Multiple sequence alignment - TraesCS3B01G009300

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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 TraesCS3B01G009300 chr3B 100.000 2414 0 0 1 2414 4460423 4458010 0.000000e+00 4458.0
1 TraesCS3B01G009300 chr3B 77.888 1108 160 49 770 1812 4434344 4433257 5.710000e-171 610.0
2 TraesCS3B01G009300 chr3B 79.788 851 118 29 765 1590 4469519 4468698 9.680000e-159 569.0
3 TraesCS3B01G009300 chr3B 76.712 292 52 9 1210 1493 4475845 4475562 5.380000e-32 148.0
4 TraesCS3B01G009300 chr3A 83.076 1684 168 55 222 1822 1779574 1781223 0.000000e+00 1423.0
5 TraesCS3B01G009300 chr3A 77.655 904 132 37 967 1812 1789554 1790445 1.000000e-133 486.0
6 TraesCS3B01G009300 chr3A 78.824 680 121 15 848 1519 1851827 1852491 1.020000e-118 436.0
7 TraesCS3B01G009300 chr3A 76.304 671 120 23 871 1521 1769469 1770120 2.990000e-84 322.0
8 TraesCS3B01G009300 chr3A 87.222 180 18 4 1 177 1779381 1779558 1.460000e-47 200.0
9 TraesCS3B01G009300 chr3A 77.215 237 42 10 1007 1238 1859292 1859521 7.010000e-26 128.0
10 TraesCS3B01G009300 chr3A 90.411 73 4 3 1888 1958 1782037 1782108 2.560000e-15 93.5
11 TraesCS3B01G009300 chr3D 88.019 1060 84 24 799 1822 2256848 2255796 0.000000e+00 1214.0
12 TraesCS3B01G009300 chr3D 79.314 1020 138 43 846 1812 2243503 2242504 0.000000e+00 647.0
13 TraesCS3B01G009300 chr3D 78.587 920 129 38 942 1821 2239566 2238675 1.630000e-151 545.0
14 TraesCS3B01G009300 chr3D 86.553 409 45 8 1852 2259 2253304 2252905 2.200000e-120 442.0
15 TraesCS3B01G009300 chr3D 77.845 659 105 25 846 1493 2201942 2201314 1.050000e-98 370.0
16 TraesCS3B01G009300 chr3D 76.654 514 97 17 931 1434 2259186 2258686 1.840000e-66 263.0
17 TraesCS3B01G009300 chr3D 78.455 246 41 9 1007 1247 2201195 2200957 1.500000e-32 150.0
18 TraesCS3B01G009300 chr3D 87.671 73 7 2 2290 2361 346355821 346355750 1.540000e-12 84.2
19 TraesCS3B01G009300 chr5B 91.667 72 6 0 2290 2361 594231269 594231198 1.530000e-17 100.0
20 TraesCS3B01G009300 chr5B 94.595 37 2 0 2290 2326 526672756 526672792 9.320000e-05 58.4
21 TraesCS3B01G009300 chr2A 89.474 76 8 0 2290 2365 676127853 676127928 1.980000e-16 97.1
22 TraesCS3B01G009300 chr4A 86.842 76 10 0 2290 2365 188609932 188610007 4.280000e-13 86.1
23 TraesCS3B01G009300 chr5D 94.231 52 3 0 2310 2361 396485025 396484974 1.990000e-11 80.5
24 TraesCS3B01G009300 chr7A 86.111 72 10 0 2290 2361 31196760 31196831 7.160000e-11 78.7
25 TraesCS3B01G009300 chr7A 95.000 40 2 0 2290 2329 24380973 24380934 2.000000e-06 63.9
26 TraesCS3B01G009300 chr7A 95.000 40 2 0 2290 2329 24400712 24400673 2.000000e-06 63.9
27 TraesCS3B01G009300 chr6A 94.118 51 3 0 2311 2361 608556187 608556137 7.160000e-11 78.7


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 TraesCS3B01G009300 chr3B 4458010 4460423 2413 True 4458.000000 4458 100.0000 1 2414 1 chr3B.!!$R2 2413
1 TraesCS3B01G009300 chr3B 4433257 4434344 1087 True 610.000000 610 77.8880 770 1812 1 chr3B.!!$R1 1042
2 TraesCS3B01G009300 chr3B 4468698 4469519 821 True 569.000000 569 79.7880 765 1590 1 chr3B.!!$R3 825
3 TraesCS3B01G009300 chr3A 1779381 1782108 2727 False 572.166667 1423 86.9030 1 1958 3 chr3A.!!$F5 1957
4 TraesCS3B01G009300 chr3A 1789554 1790445 891 False 486.000000 486 77.6550 967 1812 1 chr3A.!!$F2 845
5 TraesCS3B01G009300 chr3A 1851827 1852491 664 False 436.000000 436 78.8240 848 1519 1 chr3A.!!$F3 671
6 TraesCS3B01G009300 chr3A 1769469 1770120 651 False 322.000000 322 76.3040 871 1521 1 chr3A.!!$F1 650
7 TraesCS3B01G009300 chr3D 2252905 2259186 6281 True 639.666667 1214 83.7420 799 2259 3 chr3D.!!$R4 1460
8 TraesCS3B01G009300 chr3D 2238675 2243503 4828 True 596.000000 647 78.9505 846 1821 2 chr3D.!!$R3 975
9 TraesCS3B01G009300 chr3D 2200957 2201942 985 True 260.000000 370 78.1500 846 1493 2 chr3D.!!$R2 647

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
206 209 0.035458 CATAATCGCCCCTCCCTCAC 59.965 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 10015 0.321564 TCACCCATTTGCCTGTCGAG 60.322 55.0 0.0 0.0 0.0 4.04 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 6.947733 TGTTCAAGATAGTCCATGGAATTGTT 59.052 34.615 21.50 10.02 0.00 2.83
94 95 5.354513 CCAATCTATCCATCATCTGTCATGC 59.645 44.000 0.00 0.00 0.00 4.06
102 103 4.581409 CCATCATCTGTCATGCCAATACAA 59.419 41.667 0.00 0.00 0.00 2.41
112 113 6.032094 GTCATGCCAATACAAAGAACATCAG 58.968 40.000 0.00 0.00 0.00 2.90
165 168 6.418101 ACCATCTAGTGACAAATACAAGCAT 58.582 36.000 0.00 0.00 0.00 3.79
179 182 0.517316 AAGCATTGGAGCGAAACGAC 59.483 50.000 0.00 0.00 40.15 4.34
181 184 1.897398 GCATTGGAGCGAAACGACGT 61.897 55.000 0.00 0.00 35.59 4.34
182 185 0.179250 CATTGGAGCGAAACGACGTG 60.179 55.000 0.00 0.00 35.59 4.49
183 186 0.599204 ATTGGAGCGAAACGACGTGT 60.599 50.000 0.00 0.00 35.59 4.49
194 197 1.837450 CGACGTGTCGCCATAATCG 59.163 57.895 9.68 0.00 46.50 3.34
195 198 1.558383 GACGTGTCGCCATAATCGC 59.442 57.895 0.00 0.00 0.00 4.58
198 201 2.110213 TGTCGCCATAATCGCCCC 59.890 61.111 0.00 0.00 0.00 5.80
199 202 2.426023 GTCGCCATAATCGCCCCT 59.574 61.111 0.00 0.00 0.00 4.79
200 203 1.668151 GTCGCCATAATCGCCCCTC 60.668 63.158 0.00 0.00 0.00 4.30
201 204 2.358737 CGCCATAATCGCCCCTCC 60.359 66.667 0.00 0.00 0.00 4.30
202 205 2.034221 GCCATAATCGCCCCTCCC 59.966 66.667 0.00 0.00 0.00 4.30
203 206 2.529744 GCCATAATCGCCCCTCCCT 61.530 63.158 0.00 0.00 0.00 4.20
204 207 1.679898 CCATAATCGCCCCTCCCTC 59.320 63.158 0.00 0.00 0.00 4.30
