Multiple sequence alignment - TraesCS2D01G547500

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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 TraesCS2D01G547500 chr2D 100.000 5254 0 0 554 5807 623910383 623915636 0.000000e+00 9703
1 TraesCS2D01G547500 chr2D 90.522 939 80 6 1016 1948 623895248 623896183 0.000000e+00 1232
2 TraesCS2D01G547500 chr2D 87.942 904 103 4 1039 1936 623958499 623957596 0.000000e+00 1061
3 TraesCS2D01G547500 chr2D 85.804 951 107 14 3975 4916 623896412 623897343 0.000000e+00 983
4 TraesCS2D01G547500 chr2D 100.000 290 0 0 1 290 623909830 623910119 2.380000e-148 536
5 TraesCS2D01G547500 chr7D 96.199 2289 71 10 3526 5807 534469454 534467175 0.000000e+00 3731
6 TraesCS2D01G547500 chr7D 93.832 1751 94 5 3221 4965 534371410 534369668 0.000000e+00 2623
7 TraesCS2D01G547500 chr7D 92.185 1062 68 8 932 1985 534473158 534472104 0.000000e+00 1487
8 TraesCS2D01G547500 chr7D 82.423 1337 183 33 3864 5169 534620949 534619634 0.000000e+00 1120
9 TraesCS2D01G547500 chr7D 91.459 281 16 2 3 281 534525278 534525004 4.250000e-101 379
10 TraesCS2D01G547500 chr7D 88.217 314 20 6 3221 3532 534470930 534470632 5.530000e-95 359
11 TraesCS2D01G547500 chr7D 85.669 314 15 13 2046 2331 534472107 534471796 2.630000e-78 303
12 TraesCS2D01G547500 chr7D 84.561 285 19 9 2084 2344 534371685 534371402 5.770000e-65 259
13 TraesCS2D01G547500 chr2B 88.896 1666 155 17 3277 4938 765581574 765583213 0.000000e+00 2025
14 TraesCS2D01G547500 chr2B 88.457 1542 114 32 836 2339 765580017 765581532 0.000000e+00 1803
15 TraesCS2D01G547500 chr2B 90.234 942 85 5 1016 1951 765572178 765573118 0.000000e+00 1223
16 TraesCS2D01G547500 chr2B 87.704 919 107 4 1036 1950 753829994 753829078 0.000000e+00 1066
17 TraesCS2D01G547500 chr2B 87.140 902 113 1 1036 1934 753747999 753748900 0.000000e+00 1020
18 TraesCS2D01G547500 chr2B 85.338 948 115 14 3983 4916 765573343 765574280 0.000000e+00 959
19 TraesCS2D01G547500 chr2B 90.476 210 17 3 1 208 765579494 765579702 2.060000e-69 274
20 TraesCS2D01G547500 chr2B 82.119 151 20 3 611 759 765579718 765579863 7.900000e-24 122
21 TraesCS2D01G547500 chr2A 89.115 1525 145 11 3417 4938 755113966 755115472 0.000000e+00 1877
22 TraesCS2D01G547500 chr2A 92.446 887 59 3 2344 3223 732991034 732990149 0.000000e+00 1260
23 TraesCS2D01G547500 chr2A 83.004 1418 184 33 3784 5169 755087282 755088674 0.000000e+00 1230
24 TraesCS2D01G547500 chr2A 90.889 922 77 6 1034 1950 755251677 755250758 0.000000e+00 1230
25 TraesCS2D01G547500 chr2A 87.432 923 110 4 1035 1954 748078214 748079133 0.000000e+00 1057
26 TraesCS2D01G547500 chr2A 83.621 1044 150 17 3892 4927 755247710 755246680 0.000000e+00 961
27 TraesCS2D01G547500 chr6D 93.243 888 49 5 2345 3223 30534560 30533675 0.000000e+00 1297
28 TraesCS2D01G547500 chr7B 92.857 882 55 3 2345 3218 634288581 634287700 0.000000e+00 1273
29 TraesCS2D01G547500 chrUn 92.768 885 55 4 2345 3221 110780341 110779458 0.000000e+00 1271
30 TraesCS2D01G547500 chr3B 92.686 875 57 2 2353 3220 764783402 764782528 0.000000e+00 1254
31 TraesCS2D01G547500 chr6A 92.588 877 57 3 2353 3222 2044961 2044086 0.000000e+00 1253
32 TraesCS2D01G547500 chr7A 92.308 884 61 2 2345 3221 682327954 682327071 0.000000e+00 1249
33 TraesCS2D01G547500 chr6B 91.713 905 66 4 2335 3231 57715881 57716784 0.000000e+00 1247
34 TraesCS2D01G547500 chr5D 92.031 891 61 4 2343 3223 534087082 534087972 0.000000e+00 1243


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 TraesCS2D01G547500 chr2D 623909830 623915636 5806 False 5119.5 9703 100.0000 1 5807 2 chr2D.!!$F2 5806
1 TraesCS2D01G547500 chr2D 623895248 623897343 2095 False 1107.5 1232 88.1630 1016 4916 2 chr2D.!!$F1 3900
2 TraesCS2D01G547500 chr2D 623957596 623958499 903 True 1061.0 1061 87.9420 1039 1936 1 chr2D.!!$R1 897
3 TraesCS2D01G547500 chr7D 534467175 534473158 5983 True 1470.0 3731 90.5675 932 5807 4 chr7D.!!$R4 4875
4 TraesCS2D01G547500 chr7D 534369668 534371685 2017 True 1441.0 2623 89.1965 2084 4965 2 chr7D.!!$R3 2881
5 TraesCS2D01G547500 chr7D 534619634 534620949 1315 True 1120.0 1120 82.4230 3864 5169 1 chr7D.!!$R2 1305
