Multiple sequence alignment - TraesCS3B01G544200

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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 TraesCS3B01G544200 chr3B 100.000 2919 0 0 1 2919 781495863 781492945 0.000000e+00 5391.0
1 TraesCS3B01G544200 chr3B 87.201 1172 103 30 980 2110 781210449 781211614 0.000000e+00 1290.0
2 TraesCS3B01G544200 chr3B 88.040 995 79 23 909 1871 781356082 781357068 0.000000e+00 1142.0
3 TraesCS3B01G544200 chr3B 89.819 717 53 8 1277 1981 781344839 781345547 0.000000e+00 902.0
4 TraesCS3B01G544200 chr3B 85.175 371 44 7 913 1280 781344446 781344808 1.280000e-98 370.0
5 TraesCS3B01G544200 chr3B 93.671 237 12 2 1 237 235917068 235916835 4.630000e-93 351.0
6 TraesCS3B01G544200 chr3B 94.667 75 3 1 1896 1970 781362372 781362445 6.610000e-22 115.0
7 TraesCS3B01G544200 chr3D 91.682 1587 80 18 928 2478 584457011 584455441 0.000000e+00 2152.0
8 TraesCS3B01G544200 chr3D 88.314 1044 89 19 962 1981 584048670 584049704 0.000000e+00 1221.0
9 TraesCS3B01G544200 chr3D 86.917 1093 98 25 909 1970 584129725 584130803 0.000000e+00 1184.0
10 TraesCS3B01G544200 chr3D 89.130 460 30 5 2478 2917 584455404 584454945 3.290000e-154 555.0
11 TraesCS3B01G544200 chr3D 79.708 616 86 16 1884 2477 584453907 584453309 2.710000e-110 409.0
12 TraesCS3B01G544200 chr3D 85.609 271 31 5 2470 2739 584453276 584453013 7.970000e-71 278.0
13 TraesCS3B01G544200 chrUn 94.454 1208 59 5 1278 2478 45482982 45481776 0.000000e+00 1853.0
14 TraesCS3B01G544200 chrUn 85.562 658 56 20 652 1277 45483675 45483025 0.000000e+00 652.0
15 TraesCS3B01G544200 chrUn 89.336 422 24 6 2470 2870 45481744 45481323 7.220000e-141 510.0
16 TraesCS3B01G544200 chrUn 78.706 371 35 20 269 604 45484041 45483680 1.060000e-49 207.0
17 TraesCS3B01G544200 chr3A 86.808 1084 91 33 945 1981 21360408 21359330 0.000000e+00 1162.0
18 TraesCS3B01G544200 chr7D 84.487 1199 108 44 934 2070 588419712 588420894 0.000000e+00 1112.0
19 TraesCS3B01G544200 chr7D 95.726 234 9 1 1 234 30392974 30393206 2.750000e-100 375.0
20 TraesCS3B01G544200 chr1B 96.581 234 8 0 1 234 337940729 337940962 3.530000e-104 388.0
21 TraesCS3B01G544200 chr1B 92.797 236 16 1 1 235 619103138 619103373 1.000000e-89 340.0
22 TraesCS3B01G544200 chr2B 94.167 240 14 0 4 243 200577380 200577141 1.650000e-97 366.0
23 TraesCS3B01G544200 chr2B 92.887 239 15 2 1 239 725131828 725131592 2.150000e-91 346.0
24 TraesCS3B01G544200 chr5B 93.033 244 15 2 1 244 31267090 31267331 3.580000e-94 355.0
25 TraesCS3B01G544200 chr6D 94.397 232 8 3 15 245 25833724 25833951 4.630000e-93 351.0
26 TraesCS3B01G544200 chr6B 92.593 243 12 6 1 243 583290983 583290747 7.740000e-91 344.0
27 TraesCS3B01G544200 chr6A 89.831 59 6 0 1178 1236 602131537 602131595 3.120000e-10 76.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G544200 chr3B 781492945 781495863 2918 True 5391.0 5391 100.00000 1 2919 1 chr3B.!!$R2 2918
1 TraesCS3B01G544200 chr3B 781210449 781211614 1165 False 1290.0 1290 87.20100 980 2110 1 chr3B.!!$F1 1130
2 TraesCS3B01G544200 chr3B 781356082 781357068 986 False 1142.0 1142 88.04000 909 1871 1 chr3B.!!$F2 962
3 TraesCS3B01G544200 chr3B 781344446 781345547 1101 False 636.0 902 87.49700 913 1981 2 chr3B.!!$F4 1068
4 TraesCS3B01G544200 chr3D 584048670 584049704 1034 False 1221.0 1221 88.31400 962 1981 1 chr3D.!!$F1 1019
5 TraesCS3B01G544200 chr3D 584129725 584130803 1078 False 1184.0 1184 86.91700 909 1970 1 chr3D.!!$F2 1061
6 TraesCS3B01G544200 chr3D 584453013 584457011 3998 True 848.5 2152 86.53225 928 2917 4 chr3D.!!$R1 1989
7 TraesCS3B01G544200 chrUn 45481323 45484041 2718 True 805.5 1853 87.01450 269 2870 4 chrUn.!!$R1 2601
8 TraesCS3B01G544200 chr3A 21359330 21360408 1078 True 1162.0 1162 86.80800 945 1981 1 chr3A.!!$R1 1036
9 TraesCS3B01G544200 chr7D 588419712 588420894 1182 False 1112.0 1112 84.48700 934 2070 1 chr7D.!!$F2 1136

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
260 261 0.171231 GGGACTACGTACGGTTGGAC 59.829 60.0 21.06 4.96 0.00 4.02 F
322 323 0.179217 CGTGACGCATCCACACATTG 60.179 55.0 0.00 0.00 34.36 2.82 F
729 765 0.315568 CCCGCTCCTGTATCAGTAGC 59.684 60.0 4.62 4.62 39.53 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1128 1211 0.460459 GGACGGTAGGAAGCTGCTTC 60.460 60.0 29.50 29.50 39.52 3.86 R
1845 1993 0.891904 TACTTTGGCGGGAACTTGGC 60.892 55.0 0.00 0.00 0.00 4.52 R
2328 2530 0.850856 GTGCTACGGCGTACATAAGC 59.149 55.0 21.31 21.31 42.25 3.09 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
