Multiple sequence alignment - TraesCS1B01G116100

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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 TraesCS1B01G116100 chr1B 100.000 6125 0 0 1 6125 136653141 136647017 0.000000e+00 11311.0
1 TraesCS1B01G116100 chr1B 82.069 725 108 18 2 714 131797072 131797786 3.160000e-167 599.0
2 TraesCS1B01G116100 chr1D 94.137 3957 161 25 1411 5312 83728636 83724696 0.000000e+00 5956.0
3 TraesCS1B01G116100 chr1D 92.948 553 24 9 889 1426 83729227 83728675 0.000000e+00 791.0
4 TraesCS1B01G116100 chr1D 78.049 369 70 8 486 848 483355250 483355613 7.990000e-54 222.0
5 TraesCS1B01G116100 chr1D 83.436 163 14 6 5857 6018 83721952 83721802 8.280000e-29 139.0
6 TraesCS1B01G116100 chr1A 94.207 3470 113 37 881 4292 100297203 100293764 0.000000e+00 5214.0
7 TraesCS1B01G116100 chr1A 95.273 1227 56 2 4294 5520 100293503 100292279 0.000000e+00 1943.0
8 TraesCS1B01G116100 chr1A 88.978 499 42 5 5531 6018 100292238 100291742 6.790000e-169 604.0
9 TraesCS1B01G116100 chr2D 81.154 849 117 29 57 885 651369693 651370518 5.180000e-180 641.0
10 TraesCS1B01G116100 chr2D 75.306 490 82 25 419 885 494647626 494648099 1.350000e-46 198.0
11 TraesCS1B01G116100 chr2D 97.872 47 1 0 1684 1730 485075163 485075117 1.420000e-11 82.4
12 TraesCS1B01G116100 chr6D 79.002 862 135 36 2 833 316628728 316627883 1.160000e-151 547.0
13 TraesCS1B01G116100 chr3B 82.250 631 70 26 1275 1870 228501442 228502065 1.970000e-139 507.0
14 TraesCS1B01G116100 chr2B 79.494 751 119 29 4 738 19378451 19379182 9.170000e-138 501.0
15 TraesCS1B01G116100 chr2B 86.167 347 47 1 2 347 249238223 249237877 2.080000e-99 374.0
16 TraesCS1B01G116100 chr3A 82.403 591 65 25 1275 1829 644715830 644716417 4.290000e-131 479.0
17 TraesCS1B01G116100 chr7B 87.906 339 39 2 3 341 674077159 674077495 1.240000e-106 398.0
18 TraesCS1B01G116100 chr5D 76.023 855 152 37 2 824 542754308 542753475 1.600000e-105 394.0
19 TraesCS1B01G116100 chrUn 87.278 338 43 0 4 341 78904916 78905253 2.680000e-103 387.0
20 TraesCS1B01G116100 chrUn 78.209 335 59 14 456 782 78905360 78905688 1.040000e-47 202.0
21 TraesCS1B01G116100 chr7A 75.517 870 163 39 2 846 646971758 646970914 1.250000e-101 381.0
22 TraesCS1B01G116100 chr7D 78.657 417 66 20 419 823 21031658 21031253 7.880000e-64 255.0
23 TraesCS1B01G116100 chr6B 75.535 327 46 21 417 731 96349353 96349049 4.980000e-26 130.0
24 TraesCS1B01G116100 chr5B 92.683 41 2 1 524 564 372172399 372172360 2.380000e-04 58.4


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 TraesCS1B01G116100 chr1B 136647017 136653141 6124 True 11311.000000 11311 100.000000 1 6125 1 chr1B.!!$R1 6124
1 TraesCS1B01G116100 chr1B 131797072 131797786 714 False 599.000000 599 82.069000 2 714 1 chr1B.!!$F1 712
2 TraesCS1B01G116100 chr1D 83721802 83729227 7425 True 2295.333333 5956 90.173667 889 6018 3 chr1D.!!$R1 5129
3 TraesCS1B01G116100 chr1A 100291742 100297203 5461 True 2587.000000 5214 92.819333 881 6018 3 chr1A.!!$R1 5137
4 TraesCS1B01G116100 chr2D 651369693 651370518 825 False 641.000000 641 81.154000 57 885 1 chr2D.!!$F2 828
5 TraesCS1B01G116100 chr6D 316627883 316628728 845 True 547.000000 547 79.002000 2 833 1 chr6D.!!$R1 831
6 TraesCS1B01G116100 chr3B 228501442 228502065 623 False 507.000000 507 82.250000 1275 1870 1 chr3B.!!$F1 595
7 TraesCS1B01G116100 chr2B 19378451 19379182 731 False 501.000000 501 79.494000 4 738 1 chr2B.!!$F1 734
8 TraesCS1B01G116100 chr3A 644715830 644716417 587 False 479.000000 479 82.403000 1275 1829 1 chr3A.!!$F1 554
9 TraesCS1B01G116100 chr5D 542753475 542754308 833 True 394.000000 394 76.023000 2 824 1 chr5D.!!$R1 822
10 TraesCS1B01G116100 chrUn 78904916 78905688 772 False 294.500000 387 82.743500 4 782 2 chrUn.!!$F1 778
11 TraesCS1B01G116100 chr7A 646970914 646971758 844 True 381.000000 381 75.517000 2 846 1 chr7A.!!$R1 844

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
852 956 0.442699 CGCGGGCTCTAAAAACAGAC 59.557 55.000 0.00 0.00 0.00 3.51 F
1095 1208 0.306533 GCAACCGTGTCGTGAACAAT 59.693 50.000 0.00 0.00 40.31 2.71 F
1184 1297 0.748729 GTCCGTCGATCTGGTCCTCT 60.749 60.000 0.00 0.00 0.00 3.69 F
1974 2203 1.070758 GTCACCTGTCTTGCTGGAAGA 59.929 52.381 7.58 7.58 38.45 2.87 F
2811 3053 2.741145 CCTCCTAGACTGCTACTTGGT 58.259 52.381 0.00 0.00 33.40 3.67 F
4615 5149 0.105760 TGTTGGTGCCATCCCACTTT 60.106 50.000 0.00 0.00 36.03 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2811 3053 0.401356 TTGGCTGATGAGCTTCACCA 59.599 50.0 3.60 0.00 45.44 4.17 R
