Multiple sequence alignment - TraesCS5B01G457500

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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 TraesCS5B01G457500 chr5B 100.000 4076 0 0 1 4076 632125881 632129956 0.000000e+00 7528.0
1 TraesCS5B01G457500 chr5D 89.163 3165 272 32 566 3697 503470202 503473328 0.000000e+00 3879.0
2 TraesCS5B01G457500 chr5D 86.814 2404 258 34 633 3011 503502184 503504553 0.000000e+00 2628.0
3 TraesCS5B01G457500 chr5D 87.968 2244 235 19 788 3011 503431222 503433450 0.000000e+00 2615.0
4 TraesCS5B01G457500 chr5D 86.233 2397 299 19 630 3011 503641966 503644346 0.000000e+00 2569.0
5 TraesCS5B01G457500 chr5D 88.682 2041 214 9 880 2908 503651234 503653269 0.000000e+00 2473.0
6 TraesCS5B01G457500 chr5D 85.896 1177 112 27 397 1566 503635990 503637119 0.000000e+00 1205.0
7 TraesCS5B01G457500 chr5D 84.889 1211 149 20 1814 3011 503637112 503638301 0.000000e+00 1192.0
8 TraesCS5B01G457500 chr5D 84.070 973 141 10 2039 3001 503644445 503645413 0.000000e+00 926.0
9 TraesCS5B01G457500 chr5D 92.997 614 33 5 3093 3697 503654638 503655250 0.000000e+00 887.0
10 TraesCS5B01G457500 chr5D 88.594 377 22 12 3155 3530 503433593 503433949 4.840000e-119 438.0
11 TraesCS5B01G457500 chr5D 95.686 255 2 3 1 255 503469436 503469681 6.350000e-108 401.0
12 TraesCS5B01G457500 chr5D 82.803 314 21 17 284 565 503469660 503469972 2.430000e-62 250.0
13 TraesCS5B01G457500 chr5D 90.055 181 5 8 3884 4052 503655852 503656031 5.300000e-54 222.0
14 TraesCS5B01G457500 chr5D 90.698 86 4 1 3612 3697 503199641 503199722 1.200000e-20 111.0
15 TraesCS5B01G457500 chr5D 95.000 60 3 0 3031 3090 503433509 503433568 1.210000e-15 95.3
16 TraesCS5B01G457500 chr5A 89.182 2163 215 11 862 3011 631641593 631643749 0.000000e+00 2680.0
17 TraesCS5B01G457500 chr5A 85.888 2140 253 24 554 2683 631530332 631532432 0.000000e+00 2233.0
18 TraesCS5B01G457500 chr5A 89.423 1040 108 2 1499 2537 631629209 631630247 0.000000e+00 1310.0
19 TraesCS5B01G457500 chr5A 89.468 864 71 12 663 1521 631627295 631628143 0.000000e+00 1074.0
20 TraesCS5B01G457500 chr5A 76.131 884 195 15 998 1873 706436343 706437218 2.230000e-122 449.0
21 TraesCS5B01G457500 chr5A 94.737 285 15 0 3413 3697 631644668 631644384 1.040000e-120 444.0
22 TraesCS5B01G457500 chr5A 87.895 380 37 4 2573 2943 631654920 631654541 4.840000e-119 438.0
23 TraesCS5B01G457500 chr5A 86.753 385 30 7 3031 3409 631643808 631644177 3.790000e-110 409.0
24 TraesCS5B01G457500 chr5A 82.911 316 53 1 2602 2917 631630272 631630586 2.400000e-72 283.0
25 TraesCS5B01G457500 chr5A 85.663 279 23 7 3101 3373 631631883 631632150 1.120000e-70 278.0
26 TraesCS5B01G457500 chr2D 75.228 876 203 13 1049 1917 603129364 603128496 1.760000e-108 403.0
27 TraesCS5B01G457500 chr2D 97.297 37 1 0 61 97 66433999 66434035 3.400000e-06 63.9
28 TraesCS5B01G457500 chr7D 87.451 255 11 13 3742 3981 45271569 45271817 1.440000e-69 274.0
29 TraesCS5B01G457500 chr7D 86.260 262 17 13 3743 3987 44548239 44547980 2.420000e-67 267.0
30 TraesCS5B01G457500 chr7D 86.047 258 16 12 3742 3984 44702797 44702545 4.040000e-65 259.0
31 TraesCS5B01G457500 chr7D 85.417 240 16 11 3740 3964 44580232 44580467 8.810000e-57 231.0
32 TraesCS5B01G457500 chrUn 86.260 262 8 12 3739 3984 48984421 48984670 4.040000e-65 259.0
33 TraesCS5B01G457500 chr4A 87.554 233 16 10 3742 3964 656846961 656847190 1.450000e-64 257.0
34 TraesCS5B01G457500 chr4A 85.833 240 20 12 3742 3971 656816849 656817084 4.070000e-60 243.0
35 TraesCS5B01G457500 chr4A 90.244 123 6 5 3739 3859 656553554 656553672 5.450000e-34 156.0
36 TraesCS5B01G457500 chr4A 90.598 117 8 3 3742 3858 656475669 656475556 7.060000e-33 152.0
37 TraesCS5B01G457500 chr7A 84.337 249 27 11 3743 3987 46961857 46961617 2.450000e-57 233.0
38 TraesCS5B01G457500 chr7A 84.146 246 27 11 3743 3984 47498185 47498422 1.140000e-55 228.0
39 TraesCS5B01G457500 chr7A 92.308 117 3 4 3742 3858 46777875 46777765 1.170000e-35 161.0
40 TraesCS5B01G457500 chr6A 90.833 120 9 2 3743 3861 33302284 33302402 4.220000e-35 159.0
41 TraesCS5B01G457500 chr2A 94.444 72 4 0 50 121 47068861 47068790 1.200000e-20 111.0
42 TraesCS5B01G457500 chr2A 94.444 72 4 0 50 121 73495181 73495110 1.200000e-20 111.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G457500 chr5B 632125881 632129956 4075 False 7528.000000 7528 100.000000 1 4076 1 chr5B.!!$F1 4075
1 TraesCS5B01G457500 chr5D 503502184 503504553 2369 False 2628.000000 2628 86.814000 633 3011 1 chr5D.!!$F2 2378
2 TraesCS5B01G457500 chr5D 503469436 503473328 3892 False 1510.000000 3879 89.217333 1 3697 3 chr5D.!!$F4 3696
3 TraesCS5B01G457500 chr5D 503635990 503645413 9423 False 1473.000000 2569 85.272000 397 3011 4 chr5D.!!$F5 2614
4 TraesCS5B01G457500 chr5D 503651234 503656031 4797 False 1194.000000 2473 90.578000 880 4052 3 chr5D.!!$F6 3172
5 TraesCS5B01G457500 chr5D 503431222 503433949 2727 False 1049.433333 2615 90.520667 788 3530 3 chr5D.!!$F3 2742
6 TraesCS5B01G457500 chr5A 631530332 631532432 2100 False 2233.000000 2233 85.888000 554 2683 1 chr5A.!!$F1 2129
7 TraesCS5B01G457500 chr5A 631641593 631644177 2584 False 1544.500000 2680 87.967500 862 3409 2 chr5A.!!$F4 2547
