Multiple sequence alignment - TraesCS6D01G056400

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 TraesCS6D01G056400 chr6D 100.000 3191 0 0 1 3191 27033841 27030651 0.000000e+00 5893.0
1 TraesCS6D01G056400 chr6D 84.848 1749 225 21 620 2348 26860963 26859235 0.000000e+00 1725.0
2 TraesCS6D01G056400 chr6D 84.791 1749 226 21 620 2348 26817215 26815487 0.000000e+00 1720.0
3 TraesCS6D01G056400 chr6D 84.734 1749 227 21 620 2348 26897303 26895575 0.000000e+00 1714.0
4 TraesCS6D01G056400 chr6D 81.983 1654 251 31 670 2309 26515887 26517507 0.000000e+00 1360.0
5 TraesCS6D01G056400 chr6D 81.780 1652 260 28 670 2309 26531871 26533493 0.000000e+00 1345.0
6 TraesCS6D01G056400 chr6D 89.489 333 18 7 4 319 68329049 68329381 3.830000e-109 405.0
7 TraesCS6D01G056400 chr6A 93.529 2040 94 10 912 2932 28319318 28317298 0.000000e+00 3001.0
8 TraesCS6D01G056400 chr6A 83.744 1747 226 31 620 2348 28258933 28257227 0.000000e+00 1600.0
9 TraesCS6D01G056400 chr6A 95.005 1001 34 10 1505 2493 28317312 28316316 0.000000e+00 1557.0
10 TraesCS6D01G056400 chr6A 90.510 706 36 11 2496 3191 28285278 28284594 0.000000e+00 904.0
11 TraesCS6D01G056400 chr6A 90.957 575 33 11 319 883 28319873 28319308 0.000000e+00 756.0
12 TraesCS6D01G056400 chr6B 85.749 2042 230 28 337 2348 49239423 49237413 0.000000e+00 2102.0
13 TraesCS6D01G056400 chr6B 84.000 1275 175 19 1083 2348 49052913 49051659 0.000000e+00 1197.0
14 TraesCS6D01G056400 chr6B 84.035 1140 162 12 1057 2189 49551750 49552876 0.000000e+00 1079.0
15 TraesCS6D01G056400 chr6B 88.321 685 56 12 1809 2473 49331949 49331269 0.000000e+00 800.0
16 TraesCS6D01G056400 chr6B 94.800 500 17 8 504 997 49236491 49235995 0.000000e+00 771.0
17 TraesCS6D01G056400 chr6B 90.068 584 29 16 2585 3154 49231049 49230481 0.000000e+00 730.0
18 TraesCS6D01G056400 chr6B 94.444 468 18 6 2044 2506 49235973 49235509 0.000000e+00 713.0
19 TraesCS6D01G056400 chr6B 85.034 294 24 11 636 920 49392047 49391765 6.740000e-72 281.0
20 TraesCS6D01G056400 chr6B 86.585 246 26 5 619 859 49199837 49199594 6.790000e-67 265.0
21 TraesCS6D01G056400 chr6B 83.444 302 25 14 313 610 49550053 49550333 1.140000e-64 257.0
22 TraesCS6D01G056400 chr6B 91.111 45 3 1 2889 2932 48980529 48980485 3.440000e-05 60.2
23 TraesCS6D01G056400 chr2D 88.955 335 20 7 1 319 596575956 596575623 6.410000e-107 398.0
24 TraesCS6D01G056400 chr2D 92.490 253 19 0 1 253 1613037 1613289 2.340000e-96 363.0
25 TraesCS6D01G056400 chr4D 88.889 333 21 6 3 319 447333880 447333548 2.310000e-106 396.0
26 TraesCS6D01G056400 chr4D 88.554 332 21 7 4 319 357507543 357507213 1.390000e-103 387.0
27 TraesCS6D01G056400 chr7D 88.358 335 23 5 1 319 80326757 80327091 3.860000e-104 388.0
28 TraesCS6D01G056400 chr7D 86.866 335 28 6 1 319 548054702 548055036 8.410000e-96 361.0
29 TraesCS6D01G056400 chr7A 88.957 326 20 7 4 313 670686301 670685976 3.860000e-104 388.0
30 TraesCS6D01G056400 chr7A 87.349 332 26 1 4 319 6799389 6799058 1.810000e-97 366.0
31 TraesCS6D01G056400 chr1D 88.288 333 25 1 1 319 469610457 469610789 1.390000e-103 387.0
32 TraesCS6D01G056400 chr1D 88.146 329 23 5 7 319 325966404 325966732 8.360000e-101 377.0
33 TraesCS6D01G056400 chr1D 87.761 335 25 7 1 319 375353008 375353342 8.360000e-101 377.0
34 TraesCS6D01G056400 chr1D 87.768 327 24 5 4 314 487022890 487022564 5.030000e-98 368.0
35 TraesCS6D01G056400 chr3B 87.915 331 24 3 1 315 749488953 749489283 3.010000e-100 375.0
36 TraesCS6D01G056400 chr2B 88.746 311 19 1 25 319 210461612 210461302 1.810000e-97 366.0
37 TraesCS6D01G056400 chr3D 87.009 331 27 6 5 319 539925222 539924892 3.030000e-95 359.0
38 TraesCS6D01G056400 chr4B 86.747 332 28 4 4 319 526721675 526721344 3.920000e-94 355.0


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 TraesCS6D01G056400 chr6D 27030651 27033841 3190 True 5893.000000 5893 100.000000 1 3191 1 chr6D.!!$R4 3190
1 TraesCS6D01G056400 chr6D 26859235 26860963 1728 True 1725.000000 1725 84.848000 620 2348 1 chr6D.!!$R2 1728
2 TraesCS6D01G056400 chr6D 26815487 26817215 1728 True 1720.000000 1720 84.791000 620 2348 1 chr6D.!!$R1 1728
3 TraesCS6D01G056400 chr6D 26895575 26897303 1728 True 1714.000000 1714 84.734000 620 2348 1 chr6D.!!$R3 1728
4 TraesCS6D01G056400 chr6D 26515887 26517507 1620 False 1360.000000 1360 81.983000 670 2309 1 chr6D.!!$F1 1639
5 TraesCS6D01G056400 chr6D 26531871 26533493 1622 False 1345.000000 1345 81.780000 670 2309 1 chr6D.!!$F2 1639
6 TraesCS6D01G056400 chr6A 28316316 28319873 3557 True 1771.333333 3001 93.163667 319 2932 3 chr6A.!!$R3 2613
7 TraesCS6D01G056400 chr6A 28257227 28258933 1706 True 1600.000000 1600 83.744000 620 2348 1 chr6A.!!$R1 1728
8 TraesCS6D01G056400 chr6A 28284594 28285278 684 True 904.000000 904 90.510000 2496 3191 1 chr6A.!!$R2 695
9 TraesCS6D01G056400 chr6B 49051659 49052913 1254 True 1197.000000 1197 84.000000 1083 2348 1 chr6B.!!$R2 1265
10 TraesCS6D01G056400 chr6B 49235509 49239423 3914 True 1195.333333 2102 91.664333 337 2506 3 chr6B.!!$R7 2169
11 TraesCS6D01G056400 chr6B 49331269 49331949 680 True 800.000000 800 88.321000 1809 2473 1 chr6B.!!$R5 664
12 TraesCS6D01G056400 chr6B 49230481 49231049 568 True 730.000000 730 90.068000 2585 3154 1 chr6B.!!$R4 569
13 TraesCS6D01G056400 chr6B 49550053 49552876 2823 False 668.000000 1079 83.739500 313 2189 2 chr6B.!!$F1 1876

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