71 72 2.851045 GGAACCAAGGCCCTCCAA 59.149 61.111 0.00 0.00 33.74 3.53
72 73 1.155155 GGAACCAAGGCCCTCCAAA 59.845 57.895 0.00 0.00 33.74 3.28
73 74 0.900182 GGAACCAAGGCCCTCCAAAG 60.900 60.000 0.00 0.00 33.74 2.77
74 75 0.900182 GAACCAAGGCCCTCCAAAGG 60.900 60.000 0.00 0.00 42.95 3.11
75 76 1.368268 AACCAAGGCCCTCCAAAGGA 61.368 55.000 0.00 0.00 46.67 3.36
76 77 1.000396 CCAAGGCCCTCCAAAGGAG 60.000 63.158 0.00 6.08 46.67 3.69
84 85 3.713650 TCCAAAGGAGAGGAGGCG 58.286 61.111 0.00 0.00 0.00 5.52
85 86 2.124942 CCAAAGGAGAGGAGGCGC 60.125 66.667 0.00 0.00 0.00 6.53
86 87 2.124942 CAAAGGAGAGGAGGCGCC 60.125 66.667 21.89 21.89 0.00 6.53
87 88 2.607750 AAAGGAGAGGAGGCGCCA 60.608 61.111 31.54 0.00 40.02 5.69
88 89 2.664081 AAAGGAGAGGAGGCGCCAG 61.664 63.158 31.54 0.00 40.02 4.85
89 90 3.608759 AAGGAGAGGAGGCGCCAGA 62.609 63.158 31.54 0.00 40.02 3.86
90 91 2.841988 GGAGAGGAGGCGCCAGAT 60.842 66.667 31.54 13.79 40.02 2.90
91 92 2.733945 GAGAGGAGGCGCCAGATC 59.266 66.667 31.54 21.92 40.02 2.75
92 93 2.841988 AGAGGAGGCGCCAGATCC 60.842 66.667 31.54 26.43 40.02 3.36
93 94 3.934962 GAGGAGGCGCCAGATCCC 61.935 72.222 31.54 20.03 40.02 3.85
109 110 3.891400 CCGCCGCCACCATCATTG 61.891 66.667 0.00 0.00 0.00 2.82
113 114 3.530260 CGCCACCATCATTGGGGC 61.530 66.667 12.03 12.03 45.95 5.80
114 115 3.156556 GCCACCATCATTGGGGCC 61.157 66.667 11.33 0.00 45.95 5.80
115 116 2.834505 CCACCATCATTGGGGCCG 60.835 66.667 0.00 0.00 45.95 6.13
116 117 3.357444 CCACCATCATTGGGGCCGA 62.357 63.158 0.00 0.00 45.95 5.54
118 119 2.908940 CCATCATTGGGGCCGAGC 60.909 66.667 0.00 0.00 39.56 5.03
119 120 2.124193 CATCATTGGGGCCGAGCA 60.124 61.111 0.00 0.00 0.00 4.26
120 121 2.124151 ATCATTGGGGCCGAGCAC 60.124 61.111 0.00 0.00 0.00 4.40
164 165 4.798682 GGCGGAGGAAGGGGAGGA 62.799 72.222 0.00 0.00 0.00 3.71
165 166 3.157949 GCGGAGGAAGGGGAGGAG 61.158 72.222 0.00 0.00 0.00 3.69
166 167 2.690452 CGGAGGAAGGGGAGGAGA 59.310 66.667 0.00 0.00 0.00 3.71
167 168 1.456705 CGGAGGAAGGGGAGGAGAG 60.457 68.421 0.00 0.00 0.00 3.20
168 169 1.074850 GGAGGAAGGGGAGGAGAGG 60.075 68.421 0.00 0.00 0.00 3.69
169 170 1.074850 GAGGAAGGGGAGGAGAGGG 60.075 68.421 0.00 0.00 0.00 4.30
170 171 1.550374 AGGAAGGGGAGGAGAGGGA 60.550 63.158 0.00 0.00 0.00 4.20
171 172 0.938926 AGGAAGGGGAGGAGAGGGAT 60.939 60.000 0.00 0.00 0.00 3.85
172 173 0.868186 GGAAGGGGAGGAGAGGGATA 59.132 60.000 0.00 0.00 0.00 2.59
173 174 1.223337 GGAAGGGGAGGAGAGGGATAA 59.777 57.143 0.00 0.00 0.00 1.75
174 175 2.361504 GGAAGGGGAGGAGAGGGATAAA 60.362 54.545 0.00 0.00 0.00 1.40
175 176 3.394645 GAAGGGGAGGAGAGGGATAAAA 58.605 50.000 0.00 0.00 0.00 1.52
176 177 2.777913 AGGGGAGGAGAGGGATAAAAC 58.222 52.381 0.00 0.00 0.00 2.43
177 178 1.416772 GGGGAGGAGAGGGATAAAACG 59.583 57.143 0.00 0.00 0.00 3.60
178 179 1.202663 GGGAGGAGAGGGATAAAACGC 60.203 57.143 0.00 0.00 0.00 4.84
179 180 1.538419 GGAGGAGAGGGATAAAACGCG 60.538 57.143 3.53 3.53 0.00 6.01
180 181 0.464452 AGGAGAGGGATAAAACGCGG 59.536 55.000 12.47 0.00 0.00 6.46
181 182 1.158484 GGAGAGGGATAAAACGCGGC 61.158 60.000 12.47 0.00 0.00 6.53
182 183 1.488261 GAGAGGGATAAAACGCGGCG 61.488 60.000 22.36 22.36 0.00 6.46
183 184 2.512974 AGGGATAAAACGCGGCGG 60.513 61.111 27.37 8.79 0.00 6.13
184 185 4.246206 GGGATAAAACGCGGCGGC 62.246 66.667 27.37 6.12 0.00 6.53
217 218 3.522731 CCCCGAGTCGCCTCAGAG 61.523 72.222 7.12 0.00 37.59 3.35
218 219 3.522731 CCCGAGTCGCCTCAGAGG 61.523 72.222 12.81 12.81 37.59 3.69
219 220 2.438614 CCGAGTCGCCTCAGAGGA 60.439 66.667 21.89 0.00 37.67 3.71
220 221 2.477176 CCGAGTCGCCTCAGAGGAG 61.477 68.421 21.89 17.79 37.67 3.69
228 229 4.544689 CTCAGAGGAGGCGACGCG 62.545 72.222 14.61 3.53 37.51 6.01
256 257 4.018409 GGGGGACTACGTACGGTT 57.982 61.111 21.06 2.38 0.00 4.44
257 258 1.512694 GGGGGACTACGTACGGTTG 59.487 63.158 21.06 11.20 0.00 3.77
258 259 1.512694 GGGGACTACGTACGGTTGG 59.487 63.158 21.06 3.82 0.00 3.77
259 260 0.965363 GGGGACTACGTACGGTTGGA 60.965 60.000 21.06 0.00 0.00 3.53
260 261 0.171231 GGGACTACGTACGGTTGGAC 59.829 60.000 21.06 4.96 0.00 4.02
261 262 0.171231 GGACTACGTACGGTTGGACC 59.829 60.000 21.06 7.56 34.05 4.46
262 263 0.171231 GACTACGTACGGTTGGACCC 59.829 60.000 21.06 0.00 33.75 4.46
263 264 1.250840 ACTACGTACGGTTGGACCCC 61.251 60.000 21.06 0.00 33.75 4.95
264 265 1.948721 CTACGTACGGTTGGACCCCC 61.949 65.000 21.06 0.00 33.75 5.40
265 266 2.439553 TACGTACGGTTGGACCCCCT 62.440 60.000 21.06 0.00 33.75 4.79
266 267 2.586293 CGTACGGTTGGACCCCCTT 61.586 63.158 7.57 0.00 33.75 3.95
267 268 1.257055 CGTACGGTTGGACCCCCTTA 61.257 60.000 7.57 0.00 33.75 2.69
