Multiple sequence alignment - TraesCS5D01G520500

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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 TraesCS5D01G520500 chr5D 100.000 5215 0 0 1 5215 541938626 541933412 0.000000e+00 9631
1 TraesCS5D01G520500 chr5D 96.565 3319 92 8 1231 4533 541860616 541857304 0.000000e+00 5478
2 TraesCS5D01G520500 chr5D 83.644 1718 244 25 2667 4355 541944840 541943131 0.000000e+00 1581
3 TraesCS5D01G520500 chr5D 82.851 1726 255 35 2669 4370 541953877 541952169 0.000000e+00 1509
4 TraesCS5D01G520500 chr5D 80.841 1070 200 5 1300 2368 541950725 541949660 0.000000e+00 835
5 TraesCS5D01G520500 chr5D 90.110 364 27 4 872 1226 541944553 541944190 1.020000e-126 464
6 TraesCS5D01G520500 chr5D 99.184 245 1 1 4972 5215 541857043 541856799 1.720000e-119 440
7 TraesCS5D01G520500 chr5D 87.097 403 32 14 839 1226 541949077 541948680 6.200000e-119 438
8 TraesCS5D01G520500 chr5D 95.192 208 10 0 4708 4915 541857258 541857051 3.890000e-86 329
9 TraesCS5D01G520500 chr5D 94.706 170 9 0 299 468 498721902 498722071 1.110000e-66 265
10 TraesCS5D01G520500 chr5D 95.152 165 8 0 304 468 60140927 60140763 1.440000e-65 261
11 TraesCS5D01G520500 chr5B 95.204 4149 145 20 465 4595 683984354 683980242 0.000000e+00 6510
12 TraesCS5D01G520500 chr5B 83.977 1916 259 30 2667 4552 683993905 683992008 0.000000e+00 1794
13 TraesCS5D01G520500 chr5B 84.233 1611 210 36 2667 4261 683998365 683996783 0.000000e+00 1528
14 TraesCS5D01G520500 chr5B 79.672 1097 212 10 1290 2382 683995268 683994179 0.000000e+00 780
15 TraesCS5D01G520500 chr5B 90.421 522 25 8 4708 5215 683980245 683979735 0.000000e+00 664
16 TraesCS5D01G520500 chr5B 84.742 485 57 9 754 1226 683993724 683993245 2.200000e-128 470
17 TraesCS5D01G520500 chr5B 87.626 396 36 8 839 1226 683998137 683997747 1.030000e-121 448
18 TraesCS5D01G520500 chr5B 93.160 307 16 4 1 305 683984656 683984353 3.710000e-121 446
19 TraesCS5D01G520500 chr5B 84.286 140 21 1 609 747 684003486 684003347 9.110000e-28 135
20 TraesCS5D01G520500 chr4A 89.870 2162 172 13 748 2899 627386077 627388201 0.000000e+00 2736
21 TraesCS5D01G520500 chr4A 93.144 1721 89 14 2886 4587 627388659 627390369 0.000000e+00 2497
22 TraesCS5D01G520500 chr4A 86.998 1469 168 13 3050 4517 627366488 627367934 0.000000e+00 1633
23 TraesCS5D01G520500 chr4A 85.164 1375 187 15 3028 4392 627357355 627358722 0.000000e+00 1393
24 TraesCS5D01G520500 chr4A 83.007 1071 165 9 1222 2285 627376058 627377118 0.000000e+00 953
25 TraesCS5D01G520500 chr4A 84.068 885 98 26 2616 3464 627377233 627378110 0.000000e+00 813
26 TraesCS5D01G520500 chr4A 80.398 1056 194 7 1297 2351 627360238 627361281 0.000000e+00 791
27 TraesCS5D01G520500 chr4A 81.153 971 178 5 1408 2376 627381579 627382546 0.000000e+00 774
28 TraesCS5D01G520500 chr4A 79.292 1101 211 13 1290 2379 627364477 627365571 0.000000e+00 754
29 TraesCS5D01G520500 chr4A 92.731 509 29 5 4710 5215 627390376 627390879 0.000000e+00 728
30 TraesCS5D01G520500 chr4A 89.160 369 33 4 865 1226 627361986 627362354 2.210000e-123 453
31 TraesCS5D01G520500 chr4A 78.681 652 116 16 2667 3301 627385902 627386547 3.760000e-111 412
32 TraesCS5D01G520500 chr4A 92.086 278 16 3 955 1226 627366462 627366739 2.280000e-103 387
33 TraesCS5D01G520500 chr4A 90.288 278 24 2 472 748 627364489 627364764 1.380000e-95 361
34 TraesCS5D01G520500 chr4A 83.805 389 38 15 855 1226 627377567 627377947 3.870000e-91 346
35 TraesCS5D01G520500 chr4A 88.372 258 30 0 493 750 627360263 627360520 1.410000e-80 311
36 TraesCS5D01G520500 chr4A 85.714 210 24 2 1224 1432 627368800 627369004 3.160000e-52 217
37 TraesCS5D01G520500 chr4A 82.470 251 32 1 497 747 627381509 627381747 5.290000e-50 209
38 TraesCS5D01G520500 chr4A 89.630 135 10 4 4576 4710 153242482 153242612 8.980000e-38 169
39 TraesCS5D01G520500 chr4A 82.447 188 33 0 557 744 627355693 627355880 1.160000e-36 165
40 TraesCS5D01G520500 chr4A 75.510 343 79 5 2616 2958 627382817 627383154 4.180000e-36 163
41 TraesCS5D01G520500 chr1A 94.144 222 8 2 4995 5215 460853279 460853496 3.010000e-87 333
42 TraesCS5D01G520500 chr7A 93.182 220 10 2 4997 5215 414847460 414847245 8.430000e-83 318
43 TraesCS5D01G520500 chr7A 92.000 150 7 3 4982 5130 685468793 685468938 6.850000e-49 206
44 TraesCS5D01G520500 chr7D 95.266 169 6 2 299 466 171307984 171308151 3.100000e-67 267
45 TraesCS5D01G520500 chr7D 93.388 121 7 1 4592 4712 176125158 176125277 1.490000e-40 178
46 TraesCS5D01G520500 chr7D 92.683 123 7 2 4589 4710 192019148 192019269 5.370000e-40 176
