Multiple sequence alignment - TraesCS7B01G169900

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 TraesCS7B01G169900 chr7B 100.000 2853 0 0 1 2853 241106546 241109398 0.000000e+00 5269.0
1 TraesCS7B01G169900 chr7D 91.335 2666 130 47 114 2726 262699981 262697364 0.000000e+00 3550.0
2 TraesCS7B01G169900 chr7D 90.196 102 10 0 1427 1528 13029137 13029036 1.780000e-27 134.0
3 TraesCS7B01G169900 chr7D 88.235 102 12 0 1427 1528 13066868 13066767 3.860000e-24 122.0
4 TraesCS7B01G169900 chr7A 87.451 2303 94 88 518 2724 285577215 285575012 0.000000e+00 2471.0
5 TraesCS7B01G169900 chr7A 90.196 102 10 0 1427 1528 12429272 12429171 1.780000e-27 134.0
6 TraesCS7B01G169900 chr7A 90.196 102 10 0 1427 1528 12454961 12454860 1.780000e-27 134.0
7 TraesCS7B01G169900 chr7A 90.196 102 10 0 1427 1528 12652356 12652255 1.780000e-27 134.0
8 TraesCS7B01G169900 chr7A 84.932 73 5 3 342 408 285577284 285577212 5.100000e-08 69.4
9 TraesCS7B01G169900 chr3A 89.299 271 26 3 1131 1400 633922097 633922365 1.270000e-88 337.0
10 TraesCS7B01G169900 chr3A 80.952 105 13 2 2732 2829 214272287 214272183 3.050000e-10 76.8
11 TraesCS7B01G169900 chr5D 88.679 265 30 0 1136 1400 425077485 425077221 9.860000e-85 324.0
12 TraesCS7B01G169900 chr3D 88.192 271 29 3 1131 1400 492131420 492131688 1.280000e-83 320.0
13 TraesCS7B01G169900 chr5B 86.806 288 35 3 1114 1400 514279648 514279363 4.590000e-83 318.0
14 TraesCS7B01G169900 chr3B 87.823 271 30 3 1131 1400 653152047 653152315 5.930000e-82 315.0
15 TraesCS7B01G169900 chr5A 87.925 265 32 0 1136 1400 539093485 539093221 2.130000e-81 313.0
16 TraesCS7B01G169900 chr6D 81.271 299 48 8 1177 1471 298207239 298206945 4.750000e-58 235.0
17 TraesCS7B01G169900 chr6D 81.063 301 45 12 1177 1471 298399280 298398986 2.210000e-56 230.0
18 TraesCS7B01G169900 chr6D 78.761 339 66 6 1136 1471 297407374 297407039 3.700000e-54 222.0
19 TraesCS7B01G169900 chr6B 80.936 299 49 8 1177 1471 461961823 461961529 2.210000e-56 230.0
20 TraesCS7B01G169900 chr6B 79.933 299 52 8 1177 1471 461903629 461903335 2.230000e-51 213.0
21 TraesCS7B01G169900 chr6A 79.801 302 53 8 1171 1468 420973745 420974042 2.230000e-51 213.0
22 TraesCS7B01G169900 chr4A 88.889 108 12 0 1421 1528 724782995 724783102 1.780000e-27 134.0
23 TraesCS7B01G169900 chr4D 88.235 102 12 0 1427 1528 506606733 506606632 3.860000e-24 122.0


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 TraesCS7B01G169900 chr7B 241106546 241109398 2852 False 5269.0 5269 100.0000 1 2853 1 chr7B.!!$F1 2852
1 TraesCS7B01G169900 chr7D 262697364 262699981 2617 True 3550.0 3550 91.3350 114 2726 1 chr7D.!!$R3 2612
2 TraesCS7B01G169900 chr7A 285575012 285577284 2272 True 1270.2 2471 86.1915 342 2724 2 chr7A.!!$R4 2382

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
307 322 0.03467 ATGAGGCACTTTGAGAGGCC 60.035 55.0 0.0 0.0 41.55 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 2044 0.178987 TCTCCTCCTCGCCATCTACC 60.179 60.0 0.0 0.0 0.0 3.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 6.710597 ATGCAGAGGTAGAAAGACGTATAA 57.289 37.500 0.00 0.00 0.00 0.98
25 26 5.888105 TGCAGAGGTAGAAAGACGTATAAC 58.112 41.667 0.00 0.00 0.00 1.89
26 27 5.416639 TGCAGAGGTAGAAAGACGTATAACA 59.583 40.000 0.00 0.00 0.00 2.41
27 28 6.071784 TGCAGAGGTAGAAAGACGTATAACAA 60.072 38.462 0.00 0.00 0.00 2.83
28 29 6.472808 GCAGAGGTAGAAAGACGTATAACAAG 59.527 42.308 0.00 0.00 0.00 3.16
29 30 7.536855 CAGAGGTAGAAAGACGTATAACAAGT 58.463 38.462 0.00 0.00 0.00 3.16
30 31 8.671921 CAGAGGTAGAAAGACGTATAACAAGTA 58.328 37.037 0.00 0.00 0.00 2.24
31 32 8.672815 AGAGGTAGAAAGACGTATAACAAGTAC 58.327 37.037 0.00 0.00 0.00 2.73
32 33 7.766283 AGGTAGAAAGACGTATAACAAGTACC 58.234 38.462 0.00 0.00 0.00 3.34
33 34 6.688813 GGTAGAAAGACGTATAACAAGTACCG 59.311 42.308 0.00 0.00 0.00 4.02
34 35 6.500684 AGAAAGACGTATAACAAGTACCGA 57.499 37.500 0.00 0.00 0.00 4.69
35 36 6.317857 AGAAAGACGTATAACAAGTACCGAC 58.682 40.000 0.00 0.00 0.00 4.79
36 37 5.627499 AAGACGTATAACAAGTACCGACA 57.373 39.130 0.00 0.00 0.00 4.35
37 38 5.627499 AGACGTATAACAAGTACCGACAA 57.373 39.130 0.00 0.00 0.00 3.18
38 39 6.012658 AGACGTATAACAAGTACCGACAAA 57.987 37.500 0.00 0.00 0.00 2.83
39 40 6.446318 AGACGTATAACAAGTACCGACAAAA 58.554 36.000 0.00 0.00 0.00 2.44
40 41 6.583806 AGACGTATAACAAGTACCGACAAAAG 59.416 38.462 0.00 0.00 0.00 2.27
41 42 6.215845 ACGTATAACAAGTACCGACAAAAGT 58.784 36.000 0.00 0.00 0.00 2.66
42 43 7.367285 ACGTATAACAAGTACCGACAAAAGTA 58.633 34.615 0.00 0.00 0.00 2.24
43 44 8.028938 ACGTATAACAAGTACCGACAAAAGTAT 58.971 33.333 0.00 0.00 0.00 2.12
44 45 8.863049 CGTATAACAAGTACCGACAAAAGTATT 58.137 33.333 0.00 0.00 0.00 1.89
60 61 8.364480 CAAAAGTATTTGTACTGAATACACGC 57.636 34.615 22.90 7.24 43.71 5.34
