Multiple sequence alignment - TraesCS7A01G140000

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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 TraesCS7A01G140000 chr7A 100.000 3284 0 0 1 3284 91684075 91687358 0.000000e+00 6065.0
1 TraesCS7A01G140000 chr7A 91.563 1695 109 17 819 2499 92841190 92839516 0.000000e+00 2307.0
2 TraesCS7A01G140000 chr7A 96.357 796 13 7 2500 3284 605482064 605481274 0.000000e+00 1295.0
3 TraesCS7A01G140000 chr7A 95.970 794 20 6 2500 3284 30611668 30612458 0.000000e+00 1279.0
4 TraesCS7A01G140000 chr7A 95.833 792 23 6 2500 3284 21937098 21937886 0.000000e+00 1271.0
5 TraesCS7A01G140000 chr7A 85.891 808 99 5 1014 1806 91724809 91725616 0.000000e+00 846.0
6 TraesCS7A01G140000 chr7A 74.906 1064 209 30 1136 2179 91633117 91634142 1.810000e-117 433.0
7 TraesCS7A01G140000 chr7A 87.368 380 45 1 1802 2181 91741549 91741925 1.810000e-117 433.0
8 TraesCS7A01G140000 chr7D 93.261 1929 112 9 581 2496 90508344 90510267 0.000000e+00 2826.0
9 TraesCS7A01G140000 chr7D 91.171 1699 123 17 819 2499 90748199 90746510 0.000000e+00 2281.0
10 TraesCS7A01G140000 chr7D 75.842 1188 226 33 1014 2179 90257250 90258398 6.200000e-152 547.0
11 TraesCS7A01G140000 chr7D 90.394 406 32 4 2020 2420 90541914 90542317 8.070000e-146 527.0
12 TraesCS7A01G140000 chr7D 89.873 237 24 0 1 237 90425769 90426005 4.120000e-79 305.0
13 TraesCS7A01G140000 chr7D 100.000 29 0 0 907 935 90257132 90257160 2.000000e-03 54.7
14 TraesCS7A01G140000 chr7B 91.003 1945 125 22 584 2484 41297242 41299180 0.000000e+00 2577.0
15 TraesCS7A01G140000 chr7B 80.556 576 78 23 830 1383 41275795 41276358 2.360000e-111 412.0
16 TraesCS7A01G140000 chr7B 75.028 909 171 33 1016 1881 41309750 41310645 1.440000e-98 370.0
17 TraesCS7A01G140000 chr7B 75.993 604 123 11 1584 2179 41277761 41278350 3.210000e-75 292.0
18 TraesCS7A01G140000 chr7B 89.593 221 23 0 1 221 41296403 41296623 6.940000e-72 281.0
19 TraesCS7A01G140000 chr7B 88.158 76 7 2 184 258 272565401 272565327 4.510000e-14 89.8
20 TraesCS7A01G140000 chr5A 96.595 793 15 7 2500 3284 174951714 174950926 0.000000e+00 1304.0
21 TraesCS7A01G140000 chr4A 96.071 789 24 5 2500 3284 523021032 523020247 0.000000e+00 1279.0
22 TraesCS7A01G140000 chr4A 80.745 161 30 1 3 163 567564132 567564291 1.240000e-24 124.0
23 TraesCS7A01G140000 chr4A 86.842 76 8 2 184 258 179595659 179595585 2.100000e-12 84.2
24 TraesCS7A01G140000 chr1A 96.071 789 23 4 2500 3284 1086821 1087605 0.000000e+00 1279.0
25 TraesCS7A01G140000 chr1A 99.320 147 1 0 378 524 278521587 278521733 1.940000e-67 267.0
26 TraesCS7A01G140000 chr3A 95.949 790 22 6 2500 3284 240392267 240391483 0.000000e+00 1273.0
27 TraesCS7A01G140000 chr3A 95.739 798 19 6 2500 3284 700658888 700658093 0.000000e+00 1271.0
28 TraesCS7A01G140000 chr6A 95.723 795 22 5 2499 3284 36546811 36546020 0.000000e+00 1269.0
29 TraesCS7A01G140000 chr6A 99.320 147 1 0 378 524 597252600 597252454 1.940000e-67 267.0
30 TraesCS7A01G140000 chr6A 94.737 57 3 0 184 240 424344766 424344822 4.510000e-14 89.8
31 TraesCS7A01G140000 chrUn 86.123 1189 138 12 1014 2184 103266637 103265458 0.000000e+00 1256.0
32 TraesCS7A01G140000 chrUn 83.444 453 57 7 1014 1451 312333840 312334289 3.950000e-109 405.0
33 TraesCS7A01G140000 chrUn 98.639 147 2 0 378 524 217908061 217908207 9.040000e-66 261.0
34 TraesCS7A01G140000 chrUn 83.478 115 7 5 805 916 312333601 312333706 2.700000e-16 97.1
35 TraesCS7A01G140000 chrUn 83.478 115 7 5 805 916 339126918 339127023 2.700000e-16 97.1
36 TraesCS7A01G140000 chrUn 83.478 115 7 5 805 916 404732772 404732877 2.700000e-16 97.1
37 TraesCS7A01G140000 chr6B 85.835 1186 146 8 1014 2184 52440667 52439489 0.000000e+00 1240.0
38 TraesCS7A01G140000 chr6B 85.567 97 12 2 276 372 46509993 46509899 2.090000e-17 100.0
39 TraesCS7A01G140000 chr6B 83.478 115 7 5 805 916 52440906 52440801 2.700000e-16 97.1
40 TraesCS7A01G140000 chr6B 83.478 115 7 5 805 916 52441533 52441428 2.700000e-16 97.1
41 TraesCS7A01G140000 chr3B 99.320 147 1 0 378 524 92296341 92296195 1.940000e-67 267.0
42 TraesCS7A01G140000 chr2B 99.320 147 1 0 378 524 234540767 234540621 1.940000e-67 267.0
43 TraesCS7A01G140000 chr6D 98.639 147 2 0 378 524 458940961 458940815 9.040000e-66 261.0
44 TraesCS7A01G140000 chr4B 98.639 147 2 0 378 524 209107051 209107197 9.040000e-66 261.0
45 TraesCS7A01G140000 chr4B 98.639 147 2 0 378 524 495479319 495479173 9.040000e-66 261.0
46 TraesCS7A01G140000 chr3D 98.639 147 2 0 378 524 501837987 501837841 9.040000e-66 261.0
47 TraesCS7A01G140000 chr3D 83.815 173 28 0 1 173 406411191 406411363 7.290000e-37 165.0
48 TraesCS7A01G140000 chr5D 87.742 155 16 3 29 182 409729581 409729429 9.360000e-41 178.0
