Multiple sequence alignment - TraesCS2D01G290200

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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 TraesCS2D01G290200 chr2D 100.000 3662 0 0 1 3662 372320622 372324283 0.000000e+00 6763.0
1 TraesCS2D01G290200 chr2A 91.462 2530 111 33 1183 3662 503453917 503456391 0.000000e+00 3378.0
2 TraesCS2D01G290200 chr2A 85.397 315 18 13 33 330 503452941 503453244 5.940000e-78 302.0
3 TraesCS2D01G290200 chr2A 89.189 222 13 5 486 696 503453295 503453516 2.170000e-67 267.0
4 TraesCS2D01G290200 chr2A 89.286 224 8 5 816 1023 503453622 503453845 2.170000e-67 267.0
5 TraesCS2D01G290200 chr2A 100.000 51 0 0 717 767 503453509 503453559 1.080000e-15 95.3
6 TraesCS2D01G290200 chr2A 97.917 48 1 0 1097 1144 503453873 503453920 2.340000e-12 84.2
7 TraesCS2D01G290200 chr2B 93.079 2153 71 22 1004 3117 441872708 441874821 0.000000e+00 3079.0
8 TraesCS2D01G290200 chr2B 83.598 567 25 26 478 1006 441871865 441872401 1.540000e-128 470.0
9 TraesCS2D01G290200 chr2B 83.521 267 16 14 1 256 441871232 441871481 1.320000e-54 224.0
10 TraesCS2D01G290200 chr2B 88.356 146 12 5 339 480 787751677 787751533 1.750000e-38 171.0
11 TraesCS2D01G290200 chr2B 82.540 189 12 10 3303 3477 441874969 441875150 2.950000e-31 147.0
12 TraesCS2D01G290200 chr2B 100.000 46 0 0 279 324 441871819 441871864 6.520000e-13 86.1
13 TraesCS2D01G290200 chr7B 89.404 151 12 2 335 481 85624478 85624328 1.740000e-43 187.0
14 TraesCS2D01G290200 chr7B 87.179 156 9 4 335 479 502893570 502893725 2.260000e-37 167.0
15 TraesCS2D01G290200 chr7B 94.915 59 2 1 3602 3660 297400637 297400580 1.400000e-14 91.6
16 TraesCS2D01G290200 chr7B 81.897 116 11 2 3556 3661 156706800 156706685 5.040000e-14 89.8
17 TraesCS2D01G290200 chr1D 92.126 127 8 1 335 459 227022343 227022217 1.040000e-40 178.0
18 TraesCS2D01G290200 chr1D 93.333 60 4 0 3603 3662 145941596 145941655 5.040000e-14 89.8
19 TraesCS2D01G290200 chr1D 89.394 66 4 3 433 497 352399994 352399931 3.030000e-11 80.5
20 TraesCS2D01G290200 chr1D 76.730 159 21 8 335 479 160451501 160451657 1.410000e-09 75.0
21 TraesCS2D01G290200 chr7A 91.538 130 8 2 335 461 420620814 420620943 3.760000e-40 176.0
22 TraesCS2D01G290200 chr7A 93.220 59 3 1 3602 3660 391906592 391906649 6.520000e-13 86.1
23 TraesCS2D01G290200 chr6A 90.909 132 10 1 335 464 494930046 494929915 3.760000e-40 176.0
24 TraesCS2D01G290200 chr3A 91.538 130 8 1 335 461 337267651 337267780 3.760000e-40 176.0
25 TraesCS2D01G290200 chr3A 88.356 146 14 1 322 464 24352478 24352333 4.860000e-39 172.0
26 TraesCS2D01G290200 chr6D 88.652 141 13 1 322 459 403091545 403091685 6.290000e-38 169.0
27 TraesCS2D01G290200 chr5A 87.671 146 15 1 322 464 140975435 140975290 2.260000e-37 167.0
28 TraesCS2D01G290200 chr5B 96.364 55 2 0 3608 3662 271946305 271946251 1.400000e-14 91.6
29 TraesCS2D01G290200 chr1A 93.333 60 3 1 3603 3662 143819124 143819182 1.810000e-13 87.9
30 TraesCS2D01G290200 chr1A 94.545 55 2 1 3609 3662 58289689 58289635 2.340000e-12 84.2
31 TraesCS2D01G290200 chr7D 87.324 71 8 1 3593 3662 43214931 43214861 3.030000e-11 80.5
32 TraesCS2D01G290200 chr4A 85.000 80 10 2 3585 3662 651368107 651368028 3.030000e-11 80.5
33 TraesCS2D01G290200 chr3B 84.848 66 7 2 434 497 291100734 291100670 3.050000e-06 63.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G290200 chr2D 372320622 372324283 3661 False 6763.00 6763 100.0000 1 3662 1 chr2D.!!$F1 3661
1 TraesCS2D01G290200 chr2A 503452941 503456391 3450 False 732.25 3378 92.2085 33 3662 6 chr2A.!!$F1 3629
2 TraesCS2D01G290200 chr2B 441871232 441875150 3918 False 801.22 3079 88.5476 1 3477 5 chr2B.!!$F1 3476

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
85 93 0.094730 GTACGTGCGAAATGGTCTGC 59.905 55.0 0.00 0.00 0.00 4.26 F
229 245 0.388520 CGACCATGCACGTCTTCTCA 60.389 55.0 12.56 0.00 0.00 3.27 F
659 1011 0.391130 GCGTTCCTAGTGCATGGACA 60.391 55.0 20.21 4.83 31.24 4.02 F
1089 1801 0.601046 TCGAGCACAAGCACAAGAGG 60.601 55.0 0.00 0.00 45.49 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1314 2030 0.031449 CGAGGAGGAGGAATCGCTTC 59.969 60.000 0.00 0.00 0.00 3.86 R
1945 2679 1.133458 CTCCAAGAAGCGCGCTTTC 59.867 57.895 42.93 33.12 36.26 2.62 R
2466 3219 3.200605 ACCAGCATCAATCAGTACATCCA 59.799 43.478 0.00 0.00 0.00 3.41 R
