Multiple sequence alignment - TraesCS4B01G274300

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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 TraesCS4B01G274300 chr4B 100.000 3192 0 0 1 3192 552020412 552017221 0.000000e+00 5895.0
1 TraesCS4B01G274300 chr4B 91.270 126 10 1 232 357 552025538 552025414 1.520000e-38 171.0
2 TraesCS4B01G274300 chr4B 95.050 101 3 2 586 685 23834139 23834040 1.190000e-34 158.0
3 TraesCS4B01G274300 chr4D 89.950 2398 107 59 737 3069 442900657 442898329 0.000000e+00 2970.0
4 TraesCS4B01G274300 chr4D 90.785 293 22 5 232 521 442901002 442900712 1.390000e-103 387.0
5 TraesCS4B01G274300 chr4D 91.892 111 3 3 3085 3192 442898269 442898162 1.980000e-32 150.0
6 TraesCS4B01G274300 chr4D 100.000 28 0 0 501 528 121432368 121432341 6.000000e-03 52.8
7 TraesCS4B01G274300 chr4A 89.711 2284 123 61 844 3069 24762574 24764803 0.000000e+00 2813.0
8 TraesCS4B01G274300 chr4A 88.415 164 19 0 2541 2704 621564031 621564194 6.980000e-47 198.0
9 TraesCS4B01G274300 chr4A 91.406 128 7 3 3065 3192 24764844 24764967 4.230000e-39 172.0
10 TraesCS4B01G274300 chr4A 93.578 109 4 3 578 683 163914579 163914471 3.300000e-35 159.0
11 TraesCS4B01G274300 chr4A 100.000 53 0 0 3140 3192 621564733 621564785 7.290000e-17 99.0
12 TraesCS4B01G274300 chr4A 97.727 44 0 1 232 275 24759783 24759825 1.230000e-09 75.0
13 TraesCS4B01G274300 chr2B 88.085 235 19 8 1 229 106093606 106093837 1.460000e-68 270.0
14 TraesCS4B01G274300 chr2B 86.611 239 22 8 1 234 510790870 510790637 4.090000e-64 255.0
15 TraesCS4B01G274300 chr2B 86.441 236 24 7 1 232 800237172 800236941 5.290000e-63 252.0
16 TraesCS4B01G274300 chr2B 94.000 100 5 1 585 684 31741628 31741726 1.980000e-32 150.0
17 TraesCS4B01G274300 chr6B 87.660 235 18 8 1 234 44789516 44789740 2.440000e-66 263.0
18 TraesCS4B01G274300 chr6B 86.008 243 21 11 1 232 687053431 687053671 6.840000e-62 248.0
19 TraesCS4B01G274300 chr6B 96.703 91 3 0 585 675 38003945 38004035 5.510000e-33 152.0
20 TraesCS4B01G274300 chr7D 86.667 240 24 6 1 234 539840707 539840944 3.160000e-65 259.0
21 TraesCS4B01G274300 chr5B 86.809 235 24 7 1 232 131019081 131018851 4.090000e-64 255.0
22 TraesCS4B01G274300 chr5B 85.837 233 25 7 3 232 596986137 596985910 1.140000e-59 241.0
23 TraesCS4B01G274300 chr5B 85.475 179 26 0 2541 2719 690909500 690909322 1.510000e-43 187.0
24 TraesCS4B01G274300 chr5B 100.000 53 0 0 3140 3192 690908799 690908747 7.290000e-17 99.0
25 TraesCS4B01G274300 chr5B 90.323 62 5 1 670 730 70793445 70793384 2.640000e-11 80.5
26 TraesCS4B01G274300 chr5B 100.000 36 0 0 232 267 653786083 653786048 2.050000e-07 67.6
27 TraesCS4B01G274300 chr5A 86.017 236 24 9 1 232 18565278 18565048 8.840000e-61 244.0
28 TraesCS4B01G274300 chr5A 90.769 65 4 2 670 733 48469138 48469201 5.670000e-13 86.1
29 TraesCS4B01G274300 chr5A 100.000 37 0 0 232 268 321891759 321891795 5.710000e-08 69.4
30 TraesCS4B01G274300 chr5D 88.415 164 19 0 2541 2704 547607269 547607432 6.980000e-47 198.0
31 TraesCS4B01G274300 chr5D 98.113 53 1 0 3140 3192 547607976 547608028 3.390000e-15 93.5
32 TraesCS4B01G274300 chr5D 91.045 67 5 1 670 735 59947779 59947845 4.390000e-14 89.8
33 TraesCS4B01G274300 chr5D 100.000 37 0 0 232 268 233158940 233158904 5.710000e-08 69.4
34 TraesCS4B01G274300 chrUn 87.805 164 20 0 2541 2704 68495178 68495341 3.250000e-45 193.0
35 TraesCS4B01G274300 chrUn 98.113 53 1 0 3140 3192 68495885 68495937 3.390000e-15 93.5
36 TraesCS4B01G274300 chr7B 96.939 98 3 0 578 675 414314548 414314451 7.080000e-37 165.0
37 TraesCS4B01G274300 chr7B 91.667 60 4 1 675 733 103571088 103571029 7.340000e-12 82.4
38 TraesCS4B01G274300 chr2D 98.901 91 1 0 585 675 433984845 433984755 2.550000e-36 163.0
39 TraesCS4B01G274300 chr2D 82.486 177 24 6 499 672 683347 683519 7.130000e-32 148.0
40 TraesCS4B01G274300 chr3B 95.146 103 3 2 576 676 15111010 15111112 9.160000e-36 161.0
41 TraesCS4B01G274300 chr3B 87.097 62 7 1 496 557 790189485 790189425 5.710000e-08 69.4
42 TraesCS4B01G274300 chr3B 100.000 36 0 0 232 267 7236579 7236614 2.050000e-07 67.6
43 TraesCS4B01G274300 chr3A 97.849 93 2 0 581 673 11617174 11617266 9.160000e-36 161.0
44 TraesCS4B01G274300 chr3A 87.013 77 9 1 499 575 12912168 12912243 5.670000e-13 86.1
45 TraesCS4B01G274300 chr3D 76.772 254 30 12 494 733 20751616 20751854 7.240000e-22 115.0
46 TraesCS4B01G274300 chr3D 84.615 91 13 1 499 589 274654233 274654144 4.390000e-14 89.8
47 TraesCS4B01G274300 chr3D 100.000 35 0 0 232 266 6226797 6226763 7.390000e-07 65.8
48 TraesCS4B01G274300 chr3D 100.000 35 0 0 232 266 535582210 535582176 7.390000e-07 65.8
49 TraesCS4B01G274300 chr3D 93.023 43 3 0 495 537 417212854 417212896 2.660000e-06 63.9
50 TraesCS4B01G274300 chr6D 93.750 64 4 0 670 733 305021342 305021405 2.620000e-16 97.1
51 TraesCS4B01G274300 chr1D 92.857 56 4 0 678 733 137636120 137636175 7.340000e-12 82.4
52 TraesCS4B01G274300 chr1D 91.667 60 4 1 675 734 451032987 451033045 7.340000e-12 82.4
53 TraesCS4B01G274300 chr1B 91.525 59 5 0 678 736 209993930 209993872 7.340000e-12 82.4
54 TraesCS4B01G274300 chr7A 83.871 62 9 1 495 556 8325335 8325395 1.240000e-04 58.4


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 TraesCS4B01G274300 chr4B 552017221 552020412 3191 True 5895 5895 100.000000 1 3192 1 chr4B.!!$R2 3191