61 62 5.944049 AGTATTTGTACTGAATACACGCG 57.056 39.130 22.90 3.53 43.71 6.01
62 63 5.404946 AGTATTTGTACTGAATACACGCGT 58.595 37.500 22.90 5.58 43.71 6.01
63 64 6.554419 AGTATTTGTACTGAATACACGCGTA 58.446 36.000 13.44 0.00 43.71 4.42
64 65 7.198390 AGTATTTGTACTGAATACACGCGTAT 58.802 34.615 13.44 1.77 43.71 3.06
65 66 8.344831 AGTATTTGTACTGAATACACGCGTATA 58.655 33.333 13.44 5.15 43.71 1.47
66 67 6.795053 TTTGTACTGAATACACGCGTATAC 57.205 37.500 13.44 5.41 43.71 1.47
67 68 5.739752 TGTACTGAATACACGCGTATACT 57.260 39.130 13.44 0.00 38.95 2.12
68 69 5.504392 TGTACTGAATACACGCGTATACTG 58.496 41.667 13.44 0.59 38.95 2.74
69 70 4.627611 ACTGAATACACGCGTATACTGT 57.372 40.909 13.44 8.17 37.34 3.55
70 71 4.595116 ACTGAATACACGCGTATACTGTC 58.405 43.478 13.44 4.52 37.34 3.51
71 72 4.334759 ACTGAATACACGCGTATACTGTCT 59.665 41.667 13.44 0.00 37.34 3.41
72 73 4.840911 TGAATACACGCGTATACTGTCTC 58.159 43.478 13.44 6.65 37.34 3.36
73 74 3.516681 ATACACGCGTATACTGTCTCG 57.483 47.619 13.44 0.00 36.53 4.04
74 75 1.081892 ACACGCGTATACTGTCTCGT 58.918 50.000 13.44 0.00 0.00 4.18
75 76 2.270923 ACACGCGTATACTGTCTCGTA 58.729 47.619 13.44 0.00 0.00 3.43
76 77 2.868583 ACACGCGTATACTGTCTCGTAT 59.131 45.455 13.44 0.00 34.63 3.06
77 78 3.310774 ACACGCGTATACTGTCTCGTATT 59.689 43.478 13.44 0.00 32.63 1.89
78 79 3.898946 CACGCGTATACTGTCTCGTATTC 59.101 47.826 13.44 0.00 32.63 1.75
79 80 3.806521 ACGCGTATACTGTCTCGTATTCT 59.193 43.478 11.67 0.00 32.63 2.40
80 81 4.084641 ACGCGTATACTGTCTCGTATTCTC 60.085 45.833 11.67 0.00 32.63 2.87
81 82 4.150274 CGCGTATACTGTCTCGTATTCTCT 59.850 45.833 0.00 0.00 32.63 3.10
82 83 5.333187 CGCGTATACTGTCTCGTATTCTCTT 60.333 44.000 0.00 0.00 32.63 2.85
83 84 6.128982 CGCGTATACTGTCTCGTATTCTCTTA 60.129 42.308 0.00 0.00 32.63 2.10
84 85 7.411696 CGCGTATACTGTCTCGTATTCTCTTAT 60.412 40.741 0.00 0.00 32.63 1.73
85 86 8.229137 GCGTATACTGTCTCGTATTCTCTTATT 58.771 37.037 0.56 0.00 32.63 1.40
91 92 9.141400 ACTGTCTCGTATTCTCTTATTTTGAAC 57.859 33.333 0.00 0.00 0.00 3.18
92 93 8.475331 TGTCTCGTATTCTCTTATTTTGAACC 57.525 34.615 0.00 0.00 0.00 3.62
93 94 7.548075 TGTCTCGTATTCTCTTATTTTGAACCC 59.452 37.037 0.00 0.00 0.00 4.11
94 95 7.764901 GTCTCGTATTCTCTTATTTTGAACCCT 59.235 37.037 0.00 0.00 0.00 4.34
95 96 8.974238 TCTCGTATTCTCTTATTTTGAACCCTA 58.026 33.333 0.00 0.00 0.00 3.53
96 97 8.937634 TCGTATTCTCTTATTTTGAACCCTAC 57.062 34.615 0.00 0.00 0.00 3.18
97 98 8.755977 TCGTATTCTCTTATTTTGAACCCTACT 58.244 33.333 0.00 0.00 0.00 2.57
98 99 8.818057 CGTATTCTCTTATTTTGAACCCTACTG 58.182 37.037 0.00 0.00 0.00 2.74
99 100 9.668497 GTATTCTCTTATTTTGAACCCTACTGT 57.332 33.333 0.00 0.00 0.00 3.55
100 101 8.794335 ATTCTCTTATTTTGAACCCTACTGTC 57.206 34.615 0.00 0.00 0.00 3.51
101 102 7.554959 TCTCTTATTTTGAACCCTACTGTCT 57.445 36.000 0.00 0.00 0.00 3.41
102 103 7.612677 TCTCTTATTTTGAACCCTACTGTCTC 58.387 38.462 0.00 0.00 0.00 3.36
103 104 6.395629 TCTTATTTTGAACCCTACTGTCTCG 58.604 40.000 0.00 0.00 0.00 4.04
104 105 4.618920 ATTTTGAACCCTACTGTCTCGT 57.381 40.909 0.00 0.00 0.00 4.18
105 106 5.733620 ATTTTGAACCCTACTGTCTCGTA 57.266 39.130 0.00 0.00 0.00 3.43
106 107 5.733620 TTTTGAACCCTACTGTCTCGTAT 57.266 39.130 0.00 0.00 0.00 3.06
107 108 5.733620 TTTGAACCCTACTGTCTCGTATT 57.266 39.130 0.00 0.00 0.00 1.89
108 109 4.978083 TGAACCCTACTGTCTCGTATTC 57.022 45.455 0.00 0.00 0.00 1.75
109 110 3.376234 TGAACCCTACTGTCTCGTATTCG 59.624 47.826 0.00 0.00 38.55 3.34
110 111 2.996631 ACCCTACTGTCTCGTATTCGT 58.003 47.619 0.00 0.00 38.33 3.85
111 112 4.142609 ACCCTACTGTCTCGTATTCGTA 57.857 45.455 0.00 0.00 38.33 3.43
112 113 4.712476 ACCCTACTGTCTCGTATTCGTAT 58.288 43.478 0.00 0.00 38.33 3.06
121 122 6.067039 TGTCTCGTATTCGTATTCGTATTCG 58.933 40.000 4.59 4.59 38.28 3.34
132 133 5.793952 CGTATTCGTATTCGTATTCAGAGGG 59.206 44.000 0.00 0.00 38.33 4.30
134 135 5.587388 TTCGTATTCGTATTCAGAGGGTT 57.413 39.130 0.00 0.00 38.33 4.11
135 136 6.698008 TTCGTATTCGTATTCAGAGGGTTA 57.302 37.500 0.00 0.00 38.33 2.85
136 137 6.698008 TCGTATTCGTATTCAGAGGGTTAA 57.302 37.500 0.00 0.00 38.33 2.01
139 140 6.420008 CGTATTCGTATTCAGAGGGTTAAAGG 59.580 42.308 0.00 0.00 0.00 3.11
181 182 3.575965 ATTTTCGTTGGATCAAGGTGC 57.424 42.857 0.00 0.00 32.10 5.01
184 185 1.375396 CGTTGGATCAAGGTGCCGA 60.375 57.895 0.00 0.00 0.00 5.54
185 186 0.744414 CGTTGGATCAAGGTGCCGAT 60.744 55.000 0.00 0.00 0.00 4.18
186 187 1.017387 GTTGGATCAAGGTGCCGATC 58.983 55.000 0.00 0.00 37.83 3.69
187 188 0.461870 TTGGATCAAGGTGCCGATCG 60.462 55.000 8.51 8.51 39.16 3.69
188 189 1.595382 GGATCAAGGTGCCGATCGG 60.595 63.158 30.03 30.03 39.16 4.18
199 200 3.039988 CGATCGGCGGTCATAGGT 58.960 61.111 21.38 0.00 36.03 3.08
201 202 1.740285 GATCGGCGGTCATAGGTGT 59.260 57.895 16.56 0.00 0.00 4.16
