Multiple sequence alignment - TraesCS2D01G345700

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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 TraesCS2D01G345700 chr2D 100.000 3960 0 0 1 3960 441577143 441573184 0.000000e+00 7313
1 TraesCS2D01G345700 chr2D 96.748 123 3 1 355 476 377306125 377306003 1.870000e-48 204
2 TraesCS2D01G345700 chr2D 91.781 146 7 4 330 471 579092493 579092349 8.680000e-47 198
3 TraesCS2D01G345700 chr2B 92.395 3537 195 33 469 3960 519187370 519183863 0.000000e+00 4974
4 TraesCS2D01G345700 chr2B 95.787 356 12 2 4 356 519187723 519187368 4.440000e-159 571
5 TraesCS2D01G345700 chr2A 91.631 3549 201 37 469 3960 585214844 585211335 0.000000e+00 4820
6 TraesCS2D01G345700 chr2A 97.191 356 10 0 1 356 585215197 585214842 1.570000e-168 603
7 TraesCS2D01G345700 chr2A 92.647 136 8 2 337 472 206444484 206444617 1.120000e-45 195
8 TraesCS2D01G345700 chr5B 89.202 852 79 8 2134 2975 19791268 19790420 0.000000e+00 1051
9 TraesCS2D01G345700 chr5B 85.271 516 38 7 762 1262 19792789 19792297 7.640000e-137 497
10 TraesCS2D01G345700 chr5B 80.245 653 82 24 1457 2091 19792018 19791395 7.810000e-122 448
11 TraesCS2D01G345700 chr5B 87.179 195 20 4 4 193 19793081 19792887 2.400000e-52 217
12 TraesCS2D01G345700 chr6B 84.549 233 32 4 2728 2958 435832622 435832392 1.110000e-55 228
13 TraesCS2D01G345700 chr6A 84.549 233 32 4 2728 2958 392193952 392193722 1.110000e-55 228
14 TraesCS2D01G345700 chr6D 99.167 120 1 0 353 472 348647336 348647455 2.400000e-52 217
15 TraesCS2D01G345700 chr6D 96.000 125 4 1 348 471 9063698 9063574 6.710000e-48 202
16 TraesCS2D01G345700 chr4A 94.245 139 6 2 338 474 624989661 624989523 1.110000e-50 211
17 TraesCS2D01G345700 chr3D 98.291 117 2 0 355 471 337959509 337959625 5.190000e-49 206
18 TraesCS2D01G345700 chr3B 96.721 122 4 0 355 476 588418291 588418170 1.870000e-48 204
19 TraesCS2D01G345700 chr1B 96.032 126 4 1 348 472 330233056 330232931 1.870000e-48 204


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 TraesCS2D01G345700 chr2D 441573184 441577143 3959 True 7313.00 7313 100.00000 1 3960 1 chr2D.!!$R2 3959
1 TraesCS2D01G345700 chr2B 519183863 519187723 3860 True 2772.50 4974 94.09100 4 3960 2 chr2B.!!$R1 3956
2 TraesCS2D01G345700 chr2A 585211335 585215197 3862 True 2711.50 4820 94.41100 1 3960 2 chr2A.!!$R1 3959
3 TraesCS2D01G345700 chr5B 19790420 19793081 2661 True 553.25 1051 85.47425 4 2975 4 chr5B.!!$R1 2971

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
467 476 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 F
1883 2054 0.035247 AGAAGGCGACCGTCTAGTCT 60.035 55.0 11.34 0.00 40.35 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 2154 0.259065 ACTGGATGCTAGTCGGGAGA 59.741 55.0 0.0 0.0 0.0 3.71 R
3808 4128 0.692476 TGGGTGAGTGGGTGATCAAG 59.308 55.0 0.0 0.0 0.0 3.02 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
86 93 5.631119 TCTGTATTCTAGATGTCGGGATGA 58.369 41.667 0.00 0.00 0.00 2.92
120 127 4.594062 ACCACACACCTGTACCACTAATTA 59.406 41.667 0.00 0.00 0.00 1.40
279 288 2.350192 GGTTGAAAAACCACTTTTGCCG 59.650 45.455 2.75 0.00 42.38 5.69
353 362 8.532341 CGTTTGTAGTATGTATGCTCTAACTTG 58.468 37.037 0.00 0.00 0.00 3.16
354 363 9.367444 GTTTGTAGTATGTATGCTCTAACTTGT 57.633 33.333 0.00 0.00 0.00 3.16
357 366 9.404848 TGTAGTATGTATGCTCTAACTTGTACT 57.595 33.333 0.00 0.00 0.00 2.73
358 367 9.881529 GTAGTATGTATGCTCTAACTTGTACTC 57.118 37.037 0.00 0.00 0.00 2.59
359 368 7.942990 AGTATGTATGCTCTAACTTGTACTCC 58.057 38.462 0.00 0.00 0.00 3.85
360 369 5.593679 TGTATGCTCTAACTTGTACTCCC 57.406 43.478 0.00 0.00 0.00 4.30
361 370 5.269991 TGTATGCTCTAACTTGTACTCCCT 58.730 41.667 0.00 0.00 0.00 4.20
362 371 5.360144 TGTATGCTCTAACTTGTACTCCCTC 59.640 44.000 0.00 0.00 0.00 4.30
363 372 3.097614 TGCTCTAACTTGTACTCCCTCC 58.902 50.000 0.00 0.00 0.00 4.30
364 373 2.099427 GCTCTAACTTGTACTCCCTCCG 59.901 54.545 0.00 0.00 0.00 4.63