1 TraesCS4B01G274300 chr4D 442898162 442901002 2840 True 1169 2970 90.875667 232 3192 3 chr4D.!!$R2 2960
2 TraesCS4B01G274300 chr4A 24759783 24764967 5184 False 1020 2813 92.948000 232 3192 3 chr4A.!!$F1 2960

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
153 154 0.419459 AGACAATGAGGAGGGGAGGT 59.581 55.0 0.0 0.0 0.00 3.85 F
186 187 0.475044 TGCCCTTTAGTCCCGTTTGT 59.525 50.0 0.0 0.0 0.00 2.83 F
475 493 0.747255 TTAGCATCGGCCTCAGAGTC 59.253 55.0 0.0 0.0 42.56 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 4387 0.659427 AATGCGGCTGACGAATGATG 59.341 50.000 7.31 0.0 40.93 3.07 R
1952 4399 1.063649 CATCACTGAGCAATGCGGC 59.936 57.895 0.00 0.0 0.00 6.53 R
2464 4961 0.961753 CCAGCACTTGGGTTCTTTCC 59.038 55.000 0.00 0.0 43.75 3.13 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 9.512435 TTTTTGCAAACCATGTCAAAATTTATG 57.488 25.926 12.39 0.00 40.87 1.90
27 28 7.798596 TTGCAAACCATGTCAAAATTTATGT 57.201 28.000 0.00 0.00 0.00 2.29
28 29 7.798596 TGCAAACCATGTCAAAATTTATGTT 57.201 28.000 0.00 0.00 0.00 2.71
29 30 8.218338 TGCAAACCATGTCAAAATTTATGTTT 57.782 26.923 0.00 0.00 0.00 2.83
30 31 8.680903 TGCAAACCATGTCAAAATTTATGTTTT 58.319 25.926 0.00 0.00 0.00 2.43
78 79 9.653287 TGTAGAAACATAACTACATCTCAAAGG 57.347 33.333 0.00 0.00 42.27 3.11
79 80 9.871238 GTAGAAACATAACTACATCTCAAAGGA 57.129 33.333 0.00 0.00 38.84 3.36
81 82 9.965902 AGAAACATAACTACATCTCAAAGGATT 57.034 29.630 0.00 0.00 0.00 3.01
146 147 9.801873 TTTTAAAACAGAAAAGACAATGAGGAG 57.198 29.630 0.00 0.00 0.00 3.69
147 148 6.396829 AAAACAGAAAAGACAATGAGGAGG 57.603 37.500 0.00 0.00 0.00 4.30
148 149 4.026356 ACAGAAAAGACAATGAGGAGGG 57.974 45.455 0.00 0.00 0.00 4.30
149 150 3.245052 ACAGAAAAGACAATGAGGAGGGG 60.245 47.826 0.00 0.00 0.00 4.79
150 151 3.009473 CAGAAAAGACAATGAGGAGGGGA 59.991 47.826 0.00 0.00 0.00 4.81
151 152 3.265479 AGAAAAGACAATGAGGAGGGGAG 59.735 47.826 0.00 0.00 0.00 4.30
152 153 1.589414 AAGACAATGAGGAGGGGAGG 58.411 55.000 0.00 0.00 0.00 4.30
153 154 0.419459 AGACAATGAGGAGGGGAGGT 59.581 55.000 0.00 0.00 0.00 3.85
154 155 1.651770 AGACAATGAGGAGGGGAGGTA 59.348 52.381 0.00 0.00 0.00 3.08
155 156 2.043227 GACAATGAGGAGGGGAGGTAG 58.957 57.143 0.00 0.00 0.00 3.18
156 157 1.651770 ACAATGAGGAGGGGAGGTAGA 59.348 52.381 0.00 0.00 0.00 2.59
157 158 2.324541 CAATGAGGAGGGGAGGTAGAG 58.675 57.143 0.00 0.00 0.00 2.43
158 159 1.626621 ATGAGGAGGGGAGGTAGAGT 58.373 55.000 0.00 0.00 0.00 3.24
159 160 1.394532 TGAGGAGGGGAGGTAGAGTT 58.605 55.000 0.00 0.00 0.00 3.01
160 161 1.722851 TGAGGAGGGGAGGTAGAGTTT 59.277 52.381 0.00 0.00 0.00 2.66
161 162 2.112190 GAGGAGGGGAGGTAGAGTTTG 58.888 57.143 0.00 0.00 0.00 2.93
162 163 1.722851 AGGAGGGGAGGTAGAGTTTGA 59.277 52.381 0.00 0.00 0.00 2.69
163 164 2.113777 AGGAGGGGAGGTAGAGTTTGAA 59.886 50.000 0.00 0.00 0.00 2.69
164 165 2.910977 GGAGGGGAGGTAGAGTTTGAAA 59.089 50.000 0.00 0.00 0.00 2.69
165 166 3.329814 GGAGGGGAGGTAGAGTTTGAAAA 59.670 47.826 0.00 0.00 0.00 2.29
166 167 4.018324 GGAGGGGAGGTAGAGTTTGAAAAT 60.018 45.833 0.00 0.00 0.00 1.82
167 168 5.516768 GGAGGGGAGGTAGAGTTTGAAAATT 60.517 44.000 0.00 0.00 0.00 1.82
168 169 5.325239 AGGGGAGGTAGAGTTTGAAAATTG 58.675 41.667 0.00 0.00 0.00 2.32
169 170 4.082190 GGGGAGGTAGAGTTTGAAAATTGC 60.082 45.833 0.00 0.00 0.00 3.56
170 171 4.082190 GGGAGGTAGAGTTTGAAAATTGCC 60.082 45.833 0.00 0.00 0.00 4.52
171 172 4.082190 GGAGGTAGAGTTTGAAAATTGCCC 60.082 45.833 0.00 0.00 0.00 5.36
172 173 4.740902 AGGTAGAGTTTGAAAATTGCCCT 58.259 39.130 0.00 0.00 0.00 5.19
173 174 5.147767 AGGTAGAGTTTGAAAATTGCCCTT 58.852 37.500 0.00 0.00 0.00 3.95
174 175 5.602561 AGGTAGAGTTTGAAAATTGCCCTTT 59.397 36.000 0.00 0.00 0.00 3.11
175 176 6.780522 AGGTAGAGTTTGAAAATTGCCCTTTA 59.219 34.615 0.00 0.00 0.00 1.85
176 177 7.039714 AGGTAGAGTTTGAAAATTGCCCTTTAG 60.040 37.037 0.00 0.00 0.00 1.85
177 178 6.731292 AGAGTTTGAAAATTGCCCTTTAGT 57.269 33.333 0.00 0.00 0.00 2.24
178 179 6.749139 AGAGTTTGAAAATTGCCCTTTAGTC 58.251 36.000 0.00 0.00 0.00 2.59
179 180 5.853936 AGTTTGAAAATTGCCCTTTAGTCC 58.146 37.500 0.00 0.00 0.00 3.85
180 181 4.882842 TTGAAAATTGCCCTTTAGTCCC 57.117 40.909 0.00 0.00 0.00 4.46
181 182 2.823154 TGAAAATTGCCCTTTAGTCCCG 59.177 45.455 0.00 0.00 0.00 5.14
182 183 2.597578 AAATTGCCCTTTAGTCCCGT 57.402 45.000 0.00 0.00 0.00 5.28
183 184 2.597578 AATTGCCCTTTAGTCCCGTT 57.402 45.000 0.00 0.00 0.00 4.44
184 185 2.597578 ATTGCCCTTTAGTCCCGTTT 57.402 45.000 0.00 0.00 0.00 3.60
185 186 1.611519 TTGCCCTTTAGTCCCGTTTG 58.388 50.000 0.00 0.00 0.00 2.93
186 187 0.475044 TGCCCTTTAGTCCCGTTTGT 59.525 50.000 0.00 0.00 0.00 2.83
187 188 0.879090 GCCCTTTAGTCCCGTTTGTG 59.121 55.000 0.00 0.00 0.00 3.33
188 189 1.543871 GCCCTTTAGTCCCGTTTGTGA 60.544 52.381 0.00 0.00 0.00 3.58
189 190 2.878526 GCCCTTTAGTCCCGTTTGTGAT 60.879 50.000 0.00 0.00 0.00 3.06
190 191 3.620472 GCCCTTTAGTCCCGTTTGTGATA 60.620 47.826 0.00 0.00 0.00 2.15
191 192 3.937079 CCCTTTAGTCCCGTTTGTGATAC 59.063 47.826 0.00 0.00 0.00 2.24
192 193 4.563993 CCCTTTAGTCCCGTTTGTGATACA 60.564 45.833 0.00 0.00 0.00 2.29
193 194 4.998672 CCTTTAGTCCCGTTTGTGATACAA 59.001 41.667 0.00 0.00 36.11 2.41
194 195 5.470777 CCTTTAGTCCCGTTTGTGATACAAA 59.529 40.000 3.20 3.20 44.91 2.83
210 211 9.483916 TGTGATACAAACCGGAACTATATATTG 57.516 33.333 9.46 1.60 0.00 1.90