49 TraesCS7A01G140000 chr1D 85.870 92 10 3 67 157 478035555 478035644 9.700000e-16 95.3
50 TraesCS7A01G140000 chr1D 88.158 76 7 2 184 258 134529895 134529821 4.510000e-14 89.8
51 TraesCS7A01G140000 chr4D 86.842 76 8 2 184 258 306544388 306544314 2.100000e-12 84.2
52 TraesCS7A01G140000 chr4D 86.667 75 10 0 184 258 362571907 362571833 2.100000e-12 84.2
53 TraesCS7A01G140000 chr2D 86.667 75 10 0 184 258 525918727 525918653 2.100000e-12 84.2


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 TraesCS7A01G140000 chr7A 91684075 91687358 3283 False 6065.000000 6065 100.000000 1 3284 1 chr7A.!!$F4 3283
1 TraesCS7A01G140000 chr7A 92839516 92841190 1674 True 2307.000000 2307 91.563000 819 2499 1 chr7A.!!$R1 1680
2 TraesCS7A01G140000 chr7A 605481274 605482064 790 True 1295.000000 1295 96.357000 2500 3284 1 chr7A.!!$R2 784
3 TraesCS7A01G140000 chr7A 30611668 30612458 790 False 1279.000000 1279 95.970000 2500 3284 1 chr7A.!!$F2 784
4 TraesCS7A01G140000 chr7A 21937098 21937886 788 False 1271.000000 1271 95.833000 2500 3284 1 chr7A.!!$F1 784
5 TraesCS7A01G140000 chr7A 91724809 91725616 807 False 846.000000 846 85.891000 1014 1806 1 chr7A.!!$F5 792
6 TraesCS7A01G140000 chr7A 91633117 91634142 1025 False 433.000000 433 74.906000 1136 2179 1 chr7A.!!$F3 1043
7 TraesCS7A01G140000 chr7D 90508344 90510267 1923 False 2826.000000 2826 93.261000 581 2496 1 chr7D.!!$F2 1915
8 TraesCS7A01G140000 chr7D 90746510 90748199 1689 True 2281.000000 2281 91.171000 819 2499 1 chr7D.!!$R1 1680
9 TraesCS7A01G140000 chr7D 90257132 90258398 1266 False 300.850000 547 87.921000 907 2179 2 chr7D.!!$F4 1272
10 TraesCS7A01G140000 chr7B 41296403 41299180 2777 False 1429.000000 2577 90.298000 1 2484 2 chr7B.!!$F3 2483
11 TraesCS7A01G140000 chr7B 41309750 41310645 895 False 370.000000 370 75.028000 1016 1881 1 chr7B.!!$F1 865
12 TraesCS7A01G140000 chr7B 41275795 41278350 2555 False 352.000000 412 78.274500 830 2179 2 chr7B.!!$F2 1349
13 TraesCS7A01G140000 chr5A 174950926 174951714 788 True 1304.000000 1304 96.595000 2500 3284 1 chr5A.!!$R1 784
14 TraesCS7A01G140000 chr4A 523020247 523021032 785 True 1279.000000 1279 96.071000 2500 3284 1 chr4A.!!$R2 784
15 TraesCS7A01G140000 chr1A 1086821 1087605 784 False 1279.000000 1279 96.071000 2500 3284 1 chr1A.!!$F1 784
16 TraesCS7A01G140000 chr3A 240391483 240392267 784 True 1273.000000 1273 95.949000 2500 3284 1 chr3A.!!$R1 784
17 TraesCS7A01G140000 chr3A 700658093 700658888 795 True 1271.000000 1271 95.739000 2500 3284 1 chr3A.!!$R2 784
18 TraesCS7A01G140000 chr6A 36546020 36546811 791 True 1269.000000 1269 95.723000 2499 3284 1 chr6A.!!$R1 785
19 TraesCS7A01G140000 chrUn 103265458 103266637 1179 True 1256.000000 1256 86.123000 1014 2184 1 chrUn.!!$R1 1170
20 TraesCS7A01G140000 chrUn 312333601 312334289 688 False 251.050000 405 83.461000 805 1451 2 chrUn.!!$F4 646
21 TraesCS7A01G140000 chr6B 52439489 52441533 2044 True 478.066667 1240 84.263667 805 2184 3 chr6B.!!$R2 1379

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
550 868 0.031043 CACAACACGTCTGGACCGTA 59.969 55.0 0.00 0.00 36.65 4.02 F
555 873 0.169672 CACGTCTGGACCGTACGATT 59.830 55.0 18.76 2.38 39.80 3.34 F
1514 3167 0.318614 GACCGGTCCGTTTACGACAA 60.319 55.0 24.75 0.00 43.02 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 2964 0.038709 GCCAGCTCCTATCGTAGCAG 60.039 60.000 0.00 0.0 41.32 4.24 R
1577 3230 0.739813 GTTGTCGCCGAGGCTACATT 60.740 55.000 19.81 0.0 44.27 2.71 R
2670 4375 1.149627 CACCAACCGGGACCAAAGA 59.850 57.895 6.32 0.0 41.15 2.52 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
72 73 4.052518 AGGCCATGGTGGGAGTGC 62.053 66.667 14.67 0.00 38.19 4.40
75 76 2.044650 CCATGGTGGGAGTGCTGG 60.045 66.667 2.57 0.00 32.67 4.85
94 95 1.610327 GGAAGAGGAGAAAGGGCCC 59.390 63.158 16.46 16.46 0.00 5.80
98 99 2.689034 AGGAGAAAGGGCCCGGAG 60.689 66.667 18.44 0.00 0.00 4.63
119 120 2.157738 GAGGATGAATGTGGCTATGGC 58.842 52.381 0.00 0.00 37.82 4.40
120 121 1.779092 AGGATGAATGTGGCTATGGCT 59.221 47.619 0.00 0.00 38.73 4.75
130 131 2.203308 CTATGGCTGGGGCTGCAG 60.203 66.667 10.11 10.11 38.73 4.41
163 164 3.645660 TGAGGCAATGGTGGGCGA 61.646 61.111 0.00 0.00 35.71 5.54
164 165 2.361104 GAGGCAATGGTGGGCGAA 60.361 61.111 0.00 0.00 35.71 4.70
174 175 2.602267 TGGGCGAAAGAGGGACGA 60.602 61.111 0.00 0.00 0.00 4.20
176 177 1.740664 GGGCGAAAGAGGGACGAAC 60.741 63.158 0.00 0.00 0.00 3.95
198 199 0.438830 GTGTCTTCAATGTCGACGCC 59.561 55.000 11.62 0.00 33.36 5.68
199 200 0.032815 TGTCTTCAATGTCGACGCCA 59.967 50.000 11.62 0.00 0.00 5.69
201 202 0.389817 TCTTCAATGTCGACGCCAGG 60.390 55.000 11.62 0.00 0.00 4.45
209 210 3.382832 CGACGCCAGGGAGAGGTT 61.383 66.667 0.00 0.00 0.00 3.50
211 212 2.526873 ACGCCAGGGAGAGGTTGT 60.527 61.111 0.00 0.00 0.00 3.32
