Multiple sequence alignment - TraesCS4D01G319800

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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 TraesCS4D01G319800 chr4D 100.000 2791 0 0 1 2791 483429577 483432367 0.000000e+00 5155.0
1 TraesCS4D01G319800 chr4D 89.324 562 37 12 980 1529 483369157 483369707 0.000000e+00 684.0
2 TraesCS4D01G319800 chr4D 85.377 636 46 19 1525 2131 483369733 483370350 1.420000e-172 616.0
3 TraesCS4D01G319800 chr4D 87.676 284 32 3 1242 1522 381404272 381403989 7.450000e-86 327.0
4 TraesCS4D01G319800 chr4D 90.751 173 14 1 2377 2547 483370391 483370563 2.160000e-56 230.0
5 TraesCS4D01G319800 chr4D 88.889 162 15 2 740 900 483390505 483390664 2.190000e-46 196.0
6 TraesCS4D01G319800 chr4D 86.986 146 17 2 754 897 483368839 483368984 2.220000e-36 163.0
7 TraesCS4D01G319800 chr4D 92.035 113 9 0 1027 1139 381404434 381404322 2.880000e-35 159.0
8 TraesCS4D01G319800 chr5D 93.136 743 45 6 1 738 57377508 57376767 0.000000e+00 1085.0
9 TraesCS4D01G319800 chr5D 94.188 585 23 4 165 738 469426090 469425506 0.000000e+00 881.0
10 TraesCS4D01G319800 chr5D 82.075 106 19 0 1245 1350 110794091 110794196 1.060000e-14 91.6
11 TraesCS4D01G319800 chr7D 92.358 759 34 7 1 740 17324619 17323866 0.000000e+00 1059.0
12 TraesCS4D01G319800 chr7D 92.463 743 46 7 3 737 594807392 594806652 0.000000e+00 1053.0
13 TraesCS4D01G319800 chr7D 91.732 762 38 5 1 739 154613289 154614048 0.000000e+00 1035.0
14 TraesCS4D01G319800 chr7D 94.624 651 31 1 18 668 27564103 27563457 0.000000e+00 1005.0
15 TraesCS4D01G319800 chr7D 93.088 651 32 7 99 737 10125134 10124485 0.000000e+00 941.0
16 TraesCS4D01G319800 chr7D 89.771 743 45 10 1 738 36262140 36261424 0.000000e+00 922.0
17 TraesCS4D01G319800 chr7D 89.125 754 45 3 3 737 574466603 574467338 0.000000e+00 904.0
18 TraesCS4D01G319800 chr7D 86.957 345 21 8 1 343 43659452 43659774 1.580000e-97 366.0
19 TraesCS4D01G319800 chr7D 85.714 322 16 2 1 292 60341885 60341564 2.090000e-81 313.0
20 TraesCS4D01G319800 chr7D 94.118 204 12 0 1266 1469 117245068 117245271 7.510000e-81 311.0
21 TraesCS4D01G319800 chr7D 95.804 143 5 1 1 142 631013870 631014012 2.160000e-56 230.0
22 TraesCS4D01G319800 chr7D 91.304 161 8 4 1 156 574023808 574023967 6.050000e-52 215.0
23 TraesCS4D01G319800 chr7D 93.443 61 3 1 1577 1637 117245401 117245460 3.830000e-14 89.8
24 TraesCS4D01G319800 chr7D 100.000 30 0 0 1245 1274 117243054 117243083 3.880000e-04 56.5
25 TraesCS4D01G319800 chrUn 92.185 755 39 3 1 737 96730085 96730837 0.000000e+00 1050.0
26 TraesCS4D01G319800 chrUn 82.474 97 15 2 1267 1362 58870812 58870717 1.780000e-12 84.2
27 TraesCS4D01G319800 chr6D 91.722 749 48 7 3 738 25477 26224 0.000000e+00 1027.0
28 TraesCS4D01G319800 chr3D 89.597 769 46 18 1 737 5749032 5749798 0.000000e+00 946.0
29 TraesCS4D01G319800 chr3D 92.453 53 4 0 1259 1311 63460728 63460676 2.980000e-10 76.8
30 TraesCS4D01G319800 chr4B 90.552 688 43 11 1640 2309 613754004 613753321 0.000000e+00 891.0
31 TraesCS4D01G319800 chr4B 96.146 493 16 2 2302 2791 613753144 613752652 0.000000e+00 802.0
32 TraesCS4D01G319800 chr4B 87.321 560 45 12 981 1531 613754709 613754167 3.950000e-173 617.0
33 TraesCS4D01G319800 chr4B 82.971 276 36 6 982 1253 613757747 613757479 3.590000e-59 239.0
34 TraesCS4D01G319800 chr2D 87.534 746 37 9 1 739 599010912 599010216 0.000000e+00 811.0
35 TraesCS4D01G319800 chr5A 90.179 560 43 7 980 1531 663379099 663379654 0.000000e+00 719.0
36 TraesCS4D01G319800 chr5A 89.631 434 22 10 1640 2069 663379820 663380234 5.290000e-147 531.0
37 TraesCS4D01G319800 chr5A 87.333 150 16 3 754 901 663378581 663378729 4.780000e-38 169.0
38 TraesCS4D01G319800 chr7B 82.540 441 58 14 1046 1469 77431942 77432380 1.220000e-98 370.0
39 TraesCS4D01G319800 chr7B 86.667 90 8 2 1551 1637 77432496 77432584 2.290000e-16 97.1
40 TraesCS4D01G319800 chr7A 93.333 225 15 0 1245 1469 121398162 121398386 1.600000e-87 333.0
41 TraesCS4D01G319800 chr7A 94.915 59 3 0 1579 1637 121398532 121398590 2.960000e-15 93.5
42 TraesCS4D01G319800 chr2A 93.038 158 9 2 1 157 23698766 23698610 2.160000e-56 230.0
43 TraesCS4D01G319800 chr3B 89.855 138 14 0 1245 1382 757918709 757918846 7.940000e-41 178.0
44 TraesCS4D01G319800 chr5B 80.508 118 23 0 1245 1362 122101444 122101327 1.060000e-14 91.6


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 TraesCS4D01G319800 chr4D 483429577 483432367 2790 False 5155.00 5155 100.000000 1 2791 1 chr4D.!!$F2 2790
1 TraesCS4D01G319800 chr4D 483368839 483370563 1724 False 423.25 684 88.109500 754 2547 4 chr4D.!!$F3 1793
