Multiple sequence alignment - TraesCS3D01G357800

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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 TraesCS3D01G357800 chr3D 100.000 7117 0 0 1 7117 470896118 470889002 0.000000e+00 13143
1 TraesCS3D01G357800 chr3D 98.277 2147 33 4 3361 5505 470891687 470889543 0.000000e+00 3757
2 TraesCS3D01G357800 chr3D 98.277 2147 33 4 4432 6576 470892758 470890614 0.000000e+00 3757
3 TraesCS3D01G357800 chr3D 98.417 1074 17 0 3361 4434 470890616 470889543 0.000000e+00 1890
4 TraesCS3D01G357800 chr3D 98.417 1074 17 0 5503 6576 470892758 470891685 0.000000e+00 1890
5 TraesCS3D01G357800 chr3A 91.251 1966 114 21 2516 4434 613174193 613172239 0.000000e+00 2625
6 TraesCS3D01G357800 chr3A 86.593 1820 143 57 483 2222 613176395 613174597 0.000000e+00 1916
7 TraesCS3D01G357800 chr3A 90.255 1139 71 15 5511 6617 613173327 613172197 0.000000e+00 1452
8 TraesCS3D01G357800 chr3A 89.973 1097 71 14 4440 5505 613173327 613172239 0.000000e+00 1380
9 TraesCS3D01G357800 chr3A 85.199 527 49 22 6614 7117 613172158 613171638 1.370000e-141 514
10 TraesCS3D01G357800 chr3A 82.990 388 33 15 27 403 613176782 613176417 3.200000e-83 320
11 TraesCS3D01G357800 chr3A 86.977 215 20 3 2310 2524 613174448 613174242 1.190000e-57 235
12 TraesCS3D01G357800 chr3B 90.274 1974 130 24 2496 4434 625335759 625333813 0.000000e+00 2525
13 TraesCS3D01G357800 chr3B 89.493 1656 107 25 5503 7117 625334893 625333264 0.000000e+00 2032
14 TraesCS3D01G357800 chr3B 86.548 1576 104 46 373 1886 625337860 625336331 0.000000e+00 1637
15 TraesCS3D01G357800 chr3B 88.273 1100 84 18 4432 5505 625334893 625333813 0.000000e+00 1275
16 TraesCS3D01G357800 chr3B 88.690 336 23 7 46 379 625359861 625359539 5.170000e-106 396
17 TraesCS3D01G357800 chr3B 91.912 272 14 4 1885 2151 625336227 625335959 2.420000e-99 374
18 TraesCS3D01G357800 chr3B 97.605 167 3 1 2267 2433 625335932 625335767 1.170000e-72 285
19 TraesCS3D01G357800 chr1A 83.820 377 43 15 1281 1644 478567439 478567810 6.840000e-90 342
20 TraesCS3D01G357800 chr1A 88.136 118 14 0 1285 1402 370110230 370110113 2.680000e-29 141
21 TraesCS3D01G357800 chr1D 92.025 163 13 0 1482 1644 377974177 377974339 5.550000e-56 230
22 TraesCS3D01G357800 chr1D 95.161 124 6 0 1281 1404 377973953 377974076 5.630000e-46 196
23 TraesCS3D01G357800 chr1B 90.798 163 15 0 1482 1644 505626565 505626727 1.200000e-52 219
24 TraesCS3D01G357800 chr1B 95.161 124 6 0 1281 1404 505626342 505626465 5.630000e-46 196
25 TraesCS3D01G357800 chr4D 91.216 148 9 3 6970 7117 307236498 307236355 1.570000e-46 198
26 TraesCS3D01G357800 chr5D 91.057 123 11 0 1282 1404 432514646 432514524 4.420000e-37 167
27 TraesCS3D01G357800 chr5A 90.551 127 11 1 1278 1404 547332377 547332252 4.420000e-37 167
28 TraesCS3D01G357800 chr5B 89.431 123 13 0 1282 1404 523213437 523213559 9.560000e-34 156


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 TraesCS3D01G357800 chr3D 470889002 470896118 7116 True 13143.000000 13143 100.000000 1 7117 1 chr3D.!!$R1 7116
1 TraesCS3D01G357800 chr3D 470889543 470892758 3215 True 2823.500000 3757 98.347000 3361 6576 4 chr3D.!!$R2 3215
2 TraesCS3D01G357800 chr3A 613171638 613176782 5144 True 1206.000000 2625 87.605429 27 7117 7 chr3A.!!$R1 7090
3 TraesCS3D01G357800 chr3B 625333264 625337860 4596 True 1354.666667 2525 90.684167 373 7117 6 chr3B.!!$R2 6744

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
228 237 0.034767 TCTACCGTCACGAGTGGGAT 60.035 55.0 0.00 0.0 0.00 3.85 F
1902 2156 0.040942 TTAGCAACCATGGCACCCAT 59.959 50.0 13.04 0.0 46.37 4.00 F
1989 2248 0.172127 TGCTGTTGTGCTTGCGAAAA 59.828 45.0 0.00 0.0 0.00 2.29 F
2542 3011 0.514255 GGCTTACACGTTTTCCGGAC 59.486 55.0 1.83 0.0 42.24 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1982 2241 0.385751 TCCGGCAACAAATTTTCGCA 59.614 45.000 0.00 0.00 0.00 5.10 R
2934 3407 0.244450 CGTTGCTGTTGATGGCCATT 59.756 50.000 21.84 3.11 0.00 3.16 R
3304 3793 0.610174 TGTCTCTCACCATGCTCCAC 59.390 55.000 0.00 0.00 0.00 4.02 R