316 317 0.035439 CCTAGCCGCCTTTTCTTGGA 60.035 55.0 0.0 0.0 0.0 3.53 F
1393 2482 0.100682 CGTACTGGTCCATGTCCGAG 59.899 60.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2101 3194 0.601057 TGCAACGACTCGAGATGGAA 59.399 50.0 21.68 0.0 0.00 3.53 R
2711 3989 0.725784 GCAGACGCATTTGTTGTCGG 60.726 55.0 0.00 0.0 37.69 4.79 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
19 20 2.609427 TCTGAGCGGATCCATCAAAG 57.391 50.000 13.41 4.90 0.00 2.77
20 21 2.110578 TCTGAGCGGATCCATCAAAGA 58.889 47.619 13.41 7.12 0.00 2.52
21 22 2.159043 TCTGAGCGGATCCATCAAAGAC 60.159 50.000 13.41 0.00 0.00 3.01
22 23 1.554617 TGAGCGGATCCATCAAAGACA 59.445 47.619 13.41 0.00 0.00 3.41
23 24 2.027285 TGAGCGGATCCATCAAAGACAA 60.027 45.455 13.41 0.00 0.00 3.18
24 25 2.352960 GAGCGGATCCATCAAAGACAAC 59.647 50.000 13.41 0.00 0.00 3.32
25 26 1.401905 GCGGATCCATCAAAGACAACC 59.598 52.381 13.41 0.00 0.00 3.77
26 27 2.710377 CGGATCCATCAAAGACAACCA 58.290 47.619 13.41 0.00 0.00 3.67
27 28 2.420022 CGGATCCATCAAAGACAACCAC 59.580 50.000 13.41 0.00 0.00 4.16
28 29 2.755103 GGATCCATCAAAGACAACCACC 59.245 50.000 6.95 0.00 0.00 4.61
29 30 1.890876 TCCATCAAAGACAACCACCG 58.109 50.000 0.00 0.00 0.00 4.94
30 31 1.418264 TCCATCAAAGACAACCACCGA 59.582 47.619 0.00 0.00 0.00 4.69
31 32 1.535462 CCATCAAAGACAACCACCGAC 59.465 52.381 0.00 0.00 0.00 4.79
32 33 1.535462 CATCAAAGACAACCACCGACC 59.465 52.381 0.00 0.00 0.00 4.79
33 34 0.542333 TCAAAGACAACCACCGACCA 59.458 50.000 0.00 0.00 0.00 4.02
34 35 1.065345 TCAAAGACAACCACCGACCAA 60.065 47.619 0.00 0.00 0.00 3.67
35 36 1.746220 CAAAGACAACCACCGACCAAA 59.254 47.619 0.00 0.00 0.00 3.28
36 37 2.358322 AAGACAACCACCGACCAAAT 57.642 45.000 0.00 0.00 0.00 2.32
37 38 1.892209 AGACAACCACCGACCAAATC 58.108 50.000 0.00 0.00 0.00 2.17
38 39 1.420138 AGACAACCACCGACCAAATCT 59.580 47.619 0.00 0.00 0.00 2.40
39 40 1.804748 GACAACCACCGACCAAATCTC 59.195 52.381 0.00 0.00 0.00 2.75
40 41 0.796312 CAACCACCGACCAAATCTCG 59.204 55.000 0.00 0.00 0.00 4.04
41 42 0.395312 AACCACCGACCAAATCTCGT 59.605 50.000 0.00 0.00 0.00 4.18
42 43 0.320421 ACCACCGACCAAATCTCGTG 60.320 55.000 0.00 0.00 0.00 4.35
43 44 0.037697 CCACCGACCAAATCTCGTGA 60.038 55.000 0.00 0.00 30.46 4.35
44 45 1.350193 CACCGACCAAATCTCGTGAG 58.650 55.000 0.00 0.00 30.46 3.51
45 46 1.067846 CACCGACCAAATCTCGTGAGA 60.068 52.381 1.43 1.43 42.37 3.27
47 48 2.159226 ACCGACCAAATCTCGTGAGATC 60.159 50.000 12.50 0.70 46.75 2.75
48 49 2.099921 CCGACCAAATCTCGTGAGATCT 59.900 50.000 12.50 0.00 46.75 2.75
49 50 3.111838 CGACCAAATCTCGTGAGATCTG 58.888 50.000 12.50 9.24 46.75 2.90
50 51 2.863137 GACCAAATCTCGTGAGATCTGC 59.137 50.000 12.50 0.00 46.75 4.26
51 52 2.499289 ACCAAATCTCGTGAGATCTGCT 59.501 45.455 12.50 0.00 46.75 4.24
52 53 2.864946 CCAAATCTCGTGAGATCTGCTG 59.135 50.000 12.50 8.06 46.75 4.41
53 54 3.429960 CCAAATCTCGTGAGATCTGCTGA 60.430 47.826 12.50 0.00 46.75 4.26
54 55 4.179298 CAAATCTCGTGAGATCTGCTGAA 58.821 43.478 12.50 0.00 46.75 3.02
55 56 3.713858 ATCTCGTGAGATCTGCTGAAG 57.286 47.619 0.00 0.00 44.37 3.02
56 57 2.716217 TCTCGTGAGATCTGCTGAAGA 58.284 47.619 0.00 0.00 40.84 2.87
57 58 2.421775 TCTCGTGAGATCTGCTGAAGAC 59.578 50.000 0.00 0.00 37.88 3.01
58 59 2.162681 TCGTGAGATCTGCTGAAGACA 58.837 47.619 0.00 0.00 37.88 3.41
59 60 2.095008 TCGTGAGATCTGCTGAAGACAC 60.095 50.000 0.00 7.24 37.88 3.67
60 61 2.352127 CGTGAGATCTGCTGAAGACACA 60.352 50.000 0.00 8.77 37.88 3.72
61 62 2.992543 GTGAGATCTGCTGAAGACACAC 59.007 50.000 0.00 12.63 37.88 3.82
62 63 2.028658 TGAGATCTGCTGAAGACACACC 60.029 50.000 0.00 0.00 37.88 4.16
63 64 2.233431 GAGATCTGCTGAAGACACACCT 59.767 50.000 0.00 0.00 37.88 4.00
64 65 2.233431 AGATCTGCTGAAGACACACCTC 59.767 50.000 0.00 0.00 37.88 3.85
65 66 0.681733 TCTGCTGAAGACACACCTCC 59.318 55.000 0.00 0.00 0.00 4.30
66 67 0.394192 CTGCTGAAGACACACCTCCA 59.606 55.000 0.00 0.00 0.00 3.86
67 68 0.106708 TGCTGAAGACACACCTCCAC 59.893 55.000 0.00 0.00 0.00 4.02
68 69 0.106708 GCTGAAGACACACCTCCACA 59.893 55.000 0.00 0.00 0.00 4.17
69 70 1.871080 CTGAAGACACACCTCCACAC 58.129 55.000 0.00 0.00 0.00 3.82
70 71 0.104120 TGAAGACACACCTCCACACG 59.896 55.000 0.00 0.00 0.00 4.49
71 72 1.222115 GAAGACACACCTCCACACGC 61.222 60.000 0.00 0.00 0.00 5.34
72 73 1.686325 AAGACACACCTCCACACGCT 61.686 55.000 0.00 0.00 0.00 5.07
73 74 1.664965 GACACACCTCCACACGCTC 60.665 63.158 0.00 0.00 0.00 5.03
74 75 2.088674 GACACACCTCCACACGCTCT 62.089 60.000 0.00 0.00 0.00 4.09
75 76 1.373497 CACACCTCCACACGCTCTC 60.373 63.158 0.00 0.00 0.00 3.20
76 77 2.262915 CACCTCCACACGCTCTCC 59.737 66.667 0.00 0.00 0.00 3.71
77 78 3.374402 ACCTCCACACGCTCTCCG 61.374 66.667 0.00 0.00 44.21 4.63
78 79 3.062466 CCTCCACACGCTCTCCGA 61.062 66.667 0.00 0.00 41.02 4.55
79 80 2.179517 CTCCACACGCTCTCCGAC 59.820 66.667 0.00 0.00 41.02 4.79
80 81 3.669036 CTCCACACGCTCTCCGACG 62.669 68.421 0.00 0.00 41.02 5.12
81 82 3.733960 CCACACGCTCTCCGACGA 61.734 66.667 0.00 0.00 41.02 4.20
82 83 2.485582 CACACGCTCTCCGACGAT 59.514 61.111 0.00 0.00 41.02 3.73
83 84 1.869574 CACACGCTCTCCGACGATG 60.870 63.158 0.00 0.00 41.02 3.84
84 85 2.951745 CACGCTCTCCGACGATGC 60.952 66.667 0.00 0.00 41.02 3.91
85 86 3.134792 ACGCTCTCCGACGATGCT 61.135 61.111 0.00 0.00 41.02 3.79
86 87 1.818363 ACGCTCTCCGACGATGCTA 60.818 57.895 0.00 0.00 41.02 3.49
87 88 1.082431 CGCTCTCCGACGATGCTAG 60.082 63.158 0.00 0.00 40.02 3.42
88 89 1.499688 CGCTCTCCGACGATGCTAGA 61.500 60.000 0.00 0.00 40.02 2.43