2 TraesCS4D01G319800 chr5D 57376767 57377508 741 True 1085.00 1085 93.136000 1 738 1 chr5D.!!$R1 737
3 TraesCS4D01G319800 chr5D 469425506 469426090 584 True 881.00 881 94.188000 165 738 1 chr5D.!!$R2 573
4 TraesCS4D01G319800 chr7D 17323866 17324619 753 True 1059.00 1059 92.358000 1 740 1 chr7D.!!$R2 739
5 TraesCS4D01G319800 chr7D 594806652 594807392 740 True 1053.00 1053 92.463000 3 737 1 chr7D.!!$R6 734
6 TraesCS4D01G319800 chr7D 154613289 154614048 759 False 1035.00 1035 91.732000 1 739 1 chr7D.!!$F2 738
7 TraesCS4D01G319800 chr7D 27563457 27564103 646 True 1005.00 1005 94.624000 18 668 1 chr7D.!!$R3 650
8 TraesCS4D01G319800 chr7D 10124485 10125134 649 True 941.00 941 93.088000 99 737 1 chr7D.!!$R1 638
9 TraesCS4D01G319800 chr7D 36261424 36262140 716 True 922.00 922 89.771000 1 738 1 chr7D.!!$R4 737
10 TraesCS4D01G319800 chr7D 574466603 574467338 735 False 904.00 904 89.125000 3 737 1 chr7D.!!$F4 734
11 TraesCS4D01G319800 chrUn 96730085 96730837 752 False 1050.00 1050 92.185000 1 737 1 chrUn.!!$F1 736
12 TraesCS4D01G319800 chr6D 25477 26224 747 False 1027.00 1027 91.722000 3 738 1 chr6D.!!$F1 735
13 TraesCS4D01G319800 chr3D 5749032 5749798 766 False 946.00 946 89.597000 1 737 1 chr3D.!!$F1 736
14 TraesCS4D01G319800 chr4B 613752652 613757747 5095 True 637.25 891 89.247500 981 2791 4 chr4B.!!$R1 1810
15 TraesCS4D01G319800 chr2D 599010216 599010912 696 True 811.00 811 87.534000 1 739 1 chr2D.!!$R1 738
16 TraesCS4D01G319800 chr5A 663378581 663380234 1653 False 473.00 719 89.047667 754 2069 3 chr5A.!!$F1 1315
17 TraesCS4D01G319800 chr7B 77431942 77432584 642 False 233.55 370 84.603500 1046 1637 2 chr7B.!!$F1 591

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
848 937 0.037975 GGTTGAGGGTGCAAAGCATG 60.038 55.0 0.0 0.0 41.91 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2708 5348 1.153349 GGGTCTAGGGCTTTCGCTG 60.153 63.158 0.0 0.0 36.78 5.18 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
547 635 3.900892 CGCCTATGCCGACGGTCT 61.901 66.667 16.73 5.65 0.00 3.85
744 833 6.599437 CAGTTATTCTGGTAGTGAAAAACGG 58.401 40.000 0.00 0.00 40.23 4.44
746 835 1.886886 TCTGGTAGTGAAAAACGGCC 58.113 50.000 0.00 0.00 0.00 6.13
747 836 0.515564 CTGGTAGTGAAAAACGGCCG 59.484 55.000 26.86 26.86 32.33 6.13
748 837 1.208358 GGTAGTGAAAAACGGCCGC 59.792 57.895 28.58 9.24 0.00 6.53
749 838 1.154543 GTAGTGAAAAACGGCCGCG 60.155 57.895 28.58 1.99 0.00 6.46
752 841 4.320928 TGAAAAACGGCCGCGCTG 62.321 61.111 28.58 0.00 41.29 5.18
759 848 4.817063 CGGCCGCGCTGTTCATTG 62.817 66.667 14.67 0.00 0.00 2.82
761 850 4.403137 GCCGCGCTGTTCATTGCA 62.403 61.111 5.56 0.00 0.00 4.08
763 852 2.251963 CGCGCTGTTCATTGCACA 59.748 55.556 5.56 0.00 0.00 4.57
764 853 1.794785 CGCGCTGTTCATTGCACAG 60.795 57.895 11.50 11.50 43.99 3.66
765 854 1.575922 GCGCTGTTCATTGCACAGA 59.424 52.632 18.78 0.00 43.90 3.41
766 855 0.169672 GCGCTGTTCATTGCACAGAT 59.830 50.000 18.78 0.00 43.90 2.90
767 856 1.891178 CGCTGTTCATTGCACAGATG 58.109 50.000 18.78 7.49 43.90 2.90
768 857 1.466866 CGCTGTTCATTGCACAGATGG 60.467 52.381 18.78 4.82 43.90 3.51
769 858 1.814394 GCTGTTCATTGCACAGATGGA 59.186 47.619 18.78 0.00 43.90 3.41
770 859 2.159421 GCTGTTCATTGCACAGATGGAG 60.159 50.000 18.78 0.00 43.90 3.86
771 860 3.079578 CTGTTCATTGCACAGATGGAGT 58.920 45.455 10.47 0.00 43.90 3.85
773 862 3.244665 TGTTCATTGCACAGATGGAGTCT 60.245 43.478 0.00 0.00 37.80 3.24
776 865 2.479566 TTGCACAGATGGAGTCTTCC 57.520 50.000 0.00 0.00 44.31 3.46
778 867 2.820178 TGCACAGATGGAGTCTTCCTA 58.180 47.619 0.00 0.00 44.36 2.94
779 868 2.762887 TGCACAGATGGAGTCTTCCTAG 59.237 50.000 0.00 0.00 44.36 3.02
780 869 2.482839 GCACAGATGGAGTCTTCCTAGC 60.483 54.545 0.00 0.00 44.36 3.42
781 870 2.102252 CACAGATGGAGTCTTCCTAGCC 59.898 54.545 0.00 0.00 44.36 3.93
782 871 2.023501 ACAGATGGAGTCTTCCTAGCCT 60.024 50.000 0.00 0.00 44.36 4.58
783 872 3.037549 CAGATGGAGTCTTCCTAGCCTT 58.962 50.000 0.00 0.00 44.36 4.35
784 873 3.454082 CAGATGGAGTCTTCCTAGCCTTT 59.546 47.826 0.00 0.00 44.36 3.11
785 874 4.080638 CAGATGGAGTCTTCCTAGCCTTTT 60.081 45.833 0.00 0.00 44.36 2.27
788 877 3.846588 TGGAGTCTTCCTAGCCTTTTGAT 59.153 43.478 0.00 0.00 44.36 2.57
789 878 4.080863 TGGAGTCTTCCTAGCCTTTTGATC 60.081 45.833 0.00 0.00 44.36 2.92
790 879 4.447290 GAGTCTTCCTAGCCTTTTGATCC 58.553 47.826 0.00 0.00 0.00 3.36
791 880 3.846588 AGTCTTCCTAGCCTTTTGATCCA 59.153 43.478 0.00 0.00 0.00 3.41
792 881 4.476479 AGTCTTCCTAGCCTTTTGATCCAT 59.524 41.667 0.00 0.00 0.00 3.41