6729 7289 1.377987 CCGGGTAACATGGTGTGGG 60.378 63.158 0.00 0.00 39.74 4.61 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
18 19 3.489813 TCGTGACCGTTCATGTCAG 57.510 52.632 1.85 0.00 42.99 3.51
19 20 0.038618 TCGTGACCGTTCATGTCAGG 60.039 55.000 1.85 3.92 42.99 3.86
20 21 0.038618 CGTGACCGTTCATGTCAGGA 60.039 55.000 7.17 0.00 46.31 3.86
21 22 1.604438 CGTGACCGTTCATGTCAGGAA 60.604 52.381 7.17 0.00 46.31 3.36
22 23 2.489971 GTGACCGTTCATGTCAGGAAA 58.510 47.619 0.67 0.00 42.99 3.13
23 24 2.875933 GTGACCGTTCATGTCAGGAAAA 59.124 45.455 0.67 0.00 42.99 2.29
24 25 3.314080 GTGACCGTTCATGTCAGGAAAAA 59.686 43.478 0.67 0.00 42.99 1.94
25 26 3.314080 TGACCGTTCATGTCAGGAAAAAC 59.686 43.478 0.67 0.00 37.80 2.43
35 36 3.563808 TGTCAGGAAAAACGAACATCTGG 59.436 43.478 0.00 0.00 0.00 3.86
37 38 3.813166 TCAGGAAAAACGAACATCTGGTC 59.187 43.478 0.00 0.00 0.00 4.02
42 43 5.048713 GGAAAAACGAACATCTGGTCAGAAT 60.049 40.000 4.67 0.00 41.36 2.40
43 44 6.391227 AAAAACGAACATCTGGTCAGAATT 57.609 33.333 4.67 3.08 41.36 2.17
44 45 6.391227 AAAACGAACATCTGGTCAGAATTT 57.609 33.333 4.67 1.53 41.36 1.82
65 66 2.661594 TCTGTCATCAGTTTGACGACG 58.338 47.619 0.00 0.00 41.95 5.12
68 69 1.136611 GTCATCAGTTTGACGACGTGC 60.137 52.381 4.58 0.00 36.93 5.34
71 72 1.083401 CAGTTTGACGACGTGCTGC 60.083 57.895 4.58 0.00 0.00 5.25
76 77 0.526211 TTGACGACGTGCTGCTCTAT 59.474 50.000 4.58 0.00 0.00 1.98
91 93 6.072008 TGCTGCTCTATAAGATTTTGTTTGCA 60.072 34.615 0.00 0.00 0.00 4.08
111 113 2.817258 CACAAACAGAAGGCCGGATTTA 59.183 45.455 5.05 0.00 0.00 1.40
116 118 1.766496 CAGAAGGCCGGATTTAGGGTA 59.234 52.381 5.05 0.00 0.00 3.69
124 126 3.181457 GCCGGATTTAGGGTAAAGCTACT 60.181 47.826 5.05 0.00 34.67 2.57
126 128 5.279859 GCCGGATTTAGGGTAAAGCTACTAT 60.280 44.000 5.05 0.00 34.67 2.12
142 145 4.458642 GCTACTATAGTAGGTGGTACAGGC 59.541 50.000 31.65 16.40 46.07 4.85
143 146 4.531357 ACTATAGTAGGTGGTACAGGCA 57.469 45.455 2.75 0.00 41.80 4.75
189 195 5.762218 CCATCCAGAATAAATGAGACCTCAC 59.238 44.000 1.31 0.00 43.11 3.51
190 196 6.351711 CATCCAGAATAAATGAGACCTCACA 58.648 40.000 1.31 0.00 43.11 3.58
195 201 7.493971 CCAGAATAAATGAGACCTCACACTAAG 59.506 40.741 1.31 0.00 43.11 2.18
202 211 1.540267 GACCTCACACTAAGCTCGACA 59.460 52.381 0.00 0.00 0.00 4.35
212 221 2.145397 AAGCTCGACATGGGTCTCTA 57.855 50.000 0.00 0.00 42.05 2.43
214 223 0.386113 GCTCGACATGGGTCTCTACC 59.614 60.000 0.00 0.00 45.97 3.18
227 236 0.675837 CTCTACCGTCACGAGTGGGA 60.676 60.000 0.00 0.00 0.00 4.37
228 237 0.034767 TCTACCGTCACGAGTGGGAT 60.035 55.000 0.00 0.00 0.00 3.85
251 262 4.864806 TGGAAAGAAGAGAAATCGATCGTG 59.135 41.667 15.94 0.00 0.00 4.35
259 270 3.190874 AGAAATCGATCGTGAAAGGAGC 58.809 45.455 15.94 0.00 32.39 4.70
268 279 2.433868 GTGAAAGGAGCACGTACTCA 57.566 50.000 17.37 0.00 38.50 3.41
269 280 2.960819 GTGAAAGGAGCACGTACTCAT 58.039 47.619 17.37 7.69 38.50 2.90
270 281 2.924290 GTGAAAGGAGCACGTACTCATC 59.076 50.000 17.37 12.01 38.50 2.92
271 282 2.560981 TGAAAGGAGCACGTACTCATCA 59.439 45.455 17.37 14.17 38.50 3.07
298 309 7.484641 TCATCATCACAATTAAAACTTTAGCGC 59.515 33.333 0.00 0.00 0.00 5.92
312 323 4.389077 ACTTTAGCGCTGGATATTAATCGC 59.611 41.667 22.90 8.45 42.46 4.58
313 324 1.726853 AGCGCTGGATATTAATCGCC 58.273 50.000 10.39 6.48 43.05 5.54
314 325 0.370273 GCGCTGGATATTAATCGCCG 59.630 55.000 0.00 1.65 37.02 6.46
316 327 2.066262 CGCTGGATATTAATCGCCGTT 58.934 47.619 0.00 0.00 32.44 4.44
318 329 3.064207 GCTGGATATTAATCGCCGTTCA 58.936 45.455 0.00 0.00 32.44 3.18
319 330 3.120649 GCTGGATATTAATCGCCGTTCAC 60.121 47.826 0.00 0.00 32.44 3.18
320 331 3.395639 TGGATATTAATCGCCGTTCACC 58.604 45.455 0.00 0.00 32.44 4.02
321 332 3.070446 TGGATATTAATCGCCGTTCACCT 59.930 43.478 0.00 0.00 32.44 4.00
322 333 3.678548 GGATATTAATCGCCGTTCACCTC 59.321 47.826 0.00 0.00 32.44 3.85
323 334 1.949465 ATTAATCGCCGTTCACCTCC 58.051 50.000 0.00 0.00 0.00 4.30
324 335 0.609151 TTAATCGCCGTTCACCTCCA 59.391 50.000 0.00 0.00 0.00 3.86
