Multiple sequence alignment - TraesCS3B01G239000

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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 TraesCS3B01G239000 chr3B 100.000 5731 0 0 1 5731 376636665 376630935 0.000000e+00 10584.0
1 TraesCS3B01G239000 chr3B 94.932 296 12 2 5335 5628 781734063 781733769 1.450000e-125 460.0
2 TraesCS3B01G239000 chr3B 96.190 105 4 0 5627 5731 781733730 781733626 7.630000e-39 172.0
3 TraesCS3B01G239000 chr3B 90.741 54 4 1 4108 4160 112276973 112277026 2.860000e-08 71.3
4 TraesCS3B01G239000 chr3B 89.474 57 5 1 4121 4177 482487886 482487831 2.860000e-08 71.3
5 TraesCS3B01G239000 chr3A 97.730 2467 44 2 877 3343 260070662 260068208 0.000000e+00 4235.0
6 TraesCS3B01G239000 chr3A 95.398 1282 39 8 3893 5166 260067435 260066166 0.000000e+00 2023.0
7 TraesCS3B01G239000 chr3A 96.064 559 18 3 3338 3894 260068186 260067630 0.000000e+00 907.0
8 TraesCS3B01G239000 chr3A 95.181 166 8 0 5170 5335 260032084 260031919 4.400000e-66 263.0
9 TraesCS3B01G239000 chr3A 90.741 54 3 2 3841 3894 260067603 260067552 2.860000e-08 71.3
10 TraesCS3B01G239000 chr3D 98.032 1829 27 1 900 2728 241669554 241667735 0.000000e+00 3169.0
11 TraesCS3B01G239000 chr3D 96.074 1452 41 5 3893 5335 241666274 241664830 0.000000e+00 2351.0
12 TraesCS3B01G239000 chr3D 91.579 1235 49 26 2714 3894 241667702 241666469 0.000000e+00 1653.0
13 TraesCS3B01G239000 chr3D 90.402 771 67 5 1 765 407639141 407639910 0.000000e+00 1007.0
14 TraesCS3B01G239000 chr3D 90.445 764 68 3 4 763 245055399 245056161 0.000000e+00 1002.0
15 TraesCS3B01G239000 chr3D 93.814 194 12 0 3040 3233 263812183 263812376 5.620000e-75 292.0
16 TraesCS3B01G239000 chr3D 87.500 64 5 3 4113 4174 131489157 131489219 2.860000e-08 71.3
17 TraesCS3B01G239000 chr3D 90.741 54 3 2 3841 3894 241666442 241666391 2.860000e-08 71.3
18 TraesCS3B01G239000 chrUn 91.678 769 60 2 1 765 44919403 44918635 0.000000e+00 1062.0
19 TraesCS3B01G239000 chr2D 91.440 771 56 6 1 765 366554554 366553788 0.000000e+00 1050.0
20 TraesCS3B01G239000 chr2D 94.211 190 10 1 3044 3233 380416532 380416720 7.270000e-74 289.0
21 TraesCS3B01G239000 chr2D 88.525 61 6 1 4114 4174 310405790 310405849 7.970000e-09 73.1
22 TraesCS3B01G239000 chr7A 90.767 769 64 4 1 765 330156741 330155976 0.000000e+00 1020.0
23 TraesCS3B01G239000 chr7A 82.230 287 35 10 5342 5625 516113568 516113295 3.450000e-57 233.0
24 TraesCS3B01G239000 chr2B 90.637 769 65 5 1 765 216517319 216516554 0.000000e+00 1014.0
25 TraesCS3B01G239000 chr1B 90.625 768 66 4 1 763 482865869 482865103 0.000000e+00 1014.0
26 TraesCS3B01G239000 chr1B 91.275 298 17 3 5333 5628 282346334 282346044 1.160000e-106 398.0
27 TraesCS3B01G239000 chr1B 86.614 127 17 0 3350 3476 632208831 632208705 2.150000e-29 141.0
28 TraesCS3B01G239000 chr1B 85.156 128 16 2 3350 3474 60451477 60451604 1.680000e-25 128.0
29 TraesCS3B01G239000 chr5D 90.507 769 68 3 1 765 175483869 175484636 0.000000e+00 1011.0
30 TraesCS3B01G239000 chr4D 90.013 781 62 7 1 765 36080102 36080882 0.000000e+00 996.0
31 TraesCS3B01G239000 chr4D 91.960 199 14 1 3032 3230 351573955 351574151 1.570000e-70 278.0
32 TraesCS3B01G239000 chr4D 93.878 49 3 0 4112 4160 107696514 107696562 2.210000e-09 75.0
33 TraesCS3B01G239000 chr4B 95.620 411 12 2 5327 5731 8691034 8690624 0.000000e+00 654.0
34 TraesCS3B01G239000 chr4B 94.444 54 3 0 5282 5335 520914557 520914504 3.680000e-12 84.2
35 TraesCS3B01G239000 chr6D 94.863 292 11 3 5335 5624 311306417 311306128 2.430000e-123 453.0
36 TraesCS3B01G239000 chr6D 92.079 202 14 1 3032 3233 267532806 267533005 3.380000e-72 283.0
37 TraesCS3B01G239000 chr6D 83.165 297 33 12 5334 5625 267477364 267477080 7.370000e-64 255.0
38 TraesCS3B01G239000 chr6D 96.739 92 3 0 5640 5731 311305874 311305783 2.770000e-33 154.0
39 TraesCS3B01G239000 chr6D 91.111 90 8 0 5246 5335 459045397 459045486 7.800000e-24 122.0
40 TraesCS3B01G239000 chr1D 90.725 345 21 6 5338 5676 465598570 465598909 3.150000e-122 449.0
41 TraesCS3B01G239000 chr1D 81.931 404 53 12 5329 5722 451981753 451982146 1.990000e-84 324.0