8 TraesCS5B01G457500 chr5A 631627295 631632150 4855 False 736.250000 1310 86.866250 663 3373 4 chr5A.!!$F3 2710
9 TraesCS5B01G457500 chr5A 706436343 706437218 875 False 449.000000 449 76.131000 998 1873 1 chr5A.!!$F2 875
10 TraesCS5B01G457500 chr2D 603128496 603129364 868 True 403.000000 403 75.228000 1049 1917 1 chr2D.!!$R1 868

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
749 1021 0.473755 TTCAGCAACAAGAGGAGGCA 59.526 50.0 0.0 0.0 0.0 4.75 F
1631 8784 0.317854 GACCCTTTGTTTGCTCGCAC 60.318 55.0 0.0 0.0 0.0 5.34 F
1890 9043 0.331278 AAATGGATGGACGCCCTGAA 59.669 50.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2219 9378 0.037590 TGCCACCGCCACTATCTTTT 59.962 50.0 0.00 0.00 0.00 2.27 R
2522 10752 0.105593 CGTGCTATCCTGTGGCAGAT 59.894 55.0 0.00 0.00 45.61 2.90 R
3884 14520 0.036164 TACACCAGATGCGCTTTGGT 59.964 50.0 20.33 20.33 45.77 3.67 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 3.007290 TGATGCAGTCTTTGTCAGCTAGT 59.993 43.478 0.00 0.00 0.00 2.57
168 169 5.637006 TTGGCATATAACCAAACACAGTC 57.363 39.130 7.87 0.00 44.11 3.51
174 175 7.414098 GGCATATAACCAAACACAGTCAAGTAG 60.414 40.741 0.00 0.00 0.00 2.57
175 176 7.414098 GCATATAACCAAACACAGTCAAGTAGG 60.414 40.741 0.00 0.00 0.00 3.18
176 177 4.497291 AACCAAACACAGTCAAGTAGGA 57.503 40.909 0.00 0.00 0.00 2.94
177 178 4.073293 ACCAAACACAGTCAAGTAGGAG 57.927 45.455 0.00 0.00 0.00 3.69
178 179 3.454812 ACCAAACACAGTCAAGTAGGAGT 59.545 43.478 0.00 0.00 0.00 3.85
180 181 5.129815 ACCAAACACAGTCAAGTAGGAGTAA 59.870 40.000 0.00 0.00 0.00 2.24
181 182 6.183361 ACCAAACACAGTCAAGTAGGAGTAAT 60.183 38.462 0.00 0.00 0.00 1.89
182 183 6.710744 CCAAACACAGTCAAGTAGGAGTAATT 59.289 38.462 0.00 0.00 0.00 1.40
183 184 7.228706 CCAAACACAGTCAAGTAGGAGTAATTT 59.771 37.037 0.00 0.00 0.00 1.82
184 185 7.730364 AACACAGTCAAGTAGGAGTAATTTG 57.270 36.000 0.00 0.00 0.00 2.32
185 186 7.062749 ACACAGTCAAGTAGGAGTAATTTGA 57.937 36.000 0.00 0.00 0.00 2.69
186 187 7.680730 ACACAGTCAAGTAGGAGTAATTTGAT 58.319 34.615 0.00 0.00 31.28 2.57
187 188 8.812972 ACACAGTCAAGTAGGAGTAATTTGATA 58.187 33.333 0.00 0.00 31.28 2.15
188 189 9.088512 CACAGTCAAGTAGGAGTAATTTGATAC 57.911 37.037 0.00 0.00 31.28 2.24
254 255 8.534496 ACTTTACATACCAATACTCTTTACGGT 58.466 33.333 0.00 0.00 0.00 4.83
255 256 8.706492 TTTACATACCAATACTCTTTACGGTG 57.294 34.615 0.00 0.00 0.00 4.94
256 257 6.534475 ACATACCAATACTCTTTACGGTGA 57.466 37.500 0.00 0.00 0.00 4.02
257 258 6.938507 ACATACCAATACTCTTTACGGTGAA 58.061 36.000 0.00 0.00 0.00 3.18
258 259 7.039882 ACATACCAATACTCTTTACGGTGAAG 58.960 38.462 6.33 6.33 0.00 3.02
259 260 5.733620 ACCAATACTCTTTACGGTGAAGA 57.266 39.130 13.80 13.80 0.00 2.87
266 267 4.649977 CTCTTTACGGTGAAGAGTAGTCG 58.350 47.826 26.04 8.23 43.18 4.18
267 268 4.067896 TCTTTACGGTGAAGAGTAGTCGT 58.932 43.478 10.90 0.00 35.07 4.34
268 269 5.237815 TCTTTACGGTGAAGAGTAGTCGTA 58.762 41.667 10.90 0.00 32.94 3.43
269 270 5.349817 TCTTTACGGTGAAGAGTAGTCGTAG 59.650 44.000 10.90 0.00 35.14 3.51
270 271 3.325293 ACGGTGAAGAGTAGTCGTAGA 57.675 47.619 0.00 0.00 0.00 2.59
271 272 3.871485 ACGGTGAAGAGTAGTCGTAGAT 58.129 45.455 0.00 0.00 40.67 1.98
272 273 3.622163 ACGGTGAAGAGTAGTCGTAGATG 59.378 47.826 0.00 0.00 40.67 2.90
273 274 3.002451 CGGTGAAGAGTAGTCGTAGATGG 59.998 52.174 0.00 0.00 40.67 3.51
274 275 3.946558 GGTGAAGAGTAGTCGTAGATGGT 59.053 47.826 0.00 0.00 40.67 3.55
275 276 4.398673 GGTGAAGAGTAGTCGTAGATGGTT 59.601 45.833 0.00 0.00 40.67 3.67
276 277 5.333513 GTGAAGAGTAGTCGTAGATGGTTG 58.666 45.833 0.00 0.00 40.67 3.77
277 278 4.398358 TGAAGAGTAGTCGTAGATGGTTGG 59.602 45.833 0.00 0.00 40.67 3.77
278 279 3.965694 AGAGTAGTCGTAGATGGTTGGT 58.034 45.455 0.00 0.00 40.67 3.67
279 280 5.108187 AGAGTAGTCGTAGATGGTTGGTA 57.892 43.478 0.00 0.00 40.67 3.25
280 281 4.880696 AGAGTAGTCGTAGATGGTTGGTAC 59.119 45.833 0.00 0.00 40.67 3.34
281 282 3.950395 AGTAGTCGTAGATGGTTGGTACC 59.050 47.826 4.43 4.43 45.26 3.34
282 283 2.105766 AGTCGTAGATGGTTGGTACCC 58.894 52.381 10.07 0.00 44.35 3.69
283 284 1.826720 GTCGTAGATGGTTGGTACCCA 59.173 52.381 10.07 0.00 44.35 4.51
284 285 1.826720 TCGTAGATGGTTGGTACCCAC 59.173 52.381 10.07 8.74 44.35 4.61
285 286 1.551430 CGTAGATGGTTGGTACCCACA 59.449 52.381 17.32 10.17 44.35 4.17
286 287 2.169769 CGTAGATGGTTGGTACCCACAT 59.830 50.000 17.32 14.23 44.35 3.21
287 288 3.385433 CGTAGATGGTTGGTACCCACATA 59.615 47.826 17.32 6.61 44.35 2.29
288 289 3.926058 AGATGGTTGGTACCCACATAC 57.074 47.619 17.32 7.75 44.35 2.39
289 290 2.508300 AGATGGTTGGTACCCACATACC 59.492 50.000 17.32 12.74 44.35 2.73
298 299 5.625568 GGTACCCACATACCAATACTCTT 57.374 43.478 0.00 0.00 43.69 2.85
299 300 5.997843 GGTACCCACATACCAATACTCTTT 58.002 41.667 0.00 0.00 43.69 2.52
300 301 7.128234 GGTACCCACATACCAATACTCTTTA 57.872 40.000 0.00 0.00 43.69 1.85
301 302 6.988580 GGTACCCACATACCAATACTCTTTAC 59.011 42.308 0.00 0.00 43.69 2.01
302 303 5.667466 ACCCACATACCAATACTCTTTACG 58.333 41.667 0.00 0.00 0.00 3.18
303 304 5.054477 CCCACATACCAATACTCTTTACGG 58.946 45.833 0.00 0.00 0.00 4.02
336 337 0.807496 GTCAGAAAGCACCTGGATGC 59.193 55.000 0.00 6.93 46.50 3.91
343 344 2.758089 GCACCTGGATGCTGCTTCG 61.758 63.158 0.00 0.00 42.62 3.79
