Multiple sequence alignment - TraesCS7B01G452400

Loading Multiple Alignment...

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 TraesCS7B01G452400 chr7B 100.000 4282 0 0 1 4282 713661115 713665396 0.000000e+00 7908.0
1 TraesCS7B01G452400 chr7B 84.743 662 61 18 857 1493 243783197 243782551 1.010000e-175 627.0
2 TraesCS7B01G452400 chr7B 82.437 279 33 10 3910 4183 713725948 713726215 3.330000e-56 230.0
3 TraesCS7B01G452400 chr7B 88.112 143 7 5 3344 3478 713377663 713377523 1.230000e-35 161.0
4 TraesCS7B01G452400 chr7B 80.402 199 28 6 1507 1705 243782507 243782320 1.610000e-29 141.0
5 TraesCS7B01G452400 chr7B 78.713 202 26 11 1507 1705 347592272 347592085 7.520000e-23 119.0
6 TraesCS7B01G452400 chr7B 100.000 34 0 0 2327 2360 714464781 714464814 3.570000e-06 63.9
7 TraesCS7B01G452400 chr7D 89.021 2851 187 41 1507 4282 619041441 619044240 0.000000e+00 3415.0
8 TraesCS7B01G452400 chr7D 82.481 1564 140 68 2 1496 619039898 619041396 0.000000e+00 1247.0
9 TraesCS7B01G452400 chr7D 100.000 28 0 0 1143 1170 263833021 263832994 8.000000e-03 52.8
10 TraesCS7B01G452400 chr7A 89.337 2457 145 50 1522 3923 712770102 712772496 0.000000e+00 2977.0
11 TraesCS7B01G452400 chr7A 82.977 1122 82 49 416 1493 712768978 712770034 0.000000e+00 913.0
12 TraesCS7B01G452400 chr7A 91.268 355 24 6 1694 2048 728248944 728248597 1.080000e-130 477.0
13 TraesCS7B01G452400 chr7A 83.633 501 59 11 2273 2753 728248510 728248013 2.350000e-122 449.0
14 TraesCS7B01G452400 chr7A 91.748 206 11 3 4078 4282 712773214 712773414 9.070000e-72 281.0
15 TraesCS7B01G452400 chr7A 84.100 239 35 1 2273 2508 728247729 728247491 1.200000e-55 228.0
16 TraesCS7B01G452400 chr7A 79.279 222 16 15 2539 2755 712979329 712979525 1.250000e-25 128.0
17 TraesCS7B01G452400 chr7A 100.000 30 0 0 1143 1172 286819164 286819135 5.980000e-04 56.5
18 TraesCS7B01G452400 chr5B 86.405 331 27 5 857 1178 91774283 91773962 3.170000e-91 346.0
19 TraesCS7B01G452400 chr5B 80.597 201 24 9 1507 1705 91768383 91768196 1.610000e-29 141.0
20 TraesCS7B01G452400 chr2B 83.444 151 24 1 2275 2424 744087698 744087548 5.770000e-29 139.0
21 TraesCS7B01G452400 chr5D 85.366 82 8 4 1125 1204 432533159 432533080 9.870000e-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 TraesCS7B01G452400 chr7B 713661115 713665396 4281 False 7908.000000 7908 100.000000 1 4282 1 chr7B.!!$F1 4281
1 TraesCS7B01G452400 chr7B 243782320 243783197 877 True 384.000000 627 82.572500 857 1705 2 chr7B.!!$R3 848
2 TraesCS7B01G452400 chr7D 619039898 619044240 4342 False 2331.000000 3415 85.751000 2 4282 2 chr7D.!!$F1 4280
3 TraesCS7B01G452400 chr7A 712768978 712773414 4436 False 1390.333333 2977 88.020667 416 4282 3 chr7A.!!$F2 3866
4 TraesCS7B01G452400 chr7A 728247491 728248944 1453 True 384.666667 477 86.333667 1694 2753 3 chr7A.!!$R2 1059

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
814 875 0.036306 TTCTTTGCTTCCGTCCCTCC 59.964 55.0 0.0 0.0 0.00 4.30 F
1215 1301 0.179134 CCTCCTCTGTTTCGCCTACG 60.179 60.0 0.0 0.0 42.01 3.51 F
1544 1696 0.385390 GTGCAGTGTGTTTTCCCCTG 59.615 55.0 0.0 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 2127 0.586319 GCAAGCAAGCGTGTCAGTTA 59.414 50.000 9.56 0.00 0.00 2.24 R
2476 2683 1.133976 AGCAACTGGTTTCAGACAGCT 60.134 47.619 0.00 3.88 43.49 4.24 R
3300 3817 0.030773 CGTCGGTCGTGGATGATGAT 59.969 55.000 0.00 0.00 34.52 2.45 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
34 35 7.329588 ACCTAAAATATTTTAGCAGGTTCGG 57.670 36.000 30.38 21.55 45.11 4.30
37 38 5.576447 AAATATTTTAGCAGGTTCGGTGG 57.424 39.130 0.00 0.00 0.00 4.61
42 43 1.823169 TAGCAGGTTCGGTGGTCCAC 61.823 60.000 14.13 14.13 0.00 4.02
46 47 1.278127 CAGGTTCGGTGGTCCACTAAT 59.722 52.381 21.40 0.75 34.40 1.73
54 56 3.692690 GGTGGTCCACTAATAAGGCAAA 58.307 45.455 21.40 0.00 34.40 3.68
55 57 4.278310 GGTGGTCCACTAATAAGGCAAAT 58.722 43.478 21.40 0.00 34.40 2.32
59 61 3.564225 GTCCACTAATAAGGCAAATCGGG 59.436 47.826 0.00 0.00 0.00 5.14
68 70 1.455383 GGCAAATCGGGCCGAATCAT 61.455 55.000 34.58 14.21 42.39 2.45
79 81 3.381272 GGGCCGAATCATTTGAATCTTGA 59.619 43.478 0.00 0.00 0.00 3.02
80 82 4.354587 GGCCGAATCATTTGAATCTTGAC 58.645 43.478 0.00 0.00 0.00 3.18
81 83 4.142403 GGCCGAATCATTTGAATCTTGACA 60.142 41.667 0.00 0.00 0.00 3.58
82 84 4.795278 GCCGAATCATTTGAATCTTGACAC 59.205 41.667 0.00 0.00 0.00 3.67
83 85 5.392380 GCCGAATCATTTGAATCTTGACACT 60.392 40.000 0.00 0.00 0.00 3.55
84 86 6.253746 CCGAATCATTTGAATCTTGACACTC 58.746 40.000 0.00 0.00 0.00 3.51
97 99 2.977914 TGACACTCAAGCATCCTAAGC 58.022 47.619 0.00 0.00 0.00 3.09
105 107 0.461961 AGCATCCTAAGCGTGAGGAC 59.538 55.000 6.45 0.00 45.90 3.85
110 112 0.888619 CCTAAGCGTGAGGACTGACA 59.111 55.000 0.00 0.00 35.99 3.58
118 120 1.375326 GAGGACTGACAACACCCCC 59.625 63.158 0.00 0.00 0.00 5.40
135 137 4.373116 CGTGTCCCCAGTCCGGTG 62.373 72.222 0.00 0.00 0.00 4.94
136 138 4.699522 GTGTCCCCAGTCCGGTGC 62.700 72.222 0.00 0.00 0.00 5.01
