Multiple sequence alignment - TraesCS4B01G190300

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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 TraesCS4B01G190300 chr4B 100.000 4611 0 0 1 4611 413117730 413113120 0.000000e+00 8516.0
1 TraesCS4B01G190300 chr4D 92.512 2150 116 24 2099 4222 335039616 335037486 0.000000e+00 3037.0
2 TraesCS4B01G190300 chr4D 90.258 1899 74 39 205 2027 335041981 335040118 0.000000e+00 2379.0
3 TraesCS4B01G190300 chr4D 87.648 421 38 5 2038 2458 335040055 335039649 1.160000e-130 477.0
4 TraesCS4B01G190300 chr4D 92.746 193 7 4 4325 4511 335037433 335037242 5.880000e-69 272.0
5 TraesCS4B01G190300 chr4D 89.796 147 10 4 3 145 335042135 335041990 2.830000e-42 183.0
6 TraesCS4B01G190300 chr4D 89.764 127 8 4 4090 4214 334968153 334968030 1.720000e-34 158.0
7 TraesCS4B01G190300 chr4D 94.792 96 5 0 4086 4181 507479812 507479907 2.870000e-32 150.0
8 TraesCS4B01G190300 chr4D 95.604 91 2 2 4098 4188 493345653 493345741 1.340000e-30 145.0
9 TraesCS4B01G190300 chr4A 90.192 2131 88 43 212 2290 137963699 137965760 0.000000e+00 2665.0
10 TraesCS4B01G190300 chr4A 88.854 1256 78 31 3101 4318 137967478 137968709 0.000000e+00 1487.0
11 TraesCS4B01G190300 chr4A 87.394 587 56 10 2047 2630 137966172 137966743 0.000000e+00 658.0
12 TraesCS4B01G190300 chr4A 89.100 422 34 7 2318 2732 137965752 137966168 8.850000e-142 514.0
13 TraesCS4B01G190300 chr4A 87.356 174 15 4 2810 2977 137972670 137972498 4.710000e-45 193.0
14 TraesCS4B01G190300 chr4A 100.000 104 0 0 4508 4611 727723566 727723463 4.710000e-45 193.0
15 TraesCS4B01G190300 chr4A 84.946 186 21 4 2627 2812 137973006 137972828 1.020000e-41 182.0
16 TraesCS4B01G190300 chr4A 84.409 186 22 4 2627 2812 137966803 137966981 4.740000e-40 176.0
17 TraesCS4B01G190300 chr4A 90.909 121 6 4 4095 4214 138312944 138313060 1.720000e-34 158.0
18 TraesCS4B01G190300 chr4A 86.986 146 7 5 11 145 137963535 137963679 2.220000e-33 154.0
19 TraesCS4B01G190300 chr4A 100.000 75 0 0 2983 3057 137967401 137967475 6.220000e-29 139.0
20 TraesCS4B01G190300 chr4A 98.667 75 1 0 2983 3057 137972408 137972334 2.890000e-27 134.0
21 TraesCS4B01G190300 chr4A 100.000 35 0 0 4330 4364 137968695 137968729 1.070000e-06 65.8
22 TraesCS4B01G190300 chrUn 100.000 104 0 0 4508 4611 266374182 266374079 4.710000e-45 193.0
23 TraesCS4B01G190300 chr7B 100.000 104 0 0 4508 4611 79398858 79398755 4.710000e-45 193.0
24 TraesCS4B01G190300 chr7A 100.000 104 0 0 4508 4611 37105159 37105262 4.710000e-45 193.0
25 TraesCS4B01G190300 chr6B 100.000 104 0 0 4508 4611 702274898 702275001 4.710000e-45 193.0
26 TraesCS4B01G190300 chr5A 100.000 104 0 0 4508 4611 680987520 680987623 4.710000e-45 193.0
27 TraesCS4B01G190300 chr1B 100.000 104 0 0 4508 4611 169776230 169776333 4.710000e-45 193.0
28 TraesCS4B01G190300 chr1B 92.453 106 7 1 4083 4187 665493109 665493004 2.870000e-32 150.0
29 TraesCS4B01G190300 chr5B 97.321 112 3 0 4500 4611 535106007 535106118 1.690000e-44 191.0
30 TraesCS4B01G190300 chr5B 97.297 111 3 0 4501 4611 678165655 678165545 6.090000e-44 189.0
31 TraesCS4B01G190300 chr1A 96.809 94 0 3 4089 4182 256826586 256826496 2.220000e-33 154.0
32 TraesCS4B01G190300 chr1D 96.739 92 1 2 4089 4180 202569098 202569009 7.990000e-33 152.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G190300 chr4B 413113120 413117730 4610 True 8516.00 8516 100.000000 1 4611 1 chr4B.!!$R1 4610
1 TraesCS4B01G190300 chr4D 335037242 335042135 4893 True 1269.60 3037 90.592000 3 4511 5 chr4D.!!$R2 4508
2 TraesCS4B01G190300 chr4A 137963535 137968729 5194 False 732.35 2665 90.866875 11 4364 8 chr4A.!!$F2 4353

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
331 343 0.110295 TGGATCTGGGTTGTGTGTGG 59.890 55.000 0.00 0.0 0.00 4.17 F
1999 2108 0.325933 CCAGGTGAGGATCTTGCACA 59.674 55.000 12.67 0.0 34.92 4.57 F
2402 3591 0.391661 TGGCGCTTTCTGCTAGGAAG 60.392 55.000 7.64 0.0 40.11 3.46 F
2680 3933 1.730064 CGCGTACTTATGTGGCTTGTT 59.270 47.619 0.00 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2263 2807 0.319813 AGCGCAACCAAAAAGATGCC 60.320 50.0 11.47 0.00 35.41 4.40 R
3057 4561 0.322008 TGCAACACACACACACCAGA 60.322 50.0 0.00 0.00 0.00 3.86 R
3475 5002 1.199615 TGAGCCCAACGTATCCATCA 58.800 50.0 0.00 0.00 0.00 3.07 R
4533 6089 0.035458 CTCTATTTAGGCGCCCTGGG 59.965 60.0 26.15 8.86 34.61 4.45 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
53 54 3.264947 TGTTCATGATGCTGTAGACTGC 58.735 45.455 0.00 4.71 40.61 4.40
63 64 4.112634 TGCTGTAGACTGCACGAATTATC 58.887 43.478 9.84 0.00 44.12 1.75
82 83 2.475155 TCAGGATGGCAGAAGAGTCAT 58.525 47.619 0.00 0.00 36.16 3.06
85 86 1.476471 GGATGGCAGAAGAGTCATGGG 60.476 57.143 0.00 0.00 0.00 4.00
92 93 2.114616 AGAAGAGTCATGGGCTCGAAT 58.885 47.619 10.90 4.26 37.99 3.34
93 94 2.102252 AGAAGAGTCATGGGCTCGAATC 59.898 50.000 10.90 10.65 37.99 2.52
96 97 1.043116 AGTCATGGGCTCGAATCGGA 61.043 55.000 1.76 0.00 0.00 4.55
140 152 7.043961 TCTGTAAGTATAGGAGCTGACATTG 57.956 40.000 0.00 0.00 33.76 2.82
141 153 6.607600 TCTGTAAGTATAGGAGCTGACATTGT 59.392 38.462 0.00 0.00 33.76 2.71