42 TraesCS3B01G239000 chr5B 95.378 238 9 1 5332 5567 518668996 518669233 1.510000e-100 377.0
43 TraesCS3B01G239000 chr5B 92.118 203 12 2 3033 3233 464890240 464890440 3.380000e-72 283.0
44 TraesCS3B01G239000 chr5B 87.037 108 14 0 3354 3461 493936240 493936133 7.800000e-24 122.0
45 TraesCS3B01G239000 chr6A 92.424 198 13 1 3036 3233 381088703 381088898 1.220000e-71 281.0
46 TraesCS3B01G239000 chr6A 91.960 199 14 1 3032 3230 178519247 178519443 1.570000e-70 278.0
47 TraesCS3B01G239000 chr2A 91.071 56 5 0 4114 4169 610689404 610689459 6.160000e-10 76.8
48 TraesCS3B01G239000 chr1A 85.915 71 6 4 4119 4187 71070793 71070861 7.970000e-09 73.1


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 TraesCS3B01G239000 chr3B 376630935 376636665 5730 True 10584.000 10584 100.00000 1 5731 1 chr3B.!!$R1 5730
1 TraesCS3B01G239000 chr3A 260066166 260070662 4496 True 1809.075 4235 94.98325 877 5166 4 chr3A.!!$R2 4289
2 TraesCS3B01G239000 chr3D 241664830 241669554 4724 True 1811.075 3169 94.10650 900 5335 4 chr3D.!!$R1 4435
3 TraesCS3B01G239000 chr3D 407639141 407639910 769 False 1007.000 1007 90.40200 1 765 1 chr3D.!!$F4 764
4 TraesCS3B01G239000 chr3D 245055399 245056161 762 False 1002.000 1002 90.44500 4 763 1 chr3D.!!$F2 759
5 TraesCS3B01G239000 chrUn 44918635 44919403 768 True 1062.000 1062 91.67800 1 765 1 chrUn.!!$R1 764
6 TraesCS3B01G239000 chr2D 366553788 366554554 766 True 1050.000 1050 91.44000 1 765 1 chr2D.!!$R1 764
7 TraesCS3B01G239000 chr7A 330155976 330156741 765 True 1020.000 1020 90.76700 1 765 1 chr7A.!!$R1 764
8 TraesCS3B01G239000 chr2B 216516554 216517319 765 True 1014.000 1014 90.63700 1 765 1 chr2B.!!$R1 764
9 TraesCS3B01G239000 chr1B 482865103 482865869 766 True 1014.000 1014 90.62500 1 763 1 chr1B.!!$R2 762
10 TraesCS3B01G239000 chr5D 175483869 175484636 767 False 1011.000 1011 90.50700 1 765 1 chr5D.!!$F1 764
11 TraesCS3B01G239000 chr4D 36080102 36080882 780 False 996.000 996 90.01300 1 765 1 chr4D.!!$F1 764
12 TraesCS3B01G239000 chr6D 311305783 311306417 634 True 303.500 453 95.80100 5335 5731 2 chr6D.!!$R2 396

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
824 846 0.108756 GAGGCCGTGTTGGTAGAGAC 60.109 60.000 0.00 0.00 41.21 3.36 F
829 851 0.318360 CGTGTTGGTAGAGACGTGCA 60.318 55.000 0.00 0.00 32.36 4.57 F
834 856 0.320050 TGGTAGAGACGTGCATTGCA 59.680 50.000 7.38 7.38 35.60 4.08 F
1557 1579 0.474184 CCTCCCCTGACGCCATTATT 59.526 55.000 0.00 0.00 0.00 1.40 F
2031 2053 0.539986 GCCGGAACCATGAGAAGGTA 59.460 55.000 5.05 0.00 38.76 3.08 F
2494 2516 1.064314 ACTGGTTGTGTTGGTTAGCCA 60.064 47.619 0.00 0.00 44.38 4.75 F
3643 3793 0.521291 GCTGTTTTGCTGGCGTATCA 59.479 50.000 0.00 0.00 0.00 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2258 2280 0.460311 CCCCGTCACTGGATCACTAC 59.540 60.000 0.00 0.00 0.00 2.73 R
2274 2296 4.163458 TGGTGTGAGATTCTTACATACCCC 59.837 45.833 13.65 10.65 42.35 4.95 R
2493 2515 6.306356 CGGTTTCTGCATCTTGAAAAAGTATG 59.694 38.462 0.86 0.00 34.52 2.39 R
3048 3142 2.593026 TGGGACTAAAGGCTTTGTTGG 58.407 47.619 22.32 11.54 0.00 3.77 R
3564 3713 1.623811 GACTAACCCTGACTTCTGCCA 59.376 52.381 0.00 0.00 0.00 4.92 R
3856 4006 2.238646 ACAAGTTCCCAGTGAGACACAA 59.761 45.455 4.75 0.00 36.74 3.33 R
5464 5821 0.032403 CGTGGTAAAGACGTGGGTCA 59.968 55.000 0.00 0.00 45.92 4.02 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
36 37 3.316573 CTCCTTCCCCGCCAGTGAC 62.317 68.421 0.00 0.00 0.00 3.67
72 73 3.399330 GGTTGCTGCTGTAGTGAACTTA 58.601 45.455 0.00 0.00 0.00 2.24
168 171 7.230913 TGGTCGTTTGGAAAAAGATGGTAATTA 59.769 33.333 0.00 0.00 0.00 1.40
205 209 1.872952 TGAATGCTTGGTCGTGACAAG 59.127 47.619 2.00 10.59 46.15 3.16
211 215 2.668550 GGTCGTGACAAGCACCCC 60.669 66.667 2.00 0.00 44.85 4.95
343 348 5.416639 ACATGTACGACCAGTTACATCACTA 59.583 40.000 0.00 0.00 31.51 2.74
350 355 5.345202 CGACCAGTTACATCACTAACTTGTC 59.655 44.000 10.91 10.91 41.58 3.18
383 388 9.683069 CATTTGAGCAGTAGTACTTGAAATTTT 57.317 29.630 0.00 0.00 0.00 1.82
388 393 8.856490 AGCAGTAGTACTTGAAATTTTTGTTG 57.144 30.769 0.00 0.00 0.00 3.33
