Multiple sequence alignment - TraesCS3A01G212900

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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 TraesCS3A01G212900 chr3A 100.000 4641 0 0 1 4641 384201949 384197309 0.000000e+00 8571.0
1 TraesCS3A01G212900 chr3A 72.034 354 78 16 4291 4641 8668630 8668965 8.270000e-13 86.1
2 TraesCS3A01G212900 chr3A 71.751 354 79 16 4291 4641 474676260 474676595 3.850000e-11 80.5
3 TraesCS3A01G212900 chr3B 93.731 3334 144 22 825 4113 384333617 384330304 0.000000e+00 4939.0
4 TraesCS3A01G212900 chr3B 90.686 204 6 5 4438 4641 384314844 384314654 4.610000e-65 259.0
5 TraesCS3A01G212900 chr3B 91.061 179 12 3 4107 4281 384317074 384316896 6.000000e-59 239.0
6 TraesCS3A01G212900 chr3D 93.918 2121 103 16 2077 4189 291230613 291228511 0.000000e+00 3179.0
7 TraesCS3A01G212900 chr3D 93.172 1157 44 13 825 1956 291231894 291230748 0.000000e+00 1666.0
8 TraesCS3A01G212900 chr3D 92.531 241 12 3 4401 4641 291228004 291227770 1.600000e-89 340.0
9 TraesCS3A01G212900 chr3D 91.463 82 4 1 1956 2037 291230692 291230614 4.910000e-20 110.0
10 TraesCS3A01G212900 chr5B 91.497 788 65 2 1 787 678641865 678641079 0.000000e+00 1083.0
11 TraesCS3A01G212900 chr6D 91.195 795 65 5 1 792 378740785 378739993 0.000000e+00 1075.0
12 TraesCS3A01G212900 chr6D 90.886 779 68 2 1 778 456734127 456734903 0.000000e+00 1042.0
13 TraesCS3A01G212900 chr5D 91.506 777 64 2 1 776 59355969 59355194 0.000000e+00 1068.0
14 TraesCS3A01G212900 chr5D 90.736 788 71 2 1 787 537983075 537982289 0.000000e+00 1050.0
15 TraesCS3A01G212900 chr2D 91.399 779 65 2 1 778 589514411 589515188 0.000000e+00 1066.0
16 TraesCS3A01G212900 chr2D 91.014 779 68 2 1 778 538072066 538072843 0.000000e+00 1050.0
17 TraesCS3A01G212900 chr2D 90.629 779 64 5 1 778 648339841 648340611 0.000000e+00 1026.0
18 TraesCS3A01G212900 chr4D 90.605 777 65 4 1 776 303074569 303075338 0.000000e+00 1024.0
19 TraesCS3A01G212900 chr1B 91.304 69 6 0 3975 4043 26129256 26129324 1.370000e-15 95.3
20 TraesCS3A01G212900 chr7B 71.831 355 77 19 4291 4641 608191323 608191658 3.850000e-11 80.5
21 TraesCS3A01G212900 chr6B 71.671 353 81 14 4291 4641 694414505 694414170 3.850000e-11 80.5
22 TraesCS3A01G212900 chr2A 75.138 181 36 6 4462 4641 96143812 96143640 4.980000e-10 76.8
23 TraesCS3A01G212900 chr1A 94.118 34 2 0 4546 4579 346750928 346750895 8.000000e-03 52.8


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 TraesCS3A01G212900 chr3A 384197309 384201949 4640 True 8571.00 8571 100.0000 1 4641 1 chr3A.!!$R1 4640
1 TraesCS3A01G212900 chr3B 384330304 384333617 3313 True 4939.00 4939 93.7310 825 4113 1 chr3B.!!$R1 3288
2 TraesCS3A01G212900 chr3B 384314654 384317074 2420 True 249.00 259 90.8735 4107 4641 2 chr3B.!!$R2 534
3 TraesCS3A01G212900 chr3D 291227770 291231894 4124 True 1323.75 3179 92.7710 825 4641 4 chr3D.!!$R1 3816
4 TraesCS3A01G212900 chr5B 678641079 678641865 786 True 1083.00 1083 91.4970 1 787 1 chr5B.!!$R1 786
5 TraesCS3A01G212900 chr6D 378739993 378740785 792 True 1075.00 1075 91.1950 1 792 1 chr6D.!!$R1 791
6 TraesCS3A01G212900 chr6D 456734127 456734903 776 False 1042.00 1042 90.8860 1 778 1 chr6D.!!$F1 777
7 TraesCS3A01G212900 chr5D 59355194 59355969 775 True 1068.00 1068 91.5060 1 776 1 chr5D.!!$R1 775
8 TraesCS3A01G212900 chr5D 537982289 537983075 786 True 1050.00 1050 90.7360 1 787 1 chr5D.!!$R2 786
9 TraesCS3A01G212900 chr2D 589514411 589515188 777 False 1066.00 1066 91.3990 1 778 1 chr2D.!!$F2 777
10 TraesCS3A01G212900 chr2D 538072066 538072843 777 False 1050.00 1050 91.0140 1 778 1 chr2D.!!$F1 777
11 TraesCS3A01G212900 chr2D 648339841 648340611 770 False 1026.00 1026 90.6290 1 778 1 chr2D.!!$F3 777
12 TraesCS3A01G212900 chr4D 303074569 303075338 769 False 1024.00 1024 90.6050 1 776 1 chr4D.!!$F1 775

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
39 40 0.034337 GGTGAACTTGCGGTGGTAGA 59.966 55.000 0.00 0.0 0.00 2.59 F
813 818 0.107456 CGCCTCATTGTAGATGCCCT 59.893 55.000 0.00 0.0 0.00 5.19 F
931 953 0.734889 CCAAAGTCGGCCATCATCAC 59.265 55.000 2.24 0.0 0.00 3.06 F
2084 2173 1.404391 CAGAGCATCCATTCCAAGTGC 59.596 52.381 0.00 0.0 33.66 4.40 F
2196 2286 1.560923 CTCTTGGGTGATCGTTAGCG 58.439 55.000 0.00 0.0 39.92 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1550 1580 2.586425 GAAATGCCAAGCCCAGCTATA 58.414 47.619 0.00 0.00 38.25 1.31 R
2537 2630 0.606604 GTCAAGGAACCAGCTCCGTA 59.393 55.000 0.00 0.00 40.75 4.02 R
2904 2999 5.411831 AGATGCATCATCGGTATACATGT 57.588 39.130 27.81 2.69 44.67 3.21 R
3099 3201 0.676736 AGGCCTTCTCGCTAGCATAC 59.323 55.000 16.45 0.00 0.00 2.39 R
