Multiple sequence alignment - TraesCS5B01G541500

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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 TraesCS5B01G541500 chr5B 100.000 5212 0 0 1 5212 695988819 695994030 0.000000e+00 9625.0
1 TraesCS5B01G541500 chr5B 91.292 2090 166 12 2135 4216 695704663 695706744 0.000000e+00 2837.0
2 TraesCS5B01G541500 chr5B 86.322 1857 233 14 2168 4015 695963004 695964848 0.000000e+00 2002.0
3 TraesCS5B01G541500 chr5B 86.749 1298 140 21 860 2138 695703284 695704568 0.000000e+00 1415.0
4 TraesCS5B01G541500 chr5B 78.505 1498 299 19 2157 3642 710344210 710345696 0.000000e+00 961.0
5 TraesCS5B01G541500 chr5B 76.420 1620 339 39 2182 3780 695951046 695952643 0.000000e+00 835.0
6 TraesCS5B01G541500 chr5B 84.223 824 122 8 1012 1831 695961092 695961911 0.000000e+00 795.0
7 TraesCS5B01G541500 chr5B 84.605 773 101 6 996 1764 695834549 695835307 0.000000e+00 752.0
8 TraesCS5B01G541500 chr5B 79.357 809 157 10 1028 1831 695422403 695423206 1.270000e-155 560.0
9 TraesCS5B01G541500 chr5B 87.205 297 17 9 4394 4670 695706863 695707158 8.420000e-83 318.0
10 TraesCS5B01G541500 chr5B 78.958 518 48 32 4722 5212 695553211 695553694 3.950000e-76 296.0
11 TraesCS5B01G541500 chr5B 94.444 126 7 0 386 511 680998601 680998726 1.480000e-45 195.0
12 TraesCS5B01G541500 chr5B 85.556 90 10 1 606 692 577020155 577020244 2.000000e-14 91.6
13 TraesCS5B01G541500 chr5B 100.000 29 0 0 4990 5018 695719273 695719301 3.000000e-03 54.7
14 TraesCS5B01G541500 chr5D 95.936 4134 139 7 512 4636 555932445 555928332 0.000000e+00 6676.0
15 TraesCS5B01G541500 chr5D 92.250 2000 152 3 2135 4133 555070359 555068362 0.000000e+00 2832.0
16 TraesCS5B01G541500 chr5D 86.437 1858 230 13 2172 4021 555659573 555657730 0.000000e+00 2015.0
17 TraesCS5B01G541500 chr5D 88.189 1016 108 7 1006 2018 556035826 556034820 0.000000e+00 1201.0
18 TraesCS5B01G541500 chr5D 86.544 1085 131 9 1012 2086 555071574 555070495 0.000000e+00 1181.0
19 TraesCS5B01G541500 chr5D 76.351 1962 395 62 2183 4113 558718906 558720829 0.000000e+00 989.0
20 TraesCS5B01G541500 chr5D 83.836 829 129 5 1012 1838 555660820 555659995 0.000000e+00 784.0
21 TraesCS5B01G541500 chr5D 79.398 830 162 9 1035 1861 555916793 555915970 1.260000e-160 577.0
22 TraesCS5B01G541500 chr5D 94.495 327 12 2 3 323 555932792 555932466 2.800000e-137 499.0
23 TraesCS5B01G541500 chr5D 86.547 446 43 8 4191 4636 555068339 555067911 4.720000e-130 475.0
24 TraesCS5B01G541500 chr5D 95.455 66 2 1 331 395 555932493 555932428 2.570000e-18 104.0
25 TraesCS5B01G541500 chr4A 90.090 2886 197 36 2135 4999 613766327 613769144 0.000000e+00 3663.0
26 TraesCS5B01G541500 chr4A 89.840 1378 122 11 696 2064 613764859 613766227 0.000000e+00 1753.0
27 TraesCS5B01G541500 chr4A 91.266 229 6 3 4984 5212 613770644 613770858 3.050000e-77 300.0
28 TraesCS5B01G541500 chr4A 89.381 226 17 4 102 320 613764484 613764709 1.430000e-70 278.0
29 TraesCS5B01G541500 chr1B 77.989 1999 387 44 2176 4147 597535582 597537554 0.000000e+00 1205.0
30 TraesCS5B01G541500 chr7D 94.262 122 6 1 391 512 634071200 634071080 8.910000e-43 185.0
31 TraesCS5B01G541500 chr2B 93.548 124 8 0 388 511 745041657 745041780 8.910000e-43 185.0
32 TraesCS5B01G541500 chr2B 86.139 101 10 4 602 699 547862113 547862212 7.140000e-19 106.0
33 TraesCS5B01G541500 chr2B 88.608 79 8 1 615 692 335527257 335527179 1.550000e-15 95.3
34 TraesCS5B01G541500 chr2B 84.211 95 14 1 609 702 646110927 646111021 2.000000e-14 91.6
35 TraesCS5B01G541500 chr3B 94.624 93 5 0 388 480 14462422 14462514 1.510000e-30 145.0
36 TraesCS5B01G541500 chr3B 86.585 82 10 1 615 695 651725118 651725037 7.190000e-14 89.8
37 TraesCS5B01G541500 chr5A 95.238 84 4 0 394 477 445256403 445256320 3.270000e-27 134.0
38 TraesCS5B01G541500 chr4B 88.235 85 9 1 609 692 461693544 461693460 3.320000e-17 100.0
39 TraesCS5B01G541500 chr7B 86.022 93 10 3 608 699 15307970 15307880 4.300000e-16 97.1
40 TraesCS5B01G541500 chr7A 88.608 79 8 1 615 692 112977546 112977468 1.550000e-15 95.3
41 TraesCS5B01G541500 chr2A 94.737 57 2 1 388 443 106655148 106655204 2.590000e-13 87.9