6 TraesCS2D01G547500 chr2B 765572178 765574280 2102 False 1091.0 1223 87.7860 1016 4916 2 chr2B.!!$F2 3900
7 TraesCS2D01G547500 chr2B 753829078 753829994 916 True 1066.0 1066 87.7040 1036 1950 1 chr2B.!!$R1 914
8 TraesCS2D01G547500 chr2B 765579494 765583213 3719 False 1056.0 2025 87.4870 1 4938 4 chr2B.!!$F3 4937
9 TraesCS2D01G547500 chr2B 753747999 753748900 901 False 1020.0 1020 87.1400 1036 1934 1 chr2B.!!$F1 898
10 TraesCS2D01G547500 chr2A 755113966 755115472 1506 False 1877.0 1877 89.1150 3417 4938 1 chr2A.!!$F3 1521
11 TraesCS2D01G547500 chr2A 732990149 732991034 885 True 1260.0 1260 92.4460 2344 3223 1 chr2A.!!$R1 879
12 TraesCS2D01G547500 chr2A 755087282 755088674 1392 False 1230.0 1230 83.0040 3784 5169 1 chr2A.!!$F2 1385
13 TraesCS2D01G547500 chr2A 755246680 755251677 4997 True 1095.5 1230 87.2550 1034 4927 2 chr2A.!!$R2 3893
14 TraesCS2D01G547500 chr2A 748078214 748079133 919 False 1057.0 1057 87.4320 1035 1954 1 chr2A.!!$F1 919
15 TraesCS2D01G547500 chr6D 30533675 30534560 885 True 1297.0 1297 93.2430 2345 3223 1 chr6D.!!$R1 878
16 TraesCS2D01G547500 chr7B 634287700 634288581 881 True 1273.0 1273 92.8570 2345 3218 1 chr7B.!!$R1 873
17 TraesCS2D01G547500 chrUn 110779458 110780341 883 True 1271.0 1271 92.7680 2345 3221 1 chrUn.!!$R1 876
18 TraesCS2D01G547500 chr3B 764782528 764783402 874 True 1254.0 1254 92.6860 2353 3220 1 chr3B.!!$R1 867
19 TraesCS2D01G547500 chr6A 2044086 2044961 875 True 1253.0 1253 92.5880 2353 3222 1 chr6A.!!$R1 869
20 TraesCS2D01G547500 chr7A 682327071 682327954 883 True 1249.0 1249 92.3080 2345 3221 1 chr7A.!!$R1 876
21 TraesCS2D01G547500 chr6B 57715881 57716784 903 False 1247.0 1247 91.7130 2335 3231 1 chr6B.!!$F1 896
22 TraesCS2D01G547500 chr5D 534087082 534087972 890 False 1243.0 1243 92.0310 2343 3223 1 chr5D.!!$F1 880

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
225 228 0.177141 TACACGGGCAATGCTAGACC 59.823 55.000 4.82 0.00 0.00 3.85 F
227 230 0.464036 CACGGGCAATGCTAGACCTA 59.536 55.000 4.82 0.00 0.00 3.08 F
1089 1177 0.312102 TAGCATGGCTCGTCATCTCG 59.688 55.000 0.00 0.00 40.44 4.04 F
2065 2165 1.002257 ATGAACCGCACATGAGCCA 60.002 52.632 9.65 2.05 0.00 4.75 F
2803 3852 0.320073 TACCTAGTTGCCACGTGTGC 60.320 55.000 15.65 17.32 0.00 4.57 F
3204 4859 1.616620 CAATGTTGCCATACGTGTGC 58.383 50.000 6.80 2.78 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1031 1119 0.174845 CATGGCCACCATTGCTTCAG 59.825 55.000 8.16 0.00 42.23 3.02 R
2072 2172 0.248289 GCTGGCCATGTGCTTTGATT 59.752 50.000 5.51 0.00 40.92 2.57 R
2341 2529 1.053424 GGTGGATATGGGCGTCCTTA 58.947 55.000 7.97 5.71 35.49 2.69 R
2995 4125 2.361610 CTGCCCACACATCCACCC 60.362 66.667 0.00 0.00 0.00 4.61 R
4162 7360 1.342174 ACCAGCAGCAAACAAATCCTG 59.658 47.619 0.00 0.00 0.00 3.86 R
5150 8383 0.811616 GTAGCCTGGTTGATCGCCTG 60.812 60.000 7.51 6.81 0.00 4.85 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.341383 GGATTCCCTGTCAATGCCACT 60.341 52.381 0.00 0.00 0.00 4.00
26 27 1.951209 TCCCTGTCAATGCCACTAGA 58.049 50.000 0.00 0.00 0.00 2.43
34 35 6.258230 TGTCAATGCCACTAGAAAAAGATG 57.742 37.500 0.00 0.00 0.00 2.90
52 53 0.473755 TGCCACCTTGCTTCAGAAGA 59.526 50.000 14.86 0.00 0.00 2.87
57 58 3.370315 CCACCTTGCTTCAGAAGATAGCT 60.370 47.826 14.86 0.00 35.93 3.32
102 103 8.881743 TGTGATGCAATTTATTTTCATTAAGCC 58.118 29.630 0.00 0.00 0.00 4.35
146 147 2.333688 TTGATGTTGTGGACGTTGGA 57.666 45.000 0.00 0.00 0.00 3.53
215 218 6.933521 TGTAACTATAAAGTTTTACACGGGCA 59.066 34.615 0.00 0.00 43.60 5.36
218 221 6.848451 ACTATAAAGTTTTACACGGGCAATG 58.152 36.000 0.00 0.00 29.00 2.82
219 222 2.432206 AAGTTTTACACGGGCAATGC 57.568 45.000 0.00 0.00 0.00 3.56
220 223 1.616159 AGTTTTACACGGGCAATGCT 58.384 45.000 4.82 0.00 0.00 3.79
222 225 2.747446 AGTTTTACACGGGCAATGCTAG 59.253 45.455 4.82 1.85 0.00 3.42
223 226 2.745281 GTTTTACACGGGCAATGCTAGA 59.255 45.455 4.82 0.00 0.00 2.43
224 227 2.018542 TTACACGGGCAATGCTAGAC 57.981 50.000 4.82 0.00 0.00 2.59
225 228 0.177141 TACACGGGCAATGCTAGACC 59.823 55.000 4.82 0.00 0.00 3.85
226 229 1.221840 CACGGGCAATGCTAGACCT 59.778 57.895 4.82 0.00 0.00 3.85