355 356 1.741993 CTGCTTCGTGTTTTGTTCCG 58.258 50.000 0.00 0.00 0.00 4.30
358 359 1.843753 GCTTCGTGTTTTGTTCCGTTG 59.156 47.619 0.00 0.00 0.00 4.10
363 364 2.538132 CGTGTTTTGTTCCGTTGTCTCC 60.538 50.000 0.00 0.00 0.00 3.71
384 385 3.439129 CCTTGGTAATGGAAGGTCGTTTC 59.561 47.826 0.00 0.00 35.01 2.78
385 386 2.690786 TGGTAATGGAAGGTCGTTTCG 58.309 47.619 0.00 0.00 0.00 3.46
390 391 4.483476 AATGGAAGGTCGTTTCGAAAAG 57.517 40.909 13.10 14.99 37.72 2.27
410 441 8.739461 CGAAAAGAAAAACAGTTAATACCACAC 58.261 33.333 0.00 0.00 0.00 3.82
422 453 7.061905 CAGTTAATACCACACTAGAACTGAACG 59.938 40.741 8.67 0.00 43.06 3.95
447 478 9.039870 CGATAATGATTTATCTTGCTATCTCCC 57.960 37.037 4.70 0.00 41.00 4.30
453 484 8.756927 TGATTTATCTTGCTATCTCCCATCTAG 58.243 37.037 0.00 0.00 0.00 2.43
454 485 8.677870 ATTTATCTTGCTATCTCCCATCTAGT 57.322 34.615 0.00 0.00 0.00 2.57
462 493 6.375736 TGCTATCTCCCATCTAGTATTTCGAG 59.624 42.308 0.00 0.00 0.00 4.04
491 522 1.224436 TGGATGCATTCCCTCCATCA 58.776 50.000 1.51 0.00 44.77 3.07
513 544 5.754406 TCAATGAAGTCCAGCAACAAAATTG 59.246 36.000 0.00 0.00 0.00 2.32
557 591 5.068987 TGCAAATTACTGAAGAAGCAACCTT 59.931 36.000 0.00 0.00 0.00 3.50
558 592 5.985530 GCAAATTACTGAAGAAGCAACCTTT 59.014 36.000 0.00 0.00 0.00 3.11
624 887 9.924010 ACCTAGAGAGTATGTTCTGTTATTAGT 57.076 33.333 0.00 0.00 0.00 2.24
699 970 8.154203 TGTGTTGGACTCAAATCAACTCTTATA 58.846 33.333 0.00 0.00 40.75 0.98
737 1009 2.371841 TCAGCTTCCTAACCTTCAGCAA 59.628 45.455 0.00 0.00 32.58 3.91
747 1019 1.072965 ACCTTCAGCAACAAGAGGAGG 59.927 52.381 0.00 0.00 0.00 4.30
748 1020 1.163554 CTTCAGCAACAAGAGGAGGC 58.836 55.000 0.00 0.00 0.00 4.70
749 1021 0.473755 TTCAGCAACAAGAGGAGGCA 59.526 50.000 0.00 0.00 0.00 4.75
782 1058 6.019398 GCAAACTACCTTTAAAAACGCACATT 60.019 34.615 0.00 0.00 0.00 2.71
802 1079 7.201574 GCACATTAATGGTTTCGTCAGTACATA 60.202 37.037 19.37 0.00 0.00 2.29
803 1080 8.328146 CACATTAATGGTTTCGTCAGTACATAG 58.672 37.037 19.37 0.00 0.00 2.23
804 1081 7.494625 ACATTAATGGTTTCGTCAGTACATAGG 59.505 37.037 19.37 0.00 0.00 2.57
805 1082 3.241067 TGGTTTCGTCAGTACATAGGC 57.759 47.619 0.00 0.00 0.00 3.93
807 1084 3.196901 TGGTTTCGTCAGTACATAGGCAT 59.803 43.478 0.00 0.00 0.00 4.40
809 1086 4.441634 GGTTTCGTCAGTACATAGGCATCT 60.442 45.833 0.00 0.00 0.00 2.90
810 1087 5.221185 GGTTTCGTCAGTACATAGGCATCTA 60.221 44.000 0.00 0.00 0.00 1.98
811 1088 6.270815 GTTTCGTCAGTACATAGGCATCTAA 58.729 40.000 0.00 0.00 0.00 2.10
824 1102 2.816087 GGCATCTAATATGTGGCCACAG 59.184 50.000 39.29 26.75 45.48 3.66
830 1108 2.645838 ATATGTGGCCACAGATCACC 57.354 50.000 39.29 11.77 45.48 4.02
837 1115 1.589716 GCCACAGATCACCTGCCAAC 61.590 60.000 0.00 0.00 46.81 3.77
896 1185 5.669477 ACTCTGGTTATCTGAGATTTGAGC 58.331 41.667 0.00 0.00 42.04 4.26
902 1191 5.006165 GGTTATCTGAGATTTGAGCTTCACG 59.994 44.000 0.00 0.00 0.00 4.35
904 1193 1.396301 CTGAGATTTGAGCTTCACGCC 59.604 52.381 0.00 0.00 40.39 5.68
915 1204 1.600413 GCTTCACGCCTTTGGAAACTG 60.600 52.381 0.00 0.00 0.00 3.16
950 1241 6.326323 TCAAGTCCATGTATCCAGCATACTAA 59.674 38.462 0.00 0.00 38.64 2.24
1100 1391 4.708726 ACATAAAATGCTTCACAGAGGC 57.291 40.909 0.00 0.00 35.17 4.70
1108 1399 1.269517 GCTTCACAGAGGCCGAGATAG 60.270 57.143 0.00 0.00 0.00 2.08
1213 1504 8.807667 AAGAATAGTTGCAGTCAAGAAATTTG 57.192 30.769 0.00 0.00 31.93 2.32
1248 1539 6.351711 AGAAGAAAATTTTGCCAAAGAGCTT 58.648 32.000 8.47 1.96 0.00 3.74
1293 1584 5.882557 CCACAAGAATGTAGTTAGGCTCATT 59.117 40.000 0.00 0.00 37.82 2.57
1393 7460 3.133183 CCATGAATGCATTCCCATCACAA 59.867 43.478 31.35 14.34 35.97 3.33
1569 8722 4.081697 TCAAGACTTGTCAACACAGACTCA 60.082 41.667 14.75 0.00 39.27 3.41
1570 8723 4.052159 AGACTTGTCAACACAGACTCAG 57.948 45.455 3.49 0.00 39.27 3.35
1631 8784 0.317854 GACCCTTTGTTTGCTCGCAC 60.318 55.000 0.00 0.00 0.00 5.34
1719 8872 7.875554 ACAAAGAAAAAGGCAACAGTAAGAAAA 59.124 29.630 0.00 0.00 41.41 2.29
1740 8893 0.759346 GGGAGACCGGCATAGTTGAT 59.241 55.000 0.00 0.00 43.64 2.57
1879 9032 7.101054 ACAATGTTTGAAGATGGAAATGGATG 58.899 34.615 0.00 0.00 0.00 3.51
1890 9043 0.331278 AAATGGATGGACGCCCTGAA 59.669 50.000 0.00 0.00 0.00 3.02
1944 9097 3.211045 TCGGAAAACTCAAGTTCAAGGG 58.789 45.455 0.00 0.00 37.25 3.95
1968 9127 6.408776 GGAAACAAACTATTTTTCCTTGGGGT 60.409 38.462 5.29 0.00 43.39 4.95
1997 9156 3.576004 GCCAGCAGCTCAGAACAG 58.424 61.111 0.00 0.00 38.99 3.16
2041 9200 1.188863 GCCACAATCTTTGCCATCCT 58.811 50.000 0.00 0.00 0.00 3.24
2066 9225 1.130561 GTGCCGCCATTTCTCACTTAC 59.869 52.381 0.00 0.00 0.00 2.34
2070 9229 3.334691 CCGCCATTTCTCACTTACAGAA 58.665 45.455 0.00 0.00 0.00 3.02
2082 9241 6.372659 TCTCACTTACAGAAATGAAATCAGCC 59.627 38.462 0.00 0.00 0.00 4.85
2087 9246 5.534207 ACAGAAATGAAATCAGCCACAAA 57.466 34.783 0.00 0.00 0.00 2.83
2133 9292 2.647299 TGGTGTGGGTGGATCTTGTAAT 59.353 45.455 0.00 0.00 0.00 1.89
2184 9343 0.451783 CCAAGGTGGCTATCAAACGC 59.548 55.000 0.00 0.00 0.00 4.84
2187 9346 1.743995 GGTGGCTATCAAACGCGGT 60.744 57.895 12.47 0.00 0.00 5.68
2200 9359 1.213013 CGCGGTAGAGTTCAGCAGT 59.787 57.895 0.00 0.00 0.00 4.40
2210 9369 3.005261 AGAGTTCAGCAGTGTGTGAGTAG 59.995 47.826 0.00 0.00 0.00 2.57
2211 9370 2.959030 AGTTCAGCAGTGTGTGAGTAGA 59.041 45.455 0.00 0.00 0.00 2.59
