Multiple sequence alignment - TraesCS3D01G545400

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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 TraesCS3D01G545400 chr3D 100.000 3371 0 0 1 3371 615008999 615005629 0.000000e+00 6226.0
1 TraesCS3D01G545400 chr3D 93.036 718 49 1 2654 3371 30688957 30688241 0.000000e+00 1048.0
2 TraesCS3D01G545400 chr3B 94.097 1711 92 3 951 2653 28798492 28796783 0.000000e+00 2591.0
3 TraesCS3D01G545400 chr3B 93.387 741 49 0 1485 2225 813144077 813144817 0.000000e+00 1098.0
4 TraesCS3D01G545400 chr3B 90.433 554 43 3 949 1492 813142807 813143360 0.000000e+00 721.0
5 TraesCS3D01G545400 chr3B 89.242 409 38 3 22 430 813141866 813142268 1.080000e-139 507.0
6 TraesCS3D01G545400 chr3B 89.189 407 42 2 2223 2629 813148447 813148851 1.080000e-139 507.0
7 TraesCS3D01G545400 chr3B 85.879 347 47 1 2270 2616 28796601 28796257 5.310000e-98 368.0
8 TraesCS3D01G545400 chr3B 83.912 317 26 7 498 802 813142291 813142594 2.560000e-71 279.0
9 TraesCS3D01G545400 chr3B 84.716 229 34 1 2265 2493 813277274 813277047 9.410000e-56 228.0
10 TraesCS3D01G545400 chr3B 92.063 63 5 0 719 781 28800151 28800089 4.630000e-14 89.8
11 TraesCS3D01G545400 chr2D 93.602 719 45 1 2653 3371 174953635 174954352 0.000000e+00 1072.0
12 TraesCS3D01G545400 chr2D 93.324 719 47 1 2653 3371 175740242 175739525 0.000000e+00 1061.0
13 TraesCS3D01G545400 chr6D 93.463 719 46 1 2653 3371 379499626 379498909 0.000000e+00 1066.0
14 TraesCS3D01G545400 chr6D 92.907 719 50 1 2653 3371 413783044 413782327 0.000000e+00 1044.0
15 TraesCS3D01G545400 chr5D 93.324 719 47 1 2653 3371 419410203 419410920 0.000000e+00 1061.0
16 TraesCS3D01G545400 chr7D 93.185 719 48 1 2653 3371 50412335 50413052 0.000000e+00 1055.0
17 TraesCS3D01G545400 chr7D 93.185 719 48 1 2653 3371 207227169 207226452 0.000000e+00 1055.0
18 TraesCS3D01G545400 chr4D 92.907 719 49 2 2653 3371 485606441 485605725 0.000000e+00 1044.0
19 TraesCS3D01G545400 chr1D 91.139 79 7 0 1935 2013 461830400 461830478 1.280000e-19 108.0
20 TraesCS3D01G545400 chr1B 89.873 79 8 0 1935 2013 635492299 635492377 5.950000e-18 102.0


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 TraesCS3D01G545400 chr3D 615005629 615008999 3370 True 6226.000000 6226 100.000000 1 3371 1 chr3D.!!$R2 3370
1 TraesCS3D01G545400 chr3D 30688241 30688957 716 True 1048.000000 1048 93.036000 2654 3371 1 chr3D.!!$R1 717
2 TraesCS3D01G545400 chr3B 28796257 28800151 3894 True 1016.266667 2591 90.679667 719 2653 3 chr3B.!!$R2 1934
3 TraesCS3D01G545400 chr3B 813141866 813148851 6985 False 622.400000 1098 89.232600 22 2629 5 chr3B.!!$F1 2607
4 TraesCS3D01G545400 chr2D 174953635 174954352 717 False 1072.000000 1072 93.602000 2653 3371 1 chr2D.!!$F1 718
5 TraesCS3D01G545400 chr2D 175739525 175740242 717 True 1061.000000 1061 93.324000 2653 3371 1 chr2D.!!$R1 718
6 TraesCS3D01G545400 chr6D 379498909 379499626 717 True 1066.000000 1066 93.463000 2653 3371 1 chr6D.!!$R1 718
7 TraesCS3D01G545400 chr6D 413782327 413783044 717 True 1044.000000 1044 92.907000 2653 3371 1 chr6D.!!$R2 718
8 TraesCS3D01G545400 chr5D 419410203 419410920 717 False 1061.000000 1061 93.324000 2653 3371 1 chr5D.!!$F1 718
9 TraesCS3D01G545400 chr7D 50412335 50413052 717 False 1055.000000 1055 93.185000 2653 3371 1 chr7D.!!$F1 718
10 TraesCS3D01G545400 chr7D 207226452 207227169 717 True 1055.000000 1055 93.185000 2653 3371 1 chr7D.!!$R1 718
11 TraesCS3D01G545400 chr4D 485605725 485606441 716 True 1044.000000 1044 92.907000 2653 3371 1 chr4D.!!$R1 718

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
859 947 0.037697 TCCAATAGCAAGCACGTCGT 60.038 50.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2839 8787 0.036875 ACCACCAAGCTGCTAAGGAC 59.963 55.0 23.02 0.0 0.0 3.85 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
17 18 4.016706 CCCAGACCGTGTCCACCC 62.017 72.222 1.06 0.00 32.18 4.61
18 19 2.923035 CCAGACCGTGTCCACCCT 60.923 66.667 1.06 0.00 32.18 4.34