227 230 0.464036 CACGGGCAATGCTAGACCTA 59.536 55.000 4.82 0.00 0.00 3.08
228 231 0.464452 ACGGGCAATGCTAGACCTAC 59.536 55.000 4.82 0.00 0.00 3.18
229 232 0.597637 CGGGCAATGCTAGACCTACG 60.598 60.000 4.82 0.00 0.00 3.51
230 233 0.464452 GGGCAATGCTAGACCTACGT 59.536 55.000 4.82 0.00 0.00 3.57
231 234 1.684983 GGGCAATGCTAGACCTACGTA 59.315 52.381 4.82 0.00 0.00 3.57
232 235 2.101917 GGGCAATGCTAGACCTACGTAA 59.898 50.000 4.82 0.00 0.00 3.18
233 236 3.431207 GGGCAATGCTAGACCTACGTAAA 60.431 47.826 4.82 0.00 0.00 2.01
234 237 3.802685 GGCAATGCTAGACCTACGTAAAG 59.197 47.826 4.82 0.00 0.00 1.85
235 238 4.441079 GGCAATGCTAGACCTACGTAAAGA 60.441 45.833 4.82 0.00 0.00 2.52
236 239 5.107133 GCAATGCTAGACCTACGTAAAGAA 58.893 41.667 0.00 0.00 0.00 2.52
237 240 5.232414 GCAATGCTAGACCTACGTAAAGAAG 59.768 44.000 0.00 0.00 0.00 2.85
238 241 4.978083 TGCTAGACCTACGTAAAGAAGG 57.022 45.455 0.00 0.00 36.42 3.46
239 242 4.338879 TGCTAGACCTACGTAAAGAAGGT 58.661 43.478 6.67 6.67 46.33 3.50
240 243 5.500234 TGCTAGACCTACGTAAAGAAGGTA 58.500 41.667 6.94 0.00 43.69 3.08
241 244 5.355350 TGCTAGACCTACGTAAAGAAGGTAC 59.645 44.000 6.94 2.27 43.69 3.34
242 245 4.954092 AGACCTACGTAAAGAAGGTACG 57.046 45.455 6.94 2.65 43.69 3.67
252 255 7.146368 CGTAAAGAAGGTACGTAAGCTAATG 57.854 40.000 0.00 0.00 39.54 1.90
253 256 6.197842 CGTAAAGAAGGTACGTAAGCTAATGG 59.802 42.308 0.00 0.00 39.54 3.16
254 257 4.667519 AGAAGGTACGTAAGCTAATGGG 57.332 45.455 0.00 0.00 45.62 4.00
255 258 4.284178 AGAAGGTACGTAAGCTAATGGGA 58.716 43.478 0.00 0.00 45.62 4.37
256 259 4.900054 AGAAGGTACGTAAGCTAATGGGAT 59.100 41.667 0.00 0.00 45.62 3.85
257 260 4.602340 AGGTACGTAAGCTAATGGGATG 57.398 45.455 0.00 0.00 45.62 3.51
258 261 3.965347 AGGTACGTAAGCTAATGGGATGT 59.035 43.478 0.00 0.00 45.62 3.06
259 262 4.038883 AGGTACGTAAGCTAATGGGATGTC 59.961 45.833 0.00 0.00 45.62 3.06
260 263 3.470645 ACGTAAGCTAATGGGATGTCC 57.529 47.619 0.00 0.00 45.62 4.02
262 265 3.199071 ACGTAAGCTAATGGGATGTCCAA 59.801 43.478 0.86 0.00 46.91 3.53
263 266 4.922134 ACGTAAGCTAATGGGATGTCCAAC 60.922 45.833 0.86 0.00 46.91 3.77
264 267 8.826241 TACGTAAGCTAATGGGATGTCCAACG 62.826 46.154 0.86 0.00 46.91 4.10
268 271 2.753701 TGGGATGTCCAACGTGGG 59.246 61.111 1.09 1.09 43.84 4.61
269 272 2.045340 GGGATGTCCAACGTGGGG 60.045 66.667 9.71 4.45 38.32 4.96
270 273 2.045340 GGATGTCCAACGTGGGGG 60.045 66.667 9.71 1.53 38.32 5.40
575 578 4.070224 CGTAAAGCTGCGTAAAAGTTACG 58.930 43.478 14.54 14.54 43.13 3.18
576 579 4.375305 CGTAAAGCTGCGTAAAAGTTACGT 60.375 41.667 18.59 0.00 42.35 3.57
577 580 5.164196 CGTAAAGCTGCGTAAAAGTTACGTA 60.164 40.000 18.59 14.49 42.35 3.57
581 584 4.557276 CTGCGTAAAAGTTACGTAGGTG 57.443 45.455 22.79 6.43 45.39 4.00
582 585 3.976169 TGCGTAAAAGTTACGTAGGTGT 58.024 40.909 18.59 0.00 42.35 4.16
583 586 5.114785 TGCGTAAAAGTTACGTAGGTGTA 57.885 39.130 18.59 0.00 42.35 2.90
584 587 5.153513 TGCGTAAAAGTTACGTAGGTGTAG 58.846 41.667 18.59 0.00 42.35 2.74
585 588 5.154222 GCGTAAAAGTTACGTAGGTGTAGT 58.846 41.667 18.59 0.00 42.35 2.73
586 589 6.072948 TGCGTAAAAGTTACGTAGGTGTAGTA 60.073 38.462 18.59 0.00 42.35 1.82
587 590 6.967199 GCGTAAAAGTTACGTAGGTGTAGTAT 59.033 38.462 18.59 0.00 42.35 2.12
588 591 7.484959 GCGTAAAAGTTACGTAGGTGTAGTATT 59.515 37.037 18.59 0.00 42.35 1.89
589 592 9.982291 CGTAAAAGTTACGTAGGTGTAGTATTA 57.018 33.333 11.42 0.00 36.31 0.98
592 595 9.722056 AAAAGTTACGTAGGTGTAGTATTATCG 57.278 33.333 0.00 0.00 0.00 2.92
593 596 7.426929 AGTTACGTAGGTGTAGTATTATCGG 57.573 40.000 0.00 0.00 0.00 4.18
594 597 6.992715 AGTTACGTAGGTGTAGTATTATCGGT 59.007 38.462 0.00 0.00 0.00 4.69
595 598 7.499232 AGTTACGTAGGTGTAGTATTATCGGTT 59.501 37.037 0.00 0.00 0.00 4.44
596 599 6.699575 ACGTAGGTGTAGTATTATCGGTTT 57.300 37.500 0.00 0.00 0.00 3.27
597 600 7.100458 ACGTAGGTGTAGTATTATCGGTTTT 57.900 36.000 0.00 0.00 0.00 2.43
598 601 8.220755 ACGTAGGTGTAGTATTATCGGTTTTA 57.779 34.615 0.00 0.00 0.00 1.52
599 602 8.129211 ACGTAGGTGTAGTATTATCGGTTTTAC 58.871 37.037 0.00 0.00 0.00 2.01
600 603 8.128582 CGTAGGTGTAGTATTATCGGTTTTACA 58.871 37.037 0.00 0.00 0.00 2.41