365 374 3.354467 CTCTAACTTGTACTCCCTCCGT 58.646 50.000 0.00 0.00 0.00 4.69
366 375 3.350833 TCTAACTTGTACTCCCTCCGTC 58.649 50.000 0.00 0.00 0.00 4.79
367 376 1.264295 AACTTGTACTCCCTCCGTCC 58.736 55.000 0.00 0.00 0.00 4.79
368 377 0.964358 ACTTGTACTCCCTCCGTCCG 60.964 60.000 0.00 0.00 0.00 4.79
369 378 0.679002 CTTGTACTCCCTCCGTCCGA 60.679 60.000 0.00 0.00 0.00 4.55
370 379 0.251297 TTGTACTCCCTCCGTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
371 380 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
372 381 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
373 382 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
374 383 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
375 384 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
376 385 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
377 386 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
378 387 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
379 388 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
380 389 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
381 390 2.928116 CTCCGTCCGAAAATACTTGTCC 59.072 50.000 0.00 0.00 0.00 4.02
382 391 1.657094 CCGTCCGAAAATACTTGTCCG 59.343 52.381 0.00 0.00 0.00 4.79
383 392 2.598589 CGTCCGAAAATACTTGTCCGA 58.401 47.619 0.00 0.00 0.00 4.55
384 393 2.597305 CGTCCGAAAATACTTGTCCGAG 59.403 50.000 0.00 0.00 0.00 4.63
385 394 2.928116 GTCCGAAAATACTTGTCCGAGG 59.072 50.000 0.00 0.00 0.00 4.63
386 395 2.827322 TCCGAAAATACTTGTCCGAGGA 59.173 45.455 0.00 0.00 0.00 3.71
387 396 3.258872 TCCGAAAATACTTGTCCGAGGAA 59.741 43.478 0.00 0.00 0.00 3.36
388 397 4.081309 TCCGAAAATACTTGTCCGAGGAAT 60.081 41.667 0.00 0.00 0.00 3.01
389 398 4.034048 CCGAAAATACTTGTCCGAGGAATG 59.966 45.833 0.00 0.00 0.00 2.67
390 399 4.034048 CGAAAATACTTGTCCGAGGAATGG 59.966 45.833 0.00 0.00 0.00 3.16
391 400 4.837093 AAATACTTGTCCGAGGAATGGA 57.163 40.909 0.00 0.00 0.00 3.41
392 401 5.373812 AAATACTTGTCCGAGGAATGGAT 57.626 39.130 0.00 0.00 37.93 3.41
393 402 2.698855 ACTTGTCCGAGGAATGGATG 57.301 50.000 0.00 0.00 37.93 3.51
394 403 1.909302 ACTTGTCCGAGGAATGGATGT 59.091 47.619 0.00 0.00 37.93 3.06
395 404 3.104512 ACTTGTCCGAGGAATGGATGTA 58.895 45.455 0.00 0.00 37.93 2.29
396 405 3.711704 ACTTGTCCGAGGAATGGATGTAT 59.288 43.478 0.00 0.00 37.93 2.29
397 406 4.202264 ACTTGTCCGAGGAATGGATGTATC 60.202 45.833 0.00 0.00 37.93 2.24
398 407 3.576861 TGTCCGAGGAATGGATGTATCT 58.423 45.455 0.00 0.00 37.93 1.98
399 408 4.736473 TGTCCGAGGAATGGATGTATCTA 58.264 43.478 0.00 0.00 37.93 1.98
400 409 4.767409 TGTCCGAGGAATGGATGTATCTAG 59.233 45.833 0.00 0.00 37.93 2.43
401 410 5.010933 GTCCGAGGAATGGATGTATCTAGA 58.989 45.833 0.00 0.00 37.93 2.43
402 411 5.654650 GTCCGAGGAATGGATGTATCTAGAT 59.345 44.000 10.73 10.73 37.93 1.98
403 412 5.654209 TCCGAGGAATGGATGTATCTAGATG 59.346 44.000 15.79 0.00 0.00 2.90
404 413 5.420421 CCGAGGAATGGATGTATCTAGATGT 59.580 44.000 15.79 1.25 0.00 3.06
405 414 6.603599 CCGAGGAATGGATGTATCTAGATGTA 59.396 42.308 15.79 4.44 0.00 2.29
406 415 7.286546 CCGAGGAATGGATGTATCTAGATGTAT 59.713 40.741 15.79 9.11 0.00 2.29
407 416 8.690884 CGAGGAATGGATGTATCTAGATGTATT 58.309 37.037 15.79 6.57 0.00 1.89
436 445 8.713971 AGTTCTACATACATCCATTTGTATCCA 58.286 33.333 0.00 0.00 40.07 3.41
437 446 9.507329 GTTCTACATACATCCATTTGTATCCAT 57.493 33.333 0.00 0.00 40.07 3.41
444 453 7.496529 ACATCCATTTGTATCCATTTCTACG 57.503 36.000 0.00 0.00 0.00 3.51
445 454 7.279615 ACATCCATTTGTATCCATTTCTACGA 58.720 34.615 0.00 0.00 0.00 3.43
446 455 7.226720 ACATCCATTTGTATCCATTTCTACGAC 59.773 37.037 0.00 0.00 0.00 4.34
447 456 6.645306 TCCATTTGTATCCATTTCTACGACA 58.355 36.000 0.00 0.00 0.00 4.35
448 457 7.106890 TCCATTTGTATCCATTTCTACGACAA 58.893 34.615 0.00 0.00 0.00 3.18
449 458 7.279981 TCCATTTGTATCCATTTCTACGACAAG 59.720 37.037 0.00 0.00 0.00 3.16