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 TraesCS5B01G541500 chr5B 695988819 695994030 5211 False 9625.000000 9625 100.000000 1 5212 1 chr5B.!!$F8 5211
1 TraesCS5B01G541500 chr5B 695703284 695707158 3874 False 1523.333333 2837 88.415333 860 4670 3 chr5B.!!$F10 3810
2 TraesCS5B01G541500 chr5B 695961092 695964848 3756 False 1398.500000 2002 85.272500 1012 4015 2 chr5B.!!$F11 3003
3 TraesCS5B01G541500 chr5B 710344210 710345696 1486 False 961.000000 961 78.505000 2157 3642 1 chr5B.!!$F9 1485
4 TraesCS5B01G541500 chr5B 695951046 695952643 1597 False 835.000000 835 76.420000 2182 3780 1 chr5B.!!$F7 1598
5 TraesCS5B01G541500 chr5B 695834549 695835307 758 False 752.000000 752 84.605000 996 1764 1 chr5B.!!$F6 768
6 TraesCS5B01G541500 chr5B 695422403 695423206 803 False 560.000000 560 79.357000 1028 1831 1 chr5B.!!$F3 803
7 TraesCS5B01G541500 chr5D 555928332 555932792 4460 True 2426.333333 6676 95.295333 3 4636 3 chr5D.!!$R5 4633
8 TraesCS5B01G541500 chr5D 555067911 555071574 3663 True 1496.000000 2832 88.447000 1012 4636 3 chr5D.!!$R3 3624
9 TraesCS5B01G541500 chr5D 555657730 555660820 3090 True 1399.500000 2015 85.136500 1012 4021 2 chr5D.!!$R4 3009
10 TraesCS5B01G541500 chr5D 556034820 556035826 1006 True 1201.000000 1201 88.189000 1006 2018 1 chr5D.!!$R2 1012
11 TraesCS5B01G541500 chr5D 558718906 558720829 1923 False 989.000000 989 76.351000 2183 4113 1 chr5D.!!$F1 1930
12 TraesCS5B01G541500 chr5D 555915970 555916793 823 True 577.000000 577 79.398000 1035 1861 1 chr5D.!!$R1 826
13 TraesCS5B01G541500 chr4A 613764484 613770858 6374 False 1498.500000 3663 90.144250 102 5212 4 chr4A.!!$F1 5110
14 TraesCS5B01G541500 chr1B 597535582 597537554 1972 False 1205.000000 1205 77.989000 2176 4147 1 chr1B.!!$F1 1971

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
482 488 0.032952 TGTCAGTGGCCGAACAGTAC 59.967 55.000 0.00 0.0 0.00 2.73 F
483 489 0.669625 GTCAGTGGCCGAACAGTACC 60.670 60.000 0.00 0.0 0.00 3.34 F
1336 1368 0.246360 TCGCTTCCTCAAATCGCTCA 59.754 50.000 0.00 0.0 0.00 4.26 F
1435 1467 2.697654 ACAAGCTGAGTGAGATTCTGC 58.302 47.619 0.00 0.0 39.09 4.26 F
3080 3932 2.309613 TCTTCAGCTTGCACCAAACAT 58.690 42.857 0.00 0.0 0.00 2.71 F
3422 4283 5.048507 GGCTTTAGTATTACCAAGAGTCCG 58.951 45.833 7.31 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1336 1368 1.474077 GGCAATTCCACAGCGAGAATT 59.526 47.619 0.00 0.00 42.08 2.17 R
1435 1467 2.816958 ATGCTCGGTCTTGCTGCG 60.817 61.111 0.00 0.00 0.00 5.18 R
3073 3925 3.256631 AGCAAGACTAGGCAAATGTTTGG 59.743 43.478 0.00 0.00 38.57 3.28 R
3422 4283 3.112205 ATCCTCCACCGCATCTGCC 62.112 63.158 0.00 0.00 37.91 4.85 R
4046 4922 0.742635 CAGCCTTTCTCTCGGAAGGC 60.743 60.000 15.04 15.04 42.78 4.35 R
5101 7522 0.324738 AGACGGCCAGGAAGAGATCA 60.325 55.000 2.24 0.00 0.00 2.92 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
28 29 3.729108 AGGGAGAGATCATGGAGTTTCA 58.271 45.455 0.00 0.00 0.00 2.69
41 42 4.608269 TGGAGTTTCATGCAAATATGGGA 58.392 39.130 0.00 0.00 0.00 4.37
175 176 9.807921 TCCTTGACAAAACTCCTTATCTAAAAT 57.192 29.630 0.00 0.00 0.00 1.82
265 266 3.520569 GCTGTTGTCAAAAAGCTTGGAA 58.479 40.909 0.00 0.00 42.56 3.53
273 274 3.130340 TCAAAAAGCTTGGAACACTCACC 59.870 43.478 0.00 0.00 39.29 4.02
284 285 4.262617 GGAACACTCACCTATTCCTTTCC 58.737 47.826 0.00 0.00 38.08 3.13
296 297 3.409026 TTCCTTTCCTCTTGCTCTGAC 57.591 47.619 0.00 0.00 0.00 3.51
298 299 1.674221 CCTTTCCTCTTGCTCTGACGG 60.674 57.143 0.00 0.00 0.00 4.79
299 300 1.001406 CTTTCCTCTTGCTCTGACGGT 59.999 52.381 0.00 0.00 0.00 4.83
300 301 1.048601 TTCCTCTTGCTCTGACGGTT 58.951 50.000 0.00 0.00 0.00 4.44
301 302 0.603569 TCCTCTTGCTCTGACGGTTC 59.396 55.000 0.00 0.00 0.00 3.62
302 303 0.605589 CCTCTTGCTCTGACGGTTCT 59.394 55.000 0.00 0.00 0.00 3.01
303 304 1.403514 CCTCTTGCTCTGACGGTTCTC 60.404 57.143 0.00 0.00 0.00 2.87
304 305 1.543802 CTCTTGCTCTGACGGTTCTCT 59.456 52.381 0.00 0.00 0.00 3.10
305 306 1.542030 TCTTGCTCTGACGGTTCTCTC 59.458 52.381 0.00 0.00 0.00 3.20
306 307 0.603569 TTGCTCTGACGGTTCTCTCC 59.396 55.000 0.00 0.00 0.00 3.71
