Multiple sequence alignment - TraesCS7A01G215700

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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 TraesCS7A01G215700 chr7A 100.000 3835 0 0 1 3835 182021131 182017297 0.000000e+00 7083.0
1 TraesCS7A01G215700 chr7A 97.938 97 2 0 2866 2962 461038441 461038537 6.590000e-38 169.0
2 TraesCS7A01G215700 chr7A 100.000 87 0 0 2869 2955 694046834 694046920 1.100000e-35 161.0
3 TraesCS7A01G215700 chr7D 91.508 2897 149 44 36 2871 178011526 178008666 0.000000e+00 3897.0
4 TraesCS7A01G215700 chr7D 87.706 667 35 19 3175 3835 178008332 178007707 0.000000e+00 734.0
5 TraesCS7A01G215700 chr7D 83.603 433 64 6 1484 1911 629824292 629824722 2.150000e-107 399.0
6 TraesCS7A01G215700 chr7D 94.273 227 8 2 2953 3177 178008668 178008445 3.670000e-90 342.0
7 TraesCS7A01G215700 chr7B 90.075 2519 128 54 388 2871 144079024 144076593 0.000000e+00 3155.0
8 TraesCS7A01G215700 chr7B 91.525 413 31 4 3425 3835 144075307 144074897 2.000000e-157 566.0
9 TraesCS7A01G215700 chr7B 82.910 433 67 6 1484 1911 732644809 732645239 2.160000e-102 383.0
10 TraesCS7A01G215700 chr7B 90.592 287 16 3 3012 3298 144075644 144075369 1.680000e-98 370.0
11 TraesCS7A01G215700 chr3A 81.992 261 30 12 128 374 111840102 111839845 5.020000e-49 206.0
12 TraesCS7A01G215700 chr3A 78.541 233 30 10 140 361 208722480 208722703 6.680000e-28 135.0
13 TraesCS7A01G215700 chr5A 82.031 256 29 9 134 374 281137476 281137729 6.500000e-48 202.0
14 TraesCS7A01G215700 chr4A 82.101 257 27 11 134 374 572708417 572708670 6.500000e-48 202.0
15 TraesCS7A01G215700 chr4A 93.878 98 5 1 2867 2964 42254271 42254367 3.090000e-31 147.0
16 TraesCS7A01G215700 chr1B 81.250 256 30 11 134 374 615402435 615402183 1.410000e-44 191.0
17 TraesCS7A01G215700 chr1B 79.508 244 44 5 134 375 505109530 505109291 6.590000e-38 169.0
18 TraesCS7A01G215700 chr1D 89.865 148 13 1 133 278 408464306 408464453 5.060000e-44 189.0
19 TraesCS7A01G215700 chr2D 81.333 225 34 6 134 352 18635941 18636163 3.940000e-40 176.0
20 TraesCS7A01G215700 chr1A 88.435 147 15 1 134 278 314432524 314432670 3.940000e-40 176.0
21 TraesCS7A01G215700 chr4B 79.747 237 34 9 134 368 656136180 656136404 3.970000e-35 159.0
22 TraesCS7A01G215700 chr5D 94.898 98 5 0 2862 2959 430647534 430647631 1.840000e-33 154.0
23 TraesCS7A01G215700 chr2B 95.789 95 4 0 2864 2958 77856058 77856152 1.840000e-33 154.0
24 TraesCS7A01G215700 chr2B 93.878 98 6 0 2869 2966 245476400 245476497 8.580000e-32 148.0
25 TraesCS7A01G215700 chr5B 92.308 104 7 1 2852 2954 612333407 612333510 3.090000e-31 147.0
26 TraesCS7A01G215700 chr5B 97.143 35 1 0 299 333 638760494 638760460 4.140000e-05 60.2
27 TraesCS7A01G215700 chr2A 91.346 104 8 1 2852 2954 747678020 747677917 1.440000e-29 141.0
28 TraesCS7A01G215700 chr6A 89.815 108 9 2 2869 2976 249160194 249160299 1.860000e-28 137.0
29 TraesCS7A01G215700 chr3D 85.185 81 10 2 289 369 69828961 69828883 8.830000e-12 82.4


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 TraesCS7A01G215700 chr7A 182017297 182021131 3834 True 7083.000000 7083 100.000000 1 3835 1 chr7A.!!$R1 3834
1 TraesCS7A01G215700 chr7D 178007707 178011526 3819 True 1657.666667 3897 91.162333 36 3835 3 chr7D.!!$R1 3799
2 TraesCS7A01G215700 chr7B 144074897 144079024 4127 True 1363.666667 3155 90.730667 388 3835 3 chr7B.!!$R1 3447

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
190 195 0.179073 GCGCATACACTCATCCCTGT 60.179 55.000 0.30 0.00 0.00 4.00 F
1077 1124 0.252742 TGGAGGAAGGGAGGAAGGAC 60.253 60.000 0.00 0.00 0.00 3.85 F
1371 1420 1.149361 CCAAATGGCATGTCGCATGC 61.149 55.000 26.43 26.43 45.17 4.06 F
2139 2201 1.266446 CACACATTTGCACGTCCATCA 59.734 47.619 0.00 0.00 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1219 1266 0.029300 CGGGCATGCAAAGATAACCG 59.971 55.0 21.36 16.17 0.0 4.44 R
2361 2431 0.032267 GACAGCCGCATCTACTACCC 59.968 60.0 0.00 0.00 0.0 3.69 R
2362 2432 0.032267 GGACAGCCGCATCTACTACC 59.968 60.0 0.00 0.00 0.0 3.18 R
2940 3036 0.108281 GCCTTGTACTCCCTCCGTTC 60.108 60.0 0.00 0.00 0.0 3.95 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
24 25 7.737972 TTGAAGAAATATTCTCGTGTTTCCA 57.262 32.000 0.00 0.00 39.61 3.53
25 26 7.737972 TGAAGAAATATTCTCGTGTTTCCAA 57.262 32.000 0.00 0.00 39.61 3.53
26 27 8.160521 TGAAGAAATATTCTCGTGTTTCCAAA 57.839 30.769 0.00 0.00 39.61 3.28
27 28 8.625651 TGAAGAAATATTCTCGTGTTTCCAAAA 58.374 29.630 0.00 0.00 39.61 2.44
28 29 9.626045 GAAGAAATATTCTCGTGTTTCCAAAAT 57.374 29.630 0.00 0.00 39.61 1.82
29 30 9.981114 AAGAAATATTCTCGTGTTTCCAAAATT 57.019 25.926 0.00 0.00 39.61 1.82
30 31 9.981114 AGAAATATTCTCGTGTTTCCAAAATTT 57.019 25.926 0.00 0.00 34.07 1.82
32 33 9.981114 AAATATTCTCGTGTTTCCAAAATTTCT 57.019 25.926 0.00 0.00 0.00 2.52
33 34 8.970691 ATATTCTCGTGTTTCCAAAATTTCTG 57.029 30.769 0.00 0.00 0.00 3.02
34 35 5.828299 TCTCGTGTTTCCAAAATTTCTGT 57.172 34.783 0.00 0.00 0.00 3.41
38 39 6.390721 TCGTGTTTCCAAAATTTCTGTGAAA 58.609 32.000 0.00 0.00 0.00 2.69
118 120 2.356125 GGCTTGCAGATAAGGGAGTTGA 60.356 50.000 0.00 0.00 0.00 3.18