19 20 2.343758 CAGACCGTGTCCACCCTG 59.656 66.667 1.06 0.00 32.18 4.45
20 21 2.200370 AGACCGTGTCCACCCTGA 59.800 61.111 1.06 0.00 32.18 3.86
49 50 2.602211 GACTCATGTTCATGCTCACTCG 59.398 50.000 7.80 0.00 0.00 4.18
51 52 1.550072 TCATGTTCATGCTCACTCGGA 59.450 47.619 7.80 0.00 0.00 4.55
72 73 1.006758 TGGTCCCCGTACTCATTCTCT 59.993 52.381 0.00 0.00 0.00 3.10
97 98 2.427753 GATCCTGCCCATCCGTCC 59.572 66.667 0.00 0.00 0.00 4.79
109 110 3.550820 CCATCCGTCCAATAATCACCAA 58.449 45.455 0.00 0.00 0.00 3.67
114 115 3.352648 CGTCCAATAATCACCAAGGGTT 58.647 45.455 0.00 0.00 31.02 4.11
122 123 0.107831 TCACCAAGGGTTTGTCGAGG 59.892 55.000 0.00 0.00 31.02 4.63
127 128 1.789576 AAGGGTTTGTCGAGGCCCAT 61.790 55.000 0.00 1.94 43.42 4.00
156 157 2.198827 TGACGGTTCAAAGGCATGAT 57.801 45.000 0.00 0.00 0.00 2.45
157 158 3.342377 TGACGGTTCAAAGGCATGATA 57.658 42.857 0.00 0.00 0.00 2.15
170 171 3.532892 GCATGATAGCCTGAATGTTCG 57.467 47.619 0.00 0.00 0.00 3.95
171 172 2.874701 GCATGATAGCCTGAATGTTCGT 59.125 45.455 0.00 0.00 0.00 3.85
172 173 3.303593 GCATGATAGCCTGAATGTTCGTG 60.304 47.826 0.00 0.00 0.00 4.35
173 174 3.885724 TGATAGCCTGAATGTTCGTGA 57.114 42.857 0.00 0.00 0.00 4.35
174 175 3.785486 TGATAGCCTGAATGTTCGTGAG 58.215 45.455 0.00 0.00 0.00 3.51
175 176 2.672961 TAGCCTGAATGTTCGTGAGG 57.327 50.000 0.00 0.00 0.00 3.86
176 177 1.796796 GCCTGAATGTTCGTGAGGC 59.203 57.895 6.79 6.79 42.37 4.70
177 178 3.231734 CCTGAATGTTCGTGAGGCA 57.768 52.632 0.00 0.00 0.00 4.75
182 183 0.670546 AATGTTCGTGAGGCAGACCG 60.671 55.000 0.00 0.00 42.76 4.79
210 211 1.622607 CGGTGGGGTTGCTCCTGATA 61.623 60.000 0.00 0.00 36.25 2.15
215 216 1.883084 GGTTGCTCCTGATACGGCG 60.883 63.158 4.80 4.80 0.00 6.46
221 222 1.000607 GCTCCTGATACGGCGACATAA 60.001 52.381 16.62 0.00 0.00 1.90
256 257 5.393461 CGTTGTACGGGATTTCTAGTTAGGT 60.393 44.000 0.00 0.00 38.08 3.08
313 314 0.179045 CCACCGAGGGGATCAATGAC 60.179 60.000 0.00 0.00 36.97 3.06
329 330 2.925170 ACGGCCAGGCTCTTGAGT 60.925 61.111 12.43 0.00 0.00 3.41
335 336 1.673665 CAGGCTCTTGAGTGTGGGC 60.674 63.158 0.00 0.00 0.00 5.36
355 356 1.063806 GAGTCGACAGTGTGCATGTC 58.936 55.000 19.50 8.58 42.94 3.06
356 357 0.319900 AGTCGACAGTGTGCATGTCC 60.320 55.000 19.50 1.32 43.36 4.02
358 359 0.105778 TCGACAGTGTGCATGTCCAA 59.894 50.000 12.20 0.21 43.36 3.53
370 371 1.068055 CATGTCCAAGCTGCACCTTTC 60.068 52.381 1.02 0.00 0.00 2.62
385 386 1.065854 CCTTTCGACATGGAGCTCCTT 60.066 52.381 32.28 24.06 36.82 3.36
386 387 2.005451 CTTTCGACATGGAGCTCCTTG 58.995 52.381 35.34 35.34 44.21 3.61
418 419 0.116342 TAGGTGCAGAGACCCTCCAA 59.884 55.000 0.00 0.00 36.56 3.53
427 428 1.219393 GACCCTCCAAGAAGCCGAG 59.781 63.158 0.00 0.00 0.00 4.63
428 429 2.124942 CCCTCCAAGAAGCCGAGC 60.125 66.667 0.00 0.00 0.00 5.03
429 430 2.665000 CCTCCAAGAAGCCGAGCA 59.335 61.111 0.00 0.00 0.00 4.26
430 431 1.003355 CCTCCAAGAAGCCGAGCAA 60.003 57.895 0.00 0.00 0.00 3.91
431 432 0.393537 CCTCCAAGAAGCCGAGCAAT 60.394 55.000 0.00 0.00 0.00 3.56
432 433 1.012841 CTCCAAGAAGCCGAGCAATC 58.987 55.000 0.00 0.00 0.00 2.67
433 434 0.615331 TCCAAGAAGCCGAGCAATCT 59.385 50.000 0.00 0.00 0.00 2.40
434 435 0.731417 CCAAGAAGCCGAGCAATCTG 59.269 55.000 0.00 0.00 29.88 2.90
435 436 1.446907 CAAGAAGCCGAGCAATCTGT 58.553 50.000 0.00 0.00 29.88 3.41
436 437 1.808945 CAAGAAGCCGAGCAATCTGTT 59.191 47.619 0.00 0.00 29.88 3.16
437 438 1.446907 AGAAGCCGAGCAATCTGTTG 58.553 50.000 0.00 0.00 38.39 3.33
438 439 1.002430 AGAAGCCGAGCAATCTGTTGA 59.998 47.619 0.00 0.00 37.53 3.18
439 440 1.129437 GAAGCCGAGCAATCTGTTGAC 59.871 52.381 0.00 0.00 37.53 3.18
440 441 0.322975 AGCCGAGCAATCTGTTGACT 59.677 50.000 0.00 0.00 37.53 3.41
441 442 1.550524 AGCCGAGCAATCTGTTGACTA 59.449 47.619 0.00 0.00 37.53 2.59
442 443 2.169352 AGCCGAGCAATCTGTTGACTAT 59.831 45.455 0.00 0.00 37.53 2.12
443 444 2.286294 GCCGAGCAATCTGTTGACTATG 59.714 50.000 0.00 0.00 37.53 2.23
444 445 3.785486 CCGAGCAATCTGTTGACTATGA 58.215 45.455 0.00 0.00 37.53 2.15
445 446 3.553511 CCGAGCAATCTGTTGACTATGAC 59.446 47.826 0.00 0.00 37.53 3.06
