Multiple sequence alignment - TraesCS2B01G393700

Loading Multiple Alignment...

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 TraesCS2B01G393700 chr2B 100.000 3563 0 0 1 3563 558006414 558002852 0.000000e+00 6580
1 TraesCS2B01G393700 chr2B 76.441 590 99 22 3000 3560 496977518 496976940 2.090000e-72 283
2 TraesCS2B01G393700 chr2A 91.184 1849 110 23 1108 2924 619196862 619198689 0.000000e+00 2462
3 TraesCS2B01G393700 chr2A 84.048 909 88 28 85 973 619183240 619184111 0.000000e+00 822
4 TraesCS2B01G393700 chr2A 100.000 82 0 0 1035 1116 619196478 619196559 6.160000e-33 152
5 TraesCS2B01G393700 chr2D 90.336 1873 106 26 971 2814 476828058 476829884 0.000000e+00 2386
6 TraesCS2B01G393700 chr2D 89.866 523 35 7 381 889 476826155 476826673 0.000000e+00 656
7 TraesCS2B01G393700 chr2D 89.679 436 32 3 398 820 476806040 476806475 8.700000e-151 544
8 TraesCS2B01G393700 chr2D 77.537 601 91 24 2990 3560 80110453 80109867 4.440000e-84 322
9 TraesCS2B01G393700 chr2D 87.451 255 26 6 9 259 476800265 476800517 4.500000e-74 289
10 TraesCS2B01G393700 chr2D 76.596 376 73 12 2990 3360 36553577 36553212 3.630000e-45 193
11 TraesCS2B01G393700 chr5D 79.658 585 81 20 3003 3559 554158356 554157782 1.550000e-103 387
12 TraesCS2B01G393700 chr5D 77.572 593 93 25 3000 3563 374259255 374259836 4.440000e-84 322
13 TraesCS2B01G393700 chr5D 75.584 471 88 17 3114 3563 385516562 385517026 1.300000e-49 207
14 TraesCS2B01G393700 chr1D 80.855 491 80 13 2992 3473 219732144 219731659 1.210000e-99 374
15 TraesCS2B01G393700 chr6D 78.328 586 86 20 3003 3560 446438972 446438400 1.230000e-89 340
16 TraesCS2B01G393700 chrUn 77.907 602 88 29 2990 3560 41163817 41164404 2.050000e-87 333
17 TraesCS2B01G393700 chr4D 77.172 587 94 26 2999 3558 138702162 138701589 4.470000e-79 305
18 TraesCS2B01G393700 chr3A 77.055 584 96 24 3003 3560 523622307 523621736 5.780000e-78 302
19 TraesCS2B01G393700 chr3A 78.451 297 54 8 2999 3290 706281403 706281694 6.070000e-43 185
20 TraesCS2B01G393700 chr3A 85.965 114 15 1 3446 3559 658888614 658888726 1.740000e-23 121
21 TraesCS2B01G393700 chr7B 76.391 593 95 30 3003 3563 510736955 510736376 9.740000e-71 278
22 TraesCS2B01G393700 chr3D 79.648 398 68 10 2994 3381 566109839 566110233 1.260000e-69 274
23 TraesCS2B01G393700 chr3D 77.810 347 61 13 2990 3332 19717195 19717529 2.170000e-47 200
24 TraesCS2B01G393700 chr7D 84.049 163 26 0 3383 3545 596962025 596961863 1.320000e-34 158


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 TraesCS2B01G393700 chr2B 558002852 558006414 3562 True 6580 6580 100.000 1 3563 1 chr2B.!!$R2 3562
1 TraesCS2B01G393700 chr2B 496976940 496977518 578 True 283 283 76.441 3000 3560 1 chr2B.!!$R1 560
2 TraesCS2B01G393700 chr2A 619196478 619198689 2211 False 1307 2462 95.592 1035 2924 2 chr2A.!!$F2 1889
3 TraesCS2B01G393700 chr2A 619183240 619184111 871 False 822 822 84.048 85 973 1 chr2A.!!$F1 888
4 TraesCS2B01G393700 chr2D 476826155 476829884 3729 False 1521 2386 90.101 381 2814 2 chr2D.!!$F3 2433
5 TraesCS2B01G393700 chr2D 80109867 80110453 586 True 322 322 77.537 2990 3560 1 chr2D.!!$R2 570
6 TraesCS2B01G393700 chr5D 554157782 554158356 574 True 387 387 79.658 3003 3559 1 chr5D.!!$R1 556
7 TraesCS2B01G393700 chr5D 374259255 374259836 581 False 322 322 77.572 3000 3563 1 chr5D.!!$F1 563
8 TraesCS2B01G393700 chr6D 446438400 446438972 572 True 340 340 78.328 3003 3560 1 chr6D.!!$R1 557
9 TraesCS2B01G393700 chrUn 41163817 41164404 587 False 333 333 77.907 2990 3560 1 chrUn.!!$F1 570
10 TraesCS2B01G393700 chr4D 138701589 138702162 573 True 305 305 77.172 2999 3558 1 chr4D.!!$R1 559
11 TraesCS2B01G393700 chr3A 523621736 523622307 571 True 302 302 77.055 3003 3560 1 chr3A.!!$R1 557
12 TraesCS2B01G393700 chr7B 510736376 510736955 579 True 278 278 76.391 3003 3563 1 chr7B.!!$R1 560

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
828 901 0.988145 TGGAAGCTGGGATCCGGATT 60.988 55.0 20.22 6.1 41.59 3.01 F
1374 3112 0.107945 ACGGAAGATGCAGAAGCCTC 60.108 55.0 0.00 0.0 41.13 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2384 4155 1.202582 TGCAGCTCGTCTTAGTCCTTC 59.797 52.381 0.0 0.0 0.00 3.46 R
3001 4783 0.039437 GTGCTGGACGAAGACGAAGA 60.039 55.000 0.0 0.0 42.66 2.87 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
28 29 8.662781 TTCCTCTATTATGTGTGTATTCTTGC 57.337 34.615 0.00 0.00 0.00 4.01
29 30 7.791029 TCCTCTATTATGTGTGTATTCTTGCA 58.209 34.615 0.00 0.00 0.00 4.08
30 31 8.432013 TCCTCTATTATGTGTGTATTCTTGCAT 58.568 33.333 0.00 0.00 0.00 3.96
31 32 9.710900 CCTCTATTATGTGTGTATTCTTGCATA 57.289 33.333 0.00 0.00 0.00 3.14
39 40 9.783081 ATGTGTGTATTCTTGCATATGATAAGA 57.217 29.630 6.97 12.15 0.00 2.10
40 41 9.612066 TGTGTGTATTCTTGCATATGATAAGAA 57.388 29.630 25.08 25.08 42.56 2.52