2214 9373 3.917988 TCAGCAGTGTGTGAGTAGATTG 58.082 45.455 0.00 0.00 0.00 2.67
2217 9376 4.751600 CAGCAGTGTGTGAGTAGATTGAAA 59.248 41.667 0.00 0.00 0.00 2.69
2218 9377 4.993584 AGCAGTGTGTGAGTAGATTGAAAG 59.006 41.667 0.00 0.00 0.00 2.62
2219 9378 4.991056 GCAGTGTGTGAGTAGATTGAAAGA 59.009 41.667 0.00 0.00 0.00 2.52
2230 9389 9.658799 TGAGTAGATTGAAAGAAAAGATAGTGG 57.341 33.333 0.00 0.00 0.00 4.00
2233 9392 5.355350 AGATTGAAAGAAAAGATAGTGGCGG 59.645 40.000 0.00 0.00 0.00 6.13
2283 9442 0.865769 CACTGGTCGGTTACTGCAAC 59.134 55.000 0.00 0.00 36.32 4.17
2313 9472 6.862711 AACGAGATGATACTGATCTACGAA 57.137 37.500 0.00 0.00 32.79 3.85
2361 9520 5.585445 TGAGAACCTTTACGCTAACAAAACA 59.415 36.000 0.00 0.00 0.00 2.83
2522 10752 5.636123 TGGCAAGGTTCCAATTAAAGTCTA 58.364 37.500 0.00 0.00 0.00 2.59
2544 10774 2.203070 CCACAGGATAGCACGGGC 60.203 66.667 0.00 0.00 41.61 6.13
2683 10919 0.533531 TGCTCGGGCTGCTTATGATG 60.534 55.000 9.62 0.00 39.59 3.07
2770 11006 3.397482 CTTGATCTGATTGTCGATCCCC 58.603 50.000 0.00 0.00 36.15 4.81
2798 11034 1.706287 GGAAAGATTGCTCCGCGGTC 61.706 60.000 27.15 18.51 0.00 4.79
2876 11112 2.162408 GCCCTACAATGCAAGAAGTGTC 59.838 50.000 0.00 0.00 0.00 3.67
2898 11134 2.103094 TGAGAACCTGGAGTTGTGTCTG 59.897 50.000 0.00 0.00 39.40 3.51
2980 12228 1.166531 AAGGACAGAACGTTGGCTGC 61.167 55.000 5.00 4.40 35.57 5.25
3004 12252 3.191371 CCTGGAGATGTACCTTGCAAAAC 59.809 47.826 0.00 0.00 0.00 2.43
3016 12264 1.850377 TGCAAAACACGATGCTTTGG 58.150 45.000 12.49 2.14 42.97 3.28
3023 12271 1.812571 ACACGATGCTTTGGAATGGTC 59.187 47.619 0.00 0.00 0.00 4.02
3025 12273 3.270027 CACGATGCTTTGGAATGGTCTA 58.730 45.455 0.00 0.00 0.00 2.59
3027 12275 2.874701 CGATGCTTTGGAATGGTCTAGG 59.125 50.000 0.00 0.00 0.00 3.02
3028 12276 3.432186 CGATGCTTTGGAATGGTCTAGGA 60.432 47.826 0.00 0.00 0.00 2.94
3032 12603 3.067320 GCTTTGGAATGGTCTAGGAATGC 59.933 47.826 0.00 0.00 0.00 3.56
3061 12636 2.290641 GTGGATTCCGATTCCGAATTGG 59.709 50.000 18.42 18.42 42.85 3.16
3109 12685 1.068541 GCCGAAGTGGTCACCAATTTC 60.069 52.381 11.61 11.20 42.06 2.17
3116 12692 4.172807 AGTGGTCACCAATTTCCCTACTA 58.827 43.478 0.00 0.00 34.18 1.82
3129 12705 8.370940 CAATTTCCCTACTATCAATGCTCTCTA 58.629 37.037 0.00 0.00 0.00 2.43
3131 12707 6.207509 TCCCTACTATCAATGCTCTCTACT 57.792 41.667 0.00 0.00 0.00 2.57
3133 12709 5.417580 CCCTACTATCAATGCTCTCTACTCC 59.582 48.000 0.00 0.00 0.00 3.85
3134 12710 6.007076 CCTACTATCAATGCTCTCTACTCCA 58.993 44.000 0.00 0.00 0.00 3.86
3135 12711 5.782893 ACTATCAATGCTCTCTACTCCAC 57.217 43.478 0.00 0.00 0.00 4.02
3136 12712 5.454062 ACTATCAATGCTCTCTACTCCACT 58.546 41.667 0.00 0.00 0.00 4.00
3137 12713 4.669206 ATCAATGCTCTCTACTCCACTG 57.331 45.455 0.00 0.00 0.00 3.66
3138 12714 3.701664 TCAATGCTCTCTACTCCACTGA 58.298 45.455 0.00 0.00 0.00 3.41
3139 12715 3.445450 TCAATGCTCTCTACTCCACTGAC 59.555 47.826 0.00 0.00 0.00 3.51
3140 12716 1.454201 TGCTCTCTACTCCACTGACG 58.546 55.000 0.00 0.00 0.00 4.35
3141 12717 0.736053 GCTCTCTACTCCACTGACGG 59.264 60.000 0.00 0.00 0.00 4.79
3184 13548 8.623903 CCATACATGTATACTGCAATTTCTGTT 58.376 33.333 17.86 0.00 0.00 3.16
3218 13582 8.447787 TTCTGAAGCGAGTATTTTATTTTTGC 57.552 30.769 0.00 0.00 0.00 3.68
3259 13629 4.783242 CTTTTCGTTATCAGGGTGTTGTG 58.217 43.478 0.00 0.00 0.00 3.33
3307 13678 7.604164 CCTGCACTATTATTATGTCCTGTTAGG 59.396 40.741 0.00 0.00 36.46 2.69
3366 13747 5.357878 TCATTATGCATGAAACTGGTTCCTC 59.642 40.000 10.16 0.00 39.11 3.71
3409 13793 7.511959 AAGACATTATCGATAGTGCTCTACA 57.488 36.000 23.38 0.00 37.40 2.74
3697 14081 2.165030 CGCCTGCTCAATCTTCCATTTT 59.835 45.455 0.00 0.00 0.00 1.82
3699 14083 3.446516 GCCTGCTCAATCTTCCATTTTCT 59.553 43.478 0.00 0.00 0.00 2.52
3700 14084 4.439837 GCCTGCTCAATCTTCCATTTTCTC 60.440 45.833 0.00 0.00 0.00 2.87
3701 14085 4.703575 CCTGCTCAATCTTCCATTTTCTCA 59.296 41.667 0.00 0.00 0.00 3.27
3703 14087 5.319453 TGCTCAATCTTCCATTTTCTCAGT 58.681 37.500 0.00 0.00 0.00 3.41
3704 14088 5.413833 TGCTCAATCTTCCATTTTCTCAGTC 59.586 40.000 0.00 0.00 0.00 3.51
3705 14089 5.413833 GCTCAATCTTCCATTTTCTCAGTCA 59.586 40.000 0.00 0.00 0.00 3.41
3708 14092 7.000472 TCAATCTTCCATTTTCTCAGTCAGTT 59.000 34.615 0.00 0.00 0.00 3.16
3709 14093 6.814506 ATCTTCCATTTTCTCAGTCAGTTG 57.185 37.500 0.00 0.00 0.00 3.16
3710 14094 5.928976 TCTTCCATTTTCTCAGTCAGTTGA 58.071 37.500 0.00 0.00 0.00 3.18
3711 14095 6.356556 TCTTCCATTTTCTCAGTCAGTTGAA 58.643 36.000 0.00 0.00 0.00 2.69
3712 14096 6.484643 TCTTCCATTTTCTCAGTCAGTTGAAG 59.515 38.462 0.00 0.00 0.00 3.02
3715 14099 6.931281 TCCATTTTCTCAGTCAGTTGAAGTAG 59.069 38.462 0.00 0.00 0.00 2.57
3718 14102 5.854010 TTCTCAGTCAGTTGAAGTAGTGT 57.146 39.130 0.00 0.00 0.00 3.55
3720 14104 5.592054 TCTCAGTCAGTTGAAGTAGTGTTG 58.408 41.667 0.00 0.00 0.00 3.33
3721 14105 5.127194 TCTCAGTCAGTTGAAGTAGTGTTGT 59.873 40.000 0.00 0.00 0.00 3.32
3723 14107 5.105513 TCAGTCAGTTGAAGTAGTGTTGTCA 60.106 40.000 0.00 0.00 0.00 3.58
3724 14108 5.580691 CAGTCAGTTGAAGTAGTGTTGTCAA 59.419 40.000 0.00 0.00 0.00 3.18
3725 14109 6.258727 CAGTCAGTTGAAGTAGTGTTGTCAAT 59.741 38.462 0.00 0.00 32.93 2.57
3726 14110 6.823689 AGTCAGTTGAAGTAGTGTTGTCAATT 59.176 34.615 0.00 0.00 32.93 2.32
3727 14111 7.336931 AGTCAGTTGAAGTAGTGTTGTCAATTT 59.663 33.333 0.00 0.00 32.93 1.82