202 203 0.597637 GATCGGCGGTCATAGGTGTG 60.598 60.000 16.56 0.00 0.00 3.82
203 204 2.644555 ATCGGCGGTCATAGGTGTGC 62.645 60.000 7.21 0.00 0.00 4.57
204 205 2.267642 GGCGGTCATAGGTGTGCA 59.732 61.111 0.00 0.00 0.00 4.57
220 234 2.752354 TGTGCACCCCTATGAATTTTCG 59.248 45.455 15.69 0.00 0.00 3.46
229 243 4.062293 CCTATGAATTTTCGCCCGACATA 58.938 43.478 0.00 0.00 0.00 2.29
237 251 0.467474 TCGCCCGACATATGAGGAGT 60.467 55.000 18.85 0.00 0.00 3.85
245 259 5.278858 CCCGACATATGAGGAGTTAAGGTAC 60.279 48.000 18.85 0.00 0.00 3.34
247 261 6.015350 CCGACATATGAGGAGTTAAGGTACAT 60.015 42.308 10.38 0.00 0.00 2.29
260 274 3.788227 AGGTACATGAGGCAGTTTGAA 57.212 42.857 0.00 0.00 0.00 2.69
300 315 6.201044 CGAGTTAAGGTATATGAGGCACTTTG 59.799 42.308 0.00 0.00 41.55 2.77
305 320 4.346418 AGGTATATGAGGCACTTTGAGAGG 59.654 45.833 0.00 0.00 41.55 3.69
306 321 2.698855 TATGAGGCACTTTGAGAGGC 57.301 50.000 0.00 0.00 41.55 4.70
307 322 0.034670 ATGAGGCACTTTGAGAGGCC 60.035 55.000 0.00 0.00 41.55 5.19
317 332 6.183360 GGCACTTTGAGAGGCCAAATTATAAT 60.183 38.462 5.01 0.00 39.87 1.28
318 333 7.014230 GGCACTTTGAGAGGCCAAATTATAATA 59.986 37.037 5.01 0.00 39.87 0.98
335 350 9.844257 AATTATAATAGATTGGCTAGAGATGGC 57.156 33.333 0.00 0.00 31.33 4.40
367 382 3.815401 CCAATCTTCGTTGAAGGACACTT 59.185 43.478 6.71 0.00 39.82 3.16
474 500 3.370633 GGAAGGGAGTAGGAACCATGTTC 60.371 52.174 0.00 0.00 0.00 3.18
554 590 4.128388 GGTGGCGGCGGGAAAATG 62.128 66.667 9.78 0.00 0.00 2.32
703 748 0.686112 ACTCTCCAGCAGCCTACCTC 60.686 60.000 0.00 0.00 0.00 3.85
707 752 2.366167 CAGCAGCCTACCTCCCCT 60.366 66.667 0.00 0.00 0.00 4.79
708 753 1.075226 CAGCAGCCTACCTCCCCTA 60.075 63.158 0.00 0.00 0.00 3.53
710 755 1.167943 AGCAGCCTACCTCCCCTATA 58.832 55.000 0.00 0.00 0.00 1.31
711 756 1.077993 AGCAGCCTACCTCCCCTATAG 59.922 57.143 0.00 0.00 0.00 1.31
712 757 1.077334 GCAGCCTACCTCCCCTATAGA 59.923 57.143 0.00 0.00 0.00 1.98
713 758 2.886391 GCAGCCTACCTCCCCTATAGAG 60.886 59.091 0.00 0.00 0.00 2.43
715 760 3.592427 CAGCCTACCTCCCCTATAGAGTA 59.408 52.174 0.00 0.00 0.00 2.59
716 761 4.230964 CAGCCTACCTCCCCTATAGAGTAT 59.769 50.000 0.00 0.00 0.00 2.12
718 763 4.686670 GCCTACCTCCCCTATAGAGTATCG 60.687 54.167 0.00 0.00 42.67 2.92
719 764 4.474287 CCTACCTCCCCTATAGAGTATCGT 59.526 50.000 0.00 0.00 42.67 3.73
720 765 5.664908 CCTACCTCCCCTATAGAGTATCGTA 59.335 48.000 0.00 0.00 42.67 3.43
724 772 6.183361 ACCTCCCCTATAGAGTATCGTATAGC 60.183 46.154 0.00 0.00 42.67 2.97
903 958 1.157751 ACCTCGACTCCCCTTCCAA 59.842 57.895 0.00 0.00 0.00 3.53
951 1015 0.333312 TCCTCTCTTTCTCTCCCGCT 59.667 55.000 0.00 0.00 0.00 5.52
973 1037 2.368011 GCGCCTACCTTCCCTTCCT 61.368 63.158 0.00 0.00 0.00 3.36
974 1038 1.823976 CGCCTACCTTCCCTTCCTC 59.176 63.158 0.00 0.00 0.00 3.71
975 1039 1.687297 CGCCTACCTTCCCTTCCTCC 61.687 65.000 0.00 0.00 0.00 4.30
1049 1118 2.511600 AATCTAGCCCGCACACGC 60.512 61.111 0.00 0.00 38.22 5.34
1050 1119 3.019003 AATCTAGCCCGCACACGCT 62.019 57.895 0.00 0.00 38.22 5.07
1066 1135 4.673298 CTACGCCACGCCACACCA 62.673 66.667 0.00 0.00 0.00 4.17
1081 1150 1.411246 ACACCAACACGTGAGCTAAGA 59.589 47.619 25.01 0.00 37.20 2.10
1082 1151 2.159014 ACACCAACACGTGAGCTAAGAA 60.159 45.455 25.01 0.00 37.20 2.52
1083 1152 2.476619 CACCAACACGTGAGCTAAGAAG 59.523 50.000 25.01 2.58 35.68 2.85
1099 1168 0.244721 GAAGCAAAAGCAAGGCGGAT 59.755 50.000 0.00 0.00 0.00 4.18
1101 1170 1.767759 AGCAAAAGCAAGGCGGATAT 58.232 45.000 0.00 0.00 0.00 1.63
1107 1176 2.614829 AGCAAGGCGGATATACGTTT 57.385 45.000 9.53 1.28 35.98 3.60
1124 1193 3.813166 ACGTTTACACCACCATCAAAGAG 59.187 43.478 0.00 0.00 0.00 2.85
1125 1194 3.364964 CGTTTACACCACCATCAAAGAGC 60.365 47.826 0.00 0.00 0.00 4.09
1126 1195 3.788227 TTACACCACCATCAAAGAGCT 57.212 42.857 0.00 0.00 0.00 4.09
1127 1196 2.664402 ACACCACCATCAAAGAGCTT 57.336 45.000 0.00 0.00 0.00 3.74
1128 1197 3.788227 ACACCACCATCAAAGAGCTTA 57.212 42.857 0.00 0.00 0.00 3.09
1129 1198 3.679389 ACACCACCATCAAAGAGCTTAG 58.321 45.455 0.00 0.00 0.00 2.18
1204 1273 2.254737 GACGAGGGAGGAGGACGAGA 62.255 65.000 0.00 0.00 0.00 4.04
1326 1395 2.042230 AACTACCTCCGCCCCGAT 60.042 61.111 0.00 0.00 0.00 4.18
1566 1644 4.478371 CATCCTGCAGAGGCGCCA 62.478 66.667 31.54 6.15 45.35 5.69
1569 1647 3.437795 CCTGCAGAGGCGCCAAAG 61.438 66.667 31.54 18.35 45.35 2.77
1570 1648 2.359107 CTGCAGAGGCGCCAAAGA 60.359 61.111 31.54 7.14 45.35 2.52
1571 1649 2.669569 TGCAGAGGCGCCAAAGAC 60.670 61.111 31.54 14.36 45.35 3.01
1639 1720 1.624479 CCTGGACCTCTGCATCAGCT 61.624 60.000 0.00 0.00 42.74 4.24
1903 2000 0.690762 TTGTTGCTCCCTCCTACCAC 59.309 55.000 0.00 0.00 0.00 4.16
1915 2012 6.172630 TCCCTCCTACCACGTTTTTATTTAC 58.827 40.000 0.00 0.00 0.00 2.01