404 409 3.394674 TGTTGCAGTAAACTCATCGGA 57.605 42.857 0.00 0.00 0.00 4.55
451 456 9.305925 CCAAAACCATCAATTAATCTTTAGCTC 57.694 33.333 0.00 0.00 0.00 4.09
460 465 8.208224 TCAATTAATCTTTAGCTCGTTCCCATA 58.792 33.333 0.00 0.00 0.00 2.74
462 467 8.974060 ATTAATCTTTAGCTCGTTCCCATAAA 57.026 30.769 0.00 0.00 0.00 1.40
503 515 6.494842 ACCATGCTATAATTAAGTGCAAACG 58.505 36.000 12.22 7.16 37.20 3.60
539 557 5.992829 TGTATGTATCAAACCTGACGTGTTT 59.007 36.000 0.00 0.00 36.40 2.83
569 587 6.349243 TGCAGGTTTTAGTACTAGTGCTAA 57.651 37.500 24.38 24.38 36.28 3.09
611 632 7.065923 GGAACTACCTAGCCAAAAATTACTCTG 59.934 40.741 0.00 0.00 35.41 3.35
613 634 3.689649 ACCTAGCCAAAAATTACTCTGCG 59.310 43.478 0.00 0.00 0.00 5.18
627 648 2.832129 ACTCTGCGTTCCTCCTCATAAA 59.168 45.455 0.00 0.00 0.00 1.40
670 691 4.415150 ATGGCCGGTGTGCAGAGG 62.415 66.667 1.90 0.00 0.00 3.69
690 711 5.727766 AGAGGTCTAGGTTGAGTACTACTCT 59.272 44.000 15.76 0.00 45.27 3.24
765 787 2.794282 CGCAGAGACCTCGAAAGATCTG 60.794 54.545 0.00 11.16 40.84 2.90
766 788 2.425312 GCAGAGACCTCGAAAGATCTGA 59.575 50.000 17.01 0.00 40.84 3.27
767 789 3.119316 GCAGAGACCTCGAAAGATCTGAA 60.119 47.826 17.01 0.00 40.84 3.02
768 790 4.441356 GCAGAGACCTCGAAAGATCTGAAT 60.441 45.833 17.01 0.00 40.84 2.57
769 791 5.280945 CAGAGACCTCGAAAGATCTGAATC 58.719 45.833 10.34 0.00 40.84 2.52
770 792 4.036262 AGAGACCTCGAAAGATCTGAATCG 59.964 45.833 15.80 15.80 40.84 3.34
771 793 3.067461 AGACCTCGAAAGATCTGAATCGG 59.933 47.826 19.56 10.93 40.84 4.18
772 794 2.761208 ACCTCGAAAGATCTGAATCGGT 59.239 45.455 19.56 11.45 40.84 4.69
773 795 3.195825 ACCTCGAAAGATCTGAATCGGTT 59.804 43.478 19.56 0.48 40.84 4.44
774 796 3.553511 CCTCGAAAGATCTGAATCGGTTG 59.446 47.826 19.56 12.71 40.84 3.77
775 797 4.177026 CTCGAAAGATCTGAATCGGTTGT 58.823 43.478 19.56 0.00 40.84 3.32
776 798 4.174009 TCGAAAGATCTGAATCGGTTGTC 58.826 43.478 19.56 0.00 36.97 3.18
777 799 3.307242 CGAAAGATCTGAATCGGTTGTCC 59.693 47.826 14.67 0.00 36.97 4.02
778 800 2.990066 AGATCTGAATCGGTTGTCCC 57.010 50.000 0.00 0.00 36.97 4.46
779 801 2.472029 AGATCTGAATCGGTTGTCCCT 58.528 47.619 0.00 0.00 36.97 4.20
780 802 2.840651 AGATCTGAATCGGTTGTCCCTT 59.159 45.455 0.00 0.00 36.97 3.95
781 803 2.762535 TCTGAATCGGTTGTCCCTTC 57.237 50.000 0.00 0.00 0.00 3.46
782 804 1.278127 TCTGAATCGGTTGTCCCTTCC 59.722 52.381 0.00 0.00 0.00 3.46
783 805 1.003118 CTGAATCGGTTGTCCCTTCCA 59.997 52.381 0.00 0.00 0.00 3.53
784 806 1.003118 TGAATCGGTTGTCCCTTCCAG 59.997 52.381 0.00 0.00 0.00 3.86
785 807 1.003233 GAATCGGTTGTCCCTTCCAGT 59.997 52.381 0.00 0.00 0.00 4.00
786 808 0.324943 ATCGGTTGTCCCTTCCAGTG 59.675 55.000 0.00 0.00 0.00 3.66
787 809 1.052124 TCGGTTGTCCCTTCCAGTGT 61.052 55.000 0.00 0.00 0.00 3.55
788 810 0.884704 CGGTTGTCCCTTCCAGTGTG 60.885 60.000 0.00 0.00 0.00 3.82
789 811 0.537371 GGTTGTCCCTTCCAGTGTGG 60.537 60.000 0.00 0.00 39.43 4.17
790 812 0.182775 GTTGTCCCTTCCAGTGTGGT 59.817 55.000 0.00 0.00 39.03 4.16
791 813 0.182537 TTGTCCCTTCCAGTGTGGTG 59.817 55.000 0.00 0.00 39.03 4.17
792 814 1.073199 GTCCCTTCCAGTGTGGTGG 59.927 63.158 0.00 0.00 39.03 4.61
793 815 2.282462 CCCTTCCAGTGTGGTGGC 60.282 66.667 0.00 0.00 39.03 5.01
794 816 2.833913 CCCTTCCAGTGTGGTGGCT 61.834 63.158 0.00 0.00 39.03 4.75
795 817 1.488705 CCCTTCCAGTGTGGTGGCTA 61.489 60.000 0.00 0.00 39.03 3.93
796 818 0.400213 CCTTCCAGTGTGGTGGCTAA 59.600 55.000 0.00 0.00 39.03 3.09
797 819 1.523758 CTTCCAGTGTGGTGGCTAAC 58.476 55.000 0.00 0.00 39.03 2.34
809 831 2.038689 GGTGGCTAACCCTAATAGAGGC 59.961 54.545 0.00 0.00 45.17 4.70
810 832 2.038689 GTGGCTAACCCTAATAGAGGCC 59.961 54.545 0.00 0.00 45.17 5.19
811 833 1.275573 GGCTAACCCTAATAGAGGCCG 59.724 57.143 0.00 0.00 45.17 6.13
812 834 1.969208 GCTAACCCTAATAGAGGCCGT 59.031 52.381 0.00 0.00 45.17 5.68
813 835 2.288886 GCTAACCCTAATAGAGGCCGTG 60.289 54.545 0.00 0.00 45.17 4.94
814 836 1.875488 AACCCTAATAGAGGCCGTGT 58.125 50.000 0.00 0.00 45.17 4.49
815 837 1.875488 ACCCTAATAGAGGCCGTGTT 58.125 50.000 0.00 0.00 45.17 3.32
816 838 1.485066 ACCCTAATAGAGGCCGTGTTG 59.515 52.381 0.00 0.00 45.17 3.33