89 90 0.040781 GCTCTCCGACGATGCTAGAC 60.041 60.000 0.00 0.00 0.00 2.59
90 91 1.300481 CTCTCCGACGATGCTAGACA 58.700 55.000 0.00 0.00 0.00 3.41
91 92 1.003331 CTCTCCGACGATGCTAGACAC 60.003 57.143 0.00 0.00 0.00 3.67
92 93 0.733150 CTCCGACGATGCTAGACACA 59.267 55.000 0.00 0.00 0.00 3.72
93 94 0.450583 TCCGACGATGCTAGACACAC 59.549 55.000 0.00 0.00 0.00 3.82
94 95 0.525668 CCGACGATGCTAGACACACC 60.526 60.000 0.00 0.00 0.00 4.16
95 96 0.170339 CGACGATGCTAGACACACCA 59.830 55.000 0.00 0.00 0.00 4.17
96 97 1.202302 CGACGATGCTAGACACACCAT 60.202 52.381 0.00 0.00 0.00 3.55
97 98 2.735444 CGACGATGCTAGACACACCATT 60.735 50.000 0.00 0.00 0.00 3.16
98 99 2.604914 GACGATGCTAGACACACCATTG 59.395 50.000 0.00 0.00 0.00 2.82
99 100 1.935873 CGATGCTAGACACACCATTGG 59.064 52.381 0.00 0.00 0.00 3.16
100 101 2.292267 GATGCTAGACACACCATTGGG 58.708 52.381 7.78 0.00 41.29 4.12
101 102 1.357137 TGCTAGACACACCATTGGGA 58.643 50.000 7.78 0.00 38.05 4.37
102 103 1.003118 TGCTAGACACACCATTGGGAC 59.997 52.381 7.78 0.00 38.05 4.46
103 104 2.007049 GCTAGACACACCATTGGGACG 61.007 57.143 7.78 0.00 38.05 4.79
104 105 0.611200 TAGACACACCATTGGGACGG 59.389 55.000 7.78 0.00 38.05 4.79
105 106 1.674322 GACACACCATTGGGACGGG 60.674 63.158 7.78 0.00 38.05 5.28
106 107 2.361104 CACACCATTGGGACGGGG 60.361 66.667 7.78 0.00 38.05 5.73
107 108 3.657350 ACACCATTGGGACGGGGG 61.657 66.667 7.78 0.00 38.05 5.40
110 111 3.093835 CCATTGGGACGGGGGCTA 61.094 66.667 0.00 0.00 35.59 3.93
111 112 2.510906 CATTGGGACGGGGGCTAG 59.489 66.667 0.00 0.00 0.00 3.42
112 113 2.772622 ATTGGGACGGGGGCTAGG 60.773 66.667 0.00 0.00 0.00 3.02
120 121 4.499116 GGGGGCTAGGCAGGGAGA 62.499 72.222 19.14 0.00 0.00 3.71
121 122 2.366972 GGGGCTAGGCAGGGAGAA 60.367 66.667 19.14 0.00 0.00 2.87
122 123 2.747443 GGGGCTAGGCAGGGAGAAC 61.747 68.421 19.14 0.00 0.00 3.01
123 124 2.747443 GGGCTAGGCAGGGAGAACC 61.747 68.421 19.14 0.00 40.67 3.62
137 138 5.373812 GGGAGAACCTTATTCCATCTTCA 57.626 43.478 0.00 0.00 35.85 3.02
138 139 5.755849 GGGAGAACCTTATTCCATCTTCAA 58.244 41.667 0.00 0.00 35.85 2.69
139 140 5.825151 GGGAGAACCTTATTCCATCTTCAAG 59.175 44.000 0.00 0.00 35.85 3.02
140 141 6.353082 GGGAGAACCTTATTCCATCTTCAAGA 60.353 42.308 0.00 0.00 35.85 3.02
141 142 7.112779 GGAGAACCTTATTCCATCTTCAAGAA 58.887 38.462 0.00 0.00 0.00 2.52
142 143 7.281999 GGAGAACCTTATTCCATCTTCAAGAAG 59.718 40.741 3.43 3.43 39.71 2.85
143 144 6.601217 AGAACCTTATTCCATCTTCAAGAAGC 59.399 38.462 4.95 0.00 38.28 3.86
144 145 5.196695 ACCTTATTCCATCTTCAAGAAGCC 58.803 41.667 4.95 0.00 38.28 4.35
145 146 5.195940 CCTTATTCCATCTTCAAGAAGCCA 58.804 41.667 4.95 0.00 38.28 4.75
146 147 5.067023 CCTTATTCCATCTTCAAGAAGCCAC 59.933 44.000 4.95 0.00 38.28 5.01
147 148 2.496899 TCCATCTTCAAGAAGCCACC 57.503 50.000 4.95 0.00 38.28 4.61
148 149 1.089920 CCATCTTCAAGAAGCCACCG 58.910 55.000 4.95 0.00 38.28 4.94
149 150 0.449388 CATCTTCAAGAAGCCACCGC 59.551 55.000 4.95 0.00 38.28 5.68
150 151 0.678048 ATCTTCAAGAAGCCACCGCC 60.678 55.000 4.95 0.00 38.28 6.13
151 152 2.668212 TTCAAGAAGCCACCGCCG 60.668 61.111 0.00 0.00 34.57 6.46
152 153 3.469863 TTCAAGAAGCCACCGCCGT 62.470 57.895 0.00 0.00 34.57 5.68
153 154 3.423154 CAAGAAGCCACCGCCGTC 61.423 66.667 0.00 0.00 34.57 4.79
154 155 3.626924 AAGAAGCCACCGCCGTCT 61.627 61.111 0.00 0.00 34.57 4.18
155 156 3.591254 AAGAAGCCACCGCCGTCTC 62.591 63.158 0.00 0.00 34.57 3.36
160 161 4.052229 CCACCGCCGTCTCGTCTT 62.052 66.667 0.00 0.00 0.00 3.01
161 162 2.504244 CACCGCCGTCTCGTCTTC 60.504 66.667 0.00 0.00 0.00 2.87
162 163 2.672307 ACCGCCGTCTCGTCTTCT 60.672 61.111 0.00 0.00 0.00 2.85
163 164 2.266627 ACCGCCGTCTCGTCTTCTT 61.267 57.895 0.00 0.00 0.00 2.52
164 165 1.801913 CCGCCGTCTCGTCTTCTTG 60.802 63.158 0.00 0.00 0.00 3.02
165 166 1.209383 CGCCGTCTCGTCTTCTTGA 59.791 57.895 0.00 0.00 0.00 3.02
166 167 0.794981 CGCCGTCTCGTCTTCTTGAG 60.795 60.000 0.00 0.00 0.00 3.02
167 168 0.241481 GCCGTCTCGTCTTCTTGAGT 59.759 55.000 0.00 0.00 33.88 3.41
168 169 1.467734 GCCGTCTCGTCTTCTTGAGTA 59.532 52.381 0.00 0.00 33.88 2.59
169 170 2.476519 GCCGTCTCGTCTTCTTGAGTAG 60.477 54.545 0.00 0.00 33.88 2.57
170 171 2.096174 CCGTCTCGTCTTCTTGAGTAGG 59.904 54.545 0.00 0.00 33.88 3.18
171 172 3.001414 CGTCTCGTCTTCTTGAGTAGGA 58.999 50.000 0.00 0.00 33.88 2.94
172 173 3.181518 CGTCTCGTCTTCTTGAGTAGGAC 60.182 52.174 0.00 0.00 33.88 3.85
173 174 3.752222 GTCTCGTCTTCTTGAGTAGGACA 59.248 47.826 0.00 0.00 33.88 4.02
174 175 3.752222 TCTCGTCTTCTTGAGTAGGACAC 59.248 47.826 0.00 0.00 33.88 3.67
175 176 3.483421 TCGTCTTCTTGAGTAGGACACA 58.517 45.455 0.00 0.00 0.00 3.72
176 177 3.887110 TCGTCTTCTTGAGTAGGACACAA 59.113 43.478 0.00 0.00 0.00 3.33
177 178 4.340097 TCGTCTTCTTGAGTAGGACACAAA 59.660 41.667 0.00 0.00 28.81 2.83
178 179 4.444720 CGTCTTCTTGAGTAGGACACAAAC 59.555 45.833 0.00 0.00 28.81 2.93
179 180 4.750598 GTCTTCTTGAGTAGGACACAAACC 59.249 45.833 0.00 0.00 28.81 3.27
180 181 3.764237 TCTTGAGTAGGACACAAACCC 57.236 47.619 0.00 0.00 28.81 4.11
181 182 3.314693 TCTTGAGTAGGACACAAACCCT 58.685 45.455 0.00 0.00 36.60 4.34
182 183 4.485875 TCTTGAGTAGGACACAAACCCTA 58.514 43.478 0.00 0.00 34.11 3.53
183 184 4.903049 TCTTGAGTAGGACACAAACCCTAA 59.097 41.667 0.00 0.00 36.84 2.69
184 185 4.612264 TGAGTAGGACACAAACCCTAAC 57.388 45.455 0.00 0.00 36.84 2.34
185 186 3.968649 TGAGTAGGACACAAACCCTAACA 59.031 43.478 0.00 0.00 36.84 2.41
186 187 4.409574 TGAGTAGGACACAAACCCTAACAA 59.590 41.667 0.00 0.00 36.84 2.83