211 212 9.701098 GTGATACAAACCGGAACTATATATTGA 57.299 33.333 9.46 0.00 0.00 2.57
212 213 9.701098 TGATACAAACCGGAACTATATATTGAC 57.299 33.333 9.46 0.00 0.00 3.18
213 214 9.148104 GATACAAACCGGAACTATATATTGACC 57.852 37.037 9.46 3.83 0.00 4.02
214 215 6.293698 ACAAACCGGAACTATATATTGACCC 58.706 40.000 9.46 1.46 0.00 4.46
215 216 6.100714 ACAAACCGGAACTATATATTGACCCT 59.899 38.462 9.46 0.00 0.00 4.34
216 217 6.758806 AACCGGAACTATATATTGACCCTT 57.241 37.500 9.46 0.00 0.00 3.95
217 218 6.758806 ACCGGAACTATATATTGACCCTTT 57.241 37.500 9.46 0.00 0.00 3.11
218 219 7.860649 ACCGGAACTATATATTGACCCTTTA 57.139 36.000 9.46 0.00 0.00 1.85
219 220 7.904205 ACCGGAACTATATATTGACCCTTTAG 58.096 38.462 9.46 0.00 0.00 1.85
220 221 7.511714 ACCGGAACTATATATTGACCCTTTAGT 59.488 37.037 9.46 0.00 0.00 2.24
221 222 8.033626 CCGGAACTATATATTGACCCTTTAGTC 58.966 40.741 0.00 0.00 37.28 2.59
222 223 8.033626 CGGAACTATATATTGACCCTTTAGTCC 58.966 40.741 0.95 0.00 35.83 3.85
223 224 9.102453 GGAACTATATATTGACCCTTTAGTCCT 57.898 37.037 0.95 0.00 35.83 3.85
224 225 9.930693 GAACTATATATTGACCCTTTAGTCCTG 57.069 37.037 0.95 0.00 35.83 3.86
225 226 8.437274 ACTATATATTGACCCTTTAGTCCTGG 57.563 38.462 0.95 0.00 35.83 4.45
226 227 8.017251 ACTATATATTGACCCTTTAGTCCTGGT 58.983 37.037 0.95 0.00 35.83 4.00
227 228 7.707467 ATATATTGACCCTTTAGTCCTGGTT 57.293 36.000 0.00 0.00 35.83 3.67
228 229 4.741928 ATTGACCCTTTAGTCCTGGTTT 57.258 40.909 0.00 0.00 35.83 3.27
229 230 5.853572 ATTGACCCTTTAGTCCTGGTTTA 57.146 39.130 0.00 0.00 35.83 2.01
230 231 5.853572 TTGACCCTTTAGTCCTGGTTTAT 57.146 39.130 0.00 0.00 35.83 1.40
279 280 4.139786 TCCTGACTTGTACGTACAGTTCT 58.860 43.478 26.04 11.46 37.52 3.01
287 288 7.898946 ACTTGTACGTACAGTTCTGTTTTAAC 58.101 34.615 26.04 2.67 37.52 2.01
301 302 8.711457 GTTCTGTTTTAACGCCTTAATGTAGTA 58.289 33.333 0.00 0.00 0.00 1.82
302 303 8.470040 TCTGTTTTAACGCCTTAATGTAGTAG 57.530 34.615 0.00 0.00 0.00 2.57
356 357 9.854668 AGTCTATCACTGTACATATACTTGTCT 57.145 33.333 0.00 0.00 32.26 3.41
378 379 4.376450 TTTTGTTGTTGTTGTTGCGAAC 57.624 36.364 0.00 0.00 0.00 3.95
395 396 4.794762 TGCGAACGTGTACATATACTTGTC 59.205 41.667 0.00 0.00 32.00 3.18
405 406 7.428761 GTGTACATATACTTGTCGAACTCTCAC 59.571 40.741 0.00 0.00 32.00 3.51
422 439 4.537751 TCTCACTTGAGATCCGTTCCTAT 58.462 43.478 4.76 0.00 45.48 2.57
424 441 5.765677 TCTCACTTGAGATCCGTTCCTATAG 59.234 44.000 4.76 0.00 45.48 1.31
430 447 6.645790 TGAGATCCGTTCCTATAGGTAAAC 57.354 41.667 18.51 14.61 36.34 2.01
475 493 0.747255 TTAGCATCGGCCTCAGAGTC 59.253 55.000 0.00 0.00 42.56 3.36
502 520 8.394121 CCTCTGAATAAAAGCTGAAACATACTC 58.606 37.037 0.00 0.00 0.00 2.59
504 522 7.336931 TCTGAATAAAAGCTGAAACATACTCCC 59.663 37.037 0.00 0.00 0.00 4.30
505 523 7.175104 TGAATAAAAGCTGAAACATACTCCCT 58.825 34.615 0.00 0.00 0.00 4.20
506 524 7.336931 TGAATAAAAGCTGAAACATACTCCCTC 59.663 37.037 0.00 0.00 0.00 4.30
507 525 4.917906 AAAGCTGAAACATACTCCCTCT 57.082 40.909 0.00 0.00 0.00 3.69
508 526 3.902881 AGCTGAAACATACTCCCTCTG 57.097 47.619 0.00 0.00 0.00 3.35
509 527 3.177228 AGCTGAAACATACTCCCTCTGT 58.823 45.455 0.00 0.00 0.00 3.41
510 528 3.584848 AGCTGAAACATACTCCCTCTGTT 59.415 43.478 0.00 0.00 34.71 3.16
511 529 4.042187 AGCTGAAACATACTCCCTCTGTTT 59.958 41.667 0.00 0.00 43.68 2.83
569 587 3.149196 CAACATACAGAGCAAAGTGGGT 58.851 45.455 0.00 0.00 0.00 4.51
570 588 2.783135 ACATACAGAGCAAAGTGGGTG 58.217 47.619 0.00 0.00 0.00 4.61
571 589 2.371841 ACATACAGAGCAAAGTGGGTGA 59.628 45.455 0.00 0.00 0.00 4.02
575 593 2.158623 ACAGAGCAAAGTGGGTGAATCA 60.159 45.455 0.00 0.00 0.00 2.57
576 594 2.486982 CAGAGCAAAGTGGGTGAATCAG 59.513 50.000 0.00 0.00 0.00 2.90
577 595 1.200948 GAGCAAAGTGGGTGAATCAGC 59.799 52.381 3.49 3.49 0.00 4.26
578 596 0.961019 GCAAAGTGGGTGAATCAGCA 59.039 50.000 14.70 0.00 33.07 4.41
579 597 1.336240 GCAAAGTGGGTGAATCAGCAC 60.336 52.381 14.70 10.18 38.05 4.40
581 599 2.191128 AAGTGGGTGAATCAGCACTC 57.809 50.000 14.70 5.10 39.73 3.51
582 600 1.356124 AGTGGGTGAATCAGCACTCT 58.644 50.000 14.70 7.12 39.98 3.24
583 601 1.002888 AGTGGGTGAATCAGCACTCTG 59.997 52.381 14.70 0.00 39.98 3.35
593 611 2.171840 TCAGCACTCTGAACTACTCCC 58.828 52.381 0.00 0.00 45.69 4.30
594 612 2.175202 CAGCACTCTGAACTACTCCCT 58.825 52.381 0.00 0.00 42.95 4.20
595 613 2.165437 CAGCACTCTGAACTACTCCCTC 59.835 54.545 0.00 0.00 42.95 4.30
596 614 2.042433 AGCACTCTGAACTACTCCCTCT 59.958 50.000 0.00 0.00 0.00 3.69
597 615 2.165437 GCACTCTGAACTACTCCCTCTG 59.835 54.545 0.00 0.00 0.00 3.35
598 616 3.426615 CACTCTGAACTACTCCCTCTGT 58.573 50.000 0.00 0.00 0.00 3.41
599 617 4.590918 CACTCTGAACTACTCCCTCTGTA 58.409 47.826 0.00 0.00 0.00 2.74
600 618 5.010933 CACTCTGAACTACTCCCTCTGTAA 58.989 45.833 0.00 0.00 0.00 2.41
601 619 5.477291 CACTCTGAACTACTCCCTCTGTAAA 59.523 44.000 0.00 0.00 0.00 2.01
602 620 5.477637 ACTCTGAACTACTCCCTCTGTAAAC 59.522 44.000 0.00 0.00 0.00 2.01
603 621 5.642165 TCTGAACTACTCCCTCTGTAAACT 58.358 41.667 0.00 0.00 0.00 2.66
604 622 6.787170 TCTGAACTACTCCCTCTGTAAACTA 58.213 40.000 0.00 0.00 0.00 2.24
605 623 7.236529 TCTGAACTACTCCCTCTGTAAACTAA 58.763 38.462 0.00 0.00 0.00 2.24
606 624 7.894364 TCTGAACTACTCCCTCTGTAAACTAAT 59.106 37.037 0.00 0.00 0.00 1.73
607 625 9.186837 CTGAACTACTCCCTCTGTAAACTAATA 57.813 37.037 0.00 0.00 0.00 0.98