288 289 2.473070 TGGGAGTCCGGATATTCACAA 58.527 47.619 7.81 0.00 35.24 3.33
290 291 2.224305 GGGAGTCCGGATATTCACAAGG 60.224 54.545 7.81 0.00 0.00 3.61
299 300 3.632145 GGATATTCACAAGGCGAACCAAT 59.368 43.478 0.00 0.00 39.06 3.16
306 307 3.098555 GGCGAACCAATAGCCGTG 58.901 61.111 0.00 0.00 41.53 4.94
310 311 1.713830 GAACCAATAGCCGTGACGC 59.286 57.895 0.00 0.00 0.00 5.19
317 318 1.955495 ATAGCCGTGACGCATCCACA 61.955 55.000 0.00 0.00 34.36 4.17
320 321 1.741401 CCGTGACGCATCCACACAT 60.741 57.895 0.00 0.00 34.36 3.21
322 323 0.179217 CGTGACGCATCCACACATTG 60.179 55.000 0.00 0.00 34.36 2.82
328 329 2.747460 ATCCACACATTGCGCGCT 60.747 55.556 33.29 10.46 0.00 5.92
338 339 2.348605 ATTGCGCGCTCTCCTCTCTC 62.349 60.000 33.29 0.00 0.00 3.20
339 340 3.209097 GCGCGCTCTCCTCTCTCT 61.209 66.667 26.67 0.00 0.00 3.10
351 352 4.078922 TCTCCTCTCTCTCTCTCTCTCTCT 60.079 50.000 0.00 0.00 0.00 3.10
352 353 4.219115 TCCTCTCTCTCTCTCTCTCTCTC 58.781 52.174 0.00 0.00 0.00 3.20
353 354 4.078922 TCCTCTCTCTCTCTCTCTCTCTCT 60.079 50.000 0.00 0.00 0.00 3.10
354 355 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
355 356 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
356 357 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
357 358 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
358 359 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
413 427 3.935993 GCTGAAGCCTGAAGGTGTA 57.064 52.632 0.00 0.00 37.57 2.90
420 434 4.202419 TGAAGCCTGAAGGTGTAGCTAAAA 60.202 41.667 0.00 0.00 37.57 1.52
424 438 3.947834 CCTGAAGGTGTAGCTAAAATGGG 59.052 47.826 0.00 0.00 0.00 4.00
432 446 4.816925 GTGTAGCTAAAATGGGGAAGCTAG 59.183 45.833 0.00 0.00 35.85 3.42
434 448 2.511637 AGCTAAAATGGGGAAGCTAGCT 59.488 45.455 12.68 12.68 37.78 3.32
496 519 2.492012 GCCAAAAATGGTGCAACATGA 58.508 42.857 20.07 0.00 39.98 3.07
497 520 2.223845 GCCAAAAATGGTGCAACATGAC 59.776 45.455 20.07 0.00 39.98 3.06
516 539 5.351233 TGACATAGTAAACTTGTTTGGCG 57.649 39.130 8.79 0.00 0.00 5.69
517 540 5.057819 TGACATAGTAAACTTGTTTGGCGA 58.942 37.500 8.79 0.07 0.00 5.54
518 541 5.527951 TGACATAGTAAACTTGTTTGGCGAA 59.472 36.000 8.79 0.00 0.00 4.70
526 549 1.592543 CTTGTTTGGCGAAAGGTTTGC 59.407 47.619 0.00 0.00 0.00 3.68
530 553 4.081050 GGCGAAAGGTTTGCCTCT 57.919 55.556 11.36 0.00 46.33 3.69
542 565 8.706322 AAAGGTTTGCCTCTCTTTTCTTTATA 57.294 30.769 0.00 0.00 46.33 0.98
543 566 8.706322 AAGGTTTGCCTCTCTTTTCTTTATAA 57.294 30.769 0.00 0.00 46.33 0.98
544 567 8.112016 AGGTTTGCCTCTCTTTTCTTTATAAC 57.888 34.615 0.00 0.00 42.67 1.89
545 568 7.724061 AGGTTTGCCTCTCTTTTCTTTATAACA 59.276 33.333 0.00 0.00 42.67 2.41
546 569 8.523658 GGTTTGCCTCTCTTTTCTTTATAACAT 58.476 33.333 0.00 0.00 0.00 2.71
547 570 9.346725 GTTTGCCTCTCTTTTCTTTATAACATG 57.653 33.333 0.00 0.00 0.00 3.21
548 571 8.862325 TTGCCTCTCTTTTCTTTATAACATGA 57.138 30.769 0.00 0.00 0.00 3.07
549 572 8.498054 TGCCTCTCTTTTCTTTATAACATGAG 57.502 34.615 0.00 0.00 0.00 2.90
550 573 8.103305 TGCCTCTCTTTTCTTTATAACATGAGT 58.897 33.333 0.00 0.00 0.00 3.41
558 594 9.739276 TTTTCTTTATAACATGAGTCCACTGAT 57.261 29.630 0.00 0.00 0.00 2.90
585 621 8.750515 TGGAATGATAATCTGCAATTGTCTAA 57.249 30.769 7.40 0.00 0.00 2.10
604 640 6.033966 GTCTAAACATATTTTTGGCGGAAGG 58.966 40.000 0.00 0.00 0.00 3.46
615 651 3.061093 GCGGAAGGCACTACTAACC 57.939 57.895 0.00 0.00 38.49 2.85
616 652 0.804933 GCGGAAGGCACTACTAACCG 60.805 60.000 0.00 0.00 38.49 4.44
617 653 0.804933 CGGAAGGCACTACTAACCGC 60.805 60.000 0.00 0.00 38.49 5.68
618 654 0.535797 GGAAGGCACTACTAACCGCT 59.464 55.000 0.00 0.00 38.49 5.52
619 655 1.471153 GGAAGGCACTACTAACCGCTC 60.471 57.143 0.00 0.00 38.49 5.03
620 656 1.477295 GAAGGCACTACTAACCGCTCT 59.523 52.381 0.00 0.00 38.49 4.09
621 657 2.431954 AGGCACTACTAACCGCTCTA 57.568 50.000 0.00 0.00 36.02 2.43
622 658 2.299521 AGGCACTACTAACCGCTCTAG 58.700 52.381 0.00 0.00 36.02 2.43
623 659 1.269154 GGCACTACTAACCGCTCTAGC 60.269 57.143 0.00 0.00 37.78 3.42
624 660 1.404391 GCACTACTAACCGCTCTAGCA 59.596 52.381 2.44 0.00 42.21 3.49
625 661 2.034812 GCACTACTAACCGCTCTAGCAT 59.965 50.000 2.44 0.00 42.21 3.79
626 662 3.491104 GCACTACTAACCGCTCTAGCATT 60.491 47.826 2.44 0.00 42.21 3.56
627 663 4.683832 CACTACTAACCGCTCTAGCATTT 58.316 43.478 2.44 0.00 42.21 2.32
628 664 5.109903 CACTACTAACCGCTCTAGCATTTT 58.890 41.667 2.44 0.00 42.21 1.82
629 665 5.005779 CACTACTAACCGCTCTAGCATTTTG 59.994 44.000 2.44 0.00 42.21 2.44
630 666 3.270877 ACTAACCGCTCTAGCATTTTGG 58.729 45.455 2.44 0.00 42.21 3.28
