Multiple sequence alignment - TraesCS6D01G123600

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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 TraesCS6D01G123600 chr6D 100.000 3518 0 0 1 3518 88773936 88777453 0.000000e+00 6497
1 TraesCS6D01G123600 chr6D 100.000 1288 0 0 3776 5063 88777711 88778998 0.000000e+00 2379
2 TraesCS6D01G123600 chr6D 86.310 935 87 20 1087 2003 5762632 5761721 0.000000e+00 979
3 TraesCS6D01G123600 chr6D 91.579 95 7 1 2562 2655 389976960 389976866 4.110000e-26 130
4 TraesCS6D01G123600 chr6A 94.325 1586 68 7 988 2563 106798292 106799865 0.000000e+00 2410
5 TraesCS6D01G123600 chr6A 93.502 1308 46 15 3776 5063 106800754 106802042 0.000000e+00 1908
6 TraesCS6D01G123600 chr6A 91.800 878 31 10 2642 3518 106799861 106800698 0.000000e+00 1184
7 TraesCS6D01G123600 chr6A 84.071 678 78 19 1 674 106781245 106781896 1.200000e-175 627
8 TraesCS6D01G123600 chr6B 90.353 1586 101 13 988 2556 169108174 169109724 0.000000e+00 2034
9 TraesCS6D01G123600 chr6B 92.466 876 46 3 2645 3518 169109737 169110594 0.000000e+00 1234
10 TraesCS6D01G123600 chr6B 94.781 594 25 2 3776 4368 169110658 169111246 0.000000e+00 920
11 TraesCS6D01G123600 chr6B 90.516 601 24 9 4475 5063 169111275 169111854 0.000000e+00 763
12 TraesCS6D01G123600 chr6B 87.566 378 29 10 1 368 169105543 169105912 6.060000e-114 422
13 TraesCS6D01G123600 chr6B 85.915 355 27 9 610 942 169107817 169108170 1.730000e-94 357
14 TraesCS6D01G123600 chr7A 83.024 1561 187 40 1000 2512 192663131 192664661 0.000000e+00 1343
15 TraesCS6D01G123600 chr7A 86.804 341 37 1 3777 4109 192665829 192666169 1.720000e-99 374
16 TraesCS6D01G123600 chr7A 81.667 180 21 5 2688 2864 192664841 192665011 6.840000e-29 139
17 TraesCS6D01G123600 chr7D 82.750 1513 188 36 1000 2466 185131309 185132794 0.000000e+00 1280
18 TraesCS6D01G123600 chr7D 87.121 396 44 7 2685 3075 185133003 185133396 4.650000e-120 442
19 TraesCS6D01G123600 chr7D 89.062 320 35 0 3779 4098 185134342 185134661 1.020000e-106 398
20 TraesCS6D01G123600 chr7B 82.292 1553 205 37 1000 2512 327268215 327269737 0.000000e+00 1280
21 TraesCS6D01G123600 chr7B 85.211 426 54 8 2691 3111 327269923 327270344 3.620000e-116 429
22 TraesCS6D01G123600 chr7B 89.124 331 36 0 3779 4109 327270912 327271242 3.650000e-111 412
23 TraesCS6D01G123600 chr2B 85.714 420 31 14 1084 1502 103894203 103894594 2.820000e-112 416
24 TraesCS6D01G123600 chr2B 85.083 362 27 10 1087 1448 755624908 755624574 1.350000e-90 344
25 TraesCS6D01G123600 chr4B 96.512 86 3 0 2561 2646 41531416 41531501 5.280000e-30 143
26 TraesCS6D01G123600 chr1D 94.382 89 5 0 2560 2648 138347293 138347205 2.460000e-28 137
27 TraesCS6D01G123600 chr1A 94.382 89 5 0 2560 2648 154576867 154576779 2.460000e-28 137
28 TraesCS6D01G123600 chr5B 92.473 93 6 1 2562 2653 390700633 390700541 1.140000e-26 132
29 TraesCS6D01G123600 chr4A 93.182 88 6 0 2563 2650 724857590 724857677 4.110000e-26 130
30 TraesCS6D01G123600 chr3D 90.722 97 9 0 2558 2654 477907447 477907351 4.110000e-26 130
31 TraesCS6D01G123600 chr3B 90.722 97 9 0 2558 2654 637089785 637089689 4.110000e-26 130
32 TraesCS6D01G123600 chr3A 90.722 97 9 0 2558 2654 621324965 621324869 4.110000e-26 130


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 TraesCS6D01G123600 chr6D 88773936 88778998 5062 False 4438.000000 6497 100.000000 1 5063 2 chr6D.!!$F1 5062
1 TraesCS6D01G123600 chr6D 5761721 5762632 911 True 979.000000 979 86.310000 1087 2003 1 chr6D.!!$R1 916
2 TraesCS6D01G123600 chr6A 106798292 106802042 3750 False 1834.000000 2410 93.209000 988 5063 3 chr6A.!!$F2 4075
3 TraesCS6D01G123600 chr6A 106781245 106781896 651 False 627.000000 627 84.071000 1 674 1 chr6A.!!$F1 673
4 TraesCS6D01G123600 chr6B 169105543 169111854 6311 False 955.000000 2034 90.266167 1 5063 6 chr6B.!!$F1 5062
5 TraesCS6D01G123600 chr7A 192663131 192666169 3038 False 618.666667 1343 83.831667 1000 4109 3 chr7A.!!$F1 3109
6 TraesCS6D01G123600 chr7D 185131309 185134661 3352 False 706.666667 1280 86.311000 1000 4098 3 chr7D.!!$F1 3098
7 TraesCS6D01G123600 chr7B 327268215 327271242 3027 False 707.000000 1280 85.542333 1000 4109 3 chr7B.!!$F1 3109