4152 4261 0.967662 TGTGTCCCAAATGTGCCATG 59.032 50.000 0.00 0.00 0.00 3.66 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
39 40 0.034337 GGTGAACTTGCGGTGGTAGA 59.966 55.000 0.00 0.00 0.00 2.59
45 46 1.342082 CTTGCGGTGGTAGAACGACG 61.342 60.000 0.00 0.00 0.00 5.12
101 102 6.428159 CCAAAGTAGTGCTATGAAGAACTTGT 59.572 38.462 0.00 0.00 38.62 3.16
131 132 7.362315 GCCATATGATCATGCATGCTTTACTTA 60.362 37.037 22.25 12.16 0.00 2.24
164 165 4.559300 GCTCCATTGTTGTTTGTGTGCTAT 60.559 41.667 0.00 0.00 0.00 2.97
215 216 0.520847 GCTGCTTCAACTCTTGCTCC 59.479 55.000 0.00 0.00 0.00 4.70
230 231 0.107508 GCTCCTGTGCATTGCTAGGA 60.108 55.000 24.18 24.18 39.12 2.94
237 238 2.224499 TGTGCATTGCTAGGACAAGTGA 60.224 45.455 10.49 0.00 34.30 3.41
253 254 3.541996 AGTGATATGCCGTGTTCATCA 57.458 42.857 0.00 0.00 0.00 3.07
254 255 3.198068 AGTGATATGCCGTGTTCATCAC 58.802 45.455 5.14 5.14 43.67 3.06
262 263 2.812011 GCCGTGTTCATCACTAAGGTTT 59.188 45.455 0.00 0.00 44.16 3.27
266 267 4.988540 CGTGTTCATCACTAAGGTTTCAGA 59.011 41.667 0.00 0.00 44.16 3.27
333 334 1.630369 AGCAACAGCAACCATAGAGGA 59.370 47.619 0.00 0.00 41.22 3.71
348 349 5.070981 CCATAGAGGATTCAAGACTAGGCAA 59.929 44.000 0.00 0.00 41.22 4.52
419 420 1.340502 TGTTGACAGTGGCAAGGTTGA 60.341 47.619 12.94 0.00 0.00 3.18
462 464 2.560105 GTTTGGGCTGAAGCTGAAGAAT 59.440 45.455 1.74 0.00 41.70 2.40
615 619 3.693471 CCGCTTGGGCCAATGCAA 61.693 61.111 28.08 5.45 40.13 4.08
629 633 4.616835 GCCAATGCAAACAACCAAACAAAA 60.617 37.500 0.00 0.00 37.47 2.44
645 649 6.090628 CCAAACAAAATGCACTTGCGTATTAT 59.909 34.615 9.70 0.00 45.83 1.28
651 655 9.877137 CAAAATGCACTTGCGTATTATCTAATA 57.123 29.630 0.00 0.00 45.83 0.98
704 708 4.081087 AGTTGCAGATGACGTATTAGGGTT 60.081 41.667 0.00 0.00 0.00 4.11
707 711 3.002348 GCAGATGACGTATTAGGGTTTGC 59.998 47.826 0.00 0.00 0.00 3.68
780 785 1.018148 AACGGCAATCAAACACGTCA 58.982 45.000 0.00 0.00 36.69 4.35
787 792 3.488384 GCAATCAAACACGTCAAAGGTGA 60.488 43.478 6.77 0.00 37.42 4.02
789 794 5.280945 CAATCAAACACGTCAAAGGTGATT 58.719 37.500 6.77 0.00 37.42 2.57
790 795 4.545823 TCAAACACGTCAAAGGTGATTC 57.454 40.909 6.77 0.00 37.42 2.52
791 796 3.942115 TCAAACACGTCAAAGGTGATTCA 59.058 39.130 6.77 0.00 37.42 2.57
792 797 4.396478 TCAAACACGTCAAAGGTGATTCAA 59.604 37.500 6.77 0.00 37.42 2.69
793 798 4.974368 AACACGTCAAAGGTGATTCAAA 57.026 36.364 6.77 0.00 37.42 2.69
794 799 4.287238 ACACGTCAAAGGTGATTCAAAC 57.713 40.909 6.77 0.00 37.42 2.93
795 800 3.242608 ACACGTCAAAGGTGATTCAAACG 60.243 43.478 6.77 0.00 37.42 3.60
796 801 2.286772 ACGTCAAAGGTGATTCAAACGC 60.287 45.455 0.00 0.00 35.80 4.84
797 802 2.661594 GTCAAAGGTGATTCAAACGCC 58.338 47.619 0.00 0.00 35.80 5.68
799 804 2.552315 TCAAAGGTGATTCAAACGCCTC 59.448 45.455 0.00 0.00 45.83 4.70
800 805 2.270352 AAGGTGATTCAAACGCCTCA 57.730 45.000 0.00 0.00 45.83 3.86
801 806 2.496899 AGGTGATTCAAACGCCTCAT 57.503 45.000 0.00 0.00 43.60 2.90
802 807 2.795329 AGGTGATTCAAACGCCTCATT 58.205 42.857 0.00 0.00 43.60 2.57
803 808 2.489329 AGGTGATTCAAACGCCTCATTG 59.511 45.455 0.00 0.00 43.60 2.82
804 809 2.228822 GGTGATTCAAACGCCTCATTGT 59.771 45.455 0.00 0.00 35.35 2.71
805 810 3.438781 GGTGATTCAAACGCCTCATTGTA 59.561 43.478 0.00 0.00 35.35 2.41
806 811 4.437390 GGTGATTCAAACGCCTCATTGTAG 60.437 45.833 0.00 0.00 35.35 2.74
807 812 4.391830 GTGATTCAAACGCCTCATTGTAGA 59.608 41.667 0.00 0.00 0.00 2.59
808 813 5.065218 GTGATTCAAACGCCTCATTGTAGAT 59.935 40.000 0.00 0.00 0.00 1.98
809 814 4.944962 TTCAAACGCCTCATTGTAGATG 57.055 40.909 0.00 0.00 0.00 2.90
810 815 2.677836 TCAAACGCCTCATTGTAGATGC 59.322 45.455 0.00 0.00 0.00 3.91
811 816 1.668419 AACGCCTCATTGTAGATGCC 58.332 50.000 0.00 0.00 0.00 4.40
812 817 0.179045 ACGCCTCATTGTAGATGCCC 60.179 55.000 0.00 0.00 0.00 5.36
813 818 0.107456 CGCCTCATTGTAGATGCCCT 59.893 55.000 0.00 0.00 0.00 5.19
814 819 1.344438 CGCCTCATTGTAGATGCCCTA 59.656 52.381 0.00 0.00 0.00 3.53
815 820 2.224281 CGCCTCATTGTAGATGCCCTAA 60.224 50.000 0.00 0.00 0.00 2.69
816 821 3.744214 CGCCTCATTGTAGATGCCCTAAA 60.744 47.826 0.00 0.00 0.00 1.85
817 822 4.207165 GCCTCATTGTAGATGCCCTAAAA 58.793 43.478 0.00 0.00 0.00 1.52
818 823 4.829492 GCCTCATTGTAGATGCCCTAAAAT 59.171 41.667 0.00 0.00 36.05 1.82
820 825 5.242393 CCTCATTGTAGATGCCCTAAAATGG 59.758 44.000 18.47 12.49 46.26 3.16
821 826 6.012337 TCATTGTAGATGCCCTAAAATGGA 57.988 37.500 18.47 8.76 46.26 3.41
822 827 6.430864 TCATTGTAGATGCCCTAAAATGGAA 58.569 36.000 18.47 5.48 46.26 3.53
823 828 6.547141 TCATTGTAGATGCCCTAAAATGGAAG 59.453 38.462 18.47 2.67 46.26 3.46
838 843 1.221021 GAAGGCCTTCCTACCCACG 59.779 63.158 31.91 0.00 43.40 4.94
862 868 1.380380 CTCCCCATTCAGGCCCAAC 60.380 63.158 0.00 0.00 35.39 3.77
866 872 1.984026 CCATTCAGGCCCAACACCC 60.984 63.158 0.00 0.00 0.00 4.61
