Multiple sequence alignment - TraesCS2D01G280500

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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 TraesCS2D01G280500 chr2D 100.000 4052 0 0 1 4052 352703148 352707199 0.000000e+00 7483.0
1 TraesCS2D01G280500 chr2B 94.134 3597 102 29 246 3764 418947254 418950819 0.000000e+00 5373.0
2 TraesCS2D01G280500 chr2B 88.841 233 20 4 3822 4052 418950845 418951073 8.570000e-72 281.0
3 TraesCS2D01G280500 chr2A 95.677 3169 81 20 617 3765 470638710 470641842 0.000000e+00 5042.0
4 TraesCS2D01G280500 chr2A 93.617 235 11 3 305 535 470638398 470638632 8.340000e-92 348.0
5 TraesCS2D01G280500 chr2A 90.583 223 19 1 3818 4038 470641861 470642083 1.100000e-75 294.0
6 TraesCS2D01G280500 chr7A 77.523 2140 386 59 990 3095 86048188 86050266 0.000000e+00 1199.0
7 TraesCS2D01G280500 chr7D 77.487 2141 384 65 990 3095 84986117 84988194 0.000000e+00 1194.0
8 TraesCS2D01G280500 chr7D 96.791 187 5 1 57 242 118926291 118926105 1.090000e-80 311.0
9 TraesCS2D01G280500 chr7B 77.207 2141 381 64 990 3095 34610040 34612108 0.000000e+00 1151.0
10 TraesCS2D01G280500 chr7B 100.000 54 0 0 3764 3817 675111344 675111291 2.580000e-17 100.0
11 TraesCS2D01G280500 chr7B 95.000 60 2 1 3761 3819 208844768 208844827 4.310000e-15 93.5
12 TraesCS2D01G280500 chr3D 97.326 187 4 1 57 242 77585264 77585078 2.350000e-82 316.0
13 TraesCS2D01G280500 chr3D 96.809 188 5 1 57 244 413181337 413181523 3.040000e-81 313.0
14 TraesCS2D01G280500 chr3D 96.791 187 5 1 57 242 420106556 420106370 1.090000e-80 311.0
15 TraesCS2D01G280500 chr6D 96.791 187 5 1 57 242 244681798 244681612 1.090000e-80 311.0
16 TraesCS2D01G280500 chr5D 96.791 187 5 1 57 242 332408832 332408646 1.090000e-80 311.0
17 TraesCS2D01G280500 chr5D 95.312 64 2 1 3764 3827 458691525 458691587 2.580000e-17 100.0
18 TraesCS2D01G280500 chr5D 98.182 55 1 0 3764 3818 258002320 258002374 3.330000e-16 97.1
19 TraesCS2D01G280500 chr4D 96.791 187 5 1 57 242 437395590 437395404 1.090000e-80 311.0
20 TraesCS2D01G280500 chr1D 96.277 188 5 2 57 242 41295321 41295134 1.410000e-79 307.0
21 TraesCS2D01G280500 chr6A 96.257 187 6 1 57 242 162993743 162993929 5.090000e-79 305.0
22 TraesCS2D01G280500 chr4B 98.182 55 1 0 3764 3818 633301946 633302000 3.330000e-16 97.1
23 TraesCS2D01G280500 chrUn 98.148 54 1 0 3764 3817 26261168 26261221 1.200000e-15 95.3
24 TraesCS2D01G280500 chrUn 94.915 59 3 0 3764 3822 103314813 103314755 4.310000e-15 93.5
25 TraesCS2D01G280500 chr3B 88.312 77 6 3 3760 3835 5375610 5375684 5.580000e-14 89.8
26 TraesCS2D01G280500 chr6B 89.706 68 6 1 3764 3830 124633735 124633668 7.220000e-13 86.1


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 TraesCS2D01G280500 chr2D 352703148 352707199 4051 False 7483.000000 7483 100.000000 1 4052 1 chr2D.!!$F1 4051
1 TraesCS2D01G280500 chr2B 418947254 418951073 3819 False 2827.000000 5373 91.487500 246 4052 2 chr2B.!!$F1 3806
2 TraesCS2D01G280500 chr2A 470638398 470642083 3685 False 1894.666667 5042 93.292333 305 4038 3 chr2A.!!$F1 3733
3 TraesCS2D01G280500 chr7A 86048188 86050266 2078 False 1199.000000 1199 77.523000 990 3095 1 chr7A.!!$F1 2105
4 TraesCS2D01G280500 chr7D 84986117 84988194 2077 False 1194.000000 1194 77.487000 990 3095 1 chr7D.!!$F1 2105
5 TraesCS2D01G280500 chr7B 34610040 34612108 2068 False 1151.000000 1151 77.207000 990 3095 1 chr7B.!!$F1 2105

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
66 67 0.322366 TGGATGAGCGTTTGATGCCA 60.322 50.0 0.0 0.0 0.00 4.92 F
950 1060 0.620556 TAACTCCCGTCCCGAGTAGT 59.379 55.0 0.0 0.0 39.69 2.73 F
1198 1320 0.458543 CAACATCACCTCCGACCTCG 60.459 60.0 0.0 0.0 39.44 4.63 F
1199 1321 0.611062 AACATCACCTCCGACCTCGA 60.611 55.0 0.0 0.0 43.02 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1198 1320 0.812549 GAGGTCGAGTGGAAGAGGTC 59.187 60.000 0.00 0.0 0.00 3.85 R
2443 2574 0.111253 CCAAGTGGGGTCAAGCTCTT 59.889 55.000 0.00 0.0 0.00 2.85 R
2850 3002 2.621055 AGATATCTTGAGCTCTTCGCGT 59.379 45.455 16.19 0.0 45.59 6.01 R
3052 3204 6.316390 CCTGTAACCAAATTCTGTCATAGGAC 59.684 42.308 0.00 0.0 44.57 3.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 8.664798 GTGACAGTAATATAACACAGAAATGCA 58.335 33.333 0.00 0.00 0.00 3.96
27 28 9.394767 TGACAGTAATATAACACAGAAATGCAT 57.605 29.630 0.00 0.00 0.00 3.96
30 31 9.797473 CAGTAATATAACACAGAAATGCATACG 57.203 33.333 0.00 0.00 0.00 3.06
31 32 9.758651 AGTAATATAACACAGAAATGCATACGA 57.241 29.630 0.00 0.00 0.00 3.43
53 54 6.841119 CGATAGTTTCACAATGTTTGGATGA 58.159 36.000 0.00 0.00 34.12 2.92
54 55 6.963242 CGATAGTTTCACAATGTTTGGATGAG 59.037 38.462 0.00 0.00 34.12 2.90
55 56 4.874970 AGTTTCACAATGTTTGGATGAGC 58.125 39.130 0.00 0.00 34.12 4.26