307 308 0.539669 TGCTCTGACGGTTCTCTCCA 60.540 55.000 0.00 0.00 0.00 3.86
308 309 0.109039 GCTCTGACGGTTCTCTCCAC 60.109 60.000 0.00 0.00 0.00 4.02
309 310 1.540267 CTCTGACGGTTCTCTCCACT 58.460 55.000 0.00 0.00 0.00 4.00
310 311 1.889829 CTCTGACGGTTCTCTCCACTT 59.110 52.381 0.00 0.00 0.00 3.16
311 312 2.297597 CTCTGACGGTTCTCTCCACTTT 59.702 50.000 0.00 0.00 0.00 2.66
312 313 2.296471 TCTGACGGTTCTCTCCACTTTC 59.704 50.000 0.00 0.00 0.00 2.62
313 314 1.343465 TGACGGTTCTCTCCACTTTCC 59.657 52.381 0.00 0.00 0.00 3.13
314 315 0.685660 ACGGTTCTCTCCACTTTCCC 59.314 55.000 0.00 0.00 0.00 3.97
315 316 0.685097 CGGTTCTCTCCACTTTCCCA 59.315 55.000 0.00 0.00 0.00 4.37
316 317 1.608283 CGGTTCTCTCCACTTTCCCAC 60.608 57.143 0.00 0.00 0.00 4.61
317 318 1.420138 GGTTCTCTCCACTTTCCCACA 59.580 52.381 0.00 0.00 0.00 4.17
318 319 2.495084 GTTCTCTCCACTTTCCCACAC 58.505 52.381 0.00 0.00 0.00 3.82
319 320 1.801242 TCTCTCCACTTTCCCACACA 58.199 50.000 0.00 0.00 0.00 3.72
320 321 2.123589 TCTCTCCACTTTCCCACACAA 58.876 47.619 0.00 0.00 0.00 3.33
321 322 2.711009 TCTCTCCACTTTCCCACACAAT 59.289 45.455 0.00 0.00 0.00 2.71
322 323 3.907474 TCTCTCCACTTTCCCACACAATA 59.093 43.478 0.00 0.00 0.00 1.90
323 324 4.536090 TCTCTCCACTTTCCCACACAATAT 59.464 41.667 0.00 0.00 0.00 1.28
324 325 5.724370 TCTCTCCACTTTCCCACACAATATA 59.276 40.000 0.00 0.00 0.00 0.86
325 326 6.386927 TCTCTCCACTTTCCCACACAATATAT 59.613 38.462 0.00 0.00 0.00 0.86
326 327 6.356556 TCTCCACTTTCCCACACAATATATG 58.643 40.000 0.00 0.00 0.00 1.78
327 328 6.069673 TCTCCACTTTCCCACACAATATATGT 60.070 38.462 0.00 0.00 45.34 2.29
328 329 7.126573 TCTCCACTTTCCCACACAATATATGTA 59.873 37.037 0.00 0.00 41.46 2.29
329 330 7.634718 TCCACTTTCCCACACAATATATGTAA 58.365 34.615 0.00 0.00 41.46 2.41
378 384 8.615211 ACAGTACGTATATTGTGTTTCGATCTA 58.385 33.333 0.00 0.00 30.56 1.98
379 385 9.608617 CAGTACGTATATTGTGTTTCGATCTAT 57.391 33.333 0.00 0.00 0.00 1.98
382 388 8.651200 ACGTATATTGTGTTTCGATCTATACG 57.349 34.615 17.07 17.07 38.96 3.06
383 389 8.498358 ACGTATATTGTGTTTCGATCTATACGA 58.502 33.333 21.96 1.74 37.21 3.43
384 390 9.486857 CGTATATTGTGTTTCGATCTATACGAT 57.513 33.333 15.04 6.78 37.21 3.73
387 393 6.822073 TTGTGTTTCGATCTATACGATTGG 57.178 37.500 0.00 0.00 39.45 3.16
388 394 5.286438 TGTGTTTCGATCTATACGATTGGG 58.714 41.667 0.00 0.00 39.45 4.12
389 395 4.684703 GTGTTTCGATCTATACGATTGGGG 59.315 45.833 0.00 0.00 39.45 4.96
390 396 4.585581 TGTTTCGATCTATACGATTGGGGA 59.414 41.667 0.00 0.00 39.45 4.81
391 397 5.162075 GTTTCGATCTATACGATTGGGGAG 58.838 45.833 0.00 0.00 39.45 4.30
392 398 2.753452 TCGATCTATACGATTGGGGAGC 59.247 50.000 0.00 0.00 34.74 4.70
393 399 2.492088 CGATCTATACGATTGGGGAGCA 59.508 50.000 0.00 0.00 30.84 4.26
394 400 3.428180 CGATCTATACGATTGGGGAGCAG 60.428 52.174 0.00 0.00 30.84 4.24
395 401 1.618837 TCTATACGATTGGGGAGCAGC 59.381 52.381 0.00 0.00 0.00 5.25
396 402 1.620819 CTATACGATTGGGGAGCAGCT 59.379 52.381 0.00 0.00 0.00 4.24
397 403 0.394565 ATACGATTGGGGAGCAGCTC 59.605 55.000 14.69 14.69 0.00 4.09
405 411 4.154347 GGAGCAGCTCCCCTGACG 62.154 72.222 29.22 0.00 44.36 4.35
406 412 3.386237 GAGCAGCTCCCCTGACGT 61.386 66.667 11.84 0.00 44.64 4.34
407 413 2.037367 AGCAGCTCCCCTGACGTA 59.963 61.111 0.00 0.00 44.64 3.57
408 414 2.184579 GCAGCTCCCCTGACGTAC 59.815 66.667 0.00 0.00 44.64 3.67
409 415 2.352032 GCAGCTCCCCTGACGTACT 61.352 63.158 0.00 0.00 44.64 2.73
410 416 1.513158 CAGCTCCCCTGACGTACTG 59.487 63.158 0.00 0.00 44.64 2.74
411 417 2.184579 GCTCCCCTGACGTACTGC 59.815 66.667 0.00 0.00 0.00 4.40
412 418 2.646175 GCTCCCCTGACGTACTGCA 61.646 63.158 0.00 0.00 0.00 4.41
413 419 1.215647 CTCCCCTGACGTACTGCAC 59.784 63.158 0.00 0.00 0.00 4.57
414 420 1.532078 TCCCCTGACGTACTGCACA 60.532 57.895 0.00 0.00 0.00 4.57
415 421 0.902984 TCCCCTGACGTACTGCACAT 60.903 55.000 0.00 0.00 0.00 3.21
416 422 0.740868 CCCCTGACGTACTGCACATG 60.741 60.000 0.00 0.00 0.00 3.21
417 423 1.361668 CCCTGACGTACTGCACATGC 61.362 60.000 0.00 0.00 42.50 4.06
418 424 1.361668 CCTGACGTACTGCACATGCC 61.362 60.000 0.49 0.00 41.18 4.40
419 425 1.686566 CTGACGTACTGCACATGCCG 61.687 60.000 0.49 0.00 41.18 5.69
