Multiple sequence alignment - TraesCS7B01G373000

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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 TraesCS7B01G373000 chr7B 100.000 4658 0 0 1 4658 638881526 638886183 0.000000e+00 8602
1 TraesCS7B01G373000 chr7B 91.391 302 24 1 938 1239 656308059 656307760 3.350000e-111 412
2 TraesCS7B01G373000 chr7D 95.984 2490 70 16 2185 4658 576283711 576286186 0.000000e+00 4017
3 TraesCS7B01G373000 chr7D 86.974 2303 170 81 1 2227 576281173 576283421 0.000000e+00 2471
4 TraesCS7B01G373000 chr7D 74.453 548 140 0 1583 2130 142610841 142611388 2.170000e-58 237
5 TraesCS7B01G373000 chr7A 92.325 1746 82 21 2338 4039 667212861 667214598 0.000000e+00 2435
6 TraesCS7B01G373000 chr7A 90.884 1821 109 38 531 2315 667210732 667212531 0.000000e+00 2390
7 TraesCS7B01G373000 chr7A 86.196 326 28 10 4345 4655 667214605 667214928 2.080000e-88 337
8 TraesCS7B01G373000 chr7A 75.785 446 108 0 1583 2028 144603876 144604321 4.690000e-55 226
9 TraesCS7B01G373000 chr3B 91.531 307 24 1 933 1239 11697722 11698026 5.570000e-114 422
10 TraesCS7B01G373000 chr5B 91.447 304 24 1 938 1241 702324816 702324515 2.590000e-112 416
11 TraesCS7B01G373000 chr5B 90.820 305 25 2 938 1241 344150967 344150665 5.610000e-109 405
12 TraesCS7B01G373000 chr4B 90.397 302 27 1 938 1239 477965297 477964998 3.380000e-106 396
13 TraesCS7B01G373000 chr4A 90.397 302 27 1 938 1239 313507384 313507683 3.380000e-106 396
14 TraesCS7B01G373000 chr4A 90.397 302 27 1 938 1239 677531418 677531119 3.380000e-106 396


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 TraesCS7B01G373000 chr7B 638881526 638886183 4657 False 8602.000000 8602 100.000000 1 4658 1 chr7B.!!$F1 4657
1 TraesCS7B01G373000 chr7D 576281173 576286186 5013 False 3244.000000 4017 91.479000 1 4658 2 chr7D.!!$F2 4657
2 TraesCS7B01G373000 chr7D 142610841 142611388 547 False 237.000000 237 74.453000 1583 2130 1 chr7D.!!$F1 547
3 TraesCS7B01G373000 chr7A 667210732 667214928 4196 False 1720.666667 2435 89.801667 531 4655 3 chr7A.!!$F2 4124

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
472 509 0.034616 GCTCTTGCTCAGGTGTCAGT 59.965 55.0 0.00 0.00 36.03 3.41 F
607 644 0.109723 GTTGGTTGGTGGCACCTCTA 59.890 55.0 34.69 22.62 39.58 2.43 F
724 765 0.179062 CAAGGGCTGGTGCTAGCTAG 60.179 60.0 16.84 16.84 43.22 3.42 F
725 766 0.618968 AAGGGCTGGTGCTAGCTAGT 60.619 55.0 21.62 0.00 43.22 2.57 F
795 849 0.971959 TTTGTGATGCTGATGGGGCC 60.972 55.0 0.00 0.00 0.00 5.80 F
3120 3872 0.826715 AGCAGCTCTTCGCCAGAATA 59.173 50.0 0.00 0.00 40.39 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1560 1623 0.853530 AACCAAGAGGAAAGCCAGGT 59.146 50.000 0.00 0.0 38.69 4.00 R
1629 1692 2.079158 ACACCAGCAACATCATCGAAG 58.921 47.619 0.00 0.0 0.00 3.79 R
2164 2375 4.874970 ACATGCAAAAATTCCAGACTGAC 58.125 39.130 3.32 0.0 0.00 3.51 R
2358 3071 8.469200 CCAAATGTTAAGCAAGATCCAGAATAA 58.531 33.333 0.00 0.0 0.00 1.40 R
3192 3944 1.297689 GATCTGCTGCAGGTCACCA 59.702 57.895 32.17 12.9 40.93 4.17 R
4092 4848 1.676006 GCAACGGATACATTTCCTGGG 59.324 52.381 0.00 0.0 33.30 4.45 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 2.596338 TCGTCGGCCAGTCAGTCA 60.596 61.111 2.24 0.00 0.00 3.41
78 79 2.430921 CGTCGGCCAGTCAGTCAC 60.431 66.667 2.24 0.00 0.00 3.67
79 80 2.048127 GTCGGCCAGTCAGTCACC 60.048 66.667 2.24 0.00 0.00 4.02
80 81 3.680786 TCGGCCAGTCAGTCACCG 61.681 66.667 2.24 0.00 45.15 4.94
96 97 0.756442 ACCGCCCCGCTACTTATACA 60.756 55.000 0.00 0.00 0.00 2.29
100 101 1.335689 GCCCCGCTACTTATACACTCG 60.336 57.143 0.00 0.00 0.00 4.18
134 140 1.604378 CTTCCCTCACAATCGCCCT 59.396 57.895 0.00 0.00 0.00 5.19
143 149 2.042930 AATCGCCCTCTTCCCCCT 59.957 61.111 0.00 0.00 0.00 4.79
144 150 2.073101 AATCGCCCTCTTCCCCCTC 61.073 63.158 0.00 0.00 0.00 4.30
145 151 2.553438 AATCGCCCTCTTCCCCCTCT 62.553 60.000 0.00 0.00 0.00 3.69
203 236 4.406943 GTCACGCCTCTTTGATTTGATTC 58.593 43.478 0.00 0.00 0.00 2.52
209 242 5.228635 CGCCTCTTTGATTTGATTCGATTTG 59.771 40.000 0.00 0.00 0.00 2.32
229 262 4.909696 TGTTCCGAATTTCAGCTTCAAA 57.090 36.364 0.00 0.00 0.00 2.69
235 268 3.320626 GAATTTCAGCTTCAAACCTGCC 58.679 45.455 0.00 0.00 0.00 4.85
236 269 1.039856 TTTCAGCTTCAAACCTGCCC 58.960 50.000 0.00 0.00 0.00 5.36
240 273 2.982744 GCTTCAAACCTGCCCGCTC 61.983 63.158 0.00 0.00 0.00 5.03