47 TraesCS5D01G520500 chr6D 94.706 170 9 0 304 473 266777641 266777472 1.110000e-66 265
48 TraesCS5D01G520500 chr6D 94.186 172 10 0 304 475 90890282 90890453 4.000000e-66 263
49 TraesCS5D01G520500 chr6D 94.068 118 6 1 4592 4709 464836806 464836690 1.490000e-40 178
50 TraesCS5D01G520500 chr2D 95.238 168 5 2 300 466 445733667 445733832 4.000000e-66 263
51 TraesCS5D01G520500 chr2D 90.576 191 12 6 279 466 425155706 425155519 1.120000e-61 248
52 TraesCS5D01G520500 chr2B 94.118 170 10 0 304 473 485894319 485894150 5.180000e-65 259
53 TraesCS5D01G520500 chr2B 91.146 192 10 4 4993 5182 330003839 330003653 2.410000e-63 254
54 TraesCS5D01G520500 chr2B 92.655 177 11 2 292 468 798164507 798164681 2.410000e-63 254
55 TraesCS5D01G520500 chr2B 86.897 145 16 3 4575 4719 468557033 468557174 5.410000e-35 159
56 TraesCS5D01G520500 chr2A 94.167 120 6 1 4592 4711 739282659 739282541 1.150000e-41 182
57 TraesCS5D01G520500 chr7B 92.063 126 9 1 4584 4709 434926031 434925907 5.370000e-40 176
58 TraesCS5D01G520500 chr4B 91.473 129 8 3 4589 4716 322692939 322693065 1.930000e-39 174
59 TraesCS5D01G520500 chr1B 91.339 127 9 2 4592 4717 481708561 481708436 6.940000e-39 172


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 TraesCS5D01G520500 chr5D 541933412 541938626 5214 True 9631.000000 9631 100.000000 1 5215 1 chr5D.!!$R2 5214
1 TraesCS5D01G520500 chr5D 541856799 541860616 3817 True 2082.333333 5478 96.980333 1231 5215 3 chr5D.!!$R3 3984
2 TraesCS5D01G520500 chr5D 541943131 541944840 1709 True 1022.500000 1581 86.877000 872 4355 2 chr5D.!!$R4 3483
3 TraesCS5D01G520500 chr5D 541948680 541953877 5197 True 927.333333 1509 83.596333 839 4370 3 chr5D.!!$R5 3531
4 TraesCS5D01G520500 chr5B 683979735 683984656 4921 True 2540.000000 6510 92.928333 1 5215 3 chr5B.!!$R2 5214
5 TraesCS5D01G520500 chr5B 683992008 683998365 6357 True 1004.000000 1794 84.050000 754 4552 5 chr5B.!!$R3 3798
6 TraesCS5D01G520500 chr4A 627376058 627390879 14821 False 963.100000 2736 84.443900 497 5215 10 chr4A.!!$F3 4718
7 TraesCS5D01G520500 chr4A 627355693 627369004 13311 False 646.500000 1633 85.991900 472 4517 10 chr4A.!!$F2 4045

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
572 6541 0.540133 TTTCCAGCAATGGCAGCAGA 60.540 50.000 0.00 0.00 44.61 4.26 F
675 6644 0.610232 GCATTGGGGAAGACTGCACT 60.610 55.000 0.00 0.00 33.13 4.40 F
1651 9056 1.416401 CACCTATACAGCCCCGTCAAT 59.584 52.381 0.00 0.00 0.00 2.57 F
1803 9208 0.107268 ACCGGCTACAAAGAAACCGT 59.893 50.000 0.00 0.00 42.29 4.83 F
1978 14654 0.529378 GGAGCTTCAACCCATGCTTG 59.471 55.000 0.00 0.00 35.76 4.01 F
2188 14864 2.817470 ATTGCATGGCCGCGAACAAC 62.817 55.000 8.23 3.62 33.35 3.32 F
3441 23610 1.717032 ACTAGGCTGTTGTCTGGACA 58.283 50.000 0.00 0.00 39.98 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 9056 0.596082 TCGACGTGAAGCAGATGTGA 59.404 50.000 0.00 0.00 0.00 3.58 R
1736 9141 1.010125 CTGTGAAACGGTTGCGTGG 60.010 57.895 0.00 0.00 42.39 4.94 R
2750 15542 1.071814 TAGTTCCCGGGTGTGTTGC 59.928 57.895 22.86 4.06 0.00 4.17 R
3226 18835 1.269723 TGTAGTTGTCAGTGGCTCTCG 59.730 52.381 0.00 0.00 0.00 4.04 R
3270 23439 2.429250 TGTAGACCATACCATGACCACG 59.571 50.000 0.00 0.00 0.00 4.94 R
3890 24067 4.009675 TCCGATGAAACATCAAGGGAAAG 58.990 43.478 11.39 0.00 0.00 2.62 R
4589 24791 0.032813 TTCCGGACGGAGGGAGTATT 60.033 55.000 13.64 0.00 46.06 1.89 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
31 33 1.398390 GCTTCAACCAGCCAATCTACG 59.602 52.381 0.00 0.00 33.21 3.51
60 62 0.682852 CCTCCTTCACGTTACCACCA 59.317 55.000 0.00 0.00 0.00 4.17
75 77 1.340889 CCACCAACACCAAACCATCTG 59.659 52.381 0.00 0.00 0.00 2.90
89 91 3.701664 ACCATCTGATTTCCTGGAAACC 58.298 45.455 23.29 15.34 34.23 3.27
98 100 6.973642 TGATTTCCTGGAAACCATAGAAGAT 58.026 36.000 23.29 4.24 34.23 2.40
99 101 7.056635 TGATTTCCTGGAAACCATAGAAGATC 58.943 38.462 23.29 13.17 34.23 2.75
105 107 6.462768 CCTGGAAACCATAGAAGATCTCAGAG 60.463 46.154 0.00 0.00 30.82 3.35
138 140 3.756933 ACCATTGACAAAAGCAGCAAT 57.243 38.095 0.00 0.00 0.00 3.56
146 148 4.445052 TGACAAAAGCAGCAATTCGAAATG 59.555 37.500 8.90 8.90 0.00 2.32
151 153 1.922545 GCAGCAATTCGAAATGAAGGC 59.077 47.619 17.30 11.91 40.65 4.35
168 170 1.654220 GCAAGCACACAATCACGGT 59.346 52.632 0.00 0.00 0.00 4.83
179 181 2.076863 CAATCACGGTCAAAGTCTCCC 58.923 52.381 0.00 0.00 0.00 4.30
205 207 5.904872 CGTGTTAACGTACACTCTGATAC 57.095 43.478 17.13 0.00 44.85 2.24
278 280 6.307170 GATGAATCACATGGCAACTTGCAAA 61.307 40.000 15.61 3.63 45.21 3.68