330 341 2.738480 CGTTCACCTCCACCGGAA 59.262 61.111 9.46 0.00 0.00 4.30
349 360 4.811557 CGGAACAAGAGAAGAGAAACACTT 59.188 41.667 0.00 0.00 0.00 3.16
351 362 5.586643 GGAACAAGAGAAGAGAAACACTTGT 59.413 40.000 0.00 0.00 45.94 3.16
353 364 7.442666 GGAACAAGAGAAGAGAAACACTTGTAT 59.557 37.037 0.00 0.00 44.17 2.29
354 365 8.738645 AACAAGAGAAGAGAAACACTTGTATT 57.261 30.769 0.00 0.00 44.17 1.89
355 366 8.147642 ACAAGAGAAGAGAAACACTTGTATTG 57.852 34.615 0.00 0.00 43.49 1.90
356 367 6.793492 AGAGAAGAGAAACACTTGTATTGC 57.207 37.500 0.00 0.00 0.00 3.56
357 368 6.291377 AGAGAAGAGAAACACTTGTATTGCA 58.709 36.000 0.00 0.00 0.00 4.08
372 383 1.264749 TTGCAGTAGGTCAGGGCGAT 61.265 55.000 0.00 0.00 0.00 4.58
387 398 1.712081 CGATGCACTCGCTCCTTTG 59.288 57.895 0.00 0.00 41.14 2.77
406 417 1.398739 TGCTGCACGAACGAAAAAGAA 59.601 42.857 0.00 0.00 0.00 2.52
407 418 2.036933 GCTGCACGAACGAAAAAGAAG 58.963 47.619 0.14 0.00 0.00 2.85
410 421 3.935450 TGCACGAACGAAAAAGAAGAAG 58.065 40.909 0.14 0.00 0.00 2.85
443 454 5.071519 CCATGATGAGAATACCAACTCTCCT 59.928 44.000 0.00 0.00 37.82 3.69
445 456 7.038445 CCATGATGAGAATACCAACTCTCCTAT 60.038 40.741 0.00 0.00 37.82 2.57
446 457 7.531857 TGATGAGAATACCAACTCTCCTATC 57.468 40.000 0.00 0.00 37.82 2.08
447 458 6.495181 TGATGAGAATACCAACTCTCCTATCC 59.505 42.308 0.00 0.00 37.82 2.59
448 459 5.777449 TGAGAATACCAACTCTCCTATCCA 58.223 41.667 0.00 0.00 37.82 3.41
449 460 5.835819 TGAGAATACCAACTCTCCTATCCAG 59.164 44.000 0.00 0.00 37.82 3.86
450 461 5.151454 AGAATACCAACTCTCCTATCCAGG 58.849 45.833 0.00 0.00 44.17 4.45
451 462 1.501582 ACCAACTCTCCTATCCAGGC 58.498 55.000 0.00 0.00 42.30 4.85
452 463 1.273838 ACCAACTCTCCTATCCAGGCA 60.274 52.381 0.00 0.00 42.30 4.75
453 464 2.053244 CCAACTCTCCTATCCAGGCAT 58.947 52.381 0.00 0.00 42.30 4.40
493 504 5.221541 ACCTGTATTTCTATAGCTGGAGCAC 60.222 44.000 0.00 0.00 45.16 4.40
544 555 0.320771 GCAAAAGCGTGAGGAGGAGA 60.321 55.000 0.00 0.00 0.00 3.71
770 787 2.094675 CAGCTACCCACATTTTCCCAG 58.905 52.381 0.00 0.00 0.00 4.45
827 867 1.333791 CGAGACCAAGACGCCAAAAAC 60.334 52.381 0.00 0.00 0.00 2.43
830 870 0.458260 ACCAAGACGCCAAAAACACC 59.542 50.000 0.00 0.00 0.00 4.16
853 893 0.960861 ACAGAGACGCTCGATCACCA 60.961 55.000 0.00 0.00 35.36 4.17
1141 1208 2.742372 CACCCAAGAAGACGCCGG 60.742 66.667 0.00 0.00 0.00 6.13
1172 1239 4.271816 CCCCGACGCCGAGATGAG 62.272 72.222 0.00 0.00 38.22 2.90
1209 1276 4.778143 GCTGGGCCAGGTACACGG 62.778 72.222 33.43 8.27 31.21 4.94
1220 1287 0.108756 GGTACACGGGCTTCTCACTC 60.109 60.000 0.00 0.00 0.00 3.51
1275 1370 6.801718 TGTAGGTACTGGTGCTAATGTTAT 57.198 37.500 0.00 0.00 41.52 1.89
1293 1401 1.747709 ATTGTGTGCAGAGATGGAGC 58.252 50.000 0.00 0.00 0.00 4.70
1391 1499 2.108514 CATCGCCAACGCCATCACT 61.109 57.895 0.00 0.00 39.84 3.41
1410 1518 2.688958 ACTAACCTCTGCGGTCAGTATC 59.311 50.000 0.00 0.00 42.77 2.24
1477 1590 1.268352 AGAGAGTTGTCAGCGAGTGTC 59.732 52.381 0.00 0.00 0.00 3.67
1480 1593 1.789464 GAGTTGTCAGCGAGTGTCTTG 59.211 52.381 0.00 0.00 0.00 3.02
1481 1594 1.137086 AGTTGTCAGCGAGTGTCTTGT 59.863 47.619 0.00 0.00 0.00 3.16
1637 1759 4.016706 CCCGACGGAACCAGGCTT 62.017 66.667 17.49 0.00 0.00 4.35
1688 1811 1.514678 AACCAGCGCTGCGATTTTCA 61.515 50.000 31.96 0.00 0.00 2.69
1689 1812 1.209898 CCAGCGCTGCGATTTTCAA 59.790 52.632 31.96 0.00 0.00 2.69
1690 1813 1.067199 CCAGCGCTGCGATTTTCAAC 61.067 55.000 31.96 4.97 0.00 3.18
1691 1814 1.067199 CAGCGCTGCGATTTTCAACC 61.067 55.000 26.68 4.17 0.00 3.77
1692 1815 2.145905 GCGCTGCGATTTTCAACCG 61.146 57.895 28.07 0.00 0.00 4.44
1693 1816 1.511887 CGCTGCGATTTTCAACCGG 60.512 57.895 18.66 0.00 0.00 5.28
1694 1817 1.801512 GCTGCGATTTTCAACCGGC 60.802 57.895 0.00 0.00 0.00 6.13
1695 1818 1.578926 CTGCGATTTTCAACCGGCA 59.421 52.632 0.00 0.00 0.00 5.69
1697 1820 0.886938 TGCGATTTTCAACCGGCAGA 60.887 50.000 0.00 0.00 0.00 4.26
1698 1821 0.454452 GCGATTTTCAACCGGCAGAC 60.454 55.000 0.00 0.00 0.00 3.51
1825 1974 1.071471 CCAGAGCACGGGAACAGTT 59.929 57.895 0.00 0.00 33.26 3.16