601 604 9.237846 GTAGGTGTAGTATTATCGGTTTTACAC 57.762 37.037 3.89 3.89 38.91 2.90
602 605 7.468922 GGTGTAGTATTATCGGTTTTACACC 57.531 40.000 13.24 13.24 46.85 4.16
603 606 6.479990 GGTGTAGTATTATCGGTTTTACACCC 59.520 42.308 16.25 3.35 46.98 4.61
604 607 7.267857 GTGTAGTATTATCGGTTTTACACCCT 58.732 38.462 0.00 0.00 43.83 4.34
605 608 7.436376 GTGTAGTATTATCGGTTTTACACCCTC 59.564 40.741 0.00 0.00 43.83 4.30
606 609 5.922053 AGTATTATCGGTTTTACACCCTCC 58.078 41.667 0.00 0.00 43.83 4.30
607 610 4.847990 ATTATCGGTTTTACACCCTCCA 57.152 40.909 0.00 0.00 43.83 3.86
608 611 4.847990 TTATCGGTTTTACACCCTCCAT 57.152 40.909 0.00 0.00 43.83 3.41
609 612 2.483014 TCGGTTTTACACCCTCCATG 57.517 50.000 0.00 0.00 43.83 3.66
613 616 4.225492 TCGGTTTTACACCCTCCATGAATA 59.775 41.667 0.00 0.00 43.83 1.75
639 642 9.860898 ATGAGGTGTTCTAAAATTTTCATAAGC 57.139 29.630 6.72 1.29 0.00 3.09
641 644 8.189119 AGGTGTTCTAAAATTTTCATAAGCCA 57.811 30.769 6.72 0.00 0.00 4.75
646 649 9.561270 GTTCTAAAATTTTCATAAGCCAGACTC 57.439 33.333 6.72 0.00 0.00 3.36
647 650 9.520515 TTCTAAAATTTTCATAAGCCAGACTCT 57.479 29.630 6.72 0.00 0.00 3.24
817 889 8.919777 AATTTAGAACAAAGCAAGTAGGTACT 57.080 30.769 0.00 0.00 46.37 2.73
827 899 8.999431 CAAAGCAAGTAGGTACTTAAATCAGAA 58.001 33.333 2.06 0.00 44.19 3.02
859 942 5.734720 ACTTCTTCATCACATATCGGTTGT 58.265 37.500 0.00 0.00 0.00 3.32
864 947 9.476202 TTCTTCATCACATATCGGTTGTAATAG 57.524 33.333 0.00 0.00 0.00 1.73
865 948 7.598869 TCTTCATCACATATCGGTTGTAATAGC 59.401 37.037 0.00 0.00 0.00 2.97
866 949 6.754193 TCATCACATATCGGTTGTAATAGCA 58.246 36.000 0.00 0.00 0.00 3.49
867 950 7.386059 TCATCACATATCGGTTGTAATAGCAT 58.614 34.615 0.00 0.00 0.00 3.79
868 951 7.877612 TCATCACATATCGGTTGTAATAGCATT 59.122 33.333 0.00 0.00 0.00 3.56
870 953 9.719355 ATCACATATCGGTTGTAATAGCATTTA 57.281 29.630 0.00 0.00 0.00 1.40
871 954 9.719355 TCACATATCGGTTGTAATAGCATTTAT 57.281 29.630 0.00 0.00 0.00 1.40
886 969 8.988064 ATAGCATTTATAGTAATGACACGGAG 57.012 34.615 1.99 0.00 37.65 4.63
889 972 6.740401 GCATTTATAGTAATGACACGGAGGGA 60.740 42.308 1.99 0.00 37.65 4.20
897 980 3.377253 TGACACGGAGGGAGTACTATT 57.623 47.619 0.00 0.00 0.00 1.73
898 981 3.285484 TGACACGGAGGGAGTACTATTC 58.715 50.000 0.00 0.00 0.00 1.75
900 983 3.288964 ACACGGAGGGAGTACTATTCTG 58.711 50.000 0.00 1.77 0.00 3.02
1011 1098 9.772973 TCTATTTAGTGTTTCATGTGTTGTACT 57.227 29.630 0.00 0.00 0.00 2.73
1026 1114 1.337703 TGTACTTGTACGCCGAACTGT 59.662 47.619 0.00 0.00 0.00 3.55
1031 1119 1.769733 TGTACGCCGAACTGTACAAC 58.230 50.000 0.00 0.00 45.68 3.32
1032 1120 1.337703 TGTACGCCGAACTGTACAACT 59.662 47.619 0.00 0.00 45.68 3.16
1056 1144 0.683828 CAATGGTGGCCATGGCTGTA 60.684 55.000 34.70 19.27 44.40 2.74
1084 1172 2.358372 TGGCTAGCATGGCTCGTCA 61.358 57.895 18.24 0.00 44.74 4.35
1089 1177 0.312102 TAGCATGGCTCGTCATCTCG 59.688 55.000 0.00 0.00 40.44 4.04
1101 1189 1.066908 GTCATCTCGCTCCTCTCCTTG 59.933 57.143 0.00 0.00 0.00 3.61
1249 1340 4.129737 ACGGTCCGCTCATGTCCG 62.130 66.667 12.28 0.00 45.53 4.79
1496 1591 2.584391 GGAGCGACAAGGTGAGGGT 61.584 63.158 0.00 0.00 0.00 4.34
1863 1958 1.515088 CTACCTCGACGTGCTGCTG 60.515 63.158 0.00 0.00 0.00 4.41
1908 2003 2.126424 GACCTGCTCGACCGTGAC 60.126 66.667 0.00 0.00 0.00 3.67
1920 2015 2.423031 CCGTGACACGCTACGTTCG 61.423 63.158 22.46 0.00 40.91 3.95
2065 2165 1.002257 ATGAACCGCACATGAGCCA 60.002 52.632 9.65 2.05 0.00 4.75
2072 2172 4.100084 CACATGAGCCAGCCGGGA 62.100 66.667 2.18 0.00 40.01 5.14
2133 2260 2.256306 GGGGATCAAACAAATGGTGGT 58.744 47.619 0.00 0.00 0.00 4.16
2134 2261 2.233676 GGGGATCAAACAAATGGTGGTC 59.766 50.000 0.00 0.00 0.00 4.02
2135 2262 2.896685 GGGATCAAACAAATGGTGGTCA 59.103 45.455 0.00 0.00 0.00 4.02
2140 2282 6.486320 GGATCAAACAAATGGTGGTCAAAAAT 59.514 34.615 0.00 0.00 0.00 1.82
2143 2289 8.970859 TCAAACAAATGGTGGTCAAAAATAAT 57.029 26.923 0.00 0.00 0.00 1.28
2185 2359 9.860898 AGCTATTTCAATAACCAATTTTGACTC 57.139 29.630 0.00 0.00 0.00 3.36
2332 2520 8.577296 TCTGCATGTTAATCATCTACTACTACC 58.423 37.037 0.00 0.00 34.09 3.18
2333 2521 8.245195 TGCATGTTAATCATCTACTACTACCA 57.755 34.615 0.00 0.00 34.09 3.25