312 315 4.156477 AGAGACAAGCATATACTCCCTCC 58.844 47.826 0.00 0.00 0.00 4.30
313 316 2.894126 AGACAAGCATATACTCCCTCCG 59.106 50.000 0.00 0.00 0.00 4.63
314 317 2.628657 GACAAGCATATACTCCCTCCGT 59.371 50.000 0.00 0.00 0.00 4.69
316 319 3.069729 ACAAGCATATACTCCCTCCGTTC 59.930 47.826 0.00 0.00 0.00 3.95
318 321 2.158295 AGCATATACTCCCTCCGTTCCT 60.158 50.000 0.00 0.00 0.00 3.36
320 323 3.830755 GCATATACTCCCTCCGTTCCTAA 59.169 47.826 0.00 0.00 0.00 2.69
321 324 4.282703 GCATATACTCCCTCCGTTCCTAAA 59.717 45.833 0.00 0.00 0.00 1.85
322 325 5.046520 GCATATACTCCCTCCGTTCCTAAAT 60.047 44.000 0.00 0.00 0.00 1.40
323 326 6.154021 GCATATACTCCCTCCGTTCCTAAATA 59.846 42.308 0.00 0.00 0.00 1.40
324 327 7.147707 GCATATACTCCCTCCGTTCCTAAATAT 60.148 40.741 0.00 0.00 0.00 1.28
325 328 9.417561 CATATACTCCCTCCGTTCCTAAATATA 57.582 37.037 0.00 0.00 0.00 0.86
327 330 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
330 333 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
331 334 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
333 336 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
334 337 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
369 372 7.870954 CACTAAATGGACTATATACGGAGCAAA 59.129 37.037 0.00 0.00 0.00 3.68
374 377 6.822442 TGGACTATATACGGAGCAAAATGAA 58.178 36.000 0.00 0.00 0.00 2.57
375 378 7.450074 TGGACTATATACGGAGCAAAATGAAT 58.550 34.615 0.00 0.00 0.00 2.57
376 379 7.387673 TGGACTATATACGGAGCAAAATGAATG 59.612 37.037 0.00 0.00 0.00 2.67
377 380 7.602644 GGACTATATACGGAGCAAAATGAATGA 59.397 37.037 0.00 0.00 0.00 2.57
381 384 6.949352 ATACGGAGCAAAATGAATGAATCT 57.051 33.333 0.00 0.00 0.00 2.40
385 388 5.967674 CGGAGCAAAATGAATGAATCTACAC 59.032 40.000 0.00 0.00 0.00 2.90
386 389 6.183360 CGGAGCAAAATGAATGAATCTACACT 60.183 38.462 0.00 0.00 0.00 3.55
387 390 7.192232 GGAGCAAAATGAATGAATCTACACTC 58.808 38.462 0.00 0.00 0.00 3.51
388 391 7.148188 GGAGCAAAATGAATGAATCTACACTCA 60.148 37.037 0.00 0.00 30.94 3.41
390 393 8.579006 AGCAAAATGAATGAATCTACACTCAAA 58.421 29.630 0.00 0.00 30.22 2.69
391 394 9.195411 GCAAAATGAATGAATCTACACTCAAAA 57.805 29.630 0.00 0.00 30.22 2.44
394 397 8.922058 AATGAATGAATCTACACTCAAAATGC 57.078 30.769 0.00 0.00 30.22 3.56
395 398 7.451501 TGAATGAATCTACACTCAAAATGCA 57.548 32.000 0.00 0.00 0.00 3.96
396 399 8.058667 TGAATGAATCTACACTCAAAATGCAT 57.941 30.769 0.00 0.00 0.00 3.96
397 400 8.186163 TGAATGAATCTACACTCAAAATGCATC 58.814 33.333 0.00 0.00 0.00 3.91
398 401 7.876936 ATGAATCTACACTCAAAATGCATCT 57.123 32.000 0.00 0.00 0.00 2.90
399 402 8.969260 ATGAATCTACACTCAAAATGCATCTA 57.031 30.769 0.00 0.00 0.00 1.98
400 403 8.969260 TGAATCTACACTCAAAATGCATCTAT 57.031 30.769 0.00 0.00 0.00 1.98
411 414 9.586435 CTCAAAATGCATCTATATACATCCGTA 57.414 33.333 0.00 0.00 0.00 4.02
415 418 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
416 419 6.805713 TGCATCTATATACATCCGTATGTGG 58.194 40.000 3.56 0.00 45.99 4.17
417 420 6.379988 TGCATCTATATACATCCGTATGTGGT 59.620 38.462 3.56 0.00 45.99 4.16
418 421 7.093509 TGCATCTATATACATCCGTATGTGGTT 60.094 37.037 3.56 0.00 45.99 3.67
420 423 8.466798 CATCTATATACATCCGTATGTGGTTCA 58.533 37.037 3.56 0.00 45.99 3.18
421 424 8.589701 TCTATATACATCCGTATGTGGTTCAT 57.410 34.615 3.56 0.00 45.99 2.57
422 425 9.689501 TCTATATACATCCGTATGTGGTTCATA 57.310 33.333 3.56 0.00 45.99 2.15
426 429 5.116180 ACATCCGTATGTGGTTCATAGTTG 58.884 41.667 0.00 0.00 44.79 3.16
428 431 5.408880 TCCGTATGTGGTTCATAGTTGAA 57.591 39.130 0.00 0.00 39.36 2.69
429 432 5.416083 TCCGTATGTGGTTCATAGTTGAAG 58.584 41.667 0.00 0.00 42.41 3.02
440 443 7.891183 GTTCATAGTTGAAGCTCTACAAAGA 57.109 36.000 0.00 0.00 42.41 2.52
441 444 7.734554 GTTCATAGTTGAAGCTCTACAAAGAC 58.265 38.462 0.00 0.00 42.41 3.01
444 447 8.749354 TCATAGTTGAAGCTCTACAAAGACATA 58.251 33.333 0.00 0.00 0.00 2.29
445 448 9.539825 CATAGTTGAAGCTCTACAAAGACATAT 57.460 33.333 0.00 0.00 0.00 1.78
457 460 9.976511 TCTACAAAGACATATATTTAGGAACGG 57.023 33.333 0.00 0.00 0.00 4.44
458 461 9.976511 CTACAAAGACATATATTTAGGAACGGA 57.023 33.333 0.00 0.00 0.00 4.69
459 462 8.888579 ACAAAGACATATATTTAGGAACGGAG 57.111 34.615 0.00 0.00 0.00 4.63
461 464 6.607004 AGACATATATTTAGGAACGGAGGG 57.393 41.667 0.00 0.00 0.00 4.30
572 6541 0.540133 TTTCCAGCAATGGCAGCAGA 60.540 50.000 0.00 0.00 44.61 4.26
601 6570 2.969238 CATCCGACCGCTCCATGC 60.969 66.667 0.00 0.00 38.57 4.06
673 6642 1.304381 GGCATTGGGGAAGACTGCA 60.304 57.895 0.00 0.00 34.56 4.41
675 6644 0.610232 GCATTGGGGAAGACTGCACT 60.610 55.000 0.00 0.00 33.13 4.40