46 47 7.468922 TTCTTGCATATGATAAGAAGACACG 57.531 36.000 21.80 2.83 36.00 4.49
47 48 6.573434 TCTTGCATATGATAAGAAGACACGT 58.427 36.000 16.09 0.00 0.00 4.49
48 49 7.041721 TCTTGCATATGATAAGAAGACACGTT 58.958 34.615 16.09 0.00 0.00 3.99
49 50 6.828502 TGCATATGATAAGAAGACACGTTC 57.171 37.500 6.97 0.00 0.00 3.95
50 51 6.573434 TGCATATGATAAGAAGACACGTTCT 58.427 36.000 6.97 0.00 38.48 3.01
51 52 6.476706 TGCATATGATAAGAAGACACGTTCTG 59.523 38.462 6.97 0.00 36.86 3.02
52 53 6.477033 GCATATGATAAGAAGACACGTTCTGT 59.523 38.462 6.97 0.00 36.86 3.41
65 66 3.723764 CACGTTCTGTGTAAATTGTGTGC 59.276 43.478 0.00 0.00 43.88 4.57
66 67 3.375610 ACGTTCTGTGTAAATTGTGTGCA 59.624 39.130 0.00 0.00 0.00 4.57
67 68 4.036262 ACGTTCTGTGTAAATTGTGTGCAT 59.964 37.500 0.00 0.00 0.00 3.96
68 69 5.237561 ACGTTCTGTGTAAATTGTGTGCATA 59.762 36.000 0.00 0.00 0.00 3.14
69 70 6.072728 ACGTTCTGTGTAAATTGTGTGCATAT 60.073 34.615 0.00 0.00 0.00 1.78
70 71 6.801377 CGTTCTGTGTAAATTGTGTGCATATT 59.199 34.615 0.00 0.00 0.00 1.28
71 72 7.325821 CGTTCTGTGTAAATTGTGTGCATATTT 59.674 33.333 0.00 0.00 0.00 1.40
72 73 8.977505 GTTCTGTGTAAATTGTGTGCATATTTT 58.022 29.630 0.00 0.00 0.00 1.82
73 74 9.539825 TTCTGTGTAAATTGTGTGCATATTTTT 57.460 25.926 0.00 0.00 0.00 1.94
279 338 8.986847 CCAATGTTTGTTTTTGCATACTATGAA 58.013 29.630 0.00 0.00 0.00 2.57
306 365 2.031157 GCAATTTAGGTGCGAACTGTGT 60.031 45.455 0.00 0.00 31.20 3.72
318 378 3.490526 GCGAACTGTGTGCAATTTTTCAT 59.509 39.130 0.00 0.00 0.00 2.57
376 438 6.048509 GGCCCAATTTCTGTGTAAAATATGG 58.951 40.000 0.00 0.00 0.00 2.74
379 441 5.748152 CCAATTTCTGTGTAAAATATGGGCG 59.252 40.000 0.00 0.00 0.00 6.13
428 490 7.795482 TTTTTCTGAAACGAGTTTCTATCCA 57.205 32.000 23.73 8.11 46.67 3.41
430 492 7.979444 TTTCTGAAACGAGTTTCTATCCAAT 57.021 32.000 23.73 0.00 46.67 3.16
431 493 7.596749 TTCTGAAACGAGTTTCTATCCAATC 57.403 36.000 23.73 1.95 46.67 2.67
444 508 9.160496 GTTTCTATCCAATCTCTATATGCTTGG 57.840 37.037 0.00 0.00 38.14 3.61
489 553 7.642071 ATCAACTGACCGAAAATTCATTTTG 57.358 32.000 2.17 0.00 39.86 2.44
490 554 6.800543 TCAACTGACCGAAAATTCATTTTGA 58.199 32.000 2.17 0.00 39.86 2.69
491 555 7.261325 TCAACTGACCGAAAATTCATTTTGAA 58.739 30.769 2.17 0.00 39.86 2.69
496 560 4.979815 ACCGAAAATTCATTTTGAACCGAC 59.020 37.500 2.17 0.00 39.45 4.79
503 567 4.610605 TCATTTTGAACCGACTGACCTA 57.389 40.909 0.00 0.00 0.00 3.08
551 615 1.678635 TGGAAATGCCTGCCCTTCG 60.679 57.895 0.00 0.00 37.63 3.79
555 619 1.039233 AAATGCCTGCCCTTCGGATG 61.039 55.000 0.00 0.00 0.00 3.51
585 649 2.052690 ACGATACGGGCAGTCTGCT 61.053 57.895 23.68 7.52 44.28 4.24
614 678 3.247173 GCCAGAAAAGTGATGATCTAGCG 59.753 47.826 0.00 0.00 0.00 4.26
618 682 5.460419 CAGAAAAGTGATGATCTAGCGGTAC 59.540 44.000 0.00 0.00 0.00 3.34
648 712 3.436015 GGCCGAAAAGTAGAAAGGAAGAC 59.564 47.826 0.00 0.00 0.00 3.01
668 732 3.487372 ACATGGAATCCGATCGAGAGTA 58.513 45.455 18.66 0.00 0.00 2.59
671 735 2.293677 TGGAATCCGATCGAGAGTAAGC 59.706 50.000 18.66 0.25 0.00 3.09
673 737 1.880271 ATCCGATCGAGAGTAAGCGA 58.120 50.000 18.66 1.66 41.14 4.93
740 804 2.450476 GGAGCTTTGGAATGGTGATGT 58.550 47.619 0.00 0.00 0.00 3.06
770 843 1.262417 TGCCCACTGAACTGATACGA 58.738 50.000 0.00 0.00 0.00 3.43
786 859 2.397252 GACGATGAAGCTGCGTGC 59.603 61.111 8.58 0.00 38.51 5.34
828 901 0.988145 TGGAAGCTGGGATCCGGATT 60.988 55.000 20.22 6.10 41.59 3.01
908 2301 4.459089 GCAGAGACGGGCCCTGAC 62.459 72.222 22.43 13.76 0.00 3.51
909 2302 2.681778 CAGAGACGGGCCCTGACT 60.682 66.667 22.43 18.39 0.00 3.41
975 2390 2.202987 GGTGGATGCTCAGAGCCG 60.203 66.667 20.16 0.00 41.51 5.52
1022 2437 0.112412 GGGGCTTTGAACCTCTTCCA 59.888 55.000 0.00 0.00 0.00 3.53
1030 2445 2.306847 TGAACCTCTTCCAAAACCTGC 58.693 47.619 0.00 0.00 0.00 4.85
1147 2870 0.536233 TAAACGCACCATGCACCAGT 60.536 50.000 1.20 0.00 45.36 4.00
1159 2882 1.270785 TGCACCAGTACCACACATCAG 60.271 52.381 0.00 0.00 0.00 2.90
1196 2928 3.133901 TGCAAGAGGATAAGGCAATCGTA 59.866 43.478 0.00 0.00 0.00 3.43
1202 2934 2.304761 GGATAAGGCAATCGTATCCCCA 59.695 50.000 6.69 0.00 45.37 4.96
1214 2946 2.561569 GTATCCCCATGACTCCGTTTG 58.438 52.381 0.00 0.00 0.00 2.93
1270 3002 0.525311 CTCTGCTCTCAGCTCGACAA 59.475 55.000 0.00 0.00 42.97 3.18
1329 3061 1.067416 GCTGCCGTATCCGATCACA 59.933 57.895 0.00 0.00 35.63 3.58
1374 3112 0.107945 ACGGAAGATGCAGAAGCCTC 60.108 55.000 0.00 0.00 41.13 4.70
1416 3160 1.004918 CGAGGATGATTACCCCGCC 60.005 63.158 0.00 0.00 0.00 6.13
1454 3198 3.502211 GTCCAGGTTACACAGGTGAATTG 59.498 47.826 6.40 0.00 0.00 2.32
1466 3210 3.875727 CAGGTGAATTGCTGATCTACTGG 59.124 47.826 0.00 0.00 0.00 4.00
1493 3238 0.981183 TGCTTGGATAACTCGTGGGT 59.019 50.000 0.00 0.00 0.00 4.51
1497 3242 1.855295 TGGATAACTCGTGGGTAGCA 58.145 50.000 0.00 0.00 0.00 3.49
1504 3249 1.000955 ACTCGTGGGTAGCAGTTTGAG 59.999 52.381 0.00 0.00 0.00 3.02