56 57 3.557577 TTCACAATGTTTGGATGAGCG 57.442 42.857 0.00 0.00 34.12 5.03
57 58 2.503331 TCACAATGTTTGGATGAGCGT 58.497 42.857 0.00 0.00 34.12 5.07
58 59 2.884012 TCACAATGTTTGGATGAGCGTT 59.116 40.909 0.00 0.00 34.12 4.84
59 60 3.317711 TCACAATGTTTGGATGAGCGTTT 59.682 39.130 0.00 0.00 34.12 3.60
60 61 3.426191 CACAATGTTTGGATGAGCGTTTG 59.574 43.478 0.00 0.00 34.12 2.93
61 62 3.317711 ACAATGTTTGGATGAGCGTTTGA 59.682 39.130 0.00 0.00 34.12 2.69
62 63 4.022068 ACAATGTTTGGATGAGCGTTTGAT 60.022 37.500 0.00 0.00 34.12 2.57
63 64 3.557577 TGTTTGGATGAGCGTTTGATG 57.442 42.857 0.00 0.00 0.00 3.07
64 65 2.253603 GTTTGGATGAGCGTTTGATGC 58.746 47.619 0.00 0.00 0.00 3.91
65 66 0.810648 TTGGATGAGCGTTTGATGCC 59.189 50.000 0.00 0.00 0.00 4.40
66 67 0.322366 TGGATGAGCGTTTGATGCCA 60.322 50.000 0.00 0.00 0.00 4.92
67 68 0.810648 GGATGAGCGTTTGATGCCAA 59.189 50.000 0.00 0.00 0.00 4.52
68 69 1.468054 GGATGAGCGTTTGATGCCAAC 60.468 52.381 0.00 0.00 30.88 3.77
69 70 1.199789 GATGAGCGTTTGATGCCAACA 59.800 47.619 0.00 0.00 30.88 3.33
70 71 1.028130 TGAGCGTTTGATGCCAACAA 58.972 45.000 0.00 0.00 30.88 2.83
71 72 1.612950 TGAGCGTTTGATGCCAACAAT 59.387 42.857 0.00 0.00 30.88 2.71
72 73 2.035704 TGAGCGTTTGATGCCAACAATT 59.964 40.909 0.00 0.00 30.88 2.32
73 74 2.406130 AGCGTTTGATGCCAACAATTG 58.594 42.857 3.24 3.24 30.88 2.32
119 120 7.396190 CCAACATTTGGCAAATCAAAAATTG 57.604 32.000 22.02 16.84 45.17 2.32
120 121 6.979238 CCAACATTTGGCAAATCAAAAATTGT 59.021 30.769 22.02 13.26 45.17 2.71
121 122 7.167801 CCAACATTTGGCAAATCAAAAATTGTC 59.832 33.333 22.02 0.00 45.17 3.18
122 123 7.330900 ACATTTGGCAAATCAAAAATTGTCA 57.669 28.000 22.02 0.00 39.22 3.58
123 124 7.769220 ACATTTGGCAAATCAAAAATTGTCAA 58.231 26.923 22.02 1.77 46.13 3.18
127 128 7.330900 TGGCAAATCAAAAATTGTCAAATGT 57.669 28.000 0.00 0.00 38.13 2.71
128 129 7.769220 TGGCAAATCAAAAATTGTCAAATGTT 58.231 26.923 0.00 0.00 38.13 2.71
129 130 7.701078 TGGCAAATCAAAAATTGTCAAATGTTG 59.299 29.630 0.00 0.00 38.13 3.33
130 131 7.914346 GGCAAATCAAAAATTGTCAAATGTTGA 59.086 29.630 8.39 8.39 36.14 3.18
144 145 7.579589 TCAAATGTTGACAACTTTTTGTGAG 57.420 32.000 27.55 18.37 46.43 3.51
145 146 6.589523 TCAAATGTTGACAACTTTTTGTGAGG 59.410 34.615 27.55 17.93 46.43 3.86
146 147 5.659440 ATGTTGACAACTTTTTGTGAGGT 57.341 34.783 18.73 0.00 46.43 3.85
147 148 5.461032 TGTTGACAACTTTTTGTGAGGTT 57.539 34.783 18.73 0.00 46.43 3.50
148 149 5.226396 TGTTGACAACTTTTTGTGAGGTTG 58.774 37.500 18.73 0.00 46.43 3.77
149 150 5.010112 TGTTGACAACTTTTTGTGAGGTTGA 59.990 36.000 18.73 0.00 46.43 3.18
150 151 5.309323 TGACAACTTTTTGTGAGGTTGAG 57.691 39.130 10.89 0.00 46.43 3.02
151 152 5.007034 TGACAACTTTTTGTGAGGTTGAGA 58.993 37.500 10.89 0.00 46.43 3.27
152 153 5.475220 TGACAACTTTTTGTGAGGTTGAGAA 59.525 36.000 10.89 0.00 46.43 2.87
153 154 5.954335 ACAACTTTTTGTGAGGTTGAGAAG 58.046 37.500 10.89 0.00 44.66 2.85
154 155 5.710099 ACAACTTTTTGTGAGGTTGAGAAGA 59.290 36.000 10.89 0.00 44.66 2.87
155 156 6.208599 ACAACTTTTTGTGAGGTTGAGAAGAA 59.791 34.615 10.89 0.00 44.66 2.52
156 157 6.834168 ACTTTTTGTGAGGTTGAGAAGAAA 57.166 33.333 0.00 0.00 0.00 2.52
157 158 7.227049 ACTTTTTGTGAGGTTGAGAAGAAAA 57.773 32.000 0.00 0.00 0.00 2.29
158 159 7.315890 ACTTTTTGTGAGGTTGAGAAGAAAAG 58.684 34.615 0.00 0.00 37.50 2.27
159 160 6.834168 TTTTGTGAGGTTGAGAAGAAAAGT 57.166 33.333 0.00 0.00 0.00 2.66
160 161 6.834168 TTTGTGAGGTTGAGAAGAAAAGTT 57.166 33.333 0.00 0.00 0.00 2.66
161 162 5.818136 TGTGAGGTTGAGAAGAAAAGTTG 57.182 39.130 0.00 0.00 0.00 3.16
162 163 4.640201 TGTGAGGTTGAGAAGAAAAGTTGG 59.360 41.667 0.00 0.00 0.00 3.77
163 164 4.640647 GTGAGGTTGAGAAGAAAAGTTGGT 59.359 41.667 0.00 0.00 0.00 3.67
164 165 5.820947 GTGAGGTTGAGAAGAAAAGTTGGTA 59.179 40.000 0.00 0.00 0.00 3.25
165 166 6.017852 GTGAGGTTGAGAAGAAAAGTTGGTAG 60.018 42.308 0.00 0.00 0.00 3.18
166 167 4.822350 AGGTTGAGAAGAAAAGTTGGTAGC 59.178 41.667 0.00 0.00 0.00 3.58
167 168 4.023107 GGTTGAGAAGAAAAGTTGGTAGCC 60.023 45.833 0.00 0.00 0.00 3.93
168 169 4.431416 TGAGAAGAAAAGTTGGTAGCCA 57.569 40.909 0.00 0.00 0.00 4.75
169 170 4.787551 TGAGAAGAAAAGTTGGTAGCCAA 58.212 39.130 0.00 0.00 41.69 4.52
182 183 2.289565 GTAGCCAACCAATCACTAGCC 58.710 52.381 0.00 0.00 0.00 3.93
183 184 0.698238 AGCCAACCAATCACTAGCCA 59.302 50.000 0.00 0.00 0.00 4.75
184 185 1.075374 AGCCAACCAATCACTAGCCAA 59.925 47.619 0.00 0.00 0.00 4.52
185 186 1.202348 GCCAACCAATCACTAGCCAAC 59.798 52.381 0.00 0.00 0.00 3.77
186 187 2.513753 CCAACCAATCACTAGCCAACA 58.486 47.619 0.00 0.00 0.00 3.33
187 188 3.091545 CCAACCAATCACTAGCCAACAT 58.908 45.455 0.00 0.00 0.00 2.71
188 189 3.511146 CCAACCAATCACTAGCCAACATT 59.489 43.478 0.00 0.00 0.00 2.71
189 190 4.021192 CCAACCAATCACTAGCCAACATTT 60.021 41.667 0.00 0.00 0.00 2.32