876 882 1.748879 CCAACACCCATAGCCCACG 60.749 63.158 0.00 0.00 0.00 4.94
890 896 1.584495 CCACGCAAAGCCCTAAACC 59.416 57.895 0.00 0.00 0.00 3.27
891 897 1.175983 CCACGCAAAGCCCTAAACCA 61.176 55.000 0.00 0.00 0.00 3.67
892 898 0.887933 CACGCAAAGCCCTAAACCAT 59.112 50.000 0.00 0.00 0.00 3.55
893 899 1.135402 CACGCAAAGCCCTAAACCATC 60.135 52.381 0.00 0.00 0.00 3.51
894 900 1.173043 CGCAAAGCCCTAAACCATCA 58.827 50.000 0.00 0.00 0.00 3.07
896 902 1.204704 GCAAAGCCCTAAACCATCACC 59.795 52.381 0.00 0.00 0.00 4.02
897 903 2.524306 CAAAGCCCTAAACCATCACCA 58.476 47.619 0.00 0.00 0.00 4.17
898 904 3.099141 CAAAGCCCTAAACCATCACCAT 58.901 45.455 0.00 0.00 0.00 3.55
902 908 2.952310 GCCCTAAACCATCACCATTCTC 59.048 50.000 0.00 0.00 0.00 2.87
903 909 3.206150 CCCTAAACCATCACCATTCTCG 58.794 50.000 0.00 0.00 0.00 4.04
918 940 3.546714 CTCGCCGAACCCCCAAAGT 62.547 63.158 0.00 0.00 0.00 2.66
931 953 0.734889 CCAAAGTCGGCCATCATCAC 59.265 55.000 2.24 0.00 0.00 3.06
1521 1544 2.298411 TAACCCGGTATTTGTCTCGC 57.702 50.000 0.00 0.00 0.00 5.03
1560 1590 7.917505 GCATGATAAACATTTATATAGCTGGGC 59.082 37.037 0.00 0.00 37.07 5.36
1596 1626 8.512138 CGGAATGAAATACTTCTGTTTTAGGTT 58.488 33.333 0.00 0.00 32.33 3.50
1612 1642 3.375782 AGGTTGCAATTTGAGAACTGC 57.624 42.857 0.59 0.00 35.32 4.40
1646 1676 7.441836 AGAAAACCATTGAGGAACAAATAACC 58.558 34.615 0.00 0.00 42.03 2.85
1699 1729 6.861055 TGATTGAAAAGTTCTAATTGTTCGGC 59.139 34.615 0.00 0.00 0.00 5.54
1728 1758 8.625651 TCTAATCAGCTAGTTGATCTGTAAGTC 58.374 37.037 20.74 0.00 36.81 3.01
1762 1792 3.009143 GGGACAGTGTTTCCTACCTCAAT 59.991 47.826 0.00 0.00 33.17 2.57
1782 1812 7.063780 CCTCAATTCAAGACAATAAAATGGTGC 59.936 37.037 0.00 0.00 0.00 5.01
1875 1907 8.062065 TGTGAAATACTGGAAAATAATGGACC 57.938 34.615 0.00 0.00 0.00 4.46
1880 1912 4.415596 ACTGGAAAATAATGGACCTGCAA 58.584 39.130 0.00 0.00 0.00 4.08
2084 2173 1.404391 CAGAGCATCCATTCCAAGTGC 59.596 52.381 0.00 0.00 33.66 4.40
2135 2225 3.238788 TCTTATGTGCCGAGGAGGATA 57.761 47.619 0.00 0.00 45.00 2.59
2196 2286 1.560923 CTCTTGGGTGATCGTTAGCG 58.439 55.000 0.00 0.00 39.92 4.26
2251 2344 3.484407 AGCATGATAGATGAAGGGTTGC 58.516 45.455 0.00 0.00 0.00 4.17
2537 2630 1.605712 GCGAACACTGTCCAGCTTACT 60.606 52.381 0.00 0.00 0.00 2.24
2610 2703 2.753452 CACTGCAAGAAATCAGCCAGAT 59.247 45.455 0.00 0.00 36.27 2.90
2615 2708 3.950395 GCAAGAAATCAGCCAGATACCTT 59.050 43.478 0.00 0.00 35.39 3.50
2733 2827 7.125659 TCAATGGAATGTGGTACTGAGAATCTA 59.874 37.037 0.00 0.00 34.92 1.98
2904 2999 3.186283 TGGCCTCAGGAAAGGTATGTAA 58.814 45.455 3.32 0.00 38.79 2.41
2915 3017 7.384115 CAGGAAAGGTATGTAACATGTATACCG 59.616 40.741 22.21 9.81 46.91 4.02
2974 3076 6.331369 TGCTAAATTGAAAAGTTCTCCAGG 57.669 37.500 0.00 0.00 34.98 4.45
2986 3088 5.319043 AGTTCTCCAGGTTTTTCCACATA 57.681 39.130 0.00 0.00 39.02 2.29
2994 3096 7.796054 TCCAGGTTTTTCCACATAAAAATTGA 58.204 30.769 0.00 0.00 39.70 2.57
3046 3148 5.717119 ACAATTTCTTCATCATGCCAGTTC 58.283 37.500 0.00 0.00 0.00 3.01
3087 3189 8.730093 AAAACAATATTTAGGTTACTTGGGGT 57.270 30.769 0.00 0.00 0.00 4.95
3099 3201 6.719829 AGGTTACTTGGGGTAATTTCTTGAAG 59.280 38.462 0.00 0.00 41.68 3.02
3108 3210 6.017026 GGGGTAATTTCTTGAAGTATGCTAGC 60.017 42.308 8.10 8.10 0.00 3.42
3122 3224 0.319469 GCTAGCGAGAAGGCCTCATC 60.319 60.000 5.23 6.39 42.06 2.92
3610 3714 3.090532 GGGTCAAGAGCCCCCGAT 61.091 66.667 7.05 0.00 42.92 4.18
3615 3719 0.617535 TCAAGAGCCCCCGATCAGAA 60.618 55.000 0.00 0.00 0.00 3.02
3616 3720 0.179062 CAAGAGCCCCCGATCAGAAG 60.179 60.000 0.00 0.00 0.00 2.85
3617 3721 0.325671 AAGAGCCCCCGATCAGAAGA 60.326 55.000 0.00 0.00 0.00 2.87
3618 3722 0.325671 AGAGCCCCCGATCAGAAGAA 60.326 55.000 0.00 0.00 0.00 2.52
3619 3723 0.541863 GAGCCCCCGATCAGAAGAAA 59.458 55.000 0.00 0.00 0.00 2.52
3620 3724 0.543749 AGCCCCCGATCAGAAGAAAG 59.456 55.000 0.00 0.00 0.00 2.62
3723 3827 8.696374 TCGAGTTATTCAGTTCTTGATTATCCT 58.304 33.333 0.00 0.00 35.27 3.24
3724 3828 9.319143 CGAGTTATTCAGTTCTTGATTATCCTT 57.681 33.333 0.00 0.00 35.27 3.36
3742 3846 6.897706 ATCCTTCCTAGAACGAATACTACC 57.102 41.667 0.00 0.00 0.00 3.18
3745 3849 5.593502 CCTTCCTAGAACGAATACTACCAGT 59.406 44.000 0.00 0.00 0.00 4.00
3762 3866 6.823689 ACTACCAGTATGATTTTGTAGCAAGG 59.176 38.462 0.00 0.00 39.69 3.61
3880 3984 9.478019 GAAACTTCACTGTGATGTATTTTATCG 57.522 33.333 24.11 0.00 34.23 2.92
3933 4039 4.306600 GTTTTCCATTGTGGGATTGTGTC 58.693 43.478 0.00 0.00 38.32 3.67
3949 4055 6.073222 GGATTGTGTCACGTGATTTTCTAGTT 60.073 38.462 23.12 0.92 0.00 2.24
3991 4099 5.242171 TGCACTGTTTTGTCATGATCTTGAT 59.758 36.000 13.82 0.00 0.00 2.57
4050 4158 5.507985 GCACCAATATTGCTAAATCCTGGTC 60.508 44.000 10.11 0.00 38.16 4.02