3042 3284 0.904394 TCTGGGGCTGCCAATTTTCC 60.904 55.0 22.05 11.67 0.00 3.13 R
3463 3706 2.031495 AGTTGCTTCCTGTAGGGTCT 57.969 50.0 0.00 0.00 36.25 3.85 R
3513 3756 1.251251 GCTCCAAGGACTTGCACATT 58.749 50.0 6.54 0.00 39.16 2.71 R
4635 5169 0.322456 TAACCAGGTGATGCTGTGCC 60.322 55.0 0.00 0.00 0.00 5.01 R
5526 6334 0.459489 TGCTTGAGGTTGTGGCAAAC 59.541 50.0 0.00 0.00 0.00 2.93 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
125 127 2.804167 CTTGCGTGGTTGTTGGCA 59.196 55.556 0.00 0.00 0.00 4.92
195 197 3.984241 CGATCTCGTCGTGGAAGC 58.016 61.111 0.00 0.00 45.19 3.86
285 289 3.185365 CGCGCATGTCTAACGGCA 61.185 61.111 8.75 0.00 0.00 5.69
341 345 2.295692 CTCATGTAGAGTGCAGCGC 58.704 57.895 0.00 0.00 39.62 5.92
344 348 3.391665 ATGTAGAGTGCAGCGCCCC 62.392 63.158 2.29 0.00 0.00 5.80
347 351 3.605749 TAGAGTGCAGCGCCCCAAC 62.606 63.158 2.29 0.00 0.00 3.77
373 429 1.224315 CCATCGGAGATTGGTGGCA 59.776 57.895 0.00 0.00 45.12 4.92
390 446 1.610327 CAGGGGGAGAGAGAGACGA 59.390 63.158 0.00 0.00 0.00 4.20
393 449 0.818938 GGGGGAGAGAGAGACGAAAC 59.181 60.000 0.00 0.00 0.00 2.78
400 456 4.736896 AGAGACGAAACGGGGCGC 62.737 66.667 0.00 0.00 0.00 6.53
422 478 1.673920 GGCGACGAGAGAAAGAGAGAT 59.326 52.381 0.00 0.00 0.00 2.75
427 483 4.668289 GACGAGAGAAAGAGAGATGGAAC 58.332 47.826 0.00 0.00 0.00 3.62
480 542 2.811317 GCGAGGAGAGTGCCAACG 60.811 66.667 0.00 0.00 34.72 4.10
481 543 2.962569 CGAGGAGAGTGCCAACGA 59.037 61.111 0.00 0.00 33.94 3.85
484 553 0.603569 GAGGAGAGTGCCAACGAGAA 59.396 55.000 0.00 0.00 0.00 2.87
510 580 2.561569 GCTTTTTATAGCCGCTGAGGA 58.438 47.619 2.16 0.00 45.00 3.71
573 653 2.438434 GCCTGGCCATTACTGCGT 60.438 61.111 5.51 0.00 0.00 5.24
574 654 2.046285 GCCTGGCCATTACTGCGTT 61.046 57.895 5.51 0.00 0.00 4.84
578 658 2.339556 GGCCATTACTGCGTTGCCA 61.340 57.895 0.00 0.00 38.73 4.92
579 659 1.583986 GCCATTACTGCGTTGCCAA 59.416 52.632 0.00 0.00 0.00 4.52
589 669 1.322538 GCGTTGCCAATGGGGAATCT 61.323 55.000 0.00 0.00 46.89 2.40
590 670 1.185315 CGTTGCCAATGGGGAATCTT 58.815 50.000 0.00 0.00 46.89 2.40
649 745 3.785499 GCGGGAAAACGAGGCGAC 61.785 66.667 0.00 0.00 35.47 5.19
658 758 4.225340 CGAGGCGACGAGGACGAG 62.225 72.222 0.00 0.00 42.66 4.18
683 783 4.736631 CGTGCGTCGCTGACTCGA 62.737 66.667 19.50 0.00 35.95 4.04
717 817 2.214690 GCTTTCGCGCTAAAAACGTTTT 59.785 40.909 20.26 20.26 0.00 2.43
800 904 3.131240 GGACCGAACCGATGAAAATTG 57.869 47.619 0.00 0.00 0.00 2.32
801 905 2.159435 GGACCGAACCGATGAAAATTGG 60.159 50.000 0.00 0.00 0.00 3.16
802 906 2.745281 GACCGAACCGATGAAAATTGGA 59.255 45.455 0.00 0.00 0.00 3.53
803 907 3.352648 ACCGAACCGATGAAAATTGGAT 58.647 40.909 0.00 0.00 0.00 3.41
804 908 3.761752 ACCGAACCGATGAAAATTGGATT 59.238 39.130 0.00 0.00 0.00 3.01
805 909 4.219725 ACCGAACCGATGAAAATTGGATTT 59.780 37.500 0.00 0.00 0.00 2.17
806 910 5.167845 CCGAACCGATGAAAATTGGATTTT 58.832 37.500 0.00 0.00 44.56 1.82
807 911 5.637387 CCGAACCGATGAAAATTGGATTTTT 59.363 36.000 0.00 0.00 42.15 1.94
808 912 6.400940 CCGAACCGATGAAAATTGGATTTTTG 60.401 38.462 0.00 0.00 42.15 2.44
809 913 6.364706 CGAACCGATGAAAATTGGATTTTTGA 59.635 34.615 0.00 0.00 42.15 2.69
810 914 7.095857 CGAACCGATGAAAATTGGATTTTTGAA 60.096 33.333 0.00 0.00 42.15 2.69
811 915 7.656707 ACCGATGAAAATTGGATTTTTGAAG 57.343 32.000 0.00 0.00 42.15 3.02
812 916 6.650390 ACCGATGAAAATTGGATTTTTGAAGG 59.350 34.615 0.00 5.55 42.15 3.46
813 917 6.402442 CCGATGAAAATTGGATTTTTGAAGGC 60.402 38.462 0.73 0.00 42.15 4.35
814 918 5.921004 TGAAAATTGGATTTTTGAAGGCG 57.079 34.783 0.73 0.00 42.15 5.52
815 919 5.363939 TGAAAATTGGATTTTTGAAGGCGT 58.636 33.333 0.73 0.00 42.15 5.68
816 920 5.236047 TGAAAATTGGATTTTTGAAGGCGTG 59.764 36.000 0.73 0.00 42.15 5.34
817 921 4.599047 AATTGGATTTTTGAAGGCGTGA 57.401 36.364 0.00 0.00 0.00 4.35
818 922 3.363341 TTGGATTTTTGAAGGCGTGAC 57.637 42.857 0.00 0.00 0.00 3.67
819 923 2.582052 TGGATTTTTGAAGGCGTGACT 58.418 42.857 0.00 0.00 0.00 3.41
820 924 3.745799 TGGATTTTTGAAGGCGTGACTA 58.254 40.909 0.00 0.00 0.00 2.59
821 925 3.751175 TGGATTTTTGAAGGCGTGACTAG 59.249 43.478 0.00 0.00 0.00 2.57
822 926 3.127030 GGATTTTTGAAGGCGTGACTAGG 59.873 47.826 0.00 0.00 0.00 3.02
823 927 1.519408 TTTTGAAGGCGTGACTAGGC 58.481 50.000 0.00 0.00 36.98 3.93
824 928 0.685097 TTTGAAGGCGTGACTAGGCT 59.315 50.000 0.00 0.00 46.93 4.58
849 953 3.259930 GCGCGGGCTCTAAAAACA 58.740 55.556 18.33 0.00 35.83 2.83