818 8135 9.282247 CTATGTTCATGCTTTCATCTACAAAAC 57.718 33.333 0.00 0.00 31.15 2.43
883 8280 3.728845 TGAACTCTGAACACTGCTTACC 58.271 45.455 0.00 0.00 0.00 2.85
1075 8479 8.023706 GGGAGAAAGATGAGTATTTCAAACAAC 58.976 37.037 0.00 0.00 37.87 3.32
1115 8519 3.382048 TGATGAGATGAGATCAAGGCG 57.618 47.619 0.00 0.00 0.00 5.52
1160 8564 8.466798 ACTTACAGAGAAAGAGATAAAGAGAGC 58.533 37.037 0.00 0.00 0.00 4.09
1200 8604 5.357032 GGAAAATCGAGTTATTGGATGTGGT 59.643 40.000 0.00 0.00 0.00 4.16
1286 8690 6.569127 TGATTTAACCCTGTCCAGCTAATA 57.431 37.500 0.00 0.00 0.00 0.98
1288 8692 8.270137 TGATTTAACCCTGTCCAGCTAATATA 57.730 34.615 0.00 0.00 0.00 0.86
1289 8693 8.719596 TGATTTAACCCTGTCCAGCTAATATAA 58.280 33.333 0.00 0.00 0.00 0.98
1291 8695 8.918202 TTTAACCCTGTCCAGCTAATATAATG 57.082 34.615 0.00 0.00 0.00 1.90
1292 8696 6.515512 AACCCTGTCCAGCTAATATAATGT 57.484 37.500 0.00 0.00 0.00 2.71
1293 8697 5.869579 ACCCTGTCCAGCTAATATAATGTG 58.130 41.667 0.00 0.00 0.00 3.21
1294 8698 4.697352 CCCTGTCCAGCTAATATAATGTGC 59.303 45.833 0.00 0.00 0.00 4.57
1295 8699 5.308014 CCTGTCCAGCTAATATAATGTGCA 58.692 41.667 0.00 0.00 0.00 4.57
1601 9006 2.223900 CCGAATGTAGCAGCTGAGATCA 60.224 50.000 20.43 10.64 0.00 2.92
1651 9056 1.416401 CACCTATACAGCCCCGTCAAT 59.584 52.381 0.00 0.00 0.00 2.57
1736 9141 4.452733 CCTTCCTCCCGTCACCGC 62.453 72.222 0.00 0.00 0.00 5.68
1803 9208 0.107268 ACCGGCTACAAAGAAACCGT 59.893 50.000 0.00 0.00 42.29 4.83
1863 9268 2.754472 CATCAACAACACGTCTGAGGA 58.246 47.619 4.12 0.00 0.00 3.71
1978 14654 0.529378 GGAGCTTCAACCCATGCTTG 59.471 55.000 0.00 0.00 35.76 4.01
2038 14714 4.641645 CAGGACCTTGCCGGCACA 62.642 66.667 32.95 19.43 35.61 4.57
2148 14824 5.407407 AAAGACACACCTACTGACTATGG 57.593 43.478 0.00 0.00 0.00 2.74
2188 14864 2.817470 ATTGCATGGCCGCGAACAAC 62.817 55.000 8.23 3.62 33.35 3.32
2898 15696 5.880054 AACAGTGAATCCCTTTTCATACG 57.120 39.130 0.00 0.00 37.88 3.06
2996 16074 7.880059 AGAAAATAGTGAGCTCAAAATTTGC 57.120 32.000 26.29 24.97 0.00 3.68
3109 16195 8.692110 TTGCTACTCATGCAATTTCAAATAAG 57.308 30.769 0.00 0.00 44.24 1.73
3226 18835 6.360148 CGCATACTTACGGAGAAAGAGATAAC 59.640 42.308 0.00 0.00 0.00 1.89
3270 23439 7.225538 ACAATGAAGATCGAGTTATTGGATGTC 59.774 37.037 12.58 0.00 31.64 3.06
3405 23574 9.889128 TTATAATCTTGTCACAGATCAATCACA 57.111 29.630 0.00 0.00 31.87 3.58
3440 23609 3.586892 GTTACTAGGCTGTTGTCTGGAC 58.413 50.000 0.00 0.00 30.57 4.02
3441 23610 1.717032 ACTAGGCTGTTGTCTGGACA 58.283 50.000 0.00 0.00 39.98 4.02
3842 24019 3.439129 TCGAGCTAATGACACGAAAGAGA 59.561 43.478 0.00 0.00 0.00 3.10
3855 24032 7.664318 TGACACGAAAGAGAGCTATATATACCA 59.336 37.037 0.00 0.00 0.00 3.25
3890 24067 4.509600 GGAAAGCACTCACTGTCATATAGC 59.490 45.833 0.00 0.00 0.00 2.97
3981 24158 1.774254 TGGTGGTCCTTGAGAACATGT 59.226 47.619 0.00 0.00 46.18 3.21
4052 24229 2.847327 TGAAGGAAGTTGCAGAGAGG 57.153 50.000 0.00 0.00 0.00 3.69
4270 24447 8.354711 TGTTTGGGATATGCAACACTAAATAA 57.645 30.769 0.00 0.00 0.00 1.40
4298 24475 4.331137 CCGCACATTGTCGTAATAAGTTG 58.669 43.478 7.51 0.00 0.00 3.16
4410 24605 9.562408 TTACACCATTGTAGTAAATTTGTGAGA 57.438 29.630 0.00 0.00 39.44 3.27
4421 24616 6.912591 AGTAAATTTGTGAGAAACGAGCTTTG 59.087 34.615 0.00 0.00 0.00 2.77
4507 24702 5.702670 TCTGATGGCTCAAACTAACTTCAAG 59.297 40.000 0.00 0.00 0.00 3.02
4509 24704 6.530120 TGATGGCTCAAACTAACTTCAAGTA 58.470 36.000 0.00 0.00 0.00 2.24
4560 24761 2.744787 GCATCGTCTGCCAGTTTATG 57.255 50.000 0.00 0.00 45.66 1.90
4561 24762 1.268234 GCATCGTCTGCCAGTTTATGC 60.268 52.381 10.47 10.47 45.66 3.14
4562 24763 2.283298 CATCGTCTGCCAGTTTATGCT 58.717 47.619 0.00 0.00 0.00 3.79
4564 24765 3.603158 TCGTCTGCCAGTTTATGCTTA 57.397 42.857 0.00 0.00 0.00 3.09
4599 24801 9.732130 AGATAGCAATAAAATGAATACTCCCTC 57.268 33.333 0.00 0.00 0.00 4.30
4600 24802 8.870075 ATAGCAATAAAATGAATACTCCCTCC 57.130 34.615 0.00 0.00 0.00 4.30
4602 24804 5.531287 GCAATAAAATGAATACTCCCTCCGT 59.469 40.000 0.00 0.00 0.00 4.69
4603 24805 6.293462 GCAATAAAATGAATACTCCCTCCGTC 60.293 42.308 0.00 0.00 0.00 4.79
4604 24806 3.840124 AAATGAATACTCCCTCCGTCC 57.160 47.619 0.00 0.00 0.00 4.79
4606 24808 0.754217 TGAATACTCCCTCCGTCCGG 60.754 60.000 0.00 0.00 0.00 5.14
4607 24809 0.466922 GAATACTCCCTCCGTCCGGA 60.467 60.000 0.00 0.00 42.90 5.14
4608 24810 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
4610 24812 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
4611 24813 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
4612 24814 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