631 667 0.811281 AACCGCTCTAGCATTTTGGC 59.189 50.000 2.44 0.00 42.21 4.52
632 668 1.353103 CCGCTCTAGCATTTTGGCG 59.647 57.895 2.44 0.00 42.21 5.69
633 669 1.353103 CGCTCTAGCATTTTGGCGG 59.647 57.895 2.44 0.00 42.21 6.13
634 670 1.089481 CGCTCTAGCATTTTGGCGGA 61.089 55.000 2.44 0.00 42.21 5.54
635 671 1.094785 GCTCTAGCATTTTGGCGGAA 58.905 50.000 0.00 0.00 41.59 4.30
636 672 1.064654 GCTCTAGCATTTTGGCGGAAG 59.935 52.381 0.00 0.00 41.59 3.46
637 673 1.672881 CTCTAGCATTTTGGCGGAAGG 59.327 52.381 0.00 0.00 39.27 3.46
647 683 4.421952 GCGGAAGGCACTACTAGC 57.578 61.111 0.00 0.00 38.49 3.42
665 701 1.832411 GCCGCGCTAGCTATTTGACC 61.832 60.000 13.93 0.00 42.32 4.02
697 733 4.647611 TGTTTGACGTGGATTTGAGGTAT 58.352 39.130 0.00 0.00 0.00 2.73
712 748 0.404426 GGTATAGGGTTGGATGGCCC 59.596 60.000 0.00 0.00 45.16 5.80
725 761 1.762522 ATGGCCCGCTCCTGTATCAG 61.763 60.000 0.00 0.00 0.00 2.90
729 765 0.315568 CCCGCTCCTGTATCAGTAGC 59.684 60.000 4.62 4.62 39.53 3.58
731 767 3.875838 GCTCCTGTATCAGTAGCGG 57.124 57.895 0.00 0.00 34.08 5.52
732 768 0.315568 GCTCCTGTATCAGTAGCGGG 59.684 60.000 0.00 0.00 34.08 6.13
733 769 1.982660 CTCCTGTATCAGTAGCGGGA 58.017 55.000 0.00 0.00 36.37 5.14
736 772 1.964223 CCTGTATCAGTAGCGGGACAT 59.036 52.381 0.00 0.00 0.00 3.06
740 778 0.755698 ATCAGTAGCGGGACATCGGT 60.756 55.000 0.00 0.00 43.51 4.69
751 789 2.825086 GACATCGGTCCAATTTTCGG 57.175 50.000 0.00 0.00 38.12 4.30
766 804 8.247562 TCCAATTTTCGGACAATTAAATACAGG 58.752 33.333 2.07 0.00 0.00 4.00
769 807 6.746745 TTTCGGACAATTAAATACAGGGTC 57.253 37.500 0.00 0.00 0.00 4.46
770 808 4.435425 TCGGACAATTAAATACAGGGTCG 58.565 43.478 0.00 0.00 0.00 4.79
772 810 4.520179 GGACAATTAAATACAGGGTCGGT 58.480 43.478 0.00 0.00 0.00 4.69
773 811 4.945543 GGACAATTAAATACAGGGTCGGTT 59.054 41.667 0.00 0.00 0.00 4.44
774 812 5.416639 GGACAATTAAATACAGGGTCGGTTT 59.583 40.000 0.00 0.00 0.00 3.27
775 813 6.262193 ACAATTAAATACAGGGTCGGTTTG 57.738 37.500 0.00 0.00 0.00 2.93
776 814 4.976224 ATTAAATACAGGGTCGGTTTGC 57.024 40.909 0.00 0.00 0.00 3.68
777 815 2.279935 AAATACAGGGTCGGTTTGCA 57.720 45.000 0.00 0.00 0.00 4.08
818 857 6.817140 CCCTTACTACACAATACCAAGTTCTC 59.183 42.308 0.00 0.00 0.00 2.87
834 873 4.873010 AGTTCTCCTCATCCAGCTTAGTA 58.127 43.478 0.00 0.00 0.00 1.82
847 886 5.369993 TCCAGCTTAGTAGATACCTCTCTGA 59.630 44.000 0.00 0.00 32.66 3.27
862 901 4.142271 CCTCTCTGACCACAAGAGTACATC 60.142 50.000 0.00 0.00 35.76 3.06
880 919 4.009675 ACATCACACAAATGGTAGCGATT 58.990 39.130 0.00 0.00 0.00 3.34
926 981 6.102897 ACCCTATCCATCGTCTTCATTAAG 57.897 41.667 0.00 0.00 0.00 1.85
939 998 5.739161 GTCTTCATTAAGCCGTGCAATTAAG 59.261 40.000 0.00 0.00 32.36 1.85
972 1031 3.253677 GTCCATCGATCAACTACCGATCT 59.746 47.826 0.00 0.00 40.54 2.75
1048 1113 2.171568 TCATCATCCAGTCAGCCTCT 57.828 50.000 0.00 0.00 0.00 3.69
1111 1186 5.221843 ACCAACCAGTAGTCAATTAAGCAGA 60.222 40.000 0.00 0.00 0.00 4.26
1114 1197 5.246307 ACCAGTAGTCAATTAAGCAGAACC 58.754 41.667 0.00 0.00 0.00 3.62
1154 1237 0.394080 CTTCCTACCGTCCTCCTCGT 60.394 60.000 0.00 0.00 0.00 4.18
1215 1298 4.778143 GGCGACCCCGACATGCTT 62.778 66.667 0.00 0.00 44.91 3.91
1263 1346 1.656818 CCCTCGACGGCCGTAAGTTA 61.657 60.000 34.36 13.83 39.75 2.24
1302 1440 1.929836 GCCTGAACAGAGAGTAATGCG 59.070 52.381 3.19 0.00 0.00 4.73
1388 1536 1.585006 GGCGGACGACTTCTTCTCA 59.415 57.895 0.00 0.00 0.00 3.27
1415 1563 2.110352 GGCATTCCCGGGTAACACG 61.110 63.158 22.86 5.56 39.74 4.49
1496 1644 2.981302 CTGGGCGTCTCCATGTCA 59.019 61.111 0.00 0.00 36.05 3.58
1697 1845 2.668550 AAGAACAACGGAGGCGCC 60.669 61.111 21.89 21.89 0.00 6.53
1845 1993 1.077212 CTGGTGGAGGCCATCAAGG 60.077 63.158 5.01 0.00 44.73 3.61
1876 2030 1.669795 GCCAAAGTAACCAGCATGCAC 60.670 52.381 21.98 8.85 31.97 4.57
1890 2052 1.177895 ATGCACGCATGTTGGTTGGA 61.178 50.000 3.17 0.00 35.03 3.53
1894 2056 1.269174 CACGCATGTTGGTTGGATCAA 59.731 47.619 0.00 0.00 0.00 2.57
1935 2099 3.713288 TGCTAATAATGACGAAGGACCG 58.287 45.455 0.00 0.00 0.00 4.79
2029 2230 6.257411 TCGTCGGTTTTACTGTTAATTGTTGA 59.743 34.615 0.00 0.00 0.00 3.18
2185 2387 3.438216 TTGCAGATCCATTCCAAGACA 57.562 42.857 0.00 0.00 0.00 3.41
2210 2412 3.840890 TTGAAAGTTTCGCTGTGTTGT 57.159 38.095 10.92 0.00 0.00 3.32
2328 2530 4.383850 ACTCTCAGTGGATCGATCTTTG 57.616 45.455 23.96 18.26 0.00 2.77
2339 2541 4.143305 GGATCGATCTTTGCTTATGTACGC 60.143 45.833 23.96 0.00 0.00 4.42
2383 2585 3.404899 GTGTTATTTCGGTGGAGTTCCA 58.595 45.455 0.00 0.00 45.30 3.53
2395 2597 2.811431 TGGAGTTCCACATTAGCGTTTG 59.189 45.455 0.00 0.00 42.01 2.93
