Multiple sequence alignment - TraesCS3A01G481200

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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 TraesCS3A01G481200 chr3A 100.000 4639 0 0 1 4639 712321151 712325789 0.000000e+00 8567.0
1 TraesCS3A01G481200 chr3A 93.154 818 47 5 3085 3900 712454972 712455782 0.000000e+00 1192.0
2 TraesCS3A01G481200 chr3A 82.704 1191 99 44 906 2058 712379021 712380142 0.000000e+00 959.0
3 TraesCS3A01G481200 chr3A 85.681 852 63 28 2220 3020 712454135 712454978 0.000000e+00 843.0
4 TraesCS3A01G481200 chr3A 84.531 640 46 22 951 1576 712452714 712453314 6.690000e-163 584.0
5 TraesCS3A01G481200 chr3A 82.016 734 81 31 3090 3806 711381458 711380759 1.120000e-160 577.0
6 TraesCS3A01G481200 chr3A 86.820 478 44 12 2220 2689 712380510 712380976 2.470000e-142 516.0
7 TraesCS3A01G481200 chr3A 86.458 480 51 8 2220 2690 711382954 711382480 8.900000e-142 514.0
8 TraesCS3A01G481200 chr3A 90.028 361 23 8 410 758 712320746 712320387 5.470000e-124 455.0
9 TraesCS3A01G481200 chr3A 94.828 290 13 1 3127 3414 712381374 712381663 7.080000e-123 451.0
10 TraesCS3A01G481200 chr3A 83.402 482 60 13 2220 2691 711384524 711384053 3.320000e-116 429.0
11 TraesCS3A01G481200 chr3A 89.506 324 31 2 2704 3024 712381040 712381363 1.550000e-109 407.0
12 TraesCS3A01G481200 chr3A 81.667 540 47 31 1706 2225 711385078 711384571 7.230000e-108 401.0
13 TraesCS3A01G481200 chr3A 87.241 290 30 5 3379 3661 711302381 711302092 1.610000e-84 324.0
14 TraesCS3A01G481200 chr3A 89.627 241 21 3 1043 1282 711385633 711385396 2.100000e-78 303.0
15 TraesCS3A01G481200 chr3A 87.192 203 20 3 2797 2998 711381668 711381471 4.670000e-55 226.0
16 TraesCS3A01G481200 chr3A 91.176 136 12 0 4031 4166 600920878 600921013 7.930000e-43 185.0
17 TraesCS3A01G481200 chr3A 90.647 139 13 0 4031 4169 660858504 660858366 7.930000e-43 185.0
18 TraesCS3A01G481200 chr3A 83.696 184 9 7 2060 2222 712453900 712454083 2.240000e-33 154.0
19 TraesCS3A01G481200 chr3A 91.111 90 6 2 3853 3941 712455779 712455867 2.270000e-23 121.0
20 TraesCS3A01G481200 chr3A 86.316 95 5 3 2060 2150 712380315 712380405 3.820000e-16 97.1
21 TraesCS3A01G481200 chr3A 90.411 73 6 1 2704 2775 711381737 711381665 1.370000e-15 95.3
22 TraesCS3A01G481200 chr3D 93.507 2264 100 23 774 3028 577026109 577023884 0.000000e+00 3323.0
23 TraesCS3A01G481200 chr3D 97.422 892 17 2 3052 3941 577023902 577023015 0.000000e+00 1515.0
24 TraesCS3A01G481200 chr3D 93.818 825 41 6 3078 3900 577179151 577179967 0.000000e+00 1232.0
25 TraesCS3A01G481200 chr3D 88.271 827 59 18 2220 3018 577178347 577179163 0.000000e+00 955.0
26 TraesCS3A01G481200 chr3D 84.706 680 56 24 906 1576 577176862 577177502 1.820000e-178 636.0
27 TraesCS3A01G481200 chr3D 85.057 522 43 21 3134 3641 577153749 577153249 2.490000e-137 499.0
28 TraesCS3A01G481200 chr3D 84.601 526 54 13 3428 3931 576853457 576852937 8.960000e-137 497.0
29 TraesCS3A01G481200 chr3D 84.696 477 43 16 3210 3661 577144386 577143915 2.550000e-122 449.0
30 TraesCS3A01G481200 chr3D 89.634 328 30 3 2704 3028 576854096 576853770 9.290000e-112 414.0
31 TraesCS3A01G481200 chr3D 78.393 722 74 35 908 1590 576856283 576855605 1.210000e-105 394.0
32 TraesCS3A01G481200 chr3D 85.714 343 40 2 2356 2690 575838607 575838266 2.050000e-93 353.0
33 TraesCS3A01G481200 chr3D 83.578 341 40 9 1616 1955 576855612 576855287 5.830000e-79 305.0
34 TraesCS3A01G481200 chr3D 93.846 195 12 0 1043 1237 577145532 577145338 1.260000e-75 294.0
35 TraesCS3A01G481200 chr3D 88.797 241 24 3 1043 1282 575840344 575840106 4.540000e-75 292.0
36 TraesCS3A01G481200 chr3D 81.250 384 49 15 2220 2591 575839261 575838889 5.870000e-74 289.0
37 TraesCS3A01G481200 chr3D 84.158 303 30 11 1706 1999 575839789 575839496 1.270000e-70 278.0
38 TraesCS3A01G481200 chr3D 88.780 205 22 1 2797 3000 575837332 575837128 2.770000e-62 250.0
39 TraesCS3A01G481200 chr3D 89.922 129 13 0 1838 1966 577177833 577177961 2.870000e-37 167.0
40 TraesCS3A01G481200 chr3D 94.231 104 5 1 2894 2996 575765500 575765397 1.730000e-34 158.0
41 TraesCS3A01G481200 chr3D 79.902 204 37 3 4440 4639 577180253 577180456 3.740000e-31 147.0
42 TraesCS3A01G481200 chr3D 92.308 91 3 1 2060 2150 576854970 576854884 4.870000e-25 126.0
43 TraesCS3A01G481200 chr3D 78.873 213 20 13 2029 2225 575839511 575839308 2.270000e-23 121.0
44 TraesCS3A01G481200 chr3D 100.000 32 0 0 2704 2735 575837391 575837360 5.010000e-05 60.2