3729 14113 6.628856 CAGTTGAAGTAGTGTTGTCAATTTCG 59.371 38.462 0.00 0.00 32.93 3.46
3730 14114 6.315393 AGTTGAAGTAGTGTTGTCAATTTCGT 59.685 34.615 0.00 0.00 32.93 3.85
3731 14115 6.281848 TGAAGTAGTGTTGTCAATTTCGTC 57.718 37.500 0.00 0.00 0.00 4.20
3734 14118 6.092955 AGTAGTGTTGTCAATTTCGTCCTA 57.907 37.500 0.00 0.00 0.00 2.94
3735 14119 5.924825 AGTAGTGTTGTCAATTTCGTCCTAC 59.075 40.000 0.00 0.00 0.00 3.18
3736 14120 4.957296 AGTGTTGTCAATTTCGTCCTACT 58.043 39.130 0.00 0.00 0.00 2.57
3737 14121 4.989168 AGTGTTGTCAATTTCGTCCTACTC 59.011 41.667 0.00 0.00 0.00 2.59
3738 14122 4.748102 GTGTTGTCAATTTCGTCCTACTCA 59.252 41.667 0.00 0.00 0.00 3.41
3739 14123 5.408604 GTGTTGTCAATTTCGTCCTACTCAT 59.591 40.000 0.00 0.00 0.00 2.90
3740 14124 5.995282 TGTTGTCAATTTCGTCCTACTCATT 59.005 36.000 0.00 0.00 0.00 2.57
3815 14451 1.481871 TCGATACCCCACTTCTCCAC 58.518 55.000 0.00 0.00 0.00 4.02
3816 14452 1.006758 TCGATACCCCACTTCTCCACT 59.993 52.381 0.00 0.00 0.00 4.00
3817 14453 1.409427 CGATACCCCACTTCTCCACTC 59.591 57.143 0.00 0.00 0.00 3.51
3818 14454 1.763545 GATACCCCACTTCTCCACTCC 59.236 57.143 0.00 0.00 0.00 3.85
3819 14455 0.790993 TACCCCACTTCTCCACTCCT 59.209 55.000 0.00 0.00 0.00 3.69
3820 14456 0.104409 ACCCCACTTCTCCACTCCTT 60.104 55.000 0.00 0.00 0.00 3.36
3821 14457 0.615850 CCCCACTTCTCCACTCCTTC 59.384 60.000 0.00 0.00 0.00 3.46
3822 14458 1.650528 CCCACTTCTCCACTCCTTCT 58.349 55.000 0.00 0.00 0.00 2.85
3823 14459 1.981495 CCCACTTCTCCACTCCTTCTT 59.019 52.381 0.00 0.00 0.00 2.52
3824 14460 2.373502 CCCACTTCTCCACTCCTTCTTT 59.626 50.000 0.00 0.00 0.00 2.52
3825 14461 3.181439 CCCACTTCTCCACTCCTTCTTTT 60.181 47.826 0.00 0.00 0.00 2.27
3826 14462 4.464947 CCACTTCTCCACTCCTTCTTTTT 58.535 43.478 0.00 0.00 0.00 1.94
3862 14498 7.945033 TTTTGTTTTTGCAGATCTGAATACC 57.055 32.000 27.04 8.57 0.00 2.73
3863 14499 6.647334 TTGTTTTTGCAGATCTGAATACCA 57.353 33.333 27.04 11.23 0.00 3.25
3866 14502 6.922957 TGTTTTTGCAGATCTGAATACCAAAC 59.077 34.615 27.04 19.63 0.00 2.93
3867 14503 6.647334 TTTTGCAGATCTGAATACCAAACA 57.353 33.333 27.04 8.27 0.00 2.83
3868 14504 5.627499 TTGCAGATCTGAATACCAAACAC 57.373 39.130 27.04 4.35 0.00 3.32
3869 14505 4.009675 TGCAGATCTGAATACCAAACACC 58.990 43.478 27.04 4.14 0.00 4.16
3871 14507 4.458989 GCAGATCTGAATACCAAACACCAA 59.541 41.667 27.04 0.00 0.00 3.67
3872 14508 5.048083 GCAGATCTGAATACCAAACACCAAA 60.048 40.000 27.04 0.00 0.00 3.28
3873 14509 6.516527 GCAGATCTGAATACCAAACACCAAAA 60.517 38.462 27.04 0.00 0.00 2.44
3874 14510 7.432869 CAGATCTGAATACCAAACACCAAAAA 58.567 34.615 18.34 0.00 0.00 1.94
3976 14792 6.183360 TGGATGCGCATTTATTTTCTCATCTT 60.183 34.615 26.12 0.00 32.19 2.40
3977 14793 6.698766 GGATGCGCATTTATTTTCTCATCTTT 59.301 34.615 26.12 0.00 32.19 2.52
3979 14795 7.887996 TGCGCATTTATTTTCTCATCTTTTT 57.112 28.000 5.66 0.00 0.00 1.94
4035 14859 3.139603 TGACGCACGATCGATTTCTTA 57.860 42.857 24.34 0.00 0.00 2.10
4046 14870 5.276114 CGATCGATTTCTTACTCTGCTGTTG 60.276 44.000 10.26 0.00 0.00 3.33
4048 14872 5.297547 TCGATTTCTTACTCTGCTGTTGTT 58.702 37.500 0.00 0.00 0.00 2.83
4049 14873 5.177511 TCGATTTCTTACTCTGCTGTTGTTG 59.822 40.000 0.00 0.00 0.00 3.33
4051 14875 6.511767 CGATTTCTTACTCTGCTGTTGTTGTT 60.512 38.462 0.00 0.00 0.00 2.83
4052 14876 5.734855 TTCTTACTCTGCTGTTGTTGTTC 57.265 39.130 0.00 0.00 0.00 3.18
4053 14877 5.023533 TCTTACTCTGCTGTTGTTGTTCT 57.976 39.130 0.00 0.00 0.00 3.01
4054 14878 5.428253 TCTTACTCTGCTGTTGTTGTTCTT 58.572 37.500 0.00 0.00 0.00 2.52
4055 14879 5.294306 TCTTACTCTGCTGTTGTTGTTCTTG 59.706 40.000 0.00 0.00 0.00 3.02
4056 14880 3.347216 ACTCTGCTGTTGTTGTTCTTGT 58.653 40.909 0.00 0.00 0.00 3.16
4057 14881 3.758554 ACTCTGCTGTTGTTGTTCTTGTT 59.241 39.130 0.00 0.00 0.00 2.83
4058 14882 4.095410 TCTGCTGTTGTTGTTCTTGTTG 57.905 40.909 0.00 0.00 0.00 3.33
4059 14883 3.505680 TCTGCTGTTGTTGTTCTTGTTGT 59.494 39.130 0.00 0.00 0.00 3.32
4060 14884 4.697828 TCTGCTGTTGTTGTTCTTGTTGTA 59.302 37.500 0.00 0.00 0.00 2.41
4061 14885 5.356751 TCTGCTGTTGTTGTTCTTGTTGTAT 59.643 36.000 0.00 0.00 0.00 2.29
4062 14886 5.960113 TGCTGTTGTTGTTCTTGTTGTATT 58.040 33.333 0.00 0.00 0.00 1.89
4063 14887 6.393990 TGCTGTTGTTGTTCTTGTTGTATTT 58.606 32.000 0.00 0.00 0.00 1.40
4064 14888 6.309980 TGCTGTTGTTGTTCTTGTTGTATTTG 59.690 34.615 0.00 0.00 0.00 2.32
4065 14889 6.310224 GCTGTTGTTGTTCTTGTTGTATTTGT 59.690 34.615 0.00 0.00 0.00 2.83
4066 14890 7.148656 GCTGTTGTTGTTCTTGTTGTATTTGTT 60.149 33.333 0.00 0.00 0.00 2.83
4067 14891 8.594881 TGTTGTTGTTCTTGTTGTATTTGTTT 57.405 26.923 0.00 0.00 0.00 2.83
4068 14892 9.046296 TGTTGTTGTTCTTGTTGTATTTGTTTT 57.954 25.926 0.00 0.00 0.00 2.43
4069 14893 9.871299 GTTGTTGTTCTTGTTGTATTTGTTTTT 57.129 25.926 0.00 0.00 0.00 1.94
4071 14895 9.261180 TGTTGTTCTTGTTGTATTTGTTTTTCA 57.739 25.926 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 5.534278 TGCACTTCAGTAATGAATTTCACCA 59.466 36.000 6.00 0.00 0.00 4.17
180 181 7.341256 TCGGACCAGTAAAGAGTAGTATCAAAT 59.659 37.037 0.00 0.00 0.00 2.32
181 182 6.660521 TCGGACCAGTAAAGAGTAGTATCAAA 59.339 38.462 0.00 0.00 0.00 2.69
182 183 6.182627 TCGGACCAGTAAAGAGTAGTATCAA 58.817 40.000 0.00 0.00 0.00 2.57