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
552 604 0.250513 GCTCTGGTACCCTTGTCAGG 59.749 60.000 10.07 0.0 40.45 3.86 F
810 2511 0.898789 TTCTTCCTCTCGGCGGTCTT 60.899 55.000 7.21 0.0 0.00 3.01 F
988 2700 1.115467 ACAGTTCTATCCAGGAGCGG 58.885 55.000 0.00 0.0 0.00 5.52 F
1690 3451 1.277842 AGTTGTACCATCGGCATGTGA 59.722 47.619 0.00 0.0 0.00 3.58 F
1757 3518 1.423541 ACTAATGGGTGTTGGTGCTGA 59.576 47.619 0.00 0.0 0.00 4.26 F
2608 4461 3.004002 ACGTTTTTGTAGGCTAGTTTGGC 59.996 43.478 0.00 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1772 3533 0.394352 ATGATGTTGAAGCCCCCGAC 60.394 55.000 0.0 0.0 0.0 4.79 R
2586 4439 3.004002 GCCAAACTAGCCTACAAAAACGT 59.996 43.478 0.0 0.0 0.0 3.99 R
2587 4440 3.561503 GCCAAACTAGCCTACAAAAACG 58.438 45.455 0.0 0.0 0.0 3.60 R
3323 5375 0.810031 CGCTATGTACTGGGTGGTGC 60.810 60.000 0.0 0.0 0.0 5.01 R
3332 5384 1.141019 CGTGTGCCCGCTATGTACT 59.859 57.895 0.0 0.0 0.0 2.73 R
4559 6995 0.038166 ATGCCCAGTGTTGGTAGGTG 59.962 55.000 0.0 0.0 43.4 4.00 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
122 129 9.987272 CAGAAGAAAAACCCAATCTAAAAAGAT 57.013 29.630 0.00 0.00 0.00 2.40
294 304 3.334583 TTGCCTAAACTCGAGAGCATT 57.665 42.857 21.68 10.64 0.00 3.56
296 306 2.028112 TGCCTAAACTCGAGAGCATTGT 60.028 45.455 21.68 0.00 0.00 2.71
297 307 2.605366 GCCTAAACTCGAGAGCATTGTC 59.395 50.000 21.68 0.00 0.00 3.18
382 434 4.274950 GCTCTTAAGCCTACACACACAAAA 59.725 41.667 0.00 0.00 43.10 2.44
390 442 3.311322 CCTACACACACAAAAGCTCGAAA 59.689 43.478 0.00 0.00 0.00 3.46
394 446 3.311322 CACACACAAAAGCTCGAAACCTA 59.689 43.478 0.00 0.00 0.00 3.08
395 447 3.311596 ACACACAAAAGCTCGAAACCTAC 59.688 43.478 0.00 0.00 0.00 3.18
396 448 3.311322 CACACAAAAGCTCGAAACCTACA 59.689 43.478 0.00 0.00 0.00 2.74
397 449 3.311596 ACACAAAAGCTCGAAACCTACAC 59.688 43.478 0.00 0.00 0.00 2.90
398 450 3.311322 CACAAAAGCTCGAAACCTACACA 59.689 43.478 0.00 0.00 0.00 3.72
399 451 3.311596 ACAAAAGCTCGAAACCTACACAC 59.688 43.478 0.00 0.00 0.00 3.82
400 452 2.902705 AAGCTCGAAACCTACACACA 57.097 45.000 0.00 0.00 0.00 3.72
401 453 2.150397 AGCTCGAAACCTACACACAC 57.850 50.000 0.00 0.00 0.00 3.82
402 454 1.687123 AGCTCGAAACCTACACACACT 59.313 47.619 0.00 0.00 0.00 3.55
403 455 2.889045 AGCTCGAAACCTACACACACTA 59.111 45.455 0.00 0.00 0.00 2.74
404 456 3.319972 AGCTCGAAACCTACACACACTAA 59.680 43.478 0.00 0.00 0.00 2.24
405 457 3.673809 GCTCGAAACCTACACACACTAAG 59.326 47.826 0.00 0.00 0.00 2.18
406 458 4.235360 CTCGAAACCTACACACACTAAGG 58.765 47.826 0.00 0.00 35.14 2.69
407 459 2.735134 CGAAACCTACACACACTAAGGC 59.265 50.000 0.00 0.00 31.98 4.35
408 460 3.554337 CGAAACCTACACACACTAAGGCT 60.554 47.826 0.00 0.00 31.98 4.58
409 461 3.402628 AACCTACACACACTAAGGCTG 57.597 47.619 0.00 0.00 31.98 4.85
411 463 1.676014 CCTACACACACTAAGGCTGCC 60.676 57.143 11.65 11.65 0.00 4.85
412 464 0.323629 TACACACACTAAGGCTGCCC 59.676 55.000 16.57 0.00 0.00 5.36
413 465 1.376466 CACACACTAAGGCTGCCCT 59.624 57.895 16.57 4.69 45.77 5.19
437 489 1.272490 TCGAATCGCCTCTTGAACTGT 59.728 47.619 0.00 0.00 0.00 3.55
451 503 2.425312 TGAACTGTTGTCGCCACAAATT 59.575 40.909 0.00 0.00 44.32 1.82
465 517 4.651778 CCACAAATTGGGAGAGTACAGAA 58.348 43.478 0.00 0.00 42.54 3.02
469 521 4.828072 AATTGGGAGAGTACAGAAGGAC 57.172 45.455 0.00 0.00 0.00 3.85
500 552 2.033194 CCCAACCTTTCGGCTCGAC 61.033 63.158 0.00 0.00 34.89 4.20
506 558 0.457853 CCTTTCGGCTCGACGATTCA 60.458 55.000 0.00 0.00 43.11 2.57
509 561 1.277326 TTCGGCTCGACGATTCAATG 58.723 50.000 0.00 0.00 43.11 2.82
516 568 1.012234 GACGATTCAATGTCGCCGC 60.012 57.895 0.00 0.00 42.56 6.53
536 588 1.672881 CCGAGGATTGAACCATTGCTC 59.327 52.381 0.00 0.00 31.93 4.26
552 604 0.250513 GCTCTGGTACCCTTGTCAGG 59.749 60.000 10.07 0.00 40.45 3.86
557 609 1.923909 GTACCCTTGTCAGGCCCCT 60.924 63.158 0.00 0.00 39.20 4.79
565 617 3.640407 TCAGGCCCCTGAGTGTGC 61.640 66.667 12.86 0.00 46.80 4.57
569 621 2.270986 GGCCCCTGAGTGTGCTTTG 61.271 63.158 0.00 0.00 0.00 2.77
613 2303 6.315891 GGGAAGAATGAGAGAGAAATTGAGTG 59.684 42.308 0.00 0.00 0.00 3.51
616 2306 6.405538 AGAATGAGAGAGAAATTGAGTGACC 58.594 40.000 0.00 0.00 0.00 4.02
649 2340 4.682787 ACTTGCTCAAAGGTTAAACAAGC 58.317 39.130 0.00 0.00 40.51 4.01