1513 3258 4.278419 GGGTAGCAGTTTGAGTTTGAATGT 59.722 41.667 0.00 0.00 0.00 2.71
1730 3475 0.830444 ACGTCCTGGTGCACCTTCTA 60.830 55.000 34.75 15.31 36.82 2.10
1782 3546 2.868920 GAGCAAGTGAGCAGCTGC 59.131 61.111 31.53 31.53 39.02 5.25
1790 3554 1.145598 TGAGCAGCTGCCTGATAGC 59.854 57.895 34.39 15.28 41.77 2.97
1799 3563 2.756829 CTGCCTGATAGCTGTGAGATG 58.243 52.381 0.00 0.00 0.00 2.90
1916 3680 1.065053 TGCACAAAGGTACACCACACT 60.065 47.619 0.38 0.00 38.89 3.55
1919 3683 1.211949 ACAAAGGTACACCACACTGCT 59.788 47.619 0.38 0.00 38.89 4.24
1925 3689 2.932622 GGTACACCACACTGCTGATCAG 60.933 54.545 18.84 18.84 41.35 2.90
1995 3759 8.220755 ACTGTTCAAGTTAACTGAAAGCATTA 57.779 30.769 9.34 0.00 34.57 1.90
2073 3837 1.743252 CAGGAAAGACCAGAGCGGC 60.743 63.158 0.00 0.00 42.04 6.53
2140 3904 8.473219 TGATTTACCTAGCTCTGATGCTATATG 58.527 37.037 0.00 5.01 43.54 1.78
2145 3909 8.372877 ACCTAGCTCTGATGCTATATGTAATT 57.627 34.615 0.00 0.00 43.54 1.40
2186 3950 8.066595 CGATTATTTCTTTTAGAGCAGGTCATG 58.933 37.037 1.66 0.00 0.00 3.07
2325 4096 6.018262 TCGACAAACAAACCTCTTACTGATTG 60.018 38.462 0.00 0.00 0.00 2.67
2384 4155 0.944311 CTCCTGTCGTGTGGAAACGG 60.944 60.000 0.00 0.00 43.73 4.44
2388 4159 0.531090 TGTCGTGTGGAAACGGAAGG 60.531 55.000 0.00 0.00 43.73 3.46
2389 4160 0.249573 GTCGTGTGGAAACGGAAGGA 60.250 55.000 0.00 0.00 43.73 3.36
2459 4230 4.446385 TGTACATCGCTGTAACAGTTGTTC 59.554 41.667 0.00 0.00 39.51 3.18
2555 4326 1.137086 GAGAACTCTGGATAAGGCGCA 59.863 52.381 10.83 0.00 0.00 6.09
2593 4368 1.394917 GCGATGCAGTTTCAACTCGAT 59.605 47.619 6.28 0.00 37.08 3.59
2619 4398 6.183360 GCCACTGATTATCTGATATGAATGCC 60.183 42.308 6.11 0.00 0.00 4.40
2648 4427 6.841286 GTGTGATATATCGAACAAAAAGCTCG 59.159 38.462 8.19 0.00 37.18 5.03
2670 4449 4.260212 CGTGTGACCGGATGATTAATCAAC 60.260 45.833 21.50 18.25 40.69 3.18
2706 4485 5.131642 TCCAGTGATTGCTTCTCTCCATAAT 59.868 40.000 0.00 0.00 0.00 1.28
2707 4486 6.327365 TCCAGTGATTGCTTCTCTCCATAATA 59.673 38.462 0.00 0.00 0.00 0.98
2708 4487 6.426328 CCAGTGATTGCTTCTCTCCATAATAC 59.574 42.308 0.00 0.00 0.00 1.89
2709 4488 7.215789 CAGTGATTGCTTCTCTCCATAATACT 58.784 38.462 0.00 0.00 0.00 2.12
2710 4489 7.714377 CAGTGATTGCTTCTCTCCATAATACTT 59.286 37.037 0.00 0.00 0.00 2.24
2713 4492 9.770097 TGATTGCTTCTCTCCATAATACTTTAG 57.230 33.333 0.00 0.00 0.00 1.85
2891 4673 8.542953 GTTTTTCAAGGCTACTGATTTTTCTTG 58.457 33.333 0.00 0.00 33.55 3.02
2906 4688 8.587608 TGATTTTTCTTGCAAGGATTTACTCAT 58.412 29.630 25.73 6.51 0.00 2.90
2912 4694 7.112122 TCTTGCAAGGATTTACTCATACATGT 58.888 34.615 25.73 2.69 0.00 3.21
2913 4695 7.611467 TCTTGCAAGGATTTACTCATACATGTT 59.389 33.333 25.73 0.00 0.00 2.71
2914 4696 7.701539 TGCAAGGATTTACTCATACATGTTT 57.298 32.000 2.30 0.00 0.00 2.83
2924 4706 3.669536 TCATACATGTTTCCGCTCACAA 58.330 40.909 2.30 0.00 0.00 3.33
2925 4707 4.068599 TCATACATGTTTCCGCTCACAAA 58.931 39.130 2.30 0.00 0.00 2.83
2926 4708 4.699735 TCATACATGTTTCCGCTCACAAAT 59.300 37.500 2.30 0.00 0.00 2.32
2927 4709 5.182950 TCATACATGTTTCCGCTCACAAATT 59.817 36.000 2.30 0.00 0.00 1.82
2928 4710 4.320608 ACATGTTTCCGCTCACAAATTT 57.679 36.364 0.00 0.00 0.00 1.82
2929 4711 4.298332 ACATGTTTCCGCTCACAAATTTC 58.702 39.130 0.00 0.00 0.00 2.17
2930 4712 3.363341 TGTTTCCGCTCACAAATTTCC 57.637 42.857 0.00 0.00 0.00 3.13
2931 4713 2.955660 TGTTTCCGCTCACAAATTTCCT 59.044 40.909 0.00 0.00 0.00 3.36
2932 4714 3.383185 TGTTTCCGCTCACAAATTTCCTT 59.617 39.130 0.00 0.00 0.00 3.36
2933 4715 4.142049 TGTTTCCGCTCACAAATTTCCTTT 60.142 37.500 0.00 0.00 0.00 3.11
2934 4716 5.067936 TGTTTCCGCTCACAAATTTCCTTTA 59.932 36.000 0.00 0.00 0.00 1.85
2935 4717 5.371115 TTCCGCTCACAAATTTCCTTTAG 57.629 39.130 0.00 0.00 0.00 1.85
2936 4718 4.647611 TCCGCTCACAAATTTCCTTTAGA 58.352 39.130 0.00 0.00 0.00 2.10
2937 4719 5.067273 TCCGCTCACAAATTTCCTTTAGAA 58.933 37.500 0.00 0.00 0.00 2.10
2938 4720 5.048991 TCCGCTCACAAATTTCCTTTAGAAC 60.049 40.000 0.00 0.00 32.95 3.01
2939 4721 5.048713 CCGCTCACAAATTTCCTTTAGAACT 60.049 40.000 0.00 0.00 32.95 3.01
2940 4722 5.853282 CGCTCACAAATTTCCTTTAGAACTG 59.147 40.000 0.00 0.00 32.95 3.16
2941 4723 6.513393 CGCTCACAAATTTCCTTTAGAACTGT 60.513 38.462 0.00 0.00 32.95 3.55
2942 4724 7.203218 GCTCACAAATTTCCTTTAGAACTGTT 58.797 34.615 0.00 0.00 32.95 3.16
2943 4725 7.168135 GCTCACAAATTTCCTTTAGAACTGTTG 59.832 37.037 0.00 0.00 32.95 3.33
2944 4726 8.287439 TCACAAATTTCCTTTAGAACTGTTGA 57.713 30.769 0.00 0.00 32.95 3.18
2945 4727 8.405531 TCACAAATTTCCTTTAGAACTGTTGAG 58.594 33.333 0.00 0.00 32.95 3.02
2946 4728 8.190784 CACAAATTTCCTTTAGAACTGTTGAGT 58.809 33.333 0.00 0.00 32.95 3.41
2947 4729 9.403583 ACAAATTTCCTTTAGAACTGTTGAGTA 57.596 29.630 0.00 0.00 32.95 2.59
2950 4732 9.793259 AATTTCCTTTAGAACTGTTGAGTATCA 57.207 29.630 0.00 0.00 37.55 2.15
2951 4733 9.965902 ATTTCCTTTAGAACTGTTGAGTATCAT 57.034 29.630 0.00 0.00 38.75 2.45