793 882 4.819088 GTCTTCCTAGCCTTTTGATCCATC 59.181 45.833 0.00 0.00 0.00 3.51
795 884 5.905331 TCTTCCTAGCCTTTTGATCCATCTA 59.095 40.000 0.00 0.00 0.00 1.98
796 885 6.386927 TCTTCCTAGCCTTTTGATCCATCTAA 59.613 38.462 0.00 0.00 0.00 2.10
797 886 5.930135 TCCTAGCCTTTTGATCCATCTAAC 58.070 41.667 0.00 0.00 0.00 2.34
799 888 5.994668 CCTAGCCTTTTGATCCATCTAACTC 59.005 44.000 0.00 0.00 0.00 3.01
800 889 5.707066 AGCCTTTTGATCCATCTAACTCT 57.293 39.130 0.00 0.00 0.00 3.24
801 890 5.435291 AGCCTTTTGATCCATCTAACTCTG 58.565 41.667 0.00 0.00 0.00 3.35
803 892 5.526846 GCCTTTTGATCCATCTAACTCTGAG 59.473 44.000 2.45 2.45 0.00 3.35
804 893 6.631314 GCCTTTTGATCCATCTAACTCTGAGA 60.631 42.308 12.44 0.00 0.00 3.27
805 894 7.507829 CCTTTTGATCCATCTAACTCTGAGAT 58.492 38.462 12.44 1.53 33.82 2.75
809 898 8.774546 TTGATCCATCTAACTCTGAGATAAGT 57.225 34.615 12.44 0.00 32.27 2.24
810 899 8.175925 TGATCCATCTAACTCTGAGATAAGTG 57.824 38.462 12.44 5.64 32.27 3.16
811 900 7.782168 TGATCCATCTAACTCTGAGATAAGTGT 59.218 37.037 12.44 0.00 32.27 3.55
812 901 7.575414 TCCATCTAACTCTGAGATAAGTGTC 57.425 40.000 12.44 0.00 32.27 3.67
813 902 6.261158 TCCATCTAACTCTGAGATAAGTGTCG 59.739 42.308 12.44 0.00 32.27 4.35
814 903 5.487153 TCTAACTCTGAGATAAGTGTCGC 57.513 43.478 12.44 0.00 0.00 5.19
818 907 3.127895 ACTCTGAGATAAGTGTCGCTCAC 59.872 47.826 12.44 3.06 46.46 3.51
835 924 2.819595 CGATGGCCGTGGGTTGAG 60.820 66.667 0.00 0.00 0.00 3.02
836 925 2.438434 GATGGCCGTGGGTTGAGG 60.438 66.667 0.00 0.00 0.00 3.86
837 926 3.995506 GATGGCCGTGGGTTGAGGG 62.996 68.421 0.00 0.00 0.00 4.30
842 931 2.203280 CGTGGGTTGAGGGTGCAA 60.203 61.111 0.00 0.00 0.00 4.08
844 933 1.795170 CGTGGGTTGAGGGTGCAAAG 61.795 60.000 0.00 0.00 0.00 2.77
845 934 1.832167 TGGGTTGAGGGTGCAAAGC 60.832 57.895 0.00 0.00 0.00 3.51
847 936 1.187567 GGGTTGAGGGTGCAAAGCAT 61.188 55.000 0.00 0.00 41.91 3.79
848 937 0.037975 GGTTGAGGGTGCAAAGCATG 60.038 55.000 0.00 0.00 41.91 4.06
849 938 0.675633 GTTGAGGGTGCAAAGCATGT 59.324 50.000 0.00 0.00 41.91 3.21
850 939 0.961019 TTGAGGGTGCAAAGCATGTC 59.039 50.000 0.00 0.00 41.91 3.06
851 940 0.895100 TGAGGGTGCAAAGCATGTCC 60.895 55.000 0.00 0.00 41.91 4.02
852 941 0.895100 GAGGGTGCAAAGCATGTCCA 60.895 55.000 0.00 0.00 41.91 4.02
853 942 1.181098 AGGGTGCAAAGCATGTCCAC 61.181 55.000 0.00 0.00 41.91 4.02
854 943 1.081242 GGTGCAAAGCATGTCCACG 60.081 57.895 0.00 0.00 41.91 4.94
856 945 0.871722 GTGCAAAGCATGTCCACGTA 59.128 50.000 0.00 0.00 41.91 3.57
857 946 1.135972 GTGCAAAGCATGTCCACGTAG 60.136 52.381 0.00 0.00 41.91 3.51
858 947 1.270571 TGCAAAGCATGTCCACGTAGA 60.271 47.619 0.00 0.00 31.71 2.59
859 948 1.128692 GCAAAGCATGTCCACGTAGAC 59.871 52.381 7.22 7.22 37.28 2.59
860 949 1.390123 CAAAGCATGTCCACGTAGACG 59.610 52.381 9.56 0.00 46.33 4.18
861 950 0.736325 AAGCATGTCCACGTAGACGC 60.736 55.000 9.56 7.65 44.43 5.19
862 951 2.505498 GCATGTCCACGTAGACGCG 61.505 63.158 3.53 3.53 44.43 6.01
863 952 2.202570 ATGTCCACGTAGACGCGC 60.203 61.111 5.73 0.00 44.43 6.86
866 955 1.582168 GTCCACGTAGACGCGCTAC 60.582 63.158 22.55 22.55 44.90 3.58
868 957 1.582937 CCACGTAGACGCGCTACTG 60.583 63.158 26.51 22.85 45.92 2.74
870 959 0.371301 CACGTAGACGCGCTACTGTA 59.629 55.000 26.51 3.72 45.92 2.74
874 963 2.538333 CGTAGACGCGCTACTGTACAAT 60.538 50.000 26.51 0.00 45.92 2.71
875 964 1.909376 AGACGCGCTACTGTACAATG 58.091 50.000 5.73 0.00 0.00 2.82
877 966 2.099263 AGACGCGCTACTGTACAATGAT 59.901 45.455 5.73 0.00 0.00 2.45
880 969 3.795101 ACGCGCTACTGTACAATGATAAC 59.205 43.478 5.73 0.00 0.00 1.89
881 970 3.794564 CGCGCTACTGTACAATGATAACA 59.205 43.478 5.56 0.00 0.00 2.41
885 974 5.459107 CGCTACTGTACAATGATAACAGGTC 59.541 44.000 15.34 6.72 43.91 3.85
886 975 5.753921 GCTACTGTACAATGATAACAGGTCC 59.246 44.000 15.34 0.00 43.91 4.46
887 976 5.755409 ACTGTACAATGATAACAGGTCCA 57.245 39.130 15.34 0.00 43.91 4.02
889 978 4.500127 TGTACAATGATAACAGGTCCACG 58.500 43.478 0.00 0.00 0.00 4.94
891 980 4.015872 ACAATGATAACAGGTCCACGTT 57.984 40.909 0.00 0.00 0.00 3.99
892 981 3.751175 ACAATGATAACAGGTCCACGTTG 59.249 43.478 6.90 0.00 0.00 4.10
893 982 3.973206 ATGATAACAGGTCCACGTTGA 57.027 42.857 6.90 0.00 0.00 3.18
894 983 3.034721 TGATAACAGGTCCACGTTGAC 57.965 47.619 11.18 11.18 34.42 3.18
903 992 4.354212 CACGTTGACGCGCTGGTG 62.354 66.667 5.73 3.82 44.43 4.17
904 993 4.578898 ACGTTGACGCGCTGGTGA 62.579 61.111 5.73 0.00 44.43 4.02
905 994 3.334751 CGTTGACGCGCTGGTGAA 61.335 61.111 5.73 0.00 0.00 3.18
906 995 2.667318 CGTTGACGCGCTGGTGAAT 61.667 57.895 5.73 0.00 0.00 2.57
