Multiple sequence alignment - TraesCS3B01G424400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G424400 chr3B 100.000 2695 0 0 1 2695 662418783 662421477 0.000000e+00 4977.0
1 TraesCS3B01G424400 chr3B 89.225 761 72 7 1265 2018 662466645 662467402 0.000000e+00 942.0
2 TraesCS3B01G424400 chr3B 89.744 702 47 15 5 695 16081102 16081789 0.000000e+00 874.0
3 TraesCS3B01G424400 chr3B 91.809 586 44 4 1284 1867 661989203 661988620 0.000000e+00 813.0
4 TraesCS3B01G424400 chr3B 87.781 622 61 9 1265 1883 662366944 662367553 0.000000e+00 713.0
5 TraesCS3B01G424400 chr3B 82.602 615 62 24 94 695 404621402 404621984 4.010000e-138 501.0
6 TraesCS3B01G424400 chr3B 97.531 243 6 0 1025 1267 194636828 194637070 1.490000e-112 416.0
7 TraesCS3B01G424400 chr3B 85.714 399 51 6 1330 1724 662446130 662446526 1.490000e-112 416.0
8 TraesCS3B01G424400 chr3B 96.371 248 8 1 1026 1272 612798927 612798680 8.980000e-110 407.0
9 TraesCS3B01G424400 chr3B 82.065 184 30 2 1744 1926 661991839 661991658 1.290000e-33 154.0
10 TraesCS3B01G424400 chr3D 92.259 956 39 14 1265 2219 500841353 500842274 0.000000e+00 1323.0
11 TraesCS3B01G424400 chr3D 94.433 467 23 3 2229 2693 500843070 500843535 0.000000e+00 715.0
12 TraesCS3B01G424400 chr3D 89.163 203 9 2 837 1027 500841153 500841354 9.640000e-60 241.0
13 TraesCS3B01G424400 chr3D 90.964 166 14 1 837 1001 500847186 500847351 3.490000e-54 222.0
14 TraesCS3B01G424400 chr3A 89.623 954 78 14 1266 2217 640554879 640553945 0.000000e+00 1194.0
15 TraesCS3B01G424400 chr3A 84.294 694 77 18 1 674 529108740 529108059 0.000000e+00 649.0
16 TraesCS3B01G424400 chr3A 92.258 310 23 1 2228 2536 640553206 640552897 3.190000e-119 438.0
17 TraesCS3B01G424400 chr3A 95.257 253 11 1 1026 1277 644616803 644616551 1.500000e-107 399.0
18 TraesCS3B01G424400 chr3A 88.265 196 11 1 837 1020 640555081 640554886 9.710000e-55 224.0
19 TraesCS3B01G424400 chr3A 82.883 222 36 2 1744 1964 640513425 640513205 5.890000e-47 198.0
20 TraesCS3B01G424400 chr3A 84.058 207 22 7 1590 1792 640513620 640513421 3.540000e-44 189.0
21 TraesCS3B01G424400 chr3A 81.690 142 16 5 2077 2217 555388655 555388787 2.840000e-20 110.0
22 TraesCS3B01G424400 chr2B 90.309 712 42 11 1 698 725813013 725812315 0.000000e+00 907.0
23 TraesCS3B01G424400 chr2B 90.483 683 41 11 25 695 479990835 479991505 0.000000e+00 880.0
24 TraesCS3B01G424400 chr2B 89.235 706 53 10 1 695 618049685 618048992 0.000000e+00 861.0
25 TraesCS3B01G424400 chr2B 88.532 654 48 13 66 695 237591094 237591744 0.000000e+00 767.0
26 TraesCS3B01G424400 chr7B 89.266 708 47 17 1 695 530365979 530365288 0.000000e+00 859.0
27 TraesCS3B01G424400 chr7B 88.746 702 50 15 1 695 591727085 591727764 0.000000e+00 832.0
28 TraesCS3B01G424400 chr1B 88.967 707 52 15 1 695 576600542 576599850 0.000000e+00 850.0
29 TraesCS3B01G424400 chr1B 88.873 692 53 11 10 695 648107895 648108568 0.000000e+00 830.0
30 TraesCS3B01G424400 chr1B 97.119 243 7 0 1025 1267 575885354 575885112 6.940000e-111 411.0
31 TraesCS3B01G424400 chr1B 96.694 242 8 0 1025 1266 368225576 368225817 1.160000e-108 403.0
32 TraesCS3B01G424400 chr1B 77.931 145 18 8 2077 2217 613721013 613720879 8.000000e-11 78.7
33 TraesCS3B01G424400 chr4D 84.831 712 76 21 1 695 57896791 57897487 0.000000e+00 688.0
34 TraesCS3B01G424400 chr4D 87.692 65 7 1 2228 2291 277422987 277422923 1.030000e-09 75.0
35 TraesCS3B01G424400 chr7A 83.452 701 85 24 14 695 648893483 648892795 8.190000e-175 623.0
36 TraesCS3B01G424400 chr6D 84.967 612 79 10 88 695 100344787 100344185 2.290000e-170 608.0
37 TraesCS3B01G424400 chr6D 86.076 79 8 3 2143 2220 20407102 20407026 6.180000e-12 82.4
38 TraesCS3B01G424400 chr6B 83.333 636 56 13 80 695 1568893 1568288 2.360000e-150 542.0
39 TraesCS3B01G424400 chr6B 98.039 51 0 1 2242 2291 19141111 19141161 1.330000e-13 87.9
40 TraesCS3B01G424400 chr5A 97.531 243 6 0 1024 1266 840168 839926 1.490000e-112 416.0
41 TraesCS3B01G424400 chr5A 96.078 51 1 1 2242 2291 645267211 645267161 6.180000e-12 82.4
42 TraesCS3B01G424400 chr5B 97.510 241 6 0 1026 1266 648357426 648357666 1.930000e-111 412.0
43 TraesCS3B01G424400 chr5B 96.386 249 9 0 1026 1274 375130311 375130063 6.940000e-111 411.0
44 TraesCS3B01G424400 chr5B 94.118 51 2 1 2242 2291 650551832 650551782 2.880000e-10 76.8
45 TraesCS3B01G424400 chr5D 82.708 480 53 15 218 693 497016620 497017073 1.500000e-107 399.0
46 TraesCS3B01G424400 chr2A 92.222 270 18 3 1017 1284 350731876 350732144 1.960000e-101 379.0
47 TraesCS3B01G424400 chr2A 76.774 155 25 6 2064 2217 575675325 575675469 2.880000e-10 76.8
48 TraesCS3B01G424400 chr2D 81.391 489 65 19 218 695 630626548 630626075 2.530000e-100 375.0
49 TraesCS3B01G424400 chr4B 80.469 128 17 4 2091 2217 360233793 360233673 1.030000e-14 91.6
50 TraesCS3B01G424400 chr4B 84.146 82 6 6 2139 2217 44183741 44183818 3.720000e-09 73.1
51 TraesCS3B01G424400 chr1D 86.250 80 5 5 2140 2217 411061562 411061637 6.180000e-12 82.4
52 TraesCS3B01G424400 chrUn 80.909 110 8 8 2077 2184 26606370 26606272 1.030000e-09 75.0