147 149 4.335647 CCGGTGCCAGTGAGCCTT 62.336 66.667 0.00 0.00 0.00 4.35
148 150 3.052082 CGGTGCCAGTGAGCCTTG 61.052 66.667 0.00 0.00 0.00 3.61
149 151 3.368571 GGTGCCAGTGAGCCTTGC 61.369 66.667 0.00 0.00 32.51 4.01
150 152 2.595463 GTGCCAGTGAGCCTTGCA 60.595 61.111 0.00 0.00 39.36 4.08
159 161 1.135689 GTGAGCCTTGCACAATTACGG 60.136 52.381 0.00 0.00 36.31 4.02
160 162 1.165270 GAGCCTTGCACAATTACGGT 58.835 50.000 0.00 0.00 0.00 4.83
162 164 0.878416 GCCTTGCACAATTACGGTCA 59.122 50.000 0.00 0.00 0.00 4.02
163 165 1.472480 GCCTTGCACAATTACGGTCAT 59.528 47.619 0.00 0.00 0.00 3.06
176 178 1.872679 GGTCATCGTCGACTTCCGC 60.873 63.158 14.70 1.02 38.37 5.54
181 184 0.108329 ATCGTCGACTTCCGCCAAAT 60.108 50.000 14.70 0.00 38.37 2.32
191 194 2.480555 CGCCAAATCACGCCTCAC 59.519 61.111 0.00 0.00 0.00 3.51
196 199 2.393764 CCAAATCACGCCTCACAAAAC 58.606 47.619 0.00 0.00 0.00 2.43
197 200 2.393764 CAAATCACGCCTCACAAAACC 58.606 47.619 0.00 0.00 0.00 3.27
198 201 0.958822 AATCACGCCTCACAAAACCC 59.041 50.000 0.00 0.00 0.00 4.11
204 208 1.254026 GCCTCACAAAACCCCCTTAC 58.746 55.000 0.00 0.00 0.00 2.34
211 215 2.753009 AAAACCCCCTTACGGCGACC 62.753 60.000 16.62 0.00 0.00 4.79
224 228 4.471726 CGACCGTCGAAGTCCCCG 62.472 72.222 16.03 0.00 43.74 5.73
225 229 3.368571 GACCGTCGAAGTCCCCGT 61.369 66.667 5.70 0.00 0.00 5.28
228 232 3.367743 CGTCGAAGTCCCCGTCCA 61.368 66.667 0.00 0.00 0.00 4.02
232 236 1.080025 CGAAGTCCCCGTCCAAGAC 60.080 63.158 0.00 0.00 0.00 3.01
238 242 0.252789 TCCCCGTCCAAGACCCATTA 60.253 55.000 0.00 0.00 0.00 1.90
241 245 2.357777 CCCCGTCCAAGACCCATTATTT 60.358 50.000 0.00 0.00 0.00 1.40
243 247 2.949644 CCGTCCAAGACCCATTATTTCC 59.050 50.000 0.00 0.00 0.00 3.13
252 281 3.463704 GACCCATTATTTCCCTTCCTCCT 59.536 47.826 0.00 0.00 0.00 3.69
255 284 3.724209 CCATTATTTCCCTTCCTCCTCCT 59.276 47.826 0.00 0.00 0.00 3.69
259 288 0.800239 TTCCCTTCCTCCTCCTCCTT 59.200 55.000 0.00 0.00 0.00 3.36
262 291 0.341609 CCTTCCTCCTCCTCCTTCCT 59.658 60.000 0.00 0.00 0.00 3.36
264 293 0.340208 TTCCTCCTCCTCCTTCCTCC 59.660 60.000 0.00 0.00 0.00 4.30
265 294 0.556380 TCCTCCTCCTCCTTCCTCCT 60.556 60.000 0.00 0.00 0.00 3.69
266 295 0.105709 CCTCCTCCTCCTTCCTCCTC 60.106 65.000 0.00 0.00 0.00 3.71
267 296 0.933700 CTCCTCCTCCTTCCTCCTCT 59.066 60.000 0.00 0.00 0.00 3.69
268 297 0.930726 TCCTCCTCCTTCCTCCTCTC 59.069 60.000 0.00 0.00 0.00 3.20
269 298 0.467290 CCTCCTCCTTCCTCCTCTCG 60.467 65.000 0.00 0.00 0.00 4.04
270 299 0.467290 CTCCTCCTTCCTCCTCTCGG 60.467 65.000 0.00 0.00 0.00 4.63
271 300 1.456705 CCTCCTTCCTCCTCTCGGG 60.457 68.421 0.00 0.00 0.00 5.14
272 301 1.308326 CTCCTTCCTCCTCTCGGGT 59.692 63.158 0.00 0.00 36.25 5.28
273 302 0.551879 CTCCTTCCTCCTCTCGGGTA 59.448 60.000 0.00 0.00 36.25 3.69
289 318 3.151710 TAGACCCCATGACGGCCG 61.152 66.667 26.86 26.86 0.00 6.13
313 342 2.161808 CGTTCGCTCTCTAAGACCAAGA 59.838 50.000 0.00 0.00 0.00 3.02
314 343 3.729462 CGTTCGCTCTCTAAGACCAAGAG 60.729 52.174 0.00 0.00 41.59 2.85
322 351 4.767928 TCTCTAAGACCAAGAGGAGAACAC 59.232 45.833 0.60 0.00 40.77 3.32
327 356 2.365617 GACCAAGAGGAGAACACTCACA 59.634 50.000 0.00 0.00 37.43 3.58
330 359 4.593206 ACCAAGAGGAGAACACTCACAATA 59.407 41.667 0.00 0.00 37.43 1.90
336 365 6.031751 AGGAGAACACTCACAATAGAGAAC 57.968 41.667 0.00 0.00 38.98 3.01
339 368 6.031751 AGAACACTCACAATAGAGAACTCC 57.968 41.667 0.00 0.00 38.98 3.85
342 371 3.108376 ACTCACAATAGAGAACTCCCCC 58.892 50.000 0.00 0.00 38.98 5.40
343 372 3.246167 ACTCACAATAGAGAACTCCCCCT 60.246 47.826 0.00 0.00 38.98 4.79
347 376 3.519913 ACAATAGAGAACTCCCCCTTCAC 59.480 47.826 0.00 0.00 0.00 3.18
349 378 0.193574 AGAGAACTCCCCCTTCACCA 59.806 55.000 0.00 0.00 0.00 4.17
352 381 1.145119 AGAACTCCCCCTTCACCAAAC 59.855 52.381 0.00 0.00 0.00 2.93
353 382 0.187606 AACTCCCCCTTCACCAAACC 59.812 55.000 0.00 0.00 0.00 3.27
373 402 5.456548 ACCTAACCAACCAATAAAAACGG 57.543 39.130 0.00 0.00 0.00 4.44
374 403 5.139001 ACCTAACCAACCAATAAAAACGGA 58.861 37.500 0.00 0.00 0.00 4.69
375 404 5.242171 ACCTAACCAACCAATAAAAACGGAG 59.758 40.000 0.00 0.00 0.00 4.63
376 405 5.474189 CCTAACCAACCAATAAAAACGGAGA 59.526 40.000 0.00 0.00 0.00 3.71
389 418 4.773117 GGAGACGTCACCGCGACC 62.773 72.222 19.50 5.48 42.07 4.79
390 419 3.735029 GAGACGTCACCGCGACCT 61.735 66.667 19.50 0.00 42.07 3.85
393 422 3.264866 GACGTCACCGCGACCTTCT 62.265 63.158 8.23 0.00 42.07 2.85
394 423 2.504244 CGTCACCGCGACCTTCTC 60.504 66.667 8.23 0.00 42.07 2.87
395 424 2.126031 GTCACCGCGACCTTCTCC 60.126 66.667 8.23 0.00 38.85 3.71
396 425 3.379445 TCACCGCGACCTTCTCCC 61.379 66.667 8.23 0.00 0.00 4.30
397 426 4.452733 CACCGCGACCTTCTCCCC 62.453 72.222 8.23 0.00 0.00 4.81
400 429 4.065281 CGCGACCTTCTCCCCGTT 62.065 66.667 0.00 0.00 0.00 4.44
401 430 2.125633 GCGACCTTCTCCCCGTTC 60.126 66.667 0.00 0.00 0.00 3.95
402 431 2.181021 CGACCTTCTCCCCGTTCG 59.819 66.667 0.00 0.00 0.00 3.95
403 432 2.125633 GACCTTCTCCCCGTTCGC 60.126 66.667 0.00 0.00 0.00 4.70
404 433 2.920912 ACCTTCTCCCCGTTCGCA 60.921 61.111 0.00 0.00 0.00 5.10