183 184 5.748402 TCGGACCAGTAAAGAGTAGTATCA 58.252 41.667 0.00 0.00 0.00 2.15
184 185 6.459435 GGTTCGGACCAGTAAAGAGTAGTATC 60.459 46.154 8.43 0.00 45.77 2.24
185 186 5.359292 GGTTCGGACCAGTAAAGAGTAGTAT 59.641 44.000 8.43 0.00 45.77 2.12
186 187 4.702131 GGTTCGGACCAGTAAAGAGTAGTA 59.298 45.833 8.43 0.00 45.77 1.82
187 188 3.509184 GGTTCGGACCAGTAAAGAGTAGT 59.491 47.826 8.43 0.00 45.77 2.73
188 189 4.107363 GGTTCGGACCAGTAAAGAGTAG 57.893 50.000 8.43 0.00 45.77 2.57
213 214 9.158233 GGTATGTAAAGTGTGAGTAGCATTTTA 57.842 33.333 0.00 0.00 30.43 1.52
254 255 4.398358 CCAACCATCTACGACTACTCTTCA 59.602 45.833 0.00 0.00 0.00 3.02
255 256 4.398673 ACCAACCATCTACGACTACTCTTC 59.601 45.833 0.00 0.00 0.00 2.87
256 257 4.342359 ACCAACCATCTACGACTACTCTT 58.658 43.478 0.00 0.00 0.00 2.85
257 258 3.965694 ACCAACCATCTACGACTACTCT 58.034 45.455 0.00 0.00 0.00 3.24
258 259 4.036144 GGTACCAACCATCTACGACTACTC 59.964 50.000 7.15 0.00 45.98 2.59
259 260 3.950395 GGTACCAACCATCTACGACTACT 59.050 47.826 7.15 0.00 45.98 2.57
260 261 4.298744 GGTACCAACCATCTACGACTAC 57.701 50.000 7.15 0.00 45.98 2.73
277 278 6.698766 CGTAAAGAGTATTGGTATGTGGGTAC 59.301 42.308 0.00 0.00 0.00 3.34
278 279 6.183360 CCGTAAAGAGTATTGGTATGTGGGTA 60.183 42.308 0.00 0.00 0.00 3.69
279 280 5.395990 CCGTAAAGAGTATTGGTATGTGGGT 60.396 44.000 0.00 0.00 0.00 4.51
280 281 5.054477 CCGTAAAGAGTATTGGTATGTGGG 58.946 45.833 0.00 0.00 0.00 4.61
281 282 5.667466 ACCGTAAAGAGTATTGGTATGTGG 58.333 41.667 0.00 0.00 0.00 4.17
282 283 8.882415 AATACCGTAAAGAGTATTGGTATGTG 57.118 34.615 2.74 0.00 40.74 3.21
283 284 8.146412 GGAATACCGTAAAGAGTATTGGTATGT 58.854 37.037 2.74 0.00 40.74 2.29
284 285 8.365647 AGGAATACCGTAAAGAGTATTGGTATG 58.634 37.037 2.74 0.00 40.74 2.39
285 286 8.488308 AGGAATACCGTAAAGAGTATTGGTAT 57.512 34.615 0.42 0.00 42.79 2.73
286 287 7.902920 AGGAATACCGTAAAGAGTATTGGTA 57.097 36.000 0.42 0.00 38.86 3.25
287 288 6.803366 AGGAATACCGTAAAGAGTATTGGT 57.197 37.500 0.42 0.00 38.86 3.67
288 289 8.502105 AAAAGGAATACCGTAAAGAGTATTGG 57.498 34.615 0.42 0.00 38.86 3.16
289 290 8.610035 GGAAAAGGAATACCGTAAAGAGTATTG 58.390 37.037 0.42 0.00 38.86 1.90
290 291 8.546322 AGGAAAAGGAATACCGTAAAGAGTATT 58.454 33.333 0.00 0.00 40.88 1.89
291 292 7.985752 CAGGAAAAGGAATACCGTAAAGAGTAT 59.014 37.037 0.00 0.00 41.83 2.12
292 293 7.038799 ACAGGAAAAGGAATACCGTAAAGAGTA 60.039 37.037 0.00 0.00 41.83 2.59
293 294 6.171213 CAGGAAAAGGAATACCGTAAAGAGT 58.829 40.000 0.00 0.00 41.83 3.24
294 295 6.171213 ACAGGAAAAGGAATACCGTAAAGAG 58.829 40.000 0.00 0.00 41.83 2.85
295 296 6.117975 ACAGGAAAAGGAATACCGTAAAGA 57.882 37.500 0.00 0.00 41.83 2.52
296 297 5.935789 TGACAGGAAAAGGAATACCGTAAAG 59.064 40.000 0.00 0.00 41.83 1.85
297 298 5.867330 TGACAGGAAAAGGAATACCGTAAA 58.133 37.500 0.00 0.00 41.83 2.01
298 299 5.246656 TCTGACAGGAAAAGGAATACCGTAA 59.753 40.000 1.81 0.00 41.83 3.18
299 300 4.773674 TCTGACAGGAAAAGGAATACCGTA 59.226 41.667 1.81 0.00 41.83 4.02
300 301 3.581332 TCTGACAGGAAAAGGAATACCGT 59.419 43.478 1.81 0.00 41.83 4.83
301 302 4.202245 TCTGACAGGAAAAGGAATACCG 57.798 45.455 1.81 0.00 41.83 4.02
302 303 5.106118 GCTTTCTGACAGGAAAAGGAATACC 60.106 44.000 14.96 0.00 35.22 2.73
303 304 5.473504 TGCTTTCTGACAGGAAAAGGAATAC 59.526 40.000 14.96 3.11 35.22 1.89
336 337 1.063469 ACGGAACAAAACACGAAGCAG 59.937 47.619 0.00 0.00 0.00 4.24
343 344 2.681344 AGGAGACAACGGAACAAAACAC 59.319 45.455 0.00 0.00 0.00 3.32
355 356 4.010349 CCTTCCATTACCAAGGAGACAAC 58.990 47.826 0.00 0.00 41.74 3.32
358 359 3.679083 CGACCTTCCATTACCAAGGAGAC 60.679 52.174 4.71 0.00 41.74 3.36
363 364 3.124636 CGAAACGACCTTCCATTACCAAG 59.875 47.826 0.00 0.00 0.00 3.61
384 385 8.739461 GTGTGGTATTAACTGTTTTTCTTTTCG 58.261 33.333 0.00 0.00 0.00 3.46
385 386 9.797556 AGTGTGGTATTAACTGTTTTTCTTTTC 57.202 29.630 0.00 0.00 0.00 2.29
390 391 9.874215 GTTCTAGTGTGGTATTAACTGTTTTTC 57.126 33.333 0.00 0.00 0.00 2.29
422 453 9.896645 TGGGAGATAGCAAGATAAATCATTATC 57.103 33.333 1.26 1.26 45.17 1.75
447 478 8.920665 CATAAGGAAAGCTCGAAATACTAGATG 58.079 37.037 0.00 0.00 0.00 2.90
491 522 5.916318 TCAATTTTGTTGCTGGACTTCATT 58.084 33.333 0.00 0.00 0.00 2.57
623 886 7.067859 GGACTTCCCCCATTTAATAACTGTTAC 59.932 40.741 1.73 0.00 0.00 2.50
624 887 7.120716 GGACTTCCCCCATTTAATAACTGTTA 58.879 38.462 2.26 2.26 0.00 2.41
625 888 5.955959 GGACTTCCCCCATTTAATAACTGTT 59.044 40.000 0.00 0.00 0.00 3.16
626 889 5.015817 TGGACTTCCCCCATTTAATAACTGT 59.984 40.000 0.00 0.00 34.29 3.55
627 890 5.515106 TGGACTTCCCCCATTTAATAACTG 58.485 41.667 0.00 0.00 34.29 3.16
628 891 5.766590 CTGGACTTCCCCCATTTAATAACT 58.233 41.667 0.00 0.00 32.49 2.24
629 892 4.341235 GCTGGACTTCCCCCATTTAATAAC 59.659 45.833 0.00 0.00 32.49 1.89
630 893 4.017037 TGCTGGACTTCCCCCATTTAATAA 60.017 41.667 0.00 0.00 32.49 1.40
631 894 3.529734 TGCTGGACTTCCCCCATTTAATA 59.470 43.478 0.00 0.00 32.49 0.98
634 897 1.005450 GTGCTGGACTTCCCCCATTTA 59.995 52.381 0.00 0.00 32.49 1.40
699 970 5.134725 AGCTGATCAAAAGATGGGGTAAT 57.865 39.130 0.00 0.00 0.00 1.89
719 991 2.504367 TGTTGCTGAAGGTTAGGAAGC 58.496 47.619 0.00 0.00 0.00 3.86
737 1009 3.026694 GCCATAAAATGCCTCCTCTTGT 58.973 45.455 0.00 0.00 0.00 3.16
747 1019 8.541133 TTTAAAGGTAGTTTGCCATAAAATGC 57.459 30.769 0.00 0.00 0.00 3.56