214 215 1.003233 GCCAGGGAGAGGTTGTGTC 60.003 63.158 0.00 0.00 0.00 3.67
221 222 0.389166 GAGAGGTTGTGTCCGCTCTG 60.389 60.000 8.73 0.00 46.10 3.35
223 224 3.050275 GGTTGTGTCCGCTCTGGC 61.050 66.667 0.00 0.00 37.80 4.85
224 225 2.031163 GTTGTGTCCGCTCTGGCT 59.969 61.111 0.00 0.00 37.80 4.75
225 226 2.031012 TTGTGTCCGCTCTGGCTG 59.969 61.111 0.00 0.00 37.80 4.85
226 227 3.535629 TTGTGTCCGCTCTGGCTGG 62.536 63.158 0.00 0.00 37.80 4.85
227 228 4.767255 GTGTCCGCTCTGGCTGGG 62.767 72.222 0.00 0.00 37.80 4.45
232 233 4.478371 CGCTCTGGCTGGGCATGA 62.478 66.667 16.79 0.00 36.09 3.07
233 234 2.044650 GCTCTGGCTGGGCATGAA 60.045 61.111 11.75 0.00 35.22 2.57
234 235 1.455217 GCTCTGGCTGGGCATGAAT 60.455 57.895 11.75 0.00 35.22 2.57
235 236 1.735376 GCTCTGGCTGGGCATGAATG 61.735 60.000 11.75 0.00 35.22 2.67
244 245 2.715005 GCATGAATGCGGCGCTAA 59.285 55.556 33.26 14.71 44.67 3.09
245 246 1.655350 GCATGAATGCGGCGCTAAC 60.655 57.895 33.26 21.97 44.67 2.34
246 247 1.368019 CATGAATGCGGCGCTAACG 60.368 57.895 33.26 12.47 44.07 3.18
273 274 2.851104 GGCGACGACCGTTTCAAG 59.149 61.111 0.00 0.00 41.15 3.02
274 275 2.170273 GCGACGACCGTTTCAAGC 59.830 61.111 0.00 0.00 41.15 4.01
275 276 2.464189 CGACGACCGTTTCAAGCG 59.536 61.111 0.00 0.00 0.00 4.68
306 307 3.003763 GCGAGGGTGGAGGGTCTT 61.004 66.667 0.00 0.00 0.00 3.01
307 308 2.982130 CGAGGGTGGAGGGTCTTG 59.018 66.667 0.00 0.00 0.00 3.02
308 309 2.660064 CGAGGGTGGAGGGTCTTGG 61.660 68.421 0.00 0.00 0.00 3.61
310 311 2.204090 GGGTGGAGGGTCTTGGGA 60.204 66.667 0.00 0.00 0.00 4.37
311 312 1.619669 GGGTGGAGGGTCTTGGGAT 60.620 63.158 0.00 0.00 0.00 3.85
312 313 1.609783 GGTGGAGGGTCTTGGGATG 59.390 63.158 0.00 0.00 0.00 3.51
313 314 0.914417 GGTGGAGGGTCTTGGGATGA 60.914 60.000 0.00 0.00 0.00 2.92
314 315 0.543749 GTGGAGGGTCTTGGGATGAG 59.456 60.000 0.00 0.00 0.00 2.90
315 316 1.274703 TGGAGGGTCTTGGGATGAGC 61.275 60.000 0.00 0.00 0.00 4.26
318 319 4.972875 GGTCTTGGGATGAGCCAG 57.027 61.111 0.00 0.00 38.95 4.85
319 320 1.225704 GGTCTTGGGATGAGCCAGG 59.774 63.158 0.00 0.00 38.95 4.45
320 321 1.225704 GTCTTGGGATGAGCCAGGG 59.774 63.158 0.00 0.00 38.95 4.45
321 322 1.229951 TCTTGGGATGAGCCAGGGT 60.230 57.895 0.00 0.00 38.95 4.34
322 323 0.846427 TCTTGGGATGAGCCAGGGTT 60.846 55.000 0.00 0.00 38.95 4.11
323 324 0.682209 CTTGGGATGAGCCAGGGTTG 60.682 60.000 0.00 0.00 38.95 3.77
326 327 0.623723 GGGATGAGCCAGGGTTGTTA 59.376 55.000 0.00 0.00 38.95 2.41
328 329 1.559682 GGATGAGCCAGGGTTGTTAGA 59.440 52.381 0.00 0.00 36.34 2.10
329 330 2.026262 GGATGAGCCAGGGTTGTTAGAA 60.026 50.000 0.00 0.00 36.34 2.10
330 331 3.561313 GGATGAGCCAGGGTTGTTAGAAA 60.561 47.826 0.00 0.00 36.34 2.52
331 332 2.858745 TGAGCCAGGGTTGTTAGAAAC 58.141 47.619 0.00 0.00 0.00 2.78
332 333 1.804748 GAGCCAGGGTTGTTAGAAACG 59.195 52.381 0.00 0.00 0.00 3.60
333 334 0.879090 GCCAGGGTTGTTAGAAACGG 59.121 55.000 0.00 0.00 0.00 4.44
335 336 0.879090 CAGGGTTGTTAGAAACGGGC 59.121 55.000 0.00 0.00 0.00 6.13
337 338 0.886043 GGGTTGTTAGAAACGGGCGT 60.886 55.000 0.00 0.00 0.00 5.68
340 658 0.106335 TTGTTAGAAACGGGCGTGGA 59.894 50.000 0.00 0.00 0.00 4.02
347 665 4.760047 ACGGGCGTGGATGCTGTC 62.760 66.667 0.00 0.00 34.52 3.51
348 666 4.457496 CGGGCGTGGATGCTGTCT 62.457 66.667 0.00 0.00 34.52 3.41
354 672 1.293498 GTGGATGCTGTCTGGACGT 59.707 57.895 0.00 0.00 0.00 4.34
382 700 3.546543 CCTCCCCCGCGCTTGATA 61.547 66.667 5.56 0.00 0.00 2.15
383 701 2.029666 CTCCCCCGCGCTTGATAG 59.970 66.667 5.56 0.00 0.00 2.08
384 702 4.235762 TCCCCCGCGCTTGATAGC 62.236 66.667 5.56 0.00 44.21 2.97
395 713 3.439857 GCTTGATAGCAATATGGGGGA 57.560 47.619 0.00 0.00 46.95 4.81
397 715 3.760684 GCTTGATAGCAATATGGGGGAAG 59.239 47.826 0.00 0.00 46.95 3.46
398 716 4.751028 GCTTGATAGCAATATGGGGGAAGT 60.751 45.833 0.00 0.00 46.95 3.01
399 717 5.388654 CTTGATAGCAATATGGGGGAAGTT 58.611 41.667 0.00 0.00 32.68 2.66
400 718 4.985538 TGATAGCAATATGGGGGAAGTTC 58.014 43.478 0.00 0.00 0.00 3.01
401 719 2.755952 AGCAATATGGGGGAAGTTCC 57.244 50.000 13.99 13.99 35.23 3.62
411 729 3.670105 GGAAGTTCCCATCAGGCAA 57.330 52.632 11.17 0.00 34.51 4.52
412 730 1.177401 GGAAGTTCCCATCAGGCAAC 58.823 55.000 11.17 0.00 34.51 4.17
413 731 1.547675 GGAAGTTCCCATCAGGCAACA 60.548 52.381 11.17 0.00 41.41 3.33
416 734 0.240945 GTTCCCATCAGGCAACAACG 59.759 55.000 0.00 0.00 41.41 4.10
418 736 1.603455 CCCATCAGGCAACAACGGT 60.603 57.895 0.00 0.00 41.41 4.83
419 737 1.178534 CCCATCAGGCAACAACGGTT 61.179 55.000 0.00 0.00 37.87 4.44
420 738 0.240945 CCATCAGGCAACAACGGTTC 59.759 55.000 0.00 0.00 34.21 3.62
421 739 1.238439 CATCAGGCAACAACGGTTCT 58.762 50.000 0.00 0.00 34.21 3.01
422 740 1.069022 CATCAGGCAACAACGGTTCTG 60.069 52.381 0.00 0.00 34.21 3.02
423 741 1.008538 CAGGCAACAACGGTTCTGC 60.009 57.895 13.52 13.52 34.21 4.26