2721 3486 2.892852 ACAAAATGCTGTGGCTATGTGT 59.107 40.909 0.00 0.00 39.59 3.72 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
55 59 0.865111 TCATGTTTGAACGAGCGTGG 59.135 50.000 0.00 0.00 0.00 4.94
84 92 0.365523 CGTACGTGCGAAATGGTCTG 59.634 55.000 21.98 0.00 0.00 3.51
85 93 0.094730 GTACGTGCGAAATGGTCTGC 59.905 55.000 0.00 0.00 0.00 4.26
86 94 1.348538 TACGTGCGAAATGGTCTGCG 61.349 55.000 0.00 0.00 0.00 5.18
90 98 1.154225 GCGAAATGGTCTGCGTTGG 60.154 57.895 0.00 0.00 0.00 3.77
130 146 4.681978 GAACGCAGACTGCCCGGT 62.682 66.667 21.55 11.02 41.12 5.28
229 245 0.388520 CGACCATGCACGTCTTCTCA 60.389 55.000 12.56 0.00 0.00 3.27
233 249 2.290641 ACCATGCACGTCTTCTCAAAAC 59.709 45.455 0.00 0.00 0.00 2.43
236 252 4.350346 CATGCACGTCTTCTCAAAACAAA 58.650 39.130 0.00 0.00 0.00 2.83
247 263 7.222805 GTCTTCTCAAAACAAAAGAAATCCACC 59.777 37.037 0.00 0.00 30.10 4.61
250 266 5.587289 TCAAAACAAAAGAAATCCACCGAG 58.413 37.500 0.00 0.00 0.00 4.63
251 267 5.126384 TCAAAACAAAAGAAATCCACCGAGT 59.874 36.000 0.00 0.00 0.00 4.18
252 268 5.592104 AAACAAAAGAAATCCACCGAGTT 57.408 34.783 0.00 0.00 0.00 3.01
253 269 5.592104 AACAAAAGAAATCCACCGAGTTT 57.408 34.783 0.00 0.00 0.00 2.66
271 287 1.658994 TTGTTTGTGGTCTCGACACC 58.341 50.000 2.41 2.41 38.05 4.16
330 665 4.451096 CGTGCGCCAAAATAATACTCCTAT 59.549 41.667 4.18 0.00 0.00 2.57
332 667 6.312918 CGTGCGCCAAAATAATACTCCTATAT 59.687 38.462 4.18 0.00 0.00 0.86
333 668 7.490079 CGTGCGCCAAAATAATACTCCTATATA 59.510 37.037 4.18 0.00 0.00 0.86
335 670 8.537016 TGCGCCAAAATAATACTCCTATATACT 58.463 33.333 4.18 0.00 0.00 2.12
336 671 9.032420 GCGCCAAAATAATACTCCTATATACTC 57.968 37.037 0.00 0.00 0.00 2.59
337 672 9.530633 CGCCAAAATAATACTCCTATATACTCC 57.469 37.037 0.00 0.00 0.00 3.85
338 673 9.530633 GCCAAAATAATACTCCTATATACTCCG 57.469 37.037 0.00 0.00 0.00 4.63
358 693 8.943909 ACTCCGTTCCTAAATATAAGTCTTTG 57.056 34.615 0.00 0.00 0.00 2.77
359 694 8.537858 ACTCCGTTCCTAAATATAAGTCTTTGT 58.462 33.333 0.00 0.00 0.00 2.83
375 710 7.187824 AGTCTTTGTAGAGCTTCCATTATGA 57.812 36.000 0.00 0.00 0.00 2.15
376 711 7.624549 AGTCTTTGTAGAGCTTCCATTATGAA 58.375 34.615 0.00 0.00 0.00 2.57
377 712 7.550906 AGTCTTTGTAGAGCTTCCATTATGAAC 59.449 37.037 0.00 0.00 0.00 3.18
379 714 5.692115 TGTAGAGCTTCCATTATGAACCA 57.308 39.130 0.00 0.00 0.00 3.67
380 715 5.428253 TGTAGAGCTTCCATTATGAACCAC 58.572 41.667 0.00 0.00 0.00 4.16
381 716 4.574674 AGAGCTTCCATTATGAACCACA 57.425 40.909 0.00 0.00 0.00 4.17
382 717 5.121380 AGAGCTTCCATTATGAACCACAT 57.879 39.130 0.00 0.00 42.39 3.21
383 718 6.252599 AGAGCTTCCATTATGAACCACATA 57.747 37.500 0.00 0.00 40.07 2.29
384 719 6.058183 AGAGCTTCCATTATGAACCACATAC 58.942 40.000 0.00 0.00 40.62 2.39
385 720 4.816385 AGCTTCCATTATGAACCACATACG 59.184 41.667 0.00 0.00 40.62 3.06
386 721 4.814234 GCTTCCATTATGAACCACATACGA 59.186 41.667 0.00 0.00 40.62 3.43
387 722 5.295787 GCTTCCATTATGAACCACATACGAA 59.704 40.000 0.00 0.00 40.62 3.85
388 723 6.017109 GCTTCCATTATGAACCACATACGAAT 60.017 38.462 0.00 0.00 40.62 3.34
389 724 6.859420 TCCATTATGAACCACATACGAATG 57.141 37.500 0.00 0.00 40.62 2.67
391 726 7.501844 TCCATTATGAACCACATACGAATGTA 58.498 34.615 0.00 0.00 44.70 2.29
392 727 8.154203 TCCATTATGAACCACATACGAATGTAT 58.846 33.333 0.00 0.00 44.70 2.29
393 728 9.430623 CCATTATGAACCACATACGAATGTATA 57.569 33.333 0.00 0.00 44.70 1.47
399 734 9.855021 TGAACCACATACGAATGTATATAGATG 57.145 33.333 0.00 0.00 44.70 2.90
400 735 8.703604 AACCACATACGAATGTATATAGATGC 57.296 34.615 0.00 0.00 44.70 3.91
401 736 7.836842 ACCACATACGAATGTATATAGATGCA 58.163 34.615 0.00 0.00 44.70 3.96
402 737 8.478066 ACCACATACGAATGTATATAGATGCAT 58.522 33.333 0.00 0.00 44.70 3.96
437 772 8.749026 AGATTCATTCATTTTGCTCATCTAGT 57.251 30.769 0.00 0.00 0.00 2.57
438 773 8.622157 AGATTCATTCATTTTGCTCATCTAGTG 58.378 33.333 0.00 0.00 0.00 2.74
439 774 6.688637 TCATTCATTTTGCTCATCTAGTGG 57.311 37.500 0.00 0.00 0.00 4.00
440 775 6.417258 TCATTCATTTTGCTCATCTAGTGGA 58.583 36.000 0.00 0.00 0.00 4.02
441 776 6.885918 TCATTCATTTTGCTCATCTAGTGGAA 59.114 34.615 0.00 0.00 0.00 3.53
442 777 7.558807 TCATTCATTTTGCTCATCTAGTGGAAT 59.441 33.333 0.00 0.00 0.00 3.01
443 778 6.932356 TCATTTTGCTCATCTAGTGGAATC 57.068 37.500 0.00 0.00 0.00 2.52
444 779 6.656902 TCATTTTGCTCATCTAGTGGAATCT 58.343 36.000 0.00 0.00 0.00 2.40
445 780 6.765036 TCATTTTGCTCATCTAGTGGAATCTC 59.235 38.462 0.00 0.00 0.00 2.75