45 TraesCS3A01G481200 chr3B 93.212 825 43 8 3085 3900 768725801 768726621 0.000000e+00 1201.0
46 TraesCS3A01G481200 chr3B 87.170 834 61 25 2220 3020 768724985 768725805 0.000000e+00 905.0
47 TraesCS3A01G481200 chr3B 86.247 778 77 17 3127 3896 768672208 768672963 0.000000e+00 817.0
48 TraesCS3A01G481200 chr3B 84.451 701 74 22 3146 3831 768264590 768265270 0.000000e+00 658.0
49 TraesCS3A01G481200 chr3B 79.480 1038 125 49 1706 2690 768511163 768512165 0.000000e+00 656.0
50 TraesCS3A01G481200 chr3B 82.602 638 59 23 1043 1670 768723614 768724209 2.470000e-142 516.0
51 TraesCS3A01G481200 chr3B 77.778 810 100 35 902 1675 768572501 768573266 4.290000e-115 425.0
52 TraesCS3A01G481200 chr3B 81.031 543 47 22 1706 2225 768261969 768262478 9.420000e-102 381.0
53 TraesCS3A01G481200 chr3B 88.779 303 31 2 2715 3015 768671826 768672127 7.330000e-98 368.0
54 TraesCS3A01G481200 chr3B 78.161 696 66 37 906 1563 768670064 768670711 9.490000e-97 364.0
55 TraesCS3A01G481200 chr3B 83.990 406 32 9 1706 2098 766835337 766834952 4.410000e-95 359.0
56 TraesCS3A01G481200 chr3B 81.128 461 52 19 1697 2152 768670852 768671282 2.070000e-88 337.0
57 TraesCS3A01G481200 chr3B 85.531 311 44 1 43 353 207126779 207126470 1.610000e-84 324.0
58 TraesCS3A01G481200 chr3B 90.222 225 19 2 1043 1267 768261418 768261639 1.630000e-74 291.0
59 TraesCS3A01G481200 chr3B 83.333 186 22 7 2506 2690 768573409 768573586 3.710000e-36 163.0
60 TraesCS3A01G481200 chr3B 80.978 184 13 8 2060 2221 768724749 768724932 4.870000e-25 126.0
61 TraesCS3A01G481200 chr3B 97.015 67 2 0 2060 2126 768671282 768671348 3.790000e-21 113.0
62 TraesCS3A01G481200 chr3B 100.000 32 0 0 2704 2735 768264261 768264292 5.010000e-05 60.2
63 TraesCS3A01G481200 chr2B 93.726 797 40 4 3147 3941 657053176 657052388 0.000000e+00 1186.0
64 TraesCS3A01G481200 chr2B 84.632 950 74 30 788 1675 657055312 657054373 0.000000e+00 880.0
65 TraesCS3A01G481200 chr2B 91.786 560 39 5 1671 2229 657054310 657053757 0.000000e+00 773.0
66 TraesCS3A01G481200 chr2B 92.308 299 20 2 4342 4639 657052029 657051733 5.550000e-114 422.0
67 TraesCS3A01G481200 chr2B 86.243 378 26 9 2220 2595 657053711 657053358 2.020000e-103 387.0
68 TraesCS3A01G481200 chr2B 96.341 164 6 0 2844 3007 657053337 657053174 2.130000e-68 270.0
69 TraesCS3A01G481200 chr2B 83.462 260 20 4 3946 4191 657052353 657052103 2.170000e-53 220.0
70 TraesCS3A01G481200 chr2B 89.899 99 9 1 4235 4332 657052111 657052013 4.870000e-25 126.0
71 TraesCS3A01G481200 chr5A 94.466 777 25 8 1 761 525127108 525127882 0.000000e+00 1181.0
72 TraesCS3A01G481200 chr5A 87.705 366 30 7 411 764 525126715 525126353 3.340000e-111 412.0
73 TraesCS3A01G481200 chr2D 87.077 797 63 20 1 759 441544616 441545410 0.000000e+00 865.0
74 TraesCS3A01G481200 chr2D 87.368 380 28 8 402 761 441544346 441543967 7.180000e-113 418.0
75 TraesCS3A01G481200 chr7D 90.816 392 36 0 1 392 414424704 414425095 4.110000e-145 525.0
76 TraesCS3A01G481200 chr7D 86.807 379 29 10 402 760 414424431 414424054 2.010000e-108 403.0
77 TraesCS3A01G481200 chr7D 86.579 380 27 9 402 759 414425160 414425537 9.350000e-107 398.0
78 TraesCS3A01G481200 chr6B 85.161 310 45 1 43 352 15802850 15803158 2.690000e-82 316.0
79 TraesCS3A01G481200 chr4A 91.367 139 11 1 4032 4169 5222868 5222730 6.130000e-44 189.0
80 TraesCS3A01G481200 chr5D 90.278 144 12 2 4031 4172 526253972 526253829 2.200000e-43 187.0
81 TraesCS3A01G481200 chr4D 90.278 144 13 1 4033 4175 386984804 386984661 2.200000e-43 187.0
82 TraesCS3A01G481200 chr1D 90.714 140 13 0 4031 4170 332997198 332997337 2.200000e-43 187.0
83 TraesCS3A01G481200 chr1D 90.647 139 13 0 4031 4169 443117332 443117194 7.930000e-43 185.0
84 TraesCS3A01G481200 chr1D 83.784 185 23 7 3993 4172 423040559 423040741 7.980000e-38 169.0
85 TraesCS3A01G481200 chr4B 90.647 139 13 0 4031 4169 142427518 142427380 7.930000e-43 185.0


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 TraesCS3A01G481200 chr3A 712321151 712325789 4638 False 8567.000000 8567 100.000000 1 4639 1 chr3A.!!$F2 4638
1 TraesCS3A01G481200 chr3A 712452714 712455867 3153 False 578.800000 1192 87.634600 951 3941 5 chr3A.!!$F4 2990
2 TraesCS3A01G481200 chr3A 712379021 712381663 2642 False 486.020000 959 88.034800 906 3414 5 chr3A.!!$F3 2508
3 TraesCS3A01G481200 chr3A 711380759 711385633 4874 True 363.614286 577 85.824714 1043 3806 7 chr3A.!!$R4 2763