164 169 4.153655 CACAATATAGATGCAAGCGCTCAT 59.846 41.667 12.06 11.47 39.64 2.90
182 187 4.438145 GCTCATATATACGCGCATACACTC 59.562 45.833 5.73 0.00 0.00 3.51
184 189 6.131544 TCATATATACGCGCATACACTCAT 57.868 37.500 5.73 0.00 0.00 2.90
189 194 1.217585 CGCGCATACACTCATCCCTG 61.218 60.000 8.75 0.00 0.00 4.45
190 195 0.179073 GCGCATACACTCATCCCTGT 60.179 55.000 0.30 0.00 0.00 4.00
194 199 2.939103 GCATACACTCATCCCTGTGAAC 59.061 50.000 0.00 0.00 37.59 3.18
195 200 3.619733 GCATACACTCATCCCTGTGAACA 60.620 47.826 0.00 0.00 37.59 3.18
197 202 1.270305 ACACTCATCCCTGTGAACACG 60.270 52.381 0.00 0.00 37.59 4.49
199 204 1.354337 CTCATCCCTGTGAACACGCG 61.354 60.000 3.53 3.53 0.00 6.01
203 208 3.268603 CCTGTGAACACGCGCACA 61.269 61.111 14.97 14.97 42.25 4.57
206 211 2.350760 GTGAACACGCGCACACAC 60.351 61.111 5.73 8.71 35.19 3.82
207 212 3.568743 TGAACACGCGCACACACC 61.569 61.111 5.73 0.00 0.00 4.16
208 213 4.307908 GAACACGCGCACACACCC 62.308 66.667 5.73 0.00 0.00 4.61
209 214 4.849310 AACACGCGCACACACCCT 62.849 61.111 5.73 0.00 0.00 4.34
210 215 3.448533 AACACGCGCACACACCCTA 62.449 57.895 5.73 0.00 0.00 3.53
211 216 3.411351 CACGCGCACACACCCTAC 61.411 66.667 5.73 0.00 0.00 3.18
214 220 4.323477 GCGCACACACCCTACCCA 62.323 66.667 0.30 0.00 0.00 4.51
220 226 2.106511 GCACACACCCTACCCATATGAT 59.893 50.000 3.65 0.00 0.00 2.45
226 232 3.261897 CACCCTACCCATATGATCACCTC 59.738 52.174 3.65 0.00 0.00 3.85
241 247 1.379176 CCTCCGAGAGACTGAGCCA 60.379 63.158 0.00 0.00 0.00 4.75
248 254 2.035704 CGAGAGACTGAGCCAGCATATT 59.964 50.000 2.50 0.00 34.37 1.28
254 260 5.549347 AGACTGAGCCAGCATATTATCTTG 58.451 41.667 2.50 0.00 34.37 3.02
263 269 9.007901 AGCCAGCATATTATCTTGAGATTTTAC 57.992 33.333 0.00 0.00 36.05 2.01
273 279 8.561932 TATCTTGAGATTTTACGAAGTCATCG 57.438 34.615 0.00 0.00 44.98 3.84
282 299 2.913777 CGAAGTCATCGTAGGTGACA 57.086 50.000 14.80 0.00 46.46 3.58
284 301 2.418976 CGAAGTCATCGTAGGTGACAGA 59.581 50.000 14.80 0.00 46.46 3.41
287 304 5.407407 AAGTCATCGTAGGTGACAGAAAT 57.593 39.130 14.80 0.00 46.46 2.17
296 313 5.336055 CGTAGGTGACAGAAATGTCTCTTCT 60.336 44.000 9.57 3.22 39.41 2.85
305 322 6.642950 ACAGAAATGTCTCTTCTCACTAAACG 59.357 38.462 0.00 0.00 30.58 3.60
307 324 2.929960 TGTCTCTTCTCACTAAACGCG 58.070 47.619 3.53 3.53 0.00 6.01
308 325 1.649662 GTCTCTTCTCACTAAACGCGC 59.350 52.381 5.73 0.00 0.00 6.86
324 341 1.574477 CGCGCATCGTCAAAAATTCTG 59.426 47.619 8.75 0.00 0.00 3.02
358 375 5.431765 AGAATAAATGCGATCACCAAGACT 58.568 37.500 0.00 0.00 0.00 3.24
385 431 1.454847 TGGTGGGCACACTGTTTCC 60.455 57.895 20.52 0.70 46.85 3.13
456 502 3.486209 GCCGTCAGTCAAAAAGAAACGAA 60.486 43.478 0.00 0.00 33.34 3.85
471 517 2.365408 ACGAAACGAGATCCTTGGAC 57.635 50.000 0.00 0.00 0.00 4.02
570 616 1.227999 CGGCGGTGTTGATGAGTGTT 61.228 55.000 0.00 0.00 0.00 3.32
678 724 2.117156 ACGCAGCCAATGGAGATGC 61.117 57.895 2.05 8.97 0.00 3.91
680 726 2.719979 CAGCCAATGGAGATGCGC 59.280 61.111 2.05 0.00 0.00 6.09
681 727 1.822613 CAGCCAATGGAGATGCGCT 60.823 57.895 9.73 0.00 0.00 5.92
729 775 1.154672 CCGTGTCGTGTGAAATGCG 60.155 57.895 0.00 0.00 0.00 4.73
732 778 0.579630 GTGTCGTGTGAAATGCGTCA 59.420 50.000 0.00 0.00 0.00 4.35
754 800 4.744795 AGCATACTACACCTTCTGGAAG 57.255 45.455 3.57 3.57 38.14 3.46
755 801 4.353777 AGCATACTACACCTTCTGGAAGA 58.646 43.478 11.44 0.00 44.68 2.87
771 817 4.876125 TGGAAGAGAGAATATCATCGCAC 58.124 43.478 0.00 0.00 0.00 5.34
772 818 4.586421 TGGAAGAGAGAATATCATCGCACT 59.414 41.667 0.00 0.00 0.00 4.40
773 819 4.922692 GGAAGAGAGAATATCATCGCACTG 59.077 45.833 0.00 0.00 0.00 3.66
774 820 5.508825 GGAAGAGAGAATATCATCGCACTGT 60.509 44.000 0.00 0.00 0.00 3.55
775 821 6.294231 GGAAGAGAGAATATCATCGCACTGTA 60.294 42.308 0.00 0.00 0.00 2.74
776 822 6.641169 AGAGAGAATATCATCGCACTGTAA 57.359 37.500 0.00 0.00 0.00 2.41
777 823 6.676950 AGAGAGAATATCATCGCACTGTAAG 58.323 40.000 0.00 0.00 42.29 2.34
821 867 1.115326 AACCAAAGCAGAGGTTGGCC 61.115 55.000 0.00 0.00 46.96 5.36
847 893 2.652313 TCCAAACGGCATGGAAAGG 58.348 52.632 3.89 0.00 43.84 3.11
853 899 0.474184 ACGGCATGGAAAGGGATAGG 59.526 55.000 0.00 0.00 0.00 2.57
1077 1124 0.252742 TGGAGGAAGGGAGGAAGGAC 60.253 60.000 0.00 0.00 0.00 3.85
1167 1214 3.742433 AGATCGCTTCTAGGGTTCATG 57.258 47.619 0.00 0.00 31.59 3.07
1185 1232 1.500474 TGAATCCGCATCTCTCCCTT 58.500 50.000 0.00 0.00 0.00 3.95
1215 1262 4.998671 TGCAGATCTCTCTTCGATCTTT 57.001 40.909 0.00 0.00 43.74 2.52
1217 1264 6.070897 TGCAGATCTCTCTTCGATCTTTAG 57.929 41.667 0.00 0.00 43.74 1.85
1219 1266 6.142817 GCAGATCTCTCTTCGATCTTTAGAC 58.857 44.000 0.00 0.00 43.74 2.59
1220 1267 6.362686 CAGATCTCTCTTCGATCTTTAGACG 58.637 44.000 0.00 0.00 43.74 4.18
1225 1272 6.766944 TCTCTCTTCGATCTTTAGACGGTTAT 59.233 38.462 0.00 0.00 0.00 1.89
1258 1305 3.564511 CGCACAAACTTCTGGTAATTGG 58.435 45.455 0.00 0.00 0.00 3.16
1354 1403 1.799157 AAGCCATTAGCCACCCACCA 61.799 55.000 0.00 0.00 45.47 4.17
1371 1420 1.149361 CCAAATGGCATGTCGCATGC 61.149 55.000 26.43 26.43 45.17 4.06
1451 1501 4.266502 TGTTGTTGCGTGAAAGTTAATTGC 59.733 37.500 0.00 0.00 0.00 3.56