608 626 9.710818 TGAACTACTCCCTCTGTAAACTAATAT 57.289 33.333 0.00 0.00 0.00 1.28
614 632 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
616 634 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
648 666 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
649 667 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
650 668 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
651 669 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
663 681 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
664 682 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
665 683 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
666 684 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
667 685 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
668 686 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
669 687 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
670 688 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
671 689 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
708 726 9.682465 AGTCCATAGTAAAATCCCTAAAAAGAC 57.318 33.333 0.00 0.00 0.00 3.01
709 727 9.682465 GTCCATAGTAAAATCCCTAAAAAGACT 57.318 33.333 0.00 0.00 0.00 3.24
729 747 9.731001 AAAGACTTATATTTAGGAAGAGAGGGA 57.269 33.333 0.00 0.00 0.00 4.20
730 748 8.950007 AGACTTATATTTAGGAAGAGAGGGAG 57.050 38.462 0.00 0.00 0.00 4.30
784 806 4.859304 TGTTCTTTTCTGCATGCTCATT 57.141 36.364 20.33 0.00 0.00 2.57
785 807 4.801891 TGTTCTTTTCTGCATGCTCATTC 58.198 39.130 20.33 1.58 0.00 2.67
786 808 4.171754 GTTCTTTTCTGCATGCTCATTCC 58.828 43.478 20.33 0.00 0.00 3.01
794 816 1.871080 CATGCTCATTCCTCCGGTAC 58.129 55.000 0.00 0.00 0.00 3.34
816 838 3.806591 GCTGTTGCTACCGTAGACA 57.193 52.632 9.88 5.02 36.03 3.41
817 839 1.630148 GCTGTTGCTACCGTAGACAG 58.370 55.000 17.36 17.36 36.03 3.51
818 840 1.736032 GCTGTTGCTACCGTAGACAGG 60.736 57.143 20.73 9.31 36.03 4.00
873 3285 1.863662 GACACGGACAAGGAGCGAGA 61.864 60.000 0.00 0.00 0.00 4.04
875 3287 1.303398 ACGGACAAGGAGCGAGAGA 60.303 57.895 0.00 0.00 0.00 3.10
896 3311 1.227674 CACCTATCCTCAAGCCGGC 60.228 63.158 21.89 21.89 0.00 6.13
897 3312 1.383248 ACCTATCCTCAAGCCGGCT 60.383 57.895 27.08 27.08 0.00 5.52
931 3350 2.124695 GACACCCAATCGGCCTCC 60.125 66.667 0.00 0.00 33.26 4.30
934 3353 4.115199 ACCCAATCGGCCTCCAGC 62.115 66.667 0.00 0.00 42.60 4.85
948 3367 2.679716 CAGCCTCAAGGGGAAGGG 59.320 66.667 0.00 0.00 35.18 3.95
967 3394 2.294449 GAAGCACCTTCCCCTTCTTT 57.706 50.000 0.00 0.00 34.71 2.52
982 3409 4.047822 CCTTCTTTGCTAGCTATCACTCG 58.952 47.826 17.23 0.00 0.00 4.18
1109 3540 4.886121 GGTGCCCGCCGCTACTAC 62.886 72.222 0.00 0.00 38.78 2.73
1731 4174 2.222013 GGAGGAGTCCGGGTGGTTT 61.222 63.158 0.00 0.00 36.30 3.27
1934 4381 4.959399 TGCATCCATCGTGCATGA 57.041 50.000 11.83 11.83 46.76 3.07
1940 4387 3.669824 GCATCCATCGTGCATGAATGATC 60.670 47.826 18.93 11.35 42.08 2.92
1965 4412 2.789917 GTCAGCCGCATTGCTCAG 59.210 61.111 7.12 0.00 40.32 3.35
1975 4422 3.120304 CCGCATTGCTCAGTGATGATATG 60.120 47.826 7.12 0.00 0.00 1.78
1976 4423 3.667166 CGCATTGCTCAGTGATGATATGC 60.667 47.826 7.12 14.66 0.00 3.14
1977 4424 3.502595 GCATTGCTCAGTGATGATATGCT 59.497 43.478 16.25 0.00 0.00 3.79
2008 4457 1.605058 TTGGACAGTCTAGCGGGCTC 61.605 60.000 0.00 0.00 0.00 4.70
2020 4469 4.035102 GGGCTCGGGTTCAGGCTT 62.035 66.667 0.00 0.00 36.67 4.35
2137 4586 4.695231 CTCGTGCCCGTCGTCGTT 62.695 66.667 0.71 0.00 35.01 3.85
2197 4646 3.687698 AGCACGACAACTTGTAACTGTTT 59.312 39.130 0.00 0.00 0.00 2.83
2198 4647 4.155280 AGCACGACAACTTGTAACTGTTTT 59.845 37.500 0.00 0.00 0.00 2.43
2213 4681 6.436843 AACTGTTTTGAGTTACACAAGGAG 57.563 37.500 0.00 0.00 34.29 3.69
2214 4682 4.881850 ACTGTTTTGAGTTACACAAGGAGG 59.118 41.667 0.00 0.00 0.00 4.30
2215 4683 5.105567 TGTTTTGAGTTACACAAGGAGGA 57.894 39.130 0.00 0.00 0.00 3.71
2231 4699 6.825721 ACAAGGAGGAAATCATGTACATTCTC 59.174 38.462 5.37 0.00 30.30 2.87
2241 4709 4.224818 TCATGTACATTCTCACACATGGGA 59.775 41.667 5.37 0.00 45.30 4.37
2242 4710 4.206477 TGTACATTCTCACACATGGGAG 57.794 45.455 0.00 4.66 46.71 4.30
2260 4728 3.559171 GGGAGTGAATCTTGTAACTGCCA 60.559 47.826 7.26 0.00 46.91 4.92
2289 4757 3.517602 TCAATCTGTACACATGCGGTAC 58.482 45.455 17.11 17.11 41.11 3.34
2395 4887 3.749088 ACGAACGAGCATAAAAATGGACA 59.251 39.130 0.14 0.00 0.00 4.02
2396 4888 4.088648 CGAACGAGCATAAAAATGGACAC 58.911 43.478 0.00 0.00 0.00 3.67
2401 4893 4.393062 CGAGCATAAAAATGGACACACTCT 59.607 41.667 0.00 0.00 0.00 3.24
2428 4920 3.132160 AGAATTCATCGCATCAGCTCAG 58.868 45.455 8.44 0.00 39.10 3.35
2490 4987 0.466189 ACCCAAGTGCTGGTGACAAG 60.466 55.000 0.00 0.00 44.76 3.16
2534 5032 1.097547 CGCCACCTATTTCTGCCAGG 61.098 60.000 0.00 0.00 35.45 4.45
2547 5046 1.459592 CTGCCAGGAAACGTTTACTCG 59.540 52.381 23.01 17.77 0.00 4.18
2653 5152 3.862267 GTCCTCGATCTTTGTCATCACAG 59.138 47.826 0.00 0.00 32.71 3.66
2702 5201 0.107456 AACACAGCTCCTGTCACCAG 59.893 55.000 0.00 0.00 43.43 4.00
2704 5203 2.433838 CAGCTCCTGTCACCAGCG 60.434 66.667 0.00 0.00 38.26 5.18
2775 5275 6.389906 AGCTGATAAACTGGCATAACAAAAC 58.610 36.000 0.00 0.00 0.00 2.43
2776 5276 6.209391 AGCTGATAAACTGGCATAACAAAACT 59.791 34.615 0.00 0.00 0.00 2.66
2832 5337 7.509141 TCAAAGCAAATCAATTGACAGTCTA 57.491 32.000 11.07 0.00 41.85 2.59