190 191 4.789012 ACCAATCACTAGCCAACATTTG 57.211 40.909 0.00 0.00 0.00 2.32
200 201 2.855209 CCAACATTTGGCATTTCCCA 57.145 45.000 0.00 0.00 45.17 4.37
201 202 3.137446 CCAACATTTGGCATTTCCCAA 57.863 42.857 0.00 0.00 45.17 4.12
232 233 2.064573 CCAACTTTTGGCATCGAACC 57.935 50.000 0.00 0.00 45.17 3.62
233 234 1.339610 CCAACTTTTGGCATCGAACCA 59.660 47.619 6.45 6.45 45.17 3.67
234 235 2.223923 CCAACTTTTGGCATCGAACCAA 60.224 45.455 16.88 16.88 45.17 3.67
235 236 3.554752 CCAACTTTTGGCATCGAACCAAT 60.555 43.478 20.29 6.70 46.25 3.16
236 237 3.575965 ACTTTTGGCATCGAACCAATC 57.424 42.857 20.29 0.00 46.25 2.67
237 238 2.890311 ACTTTTGGCATCGAACCAATCA 59.110 40.909 20.29 11.54 46.25 2.57
238 239 3.511146 ACTTTTGGCATCGAACCAATCAT 59.489 39.130 20.29 8.83 46.25 2.45
239 240 3.507103 TTTGGCATCGAACCAATCATG 57.493 42.857 20.29 0.00 46.25 3.07
240 241 0.740149 TGGCATCGAACCAATCATGC 59.260 50.000 8.01 1.52 39.64 4.06
241 242 1.027357 GGCATCGAACCAATCATGCT 58.973 50.000 3.08 0.00 39.96 3.79
242 243 1.406539 GGCATCGAACCAATCATGCTT 59.593 47.619 3.08 0.00 39.96 3.91
243 244 2.456989 GCATCGAACCAATCATGCTTG 58.543 47.619 2.20 2.20 38.47 4.01
244 245 2.159338 GCATCGAACCAATCATGCTTGT 60.159 45.455 8.38 0.00 38.47 3.16
252 253 3.236816 CCAATCATGCTTGTGACGTTTC 58.763 45.455 8.38 0.00 0.00 2.78
263 264 2.869801 TGTGACGTTTCTGAACATCCAC 59.130 45.455 0.00 0.00 35.44 4.02
285 294 0.981183 TAAGTGCGACCCCAAGTGAT 59.019 50.000 0.00 0.00 0.00 3.06
293 302 1.315257 ACCCCAAGTGATGCGAATGC 61.315 55.000 0.00 0.00 43.20 3.56
392 411 3.341263 GGGACTTTGTGGTTCCCTC 57.659 57.895 0.00 0.00 37.63 4.30
443 462 4.322123 GGGATCTAATACGAGGAGGAAAGC 60.322 50.000 0.00 0.00 0.00 3.51
489 508 2.665185 AGCGACCGCCAAGAACAC 60.665 61.111 11.03 0.00 43.17 3.32
538 563 1.706305 TCCAACGGGGTTAGATTTGGT 59.294 47.619 0.00 0.00 38.32 3.67
539 564 2.089201 CCAACGGGGTTAGATTTGGTC 58.911 52.381 0.00 0.00 33.39 4.02
574 617 5.697826 CCAAACCAATTGCGCAATTTATTT 58.302 33.333 38.50 33.77 38.84 1.40
577 620 7.805071 CCAAACCAATTGCGCAATTTATTTTTA 59.195 29.630 38.50 9.68 38.84 1.52
578 621 8.838961 CAAACCAATTGCGCAATTTATTTTTAG 58.161 29.630 38.50 25.81 38.84 1.85
581 632 7.064490 ACCAATTGCGCAATTTATTTTTAGGAG 59.936 33.333 38.50 24.15 38.84 3.69
585 636 8.770438 TTGCGCAATTTATTTTTAGGAGAAAT 57.230 26.923 21.02 0.00 0.00 2.17
609 660 1.736126 TCGTCGTCAAGCTCGATACTT 59.264 47.619 0.00 0.00 39.45 2.24
610 661 1.840741 CGTCGTCAAGCTCGATACTTG 59.159 52.381 17.83 17.83 44.76 3.16
612 663 2.594654 GTCGTCAAGCTCGATACTTGTG 59.405 50.000 21.19 16.57 43.97 3.33
792 886 1.912763 TGGTGCCATTTGCTTCCCC 60.913 57.895 0.00 0.00 42.00 4.81
859 966 1.202533 GCACCGGCACACATATCTACT 60.203 52.381 0.00 0.00 40.72 2.57
860 967 2.035449 GCACCGGCACACATATCTACTA 59.965 50.000 0.00 0.00 40.72 1.82
861 968 3.857383 GCACCGGCACACATATCTACTAG 60.857 52.174 0.00 0.00 40.72 2.57
862 969 3.318275 CACCGGCACACATATCTACTAGT 59.682 47.826 0.00 0.00 0.00 2.57
863 970 4.517832 CACCGGCACACATATCTACTAGTA 59.482 45.833 0.00 1.89 0.00 1.82
864 971 5.183331 CACCGGCACACATATCTACTAGTAT 59.817 44.000 0.00 0.00 0.00 2.12
865 972 5.415077 ACCGGCACACATATCTACTAGTATC 59.585 44.000 0.00 0.00 0.00 2.24
866 973 5.648526 CCGGCACACATATCTACTAGTATCT 59.351 44.000 2.33 0.00 0.00 1.98
867 974 6.183360 CCGGCACACATATCTACTAGTATCTC 60.183 46.154 2.33 0.00 0.00 2.75
868 975 6.596106 CGGCACACATATCTACTAGTATCTCT 59.404 42.308 2.33 0.00 0.00 3.10
869 976 7.119992 CGGCACACATATCTACTAGTATCTCTT 59.880 40.741 2.33 0.00 0.00 2.85
870 977 8.798402 GGCACACATATCTACTAGTATCTCTTT 58.202 37.037 2.33 0.00 0.00 2.52
949 1059 1.020437 GTAACTCCCGTCCCGAGTAG 58.980 60.000 0.00 0.00 39.69 2.57
950 1060 0.620556 TAACTCCCGTCCCGAGTAGT 59.379 55.000 0.00 0.00 39.69 2.73
951 1061 0.964358 AACTCCCGTCCCGAGTAGTG 60.964 60.000 0.00 0.00 39.69 2.74
962 1072 0.789753 CGAGTAGTGTCGCGTCAGTG 60.790 60.000 21.38 3.30 32.22 3.66
1198 1320 0.458543 CAACATCACCTCCGACCTCG 60.459 60.000 0.00 0.00 39.44 4.63
1199 1321 0.611062 AACATCACCTCCGACCTCGA 60.611 55.000 0.00 0.00 43.02 4.04
1200 1322 1.313812 ACATCACCTCCGACCTCGAC 61.314 60.000 0.00 0.00 43.02 4.20
1201 1323 1.753463 ATCACCTCCGACCTCGACC 60.753 63.158 0.00 0.00 43.02 4.79
1202 1324 2.212794 ATCACCTCCGACCTCGACCT 62.213 60.000 0.00 0.00 43.02 3.85
1203 1325 2.045143 ACCTCCGACCTCGACCTC 60.045 66.667 0.00 0.00 43.02 3.85
1707 1838 4.101448 GACCTGGTGCGGCCTGAT 62.101 66.667 2.82 0.00 38.33 2.90
2097 2228 0.754217 CCGAGAAGGTGTCCCGGATA 60.754 60.000 0.73 0.00 42.49 2.59
2269 2400 1.905637 TCTACAGCAGGAGTCGTCAA 58.094 50.000 0.00 0.00 0.00 3.18
2364 2495 5.609088 GTTTACAGTGATACGCTTGACAAG 58.391 41.667 11.02 11.02 0.00 3.16