1468 1522 7.915397 AGTTAATTGCGTGTGGATTATTGATTC 59.085 33.333 0.00 0.00 0.00 2.52
1476 1530 6.845782 CGTGTGGATTATTGATTCATTGTACG 59.154 38.462 0.00 0.00 0.00 3.67
1482 1536 8.212495 GGATTATTGATTCATTGTACGTACGTC 58.788 37.037 26.53 16.55 0.00 4.34
1483 1537 5.961395 ATTGATTCATTGTACGTACGTCC 57.039 39.130 26.53 15.03 0.00 4.79
1860 1914 3.515502 TCCTCGAGTTCATCATCACCTTT 59.484 43.478 12.31 0.00 0.00 3.11
1927 1981 3.423776 CGTAAGCAGATCTATCTCGGTCG 60.424 52.174 0.00 0.00 34.22 4.79
1954 2008 6.949327 CGAATTAACAACAAAACTCGCGTATA 59.051 34.615 5.77 0.00 0.00 1.47
1958 2012 8.644264 TTAACAACAAAACTCGCGTATAATTC 57.356 30.769 5.77 0.00 0.00 2.17
1978 2032 3.054878 TCGCTAACGAGTTGAGAAAACC 58.945 45.455 0.00 0.00 45.12 3.27
1979 2033 2.160013 CGCTAACGAGTTGAGAAAACCG 60.160 50.000 0.00 0.00 43.93 4.44
1980 2034 2.798847 GCTAACGAGTTGAGAAAACCGT 59.201 45.455 0.00 0.00 0.00 4.83
2139 2201 1.266446 CACACATTTGCACGTCCATCA 59.734 47.619 0.00 0.00 0.00 3.07
2178 2247 2.238942 TACAGCCGCATAAGTCCATG 57.761 50.000 0.00 0.00 0.00 3.66
2189 2258 6.038161 CCGCATAAGTCCATGTAGAATTTTCA 59.962 38.462 0.00 0.00 0.00 2.69
2307 2376 6.846283 GTCGTGTTTCAGTCAAAAAGATAGTG 59.154 38.462 0.00 0.00 0.00 2.74
2309 2378 5.915196 GTGTTTCAGTCAAAAAGATAGTGGC 59.085 40.000 0.00 0.00 0.00 5.01
2354 2424 6.966632 TCGTGTTTCATCAGTCAAAAAGAAAG 59.033 34.615 0.00 0.00 0.00 2.62
2355 2425 6.197096 CGTGTTTCATCAGTCAAAAAGAAAGG 59.803 38.462 0.00 0.00 0.00 3.11
2356 2426 7.257722 GTGTTTCATCAGTCAAAAAGAAAGGA 58.742 34.615 0.00 0.00 0.00 3.36
2357 2427 7.759433 GTGTTTCATCAGTCAAAAAGAAAGGAA 59.241 33.333 0.00 0.00 0.00 3.36
2358 2428 8.310382 TGTTTCATCAGTCAAAAAGAAAGGAAA 58.690 29.630 0.00 0.00 0.00 3.13
2359 2429 9.317936 GTTTCATCAGTCAAAAAGAAAGGAAAT 57.682 29.630 0.00 0.00 0.00 2.17
2360 2430 9.889128 TTTCATCAGTCAAAAAGAAAGGAAATT 57.111 25.926 0.00 0.00 0.00 1.82
2361 2431 8.876275 TCATCAGTCAAAAAGAAAGGAAATTG 57.124 30.769 0.00 0.00 0.00 2.32
2362 2432 7.927629 TCATCAGTCAAAAAGAAAGGAAATTGG 59.072 33.333 0.00 0.00 0.00 3.16
2363 2433 6.581712 TCAGTCAAAAAGAAAGGAAATTGGG 58.418 36.000 0.00 0.00 0.00 4.12
2364 2434 6.156083 TCAGTCAAAAAGAAAGGAAATTGGGT 59.844 34.615 0.00 0.00 0.00 4.51
2365 2435 7.343316 TCAGTCAAAAAGAAAGGAAATTGGGTA 59.657 33.333 0.00 0.00 0.00 3.69
2366 2436 7.653311 CAGTCAAAAAGAAAGGAAATTGGGTAG 59.347 37.037 0.00 0.00 0.00 3.18
2383 2453 1.409427 GTAGTAGATGCGGCTGTCCTT 59.591 52.381 0.00 0.00 0.00 3.36
2384 2454 0.905357 AGTAGATGCGGCTGTCCTTT 59.095 50.000 0.00 0.00 0.00 3.11
2385 2455 1.009829 GTAGATGCGGCTGTCCTTTG 58.990 55.000 0.00 0.00 0.00 2.77
2458 2539 2.046023 TTGATGGCTGTCCGCTGG 60.046 61.111 0.00 0.00 39.13 4.85
2477 2558 3.286751 CCTGCCACGGTTGGTGTG 61.287 66.667 0.00 0.00 45.98 3.82
2835 2924 1.096416 GAACTCCGTCTCCGTCTGAT 58.904 55.000 0.00 0.00 0.00 2.90
2836 2925 1.473278 GAACTCCGTCTCCGTCTGATT 59.527 52.381 0.00 0.00 0.00 2.57
2871 2967 8.180267 CACTAGCAACGTTGTATTACTACTACT 58.820 37.037 27.78 14.39 33.22 2.57
2872 2968 8.394121 ACTAGCAACGTTGTATTACTACTACTC 58.606 37.037 27.78 7.33 33.22 2.59
2873 2969 6.558909 AGCAACGTTGTATTACTACTACTCC 58.441 40.000 27.78 6.71 33.22 3.85
2874 2970 5.745769 GCAACGTTGTATTACTACTACTCCC 59.254 44.000 27.78 2.76 33.22 4.30
2875 2971 6.405176 GCAACGTTGTATTACTACTACTCCCT 60.405 42.308 27.78 0.00 33.22 4.20
2876 2972 6.934048 ACGTTGTATTACTACTACTCCCTC 57.066 41.667 6.80 0.00 33.22 4.30
2877 2973 5.825151 ACGTTGTATTACTACTACTCCCTCC 59.175 44.000 6.80 0.00 33.22 4.30
2878 2974 5.049818 CGTTGTATTACTACTACTCCCTCCG 60.050 48.000 6.80 0.00 33.22 4.63
2879 2975 5.636903 TGTATTACTACTACTCCCTCCGT 57.363 43.478 0.00 0.00 0.00 4.69
2880 2976 6.006275 TGTATTACTACTACTCCCTCCGTT 57.994 41.667 0.00 0.00 0.00 4.44
2881 2977 6.058183 TGTATTACTACTACTCCCTCCGTTC 58.942 44.000 0.00 0.00 0.00 3.95
2882 2978 2.433662 ACTACTACTCCCTCCGTTCC 57.566 55.000 0.00 0.00 0.00 3.62
2883 2979 1.637553 ACTACTACTCCCTCCGTTCCA 59.362 52.381 0.00 0.00 0.00 3.53
2884 2980 2.299521 CTACTACTCCCTCCGTTCCAG 58.700 57.143 0.00 0.00 0.00 3.86
2885 2981 0.702902 ACTACTCCCTCCGTTCCAGA 59.297 55.000 0.00 0.00 0.00 3.86
2886 2982 1.076677 ACTACTCCCTCCGTTCCAGAA 59.923 52.381 0.00 0.00 0.00 3.02
2887 2983 2.292323 ACTACTCCCTCCGTTCCAGAAT 60.292 50.000 0.00 0.00 0.00 2.40
2888 2984 2.544844 ACTCCCTCCGTTCCAGAATA 57.455 50.000 0.00 0.00 0.00 1.75
2889 2985 2.389715 ACTCCCTCCGTTCCAGAATAG 58.610 52.381 0.00 0.00 0.00 1.73
2890 2986 2.024273 ACTCCCTCCGTTCCAGAATAGA 60.024 50.000 0.00 0.00 0.00 1.98
2891 2987 3.235200 CTCCCTCCGTTCCAGAATAGAT 58.765 50.000 0.00 0.00 0.00 1.98
2892 2988 2.965831 TCCCTCCGTTCCAGAATAGATG 59.034 50.000 0.00 0.00 0.00 2.90
2893 2989 2.965831 CCCTCCGTTCCAGAATAGATGA 59.034 50.000 0.00 0.00 0.00 2.92
2894 2990 3.243907 CCCTCCGTTCCAGAATAGATGAC 60.244 52.174 0.00 0.00 0.00 3.06
2895 2991 3.639094 CCTCCGTTCCAGAATAGATGACT 59.361 47.826 0.00 0.00 0.00 3.41
2896 2992 4.261825 CCTCCGTTCCAGAATAGATGACTC 60.262 50.000 0.00 0.00 0.00 3.36
2897 2993 4.278310 TCCGTTCCAGAATAGATGACTCA 58.722 43.478 0.00 0.00 0.00 3.41