142 154 7.124298 TCTGTAAGTATAGGAGCTGACATTGTT 59.876 37.037 0.00 0.00 33.76 2.83
143 155 7.265673 TGTAAGTATAGGAGCTGACATTGTTC 58.734 38.462 0.00 0.00 0.00 3.18
144 156 6.552445 AAGTATAGGAGCTGACATTGTTCT 57.448 37.500 0.00 0.00 0.00 3.01
145 157 5.911752 AGTATAGGAGCTGACATTGTTCTG 58.088 41.667 0.00 0.00 0.00 3.02
146 158 5.658634 AGTATAGGAGCTGACATTGTTCTGA 59.341 40.000 0.00 0.00 0.00 3.27
147 159 3.777106 AGGAGCTGACATTGTTCTGAA 57.223 42.857 0.00 0.00 0.00 3.02
148 160 4.298103 AGGAGCTGACATTGTTCTGAAT 57.702 40.909 0.00 0.00 0.00 2.57
149 161 5.426689 AGGAGCTGACATTGTTCTGAATA 57.573 39.130 0.00 0.00 0.00 1.75
150 162 5.999044 AGGAGCTGACATTGTTCTGAATAT 58.001 37.500 0.00 0.00 0.00 1.28
151 163 6.421485 AGGAGCTGACATTGTTCTGAATATT 58.579 36.000 0.00 0.00 0.00 1.28
152 164 6.888632 AGGAGCTGACATTGTTCTGAATATTT 59.111 34.615 0.00 0.00 0.00 1.40
153 165 6.971184 GGAGCTGACATTGTTCTGAATATTTG 59.029 38.462 0.00 0.00 0.00 2.32
154 166 6.327934 AGCTGACATTGTTCTGAATATTTGC 58.672 36.000 0.00 0.00 0.00 3.68
155 167 6.152323 AGCTGACATTGTTCTGAATATTTGCT 59.848 34.615 0.00 0.00 0.00 3.91
156 168 6.252869 GCTGACATTGTTCTGAATATTTGCTG 59.747 38.462 0.00 0.00 0.00 4.41
157 169 7.451501 TGACATTGTTCTGAATATTTGCTGA 57.548 32.000 0.00 0.00 0.00 4.26
158 170 8.058667 TGACATTGTTCTGAATATTTGCTGAT 57.941 30.769 0.00 0.00 0.00 2.90
159 171 7.971722 TGACATTGTTCTGAATATTTGCTGATG 59.028 33.333 0.00 0.00 0.00 3.07
160 172 8.058667 ACATTGTTCTGAATATTTGCTGATGA 57.941 30.769 0.00 0.00 0.00 2.92
161 173 7.972277 ACATTGTTCTGAATATTTGCTGATGAC 59.028 33.333 0.00 0.00 0.00 3.06
162 174 7.692460 TTGTTCTGAATATTTGCTGATGACT 57.308 32.000 0.00 0.00 0.00 3.41
163 175 7.080353 TGTTCTGAATATTTGCTGATGACTG 57.920 36.000 0.00 0.00 0.00 3.51
164 176 5.746307 TCTGAATATTTGCTGATGACTGC 57.254 39.130 0.00 0.00 40.53 4.40
171 183 1.718396 TGCTGATGACTGCTTCTTCG 58.282 50.000 0.00 0.00 40.71 3.79
173 185 2.072298 GCTGATGACTGCTTCTTCGTT 58.928 47.619 0.00 0.00 37.84 3.85
174 186 3.254060 GCTGATGACTGCTTCTTCGTTA 58.746 45.455 0.00 0.00 37.84 3.18
181 193 4.515191 TGACTGCTTCTTCGTTATTTTGCT 59.485 37.500 0.00 0.00 0.00 3.91
182 194 5.699001 TGACTGCTTCTTCGTTATTTTGCTA 59.301 36.000 0.00 0.00 0.00 3.49
186 198 7.750903 ACTGCTTCTTCGTTATTTTGCTATTTC 59.249 33.333 0.00 0.00 0.00 2.17
187 199 7.589395 TGCTTCTTCGTTATTTTGCTATTTCA 58.411 30.769 0.00 0.00 0.00 2.69
190 202 9.773328 CTTCTTCGTTATTTTGCTATTTCATCA 57.227 29.630 0.00 0.00 0.00 3.07
192 204 9.935682 TCTTCGTTATTTTGCTATTTCATCATC 57.064 29.630 0.00 0.00 0.00 2.92
193 205 8.766493 TTCGTTATTTTGCTATTTCATCATCG 57.234 30.769 0.00 0.00 0.00 3.84
195 207 8.275632 TCGTTATTTTGCTATTTCATCATCGAG 58.724 33.333 0.00 0.00 0.00 4.04
199 211 8.668510 ATTTTGCTATTTCATCATCGAGTAGT 57.331 30.769 0.00 0.00 0.00 2.73
200 212 9.764363 ATTTTGCTATTTCATCATCGAGTAGTA 57.236 29.630 0.00 0.00 0.00 1.82
201 213 9.594478 TTTTGCTATTTCATCATCGAGTAGTAA 57.406 29.630 0.00 0.00 0.00 2.24
202 214 8.803201 TTGCTATTTCATCATCGAGTAGTAAG 57.197 34.615 0.00 0.00 0.00 2.34
203 215 6.863645 TGCTATTTCATCATCGAGTAGTAAGC 59.136 38.462 0.00 0.00 0.00 3.09
204 216 7.087639 GCTATTTCATCATCGAGTAGTAAGCT 58.912 38.462 0.00 0.00 0.00 3.74
205 217 7.596995 GCTATTTCATCATCGAGTAGTAAGCTT 59.403 37.037 3.48 3.48 0.00 3.74
206 218 7.706281 ATTTCATCATCGAGTAGTAAGCTTG 57.294 36.000 9.86 0.00 0.00 4.01
207 219 4.611943 TCATCATCGAGTAGTAAGCTTGC 58.388 43.478 9.86 8.07 0.00 4.01
208 220 4.097892 TCATCATCGAGTAGTAAGCTTGCA 59.902 41.667 17.21 0.09 0.00 4.08
209 221 4.033990 TCATCGAGTAGTAAGCTTGCAG 57.966 45.455 17.21 2.97 0.00 4.41
210 222 3.444034 TCATCGAGTAGTAAGCTTGCAGT 59.556 43.478 17.21 5.77 0.00 4.40
272 284 5.094134 GTGAACTACCGACAACTGTATCTC 58.906 45.833 0.00 0.00 0.00 2.75
282 294 5.317733 ACAACTGTATCTCCTCTTTCGAG 57.682 43.478 0.00 0.00 37.01 4.04
293 305 2.352960 CCTCTTTCGAGCCAGCAAATAC 59.647 50.000 0.00 0.00 35.90 1.89
294 306 3.265791 CTCTTTCGAGCCAGCAAATACT 58.734 45.455 0.00 0.00 0.00 2.12
295 307 4.433615 CTCTTTCGAGCCAGCAAATACTA 58.566 43.478 0.00 0.00 0.00 1.82
296 308 4.827692 TCTTTCGAGCCAGCAAATACTAA 58.172 39.130 0.00 0.00 0.00 2.24
297 309 5.428253 TCTTTCGAGCCAGCAAATACTAAT 58.572 37.500 0.00 0.00 0.00 1.73
298 310 6.578944 TCTTTCGAGCCAGCAAATACTAATA 58.421 36.000 0.00 0.00 0.00 0.98
330 342 1.202806 AGTGGATCTGGGTTGTGTGTG 60.203 52.381 0.00 0.00 0.00 3.82
331 343 0.110295 TGGATCTGGGTTGTGTGTGG 59.890 55.000 0.00 0.00 0.00 4.17
346 360 4.037565 TGTGTGTGGGATCGTATCAGTATC 59.962 45.833 0.00 0.00 0.00 2.24
407 423 4.681978 GGCCACCGCGTCACTCTT 62.682 66.667 4.92 0.00 35.02 2.85
414 430 3.247442 CACCGCGTCACTCTTATTTGTA 58.753 45.455 4.92 0.00 0.00 2.41
415 431 3.060363 CACCGCGTCACTCTTATTTGTAC 59.940 47.826 4.92 0.00 0.00 2.90
417 433 4.156556 ACCGCGTCACTCTTATTTGTACTA 59.843 41.667 4.92 0.00 0.00 1.82
419 435 5.747197 CCGCGTCACTCTTATTTGTACTATT 59.253 40.000 4.92 0.00 0.00 1.73
420 436 6.255020 CCGCGTCACTCTTATTTGTACTATTT 59.745 38.462 4.92 0.00 0.00 1.40
421 437 7.201496 CCGCGTCACTCTTATTTGTACTATTTT 60.201 37.037 4.92 0.00 0.00 1.82
422 438 7.839837 CGCGTCACTCTTATTTGTACTATTTTC 59.160 37.037 0.00 0.00 0.00 2.29