4051 4159 4.821805 ACCAATATTGCTAAATCCTGGTCG 59.178 41.667 10.11 0.00 36.70 4.79
4105 4214 4.097437 CCTGCACTCACAAATCTGCATAAT 59.903 41.667 0.00 0.00 38.89 1.28
4152 4261 3.428045 GCTACATTGTTGGCAATCACTCC 60.428 47.826 1.92 0.00 42.91 3.85
4203 4315 7.201857 GGAGGAGTACGTAATAATGGTACTGTT 60.202 40.741 7.71 0.00 44.93 3.16
4209 4321 5.701750 ACGTAATAATGGTACTGTTGTGCAA 59.298 36.000 0.00 0.00 0.00 4.08
4234 4346 3.237628 GCGAGAACTGCTTCAAAAATCC 58.762 45.455 0.00 0.00 0.00 3.01
4245 4358 4.574828 GCTTCAAAAATCCGAGCCTATGTA 59.425 41.667 0.00 0.00 0.00 2.29
4281 4394 2.711542 CATTGTTCTAAGCCCGAACCT 58.288 47.619 7.60 0.00 39.92 3.50
4282 4395 2.943036 TTGTTCTAAGCCCGAACCTT 57.057 45.000 7.60 0.00 39.92 3.50
4283 4396 2.178912 TGTTCTAAGCCCGAACCTTG 57.821 50.000 7.60 0.00 39.92 3.61
4284 4397 0.803117 GTTCTAAGCCCGAACCTTGC 59.197 55.000 0.00 0.00 35.81 4.01
4285 4398 0.672401 TTCTAAGCCCGAACCTTGCG 60.672 55.000 0.00 0.00 0.00 4.85
4286 4399 2.744709 TAAGCCCGAACCTTGCGC 60.745 61.111 0.00 0.00 0.00 6.09
4290 4403 3.124921 CCCGAACCTTGCGCGAAT 61.125 61.111 12.10 0.00 0.00 3.34
4291 4404 2.399611 CCGAACCTTGCGCGAATC 59.600 61.111 12.10 0.00 0.00 2.52
4292 4405 2.100631 CCGAACCTTGCGCGAATCT 61.101 57.895 12.10 0.00 0.00 2.40
4293 4406 1.635663 CCGAACCTTGCGCGAATCTT 61.636 55.000 12.10 0.00 0.00 2.40
4294 4407 0.519175 CGAACCTTGCGCGAATCTTG 60.519 55.000 12.10 0.00 0.00 3.02
4295 4408 0.517316 GAACCTTGCGCGAATCTTGT 59.483 50.000 12.10 0.00 0.00 3.16
4296 4409 0.951558 AACCTTGCGCGAATCTTGTT 59.048 45.000 12.10 1.40 0.00 2.83
4298 4411 0.516877 CCTTGCGCGAATCTTGTTCA 59.483 50.000 12.10 0.00 0.00 3.18
4299 4412 1.069296 CCTTGCGCGAATCTTGTTCAA 60.069 47.619 12.10 0.00 0.00 2.69
4302 4415 2.409012 TGCGCGAATCTTGTTCAACTA 58.591 42.857 12.10 0.00 0.00 2.24
4303 4416 3.000041 TGCGCGAATCTTGTTCAACTAT 59.000 40.909 12.10 0.00 0.00 2.12
4304 4417 3.062099 TGCGCGAATCTTGTTCAACTATC 59.938 43.478 12.10 0.00 0.00 2.08
4306 4419 4.260375 GCGCGAATCTTGTTCAACTATCAT 60.260 41.667 12.10 0.00 0.00 2.45
4308 4421 6.250819 CGCGAATCTTGTTCAACTATCATTT 58.749 36.000 0.00 0.00 0.00 2.32
4309 4422 6.193410 CGCGAATCTTGTTCAACTATCATTTG 59.807 38.462 0.00 0.00 0.00 2.32
4310 4423 6.470235 GCGAATCTTGTTCAACTATCATTTGG 59.530 38.462 0.00 0.00 0.00 3.28
4311 4424 7.626240 GCGAATCTTGTTCAACTATCATTTGGA 60.626 37.037 0.00 0.00 0.00 3.53
4312 4425 7.693951 CGAATCTTGTTCAACTATCATTTGGAC 59.306 37.037 0.00 0.00 33.60 4.02
4313 4426 8.641498 AATCTTGTTCAACTATCATTTGGACT 57.359 30.769 0.00 0.00 34.06 3.85
4315 4428 6.655003 TCTTGTTCAACTATCATTTGGACTCC 59.345 38.462 0.00 0.00 34.06 3.85
4316 4429 4.935205 TGTTCAACTATCATTTGGACTCCG 59.065 41.667 0.00 0.00 34.06 4.63
4317 4430 3.531538 TCAACTATCATTTGGACTCCGC 58.468 45.455 0.00 0.00 0.00 5.54
4318 4431 2.614057 CAACTATCATTTGGACTCCGCC 59.386 50.000 0.00 0.00 0.00 6.13
4319 4432 1.837439 ACTATCATTTGGACTCCGCCA 59.163 47.619 0.00 0.00 35.78 5.69
4320 4433 2.213499 CTATCATTTGGACTCCGCCAC 58.787 52.381 0.00 0.00 37.75 5.01
4321 4434 0.394352 ATCATTTGGACTCCGCCACC 60.394 55.000 0.00 0.00 37.75 4.61
4322 4435 1.303236 CATTTGGACTCCGCCACCA 60.303 57.895 0.00 0.00 37.75 4.17
4323 4436 1.002134 ATTTGGACTCCGCCACCAG 60.002 57.895 0.00 0.00 37.75 4.00
4324 4437 3.842925 TTTGGACTCCGCCACCAGC 62.843 63.158 0.00 0.00 37.75 4.85
4326 4439 4.767255 GGACTCCGCCACCAGCAG 62.767 72.222 0.00 0.00 44.04 4.24
4327 4440 4.767255 GACTCCGCCACCAGCAGG 62.767 72.222 0.00 0.00 44.04 4.85
4344 4691 2.821366 GCTCGGTGGCTGTGGATG 60.821 66.667 0.00 0.00 0.00 3.51
4347 4694 1.300971 CTCGGTGGCTGTGGATGTTG 61.301 60.000 0.00 0.00 0.00 3.33
4354 4701 1.308069 GCTGTGGATGTTGATGCGGT 61.308 55.000 0.00 0.00 0.00 5.68
4359 4706 1.308069 GGATGTTGATGCGGTGCTGT 61.308 55.000 0.00 0.00 0.00 4.40
4360 4707 0.523072 GATGTTGATGCGGTGCTGTT 59.477 50.000 0.00 0.00 0.00 3.16
4361 4708 0.961019 ATGTTGATGCGGTGCTGTTT 59.039 45.000 0.00 0.00 0.00 2.83
4362 4709 0.310543 TGTTGATGCGGTGCTGTTTC 59.689 50.000 0.00 0.00 0.00 2.78
4363 4710 0.387239 GTTGATGCGGTGCTGTTTCC 60.387 55.000 0.00 0.00 0.00 3.13
4364 4711 1.523154 TTGATGCGGTGCTGTTTCCC 61.523 55.000 0.00 0.00 0.00 3.97
4365 4712 1.675641 GATGCGGTGCTGTTTCCCT 60.676 57.895 0.00 0.00 0.00 4.20
4366 4713 1.648467 GATGCGGTGCTGTTTCCCTC 61.648 60.000 0.00 0.00 0.00 4.30
4367 4714 2.032681 GCGGTGCTGTTTCCCTCT 59.967 61.111 0.00 0.00 0.00 3.69
4368 4715 1.295423 GCGGTGCTGTTTCCCTCTA 59.705 57.895 0.00 0.00 0.00 2.43
4369 4716 0.741221 GCGGTGCTGTTTCCCTCTAG 60.741 60.000 0.00 0.00 0.00 2.43
4370 4717 0.608640 CGGTGCTGTTTCCCTCTAGT 59.391 55.000 0.00 0.00 0.00 2.57
4371 4718 1.404315 CGGTGCTGTTTCCCTCTAGTC 60.404 57.143 0.00 0.00 0.00 2.59
4372 4719 1.066071 GGTGCTGTTTCCCTCTAGTCC 60.066 57.143 0.00 0.00 0.00 3.85