205 208 1.127567 CCATAATCGCCCCTCCCTCA 61.128 60.000 0.00 0.00 0.00 3.86
206 209 0.035458 CATAATCGCCCCTCCCTCAC 59.965 60.000 0.00 0.00 0.00 3.51
207 210 1.128188 ATAATCGCCCCTCCCTCACC 61.128 60.000 0.00 0.00 0.00 4.02
209 212 3.721172 ATCGCCCCTCCCTCACCAT 62.721 63.158 0.00 0.00 0.00 3.55
210 213 4.181010 CGCCCCTCCCTCACCATG 62.181 72.222 0.00 0.00 0.00 3.66
211 214 3.813724 GCCCCTCCCTCACCATGG 61.814 72.222 11.19 11.19 0.00 3.66
212 215 2.286425 CCCCTCCCTCACCATGGT 60.286 66.667 13.00 13.00 0.00 3.55
213 216 1.930656 CCCCTCCCTCACCATGGTT 60.931 63.158 16.84 0.00 0.00 3.67
214 217 1.304282 CCCTCCCTCACCATGGTTG 59.696 63.158 16.84 11.20 0.00 3.77
253 256 4.667420 GTCGAAAAGACGCCCTGA 57.333 55.556 0.00 0.00 40.43 3.86
254 257 2.908817 GTCGAAAAGACGCCCTGAA 58.091 52.632 0.00 0.00 40.43 3.02
257 260 2.225727 GTCGAAAAGACGCCCTGAAAAT 59.774 45.455 0.00 0.00 40.43 1.82
265 268 3.005540 GCCCTGAAAATGCCCCACG 62.006 63.158 0.00 0.00 0.00 4.94
270 273 0.608035 TGAAAATGCCCCACGAGACC 60.608 55.000 0.00 0.00 0.00 3.85
277 280 2.362369 CCCCACGAGACCAGCAGAT 61.362 63.158 0.00 0.00 0.00 2.90
288 291 3.647113 AGACCAGCAGATCAGAATAGCAT 59.353 43.478 0.00 0.00 0.00 3.79
292 295 2.896044 AGCAGATCAGAATAGCATCCGA 59.104 45.455 0.00 0.00 0.00 4.55
293 296 3.514706 AGCAGATCAGAATAGCATCCGAT 59.485 43.478 0.00 0.00 0.00 4.18
294 297 3.617706 GCAGATCAGAATAGCATCCGATG 59.382 47.826 3.82 3.82 0.00 3.84
310 313 4.196971 TCCGATGTCGATGAAGAGAAGTA 58.803 43.478 3.62 0.00 43.02 2.24
338 341 4.253685 CGAAAGGATCCAACATGTACACT 58.746 43.478 15.82 0.00 0.00 3.55
353 356 7.840931 ACATGTACACTCATGAGTAAAGATGA 58.159 34.615 32.03 16.50 45.41 2.92
364 367 9.506018 TCATGAGTAAAGATGAACAAAGATTGA 57.494 29.630 0.00 0.00 0.00 2.57
378 381 5.206587 CAAAGATTGATTCCAAGGGGATCT 58.793 41.667 5.20 0.00 44.48 2.75
390 393 2.850833 AGGGGATCTGATGAAGACCAA 58.149 47.619 0.00 0.00 37.88 3.67
393 396 3.274288 GGGATCTGATGAAGACCAACAC 58.726 50.000 0.00 0.00 37.88 3.32
418 421 2.801111 CTGAATCATGTGAGATCCGCTG 59.199 50.000 0.00 0.00 0.00 5.18
424 427 0.611896 TGTGAGATCCGCTGGAGACA 60.612 55.000 3.76 1.96 34.05 3.41
448 451 0.596600 TCCACACGCTCTTCAACGAC 60.597 55.000 0.00 0.00 0.00 4.34
450 453 1.300697 ACACGCTCTTCAACGACCC 60.301 57.895 0.00 0.00 0.00 4.46
451 454 2.027625 CACGCTCTTCAACGACCCC 61.028 63.158 0.00 0.00 0.00 4.95
463 466 2.763215 GACCCCCAAGATGCACCA 59.237 61.111 0.00 0.00 0.00 4.17
467 470 1.570857 CCCCCAAGATGCACCACCTA 61.571 60.000 0.00 0.00 0.00 3.08
468 471 0.107017 CCCCAAGATGCACCACCTAG 60.107 60.000 0.00 0.00 0.00 3.02
471 474 1.134280 CCAAGATGCACCACCTAGAGG 60.134 57.143 0.00 0.00 42.17 3.69
490 493 4.484872 GGGTTAGGCGGGCAGGAC 62.485 72.222 3.78 0.00 0.00 3.85
491 494 3.712907 GGTTAGGCGGGCAGGACA 61.713 66.667 3.78 0.00 0.00 4.02
492 495 2.349755 GTTAGGCGGGCAGGACAA 59.650 61.111 3.78 0.00 0.00 3.18
493 496 1.302993 GTTAGGCGGGCAGGACAAA 60.303 57.895 3.78 0.00 0.00 2.83
525 549 3.381590 ACCTTTCTGAGCAGGACAAAAAC 59.618 43.478 10.98 0.00 33.90 2.43
533 557 2.441750 AGCAGGACAAAAACCCTACTCA 59.558 45.455 0.00 0.00 0.00 3.41
539 563 2.359848 ACAAAAACCCTACTCAAACGGC 59.640 45.455 0.00 0.00 0.00 5.68
540 564 1.612676 AAAACCCTACTCAAACGGCC 58.387 50.000 0.00 0.00 0.00 6.13
541 565 0.251033 AAACCCTACTCAAACGGCCC 60.251 55.000 0.00 0.00 0.00 5.80
567 591 6.641176 AAAAAGCACCTAAAAACAACGAAG 57.359 33.333 0.00 0.00 0.00 3.79
571 595 5.337554 AGCACCTAAAAACAACGAAGAAAC 58.662 37.500 0.00 0.00 0.00 2.78
574 598 4.951715 ACCTAAAAACAACGAAGAAACCCT 59.048 37.500 0.00 0.00 0.00 4.34
590 614 1.821332 CCTTCTCATCGCAAGGGCC 60.821 63.158 0.00 0.00 36.29 5.80
599 623 4.344865 GCAAGGGCCGAGGTCCAA 62.345 66.667 15.96 0.00 43.56 3.53
611 635 3.423154 GTCCAACGCGCCTCCAAG 61.423 66.667 5.73 0.00 0.00 3.61
612 636 3.621805 TCCAACGCGCCTCCAAGA 61.622 61.111 5.73 0.00 0.00 3.02
619 643 0.462047 CGCGCCTCCAAGACCTTAAT 60.462 55.000 0.00 0.00 0.00 1.40
621 645 2.210961 GCGCCTCCAAGACCTTAATAC 58.789 52.381 0.00 0.00 0.00 1.89
625 649 3.684697 GCCTCCAAGACCTTAATACCACC 60.685 52.174 0.00 0.00 0.00 4.61
626 650 3.431766 CCTCCAAGACCTTAATACCACCG 60.432 52.174 0.00 0.00 0.00 4.94
687 713 1.173913 GAAACCATAGCCGCCTGTTT 58.826 50.000 0.00 0.00 32.23 2.83
690 716 2.045708 CCATAGCCGCCTGTTTGCA 61.046 57.895 0.00 0.00 0.00 4.08
735 762 3.714391 AGAAATACCGATAACAGCCGAC 58.286 45.455 0.00 0.00 0.00 4.79
814 2355 4.096984 AGCTAAATTGTAACATGGAGCAGC 59.903 41.667 0.00 0.00 0.00 5.25
824 2365 3.813443 ACATGGAGCAGCTTACATTAGG 58.187 45.455 10.05 3.94 0.00 2.69
840 2391 9.102757 CTTACATTAGGTCTACGTACTCAAGTA 57.897 37.037 0.00 0.00 0.00 2.24
843 2394 9.790344 ACATTAGGTCTACGTACTCAAGTATAT 57.210 33.333 0.00 0.00 32.54 0.86
858 2437 5.296531 TCAAGTATATGTACGTACGCTCCAA 59.703 40.000 20.18 2.43 35.92 3.53
890 2477 9.127277 GCTAGCTAGCCTATAAATACTATCAGT 57.873 37.037 31.67 0.00 43.39 3.41
927 2552 3.619038 GTCACCAGCTAGCTTATTCACAC 59.381 47.826 16.46 1.91 0.00 3.82
928 2553 2.939103 CACCAGCTAGCTTATTCACACC 59.061 50.000 16.46 0.00 0.00 4.16
929 2554 2.571653 ACCAGCTAGCTTATTCACACCA 59.428 45.455 16.46 0.00 0.00 4.17
981 2618 9.290988 CACATATTTACCTCTCTCTCTAGCTAA 57.709 37.037 0.00 0.00 0.00 3.09
1419 3081 2.056906 GCCACCATGCCTAGGTAGGG 62.057 65.000 26.68 26.68 43.82 3.53
1440 3114 6.601332 AGGGATAACATGTAATTGATCGGTT 58.399 36.000 0.00 0.00 0.00 4.44
1441 3115 6.486657 AGGGATAACATGTAATTGATCGGTTG 59.513 38.462 0.00 0.00 0.00 3.77