420 426 1.736645 GACGTACTGCACATGCCGT 60.737 57.895 6.19 6.19 41.33 5.68
421 427 1.289109 GACGTACTGCACATGCCGTT 61.289 55.000 6.24 0.00 39.23 4.44
422 428 1.132436 CGTACTGCACATGCCGTTG 59.868 57.895 6.24 0.00 39.23 4.10
423 429 1.501741 GTACTGCACATGCCGTTGG 59.498 57.895 6.24 0.00 39.23 3.77
424 430 1.673993 TACTGCACATGCCGTTGGG 60.674 57.895 6.24 0.00 39.23 4.12
425 431 3.751246 CTGCACATGCCGTTGGGG 61.751 66.667 0.49 0.00 41.18 4.96
434 440 4.263572 CCGTTGGGGCCACTGACA 62.264 66.667 6.53 0.00 0.00 3.58
435 441 2.034066 CGTTGGGGCCACTGACAT 59.966 61.111 6.53 0.00 0.00 3.06
436 442 2.334946 CGTTGGGGCCACTGACATG 61.335 63.158 6.53 0.00 0.00 3.21
437 443 1.228552 GTTGGGGCCACTGACATGT 60.229 57.895 6.53 0.00 0.00 3.21
438 444 1.228521 TTGGGGCCACTGACATGTG 60.229 57.895 6.53 0.00 37.66 3.21
444 450 3.991999 CACTGACATGTGGGCCTG 58.008 61.111 1.15 0.00 34.56 4.85
445 451 1.376086 CACTGACATGTGGGCCTGA 59.624 57.895 1.15 0.00 34.56 3.86
446 452 0.034767 CACTGACATGTGGGCCTGAT 60.035 55.000 1.15 0.00 34.56 2.90
447 453 0.700564 ACTGACATGTGGGCCTGATT 59.299 50.000 1.15 0.00 0.00 2.57
448 454 1.340405 ACTGACATGTGGGCCTGATTC 60.340 52.381 1.15 0.00 0.00 2.52
449 455 0.034186 TGACATGTGGGCCTGATTCC 60.034 55.000 1.15 0.00 0.00 3.01
450 456 0.753111 GACATGTGGGCCTGATTCCC 60.753 60.000 1.15 0.00 44.17 3.97
451 457 1.825191 CATGTGGGCCTGATTCCCG 60.825 63.158 4.53 0.00 46.92 5.14
452 458 3.060614 ATGTGGGCCTGATTCCCGG 62.061 63.158 4.53 0.00 46.92 5.73
458 464 4.883354 CCTGATTCCCGGCAGGCC 62.883 72.222 12.24 0.00 44.53 5.19
459 465 4.883354 CTGATTCCCGGCAGGCCC 62.883 72.222 0.00 0.00 35.76 5.80
476 482 2.425592 CACCTGTCAGTGGCCGAA 59.574 61.111 0.00 0.00 33.95 4.30
477 483 1.961277 CACCTGTCAGTGGCCGAAC 60.961 63.158 0.00 0.00 33.95 3.95
478 484 2.425592 CCTGTCAGTGGCCGAACA 59.574 61.111 0.00 0.00 0.00 3.18
479 485 1.669115 CCTGTCAGTGGCCGAACAG 60.669 63.158 15.79 15.79 39.04 3.16
480 486 1.069765 CTGTCAGTGGCCGAACAGT 59.930 57.895 14.93 0.00 35.51 3.55
481 487 0.317160 CTGTCAGTGGCCGAACAGTA 59.683 55.000 14.93 0.00 35.51 2.74
482 488 0.032952 TGTCAGTGGCCGAACAGTAC 59.967 55.000 0.00 0.00 0.00 2.73
483 489 0.669625 GTCAGTGGCCGAACAGTACC 60.670 60.000 0.00 0.00 0.00 3.34
484 490 1.375523 CAGTGGCCGAACAGTACCC 60.376 63.158 0.00 0.00 0.00 3.69
485 491 1.535687 AGTGGCCGAACAGTACCCT 60.536 57.895 0.00 0.00 0.00 4.34
486 492 1.375523 GTGGCCGAACAGTACCCTG 60.376 63.158 0.00 0.00 44.68 4.45
487 493 2.436115 GGCCGAACAGTACCCTGC 60.436 66.667 0.00 0.00 42.81 4.85
488 494 2.663196 GCCGAACAGTACCCTGCT 59.337 61.111 0.00 0.00 42.81 4.24
489 495 1.741770 GCCGAACAGTACCCTGCTG 60.742 63.158 0.00 0.00 42.81 4.41
490 496 1.741770 CCGAACAGTACCCTGCTGC 60.742 63.158 0.00 0.00 42.81 5.25
491 497 1.005037 CGAACAGTACCCTGCTGCA 60.005 57.895 0.88 0.88 42.81 4.41
492 498 1.291877 CGAACAGTACCCTGCTGCAC 61.292 60.000 0.00 0.00 42.81 4.57
493 499 1.291877 GAACAGTACCCTGCTGCACG 61.292 60.000 0.00 0.00 42.81 5.34
494 500 2.434884 CAGTACCCTGCTGCACGG 60.435 66.667 14.90 14.90 0.00 4.94
495 501 4.394712 AGTACCCTGCTGCACGGC 62.395 66.667 16.17 2.97 0.00 5.68
496 502 4.697756 GTACCCTGCTGCACGGCA 62.698 66.667 16.17 3.76 40.15 5.69
509 515 4.933064 CGGCAGAGGATCCGCGTC 62.933 72.222 10.07 5.91 39.14 5.19
510 516 4.593864 GGCAGAGGATCCGCGTCC 62.594 72.222 10.07 11.09 38.62 4.79
542 558 3.058160 GCAGTGCTCCAACGCCAT 61.058 61.111 8.18 0.00 0.00 4.40
574 590 5.260424 TCCTACCAACATTTGCACACATAT 58.740 37.500 0.00 0.00 0.00 1.78
612 628 9.236006 ACTAGTCATCTGCATTTTGAAATACTT 57.764 29.630 0.00 0.00 0.00 2.24
772 791 6.014584 TCTGTGCACTCCTTATCTAAAACAGA 60.015 38.462 19.41 3.41 38.30 3.41
1236 1268 1.618837 GAGCTGGCCTATGATACCGAA 59.381 52.381 3.32 0.00 0.00 4.30
1336 1368 0.246360 TCGCTTCCTCAAATCGCTCA 59.754 50.000 0.00 0.00 0.00 4.26
1433 1465 5.474578 TGTTACAAGCTGAGTGAGATTCT 57.525 39.130 2.51 0.00 0.00 2.40
1435 1467 2.697654 ACAAGCTGAGTGAGATTCTGC 58.302 47.619 0.00 0.00 39.09 4.26
2098 2851 6.981762 TGAGTACTAGTAGACTTGTGTAGC 57.018 41.667 1.87 0.00 34.09 3.58
2554 3406 4.567987 AGGAGGAGTGGGAGAAGATTAT 57.432 45.455 0.00 0.00 0.00 1.28