2498 2740 5.928976 TGACCATATGTGTCCTCCAATAAG 58.071 41.667 16.79 0.00 31.60 1.73
2529 2771 8.109705 ACTTGATGCATCTTAAACATGTACAA 57.890 30.769 26.32 8.14 0.00 2.41
2590 2832 3.267483 GTTGGTTGTAGCATGTATCCGT 58.733 45.455 0.00 0.00 0.00 4.69
2647 2889 7.660617 GGCCCCTTCTCTAAAAGTATATGTAAC 59.339 40.741 0.00 0.00 0.00 2.50
2739 2982 1.873698 TTATCGAGCGGGCATTAACC 58.126 50.000 0.00 0.00 0.00 2.85
2740 2983 0.753867 TATCGAGCGGGCATTAACCA 59.246 50.000 0.00 0.00 0.00 3.67
2832 3094 5.309323 TGACCGAAATTTTCATAAGGCAG 57.691 39.130 9.66 0.00 0.00 4.85
2871 3133 1.816224 TGCGGTTCCTGCTTTATTTCC 59.184 47.619 0.00 0.00 0.00 3.13
2882 3144 3.290710 GCTTTATTTCCCTCTGATGGCA 58.709 45.455 0.00 0.00 0.00 4.92
2902 3164 4.479619 GCAAAGGTAATTCTTGTGCTGAG 58.520 43.478 0.00 0.00 32.92 3.35
2917 3179 1.136141 GCTGAGCACACGTGAGAATTG 60.136 52.381 25.01 10.84 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 4.778143 CCTTGGTTCCCCGGAGCG 62.778 72.222 0.73 0.00 0.00 5.03
48 49 4.426313 GGCCTTGGTTCCCCGGAG 62.426 72.222 0.73 0.00 0.00 4.63
51 52 4.426313 GAGGGCCTTGGTTCCCCG 62.426 72.222 7.89 0.00 43.67 5.73
52 53 4.062032 GGAGGGCCTTGGTTCCCC 62.062 72.222 7.89 0.00 43.67 4.81
53 54 2.380571 TTTGGAGGGCCTTGGTTCCC 62.381 60.000 7.89 3.10 42.94 3.97
54 55 0.900182 CTTTGGAGGGCCTTGGTTCC 60.900 60.000 7.89 4.32 34.31 3.62
55 56 0.900182 CCTTTGGAGGGCCTTGGTTC 60.900 60.000 7.89 0.00 39.55 3.62
56 57 1.156095 CCTTTGGAGGGCCTTGGTT 59.844 57.895 7.89 0.00 39.55 3.67
57 58 1.778383 TCCTTTGGAGGGCCTTGGT 60.778 57.895 7.89 0.00 43.72 3.67
58 59 1.000396 CTCCTTTGGAGGGCCTTGG 60.000 63.158 7.89 5.83 45.43 3.61
59 60 4.751431 CTCCTTTGGAGGGCCTTG 57.249 61.111 7.89 0.00 45.43 3.61
67 68 2.660064 GCGCCTCCTCTCCTTTGGA 61.660 63.158 0.00 0.00 0.00 3.53
68 69 2.124942 GCGCCTCCTCTCCTTTGG 60.125 66.667 0.00 0.00 0.00 3.28
69 70 2.124942 GGCGCCTCCTCTCCTTTG 60.125 66.667 22.15 0.00 0.00 2.77
70 71 2.607750 TGGCGCCTCCTCTCCTTT 60.608 61.111 29.70 0.00 35.26 3.11
71 72 2.887738 ATCTGGCGCCTCCTCTCCTT 62.888 60.000 29.70 0.00 35.26 3.36
72 73 3.387609 ATCTGGCGCCTCCTCTCCT 62.388 63.158 29.70 0.27 35.26 3.69
73 74 2.841988 ATCTGGCGCCTCCTCTCC 60.842 66.667 29.70 0.00 35.26 3.71
74 75 2.733945 GATCTGGCGCCTCCTCTC 59.266 66.667 29.70 13.15 35.26 3.20
75 76 2.841988 GGATCTGGCGCCTCCTCT 60.842 66.667 29.70 7.68 35.26 3.69
76 77 3.934962 GGGATCTGGCGCCTCCTC 61.935 72.222 29.70 19.66 35.26 3.71
92 93 3.891400 CAATGATGGTGGCGGCGG 61.891 66.667 9.78 0.00 0.00 6.13
93 94 3.891400 CCAATGATGGTGGCGGCG 61.891 66.667 0.51 0.51 42.18 6.46
94 95 3.530260 CCCAATGATGGTGGCGGC 61.530 66.667 0.00 0.00 46.01 6.53
95 96 2.834505 CCCCAATGATGGTGGCGG 60.835 66.667 0.00 0.00 46.01 6.13
96 97 3.530260 GCCCCAATGATGGTGGCG 61.530 66.667 10.30 0.00 46.35 5.69
98 99 2.834505 CGGCCCCAATGATGGTGG 60.835 66.667 0.00 0.00 46.01 4.61
99 100 1.825191 CTCGGCCCCAATGATGGTG 60.825 63.158 0.00 0.00 46.01 4.17
100 101 2.597340 CTCGGCCCCAATGATGGT 59.403 61.111 0.00 0.00 46.01 3.55
102 103 2.124193 TGCTCGGCCCCAATGATG 60.124 61.111 0.00 0.00 0.00 3.07
103 104 2.124151 GTGCTCGGCCCCAATGAT 60.124 61.111 0.00 0.00 0.00 2.45
104 105 4.424711 GGTGCTCGGCCCCAATGA 62.425 66.667 0.00 0.00 0.00 2.57
147 148 4.798682 TCCTCCCCTTCCTCCGCC 62.799 72.222 0.00 0.00 0.00 6.13
148 149 3.157949 CTCCTCCCCTTCCTCCGC 61.158 72.222 0.00 0.00 0.00 5.54
149 150 1.456705 CTCTCCTCCCCTTCCTCCG 60.457 68.421 0.00 0.00 0.00 4.63
150 151 1.074850 CCTCTCCTCCCCTTCCTCC 60.075 68.421 0.00 0.00 0.00 4.30
151 152 1.074850 CCCTCTCCTCCCCTTCCTC 60.075 68.421 0.00 0.00 0.00 3.71
152 153 0.938926 ATCCCTCTCCTCCCCTTCCT 60.939 60.000 0.00 0.00 0.00 3.36
153 154 0.868186 TATCCCTCTCCTCCCCTTCC 59.132 60.000 0.00 0.00 0.00 3.46
154 155 2.797285 TTATCCCTCTCCTCCCCTTC 57.203 55.000 0.00 0.00 0.00 3.46
155 156 3.124066 GTTTTATCCCTCTCCTCCCCTT 58.876 50.000 0.00 0.00 0.00 3.95
156 157 2.777913 GTTTTATCCCTCTCCTCCCCT 58.222 52.381 0.00 0.00 0.00 4.79
157 158 1.416772 CGTTTTATCCCTCTCCTCCCC 59.583 57.143 0.00 0.00 0.00 4.81
158 159 1.202663 GCGTTTTATCCCTCTCCTCCC 60.203 57.143 0.00 0.00 0.00 4.30
159 160 1.538419 CGCGTTTTATCCCTCTCCTCC 60.538 57.143 0.00 0.00 0.00 4.30
160 161 1.538419 CCGCGTTTTATCCCTCTCCTC 60.538 57.143 4.92 0.00 0.00 3.71
161 162 0.464452 CCGCGTTTTATCCCTCTCCT 59.536 55.000 4.92 0.00 0.00 3.69
162 163 1.158484 GCCGCGTTTTATCCCTCTCC 61.158 60.000 4.92 0.00 0.00 3.71
163 164 1.488261 CGCCGCGTTTTATCCCTCTC 61.488 60.000 4.92 0.00 0.00 3.20
164 165 1.520787 CGCCGCGTTTTATCCCTCT 60.521 57.895 4.92 0.00 0.00 3.69