423 439 8.870879 GCGTCACTCTTATTTGTACTATTTTCT 58.129 33.333 0.00 0.00 0.00 2.52
453 469 0.672401 GAAACGATCCCGGAGCAACA 60.672 55.000 0.73 0.00 40.78 3.33
462 479 4.067972 TCCCGGAGCAACAGATTTATAC 57.932 45.455 0.73 0.00 0.00 1.47
473 490 1.493022 AGATTTATACGGCCCCTGCAA 59.507 47.619 0.00 0.00 40.13 4.08
476 493 1.465794 TTATACGGCCCCTGCAAAAC 58.534 50.000 0.00 0.00 40.13 2.43
479 496 1.175983 TACGGCCCCTGCAAAACTTG 61.176 55.000 0.00 0.00 40.13 3.16
497 514 1.375326 GGTCCGCCCTTCTCAAGTT 59.625 57.895 0.00 0.00 0.00 2.66
517 534 9.405587 TCAAGTTCGATCCATTAACAAAATTTC 57.594 29.630 0.00 0.00 0.00 2.17
537 554 4.963878 CCACCTGGCACATAGACC 57.036 61.111 0.00 0.00 38.20 3.85
538 555 1.153369 CCACCTGGCACATAGACCG 60.153 63.158 0.00 0.00 38.20 4.79
539 556 1.815421 CACCTGGCACATAGACCGC 60.815 63.158 0.00 0.00 38.20 5.68
544 561 1.220749 GGCACATAGACCGCCTCAA 59.779 57.895 0.00 0.00 42.78 3.02
549 566 2.017049 ACATAGACCGCCTCAATTTGC 58.983 47.619 0.00 0.00 0.00 3.68
572 589 0.807667 CTTTGACCTGCGGATCCTCG 60.808 60.000 10.75 0.00 0.00 4.63
630 648 3.410631 TCCAAGCACAATCCGAACTTA 57.589 42.857 0.00 0.00 0.00 2.24
632 650 4.331968 TCCAAGCACAATCCGAACTTAAT 58.668 39.130 0.00 0.00 0.00 1.40
635 653 5.345741 CCAAGCACAATCCGAACTTAATTTG 59.654 40.000 0.00 0.00 0.00 2.32
653 671 1.464734 TGGAGAGCTCGGACAGTTAG 58.535 55.000 8.37 0.00 0.00 2.34
751 788 7.740519 ACGTAACGTGTACAATTCCTATTAC 57.259 36.000 0.00 0.00 39.18 1.89
752 789 7.538575 ACGTAACGTGTACAATTCCTATTACT 58.461 34.615 0.00 0.00 39.18 2.24
753 790 7.485913 ACGTAACGTGTACAATTCCTATTACTG 59.514 37.037 0.00 0.25 39.18 2.74
787 824 7.132128 AGATTGATCTCTAGAATATCCCTCCC 58.868 42.308 10.70 0.21 29.30 4.30
788 825 5.213868 TGATCTCTAGAATATCCCTCCCC 57.786 47.826 10.70 0.00 0.00 4.81
822 859 3.369892 GGCAACTCTCCTTGCTCATAGAA 60.370 47.826 4.06 0.00 45.07 2.10
825 862 3.357203 ACTCTCCTTGCTCATAGAACGA 58.643 45.455 0.00 0.00 0.00 3.85
829 866 6.096987 ACTCTCCTTGCTCATAGAACGAATAA 59.903 38.462 0.00 0.00 0.00 1.40
830 867 7.055667 TCTCCTTGCTCATAGAACGAATAAT 57.944 36.000 0.00 0.00 0.00 1.28
831 868 7.500992 TCTCCTTGCTCATAGAACGAATAATT 58.499 34.615 0.00 0.00 0.00 1.40
867 924 3.380479 AAGGAAGTTCATTGACGACGA 57.620 42.857 0.00 0.00 0.00 4.20
930 997 4.881019 TGGAAACCTGAAAGAGAGAGAG 57.119 45.455 0.00 0.00 34.07 3.20
942 1019 2.236146 AGAGAGAGAGACGAGCAGAGAA 59.764 50.000 0.00 0.00 0.00 2.87
993 1080 4.851214 AGGCGAGAGAGGAGGCCC 62.851 72.222 0.00 0.00 46.75 5.80
1004 1098 2.203126 GAGGCCCAAGAGGATGCG 60.203 66.667 0.00 0.00 38.24 4.73
1048 1142 4.410400 CCACCAACGCCTCCTCCC 62.410 72.222 0.00 0.00 0.00 4.30
1049 1143 4.410400 CACCAACGCCTCCTCCCC 62.410 72.222 0.00 0.00 0.00 4.81
1812 1921 3.422303 GTGCTCATGAACGCGCCA 61.422 61.111 5.73 4.84 0.00 5.69
1995 2104 0.617413 AGTGCCAGGTGAGGATCTTG 59.383 55.000 0.00 0.00 34.92 3.02
1999 2108 0.325933 CCAGGTGAGGATCTTGCACA 59.674 55.000 12.67 0.00 34.92 4.57
2028 2137 1.467342 GGCCGTCACCTTTAATGACAC 59.533 52.381 8.10 0.61 45.64 3.67
2036 2198 7.255569 CGTCACCTTTAATGACACATAGTAGA 58.744 38.462 8.10 0.00 45.64 2.59
2060 2222 1.552337 TCATTGGAGCTGGTCTGAGTC 59.448 52.381 6.83 0.00 0.00 3.36
2101 2263 6.938507 TCAGCAAATGGAGAAATTTTATGCT 58.061 32.000 0.00 0.00 30.59 3.79
2180 2724 4.615588 TTTTTATTTTCCAGTGGCCCTG 57.384 40.909 3.51 12.83 41.15 4.45
2208 2752 6.935167 TCTGTTAGTGACTTATTGCTGATCA 58.065 36.000 0.00 0.00 0.00 2.92
2263 2807 5.112686 GTTGAAGAGCTAGTGATACAAGGG 58.887 45.833 0.00 0.00 0.00 3.95
2277 2821 2.407562 ACAAGGGGCATCTTTTTGGTT 58.592 42.857 0.00 0.00 0.00 3.67
2294 2838 1.128692 GGTTGCGCTAAGTGCTTACTG 59.871 52.381 9.73 0.00 40.03 2.74
2295 2839 1.798813 GTTGCGCTAAGTGCTTACTGT 59.201 47.619 9.73 0.00 40.03 3.55
2296 2840 1.710013 TGCGCTAAGTGCTTACTGTC 58.290 50.000 9.73 0.00 40.03 3.51
2297 2841 1.272490 TGCGCTAAGTGCTTACTGTCT 59.728 47.619 9.73 0.00 40.03 3.41
2298 2842 2.288825 TGCGCTAAGTGCTTACTGTCTT 60.289 45.455 9.73 0.00 40.03 3.01
2309 3496 4.238514 GCTTACTGTCTTACTGACCAGTG 58.761 47.826 12.54 0.00 44.75 3.66
2337 3524 4.526438 AGATATGCTAAACTTGGGCCTT 57.474 40.909 4.53 0.00 0.00 4.35
2351 3538 0.675633 GGCCTTTTCTGAAGCTGCAA 59.324 50.000 1.02 0.00 0.00 4.08
2352 3539 1.603931 GGCCTTTTCTGAAGCTGCAAC 60.604 52.381 1.02 0.00 0.00 4.17
2402 3591 0.391661 TGGCGCTTTCTGCTAGGAAG 60.392 55.000 7.64 0.00 40.11 3.46
2411 3602 6.089476 GCTTTCTGCTAGGAAGAATCAAAAC 58.911 40.000 8.01 0.00 38.95 2.43
2412 3603 6.294176 GCTTTCTGCTAGGAAGAATCAAAACA 60.294 38.462 8.01 0.00 38.95 2.83
2435 3626 8.494016 ACAAATTACTATAAGACTCAAGGTGC 57.506 34.615 0.00 0.00 0.00 5.01
2448 3639 1.963515 CAAGGTGCAAGTTTTAGGCCT 59.036 47.619 11.78 11.78 0.00 5.19
2486 3677 2.221169 TGACATCAACAGTCAACAGCC 58.779 47.619 0.00 0.00 42.57 4.85
2611 3802 4.906664 ACATCTCAATATCCTCAGCTCCTT 59.093 41.667 0.00 0.00 0.00 3.36
2612 3803 4.952071 TCTCAATATCCTCAGCTCCTTG 57.048 45.455 0.00 0.00 0.00 3.61
2650 3903 3.274095 TCTGTTTGACATGACACACCA 57.726 42.857 11.08 2.29 0.00 4.17
2660 3913 5.238432 TGACATGACACACCAATTGTCTTAC 59.762 40.000 0.00 0.00 43.30 2.34