691 2382 4.479993 CCCAGGCGCTTCCTCTGG 62.480 72.222 19.29 19.29 45.52 3.86
698 2390 1.153289 CGCTTCCTCTGGGGTGATG 60.153 63.158 0.00 0.00 36.25 3.07
722 2414 2.159382 GCCGTTGGATTCCTTCTTTCA 58.841 47.619 3.95 0.00 0.00 2.69
744 2436 2.550978 AGCCGTTGGATAACTGAATCG 58.449 47.619 0.00 0.00 34.60 3.34
766 2458 3.128242 GCATGACACCCATTCTTCAGAAG 59.872 47.826 3.45 3.45 37.48 2.85
800 2501 5.902431 AGTATTGGCTGTATCTTCTTCCTCT 59.098 40.000 0.00 0.00 0.00 3.69
801 2502 4.744795 TTGGCTGTATCTTCTTCCTCTC 57.255 45.455 0.00 0.00 0.00 3.20
809 2510 1.304217 TTCTTCCTCTCGGCGGTCT 60.304 57.895 7.21 0.00 0.00 3.85
810 2511 0.898789 TTCTTCCTCTCGGCGGTCTT 60.899 55.000 7.21 0.00 0.00 3.01
838 2539 4.154347 CGAGCCCAGCCTCCAGTC 62.154 72.222 0.00 0.00 0.00 3.51
840 2541 4.345286 AGCCCAGCCTCCAGTCCT 62.345 66.667 0.00 0.00 0.00 3.85
841 2542 3.791586 GCCCAGCCTCCAGTCCTC 61.792 72.222 0.00 0.00 0.00 3.71
951 2663 8.052930 GCTCGAAAGCACAGATAATTTCTGGT 62.053 42.308 16.73 5.43 46.38 4.00
952 2664 9.427079 GCTCGAAAGCACAGATAATTTCTGGTT 62.427 40.741 16.73 8.34 46.38 3.67
961 2673 7.709149 CAGATAATTTCTGGTTTCCTTCCTT 57.291 36.000 8.79 0.00 46.89 3.36
962 2674 8.807948 CAGATAATTTCTGGTTTCCTTCCTTA 57.192 34.615 8.79 0.00 46.89 2.69
963 2675 8.678199 CAGATAATTTCTGGTTTCCTTCCTTAC 58.322 37.037 8.79 0.00 46.89 2.34
964 2676 8.390921 AGATAATTTCTGGTTTCCTTCCTTACA 58.609 33.333 0.00 0.00 31.79 2.41
965 2677 9.190317 GATAATTTCTGGTTTCCTTCCTTACAT 57.810 33.333 0.00 0.00 0.00 2.29
966 2678 7.855784 AATTTCTGGTTTCCTTCCTTACATT 57.144 32.000 0.00 0.00 0.00 2.71
967 2679 6.894339 TTTCTGGTTTCCTTCCTTACATTC 57.106 37.500 0.00 0.00 0.00 2.67
968 2680 5.843019 TCTGGTTTCCTTCCTTACATTCT 57.157 39.130 0.00 0.00 0.00 2.40
969 2681 6.945636 TCTGGTTTCCTTCCTTACATTCTA 57.054 37.500 0.00 0.00 0.00 2.10
970 2682 6.708285 TCTGGTTTCCTTCCTTACATTCTAC 58.292 40.000 0.00 0.00 0.00 2.59
971 2683 6.271391 TCTGGTTTCCTTCCTTACATTCTACA 59.729 38.462 0.00 0.00 0.00 2.74
972 2684 6.472887 TGGTTTCCTTCCTTACATTCTACAG 58.527 40.000 0.00 0.00 0.00 2.74
973 2685 6.043938 TGGTTTCCTTCCTTACATTCTACAGT 59.956 38.462 0.00 0.00 0.00 3.55
974 2686 6.940867 GGTTTCCTTCCTTACATTCTACAGTT 59.059 38.462 0.00 0.00 0.00 3.16
975 2687 7.119407 GGTTTCCTTCCTTACATTCTACAGTTC 59.881 40.741 0.00 0.00 0.00 3.01
976 2688 7.554959 TTCCTTCCTTACATTCTACAGTTCT 57.445 36.000 0.00 0.00 0.00 3.01
977 2689 8.660295 TTCCTTCCTTACATTCTACAGTTCTA 57.340 34.615 0.00 0.00 0.00 2.10
978 2690 8.840200 TCCTTCCTTACATTCTACAGTTCTAT 57.160 34.615 0.00 0.00 0.00 1.98
979 2691 8.915036 TCCTTCCTTACATTCTACAGTTCTATC 58.085 37.037 0.00 0.00 0.00 2.08
980 2692 8.145122 CCTTCCTTACATTCTACAGTTCTATCC 58.855 40.741 0.00 0.00 0.00 2.59
981 2693 8.603898 TTCCTTACATTCTACAGTTCTATCCA 57.396 34.615 0.00 0.00 0.00 3.41
982 2694 8.239038 TCCTTACATTCTACAGTTCTATCCAG 57.761 38.462 0.00 0.00 0.00 3.86
983 2695 7.287927 TCCTTACATTCTACAGTTCTATCCAGG 59.712 40.741 0.00 0.00 0.00 4.45
984 2696 7.287927 CCTTACATTCTACAGTTCTATCCAGGA 59.712 40.741 0.00 0.00 0.00 3.86
985 2697 6.723298 ACATTCTACAGTTCTATCCAGGAG 57.277 41.667 0.00 0.00 0.00 3.69
986 2698 5.069781 ACATTCTACAGTTCTATCCAGGAGC 59.930 44.000 0.00 0.00 0.00 4.70
987 2699 3.215151 TCTACAGTTCTATCCAGGAGCG 58.785 50.000 0.00 0.00 0.00 5.03
988 2700 1.115467 ACAGTTCTATCCAGGAGCGG 58.885 55.000 0.00 0.00 0.00 5.52
989 2701 1.342076 ACAGTTCTATCCAGGAGCGGA 60.342 52.381 0.00 0.00 40.07 5.54
991 2703 3.157881 CAGTTCTATCCAGGAGCGGATA 58.842 50.000 0.00 0.00 44.26 2.59
1038 2750 1.575447 ATCCTTGCCCCCACTTCTCC 61.575 60.000 0.00 0.00 0.00 3.71
1048 2769 4.699522 ACTTCTCCCCGCCGCAAC 62.700 66.667 0.00 0.00 0.00 4.17
1114 2835 3.420482 CCCCCTTTCCATCCGCCT 61.420 66.667 0.00 0.00 0.00 5.52
1346 3089 2.997986 GCAATGCTTTTCTGTTCCCATG 59.002 45.455 0.00 0.00 0.00 3.66
1349 3092 1.962807 TGCTTTTCTGTTCCCATGTGG 59.037 47.619 0.00 0.00 0.00 4.17
1653 3412 4.141228 TCTGGTAAGTATCTCCTCCGTGAT 60.141 45.833 0.00 0.00 0.00 3.06
1668 3429 7.875971 TCCTCCGTGATATATGATTCATATCG 58.124 38.462 19.90 16.60 38.00 2.92
1690 3451 1.277842 AGTTGTACCATCGGCATGTGA 59.722 47.619 0.00 0.00 0.00 3.58
1694 3455 3.462982 TGTACCATCGGCATGTGATTAC 58.537 45.455 0.00 0.70 0.00 1.89