446 781 5.946942 TTTGCTCATCTAGTGGAATCTCT 57.053 39.130 0.00 0.00 0.00 3.10
447 782 7.423844 TTTTGCTCATCTAGTGGAATCTCTA 57.576 36.000 0.00 0.00 0.00 2.43
448 783 6.398234 TTGCTCATCTAGTGGAATCTCTAC 57.602 41.667 0.00 0.00 0.00 2.59
449 784 5.449553 TGCTCATCTAGTGGAATCTCTACA 58.550 41.667 0.00 0.00 29.47 2.74
450 785 5.893824 TGCTCATCTAGTGGAATCTCTACAA 59.106 40.000 0.00 0.00 29.47 2.41
451 786 6.381133 TGCTCATCTAGTGGAATCTCTACAAA 59.619 38.462 0.00 0.00 29.47 2.83
452 787 6.922957 GCTCATCTAGTGGAATCTCTACAAAG 59.077 42.308 0.00 0.00 29.47 2.77
453 788 7.201866 GCTCATCTAGTGGAATCTCTACAAAGA 60.202 40.741 0.00 0.00 30.91 2.52
454 789 8.001881 TCATCTAGTGGAATCTCTACAAAGAC 57.998 38.462 0.00 0.00 29.78 3.01
455 790 7.836685 TCATCTAGTGGAATCTCTACAAAGACT 59.163 37.037 0.00 0.00 29.78 3.24
456 791 8.474025 CATCTAGTGGAATCTCTACAAAGACTT 58.526 37.037 0.00 0.00 29.78 3.01
457 792 9.702253 ATCTAGTGGAATCTCTACAAAGACTTA 57.298 33.333 0.00 0.00 29.78 2.24
458 793 9.702253 TCTAGTGGAATCTCTACAAAGACTTAT 57.298 33.333 0.00 0.00 29.47 1.73
473 808 8.414778 ACAAAGACTTATATTTAGAGACGGAGG 58.585 37.037 0.00 0.00 0.00 4.30
474 809 7.527568 AAGACTTATATTTAGAGACGGAGGG 57.472 40.000 0.00 0.00 0.00 4.30
475 810 6.850234 AGACTTATATTTAGAGACGGAGGGA 58.150 40.000 0.00 0.00 0.00 4.20
476 811 6.943718 AGACTTATATTTAGAGACGGAGGGAG 59.056 42.308 0.00 0.00 0.00 4.30
477 812 6.612741 ACTTATATTTAGAGACGGAGGGAGT 58.387 40.000 0.00 0.00 0.00 3.85
478 813 7.753630 ACTTATATTTAGAGACGGAGGGAGTA 58.246 38.462 0.00 0.00 0.00 2.59
479 814 7.665145 ACTTATATTTAGAGACGGAGGGAGTAC 59.335 40.741 0.00 0.00 0.00 2.73
480 815 4.523168 ATTTAGAGACGGAGGGAGTACT 57.477 45.455 0.00 0.00 0.00 2.73
481 816 4.313020 TTTAGAGACGGAGGGAGTACTT 57.687 45.455 0.00 0.00 0.00 2.24
482 817 5.441718 TTTAGAGACGGAGGGAGTACTTA 57.558 43.478 0.00 0.00 0.00 2.24
483 818 3.280197 AGAGACGGAGGGAGTACTTAC 57.720 52.381 0.00 0.00 0.00 2.34
484 819 2.092484 AGAGACGGAGGGAGTACTTACC 60.092 54.545 8.99 8.99 0.00 2.85
508 843 5.391950 CGTACATACAAAATCTGCAAAGCCT 60.392 40.000 0.00 0.00 0.00 4.58
578 913 1.151450 CTGTTGGACCCAGTGGCTT 59.849 57.895 2.61 0.00 33.59 4.35
639 982 2.978824 CTGGTGGGTCCGTACAGG 59.021 66.667 0.00 0.00 42.97 4.00
640 983 2.605295 TGGTGGGTCCGTACAGGG 60.605 66.667 0.00 0.00 41.52 4.45
659 1011 0.391130 GCGTTCCTAGTGCATGGACA 60.391 55.000 20.21 4.83 31.24 4.02
683 1035 2.760385 ACTAGTCGGCTGCCCTCC 60.760 66.667 14.12 0.58 0.00 4.30
705 1057 1.186917 TTCCGTTTCGCCCCTACAGA 61.187 55.000 0.00 0.00 0.00 3.41
708 1060 1.269621 CCGTTTCGCCCCTACAGATAG 60.270 57.143 0.00 0.00 0.00 2.08
709 1061 1.269621 CGTTTCGCCCCTACAGATAGG 60.270 57.143 0.00 0.00 46.99 2.57
710 1062 1.761198 GTTTCGCCCCTACAGATAGGT 59.239 52.381 0.00 0.00 46.11 3.08
712 1064 1.113517 TCGCCCCTACAGATAGGTGC 61.114 60.000 0.00 0.00 45.75 5.01
713 1065 1.755384 GCCCCTACAGATAGGTGCC 59.245 63.158 0.00 0.00 44.04 5.01
766 1120 5.710099 CCATTTAGGAAAGCAGTAAAGACCA 59.290 40.000 0.00 0.00 41.22 4.02
845 1232 5.358725 CGTTTACCCATGTTTTATAGGCCTT 59.641 40.000 12.58 0.81 0.00 4.35
1026 1738 6.342111 ACTAAAGCAGAAGGAAGCATACTAC 58.658 40.000 0.00 0.00 0.00 2.73
1027 1739 5.428184 AAAGCAGAAGGAAGCATACTACT 57.572 39.130 0.00 0.00 0.00 2.57
1028 1740 6.546428 AAAGCAGAAGGAAGCATACTACTA 57.454 37.500 0.00 0.00 0.00 1.82
1029 1741 5.523438 AGCAGAAGGAAGCATACTACTAC 57.477 43.478 0.00 0.00 0.00 2.73
1055 1767 6.603224 AGGAGGGAATACAGTACAGTACTAG 58.397 44.000 13.12 10.08 37.23 2.57
1059 1771 8.329346 AGGGAATACAGTACAGTACTAGAGTA 57.671 38.462 13.12 11.50 37.23 2.59
1086 1798 0.882042 AGGTCGAGCACAAGCACAAG 60.882 55.000 18.15 0.00 45.49 3.16
1089 1801 0.601046 TCGAGCACAAGCACAAGAGG 60.601 55.000 0.00 0.00 45.49 3.69
1091 1803 1.152902 AGCACAAGCACAAGAGGCA 60.153 52.632 0.00 0.00 45.49 4.75
1130 1842 2.290577 ACCCCTGCAGAAAGTGAAGATC 60.291 50.000 17.39 0.00 32.55 2.75
1246 1958 2.127708 GCTTCATTCCCTCCCTTCCTA 58.872 52.381 0.00 0.00 0.00 2.94
1314 2030 2.036571 GGTTAGTCGCCAAACCCCG 61.037 63.158 2.29 0.00 39.43 5.73
1331 2047 1.395826 CCGAAGCGATTCCTCCTCCT 61.396 60.000 8.00 0.00 0.00 3.69
1347 2069 4.363990 CTCGTGCTCCTGGCGTGT 62.364 66.667 0.00 0.00 45.43 4.49
1368 2090 3.041940 GCCTGCACGCACGTAACT 61.042 61.111 2.56 0.00 0.00 2.24
1371 2093 1.372997 CTGCACGCACGTAACTCCT 60.373 57.895 0.00 0.00 0.00 3.69
1375 2097 2.879462 CGCACGTAACTCCTCCGC 60.879 66.667 0.00 0.00 0.00 5.54