907 996 1.348538 CGTTGACGCGCTGGTGAATA 61.349 55.000 5.73 0.00 0.00 1.75
908 997 0.793861 GTTGACGCGCTGGTGAATAA 59.206 50.000 5.73 0.00 0.00 1.40
909 998 1.195900 GTTGACGCGCTGGTGAATAAA 59.804 47.619 5.73 0.00 0.00 1.40
910 999 1.732941 TGACGCGCTGGTGAATAAAT 58.267 45.000 5.73 0.00 0.00 1.40
911 1000 2.894902 TGACGCGCTGGTGAATAAATA 58.105 42.857 5.73 0.00 0.00 1.40
912 1001 2.605818 TGACGCGCTGGTGAATAAATAC 59.394 45.455 5.73 0.00 0.00 1.89
913 1002 1.591158 ACGCGCTGGTGAATAAATACG 59.409 47.619 5.73 0.00 0.00 3.06
915 1004 1.333791 GCGCTGGTGAATAAATACGGC 60.334 52.381 0.00 0.00 0.00 5.68
916 1005 1.937223 CGCTGGTGAATAAATACGGCA 59.063 47.619 0.00 0.00 0.00 5.69
917 1006 2.353269 CGCTGGTGAATAAATACGGCAA 59.647 45.455 0.00 0.00 0.00 4.52
918 1007 3.691498 GCTGGTGAATAAATACGGCAAC 58.309 45.455 0.00 0.00 0.00 4.17
919 1008 3.127895 GCTGGTGAATAAATACGGCAACA 59.872 43.478 0.00 0.00 0.00 3.33
920 1009 4.380023 GCTGGTGAATAAATACGGCAACAA 60.380 41.667 0.00 0.00 0.00 2.83
921 1010 5.049398 TGGTGAATAAATACGGCAACAAC 57.951 39.130 0.00 0.00 0.00 3.32
922 1011 4.082679 TGGTGAATAAATACGGCAACAACC 60.083 41.667 0.00 0.00 0.00 3.77
923 1012 4.417506 GTGAATAAATACGGCAACAACCC 58.582 43.478 0.00 0.00 0.00 4.11
924 1013 3.444388 TGAATAAATACGGCAACAACCCC 59.556 43.478 0.00 0.00 0.00 4.95
944 1033 1.812922 CTGCCCGCAGATGACAGAC 60.813 63.158 11.32 0.00 46.30 3.51
945 1034 2.512515 GCCCGCAGATGACAGACC 60.513 66.667 0.00 0.00 0.00 3.85
946 1035 2.187946 CCCGCAGATGACAGACCC 59.812 66.667 0.00 0.00 0.00 4.46
947 1036 2.362369 CCCGCAGATGACAGACCCT 61.362 63.158 0.00 0.00 0.00 4.34
948 1037 1.142748 CCGCAGATGACAGACCCTC 59.857 63.158 0.00 0.00 0.00 4.30
950 1039 1.520342 GCAGATGACAGACCCTCGC 60.520 63.158 0.00 0.00 0.00 5.03
951 1040 1.954362 GCAGATGACAGACCCTCGCT 61.954 60.000 0.00 0.00 0.00 4.93
952 1041 0.102120 CAGATGACAGACCCTCGCTC 59.898 60.000 0.00 0.00 0.00 5.03
953 1042 0.323816 AGATGACAGACCCTCGCTCA 60.324 55.000 0.00 0.00 0.00 4.26
954 1043 0.179124 GATGACAGACCCTCGCTCAC 60.179 60.000 0.00 0.00 0.00 3.51
955 1044 0.613292 ATGACAGACCCTCGCTCACT 60.613 55.000 0.00 0.00 0.00 3.41
956 1045 1.244697 TGACAGACCCTCGCTCACTC 61.245 60.000 0.00 0.00 0.00 3.51
957 1046 2.259875 GACAGACCCTCGCTCACTCG 62.260 65.000 0.00 0.00 0.00 4.18
958 1047 3.444805 AGACCCTCGCTCACTCGC 61.445 66.667 0.00 0.00 0.00 5.03
960 1049 3.404141 GACCCTCGCTCACTCGCTC 62.404 68.421 0.00 0.00 0.00 5.03
961 1050 3.137459 CCCTCGCTCACTCGCTCT 61.137 66.667 0.00 0.00 0.00 4.09
964 1053 0.812014 CCTCGCTCACTCGCTCTCTA 60.812 60.000 0.00 0.00 0.00 2.43
965 1054 1.010580 CTCGCTCACTCGCTCTCTAA 58.989 55.000 0.00 0.00 0.00 2.10
966 1055 0.727970 TCGCTCACTCGCTCTCTAAC 59.272 55.000 0.00 0.00 0.00 2.34
967 1056 0.448197 CGCTCACTCGCTCTCTAACA 59.552 55.000 0.00 0.00 0.00 2.41
968 1057 1.792273 CGCTCACTCGCTCTCTAACAC 60.792 57.143 0.00 0.00 0.00 3.32
969 1058 1.200252 GCTCACTCGCTCTCTAACACA 59.800 52.381 0.00 0.00 0.00 3.72
970 1059 2.351835 GCTCACTCGCTCTCTAACACAA 60.352 50.000 0.00 0.00 0.00 3.33
971 1060 3.238441 CTCACTCGCTCTCTAACACAAC 58.762 50.000 0.00 0.00 0.00 3.32
974 1063 2.288273 ACTCGCTCTCTAACACAACACC 60.288 50.000 0.00 0.00 0.00 4.16
976 1065 1.270094 CGCTCTCTAACACAACACCCA 60.270 52.381 0.00 0.00 0.00 4.51
977 1066 2.143925 GCTCTCTAACACAACACCCAC 58.856 52.381 0.00 0.00 0.00 4.61
979 1068 3.393800 CTCTCTAACACAACACCCACTG 58.606 50.000 0.00 0.00 0.00 3.66
980 1069 2.104111 TCTCTAACACAACACCCACTGG 59.896 50.000 0.00 0.00 37.80 4.00
982 1071 2.104111 TCTAACACAACACCCACTGGAG 59.896 50.000 0.00 0.00 34.81 3.86
983 1072 0.916086 AACACAACACCCACTGGAGA 59.084 50.000 0.00 0.00 34.81 3.71
984 1073 0.469917 ACACAACACCCACTGGAGAG 59.530 55.000 0.00 0.00 34.81 3.20
1114 3430 3.105659 GCGAAGGCAGATGGAAGC 58.894 61.111 0.00 0.00 39.62 3.86
1122 3438 0.322816 GCAGATGGAAGCAAGTCCCA 60.323 55.000 0.00 0.00 36.80 4.37
1181 3505 3.526430 TCCCTAGCTTGGTAGACACTAGA 59.474 47.826 13.38 0.00 30.97 2.43
1182 3506 3.633065 CCCTAGCTTGGTAGACACTAGAC 59.367 52.174 13.38 0.00 30.97 2.59
1183 3507 4.270834 CCTAGCTTGGTAGACACTAGACA 58.729 47.826 5.98 0.00 30.97 3.41
1184 3508 4.336993 CCTAGCTTGGTAGACACTAGACAG 59.663 50.000 5.98 0.00 30.97 3.51
1185 3509 3.768878 AGCTTGGTAGACACTAGACAGT 58.231 45.455 0.00 0.00 34.42 3.55
1186 3510 4.919793 AGCTTGGTAGACACTAGACAGTA 58.080 43.478 0.00 0.00 32.21 2.74
1187 3511 4.944930 AGCTTGGTAGACACTAGACAGTAG 59.055 45.833 0.00 0.00 32.21 2.57
1188 3512 4.096682 GCTTGGTAGACACTAGACAGTAGG 59.903 50.000 0.00 0.00 32.21 3.18
1195 3522 6.623979 AGACACTAGACAGTAGGAGTAGAA 57.376 41.667 0.00 0.00 32.21 2.10