446 447 3.241553 CGAGCAATCTGTTGACTATGACG 59.758 47.826 0.00 0.00 37.53 4.35
447 448 4.424626 GAGCAATCTGTTGACTATGACGA 58.575 43.478 0.00 0.00 37.53 4.20
448 449 4.428209 AGCAATCTGTTGACTATGACGAG 58.572 43.478 0.00 0.00 37.53 4.18
449 450 3.553511 GCAATCTGTTGACTATGACGAGG 59.446 47.826 0.00 0.00 37.53 4.63
450 451 2.941453 TCTGTTGACTATGACGAGGC 57.059 50.000 0.00 0.00 0.00 4.70
451 452 1.132453 TCTGTTGACTATGACGAGGCG 59.868 52.381 0.00 0.00 0.00 5.52
452 453 0.457853 TGTTGACTATGACGAGGCGC 60.458 55.000 0.00 0.00 0.00 6.53
453 454 0.457853 GTTGACTATGACGAGGCGCA 60.458 55.000 10.83 0.00 0.00 6.09
475 476 4.710695 CGTCAGGCGGCGTGTGTA 62.711 66.667 20.62 0.66 36.85 2.90
476 477 2.809601 GTCAGGCGGCGTGTGTAG 60.810 66.667 20.62 0.00 0.00 2.74
477 478 4.735132 TCAGGCGGCGTGTGTAGC 62.735 66.667 20.62 0.00 0.00 3.58
484 485 3.124921 GCGTGTGTAGCCGGCAAT 61.125 61.111 31.54 12.06 0.00 3.56
485 486 2.784596 CGTGTGTAGCCGGCAATG 59.215 61.111 31.54 9.96 0.00 2.82
486 487 2.485122 GTGTGTAGCCGGCAATGC 59.515 61.111 31.54 13.51 0.00 3.56
487 488 2.033294 TGTGTAGCCGGCAATGCA 59.967 55.556 31.54 16.38 0.00 3.96
488 489 2.039974 TGTGTAGCCGGCAATGCAG 61.040 57.895 31.54 2.15 0.00 4.41
489 490 3.133464 TGTAGCCGGCAATGCAGC 61.133 61.111 31.54 9.59 0.00 5.25
490 491 3.133464 GTAGCCGGCAATGCAGCA 61.133 61.111 31.54 0.00 35.83 4.41
491 492 2.360978 TAGCCGGCAATGCAGCAA 60.361 55.556 31.54 0.00 35.83 3.91
492 493 2.699768 TAGCCGGCAATGCAGCAAC 61.700 57.895 31.54 3.24 35.83 4.17
494 495 4.440127 CCGGCAATGCAGCAACCC 62.440 66.667 7.79 0.00 35.83 4.11
495 496 3.376078 CGGCAATGCAGCAACCCT 61.376 61.111 7.79 0.00 35.83 4.34
496 497 2.934570 CGGCAATGCAGCAACCCTT 61.935 57.895 7.79 0.00 35.83 3.95
499 500 2.051941 CAATGCAGCAACCCTTGGT 58.948 52.632 0.00 0.00 43.12 3.67
506 507 2.439104 GCAACCCTTGGTGGCCAAA 61.439 57.895 7.24 0.00 46.35 3.28
526 527 3.179265 CGGCTCAGTGTAACGGCG 61.179 66.667 4.80 4.80 45.86 6.46
528 529 2.736995 GCTCAGTGTAACGGCGCA 60.737 61.111 10.83 0.00 42.30 6.09
532 533 1.959226 CAGTGTAACGGCGCAAGGT 60.959 57.895 10.83 3.26 45.86 3.50
542 543 2.317609 GCGCAAGGTCGACACATGT 61.318 57.895 18.91 0.00 38.28 3.21
567 568 2.900546 TCCCAATAATTTTGGTGCCGTT 59.099 40.909 14.39 0.00 37.88 4.44
596 597 3.785859 GGATCTCCACGGCAGCCA 61.786 66.667 13.30 0.00 35.64 4.75
686 697 1.139734 ACGTCAGCGCATCAGGTAG 59.860 57.895 11.47 0.00 42.83 3.18
687 698 1.313091 ACGTCAGCGCATCAGGTAGA 61.313 55.000 11.47 0.00 42.83 2.59
705 716 2.723746 GCGGCTGGCATTGTATGG 59.276 61.111 1.08 0.00 42.87 2.74
706 717 2.120909 GCGGCTGGCATTGTATGGT 61.121 57.895 1.08 0.00 42.87 3.55
707 718 1.666209 GCGGCTGGCATTGTATGGTT 61.666 55.000 1.08 0.00 42.87 3.67
708 719 0.101040 CGGCTGGCATTGTATGGTTG 59.899 55.000 1.08 0.00 0.00 3.77
712 725 1.406539 CTGGCATTGTATGGTTGAGCC 59.593 52.381 0.00 0.00 40.93 4.70
717 730 3.738982 CATTGTATGGTTGAGCCGGATA 58.261 45.455 5.05 0.00 41.21 2.59
728 741 3.214123 CCGGATAGGTCGGCGTGA 61.214 66.667 6.85 0.00 41.07 4.35
736 749 2.576317 GTCGGCGTGACGTAGAGC 60.576 66.667 6.91 0.00 37.96 4.09
747 760 2.508663 GTAGAGCAACCGGACGCC 60.509 66.667 9.46 4.39 0.00 5.68
791 804 7.549615 ACTACACCTTCTTTCTGTGTTAAAC 57.450 36.000 0.00 0.00 42.75 2.01
796 809 8.145122 ACACCTTCTTTCTGTGTTAAACAAAAA 58.855 29.630 0.00 0.00 40.12 1.94
797 810 9.150348 CACCTTCTTTCTGTGTTAAACAAAAAT 57.850 29.630 0.00 0.00 38.67 1.82
801 814 8.865590 TCTTTCTGTGTTAAACAAAAATAGGC 57.134 30.769 0.00 0.00 38.67 3.93
802 815 8.691797 TCTTTCTGTGTTAAACAAAAATAGGCT 58.308 29.630 0.00 0.00 38.67 4.58
803 816 9.959749 CTTTCTGTGTTAAACAAAAATAGGCTA 57.040 29.630 0.00 0.00 38.67 3.93
804 817 9.738832 TTTCTGTGTTAAACAAAAATAGGCTAC 57.261 29.630 0.00 0.00 38.67 3.58
805 818 8.453238 TCTGTGTTAAACAAAAATAGGCTACA 57.547 30.769 0.00 0.00 38.67 2.74
807 820 8.859517 TGTGTTAAACAAAAATAGGCTACAAC 57.140 30.769 0.00 0.00 35.24 3.32
808 821 8.688151 TGTGTTAAACAAAAATAGGCTACAACT 58.312 29.630 0.00 0.00 35.24 3.16
810 823 9.738832 TGTTAAACAAAAATAGGCTACAACTTC 57.261 29.630 0.00 0.00 0.00 3.01