1829 1978 3.369052 CCAGAGCACGGGAACAGTTTATA 60.369 47.826 0.00 0.00 33.26 0.98
1902 2156 0.040942 TTAGCAACCATGGCACCCAT 59.959 50.000 13.04 0.00 46.37 4.00
1909 2163 3.678965 ACCATGGCACCCATATAAACA 57.321 42.857 13.04 0.00 43.15 2.83
1931 2185 0.733150 GAGAAATGTTAGGTGCGCCC 59.267 55.000 14.07 5.76 34.57 6.13
1946 2200 2.099592 TGCGCCCATGATTTTTCTGATC 59.900 45.455 4.18 0.00 0.00 2.92
1965 2224 1.206115 CGAAACTTTGCGGTTGTGGC 61.206 55.000 0.00 0.00 0.00 5.01
1982 2241 2.646719 CGCCATGCTGTTGTGCTT 59.353 55.556 0.00 0.00 0.00 3.91
1989 2248 0.172127 TGCTGTTGTGCTTGCGAAAA 59.828 45.000 0.00 0.00 0.00 2.29
2006 2265 3.253230 GAAAATTTGTTGCCGGATGAGG 58.747 45.455 5.05 0.00 0.00 3.86
2033 2292 4.141801 ACTGCCCGTGCTGTCTTAATTATA 60.142 41.667 0.00 0.00 45.30 0.98
2065 2324 9.203421 GCAAATGGTAGCAGTTTAATTAAAAGT 57.797 29.630 12.14 0.66 0.00 2.66
2105 2364 4.054780 TGCTGGTGATACGAGGTATTTC 57.945 45.455 0.00 0.00 0.00 2.17
2143 2419 1.737793 CTCCACAACGGTAATGAAGCC 59.262 52.381 0.00 0.00 35.57 4.35
2146 2422 2.294791 CCACAACGGTAATGAAGCCAAA 59.705 45.455 0.00 0.00 0.00 3.28
2147 2423 3.243569 CCACAACGGTAATGAAGCCAAAA 60.244 43.478 0.00 0.00 0.00 2.44
2148 2424 4.363999 CACAACGGTAATGAAGCCAAAAA 58.636 39.130 0.00 0.00 0.00 1.94
2170 2446 6.515043 AAAAATGCAATTGAAGACAGAACG 57.485 33.333 10.34 0.00 36.10 3.95
2171 2447 4.836125 AATGCAATTGAAGACAGAACGT 57.164 36.364 10.34 0.00 33.44 3.99
2172 2448 5.940192 AATGCAATTGAAGACAGAACGTA 57.060 34.783 10.34 0.00 33.44 3.57
2173 2449 6.500684 AATGCAATTGAAGACAGAACGTAT 57.499 33.333 10.34 0.00 33.44 3.06
2174 2450 5.940192 TGCAATTGAAGACAGAACGTATT 57.060 34.783 10.34 0.00 0.00 1.89
2175 2451 5.688823 TGCAATTGAAGACAGAACGTATTG 58.311 37.500 10.34 0.00 0.00 1.90
2176 2452 5.238432 TGCAATTGAAGACAGAACGTATTGT 59.762 36.000 10.34 4.70 0.00 2.71
2177 2453 5.565259 GCAATTGAAGACAGAACGTATTGTG 59.435 40.000 10.34 0.00 35.23 3.33
2178 2454 6.565811 GCAATTGAAGACAGAACGTATTGTGA 60.566 38.462 10.34 0.00 33.34 3.58
2179 2455 7.351981 CAATTGAAGACAGAACGTATTGTGAA 58.648 34.615 9.32 0.00 33.34 3.18
2180 2456 7.672983 ATTGAAGACAGAACGTATTGTGAAT 57.327 32.000 9.32 1.47 33.34 2.57
2181 2457 8.771920 ATTGAAGACAGAACGTATTGTGAATA 57.228 30.769 9.32 0.00 33.34 1.75
2182 2458 8.596271 TTGAAGACAGAACGTATTGTGAATAA 57.404 30.769 9.32 0.00 33.34 1.40
2183 2459 8.771920 TGAAGACAGAACGTATTGTGAATAAT 57.228 30.769 9.32 0.00 33.34 1.28
2184 2460 9.863845 TGAAGACAGAACGTATTGTGAATAATA 57.136 29.630 9.32 0.00 33.34 0.98
2186 2462 9.871238 AAGACAGAACGTATTGTGAATAATAGT 57.129 29.630 9.32 0.00 33.34 2.12
2195 2471 9.125906 CGTATTGTGAATAATAGTACTACTGGC 57.874 37.037 4.31 0.00 0.00 4.85
2228 2557 8.650143 AACAAACCAAATCTCCAGTACATATT 57.350 30.769 0.00 0.00 0.00 1.28
2229 2558 8.055279 ACAAACCAAATCTCCAGTACATATTG 57.945 34.615 0.00 0.00 0.00 1.90
2231 2560 7.630242 AACCAAATCTCCAGTACATATTGTG 57.370 36.000 0.00 0.00 0.00 3.33
2232 2561 6.957631 ACCAAATCTCCAGTACATATTGTGA 58.042 36.000 0.00 0.00 0.00 3.58
2233 2562 7.577303 ACCAAATCTCCAGTACATATTGTGAT 58.423 34.615 0.00 0.00 0.00 3.06
2236 2565 9.334947 CAAATCTCCAGTACATATTGTGATTCT 57.665 33.333 0.00 0.00 0.00 2.40
2237 2566 8.899427 AATCTCCAGTACATATTGTGATTCTG 57.101 34.615 0.00 0.00 0.00 3.02
2238 2567 7.423844 TCTCCAGTACATATTGTGATTCTGT 57.576 36.000 0.00 0.00 0.00 3.41
2239 2568 8.533569 TCTCCAGTACATATTGTGATTCTGTA 57.466 34.615 0.00 0.00 0.00 2.74
2240 2569 8.633561 TCTCCAGTACATATTGTGATTCTGTAG 58.366 37.037 0.00 0.00 0.00 2.74
2241 2570 8.533569 TCCAGTACATATTGTGATTCTGTAGA 57.466 34.615 0.00 0.00 0.00 2.59
2242 2571 8.977412 TCCAGTACATATTGTGATTCTGTAGAA 58.023 33.333 0.00 0.00 38.56 2.10
2244 2573 9.586435 CAGTACATATTGTGATTCTGTAGAACA 57.414 33.333 0.00 0.00 36.80 3.18
2246 2575 9.035607 GTACATATTGTGATTCTGTAGAACAGG 57.964 37.037 7.18 0.00 45.94 4.00
2247 2576 7.624549 ACATATTGTGATTCTGTAGAACAGGT 58.375 34.615 7.18 0.00 45.94 4.00
2249 2578 8.607459 CATATTGTGATTCTGTAGAACAGGTTC 58.393 37.037 7.18 4.00 45.94 3.62
2250 2579 4.894784 TGTGATTCTGTAGAACAGGTTCC 58.105 43.478 8.47 0.00 45.94 3.62