1916 2013 6.013466 TCCCTCCTACCACGTTTTTATTTACT 60.013 38.462 0.00 0.00 0.00 2.24
1953 2053 6.651975 AATACTACAGTACTGGTAGATGGC 57.348 41.667 26.12 0.00 40.49 4.40
2011 2116 2.851588 GATCCTCCCTGCCCTCCC 60.852 72.222 0.00 0.00 0.00 4.30
2016 2121 4.431524 TCCCTGCCCTCCCCGATT 62.432 66.667 0.00 0.00 0.00 3.34
2080 2193 9.233232 GAAATGGAACGGAATGAAATAATACAC 57.767 33.333 0.00 0.00 0.00 2.90
2124 2240 1.280133 CCCATGGTCTCATGTCTGTGT 59.720 52.381 11.73 0.00 46.96 3.72
2125 2241 2.353323 CCATGGTCTCATGTCTGTGTG 58.647 52.381 2.57 0.00 46.96 3.82
2126 2242 2.027837 CCATGGTCTCATGTCTGTGTGA 60.028 50.000 2.57 0.00 46.96 3.58
2128 2244 3.111853 TGGTCTCATGTCTGTGTGAAC 57.888 47.619 0.00 0.00 31.69 3.18
2129 2245 2.433970 TGGTCTCATGTCTGTGTGAACA 59.566 45.455 0.00 0.00 37.08 3.18
2143 2260 3.058914 GTGTGAACATCTCAAACTTCCCG 60.059 47.826 0.00 0.00 39.01 5.14
2181 2298 1.021968 GAAACACGTCCCAAGCAAGT 58.978 50.000 0.00 0.00 0.00 3.16
2201 2319 7.042335 GCAAGTGTATGAAATGAGTACTAGGT 58.958 38.462 0.00 0.00 0.00 3.08
2215 2333 8.418597 TGAGTACTAGGTCTTGTCATTAGTTT 57.581 34.615 0.00 0.00 0.00 2.66
2230 2348 6.253083 GTCATTAGTTTGTTACTACTCGCTCC 59.747 42.308 0.00 0.00 39.05 4.70
2264 2382 5.118642 AGTGTCGTAGTTTCAGTTAGACC 57.881 43.478 0.00 0.00 0.00 3.85
2270 2388 2.755650 AGTTTCAGTTAGACCGTGCTG 58.244 47.619 0.00 0.00 0.00 4.41
2329 2447 3.964875 CCGTTGTGCTGGTGGTGC 61.965 66.667 0.00 0.00 0.00 5.01
2330 2448 3.208383 CGTTGTGCTGGTGGTGCA 61.208 61.111 0.00 0.00 38.19 4.57
2331 2449 2.723746 GTTGTGCTGGTGGTGCAG 59.276 61.111 0.00 0.00 41.41 4.41
2332 2450 1.823470 GTTGTGCTGGTGGTGCAGA 60.823 57.895 0.00 0.00 41.41 4.26
2333 2451 1.077140 TTGTGCTGGTGGTGCAGAA 60.077 52.632 0.00 0.00 41.41 3.02
2349 2467 1.466167 CAGAACAGATTGGTTGGAGCG 59.534 52.381 0.00 0.00 0.00 5.03
2410 2537 1.467713 CGTACGTCTTGCCCTCTTCTC 60.468 57.143 7.22 0.00 0.00 2.87
2425 2552 5.241662 CCTCTTCTCTTCTGTTTTGGGTAG 58.758 45.833 0.00 0.00 0.00 3.18
2560 2697 0.179045 GTGTTGGTGCACTCCTGTCT 60.179 55.000 17.98 0.00 36.51 3.41
2562 2699 1.230324 GTTGGTGCACTCCTGTCTTC 58.770 55.000 17.98 0.00 0.00 2.87
2594 2731 1.227527 GCCGCTTTTGGGTTGCTTT 60.228 52.632 0.00 0.00 0.00 3.51
2642 2779 5.602561 ACTAACCAAAAGGCTGAATTTCCTT 59.397 36.000 0.00 2.80 44.07 3.36
2673 2812 6.578023 TCTTTTACCAACAAAAATGGACCTG 58.422 36.000 0.00 0.00 40.56 4.00
2686 2828 9.626045 CAAAAATGGACCTGTTTTTCTAGATAC 57.374 33.333 14.21 0.00 35.87 2.24
2693 2835 9.668497 GGACCTGTTTTTCTAGATACATAAACT 57.332 33.333 0.00 0.00 0.00 2.66
2721 2863 1.581934 TCGGCCGATTTCTTAGCATG 58.418 50.000 27.28 0.00 0.00 4.06
2726 2868 4.377431 CGGCCGATTTCTTAGCATGTATTC 60.377 45.833 24.07 0.00 0.00 1.75
2727 2869 4.083271 GGCCGATTTCTTAGCATGTATTCC 60.083 45.833 0.00 0.00 0.00 3.01
2728 2870 4.083271 GCCGATTTCTTAGCATGTATTCCC 60.083 45.833 0.00 0.00 0.00 3.97
2729 2871 5.308825 CCGATTTCTTAGCATGTATTCCCT 58.691 41.667 0.00 0.00 0.00 4.20
2730 2872 5.409826 CCGATTTCTTAGCATGTATTCCCTC 59.590 44.000 0.00 0.00 0.00 4.30
2731 2873 5.409826 CGATTTCTTAGCATGTATTCCCTCC 59.590 44.000 0.00 0.00 0.00 4.30
2732 2874 4.336889 TTCTTAGCATGTATTCCCTCCG 57.663 45.455 0.00 0.00 0.00 4.63
2733 2875 3.305720 TCTTAGCATGTATTCCCTCCGT 58.694 45.455 0.00 0.00 0.00 4.69
2734 2876 3.321111 TCTTAGCATGTATTCCCTCCGTC 59.679 47.826 0.00 0.00 0.00 4.79
2735 2877 1.794714 AGCATGTATTCCCTCCGTCT 58.205 50.000 0.00 0.00 0.00 4.18
2736 2878 1.414181 AGCATGTATTCCCTCCGTCTG 59.586 52.381 0.00 0.00 0.00 3.51
2737 2879 1.412710 GCATGTATTCCCTCCGTCTGA 59.587 52.381 0.00 0.00 0.00 3.27
2738 2880 2.158957 GCATGTATTCCCTCCGTCTGAA 60.159 50.000 0.00 0.00 0.00 3.02
2739 2881 3.681594 GCATGTATTCCCTCCGTCTGAAA 60.682 47.826 0.00 0.00 0.00 2.69
2740 2882 4.513442 CATGTATTCCCTCCGTCTGAAAA 58.487 43.478 0.00 0.00 0.00 2.29
2741 2883 4.627284 TGTATTCCCTCCGTCTGAAAAA 57.373 40.909 0.00 0.00 0.00 1.94
2764 2906 9.508642 AAAAACTTATCCCAAACTTGTTTTTCA 57.491 25.926 0.00 0.00 40.02 2.69
2765 2907 9.508642 AAAACTTATCCCAAACTTGTTTTTCAA 57.491 25.926 0.00 0.00 34.01 2.69
2766 2908 9.508642 AAACTTATCCCAAACTTGTTTTTCAAA 57.491 25.926 0.00 0.00 35.48 2.69
2767 2909 9.679661 AACTTATCCCAAACTTGTTTTTCAAAT 57.320 25.926 0.00 0.00 35.48 2.32
2768 2910 9.679661 ACTTATCCCAAACTTGTTTTTCAAATT 57.320 25.926 0.00 0.00 35.48 1.82
2769 2911 9.934190 CTTATCCCAAACTTGTTTTTCAAATTG 57.066 29.630 0.00 0.00 35.48 2.32
2770 2912 9.672673 TTATCCCAAACTTGTTTTTCAAATTGA 57.327 25.926 0.00 0.00 36.17 2.57
2771 2913 8.750515 ATCCCAAACTTGTTTTTCAAATTGAT 57.249 26.923 0.00 0.00 36.17 2.57
2772 2914 7.983307 TCCCAAACTTGTTTTTCAAATTGATG 58.017 30.769 0.00 0.00 36.17 3.07
2773 2915 7.609532 TCCCAAACTTGTTTTTCAAATTGATGT 59.390 29.630 0.00 0.00 36.17 3.06