850 954 1.134694 GCGCGGGCTCTAAAAACAG 59.865 57.895 18.33 0.00 35.83 3.16
851 955 1.296056 GCGCGGGCTCTAAAAACAGA 61.296 55.000 18.33 0.00 35.83 3.41
852 956 0.442699 CGCGGGCTCTAAAAACAGAC 59.557 55.000 0.00 0.00 0.00 3.51
853 957 0.803117 GCGGGCTCTAAAAACAGACC 59.197 55.000 0.00 0.00 0.00 3.85
854 958 1.076332 CGGGCTCTAAAAACAGACCG 58.924 55.000 0.00 0.00 30.70 4.79
855 959 1.450025 GGGCTCTAAAAACAGACCGG 58.550 55.000 0.00 0.00 0.00 5.28
856 960 1.450025 GGCTCTAAAAACAGACCGGG 58.550 55.000 6.32 0.00 0.00 5.73
857 961 1.450025 GCTCTAAAAACAGACCGGGG 58.550 55.000 6.32 0.00 0.00 5.73
858 962 1.949079 GCTCTAAAAACAGACCGGGGG 60.949 57.143 6.32 0.00 0.00 5.40
859 963 1.626825 CTCTAAAAACAGACCGGGGGA 59.373 52.381 6.32 0.00 0.00 4.81
860 964 1.348696 TCTAAAAACAGACCGGGGGAC 59.651 52.381 6.32 0.00 0.00 4.46
861 965 1.350019 CTAAAAACAGACCGGGGGACT 59.650 52.381 6.32 0.00 0.00 3.85
865 969 2.347490 CAGACCGGGGGACTGTTG 59.653 66.667 6.32 0.00 39.80 3.33
866 970 2.928396 AGACCGGGGGACTGTTGG 60.928 66.667 6.32 0.00 33.66 3.77
867 971 4.029809 GACCGGGGGACTGTTGGG 62.030 72.222 6.32 0.00 33.66 4.12
1095 1208 0.306533 GCAACCGTGTCGTGAACAAT 59.693 50.000 0.00 0.00 40.31 2.71
1184 1297 0.748729 GTCCGTCGATCTGGTCCTCT 60.749 60.000 0.00 0.00 0.00 3.69
1206 1320 8.107729 CCTCTTACCCTTCTGTTTTTAGGTATT 58.892 37.037 0.00 0.00 30.34 1.89
1380 1494 7.175990 TGCTACCTCCTTTTTACACCTATTTTG 59.824 37.037 0.00 0.00 0.00 2.44
1383 1502 6.156519 CCTCCTTTTTACACCTATTTTGTGC 58.843 40.000 0.00 0.00 37.22 4.57
1392 1511 5.246307 ACACCTATTTTGTGCCTCTCTTAC 58.754 41.667 0.00 0.00 37.22 2.34
1428 1612 5.066893 TGCATCTGAACTGAAATGATTAGCC 59.933 40.000 0.00 0.00 0.00 3.93
1466 1650 6.299922 TGAAACAATACCATGTCTTGTACCA 58.700 36.000 5.52 4.75 32.99 3.25
1543 1734 8.483307 AAATTGTCTCAATGAATAATTGGTGC 57.517 30.769 0.00 0.00 45.00 5.01
1572 1788 7.134362 TGAGAGGAGATAGATCAAGCAAAAT 57.866 36.000 0.00 0.00 0.00 1.82
1770 1988 8.035984 TCACCATATATGAGTTTGTTGTCGTTA 58.964 33.333 14.54 0.00 0.00 3.18
1823 2043 4.162320 TCGTGGCATTAGATTTCTCCTTCT 59.838 41.667 0.00 0.00 0.00 2.85
1956 2185 1.268743 GCCATGCATAAGAAAGGCGTC 60.269 52.381 7.63 0.00 31.88 5.19
1974 2203 1.070758 GTCACCTGTCTTGCTGGAAGA 59.929 52.381 7.58 7.58 38.45 2.87
2025 2254 4.483950 CTTCCACCTCCTCAGATGGTATA 58.516 47.826 0.00 0.00 33.67 1.47
2087 2316 5.773575 TGGTAAGATGATCGACTAGCATTC 58.226 41.667 0.00 0.00 33.33 2.67
2099 2328 6.266323 TCGACTAGCATTCTGATACTTTGTC 58.734 40.000 0.00 0.00 0.00 3.18
2244 2481 6.511767 CGTGCTGTCATCCCATTTAAGTTATC 60.512 42.308 0.00 0.00 0.00 1.75
2331 2568 6.976934 ACCAATGGTTTCACTTTCATTAGT 57.023 33.333 0.00 0.00 27.29 2.24
2371 2611 3.308401 AGGCCTAATTTTAGCAATGGGG 58.692 45.455 1.29 0.00 0.00 4.96
2436 2676 6.016276 TCAGGCAAGGTTTGTAAGATTTCTTC 60.016 38.462 0.00 0.00 37.40 2.87
2553 2795 8.871125 TCTGACTGGATTAGAAGTTTAGACTTT 58.129 33.333 0.00 0.00 45.88 2.66
2811 3053 2.741145 CCTCCTAGACTGCTACTTGGT 58.259 52.381 0.00 0.00 33.40 3.67
3042 3284 3.452474 GAGAGATGTTGGACTGGATTCG 58.548 50.000 0.00 0.00 0.00 3.34
3461 3704 8.608317 GTCTTTGAAGCTACTTTATCATTCCTC 58.392 37.037 0.00 0.00 0.00 3.71
3463 3706 8.862325 TTTGAAGCTACTTTATCATTCCTCAA 57.138 30.769 0.00 0.00 0.00 3.02
3513 3756 4.728772 ACCTGACAATGAGGATTTTGACA 58.271 39.130 0.00 0.00 34.37 3.58
3634 3878 9.677567 TGTCTTGTTAGCTTTTCATAACAAATC 57.322 29.630 10.53 7.66 45.96 2.17
3681 3925 8.647143 TTTCAGTGATTCTTTTTCATTTGACC 57.353 30.769 0.00 0.00 0.00 4.02
3686 3930 8.960591 AGTGATTCTTTTTCATTTGACCGATAT 58.039 29.630 0.00 0.00 0.00 1.63
3687 3931 9.573133 GTGATTCTTTTTCATTTGACCGATATT 57.427 29.630 0.00 0.00 0.00 1.28
3908 4153 0.913924 TGATCATGCAGGGAAGCTCA 59.086 50.000 0.00 0.00 34.99 4.26
3948 4193 5.355350 AGGTATTACTGCATGCTTTCTTGTC 59.645 40.000 20.33 3.53 0.00 3.18
3990 4236 6.718522 TGATATCCGGTATCAGTTGTGTTA 57.281 37.500 17.50 0.00 43.25 2.41
4003 4249 4.067896 AGTTGTGTTAAGCCAGACATCAG 58.932 43.478 0.00 0.00 0.00 2.90
4116 4377 9.305110 GCAAACAGATGTTATTTTTCATTTTCG 57.695 29.630 0.00 0.00 37.25 3.46
4196 4465 4.161377 ACCACTTAAATGTTTTGCCACTGT 59.839 37.500 0.00 0.00 0.00 3.55
4243 4512 3.216800 GCATCCTCATGTGGCAAGAATA 58.783 45.455 9.02 0.00 31.86 1.75
4278 4547 9.605275 AGTACTATTTGTCGTCATACTACTACA 57.395 33.333 0.00 0.00 0.00 2.74
4354 4888 1.730501 TTCTCTTGCAGGCTCAATCG 58.269 50.000 0.00 0.00 0.00 3.34
4432 4966 2.070262 TGCAGTCTCACAATCTGACG 57.930 50.000 0.00 0.00 36.01 4.35
4529 5063 6.554334 TTTCGATTAAGAAAACTGGTGAGG 57.446 37.500 0.00 0.00 37.20 3.86