2680 3933 1.730064 CGCGTACTTATGTGGCTTGTT 59.270 47.619 0.00 0.00 0.00 2.83
2856 4272 3.376546 GCAATCTCTTGGTCTTTAGGCAG 59.623 47.826 0.00 0.00 32.72 4.85
2880 4296 6.830838 AGAAGGGCTTGTATATTTCCTTTCTG 59.169 38.462 3.63 0.00 40.33 3.02
2981 4485 5.986135 ACAGAGAGAAACACACACAATAGAC 59.014 40.000 0.00 0.00 0.00 2.59
3058 4562 7.573968 AGAGTAATTGGCTACCATGAAAATC 57.426 36.000 0.00 0.00 31.53 2.17
3059 4563 7.349598 AGAGTAATTGGCTACCATGAAAATCT 58.650 34.615 0.00 0.00 31.53 2.40
3060 4564 7.284034 AGAGTAATTGGCTACCATGAAAATCTG 59.716 37.037 0.00 0.00 31.53 2.90
3061 4565 5.603170 AATTGGCTACCATGAAAATCTGG 57.397 39.130 0.00 0.00 38.55 3.86
3063 4567 3.355378 TGGCTACCATGAAAATCTGGTG 58.645 45.455 4.52 0.00 45.28 4.17
3064 4568 3.245229 TGGCTACCATGAAAATCTGGTGT 60.245 43.478 4.52 0.00 45.28 4.16
3086 4590 2.992543 GTGTGTGTTGCATGTGTTGTTT 59.007 40.909 0.00 0.00 0.00 2.83
3090 4594 4.862018 GTGTGTTGCATGTGTTGTTTAGTT 59.138 37.500 0.00 0.00 0.00 2.24
3203 4717 5.235516 CCAGTTAGTGTTGTTACCTGTAGG 58.764 45.833 0.00 0.00 42.17 3.18
3204 4718 4.689345 CAGTTAGTGTTGTTACCTGTAGGC 59.311 45.833 0.00 0.00 39.32 3.93
3205 4719 4.591924 AGTTAGTGTTGTTACCTGTAGGCT 59.408 41.667 0.00 0.00 39.32 4.58
3206 4720 3.402628 AGTGTTGTTACCTGTAGGCTG 57.597 47.619 0.00 0.00 39.32 4.85
3207 4721 2.704065 AGTGTTGTTACCTGTAGGCTGT 59.296 45.455 0.00 0.00 39.32 4.40
3208 4722 3.899360 AGTGTTGTTACCTGTAGGCTGTA 59.101 43.478 0.00 0.00 39.32 2.74
3209 4723 4.021368 AGTGTTGTTACCTGTAGGCTGTAG 60.021 45.833 0.00 0.00 39.32 2.74
3210 4724 3.259902 GTTGTTACCTGTAGGCTGTAGC 58.740 50.000 0.00 0.00 39.32 3.58
3211 4725 2.816411 TGTTACCTGTAGGCTGTAGCT 58.184 47.619 0.00 0.00 41.70 3.32
3212 4726 3.972133 TGTTACCTGTAGGCTGTAGCTA 58.028 45.455 0.00 0.00 41.70 3.32
3213 4727 4.543689 TGTTACCTGTAGGCTGTAGCTAT 58.456 43.478 0.00 0.00 41.70 2.97
3266 4792 8.220559 AGTTGCTTATATCATGGTTCCATAAGT 58.779 33.333 3.88 0.00 33.61 2.24
3311 4837 2.548057 TGTCCTCGCACATTTTCAACTC 59.452 45.455 0.00 0.00 0.00 3.01
3334 4860 8.695456 ACTCTGGATAACTTGTTCATTTTTGTT 58.305 29.630 0.00 0.00 0.00 2.83
3451 4978 6.349033 GCTTTGCTAGTAGCTCTATAGGAGAC 60.349 46.154 22.34 0.00 44.45 3.36
3634 5161 5.178096 TGGAGCATTTCTTGGAAGTGATA 57.822 39.130 6.90 0.00 0.00 2.15
3923 5455 4.365514 TGGCCTTCTTTGTGTCAGATTA 57.634 40.909 3.32 0.00 0.00 1.75
3958 5490 7.595130 GTGAAATGAGATTTTGGTTCTGTTACC 59.405 37.037 0.00 0.00 34.02 2.85
3996 5529 0.732571 CCCGTCACCATATGTTGTGC 59.267 55.000 1.24 0.48 32.51 4.57
4002 5535 3.753272 GTCACCATATGTTGTGCAGAACT 59.247 43.478 25.13 14.20 32.51 3.01
4013 5546 4.350620 CAGAACTCTGCGTGCAGT 57.649 55.556 20.33 2.43 43.96 4.40
4014 5547 3.496898 CAGAACTCTGCGTGCAGTA 57.503 52.632 20.33 7.61 43.96 2.74
4016 5549 3.150848 CAGAACTCTGCGTGCAGTATA 57.849 47.619 20.33 1.85 43.96 1.47
4017 5550 3.711086 CAGAACTCTGCGTGCAGTATAT 58.289 45.455 20.33 6.79 43.96 0.86
4018 5551 4.115516 CAGAACTCTGCGTGCAGTATATT 58.884 43.478 20.33 10.95 43.96 1.28
4020 5553 5.063944 CAGAACTCTGCGTGCAGTATATTTT 59.936 40.000 20.33 6.84 43.96 1.82
4021 5554 6.255670 CAGAACTCTGCGTGCAGTATATTTTA 59.744 38.462 20.33 0.00 43.96 1.52
4022 5555 6.986817 AGAACTCTGCGTGCAGTATATTTTAT 59.013 34.615 20.33 2.52 43.96 1.40
4023 5556 6.771188 ACTCTGCGTGCAGTATATTTTATC 57.229 37.500 20.33 0.00 43.96 1.75
4024 5557 5.402568 ACTCTGCGTGCAGTATATTTTATCG 59.597 40.000 20.33 0.00 43.96 2.92
4026 5559 3.743911 TGCGTGCAGTATATTTTATCGGG 59.256 43.478 0.00 0.00 0.00 5.14
4028 5561 4.562082 CGTGCAGTATATTTTATCGGGGA 58.438 43.478 0.00 0.00 0.00 4.81
4056 5597 2.290960 GCTGGGTGTAAAGGTCTGGAAT 60.291 50.000 0.00 0.00 0.00 3.01
4170 5711 2.008268 GATTCCCGGCTGGTGCAATG 62.008 60.000 11.58 0.00 41.91 2.82
4176 5717 0.860533 CGGCTGGTGCAATGTTTTTG 59.139 50.000 0.00 0.00 41.91 2.44
4187 5728 6.183359 GGTGCAATGTTTTTGTTTTCGTTTTG 60.183 34.615 0.00 0.00 0.00 2.44
4229 5771 1.909700 TGCCCAAATCAGAACACCTC 58.090 50.000 0.00 0.00 0.00 3.85
4234 5776 3.084786 CCAAATCAGAACACCTCCTTCC 58.915 50.000 0.00 0.00 0.00 3.46
4236 5778 2.044793 ATCAGAACACCTCCTTCCCA 57.955 50.000 0.00 0.00 0.00 4.37
4244 5786 1.425448 CACCTCCTTCCCAAAACTCCT 59.575 52.381 0.00 0.00 0.00 3.69
4252 5794 1.118838 CCCAAAACTCCTGTTTGGCA 58.881 50.000 9.89 0.00 44.70 4.92
4254 5796 2.104622 CCCAAAACTCCTGTTTGGCATT 59.895 45.455 9.89 0.00 44.70 3.56
4279 5829 6.378564 TGTGTGTTTTCCAGTCCATTTTTCTA 59.621 34.615 0.00 0.00 0.00 2.10
4299 5849 2.587612 TTTTTACGTCATGTGCTCGC 57.412 45.000 0.00 0.00 0.00 5.03
4305 5855 1.280982 CGTCATGTGCTCGCTGTATT 58.719 50.000 0.00 0.00 0.00 1.89
4306 5856 1.660607 CGTCATGTGCTCGCTGTATTT 59.339 47.619 0.00 0.00 0.00 1.40
4307 5857 2.094258 CGTCATGTGCTCGCTGTATTTT 59.906 45.455 0.00 0.00 0.00 1.82
4308 5858 3.674423 GTCATGTGCTCGCTGTATTTTC 58.326 45.455 0.00 0.00 0.00 2.29
4309 5859 3.372206 GTCATGTGCTCGCTGTATTTTCT 59.628 43.478 0.00 0.00 0.00 2.52
4310 5860 3.371898 TCATGTGCTCGCTGTATTTTCTG 59.628 43.478 0.00 0.00 0.00 3.02
4311 5861 2.766313 TGTGCTCGCTGTATTTTCTGT 58.234 42.857 0.00 0.00 0.00 3.41
4312 5862 3.138304 TGTGCTCGCTGTATTTTCTGTT 58.862 40.909 0.00 0.00 0.00 3.16