2857 5362 7.327214 ACAGAAATAGGAGATCACAACTTCTC 58.673 38.462 0.00 0.00 38.10 2.87
2886 5394 5.674215 AAACGAAAACGAACAAACATGAC 57.326 34.783 0.00 0.00 0.00 3.06
2890 5398 1.018148 AACGAACAAACATGACGCCA 58.982 45.000 0.00 0.00 0.00 5.69
2895 5407 4.222886 CGAACAAACATGACGCCAATAAA 58.777 39.130 0.00 0.00 0.00 1.40
2981 5493 5.643777 GCAAAATCCTACTTGCAGAAGACTA 59.356 40.000 2.07 0.00 45.81 2.59
3025 5537 1.065126 AGGCTAGGACAAACAGGCATC 60.065 52.381 0.00 0.00 37.32 3.91
3030 5542 1.168714 GGACAAACAGGCATCAGGAC 58.831 55.000 0.00 0.00 0.00 3.85
3032 5544 2.027192 GGACAAACAGGCATCAGGACTA 60.027 50.000 0.00 0.00 29.10 2.59
3048 5560 4.267928 CAGGACTAACTAAATGTAGCGTGC 59.732 45.833 0.00 0.00 0.00 5.34
3083 5641 8.810427 CAATGATAACAGCATTAATGTTTGTCC 58.190 33.333 20.57 15.24 41.08 4.02
3103 5661 1.132262 CCGGCGTTGACAAAATATGCT 59.868 47.619 6.01 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.512435 CATAAATTTTGACATGGTTTGCAAAAA 57.488 25.926 14.67 5.83 40.87 1.94
1 2 8.680903 ACATAAATTTTGACATGGTTTGCAAAA 58.319 25.926 14.67 0.00 41.30 2.44
2 3 8.218338 ACATAAATTTTGACATGGTTTGCAAA 57.782 26.923 8.05 8.05 32.92 3.68
3 4 7.798596 ACATAAATTTTGACATGGTTTGCAA 57.201 28.000 0.00 0.00 0.00 4.08
4 5 7.798596 AACATAAATTTTGACATGGTTTGCA 57.201 28.000 0.00 0.00 0.00 4.08
52 53 9.653287 CCTTTGAGATGTAGTTATGTTTCTACA 57.347 33.333 7.34 7.34 46.45 2.74
53 54 9.871238 TCCTTTGAGATGTAGTTATGTTTCTAC 57.129 33.333 0.00 0.00 37.58 2.59
55 56 9.965902 AATCCTTTGAGATGTAGTTATGTTTCT 57.034 29.630 0.00 0.00 0.00 2.52
120 121 9.801873 CTCCTCATTGTCTTTTCTGTTTTAAAA 57.198 29.630 0.00 0.00 0.00 1.52
121 122 8.413229 CCTCCTCATTGTCTTTTCTGTTTTAAA 58.587 33.333 0.00 0.00 0.00 1.52
122 123 7.014230 CCCTCCTCATTGTCTTTTCTGTTTTAA 59.986 37.037 0.00 0.00 0.00 1.52
123 124 6.490040 CCCTCCTCATTGTCTTTTCTGTTTTA 59.510 38.462 0.00 0.00 0.00 1.52
124 125 5.302823 CCCTCCTCATTGTCTTTTCTGTTTT 59.697 40.000 0.00 0.00 0.00 2.43
125 126 4.829492 CCCTCCTCATTGTCTTTTCTGTTT 59.171 41.667 0.00 0.00 0.00 2.83
126 127 4.401925 CCCTCCTCATTGTCTTTTCTGTT 58.598 43.478 0.00 0.00 0.00 3.16
127 128 3.245052 CCCCTCCTCATTGTCTTTTCTGT 60.245 47.826 0.00 0.00 0.00 3.41
128 129 3.009473 TCCCCTCCTCATTGTCTTTTCTG 59.991 47.826 0.00 0.00 0.00 3.02
129 130 3.260205 TCCCCTCCTCATTGTCTTTTCT 58.740 45.455 0.00 0.00 0.00 2.52
130 131 3.615155 CTCCCCTCCTCATTGTCTTTTC 58.385 50.000 0.00 0.00 0.00 2.29
131 132 2.310052 CCTCCCCTCCTCATTGTCTTTT 59.690 50.000 0.00 0.00 0.00 2.27
132 133 1.918957 CCTCCCCTCCTCATTGTCTTT 59.081 52.381 0.00 0.00 0.00 2.52
133 134 1.203492 ACCTCCCCTCCTCATTGTCTT 60.203 52.381 0.00 0.00 0.00 3.01
134 135 0.419459 ACCTCCCCTCCTCATTGTCT 59.581 55.000 0.00 0.00 0.00 3.41
135 136 2.043227 CTACCTCCCCTCCTCATTGTC 58.957 57.143 0.00 0.00 0.00 3.18
136 137 1.651770 TCTACCTCCCCTCCTCATTGT 59.348 52.381 0.00 0.00 0.00 2.71
137 138 2.324541 CTCTACCTCCCCTCCTCATTG 58.675 57.143 0.00 0.00 0.00 2.82
138 139 1.940957 ACTCTACCTCCCCTCCTCATT 59.059 52.381 0.00 0.00 0.00 2.57
139 140 1.626621 ACTCTACCTCCCCTCCTCAT 58.373 55.000 0.00 0.00 0.00 2.90
140 141 1.394532 AACTCTACCTCCCCTCCTCA 58.605 55.000 0.00 0.00 0.00 3.86
141 142 2.112190 CAAACTCTACCTCCCCTCCTC 58.888 57.143 0.00 0.00 0.00 3.71
142 143 1.722851 TCAAACTCTACCTCCCCTCCT 59.277 52.381 0.00 0.00 0.00 3.69
143 144 2.249309 TCAAACTCTACCTCCCCTCC 57.751 55.000 0.00 0.00 0.00 4.30
144 145 4.635699 TTTTCAAACTCTACCTCCCCTC 57.364 45.455 0.00 0.00 0.00 4.30
145 146 5.325239 CAATTTTCAAACTCTACCTCCCCT 58.675 41.667 0.00 0.00 0.00 4.79
146 147 4.082190 GCAATTTTCAAACTCTACCTCCCC 60.082 45.833 0.00 0.00 0.00 4.81
147 148 4.082190 GGCAATTTTCAAACTCTACCTCCC 60.082 45.833 0.00 0.00 0.00 4.30
148 149 4.082190 GGGCAATTTTCAAACTCTACCTCC 60.082 45.833 0.00 0.00 0.00 4.30
149 150 4.767409 AGGGCAATTTTCAAACTCTACCTC 59.233 41.667 0.00 0.00 0.00 3.85
150 151 4.740902 AGGGCAATTTTCAAACTCTACCT 58.259 39.130 0.00 0.00 0.00 3.08
151 152 5.468540 AAGGGCAATTTTCAAACTCTACC 57.531 39.130 0.00 0.00 0.00 3.18
152 153 7.658261 ACTAAAGGGCAATTTTCAAACTCTAC 58.342 34.615 0.00 0.00 0.00 2.59
153 154 7.039993 GGACTAAAGGGCAATTTTCAAACTCTA 60.040 37.037 0.00 0.00 0.00 2.43
154 155 6.239317 GGACTAAAGGGCAATTTTCAAACTCT 60.239 38.462 0.00 0.00 0.00 3.24
155 156 5.926542 GGACTAAAGGGCAATTTTCAAACTC 59.073 40.000 0.00 0.00 0.00 3.01
156 157 5.221641 GGGACTAAAGGGCAATTTTCAAACT 60.222 40.000 0.00 0.00 0.00 2.66
157 158 4.994852 GGGACTAAAGGGCAATTTTCAAAC 59.005 41.667 0.00 0.00 0.00 2.93
158 159 4.262249 CGGGACTAAAGGGCAATTTTCAAA 60.262 41.667 0.00 0.00 0.00 2.69
159 160 3.257127 CGGGACTAAAGGGCAATTTTCAA 59.743 43.478 0.00 0.00 0.00 2.69
160 161 2.823154 CGGGACTAAAGGGCAATTTTCA 59.177 45.455 0.00 0.00 0.00 2.69
161 162 2.823747 ACGGGACTAAAGGGCAATTTTC 59.176 45.455 0.00 0.00 0.00 2.29
162 163 2.884320 ACGGGACTAAAGGGCAATTTT 58.116 42.857 0.00 0.00 0.00 1.82
163 164 2.597578 ACGGGACTAAAGGGCAATTT 57.402 45.000 0.00 0.00 0.00 1.82
164 165 2.560981 CAAACGGGACTAAAGGGCAATT 59.439 45.455 0.00 0.00 0.00 2.32
165 166 2.167662 CAAACGGGACTAAAGGGCAAT 58.832 47.619 0.00 0.00 0.00 3.56
166 167 1.133730 ACAAACGGGACTAAAGGGCAA 60.134 47.619 0.00 0.00 0.00 4.52
167 168 0.475044 ACAAACGGGACTAAAGGGCA 59.525 50.000 0.00 0.00 0.00 5.36
168 169 0.879090 CACAAACGGGACTAAAGGGC 59.121 55.000 0.00 0.00 0.00 5.19
