Multiple sequence alignment - TraesCS5B01G359500

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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 TraesCS5B01G359500 chr5B 100.000 4639 0 0 1 4639 539291231 539295869 0.000000e+00 8567.0
1 TraesCS5B01G359500 chr5B 80.214 187 17 6 4447 4625 539301624 539301798 6.300000e-24 122.0
2 TraesCS5B01G359500 chr5B 79.581 191 15 7 4443 4625 539306764 539306938 1.050000e-21 115.0
3 TraesCS5B01G359500 chr5B 85.526 76 7 3 4336 4407 661232216 661232291 4.980000e-10 76.8
4 TraesCS5B01G359500 chr5A 93.697 3903 154 41 776 4639 559069730 559073579 0.000000e+00 5760.0
5 TraesCS5B01G359500 chr5A 81.081 259 18 10 489 733 559069417 559069658 1.330000e-40 178.0
6 TraesCS5B01G359500 chr5A 84.034 119 12 5 174 286 559069181 559069298 1.770000e-19 108.0
7 TraesCS5B01G359500 chr5A 96.078 51 2 0 313 363 559069297 559069347 2.970000e-12 84.2
8 TraesCS5B01G359500 chr5A 92.105 38 1 2 4372 4407 653297946 653297983 8.000000e-03 52.8
9 TraesCS5B01G359500 chr5D 93.581 3848 166 35 837 4639 443011484 443015295 0.000000e+00 5662.0
10 TraesCS5B01G359500 chr5D 90.417 240 7 4 499 732 443011042 443011271 7.540000e-78 302.0
11 TraesCS5B01G359500 chr5D 90.541 222 9 7 191 408 443010799 443011012 2.730000e-72 283.0
12 TraesCS5B01G359500 chr5D 84.681 235 21 7 4399 4625 443018938 443019165 2.170000e-53 220.0
13 TraesCS5B01G359500 chrUn 93.220 413 28 0 1355 1767 34768664 34768252 3.970000e-170 608.0
14 TraesCS5B01G359500 chrUn 96.774 93 3 0 1969 2061 34768254 34768162 6.210000e-34 156.0
15 TraesCS5B01G359500 chr6D 90.698 43 3 1 4367 4408 13994265 13994223 6.480000e-04 56.5


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 TraesCS5B01G359500 chr5B 539291231 539295869 4638 False 8567.00 8567 100.0000 1 4639 1 chr5B.!!$F1 4638
1 TraesCS5B01G359500 chr5A 559069181 559073579 4398 False 1532.55 5760 88.7225 174 4639 4 chr5A.!!$F2 4465
2 TraesCS5B01G359500 chr5D 443010799 443019165 8366 False 1616.75 5662 89.8050 191 4639 4 chr5D.!!$F1 4448
3 TraesCS5B01G359500 chrUn 34768162 34768664 502 True 382.00 608 94.9970 1355 2061 2 chrUn.!!$R1 706

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
64 65 0.034670 ATGGAGCTCTGGGCAACTTC 60.035 55.000 14.64 0.0 44.79 3.01 F
790 916 0.036858 GCGTTGCTTTCCTCTCCTCT 60.037 55.000 0.00 0.0 0.00 3.69 F
1314 1518 0.108207 GCTACATGCAGATGAGCCCT 59.892 55.000 0.00 0.0 42.31 5.19 F
2127 2331 1.864029 GCACGCCTTTTCAAGAACCAC 60.864 52.381 0.00 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1125 1329 0.378257 CCATCTCCGCGAAAATGGTG 59.622 55.000 8.23 0.0 35.08 4.17 R
2310 2514 0.325110 AGAGCAGCCTCTTCCTAGCA 60.325 55.000 0.00 0.0 46.16 3.49 R
2921 3125 2.036217 TCTTGGGCAGTTTCATTTGCAG 59.964 45.455 0.00 0.0 42.02 4.41 R
3974 4193 1.949525 CCAAAAGGCATCTATGGACCG 59.050 52.381 0.00 0.0 34.05 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 0.605083 CAAGGGCCCTTCTTTCTTGC 59.395 55.000 35.15 0.00 33.42 4.01