1502 3850 3.321648 AGGATGGTCAGCACGCCA 61.322 61.111 0.85 0.00 39.33 5.69
1534 3931 1.513622 GCTCCGTCTCCTCCAACTC 59.486 63.158 0.00 0.00 0.00 3.01
1543 3940 4.785453 CTCCAACTCCGGGGCTGC 62.785 72.222 0.00 0.00 0.00 5.25
1550 3947 4.096003 TCCGGGGCTGCTACAAGC 62.096 66.667 0.00 0.00 42.82 4.01
1551 3948 4.101448 CCGGGGCTGCTACAAGCT 62.101 66.667 0.00 0.00 42.97 3.74
1563 3960 2.428960 TACAAGCTCCAACGCTGCGA 62.429 55.000 30.47 4.83 40.79 5.10
1630 4030 3.717294 GGGCGGCCTCTTCTTCCA 61.717 66.667 22.87 0.00 0.00 3.53
1757 4184 1.050767 CGTTTCTTGAGTCCGACGAC 58.949 55.000 0.00 0.00 39.50 4.34
1802 4235 0.511221 CGGGTTAACGCTCACACTTG 59.489 55.000 19.13 0.00 0.00 3.16
1851 4289 2.541178 CGTACGAACAGGGAGCTGTATC 60.541 54.545 10.44 0.00 36.42 2.24
1855 4293 2.541178 CGAACAGGGAGCTGTATCGTAC 60.541 54.545 0.00 0.00 36.42 3.67
1856 4294 1.400737 ACAGGGAGCTGTATCGTACC 58.599 55.000 0.00 0.00 35.56 3.34
1857 4295 0.674534 CAGGGAGCTGTATCGTACCC 59.325 60.000 0.00 0.00 37.79 3.69
1858 4296 0.469518 AGGGAGCTGTATCGTACCCC 60.470 60.000 0.00 0.00 38.22 4.95
1859 4297 0.757935 GGGAGCTGTATCGTACCCCA 60.758 60.000 0.00 0.00 32.77 4.96
1860 4298 0.388294 GGAGCTGTATCGTACCCCAC 59.612 60.000 0.00 0.00 0.00 4.61
1863 4301 1.903860 AGCTGTATCGTACCCCACAAA 59.096 47.619 0.00 0.00 0.00 2.83
1864 4302 2.504175 AGCTGTATCGTACCCCACAAAT 59.496 45.455 0.00 0.00 0.00 2.32
1865 4303 2.612212 GCTGTATCGTACCCCACAAATG 59.388 50.000 0.00 0.00 0.00 2.32
1866 4304 3.869065 CTGTATCGTACCCCACAAATGT 58.131 45.455 0.00 0.00 0.00 2.71
1867 4305 4.681244 GCTGTATCGTACCCCACAAATGTA 60.681 45.833 0.00 0.00 0.00 2.29
1895 4337 2.358957 ACAGCTCCATGTACGTACGTA 58.641 47.619 23.60 23.60 0.00 3.57
1988 4437 6.516693 CGAGCTGTTTAGATGGATGGTGTATA 60.517 42.308 0.00 0.00 0.00 1.47
2003 4452 4.000988 GGTGTATAAGTGGGTGTGTTCAG 58.999 47.826 0.00 0.00 0.00 3.02
2056 4505 9.369904 GAGCATCCACATTTTGTATTGTATTTT 57.630 29.630 0.00 0.00 0.00 1.82
2126 4576 8.705594 TCTTTGAAAAGAAGGATATCTACCGAT 58.294 33.333 2.05 0.00 41.75 4.18
2204 4654 9.507329 GGATCTAGATGACAATAAATGCCTAAA 57.493 33.333 10.74 0.00 0.00 1.85
2216 4666 9.563748 CAATAAATGCCTAAAAATTGGATGGAT 57.436 29.630 0.00 0.00 0.00 3.41
2246 4699 1.400494 GTTGGAGACGTGCTTTGTTGT 59.600 47.619 0.00 0.00 0.00 3.32
2249 4702 3.472652 TGGAGACGTGCTTTGTTGTAAT 58.527 40.909 0.00 0.00 0.00 1.89
2250 4703 4.633175 TGGAGACGTGCTTTGTTGTAATA 58.367 39.130 0.00 0.00 0.00 0.98
2328 4965 2.145536 GGCAAGGGAAACAATGCTTTG 58.854 47.619 10.58 10.58 41.55 2.77
2452 5089 1.290009 GGTGGTTTGATGGCAGTGC 59.710 57.895 6.55 6.55 0.00 4.40
2494 5131 1.921243 TGCCATGACTATCGTTGACG 58.079 50.000 0.00 0.00 41.45 4.35
2541 5180 2.639065 TGTTTTCCTTGTTGAGACGCT 58.361 42.857 0.00 0.00 0.00 5.07
2608 5248 2.821969 GTGAATTTCACTGGATGTGCCT 59.178 45.455 19.90 0.00 43.73 4.75
2618 5258 2.751806 CTGGATGTGCCTTCTTCCTTTC 59.248 50.000 0.00 0.00 37.63 2.62
2650 5290 2.063015 AACCCCGCCACATCAGTTCA 62.063 55.000 0.00 0.00 0.00 3.18
2687 5327 7.934665 CCTGTAGATGTAGCTTTACTCTCTCTA 59.065 40.741 0.00 0.00 0.00 2.43
2708 5348 9.507329 TCTCTATATTAATGTGATTGCTTTCCC 57.493 33.333 0.00 0.00 0.00 3.97
2732 5372 0.329596 AAAGCCCTAGACCCAGCTTG 59.670 55.000 0.00 0.00 44.48 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 210 0.744057 TGTGTGCACAGATATGCCGG 60.744 55.000 22.40 0.00 45.50 6.13
547 635 0.029834 GCTCGAAATACGCCTACGGA 59.970 55.000 0.00 0.00 46.04 4.69
742 831 4.817063 CAATGAACAGCGCGGCCG 62.817 66.667 24.05 24.05 37.57 6.13
744 833 4.403137 TGCAATGAACAGCGCGGC 62.403 61.111 8.83 0.00 0.00 6.53
746 835 1.794785 CTGTGCAATGAACAGCGCG 60.795 57.895 8.65 0.00 43.81 6.86
747 836 0.169672 ATCTGTGCAATGAACAGCGC 59.830 50.000 16.43 0.00 43.88 5.92
748 837 1.466866 CCATCTGTGCAATGAACAGCG 60.467 52.381 16.43 9.66 43.88 5.18
749 838 1.814394 TCCATCTGTGCAATGAACAGC 59.186 47.619 16.43 0.00 43.88 4.40
752 841 3.341823 AGACTCCATCTGTGCAATGAAC 58.658 45.455 0.00 0.00 35.81 3.18
753 842 3.708403 AGACTCCATCTGTGCAATGAA 57.292 42.857 0.00 0.00 35.81 2.57
754 843 3.603532 GAAGACTCCATCTGTGCAATGA 58.396 45.455 0.00 0.00 37.88 2.57
755 844 2.681848 GGAAGACTCCATCTGTGCAATG 59.318 50.000 0.00 0.00 41.96 2.82
756 845 2.575279 AGGAAGACTCCATCTGTGCAAT 59.425 45.455 0.00 0.00 45.24 3.56
757 846 1.980765 AGGAAGACTCCATCTGTGCAA 59.019 47.619 0.00 0.00 45.24 4.08
758 847 1.649321 AGGAAGACTCCATCTGTGCA 58.351 50.000 0.00 0.00 45.24 4.57
759 848 2.482839 GCTAGGAAGACTCCATCTGTGC 60.483 54.545 0.00 0.00 45.24 4.57
760 849 2.102252 GGCTAGGAAGACTCCATCTGTG 59.898 54.545 0.00 0.00 45.24 3.66