4 TraesCS3A01G481200 chr3D 577023015 577026109 3094 True 2419.000000 3323 95.464500 774 3941 2 chr3D.!!$R5 3167
5 TraesCS3A01G481200 chr3D 577176862 577180456 3594 False 627.400000 1232 87.323800 906 4639 5 chr3D.!!$F1 3733
6 TraesCS3A01G481200 chr3D 577153249 577153749 500 True 499.000000 499 85.057000 3134 3641 1 chr3D.!!$R2 507
7 TraesCS3A01G481200 chr3D 577143915 577145532 1617 True 371.500000 449 89.271000 1043 3661 2 chr3D.!!$R6 2618
8 TraesCS3A01G481200 chr3D 576852937 576856283 3346 True 347.200000 497 85.702800 908 3931 5 chr3D.!!$R4 3023
9 TraesCS3A01G481200 chr3D 575837128 575840344 3216 True 234.742857 353 86.796000 1043 3000 7 chr3D.!!$R3 1957
10 TraesCS3A01G481200 chr3B 768723614 768726621 3007 False 687.000000 1201 85.990500 1043 3900 4 chr3B.!!$F5 2857
11 TraesCS3A01G481200 chr3B 768511163 768512165 1002 False 656.000000 656 79.480000 1706 2690 1 chr3B.!!$F1 984
12 TraesCS3A01G481200 chr3B 768670064 768672963 2899 False 399.800000 817 86.266000 906 3896 5 chr3B.!!$F4 2990
13 TraesCS3A01G481200 chr3B 768261418 768265270 3852 False 347.550000 658 88.926000 1043 3831 4 chr3B.!!$F2 2788
14 TraesCS3A01G481200 chr3B 768572501 768573586 1085 False 294.000000 425 80.555500 902 2690 2 chr3B.!!$F3 1788
15 TraesCS3A01G481200 chr2B 657051733 657055312 3579 True 533.000000 1186 89.799625 788 4639 8 chr2B.!!$R1 3851
16 TraesCS3A01G481200 chr5A 525127108 525127882 774 False 1181.000000 1181 94.466000 1 761 1 chr5A.!!$F1 760
17 TraesCS3A01G481200 chr2D 441544616 441545410 794 False 865.000000 865 87.077000 1 759 1 chr2D.!!$F1 758
18 TraesCS3A01G481200 chr7D 414424704 414425537 833 False 461.500000 525 88.697500 1 759 2 chr7D.!!$F1 758

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
702 797 0.183014 TTTGGGTGCCGGAGTGTTTA 59.817 50.0 5.05 0.00 0.00 2.01 F
904 1007 0.249238 CTAGGTGTCAGCTGATCCGC 60.249 60.0 21.47 14.26 0.00 5.54 F
1441 1731 0.455410 TGCACAATTATCGCAAGCCC 59.545 50.0 0.00 0.00 31.46 5.19 F
2044 2938 0.738063 CTCACTCTGCTCTGCTGCTG 60.738 60.0 0.00 0.00 0.00 4.41 F
2166 3287 0.878416 TGTGCGGCAATTGGTAGTTC 59.122 50.0 3.23 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 2344 0.524862 CTCCCAGCTGCAATTCACAC 59.475 55.000 8.66 0.00 0.0 3.82 R
1898 2504 0.601046 CTGTGAAGACGCCAAGCAGA 60.601 55.000 0.00 0.00 0.0 4.26 R
3207 9179 1.542108 GCAGTGAGGCTCAAGACAACT 60.542 52.381 20.62 8.06 0.0 3.16 R
3461 9462 0.108662 CCAGCGCGCCATAGATCATA 60.109 55.000 30.33 0.00 0.0 2.15 R
3948 10054 0.830444 AACGCCACCCACTAGACAGA 60.830 55.000 0.00 0.00 0.0 3.41 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
76 77 2.676744 CGCAACTATGATGGCGTCA 58.323 52.632 12.53 12.53 44.11 4.35
190 191 0.742505 CGTCAGGCGGTAGGTATTCA 59.257 55.000 0.00 0.00 36.85 2.57
290 291 4.778415 CGTGCTCCCGACGGACAG 62.778 72.222 17.49 11.91 33.32 3.51
486 558 2.043752 TCGGGCGATACAGTGGGA 60.044 61.111 0.00 0.00 0.00 4.37
528 600 2.511545 GATTTGGCTGGGGCTGCAAC 62.512 60.000 0.50 0.00 38.73 4.17
570 642 2.093869 GTGGAGTGCGGGTTCATTACTA 60.094 50.000 0.00 0.00 0.00 1.82
604 677 0.380378 GGTTTCTGCAAAGTCACGCA 59.620 50.000 0.00 0.00 36.52 5.24
702 797 0.183014 TTTGGGTGCCGGAGTGTTTA 59.817 50.000 5.05 0.00 0.00 2.01
713 808 3.570550 CCGGAGTGTTTATGGGTCAAAAA 59.429 43.478 0.00 0.00 0.00 1.94
754 849 2.052104 GGGCCTGCCGTGCTTTTAT 61.052 57.895 0.84 0.00 36.85 1.40
759 854 2.359900 CCTGCCGTGCTTTTATCTCTT 58.640 47.619 0.00 0.00 0.00 2.85
761 856 3.426695 CCTGCCGTGCTTTTATCTCTTTG 60.427 47.826 0.00 0.00 0.00 2.77
762 857 3.407698 TGCCGTGCTTTTATCTCTTTGA 58.592 40.909 0.00 0.00 0.00 2.69
763 858 3.818210 TGCCGTGCTTTTATCTCTTTGAA 59.182 39.130 0.00 0.00 0.00 2.69
764 859 4.458989 TGCCGTGCTTTTATCTCTTTGAAT 59.541 37.500 0.00 0.00 0.00 2.57
765 860 5.048083 TGCCGTGCTTTTATCTCTTTGAATT 60.048 36.000 0.00 0.00 0.00 2.17
766 861 5.287035 GCCGTGCTTTTATCTCTTTGAATTG 59.713 40.000 0.00 0.00 0.00 2.32
767 862 5.287035 CCGTGCTTTTATCTCTTTGAATTGC 59.713 40.000 0.00 0.00 0.00 3.56
768 863 5.287035 CGTGCTTTTATCTCTTTGAATTGCC 59.713 40.000 0.00 0.00 0.00 4.52
769 864 6.393171 GTGCTTTTATCTCTTTGAATTGCCT 58.607 36.000 0.00 0.00 0.00 4.75
770 865 6.309737 GTGCTTTTATCTCTTTGAATTGCCTG 59.690 38.462 0.00 0.00 0.00 4.85
771 866 6.015180 TGCTTTTATCTCTTTGAATTGCCTGT 60.015 34.615 0.00 0.00 0.00 4.00
772 867 6.309737 GCTTTTATCTCTTTGAATTGCCTGTG 59.690 38.462 0.00 0.00 0.00 3.66