2605 3013 3.342377 TGACGATTTAGTTGCCATCCA 57.658 42.857 0.00 0.00 0.00 3.41
2674 3082 3.558931 TGGCAACTCTCTCTGTTTTGA 57.441 42.857 0.00 0.00 37.61 2.69
2714 3127 3.797256 GTCTATGGTAGTTGTCGCATGTC 59.203 47.826 0.00 0.00 0.00 3.06
2803 3852 0.320073 TACCTAGTTGCCACGTGTGC 60.320 55.000 15.65 17.32 0.00 4.57
2890 3939 4.158394 AGCAAACGAATCATAGTTGCCATT 59.842 37.500 3.24 0.00 0.00 3.16
2995 4125 2.126071 CACACGCGTGGACTAGGG 60.126 66.667 39.21 15.50 39.64 3.53
3204 4859 1.616620 CAATGTTGCCATACGTGTGC 58.383 50.000 6.80 2.78 0.00 4.57
3292 5001 1.899814 TCAGGAGCGTGGTGAAACTAT 59.100 47.619 0.00 0.00 36.74 2.12
3557 6725 4.879545 AGTTTAGAAACACGACAACATGGT 59.120 37.500 7.82 0.00 41.30 3.55
3729 6898 8.839343 TGACATGCTATTCATATGTTACAAAGG 58.161 33.333 1.90 0.00 35.35 3.11
3765 6934 9.428097 TCTAAAACTAAGTACGGATTTCCTTTC 57.572 33.333 0.00 0.00 0.00 2.62
3774 6943 8.358582 AGTACGGATTTCCTTTCTAAGAACTA 57.641 34.615 0.00 0.00 0.00 2.24
3928 7100 8.067488 AGGGAAATATTGGGTCAAGAACAATAT 58.933 33.333 12.04 12.04 44.98 1.28
3929 7101 9.362151 GGGAAATATTGGGTCAAGAACAATATA 57.638 33.333 15.59 0.97 43.31 0.86
3939 7111 8.778358 GGGTCAAGAACAATATATAGCTTCTTG 58.222 37.037 20.93 20.93 44.78 3.02
4050 7226 5.681880 CAATGTGCAGTTTTAAAGCAATGG 58.318 37.500 4.79 0.00 40.35 3.16
4073 7249 7.629157 TGGTGATTCTTCTATACCACATTCAA 58.371 34.615 0.00 0.00 36.56 2.69
4263 7461 5.263599 TCATCAATGGCTAAGGTTTGTGAT 58.736 37.500 0.00 0.00 0.00 3.06
4493 7691 6.978674 AGGTCGAGATAAAGATGTATGGAA 57.021 37.500 0.00 0.00 0.00 3.53
4690 7888 1.198094 TCCCATTGAGCTGGAACGGA 61.198 55.000 0.00 0.00 38.69 4.69
5060 8293 5.518848 ACTGACACATTTTCAGATGCAAA 57.481 34.783 6.37 0.00 42.81 3.68
5192 8425 1.736645 GGACGGTGATGGTGACGTG 60.737 63.158 0.00 0.00 39.95 4.49
5247 8480 2.170166 TGCTTTTGGATGGTGATGGAC 58.830 47.619 0.00 0.00 0.00 4.02
5293 8526 9.677567 GTGCTTCTTCAAATAACAGAATAAACA 57.322 29.630 0.00 0.00 0.00 2.83
5450 8683 7.816945 TCGTTCTCCTTTTAATAGTAAACCG 57.183 36.000 0.00 0.00 0.00 4.44
5462 8695 3.619233 AGTAAACCGCACAACAATCAC 57.381 42.857 0.00 0.00 0.00 3.06
5500 8733 6.681368 GCCACCAACATCTTTCAATAATCTCC 60.681 42.308 0.00 0.00 0.00 3.71
5557 8790 6.863275 GGTAGTGACCAAATAAAAATCAGGG 58.137 40.000 0.00 0.00 46.12 4.45
5635 8868 1.837439 TCACCCGATTGCCTAGTGATT 59.163 47.619 0.00 0.00 32.75 2.57
5637 8870 1.202533 ACCCGATTGCCTAGTGATTCG 60.203 52.381 0.00 0.00 0.00 3.34
5646 8879 7.373441 CGATTGCCTAGTGATTCGAAAATTAAC 59.627 37.037 0.00 0.00 0.00 2.01
5672 8905 2.562738 ACTTTGCATCTGTTTTAGCCCC 59.437 45.455 0.00 0.00 0.00 5.80
5744 8977 2.109834 TCCCATCTCCCTTGCTTTTTCA 59.890 45.455 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.787473 TTCTAGTGGCATTGACAGGG 57.213 50.000 0.00 0.00 0.00 4.45
16 17 3.445096 GTGGCATCTTTTTCTAGTGGCAT 59.555 43.478 6.75 0.00 45.16 4.40
23 24 3.766545 AGCAAGGTGGCATCTTTTTCTA 58.233 40.909 11.03 0.00 35.83 2.10
26 27 2.699846 TGAAGCAAGGTGGCATCTTTTT 59.300 40.909 11.03 8.46 32.97 1.94
34 35 1.831580 ATCTTCTGAAGCAAGGTGGC 58.168 50.000 12.54 0.00 0.00 5.01
57 58 7.474190 CATCACATATCAACATAGCACAACAA 58.526 34.615 0.00 0.00 0.00 2.83
115 116 9.186323 CGTCCACAACATCAAATTGTTATAAAA 57.814 29.630 0.00 0.00 38.22 1.52
195 198 5.741982 GCATTGCCCGTGTAAAACTTTATAG 59.258 40.000 0.00 0.00 0.00 1.31
200 203 1.960689 AGCATTGCCCGTGTAAAACTT 59.039 42.857 4.70 0.00 0.00 2.66
202 205 2.745281 TCTAGCATTGCCCGTGTAAAAC 59.255 45.455 4.70 0.00 0.00 2.43
208 211 0.464036 TAGGTCTAGCATTGCCCGTG 59.536 55.000 4.70 0.00 0.00 4.94
210 213 0.597637 CGTAGGTCTAGCATTGCCCG 60.598 60.000 4.70 0.00 0.00 6.13
211 214 0.464452 ACGTAGGTCTAGCATTGCCC 59.536 55.000 4.70 0.00 0.00 5.36
212 215 3.447918 TTACGTAGGTCTAGCATTGCC 57.552 47.619 4.70 0.00 0.00 4.52
213 216 4.679662 TCTTTACGTAGGTCTAGCATTGC 58.320 43.478 0.00 0.00 0.00 3.56
215 218 5.421374 ACCTTCTTTACGTAGGTCTAGCATT 59.579 40.000 0.94 0.00 38.92 3.56
218 221 4.979943 ACCTTCTTTACGTAGGTCTAGC 57.020 45.455 0.94 0.00 38.92 3.42
219 222 6.042144 CGTACCTTCTTTACGTAGGTCTAG 57.958 45.833 10.20 0.78 41.87 2.43
228 231 6.197842 CCATTAGCTTACGTACCTTCTTTACG 59.802 42.308 0.00 0.55 46.25 3.18