187 188 5.104444 TGAGTAGGACACAAACCCTAACAAA 60.104 40.000 0.00 0.00 36.84 2.83
188 189 5.757988 AGTAGGACACAAACCCTAACAAAA 58.242 37.500 0.00 0.00 36.84 2.44
189 190 4.994907 AGGACACAAACCCTAACAAAAC 57.005 40.909 0.00 0.00 0.00 2.43
190 191 4.606210 AGGACACAAACCCTAACAAAACT 58.394 39.130 0.00 0.00 0.00 2.66
191 192 5.020795 AGGACACAAACCCTAACAAAACTT 58.979 37.500 0.00 0.00 0.00 2.66
192 193 5.105513 AGGACACAAACCCTAACAAAACTTG 60.106 40.000 0.00 0.00 0.00 3.16
193 194 5.105675 GGACACAAACCCTAACAAAACTTGA 60.106 40.000 0.00 0.00 0.00 3.02
194 195 6.347859 ACACAAACCCTAACAAAACTTGAA 57.652 33.333 0.00 0.00 0.00 2.69
195 196 6.394809 ACACAAACCCTAACAAAACTTGAAG 58.605 36.000 0.00 0.00 0.00 3.02
196 197 6.209788 ACACAAACCCTAACAAAACTTGAAGA 59.790 34.615 0.00 0.00 0.00 2.87
197 198 7.093992 CACAAACCCTAACAAAACTTGAAGAA 58.906 34.615 0.00 0.00 0.00 2.52
198 199 7.275560 CACAAACCCTAACAAAACTTGAAGAAG 59.724 37.037 0.00 0.00 35.07 2.85
199 200 5.515797 ACCCTAACAAAACTTGAAGAAGC 57.484 39.130 0.00 0.00 31.68 3.86
200 201 4.953579 ACCCTAACAAAACTTGAAGAAGCA 59.046 37.500 0.00 0.00 31.68 3.91
201 202 5.163550 ACCCTAACAAAACTTGAAGAAGCAC 60.164 40.000 0.00 0.00 31.68 4.40
202 203 5.281727 CCTAACAAAACTTGAAGAAGCACC 58.718 41.667 0.00 0.00 31.68 5.01
203 204 5.067805 CCTAACAAAACTTGAAGAAGCACCT 59.932 40.000 0.00 0.00 31.68 4.00
204 205 4.376340 ACAAAACTTGAAGAAGCACCTG 57.624 40.909 0.00 0.00 31.68 4.00
205 206 4.016444 ACAAAACTTGAAGAAGCACCTGA 58.984 39.130 0.00 0.00 31.68 3.86
206 207 4.462483 ACAAAACTTGAAGAAGCACCTGAA 59.538 37.500 0.00 0.00 31.68 3.02
207 208 5.047377 ACAAAACTTGAAGAAGCACCTGAAA 60.047 36.000 0.00 0.00 31.68 2.69
208 209 5.659440 AAACTTGAAGAAGCACCTGAAAA 57.341 34.783 0.00 0.00 31.68 2.29
209 210 4.639135 ACTTGAAGAAGCACCTGAAAAC 57.361 40.909 0.00 0.00 31.68 2.43
210 211 3.065371 ACTTGAAGAAGCACCTGAAAACG 59.935 43.478 0.00 0.00 31.68 3.60
211 212 1.946768 TGAAGAAGCACCTGAAAACGG 59.053 47.619 0.00 0.00 0.00 4.44
212 213 2.218603 GAAGAAGCACCTGAAAACGGA 58.781 47.619 0.00 0.00 0.00 4.69
213 214 1.884235 AGAAGCACCTGAAAACGGAG 58.116 50.000 0.00 0.00 0.00 4.63
214 215 0.238553 GAAGCACCTGAAAACGGAGC 59.761 55.000 0.00 0.00 38.25 4.70
215 216 1.172812 AAGCACCTGAAAACGGAGCC 61.173 55.000 0.00 0.00 38.67 4.70
216 217 2.626780 GCACCTGAAAACGGAGCCC 61.627 63.158 0.00 0.00 32.83 5.19
217 218 1.073199 CACCTGAAAACGGAGCCCT 59.927 57.895 0.00 0.00 0.00 5.19
218 219 0.955919 CACCTGAAAACGGAGCCCTC 60.956 60.000 0.00 0.00 0.00 4.30
219 220 1.377333 CCTGAAAACGGAGCCCTCC 60.377 63.158 4.19 4.19 46.18 4.30
220 221 1.377333 CTGAAAACGGAGCCCTCCC 60.377 63.158 8.68 0.00 46.96 4.30
221 222 2.124507 CTGAAAACGGAGCCCTCCCA 62.125 60.000 8.68 0.20 46.96 4.37
222 223 1.674651 GAAAACGGAGCCCTCCCAC 60.675 63.158 8.68 0.00 46.96 4.61
223 224 3.205851 AAAACGGAGCCCTCCCACC 62.206 63.158 8.68 0.00 46.96 4.61
260 261 4.457496 CGCGCACCCAGGAGATGT 62.457 66.667 8.75 0.00 0.00 3.06
261 262 2.821366 GCGCACCCAGGAGATGTG 60.821 66.667 0.30 0.00 0.00 3.21
262 263 2.124983 CGCACCCAGGAGATGTGG 60.125 66.667 0.00 0.00 34.52 4.17
269 270 0.678395 CCAGGAGATGTGGGAGATCG 59.322 60.000 0.00 0.00 0.00 3.69
270 271 0.678395 CAGGAGATGTGGGAGATCGG 59.322 60.000 0.00 0.00 0.00 4.18
271 272 1.118356 AGGAGATGTGGGAGATCGGC 61.118 60.000 0.00 0.00 0.00 5.54
272 273 1.006805 GAGATGTGGGAGATCGGCG 60.007 63.158 0.00 0.00 0.00 6.46
273 274 2.029666 GATGTGGGAGATCGGCGG 59.970 66.667 7.21 0.00 0.00 6.13
274 275 4.241555 ATGTGGGAGATCGGCGGC 62.242 66.667 7.21 0.00 0.00 6.53
296 297 3.668386 CCAACGGGAGGCAGAAAC 58.332 61.111 0.00 0.00 35.59 2.78
297 298 1.971695 CCAACGGGAGGCAGAAACC 60.972 63.158 0.00 0.00 35.59 3.27
298 299 1.971695 CAACGGGAGGCAGAAACCC 60.972 63.158 0.00 0.00 40.17 4.11
299 300 2.154074 AACGGGAGGCAGAAACCCT 61.154 57.895 0.00 0.00 41.28 4.34
300 301 0.838987 AACGGGAGGCAGAAACCCTA 60.839 55.000 0.00 0.00 41.28 3.53
301 302 1.265454 ACGGGAGGCAGAAACCCTAG 61.265 60.000 0.00 0.00 41.28 3.02
302 303 1.224870 GGGAGGCAGAAACCCTAGC 59.775 63.158 0.00 0.00 40.39 3.42
305 306 2.824489 GGCAGAAACCCTAGCCGC 60.824 66.667 0.00 0.00 37.41 6.53
306 307 2.824489 GCAGAAACCCTAGCCGCC 60.824 66.667 0.00 0.00 0.00 6.13
307 308 2.990479 CAGAAACCCTAGCCGCCT 59.010 61.111 0.00 0.00 0.00 5.52
308 309 1.299976 CAGAAACCCTAGCCGCCTT 59.700 57.895 0.00 0.00 0.00 4.35
309 310 0.322546 CAGAAACCCTAGCCGCCTTT 60.323 55.000 0.00 0.00 0.00 3.11
310 311 0.404426 AGAAACCCTAGCCGCCTTTT 59.596 50.000 0.00 0.00 0.00 2.27
311 312 0.809385 GAAACCCTAGCCGCCTTTTC 59.191 55.000 0.00 0.00 0.00 2.29
312 313 0.404426 AAACCCTAGCCGCCTTTTCT 59.596 50.000 0.00 0.00 0.00 2.52
313 314 0.404426 AACCCTAGCCGCCTTTTCTT 59.596 50.000 0.00 0.00 0.00 2.52
314 315 0.322546 ACCCTAGCCGCCTTTTCTTG 60.323 55.000 0.00 0.00 0.00 3.02
315 316 1.032114 CCCTAGCCGCCTTTTCTTGG 61.032 60.000 0.00 0.00 0.00 3.61
316 317 0.035439 CCTAGCCGCCTTTTCTTGGA 60.035 55.000 0.00 0.00 0.00 3.53
317 318 1.373570 CTAGCCGCCTTTTCTTGGAG 58.626 55.000 0.00 0.00 0.00 3.86
364 365 2.674796 ACAATGTAGCGTTCTCTCCC 57.325 50.000 0.00 0.00 0.00 4.30
639 1354 8.408601 CCTTTGAATGTTTGATAATAGGTGAGG 58.591 37.037 0.00 0.00 0.00 3.86
698 1416 3.744426 AGTTCAGGTTGTATACGTGCAAC 59.256 43.478 18.03 18.03 46.32 4.17
868 1615 9.118300 GGGATTCAGATATGGATATTTGATCAC 57.882 37.037 0.00 1.02 34.91 3.06
901 1648 1.427592 GCTCCGCTCAGCAGTTCATC 61.428 60.000 0.00 0.00 39.43 2.92
1201 2287 4.459089 GCTTCTCCCGCCGCTTCT 62.459 66.667 0.00 0.00 0.00 2.85