2558 3314 1.515736 GGTAGGTAGACGTGCGTGC 60.516 63.158 0.67 0.00 0.00 5.34
2672 3437 7.936496 TGTGGATTTCAGAAATATACAGCAA 57.064 32.000 8.45 0.00 0.00 3.91
2673 3438 8.347004 TGTGGATTTCAGAAATATACAGCAAA 57.653 30.769 8.45 0.00 0.00 3.68
2674 3439 8.461222 TGTGGATTTCAGAAATATACAGCAAAG 58.539 33.333 8.45 0.00 0.00 2.77
2675 3440 7.917505 GTGGATTTCAGAAATATACAGCAAAGG 59.082 37.037 8.45 0.00 0.00 3.11
2676 3441 7.833682 TGGATTTCAGAAATATACAGCAAAGGA 59.166 33.333 8.45 0.00 0.00 3.36
2677 3442 8.131731 GGATTTCAGAAATATACAGCAAAGGAC 58.868 37.037 8.45 0.00 0.00 3.85
2678 3443 7.994425 TTTCAGAAATATACAGCAAAGGACA 57.006 32.000 0.00 0.00 0.00 4.02
2699 3464 6.324561 ACAAAGGTTGCAACATTTTGTTTT 57.675 29.167 34.73 23.57 40.47 2.43
2721 3486 6.636562 TTAACCGTTTGCTCCTTTTCATTA 57.363 33.333 0.00 0.00 0.00 1.90
2817 3591 1.514678 TTTGGGATGCTGACACGTGC 61.515 55.000 17.22 9.30 0.00 5.34
2821 3595 1.656652 GGATGCTGACACGTGCTAAT 58.343 50.000 17.22 2.31 0.00 1.73
2875 3649 2.203252 CGGGTGGAGATGGGCATG 60.203 66.667 0.00 0.00 0.00 4.06
2923 3697 7.277539 CCTTGTCATTCTCTAGCTTTGAGTAAG 59.722 40.741 13.71 4.80 36.90 2.34
2987 3763 7.439655 TGAGCTTTAAACAAAACTTGTGTTTGT 59.560 29.630 17.19 7.30 46.10 2.83
3100 3876 4.142730 CCCGAAGAGAAGAAGCAAATGAAG 60.143 45.833 0.00 0.00 0.00 3.02
3117 3893 0.698238 AAGCATGGTCCAGCCTTACA 59.302 50.000 0.00 0.00 38.35 2.41
3119 3895 1.285962 AGCATGGTCCAGCCTTACAAT 59.714 47.619 0.00 0.00 38.35 2.71
3120 3896 1.678101 GCATGGTCCAGCCTTACAATC 59.322 52.381 0.00 0.00 38.35 2.67
3143 3919 6.380995 TCGTGGAATTCTGAAATGAAACATG 58.619 36.000 5.23 0.00 0.00 3.21
3144 3920 5.574055 CGTGGAATTCTGAAATGAAACATGG 59.426 40.000 5.23 0.00 0.00 3.66
3145 3921 5.349543 GTGGAATTCTGAAATGAAACATGGC 59.650 40.000 5.23 0.00 0.00 4.40
3146 3922 4.872124 GGAATTCTGAAATGAAACATGGCC 59.128 41.667 5.23 0.00 0.00 5.36
3147 3923 3.959535 TTCTGAAATGAAACATGGCCC 57.040 42.857 0.00 0.00 0.00 5.80
3148 3924 2.178580 TCTGAAATGAAACATGGCCCC 58.821 47.619 0.00 0.00 0.00 5.80
3149 3925 2.181975 CTGAAATGAAACATGGCCCCT 58.818 47.619 0.00 0.00 0.00 4.79
3150 3926 3.011144 TCTGAAATGAAACATGGCCCCTA 59.989 43.478 0.00 0.00 0.00 3.53
3151 3927 3.096092 TGAAATGAAACATGGCCCCTAC 58.904 45.455 0.00 0.00 0.00 3.18
3152 3928 3.245586 TGAAATGAAACATGGCCCCTACT 60.246 43.478 0.00 0.00 0.00 2.57
3153 3929 2.736670 ATGAAACATGGCCCCTACTC 57.263 50.000 0.00 0.00 0.00 2.59
3154 3930 1.367346 TGAAACATGGCCCCTACTCA 58.633 50.000 0.00 0.00 0.00 3.41
3155 3931 1.707989 TGAAACATGGCCCCTACTCAA 59.292 47.619 0.00 0.00 0.00 3.02
3156 3932 2.109128 TGAAACATGGCCCCTACTCAAA 59.891 45.455 0.00 0.00 0.00 2.69
3157 3933 3.245586 TGAAACATGGCCCCTACTCAAAT 60.246 43.478 0.00 0.00 0.00 2.32
3158 3934 2.442236 ACATGGCCCCTACTCAAATG 57.558 50.000 0.00 0.00 0.00 2.32
3159 3935 1.922447 ACATGGCCCCTACTCAAATGA 59.078 47.619 0.00 0.00 0.00 2.57
3160 3936 2.311542 ACATGGCCCCTACTCAAATGAA 59.688 45.455 0.00 0.00 0.00 2.57
3192 3968 6.765512 TGGGATTCTGAAAAACAAAACCAATC 59.234 34.615 0.00 0.00 0.00 2.67
3317 4114 4.904251 CCTTCCTCCCTCTTGATCAAGATA 59.096 45.833 32.75 21.44 45.40 1.98
3348 4145 4.853924 AATTTGTTGACCTACTGCTTGG 57.146 40.909 0.00 0.00 0.00 3.61
3411 4220 3.933332 GGTCAACATGTTAGGCTAGTGAC 59.067 47.826 11.53 12.13 0.00 3.67
3441 4250 1.663379 GCCCAACTAACCGGCCATTC 61.663 60.000 0.00 0.00 36.63 2.67
3470 4281 4.595762 TCACAGTAACACAAGAGTACCC 57.404 45.455 0.00 0.00 0.00 3.69
3478 4289 2.224305 ACACAAGAGTACCCACTTCAGC 60.224 50.000 0.00 0.00 34.21 4.26
3498 4309 6.827727 TCAGCAAAGTCTCCTAGTTTTAACT 58.172 36.000 0.29 0.29 42.91 2.24
3499 4310 6.706270 TCAGCAAAGTCTCCTAGTTTTAACTG 59.294 38.462 5.41 0.00 40.07 3.16
3500 4311 6.483640 CAGCAAAGTCTCCTAGTTTTAACTGT 59.516 38.462 5.41 0.00 40.07 3.55
3501 4312 7.656137 CAGCAAAGTCTCCTAGTTTTAACTGTA 59.344 37.037 5.41 0.00 40.07 2.74
3516 4327 9.712359 GTTTTAACTGTACTAGGTGTTTTCTTG 57.288 33.333 0.00 0.00 0.00 3.02
3520 4331 7.128234 ACTGTACTAGGTGTTTTCTTGGTTA 57.872 36.000 0.00 0.00 0.00 2.85
3521 4332 7.567458 ACTGTACTAGGTGTTTTCTTGGTTAA 58.433 34.615 0.00 0.00 0.00 2.01
3522 4333 8.215736 ACTGTACTAGGTGTTTTCTTGGTTAAT 58.784 33.333 0.00 0.00 0.00 1.40
3523 4334 8.983702 TGTACTAGGTGTTTTCTTGGTTAATT 57.016 30.769 0.00 0.00 0.00 1.40
3524 4335 9.059260 TGTACTAGGTGTTTTCTTGGTTAATTC 57.941 33.333 0.00 0.00 0.00 2.17
3525 4336 9.059260 GTACTAGGTGTTTTCTTGGTTAATTCA 57.941 33.333 0.00 0.00 0.00 2.57