241 274 1.600636 CTTCAAACCTGCCCGCTCA 60.601 57.895 0.00 0.00 0.00 4.26
242 275 1.580845 CTTCAAACCTGCCCGCTCAG 61.581 60.000 0.00 0.00 0.00 3.35
248 281 2.759973 CTGCCCGCTCAGGTCCTA 60.760 66.667 0.00 0.00 38.74 2.94
249 282 3.075005 TGCCCGCTCAGGTCCTAC 61.075 66.667 0.00 0.00 38.74 3.18
252 285 3.449227 CCGCTCAGGTCCTACGCA 61.449 66.667 11.03 0.00 34.51 5.24
254 287 2.407428 CGCTCAGGTCCTACGCAGA 61.407 63.158 11.03 0.00 0.00 4.26
257 290 0.394488 CTCAGGTCCTACGCAGAGGA 60.394 60.000 0.00 0.00 43.67 3.71
258 291 0.394488 TCAGGTCCTACGCAGAGGAG 60.394 60.000 3.80 0.00 46.54 3.69
260 293 3.604629 GTCCTACGCAGAGGAGCA 58.395 61.111 3.80 0.00 46.54 4.26
261 294 2.119886 GTCCTACGCAGAGGAGCAT 58.880 57.895 3.80 0.00 46.54 3.79
282 315 1.664151 CCCGCTAGATTCCGTTGTTTC 59.336 52.381 0.00 0.00 0.00 2.78
283 316 2.618053 CCGCTAGATTCCGTTGTTTCT 58.382 47.619 0.00 0.00 0.00 2.52
314 349 2.328099 GGGTCTGGAGCAAGCGTTG 61.328 63.158 2.27 0.00 0.00 4.10
315 350 2.328099 GGTCTGGAGCAAGCGTTGG 61.328 63.158 0.00 0.00 0.00 3.77
316 351 1.598130 GTCTGGAGCAAGCGTTGGT 60.598 57.895 2.78 2.78 45.34 3.67
317 352 1.597854 TCTGGAGCAAGCGTTGGTG 60.598 57.895 7.07 0.00 42.23 4.17
318 353 1.893808 CTGGAGCAAGCGTTGGTGT 60.894 57.895 7.07 0.00 42.23 4.16
319 354 2.121564 CTGGAGCAAGCGTTGGTGTG 62.122 60.000 7.07 0.00 42.23 3.82
321 356 2.124320 AGCAAGCGTTGGTGTGGT 60.124 55.556 2.41 0.00 40.37 4.16
322 357 2.026014 GCAAGCGTTGGTGTGGTG 59.974 61.111 1.01 0.00 0.00 4.17
325 361 2.480610 AAGCGTTGGTGTGGTGCTG 61.481 57.895 0.00 0.00 35.77 4.41
352 388 1.915266 CTGGGTGTCTGCCTGGAGA 60.915 63.158 0.00 0.00 0.00 3.71
359 395 2.746362 GTGTCTGCCTGGAGAGATTTTG 59.254 50.000 0.00 0.00 0.00 2.44
361 397 1.283029 TCTGCCTGGAGAGATTTTGGG 59.717 52.381 0.00 0.00 0.00 4.12
362 398 1.283029 CTGCCTGGAGAGATTTTGGGA 59.717 52.381 0.00 0.00 0.00 4.37
365 401 1.213926 CCTGGAGAGATTTTGGGAGGG 59.786 57.143 0.00 0.00 0.00 4.30
366 402 1.213926 CTGGAGAGATTTTGGGAGGGG 59.786 57.143 0.00 0.00 0.00 4.79
368 404 1.299939 GAGAGATTTTGGGAGGGGGT 58.700 55.000 0.00 0.00 0.00 4.95
369 405 1.002857 AGAGATTTTGGGAGGGGGTG 58.997 55.000 0.00 0.00 0.00 4.61
370 406 0.999712 GAGATTTTGGGAGGGGGTGA 59.000 55.000 0.00 0.00 0.00 4.02
371 407 1.357761 GAGATTTTGGGAGGGGGTGAA 59.642 52.381 0.00 0.00 0.00 3.18
372 408 1.077169 AGATTTTGGGAGGGGGTGAAC 59.923 52.381 0.00 0.00 0.00 3.18
386 422 2.683933 GAACTCGGGCTGGGGAGA 60.684 66.667 0.00 0.00 34.40 3.71
387 423 2.041265 AACTCGGGCTGGGGAGAT 59.959 61.111 0.00 0.00 34.40 2.75
394 430 2.114838 GCTGGGGAGATGGATGGC 59.885 66.667 0.00 0.00 0.00 4.40
395 431 2.429058 CTGGGGAGATGGATGGCG 59.571 66.667 0.00 0.00 0.00 5.69
396 432 2.366837 TGGGGAGATGGATGGCGT 60.367 61.111 0.00 0.00 0.00 5.68
397 433 2.111878 GGGGAGATGGATGGCGTG 59.888 66.667 0.00 0.00 0.00 5.34
399 435 1.524621 GGGAGATGGATGGCGTGTG 60.525 63.158 0.00 0.00 0.00 3.82
401 437 0.464036 GGAGATGGATGGCGTGTGTA 59.536 55.000 0.00 0.00 0.00 2.90
405 441 0.107703 ATGGATGGCGTGTGTACTGG 60.108 55.000 0.00 0.00 0.00 4.00
406 442 1.188871 TGGATGGCGTGTGTACTGGA 61.189 55.000 0.00 0.00 0.00 3.86
407 443 0.739813 GGATGGCGTGTGTACTGGAC 60.740 60.000 0.00 0.00 0.00 4.02
417 454 4.497674 CGTGTGTACTGGACTAATCTAGGC 60.498 50.000 0.00 0.00 37.75 3.93
422 459 4.528076 ACTGGACTAATCTAGGCTCTGA 57.472 45.455 0.00 0.00 37.75 3.27
447 484 1.060622 CGAGCGTAGTGAGACCGTC 59.939 63.158 0.00 0.00 0.00 4.79
449 486 0.097325 GAGCGTAGTGAGACCGTCTG 59.903 60.000 5.57 0.00 0.00 3.51
450 487 0.321387 AGCGTAGTGAGACCGTCTGA 60.321 55.000 5.57 0.00 0.00 3.27
451 488 0.733729 GCGTAGTGAGACCGTCTGAT 59.266 55.000 5.57 0.00 0.00 2.90
453 490 2.786854 CGTAGTGAGACCGTCTGATTG 58.213 52.381 5.57 0.00 0.00 2.67
454 491 2.531206 GTAGTGAGACCGTCTGATTGC 58.469 52.381 5.57 0.00 0.00 3.56
455 492 1.261480 AGTGAGACCGTCTGATTGCT 58.739 50.000 5.57 0.00 0.00 3.91
456 493 1.203523 AGTGAGACCGTCTGATTGCTC 59.796 52.381 5.57 0.00 0.00 4.26
457 494 1.203523 GTGAGACCGTCTGATTGCTCT 59.796 52.381 5.57 0.00 0.00 4.09
458 495 1.895798 TGAGACCGTCTGATTGCTCTT 59.104 47.619 5.57 0.00 0.00 2.85
459 496 2.266554 GAGACCGTCTGATTGCTCTTG 58.733 52.381 5.57 0.00 0.00 3.02
463 500 1.673923 CCGTCTGATTGCTCTTGCTCA 60.674 52.381 0.00 0.00 40.48 4.26
464 501 1.659601 CGTCTGATTGCTCTTGCTCAG 59.340 52.381 0.00 0.00 40.62 3.35
465 502 2.008329 GTCTGATTGCTCTTGCTCAGG 58.992 52.381 7.21 0.00 40.07 3.86