1529 3226 0.980754 TATGGGATGGCAGGTCGTGT 60.981 55.000 0.00 0.00 0.00 4.49
1676 3386 1.662629 CTTCGCCATAGAGCTTGTGTG 59.337 52.381 0.00 0.00 0.00 3.82
1677 3387 0.740868 TCGCCATAGAGCTTGTGTGC 60.741 55.000 0.00 0.00 0.00 4.57
1680 3390 1.442769 CCATAGAGCTTGTGTGCGTT 58.557 50.000 0.00 0.00 38.13 4.84
1681 3391 1.394917 CCATAGAGCTTGTGTGCGTTC 59.605 52.381 0.00 0.00 38.13 3.95
1686 3400 1.264020 GAGCTTGTGTGCGTTCATTGA 59.736 47.619 0.00 0.00 38.13 2.57
1711 3425 5.876651 TGTATACATCAGCTTGTCCATCT 57.123 39.130 0.08 0.00 0.00 2.90
1717 3431 5.665459 ACATCAGCTTGTCCATCTAAGTAC 58.335 41.667 0.00 0.00 0.00 2.73
1723 3437 4.025647 GCTTGTCCATCTAAGTACGCATTC 60.026 45.833 0.00 0.00 0.00 2.67
1745 3459 3.242220 CGTACGTCGCTGTAGACTTGTAT 60.242 47.826 7.22 0.00 38.90 2.29
1758 7313 2.544267 GACTTGTATATGTGCGCCTTCC 59.456 50.000 4.18 0.00 0.00 3.46
1775 7330 3.628257 CCTTCCCCATGCCATTTACTCTT 60.628 47.826 0.00 0.00 0.00 2.85
1785 7340 7.063780 CCATGCCATTTACTCTTTTTCATTGTC 59.936 37.037 0.00 0.00 0.00 3.18
1822 7379 8.454106 CACTTTTCTATGTAAATCACCTTCTGG 58.546 37.037 0.00 0.00 39.83 3.86
1823 7380 7.121315 ACTTTTCTATGTAAATCACCTTCTGGC 59.879 37.037 0.00 0.00 36.63 4.85
1824 7381 5.957771 TCTATGTAAATCACCTTCTGGCT 57.042 39.130 0.00 0.00 36.63 4.75
1827 7384 8.034313 TCTATGTAAATCACCTTCTGGCTATT 57.966 34.615 0.00 0.00 36.63 1.73
1828 7385 8.150945 TCTATGTAAATCACCTTCTGGCTATTC 58.849 37.037 0.00 0.00 36.63 1.75
1829 7386 5.437060 TGTAAATCACCTTCTGGCTATTCC 58.563 41.667 0.00 0.00 36.63 3.01
1830 7387 4.591321 AAATCACCTTCTGGCTATTCCA 57.409 40.909 0.00 0.00 44.18 3.53
1835 8473 4.522789 TCACCTTCTGGCTATTCCAAAAAC 59.477 41.667 0.00 0.00 46.01 2.43
1841 8479 7.254761 CCTTCTGGCTATTCCAAAAACAAAAAC 60.255 37.037 0.00 0.00 46.01 2.43
1843 8481 4.271291 TGGCTATTCCAAAAACAAAAACGC 59.729 37.500 0.00 0.00 43.21 4.84
1848 8486 4.008539 TCCAAAAACAAAAACGCAATGC 57.991 36.364 0.00 0.00 0.00 3.56
1850 8488 3.784994 CCAAAAACAAAAACGCAATGCTG 59.215 39.130 2.94 0.00 0.00 4.41
1883 9912 0.318120 CCTTTTTGACTGGCGCCATT 59.682 50.000 32.87 26.63 0.00 3.16
1930 9959 6.820335 AGAAAAGCTTGCTGAATAAAAAGGT 58.180 32.000 0.00 0.00 32.04 3.50
1934 9963 6.018589 AGCTTGCTGAATAAAAAGGTCTTC 57.981 37.500 0.00 0.00 0.00 2.87
1951 9980 0.895100 TTCCCAGTTGCCATGTGAGC 60.895 55.000 0.00 0.00 0.00 4.26
1966 9995 2.670592 AGCATGCTCGCTGTTGCA 60.671 55.556 16.30 0.00 41.85 4.08
1986 10015 1.210155 GCGCATGAACACCCTGAAC 59.790 57.895 0.30 0.00 0.00 3.18
1989 10018 0.798776 GCATGAACACCCTGAACTCG 59.201 55.000 0.00 0.00 0.00 4.18
2055 10084 5.931441 AAAGTAACTGCTGACTTGATGTC 57.069 39.130 0.00 0.00 45.54 3.06
2067 10096 5.100751 GACTTGATGTCAACAAAGTCTGG 57.899 43.478 15.59 0.00 44.73 3.86
2103 10132 4.549458 CAAATTTAGTGTGTGAAGGCTGG 58.451 43.478 0.00 0.00 0.00 4.85
2136 10165 8.593492 AGTAATTTCTTTTCTGGTTGATTTGC 57.407 30.769 0.00 0.00 0.00 3.68
2137 10166 8.203485 AGTAATTTCTTTTCTGGTTGATTTGCA 58.797 29.630 0.00 0.00 0.00 4.08
2138 10167 6.849588 ATTTCTTTTCTGGTTGATTTGCAC 57.150 33.333 0.00 0.00 0.00 4.57
2146 10175 7.517614 TTCTGGTTGATTTGCACTTACATAA 57.482 32.000 0.00 0.00 0.00 1.90
2153 10182 9.277565 GTTGATTTGCACTTACATAACTGTATG 57.722 33.333 0.00 0.00 42.55 2.39
2168 10197 9.226606 CATAACTGTATGGTTGGAGTTAAAGAA 57.773 33.333 0.00 0.00 35.20 2.52
2184 10213 0.037877 AGAAACTGGCTGCTGCTCAT 59.962 50.000 15.64 0.00 39.59 2.90
2186 10215 2.092538 AGAAACTGGCTGCTGCTCATAT 60.093 45.455 15.64 0.00 39.59 1.78
2190 10219 3.474600 ACTGGCTGCTGCTCATATAAAG 58.525 45.455 15.64 2.28 39.59 1.85
2216 10245 4.214119 AGTTAATGTACTGTGCTGTTGCTG 59.786 41.667 0.00 0.00 40.48 4.41
2231 10261 4.782156 TGTTGCTGACATTATGTTGAACG 58.218 39.130 0.00 0.00 32.00 3.95
2232 10262 4.513318 TGTTGCTGACATTATGTTGAACGA 59.487 37.500 0.00 0.00 32.00 3.85
2244 10274 2.881513 TGTTGAACGAAGCCATGCTAAA 59.118 40.909 0.00 0.00 38.25 1.85
2259 10289 8.859090 AGCCATGCTAAAATATTTATAACTGCA 58.141 29.630 0.01 6.63 36.99 4.41
2260 10290 8.915654 GCCATGCTAAAATATTTATAACTGCAC 58.084 33.333 0.01 0.00 0.00 4.57
2261 10291 9.117145 CCATGCTAAAATATTTATAACTGCACG 57.883 33.333 0.01 0.00 0.00 5.34
2262 10292 9.117145 CATGCTAAAATATTTATAACTGCACGG 57.883 33.333 0.01 0.59 0.00 4.94
2263 10293 8.439993 TGCTAAAATATTTATAACTGCACGGA 57.560 30.769 0.01 0.00 0.00 4.69
2264 10294 8.894731 TGCTAAAATATTTATAACTGCACGGAA 58.105 29.630 0.01 0.00 0.00 4.30
2265 10295 9.382244 GCTAAAATATTTATAACTGCACGGAAG 57.618 33.333 0.01 0.00 0.00 3.46
2269 10299 9.783256 AAATATTTATAACTGCACGGAAGTTTC 57.217 29.630 0.00 0.00 46.40 2.78
2270 10300 8.732746 ATATTTATAACTGCACGGAAGTTTCT 57.267 30.769 3.03 0.00 46.40 2.52
2271 10301 6.476243 TTTATAACTGCACGGAAGTTTCTC 57.524 37.500 3.03 0.00 46.40 2.87
2272 10302 2.622064 AACTGCACGGAAGTTTCTCT 57.378 45.000 0.00 0.00 46.40 3.10
2273 10303 2.156343 ACTGCACGGAAGTTTCTCTC 57.844 50.000 0.00 0.00 46.40 3.20
2274 10304 1.689273 ACTGCACGGAAGTTTCTCTCT 59.311 47.619 0.00 0.00 46.40 3.10
2275 10305 2.103263 ACTGCACGGAAGTTTCTCTCTT 59.897 45.455 0.00 0.00 46.40 2.85
2276 10306 3.321111 ACTGCACGGAAGTTTCTCTCTTA 59.679 43.478 0.00 0.00 46.40 2.10
2277 10307 4.202223 ACTGCACGGAAGTTTCTCTCTTAA 60.202 41.667 0.00 0.00 46.40 1.85
2278 10308 4.894784 TGCACGGAAGTTTCTCTCTTAAT 58.105 39.130 0.00 0.00 46.40 1.40
2279 10309 5.305585 TGCACGGAAGTTTCTCTCTTAATT 58.694 37.500 0.00 0.00 46.40 1.40
2280 10310 6.460781 TGCACGGAAGTTTCTCTCTTAATTA 58.539 36.000 0.00 0.00 46.40 1.40
2281 10311 6.932400 TGCACGGAAGTTTCTCTCTTAATTAA 59.068 34.615 0.00 0.00 46.40 1.40