817 839 1.202651 CCCTAATAGAGGCCGTGTTGG 60.203 57.143 0.00 0.00 45.17 3.77
818 840 1.485066 CCTAATAGAGGCCGTGTTGGT 59.515 52.381 0.00 0.00 38.96 3.67
819 841 2.696707 CCTAATAGAGGCCGTGTTGGTA 59.303 50.000 0.00 0.00 38.96 3.25
820 842 2.981859 AATAGAGGCCGTGTTGGTAG 57.018 50.000 0.00 0.00 41.21 3.18
821 843 2.154567 ATAGAGGCCGTGTTGGTAGA 57.845 50.000 0.00 0.00 41.21 2.59
822 844 1.471119 TAGAGGCCGTGTTGGTAGAG 58.529 55.000 0.00 0.00 41.21 2.43
823 845 0.251653 AGAGGCCGTGTTGGTAGAGA 60.252 55.000 0.00 0.00 41.21 3.10
824 846 0.108756 GAGGCCGTGTTGGTAGAGAC 60.109 60.000 0.00 0.00 41.21 3.36
825 847 1.445582 GGCCGTGTTGGTAGAGACG 60.446 63.158 0.00 0.00 41.21 4.18
826 848 1.288127 GCCGTGTTGGTAGAGACGT 59.712 57.895 0.00 0.00 41.21 4.34
827 849 1.007336 GCCGTGTTGGTAGAGACGTG 61.007 60.000 0.00 0.00 41.21 4.49
828 850 1.007336 CCGTGTTGGTAGAGACGTGC 61.007 60.000 0.00 0.00 34.85 5.34
829 851 0.318360 CGTGTTGGTAGAGACGTGCA 60.318 55.000 0.00 0.00 32.36 4.57
830 852 1.668919 CGTGTTGGTAGAGACGTGCAT 60.669 52.381 0.00 0.00 32.36 3.96
831 853 2.413837 GTGTTGGTAGAGACGTGCATT 58.586 47.619 0.00 0.00 0.00 3.56
832 854 2.157668 GTGTTGGTAGAGACGTGCATTG 59.842 50.000 0.00 0.00 0.00 2.82
833 855 1.128692 GTTGGTAGAGACGTGCATTGC 59.871 52.381 0.46 0.46 0.00 3.56
834 856 0.320050 TGGTAGAGACGTGCATTGCA 59.680 50.000 7.38 7.38 35.60 4.08
835 857 1.270571 TGGTAGAGACGTGCATTGCAA 60.271 47.619 13.94 0.00 41.47 4.08
836 858 1.394917 GGTAGAGACGTGCATTGCAAG 59.605 52.381 20.74 20.74 41.47 4.01
872 894 3.944871 AAAAACCACGAAGCTGCTG 57.055 47.368 1.35 0.00 0.00 4.41
873 895 1.102978 AAAAACCACGAAGCTGCTGT 58.897 45.000 1.35 0.00 0.00 4.40
874 896 1.961793 AAAACCACGAAGCTGCTGTA 58.038 45.000 1.35 0.00 0.00 2.74
875 897 1.961793 AAACCACGAAGCTGCTGTAA 58.038 45.000 1.35 0.00 0.00 2.41
1464 1486 1.335810 CATTACGCCTACGGAGCAGTA 59.664 52.381 0.00 0.00 46.04 2.74
1533 1555 3.464494 GTACCCCTCCCGTTCCCG 61.464 72.222 0.00 0.00 0.00 5.14
1557 1579 0.474184 CCTCCCCTGACGCCATTATT 59.526 55.000 0.00 0.00 0.00 1.40
1689 1711 1.745087 CTAGTTGCCATTTGTCGCCAT 59.255 47.619 0.00 0.00 0.00 4.40
1695 1717 0.680921 CCATTTGTCGCCATGAGGGT 60.681 55.000 0.00 0.00 39.65 4.34
1896 1918 4.700268 TGTGTCACATGAATATGGCAAC 57.300 40.909 0.18 0.00 38.66 4.17
2031 2053 0.539986 GCCGGAACCATGAGAAGGTA 59.460 55.000 5.05 0.00 38.76 3.08
2071 2093 2.124570 CCGAAGCATGGGGGACAG 60.125 66.667 0.00 0.00 0.00 3.51
2085 2107 1.630878 GGGACAGTTCTTGGATCACCT 59.369 52.381 0.00 0.00 37.04 4.00
2258 2280 5.766670 TGCAAGAGATGGCAAAGGATAATAG 59.233 40.000 0.00 0.00 37.03 1.73
2274 2296 6.431543 AGGATAATAGTAGTGATCCAGTGACG 59.568 42.308 9.35 0.00 40.38 4.35
2484 2506 7.175104 ACTATAATTTCATGGACTGGTTGTGT 58.825 34.615 0.00 0.00 0.00 3.72
2493 2515 1.607148 GACTGGTTGTGTTGGTTAGCC 59.393 52.381 0.00 0.00 0.00 3.93
2494 2516 1.064314 ACTGGTTGTGTTGGTTAGCCA 60.064 47.619 0.00 0.00 44.38 4.75
2665 2687 7.459795 TGTGCATTTATTTGACATTCTACCA 57.540 32.000 0.00 0.00 0.00 3.25
2698 2720 9.778741 AGTTTATCTGTCTGAAATGTTGAACTA 57.221 29.630 0.00 0.00 0.00 2.24
2732 2801 2.761767 TCTGCAAATGGCTGTATGCATT 59.238 40.909 3.54 0.00 46.59 3.56
2839 2933 1.805428 ATGGCGCCCAAAGTGTCAAC 61.805 55.000 26.77 0.00 45.33 3.18
2850 2944 6.821665 GCCCAAAGTGTCAACTTACTATGATA 59.178 38.462 0.00 0.00 46.15 2.15
2862 2956 9.553064 CAACTTACTATGATATCTTTTGAGCCT 57.447 33.333 3.98 0.00 0.00 4.58
3009 3103 6.586751 TCGAGAAACAAAATAACGATGACAC 58.413 36.000 0.00 0.00 0.00 3.67
3048 3142 8.342634 AGTCATAATACAACAACAAGTCAACAC 58.657 33.333 0.00 0.00 0.00 3.32
3191 3285 5.885912 GGCTAGTTCTTTGGTGATATTCCAA 59.114 40.000 8.59 8.59 42.29 3.53
3420 3569 3.073678 CACGGGACATGACAATTTCTGA 58.926 45.455 0.00 0.00 0.00 3.27
3489 3638 2.910199 TGACATGTCTCCTGCTATTGC 58.090 47.619 25.55 0.00 40.20 3.56
3502 3651 4.334203 CCTGCTATTGCCGTAACATGTTTA 59.666 41.667 17.78 0.00 38.71 2.01
3564 3713 4.407296 CCTCTTCACCTATGCCTTCTACTT 59.593 45.833 0.00 0.00 0.00 2.24
3643 3793 0.521291 GCTGTTTTGCTGGCGTATCA 59.479 50.000 0.00 0.00 0.00 2.15
3660 3810 6.348540 GGCGTATCAGTGTTTTCTTCATTTCT 60.349 38.462 0.00 0.00 0.00 2.52