2898 2994 4.709886 TCCGTTCCAGAATAGATGACTCAA 59.290 41.667 0.00 0.00 0.00 3.02
2899 2995 4.806247 CCGTTCCAGAATAGATGACTCAAC 59.194 45.833 0.00 0.00 0.00 3.18
2900 2996 5.394663 CCGTTCCAGAATAGATGACTCAACT 60.395 44.000 0.00 0.00 0.00 3.16
2901 2997 6.102663 CGTTCCAGAATAGATGACTCAACTT 58.897 40.000 0.00 0.00 0.00 2.66
2902 2998 6.591834 CGTTCCAGAATAGATGACTCAACTTT 59.408 38.462 0.00 0.00 0.00 2.66
2903 2999 7.412346 CGTTCCAGAATAGATGACTCAACTTTG 60.412 40.741 0.00 0.00 0.00 2.77
2904 3000 7.009179 TCCAGAATAGATGACTCAACTTTGT 57.991 36.000 0.00 0.00 0.00 2.83
2905 3001 8.134202 TCCAGAATAGATGACTCAACTTTGTA 57.866 34.615 0.00 0.00 0.00 2.41
2906 3002 8.035394 TCCAGAATAGATGACTCAACTTTGTAC 58.965 37.037 0.00 0.00 0.00 2.90
2907 3003 8.037758 CCAGAATAGATGACTCAACTTTGTACT 58.962 37.037 0.00 0.00 0.00 2.73
2930 3026 7.567458 ACTAACTTTAGTACAAACTTGGGTCA 58.433 34.615 0.00 0.00 41.92 4.02
2931 3027 8.215736 ACTAACTTTAGTACAAACTTGGGTCAT 58.784 33.333 0.00 0.00 41.92 3.06
2932 3028 7.506328 AACTTTAGTACAAACTTGGGTCATC 57.494 36.000 0.00 0.00 37.15 2.92
2933 3029 6.002082 ACTTTAGTACAAACTTGGGTCATCC 58.998 40.000 0.00 0.00 37.15 3.51
2934 3030 5.570205 TTAGTACAAACTTGGGTCATCCA 57.430 39.130 0.00 0.00 45.43 3.41
2935 3031 4.657814 AGTACAAACTTGGGTCATCCAT 57.342 40.909 0.00 0.00 46.52 3.41
2936 3032 4.998051 AGTACAAACTTGGGTCATCCATT 58.002 39.130 0.00 0.00 46.52 3.16
2937 3033 5.393866 AGTACAAACTTGGGTCATCCATTT 58.606 37.500 0.00 0.00 46.52 2.32
2938 3034 5.838521 AGTACAAACTTGGGTCATCCATTTT 59.161 36.000 0.00 0.00 46.52 1.82
2939 3035 4.959723 ACAAACTTGGGTCATCCATTTTG 58.040 39.130 9.22 9.22 46.52 2.44
2940 3036 4.202346 ACAAACTTGGGTCATCCATTTTGG 60.202 41.667 13.69 0.00 46.52 3.28
2949 3045 3.662290 TCCATTTTGGAACGGAGGG 57.338 52.632 0.00 0.00 45.00 4.30
2950 3046 1.068948 TCCATTTTGGAACGGAGGGA 58.931 50.000 0.00 0.00 45.00 4.20
2951 3047 1.004277 TCCATTTTGGAACGGAGGGAG 59.996 52.381 0.00 0.00 45.00 4.30
2952 3048 1.271926 CCATTTTGGAACGGAGGGAGT 60.272 52.381 0.00 0.00 40.96 3.85
2953 3049 2.026636 CCATTTTGGAACGGAGGGAGTA 60.027 50.000 0.00 0.00 40.96 2.59
2954 3050 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
2986 3082 2.516589 CGTCGTCATCGTGGCCATG 61.517 63.158 19.62 19.62 38.33 3.66
2992 3088 0.033366 TCATCGTGGCCATGTATCCG 59.967 55.000 24.24 14.60 0.00 4.18
3096 4084 4.319139 TGTGTTTTGGAACCATGTGATG 57.681 40.909 0.00 0.00 34.80 3.07
3198 4301 5.652744 AGTAGCTTAATTAATTCCGTGCG 57.347 39.130 3.39 0.00 0.00 5.34
3213 4316 1.117234 GTGCGGTTGTTGTTTTAGCG 58.883 50.000 0.00 0.00 36.02 4.26
3216 4319 0.664224 CGGTTGTTGTTTTAGCGGGT 59.336 50.000 0.00 0.00 0.00 5.28
3217 4320 1.598430 CGGTTGTTGTTTTAGCGGGTG 60.598 52.381 0.00 0.00 0.00 4.61
3218 4321 1.677052 GGTTGTTGTTTTAGCGGGTGA 59.323 47.619 0.00 0.00 0.00 4.02
3219 4322 2.099427 GGTTGTTGTTTTAGCGGGTGAA 59.901 45.455 0.00 0.00 0.00 3.18
3306 4413 3.501396 CCTTGTGGCGCATTCGAT 58.499 55.556 10.83 0.00 38.10 3.59
3307 4414 2.689083 CCTTGTGGCGCATTCGATA 58.311 52.632 10.83 0.00 38.10 2.92
3308 4415 0.583438 CCTTGTGGCGCATTCGATAG 59.417 55.000 10.83 0.00 38.10 2.08
3309 4416 0.583438 CTTGTGGCGCATTCGATAGG 59.417 55.000 10.83 0.00 38.10 2.57
3310 4417 0.176910 TTGTGGCGCATTCGATAGGA 59.823 50.000 10.83 0.00 38.10 2.94
3311 4418 0.176910 TGTGGCGCATTCGATAGGAA 59.823 50.000 10.83 0.00 39.42 3.36
3312 4419 1.202639 TGTGGCGCATTCGATAGGAAT 60.203 47.619 10.83 0.00 46.29 3.01
3313 4420 1.461127 GTGGCGCATTCGATAGGAATC 59.539 52.381 10.83 0.00 43.52 2.52
3314 4421 1.344438 TGGCGCATTCGATAGGAATCT 59.656 47.619 10.83 0.00 43.52 2.40
3315 4422 1.996191 GGCGCATTCGATAGGAATCTC 59.004 52.381 10.83 0.00 43.52 2.75
3316 4423 2.610479 GGCGCATTCGATAGGAATCTCA 60.610 50.000 10.83 0.00 43.52 3.27
3317 4424 2.665537 GCGCATTCGATAGGAATCTCAG 59.334 50.000 0.30 0.00 43.52 3.35
3318 4425 2.665537 CGCATTCGATAGGAATCTCAGC 59.334 50.000 0.00 0.00 43.52 4.26
3319 4426 2.665537 GCATTCGATAGGAATCTCAGCG 59.334 50.000 0.00 0.00 43.52 5.18
3320 4427 2.423926 TTCGATAGGAATCTCAGCGC 57.576 50.000 0.00 0.00 0.00 5.92
3321 4428 1.318576 TCGATAGGAATCTCAGCGCA 58.681 50.000 11.47 0.00 0.00 6.09
3355 4462 1.753073 CCATTGGGAGGAAACATCTGC 59.247 52.381 0.00 0.00 35.59 4.26
3377 4484 1.726248 CATGACACAATCGTTCGCTCA 59.274 47.619 0.00 0.00 0.00 4.26
3395 4502 1.207089 TCATTTGACGCTACCTGAGGG 59.793 52.381 2.38 0.00 43.73 4.30
3396 4503 1.207089 CATTTGACGCTACCTGAGGGA 59.793 52.381 2.38 0.00 40.59 4.20
3398 4505 0.606604 TTGACGCTACCTGAGGGAAC 59.393 55.000 2.38 0.00 40.59 3.62
3399 4506 0.541063 TGACGCTACCTGAGGGAACA 60.541 55.000 2.38 0.00 40.59 3.18
3401 4508 0.320697 ACGCTACCTGAGGGAACAAC 59.679 55.000 2.38 0.00 40.59 3.32
3402 4509 0.391263 CGCTACCTGAGGGAACAACC 60.391 60.000 2.38 0.00 40.59 3.77
3403 4510 0.984995 GCTACCTGAGGGAACAACCT 59.015 55.000 2.38 0.00 45.57 3.50
3405 4512 2.876079 GCTACCTGAGGGAACAACCTTG 60.876 54.545 2.38 0.00 42.10 3.61
3406 4513 0.478507 ACCTGAGGGAACAACCTTGG 59.521 55.000 2.38 0.00 42.10 3.61
3407 4514 0.478507 CCTGAGGGAACAACCTTGGT 59.521 55.000 0.00 0.00 42.10 3.67
