Multiple sequence alignment - TraesCS3B01G035000

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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 TraesCS3B01G035000 chr3B 100.000 5734 0 0 1 5734 16979406 16985139 0.000000e+00 10589.0
1 TraesCS3B01G035000 chr3B 88.250 2068 142 41 1 1999 16832015 16829980 0.000000e+00 2379.0
2 TraesCS3B01G035000 chr3B 88.091 1755 180 24 1999 3736 747934906 747933164 0.000000e+00 2056.0
3 TraesCS3B01G035000 chr3B 80.316 1265 197 23 3759 4991 16757705 16756461 0.000000e+00 909.0
4 TraesCS3B01G035000 chr3B 80.151 1058 152 22 3759 4795 16693071 16694091 0.000000e+00 737.0
5 TraesCS3B01G035000 chr3B 81.277 705 77 21 1158 1830 16957483 16958164 2.370000e-143 520.0
6 TraesCS3B01G035000 chr3B 85.991 464 53 10 4531 4991 16850933 16850479 2.400000e-133 486.0
7 TraesCS3B01G035000 chr3B 83.534 498 69 11 4497 4991 16733770 16734257 2.440000e-123 453.0
8 TraesCS3B01G035000 chr3B 80.569 633 74 19 1224 1830 16759157 16758548 5.270000e-120 442.0
9 TraesCS3B01G035000 chr3B 91.336 277 23 1 3765 4041 16829758 16829483 1.510000e-100 377.0
10 TraesCS3B01G035000 chr3B 79.588 485 71 10 3759 4224 16959041 16959516 7.170000e-84 322.0
11 TraesCS3B01G035000 chr3B 84.642 293 34 6 1530 1812 16676471 16676762 1.220000e-71 281.0
12 TraesCS3B01G035000 chr3B 82.677 127 17 4 1844 1966 86565894 86565769 2.180000e-19 108.0
13 TraesCS3B01G035000 chr6D 91.652 1761 124 19 1992 3736 437849982 437851735 0.000000e+00 2416.0
14 TraesCS3B01G035000 chr6D 87.432 740 83 6 4996 5734 80336365 80335635 0.000000e+00 843.0
15 TraesCS3B01G035000 chr1B 90.878 1754 143 11 1992 3734 666216702 666214955 0.000000e+00 2337.0
16 TraesCS3B01G035000 chr1B 88.451 736 74 8 5001 5734 339361748 339361022 0.000000e+00 878.0
17 TraesCS3B01G035000 chr2A 90.126 1752 152 18 1999 3734 566641432 566639686 0.000000e+00 2257.0
18 TraesCS3B01G035000 chr2A 92.369 629 45 3 3113 3738 570576695 570576067 0.000000e+00 893.0
19 TraesCS3B01G035000 chr7A 89.840 1752 150 22 1997 3736 639255830 639254095 0.000000e+00 2224.0
20 TraesCS3B01G035000 chr1D 88.635 1751 164 26 1999 3736 298482564 298480836 0.000000e+00 2098.0
21 TraesCS3B01G035000 chr1D 88.554 1756 166 27 1997 3738 298475728 298473994 0.000000e+00 2097.0
22 TraesCS3B01G035000 chr1D 88.859 745 69 9 4991 5734 417912620 417913351 0.000000e+00 904.0
23 TraesCS3B01G035000 chr1D 87.015 747 82 11 4991 5734 481423090 481422356 0.000000e+00 828.0
24 TraesCS3B01G035000 chr3D 88.319 1755 171 26 1998 3736 429812688 429814424 0.000000e+00 2074.0
25 TraesCS3B01G035000 chr3D 88.415 751 73 10 4988 5734 350674228 350674968 0.000000e+00 893.0
26 TraesCS3B01G035000 chr3D 88.282 751 75 8 4986 5734 381006824 381007563 0.000000e+00 887.0
27 TraesCS3B01G035000 chr3D 87.368 760 84 9 4977 5734 567668663 567669412 0.000000e+00 861.0
28 TraesCS3B01G035000 chr3D 82.437 985 142 8 3758 4720 11795587 11796562 0.000000e+00 832.0
29 TraesCS3B01G035000 chr3D 83.237 173 20 4 1828 1999 161989952 161990116 3.580000e-32 150.0
30 TraesCS3B01G035000 chr5B 90.953 1437 106 16 1997 3421 89578325 89576901 0.000000e+00 1912.0
31 TraesCS3B01G035000 chr5B 80.795 151 19 7 1843 1986 472938190 472938043 6.070000e-20 110.0
32 TraesCS3B01G035000 chr5A 87.802 746 80 8 4991 5734 142745091 142745827 0.000000e+00 863.0
33 TraesCS3B01G035000 chr4B 87.248 745 79 8 4991 5734 10472406 10471677 0.000000e+00 835.0
34 TraesCS3B01G035000 chr3A 81.243 837 140 9 3870 4700 25770241 25771066 0.000000e+00 660.0
35 TraesCS3B01G035000 chr3A 84.194 620 86 11 4379 4992 25213306 25212693 4.950000e-165 592.0
36 TraesCS3B01G035000 chr3A 79.278 637 100 11 3759 4372 25232331 25231704 3.200000e-112 416.0
37 TraesCS3B01G035000 chr3A 80.000 615 72 18 1236 1830 25234020 25233437 1.920000e-109 407.0
38 TraesCS3B01G035000 chr3A 81.046 153 18 7 1843 1986 512702539 512702389 1.690000e-20 111.0
39 TraesCS3B01G035000 chr7D 83.929 168 21 3 1830 1997 111325173 111325012 7.690000e-34 156.0
40 TraesCS3B01G035000 chr6B 83.471 121 16 1 1850 1970 135849655 135849771 6.070000e-20 110.0
41 TraesCS3B01G035000 chr1A 81.752 137 16 6 1843 1970 70494884 70495020 7.860000e-19 106.0
42 TraesCS3B01G035000 chr2D 79.856 139 22 3 1848 1986 11022087 11021955 4.730000e-16 97.1


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 TraesCS3B01G035000 chr3B 16979406 16985139 5733 False 10589.0 10589 100.0000 1 5734 1 chr3B.!!$F4 5733
1 TraesCS3B01G035000 chr3B 747933164 747934906 1742 True 2056.0 2056 88.0910 1999 3736 1 chr3B.!!$R3 1737
2 TraesCS3B01G035000 chr3B 16829483 16832015 2532 True 1378.0 2379 89.7930 1 4041 2 chr3B.!!$R5 4040
3 TraesCS3B01G035000 chr3B 16693071 16694091 1020 False 737.0 737 80.1510 3759 4795 1 chr3B.!!$F2 1036