466 503 1.627329 TCTGATTGCTCTTGCTCAGGT 59.373 47.619 7.21 0.00 40.07 4.00
469 506 1.736681 GATTGCTCTTGCTCAGGTGTC 59.263 52.381 0.00 0.00 40.48 3.67
472 509 0.034616 GCTCTTGCTCAGGTGTCAGT 59.965 55.000 0.00 0.00 36.03 3.41
491 528 8.732531 GTGTCAGTTAGTAGAGTAATCTGAAGT 58.267 37.037 2.23 0.00 33.36 3.01
512 549 7.505923 TGAAGTACATACATACAGATACAGGCT 59.494 37.037 0.00 0.00 0.00 4.58
513 550 7.220741 AGTACATACATACAGATACAGGCTG 57.779 40.000 14.16 14.16 39.26 4.85
514 551 4.887748 ACATACATACAGATACAGGCTGC 58.112 43.478 15.89 0.00 36.86 5.25
516 553 3.465742 ACATACAGATACAGGCTGCTG 57.534 47.619 15.89 16.02 36.86 4.41
518 555 0.465705 TACAGATACAGGCTGCTGGC 59.534 55.000 15.89 9.27 36.86 4.85
521 558 4.864334 ATACAGGCTGCTGGCGGC 62.864 66.667 15.89 17.03 46.87 6.53
546 583 6.763610 CACTTTGAGTTTGAGGGGATAGATAC 59.236 42.308 0.00 0.00 0.00 2.24
550 587 5.221722 TGAGTTTGAGGGGATAGATACATGC 60.222 44.000 0.00 0.00 0.00 4.06
573 610 3.926616 TCTAGTTGCTTGTAGTTGGAGC 58.073 45.455 0.00 0.00 36.95 4.70
574 611 2.638480 AGTTGCTTGTAGTTGGAGCA 57.362 45.000 0.00 0.00 44.03 4.26
581 618 3.690460 CTTGTAGTTGGAGCAAAGGGAT 58.310 45.455 0.00 0.00 0.00 3.85
588 625 2.459644 TGGAGCAAAGGGATGAAATGG 58.540 47.619 0.00 0.00 0.00 3.16
600 637 0.755686 TGAAATGGTTGGTTGGTGGC 59.244 50.000 0.00 0.00 0.00 5.01
601 638 0.755686 GAAATGGTTGGTTGGTGGCA 59.244 50.000 0.00 0.00 0.00 4.92
602 639 0.467804 AAATGGTTGGTTGGTGGCAC 59.532 50.000 9.70 9.70 0.00 5.01
604 641 2.123468 GGTTGGTTGGTGGCACCT 60.123 61.111 34.69 0.00 39.58 4.00
606 643 1.152756 GTTGGTTGGTGGCACCTCT 60.153 57.895 34.69 0.00 39.58 3.69
607 644 0.109723 GTTGGTTGGTGGCACCTCTA 59.890 55.000 34.69 22.62 39.58 2.43
623 664 3.515901 ACCTCTAGTTGTCTGGTTCCATC 59.484 47.826 0.00 0.00 0.00 3.51
637 678 4.164221 TGGTTCCATCCTAGTTCTTCATCC 59.836 45.833 0.00 0.00 0.00 3.51
638 679 4.445019 GGTTCCATCCTAGTTCTTCATCCC 60.445 50.000 0.00 0.00 0.00 3.85
639 680 4.007581 TCCATCCTAGTTCTTCATCCCA 57.992 45.455 0.00 0.00 0.00 4.37
641 682 4.788075 TCCATCCTAGTTCTTCATCCCAAA 59.212 41.667 0.00 0.00 0.00 3.28
642 683 5.433051 TCCATCCTAGTTCTTCATCCCAAAT 59.567 40.000 0.00 0.00 0.00 2.32
644 685 6.939163 CCATCCTAGTTCTTCATCCCAAATAG 59.061 42.308 0.00 0.00 0.00 1.73
681 722 2.358898 CACCATACCATACCTTTGCTGC 59.641 50.000 0.00 0.00 0.00 5.25
692 733 2.865551 ACCTTTGCTGCGAAACATTTTG 59.134 40.909 3.56 0.00 0.00 2.44
702 743 3.860378 GCGAAACATTTTGCATCCCAAGA 60.860 43.478 11.04 0.00 44.97 3.02
704 745 3.683365 AACATTTTGCATCCCAAGACC 57.317 42.857 0.00 0.00 34.34 3.85
705 746 1.901833 ACATTTTGCATCCCAAGACCC 59.098 47.619 0.00 0.00 34.34 4.46
706 747 1.901159 CATTTTGCATCCCAAGACCCA 59.099 47.619 0.00 0.00 34.34 4.51
707 748 2.094100 TTTTGCATCCCAAGACCCAA 57.906 45.000 0.00 0.00 34.34 4.12
708 749 1.631405 TTTGCATCCCAAGACCCAAG 58.369 50.000 0.00 0.00 34.34 3.61
711 752 1.380380 CATCCCAAGACCCAAGGGC 60.380 63.158 4.70 0.00 42.52 5.19
712 753 1.544917 ATCCCAAGACCCAAGGGCT 60.545 57.895 4.70 0.44 42.52 5.19
714 755 2.036256 CCAAGACCCAAGGGCTGG 59.964 66.667 4.70 6.10 45.97 4.85
715 756 2.845345 CCAAGACCCAAGGGCTGGT 61.845 63.158 4.70 0.00 44.76 4.00
718 759 3.971702 GACCCAAGGGCTGGTGCT 61.972 66.667 4.70 0.00 44.76 4.40
719 760 2.531685 ACCCAAGGGCTGGTGCTA 60.532 61.111 4.70 0.00 44.76 3.49
720 761 2.273449 CCCAAGGGCTGGTGCTAG 59.727 66.667 0.00 0.00 44.76 3.42
721 762 2.439156 CCAAGGGCTGGTGCTAGC 60.439 66.667 8.10 8.10 40.78 3.42
722 763 2.673523 CAAGGGCTGGTGCTAGCT 59.326 61.111 17.23 0.00 43.22 3.32
723 764 1.626356 CCAAGGGCTGGTGCTAGCTA 61.626 60.000 17.23 0.00 43.22 3.32
724 765 0.179062 CAAGGGCTGGTGCTAGCTAG 60.179 60.000 16.84 16.84 43.22 3.42
725 766 0.618968 AAGGGCTGGTGCTAGCTAGT 60.619 55.000 21.62 0.00 43.22 2.57
726 767 1.045911 AGGGCTGGTGCTAGCTAGTC 61.046 60.000 21.62 14.14 43.22 2.59
727 768 1.045911 GGGCTGGTGCTAGCTAGTCT 61.046 60.000 21.62 0.00 43.22 3.24
728 769 1.693627 GGCTGGTGCTAGCTAGTCTA 58.306 55.000 21.62 12.04 43.22 2.59
743 784 6.951971 AGCTAGTCTAGTGTCCAAAATGAAT 58.048 36.000 8.68 0.00 0.00 2.57
744 785 6.820656 AGCTAGTCTAGTGTCCAAAATGAATG 59.179 38.462 8.68 0.00 0.00 2.67
746 787 7.010923 GCTAGTCTAGTGTCCAAAATGAATGAG 59.989 40.741 8.68 0.00 0.00 2.90
747 788 6.773638 AGTCTAGTGTCCAAAATGAATGAGT 58.226 36.000 0.00 0.00 0.00 3.41