405 434 2.345991 CCTTCTCCCCGTTCGCAA 59.654 61.111 0.00 0.00 0.00 4.85
406 435 1.302192 CCTTCTCCCCGTTCGCAAA 60.302 57.895 0.00 0.00 0.00 3.68
407 436 0.676782 CCTTCTCCCCGTTCGCAAAT 60.677 55.000 0.00 0.00 0.00 2.32
408 437 0.727398 CTTCTCCCCGTTCGCAAATC 59.273 55.000 0.00 0.00 0.00 2.17
409 438 0.675522 TTCTCCCCGTTCGCAAATCC 60.676 55.000 0.00 0.00 0.00 3.01
410 439 1.376683 CTCCCCGTTCGCAAATCCA 60.377 57.895 0.00 0.00 0.00 3.41
417 446 1.259316 GTTCGCAAATCCATCGCAAC 58.741 50.000 0.00 0.00 0.00 4.17
439 468 4.157840 ACAACAAACAAGACTCCCAAAGAC 59.842 41.667 0.00 0.00 0.00 3.01
448 477 4.770795 AGACTCCCAAAGACATTAATCCG 58.229 43.478 0.00 0.00 0.00 4.18
449 478 3.877508 GACTCCCAAAGACATTAATCCGG 59.122 47.826 0.00 0.00 0.00 5.14
450 479 3.521937 ACTCCCAAAGACATTAATCCGGA 59.478 43.478 6.61 6.61 0.00 5.14
451 480 4.130118 CTCCCAAAGACATTAATCCGGAG 58.870 47.826 11.34 0.00 0.00 4.63
453 482 3.545703 CCAAAGACATTAATCCGGAGCT 58.454 45.455 11.34 1.53 0.00 4.09
458 493 1.202698 ACATTAATCCGGAGCTCAGCC 60.203 52.381 17.19 0.00 0.00 4.85
521 562 3.577805 AGGGGGACGAAAATATCTTGG 57.422 47.619 0.00 0.00 0.00 3.61
625 670 4.386951 CGCCATGACCACGGTGGA 62.387 66.667 32.72 12.70 40.96 4.02
626 671 2.272146 GCCATGACCACGGTGGAT 59.728 61.111 32.72 17.06 40.96 3.41
627 672 2.114670 GCCATGACCACGGTGGATG 61.115 63.158 32.72 24.14 40.96 3.51
630 675 1.923395 ATGACCACGGTGGATGGGT 60.923 57.895 32.72 10.71 40.96 4.51
631 676 2.046314 GACCACGGTGGATGGGTG 60.046 66.667 32.72 5.47 40.96 4.61
672 733 2.828877 TCGCCACGAAGAAAAGAAAGA 58.171 42.857 0.00 0.00 31.06 2.52
673 734 2.800544 TCGCCACGAAGAAAAGAAAGAG 59.199 45.455 0.00 0.00 31.06 2.85
674 735 2.800544 CGCCACGAAGAAAAGAAAGAGA 59.199 45.455 0.00 0.00 0.00 3.10
675 736 3.120854 CGCCACGAAGAAAAGAAAGAGAG 60.121 47.826 0.00 0.00 0.00 3.20
676 737 3.364465 GCCACGAAGAAAAGAAAGAGAGC 60.364 47.826 0.00 0.00 0.00 4.09
677 738 3.120854 CCACGAAGAAAAGAAAGAGAGCG 60.121 47.826 0.00 0.00 0.00 5.03
678 739 3.736252 CACGAAGAAAAGAAAGAGAGCGA 59.264 43.478 0.00 0.00 0.00 4.93
679 740 3.984633 ACGAAGAAAAGAAAGAGAGCGAG 59.015 43.478 0.00 0.00 0.00 5.03
680 741 3.366422 CGAAGAAAAGAAAGAGAGCGAGG 59.634 47.826 0.00 0.00 0.00 4.63
681 742 2.694213 AGAAAAGAAAGAGAGCGAGGC 58.306 47.619 0.00 0.00 0.00 4.70
682 743 2.037772 AGAAAAGAAAGAGAGCGAGGCA 59.962 45.455 0.00 0.00 0.00 4.75
683 744 2.550830 AAAGAAAGAGAGCGAGGCAA 57.449 45.000 0.00 0.00 0.00 4.52
684 745 2.091852 AAGAAAGAGAGCGAGGCAAG 57.908 50.000 0.00 0.00 0.00 4.01
685 746 0.248843 AGAAAGAGAGCGAGGCAAGG 59.751 55.000 0.00 0.00 0.00 3.61
686 747 1.365368 GAAAGAGAGCGAGGCAAGGC 61.365 60.000 0.00 0.00 0.00 4.35
769 830 1.302383 TGGTTGGCGCCATAAAGTCG 61.302 55.000 33.25 0.00 32.81 4.18
781 842 2.187896 TAAAGTCGCCCCCTTTCCCG 62.188 60.000 0.00 0.00 34.20 5.14
790 851 3.408853 CCTTTCCCGTCCCCCTCC 61.409 72.222 0.00 0.00 0.00 4.30
804 865 0.701147 CCCTCCCCTCTTCTTTGCTT 59.299 55.000 0.00 0.00 0.00 3.91
814 875 0.036306 TTCTTTGCTTCCGTCCCTCC 59.964 55.000 0.00 0.00 0.00 4.30
815 876 1.125093 TCTTTGCTTCCGTCCCTCCA 61.125 55.000 0.00 0.00 0.00 3.86
818 879 4.097361 GCTTCCGTCCCTCCACCC 62.097 72.222 0.00 0.00 0.00 4.61
835 896 1.048160 CCCCTCTCTCTCTTCCTGCC 61.048 65.000 0.00 0.00 0.00 4.85
844 905 0.682855 CTCTTCCTGCCTCGTCCTCT 60.683 60.000 0.00 0.00 0.00 3.69
845 906 0.681564 TCTTCCTGCCTCGTCCTCTC 60.682 60.000 0.00 0.00 0.00 3.20
846 907 1.671901 CTTCCTGCCTCGTCCTCTCC 61.672 65.000 0.00 0.00 0.00 3.71
847 908 2.043450 CCTGCCTCGTCCTCTCCT 60.043 66.667 0.00 0.00 0.00 3.69
848 909 2.124693 CCTGCCTCGTCCTCTCCTC 61.125 68.421 0.00 0.00 0.00 3.71
949 1016 3.068881 CGTGTGGGTGGGTGATCT 58.931 61.111 0.00 0.00 0.00 2.75
956 1023 0.623617 GGGTGGGTGATCTAAGGGGT 60.624 60.000 0.00 0.00 0.00 4.95
978 1046 2.689034 GGAGGAGTGGGGAGTGGG 60.689 72.222 0.00 0.00 0.00 4.61
983 1051 2.203998 AGTGGGGAGTGGGGAGTG 60.204 66.667 0.00 0.00 0.00 3.51
988 1056 4.348495 GGAGTGGGGAGTGGGGGA 62.348 72.222 0.00 0.00 0.00 4.81
1092 1169 4.228567 GGGAGCAGCGGGAGTAGC 62.229 72.222 0.00 0.00 0.00 3.58
1215 1301 0.179134 CCTCCTCTGTTTCGCCTACG 60.179 60.000 0.00 0.00 42.01 3.51
1255 1341 8.420222 AGTCGTGATTTCTTCAGATATCTTCAT 58.580 33.333 1.33 0.00 34.81 2.57
1256 1342 8.486383 GTCGTGATTTCTTCAGATATCTTCATG 58.514 37.037 1.33 8.15 34.81 3.07
1264 1350 8.634335 TCTTCAGATATCTTCATGTAGAGAGG 57.366 38.462 1.33 0.82 0.00 3.69
1265 1351 8.443979 TCTTCAGATATCTTCATGTAGAGAGGA 58.556 37.037 1.33 2.97 0.00 3.71
1290 1380 3.396260 TTACTGTCAAGTGCACCCTAC 57.604 47.619 14.63 9.60 37.19 3.18
1296 1386 1.985159 TCAAGTGCACCCTACCTTCAT 59.015 47.619 14.63 0.00 0.00 2.57
1300 1390 0.698238 TGCACCCTACCTTCATGCTT 59.302 50.000 0.00 0.00 37.20 3.91
1307 1397 2.932614 CCTACCTTCATGCTTCAGTTCG 59.067 50.000 0.00 0.00 0.00 3.95
1313 1413 2.071540 TCATGCTTCAGTTCGCTTCTG 58.928 47.619 0.00 0.00 0.00 3.02
1316 1416 0.441921 GCTTCAGTTCGCTTCTGAGC 59.558 55.000 0.00 0.00 45.65 4.26
1346 1447 8.424133 ACAAAGGGGATATTTTGATGATTTAGC 58.576 33.333 4.92 0.00 37.63 3.09