3041 3893 5.118990 GCACAAGAAGATCTAAGCCATGTA 58.881 41.667 0.00 0.00 0.00 2.29
3073 3925 3.499918 ACAGTAACATCTTCAGCTTGCAC 59.500 43.478 0.00 0.00 0.00 4.57
3080 3932 2.309613 TCTTCAGCTTGCACCAAACAT 58.690 42.857 0.00 0.00 0.00 2.71
3188 4040 8.207545 AGTATTGGCAAATTGTTCCAACTAAAA 58.792 29.630 3.01 0.00 42.02 1.52
3422 4283 5.048507 GGCTTTAGTATTACCAAGAGTCCG 58.951 45.833 7.31 0.00 0.00 4.79
3814 4684 7.558444 TCACCTTGTACTGTGGTTTAGAAAAAT 59.442 33.333 9.73 0.00 33.29 1.82
3973 4849 9.887629 AAATGTATCAATGGCAAAAACATATGA 57.112 25.926 10.38 0.00 0.00 2.15
4046 4922 0.179094 TTGACAATAGGGGCGCTACG 60.179 55.000 13.97 10.46 0.00 3.51
4120 4996 3.885976 TCCAAACCATCCCACAGTTAA 57.114 42.857 0.00 0.00 0.00 2.01
4135 5017 8.778059 TCCCACAGTTAATATTTATGAGGAGTT 58.222 33.333 0.00 0.00 0.00 3.01
4218 5100 5.431765 ACGCTGATGAGAATTAAGATGGTT 58.568 37.500 0.00 0.00 0.00 3.67
4220 5102 6.703607 ACGCTGATGAGAATTAAGATGGTTAG 59.296 38.462 0.00 0.00 0.00 2.34
4224 5106 9.770097 CTGATGAGAATTAAGATGGTTAGCTTA 57.230 33.333 0.00 0.00 33.89 3.09
4238 5120 4.201950 GGTTAGCTTACGAGTGGAACGATA 60.202 45.833 0.00 0.00 45.86 2.92
4280 5162 9.427821 AAGAGGTATTAATACAGACTGTGATCT 57.572 33.333 23.59 9.81 34.98 2.75
4298 5180 7.806690 TGTGATCTTTCTTTCTTTTACCATCG 58.193 34.615 0.00 0.00 0.00 3.84
4315 5197 3.787634 CCATCGAAATGCATCTTTTGTCG 59.212 43.478 0.00 3.28 0.00 4.35
4319 5201 4.909305 TCGAAATGCATCTTTTGTCGAAAC 59.091 37.500 0.00 0.00 0.00 2.78
4341 5223 8.607441 AAACCTGATTTTGGCTTCTAAAATTC 57.393 30.769 3.13 0.00 37.73 2.17
4414 5296 2.012673 CTTGGAGTGGCATACTGAAGC 58.987 52.381 0.00 0.00 40.53 3.86
4506 5391 6.304788 GTTGCTAATTGCTACGTTGAATTG 57.695 37.500 0.00 2.20 43.37 2.32
4509 5394 2.939460 ATTGCTACGTTGAATTGCCC 57.061 45.000 0.00 0.00 0.00 5.36
4558 5443 5.431765 ACATAATCTCTCTGTTTCGGCATT 58.568 37.500 0.00 0.00 0.00 3.56
4586 5471 5.366460 AGTGTGGATTATCTCTGCTGAATG 58.634 41.667 0.00 0.00 0.00 2.67
4606 5499 9.791820 CTGAATGCTCTTCTATATAGAGATGTG 57.208 37.037 12.16 8.43 41.32 3.21
4631 5524 0.179073 GATCCTGGCTTTGCTCGCTA 60.179 55.000 0.00 0.00 0.00 4.26
4697 5603 5.070313 TCAATTGCCTTTCTTGCTTACCTTT 59.930 36.000 0.00 0.00 0.00 3.11
4718 5624 5.784750 TTTGCGATTATGACTCAAGAGTG 57.215 39.130 7.57 0.00 42.66 3.51
4810 5716 9.797556 TGAATTCTGAATTATTTCTGCTGAATG 57.202 29.630 15.14 0.00 32.50 2.67
4814 5720 7.478322 TCTGAATTATTTCTGCTGAATGCTTC 58.522 34.615 6.88 8.56 43.37 3.86
4815 5721 6.567050 TGAATTATTTCTGCTGAATGCTTCC 58.433 36.000 6.88 0.00 43.37 3.46
4834 5740 6.040054 TGCTTCCTGATGATGGAAATGTAATG 59.960 38.462 0.00 0.00 42.29 1.90
4866 5772 1.691196 TGCTTGCTTACTTGCTTGGT 58.309 45.000 0.00 0.00 0.00 3.67
4889 5795 2.945008 CCTGTTTGTCTGAGCAAGTTGA 59.055 45.455 7.16 0.00 0.00 3.18
4892 5798 5.239306 CCTGTTTGTCTGAGCAAGTTGAATA 59.761 40.000 7.16 0.00 0.00 1.75
4899 5805 5.639506 GTCTGAGCAAGTTGAATAGCTGTAA 59.360 40.000 7.16 0.00 37.48 2.41
4903 5809 4.627467 AGCAAGTTGAATAGCTGTAAGTCG 59.373 41.667 7.16 0.00 35.72 4.18
4917 5823 5.176958 GCTGTAAGTCGTTGCTTCTTCTTTA 59.823 40.000 0.00 0.00 35.30 1.85
4926 5832 8.217778 GTCGTTGCTTCTTCTTTATATCTATGC 58.782 37.037 0.00 0.00 0.00 3.14
5004 7425 8.944029 ACTGTAGATGAAACTGAAGATGAATTG 58.056 33.333 0.00 0.00 0.00 2.32
5006 7427 6.205101 AGATGAAACTGAAGATGAATTGCC 57.795 37.500 0.00 0.00 0.00 4.52
5016 7437 4.210724 AGATGAATTGCCATTTGGTTGG 57.789 40.909 0.00 0.00 39.94 3.77
5041 7462 2.473984 GCTTCAAAACACAAGCTGCATC 59.526 45.455 1.02 0.00 41.61 3.91
5042 7463 3.797865 GCTTCAAAACACAAGCTGCATCT 60.798 43.478 1.02 0.00 41.61 2.90
5043 7464 3.358707 TCAAAACACAAGCTGCATCTG 57.641 42.857 1.02 0.00 0.00 2.90
5044 7465 1.790623 CAAAACACAAGCTGCATCTGC 59.209 47.619 1.02 0.00 42.50 4.26
5178 7599 2.123251 ATCTCCGGCCGATCCACT 60.123 61.111 30.73 2.48 34.01 4.00
5179 7600 2.203771 ATCTCCGGCCGATCCACTC 61.204 63.158 30.73 0.00 34.01 3.51
5180 7601 3.917760 CTCCGGCCGATCCACTCC 61.918 72.222 30.73 0.00 34.01 3.85
5181 7602 4.458829 TCCGGCCGATCCACTCCT 62.459 66.667 30.73 0.00 34.01 3.69
5182 7603 3.917760 CCGGCCGATCCACTCCTC 61.918 72.222 30.73 0.00 34.01 3.71