749 790 7.173907 AGTCTAGTGTCCAAAATGAATGAGTTG 59.826 37.037 0.00 0.00 0.00 3.16
750 791 7.173218 GTCTAGTGTCCAAAATGAATGAGTTGA 59.827 37.037 0.00 0.00 0.00 3.18
752 793 6.917533 AGTGTCCAAAATGAATGAGTTGATC 58.082 36.000 0.00 0.00 0.00 2.92
753 794 5.796935 GTGTCCAAAATGAATGAGTTGATCG 59.203 40.000 0.00 0.00 0.00 3.69
755 796 6.375174 TGTCCAAAATGAATGAGTTGATCGAT 59.625 34.615 0.00 0.00 0.00 3.59
757 798 6.375174 TCCAAAATGAATGAGTTGATCGATGT 59.625 34.615 0.54 0.00 0.00 3.06
758 799 7.552330 TCCAAAATGAATGAGTTGATCGATGTA 59.448 33.333 0.54 0.00 0.00 2.29
761 815 4.371786 TGAATGAGTTGATCGATGTAGGC 58.628 43.478 0.54 0.00 0.00 3.93
764 818 2.946990 TGAGTTGATCGATGTAGGCGTA 59.053 45.455 0.54 0.00 0.00 4.42
790 844 5.730847 GCTCTTCTGATTTGTGATGCTGATG 60.731 44.000 0.00 0.00 0.00 3.07
793 847 2.361119 CTGATTTGTGATGCTGATGGGG 59.639 50.000 0.00 0.00 0.00 4.96
795 849 0.971959 TTTGTGATGCTGATGGGGCC 60.972 55.000 0.00 0.00 0.00 5.80
812 867 1.300481 GCCTTCTGCCCGTAGAATTC 58.700 55.000 0.00 0.00 36.21 2.17
815 870 2.618053 CTTCTGCCCGTAGAATTCGTT 58.382 47.619 0.00 0.00 36.21 3.85
821 876 2.933906 GCCCGTAGAATTCGTTGATTCA 59.066 45.455 0.00 0.00 38.27 2.57
824 879 4.630069 CCCGTAGAATTCGTTGATTCAGTT 59.370 41.667 0.00 0.00 38.27 3.16
875 932 3.587506 ACTTAGGGAAAGTACATGGCTGT 59.412 43.478 0.00 0.00 46.85 4.40
876 933 2.789409 AGGGAAAGTACATGGCTGTC 57.211 50.000 0.00 0.00 36.79 3.51
879 936 2.359900 GGAAAGTACATGGCTGTCTGG 58.640 52.381 0.00 0.00 36.79 3.86
880 937 2.359900 GAAAGTACATGGCTGTCTGGG 58.640 52.381 0.00 0.00 36.79 4.45
881 938 1.362224 AAGTACATGGCTGTCTGGGT 58.638 50.000 0.00 0.00 36.79 4.51
883 940 1.831736 AGTACATGGCTGTCTGGGTAC 59.168 52.381 0.00 0.00 36.79 3.34
884 941 1.134491 GTACATGGCTGTCTGGGTACC 60.134 57.143 2.17 2.17 42.92 3.34
1113 1176 2.853542 TCCCTGGAGCACAAGCCA 60.854 61.111 0.00 0.00 43.56 4.75
1134 1197 5.661458 CCAAACGATTCTAAGAGGAAGCTA 58.339 41.667 0.00 0.00 30.48 3.32
1185 1248 2.960170 GCCTTGCTGAGTGCCAAG 59.040 61.111 0.00 0.00 42.00 3.61
1209 1272 2.825836 CTTGCGGATGACCAGGGC 60.826 66.667 0.00 0.00 35.59 5.19
1215 1278 2.501610 GATGACCAGGGCGTCTCC 59.498 66.667 7.36 0.00 33.70 3.71
1368 1431 3.414700 GTCCGTGTGCAGCTTCCG 61.415 66.667 0.00 0.00 0.00 4.30
2352 3065 8.442374 ACTTGGAACCTGTTAGAACCTATTTTA 58.558 33.333 0.00 0.00 0.00 1.52
3111 3863 1.110442 TCTCTAGGCAGCAGCTCTTC 58.890 55.000 0.00 0.00 41.70 2.87
3120 3872 0.826715 AGCAGCTCTTCGCCAGAATA 59.173 50.000 0.00 0.00 40.39 1.75
3192 3944 2.746359 GTGACCACTGGAGCTGCT 59.254 61.111 6.82 0.00 0.00 4.24
3213 3965 2.369654 TGACCTGCAGCAGATCACT 58.630 52.632 24.90 0.08 27.55 3.41
3302 4054 3.482722 ACGTTTCATCGTACTGATCGT 57.517 42.857 8.76 8.76 42.35 3.73
3330 4082 1.302752 GCTGCAGATGGTGGTGACA 60.303 57.895 20.43 0.00 38.70 3.58
3333 4085 2.165167 CTGCAGATGGTGGTGACATTT 58.835 47.619 8.42 0.00 46.14 2.32
3495 4247 1.522092 CTACCAGATCGCCCTGCAA 59.478 57.895 0.00 0.00 32.97 4.08
3668 4420 3.766691 GGTCTAGGTTCGCCCGCA 61.767 66.667 0.00 0.00 38.74 5.69
3806 4558 9.547279 AAGATGTAATTACTTGGGAAGGATTTT 57.453 29.630 16.33 0.00 0.00 1.82
3921 4674 1.265905 GTTTCGGCATTTCGAACCTGT 59.734 47.619 0.00 0.00 46.85 4.00
3975 4730 6.258287 TGATCTTTCGAACGAACTTTGGTTTA 59.742 34.615 8.54 0.00 35.58 2.01
4065 4821 1.751351 CTCGGATGCCAAGTCTACTCA 59.249 52.381 0.00 0.00 0.00 3.41
4066 4822 1.476891 TCGGATGCCAAGTCTACTCAC 59.523 52.381 0.00 0.00 0.00 3.51
4087 4843 4.915704 ACGTGTGATGTTTCGTGAAAAAT 58.084 34.783 0.00 0.00 35.24 1.82
4091 4847 7.485277 ACGTGTGATGTTTCGTGAAAAATAAAA 59.515 29.630 0.00 0.00 35.24 1.52
4092 4848 7.781156 CGTGTGATGTTTCGTGAAAAATAAAAC 59.219 33.333 0.00 0.00 28.83 2.43
4110 4866 3.732048 AACCCAGGAAATGTATCCGTT 57.268 42.857 0.00 0.00 44.60 4.44
4123 4879 6.861065 ATGTATCCGTTGCGAAGAAAATAT 57.139 33.333 0.00 0.00 0.00 1.28
4130 4886 5.276868 CCGTTGCGAAGAAAATATAGTCTGG 60.277 44.000 0.00 0.00 0.00 3.86
4132 4888 4.127171 TGCGAAGAAAATATAGTCTGGCC 58.873 43.478 0.00 0.00 0.00 5.36
4137 4893 7.523380 GCGAAGAAAATATAGTCTGGCCTACTA 60.523 40.741 17.46 17.46 34.11 1.82
4147 4903 3.007398 GTCTGGCCTACTATCCATCCAAG 59.993 52.174 3.32 0.00 0.00 3.61
4206 4962 6.978343 TTTTGTCACGGATACATTTCCTAG 57.022 37.500 0.00 0.00 33.30 3.02
4208 4964 6.778834 TTGTCACGGATACATTTCCTAGTA 57.221 37.500 0.00 0.00 33.30 1.82
4209 4965 6.971726 TGTCACGGATACATTTCCTAGTAT 57.028 37.500 0.00 0.00 33.30 2.12