424 742 2.193536 AGGCAACAACGGTTCTGCC 61.194 57.895 25.62 25.62 46.70 4.85
425 743 2.193536 GGCAACAACGGTTCTGCCT 61.194 57.895 25.65 0.00 44.19 4.75
426 744 1.008538 GCAACAACGGTTCTGCCTG 60.009 57.895 11.61 0.00 34.21 4.85
427 745 1.444119 GCAACAACGGTTCTGCCTGA 61.444 55.000 11.61 0.00 34.21 3.86
428 746 0.307760 CAACAACGGTTCTGCCTGAC 59.692 55.000 0.00 0.00 34.21 3.51
429 747 0.818040 AACAACGGTTCTGCCTGACC 60.818 55.000 0.00 0.00 29.00 4.02
430 748 1.966451 CAACGGTTCTGCCTGACCC 60.966 63.158 0.00 0.00 34.25 4.46
431 749 2.147387 AACGGTTCTGCCTGACCCT 61.147 57.895 0.00 0.00 34.25 4.34
432 750 0.834687 AACGGTTCTGCCTGACCCTA 60.835 55.000 0.00 0.00 34.25 3.53
433 751 1.218316 CGGTTCTGCCTGACCCTAC 59.782 63.158 0.00 0.00 34.25 3.18
434 752 1.541310 CGGTTCTGCCTGACCCTACA 61.541 60.000 0.00 0.00 34.25 2.74
435 753 0.690762 GGTTCTGCCTGACCCTACAA 59.309 55.000 0.00 0.00 0.00 2.41
436 754 1.073284 GGTTCTGCCTGACCCTACAAA 59.927 52.381 0.00 0.00 0.00 2.83
437 755 2.290960 GGTTCTGCCTGACCCTACAAAT 60.291 50.000 0.00 0.00 0.00 2.32
438 756 2.749621 GTTCTGCCTGACCCTACAAATG 59.250 50.000 0.00 0.00 0.00 2.32
439 757 1.098050 CTGCCTGACCCTACAAATGC 58.902 55.000 0.00 0.00 0.00 3.56
440 758 0.403655 TGCCTGACCCTACAAATGCA 59.596 50.000 0.00 0.00 0.00 3.96
441 759 1.005805 TGCCTGACCCTACAAATGCAT 59.994 47.619 0.00 0.00 0.00 3.96
442 760 1.406539 GCCTGACCCTACAAATGCATG 59.593 52.381 0.00 0.00 0.00 4.06
443 761 1.406539 CCTGACCCTACAAATGCATGC 59.593 52.381 11.82 11.82 0.00 4.06
444 762 2.093890 CTGACCCTACAAATGCATGCA 58.906 47.619 25.04 25.04 0.00 3.96
445 763 2.691526 CTGACCCTACAAATGCATGCAT 59.308 45.455 27.46 27.46 38.46 3.96
446 764 3.884693 CTGACCCTACAAATGCATGCATA 59.115 43.478 32.36 16.51 35.31 3.14
447 765 4.472496 TGACCCTACAAATGCATGCATAT 58.528 39.130 32.36 22.17 35.31 1.78
448 766 4.278919 TGACCCTACAAATGCATGCATATG 59.721 41.667 32.36 18.99 35.31 1.78
449 767 4.217510 ACCCTACAAATGCATGCATATGT 58.782 39.130 32.36 18.15 36.65 2.29
450 768 4.650588 ACCCTACAAATGCATGCATATGTT 59.349 37.500 32.36 20.48 36.65 2.71
451 769 4.986034 CCCTACAAATGCATGCATATGTTG 59.014 41.667 32.36 30.51 36.65 3.33
452 770 5.452216 CCCTACAAATGCATGCATATGTTGT 60.452 40.000 34.35 34.35 38.05 3.32
453 771 5.688621 CCTACAAATGCATGCATATGTTGTC 59.311 40.000 35.31 3.12 36.71 3.18
454 772 5.074584 ACAAATGCATGCATATGTTGTCA 57.925 34.783 30.26 6.47 32.64 3.58
455 773 5.106442 ACAAATGCATGCATATGTTGTCAG 58.894 37.500 30.26 15.84 32.64 3.51
456 774 4.994907 AATGCATGCATATGTTGTCAGT 57.005 36.364 32.36 10.88 36.65 3.41
457 775 3.768468 TGCATGCATATGTTGTCAGTG 57.232 42.857 18.46 0.00 36.65 3.66
458 776 3.345414 TGCATGCATATGTTGTCAGTGA 58.655 40.909 18.46 0.00 36.65 3.41
459 777 3.757493 TGCATGCATATGTTGTCAGTGAA 59.243 39.130 18.46 0.00 36.65 3.18
460 778 4.142556 TGCATGCATATGTTGTCAGTGAAG 60.143 41.667 18.46 0.00 36.65 3.02
461 779 4.095334 GCATGCATATGTTGTCAGTGAAGA 59.905 41.667 14.21 0.00 36.65 2.87
462 780 5.220989 GCATGCATATGTTGTCAGTGAAGAT 60.221 40.000 14.21 0.00 36.65 2.40
463 781 6.679638 GCATGCATATGTTGTCAGTGAAGATT 60.680 38.462 14.21 0.00 36.65 2.40
464 782 6.822667 TGCATATGTTGTCAGTGAAGATTT 57.177 33.333 4.29 0.00 0.00 2.17
465 783 7.218228 TGCATATGTTGTCAGTGAAGATTTT 57.782 32.000 4.29 0.00 0.00 1.82
466 784 7.085746 TGCATATGTTGTCAGTGAAGATTTTG 58.914 34.615 4.29 0.00 0.00 2.44
467 785 7.086376 GCATATGTTGTCAGTGAAGATTTTGT 58.914 34.615 4.29 0.00 0.00 2.83
468 786 7.061441 GCATATGTTGTCAGTGAAGATTTTGTG 59.939 37.037 4.29 0.00 0.00 3.33
469 787 5.895636 TGTTGTCAGTGAAGATTTTGTGT 57.104 34.783 0.00 0.00 0.00 3.72
470 788 5.639757 TGTTGTCAGTGAAGATTTTGTGTG 58.360 37.500 0.00 0.00 0.00 3.82
471 789 5.414144 TGTTGTCAGTGAAGATTTTGTGTGA 59.586 36.000 0.00 0.00 0.00 3.58
472 790 6.072230 TGTTGTCAGTGAAGATTTTGTGTGAA 60.072 34.615 0.00 0.00 0.00 3.18
473 791 6.122850 TGTCAGTGAAGATTTTGTGTGAAG 57.877 37.500 0.00 0.00 0.00 3.02
474 792 4.972440 GTCAGTGAAGATTTTGTGTGAAGC 59.028 41.667 0.00 0.00 0.00 3.86
475 793 4.036734 TCAGTGAAGATTTTGTGTGAAGCC 59.963 41.667 0.00 0.00 0.00 4.35
476 794 4.037208 CAGTGAAGATTTTGTGTGAAGCCT 59.963 41.667 0.00 0.00 0.00 4.58
477 795 4.646492 AGTGAAGATTTTGTGTGAAGCCTT 59.354 37.500 0.00 0.00 0.00 4.35
478 796 4.741676 GTGAAGATTTTGTGTGAAGCCTTG 59.258 41.667 0.00 0.00 0.00 3.61
479 797 4.202141 TGAAGATTTTGTGTGAAGCCTTGG 60.202 41.667 0.00 0.00 0.00 3.61
480 798 3.565307 AGATTTTGTGTGAAGCCTTGGA 58.435 40.909 0.00 0.00 0.00 3.53
481 799 3.571401 AGATTTTGTGTGAAGCCTTGGAG 59.429 43.478 0.00 0.00 0.00 3.86
482 800 2.727123 TTTGTGTGAAGCCTTGGAGA 57.273 45.000 0.00 0.00 0.00 3.71
483 801 1.967319 TTGTGTGAAGCCTTGGAGAC 58.033 50.000 0.00 0.00 0.00 3.36
484 802 0.249868 TGTGTGAAGCCTTGGAGACG 60.250 55.000 0.00 0.00 0.00 4.18