450 459 7.065803 CCATTTGTATCCATTTCTACGACAAGT 59.934 37.037 0.00 0.00 0.00 3.16
451 460 9.093970 CATTTGTATCCATTTCTACGACAAGTA 57.906 33.333 0.00 0.00 0.00 2.24
452 461 9.832445 ATTTGTATCCATTTCTACGACAAGTAT 57.168 29.630 0.00 0.00 34.34 2.12
453 462 9.661563 TTTGTATCCATTTCTACGACAAGTATT 57.338 29.630 0.00 0.00 34.34 1.89
454 463 9.661563 TTGTATCCATTTCTACGACAAGTATTT 57.338 29.630 0.00 0.00 34.34 1.40
455 464 9.309516 TGTATCCATTTCTACGACAAGTATTTC 57.690 33.333 0.00 0.00 34.34 2.17
456 465 7.787725 ATCCATTTCTACGACAAGTATTTCC 57.212 36.000 0.00 0.00 34.34 3.13
457 466 5.808540 TCCATTTCTACGACAAGTATTTCCG 59.191 40.000 0.00 0.00 34.34 4.30
458 467 5.006358 CCATTTCTACGACAAGTATTTCCGG 59.994 44.000 0.00 0.00 34.34 5.14
459 468 5.389859 TTTCTACGACAAGTATTTCCGGA 57.610 39.130 0.00 0.00 34.34 5.14
460 469 4.361451 TCTACGACAAGTATTTCCGGAC 57.639 45.455 1.83 0.00 34.34 4.79
461 470 1.986698 ACGACAAGTATTTCCGGACG 58.013 50.000 1.83 3.25 0.00 4.79
462 471 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
463 472 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
464 473 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
465 474 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
466 475 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
467 476 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
497 506 2.800544 CAGCGAAATATAACACGGGGAG 59.199 50.000 0.00 0.00 0.00 4.30
521 530 2.228822 ACTTGGCCTTTTGATGCTTACG 59.771 45.455 3.32 0.00 0.00 3.18
565 574 2.668850 TTGAGGAAGAGGGAGGGAAT 57.331 50.000 0.00 0.00 0.00 3.01
653 662 5.532557 TCATTAGGAACGCATCATGTCTAG 58.467 41.667 0.00 0.00 0.00 2.43
945 965 7.715249 TCACATCTCAAACTAAGTTAGCTTGTT 59.285 33.333 20.23 8.58 34.40 2.83
1005 1025 6.961359 TGTTAATCTTCACTAACCATGTCG 57.039 37.500 0.00 0.00 0.00 4.35
1201 1227 4.657039 ACCTTTACACTCTGGTAAGTCCAA 59.343 41.667 0.00 0.00 46.59 3.53
1203 1229 6.059484 CCTTTACACTCTGGTAAGTCCAAAA 58.941 40.000 0.00 0.00 46.59 2.44
1374 1406 3.189910 CGCAATCTCCCATCCATAACATG 59.810 47.826 0.00 0.00 0.00 3.21
1407 1439 0.859232 CGCGCACTTCAGTTGTTACT 59.141 50.000 8.75 0.00 34.00 2.24
1441 1473 3.936564 ACACTGAGAGCAAAGAATCTCC 58.063 45.455 0.12 0.00 41.07 3.71
1461 1621 4.567971 TCCACGTTCCGTAATTTGTACAT 58.432 39.130 0.00 0.00 38.32 2.29
1488 1648 8.768955 CCTCATCTATACGGATTGAAAAAGAAG 58.231 37.037 0.00 0.00 0.00 2.85
1504 1664 9.862371 TGAAAAAGAAGTTTGCACTTACATTTA 57.138 25.926 0.00 0.00 43.79 1.40
1575 1736 2.213499 GGTCTGCACATATACCTGCAC 58.787 52.381 2.63 0.00 38.49 4.57
1576 1737 2.158900 GGTCTGCACATATACCTGCACT 60.159 50.000 2.63 0.00 38.49 4.40
1593 1754 3.244976 GCACTTTTTCATTCGGTGATGG 58.755 45.455 0.00 0.00 36.54 3.51
1595 1759 2.231235 ACTTTTTCATTCGGTGATGGCC 59.769 45.455 0.00 0.00 36.54 5.36
1746 1913 5.220098 GCGATACTACCGTGAAACTTACAAC 60.220 44.000 0.00 0.00 31.75 3.32
1758 1925 7.013529 GTGAAACTTACAACGTAATAGCCTTG 58.986 38.462 0.00 0.00 0.00 3.61
1771 1941 7.551617 ACGTAATAGCCTTGCAGTTATTTAACT 59.448 33.333 0.00 0.00 46.76 2.24
1871 2041 8.475331 TTTCTTTAATACTGTTCTAGAAGGCG 57.525 34.615 5.12 0.00 0.00 5.52
1876 2046 0.526662 CTGTTCTAGAAGGCGACCGT 59.473 55.000 5.12 0.00 0.00 4.83
1881 2052 3.869623 TAGAAGGCGACCGTCTAGT 57.130 52.632 14.17 0.00 40.35 2.57
1883 2054 0.035247 AGAAGGCGACCGTCTAGTCT 60.035 55.000 11.34 0.00 40.35 3.24
1885 2056 1.598601 GAAGGCGACCGTCTAGTCTAG 59.401 57.143 0.00 0.00 34.46 2.43
1887 2058 1.648174 GCGACCGTCTAGTCTAGCC 59.352 63.158 1.60 0.00 34.46 3.93
1888 2059 1.784036 GCGACCGTCTAGTCTAGCCC 61.784 65.000 1.60 0.00 34.46 5.19
1890 2061 1.023502 GACCGTCTAGTCTAGCCCAC 58.976 60.000 1.60 0.00 33.79 4.61
1892 2063 0.106619 CCGTCTAGTCTAGCCCACCT 60.107 60.000 1.60 0.00 0.00 4.00
1893 2064 1.025812 CGTCTAGTCTAGCCCACCTG 58.974 60.000 1.60 0.00 0.00 4.00
1896 2067 1.062886 TCTAGTCTAGCCCACCTGCAT 60.063 52.381 1.60 0.00 0.00 3.96