3408 4515 1.609208 CTGAGGGAACAACCTTGGTG 58.391 55.000 0.00 0.00 42.10 4.17
3409 4516 1.142870 CTGAGGGAACAACCTTGGTGA 59.857 52.381 0.00 0.00 42.10 4.02
3410 4517 1.142870 TGAGGGAACAACCTTGGTGAG 59.857 52.381 0.00 0.00 42.10 3.51
3432 4539 8.057011 GTGAGGAAACTTTTTCCCCCTATATTA 58.943 37.037 13.05 0.00 44.43 0.98
3434 4541 7.067421 AGGAAACTTTTTCCCCCTATATTAGC 58.933 38.462 13.05 0.00 37.44 3.09
3470 4578 6.711277 TCTATGTGAAGTATGGCAGTTCTTT 58.289 36.000 0.00 0.00 37.46 2.52
3479 4587 3.096489 TGGCAGTTCTTTTGATGCAAC 57.904 42.857 0.00 0.00 36.46 4.17
3518 4626 4.456911 AGACATGCGTGACAAATTCTCATT 59.543 37.500 14.17 0.00 0.00 2.57
3538 4646 2.459060 TGCAACATGGCAATTCTTGG 57.541 45.000 0.00 0.00 41.65 3.61
3540 4648 2.367894 TGCAACATGGCAATTCTTGGAA 59.632 40.909 0.00 0.00 41.65 3.53
3541 4649 3.181457 TGCAACATGGCAATTCTTGGAAA 60.181 39.130 0.00 0.00 41.65 3.13
3542 4650 3.814283 GCAACATGGCAATTCTTGGAAAA 59.186 39.130 0.00 0.00 0.00 2.29
3543 4651 4.319694 GCAACATGGCAATTCTTGGAAAAC 60.320 41.667 0.00 0.00 0.00 2.43
3570 4681 2.224523 TGAAACAATGAGCCTCCTCGTT 60.225 45.455 0.00 0.00 45.79 3.85
3581 4692 2.098117 GCCTCCTCGTTGATTTCCATTG 59.902 50.000 0.00 0.00 0.00 2.82
3585 4696 2.684881 CCTCGTTGATTTCCATTGGAGG 59.315 50.000 5.36 0.00 32.96 4.30
3590 4701 2.722094 TGATTTCCATTGGAGGAACCG 58.278 47.619 5.36 0.00 46.85 4.44
3626 4738 3.904136 AGCACAAAAGAAAGATGTCCG 57.096 42.857 0.00 0.00 0.00 4.79
3629 4741 3.853307 GCACAAAAGAAAGATGTCCGGTG 60.853 47.826 0.00 0.00 0.00 4.94
3638 4750 2.816411 AGATGTCCGGTGTTCTAGGAA 58.184 47.619 0.00 0.00 35.60 3.36
3639 4751 2.496470 AGATGTCCGGTGTTCTAGGAAC 59.504 50.000 0.00 3.75 35.60 3.62
3663 4775 3.652581 GGACTAAGCCCAGCAAACT 57.347 52.632 0.00 0.00 0.00 2.66
3701 4813 7.518848 CGAAAGAAGAAAGACATGATCACACAA 60.519 37.037 0.00 0.00 0.00 3.33
3717 4829 1.001181 CACAAAATCAGCACAAGGGGG 59.999 52.381 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.737972 TGGAAACACGAGAATATTTCTTCAA 57.262 32.000 0.00 0.00 36.01 2.69
1 2 7.737972 TTGGAAACACGAGAATATTTCTTCA 57.262 32.000 0.00 0.00 42.67 3.02
2 3 9.626045 ATTTTGGAAACACGAGAATATTTCTTC 57.374 29.630 0.00 0.00 42.67 2.87
3 4 9.981114 AATTTTGGAAACACGAGAATATTTCTT 57.019 25.926 0.00 0.00 42.67 2.52
4 5 9.981114 AAATTTTGGAAACACGAGAATATTTCT 57.019 25.926 0.00 0.00 42.67 2.52
6 7 9.981114 AGAAATTTTGGAAACACGAGAATATTT 57.019 25.926 0.00 0.00 42.67 1.40
7 8 9.410556 CAGAAATTTTGGAAACACGAGAATATT 57.589 29.630 0.00 0.00 42.67 1.28
8 9 8.576442 ACAGAAATTTTGGAAACACGAGAATAT 58.424 29.630 0.00 0.00 42.67 1.28
9 10 7.860373 CACAGAAATTTTGGAAACACGAGAATA 59.140 33.333 0.00 0.00 42.67 1.75
10 11 6.697019 CACAGAAATTTTGGAAACACGAGAAT 59.303 34.615 0.00 0.00 42.67 2.40
11 12 6.033341 CACAGAAATTTTGGAAACACGAGAA 58.967 36.000 0.00 0.00 42.67 2.87
12 13 5.355630 TCACAGAAATTTTGGAAACACGAGA 59.644 36.000 0.00 0.00 42.67 4.04
13 14 5.577835 TCACAGAAATTTTGGAAACACGAG 58.422 37.500 0.00 0.00 42.67 4.18
14 15 5.568685 TCACAGAAATTTTGGAAACACGA 57.431 34.783 0.00 0.00 42.67 4.35
15 16 6.639671 TTTCACAGAAATTTTGGAAACACG 57.360 33.333 0.00 0.00 42.67 4.49
16 17 9.838975 AAAATTTCACAGAAATTTTGGAAACAC 57.161 25.926 28.38 0.00 43.87 3.32
164 169 4.201980 GGGATGAGTGTATGCGCGTATATA 60.202 45.833 19.79 14.59 0.00 0.86
172 177 1.136891 TCACAGGGATGAGTGTATGCG 59.863 52.381 0.00 0.00 37.07 4.73
174 179 3.935203 GTGTTCACAGGGATGAGTGTATG 59.065 47.826 0.00 0.00 37.07 2.39
182 187 3.027170 GCGCGTGTTCACAGGGATG 62.027 63.158 8.43 0.00 32.80 3.51
184 189 4.228567 TGCGCGTGTTCACAGGGA 62.229 61.111 8.43 0.00 32.80 4.20
189 194 2.350760 GTGTGTGCGCGTGTTCAC 60.351 61.111 8.43 7.89 0.00 3.18
190 195 3.568743 GGTGTGTGCGCGTGTTCA 61.569 61.111 8.43 0.00 0.00 3.18
194 199 3.411351 GTAGGGTGTGTGCGCGTG 61.411 66.667 8.43 0.00 0.00 5.34
195 200 4.675029 GGTAGGGTGTGTGCGCGT 62.675 66.667 8.43 0.00 0.00 6.01
197 202 2.246761 TATGGGTAGGGTGTGTGCGC 62.247 60.000 0.00 0.00 0.00 6.09
199 204 1.488812 TCATATGGGTAGGGTGTGTGC 59.511 52.381 2.13 0.00 0.00 4.57
203 208 2.979678 GGTGATCATATGGGTAGGGTGT 59.020 50.000 0.00 0.00 0.00 4.16
206 211 2.840651 GGAGGTGATCATATGGGTAGGG 59.159 54.545 0.00 0.00 0.00 3.53
207 212 2.497675 CGGAGGTGATCATATGGGTAGG 59.502 54.545 0.00 0.00 0.00 3.18
208 213 3.431415 TCGGAGGTGATCATATGGGTAG 58.569 50.000 0.00 0.00 0.00 3.18
209 214 3.075432 TCTCGGAGGTGATCATATGGGTA 59.925 47.826 4.96 0.00 0.00 3.69
210 215 2.158310 TCTCGGAGGTGATCATATGGGT 60.158 50.000 4.96 0.00 0.00 4.51
211 216 2.495270 CTCTCGGAGGTGATCATATGGG 59.505 54.545 4.96 0.00 0.00 4.00
214 220 4.078537 CAGTCTCTCGGAGGTGATCATAT 58.921 47.826 4.96 0.00 0.00 1.78
220 226 0.678366 GCTCAGTCTCTCGGAGGTGA 60.678 60.000 4.96 1.54 38.48 4.02
226 232 1.674764 ATGCTGGCTCAGTCTCTCGG 61.675 60.000 4.45 0.00 33.43 4.63
248 254 8.561932 CGATGACTTCGTAAAATCTCAAGATA 57.438 34.615 2.72 0.00 43.01 1.98
282 299 5.635700 GCGTTTAGTGAGAAGAGACATTTCT 59.364 40.000 0.00 0.00 37.59 2.52
284 301 4.386049 CGCGTTTAGTGAGAAGAGACATTT 59.614 41.667 0.00 0.00 0.00 2.32
287 304 2.921069 GCGCGTTTAGTGAGAAGAGACA 60.921 50.000 8.43 0.00 0.00 3.41