785 880 1.239347 GCCTGTGTCCTTCCTTGAAC 58.761 55.000 0.00 0.00 0.00 3.18
790 885 2.025793 TGTGTCCTTCCTTGAACCAACA 60.026 45.455 0.00 0.00 0.00 3.33
797 892 4.277423 CCTTCCTTGAACCAACAAACGTAT 59.723 41.667 0.00 0.00 0.00 3.06
825 920 2.094906 GCGTAGACCCCAATTTTCCAAC 60.095 50.000 0.00 0.00 0.00 3.77
852 955 2.332654 GCGAAACATTCCCACGCCT 61.333 57.895 0.00 0.00 42.79 5.52
876 979 1.992277 CTGCCTGACTAGTGGGCCT 60.992 63.158 24.89 0.00 44.71 5.19
885 988 1.041437 CTAGTGGGCCTAGCTGGTAC 58.959 60.000 4.53 0.00 36.98 3.34
886 989 0.635009 TAGTGGGCCTAGCTGGTACT 59.365 55.000 4.53 0.00 38.35 2.73
887 990 0.635009 AGTGGGCCTAGCTGGTACTA 59.365 55.000 4.53 0.00 38.35 1.82
902 1005 2.362717 GGTACTAGGTGTCAGCTGATCC 59.637 54.545 21.47 23.26 0.00 3.36
904 1007 0.249238 CTAGGTGTCAGCTGATCCGC 60.249 60.000 21.47 14.26 0.00 5.54
911 1027 3.390521 AGCTGATCCGCCCGTTCA 61.391 61.111 5.40 0.00 0.00 3.18
1148 1371 2.870161 CGCGGTCGTCTTCGTCAG 60.870 66.667 0.00 0.00 38.33 3.51
1161 1384 3.845259 GTCAGGGTCCGCGCCATA 61.845 66.667 0.00 0.00 0.00 2.74
1308 1571 2.116125 GCAGTTTGCAGGGAGGGT 59.884 61.111 0.00 0.00 44.26 4.34
1309 1572 1.531602 GCAGTTTGCAGGGAGGGTT 60.532 57.895 0.00 0.00 44.26 4.11
1310 1573 1.115326 GCAGTTTGCAGGGAGGGTTT 61.115 55.000 0.00 0.00 44.26 3.27
1311 1574 1.413118 CAGTTTGCAGGGAGGGTTTT 58.587 50.000 0.00 0.00 0.00 2.43
1312 1575 1.341209 CAGTTTGCAGGGAGGGTTTTC 59.659 52.381 0.00 0.00 0.00 2.29
1313 1576 1.063266 AGTTTGCAGGGAGGGTTTTCA 60.063 47.619 0.00 0.00 0.00 2.69
1314 1577 1.970640 GTTTGCAGGGAGGGTTTTCAT 59.029 47.619 0.00 0.00 0.00 2.57
1356 1637 4.872691 AGAAACAGAGCATGTATGTACAGC 59.127 41.667 0.33 0.00 43.00 4.40
1435 1725 6.712241 ACTACTATGATGCACAATTATCGC 57.288 37.500 0.00 0.00 0.00 4.58
1441 1731 0.455410 TGCACAATTATCGCAAGCCC 59.545 50.000 0.00 0.00 31.46 5.19
1592 1972 4.304110 GTCGTTCTGTGTATTCCAACTGA 58.696 43.478 0.00 0.00 0.00 3.41
1675 2055 4.104776 CGTGCGATTTCATTATGGCTTTT 58.895 39.130 0.00 0.00 31.42 2.27
1676 2056 4.027458 CGTGCGATTTCATTATGGCTTTTG 60.027 41.667 0.00 0.00 31.42 2.44
1784 2344 1.843368 AGAATGGGATGTGGTTGCTG 58.157 50.000 0.00 0.00 0.00 4.41
1818 2383 6.451393 CAGCTGGGAGTATAATCTGTTACTC 58.549 44.000 5.57 2.26 42.27 2.59
1836 2402 4.410492 ACTCATGAAACGCTTGTCAATC 57.590 40.909 0.00 0.00 0.00 2.67
1852 2418 6.000891 TGTCAATCTTTTGTATGCAGTGAC 57.999 37.500 0.00 0.00 34.32 3.67
1898 2504 1.529244 GCACCCAGTCAACCTGCTT 60.529 57.895 0.00 0.00 40.06 3.91
2044 2938 0.738063 CTCACTCTGCTCTGCTGCTG 60.738 60.000 0.00 0.00 0.00 4.41
2166 3287 0.878416 TGTGCGGCAATTGGTAGTTC 59.122 50.000 3.23 0.00 0.00 3.01
2170 3291 1.094785 CGGCAATTGGTAGTTCCCTG 58.905 55.000 7.72 0.00 34.77 4.45
2261 4649 5.551233 CATTTTCCTAGTCTGTGTTGAGGA 58.449 41.667 0.00 0.00 34.46 3.71
2279 4668 4.072131 GAGGACAAATTGTAGCTGTTGGA 58.928 43.478 0.00 0.00 0.00 3.53
2391 5870 8.337532 GCAAATTTCAGCTGTTACTTTTTGAAT 58.662 29.630 14.67 0.00 0.00 2.57
2396 5875 6.738114 TCAGCTGTTACTTTTTGAATTCAGG 58.262 36.000 14.67 3.66 0.00 3.86
2617 6136 2.747989 GGTTGCAGGACTAGCTTAAACC 59.252 50.000 0.00 0.00 31.33 3.27
2618 6137 2.747989 GTTGCAGGACTAGCTTAAACCC 59.252 50.000 0.00 0.00 0.00 4.11
3009 8969 6.613153 AGTTCATTTAGTAGTCCTGCTCTT 57.387 37.500 0.00 0.00 0.00 2.85
3010 8970 6.635755 AGTTCATTTAGTAGTCCTGCTCTTC 58.364 40.000 0.00 0.00 0.00 2.87
3011 8971 6.439058 AGTTCATTTAGTAGTCCTGCTCTTCT 59.561 38.462 0.00 0.00 0.00 2.85
3012 8972 7.616150 AGTTCATTTAGTAGTCCTGCTCTTCTA 59.384 37.037 0.00 0.00 0.00 2.10
3013 8973 8.417884 GTTCATTTAGTAGTCCTGCTCTTCTAT 58.582 37.037 0.00 0.00 0.00 1.98
3014 8974 9.642343 TTCATTTAGTAGTCCTGCTCTTCTATA 57.358 33.333 0.00 0.00 0.00 1.31
3015 8975 9.815306 TCATTTAGTAGTCCTGCTCTTCTATAT 57.185 33.333 0.00 0.00 0.00 0.86
3131 9091 4.258543 TGTCGGTATGATGGGTTTTCTTC 58.741 43.478 0.00 0.00 0.00 2.87
3207 9179 3.709653 AGGCTGGGATTCTTACAATCGTA 59.290 43.478 0.00 0.00 0.00 3.43
3384 9372 5.346281 GTGTGTCGCCTATTTATCTATCAGC 59.654 44.000 0.00 0.00 0.00 4.26
3385 9373 5.010617 TGTGTCGCCTATTTATCTATCAGCA 59.989 40.000 0.00 0.00 0.00 4.41
3549 9550 5.474825 TCATCAAGCGTTACAAGTATGACA 58.525 37.500 0.00 0.00 0.00 3.58
3741 9750 7.726033 AGAATTGTATAGTCTGGTCTGTCTT 57.274 36.000 0.00 0.00 0.00 3.01
3782 9791 7.801716 TGTTGCTTACTTTAGTTCAGTTGAT 57.198 32.000 0.00 0.00 0.00 2.57
3783 9792 8.220755 TGTTGCTTACTTTAGTTCAGTTGATT 57.779 30.769 0.00 0.00 0.00 2.57