485 803 0.033504 GTGTGAAGCCTTGGAGACGA 59.966 55.000 0.00 0.00 0.00 4.20
486 804 0.033504 TGTGAAGCCTTGGAGACGAC 59.966 55.000 0.00 0.00 0.00 4.34
487 805 1.009389 GTGAAGCCTTGGAGACGACG 61.009 60.000 0.00 0.00 0.00 5.12
488 806 1.289380 GAAGCCTTGGAGACGACGT 59.711 57.895 0.00 0.00 0.00 4.34
489 807 0.524862 GAAGCCTTGGAGACGACGTA 59.475 55.000 0.00 0.00 0.00 3.57
490 808 0.243095 AAGCCTTGGAGACGACGTAC 59.757 55.000 0.00 0.00 0.00 3.67
491 809 1.153881 GCCTTGGAGACGACGTACC 60.154 63.158 14.30 14.30 0.00 3.34
492 810 1.509923 CCTTGGAGACGACGTACCC 59.490 63.158 17.21 13.92 0.00 3.69
493 811 1.136147 CTTGGAGACGACGTACCCG 59.864 63.158 17.21 0.00 40.83 5.28
494 812 2.262471 CTTGGAGACGACGTACCCGG 62.262 65.000 17.21 0.00 38.78 5.73
495 813 3.512516 GGAGACGACGTACCCGGG 61.513 72.222 22.25 22.25 38.78 5.73
496 814 3.512516 GAGACGACGTACCCGGGG 61.513 72.222 27.92 12.73 38.78 5.73
499 817 4.424711 ACGACGTACCCGGGGCTA 62.425 66.667 27.92 5.98 38.78 3.93
500 818 3.589881 CGACGTACCCGGGGCTAG 61.590 72.222 27.92 15.53 38.78 3.42
501 819 3.222121 GACGTACCCGGGGCTAGG 61.222 72.222 27.92 16.84 38.78 3.02
511 829 2.439104 GGGGCTAGGGTGAGCTGAG 61.439 68.421 0.00 0.00 42.43 3.35
514 832 2.439104 GCTAGGGTGAGCTGAGGGG 61.439 68.421 0.00 0.00 39.50 4.79
530 848 2.046285 GGGGGACAGCGTTTGATGG 61.046 63.158 0.00 0.00 35.27 3.51
549 867 1.227147 CACAACACGTCTGGACCGT 60.227 57.895 0.00 0.00 39.52 4.83
550 868 0.031043 CACAACACGTCTGGACCGTA 59.969 55.000 0.00 0.00 36.65 4.02
553 871 1.165907 AACACGTCTGGACCGTACGA 61.166 55.000 18.76 0.00 39.80 3.43
555 873 0.169672 CACGTCTGGACCGTACGATT 59.830 55.000 18.76 2.38 39.80 3.34
557 875 0.588233 CGTCTGGACCGTACGATTCG 60.588 60.000 18.76 4.14 38.89 3.34
569 887 0.734942 ACGATTCGAACGATTGCGGT 60.735 50.000 21.26 0.00 42.43 5.68
640 982 2.550978 GCGTGTAGCCAAGTATCACAT 58.449 47.619 0.00 0.00 40.81 3.21
641 983 3.713288 GCGTGTAGCCAAGTATCACATA 58.287 45.455 0.00 0.00 40.81 2.29
760 1105 1.523095 GCGTGCTCTATCCGAAATCAC 59.477 52.381 0.00 0.00 0.00 3.06
762 1107 2.128035 GTGCTCTATCCGAAATCACCG 58.872 52.381 0.00 0.00 0.00 4.94
777 1138 3.685139 TCACCGCAAATTCTCTCTCTT 57.315 42.857 0.00 0.00 0.00 2.85
795 1156 5.982356 TCTCTTTCTCTCTCTCTCTCTCTG 58.018 45.833 0.00 0.00 0.00 3.35
796 1157 5.721480 TCTCTTTCTCTCTCTCTCTCTCTGA 59.279 44.000 0.00 0.00 0.00 3.27
812 1175 8.522830 TCTCTCTCTGACAAAACAAAAACAAAT 58.477 29.630 0.00 0.00 0.00 2.32
1113 1534 2.430244 CACTGGCGCTACGTCGTT 60.430 61.111 7.64 0.00 32.50 3.85
1240 1667 1.315257 GCTGTGGCCGGAATTCATGT 61.315 55.000 5.05 0.00 0.00 3.21
1404 2964 2.663119 GCGTTTTGATGATCAAAGCACC 59.337 45.455 26.57 16.60 45.77 5.01
1494 3147 4.394712 CACGTCCCCTGCCACCTC 62.395 72.222 0.00 0.00 0.00 3.85
1514 3167 0.318614 GACCGGTCCGTTTACGACAA 60.319 55.000 24.75 0.00 43.02 3.18
1549 3202 1.910580 GCTGGGGGAGAAATCGTGGA 61.911 60.000 0.00 0.00 0.00 4.02
1632 3315 1.080974 CGTCACGTACTGGACCACC 60.081 63.158 0.00 0.00 0.00 4.61
1815 3504 1.202903 GCTATGGAGAGGACGGAGGTA 60.203 57.143 0.00 0.00 0.00 3.08
2007 3699 6.126568 TCGTTGTATGAACGAGATCATGTA 57.873 37.500 9.70 1.24 46.21 2.29
2037 3729 1.804151 CACAAACCGATTGACGACCAT 59.196 47.619 7.74 0.00 45.77 3.55
2046 3738 3.306166 CGATTGACGACCATACAAGGAAC 59.694 47.826 0.00 0.00 45.77 3.62
2049 3741 0.390735 ACGACCATACAAGGAACGCC 60.391 55.000 0.00 0.00 36.26 5.68
2174 3866 0.179029 ACCAAGGAACCGTTGAGTGG 60.179 55.000 0.00 0.00 0.00 4.00
2203 3895 2.086869 CTCTTGCGTCACCATTTCCAT 58.913 47.619 0.00 0.00 0.00 3.41
2236 3928 2.876550 TCATCGTCGTCGTCATTATCCT 59.123 45.455 1.33 0.00 38.33 3.24
2317 4012 0.391927 CGGCCTTGTTATCCGGTTCA 60.392 55.000 0.00 0.00 39.52 3.18
2337 4032 8.458843 CGGTTCACAGGAATAGAAAACATATTT 58.541 33.333 0.00 0.00 35.05 1.40
2389 4088 4.639755 TGGATTGTTTATCGCATGTGTCAT 59.360 37.500 6.09 0.00 33.82 3.06
2393 4092 3.750652 TGTTTATCGCATGTGTCATGTGT 59.249 39.130 18.39 11.09 0.00 3.72
2397 4096 1.530720 TCGCATGTGTCATGTGTTCAC 59.469 47.619 18.39 0.00 0.00 3.18
2815 4537 9.899661 AGGTGTTTCATATATTGTGTTAGCTAA 57.100 29.630 0.86 0.86 0.00 3.09
2907 4629 1.937278 TAGAGAGGACTAGACACGCG 58.063 55.000 3.53 3.53 0.00 6.01
3172 4894 1.066152 GAATGCCGCCAATTCCTCTTC 59.934 52.381 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.032799 CGACCTGTAGCTAGAGCAGAAG 59.967 54.545 12.38 1.32 45.16 2.85
13 14 0.664224 GGACGACCTGTAGCTAGAGC 59.336 60.000 12.38 0.00 42.49 4.09
19 20 0.680280 TCTCTGGGACGACCTGTAGC 60.680 60.000 3.44 0.00 41.11 3.58
72 73 0.915364 CCCTTTCTCCTCTTCCCCAG 59.085 60.000 0.00 0.00 0.00 4.45
75 76 1.610327 GGCCCTTTCTCCTCTTCCC 59.390 63.158 0.00 0.00 0.00 3.97
94 95 0.533755 GCCACATTCATCCTCCTCCG 60.534 60.000 0.00 0.00 0.00 4.63
98 99 2.787994 CCATAGCCACATTCATCCTCC 58.212 52.381 0.00 0.00 0.00 4.30
110 111 3.812544 CAGCCCCAGCCATAGCCA 61.813 66.667 0.00 0.00 41.25 4.75