2393 2524 2.037620 GAGGATGCTGCCGGAGATGT 62.038 60.000 5.05 0.00 0.00 3.06
2443 2574 4.718961 TGATGATGACGAGGAGTATCTGA 58.281 43.478 0.00 0.00 33.73 3.27
2807 2959 5.360714 ACTTCAACTTTGCCTTTGATGAGAA 59.639 36.000 0.00 0.00 33.35 2.87
2850 3002 3.294214 GAAGGTACCGGATCCTCAACTA 58.706 50.000 9.46 0.00 33.09 2.24
3052 3204 6.253946 ACCATTCCAGAAGAAGGTTATAGG 57.746 41.667 0.00 0.00 38.07 2.57
3327 3481 4.450305 AGAGGCATGCTTCTTGGAATAT 57.550 40.909 25.35 2.30 0.00 1.28
3328 3482 5.573380 AGAGGCATGCTTCTTGGAATATA 57.427 39.130 25.35 0.00 0.00 0.86
3329 3483 5.312079 AGAGGCATGCTTCTTGGAATATAC 58.688 41.667 25.35 0.00 0.00 1.47
3466 3621 7.492344 AGAAAATGAAGTGAAACAAACATGTCC 59.508 33.333 0.00 0.00 41.43 4.02
3470 3625 7.202016 TGAAGTGAAACAAACATGTCCTATC 57.798 36.000 0.00 0.00 41.43 2.08
3507 3662 5.272283 ACGGATCGTAAAACTGACCATAT 57.728 39.130 0.00 0.00 38.73 1.78
3546 3701 6.365247 TGATCGTACTGTTGAAGAAAGTAAGC 59.635 38.462 0.00 0.00 0.00 3.09
3549 3704 6.704493 TCGTACTGTTGAAGAAAGTAAGCATT 59.296 34.615 0.00 0.00 0.00 3.56
3609 3764 7.816640 TCTTTTCTTTATGCTCACATACAACC 58.183 34.615 0.00 0.00 38.50 3.77
3730 3885 3.027412 AGACTGTAGGGCATAGTGTCAG 58.973 50.000 11.98 4.24 0.00 3.51
3768 3923 5.857822 CTGTAGGGCAGTAGTACAAAAAC 57.142 43.478 2.52 0.00 40.27 2.43
3769 3924 4.644498 TGTAGGGCAGTAGTACAAAAACC 58.356 43.478 2.52 0.00 0.00 3.27
3770 3925 2.774687 AGGGCAGTAGTACAAAAACCG 58.225 47.619 2.52 0.00 0.00 4.44
3774 3929 4.937015 GGGCAGTAGTACAAAAACCGAATA 59.063 41.667 2.52 0.00 0.00 1.75
3776 3931 6.072563 GGGCAGTAGTACAAAAACCGAATAAA 60.073 38.462 2.52 0.00 0.00 1.40
3778 3933 6.798476 GCAGTAGTACAAAAACCGAATAAACC 59.202 38.462 2.52 0.00 0.00 3.27
3779 3934 7.011189 CAGTAGTACAAAAACCGAATAAACCG 58.989 38.462 2.52 0.00 0.00 4.44
3780 3935 6.928492 AGTAGTACAAAAACCGAATAAACCGA 59.072 34.615 2.52 0.00 0.00 4.69
3782 3937 6.429624 AGTACAAAAACCGAATAAACCGAAC 58.570 36.000 0.00 0.00 0.00 3.95
3783 3938 4.609947 ACAAAAACCGAATAAACCGAACC 58.390 39.130 0.00 0.00 0.00 3.62
3784 3939 3.541071 AAAACCGAATAAACCGAACCG 57.459 42.857 0.00 0.00 0.00 4.44
3785 3940 2.168326 AACCGAATAAACCGAACCGT 57.832 45.000 0.00 0.00 0.00 4.83
3786 3941 3.311486 AACCGAATAAACCGAACCGTA 57.689 42.857 0.00 0.00 0.00 4.02
3787 3942 3.525268 ACCGAATAAACCGAACCGTAT 57.475 42.857 0.00 0.00 0.00 3.06
3788 3943 3.860641 ACCGAATAAACCGAACCGTATT 58.139 40.909 0.00 0.00 0.00 1.89
3789 3944 5.004922 ACCGAATAAACCGAACCGTATTA 57.995 39.130 0.00 0.00 0.00 0.98
3790 3945 5.415221 ACCGAATAAACCGAACCGTATTAA 58.585 37.500 0.00 0.00 0.00 1.40
3791 3946 5.290885 ACCGAATAAACCGAACCGTATTAAC 59.709 40.000 0.00 0.00 0.00 2.01
3792 3947 5.276820 CCGAATAAACCGAACCGTATTAACC 60.277 44.000 0.00 0.00 0.00 2.85
3793 3948 5.290643 CGAATAAACCGAACCGTATTAACCA 59.709 40.000 0.00 0.00 0.00 3.67
3794 3949 6.018832 CGAATAAACCGAACCGTATTAACCAT 60.019 38.462 0.00 0.00 0.00 3.55
3795 3950 7.168972 CGAATAAACCGAACCGTATTAACCATA 59.831 37.037 0.00 0.00 0.00 2.74
3796 3951 8.907222 AATAAACCGAACCGTATTAACCATAT 57.093 30.769 0.00 0.00 0.00 1.78
3797 3952 8.907222 ATAAACCGAACCGTATTAACCATATT 57.093 30.769 0.00 0.00 0.00 1.28
3798 3953 9.995003 ATAAACCGAACCGTATTAACCATATTA 57.005 29.630 0.00 0.00 0.00 0.98
3799 3954 8.729805 AAACCGAACCGTATTAACCATATTAA 57.270 30.769 0.00 0.00 0.00 1.40
3800 3955 7.713764 ACCGAACCGTATTAACCATATTAAC 57.286 36.000 0.00 0.00 0.00 2.01
3801 3956 6.705825 ACCGAACCGTATTAACCATATTAACC 59.294 38.462 0.00 0.00 0.00 2.85
3802 3957 6.128849 CCGAACCGTATTAACCATATTAACCG 60.129 42.308 0.00 0.00 0.00 4.44
3803 3958 6.640499 CGAACCGTATTAACCATATTAACCGA 59.360 38.462 0.00 0.00 0.00 4.69
3804 3959 7.168972 CGAACCGTATTAACCATATTAACCGAA 59.831 37.037 0.00 0.00 0.00 4.30
3805 3960 7.713764 ACCGTATTAACCATATTAACCGAAC 57.286 36.000 0.00 0.00 0.00 3.95
3806 3961 6.420604 ACCGTATTAACCATATTAACCGAACG 59.579 38.462 0.00 0.00 0.00 3.95
3807 3962 6.291385 CGTATTAACCATATTAACCGAACGC 58.709 40.000 0.00 0.00 0.00 4.84
3808 3963 5.678132 ATTAACCATATTAACCGAACGCC 57.322 39.130 0.00 0.00 0.00 5.68
3809 3964 1.957668 ACCATATTAACCGAACGCCC 58.042 50.000 0.00 0.00 0.00 6.13
3810 3965 1.209990 ACCATATTAACCGAACGCCCA 59.790 47.619 0.00 0.00 0.00 5.36
3811 3966 1.871039 CCATATTAACCGAACGCCCAG 59.129 52.381 0.00 0.00 0.00 4.45
3812 3967 1.263217 CATATTAACCGAACGCCCAGC 59.737 52.381 0.00 0.00 0.00 4.85
3813 3968 0.462403 TATTAACCGAACGCCCAGCC 60.462 55.000 0.00 0.00 0.00 4.85
3814 3969 3.781432 TATTAACCGAACGCCCAGCCC 62.781 57.143 0.00 0.00 0.00 5.19
3861 4018 7.118723 AGGTGTCATTCATACATTGGTGTTAT 58.881 34.615 0.00 0.00 39.77 1.89
3872 4029 6.500684 ACATTGGTGTTATTACTCTTGCTG 57.499 37.500 0.00 0.00 34.01 4.41
3891 4048 8.015087 TCTTGCTGTTTTACTGACGAAAATATG 58.985 33.333 0.00 0.00 0.00 1.78