811 824 9.188588 GTTAAACAAAAATAGGCTACAACTTCC 57.811 33.333 0.00 0.00 0.00 3.46
837 925 4.380841 TTTGCATGGCTCATGAGAAATC 57.619 40.909 27.04 12.01 43.81 2.17
859 947 0.037697 TCCAATAGCAAGCACGTCGT 60.038 50.000 0.00 0.00 0.00 4.34
863 951 3.296628 CAATAGCAAGCACGTCGTTTTT 58.703 40.909 0.00 0.00 0.00 1.94
892 991 1.681538 TGTAGCAGAGGAGACCGATC 58.318 55.000 0.00 0.00 0.00 3.69
918 2476 5.591877 GGTAGGTACATATATACCCTCACCG 59.408 48.000 6.57 0.00 45.13 4.94
919 2477 5.525454 AGGTACATATATACCCTCACCGA 57.475 43.478 6.57 0.00 45.13 4.69
921 2479 6.500336 AGGTACATATATACCCTCACCGATT 58.500 40.000 6.57 0.00 45.13 3.34
922 2480 7.645942 AGGTACATATATACCCTCACCGATTA 58.354 38.462 6.57 0.00 45.13 1.75
923 2481 8.287350 AGGTACATATATACCCTCACCGATTAT 58.713 37.037 6.57 0.00 45.13 1.28
924 2482 8.574737 GGTACATATATACCCTCACCGATTATC 58.425 40.741 0.00 0.00 39.05 1.75
925 2483 9.352191 GTACATATATACCCTCACCGATTATCT 57.648 37.037 0.00 0.00 0.00 1.98
934 2492 8.522542 ACCCTCACCGATTATCTATATCTAAC 57.477 38.462 0.00 0.00 0.00 2.34
935 2493 7.560626 ACCCTCACCGATTATCTATATCTAACC 59.439 40.741 0.00 0.00 0.00 2.85
936 2494 7.255173 CCCTCACCGATTATCTATATCTAACCG 60.255 44.444 0.00 0.00 0.00 4.44
937 2495 7.498239 CCTCACCGATTATCTATATCTAACCGA 59.502 40.741 0.00 0.00 0.00 4.69
938 2496 8.975663 TCACCGATTATCTATATCTAACCGAT 57.024 34.615 0.00 0.00 36.11 4.18
939 2497 9.053840 TCACCGATTATCTATATCTAACCGATC 57.946 37.037 0.00 0.00 33.48 3.69
940 2498 8.010540 CACCGATTATCTATATCTAACCGATCG 58.989 40.741 8.51 8.51 33.48 3.69
941 2499 7.519843 CCGATTATCTATATCTAACCGATCGG 58.480 42.308 32.20 32.20 43.94 4.18
942 2500 7.361031 CCGATTATCTATATCTAACCGATCGGG 60.361 44.444 35.87 19.75 45.00 5.14
943 2501 6.630444 TTATCTATATCTAACCGATCGGGC 57.370 41.667 35.87 0.00 40.62 6.13
944 2502 3.959293 TCTATATCTAACCGATCGGGCA 58.041 45.455 35.87 22.23 40.62 5.36
945 2503 3.945921 TCTATATCTAACCGATCGGGCAG 59.054 47.826 35.87 29.26 40.62 4.85
946 2504 2.281539 TATCTAACCGATCGGGCAGA 57.718 50.000 35.87 32.73 40.62 4.26
947 2505 0.962489 ATCTAACCGATCGGGCAGAG 59.038 55.000 35.87 24.91 40.62 3.35
960 2518 2.967270 GCAGAGGAGCCAACCAATT 58.033 52.632 0.00 0.00 0.00 2.32
961 2519 2.128771 GCAGAGGAGCCAACCAATTA 57.871 50.000 0.00 0.00 0.00 1.40
1048 2612 4.465512 CTGCGGTCGCCAACATGC 62.466 66.667 12.94 0.00 41.09 4.06
1129 2699 3.048941 GCTACGGCCGACTTCGTCT 62.049 63.158 35.90 9.38 40.31 4.18
1130 2700 1.709147 GCTACGGCCGACTTCGTCTA 61.709 60.000 35.90 10.16 40.31 2.59
1137 2707 1.731750 GCCGACTTCGTCTACTTCCAC 60.732 57.143 0.00 0.00 37.74 4.02
1159 2729 2.514592 TCTGCAAGCTATGGCGCC 60.515 61.111 22.73 22.73 44.37 6.53
1316 2889 2.542907 CGCCACCAATATCCGGCAC 61.543 63.158 0.00 0.00 45.14 5.01
1391 2964 4.195334 CCCCTCCATCCGCCCAAG 62.195 72.222 0.00 0.00 0.00 3.61
1415 2988 2.656002 CCTCTATGACCCTCTGTTCGA 58.344 52.381 0.00 0.00 0.00 3.71
1446 3019 1.153756 CCACCTGCCACTTTTCCCT 59.846 57.895 0.00 0.00 0.00 4.20
1488 3061 0.755698 ACCCGAGTGGCATCGTCTAT 60.756 55.000 14.88 0.11 41.12 1.98
1556 3853 1.991121 TACGTGTCTGAGTTCAGGGT 58.009 50.000 9.13 5.60 43.91 4.34
1605 3902 1.123928 GGACGGTCATCCAGAGGAAT 58.876 55.000 10.76 0.00 38.77 3.01
1653 3950 2.351418 CTGCATCGCGTATTTTTCTGGA 59.649 45.455 5.77 0.00 0.00 3.86
1668 3965 4.591321 TTCTGGAAATATCCTTGTGGCT 57.409 40.909 0.00 0.00 46.70 4.75
1716 4013 0.254462 TGAAGTCCACCACAGCAACA 59.746 50.000 0.00 0.00 0.00 3.33
1761 4058 4.752879 CCGTGGTCGTTGCCGGAT 62.753 66.667 5.05 0.00 43.01 4.18
1838 4135 1.663388 TGACGGTGCACATCACGAC 60.663 57.895 20.43 13.28 46.56 4.34
1902 4199 5.705441 TGGTGTCTTGATGTTTATTCACTCC 59.295 40.000 0.00 0.00 0.00 3.85
1953 4250 0.545309 TGAGGTGGGTGAGGAAGGAG 60.545 60.000 0.00 0.00 0.00 3.69
2076 4373 0.536687 TCTCGGACGACAAGGACAGT 60.537 55.000 0.00 0.00 0.00 3.55
2179 4476 0.324645 ATGGCTTAACCCCCAGCTTG 60.325 55.000 0.00 0.00 37.83 4.01
2240 8169 3.151554 GCAATAGCATGATCCACATCCA 58.848 45.455 0.00 0.00 41.58 3.41
2245 8174 2.980379 AGCATGATCCACATCCAGAGAT 59.020 45.455 0.00 0.00 37.07 2.75