4587 5121 3.200605 TGTATTGGATCCAGTGCTCATGT 59.799 43.478 22.59 3.34 0.00 3.21
4589 5123 2.118313 TGGATCCAGTGCTCATGTTG 57.882 50.000 11.44 0.00 0.00 3.33
4604 5138 1.649664 TGTTGTGCAATTGTTGGTGC 58.350 45.000 7.40 0.00 41.29 5.01
4615 5149 0.105760 TGTTGGTGCCATCCCACTTT 60.106 50.000 0.00 0.00 36.03 2.66
4635 5169 6.651225 CACTTTTGTAACTCTTAGAGGAAGGG 59.349 42.308 14.24 5.23 41.98 3.95
4950 5484 3.372440 TCAGACAGTAGCTCAGATCCA 57.628 47.619 0.00 0.00 0.00 3.41
4951 5485 3.020274 TCAGACAGTAGCTCAGATCCAC 58.980 50.000 0.00 0.00 0.00 4.02
4955 5489 0.639392 AGTAGCTCAGATCCACCCCT 59.361 55.000 0.00 0.00 0.00 4.79
5112 5646 1.648720 CGTCAGGGTGTTTGCAGTG 59.351 57.895 0.00 0.00 0.00 3.66
5130 5664 4.499188 GCAGTGCGTGATACTTGAGGTATA 60.499 45.833 0.00 0.00 40.82 1.47
5199 5733 5.818887 TGTTGGCATGACATAGGCATATAT 58.181 37.500 0.00 0.00 40.17 0.86
5350 5900 0.311790 CTGGTGAATGCAGTGCGTTT 59.688 50.000 22.97 13.04 37.94 3.60
5435 6197 7.281774 ACAACTTTTGCTCCATGTATCATCTAG 59.718 37.037 0.00 0.00 0.00 2.43
5458 6266 9.478019 CTAGTCTGCAACAACTTTATATTTTCG 57.522 33.333 1.84 0.00 0.00 3.46
5504 6312 3.766545 AGCCATTCCAGCTGTTTTAAGA 58.233 40.909 13.81 0.00 39.69 2.10
5526 6334 2.575805 AGCTTTCAGGTTCTTCCAGG 57.424 50.000 0.00 0.00 39.02 4.45
5527 6335 1.777272 AGCTTTCAGGTTCTTCCAGGT 59.223 47.619 0.00 0.00 39.02 4.00
5528 6336 2.175715 AGCTTTCAGGTTCTTCCAGGTT 59.824 45.455 0.00 0.00 39.02 3.50
5537 6375 1.398692 TCTTCCAGGTTTGCCACAAC 58.601 50.000 0.00 0.00 37.19 3.32
5543 6381 1.067516 CAGGTTTGCCACAACCTCAAG 59.932 52.381 8.72 0.00 45.80 3.02
5555 6393 2.880890 CAACCTCAAGCAGCACTAGTTT 59.119 45.455 0.00 0.00 0.00 2.66
5580 6418 5.840693 TCTAGGAATAGGATGCATGAAGTGA 59.159 40.000 2.46 0.00 0.00 3.41
5594 6432 6.642683 CATGAAGTGAATCAGGCAATTTTC 57.357 37.500 0.00 0.00 31.76 2.29
5624 6472 2.828877 TCGACAAAATGTCCGACACTT 58.171 42.857 2.57 0.00 44.20 3.16
5638 6486 5.515626 GTCCGACACTTGAACTGTATATGAC 59.484 44.000 0.00 0.00 0.00 3.06
5640 6488 6.042777 CCGACACTTGAACTGTATATGACAT 58.957 40.000 0.00 0.00 37.45 3.06
5672 6520 4.709397 TCGGGCAATTTTAGTGATGGAATT 59.291 37.500 0.00 0.00 0.00 2.17
5725 6573 2.361757 CTGGACTCCTGACAGCATCTAG 59.638 54.545 0.00 0.00 0.00 2.43
5762 6610 4.803098 TTGCTTCACTAGTACTCCTTCC 57.197 45.455 0.00 0.00 0.00 3.46
5774 6622 8.681806 ACTAGTACTCCTTCCGTTTCTAAATAC 58.318 37.037 0.00 0.00 0.00 1.89
5780 6628 8.101419 ACTCCTTCCGTTTCTAAATACTTGAAT 58.899 33.333 0.00 0.00 0.00 2.57
5932 8791 4.644685 TCCATGCTTTTATTGTTCCCTAGC 59.355 41.667 0.00 0.00 0.00 3.42
5938 8797 5.730568 GCTTTTATTGTTCCCTAGCATGTCG 60.731 44.000 0.00 0.00 0.00 4.35
5943 8802 1.207329 GTTCCCTAGCATGTCGAAGGT 59.793 52.381 0.00 0.00 0.00 3.50
5946 8805 2.092049 TCCCTAGCATGTCGAAGGTAGA 60.092 50.000 16.81 0.00 37.89 2.59
5984 8843 9.587772 CACACTACATAATAGGCCATCTAATAC 57.412 37.037 5.01 0.00 0.00 1.89
6011 8870 8.446599 AAAAAGTAGCTTTGCTTCACTAGTAA 57.553 30.769 0.00 0.00 40.44 2.24
6018 8877 8.622948 AGCTTTGCTTCACTAGTAATTTACTT 57.377 30.769 14.00 0.00 36.41 2.24
6019 8878 9.067986 AGCTTTGCTTCACTAGTAATTTACTTT 57.932 29.630 14.00 0.17 36.41 2.66
6020 8879 9.678941 GCTTTGCTTCACTAGTAATTTACTTTT 57.321 29.630 14.00 0.00 40.14 2.27
6043 8902 6.952773 TTTTTGCCTGTGTTCACTAGTAAT 57.047 33.333 0.00 0.00 0.00 1.89
6044 8903 6.952773 TTTTGCCTGTGTTCACTAGTAATT 57.047 33.333 0.00 0.00 0.00 1.40
6045 8904 6.952773 TTTGCCTGTGTTCACTAGTAATTT 57.047 33.333 0.00 0.00 0.00 1.82
6046 8905 8.453238 TTTTGCCTGTGTTCACTAGTAATTTA 57.547 30.769 0.00 0.00 0.00 1.40
6047 8906 7.429636 TTGCCTGTGTTCACTAGTAATTTAC 57.570 36.000 0.00 0.00 0.00 2.01
6048 8907 6.765403 TGCCTGTGTTCACTAGTAATTTACT 58.235 36.000 13.36 13.36 42.68 2.24
6049 8908 6.649141 TGCCTGTGTTCACTAGTAATTTACTG 59.351 38.462 17.47 10.60 39.81 2.74
6050 8909 6.649557 GCCTGTGTTCACTAGTAATTTACTGT 59.350 38.462 17.47 11.12 39.81 3.55
6051 8910 7.816031 GCCTGTGTTCACTAGTAATTTACTGTA 59.184 37.037 17.47 0.00 39.81 2.74
6052 8911 9.136952 CCTGTGTTCACTAGTAATTTACTGTAC 57.863 37.037 17.47 7.82 39.81 2.90
6053 8912 9.687210 CTGTGTTCACTAGTAATTTACTGTACA 57.313 33.333 17.47 9.89 39.81 2.90
6075 8934 9.916397 GTACATAACATTACATAGTTTGAGTGC 57.084 33.333 0.00 0.00 0.00 4.40
6076 8935 8.560355 ACATAACATTACATAGTTTGAGTGCA 57.440 30.769 0.00 0.00 0.00 4.57
6077 8936 8.450964 ACATAACATTACATAGTTTGAGTGCAC 58.549 33.333 9.40 9.40 0.00 4.57
6078 8937 6.875948 AACATTACATAGTTTGAGTGCACA 57.124 33.333 21.04 0.00 0.00 4.57