4 TraesCS3B01G035000 chr3B 16756461 16759157 2696 True 675.5 909 80.4425 1224 4991 2 chr3B.!!$R4 3767
5 TraesCS3B01G035000 chr3B 16957483 16959516 2033 False 421.0 520 80.4325 1158 4224 2 chr3B.!!$F5 3066
6 TraesCS3B01G035000 chr6D 437849982 437851735 1753 False 2416.0 2416 91.6520 1992 3736 1 chr6D.!!$F1 1744
7 TraesCS3B01G035000 chr6D 80335635 80336365 730 True 843.0 843 87.4320 4996 5734 1 chr6D.!!$R1 738
8 TraesCS3B01G035000 chr1B 666214955 666216702 1747 True 2337.0 2337 90.8780 1992 3734 1 chr1B.!!$R2 1742
9 TraesCS3B01G035000 chr1B 339361022 339361748 726 True 878.0 878 88.4510 5001 5734 1 chr1B.!!$R1 733
10 TraesCS3B01G035000 chr2A 566639686 566641432 1746 True 2257.0 2257 90.1260 1999 3734 1 chr2A.!!$R1 1735
11 TraesCS3B01G035000 chr2A 570576067 570576695 628 True 893.0 893 92.3690 3113 3738 1 chr2A.!!$R2 625
12 TraesCS3B01G035000 chr7A 639254095 639255830 1735 True 2224.0 2224 89.8400 1997 3736 1 chr7A.!!$R1 1739
13 TraesCS3B01G035000 chr1D 298480836 298482564 1728 True 2098.0 2098 88.6350 1999 3736 1 chr1D.!!$R2 1737
14 TraesCS3B01G035000 chr1D 298473994 298475728 1734 True 2097.0 2097 88.5540 1997 3738 1 chr1D.!!$R1 1741
15 TraesCS3B01G035000 chr1D 417912620 417913351 731 False 904.0 904 88.8590 4991 5734 1 chr1D.!!$F1 743
16 TraesCS3B01G035000 chr1D 481422356 481423090 734 True 828.0 828 87.0150 4991 5734 1 chr1D.!!$R3 743
17 TraesCS3B01G035000 chr3D 429812688 429814424 1736 False 2074.0 2074 88.3190 1998 3736 1 chr3D.!!$F5 1738
18 TraesCS3B01G035000 chr3D 350674228 350674968 740 False 893.0 893 88.4150 4988 5734 1 chr3D.!!$F3 746
19 TraesCS3B01G035000 chr3D 381006824 381007563 739 False 887.0 887 88.2820 4986 5734 1 chr3D.!!$F4 748
20 TraesCS3B01G035000 chr3D 567668663 567669412 749 False 861.0 861 87.3680 4977 5734 1 chr3D.!!$F6 757
21 TraesCS3B01G035000 chr3D 11795587 11796562 975 False 832.0 832 82.4370 3758 4720 1 chr3D.!!$F1 962
22 TraesCS3B01G035000 chr5B 89576901 89578325 1424 True 1912.0 1912 90.9530 1997 3421 1 chr5B.!!$R1 1424
23 TraesCS3B01G035000 chr5A 142745091 142745827 736 False 863.0 863 87.8020 4991 5734 1 chr5A.!!$F1 743
24 TraesCS3B01G035000 chr4B 10471677 10472406 729 True 835.0 835 87.2480 4991 5734 1 chr4B.!!$R1 743
25 TraesCS3B01G035000 chr3A 25770241 25771066 825 False 660.0 660 81.2430 3870 4700 1 chr3A.!!$F1 830
26 TraesCS3B01G035000 chr3A 25212693 25213306 613 True 592.0 592 84.1940 4379 4992 1 chr3A.!!$R1 613
27 TraesCS3B01G035000 chr3A 25231704 25234020 2316 True 411.5 416 79.6390 1236 4372 2 chr3A.!!$R3 3136

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
257 258 0.035439 CGGCCCAACAAGATGTACCT 60.035 55.0 0.00 0.00 0.00 3.08 F
1087 1122 0.035152 TGCATCAGTGTTGGGCTAGG 60.035 55.0 3.45 0.00 0.00 3.02 F
2261 3160 0.040499 AGCTTCGAGGGAGAGTTCCT 59.960 55.0 0.00 0.00 43.49 3.36 F
2306 3205 0.530744 TTGATGAAGCTACCGACGCT 59.469 50.0 0.00 0.00 39.94 5.07 F
3234 4166 0.834261 GAGAGGGCCCAGAGATACCC 60.834 65.0 27.56 0.76 43.17 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 1851 0.528684 GGAGCTCGTCCATCTTTCCG 60.529 60.0 7.83 0.0 46.10 4.30 R
2527 3451 0.464373 CCATGTGGGAGGTGGAATCG 60.464 60.0 0.00 0.0 40.01 3.34 R
3755 4699 0.178767 CGGGAGGTGAAGCATGATGA 59.821 55.0 0.00 0.0 0.00 2.92 R
3922 4884 0.181350 GAGTTGATCGGGATGGCCTT 59.819 55.0 3.32 0.0 0.00 4.35 R
4913 5881 0.106769 TGTTCCTTGCTCTTGTGGCA 60.107 50.0 0.00 0.0 37.97 4.92 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
20 21 0.103208 CTGTAGTCCGCCTGATCCAC 59.897 60.000 0.00 0.00 0.00 4.02
25 26 1.040646 GTCCGCCTGATCCACTATCA 58.959 55.000 0.00 0.00 42.48 2.15
26 27 1.620819 GTCCGCCTGATCCACTATCAT 59.379 52.381 0.00 0.00 43.70 2.45
27 28 1.620323 TCCGCCTGATCCACTATCATG 59.380 52.381 0.00 0.00 43.70 3.07
28 29 1.436600 CGCCTGATCCACTATCATGC 58.563 55.000 5.50 5.50 46.78 4.06
29 30 2.855209 GCCTGATCCACTATCATGCT 57.145 50.000 7.68 0.00 46.75 3.79
30 31 3.969287 GCCTGATCCACTATCATGCTA 57.031 47.619 7.68 0.00 46.75 3.49
31 32 3.594134 GCCTGATCCACTATCATGCTAC 58.406 50.000 7.68 0.00 46.75 3.58
37 38 3.392882 TCCACTATCATGCTACGCAATG 58.607 45.455 0.00 0.00 43.62 2.82
40 41 4.035558 CCACTATCATGCTACGCAATGTTT 59.964 41.667 0.00 0.00 43.62 2.83
90 91 5.385198 AGGTAGAATCTCATCTGAGGTCTC 58.615 45.833 13.97 6.24 42.30 3.36
98 99 3.444029 TCATCTGAGGTCTCCATTGACA 58.556 45.455 0.00 0.00 38.61 3.58
103 104 2.894765 TGAGGTCTCCATTGACACGTAA 59.105 45.455 0.00 0.00 38.61 3.18
112 113 2.722936 TTGACACGTAACAACGCTTG 57.277 45.000 0.00 0.00 36.44 4.01
160 161 7.288672 TCTATTTTCTTCTTCTTTTTCGACGC 58.711 34.615 0.00 0.00 0.00 5.19
176 177 2.331893 CGCCTGGTTCATTTGCCGA 61.332 57.895 0.00 0.00 0.00 5.54
257 258 0.035439 CGGCCCAACAAGATGTACCT 60.035 55.000 0.00 0.00 0.00 3.08