3784 9793 8.128582 TGTTGCTTACTTTAGTTCAGTTGATTG 58.871 33.333 0.00 0.00 0.00 2.67
3785 9794 8.342634 GTTGCTTACTTTAGTTCAGTTGATTGA 58.657 33.333 0.00 0.00 0.00 2.57
3843 9866 5.182570 CGTCGGTTCTATTCTATGGATGGTA 59.817 44.000 0.00 0.00 0.00 3.25
3941 10017 3.394836 GGCTTCTGGACGAGGGCT 61.395 66.667 0.00 0.00 40.56 5.19
3942 10018 2.665603 GCTTCTGGACGAGGGCTT 59.334 61.111 0.00 0.00 0.00 4.35
3944 10020 1.021920 GCTTCTGGACGAGGGCTTTC 61.022 60.000 0.00 0.00 0.00 2.62
3948 10054 1.831652 CTGGACGAGGGCTTTCTGGT 61.832 60.000 0.00 0.00 0.00 4.00
4016 10122 4.594920 CCAGATTCTAAGCTATTCCCTCCA 59.405 45.833 0.00 0.00 0.00 3.86
4019 10125 7.127032 CCAGATTCTAAGCTATTCCCTCCATAT 59.873 40.741 0.00 0.00 0.00 1.78
4021 10127 9.965983 AGATTCTAAGCTATTCCCTCCATATAT 57.034 33.333 0.00 0.00 0.00 0.86
4022 10128 9.995003 GATTCTAAGCTATTCCCTCCATATATG 57.005 37.037 5.68 5.68 0.00 1.78
4023 10129 8.917414 TTCTAAGCTATTCCCTCCATATATGT 57.083 34.615 11.73 0.00 0.00 2.29
4024 10130 8.540507 TCTAAGCTATTCCCTCCATATATGTC 57.459 38.462 11.73 0.00 0.00 3.06
4025 10131 6.567602 AAGCTATTCCCTCCATATATGTCC 57.432 41.667 11.73 0.00 0.00 4.02
4026 10132 5.859429 AGCTATTCCCTCCATATATGTCCT 58.141 41.667 11.73 0.00 0.00 3.85
4028 10134 6.737608 AGCTATTCCCTCCATATATGTCCTTT 59.262 38.462 11.73 0.00 0.00 3.11
4029 10135 7.240616 AGCTATTCCCTCCATATATGTCCTTTT 59.759 37.037 11.73 0.00 0.00 2.27
4047 10153 9.635404 TGTCCTTTTAGTCTTTTTGGAGATTTA 57.365 29.630 0.00 0.00 0.00 1.40
4111 10218 7.828223 AGAATGTAGATTCACTCATTTTGCTCT 59.172 33.333 14.46 0.00 40.59 4.09
4128 10248 5.183014 TGCTCTGTATGTAGTCCGTATTG 57.817 43.478 0.00 0.00 0.00 1.90
4166 10286 9.467030 AAGACTTATATTTAGGAAAGGAGGGAT 57.533 33.333 0.00 0.00 0.00 3.85
4167 10287 9.467030 AGACTTATATTTAGGAAAGGAGGGATT 57.533 33.333 0.00 0.00 0.00 3.01
4181 10301 6.075949 AGGAGGGATTAAAACTAAAGGGAC 57.924 41.667 0.00 0.00 0.00 4.46
4186 10306 5.449999 GGGATTAAAACTAAAGGGACGCATG 60.450 44.000 0.00 0.00 0.00 4.06
4187 10307 5.124936 GGATTAAAACTAAAGGGACGCATGT 59.875 40.000 0.00 0.00 0.00 3.21
4188 10308 6.349860 GGATTAAAACTAAAGGGACGCATGTT 60.350 38.462 0.00 0.00 0.00 2.71
4189 10309 4.929819 AAAACTAAAGGGACGCATGTTT 57.070 36.364 0.00 0.00 0.00 2.83
4190 10310 4.929819 AAACTAAAGGGACGCATGTTTT 57.070 36.364 0.00 0.00 0.00 2.43
4191 10311 4.929819 AACTAAAGGGACGCATGTTTTT 57.070 36.364 0.00 0.00 0.00 1.94
4210 10330 4.377839 TTTTTGATGAAACGCTGGTGAA 57.622 36.364 0.00 0.00 0.00 3.18
4211 10331 3.624326 TTTGATGAAACGCTGGTGAAG 57.376 42.857 0.00 0.00 0.00 3.02
4223 10343 3.722728 CTGGTGAAGCAGCTTTTCTTT 57.277 42.857 9.62 0.00 32.61 2.52
4224 10344 4.050852 CTGGTGAAGCAGCTTTTCTTTT 57.949 40.909 9.62 0.00 32.61 2.27
4225 10345 4.045636 TGGTGAAGCAGCTTTTCTTTTC 57.954 40.909 9.62 0.00 32.61 2.29
4226 10346 3.446873 TGGTGAAGCAGCTTTTCTTTTCA 59.553 39.130 9.62 0.00 32.61 2.69
4227 10347 4.081752 TGGTGAAGCAGCTTTTCTTTTCAA 60.082 37.500 9.62 0.00 31.52 2.69
4228 10348 5.052481 GGTGAAGCAGCTTTTCTTTTCAAT 58.948 37.500 9.62 0.00 31.52 2.57
4229 10349 5.525012 GGTGAAGCAGCTTTTCTTTTCAATT 59.475 36.000 9.62 0.00 31.52 2.32
4230 10350 6.701400 GGTGAAGCAGCTTTTCTTTTCAATTA 59.299 34.615 9.62 0.00 31.52 1.40
4231 10351 7.095899 GGTGAAGCAGCTTTTCTTTTCAATTAG 60.096 37.037 9.62 0.00 31.52 1.73
4234 10354 6.145535 AGCAGCTTTTCTTTTCAATTAGACG 58.854 36.000 0.00 0.00 0.00 4.18
4236 10356 5.914635 CAGCTTTTCTTTTCAATTAGACGCA 59.085 36.000 0.00 0.00 0.00 5.24
4275 10395 3.130340 ACTTAGAGCAACTCTAGCAGAGC 59.870 47.826 11.60 1.84 46.12 4.09
4276 10396 0.823460 AGAGCAACTCTAGCAGAGCC 59.177 55.000 11.60 3.34 46.12 4.70
4295 10416 1.862123 GTCATGTGTGGTCGCTGTG 59.138 57.895 0.00 0.00 0.00 3.66
4301 10422 0.652592 GTGTGGTCGCTGTGATATGC 59.347 55.000 0.00 0.00 0.00 3.14
4304 10425 0.179076 TGGTCGCTGTGATATGCCAG 60.179 55.000 0.00 0.00 0.00 4.85
4314 10435 3.135167 TGTGATATGCCAGAGAGATTGCA 59.865 43.478 0.00 0.00 38.23 4.08
4315 10436 4.132336 GTGATATGCCAGAGAGATTGCAA 58.868 43.478 0.00 0.00 37.27 4.08
4316 10437 4.577693 GTGATATGCCAGAGAGATTGCAAA 59.422 41.667 1.71 0.00 37.27 3.68
4317 10438 4.820173 TGATATGCCAGAGAGATTGCAAAG 59.180 41.667 1.71 0.00 37.27 2.77
4318 10439 1.830279 TGCCAGAGAGATTGCAAAGG 58.170 50.000 1.71 0.00 0.00 3.11
4319 10440 0.455005 GCCAGAGAGATTGCAAAGGC 59.545 55.000 1.71 5.10 41.68 4.35
4331 10452 1.952193 GCAAAGGCAAAATGTGTGGT 58.048 45.000 0.00 0.00 40.72 4.16
4332 10453 3.104843 GCAAAGGCAAAATGTGTGGTA 57.895 42.857 0.00 0.00 40.72 3.25