2253 2582 4.020218 TGATTCTGTAGAACAGGTTCCCAG 60.020 45.833 17.01 17.01 45.94 4.45
2254 2583 2.972348 TCTGTAGAACAGGTTCCCAGT 58.028 47.619 20.01 4.05 45.94 4.00
2256 2585 4.485875 TCTGTAGAACAGGTTCCCAGTTA 58.514 43.478 20.01 7.52 45.94 2.24
2257 2586 4.282703 TCTGTAGAACAGGTTCCCAGTTAC 59.717 45.833 20.01 12.27 45.94 2.50
2258 2587 4.228824 TGTAGAACAGGTTCCCAGTTACT 58.771 43.478 8.47 0.00 40.33 2.24
2299 2711 6.699204 GCAATGAGTCGATTGAGAAATCTAGA 59.301 38.462 15.29 0.00 35.65 2.43
2480 2892 1.431496 AATTGTCAAGGCGCAAATGC 58.569 45.000 10.83 0.00 37.78 3.56
2524 2936 2.704572 CCTTCACCTCTAAGCAACTGG 58.295 52.381 0.00 0.00 0.00 4.00
2538 3007 2.857104 GCAACTGGCTTACACGTTTTCC 60.857 50.000 0.00 0.00 40.25 3.13
2542 3011 0.514255 GGCTTACACGTTTTCCGGAC 59.486 55.000 1.83 0.00 42.24 4.79
2599 3068 4.571984 TCAGATTTGTACATCAATCTGCCG 59.428 41.667 29.52 16.60 39.12 5.69
2602 3071 0.809636 TGTACATCAATCTGCCGGCG 60.810 55.000 23.90 16.91 0.00 6.46
2706 3179 5.478407 ACATCTAACAACATGATCGACACA 58.522 37.500 0.00 0.00 0.00 3.72
2709 3182 4.869861 TCTAACAACATGATCGACACATGG 59.130 41.667 26.74 17.48 46.19 3.66
2934 3407 1.203441 ACCAGATCCTCAAGGCTGCA 61.203 55.000 0.50 0.00 34.44 4.41
2979 3452 0.678395 CAGAGATGGATGTCCCCGAG 59.322 60.000 0.00 0.00 34.29 4.63
2982 3455 1.109920 AGATGGATGTCCCCGAGTCG 61.110 60.000 5.29 5.29 34.29 4.18
3067 3548 3.610242 GTCAGTAATGTCTCTTGCTCACG 59.390 47.826 0.00 0.00 0.00 4.35
3334 3823 2.548875 GTGAGAGACATGCTGATGGAC 58.451 52.381 0.00 0.00 33.39 4.02
6590 7103 1.939974 CGAGCCGAATCTTTCCATCA 58.060 50.000 0.00 0.00 0.00 3.07
6697 7254 1.068954 GCGGGCAAAAGAGAAGTGAAG 60.069 52.381 0.00 0.00 0.00 3.02
6752 7312 2.203015 CCATGTTACCCGGGCGAG 60.203 66.667 24.08 4.54 0.00 5.03
6875 7455 4.661222 TGCAGAGAGAGAAGAGAAGAGAA 58.339 43.478 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.163818 TTCCTGACATGAACGGTCAC 57.836 50.000 4.62 0.00 40.16 3.67
4 5 3.606153 CGTTTTTCCTGACATGAACGGTC 60.606 47.826 0.00 0.00 36.99 4.79
5 6 2.289547 CGTTTTTCCTGACATGAACGGT 59.710 45.455 0.00 0.00 36.99 4.83
7 8 3.870723 TCGTTTTTCCTGACATGAACG 57.129 42.857 0.00 2.46 40.63 3.95
8 9 4.915704 TGTTCGTTTTTCCTGACATGAAC 58.084 39.130 0.00 0.00 36.06 3.18
10 11 5.049474 CAGATGTTCGTTTTTCCTGACATGA 60.049 40.000 0.00 0.00 0.00 3.07
11 12 5.149273 CAGATGTTCGTTTTTCCTGACATG 58.851 41.667 0.00 0.00 0.00 3.21
12 13 4.216257 CCAGATGTTCGTTTTTCCTGACAT 59.784 41.667 0.00 0.00 0.00 3.06
13 14 3.563808 CCAGATGTTCGTTTTTCCTGACA 59.436 43.478 0.00 0.00 0.00 3.58
14 15 3.564225 ACCAGATGTTCGTTTTTCCTGAC 59.436 43.478 0.00 0.00 0.00 3.51
15 16 3.813166 GACCAGATGTTCGTTTTTCCTGA 59.187 43.478 0.00 0.00 0.00 3.86
16 17 3.563808 TGACCAGATGTTCGTTTTTCCTG 59.436 43.478 0.00 0.00 0.00 3.86
17 18 3.815401 CTGACCAGATGTTCGTTTTTCCT 59.185 43.478 0.00 0.00 0.00 3.36
18 19 3.813166 TCTGACCAGATGTTCGTTTTTCC 59.187 43.478 0.00 0.00 31.41 3.13
19 20 5.418310 TTCTGACCAGATGTTCGTTTTTC 57.582 39.130 0.01 0.00 37.29 2.29
20 21 6.391227 AATTCTGACCAGATGTTCGTTTTT 57.609 33.333 0.01 0.00 37.29 1.94
21 22 6.391227 AAATTCTGACCAGATGTTCGTTTT 57.609 33.333 0.01 0.00 37.29 2.43
22 23 6.263168 AGAAAATTCTGACCAGATGTTCGTTT 59.737 34.615 0.01 0.00 37.29 3.60
23 24 5.765182 AGAAAATTCTGACCAGATGTTCGTT 59.235 36.000 0.01 0.00 37.29 3.85
24 25 5.308825 AGAAAATTCTGACCAGATGTTCGT 58.691 37.500 0.01 0.00 37.29 3.85
25 26 5.869753 AGAAAATTCTGACCAGATGTTCG 57.130 39.130 0.01 0.00 37.29 3.95
50 51 1.136529 CAGCACGTCGTCAAACTGATG 60.137 52.381 0.00 0.00 34.78 3.07
55 56 1.201825 GAGCAGCACGTCGTCAAAC 59.798 57.895 0.00 0.00 0.00 2.93
58 59 1.375551 TATAGAGCAGCACGTCGTCA 58.624 50.000 0.00 0.00 0.00 4.35
65 66 6.252228 GCAAACAAAATCTTATAGAGCAGCAC 59.748 38.462 0.00 0.00 0.00 4.40
68 69 7.307694 TGTGCAAACAAAATCTTATAGAGCAG 58.692 34.615 0.00 0.00 0.00 4.24
91 93 1.995376 AAATCCGGCCTTCTGTTTGT 58.005 45.000 0.00 0.00 0.00 2.83
111 113 6.125949 ACCACCTACTATAGTAGCTTTACCCT 60.126 42.308 27.84 7.17 44.97 4.34