20 21 0.188342 AAGGGCCCTTCTTTCTTGCA 59.812 50.000 32.48 0.00 0.00 4.08
21 22 0.411058 AGGGCCCTTCTTTCTTGCAT 59.589 50.000 22.28 0.00 0.00 3.96
22 23 1.640670 AGGGCCCTTCTTTCTTGCATA 59.359 47.619 22.28 0.00 0.00 3.14
23 24 1.751351 GGGCCCTTCTTTCTTGCATAC 59.249 52.381 17.04 0.00 0.00 2.39
24 25 1.401905 GGCCCTTCTTTCTTGCATACG 59.598 52.381 0.00 0.00 0.00 3.06
25 26 1.202188 GCCCTTCTTTCTTGCATACGC 60.202 52.381 0.00 0.00 39.24 4.42
26 27 1.401905 CCCTTCTTTCTTGCATACGCC 59.598 52.381 0.00 0.00 37.32 5.68
27 28 1.062587 CCTTCTTTCTTGCATACGCCG 59.937 52.381 0.00 0.00 37.32 6.46
28 29 1.062587 CTTCTTTCTTGCATACGCCGG 59.937 52.381 0.00 0.00 37.32 6.13
29 30 1.062525 CTTTCTTGCATACGCCGGC 59.937 57.895 19.07 19.07 37.32 6.13
30 31 2.631696 CTTTCTTGCATACGCCGGCG 62.632 60.000 44.88 44.88 46.03 6.46
45 46 4.400109 GCGACGGCAGTCTCGACA 62.400 66.667 15.11 0.00 44.93 4.35
46 47 2.485582 CGACGGCAGTCTCGACAT 59.514 61.111 15.11 0.00 44.93 3.06
47 48 1.869574 CGACGGCAGTCTCGACATG 60.870 63.158 15.11 0.00 44.93 3.21
48 49 1.517257 GACGGCAGTCTCGACATGG 60.517 63.158 9.95 0.00 43.80 3.66
49 50 1.934220 GACGGCAGTCTCGACATGGA 61.934 60.000 9.95 0.00 43.80 3.41
50 51 1.226802 CGGCAGTCTCGACATGGAG 60.227 63.158 0.00 0.00 35.32 3.86
51 52 1.520342 GGCAGTCTCGACATGGAGC 60.520 63.158 0.00 0.00 33.98 4.70
52 53 1.515020 GCAGTCTCGACATGGAGCT 59.485 57.895 0.00 0.00 33.98 4.09
53 54 0.527385 GCAGTCTCGACATGGAGCTC 60.527 60.000 4.71 4.71 33.98 4.09
54 55 1.102154 CAGTCTCGACATGGAGCTCT 58.898 55.000 14.64 0.00 33.98 4.09
55 56 1.102154 AGTCTCGACATGGAGCTCTG 58.898 55.000 14.64 7.59 33.98 3.35
56 57 0.102120 GTCTCGACATGGAGCTCTGG 59.898 60.000 14.64 5.99 33.98 3.86
57 58 1.039785 TCTCGACATGGAGCTCTGGG 61.040 60.000 14.64 5.62 33.98 4.45
58 59 2.202987 CGACATGGAGCTCTGGGC 60.203 66.667 14.64 4.63 42.19 5.36
59 60 2.993008 GACATGGAGCTCTGGGCA 59.007 61.111 14.64 2.97 44.79 5.36
60 61 1.300963 GACATGGAGCTCTGGGCAA 59.699 57.895 14.64 0.00 44.79 4.52
61 62 1.001641 ACATGGAGCTCTGGGCAAC 60.002 57.895 14.64 0.00 44.79 4.17
62 63 1.302285 CATGGAGCTCTGGGCAACT 59.698 57.895 14.64 0.00 44.79 3.16
63 64 0.323178 CATGGAGCTCTGGGCAACTT 60.323 55.000 14.64 0.00 44.79 2.66
64 65 0.034670 ATGGAGCTCTGGGCAACTTC 60.035 55.000 14.64 0.00 44.79 3.01
65 66 1.377856 GGAGCTCTGGGCAACTTCC 60.378 63.158 14.64 0.00 44.79 3.46
66 67 1.682257 GAGCTCTGGGCAACTTCCT 59.318 57.895 6.43 0.00 44.79 3.36
67 68 0.037447 GAGCTCTGGGCAACTTCCTT 59.963 55.000 6.43 0.00 44.79 3.36
68 69 0.480252 AGCTCTGGGCAACTTCCTTT 59.520 50.000 0.74 0.00 44.79 3.11
69 70 1.705186 AGCTCTGGGCAACTTCCTTTA 59.295 47.619 0.74 0.00 44.79 1.85
70 71 2.310052 AGCTCTGGGCAACTTCCTTTAT 59.690 45.455 0.74 0.00 44.79 1.40
71 72 2.424956 GCTCTGGGCAACTTCCTTTATG 59.575 50.000 0.00 0.00 41.35 1.90
72 73 3.690460 CTCTGGGCAACTTCCTTTATGT 58.310 45.455 0.00 0.00 0.00 2.29
73 74 3.420893 TCTGGGCAACTTCCTTTATGTG 58.579 45.455 0.00 0.00 0.00 3.21