258 259 1.751437 GGCCCAACAAGATGTACCTC 58.249 55.000 0.00 0.00 0.00 3.85
260 261 1.338769 GCCCAACAAGATGTACCTCGT 60.339 52.381 0.00 0.00 0.00 4.18
268 269 4.695455 ACAAGATGTACCTCGTGATTTTGG 59.305 41.667 18.02 0.00 0.00 3.28
269 270 3.873910 AGATGTACCTCGTGATTTTGGG 58.126 45.455 0.00 0.00 0.00 4.12
295 296 7.687941 ACCTTTTGATATCTTGTTCGTGAAT 57.312 32.000 3.98 0.00 0.00 2.57
296 297 8.110860 ACCTTTTGATATCTTGTTCGTGAATT 57.889 30.769 3.98 0.00 0.00 2.17
332 333 7.894753 ATTTTGATTGGTTTTGGAATGGTTT 57.105 28.000 0.00 0.00 0.00 3.27
339 340 6.240549 TGGTTTTGGAATGGTTTTACATGT 57.759 33.333 2.69 2.69 0.00 3.21
340 341 6.653989 TGGTTTTGGAATGGTTTTACATGTT 58.346 32.000 2.30 0.00 0.00 2.71
429 430 2.428491 TCCCGAATGCACGTTTAACAT 58.572 42.857 0.00 0.00 0.00 2.71
706 735 5.994887 TTACAGTTCATAAGCGTTTGTGT 57.005 34.783 8.48 0.00 0.00 3.72
722 751 7.168469 AGCGTTTGTGTAAAATGTCATTAAACC 59.832 33.333 0.00 0.79 0.00 3.27
843 873 9.903185 GTAGCTTTCTTAGAAAATATCGTGAAC 57.097 33.333 8.82 0.00 0.00 3.18
911 944 9.203421 GGCACAAACTTTTGCTAATAAAATAGT 57.797 29.630 1.49 0.00 41.79 2.12
942 975 7.929159 CAGGTTTTAAAAACTGCATGGATTTT 58.071 30.769 28.07 4.31 45.62 1.82
1087 1122 0.035152 TGCATCAGTGTTGGGCTAGG 60.035 55.000 3.45 0.00 0.00 3.02
1131 1178 3.063588 GGCAAGGTTACAATAAGCGAGAC 59.936 47.826 0.00 0.00 0.00 3.36
1136 1183 4.020485 AGGTTACAATAAGCGAGACCTTGT 60.020 41.667 0.00 0.00 32.38 3.16
1141 1188 0.454600 TAAGCGAGACCTTGTAGCGG 59.545 55.000 0.00 0.00 0.00 5.52
1220 1275 2.496111 GTGGTCACAATAACCCGACAA 58.504 47.619 0.00 0.00 35.84 3.18
1433 1504 4.994852 GTGTTTGGATGTGAAGCACTACTA 59.005 41.667 0.00 0.00 35.11 1.82
1438 1509 4.100035 TGGATGTGAAGCACTACTAGGATG 59.900 45.833 0.00 0.00 35.11 3.51
1481 1554 3.516615 GCACTCGAGGATGATATTAGGC 58.483 50.000 18.41 0.00 0.00 3.93
1483 1556 4.489810 CACTCGAGGATGATATTAGGCAC 58.510 47.826 18.41 0.00 0.00 5.01
1486 1559 3.190744 TCGAGGATGATATTAGGCACGAC 59.809 47.826 0.00 0.00 0.00 4.34
1492 1565 7.624549 AGGATGATATTAGGCACGACATTAAT 58.375 34.615 0.00 0.00 0.00 1.40
1590 1665 7.475840 AGATTAATTGAATTTGCTCCTTCGAC 58.524 34.615 0.00 0.00 0.00 4.20
1756 1851 6.090493 GTCGGTGAAAAGATAAGGTTGTAGAC 59.910 42.308 0.00 0.00 0.00 2.59
1768 1863 3.056035 AGGTTGTAGACGGAAAGATGGAC 60.056 47.826 0.00 0.00 0.00 4.02
1848 1944 0.178903 AGGCTACTCACAGTGGGGAA 60.179 55.000 5.13 0.00 0.00 3.97
1862 1958 9.782900 TCACAGTGGGGAATATCATATATTAGA 57.217 33.333 0.00 0.00 0.00 2.10
1963 2059 5.905480 TGCATGACACATATTAGCGTAAG 57.095 39.130 0.00 0.00 43.44 2.34
2012 2108 3.834489 TGTTACTGTTGGGGAACGTAA 57.166 42.857 0.00 0.00 0.00 3.18
2080 2226 1.338655 GCAACGAGAGGGGAGAGTATC 59.661 57.143 0.00 0.00 0.00 2.24
2161 3060 4.379221 GTCTTCACGATCGACCGG 57.621 61.111 24.34 0.00 0.00 5.28
2244 3143 3.067461 ACGAACTCATGATCCAGTAGAGC 59.933 47.826 0.00 0.00 0.00 4.09
2245 3144 3.317711 CGAACTCATGATCCAGTAGAGCT 59.682 47.826 0.00 0.00 0.00 4.09
2259 3158 1.470051 AGAGCTTCGAGGGAGAGTTC 58.530 55.000 0.00 0.00 0.00 3.01
2261 3160 0.040499 AGCTTCGAGGGAGAGTTCCT 59.960 55.000 0.00 0.00 43.49 3.36
2306 3205 0.530744 TTGATGAAGCTACCGACGCT 59.469 50.000 0.00 0.00 39.94 5.07
2449 3357 0.990818 AAAGGATGGAGGGAGGAGGC 60.991 60.000 0.00 0.00 0.00 4.70
2450 3358 1.907470 AAGGATGGAGGGAGGAGGCT 61.907 60.000 0.00 0.00 0.00 4.58
2591 3516 2.531942 AAGGAAGGAAGGGGGCGT 60.532 61.111 0.00 0.00 0.00 5.68
2764 3691 4.879598 ACCTTTCCGATGTCCGAATATAC 58.120 43.478 0.00 0.00 41.76 1.47
2789 3716 6.757010 CCCTTCCAATATATCGATCTTTACGG 59.243 42.308 0.00 0.00 0.00 4.02
2792 3719 6.931838 TCCAATATATCGATCTTTACGGCTT 58.068 36.000 0.00 0.00 0.00 4.35
2795 3722 7.492669 CCAATATATCGATCTTTACGGCTTGAT 59.507 37.037 0.00 0.00 0.00 2.57
2812 3739 4.679106 GCTTGATCATTTCGAGACTCCTCA 60.679 45.833 0.00 0.00 38.01 3.86
3003 3932 4.277515 TGCTCATATTGGCTCCTACATC 57.722 45.455 0.00 0.00 0.00 3.06
3145 4077 3.069016 TGGCAAGTCTCTTTACTCGTTCA 59.931 43.478 0.00 0.00 0.00 3.18
3177 4109 3.536956 TCCCGCAACTAACTCATTAGG 57.463 47.619 0.00 0.00 41.98 2.69
3181 4113 2.029244 CGCAACTAACTCATTAGGCACG 59.971 50.000 0.00 0.00 41.98 5.34
3234 4166 0.834261 GAGAGGGCCCAGAGATACCC 60.834 65.000 27.56 0.76 43.17 3.69
3245 4177 2.700897 CAGAGATACCCCTCCGACAATT 59.299 50.000 0.00 0.00 33.76 2.32
3249 4181 1.887797 TACCCCTCCGACAATTGGAT 58.112 50.000 10.83 0.00 34.32 3.41
3293 4225 2.294074 TGCCAACTCAACAAGTACCAC 58.706 47.619 0.00 0.00 37.17 4.16
3472 4407 3.611766 AGTGCTAAGCTAACGGAATGT 57.388 42.857 0.00 0.00 0.00 2.71
3478 4413 4.153475 GCTAAGCTAACGGAATGTGTCAAA 59.847 41.667 0.00 0.00 0.00 2.69
3486 4421 5.300969 ACGGAATGTGTCAAATCAATCAG 57.699 39.130 0.00 0.00 0.00 2.90
3496 4433 7.066645 TGTGTCAAATCAATCAGATCATTCTCC 59.933 37.037 0.00 0.00 35.39 3.71