1289 2375 2.575279 TCGTACCTACTCTGAAGGACCT 59.425 50.000 2.45 0.00 37.57 3.85
1329 2415 1.538047 GATTGTCCTTGCAGCCTCAA 58.462 50.000 0.00 0.00 0.00 3.02
1371 2460 2.037049 TTTGGATGCCGCCATGGT 59.963 55.556 14.67 0.00 41.21 3.55
1393 2482 0.100682 CGTACTGGTCCATGTCCGAG 59.899 60.000 0.00 0.00 0.00 4.63
1522 2611 1.192146 AGTGCTTCGGGCTACAGGAA 61.192 55.000 3.33 0.00 42.39 3.36
1673 2762 2.224450 ACACTACAGACCCTTTTTCCGG 60.224 50.000 0.00 0.00 0.00 5.14
1740 2829 3.406764 GAATTCCCTATACTGGCTGCTG 58.593 50.000 0.00 0.00 0.00 4.41
1813 2902 1.298667 GTGATAGGGTTGCCGGTGT 59.701 57.895 1.90 0.00 0.00 4.16
1835 2924 2.217038 TGGGTGCTGGGAGTGAGAC 61.217 63.158 0.00 0.00 0.00 3.36
1896 2985 2.231380 TGGGCTGGGTTTCCTCTCC 61.231 63.158 0.00 0.00 0.00 3.71
2019 3109 6.327104 TGAAAATTCCCATGGATCCAAATAGG 59.673 38.462 20.67 17.34 39.47 2.57
2101 3194 1.632046 AAAAATCGGCATCGTCGCGT 61.632 50.000 5.77 0.00 37.69 6.01
2337 3443 6.092670 CAGACATTGTAGAATTCATGACCGTT 59.907 38.462 8.44 0.00 0.00 4.44
2380 3486 8.251721 AGCTAGGGTGATATCAACGATTATTAC 58.748 37.037 14.52 0.00 33.46 1.89
2393 3499 4.041567 ACGATTATTACATGGGAGGCATGA 59.958 41.667 0.00 0.00 34.39 3.07
2396 3502 6.403964 CGATTATTACATGGGAGGCATGATTG 60.404 42.308 0.00 0.00 34.39 2.67
2405 3511 5.083122 TGGGAGGCATGATTGTTTTCTTAA 58.917 37.500 0.00 0.00 0.00 1.85
2451 3561 7.499438 TGTCGTCTTTGTTTGTTACATTTTG 57.501 32.000 0.00 0.00 36.44 2.44
2477 3587 2.680312 AATGCATGTACTCTGCGACT 57.320 45.000 0.00 2.24 42.62 4.18
2478 3588 3.801114 AATGCATGTACTCTGCGACTA 57.199 42.857 0.00 0.63 42.62 2.59
2479 3589 4.327982 AATGCATGTACTCTGCGACTAT 57.672 40.909 0.00 2.55 42.62 2.12
2480 3590 5.453567 AATGCATGTACTCTGCGACTATA 57.546 39.130 0.00 0.00 42.62 1.31
2481 3591 5.651387 ATGCATGTACTCTGCGACTATAT 57.349 39.130 0.00 1.72 42.62 0.86
2482 3592 6.759497 ATGCATGTACTCTGCGACTATATA 57.241 37.500 0.00 0.00 42.62 0.86
2483 3593 6.759497 TGCATGTACTCTGCGACTATATAT 57.241 37.500 13.79 0.00 42.62 0.86
2484 3594 7.859325 TGCATGTACTCTGCGACTATATATA 57.141 36.000 13.79 0.00 42.62 0.86
2485 3595 8.451908 TGCATGTACTCTGCGACTATATATAT 57.548 34.615 13.79 0.00 42.62 0.86
2486 3596 9.555727 TGCATGTACTCTGCGACTATATATATA 57.444 33.333 13.79 2.49 42.62 0.86
2651 3769 3.805207 AGACTTAATATTGGTGGTCGCC 58.195 45.455 0.00 0.00 0.00 5.54
2654 3932 4.196971 ACTTAATATTGGTGGTCGCCTTC 58.803 43.478 0.00 0.00 0.00 3.46
2747 4025 2.352457 CGGCGACTTCCTCGATCG 60.352 66.667 9.36 9.36 46.14 3.69
2795 4073 2.172717 GGAGGTGCTTATAAGGGCAAGA 59.827 50.000 14.28 0.00 40.26 3.02
2840 4128 5.220739 GGATTGAGTGTGTGTGAATATCTGC 60.221 44.000 0.00 0.00 0.00 4.26
2939 4603 1.078214 CCTGGGCTTCAATCTCGCA 60.078 57.895 0.00 0.00 0.00 5.10
3151 5766 2.277072 CTCCTCCGCCTCTCTCCA 59.723 66.667 0.00 0.00 0.00 3.86
3154 5769 1.684049 CCTCCGCCTCTCTCCACTT 60.684 63.158 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.208431 GTCTTTGATGGATCCGCTCAG 58.792 52.381 14.46 6.89 0.00 3.35
5 6 1.401905 GGTTGTCTTTGATGGATCCGC 59.598 52.381 7.39 2.06 0.00 5.54
6 7 2.420022 GTGGTTGTCTTTGATGGATCCG 59.580 50.000 7.39 0.00 0.00 4.18
8 9 2.420022 CGGTGGTTGTCTTTGATGGATC 59.580 50.000 0.00 0.00 0.00 3.36
9 10 2.039746 TCGGTGGTTGTCTTTGATGGAT 59.960 45.455 0.00 0.00 0.00 3.41
10 11 1.418264 TCGGTGGTTGTCTTTGATGGA 59.582 47.619 0.00 0.00 0.00 3.41
11 12 1.535462 GTCGGTGGTTGTCTTTGATGG 59.465 52.381 0.00 0.00 0.00 3.51
12 13 1.535462 GGTCGGTGGTTGTCTTTGATG 59.465 52.381 0.00 0.00 0.00 3.07
13 14 1.142060 TGGTCGGTGGTTGTCTTTGAT 59.858 47.619 0.00 0.00 0.00 2.57
14 15 0.542333 TGGTCGGTGGTTGTCTTTGA 59.458 50.000 0.00 0.00 0.00 2.69
15 16 1.384525 TTGGTCGGTGGTTGTCTTTG 58.615 50.000 0.00 0.00 0.00 2.77
16 17 2.131776 TTTGGTCGGTGGTTGTCTTT 57.868 45.000 0.00 0.00 0.00 2.52
17 18 2.158667 AGATTTGGTCGGTGGTTGTCTT 60.159 45.455 0.00 0.00 0.00 3.01
18 19 1.420138 AGATTTGGTCGGTGGTTGTCT 59.580 47.619 0.00 0.00 0.00 3.41
19 20 1.804748 GAGATTTGGTCGGTGGTTGTC 59.195 52.381 0.00 0.00 0.00 3.18
20 21 1.876416 CGAGATTTGGTCGGTGGTTGT 60.876 52.381 0.00 0.00 33.66 3.32
21 22 0.796312 CGAGATTTGGTCGGTGGTTG 59.204 55.000 0.00 0.00 33.66 3.77
22 23 0.395312 ACGAGATTTGGTCGGTGGTT 59.605 50.000 0.00 0.00 41.88 3.67
23 24 0.320421 CACGAGATTTGGTCGGTGGT 60.320 55.000 0.00 0.00 41.88 4.16
24 25 0.037697 TCACGAGATTTGGTCGGTGG 60.038 55.000 0.00 0.00 41.88 4.61
25 26 1.067846 TCTCACGAGATTTGGTCGGTG 60.068 52.381 0.00 0.00 41.88 4.94
26 27 1.254026 TCTCACGAGATTTGGTCGGT 58.746 50.000 0.00 0.00 41.88 4.69
27 28 2.586258 ATCTCACGAGATTTGGTCGG 57.414 50.000 3.64 0.00 45.31 4.79
36 37 2.421775 GTCTTCAGCAGATCTCACGAGA 59.578 50.000 0.00 0.00 42.37 4.04
37 38 2.163211 TGTCTTCAGCAGATCTCACGAG 59.837 50.000 0.00 0.00 32.60 4.18
38 39 2.095008 GTGTCTTCAGCAGATCTCACGA 60.095 50.000 0.00 0.00 32.60 4.35
39 40 2.257894 GTGTCTTCAGCAGATCTCACG 58.742 52.381 0.00 0.00 32.60 4.35
40 41 2.992543 GTGTGTCTTCAGCAGATCTCAC 59.007 50.000 0.00 0.00 32.60 3.51
41 42 2.028658 GGTGTGTCTTCAGCAGATCTCA 60.029 50.000 0.00 0.00 36.09 3.27
42 43 2.233431 AGGTGTGTCTTCAGCAGATCTC 59.767 50.000 0.00 0.00 38.15 2.75
43 44 2.233431 GAGGTGTGTCTTCAGCAGATCT 59.767 50.000 0.00 0.00 38.15 2.75
44 45 2.615869 GAGGTGTGTCTTCAGCAGATC 58.384 52.381 0.00 0.00 38.15 2.75
45 46 1.277557 GGAGGTGTGTCTTCAGCAGAT 59.722 52.381 0.00 0.00 38.15 2.90
46 47 0.681733 GGAGGTGTGTCTTCAGCAGA 59.318 55.000 0.00 0.00 38.15 4.26
47 48 0.394192 TGGAGGTGTGTCTTCAGCAG 59.606 55.000 0.00 0.00 38.15 4.24