4613 24815 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
4615 24817 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4616 24818 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4618 24820 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
4619 24821 1.135315 CCGTCCGGAAATACTTGTCGA 60.135 52.381 5.23 0.00 37.50 4.20
4622 24824 3.319755 GTCCGGAAATACTTGTCGAACA 58.680 45.455 5.23 0.00 0.00 3.18
4623 24825 3.742369 GTCCGGAAATACTTGTCGAACAA 59.258 43.478 5.23 0.00 36.54 2.83
4624 24826 4.211794 GTCCGGAAATACTTGTCGAACAAA 59.788 41.667 5.23 0.00 37.69 2.83
4627 24829 5.086058 CGGAAATACTTGTCGAACAAATGG 58.914 41.667 0.00 0.00 37.69 3.16
4628 24830 5.106869 CGGAAATACTTGTCGAACAAATGGA 60.107 40.000 0.00 0.00 37.69 3.41
4629 24831 6.403200 CGGAAATACTTGTCGAACAAATGGAT 60.403 38.462 0.00 0.00 37.69 3.41
4630 24832 6.747280 GGAAATACTTGTCGAACAAATGGATG 59.253 38.462 0.00 0.00 37.69 3.51
4631 24833 6.817765 AATACTTGTCGAACAAATGGATGT 57.182 33.333 0.00 0.00 37.69 3.06
4632 24834 7.915293 AATACTTGTCGAACAAATGGATGTA 57.085 32.000 0.00 0.00 37.69 2.29
4634 24836 6.422776 ACTTGTCGAACAAATGGATGTATC 57.577 37.500 0.00 0.00 37.69 2.24
4635 24837 6.173339 ACTTGTCGAACAAATGGATGTATCT 58.827 36.000 0.00 0.00 37.69 1.98
4637 24839 7.492669 ACTTGTCGAACAAATGGATGTATCTAG 59.507 37.037 0.00 0.00 37.69 2.43
4639 24841 7.726216 TGTCGAACAAATGGATGTATCTAGAT 58.274 34.615 10.73 10.73 32.02 1.98
4640 24842 7.653311 TGTCGAACAAATGGATGTATCTAGATG 59.347 37.037 15.79 0.00 32.02 2.90
4642 24844 8.856103 TCGAACAAATGGATGTATCTAGATGTA 58.144 33.333 15.79 4.44 32.02 2.29
4682 24884 6.668323 ACATCTATTTTTATCCATTTCCGCG 58.332 36.000 0.00 0.00 0.00 6.46
4683 24885 6.485313 ACATCTATTTTTATCCATTTCCGCGA 59.515 34.615 8.23 0.00 0.00 5.87
4684 24886 6.295039 TCTATTTTTATCCATTTCCGCGAC 57.705 37.500 8.23 0.00 0.00 5.19
4685 24887 4.974368 ATTTTTATCCATTTCCGCGACA 57.026 36.364 8.23 0.00 0.00 4.35
4686 24888 4.768130 TTTTTATCCATTTCCGCGACAA 57.232 36.364 8.23 0.00 0.00 3.18
4687 24889 4.349663 TTTTATCCATTTCCGCGACAAG 57.650 40.909 8.23 0.00 0.00 3.16
4688 24890 2.684001 TATCCATTTCCGCGACAAGT 57.316 45.000 8.23 0.00 0.00 3.16
4689 24891 2.684001 ATCCATTTCCGCGACAAGTA 57.316 45.000 8.23 0.00 0.00 2.24
4690 24892 2.459060 TCCATTTCCGCGACAAGTAA 57.541 45.000 8.23 0.00 0.00 2.24
4693 24895 3.372822 TCCATTTCCGCGACAAGTAATTC 59.627 43.478 8.23 0.00 0.00 2.17
4695 24897 4.569162 CCATTTCCGCGACAAGTAATTCTA 59.431 41.667 8.23 0.00 0.00 2.10
4696 24898 5.276868 CCATTTCCGCGACAAGTAATTCTAG 60.277 44.000 8.23 0.00 0.00 2.43
4697 24899 4.707030 TTCCGCGACAAGTAATTCTAGA 57.293 40.909 8.23 0.00 0.00 2.43
4698 24900 4.025015 TCCGCGACAAGTAATTCTAGAC 57.975 45.455 8.23 0.00 0.00 2.59
4701 24903 3.486375 CGCGACAAGTAATTCTAGACGGA 60.486 47.826 0.00 0.00 0.00 4.69
4702 24904 4.036352 GCGACAAGTAATTCTAGACGGAG 58.964 47.826 0.00 0.00 0.00 4.63
4703 24905 4.599047 CGACAAGTAATTCTAGACGGAGG 58.401 47.826 0.00 0.00 0.00 4.30
4704 24906 4.497674 CGACAAGTAATTCTAGACGGAGGG 60.498 50.000 0.00 0.00 0.00 4.30
4705 24907 4.607239 ACAAGTAATTCTAGACGGAGGGA 58.393 43.478 0.00 0.00 0.00 4.20
4706 24908 4.645588 ACAAGTAATTCTAGACGGAGGGAG 59.354 45.833 0.00 0.00 0.00 4.30
4773 25496 3.437741 TGAAGACAACAGCTATGCACATG 59.562 43.478 0.00 0.00 0.00 3.21
4810 25536 4.818534 TCATCTTCAGTTGTTGTCTTGC 57.181 40.909 0.00 0.00 0.00 4.01
4835 25561 0.405585 AAGGGAACACATGGGACCAG 59.594 55.000 0.00 0.00 0.00 4.00
4892 25618 6.095440 AGGTGATGTTTGTAATCTTGTATGCC 59.905 38.462 0.00 0.00 0.00 4.40
4955 25683 6.477688 CCAGCCATTGTTATGATTGTGAATTC 59.522 38.462 0.00 0.00 33.37 2.17
4956 25684 6.477688 CAGCCATTGTTATGATTGTGAATTCC 59.522 38.462 2.27 0.00 33.37 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.398390 CGTAGATTGGCTGGTTGAAGC 59.602 52.381 0.00 0.00 42.75 3.86
31 33 4.065321 ACGTGAAGGAGGATGAATCATC 57.935 45.455 14.51 14.51 39.87 2.92
60 62 4.281688 CAGGAAATCAGATGGTTTGGTGTT 59.718 41.667 0.00 0.00 0.00 3.32
75 77 7.286313 AGATCTTCTATGGTTTCCAGGAAATC 58.714 38.462 17.99 17.69 36.75 2.17
89 91 4.088634 CCCCTCCTCTGAGATCTTCTATG 58.911 52.174 6.17 0.00 41.42 2.23
98 100 0.487325 TTCACACCCCTCCTCTGAGA 59.513 55.000 6.17 0.00 41.42 3.27
99 101 1.002544 GTTTCACACCCCTCCTCTGAG 59.997 57.143 0.00 0.00 38.42 3.35
105 107 1.203001 TCAATGGTTTCACACCCCTCC 60.203 52.381 0.00 0.00 46.68 4.30
138 140 1.952990 TGTGCTTGCCTTCATTTCGAA 59.047 42.857 0.00 0.00 0.00 3.71
146 148 1.664016 CGTGATTGTGTGCTTGCCTTC 60.664 52.381 0.00 0.00 0.00 3.46