3510 4447 1.002069 TTCTCCAATGATGTGGCCCT 58.998 50.000 0.00 0.00 38.68 5.19
3591 4529 4.083537 CGAGCTAGTCAAGTAGAGGCATAG 60.084 50.000 0.00 0.00 0.00 2.23
3738 4682 8.586744 CCTCTAGGGTATATTTCCTTCAGTTAC 58.413 40.741 2.45 0.00 34.75 2.50
3739 4683 9.369672 CTCTAGGGTATATTTCCTTCAGTTACT 57.630 37.037 2.45 0.00 34.75 2.24
3740 4684 9.364653 TCTAGGGTATATTTCCTTCAGTTACTC 57.635 37.037 2.45 0.00 34.75 2.59
3741 4685 9.369672 CTAGGGTATATTTCCTTCAGTTACTCT 57.630 37.037 2.45 0.00 34.75 3.24
3743 4687 9.725206 AGGGTATATTTCCTTCAGTTACTCTAA 57.275 33.333 0.00 0.00 0.00 2.10
3744 4688 9.984190 GGGTATATTTCCTTCAGTTACTCTAAG 57.016 37.037 0.00 0.00 0.00 2.18
3745 4689 9.478768 GGTATATTTCCTTCAGTTACTCTAAGC 57.521 37.037 0.00 0.00 0.00 3.09
3746 4690 9.478768 GTATATTTCCTTCAGTTACTCTAAGCC 57.521 37.037 0.00 0.00 0.00 4.35
3747 4691 6.628644 ATTTCCTTCAGTTACTCTAAGCCT 57.371 37.500 0.00 0.00 0.00 4.58
3748 4692 5.662674 TTCCTTCAGTTACTCTAAGCCTC 57.337 43.478 0.00 0.00 0.00 4.70
3749 4693 4.936802 TCCTTCAGTTACTCTAAGCCTCT 58.063 43.478 0.00 0.00 0.00 3.69
3750 4694 4.951094 TCCTTCAGTTACTCTAAGCCTCTC 59.049 45.833 0.00 0.00 0.00 3.20
3751 4695 4.953579 CCTTCAGTTACTCTAAGCCTCTCT 59.046 45.833 0.00 0.00 0.00 3.10
3752 4696 5.067283 CCTTCAGTTACTCTAAGCCTCTCTC 59.933 48.000 0.00 0.00 0.00 3.20
3753 4697 5.444744 TCAGTTACTCTAAGCCTCTCTCT 57.555 43.478 0.00 0.00 0.00 3.10
3754 4698 5.433526 TCAGTTACTCTAAGCCTCTCTCTC 58.566 45.833 0.00 0.00 0.00 3.20
3755 4699 5.190925 TCAGTTACTCTAAGCCTCTCTCTCT 59.809 44.000 0.00 0.00 0.00 3.10
3756 4700 5.527582 CAGTTACTCTAAGCCTCTCTCTCTC 59.472 48.000 0.00 0.00 0.00 3.20
3784 4728 4.361971 ACCTCCCGGAGCTCGACA 62.362 66.667 9.17 0.00 42.43 4.35
3793 4737 3.822607 GAGCTCGACAACTCCATGT 57.177 52.632 0.00 0.00 35.90 3.21
3922 4884 1.149627 AAACGCTACCACAAGGCCA 59.850 52.632 5.01 0.00 39.06 5.36
3950 4912 1.103803 CCGATCAACTCCTTCGAGGA 58.896 55.000 0.00 0.00 43.43 3.71
3997 4960 1.002533 TCTTACCCTAAGCCCGGCT 59.997 57.895 5.94 5.94 42.56 5.52
4059 5022 4.498520 CCGACGCCAGCGATGAGT 62.499 66.667 20.32 0.99 42.83 3.41
4070 5033 3.188786 GATGAGTCGTGCGCCACC 61.189 66.667 4.18 0.00 0.00 4.61
4072 5035 3.240134 ATGAGTCGTGCGCCACCTT 62.240 57.895 4.18 0.00 0.00 3.50
4083 5046 2.224159 GCCACCTTCCTGGACTGGA 61.224 63.158 18.45 0.00 34.77 3.86
4088 5051 1.343478 ACCTTCCTGGACTGGATCGAT 60.343 52.381 18.45 0.00 39.71 3.59
4097 5060 2.839632 TGGATCGATCGGCAGCCT 60.840 61.111 18.81 0.00 0.00 4.58
4121 5084 1.822506 AGTCGGTCATCTTCGTCTCA 58.177 50.000 0.00 0.00 0.00 3.27
4128 5091 2.352960 GTCATCTTCGTCTCATTTGGCC 59.647 50.000 0.00 0.00 0.00 5.36
4131 5094 0.322456 CTTCGTCTCATTTGGCCCCA 60.322 55.000 0.00 0.00 0.00 4.96
4136 5099 0.846427 TCTCATTTGGCCCCAGAGGT 60.846 55.000 0.00 0.00 38.26 3.85
4138 5101 0.486879 TCATTTGGCCCCAGAGGTTT 59.513 50.000 0.00 0.00 38.26 3.27
4149 5112 0.318699 CAGAGGTTTGCTGTCGACGA 60.319 55.000 11.62 0.00 0.00 4.20
4204 5167 2.203070 CGGGCAGCGCTTCCTATT 60.203 61.111 25.32 0.00 0.00 1.73
4241 5204 3.728373 GACCAGGGGGCCGTGAAT 61.728 66.667 6.10 0.00 37.90 2.57
4259 5222 0.253044 ATGCCAACCACTATGACGCT 59.747 50.000 0.00 0.00 0.00 5.07
4271 5234 1.719600 ATGACGCTGAGAGCAAGAAC 58.280 50.000 0.00 0.00 42.58 3.01
4287 5250 3.557695 AACGACCCCCTGGCCTACT 62.558 63.158 3.32 0.00 33.59 2.57
4292 5255 2.286121 CCCCTGGCCTACTTCCCA 60.286 66.667 3.32 0.00 0.00 4.37
4296 5259 3.727387 TGGCCTACTTCCCAGAGC 58.273 61.111 3.32 0.00 0.00 4.09
4307 5270 2.432628 CCAGAGCGGTTCGTGGAC 60.433 66.667 5.86 0.00 31.04 4.02
4310 5273 3.112709 GAGCGGTTCGTGGACAGC 61.113 66.667 0.00 0.00 40.38 4.40
4312 5275 2.970324 GCGGTTCGTGGACAGCAA 60.970 61.111 0.00 0.00 39.93 3.91
4313 5276 2.325082 GCGGTTCGTGGACAGCAAT 61.325 57.895 0.00 0.00 39.93 3.56
4314 5277 1.497278 CGGTTCGTGGACAGCAATG 59.503 57.895 0.00 0.00 0.00 2.82
4316 5279 0.517316 GGTTCGTGGACAGCAATGAC 59.483 55.000 0.00 0.00 0.00 3.06
4317 5280 1.225855 GTTCGTGGACAGCAATGACA 58.774 50.000 0.00 0.00 0.00 3.58
4318 5281 1.069906 GTTCGTGGACAGCAATGACAC 60.070 52.381 0.00 0.00 0.00 3.67
4362 5328 3.587095 CGCAGACGGAGGTACTGA 58.413 61.111 0.00 0.00 41.55 3.41
4369 5335 0.959372 ACGGAGGTACTGACTCACGG 60.959 60.000 0.00 0.00 41.55 4.94
4376 5342 3.625897 CTGACTCACGGGGCCACA 61.626 66.667 5.46 0.00 0.00 4.17
4377 5343 2.927856 TGACTCACGGGGCCACAT 60.928 61.111 5.46 0.00 0.00 3.21
4390 5356 1.466856 GCCACATGATGCTTCTTGGA 58.533 50.000 16.65 0.00 32.66 3.53
4408 5374 1.228552 AGCATTGCGGGTGGAACTT 60.229 52.632 2.38 0.00 36.74 2.66
4420 5386 1.056660 TGGAACTTGGTCCTGGAGAC 58.943 55.000 6.25 0.00 45.51 3.36
4430 5396 0.842030 TCCTGGAGACCTTGGTGCAT 60.842 55.000 0.00 0.00 0.00 3.96
4479 5445 1.211969 GCCGAGTAGCGACAGAACA 59.788 57.895 0.00 0.00 44.57 3.18