48 49 0.106708 GTGGAGGTGTGTCTTCAGCA 59.893 55.000 0.00 0.00 38.15 4.41
49 50 0.106708 TGTGGAGGTGTGTCTTCAGC 59.893 55.000 0.00 0.00 36.27 4.26
50 51 1.869754 CGTGTGGAGGTGTGTCTTCAG 60.870 57.143 0.00 0.00 0.00 3.02
51 52 0.104120 CGTGTGGAGGTGTGTCTTCA 59.896 55.000 0.00 0.00 0.00 3.02
52 53 1.222115 GCGTGTGGAGGTGTGTCTTC 61.222 60.000 0.00 0.00 0.00 2.87
53 54 1.227556 GCGTGTGGAGGTGTGTCTT 60.228 57.895 0.00 0.00 0.00 3.01
54 55 2.088674 GAGCGTGTGGAGGTGTGTCT 62.089 60.000 0.00 0.00 0.00 3.41
55 56 1.664965 GAGCGTGTGGAGGTGTGTC 60.665 63.158 0.00 0.00 0.00 3.67
56 57 2.088674 GAGAGCGTGTGGAGGTGTGT 62.089 60.000 0.00 0.00 0.00 3.72
57 58 1.373497 GAGAGCGTGTGGAGGTGTG 60.373 63.158 0.00 0.00 0.00 3.82
58 59 2.574955 GGAGAGCGTGTGGAGGTGT 61.575 63.158 0.00 0.00 0.00 4.16
59 60 2.262915 GGAGAGCGTGTGGAGGTG 59.737 66.667 0.00 0.00 0.00 4.00
60 61 3.374402 CGGAGAGCGTGTGGAGGT 61.374 66.667 0.00 0.00 0.00 3.85
61 62 3.062466 TCGGAGAGCGTGTGGAGG 61.062 66.667 0.00 0.00 0.00 4.30
62 63 2.179517 GTCGGAGAGCGTGTGGAG 59.820 66.667 0.00 0.00 36.95 3.86
63 64 3.733960 CGTCGGAGAGCGTGTGGA 61.734 66.667 0.00 0.00 36.95 4.02
64 65 3.052620 ATCGTCGGAGAGCGTGTGG 62.053 63.158 0.00 0.00 36.95 4.17
65 66 1.869574 CATCGTCGGAGAGCGTGTG 60.870 63.158 0.00 0.00 36.95 3.82
66 67 2.485582 CATCGTCGGAGAGCGTGT 59.514 61.111 0.00 0.00 36.95 4.49
67 68 2.048312 TAGCATCGTCGGAGAGCGTG 62.048 60.000 0.00 0.00 36.95 5.34
68 69 1.777030 CTAGCATCGTCGGAGAGCGT 61.777 60.000 0.00 0.00 36.95 5.07
69 70 1.082431 CTAGCATCGTCGGAGAGCG 60.082 63.158 0.00 0.00 36.95 5.03
70 71 0.040781 GTCTAGCATCGTCGGAGAGC 60.041 60.000 0.00 0.00 36.95 4.09
71 72 1.003331 GTGTCTAGCATCGTCGGAGAG 60.003 57.143 0.00 0.00 36.95 3.20
72 73 1.015109 GTGTCTAGCATCGTCGGAGA 58.985 55.000 0.00 0.00 0.00 3.71
73 74 0.733150 TGTGTCTAGCATCGTCGGAG 59.267 55.000 0.00 0.00 0.00 4.63
74 75 0.450583 GTGTGTCTAGCATCGTCGGA 59.549 55.000 0.00 0.00 0.00 4.55
75 76 0.525668 GGTGTGTCTAGCATCGTCGG 60.526 60.000 0.00 0.00 0.00 4.79
76 77 0.170339 TGGTGTGTCTAGCATCGTCG 59.830 55.000 0.00 0.00 0.00 5.12
77 78 2.586258 ATGGTGTGTCTAGCATCGTC 57.414 50.000 0.00 0.00 33.85 4.20
78 79 2.621338 CAATGGTGTGTCTAGCATCGT 58.379 47.619 0.00 0.00 37.77 3.73
79 80 1.935873 CCAATGGTGTGTCTAGCATCG 59.064 52.381 0.00 0.00 37.77 3.84
80 81 2.092968 TCCCAATGGTGTGTCTAGCATC 60.093 50.000 0.00 0.00 37.77 3.91
81 82 1.915489 TCCCAATGGTGTGTCTAGCAT 59.085 47.619 0.00 0.00 40.24 3.79
82 83 1.003118 GTCCCAATGGTGTGTCTAGCA 59.997 52.381 0.00 0.00 0.00 3.49
83 84 1.739067 GTCCCAATGGTGTGTCTAGC 58.261 55.000 0.00 0.00 0.00 3.42
84 85 1.405526 CCGTCCCAATGGTGTGTCTAG 60.406 57.143 0.00 0.00 0.00 2.43
85 86 0.611200 CCGTCCCAATGGTGTGTCTA 59.389 55.000 0.00 0.00 0.00 2.59
86 87 1.374947 CCGTCCCAATGGTGTGTCT 59.625 57.895 0.00 0.00 0.00 3.41
87 88 1.674322 CCCGTCCCAATGGTGTGTC 60.674 63.158 0.00 0.00 0.00 3.67
88 89 2.434331 CCCGTCCCAATGGTGTGT 59.566 61.111 0.00 0.00 0.00 3.72
89 90 2.361104 CCCCGTCCCAATGGTGTG 60.361 66.667 0.00 0.00 0.00 3.82
90 91 3.657350 CCCCCGTCCCAATGGTGT 61.657 66.667 0.00 0.00 0.00 4.16
92 93 3.954740 TAGCCCCCGTCCCAATGGT 62.955 63.158 0.00 0.00 0.00 3.55
93 94 3.093835 TAGCCCCCGTCCCAATGG 61.094 66.667 0.00 0.00 0.00 3.16
94 95 2.510906 CTAGCCCCCGTCCCAATG 59.489 66.667 0.00 0.00 0.00 2.82
95 96 2.772622 CCTAGCCCCCGTCCCAAT 60.773 66.667 0.00 0.00 0.00 3.16
103 104 4.499116 TCTCCCTGCCTAGCCCCC 62.499 72.222 0.00 0.00 0.00 5.40
104 105 2.366972 TTCTCCCTGCCTAGCCCC 60.367 66.667 0.00 0.00 0.00 5.80
105 106 2.747443 GGTTCTCCCTGCCTAGCCC 61.747 68.421 0.00 0.00 0.00 5.19
106 107 1.275421 AAGGTTCTCCCTGCCTAGCC 61.275 60.000 0.00 0.00 45.47 3.93
107 108 1.497161 TAAGGTTCTCCCTGCCTAGC 58.503 55.000 0.00 0.00 45.47 3.42
108 109 3.071747 GGAATAAGGTTCTCCCTGCCTAG 59.928 52.174 0.00 0.00 45.47 3.02
109 110 3.046374 GGAATAAGGTTCTCCCTGCCTA 58.954 50.000 0.00 0.00 45.47 3.93
110 111 1.847088 GGAATAAGGTTCTCCCTGCCT 59.153 52.381 0.00 0.00 45.47 4.75
111 112 1.564348 TGGAATAAGGTTCTCCCTGCC 59.436 52.381 0.00 0.00 45.47 4.85
112 113 3.137360 AGATGGAATAAGGTTCTCCCTGC 59.863 47.826 0.00 0.00 45.47 4.85
113 114 5.104360 TGAAGATGGAATAAGGTTCTCCCTG 60.104 44.000 0.00 0.00 45.47 4.45
115 116 5.373812 TGAAGATGGAATAAGGTTCTCCC 57.626 43.478 0.00 0.00 0.00 4.30
116 117 6.653989 TCTTGAAGATGGAATAAGGTTCTCC 58.346 40.000 0.00 0.00 0.00 3.71
117 118 7.201688 GCTTCTTGAAGATGGAATAAGGTTCTC 60.202 40.741 13.87 0.00 0.00 2.87
118 119 6.601217 GCTTCTTGAAGATGGAATAAGGTTCT 59.399 38.462 13.87 0.00 0.00 3.01
119 120 6.183360 GGCTTCTTGAAGATGGAATAAGGTTC 60.183 42.308 13.87 0.00 0.00 3.62
120 121 5.654209 GGCTTCTTGAAGATGGAATAAGGTT 59.346 40.000 13.87 0.00 0.00 3.50
121 122 5.196695 GGCTTCTTGAAGATGGAATAAGGT 58.803 41.667 13.87 0.00 0.00 3.50
122 123 5.067023 GTGGCTTCTTGAAGATGGAATAAGG 59.933 44.000 13.87 0.00 0.00 2.69
123 124 5.067023 GGTGGCTTCTTGAAGATGGAATAAG 59.933 44.000 13.87 0.00 0.00 1.73
124 125 4.949856 GGTGGCTTCTTGAAGATGGAATAA 59.050 41.667 13.87 0.00 0.00 1.40
125 126 4.526970 GGTGGCTTCTTGAAGATGGAATA 58.473 43.478 13.87 0.00 0.00 1.75
126 127 3.359950 GGTGGCTTCTTGAAGATGGAAT 58.640 45.455 13.87 0.00 0.00 3.01
127 128 2.795329 GGTGGCTTCTTGAAGATGGAA 58.205 47.619 13.87 0.00 0.00 3.53
128 129 1.339055 CGGTGGCTTCTTGAAGATGGA 60.339 52.381 13.87 0.00 0.00 3.41
129 130 1.089920 CGGTGGCTTCTTGAAGATGG 58.910 55.000 13.87 1.57 0.00 3.51