151 153 0.943673 TGACCGTGATTGTGTGCTTG 59.056 50.000 0.00 0.00 0.00 4.01
168 170 1.371183 CACGCAGGGGAGACTTTGA 59.629 57.895 0.00 0.00 0.00 2.69
304 307 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
306 309 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
307 310 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
325 328 9.442047 CATTTAGTGGAATCTCTACAAAGACTT 57.558 33.333 0.00 0.00 29.47 3.01
345 348 8.827177 TTTTGCTCCGTATATAGTCCATTTAG 57.173 34.615 0.00 0.00 0.00 1.85
347 350 7.936847 TCATTTTGCTCCGTATATAGTCCATTT 59.063 33.333 0.00 0.00 0.00 2.32
348 351 7.450074 TCATTTTGCTCCGTATATAGTCCATT 58.550 34.615 0.00 0.00 0.00 3.16
349 352 7.004555 TCATTTTGCTCCGTATATAGTCCAT 57.995 36.000 0.00 0.00 0.00 3.41
353 356 8.902540 TTCATTCATTTTGCTCCGTATATAGT 57.097 30.769 0.00 0.00 0.00 2.12
354 357 9.979270 GATTCATTCATTTTGCTCCGTATATAG 57.021 33.333 0.00 0.00 0.00 1.31
355 358 9.725019 AGATTCATTCATTTTGCTCCGTATATA 57.275 29.630 0.00 0.00 0.00 0.86
356 359 8.627208 AGATTCATTCATTTTGCTCCGTATAT 57.373 30.769 0.00 0.00 0.00 0.86
357 360 8.988934 GTAGATTCATTCATTTTGCTCCGTATA 58.011 33.333 0.00 0.00 0.00 1.47
359 362 6.821160 TGTAGATTCATTCATTTTGCTCCGTA 59.179 34.615 0.00 0.00 0.00 4.02
360 363 5.647658 TGTAGATTCATTCATTTTGCTCCGT 59.352 36.000 0.00 0.00 0.00 4.69
361 364 5.967674 GTGTAGATTCATTCATTTTGCTCCG 59.032 40.000 0.00 0.00 0.00 4.63
364 367 7.692460 TGAGTGTAGATTCATTCATTTTGCT 57.308 32.000 0.00 0.00 31.09 3.91
365 368 8.746922 TTTGAGTGTAGATTCATTCATTTTGC 57.253 30.769 0.00 0.00 34.88 3.68
369 372 8.525316 TGCATTTTGAGTGTAGATTCATTCATT 58.475 29.630 0.00 0.00 34.88 2.57
374 377 7.876936 AGATGCATTTTGAGTGTAGATTCAT 57.123 32.000 0.00 0.00 0.00 2.57
375 378 8.969260 ATAGATGCATTTTGAGTGTAGATTCA 57.031 30.769 0.00 0.00 0.00 2.57
385 388 8.484641 ACGGATGTATATAGATGCATTTTGAG 57.515 34.615 11.19 0.00 38.38 3.02
388 391 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
390 393 7.928167 CCACATACGGATGTATATAGATGCATT 59.072 37.037 14.23 1.23 44.82 3.56
391 394 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
392 395 6.379988 ACCACATACGGATGTATATAGATGCA 59.620 38.462 14.23 0.00 44.82 3.96
394 397 8.466798 TGAACCACATACGGATGTATATAGATG 58.533 37.037 14.23 0.00 44.82 2.90
395 398 8.589701 TGAACCACATACGGATGTATATAGAT 57.410 34.615 14.23 0.00 44.82 1.98
396 399 8.589701 ATGAACCACATACGGATGTATATAGA 57.410 34.615 14.23 0.00 44.82 1.98
397 400 9.952188 CTATGAACCACATACGGATGTATATAG 57.048 37.037 14.23 12.28 44.82 1.31
398 401 9.470399 ACTATGAACCACATACGGATGTATATA 57.530 33.333 14.23 7.10 44.82 0.86
399 402 8.362464 ACTATGAACCACATACGGATGTATAT 57.638 34.615 14.23 1.68 44.82 0.86
400 403 7.770366 ACTATGAACCACATACGGATGTATA 57.230 36.000 14.23 6.48 44.82 1.47
401 404 6.665992 ACTATGAACCACATACGGATGTAT 57.334 37.500 14.23 5.54 44.82 2.29
402 405 6.097129 TCAACTATGAACCACATACGGATGTA 59.903 38.462 14.23 0.00 37.07 2.29
404 407 5.356426 TCAACTATGAACCACATACGGATG 58.644 41.667 5.94 5.94 40.07 3.51
407 410 4.034048 GCTTCAACTATGAACCACATACGG 59.966 45.833 0.00 0.00 40.59 4.02
411 414 5.171339 AGAGCTTCAACTATGAACCACAT 57.829 39.130 0.00 0.00 40.59 3.21
415 418 6.874134 TCTTTGTAGAGCTTCAACTATGAACC 59.126 38.462 0.00 0.00 40.59 3.62
416 419 7.385205 TGTCTTTGTAGAGCTTCAACTATGAAC 59.615 37.037 0.00 0.00 40.59 3.18
417 420 7.441836 TGTCTTTGTAGAGCTTCAACTATGAA 58.558 34.615 0.00 0.00 43.18 2.57
418 421 6.993079 TGTCTTTGTAGAGCTTCAACTATGA 58.007 36.000 0.00 0.00 0.00 2.15
431 434 9.976511 CCGTTCCTAAATATATGTCTTTGTAGA 57.023 33.333 0.00 0.00 0.00 2.59
432 435 9.976511 TCCGTTCCTAAATATATGTCTTTGTAG 57.023 33.333 0.00 0.00 0.00 2.74
435 438 7.387948 CCCTCCGTTCCTAAATATATGTCTTTG 59.612 40.741 0.00 0.00 0.00 2.77
436 439 7.291651 TCCCTCCGTTCCTAAATATATGTCTTT 59.708 37.037 0.00 0.00 0.00 2.52
437 440 6.785963 TCCCTCCGTTCCTAAATATATGTCTT 59.214 38.462 0.00 0.00 0.00 3.01
438 441 6.320518 TCCCTCCGTTCCTAAATATATGTCT 58.679 40.000 0.00 0.00 0.00 3.41
439 442 6.210984 ACTCCCTCCGTTCCTAAATATATGTC 59.789 42.308 0.00 0.00 0.00 3.06
440 443 6.082707 ACTCCCTCCGTTCCTAAATATATGT 58.917 40.000 0.00 0.00 0.00 2.29
441 444 6.607004 ACTCCCTCCGTTCCTAAATATATG 57.393 41.667 0.00 0.00 0.00 1.78
444 447 6.666980 GGTATACTCCCTCCGTTCCTAAATAT 59.333 42.308 2.25 0.00 0.00 1.28
445 448 6.012745 GGTATACTCCCTCCGTTCCTAAATA 58.987 44.000 2.25 0.00 0.00 1.40
446 449 4.837298 GGTATACTCCCTCCGTTCCTAAAT 59.163 45.833 2.25 0.00 0.00 1.40
447 450 4.218312 GGTATACTCCCTCCGTTCCTAAA 58.782 47.826 2.25 0.00 0.00 1.85
448 451 3.205056 TGGTATACTCCCTCCGTTCCTAA 59.795 47.826 2.25 0.00 0.00 2.69