4482 5448 1.736126 CCGAGTAGCGACAGAACACTA 59.264 52.381 0.00 0.00 44.57 2.74
4484 5450 3.546417 CCGAGTAGCGACAGAACACTATC 60.546 52.174 0.00 0.00 44.57 2.08
4492 5458 4.366586 CGACAGAACACTATCATGCTGAT 58.633 43.478 0.00 4.45 40.72 2.90
4493 5459 4.807834 CGACAGAACACTATCATGCTGATT 59.192 41.667 0.00 0.00 38.26 2.57
4496 5462 6.175471 ACAGAACACTATCATGCTGATTGAA 58.825 36.000 12.02 0.00 38.26 2.69
4519 5485 1.688772 GTCAGGGTAGCCATACGAGA 58.311 55.000 14.62 0.00 32.24 4.04
4521 5487 0.962489 CAGGGTAGCCATACGAGAGG 59.038 60.000 14.62 0.00 32.24 3.69
4549 5515 2.763448 CCAAGAGAAAGGAGGAGATCGT 59.237 50.000 0.00 0.00 0.00 3.73
4565 5531 2.262915 GTCGTGGCAGTGAGGGAG 59.737 66.667 0.00 0.00 0.00 4.30
4570 5536 2.217038 TGGCAGTGAGGGAGGTGAC 61.217 63.158 0.00 0.00 0.00 3.67
4580 5546 2.351276 GAGGTGACGGTTGGCCAT 59.649 61.111 6.09 0.00 34.09 4.40
4617 5583 4.143333 GAGCTAAGGTGGCGGCGA 62.143 66.667 12.98 0.00 34.52 5.54
4704 5670 1.004628 TGCATAAGTGGACATGTGGCT 59.995 47.619 1.15 0.00 0.00 4.75
4705 5671 1.402968 GCATAAGTGGACATGTGGCTG 59.597 52.381 1.15 0.00 0.00 4.85
4732 5698 2.607187 CTAGGTGTCAGCAAACCTACG 58.393 52.381 4.59 0.00 45.15 3.51
4742 5708 5.232414 GTCAGCAAACCTACGAATACATCTC 59.768 44.000 0.00 0.00 0.00 2.75
4752 5718 4.135306 ACGAATACATCTCGCTCCTTCTA 58.865 43.478 0.00 0.00 39.97 2.10
4754 5720 5.241949 ACGAATACATCTCGCTCCTTCTATT 59.758 40.000 0.00 0.00 39.97 1.73
4758 5724 4.688021 ACATCTCGCTCCTTCTATTTGTC 58.312 43.478 0.00 0.00 0.00 3.18
4766 5732 3.198068 TCCTTCTATTTGTCTGCATCGC 58.802 45.455 0.00 0.00 0.00 4.58
4905 5873 9.586435 TTTCATATACTATATCGACATGGCAAG 57.414 33.333 0.00 0.00 0.00 4.01
4913 5881 1.344438 TCGACATGGCAAGAGTCAAGT 59.656 47.619 15.28 0.00 33.41 3.16
4920 5888 1.024271 GCAAGAGTCAAGTGCCACAA 58.976 50.000 0.00 0.00 31.94 3.33
4926 5894 1.024271 GTCAAGTGCCACAAGAGCAA 58.976 50.000 0.00 0.00 43.02 3.91
4928 5896 0.313043 CAAGTGCCACAAGAGCAAGG 59.687 55.000 0.00 0.00 43.02 3.61
4940 5909 2.609747 AGAGCAAGGAACACTGGTCTA 58.390 47.619 2.14 0.00 35.11 2.59
4961 5930 1.539280 GGCAAGTTAGGGCTCTCGATC 60.539 57.143 0.00 0.00 0.00 3.69
4972 5941 3.557595 GGGCTCTCGATCAACAACTTATG 59.442 47.826 0.00 0.00 0.00 1.90
5011 5987 6.283694 ACTTTTTCTTTGAAAAGGAGGATGC 58.716 36.000 17.52 0.00 46.10 3.91
5141 6120 2.431057 ACTTGTTGCTACTCCTATCCCG 59.569 50.000 0.00 0.00 0.00 5.14
5157 6136 1.378762 CCGGTGATGAAGGGGTGTT 59.621 57.895 0.00 0.00 0.00 3.32
5185 6164 5.112686 GTCTGAGCCTAATACCAAACAGAG 58.887 45.833 0.00 0.00 34.58 3.35
5242 6221 2.357050 CCATCCAAGCCACAATACCTGA 60.357 50.000 0.00 0.00 0.00 3.86
5247 6226 3.411446 CAAGCCACAATACCTGAACTGA 58.589 45.455 0.00 0.00 0.00 3.41
5252 6231 4.631813 GCCACAATACCTGAACTGAGTTAG 59.368 45.833 0.00 0.00 0.00 2.34
5298 6277 2.203195 ACCACATGTGCACGCTGT 60.203 55.556 20.81 16.62 0.00 4.40
5300 6279 1.227999 ACCACATGTGCACGCTGTAC 61.228 55.000 20.81 0.00 33.42 2.90
5325 6305 2.122768 GGTCACCTCCTTCATCCATCT 58.877 52.381 0.00 0.00 0.00 2.90
5328 6308 4.349342 GGTCACCTCCTTCATCCATCTATT 59.651 45.833 0.00 0.00 0.00 1.73
5337 6317 6.734281 TCCTTCATCCATCTATTCATCCTCAT 59.266 38.462 0.00 0.00 0.00 2.90
5372 6352 1.403687 ATCGACCTTGCTAGGCCTCC 61.404 60.000 9.68 1.52 46.22 4.30
5389 6369 4.758251 CCTGCCATCGACGCCACA 62.758 66.667 4.01 0.00 0.00 4.17
5420 6400 0.320683 CAACATCGTCCTCCTGCACA 60.321 55.000 0.00 0.00 0.00 4.57
5422 6402 0.615331 ACATCGTCCTCCTGCACAAT 59.385 50.000 0.00 0.00 0.00 2.71
5444 6425 1.987855 ATCACCACCCATCGGACGT 60.988 57.895 0.00 0.00 0.00 4.34
5445 6426 2.238847 ATCACCACCCATCGGACGTG 62.239 60.000 0.00 0.00 34.77 4.49
5497 6478 0.104120 CCGCCATCGATGTGTAGGAA 59.896 55.000 23.27 0.00 38.10 3.36
5525 6506 1.975407 CTCCACCACCTACCGACGT 60.975 63.158 0.00 0.00 0.00 4.34
5606 6588 0.541863 ATGGGGGTGACGATGAAGAC 59.458 55.000 0.00 0.00 0.00 3.01
5607 6589 0.544357 TGGGGGTGACGATGAAGACT 60.544 55.000 0.00 0.00 0.00 3.24
5608 6590 0.613777 GGGGGTGACGATGAAGACTT 59.386 55.000 0.00 0.00 0.00 3.01
5629 6611 0.036952 GTCGCCATCATCCGATCCAT 60.037 55.000 0.00 0.00 35.76 3.41
5630 6612 0.037046 TCGCCATCATCCGATCCATG 60.037 55.000 0.00 0.00 0.00 3.66
5631 6613 1.642037 CGCCATCATCCGATCCATGC 61.642 60.000 0.00 0.00 0.00 4.06
5632 6614 0.607217 GCCATCATCCGATCCATGCA 60.607 55.000 0.00 0.00 0.00 3.96
5633 6615 1.953785 GCCATCATCCGATCCATGCAT 60.954 52.381 0.00 0.00 0.00 3.96
5667 6649 3.442996 CTCCAACGAGGGCTACAAG 57.557 57.895 0.00 0.00 38.24 3.16
5712 6694 3.181427 GGTAGCCTCCTCCAGATCTAAGA 60.181 52.174 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 6.214005 CCTATAAGGGGGTCGTATGGATAAAA 59.786 42.308 0.00 0.00 0.00 1.52
112 113 2.728007 AGAAATTAAGGCTGGCCAGAC 58.272 47.619 37.21 35.11 38.92 3.51
155 156 1.154225 GCAAATGAACCAGGCGTCG 60.154 57.895 0.00 0.00 0.00 5.12