130 131 0.449388 GCGGTGGCTTCTTGAAGATG 59.551 55.000 13.87 0.00 35.83 2.90
131 132 0.678048 GGCGGTGGCTTCTTGAAGAT 60.678 55.000 13.87 0.00 39.81 2.40
132 133 1.302511 GGCGGTGGCTTCTTGAAGA 60.303 57.895 13.87 0.00 39.81 2.87
133 134 2.680913 CGGCGGTGGCTTCTTGAAG 61.681 63.158 0.00 6.04 39.81 3.02
134 135 2.668212 CGGCGGTGGCTTCTTGAA 60.668 61.111 0.00 0.00 39.81 2.69
135 136 3.876589 GACGGCGGTGGCTTCTTGA 62.877 63.158 13.24 0.00 39.81 3.02
136 137 3.423154 GACGGCGGTGGCTTCTTG 61.423 66.667 13.24 0.00 39.81 3.02
137 138 3.591254 GAGACGGCGGTGGCTTCTT 62.591 63.158 13.24 0.00 39.81 2.52
138 139 4.070552 GAGACGGCGGTGGCTTCT 62.071 66.667 13.24 2.99 39.81 2.85
143 144 3.966026 GAAGACGAGACGGCGGTGG 62.966 68.421 13.24 1.41 41.28 4.61
144 145 2.473664 AAGAAGACGAGACGGCGGTG 62.474 60.000 13.24 0.00 41.28 4.94
145 146 2.266627 AAGAAGACGAGACGGCGGT 61.267 57.895 13.24 0.00 41.28 5.68
146 147 1.801913 CAAGAAGACGAGACGGCGG 60.802 63.158 13.24 0.00 41.28 6.13
147 148 0.794981 CTCAAGAAGACGAGACGGCG 60.795 60.000 4.80 4.80 41.28 6.46
148 149 0.241481 ACTCAAGAAGACGAGACGGC 59.759 55.000 0.00 0.00 33.33 5.68
149 150 2.096174 CCTACTCAAGAAGACGAGACGG 59.904 54.545 0.00 0.00 33.33 4.79
150 151 3.001414 TCCTACTCAAGAAGACGAGACG 58.999 50.000 0.00 0.00 33.33 4.18
151 152 3.752222 TGTCCTACTCAAGAAGACGAGAC 59.248 47.826 0.00 0.00 33.33 3.36
152 153 3.752222 GTGTCCTACTCAAGAAGACGAGA 59.248 47.826 0.00 0.00 33.33 4.04
153 154 3.502595 TGTGTCCTACTCAAGAAGACGAG 59.497 47.826 0.00 0.00 35.30 4.18
154 155 3.483421 TGTGTCCTACTCAAGAAGACGA 58.517 45.455 0.00 0.00 0.00 4.20
155 156 3.917329 TGTGTCCTACTCAAGAAGACG 57.083 47.619 0.00 0.00 0.00 4.18
156 157 4.750598 GGTTTGTGTCCTACTCAAGAAGAC 59.249 45.833 0.00 0.00 33.80 3.01
157 158 4.202326 GGGTTTGTGTCCTACTCAAGAAGA 60.202 45.833 0.00 0.00 33.80 2.87
158 159 4.065789 GGGTTTGTGTCCTACTCAAGAAG 58.934 47.826 0.00 0.00 33.80 2.85
159 160 3.714798 AGGGTTTGTGTCCTACTCAAGAA 59.285 43.478 0.00 0.00 33.80 2.52
160 161 3.314693 AGGGTTTGTGTCCTACTCAAGA 58.685 45.455 0.00 0.00 33.80 3.02
161 162 3.771577 AGGGTTTGTGTCCTACTCAAG 57.228 47.619 0.00 0.00 33.80 3.02
162 163 4.409574 TGTTAGGGTTTGTGTCCTACTCAA 59.590 41.667 0.00 0.00 35.56 3.02
163 164 3.968649 TGTTAGGGTTTGTGTCCTACTCA 59.031 43.478 0.00 0.00 35.56 3.41
164 165 4.612264 TGTTAGGGTTTGTGTCCTACTC 57.388 45.455 0.00 0.00 35.56 2.59
165 166 5.376756 TTTGTTAGGGTTTGTGTCCTACT 57.623 39.130 0.00 0.00 35.56 2.57
166 167 5.591472 AGTTTTGTTAGGGTTTGTGTCCTAC 59.409 40.000 0.00 0.00 35.56 3.18
167 168 5.757988 AGTTTTGTTAGGGTTTGTGTCCTA 58.242 37.500 0.00 0.00 34.75 2.94
168 169 4.606210 AGTTTTGTTAGGGTTTGTGTCCT 58.394 39.130 0.00 0.00 37.18 3.85
169 170 4.994907 AGTTTTGTTAGGGTTTGTGTCC 57.005 40.909 0.00 0.00 0.00 4.02
170 171 5.956642 TCAAGTTTTGTTAGGGTTTGTGTC 58.043 37.500 0.00 0.00 0.00 3.67
171 172 5.986501 TCAAGTTTTGTTAGGGTTTGTGT 57.013 34.783 0.00 0.00 0.00 3.72
172 173 6.626302 TCTTCAAGTTTTGTTAGGGTTTGTG 58.374 36.000 0.00 0.00 0.00 3.33
173 174 6.844097 TCTTCAAGTTTTGTTAGGGTTTGT 57.156 33.333 0.00 0.00 0.00 2.83
174 175 6.255670 GCTTCTTCAAGTTTTGTTAGGGTTTG 59.744 38.462 0.00 0.00 31.45 2.93
175 176 6.071051 TGCTTCTTCAAGTTTTGTTAGGGTTT 60.071 34.615 0.00 0.00 31.45 3.27
176 177 5.420739 TGCTTCTTCAAGTTTTGTTAGGGTT 59.579 36.000 0.00 0.00 31.45 4.11
177 178 4.953579 TGCTTCTTCAAGTTTTGTTAGGGT 59.046 37.500 0.00 0.00 31.45 4.34
178 179 5.281727 GTGCTTCTTCAAGTTTTGTTAGGG 58.718 41.667 0.00 0.00 31.45 3.53
179 180 5.067805 AGGTGCTTCTTCAAGTTTTGTTAGG 59.932 40.000 0.00 0.00 31.45 2.69
180 181 5.973565 CAGGTGCTTCTTCAAGTTTTGTTAG 59.026 40.000 0.00 0.00 31.45 2.34
181 182 5.650266 TCAGGTGCTTCTTCAAGTTTTGTTA 59.350 36.000 0.00 0.00 31.45 2.41
182 183 4.462483 TCAGGTGCTTCTTCAAGTTTTGTT 59.538 37.500 0.00 0.00 31.45 2.83
183 184 4.016444 TCAGGTGCTTCTTCAAGTTTTGT 58.984 39.130 0.00 0.00 31.45 2.83
184 185 4.637483 TCAGGTGCTTCTTCAAGTTTTG 57.363 40.909 0.00 0.00 31.45 2.44
185 186 5.659440 TTTCAGGTGCTTCTTCAAGTTTT 57.341 34.783 0.00 0.00 31.45 2.43
186 187 5.410924 GTTTTCAGGTGCTTCTTCAAGTTT 58.589 37.500 0.00 0.00 31.45 2.66
187 188 4.438744 CGTTTTCAGGTGCTTCTTCAAGTT 60.439 41.667 0.00 0.00 31.45 2.66
188 189 3.065371 CGTTTTCAGGTGCTTCTTCAAGT 59.935 43.478 0.00 0.00 31.45 3.16
189 190 3.548818 CCGTTTTCAGGTGCTTCTTCAAG 60.549 47.826 0.00 0.00 0.00 3.02
190 191 2.357637 CCGTTTTCAGGTGCTTCTTCAA 59.642 45.455 0.00 0.00 0.00 2.69
191 192 1.946768 CCGTTTTCAGGTGCTTCTTCA 59.053 47.619 0.00 0.00 0.00 3.02
192 193 2.218603 TCCGTTTTCAGGTGCTTCTTC 58.781 47.619 0.00 0.00 0.00 2.87
193 194 2.222027 CTCCGTTTTCAGGTGCTTCTT 58.778 47.619 0.00 0.00 0.00 2.52
194 195 1.884235 CTCCGTTTTCAGGTGCTTCT 58.116 50.000 0.00 0.00 0.00 2.85
195 196 0.238553 GCTCCGTTTTCAGGTGCTTC 59.761 55.000 2.49 0.00 42.91 3.86
196 197 1.172812 GGCTCCGTTTTCAGGTGCTT 61.173 55.000 8.81 0.00 44.86 3.91
197 198 1.600916 GGCTCCGTTTTCAGGTGCT 60.601 57.895 8.81 0.00 44.86 4.40
198 199 2.626780 GGGCTCCGTTTTCAGGTGC 61.627 63.158 1.16 1.16 44.78 5.01
199 200 0.955919 GAGGGCTCCGTTTTCAGGTG 60.956 60.000 0.00 0.00 0.00 4.00
200 201 1.375326 GAGGGCTCCGTTTTCAGGT 59.625 57.895 0.00 0.00 0.00 4.00
201 202 1.377333 GGAGGGCTCCGTTTTCAGG 60.377 63.158 0.00 0.00 40.36 3.86
202 203 4.303257 GGAGGGCTCCGTTTTCAG 57.697 61.111 0.00 0.00 40.36 3.02
243 244 4.457496 ACATCTCCTGGGTGCGCG 62.457 66.667 0.00 0.00 0.00 6.86
244 245 2.821366 CACATCTCCTGGGTGCGC 60.821 66.667 0.00 0.00 0.00 6.09