2282 10312 7.117812 TGCACGGAAGTTTCTCTCTTAATTAAG 59.882 37.037 17.60 17.60 46.40 1.85
2283 10313 7.117956 GCACGGAAGTTTCTCTCTTAATTAAGT 59.882 37.037 21.69 2.54 46.40 2.24
2284 10314 8.989980 CACGGAAGTTTCTCTCTTAATTAAGTT 58.010 33.333 21.69 8.66 46.40 2.66
2285 10315 9.557061 ACGGAAGTTTCTCTCTTAATTAAGTTT 57.443 29.630 21.69 7.51 46.40 2.66
2294 10324 9.668497 TCTCTCTTAATTAAGTTTCCTTTAGGC 57.332 33.333 21.69 0.00 34.93 3.93
2295 10325 9.674068 CTCTCTTAATTAAGTTTCCTTTAGGCT 57.326 33.333 21.69 0.00 34.93 4.58
2296 10326 9.449719 TCTCTTAATTAAGTTTCCTTTAGGCTG 57.550 33.333 21.69 0.00 34.93 4.85
2297 10327 8.575649 TCTTAATTAAGTTTCCTTTAGGCTGG 57.424 34.615 21.69 0.00 34.93 4.85
2298 10328 8.168058 TCTTAATTAAGTTTCCTTTAGGCTGGT 58.832 33.333 21.69 0.00 34.93 4.00
2299 10329 6.835819 AATTAAGTTTCCTTTAGGCTGGTC 57.164 37.500 0.00 0.00 34.44 4.02
2300 10330 3.876309 AAGTTTCCTTTAGGCTGGTCA 57.124 42.857 0.00 0.00 34.44 4.02
2301 10331 4.388577 AAGTTTCCTTTAGGCTGGTCAT 57.611 40.909 0.00 0.00 34.44 3.06
2302 10332 5.514500 AAGTTTCCTTTAGGCTGGTCATA 57.486 39.130 0.00 0.00 34.44 2.15
2303 10333 5.104259 AGTTTCCTTTAGGCTGGTCATAG 57.896 43.478 0.00 0.00 34.44 2.23
2304 10334 4.536489 AGTTTCCTTTAGGCTGGTCATAGT 59.464 41.667 0.00 0.00 34.44 2.12
2305 10335 4.487714 TTCCTTTAGGCTGGTCATAGTG 57.512 45.455 0.00 0.00 34.44 2.74
2306 10336 2.771943 TCCTTTAGGCTGGTCATAGTGG 59.228 50.000 0.00 0.00 34.44 4.00
2307 10337 2.158755 CCTTTAGGCTGGTCATAGTGGG 60.159 54.545 0.00 0.00 0.00 4.61
2308 10338 1.507140 TTAGGCTGGTCATAGTGGGG 58.493 55.000 0.00 0.00 0.00 4.96
2309 10339 0.399949 TAGGCTGGTCATAGTGGGGG 60.400 60.000 0.00 0.00 0.00 5.40
2310 10340 2.001269 GGCTGGTCATAGTGGGGGT 61.001 63.158 0.00 0.00 0.00 4.95
2311 10341 0.693092 GGCTGGTCATAGTGGGGGTA 60.693 60.000 0.00 0.00 0.00 3.69
2312 10342 1.209621 GCTGGTCATAGTGGGGGTAA 58.790 55.000 0.00 0.00 0.00 2.85
2313 10343 1.134189 GCTGGTCATAGTGGGGGTAAC 60.134 57.143 0.00 0.00 0.00 2.50
2314 10344 2.478292 CTGGTCATAGTGGGGGTAACT 58.522 52.381 0.00 0.00 0.00 2.24
2315 10345 2.844348 CTGGTCATAGTGGGGGTAACTT 59.156 50.000 0.00 0.00 0.00 2.66
2316 10346 4.035112 CTGGTCATAGTGGGGGTAACTTA 58.965 47.826 0.00 0.00 0.00 2.24
2317 10347 4.437023 TGGTCATAGTGGGGGTAACTTAA 58.563 43.478 0.00 0.00 0.00 1.85
2318 10348 4.225717 TGGTCATAGTGGGGGTAACTTAAC 59.774 45.833 0.00 0.00 0.00 2.01
2319 10349 4.472470 GGTCATAGTGGGGGTAACTTAACT 59.528 45.833 0.00 0.00 0.00 2.24
2320 10350 5.662657 GGTCATAGTGGGGGTAACTTAACTA 59.337 44.000 0.00 0.00 0.00 2.24
2321 10351 6.183360 GGTCATAGTGGGGGTAACTTAACTAG 60.183 46.154 0.00 0.00 31.42 2.57
2322 10352 6.382282 GTCATAGTGGGGGTAACTTAACTAGT 59.618 42.308 0.00 0.00 39.32 2.57
2323 10353 7.561356 GTCATAGTGGGGGTAACTTAACTAGTA 59.439 40.741 0.00 0.00 35.54 1.82
2324 10354 8.121833 TCATAGTGGGGGTAACTTAACTAGTAA 58.878 37.037 0.00 0.00 35.54 2.24
2325 10355 6.611613 AGTGGGGGTAACTTAACTAGTAAC 57.388 41.667 0.00 0.00 35.54 2.50
2326 10356 6.084060 AGTGGGGGTAACTTAACTAGTAACA 58.916 40.000 0.00 0.00 35.54 2.41
2327 10357 6.732390 AGTGGGGGTAACTTAACTAGTAACAT 59.268 38.462 0.00 0.00 35.54 2.71
2328 10358 7.900784 AGTGGGGGTAACTTAACTAGTAACATA 59.099 37.037 0.00 0.00 35.54 2.29
2329 10359 8.539544 GTGGGGGTAACTTAACTAGTAACATAA 58.460 37.037 0.00 0.00 35.54 1.90
2330 10360 8.539544 TGGGGGTAACTTAACTAGTAACATAAC 58.460 37.037 0.00 0.00 35.54 1.89
2331 10361 8.539544 GGGGGTAACTTAACTAGTAACATAACA 58.460 37.037 0.00 0.00 35.54 2.41
2332 10362 9.371136 GGGGTAACTTAACTAGTAACATAACAC 57.629 37.037 0.00 0.00 35.54 3.32
2333 10363 9.927668 GGGTAACTTAACTAGTAACATAACACA 57.072 33.333 0.00 0.00 35.54 3.72
2342 10372 9.640963 AACTAGTAACATAACACATCTCAAGAC 57.359 33.333 0.00 0.00 0.00 3.01
2343 10373 8.803235 ACTAGTAACATAACACATCTCAAGACA 58.197 33.333 0.00 0.00 0.00 3.41
2344 10374 9.639601 CTAGTAACATAACACATCTCAAGACAA 57.360 33.333 0.00 0.00 0.00 3.18
2345 10375 8.902540 AGTAACATAACACATCTCAAGACAAA 57.097 30.769 0.00 0.00 0.00 2.83
2346 10376 8.993121 AGTAACATAACACATCTCAAGACAAAG 58.007 33.333 0.00 0.00 0.00 2.77
2347 10377 7.807977 AACATAACACATCTCAAGACAAAGT 57.192 32.000 0.00 0.00 0.00 2.66
2348 10378 7.807977 ACATAACACATCTCAAGACAAAGTT 57.192 32.000 0.00 0.00 0.00 2.66
2349 10379 7.642669 ACATAACACATCTCAAGACAAAGTTG 58.357 34.615 0.00 0.00 0.00 3.16
2350 10380 4.558538 ACACATCTCAAGACAAAGTTGC 57.441 40.909 0.00 0.00 0.00 4.17
2351 10381 4.202441 ACACATCTCAAGACAAAGTTGCT 58.798 39.130 0.00 0.00 0.00 3.91
2352 10382 4.641989 ACACATCTCAAGACAAAGTTGCTT 59.358 37.500 0.00 0.00 0.00 3.91
2353 10383 5.822519 ACACATCTCAAGACAAAGTTGCTTA 59.177 36.000 0.00 0.00 0.00 3.09
2354 10384 6.488006 ACACATCTCAAGACAAAGTTGCTTAT 59.512 34.615 0.00 0.00 0.00 1.73
2355 10385 6.800408 CACATCTCAAGACAAAGTTGCTTATG 59.200 38.462 0.00 1.20 0.00 1.90
2356 10386 6.488006 ACATCTCAAGACAAAGTTGCTTATGT 59.512 34.615 0.00 1.70 0.00 2.29
2357 10387 6.304356 TCTCAAGACAAAGTTGCTTATGTG 57.696 37.500 0.00 0.00 0.00 3.21
2358 10388 5.239306 TCTCAAGACAAAGTTGCTTATGTGG 59.761 40.000 0.00 0.00 0.00 4.17
2359 10389 3.923017 AGACAAAGTTGCTTATGTGGC 57.077 42.857 0.00 0.00 0.00 5.01
2360 10390 3.221771 AGACAAAGTTGCTTATGTGGCA 58.778 40.909 0.00 0.00 37.97 4.92
2361 10391 3.828451 AGACAAAGTTGCTTATGTGGCAT 59.172 39.130 0.00 0.00 39.54 4.40
2362 10392 3.916761 ACAAAGTTGCTTATGTGGCATG 58.083 40.909 0.00 0.00 39.54 4.06
2363 10393 3.321682 ACAAAGTTGCTTATGTGGCATGT 59.678 39.130 0.00 0.00 39.54 3.21