2952 4734 9.219603 TTTCCTTTAGAACTGTTGAGTATCATG 57.780 33.333 0.00 0.00 38.75 3.07
2967 4749 6.881065 TGAGTATCATGATTATTTAGGGCTGC 59.119 38.462 14.65 0.00 42.56 5.25
2968 4750 6.183347 AGTATCATGATTATTTAGGGCTGCC 58.817 40.000 14.65 11.05 0.00 4.85
2969 4751 4.729552 TCATGATTATTTAGGGCTGCCT 57.270 40.909 19.68 7.25 0.00 4.75
2970 4752 4.655963 TCATGATTATTTAGGGCTGCCTC 58.344 43.478 19.68 8.86 0.00 4.70
2971 4753 3.508845 TGATTATTTAGGGCTGCCTCC 57.491 47.619 19.68 2.28 0.00 4.30
2972 4754 2.782925 TGATTATTTAGGGCTGCCTCCA 59.217 45.455 19.68 0.66 0.00 3.86
2973 4755 2.729028 TTATTTAGGGCTGCCTCCAC 57.271 50.000 19.68 1.03 0.00 4.02
2974 4756 1.590591 TATTTAGGGCTGCCTCCACA 58.409 50.000 19.68 0.00 0.00 4.17
2975 4757 0.257039 ATTTAGGGCTGCCTCCACAG 59.743 55.000 19.68 0.00 40.80 3.66
2976 4758 0.840288 TTTAGGGCTGCCTCCACAGA 60.840 55.000 19.68 0.00 40.25 3.41
2977 4759 1.553690 TTAGGGCTGCCTCCACAGAC 61.554 60.000 19.68 0.00 45.62 3.51
2979 4761 2.431683 GGCTGCCTCCACAGACAA 59.568 61.111 12.43 0.00 45.65 3.18
2980 4762 1.968540 GGCTGCCTCCACAGACAAC 60.969 63.158 12.43 0.00 45.65 3.32
2981 4763 1.968540 GCTGCCTCCACAGACAACC 60.969 63.158 0.00 0.00 40.25 3.77
2982 4764 1.757306 CTGCCTCCACAGACAACCT 59.243 57.895 0.00 0.00 40.25 3.50
2983 4765 0.321122 CTGCCTCCACAGACAACCTC 60.321 60.000 0.00 0.00 40.25 3.85
2984 4766 0.764369 TGCCTCCACAGACAACCTCT 60.764 55.000 0.00 0.00 0.00 3.69
2991 4773 3.217242 CAGACAACCTCTGGTTCCG 57.783 57.895 0.00 0.00 43.05 4.30
2992 4774 0.951040 CAGACAACCTCTGGTTCCGC 60.951 60.000 0.00 0.00 43.05 5.54
2993 4775 1.671379 GACAACCTCTGGTTCCGCC 60.671 63.158 0.00 0.00 43.05 6.13
2994 4776 2.742372 CAACCTCTGGTTCCGCCG 60.742 66.667 0.00 0.00 43.05 6.46
2995 4777 2.920912 AACCTCTGGTTCCGCCGA 60.921 61.111 0.00 0.00 43.05 5.54
2996 4778 3.236003 AACCTCTGGTTCCGCCGAC 62.236 63.158 0.00 0.00 43.05 4.79
2997 4779 3.382832 CCTCTGGTTCCGCCGACT 61.383 66.667 0.00 0.00 41.21 4.18
2998 4780 2.050350 CCTCTGGTTCCGCCGACTA 61.050 63.158 0.00 0.00 41.21 2.59
2999 4781 1.139095 CTCTGGTTCCGCCGACTAC 59.861 63.158 0.00 0.00 41.21 2.73
3000 4782 2.183555 CTGGTTCCGCCGACTACC 59.816 66.667 0.00 0.00 41.21 3.18
3001 4783 2.283388 TGGTTCCGCCGACTACCT 60.283 61.111 0.00 0.00 41.21 3.08
3023 4805 1.300620 CGTCTTCGTCCAGCACCAA 60.301 57.895 0.00 0.00 0.00 3.67
3027 4809 0.249868 CTTCGTCCAGCACCAACTCA 60.250 55.000 0.00 0.00 0.00 3.41
3031 4813 0.320771 GTCCAGCACCAACTCATCGT 60.321 55.000 0.00 0.00 0.00 3.73
3047 4829 1.796355 CGTCAGCGTCGTCGTCATT 60.796 57.895 3.66 0.00 39.49 2.57
3049 4831 0.782384 GTCAGCGTCGTCGTCATTTT 59.218 50.000 3.66 0.00 39.49 1.82
3065 4847 2.668144 TTTTCCCCGACCACTTCATT 57.332 45.000 0.00 0.00 0.00 2.57
3068 4850 4.310022 TTTCCCCGACCACTTCATTTAT 57.690 40.909 0.00 0.00 0.00 1.40
3082 4864 4.459390 TCATTTATTCCGACAACCGAGA 57.541 40.909 0.00 0.00 41.76 4.04
3083 4865 4.823157 TCATTTATTCCGACAACCGAGAA 58.177 39.130 0.00 0.00 41.76 2.87
3086 4868 1.012486 ATTCCGACAACCGAGAACGC 61.012 55.000 0.00 0.00 41.76 4.84
3087 4869 2.352704 TTCCGACAACCGAGAACGCA 62.353 55.000 0.00 0.00 41.76 5.24
3088 4870 1.736645 CCGACAACCGAGAACGCAT 60.737 57.895 0.00 0.00 41.76 4.73
3089 4871 1.683790 CCGACAACCGAGAACGCATC 61.684 60.000 0.00 0.00 41.76 3.91
3090 4872 1.702299 GACAACCGAGAACGCATCG 59.298 57.895 0.00 0.00 39.86 3.84
3095 4877 2.809174 CGAGAACGCATCGGCACA 60.809 61.111 0.00 0.00 41.24 4.57
3096 4878 2.167219 CGAGAACGCATCGGCACAT 61.167 57.895 0.00 0.00 41.24 3.21
3097 4879 1.695893 CGAGAACGCATCGGCACATT 61.696 55.000 0.00 0.00 41.24 2.71
3098 4880 0.026803 GAGAACGCATCGGCACATTC 59.973 55.000 0.00 0.00 41.24 2.67
3099 4881 0.391661 AGAACGCATCGGCACATTCT 60.392 50.000 0.00 0.00 41.24 2.40
3100 4882 1.134818 AGAACGCATCGGCACATTCTA 60.135 47.619 0.00 0.00 41.24 2.10
3147 4931 0.112606 TCGACTCCTCCTCTGTTGGT 59.887 55.000 0.00 0.00 0.00 3.67
3149 4942 0.899019 GACTCCTCCTCTGTTGGTCC 59.101 60.000 0.00 0.00 0.00 4.46
3174 4967 0.032952 ACATGGCGTACAACTCGTGT 59.967 50.000 0.00 0.00 44.82 4.49
3175 4968 1.144969 CATGGCGTACAACTCGTGTT 58.855 50.000 0.00 0.00 41.98 3.32
3198 4993 4.201679 CGTCTACGCATGCCCGGA 62.202 66.667 13.15 4.55 0.00 5.14
3276 5072 4.136511 TGCGGCGCCTCGTCAATA 62.137 61.111 30.82 3.60 0.00 1.90
3277 5073 3.627218 GCGGCGCCTCGTCAATAC 61.627 66.667 26.68 0.00 0.00 1.89
3280 5076 2.103538 GCGCCTCGTCAATACCGA 59.896 61.111 0.00 0.00 0.00 4.69
3285 5081 1.134560 GCCTCGTCAATACCGACTTCT 59.865 52.381 0.00 0.00 33.54 2.85
3287 5083 3.436496 CCTCGTCAATACCGACTTCTTC 58.564 50.000 0.00 0.00 33.54 2.87
3304 5100 3.849951 CCCGTCTACGCATGCCCT 61.850 66.667 13.15 0.00 38.18 5.19
3318 5114 2.203394 CCCTGTGCTGCCAACACT 60.203 61.111 0.00 0.00 38.86 3.55
3322 5118 1.077858 TGTGCTGCCAACACTGACA 60.078 52.632 0.00 0.00 38.86 3.58