4373 4720 0.895530 TGCTGTTTCCCTCTAGTCCG 59.104 55.000 0.00 0.00 0.00 4.79
4374 4721 0.460459 GCTGTTTCCCTCTAGTCCGC 60.460 60.000 0.00 0.00 0.00 5.54
4375 4722 0.179134 CTGTTTCCCTCTAGTCCGCG 60.179 60.000 0.00 0.00 0.00 6.46
4376 4723 1.141234 GTTTCCCTCTAGTCCGCGG 59.859 63.158 22.12 22.12 0.00 6.46
4377 4724 1.000521 TTTCCCTCTAGTCCGCGGA 60.001 57.895 27.28 27.28 0.00 5.54
4378 4725 0.396695 TTTCCCTCTAGTCCGCGGAT 60.397 55.000 33.58 21.74 0.00 4.18
4379 4726 1.107538 TTCCCTCTAGTCCGCGGATG 61.108 60.000 33.58 23.33 0.00 3.51
4380 4727 2.565645 CCCTCTAGTCCGCGGATGG 61.566 68.421 33.58 24.92 0.00 3.51
4381 4728 1.528542 CCTCTAGTCCGCGGATGGA 60.529 63.158 33.58 25.50 35.04 3.41
4387 4734 3.860605 TCCGCGGATGGACATGGG 61.861 66.667 27.28 0.00 31.53 4.00
4389 4736 4.552365 CGCGGATGGACATGGGCT 62.552 66.667 0.00 0.00 0.00 5.19
4390 4737 2.124151 GCGGATGGACATGGGCTT 60.124 61.111 0.00 0.00 0.00 4.35
4391 4738 1.754234 GCGGATGGACATGGGCTTT 60.754 57.895 0.00 0.00 0.00 3.51
4392 4739 2.008268 GCGGATGGACATGGGCTTTG 62.008 60.000 0.00 0.00 0.00 2.77
4393 4740 0.680921 CGGATGGACATGGGCTTTGT 60.681 55.000 0.00 0.00 0.00 2.83
4395 4742 0.819582 GATGGACATGGGCTTTGTGG 59.180 55.000 0.00 0.00 0.00 4.17
4396 4743 1.259840 ATGGACATGGGCTTTGTGGC 61.260 55.000 0.00 0.00 40.96 5.01
4397 4744 1.607467 GGACATGGGCTTTGTGGCT 60.607 57.895 0.00 0.00 41.48 4.75
4399 4746 0.811281 GACATGGGCTTTGTGGCTAC 59.189 55.000 0.00 0.00 41.48 3.58
4435 6524 2.674380 CCTCTGTGCCTGGTTGCC 60.674 66.667 0.00 0.00 0.00 4.52
4436 6525 2.113774 CTCTGTGCCTGGTTGCCA 59.886 61.111 0.00 0.00 0.00 4.92
4537 6626 4.997395 TGAACTGAAGGCTTTATGACAGAC 59.003 41.667 16.92 11.47 0.00 3.51
4562 6651 1.830477 GAGGTGTCAGATTGCCTCTCT 59.170 52.381 9.43 0.00 42.99 3.10
4583 6679 4.777366 TCTATGGTGAACAGGATCAAGTCA 59.223 41.667 0.00 0.00 0.00 3.41
4584 6680 3.855255 TGGTGAACAGGATCAAGTCAA 57.145 42.857 0.00 0.00 0.00 3.18
4585 6681 3.743521 TGGTGAACAGGATCAAGTCAAG 58.256 45.455 0.00 0.00 0.00 3.02
4586 6682 3.136443 TGGTGAACAGGATCAAGTCAAGT 59.864 43.478 0.00 0.00 0.00 3.16
4587 6683 3.748568 GGTGAACAGGATCAAGTCAAGTC 59.251 47.826 0.00 0.00 0.00 3.01
4588 6684 4.503991 GGTGAACAGGATCAAGTCAAGTCT 60.504 45.833 0.00 0.00 0.00 3.24
4589 6685 5.279506 GGTGAACAGGATCAAGTCAAGTCTA 60.280 44.000 0.00 0.00 0.00 2.59
4590 6686 6.223852 GTGAACAGGATCAAGTCAAGTCTAA 58.776 40.000 0.00 0.00 0.00 2.10
4591 6687 6.367422 GTGAACAGGATCAAGTCAAGTCTAAG 59.633 42.308 0.00 0.00 0.00 2.18
4592 6688 5.413309 ACAGGATCAAGTCAAGTCTAAGG 57.587 43.478 0.00 0.00 0.00 2.69
4593 6689 4.841246 ACAGGATCAAGTCAAGTCTAAGGT 59.159 41.667 0.00 0.00 0.00 3.50
4594 6690 5.046950 ACAGGATCAAGTCAAGTCTAAGGTC 60.047 44.000 0.00 0.00 0.00 3.85
4606 6702 4.537751 AGTCTAAGGTCCAAGATCGATCA 58.462 43.478 26.47 3.51 0.00 2.92
4617 6713 1.765314 AGATCGATCAAAGAGTGGGGG 59.235 52.381 26.47 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.154150 GCAAGTTCACCATCAGCGC 60.154 57.895 0.00 0.00 0.00 5.92
39 40 0.036306 ATCCAAAAGAGGGCGTCGTT 59.964 50.000 2.53 2.53 0.00 3.85
45 46 0.890683 CACCACATCCAAAAGAGGGC 59.109 55.000 0.00 0.00 0.00 5.19
80 81 7.278868 GCATAACAAGTTCTTCATAGCACTACT 59.721 37.037 0.00 0.00 27.31 2.57
90 91 7.774625 TGATCATATGGCATAACAAGTTCTTCA 59.225 33.333 11.86 2.78 0.00 3.02
101 102 4.953579 AGCATGCATGATCATATGGCATAA 59.046 37.500 30.64 5.02 0.00 1.90
131 132 4.660168 ACAACAATGGAGCAGAAGAGAAT 58.340 39.130 0.00 0.00 0.00 2.40
164 165 2.426738 AGCACACAAGTAGCAAGCAAAA 59.573 40.909 0.00 0.00 0.00 2.44
215 216 2.161012 CACTTGTCCTAGCAATGCACAG 59.839 50.000 8.35 3.82 0.00 3.66
230 231 3.052455 TGAACACGGCATATCACTTGT 57.948 42.857 0.00 0.00 0.00 3.16
275 276 3.054139 TGCACTAGCTTCTTCCCATGAAT 60.054 43.478 0.00 0.00 42.74 2.57
333 334 2.290514 TGCTGCTTGCCTAGTCTTGAAT 60.291 45.455 0.00 0.00 42.00 2.57
348 349 2.421619 GAGTAAGCTTGTTCTGCTGCT 58.578 47.619 9.86 0.00 41.03 4.24
393 394 0.467804 TGCCACTGTCAACACTGCTA 59.532 50.000 0.00 0.00 0.00 3.49
419 420 1.002087 GACGATCCACCTTGACACCTT 59.998 52.381 0.00 0.00 0.00 3.50
462 464 4.984295 TGAACTGGGTGAAGATGATGAAA 58.016 39.130 0.00 0.00 0.00 2.69
475 477 2.158325 ACAACAATGGGATGAACTGGGT 60.158 45.455 0.00 0.00 0.00 4.51
615 619 4.379290 GCAAGTGCATTTTGTTTGGTTGTT 60.379 37.500 13.36 0.00 41.59 2.83
645 649 7.201974 GCCTGTATTTAGTGTCCCTGTATTAGA 60.202 40.741 0.00 0.00 0.00 2.10
651 655 2.910319 TGCCTGTATTTAGTGTCCCTGT 59.090 45.455 0.00 0.00 0.00 4.00
666 670 2.671130 CAACTTGTTTGGTTGCCTGT 57.329 45.000 0.00 0.00 37.76 4.00
704 708 1.481772 AGCTTGGTTGAGCAAAAGCAA 59.518 42.857 17.16 13.28 45.89 3.91
707 711 2.887152 ACCTAGCTTGGTTGAGCAAAAG 59.113 45.455 14.58 0.00 45.12 2.27