3526 4337 7.937649 ACTAGGTGTTTTCTTGGTTAATTCAC 58.062 34.615 0.00 0.00 0.00 3.18
3527 4338 6.783708 AGGTGTTTTCTTGGTTAATTCACA 57.216 33.333 0.00 0.00 0.00 3.58
3528 4339 6.569780 AGGTGTTTTCTTGGTTAATTCACAC 58.430 36.000 0.00 0.00 32.88 3.82
3529 4340 6.379988 AGGTGTTTTCTTGGTTAATTCACACT 59.620 34.615 0.00 0.00 33.91 3.55
3530 4341 6.695713 GGTGTTTTCTTGGTTAATTCACACTC 59.304 38.462 0.00 0.00 33.91 3.51
3531 4342 6.695713 GTGTTTTCTTGGTTAATTCACACTCC 59.304 38.462 0.00 0.00 31.34 3.85
3532 4343 6.183360 TGTTTTCTTGGTTAATTCACACTCCC 60.183 38.462 0.00 0.00 0.00 4.30
3533 4344 4.993705 TCTTGGTTAATTCACACTCCCT 57.006 40.909 0.00 0.00 0.00 4.20
3534 4345 4.906618 TCTTGGTTAATTCACACTCCCTC 58.093 43.478 0.00 0.00 0.00 4.30
3535 4346 3.328382 TGGTTAATTCACACTCCCTCG 57.672 47.619 0.00 0.00 0.00 4.63
3539 4350 0.693049 AATTCACACTCCCTCGGCTT 59.307 50.000 0.00 0.00 0.00 4.35
3549 4360 1.026718 CCCTCGGCTTCGAAATGCTT 61.027 55.000 9.01 0.00 42.80 3.91
3560 4371 4.928661 TCGAAATGCTTGAAGTTCTAGC 57.071 40.909 26.22 26.22 43.76 3.42
3572 4383 2.784347 AGTTCTAGCTTTGTCCCAAGC 58.216 47.619 0.00 0.00 42.10 4.01
3573 4384 1.813178 GTTCTAGCTTTGTCCCAAGCC 59.187 52.381 0.00 0.00 42.74 4.35
3575 4386 1.003580 TCTAGCTTTGTCCCAAGCCAG 59.996 52.381 0.00 0.00 42.74 4.85
3598 4409 6.016777 CAGACATCTTAAAGTTTGGCAAGTCT 60.017 38.462 0.00 2.91 32.23 3.24
3600 4411 7.173390 AGACATCTTAAAGTTTGGCAAGTCTAC 59.827 37.037 8.97 1.33 30.50 2.59
3601 4412 6.998673 ACATCTTAAAGTTTGGCAAGTCTACT 59.001 34.615 0.00 0.00 0.00 2.57
3603 4414 7.958053 TCTTAAAGTTTGGCAAGTCTACTAC 57.042 36.000 0.00 0.00 0.00 2.73
3604 4415 6.932960 TCTTAAAGTTTGGCAAGTCTACTACC 59.067 38.462 0.00 0.00 0.00 3.18
3606 4417 4.273148 AGTTTGGCAAGTCTACTACCAG 57.727 45.455 0.00 0.00 34.88 4.00
3608 4419 4.836736 AGTTTGGCAAGTCTACTACCAGTA 59.163 41.667 0.00 0.00 34.88 2.74
3610 4421 5.593679 TTGGCAAGTCTACTACCAGTATC 57.406 43.478 0.00 0.00 34.88 2.24
3611 4422 4.868268 TGGCAAGTCTACTACCAGTATCT 58.132 43.478 1.64 0.00 29.08 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.887568 GGAGATGGCGTCTGTGCG 60.888 66.667 15.23 0.00 37.29 5.34
65 73 0.365523 CAGACCATTTCGCACGTACG 59.634 55.000 15.01 15.01 0.00 3.67
86 94 4.410400 CAGGCGGTCCCTCCCAAC 62.410 72.222 0.00 0.00 44.09 3.77
90 98 4.785453 CAAGCAGGCGGTCCCTCC 62.785 72.222 0.00 0.00 44.09 4.30
229 245 5.592104 ACTCGGTGGATTTCTTTTGTTTT 57.408 34.783 0.00 0.00 0.00 2.43
233 249 4.932146 ACAAACTCGGTGGATTTCTTTTG 58.068 39.130 0.00 0.00 0.00 2.44
236 252 4.401202 ACAAACAAACTCGGTGGATTTCTT 59.599 37.500 0.00 0.00 0.00 2.52
247 263 2.034001 GTCGAGACCACAAACAAACTCG 60.034 50.000 0.00 0.00 45.20 4.18
250 266 2.223180 GGTGTCGAGACCACAAACAAAC 60.223 50.000 25.82 0.00 35.88 2.93
251 267 2.011222 GGTGTCGAGACCACAAACAAA 58.989 47.619 25.82 0.00 35.88 2.83
252 268 1.066071 TGGTGTCGAGACCACAAACAA 60.066 47.619 29.12 5.94 41.30 2.83
253 269 0.537653 TGGTGTCGAGACCACAAACA 59.462 50.000 29.12 6.72 41.30 2.83
348 683 9.553064 CATAATGGAAGCTCTACAAAGACTTAT 57.447 33.333 0.00 0.00 0.00 1.73
349 684 8.758829 TCATAATGGAAGCTCTACAAAGACTTA 58.241 33.333 0.00 0.00 0.00 2.24
350 685 7.624549 TCATAATGGAAGCTCTACAAAGACTT 58.375 34.615 0.00 0.00 0.00 3.01
351 686 7.187824 TCATAATGGAAGCTCTACAAAGACT 57.812 36.000 0.00 0.00 0.00 3.24
352 687 7.201652 GGTTCATAATGGAAGCTCTACAAAGAC 60.202 40.741 0.00 0.00 40.99 3.01
353 688 6.823689 GGTTCATAATGGAAGCTCTACAAAGA 59.176 38.462 0.00 0.00 40.99 2.52
354 689 6.599244 TGGTTCATAATGGAAGCTCTACAAAG 59.401 38.462 6.65 0.00 43.72 2.77
355 690 6.374333 GTGGTTCATAATGGAAGCTCTACAAA 59.626 38.462 6.65 0.00 43.72 2.83
356 691 5.880332 GTGGTTCATAATGGAAGCTCTACAA 59.120 40.000 6.65 0.00 43.72 2.41
358 693 5.428253 TGTGGTTCATAATGGAAGCTCTAC 58.572 41.667 6.65 0.00 43.72 2.59
359 694 5.692115 TGTGGTTCATAATGGAAGCTCTA 57.308 39.130 6.65 0.00 43.72 2.43
360 695 4.574674 TGTGGTTCATAATGGAAGCTCT 57.425 40.909 6.65 0.00 43.72 4.09
361 696 5.050091 CGTATGTGGTTCATAATGGAAGCTC 60.050 44.000 6.65 4.03 43.72 4.09
363 698 4.814234 TCGTATGTGGTTCATAATGGAAGC 59.186 41.667 0.00 0.00 43.66 3.86
364 699 6.918892 TTCGTATGTGGTTCATAATGGAAG 57.081 37.500 0.00 0.00 40.21 3.46
365 700 6.826231 ACATTCGTATGTGGTTCATAATGGAA 59.174 34.615 6.89 0.00 43.29 3.53
366 701 6.353323 ACATTCGTATGTGGTTCATAATGGA 58.647 36.000 6.89 0.00 43.29 3.41