3717 3867 0.756294 ATATCCCGGTTGTCATGCGA 59.244 50.000 0.00 0.00 0.00 5.10
3782 3932 7.985184 TGTATAGGTGTTTCATACATTCTGACC 59.015 37.037 0.00 0.00 39.39 4.02
3856 4006 7.141363 GGTAACGTCGTGTGGATTATATTAGT 58.859 38.462 0.00 0.00 0.00 2.24
3930 4276 9.113838 CTTATTGCTTGTAGTGATATTGTTCCT 57.886 33.333 0.00 0.00 0.00 3.36
4027 4373 9.959749 TCACGCTTTAAAAGTTTATCTTTCATT 57.040 25.926 0.00 0.00 44.50 2.57
4105 4452 3.610911 GGTGCTTGTACTAGCCAAAGAT 58.389 45.455 23.56 0.00 40.49 2.40
4131 4478 3.054948 CCGTAAAAATGGTACTCCCTCCA 60.055 47.826 0.00 0.00 38.14 3.86
4339 4686 6.254281 ACTTATGTGCACTTACCATGTTTC 57.746 37.500 19.41 0.00 0.00 2.78
4355 4702 7.170965 ACCATGTTTCATTGAACTCACTATCT 58.829 34.615 0.00 0.00 0.00 1.98
4379 4726 6.910536 ATGTCAGAAACGACTAATGGAATC 57.089 37.500 0.00 0.00 36.82 2.52
4381 4728 5.637810 TGTCAGAAACGACTAATGGAATCAC 59.362 40.000 0.00 0.00 36.82 3.06
4388 4735 6.525578 ACGACTAATGGAATCACTGAACTA 57.474 37.500 0.00 0.00 0.00 2.24
4529 4876 1.211457 GATGTCCCAAGTCTGAGGCAT 59.789 52.381 0.00 0.00 0.00 4.40
4573 4920 2.633967 TCATTGCCTTTTCATGCTTGGT 59.366 40.909 0.00 0.00 0.00 3.67
4719 5066 3.593096 TGACTATGTCTGCAGCAAGAAG 58.407 45.455 9.47 11.58 33.15 2.85
4816 5171 2.125952 TGTGCTGCACCGAGATCG 60.126 61.111 28.17 0.00 39.44 3.69
4824 5179 1.272490 TGCACCGAGATCGAGTTCTTT 59.728 47.619 3.31 0.00 43.02 2.52
4917 5272 2.919666 GCAATAACGTGCACTGGAAT 57.080 45.000 16.19 0.10 44.29 3.01
4918 5273 2.518949 GCAATAACGTGCACTGGAATG 58.481 47.619 16.19 9.57 44.29 2.67
4919 5274 2.731968 GCAATAACGTGCACTGGAATGG 60.732 50.000 16.19 0.00 44.29 3.16
4920 5275 2.746904 CAATAACGTGCACTGGAATGGA 59.253 45.455 16.19 0.00 0.00 3.41
4951 5306 4.895297 TCTTCTCCCTTCACTTGCATTTTT 59.105 37.500 0.00 0.00 0.00 1.94
5016 5371 4.399934 TGCATGCTTTCTAGATTGATTGCA 59.600 37.500 20.33 13.15 34.33 4.08
5098 5453 1.729586 AGCAACCAGTAGGAGGTCAA 58.270 50.000 0.00 0.00 38.76 3.18
5160 5515 5.069119 GGAAAACTGGTTGAAGAGAATTGGT 59.931 40.000 0.00 0.00 0.00 3.67
5194 5549 5.535030 AGGAAAACTGGTTGGAAAGTGATAC 59.465 40.000 0.00 0.00 0.00 2.24
5217 5572 5.296780 ACAAGCGAGAACAAGATTCAGAAAA 59.703 36.000 0.00 0.00 0.00 2.29
5222 5577 6.073765 GCGAGAACAAGATTCAGAAAACAGTA 60.074 38.462 0.00 0.00 0.00 2.74
5274 5629 3.330701 TGGGCAAAATCAGGAGTTCTAGT 59.669 43.478 0.00 0.00 0.00 2.57
5288 5643 4.270834 AGTTCTAGTGCGATACAAGAGGA 58.729 43.478 0.00 0.00 0.00 3.71
5349 5704 1.279846 CCCTAAGGCCTCGTTTGGTTA 59.720 52.381 5.23 0.00 0.00 2.85
5350 5705 2.290450 CCCTAAGGCCTCGTTTGGTTAA 60.290 50.000 5.23 0.00 0.00 2.01
5358 5715 2.224784 CCTCGTTTGGTTAAGGTTTCCG 59.775 50.000 0.00 0.00 0.00 4.30
5557 5914 2.573689 GCGAGAGACGACCGAACG 60.574 66.667 0.00 0.00 45.77 3.95
5582 5939 2.511600 GTCGGCCAAGATCCGGTG 60.512 66.667 2.24 0.00 46.43 4.94
5588 5945 2.438434 CAAGATCCGGTGCCCCAC 60.438 66.667 0.00 0.00 0.00 4.61
5628 5985 4.520846 CGCCGGCGACAGAAATGC 62.521 66.667 44.86 1.62 42.83 3.56
5629 5986 3.127533 GCCGGCGACAGAAATGCT 61.128 61.111 12.58 0.00 0.00 3.79
5630 5987 3.093278 CCGGCGACAGAAATGCTC 58.907 61.111 9.30 0.00 0.00 4.26
5631 5988 1.741401 CCGGCGACAGAAATGCTCA 60.741 57.895 9.30 0.00 0.00 4.26
5632 5989 1.699656 CCGGCGACAGAAATGCTCAG 61.700 60.000 9.30 0.00 0.00 3.35
5633 5990 1.699656 CGGCGACAGAAATGCTCAGG 61.700 60.000 0.00 0.00 0.00 3.86
5634 5991 0.391661 GGCGACAGAAATGCTCAGGA 60.392 55.000 0.00 0.00 0.00 3.86
5635 5992 1.661341 GCGACAGAAATGCTCAGGAT 58.339 50.000 0.00 0.00 0.00 3.24
5636 5993 1.596727 GCGACAGAAATGCTCAGGATC 59.403 52.381 0.00 0.00 0.00 3.36
5637 5994 2.208431 CGACAGAAATGCTCAGGATCC 58.792 52.381 2.48 2.48 0.00 3.36
5638 5995 2.419159 CGACAGAAATGCTCAGGATCCA 60.419 50.000 15.82 0.00 0.00 3.41
5652 6247 1.074167 ATCCAAGATCCGCCCCTCT 60.074 57.895 0.00 0.00 0.00 3.69
5655 6250 0.760945 CCAAGATCCGCCCCTCTAGT 60.761 60.000 0.00 0.00 0.00 2.57
5708 6303 2.012794 TCCCCGGATCTCTCCTCCA 61.013 63.158 0.73 0.00 39.65 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
205 209 3.615709 GGTTGTGGCTTGGGGTGC 61.616 66.667 0.00 0.00 0.00 5.01
211 215 1.876156 GAGACTTCTGGTTGTGGCTTG 59.124 52.381 0.00 0.00 0.00 4.01