3896 4053 7.295201 TGTTTTACTGACGAAAATATGAGTGC 58.705 34.615 0.00 0.00 0.00 4.40
3909 4066 9.869844 GAAAATATGAGTGCTGATGTGTTATAC 57.130 33.333 0.00 0.00 0.00 1.47
3962 4121 9.747293 GTATTTCATTAGTACTGTTAGGACTCC 57.253 37.037 5.39 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.664798 TGCATTTCTGTGTTATATTACTGTCAC 58.335 33.333 0.00 0.00 0.00 3.67
1 2 8.785329 TGCATTTCTGTGTTATATTACTGTCA 57.215 30.769 0.00 0.00 0.00 3.58
4 5 9.797473 CGTATGCATTTCTGTGTTATATTACTG 57.203 33.333 3.54 0.00 0.00 2.74
5 6 9.758651 TCGTATGCATTTCTGTGTTATATTACT 57.241 29.630 3.54 0.00 0.00 2.24
9 10 9.929180 ACTATCGTATGCATTTCTGTGTTATAT 57.071 29.630 3.54 0.00 0.00 0.86
10 11 9.758651 AACTATCGTATGCATTTCTGTGTTATA 57.241 29.630 3.54 0.00 0.00 0.98
11 12 8.662781 AACTATCGTATGCATTTCTGTGTTAT 57.337 30.769 3.54 0.00 0.00 1.89
12 13 8.487313 AAACTATCGTATGCATTTCTGTGTTA 57.513 30.769 3.54 0.00 0.00 2.41
13 14 6.985188 AACTATCGTATGCATTTCTGTGTT 57.015 33.333 3.54 1.83 0.00 3.32
14 15 6.593770 TGAAACTATCGTATGCATTTCTGTGT 59.406 34.615 3.54 0.00 0.00 3.72
15 16 6.901887 GTGAAACTATCGTATGCATTTCTGTG 59.098 38.462 3.54 0.00 0.00 3.66
16 17 6.593770 TGTGAAACTATCGTATGCATTTCTGT 59.406 34.615 3.54 0.00 38.04 3.41
17 18 7.003939 TGTGAAACTATCGTATGCATTTCTG 57.996 36.000 3.54 0.00 38.04 3.02
18 19 7.609760 TTGTGAAACTATCGTATGCATTTCT 57.390 32.000 3.54 0.00 38.04 2.52
19 20 7.910162 ACATTGTGAAACTATCGTATGCATTTC 59.090 33.333 3.54 0.96 38.04 2.17
20 21 7.761409 ACATTGTGAAACTATCGTATGCATTT 58.239 30.769 3.54 0.00 38.04 2.32
21 22 7.320443 ACATTGTGAAACTATCGTATGCATT 57.680 32.000 3.54 0.00 38.04 3.56
22 23 6.925610 ACATTGTGAAACTATCGTATGCAT 57.074 33.333 3.79 3.79 38.04 3.96
23 24 6.735678 AACATTGTGAAACTATCGTATGCA 57.264 33.333 0.00 0.00 38.04 3.96
24 25 6.468956 CCAAACATTGTGAAACTATCGTATGC 59.531 38.462 0.00 0.00 38.04 3.14
25 26 7.747888 TCCAAACATTGTGAAACTATCGTATG 58.252 34.615 0.00 0.00 38.04 2.39
26 27 7.915293 TCCAAACATTGTGAAACTATCGTAT 57.085 32.000 0.00 0.00 38.04 3.06
27 28 7.604545 TCATCCAAACATTGTGAAACTATCGTA 59.395 33.333 0.00 0.00 38.04 3.43
28 29 6.429692 TCATCCAAACATTGTGAAACTATCGT 59.570 34.615 0.00 0.00 38.04 3.73
29 30 6.841119 TCATCCAAACATTGTGAAACTATCG 58.159 36.000 0.00 0.00 38.04 2.92
30 31 6.749118 GCTCATCCAAACATTGTGAAACTATC 59.251 38.462 0.00 0.00 38.04 2.08
31 32 6.623549 CGCTCATCCAAACATTGTGAAACTAT 60.624 38.462 0.00 0.00 38.04 2.12
32 33 5.334802 CGCTCATCCAAACATTGTGAAACTA 60.335 40.000 0.00 0.00 38.04 2.24
33 34 4.557296 CGCTCATCCAAACATTGTGAAACT 60.557 41.667 0.00 0.00 38.04 2.66
34 35 3.670055 CGCTCATCCAAACATTGTGAAAC 59.330 43.478 0.00 0.00 37.35 2.78
35 36 3.317711 ACGCTCATCCAAACATTGTGAAA 59.682 39.130 0.00 0.00 0.00 2.69
36 37 2.884012 ACGCTCATCCAAACATTGTGAA 59.116 40.909 0.00 0.00 0.00 3.18
37 38 2.503331 ACGCTCATCCAAACATTGTGA 58.497 42.857 0.00 0.00 0.00 3.58
38 39 2.995466 ACGCTCATCCAAACATTGTG 57.005 45.000 0.00 0.00 0.00 3.33
39 40 3.317711 TCAAACGCTCATCCAAACATTGT 59.682 39.130 0.00 0.00 0.00 2.71
40 41 3.899734 TCAAACGCTCATCCAAACATTG 58.100 40.909 0.00 0.00 0.00 2.82
41 42 4.487948 CATCAAACGCTCATCCAAACATT 58.512 39.130 0.00 0.00 0.00 2.71
42 43 3.674138 GCATCAAACGCTCATCCAAACAT 60.674 43.478 0.00 0.00 0.00 2.71
43 44 2.351641 GCATCAAACGCTCATCCAAACA 60.352 45.455 0.00 0.00 0.00 2.83
44 45 2.253603 GCATCAAACGCTCATCCAAAC 58.746 47.619 0.00 0.00 0.00 2.93
45 46 1.202114 GGCATCAAACGCTCATCCAAA 59.798 47.619 0.00 0.00 0.00 3.28
46 47 0.810648 GGCATCAAACGCTCATCCAA 59.189 50.000 0.00 0.00 0.00 3.53
47 48 0.322366 TGGCATCAAACGCTCATCCA 60.322 50.000 0.00 0.00 0.00 3.41
48 49 0.810648 TTGGCATCAAACGCTCATCC 59.189 50.000 0.00 0.00 0.00 3.51
49 50 1.199789 TGTTGGCATCAAACGCTCATC 59.800 47.619 0.00 0.00 34.28 2.92
50 51 1.246649 TGTTGGCATCAAACGCTCAT 58.753 45.000 0.00 0.00 34.28 2.90
51 52 1.028130 TTGTTGGCATCAAACGCTCA 58.972 45.000 8.48 0.00 34.28 4.26
52 53 2.352503 ATTGTTGGCATCAAACGCTC 57.647 45.000 14.40 0.00 34.28 5.03
53 54 2.406130 CAATTGTTGGCATCAAACGCT 58.594 42.857 14.40 0.00 34.28 5.07
54 55 1.460359 CCAATTGTTGGCATCAAACGC 59.540 47.619 14.40 0.00 45.17 4.84
81 82 5.392165 CCAAATGTTGGCTTGCCAAATATTG 60.392 40.000 26.12 25.13 45.17 1.90
82 83 4.701171 CCAAATGTTGGCTTGCCAAATATT 59.299 37.500 26.12 23.52 45.17 1.28
83 84 4.263435 CCAAATGTTGGCTTGCCAAATAT 58.737 39.130 26.12 19.92 45.17 1.28
84 85 3.672808 CCAAATGTTGGCTTGCCAAATA 58.327 40.909 26.12 18.73 45.17 1.40
85 86 2.506444 CCAAATGTTGGCTTGCCAAAT 58.494 42.857 26.12 18.32 45.17 2.32
86 87 1.964552 CCAAATGTTGGCTTGCCAAA 58.035 45.000 26.12 17.09 45.17 3.28
87 88 3.702147 CCAAATGTTGGCTTGCCAA 57.298 47.368 21.59 21.59 45.17 4.52
96 97 7.701078 TGACAATTTTTGATTTGCCAAATGTTG 59.299 29.630 7.53 5.67 37.11 3.33