116 118 6.776603 CCTGTACCACCTACTATAGTAGCTTT 59.223 42.308 27.84 14.93 44.97 3.51
124 126 3.216800 CGTGCCTGTACCACCTACTATA 58.783 50.000 0.00 0.00 0.00 1.31
126 128 1.466856 CGTGCCTGTACCACCTACTA 58.533 55.000 0.00 0.00 0.00 1.82
133 135 2.845317 ACCACCGTGCCTGTACCA 60.845 61.111 0.00 0.00 0.00 3.25
142 145 2.274437 CTCTGAATCATCACCACCGTG 58.726 52.381 0.00 0.00 41.72 4.94
143 146 1.406069 GCTCTGAATCATCACCACCGT 60.406 52.381 0.00 0.00 0.00 4.83
189 195 1.478510 AGACCCATGTCGAGCTTAGTG 59.521 52.381 0.00 0.00 46.51 2.74
190 196 1.751924 GAGACCCATGTCGAGCTTAGT 59.248 52.381 0.00 0.00 46.51 2.24
195 201 0.386113 GGTAGAGACCCATGTCGAGC 59.614 60.000 0.00 0.00 46.51 5.03
202 211 0.034767 TCGTGACGGTAGAGACCCAT 60.035 55.000 4.70 0.00 43.64 4.00
212 221 2.646175 CCATCCCACTCGTGACGGT 61.646 63.158 4.70 0.00 0.00 4.83
214 223 0.037697 TTTCCATCCCACTCGTGACG 60.038 55.000 0.00 0.00 0.00 4.35
227 236 5.521735 CACGATCGATTTCTCTTCTTTCCAT 59.478 40.000 24.34 0.00 0.00 3.41
228 237 4.864806 CACGATCGATTTCTCTTCTTTCCA 59.135 41.667 24.34 0.00 0.00 3.53
251 262 3.232213 TGATGAGTACGTGCTCCTTTC 57.768 47.619 27.59 21.10 34.74 2.62
259 270 5.284079 TGTGATGATGATGATGAGTACGTG 58.716 41.667 0.00 0.00 0.00 4.49
271 282 9.507280 CGCTAAAGTTTTAATTGTGATGATGAT 57.493 29.630 0.00 0.00 0.00 2.45
294 305 1.726853 GGCGATTAATATCCAGCGCT 58.273 50.000 2.64 2.64 43.49 5.92
298 309 3.432252 GGTGAACGGCGATTAATATCCAG 59.568 47.826 16.62 2.73 0.00 3.86
312 323 2.874664 TTCCGGTGGAGGTGAACGG 61.875 63.158 0.00 0.00 45.52 4.44
313 324 1.666872 GTTCCGGTGGAGGTGAACG 60.667 63.158 0.00 0.00 31.21 3.95
314 325 0.179040 TTGTTCCGGTGGAGGTGAAC 60.179 55.000 0.00 0.00 38.03 3.18
316 327 0.761323 TCTTGTTCCGGTGGAGGTGA 60.761 55.000 0.00 0.00 31.21 4.02
318 329 0.471211 TCTCTTGTTCCGGTGGAGGT 60.471 55.000 0.00 0.00 31.21 3.85
319 330 0.685097 TTCTCTTGTTCCGGTGGAGG 59.315 55.000 0.00 0.00 31.21 4.30
320 331 1.618837 TCTTCTCTTGTTCCGGTGGAG 59.381 52.381 0.00 3.61 31.21 3.86
321 332 1.618837 CTCTTCTCTTGTTCCGGTGGA 59.381 52.381 0.00 0.00 0.00 4.02
322 333 1.618837 TCTCTTCTCTTGTTCCGGTGG 59.381 52.381 0.00 0.00 0.00 4.61
323 334 3.386768 TTCTCTTCTCTTGTTCCGGTG 57.613 47.619 0.00 0.00 0.00 4.94
324 335 3.134081 TGTTTCTCTTCTCTTGTTCCGGT 59.866 43.478 0.00 0.00 0.00 5.28
330 341 7.254932 GCAATACAAGTGTTTCTCTTCTCTTGT 60.255 37.037 11.88 11.88 44.63 3.16
349 360 1.209504 GCCCTGACCTACTGCAATACA 59.790 52.381 0.00 0.00 0.00 2.29
351 362 0.464036 CGCCCTGACCTACTGCAATA 59.536 55.000 0.00 0.00 0.00 1.90
353 364 1.264749 ATCGCCCTGACCTACTGCAA 61.265 55.000 0.00 0.00 0.00 4.08
354 365 1.685765 ATCGCCCTGACCTACTGCA 60.686 57.895 0.00 0.00 0.00 4.41
355 366 1.227380 CATCGCCCTGACCTACTGC 60.227 63.158 0.00 0.00 0.00 4.40
356 367 1.227380 GCATCGCCCTGACCTACTG 60.227 63.158 0.00 0.00 0.00 2.74
357 368 1.685765 TGCATCGCCCTGACCTACT 60.686 57.895 0.00 0.00 0.00 2.57
372 383 1.962822 CAGCAAAGGAGCGAGTGCA 60.963 57.895 0.00 0.00 46.23 4.57
387 398 2.036933 CTTCTTTTTCGTTCGTGCAGC 58.963 47.619 0.00 0.00 0.00 5.25
406 417 5.634118 TCTCATCATGGGTGTTTTTCTTCT 58.366 37.500 0.00 0.00 0.00 2.85
407 418 5.964958 TCTCATCATGGGTGTTTTTCTTC 57.035 39.130 0.00 0.00 0.00 2.87
410 421 6.152661 TGGTATTCTCATCATGGGTGTTTTTC 59.847 38.462 0.00 0.00 0.00 2.29
443 454 1.699634 GGTTAGCTGGATGCCTGGATA 59.300 52.381 0.00 0.00 44.23 2.59
445 456 1.635817 GGGTTAGCTGGATGCCTGGA 61.636 60.000 0.00 0.00 44.23 3.86
446 457 1.152881 GGGTTAGCTGGATGCCTGG 60.153 63.158 0.00 0.00 44.23 4.45
447 458 1.152881 GGGGTTAGCTGGATGCCTG 60.153 63.158 0.00 0.00 44.23 4.85
448 459 1.619363 TGGGGTTAGCTGGATGCCT 60.619 57.895 0.00 0.00 44.23 4.75
449 460 1.453928 GTGGGGTTAGCTGGATGCC 60.454 63.158 0.00 0.00 44.23 4.40
450 461 1.819632 CGTGGGGTTAGCTGGATGC 60.820 63.158 0.00 0.00 43.29 3.91
451 462 0.462047 GTCGTGGGGTTAGCTGGATG 60.462 60.000 0.00 0.00 0.00 3.51
452 463 1.623542 GGTCGTGGGGTTAGCTGGAT 61.624 60.000 0.00 0.00 0.00 3.41
453 464 2.288025 GGTCGTGGGGTTAGCTGGA 61.288 63.158 0.00 0.00 0.00 3.86