1897 2068 1.765314 CTAGTCTAGCCCACCTGCATT 59.235 52.381 0.00 0.00 0.00 3.56
1898 2069 1.879575 AGTCTAGCCCACCTGCATTA 58.120 50.000 0.00 0.00 0.00 1.90
1899 2070 1.765314 AGTCTAGCCCACCTGCATTAG 59.235 52.381 0.00 0.00 0.00 1.73
1924 2106 3.655777 CCCCTCCTAGCCAAAATATACCA 59.344 47.826 0.00 0.00 0.00 3.25
1925 2107 4.263506 CCCCTCCTAGCCAAAATATACCAG 60.264 50.000 0.00 0.00 0.00 4.00
1926 2108 4.597507 CCCTCCTAGCCAAAATATACCAGA 59.402 45.833 0.00 0.00 0.00 3.86
1927 2109 5.513267 CCCTCCTAGCCAAAATATACCAGAC 60.513 48.000 0.00 0.00 0.00 3.51
1928 2110 5.308237 CCTCCTAGCCAAAATATACCAGACT 59.692 44.000 0.00 0.00 0.00 3.24
1929 2111 6.420913 TCCTAGCCAAAATATACCAGACTC 57.579 41.667 0.00 0.00 0.00 3.36
1965 2154 5.939764 TTATGTGCTAGGAACTGATCTGT 57.060 39.130 0.00 0.00 41.52 3.41
1970 2159 2.364002 GCTAGGAACTGATCTGTCTCCC 59.636 54.545 20.19 15.20 41.52 4.30
2008 2197 0.250727 TGGTGGGCACAGCTTCTTAC 60.251 55.000 20.49 0.00 45.14 2.34
2024 2213 5.915196 GCTTCTTACTTACAAGGCAAAAGTG 59.085 40.000 0.00 0.00 35.23 3.16
2039 2228 4.624015 CAAAAGTGCATTTCAGGATGTGT 58.376 39.130 0.00 0.00 37.40 3.72
2048 2237 6.936335 TGCATTTCAGGATGTGTATATCGATT 59.064 34.615 1.71 0.00 37.40 3.34
2057 2246 5.966636 TGTGTATATCGATTTGTCTGCAC 57.033 39.130 1.71 4.81 0.00 4.57
2093 2284 5.950544 TGCTTCCATGGTAACTAGTATGT 57.049 39.130 12.58 0.00 37.61 2.29
2096 2287 5.758784 GCTTCCATGGTAACTAGTATGTTCC 59.241 44.000 12.58 0.00 37.61 3.62
2200 2475 6.670695 AGCAACCCAACAAAAAGAGAATAT 57.329 33.333 0.00 0.00 0.00 1.28
2203 2478 6.587608 GCAACCCAACAAAAAGAGAATATCTG 59.412 38.462 0.00 0.00 38.67 2.90
2225 2500 3.129287 GCATTGGTAAGACCTGGAACATG 59.871 47.826 0.00 0.00 39.58 3.21
2257 2535 9.052759 ACTAGTACAAGTTACTCAACCAAATTG 57.947 33.333 0.00 0.00 39.94 2.32
2267 2545 9.129209 GTTACTCAACCAAATTGCTTTTCTATC 57.871 33.333 0.00 0.00 38.29 2.08
2274 2552 8.742554 ACCAAATTGCTTTTCTATCTTTTACG 57.257 30.769 0.00 0.00 0.00 3.18
2303 2581 5.308825 ACACCTCCAGAGTTAAAAGTGATG 58.691 41.667 6.52 0.00 0.00 3.07
2387 2665 7.227512 CAGTTATGGTGGGTTCTTCATATTCTC 59.772 40.741 0.00 0.00 0.00 2.87
2398 2676 9.674068 GGTTCTTCATATTCTCTTTCCTTTACT 57.326 33.333 0.00 0.00 0.00 2.24
2477 2756 7.614583 TGTATAGTAAGCTGGTTCAGAAGTACT 59.385 37.037 0.00 0.00 32.44 2.73
2545 2829 8.324191 TCATCAGTGATTACTTAAGGGAGAAT 57.676 34.615 1.86 1.04 34.07 2.40
2550 2834 9.319143 CAGTGATTACTTAAGGGAGAATAACTG 57.681 37.037 16.65 16.65 34.31 3.16
2564 2848 6.981559 GGAGAATAACTGGAGATGACAACTAC 59.018 42.308 0.00 0.00 0.00 2.73
2585 2869 3.244911 ACAGTAAGTGCTTAGGGTGCAAT 60.245 43.478 0.00 0.00 42.41 3.56
2587 2871 4.941263 CAGTAAGTGCTTAGGGTGCAATTA 59.059 41.667 4.83 4.83 44.98 1.40
2589 2873 4.783764 AAGTGCTTAGGGTGCAATTAAC 57.216 40.909 0.00 0.00 44.98 2.01
2618 2904 3.493699 GGCACGTAAATAGCATACCTGGA 60.494 47.826 0.00 0.00 0.00 3.86
2630 2916 4.526262 AGCATACCTGGATAGTAAGCAGAG 59.474 45.833 0.00 0.00 36.99 3.35
2640 2926 5.011125 GGATAGTAAGCAGAGCATTGTCCTA 59.989 44.000 0.00 0.00 0.00 2.94
2643 2929 2.522836 AGCAGAGCATTGTCCTATCG 57.477 50.000 0.00 0.00 0.00 2.92
2667 2953 5.319140 TCACATCAATTCATGGCAGAAAG 57.681 39.130 0.00 0.00 0.00 2.62
2681 2967 6.627395 TGGCAGAAAGTTCTTCGAATTTAA 57.373 33.333 0.00 0.00 34.74 1.52
2880 3170 3.118956 AGAGACTTCTCCGCACTTTATGG 60.119 47.826 2.47 0.00 43.88 2.74
2990 3280 6.763715 AGCATTATTACCCATCCTCTACAA 57.236 37.500 0.00 0.00 0.00 2.41
2997 3287 1.415659 CCCATCCTCTACAAGCAGGAG 59.584 57.143 0.00 0.00 42.28 3.69
3009 3299 7.159372 TCTACAAGCAGGAGGTTTAACTAAAG 58.841 38.462 0.00 0.00 32.07 1.85
3018 3308 7.171678 CAGGAGGTTTAACTAAAGTGTGAGAAG 59.828 40.741 0.00 0.00 0.00 2.85
3110 3400 8.560355 TTTACATTGTCATGTATGCAAGTACT 57.440 30.769 0.00 0.00 43.96 2.73
3111 3401 9.660180 TTTACATTGTCATGTATGCAAGTACTA 57.340 29.630 0.00 0.00 43.96 1.82
3112 3402 9.660180 TTACATTGTCATGTATGCAAGTACTAA 57.340 29.630 0.00 0.00 43.96 2.24