721 726 3.429547 CGCATACACTTCTCAACCTAGCT 60.430 47.826 0.00 0.00 0.00 3.32
725 730 3.525537 CATCGCATACACTTCTCAACCT 58.474 45.455 0.00 0.00 0.00 3.50
749 754 1.098129 TTGCCGTTTGCTACAGTGCA 61.098 50.000 0.00 0.00 42.00 4.57
769 774 3.942115 TGAATCACCTTTGACGTGTTTGA 59.058 39.130 0.00 0.00 33.38 2.69
780 785 2.582052 TGAGGCGTTTGAATCACCTTT 58.418 42.857 0.00 0.00 0.00 3.11
787 792 4.201950 GCATCTACAATGAGGCGTTTGAAT 60.202 41.667 0.00 0.00 34.13 2.57
789 794 2.677836 GCATCTACAATGAGGCGTTTGA 59.322 45.455 0.00 0.00 34.13 2.69
790 795 2.223340 GGCATCTACAATGAGGCGTTTG 60.223 50.000 0.00 0.00 43.65 2.93
791 796 2.017049 GGCATCTACAATGAGGCGTTT 58.983 47.619 0.00 0.00 43.65 3.60
792 797 1.668419 GGCATCTACAATGAGGCGTT 58.332 50.000 0.00 0.00 43.65 4.84
793 798 0.179045 GGGCATCTACAATGAGGCGT 60.179 55.000 0.00 0.00 43.65 5.68
794 799 0.107456 AGGGCATCTACAATGAGGCG 59.893 55.000 0.00 0.00 43.65 5.52
795 800 3.492102 TTAGGGCATCTACAATGAGGC 57.508 47.619 0.00 0.00 42.23 4.70
796 801 5.242393 CCATTTTAGGGCATCTACAATGAGG 59.758 44.000 18.62 6.84 43.57 3.86
797 802 6.064060 TCCATTTTAGGGCATCTACAATGAG 58.936 40.000 18.62 12.42 43.57 2.90
798 803 6.012337 TCCATTTTAGGGCATCTACAATGA 57.988 37.500 18.62 8.57 43.57 2.57
799 804 6.239120 CCTTCCATTTTAGGGCATCTACAATG 60.239 42.308 13.67 13.67 41.93 2.82
800 805 5.835280 CCTTCCATTTTAGGGCATCTACAAT 59.165 40.000 0.00 0.00 30.73 2.71
801 806 5.200483 CCTTCCATTTTAGGGCATCTACAA 58.800 41.667 0.00 0.00 0.00 2.41
802 807 4.792068 CCTTCCATTTTAGGGCATCTACA 58.208 43.478 0.00 0.00 0.00 2.74
803 808 3.570125 GCCTTCCATTTTAGGGCATCTAC 59.430 47.826 0.00 0.00 42.08 2.59
804 809 3.832527 GCCTTCCATTTTAGGGCATCTA 58.167 45.455 0.00 0.00 42.08 1.98
805 810 2.670939 GCCTTCCATTTTAGGGCATCT 58.329 47.619 0.00 0.00 42.08 2.90
820 825 1.221021 CGTGGGTAGGAAGGCCTTC 59.779 63.158 33.67 33.67 43.90 3.46
821 826 1.229400 TCGTGGGTAGGAAGGCCTT 60.229 57.895 20.65 20.65 43.90 4.35
823 828 2.582978 GTCGTGGGTAGGAAGGCC 59.417 66.667 0.00 0.00 0.00 5.19
847 853 1.984026 GGTGTTGGGCCTGAATGGG 60.984 63.158 4.53 0.00 36.00 4.00
862 868 1.656818 CTTTGCGTGGGCTATGGGTG 61.657 60.000 0.00 0.00 40.82 4.61
866 872 2.774799 GGGCTTTGCGTGGGCTATG 61.775 63.158 0.00 0.00 40.82 2.23
876 882 1.204704 GGTGATGGTTTAGGGCTTTGC 59.795 52.381 0.00 0.00 0.00 3.68
890 896 0.652592 GTTCGGCGAGAATGGTGATG 59.347 55.000 10.46 0.00 41.49 3.07
891 897 0.462047 GGTTCGGCGAGAATGGTGAT 60.462 55.000 10.46 0.00 41.49 3.06
892 898 1.079405 GGTTCGGCGAGAATGGTGA 60.079 57.895 10.46 0.00 41.49 4.02
893 899 2.106683 GGGTTCGGCGAGAATGGTG 61.107 63.158 10.46 0.00 41.49 4.17
894 900 2.267961 GGGTTCGGCGAGAATGGT 59.732 61.111 10.46 0.00 41.49 3.55
896 902 2.513897 GGGGGTTCGGCGAGAATG 60.514 66.667 10.46 0.00 41.49 2.67
897 903 2.132089 TTTGGGGGTTCGGCGAGAAT 62.132 55.000 10.46 0.00 41.49 2.40
898 904 2.741486 CTTTGGGGGTTCGGCGAGAA 62.741 60.000 10.46 0.00 36.31 2.87
902 908 3.053896 GACTTTGGGGGTTCGGCG 61.054 66.667 0.00 0.00 0.00 6.46
903 909 3.053896 CGACTTTGGGGGTTCGGC 61.054 66.667 0.00 0.00 0.00 5.54
943 965 0.991920 TGGGAGGTGGGATGAAGAAC 59.008 55.000 0.00 0.00 0.00 3.01
944 966 1.753903 TTGGGAGGTGGGATGAAGAA 58.246 50.000 0.00 0.00 0.00 2.52
945 967 1.753903 TTTGGGAGGTGGGATGAAGA 58.246 50.000 0.00 0.00 0.00 2.87
950 972 0.116342 GGGTTTTTGGGAGGTGGGAT 59.884 55.000 0.00 0.00 0.00 3.85
1212 1235 4.404654 GCCTTGCGTTCCTTGGCG 62.405 66.667 0.00 0.00 33.96 5.69
1521 1544 5.799435 TGTTTATCATGCACATTAACAAGCG 59.201 36.000 8.77 0.00 0.00 4.68
1550 1580 2.586425 GAAATGCCAAGCCCAGCTATA 58.414 47.619 0.00 0.00 38.25 1.31
1612 1642 7.921786 TCCTCAATGGTTTTCTACTACAATG 57.078 36.000 0.00 0.00 37.07 2.82
1646 1676 7.284034 AGGCACCTTCAAATTATCACTAATCAG 59.716 37.037 0.00 0.00 0.00 2.90
1699 1729 6.676950 ACAGATCAACTAGCTGATTAGATCG 58.323 40.000 9.92 3.18 44.73 3.69
1728 1758 4.870650 AACACTGTCCCCGAACAGAGTAG 61.871 52.174 16.23 7.87 46.11 2.57
1762 1792 7.288810 AGAAGCACCATTTTATTGTCTTGAA 57.711 32.000 0.00 0.00 0.00 2.69
1782 1812 7.691877 GCAAAACAATAAACACAAACCAAGAAG 59.308 33.333 0.00 0.00 0.00 2.85
1841 1873 9.606631 ATTTTCCAGTATTTCACAGACTAGATC 57.393 33.333 0.00 0.00 0.00 2.75
1875 1907 6.017109 ACACAACCTATCAACTAAACTTGCAG 60.017 38.462 0.00 0.00 0.00 4.41
2049 2138 4.365514 TGCTCTGATTCACCCTTAAACA 57.634 40.909 0.00 0.00 0.00 2.83
2084 2173 3.184581 GTGTTACTTCGTCAAGAGCTTGG 59.815 47.826 10.09 0.00 40.78 3.61
2135 2225 4.870123 TTTGCTTGCACCATGTTAATCT 57.130 36.364 0.00 0.00 0.00 2.40
2158 2248 6.151648 CCAAGAGCAATAAAAGGATGAACTGA 59.848 38.462 0.00 0.00 0.00 3.41
2251 2344 2.320745 TGGATGCTCTATGTGCACTG 57.679 50.000 19.41 8.48 43.59 3.66
2497 2590 1.671328 CTGCTGCCAACATCAGAGATG 59.329 52.381 5.50 5.50 41.58 2.90