165 166 2.531376 CCGCCGCGTTTTATCCCTC 61.531 63.158 12.58 0.00 0.00 4.30
166 167 2.512974 CCGCCGCGTTTTATCCCT 60.513 61.111 12.58 0.00 0.00 4.20
167 168 4.246206 GCCGCCGCGTTTTATCCC 62.246 66.667 12.58 0.00 0.00 3.85
211 212 4.544689 CGCGTCGCCTCCTCTGAG 62.545 72.222 12.44 0.00 38.42 3.35
239 240 1.512694 CAACCGTACGTAGTCCCCC 59.487 63.158 15.21 0.00 43.93 5.40
240 241 0.965363 TCCAACCGTACGTAGTCCCC 60.965 60.000 15.21 0.00 43.93 4.81
241 242 0.171231 GTCCAACCGTACGTAGTCCC 59.829 60.000 15.21 0.00 43.93 4.46
242 243 0.171231 GGTCCAACCGTACGTAGTCC 59.829 60.000 15.21 5.24 43.93 3.85
243 244 0.171231 GGGTCCAACCGTACGTAGTC 59.829 60.000 15.21 0.00 39.07 2.59
244 245 1.250840 GGGGTCCAACCGTACGTAGT 61.251 60.000 15.21 2.62 42.22 2.73
245 246 1.512694 GGGGTCCAACCGTACGTAG 59.487 63.158 15.21 1.90 39.83 3.51
246 247 1.981853 GGGGGTCCAACCGTACGTA 60.982 63.158 15.21 0.00 39.83 3.57
247 248 3.313524 GGGGGTCCAACCGTACGT 61.314 66.667 15.21 0.00 39.83 3.57
248 249 1.257055 TAAGGGGGTCCAACCGTACG 61.257 60.000 8.69 8.69 39.83 3.67
249 250 1.134310 CATAAGGGGGTCCAACCGTAC 60.134 57.143 0.00 0.00 39.83 3.67
250 251 1.205966 CATAAGGGGGTCCAACCGTA 58.794 55.000 0.00 0.00 39.83 4.02
251 252 1.568118 CCATAAGGGGGTCCAACCGT 61.568 60.000 0.00 0.00 39.83 4.83
252 253 1.226262 CCATAAGGGGGTCCAACCG 59.774 63.158 0.00 0.00 39.83 4.44
263 264 3.838317 TGAATATCCGGACTCCCATAAGG 59.162 47.826 6.12 0.00 0.00 2.69
264 265 4.283467 TGTGAATATCCGGACTCCCATAAG 59.717 45.833 6.12 0.00 0.00 1.73
265 266 4.228010 TGTGAATATCCGGACTCCCATAA 58.772 43.478 6.12 0.00 0.00 1.90
266 267 3.851979 TGTGAATATCCGGACTCCCATA 58.148 45.455 6.12 0.00 0.00 2.74
267 268 2.689658 TGTGAATATCCGGACTCCCAT 58.310 47.619 6.12 0.00 0.00 4.00
277 278 2.639065 TGGTTCGCCTTGTGAATATCC 58.361 47.619 0.00 0.00 34.54 2.59
278 279 4.900635 ATTGGTTCGCCTTGTGAATATC 57.099 40.909 0.00 0.00 34.54 1.63
280 281 3.625764 GCTATTGGTTCGCCTTGTGAATA 59.374 43.478 0.00 0.00 34.54 1.75
283 284 1.448985 GCTATTGGTTCGCCTTGTGA 58.551 50.000 0.00 0.00 38.36 3.58
288 289 1.449601 CACGGCTATTGGTTCGCCT 60.450 57.895 0.00 0.00 41.61 5.52
290 291 1.713830 GTCACGGCTATTGGTTCGC 59.286 57.895 0.00 0.00 0.00 4.70
299 300 2.183300 GTGGATGCGTCACGGCTA 59.817 61.111 8.47 0.00 0.00 3.93
303 304 0.179217 CAATGTGTGGATGCGTCACG 60.179 55.000 8.47 0.00 37.91 4.35
305 306 1.875262 GCAATGTGTGGATGCGTCA 59.125 52.632 8.47 0.00 0.00 4.35
306 307 4.771684 GCAATGTGTGGATGCGTC 57.228 55.556 0.00 0.00 0.00 5.19
310 311 2.577644 GCGCGCAATGTGTGGATG 60.578 61.111 29.10 0.00 0.00 3.51
317 318 2.510238 GAGGAGAGCGCGCAATGT 60.510 61.111 35.10 13.12 0.00 2.71
320 321 3.057547 GAGAGAGGAGAGCGCGCAA 62.058 63.158 35.10 0.00 0.00 4.85
322 323 3.181169 GAGAGAGAGGAGAGCGCGC 62.181 68.421 26.66 26.66 0.00 6.86
325 326 1.414181 AGAGAGAGAGAGAGGAGAGCG 59.586 57.143 0.00 0.00 0.00 5.03
328 329 4.078922 AGAGAGAGAGAGAGAGAGAGGAGA 60.079 50.000 0.00 0.00 0.00 3.71
338 339 3.963374 TGGAGAGAGAGAGAGAGAGAGAG 59.037 52.174 0.00 0.00 0.00 3.20
339 340 3.994317 TGGAGAGAGAGAGAGAGAGAGA 58.006 50.000 0.00 0.00 0.00 3.10
351 352 3.118261 GCCATTTGGTGTATGGAGAGAGA 60.118 47.826 6.07 0.00 44.36 3.10
352 353 3.209410 GCCATTTGGTGTATGGAGAGAG 58.791 50.000 6.07 0.00 44.36 3.20
353 354 2.419990 CGCCATTTGGTGTATGGAGAGA 60.420 50.000 6.07 0.00 44.36 3.10
354 355 1.942657 CGCCATTTGGTGTATGGAGAG 59.057 52.381 6.07 0.00 44.36 3.20
355 356 1.557371 TCGCCATTTGGTGTATGGAGA 59.443 47.619 9.82 5.25 45.72 3.71
356 357 2.036958 TCGCCATTTGGTGTATGGAG 57.963 50.000 9.82 2.91 44.36 3.86
357 358 2.498644 TTCGCCATTTGGTGTATGGA 57.501 45.000 9.82 0.00 44.36 3.41
358 359 2.159254 CCTTTCGCCATTTGGTGTATGG 60.159 50.000 9.82 8.31 45.57 2.74
402 403 3.947834 CCCATTTTAGCTACACCTTCAGG 59.052 47.826 0.00 0.00 42.17 3.86
403 404 3.947834 CCCCATTTTAGCTACACCTTCAG 59.052 47.826 0.00 0.00 0.00 3.02
404 405 3.589735 TCCCCATTTTAGCTACACCTTCA 59.410 43.478 0.00 0.00 0.00 3.02
405 406 4.230745 TCCCCATTTTAGCTACACCTTC 57.769 45.455 0.00 0.00 0.00 3.46
413 427 2.511637 AGCTAGCTTCCCCATTTTAGCT 59.488 45.455 12.68 0.00 45.32 3.32
420 434 1.695597 AGCCAGCTAGCTTCCCCAT 60.696 57.895 16.46 0.00 41.41 4.00
424 438 2.121291 AAAAGAGCCAGCTAGCTTCC 57.879 50.000 16.46 8.96 45.15 3.46
447 461 6.934645 AGCTAGCTAGTGTGTATGTTTTTGAA 59.065 34.615 17.69 0.00 0.00 2.69
449 463 6.727824 AGCTAGCTAGTGTGTATGTTTTTG 57.272 37.500 17.69 0.00 0.00 2.44
450 464 6.090898 CGAAGCTAGCTAGTGTGTATGTTTTT 59.909 38.462 19.70 0.00 0.00 1.94
451 465 5.577164 CGAAGCTAGCTAGTGTGTATGTTTT 59.423 40.000 19.70 0.00 0.00 2.43