2318 8247 4.577988 AGAGTTCTCAGCTCCTACACTA 57.422 45.455 2.64 0.00 33.69 2.74
2331 8260 4.817517 TCCTACACTAGTTTAGCAAGCAC 58.182 43.478 10.11 0.00 0.00 4.40
2409 8338 1.136565 CGGCCTTGTAACAATGGCG 59.863 57.895 0.00 11.35 45.75 5.69
2451 8380 3.712881 GCCGTTGCCACACTCGAC 61.713 66.667 0.00 0.00 0.00 4.20
2558 8487 4.883083 TCCGTTGGAGCAATGTAGATATC 58.117 43.478 0.00 0.00 0.00 1.63
2696 8625 0.535102 CTGACAACCGGAAGCACCTT 60.535 55.000 9.46 0.00 36.31 3.50
2723 8671 1.594021 CCCCGCCAAAAACAACAGC 60.594 57.895 0.00 0.00 0.00 4.40
2782 8730 1.530720 CGCGCATGCTATTGTCCAATA 59.469 47.619 17.13 0.22 39.65 1.90
2784 8732 2.549754 GCGCATGCTATTGTCCAATACT 59.450 45.455 17.13 0.00 38.39 2.12
2818 8766 1.153369 TTAGTCATGCTGGCCTCGC 60.153 57.895 3.32 7.56 0.00 5.03
2819 8767 1.898330 TTAGTCATGCTGGCCTCGCA 61.898 55.000 19.97 19.97 42.25 5.10
2835 8783 3.990469 CCTCGCACCATAGTATCAATGAC 59.010 47.826 0.00 0.00 0.00 3.06
2839 8787 2.731451 CACCATAGTATCAATGACGCCG 59.269 50.000 0.00 0.00 0.00 6.46
2855 8803 1.296715 CCGTCCTTAGCAGCTTGGT 59.703 57.895 0.00 0.00 0.00 3.67
2901 8849 1.664017 CGAGGCTCCATCATCGCAG 60.664 63.158 9.32 0.00 0.00 5.18
3088 9036 0.544697 GAATACACCCCCATCACCGT 59.455 55.000 0.00 0.00 0.00 4.83
3090 9038 1.882308 ATACACCCCCATCACCGTAA 58.118 50.000 0.00 0.00 0.00 3.18
3283 9231 3.433306 TGTTCTTTACCCATGGACTGG 57.567 47.619 15.22 0.00 45.51 4.00
3307 9255 4.526970 ACATACCCCTAATGTCAAGCAAG 58.473 43.478 0.00 0.00 32.02 4.01
3322 9270 3.904136 AGCAAGACAATTTTCTCCACG 57.096 42.857 0.00 0.00 0.00 4.94
3325 9273 3.003275 GCAAGACAATTTTCTCCACGTCA 59.997 43.478 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.016706 GGGTGGACACGGTCTGGG 62.017 72.222 4.41 0.00 32.47 4.45
1 2 2.923035 AGGGTGGACACGGTCTGG 60.923 66.667 4.41 0.00 32.47 3.86
2 3 2.207229 TCAGGGTGGACACGGTCTG 61.207 63.158 10.62 10.62 32.47 3.51
3 4 2.200370 TCAGGGTGGACACGGTCT 59.800 61.111 4.41 0.00 32.47 3.85
4 5 2.342648 GTCAGGGTGGACACGGTC 59.657 66.667 0.00 0.00 37.73 4.79
5 6 3.239253 GGTCAGGGTGGACACGGT 61.239 66.667 0.00 0.00 39.59 4.83
6 7 4.016706 GGGTCAGGGTGGACACGG 62.017 72.222 0.00 0.00 39.59 4.94
7 8 2.521958 GATGGGTCAGGGTGGACACG 62.522 65.000 0.00 0.00 44.26 4.49
8 9 1.299976 GATGGGTCAGGGTGGACAC 59.700 63.158 0.00 0.00 41.65 3.67
9 10 1.151921 TGATGGGTCAGGGTGGACA 60.152 57.895 0.00 0.00 39.59 4.02
10 11 1.604378 CTGATGGGTCAGGGTGGAC 59.396 63.158 0.00 0.00 46.56 4.02
11 12 4.152248 CTGATGGGTCAGGGTGGA 57.848 61.111 0.00 0.00 46.56 4.02
17 18 6.425776 CATGAACATGAGTCTGATGGGTCAG 61.426 48.000 8.89 0.00 45.36 3.51
18 19 2.905736 TGAACATGAGTCTGATGGGTCA 59.094 45.455 0.00 4.40 0.00 4.02
19 20 3.616956 TGAACATGAGTCTGATGGGTC 57.383 47.619 0.00 1.96 0.00 4.46
20 21 3.882444 CATGAACATGAGTCTGATGGGT 58.118 45.455 8.89 0.00 41.20 4.51
60 61 3.280295 TCACCCGAGAGAGAATGAGTAC 58.720 50.000 0.00 0.00 0.00 2.73
72 73 2.764128 GGGCAGGATCACCCGAGA 60.764 66.667 2.25 0.00 40.87 4.04
97 98 4.457603 TCGACAAACCCTTGGTGATTATTG 59.542 41.667 0.00 0.00 35.34 1.90
109 110 0.912487 TATGGGCCTCGACAAACCCT 60.912 55.000 4.53 0.00 43.25 4.34
114 115 0.758734 CATCCTATGGGCCTCGACAA 59.241 55.000 4.53 0.00 0.00 3.18
127 128 2.168458 TGAACCGTCATCCCATCCTA 57.832 50.000 0.00 0.00 0.00 2.94
137 138 2.198827 ATCATGCCTTTGAACCGTCA 57.801 45.000 0.00 0.00 0.00 4.35
140 141 2.763249 GCTATCATGCCTTTGAACCG 57.237 50.000 0.00 0.00 0.00 4.44
156 157 1.405526 GCCTCACGAACATTCAGGCTA 60.406 52.381 12.13 0.00 45.40 3.93
157 158 0.674895 GCCTCACGAACATTCAGGCT 60.675 55.000 12.13 0.00 45.40 4.58
160 161 1.728971 GTCTGCCTCACGAACATTCAG 59.271 52.381 0.00 0.00 0.00 3.02
170 171 1.369625 CATTAACCGGTCTGCCTCAC 58.630 55.000 8.04 0.00 0.00 3.51
171 172 0.392461 GCATTAACCGGTCTGCCTCA 60.392 55.000 20.37 0.00 0.00 3.86
172 173 2.394604 GCATTAACCGGTCTGCCTC 58.605 57.895 20.37 2.04 0.00 4.70
173 174 4.637771 GCATTAACCGGTCTGCCT 57.362 55.556 20.37 3.42 0.00 4.75
174 175 3.509659 GGCATTAACCGGTCTGCC 58.490 61.111 29.15 29.15 46.54 4.85
182 183 1.304630 AACCCCACCGGCATTAACC 60.305 57.895 0.00 0.00 33.26 2.85