1443 1552 6.698008 TCTGTTTCTGCTTCATTTCTCAAA 57.302 33.333 0.00 0.00 0.00 2.69
1460 1569 5.178061 TCTCAAATCTTTGCTCGCAATCTA 58.822 37.500 5.03 0.00 38.05 1.98
1493 1603 7.945134 AGTAACAGATTCTTGAGTTGCAAAAT 58.055 30.769 0.00 0.00 35.74 1.82
1544 1696 0.385390 GTGCAGTGTGTTTTCCCCTG 59.615 55.000 0.00 0.00 0.00 4.45
1590 1742 1.522668 TTGGGTTGATCTGCTTCACG 58.477 50.000 0.00 0.00 0.00 4.35
1593 1745 2.236146 TGGGTTGATCTGCTTCACGTAT 59.764 45.455 0.00 0.00 0.00 3.06
1614 1766 6.950428 CGTATCGTGCAATCTTATTCTTATGC 59.050 38.462 0.00 0.00 0.00 3.14
1615 1767 6.866010 ATCGTGCAATCTTATTCTTATGCA 57.134 33.333 0.00 0.00 41.08 3.96
1645 1797 7.041508 ACACTCTGCTTTTGAGAAATTCTGTAG 60.042 37.037 0.00 0.00 35.66 2.74
1653 1805 9.921637 CTTTTGAGAAATTCTGTAGAGACTACT 57.078 33.333 0.00 0.00 0.00 2.57
1656 1808 9.516546 TTGAGAAATTCTGTAGAGACTACTACA 57.483 33.333 0.00 0.00 46.65 2.74
1687 1839 6.380995 TGTTCTGAACATTTGACATATGTGC 58.619 36.000 18.69 10.50 36.41 4.57
1731 1884 3.691342 TTCCTGGGAGCCGTCACG 61.691 66.667 0.00 0.00 0.00 4.35
1960 2127 0.601311 GAGCAGGACAGCAACTTCGT 60.601 55.000 0.00 0.00 36.85 3.85
2000 2171 2.356665 TGCCTGCACTTCCTTTGTTA 57.643 45.000 0.00 0.00 0.00 2.41
2001 2172 2.660572 TGCCTGCACTTCCTTTGTTAA 58.339 42.857 0.00 0.00 0.00 2.01
2003 2174 4.402829 TGCCTGCACTTCCTTTGTTAATA 58.597 39.130 0.00 0.00 0.00 0.98
2004 2175 5.016173 TGCCTGCACTTCCTTTGTTAATAT 58.984 37.500 0.00 0.00 0.00 1.28
2007 2178 7.013274 TGCCTGCACTTCCTTTGTTAATATATC 59.987 37.037 0.00 0.00 0.00 1.63
2008 2179 7.013274 GCCTGCACTTCCTTTGTTAATATATCA 59.987 37.037 0.00 0.00 0.00 2.15
2009 2180 9.071276 CCTGCACTTCCTTTGTTAATATATCAT 57.929 33.333 0.00 0.00 0.00 2.45
2048 2224 8.243426 TGTTGCTTGATTTACATGGACTAATTC 58.757 33.333 0.00 0.00 0.00 2.17
2058 2234 5.809001 ACATGGACTAATTCTTGCTCTCAA 58.191 37.500 0.00 0.00 0.00 3.02
2167 2343 8.695456 AGATTATAATTTGCAAGTAACTTGGGG 58.305 33.333 0.00 0.00 41.31 4.96
2168 2344 5.675684 ATAATTTGCAAGTAACTTGGGGG 57.324 39.130 0.00 0.00 41.31 5.40
2203 2379 4.278669 GCTTATCTATCCTTGTCGTCCTCA 59.721 45.833 0.00 0.00 0.00 3.86
2204 2380 5.047660 GCTTATCTATCCTTGTCGTCCTCAT 60.048 44.000 0.00 0.00 0.00 2.90
2205 2381 6.151312 GCTTATCTATCCTTGTCGTCCTCATA 59.849 42.308 0.00 0.00 0.00 2.15
2227 2403 9.883142 TCATAATCATCATGTTGTAGTTGTACA 57.117 29.630 3.76 0.00 37.38 2.90
2228 2404 9.920826 CATAATCATCATGTTGTAGTTGTACAC 57.079 33.333 0.00 0.00 38.95 2.90
2230 2406 5.774630 TCATCATGTTGTAGTTGTACACGA 58.225 37.500 0.00 0.00 38.95 4.35
2231 2407 6.394809 TCATCATGTTGTAGTTGTACACGAT 58.605 36.000 0.00 0.00 38.95 3.73
2232 2408 6.871492 TCATCATGTTGTAGTTGTACACGATT 59.129 34.615 0.00 0.00 38.95 3.34
2233 2409 6.699895 TCATGTTGTAGTTGTACACGATTC 57.300 37.500 0.00 0.00 38.95 2.52
2234 2410 5.343860 TCATGTTGTAGTTGTACACGATTCG 59.656 40.000 4.14 4.14 38.95 3.34
2235 2411 4.609947 TGTTGTAGTTGTACACGATTCGT 58.390 39.130 5.75 5.75 38.95 3.85
2236 2412 5.042593 TGTTGTAGTTGTACACGATTCGTT 58.957 37.500 9.40 4.24 38.95 3.85
2243 2425 6.384224 AGTTGTACACGATTCGTTTGAGATA 58.616 36.000 9.40 0.00 38.32 1.98
2245 2427 6.185852 TGTACACGATTCGTTTGAGATAGA 57.814 37.500 9.40 0.00 38.32 1.98
2246 2428 6.792326 TGTACACGATTCGTTTGAGATAGAT 58.208 36.000 9.40 0.00 38.32 1.98
2262 2444 9.914131 TTGAGATAGATACCTGAATAATGAACG 57.086 33.333 0.00 0.00 0.00 3.95
2313 2515 4.083271 GGTCTGATTGAGCCTAACACAAAC 60.083 45.833 0.00 0.00 37.22 2.93
2468 2675 3.572682 ATCAGGCATATGCATGGTTTGAG 59.427 43.478 34.46 13.70 44.45 3.02
2471 2678 1.684983 GCATATGCATGGTTTGAGCCT 59.315 47.619 22.84 0.00 41.59 4.58
2476 2683 1.176527 GCATGGTTTGAGCCTAAGCA 58.823 50.000 0.00 4.45 43.56 3.91
2534 2757 3.243035 TGTCATGCTTGTTTTTCTGGACG 60.243 43.478 0.00 0.00 0.00 4.79
2629 2852 4.271816 CCGAGGGCGTCCATCGAG 62.272 72.222 26.46 16.19 42.86 4.04
2688 2911 0.968901 AATGCCGTCGGTGACCTCTA 60.969 55.000 13.94 0.00 0.00 2.43
2753 2976 4.077982 TCTCTGAAACCCACTATCCCCTAT 60.078 45.833 0.00 0.00 0.00 2.57
2760 2983 3.248024 CCCACTATCCCCTATTAGCACA 58.752 50.000 0.00 0.00 0.00 4.57
2776 3016 3.545703 AGCACAAACTCTGCTTACTTGT 58.454 40.909 0.00 0.00 42.54 3.16
2832 3079 4.516323 TCTGAATTTCCGCTCATTCATCA 58.484 39.130 0.00 0.00 38.45 3.07
2833 3080 4.573607 TCTGAATTTCCGCTCATTCATCAG 59.426 41.667 0.00 0.00 38.45 2.90
2835 3082 5.427378 TGAATTTCCGCTCATTCATCAGTA 58.573 37.500 0.00 0.00 35.02 2.74
2859 3108 9.000018 GTAGTCATTTATTTGATTTCTTCACGC 58.000 33.333 0.00 0.00 32.84 5.34
2862 3111 7.750458 GTCATTTATTTGATTTCTTCACGCTCA 59.250 33.333 0.00 0.00 32.84 4.26
2870 3119 6.948353 TGATTTCTTCACGCTCATTTATAGC 58.052 36.000 0.00 0.00 36.60 2.97
2891 3140 4.279420 AGCCTGAATTTCTTTTGGTCTGTC 59.721 41.667 0.00 0.00 0.00 3.51
2941 3454 0.250252 TCTGCCGTGTTGCTCATTCA 60.250 50.000 0.00 0.00 0.00 2.57
3020 3533 6.031471 CACATACCTTAAAACATAAACCGCC 58.969 40.000 0.00 0.00 0.00 6.13
3033 3546 3.130160 CCGCCCAGCTCTTTCTGC 61.130 66.667 0.00 0.00 32.87 4.26