2519 2612 3.243336 CGTAGTAAGCTGGACAGTGTTC 58.757 50.000 0.00 0.00 0.00 3.18
2537 2630 0.606604 GTCAAGGAACCAGCTCCGTA 59.393 55.000 0.00 0.00 40.75 4.02
2610 2703 9.656323 ACTGATATTGTAAGGTAGATGAAGGTA 57.344 33.333 0.00 0.00 0.00 3.08
2904 2999 5.411831 AGATGCATCATCGGTATACATGT 57.588 39.130 27.81 2.69 44.67 3.21
2915 3017 7.810282 AGTGTTACGTAAGATAGATGCATCATC 59.190 37.037 27.81 24.14 40.16 2.92
2974 3076 6.347321 CCCGCTCAATTTTTATGTGGAAAAAC 60.347 38.462 0.00 0.00 34.01 2.43
2986 3088 0.761802 TTTGGGCCCGCTCAATTTTT 59.238 45.000 19.37 0.00 36.18 1.94
3087 3189 7.489160 TCTCGCTAGCATACTTCAAGAAATTA 58.511 34.615 16.45 0.00 0.00 1.40
3099 3201 0.676736 AGGCCTTCTCGCTAGCATAC 59.323 55.000 16.45 0.00 0.00 2.39
3108 3210 1.110442 ACAGAGATGAGGCCTTCTCG 58.890 55.000 23.02 19.95 45.32 4.04
3122 3224 3.561310 TGTTAGTGCTTTGCTCAACAGAG 59.439 43.478 0.00 0.00 33.61 3.35
3610 3714 9.618890 TTTGATTTCTCTTTCTCTTTCTTCTGA 57.381 29.630 0.00 0.00 0.00 3.27
3619 3723 8.447053 GCGAGTTATTTTGATTTCTCTTTCTCT 58.553 33.333 0.00 0.00 0.00 3.10
3620 3724 8.447053 AGCGAGTTATTTTGATTTCTCTTTCTC 58.553 33.333 0.00 0.00 0.00 2.87
3723 3827 7.994911 TCATACTGGTAGTATTCGTTCTAGGAA 59.005 37.037 0.00 0.00 39.26 3.36
3724 3828 7.512130 TCATACTGGTAGTATTCGTTCTAGGA 58.488 38.462 0.00 0.00 39.26 2.94
3742 3846 5.066505 GGTCCCTTGCTACAAAATCATACTG 59.933 44.000 0.00 0.00 0.00 2.74
3745 3849 4.947388 GTGGTCCCTTGCTACAAAATCATA 59.053 41.667 0.00 0.00 0.00 2.15
3762 3866 2.370849 TCCTCAGGTAAAACAGTGGTCC 59.629 50.000 0.00 0.00 0.00 4.46
3880 3984 3.065648 TGTCAACAGGTAAACGCTTTTCC 59.934 43.478 0.00 0.00 0.00 3.13
3923 4029 3.502211 AGAAAATCACGTGACACAATCCC 59.498 43.478 22.71 5.07 0.00 3.85
3933 4039 5.140177 GCTTGACAACTAGAAAATCACGTG 58.860 41.667 9.94 9.94 0.00 4.49
3949 4055 2.364647 TGCAAATTCCATGTGCTTGACA 59.635 40.909 6.77 0.00 39.09 3.58
3976 4084 7.229106 TGACAAGAACAATCAAGATCATGACAA 59.771 33.333 2.13 0.00 30.82 3.18
3977 4085 6.711645 TGACAAGAACAATCAAGATCATGACA 59.288 34.615 2.13 0.00 30.82 3.58
4050 4158 2.668457 GCATCAGTGTGAACTAGAACCG 59.332 50.000 0.00 0.00 0.00 4.44
4051 4159 3.664107 TGCATCAGTGTGAACTAGAACC 58.336 45.455 0.00 0.00 0.00 3.62
4105 4214 8.345565 GCTTGAAGTTTCAAAGAGAGTTGATAA 58.654 33.333 8.48 0.00 45.61 1.75
4127 4236 3.922240 GTGATTGCCAACAATGTAGCTTG 59.078 43.478 9.29 0.00 46.59 4.01
4152 4261 0.967662 TGTGTCCCAAATGTGCCATG 59.032 50.000 0.00 0.00 0.00 3.66
4162 4272 2.106511 CTCCTCCTTTCTTGTGTCCCAA 59.893 50.000 0.00 0.00 0.00 4.12
4163 4273 1.699634 CTCCTCCTTTCTTGTGTCCCA 59.300 52.381 0.00 0.00 0.00 4.37
4169 4279 5.997384 ATTACGTACTCCTCCTTTCTTGT 57.003 39.130 0.00 0.00 0.00 3.16
4203 4315 1.146041 AGTTCTCGCAGGTTGCACA 59.854 52.632 1.69 0.00 45.36 4.57
4209 4321 0.106708 TTGAAGCAGTTCTCGCAGGT 59.893 50.000 0.00 0.00 33.38 4.00
4234 4346 5.164233 CACCATCATAAGTACATAGGCTCG 58.836 45.833 0.00 0.00 0.00 5.03
4245 4358 3.359033 ACAATGCTGCACCATCATAAGT 58.641 40.909 3.57 0.00 0.00 2.24
4281 4394 1.601903 AGTTGAACAAGATTCGCGCAA 59.398 42.857 8.75 0.78 0.00 4.85
4282 4395 1.225855 AGTTGAACAAGATTCGCGCA 58.774 45.000 8.75 0.00 0.00 6.09
4283 4396 3.062099 TGATAGTTGAACAAGATTCGCGC 59.938 43.478 0.00 0.00 0.00 6.86
4284 4397 4.840401 TGATAGTTGAACAAGATTCGCG 57.160 40.909 0.00 0.00 0.00 5.87
4285 4398 6.470235 CCAAATGATAGTTGAACAAGATTCGC 59.530 38.462 0.00 0.00 0.00 4.70
4286 4399 7.693951 GTCCAAATGATAGTTGAACAAGATTCG 59.306 37.037 0.00 0.00 0.00 3.34
4287 4400 8.734386 AGTCCAAATGATAGTTGAACAAGATTC 58.266 33.333 0.00 0.00 0.00 2.52
4289 4402 7.337942 GGAGTCCAAATGATAGTTGAACAAGAT 59.662 37.037 3.60 0.00 0.00 2.40
4290 4403 6.655003 GGAGTCCAAATGATAGTTGAACAAGA 59.345 38.462 3.60 0.00 0.00 3.02
4291 4404 6.402550 CGGAGTCCAAATGATAGTTGAACAAG 60.403 42.308 10.49 0.00 0.00 3.16
4292 4405 5.411361 CGGAGTCCAAATGATAGTTGAACAA 59.589 40.000 10.49 0.00 0.00 2.83
4293 4406 4.935205 CGGAGTCCAAATGATAGTTGAACA 59.065 41.667 10.49 0.00 0.00 3.18
4294 4407 4.201822 GCGGAGTCCAAATGATAGTTGAAC 60.202 45.833 10.49 0.00 0.00 3.18
4295 4408 3.938963 GCGGAGTCCAAATGATAGTTGAA 59.061 43.478 10.49 0.00 0.00 2.69
4296 4409 3.531538 GCGGAGTCCAAATGATAGTTGA 58.468 45.455 10.49 0.00 0.00 3.18
4298 4411 2.238646 TGGCGGAGTCCAAATGATAGTT 59.761 45.455 10.49 0.00 31.31 2.24
4299 4412 1.837439 TGGCGGAGTCCAAATGATAGT 59.163 47.619 10.49 0.00 31.31 2.12
4302 4415 0.394352 GGTGGCGGAGTCCAAATGAT 60.394 55.000 10.49 0.00 35.67 2.45
4303 4416 1.002624 GGTGGCGGAGTCCAAATGA 60.003 57.895 10.49 0.00 35.67 2.57
4304 4417 1.303236 TGGTGGCGGAGTCCAAATG 60.303 57.895 10.49 0.00 35.67 2.32
4306 4419 2.429930 CTGGTGGCGGAGTCCAAA 59.570 61.111 10.49 0.00 35.67 3.28
4326 4439 4.101448 ATCCACAGCCACCGAGCC 62.101 66.667 0.00 0.00 0.00 4.70