4313 5863 3.563808 TGTGCTCGCTGTATTTTCTGTTT 59.436 39.130 0.00 0.00 0.00 2.83
4314 5864 4.036262 TGTGCTCGCTGTATTTTCTGTTTT 59.964 37.500 0.00 0.00 0.00 2.43
4315 5865 4.976116 GTGCTCGCTGTATTTTCTGTTTTT 59.024 37.500 0.00 0.00 0.00 1.94
4390 5940 4.217118 GTGTGATCTTGCCACAATCTCTTT 59.783 41.667 0.00 0.00 44.91 2.52
4391 5941 4.828939 TGTGATCTTGCCACAATCTCTTTT 59.171 37.500 0.00 0.00 41.07 2.27
4392 5942 6.003326 TGTGATCTTGCCACAATCTCTTTTA 58.997 36.000 0.00 0.00 41.07 1.52
4394 5944 7.148188 TGTGATCTTGCCACAATCTCTTTTATC 60.148 37.037 0.00 0.00 41.07 1.75
4458 6012 3.828451 CCACATGGGATTGGATTATGGAC 59.172 47.826 0.00 0.00 40.01 4.02
4492 6048 4.641396 TGTTCCTACAAAGAGTGGTGATG 58.359 43.478 0.00 0.00 0.00 3.07
4514 6070 2.668632 CGGAGCAGGTTAAGGGCA 59.331 61.111 0.00 0.00 0.00 5.36
4515 6071 1.224592 CGGAGCAGGTTAAGGGCAT 59.775 57.895 0.00 0.00 0.00 4.40
4516 6072 0.815615 CGGAGCAGGTTAAGGGCATC 60.816 60.000 0.00 0.00 0.00 3.91
4517 6073 0.548510 GGAGCAGGTTAAGGGCATCT 59.451 55.000 0.00 0.00 0.00 2.90
4518 6074 1.475930 GGAGCAGGTTAAGGGCATCTC 60.476 57.143 0.00 0.00 0.00 2.75
4519 6075 0.548510 AGCAGGTTAAGGGCATCTCC 59.451 55.000 0.00 0.00 0.00 3.71
4520 6076 0.255890 GCAGGTTAAGGGCATCTCCA 59.744 55.000 0.00 0.00 36.21 3.86
4521 6077 1.748591 GCAGGTTAAGGGCATCTCCAG 60.749 57.143 0.00 0.00 36.21 3.86
4522 6078 0.548510 AGGTTAAGGGCATCTCCAGC 59.451 55.000 0.00 0.00 36.21 4.85
4528 6084 2.892425 GGCATCTCCAGCCGTTCG 60.892 66.667 0.00 0.00 43.15 3.95
4529 6085 2.892425 GCATCTCCAGCCGTTCGG 60.892 66.667 6.90 6.90 0.00 4.30
4548 6104 3.820843 CCCCCAGGGCGCCTAAAT 61.821 66.667 28.56 7.33 35.35 1.40
4549 6105 2.457323 CCCCCAGGGCGCCTAAATA 61.457 63.158 28.56 0.00 35.35 1.40
4550 6106 1.073199 CCCCAGGGCGCCTAAATAG 59.927 63.158 28.56 10.47 29.64 1.73
4551 6107 1.415672 CCCCAGGGCGCCTAAATAGA 61.416 60.000 28.56 0.00 29.64 1.98
4552 6108 0.035458 CCCAGGGCGCCTAAATAGAG 59.965 60.000 28.56 6.58 29.64 2.43
4553 6109 0.603975 CCAGGGCGCCTAAATAGAGC 60.604 60.000 28.56 5.83 29.64 4.09
4557 6113 3.952811 CGCCTAAATAGAGCGGCC 58.047 61.111 12.51 0.00 45.88 6.13
4558 6114 1.367840 CGCCTAAATAGAGCGGCCT 59.632 57.895 0.00 0.00 45.88 5.19
4559 6115 0.946221 CGCCTAAATAGAGCGGCCTG 60.946 60.000 0.00 0.00 45.88 4.85
4560 6116 0.603975 GCCTAAATAGAGCGGCCTGG 60.604 60.000 0.00 0.00 36.56 4.45
4561 6117 0.035458 CCTAAATAGAGCGGCCTGGG 59.965 60.000 0.00 0.00 0.00 4.45
4562 6118 0.035458 CTAAATAGAGCGGCCTGGGG 59.965 60.000 0.00 0.00 0.00 4.96
4563 6119 1.415672 TAAATAGAGCGGCCTGGGGG 61.416 60.000 0.00 0.00 0.00 5.40
4589 6145 4.530857 CGCTAGTTCGGCCCCTGG 62.531 72.222 0.00 0.00 0.00 4.45
4590 6146 4.176752 GCTAGTTCGGCCCCTGGG 62.177 72.222 5.50 5.50 38.57 4.45
4608 6164 2.760385 GGCGACCTAGCTCCCAGT 60.760 66.667 0.00 0.00 37.29 4.00
4609 6165 2.787567 GGCGACCTAGCTCCCAGTC 61.788 68.421 0.00 0.00 37.29 3.51
4610 6166 2.052690 GCGACCTAGCTCCCAGTCA 61.053 63.158 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.321156 GGCAGCACAAACTATTGTCATCAA 60.321 41.667 0.00 0.00 46.78 2.57
1 2 3.191162 GGCAGCACAAACTATTGTCATCA 59.809 43.478 0.00 0.00 46.78 3.07
2 3 3.728864 CGGCAGCACAAACTATTGTCATC 60.729 47.826 0.00 0.00 46.78 2.92
3 4 2.162208 CGGCAGCACAAACTATTGTCAT 59.838 45.455 0.00 0.00 46.78 3.06
4 5 1.535028 CGGCAGCACAAACTATTGTCA 59.465 47.619 0.00 0.00 46.78 3.58
5 6 1.804151 TCGGCAGCACAAACTATTGTC 59.196 47.619 0.00 0.00 46.78 3.18
7 8 2.987413 TTCGGCAGCACAAACTATTG 57.013 45.000 0.00 0.00 42.46 1.90
8 9 5.590259 AGAATATTCGGCAGCACAAACTATT 59.410 36.000 9.78 0.00 0.00 1.73
9 10 5.008019 CAGAATATTCGGCAGCACAAACTAT 59.992 40.000 9.78 0.00 0.00 2.12
53 54 3.732212 TCTGCCATCCTGATAATTCGTG 58.268 45.455 0.00 0.00 0.00 4.35
63 64 2.562635 CATGACTCTTCTGCCATCCTG 58.437 52.381 0.00 0.00 0.00 3.86
82 83 1.187974 TACTTTCCGATTCGAGCCCA 58.812 50.000 7.83 0.00 0.00 5.36
85 86 4.238514 AGCATATACTTTCCGATTCGAGC 58.761 43.478 7.83 0.00 0.00 5.03
92 93 4.161565 ACACAGGAAGCATATACTTTCCGA 59.838 41.667 6.24 0.00 0.00 4.55
93 94 4.442706 ACACAGGAAGCATATACTTTCCG 58.557 43.478 6.24 4.99 0.00 4.30
96 97 6.476378 ACAGAACACAGGAAGCATATACTTT 58.524 36.000 0.00 0.00 0.00 2.66
140 152 5.970023 GCAGTCATCAGCAAATATTCAGAAC 59.030 40.000 0.00 0.00 0.00 3.01
141 153 5.884232 AGCAGTCATCAGCAAATATTCAGAA 59.116 36.000 0.00 0.00 0.00 3.02
142 154 5.434408 AGCAGTCATCAGCAAATATTCAGA 58.566 37.500 0.00 0.00 0.00 3.27
143 155 5.752892 AGCAGTCATCAGCAAATATTCAG 57.247 39.130 0.00 0.00 0.00 3.02
144 156 5.884232 AGAAGCAGTCATCAGCAAATATTCA 59.116 36.000 0.00 0.00 0.00 2.57
145 157 6.374565 AGAAGCAGTCATCAGCAAATATTC 57.625 37.500 0.00 0.00 0.00 1.75
146 158 6.457934 CGAAGAAGCAGTCATCAGCAAATATT 60.458 38.462 0.00 0.00 0.00 1.28
147 159 5.007430 CGAAGAAGCAGTCATCAGCAAATAT 59.993 40.000 0.00 0.00 0.00 1.28
148 160 4.330894 CGAAGAAGCAGTCATCAGCAAATA 59.669 41.667 0.00 0.00 0.00 1.40
149 161 3.126514 CGAAGAAGCAGTCATCAGCAAAT 59.873 43.478 0.00 0.00 0.00 2.32
150 162 2.481568 CGAAGAAGCAGTCATCAGCAAA 59.518 45.455 0.00 0.00 0.00 3.68
151 163 2.071540 CGAAGAAGCAGTCATCAGCAA 58.928 47.619 0.00 0.00 0.00 3.91
152 164 1.001293 ACGAAGAAGCAGTCATCAGCA 59.999 47.619 0.00 0.00 0.00 4.41