3048 3561 6.348786 GCTCTTTCTGCAACATGAACATTCTA 60.349 38.462 0.00 0.00 0.00 2.10
3084 3598 4.091220 CACTCTCGAGCTCATTGTTTCTTC 59.909 45.833 15.40 0.00 0.00 2.87
3087 3601 3.993081 CTCGAGCTCATTGTTTCTTCAGT 59.007 43.478 15.40 0.00 0.00 3.41
3088 3602 3.742882 TCGAGCTCATTGTTTCTTCAGTG 59.257 43.478 15.40 0.00 0.00 3.66
3089 3603 3.666374 CGAGCTCATTGTTTCTTCAGTGC 60.666 47.826 15.40 0.00 0.00 4.40
3148 3665 6.998074 TCTCAACTTTCTATTCATGTTGGTGT 59.002 34.615 0.00 0.00 38.64 4.16
3173 3690 4.528206 GGTTTTCAGGATTTCCAGATTGGT 59.472 41.667 0.00 0.00 39.03 3.67
3292 3809 5.336690 GGAGGAAGCTCTAGATCATCATCAC 60.337 48.000 13.42 2.54 0.00 3.06
3295 3812 5.046448 GGAAGCTCTAGATCATCATCACCAT 60.046 44.000 0.00 0.00 0.00 3.55
3296 3813 5.664294 AGCTCTAGATCATCATCACCATC 57.336 43.478 0.00 0.00 0.00 3.51
3297 3814 5.085219 AGCTCTAGATCATCATCACCATCA 58.915 41.667 0.00 0.00 0.00 3.07
3298 3815 5.722441 AGCTCTAGATCATCATCACCATCAT 59.278 40.000 0.00 0.00 0.00 2.45
3299 3816 6.044046 GCTCTAGATCATCATCACCATCATC 58.956 44.000 0.00 0.00 0.00 2.92
3300 3817 6.351117 GCTCTAGATCATCATCACCATCATCA 60.351 42.308 0.00 0.00 0.00 3.07
3301 3818 7.633991 GCTCTAGATCATCATCACCATCATCAT 60.634 40.741 0.00 0.00 0.00 2.45
3331 3848 3.857854 CCGACGACGACGACCGAT 61.858 66.667 20.63 0.00 42.66 4.18
3491 4008 7.927092 ACGAACCCTAAATTTATAGAGCTCTTC 59.073 37.037 23.84 6.88 0.00 2.87
3536 4062 7.493499 TGATTTTTGATCTCTCTCTTCTCCT 57.507 36.000 0.00 0.00 0.00 3.69
3572 4098 0.742990 TAGTACGTACGACCACCGGG 60.743 60.000 24.41 0.00 43.93 5.73
3573 4099 2.749839 TACGTACGACCACCGGGG 60.750 66.667 24.41 0.00 43.93 5.73
3574 4100 3.261039 TACGTACGACCACCGGGGA 62.261 63.158 24.41 0.00 43.93 4.81
3702 4228 2.741985 CGTGCATGGGCTTCGTGA 60.742 61.111 0.00 0.00 41.91 4.35
3706 4232 1.067635 GTGCATGGGCTTCGTGAAATT 60.068 47.619 0.00 0.00 41.91 1.82
3717 4243 6.349363 GGGCTTCGTGAAATTTTGATCTACTT 60.349 38.462 0.00 0.00 0.00 2.24
3775 4304 5.283012 GCGTCGTATCTTGAAATTTTGGAAC 59.717 40.000 0.00 0.00 0.00 3.62
3795 4324 2.092103 ACCCCAGCTCTCTAGTGAGTAG 60.092 54.545 20.03 13.56 40.98 2.57
3809 4338 7.655490 TCTAGTGAGTAGTAACAACTTGAACC 58.345 38.462 0.00 0.00 29.84 3.62
3810 4339 6.229936 AGTGAGTAGTAACAACTTGAACCA 57.770 37.500 0.00 0.00 0.00 3.67
3835 4364 1.227556 GACCGCGCAATGGATACCT 60.228 57.895 8.75 0.00 0.00 3.08
3844 4373 4.024809 GCGCAATGGATACCTAAGTTCTTC 60.025 45.833 0.30 0.00 0.00 2.87
3847 4376 6.260936 CGCAATGGATACCTAAGTTCTTCATT 59.739 38.462 0.00 0.00 0.00 2.57
3900 4433 5.552870 ACAATGTCCATAGTATGAGGGTC 57.447 43.478 11.91 0.00 0.00 4.46
3914 4447 3.149196 TGAGGGTCAAATCAACAGCTTC 58.851 45.455 0.00 0.00 0.00 3.86
3968 4502 4.679373 ATGTAATGAGTTCGGATGAGCT 57.321 40.909 0.00 0.00 38.51 4.09
3974 4508 2.886862 AGTTCGGATGAGCTCATGAG 57.113 50.000 33.33 24.19 36.57 2.90
4071 5197 6.620678 CAATGTATACCAAAGTTCAACCTGG 58.379 40.000 4.94 4.94 34.95 4.45
4104 5245 3.891366 ACAAGGGGAAGTCAACATCTTTG 59.109 43.478 0.00 0.00 0.00 2.77
4183 5327 3.405831 CTTCTGGCTTGATCAGTCAACA 58.594 45.455 0.00 0.00 36.38 3.33
4185 5329 3.340928 TCTGGCTTGATCAGTCAACATG 58.659 45.455 0.00 0.00 36.38 3.21
4212 5356 2.390599 CGCGTCATCACCCTGTTGG 61.391 63.158 0.00 0.00 41.37 3.77
4238 5382 2.677836 GCTGGTTCAAATATCAGCGTGA 59.322 45.455 0.00 0.00 42.24 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.749354 CCTGCTAAAATATTTTAGGTTCAAGGT 58.251 33.333 33.56 7.66 46.03 3.50
11 12 7.193595 CACCGAACCTGCTAAAATATTTTAGG 58.806 38.462 33.56 26.98 46.03 2.69
18 19 3.602483 GACCACCGAACCTGCTAAAATA 58.398 45.455 0.00 0.00 0.00 1.40
22 23 1.122632 TGGACCACCGAACCTGCTAA 61.123 55.000 0.00 0.00 39.42 3.09
25 26 1.823169 TAGTGGACCACCGAACCTGC 61.823 60.000 21.32 0.00 39.42 4.85
28 29 3.528532 CTTATTAGTGGACCACCGAACC 58.471 50.000 21.32 0.00 39.42 3.62
34 35 4.035208 CGATTTGCCTTATTAGTGGACCAC 59.965 45.833 17.43 17.43 34.10 4.16
37 38 3.564225 CCCGATTTGCCTTATTAGTGGAC 59.436 47.826 0.00 0.00 0.00 4.02
54 56 2.051334 TTCAAATGATTCGGCCCGAT 57.949 45.000 6.69 0.00 35.23 4.18
55 57 1.946768 GATTCAAATGATTCGGCCCGA 59.053 47.619 0.00 0.00 0.00 5.14
59 61 4.795278 GTGTCAAGATTCAAATGATTCGGC 59.205 41.667 1.02 0.00 31.69 5.54
61 63 6.834876 TGAGTGTCAAGATTCAAATGATTCG 58.165 36.000 1.02 0.00 31.69 3.34
79 81 1.276421 ACGCTTAGGATGCTTGAGTGT 59.724 47.619 9.63 9.63 0.00 3.55
80 82 1.662629 CACGCTTAGGATGCTTGAGTG 59.337 52.381 0.00 0.67 32.43 3.51
81 83 1.550524 TCACGCTTAGGATGCTTGAGT 59.449 47.619 0.00 0.00 34.53 3.41
82 84 2.200067 CTCACGCTTAGGATGCTTGAG 58.800 52.381 7.59 7.59 45.48 3.02
83 85 1.134699 CCTCACGCTTAGGATGCTTGA 60.135 52.381 0.00 0.00 36.57 3.02
84 86 1.134699 TCCTCACGCTTAGGATGCTTG 60.135 52.381 0.00 0.00 38.24 4.01
87 89 0.461961 AGTCCTCACGCTTAGGATGC 59.538 55.000 4.49 0.00 44.79 3.91
88 90 1.751351 TCAGTCCTCACGCTTAGGATG 59.249 52.381 4.49 4.96 44.79 3.51
89 91 1.751924 GTCAGTCCTCACGCTTAGGAT 59.248 52.381 4.49 0.00 44.79 3.24
90 92 1.174783 GTCAGTCCTCACGCTTAGGA 58.825 55.000 0.00 0.00 40.92 2.94
97 99 0.600255 GGGTGTTGTCAGTCCTCACG 60.600 60.000 0.00 0.00 0.00 4.35