198 199 1.141019 TCGCCGTATCAGGAGCAAC 59.859 57.895 0.00 0.00 0.00 4.17
206 207 5.392703 GGAGTATGATTATGTCGCCGTATCA 60.393 44.000 0.00 0.00 0.00 2.15
210 211 2.029290 GGGAGTATGATTATGTCGCCGT 60.029 50.000 0.00 0.00 0.00 5.68
215 216 4.957296 ACAACGGGGAGTATGATTATGTC 58.043 43.478 0.00 0.00 0.00 3.06
245 246 4.019501 ACTCCGAGACTCACCTAACTAGAA 60.020 45.833 1.33 0.00 0.00 2.10
251 252 1.002888 ACGACTCCGAGACTCACCTAA 59.997 52.381 1.33 0.00 39.50 2.69
256 257 1.299562 GCTCACGACTCCGAGACTCA 61.300 60.000 1.33 0.00 39.50 3.41
292 293 3.106986 ATTGATCCCCTCGGTGGCG 62.107 63.158 0.00 0.00 0.00 5.69
313 314 2.435586 CACTCAAGAGCCTGGCCG 60.436 66.667 16.57 1.57 0.00 6.13
329 330 2.910479 ACTGTCGACTCGCCCACA 60.910 61.111 17.92 0.00 0.00 4.17
335 336 0.664466 ACATGCACACTGTCGACTCG 60.664 55.000 17.92 10.33 0.00 4.18
355 356 1.165907 TGTCGAAAGGTGCAGCTTGG 61.166 55.000 30.27 23.73 0.00 3.61
356 357 0.877071 ATGTCGAAAGGTGCAGCTTG 59.123 50.000 30.27 19.11 0.00 4.01
358 359 0.957395 CCATGTCGAAAGGTGCAGCT 60.957 55.000 13.85 13.85 0.00 4.24
370 371 3.359194 CTCAAGGAGCTCCATGTCG 57.641 57.895 33.90 21.85 36.22 4.35
385 386 0.035152 CACCTATTGCCCAGTGCTCA 60.035 55.000 0.00 0.00 42.00 4.26
386 387 2.785868 CACCTATTGCCCAGTGCTC 58.214 57.895 0.00 0.00 42.00 4.26
404 405 0.392327 GCTTCTTGGAGGGTCTCTGC 60.392 60.000 0.00 0.00 0.00 4.26
406 407 1.261238 CGGCTTCTTGGAGGGTCTCT 61.261 60.000 0.00 0.00 0.00 3.10
418 419 1.002430 TCAACAGATTGCTCGGCTTCT 59.998 47.619 0.00 0.00 35.63 2.85
427 428 3.553511 CCTCGTCATAGTCAACAGATTGC 59.446 47.826 0.00 0.00 35.63 3.56
428 429 3.553511 GCCTCGTCATAGTCAACAGATTG 59.446 47.826 0.00 0.00 37.14 2.67
429 430 3.735208 CGCCTCGTCATAGTCAACAGATT 60.735 47.826 0.00 0.00 0.00 2.40
430 431 2.223595 CGCCTCGTCATAGTCAACAGAT 60.224 50.000 0.00 0.00 0.00 2.90
431 432 1.132453 CGCCTCGTCATAGTCAACAGA 59.868 52.381 0.00 0.00 0.00 3.41
432 433 1.550065 CGCCTCGTCATAGTCAACAG 58.450 55.000 0.00 0.00 0.00 3.16
433 434 0.457853 GCGCCTCGTCATAGTCAACA 60.458 55.000 0.00 0.00 0.00 3.33
434 435 0.457853 TGCGCCTCGTCATAGTCAAC 60.458 55.000 4.18 0.00 0.00 3.18
435 436 0.179137 CTGCGCCTCGTCATAGTCAA 60.179 55.000 4.18 0.00 0.00 3.18
436 437 1.433471 CTGCGCCTCGTCATAGTCA 59.567 57.895 4.18 0.00 0.00 3.41
437 438 1.946650 GCTGCGCCTCGTCATAGTC 60.947 63.158 4.18 0.00 0.00 2.59
438 439 2.105128 GCTGCGCCTCGTCATAGT 59.895 61.111 4.18 0.00 0.00 2.12
439 440 3.026879 CGCTGCGCCTCGTCATAG 61.027 66.667 9.88 0.00 0.00 2.23
440 441 3.822192 ACGCTGCGCCTCGTCATA 61.822 61.111 23.51 0.00 33.09 2.15
469 470 2.257286 CTGCATTGCCGGCTACACAC 62.257 60.000 29.70 12.64 0.00 3.82
473 474 2.699768 TTGCTGCATTGCCGGCTAC 61.700 57.895 29.70 14.53 0.00 3.58
475 476 4.060038 GTTGCTGCATTGCCGGCT 62.060 61.111 29.70 4.80 0.00 5.52
477 478 4.440127 GGGTTGCTGCATTGCCGG 62.440 66.667 1.84 0.00 0.00 6.13
478 479 2.934570 AAGGGTTGCTGCATTGCCG 61.935 57.895 1.84 0.16 0.00 5.69
479 480 1.375013 CAAGGGTTGCTGCATTGCC 60.375 57.895 1.84 6.52 0.00 4.52
480 481 1.375013 CCAAGGGTTGCTGCATTGC 60.375 57.895 1.84 0.46 0.00 3.56
481 482 0.320073 CACCAAGGGTTGCTGCATTG 60.320 55.000 1.84 4.88 31.02 2.82
482 483 1.474332 CCACCAAGGGTTGCTGCATT 61.474 55.000 1.84 0.00 31.02 3.56
483 484 1.909781 CCACCAAGGGTTGCTGCAT 60.910 57.895 1.84 0.00 31.02 3.96
484 485 2.521465 CCACCAAGGGTTGCTGCA 60.521 61.111 0.00 0.00 31.02 4.41
485 486 3.994853 GCCACCAAGGGTTGCTGC 61.995 66.667 4.37 0.00 40.60 5.25
486 487 3.305516 GGCCACCAAGGGTTGCTG 61.306 66.667 10.76 0.00 42.92 4.41
487 488 2.887738 TTTGGCCACCAAGGGTTGCT 62.888 55.000 3.88 0.00 44.84 3.91
488 489 1.767654 ATTTGGCCACCAAGGGTTGC 61.768 55.000 3.88 3.04 44.84 4.17
489 490 0.321346 GATTTGGCCACCAAGGGTTG 59.679 55.000 3.88 0.00 44.84 3.77
490 491 0.835971 GGATTTGGCCACCAAGGGTT 60.836 55.000 3.88 0.00 44.84 4.11
491 492 1.229177 GGATTTGGCCACCAAGGGT 60.229 57.895 3.88 0.00 44.84 4.34
492 493 2.350458 CGGATTTGGCCACCAAGGG 61.350 63.158 3.88 0.00 44.84 3.95
493 494 2.350458 CCGGATTTGGCCACCAAGG 61.350 63.158 3.88 1.29 44.84 3.61