4333 10454 3.059166 GCAAAGGCAAAATGTGTGGTAG 58.941 45.455 0.00 0.00 40.72 3.18
4334 10455 3.059166 CAAAGGCAAAATGTGTGGTAGC 58.941 45.455 0.00 0.00 0.00 3.58
4335 10456 1.256812 AGGCAAAATGTGTGGTAGCC 58.743 50.000 0.00 0.00 40.85 3.93
4336 10457 0.965439 GGCAAAATGTGTGGTAGCCA 59.035 50.000 0.00 0.00 40.29 4.75
4337 10458 1.550072 GGCAAAATGTGTGGTAGCCAT 59.450 47.619 0.00 0.00 40.29 4.40
4338 10459 2.417243 GGCAAAATGTGTGGTAGCCATC 60.417 50.000 0.00 0.00 40.29 3.51
4339 10460 2.230992 GCAAAATGTGTGGTAGCCATCA 59.769 45.455 0.00 0.00 35.28 3.07
4340 10461 3.119029 GCAAAATGTGTGGTAGCCATCAT 60.119 43.478 0.00 0.00 35.28 2.45
4359 10480 0.940519 TAAGGCGAAACGTGTGGTCG 60.941 55.000 0.00 0.00 37.82 4.79
4375 10496 2.560981 TGGTCGCCGTCATATGACATAT 59.439 45.455 30.15 1.87 44.99 1.78
4376 10497 3.759618 TGGTCGCCGTCATATGACATATA 59.240 43.478 30.15 13.55 44.99 0.86
4387 10508 9.500864 CGTCATATGACATATAGAGATTGTGAG 57.499 37.037 30.15 8.44 44.99 3.51
4458 10579 1.610038 CACACGTGTGTCCTACCTGTA 59.390 52.381 35.03 0.00 42.83 2.74
4466 10587 4.929808 GTGTGTCCTACCTGTAATTGACTG 59.070 45.833 0.00 0.00 0.00 3.51
4564 10689 7.239763 TGTTCATTGTAGACCTCTTACATCA 57.760 36.000 0.00 0.00 0.00 3.07
4615 10740 5.783111 AGATCCACCATTTACAAAGCAAAC 58.217 37.500 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.459089 GTCCTCCGTCAGGCTGCC 62.459 72.222 11.65 11.65 43.08 4.85
190 191 4.488911 AGGGAGGCTGGAGGCGAT 62.489 66.667 0.00 0.00 46.23 4.58
375 376 0.888619 TCGCTCGTCTTCAAGGACAT 59.111 50.000 0.00 0.00 36.12 3.06
433 505 1.005394 CTAGGTCAACAACGGCGGT 60.005 57.895 13.24 0.00 0.00 5.68
441 513 2.182827 AGCATGAGAGCTAGGTCAACA 58.817 47.619 23.18 20.66 44.50 3.33
486 558 3.764972 CCTAGTTTCTCTCCCTCTCGTTT 59.235 47.826 0.00 0.00 0.00 3.60
528 600 2.044252 TCTCCCTCTCGTTCCCCG 60.044 66.667 0.00 0.00 38.13 5.73
754 849 3.149196 GGACACAGGCAATTCAAAGAGA 58.851 45.455 0.00 0.00 0.00 3.10
759 854 2.158475 AGGAAGGACACAGGCAATTCAA 60.158 45.455 0.00 0.00 0.00 2.69
761 856 2.206576 AGGAAGGACACAGGCAATTC 57.793 50.000 0.00 0.00 0.00 2.17
762 857 2.158475 TCAAGGAAGGACACAGGCAATT 60.158 45.455 0.00 0.00 0.00 2.32
763 858 1.425066 TCAAGGAAGGACACAGGCAAT 59.575 47.619 0.00 0.00 0.00 3.56
764 859 0.843309 TCAAGGAAGGACACAGGCAA 59.157 50.000 0.00 0.00 0.00 4.52
765 860 0.843309 TTCAAGGAAGGACACAGGCA 59.157 50.000 0.00 0.00 0.00 4.75
766 861 1.239347 GTTCAAGGAAGGACACAGGC 58.761 55.000 0.00 0.00 0.00 4.85
767 862 1.142870 TGGTTCAAGGAAGGACACAGG 59.857 52.381 0.00 0.00 0.00 4.00
768 863 2.618709 GTTGGTTCAAGGAAGGACACAG 59.381 50.000 0.00 0.00 0.00 3.66
769 864 2.025793 TGTTGGTTCAAGGAAGGACACA 60.026 45.455 0.00 0.00 0.00 3.72
770 865 2.650322 TGTTGGTTCAAGGAAGGACAC 58.350 47.619 0.00 0.00 0.00 3.67
771 866 3.374042 TTGTTGGTTCAAGGAAGGACA 57.626 42.857 0.00 0.00 0.00 4.02
772 867 3.488553 CGTTTGTTGGTTCAAGGAAGGAC 60.489 47.826 0.00 0.00 0.00 3.85
785 880 0.446222 CGGCTCCATACGTTTGTTGG 59.554 55.000 5.27 3.14 0.00 3.77
790 885 0.526954 CTACGCGGCTCCATACGTTT 60.527 55.000 12.47 0.00 39.78 3.60
825 920 1.401018 GGAATGTTTCGCGGTTCCTTG 60.401 52.381 6.13 0.00 37.67 3.61
852 955 1.065926 CCACTAGTCAGGCAGATGCAA 60.066 52.381 7.19 0.00 44.36 4.08
876 979 2.376109 GCTGACACCTAGTACCAGCTA 58.624 52.381 9.83 0.00 44.75 3.32
885 988 0.249238 GCGGATCAGCTGACACCTAG 60.249 60.000 27.81 19.10 0.00 3.02
886 989 1.676678 GGCGGATCAGCTGACACCTA 61.677 60.000 27.81 6.60 37.29 3.08
887 990 2.581354 GCGGATCAGCTGACACCT 59.419 61.111 27.81 12.61 0.00 4.00
892 995 3.371097 GAACGGGCGGATCAGCTGA 62.371 63.158 20.79 20.79 37.29 4.26
895 998 3.195698 GTGAACGGGCGGATCAGC 61.196 66.667 9.58 9.58 0.00 4.26
902 1005 2.480555 GAGCAATGTGAACGGGCG 59.519 61.111 0.00 0.00 0.00 6.13
904 1007 1.026718 GGAGGAGCAATGTGAACGGG 61.027 60.000 0.00 0.00 0.00 5.28
911 1027 0.842030 TGACTGGGGAGGAGCAATGT 60.842 55.000 0.00 0.00 0.00 2.71
998 1161 4.812476 CGTCGCCGCCCTTCATCA 62.812 66.667 0.00 0.00 0.00 3.07
1034 1242 3.688159 CCGTCGTCCCCTTCGGTT 61.688 66.667 0.00 0.00 38.45 4.44
1161 1384 0.178929 AGGAGACGAAGAAGTGGGGT 60.179 55.000 0.00 0.00 0.00 4.95
1329 1602 8.165239 TGTACATACATGCTCTGTTTCTTTTT 57.835 30.769 0.00 0.00 39.39 1.94
1356 1637 7.810766 ATGTCGCAATTTAATTTTGTACAGG 57.189 32.000 0.00 0.00 30.86 4.00
1475 1777 2.368439 AGCAGTTGACAGAGCAAAACA 58.632 42.857 0.00 0.00 0.00 2.83
1488 1802 0.036577 AGCTCAGTGGCTAGCAGTTG 60.037 55.000 18.24 10.86 41.16 3.16