367 702 6.618287 ACATTCGTATGTGGTTCATAATGG 57.382 37.500 6.89 0.00 43.29 3.16
375 710 8.311109 TGCATCTATATACATTCGTATGTGGTT 58.689 33.333 16.91 5.39 44.56 3.67
376 711 7.836842 TGCATCTATATACATTCGTATGTGGT 58.163 34.615 16.91 8.59 44.56 4.16
377 712 8.877808 ATGCATCTATATACATTCGTATGTGG 57.122 34.615 16.91 3.59 44.56 4.17
411 746 9.842775 ACTAGATGAGCAAAATGAATGAATCTA 57.157 29.630 0.00 0.00 0.00 1.98
412 747 8.622157 CACTAGATGAGCAAAATGAATGAATCT 58.378 33.333 0.00 0.00 0.00 2.40
413 748 7.861372 CCACTAGATGAGCAAAATGAATGAATC 59.139 37.037 0.00 0.00 0.00 2.52
414 749 7.558807 TCCACTAGATGAGCAAAATGAATGAAT 59.441 33.333 0.00 0.00 0.00 2.57
415 750 6.885918 TCCACTAGATGAGCAAAATGAATGAA 59.114 34.615 0.00 0.00 0.00 2.57
416 751 6.417258 TCCACTAGATGAGCAAAATGAATGA 58.583 36.000 0.00 0.00 0.00 2.57
417 752 6.688637 TCCACTAGATGAGCAAAATGAATG 57.311 37.500 0.00 0.00 0.00 2.67
418 753 7.778853 AGATTCCACTAGATGAGCAAAATGAAT 59.221 33.333 0.00 0.00 0.00 2.57
419 754 7.114754 AGATTCCACTAGATGAGCAAAATGAA 58.885 34.615 0.00 0.00 0.00 2.57
420 755 6.656902 AGATTCCACTAGATGAGCAAAATGA 58.343 36.000 0.00 0.00 0.00 2.57
421 756 6.766944 AGAGATTCCACTAGATGAGCAAAATG 59.233 38.462 0.00 0.00 0.00 2.32
422 757 6.897986 AGAGATTCCACTAGATGAGCAAAAT 58.102 36.000 0.00 0.00 0.00 1.82
423 758 6.305272 AGAGATTCCACTAGATGAGCAAAA 57.695 37.500 0.00 0.00 0.00 2.44
424 759 5.946942 AGAGATTCCACTAGATGAGCAAA 57.053 39.130 0.00 0.00 0.00 3.68
425 760 5.893824 TGTAGAGATTCCACTAGATGAGCAA 59.106 40.000 0.00 0.00 0.00 3.91
426 761 5.449553 TGTAGAGATTCCACTAGATGAGCA 58.550 41.667 0.00 0.00 0.00 4.26
427 762 6.398234 TTGTAGAGATTCCACTAGATGAGC 57.602 41.667 0.00 0.00 0.00 4.26
428 763 8.134895 GTCTTTGTAGAGATTCCACTAGATGAG 58.865 40.741 0.00 0.00 0.00 2.90
429 764 7.836685 AGTCTTTGTAGAGATTCCACTAGATGA 59.163 37.037 0.00 0.00 0.00 2.92
430 765 8.006298 AGTCTTTGTAGAGATTCCACTAGATG 57.994 38.462 0.00 0.00 0.00 2.90
431 766 8.602472 AAGTCTTTGTAGAGATTCCACTAGAT 57.398 34.615 0.00 0.00 0.00 1.98
432 767 9.702253 ATAAGTCTTTGTAGAGATTCCACTAGA 57.298 33.333 0.00 0.00 0.00 2.43
447 782 8.414778 CCTCCGTCTCTAAATATAAGTCTTTGT 58.585 37.037 0.00 0.00 0.00 2.83
448 783 7.868415 CCCTCCGTCTCTAAATATAAGTCTTTG 59.132 40.741 0.00 0.00 0.00 2.77
449 784 7.783596 TCCCTCCGTCTCTAAATATAAGTCTTT 59.216 37.037 0.00 0.00 0.00 2.52
450 785 7.296098 TCCCTCCGTCTCTAAATATAAGTCTT 58.704 38.462 0.00 0.00 0.00 3.01
451 786 6.850234 TCCCTCCGTCTCTAAATATAAGTCT 58.150 40.000 0.00 0.00 0.00 3.24
452 787 6.716173 ACTCCCTCCGTCTCTAAATATAAGTC 59.284 42.308 0.00 0.00 0.00 3.01
453 788 6.612741 ACTCCCTCCGTCTCTAAATATAAGT 58.387 40.000 0.00 0.00 0.00 2.24
454 789 7.884354 AGTACTCCCTCCGTCTCTAAATATAAG 59.116 40.741 0.00 0.00 0.00 1.73
455 790 7.753630 AGTACTCCCTCCGTCTCTAAATATAA 58.246 38.462 0.00 0.00 0.00 0.98
456 791 7.327064 AGTACTCCCTCCGTCTCTAAATATA 57.673 40.000 0.00 0.00 0.00 0.86
457 792 6.203526 AGTACTCCCTCCGTCTCTAAATAT 57.796 41.667 0.00 0.00 0.00 1.28
458 793 5.643421 AGTACTCCCTCCGTCTCTAAATA 57.357 43.478 0.00 0.00 0.00 1.40
459 794 4.523168 AGTACTCCCTCCGTCTCTAAAT 57.477 45.455 0.00 0.00 0.00 1.40
460 795 4.313020 AAGTACTCCCTCCGTCTCTAAA 57.687 45.455 0.00 0.00 0.00 1.85
461 796 4.384647 GGTAAGTACTCCCTCCGTCTCTAA 60.385 50.000 0.00 0.00 0.00 2.10
462 797 3.135530 GGTAAGTACTCCCTCCGTCTCTA 59.864 52.174 0.00 0.00 0.00 2.43
463 798 2.092484 GGTAAGTACTCCCTCCGTCTCT 60.092 54.545 0.00 0.00 0.00 3.10
464 799 2.296792 GGTAAGTACTCCCTCCGTCTC 58.703 57.143 0.00 0.00 0.00 3.36
465 800 1.407989 CGGTAAGTACTCCCTCCGTCT 60.408 57.143 15.13 0.00 34.38 4.18
466 801 1.020437 CGGTAAGTACTCCCTCCGTC 58.980 60.000 15.13 0.00 34.38 4.79
467 802 0.329596 ACGGTAAGTACTCCCTCCGT 59.670 55.000 20.05 20.05 44.87 4.69
468 803 2.332063 TACGGTAAGTACTCCCTCCG 57.668 55.000 19.12 19.12 42.94 4.63
477 812 7.321908 TGCAGATTTTGTATGTACGGTAAGTA 58.678 34.615 0.00 0.00 0.00 2.24
478 813 6.167685 TGCAGATTTTGTATGTACGGTAAGT 58.832 36.000 0.00 0.00 0.00 2.24
479 814 6.656314 TGCAGATTTTGTATGTACGGTAAG 57.344 37.500 0.00 0.00 0.00 2.34
480 815 7.436430 TTTGCAGATTTTGTATGTACGGTAA 57.564 32.000 0.00 0.00 0.00 2.85
481 816 6.402766 GCTTTGCAGATTTTGTATGTACGGTA 60.403 38.462 0.00 0.00 0.00 4.02
482 817 5.619086 GCTTTGCAGATTTTGTATGTACGGT 60.619 40.000 0.00 0.00 0.00 4.83
483 818 4.793216 GCTTTGCAGATTTTGTATGTACGG 59.207 41.667 0.00 0.00 0.00 4.02
484 819 4.793216 GGCTTTGCAGATTTTGTATGTACG 59.207 41.667 0.00 0.00 0.00 3.67