2774 2916 8.887717 CCCAAACTTGTTTTTCAAATTGATGTA 58.112 29.630 0.00 0.00 36.17 2.29
2820 2962 9.528018 AAATCTATTTGAAGCAAACTTTTTCGA 57.472 25.926 0.00 0.00 36.13 3.71
2821 2963 9.528018 AATCTATTTGAAGCAAACTTTTTCGAA 57.472 25.926 0.00 0.00 36.13 3.71
2822 2964 8.335256 TCTATTTGAAGCAAACTTTTTCGAAC 57.665 30.769 0.00 0.00 36.13 3.95
2823 2965 5.428793 TTTGAAGCAAACTTTTTCGAACG 57.571 34.783 0.00 0.00 35.82 3.95
2824 2966 4.343811 TGAAGCAAACTTTTTCGAACGA 57.656 36.364 0.00 0.00 35.82 3.85
2825 2967 4.724303 TGAAGCAAACTTTTTCGAACGAA 58.276 34.783 0.00 5.53 35.82 3.85
2826 2968 5.336744 TGAAGCAAACTTTTTCGAACGAAT 58.663 33.333 10.33 0.00 35.82 3.34
2827 2969 6.487960 TGAAGCAAACTTTTTCGAACGAATA 58.512 32.000 10.33 3.45 35.82 1.75
2828 2970 6.967767 TGAAGCAAACTTTTTCGAACGAATAA 59.032 30.769 10.33 10.68 35.82 1.40
2829 2971 6.969669 AGCAAACTTTTTCGAACGAATAAG 57.030 33.333 25.70 25.70 43.67 1.73
2830 2972 6.721321 AGCAAACTTTTTCGAACGAATAAGA 58.279 32.000 30.33 9.94 42.01 2.10
2831 2973 6.851330 AGCAAACTTTTTCGAACGAATAAGAG 59.149 34.615 30.33 22.99 42.01 2.85
2832 2974 6.397584 GCAAACTTTTTCGAACGAATAAGAGC 60.398 38.462 30.33 26.11 42.01 4.09
2833 2975 5.917541 ACTTTTTCGAACGAATAAGAGCA 57.082 34.783 30.33 8.50 42.01 4.26
2834 2976 6.481954 ACTTTTTCGAACGAATAAGAGCAT 57.518 33.333 30.33 15.66 42.01 3.79
2835 2977 6.899114 ACTTTTTCGAACGAATAAGAGCATT 58.101 32.000 30.33 15.41 42.01 3.56
2836 2978 7.360361 ACTTTTTCGAACGAATAAGAGCATTT 58.640 30.769 30.33 14.92 42.01 2.32
2837 2979 7.860872 ACTTTTTCGAACGAATAAGAGCATTTT 59.139 29.630 30.33 14.44 42.01 1.82
2838 2980 7.547285 TTTTCGAACGAATAAGAGCATTTTG 57.453 32.000 10.33 0.00 33.79 2.44
2839 2981 6.474819 TTCGAACGAATAAGAGCATTTTGA 57.525 33.333 5.53 0.00 0.00 2.69
2840 2982 6.662414 TCGAACGAATAAGAGCATTTTGAT 57.338 33.333 0.00 0.00 0.00 2.57
2841 2983 7.072177 TCGAACGAATAAGAGCATTTTGATT 57.928 32.000 0.00 0.00 0.00 2.57
2842 2984 8.192068 TCGAACGAATAAGAGCATTTTGATTA 57.808 30.769 0.00 0.00 0.00 1.75
2843 2985 8.661257 TCGAACGAATAAGAGCATTTTGATTAA 58.339 29.630 0.00 0.00 0.00 1.40
2844 2986 9.272901 CGAACGAATAAGAGCATTTTGATTAAA 57.727 29.630 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.283807 TGTTATACGTCTTTCTACCTCTGCATA 59.716 37.037 0.00 0.00 0.00 3.14
1 2 6.096423 TGTTATACGTCTTTCTACCTCTGCAT 59.904 38.462 0.00 0.00 0.00 3.96
2 3 5.416639 TGTTATACGTCTTTCTACCTCTGCA 59.583 40.000 0.00 0.00 0.00 4.41
3 4 5.888105 TGTTATACGTCTTTCTACCTCTGC 58.112 41.667 0.00 0.00 0.00 4.26
4 5 7.536855 ACTTGTTATACGTCTTTCTACCTCTG 58.463 38.462 0.00 0.00 0.00 3.35
5 6 7.700022 ACTTGTTATACGTCTTTCTACCTCT 57.300 36.000 0.00 0.00 0.00 3.69
6 7 7.912773 GGTACTTGTTATACGTCTTTCTACCTC 59.087 40.741 0.00 0.00 0.00 3.85
7 8 7.414540 CGGTACTTGTTATACGTCTTTCTACCT 60.415 40.741 0.00 0.00 0.00 3.08
8 9 6.688813 CGGTACTTGTTATACGTCTTTCTACC 59.311 42.308 0.00 0.00 0.00 3.18
9 10 7.426743 GTCGGTACTTGTTATACGTCTTTCTAC 59.573 40.741 0.00 0.00 0.00 2.59
10 11 7.119116 TGTCGGTACTTGTTATACGTCTTTCTA 59.881 37.037 0.00 0.00 0.00 2.10
11 12 6.072508 TGTCGGTACTTGTTATACGTCTTTCT 60.073 38.462 0.00 0.00 0.00 2.52
12 13 6.086222 TGTCGGTACTTGTTATACGTCTTTC 58.914 40.000 0.00 0.00 0.00 2.62
13 14 6.012658 TGTCGGTACTTGTTATACGTCTTT 57.987 37.500 0.00 0.00 0.00 2.52
14 15 5.627499 TGTCGGTACTTGTTATACGTCTT 57.373 39.130 0.00 0.00 0.00 3.01
15 16 5.627499 TTGTCGGTACTTGTTATACGTCT 57.373 39.130 0.00 0.00 0.00 4.18
16 17 6.363357 ACTTTTGTCGGTACTTGTTATACGTC 59.637 38.462 0.00 0.00 0.00 4.34
17 18 6.215845 ACTTTTGTCGGTACTTGTTATACGT 58.784 36.000 0.00 0.00 0.00 3.57
18 19 6.695292 ACTTTTGTCGGTACTTGTTATACG 57.305 37.500 0.00 0.00 0.00 3.06
35 36 7.213706 CGCGTGTATTCAGTACAAATACTTTTG 59.786 37.037 21.83 14.15 44.52 2.44
36 37 7.095523 ACGCGTGTATTCAGTACAAATACTTTT 60.096 33.333 12.93 8.06 44.52 2.27
37 38 6.366877 ACGCGTGTATTCAGTACAAATACTTT 59.633 34.615 12.93 7.84 44.52 2.66
38 39 5.865552 ACGCGTGTATTCAGTACAAATACTT 59.134 36.000 12.93 7.62 44.52 2.24
39 40 5.404946 ACGCGTGTATTCAGTACAAATACT 58.595 37.500 12.93 7.72 44.52 2.12
40 41 5.691508 ACGCGTGTATTCAGTACAAATAC 57.308 39.130 12.93 17.69 44.52 1.89
41 42 8.344831 AGTATACGCGTGTATTCAGTACAAATA 58.655 33.333 25.31 3.06 44.52 1.40
42 43 7.166970 CAGTATACGCGTGTATTCAGTACAAAT 59.833 37.037 25.31 4.16 44.52 2.32
43 44 6.469915 CAGTATACGCGTGTATTCAGTACAAA 59.530 38.462 25.31 2.82 44.52 2.83
44 45 5.967088 CAGTATACGCGTGTATTCAGTACAA 59.033 40.000 25.31 3.54 44.52 2.41
45 46 5.065090 ACAGTATACGCGTGTATTCAGTACA 59.935 40.000 25.31 4.27 41.50 2.90
46 47 5.505286 ACAGTATACGCGTGTATTCAGTAC 58.495 41.667 25.31 16.81 41.50 2.73
47 48 5.525012 AGACAGTATACGCGTGTATTCAGTA 59.475 40.000 25.31 5.72 41.50 2.74
48 49 4.334759 AGACAGTATACGCGTGTATTCAGT 59.665 41.667 25.31 21.68 41.50 3.41