3113 3403 8.560355 ACATTGTCATGTATGCAAGTACTAAA 57.440 30.769 0.00 0.00 42.24 1.85
3130 3420 7.331791 AGTACTAAATAGGGTGCTTTCAGAAG 58.668 38.462 0.00 0.00 35.92 2.85
3142 3432 7.362142 GGGTGCTTTCAGAAGGAATTTAACTAG 60.362 40.741 0.00 0.00 34.84 2.57
3143 3433 7.175119 GGTGCTTTCAGAAGGAATTTAACTAGT 59.825 37.037 0.00 0.00 34.84 2.57
3378 3673 2.828520 CACTTCACTCCTAGGCTTCAGA 59.171 50.000 2.96 0.00 0.00 3.27
3391 3686 6.267471 CCTAGGCTTCAGAGATAACTTCAGAT 59.733 42.308 0.00 0.00 0.00 2.90
3427 3729 6.183360 GGCATGTTTACAAGGCTGGTATATTT 60.183 38.462 1.80 0.00 37.20 1.40
3428 3730 7.013846 GGCATGTTTACAAGGCTGGTATATTTA 59.986 37.037 1.80 0.00 37.20 1.40
3429 3731 8.076178 GCATGTTTACAAGGCTGGTATATTTAG 58.924 37.037 1.80 0.00 0.00 1.85
3430 3732 7.562454 TGTTTACAAGGCTGGTATATTTAGC 57.438 36.000 1.80 0.00 36.74 3.09
3431 3733 7.343357 TGTTTACAAGGCTGGTATATTTAGCT 58.657 34.615 1.80 0.00 37.58 3.32
3456 3758 3.014856 GCTCTTGGCGCGGTTATC 58.985 61.111 8.83 0.00 0.00 1.75
3458 3760 0.249322 GCTCTTGGCGCGGTTATCTA 60.249 55.000 8.83 0.00 0.00 1.98
3460 3762 0.103572 TCTTGGCGCGGTTATCTACC 59.896 55.000 8.83 0.00 44.03 3.18
3488 3799 6.014755 TCTCAACTCTCAACTCAATCTGATGT 60.015 38.462 0.00 0.00 0.00 3.06
3581 3892 2.028020 CCTTGTAAGGGTCAGAGTCCAC 60.028 54.545 2.63 0.00 42.66 4.02
3605 3917 2.121948 TCCATCCAGGAGTTCTGATGG 58.878 52.381 17.54 17.54 46.18 3.51
3643 3955 7.219322 TCAATCATGTTCAAGAACTGAAGAGA 58.781 34.615 13.49 10.41 44.83 3.10
3679 3999 3.701040 ACCCAACAATGGCTGATATTCAC 59.299 43.478 0.00 0.00 46.09 3.18
3748 4068 0.237235 TTAACGCCAGAAAAGCTGCG 59.763 50.000 11.78 11.78 43.50 5.18
3808 4128 4.095036 GCAGTAGCAATTCCAAGGTTAGAC 59.905 45.833 0.00 0.00 41.58 2.59
3820 4140 3.983044 AGGTTAGACTTGATCACCCAC 57.017 47.619 0.00 0.00 0.00 4.61
3859 4179 3.806521 GTGTAGCCAGATGATGCTAACAG 59.193 47.826 0.00 0.00 41.42 3.16
3861 4181 4.649218 TGTAGCCAGATGATGCTAACAGTA 59.351 41.667 0.00 0.00 41.42 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 93 6.478512 ACAGGTGTGTGGTTTATTTCAATT 57.521 33.333 0.00 0.00 34.75 2.32
261 270 3.254892 GAACGGCAAAAGTGGTTTTTCA 58.745 40.909 0.00 0.00 36.87 2.69
332 341 9.881529 GAGTACAAGTTAGAGCATACATACTAC 57.118 37.037 0.00 0.00 0.00 2.73
353 362 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
354 363 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
355 364 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
356 365 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
357 366 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
358 367 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
359 368 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
360 369 2.928116 GGACAAGTATTTTCGGACGGAG 59.072 50.000 0.00 0.00 0.00 4.63
361 370 2.671914 CGGACAAGTATTTTCGGACGGA 60.672 50.000 0.00 0.00 0.00 4.69
362 371 1.657094 CGGACAAGTATTTTCGGACGG 59.343 52.381 0.00 0.00 0.00 4.79
363 372 2.597305 CTCGGACAAGTATTTTCGGACG 59.403 50.000 0.00 0.00 0.00 4.79
364 373 2.928116 CCTCGGACAAGTATTTTCGGAC 59.072 50.000 0.00 0.00 0.00 4.79
365 374 2.827322 TCCTCGGACAAGTATTTTCGGA 59.173 45.455 0.00 0.00 0.00 4.55
366 375 3.241067 TCCTCGGACAAGTATTTTCGG 57.759 47.619 0.00 0.00 0.00 4.30
367 376 4.034048 CCATTCCTCGGACAAGTATTTTCG 59.966 45.833 0.00 0.00 0.00 3.46
368 377 5.183228 TCCATTCCTCGGACAAGTATTTTC 58.817 41.667 0.00 0.00 0.00 2.29
369 378 5.174037 TCCATTCCTCGGACAAGTATTTT 57.826 39.130 0.00 0.00 0.00 1.82
370 379 4.837093 TCCATTCCTCGGACAAGTATTT 57.163 40.909 0.00 0.00 0.00 1.40
371 380 4.164221 ACATCCATTCCTCGGACAAGTATT 59.836 41.667 0.00 0.00 34.69 1.89
372 381 3.711704 ACATCCATTCCTCGGACAAGTAT 59.288 43.478 0.00 0.00 34.69 2.12
373 382 3.104512 ACATCCATTCCTCGGACAAGTA 58.895 45.455 0.00 0.00 34.69 2.24
374 383 1.909302 ACATCCATTCCTCGGACAAGT 59.091 47.619 0.00 0.00 34.69 3.16
375 384 2.698855 ACATCCATTCCTCGGACAAG 57.301 50.000 0.00 0.00 34.69 3.16