169 170 2.554370 TCACAAACGGGACTAAAGGG 57.446 50.000 0.00 0.00 0.00 3.95
170 171 4.571919 TGTATCACAAACGGGACTAAAGG 58.428 43.478 0.00 0.00 0.00 3.11
171 172 6.548441 TTTGTATCACAAACGGGACTAAAG 57.452 37.500 0.45 0.00 42.55 1.85
184 185 9.483916 CAATATATAGTTCCGGTTTGTATCACA 57.516 33.333 0.00 0.00 0.00 3.58
185 186 9.701098 TCAATATATAGTTCCGGTTTGTATCAC 57.299 33.333 0.00 0.00 0.00 3.06
186 187 9.701098 GTCAATATATAGTTCCGGTTTGTATCA 57.299 33.333 0.00 0.00 0.00 2.15
187 188 9.148104 GGTCAATATATAGTTCCGGTTTGTATC 57.852 37.037 0.00 0.00 0.00 2.24
188 189 8.098912 GGGTCAATATATAGTTCCGGTTTGTAT 58.901 37.037 0.00 0.00 0.00 2.29
189 190 7.290714 AGGGTCAATATATAGTTCCGGTTTGTA 59.709 37.037 0.00 0.00 0.00 2.41
190 191 6.100714 AGGGTCAATATATAGTTCCGGTTTGT 59.899 38.462 0.00 0.00 0.00 2.83
191 192 6.531021 AGGGTCAATATATAGTTCCGGTTTG 58.469 40.000 0.00 0.00 0.00 2.93
192 193 6.758806 AGGGTCAATATATAGTTCCGGTTT 57.241 37.500 0.00 0.00 0.00 3.27
193 194 6.758806 AAGGGTCAATATATAGTTCCGGTT 57.241 37.500 0.00 0.00 0.00 4.44
194 195 6.758806 AAAGGGTCAATATATAGTTCCGGT 57.241 37.500 0.00 0.00 0.00 5.28
195 196 7.904205 ACTAAAGGGTCAATATATAGTTCCGG 58.096 38.462 0.00 0.00 0.00 5.14
196 197 8.033626 GGACTAAAGGGTCAATATATAGTTCCG 58.966 40.741 0.00 0.00 37.91 4.30
197 198 9.102453 AGGACTAAAGGGTCAATATATAGTTCC 57.898 37.037 0.00 0.00 37.91 3.62
198 199 9.930693 CAGGACTAAAGGGTCAATATATAGTTC 57.069 37.037 0.00 0.00 37.91 3.01
199 200 8.881262 CCAGGACTAAAGGGTCAATATATAGTT 58.119 37.037 0.00 0.00 37.91 2.24
200 201 8.017251 ACCAGGACTAAAGGGTCAATATATAGT 58.983 37.037 0.00 0.00 37.91 2.12
201 202 8.437274 ACCAGGACTAAAGGGTCAATATATAG 57.563 38.462 0.00 0.00 37.91 1.31
202 203 8.808240 AACCAGGACTAAAGGGTCAATATATA 57.192 34.615 0.00 0.00 37.91 0.86
203 204 7.707467 AACCAGGACTAAAGGGTCAATATAT 57.293 36.000 0.00 0.00 37.91 0.86
204 205 7.519347 AAACCAGGACTAAAGGGTCAATATA 57.481 36.000 0.00 0.00 37.91 0.86
205 206 6.402981 AAACCAGGACTAAAGGGTCAATAT 57.597 37.500 0.00 0.00 37.91 1.28
206 207 5.853572 AAACCAGGACTAAAGGGTCAATA 57.146 39.130 0.00 0.00 37.91 1.90
207 208 4.741928 AAACCAGGACTAAAGGGTCAAT 57.258 40.909 0.00 0.00 37.91 2.57
208 209 5.073965 ACATAAACCAGGACTAAAGGGTCAA 59.926 40.000 0.00 0.00 37.91 3.18
209 210 4.600111 ACATAAACCAGGACTAAAGGGTCA 59.400 41.667 0.00 0.00 37.91 4.02
210 211 5.045797 AGACATAAACCAGGACTAAAGGGTC 60.046 44.000 0.00 0.00 32.01 4.46
211 212 4.850386 AGACATAAACCAGGACTAAAGGGT 59.150 41.667 0.00 0.00 34.43 4.34
212 213 5.186198 CAGACATAAACCAGGACTAAAGGG 58.814 45.833 0.00 0.00 0.00 3.95
213 214 5.186198 CCAGACATAAACCAGGACTAAAGG 58.814 45.833 0.00 0.00 0.00 3.11
214 215 4.636206 GCCAGACATAAACCAGGACTAAAG 59.364 45.833 0.00 0.00 0.00 1.85
215 216 4.585879 GCCAGACATAAACCAGGACTAAA 58.414 43.478 0.00 0.00 0.00 1.85
216 217 3.369052 CGCCAGACATAAACCAGGACTAA 60.369 47.826 0.00 0.00 0.00 2.24
217 218 2.167693 CGCCAGACATAAACCAGGACTA 59.832 50.000 0.00 0.00 0.00 2.59
218 219 1.066143 CGCCAGACATAAACCAGGACT 60.066 52.381 0.00 0.00 0.00 3.85
219 220 1.369625 CGCCAGACATAAACCAGGAC 58.630 55.000 0.00 0.00 0.00 3.85
220 221 0.392461 GCGCCAGACATAAACCAGGA 60.392 55.000 0.00 0.00 0.00 3.86
221 222 1.376609 GGCGCCAGACATAAACCAGG 61.377 60.000 24.80 0.00 0.00 4.45
222 223 0.392998 AGGCGCCAGACATAAACCAG 60.393 55.000 31.54 0.00 0.00 4.00
223 224 0.037590 AAGGCGCCAGACATAAACCA 59.962 50.000 31.54 0.00 0.00 3.67
224 225 1.940613 CTAAGGCGCCAGACATAAACC 59.059 52.381 31.54 0.00 0.00 3.27
225 226 2.608090 GTCTAAGGCGCCAGACATAAAC 59.392 50.000 31.55 15.31 40.74 2.01
226 227 2.419574 GGTCTAAGGCGCCAGACATAAA 60.420 50.000 34.79 11.19 42.45 1.40
227 228 1.138266 GGTCTAAGGCGCCAGACATAA 59.862 52.381 34.79 12.63 42.45 1.90
228 229 0.750850 GGTCTAAGGCGCCAGACATA 59.249 55.000 34.79 18.17 42.45 2.29
229 230 1.264749 TGGTCTAAGGCGCCAGACAT 61.265 55.000 34.79 18.04 42.45 3.06
230 231 1.911269 TGGTCTAAGGCGCCAGACA 60.911 57.895 34.79 23.37 42.45 3.41
279 280 9.874205 ATACTACTACATTAAGGCGTTAAAACA 57.126 29.630 14.95 3.34 31.81 2.83
356 357 4.606232 CGTTCGCAACAACAACAACAAAAA 60.606 37.500 0.00 0.00 0.00 1.94
363 364 0.517755 ACACGTTCGCAACAACAACA 59.482 45.000 0.00 0.00 0.00 3.33
378 379 6.484540 AGAGTTCGACAAGTATATGTACACG 58.515 40.000 0.00 0.00 32.57 4.49
405 406 6.896021 TTACCTATAGGAACGGATCTCAAG 57.104 41.667 26.01 0.00 38.94 3.02
422 439 3.947196 TCGCGTTGATAGGAGTTTACCTA 59.053 43.478 5.77 0.00 45.05 3.08
424 441 3.155093 TCGCGTTGATAGGAGTTTACC 57.845 47.619 5.77 0.00 0.00 2.85
430 447 3.186909 TGAATGTTCGCGTTGATAGGAG 58.813 45.455 5.77 0.00 0.00 3.69
475 493 5.964958 TGTTTCAGCTTTTATTCAGAGGG 57.035 39.130 0.00 0.00 0.00 4.30
489 507 3.618690 ACAGAGGGAGTATGTTTCAGC 57.381 47.619 0.00 0.00 0.00 4.26
543 561 6.042143 CCACTTTGCTCTGTATGTTGTTTTT 58.958 36.000 0.00 0.00 0.00 1.94
544 562 5.451798 CCCACTTTGCTCTGTATGTTGTTTT 60.452 40.000 0.00 0.00 0.00 2.43
546 564 3.569701 CCCACTTTGCTCTGTATGTTGTT 59.430 43.478 0.00 0.00 0.00 2.83
548 566 3.058016 CACCCACTTTGCTCTGTATGTTG 60.058 47.826 0.00 0.00 0.00 3.33
549 567 3.149196 CACCCACTTTGCTCTGTATGTT 58.851 45.455 0.00 0.00 0.00 2.71
551 569 3.057969 TCACCCACTTTGCTCTGTATG 57.942 47.619 0.00 0.00 0.00 2.39
553 571 3.072330 TGATTCACCCACTTTGCTCTGTA 59.928 43.478 0.00 0.00 0.00 2.74
554 572 2.158623 TGATTCACCCACTTTGCTCTGT 60.159 45.455 0.00 0.00 0.00 3.41