494 495 3.287445 CCGGATTTGGCCACCAAG 58.713 61.111 3.88 0.00 44.84 3.61
506 507 1.515954 CCGTTACACTGAGCCGGAT 59.484 57.895 5.05 0.00 41.08 4.18
526 527 0.884704 ACCACATGTGTCGACCTTGC 60.885 55.000 23.79 1.36 0.00 4.01
528 529 1.542547 GGAACCACATGTGTCGACCTT 60.543 52.381 23.79 5.62 0.00 3.50
567 568 2.758327 AGATCCACGCCGCCTACA 60.758 61.111 0.00 0.00 0.00 2.74
615 616 4.832608 GACCGCCGTGGATCCACC 62.833 72.222 34.05 22.06 43.49 4.61
641 642 2.107141 GGGATGGACTCGCCGAAG 59.893 66.667 0.00 0.00 40.66 3.79
642 643 3.833645 CGGGATGGACTCGCCGAA 61.834 66.667 0.00 0.00 38.97 4.30
644 645 3.774959 CTTCGGGATGGACTCGCCG 62.775 68.421 0.00 0.00 42.91 6.46
645 646 2.107141 CTTCGGGATGGACTCGCC 59.893 66.667 0.00 0.00 42.91 5.54
646 647 1.389609 TACCTTCGGGATGGACTCGC 61.390 60.000 7.53 0.00 42.91 5.03
664 675 0.249031 CCTGATGCGCTGACGTGATA 60.249 55.000 9.73 0.00 42.83 2.15
674 685 2.659897 CCGCTCTACCTGATGCGC 60.660 66.667 0.00 0.00 45.97 6.09
686 697 1.650912 CATACAATGCCAGCCGCTC 59.349 57.895 0.00 0.00 38.78 5.03
687 698 1.825191 CCATACAATGCCAGCCGCT 60.825 57.895 0.00 0.00 38.78 5.52
704 715 1.067582 CGACCTATCCGGCTCAACC 59.932 63.158 0.00 0.00 35.61 3.77
705 716 1.067582 CCGACCTATCCGGCTCAAC 59.932 63.158 0.00 0.00 40.54 3.18
706 717 3.533720 CCGACCTATCCGGCTCAA 58.466 61.111 0.00 0.00 40.54 3.02
712 725 2.025727 GTCACGCCGACCTATCCG 59.974 66.667 0.00 0.00 38.85 4.18
717 730 2.359107 TCTACGTCACGCCGACCT 60.359 61.111 0.00 0.00 42.07 3.85
728 741 2.564975 CGTCCGGTTGCTCTACGT 59.435 61.111 0.00 0.00 0.00 3.57
736 749 1.956629 ATAGTCCAGGCGTCCGGTTG 61.957 60.000 0.00 0.00 0.00 3.77
791 804 8.887036 AAAAAGGAAGTTGTAGCCTATTTTTG 57.113 30.769 0.00 0.00 0.00 2.44
826 872 4.141733 TGCTATTGGACGGATTTCTCATGA 60.142 41.667 0.00 0.00 0.00 3.07
827 873 4.129380 TGCTATTGGACGGATTTCTCATG 58.871 43.478 0.00 0.00 0.00 3.07
837 925 1.715585 CGTGCTTGCTATTGGACGG 59.284 57.895 0.00 0.00 42.67 4.79
870 958 2.244695 TCGGTCTCCTCTGCTACAAAA 58.755 47.619 0.00 0.00 0.00 2.44
872 960 2.025155 GATCGGTCTCCTCTGCTACAA 58.975 52.381 0.00 0.00 0.00 2.41
914 2472 8.010540 CGATCGGTTAGATATAGATAATCGGTG 58.989 40.741 7.38 1.47 40.26 4.94
916 2474 7.519843 CCGATCGGTTAGATATAGATAATCGG 58.480 42.308 26.35 0.00 43.84 4.18
917 2475 7.519843 CCCGATCGGTTAGATATAGATAATCG 58.480 42.308 31.22 6.68 40.26 3.34
918 2476 7.040617 TGCCCGATCGGTTAGATATAGATAATC 60.041 40.741 31.22 1.83 40.26 1.75
919 2477 6.776116 TGCCCGATCGGTTAGATATAGATAAT 59.224 38.462 31.22 0.00 40.26 1.28
921 2479 5.687780 TGCCCGATCGGTTAGATATAGATA 58.312 41.667 31.22 4.32 40.26 1.98
922 2480 4.533815 TGCCCGATCGGTTAGATATAGAT 58.466 43.478 31.22 0.00 40.26 1.98
923 2481 3.945921 CTGCCCGATCGGTTAGATATAGA 59.054 47.826 31.22 3.06 40.26 1.98
924 2482 3.945921 TCTGCCCGATCGGTTAGATATAG 59.054 47.826 31.22 14.39 40.26 1.31
925 2483 3.945921 CTCTGCCCGATCGGTTAGATATA 59.054 47.826 31.22 12.24 40.26 0.86
926 2484 2.755655 CTCTGCCCGATCGGTTAGATAT 59.244 50.000 31.22 0.00 40.26 1.63
927 2485 2.160205 CTCTGCCCGATCGGTTAGATA 58.840 52.381 31.22 13.18 40.26 1.98
928 2486 0.962489 CTCTGCCCGATCGGTTAGAT 59.038 55.000 31.22 0.00 43.51 1.98
929 2487 1.107538 CCTCTGCCCGATCGGTTAGA 61.108 60.000 31.22 28.37 0.00 2.10
930 2488 1.107538 TCCTCTGCCCGATCGGTTAG 61.108 60.000 31.22 26.15 0.00 2.34
931 2489 1.076559 TCCTCTGCCCGATCGGTTA 60.077 57.895 31.22 18.76 0.00 2.85
932 2490 2.363795 TCCTCTGCCCGATCGGTT 60.364 61.111 31.22 0.00 0.00 4.44
933 2491 2.835431 CTCCTCTGCCCGATCGGT 60.835 66.667 31.22 0.00 0.00 4.69
934 2492 4.292178 GCTCCTCTGCCCGATCGG 62.292 72.222 27.65 27.65 0.00 4.18
935 2493 4.292178 GGCTCCTCTGCCCGATCG 62.292 72.222 8.51 8.51 46.82 3.69
942 2500 2.128771 TAATTGGTTGGCTCCTCTGC 57.871 50.000 0.00 0.00 0.00 4.26
943 2501 6.966534 ATAAATAATTGGTTGGCTCCTCTG 57.033 37.500 0.00 0.00 0.00 3.35
944 2502 8.673251 AGATATAAATAATTGGTTGGCTCCTCT 58.327 33.333 0.00 0.00 0.00 3.69
945 2503 8.870075 AGATATAAATAATTGGTTGGCTCCTC 57.130 34.615 0.00 0.00 0.00 3.71