4212 4968 9.085645 TGTCACGGATACATTTCCTAGTATATT 57.914 33.333 0.00 0.00 33.30 1.28
4213 4969 9.924650 GTCACGGATACATTTCCTAGTATATTT 57.075 33.333 0.00 0.00 33.30 1.40
4250 5006 5.183904 ACAAAAATAGATTGGACACTCAGGC 59.816 40.000 0.00 0.00 32.02 4.85
4259 5015 3.378512 TGGACACTCAGGCTTGATATCT 58.621 45.455 0.00 0.00 31.68 1.98
4266 5023 6.995091 ACACTCAGGCTTGATATCTAAAATCC 59.005 38.462 0.00 0.00 31.68 3.01
4314 5075 8.903059 TTTAACTTAATGTTCATATTGGGGGT 57.097 30.769 0.00 0.00 39.89 4.95
4335 5096 4.290622 AGCACCCAGTTGCCCCAG 62.291 66.667 0.00 0.00 44.14 4.45
4426 5189 6.177610 AGACTTTTTGTAGGACTGTTCACAA 58.822 36.000 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.837291 CCTCCTCCTCCGGCTCTG 60.837 72.222 0.00 0.00 0.00 3.35
20 21 2.169590 TTTCCTCCTCCTCCGGCTCT 62.170 60.000 0.00 0.00 0.00 4.09
21 22 1.265454 TTTTCCTCCTCCTCCGGCTC 61.265 60.000 0.00 0.00 0.00 4.70
22 23 0.840722 TTTTTCCTCCTCCTCCGGCT 60.841 55.000 0.00 0.00 0.00 5.52
77 78 0.756442 TGTATAAGTAGCGGGGCGGT 60.756 55.000 0.00 0.00 41.50 5.68
78 79 0.319297 GTGTATAAGTAGCGGGGCGG 60.319 60.000 0.00 0.00 0.00 6.13
79 80 0.672342 AGTGTATAAGTAGCGGGGCG 59.328 55.000 0.00 0.00 0.00 6.13
80 81 1.335689 CGAGTGTATAAGTAGCGGGGC 60.336 57.143 0.00 0.00 0.00 5.80
81 82 1.268899 CCGAGTGTATAAGTAGCGGGG 59.731 57.143 0.00 0.00 34.08 5.73
111 112 0.179000 CGATTGTGAGGGAAGGGGAG 59.821 60.000 0.00 0.00 0.00 4.30
112 113 1.910580 GCGATTGTGAGGGAAGGGGA 61.911 60.000 0.00 0.00 0.00 4.81
115 121 1.452108 GGGCGATTGTGAGGGAAGG 60.452 63.158 0.00 0.00 0.00 3.46
118 124 0.909610 AAGAGGGCGATTGTGAGGGA 60.910 55.000 0.00 0.00 0.00 4.20
134 140 2.687566 GGCGGAAGAGGGGGAAGA 60.688 66.667 0.00 0.00 0.00 2.87
191 202 6.673106 TCGGAACAAATCGAATCAAATCAAA 58.327 32.000 0.00 0.00 32.11 2.69
192 203 6.247727 TCGGAACAAATCGAATCAAATCAA 57.752 33.333 0.00 0.00 32.11 2.57
194 205 7.740519 AATTCGGAACAAATCGAATCAAATC 57.259 32.000 10.64 0.00 40.31 2.17
195 206 7.812191 TGAAATTCGGAACAAATCGAATCAAAT 59.188 29.630 10.64 0.44 40.31 2.32
196 207 7.142021 TGAAATTCGGAACAAATCGAATCAAA 58.858 30.769 10.64 0.00 40.31 2.69
197 208 6.673106 TGAAATTCGGAACAAATCGAATCAA 58.327 32.000 10.64 0.00 40.31 2.57
203 236 4.083581 AGCTGAAATTCGGAACAAATCG 57.916 40.909 5.91 0.00 0.00 3.34
209 242 3.981416 GGTTTGAAGCTGAAATTCGGAAC 59.019 43.478 5.91 0.75 0.00 3.62
221 254 2.985847 GCGGGCAGGTTTGAAGCT 60.986 61.111 0.00 0.00 37.19 3.74
235 268 3.417275 CTGCGTAGGACCTGAGCGG 62.417 68.421 14.76 14.76 39.35 5.52
236 269 2.103143 CTGCGTAGGACCTGAGCG 59.897 66.667 3.53 7.39 0.00 5.03
240 273 2.010582 GCTCCTCTGCGTAGGACCTG 62.011 65.000 3.53 0.00 40.86 4.00
241 274 1.755008 GCTCCTCTGCGTAGGACCT 60.755 63.158 0.00 0.00 40.86 3.85
242 275 1.395826 ATGCTCCTCTGCGTAGGACC 61.396 60.000 0.00 0.00 40.86 4.46
244 277 1.109920 GGATGCTCCTCTGCGTAGGA 61.110 60.000 0.00 6.67 43.58 2.94
248 281 3.842923 CGGGATGCTCCTCTGCGT 61.843 66.667 2.79 0.00 36.57 5.24
258 291 0.249911 AACGGAATCTAGCGGGATGC 60.250 55.000 0.00 0.00 46.98 3.91
260 293 1.120530 ACAACGGAATCTAGCGGGAT 58.879 50.000 0.00 0.00 0.00 3.85
261 294 0.899720 AACAACGGAATCTAGCGGGA 59.100 50.000 0.00 0.00 0.00 5.14
267 300 3.197116 GGGAGGAGAAACAACGGAATCTA 59.803 47.826 0.00 0.00 0.00 1.98
298 333 1.598130 ACCAACGCTTGCTCCAGAC 60.598 57.895 0.00 0.00 0.00 3.51
304 339 2.124320 ACCACACCAACGCTTGCT 60.124 55.556 0.00 0.00 0.00 3.91
314 349 2.542907 CGAACACCAGCACCACACC 61.543 63.158 0.00 0.00 0.00 4.16
315 350 1.772063 GACGAACACCAGCACCACAC 61.772 60.000 0.00 0.00 0.00 3.82
316 351 1.522806 GACGAACACCAGCACCACA 60.523 57.895 0.00 0.00 0.00 4.17
317 352 1.227556 AGACGAACACCAGCACCAC 60.228 57.895 0.00 0.00 0.00 4.16
318 353 1.227527 CAGACGAACACCAGCACCA 60.228 57.895 0.00 0.00 0.00 4.17
319 354 1.961277 CCAGACGAACACCAGCACC 60.961 63.158 0.00 0.00 0.00 5.01
321 356 2.425592 CCCAGACGAACACCAGCA 59.574 61.111 0.00 0.00 0.00 4.41
322 357 1.961277 CACCCAGACGAACACCAGC 60.961 63.158 0.00 0.00 0.00 4.85
325 361 0.600255 CAGACACCCAGACGAACACC 60.600 60.000 0.00 0.00 0.00 4.16
352 388 1.077169 GTTCACCCCCTCCCAAAATCT 59.923 52.381 0.00 0.00 0.00 2.40
359 395 3.400054 CCGAGTTCACCCCCTCCC 61.400 72.222 0.00 0.00 0.00 4.30
361 397 4.097361 GCCCGAGTTCACCCCCTC 62.097 72.222 0.00 0.00 0.00 4.30
362 398 4.658786 AGCCCGAGTTCACCCCCT 62.659 66.667 0.00 0.00 0.00 4.79