251 255 2.047274 ATCTGTTGGTGCGACCGG 60.047 61.111 0.00 0.00 42.58 5.28
343 348 0.591170 CAAATGCGGTCGGACAAGTT 59.409 50.000 10.76 0.00 0.00 2.66
350 355 2.787249 CTGCTCAAATGCGGTCGG 59.213 61.111 0.00 0.00 34.82 4.79
383 388 3.734463 TCCGATGAGTTTACTGCAACAA 58.266 40.909 0.00 0.00 0.00 2.83
388 393 1.666189 GGCTTCCGATGAGTTTACTGC 59.334 52.381 0.00 0.00 0.00 4.40
451 456 7.153217 ACTACTTTGGAATTTTATGGGAACG 57.847 36.000 0.00 0.00 0.00 3.95
460 465 7.888546 AGCATGGTAGTACTACTTTGGAATTTT 59.111 33.333 27.71 5.77 36.36 1.82
462 467 6.958767 AGCATGGTAGTACTACTTTGGAATT 58.041 36.000 27.71 8.04 36.36 2.17
503 515 4.503910 TGATACATACAAGGTGTGAGCAC 58.496 43.478 0.01 0.00 44.53 4.40
539 557 6.666546 ACTAGTACTAAAACCTGCATAGTGGA 59.333 38.462 3.76 0.00 32.44 4.02
584 602 5.878669 AGTAATTTTTGGCTAGGTAGTTCCG 59.121 40.000 0.00 0.00 41.99 4.30
611 632 5.119694 AGAAAGATTTATGAGGAGGAACGC 58.880 41.667 0.00 0.00 0.00 4.84
613 634 7.929941 ACAAGAAAGATTTATGAGGAGGAAC 57.070 36.000 0.00 0.00 0.00 3.62
627 648 4.608948 AGGACAGACGAACAAGAAAGAT 57.391 40.909 0.00 0.00 0.00 2.40
690 711 2.031314 TCGCCGCTGCCTTGTTAA 59.969 55.556 0.00 0.00 0.00 2.01
765 787 1.003233 ACTGGAAGGGACAACCGATTC 59.997 52.381 0.00 0.00 46.96 2.52
766 788 1.064825 ACTGGAAGGGACAACCGATT 58.935 50.000 0.00 0.00 46.96 3.34
767 789 0.324943 CACTGGAAGGGACAACCGAT 59.675 55.000 0.00 0.00 43.23 4.18
768 790 1.052124 ACACTGGAAGGGACAACCGA 61.052 55.000 0.00 0.00 43.23 4.69
769 791 0.884704 CACACTGGAAGGGACAACCG 60.885 60.000 0.00 0.00 43.23 4.44
770 792 0.537371 CCACACTGGAAGGGACAACC 60.537 60.000 0.00 0.00 43.23 3.77
771 793 0.182775 ACCACACTGGAAGGGACAAC 59.817 55.000 0.00 0.00 43.23 3.32
772 794 0.182537 CACCACACTGGAAGGGACAA 59.817 55.000 0.00 0.00 43.23 3.18
773 795 1.705002 CCACCACACTGGAAGGGACA 61.705 60.000 0.00 0.00 43.23 4.02
774 796 1.073199 CCACCACACTGGAAGGGAC 59.927 63.158 0.00 0.00 43.23 4.46
775 797 2.829384 GCCACCACACTGGAAGGGA 61.829 63.158 0.00 0.00 43.23 4.20
777 799 0.400213 TTAGCCACCACACTGGAAGG 59.600 55.000 0.00 0.00 40.96 3.46
778 800 1.523758 GTTAGCCACCACACTGGAAG 58.476 55.000 0.00 0.00 40.96 3.46
779 801 0.109723 GGTTAGCCACCACACTGGAA 59.890 55.000 0.00 0.00 46.42 3.53
780 802 1.758592 GGTTAGCCACCACACTGGA 59.241 57.895 0.00 0.00 46.42 3.86
781 803 4.397348 GGTTAGCCACCACACTGG 57.603 61.111 0.00 0.00 46.42 4.00
788 810 2.038689 GCCTCTATTAGGGTTAGCCACC 59.961 54.545 2.44 0.00 46.65 4.61
789 811 2.038689 GGCCTCTATTAGGGTTAGCCAC 59.961 54.545 2.44 0.00 46.65 5.01
790 812 2.335933 GGCCTCTATTAGGGTTAGCCA 58.664 52.381 2.44 0.00 46.65 4.75
791 813 1.275573 CGGCCTCTATTAGGGTTAGCC 59.724 57.143 0.00 0.00 46.65 3.93
792 814 1.969208 ACGGCCTCTATTAGGGTTAGC 59.031 52.381 0.00 0.00 46.65 3.09
793 815 2.963782 ACACGGCCTCTATTAGGGTTAG 59.036 50.000 0.00 0.00 46.65 2.34
794 816 3.036452 ACACGGCCTCTATTAGGGTTA 57.964 47.619 0.00 0.00 46.65 2.85
795 817 1.875488 ACACGGCCTCTATTAGGGTT 58.125 50.000 0.00 0.00 46.65 4.11
796 818 1.485066 CAACACGGCCTCTATTAGGGT 59.515 52.381 0.00 0.00 46.65 4.34
797 819 1.202651 CCAACACGGCCTCTATTAGGG 60.203 57.143 0.00 0.00 46.65 3.53
799 821 2.981859 ACCAACACGGCCTCTATTAG 57.018 50.000 0.00 0.00 39.03 1.73
800 822 3.634504 TCTACCAACACGGCCTCTATTA 58.365 45.455 0.00 0.00 39.03 0.98
801 823 2.431057 CTCTACCAACACGGCCTCTATT 59.569 50.000 0.00 0.00 39.03 1.73
802 824 2.032620 CTCTACCAACACGGCCTCTAT 58.967 52.381 0.00 0.00 39.03 1.98
803 825 1.005097 TCTCTACCAACACGGCCTCTA 59.995 52.381 0.00 0.00 39.03 2.43
804 826 0.251653 TCTCTACCAACACGGCCTCT 60.252 55.000 0.00 0.00 39.03 3.69
805 827 0.108756 GTCTCTACCAACACGGCCTC 60.109 60.000 0.00 0.00 39.03 4.70
806 828 1.874345 CGTCTCTACCAACACGGCCT 61.874 60.000 0.00 0.00 39.03 5.19
807 829 1.445582 CGTCTCTACCAACACGGCC 60.446 63.158 0.00 0.00 39.03 6.13
808 830 1.007336 CACGTCTCTACCAACACGGC 61.007 60.000 0.00 0.00 39.03 5.68
809 831 1.007336 GCACGTCTCTACCAACACGG 61.007 60.000 0.00 0.00 42.50 4.94
810 832 0.318360 TGCACGTCTCTACCAACACG 60.318 55.000 0.00 0.00 38.24 4.49