5183 7604 4.271816 CGGCCGATCCACTCCTCG 62.272 72.222 24.07 0.00 34.01 4.63
5184 7605 4.593864 GGCCGATCCACTCCTCGC 62.594 72.222 0.00 0.00 33.63 5.03
5185 7606 4.933064 GCCGATCCACTCCTCGCG 62.933 72.222 0.00 0.00 33.63 5.87
5186 7607 4.271816 CCGATCCACTCCTCGCGG 62.272 72.222 6.13 0.00 33.63 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.118112 TCCATGATCTCTCCCTTTCAAGC 60.118 47.826 0.00 0.00 0.00 4.01
1 2 4.163839 ACTCCATGATCTCTCCCTTTCAAG 59.836 45.833 0.00 0.00 0.00 3.02
28 29 1.321474 CGCCACTCCCATATTTGCAT 58.679 50.000 0.00 0.00 0.00 3.96
41 42 3.030652 CAAAAAGACGCCGCCACT 58.969 55.556 0.00 0.00 0.00 4.00
265 266 4.430441 AGAGGAAAGGAATAGGTGAGTGT 58.570 43.478 0.00 0.00 0.00 3.55
273 274 5.115480 GTCAGAGCAAGAGGAAAGGAATAG 58.885 45.833 0.00 0.00 0.00 1.73
284 285 1.543802 AGAGAACCGTCAGAGCAAGAG 59.456 52.381 0.00 0.00 0.00 2.85
296 297 0.685097 TGGGAAAGTGGAGAGAACCG 59.315 55.000 0.00 0.00 0.00 4.44
298 299 2.158813 TGTGTGGGAAAGTGGAGAGAAC 60.159 50.000 0.00 0.00 0.00 3.01
299 300 2.123589 TGTGTGGGAAAGTGGAGAGAA 58.876 47.619 0.00 0.00 0.00 2.87
300 301 1.801242 TGTGTGGGAAAGTGGAGAGA 58.199 50.000 0.00 0.00 0.00 3.10
301 302 2.638480 TTGTGTGGGAAAGTGGAGAG 57.362 50.000 0.00 0.00 0.00 3.20
302 303 4.927267 ATATTGTGTGGGAAAGTGGAGA 57.073 40.909 0.00 0.00 0.00 3.71
303 304 6.122277 ACATATATTGTGTGGGAAAGTGGAG 58.878 40.000 0.00 0.00 37.11 3.86
304 305 6.073447 ACATATATTGTGTGGGAAAGTGGA 57.927 37.500 0.00 0.00 37.11 4.02
305 306 7.873719 TTACATATATTGTGTGGGAAAGTGG 57.126 36.000 4.26 0.00 39.48 4.00
306 307 8.735315 TGTTTACATATATTGTGTGGGAAAGTG 58.265 33.333 4.26 0.00 39.48 3.16
307 308 8.871629 TGTTTACATATATTGTGTGGGAAAGT 57.128 30.769 4.26 0.00 39.48 2.66
311 312 9.693739 AGAATTGTTTACATATATTGTGTGGGA 57.306 29.630 4.26 0.00 39.48 4.37
312 313 9.950680 GAGAATTGTTTACATATATTGTGTGGG 57.049 33.333 4.26 0.00 39.48 4.61
322 323 9.178758 GGAAAGTGGAGAGAATTGTTTACATAT 57.821 33.333 0.00 0.00 0.00 1.78
323 324 7.610305 GGGAAAGTGGAGAGAATTGTTTACATA 59.390 37.037 0.00 0.00 0.00 2.29
324 325 6.434340 GGGAAAGTGGAGAGAATTGTTTACAT 59.566 38.462 0.00 0.00 0.00 2.29
325 326 5.768164 GGGAAAGTGGAGAGAATTGTTTACA 59.232 40.000 0.00 0.00 0.00 2.41
326 327 5.768164 TGGGAAAGTGGAGAGAATTGTTTAC 59.232 40.000 0.00 0.00 0.00 2.01
327 328 5.768164 GTGGGAAAGTGGAGAGAATTGTTTA 59.232 40.000 0.00 0.00 0.00 2.01
328 329 4.584743 GTGGGAAAGTGGAGAGAATTGTTT 59.415 41.667 0.00 0.00 0.00 2.83
329 330 4.145052 GTGGGAAAGTGGAGAGAATTGTT 58.855 43.478 0.00 0.00 0.00 2.83
378 384 0.394565 GAGCTGCTCCCCAATCGTAT 59.605 55.000 18.80 0.00 0.00 3.06
379 385 1.686325 GGAGCTGCTCCCCAATCGTA 61.686 60.000 33.62 0.00 44.36 3.43
380 386 2.586792 GAGCTGCTCCCCAATCGT 59.413 61.111 18.80 0.00 0.00 3.73
381 387 2.203126 GGAGCTGCTCCCCAATCG 60.203 66.667 33.62 0.00 44.36 3.34
389 395 2.052690 TACGTCAGGGGAGCTGCTC 61.053 63.158 21.17 21.17 0.00 4.26
390 396 2.037367 TACGTCAGGGGAGCTGCT 59.963 61.111 0.00 0.00 0.00 4.24
391 397 2.184579 GTACGTCAGGGGAGCTGC 59.815 66.667 0.00 0.00 0.00 5.25
392 398 1.513158 CAGTACGTCAGGGGAGCTG 59.487 63.158 0.00 0.00 0.00 4.24
393 399 2.352032 GCAGTACGTCAGGGGAGCT 61.352 63.158 0.00 0.00 0.00 4.09
394 400 2.184579 GCAGTACGTCAGGGGAGC 59.815 66.667 0.00 0.00 0.00 4.70
395 401 1.215647 GTGCAGTACGTCAGGGGAG 59.784 63.158 0.00 0.00 0.00 4.30
396 402 0.902984 ATGTGCAGTACGTCAGGGGA 60.903 55.000 0.00 0.00 0.00 4.81
397 403 0.740868 CATGTGCAGTACGTCAGGGG 60.741 60.000 0.00 0.00 0.00 4.79
398 404 1.361668 GCATGTGCAGTACGTCAGGG 61.362 60.000 0.00 0.00 41.59 4.45
399 405 1.361668 GGCATGTGCAGTACGTCAGG 61.362 60.000 7.36 0.00 44.36 3.86
400 406 1.686566 CGGCATGTGCAGTACGTCAG 61.687 60.000 7.36 0.00 44.36 3.51
401 407 1.736282 CGGCATGTGCAGTACGTCA 60.736 57.895 7.36 0.00 44.36 4.35
402 408 3.081133 CGGCATGTGCAGTACGTC 58.919 61.111 7.36 0.00 44.36 4.34
408 414 3.751246 CCCCAACGGCATGTGCAG 61.751 66.667 7.36 5.43 44.36 4.41
417 423 3.567579 ATGTCAGTGGCCCCAACGG 62.568 63.158 0.00 0.00 0.00 4.44
418 424 2.034066 ATGTCAGTGGCCCCAACG 59.966 61.111 0.00 0.00 0.00 4.10
419 425 1.228552 ACATGTCAGTGGCCCCAAC 60.229 57.895 0.00 0.00 0.00 3.77