3338 5134 2.279851 CACGTGCCTTCGTCCACA 60.280 61.111 0.82 0.00 42.27 4.17
3354 5150 0.828022 CACAACGTATCCCCAGGCTA 59.172 55.000 0.00 0.00 0.00 3.93
3369 5166 1.675641 GCTAGGCAACCTGGTGTGG 60.676 63.158 0.00 0.00 34.44 4.17
3381 5178 1.374252 GGTGTGGCGTCTCGTCAAT 60.374 57.895 0.00 0.00 44.86 2.57
3394 5192 4.735822 GTCTCGTCAATACCATCTTCTTCG 59.264 45.833 0.00 0.00 0.00 3.79
3420 5232 1.741770 CAACTGCGCCCCTGACTAC 60.742 63.158 4.18 0.00 0.00 2.73
3421 5233 2.214216 AACTGCGCCCCTGACTACA 61.214 57.895 4.18 0.00 0.00 2.74
3423 5235 1.522355 CTGCGCCCCTGACTACATG 60.522 63.158 4.18 0.00 0.00 3.21
3425 5237 3.031417 GCGCCCCTGACTACATGGT 62.031 63.158 0.00 0.00 31.36 3.55
3426 5238 1.153369 CGCCCCTGACTACATGGTG 60.153 63.158 0.00 0.00 31.36 4.17
3428 5240 1.915078 GCCCCTGACTACATGGTGCT 61.915 60.000 0.00 0.00 31.36 4.40
3469 5282 0.957395 GGTGACTACCTCGACACCGA 60.957 60.000 5.03 0.00 43.97 4.69
3471 5284 0.957395 TGACTACCTCGACACCGACC 60.957 60.000 0.00 0.00 40.30 4.79
3472 5285 0.957395 GACTACCTCGACACCGACCA 60.957 60.000 0.00 0.00 40.30 4.02
3500 5314 2.963498 TCGACATCGATCACGGTATC 57.037 50.000 16.85 0.00 44.22 2.24
3502 5316 1.401148 CGACATCGATCACGGTATCCC 60.401 57.143 11.40 0.00 43.02 3.85
3517 5331 1.562672 ATCCCTTGCACGGCTACCTT 61.563 55.000 3.07 0.00 0.00 3.50
3520 5334 0.392998 CCTTGCACGGCTACCTTGAT 60.393 55.000 0.00 0.00 0.00 2.57
3523 5338 0.541392 TGCACGGCTACCTTGATCAT 59.459 50.000 0.00 0.00 0.00 2.45
3525 5340 1.473257 GCACGGCTACCTTGATCATGA 60.473 52.381 10.07 0.00 0.00 3.07
3529 5344 3.704566 ACGGCTACCTTGATCATGACTAA 59.295 43.478 10.07 0.00 0.00 2.24
3540 5355 4.163458 TGATCATGACTAAACCACCCTACC 59.837 45.833 0.00 0.00 0.00 3.18
3546 5361 2.113052 ACTAAACCACCCTACCCTCTCA 59.887 50.000 0.00 0.00 0.00 3.27
3560 5375 2.028130 CCTCTCAGCTACCTCGACAAT 58.972 52.381 0.00 0.00 0.00 2.71
3561 5376 2.223688 CCTCTCAGCTACCTCGACAATG 60.224 54.545 0.00 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.783081 TCTTATCATATGCAAGAATACACACAT 57.217 29.630 13.94 0.00 0.00 3.21
14 15 9.612066 TTCTTATCATATGCAAGAATACACACA 57.388 29.630 19.97 4.82 34.28 3.72
20 21 9.196552 CGTGTCTTCTTATCATATGCAAGAATA 57.803 33.333 22.26 16.53 37.58 1.75
21 22 7.712639 ACGTGTCTTCTTATCATATGCAAGAAT 59.287 33.333 22.26 11.16 37.58 2.40
22 23 7.041721 ACGTGTCTTCTTATCATATGCAAGAA 58.958 34.615 21.38 21.38 36.27 2.52
23 24 6.573434 ACGTGTCTTCTTATCATATGCAAGA 58.427 36.000 12.84 12.84 0.00 3.02
24 25 6.834959 ACGTGTCTTCTTATCATATGCAAG 57.165 37.500 0.00 4.36 0.00 4.01
25 26 7.010460 CAGAACGTGTCTTCTTATCATATGCAA 59.990 37.037 0.00 0.00 32.70 4.08
26 27 6.476706 CAGAACGTGTCTTCTTATCATATGCA 59.523 38.462 0.00 0.00 32.70 3.96
27 28 6.477033 ACAGAACGTGTCTTCTTATCATATGC 59.523 38.462 0.00 0.00 31.90 3.14
28 29 7.835520 CACAGAACGTGTCTTCTTATCATATG 58.164 38.462 0.00 0.00 41.03 1.78
29 30 7.993821 CACAGAACGTGTCTTCTTATCATAT 57.006 36.000 0.00 0.00 41.03 1.78
44 45 3.375610 TGCACACAATTTACACAGAACGT 59.624 39.130 0.00 0.00 0.00 3.99
45 46 3.946402 TGCACACAATTTACACAGAACG 58.054 40.909 0.00 0.00 0.00 3.95
46 47 8.519492 AAATATGCACACAATTTACACAGAAC 57.481 30.769 0.00 0.00 0.00 3.01
47 48 9.539825 AAAAATATGCACACAATTTACACAGAA 57.460 25.926 0.00 0.00 0.00 3.02
249 251 7.496747 AGTATGCAAAAACAAACATTGGTACT 58.503 30.769 0.00 0.00 34.12 2.73
262 321 6.128956 TGCGCTTTTTCATAGTATGCAAAAAC 60.129 34.615 17.56 13.65 35.56 2.43
341 401 9.212593 ACACAGAAATTGGGCCTTTTATAATAT 57.787 29.630 4.53 0.00 31.46 1.28
355 417 5.748152 CGCCCATATTTTACACAGAAATTGG 59.252 40.000 0.00 0.00 31.65 3.16
427 489 6.565435 CGTTTCAGCCAAGCATATAGAGATTG 60.565 42.308 0.00 0.39 0.00 2.67
428 490 5.468072 CGTTTCAGCCAAGCATATAGAGATT 59.532 40.000 0.00 0.00 0.00 2.40
430 492 4.099419 TCGTTTCAGCCAAGCATATAGAGA 59.901 41.667 0.00 0.00 0.00 3.10
431 493 4.371786 TCGTTTCAGCCAAGCATATAGAG 58.628 43.478 0.00 0.00 0.00 2.43
437 501 3.319755 CAAAATCGTTTCAGCCAAGCAT 58.680 40.909 0.00 0.00 0.00 3.79
444 508 1.611491 TGACCCCAAAATCGTTTCAGC 59.389 47.619 0.00 0.00 0.00 4.26
476 540 6.143919 GGTCAGTCGGTTCAAAATGAATTTTC 59.856 38.462 0.00 0.00 38.79 2.29
489 553 1.001597 CGGCTATAGGTCAGTCGGTTC 60.002 57.143 1.04 0.00 37.47 3.62
490 554 1.030457 CGGCTATAGGTCAGTCGGTT 58.970 55.000 1.04 0.00 37.47 4.44
491 555 0.182061 TCGGCTATAGGTCAGTCGGT 59.818 55.000 1.04 0.00 41.36 4.69
496 560 2.223803 AGGGATCGGCTATAGGTCAG 57.776 55.000 1.04 0.00 0.00 3.51
503 567 4.965532 AGCAATCTATAAGGGATCGGCTAT 59.034 41.667 0.00 0.00 34.39 2.97
585 649 0.746204 TCACTTTTCTGGCGTGTGCA 60.746 50.000 0.00 0.00 45.35 4.57
614 678 0.037975 TTTCGGCCTTCAGACGTACC 60.038 55.000 0.00 0.00 0.00 3.34
618 682 1.993370 CTACTTTTCGGCCTTCAGACG 59.007 52.381 0.00 0.00 0.00 4.18
648 712 4.480541 CTTACTCTCGATCGGATTCCATG 58.519 47.826 16.41 1.61 0.00 3.66