105 107 1.597027 GACACGGGGGTGTTGTCAG 60.597 63.158 0.98 0.00 37.74 3.51
124 126 4.704833 CACTGGCACCGGACTGGG 62.705 72.222 9.46 0.00 44.64 4.45
131 133 3.052082 CAAGGCTCACTGGCACCG 61.052 66.667 0.00 0.00 44.55 4.94
135 137 1.530013 ATTGTGCAAGGCTCACTGGC 61.530 55.000 7.71 0.00 46.97 4.85
136 138 0.963962 AATTGTGCAAGGCTCACTGG 59.036 50.000 7.71 0.00 35.58 4.00
140 142 1.164411 CCGTAATTGTGCAAGGCTCA 58.836 50.000 0.00 0.00 0.00 4.26
159 161 1.872679 GGCGGAAGTCGACGATGAC 60.873 63.158 10.46 0.00 42.43 3.06
160 162 2.488355 GGCGGAAGTCGACGATGA 59.512 61.111 10.46 0.00 42.43 2.92
172 174 2.435938 GAGGCGTGATTTGGCGGA 60.436 61.111 0.00 0.00 36.92 5.54
176 178 2.393764 GTTTTGTGAGGCGTGATTTGG 58.606 47.619 0.00 0.00 0.00 3.28
181 184 1.527380 GGGGTTTTGTGAGGCGTGA 60.527 57.895 0.00 0.00 0.00 4.35
211 215 2.814183 CTTGGACGGGGACTTCGACG 62.814 65.000 0.00 0.00 0.00 5.12
215 219 1.295746 GGTCTTGGACGGGGACTTC 59.704 63.158 0.00 0.00 32.65 3.01
216 220 2.222013 GGGTCTTGGACGGGGACTT 61.222 63.158 0.00 0.00 32.65 3.01
217 221 2.606826 GGGTCTTGGACGGGGACT 60.607 66.667 0.00 0.00 32.65 3.85
221 225 2.729028 AATAATGGGTCTTGGACGGG 57.271 50.000 0.00 0.00 32.65 5.28
224 228 4.251103 AGGGAAATAATGGGTCTTGGAC 57.749 45.455 0.00 0.00 0.00 4.02
225 229 4.325816 GGAAGGGAAATAATGGGTCTTGGA 60.326 45.833 0.00 0.00 0.00 3.53
228 232 4.079154 GGAGGAAGGGAAATAATGGGTCTT 60.079 45.833 0.00 0.00 0.00 3.01
232 236 3.181428 GGAGGAGGAAGGGAAATAATGGG 60.181 52.174 0.00 0.00 0.00 4.00
238 242 1.371415 AGGAGGAGGAGGAAGGGAAAT 59.629 52.381 0.00 0.00 0.00 2.17
241 245 0.340208 GAAGGAGGAGGAGGAAGGGA 59.660 60.000 0.00 0.00 0.00 4.20
243 247 0.341609 AGGAAGGAGGAGGAGGAAGG 59.658 60.000 0.00 0.00 0.00 3.46
270 299 2.504519 GCCGTCATGGGGTCTACC 59.495 66.667 5.74 0.00 38.63 3.18
271 300 2.504519 GGCCGTCATGGGGTCTAC 59.495 66.667 0.00 0.00 38.63 2.59
272 301 3.151710 CGGCCGTCATGGGGTCTA 61.152 66.667 19.50 0.00 38.63 2.59
289 318 1.202166 GGTCTTAGAGAGCGAACGGTC 60.202 57.143 16.74 16.74 42.36 4.79
313 342 5.777732 AGTTCTCTATTGTGAGTGTTCTCCT 59.222 40.000 0.00 0.00 39.75 3.69
314 343 6.031751 AGTTCTCTATTGTGAGTGTTCTCC 57.968 41.667 0.00 0.00 39.75 3.71
322 351 3.379452 AGGGGGAGTTCTCTATTGTGAG 58.621 50.000 0.00 0.00 35.52 3.51
327 356 3.116174 GGTGAAGGGGGAGTTCTCTATT 58.884 50.000 0.00 0.00 0.00 1.73
330 359 0.193574 TGGTGAAGGGGGAGTTCTCT 59.806 55.000 0.00 0.00 0.00 3.10
336 365 1.368374 TAGGTTTGGTGAAGGGGGAG 58.632 55.000 0.00 0.00 0.00 4.30
339 368 1.146152 TGGTTAGGTTTGGTGAAGGGG 59.854 52.381 0.00 0.00 0.00 4.79
342 371 3.292460 TGGTTGGTTAGGTTTGGTGAAG 58.708 45.455 0.00 0.00 0.00 3.02
343 372 3.383698 TGGTTGGTTAGGTTTGGTGAA 57.616 42.857 0.00 0.00 0.00 3.18
347 376 6.201234 CGTTTTTATTGGTTGGTTAGGTTTGG 59.799 38.462 0.00 0.00 0.00 3.28
349 378 6.097981 TCCGTTTTTATTGGTTGGTTAGGTTT 59.902 34.615 0.00 0.00 0.00 3.27
352 381 5.474189 TCTCCGTTTTTATTGGTTGGTTAGG 59.526 40.000 0.00 0.00 0.00 2.69
353 382 6.376177 GTCTCCGTTTTTATTGGTTGGTTAG 58.624 40.000 0.00 0.00 0.00 2.34
380 409 4.452733 GGGGAGAAGGTCGCGGTG 62.453 72.222 6.13 0.00 39.06 4.94
384 413 2.125633 GAACGGGGAGAAGGTCGC 60.126 66.667 0.00 0.00 37.39 5.19
385 414 2.181021 CGAACGGGGAGAAGGTCG 59.819 66.667 0.00 0.00 0.00 4.79
386 415 2.125633 GCGAACGGGGAGAAGGTC 60.126 66.667 0.00 0.00 0.00 3.85
387 416 2.047213 TTTGCGAACGGGGAGAAGGT 62.047 55.000 0.00 0.00 0.00 3.50
389 418 0.727398 GATTTGCGAACGGGGAGAAG 59.273 55.000 0.00 0.00 0.00 2.85
390 419 0.675522 GGATTTGCGAACGGGGAGAA 60.676 55.000 0.00 0.00 0.00 2.87
393 422 0.746563 GATGGATTTGCGAACGGGGA 60.747 55.000 0.00 0.00 0.00 4.81
394 423 1.727467 GATGGATTTGCGAACGGGG 59.273 57.895 0.00 0.00 0.00 5.73
395 424 1.351707 CGATGGATTTGCGAACGGG 59.648 57.895 0.00 0.00 0.00 5.28
396 425 1.297598 GCGATGGATTTGCGAACGG 60.298 57.895 0.00 0.00 0.00 4.44
397 426 0.179202 TTGCGATGGATTTGCGAACG 60.179 50.000 0.00 0.00 37.57 3.95
398 427 1.259316 GTTGCGATGGATTTGCGAAC 58.741 50.000 0.00 0.00 37.57 3.95
399 428 0.877743 TGTTGCGATGGATTTGCGAA 59.122 45.000 0.00 0.00 37.57 4.70
400 429 0.877743 TTGTTGCGATGGATTTGCGA 59.122 45.000 0.00 0.00 37.57 5.10
401 430 0.984109 GTTGTTGCGATGGATTTGCG 59.016 50.000 0.00 0.00 37.57 4.85
402 431 2.063156 TGTTGTTGCGATGGATTTGC 57.937 45.000 0.00 0.00 35.05 3.68
403 432 3.801050 TGTTTGTTGTTGCGATGGATTTG 59.199 39.130 0.00 0.00 0.00 2.32
404 433 4.052159 TGTTTGTTGTTGCGATGGATTT 57.948 36.364 0.00 0.00 0.00 2.17
405 434 3.724508 TGTTTGTTGTTGCGATGGATT 57.275 38.095 0.00 0.00 0.00 3.01
406 435 3.317711 TCTTGTTTGTTGTTGCGATGGAT 59.682 39.130 0.00 0.00 0.00 3.41
407 436 2.685388 TCTTGTTTGTTGTTGCGATGGA 59.315 40.909 0.00 0.00 0.00 3.41
408 437 2.788786 GTCTTGTTTGTTGTTGCGATGG 59.211 45.455 0.00 0.00 0.00 3.51
409 438 3.694734 AGTCTTGTTTGTTGTTGCGATG 58.305 40.909 0.00 0.00 0.00 3.84
410 439 3.243068 GGAGTCTTGTTTGTTGTTGCGAT 60.243 43.478 0.00 0.00 0.00 4.58
417 446 4.157656 TGTCTTTGGGAGTCTTGTTTGTTG 59.842 41.667 0.00 0.00 0.00 3.33