6079 8938 6.875948 ACATTACATAGTTTGAGTGCACAA 57.124 33.333 21.04 3.51 0.00 3.33
6080 8939 6.668323 ACATTACATAGTTTGAGTGCACAAC 58.332 36.000 21.04 14.68 0.00 3.32
6081 8940 6.262049 ACATTACATAGTTTGAGTGCACAACA 59.738 34.615 21.04 15.68 0.00 3.33
6082 8941 6.685527 TTACATAGTTTGAGTGCACAACAA 57.314 33.333 21.04 20.46 0.00 2.83
6083 8942 5.173774 ACATAGTTTGAGTGCACAACAAG 57.826 39.130 21.04 13.64 0.00 3.16
6084 8943 4.640201 ACATAGTTTGAGTGCACAACAAGT 59.360 37.500 21.04 16.16 0.00 3.16
6085 8944 5.125417 ACATAGTTTGAGTGCACAACAAGTT 59.875 36.000 21.04 16.46 0.00 2.66
6086 8945 4.519540 AGTTTGAGTGCACAACAAGTTT 57.480 36.364 21.04 10.64 0.00 2.66
6087 8946 4.485163 AGTTTGAGTGCACAACAAGTTTC 58.515 39.130 21.04 14.26 0.00 2.78
6088 8947 4.022416 AGTTTGAGTGCACAACAAGTTTCA 60.022 37.500 21.04 8.37 0.00 2.69
6089 8948 4.511617 TTGAGTGCACAACAAGTTTCAA 57.488 36.364 21.04 14.11 0.00 2.69
6090 8949 3.832276 TGAGTGCACAACAAGTTTCAAC 58.168 40.909 21.04 0.00 0.00 3.18
6091 8950 3.254411 TGAGTGCACAACAAGTTTCAACA 59.746 39.130 21.04 0.00 0.00 3.33
6092 8951 4.082300 TGAGTGCACAACAAGTTTCAACAT 60.082 37.500 21.04 0.00 0.00 2.71
6093 8952 5.124617 TGAGTGCACAACAAGTTTCAACATA 59.875 36.000 21.04 0.00 0.00 2.29
6094 8953 5.960113 AGTGCACAACAAGTTTCAACATAA 58.040 33.333 21.04 0.00 0.00 1.90
6095 8954 6.393990 AGTGCACAACAAGTTTCAACATAAA 58.606 32.000 21.04 0.00 0.00 1.40
6096 8955 6.310224 AGTGCACAACAAGTTTCAACATAAAC 59.690 34.615 21.04 0.00 39.22 2.01
6097 8956 5.578727 TGCACAACAAGTTTCAACATAAACC 59.421 36.000 0.00 0.00 39.66 3.27
6098 8957 5.006261 GCACAACAAGTTTCAACATAAACCC 59.994 40.000 0.00 0.00 39.66 4.11
6099 8958 5.522097 CACAACAAGTTTCAACATAAACCCC 59.478 40.000 0.00 0.00 39.66 4.95
6100 8959 5.423931 ACAACAAGTTTCAACATAAACCCCT 59.576 36.000 0.00 0.00 39.66 4.79
6101 8960 5.784578 ACAAGTTTCAACATAAACCCCTC 57.215 39.130 0.00 0.00 39.66 4.30
6102 8961 4.587262 ACAAGTTTCAACATAAACCCCTCC 59.413 41.667 0.00 0.00 39.66 4.30
6103 8962 4.463050 AGTTTCAACATAAACCCCTCCA 57.537 40.909 0.00 0.00 39.66 3.86
6104 8963 4.810345 AGTTTCAACATAAACCCCTCCAA 58.190 39.130 0.00 0.00 39.66 3.53
6105 8964 5.212745 AGTTTCAACATAAACCCCTCCAAA 58.787 37.500 0.00 0.00 39.66 3.28
6106 8965 5.663556 AGTTTCAACATAAACCCCTCCAAAA 59.336 36.000 0.00 0.00 39.66 2.44
6107 8966 6.157123 AGTTTCAACATAAACCCCTCCAAAAA 59.843 34.615 0.00 0.00 39.66 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 54 3.164977 TCGCCTCCACCAACCACA 61.165 61.111 0.00 0.00 0.00 4.17
55 57 1.966451 CAACTCGCCTCCACCAACC 60.966 63.158 0.00 0.00 0.00 3.77
245 249 1.307084 GGGGAGGTGGAGGCTTAGT 60.307 63.158 0.00 0.00 0.00 2.24
280 284 4.011517 CCAACTACCCGGTGCCGT 62.012 66.667 9.90 0.00 37.81 5.68
285 289 3.387947 CGAGGCCAACTACCCGGT 61.388 66.667 5.01 0.00 0.00 5.28
341 345 1.382522 CGATGGATGAACTGTTGGGG 58.617 55.000 0.00 0.00 0.00 4.96
344 348 3.251479 TCTCCGATGGATGAACTGTTG 57.749 47.619 0.00 0.00 0.00 3.33
347 351 3.136763 CCAATCTCCGATGGATGAACTG 58.863 50.000 0.00 0.00 39.12 3.16
348 352 2.774234 ACCAATCTCCGATGGATGAACT 59.226 45.455 0.00 0.00 39.12 3.01
373 429 0.705253 TTTCGTCTCTCTCTCCCCCT 59.295 55.000 0.00 0.00 0.00 4.79
400 456 1.226435 CTCTTTCTCTCGTCGCCGG 60.226 63.158 0.00 0.00 33.95 6.13
414 470 1.908483 GCCCCGTTCCATCTCTCTT 59.092 57.895 0.00 0.00 0.00 2.85
415 471 2.427245 CGCCCCGTTCCATCTCTCT 61.427 63.158 0.00 0.00 0.00 3.10
476 538 0.954452 AAAAGCCAGCCTTCTCGTTG 59.046 50.000 0.00 0.00 31.99 4.10
477 539 1.692411 AAAAAGCCAGCCTTCTCGTT 58.308 45.000 0.00 0.00 31.99 3.85
478 540 2.561478 TAAAAAGCCAGCCTTCTCGT 57.439 45.000 0.00 0.00 31.99 4.18
480 542 4.560136 GCTATAAAAAGCCAGCCTTCTC 57.440 45.455 0.00 0.00 36.45 2.87
509 579 1.275657 CACACACGTTTGTCGCCTC 59.724 57.895 3.93 0.00 44.19 4.70
510 580 0.179105 TACACACACGTTTGTCGCCT 60.179 50.000 3.93 0.00 44.19 5.52
515 588 1.077645 ACGCGTACACACACGTTTGT 61.078 50.000 11.67 0.44 40.34 2.83
518 591 2.232296 CCACGCGTACACACACGTT 61.232 57.895 13.44 0.00 40.34 3.99
559 639 2.339556 GGCAACGCAGTAATGGCCA 61.340 57.895 8.56 8.56 45.00 5.36
573 653 2.387757 GCTAAGATTCCCCATTGGCAA 58.612 47.619 0.68 0.68 31.48 4.52
574 654 1.750332 CGCTAAGATTCCCCATTGGCA 60.750 52.381 0.00 0.00 31.48 4.92
578 658 2.158608 CCTTCCGCTAAGATTCCCCATT 60.159 50.000 0.00 0.00 37.38 3.16
579 659 1.421646 CCTTCCGCTAAGATTCCCCAT 59.578 52.381 0.00 0.00 37.38 4.00
649 745 2.638154 GGCGTATCCTCGTCCTCG 59.362 66.667 0.00 0.00 38.55 4.63
706 806 2.357323 GGTGTCGGGGAAAACGTTTTTA 59.643 45.455 25.86 8.32 0.00 1.52