782 1058 5.105269 TGCCTATGTACTGACGAAACCATTA 60.105 40.000 0.00 0.00 0.00 1.90
802 1079 2.442878 TGTGGCCACATATTAGATGCCT 59.557 45.455 34.74 0.00 39.60 4.75
803 1080 2.816087 CTGTGGCCACATATTAGATGCC 59.184 50.000 37.66 6.61 41.01 4.40
804 1081 3.743521 TCTGTGGCCACATATTAGATGC 58.256 45.455 37.66 6.84 41.01 3.91
805 1082 5.410746 GTGATCTGTGGCCACATATTAGATG 59.589 44.000 37.66 23.12 41.01 2.90
807 1084 4.202357 GGTGATCTGTGGCCACATATTAGA 60.202 45.833 37.66 29.37 41.01 2.10
809 1086 3.716353 AGGTGATCTGTGGCCACATATTA 59.284 43.478 37.66 28.25 41.01 0.98
810 1087 2.511218 AGGTGATCTGTGGCCACATATT 59.489 45.455 37.66 24.54 41.01 1.28
811 1088 2.130193 AGGTGATCTGTGGCCACATAT 58.870 47.619 37.66 33.93 41.01 1.78
824 1102 1.838112 TCAATGGTTGGCAGGTGATC 58.162 50.000 0.00 0.00 0.00 2.92
830 1108 1.546923 TGCAGAATCAATGGTTGGCAG 59.453 47.619 0.00 0.00 0.00 4.85
837 1115 5.021033 AGAGTACTCTGCAGAATCAATGG 57.979 43.478 24.62 6.60 38.75 3.16
896 1185 1.676006 ACAGTTTCCAAAGGCGTGAAG 59.324 47.619 0.00 0.00 0.00 3.02
902 1191 3.871006 CCTGAAAAACAGTTTCCAAAGGC 59.129 43.478 0.00 0.00 44.40 4.35
904 1193 5.719173 TGACCTGAAAAACAGTTTCCAAAG 58.281 37.500 0.00 0.00 44.40 2.77
915 1204 4.918810 ACATGGACTTGACCTGAAAAAC 57.081 40.909 0.00 0.00 0.00 2.43
950 1241 7.283580 AGACTGAGTATAACAGTTAGCTTCGAT 59.716 37.037 12.88 0.00 0.00 3.59
1100 1391 4.039245 TGCTGGTAATTCTTCCTATCTCGG 59.961 45.833 0.00 0.00 0.00 4.63
1108 1399 7.121315 AGTTTCATAGTTGCTGGTAATTCTTCC 59.879 37.037 0.00 0.00 0.00 3.46
1213 1504 8.699749 GGCAAAATTTTCTTCTACATTACACAC 58.300 33.333 0.00 0.00 0.00 3.82
1248 1539 5.298276 GTGGTTGATTTCACAGTGGACTTTA 59.702 40.000 0.00 0.00 34.32 1.85
1393 7460 2.866156 CAATTCGCAGTCGTGTATCCAT 59.134 45.455 0.00 0.00 36.96 3.41
1569 8722 1.202976 ACATGCTCAGTGAAAAGGGCT 60.203 47.619 0.00 0.00 0.00 5.19
1570 8723 1.251251 ACATGCTCAGTGAAAAGGGC 58.749 50.000 0.00 0.00 0.00 5.19
1631 8784 3.818121 TTTGTGGTGAGACGCCCGG 62.818 63.158 0.00 0.00 32.22 5.73
1645 8798 6.238374 CCGAAACTGTAAACATCACTCTTTGT 60.238 38.462 0.00 0.00 0.00 2.83
1719 8872 1.003051 AACTATGCCGGTCTCCCCT 59.997 57.895 1.90 0.00 0.00 4.79
1740 8893 2.957680 TGCAAGAGCTTGGATGAAACAA 59.042 40.909 11.78 0.00 42.74 2.83
1879 9032 0.537188 TCTCTCATTTCAGGGCGTCC 59.463 55.000 0.00 0.00 0.00 4.79
1890 9043 2.027745 ACGTTCTGCCACATCTCTCATT 60.028 45.455 0.00 0.00 0.00 2.57
1944 9097 6.588204 ACCCCAAGGAAAAATAGTTTGTTTC 58.412 36.000 0.00 0.00 36.73 2.78
1968 9127 0.538057 CTGCTGGCTTGTTCCTCCAA 60.538 55.000 0.00 0.00 0.00 3.53
1997 9156 2.211806 CTGAGCTAGAAGATTGCCAGC 58.788 52.381 0.00 0.00 0.00 4.85
2041 9200 1.271108 TGAGAAATGGCGGCACAAGTA 60.271 47.619 16.34 0.00 0.00 2.24
2066 9225 6.847956 TTTTTGTGGCTGATTTCATTTCTG 57.152 33.333 0.00 0.00 0.00 3.02
2087 9246 7.823745 ATAAGGTGTGACTCATCAAAGTTTT 57.176 32.000 0.00 0.00 36.31 2.43
2133 9292 6.777091 CCCCATCAATCATTCCATAGTAAACA 59.223 38.462 0.00 0.00 0.00 2.83
2184 9343 1.000163 ACACACTGCTGAACTCTACCG 60.000 52.381 0.00 0.00 0.00 4.02
2187 9346 2.959030 ACTCACACACTGCTGAACTCTA 59.041 45.455 0.00 0.00 0.00 2.43
2200 9359 8.908786 ATCTTTTCTTTCAATCTACTCACACA 57.091 30.769 0.00 0.00 0.00 3.72
2210 9369 5.123979 ACCGCCACTATCTTTTCTTTCAATC 59.876 40.000 0.00 0.00 0.00 2.67
2211 9370 5.010282 ACCGCCACTATCTTTTCTTTCAAT 58.990 37.500 0.00 0.00 0.00 2.57
2214 9373 3.127030 CCACCGCCACTATCTTTTCTTTC 59.873 47.826 0.00 0.00 0.00 2.62
2217 9376 1.679032 GCCACCGCCACTATCTTTTCT 60.679 52.381 0.00 0.00 0.00 2.52
2218 9377 0.733150 GCCACCGCCACTATCTTTTC 59.267 55.000 0.00 0.00 0.00 2.29
2219 9378 0.037590 TGCCACCGCCACTATCTTTT 59.962 50.000 0.00 0.00 0.00 2.27
2283 9442 4.921547 TCAGTATCATCTCGTTTTCCTCG 58.078 43.478 0.00 0.00 0.00 4.63
2313 9472 1.153168 GGTGCCACGAGCCATGTAT 60.153 57.895 0.00 0.00 42.71 2.29
2522 10752 0.105593 CGTGCTATCCTGTGGCAGAT 59.894 55.000 0.00 0.00 45.61 2.90
2544 10774 1.868997 CACAGGCTGCGTGGTAAAG 59.131 57.895 24.13 6.88 0.00 1.85
2545 10775 4.057224 CACAGGCTGCGTGGTAAA 57.943 55.556 24.13 0.00 0.00 2.01
2641 10877 4.183101 CACAAAACCTCAAACAGCACAAT 58.817 39.130 0.00 0.00 0.00 2.71
2683 10919 3.680196 GCTTGTCTCCATGGAAGACTACC 60.680 52.174 28.95 17.81 34.03 3.18
2707 10943 2.770164 AGGGCGCAATATACCAGATC 57.230 50.000 10.83 0.00 0.00 2.75
2770 11006 4.142730 CGGAGCAATCTTTCCTTCAAGAAG 60.143 45.833 2.83 2.83 36.36 2.85
2798 11034 5.766222 CAATCTCCACAAACTTCTTCAAGG 58.234 41.667 0.00 0.00 33.37 3.61
2876 11112 2.366916 AGACACAACTCCAGGTTCTCAG 59.633 50.000 0.00 0.00 35.74 3.35
2898 11134 1.081175 GCTTCCGCTTTGTTCTGCC 60.081 57.895 0.00 0.00 0.00 4.85
2974 12222 0.909133 TACATCTCCAGGTGCAGCCA 60.909 55.000 13.29 0.00 40.61 4.75
2980 12228 1.278985 TGCAAGGTACATCTCCAGGTG 59.721 52.381 0.00 0.00 0.00 4.00
3004 12252 2.086869 AGACCATTCCAAAGCATCGTG 58.913 47.619 0.00 0.00 0.00 4.35
3016 12264 3.209410 CACCAGCATTCCTAGACCATTC 58.791 50.000 0.00 0.00 0.00 2.67
3023 12271 1.679944 CCACACCACCAGCATTCCTAG 60.680 57.143 0.00 0.00 0.00 3.02
3025 12273 1.075482 CCACACCACCAGCATTCCT 59.925 57.895 0.00 0.00 0.00 3.36
3027 12275 1.474077 GAATCCACACCACCAGCATTC 59.526 52.381 0.00 0.00 0.00 2.67
3028 12276 1.549203 GAATCCACACCACCAGCATT 58.451 50.000 0.00 0.00 0.00 3.56