452 466 5.103000 CGAAGCTAGCTAGTGTGTATGTTT 58.897 41.667 19.70 0.00 0.00 2.83
453 467 4.440250 CCGAAGCTAGCTAGTGTGTATGTT 60.440 45.833 19.70 0.00 0.00 2.71
454 468 3.066900 CCGAAGCTAGCTAGTGTGTATGT 59.933 47.826 19.70 0.00 0.00 2.29
455 469 3.633235 CCGAAGCTAGCTAGTGTGTATG 58.367 50.000 19.70 6.13 0.00 2.39
456 470 2.034812 GCCGAAGCTAGCTAGTGTGTAT 59.965 50.000 19.70 0.00 35.50 2.29
464 487 2.483014 TTTTTGGCCGAAGCTAGCTA 57.517 45.000 19.70 0.00 39.73 3.32
496 519 6.380095 TTTCGCCAAACAAGTTTACTATGT 57.620 33.333 0.00 0.00 0.00 2.29
497 520 5.856455 CCTTTCGCCAAACAAGTTTACTATG 59.144 40.000 0.00 0.00 0.00 2.23
526 549 9.103861 GGACTCATGTTATAAAGAAAAGAGAGG 57.896 37.037 0.00 0.00 0.00 3.69
528 551 9.436957 GTGGACTCATGTTATAAAGAAAAGAGA 57.563 33.333 0.00 0.00 0.00 3.10
530 553 9.219603 CAGTGGACTCATGTTATAAAGAAAAGA 57.780 33.333 0.00 0.00 0.00 2.52
542 565 4.371624 TCCAAATCAGTGGACTCATGTT 57.628 40.909 0.00 0.00 42.97 2.71
550 573 6.263842 GCAGATTATCATTCCAAATCAGTGGA 59.736 38.462 0.00 0.00 46.24 4.02
558 594 8.070034 AGACAATTGCAGATTATCATTCCAAA 57.930 30.769 5.05 0.00 0.00 3.28
585 621 2.564947 TGCCTTCCGCCAAAAATATGTT 59.435 40.909 0.00 0.00 36.24 2.71
592 628 0.109723 AGTAGTGCCTTCCGCCAAAA 59.890 50.000 0.00 0.00 36.24 2.44
604 640 1.404391 TGCTAGAGCGGTTAGTAGTGC 59.596 52.381 0.00 0.00 45.83 4.40
605 641 3.992260 ATGCTAGAGCGGTTAGTAGTG 57.008 47.619 0.00 0.00 45.83 2.74
607 643 4.508124 CCAAAATGCTAGAGCGGTTAGTAG 59.492 45.833 0.00 0.00 45.83 2.57
608 644 4.439057 CCAAAATGCTAGAGCGGTTAGTA 58.561 43.478 0.00 0.00 45.83 1.82
609 645 3.270877 CCAAAATGCTAGAGCGGTTAGT 58.729 45.455 0.00 0.00 45.83 2.24
610 646 2.032178 GCCAAAATGCTAGAGCGGTTAG 59.968 50.000 0.00 0.00 45.83 2.34
611 647 2.014128 GCCAAAATGCTAGAGCGGTTA 58.986 47.619 0.00 0.00 45.83 2.85
612 648 0.811281 GCCAAAATGCTAGAGCGGTT 59.189 50.000 0.00 0.00 45.83 4.44
613 649 1.369091 CGCCAAAATGCTAGAGCGGT 61.369 55.000 0.00 0.00 45.83 5.68
614 650 1.353103 CGCCAAAATGCTAGAGCGG 59.647 57.895 0.00 0.00 45.83 5.52
615 651 1.089481 TCCGCCAAAATGCTAGAGCG 61.089 55.000 0.00 0.00 45.83 5.03
616 652 1.064654 CTTCCGCCAAAATGCTAGAGC 59.935 52.381 0.00 0.00 42.50 4.09
617 653 1.672881 CCTTCCGCCAAAATGCTAGAG 59.327 52.381 0.00 0.00 0.00 2.43
618 654 1.750193 CCTTCCGCCAAAATGCTAGA 58.250 50.000 0.00 0.00 0.00 2.43
619 655 0.101219 GCCTTCCGCCAAAATGCTAG 59.899 55.000 0.00 0.00 0.00 3.42
620 656 0.610509 TGCCTTCCGCCAAAATGCTA 60.611 50.000 0.00 0.00 36.24 3.49
621 657 1.907807 TGCCTTCCGCCAAAATGCT 60.908 52.632 0.00 0.00 36.24 3.79
622 658 1.737735 GTGCCTTCCGCCAAAATGC 60.738 57.895 0.00 0.00 36.24 3.56
623 659 1.135402 GTAGTGCCTTCCGCCAAAATG 60.135 52.381 0.00 0.00 36.24 2.32
624 660 1.173913 GTAGTGCCTTCCGCCAAAAT 58.826 50.000 0.00 0.00 36.24 1.82
625 661 0.109723 AGTAGTGCCTTCCGCCAAAA 59.890 50.000 0.00 0.00 36.24 2.44
626 662 0.978151 TAGTAGTGCCTTCCGCCAAA 59.022 50.000 0.00 0.00 36.24 3.28
627 663 0.535335 CTAGTAGTGCCTTCCGCCAA 59.465 55.000 0.00 0.00 36.24 4.52
628 664 1.956629 GCTAGTAGTGCCTTCCGCCA 61.957 60.000 0.00 0.00 36.24 5.69
629 665 1.227292 GCTAGTAGTGCCTTCCGCC 60.227 63.158 0.00 0.00 36.24 6.13
630 666 1.227292 GGCTAGTAGTGCCTTCCGC 60.227 63.158 0.00 0.00 46.38 5.54
636 672 2.842256 TAGCGCGGCTAGTAGTGCC 61.842 63.158 8.83 1.20 44.16 5.01
637 673 2.719979 TAGCGCGGCTAGTAGTGC 59.280 61.111 8.83 14.42 40.44 4.40
644 680 0.671796 TCAAATAGCTAGCGCGGCTA 59.328 50.000 29.47 29.47 44.76 3.93
645 681 0.876342 GTCAAATAGCTAGCGCGGCT 60.876 55.000 27.63 27.63 43.41 5.52
646 682 1.565106 GTCAAATAGCTAGCGCGGC 59.435 57.895 18.05 18.05 42.32 6.53
647 683 1.548973 CGGTCAAATAGCTAGCGCGG 61.549 60.000 8.83 0.00 42.32 6.46
648 684 0.594028 TCGGTCAAATAGCTAGCGCG 60.594 55.000 9.55 0.00 42.32 6.86
649 685 1.258197 GTTCGGTCAAATAGCTAGCGC 59.742 52.381 9.55 0.00 34.35 5.92
650 686 1.517276 CGTTCGGTCAAATAGCTAGCG 59.483 52.381 9.55 0.00 35.57 4.26
665 701 1.829457 CACGTCAAACAACAACGTTCG 59.171 47.619 0.00 0.00 46.56 3.95
684 720 4.376223 TCCAACCCTATACCTCAAATCCA 58.624 43.478 0.00 0.00 0.00 3.41
697 733 3.804329 GCGGGCCATCCAACCCTA 61.804 66.667 4.39 0.00 44.63 3.53
732 768 2.352388 TCCGAAAATTGGACCGATGTC 58.648 47.619 0.00 0.00 40.98 3.06
733 769 2.483014 TCCGAAAATTGGACCGATGT 57.517 45.000 0.00 0.00 0.00 3.06
740 778 8.247562 CCTGTATTTAATTGTCCGAAAATTGGA 58.752 33.333 6.77 0.00 0.00 3.53
743 781 8.129496 ACCCTGTATTTAATTGTCCGAAAATT 57.871 30.769 2.10 2.10 0.00 1.82
751 789 6.319399 CAAACCGACCCTGTATTTAATTGTC 58.681 40.000 0.00 0.00 0.00 3.18