365 401 4.410400 CCCAGCCCGAGTTCACCC 62.410 72.222 0.00 0.00 0.00 4.61
366 402 4.410400 CCCCAGCCCGAGTTCACC 62.410 72.222 0.00 0.00 0.00 4.02
368 404 2.822643 ATCTCCCCAGCCCGAGTTCA 62.823 60.000 0.00 0.00 0.00 3.18
369 405 2.066999 ATCTCCCCAGCCCGAGTTC 61.067 63.158 0.00 0.00 0.00 3.01
370 406 2.041265 ATCTCCCCAGCCCGAGTT 59.959 61.111 0.00 0.00 0.00 3.01
371 407 2.765807 CATCTCCCCAGCCCGAGT 60.766 66.667 0.00 0.00 0.00 4.18
372 408 3.554342 CCATCTCCCCAGCCCGAG 61.554 72.222 0.00 0.00 0.00 4.63
386 422 0.107703 CCAGTACACACGCCATCCAT 60.108 55.000 0.00 0.00 0.00 3.41
387 423 1.188871 TCCAGTACACACGCCATCCA 61.189 55.000 0.00 0.00 0.00 3.41
394 430 4.497674 GCCTAGATTAGTCCAGTACACACG 60.498 50.000 0.00 0.00 0.00 4.49
395 431 4.645588 AGCCTAGATTAGTCCAGTACACAC 59.354 45.833 0.00 0.00 0.00 3.82
396 432 4.868268 AGCCTAGATTAGTCCAGTACACA 58.132 43.478 0.00 0.00 0.00 3.72
397 433 5.009210 CAGAGCCTAGATTAGTCCAGTACAC 59.991 48.000 0.00 0.00 0.00 2.90
399 435 5.378332 TCAGAGCCTAGATTAGTCCAGTAC 58.622 45.833 0.00 0.00 0.00 2.73
401 437 4.528076 TCAGAGCCTAGATTAGTCCAGT 57.472 45.455 0.00 0.00 0.00 4.00
417 454 0.588737 TACGCTCGCAGCTATCAGAG 59.411 55.000 6.58 0.00 39.60 3.35
422 459 0.309302 CTCACTACGCTCGCAGCTAT 59.691 55.000 6.58 0.00 39.60 2.97
433 470 2.786854 CAATCAGACGGTCTCACTACG 58.213 52.381 7.89 0.00 0.00 3.51
434 471 2.164624 AGCAATCAGACGGTCTCACTAC 59.835 50.000 7.89 0.00 0.00 2.73
447 484 1.738350 CACCTGAGCAAGAGCAATCAG 59.262 52.381 0.00 0.00 45.49 2.90
449 486 1.736681 GACACCTGAGCAAGAGCAATC 59.263 52.381 0.00 0.00 45.49 2.67
450 487 1.072806 TGACACCTGAGCAAGAGCAAT 59.927 47.619 0.00 0.00 45.49 3.56
451 488 0.469494 TGACACCTGAGCAAGAGCAA 59.531 50.000 0.00 0.00 45.49 3.91
453 490 0.034616 ACTGACACCTGAGCAAGAGC 59.965 55.000 0.00 0.00 42.56 4.09
454 491 2.540265 AACTGACACCTGAGCAAGAG 57.460 50.000 0.00 0.00 0.00 2.85
455 492 2.965831 ACTAACTGACACCTGAGCAAGA 59.034 45.455 0.00 0.00 0.00 3.02
456 493 3.393089 ACTAACTGACACCTGAGCAAG 57.607 47.619 0.00 0.00 0.00 4.01
457 494 4.149598 TCTACTAACTGACACCTGAGCAA 58.850 43.478 0.00 0.00 0.00 3.91
458 495 3.759086 CTCTACTAACTGACACCTGAGCA 59.241 47.826 0.00 0.00 0.00 4.26
459 496 3.759618 ACTCTACTAACTGACACCTGAGC 59.240 47.826 0.00 0.00 0.00 4.26
463 500 7.403671 TCAGATTACTCTACTAACTGACACCT 58.596 38.462 0.00 0.00 0.00 4.00
464 501 7.627298 TCAGATTACTCTACTAACTGACACC 57.373 40.000 0.00 0.00 0.00 4.16
465 502 8.732531 ACTTCAGATTACTCTACTAACTGACAC 58.267 37.037 0.00 0.00 33.64 3.67
466 503 8.865420 ACTTCAGATTACTCTACTAACTGACA 57.135 34.615 0.00 0.00 33.64 3.58
491 528 5.775195 AGCAGCCTGTATCTGTATGTATGTA 59.225 40.000 0.00 0.00 34.21 2.29
496 533 2.103771 CCAGCAGCCTGTATCTGTATGT 59.896 50.000 0.00 0.00 37.38 2.29
499 536 0.465705 GCCAGCAGCCTGTATCTGTA 59.534 55.000 0.00 0.00 37.38 2.74
500 537 1.222936 GCCAGCAGCCTGTATCTGT 59.777 57.895 0.00 0.00 37.38 3.41
502 539 2.503061 CGCCAGCAGCCTGTATCT 59.497 61.111 0.00 0.00 38.78 1.98
503 540 2.590007 CCGCCAGCAGCCTGTATC 60.590 66.667 0.00 0.00 38.78 2.24
504 541 4.864334 GCCGCCAGCAGCCTGTAT 62.864 66.667 0.00 0.00 42.97 2.29
513 550 2.075426 AAACTCAAAGTGCCGCCAGC 62.075 55.000 0.00 0.00 44.14 4.85
514 551 0.318107 CAAACTCAAAGTGCCGCCAG 60.318 55.000 0.00 0.00 0.00 4.85
516 553 0.040067 CTCAAACTCAAAGTGCCGCC 60.040 55.000 0.00 0.00 0.00 6.13
518 555 0.593128 CCCTCAAACTCAAAGTGCCG 59.407 55.000 0.00 0.00 0.00 5.69
521 558 5.165961 TCTATCCCCTCAAACTCAAAGTG 57.834 43.478 0.00 0.00 0.00 3.16
522 559 6.443849 TGTATCTATCCCCTCAAACTCAAAGT 59.556 38.462 0.00 0.00 0.00 2.66
525 562 6.688922 GCATGTATCTATCCCCTCAAACTCAA 60.689 42.308 0.00 0.00 0.00 3.02
526 563 5.221722 GCATGTATCTATCCCCTCAAACTCA 60.222 44.000 0.00 0.00 0.00 3.41
527 564 5.241662 GCATGTATCTATCCCCTCAAACTC 58.758 45.833 0.00 0.00 0.00 3.01
528 565 4.042187 GGCATGTATCTATCCCCTCAAACT 59.958 45.833 0.00 0.00 0.00 2.66
529 566 4.042187 AGGCATGTATCTATCCCCTCAAAC 59.958 45.833 0.00 0.00 0.00 2.93
546 583 3.866651 ACTACAAGCAACTAGAGGCATG 58.133 45.455 11.78 11.84 35.08 4.06
550 587 4.499183 CTCCAACTACAAGCAACTAGAGG 58.501 47.826 0.00 0.00 0.00 3.69
573 610 4.317488 CAACCAACCATTTCATCCCTTTG 58.683 43.478 0.00 0.00 0.00 2.77
574 611 3.327464 CCAACCAACCATTTCATCCCTTT 59.673 43.478 0.00 0.00 0.00 3.11
575 612 2.905736 CCAACCAACCATTTCATCCCTT 59.094 45.455 0.00 0.00 0.00 3.95