668 732 1.674611 CGAATCGTTGACGCTCGCTT 61.675 55.000 12.45 0.00 37.51 4.68
671 735 0.291989 CTTCGAATCGTTGACGCTCG 59.708 55.000 16.45 16.45 41.98 5.03
673 737 2.279582 ATCTTCGAATCGTTGACGCT 57.720 45.000 1.52 0.00 39.60 5.07
770 843 3.481903 CGCACGCAGCTTCATCGT 61.482 61.111 0.00 0.00 42.61 3.73
786 859 1.602668 CCTGCAAACACATGGGAAACG 60.603 52.381 0.00 0.00 0.00 3.60
828 901 1.358103 AGGGAGCTAGCGGGATATACA 59.642 52.381 9.55 0.00 0.00 2.29
908 2301 0.460987 GGAATGCACGGTCAGGAGAG 60.461 60.000 0.00 0.00 0.00 3.20
909 2302 1.596934 GGAATGCACGGTCAGGAGA 59.403 57.895 0.00 0.00 0.00 3.71
939 2334 2.813754 ACCAGGACATGTCGTTCAAATG 59.186 45.455 18.07 6.35 0.00 2.32
975 2390 5.970317 TTGCATGATGATATGGTCAATCC 57.030 39.130 0.00 0.00 40.97 3.01
1022 2437 1.227853 AAGCTCGACGGCAGGTTTT 60.228 52.632 10.28 0.00 34.17 2.43
1133 2856 1.303236 TGGTACTGGTGCATGGTGC 60.303 57.895 0.00 0.00 45.29 5.01
1147 2870 0.037697 GGCGTCACTGATGTGTGGTA 60.038 55.000 0.21 0.00 44.14 3.25
1159 2882 3.050275 GCAACTCCCTGGCGTCAC 61.050 66.667 0.00 0.00 0.00 3.67
1196 2928 0.394352 GCAAACGGAGTCATGGGGAT 60.394 55.000 0.00 0.00 45.00 3.85
1214 2946 2.871427 GCTGCATGCGTACCGTAGC 61.871 63.158 14.09 10.68 0.00 3.58
1318 3050 1.114627 AGCTGTGCTGTGATCGGATA 58.885 50.000 0.00 0.00 37.57 2.59
1320 3052 3.380995 AGCTGTGCTGTGATCGGA 58.619 55.556 0.00 0.00 37.57 4.55
1345 3077 1.992277 ATCTTCCGTGGCTCCTGCT 60.992 57.895 0.00 0.00 39.59 4.24
1416 3160 0.669625 GGACCCTTTTCGGTGACTCG 60.670 60.000 0.00 0.00 35.79 4.18
1454 3198 2.810439 CTGGCTACCAGTAGATCAGC 57.190 55.000 9.02 0.00 45.82 4.26
1476 3220 2.167693 TGCTACCCACGAGTTATCCAAG 59.832 50.000 0.00 0.00 0.00 3.61
1478 3222 1.754803 CTGCTACCCACGAGTTATCCA 59.245 52.381 0.00 0.00 0.00 3.41
1493 3238 5.129634 TGGACATTCAAACTCAAACTGCTA 58.870 37.500 0.00 0.00 0.00 3.49
1497 3242 5.278660 GCTCATGGACATTCAAACTCAAACT 60.279 40.000 0.00 0.00 0.00 2.66
1504 3249 2.490903 AGCAGCTCATGGACATTCAAAC 59.509 45.455 0.00 0.00 0.00 2.93
1513 3258 2.580815 CGGTGAGCAGCTCATGGA 59.419 61.111 27.86 1.76 42.73 3.41
1730 3475 1.620819 CTGTCAGTTACCTGCTGGACT 59.379 52.381 17.64 7.40 38.66 3.85
1748 3493 3.599046 GCTCGGTGCATATTTTCTCTG 57.401 47.619 0.00 0.00 42.31 3.35
1782 3546 3.181482 ACGAACATCTCACAGCTATCAGG 60.181 47.826 0.00 0.00 0.00 3.86
1790 3554 2.360553 AGCAGACGAACATCTCACAG 57.639 50.000 0.00 0.00 0.00 3.66
1946 3710 4.410099 TCCAAATGTGCCATCTTTTCTCT 58.590 39.130 0.00 0.00 0.00 3.10
1947 3711 4.789012 TCCAAATGTGCCATCTTTTCTC 57.211 40.909 0.00 0.00 0.00 2.87
1995 3759 1.995626 CAACGGGGTCCCAGGATCT 60.996 63.158 13.16 0.00 35.37 2.75
2064 3828 3.907260 TTCAGGCAAGCCGCTCTGG 62.907 63.158 5.28 0.00 41.91 3.86
2073 3837 2.005451 CTGTCTCCGATTTCAGGCAAG 58.995 52.381 0.00 0.00 0.00 4.01
2163 3927 9.905713 ATACATGACCTGCTCTAAAAGAAATAA 57.094 29.630 0.00 0.00 0.00 1.40
2177 3941 1.672881 GGCTTCACATACATGACCTGC 59.327 52.381 0.00 0.00 0.00 4.85
2186 3950 3.334583 TCTGTTCCTGGCTTCACATAC 57.665 47.619 0.00 0.00 0.00 2.39
2297 4061 5.064198 CAGTAAGAGGTTTGTTTGTCGACAA 59.936 40.000 26.53 26.53 37.73 3.18
2306 4070 6.998074 TGATGACAATCAGTAAGAGGTTTGTT 59.002 34.615 0.00 0.00 37.91 2.83
2325 4096 5.220548 CCGAACATGAACTCTGAATGATGAC 60.221 44.000 0.00 0.00 0.00 3.06
2384 4155 1.202582 TGCAGCTCGTCTTAGTCCTTC 59.797 52.381 0.00 0.00 0.00 3.46
2388 4159 2.065993 TGTTGCAGCTCGTCTTAGTC 57.934 50.000 1.17 0.00 0.00 2.59
2389 4160 2.135933 GTTGTTGCAGCTCGTCTTAGT 58.864 47.619 1.17 0.00 0.00 2.24
2459 4230 2.991190 GCACCTGCAAATTCACAAGATG 59.009 45.455 0.00 0.00 41.59 2.90
2555 4326 3.670625 TCGCCAACAGTAATTTAGCTGT 58.329 40.909 0.00 4.76 46.61 4.40
2593 4368 6.373495 GCATTCATATCAGATAATCAGTGGCA 59.627 38.462 0.00 0.00 0.00 4.92
2619 4398 7.426456 GCTTTTTGTTCGATATATCACACTGTG 59.574 37.037 13.11 6.19 34.45 3.66
2648 4427 4.260212 CGTTGATTAATCATCCGGTCACAC 60.260 45.833 18.61 9.50 36.56 3.82
2670 4449 2.979814 TCACTGGATAACCATGTCCG 57.020 50.000 0.00 0.00 45.87 4.79
2710 4489 9.736414 AGTCTCTGTGAGTATACAGTTAACTAA 57.264 33.333 8.04 0.00 46.32 2.24
2713 4492 9.165035 AGTAGTCTCTGTGAGTATACAGTTAAC 57.835 37.037 5.50 0.00 46.32 2.01
2765 4547 7.715249 CCACAGGAAATATATTCGAGGAAAGAA 59.285 37.037 0.00 0.00 0.00 2.52
2841 4623 2.415512 GCCGTAGTTGTGGAATGACTTC 59.584 50.000 0.00 0.00 0.00 3.01
2844 4626 2.094762 AGCCGTAGTTGTGGAATGAC 57.905 50.000 0.00 0.00 0.00 3.06
2875 4657 5.376854 TCCTTGCAAGAAAAATCAGTAGC 57.623 39.130 28.05 0.00 0.00 3.58
2891 4673 7.196331 GGAAACATGTATGAGTAAATCCTTGC 58.804 38.462 0.00 0.00 0.00 4.01
2906 4688 5.446143 AAATTTGTGAGCGGAAACATGTA 57.554 34.783 0.00 0.00 0.00 2.29
2907 4689 4.298332 GAAATTTGTGAGCGGAAACATGT 58.702 39.130 0.00 0.00 0.00 3.21
2912 4694 4.664150 AAAGGAAATTTGTGAGCGGAAA 57.336 36.364 0.00 0.00 0.00 3.13
2913 4695 5.067273 TCTAAAGGAAATTTGTGAGCGGAA 58.933 37.500 0.00 0.00 32.01 4.30