119 120 3.077359 GCTATATAAACTGCAGCCCCAG 58.923 50.000 15.27 3.34 38.78 4.45
120 121 2.549992 CGCTATATAAACTGCAGCCCCA 60.550 50.000 15.27 0.00 0.00 4.96
130 131 2.334838 CCTCACGCCCGCTATATAAAC 58.665 52.381 0.00 0.00 0.00 2.01
163 164 1.370064 CACCCGTTCGTCCCTCTTT 59.630 57.895 0.00 0.00 0.00 2.52
164 165 1.813728 GACACCCGTTCGTCCCTCTT 61.814 60.000 0.00 0.00 0.00 2.85
174 175 1.069513 TCGACATTGAAGACACCCGTT 59.930 47.619 0.00 0.00 0.00 4.44
176 177 1.068474 GTCGACATTGAAGACACCCG 58.932 55.000 11.55 0.00 35.19 5.28
198 199 1.293498 CGGACACAACCTCTCCCTG 59.707 63.158 0.00 0.00 0.00 4.45
199 200 2.584391 GCGGACACAACCTCTCCCT 61.584 63.158 0.00 0.00 0.00 4.20
201 202 1.079750 GAGCGGACACAACCTCTCC 60.080 63.158 0.00 0.00 36.22 3.71
209 210 4.007644 CCAGCCAGAGCGGACACA 62.008 66.667 0.00 0.00 46.67 3.72
228 229 1.368019 CGTTAGCGCCGCATTCATG 60.368 57.895 13.36 0.00 0.00 3.07
229 230 3.014036 CGTTAGCGCCGCATTCAT 58.986 55.556 13.36 0.00 0.00 2.57
247 248 3.479269 GTCGTCGCCGCTCCAAAG 61.479 66.667 0.00 0.00 0.00 2.77
256 257 2.851104 CTTGAAACGGTCGTCGCC 59.149 61.111 0.00 0.00 43.89 5.54
257 258 2.170273 GCTTGAAACGGTCGTCGC 59.830 61.111 0.00 0.00 43.89 5.19
258 259 2.464189 CGCTTGAAACGGTCGTCG 59.536 61.111 0.00 0.00 45.88 5.12
259 260 2.851104 CCGCTTGAAACGGTCGTC 59.149 61.111 0.00 0.00 45.70 4.20
293 294 1.619669 ATCCCAAGACCCTCCACCC 60.620 63.158 0.00 0.00 0.00 4.61
295 296 0.543749 CTCATCCCAAGACCCTCCAC 59.456 60.000 0.00 0.00 0.00 4.02
296 297 1.274703 GCTCATCCCAAGACCCTCCA 61.275 60.000 0.00 0.00 0.00 3.86
297 298 1.529309 GCTCATCCCAAGACCCTCC 59.471 63.158 0.00 0.00 0.00 4.30
298 299 1.274703 TGGCTCATCCCAAGACCCTC 61.275 60.000 0.00 0.00 30.32 4.30
299 300 1.229951 TGGCTCATCCCAAGACCCT 60.230 57.895 0.00 0.00 30.32 4.34
300 301 1.225704 CTGGCTCATCCCAAGACCC 59.774 63.158 0.00 0.00 33.73 4.46
301 302 1.225704 CCTGGCTCATCCCAAGACC 59.774 63.158 0.00 0.00 33.73 3.85
302 303 1.225704 CCCTGGCTCATCCCAAGAC 59.774 63.158 0.00 0.00 33.73 3.01
303 304 0.846427 AACCCTGGCTCATCCCAAGA 60.846 55.000 0.00 0.00 33.73 3.02
304 305 0.682209 CAACCCTGGCTCATCCCAAG 60.682 60.000 0.00 0.00 33.73 3.61
306 307 1.434513 AACAACCCTGGCTCATCCCA 61.435 55.000 0.00 0.00 0.00 4.37
307 308 0.623723 TAACAACCCTGGCTCATCCC 59.376 55.000 0.00 0.00 0.00 3.85
308 309 1.559682 TCTAACAACCCTGGCTCATCC 59.440 52.381 0.00 0.00 0.00 3.51
310 311 3.421844 GTTTCTAACAACCCTGGCTCAT 58.578 45.455 0.00 0.00 0.00 2.90
311 312 2.808933 CGTTTCTAACAACCCTGGCTCA 60.809 50.000 0.00 0.00 0.00 4.26
312 313 1.804748 CGTTTCTAACAACCCTGGCTC 59.195 52.381 0.00 0.00 0.00 4.70
313 314 1.544759 CCGTTTCTAACAACCCTGGCT 60.545 52.381 0.00 0.00 0.00 4.75
314 315 0.879090 CCGTTTCTAACAACCCTGGC 59.121 55.000 0.00 0.00 0.00 4.85
315 316 1.530323 CCCGTTTCTAACAACCCTGG 58.470 55.000 0.00 0.00 0.00 4.45
316 317 0.879090 GCCCGTTTCTAACAACCCTG 59.121 55.000 0.00 0.00 0.00 4.45
317 318 0.604511 CGCCCGTTTCTAACAACCCT 60.605 55.000 0.00 0.00 0.00 4.34
318 319 0.886043 ACGCCCGTTTCTAACAACCC 60.886 55.000 0.00 0.00 0.00 4.11
319 320 0.236449 CACGCCCGTTTCTAACAACC 59.764 55.000 0.00 0.00 0.00 3.77
320 321 0.236449 CCACGCCCGTTTCTAACAAC 59.764 55.000 0.00 0.00 0.00 3.32
321 322 0.106335 TCCACGCCCGTTTCTAACAA 59.894 50.000 0.00 0.00 0.00 2.83
322 323 0.322322 ATCCACGCCCGTTTCTAACA 59.678 50.000 0.00 0.00 0.00 2.41
323 324 0.725117 CATCCACGCCCGTTTCTAAC 59.275 55.000 0.00 0.00 0.00 2.34
326 327 2.746277 GCATCCACGCCCGTTTCT 60.746 61.111 0.00 0.00 0.00 2.52
328 329 3.055719 CAGCATCCACGCCCGTTT 61.056 61.111 0.00 0.00 0.00 3.60
329 330 4.329545 ACAGCATCCACGCCCGTT 62.330 61.111 0.00 0.00 0.00 4.44
330 331 4.760047 GACAGCATCCACGCCCGT 62.760 66.667 0.00 0.00 0.00 5.28
331 332 4.457496 AGACAGCATCCACGCCCG 62.457 66.667 0.00 0.00 0.00 6.13
332 333 2.821366 CAGACAGCATCCACGCCC 60.821 66.667 0.00 0.00 0.00 6.13
333 334 2.821366 CCAGACAGCATCCACGCC 60.821 66.667 0.00 0.00 0.00 5.68
335 336 1.807165 CGTCCAGACAGCATCCACG 60.807 63.158 0.00 0.00 0.00 4.94
337 338 1.591703 GACGTCCAGACAGCATCCA 59.408 57.895 3.51 0.00 0.00 3.41
340 658 2.573869 CGGACGTCCAGACAGCAT 59.426 61.111 32.80 0.00 35.14 3.79
347 665 3.423154 GGCTTTGCGGACGTCCAG 61.423 66.667 32.80 24.88 35.14 3.86
376 694 4.990526 ACTTCCCCCATATTGCTATCAAG 58.009 43.478 0.00 0.00 35.37 3.02
378 696 4.202567 GGAACTTCCCCCATATTGCTATCA 60.203 45.833 0.00 0.00 0.00 2.15
379 697 4.336280 GGAACTTCCCCCATATTGCTATC 58.664 47.826 0.00 0.00 0.00 2.08
380 698 4.388577 GGAACTTCCCCCATATTGCTAT 57.611 45.455 0.00 0.00 0.00 2.97
382 700 2.755952 GGAACTTCCCCCATATTGCT 57.244 50.000 0.00 0.00 0.00 3.91
398 716 0.893270 CCGTTGTTGCCTGATGGGAA 60.893 55.000 0.00 0.00 41.50 3.97
399 717 1.303236 CCGTTGTTGCCTGATGGGA 60.303 57.895 0.00 0.00 37.23 4.37