741 843 4.322385 AAAGCAAACCCGCGCGTC 62.322 61.111 29.95 9.94 36.85 5.19
744 846 3.281359 ATCCAAAGCAAACCCGCGC 62.281 57.895 0.00 0.00 36.85 6.86
745 847 1.154035 GATCCAAAGCAAACCCGCG 60.154 57.895 0.00 0.00 36.85 6.46
746 848 1.215382 GGATCCAAAGCAAACCCGC 59.785 57.895 6.95 0.00 0.00 6.13
792 896 5.236047 CACGCCTTCAAAAATCCAATTTTCA 59.764 36.000 0.00 0.00 41.30 2.69
798 902 2.955660 AGTCACGCCTTCAAAAATCCAA 59.044 40.909 0.00 0.00 0.00 3.53
799 903 2.582052 AGTCACGCCTTCAAAAATCCA 58.418 42.857 0.00 0.00 0.00 3.41
800 904 3.127030 CCTAGTCACGCCTTCAAAAATCC 59.873 47.826 0.00 0.00 0.00 3.01
801 905 3.426292 GCCTAGTCACGCCTTCAAAAATC 60.426 47.826 0.00 0.00 0.00 2.17
802 906 2.488153 GCCTAGTCACGCCTTCAAAAAT 59.512 45.455 0.00 0.00 0.00 1.82
803 907 1.877443 GCCTAGTCACGCCTTCAAAAA 59.123 47.619 0.00 0.00 0.00 1.94
804 908 1.071699 AGCCTAGTCACGCCTTCAAAA 59.928 47.619 0.00 0.00 0.00 2.44
805 909 0.685097 AGCCTAGTCACGCCTTCAAA 59.315 50.000 0.00 0.00 0.00 2.69
806 910 0.685097 AAGCCTAGTCACGCCTTCAA 59.315 50.000 0.00 0.00 0.00 2.69
807 911 0.685097 AAAGCCTAGTCACGCCTTCA 59.315 50.000 0.00 0.00 0.00 3.02
808 912 1.809684 AAAAGCCTAGTCACGCCTTC 58.190 50.000 0.00 0.00 0.00 3.46
809 913 2.271944 AAAAAGCCTAGTCACGCCTT 57.728 45.000 0.00 0.00 0.00 4.35
832 936 1.134694 CTGTTTTTAGAGCCCGCGC 59.865 57.895 0.00 0.00 0.00 6.86
833 937 0.442699 GTCTGTTTTTAGAGCCCGCG 59.557 55.000 0.00 0.00 0.00 6.46
834 938 0.803117 GGTCTGTTTTTAGAGCCCGC 59.197 55.000 0.00 0.00 38.83 6.13
835 939 1.076332 CGGTCTGTTTTTAGAGCCCG 58.924 55.000 0.00 0.00 41.03 6.13
836 940 1.450025 CCGGTCTGTTTTTAGAGCCC 58.550 55.000 0.00 0.00 41.03 5.19
837 941 1.450025 CCCGGTCTGTTTTTAGAGCC 58.550 55.000 0.00 0.00 41.03 4.70
838 942 1.450025 CCCCGGTCTGTTTTTAGAGC 58.550 55.000 0.00 0.00 40.77 4.09
839 943 1.626825 TCCCCCGGTCTGTTTTTAGAG 59.373 52.381 0.00 0.00 0.00 2.43
840 944 1.348696 GTCCCCCGGTCTGTTTTTAGA 59.651 52.381 0.00 0.00 0.00 2.10
841 945 1.350019 AGTCCCCCGGTCTGTTTTTAG 59.650 52.381 0.00 0.00 0.00 1.85
842 946 1.072648 CAGTCCCCCGGTCTGTTTTTA 59.927 52.381 0.00 0.00 34.92 1.52
843 947 0.179001 CAGTCCCCCGGTCTGTTTTT 60.179 55.000 0.00 0.00 34.92 1.94
844 948 1.350310 ACAGTCCCCCGGTCTGTTTT 61.350 55.000 0.00 0.00 46.50 2.43
845 949 1.768888 ACAGTCCCCCGGTCTGTTT 60.769 57.895 0.00 0.00 46.50 2.83
846 950 2.122547 ACAGTCCCCCGGTCTGTT 60.123 61.111 0.00 0.00 46.50 3.16
848 952 2.347490 CAACAGTCCCCCGGTCTG 59.653 66.667 0.00 6.19 42.80 3.51
849 953 2.928396 CCAACAGTCCCCCGGTCT 60.928 66.667 0.00 0.00 0.00 3.85
850 954 4.029809 CCCAACAGTCCCCCGGTC 62.030 72.222 0.00 0.00 0.00 4.79
874 978 2.476854 GCCACGCTAAAAGCATCTCTTG 60.477 50.000 0.00 0.00 42.58 3.02
875 979 1.740025 GCCACGCTAAAAGCATCTCTT 59.260 47.619 0.00 0.00 42.58 2.85
876 980 1.065854 AGCCACGCTAAAAGCATCTCT 60.066 47.619 0.00 0.00 42.58 3.10
877 981 1.063174 CAGCCACGCTAAAAGCATCTC 59.937 52.381 0.00 0.00 42.58 2.75
878 982 1.089920 CAGCCACGCTAAAAGCATCT 58.910 50.000 0.00 0.00 42.58 2.90
879 983 1.063174 CTCAGCCACGCTAAAAGCATC 59.937 52.381 0.00 0.00 42.58 3.91
880 984 1.089920 CTCAGCCACGCTAAAAGCAT 58.910 50.000 0.00 0.00 42.58 3.79
881 985 1.577328 GCTCAGCCACGCTAAAAGCA 61.577 55.000 0.00 0.00 42.58 3.91
882 986 1.135523 GCTCAGCCACGCTAAAAGC 59.864 57.895 0.00 0.00 36.40 3.51
1184 1297 7.392393 GCAGAATACCTAAAAACAGAAGGGTAA 59.608 37.037 0.00 0.00 34.52 2.85
1206 1320 5.591099 GGATCAAACAAAGAAAACAGCAGA 58.409 37.500 0.00 0.00 0.00 4.26
1380 1494 4.221041 ACAGGAAACTAGTAAGAGAGGCAC 59.779 45.833 0.00 0.00 40.21 5.01
1383 1502 5.172205 GCAACAGGAAACTAGTAAGAGAGG 58.828 45.833 0.00 0.00 40.21 3.69
1392 1511 4.999950 AGTTCAGATGCAACAGGAAACTAG 59.000 41.667 0.00 0.00 40.21 2.57
1428 1612 6.369065 GGTATTGTTTCAGACTGGTTACTCTG 59.631 42.308 1.81 0.00 36.07 3.35
1478 1662 4.503741 TTTACCTCAAAATGCAGCTCAC 57.496 40.909 0.00 0.00 0.00 3.51
1543 1734 5.562696 GCTTGATCTATCTCCTCTCAAGTCG 60.563 48.000 11.06 0.00 42.92 4.18
1756 1974 5.365619 ACAGAATCCTAACGACAACAAACT 58.634 37.500 0.00 0.00 0.00 2.66
1823 2043 3.748083 AGCAAGCACATGAGAAGAAGAA 58.252 40.909 0.00 0.00 0.00 2.52
1874 2103 9.979578 ACATAAACAGCAAAATCAATCAACTTA 57.020 25.926 0.00 0.00 0.00 2.24
1956 2185 2.260844 TTCTTCCAGCAAGACAGGTG 57.739 50.000 0.00 0.00 41.13 4.00
1974 2203 3.583228 TGATACCCTATCCGACACCATT 58.417 45.455 0.00 0.00 34.26 3.16
2025 2254 3.837731 CCACCATTTCCCAAATAACCACT 59.162 43.478 0.00 0.00 0.00 4.00