158 159 2.179018 CGGCAAATGAACCAGGCG 59.821 61.111 0.00 0.00 43.34 5.52
160 161 2.810439 TTTTCGGCAAATGAACCAGG 57.190 45.000 0.00 0.00 0.00 4.45
194 195 1.629013 CGAGCGTTGCTACATTCTCA 58.371 50.000 0.00 0.00 39.88 3.27
199 200 1.519455 GAGGCGAGCGTTGCTACAT 60.519 57.895 0.00 0.00 39.88 2.29
200 201 2.126071 GAGGCGAGCGTTGCTACA 60.126 61.111 0.00 0.00 39.88 2.74
201 202 1.687494 CTTGAGGCGAGCGTTGCTAC 61.687 60.000 0.00 0.00 39.88 3.58
251 252 3.404899 GTTCCCAAAATCACGAGGTACA 58.595 45.455 0.00 0.00 0.00 2.90
257 258 3.954904 TCAAAAGGTTCCCAAAATCACGA 59.045 39.130 0.00 0.00 0.00 4.35
258 259 4.314740 TCAAAAGGTTCCCAAAATCACG 57.685 40.909 0.00 0.00 0.00 4.35
260 261 8.313292 CAAGATATCAAAAGGTTCCCAAAATCA 58.687 33.333 5.32 0.00 0.00 2.57
268 269 6.148811 TCACGAACAAGATATCAAAAGGTTCC 59.851 38.462 5.32 0.00 31.86 3.62
269 270 7.129109 TCACGAACAAGATATCAAAAGGTTC 57.871 36.000 5.32 9.46 0.00 3.62
387 388 7.171678 CGGGAAAACTTGGCATGTAAATAAAAA 59.828 33.333 6.44 0.00 0.00 1.94
388 389 6.647067 CGGGAAAACTTGGCATGTAAATAAAA 59.353 34.615 6.44 0.00 0.00 1.52
398 399 1.066929 GCATTCGGGAAAACTTGGCAT 60.067 47.619 0.00 0.00 0.00 4.40
651 680 9.591792 TGTTCACACAATTTCAAAACATATTCA 57.408 25.926 0.00 0.00 0.00 2.57
658 687 9.444534 AAAAAGTTGTTCACACAATTTCAAAAC 57.555 25.926 0.00 0.00 44.85 2.43
748 778 8.661352 AACTCGAAAATTTGTTGATGGAATTT 57.339 26.923 0.00 0.00 35.22 1.82
750 780 8.661352 AAAACTCGAAAATTTGTTGATGGAAT 57.339 26.923 0.00 0.00 0.00 3.01
817 847 9.903185 GTTCACGATATTTTCTAAGAAAGCTAC 57.097 33.333 0.00 0.00 0.00 3.58
871 904 8.449251 AAAGTTTGTGCCATTAAAAATGTGAT 57.551 26.923 0.00 0.00 0.00 3.06
873 906 7.044183 GCAAAAGTTTGTGCCATTAAAAATGTG 60.044 33.333 5.71 0.00 40.24 3.21
911 944 9.482627 CCATGCAGTTTTTAAAACCTGTTAATA 57.517 29.630 21.95 8.40 0.00 0.98
914 947 7.113658 TCCATGCAGTTTTTAAAACCTGTTA 57.886 32.000 21.95 14.15 0.00 2.41
917 950 7.495135 AAATCCATGCAGTTTTTAAAACCTG 57.505 32.000 18.30 18.30 0.00 4.00
1104 1139 4.201783 CGCTTATTGTAACCTTGCCTACAC 60.202 45.833 0.00 0.00 0.00 2.90
1131 1178 0.734889 CAAATGAGGCCGCTACAAGG 59.265 55.000 8.34 0.00 0.00 3.61
1136 1183 2.706636 GCATCAAATGAGGCCGCTA 58.293 52.632 8.34 0.00 45.12 4.26
1141 1188 9.398031 ACTTCAAAGTTAGGCATCAAATGAGGC 62.398 40.741 11.33 11.33 42.81 4.70
1220 1275 3.134574 TGTTGTTGCCGGAGAATAAGT 57.865 42.857 5.05 0.00 0.00 2.24
1268 1325 1.001378 CCTCGGCAAACAAAGGTGAAG 60.001 52.381 0.00 0.00 0.00 3.02
1433 1504 5.769662 TGACACTAGCAAAATCAAACATCCT 59.230 36.000 0.00 0.00 0.00 3.24
1438 1509 4.798574 CCCTGACACTAGCAAAATCAAAC 58.201 43.478 0.00 0.00 0.00 2.93
1481 1554 8.946935 CATGTTTAGCATACAATTAATGTCGTG 58.053 33.333 0.00 0.00 42.70 4.35
1483 1556 9.502145 AACATGTTTAGCATACAATTAATGTCG 57.498 29.630 4.92 0.00 42.70 4.35
1517 1590 9.121658 CCATCGAGCTATATTACTCTAATGGTA 57.878 37.037 17.32 0.00 38.17 3.25
1756 1851 0.528684 GGAGCTCGTCCATCTTTCCG 60.529 60.000 7.83 0.00 46.10 4.30
1926 2022 6.757478 TGTGTCATGCATGGCAATAAATAAAG 59.243 34.615 34.01 0.00 44.94 1.85
1936 2032 3.253921 GCTAATATGTGTCATGCATGGCA 59.746 43.478 29.45 29.45 44.86 4.92
1985 2081 5.425630 GTTCCCCAACAGTAACATAGGTAG 58.574 45.833 0.00 0.00 32.14 3.18
2080 2226 0.740868 TCTACGAGGGTACGTGGACG 60.741 60.000 0.00 0.00 45.53 4.79
2179 3078 4.147449 CAGATCGCGGAGGTGCCA 62.147 66.667 6.13 0.00 35.94 4.92
2244 3143 2.165437 CTGAAGGAACTCTCCCTCGAAG 59.835 54.545 0.00 0.00 43.64 3.79
2245 3144 2.171840 CTGAAGGAACTCTCCCTCGAA 58.828 52.381 0.00 0.00 43.64 3.71
2287 3186 0.530744 AGCGTCGGTAGCTTCATCAA 59.469 50.000 0.00 0.00 43.24 2.57
2424 3332 6.457011 CCTCCTCCCTCCATCCTTTATATAT 58.543 44.000 0.00 0.00 0.00 0.86
2449 3357 3.142393 CCCTATGAGGACCGGCAG 58.858 66.667 0.00 0.00 37.67 4.85
2450 3358 3.161450 GCCCTATGAGGACCGGCA 61.161 66.667 0.00 0.00 37.67 5.69
2516 3440 3.288964 AGGTGGAATCGTACTAGGACTG 58.711 50.000 2.99 0.00 0.00 3.51
2527 3451 0.464373 CCATGTGGGAGGTGGAATCG 60.464 60.000 0.00 0.00 40.01 3.34
2618 3544 3.797353 CACCCCTCCCCATGGACG 61.797 72.222 15.22 2.40 35.03 4.79
2653 3580 3.621461 GCCATACGGGAAAGGAGAGAAAA 60.621 47.826 0.00 0.00 40.01 2.29
2764 3691 6.757010 CCGTAAAGATCGATATATTGGAAGGG 59.243 42.308 0.00 0.00 0.00 3.95
2789 3716 3.791245 AGGAGTCTCGAAATGATCAAGC 58.209 45.455 0.00 0.00 0.00 4.01
2792 3719 4.646492 TGATGAGGAGTCTCGAAATGATCA 59.354 41.667 0.00 0.00 42.79 2.92
2795 3722 4.403752 ACATGATGAGGAGTCTCGAAATGA 59.596 41.667 0.00 0.00 42.79 2.57
2812 3739 1.905215 GGATGAGATCGGGGACATGAT 59.095 52.381 0.00 0.00 0.00 2.45
2957 3886 3.315191 CAGGTTCCGCTATTGGTTATTGG 59.685 47.826 0.00 0.00 0.00 3.16
3003 3932 6.726230 TGACCGATAAAGATCTTCGTAGAAG 58.274 40.000 8.78 3.56 45.90 2.85
3051 3981 2.038387 ACATACCGATGACAAAGGGC 57.962 50.000 4.83 0.00 36.48 5.19