811 833 2.080286 ATGCACGTCTCTACCAACAC 57.920 50.000 0.00 0.00 0.00 3.32
812 834 2.412870 CAATGCACGTCTCTACCAACA 58.587 47.619 0.00 0.00 0.00 3.33
813 835 1.128692 GCAATGCACGTCTCTACCAAC 59.871 52.381 0.00 0.00 0.00 3.77
814 836 1.270571 TGCAATGCACGTCTCTACCAA 60.271 47.619 2.72 0.00 31.71 3.67
815 837 0.320050 TGCAATGCACGTCTCTACCA 59.680 50.000 2.72 0.00 31.71 3.25
816 838 1.394917 CTTGCAATGCACGTCTCTACC 59.605 52.381 7.72 0.00 38.71 3.18
817 839 2.069273 ACTTGCAATGCACGTCTCTAC 58.931 47.619 11.71 0.00 36.28 2.59
818 840 2.068519 CACTTGCAATGCACGTCTCTA 58.931 47.619 14.56 0.00 38.94 2.43
819 841 0.870393 CACTTGCAATGCACGTCTCT 59.130 50.000 14.56 0.00 38.94 3.10
820 842 0.727122 GCACTTGCAATGCACGTCTC 60.727 55.000 14.56 6.18 38.94 3.36
821 843 1.283793 GCACTTGCAATGCACGTCT 59.716 52.632 14.56 0.00 38.94 4.18
822 844 3.832981 GCACTTGCAATGCACGTC 58.167 55.556 14.56 6.49 38.94 4.34
854 876 1.102978 ACAGCAGCTTCGTGGTTTTT 58.897 45.000 0.00 0.00 0.00 1.94
855 877 1.961793 TACAGCAGCTTCGTGGTTTT 58.038 45.000 0.00 0.00 0.00 2.43
856 878 1.961793 TTACAGCAGCTTCGTGGTTT 58.038 45.000 0.00 0.00 0.00 3.27
857 879 2.185004 ATTACAGCAGCTTCGTGGTT 57.815 45.000 0.00 0.00 0.00 3.67
858 880 2.893637 CTATTACAGCAGCTTCGTGGT 58.106 47.619 0.00 0.00 0.00 4.16
870 892 2.451132 CGACCACTCACGCTATTACAG 58.549 52.381 0.00 0.00 0.00 2.74
871 893 1.133598 CCGACCACTCACGCTATTACA 59.866 52.381 0.00 0.00 0.00 2.41
872 894 1.836383 CCGACCACTCACGCTATTAC 58.164 55.000 0.00 0.00 0.00 1.89
873 895 0.101759 GCCGACCACTCACGCTATTA 59.898 55.000 0.00 0.00 0.00 0.98
874 896 1.153628 GCCGACCACTCACGCTATT 60.154 57.895 0.00 0.00 0.00 1.73
875 897 2.348104 TGCCGACCACTCACGCTAT 61.348 57.895 0.00 0.00 0.00 2.97
1008 1030 2.354773 GACGGGATCGACGCCATC 60.355 66.667 8.28 2.14 40.11 3.51
1009 1031 2.833582 AGACGGGATCGACGCCAT 60.834 61.111 8.28 0.00 40.11 4.40
1140 1162 4.980805 GCAACTGCGGGGTCGTGA 62.981 66.667 0.00 0.00 38.89 4.35
1464 1486 4.409247 ACGTAGGCCTGGATAGATTTCTTT 59.591 41.667 17.99 0.00 0.00 2.52
1533 1555 4.083862 GCGTCAGGGGAGGTGACC 62.084 72.222 0.00 0.00 41.17 4.02
1557 1579 2.747460 GCAGCATGGAACTCCGCA 60.747 61.111 0.00 0.00 39.43 5.69
1689 1711 2.702592 AAACTTTGTCGACACCCTCA 57.297 45.000 19.90 0.00 0.00 3.86
1695 1717 4.560819 GCATCAACAAAAACTTTGTCGACA 59.439 37.500 15.76 15.76 0.00 4.35
1896 1918 0.962489 CACTCTCCATAGGTAGCCCG 59.038 60.000 0.00 0.00 35.12 6.13
2031 2053 2.141911 AGCATCCTCCCCATCTCAATT 58.858 47.619 0.00 0.00 0.00 2.32
2085 2107 3.346315 CATGCTTCCACACATTACTGGA 58.654 45.455 0.00 0.00 34.58 3.86
2258 2280 0.460311 CCCCGTCACTGGATCACTAC 59.540 60.000 0.00 0.00 0.00 2.73
2274 2296 4.163458 TGGTGTGAGATTCTTACATACCCC 59.837 45.833 13.65 10.65 42.35 4.95
2493 2515 6.306356 CGGTTTCTGCATCTTGAAAAAGTATG 59.694 38.462 0.86 0.00 34.52 2.39
2494 2516 6.381801 CGGTTTCTGCATCTTGAAAAAGTAT 58.618 36.000 0.86 0.00 34.52 2.12
2698 2720 7.436080 CAGCCATTTGCAGATAAATATTTTCGT 59.564 33.333 5.91 0.00 44.83 3.85
2795 2864 7.753309 AGTAGTATATCATCTCTTTGTCGCT 57.247 36.000 0.00 0.00 0.00 4.93
2890 2984 8.421784 CCTAGCAGGTATTGTTAATCTCAGTAA 58.578 37.037 0.00 0.00 0.00 2.24
3048 3142 2.593026 TGGGACTAAAGGCTTTGTTGG 58.407 47.619 22.32 11.54 0.00 3.77
3191 3285 7.168905 AGTCCGTAAAGAAAGATTTGAAGGAT 58.831 34.615 0.00 0.00 0.00 3.24
3420 3569 4.565564 GTCGTATCACCGTATTGCTCTTTT 59.434 41.667 0.00 0.00 0.00 2.27
3489 3638 6.737254 ATCCTTTCTGTAAACATGTTACGG 57.263 37.500 12.39 14.33 33.65 4.02
3502 3651 6.554605 TCCCAAATCTGAAAAATCCTTTCTGT 59.445 34.615 0.00 0.00 0.00 3.41
3564 3713 1.623811 GACTAACCCTGACTTCTGCCA 59.376 52.381 0.00 0.00 0.00 4.92
3683 3833 4.405680 CCGGGATATGCATATAACAGGAGA 59.594 45.833 23.79 0.00 0.00 3.71
3717 3867 3.561120 TTTCCTGATGGCGCCGGTT 62.561 57.895 23.90 9.31 0.00 4.44
3782 3932 6.857964 CACTCTTTAAACACAAGGTGCTAATG 59.142 38.462 0.00 0.00 36.98 1.90
3856 4006 2.238646 ACAAGTTCCCAGTGAGACACAA 59.761 45.455 4.75 0.00 36.74 3.33
3887 4115 6.264067 AGCAATAAGGTTATCCAGCATTTCTC 59.736 38.462 0.00 0.00 35.89 2.87
3939 4285 6.843069 AAAATCACATACAAACCTTGTTGC 57.157 33.333 0.00 0.00 42.22 4.17