97 98 7.769220 TGACAATTTTTGATTTGCCAAATGTT 58.231 26.923 7.53 0.00 36.12 2.71
98 99 7.330900 TGACAATTTTTGATTTGCCAAATGT 57.669 28.000 7.53 0.00 36.12 2.71
99 100 8.630278 TTTGACAATTTTTGATTTGCCAAATG 57.370 26.923 7.53 0.00 32.59 2.32
100 101 9.250624 CATTTGACAATTTTTGATTTGCCAAAT 57.749 25.926 1.47 1.47 42.67 2.32
101 102 8.248945 ACATTTGACAATTTTTGATTTGCCAAA 58.751 25.926 0.00 0.00 38.78 3.28
102 103 7.769220 ACATTTGACAATTTTTGATTTGCCAA 58.231 26.923 0.00 0.00 0.00 4.52
103 104 7.330900 ACATTTGACAATTTTTGATTTGCCA 57.669 28.000 0.00 0.00 0.00 4.92
104 105 7.914346 TCAACATTTGACAATTTTTGATTTGCC 59.086 29.630 7.30 0.00 34.08 4.52
105 106 8.838452 TCAACATTTGACAATTTTTGATTTGC 57.162 26.923 7.30 0.00 34.08 3.68
120 121 6.589523 CCTCACAAAAAGTTGTCAACATTTGA 59.410 34.615 32.09 20.74 45.00 2.69
121 122 6.368516 ACCTCACAAAAAGTTGTCAACATTTG 59.631 34.615 27.87 27.87 45.00 2.32
122 123 6.463360 ACCTCACAAAAAGTTGTCAACATTT 58.537 32.000 17.78 14.74 45.00 2.32
123 124 6.036577 ACCTCACAAAAAGTTGTCAACATT 57.963 33.333 17.78 9.33 45.00 2.71
124 125 5.659440 ACCTCACAAAAAGTTGTCAACAT 57.341 34.783 17.78 2.81 45.00 2.71
125 126 5.010112 TCAACCTCACAAAAAGTTGTCAACA 59.990 36.000 17.78 0.00 45.00 3.33
126 127 5.465935 TCAACCTCACAAAAAGTTGTCAAC 58.534 37.500 7.68 7.68 45.00 3.18
127 128 5.475220 TCTCAACCTCACAAAAAGTTGTCAA 59.525 36.000 0.00 0.00 45.00 3.18
128 129 5.007034 TCTCAACCTCACAAAAAGTTGTCA 58.993 37.500 0.00 0.00 45.00 3.58
129 130 5.560966 TCTCAACCTCACAAAAAGTTGTC 57.439 39.130 0.00 0.00 45.00 3.18
131 132 6.194796 TCTTCTCAACCTCACAAAAAGTTG 57.805 37.500 0.00 0.00 40.72 3.16
132 133 6.834168 TTCTTCTCAACCTCACAAAAAGTT 57.166 33.333 0.00 0.00 0.00 2.66
133 134 6.834168 TTTCTTCTCAACCTCACAAAAAGT 57.166 33.333 0.00 0.00 0.00 2.66
134 135 7.315890 ACTTTTCTTCTCAACCTCACAAAAAG 58.684 34.615 0.00 0.00 37.27 2.27
135 136 7.227049 ACTTTTCTTCTCAACCTCACAAAAA 57.773 32.000 0.00 0.00 0.00 1.94
136 137 6.834168 ACTTTTCTTCTCAACCTCACAAAA 57.166 33.333 0.00 0.00 0.00 2.44
137 138 6.350110 CCAACTTTTCTTCTCAACCTCACAAA 60.350 38.462 0.00 0.00 0.00 2.83
138 139 5.125417 CCAACTTTTCTTCTCAACCTCACAA 59.875 40.000 0.00 0.00 0.00 3.33
139 140 4.640201 CCAACTTTTCTTCTCAACCTCACA 59.360 41.667 0.00 0.00 0.00 3.58
140 141 4.640647 ACCAACTTTTCTTCTCAACCTCAC 59.359 41.667 0.00 0.00 0.00 3.51
141 142 4.855340 ACCAACTTTTCTTCTCAACCTCA 58.145 39.130 0.00 0.00 0.00 3.86
142 143 5.049336 GCTACCAACTTTTCTTCTCAACCTC 60.049 44.000 0.00 0.00 0.00 3.85
143 144 4.822350 GCTACCAACTTTTCTTCTCAACCT 59.178 41.667 0.00 0.00 0.00 3.50
144 145 4.023107 GGCTACCAACTTTTCTTCTCAACC 60.023 45.833 0.00 0.00 0.00 3.77
145 146 4.578928 TGGCTACCAACTTTTCTTCTCAAC 59.421 41.667 0.00 0.00 0.00 3.18
146 147 4.787551 TGGCTACCAACTTTTCTTCTCAA 58.212 39.130 0.00 0.00 0.00 3.02
147 148 4.431416 TGGCTACCAACTTTTCTTCTCA 57.569 40.909 0.00 0.00 0.00 3.27
162 163 2.289565 GGCTAGTGATTGGTTGGCTAC 58.710 52.381 0.00 0.00 0.00 3.58
163 164 1.912731 TGGCTAGTGATTGGTTGGCTA 59.087 47.619 0.00 0.00 0.00 3.93
164 165 0.698238 TGGCTAGTGATTGGTTGGCT 59.302 50.000 0.00 0.00 0.00 4.75
165 166 1.202348 GTTGGCTAGTGATTGGTTGGC 59.798 52.381 0.00 0.00 0.00 4.52
166 167 2.513753 TGTTGGCTAGTGATTGGTTGG 58.486 47.619 0.00 0.00 0.00 3.77
167 168 4.789012 AATGTTGGCTAGTGATTGGTTG 57.211 40.909 0.00 0.00 0.00 3.77
168 169 4.021192 CCAAATGTTGGCTAGTGATTGGTT 60.021 41.667 0.00 0.00 45.17 3.67
169 170 3.511146 CCAAATGTTGGCTAGTGATTGGT 59.489 43.478 0.00 0.00 45.17 3.67
170 171 4.114058 CCAAATGTTGGCTAGTGATTGG 57.886 45.455 0.00 0.00 45.17 3.16
181 182 5.251764 TATTTGGGAAATGCCAAATGTTGG 58.748 37.500 30.58 2.50 43.58 3.77
182 183 7.393841 AATATTTGGGAAATGCCAAATGTTG 57.606 32.000 30.58 0.00 42.05 3.33
183 184 7.393841 CAATATTTGGGAAATGCCAAATGTT 57.606 32.000 30.58 27.75 43.31 2.71
214 215 2.791383 TGGTTCGATGCCAAAAGTTG 57.209 45.000 6.75 0.00 32.29 3.16
221 222 0.740149 GCATGATTGGTTCGATGCCA 59.260 50.000 0.00 5.26 35.03 4.92
222 223 1.027357 AGCATGATTGGTTCGATGCC 58.973 50.000 0.00 0.05 38.53 4.40
223 224 2.159338 ACAAGCATGATTGGTTCGATGC 60.159 45.455 26.12 0.00 41.48 3.91
224 225 3.127376 TCACAAGCATGATTGGTTCGATG 59.873 43.478 26.12 14.61 41.48 3.84
225 226 3.127548 GTCACAAGCATGATTGGTTCGAT 59.872 43.478 26.12 2.54 41.48 3.59
226 227 2.483877 GTCACAAGCATGATTGGTTCGA 59.516 45.455 26.12 14.27 41.48 3.71
227 228 2.725759 CGTCACAAGCATGATTGGTTCG 60.726 50.000 26.12 20.79 41.48 3.95
228 229 2.226437 ACGTCACAAGCATGATTGGTTC 59.774 45.455 26.12 14.39 41.48 3.62
229 230 2.229792 ACGTCACAAGCATGATTGGTT 58.770 42.857 26.12 4.81 44.12 3.67
230 231 1.896220 ACGTCACAAGCATGATTGGT 58.104 45.000 26.12 12.36 34.36 3.67
231 232 2.995466 AACGTCACAAGCATGATTGG 57.005 45.000 26.12 15.49 34.36 3.16