376 385 3.967326 AGATACATCCATTCCTCGGACAA 59.033 43.478 0.00 0.00 34.69 3.18
377 386 3.576861 AGATACATCCATTCCTCGGACA 58.423 45.455 0.00 0.00 34.69 4.02
378 387 5.010933 TCTAGATACATCCATTCCTCGGAC 58.989 45.833 0.00 0.00 34.69 4.79
379 388 5.256806 TCTAGATACATCCATTCCTCGGA 57.743 43.478 0.00 0.00 36.84 4.55
380 389 5.420421 ACATCTAGATACATCCATTCCTCGG 59.580 44.000 4.54 0.00 0.00 4.63
381 390 6.522625 ACATCTAGATACATCCATTCCTCG 57.477 41.667 4.54 0.00 0.00 4.63
430 439 8.762426 GGAAATACTTGTCGTAGAAATGGATAC 58.238 37.037 0.00 0.00 39.69 2.24
431 440 7.650504 CGGAAATACTTGTCGTAGAAATGGATA 59.349 37.037 0.00 0.00 39.69 2.59
432 441 6.479001 CGGAAATACTTGTCGTAGAAATGGAT 59.521 38.462 0.00 0.00 39.69 3.41
433 442 5.808540 CGGAAATACTTGTCGTAGAAATGGA 59.191 40.000 0.00 0.00 39.69 3.41
434 443 5.006358 CCGGAAATACTTGTCGTAGAAATGG 59.994 44.000 0.00 0.00 39.69 3.16
435 444 5.808540 TCCGGAAATACTTGTCGTAGAAATG 59.191 40.000 0.00 0.00 39.69 2.32
436 445 5.809051 GTCCGGAAATACTTGTCGTAGAAAT 59.191 40.000 5.23 0.00 39.69 2.17
437 446 5.163513 GTCCGGAAATACTTGTCGTAGAAA 58.836 41.667 5.23 0.00 39.69 2.52
438 447 4.672542 CGTCCGGAAATACTTGTCGTAGAA 60.673 45.833 5.23 0.00 39.69 2.10
439 448 3.181507 CGTCCGGAAATACTTGTCGTAGA 60.182 47.826 5.23 0.00 0.00 2.59
440 449 3.103738 CGTCCGGAAATACTTGTCGTAG 58.896 50.000 5.23 0.00 0.00 3.51
441 450 2.159393 CCGTCCGGAAATACTTGTCGTA 60.159 50.000 5.23 0.00 37.50 3.43
442 451 1.403249 CCGTCCGGAAATACTTGTCGT 60.403 52.381 5.23 0.00 37.50 4.34
443 452 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
444 453 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
445 454 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
446 455 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
447 456 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
448 457 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
449 458 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
450 459 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
451 460 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
452 461 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
453 462 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
454 463 0.109342 GTATACTCCCTCCGTCCGGA 59.891 60.000 0.00 0.00 42.90 5.14
455 464 0.179009 TGTATACTCCCTCCGTCCGG 60.179 60.000 4.17 0.00 0.00 5.14
456 465 1.236628 CTGTATACTCCCTCCGTCCG 58.763 60.000 4.17 0.00 0.00 4.79
457 466 0.960286 GCTGTATACTCCCTCCGTCC 59.040 60.000 4.17 0.00 0.00 4.79
458 467 1.609555 CTGCTGTATACTCCCTCCGTC 59.390 57.143 4.17 0.00 0.00 4.79
459 468 1.693627 CTGCTGTATACTCCCTCCGT 58.306 55.000 4.17 0.00 0.00 4.69
460 469 0.315568 GCTGCTGTATACTCCCTCCG 59.684 60.000 4.17 0.00 0.00 4.63
461 470 0.315568 CGCTGCTGTATACTCCCTCC 59.684 60.000 4.17 0.00 0.00 4.30
462 471 1.319541 TCGCTGCTGTATACTCCCTC 58.680 55.000 4.17 0.00 0.00 4.30
463 472 1.776662 TTCGCTGCTGTATACTCCCT 58.223 50.000 4.17 0.00 0.00 4.20
464 473 2.596904 TTTCGCTGCTGTATACTCCC 57.403 50.000 4.17 0.00 0.00 4.30
465 474 6.866770 TGTTATATTTCGCTGCTGTATACTCC 59.133 38.462 4.17 0.00 0.00 3.85
466 475 7.409449 CGTGTTATATTTCGCTGCTGTATACTC 60.409 40.741 4.17 0.00 0.00 2.59
467 476 6.362551 CGTGTTATATTTCGCTGCTGTATACT 59.637 38.462 4.17 0.00 0.00 2.12
497 506 2.171003 AGCATCAAAAGGCCAAGTACC 58.829 47.619 5.01 0.00 30.82 3.34
521 530 9.740710 AATAATAGTTCTAGGCAAATGGGATAC 57.259 33.333 0.00 0.00 0.00 2.24
565 574 4.704540 TGTTCTTCAGGCTCAACAAGAAAA 59.295 37.500 8.34 2.71 36.79 2.29
653 662 7.569599 TTCTTATTCCCTATATCTGGAACCC 57.430 40.000 7.78 0.00 43.11 4.11
945 965 1.075601 AAGAATGGGTTGGGCTCTGA 58.924 50.000 0.00 0.00 0.00 3.27
1005 1025 1.346068 CCTATAGCAAGTGCCTCCCTC 59.654 57.143 0.00 0.00 43.38 4.30
1282 1308 2.237643 TGAAGCCTGTGCAATTAAGCA 58.762 42.857 0.00 0.00 43.35 3.91
1283 1309 2.989166 GTTGAAGCCTGTGCAATTAAGC 59.011 45.455 0.00 0.00 41.13 3.09