229 232 6.478016 CCCATTAGCTTACGTACCTTCTTTAC 59.522 42.308 0.00 0.00 0.00 2.01
230 233 6.380846 TCCCATTAGCTTACGTACCTTCTTTA 59.619 38.462 0.00 0.00 0.00 1.85
231 234 5.188359 TCCCATTAGCTTACGTACCTTCTTT 59.812 40.000 0.00 0.00 0.00 2.52
232 235 4.713321 TCCCATTAGCTTACGTACCTTCTT 59.287 41.667 0.00 0.00 0.00 2.52
233 236 4.284178 TCCCATTAGCTTACGTACCTTCT 58.716 43.478 0.00 0.00 0.00 2.85
234 237 4.660789 TCCCATTAGCTTACGTACCTTC 57.339 45.455 0.00 0.00 0.00 3.46
235 238 4.407945 ACATCCCATTAGCTTACGTACCTT 59.592 41.667 0.00 0.00 0.00 3.50
236 239 3.965347 ACATCCCATTAGCTTACGTACCT 59.035 43.478 0.00 0.00 0.00 3.08
237 240 4.304939 GACATCCCATTAGCTTACGTACC 58.695 47.826 0.00 0.00 0.00 3.34
238 241 4.202182 TGGACATCCCATTAGCTTACGTAC 60.202 45.833 0.00 0.00 40.82 3.67
239 242 3.962063 TGGACATCCCATTAGCTTACGTA 59.038 43.478 0.00 0.00 40.82 3.57
240 243 2.769663 TGGACATCCCATTAGCTTACGT 59.230 45.455 0.00 0.00 40.82 3.57
241 244 3.469008 TGGACATCCCATTAGCTTACG 57.531 47.619 0.00 0.00 40.82 3.18
242 245 3.560068 CGTTGGACATCCCATTAGCTTAC 59.440 47.826 0.00 0.00 46.10 2.34
243 246 3.199071 ACGTTGGACATCCCATTAGCTTA 59.801 43.478 0.00 0.00 46.10 3.09
244 247 2.026262 ACGTTGGACATCCCATTAGCTT 60.026 45.455 0.00 0.00 46.10 3.74
245 248 1.559682 ACGTTGGACATCCCATTAGCT 59.440 47.619 0.00 0.00 46.10 3.32
246 249 1.670811 CACGTTGGACATCCCATTAGC 59.329 52.381 0.00 0.00 46.10 3.09
247 250 2.288666 CCACGTTGGACATCCCATTAG 58.711 52.381 0.00 0.00 46.10 1.73
248 251 1.065053 CCCACGTTGGACATCCCATTA 60.065 52.381 0.00 0.00 46.10 1.90
249 252 0.323360 CCCACGTTGGACATCCCATT 60.323 55.000 0.00 0.00 46.10 3.16
250 253 1.302949 CCCACGTTGGACATCCCAT 59.697 57.895 0.00 0.00 46.10 4.00
251 254 2.753701 CCCACGTTGGACATCCCA 59.246 61.111 0.00 0.00 40.96 4.37
252 255 2.045340 CCCCACGTTGGACATCCC 60.045 66.667 7.36 0.00 40.96 3.85
253 256 2.045340 CCCCCACGTTGGACATCC 60.045 66.667 7.36 0.00 40.96 3.51
553 556 4.070224 CGTAACTTTTACGCAGCTTTACG 58.930 43.478 5.61 7.04 35.77 3.18
554 557 5.010249 ACGTAACTTTTACGCAGCTTTAC 57.990 39.130 16.33 0.00 43.97 2.01
555 558 5.345741 CCTACGTAACTTTTACGCAGCTTTA 59.654 40.000 16.33 2.40 43.97 1.85
556 559 4.151157 CCTACGTAACTTTTACGCAGCTTT 59.849 41.667 16.33 1.43 43.97 3.51
557 560 3.676646 CCTACGTAACTTTTACGCAGCTT 59.323 43.478 16.33 2.05 43.97 3.74
558 561 3.248266 CCTACGTAACTTTTACGCAGCT 58.752 45.455 16.33 2.37 43.97 4.24
559 562 2.989166 ACCTACGTAACTTTTACGCAGC 59.011 45.455 16.33 0.00 43.97 5.25
560 563 3.983344 ACACCTACGTAACTTTTACGCAG 59.017 43.478 16.33 13.27 43.97 5.18
561 564 3.976169 ACACCTACGTAACTTTTACGCA 58.024 40.909 16.33 5.04 43.97 5.24
562 565 5.154222 ACTACACCTACGTAACTTTTACGC 58.846 41.667 16.33 0.00 43.97 4.42
563 566 8.895932 AATACTACACCTACGTAACTTTTACG 57.104 34.615 15.13 15.13 45.44 3.18
566 569 9.722056 CGATAATACTACACCTACGTAACTTTT 57.278 33.333 0.00 0.00 0.00 2.27
567 570 8.345565 CCGATAATACTACACCTACGTAACTTT 58.654 37.037 0.00 0.00 0.00 2.66
568 571 7.499232 ACCGATAATACTACACCTACGTAACTT 59.501 37.037 0.00 0.00 0.00 2.66
569 572 6.992715 ACCGATAATACTACACCTACGTAACT 59.007 38.462 0.00 0.00 0.00 2.24
570 573 7.190920 ACCGATAATACTACACCTACGTAAC 57.809 40.000 0.00 0.00 0.00 2.50
571 574 7.801716 AACCGATAATACTACACCTACGTAA 57.198 36.000 0.00 0.00 0.00 3.18
572 575 7.801716 AAACCGATAATACTACACCTACGTA 57.198 36.000 0.00 0.00 0.00 3.57
573 576 6.699575 AAACCGATAATACTACACCTACGT 57.300 37.500 0.00 0.00 0.00 3.57
574 577 8.128582 TGTAAAACCGATAATACTACACCTACG 58.871 37.037 0.00 0.00 0.00 3.51
575 578 9.237846 GTGTAAAACCGATAATACTACACCTAC 57.762 37.037 0.00 0.00 34.32 3.18
578 581 7.468922 GGTGTAAAACCGATAATACTACACC 57.531 40.000 11.51 11.51 46.12 4.16
590 593 9.215769 TCATATTCATGGAGGGTGTAAAACCGA 62.216 40.741 0.00 0.00 40.22 4.69
591 594 7.133346 TCATATTCATGGAGGGTGTAAAACCG 61.133 42.308 0.00 0.00 40.22 4.44
592 595 6.126409 TCATATTCATGGAGGGTGTAAAACC 58.874 40.000 0.00 0.00 39.34 3.27
593 596 6.263168 CCTCATATTCATGGAGGGTGTAAAAC 59.737 42.308 6.98 0.00 31.23 2.43
594 597 6.069088 ACCTCATATTCATGGAGGGTGTAAAA 60.069 38.462 16.45 0.00 35.46 1.52
595 598 5.431731 ACCTCATATTCATGGAGGGTGTAAA 59.568 40.000 16.45 0.00 35.46 2.01