449 452 2.785269 TGGTATACTCCCTCCGTTCCTA 59.215 50.000 2.25 0.00 0.00 2.94
451 454 1.685517 GTGGTATACTCCCTCCGTTCC 59.314 57.143 2.25 0.00 0.00 3.62
452 455 2.381911 TGTGGTATACTCCCTCCGTTC 58.618 52.381 2.25 0.00 0.00 3.95
454 457 2.769602 ATGTGGTATACTCCCTCCGT 57.230 50.000 2.25 0.00 0.00 4.69
455 458 3.506455 CAGTATGTGGTATACTCCCTCCG 59.494 52.174 2.25 0.00 32.93 4.63
456 459 4.737578 TCAGTATGTGGTATACTCCCTCC 58.262 47.826 2.25 0.00 37.40 4.30
457 460 6.919775 AATCAGTATGTGGTATACTCCCTC 57.080 41.667 2.25 0.00 37.40 4.30
458 461 8.648693 GTTAAATCAGTATGTGGTATACTCCCT 58.351 37.037 2.25 0.00 37.40 4.20
459 462 8.648693 AGTTAAATCAGTATGTGGTATACTCCC 58.351 37.037 2.25 0.00 37.40 4.30
461 464 9.477484 CCAGTTAAATCAGTATGTGGTATACTC 57.523 37.037 2.25 0.00 37.40 2.59
632 6601 1.151450 GGGTATGGGATGGGCACTG 59.849 63.158 0.00 0.00 0.00 3.66
673 6642 2.358003 GTTCTGGCTGCTCGCAGT 60.358 61.111 19.00 0.00 45.24 4.40
675 6644 2.357881 CTGTTCTGGCTGCTCGCA 60.358 61.111 0.00 0.00 41.67 5.10
720 6692 0.322098 TTGGGCGTGGTGAATCGATT 60.322 50.000 11.20 11.20 0.00 3.34
862 8179 3.133901 TGGTAAGCAGTGTTCAGAGTTCA 59.866 43.478 0.00 0.00 0.00 3.18
863 8180 3.728845 TGGTAAGCAGTGTTCAGAGTTC 58.271 45.455 0.00 0.00 0.00 3.01
883 8280 5.050159 GCTATTTTCCTTTTGGTTGCAACTG 60.050 40.000 27.64 13.10 41.38 3.16
942 8342 8.849168 CCTGCAATAATATATTTGTGAGGAACA 58.151 33.333 2.68 0.00 36.85 3.18
1075 8479 7.674120 TCATCATATAACTTGAGACCTCCATG 58.326 38.462 0.00 0.00 0.00 3.66
1115 8519 1.323534 GTATGCGGATTGTGTCGACAC 59.676 52.381 36.01 36.01 46.59 3.67
1160 8564 5.334105 CGATTTTCCTTGTAGTTGTCAGTGG 60.334 44.000 0.00 0.00 0.00 4.00
1200 8604 2.090775 TCCTCTAGCCATACCATGACCA 60.091 50.000 0.00 0.00 0.00 4.02
1293 8697 4.799949 CCATGTTACATGTATGCAAACTGC 59.200 41.667 21.84 0.00 45.29 4.40
1294 8698 4.799949 GCCATGTTACATGTATGCAAACTG 59.200 41.667 21.84 5.73 31.79 3.16
1295 8699 4.706476 AGCCATGTTACATGTATGCAAACT 59.294 37.500 21.84 5.86 31.79 2.66
1507 8911 2.977772 AGTAGCTGTTGAGGCTGATC 57.022 50.000 0.00 0.00 40.52 2.92
1601 9006 3.368843 CCATTCTTCAGTGAGATGTCGGT 60.369 47.826 10.46 0.00 0.00 4.69
1651 9056 0.596082 TCGACGTGAAGCAGATGTGA 59.404 50.000 0.00 0.00 0.00 3.58
1736 9141 1.010125 CTGTGAAACGGTTGCGTGG 60.010 57.895 0.00 0.00 42.39 4.94
2038 14714 1.405526 CGACCATCGATGAACCCAAGT 60.406 52.381 26.86 13.50 43.74 3.16
2065 14741 1.893808 AACAACGGCAGCACCTCTG 60.894 57.895 0.00 0.00 45.62 3.35
2148 14824 3.904136 AGCTGTTTGTACTGATGCAAC 57.096 42.857 0.00 0.00 29.21 4.17
2188 14864 1.691976 TGGCATAAGTATCCTGGACCG 59.308 52.381 0.00 0.00 0.00 4.79
2486 15275 9.313323 CGAAATTAATATTACACCGTGCATTAG 57.687 33.333 0.00 0.00 0.00 1.73
2641 15433 7.009179 ACATTGGAAACATCTACTCAGAAGA 57.991 36.000 0.00 0.00 42.32 2.87
2750 15542 1.071814 TAGTTCCCGGGTGTGTTGC 59.928 57.895 22.86 4.06 0.00 4.17
2961 15761 9.181805 GAGCTCACTATTTTCTTTTGGTTTTAC 57.818 33.333 9.40 0.00 0.00 2.01
2964 16041 7.346751 TGAGCTCACTATTTTCTTTTGGTTT 57.653 32.000 13.74 0.00 0.00 3.27
3109 16195 2.039084 TCTTTCTCCCTCTTGTGCCTTC 59.961 50.000 0.00 0.00 0.00 3.46
3226 18835 1.269723 TGTAGTTGTCAGTGGCTCTCG 59.730 52.381 0.00 0.00 0.00 4.04
3270 23439 2.429250 TGTAGACCATACCATGACCACG 59.571 50.000 0.00 0.00 0.00 4.94
3405 23574 5.013183 AGCCTAGTAACCTCACAATGTTTCT 59.987 40.000 0.00 0.00 0.00 2.52
3855 24032 6.096846 AGTGAGTGCTTTCCATTAAAGTTGTT 59.903 34.615 0.00 0.00 45.46 2.83
3890 24067 4.009675 TCCGATGAAACATCAAGGGAAAG 58.990 43.478 11.39 0.00 0.00 2.62
4052 24229 8.752005 AATAGAGTCTCCTCATCATATCTAGC 57.248 38.462 0.00 0.00 40.40 3.42
4270 24447 1.816074 ACGACAATGTGCGGGTTAAT 58.184 45.000 0.00 0.00 0.00 1.40
4298 24475 2.032680 TTATTGCTCCGTAACTGGCC 57.967 50.000 0.00 0.00 0.00 5.36
4410 24605 1.981256 ACACATCCCAAAGCTCGTTT 58.019 45.000 0.00 0.00 0.00 3.60
4421 24616 5.690865 TCTTAATTGGACCATACACATCCC 58.309 41.667 0.00 0.00 0.00 3.85
4522 24717 6.765989 ACGATGCCAGCTGAACTATTTTATTA 59.234 34.615 17.39 0.00 0.00 0.98
4525 24720 4.513442 ACGATGCCAGCTGAACTATTTTA 58.487 39.130 17.39 0.00 0.00 1.52
4530 24726 1.134995 CAGACGATGCCAGCTGAACTA 60.135 52.381 17.39 0.00 0.00 2.24
4579 24781 6.204882 GGACGGAGGGAGTATTCATTTTATTG 59.795 42.308 0.00 0.00 0.00 1.90
4589 24791 0.032813 TTCCGGACGGAGGGAGTATT 60.033 55.000 13.64 0.00 46.06 1.89
4591 24793 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
4596 24798 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4597 24799 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