420 426 1.228521 CACATGTCAGTGGCCCCAA 60.229 57.895 0.00 0.00 35.88 4.12
421 427 2.435663 CACATGTCAGTGGCCCCA 59.564 61.111 0.00 0.00 35.88 4.96
427 433 0.034767 ATCAGGCCCACATGTCAGTG 60.035 55.000 0.00 0.00 39.21 3.66
428 434 0.700564 AATCAGGCCCACATGTCAGT 59.299 50.000 0.00 0.00 0.00 3.41
429 435 1.386533 GAATCAGGCCCACATGTCAG 58.613 55.000 0.00 0.00 0.00 3.51
430 436 0.034186 GGAATCAGGCCCACATGTCA 60.034 55.000 0.00 0.00 0.00 3.58
431 437 0.753111 GGGAATCAGGCCCACATGTC 60.753 60.000 0.00 0.00 45.31 3.06
432 438 1.307647 GGGAATCAGGCCCACATGT 59.692 57.895 0.00 0.00 45.31 3.21
433 439 1.825191 CGGGAATCAGGCCCACATG 60.825 63.158 0.00 0.00 46.36 3.21
434 440 2.597340 CGGGAATCAGGCCCACAT 59.403 61.111 0.00 0.00 46.36 3.21
435 441 3.727258 CCGGGAATCAGGCCCACA 61.727 66.667 0.00 0.00 46.36 4.17
442 448 4.883354 GGGCCTGCCGGGAATCAG 62.883 72.222 2.18 0.96 37.23 2.90
459 465 1.961277 GTTCGGCCACTGACAGGTG 60.961 63.158 2.24 2.99 37.00 4.00
460 466 2.383245 CTGTTCGGCCACTGACAGGT 62.383 60.000 2.24 0.00 36.68 4.00
461 467 1.669115 CTGTTCGGCCACTGACAGG 60.669 63.158 2.24 0.00 36.68 4.00
462 468 0.317160 TACTGTTCGGCCACTGACAG 59.683 55.000 18.04 18.04 43.81 3.51
463 469 0.032952 GTACTGTTCGGCCACTGACA 59.967 55.000 2.24 0.02 0.00 3.58
464 470 0.669625 GGTACTGTTCGGCCACTGAC 60.670 60.000 2.24 0.00 0.00 3.51
465 471 1.669440 GGTACTGTTCGGCCACTGA 59.331 57.895 2.24 0.00 0.00 3.41
466 472 1.375523 GGGTACTGTTCGGCCACTG 60.376 63.158 2.24 0.43 0.00 3.66
467 473 1.535687 AGGGTACTGTTCGGCCACT 60.536 57.895 2.24 0.00 0.00 4.00
468 474 1.375523 CAGGGTACTGTTCGGCCAC 60.376 63.158 2.24 0.00 39.92 5.01
469 475 3.065306 CAGGGTACTGTTCGGCCA 58.935 61.111 2.24 0.00 39.92 5.36
470 476 2.436115 GCAGGGTACTGTTCGGCC 60.436 66.667 0.00 0.00 46.62 6.13
471 477 1.741770 CAGCAGGGTACTGTTCGGC 60.742 63.158 0.00 0.00 46.62 5.54
472 478 1.741770 GCAGCAGGGTACTGTTCGG 60.742 63.158 0.00 0.00 46.62 4.30
473 479 1.005037 TGCAGCAGGGTACTGTTCG 60.005 57.895 0.00 0.00 46.62 3.95
474 480 1.291877 CGTGCAGCAGGGTACTGTTC 61.292 60.000 7.24 0.00 46.62 3.18
475 481 1.301716 CGTGCAGCAGGGTACTGTT 60.302 57.895 7.24 0.00 46.62 3.16
476 482 2.343758 CGTGCAGCAGGGTACTGT 59.656 61.111 7.24 0.00 46.62 3.55
478 484 4.394712 GCCGTGCAGCAGGGTACT 62.395 66.667 30.20 0.00 40.97 2.73
479 485 4.697756 TGCCGTGCAGCAGGGTAC 62.698 66.667 30.20 17.80 40.97 3.34
488 494 4.147449 CGGATCCTCTGCCGTGCA 62.147 66.667 10.75 0.00 42.49 4.57
492 498 4.933064 GACGCGGATCCTCTGCCG 62.933 72.222 12.47 7.08 45.71 5.69
493 499 4.593864 GGACGCGGATCCTCTGCC 62.594 72.222 12.47 2.02 45.71 4.85
494 500 1.806461 TATGGACGCGGATCCTCTGC 61.806 60.000 12.47 5.03 45.04 4.26
495 501 0.039074 GTATGGACGCGGATCCTCTG 60.039 60.000 12.47 1.52 39.75 3.35
496 502 1.516365 CGTATGGACGCGGATCCTCT 61.516 60.000 12.47 3.96 43.21 3.69
497 503 1.081376 CGTATGGACGCGGATCCTC 60.081 63.158 12.47 0.00 43.21 3.71
498 504 3.039988 CGTATGGACGCGGATCCT 58.960 61.111 12.47 2.18 43.21 3.24
507 513 0.818040 GCCCACCCAATCGTATGGAC 60.818 60.000 10.24 0.00 43.54 4.02
508 514 1.275421 TGCCCACCCAATCGTATGGA 61.275 55.000 10.24 0.00 43.54 3.41
509 515 0.819259 CTGCCCACCCAATCGTATGG 60.819 60.000 2.74 2.74 40.35 2.74
510 516 0.107214 ACTGCCCACCCAATCGTATG 60.107 55.000 0.00 0.00 0.00 2.39
612 628 7.406031 AATTCTTACACTATGAGACGGAGAA 57.594 36.000 0.00 0.00 0.00 2.87
681 697 8.975295 GTTACTTATTAAGAAGTACTCCCTCCA 58.025 37.037 19.62 3.09 40.72 3.86
772 791 6.883217 GGATCAAGGACAATGATATACATGCT 59.117 38.462 0.00 0.00 37.64 3.79
842 864 3.259207 CGCAGCAAGCAATAATAGGTC 57.741 47.619 0.00 0.00 46.13 3.85
1236 1268 3.624861 GGATGAACTTGTCGATGCAATCT 59.375 43.478 0.00 0.00 42.58 2.40
1336 1368 1.474077 GGCAATTCCACAGCGAGAATT 59.526 47.619 0.00 0.00 42.08 2.17
1435 1467 2.816958 ATGCTCGGTCTTGCTGCG 60.817 61.111 0.00 0.00 0.00 5.18
1844 1883 9.974980 TTGTAAGGAATGTTCTGAAAATTAACC 57.025 29.630 5.80 4.68 0.00 2.85
2554 3406 4.701651 CCAGTGCAGAACCAATTGATCTTA 59.298 41.667 7.12 0.00 0.00 2.10
3041 3893 5.416013 TGAAGATGTTACTGTCAGAGATCGT 59.584 40.000 6.91 0.00 0.00 3.73
3073 3925 3.256631 AGCAAGACTAGGCAAATGTTTGG 59.743 43.478 0.00 0.00 38.57 3.28