3032 12603 0.253044 ATCGGAATCCACACCACCAG 59.747 55.000 0.00 0.00 0.00 4.00
3061 12636 1.063649 CTGCTCATCGTGGCATTGC 59.936 57.895 0.00 0.00 37.83 3.56
3090 12665 1.539827 GGAAATTGGTGACCACTTCGG 59.460 52.381 2.46 0.00 42.50 4.30
3091 12666 1.539827 GGGAAATTGGTGACCACTTCG 59.460 52.381 2.46 0.00 30.78 3.79
3092 12667 2.876581 AGGGAAATTGGTGACCACTTC 58.123 47.619 2.46 10.41 30.78 3.01
3093 12668 3.397955 AGTAGGGAAATTGGTGACCACTT 59.602 43.478 2.46 1.54 30.78 3.16
3094 12669 2.986728 AGTAGGGAAATTGGTGACCACT 59.013 45.455 2.46 0.00 30.78 4.00
3095 12670 3.434940 AGTAGGGAAATTGGTGACCAC 57.565 47.619 2.46 0.00 30.78 4.16
3096 12671 4.785914 TGATAGTAGGGAAATTGGTGACCA 59.214 41.667 0.00 0.00 0.00 4.02
3109 12685 5.417580 GGAGTAGAGAGCATTGATAGTAGGG 59.582 48.000 0.00 0.00 0.00 3.53
3116 12692 4.099266 GTCAGTGGAGTAGAGAGCATTGAT 59.901 45.833 0.00 0.00 0.00 2.57
3129 12705 1.892819 CTGGCATCCGTCAGTGGAGT 61.893 60.000 0.00 0.00 42.45 3.85
3131 12707 1.607801 CTCTGGCATCCGTCAGTGGA 61.608 60.000 0.00 0.00 45.54 4.02
3133 12709 0.247460 TTCTCTGGCATCCGTCAGTG 59.753 55.000 0.00 0.00 45.54 3.66
3134 12710 1.198713 ATTCTCTGGCATCCGTCAGT 58.801 50.000 0.00 0.00 45.54 3.41
3135 12711 2.322355 AATTCTCTGGCATCCGTCAG 57.678 50.000 0.00 0.00 46.80 3.51
3136 12712 2.766263 AGTAATTCTCTGGCATCCGTCA 59.234 45.455 0.00 0.00 0.00 4.35
3137 12713 3.385577 GAGTAATTCTCTGGCATCCGTC 58.614 50.000 0.00 0.00 39.86 4.79
3138 12714 2.103263 GGAGTAATTCTCTGGCATCCGT 59.897 50.000 0.00 0.00 42.40 4.69
3139 12715 2.103094 TGGAGTAATTCTCTGGCATCCG 59.897 50.000 0.00 0.00 42.40 4.18
3140 12716 3.845781 TGGAGTAATTCTCTGGCATCC 57.154 47.619 0.00 0.00 42.40 3.51
3141 12717 5.858381 TGTATGGAGTAATTCTCTGGCATC 58.142 41.667 0.00 0.00 42.40 3.91
3184 13548 4.073293 ACTCGCTTCAGAAAAGAAAGGA 57.927 40.909 0.00 0.00 0.00 3.36
3213 13577 7.380536 AGCATGAAGAAAGACATAATGCAAAA 58.619 30.769 0.00 0.00 41.01 2.44
3214 13578 6.927416 AGCATGAAGAAAGACATAATGCAAA 58.073 32.000 0.00 0.00 41.01 3.68
3215 13579 6.519679 AGCATGAAGAAAGACATAATGCAA 57.480 33.333 0.00 0.00 41.01 4.08
3216 13580 6.519679 AAGCATGAAGAAAGACATAATGCA 57.480 33.333 0.00 0.00 41.01 3.96
3217 13581 7.253552 CGAAAAGCATGAAGAAAGACATAATGC 60.254 37.037 0.00 0.00 39.32 3.56
3218 13582 7.752239 ACGAAAAGCATGAAGAAAGACATAATG 59.248 33.333 0.00 0.00 0.00 1.90
3259 13629 1.401905 GAACGGCCTGACAAATCCATC 59.598 52.381 0.00 0.00 0.00 3.51
3366 13747 7.827819 TGTCTTATTATTCAGGACGAAACAG 57.172 36.000 0.00 0.00 37.12 3.16
3402 13786 3.338249 TGGAACAAGATGCTTGTAGAGC 58.662 45.455 12.64 4.24 44.65 4.09
3464 13848 0.108898 TTCTCGCTTCTGAGCTGCTC 60.109 55.000 22.38 22.38 46.96 4.26
3697 14081 5.127194 ACAACACTACTTCAACTGACTGAGA 59.873 40.000 0.00 0.00 0.00 3.27
3699 14083 5.105513 TGACAACACTACTTCAACTGACTGA 60.106 40.000 0.00 0.00 0.00 3.41
3700 14084 5.109210 TGACAACACTACTTCAACTGACTG 58.891 41.667 0.00 0.00 0.00 3.51
3701 14085 5.339008 TGACAACACTACTTCAACTGACT 57.661 39.130 0.00 0.00 0.00 3.41
3703 14087 7.465379 CGAAATTGACAACACTACTTCAACTGA 60.465 37.037 0.00 0.00 30.99 3.41
3704 14088 6.628856 CGAAATTGACAACACTACTTCAACTG 59.371 38.462 0.00 0.00 30.99 3.16
3705 14089 6.315393 ACGAAATTGACAACACTACTTCAACT 59.685 34.615 0.00 0.00 30.99 3.16
3708 14092 5.235616 GGACGAAATTGACAACACTACTTCA 59.764 40.000 0.00 0.00 0.00 3.02
3709 14093 5.465724 AGGACGAAATTGACAACACTACTTC 59.534 40.000 0.00 0.00 0.00 3.01
3710 14094 5.365619 AGGACGAAATTGACAACACTACTT 58.634 37.500 0.00 0.00 0.00 2.24
3711 14095 4.957296 AGGACGAAATTGACAACACTACT 58.043 39.130 0.00 0.00 0.00 2.57
3712 14096 5.924825 AGTAGGACGAAATTGACAACACTAC 59.075 40.000 0.00 0.00 0.00 2.73
3715 14099 4.748102 TGAGTAGGACGAAATTGACAACAC 59.252 41.667 0.00 0.00 0.00 3.32
3718 14102 7.827819 CTAATGAGTAGGACGAAATTGACAA 57.172 36.000 0.00 0.00 0.00 3.18
3734 14118 3.900601 CTGAGCTACATCCCCTAATGAGT 59.099 47.826 0.00 0.00 0.00 3.41
3735 14119 4.155709 TCTGAGCTACATCCCCTAATGAG 58.844 47.826 0.00 0.00 0.00 2.90
3736 14120 4.199002 TCTGAGCTACATCCCCTAATGA 57.801 45.455 0.00 0.00 0.00 2.57
3737 14121 4.323333 CCATCTGAGCTACATCCCCTAATG 60.323 50.000 0.00 0.00 0.00 1.90
3738 14122 3.843027 CCATCTGAGCTACATCCCCTAAT 59.157 47.826 0.00 0.00 0.00 1.73
3739 14123 3.242867 CCATCTGAGCTACATCCCCTAA 58.757 50.000 0.00 0.00 0.00 2.69
3740 14124 2.180086 ACCATCTGAGCTACATCCCCTA 59.820 50.000 0.00 0.00 0.00 3.53
3837 14473 7.984050 TGGTATTCAGATCTGCAAAAACAAAAA 59.016 29.630 18.36 3.33 0.00 1.94
3842 14478 6.922957 TGTTTGGTATTCAGATCTGCAAAAAC 59.077 34.615 18.36 18.62 0.00 2.43
3882 14518 2.629656 ACCAGATGCGCTTTGGTGC 61.630 57.895 23.64 1.20 43.32 5.01
3883 14519 3.672293 ACCAGATGCGCTTTGGTG 58.328 55.556 23.64 10.87 43.32 4.17
3884 14520 0.036164 TACACCAGATGCGCTTTGGT 59.964 50.000 20.33 20.33 45.77 3.67
3885 14521 0.729116 CTACACCAGATGCGCTTTGG 59.271 55.000 19.24 19.24 37.98 3.28
3979 14795 8.402798 TGCTTATCTGAAAGTCCATACAAAAA 57.597 30.769 0.00 0.00 33.76 1.94
4023 14847 5.578727 ACAACAGCAGAGTAAGAAATCGATC 59.421 40.000 0.00 0.00 0.00 3.69
4026 14850 5.050091 ACAACAACAGCAGAGTAAGAAATCG 60.050 40.000 0.00 0.00 0.00 3.34
4035 14859 3.347216 ACAAGAACAACAACAGCAGAGT 58.653 40.909 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.