581 618 0.755686 GCCACCAACCAACCATTTCA 59.244 50.000 0.00 0.00 0.00 2.69
588 625 0.109723 TAGAGGTGCCACCAACCAAC 59.890 55.000 17.80 0.21 41.95 3.77
600 637 2.632996 TGGAACCAGACAACTAGAGGTG 59.367 50.000 0.00 0.00 31.86 4.00
601 638 2.972348 TGGAACCAGACAACTAGAGGT 58.028 47.619 0.00 0.00 0.00 3.85
602 639 3.118592 GGATGGAACCAGACAACTAGAGG 60.119 52.174 0.00 0.00 0.00 3.69
604 641 3.791320 AGGATGGAACCAGACAACTAGA 58.209 45.455 0.00 0.00 0.00 2.43
606 643 4.684724 ACTAGGATGGAACCAGACAACTA 58.315 43.478 0.00 0.00 0.00 2.24
607 644 3.521727 ACTAGGATGGAACCAGACAACT 58.478 45.455 0.00 0.00 0.00 3.16
623 664 5.934781 AGCTATTTGGGATGAAGAACTAGG 58.065 41.667 0.00 0.00 0.00 3.02
637 678 3.012518 CCACCAGACAAGAGCTATTTGG 58.987 50.000 8.43 8.43 0.00 3.28
638 679 3.686726 GTCCACCAGACAAGAGCTATTTG 59.313 47.826 8.48 8.48 45.55 2.32
639 680 3.944087 GTCCACCAGACAAGAGCTATTT 58.056 45.455 0.00 0.00 45.55 1.40
661 702 2.654863 GCAGCAAAGGTATGGTATGGT 58.345 47.619 0.00 0.00 0.00 3.55
662 703 1.603802 CGCAGCAAAGGTATGGTATGG 59.396 52.381 0.00 0.00 0.00 2.74
663 704 2.560504 TCGCAGCAAAGGTATGGTATG 58.439 47.619 0.00 0.00 0.00 2.39
664 705 3.275617 TTCGCAGCAAAGGTATGGTAT 57.724 42.857 0.00 0.00 0.00 2.73
665 706 2.745281 GTTTCGCAGCAAAGGTATGGTA 59.255 45.455 0.00 0.00 0.00 3.25
666 707 1.539827 GTTTCGCAGCAAAGGTATGGT 59.460 47.619 0.00 0.00 0.00 3.55
667 708 1.539388 TGTTTCGCAGCAAAGGTATGG 59.461 47.619 0.00 0.00 0.00 2.74
668 709 2.987413 TGTTTCGCAGCAAAGGTATG 57.013 45.000 0.00 0.00 0.00 2.39
669 710 4.519540 AAATGTTTCGCAGCAAAGGTAT 57.480 36.364 0.00 0.00 0.00 2.73
671 712 2.865551 CAAAATGTTTCGCAGCAAAGGT 59.134 40.909 0.00 0.00 0.00 3.50
672 713 2.348779 GCAAAATGTTTCGCAGCAAAGG 60.349 45.455 0.00 0.00 0.00 3.11
673 714 2.284684 TGCAAAATGTTTCGCAGCAAAG 59.715 40.909 0.00 0.00 0.00 2.77
681 722 3.674753 GTCTTGGGATGCAAAATGTTTCG 59.325 43.478 0.00 0.00 0.00 3.46
692 733 1.380380 CCCTTGGGTCTTGGGATGC 60.380 63.158 0.00 0.00 43.47 3.91
696 737 2.036256 CAGCCCTTGGGTCTTGGG 59.964 66.667 7.61 0.00 43.62 4.12
705 746 0.179062 CTAGCTAGCACCAGCCCTTG 60.179 60.000 18.83 0.00 42.84 3.61
706 747 0.618968 ACTAGCTAGCACCAGCCCTT 60.619 55.000 20.91 0.00 42.84 3.95
707 748 1.002274 ACTAGCTAGCACCAGCCCT 59.998 57.895 20.91 0.00 42.84 5.19
708 749 1.045911 AGACTAGCTAGCACCAGCCC 61.046 60.000 20.91 6.68 42.84 5.19
718 759 7.476540 TTCATTTTGGACACTAGACTAGCTA 57.523 36.000 9.52 0.00 0.00 3.32
719 760 6.360370 TTCATTTTGGACACTAGACTAGCT 57.640 37.500 9.52 0.00 0.00 3.32
720 761 6.818644 TCATTCATTTTGGACACTAGACTAGC 59.181 38.462 9.52 0.00 0.00 3.42
721 762 8.037758 ACTCATTCATTTTGGACACTAGACTAG 58.962 37.037 8.00 8.00 0.00 2.57
722 763 7.907389 ACTCATTCATTTTGGACACTAGACTA 58.093 34.615 0.00 0.00 0.00 2.59
723 764 6.773638 ACTCATTCATTTTGGACACTAGACT 58.226 36.000 0.00 0.00 0.00 3.24
724 765 7.173218 TCAACTCATTCATTTTGGACACTAGAC 59.827 37.037 0.00 0.00 0.00 2.59
725 766 7.223584 TCAACTCATTCATTTTGGACACTAGA 58.776 34.615 0.00 0.00 0.00 2.43
726 767 7.439157 TCAACTCATTCATTTTGGACACTAG 57.561 36.000 0.00 0.00 0.00 2.57
727 768 7.148423 CGATCAACTCATTCATTTTGGACACTA 60.148 37.037 0.00 0.00 0.00 2.74
728 769 6.348786 CGATCAACTCATTCATTTTGGACACT 60.349 38.462 0.00 0.00 0.00 3.55
743 784 1.749063 ACGCCTACATCGATCAACTCA 59.251 47.619 0.00 0.00 0.00 3.41
744 785 2.493713 ACGCCTACATCGATCAACTC 57.506 50.000 0.00 0.00 0.00 3.01
746 787 2.408704 GCATACGCCTACATCGATCAAC 59.591 50.000 0.00 0.00 0.00 3.18
747 788 2.296190 AGCATACGCCTACATCGATCAA 59.704 45.455 0.00 0.00 39.83 2.57
749 790 2.162608 AGAGCATACGCCTACATCGATC 59.837 50.000 0.00 0.00 39.83 3.69
750 791 2.163509 AGAGCATACGCCTACATCGAT 58.836 47.619 0.00 0.00 39.83 3.59
752 793 2.030717 AGAAGAGCATACGCCTACATCG 60.031 50.000 0.00 0.00 39.83 3.84
753 794 3.004839 TCAGAAGAGCATACGCCTACATC 59.995 47.826 0.00 0.00 39.83 3.06
755 796 2.375146 TCAGAAGAGCATACGCCTACA 58.625 47.619 0.00 0.00 39.83 2.74
757 798 4.141937 ACAAATCAGAAGAGCATACGCCTA 60.142 41.667 0.00 0.00 39.83 3.93
758 799 3.201290 CAAATCAGAAGAGCATACGCCT 58.799 45.455 0.00 0.00 39.83 5.52
761 815 5.735324 CATCACAAATCAGAAGAGCATACG 58.265 41.667 0.00 0.00 0.00 3.06
764 818 4.096532 CAGCATCACAAATCAGAAGAGCAT 59.903 41.667 0.00 0.00 0.00 3.79
793 847 1.300481 GAATTCTACGGGCAGAAGGC 58.700 55.000 0.00 0.00 37.93 4.35
795 849 2.295253 ACGAATTCTACGGGCAGAAG 57.705 50.000 3.52 0.00 37.93 2.85