3080 3932 6.892658 TCAAATTTAGCAAGACTAGGCAAA 57.107 33.333 0.00 0.00 30.79 3.68
3188 4040 3.262405 TCGTGGCTGGAAAGTTTAGGTAT 59.738 43.478 0.00 0.00 0.00 2.73
3422 4283 3.112205 ATCCTCCACCGCATCTGCC 62.112 63.158 0.00 0.00 37.91 4.85
3780 4650 5.104652 ACCACAGTACAAGGTGAAGTAAAGT 60.105 40.000 12.26 0.29 37.18 2.66
3814 4684 6.012245 TCGGACTATAACCCTATCATCAGGTA 60.012 42.308 0.00 0.00 33.44 3.08
3947 4823 9.887629 TCATATGTTTTTGCCATTGATACATTT 57.112 25.926 1.90 0.00 0.00 2.32
3973 4849 6.599445 AGATGCTCAATGCCTAAATAGAAGT 58.401 36.000 0.00 0.00 42.00 3.01
4046 4922 0.742635 CAGCCTTTCTCTCGGAAGGC 60.743 60.000 15.04 15.04 42.78 4.35
4135 5017 9.072375 CAGTATCTTCACTGTCCTCTTCATATA 57.928 37.037 0.00 0.00 40.89 0.86
4136 5018 7.015098 CCAGTATCTTCACTGTCCTCTTCATAT 59.985 40.741 2.86 0.00 43.68 1.78
4218 5100 4.194640 AGTATCGTTCCACTCGTAAGCTA 58.805 43.478 0.00 0.00 37.18 3.32
4220 5102 3.181503 TGAGTATCGTTCCACTCGTAAGC 60.182 47.826 0.00 0.00 43.38 3.09
4224 5106 3.014623 TGATGAGTATCGTTCCACTCGT 58.985 45.455 0.00 0.00 43.38 4.18
4238 5120 2.551721 CCTCTTGCAGTTGGTGATGAGT 60.552 50.000 0.00 0.00 0.00 3.41
4280 5162 7.429633 TGCATTTCGATGGTAAAAGAAAGAAA 58.570 30.769 0.00 0.00 36.26 2.52
4298 5180 5.117592 CAGGTTTCGACAAAAGATGCATTTC 59.882 40.000 0.00 0.00 0.00 2.17
4315 5197 8.607441 AATTTTAGAAGCCAAAATCAGGTTTC 57.393 30.769 0.00 0.00 43.99 2.78
4319 5201 8.782339 AATGAATTTTAGAAGCCAAAATCAGG 57.218 30.769 0.00 0.00 35.15 3.86
4341 5223 6.539826 TCATCCTATATATCAGCGCCAAAATG 59.460 38.462 2.29 0.00 0.00 2.32
4414 5296 4.460382 TCAGCTTCTTATTTTCAGGCCTTG 59.540 41.667 0.00 0.00 0.00 3.61
4552 5437 2.593468 ATCCACACTCCCGAATGCCG 62.593 60.000 0.00 0.00 38.18 5.69
4558 5443 2.959030 CAGAGATAATCCACACTCCCGA 59.041 50.000 0.00 0.00 0.00 5.14
4606 5499 3.188048 CGAGCAAAGCCAGGATCAATATC 59.812 47.826 0.00 0.00 0.00 1.63
4615 5508 0.809241 CTCTAGCGAGCAAAGCCAGG 60.809 60.000 0.00 0.00 34.64 4.45
4631 5524 2.827921 GGTCCCAAATGCAAACATCTCT 59.172 45.455 0.00 0.00 34.62 3.10
4674 5580 4.525912 AGGTAAGCAAGAAAGGCAATTG 57.474 40.909 0.00 0.00 0.00 2.32
4675 5581 5.551305 AAAGGTAAGCAAGAAAGGCAATT 57.449 34.783 0.00 0.00 0.00 2.32
4697 5603 5.072040 TCACTCTTGAGTCATAATCGCAA 57.928 39.130 0.00 0.00 0.00 4.85
4758 5664 8.547967 AATCGACATTACAATAGTGAACAACT 57.452 30.769 0.00 0.00 43.40 3.16
4761 5667 8.541133 TCAAATCGACATTACAATAGTGAACA 57.459 30.769 0.00 0.00 0.00 3.18
4810 5716 6.040166 ACATTACATTTCCATCATCAGGAAGC 59.960 38.462 0.00 0.00 45.25 3.86
4814 5720 7.337480 TCAACATTACATTTCCATCATCAGG 57.663 36.000 0.00 0.00 0.00 3.86
4815 5721 9.459640 GAATCAACATTACATTTCCATCATCAG 57.540 33.333 0.00 0.00 0.00 2.90
4834 5740 4.762956 AAGCAAGCAAGAGAGAATCAAC 57.237 40.909 0.00 0.00 37.82 3.18
4866 5772 3.838244 ACTTGCTCAGACAAACAGGTA 57.162 42.857 0.00 0.00 0.00 3.08
4889 5795 4.822026 AGAAGCAACGACTTACAGCTATT 58.178 39.130 0.00 0.00 34.66 1.73
4892 5798 2.821991 AGAAGCAACGACTTACAGCT 57.178 45.000 0.00 0.00 37.08 4.24
4899 5805 9.469807 CATAGATATAAAGAAGAAGCAACGACT 57.530 33.333 0.00 0.00 0.00 4.18
4903 5809 8.502387 CCAGCATAGATATAAAGAAGAAGCAAC 58.498 37.037 0.00 0.00 0.00 4.17
4917 5823 7.761981 ACCTTATCATTCCCAGCATAGATAT 57.238 36.000 0.00 0.00 0.00 1.63
4926 5832 6.263168 GGACATGTAAACCTTATCATTCCCAG 59.737 42.308 0.00 0.00 0.00 4.45
4937 5843 4.469657 TGCTTTCAGGACATGTAAACCTT 58.530 39.130 0.00 0.00 31.06 3.50
4977 5883 7.895975 TTCATCTTCAGTTTCATCTACAGTG 57.104 36.000 0.00 0.00 0.00 3.66
4979 5885 7.909121 GCAATTCATCTTCAGTTTCATCTACAG 59.091 37.037 0.00 0.00 0.00 2.74
5006 7427 2.459060 TGAAGCATGCCAACCAAATG 57.541 45.000 15.66 0.00 0.00 2.32
5016 7437 2.220133 CAGCTTGTGTTTTGAAGCATGC 59.780 45.455 10.51 10.51 45.88 4.06
5059 7480 6.719365 CAGCACAACTAGCTATTAATTCCAC 58.281 40.000 0.00 0.00 41.14 4.02
5100 7521 0.755686 GACGGCCAGGAAGAGATCAT 59.244 55.000 2.24 0.00 0.00 2.45
5101 7522 0.324738 AGACGGCCAGGAAGAGATCA 60.325 55.000 2.24 0.00 0.00 2.92
5186 7607 3.363844 GAGTCCTGACAGGCGAGGC 62.364 68.421 17.33 4.44 34.61 4.70


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

AutoCloner maintained by Alex Coulton.