4599 24801 1.135315 TCGACAAGTATTTCCGGACGG 60.135 52.381 1.83 3.96 0.00 4.79
4600 24802 2.267188 TCGACAAGTATTTCCGGACG 57.733 50.000 1.83 0.27 0.00 4.79
4602 24804 3.663995 TGTTCGACAAGTATTTCCGGA 57.336 42.857 0.00 0.00 0.00 5.14
4603 24805 4.735662 TTTGTTCGACAAGTATTTCCGG 57.264 40.909 0.00 0.00 39.53 5.14
4604 24806 5.086058 CCATTTGTTCGACAAGTATTTCCG 58.914 41.667 0.00 0.00 39.53 4.30
4606 24808 7.305474 ACATCCATTTGTTCGACAAGTATTTC 58.695 34.615 0.00 0.00 39.53 2.17
4607 24809 7.214467 ACATCCATTTGTTCGACAAGTATTT 57.786 32.000 0.00 0.00 39.53 1.40
4608 24810 6.817765 ACATCCATTTGTTCGACAAGTATT 57.182 33.333 0.00 0.00 39.53 1.89
4610 24812 7.327975 AGATACATCCATTTGTTCGACAAGTA 58.672 34.615 0.00 0.00 39.53 2.24
4611 24813 6.173339 AGATACATCCATTTGTTCGACAAGT 58.827 36.000 0.00 0.00 39.53 3.16
4612 24814 6.668541 AGATACATCCATTTGTTCGACAAG 57.331 37.500 0.00 0.00 39.53 3.16
4613 24815 7.552459 TCTAGATACATCCATTTGTTCGACAA 58.448 34.615 0.00 0.00 36.11 3.18
4615 24817 7.653713 ACATCTAGATACATCCATTTGTTCGAC 59.346 37.037 4.54 0.00 0.00 4.20
4616 24818 7.726216 ACATCTAGATACATCCATTTGTTCGA 58.274 34.615 4.54 0.00 0.00 3.71
4658 24860 6.485313 TCGCGGAAATGGATAAAAATAGATGT 59.515 34.615 6.13 0.00 0.00 3.06
4659 24861 6.797033 GTCGCGGAAATGGATAAAAATAGATG 59.203 38.462 6.13 0.00 0.00 2.90
4661 24863 5.818336 TGTCGCGGAAATGGATAAAAATAGA 59.182 36.000 6.13 0.00 0.00 1.98
4662 24864 6.055231 TGTCGCGGAAATGGATAAAAATAG 57.945 37.500 6.13 0.00 0.00 1.73
4664 24866 4.974368 TGTCGCGGAAATGGATAAAAAT 57.026 36.364 6.13 0.00 0.00 1.82
4665 24867 4.216687 ACTTGTCGCGGAAATGGATAAAAA 59.783 37.500 6.13 0.00 0.00 1.94
4666 24868 3.754323 ACTTGTCGCGGAAATGGATAAAA 59.246 39.130 6.13 0.00 0.00 1.52
4668 24870 2.980568 ACTTGTCGCGGAAATGGATAA 58.019 42.857 6.13 0.00 0.00 1.75
4669 24871 2.684001 ACTTGTCGCGGAAATGGATA 57.316 45.000 6.13 0.00 0.00 2.59
4670 24872 2.684001 TACTTGTCGCGGAAATGGAT 57.316 45.000 6.13 0.00 0.00 3.41
4672 24874 3.374058 AGAATTACTTGTCGCGGAAATGG 59.626 43.478 6.13 0.00 0.00 3.16
4673 24875 4.600012 AGAATTACTTGTCGCGGAAATG 57.400 40.909 6.13 0.00 0.00 2.32
4674 24876 5.519206 GTCTAGAATTACTTGTCGCGGAAAT 59.481 40.000 6.13 0.00 0.00 2.17
4675 24877 4.860907 GTCTAGAATTACTTGTCGCGGAAA 59.139 41.667 6.13 0.00 0.00 3.13
4676 24878 4.418392 GTCTAGAATTACTTGTCGCGGAA 58.582 43.478 6.13 0.00 0.00 4.30
4678 24880 2.782192 CGTCTAGAATTACTTGTCGCGG 59.218 50.000 6.13 0.00 0.00 6.46
4679 24881 2.782192 CCGTCTAGAATTACTTGTCGCG 59.218 50.000 0.00 0.00 33.76 5.87
4682 24884 4.643784 TCCCTCCGTCTAGAATTACTTGTC 59.356 45.833 0.00 0.00 0.00 3.18
4683 24885 4.607239 TCCCTCCGTCTAGAATTACTTGT 58.393 43.478 0.00 0.00 0.00 3.16
4684 24886 4.645588 ACTCCCTCCGTCTAGAATTACTTG 59.354 45.833 0.00 0.00 0.00 3.16
4685 24887 4.869451 ACTCCCTCCGTCTAGAATTACTT 58.131 43.478 0.00 0.00 0.00 2.24
4686 24888 4.523168 ACTCCCTCCGTCTAGAATTACT 57.477 45.455 0.00 0.00 0.00 2.24
4687 24889 5.375773 AGTACTCCCTCCGTCTAGAATTAC 58.624 45.833 0.00 0.00 0.00 1.89
4688 24890 5.643421 AGTACTCCCTCCGTCTAGAATTA 57.357 43.478 0.00 0.00 0.00 1.40
4689 24891 4.523168 AGTACTCCCTCCGTCTAGAATT 57.477 45.455 0.00 0.00 0.00 2.17
4690 24892 4.208746 CAAGTACTCCCTCCGTCTAGAAT 58.791 47.826 0.00 0.00 0.00 2.40
4693 24895 2.299521 CCAAGTACTCCCTCCGTCTAG 58.700 57.143 0.00 0.00 0.00 2.43
4695 24897 0.408700 ACCAAGTACTCCCTCCGTCT 59.591 55.000 0.00 0.00 0.00 4.18
4696 24898 2.134789 TACCAAGTACTCCCTCCGTC 57.865 55.000 0.00 0.00 0.00 4.79
4697 24899 2.610438 TTACCAAGTACTCCCTCCGT 57.390 50.000 0.00 0.00 0.00 4.69
4698 24900 3.449737 TCATTTACCAAGTACTCCCTCCG 59.550 47.826 0.00 0.00 0.00 4.63
4701 24903 6.849151 AGTTTTCATTTACCAAGTACTCCCT 58.151 36.000 0.00 0.00 0.00 4.20
4702 24904 7.229907 TGAAGTTTTCATTTACCAAGTACTCCC 59.770 37.037 0.00 0.00 34.08 4.30
4703 24905 8.161699 TGAAGTTTTCATTTACCAAGTACTCC 57.838 34.615 0.00 0.00 34.08 3.85
4704 24906 7.803659 GCTGAAGTTTTCATTTACCAAGTACTC 59.196 37.037 0.00 0.00 39.30 2.59
4705 24907 7.502561 AGCTGAAGTTTTCATTTACCAAGTACT 59.497 33.333 0.00 0.00 39.30 2.73
4706 24908 7.591426 CAGCTGAAGTTTTCATTTACCAAGTAC 59.409 37.037 8.42 0.00 39.30 2.73
4773 25496 7.718753 ACTGAAGATGATCCTCCATTGTTAATC 59.281 37.037 0.00 0.00 0.00 1.75
4810 25536 1.442769 CCATGTGTTCCCTTGTCGAG 58.557 55.000 0.00 0.00 0.00 4.04
4835 25561 1.061131 CAATCAGTTCGGACATGTCGC 59.939 52.381 19.33 11.36 0.00 5.19
4892 25618 4.401202 ACCACAAACCAAAGAACTAACTGG 59.599 41.667 0.00 0.00 34.95 4.00


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

AutoCloner maintained by Alex Coulton.