761 850 2.023501 AGGCTAGGAAGACTCCATCTGT 60.024 50.000 0.00 0.00 35.55 3.41
763 852 3.413105 AAGGCTAGGAAGACTCCATCT 57.587 47.619 0.00 0.00 41.74 2.90
764 853 4.080863 TCAAAAGGCTAGGAAGACTCCATC 60.081 45.833 0.00 0.00 41.74 3.51
765 854 3.846588 TCAAAAGGCTAGGAAGACTCCAT 59.153 43.478 0.00 0.00 41.74 3.41
766 855 3.248024 TCAAAAGGCTAGGAAGACTCCA 58.752 45.455 0.00 0.00 41.74 3.86
767 856 3.983044 TCAAAAGGCTAGGAAGACTCC 57.017 47.619 0.00 0.00 41.74 3.85
768 857 4.080863 TGGATCAAAAGGCTAGGAAGACTC 60.081 45.833 0.00 0.00 41.74 3.36
769 858 3.846588 TGGATCAAAAGGCTAGGAAGACT 59.153 43.478 0.00 0.00 45.97 3.24
770 859 4.222124 TGGATCAAAAGGCTAGGAAGAC 57.778 45.455 0.00 0.00 0.00 3.01
771 860 4.723789 AGATGGATCAAAAGGCTAGGAAGA 59.276 41.667 0.00 0.00 0.00 2.87
773 862 6.158695 AGTTAGATGGATCAAAAGGCTAGGAA 59.841 38.462 0.00 0.00 0.00 3.36
776 865 6.705381 CAGAGTTAGATGGATCAAAAGGCTAG 59.295 42.308 0.00 0.00 0.00 3.42
778 867 5.190528 TCAGAGTTAGATGGATCAAAAGGCT 59.809 40.000 0.00 0.00 0.00 4.58
779 868 5.431765 TCAGAGTTAGATGGATCAAAAGGC 58.568 41.667 0.00 0.00 0.00 4.35
780 869 6.882656 TCTCAGAGTTAGATGGATCAAAAGG 58.117 40.000 0.00 0.00 0.00 3.11
783 872 9.206690 ACTTATCTCAGAGTTAGATGGATCAAA 57.793 33.333 0.00 0.00 35.36 2.69
784 873 8.637099 CACTTATCTCAGAGTTAGATGGATCAA 58.363 37.037 0.00 0.00 35.36 2.57
785 874 7.782168 ACACTTATCTCAGAGTTAGATGGATCA 59.218 37.037 0.00 0.00 35.36 2.92
788 877 6.261158 CGACACTTATCTCAGAGTTAGATGGA 59.739 42.308 0.00 0.00 35.36 3.41
789 878 6.434596 CGACACTTATCTCAGAGTTAGATGG 58.565 44.000 0.00 0.00 35.36 3.51
790 879 5.912396 GCGACACTTATCTCAGAGTTAGATG 59.088 44.000 0.00 0.00 35.36 2.90
791 880 5.825679 AGCGACACTTATCTCAGAGTTAGAT 59.174 40.000 0.00 0.00 37.46 1.98
792 881 5.186942 AGCGACACTTATCTCAGAGTTAGA 58.813 41.667 0.00 0.00 0.00 2.10
793 882 5.065346 TGAGCGACACTTATCTCAGAGTTAG 59.935 44.000 0.00 0.00 32.43 2.34
795 884 3.759086 TGAGCGACACTTATCTCAGAGTT 59.241 43.478 0.00 0.00 32.43 3.01
796 885 3.127895 GTGAGCGACACTTATCTCAGAGT 59.872 47.826 9.23 0.00 45.13 3.24
797 886 3.690422 GTGAGCGACACTTATCTCAGAG 58.310 50.000 9.23 0.00 45.13 3.35
799 888 2.096013 TCGTGAGCGACACTTATCTCAG 59.904 50.000 13.32 0.00 46.24 3.35
800 889 2.081462 TCGTGAGCGACACTTATCTCA 58.919 47.619 13.32 0.00 46.24 3.27
801 890 2.826979 TCGTGAGCGACACTTATCTC 57.173 50.000 13.32 0.00 46.24 2.75
818 907 2.819595 CTCAACCCACGGCCATCG 60.820 66.667 2.24 0.00 45.88 3.84
819 908 2.438434 CCTCAACCCACGGCCATC 60.438 66.667 2.24 0.00 0.00 3.51
820 909 4.047125 CCCTCAACCCACGGCCAT 62.047 66.667 2.24 0.00 0.00 4.40
824 913 3.783362 TTGCACCCTCAACCCACGG 62.783 63.158 0.00 0.00 0.00 4.94
825 914 1.795170 CTTTGCACCCTCAACCCACG 61.795 60.000 0.00 0.00 0.00 4.94
826 915 2.041153 CTTTGCACCCTCAACCCAC 58.959 57.895 0.00 0.00 0.00 4.61
827 916 1.832167 GCTTTGCACCCTCAACCCA 60.832 57.895 0.00 0.00 0.00 4.51
828 917 1.187567 ATGCTTTGCACCCTCAACCC 61.188 55.000 0.00 0.00 43.04 4.11
829 918 0.037975 CATGCTTTGCACCCTCAACC 60.038 55.000 0.00 0.00 43.04 3.77
830 919 0.675633 ACATGCTTTGCACCCTCAAC 59.324 50.000 0.00 0.00 43.04 3.18
832 921 0.895100 GGACATGCTTTGCACCCTCA 60.895 55.000 0.00 0.00 43.04 3.86
834 923 1.153524 TGGACATGCTTTGCACCCT 59.846 52.632 0.00 0.00 43.04 4.34
835 924 1.290009 GTGGACATGCTTTGCACCC 59.710 57.895 0.00 0.00 43.04 4.61
836 925 1.081242 CGTGGACATGCTTTGCACC 60.081 57.895 0.00 0.00 43.04 5.01
837 926 0.871722 TACGTGGACATGCTTTGCAC 59.128 50.000 0.00 0.00 43.04 4.57
838 927 1.155889 CTACGTGGACATGCTTTGCA 58.844 50.000 0.00 0.00 44.86 4.08
839 928 1.128692 GTCTACGTGGACATGCTTTGC 59.871 52.381 25.18 0.00 36.35 3.68
842 931 0.736325 GCGTCTACGTGGACATGCTT 60.736 55.000 28.34 0.00 42.22 3.91
844 933 2.505498 CGCGTCTACGTGGACATGC 61.505 63.158 28.34 22.73 45.14 4.06
845 934 3.675485 CGCGTCTACGTGGACATG 58.325 61.111 28.34 17.32 45.14 3.21
854 943 2.532531 TTGTACAGTAGCGCGTCTAC 57.467 50.000 24.04 24.04 46.30 2.59
856 945 1.471287 TCATTGTACAGTAGCGCGTCT 59.529 47.619 8.43 8.22 0.00 4.18
857 946 1.904144 TCATTGTACAGTAGCGCGTC 58.096 50.000 8.43 0.00 0.00 5.19
858 947 2.579207 ATCATTGTACAGTAGCGCGT 57.421 45.000 8.43 0.00 0.00 6.01
859 948 3.794564 TGTTATCATTGTACAGTAGCGCG 59.205 43.478 0.00 0.00 0.00 6.86
860 949 4.209288 CCTGTTATCATTGTACAGTAGCGC 59.791 45.833 0.00 0.00 38.04 5.92
861 950 5.348986 ACCTGTTATCATTGTACAGTAGCG 58.651 41.667 0.00 0.00 38.04 4.26
862 951 5.753921 GGACCTGTTATCATTGTACAGTAGC 59.246 44.000 0.00 0.00 38.04 3.58
863 952 6.757010 GTGGACCTGTTATCATTGTACAGTAG 59.243 42.308 0.00 0.00 38.04 2.57