596 599 4.975147 ACCTCATATTCATGGAGGGTGTAA 59.025 41.667 16.45 0.00 35.46 2.41
597 600 4.347876 CACCTCATATTCATGGAGGGTGTA 59.652 45.833 16.45 0.00 39.70 2.90
598 601 3.137176 CACCTCATATTCATGGAGGGTGT 59.863 47.826 16.45 0.00 39.70 4.16
599 602 3.137176 ACACCTCATATTCATGGAGGGTG 59.863 47.826 16.45 14.64 44.12 4.61
600 603 3.397527 ACACCTCATATTCATGGAGGGT 58.602 45.455 16.45 10.06 35.46 4.34
601 604 4.103785 AGAACACCTCATATTCATGGAGGG 59.896 45.833 16.45 9.58 35.46 4.30
602 605 5.301835 AGAACACCTCATATTCATGGAGG 57.698 43.478 12.02 12.02 36.40 4.30
603 606 8.737168 TTTTAGAACACCTCATATTCATGGAG 57.263 34.615 0.00 0.00 32.61 3.86
604 607 9.699410 AATTTTAGAACACCTCATATTCATGGA 57.301 29.630 0.00 0.00 32.61 3.41
613 616 9.860898 GCTTATGAAAATTTTAGAACACCTCAT 57.139 29.630 2.75 2.75 0.00 2.90
731 736 6.811253 AGAACGCTGAATTTGTACCATTAA 57.189 33.333 0.00 0.00 0.00 1.40
737 742 7.222999 AGCTTATCTAGAACGCTGAATTTGTAC 59.777 37.037 11.54 0.00 0.00 2.90
738 743 7.265673 AGCTTATCTAGAACGCTGAATTTGTA 58.734 34.615 11.54 0.00 0.00 2.41
741 746 6.818644 TCAAGCTTATCTAGAACGCTGAATTT 59.181 34.615 12.66 0.00 0.00 1.82
748 753 8.798748 TTATAAGTCAAGCTTATCTAGAACGC 57.201 34.615 0.00 0.00 44.68 4.84
793 846 8.919777 AAGTACCTACTTGCTTTGTTCTAAAT 57.080 30.769 0.00 0.00 44.30 1.40
803 856 9.740710 AATTCTGATTTAAGTACCTACTTGCTT 57.259 29.630 7.81 0.00 45.44 3.91
832 915 7.953158 ACCGATATGTGATGAAGAAGTATTG 57.047 36.000 0.00 0.00 0.00 1.90
833 916 7.987458 ACAACCGATATGTGATGAAGAAGTATT 59.013 33.333 0.00 0.00 0.00 1.89
834 917 7.500992 ACAACCGATATGTGATGAAGAAGTAT 58.499 34.615 0.00 0.00 0.00 2.12
839 922 7.598869 GCTATTACAACCGATATGTGATGAAGA 59.401 37.037 0.00 0.00 30.67 2.87
844 927 8.621532 AAATGCTATTACAACCGATATGTGAT 57.378 30.769 0.00 0.00 32.53 3.06
864 947 5.408604 CCCTCCGTGTCATTACTATAAATGC 59.591 44.000 0.00 0.00 36.89 3.56
865 948 6.755206 TCCCTCCGTGTCATTACTATAAATG 58.245 40.000 0.00 0.00 38.05 2.32
866 949 6.553852 ACTCCCTCCGTGTCATTACTATAAAT 59.446 38.462 0.00 0.00 0.00 1.40
867 950 5.895534 ACTCCCTCCGTGTCATTACTATAAA 59.104 40.000 0.00 0.00 0.00 1.40
868 951 5.452255 ACTCCCTCCGTGTCATTACTATAA 58.548 41.667 0.00 0.00 0.00 0.98
870 953 3.912248 ACTCCCTCCGTGTCATTACTAT 58.088 45.455 0.00 0.00 0.00 2.12
871 954 3.377253 ACTCCCTCCGTGTCATTACTA 57.623 47.619 0.00 0.00 0.00 1.82
872 955 2.233305 ACTCCCTCCGTGTCATTACT 57.767 50.000 0.00 0.00 0.00 2.24
873 956 3.022406 AGTACTCCCTCCGTGTCATTAC 58.978 50.000 0.00 0.00 0.00 1.89
875 958 2.233305 AGTACTCCCTCCGTGTCATT 57.767 50.000 0.00 0.00 0.00 2.57
880 963 3.552875 TCAGAATAGTACTCCCTCCGTG 58.447 50.000 0.00 0.00 0.00 4.94
882 965 4.888239 TCTTTCAGAATAGTACTCCCTCCG 59.112 45.833 0.00 0.00 0.00 4.63
886 969 7.565680 TCCATTTCTTTCAGAATAGTACTCCC 58.434 38.462 0.00 0.00 33.67 4.30
929 1012 9.416794 CTGTTTTCGACAATCAGCTATATATCT 57.583 33.333 0.00 0.00 37.93 1.98
930 1013 9.411801 TCTGTTTTCGACAATCAGCTATATATC 57.588 33.333 8.24 0.00 37.93 1.63
1006 1093 1.337703 ACAGTTCGGCGTACAAGTACA 59.662 47.619 18.71 0.00 35.87 2.90
1012 1099 1.337703 AGTTGTACAGTTCGGCGTACA 59.662 47.619 18.71 10.95 44.64 2.90
1026 1114 1.885887 GCCACCATTGCTTCAGTTGTA 59.114 47.619 0.00 0.00 0.00 2.41
1031 1119 0.174845 CATGGCCACCATTGCTTCAG 59.825 55.000 8.16 0.00 42.23 3.02
1032 1120 1.259142 CCATGGCCACCATTGCTTCA 61.259 55.000 8.16 0.00 42.23 3.02
1084 1172 2.303175 GTACAAGGAGAGGAGCGAGAT 58.697 52.381 0.00 0.00 0.00 2.75
1089 1177 2.429250 GAGAAGGTACAAGGAGAGGAGC 59.571 54.545 0.00 0.00 0.00 4.70
1101 1189 1.135053 GCGAGGAGGTTGAGAAGGTAC 60.135 57.143 0.00 0.00 0.00 3.34
1419 1514 1.162800 GCTCCGTGGCCATGATCTTC 61.163 60.000 27.13 1.26 0.00 2.87
1458 1553 3.315142 GAGGTGGTGGAGCGCATCA 62.315 63.158 11.47 4.01 0.00 3.07
1908 2003 1.272784 TGAACTGCGAACGTAGCGTG 61.273 55.000 11.67 9.09 39.99 5.34
1920 2015 1.203313 GCGTGTTACCGTGAACTGC 59.797 57.895 0.00 0.27 0.00 4.40
1962 2060 4.695217 TGAGTTGAAACTGAAACACCAC 57.305 40.909 0.00 0.00 39.88 4.16
2023 2122 9.573166 CATGGAATCAATCAAAGGGTATACTAA 57.427 33.333 2.25 0.00 0.00 2.24
2026 2125 8.352942 GTTCATGGAATCAATCAAAGGGTATAC 58.647 37.037 0.00 0.00 0.00 1.47