1697 3458 4.415881 ACCATCGGCATGTGATTACTTA 57.584 40.909 0.00 0.00 0.00 2.24
1717 3478 7.440523 ACTTAGAAACATCTAAAGTTGGCAG 57.559 36.000 0.54 0.00 32.51 4.85
1757 3518 1.423541 ACTAATGGGTGTTGGTGCTGA 59.576 47.619 0.00 0.00 0.00 4.26
1772 3533 4.202040 TGGTGCTGAAATTTGAGTGTTGAG 60.202 41.667 6.52 0.00 0.00 3.02
1825 3590 8.814038 AAATGAACACTAGCTCCATTTTCTAT 57.186 30.769 0.00 0.00 34.84 1.98
1926 3701 4.080863 AGCTATGACAGGAAGGGTTAACAG 60.081 45.833 8.10 0.00 0.00 3.16
2048 3830 5.576447 ACATATTGGTCCATTTTCGTTCC 57.424 39.130 0.00 0.00 0.00 3.62
2075 3857 7.433425 GTGTCTTCTTTGGAACTTGAAAGATTG 59.567 37.037 0.00 0.00 37.87 2.67
2095 3878 5.549742 TTGAAAGAACCCTGCATTCATTT 57.450 34.783 1.64 0.23 30.81 2.32
2254 4040 3.626930 TGGCCTGTGTCACTTAAAGTTT 58.373 40.909 3.32 0.00 0.00 2.66
2327 4113 9.831054 GTCGATTTATATTGACTTTGAGTAACG 57.169 33.333 6.35 0.00 40.59 3.18
2565 4418 9.534565 TTGTCTAGTTCATGATTGCTAATACTC 57.465 33.333 0.00 0.00 0.00 2.59
2566 4419 8.144478 TGTCTAGTTCATGATTGCTAATACTCC 58.856 37.037 0.00 0.00 0.00 3.85
2567 4420 7.600752 GTCTAGTTCATGATTGCTAATACTCCC 59.399 40.741 0.00 0.00 0.00 4.30
2568 4421 6.506538 AGTTCATGATTGCTAATACTCCCT 57.493 37.500 0.00 0.00 0.00 4.20
2569 4422 6.529220 AGTTCATGATTGCTAATACTCCCTC 58.471 40.000 0.00 0.00 0.00 4.30
2570 4423 5.489792 TCATGATTGCTAATACTCCCTCC 57.510 43.478 0.00 0.00 0.00 4.30
2571 4424 4.907269 TCATGATTGCTAATACTCCCTCCA 59.093 41.667 0.00 0.00 0.00 3.86
2572 4425 5.549228 TCATGATTGCTAATACTCCCTCCAT 59.451 40.000 0.00 0.00 0.00 3.41
2573 4426 6.730507 TCATGATTGCTAATACTCCCTCCATA 59.269 38.462 0.00 0.00 0.00 2.74
2574 4427 7.404104 TCATGATTGCTAATACTCCCTCCATAT 59.596 37.037 0.00 0.00 0.00 1.78
2575 4428 7.187824 TGATTGCTAATACTCCCTCCATATC 57.812 40.000 0.00 0.00 0.00 1.63
2576 4429 6.730507 TGATTGCTAATACTCCCTCCATATCA 59.269 38.462 0.00 0.00 0.00 2.15
2577 4430 7.237471 TGATTGCTAATACTCCCTCCATATCAA 59.763 37.037 0.00 0.00 0.00 2.57
2578 4431 7.387265 TTGCTAATACTCCCTCCATATCAAA 57.613 36.000 0.00 0.00 0.00 2.69
2579 4432 7.387265 TGCTAATACTCCCTCCATATCAAAA 57.613 36.000 0.00 0.00 0.00 2.44
2580 4433 7.988937 TGCTAATACTCCCTCCATATCAAAAT 58.011 34.615 0.00 0.00 0.00 1.82
2581 4434 9.111519 TGCTAATACTCCCTCCATATCAAAATA 57.888 33.333 0.00 0.00 0.00 1.40
2588 4441 8.314751 ACTCCCTCCATATCAAAATATAAGACG 58.685 37.037 0.00 0.00 0.00 4.18
2589 4442 8.202461 TCCCTCCATATCAAAATATAAGACGT 57.798 34.615 0.00 0.00 0.00 4.34
2590 4443 8.656806 TCCCTCCATATCAAAATATAAGACGTT 58.343 33.333 0.00 0.00 0.00 3.99
2591 4444 9.284968 CCCTCCATATCAAAATATAAGACGTTT 57.715 33.333 0.00 0.00 0.00 3.60
2599 4452 9.783256 ATCAAAATATAAGACGTTTTTGTAGGC 57.217 29.630 16.32 0.00 39.13 3.93
2600 4453 9.005777 TCAAAATATAAGACGTTTTTGTAGGCT 57.994 29.630 16.32 0.00 39.13 4.58
2603 4456 9.662947 AAATATAAGACGTTTTTGTAGGCTAGT 57.337 29.630 0.00 0.00 0.00 2.57
2604 4457 9.662947 AATATAAGACGTTTTTGTAGGCTAGTT 57.337 29.630 0.00 0.00 0.00 2.24
2605 4458 7.974482 ATAAGACGTTTTTGTAGGCTAGTTT 57.026 32.000 0.00 0.00 0.00 2.66
2606 4459 5.668558 AGACGTTTTTGTAGGCTAGTTTG 57.331 39.130 0.00 0.00 0.00 2.93
2607 4460 4.514066 AGACGTTTTTGTAGGCTAGTTTGG 59.486 41.667 0.00 0.00 0.00 3.28
2608 4461 3.004002 ACGTTTTTGTAGGCTAGTTTGGC 59.996 43.478 0.00 0.00 0.00 4.52
2628 4481 8.644374 TTTGGCCTACAAAAGTGTCTTATATT 57.356 30.769 3.32 0.00 45.59 1.28
2629 4482 8.644374 TTGGCCTACAAAAGTGTCTTATATTT 57.356 30.769 3.32 0.00 39.30 1.40
2630 4483 8.644374 TGGCCTACAAAAGTGTCTTATATTTT 57.356 30.769 3.32 0.00 39.30 1.82
2631 4484 8.519526 TGGCCTACAAAAGTGTCTTATATTTTG 58.480 33.333 3.32 7.49 44.37 2.44
2632 4485 7.973944 GGCCTACAAAAGTGTCTTATATTTTGG 59.026 37.037 12.32 0.00 43.55 3.28
2633 4486 8.520351 GCCTACAAAAGTGTCTTATATTTTGGT 58.480 33.333 12.32 0.00 43.55 3.67
2640 4493 9.449719 AAAGTGTCTTATATTTTGGTACAGAGG 57.550 33.333 0.00 0.00 42.39 3.69
2641 4494 8.147244 AGTGTCTTATATTTTGGTACAGAGGT 57.853 34.615 0.00 0.00 42.39 3.85
2642 4495 9.263446 AGTGTCTTATATTTTGGTACAGAGGTA 57.737 33.333 0.00 0.00 42.39 3.08
2643 4496 9.530633 GTGTCTTATATTTTGGTACAGAGGTAG 57.469 37.037 0.00 0.00 42.39 3.18
2644 4497 9.263446 TGTCTTATATTTTGGTACAGAGGTAGT 57.737 33.333 0.00 0.00 42.39 2.73