2063 2292 5.991933 ATGCTAGTCGATCATCTTACCAT 57.008 39.130 0.00 0.00 0.00 3.55
2087 2316 3.133003 AGGATCCGTGGACAAAGTATCAG 59.867 47.826 5.98 0.00 0.00 2.90
2099 2328 2.693591 TCACTAAGCTTAGGATCCGTGG 59.306 50.000 31.67 13.68 35.08 4.94
2217 2454 1.647545 AAATGGGATGACAGCACGCG 61.648 55.000 3.53 3.53 0.00 6.01
2244 2481 0.595095 GCCTGCAGAAGTGAAACCAG 59.405 55.000 17.39 0.00 37.80 4.00
2331 2568 2.203280 CCTGTTCCGGCAACACCA 60.203 61.111 13.34 0.00 40.29 4.17
2371 2611 5.825593 TGTGGACCTTATGATCTAATCCC 57.174 43.478 0.00 0.00 0.00 3.85
2436 2676 5.615289 AGCAGGTATAGCAATGGAAGTAAG 58.385 41.667 4.48 0.00 0.00 2.34
2493 2735 5.438761 GTTCACAGGCTTTAATGAACTGT 57.561 39.130 17.22 10.18 44.83 3.55
2553 2795 3.006430 TGCTCGTCATCACAGGTAAAGAA 59.994 43.478 0.00 0.00 0.00 2.52
2811 3053 0.401356 TTGGCTGATGAGCTTCACCA 59.599 50.000 3.60 0.00 45.44 4.17
2892 3134 3.694072 TCACTGAATTTATCCAAAGGCCG 59.306 43.478 0.00 0.00 0.00 6.13
2982 3224 3.131577 CACCATAGCCATGTGCAAGAATT 59.868 43.478 8.58 0.00 44.83 2.17
3042 3284 0.904394 TCTGGGGCTGCCAATTTTCC 60.904 55.000 22.05 11.67 0.00 3.13
3461 3704 2.039084 AGTTGCTTCCTGTAGGGTCTTG 59.961 50.000 0.00 0.00 36.25 3.02
3463 3706 2.031495 AGTTGCTTCCTGTAGGGTCT 57.969 50.000 0.00 0.00 36.25 3.85
3513 3756 1.251251 GCTCCAAGGACTTGCACATT 58.749 50.000 6.54 0.00 39.16 2.71
3948 4193 9.438291 GGATATCATACAAAAATTTCAGTCACG 57.562 33.333 4.83 0.00 0.00 4.35
3990 4236 1.681166 GGTGATGCTGATGTCTGGCTT 60.681 52.381 0.00 0.00 0.00 4.35
4003 4249 4.823442 TGAGGTAAATGATCATGGTGATGC 59.177 41.667 9.46 0.00 37.20 3.91
4116 4377 9.962783 ATACTATGTATCCGTTCAAGTTTCTAC 57.037 33.333 0.00 0.00 0.00 2.59
4129 4390 3.861840 CCCCAGCAATACTATGTATCCG 58.138 50.000 0.00 0.00 0.00 4.18
4196 4465 6.653320 ACAGATACAAAACTATTTTCCTGCGA 59.347 34.615 0.00 0.00 0.00 5.10
4309 4843 5.799827 AGTATCATTCAGAACTCCCTAGC 57.200 43.478 0.00 0.00 0.00 3.42
4408 4942 0.445436 GATTGTGAGACTGCAAGCGG 59.555 55.000 0.00 0.00 37.60 5.52
4432 4966 6.089417 CAGAAGAAAATTCCATTTGCGTAACC 59.911 38.462 0.00 0.00 32.86 2.85
4438 4972 7.515643 CATTGTCAGAAGAAAATTCCATTTGC 58.484 34.615 0.00 0.00 28.97 3.68
4587 5121 0.538584 TGGCACCAACAATTGCACAA 59.461 45.000 5.05 0.00 40.75 3.33
4589 5123 1.431496 GATGGCACCAACAATTGCAC 58.569 50.000 5.05 0.00 40.75 4.57
4604 5138 6.472887 TCTAAGAGTTACAAAAGTGGGATGG 58.527 40.000 0.00 0.00 0.00 3.51
4615 5149 3.518303 GCCCCTTCCTCTAAGAGTTACAA 59.482 47.826 0.00 0.00 37.38 2.41
4635 5169 0.322456 TAACCAGGTGATGCTGTGCC 60.322 55.000 0.00 0.00 0.00 5.01
4955 5489 3.375472 ATGCATGCGACGCTGAGGA 62.375 57.895 22.08 12.02 0.00 3.71
4983 5517 3.005554 CACATGACACAACAGAGGATCC 58.994 50.000 2.48 2.48 33.66 3.36
5064 5598 0.392193 ATCCACAAGAAGCCAGCTCG 60.392 55.000 0.00 0.00 0.00 5.03
5112 5646 6.330278 TGCATATATACCTCAAGTATCACGC 58.670 40.000 0.00 0.00 40.96 5.34
5130 5664 3.925379 TCAGAGTCACAACGTTGCATAT 58.075 40.909 27.61 11.98 0.00 1.78
5199 5733 9.268282 AGGATTTTAGTCCACTAAATCTAGACA 57.732 33.333 11.77 0.00 44.88 3.41
5212 5746 3.330701 AGAACTGCCAGGATTTTAGTCCA 59.669 43.478 0.00 0.00 40.90 4.02
5300 5836 4.883585 AGGTGTACATCATTGCAATACAGG 59.116 41.667 12.53 6.15 0.00 4.00
5367 5917 5.560724 TGTGCCAGTCTTAGAGCTTAAAAT 58.439 37.500 0.00 0.00 0.00 1.82
5435 6197 8.627428 GTTCGAAAATATAAAGTTGTTGCAGAC 58.373 33.333 0.00 0.00 0.00 3.51
5469 6277 4.592778 TGGAATGGCTGTATATAGCTGTCA 59.407 41.667 19.40 10.62 43.22 3.58
5502 6310 3.392616 TGGAAGAACCTGAAAGCTTCTCT 59.607 43.478 0.00 0.00 37.49 3.10
5504 6312 3.497584 CCTGGAAGAACCTGAAAGCTTCT 60.498 47.826 0.00 0.00 39.52 2.85
5520 6328 2.510664 GGTTGTGGCAAACCTGGAA 58.489 52.632 18.38 0.00 45.25 3.53
5521 6329 4.268720 GGTTGTGGCAAACCTGGA 57.731 55.556 18.38 0.00 45.25 3.86
5526 6334 0.459489 TGCTTGAGGTTGTGGCAAAC 59.541 50.000 0.00 0.00 0.00 2.93
5527 6335 0.746063 CTGCTTGAGGTTGTGGCAAA 59.254 50.000 0.00 0.00 32.43 3.68
5528 6336 1.737355 GCTGCTTGAGGTTGTGGCAA 61.737 55.000 0.00 0.00 32.43 4.52
5537 6375 3.406764 AGAAAACTAGTGCTGCTTGAGG 58.593 45.455 0.00 0.00 0.00 3.86
5543 6381 5.755861 CCTATTCCTAGAAAACTAGTGCTGC 59.244 44.000 0.00 0.00 0.00 5.25
5555 6393 6.327365 TCACTTCATGCATCCTATTCCTAGAA 59.673 38.462 0.00 0.00 0.00 2.10
5563 6401 5.314529 CCTGATTCACTTCATGCATCCTAT 58.685 41.667 0.00 0.00 30.52 2.57
5568 6406 2.730382 TGCCTGATTCACTTCATGCAT 58.270 42.857 0.00 0.00 40.73 3.96
5580 6418 8.133627 CGATTTGATCTAGAAAATTGCCTGATT 58.866 33.333 0.00 0.00 0.00 2.57
5614 6452 5.515626 GTCATATACAGTTCAAGTGTCGGAC 59.484 44.000 0.00 0.00 33.15 4.79