153 165 1.719600 ACGAAGAAGCAGTCATCAGC 58.280 50.000 0.00 0.00 0.00 4.26
154 166 6.414408 AAATAACGAAGAAGCAGTCATCAG 57.586 37.500 0.00 0.00 0.00 2.90
155 167 6.602179 CAAAATAACGAAGAAGCAGTCATCA 58.398 36.000 0.00 0.00 0.00 3.07
156 168 5.509622 GCAAAATAACGAAGAAGCAGTCATC 59.490 40.000 0.00 0.00 0.00 2.92
157 169 5.182001 AGCAAAATAACGAAGAAGCAGTCAT 59.818 36.000 0.00 0.00 0.00 3.06
158 170 4.515191 AGCAAAATAACGAAGAAGCAGTCA 59.485 37.500 0.00 0.00 0.00 3.41
159 171 5.035784 AGCAAAATAACGAAGAAGCAGTC 57.964 39.130 0.00 0.00 0.00 3.51
160 172 6.743575 ATAGCAAAATAACGAAGAAGCAGT 57.256 33.333 0.00 0.00 0.00 4.40
161 173 7.750458 TGAAATAGCAAAATAACGAAGAAGCAG 59.250 33.333 0.00 0.00 0.00 4.24
162 174 7.589395 TGAAATAGCAAAATAACGAAGAAGCA 58.411 30.769 0.00 0.00 0.00 3.91
163 175 8.620533 ATGAAATAGCAAAATAACGAAGAAGC 57.379 30.769 0.00 0.00 0.00 3.86
164 176 9.773328 TGATGAAATAGCAAAATAACGAAGAAG 57.227 29.630 0.00 0.00 0.00 2.85
173 185 9.764363 ACTACTCGATGATGAAATAGCAAAATA 57.236 29.630 0.00 0.00 0.00 1.40
174 186 8.668510 ACTACTCGATGATGAAATAGCAAAAT 57.331 30.769 0.00 0.00 0.00 1.82
181 193 7.382488 GCAAGCTTACTACTCGATGATGAAATA 59.618 37.037 0.00 0.00 0.00 1.40
182 194 6.201806 GCAAGCTTACTACTCGATGATGAAAT 59.798 38.462 0.00 0.00 0.00 2.17
186 198 4.363138 TGCAAGCTTACTACTCGATGATG 58.637 43.478 0.00 0.00 0.00 3.07
187 199 4.098654 ACTGCAAGCTTACTACTCGATGAT 59.901 41.667 0.00 0.00 37.60 2.45
190 202 4.457834 AACTGCAAGCTTACTACTCGAT 57.542 40.909 0.00 0.00 37.60 3.59
192 204 4.992381 AAAACTGCAAGCTTACTACTCG 57.008 40.909 0.00 0.00 37.60 4.18
295 307 9.942850 CCCAGATCCACTTTTGTTTTATTTATT 57.057 29.630 0.00 0.00 0.00 1.40
296 308 9.100197 ACCCAGATCCACTTTTGTTTTATTTAT 57.900 29.630 0.00 0.00 0.00 1.40
297 309 8.485578 ACCCAGATCCACTTTTGTTTTATTTA 57.514 30.769 0.00 0.00 0.00 1.40
298 310 7.373617 ACCCAGATCCACTTTTGTTTTATTT 57.626 32.000 0.00 0.00 0.00 1.40
308 320 2.091885 ACACACAACCCAGATCCACTTT 60.092 45.455 0.00 0.00 0.00 2.66
330 342 3.258372 TGCTTGGATACTGATACGATCCC 59.742 47.826 0.00 0.00 38.75 3.85
331 343 4.521130 TGCTTGGATACTGATACGATCC 57.479 45.455 0.00 0.00 39.77 3.36
364 378 8.973378 CACGGTAGCAAATTTTTCATAAAAGAA 58.027 29.630 0.00 0.00 36.73 2.52
365 379 7.596995 CCACGGTAGCAAATTTTTCATAAAAGA 59.403 33.333 0.00 0.00 36.73 2.52
366 380 7.621219 GCCACGGTAGCAAATTTTTCATAAAAG 60.621 37.037 0.00 0.00 36.73 2.27
379 395 2.281900 GGTGGCCACGGTAGCAAA 60.282 61.111 29.08 0.00 0.00 3.68
419 435 8.080417 CGGGATCGTTTCATCTTATACTAGAAA 58.920 37.037 0.00 0.00 0.00 2.52
420 436 7.309012 CCGGGATCGTTTCATCTTATACTAGAA 60.309 40.741 0.00 0.00 33.95 2.10
421 437 6.150641 CCGGGATCGTTTCATCTTATACTAGA 59.849 42.308 0.00 0.00 33.95 2.43
422 438 6.150641 TCCGGGATCGTTTCATCTTATACTAG 59.849 42.308 0.00 0.00 33.95 2.57
423 439 6.005823 TCCGGGATCGTTTCATCTTATACTA 58.994 40.000 0.00 0.00 33.95 1.82
424 440 4.831155 TCCGGGATCGTTTCATCTTATACT 59.169 41.667 0.00 0.00 33.95 2.12
425 441 5.130292 TCCGGGATCGTTTCATCTTATAC 57.870 43.478 0.00 0.00 33.95 1.47
434 450 0.672401 TGTTGCTCCGGGATCGTTTC 60.672 55.000 0.00 0.00 33.95 2.78
453 469 1.136828 TGCAGGGGCCGTATAAATCT 58.863 50.000 0.00 0.00 40.13 2.40
462 479 2.339712 CAAGTTTTGCAGGGGCCG 59.660 61.111 0.00 0.00 40.13 6.13
473 490 0.250770 GAGAAGGGCGGACCAAGTTT 60.251 55.000 0.92 0.00 43.89 2.66
476 493 0.674895 CTTGAGAAGGGCGGACCAAG 60.675 60.000 0.92 0.00 43.89 3.61
479 496 0.673956 GAACTTGAGAAGGGCGGACC 60.674 60.000 0.00 0.00 40.67 4.46
497 514 6.071672 TGGCTGAAATTTTGTTAATGGATCGA 60.072 34.615 0.00 0.00 0.00 3.59
538 555 1.068333 TCAAAGAGCGCAAATTGAGGC 60.068 47.619 11.47 0.00 0.00 4.70
539 556 2.589014 GTCAAAGAGCGCAAATTGAGG 58.411 47.619 18.15 2.18 32.85 3.86
544 561 0.242017 GCAGGTCAAAGAGCGCAAAT 59.758 50.000 11.47 0.00 35.00 2.32
564 581 1.002087 ACAAGTCCAACACGAGGATCC 59.998 52.381 2.48 2.48 37.52 3.36
572 589 3.665190 CCTAGGAAGACAAGTCCAACAC 58.335 50.000 1.05 0.00 37.65 3.32
630 648 1.625818 ACTGTCCGAGCTCTCCAAATT 59.374 47.619 12.85 0.00 0.00 1.82
632 650 1.048601 AACTGTCCGAGCTCTCCAAA 58.951 50.000 12.85 0.00 0.00 3.28
635 653 0.741915 CCTAACTGTCCGAGCTCTCC 59.258 60.000 12.85 0.00 0.00 3.71
637 655 1.271982 TGACCTAACTGTCCGAGCTCT 60.272 52.381 12.85 0.00 34.25 4.09
784 821 1.377690 TGCCTTTTATGTCCAGGGGA 58.622 50.000 0.00 0.00 0.00 4.81
785 822 1.824852 GTTGCCTTTTATGTCCAGGGG 59.175 52.381 0.00 0.00 0.00 4.79
786 823 2.755103 GAGTTGCCTTTTATGTCCAGGG 59.245 50.000 0.00 0.00 0.00 4.45
787 824 3.690460 AGAGTTGCCTTTTATGTCCAGG 58.310 45.455 0.00 0.00 0.00 4.45
788 825 3.691609 GGAGAGTTGCCTTTTATGTCCAG 59.308 47.826 0.00 0.00 0.00 3.86
830 867 9.470399 GAACTTCCTTAATTCCCTGGTTAATAA 57.530 33.333 0.00 0.00 0.00 1.40
831 868 8.616598 TGAACTTCCTTAATTCCCTGGTTAATA 58.383 33.333 0.00 0.00 0.00 0.98
867 924 3.297134 TGCCTCCTTTCTTTCTTGTGT 57.703 42.857 0.00 0.00 0.00 3.72
930 997 3.840890 TCTCTCTTTTCTCTGCTCGTC 57.159 47.619 0.00 0.00 0.00 4.20
942 1019 5.388599 TTCTTCCCCAAGTTTCTCTCTTT 57.611 39.130 0.00 0.00 0.00 2.52
993 1080 1.579698 CATCTCCACGCATCCTCTTG 58.420 55.000 0.00 0.00 0.00 3.02