2033 2132 4.107622 GCGGTTCATGGAATCAATCAAAG 58.892 43.478 0.00 0.00 0.00 2.77
2065 2165 0.323725 ATGTGCTTTGATTCCCGGCT 60.324 50.000 0.00 0.00 0.00 5.52
2072 2172 0.248289 GCTGGCCATGTGCTTTGATT 59.752 50.000 5.51 0.00 40.92 2.57
2143 2289 9.981114 TTGAAATAGCTATCTCGATCACAATTA 57.019 29.630 6.72 0.00 0.00 1.40
2332 2520 6.128007 GGATATGGGCGTCCTTAATGTTATTG 60.128 42.308 7.97 0.00 0.00 1.90
2333 2521 5.944007 GGATATGGGCGTCCTTAATGTTATT 59.056 40.000 7.97 0.00 0.00 1.40
2341 2529 1.053424 GGTGGATATGGGCGTCCTTA 58.947 55.000 7.97 5.71 35.49 2.69
2392 2758 1.375396 GCTCATGCCACACACGGTA 60.375 57.895 0.00 0.00 0.00 4.02
2431 2797 2.511659 TCTACTGTTCGCCTACACACT 58.488 47.619 0.00 0.00 0.00 3.55
2438 2804 1.679032 GGGCAATTCTACTGTTCGCCT 60.679 52.381 0.00 0.00 38.16 5.52
2605 3013 3.259374 CGGATAACTACATCTGCCATCCT 59.741 47.826 0.00 0.00 0.00 3.24
2714 3127 6.364976 TCACACACGACAACTATAGTTTGATG 59.635 38.462 15.60 13.16 35.83 3.07
2803 3852 6.441093 ACATACATGGCAACTGTGATTAAG 57.559 37.500 4.03 0.00 37.61 1.85
2890 3939 4.465886 ACATGGCAACTAGGTAAACACAA 58.534 39.130 0.00 0.00 37.61 3.33
2995 4125 2.361610 CTGCCCACACATCCACCC 60.362 66.667 0.00 0.00 0.00 4.61
3204 4859 3.486408 TGTTACGAAAACACTAACGCG 57.514 42.857 3.53 3.53 0.00 6.01
3292 5001 6.605194 TGGTGACAGCATATTTATTTGGCTTA 59.395 34.615 2.50 0.00 35.01 3.09
3503 5424 9.422681 GATATATATAGTACAGGGGCTCAAAGA 57.577 37.037 0.00 0.00 0.00 2.52
3557 6725 8.739039 GTGGATGCCATTATAATTATTGTGCTA 58.261 33.333 2.68 0.00 35.28 3.49
3729 6898 8.601476 CCGTACTTAGTTTTAGATGATTTGGTC 58.399 37.037 0.00 0.00 0.00 4.02
3928 7100 8.547894 CGTTGCATTATTGTACAAGAAGCTATA 58.452 33.333 24.39 14.52 0.00 1.31
3929 7101 7.279981 TCGTTGCATTATTGTACAAGAAGCTAT 59.720 33.333 24.39 9.00 0.00 2.97
3930 7102 6.592220 TCGTTGCATTATTGTACAAGAAGCTA 59.408 34.615 24.39 18.99 0.00 3.32
3931 7103 5.411361 TCGTTGCATTATTGTACAAGAAGCT 59.589 36.000 24.39 9.82 0.00 3.74
3939 7111 9.746711 GATATTCATCTCGTTGCATTATTGTAC 57.253 33.333 0.00 0.00 0.00 2.90
4050 7226 8.492673 TGTTGAATGTGGTATAGAAGAATCAC 57.507 34.615 0.00 0.00 0.00 3.06
4162 7360 1.342174 ACCAGCAGCAAACAAATCCTG 59.658 47.619 0.00 0.00 0.00 3.86
4263 7461 2.076100 CCGATAACTTGTGCAAGCTCA 58.924 47.619 11.43 0.00 41.99 4.26
4493 7691 5.006386 CAGGCATAAACTTCTCAGGTTCTT 58.994 41.667 0.00 0.00 30.24 2.52
4662 7860 1.558756 AGCTCAATGGGAAGACTCCAG 59.441 52.381 0.00 0.00 44.51 3.86
4690 7888 7.100068 ACTGATCTTCCATATCAATCCCATT 57.900 36.000 0.00 0.00 33.13 3.16
4897 8097 3.195396 TGGATAATGAAGGTGCAAAAGGC 59.805 43.478 0.00 0.00 45.13 4.35
5031 8263 5.649557 TCTGAAAATGTGTCAGTTTGGTTG 58.350 37.500 0.14 0.00 42.63 3.77
5060 8293 8.830201 TCTATGCAATATGCTTTGTTTGTTTT 57.170 26.923 3.78 0.00 45.31 2.43
5084 8317 7.824672 ACTTTCATGGTCAAAGATCTGAAATC 58.175 34.615 11.24 0.00 35.24 2.17
5150 8383 0.811616 GTAGCCTGGTTGATCGCCTG 60.812 60.000 7.51 6.81 0.00 4.85
5192 8425 6.540189 AGTTGACATCCTAATGTTGTATCTGC 59.460 38.462 0.00 0.00 46.20 4.26
5212 8445 6.946340 TCCAAAAGCATCATAGTCTAGTTGA 58.054 36.000 0.00 0.00 0.00 3.18
5247 8480 5.009010 AGCACTTTGACCTTGTGTATTTCTG 59.991 40.000 0.00 0.00 34.52 3.02
5362 8595 6.961359 TCTTAAGTGAACATGGTATTGTCG 57.039 37.500 1.63 0.00 0.00 4.35
5445 8678 2.926838 GTTTGTGATTGTTGTGCGGTTT 59.073 40.909 0.00 0.00 0.00 3.27
5450 8683 2.886081 TGGTGTTTGTGATTGTTGTGC 58.114 42.857 0.00 0.00 0.00 4.57
5462 8695 0.463204 TGGTGGCATGTTGGTGTTTG 59.537 50.000 0.00 0.00 0.00 2.93
5500 8733 2.030363 TGCCCGTAAGCAATGAACTTTG 60.030 45.455 0.00 0.00 40.56 2.77
5534 8767 7.462571 ACCCTGATTTTTATTTGGTCACTAC 57.537 36.000 0.00 0.00 0.00 2.73
5557 8790 5.392380 CCACAGATTGCCTCTCAACAATAAC 60.392 44.000 0.00 0.00 36.65 1.89
5635 8868 5.881637 GCAAAGTGCAAGTTAATTTTCGA 57.118 34.783 0.00 0.00 44.26 3.71
5659 8892 3.264964 AGGTAATTCGGGGCTAAAACAGA 59.735 43.478 0.00 0.00 0.00 3.41
5663 8896 5.176741 TGTAAGGTAATTCGGGGCTAAAA 57.823 39.130 0.00 0.00 0.00 1.52
5672 8905 5.018539 TGGACTCCATGTAAGGTAATTCG 57.981 43.478 0.00 0.00 0.00 3.34
5772 9011 9.694137 ACGAGCTATATATTAGACTTTTGGTTC 57.306 33.333 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.