578 913 0.390492 ATGCGCTACTCTATGCAGCA 59.610 50.000 9.73 0.00 41.19 4.41
618 961 3.000819 TACGGACCCACCAGCCAG 61.001 66.667 0.00 0.00 38.90 4.85
639 982 1.090052 GTCCATGCACTAGGAACGCC 61.090 60.000 5.99 0.00 35.29 5.68
640 983 0.391130 TGTCCATGCACTAGGAACGC 60.391 55.000 5.99 0.00 35.29 4.84
642 985 3.462021 GAGATGTCCATGCACTAGGAAC 58.538 50.000 5.99 2.75 35.29 3.62
659 1011 1.448922 GCAGCCGACTAGTCCGAGAT 61.449 60.000 17.23 2.31 0.00 2.75
683 1035 1.022982 GTAGGGGCGAAACGGAAAGG 61.023 60.000 0.00 0.00 0.00 3.11
709 1061 1.009335 GAAACGAAACGGTGGGCAC 60.009 57.895 0.00 0.00 0.00 5.01
710 1062 2.535788 CGAAACGAAACGGTGGGCA 61.536 57.895 0.00 0.00 0.00 5.36
712 1064 2.940561 CCGAAACGAAACGGTGGG 59.059 61.111 0.00 0.00 43.53 4.61
766 1120 3.409026 AACGCATCTTCTTCTTGAGGT 57.591 42.857 0.00 0.00 0.00 3.85
1026 1738 6.603224 ACTGTACTGTATTCCCTCCTAGTAG 58.397 44.000 3.21 0.00 0.00 2.57
1027 1739 6.587560 ACTGTACTGTATTCCCTCCTAGTA 57.412 41.667 3.21 0.00 0.00 1.82
1028 1740 5.469210 ACTGTACTGTATTCCCTCCTAGT 57.531 43.478 3.21 0.00 0.00 2.57
1029 1741 6.603224 AGTACTGTACTGTATTCCCTCCTAG 58.397 44.000 19.09 0.00 37.69 3.02
1055 1767 3.008330 TGCTCGACCTCAACTAGTACTC 58.992 50.000 0.00 0.00 0.00 2.59
1059 1771 1.617322 TGTGCTCGACCTCAACTAGT 58.383 50.000 0.00 0.00 0.00 2.57
1060 1772 2.600731 CTTGTGCTCGACCTCAACTAG 58.399 52.381 0.00 0.00 0.00 2.57
1086 1798 0.394899 CCCTCCAACTCCAATGCCTC 60.395 60.000 0.00 0.00 0.00 4.70
1089 1801 0.039618 TTCCCCTCCAACTCCAATGC 59.960 55.000 0.00 0.00 0.00 3.56
1091 1803 1.077169 GGTTTCCCCTCCAACTCCAAT 59.923 52.381 0.00 0.00 0.00 3.16
1172 1884 0.909610 ATCGGGAAGCCTGAACCTGA 60.910 55.000 0.00 0.00 42.74 3.86
1173 1885 0.035056 AATCGGGAAGCCTGAACCTG 60.035 55.000 0.00 0.00 42.74 4.00
1174 1886 1.580059 TAATCGGGAAGCCTGAACCT 58.420 50.000 0.00 0.00 42.74 3.50
1175 1887 2.093128 TCTTAATCGGGAAGCCTGAACC 60.093 50.000 0.00 0.00 42.74 3.62
1176 1888 3.118738 TCTCTTAATCGGGAAGCCTGAAC 60.119 47.826 0.00 0.00 42.74 3.18
1177 1889 3.104512 TCTCTTAATCGGGAAGCCTGAA 58.895 45.455 0.00 0.00 42.74 3.02
1246 1958 4.473520 CAGAGGGCGACGGGCAAT 62.474 66.667 0.00 0.00 46.16 3.56
1314 2030 0.031449 CGAGGAGGAGGAATCGCTTC 59.969 60.000 0.00 0.00 0.00 3.86
1331 2047 4.357947 GACACGCCAGGAGCACGA 62.358 66.667 0.00 0.00 44.04 4.35
1349 2071 3.041351 TTACGTGCGTGCAGGCAG 61.041 61.111 32.58 25.90 44.93 4.85
1360 2082 2.202570 CGGCGGAGGAGTTACGTG 60.203 66.667 0.00 0.00 0.00 4.49
1375 2097 1.450312 GTCCTTCATGCCCAGTCGG 60.450 63.158 0.00 0.00 0.00 4.79
1847 2581 3.771160 CCGCTCCACGTAGCCCTT 61.771 66.667 4.77 0.00 39.43 3.95
1945 2679 1.133458 CTCCAAGAAGCGCGCTTTC 59.867 57.895 42.93 33.12 36.26 2.62
2460 3213 5.873712 GCATCAATCAGTACATCCATCCTAG 59.126 44.000 0.00 0.00 0.00 3.02
2461 3214 5.545335 AGCATCAATCAGTACATCCATCCTA 59.455 40.000 0.00 0.00 0.00 2.94
2463 3216 4.454847 CAGCATCAATCAGTACATCCATCC 59.545 45.833 0.00 0.00 0.00 3.51
2465 3218 4.141321 ACCAGCATCAATCAGTACATCCAT 60.141 41.667 0.00 0.00 0.00 3.41
2466 3219 3.200605 ACCAGCATCAATCAGTACATCCA 59.799 43.478 0.00 0.00 0.00 3.41
2467 3220 3.813443 ACCAGCATCAATCAGTACATCC 58.187 45.455 0.00 0.00 0.00 3.51
2469 3222 4.397103 CACAACCAGCATCAATCAGTACAT 59.603 41.667 0.00 0.00 0.00 2.29
2470 3223 3.752747 CACAACCAGCATCAATCAGTACA 59.247 43.478 0.00 0.00 0.00 2.90
2471 3224 4.002982 TCACAACCAGCATCAATCAGTAC 58.997 43.478 0.00 0.00 0.00 2.73
2558 3314 3.861840 ACTATGTCAACATGAACCTCCG 58.138 45.455 0.00 0.00 37.15 4.63
2672 3437 4.486125 AAATGTTGCAACCTTTGTCCTT 57.514 36.364 25.78 6.70 0.00 3.36
2673 3438 4.190772 CAAAATGTTGCAACCTTTGTCCT 58.809 39.130 28.91 16.24 31.42 3.85
2674 3439 3.938334 ACAAAATGTTGCAACCTTTGTCC 59.062 39.130 33.03 11.65 38.49 4.02
2675 3440 5.544136 AACAAAATGTTGCAACCTTTGTC 57.456 34.783 35.57 14.45 39.45 3.18
2676 3441 5.956068 AAACAAAATGTTGCAACCTTTGT 57.044 30.435 33.03 33.03 40.14 2.83
2677 3442 7.272299 GGTTAAAACAAAATGTTGCAACCTTTG 59.728 33.333 32.16 32.16 43.92 2.77
2678 3443 7.309177 GGTTAAAACAAAATGTTGCAACCTTT 58.691 30.769 26.14 24.05 43.92 3.11
2699 3464 5.531659 TGTAATGAAAAGGAGCAAACGGTTA 59.468 36.000 0.00 0.00 0.00 2.85
2721 3486 2.892852 ACAAAATGCTGTGGCTATGTGT 59.107 40.909 0.00 0.00 39.59 3.72
2821 3595 8.908903 TCCATAAAGTTTTCTTAACTTGCTTGA 58.091 29.630 3.88 0.00 40.10 3.02