2914 4696 4.647611 TCTAAAGGAAATTTGTGAGCGGA 58.352 39.130 0.00 0.00 32.01 5.54
2924 4706 9.793259 TGATACTCAACAGTTCTAAAGGAAATT 57.207 29.630 0.00 0.00 35.51 1.82
2925 4707 9.965902 ATGATACTCAACAGTTCTAAAGGAAAT 57.034 29.630 0.00 0.00 35.51 2.17
2926 4708 9.219603 CATGATACTCAACAGTTCTAAAGGAAA 57.780 33.333 0.00 0.00 35.51 3.13
2927 4709 8.593679 TCATGATACTCAACAGTTCTAAAGGAA 58.406 33.333 0.00 0.00 33.62 3.36
2928 4710 8.134202 TCATGATACTCAACAGTTCTAAAGGA 57.866 34.615 0.00 0.00 33.62 3.36
2929 4711 8.954950 ATCATGATACTCAACAGTTCTAAAGG 57.045 34.615 6.36 0.00 33.62 3.11
2937 4719 9.784531 CCCTAAATAATCATGATACTCAACAGT 57.215 33.333 9.04 0.00 36.55 3.55
2938 4720 8.725148 GCCCTAAATAATCATGATACTCAACAG 58.275 37.037 9.04 1.26 0.00 3.16
2939 4721 8.439971 AGCCCTAAATAATCATGATACTCAACA 58.560 33.333 9.04 0.00 0.00 3.33
2940 4722 8.725148 CAGCCCTAAATAATCATGATACTCAAC 58.275 37.037 9.04 0.00 0.00 3.18
2941 4723 7.391554 GCAGCCCTAAATAATCATGATACTCAA 59.608 37.037 9.04 0.00 0.00 3.02
2942 4724 6.881065 GCAGCCCTAAATAATCATGATACTCA 59.119 38.462 9.04 0.00 0.00 3.41
2943 4725 6.317391 GGCAGCCCTAAATAATCATGATACTC 59.683 42.308 9.04 0.00 0.00 2.59
2944 4726 6.012157 AGGCAGCCCTAAATAATCATGATACT 60.012 38.462 9.04 0.00 40.58 2.12
2945 4727 6.183347 AGGCAGCCCTAAATAATCATGATAC 58.817 40.000 9.04 0.00 40.58 2.24
2946 4728 6.392911 AGGCAGCCCTAAATAATCATGATA 57.607 37.500 9.04 0.00 40.58 2.15
2947 4729 5.259632 GAGGCAGCCCTAAATAATCATGAT 58.740 41.667 8.22 1.18 43.12 2.45
2948 4730 4.507335 GGAGGCAGCCCTAAATAATCATGA 60.507 45.833 8.22 0.00 43.12 3.07
2949 4731 3.760684 GGAGGCAGCCCTAAATAATCATG 59.239 47.826 8.22 0.00 43.12 3.07
2950 4732 3.398967 TGGAGGCAGCCCTAAATAATCAT 59.601 43.478 8.22 0.00 43.12 2.45
2951 4733 2.782925 TGGAGGCAGCCCTAAATAATCA 59.217 45.455 8.22 0.00 43.12 2.57
2952 4734 3.149981 GTGGAGGCAGCCCTAAATAATC 58.850 50.000 8.22 0.00 43.12 1.75
2953 4735 2.513738 TGTGGAGGCAGCCCTAAATAAT 59.486 45.455 8.22 0.00 43.12 1.28
2954 4736 1.919654 TGTGGAGGCAGCCCTAAATAA 59.080 47.619 8.22 0.00 43.12 1.40
2955 4737 1.490490 CTGTGGAGGCAGCCCTAAATA 59.510 52.381 8.22 0.00 43.12 1.40
2956 4738 0.257039 CTGTGGAGGCAGCCCTAAAT 59.743 55.000 8.22 0.00 43.12 1.40
2957 4739 0.840288 TCTGTGGAGGCAGCCCTAAA 60.840 55.000 8.22 0.00 43.12 1.85
2958 4740 1.229496 TCTGTGGAGGCAGCCCTAA 60.229 57.895 8.22 0.00 43.12 2.69
2959 4741 1.990060 GTCTGTGGAGGCAGCCCTA 60.990 63.158 8.22 0.00 43.12 3.53
2960 4742 3.325753 GTCTGTGGAGGCAGCCCT 61.326 66.667 8.22 0.00 46.74 5.19
2961 4743 3.196207 TTGTCTGTGGAGGCAGCCC 62.196 63.158 8.22 0.00 34.53 5.19
2962 4744 1.968540 GTTGTCTGTGGAGGCAGCC 60.969 63.158 1.84 1.84 34.53 4.85
2963 4745 1.968540 GGTTGTCTGTGGAGGCAGC 60.969 63.158 0.00 0.00 34.53 5.25
2964 4746 0.321122 GAGGTTGTCTGTGGAGGCAG 60.321 60.000 0.00 0.00 34.53 4.85
2965 4747 0.764369 AGAGGTTGTCTGTGGAGGCA 60.764 55.000 0.00 0.00 32.57 4.75
2966 4748 0.321122 CAGAGGTTGTCTGTGGAGGC 60.321 60.000 0.00 0.00 46.89 4.70
2967 4749 3.923354 CAGAGGTTGTCTGTGGAGG 57.077 57.895 0.00 0.00 46.89 4.30
2973 4755 0.951040 GCGGAACCAGAGGTTGTCTG 60.951 60.000 6.10 0.00 46.95 3.51
2974 4756 1.371558 GCGGAACCAGAGGTTGTCT 59.628 57.895 6.10 0.00 46.95 3.41
2975 4757 1.671379 GGCGGAACCAGAGGTTGTC 60.671 63.158 6.10 0.00 46.95 3.18
2976 4758 2.430367 GGCGGAACCAGAGGTTGT 59.570 61.111 6.10 0.00 46.95 3.32
2977 4759 2.742372 CGGCGGAACCAGAGGTTG 60.742 66.667 6.10 0.00 46.95 3.77
2979 4761 2.776370 TAGTCGGCGGAACCAGAGGT 62.776 60.000 7.21 0.00 39.03 3.85
2980 4762 2.050350 TAGTCGGCGGAACCAGAGG 61.050 63.158 7.21 0.00 39.03 3.69
2981 4763 1.139095 GTAGTCGGCGGAACCAGAG 59.861 63.158 7.21 0.00 39.03 3.35
2982 4764 2.345760 GGTAGTCGGCGGAACCAGA 61.346 63.158 17.36 0.00 39.03 3.86
2983 4765 2.183555 GGTAGTCGGCGGAACCAG 59.816 66.667 17.36 0.00 39.03 4.00
2984 4766 2.283388 AGGTAGTCGGCGGAACCA 60.283 61.111 21.99 0.00 39.03 3.67
2985 4767 1.602327 AAGAGGTAGTCGGCGGAACC 61.602 60.000 7.21 12.43 0.00 3.62
2986 4768 0.179142 GAAGAGGTAGTCGGCGGAAC 60.179 60.000 7.21 0.00 0.00 3.62
2987 4769 1.651240 CGAAGAGGTAGTCGGCGGAA 61.651 60.000 7.21 0.00 33.62 4.30
2988 4770 2.110967 CGAAGAGGTAGTCGGCGGA 61.111 63.158 7.21 0.00 33.62 5.54
2989 4771 2.320339 GACGAAGAGGTAGTCGGCGG 62.320 65.000 7.21 0.00 41.56 6.13
2990 4772 1.062206 GACGAAGAGGTAGTCGGCG 59.938 63.158 0.00 0.00 41.56 6.46
2991 4773 0.810016 AAGACGAAGAGGTAGTCGGC 59.190 55.000 0.00 0.00 45.90 5.54
2992 4774 1.062294 CGAAGACGAAGAGGTAGTCGG 59.938 57.143 0.00 0.00 41.56 4.79
2993 4775 1.731160 ACGAAGACGAAGAGGTAGTCG 59.269 52.381 0.00 0.00 42.66 4.18
2994 4776 2.095692 GGACGAAGACGAAGAGGTAGTC 59.904 54.545 0.00 0.00 42.66 2.59
2995 4777 2.083002 GGACGAAGACGAAGAGGTAGT 58.917 52.381 0.00 0.00 42.66 2.73
2996 4778 2.082231 TGGACGAAGACGAAGAGGTAG 58.918 52.381 0.00 0.00 42.66 3.18