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 TraesCS3B01G424400 chr3B 662418783 662421477 2694 False 4977.000000 4977 100.000000 1 2695 1 chr3B.!!$F5 2694
1 TraesCS3B01G424400 chr3B 662466645 662467402 757 False 942.000000 942 89.225000 1265 2018 1 chr3B.!!$F7 753
2 TraesCS3B01G424400 chr3B 16081102 16081789 687 False 874.000000 874 89.744000 5 695 1 chr3B.!!$F1 690
3 TraesCS3B01G424400 chr3B 662366944 662367553 609 False 713.000000 713 87.781000 1265 1883 1 chr3B.!!$F4 618
4 TraesCS3B01G424400 chr3B 404621402 404621984 582 False 501.000000 501 82.602000 94 695 1 chr3B.!!$F3 601
5 TraesCS3B01G424400 chr3B 661988620 661991839 3219 True 483.500000 813 86.937000 1284 1926 2 chr3B.!!$R2 642
6 TraesCS3B01G424400 chr3D 500841153 500847351 6198 False 625.250000 1323 91.704750 837 2693 4 chr3D.!!$F1 1856
7 TraesCS3B01G424400 chr3A 529108059 529108740 681 True 649.000000 649 84.294000 1 674 1 chr3A.!!$R1 673
8 TraesCS3B01G424400 chr3A 640552897 640555081 2184 True 618.666667 1194 90.048667 837 2536 3 chr3A.!!$R4 1699
9 TraesCS3B01G424400 chr2B 725812315 725813013 698 True 907.000000 907 90.309000 1 698 1 chr2B.!!$R2 697
10 TraesCS3B01G424400 chr2B 479990835 479991505 670 False 880.000000 880 90.483000 25 695 1 chr2B.!!$F2 670
11 TraesCS3B01G424400 chr2B 618048992 618049685 693 True 861.000000 861 89.235000 1 695 1 chr2B.!!$R1 694
12 TraesCS3B01G424400 chr2B 237591094 237591744 650 False 767.000000 767 88.532000 66 695 1 chr2B.!!$F1 629
13 TraesCS3B01G424400 chr7B 530365288 530365979 691 True 859.000000 859 89.266000 1 695 1 chr7B.!!$R1 694
14 TraesCS3B01G424400 chr7B 591727085 591727764 679 False 832.000000 832 88.746000 1 695 1 chr7B.!!$F1 694
15 TraesCS3B01G424400 chr1B 576599850 576600542 692 True 850.000000 850 88.967000 1 695 1 chr1B.!!$R2 694
16 TraesCS3B01G424400 chr1B 648107895 648108568 673 False 830.000000 830 88.873000 10 695 1 chr1B.!!$F2 685
17 TraesCS3B01G424400 chr4D 57896791 57897487 696 False 688.000000 688 84.831000 1 695 1 chr4D.!!$F1 694
18 TraesCS3B01G424400 chr7A 648892795 648893483 688 True 623.000000 623 83.452000 14 695 1 chr7A.!!$R1 681
19 TraesCS3B01G424400 chr6D 100344185 100344787 602 True 608.000000 608 84.967000 88 695 1 chr6D.!!$R2 607
20 TraesCS3B01G424400 chr6B 1568288 1568893 605 True 542.000000 542 83.333000 80 695 1 chr6B.!!$R1 615

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
123 132 0.179189 CGATTTTGCTTCCGCCAGAC 60.179 55.0 0.0 0.0 34.43 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1859 3215 0.534877 ACACAATGAAGGCAGCGACA 60.535 50.0 0.0 0.0 0.0 4.35 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
123 132 0.179189 CGATTTTGCTTCCGCCAGAC 60.179 55.000 0.00 0.00 34.43 3.51
649 742 0.817634 CCACTTGTCGCAACCTGGAA 60.818 55.000 0.00 0.00 0.00 3.53
655 749 4.339814 ACTTGTCGCAACCTGGAAAAATTA 59.660 37.500 0.00 0.00 0.00 1.40
729 823 7.915508 TGATCTATAATAACAACTTTGGTGCG 58.084 34.615 0.00 0.00 0.00 5.34
730 824 7.551262 TGATCTATAATAACAACTTTGGTGCGT 59.449 33.333 0.00 0.00 0.00 5.24
733 827 4.846779 AATAACAACTTTGGTGCGTGAT 57.153 36.364 0.00 0.00 0.00 3.06
734 828 4.846779 ATAACAACTTTGGTGCGTGATT 57.153 36.364 0.00 0.00 0.00 2.57
735 829 5.950758 ATAACAACTTTGGTGCGTGATTA 57.049 34.783 0.00 0.00 0.00 1.75
736 830 4.640789 AACAACTTTGGTGCGTGATTAA 57.359 36.364 0.00 0.00 0.00 1.40
739 833 3.915437 ACTTTGGTGCGTGATTAAAGG 57.085 42.857 0.00 0.00 33.77 3.11
742 836 0.963355 TGGTGCGTGATTAAAGGGCC 60.963 55.000 0.00 0.00 0.00 5.80
743 837 0.963355 GGTGCGTGATTAAAGGGCCA 60.963 55.000 6.18 0.00 0.00 5.36
744 838 1.102978 GTGCGTGATTAAAGGGCCAT 58.897 50.000 6.18 0.00 0.00 4.40
746 840 0.668535 GCGTGATTAAAGGGCCATCC 59.331 55.000 6.18 0.00 0.00 3.51
747 841 0.944386 CGTGATTAAAGGGCCATCCG 59.056 55.000 6.18 2.45 41.52 4.18
749 843 2.650322 GTGATTAAAGGGCCATCCGAA 58.350 47.619 6.18 0.00 41.52 4.30
751 845 1.602377 GATTAAAGGGCCATCCGAACG 59.398 52.381 6.18 0.00 41.52 3.95
752 846 0.393267 TTAAAGGGCCATCCGAACGG 60.393 55.000 6.18 6.94 41.52 4.44
753 847 2.260088 TAAAGGGCCATCCGAACGGG 62.260 60.000 6.18 0.00 41.52 5.28
758 852 3.840594 CCATCCGAACGGGCCGTA 61.841 66.667 34.37 17.90 39.99 4.02
760 854 2.440796 ATCCGAACGGGCCGTAGA 60.441 61.111 34.37 27.69 39.99 2.59
761 855 2.487532 ATCCGAACGGGCCGTAGAG 61.488 63.158 34.37 24.46 39.99 2.43
763 857 3.136123 CGAACGGGCCGTAGAGGA 61.136 66.667 34.37 0.00 45.00 3.71
764 858 2.806237 GAACGGGCCGTAGAGGAG 59.194 66.667 34.37 0.00 45.00 3.69
765 859 2.036890 AACGGGCCGTAGAGGAGT 59.963 61.111 34.37 12.35 45.00 3.85
766 860 1.602327 GAACGGGCCGTAGAGGAGTT 61.602 60.000 34.37 14.52 45.00 3.01
767 861 1.190178 AACGGGCCGTAGAGGAGTTT 61.190 55.000 34.37 10.59 45.00 2.66
768 862 0.323725 ACGGGCCGTAGAGGAGTTTA 60.324 55.000 33.31 0.00 45.00 2.01
769 863 0.819582 CGGGCCGTAGAGGAGTTTAA 59.180 55.000 19.97 0.00 45.00 1.52
770 864 1.411612 CGGGCCGTAGAGGAGTTTAAT 59.588 52.381 19.97 0.00 45.00 1.40
773 867 4.441913 CGGGCCGTAGAGGAGTTTAATAAA 60.442 45.833 19.97 0.00 45.00 1.40
774 868 5.430886 GGGCCGTAGAGGAGTTTAATAAAA 58.569 41.667 0.00 0.00 45.00 1.52
775 869 5.882000 GGGCCGTAGAGGAGTTTAATAAAAA 59.118 40.000 0.00 0.00 45.00 1.94