1592 1972 1.228367 CACTGCTTGCCTCTTGGGT 60.228 57.895 0.00 0.00 37.43 4.51
1784 2344 0.524862 CTCCCAGCTGCAATTCACAC 59.475 55.000 8.66 0.00 0.00 3.82
1818 2383 5.459762 ACAAAAGATTGACAAGCGTTTCATG 59.540 36.000 13.27 7.37 38.94 3.07
1836 2402 3.364964 GGGAACGTCACTGCATACAAAAG 60.365 47.826 0.00 0.00 0.00 2.27
1898 2504 0.601046 CTGTGAAGACGCCAAGCAGA 60.601 55.000 0.00 0.00 0.00 4.26
2025 2917 0.738063 CAGCAGCAGAGCAGAGTGAG 60.738 60.000 0.00 0.00 36.85 3.51
2044 2938 7.864307 GCATTAAAGGATGCTGATTTACATC 57.136 36.000 2.79 0.00 46.85 3.06
2166 3287 2.646930 TGCTTCACAATATCAGCAGGG 58.353 47.619 0.00 0.00 37.35 4.45
2170 3291 6.956299 AACAAAATGCTTCACAATATCAGC 57.044 33.333 0.00 0.00 0.00 4.26
2261 4649 3.317993 GGTGTCCAACAGCTACAATTTGT 59.682 43.478 7.30 7.30 42.83 2.83
2279 4668 8.241497 ACAAGCATATCAATCATAAATGGTGT 57.759 30.769 0.00 0.00 0.00 4.16
2344 5819 8.794335 TTTGCAAAACAAGGTAAAAAGGTAAT 57.206 26.923 10.02 0.00 40.06 1.89
2346 5821 8.794335 AATTTGCAAAACAAGGTAAAAAGGTA 57.206 26.923 17.19 0.00 40.06 3.08
2347 5822 7.695480 AATTTGCAAAACAAGGTAAAAAGGT 57.305 28.000 17.19 0.00 40.06 3.50
2391 5870 4.038642 GGTTACTGTTTGCCAATTCCTGAA 59.961 41.667 0.00 0.00 0.00 3.02
2396 5875 5.905480 CAAAGGTTACTGTTTGCCAATTC 57.095 39.130 0.00 0.00 0.00 2.17
2520 6035 2.818751 TGGACAAATCGGCCCTTTAT 57.181 45.000 0.00 0.00 0.00 1.40
2617 6136 9.722056 CTGAAAATCCTTTCTATTTTGATACGG 57.278 33.333 0.00 0.00 41.41 4.02
3073 9033 7.929245 ACACACACACATCATACTAACAGTAAA 59.071 33.333 0.00 0.00 33.89 2.01
3131 9091 4.932268 TTTTAGCGGTGGTTCTTTATCG 57.068 40.909 0.00 0.00 0.00 2.92
3207 9179 1.542108 GCAGTGAGGCTCAAGACAACT 60.542 52.381 20.62 8.06 0.00 3.16
3384 9372 9.486497 AGTATGTGCATTGTAGAATAGAGAATG 57.514 33.333 0.00 0.00 0.00 2.67
3385 9373 9.486497 CAGTATGTGCATTGTAGAATAGAGAAT 57.514 33.333 0.00 0.00 0.00 2.40
3461 9462 0.108662 CCAGCGCGCCATAGATCATA 60.109 55.000 30.33 0.00 0.00 2.15
3549 9550 1.221840 CGGCAGCCCAGACATACTT 59.778 57.895 5.63 0.00 0.00 2.24
3741 9750 1.106351 ACATTTTCACCGTGCCAGCA 61.106 50.000 0.00 0.00 0.00 4.41
3782 9791 9.892444 TTATGTTTCCTCTATACTAGGGATCAA 57.108 33.333 0.00 0.00 34.66 2.57
3783 9792 9.535170 CTTATGTTTCCTCTATACTAGGGATCA 57.465 37.037 0.00 0.00 34.66 2.92
3784 9793 9.756571 TCTTATGTTTCCTCTATACTAGGGATC 57.243 37.037 0.00 0.00 34.66 3.36
3843 9866 5.193728 ACCCCCTAAATACAACATCACATCT 59.806 40.000 0.00 0.00 0.00 2.90
3941 10017 2.632996 CACCCACTAGACAGACCAGAAA 59.367 50.000 0.00 0.00 0.00 2.52
3942 10018 2.248248 CACCCACTAGACAGACCAGAA 58.752 52.381 0.00 0.00 0.00 3.02
3944 10020 0.898320 CCACCCACTAGACAGACCAG 59.102 60.000 0.00 0.00 0.00 4.00
3948 10054 0.830444 AACGCCACCCACTAGACAGA 60.830 55.000 0.00 0.00 0.00 3.41
4019 10125 9.807921 AATCTCCAAAAAGACTAAAAGGACATA 57.192 29.630 0.00 0.00 0.00 2.29
4021 10127 8.533569 AAATCTCCAAAAAGACTAAAAGGACA 57.466 30.769 0.00 0.00 0.00 4.02
4029 10135 9.947433 TCCGTATTTAAATCTCCAAAAAGACTA 57.053 29.630 3.39 0.00 0.00 2.59
4088 10195 6.883217 ACAGAGCAAAATGAGTGAATCTACAT 59.117 34.615 0.00 0.00 0.00 2.29
4099 10206 5.233050 CGGACTACATACAGAGCAAAATGAG 59.767 44.000 0.00 0.00 0.00 2.90
4111 10218 6.015688 GGAGATTCCAATACGGACTACATACA 60.016 42.308 0.00 0.00 46.36 2.29
4166 10286 6.394025 AAACATGCGTCCCTTTAGTTTTAA 57.606 33.333 0.00 0.00 0.00 1.52
4167 10287 6.394025 AAAACATGCGTCCCTTTAGTTTTA 57.606 33.333 0.00 0.00 36.35 1.52
4189 10309 4.358851 CTTCACCAGCGTTTCATCAAAAA 58.641 39.130 0.00 0.00 0.00 1.94
4190 10310 3.795150 GCTTCACCAGCGTTTCATCAAAA 60.795 43.478 0.00 0.00 39.29 2.44
4191 10311 2.287547 GCTTCACCAGCGTTTCATCAAA 60.288 45.455 0.00 0.00 39.29 2.69
4192 10312 1.266718 GCTTCACCAGCGTTTCATCAA 59.733 47.619 0.00 0.00 39.29 2.57
4193 10313 0.874390 GCTTCACCAGCGTTTCATCA 59.126 50.000 0.00 0.00 39.29 3.07
4194 10314 3.683581 GCTTCACCAGCGTTTCATC 57.316 52.632 0.00 0.00 39.29 2.92
4203 10323 3.722728 AAAGAAAAGCTGCTTCACCAG 57.277 42.857 16.28 0.00 35.93 4.00
4204 10324 3.446873 TGAAAAGAAAAGCTGCTTCACCA 59.553 39.130 16.28 4.70 29.18 4.17
4205 10325 4.045636 TGAAAAGAAAAGCTGCTTCACC 57.954 40.909 16.28 7.82 29.18 4.02
4206 10326 6.594284 AATTGAAAAGAAAAGCTGCTTCAC 57.406 33.333 16.28 12.31 32.17 3.18
4207 10327 7.649306 GTCTAATTGAAAAGAAAAGCTGCTTCA 59.351 33.333 16.28 4.54 31.14 3.02
4208 10328 7.149063 CGTCTAATTGAAAAGAAAAGCTGCTTC 60.149 37.037 16.28 4.13 0.00 3.86
4209 10329 6.638468 CGTCTAATTGAAAAGAAAAGCTGCTT 59.362 34.615 9.53 9.53 0.00 3.91