305 322 2.850321 TCAGAATTTTTGACGATGCGC 58.150 42.857 0.00 0.00 0.00 6.09
337 354 6.150976 TCAAAGTCTTGGTGATCGCATTTATT 59.849 34.615 8.82 0.00 33.01 1.40
348 365 2.422803 CCAGGGTTCAAAGTCTTGGTGA 60.423 50.000 0.00 0.00 33.01 4.02
351 368 1.956477 CACCAGGGTTCAAAGTCTTGG 59.044 52.381 0.00 0.00 33.01 3.61
381 427 2.819608 GCACATTAAGCACTGAGGGAAA 59.180 45.455 0.00 0.00 0.00 3.13
385 431 4.025396 CGATTAGCACATTAAGCACTGAGG 60.025 45.833 0.00 0.00 0.00 3.86
456 502 0.246635 CCACGTCCAAGGATCTCGTT 59.753 55.000 1.08 0.00 32.47 3.85
678 724 3.489059 GGTGAGAGATGAGAAGAAGAGCG 60.489 52.174 0.00 0.00 0.00 5.03
680 726 5.857471 ATGGTGAGAGATGAGAAGAAGAG 57.143 43.478 0.00 0.00 0.00 2.85
681 727 6.617782 AAATGGTGAGAGATGAGAAGAAGA 57.382 37.500 0.00 0.00 0.00 2.87
729 775 4.081642 TCCAGAAGGTGTAGTATGCTTGAC 60.082 45.833 0.00 0.00 35.89 3.18
732 778 4.777896 TCTTCCAGAAGGTGTAGTATGCTT 59.222 41.667 7.53 0.00 38.88 3.91
739 785 5.930837 ATTCTCTCTTCCAGAAGGTGTAG 57.069 43.478 7.53 0.00 38.88 2.74
754 800 6.442952 ACTTACAGTGCGATGATATTCTCTC 58.557 40.000 0.00 0.00 0.00 3.20
755 801 6.264292 AGACTTACAGTGCGATGATATTCTCT 59.736 38.462 0.00 0.00 0.00 3.10
756 802 6.362016 CAGACTTACAGTGCGATGATATTCTC 59.638 42.308 0.00 0.00 0.00 2.87
757 803 6.183360 ACAGACTTACAGTGCGATGATATTCT 60.183 38.462 0.00 0.00 0.00 2.40
758 804 5.980116 ACAGACTTACAGTGCGATGATATTC 59.020 40.000 0.00 0.00 0.00 1.75
759 805 5.907207 ACAGACTTACAGTGCGATGATATT 58.093 37.500 0.00 0.00 0.00 1.28
760 806 5.521906 ACAGACTTACAGTGCGATGATAT 57.478 39.130 0.00 0.00 0.00 1.63
771 817 4.754618 TGGTGCAATGTTACAGACTTACAG 59.245 41.667 0.00 0.00 0.00 2.74
772 818 4.709250 TGGTGCAATGTTACAGACTTACA 58.291 39.130 0.00 0.00 0.00 2.41
773 819 5.449304 GTTGGTGCAATGTTACAGACTTAC 58.551 41.667 0.00 0.00 0.00 2.34
774 820 4.517453 GGTTGGTGCAATGTTACAGACTTA 59.483 41.667 0.00 0.00 0.00 2.24
775 821 3.317993 GGTTGGTGCAATGTTACAGACTT 59.682 43.478 0.00 0.00 0.00 3.01
776 822 2.884639 GGTTGGTGCAATGTTACAGACT 59.115 45.455 0.00 0.00 0.00 3.24
777 823 2.621055 TGGTTGGTGCAATGTTACAGAC 59.379 45.455 0.00 0.00 0.00 3.51
778 824 2.937519 TGGTTGGTGCAATGTTACAGA 58.062 42.857 0.00 0.00 0.00 3.41
789 835 2.801699 GCTTTGGTTAGTTGGTTGGTGC 60.802 50.000 0.00 0.00 0.00 5.01
821 867 1.312371 ATGCCGTTTGGATTGACCGG 61.312 55.000 0.00 0.00 42.61 5.28
847 893 3.118371 CCTATTTATCGGCACCCCTATCC 60.118 52.174 0.00 0.00 0.00 2.59
853 899 1.574702 GCGCCTATTTATCGGCACCC 61.575 60.000 0.00 0.00 46.62 4.61
1077 1124 1.227380 GCAGCCCTGGTCATAGTCG 60.227 63.158 0.00 0.00 0.00 4.18
1134 1181 1.595382 CGATCTTAAGGGCGCAGGG 60.595 63.158 10.83 0.00 0.00 4.45
1167 1214 2.629336 AAAGGGAGAGATGCGGATTC 57.371 50.000 0.00 0.00 0.00 2.52
1185 1232 4.701651 AGAGAGATCTGCATGCCATTAA 57.298 40.909 16.68 0.00 0.00 1.40
1215 1262 3.202906 GGCATGCAAAGATAACCGTCTA 58.797 45.455 21.36 0.00 0.00 2.59
1217 1264 1.065551 GGGCATGCAAAGATAACCGTC 59.934 52.381 21.36 0.00 0.00 4.79
1219 1266 0.029300 CGGGCATGCAAAGATAACCG 59.971 55.000 21.36 16.17 0.00 4.44
1220 1267 0.249031 GCGGGCATGCAAAGATAACC 60.249 55.000 21.36 7.67 34.15 2.85
1354 1403 4.819082 GCATGCGACATGCCATTT 57.181 50.000 24.97 0.00 45.60 2.32
1371 1420 1.915614 GCAGTCACTGTTCATGGCGG 61.916 60.000 6.68 0.00 33.43 6.13
1451 1501 6.845782 CGTACAATGAATCAATAATCCACACG 59.154 38.462 0.00 0.00 0.00 4.49
1468 1522 4.023739 TGATCTGGACGTACGTACAATG 57.976 45.455 31.56 21.76 38.66 2.82
1476 1530 0.660595 CGGCGATGATCTGGACGTAC 60.661 60.000 0.00 0.00 0.00 3.67
1482 1536 2.160822 AAATCTCGGCGATGATCTGG 57.839 50.000 11.27 0.00 31.20 3.86
1483 1537 2.154580 CGAAAATCTCGGCGATGATCTG 59.845 50.000 11.27 0.00 44.20 2.90
1827 1881 3.800863 TCGAGGACGAGCGACTGC 61.801 66.667 0.00 0.00 43.81 4.40
1860 1914 3.181490 CGGAGATGACGAACATGAGGTAA 60.181 47.826 0.00 0.00 39.56 2.85
1927 1981 3.118972 GCGAGTTTTGTTGTTAATTCGGC 59.881 43.478 0.00 0.00 35.07 5.54
1932 1986 9.269415 GAATTATACGCGAGTTTTGTTGTTAAT 57.731 29.630 15.93 0.00 46.40 1.40
1958 2012 2.160013 CGGTTTTCTCAACTCGTTAGCG 60.160 50.000 0.00 0.00 39.92 4.26
1977 2031 2.753966 CCCGATCTGCAAGCAACGG 61.754 63.158 20.05 20.05 37.15 4.44
1978 2032 2.753966 CCCCGATCTGCAAGCAACG 61.754 63.158 0.00 2.97 0.00 4.10
1979 2033 1.372087 CTCCCCGATCTGCAAGCAAC 61.372 60.000 0.00 0.00 0.00 4.17
1980 2034 1.078214 CTCCCCGATCTGCAAGCAA 60.078 57.895 0.00 0.00 0.00 3.91
2089 2143 2.637382 TGAGGGTCTGCATCTGTGTTAA 59.363 45.455 0.00 0.00 0.00 2.01
2093 2147 2.169144 TGTATGAGGGTCTGCATCTGTG 59.831 50.000 0.00 0.00 0.00 3.66
2106 2162 5.123661 TGCAAATGTGTGTGTATGTATGAGG 59.876 40.000 0.00 0.00 0.00 3.86
2139 2201 7.974501 GGCTGTAATATAGTATGTGCTCGTAAT 59.025 37.037 0.00 0.00 0.00 1.89
2178 2247 8.256611 TGTTCTGCTGACTATGAAAATTCTAC 57.743 34.615 0.00 0.00 0.00 2.59
2189 2258 7.337689 TGCAAATATTCTTGTTCTGCTGACTAT 59.662 33.333 7.37 0.00 0.00 2.12
2252 2321 9.588096 AGGATTTTCAGTTACTGGTATCTTTTT 57.412 29.630 12.79 0.28 31.51 1.94
2307 2376 5.389516 CGATACACTAGTGTTTTCAGTTGCC 60.390 44.000 32.15 10.01 41.83 4.52