801 895 1.318576 CAAAAGAAGAACAGGGCCGT 58.681 50.000 0.00 0.00 0.00 5.68
802 896 1.001378 CAAAAGAAGAACAGGGCCGTG 60.001 52.381 23.61 23.61 0.00 4.94
803 897 0.537371 AAAGAAGAACAGGGCCGTGG 60.537 55.000 28.01 11.31 0.00 4.94
804 898 1.415672 AAGAAGAACAGGGCCGTGGA 61.416 55.000 28.01 0.00 0.00 4.02
805 899 1.376037 GAAGAACAGGGCCGTGGAG 60.376 63.158 28.01 5.02 0.00 3.86
806 900 2.804828 GAAGAACAGGGCCGTGGAGG 62.805 65.000 28.01 4.64 44.97 4.30
807 901 3.319198 GAACAGGGCCGTGGAGGA 61.319 66.667 28.01 0.00 45.00 3.71
808 902 3.316573 GAACAGGGCCGTGGAGGAG 62.317 68.421 28.01 3.48 45.00 3.69
821 915 2.365370 AGGAGGCCCTCAGCTCTG 60.365 66.667 13.90 0.00 38.86 3.35
823 917 4.527583 GAGGCCCTCAGCTCTGCG 62.528 72.222 5.69 0.00 43.05 5.18
827 921 4.504916 CCCTCAGCTCTGCGACGG 62.505 72.222 0.00 0.00 0.00 4.79
828 922 4.504916 CCTCAGCTCTGCGACGGG 62.505 72.222 0.00 0.00 0.00 5.28
829 923 3.443925 CTCAGCTCTGCGACGGGA 61.444 66.667 0.00 0.00 0.00 5.14
830 924 2.755876 TCAGCTCTGCGACGGGAT 60.756 61.111 0.00 0.00 0.00 3.85
831 925 1.448119 CTCAGCTCTGCGACGGGATA 61.448 60.000 0.00 0.00 0.00 2.59
832 926 1.035385 TCAGCTCTGCGACGGGATAA 61.035 55.000 0.00 0.00 0.00 1.75
833 927 0.596083 CAGCTCTGCGACGGGATAAG 60.596 60.000 0.00 0.00 0.00 1.73
834 928 0.752009 AGCTCTGCGACGGGATAAGA 60.752 55.000 0.00 0.00 0.00 2.10
844 938 4.142730 GCGACGGGATAAGAGTATTATCGT 60.143 45.833 10.58 7.49 33.38 3.73
939 1045 7.868922 CCTTTTCATTTTCATTGTCATCTGTCA 59.131 33.333 0.00 0.00 0.00 3.58
1006 1112 2.325484 TCCAGGACATATACATGGCGT 58.675 47.619 0.00 0.00 41.61 5.68
1020 1126 0.179234 TGGCGTTGGTCTCTGTTTCA 59.821 50.000 0.00 0.00 0.00 2.69
1025 1131 2.549754 CGTTGGTCTCTGTTTCAGCAAT 59.450 45.455 0.00 0.00 0.00 3.56
1026 1132 3.745975 CGTTGGTCTCTGTTTCAGCAATA 59.254 43.478 0.00 0.00 0.00 1.90
1028 1134 4.623932 TGGTCTCTGTTTCAGCAATACT 57.376 40.909 0.00 0.00 0.00 2.12
1029 1135 4.569943 TGGTCTCTGTTTCAGCAATACTC 58.430 43.478 0.00 0.00 0.00 2.59
1030 1136 3.935828 GGTCTCTGTTTCAGCAATACTCC 59.064 47.826 0.00 0.00 0.00 3.85
1032 1138 3.840666 TCTCTGTTTCAGCAATACTCCCT 59.159 43.478 0.00 0.00 0.00 4.20
1037 1143 4.263905 TGTTTCAGCAATACTCCCTCCATT 60.264 41.667 0.00 0.00 0.00 3.16
1038 1144 3.845781 TCAGCAATACTCCCTCCATTC 57.154 47.619 0.00 0.00 0.00 2.67
1039 1145 2.439507 TCAGCAATACTCCCTCCATTCC 59.560 50.000 0.00 0.00 0.00 3.01
1040 1146 2.173356 CAGCAATACTCCCTCCATTCCA 59.827 50.000 0.00 0.00 0.00 3.53
1041 1147 2.173569 AGCAATACTCCCTCCATTCCAC 59.826 50.000 0.00 0.00 0.00 4.02
1042 1148 2.092429 GCAATACTCCCTCCATTCCACA 60.092 50.000 0.00 0.00 0.00 4.17
1043 1149 3.624707 GCAATACTCCCTCCATTCCACAA 60.625 47.826 0.00 0.00 0.00 3.33
1044 1150 4.796606 CAATACTCCCTCCATTCCACAAT 58.203 43.478 0.00 0.00 0.00 2.71
1047 1153 3.189606 ACTCCCTCCATTCCACAATGTA 58.810 45.455 0.00 0.00 38.22 2.29
1048 1154 3.200825 ACTCCCTCCATTCCACAATGTAG 59.799 47.826 0.00 0.00 38.22 2.74
1049 1155 3.189606 TCCCTCCATTCCACAATGTAGT 58.810 45.455 0.00 0.00 38.22 2.73
1050 1156 3.054434 TCCCTCCATTCCACAATGTAGTG 60.054 47.826 0.00 0.00 38.22 2.74
1051 1157 2.684881 CCTCCATTCCACAATGTAGTGC 59.315 50.000 0.00 0.00 38.22 4.40
1053 1159 2.308570 TCCATTCCACAATGTAGTGCCT 59.691 45.455 0.00 0.00 38.22 4.75
1054 1160 2.684881 CCATTCCACAATGTAGTGCCTC 59.315 50.000 0.00 0.00 38.22 4.70
1055 1161 2.489938 TTCCACAATGTAGTGCCTCC 57.510 50.000 0.00 0.00 38.18 4.30
1056 1162 1.656587 TCCACAATGTAGTGCCTCCT 58.343 50.000 0.00 0.00 38.18 3.69
1057 1163 1.555075 TCCACAATGTAGTGCCTCCTC 59.445 52.381 0.00 0.00 38.18 3.71
1059 1165 2.766263 CCACAATGTAGTGCCTCCTCTA 59.234 50.000 0.00 0.00 38.18 2.43
1060 1166 3.389329 CCACAATGTAGTGCCTCCTCTAT 59.611 47.826 0.00 0.00 38.18 1.98
1061 1167 4.502259 CCACAATGTAGTGCCTCCTCTATC 60.502 50.000 0.00 0.00 38.18 2.08
1062 1168 3.643792 ACAATGTAGTGCCTCCTCTATCC 59.356 47.826 0.00 0.00 0.00 2.59
1063 1169 3.900601 CAATGTAGTGCCTCCTCTATCCT 59.099 47.826 0.00 0.00 0.00 3.24
1064 1170 3.231207 TGTAGTGCCTCCTCTATCCTC 57.769 52.381 0.00 0.00 0.00 3.71
1066 1172 0.553819 AGTGCCTCCTCTATCCTCGT 59.446 55.000 0.00 0.00 0.00 4.18
1068 1174 1.109920 TGCCTCCTCTATCCTCGTGC 61.110 60.000 0.00 0.00 0.00 5.34
1069 1175 0.825840 GCCTCCTCTATCCTCGTGCT 60.826 60.000 0.00 0.00 0.00 4.40
1070 1176 1.698506 CCTCCTCTATCCTCGTGCTT 58.301 55.000 0.00 0.00 0.00 3.91
1072 1178 2.302260 CTCCTCTATCCTCGTGCTTCA 58.698 52.381 0.00 0.00 0.00 3.02
1074 1180 2.427453 TCCTCTATCCTCGTGCTTCAAC 59.573 50.000 0.00 0.00 0.00 3.18
1075 1181 2.428890 CCTCTATCCTCGTGCTTCAACT 59.571 50.000 0.00 0.00 0.00 3.16
1077 1183 4.499183 CTCTATCCTCGTGCTTCAACTTT 58.501 43.478 0.00 0.00 0.00 2.66
1079 1185 2.613026 TCCTCGTGCTTCAACTTTGA 57.387 45.000 0.00 0.00 34.92 2.69
1080 1186 3.126001 TCCTCGTGCTTCAACTTTGAT 57.874 42.857 0.00 0.00 37.00 2.57
1083 1189 1.194547 TCGTGCTTCAACTTTGATCGC 59.805 47.619 6.76 6.76 37.00 4.58
1084 1190 1.069973 CGTGCTTCAACTTTGATCGCA 60.070 47.619 10.64 10.64 39.79 5.10
1086 1192 3.371168 GTGCTTCAACTTTGATCGCAAA 58.629 40.909 14.41 0.00 41.95 3.68
1087 1193 3.983344 GTGCTTCAACTTTGATCGCAAAT 59.017 39.130 14.41 0.00 42.66 2.32