3992 4338 6.366315 ACTTTTAAAGCGTGACACATGTAA 57.634 33.333 6.37 0.00 0.00 2.41
4105 4452 3.075884 GGAGTACCATTTTTACGGTGCA 58.924 45.455 0.00 0.00 40.06 4.57
4339 4686 9.591792 TTTCTGACATAGATAGTGAGTTCAATG 57.408 33.333 0.00 0.00 34.80 2.82
4355 4702 7.491372 GTGATTCCATTAGTCGTTTCTGACATA 59.509 37.037 0.00 0.00 41.41 2.29
4379 4726 5.422666 TTGCAGTGTCAATTAGTTCAGTG 57.577 39.130 0.00 0.00 35.24 3.66
4381 4728 5.344128 GCAATTGCAGTGTCAATTAGTTCAG 59.656 40.000 25.36 10.74 42.78 3.02
4388 4735 3.738830 ACAGCAATTGCAGTGTCAATT 57.261 38.095 30.89 15.42 44.77 2.32
4529 4876 1.003118 ACAGCGCCAAACATTCCTAGA 59.997 47.619 2.29 0.00 0.00 2.43
4573 4920 6.519679 AAATTTCAGCTGTGAGCATAATCA 57.480 33.333 14.67 0.00 45.56 2.57
4619 4966 6.849588 TCATCATTTACAGTGATCATTCGG 57.150 37.500 0.00 0.00 34.21 4.30
4675 5022 4.520179 TGGACAGGAAACATCAGATCATG 58.480 43.478 0.00 0.00 0.00 3.07
4719 5066 1.364626 CCACGTCATCAAGCCAGAGC 61.365 60.000 0.00 0.00 40.32 4.09
4809 5164 3.109619 GCTACCAAAGAACTCGATCTCG 58.890 50.000 0.00 0.00 41.45 4.04
4816 5171 0.036294 AGCGGGCTACCAAAGAACTC 60.036 55.000 0.00 0.00 36.13 3.01
4824 5179 2.589540 CCATTGAGCGGGCTACCA 59.410 61.111 0.00 0.00 36.13 3.25
4916 5271 5.429762 TGAAGGGAGAAGACATACATTCCAT 59.570 40.000 0.00 0.00 0.00 3.41
4917 5272 4.782691 TGAAGGGAGAAGACATACATTCCA 59.217 41.667 0.00 0.00 0.00 3.53
4918 5273 5.104735 AGTGAAGGGAGAAGACATACATTCC 60.105 44.000 0.00 0.00 0.00 3.01
4919 5274 5.983540 AGTGAAGGGAGAAGACATACATTC 58.016 41.667 0.00 0.00 0.00 2.67
4920 5275 6.176183 CAAGTGAAGGGAGAAGACATACATT 58.824 40.000 0.00 0.00 0.00 2.71
5016 5371 4.256920 GACACCAGCATTGTCTGTAATCT 58.743 43.478 5.39 0.00 40.30 2.40
5094 5449 9.593134 TCTCTTCTCTTATATGAAAAGCTTGAC 57.407 33.333 0.00 0.00 0.00 3.18
5160 5515 2.158726 ACCAGTTTTCCTTGCTAACCGA 60.159 45.455 0.00 0.00 0.00 4.69
5194 5549 4.997905 TTCTGAATCTTGTTCTCGCTTG 57.002 40.909 0.00 0.00 0.00 4.01
5217 5572 5.646577 AGCTCGAGTAAATTCAGTACTGT 57.353 39.130 21.99 5.87 31.88 3.55
5222 5577 3.447586 TGGCTAGCTCGAGTAAATTCAGT 59.552 43.478 15.72 0.00 0.00 3.41
5274 5629 4.755411 CCTTAGTTTCCTCTTGTATCGCA 58.245 43.478 0.00 0.00 0.00 5.10
5288 5643 2.091555 TGTTCCTGGTTGGCCTTAGTTT 60.092 45.455 3.32 0.00 35.26 2.66
5371 5728 3.540367 TTCGACCCGGGGAAACAGC 62.540 63.158 27.92 3.65 0.00 4.40
5409 5766 1.153086 CCAGCTCGATTTCCCTGGG 60.153 63.158 6.33 6.33 40.86 4.45
5459 5816 0.320374 TAAAGACGTGGGTCAGGCAG 59.680 55.000 0.00 0.00 45.92 4.85
5460 5817 0.034337 GTAAAGACGTGGGTCAGGCA 59.966 55.000 0.00 0.00 45.92 4.75
5461 5818 0.672711 GGTAAAGACGTGGGTCAGGC 60.673 60.000 0.00 0.00 45.92 4.85
5464 5821 0.032403 CGTGGTAAAGACGTGGGTCA 59.968 55.000 0.00 0.00 45.92 4.02
5624 5981 2.224475 CGGATCTTGGATCCTGAGCATT 60.224 50.000 20.06 0.00 36.07 3.56
5625 5982 1.347050 CGGATCTTGGATCCTGAGCAT 59.653 52.381 20.06 6.79 36.07 3.79
5626 5983 0.755079 CGGATCTTGGATCCTGAGCA 59.245 55.000 20.06 2.49 36.07 4.26
5627 5984 0.602372 GCGGATCTTGGATCCTGAGC 60.602 60.000 20.06 13.42 36.07 4.26
5628 5985 0.034616 GGCGGATCTTGGATCCTGAG 59.965 60.000 20.06 11.08 36.07 3.35
5629 5986 1.410850 GGGCGGATCTTGGATCCTGA 61.411 60.000 20.06 11.64 36.07 3.86
5630 5987 1.072159 GGGCGGATCTTGGATCCTG 59.928 63.158 20.06 15.30 36.07 3.86
5631 5988 2.150051 GGGGCGGATCTTGGATCCT 61.150 63.158 20.06 0.00 36.07 3.24
5632 5989 2.118233 GAGGGGCGGATCTTGGATCC 62.118 65.000 14.58 14.58 34.90 3.36
5633 5990 1.124477 AGAGGGGCGGATCTTGGATC 61.124 60.000 0.00 0.00 0.00 3.36
5634 5991 0.191064 TAGAGGGGCGGATCTTGGAT 59.809 55.000 0.00 0.00 0.00 3.41
5635 5992 0.470080 CTAGAGGGGCGGATCTTGGA 60.470 60.000 0.00 0.00 0.00 3.53
5636 5993 0.760945 ACTAGAGGGGCGGATCTTGG 60.761 60.000 0.00 0.00 0.00 3.61
5637 5994 0.390860 CACTAGAGGGGCGGATCTTG 59.609 60.000 0.00 0.00 0.00 3.02
5638 5995 0.261991 TCACTAGAGGGGCGGATCTT 59.738 55.000 0.00 0.00 0.00 2.40
5652 6247 2.652530 GGTCCGTTGCCGTCACTA 59.347 61.111 0.00 0.00 0.00 2.74
5708 6303 1.303888 TGTACCGGAGCTTCGAGGT 60.304 57.895 18.24 8.92 40.52 3.85


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

AutoCloner maintained by Alex Coulton.