2660 4513 4.508662 AGGTAGTAGTTGCAAATCTCTGC 58.491 43.478 1.02 7.07 42.95 4.26
2921 4827 6.201591 AGAATAGAGGTGGAAGAGTCAAGAT 58.798 40.000 0.00 0.00 0.00 2.40
2981 4887 5.844601 AGGAGAAAGGAGGTAGTTGATAGT 58.155 41.667 0.00 0.00 0.00 2.12
2986 4892 6.674419 AGAAAGGAGGTAGTTGATAGTTCCAT 59.326 38.462 0.00 0.00 0.00 3.41
3026 4932 6.477033 CAGGATCGTTGAGTGGAAATAAGTAG 59.523 42.308 0.00 0.00 0.00 2.57
3323 5375 5.479716 AACTTAACACACACTTCTTTCCG 57.520 39.130 0.00 0.00 0.00 4.30
3332 5384 1.228124 CTTCTTTCCGCACCACCCA 60.228 57.895 0.00 0.00 0.00 4.51
3890 6322 9.161629 GGTAATTTTTAAGCTGCCAAATTACAT 57.838 29.630 28.02 9.21 45.58 2.29
3921 6353 4.632153 TGAGCTGGTTCAGAAAGTAACTC 58.368 43.478 0.00 0.00 32.44 3.01
4092 6524 7.568199 AGAATGCCACCATACTAATTTGTAC 57.432 36.000 1.74 0.00 0.00 2.90
4144 6576 0.598065 GAGCATTGTTGTCCGGCTTT 59.402 50.000 0.00 0.00 34.44 3.51
4270 6702 1.070105 TATATTGCCCCGGTCACGC 59.930 57.895 0.00 0.00 39.22 5.34
4280 6712 0.109781 CCGGTCACGCCTTTCATTTG 60.110 55.000 0.00 0.00 39.22 2.32
4352 6788 5.136105 GGCATTACTCCCTTCATCTGAAAT 58.864 41.667 0.00 0.00 33.07 2.17
4441 6877 1.695242 ACATCACACCGGTTTACAGGA 59.305 47.619 2.97 0.00 35.12 3.86
4458 6894 7.658525 TTACAGGATTACATGGCATTTGAAT 57.341 32.000 0.00 0.00 31.68 2.57
4553 6989 0.322322 TACGATTGGTTTCTGCCGGT 59.678 50.000 1.90 0.00 0.00 5.28
4554 6990 1.234615 ACGATTGGTTTCTGCCGGTG 61.235 55.000 1.90 0.00 0.00 4.94
4555 6991 1.883021 GATTGGTTTCTGCCGGTGG 59.117 57.895 1.90 0.00 0.00 4.61
4569 7005 4.716003 GTGGCTCCACCTACCAAC 57.284 61.111 7.82 0.00 40.79 3.77
4570 7006 1.758592 GTGGCTCCACCTACCAACA 59.241 57.895 7.82 0.00 40.79 3.33
4571 7007 0.605589 GTGGCTCCACCTACCAACAC 60.606 60.000 7.82 0.00 40.79 3.32
4624 7060 8.884124 ATTTACCATCTCCTTTGAATTTCTCA 57.116 30.769 0.00 0.00 0.00 3.27
4688 7125 5.923733 TGTCACCCAAAACTACAAATTGT 57.076 34.783 3.43 3.43 0.00 2.71
4689 7126 7.339721 TCTTGTCACCCAAAACTACAAATTGTA 59.660 33.333 5.66 5.66 31.20 2.41
4691 7128 8.012957 TGTCACCCAAAACTACAAATTGTATT 57.987 30.769 6.27 0.00 31.66 1.89
4692 7129 8.478877 TGTCACCCAAAACTACAAATTGTATTT 58.521 29.630 6.27 4.67 31.66 1.40
4693 7130 8.974408 GTCACCCAAAACTACAAATTGTATTTC 58.026 33.333 6.27 0.00 31.66 2.17
4694 7131 8.145122 TCACCCAAAACTACAAATTGTATTTCC 58.855 33.333 6.27 0.00 31.66 3.13
4835 7284 3.058016 CAGAGGCAAACAGTGTAACCATG 60.058 47.826 0.00 0.00 37.80 3.66
4899 7348 7.095270 ACGGACTTATTACAACTTAACAGAGG 58.905 38.462 0.00 0.00 0.00 3.69
4967 7421 4.849813 ACTGGTCATCTCCAAATGATCA 57.150 40.909 0.00 0.00 42.94 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
193 201 2.144482 TTCCTTCCGTTCGTTCACTC 57.856 50.000 0.00 0.00 0.00 3.51
232 242 9.995003 AATGATGCCTTACAAACAATAGAAAAA 57.005 25.926 0.00 0.00 0.00 1.94
233 243 9.421806 CAATGATGCCTTACAAACAATAGAAAA 57.578 29.630 0.00 0.00 0.00 2.29
378 430 3.311322 TGTGTGTAGGTTTCGAGCTTTTG 59.689 43.478 0.00 0.00 0.00 2.44
382 434 1.687123 AGTGTGTGTAGGTTTCGAGCT 59.313 47.619 0.00 0.00 0.00 4.09
390 442 1.002087 GCAGCCTTAGTGTGTGTAGGT 59.998 52.381 0.00 0.00 0.00 3.08
394 446 1.073199 GGGCAGCCTTAGTGTGTGT 59.927 57.895 12.43 0.00 0.00 3.72
395 447 0.957395 CAGGGCAGCCTTAGTGTGTG 60.957 60.000 12.43 0.00 0.00 3.82
396 448 1.376466 CAGGGCAGCCTTAGTGTGT 59.624 57.895 12.43 0.00 0.00 3.72
397 449 1.377725 CCAGGGCAGCCTTAGTGTG 60.378 63.158 12.43 0.00 0.00 3.82
398 450 3.081554 CCAGGGCAGCCTTAGTGT 58.918 61.111 12.43 0.00 0.00 3.55
399 451 2.439156 GCCAGGGCAGCCTTAGTG 60.439 66.667 12.43 4.08 41.49 2.74
400 452 2.612115 AGCCAGGGCAGCCTTAGT 60.612 61.111 12.43 0.00 44.88 2.24
401 453 2.191641 GAGCCAGGGCAGCCTTAG 59.808 66.667 12.43 0.00 44.88 2.18
402 454 3.785859 CGAGCCAGGGCAGCCTTA 61.786 66.667 12.43 0.00 44.88 2.69
405 457 4.496336 ATTCGAGCCAGGGCAGCC 62.496 66.667 13.63 1.26 44.88 4.85
406 458 2.899339 GATTCGAGCCAGGGCAGC 60.899 66.667 13.63 3.11 44.88 5.25
407 459 2.587194 CGATTCGAGCCAGGGCAG 60.587 66.667 13.63 6.28 44.88 4.85
408 460 4.838152 GCGATTCGAGCCAGGGCA 62.838 66.667 13.63 0.00 44.88 5.36
451 503 3.544698 AAGTCCTTCTGTACTCTCCCA 57.455 47.619 0.00 0.00 0.00 4.37
461 513 5.046304 TGGGATCTCTTGTAAAGTCCTTCTG 60.046 44.000 0.00 0.00 46.34 3.02