439 468 1.517242 GGCTGAGCTCCGGATTAATG 58.483 55.000 12.15 0.00 0.00 1.90
449 478 2.430610 ATCACTCGGGGCTGAGCTC 61.431 63.158 6.82 6.82 39.68 4.09
450 479 2.364842 ATCACTCGGGGCTGAGCT 60.365 61.111 3.72 0.00 39.68 4.09
451 480 2.202987 CATCACTCGGGGCTGAGC 60.203 66.667 0.00 0.00 39.68 4.26
453 482 3.785859 GCCATCACTCGGGGCTGA 61.786 66.667 0.00 0.00 44.32 4.26
458 493 4.552365 ATGCCGCCATCACTCGGG 62.552 66.667 2.78 0.00 45.37 5.14
463 498 3.405592 CTGCACATGCCGCCATCAC 62.406 63.158 0.49 0.00 41.18 3.06
502 543 1.954382 GCCAAGATATTTTCGTCCCCC 59.046 52.381 0.00 0.00 0.00 5.40
747 808 0.108851 CTTTATGGCGCCAACCAACC 60.109 55.000 36.33 0.00 44.65 3.77
781 842 0.550393 AAAGAAGAGGGGAGGGGGAC 60.550 60.000 0.00 0.00 0.00 4.46
790 851 1.443802 GACGGAAGCAAAGAAGAGGG 58.556 55.000 0.00 0.00 0.00 4.30
804 865 4.393778 GAGGGGTGGAGGGACGGA 62.394 72.222 0.00 0.00 0.00 4.69
814 875 1.484038 CAGGAAGAGAGAGAGGGGTG 58.516 60.000 0.00 0.00 0.00 4.61
815 876 0.325203 GCAGGAAGAGAGAGAGGGGT 60.325 60.000 0.00 0.00 0.00 4.95
818 879 1.402787 GAGGCAGGAAGAGAGAGAGG 58.597 60.000 0.00 0.00 0.00 3.69
835 896 2.174969 CCGACGAGGAGAGGACGAG 61.175 68.421 0.00 0.00 45.00 4.18
844 905 3.379445 GGAGCCAACCGACGAGGA 61.379 66.667 8.56 0.00 45.00 3.71
846 907 4.452733 GGGGAGCCAACCGACGAG 62.453 72.222 0.00 0.00 0.00 4.18
848 909 4.452733 GAGGGGAGCCAACCGACG 62.453 72.222 0.00 0.00 0.00 5.12
949 1016 2.266279 CACTCCTCCTTCAACCCCTTA 58.734 52.381 0.00 0.00 0.00 2.69
956 1023 0.193574 ACTCCCCACTCCTCCTTCAA 59.806 55.000 0.00 0.00 0.00 2.69
994 1062 3.991051 CGACGGATCCATCCCCCG 61.991 72.222 13.41 0.00 44.24 5.73
997 1065 4.315941 GCCCGACGGATCCATCCC 62.316 72.222 17.49 0.00 44.24 3.85
1077 1145 4.577246 CCGCTACTCCCGCTGCTC 62.577 72.222 0.00 0.00 0.00 4.26
1255 1341 8.429641 ACTTGACAGTAAAATTTCCTCTCTACA 58.570 33.333 0.00 0.00 0.00 2.74
1256 1342 8.713271 CACTTGACAGTAAAATTTCCTCTCTAC 58.287 37.037 0.00 0.00 0.00 2.59
1264 1350 4.982295 GGGTGCACTTGACAGTAAAATTTC 59.018 41.667 17.98 0.00 0.00 2.17
1265 1351 4.649218 AGGGTGCACTTGACAGTAAAATTT 59.351 37.500 17.98 0.00 0.00 1.82
1272 1358 0.396811 GGTAGGGTGCACTTGACAGT 59.603 55.000 17.98 0.00 0.00 3.55
1273 1359 0.687354 AGGTAGGGTGCACTTGACAG 59.313 55.000 17.98 0.00 0.00 3.51
1290 1380 1.446907 AGCGAACTGAAGCATGAAGG 58.553 50.000 0.00 0.00 35.48 3.46
1296 1386 1.788258 CTCAGAAGCGAACTGAAGCA 58.212 50.000 10.55 0.00 42.58 3.91
1313 1413 6.463360 TCAAAATATCCCCTTTGTTTTGCTC 58.537 36.000 0.00 0.00 38.79 4.26
1316 1416 9.452287 AATCATCAAAATATCCCCTTTGTTTTG 57.548 29.630 0.00 0.00 39.73 2.44
1346 1447 1.941403 ATGAGCAGGAACCCCCATGG 61.941 60.000 4.14 4.14 41.37 3.66
1443 1552 6.767902 TCCTTAAATAGATTGCGAGCAAAGAT 59.232 34.615 14.76 5.75 39.55 2.40
1493 1603 7.089538 TGAATGAATCGCTCAAAATTTTGCTA 58.910 30.769 23.36 8.78 37.67 3.49
1544 1696 2.095919 ACAAAGACCACGCGCTTAATTC 60.096 45.455 5.73 0.00 0.00 2.17
1590 1742 7.742089 GTGCATAAGAATAAGATTGCACGATAC 59.258 37.037 9.71 0.00 46.90 2.24
1593 1745 6.048073 GTGCATAAGAATAAGATTGCACGA 57.952 37.500 9.71 0.00 46.90 4.35
1614 1766 2.938451 TCTCAAAAGCAGAGTGTGTGTG 59.062 45.455 0.00 0.00 34.73 3.82
1615 1767 3.266510 TCTCAAAAGCAGAGTGTGTGT 57.733 42.857 0.00 0.00 34.73 3.72
1645 1797 8.439993 TCAGAACATGAGTATGTAGTAGTCTC 57.560 38.462 0.00 0.00 46.54 3.36
1687 1839 1.467734 GGCTGCACAAGAACAGAGATG 59.532 52.381 0.50 0.00 35.90 2.90
1876 2029 1.271379 TCTGGTGCTTACCACGTACAG 59.729 52.381 0.00 0.00 45.62 2.74
1960 2127 0.586319 GCAAGCAAGCGTGTCAGTTA 59.414 50.000 9.56 0.00 0.00 2.24
2001 2172 9.645059 GCAACACACACTGATAGTATGATATAT 57.355 33.333 0.00 0.00 0.00 0.86
2003 2174 7.730084 AGCAACACACACTGATAGTATGATAT 58.270 34.615 0.00 0.00 0.00 1.63
2004 2175 7.112452 AGCAACACACACTGATAGTATGATA 57.888 36.000 0.00 0.00 0.00 2.15
2007 2178 5.639082 TCAAGCAACACACACTGATAGTATG 59.361 40.000 0.00 0.00 0.00 2.39
2008 2179 5.793817 TCAAGCAACACACACTGATAGTAT 58.206 37.500 0.00 0.00 0.00 2.12
2009 2180 5.208463 TCAAGCAACACACACTGATAGTA 57.792 39.130 0.00 0.00 0.00 1.82
2020 2196 4.826733 AGTCCATGTAAATCAAGCAACACA 59.173 37.500 0.00 0.00 0.00 3.72
2142 2318 7.926018 CCCCCAAGTTACTTGCAAATTATAATC 59.074 37.037 18.72 0.00 39.85 1.75
2183 2359 7.888546 TGATTATGAGGACGACAAGGATAGATA 59.111 37.037 0.00 0.00 0.00 1.98
2203 2379 8.817100 CGTGTACAACTACAACATGATGATTAT 58.183 33.333 10.29 0.00 34.53 1.28
2204 2380 8.030106 TCGTGTACAACTACAACATGATGATTA 58.970 33.333 10.29 0.00 34.95 1.75
2205 2381 6.871492 TCGTGTACAACTACAACATGATGATT 59.129 34.615 10.29 0.00 34.95 2.57
2226 2402 6.360947 CAGGTATCTATCTCAAACGAATCGTG 59.639 42.308 9.74 0.00 39.99 4.35
2227 2403 6.262496 TCAGGTATCTATCTCAAACGAATCGT 59.738 38.462 0.96 0.96 43.97 3.73
2228 2404 6.669278 TCAGGTATCTATCTCAAACGAATCG 58.331 40.000 0.00 0.00 0.00 3.34
2232 2408 9.914131 CATTATTCAGGTATCTATCTCAAACGA 57.086 33.333 0.00 0.00 0.00 3.85
2233 2409 9.914131 TCATTATTCAGGTATCTATCTCAAACG 57.086 33.333 0.00 0.00 0.00 3.60