866 955 4.566759 CGTGGACCTGTTATCATTGTACAG 59.433 45.833 0.00 0.00 39.13 2.74
868 957 4.501071 ACGTGGACCTGTTATCATTGTAC 58.499 43.478 0.00 0.00 0.00 2.90
870 959 3.695830 ACGTGGACCTGTTATCATTGT 57.304 42.857 0.00 0.00 0.00 2.71
874 963 2.608506 CGTCAACGTGGACCTGTTATCA 60.609 50.000 17.43 0.00 34.24 2.15
875 964 1.990563 CGTCAACGTGGACCTGTTATC 59.009 52.381 17.43 0.00 34.24 1.75
877 966 0.598158 GCGTCAACGTGGACCTGTTA 60.598 55.000 17.43 0.00 42.22 2.41
880 969 3.403057 CGCGTCAACGTGGACCTG 61.403 66.667 17.43 6.17 45.14 4.00
887 976 3.931317 TATTCACCAGCGCGTCAACGT 62.931 52.381 8.43 0.00 42.22 3.99
889 978 0.793861 TTATTCACCAGCGCGTCAAC 59.206 50.000 8.43 0.00 0.00 3.18
891 980 1.732941 ATTTATTCACCAGCGCGTCA 58.267 45.000 8.43 0.00 0.00 4.35
892 981 2.347292 CGTATTTATTCACCAGCGCGTC 60.347 50.000 8.43 0.00 0.00 5.19
893 982 1.591158 CGTATTTATTCACCAGCGCGT 59.409 47.619 8.43 0.00 0.00 6.01
894 983 1.070843 CCGTATTTATTCACCAGCGCG 60.071 52.381 0.00 0.00 0.00 6.86
898 987 4.955925 TGTTGCCGTATTTATTCACCAG 57.044 40.909 0.00 0.00 0.00 4.00
899 988 4.082679 GGTTGTTGCCGTATTTATTCACCA 60.083 41.667 0.00 0.00 0.00 4.17
901 990 4.417506 GGGTTGTTGCCGTATTTATTCAC 58.582 43.478 0.00 0.00 0.00 3.18
903 992 3.487879 CGGGGTTGTTGCCGTATTTATTC 60.488 47.826 0.00 0.00 0.00 1.75
904 993 2.424246 CGGGGTTGTTGCCGTATTTATT 59.576 45.455 0.00 0.00 0.00 1.40
905 994 2.018515 CGGGGTTGTTGCCGTATTTAT 58.981 47.619 0.00 0.00 0.00 1.40
906 995 1.451067 CGGGGTTGTTGCCGTATTTA 58.549 50.000 0.00 0.00 0.00 1.40
907 996 1.868987 GCGGGGTTGTTGCCGTATTT 61.869 55.000 0.00 0.00 0.00 1.40
908 997 2.337246 GCGGGGTTGTTGCCGTATT 61.337 57.895 0.00 0.00 0.00 1.89
909 998 2.748647 GCGGGGTTGTTGCCGTAT 60.749 61.111 0.00 0.00 0.00 3.06
910 999 3.943691 AGCGGGGTTGTTGCCGTA 61.944 61.111 0.00 0.00 0.00 4.02
926 1015 1.812922 GTCTGTCATCTGCGGGCAG 60.813 63.158 14.36 14.36 44.86 4.85
927 1016 2.265739 GTCTGTCATCTGCGGGCA 59.734 61.111 0.00 0.00 0.00 5.36
928 1017 2.512515 GGTCTGTCATCTGCGGGC 60.513 66.667 0.00 0.00 0.00 6.13
929 1018 2.187946 GGGTCTGTCATCTGCGGG 59.812 66.667 0.00 0.00 0.00 6.13
931 1020 1.226802 CGAGGGTCTGTCATCTGCG 60.227 63.158 0.00 0.00 0.00 5.18
932 1021 1.520342 GCGAGGGTCTGTCATCTGC 60.520 63.158 0.00 0.00 0.00 4.26
933 1022 0.102120 GAGCGAGGGTCTGTCATCTG 59.898 60.000 0.00 0.00 0.00 2.90
934 1023 0.323816 TGAGCGAGGGTCTGTCATCT 60.324 55.000 0.00 0.00 0.00 2.90
937 1026 1.228583 AGTGAGCGAGGGTCTGTCA 60.229 57.895 0.00 0.00 0.00 3.58
938 1027 1.509004 GAGTGAGCGAGGGTCTGTC 59.491 63.158 0.00 0.00 0.00 3.51
941 1030 3.444805 GCGAGTGAGCGAGGGTCT 61.445 66.667 0.00 0.00 0.00 3.85
944 1033 3.119709 GAGAGCGAGTGAGCGAGGG 62.120 68.421 0.00 0.00 43.00 4.30
945 1034 0.812014 TAGAGAGCGAGTGAGCGAGG 60.812 60.000 0.00 0.00 43.00 4.63
946 1035 1.010580 TTAGAGAGCGAGTGAGCGAG 58.989 55.000 0.00 0.00 43.00 5.03
947 1036 0.727970 GTTAGAGAGCGAGTGAGCGA 59.272 55.000 0.00 0.00 43.00 4.93
948 1037 0.448197 TGTTAGAGAGCGAGTGAGCG 59.552 55.000 0.00 0.00 43.00 5.03
950 1039 3.238441 GTTGTGTTAGAGAGCGAGTGAG 58.762 50.000 0.00 0.00 0.00 3.51
951 1040 2.621526 TGTTGTGTTAGAGAGCGAGTGA 59.378 45.455 0.00 0.00 0.00 3.41
952 1041 2.726760 GTGTTGTGTTAGAGAGCGAGTG 59.273 50.000 0.00 0.00 0.00 3.51
953 1042 2.288273 GGTGTTGTGTTAGAGAGCGAGT 60.288 50.000 0.00 0.00 0.00 4.18
954 1043 2.329379 GGTGTTGTGTTAGAGAGCGAG 58.671 52.381 0.00 0.00 0.00 5.03
955 1044 1.000506 GGGTGTTGTGTTAGAGAGCGA 59.999 52.381 0.00 0.00 0.00 4.93
956 1045 1.270094 TGGGTGTTGTGTTAGAGAGCG 60.270 52.381 0.00 0.00 0.00 5.03
957 1046 2.143925 GTGGGTGTTGTGTTAGAGAGC 58.856 52.381 0.00 0.00 0.00 4.09
958 1047 3.393800 CAGTGGGTGTTGTGTTAGAGAG 58.606 50.000 0.00 0.00 0.00 3.20
960 1049 2.104111 TCCAGTGGGTGTTGTGTTAGAG 59.896 50.000 9.92 0.00 34.93 2.43
961 1050 2.104111 CTCCAGTGGGTGTTGTGTTAGA 59.896 50.000 9.92 0.00 34.93 2.10
964 1053 0.916086 TCTCCAGTGGGTGTTGTGTT 59.084 50.000 9.92 0.00 34.93 3.32
965 1054 0.469917 CTCTCCAGTGGGTGTTGTGT 59.530 55.000 9.92 0.00 34.93 3.72
966 1055 0.758734 TCTCTCCAGTGGGTGTTGTG 59.241 55.000 9.92 0.00 34.93 3.33
967 1056 1.051812 CTCTCTCCAGTGGGTGTTGT 58.948 55.000 9.92 0.00 34.93 3.32
968 1057 1.274728 CTCTCTCTCCAGTGGGTGTTG 59.725 57.143 9.92 0.00 34.93 3.33
969 1058 1.148027 TCTCTCTCTCCAGTGGGTGTT 59.852 52.381 9.92 0.00 34.93 3.32
970 1059 0.780637 TCTCTCTCTCCAGTGGGTGT 59.219 55.000 9.92 0.00 34.93 4.16
971 1060 1.005332 TCTCTCTCTCTCCAGTGGGTG 59.995 57.143 9.92 2.90 34.93 4.61
974 1063 2.505407 TCTCTCTCTCTCTCTCCAGTGG 59.495 54.545 1.40 1.40 0.00 4.00