2364 10394 4.522405 ACAAAGTTGCTTATGTGGCATGTA 59.478 37.500 0.00 0.00 39.54 2.29
2365 10395 4.701956 AAGTTGCTTATGTGGCATGTAC 57.298 40.909 0.00 0.00 39.54 2.90
2366 10396 3.955471 AGTTGCTTATGTGGCATGTACT 58.045 40.909 0.00 0.00 39.54 2.73
2367 10397 3.941483 AGTTGCTTATGTGGCATGTACTC 59.059 43.478 0.00 0.00 39.54 2.59
2368 10398 2.917933 TGCTTATGTGGCATGTACTCC 58.082 47.619 0.00 0.00 34.56 3.85
2369 10399 2.222027 GCTTATGTGGCATGTACTCCC 58.778 52.381 0.00 0.00 0.00 4.30
2370 10400 2.158755 GCTTATGTGGCATGTACTCCCT 60.159 50.000 0.00 0.00 0.00 4.20
2371 10401 3.733337 CTTATGTGGCATGTACTCCCTC 58.267 50.000 0.00 0.00 0.00 4.30
2372 10402 0.839946 ATGTGGCATGTACTCCCTCC 59.160 55.000 0.00 0.00 0.00 4.30
2373 10403 1.144057 GTGGCATGTACTCCCTCCG 59.856 63.158 0.00 0.00 0.00 4.63
2374 10404 1.305802 TGGCATGTACTCCCTCCGT 60.306 57.895 0.00 0.00 0.00 4.69
2375 10405 0.907704 TGGCATGTACTCCCTCCGTT 60.908 55.000 0.00 0.00 0.00 4.44
2376 10406 0.179081 GGCATGTACTCCCTCCGTTC 60.179 60.000 0.00 0.00 0.00 3.95
2377 10407 0.179081 GCATGTACTCCCTCCGTTCC 60.179 60.000 0.00 0.00 0.00 3.62
2378 10408 1.191535 CATGTACTCCCTCCGTTCCA 58.808 55.000 0.00 0.00 0.00 3.53
2379 10409 1.762957 CATGTACTCCCTCCGTTCCAT 59.237 52.381 0.00 0.00 0.00 3.41
2380 10410 2.832643 TGTACTCCCTCCGTTCCATA 57.167 50.000 0.00 0.00 0.00 2.74
2381 10411 3.104519 TGTACTCCCTCCGTTCCATAA 57.895 47.619 0.00 0.00 0.00 1.90
2382 10412 3.649843 TGTACTCCCTCCGTTCCATAAT 58.350 45.455 0.00 0.00 0.00 1.28
2383 10413 3.386726 TGTACTCCCTCCGTTCCATAATG 59.613 47.826 0.00 0.00 0.00 1.90
2384 10414 2.478292 ACTCCCTCCGTTCCATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
2385 10415 3.649843 ACTCCCTCCGTTCCATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
2386 10416 4.232091 ACTCCCTCCGTTCCATAATGTAT 58.768 43.478 0.00 0.00 0.00 2.29
2387 10417 4.040461 ACTCCCTCCGTTCCATAATGTATG 59.960 45.833 0.00 0.00 35.94 2.39
2388 10418 4.228010 TCCCTCCGTTCCATAATGTATGA 58.772 43.478 0.00 0.00 38.45 2.15
2389 10419 4.039973 TCCCTCCGTTCCATAATGTATGAC 59.960 45.833 0.00 0.00 38.45 3.06
2390 10420 3.987868 CCTCCGTTCCATAATGTATGACG 59.012 47.826 0.00 0.79 38.45 4.35
2391 10421 4.500887 CCTCCGTTCCATAATGTATGACGT 60.501 45.833 0.00 0.00 38.45 4.34
2392 10422 5.013568 TCCGTTCCATAATGTATGACGTT 57.986 39.130 0.00 0.00 38.45 3.99
2393 10423 5.421277 TCCGTTCCATAATGTATGACGTTT 58.579 37.500 0.00 0.00 38.45 3.60
2394 10424 5.875910 TCCGTTCCATAATGTATGACGTTTT 59.124 36.000 0.00 0.00 38.45 2.43
2395 10425 6.372103 TCCGTTCCATAATGTATGACGTTTTT 59.628 34.615 0.00 0.00 38.45 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 5.734720 TGGACTATCTTGAACATCTCCAAC 58.265 41.667 0.00 0.00 0.00 3.77
64 65 9.075678 GACAGATGATGGATAGATTGGAAATTT 57.924 33.333 0.00 0.00 0.00 1.82
65 66 8.222637 TGACAGATGATGGATAGATTGGAAATT 58.777 33.333 0.00 0.00 0.00 1.82
66 67 7.752638 TGACAGATGATGGATAGATTGGAAAT 58.247 34.615 0.00 0.00 0.00 2.17
71 72 5.354513 GGCATGACAGATGATGGATAGATTG 59.645 44.000 0.00 0.00 0.00 2.67
72 73 5.013808 TGGCATGACAGATGATGGATAGATT 59.986 40.000 0.00 0.00 0.00 2.40
79 80 4.139038 TGTATTGGCATGACAGATGATGG 58.861 43.478 0.00 0.00 0.00 3.51
86 87 5.375417 TGTTCTTTGTATTGGCATGACAG 57.625 39.130 0.00 0.00 0.00 3.51
130 133 4.272991 GTCACTAGATGGTCTACGTACCTG 59.727 50.000 8.89 0.00 40.44 4.00
135 138 5.916661 ATTTGTCACTAGATGGTCTACGT 57.083 39.130 0.00 0.00 0.00 3.57
165 168 1.210545 GACACGTCGTTTCGCTCCAA 61.211 55.000 0.00 0.00 0.00 3.53
182 185 1.668151 GAGGGGCGATTATGGCGAC 60.668 63.158 0.00 0.00 35.64 5.19
183 186 2.741092 GAGGGGCGATTATGGCGA 59.259 61.111 0.00 0.00 34.76 5.54
186 189 1.127567 TGAGGGAGGGGCGATTATGG 61.128 60.000 0.00 0.00 0.00 2.74
188 191 1.128188 GGTGAGGGAGGGGCGATTAT 61.128 60.000 0.00 0.00 0.00 1.28
189 192 1.764854 GGTGAGGGAGGGGCGATTA 60.765 63.158 0.00 0.00 0.00 1.75
191 194 3.721172 ATGGTGAGGGAGGGGCGAT 62.721 63.158 0.00 0.00 0.00 4.58
193 196 4.181010 CATGGTGAGGGAGGGGCG 62.181 72.222 0.00 0.00 0.00 6.13
194 197 3.813724 CCATGGTGAGGGAGGGGC 61.814 72.222 2.57 0.00 0.00 5.80
195 198 1.930656 AACCATGGTGAGGGAGGGG 60.931 63.158 20.60 0.00 0.00 4.79
198 201 1.207488 TCCCAACCATGGTGAGGGAG 61.207 60.000 37.17 22.55 46.01 4.30
199 202 0.774096 TTCCCAACCATGGTGAGGGA 60.774 55.000 37.17 37.17 46.01 4.20
200 203 0.114168 TTTCCCAACCATGGTGAGGG 59.886 55.000 34.78 34.78 46.01 4.30
201 204 2.008242 TTTTCCCAACCATGGTGAGG 57.992 50.000 20.60 22.46 46.01 3.86
226 229 5.204101 GGCGTCTTTTCGACTATCTACTAC 58.796 45.833 0.00 0.00 40.59 2.73
245 248 2.679996 GGGGCATTTTCAGGGCGT 60.680 61.111 0.00 0.00 0.00 5.68
248 251 1.304052 TCGTGGGGCATTTTCAGGG 60.304 57.895 0.00 0.00 0.00 4.45
250 253 0.804989 GTCTCGTGGGGCATTTTCAG 59.195 55.000 0.00 0.00 0.00 3.02
253 256 0.609131 CTGGTCTCGTGGGGCATTTT 60.609 55.000 0.00 0.00 0.00 1.82
254 257 1.002134 CTGGTCTCGTGGGGCATTT 60.002 57.895 0.00 0.00 0.00 2.32
265 268 3.069300 TGCTATTCTGATCTGCTGGTCTC 59.931 47.826 5.39 0.00 0.00 3.36
270 273 2.994578 CGGATGCTATTCTGATCTGCTG 59.005 50.000 0.00 0.00 0.00 4.41
277 280 2.884639 TCGACATCGGATGCTATTCTGA 59.115 45.455 17.61 7.16 40.29 3.27
288 291 3.017442 ACTTCTCTTCATCGACATCGGA 58.983 45.455 0.73 0.00 40.29 4.55
292 295 6.348132 CGCTCTATACTTCTCTTCATCGACAT 60.348 42.308 0.00 0.00 0.00 3.06
293 296 5.050023 CGCTCTATACTTCTCTTCATCGACA 60.050 44.000 0.00 0.00 0.00 4.35
294 297 5.177881 TCGCTCTATACTTCTCTTCATCGAC 59.822 44.000 0.00 0.00 0.00 4.20