555 573 2.486982 CTGATTCACCCACTTTGCTCTG 59.513 50.000 0.00 0.00 0.00 3.35
558 576 1.251251 GCTGATTCACCCACTTTGCT 58.749 50.000 0.00 0.00 0.00 3.91
559 577 0.961019 TGCTGATTCACCCACTTTGC 59.039 50.000 0.00 0.00 0.00 3.68
575 593 2.042433 AGAGGGAGTAGTTCAGAGTGCT 59.958 50.000 0.00 0.00 0.00 4.40
576 594 2.165437 CAGAGGGAGTAGTTCAGAGTGC 59.835 54.545 0.00 0.00 0.00 4.40
577 595 3.426615 ACAGAGGGAGTAGTTCAGAGTG 58.573 50.000 0.00 0.00 0.00 3.51
578 596 3.818295 ACAGAGGGAGTAGTTCAGAGT 57.182 47.619 0.00 0.00 0.00 3.24
579 597 5.712917 AGTTTACAGAGGGAGTAGTTCAGAG 59.287 44.000 0.00 0.00 0.00 3.35
581 599 5.986501 AGTTTACAGAGGGAGTAGTTCAG 57.013 43.478 0.00 0.00 0.00 3.02
582 600 9.710818 ATATTAGTTTACAGAGGGAGTAGTTCA 57.289 33.333 0.00 0.00 0.00 3.18
588 606 9.939424 ACTCTTATATTAGTTTACAGAGGGAGT 57.061 33.333 0.00 0.00 32.21 3.85
590 608 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
624 642 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
625 643 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
637 655 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
638 656 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
639 657 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
640 658 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
641 659 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
642 660 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
643 661 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
644 662 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
645 663 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
650 668 9.418839 GGATATACTCCCTCCGTAAACTAATAT 57.581 37.037 0.00 0.00 38.19 1.28
651 669 8.618385 AGGATATACTCCCTCCGTAAACTAATA 58.382 37.037 0.00 0.00 46.27 0.98
652 670 7.477008 AGGATATACTCCCTCCGTAAACTAAT 58.523 38.462 0.00 0.00 46.27 1.73
653 671 6.856757 AGGATATACTCCCTCCGTAAACTAA 58.143 40.000 0.00 0.00 46.27 2.24
654 672 6.460103 AGGATATACTCCCTCCGTAAACTA 57.540 41.667 0.00 0.00 46.27 2.24
655 673 5.336491 AGGATATACTCCCTCCGTAAACT 57.664 43.478 0.00 0.00 46.27 2.66
656 674 6.662663 ACATAGGATATACTCCCTCCGTAAAC 59.337 42.308 0.00 0.00 46.27 2.01
657 675 6.797707 ACATAGGATATACTCCCTCCGTAAA 58.202 40.000 0.00 0.00 46.27 2.01
658 676 6.398655 ACATAGGATATACTCCCTCCGTAA 57.601 41.667 0.00 0.00 46.27 3.18
659 677 6.675746 ACTACATAGGATATACTCCCTCCGTA 59.324 42.308 0.00 0.00 46.27 4.02
660 678 4.949966 ACATAGGATATACTCCCTCCGT 57.050 45.455 0.00 0.00 46.27 4.69
661 679 6.003859 ACTACATAGGATATACTCCCTCCG 57.996 45.833 0.00 0.00 46.27 4.63
662 680 6.068971 TGGACTACATAGGATATACTCCCTCC 60.069 46.154 0.00 0.00 46.27 4.30
663 681 6.971340 TGGACTACATAGGATATACTCCCTC 58.029 44.000 0.00 0.00 46.27 4.30
664 682 6.989709 TGGACTACATAGGATATACTCCCT 57.010 41.667 0.00 0.00 46.27 4.20
682 700 9.682465 GTCTTTTTAGGGATTTTACTATGGACT 57.318 33.333 0.00 0.00 0.00 3.85
683 701 9.682465 AGTCTTTTTAGGGATTTTACTATGGAC 57.318 33.333 0.00 0.00 0.00 4.02
703 721 9.731001 TCCCTCTCTTCCTAAATATAAGTCTTT 57.269 33.333 0.00 0.00 0.00 2.52
704 722 9.374711 CTCCCTCTCTTCCTAAATATAAGTCTT 57.625 37.037 0.00 0.00 0.00 3.01
705 723 8.516198 ACTCCCTCTCTTCCTAAATATAAGTCT 58.484 37.037 0.00 0.00 0.00 3.24
706 724 8.715190 ACTCCCTCTCTTCCTAAATATAAGTC 57.285 38.462 0.00 0.00 0.00 3.01
707 725 9.590828 GTACTCCCTCTCTTCCTAAATATAAGT 57.409 37.037 0.00 0.00 0.00 2.24
708 726 9.589461 TGTACTCCCTCTCTTCCTAAATATAAG 57.411 37.037 0.00 0.00 0.00 1.73
710 728 9.535170 CATGTACTCCCTCTCTTCCTAAATATA 57.465 37.037 0.00 0.00 0.00 0.86
711 729 8.013667 ACATGTACTCCCTCTCTTCCTAAATAT 58.986 37.037 0.00 0.00 0.00 1.28
712 730 7.363031 ACATGTACTCCCTCTCTTCCTAAATA 58.637 38.462 0.00 0.00 0.00 1.40
713 731 6.206042 ACATGTACTCCCTCTCTTCCTAAAT 58.794 40.000 0.00 0.00 0.00 1.40
714 732 5.590818 ACATGTACTCCCTCTCTTCCTAAA 58.409 41.667 0.00 0.00 0.00 1.85
715 733 5.208294 ACATGTACTCCCTCTCTTCCTAA 57.792 43.478 0.00 0.00 0.00 2.69
716 734 4.883021 ACATGTACTCCCTCTCTTCCTA 57.117 45.455 0.00 0.00 0.00 2.94
717 735 3.767309 ACATGTACTCCCTCTCTTCCT 57.233 47.619 0.00 0.00 0.00 3.36
718 736 4.468153 AGAAACATGTACTCCCTCTCTTCC 59.532 45.833 0.00 0.00 0.00 3.46
719 737 5.186021 TCAGAAACATGTACTCCCTCTCTTC 59.814 44.000 0.00 0.00 0.00 2.87
720 738 5.087323 TCAGAAACATGTACTCCCTCTCTT 58.913 41.667 0.00 0.00 0.00 2.85
721 739 4.678256 TCAGAAACATGTACTCCCTCTCT 58.322 43.478 0.00 0.00 0.00 3.10
722 740 5.407407 TTCAGAAACATGTACTCCCTCTC 57.593 43.478 0.00 0.00 0.00 3.20
723 741 6.176183 CAATTCAGAAACATGTACTCCCTCT 58.824 40.000 0.00 0.00 0.00 3.69
724 742 5.163713 GCAATTCAGAAACATGTACTCCCTC 60.164 44.000 0.00 0.00 0.00 4.30
725 743 4.702131 GCAATTCAGAAACATGTACTCCCT 59.298 41.667 0.00 0.00 0.00 4.20
726 744 4.437390 CGCAATTCAGAAACATGTACTCCC 60.437 45.833 0.00 0.00 0.00 4.30
727 745 4.391830 TCGCAATTCAGAAACATGTACTCC 59.608 41.667 0.00 0.00 0.00 3.85
728 746 5.530519 TCGCAATTCAGAAACATGTACTC 57.469 39.130 0.00 0.00 0.00 2.59
729 747 5.940192 TTCGCAATTCAGAAACATGTACT 57.060 34.783 0.00 0.00 0.00 2.73
730 748 6.416455 TGTTTTCGCAATTCAGAAACATGTAC 59.584 34.615 0.00 0.00 36.26 2.90
786 808 1.298859 GCAACAGCTTGGTACCGGAG 61.299 60.000 9.46 9.02 0.00 4.63
794 816 1.067142 TCTACGGTAGCAACAGCTTGG 60.067 52.381 10.34 0.00 39.77 3.61
808 830 2.185350 CTGCCTGCCTGTCTACGG 59.815 66.667 0.00 0.00 0.00 4.02