4327 4440 2.821366 CATCCACAGCCACCGAGC 60.821 66.667 0.00 0.00 0.00 5.03
4329 4442 1.302431 CAACATCCACAGCCACCGA 60.302 57.895 0.00 0.00 0.00 4.69
4331 4444 0.813184 CATCAACATCCACAGCCACC 59.187 55.000 0.00 0.00 0.00 4.61
4332 4445 0.171903 GCATCAACATCCACAGCCAC 59.828 55.000 0.00 0.00 0.00 5.01
4333 4446 1.307355 CGCATCAACATCCACAGCCA 61.307 55.000 0.00 0.00 0.00 4.75
4334 4447 1.430632 CGCATCAACATCCACAGCC 59.569 57.895 0.00 0.00 0.00 4.85
4335 4448 1.308069 ACCGCATCAACATCCACAGC 61.308 55.000 0.00 0.00 0.00 4.40
4338 4451 1.137404 GCACCGCATCAACATCCAC 59.863 57.895 0.00 0.00 0.00 4.02
4339 4452 1.002257 AGCACCGCATCAACATCCA 60.002 52.632 0.00 0.00 0.00 3.41
4340 4453 1.308069 ACAGCACCGCATCAACATCC 61.308 55.000 0.00 0.00 0.00 3.51
4341 4454 0.523072 AACAGCACCGCATCAACATC 59.477 50.000 0.00 0.00 0.00 3.06
4344 4691 0.387239 GGAAACAGCACCGCATCAAC 60.387 55.000 0.00 0.00 0.00 3.18
4347 4694 1.648467 GAGGGAAACAGCACCGCATC 61.648 60.000 0.00 0.00 0.00 3.91
4354 4701 0.895530 CGGACTAGAGGGAAACAGCA 59.104 55.000 0.00 0.00 0.00 4.41
4359 4706 0.396695 ATCCGCGGACTAGAGGGAAA 60.397 55.000 33.75 2.92 0.00 3.13
4360 4707 1.107538 CATCCGCGGACTAGAGGGAA 61.108 60.000 33.75 3.58 0.00 3.97
4361 4708 1.528542 CATCCGCGGACTAGAGGGA 60.529 63.158 33.75 4.52 0.00 4.20
4362 4709 2.565645 CCATCCGCGGACTAGAGGG 61.566 68.421 33.75 20.27 0.00 4.30
4363 4710 1.528542 TCCATCCGCGGACTAGAGG 60.529 63.158 33.75 25.26 0.00 3.69
4364 4711 4.159266 TCCATCCGCGGACTAGAG 57.841 61.111 33.75 17.25 0.00 2.43
4370 4717 3.860605 CCCATGTCCATCCGCGGA 61.861 66.667 33.12 33.12 0.00 5.54
4372 4719 4.552365 AGCCCATGTCCATCCGCG 62.552 66.667 0.00 0.00 0.00 6.46
4373 4720 1.754234 AAAGCCCATGTCCATCCGC 60.754 57.895 0.00 0.00 0.00 5.54
4374 4721 0.680921 ACAAAGCCCATGTCCATCCG 60.681 55.000 0.00 0.00 0.00 4.18
4375 4722 0.819582 CACAAAGCCCATGTCCATCC 59.180 55.000 0.00 0.00 0.00 3.51
4376 4723 0.819582 CCACAAAGCCCATGTCCATC 59.180 55.000 0.00 0.00 0.00 3.51
4377 4724 1.259840 GCCACAAAGCCCATGTCCAT 61.260 55.000 0.00 0.00 0.00 3.41
4378 4725 1.907807 GCCACAAAGCCCATGTCCA 60.908 57.895 0.00 0.00 0.00 4.02
4379 4726 0.323360 TAGCCACAAAGCCCATGTCC 60.323 55.000 0.00 0.00 0.00 4.02
4380 4727 0.811281 GTAGCCACAAAGCCCATGTC 59.189 55.000 0.00 0.00 0.00 3.06
4381 4728 0.960364 CGTAGCCACAAAGCCCATGT 60.960 55.000 0.00 0.00 0.00 3.21
4382 4729 0.676466 TCGTAGCCACAAAGCCCATG 60.676 55.000 0.00 0.00 0.00 3.66
4383 4730 0.037590 TTCGTAGCCACAAAGCCCAT 59.962 50.000 0.00 0.00 0.00 4.00
4386 4733 0.887387 TGGTTCGTAGCCACAAAGCC 60.887 55.000 0.00 0.00 0.00 4.35
4387 4734 1.130561 GATGGTTCGTAGCCACAAAGC 59.869 52.381 0.00 0.00 39.03 3.51
4388 4735 2.699954 AGATGGTTCGTAGCCACAAAG 58.300 47.619 0.00 0.00 39.03 2.77
4389 4736 2.811431 CAAGATGGTTCGTAGCCACAAA 59.189 45.455 0.00 0.00 39.03 2.83
4390 4737 2.422597 CAAGATGGTTCGTAGCCACAA 58.577 47.619 0.00 0.00 39.03 3.33
4391 4738 1.338674 CCAAGATGGTTCGTAGCCACA 60.339 52.381 0.00 0.00 39.03 4.17
4392 4739 1.369625 CCAAGATGGTTCGTAGCCAC 58.630 55.000 0.00 0.00 39.03 5.01
4393 4740 3.853104 CCAAGATGGTTCGTAGCCA 57.147 52.632 0.00 0.00 40.68 4.75
4435 6524 2.530177 CATTGAAGCTGCTCATTGCTG 58.470 47.619 1.00 0.00 43.37 4.41
4436 6525 1.135083 GCATTGAAGCTGCTCATTGCT 60.135 47.619 24.73 5.63 44.02 3.91
4537 6626 1.811266 CAATCTGACACCTCGCGGG 60.811 63.158 6.13 0.59 41.89 6.13
4546 6635 3.133542 CACCATAGAGAGGCAATCTGACA 59.866 47.826 2.09 0.00 38.84 3.58
4562 6651 5.013079 ACTTGACTTGATCCTGTTCACCATA 59.987 40.000 0.00 0.00 0.00 2.74
4583 6679 4.956700 TGATCGATCTTGGACCTTAGACTT 59.043 41.667 25.02 0.00 0.00 3.01
4584 6680 4.537751 TGATCGATCTTGGACCTTAGACT 58.462 43.478 25.02 0.00 0.00 3.24
4585 6681 4.920640 TGATCGATCTTGGACCTTAGAC 57.079 45.455 25.02 0.00 0.00 2.59
4586 6682 5.656859 TCTTTGATCGATCTTGGACCTTAGA 59.343 40.000 25.02 11.27 0.00 2.10
4587 6683 5.907207 TCTTTGATCGATCTTGGACCTTAG 58.093 41.667 25.02 9.49 0.00 2.18
4588 6684 5.422331 ACTCTTTGATCGATCTTGGACCTTA 59.578 40.000 25.02 0.00 0.00 2.69
4589 6685 4.223923 ACTCTTTGATCGATCTTGGACCTT 59.776 41.667 25.02 1.65 0.00 3.50
4590 6686 3.772025 ACTCTTTGATCGATCTTGGACCT 59.228 43.478 25.02 1.14 0.00 3.85
4591 6687 3.868077 CACTCTTTGATCGATCTTGGACC 59.132 47.826 25.02 0.00 0.00 4.46
4592 6688 3.868077 CCACTCTTTGATCGATCTTGGAC 59.132 47.826 25.02 0.00 0.00 4.02
4593 6689 3.118629 CCCACTCTTTGATCGATCTTGGA 60.119 47.826 25.02 17.35 0.00 3.53
4594 6690 3.201290 CCCACTCTTTGATCGATCTTGG 58.799 50.000 25.02 18.68 0.00 3.61
4606 6702 0.178990 GACAACAGCCCCCACTCTTT 60.179 55.000 0.00 0.00 0.00 2.52
4617 6713 2.482374 GATGCCAGCGACAACAGC 59.518 61.111 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.