1088 1194 4.445385 GTGCTTCAACTTTGATCGCAAATT 59.555 37.500 14.41 0.00 42.66 1.82
1089 1195 5.049167 TGCTTCAACTTTGATCGCAAATTT 58.951 33.333 11.75 0.00 42.66 1.82
1091 1197 6.699204 TGCTTCAACTTTGATCGCAAATTTAA 59.301 30.769 11.75 0.00 42.66 1.52
1093 1199 7.096065 GCTTCAACTTTGATCGCAAATTTAACT 60.096 33.333 8.21 0.00 42.66 2.24
1094 1200 9.393249 CTTCAACTTTGATCGCAAATTTAACTA 57.607 29.630 0.00 0.00 42.66 2.24
1095 1201 8.722342 TCAACTTTGATCGCAAATTTAACTAC 57.278 30.769 0.00 0.00 42.66 2.73
1096 1202 7.806014 TCAACTTTGATCGCAAATTTAACTACC 59.194 33.333 0.00 0.00 42.66 3.18
1097 1203 7.209471 ACTTTGATCGCAAATTTAACTACCA 57.791 32.000 0.00 0.00 42.66 3.25
1101 1207 5.353123 TGATCGCAAATTTAACTACCAGGAC 59.647 40.000 0.00 0.00 0.00 3.85
1102 1208 4.004982 TCGCAAATTTAACTACCAGGACC 58.995 43.478 0.00 0.00 0.00 4.46
1103 1209 3.181514 CGCAAATTTAACTACCAGGACCG 60.182 47.826 0.00 0.00 0.00 4.79
1104 1210 4.004982 GCAAATTTAACTACCAGGACCGA 58.995 43.478 0.00 0.00 0.00 4.69
1105 1211 4.638865 GCAAATTTAACTACCAGGACCGAT 59.361 41.667 0.00 0.00 0.00 4.18
1106 1212 5.124936 GCAAATTTAACTACCAGGACCGATT 59.875 40.000 0.00 0.00 0.00 3.34
1108 1214 2.973694 TAACTACCAGGACCGATTGC 57.026 50.000 0.00 0.00 0.00 3.56
1109 1215 0.108329 AACTACCAGGACCGATTGCG 60.108 55.000 0.00 0.00 37.24 4.85
1134 1240 6.618287 CGGGAGCAAAAATTATATCAGTGA 57.382 37.500 0.00 0.00 0.00 3.41
1135 1241 7.026631 CGGGAGCAAAAATTATATCAGTGAA 57.973 36.000 0.00 0.00 0.00 3.18
1136 1242 7.651808 CGGGAGCAAAAATTATATCAGTGAAT 58.348 34.615 0.00 0.00 0.00 2.57
1138 1244 9.468532 GGGAGCAAAAATTATATCAGTGAATTC 57.531 33.333 0.00 0.00 0.00 2.17
1139 1245 9.173939 GGAGCAAAAATTATATCAGTGAATTCG 57.826 33.333 0.00 0.00 0.00 3.34
1140 1246 9.722056 GAGCAAAAATTATATCAGTGAATTCGT 57.278 29.630 0.00 0.00 0.00 3.85
1186 1292 2.112297 TTTTTCTCCCGCCGCAGT 59.888 55.556 0.00 0.00 0.00 4.40
1187 1293 1.527380 TTTTTCTCCCGCCGCAGTT 60.527 52.632 0.00 0.00 0.00 3.16
1189 1295 4.697756 TTCTCCCGCCGCAGTTGG 62.698 66.667 0.00 0.00 0.00 3.77
1196 1302 2.665185 GCCGCAGTTGGTCTCGTT 60.665 61.111 0.00 0.00 0.00 3.85
1198 1304 2.317609 CCGCAGTTGGTCTCGTTGG 61.318 63.158 0.00 0.00 0.00 3.77
1199 1305 1.594293 CGCAGTTGGTCTCGTTGGT 60.594 57.895 0.00 0.00 0.00 3.67
1200 1306 1.157870 CGCAGTTGGTCTCGTTGGTT 61.158 55.000 0.00 0.00 0.00 3.67
1201 1307 1.870580 CGCAGTTGGTCTCGTTGGTTA 60.871 52.381 0.00 0.00 0.00 2.85
1202 1308 2.215196 GCAGTTGGTCTCGTTGGTTAA 58.785 47.619 0.00 0.00 0.00 2.01
1204 1310 3.252458 GCAGTTGGTCTCGTTGGTTAAAT 59.748 43.478 0.00 0.00 0.00 1.40
1206 1312 5.735070 GCAGTTGGTCTCGTTGGTTAAATTT 60.735 40.000 0.00 0.00 0.00 1.82
1207 1313 6.513720 GCAGTTGGTCTCGTTGGTTAAATTTA 60.514 38.462 0.00 0.00 0.00 1.40
1208 1314 7.590279 CAGTTGGTCTCGTTGGTTAAATTTAT 58.410 34.615 0.00 0.00 0.00 1.40
1209 1315 7.537306 CAGTTGGTCTCGTTGGTTAAATTTATG 59.463 37.037 0.00 0.00 0.00 1.90
1210 1316 6.503589 TGGTCTCGTTGGTTAAATTTATGG 57.496 37.500 0.00 0.00 0.00 2.74
1212 1318 6.149807 TGGTCTCGTTGGTTAAATTTATGGTC 59.850 38.462 0.00 0.00 0.00 4.02
1213 1319 6.149807 GGTCTCGTTGGTTAAATTTATGGTCA 59.850 38.462 0.00 0.00 0.00 4.02
1214 1320 7.308710 GGTCTCGTTGGTTAAATTTATGGTCAA 60.309 37.037 0.00 0.00 0.00 3.18
1215 1321 8.077386 GTCTCGTTGGTTAAATTTATGGTCAAA 58.923 33.333 0.00 0.00 0.00 2.69
1217 1323 7.942990 TCGTTGGTTAAATTTATGGTCAAAGT 58.057 30.769 0.00 0.00 0.00 2.66
1218 1324 8.414778 TCGTTGGTTAAATTTATGGTCAAAGTT 58.585 29.630 0.00 0.00 31.36 2.66
1219 1325 8.484008 CGTTGGTTAAATTTATGGTCAAAGTTG 58.516 33.333 0.00 0.00 29.44 3.16
1220 1326 9.535878 GTTGGTTAAATTTATGGTCAAAGTTGA 57.464 29.630 0.00 0.00 34.20 3.18
1222 1328 9.535878 TGGTTAAATTTATGGTCAAAGTTGAAC 57.464 29.630 1.98 1.98 45.04 3.18
1223 1329 8.984764 GGTTAAATTTATGGTCAAAGTTGAACC 58.015 33.333 6.62 6.25 44.20 3.62
1224 1330 9.758651 GTTAAATTTATGGTCAAAGTTGAACCT 57.241 29.630 6.62 0.00 44.20 3.50
1225 1331 9.974980 TTAAATTTATGGTCAAAGTTGAACCTC 57.025 29.630 6.62 0.00 44.20 3.85
1226 1332 5.682943 TTTATGGTCAAAGTTGAACCTCG 57.317 39.130 6.62 0.00 44.20 4.63
1229 1335 1.202722 GGTCAAAGTTGAACCTCGGGA 60.203 52.381 0.00 0.00 38.96 5.14
1230 1336 2.567985 GTCAAAGTTGAACCTCGGGAA 58.432 47.619 0.00 0.00 39.21 3.97
1234 1340 1.301479 GTTGAACCTCGGGAAGCGT 60.301 57.895 0.00 0.00 0.00 5.07
1236 1342 2.434359 GAACCTCGGGAAGCGTGG 60.434 66.667 0.00 0.00 0.00 4.94
1237 1343 3.952628 GAACCTCGGGAAGCGTGGG 62.953 68.421 0.00 0.00 0.00 4.61
1253 1359 4.539509 CGTGGGCGCACTATATTTTAAA 57.460 40.909 28.52 0.00 0.00 1.52
1254 1360 4.911053 CGTGGGCGCACTATATTTTAAAA 58.089 39.130 28.52 2.51 0.00 1.52
1255 1361 5.516090 CGTGGGCGCACTATATTTTAAAAT 58.484 37.500 28.52 17.18 0.00 1.82
1258 1364 5.594725 TGGGCGCACTATATTTTAAAATGGA 59.405 36.000 21.19 9.38 0.00 3.41
1259 1365 6.149633 GGGCGCACTATATTTTAAAATGGAG 58.850 40.000 21.19 18.49 0.00 3.86
1261 1367 6.149633 GCGCACTATATTTTAAAATGGAGGG 58.850 40.000 21.19 18.41 0.00 4.30
1456 2812 2.761195 CCGTCGTCTGCATCCTCGA 61.761 63.158 0.00 0.00 0.00 4.04
1760 3116 6.274157 TCTGAGATTCTGTTAAGGACTGTC 57.726 41.667 0.00 0.00 0.00 3.51