310 313 4.141620 ACATGTTGGATCCTTTCGCTCTAT 60.142 41.667 14.23 0.00 0.00 1.98
338 341 9.506018 TCAATCTTTGTTCATCTTTACTCATGA 57.494 29.630 0.00 0.00 0.00 3.07
353 356 4.750941 TCCCCTTGGAATCAATCTTTGTT 58.249 39.130 0.00 0.00 37.86 2.83
364 367 4.050037 TCTTCATCAGATCCCCTTGGAAT 58.950 43.478 0.00 0.00 45.98 3.01
365 368 3.200825 GTCTTCATCAGATCCCCTTGGAA 59.799 47.826 0.00 0.00 45.98 3.53
378 381 3.387699 TCAGTCAGTGTTGGTCTTCATCA 59.612 43.478 0.00 0.00 0.00 3.07
390 393 4.879197 TCTCACATGATTCAGTCAGTGT 57.121 40.909 0.00 0.00 40.92 3.55
393 396 4.049869 CGGATCTCACATGATTCAGTCAG 58.950 47.826 0.00 0.00 40.92 3.51
424 427 0.827925 TGAAGAGCGTGTGGAGGAGT 60.828 55.000 0.00 0.00 0.00 3.85
448 451 1.570857 TAGGTGGTGCATCTTGGGGG 61.571 60.000 0.00 0.00 0.00 5.40
450 453 0.911769 TCTAGGTGGTGCATCTTGGG 59.088 55.000 0.00 0.00 0.00 4.12
451 454 1.134280 CCTCTAGGTGGTGCATCTTGG 60.134 57.143 0.00 0.00 0.00 3.61
463 466 1.761271 GCCTAACCCGCCTCTAGGT 60.761 63.158 0.00 0.00 38.27 3.08
485 488 3.490348 AGGTCTGATGGTTTTTGTCCTG 58.510 45.455 0.00 0.00 0.00 3.86
488 491 5.774498 AGAAAGGTCTGATGGTTTTTGTC 57.226 39.130 0.00 0.00 30.83 3.18
514 538 4.261031 CGTTTGAGTAGGGTTTTTGTCCTG 60.261 45.833 0.00 0.00 34.75 3.86
525 549 0.250989 TTTGGGCCGTTTGAGTAGGG 60.251 55.000 0.00 0.00 0.00 3.53
549 573 4.501559 GGTTTCTTCGTTGTTTTTAGGTGC 59.498 41.667 0.00 0.00 0.00 5.01
550 574 5.038683 GGGTTTCTTCGTTGTTTTTAGGTG 58.961 41.667 0.00 0.00 0.00 4.00
551 575 4.951715 AGGGTTTCTTCGTTGTTTTTAGGT 59.048 37.500 0.00 0.00 0.00 3.08
552 576 5.509716 AGGGTTTCTTCGTTGTTTTTAGG 57.490 39.130 0.00 0.00 0.00 2.69
565 589 2.859165 TGCGATGAGAAGGGTTTCTT 57.141 45.000 0.00 0.00 43.63 2.52
566 590 2.616510 CCTTGCGATGAGAAGGGTTTCT 60.617 50.000 0.00 0.00 46.22 2.52
567 591 1.740025 CCTTGCGATGAGAAGGGTTTC 59.260 52.381 0.00 0.00 35.93 2.78
574 598 2.125147 CGGCCCTTGCGATGAGAA 60.125 61.111 0.00 0.00 38.85 2.87
599 623 1.823169 TTAAGGTCTTGGAGGCGCGT 61.823 55.000 8.43 0.27 0.00 6.01
608 632 3.449737 TCTCCGGTGGTATTAAGGTCTTG 59.550 47.826 0.00 0.00 0.00 3.02
609 633 3.450096 GTCTCCGGTGGTATTAAGGTCTT 59.550 47.826 0.00 0.00 0.00 3.01
611 635 2.223665 CGTCTCCGGTGGTATTAAGGTC 60.224 54.545 0.00 0.00 0.00 3.85
612 636 1.753073 CGTCTCCGGTGGTATTAAGGT 59.247 52.381 0.00 0.00 0.00 3.50
619 643 1.592400 CTGCTTCGTCTCCGGTGGTA 61.592 60.000 0.00 0.00 33.95 3.25
621 645 2.125912 CTGCTTCGTCTCCGGTGG 60.126 66.667 0.00 0.00 33.95 4.61
625 649 2.202492 CGGTCTGCTTCGTCTCCG 60.202 66.667 0.00 0.00 0.00 4.63
626 650 2.182030 CCGGTCTGCTTCGTCTCC 59.818 66.667 0.00 0.00 0.00 3.71
653 679 0.462759 GTTTCATCTGCCTCCCTCCG 60.463 60.000 0.00 0.00 0.00 4.63
655 681 0.620556 TGGTTTCATCTGCCTCCCTC 59.379 55.000 0.00 0.00 0.00 4.30
656 682 1.302907 ATGGTTTCATCTGCCTCCCT 58.697 50.000 0.00 0.00 0.00 4.20
667 693 0.037590 AACAGGCGGCTATGGTTTCA 59.962 50.000 12.74 0.00 0.00 2.69
687 713 2.295909 CCCGTGGAAGAAAAGAAATGCA 59.704 45.455 0.00 0.00 0.00 3.96
735 762 1.979855 TTGTGTGGACTGTCAATGGG 58.020 50.000 10.38 0.00 0.00 4.00
794 822 6.657117 TGTAAGCTGCTCCATGTTACAATTTA 59.343 34.615 1.00 0.00 32.14 1.40
796 824 5.009631 TGTAAGCTGCTCCATGTTACAATT 58.990 37.500 1.00 0.00 32.14 2.32
799 827 3.694043 TGTAAGCTGCTCCATGTTACA 57.306 42.857 1.00 3.98 32.53 2.41
800 828 5.237344 CCTAATGTAAGCTGCTCCATGTTAC 59.763 44.000 13.46 7.53 0.00 2.50
801 829 5.104527 ACCTAATGTAAGCTGCTCCATGTTA 60.105 40.000 13.46 5.72 0.00 2.41
814 2355 7.983307 ACTTGAGTACGTAGACCTAATGTAAG 58.017 38.462 0.00 0.00 0.00 2.34
840 2391 3.499537 TCGATTGGAGCGTACGTACATAT 59.500 43.478 24.50 10.00 0.00 1.78
843 2394 1.085893 TCGATTGGAGCGTACGTACA 58.914 50.000 24.50 10.60 0.00 2.90
883 2467 6.317391 TGACTATATGATGGAGCGACTGATAG 59.683 42.308 0.00 0.00 0.00 2.08
890 2477 3.496331 TGGTGACTATATGATGGAGCGA 58.504 45.455 0.00 0.00 0.00 4.93
927 2552 3.835395 AGAGAAGGTCTCAAGGTAAGTGG 59.165 47.826 7.94 0.00 45.73 4.00
928 2553 5.233988 CAAGAGAAGGTCTCAAGGTAAGTG 58.766 45.833 7.94 0.00 45.73 3.16
929 2554 4.262678 GCAAGAGAAGGTCTCAAGGTAAGT 60.263 45.833 7.94 0.00 45.73 2.24
1419 3081 6.959361 AGCAACCGATCAATTACATGTTATC 58.041 36.000 2.30 0.00 0.00 1.75
1612 3322 9.769093 AGCAAATAACATCGTATTAACTTTGTC 57.231 29.630 0.00 0.00 0.00 3.18
1676 3386 6.344572 TGATGTATACAAGTCAATGAACGC 57.655 37.500 10.14 0.00 0.00 4.84
1677 3387 6.256539 AGCTGATGTATACAAGTCAATGAACG 59.743 38.462 10.14 0.00 0.00 3.95
1680 3390 7.105588 ACAAGCTGATGTATACAAGTCAATGA 58.894 34.615 10.14 0.00 0.00 2.57
1681 3391 7.312657 ACAAGCTGATGTATACAAGTCAATG 57.687 36.000 10.14 10.97 0.00 2.82
1686 3400 5.420725 TGGACAAGCTGATGTATACAAGT 57.579 39.130 10.14 0.00 32.57 3.16
1717 3431 0.858548 TACAGCGACGTACGAATGCG 60.859 55.000 24.41 19.01 45.77 4.73
1723 3437 1.136141 ACAAGTCTACAGCGACGTACG 60.136 52.381 15.01 15.01 45.66 3.67
1726 3440 4.334759 ACATATACAAGTCTACAGCGACGT 59.665 41.667 0.00 0.00 38.90 4.34
1732 3446 3.736252 GGCGCACATATACAAGTCTACAG 59.264 47.826 10.83 0.00 0.00 2.74
1745 3459 1.152984 CATGGGGAAGGCGCACATA 60.153 57.895 10.83 0.00 0.00 2.29
1758 7313 5.404466 TGAAAAAGAGTAAATGGCATGGG 57.596 39.130 0.00 0.00 0.00 4.00
1775 7330 3.629855 TGCAGTTTCCTCGACAATGAAAA 59.370 39.130 0.00 0.00 30.47 2.29
1785 7340 4.452455 ACATAGAAAAGTGCAGTTTCCTCG 59.548 41.667 19.51 9.98 35.92 4.63
1822 7379 5.396750 TGCGTTTTTGTTTTTGGAATAGC 57.603 34.783 0.00 0.00 0.00 2.97
1823 7380 6.356714 GCATTGCGTTTTTGTTTTTGGAATAG 59.643 34.615 0.00 0.00 0.00 1.73
1824 7381 6.037610 AGCATTGCGTTTTTGTTTTTGGAATA 59.962 30.769 2.38 0.00 0.00 1.75