756 794 3.752665 TGCAAACCGACCCTGTATTTAA 58.247 40.909 0.00 0.00 0.00 1.52
759 797 1.613255 CCTGCAAACCGACCCTGTATT 60.613 52.381 0.00 0.00 0.00 1.89
760 798 0.035439 CCTGCAAACCGACCCTGTAT 60.035 55.000 0.00 0.00 0.00 2.29
761 799 1.373435 CCTGCAAACCGACCCTGTA 59.627 57.895 0.00 0.00 0.00 2.74
762 800 1.412453 TACCTGCAAACCGACCCTGT 61.412 55.000 0.00 0.00 0.00 4.00
763 801 0.673644 CTACCTGCAAACCGACCCTG 60.674 60.000 0.00 0.00 0.00 4.45
764 802 1.677552 CTACCTGCAAACCGACCCT 59.322 57.895 0.00 0.00 0.00 4.34
765 803 2.038837 GCTACCTGCAAACCGACCC 61.039 63.158 0.00 0.00 42.31 4.46
766 804 2.388232 CGCTACCTGCAAACCGACC 61.388 63.158 0.00 0.00 43.06 4.79
769 807 1.206578 CAACGCTACCTGCAAACCG 59.793 57.895 0.00 0.00 43.06 4.44
770 808 0.887387 TCCAACGCTACCTGCAAACC 60.887 55.000 0.00 0.00 43.06 3.27
772 810 1.539388 CATTCCAACGCTACCTGCAAA 59.461 47.619 0.00 0.00 43.06 3.68
773 811 1.164411 CATTCCAACGCTACCTGCAA 58.836 50.000 0.00 0.00 43.06 4.08
774 812 1.305219 GCATTCCAACGCTACCTGCA 61.305 55.000 0.00 0.00 43.06 4.41
775 813 1.429423 GCATTCCAACGCTACCTGC 59.571 57.895 0.00 0.00 38.57 4.85
776 814 1.376609 GGGCATTCCAACGCTACCTG 61.377 60.000 0.00 0.00 35.00 4.00
777 815 1.077716 GGGCATTCCAACGCTACCT 60.078 57.895 0.00 0.00 35.00 3.08
787 825 4.820173 GGTATTGTGTAGTAAGGGCATTCC 59.180 45.833 0.00 0.00 0.00 3.01
818 857 5.329399 AGGTATCTACTAAGCTGGATGAGG 58.671 45.833 0.00 0.00 0.00 3.86
834 873 4.264172 ACTCTTGTGGTCAGAGAGGTATCT 60.264 45.833 3.96 0.00 40.89 1.98
847 886 4.415881 TTGTGTGATGTACTCTTGTGGT 57.584 40.909 0.00 0.00 0.00 4.16
862 901 3.724716 CGTGAATCGCTACCATTTGTGTG 60.725 47.826 0.00 0.00 0.00 3.82
894 933 3.181454 ACGATGGATAGGGTTGGATTGTC 60.181 47.826 0.00 0.00 0.00 3.18
895 934 2.777692 ACGATGGATAGGGTTGGATTGT 59.222 45.455 0.00 0.00 0.00 2.71
897 936 3.318313 AGACGATGGATAGGGTTGGATT 58.682 45.455 0.00 0.00 0.00 3.01
898 937 2.977808 AGACGATGGATAGGGTTGGAT 58.022 47.619 0.00 0.00 0.00 3.41
926 981 3.171277 GTGATGAACTTAATTGCACGGC 58.829 45.455 0.00 0.00 0.00 5.68
939 998 4.122046 TGATCGATGGACATGTGATGAAC 58.878 43.478 1.15 0.00 0.00 3.18
972 1031 0.396139 AGCGTAAGGGGGACGTGATA 60.396 55.000 0.00 0.00 42.31 2.15
1048 1113 0.758734 AGCTGTGTGGTGAAGTAGCA 59.241 50.000 0.00 0.00 33.81 3.49
1114 1197 3.197790 CTTCGGCGCCATGGTCAG 61.198 66.667 28.98 8.23 0.00 3.51
1128 1211 0.460459 GGACGGTAGGAAGCTGCTTC 60.460 60.000 29.50 29.50 39.52 3.86
1137 1220 1.222936 GACGAGGAGGACGGTAGGA 59.777 63.158 0.00 0.00 34.93 2.94
1215 1298 2.258591 GCGACGCAGAAGTCCTGA 59.741 61.111 16.42 0.00 45.78 3.86
1263 1346 2.552591 GGCATGATGGAAGAGCTAGCAT 60.553 50.000 18.83 1.39 34.16 3.79
1302 1440 3.792956 GCTGCACAAATACATACATGCAC 59.207 43.478 0.00 0.00 38.11 4.57
1845 1993 0.891904 TACTTTGGCGGGAACTTGGC 60.892 55.000 0.00 0.00 0.00 4.52
1876 2030 1.733389 GCTTGATCCAACCAACATGCG 60.733 52.381 0.00 0.00 0.00 4.73
1890 2052 1.531264 CGTACGCACGTAGAGCTTGAT 60.531 52.381 0.52 0.00 43.35 2.57
1935 2099 6.741448 TGAATTAAAACTGCACTTTTACGC 57.259 33.333 9.86 4.97 0.00 4.42
2029 2230 5.941948 CCAGTAGGTTCGTGAAGAAAAAT 57.058 39.130 0.00 0.00 41.10 1.82
2185 2387 6.978080 ACAACACAGCGAAACTTTCAAATAAT 59.022 30.769 2.49 0.00 0.00 1.28
2210 2412 1.960040 ATCGCGAGCCCAACTCATGA 61.960 55.000 16.66 0.00 46.63 3.07
2227 2429 6.587273 AGACCAAAGACTAAGGCTGAATATC 58.413 40.000 0.00 0.00 0.00 1.63
2328 2530 0.850856 GTGCTACGGCGTACATAAGC 59.149 55.000 21.31 21.31 42.25 3.09
2355 2557 4.317488 TCCACCGAAATAACACCAGTTAC 58.683 43.478 0.00 0.00 42.60 2.50
2383 2585 4.142138 TGTTTTGGAACCAAACGCTAATGT 60.142 37.500 17.09 0.00 44.39 2.71
2395 2597 5.457473 CACGTGAAAAGTATGTTTTGGAACC 59.543 40.000 10.90 0.00 34.80 3.62
2498 2740 7.928908 TGTTTAAGATGCATCAAGTTGTTTC 57.071 32.000 27.81 9.60 0.00 2.78
2529 2771 6.228258 CAGCCAACCGGTACTTACAATATAT 58.772 40.000 8.00 0.00 33.28 0.86
2647 2889 6.395629 TGGACAGAAAGAAACGAATAGGTAG 58.604 40.000 0.00 0.00 0.00 3.18
2720 2963 1.139256 TGGTTAATGCCCGCTCGATAA 59.861 47.619 0.00 0.00 0.00 1.75
2739 2982 3.450578 GCCCACTTGAATGTGCATAATG 58.549 45.455 0.00 0.00 36.68 1.90
2740 2983 2.431782 GGCCCACTTGAATGTGCATAAT 59.568 45.455 0.00 0.00 36.68 1.28
2841 3103 2.731217 CAGGAACCGCAAGACAAAAAG 58.269 47.619 0.00 0.00 43.02 2.27
2871 3133 4.530875 AGAATTACCTTTGCCATCAGAGG 58.469 43.478 0.91 0.91 46.84 3.69
2882 3144 4.144297 TGCTCAGCACAAGAATTACCTTT 58.856 39.130 0.00 0.00 31.71 3.11


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

AutoCloner maintained by Alex Coulton.