1854 3210 2.758979 CGGGAATCACACCTACTGTAGT 59.241 50.000 13.42 0.00 0.00 2.73
1855 3211 3.428999 CGGGAATCACACCTACTGTAGTG 60.429 52.174 13.42 12.99 39.93 2.74
1856 3212 3.767673 GGGAATCACACCTACTGTAGTGA 59.232 47.826 13.42 11.45 44.16 3.41
1857 3213 4.222145 GGGAATCACACCTACTGTAGTGAA 59.778 45.833 13.42 6.81 43.38 3.18
1858 3214 5.104900 GGGAATCACACCTACTGTAGTGAAT 60.105 44.000 13.42 5.26 43.38 2.57
1859 3215 6.407202 GGAATCACACCTACTGTAGTGAATT 58.593 40.000 13.42 14.01 43.38 2.17
1860 3216 6.313905 GGAATCACACCTACTGTAGTGAATTG 59.686 42.308 13.42 6.98 43.38 2.32
1861 3217 5.801531 TCACACCTACTGTAGTGAATTGT 57.198 39.130 13.42 5.95 37.99 2.71
1862 3218 5.779922 TCACACCTACTGTAGTGAATTGTC 58.220 41.667 13.42 0.00 37.99 3.18
1863 3219 4.621460 CACACCTACTGTAGTGAATTGTCG 59.379 45.833 13.42 0.00 37.43 4.35
1864 3220 3.612860 CACCTACTGTAGTGAATTGTCGC 59.387 47.826 13.42 0.00 36.01 5.19
1865 3221 3.510360 ACCTACTGTAGTGAATTGTCGCT 59.490 43.478 13.42 0.00 46.44 4.93
1866 3222 3.859961 CCTACTGTAGTGAATTGTCGCTG 59.140 47.826 13.42 0.00 44.45 5.18
1867 3223 2.069273 ACTGTAGTGAATTGTCGCTGC 58.931 47.619 0.12 0.00 44.45 5.25
1868 3224 1.394917 CTGTAGTGAATTGTCGCTGCC 59.605 52.381 0.00 0.00 43.93 4.85
1869 3225 1.001974 TGTAGTGAATTGTCGCTGCCT 59.998 47.619 0.00 0.00 43.93 4.75
1870 3226 2.076863 GTAGTGAATTGTCGCTGCCTT 58.923 47.619 0.00 0.00 44.45 4.35
1871 3227 1.160137 AGTGAATTGTCGCTGCCTTC 58.840 50.000 0.00 0.00 43.12 3.46
1872 3228 0.874390 GTGAATTGTCGCTGCCTTCA 59.126 50.000 0.00 0.00 0.00 3.02
1873 3229 1.470098 GTGAATTGTCGCTGCCTTCAT 59.530 47.619 0.00 0.00 0.00 2.57
1874 3230 2.095059 GTGAATTGTCGCTGCCTTCATT 60.095 45.455 0.00 0.00 0.00 2.57
1875 3231 2.095110 TGAATTGTCGCTGCCTTCATTG 60.095 45.455 0.00 0.00 0.00 2.82
1876 3232 1.538047 ATTGTCGCTGCCTTCATTGT 58.462 45.000 0.00 0.00 0.00 2.71
1877 3233 0.592637 TTGTCGCTGCCTTCATTGTG 59.407 50.000 0.00 0.00 0.00 3.33
1878 3234 0.534877 TGTCGCTGCCTTCATTGTGT 60.535 50.000 0.00 0.00 0.00 3.72
1925 3306 7.793902 TGAAAATTTTCACGTTTTCGGAAAAA 58.206 26.923 26.01 1.12 45.39 1.94
1964 3345 9.116054 GAAAAATTGCGTGCATTTTTATTGAAT 57.884 25.926 20.97 9.68 38.04 2.57
1996 3377 3.968649 AGTAAACTTGTGTGCTGCAATG 58.031 40.909 2.77 0.00 0.00 2.82
2088 3469 2.661718 TCTTTTGGCTCCTTCCGTTTT 58.338 42.857 0.00 0.00 0.00 2.43
2132 3513 9.241919 ACAGATTTCATCATAAACCACATACAA 57.758 29.630 0.00 0.00 0.00 2.41
2204 3586 5.358725 TGCTCCGTATTGTAGTTCATAGTGA 59.641 40.000 0.00 0.00 0.00 3.41
2226 3608 8.887717 AGTGAAATCTCTACAAATATGTCAAGC 58.112 33.333 0.00 0.00 41.05 4.01
2402 4574 9.809096 TTGTGTTTTAGCATGTCTTTTTGAATA 57.191 25.926 0.00 0.00 0.00 1.75
2454 4626 5.739161 GTGTTATTTAGCTCGAAAATGGCTG 59.261 40.000 6.38 0.00 37.50 4.85
2461 4634 2.805099 GCTCGAAAATGGCTGAGATAGG 59.195 50.000 0.00 0.00 0.00 2.57
2595 4768 0.467290 GCCCAACCCACTCAAACTCA 60.467 55.000 0.00 0.00 0.00 3.41
2658 4831 9.614792 GTAAGAGAATTTCTAGCAAATCCCTTA 57.385 33.333 0.00 0.00 34.14 2.69
2659 4832 8.512966 AAGAGAATTTCTAGCAAATCCCTTAC 57.487 34.615 0.00 0.00 34.14 2.34
2660 4833 7.633789 AGAGAATTTCTAGCAAATCCCTTACA 58.366 34.615 0.00 0.00 33.23 2.41
2661 4834 8.277918 AGAGAATTTCTAGCAAATCCCTTACAT 58.722 33.333 0.00 0.00 33.23 2.29
2662 4835 8.230472 AGAATTTCTAGCAAATCCCTTACATG 57.770 34.615 0.00 0.00 0.00 3.21
2663 4836 6.966534 ATTTCTAGCAAATCCCTTACATGG 57.033 37.500 0.00 0.00 0.00 3.66
2664 4837 3.820557 TCTAGCAAATCCCTTACATGGC 58.179 45.455 0.00 0.00 0.00 4.40
2665 4838 1.392589 AGCAAATCCCTTACATGGCG 58.607 50.000 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
460 513 9.598517 AGATCTTCAAAACTAGATCTCATGTTC 57.401 33.333 0.00 0.00 42.45 3.18
622 715 2.967076 CGACAAGTGGCGCACAGT 60.967 61.111 10.83 4.93 40.91 3.55
649 742 4.878397 CCTTGCGGAGATCACTCTAATTTT 59.122 41.667 0.00 0.00 42.28 1.82
655 749 3.289797 TCCTTGCGGAGATCACTCT 57.710 52.632 0.00 0.00 42.28 3.24
703 797 8.394877 CGCACCAAAGTTGTTATTATAGATCAA 58.605 33.333 0.00 0.00 0.00 2.57
704 798 7.551262 ACGCACCAAAGTTGTTATTATAGATCA 59.449 33.333 0.00 0.00 0.00 2.92
705 799 7.850982 CACGCACCAAAGTTGTTATTATAGATC 59.149 37.037 0.00 0.00 0.00 2.75
706 800 7.551262 TCACGCACCAAAGTTGTTATTATAGAT 59.449 33.333 0.00 0.00 0.00 1.98
707 801 6.874664 TCACGCACCAAAGTTGTTATTATAGA 59.125 34.615 0.00 0.00 0.00 1.98
709 803 7.618502 ATCACGCACCAAAGTTGTTATTATA 57.381 32.000 0.00 0.00 0.00 0.98
710 804 5.950758 TCACGCACCAAAGTTGTTATTAT 57.049 34.783 0.00 0.00 0.00 1.28
711 805 5.950758 ATCACGCACCAAAGTTGTTATTA 57.049 34.783 0.00 0.00 0.00 0.98
712 806 4.846779 ATCACGCACCAAAGTTGTTATT 57.153 36.364 0.00 0.00 0.00 1.40
713 807 4.846779 AATCACGCACCAAAGTTGTTAT 57.153 36.364 0.00 0.00 0.00 1.89
714 808 5.752892 TTAATCACGCACCAAAGTTGTTA 57.247 34.783 0.00 0.00 0.00 2.41
715 809 4.640789 TTAATCACGCACCAAAGTTGTT 57.359 36.364 0.00 0.00 0.00 2.83
716 810 4.499019 CCTTTAATCACGCACCAAAGTTGT 60.499 41.667 0.00 0.00 0.00 3.32
717 811 3.980775 CCTTTAATCACGCACCAAAGTTG 59.019 43.478 0.00 0.00 0.00 3.16
719 813 2.556622 CCCTTTAATCACGCACCAAAGT 59.443 45.455 0.00 0.00 0.00 2.66
721 815 1.271102 GCCCTTTAATCACGCACCAAA 59.729 47.619 0.00 0.00 0.00 3.28