1827 7384 3.686726 AGCATTGCGTTTTTGTTTTTGGA 59.313 34.783 2.38 0.00 0.00 3.53
1828 7385 3.784994 CAGCATTGCGTTTTTGTTTTTGG 59.215 39.130 2.38 0.00 0.00 3.28
1829 7386 4.401714 ACAGCATTGCGTTTTTGTTTTTG 58.598 34.783 2.38 0.00 0.00 2.44
1830 7387 4.676849 ACAGCATTGCGTTTTTGTTTTT 57.323 31.818 2.38 0.00 0.00 1.94
1835 8473 3.357770 GCATACAGCATTGCGTTTTTG 57.642 42.857 10.49 2.93 44.79 2.44
1848 8486 7.335422 AGTCAAAAAGGTAAGATCTGCATACAG 59.665 37.037 0.00 0.00 45.95 2.74
1850 8488 7.414540 CCAGTCAAAAAGGTAAGATCTGCATAC 60.415 40.741 0.00 0.00 0.00 2.39
1883 9912 3.523157 TGTCCCAGCAGAATTGATAGGAA 59.477 43.478 0.00 0.00 0.00 3.36
1923 9952 2.039418 GGCAACTGGGAAGACCTTTTT 58.961 47.619 0.00 0.00 41.11 1.94
1930 9959 0.770499 TCACATGGCAACTGGGAAGA 59.230 50.000 0.00 0.00 37.61 2.87
1934 9963 0.968901 ATGCTCACATGGCAACTGGG 60.969 55.000 0.00 0.00 43.14 4.45
1951 9980 4.452753 CTTGCAACAGCGAGCATG 57.547 55.556 0.00 0.00 40.94 4.06
1966 9995 0.537143 TTCAGGGTGTTCATGCGCTT 60.537 50.000 9.73 0.00 0.00 4.68
1970 9999 0.798776 CGAGTTCAGGGTGTTCATGC 59.201 55.000 0.00 0.00 0.00 4.06
1986 10015 0.321564 TCACCCATTTGCCTGTCGAG 60.322 55.000 0.00 0.00 0.00 4.04
1989 10018 1.106285 GGATCACCCATTTGCCTGTC 58.894 55.000 0.00 0.00 34.14 3.51
2031 10060 6.699575 ACATCAAGTCAGCAGTTACTTTTT 57.300 33.333 0.00 0.00 33.72 1.94
2055 10084 4.731773 GCACAGTTCTTCCAGACTTTGTTG 60.732 45.833 0.00 0.00 0.00 3.33
2057 10086 2.945668 GCACAGTTCTTCCAGACTTTGT 59.054 45.455 0.00 0.00 0.00 2.83
2058 10087 2.945008 TGCACAGTTCTTCCAGACTTTG 59.055 45.455 0.00 0.00 0.00 2.77
2059 10088 3.209410 CTGCACAGTTCTTCCAGACTTT 58.791 45.455 0.00 0.00 0.00 2.66
2067 10096 5.400485 CACTAAATTTGCTGCACAGTTCTTC 59.600 40.000 4.65 0.00 0.00 2.87
2079 10108 3.891366 AGCCTTCACACACTAAATTTGCT 59.109 39.130 0.00 0.00 0.00 3.91
2111 10140 8.203485 TGCAAATCAACCAGAAAAGAAATTACT 58.797 29.630 0.00 0.00 0.00 2.24
2114 10143 7.049754 AGTGCAAATCAACCAGAAAAGAAATT 58.950 30.769 0.00 0.00 0.00 1.82
2118 10147 5.596836 AAGTGCAAATCAACCAGAAAAGA 57.403 34.783 0.00 0.00 0.00 2.52
2119 10148 6.272318 TGTAAGTGCAAATCAACCAGAAAAG 58.728 36.000 0.00 0.00 0.00 2.27
2120 10149 6.214191 TGTAAGTGCAAATCAACCAGAAAA 57.786 33.333 0.00 0.00 0.00 2.29
2121 10150 5.843673 TGTAAGTGCAAATCAACCAGAAA 57.156 34.783 0.00 0.00 0.00 2.52
2124 10153 6.803320 CAGTTATGTAAGTGCAAATCAACCAG 59.197 38.462 0.00 0.00 30.75 4.00
2126 10155 6.677913 ACAGTTATGTAAGTGCAAATCAACC 58.322 36.000 7.36 0.00 39.61 3.77
2130 10159 7.985476 ACCATACAGTTATGTAAGTGCAAATC 58.015 34.615 7.36 0.00 44.85 2.17
2132 10161 7.308891 CCAACCATACAGTTATGTAAGTGCAAA 60.309 37.037 7.36 0.00 44.85 3.68
2133 10162 6.150307 CCAACCATACAGTTATGTAAGTGCAA 59.850 38.462 7.36 0.00 44.85 4.08
2134 10163 5.645929 CCAACCATACAGTTATGTAAGTGCA 59.354 40.000 7.36 0.00 44.85 4.57
2135 10164 5.878116 TCCAACCATACAGTTATGTAAGTGC 59.122 40.000 7.36 0.00 44.85 4.40
2136 10165 7.103641 ACTCCAACCATACAGTTATGTAAGTG 58.896 38.462 6.15 6.15 44.85 3.16
2137 10166 7.253905 ACTCCAACCATACAGTTATGTAAGT 57.746 36.000 0.00 0.00 44.85 2.24
2138 10167 9.661563 TTAACTCCAACCATACAGTTATGTAAG 57.338 33.333 0.00 0.00 44.85 2.34
2146 10175 7.228706 CAGTTTCTTTAACTCCAACCATACAGT 59.771 37.037 0.00 0.00 45.29 3.55
2153 10182 3.889538 AGCCAGTTTCTTTAACTCCAACC 59.110 43.478 0.00 0.00 45.29 3.77
2168 10197 3.565764 TTATATGAGCAGCAGCCAGTT 57.434 42.857 0.00 0.00 43.56 3.16
2172 10201 4.578105 ACTTTCTTTATATGAGCAGCAGCC 59.422 41.667 0.00 0.00 43.56 4.85
2186 10215 8.671384 ACAGCACAGTACATTAACTTTCTTTA 57.329 30.769 0.00 0.00 0.00 1.85
2190 10219 5.625311 GCAACAGCACAGTACATTAACTTTC 59.375 40.000 0.00 0.00 0.00 2.62
2207 10236 4.424061 TCAACATAATGTCAGCAACAGC 57.576 40.909 0.00 0.00 42.37 4.40
2208 10237 4.847757 CGTTCAACATAATGTCAGCAACAG 59.152 41.667 0.00 0.00 42.37 3.16
2216 10245 4.678509 TGGCTTCGTTCAACATAATGTC 57.321 40.909 0.00 0.00 0.00 3.06
2232 10262 9.696917 GCAGTTATAAATATTTTAGCATGGCTT 57.303 29.630 5.91 0.00 40.44 4.35
2244 10274 9.174166 AGAAACTTCCGTGCAGTTATAAATATT 57.826 29.630 0.00 0.00 33.12 1.28
2259 10289 9.557061 AAACTTAATTAAGAGAGAAACTTCCGT 57.443 29.630 27.92 2.24 37.08 4.69
2282 10312 4.636206 CACTATGACCAGCCTAAAGGAAAC 59.364 45.833 0.00 0.00 37.39 2.78
2283 10313 4.324254 CCACTATGACCAGCCTAAAGGAAA 60.324 45.833 0.00 0.00 37.39 3.13
2284 10314 3.199946 CCACTATGACCAGCCTAAAGGAA 59.800 47.826 0.00 0.00 37.39 3.36
2285 10315 2.771943 CCACTATGACCAGCCTAAAGGA 59.228 50.000 0.00 0.00 37.39 3.36
2286 10316 2.158755 CCCACTATGACCAGCCTAAAGG 60.159 54.545 0.00 0.00 38.53 3.11
2287 10317 2.158755 CCCCACTATGACCAGCCTAAAG 60.159 54.545 0.00 0.00 0.00 1.85
2288 10318 1.843851 CCCCACTATGACCAGCCTAAA 59.156 52.381 0.00 0.00 0.00 1.85
2289 10319 1.507140 CCCCACTATGACCAGCCTAA 58.493 55.000 0.00 0.00 0.00 2.69
2290 10320 0.399949 CCCCCACTATGACCAGCCTA 60.400 60.000 0.00 0.00 0.00 3.93
2291 10321 1.694169 CCCCCACTATGACCAGCCT 60.694 63.158 0.00 0.00 0.00 4.58
2292 10322 0.693092 TACCCCCACTATGACCAGCC 60.693 60.000 0.00 0.00 0.00 4.85
2293 10323 1.134189 GTTACCCCCACTATGACCAGC 60.134 57.143 0.00 0.00 0.00 4.85
2294 10324 2.478292 AGTTACCCCCACTATGACCAG 58.522 52.381 0.00 0.00 0.00 4.00
2295 10325 2.653543 AGTTACCCCCACTATGACCA 57.346 50.000 0.00 0.00 0.00 4.02
2296 10326 4.472470 AGTTAAGTTACCCCCACTATGACC 59.528 45.833 0.00 0.00 0.00 4.02
2297 10327 5.688814 AGTTAAGTTACCCCCACTATGAC 57.311 43.478 0.00 0.00 0.00 3.06