465 517 4.019231 GGTTGGGATCTCTTGTAAAGTCCT 60.019 45.833 0.00 0.00 46.34 3.85
500 552 2.324477 GGCGGCGACATTGAATCG 59.676 61.111 12.98 0.00 42.55 3.34
506 558 3.385749 AATCCTCGGCGGCGACATT 62.386 57.895 31.46 25.50 0.00 2.71
509 561 4.508128 TCAATCCTCGGCGGCGAC 62.508 66.667 31.46 7.01 0.00 5.19
516 568 1.672881 GAGCAATGGTTCAATCCTCGG 59.327 52.381 0.00 0.00 0.00 4.63
552 604 1.228245 TCAAAGCACACTCAGGGGC 60.228 57.895 0.00 0.00 0.00 5.80
565 617 6.458615 CCCCAAACTTTTCAAATTGCTCAAAG 60.459 38.462 9.23 9.23 0.00 2.77
569 621 4.702831 TCCCCAAACTTTTCAAATTGCTC 58.297 39.130 0.00 0.00 0.00 4.26
613 2303 6.554334 TTGAGCAAGTTTAACAGTATGGTC 57.446 37.500 12.11 12.11 43.62 4.02
616 2306 6.970484 ACCTTTGAGCAAGTTTAACAGTATG 58.030 36.000 0.00 0.00 46.00 2.39
649 2340 4.176271 TGTATGCTCACTCGTCATTTGAG 58.824 43.478 0.00 0.00 39.89 3.02
691 2382 2.040544 CCAACGGCTGACATCACCC 61.041 63.158 0.00 0.00 0.00 4.61
698 2390 1.087501 GAAGGAATCCAACGGCTGAC 58.912 55.000 0.61 0.00 0.00 3.51
722 2414 3.374058 CGATTCAGTTATCCAACGGCTTT 59.626 43.478 0.00 0.00 39.78 3.51
744 2436 2.715046 TCTGAAGAATGGGTGTCATGC 58.285 47.619 0.00 0.00 35.99 4.06
766 2458 7.385267 AGATACAGCCAATACTGAAGATGATC 58.615 38.462 0.00 0.00 40.25 2.92
780 2481 3.131223 CGAGAGGAAGAAGATACAGCCAA 59.869 47.826 0.00 0.00 0.00 4.52
800 2501 2.577059 GGATGTCAAGACCGCCGA 59.423 61.111 0.00 0.00 0.00 5.54
801 2502 2.885644 CGGATGTCAAGACCGCCG 60.886 66.667 13.71 13.71 40.19 6.46
898 2610 3.260100 CCAGGGTTGAGGGCTGGT 61.260 66.667 0.00 0.00 0.00 4.00
942 2654 7.730332 AGAATGTAAGGAAGGAAACCAGAAATT 59.270 33.333 0.00 0.00 0.00 1.82
943 2655 7.241628 AGAATGTAAGGAAGGAAACCAGAAAT 58.758 34.615 0.00 0.00 0.00 2.17
944 2656 6.610830 AGAATGTAAGGAAGGAAACCAGAAA 58.389 36.000 0.00 0.00 0.00 2.52
945 2657 6.200878 AGAATGTAAGGAAGGAAACCAGAA 57.799 37.500 0.00 0.00 0.00 3.02
946 2658 5.843019 AGAATGTAAGGAAGGAAACCAGA 57.157 39.130 0.00 0.00 0.00 3.86
947 2659 6.472887 TGTAGAATGTAAGGAAGGAAACCAG 58.527 40.000 0.00 0.00 0.00 4.00
949 2661 6.473758 ACTGTAGAATGTAAGGAAGGAAACC 58.526 40.000 0.00 0.00 0.00 3.27
951 2663 7.974504 AGAACTGTAGAATGTAAGGAAGGAAA 58.025 34.615 0.00 0.00 0.00 3.13
952 2664 7.554959 AGAACTGTAGAATGTAAGGAAGGAA 57.445 36.000 0.00 0.00 0.00 3.36
953 2665 8.840200 ATAGAACTGTAGAATGTAAGGAAGGA 57.160 34.615 0.00 0.00 0.00 3.36
954 2666 8.145122 GGATAGAACTGTAGAATGTAAGGAAGG 58.855 40.741 0.00 0.00 0.00 3.46
955 2667 8.696374 TGGATAGAACTGTAGAATGTAAGGAAG 58.304 37.037 0.00 0.00 0.00 3.46
956 2668 8.603898 TGGATAGAACTGTAGAATGTAAGGAA 57.396 34.615 0.00 0.00 0.00 3.36
957 2669 7.287927 CCTGGATAGAACTGTAGAATGTAAGGA 59.712 40.741 0.00 0.00 0.00 3.36
958 2670 7.287927 TCCTGGATAGAACTGTAGAATGTAAGG 59.712 40.741 0.00 0.00 0.00 2.69
959 2671 8.239038 TCCTGGATAGAACTGTAGAATGTAAG 57.761 38.462 0.00 0.00 0.00 2.34
960 2672 7.201920 GCTCCTGGATAGAACTGTAGAATGTAA 60.202 40.741 0.00 0.00 0.00 2.41
961 2673 6.265649 GCTCCTGGATAGAACTGTAGAATGTA 59.734 42.308 0.00 0.00 0.00 2.29
962 2674 5.069781 GCTCCTGGATAGAACTGTAGAATGT 59.930 44.000 0.00 0.00 0.00 2.71
963 2675 5.537188 GCTCCTGGATAGAACTGTAGAATG 58.463 45.833 0.00 0.00 0.00 2.67
964 2676 4.279671 CGCTCCTGGATAGAACTGTAGAAT 59.720 45.833 0.00 0.00 0.00 2.40
965 2677 3.632604 CGCTCCTGGATAGAACTGTAGAA 59.367 47.826 0.00 0.00 0.00 2.10
966 2678 3.215151 CGCTCCTGGATAGAACTGTAGA 58.785 50.000 0.00 0.00 0.00 2.59
967 2679 2.294791 CCGCTCCTGGATAGAACTGTAG 59.705 54.545 0.00 0.00 0.00 2.74
968 2680 2.092049 TCCGCTCCTGGATAGAACTGTA 60.092 50.000 0.00 0.00 31.53 2.74
969 2681 1.115467 CCGCTCCTGGATAGAACTGT 58.885 55.000 0.00 0.00 0.00 3.55
970 2682 1.403814 TCCGCTCCTGGATAGAACTG 58.596 55.000 0.00 0.00 31.53 3.16
971 2683 2.390225 ATCCGCTCCTGGATAGAACT 57.610 50.000 0.00 0.00 46.95 3.01
976 2688 0.041238 CCCCTATCCGCTCCTGGATA 59.959 60.000 0.00 2.75 46.95 2.59
978 2690 2.201490 CCCCTATCCGCTCCTGGA 59.799 66.667 0.00 0.00 43.58 3.86
979 2691 2.122813 ACCCCTATCCGCTCCTGG 60.123 66.667 0.00 0.00 0.00 4.45
980 2692 3.142393 CACCCCTATCCGCTCCTG 58.858 66.667 0.00 0.00 0.00 3.86
981 2693 2.020100 TAGCACCCCTATCCGCTCCT 62.020 60.000 0.00 0.00 35.93 3.69
982 2694 0.905337 ATAGCACCCCTATCCGCTCC 60.905 60.000 0.00 0.00 35.93 4.70