3145 4077 1.949525 GTTGCGGGATGATGCATTACT 59.050 47.619 0.00 0.00 41.42 2.24
3177 4109 2.959220 AAGCCTTGCAAGCAACGTGC 62.959 55.000 21.43 16.83 45.46 5.34
3181 4113 3.440173 TCACTATAAGCCTTGCAAGCAAC 59.560 43.478 21.43 12.10 0.00 4.17
3234 4166 2.710377 TGTCAATCCAATTGTCGGAGG 58.290 47.619 4.43 0.00 41.02 4.30
3249 4181 7.600375 GCATAGATCGAGATTAGGATTTGTCAA 59.400 37.037 0.00 0.00 0.00 3.18
3293 4225 0.817654 TGCTCTACATGTGTCTCCGG 59.182 55.000 9.11 0.00 0.00 5.14
3472 4407 7.114095 TGGAGAATGATCTGATTGATTTGACA 58.886 34.615 0.00 0.00 35.54 3.58
3496 4433 3.700539 TGATTAACAGGGCCACATCATTG 59.299 43.478 6.18 0.00 0.00 2.82
3506 4443 5.048083 TGAGTTGTCATTTGATTAACAGGGC 60.048 40.000 10.98 0.00 31.06 5.19
3507 4444 6.573664 TGAGTTGTCATTTGATTAACAGGG 57.426 37.500 10.98 0.00 31.06 4.45
3537 4475 7.988737 TCAAAGATGGTTATGTTTCATAGCTG 58.011 34.615 0.00 0.00 28.23 4.24
3538 4476 8.757982 ATCAAAGATGGTTATGTTTCATAGCT 57.242 30.769 0.00 0.00 28.23 3.32
3543 4481 7.807433 CGTTGAATCAAAGATGGTTATGTTTCA 59.193 33.333 2.77 0.00 32.58 2.69
3591 4529 6.448006 ACATAGACAAACAGAGTGTCACTAC 58.552 40.000 5.21 0.00 46.44 2.73
3721 4665 9.435570 AGGCTTAGAGTAACTGAAGGAAATATA 57.564 33.333 0.00 0.00 0.00 0.86
3738 4682 4.717877 TGATGAGAGAGAGAGGCTTAGAG 58.282 47.826 0.00 0.00 0.00 2.43
3739 4683 4.787135 TGATGAGAGAGAGAGGCTTAGA 57.213 45.455 0.00 0.00 0.00 2.10
3740 4684 4.321452 GCATGATGAGAGAGAGAGGCTTAG 60.321 50.000 0.00 0.00 0.00 2.18
3741 4685 3.573538 GCATGATGAGAGAGAGAGGCTTA 59.426 47.826 0.00 0.00 0.00 3.09
3742 4686 2.366266 GCATGATGAGAGAGAGAGGCTT 59.634 50.000 0.00 0.00 0.00 4.35
3743 4687 1.965643 GCATGATGAGAGAGAGAGGCT 59.034 52.381 0.00 0.00 0.00 4.58
3744 4688 1.965643 AGCATGATGAGAGAGAGAGGC 59.034 52.381 0.00 0.00 0.00 4.70
3745 4689 3.637694 TGAAGCATGATGAGAGAGAGAGG 59.362 47.826 0.00 0.00 0.00 3.69
3746 4690 4.500205 GGTGAAGCATGATGAGAGAGAGAG 60.500 50.000 0.00 0.00 0.00 3.20
3747 4691 3.384146 GGTGAAGCATGATGAGAGAGAGA 59.616 47.826 0.00 0.00 0.00 3.10
3748 4692 3.385433 AGGTGAAGCATGATGAGAGAGAG 59.615 47.826 0.00 0.00 0.00 3.20
3749 4693 3.372897 AGGTGAAGCATGATGAGAGAGA 58.627 45.455 0.00 0.00 0.00 3.10
3750 4694 3.493002 GGAGGTGAAGCATGATGAGAGAG 60.493 52.174 0.00 0.00 0.00 3.20
3751 4695 2.433604 GGAGGTGAAGCATGATGAGAGA 59.566 50.000 0.00 0.00 0.00 3.10
3752 4696 2.485124 GGGAGGTGAAGCATGATGAGAG 60.485 54.545 0.00 0.00 0.00 3.20
3753 4697 1.487976 GGGAGGTGAAGCATGATGAGA 59.512 52.381 0.00 0.00 0.00 3.27
3754 4698 1.809271 CGGGAGGTGAAGCATGATGAG 60.809 57.143 0.00 0.00 0.00 2.90
3755 4699 0.178767 CGGGAGGTGAAGCATGATGA 59.821 55.000 0.00 0.00 0.00 2.92
3756 4700 2.699073 CGGGAGGTGAAGCATGATG 58.301 57.895 0.00 0.00 0.00 3.07
3784 4728 1.827399 AACTCGCCGGACATGGAGTT 61.827 55.000 5.05 12.18 43.00 3.01
3793 4737 3.379445 GTCCAGGAACTCGCCGGA 61.379 66.667 5.05 0.00 34.60 5.14
3906 4868 1.302511 CTTGGCCTTGTGGTAGCGT 60.303 57.895 3.32 0.00 35.27 5.07
3916 4878 4.447342 CGGGATGGCCTTGGCCTT 62.447 66.667 28.37 23.06 0.00 4.35
3922 4884 0.181350 GAGTTGATCGGGATGGCCTT 59.819 55.000 3.32 0.00 0.00 4.35
3932 4894 1.202313 GGTCCTCGAAGGAGTTGATCG 60.202 57.143 4.13 0.00 46.90 3.69
3950 4912 0.892755 TGCAACGTCCTAATCGAGGT 59.107 50.000 0.00 0.00 46.76 3.85
3982 4945 3.476419 GCAGCCGGGCTTAGGGTA 61.476 66.667 21.26 0.00 36.40 3.69
4007 4970 6.069331 ACTATGAGTGGACCGATGTTATACT 58.931 40.000 0.00 0.00 0.00 2.12
4059 5022 4.680237 CAGGAAGGTGGCGCACGA 62.680 66.667 10.83 0.00 34.83 4.35
4062 5025 4.329545 GTCCAGGAAGGTGGCGCA 62.330 66.667 10.83 0.00 37.53 6.09
4070 5033 1.000827 CGATCGATCCAGTCCAGGAAG 60.001 57.143 19.51 0.00 41.92 3.46
4072 5035 0.823769 CCGATCGATCCAGTCCAGGA 60.824 60.000 18.66 0.00 43.01 3.86
4083 5046 3.620785 GGGAGGCTGCCGATCGAT 61.621 66.667 18.66 0.00 0.00 3.59
4088 5051 3.706373 GACTTGGGAGGCTGCCGA 61.706 66.667 20.76 17.87 0.00 5.54
4097 5060 0.530744 CGAAGATGACCGACTTGGGA 59.469 55.000 0.00 0.00 44.64 4.37
4121 5084 1.194121 GCAAACCTCTGGGGCCAAAT 61.194 55.000 4.39 0.00 39.10 2.32
4128 5091 0.951040 GTCGACAGCAAACCTCTGGG 60.951 60.000 11.55 0.00 35.94 4.45
4131 5094 0.387929 TTCGTCGACAGCAAACCTCT 59.612 50.000 17.16 0.00 0.00 3.69
4136 5099 4.429213 TGCTTCGTCGACAGCAAA 57.571 50.000 23.73 6.06 43.14 3.68
4149 5112 1.506493 GCTAGCTCACGCATATGCTT 58.494 50.000 24.56 13.70 39.10 3.91
4172 5135 4.020617 CCGTTGAGCTCCAGCCCA 62.021 66.667 12.15 0.00 43.38 5.36
4186 5149 3.031417 AATAGGAAGCGCTGCCCGT 62.031 57.895 31.70 17.30 39.71 5.28
4241 5204 0.673333 CAGCGTCATAGTGGTTGGCA 60.673 55.000 0.00 0.00 0.00 4.92
4248 5211 2.159324 TCTTGCTCTCAGCGTCATAGTG 60.159 50.000 0.00 0.00 46.26 2.74
4259 5222 1.671742 GGGGTCGTTCTTGCTCTCA 59.328 57.895 0.00 0.00 0.00 3.27
4271 5234 2.687566 AAGTAGGCCAGGGGGTCG 60.688 66.667 5.01 0.00 46.12 4.79