1004 1098 1.339151 GGTGGTCAAGTCCATCTCCAC 60.339 57.143 0.00 0.00 42.87 4.02
1050 1144 4.862823 GACGGAGGGGAGGGGGAG 62.863 77.778 0.00 0.00 0.00 4.30
1066 1160 2.365617 GGAGGAGATGTCGCCATTTAGA 59.634 50.000 5.59 0.00 38.37 2.10
1135 1235 4.123545 GAACGGGGTGGGGGATGG 62.124 72.222 0.00 0.00 0.00 3.51
1136 1236 4.123545 GGAACGGGGTGGGGGATG 62.124 72.222 0.00 0.00 0.00 3.51
1593 1702 2.522193 GGGTTGTTGGGGCCGAAA 60.522 61.111 1.31 0.00 0.00 3.46
1764 1873 2.943978 CGACACGAAGAGGGCCCTT 61.944 63.158 29.39 11.82 0.00 3.95
1800 1909 1.351707 GGTGTATGGCGCGTTCATG 59.648 57.895 21.31 0.00 0.00 3.07
1812 1921 1.217244 GAAGTGGACGGCGGTGTAT 59.783 57.895 13.24 0.00 0.00 2.29
1863 1972 1.812922 CTCGTCAGCTGCCATGTCC 60.813 63.158 9.47 0.00 0.00 4.02
1950 2059 1.767388 CGTCTTGACAACGTCGAGC 59.233 57.895 0.00 2.32 42.18 5.03
1995 2104 0.943835 GACGGCCAAACCAAATGTGC 60.944 55.000 2.24 0.00 39.03 4.57
1999 2108 0.469144 AGGTGACGGCCAAACCAAAT 60.469 50.000 18.10 0.00 39.03 2.32
2028 2137 7.619050 ACCAGCTCCAATGATATTCTACTATG 58.381 38.462 0.00 0.00 0.00 2.23
2036 2198 4.411540 ACTCAGACCAGCTCCAATGATATT 59.588 41.667 0.00 0.00 0.00 1.28
2060 2222 1.512734 GAGCAAGCCGCACAAATCG 60.513 57.895 0.00 0.00 46.13 3.34
2091 2253 4.605640 ACACCAGCACAAGCATAAAATT 57.394 36.364 0.00 0.00 45.49 1.82
2101 2263 2.163412 GTGAACAGAAACACCAGCACAA 59.837 45.455 0.00 0.00 0.00 3.33
2180 2724 6.813649 TCAGCAATAAGTCACTAACAGATCAC 59.186 38.462 0.00 0.00 0.00 3.06
2208 2752 3.034635 CAGAGCACCCTATAAGGACAGT 58.965 50.000 0.00 0.00 37.67 3.55
2263 2807 0.319813 AGCGCAACCAAAAAGATGCC 60.320 50.000 11.47 0.00 35.41 4.40
2294 2838 8.630054 ATCTATATCTCACTGGTCAGTAAGAC 57.370 38.462 6.14 0.00 38.45 3.01
2297 2841 8.961634 GCATATCTATATCTCACTGGTCAGTAA 58.038 37.037 3.06 0.00 40.20 2.24
2298 2842 8.332487 AGCATATCTATATCTCACTGGTCAGTA 58.668 37.037 3.06 0.00 40.20 2.74
2309 3496 7.713073 GGCCCAAGTTTAGCATATCTATATCTC 59.287 40.741 0.00 0.00 0.00 2.75
2337 3524 3.446873 TGAAAAGGTTGCAGCTTCAGAAA 59.553 39.130 0.00 0.00 34.42 2.52
2351 3538 8.531146 CAATTAATGTTCCATAGGTGAAAAGGT 58.469 33.333 0.00 0.00 0.00 3.50
2352 3539 8.531146 ACAATTAATGTTCCATAGGTGAAAAGG 58.469 33.333 0.00 0.00 40.06 3.11
2411 3602 8.492673 TGCACCTTGAGTCTTATAGTAATTTG 57.507 34.615 0.00 0.00 0.00 2.32
2412 3603 9.167311 CTTGCACCTTGAGTCTTATAGTAATTT 57.833 33.333 0.00 0.00 0.00 1.82
2435 3626 3.010250 AGGGTAAGGAGGCCTAAAACTTG 59.990 47.826 4.42 0.00 31.13 3.16
2448 3639 3.396276 TGTCATTTCAACCAGGGTAAGGA 59.604 43.478 0.00 0.00 0.00 3.36
2478 3669 1.270625 CCTTGTAAGGTCGGCTGTTGA 60.271 52.381 2.42 0.00 41.41 3.18
2553 3744 6.861065 ATGTTCCAAGTTACAACTACAGTG 57.139 37.500 0.00 0.00 38.57 3.66
2650 3903 5.290158 CCACATAAGTACGCGTAAGACAATT 59.710 40.000 22.44 8.80 43.02 2.32
2660 3913 1.355971 ACAAGCCACATAAGTACGCG 58.644 50.000 3.53 3.53 0.00 6.01
2680 3933 4.038642 TGGATCGATAATGACAACGGATCA 59.961 41.667 0.00 0.00 0.00 2.92
2747 4000 6.722328 AGGGATAGTCACGACTCATCATATA 58.278 40.000 2.26 0.00 42.54 0.86
2748 4001 5.575157 AGGGATAGTCACGACTCATCATAT 58.425 41.667 2.26 0.00 42.54 1.78
2856 4272 6.603599 ACAGAAAGGAAATATACAAGCCCTTC 59.396 38.462 0.00 0.00 33.32 3.46
2981 4485 5.180117 CCATAACTTGCATCTTCCCTTATCG 59.820 44.000 0.00 0.00 0.00 2.92
3057 4561 0.322008 TGCAACACACACACACCAGA 60.322 50.000 0.00 0.00 0.00 3.86
3058 4562 0.740149 ATGCAACACACACACACCAG 59.260 50.000 0.00 0.00 0.00 4.00
3059 4563 0.455005 CATGCAACACACACACACCA 59.545 50.000 0.00 0.00 0.00 4.17
3060 4564 0.455410 ACATGCAACACACACACACC 59.545 50.000 0.00 0.00 0.00 4.16
3061 4565 1.135431 ACACATGCAACACACACACAC 60.135 47.619 0.00 0.00 0.00 3.82
3062 4566 1.172175 ACACATGCAACACACACACA 58.828 45.000 0.00 0.00 0.00 3.72
3063 4567 1.919263 CAACACATGCAACACACACAC 59.081 47.619 0.00 0.00 0.00 3.82
3064 4568 1.543358 ACAACACATGCAACACACACA 59.457 42.857 0.00 0.00 0.00 3.72
3086 4590 7.173907 GGCCTACACTATACAAGTCGATAACTA 59.826 40.741 0.00 0.00 37.17 2.24
3090 4594 5.379187 TGGCCTACACTATACAAGTCGATA 58.621 41.667 3.32 0.00 35.76 2.92
3203 4717 5.221541 ACACATAAGAAGGGATAGCTACAGC 60.222 44.000 0.00 0.00 42.49 4.40
3204 4718 6.219473 CACACATAAGAAGGGATAGCTACAG 58.781 44.000 0.00 0.00 0.00 2.74
3205 4719 5.070446 CCACACATAAGAAGGGATAGCTACA 59.930 44.000 0.00 0.00 0.00 2.74
3206 4720 5.070580 ACCACACATAAGAAGGGATAGCTAC 59.929 44.000 0.00 0.00 0.00 3.58
3207 4721 5.216622 ACCACACATAAGAAGGGATAGCTA 58.783 41.667 0.00 0.00 0.00 3.32
3208 4722 4.040755 ACCACACATAAGAAGGGATAGCT 58.959 43.478 0.00 0.00 0.00 3.32
3209 4723 4.101741 AGACCACACATAAGAAGGGATAGC 59.898 45.833 0.00 0.00 0.00 2.97
3210 4724 5.878406 AGACCACACATAAGAAGGGATAG 57.122 43.478 0.00 0.00 0.00 2.08
3211 4725 5.304614 GCTAGACCACACATAAGAAGGGATA 59.695 44.000 0.00 0.00 0.00 2.59
3212 4726 4.101741 GCTAGACCACACATAAGAAGGGAT 59.898 45.833 0.00 0.00 0.00 3.85
3213 4727 3.451178 GCTAGACCACACATAAGAAGGGA 59.549 47.826 0.00 0.00 0.00 4.20
3266 4792 8.959548 ACAATAGAAAGATGATAACATGCACAA 58.040 29.630 0.00 0.00 36.82 3.33
3334 4860 8.821686 AACAGGTGGATGATATTCATGTAAAA 57.178 30.769 0.00 0.00 37.20 1.52