493 504 0.309302 CACGGAGTAGATGAGCCGAG 59.691 60.000 7.16 0.00 46.29 4.63
754 771 0.040499 GGCCTGGGAAAATGTGGGTA 59.960 55.000 0.00 0.00 0.00 3.69
827 867 4.363990 AGCGTCTCTGTGCGGGTG 62.364 66.667 0.00 0.00 35.87 4.61
830 870 3.402691 ATCGAGCGTCTCTGTGCGG 62.403 63.158 0.00 0.00 35.87 5.69
899 948 2.818274 CGGGTTAAGCTCCGCACC 60.818 66.667 4.41 0.00 39.78 5.01
941 990 2.202770 TGTGCCGTGTCGTCGTTT 60.203 55.556 0.00 0.00 0.00 3.60
1119 1186 2.328099 CGTCTTCTTGGGTGCTGCC 61.328 63.158 0.00 0.00 0.00 4.85
1125 1192 4.699522 GCCGGCGTCTTCTTGGGT 62.700 66.667 12.58 0.00 0.00 4.51
1209 1276 0.598562 TGACAGACGAGTGAGAAGCC 59.401 55.000 0.00 0.00 0.00 4.35
1220 1287 1.803519 GCTTCGCCTCTGACAGACG 60.804 63.158 0.00 5.08 0.00 4.18
1242 1325 3.009723 CCAGTACCTACATTGTTGCTGG 58.990 50.000 8.96 8.96 34.06 4.85
1244 1327 3.674997 CACCAGTACCTACATTGTTGCT 58.325 45.455 0.00 0.00 0.00 3.91
1275 1370 0.689055 AGCTCCATCTCTGCACACAA 59.311 50.000 0.00 0.00 0.00 3.33
1293 1401 1.800655 CGCGAACCTCTCCTTCATCAG 60.801 57.143 0.00 0.00 0.00 2.90
1410 1518 3.765511 TGAAGAAATGGAGCAAAGATGGG 59.234 43.478 0.00 0.00 0.00 4.00
1477 1590 1.662629 CGAAGATGGTAGCTGCACAAG 59.337 52.381 3.61 0.00 0.00 3.16
1480 1593 0.811616 CCCGAAGATGGTAGCTGCAC 60.812 60.000 3.61 0.00 0.00 4.57
1481 1594 1.522092 CCCGAAGATGGTAGCTGCA 59.478 57.895 3.61 0.00 0.00 4.41
1525 1647 1.997874 ATGGCCTTCTTCTCCGGCT 60.998 57.895 3.32 0.00 43.29 5.52
1637 1759 2.886134 GCCGGTTGGTGGTACCTCA 61.886 63.158 14.36 8.89 39.58 3.86
1692 1815 1.889573 GCCTATTGCTCGGTCTGCC 60.890 63.158 0.00 0.00 36.87 4.85
1693 1816 1.889573 GGCCTATTGCTCGGTCTGC 60.890 63.158 0.00 0.00 40.92 4.26
1694 1817 1.592669 CGGCCTATTGCTCGGTCTG 60.593 63.158 0.00 0.00 40.92 3.51
1695 1818 2.797278 CCGGCCTATTGCTCGGTCT 61.797 63.158 0.00 0.00 44.10 3.85
1705 1854 0.532862 CGTGATTTCAGCCGGCCTAT 60.533 55.000 26.15 11.57 0.00 2.57
1825 1974 9.244799 CATGTGCTACTAAAGTCGACATTATAA 57.755 33.333 19.50 6.57 0.00 0.98
1829 1978 4.870426 CCATGTGCTACTAAAGTCGACATT 59.130 41.667 19.50 15.11 0.00 2.71
1889 2143 3.204158 TCTGTTTATATGGGTGCCATGGT 59.796 43.478 14.67 0.00 44.84 3.55
1902 2156 7.491372 CGCACCTAACATTTCTCTCTGTTTATA 59.509 37.037 0.00 0.00 36.92 0.98
1909 2163 2.622436 GCGCACCTAACATTTCTCTCT 58.378 47.619 0.30 0.00 0.00 3.10
1946 2200 1.206115 GCCACAACCGCAAAGTTTCG 61.206 55.000 0.00 0.00 0.00 3.46
1965 2224 1.731613 CAAGCACAACAGCATGGCG 60.732 57.895 0.00 0.00 43.62 5.69
1982 2241 0.385751 TCCGGCAACAAATTTTCGCA 59.614 45.000 0.00 0.00 0.00 5.10
1989 2248 1.322538 GCCCTCATCCGGCAACAAAT 61.323 55.000 0.00 0.00 46.27 2.32
2033 2292 3.077484 ACTGCTACCATTTGCTGTCAT 57.923 42.857 0.00 0.00 36.84 3.06
2065 2324 1.059098 ATGGCATCTTCTATCGGGCA 58.941 50.000 0.00 0.00 38.44 5.36
2121 2397 3.592059 GCTTCATTACCGTTGTGGAGTA 58.408 45.455 0.00 0.00 42.00 2.59
2147 2423 6.042143 ACGTTCTGTCTTCAATTGCATTTTT 58.958 32.000 0.00 0.00 0.00 1.94
2148 2424 5.591099 ACGTTCTGTCTTCAATTGCATTTT 58.409 33.333 0.00 0.00 0.00 1.82
2149 2425 5.186996 ACGTTCTGTCTTCAATTGCATTT 57.813 34.783 0.00 0.00 0.00 2.32
2150 2426 4.836125 ACGTTCTGTCTTCAATTGCATT 57.164 36.364 0.00 0.00 0.00 3.56
2151 2427 6.072508 ACAATACGTTCTGTCTTCAATTGCAT 60.073 34.615 0.00 0.00 0.00 3.96
2152 2428 5.238432 ACAATACGTTCTGTCTTCAATTGCA 59.762 36.000 0.00 0.00 0.00 4.08
2153 2429 5.565259 CACAATACGTTCTGTCTTCAATTGC 59.435 40.000 0.00 0.00 0.00 3.56
2154 2430 6.887368 TCACAATACGTTCTGTCTTCAATTG 58.113 36.000 0.00 0.00 0.00 2.32
2155 2431 7.490962 TTCACAATACGTTCTGTCTTCAATT 57.509 32.000 0.00 0.00 0.00 2.32
2156 2432 7.672983 ATTCACAATACGTTCTGTCTTCAAT 57.327 32.000 0.00 0.00 0.00 2.57
2157 2433 8.596271 TTATTCACAATACGTTCTGTCTTCAA 57.404 30.769 0.00 0.00 0.00 2.69
2158 2434 8.771920 ATTATTCACAATACGTTCTGTCTTCA 57.228 30.769 0.00 0.00 0.00 3.02
2160 2436 9.871238 ACTATTATTCACAATACGTTCTGTCTT 57.129 29.630 0.00 0.00 0.00 3.01
2169 2445 9.125906 GCCAGTAGTACTATTATTCACAATACG 57.874 37.037 5.75 0.00 0.00 3.06
2181 2457 9.953565 TTGTTTTCATTAGCCAGTAGTACTATT 57.046 29.630 5.75 0.00 0.00 1.73