232 233 3.910170 CAGAAACGTCACAAGCATGATTG 59.090 43.478 21.63 21.63 36.22 2.67
233 234 3.814842 TCAGAAACGTCACAAGCATGATT 59.185 39.130 0.00 0.00 0.00 2.57
234 235 3.402110 TCAGAAACGTCACAAGCATGAT 58.598 40.909 0.00 0.00 0.00 2.45
235 236 2.832563 TCAGAAACGTCACAAGCATGA 58.167 42.857 0.00 0.00 0.00 3.07
236 237 3.242706 TGTTCAGAAACGTCACAAGCATG 60.243 43.478 0.00 0.00 38.28 4.06
237 238 2.942376 TGTTCAGAAACGTCACAAGCAT 59.058 40.909 0.00 0.00 38.28 3.79
238 239 2.351455 TGTTCAGAAACGTCACAAGCA 58.649 42.857 0.00 0.00 38.28 3.91
239 240 3.545633 GATGTTCAGAAACGTCACAAGC 58.454 45.455 5.80 0.00 46.39 4.01
252 253 1.394917 GCACTTAGCGTGGATGTTCAG 59.605 52.381 0.00 0.00 43.97 3.02
285 294 1.081509 GAAAAGCACGGCATTCGCA 60.082 52.632 0.00 0.00 43.89 5.10
293 302 3.506067 AGGGTAAATCTTGAAAAGCACGG 59.494 43.478 0.00 0.00 45.70 4.94
327 342 4.450419 ACGACTTGCTGAAATCTTCTTGAG 59.550 41.667 0.00 0.00 0.00 3.02
392 411 2.028420 TCACCATTTCCATGCTCTCG 57.972 50.000 0.00 0.00 0.00 4.04
443 462 1.369448 GCTGCGTAGATCTCGACGG 60.369 63.158 17.39 13.29 43.51 4.79
574 617 6.198650 TGACGACGACATATTTCTCCTAAA 57.801 37.500 0.00 0.00 0.00 1.85
577 620 4.673441 CTTGACGACGACATATTTCTCCT 58.327 43.478 0.00 0.00 0.00 3.69
578 621 3.243177 GCTTGACGACGACATATTTCTCC 59.757 47.826 0.00 0.00 0.00 3.71
581 632 3.061797 CGAGCTTGACGACGACATATTTC 60.062 47.826 0.00 0.00 0.00 2.17
585 636 1.081094 TCGAGCTTGACGACGACATA 58.919 50.000 0.00 0.00 34.85 2.29
609 660 4.321750 CCGCTTTTACTCTCTCTTACCACA 60.322 45.833 0.00 0.00 0.00 4.17
610 661 4.174762 CCGCTTTTACTCTCTCTTACCAC 58.825 47.826 0.00 0.00 0.00 4.16
612 663 3.446516 TCCCGCTTTTACTCTCTCTTACC 59.553 47.826 0.00 0.00 0.00 2.85
792 886 1.152567 AGGAGATGCGAGAGGAGGG 60.153 63.158 0.00 0.00 32.19 4.30
859 966 6.039493 GCAGCAGTAGTGGTAAAGAGATACTA 59.961 42.308 1.09 0.00 31.49 1.82
860 967 5.163499 GCAGCAGTAGTGGTAAAGAGATACT 60.163 44.000 1.09 0.00 31.49 2.12
861 968 5.044558 GCAGCAGTAGTGGTAAAGAGATAC 58.955 45.833 1.09 0.00 31.49 2.24
862 969 4.956700 AGCAGCAGTAGTGGTAAAGAGATA 59.043 41.667 1.09 0.00 31.49 1.98
863 970 3.772025 AGCAGCAGTAGTGGTAAAGAGAT 59.228 43.478 1.09 0.00 31.49 2.75
864 971 3.165875 AGCAGCAGTAGTGGTAAAGAGA 58.834 45.455 1.09 0.00 31.49 3.10
865 972 3.601443 AGCAGCAGTAGTGGTAAAGAG 57.399 47.619 1.09 0.00 31.49 2.85
866 973 3.119602 CGTAGCAGCAGTAGTGGTAAAGA 60.120 47.826 1.09 0.00 31.49 2.52
867 974 3.119602 TCGTAGCAGCAGTAGTGGTAAAG 60.120 47.826 1.09 0.00 31.49 1.85
868 975 2.821378 TCGTAGCAGCAGTAGTGGTAAA 59.179 45.455 1.09 0.00 31.49 2.01
869 976 2.422479 CTCGTAGCAGCAGTAGTGGTAA 59.578 50.000 1.09 0.00 31.49 2.85
870 977 2.014857 CTCGTAGCAGCAGTAGTGGTA 58.985 52.381 1.09 0.00 31.49 3.25
871 978 0.811915 CTCGTAGCAGCAGTAGTGGT 59.188 55.000 0.00 0.00 33.53 4.16
872 979 0.811915 ACTCGTAGCAGCAGTAGTGG 59.188 55.000 0.00 0.00 0.00 4.00
873 980 1.901538 CACTCGTAGCAGCAGTAGTG 58.098 55.000 0.00 0.00 0.00 2.74
874 981 0.171455 GCACTCGTAGCAGCAGTAGT 59.829 55.000 0.00 0.00 0.00 2.73
875 982 0.453793 AGCACTCGTAGCAGCAGTAG 59.546 55.000 0.00 0.00 0.00 2.57
876 983 0.452184 GAGCACTCGTAGCAGCAGTA 59.548 55.000 0.00 0.00 0.00 2.74
880 987 0.389166 AACAGAGCACTCGTAGCAGC 60.389 55.000 0.00 0.00 34.09 5.25
949 1059 1.590525 TGGTTCACTGACGCGACAC 60.591 57.895 15.93 4.24 0.00 3.67
950 1060 1.590525 GTGGTTCACTGACGCGACA 60.591 57.895 15.93 13.32 0.00 4.35
951 1061 2.308039 GGTGGTTCACTGACGCGAC 61.308 63.158 15.93 7.62 34.40 5.19
962 1072 4.629523 TTGGTCCGGCGGTGGTTC 62.630 66.667 27.32 12.14 0.00 3.62
1198 1320 0.812549 GAGGTCGAGTGGAAGAGGTC 59.187 60.000 0.00 0.00 0.00 3.85
1199 1321 0.961358 CGAGGTCGAGTGGAAGAGGT 60.961 60.000 0.00 0.00 43.02 3.85
1200 1322 1.803943 CGAGGTCGAGTGGAAGAGG 59.196 63.158 0.00 0.00 43.02 3.69
1201 1323 1.137825 GCGAGGTCGAGTGGAAGAG 59.862 63.158 2.94 0.00 43.02 2.85
1202 1324 2.341101 GGCGAGGTCGAGTGGAAGA 61.341 63.158 2.94 0.00 43.02 2.87
1203 1325 2.182030 GGCGAGGTCGAGTGGAAG 59.818 66.667 2.94 0.00 43.02 3.46
1279 1410 1.515519 CCGCTTCGTCGAAATCCGA 60.516 57.895 18.19 0.00 46.35 4.55
1707 1838 2.507769 CGCAGCTCATCGACAGCA 60.508 61.111 18.06 0.00 39.56 4.41
1974 2105 1.812922 CCGCAGCTCATCAGACACC 60.813 63.158 0.00 0.00 0.00 4.16
2097 2228 4.818546 GCAAGTGCCTCATACATATCAAGT 59.181 41.667 0.00 0.00 34.31 3.16
2364 2495 1.595466 CAGCATCCTCATCCAAGAGC 58.405 55.000 0.00 0.00 34.26 4.09
2393 2524 6.608405 ACCTCCATTTGAAGCATTATGATCAA 59.392 34.615 0.00 8.94 0.00 2.57
2443 2574 0.111253 CCAAGTGGGGTCAAGCTCTT 59.889 55.000 0.00 0.00 0.00 2.85
2807 2959 3.502211 CCAAAGCGTTTGACTCCTGTAAT 59.498 43.478 10.71 0.00 43.26 1.89
2850 3002 2.621055 AGATATCTTGAGCTCTTCGCGT 59.379 45.455 16.19 0.00 45.59 6.01