1284 1310 4.241590 TGTTGAAGCCTGTGCAATTAAG 57.758 40.909 0.00 0.00 41.13 1.85
1285 1311 4.280425 TGATGTTGAAGCCTGTGCAATTAA 59.720 37.500 0.00 0.00 41.13 1.40
1286 1312 3.825585 TGATGTTGAAGCCTGTGCAATTA 59.174 39.130 0.00 0.00 41.13 1.40
1407 1439 7.324354 TGCTCTCAGTGTTATATACGTACAA 57.676 36.000 0.00 0.00 0.00 2.41
1461 1621 8.018537 TCTTTTTCAATCCGTATAGATGAGGA 57.981 34.615 0.00 0.00 37.17 3.71
1575 1736 2.879826 GGCCATCACCGAATGAAAAAG 58.120 47.619 0.00 0.00 41.93 2.27
1593 1754 3.123050 GTGCATAATTTTGATTCCCGGC 58.877 45.455 0.00 0.00 0.00 6.13
1595 1759 4.027572 ACGTGCATAATTTTGATTCCCG 57.972 40.909 0.00 0.00 0.00 5.14
1692 1858 3.667960 GCACCTTCATGACGTAAGCAAAG 60.668 47.826 0.00 0.00 45.62 2.77
1733 1899 6.716898 AGGCTATTACGTTGTAAGTTTCAC 57.283 37.500 0.00 0.00 0.00 3.18
1746 1913 7.916552 AGTTAAATAACTGCAAGGCTATTACG 58.083 34.615 5.07 0.00 44.30 3.18
1758 1925 7.946655 AAAGAAGGCAAAGTTAAATAACTGC 57.053 32.000 6.60 7.58 45.17 4.40
1803 1973 5.242838 TCCATTAACTTGATGCTTTTCGGTT 59.757 36.000 0.00 0.00 0.00 4.44
1804 1974 4.764823 TCCATTAACTTGATGCTTTTCGGT 59.235 37.500 0.00 0.00 0.00 4.69
1806 1976 8.562892 AGATATCCATTAACTTGATGCTTTTCG 58.437 33.333 0.00 0.00 0.00 3.46
1850 2020 6.335777 GGTCGCCTTCTAGAACAGTATTAAA 58.664 40.000 0.00 0.00 0.00 1.52
1871 2041 1.023502 GTGGGCTAGACTAGACGGTC 58.976 60.000 13.91 0.00 33.43 4.79
1876 2046 0.335019 TGCAGGTGGGCTAGACTAGA 59.665 55.000 13.91 0.00 34.04 2.43
1881 2052 1.131638 CCTAATGCAGGTGGGCTAGA 58.868 55.000 0.00 0.00 39.91 2.43
1883 2054 2.230664 CCCTAATGCAGGTGGGCTA 58.769 57.895 7.60 0.00 43.80 3.93
1887 2058 2.123726 GGGCCCTAATGCAGGTGG 60.124 66.667 17.04 0.00 43.80 4.61
1888 2059 2.123726 GGGGCCCTAATGCAGGTG 60.124 66.667 24.38 0.00 43.80 4.00
1890 2061 2.517919 GAGGGGCCCTAATGCAGG 59.482 66.667 28.92 0.00 45.07 4.85
1892 2063 0.768221 CTAGGAGGGGCCCTAATGCA 60.768 60.000 28.92 8.39 38.26 3.96
1893 2064 2.070639 CTAGGAGGGGCCCTAATGC 58.929 63.158 28.92 13.44 38.26 3.56
1896 2067 2.289341 GGCTAGGAGGGGCCCTAA 59.711 66.667 28.92 13.54 42.30 2.69
1941 2123 6.893583 ACAGATCAGTTCCTAGCACATAATT 58.106 36.000 0.00 0.00 0.00 1.40
1965 2154 0.259065 ACTGGATGCTAGTCGGGAGA 59.741 55.000 0.00 0.00 0.00 3.71
1970 2159 2.534298 CAAGACACTGGATGCTAGTCG 58.466 52.381 0.00 0.00 34.56 4.18
2024 2213 6.974932 ATCGATATACACATCCTGAAATGC 57.025 37.500 0.00 0.00 0.00 3.56
2035 2224 5.415221 TGTGCAGACAAATCGATATACACA 58.585 37.500 0.00 4.44 32.37 3.72
2048 2237 7.441760 AGCAAAATTTGATATTTGTGCAGACAA 59.558 29.630 10.26 0.00 40.45 3.18
2057 2246 8.271312 ACCATGGAAGCAAAATTTGATATTTG 57.729 30.769 21.47 0.28 39.08 2.32
2200 2475 2.265367 TCCAGGTCTTACCAATGCAGA 58.735 47.619 0.00 0.00 41.95 4.26
2203 2478 2.790433 TGTTCCAGGTCTTACCAATGC 58.210 47.619 0.00 0.00 41.95 3.56
2257 2535 9.474249 GTGTTACATCGTAAAAGATAGAAAAGC 57.526 33.333 0.00 0.00 0.00 3.51
2267 2545 5.475719 TCTGGAGGTGTTACATCGTAAAAG 58.524 41.667 0.00 0.00 28.03 2.27
2274 2552 6.935208 ACTTTTAACTCTGGAGGTGTTACATC 59.065 38.462 0.00 0.00 34.80 3.06
2303 2581 6.094048 CCTGTGGCATGTATATAACCATAAGC 59.906 42.308 0.00 0.00 31.99 3.09
2477 2756 7.759489 AACAAGCTACAGGTTAATTTCATCA 57.241 32.000 0.00 0.00 33.98 3.07
2525 2808 8.487028 CCAGTTATTCTCCCTTAAGTAATCACT 58.513 37.037 0.97 1.17 36.19 3.41
2537 2820 4.624913 TGTCATCTCCAGTTATTCTCCCT 58.375 43.478 0.00 0.00 0.00 4.20
2540 2824 7.548097 TGTAGTTGTCATCTCCAGTTATTCTC 58.452 38.462 0.00 0.00 0.00 2.87
2541 2825 7.179338 ACTGTAGTTGTCATCTCCAGTTATTCT 59.821 37.037 3.88 0.00 0.00 2.40
2542 2826 7.324178 ACTGTAGTTGTCATCTCCAGTTATTC 58.676 38.462 3.88 0.00 0.00 1.75
2545 2829 7.450634 ACTTACTGTAGTTGTCATCTCCAGTTA 59.549 37.037 12.71 5.24 33.97 2.24
2550 2834 4.865365 GCACTTACTGTAGTTGTCATCTCC 59.135 45.833 0.00 0.00 0.00 3.71
2564 2848 2.472695 TGCACCCTAAGCACTTACTG 57.527 50.000 0.00 0.00 37.02 2.74
2585 2869 6.205076 TGCTATTTACGTGCCTTTTCTGTTAA 59.795 34.615 0.00 0.00 0.00 2.01