2997 4779 2.082231 CTGGACGAAGACGAAGAGGTA 58.918 52.381 0.00 0.00 42.66 3.08
2998 4780 0.882474 CTGGACGAAGACGAAGAGGT 59.118 55.000 0.00 0.00 42.66 3.85
2999 4781 0.456995 GCTGGACGAAGACGAAGAGG 60.457 60.000 0.00 0.00 42.66 3.69
3000 4782 0.241213 TGCTGGACGAAGACGAAGAG 59.759 55.000 0.00 0.00 42.66 2.85
3001 4783 0.039437 GTGCTGGACGAAGACGAAGA 60.039 55.000 0.00 0.00 42.66 2.87
3023 4805 1.134901 GACGACGCTGACGATGAGT 59.865 57.895 0.00 0.00 43.93 3.41
3027 4809 1.978712 ATGACGACGACGCTGACGAT 61.979 55.000 7.30 0.00 43.93 3.73
3031 4813 1.057636 GAAAATGACGACGACGCTGA 58.942 50.000 7.30 0.00 43.96 4.26
3047 4829 2.668144 AAATGAAGTGGTCGGGGAAA 57.332 45.000 0.00 0.00 0.00 3.13
3049 4831 3.371166 GGAATAAATGAAGTGGTCGGGGA 60.371 47.826 0.00 0.00 0.00 4.81
3065 4847 2.598589 CGTTCTCGGTTGTCGGAATAA 58.401 47.619 0.00 0.00 39.77 1.40
3068 4850 1.662446 GCGTTCTCGGTTGTCGGAA 60.662 57.895 0.00 0.00 39.77 4.30
3082 4864 1.006832 GTAGAATGTGCCGATGCGTT 58.993 50.000 0.00 0.00 41.78 4.84
3083 4865 0.810031 GGTAGAATGTGCCGATGCGT 60.810 55.000 0.00 0.00 41.78 5.24
3086 4868 0.880278 CGGGGTAGAATGTGCCGATG 60.880 60.000 0.00 0.00 0.00 3.84
3087 4869 1.445942 CGGGGTAGAATGTGCCGAT 59.554 57.895 0.00 0.00 0.00 4.18
3088 4870 2.897207 CGGGGTAGAATGTGCCGA 59.103 61.111 0.00 0.00 0.00 5.54
3089 4871 2.895372 GCGGGGTAGAATGTGCCG 60.895 66.667 0.00 0.00 0.00 5.69
3090 4872 2.516225 GGCGGGGTAGAATGTGCC 60.516 66.667 0.00 0.00 35.04 5.01
3092 4874 0.179056 AATCGGCGGGGTAGAATGTG 60.179 55.000 7.21 0.00 0.00 3.21
3093 4875 0.179056 CAATCGGCGGGGTAGAATGT 60.179 55.000 7.21 0.00 0.00 2.71
3095 4877 1.450211 CCAATCGGCGGGGTAGAAT 59.550 57.895 7.21 0.00 0.00 2.40
3096 4878 2.904905 CCAATCGGCGGGGTAGAA 59.095 61.111 7.21 0.00 0.00 2.10
3132 4914 0.252467 AGGGACCAACAGAGGAGGAG 60.252 60.000 0.00 0.00 0.00 3.69
3147 4931 1.195442 TGTACGCCATGTTGGAGGGA 61.195 55.000 0.00 0.00 41.96 4.20
3149 4942 0.802494 GTTGTACGCCATGTTGGAGG 59.198 55.000 0.00 0.00 41.96 4.30
3174 4967 1.216977 CATGCGTAGACGGGACCAA 59.783 57.895 3.97 0.00 40.23 3.67
3175 4968 2.889617 CATGCGTAGACGGGACCA 59.110 61.111 3.97 0.00 40.23 4.02
3198 4993 0.391661 CACATCGGTAGTTGCCAGCT 60.392 55.000 0.00 0.00 0.00 4.24
3208 5003 0.108992 GACGAAGGCACACATCGGTA 60.109 55.000 0.00 0.00 40.71 4.02
3244 5040 2.029518 GCACCAGGTTTGCCAAGC 59.970 61.111 0.00 0.00 37.19 4.01
3246 5042 3.222855 CCGCACCAGGTTTGCCAA 61.223 61.111 0.00 0.00 36.57 4.52
3267 5063 3.436496 GGAAGAAGTCGGTATTGACGAG 58.564 50.000 0.00 0.00 43.70 4.18
3275 5071 2.359900 GTAGACGGGAAGAAGTCGGTA 58.640 52.381 0.00 0.00 41.86 4.02
3276 5072 1.172175 GTAGACGGGAAGAAGTCGGT 58.828 55.000 0.00 0.00 41.86 4.69
3277 5073 0.098376 CGTAGACGGGAAGAAGTCGG 59.902 60.000 0.00 0.00 41.86 4.79
3280 5076 1.135083 CATGCGTAGACGGGAAGAAGT 60.135 52.381 3.97 0.00 40.23 3.01
3285 5081 2.185867 GGCATGCGTAGACGGGAA 59.814 61.111 12.44 0.00 40.23 3.97
3287 5083 3.849951 AGGGCATGCGTAGACGGG 61.850 66.667 12.44 0.00 40.23 5.28
3304 5100 1.077858 TGTCAGTGTTGGCAGCACA 60.078 52.632 31.47 12.44 39.17 4.57
3311 5107 1.095228 AAGGCACGTGTCAGTGTTGG 61.095 55.000 24.06 0.00 43.61 3.77
3318 5114 2.028484 GGACGAAGGCACGTGTCA 59.972 61.111 24.06 0.00 46.52 3.58
3338 5134 1.408453 GCCTAGCCTGGGGATACGTT 61.408 60.000 0.00 0.00 37.60 3.99
3343 5139 2.386935 GGTTGCCTAGCCTGGGGAT 61.387 63.158 0.00 0.00 0.00 3.85
3354 5150 4.954970 CGCCACACCAGGTTGCCT 62.955 66.667 0.00 0.00 34.79 4.75
3369 5166 2.493713 AGATGGTATTGACGAGACGC 57.506 50.000 0.00 0.00 0.00 5.19
3381 5178 1.621317 TGTGCCACGAAGAAGATGGTA 59.379 47.619 0.00 0.00 35.79 3.25
3403 5201 1.553690 ATGTAGTCAGGGGCGCAGTT 61.554 55.000 10.83 0.00 0.00 3.16
3420 5232 2.180017 GCGCAAGGAAGCACCATG 59.820 61.111 0.30 2.31 42.04 3.66
3421 5233 3.064324 GGCGCAAGGAAGCACCAT 61.064 61.111 10.83 0.00 42.04 3.55
3452 5265 0.957395 GGTCGGTGTCGAGGTAGTCA 60.957 60.000 0.00 0.00 46.91 3.41
3469 5282 1.381327 ATGTCGAGTCGGGGATGGT 60.381 57.895 13.54 0.00 0.00 3.55
3471 5284 1.008424 CGATGTCGAGTCGGGGATG 60.008 63.158 13.54 0.00 43.02 3.51
3472 5285 1.153025 TCGATGTCGAGTCGGGGAT 60.153 57.895 13.54 2.09 44.22 3.85
3500 5314 2.040544 CAAGGTAGCCGTGCAAGGG 61.041 63.158 20.72 10.75 46.87 3.95
3502 5316 1.009829 GATCAAGGTAGCCGTGCAAG 58.990 55.000 0.00 0.00 33.18 4.01
3517 5331 4.163458 GGTAGGGTGGTTTAGTCATGATCA 59.837 45.833 0.00 0.00 0.00 2.92
3520 5334 2.841881 GGGTAGGGTGGTTTAGTCATGA 59.158 50.000 0.00 0.00 0.00 3.07
3523 5338 2.113052 AGAGGGTAGGGTGGTTTAGTCA 59.887 50.000 0.00 0.00 0.00 3.41
3525 5340 2.113052 TGAGAGGGTAGGGTGGTTTAGT 59.887 50.000 0.00 0.00 0.00 2.24
3529 5344 0.910088 GCTGAGAGGGTAGGGTGGTT 60.910 60.000 0.00 0.00 0.00 3.67
3540 5355 1.464734 TTGTCGAGGTAGCTGAGAGG 58.535 55.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.