2236 2412 9.914131 CGTTCATTATTCAGGTATCTATCTCAA 57.086 33.333 0.00 0.00 0.00 3.02
2243 2425 9.915629 GAAGATACGTTCATTATTCAGGTATCT 57.084 33.333 0.00 7.58 44.62 1.98
2245 2427 9.698309 CAGAAGATACGTTCATTATTCAGGTAT 57.302 33.333 0.00 0.00 0.00 2.73
2246 2428 8.909923 TCAGAAGATACGTTCATTATTCAGGTA 58.090 33.333 0.00 0.00 0.00 3.08
2262 2444 5.241662 AGTTTCAGCCAAGTCAGAAGATAC 58.758 41.667 0.00 0.00 0.00 2.24
2313 2515 2.094545 GCATTGCCCAGTAGTTGAAAGG 60.095 50.000 0.00 0.00 0.00 3.11
2455 2662 1.753073 GCTTAGGCTCAAACCATGCAT 59.247 47.619 0.00 0.00 35.22 3.96
2456 2663 1.176527 GCTTAGGCTCAAACCATGCA 58.823 50.000 0.00 0.00 35.22 3.96
2468 2675 1.466558 GTTTCAGACAGCTGCTTAGGC 59.533 52.381 15.27 0.00 42.01 3.93
2471 2678 2.104792 ACTGGTTTCAGACAGCTGCTTA 59.895 45.455 15.27 0.53 43.49 3.09
2476 2683 1.133976 AGCAACTGGTTTCAGACAGCT 60.134 47.619 0.00 3.88 43.49 4.24
2534 2757 3.866651 AGTCCACTGCATTCATCTGTAC 58.133 45.455 0.00 0.00 0.00 2.90
2688 2911 1.990060 AGGCATACTGAGCACCCGT 60.990 57.895 0.00 0.00 0.00 5.28
2760 2983 4.523083 TGGTGAACAAGTAAGCAGAGTTT 58.477 39.130 0.00 0.00 0.00 2.66
2776 3016 6.355747 TCACATAGTGCAATGATATGGTGAA 58.644 36.000 5.39 0.00 32.98 3.18
2833 3080 9.000018 GCGTGAAGAAATCAAATAAATGACTAC 58.000 33.333 0.00 0.00 40.50 2.73
2835 3082 7.820648 AGCGTGAAGAAATCAAATAAATGACT 58.179 30.769 0.00 0.00 40.50 3.41
2856 3105 6.058183 AGAAATTCAGGCTATAAATGAGCGT 58.942 36.000 0.00 0.00 41.06 5.07
2859 3108 9.525409 CCAAAAGAAATTCAGGCTATAAATGAG 57.475 33.333 0.00 0.00 0.00 2.90
2862 3111 9.259832 AGACCAAAAGAAATTCAGGCTATAAAT 57.740 29.630 0.00 0.00 0.00 1.40
2870 3119 5.278660 CCAGACAGACCAAAAGAAATTCAGG 60.279 44.000 0.00 0.00 0.00 3.86
2891 3140 3.199677 TGTTTACAAACAGACGGACCAG 58.800 45.455 3.44 0.00 43.45 4.00
3020 3533 2.156917 TCATGTTGCAGAAAGAGCTGG 58.843 47.619 0.00 0.00 36.41 4.85
3048 3561 5.825679 AGCTCGAGAGTGTAAGAGTATGAAT 59.174 40.000 18.75 0.00 33.57 2.57
3084 3598 2.811431 TGAGAAATAACAACCGGCACTG 59.189 45.455 0.00 0.00 0.00 3.66
3087 3601 2.811431 CACTGAGAAATAACAACCGGCA 59.189 45.455 0.00 0.00 0.00 5.69
3088 3602 3.071479 TCACTGAGAAATAACAACCGGC 58.929 45.455 0.00 0.00 0.00 6.13
3089 3603 4.094887 CCATCACTGAGAAATAACAACCGG 59.905 45.833 0.00 0.00 0.00 5.28
3121 3638 8.180267 CACCAACATGAATAGAAAGTTGAGATC 58.820 37.037 0.00 0.00 41.41 2.75
3135 3652 5.350504 TGAAAACCAACACCAACATGAAT 57.649 34.783 0.00 0.00 0.00 2.57
3148 3665 5.011943 CCAATCTGGAAATCCTGAAAACCAA 59.988 40.000 12.30 0.00 45.19 3.67
3173 3690 2.604686 AGGCTCCGCACCTTCTCA 60.605 61.111 0.00 0.00 31.87 3.27
3189 3706 3.818787 GTGCAGGCAATCGGGCAG 61.819 66.667 0.00 0.00 46.44 4.85
3292 3809 3.683340 GTCGTGGATGATGATGATGATGG 59.317 47.826 0.00 0.00 0.00 3.51
3295 3812 2.288395 CGGTCGTGGATGATGATGATGA 60.288 50.000 0.00 0.00 0.00 2.92
3296 3813 2.064014 CGGTCGTGGATGATGATGATG 58.936 52.381 0.00 0.00 0.00 3.07
3297 3814 1.963515 TCGGTCGTGGATGATGATGAT 59.036 47.619 0.00 0.00 0.00 2.45
3298 3815 1.067060 GTCGGTCGTGGATGATGATGA 59.933 52.381 0.00 0.00 0.00 2.92
3299 3816 1.491670 GTCGGTCGTGGATGATGATG 58.508 55.000 0.00 0.00 0.00 3.07
3300 3817 0.030773 CGTCGGTCGTGGATGATGAT 59.969 55.000 0.00 0.00 34.52 2.45
3301 3818 1.027792 TCGTCGGTCGTGGATGATGA 61.028 55.000 0.00 0.00 40.80 2.92
3331 3848 5.994054 CAGACAGAATTTCAGAAGTTCCTCA 59.006 40.000 13.38 0.00 0.00 3.86
3500 4017 6.905578 AGATCAAAAATCAAAATGCAAAGGC 58.094 32.000 0.00 0.00 41.68 4.35
3502 4019 9.204570 AGAGAGATCAAAAATCAAAATGCAAAG 57.795 29.630 0.00 0.00 0.00 2.77
3536 4062 9.219603 GTACGTACTACTATATTACATCCACCA 57.780 37.037 18.47 0.00 0.00 4.17
3717 4243 3.904800 TGCCCTACAAATCGATCTTCA 57.095 42.857 0.00 0.00 0.00 3.02
3775 4304 2.092103 ACTACTCACTAGAGAGCTGGGG 60.092 54.545 16.13 5.75 44.98 4.96
3795 4324 4.508861 TCGCTAACTGGTTCAAGTTGTTAC 59.491 41.667 2.11 2.84 40.58 2.50
3844 4373 6.551385 AAGCTACTGTTCTGAGTTCAAATG 57.449 37.500 0.00 0.00 0.00 2.32
3847 4376 5.304614 AGGTAAGCTACTGTTCTGAGTTCAA 59.695 40.000 0.00 0.00 0.00 2.69
3900 4433 5.856126 ATGCATTTGAAGCTGTTGATTTG 57.144 34.783 0.00 0.00 0.00 2.32
3914 4447 6.128769 CGTTTAATGGCCATCATATGCATTTG 60.129 38.462 21.08 7.81 34.44 2.32
3963 4497 5.395990 TCAAGTTATGATGCTCATGAGCTCA 60.396 40.000 39.46 35.64 43.35 4.26
3967 4501 4.814771 TGCTCAAGTTATGATGCTCATGAG 59.185 41.667 18.84 18.84 37.70 2.90
3968 4502 4.773013 TGCTCAAGTTATGATGCTCATGA 58.227 39.130 0.00 0.00 37.70 3.07
3969 4503 4.554919 GCTGCTCAAGTTATGATGCTCATG 60.555 45.833 8.40 0.00 37.70 3.07
3974 4508 2.941064 TCAGCTGCTCAAGTTATGATGC 59.059 45.455 9.47 0.00 37.44 3.91
4010 4544 9.346725 CTTGAATTTTTCACTACAATCTAAGCC 57.653 33.333 0.00 0.00 39.87 4.35
4071 5197 1.652947 TCCCCTTGTACCTGTTCTCC 58.347 55.000 0.00 0.00 0.00 3.71
4084 5225 4.184649 ACAAAGATGTTGACTTCCCCTT 57.815 40.909 0.00 0.00 35.91 3.95
4212 5356 4.889832 CTGATATTTGAACCAGCACCTC 57.110 45.455 0.00 0.00 0.00 3.85
4238 5382 1.628340 TCCGATGTTGTCCAGTCCAAT 59.372 47.619 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.