400 718 1.178534 AACCGTTGTTGCCTGATGGG 61.179 55.000 0.00 0.00 32.13 4.00
401 719 0.240945 GAACCGTTGTTGCCTGATGG 59.759 55.000 0.00 0.00 33.97 3.51
403 721 1.238439 CAGAACCGTTGTTGCCTGAT 58.762 50.000 0.00 0.00 33.97 2.90
406 724 2.193536 GGCAGAACCGTTGTTGCCT 61.194 57.895 21.23 0.00 39.35 4.75
409 727 0.307760 GTCAGGCAGAACCGTTGTTG 59.692 55.000 0.00 0.00 46.52 3.33
410 728 0.818040 GGTCAGGCAGAACCGTTGTT 60.818 55.000 0.00 0.00 46.52 2.83
411 729 1.227853 GGTCAGGCAGAACCGTTGT 60.228 57.895 0.00 0.00 46.52 3.32
412 730 1.966451 GGGTCAGGCAGAACCGTTG 60.966 63.158 0.00 0.00 46.05 4.10
413 731 2.430367 GGGTCAGGCAGAACCGTT 59.570 61.111 0.00 0.00 46.05 4.44
418 736 2.879756 GCATTTGTAGGGTCAGGCAGAA 60.880 50.000 0.00 0.00 0.00 3.02
419 737 1.340017 GCATTTGTAGGGTCAGGCAGA 60.340 52.381 0.00 0.00 0.00 4.26
420 738 1.098050 GCATTTGTAGGGTCAGGCAG 58.902 55.000 0.00 0.00 0.00 4.85
421 739 0.403655 TGCATTTGTAGGGTCAGGCA 59.596 50.000 0.00 0.00 0.00 4.75
422 740 1.406539 CATGCATTTGTAGGGTCAGGC 59.593 52.381 0.00 0.00 0.00 4.85
423 741 1.406539 GCATGCATTTGTAGGGTCAGG 59.593 52.381 14.21 0.00 0.00 3.86
424 742 2.093890 TGCATGCATTTGTAGGGTCAG 58.906 47.619 18.46 0.00 0.00 3.51
425 743 2.212812 TGCATGCATTTGTAGGGTCA 57.787 45.000 18.46 0.00 0.00 4.02
426 744 4.279169 ACATATGCATGCATTTGTAGGGTC 59.721 41.667 38.75 3.42 43.28 4.46
427 745 4.217510 ACATATGCATGCATTTGTAGGGT 58.782 39.130 38.75 23.17 43.28 4.34
428 746 4.859304 ACATATGCATGCATTTGTAGGG 57.141 40.909 38.75 22.61 43.28 3.53
429 747 5.593968 ACAACATATGCATGCATTTGTAGG 58.406 37.500 39.21 34.77 43.92 3.18
430 748 6.267070 TGACAACATATGCATGCATTTGTAG 58.733 36.000 39.21 27.73 43.92 2.74
431 749 6.127675 ACTGACAACATATGCATGCATTTGTA 60.128 34.615 39.21 28.37 43.92 2.41
432 750 5.074584 TGACAACATATGCATGCATTTGT 57.925 34.783 36.20 36.20 45.62 2.83
433 751 5.005299 CACTGACAACATATGCATGCATTTG 59.995 40.000 35.13 35.13 39.90 2.32
434 752 5.105675 TCACTGACAACATATGCATGCATTT 60.106 36.000 36.23 26.36 37.82 2.32
435 753 4.399934 TCACTGACAACATATGCATGCATT 59.600 37.500 36.23 21.27 37.82 3.56
436 754 3.949113 TCACTGACAACATATGCATGCAT 59.051 39.130 33.92 33.92 40.19 3.96
437 755 3.345414 TCACTGACAACATATGCATGCA 58.655 40.909 25.04 25.04 35.39 3.96
438 756 4.095334 TCTTCACTGACAACATATGCATGC 59.905 41.667 11.82 11.82 35.39 4.06
439 757 5.806366 TCTTCACTGACAACATATGCATG 57.194 39.130 10.16 5.10 38.21 4.06
440 758 7.400599 AAATCTTCACTGACAACATATGCAT 57.599 32.000 3.79 3.79 0.00 3.96
441 759 6.822667 AAATCTTCACTGACAACATATGCA 57.177 33.333 1.58 0.00 0.00 3.96
442 760 7.061441 CACAAAATCTTCACTGACAACATATGC 59.939 37.037 1.58 0.00 0.00 3.14
443 761 8.077991 ACACAAAATCTTCACTGACAACATATG 58.922 33.333 0.00 0.00 0.00 1.78
444 762 8.077991 CACACAAAATCTTCACTGACAACATAT 58.922 33.333 0.00 0.00 0.00 1.78
445 763 7.281999 TCACACAAAATCTTCACTGACAACATA 59.718 33.333 0.00 0.00 0.00 2.29
446 764 6.095300 TCACACAAAATCTTCACTGACAACAT 59.905 34.615 0.00 0.00 0.00 2.71
447 765 5.414144 TCACACAAAATCTTCACTGACAACA 59.586 36.000 0.00 0.00 0.00 3.33
448 766 5.879237 TCACACAAAATCTTCACTGACAAC 58.121 37.500 0.00 0.00 0.00 3.32
449 767 6.507958 TTCACACAAAATCTTCACTGACAA 57.492 33.333 0.00 0.00 0.00 3.18
450 768 5.449041 GCTTCACACAAAATCTTCACTGACA 60.449 40.000 0.00 0.00 0.00 3.58
451 769 4.972440 GCTTCACACAAAATCTTCACTGAC 59.028 41.667 0.00 0.00 0.00 3.51
452 770 4.036734 GGCTTCACACAAAATCTTCACTGA 59.963 41.667 0.00 0.00 0.00 3.41
453 771 4.037208 AGGCTTCACACAAAATCTTCACTG 59.963 41.667 0.00 0.00 0.00 3.66
454 772 4.210331 AGGCTTCACACAAAATCTTCACT 58.790 39.130 0.00 0.00 0.00 3.41
455 773 4.574599 AGGCTTCACACAAAATCTTCAC 57.425 40.909 0.00 0.00 0.00 3.18
456 774 4.202141 CCAAGGCTTCACACAAAATCTTCA 60.202 41.667 0.00 0.00 0.00 3.02
457 775 4.037923 TCCAAGGCTTCACACAAAATCTTC 59.962 41.667 0.00 0.00 0.00 2.87
458 776 3.960102 TCCAAGGCTTCACACAAAATCTT 59.040 39.130 0.00 0.00 0.00 2.40
459 777 3.565307 TCCAAGGCTTCACACAAAATCT 58.435 40.909 0.00 0.00 0.00 2.40
460 778 3.569701 TCTCCAAGGCTTCACACAAAATC 59.430 43.478 0.00 0.00 0.00 2.17
461 779 3.319122 GTCTCCAAGGCTTCACACAAAAT 59.681 43.478 0.00 0.00 0.00 1.82
462 780 2.687935 GTCTCCAAGGCTTCACACAAAA 59.312 45.455 0.00 0.00 0.00 2.44
463 781 2.297701 GTCTCCAAGGCTTCACACAAA 58.702 47.619 0.00 0.00 0.00 2.83
464 782 1.810031 CGTCTCCAAGGCTTCACACAA 60.810 52.381 0.00 0.00 0.00 3.33
465 783 0.249868 CGTCTCCAAGGCTTCACACA 60.250 55.000 0.00 0.00 0.00 3.72
466 784 0.033504 TCGTCTCCAAGGCTTCACAC 59.966 55.000 0.00 0.00 0.00 3.82
467 785 0.033504 GTCGTCTCCAAGGCTTCACA 59.966 55.000 0.00 0.00 0.00 3.58
468 786 1.009389 CGTCGTCTCCAAGGCTTCAC 61.009 60.000 0.00 0.00 0.00 3.18
469 787 1.289066 CGTCGTCTCCAAGGCTTCA 59.711 57.895 0.00 0.00 0.00 3.02