2309 2378 6.200286 ACACGATACACTAGTGTTTTCAGTTG 59.800 38.462 32.15 23.26 45.60 3.16
2354 2424 3.139077 CCGCATCTACTACCCAATTTCC 58.861 50.000 0.00 0.00 0.00 3.13
2355 2425 2.548480 GCCGCATCTACTACCCAATTTC 59.452 50.000 0.00 0.00 0.00 2.17
2356 2426 2.172717 AGCCGCATCTACTACCCAATTT 59.827 45.455 0.00 0.00 0.00 1.82
2357 2427 1.768870 AGCCGCATCTACTACCCAATT 59.231 47.619 0.00 0.00 0.00 2.32
2358 2428 1.070758 CAGCCGCATCTACTACCCAAT 59.929 52.381 0.00 0.00 0.00 3.16
2359 2429 0.464036 CAGCCGCATCTACTACCCAA 59.536 55.000 0.00 0.00 0.00 4.12
2360 2430 0.686441 ACAGCCGCATCTACTACCCA 60.686 55.000 0.00 0.00 0.00 4.51
2361 2431 0.032267 GACAGCCGCATCTACTACCC 59.968 60.000 0.00 0.00 0.00 3.69
2362 2432 0.032267 GGACAGCCGCATCTACTACC 59.968 60.000 0.00 0.00 0.00 3.18
2363 2433 1.033574 AGGACAGCCGCATCTACTAC 58.966 55.000 0.00 0.00 39.96 2.73
2364 2434 1.776662 AAGGACAGCCGCATCTACTA 58.223 50.000 0.00 0.00 39.96 1.82
2365 2435 0.905357 AAAGGACAGCCGCATCTACT 59.095 50.000 0.00 0.00 39.96 2.57
2366 2436 1.009829 CAAAGGACAGCCGCATCTAC 58.990 55.000 0.00 0.00 39.96 2.59
2383 2453 1.806542 GCTCCATCAAAACGCTCTCAA 59.193 47.619 0.00 0.00 0.00 3.02
2384 2454 1.442769 GCTCCATCAAAACGCTCTCA 58.557 50.000 0.00 0.00 0.00 3.27
2385 2455 0.729690 GGCTCCATCAAAACGCTCTC 59.270 55.000 0.00 0.00 0.00 3.20
2493 2574 2.874014 TGTTCACATTCATGGCTCCAA 58.126 42.857 0.00 0.00 0.00 3.53
2547 2628 8.418597 TTCTTCTAGAGTACCTAAGCTTCAAA 57.581 34.615 0.00 0.00 0.00 2.69
2548 2629 8.418597 TTTCTTCTAGAGTACCTAAGCTTCAA 57.581 34.615 0.00 0.00 0.00 2.69
2658 2747 1.678627 CCTGTACTCACTCCCGATCAG 59.321 57.143 0.00 0.00 0.00 2.90
2669 2758 1.005569 ACCCAGATCGACCTGTACTCA 59.994 52.381 5.94 0.00 32.43 3.41
2775 2864 0.689623 AAGGAGGTGCTCTTGGTGAG 59.310 55.000 0.00 0.00 45.33 3.51
2835 2924 5.761234 ACAACGTTGCTAGTGATAAGGAAAA 59.239 36.000 27.61 0.00 0.00 2.29
2836 2925 5.302360 ACAACGTTGCTAGTGATAAGGAAA 58.698 37.500 27.61 0.00 0.00 3.13
2875 2971 4.278310 TGAGTCATCTATTCTGGAACGGA 58.722 43.478 0.00 0.00 45.11 4.69
2876 2972 4.655762 TGAGTCATCTATTCTGGAACGG 57.344 45.455 0.00 0.00 0.00 4.44
2877 2973 5.655488 AGTTGAGTCATCTATTCTGGAACG 58.345 41.667 1.70 0.00 0.00 3.95
2878 2974 7.389053 ACAAAGTTGAGTCATCTATTCTGGAAC 59.611 37.037 4.14 0.00 0.00 3.62
2879 2975 7.453393 ACAAAGTTGAGTCATCTATTCTGGAA 58.547 34.615 4.14 0.00 0.00 3.53
2880 2976 7.009179 ACAAAGTTGAGTCATCTATTCTGGA 57.991 36.000 4.14 0.00 0.00 3.86
2881 2977 8.037758 AGTACAAAGTTGAGTCATCTATTCTGG 58.962 37.037 4.14 0.00 0.00 3.86
2882 2978 8.994429 AGTACAAAGTTGAGTCATCTATTCTG 57.006 34.615 4.14 3.46 0.00 3.02
2904 3000 8.703743 TGACCCAAGTTTGTACTAAAGTTAGTA 58.296 33.333 6.81 6.81 43.36 1.82
2905 3001 7.567458 TGACCCAAGTTTGTACTAAAGTTAGT 58.433 34.615 8.67 8.67 45.39 2.24
2906 3002 8.617290 ATGACCCAAGTTTGTACTAAAGTTAG 57.383 34.615 9.21 0.00 33.17 2.34
2907 3003 7.662669 GGATGACCCAAGTTTGTACTAAAGTTA 59.337 37.037 9.21 0.00 33.17 2.24
2908 3004 6.489022 GGATGACCCAAGTTTGTACTAAAGTT 59.511 38.462 0.00 0.28 33.17 2.66
2909 3005 6.002082 GGATGACCCAAGTTTGTACTAAAGT 58.998 40.000 0.00 0.00 33.17 2.66
2910 3006 6.001460 TGGATGACCCAAGTTTGTACTAAAG 58.999 40.000 0.00 0.00 43.29 1.85
2911 3007 5.942961 TGGATGACCCAAGTTTGTACTAAA 58.057 37.500 0.00 0.00 43.29 1.85
2912 3008 5.570205 TGGATGACCCAAGTTTGTACTAA 57.430 39.130 0.00 0.00 43.29 2.24
2931 3027 1.004277 CTCCCTCCGTTCCAAAATGGA 59.996 52.381 0.00 0.00 46.61 3.41
2932 3028 1.271926 ACTCCCTCCGTTCCAAAATGG 60.272 52.381 0.00 0.00 42.15 3.16
2933 3029 2.200373 ACTCCCTCCGTTCCAAAATG 57.800 50.000 0.00 0.00 0.00 2.32
2934 3030 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
2935 3031 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
2936 3032 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
2937 3033 1.621814 CTTGTACTCCCTCCGTTCCAA 59.378 52.381 0.00 0.00 0.00 3.53
2938 3034 1.263356 CTTGTACTCCCTCCGTTCCA 58.737 55.000 0.00 0.00 0.00 3.53
2939 3035 0.535797 CCTTGTACTCCCTCCGTTCC 59.464 60.000 0.00 0.00 0.00 3.62
2940 3036 0.108281 GCCTTGTACTCCCTCCGTTC 60.108 60.000 0.00 0.00 0.00 3.95
2941 3037 0.544595 AGCCTTGTACTCCCTCCGTT 60.545 55.000 0.00 0.00 0.00 4.44
2942 3038 0.333993 TAGCCTTGTACTCCCTCCGT 59.666 55.000 0.00 0.00 0.00 4.69
2943 3039 1.341531 CATAGCCTTGTACTCCCTCCG 59.658 57.143 0.00 0.00 0.00 4.63
2944 3040 2.399580 ACATAGCCTTGTACTCCCTCC 58.600 52.381 0.00 0.00 0.00 4.30
2945 3041 5.565045 CGATTACATAGCCTTGTACTCCCTC 60.565 48.000 0.00 0.00 31.54 4.30
2946 3042 4.281182 CGATTACATAGCCTTGTACTCCCT 59.719 45.833 0.00 0.00 31.54 4.20
2947 3043 4.038883 ACGATTACATAGCCTTGTACTCCC 59.961 45.833 0.00 0.00 31.54 4.30
2948 3044 5.197682 ACGATTACATAGCCTTGTACTCC 57.802 43.478 0.00 0.00 31.54 3.85
2949 3045 4.910456 CGACGATTACATAGCCTTGTACTC 59.090 45.833 0.00 1.13 31.98 2.59
2950 3046 4.337555 ACGACGATTACATAGCCTTGTACT 59.662 41.667 0.00 0.00 31.98 2.73
2951 3047 4.604976 ACGACGATTACATAGCCTTGTAC 58.395 43.478 0.00 0.00 31.98 2.90
2952 3048 4.336153 TGACGACGATTACATAGCCTTGTA 59.664 41.667 0.00 0.00 0.00 2.41
2953 3049 3.129813 TGACGACGATTACATAGCCTTGT 59.870 43.478 0.00 0.00 0.00 3.16