49 50 4.845387 AGACAGTATACGCGTGTATTCAG 58.155 43.478 25.31 18.92 41.50 3.02
50 51 4.551410 CGAGACAGTATACGCGTGTATTCA 60.551 45.833 25.31 7.20 41.50 2.57
51 52 3.898946 CGAGACAGTATACGCGTGTATTC 59.101 47.826 25.31 20.09 41.50 1.75
52 53 3.310774 ACGAGACAGTATACGCGTGTATT 59.689 43.478 25.31 14.14 41.50 1.89
53 54 2.868583 ACGAGACAGTATACGCGTGTAT 59.131 45.455 24.59 23.84 43.62 2.29
54 55 2.270923 ACGAGACAGTATACGCGTGTA 58.729 47.619 24.59 18.01 40.43 2.90
55 56 1.081892 ACGAGACAGTATACGCGTGT 58.918 50.000 24.59 19.31 40.43 4.49
56 57 3.516681 ATACGAGACAGTATACGCGTG 57.483 47.619 24.59 7.13 41.72 5.34
57 58 3.806521 AGAATACGAGACAGTATACGCGT 59.193 43.478 19.17 19.17 43.63 6.01
58 59 4.150274 AGAGAATACGAGACAGTATACGCG 59.850 45.833 3.53 3.53 36.39 6.01
59 60 5.594724 AGAGAATACGAGACAGTATACGC 57.405 43.478 0.00 0.00 36.39 4.42
65 66 9.141400 GTTCAAAATAAGAGAATACGAGACAGT 57.859 33.333 0.00 0.00 0.00 3.55
66 67 8.596380 GGTTCAAAATAAGAGAATACGAGACAG 58.404 37.037 0.00 0.00 0.00 3.51
67 68 7.548075 GGGTTCAAAATAAGAGAATACGAGACA 59.452 37.037 0.00 0.00 0.00 3.41
68 69 7.764901 AGGGTTCAAAATAAGAGAATACGAGAC 59.235 37.037 0.00 0.00 0.00 3.36
69 70 7.848128 AGGGTTCAAAATAAGAGAATACGAGA 58.152 34.615 0.00 0.00 0.00 4.04
70 71 9.032420 GTAGGGTTCAAAATAAGAGAATACGAG 57.968 37.037 0.00 0.00 0.00 4.18
71 72 8.755977 AGTAGGGTTCAAAATAAGAGAATACGA 58.244 33.333 0.00 0.00 0.00 3.43
72 73 8.818057 CAGTAGGGTTCAAAATAAGAGAATACG 58.182 37.037 0.00 0.00 0.00 3.06
73 74 9.668497 ACAGTAGGGTTCAAAATAAGAGAATAC 57.332 33.333 0.00 0.00 0.00 1.89
74 75 9.886132 GACAGTAGGGTTCAAAATAAGAGAATA 57.114 33.333 0.00 0.00 0.00 1.75
75 76 8.606830 AGACAGTAGGGTTCAAAATAAGAGAAT 58.393 33.333 0.00 0.00 0.00 2.40
76 77 7.974504 AGACAGTAGGGTTCAAAATAAGAGAA 58.025 34.615 0.00 0.00 0.00 2.87
77 78 7.554959 AGACAGTAGGGTTCAAAATAAGAGA 57.445 36.000 0.00 0.00 0.00 3.10
78 79 6.531948 CGAGACAGTAGGGTTCAAAATAAGAG 59.468 42.308 0.00 0.00 0.00 2.85
79 80 6.014840 ACGAGACAGTAGGGTTCAAAATAAGA 60.015 38.462 0.00 0.00 0.00 2.10
80 81 6.164176 ACGAGACAGTAGGGTTCAAAATAAG 58.836 40.000 0.00 0.00 0.00 1.73
81 82 6.105397 ACGAGACAGTAGGGTTCAAAATAA 57.895 37.500 0.00 0.00 0.00 1.40
82 83 5.733620 ACGAGACAGTAGGGTTCAAAATA 57.266 39.130 0.00 0.00 0.00 1.40
83 84 4.618920 ACGAGACAGTAGGGTTCAAAAT 57.381 40.909 0.00 0.00 0.00 1.82
84 85 5.733620 ATACGAGACAGTAGGGTTCAAAA 57.266 39.130 0.00 0.00 0.00 2.44
85 86 5.620654 CGAATACGAGACAGTAGGGTTCAAA 60.621 44.000 0.00 0.00 42.66 2.69
86 87 4.142534 CGAATACGAGACAGTAGGGTTCAA 60.143 45.833 0.00 0.00 42.66 2.69
87 88 3.376234 CGAATACGAGACAGTAGGGTTCA 59.624 47.826 0.00 0.00 42.66 3.18
88 89 3.376546 ACGAATACGAGACAGTAGGGTTC 59.623 47.826 0.00 0.00 42.66 3.62
89 90 3.350833 ACGAATACGAGACAGTAGGGTT 58.649 45.455 0.00 0.00 42.66 4.11
90 91 2.996631 ACGAATACGAGACAGTAGGGT 58.003 47.619 0.00 0.00 42.66 4.34
91 92 5.614231 CGAATACGAATACGAGACAGTAGGG 60.614 48.000 0.00 0.00 42.66 3.53
92 93 5.050499 ACGAATACGAATACGAGACAGTAGG 60.050 44.000 0.00 0.00 42.66 3.18
93 94 5.972018 ACGAATACGAATACGAGACAGTAG 58.028 41.667 0.00 0.00 42.66 2.57
94 95 5.973651 ACGAATACGAATACGAGACAGTA 57.026 39.130 0.00 0.00 42.66 2.74
95 96 4.871993 ACGAATACGAATACGAGACAGT 57.128 40.909 0.00 0.00 42.66 3.55
96 97 6.243854 CGAATACGAATACGAATACGAGACAG 59.756 42.308 0.00 0.00 41.06 3.51
97 98 6.067039 CGAATACGAATACGAATACGAGACA 58.933 40.000 0.00 0.00 41.06 3.41
98 99 6.067669 ACGAATACGAATACGAATACGAGAC 58.932 40.000 0.00 0.00 41.06 3.36
99 100 6.215477 ACGAATACGAATACGAATACGAGA 57.785 37.500 0.00 0.00 41.06 4.04
100 101 8.579521 AATACGAATACGAATACGAATACGAG 57.420 34.615 0.00 0.00 41.06 4.18
101 102 8.220434 TGAATACGAATACGAATACGAATACGA 58.780 33.333 0.00 0.00 41.06 3.43
102 103 8.355809 TGAATACGAATACGAATACGAATACG 57.644 34.615 0.00 0.00 42.66 3.06
103 104 9.533983 TCTGAATACGAATACGAATACGAATAC 57.466 33.333 0.00 0.00 42.66 1.89
104 105 9.750882 CTCTGAATACGAATACGAATACGAATA 57.249 33.333 0.00 0.00 42.66 1.75
105 106 7.749570 CCTCTGAATACGAATACGAATACGAAT 59.250 37.037 0.00 0.00 42.66 3.34
106 107 7.073883 CCTCTGAATACGAATACGAATACGAA 58.926 38.462 0.00 0.00 42.66 3.85
107 108 6.347969 CCCTCTGAATACGAATACGAATACGA 60.348 42.308 0.00 0.00 42.66 3.43
108 109 5.793952 CCCTCTGAATACGAATACGAATACG 59.206 44.000 0.00 0.00 42.66 3.06
109 110 6.675987 ACCCTCTGAATACGAATACGAATAC 58.324 40.000 0.00 0.00 42.66 1.89
110 111 6.889301 ACCCTCTGAATACGAATACGAATA 57.111 37.500 0.00 0.00 42.66 1.75
111 112 5.786264 ACCCTCTGAATACGAATACGAAT 57.214 39.130 0.00 0.00 42.66 3.34
112 113 5.587388 AACCCTCTGAATACGAATACGAA 57.413 39.130 0.00 0.00 42.66 3.85
121 122 6.243148 TGGAAACCTTTAACCCTCTGAATAC 58.757 40.000 0.00 0.00 0.00 1.89
165 166 1.375396 CGGCACCTTGATCCAACGA 60.375 57.895 0.00 0.00 0.00 3.85