2182 2458 9.953565 TTTGTTTTCATTAGCCAGTAGTACTAT 57.046 29.630 5.75 0.00 0.00 2.12
2183 2459 9.211485 GTTTGTTTTCATTAGCCAGTAGTACTA 57.789 33.333 1.57 0.00 0.00 1.82
2184 2460 7.174426 GGTTTGTTTTCATTAGCCAGTAGTACT 59.826 37.037 0.00 0.00 0.00 2.73
2185 2461 7.040961 TGGTTTGTTTTCATTAGCCAGTAGTAC 60.041 37.037 0.00 0.00 0.00 2.73
2186 2462 6.999272 TGGTTTGTTTTCATTAGCCAGTAGTA 59.001 34.615 0.00 0.00 0.00 1.82
2187 2463 5.830991 TGGTTTGTTTTCATTAGCCAGTAGT 59.169 36.000 0.00 0.00 0.00 2.73
2188 2464 6.325919 TGGTTTGTTTTCATTAGCCAGTAG 57.674 37.500 0.00 0.00 0.00 2.57
2189 2465 6.716934 TTGGTTTGTTTTCATTAGCCAGTA 57.283 33.333 0.00 0.00 0.00 2.74
2190 2466 5.606348 TTGGTTTGTTTTCATTAGCCAGT 57.394 34.783 0.00 0.00 0.00 4.00
2191 2467 6.930722 AGATTTGGTTTGTTTTCATTAGCCAG 59.069 34.615 0.00 0.00 0.00 4.85
2192 2468 6.825610 AGATTTGGTTTGTTTTCATTAGCCA 58.174 32.000 0.00 0.00 0.00 4.75
2193 2469 6.368791 GGAGATTTGGTTTGTTTTCATTAGCC 59.631 38.462 0.00 0.00 0.00 3.93
2194 2470 6.928492 TGGAGATTTGGTTTGTTTTCATTAGC 59.072 34.615 0.00 0.00 0.00 3.09
2195 2471 8.143835 ACTGGAGATTTGGTTTGTTTTCATTAG 58.856 33.333 0.00 0.00 0.00 1.73
2196 2472 8.017418 ACTGGAGATTTGGTTTGTTTTCATTA 57.983 30.769 0.00 0.00 0.00 1.90
2197 2473 6.888105 ACTGGAGATTTGGTTTGTTTTCATT 58.112 32.000 0.00 0.00 0.00 2.57
2198 2474 6.484364 ACTGGAGATTTGGTTTGTTTTCAT 57.516 33.333 0.00 0.00 0.00 2.57
2199 2475 5.930837 ACTGGAGATTTGGTTTGTTTTCA 57.069 34.783 0.00 0.00 0.00 2.69
2200 2476 6.801575 TGTACTGGAGATTTGGTTTGTTTTC 58.198 36.000 0.00 0.00 0.00 2.29
2246 2575 4.013050 ACTCCGTACTAGTAACTGGGAAC 58.987 47.826 3.61 0.00 0.00 3.62
2247 2576 4.265073 GACTCCGTACTAGTAACTGGGAA 58.735 47.826 3.61 0.00 0.00 3.97
2249 2578 2.948315 GGACTCCGTACTAGTAACTGGG 59.052 54.545 3.61 4.38 0.00 4.45
2250 2579 3.376546 GTGGACTCCGTACTAGTAACTGG 59.623 52.174 3.61 7.40 0.00 4.00
2253 2582 3.181502 GCAGTGGACTCCGTACTAGTAAC 60.182 52.174 3.61 0.00 0.00 2.50
2254 2583 3.012518 GCAGTGGACTCCGTACTAGTAA 58.987 50.000 3.61 0.00 0.00 2.24
2256 2585 1.271762 TGCAGTGGACTCCGTACTAGT 60.272 52.381 0.00 0.00 0.00 2.57
2257 2586 1.460504 TGCAGTGGACTCCGTACTAG 58.539 55.000 0.00 0.00 0.00 2.57
2258 2587 1.913778 TTGCAGTGGACTCCGTACTA 58.086 50.000 0.00 0.00 0.00 1.82
2308 2720 0.815213 AGCAATCGCATGGTACGCAT 60.815 50.000 0.00 0.00 42.27 4.73
2453 2865 4.422840 TGCGCCTTGACAATTATTTCATG 58.577 39.130 4.18 0.00 0.00 3.07
2461 2873 1.431496 GCATTTGCGCCTTGACAATT 58.569 45.000 4.18 0.00 0.00 2.32
2463 2875 4.651585 GCATTTGCGCCTTGACAA 57.348 50.000 4.18 0.00 0.00 3.18
2480 2892 5.499334 GCTGAACTTTATCAATGAGTCGTCG 60.499 44.000 0.00 0.00 0.00 5.12
2482 2894 4.631813 GGCTGAACTTTATCAATGAGTCGT 59.368 41.667 0.00 0.00 0.00 4.34
2489 2901 5.574188 AGGTGAAGGCTGAACTTTATCAAT 58.426 37.500 0.00 0.00 0.00 2.57
2524 2936 0.514255 GGTCCGGAAAACGTGTAAGC 59.486 55.000 5.23 0.00 42.24 3.09
2538 3007 1.067142 TGATCTGAAACGAAGGGTCCG 60.067 52.381 0.00 0.00 0.00 4.79
2542 3011 3.599343 TGTCATGATCTGAAACGAAGGG 58.401 45.455 0.00 0.00 35.07 3.95
2934 3407 0.244450 CGTTGCTGTTGATGGCCATT 59.756 50.000 21.84 3.11 0.00 3.16
2982 3455 1.255667 TTGGCAGGGAGTCGAGGTAC 61.256 60.000 0.00 0.00 0.00 3.34
2994 3467 3.689280 ATCATGGTGATACCTTTGGCAGG 60.689 47.826 0.00 0.00 39.58 4.85
3067 3548 2.865551 CACAAAATTGCACCACCAAGTC 59.134 45.455 0.00 0.00 0.00 3.01
3304 3793 0.610174 TGTCTCTCACCATGCTCCAC 59.390 55.000 0.00 0.00 0.00 4.02
3334 3823 2.015227 GCAGCTCCCTCTTCTCCGAG 62.015 65.000 0.00 0.00 0.00 4.63
6729 7289 1.377987 CCGGGTAACATGGTGTGGG 60.378 63.158 0.00 0.00 39.74 4.61
6752 7312 0.530650 TCGATGGCCGCTTGAAGATC 60.531 55.000 0.00 0.00 38.37 2.75
6846 7423 2.809266 TTCTCTCTCTGCAGTGCGCG 62.809 60.000 14.67 0.00 46.97 6.86
6848 7425 0.525311 TCTTCTCTCTCTGCAGTGCG 59.475 55.000 14.67 6.51 0.00 5.34
6875 7455 3.241530 TTGGCCGCACCTCACTCT 61.242 61.111 0.00 0.00 40.22 3.24


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

AutoCloner maintained by Alex Coulton.