5638 6486 7.220683 CACTAAAATTGCCCGATTCACTAAATG 59.779 37.037 0.00 0.00 0.00 2.32
5640 6488 6.431543 TCACTAAAATTGCCCGATTCACTAAA 59.568 34.615 0.00 0.00 0.00 1.85
5651 6499 7.327214 TGTTAATTCCATCACTAAAATTGCCC 58.673 34.615 0.00 0.00 0.00 5.36
5696 6544 1.830477 GTCAGGAGTCCAGAGCTTCAT 59.170 52.381 12.86 0.00 0.00 2.57
5725 6573 4.810491 TGAAGCAAAACCATTCTTTTCTGC 59.190 37.500 0.00 0.00 0.00 4.26
5774 6622 7.726216 ACTTCAAAAACCCCTAGAAATTCAAG 58.274 34.615 0.00 0.00 0.00 3.02
5780 6628 6.666113 AGTTTGACTTCAAAAACCCCTAGAAA 59.334 34.615 5.98 0.00 46.08 2.52
5842 7957 2.897969 TCAGTACTCCCTCTGTTCCAAC 59.102 50.000 0.00 0.00 33.89 3.77
5906 8765 4.081476 AGGGAACAATAAAAGCATGGAAGC 60.081 41.667 0.00 0.00 0.00 3.86
5918 8777 4.746535 TCGACATGCTAGGGAACAATAA 57.253 40.909 0.00 0.00 0.00 1.40
6020 8879 6.952773 ATTACTAGTGAACACAGGCAAAAA 57.047 33.333 5.39 0.00 0.00 1.94
6021 8880 6.952773 AATTACTAGTGAACACAGGCAAAA 57.047 33.333 5.39 0.00 0.00 2.44
6022 8881 6.952773 AAATTACTAGTGAACACAGGCAAA 57.047 33.333 5.39 0.00 0.00 3.68
6023 8882 7.172532 CAGTAAATTACTAGTGAACACAGGCAA 59.827 37.037 5.39 0.00 37.23 4.52
6024 8883 6.649141 CAGTAAATTACTAGTGAACACAGGCA 59.351 38.462 5.39 0.00 37.23 4.75
6025 8884 6.649557 ACAGTAAATTACTAGTGAACACAGGC 59.350 38.462 5.39 0.00 37.23 4.85
6026 8885 9.136952 GTACAGTAAATTACTAGTGAACACAGG 57.863 37.037 5.39 2.41 37.23 4.00
6027 8886 9.687210 TGTACAGTAAATTACTAGTGAACACAG 57.313 33.333 5.39 5.54 37.23 3.66
6049 8908 9.916397 GCACTCAAACTATGTAATGTTATGTAC 57.084 33.333 0.00 0.00 0.00 2.90
6050 8909 9.660180 TGCACTCAAACTATGTAATGTTATGTA 57.340 29.630 0.00 0.00 0.00 2.29
6051 8910 8.450964 GTGCACTCAAACTATGTAATGTTATGT 58.549 33.333 10.32 0.00 0.00 2.29
6052 8911 8.450180 TGTGCACTCAAACTATGTAATGTTATG 58.550 33.333 19.41 0.00 0.00 1.90
6053 8912 8.560355 TGTGCACTCAAACTATGTAATGTTAT 57.440 30.769 19.41 0.00 0.00 1.89
6054 8913 7.971183 TGTGCACTCAAACTATGTAATGTTA 57.029 32.000 19.41 0.00 0.00 2.41
6055 8914 6.875948 TGTGCACTCAAACTATGTAATGTT 57.124 33.333 19.41 0.00 0.00 2.71
6056 8915 6.262049 TGTTGTGCACTCAAACTATGTAATGT 59.738 34.615 19.41 0.00 0.00 2.71
6057 8916 6.667370 TGTTGTGCACTCAAACTATGTAATG 58.333 36.000 19.41 0.00 0.00 1.90
6058 8917 6.875948 TGTTGTGCACTCAAACTATGTAAT 57.124 33.333 19.41 0.00 0.00 1.89
6059 8918 6.317642 ACTTGTTGTGCACTCAAACTATGTAA 59.682 34.615 19.41 3.68 0.00 2.41
6060 8919 5.820423 ACTTGTTGTGCACTCAAACTATGTA 59.180 36.000 19.41 0.00 0.00 2.29
6061 8920 4.640201 ACTTGTTGTGCACTCAAACTATGT 59.360 37.500 19.41 13.00 0.00 2.29
6062 8921 5.173774 ACTTGTTGTGCACTCAAACTATG 57.826 39.130 19.41 12.45 0.00 2.23
6063 8922 5.835113 AACTTGTTGTGCACTCAAACTAT 57.165 34.783 19.41 6.78 0.00 2.12
6064 8923 5.182190 TGAAACTTGTTGTGCACTCAAACTA 59.818 36.000 19.41 10.07 0.00 2.24
6065 8924 4.022416 TGAAACTTGTTGTGCACTCAAACT 60.022 37.500 19.41 9.85 0.00 2.66
6066 8925 4.233789 TGAAACTTGTTGTGCACTCAAAC 58.766 39.130 19.41 14.46 0.00 2.93
6067 8926 4.511617 TGAAACTTGTTGTGCACTCAAA 57.488 36.364 19.41 8.31 0.00 2.69
6068 8927 4.233789 GTTGAAACTTGTTGTGCACTCAA 58.766 39.130 19.41 20.01 0.00 3.02
6069 8928 3.254411 TGTTGAAACTTGTTGTGCACTCA 59.746 39.130 19.41 14.19 0.00 3.41
6070 8929 3.832276 TGTTGAAACTTGTTGTGCACTC 58.168 40.909 19.41 11.68 0.00 3.51
6071 8930 3.932545 TGTTGAAACTTGTTGTGCACT 57.067 38.095 19.41 0.00 0.00 4.40
6072 8931 6.454981 GGTTTATGTTGAAACTTGTTGTGCAC 60.455 38.462 10.75 10.75 38.97 4.57
6073 8932 5.578727 GGTTTATGTTGAAACTTGTTGTGCA 59.421 36.000 0.00 0.00 38.97 4.57
6074 8933 5.006261 GGGTTTATGTTGAAACTTGTTGTGC 59.994 40.000 0.00 0.00 38.97 4.57
6075 8934 5.522097 GGGGTTTATGTTGAAACTTGTTGTG 59.478 40.000 0.00 0.00 38.97 3.33
6076 8935 5.423931 AGGGGTTTATGTTGAAACTTGTTGT 59.576 36.000 0.00 0.00 38.97 3.32
6077 8936 5.912892 AGGGGTTTATGTTGAAACTTGTTG 58.087 37.500 0.00 0.00 38.97 3.33
6078 8937 5.069914 GGAGGGGTTTATGTTGAAACTTGTT 59.930 40.000 0.00 0.00 38.97 2.83
6079 8938 4.587262 GGAGGGGTTTATGTTGAAACTTGT 59.413 41.667 0.00 0.00 38.97 3.16
6080 8939 4.586841 TGGAGGGGTTTATGTTGAAACTTG 59.413 41.667 0.00 0.00 38.97 3.16
6081 8940 4.810345 TGGAGGGGTTTATGTTGAAACTT 58.190 39.130 0.00 0.00 38.97 2.66
6082 8941 4.463050 TGGAGGGGTTTATGTTGAAACT 57.537 40.909 0.00 0.00 38.97 2.66
6083 8942 5.538849 TTTGGAGGGGTTTATGTTGAAAC 57.461 39.130 0.00 0.00 38.38 2.78
6084 8943 6.561519 TTTTTGGAGGGGTTTATGTTGAAA 57.438 33.333 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.