2875 3649 7.010460 CAAGGATTGTGGAGAAAAAGTGTTTTC 59.990 37.037 4.17 4.17 45.34 2.29
2923 3697 3.381169 CTATGGTTGTGTGCGCGGC 62.381 63.158 8.83 0.00 0.00 6.53
3017 3793 5.536538 GGAATAATTGAGAGGGACCCAATTC 59.463 44.000 14.60 7.62 40.01 2.17
3021 3797 3.459598 CTGGAATAATTGAGAGGGACCCA 59.540 47.826 14.60 0.00 0.00 4.51
3100 3876 1.678101 GATTGTAAGGCTGGACCATGC 59.322 52.381 0.00 0.60 43.14 4.06
3117 3893 6.980593 TGTTTCATTTCAGAATTCCACGATT 58.019 32.000 0.65 0.00 0.00 3.34
3119 3895 6.380995 CATGTTTCATTTCAGAATTCCACGA 58.619 36.000 0.65 0.00 0.00 4.35
3120 3896 5.574055 CCATGTTTCATTTCAGAATTCCACG 59.426 40.000 0.65 0.00 0.00 4.94
3143 3919 2.802719 TGTTTCATTTGAGTAGGGGCC 58.197 47.619 0.00 0.00 0.00 5.80
3144 3920 4.220602 ACAATGTTTCATTTGAGTAGGGGC 59.779 41.667 0.00 0.00 0.00 5.80
3145 3921 5.336690 CCACAATGTTTCATTTGAGTAGGGG 60.337 44.000 0.00 0.00 0.00 4.79
3146 3922 5.336690 CCCACAATGTTTCATTTGAGTAGGG 60.337 44.000 0.00 0.00 0.00 3.53
3147 3923 5.476599 TCCCACAATGTTTCATTTGAGTAGG 59.523 40.000 0.00 0.00 0.00 3.18
3148 3924 6.573664 TCCCACAATGTTTCATTTGAGTAG 57.426 37.500 0.00 0.00 0.00 2.57
3149 3925 7.451255 AGAATCCCACAATGTTTCATTTGAGTA 59.549 33.333 0.00 0.00 0.00 2.59
3150 3926 6.268387 AGAATCCCACAATGTTTCATTTGAGT 59.732 34.615 0.00 0.00 0.00 3.41
3151 3927 6.588756 CAGAATCCCACAATGTTTCATTTGAG 59.411 38.462 0.00 0.00 0.00 3.02
3152 3928 6.267242 TCAGAATCCCACAATGTTTCATTTGA 59.733 34.615 0.00 0.00 0.00 2.69
3153 3929 6.457355 TCAGAATCCCACAATGTTTCATTTG 58.543 36.000 0.00 0.00 0.00 2.32
3154 3930 6.669125 TCAGAATCCCACAATGTTTCATTT 57.331 33.333 0.00 0.00 0.00 2.32
3155 3931 6.669125 TTCAGAATCCCACAATGTTTCATT 57.331 33.333 0.00 0.00 0.00 2.57
3156 3932 6.669125 TTTCAGAATCCCACAATGTTTCAT 57.331 33.333 0.00 0.00 0.00 2.57
3157 3933 6.477053 TTTTCAGAATCCCACAATGTTTCA 57.523 33.333 0.00 0.00 0.00 2.69
3158 3934 6.760770 TGTTTTTCAGAATCCCACAATGTTTC 59.239 34.615 0.00 0.00 0.00 2.78
3159 3935 6.648192 TGTTTTTCAGAATCCCACAATGTTT 58.352 32.000 0.00 0.00 0.00 2.83
3160 3936 6.232581 TGTTTTTCAGAATCCCACAATGTT 57.767 33.333 0.00 0.00 0.00 2.71
3218 4015 2.634600 CATCGGATAAACGTCCCCAAA 58.365 47.619 0.00 0.00 34.67 3.28
3317 4114 5.535753 AGGTCAACAAATTAGCAAAGCTT 57.464 34.783 0.00 0.00 40.44 3.74
3411 4220 4.254492 GGTTAGTTGGGCTAGTTCTCTTG 58.746 47.826 0.00 0.00 0.00 3.02
3441 4250 5.003160 TCTTGTGTTACTGTGAATCCCATG 58.997 41.667 0.00 0.00 0.00 3.66
3498 4309 8.983702 AATTAACCAAGAAAACACCTAGTACA 57.016 30.769 0.00 0.00 0.00 2.90
3499 4310 9.059260 TGAATTAACCAAGAAAACACCTAGTAC 57.941 33.333 0.00 0.00 0.00 2.73
3500 4311 9.059260 GTGAATTAACCAAGAAAACACCTAGTA 57.941 33.333 0.00 0.00 0.00 1.82
3501 4312 7.558444 TGTGAATTAACCAAGAAAACACCTAGT 59.442 33.333 0.00 0.00 0.00 2.57
3516 4327 2.629051 CCGAGGGAGTGTGAATTAACC 58.371 52.381 0.00 0.00 0.00 2.85
3520 4331 0.693049 AAGCCGAGGGAGTGTGAATT 59.307 50.000 0.00 0.00 0.00 2.17
3521 4332 0.250513 GAAGCCGAGGGAGTGTGAAT 59.749 55.000 0.00 0.00 0.00 2.57
3522 4333 1.671742 GAAGCCGAGGGAGTGTGAA 59.328 57.895 0.00 0.00 0.00 3.18
3523 4334 2.636412 CGAAGCCGAGGGAGTGTGA 61.636 63.158 0.00 0.00 38.22 3.58
3524 4335 2.125912 CGAAGCCGAGGGAGTGTG 60.126 66.667 0.00 0.00 38.22 3.82
3525 4336 1.469335 TTTCGAAGCCGAGGGAGTGT 61.469 55.000 0.00 0.00 46.39 3.55
3526 4337 0.108138 ATTTCGAAGCCGAGGGAGTG 60.108 55.000 0.00 0.00 46.39 3.51
3527 4338 0.108138 CATTTCGAAGCCGAGGGAGT 60.108 55.000 0.00 0.00 46.39 3.85
3528 4339 1.432270 GCATTTCGAAGCCGAGGGAG 61.432 60.000 0.00 0.00 46.39 4.30
3529 4340 1.449601 GCATTTCGAAGCCGAGGGA 60.450 57.895 0.00 0.00 46.39 4.20
3530 4341 1.026718 AAGCATTTCGAAGCCGAGGG 61.027 55.000 5.82 0.00 46.39 4.30
3531 4342 0.097674 CAAGCATTTCGAAGCCGAGG 59.902 55.000 5.82 0.00 46.39 4.63
3532 4343 1.078709 TCAAGCATTTCGAAGCCGAG 58.921 50.000 5.82 0.00 46.39 4.63
3533 4344 1.464608 CTTCAAGCATTTCGAAGCCGA 59.535 47.619 5.82 1.27 43.96 5.54
3534 4345 1.197721 ACTTCAAGCATTTCGAAGCCG 59.802 47.619 5.82 0.00 39.82 5.52
3535 4346 2.997485 ACTTCAAGCATTTCGAAGCC 57.003 45.000 5.82 0.00 39.82 4.35
3539 4350 4.569943 AGCTAGAACTTCAAGCATTTCGA 58.430 39.130 0.00 0.00 38.75 3.71
3572 4383 5.010012 ACTTGCCAAACTTTAAGATGTCTGG 59.990 40.000 0.00 0.00 0.00 3.86
3573 4384 6.016777 AGACTTGCCAAACTTTAAGATGTCTG 60.017 38.462 0.00 0.00 0.00 3.51
3575 4386 6.319141 AGACTTGCCAAACTTTAAGATGTC 57.681 37.500 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.