810 832 2.124942 GCCTGCCTGCCTGTCTAC 60.125 66.667 0.00 0.00 0.00 2.59
811 833 2.284921 AGCCTGCCTGCCTGTCTA 60.285 61.111 0.00 0.00 0.00 2.59
812 834 3.715097 GAGCCTGCCTGCCTGTCT 61.715 66.667 0.00 0.00 0.00 3.41
813 835 4.792804 GGAGCCTGCCTGCCTGTC 62.793 72.222 0.00 0.00 0.00 3.51
832 854 3.123620 CCTTGCTCTGCTGCGACC 61.124 66.667 0.00 0.00 35.36 4.79
873 3285 1.127343 GCTTGAGGATAGGTGGCTCT 58.873 55.000 0.00 0.00 0.00 4.09
875 3287 1.690219 CGGCTTGAGGATAGGTGGCT 61.690 60.000 0.00 0.00 0.00 4.75
896 3311 2.159000 TGTCACTGCAGCCTCATATCAG 60.159 50.000 15.27 0.00 0.00 2.90
897 3312 1.832998 TGTCACTGCAGCCTCATATCA 59.167 47.619 15.27 0.00 0.00 2.15
931 3350 1.500783 TTCCCTTCCCCTTGAGGCTG 61.501 60.000 0.00 0.00 0.00 4.85
934 3353 1.304617 GCTTCCCTTCCCCTTGAGG 59.695 63.158 0.00 0.00 0.00 3.86
948 3367 1.889170 CAAAGAAGGGGAAGGTGCTTC 59.111 52.381 0.00 0.00 39.52 3.86
966 3393 1.338337 GGAGCGAGTGATAGCTAGCAA 59.662 52.381 14.31 0.00 44.69 3.91
967 3394 0.955178 GGAGCGAGTGATAGCTAGCA 59.045 55.000 18.83 7.80 44.69 3.49
1152 3583 4.790861 GCGTCCGTCCCGAACCTC 62.791 72.222 0.00 0.00 0.00 3.85
1341 3772 4.329545 TCGTTGAGCACCAGCCCC 62.330 66.667 0.00 0.00 43.56 5.80
1405 3848 3.360340 GTCCGAGTCCACGTCCGT 61.360 66.667 0.00 0.00 0.00 4.69
1940 4387 0.659427 AATGCGGCTGACGAATGATG 59.341 50.000 7.31 0.00 40.93 3.07
1948 4395 2.037136 ACTGAGCAATGCGGCTGAC 61.037 57.895 12.83 0.00 45.99 3.51
1952 4399 1.063649 CATCACTGAGCAATGCGGC 59.936 57.895 0.00 0.00 0.00 6.53
1953 4400 1.306148 ATCATCACTGAGCAATGCGG 58.694 50.000 0.00 0.00 34.12 5.69
1965 4412 6.270815 AGCAAATCACAAAGCATATCATCAC 58.729 36.000 0.00 0.00 0.00 3.06
1975 4422 3.054878 CTGTCCAAGCAAATCACAAAGC 58.945 45.455 0.00 0.00 0.00 3.51
1976 4423 4.037208 AGACTGTCCAAGCAAATCACAAAG 59.963 41.667 3.76 0.00 0.00 2.77
1977 4424 3.953612 AGACTGTCCAAGCAAATCACAAA 59.046 39.130 3.76 0.00 0.00 2.83
2008 4457 1.672356 CCTCACAAGCCTGAACCCG 60.672 63.158 0.00 0.00 0.00 5.28
2020 4469 1.264749 CCTCGAACCCCATCCTCACA 61.265 60.000 0.00 0.00 0.00 3.58
2164 4613 2.181777 TCGTGCTCGATGACCTGC 59.818 61.111 6.80 0.00 41.35 4.85
2197 4646 5.935945 TGATTTCCTCCTTGTGTAACTCAA 58.064 37.500 0.00 0.00 38.04 3.02
2198 4647 5.560722 TGATTTCCTCCTTGTGTAACTCA 57.439 39.130 0.00 0.00 38.04 3.41
2211 4679 6.595326 TGTGTGAGAATGTACATGATTTCCTC 59.405 38.462 9.63 9.63 0.00 3.71
2213 4681 6.741992 TGTGTGAGAATGTACATGATTTCC 57.258 37.500 9.63 0.00 0.00 3.13
2231 4699 3.415212 ACAAGATTCACTCCCATGTGTG 58.585 45.455 0.00 0.00 38.90 3.82
2241 4709 5.565439 GCAATTGGCAGTTACAAGATTCACT 60.565 40.000 7.72 0.00 43.97 3.41
2242 4710 4.622740 GCAATTGGCAGTTACAAGATTCAC 59.377 41.667 7.72 0.00 43.97 3.18
2260 4728 5.731406 GCATGTGTACAGATTGATCGCAATT 60.731 40.000 2.09 0.00 44.47 2.32
2290 4758 3.250744 TGTTACTTGTGCTACGAGATGC 58.749 45.455 9.64 0.00 33.76 3.91
2291 4759 6.033966 TGTATGTTACTTGTGCTACGAGATG 58.966 40.000 9.64 0.00 33.76 2.90
2292 4760 6.203808 TGTATGTTACTTGTGCTACGAGAT 57.796 37.500 9.64 0.00 33.76 2.75
2293 4761 5.632244 TGTATGTTACTTGTGCTACGAGA 57.368 39.130 9.64 0.00 33.76 4.04
2296 4764 7.056002 TCATTTGTATGTTACTTGTGCTACG 57.944 36.000 0.00 0.00 33.34 3.51
2330 4802 1.816224 ACACACGCCCATGTAATTTCC 59.184 47.619 0.00 0.00 0.00 3.13
2395 4887 5.068329 TGCGATGAATTCTATGAGAGAGTGT 59.932 40.000 7.05 0.00 34.93 3.55
2396 4888 5.527033 TGCGATGAATTCTATGAGAGAGTG 58.473 41.667 7.05 0.00 34.93 3.51
2401 4893 4.928020 GCTGATGCGATGAATTCTATGAGA 59.072 41.667 7.05 0.00 0.00 3.27
2428 4920 3.266510 TGTGTCTGGAGTGGATTATGC 57.733 47.619 0.00 0.00 0.00 3.14
2459 4956 2.803133 GCACTTGGGTTCTTTCCTTTGC 60.803 50.000 0.00 0.00 0.00 3.68
2464 4961 0.961753 CCAGCACTTGGGTTCTTTCC 59.038 55.000 0.00 0.00 43.75 3.13
2490 4987 5.663773 GCAAATGCGCGCTTATTTGATTATC 60.664 40.000 39.14 25.91 43.51 1.75
2547 5046 4.120589 CTCTTAAGGATGCGGGTTTACTC 58.879 47.826 1.85 0.00 0.00 2.59
2653 5152 4.437930 GCTATGTGGTCAAACTGATGAAGC 60.438 45.833 0.00 0.00 0.00 3.86
2702 5201 2.227865 TGTGGCCTAACTGAATTTTCGC 59.772 45.455 3.32 0.00 0.00 4.70
2704 5203 5.705609 TCTTGTGGCCTAACTGAATTTTC 57.294 39.130 3.32 0.00 0.00 2.29
2832 5337 7.038729 TGAGAAGTTGTGATCTCCTATTTCTGT 60.039 37.037 8.73 0.00 41.10 3.41
2867 5372 2.148569 GCGTCATGTTTGTTCGTTTTCG 59.851 45.455 0.00 0.00 45.64 3.46
2873 5380 2.330231 ATTGGCGTCATGTTTGTTCG 57.670 45.000 0.00 0.00 0.00 3.95
2886 5394 4.509600 ACCATTGTTTGTTGTTTATTGGCG 59.490 37.500 0.00 0.00 0.00 5.69
2890 5398 7.984050 TGATGTGACCATTGTTTGTTGTTTATT 59.016 29.630 0.00 0.00 0.00 1.40
2895 5407 4.402155 ACTGATGTGACCATTGTTTGTTGT 59.598 37.500 0.00 0.00 0.00 3.32
2981 5493 2.325583 TTGAACTTGTCGGCAGAACT 57.674 45.000 0.00 0.00 0.00 3.01
3025 5537 4.267928 GCACGCTACATTTAGTTAGTCCTG 59.732 45.833 0.00 0.00 0.00 3.86
3030 5542 4.330074 AGCAAGCACGCTACATTTAGTTAG 59.670 41.667 0.00 0.00 41.55 2.34
3032 5544 3.074412 AGCAAGCACGCTACATTTAGTT 58.926 40.909 0.00 0.00 41.55 2.24
3048 5560 9.955208 TTAATGCTGTTATCATTGATAAGCAAG 57.045 29.630 25.63 19.65 38.35 4.01
3083 5641 1.132262 AGCATATTTTGTCAACGCCGG 59.868 47.619 0.00 0.00 0.00 6.13
3103 5661 8.248253 CAGTCTATGTACATACACCACTGTAAA 58.752 37.037 15.27 0.00 39.30 2.01


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

AutoCloner maintained by Alex Coulton.