4287 5250 2.342279 CACGAACCGCTCTGGGAA 59.658 61.111 0.00 0.00 44.64 3.97
4292 5255 2.651361 CTGTCCACGAACCGCTCT 59.349 61.111 0.00 0.00 0.00 4.09
4296 5259 0.948623 TCATTGCTGTCCACGAACCG 60.949 55.000 0.00 0.00 0.00 4.44
4307 5270 2.360350 AGGCCGGTGTCATTGCTG 60.360 61.111 1.90 0.00 0.00 4.41
4310 5273 1.450312 GAGGAGGCCGGTGTCATTG 60.450 63.158 1.90 0.00 0.00 2.82
4312 5275 3.461773 CGAGGAGGCCGGTGTCAT 61.462 66.667 1.90 0.00 0.00 3.06
4313 5276 4.988716 ACGAGGAGGCCGGTGTCA 62.989 66.667 1.90 0.00 0.00 3.58
4314 5277 4.436998 CACGAGGAGGCCGGTGTC 62.437 72.222 1.90 0.00 31.56 3.67
4362 5328 2.300967 ATCATGTGGCCCCGTGAGT 61.301 57.895 15.63 2.00 34.06 3.41
4369 5335 0.458669 CAAGAAGCATCATGTGGCCC 59.541 55.000 0.00 0.00 0.00 5.80
4390 5356 1.228552 AAGTTCCACCCGCAATGCT 60.229 52.632 2.94 0.00 0.00 3.79
4394 5360 1.527380 GACCAAGTTCCACCCGCAA 60.527 57.895 0.00 0.00 0.00 4.85
4484 5450 2.022195 CTGACCCCTTCAATCAGCATG 58.978 52.381 0.00 0.00 33.93 4.06
4492 5458 1.205460 GGCTACCCTGACCCCTTCAA 61.205 60.000 0.00 0.00 32.21 2.69
4493 5459 1.615424 GGCTACCCTGACCCCTTCA 60.615 63.158 0.00 0.00 0.00 3.02
4496 5462 0.400093 GTATGGCTACCCTGACCCCT 60.400 60.000 0.00 0.00 0.00 4.79
4519 5485 1.065854 CCTTTCTCTTGGTCATCGCCT 60.066 52.381 0.00 0.00 0.00 5.52
4521 5487 2.275318 CTCCTTTCTCTTGGTCATCGC 58.725 52.381 0.00 0.00 0.00 4.58
4549 5515 2.997315 CCTCCCTCACTGCCACGA 60.997 66.667 0.00 0.00 0.00 4.35
4565 5531 3.061848 CCATGGCCAACCGTCACC 61.062 66.667 10.96 0.00 39.70 4.02
4570 5536 3.814268 CTTCGCCATGGCCAACCG 61.814 66.667 30.79 16.42 39.70 4.44
4617 5583 1.303888 CTGTGGCCACCTTCTGCAT 60.304 57.895 32.62 0.00 0.00 3.96
4667 5633 1.376086 CACCACCTCATCCAGTGCA 59.624 57.895 0.00 0.00 32.48 4.57
4670 5636 1.583556 TATGCACCACCTCATCCAGT 58.416 50.000 0.00 0.00 0.00 4.00
4700 5666 1.209504 GACACCTAGCAATACCAGCCA 59.790 52.381 0.00 0.00 0.00 4.75
4704 5670 2.691409 GCTGACACCTAGCAATACCA 57.309 50.000 0.00 0.00 40.81 3.25
4732 5698 6.926272 ACAAATAGAAGGAGCGAGATGTATTC 59.074 38.462 0.00 0.00 0.00 1.75
4742 5708 2.621338 TGCAGACAAATAGAAGGAGCG 58.379 47.619 0.00 0.00 0.00 5.03
4752 5718 1.655484 TCATCGCGATGCAGACAAAT 58.345 45.000 37.84 4.85 38.65 2.32
4754 5720 0.932399 CATCATCGCGATGCAGACAA 59.068 50.000 37.84 23.42 44.95 3.18
4886 5854 5.768164 TGACTCTTGCCATGTCGATATAGTA 59.232 40.000 0.00 0.00 33.81 1.82
4892 5860 2.027745 ACTTGACTCTTGCCATGTCGAT 60.028 45.455 0.00 0.00 33.81 3.59
4895 5863 1.198637 GCACTTGACTCTTGCCATGTC 59.801 52.381 0.00 0.00 0.00 3.06
4902 5870 2.547211 CTCTTGTGGCACTTGACTCTTG 59.453 50.000 19.83 1.44 0.00 3.02
4905 5873 0.871057 GCTCTTGTGGCACTTGACTC 59.129 55.000 19.83 5.87 0.00 3.36
4913 5881 0.106769 TGTTCCTTGCTCTTGTGGCA 60.107 50.000 0.00 0.00 37.97 4.92
4920 5888 1.428869 AGACCAGTGTTCCTTGCTCT 58.571 50.000 0.00 0.00 0.00 4.09
4926 5894 1.625818 CTTGCCTAGACCAGTGTTCCT 59.374 52.381 0.00 0.00 0.00 3.36
4928 5896 2.841442 ACTTGCCTAGACCAGTGTTC 57.159 50.000 0.00 0.00 0.00 3.18
4940 5909 0.614979 TCGAGAGCCCTAACTTGCCT 60.615 55.000 0.00 0.00 0.00 4.75
4994 5970 2.232208 GGGTGCATCCTCCTTTTCAAAG 59.768 50.000 9.39 0.00 36.25 2.77
5126 6105 0.554305 TCACCGGGATAGGAGTAGCA 59.446 55.000 6.32 0.00 34.73 3.49
5141 6120 2.286365 TTCAACACCCCTTCATCACC 57.714 50.000 0.00 0.00 0.00 4.02
5157 6136 5.692115 TTGGTATTAGGCTCAGACATTCA 57.308 39.130 0.00 0.00 0.00 2.57
5185 6164 3.758554 AGATGTTAGGTGTTGGTGCAATC 59.241 43.478 0.00 0.00 0.00 2.67
5242 6221 3.463944 CAAACCGGTGTCTAACTCAGTT 58.536 45.455 8.52 0.00 0.00 3.16
5247 6226 0.601841 CGCCAAACCGGTGTCTAACT 60.602 55.000 8.52 0.00 40.72 2.24
5298 6277 3.892104 AAGGAGGTGACCGCCCGTA 62.892 63.158 21.26 0.00 44.82 4.02
5300 6279 4.452733 GAAGGAGGTGACCGCCCG 62.453 72.222 21.26 0.00 44.82 6.13
5305 6284 2.122768 AGATGGATGAAGGAGGTGACC 58.877 52.381 0.00 0.00 0.00 4.02
5328 6308 6.153340 TGCGTCAATATCTGATATGAGGATGA 59.847 38.462 20.87 14.43 36.14 2.92
5337 6317 4.459337 AGGTCGATGCGTCAATATCTGATA 59.541 41.667 6.75 0.00 36.14 2.15
5372 6352 4.758251 TGTGGCGTCGATGGCAGG 62.758 66.667 31.74 0.00 45.88 4.85
5420 6400 1.410083 CCGATGGGTGGTGATGGAATT 60.410 52.381 0.00 0.00 0.00 2.17
5422 6402 0.912006 TCCGATGGGTGGTGATGGAA 60.912 55.000 0.00 0.00 33.83 3.53
5497 6478 3.241530 TGGTGGAGCGGTGCTTCT 61.242 61.111 7.84 0.00 39.88 2.85
5525 6506 1.076549 GGATGGCTTGGTGGTTGGA 59.923 57.895 0.00 0.00 0.00 3.53
5606 6588 0.319040 ATCGGATGATGGCGACGAAG 60.319 55.000 0.00 0.00 37.11 3.79
5607 6589 0.318699 GATCGGATGATGGCGACGAA 60.319 55.000 0.00 0.00 37.11 3.85
5608 6590 1.285950 GATCGGATGATGGCGACGA 59.714 57.895 0.00 0.00 34.09 4.20


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

AutoCloner maintained by Alex Coulton.