802 857 5.347635 TCAACTGAATCAACGAATTCTACGG 59.652 40.000 3.52 0.00 36.73 4.02
821 876 9.846248 GCTTTGTATCATTAATTCAGTTCAACT 57.154 29.630 0.00 0.00 0.00 3.16
835 890 9.474313 TCCCTAAGTTTAATGCTTTGTATCATT 57.526 29.630 0.00 0.00 36.87 2.57
860 917 2.290323 ACCCAGACAGCCATGTACTTTC 60.290 50.000 0.00 0.00 40.68 2.62
868 925 1.298953 AATGGTACCCAGACAGCCAT 58.701 50.000 10.07 0.00 41.22 4.40
871 928 3.838244 TCATAATGGTACCCAGACAGC 57.162 47.619 10.07 0.00 36.75 4.40
875 932 6.126623 TGCTTTGTATCATAATGGTACCCAGA 60.127 38.462 10.07 0.30 36.75 3.86
876 933 6.061441 TGCTTTGTATCATAATGGTACCCAG 58.939 40.000 10.07 0.00 36.75 4.45
923 980 9.715121 AGACAGAAAATAATCGTTAGTAACCAA 57.285 29.630 7.45 0.00 0.00 3.67
931 988 9.869757 TGAATCAGAGACAGAAAATAATCGTTA 57.130 29.630 0.00 0.00 0.00 3.18
933 990 8.824781 CATGAATCAGAGACAGAAAATAATCGT 58.175 33.333 0.00 0.00 0.00 3.73
934 991 7.797587 GCATGAATCAGAGACAGAAAATAATCG 59.202 37.037 0.00 0.00 0.00 3.34
1113 1176 6.153000 TCAGTAGCTTCCTCTTAGAATCGTTT 59.847 38.462 0.00 0.00 0.00 3.60
1185 1248 1.092345 GGTCATCCGCAAGAGCCTTC 61.092 60.000 0.00 0.00 43.02 3.46
1197 1260 2.501610 GAGACGCCCTGGTCATCC 59.498 66.667 0.00 0.00 39.42 3.51
1350 1413 2.031163 GGAAGCTGCACACGGACT 59.969 61.111 1.02 0.00 0.00 3.85
1452 1515 3.031736 CCCGATAAGGTTGAAGAGGAGA 58.968 50.000 0.00 0.00 38.74 3.71
1560 1623 0.853530 AACCAAGAGGAAAGCCAGGT 59.146 50.000 0.00 0.00 38.69 4.00
1629 1692 2.079158 ACACCAGCAACATCATCGAAG 58.921 47.619 0.00 0.00 0.00 3.79
2164 2375 4.874970 ACATGCAAAAATTCCAGACTGAC 58.125 39.130 3.32 0.00 0.00 3.51
2358 3071 8.469200 CCAAATGTTAAGCAAGATCCAGAATAA 58.531 33.333 0.00 0.00 0.00 1.40
3192 3944 1.297689 GATCTGCTGCAGGTCACCA 59.702 57.895 32.17 12.90 40.93 4.17
3302 4054 2.026542 ACCATCTGCAGCAGAAGAATCA 60.027 45.455 28.78 4.56 44.04 2.57
3330 4082 1.016627 CGATGTCCGACATGCCAAAT 58.983 50.000 18.84 0.00 39.27 2.32
3333 4085 2.186644 CCGATGTCCGACATGCCA 59.813 61.111 18.84 0.00 39.27 4.92
3495 4247 3.148084 CGGTTGTCCCTCACCTGT 58.852 61.111 0.00 0.00 0.00 4.00
3668 4420 8.664669 ACAACAAATTCTCCAACCCTATAAAT 57.335 30.769 0.00 0.00 0.00 1.40
3806 4558 2.433145 CAGGAGCTCTCGCGCAAA 60.433 61.111 14.64 0.00 42.32 3.68
3921 4674 8.708742 CGATGAAAACTGTTGAATGTAGAAGTA 58.291 33.333 0.00 0.00 0.00 2.24
4008 4764 5.772672 ACACTGCCATAGTTTAATCAACCAA 59.227 36.000 0.00 0.00 37.60 3.67
4011 4767 6.086222 CACACACTGCCATAGTTTAATCAAC 58.914 40.000 0.00 0.00 37.60 3.18
4065 4821 4.343811 TTTTTCACGAAACATCACACGT 57.656 36.364 0.00 0.00 39.53 4.49
4066 4822 6.961358 TTATTTTTCACGAAACATCACACG 57.039 33.333 0.00 0.00 0.00 4.49
4087 4843 5.182169 ACGGATACATTTCCTGGGTTTTA 57.818 39.130 0.00 0.00 33.30 1.52
4091 4847 2.944094 GCAACGGATACATTTCCTGGGT 60.944 50.000 0.00 0.00 33.30 4.51
4092 4848 1.676006 GCAACGGATACATTTCCTGGG 59.324 52.381 0.00 0.00 33.30 4.45
4110 4866 4.127171 GGCCAGACTATATTTTCTTCGCA 58.873 43.478 0.00 0.00 0.00 5.10
4123 4879 3.401342 TGGATGGATAGTAGGCCAGACTA 59.599 47.826 17.23 17.23 37.64 2.59
4130 4886 2.370189 ACTGCTTGGATGGATAGTAGGC 59.630 50.000 0.00 0.00 0.00 3.93
4214 4970 9.619316 CCAATCTATTTTTGTGAAATTACGTGA 57.381 29.630 0.00 0.00 0.00 4.35
4215 4971 9.619316 TCCAATCTATTTTTGTGAAATTACGTG 57.381 29.630 0.00 0.00 0.00 4.49
4216 4972 9.620660 GTCCAATCTATTTTTGTGAAATTACGT 57.379 29.630 0.00 0.00 0.00 3.57
4217 4973 9.619316 TGTCCAATCTATTTTTGTGAAATTACG 57.381 29.630 0.00 0.00 0.00 3.18
4229 4985 5.184892 AGCCTGAGTGTCCAATCTATTTT 57.815 39.130 0.00 0.00 0.00 1.82
4232 4988 3.776969 TCAAGCCTGAGTGTCCAATCTAT 59.223 43.478 0.00 0.00 0.00 1.98
4289 5046 8.903059 ACCCCCAATATGAACATTAAGTTAAA 57.097 30.769 0.00 0.00 41.51 1.52
4299 5060 2.622977 GCTCCAACCCCCAATATGAACA 60.623 50.000 0.00 0.00 0.00 3.18
4313 5074 2.564721 GGCAACTGGGTGCTCCAAC 61.565 63.158 10.51 0.00 46.51 3.77
4314 5075 2.203480 GGCAACTGGGTGCTCCAA 60.203 61.111 10.51 0.00 46.51 3.53
4333 5094 4.392940 ACAAACTTGTGGAAGAGGATCTG 58.607 43.478 0.00 0.00 42.67 2.90
4359 5120 2.038952 TGCACTAGCCAGAACTTGTGAT 59.961 45.455 9.71 0.00 43.35 3.06
4410 5172 4.908601 ATCCATTGTGAACAGTCCTACA 57.091 40.909 0.00 0.00 0.00 2.74
4426 5189 6.784473 TGGTGAACTGACTGATAGATATCCAT 59.216 38.462 0.00 0.00 31.71 3.41


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

AutoCloner maintained by Alex Coulton.