4210 10330 6.145535 CGTCTAATTGAAAAGAAAAGCTGCT 58.854 36.000 0.00 0.00 0.00 4.24
4211 10331 5.164148 GCGTCTAATTGAAAAGAAAAGCTGC 60.164 40.000 0.00 0.00 0.00 5.25
4212 10332 5.914635 TGCGTCTAATTGAAAAGAAAAGCTG 59.085 36.000 0.00 0.00 0.00 4.24
4213 10333 5.915196 GTGCGTCTAATTGAAAAGAAAAGCT 59.085 36.000 0.00 0.00 0.00 3.74
4214 10334 5.164282 CGTGCGTCTAATTGAAAAGAAAAGC 60.164 40.000 0.00 0.00 0.00 3.51
4215 10335 5.907391 ACGTGCGTCTAATTGAAAAGAAAAG 59.093 36.000 0.00 0.00 0.00 2.27
4216 10336 5.812652 ACGTGCGTCTAATTGAAAAGAAAA 58.187 33.333 0.00 0.00 0.00 2.29
4217 10337 5.412526 ACGTGCGTCTAATTGAAAAGAAA 57.587 34.783 0.00 0.00 0.00 2.52
4218 10338 5.412526 AACGTGCGTCTAATTGAAAAGAA 57.587 34.783 0.00 0.00 0.00 2.52
4219 10339 5.412526 AAACGTGCGTCTAATTGAAAAGA 57.587 34.783 0.00 0.00 0.00 2.52
4220 10340 5.679355 TGAAAACGTGCGTCTAATTGAAAAG 59.321 36.000 0.00 0.00 0.00 2.27
4221 10341 5.570344 TGAAAACGTGCGTCTAATTGAAAA 58.430 33.333 0.00 0.00 0.00 2.29
4222 10342 5.158101 TGAAAACGTGCGTCTAATTGAAA 57.842 34.783 0.00 0.00 0.00 2.69
4223 10343 4.797693 TGAAAACGTGCGTCTAATTGAA 57.202 36.364 0.00 0.00 0.00 2.69
4224 10344 4.212425 ACATGAAAACGTGCGTCTAATTGA 59.788 37.500 0.00 0.00 0.00 2.57
4225 10345 4.463209 ACATGAAAACGTGCGTCTAATTG 58.537 39.130 0.00 0.00 0.00 2.32
4226 10346 4.742438 ACATGAAAACGTGCGTCTAATT 57.258 36.364 0.00 0.00 0.00 1.40
4227 10347 6.019318 GGTATACATGAAAACGTGCGTCTAAT 60.019 38.462 5.01 0.00 0.00 1.73
4228 10348 5.289193 GGTATACATGAAAACGTGCGTCTAA 59.711 40.000 5.01 0.00 0.00 2.10
4229 10349 4.799949 GGTATACATGAAAACGTGCGTCTA 59.200 41.667 5.01 0.00 0.00 2.59
4230 10350 3.615496 GGTATACATGAAAACGTGCGTCT 59.385 43.478 5.01 0.00 0.00 4.18
4231 10351 3.368539 TGGTATACATGAAAACGTGCGTC 59.631 43.478 5.01 0.00 0.00 5.19
4234 10354 4.939509 AGTGGTATACATGAAAACGTGC 57.060 40.909 5.01 0.00 0.00 5.34
4236 10356 6.534079 GCTCTAAGTGGTATACATGAAAACGT 59.466 38.462 5.01 0.00 0.00 3.99
4275 10395 2.048222 AGCGACCACACATGACGG 60.048 61.111 0.00 0.00 0.00 4.79
4276 10396 1.664649 ACAGCGACCACACATGACG 60.665 57.895 0.00 0.00 0.00 4.35
4295 10416 4.215827 CCTTTGCAATCTCTCTGGCATATC 59.784 45.833 0.00 0.00 35.98 1.63
4301 10422 1.830279 TGCCTTTGCAATCTCTCTGG 58.170 50.000 0.00 0.00 46.66 3.86
4314 10435 2.037121 GGCTACCACACATTTTGCCTTT 59.963 45.455 0.00 0.00 36.32 3.11
4315 10436 1.618343 GGCTACCACACATTTTGCCTT 59.382 47.619 0.00 0.00 36.32 4.35
4316 10437 1.256812 GGCTACCACACATTTTGCCT 58.743 50.000 0.00 0.00 36.32 4.75
4317 10438 0.965439 TGGCTACCACACATTTTGCC 59.035 50.000 0.00 0.00 39.33 4.52
4318 10439 2.230992 TGATGGCTACCACACATTTTGC 59.769 45.455 0.00 0.00 35.80 3.68
4319 10440 4.724074 ATGATGGCTACCACACATTTTG 57.276 40.909 0.00 0.00 35.80 2.44
4320 10441 5.360714 CCTTATGATGGCTACCACACATTTT 59.639 40.000 11.51 0.00 35.80 1.82
4321 10442 4.889409 CCTTATGATGGCTACCACACATTT 59.111 41.667 11.51 0.00 35.80 2.32
4322 10443 4.464008 CCTTATGATGGCTACCACACATT 58.536 43.478 11.51 0.00 35.80 2.71
4323 10444 3.748668 GCCTTATGATGGCTACCACACAT 60.749 47.826 11.16 11.16 46.38 3.21
4324 10445 2.421388 GCCTTATGATGGCTACCACACA 60.421 50.000 0.00 0.00 46.38 3.72
4325 10446 2.222027 GCCTTATGATGGCTACCACAC 58.778 52.381 0.00 0.00 46.38 3.82
4326 10447 2.638480 GCCTTATGATGGCTACCACA 57.362 50.000 0.00 0.00 46.38 4.17
4333 10454 1.014352 ACGTTTCGCCTTATGATGGC 58.986 50.000 0.00 0.00 46.42 4.40
4334 10455 2.006888 ACACGTTTCGCCTTATGATGG 58.993 47.619 0.00 0.00 0.00 3.51
4335 10456 2.223021 CCACACGTTTCGCCTTATGATG 60.223 50.000 0.00 0.00 0.00 3.07
4336 10457 2.006888 CCACACGTTTCGCCTTATGAT 58.993 47.619 0.00 0.00 0.00 2.45
4337 10458 1.270412 ACCACACGTTTCGCCTTATGA 60.270 47.619 0.00 0.00 0.00 2.15
4338 10459 1.127951 GACCACACGTTTCGCCTTATG 59.872 52.381 0.00 0.00 0.00 1.90
4339 10460 1.435577 GACCACACGTTTCGCCTTAT 58.564 50.000 0.00 0.00 0.00 1.73
4340 10461 0.940519 CGACCACACGTTTCGCCTTA 60.941 55.000 0.00 0.00 0.00 2.69
4375 10496 3.616560 GCGTTTCACCCTCACAATCTCTA 60.617 47.826 0.00 0.00 0.00 2.43
4376 10497 2.872038 GCGTTTCACCCTCACAATCTCT 60.872 50.000 0.00 0.00 0.00 3.10
4387 10508 1.305201 TTTGAGTCTGCGTTTCACCC 58.695 50.000 0.00 0.00 0.00 4.61
4458 10579 9.883142 TTTTGAAAAGAACCATTACAGTCAATT 57.117 25.926 0.00 0.00 0.00 2.32
4615 10740 6.093532 GAAATGTCAACTGTTTTGTTGTGG 57.906 37.500 7.17 0.00 45.26 4.17


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

AutoCloner maintained by Alex Coulton.