3052 3204 6.316390 CCTGTAACCAAATTCTGTCATAGGAC 59.684 42.308 0.00 0.00 44.57 3.85
3466 3621 5.541845 TCCGTAGCTTCATGGATTTGATAG 58.458 41.667 0.00 0.00 0.00 2.08
3470 3625 3.185188 CGATCCGTAGCTTCATGGATTTG 59.815 47.826 10.91 4.68 43.11 2.32
3666 3821 5.864474 ACAGACTCTGACGATAAATGTGTTC 59.136 40.000 13.25 0.00 35.18 3.18
3730 3885 7.826690 TGCCCTACAGTCTGAATTTATTTTTC 58.173 34.615 6.91 0.00 0.00 2.29
3758 3913 6.429624 GTTCGGTTTATTCGGTTTTTGTACT 58.570 36.000 0.00 0.00 0.00 2.73
3765 3920 2.493035 ACGGTTCGGTTTATTCGGTTT 58.507 42.857 0.00 0.00 0.00 3.27
3766 3921 2.168326 ACGGTTCGGTTTATTCGGTT 57.832 45.000 0.00 0.00 0.00 4.44
3767 3922 3.525268 ATACGGTTCGGTTTATTCGGT 57.475 42.857 0.00 0.00 0.00 4.69
3768 3923 5.276820 GGTTAATACGGTTCGGTTTATTCGG 60.277 44.000 0.00 0.00 0.00 4.30
3769 3924 5.290643 TGGTTAATACGGTTCGGTTTATTCG 59.709 40.000 0.00 0.00 0.00 3.34
3770 3925 6.660887 TGGTTAATACGGTTCGGTTTATTC 57.339 37.500 0.00 0.00 0.00 1.75
3774 3929 8.611757 GTTAATATGGTTAATACGGTTCGGTTT 58.388 33.333 0.00 0.00 0.00 3.27
3776 3931 6.705825 GGTTAATATGGTTAATACGGTTCGGT 59.294 38.462 0.00 0.00 0.00 4.69
3778 3933 6.640499 TCGGTTAATATGGTTAATACGGTTCG 59.360 38.462 0.00 0.00 0.00 3.95
3779 3934 7.945033 TCGGTTAATATGGTTAATACGGTTC 57.055 36.000 0.00 0.00 0.00 3.62
3780 3935 7.042791 CGTTCGGTTAATATGGTTAATACGGTT 60.043 37.037 0.00 0.00 0.00 4.44
3782 3937 6.616260 GCGTTCGGTTAATATGGTTAATACGG 60.616 42.308 0.00 0.00 0.00 4.02
3783 3938 6.291385 GCGTTCGGTTAATATGGTTAATACG 58.709 40.000 0.00 0.00 0.00 3.06
3784 3939 6.347644 GGGCGTTCGGTTAATATGGTTAATAC 60.348 42.308 0.00 0.00 0.00 1.89
3785 3940 5.700373 GGGCGTTCGGTTAATATGGTTAATA 59.300 40.000 0.00 0.00 0.00 0.98
3786 3941 4.516321 GGGCGTTCGGTTAATATGGTTAAT 59.484 41.667 0.00 0.00 0.00 1.40
3787 3942 3.876320 GGGCGTTCGGTTAATATGGTTAA 59.124 43.478 0.00 0.00 0.00 2.01
3788 3943 3.118482 TGGGCGTTCGGTTAATATGGTTA 60.118 43.478 0.00 0.00 0.00 2.85
3789 3944 2.291365 GGGCGTTCGGTTAATATGGTT 58.709 47.619 0.00 0.00 0.00 3.67
3790 3945 1.209990 TGGGCGTTCGGTTAATATGGT 59.790 47.619 0.00 0.00 0.00 3.55
3791 3946 1.871039 CTGGGCGTTCGGTTAATATGG 59.129 52.381 0.00 0.00 0.00 2.74
3792 3947 1.263217 GCTGGGCGTTCGGTTAATATG 59.737 52.381 0.00 0.00 0.00 1.78
3793 3948 1.589803 GCTGGGCGTTCGGTTAATAT 58.410 50.000 0.00 0.00 0.00 1.28
3794 3949 0.462403 GGCTGGGCGTTCGGTTAATA 60.462 55.000 0.00 0.00 0.00 0.98
3795 3950 1.747745 GGCTGGGCGTTCGGTTAAT 60.748 57.895 0.00 0.00 0.00 1.40
3796 3951 2.358984 GGCTGGGCGTTCGGTTAA 60.359 61.111 0.00 0.00 0.00 2.01
3797 3952 4.397832 GGGCTGGGCGTTCGGTTA 62.398 66.667 0.00 0.00 0.00 2.85
3800 3955 4.530857 CTAGGGCTGGGCGTTCGG 62.531 72.222 0.00 0.00 0.00 4.30
3802 3957 4.096003 TGCTAGGGCTGGGCGTTC 62.096 66.667 0.00 0.00 39.59 3.95
3803 3958 4.101448 CTGCTAGGGCTGGGCGTT 62.101 66.667 0.00 0.00 39.59 4.84
3804 3959 3.976490 TACTGCTAGGGCTGGGCGT 62.976 63.158 0.00 0.00 40.90 5.68
3805 3960 3.154473 TACTGCTAGGGCTGGGCG 61.154 66.667 0.00 0.00 40.90 6.13
3806 3961 2.506472 GTACTGCTAGGGCTGGGC 59.494 66.667 0.00 0.00 40.90 5.36
3807 3962 0.754217 TACGTACTGCTAGGGCTGGG 60.754 60.000 0.00 0.00 40.90 4.45
3808 3963 0.384669 GTACGTACTGCTAGGGCTGG 59.615 60.000 18.47 0.00 40.90 4.85
3809 3964 1.390565 AGTACGTACTGCTAGGGCTG 58.609 55.000 26.87 0.00 42.04 4.85
3810 3965 3.287867 TTAGTACGTACTGCTAGGGCT 57.712 47.619 33.23 10.55 37.10 5.19
3811 3966 4.581077 AATTAGTACGTACTGCTAGGGC 57.419 45.455 33.23 2.25 37.10 5.19
3812 3967 7.308469 CCTCTAAATTAGTACGTACTGCTAGGG 60.308 44.444 33.23 24.52 37.10 3.53
3813 3968 7.228308 ACCTCTAAATTAGTACGTACTGCTAGG 59.772 40.741 33.23 27.06 37.10 3.02
3814 3969 8.068977 CACCTCTAAATTAGTACGTACTGCTAG 58.931 40.741 33.23 24.78 37.10 3.42
3815 3970 7.554118 ACACCTCTAAATTAGTACGTACTGCTA 59.446 37.037 33.23 20.27 37.10 3.49
3816 3971 6.376581 ACACCTCTAAATTAGTACGTACTGCT 59.623 38.462 33.23 19.44 37.10 4.24
3853 4010 6.952773 AAAACAGCAAGAGTAATAACACCA 57.047 33.333 0.00 0.00 0.00 4.17
3861 4018 5.593968 TCGTCAGTAAAACAGCAAGAGTAA 58.406 37.500 0.00 0.00 0.00 2.24
3872 4029 7.478667 CAGCACTCATATTTTCGTCAGTAAAAC 59.521 37.037 0.00 0.00 0.00 2.43
3891 4048 2.540101 GCCGTATAACACATCAGCACTC 59.460 50.000 0.00 0.00 0.00 3.51
3896 4053 7.715265 AGAAAATAGCCGTATAACACATCAG 57.285 36.000 0.00 0.00 0.00 2.90
3936 4095 9.747293 GGAGTCCTAACAGTACTAATGAAATAC 57.253 37.037 0.41 0.00 0.00 1.89
3947 4106 5.011840 ACCAAGAAAGGAGTCCTAACAGTAC 59.988 44.000 13.43 0.00 31.13 2.73
3996 4155 5.071250 AGTCAGCGGTAATTAATATGGGTCA 59.929 40.000 0.00 0.00 0.00 4.02
3999 4158 7.159372 ACTAAGTCAGCGGTAATTAATATGGG 58.841 38.462 0.00 0.00 0.00 4.00
4011 4170 4.332428 AAAGTTGTACTAAGTCAGCGGT 57.668 40.909 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.