470 788 0.524862 TACGTCGTCTCCAAGGCTTC 59.475 55.000 0.00 0.00 0.00 3.86
471 789 0.243095 GTACGTCGTCTCCAAGGCTT 59.757 55.000 0.00 0.00 0.00 4.35
472 790 1.593296 GGTACGTCGTCTCCAAGGCT 61.593 60.000 0.00 0.00 0.00 4.58
473 791 1.153881 GGTACGTCGTCTCCAAGGC 60.154 63.158 0.00 0.00 0.00 4.35
474 792 1.509923 GGGTACGTCGTCTCCAAGG 59.490 63.158 17.32 0.00 0.00 3.61
475 793 1.136147 CGGGTACGTCGTCTCCAAG 59.864 63.158 17.32 9.51 34.81 3.61
476 794 2.334946 CCGGGTACGTCGTCTCCAA 61.335 63.158 17.32 0.00 38.78 3.53
477 795 2.747460 CCGGGTACGTCGTCTCCA 60.747 66.667 17.32 0.00 38.78 3.86
478 796 3.512516 CCCGGGTACGTCGTCTCC 61.513 72.222 14.18 6.05 38.78 3.71
479 797 3.512516 CCCCGGGTACGTCGTCTC 61.513 72.222 21.85 0.00 38.78 3.36
482 800 4.424711 TAGCCCCGGGTACGTCGT 62.425 66.667 21.85 2.21 38.78 4.34
483 801 3.589881 CTAGCCCCGGGTACGTCG 61.590 72.222 21.85 3.32 38.78 5.12
484 802 3.222121 CCTAGCCCCGGGTACGTC 61.222 72.222 21.85 2.65 38.78 4.34
485 803 4.847367 CCCTAGCCCCGGGTACGT 62.847 72.222 21.85 2.75 38.78 3.57
492 810 3.854669 CAGCTCACCCTAGCCCCG 61.855 72.222 0.00 0.00 43.86 5.73
493 811 2.365635 TCAGCTCACCCTAGCCCC 60.366 66.667 0.00 0.00 43.86 5.80
494 812 2.439104 CCTCAGCTCACCCTAGCCC 61.439 68.421 0.00 0.00 43.86 5.19
495 813 2.439104 CCCTCAGCTCACCCTAGCC 61.439 68.421 0.00 0.00 43.86 3.93
496 814 2.439104 CCCCTCAGCTCACCCTAGC 61.439 68.421 0.00 0.00 43.11 3.42
497 815 1.764054 CCCCCTCAGCTCACCCTAG 60.764 68.421 0.00 0.00 0.00 3.02
498 816 2.368594 CCCCCTCAGCTCACCCTA 59.631 66.667 0.00 0.00 0.00 3.53
514 832 1.971167 TGCCATCAAACGCTGTCCC 60.971 57.895 0.00 0.00 0.00 4.46
516 834 0.310543 TTGTGCCATCAAACGCTGTC 59.689 50.000 0.00 0.00 0.00 3.51
519 837 0.030638 GTGTTGTGCCATCAAACGCT 59.969 50.000 0.00 0.00 0.00 5.07
522 840 1.333619 AGACGTGTTGTGCCATCAAAC 59.666 47.619 0.00 0.00 0.00 2.93
530 848 2.594962 CGGTCCAGACGTGTTGTGC 61.595 63.158 0.00 0.00 0.00 4.57
539 857 0.729116 TCGAATCGTACGGTCCAGAC 59.271 55.000 16.52 0.00 0.00 3.51
541 859 1.542544 GTTCGAATCGTACGGTCCAG 58.457 55.000 16.52 3.44 0.00 3.86
542 860 0.179192 CGTTCGAATCGTACGGTCCA 60.179 55.000 23.37 0.00 44.26 4.02
544 862 2.096799 ATCGTTCGAATCGTACGGTC 57.903 50.000 28.36 12.17 46.90 4.79
549 867 1.193644 CCGCAATCGTTCGAATCGTA 58.806 50.000 16.01 0.00 0.00 3.43
550 868 0.734942 ACCGCAATCGTTCGAATCGT 60.735 50.000 16.01 5.30 0.00 3.73
553 871 0.672401 ACCACCGCAATCGTTCGAAT 60.672 50.000 0.00 0.00 0.00 3.34
555 873 0.881159 AAACCACCGCAATCGTTCGA 60.881 50.000 0.00 0.00 0.00 3.71
557 875 0.589223 TCAAACCACCGCAATCGTTC 59.411 50.000 0.00 0.00 0.00 3.95
569 887 1.906574 AGAATAGCGACCCTCAAACCA 59.093 47.619 0.00 0.00 0.00 3.67
760 1105 4.502962 AGAGAAAGAGAGAGAATTTGCGG 58.497 43.478 0.00 0.00 0.00 5.69
762 1107 6.633856 AGAGAGAGAAAGAGAGAGAATTTGC 58.366 40.000 0.00 0.00 0.00 3.68
777 1138 5.497464 TTGTCAGAGAGAGAGAGAGAGAA 57.503 43.478 0.00 0.00 0.00 2.87
812 1175 4.572795 TCGTGCTTGACTTGTTGTGATTTA 59.427 37.500 0.00 0.00 0.00 1.40
988 1393 3.762429 GATCCATGGCTGCCGCTGA 62.762 63.158 19.23 13.05 36.09 4.26
1240 1667 1.278985 CATGGGCTTGTAGTGGTCTGA 59.721 52.381 0.00 0.00 0.00 3.27
1404 2964 0.038709 GCCAGCTCCTATCGTAGCAG 60.039 60.000 0.00 0.00 41.32 4.24
1494 3147 1.797537 GTCGTAAACGGACCGGTCG 60.798 63.158 27.68 23.43 40.29 4.79
1570 3223 1.878522 CGAGGCTACATTTCGCGCT 60.879 57.895 5.56 0.00 0.00 5.92
1577 3230 0.739813 GTTGTCGCCGAGGCTACATT 60.740 55.000 19.81 0.00 44.27 2.71
1797 3486 2.225041 CCATACCTCCGTCCTCTCCATA 60.225 54.545 0.00 0.00 0.00 2.74
1815 3504 1.140252 GTACGACCCTGCATTACCCAT 59.860 52.381 0.00 0.00 0.00 4.00
1911 3603 1.424493 GCCGCATCTTGGTTCTCGAG 61.424 60.000 5.93 5.93 0.00 4.04
2007 3699 2.264005 TCGGTTTGTGCCTGTACAAT 57.736 45.000 0.00 0.00 40.00 2.71
2037 3729 1.164411 CATGCTTGGCGTTCCTTGTA 58.836 50.000 0.00 0.00 0.00 2.41
2049 3741 2.238942 TATCCACTACGCCATGCTTG 57.761 50.000 0.00 0.00 0.00 4.01
2174 3866 4.452733 ACGCAAGAGGCCCGTAGC 62.453 66.667 0.00 0.00 40.31 3.58
2203 3895 4.491763 CGACGACGATGATTGCATGTAAAA 60.492 41.667 0.00 0.00 42.66 1.52
2236 3928 2.816087 GCTTTGTTGGAAGATGAGAGCA 59.184 45.455 0.00 0.00 0.00 4.26
2280 3975 1.134965 CCGAGGTGGTGAGCTCTTTAG 60.135 57.143 16.19 0.00 43.44 1.85
2282 3977 1.674057 CCGAGGTGGTGAGCTCTTT 59.326 57.895 16.19 0.00 43.44 2.52
2317 4012 7.615365 TCTGGCAAATATGTTTTCTATTCCTGT 59.385 33.333 0.00 0.00 0.00 4.00
2377 4076 1.530720 GTGAACACATGACACATGCGA 59.469 47.619 0.00 0.00 35.06 5.10
2440 4139 9.558648 CAATCAATTGAAAAGTCGAACATATGA 57.441 29.630 13.09 0.00 40.14 2.15
2551 4256 2.354805 CCTTTAGTCCCGGTTCAGGAAG 60.355 54.545 0.00 0.00 34.43 3.46
2670 4375 1.149627 CACCAACCGGGACCAAAGA 59.850 57.895 6.32 0.00 41.15 2.52


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

AutoCloner maintained by Alex Coulton.