961 2519 9.587772 CCAGAATCGAATCGGTTAGATATAAAT 57.412 33.333 0.00 0.00 38.98 1.40
1005 2564 2.441532 TCGAGATGGACCCCCGAC 60.442 66.667 0.00 0.00 34.29 4.79
1129 2699 2.260434 GCAGACGGCGTGGAAGTA 59.740 61.111 21.19 0.00 0.00 2.24
1159 2729 0.667487 ATCGTTGCCTCGTGTGAGTG 60.667 55.000 0.00 0.00 40.85 3.51
1171 2741 4.505217 CGCTGCCGTCATCGTTGC 62.505 66.667 0.00 0.00 35.01 4.17
1316 2889 2.124570 CCAGCCAGTTCATCCCCG 60.125 66.667 0.00 0.00 0.00 5.73
1391 2964 1.062810 ACAGAGGGTCATAGAGGGTCC 60.063 57.143 0.00 0.00 0.00 4.46
1446 3019 1.725169 CCCCCAACTGGAACCCTTGA 61.725 60.000 0.00 0.00 37.39 3.02
1488 3061 1.477553 AAAGGATGGTACCGTCGCTA 58.522 50.000 24.62 0.00 33.03 4.26
1533 3830 3.172050 CCTGAACTCAGACACGTATTCG 58.828 50.000 8.33 0.00 46.59 3.34
1556 3853 2.031012 CAGGACACAAGAGCGCCA 59.969 61.111 2.29 0.00 0.00 5.69
1594 3891 5.533112 TGTTTCCTCTAGATTCCTCTGGAT 58.467 41.667 0.00 0.00 38.22 3.41
1653 3950 5.263599 TCATTCACAGCCACAAGGATATTT 58.736 37.500 0.00 0.00 36.89 1.40
1668 3965 5.567423 CGCATACCAGAGGATATCATTCACA 60.567 44.000 4.83 0.00 0.00 3.58
1716 4013 3.391049 GACCAGTACGTCTTCTTTGCTT 58.609 45.455 0.00 0.00 0.00 3.91
1838 4135 1.006832 CTGCTTCCCACGGTAATTCG 58.993 55.000 0.00 0.00 0.00 3.34
2076 4373 2.259204 CGTTCAGGCGACGGGTAA 59.741 61.111 0.00 0.00 36.90 2.85
2179 4476 2.452600 TGGGGGATTGGAGTAATTGC 57.547 50.000 0.00 0.00 0.00 3.56
2240 8169 8.440771 CCCTAAAACAAGGACCATAATATCTCT 58.559 37.037 0.00 0.00 39.15 3.10
2245 8174 7.034967 ACACCCTAAAACAAGGACCATAATA 57.965 36.000 0.00 0.00 39.15 0.98
2287 8216 0.610174 TGAGAACTCTTGGCGCTGAT 59.390 50.000 7.64 0.00 0.00 2.90
2318 8247 0.321653 CCTCCCGTGCTTGCTAAACT 60.322 55.000 0.00 0.00 0.00 2.66
2331 8260 2.722201 GGCACTAGACACCCTCCCG 61.722 68.421 0.00 0.00 0.00 5.14
2409 8338 1.277739 CCGACATGCATGCATCGTC 59.722 57.895 31.78 31.78 33.90 4.20
2437 8366 3.041940 CCCGTCGAGTGTGGCAAC 61.042 66.667 0.00 0.00 0.00 4.17
2451 8380 3.016736 ACATCCATCTAACAAAAGCCCG 58.983 45.455 0.00 0.00 0.00 6.13
2614 8543 8.540388 AGCTAAAGTGTCTCACTAAATATCCAA 58.460 33.333 2.80 0.00 44.62 3.53
2645 8574 2.230660 GGGGCCAGATAATTACACTGC 58.769 52.381 4.39 9.75 0.00 4.40
2696 8625 0.772384 TTTTGGCGGGGACTTTAGGA 59.228 50.000 0.00 0.00 0.00 2.94
2802 8750 3.709633 TGCGAGGCCAGCATGACT 61.710 61.111 20.04 0.00 39.69 3.41
2818 8766 2.731451 CGGCGTCATTGATACTATGGTG 59.269 50.000 0.00 0.00 0.00 4.17
2819 8767 2.364324 ACGGCGTCATTGATACTATGGT 59.636 45.455 6.77 0.00 0.00 3.55
2835 8783 2.125512 AAGCTGCTAAGGACGGCG 60.126 61.111 4.80 4.80 44.36 6.46
2839 8787 0.036875 ACCACCAAGCTGCTAAGGAC 59.963 55.000 23.02 0.00 0.00 3.85
2855 8803 0.472925 TACCAAGCAGAGTGGGACCA 60.473 55.000 0.00 0.00 40.75 4.02
2901 8849 2.948315 GAGGTTCAAGATCCCATTGAGC 59.052 50.000 2.58 2.58 37.91 4.26
2939 8887 0.533531 CGCTTCTATCATGCCTGGCA 60.534 55.000 25.65 25.65 44.86 4.92
2973 8921 0.673985 AGATTGCTATCGCTACCGCA 59.326 50.000 2.42 0.00 35.85 5.69
3046 8994 0.846693 GTTGATGGCCCTGGAGGTAT 59.153 55.000 0.00 0.00 38.26 2.73
3088 9036 4.320275 CGAGATACTAGCGGCTGTTGATTA 60.320 45.833 13.86 0.00 0.00 1.75
3090 9038 2.030717 CGAGATACTAGCGGCTGTTGAT 60.031 50.000 13.86 0.34 0.00 2.57
3134 9082 2.905415 ATTGGCATCTTCCCTGAACA 57.095 45.000 0.00 0.00 0.00 3.18
3216 9164 1.812571 GATGATGCGTTTGACCCAACT 59.187 47.619 0.00 0.00 0.00 3.16
3250 9198 6.263392 TGGGTAAAGAACATTGTTGATTTCGA 59.737 34.615 6.80 0.00 0.00 3.71
3283 9231 4.523083 TGCTTGACATTAGGGGTATGTTC 58.477 43.478 0.00 0.00 36.41 3.18
3307 9255 4.394795 CGAATGACGTGGAGAAAATTGTC 58.605 43.478 0.00 0.00 37.22 3.18
3310 9258 2.747446 CCCGAATGACGTGGAGAAAATT 59.253 45.455 0.00 0.00 40.78 1.82
3313 9261 0.036765 CCCCGAATGACGTGGAGAAA 60.037 55.000 0.00 0.00 41.87 2.52
3322 9270 3.186047 CGCACGTCCCCGAATGAC 61.186 66.667 0.00 0.00 37.88 3.06
3325 9273 3.524648 AACACGCACGTCCCCGAAT 62.525 57.895 6.77 0.00 37.88 3.34
3349 9433 4.153958 CGAGCCTATGTCTGATGACTAC 57.846 50.000 0.00 0.00 43.29 2.73


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

AutoCloner maintained by Alex Coulton.