983 2695 0.247736 CATAGCACCCCTATCCGCTC 59.752 60.000 0.00 0.00 34.49 5.03
984 2696 1.831652 GCATAGCACCCCTATCCGCT 61.832 60.000 0.00 0.00 34.49 5.52
985 2697 1.376037 GCATAGCACCCCTATCCGC 60.376 63.158 0.00 0.00 34.49 5.54
986 2698 0.687354 AAGCATAGCACCCCTATCCG 59.313 55.000 0.00 0.00 34.49 4.18
987 2699 1.338200 CGAAGCATAGCACCCCTATCC 60.338 57.143 0.00 0.00 34.49 2.59
988 2700 2.086054 CGAAGCATAGCACCCCTATC 57.914 55.000 0.00 0.00 34.49 2.08
1127 2848 2.047179 GCGGAGGGTTTCGAGCTT 60.047 61.111 0.00 0.00 0.00 3.74
1346 3089 8.406297 GGAATGAATAAACAGATAGAAACCCAC 58.594 37.037 0.00 0.00 0.00 4.61
1349 3092 9.178758 AGTGGAATGAATAAACAGATAGAAACC 57.821 33.333 0.00 0.00 0.00 3.27
1350 3093 9.994432 CAGTGGAATGAATAAACAGATAGAAAC 57.006 33.333 0.00 0.00 0.00 2.78
1680 3441 5.483811 TGTTTCTAAGTAATCACATGCCGA 58.516 37.500 0.00 0.00 0.00 5.54
1690 3451 9.515226 TGCCAACTTTAGATGTTTCTAAGTAAT 57.485 29.630 0.00 0.00 43.53 1.89
1694 3455 6.150140 AGCTGCCAACTTTAGATGTTTCTAAG 59.850 38.462 0.00 0.00 43.53 2.18
1697 3458 4.401925 AGCTGCCAACTTTAGATGTTTCT 58.598 39.130 0.00 0.00 35.90 2.52
1717 3478 7.843490 TTAGTTTCAAGGTACATATGTGAGC 57.157 36.000 18.81 11.47 0.00 4.26
1757 3518 2.884639 CCCCGACTCAACACTCAAATTT 59.115 45.455 0.00 0.00 0.00 1.82
1772 3533 0.394352 ATGATGTTGAAGCCCCCGAC 60.394 55.000 0.00 0.00 0.00 4.79
1889 3660 6.201226 TGTCATAGCTTGAAGTCTCTAGTG 57.799 41.667 0.00 0.00 35.70 2.74
2024 3806 7.272037 GGAACGAAAATGGACCAATATGTAT 57.728 36.000 0.00 0.00 0.00 2.29
2048 3830 4.875544 TTCAAGTTCCAAAGAAGACACG 57.124 40.909 0.00 0.00 30.91 4.49
2075 3857 4.886579 ACAAATGAATGCAGGGTTCTTTC 58.113 39.130 0.00 0.00 0.00 2.62
2095 3878 9.725019 AATGTAAGAATGTCTTCAGTCATAACA 57.275 29.630 0.00 0.00 40.55 2.41
2254 4040 6.814043 GCACCTCTGATGCAGATATATCATA 58.186 40.000 15.08 1.26 39.92 2.15
2563 4416 8.314751 ACGTCTTATATTTTGATATGGAGGGAG 58.685 37.037 0.00 0.00 0.00 4.30
2564 4417 8.202461 ACGTCTTATATTTTGATATGGAGGGA 57.798 34.615 0.00 0.00 0.00 4.20
2565 4418 8.848474 AACGTCTTATATTTTGATATGGAGGG 57.152 34.615 0.00 0.00 0.00 4.30
2573 4426 9.783256 GCCTACAAAAACGTCTTATATTTTGAT 57.217 29.630 21.46 11.72 42.48 2.57
2574 4427 9.005777 AGCCTACAAAAACGTCTTATATTTTGA 57.994 29.630 21.46 9.08 42.48 2.69
2577 4430 9.662947 ACTAGCCTACAAAAACGTCTTATATTT 57.337 29.630 0.00 0.00 0.00 1.40
2578 4431 9.662947 AACTAGCCTACAAAAACGTCTTATATT 57.337 29.630 0.00 0.00 0.00 1.28
2579 4432 9.662947 AAACTAGCCTACAAAAACGTCTTATAT 57.337 29.630 0.00 0.00 0.00 0.86
2580 4433 8.928733 CAAACTAGCCTACAAAAACGTCTTATA 58.071 33.333 0.00 0.00 0.00 0.98
2581 4434 7.094933 CCAAACTAGCCTACAAAAACGTCTTAT 60.095 37.037 0.00 0.00 0.00 1.73
2582 4435 6.203338 CCAAACTAGCCTACAAAAACGTCTTA 59.797 38.462 0.00 0.00 0.00 2.10
2583 4436 5.008316 CCAAACTAGCCTACAAAAACGTCTT 59.992 40.000 0.00 0.00 0.00 3.01
2584 4437 4.514066 CCAAACTAGCCTACAAAAACGTCT 59.486 41.667 0.00 0.00 0.00 4.18
2585 4438 4.779987 CCAAACTAGCCTACAAAAACGTC 58.220 43.478 0.00 0.00 0.00 4.34
2586 4439 3.004002 GCCAAACTAGCCTACAAAAACGT 59.996 43.478 0.00 0.00 0.00 3.99
2587 4440 3.561503 GCCAAACTAGCCTACAAAAACG 58.438 45.455 0.00 0.00 0.00 3.60
2597 4450 7.276584 GACACTTTTGTAGGCCAAACTAGCC 62.277 48.000 5.01 0.00 42.63 3.93
2598 4451 3.568430 ACACTTTTGTAGGCCAAACTAGC 59.432 43.478 5.01 0.00 42.63 3.42
2599 4452 5.063880 AGACACTTTTGTAGGCCAAACTAG 58.936 41.667 5.01 4.99 42.63 2.57
2600 4453 5.043737 AGACACTTTTGTAGGCCAAACTA 57.956 39.130 5.01 0.00 42.63 2.24
2601 4454 3.898482 AGACACTTTTGTAGGCCAAACT 58.102 40.909 5.01 0.00 42.63 2.66
2602 4455 4.649088 AAGACACTTTTGTAGGCCAAAC 57.351 40.909 5.01 2.84 42.63 2.93
2603 4456 8.644374 AATATAAGACACTTTTGTAGGCCAAA 57.356 30.769 5.01 0.00 41.25 3.28
2604 4457 8.644374 AAATATAAGACACTTTTGTAGGCCAA 57.356 30.769 5.01 0.00 35.47 4.52
2605 4458 8.519526 CAAAATATAAGACACTTTTGTAGGCCA 58.480 33.333 5.01 0.00 35.47 5.36
2606 4459 7.973944 CCAAAATATAAGACACTTTTGTAGGCC 59.026 37.037 0.00 0.00 37.04 5.19
2607 4460 8.520351 ACCAAAATATAAGACACTTTTGTAGGC 58.480 33.333 0.00 0.00 37.04 3.93
2614 4467 9.449719 CCTCTGTACCAAAATATAAGACACTTT 57.550 33.333 0.00 0.00 0.00 2.66
2615 4468 8.603304 ACCTCTGTACCAAAATATAAGACACTT 58.397 33.333 0.00 0.00 0.00 3.16