976 1065 3.708631 CTCTCTCTCTCTCTCTCTCCAGT 59.291 52.174 0.00 0.00 0.00 4.00
977 1066 3.963374 TCTCTCTCTCTCTCTCTCTCCAG 59.037 52.174 0.00 0.00 0.00 3.86
979 1068 5.303971 CATTCTCTCTCTCTCTCTCTCTCC 58.696 50.000 0.00 0.00 0.00 3.71
980 1069 5.303971 CCATTCTCTCTCTCTCTCTCTCTC 58.696 50.000 0.00 0.00 0.00 3.20
982 1071 4.392940 CCCATTCTCTCTCTCTCTCTCTC 58.607 52.174 0.00 0.00 0.00 3.20
983 1072 3.139025 CCCCATTCTCTCTCTCTCTCTCT 59.861 52.174 0.00 0.00 0.00 3.10
984 1073 3.138283 TCCCCATTCTCTCTCTCTCTCTC 59.862 52.174 0.00 0.00 0.00 3.20
1017 3333 1.303643 CACCCCTTCCTTGGCACTC 60.304 63.158 0.00 0.00 0.00 3.51
1023 3339 1.280421 CCTCTCTTCACCCCTTCCTTG 59.720 57.143 0.00 0.00 0.00 3.61
1114 3430 1.242076 CCAGCTTTCAGTGGGACTTG 58.758 55.000 0.00 0.00 0.00 3.16
1122 3438 2.755650 CAGAACGTACCAGCTTTCAGT 58.244 47.619 0.00 0.00 0.00 3.41
1181 3505 5.128008 GCTCTCCATTTTCTACTCCTACTGT 59.872 44.000 0.00 0.00 0.00 3.55
1182 3506 5.362430 AGCTCTCCATTTTCTACTCCTACTG 59.638 44.000 0.00 0.00 0.00 2.74
1183 3507 5.524535 AGCTCTCCATTTTCTACTCCTACT 58.475 41.667 0.00 0.00 0.00 2.57
1184 3508 5.862678 AGCTCTCCATTTTCTACTCCTAC 57.137 43.478 0.00 0.00 0.00 3.18
1185 3509 5.834204 GGTAGCTCTCCATTTTCTACTCCTA 59.166 44.000 0.00 0.00 32.49 2.94
1186 3510 4.651962 GGTAGCTCTCCATTTTCTACTCCT 59.348 45.833 0.00 0.00 32.49 3.69
1187 3511 4.651962 AGGTAGCTCTCCATTTTCTACTCC 59.348 45.833 9.97 0.00 32.49 3.85
1188 3512 5.361285 TCAGGTAGCTCTCCATTTTCTACTC 59.639 44.000 9.97 0.00 32.49 2.59
1195 3522 2.567615 ACGTTCAGGTAGCTCTCCATTT 59.432 45.455 9.97 0.00 0.00 2.32
1522 3870 2.038975 CCCCGGAGTTGGAGGAGA 59.961 66.667 0.73 0.00 0.00 3.71
1534 3931 4.101448 AGCTTGTAGCAGCCCCGG 62.101 66.667 0.00 0.00 45.56 5.73
1543 3940 1.790387 GCAGCGTTGGAGCTTGTAG 59.210 57.895 0.16 0.00 46.80 2.74
1786 4219 4.654015 TGAAAACAAGTGTGAGCGTTAAC 58.346 39.130 0.00 0.00 0.00 2.01
1802 4235 3.888221 CGTGCACGTGCTGAAAAC 58.112 55.556 37.59 26.25 42.66 2.43
1851 4289 3.119531 TCGTACTACATTTGTGGGGTACG 60.120 47.826 23.47 23.47 44.28 3.67
1855 4293 5.013568 TGTATCGTACTACATTTGTGGGG 57.986 43.478 0.00 0.00 0.00 4.96
1856 4294 4.506654 GCTGTATCGTACTACATTTGTGGG 59.493 45.833 0.00 0.00 31.49 4.61
1857 4295 5.348986 AGCTGTATCGTACTACATTTGTGG 58.651 41.667 0.00 0.00 31.49 4.17
1858 4296 5.459107 GGAGCTGTATCGTACTACATTTGTG 59.541 44.000 0.00 0.00 31.49 3.33
1859 4297 5.126545 TGGAGCTGTATCGTACTACATTTGT 59.873 40.000 0.00 0.00 31.49 2.83
1860 4298 5.588240 TGGAGCTGTATCGTACTACATTTG 58.412 41.667 0.00 0.00 31.49 2.32
1863 4301 4.827835 ACATGGAGCTGTATCGTACTACAT 59.172 41.667 0.00 0.00 31.49 2.29
1864 4302 4.204799 ACATGGAGCTGTATCGTACTACA 58.795 43.478 0.00 0.00 0.00 2.74
1865 4303 4.832590 ACATGGAGCTGTATCGTACTAC 57.167 45.455 0.00 0.00 0.00 2.73
1866 4304 4.450080 CGTACATGGAGCTGTATCGTACTA 59.550 45.833 0.00 0.00 34.33 1.82
1867 4305 3.250280 CGTACATGGAGCTGTATCGTACT 59.750 47.826 0.00 0.00 34.33 2.73
1988 4437 1.525995 CGGCTGAACACACCCACTT 60.526 57.895 0.00 0.00 0.00 3.16
2003 4452 2.031683 GGCACACATACACTTATTCGGC 59.968 50.000 0.00 0.00 0.00 5.54
2072 4521 2.150397 AGAGCCACGTTGAAGTACAC 57.850 50.000 0.00 0.00 0.00 2.90
2104 4554 7.726291 AGAGATCGGTAGATATCCTTCTTTTCA 59.274 37.037 0.00 0.00 44.01 2.69
2121 4571 8.848474 TCTTTATCAAAGAAAAAGAGATCGGT 57.152 30.769 0.00 0.00 44.10 4.69
2204 4654 3.016736 GACACCGACATCCATCCAATTT 58.983 45.455 0.00 0.00 0.00 1.82
2216 4666 1.361271 GTCTCCAACGACACCGACA 59.639 57.895 0.00 0.00 39.50 4.35
2237 4690 9.937175 GAGGAAATCATAGTATTACAACAAAGC 57.063 33.333 0.00 0.00 0.00 3.51
2250 4703 9.830186 ACACCTATATAGTGAGGAAATCATAGT 57.170 33.333 8.92 0.00 40.92 2.12
2328 4965 7.585210 GTGGTGTCTTCTTTGTAATCGTAAAAC 59.415 37.037 0.00 0.00 0.00 2.43
2452 5089 6.847792 GCATTACTATCATCATGAACACAACG 59.152 38.462 0.00 0.00 0.00 4.10
2517 5154 4.342772 CGTCTCAACAAGGAAAACAACTG 58.657 43.478 0.00 0.00 0.00 3.16
2541 5180 1.375013 GGCCCGTAGCTTTTCGACA 60.375 57.895 0.00 0.00 43.05 4.35
2608 5248 9.503399 GGTTAGATTAGAAACAGAAAGGAAGAA 57.497 33.333 0.00 0.00 0.00 2.52
2618 5258 3.203716 GGCGGGGTTAGATTAGAAACAG 58.796 50.000 0.00 0.00 0.00 3.16
2650 5290 3.169099 ACATCTACAGGCAGACTCTTGT 58.831 45.455 0.00 0.00 0.00 3.16
2708 5348 1.153349 GGGTCTAGGGCTTTCGCTG 60.153 63.158 0.00 0.00 36.78 5.18
2732 5372 2.822701 GCCGTTCCCGATCCAACC 60.823 66.667 0.00 0.00 35.63 3.77
2750 5390 5.874831 TCACATATATGTTTTGTTGCGGTC 58.125 37.500 15.85 0.00 39.39 4.79


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

AutoCloner maintained by Alex Coulton.