722 816 0.885196 GCCCTTTAATCACGCACCAA 59.115 50.000 0.00 0.00 0.00 3.67
723 817 0.963355 GGCCCTTTAATCACGCACCA 60.963 55.000 0.00 0.00 0.00 4.17
725 819 1.065551 GATGGCCCTTTAATCACGCAC 59.934 52.381 0.00 0.00 0.00 5.34
726 820 1.388547 GATGGCCCTTTAATCACGCA 58.611 50.000 0.00 0.00 0.00 5.24
729 823 2.341846 TCGGATGGCCCTTTAATCAC 57.658 50.000 0.00 0.00 0.00 3.06
730 824 2.650322 GTTCGGATGGCCCTTTAATCA 58.350 47.619 0.00 0.00 0.00 2.57
733 827 0.393267 CCGTTCGGATGGCCCTTTAA 60.393 55.000 5.19 0.00 0.00 1.52
734 828 1.222387 CCGTTCGGATGGCCCTTTA 59.778 57.895 5.19 0.00 0.00 1.85
735 829 2.045340 CCGTTCGGATGGCCCTTT 60.045 61.111 5.19 0.00 0.00 3.11
736 830 4.109675 CCCGTTCGGATGGCCCTT 62.110 66.667 13.08 0.00 0.00 3.95
742 836 2.279252 CTACGGCCCGTTCGGATG 60.279 66.667 16.82 4.55 41.54 3.51
743 837 2.440796 TCTACGGCCCGTTCGGAT 60.441 61.111 16.82 0.00 41.54 4.18
744 838 3.136123 CTCTACGGCCCGTTCGGA 61.136 66.667 16.82 10.03 41.54 4.55
746 840 3.122250 CTCCTCTACGGCCCGTTCG 62.122 68.421 16.82 6.50 41.54 3.95
747 841 1.602327 AACTCCTCTACGGCCCGTTC 61.602 60.000 16.82 0.00 41.54 3.95
749 843 0.323725 TAAACTCCTCTACGGCCCGT 60.324 55.000 15.63 15.63 44.35 5.28
751 845 4.677673 TTATTAAACTCCTCTACGGCCC 57.322 45.455 0.00 0.00 0.00 5.80
752 846 6.990341 TTTTTATTAAACTCCTCTACGGCC 57.010 37.500 0.00 0.00 0.00 6.13
773 867 6.072728 GCCCTGTTCTTCTTTTGTTTTGTTTT 60.073 34.615 0.00 0.00 0.00 2.43
774 868 5.411361 GCCCTGTTCTTCTTTTGTTTTGTTT 59.589 36.000 0.00 0.00 0.00 2.83
775 869 4.935205 GCCCTGTTCTTCTTTTGTTTTGTT 59.065 37.500 0.00 0.00 0.00 2.83
776 870 4.503910 GCCCTGTTCTTCTTTTGTTTTGT 58.496 39.130 0.00 0.00 0.00 2.83
780 874 1.681264 CGGCCCTGTTCTTCTTTTGTT 59.319 47.619 0.00 0.00 0.00 2.83
781 875 1.318576 CGGCCCTGTTCTTCTTTTGT 58.681 50.000 0.00 0.00 0.00 2.83
783 877 1.318576 CACGGCCCTGTTCTTCTTTT 58.681 50.000 0.00 0.00 0.00 2.27
784 878 0.537371 CCACGGCCCTGTTCTTCTTT 60.537 55.000 0.00 0.00 0.00 2.52
785 879 1.073199 CCACGGCCCTGTTCTTCTT 59.927 57.895 0.00 0.00 0.00 2.52
786 880 1.831652 CTCCACGGCCCTGTTCTTCT 61.832 60.000 0.00 0.00 0.00 2.85
787 881 1.376037 CTCCACGGCCCTGTTCTTC 60.376 63.158 0.00 0.00 0.00 2.87
788 882 2.750350 CTCCACGGCCCTGTTCTT 59.250 61.111 0.00 0.00 0.00 2.52
790 884 3.316573 CTCCTCCACGGCCCTGTTC 62.317 68.421 0.00 0.00 0.00 3.18
791 885 3.322466 CTCCTCCACGGCCCTGTT 61.322 66.667 0.00 0.00 0.00 3.16
805 899 4.173924 GCAGAGCTGAGGGCCTCC 62.174 72.222 30.03 16.01 43.05 4.30
806 900 4.527583 CGCAGAGCTGAGGGCCTC 62.528 72.222 26.95 26.95 43.05 4.70
808 902 4.828925 GTCGCAGAGCTGAGGGCC 62.829 72.222 0.00 0.00 43.05 5.80
810 904 4.504916 CCGTCGCAGAGCTGAGGG 62.505 72.222 0.85 0.00 36.95 4.30
815 909 0.752009 TCTTATCCCGTCGCAGAGCT 60.752 55.000 0.00 0.00 36.95 4.09
816 910 0.318275 CTCTTATCCCGTCGCAGAGC 60.318 60.000 0.00 0.00 36.95 4.09
818 912 2.336945 TACTCTTATCCCGTCGCAGA 57.663 50.000 0.00 0.00 0.00 4.26
820 914 4.142752 CGATAATACTCTTATCCCGTCGCA 60.143 45.833 0.00 0.00 0.00 5.10
821 915 4.142730 ACGATAATACTCTTATCCCGTCGC 60.143 45.833 0.00 0.00 0.00 5.19
823 917 6.403418 CCTCACGATAATACTCTTATCCCGTC 60.403 46.154 0.00 0.00 0.00 4.79
824 918 5.415077 CCTCACGATAATACTCTTATCCCGT 59.585 44.000 0.00 0.00 0.00 5.28
826 920 5.950549 TCCCTCACGATAATACTCTTATCCC 59.049 44.000 0.00 0.00 0.00 3.85
827 921 7.648039 ATCCCTCACGATAATACTCTTATCC 57.352 40.000 0.00 0.00 0.00 2.59
828 922 8.740906 TGAATCCCTCACGATAATACTCTTATC 58.259 37.037 0.00 0.00 0.00 1.75
829 923 8.651589 TGAATCCCTCACGATAATACTCTTAT 57.348 34.615 0.00 0.00 0.00 1.73
830 924 8.358148 GTTGAATCCCTCACGATAATACTCTTA 58.642 37.037 0.00 0.00 32.21 2.10
831 925 6.978674 TGAATCCCTCACGATAATACTCTT 57.021 37.500 0.00 0.00 0.00 2.85
832 926 6.239345 GGTTGAATCCCTCACGATAATACTCT 60.239 42.308 0.00 0.00 32.21 3.24
833 927 5.927115 GGTTGAATCCCTCACGATAATACTC 59.073 44.000 0.00 0.00 32.21 2.59
834 928 5.365605 TGGTTGAATCCCTCACGATAATACT 59.634 40.000 0.00 0.00 32.21 2.12
844 938 0.329261 CTGCCTGGTTGAATCCCTCA 59.671 55.000 0.00 0.00 0.00 3.86
1006 1112 4.973168 AGTATTGCTGAAACAGAGACCAA 58.027 39.130 2.81 0.00 32.44 3.67
1020 1126 2.173569 GTGGAATGGAGGGAGTATTGCT 59.826 50.000 0.00 0.00 0.00 3.91
1025 1131 3.189606 ACATTGTGGAATGGAGGGAGTA 58.810 45.455 0.00 0.00 43.00 2.59
1026 1132 1.995542 ACATTGTGGAATGGAGGGAGT 59.004 47.619 0.00 0.00 43.00 3.85
1028 1134 3.931907 CTACATTGTGGAATGGAGGGA 57.068 47.619 0.00 0.00 44.23 4.20
1032 1138 2.308570 AGGCACTACATTGTGGAATGGA 59.691 45.455 7.20 0.00 43.00 3.41
1037 1143 1.555075 GAGGAGGCACTACATTGTGGA 59.445 52.381 7.20 0.00 46.07 4.02
1038 1144 1.556911 AGAGGAGGCACTACATTGTGG 59.443 52.381 0.00 0.00 46.07 4.17
1039 1145 4.502259 GGATAGAGGAGGCACTACATTGTG 60.502 50.000 0.00 0.00 46.07 3.33
1040 1146 3.643792 GGATAGAGGAGGCACTACATTGT 59.356 47.826 0.00 0.00 46.07 2.71
1041 1147 3.900601 AGGATAGAGGAGGCACTACATTG 59.099 47.826 0.00 0.00 46.07 2.82
1042 1148 4.156477 GAGGATAGAGGAGGCACTACATT 58.844 47.826 0.00 0.00 46.07 2.71
1043 1149 3.773560 GAGGATAGAGGAGGCACTACAT 58.226 50.000 0.00 0.00 46.07 2.29