184 185 1.441729 CACACCTATGACCGCCGAT 59.558 57.895 0.00 0.00 0.00 4.18
185 186 2.889617 CACACCTATGACCGCCGA 59.110 61.111 0.00 0.00 0.00 5.54
186 187 2.890474 GCACACCTATGACCGCCG 60.890 66.667 0.00 0.00 0.00 6.46
187 188 2.106683 GTGCACACCTATGACCGCC 61.107 63.158 13.17 0.00 0.00 6.13
188 189 3.486263 GTGCACACCTATGACCGC 58.514 61.111 13.17 0.00 0.00 5.68
198 199 3.427503 CGAAAATTCATAGGGGTGCACAC 60.428 47.826 20.43 16.45 0.00 3.82
199 200 2.752354 CGAAAATTCATAGGGGTGCACA 59.248 45.455 20.43 0.00 0.00 4.57
201 202 1.748493 GCGAAAATTCATAGGGGTGCA 59.252 47.619 0.00 0.00 0.00 4.57
202 203 1.067060 GGCGAAAATTCATAGGGGTGC 59.933 52.381 0.00 0.00 0.00 5.01
203 204 1.681264 GGGCGAAAATTCATAGGGGTG 59.319 52.381 0.00 0.00 0.00 4.61
204 205 1.749286 CGGGCGAAAATTCATAGGGGT 60.749 52.381 0.00 0.00 0.00 4.95
210 224 4.133820 TCATATGTCGGGCGAAAATTCAT 58.866 39.130 1.90 0.00 0.00 2.57
211 225 3.536570 TCATATGTCGGGCGAAAATTCA 58.463 40.909 1.90 0.00 0.00 2.57
220 234 3.555168 CCTTAACTCCTCATATGTCGGGC 60.555 52.174 1.90 0.00 0.00 6.13
229 243 4.101741 GCCTCATGTACCTTAACTCCTCAT 59.898 45.833 0.00 0.00 0.00 2.90
237 251 5.235850 TCAAACTGCCTCATGTACCTTAA 57.764 39.130 0.00 0.00 0.00 1.85
245 259 5.452078 TTAACCTTTCAAACTGCCTCATG 57.548 39.130 0.00 0.00 0.00 3.07
247 261 6.478512 AATTTAACCTTTCAAACTGCCTCA 57.521 33.333 0.00 0.00 0.00 3.86
275 289 5.455056 AGTGCCTCATATACCTTAACTCG 57.545 43.478 0.00 0.00 0.00 4.18
290 304 0.250901 TTGGCCTCTCAAAGTGCCTC 60.251 55.000 3.32 0.00 40.24 4.70
291 305 0.185901 TTTGGCCTCTCAAAGTGCCT 59.814 50.000 3.32 0.00 40.24 4.75
335 350 3.268023 ACGAAGATTGGCCTTCTTAGG 57.732 47.619 22.96 18.13 45.02 2.69
340 355 2.162408 CCTTCAACGAAGATTGGCCTTC 59.838 50.000 3.32 0.42 41.71 3.46
352 367 5.013568 TGAACTTAAGTGTCCTTCAACGA 57.986 39.130 9.34 0.00 31.89 3.85
438 459 6.831664 ACTCCCTTCCTATCACAATGTAAT 57.168 37.500 0.00 0.00 0.00 1.89
452 478 2.197465 ACATGGTTCCTACTCCCTTCC 58.803 52.381 0.00 0.00 0.00 3.46
474 500 8.785329 ATTTCTTCCTTTCTCTAGTTTGCTAG 57.215 34.615 0.00 0.00 44.60 3.42
545 581 1.819632 CTCGCCCTCCATTTTCCCG 60.820 63.158 0.00 0.00 0.00 5.14
546 582 1.453928 CCTCGCCCTCCATTTTCCC 60.454 63.158 0.00 0.00 0.00 3.97
548 584 1.453928 CCCCTCGCCCTCCATTTTC 60.454 63.158 0.00 0.00 0.00 2.29
550 586 4.129148 GCCCCTCGCCCTCCATTT 62.129 66.667 0.00 0.00 0.00 2.32
703 748 8.377034 ACTATGCTATACGATACTCTATAGGGG 58.623 40.741 4.24 0.00 0.00 4.79
834 889 0.811281 GGGCCTCGTGGATTTTTCTG 59.189 55.000 7.92 0.00 34.57 3.02
903 958 4.214310 TGATGATGAGTTGGTTGGTTTGT 58.786 39.130 0.00 0.00 0.00 2.83
973 1037 0.612229 CTCTGCTTGCTCTCTTGGGA 59.388 55.000 0.00 0.00 0.00 4.37
974 1038 0.392729 CCTCTGCTTGCTCTCTTGGG 60.393 60.000 0.00 0.00 0.00 4.12
975 1039 0.612229 TCCTCTGCTTGCTCTCTTGG 59.388 55.000 0.00 0.00 0.00 3.61
1049 1118 4.673298 TGGTGTGGCGTGGCGTAG 62.673 66.667 0.00 0.00 0.00 3.51
1050 1119 4.237207 TTGGTGTGGCGTGGCGTA 62.237 61.111 0.00 0.00 0.00 4.42
1099 1168 6.699366 TCTTTGATGGTGGTGTAAACGTATA 58.301 36.000 0.00 0.00 0.00 1.47
1101 1170 4.958509 TCTTTGATGGTGGTGTAAACGTA 58.041 39.130 0.00 0.00 0.00 3.57
1107 1176 3.788227 AAGCTCTTTGATGGTGGTGTA 57.212 42.857 0.00 0.00 0.00 2.90
1124 1193 2.902343 GACCCATGGCCGCTAAGC 60.902 66.667 6.09 0.00 0.00 3.09
1125 1194 2.588877 CGACCCATGGCCGCTAAG 60.589 66.667 6.09 0.00 0.00 2.18
1126 1195 4.169696 CCGACCCATGGCCGCTAA 62.170 66.667 6.09 0.00 0.00 3.09
1326 1395 2.280797 AAGTTGCCGCGCTTGAGA 60.281 55.556 5.56 0.00 0.00 3.27
1434 1503 4.555360 CAGTAGTTCTTGATCTCGTTGTCG 59.445 45.833 0.00 0.00 38.55 4.35
1531 1600 2.273912 GGACGAAGGAGACGGTGGT 61.274 63.158 0.00 0.00 34.93 4.16
1566 1644 2.665185 GTCACCGGCTGCGTCTTT 60.665 61.111 0.00 0.00 0.00 2.52
1580 1661 1.682684 GGCTTCCTCTCCTCCGTCA 60.683 63.158 0.00 0.00 0.00 4.35
1639 1720 1.228124 CCTCCTGTTGGAACGGCAA 60.228 57.895 0.00 0.00 42.66 4.52
1944 2044 0.178987 TCTCCTCCTCGCCATCTACC 60.179 60.000 0.00 0.00 0.00 3.18
1953 2053 7.334921 CACCTAATAATACTAGTCTCCTCCTCG 59.665 44.444 0.00 0.00 0.00 4.63
2011 2116 3.837213 ACATGAAACTGAGCAAATCGG 57.163 42.857 0.00 0.00 40.48 4.18
2080 2193 7.042658 GGGAAACGCACTGAATTTAGTATCTAG 60.043 40.741 2.09 0.00 0.00 2.43
2124 2240 3.323691 TCTCGGGAAGTTTGAGATGTTCA 59.676 43.478 0.00 0.00 34.00 3.18
2125 2241 3.926616 TCTCGGGAAGTTTGAGATGTTC 58.073 45.455 0.00 0.00 34.00 3.18
2126 2242 4.040461 TCTTCTCGGGAAGTTTGAGATGTT 59.960 41.667 23.98 0.00 46.47 2.71
2128 2244 4.081972 TCTCTTCTCGGGAAGTTTGAGATG 60.082 45.833 23.98 6.38 46.47 2.90
2129 2245 4.090090 TCTCTTCTCGGGAAGTTTGAGAT 58.910 43.478 23.98 0.00 46.47 2.75
2143 2260 3.393089 TCAGTTGCCACTTCTCTTCTC 57.607 47.619 0.00 0.00 0.00 2.87