245 246 2.124983 CCACATCTCCTGGGTGCG 60.125 66.667 0.00 0.00 0.00 5.34
246 247 2.273449 CCCACATCTCCTGGGTGC 59.727 66.667 0.00 0.00 43.32 5.01
250 251 0.678395 CGATCTCCCACATCTCCTGG 59.322 60.000 0.00 0.00 0.00 4.45
251 252 0.678395 CCGATCTCCCACATCTCCTG 59.322 60.000 0.00 0.00 0.00 3.86
252 253 1.118356 GCCGATCTCCCACATCTCCT 61.118 60.000 0.00 0.00 0.00 3.69
253 254 1.369321 GCCGATCTCCCACATCTCC 59.631 63.158 0.00 0.00 0.00 3.71
254 255 1.006805 CGCCGATCTCCCACATCTC 60.007 63.158 0.00 0.00 0.00 2.75
255 256 2.502492 CCGCCGATCTCCCACATCT 61.502 63.158 0.00 0.00 0.00 2.90
256 257 2.029666 CCGCCGATCTCCCACATC 59.970 66.667 0.00 0.00 0.00 3.06
257 258 4.241555 GCCGCCGATCTCCCACAT 62.242 66.667 0.00 0.00 0.00 3.21
279 280 1.971695 GGTTTCTGCCTCCCGTTGG 60.972 63.158 0.00 0.00 0.00 3.77
280 281 1.971695 GGGTTTCTGCCTCCCGTTG 60.972 63.158 0.00 0.00 0.00 4.10
281 282 0.838987 TAGGGTTTCTGCCTCCCGTT 60.839 55.000 0.00 0.00 45.27 4.44
282 283 1.229400 TAGGGTTTCTGCCTCCCGT 60.229 57.895 0.00 0.00 45.27 5.28
283 284 1.522569 CTAGGGTTTCTGCCTCCCG 59.477 63.158 0.00 0.00 45.27 5.14
284 285 1.224870 GCTAGGGTTTCTGCCTCCC 59.775 63.158 0.00 0.00 41.36 4.30
285 286 1.224870 GGCTAGGGTTTCTGCCTCC 59.775 63.158 0.00 0.00 41.92 4.30
286 287 1.153349 CGGCTAGGGTTTCTGCCTC 60.153 63.158 0.00 0.00 42.90 4.70
287 288 2.990479 CGGCTAGGGTTTCTGCCT 59.010 61.111 0.00 0.00 42.90 4.75
288 289 2.824489 GCGGCTAGGGTTTCTGCC 60.824 66.667 0.00 0.00 41.76 4.85
289 290 2.821679 AAGGCGGCTAGGGTTTCTGC 62.822 60.000 13.71 0.00 0.00 4.26
290 291 0.322546 AAAGGCGGCTAGGGTTTCTG 60.323 55.000 13.71 0.00 0.00 3.02
291 292 0.404426 AAAAGGCGGCTAGGGTTTCT 59.596 50.000 13.71 0.00 0.00 2.52
292 293 0.809385 GAAAAGGCGGCTAGGGTTTC 59.191 55.000 13.71 14.79 0.00 2.78
293 294 0.404426 AGAAAAGGCGGCTAGGGTTT 59.596 50.000 13.71 9.24 0.00 3.27
294 295 0.404426 AAGAAAAGGCGGCTAGGGTT 59.596 50.000 13.71 4.23 0.00 4.11
295 296 0.322546 CAAGAAAAGGCGGCTAGGGT 60.323 55.000 13.71 0.00 0.00 4.34
296 297 1.032114 CCAAGAAAAGGCGGCTAGGG 61.032 60.000 13.71 3.98 0.00 3.53
297 298 0.035439 TCCAAGAAAAGGCGGCTAGG 60.035 55.000 13.71 7.99 0.00 3.02
298 299 1.373570 CTCCAAGAAAAGGCGGCTAG 58.626 55.000 13.71 0.00 0.00 3.42
299 300 0.035439 CCTCCAAGAAAAGGCGGCTA 60.035 55.000 13.71 0.00 0.00 3.93
300 301 1.303643 CCTCCAAGAAAAGGCGGCT 60.304 57.895 5.25 5.25 0.00 5.52
301 302 3.278157 CCTCCAAGAAAAGGCGGC 58.722 61.111 0.00 0.00 0.00 6.53
305 306 3.092301 CCCTTAAGCCTCCAAGAAAAGG 58.908 50.000 0.00 0.00 35.65 3.11
306 307 3.767711 ACCCTTAAGCCTCCAAGAAAAG 58.232 45.455 0.00 0.00 0.00 2.27
307 308 3.895704 ACCCTTAAGCCTCCAAGAAAA 57.104 42.857 0.00 0.00 0.00 2.29
308 309 4.172807 TCTACCCTTAAGCCTCCAAGAAA 58.827 43.478 0.00 0.00 0.00 2.52
309 310 3.798515 TCTACCCTTAAGCCTCCAAGAA 58.201 45.455 0.00 0.00 0.00 2.52
310 311 3.484953 TCTACCCTTAAGCCTCCAAGA 57.515 47.619 0.00 0.00 0.00 3.02
311 312 5.888982 TTATCTACCCTTAAGCCTCCAAG 57.111 43.478 0.00 0.00 0.00 3.61
312 313 6.841781 ATTTATCTACCCTTAAGCCTCCAA 57.158 37.500 0.00 0.00 0.00 3.53
313 314 7.962003 AGATATTTATCTACCCTTAAGCCTCCA 59.038 37.037 0.00 0.00 41.05 3.86
314 315 8.382058 AGATATTTATCTACCCTTAAGCCTCC 57.618 38.462 0.00 0.00 41.05 4.30
315 316 9.878667 GAAGATATTTATCTACCCTTAAGCCTC 57.121 37.037 0.00 0.00 41.96 4.70
316 317 9.393786 TGAAGATATTTATCTACCCTTAAGCCT 57.606 33.333 0.00 0.00 41.96 4.58
356 357 8.367660 AGATTATTAGCAATATCGGGAGAGAA 57.632 34.615 0.00 0.00 45.48 2.87
523 540 8.207545 TGCAGTAAATTTGTAATTTTCCCAGTT 58.792 29.630 0.00 0.00 0.00 3.16
633 1343 1.568504 TGAGACCCACATACCTCACC 58.431 55.000 0.00 0.00 31.45 4.02
639 1354 0.899720 TCCGGTTGAGACCCACATAC 59.100 55.000 0.00 0.00 43.42 2.39
698 1416 3.182967 GACACTTCTATGACGGAAGCAG 58.817 50.000 0.00 0.00 42.58 4.24
883 1630 0.809241 GGATGAACTGCTGAGCGGAG 60.809 60.000 21.86 5.10 38.46 4.63
901 1648 3.740115 ACTTGTAATATTAGCTGCCGGG 58.260 45.455 2.18 0.00 0.00 5.73
1286 2372 0.932211 AGGTGGGATACGGTCTAGGT 59.068 55.000 0.00 0.00 37.60 3.08
1289 2375 3.526211 CCAGGTGGGATACGGTCTA 57.474 57.895 0.00 0.00 40.01 2.59
1329 2415 2.199236 GAGAAGTTTTGGTCGTCACGT 58.801 47.619 0.00 0.00 0.00 4.49
1371 2460 1.471119 GGACATGGACCAGTACGAGA 58.529 55.000 0.00 0.00 0.00 4.04
1393 2482 1.126296 GTGCTTTAGCGGTTCGAAGTC 59.874 52.381 0.00 0.00 45.83 3.01
1453 2542 2.276740 CAGGGGAATGCCAGGGTC 59.723 66.667 0.00 0.00 35.15 4.46
1673 2762 5.121105 AGGATATACCGTTAAAACACCAGC 58.879 41.667 0.00 0.00 44.74 4.85
1813 2902 2.772191 ACTCCCAGCACCCACACA 60.772 61.111 0.00 0.00 0.00 3.72
1835 2924 1.134280 AGAACCGATCATTGCTCCCAG 60.134 52.381 0.00 0.00 0.00 4.45
1896 2985 3.257933 GCGTTGAAGCCTGACAGG 58.742 61.111 17.83 17.83 38.80 4.00
2019 3109 9.498307 CCAATTACCTTAATAACGTGTTCATTC 57.502 33.333 0.00 0.00 0.00 2.67
2101 3194 0.601057 TGCAACGACTCGAGATGGAA 59.399 50.000 21.68 0.00 0.00 3.53
2405 3511 7.807907 CGACAACCTTTGCTCAAAGTAAATAAT 59.192 33.333 17.88 1.27 44.66 1.28
2654 3932 7.374491 GCGAAAGATCTGAAATAAATTCCGAAG 59.626 37.037 0.00 0.00 35.31 3.79
2711 3989 0.725784 GCAGACGCATTTGTTGTCGG 60.726 55.000 0.00 0.00 37.69 4.79
2747 4025 1.734117 GAGCCGGCACAACATTTGC 60.734 57.895 31.54 0.00 39.41 3.68
2815 4097 5.295292 CAGATATTCACACACACTCAATCCC 59.705 44.000 0.00 0.00 0.00 3.85
2884 4173 4.165760 GGCCCATATACTGGTAGTTAGGT 58.834 47.826 0.00 0.00 44.30 3.08
3102 4768 1.478510 GATCTTCCTCTTCCAGCGACA 59.521 52.381 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.