3372 4898 9.391006 AGACAAAAAGAGAACACAGTTATTACA 57.609 29.630 0.00 0.00 0.00 2.41
3381 4907 4.331968 ACCACAGACAAAAAGAGAACACA 58.668 39.130 0.00 0.00 0.00 3.72
3451 4978 6.618308 CACGCTTTATAATCGTTCTAAACACG 59.382 38.462 9.64 0.00 39.08 4.49
3475 5002 1.199615 TGAGCCCAACGTATCCATCA 58.800 50.000 0.00 0.00 0.00 3.07
3634 5161 3.131046 CACTTGGCTTCCAGAAAAACACT 59.869 43.478 0.00 0.00 33.81 3.55
3698 5225 2.348666 GCACACAACTGTATCTTAGGCG 59.651 50.000 0.00 0.00 0.00 5.52
3703 5230 2.810274 CTGCTGCACACAACTGTATCTT 59.190 45.455 0.00 0.00 0.00 2.40
3958 5490 3.612479 CGGGAACAAAAGAAGCAGGAATG 60.612 47.826 0.00 0.00 0.00 2.67
3964 5497 1.673920 GTGACGGGAACAAAAGAAGCA 59.326 47.619 0.00 0.00 0.00 3.91
3996 5529 2.001812 ATACTGCACGCAGAGTTCTG 57.998 50.000 25.09 4.77 46.30 3.02
4002 5535 4.684242 CCGATAAAATATACTGCACGCAGA 59.316 41.667 25.09 9.50 46.30 4.26
4006 5539 4.387862 GTCCCCGATAAAATATACTGCACG 59.612 45.833 0.00 0.00 0.00 5.34
4007 5540 4.387862 CGTCCCCGATAAAATATACTGCAC 59.612 45.833 0.00 0.00 35.63 4.57
4008 5541 4.562082 CGTCCCCGATAAAATATACTGCA 58.438 43.478 0.00 0.00 35.63 4.41
4009 5542 3.370061 GCGTCCCCGATAAAATATACTGC 59.630 47.826 0.00 0.00 35.63 4.40
4010 5543 3.930848 GGCGTCCCCGATAAAATATACTG 59.069 47.826 0.00 0.00 35.63 2.74
4011 5544 3.055602 GGGCGTCCCCGATAAAATATACT 60.056 47.826 0.00 0.00 42.67 2.12
4013 5546 3.615224 GGGCGTCCCCGATAAAATATA 57.385 47.619 0.00 0.00 42.67 0.86
4014 5547 2.484742 GGGCGTCCCCGATAAAATAT 57.515 50.000 0.00 0.00 42.67 1.28
4016 5549 4.892002 GGGCGTCCCCGATAAAAT 57.108 55.556 0.00 0.00 42.67 1.82
4032 5565 1.376812 GACCTTTACACCCAGCCGG 60.377 63.158 0.00 0.00 37.81 6.13
4070 5611 6.209986 TGGATGAGAGAAATGCTCAACAAATT 59.790 34.615 0.00 0.00 46.45 1.82
4170 5711 9.829637 GAGATGATACAAAACGAAAACAAAAAC 57.170 29.630 0.00 0.00 0.00 2.43
4176 5717 7.323656 CCACAAGAGATGATACAAAACGAAAAC 59.676 37.037 0.00 0.00 0.00 2.43
4187 5728 2.474816 GCCGTCCACAAGAGATGATAC 58.525 52.381 0.00 0.00 0.00 2.24
4229 5771 2.365293 CCAAACAGGAGTTTTGGGAAGG 59.635 50.000 6.03 0.00 45.32 3.46
4234 5776 3.132925 CAATGCCAAACAGGAGTTTTGG 58.867 45.455 9.12 9.12 45.32 3.28
4236 5778 3.197549 ACACAATGCCAAACAGGAGTTTT 59.802 39.130 0.00 0.00 45.32 2.43
4244 5786 3.265791 GGAAAACACACAATGCCAAACA 58.734 40.909 0.00 0.00 0.00 2.83
4252 5794 5.612725 AAATGGACTGGAAAACACACAAT 57.387 34.783 0.00 0.00 0.00 2.71
4254 5796 5.186797 AGAAAAATGGACTGGAAAACACACA 59.813 36.000 0.00 0.00 0.00 3.72
4279 5829 2.742053 AGCGAGCACATGACGTAAAAAT 59.258 40.909 0.00 0.00 0.00 1.82
4315 5865 9.915629 ATAAACAGAAAATATACACCGCAAAAA 57.084 25.926 0.00 0.00 0.00 1.94
4316 5866 9.915629 AATAAACAGAAAATATACACCGCAAAA 57.084 25.926 0.00 0.00 0.00 2.44
4317 5867 9.915629 AAATAAACAGAAAATATACACCGCAAA 57.084 25.926 0.00 0.00 0.00 3.68
4318 5868 9.347934 CAAATAAACAGAAAATATACACCGCAA 57.652 29.630 0.00 0.00 0.00 4.85
4319 5869 8.516234 ACAAATAAACAGAAAATATACACCGCA 58.484 29.630 0.00 0.00 0.00 5.69
4320 5870 8.905103 ACAAATAAACAGAAAATATACACCGC 57.095 30.769 0.00 0.00 0.00 5.68
4394 5944 8.417176 CGTTGACTTTTATTTCCTGAAATTTCG 58.583 33.333 13.34 8.11 40.99 3.46
4477 6031 1.819305 GCCACCATCACCACTCTTTGT 60.819 52.381 0.00 0.00 0.00 2.83
4492 6048 1.745489 CTTAACCTGCTCCGCCACC 60.745 63.158 0.00 0.00 0.00 4.61
4511 6067 2.892425 CGAACGGCTGGAGATGCC 60.892 66.667 0.00 0.00 46.42 4.40
4512 6068 2.892425 CCGAACGGCTGGAGATGC 60.892 66.667 0.00 0.00 0.00 3.91
4532 6088 1.073199 CTATTTAGGCGCCCTGGGG 59.927 63.158 26.15 5.60 34.61 4.96
4533 6089 0.035458 CTCTATTTAGGCGCCCTGGG 59.965 60.000 26.15 8.86 34.61 4.45
4534 6090 0.603975 GCTCTATTTAGGCGCCCTGG 60.604 60.000 26.15 7.92 34.61 4.45
4535 6091 0.946221 CGCTCTATTTAGGCGCCCTG 60.946 60.000 26.15 7.22 42.28 4.45
4536 6092 1.367840 CGCTCTATTTAGGCGCCCT 59.632 57.895 26.15 13.52 42.28 5.19
4537 6093 1.668151 CCGCTCTATTTAGGCGCCC 60.668 63.158 26.15 5.07 46.29 6.13
4538 6094 2.318352 GCCGCTCTATTTAGGCGCC 61.318 63.158 21.89 21.89 46.29 6.53
4539 6095 3.245084 GCCGCTCTATTTAGGCGC 58.755 61.111 0.00 0.00 46.29 6.53
4542 6098 0.035458 CCCAGGCCGCTCTATTTAGG 59.965 60.000 0.00 0.00 0.00 2.69
4543 6099 0.035458 CCCCAGGCCGCTCTATTTAG 59.965 60.000 0.00 0.00 0.00 1.85
4544 6100 1.415672 CCCCCAGGCCGCTCTATTTA 61.416 60.000 0.00 0.00 0.00 1.40
4545 6101 2.757124 CCCCCAGGCCGCTCTATTT 61.757 63.158 0.00 0.00 0.00 1.40
4546 6102 3.171388 CCCCCAGGCCGCTCTATT 61.171 66.667 0.00 0.00 0.00 1.73
4572 6128 4.530857 CCAGGGGCCGAACTAGCG 62.531 72.222 0.00 0.00 0.00 4.26
4573 6129 4.176752 CCCAGGGGCCGAACTAGC 62.177 72.222 0.00 0.00 0.00 3.42
4574 6130 3.480133 CCCCAGGGGCCGAACTAG 61.480 72.222 13.35 0.00 35.35 2.57
4586 6142 3.541713 GAGCTAGGTCGCCCCCAG 61.542 72.222 6.12 0.00 0.00 4.45
4590 6146 3.541713 CTGGGAGCTAGGTCGCCC 61.542 72.222 29.34 20.74 45.10 6.13
4591 6147 2.760385 ACTGGGAGCTAGGTCGCC 60.760 66.667 29.34 23.22 0.00 5.54
4592 6148 2.052690 TGACTGGGAGCTAGGTCGC 61.053 63.158 26.90 26.90 0.00 5.19
4593 6149 4.338815 TGACTGGGAGCTAGGTCG 57.661 61.111 15.43 4.94 0.00 4.79


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

AutoCloner maintained by Alex Coulton.