2586 2870 5.701750 TGCTATTTACGTGCCTTTTCTGTTA 59.298 36.000 0.00 0.00 0.00 2.41
2587 2871 4.517453 TGCTATTTACGTGCCTTTTCTGTT 59.483 37.500 0.00 0.00 0.00 3.16
2588 2872 4.069304 TGCTATTTACGTGCCTTTTCTGT 58.931 39.130 0.00 0.00 0.00 3.41
2589 2873 4.678509 TGCTATTTACGTGCCTTTTCTG 57.321 40.909 0.00 0.00 0.00 3.02
2618 2904 6.571344 CGATAGGACAATGCTCTGCTTACTAT 60.571 42.308 0.00 0.00 0.00 2.12
2630 2916 3.871006 TGATGTGAACGATAGGACAATGC 59.129 43.478 0.00 0.00 43.77 3.56
2640 2926 3.695556 TGCCATGAATTGATGTGAACGAT 59.304 39.130 4.14 0.00 0.00 3.73
2643 2929 4.707030 TCTGCCATGAATTGATGTGAAC 57.293 40.909 4.14 0.00 0.00 3.18
2690 2976 6.797033 GTGCTAACATGTTAAAGTGATGTCAC 59.203 38.462 18.55 12.50 46.77 3.67
2695 2981 4.454161 TGCGTGCTAACATGTTAAAGTGAT 59.546 37.500 18.55 0.00 35.09 3.06
2880 3170 2.757077 CCACAGGGGGTCCAAGAC 59.243 66.667 0.00 0.00 34.83 3.01
2990 3280 5.063880 CACACTTTAGTTAAACCTCCTGCT 58.936 41.667 0.00 0.00 0.00 4.24
3009 3299 4.254492 GGACCCTGTTTATCTTCTCACAC 58.746 47.826 0.00 0.00 0.00 3.82
3018 3308 1.940613 GCGATGTGGACCCTGTTTATC 59.059 52.381 0.00 0.00 0.00 1.75
3026 3316 1.523154 TTGCTTTGCGATGTGGACCC 61.523 55.000 0.00 0.00 0.00 4.46
3094 3384 7.931407 CACCCTATTTAGTACTTGCATACATGA 59.069 37.037 0.00 0.00 0.00 3.07
3110 3400 5.772393 TCCTTCTGAAAGCACCCTATTTA 57.228 39.130 0.00 0.00 0.00 1.40
3111 3401 4.657814 TCCTTCTGAAAGCACCCTATTT 57.342 40.909 0.00 0.00 0.00 1.40
3112 3402 4.657814 TTCCTTCTGAAAGCACCCTATT 57.342 40.909 0.00 0.00 0.00 1.73
3113 3403 4.870021 ATTCCTTCTGAAAGCACCCTAT 57.130 40.909 0.00 0.00 36.33 2.57
3130 3420 7.145932 ACTTGCATGACACTAGTTAAATTCC 57.854 36.000 6.60 0.00 0.00 3.01
3142 3432 4.154195 CCCTGTTTAGTACTTGCATGACAC 59.846 45.833 0.00 4.08 0.00 3.67
3143 3433 4.202419 ACCCTGTTTAGTACTTGCATGACA 60.202 41.667 0.00 0.00 0.00 3.58
3244 3537 2.684881 CAGGGACAGTTGTTGGATATGC 59.315 50.000 0.00 0.00 0.00 3.14
3391 3686 7.066525 GCCTTGTAAACATGCCTGTTATTAGTA 59.933 37.037 7.84 0.00 44.83 1.82
3429 3731 1.497223 CGCCAAGAGCTATGCAGAGC 61.497 60.000 25.57 25.57 43.19 4.09
3430 3732 1.497223 GCGCCAAGAGCTATGCAGAG 61.497 60.000 3.34 3.34 40.39 3.35
3431 3733 1.522355 GCGCCAAGAGCTATGCAGA 60.522 57.895 0.00 0.00 40.39 4.26
3456 3758 4.520874 TGAGTTGAGAGTTGAGACTGGTAG 59.479 45.833 0.00 0.00 35.88 3.18
3458 3760 3.300388 TGAGTTGAGAGTTGAGACTGGT 58.700 45.455 0.00 0.00 35.88 4.00
3460 3762 5.634439 CAGATTGAGTTGAGAGTTGAGACTG 59.366 44.000 0.00 0.00 35.88 3.51
3461 3763 5.538053 TCAGATTGAGTTGAGAGTTGAGACT 59.462 40.000 0.00 0.00 39.32 3.24
3463 3765 6.014755 ACATCAGATTGAGTTGAGAGTTGAGA 60.015 38.462 0.00 0.00 0.00 3.27
3464 3766 6.164876 ACATCAGATTGAGTTGAGAGTTGAG 58.835 40.000 0.00 0.00 0.00 3.02
3465 3767 6.106648 ACATCAGATTGAGTTGAGAGTTGA 57.893 37.500 0.00 0.00 0.00 3.18
3466 3768 6.798315 AACATCAGATTGAGTTGAGAGTTG 57.202 37.500 0.00 0.00 29.78 3.16
3469 3771 8.449397 CCTTTTAACATCAGATTGAGTTGAGAG 58.551 37.037 0.00 0.00 0.00 3.20
3547 3858 3.502211 CCTTACAAGGTACTGGCACAAAG 59.498 47.826 0.00 0.00 40.86 2.77
3559 3870 2.258109 GGACTCTGACCCTTACAAGGT 58.742 52.381 7.23 0.00 44.98 3.50
3605 3917 7.092079 TGAACATGATTGATGGTGAATTTCAC 58.908 34.615 19.17 19.17 46.23 3.18
3643 3955 3.334054 GGGTGCCTCTTGGAGCCT 61.334 66.667 0.00 0.00 34.57 4.58
3679 3999 6.992063 AAGTTAGCCAGACATGATTAACAG 57.008 37.500 0.00 0.00 32.23 3.16
3748 4068 4.027572 TGTTTGTTGCTCTTGTGCTTAC 57.972 40.909 0.00 0.00 0.00 2.34
3793 4113 5.946377 GGTGATCAAGTCTAACCTTGGAATT 59.054 40.000 0.00 0.00 41.72 2.17
3808 4128 0.692476 TGGGTGAGTGGGTGATCAAG 59.308 55.000 0.00 0.00 0.00 3.02
3818 4138 3.703001 ACCTATTTCTGTGGGTGAGTG 57.297 47.619 0.00 0.00 0.00 3.51
3859 4179 7.843490 TCAACTTTAGGTAGTCATTGCATAC 57.157 36.000 0.00 0.00 0.00 2.39
3861 4181 9.277783 GATATCAACTTTAGGTAGTCATTGCAT 57.722 33.333 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.