1044 1150 2.487445 CGAGGATAGAGGAGGCACTACA 60.487 54.545 0.00 0.00 46.07 2.74
1048 1154 0.671251 CACGAGGATAGAGGAGGCAC 59.329 60.000 0.00 0.00 0.00 5.01
1049 1155 1.109920 GCACGAGGATAGAGGAGGCA 61.110 60.000 0.00 0.00 0.00 4.75
1050 1156 0.825840 AGCACGAGGATAGAGGAGGC 60.826 60.000 0.00 0.00 0.00 4.70
1051 1157 1.611491 GAAGCACGAGGATAGAGGAGG 59.389 57.143 0.00 0.00 0.00 4.30
1053 1159 2.427453 GTTGAAGCACGAGGATAGAGGA 59.573 50.000 0.00 0.00 0.00 3.71
1054 1160 2.428890 AGTTGAAGCACGAGGATAGAGG 59.571 50.000 0.00 0.00 0.00 3.69
1055 1161 3.791973 AGTTGAAGCACGAGGATAGAG 57.208 47.619 0.00 0.00 0.00 2.43
1056 1162 4.021456 TCAAAGTTGAAGCACGAGGATAGA 60.021 41.667 0.00 0.00 33.55 1.98
1057 1163 4.245660 TCAAAGTTGAAGCACGAGGATAG 58.754 43.478 0.00 0.00 33.55 2.08
1059 1165 3.126001 TCAAAGTTGAAGCACGAGGAT 57.874 42.857 0.00 0.00 33.55 3.24
1060 1166 2.613026 TCAAAGTTGAAGCACGAGGA 57.387 45.000 0.00 0.00 33.55 3.71
1061 1167 2.159787 CGATCAAAGTTGAAGCACGAGG 60.160 50.000 0.00 0.00 41.13 4.63
1062 1168 2.723010 GCGATCAAAGTTGAAGCACGAG 60.723 50.000 15.51 0.00 41.42 4.18
1063 1169 1.194547 GCGATCAAAGTTGAAGCACGA 59.805 47.619 15.51 0.00 41.42 4.35
1064 1170 1.069973 TGCGATCAAAGTTGAAGCACG 60.070 47.619 17.82 12.78 44.20 5.34
1066 1172 3.706802 TTTGCGATCAAAGTTGAAGCA 57.293 38.095 17.82 17.82 45.91 3.91
1068 1174 8.285776 AGTTAAATTTGCGATCAAAGTTGAAG 57.714 30.769 11.97 0.00 46.10 3.02
1069 1175 9.176181 GTAGTTAAATTTGCGATCAAAGTTGAA 57.824 29.630 11.97 2.95 46.10 2.69
1070 1176 7.806014 GGTAGTTAAATTTGCGATCAAAGTTGA 59.194 33.333 11.97 0.00 46.10 3.18
1074 1180 6.747280 CCTGGTAGTTAAATTTGCGATCAAAG 59.253 38.462 0.00 0.00 44.47 2.77
1075 1181 6.431543 TCCTGGTAGTTAAATTTGCGATCAAA 59.568 34.615 0.00 0.00 45.24 2.69
1077 1183 5.353123 GTCCTGGTAGTTAAATTTGCGATCA 59.647 40.000 0.00 0.00 0.00 2.92
1079 1185 4.638865 GGTCCTGGTAGTTAAATTTGCGAT 59.361 41.667 0.00 0.00 0.00 4.58
1080 1186 4.004982 GGTCCTGGTAGTTAAATTTGCGA 58.995 43.478 0.00 0.00 0.00 5.10
1083 1189 6.551736 CAATCGGTCCTGGTAGTTAAATTTG 58.448 40.000 0.00 0.00 0.00 2.32
1084 1190 5.124936 GCAATCGGTCCTGGTAGTTAAATTT 59.875 40.000 0.00 0.00 0.00 1.82
1086 1192 4.196971 GCAATCGGTCCTGGTAGTTAAAT 58.803 43.478 0.00 0.00 0.00 1.40
1087 1193 3.602483 GCAATCGGTCCTGGTAGTTAAA 58.398 45.455 0.00 0.00 0.00 1.52
1088 1194 2.417651 CGCAATCGGTCCTGGTAGTTAA 60.418 50.000 0.00 0.00 0.00 2.01
1089 1195 1.135527 CGCAATCGGTCCTGGTAGTTA 59.864 52.381 0.00 0.00 0.00 2.24
1091 1197 1.515954 CGCAATCGGTCCTGGTAGT 59.484 57.895 0.00 0.00 0.00 2.73
1103 1209 2.485188 TTTTTGCTCCCGCCGCAATC 62.485 55.000 5.33 0.00 45.67 2.67
1104 1210 1.887344 ATTTTTGCTCCCGCCGCAAT 61.887 50.000 5.33 0.00 45.67 3.56
1105 1211 2.093537 AATTTTTGCTCCCGCCGCAA 62.094 50.000 0.00 0.00 44.83 4.85
1106 1212 1.244697 TAATTTTTGCTCCCGCCGCA 61.245 50.000 0.00 0.00 35.22 5.69
1108 1214 3.252215 TGATATAATTTTTGCTCCCGCCG 59.748 43.478 0.00 0.00 34.43 6.46
1109 1215 4.278419 ACTGATATAATTTTTGCTCCCGCC 59.722 41.667 0.00 0.00 34.43 6.13
1110 1216 5.008613 TCACTGATATAATTTTTGCTCCCGC 59.991 40.000 0.00 0.00 0.00 6.13
1111 1217 6.618287 TCACTGATATAATTTTTGCTCCCG 57.382 37.500 0.00 0.00 0.00 5.14
1112 1218 9.468532 GAATTCACTGATATAATTTTTGCTCCC 57.531 33.333 0.00 0.00 0.00 4.30
1169 1275 1.527380 AACTGCGGCGGGAGAAAAA 60.527 52.632 19.55 0.00 35.29 1.94
1170 1276 2.112297 AACTGCGGCGGGAGAAAA 59.888 55.556 19.55 0.00 35.29 2.29
1172 1278 4.697756 CCAACTGCGGCGGGAGAA 62.698 66.667 19.55 0.00 35.29 2.87
1179 1285 2.665185 AACGAGACCAACTGCGGC 60.665 61.111 0.00 0.00 0.00 6.53
1180 1286 2.317609 CCAACGAGACCAACTGCGG 61.318 63.158 0.00 0.00 0.00 5.69
1182 1288 1.873698 TAACCAACGAGACCAACTGC 58.126 50.000 0.00 0.00 0.00 4.40
1184 1290 7.308951 CCATAAATTTAACCAACGAGACCAACT 60.309 37.037 1.21 0.00 0.00 3.16
1186 1292 6.490721 ACCATAAATTTAACCAACGAGACCAA 59.509 34.615 1.21 0.00 0.00 3.67
1187 1293 6.005198 ACCATAAATTTAACCAACGAGACCA 58.995 36.000 1.21 0.00 0.00 4.02
1189 1295 7.136289 TGACCATAAATTTAACCAACGAGAC 57.864 36.000 1.21 0.00 0.00 3.36
1190 1296 7.747155 TTGACCATAAATTTAACCAACGAGA 57.253 32.000 1.21 0.00 0.00 4.04
1191 1297 8.079809 ACTTTGACCATAAATTTAACCAACGAG 58.920 33.333 1.21 3.35 0.00 4.18
1192 1298 7.942990 ACTTTGACCATAAATTTAACCAACGA 58.057 30.769 1.21 0.00 0.00 3.85
1193 1299 8.484008 CAACTTTGACCATAAATTTAACCAACG 58.516 33.333 1.21 5.06 0.00 4.10
1194 1300 9.535878 TCAACTTTGACCATAAATTTAACCAAC 57.464 29.630 1.21 0.00 31.01 3.77
1196 1302 9.535878 GTTCAACTTTGACCATAAATTTAACCA 57.464 29.630 1.21 0.00 36.83 3.67
1198 1304 9.758651 AGGTTCAACTTTGACCATAAATTTAAC 57.241 29.630 1.21 0.00 36.83 2.01
1199 1305 9.974980 GAGGTTCAACTTTGACCATAAATTTAA 57.025 29.630 1.21 0.00 36.83 1.52
1200 1306 8.293867 CGAGGTTCAACTTTGACCATAAATTTA 58.706 33.333 0.00 0.00 36.83 1.40
1201 1307 7.145323 CGAGGTTCAACTTTGACCATAAATTT 58.855 34.615 0.00 0.00 36.83 1.82
1202 1308 6.294508 CCGAGGTTCAACTTTGACCATAAATT 60.295 38.462 11.01 0.00 36.83 1.82
1204 1310 4.517453 CCGAGGTTCAACTTTGACCATAAA 59.483 41.667 11.01 0.00 36.83 1.40
1206 1312 3.558321 CCCGAGGTTCAACTTTGACCATA 60.558 47.826 11.01 0.00 36.83 2.74