2298 10328 6.505754 ACTAGTTAAGTTACCCCCACTATGA 58.494 40.000 0.00 0.00 33.35 2.15
2299 10329 6.803366 ACTAGTTAAGTTACCCCCACTATG 57.197 41.667 0.00 0.00 33.35 2.23
2300 10330 7.900784 TGTTACTAGTTAAGTTACCCCCACTAT 59.099 37.037 0.00 0.00 37.01 2.12
2301 10331 7.245292 TGTTACTAGTTAAGTTACCCCCACTA 58.755 38.462 0.00 0.00 37.01 2.74
2302 10332 6.084060 TGTTACTAGTTAAGTTACCCCCACT 58.916 40.000 0.00 0.00 37.01 4.00
2303 10333 6.358974 TGTTACTAGTTAAGTTACCCCCAC 57.641 41.667 0.00 0.00 37.01 4.61
2304 10334 8.539544 GTTATGTTACTAGTTAAGTTACCCCCA 58.460 37.037 0.00 0.00 37.01 4.96
2305 10335 8.539544 TGTTATGTTACTAGTTAAGTTACCCCC 58.460 37.037 0.00 0.00 37.01 5.40
2306 10336 9.371136 GTGTTATGTTACTAGTTAAGTTACCCC 57.629 37.037 0.00 0.00 37.01 4.95
2307 10337 9.927668 TGTGTTATGTTACTAGTTAAGTTACCC 57.072 33.333 0.00 0.00 37.01 3.69
2316 10346 9.640963 GTCTTGAGATGTGTTATGTTACTAGTT 57.359 33.333 0.00 0.00 0.00 2.24
2317 10347 8.803235 TGTCTTGAGATGTGTTATGTTACTAGT 58.197 33.333 0.00 0.00 0.00 2.57
2318 10348 9.639601 TTGTCTTGAGATGTGTTATGTTACTAG 57.360 33.333 0.00 0.00 0.00 2.57
2319 10349 9.990360 TTTGTCTTGAGATGTGTTATGTTACTA 57.010 29.630 0.00 0.00 0.00 1.82
2320 10350 8.902540 TTTGTCTTGAGATGTGTTATGTTACT 57.097 30.769 0.00 0.00 0.00 2.24
2321 10351 8.774586 ACTTTGTCTTGAGATGTGTTATGTTAC 58.225 33.333 0.00 0.00 0.00 2.50
2322 10352 8.902540 ACTTTGTCTTGAGATGTGTTATGTTA 57.097 30.769 0.00 0.00 0.00 2.41
2323 10353 7.807977 ACTTTGTCTTGAGATGTGTTATGTT 57.192 32.000 0.00 0.00 0.00 2.71
2324 10354 7.642669 CAACTTTGTCTTGAGATGTGTTATGT 58.357 34.615 0.00 0.00 0.00 2.29
2325 10355 6.580041 GCAACTTTGTCTTGAGATGTGTTATG 59.420 38.462 0.00 0.00 0.00 1.90
2326 10356 6.488006 AGCAACTTTGTCTTGAGATGTGTTAT 59.512 34.615 0.00 0.00 0.00 1.89
2327 10357 5.822519 AGCAACTTTGTCTTGAGATGTGTTA 59.177 36.000 0.00 0.00 0.00 2.41
2328 10358 4.641989 AGCAACTTTGTCTTGAGATGTGTT 59.358 37.500 0.00 0.00 0.00 3.32
2329 10359 4.202441 AGCAACTTTGTCTTGAGATGTGT 58.798 39.130 0.00 0.00 0.00 3.72
2330 10360 4.825546 AGCAACTTTGTCTTGAGATGTG 57.174 40.909 0.00 0.00 0.00 3.21
2331 10361 6.488006 ACATAAGCAACTTTGTCTTGAGATGT 59.512 34.615 8.16 7.49 0.00 3.06
2332 10362 6.800408 CACATAAGCAACTTTGTCTTGAGATG 59.200 38.462 8.16 7.07 0.00 2.90
2333 10363 6.072286 CCACATAAGCAACTTTGTCTTGAGAT 60.072 38.462 8.16 0.00 0.00 2.75
2334 10364 5.239306 CCACATAAGCAACTTTGTCTTGAGA 59.761 40.000 8.16 0.00 0.00 3.27
2335 10365 5.455392 CCACATAAGCAACTTTGTCTTGAG 58.545 41.667 8.16 4.69 0.00 3.02
2336 10366 4.261572 GCCACATAAGCAACTTTGTCTTGA 60.262 41.667 8.16 0.00 0.00 3.02
2337 10367 3.983344 GCCACATAAGCAACTTTGTCTTG 59.017 43.478 8.16 0.00 0.00 3.02
2338 10368 3.636300 TGCCACATAAGCAACTTTGTCTT 59.364 39.130 0.00 4.72 37.28 3.01
2339 10369 3.221771 TGCCACATAAGCAACTTTGTCT 58.778 40.909 0.00 0.00 37.28 3.41
2340 10370 3.641437 TGCCACATAAGCAACTTTGTC 57.359 42.857 0.00 0.00 37.28 3.18
2341 10371 3.321682 ACATGCCACATAAGCAACTTTGT 59.678 39.130 0.00 0.00 44.83 2.83
2342 10372 3.916761 ACATGCCACATAAGCAACTTTG 58.083 40.909 0.00 0.00 44.83 2.77
2343 10373 4.766891 AGTACATGCCACATAAGCAACTTT 59.233 37.500 0.00 0.00 44.83 2.66
2344 10374 4.335416 AGTACATGCCACATAAGCAACTT 58.665 39.130 0.00 0.00 44.83 2.66
2345 10375 3.941483 GAGTACATGCCACATAAGCAACT 59.059 43.478 0.00 0.00 44.83 3.16
2346 10376 3.065371 GGAGTACATGCCACATAAGCAAC 59.935 47.826 0.00 0.00 44.83 4.17
2347 10377 3.278574 GGAGTACATGCCACATAAGCAA 58.721 45.455 0.00 0.00 44.83 3.91
2348 10378 2.421388 GGGAGTACATGCCACATAAGCA 60.421 50.000 0.00 0.00 45.94 3.91
2349 10379 2.158755 AGGGAGTACATGCCACATAAGC 60.159 50.000 0.00 0.00 43.31 3.09
2350 10380 3.495100 GGAGGGAGTACATGCCACATAAG 60.495 52.174 0.00 0.00 43.31 1.73
2351 10381 2.438021 GGAGGGAGTACATGCCACATAA 59.562 50.000 0.00 0.00 43.31 1.90
2352 10382 2.047061 GGAGGGAGTACATGCCACATA 58.953 52.381 0.00 0.00 43.31 2.29
2353 10383 0.839946 GGAGGGAGTACATGCCACAT 59.160 55.000 0.00 0.00 43.31 3.21
2354 10384 1.613317 CGGAGGGAGTACATGCCACA 61.613 60.000 0.00 0.00 43.31 4.17
2355 10385 1.144057 CGGAGGGAGTACATGCCAC 59.856 63.158 0.00 0.00 43.31 5.01
2356 10386 0.907704 AACGGAGGGAGTACATGCCA 60.908 55.000 0.00 0.00 43.31 4.92
2357 10387 0.179081 GAACGGAGGGAGTACATGCC 60.179 60.000 0.00 0.00 40.48 4.40
2358 10388 0.179081 GGAACGGAGGGAGTACATGC 60.179 60.000 0.00 0.00 0.00 4.06
2359 10389 1.191535 TGGAACGGAGGGAGTACATG 58.808 55.000 0.00 0.00 0.00 3.21
2360 10390 2.176247 ATGGAACGGAGGGAGTACAT 57.824 50.000 0.00 0.00 0.00 2.29
2361 10391 2.832643 TATGGAACGGAGGGAGTACA 57.167 50.000 0.00 0.00 0.00 2.90
2362 10392 3.387050 ACATTATGGAACGGAGGGAGTAC 59.613 47.826 0.00 0.00 0.00 2.73
2363 10393 3.649843 ACATTATGGAACGGAGGGAGTA 58.350 45.455 0.00 0.00 0.00 2.59
2364 10394 2.478292 ACATTATGGAACGGAGGGAGT 58.522 47.619 0.00 0.00 0.00 3.85
2365 10395 4.283467 TCATACATTATGGAACGGAGGGAG 59.717 45.833 0.00 0.00 36.81 4.30
2366 10396 4.039973 GTCATACATTATGGAACGGAGGGA 59.960 45.833 0.00 0.00 36.81 4.20
2367 10397 4.315803 GTCATACATTATGGAACGGAGGG 58.684 47.826 0.00 0.00 36.81 4.30
2368 10398 3.987868 CGTCATACATTATGGAACGGAGG 59.012 47.826 0.00 0.00 34.61 4.30
2369 10399 4.617959 ACGTCATACATTATGGAACGGAG 58.382 43.478 6.60 0.00 39.35 4.63
2370 10400 4.659111 ACGTCATACATTATGGAACGGA 57.341 40.909 6.60 0.00 39.35 4.69
2371 10401 5.728351 AAACGTCATACATTATGGAACGG 57.272 39.130 6.60 0.00 39.35 4.44


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

AutoCloner maintained by Alex Coulton.