2954 3050 3.702330 TGACGACGATTACATAGCCTTG 58.298 45.455 0.00 0.00 0.00 3.61
2986 3082 0.590195 ACTCGATACGCCACGGATAC 59.410 55.000 0.00 0.00 26.79 2.24
2992 3088 1.731433 TAGCCCACTCGATACGCCAC 61.731 60.000 0.00 0.00 0.00 5.01
3096 4084 1.586154 CCACAGGCGAATTCCACCAC 61.586 60.000 13.23 0.00 0.00 4.16
3156 4144 1.691196 ACCATTAATCCCATGCACGG 58.309 50.000 0.00 0.00 0.00 4.94
3190 4293 0.526662 AAAACAACAACCGCACGGAA 59.473 45.000 17.40 0.00 38.96 4.30
3198 4301 1.677052 TCACCCGCTAAAACAACAACC 59.323 47.619 0.00 0.00 0.00 3.77
3213 4316 4.525912 AGAAAAGTGCATTCATTCACCC 57.474 40.909 9.39 0.00 33.90 4.61
3216 4319 6.925165 GGAAGAAAGAAAAGTGCATTCATTCA 59.075 34.615 15.16 0.00 37.11 2.57
3217 4320 6.925165 TGGAAGAAAGAAAAGTGCATTCATTC 59.075 34.615 7.94 7.94 35.70 2.67
3218 4321 6.819284 TGGAAGAAAGAAAAGTGCATTCATT 58.181 32.000 0.00 0.00 0.00 2.57
3219 4322 6.409524 TGGAAGAAAGAAAAGTGCATTCAT 57.590 33.333 0.00 0.00 0.00 2.57
3298 4405 2.665537 CGCTGAGATTCCTATCGAATGC 59.334 50.000 0.00 0.00 41.47 3.56
3299 4406 2.665537 GCGCTGAGATTCCTATCGAATG 59.334 50.000 0.00 0.00 41.47 2.67
3300 4407 2.297315 TGCGCTGAGATTCCTATCGAAT 59.703 45.455 9.73 0.00 44.20 3.34
3301 4408 1.681264 TGCGCTGAGATTCCTATCGAA 59.319 47.619 9.73 0.00 35.85 3.71
3303 4410 2.360553 ATGCGCTGAGATTCCTATCG 57.639 50.000 9.73 0.00 35.85 2.92
3304 4411 3.364764 GCAAATGCGCTGAGATTCCTATC 60.365 47.826 9.73 0.00 0.00 2.08
3305 4412 2.551459 GCAAATGCGCTGAGATTCCTAT 59.449 45.455 9.73 0.00 0.00 2.57
3306 4413 1.942657 GCAAATGCGCTGAGATTCCTA 59.057 47.619 9.73 0.00 0.00 2.94
3307 4414 0.737219 GCAAATGCGCTGAGATTCCT 59.263 50.000 9.73 0.00 0.00 3.36
3308 4415 3.247033 GCAAATGCGCTGAGATTCC 57.753 52.632 9.73 0.00 0.00 3.01
3355 4462 1.460743 AGCGAACGATTGTGTCATGTG 59.539 47.619 0.00 0.00 0.00 3.21
3377 4484 1.568504 TCCCTCAGGTAGCGTCAAAT 58.431 50.000 0.00 0.00 0.00 2.32
3395 4502 3.288092 AGTTTCCTCACCAAGGTTGTTC 58.712 45.455 0.00 0.00 46.32 3.18
3396 4503 3.382083 AGTTTCCTCACCAAGGTTGTT 57.618 42.857 0.00 0.00 46.32 2.83
3398 4505 4.736126 AAAAGTTTCCTCACCAAGGTTG 57.264 40.909 0.00 0.00 46.32 3.77
3399 4506 4.161565 GGAAAAAGTTTCCTCACCAAGGTT 59.838 41.667 11.70 0.00 46.32 3.50
3402 4509 3.069586 GGGGAAAAAGTTTCCTCACCAAG 59.930 47.826 17.07 0.00 38.92 3.61
3403 4510 3.035363 GGGGAAAAAGTTTCCTCACCAA 58.965 45.455 17.07 0.00 38.92 3.67
3405 4512 1.968493 GGGGGAAAAAGTTTCCTCACC 59.032 52.381 18.89 14.26 40.88 4.02
3406 4513 2.958818 AGGGGGAAAAAGTTTCCTCAC 58.041 47.619 18.89 10.81 40.88 3.51
3407 4514 6.668133 ATATAGGGGGAAAAAGTTTCCTCA 57.332 37.500 18.89 2.64 40.88 3.86
3408 4515 7.230913 GCTAATATAGGGGGAAAAAGTTTCCTC 59.769 40.741 17.07 14.05 38.36 3.71
3409 4516 7.067421 GCTAATATAGGGGGAAAAAGTTTCCT 58.933 38.462 17.07 3.20 38.61 3.36
3410 4517 6.016527 CGCTAATATAGGGGGAAAAAGTTTCC 60.017 42.308 10.70 10.70 37.86 3.13
3411 4518 6.544931 ACGCTAATATAGGGGGAAAAAGTTTC 59.455 38.462 6.43 0.00 42.45 2.78
3421 4528 2.236146 TGCATGACGCTAATATAGGGGG 59.764 50.000 0.00 0.00 42.45 5.40
3432 4539 3.940852 TCACATAGAAATTGCATGACGCT 59.059 39.130 0.00 0.00 43.06 5.07
3434 4541 5.872635 ACTTCACATAGAAATTGCATGACG 58.127 37.500 0.00 0.00 35.40 4.35
3470 4578 0.970640 AGCTTGCCATGTTGCATCAA 59.029 45.000 0.75 0.00 41.70 2.57
3479 4587 1.093159 GTCTTCAGGAGCTTGCCATG 58.907 55.000 0.00 0.00 0.00 3.66
3487 4595 0.390340 TCACGCATGTCTTCAGGAGC 60.390 55.000 0.00 0.00 0.00 4.70
3536 4644 7.414984 GGCTCATTGTTTCAATTTTGTTTTCCA 60.415 33.333 0.00 0.00 0.00 3.53
3537 4645 6.912051 GGCTCATTGTTTCAATTTTGTTTTCC 59.088 34.615 0.00 0.00 0.00 3.13
3538 4646 7.696755 AGGCTCATTGTTTCAATTTTGTTTTC 58.303 30.769 0.00 0.00 0.00 2.29
3540 4648 6.260714 GGAGGCTCATTGTTTCAATTTTGTTT 59.739 34.615 17.69 0.00 0.00 2.83
3541 4649 5.759763 GGAGGCTCATTGTTTCAATTTTGTT 59.240 36.000 17.69 0.00 0.00 2.83
3542 4650 5.070847 AGGAGGCTCATTGTTTCAATTTTGT 59.929 36.000 17.69 0.00 0.00 2.83
3543 4651 5.544650 AGGAGGCTCATTGTTTCAATTTTG 58.455 37.500 17.69 0.00 0.00 2.44
3570 4681 2.722094 CGGTTCCTCCAATGGAAATCA 58.278 47.619 2.61 0.00 46.34 2.57
3581 4692 2.812358 AAAATTGTTGCGGTTCCTCC 57.188 45.000 0.00 0.00 0.00 4.30
3603 4714 4.261155 CGGACATCTTTCTTTTGTGCTTGA 60.261 41.667 0.00 0.00 30.49 3.02
3615 4727 3.194968 TCCTAGAACACCGGACATCTTTC 59.805 47.826 9.46 0.80 0.00 2.62
3626 4738 1.067071 CCCTGTCGTTCCTAGAACACC 60.067 57.143 8.11 0.00 0.00 4.16
3629 4741 2.169330 AGTCCCTGTCGTTCCTAGAAC 58.831 52.381 0.00 0.00 0.00 3.01
3638 4750 1.229082 TGGGCTTAGTCCCTGTCGT 60.229 57.895 0.00 0.00 46.67 4.34
3639 4751 1.517832 CTGGGCTTAGTCCCTGTCG 59.482 63.158 0.00 0.00 46.67 4.35
3663 4775 7.751793 GTCTTTCTTCTTTCGTTTTGGTGTAAA 59.248 33.333 0.00 0.00 0.00 2.01
3701 4813 1.978617 CGCCCCCTTGTGCTGATTT 60.979 57.895 0.00 0.00 0.00 2.17
3717 4829 0.667184 CTGTTGGGACATTTTGGCGC 60.667 55.000 0.00 0.00 39.30 6.53
3741 4857 7.861629 TGGAGTAGGATGACATCTTATGTTTT 58.138 34.615 14.95 0.00 45.03 2.43


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

AutoCloner maintained by Alex Coulton.