1207 1313 2.504367 CCGAGGTTCAACTTTGACCAT 58.496 47.619 11.01 0.00 36.83 3.55
1208 1314 1.476110 CCCGAGGTTCAACTTTGACCA 60.476 52.381 11.01 0.00 36.83 4.02
1209 1315 1.202722 TCCCGAGGTTCAACTTTGACC 60.203 52.381 0.00 0.00 36.83 4.02
1210 1316 2.249844 TCCCGAGGTTCAACTTTGAC 57.750 50.000 0.00 0.00 36.83 3.18
1212 1318 1.266989 GCTTCCCGAGGTTCAACTTTG 59.733 52.381 0.00 0.00 0.00 2.77
1213 1319 1.605753 GCTTCCCGAGGTTCAACTTT 58.394 50.000 0.00 0.00 0.00 2.66
1214 1320 0.602905 CGCTTCCCGAGGTTCAACTT 60.603 55.000 0.00 0.00 40.02 2.66
1215 1321 1.004918 CGCTTCCCGAGGTTCAACT 60.005 57.895 0.00 0.00 40.02 3.16
1217 1323 1.301401 CACGCTTCCCGAGGTTCAA 60.301 57.895 0.00 0.00 41.02 2.69
1218 1324 2.342279 CACGCTTCCCGAGGTTCA 59.658 61.111 0.00 0.00 41.02 3.18
1219 1325 2.434359 CCACGCTTCCCGAGGTTC 60.434 66.667 0.00 0.00 41.93 3.62
1220 1326 4.016706 CCCACGCTTCCCGAGGTT 62.017 66.667 0.00 0.00 44.85 3.50
1234 1340 5.594725 TCCATTTTAAAATATAGTGCGCCCA 59.405 36.000 12.98 0.00 0.00 5.36
1236 1342 6.149633 CCTCCATTTTAAAATATAGTGCGCC 58.850 40.000 12.98 0.00 0.00 6.53
1237 1343 6.016610 TCCCTCCATTTTAAAATATAGTGCGC 60.017 38.462 12.98 0.00 0.00 6.09
1238 1344 7.228706 ACTCCCTCCATTTTAAAATATAGTGCG 59.771 37.037 12.98 3.65 0.00 5.34
1739 3095 7.776618 TTAGACAGTCCTTAACAGAATCTCA 57.223 36.000 0.00 0.00 0.00 3.27
1747 3103 6.042781 ACAACCAGATTAGACAGTCCTTAACA 59.957 38.462 0.00 0.00 0.00 2.41
1760 3116 7.558161 TTGCATCATCTAACAACCAGATTAG 57.442 36.000 0.00 0.00 30.18 1.73
1854 3210 1.825090 ATGAAGGCAGCGACAATTCA 58.175 45.000 0.00 0.00 34.64 2.57
1855 3211 2.095059 ACAATGAAGGCAGCGACAATTC 60.095 45.455 0.00 0.00 0.00 2.17
1856 3212 1.888512 ACAATGAAGGCAGCGACAATT 59.111 42.857 0.00 0.00 0.00 2.32
1857 3213 1.200716 CACAATGAAGGCAGCGACAAT 59.799 47.619 0.00 0.00 0.00 2.71
1858 3214 0.592637 CACAATGAAGGCAGCGACAA 59.407 50.000 0.00 0.00 0.00 3.18
1859 3215 0.534877 ACACAATGAAGGCAGCGACA 60.535 50.000 0.00 0.00 0.00 4.35
1860 3216 1.394917 CTACACAATGAAGGCAGCGAC 59.605 52.381 0.00 0.00 0.00 5.19
1861 3217 1.275010 TCTACACAATGAAGGCAGCGA 59.725 47.619 0.00 0.00 0.00 4.93
1862 3218 1.725641 TCTACACAATGAAGGCAGCG 58.274 50.000 0.00 0.00 0.00 5.18
1863 3219 3.671702 GCTTTCTACACAATGAAGGCAGC 60.672 47.826 0.00 0.00 42.37 5.25
1864 3220 3.503363 TGCTTTCTACACAATGAAGGCAG 59.497 43.478 8.11 0.00 45.64 4.85
1866 3222 4.503741 TTGCTTTCTACACAATGAAGGC 57.496 40.909 0.00 0.00 42.88 4.35
1867 3223 6.071728 AGGATTTGCTTTCTACACAATGAAGG 60.072 38.462 0.00 0.00 0.00 3.46
1868 3224 6.917533 AGGATTTGCTTTCTACACAATGAAG 58.082 36.000 0.00 0.00 0.00 3.02
1869 3225 6.899393 AGGATTTGCTTTCTACACAATGAA 57.101 33.333 0.00 0.00 0.00 2.57
1870 3226 7.994425 TTAGGATTTGCTTTCTACACAATGA 57.006 32.000 0.00 0.00 0.00 2.57
1871 3227 9.474920 TTTTTAGGATTTGCTTTCTACACAATG 57.525 29.630 0.00 0.00 0.00 2.82
1872 3228 9.476202 GTTTTTAGGATTTGCTTTCTACACAAT 57.524 29.630 0.00 0.00 0.00 2.71
1873 3229 8.691797 AGTTTTTAGGATTTGCTTTCTACACAA 58.308 29.630 0.00 0.00 0.00 3.33
1874 3230 8.232913 AGTTTTTAGGATTTGCTTTCTACACA 57.767 30.769 0.00 0.00 0.00 3.72
1875 3231 8.968242 CAAGTTTTTAGGATTTGCTTTCTACAC 58.032 33.333 0.00 0.00 0.00 2.90
1876 3232 8.908903 TCAAGTTTTTAGGATTTGCTTTCTACA 58.091 29.630 0.00 0.00 0.00 2.74
1877 3233 9.744468 TTCAAGTTTTTAGGATTTGCTTTCTAC 57.256 29.630 0.00 0.00 0.00 2.59
1925 3306 8.272866 GCACGCAATTTTTCATAAAAGTAAACT 58.727 29.630 0.00 0.00 36.73 2.66
1964 3345 8.084073 AGCACACAAGTTTACTATACTAAACGA 58.916 33.333 8.48 0.00 40.26 3.85
1996 3377 1.137513 GTGTGCGAGGTTACTGTGAC 58.862 55.000 0.00 0.00 0.00 3.67
2053 3434 4.256920 CCAAAAGATGGTCAATCTCGAGT 58.743 43.478 13.13 0.00 45.37 4.18
2204 3586 8.579850 TTGGCTTGACATATTTGTAGAGATTT 57.420 30.769 0.00 0.00 35.79 2.17
2219 3601 8.801299 TCAAATATCTGTATTTTTGGCTTGACA 58.199 29.630 0.00 0.00 38.21 3.58
2220 3602 9.076596 GTCAAATATCTGTATTTTTGGCTTGAC 57.923 33.333 0.00 0.00 38.21 3.18
2280 4452 1.644337 TGAAGGCTACTACTCCCTCCA 59.356 52.381 0.00 0.00 0.00 3.86
2427 4599 6.539324 CCATTTTCGAGCTAAATAACACGAA 58.461 36.000 0.00 0.00 37.83 3.85
2430 4602 5.739161 CAGCCATTTTCGAGCTAAATAACAC 59.261 40.000 0.00 0.00 34.38 3.32
2454 4626 3.255888 TGTACCGATGTCATGCCTATCTC 59.744 47.826 0.00 0.00 0.00 2.75
2461 4634 2.893637 AGTCTTGTACCGATGTCATGC 58.106 47.619 0.00 0.00 0.00 4.06
2560 4733 1.985159 TGGGCTAGGTTCAAGTCATGT 59.015 47.619 0.00 0.00 0.00 3.21
2595 4768 1.880027 CGTTAGGGCTGCAAAAGAGTT 59.120 47.619 0.50 0.00 0.00 3.01
2658 4831 4.947388 ACTGATTTTACAATACCGCCATGT 59.053 37.500 0.00 0.00 0.00 3.21
2659 4832 5.499139 ACTGATTTTACAATACCGCCATG 57.501 39.130 0.00 0.00 0.00 3.66
2660 4833 6.524101 AAACTGATTTTACAATACCGCCAT 57.476 33.333 0.00 0.00 0.00 4.40
2661 4834 5.968528 AAACTGATTTTACAATACCGCCA 57.031 34.783 0.00 0.00 0.00 5.69
2662 4835 6.915843 CCATAAACTGATTTTACAATACCGCC 59.084 38.462 0.00 0.00 32.29 6.13
2663 4836 7.431084 CACCATAAACTGATTTTACAATACCGC 59.569 37.037 0.00 0.00 32.29 5.68
2664 4837 8.670135 TCACCATAAACTGATTTTACAATACCG 58.330 33.333 0.00 0.00 32.29 4.02


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

AutoCloner maintained by Alex Coulton.