2181 2298 8.362464 ACAAGACCTAGTACTCATTTCATACA 57.638 34.615 0.00 0.00 0.00 2.29
2201 2319 7.327761 GCGAGTAGTAACAAACTAATGACAAGA 59.672 37.037 0.00 0.00 42.37 3.02
2215 2333 2.430465 AGAACGGAGCGAGTAGTAACA 58.570 47.619 0.00 0.00 0.00 2.41
2230 2348 8.693504 TGAAACTACGACACTTATTTTAGAACG 58.306 33.333 0.00 0.00 0.00 3.95
2264 2382 0.321564 TGAAGAATCCCACCAGCACG 60.322 55.000 0.00 0.00 0.00 5.34
2270 2388 5.982890 TCTTGAAATTGAAGAATCCCACC 57.017 39.130 0.00 0.00 0.00 4.61
2329 2447 1.466167 CGCTCCAACCAATCTGTTCTG 59.534 52.381 0.00 0.00 0.00 3.02
2330 2448 1.611673 CCGCTCCAACCAATCTGTTCT 60.612 52.381 0.00 0.00 0.00 3.01
2331 2449 0.804989 CCGCTCCAACCAATCTGTTC 59.195 55.000 0.00 0.00 0.00 3.18
2332 2450 0.609131 CCCGCTCCAACCAATCTGTT 60.609 55.000 0.00 0.00 0.00 3.16
2333 2451 1.002134 CCCGCTCCAACCAATCTGT 60.002 57.895 0.00 0.00 0.00 3.41
2349 2467 1.555533 ACAGCTCTACCTAACTTGCCC 59.444 52.381 0.00 0.00 0.00 5.36
2410 2537 1.545841 GCCCCTACCCAAAACAGAAG 58.454 55.000 0.00 0.00 0.00 2.85
2463 2590 2.595754 GGGGATGGCCGCTGATTC 60.596 66.667 0.00 0.00 43.42 2.52
2560 2697 1.401148 GCGGCGATAGAATCTAGCGAA 60.401 52.381 28.78 0.00 39.76 4.70
2562 2699 0.169230 AGCGGCGATAGAATCTAGCG 59.831 55.000 21.79 21.79 39.76 4.26
2594 2731 1.606601 CAGACTGGTCCGGACTCCA 60.607 63.158 32.52 22.56 0.00 3.86
2661 2800 9.362151 TGTATCTAGAAAAACAGGTCCATTTTT 57.638 29.630 13.64 13.64 39.97 1.94
2673 2812 9.886132 TCTCCCAGTTTATGTATCTAGAAAAAC 57.114 33.333 0.00 3.60 0.00 2.43
2686 2828 2.618709 GGCCGATTTCTCCCAGTTTATG 59.381 50.000 0.00 0.00 0.00 1.90
2693 2835 1.912220 AATCGGCCGATTTCTCCCA 59.088 52.632 40.69 13.84 41.55 4.37
2703 2845 1.299541 ACATGCTAAGAAATCGGCCG 58.700 50.000 22.12 22.12 0.00 6.13
2738 2880 9.508642 TGAAAAACAAGTTTGGGATAAGTTTTT 57.491 25.926 11.45 11.45 45.05 1.94
2739 2881 9.508642 TTGAAAAACAAGTTTGGGATAAGTTTT 57.491 25.926 0.00 0.00 38.79 2.43
2740 2882 9.508642 TTTGAAAAACAAGTTTGGGATAAGTTT 57.491 25.926 0.00 0.00 39.77 2.66
2741 2883 9.679661 ATTTGAAAAACAAGTTTGGGATAAGTT 57.320 25.926 0.00 0.00 39.77 2.66
2742 2884 9.679661 AATTTGAAAAACAAGTTTGGGATAAGT 57.320 25.926 0.00 0.00 39.77 2.24
2743 2885 9.934190 CAATTTGAAAAACAAGTTTGGGATAAG 57.066 29.630 0.00 0.00 36.53 1.73
2744 2886 9.672673 TCAATTTGAAAAACAAGTTTGGGATAA 57.327 25.926 0.00 0.00 36.53 1.75
2745 2887 9.844257 ATCAATTTGAAAAACAAGTTTGGGATA 57.156 25.926 2.68 0.00 36.53 2.59
2746 2888 8.623030 CATCAATTTGAAAAACAAGTTTGGGAT 58.377 29.630 2.68 0.00 36.53 3.85
2747 2889 7.609532 ACATCAATTTGAAAAACAAGTTTGGGA 59.390 29.630 2.68 0.00 36.53 4.37
2748 2890 7.760437 ACATCAATTTGAAAAACAAGTTTGGG 58.240 30.769 2.68 0.00 36.53 4.12
2794 2936 9.528018 TCGAAAAAGTTTGCTTCAAATAGATTT 57.472 25.926 0.00 0.00 35.74 2.17
2795 2937 9.528018 TTCGAAAAAGTTTGCTTCAAATAGATT 57.472 25.926 0.00 0.00 35.74 2.40
2796 2938 8.968242 GTTCGAAAAAGTTTGCTTCAAATAGAT 58.032 29.630 0.00 0.00 35.74 1.98
2797 2939 7.165154 CGTTCGAAAAAGTTTGCTTCAAATAGA 59.835 33.333 0.00 0.00 35.74 1.98
2798 2940 7.165154 TCGTTCGAAAAAGTTTGCTTCAAATAG 59.835 33.333 0.00 0.00 35.74 1.73
2799 2941 6.967767 TCGTTCGAAAAAGTTTGCTTCAAATA 59.032 30.769 0.00 0.00 35.74 1.40
2800 2942 5.802956 TCGTTCGAAAAAGTTTGCTTCAAAT 59.197 32.000 0.00 0.00 35.74 2.32
2801 2943 5.154932 TCGTTCGAAAAAGTTTGCTTCAAA 58.845 33.333 0.00 0.00 33.01 2.69
2802 2944 4.724303 TCGTTCGAAAAAGTTTGCTTCAA 58.276 34.783 0.00 0.00 33.01 2.69
2803 2945 4.343811 TCGTTCGAAAAAGTTTGCTTCA 57.656 36.364 0.00 0.00 33.01 3.02
2804 2946 5.866503 ATTCGTTCGAAAAAGTTTGCTTC 57.133 34.783 11.50 0.00 33.01 3.86
2805 2947 7.190871 TCTTATTCGTTCGAAAAAGTTTGCTT 58.809 30.769 11.50 0.00 36.30 3.91
2806 2948 6.721321 TCTTATTCGTTCGAAAAAGTTTGCT 58.279 32.000 11.50 0.00 0.00 3.91
2807 2949 6.397584 GCTCTTATTCGTTCGAAAAAGTTTGC 60.398 38.462 11.50 7.16 0.00 3.68
2808 2950 6.631238 TGCTCTTATTCGTTCGAAAAAGTTTG 59.369 34.615 11.50 1.90 0.00 2.93
2809 2951 6.721321 TGCTCTTATTCGTTCGAAAAAGTTT 58.279 32.000 11.50 0.00 0.00 2.66
2810 2952 6.295039 TGCTCTTATTCGTTCGAAAAAGTT 57.705 33.333 11.50 0.00 0.00 2.66
2811 2953 5.917541 TGCTCTTATTCGTTCGAAAAAGT 57.082 34.783 11.50 0.00 0.00 2.66
2812 2954 7.781763 AAATGCTCTTATTCGTTCGAAAAAG 57.218 32.000 11.50 7.89 0.00 2.27
2813 2955 7.858382 TCAAAATGCTCTTATTCGTTCGAAAAA 59.142 29.630 11.50 0.00 0.00 1.94
2814 2956 7.356540 TCAAAATGCTCTTATTCGTTCGAAAA 58.643 30.769 11.50 0.00 0.00 2.29
2815 2957 6.893759 TCAAAATGCTCTTATTCGTTCGAAA 58.106 32.000 11.50 0.00 0.00 3.46
2816 2958 6.474819 TCAAAATGCTCTTATTCGTTCGAA 57.525 33.333 9.97 9.97 0.00 3.71
2817 2959 6.662414 ATCAAAATGCTCTTATTCGTTCGA 57.338 33.333 0.00 0.00 0.00 3.71
2818 2960 8.820628 TTAATCAAAATGCTCTTATTCGTTCG 57.179 30.769 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.