2616 4469 8.147244 ACCTCTGTACCAAAATATAAGACACT 57.853 34.615 0.00 0.00 0.00 3.55
2617 4470 9.530633 CTACCTCTGTACCAAAATATAAGACAC 57.469 37.037 0.00 0.00 0.00 3.67
2618 4471 9.263446 ACTACCTCTGTACCAAAATATAAGACA 57.737 33.333 0.00 0.00 0.00 3.41
2624 4477 7.985752 GCAACTACTACCTCTGTACCAAAATAT 59.014 37.037 0.00 0.00 0.00 1.28
2625 4478 7.038870 TGCAACTACTACCTCTGTACCAAAATA 60.039 37.037 0.00 0.00 0.00 1.40
2626 4479 6.171213 GCAACTACTACCTCTGTACCAAAAT 58.829 40.000 0.00 0.00 0.00 1.82
2627 4480 5.070714 TGCAACTACTACCTCTGTACCAAAA 59.929 40.000 0.00 0.00 0.00 2.44
2628 4481 4.589798 TGCAACTACTACCTCTGTACCAAA 59.410 41.667 0.00 0.00 0.00 3.28
2629 4482 4.154176 TGCAACTACTACCTCTGTACCAA 58.846 43.478 0.00 0.00 0.00 3.67
2630 4483 3.770046 TGCAACTACTACCTCTGTACCA 58.230 45.455 0.00 0.00 0.00 3.25
2631 4484 4.796038 TTGCAACTACTACCTCTGTACC 57.204 45.455 0.00 0.00 0.00 3.34
2632 4485 6.631962 AGATTTGCAACTACTACCTCTGTAC 58.368 40.000 0.00 0.00 0.00 2.90
2633 4486 6.663953 AGAGATTTGCAACTACTACCTCTGTA 59.336 38.462 0.00 0.00 0.00 2.74
2634 4487 5.482175 AGAGATTTGCAACTACTACCTCTGT 59.518 40.000 0.00 0.00 0.00 3.41
2635 4488 5.809562 CAGAGATTTGCAACTACTACCTCTG 59.190 44.000 14.10 14.10 39.07 3.35
2636 4489 5.625656 GCAGAGATTTGCAACTACTACCTCT 60.626 44.000 0.00 0.00 43.53 3.69
2637 4490 4.568760 GCAGAGATTTGCAACTACTACCTC 59.431 45.833 0.00 0.00 43.53 3.85
2638 4491 4.508662 GCAGAGATTTGCAACTACTACCT 58.491 43.478 0.00 0.00 43.53 3.08
2639 4492 4.866682 GCAGAGATTTGCAACTACTACC 57.133 45.455 0.00 0.00 43.53 3.18
2986 4892 8.860088 TCAACGATCCTGAATTCTGATATTAGA 58.140 33.333 13.45 0.00 0.00 2.10
3026 4932 5.371115 TGTTATTAGCAAAACTGGCTGTC 57.629 39.130 0.00 0.00 42.62 3.51
3095 5079 3.312697 CGGCAAGGATTTAGTTCCTAAGC 59.687 47.826 8.52 8.52 45.63 3.09
3152 5173 3.326006 TCTGCTTCTTGATCAAGTCAGGT 59.674 43.478 30.72 0.00 38.29 4.00
3295 5331 4.451096 AGAAGTGTGTGTTAAGTTATGGCG 59.549 41.667 0.00 0.00 0.00 5.69
3297 5333 7.360361 GGAAAGAAGTGTGTGTTAAGTTATGG 58.640 38.462 0.00 0.00 0.00 2.74
3323 5375 0.810031 CGCTATGTACTGGGTGGTGC 60.810 60.000 0.00 0.00 0.00 5.01
3332 5384 1.141019 CGTGTGCCCGCTATGTACT 59.859 57.895 0.00 0.00 0.00 2.73
3890 6322 6.560003 TTCTGAACCAGCTCATCCTATAAA 57.440 37.500 0.00 0.00 0.00 1.40
3939 6371 5.958955 ACAAAGAATCCAGAATTAAGCAGC 58.041 37.500 0.00 0.00 0.00 5.25
4092 6524 2.159142 GCCATGGGAGCAAATCTTCAAG 60.159 50.000 15.13 0.00 0.00 3.02
4144 6576 6.177610 GGTAAAACCACAATCATCTACCAGA 58.822 40.000 0.00 0.00 38.42 3.86
4384 6820 5.685511 TGCAGAAAATCAAACTTAAGAACGC 59.314 36.000 10.09 0.00 0.00 4.84
4458 6894 7.072202 TCTCTAGCTAGCTAGGGTTAGAGTTTA 59.928 40.741 38.51 21.19 45.03 2.01
4553 6989 0.766674 AGTGTTGGTAGGTGGAGCCA 60.767 55.000 0.00 0.00 40.61 4.75
4554 6990 0.321653 CAGTGTTGGTAGGTGGAGCC 60.322 60.000 0.00 0.00 37.58 4.70
4555 6991 0.321653 CCAGTGTTGGTAGGTGGAGC 60.322 60.000 0.00 0.00 39.79 4.70
4556 6992 0.324943 CCCAGTGTTGGTAGGTGGAG 59.675 60.000 0.00 0.00 43.40 3.86
4557 6993 1.774894 GCCCAGTGTTGGTAGGTGGA 61.775 60.000 0.00 0.00 43.40 4.02
4558 6994 1.303317 GCCCAGTGTTGGTAGGTGG 60.303 63.158 0.00 0.00 43.40 4.61
4559 6995 0.038166 ATGCCCAGTGTTGGTAGGTG 59.962 55.000 0.00 0.00 43.40 4.00
4560 6996 0.328258 GATGCCCAGTGTTGGTAGGT 59.672 55.000 0.00 0.00 43.40 3.08
4561 6997 0.394352 GGATGCCCAGTGTTGGTAGG 60.394 60.000 0.00 0.00 43.40 3.18
4562 6998 0.327924 TGGATGCCCAGTGTTGGTAG 59.672 55.000 0.00 0.00 43.40 3.18
4563 6999 2.469162 TGGATGCCCAGTGTTGGTA 58.531 52.632 0.00 0.00 43.40 3.25
4564 7000 3.260297 TGGATGCCCAGTGTTGGT 58.740 55.556 0.00 0.00 43.40 3.67
4648 7084 5.163457 GGTGACAAGATTTCTGGTTTGGAAA 60.163 40.000 0.00 0.00 37.15 3.13
4835 7284 1.009389 CGACCGAGAGCTGTTGAACC 61.009 60.000 0.00 0.00 0.00 3.62
4874 7323 7.095270 CCTCTGTTAAGTTGTAATAAGTCCGT 58.905 38.462 0.00 0.00 0.00 4.69
4899 7348 1.602377 AGCTTGTGTTCCGCTGTTTAC 59.398 47.619 0.00 0.00 31.82 2.01
4961 7415 2.641815 GTGGGGAGCTCCTTATGATCAT 59.358 50.000 31.36 13.81 35.95 2.45
4967 7421 1.003051 ACCGTGGGGAGCTCCTTAT 59.997 57.895 31.36 9.43 36.97 1.73


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

AutoCloner maintained by Alex Coulton.