74 75 3.073798 TCTGGGCAACTTCCTTTATGTGA 59.926 43.478 0.00 0.00 0.00 3.58
75 76 3.826157 CTGGGCAACTTCCTTTATGTGAA 59.174 43.478 0.00 0.00 0.00 3.18
76 77 4.219115 TGGGCAACTTCCTTTATGTGAAA 58.781 39.130 0.00 0.00 0.00 2.69
77 78 4.651503 TGGGCAACTTCCTTTATGTGAAAA 59.348 37.500 0.00 0.00 0.00 2.29
78 79 4.988540 GGGCAACTTCCTTTATGTGAAAAC 59.011 41.667 0.00 0.00 0.00 2.43
79 80 4.988540 GGCAACTTCCTTTATGTGAAAACC 59.011 41.667 0.00 0.00 0.00 3.27
80 81 5.452636 GGCAACTTCCTTTATGTGAAAACCA 60.453 40.000 0.00 0.00 0.00 3.67
81 82 6.045955 GCAACTTCCTTTATGTGAAAACCAA 58.954 36.000 0.00 0.00 0.00 3.67
82 83 6.019075 GCAACTTCCTTTATGTGAAAACCAAC 60.019 38.462 0.00 0.00 0.00 3.77
83 84 6.156748 ACTTCCTTTATGTGAAAACCAACC 57.843 37.500 0.00 0.00 0.00 3.77
84 85 5.897250 ACTTCCTTTATGTGAAAACCAACCT 59.103 36.000 0.00 0.00 0.00 3.50
85 86 7.064229 ACTTCCTTTATGTGAAAACCAACCTA 58.936 34.615 0.00 0.00 0.00 3.08
86 87 7.562088 ACTTCCTTTATGTGAAAACCAACCTAA 59.438 33.333 0.00 0.00 0.00 2.69
87 88 7.519032 TCCTTTATGTGAAAACCAACCTAAG 57.481 36.000 0.00 0.00 0.00 2.18
88 89 6.015772 TCCTTTATGTGAAAACCAACCTAAGC 60.016 38.462 0.00 0.00 0.00 3.09
89 90 6.239176 CCTTTATGTGAAAACCAACCTAAGCA 60.239 38.462 0.00 0.00 0.00 3.91
90 91 4.584327 ATGTGAAAACCAACCTAAGCAC 57.416 40.909 0.00 0.00 0.00 4.40
91 92 3.357203 TGTGAAAACCAACCTAAGCACA 58.643 40.909 0.00 0.00 33.18 4.57
92 93 3.764434 TGTGAAAACCAACCTAAGCACAA 59.236 39.130 0.00 0.00 32.74 3.33
93 94 4.220821 TGTGAAAACCAACCTAAGCACAAA 59.779 37.500 0.00 0.00 32.74 2.83
94 95 5.105146 TGTGAAAACCAACCTAAGCACAAAT 60.105 36.000 0.00 0.00 32.74 2.32
95 96 5.815222 GTGAAAACCAACCTAAGCACAAATT 59.185 36.000 0.00 0.00 0.00 1.82
96 97 6.315144 GTGAAAACCAACCTAAGCACAAATTT 59.685 34.615 0.00 0.00 0.00 1.82
97 98 6.881602 TGAAAACCAACCTAAGCACAAATTTT 59.118 30.769 0.00 0.00 0.00 1.82
98 99 6.676237 AAACCAACCTAAGCACAAATTTTG 57.324 33.333 7.59 7.59 0.00 2.44
99 100 4.126437 ACCAACCTAAGCACAAATTTTGC 58.874 39.130 9.04 13.93 40.52 3.68
100 101 4.125703 CCAACCTAAGCACAAATTTTGCA 58.874 39.130 20.12 0.00 42.83 4.08
101 102 4.211794 CCAACCTAAGCACAAATTTTGCAG 59.788 41.667 20.12 12.90 42.83 4.41
102 103 3.993920 ACCTAAGCACAAATTTTGCAGG 58.006 40.909 20.12 19.53 42.83 4.85
103 104 2.738314 CCTAAGCACAAATTTTGCAGGC 59.262 45.455 20.12 10.22 42.83 4.85
104 105 1.219646 AAGCACAAATTTTGCAGGCG 58.780 45.000 20.12 0.00 42.83 5.52
105 106 0.388659 AGCACAAATTTTGCAGGCGA 59.611 45.000 20.12 0.00 42.83 5.54
106 107 1.001181 AGCACAAATTTTGCAGGCGAT 59.999 42.857 20.12 3.76 42.83 4.58
107 108 1.799994 GCACAAATTTTGCAGGCGATT 59.200 42.857 9.04 0.00 39.93 3.34
108 109 2.223845 GCACAAATTTTGCAGGCGATTT 59.776 40.909 9.04 0.00 39.93 2.17
109 110 3.801293 CACAAATTTTGCAGGCGATTTG 58.199 40.909 17.95 17.95 42.33 2.32
110 111 3.465871 ACAAATTTTGCAGGCGATTTGT 58.534 36.364 18.81 18.81 43.83 2.83
111 112 4.447054 CACAAATTTTGCAGGCGATTTGTA 59.553 37.500 21.60 0.00 45.67 2.41
112 113 5.050499 CACAAATTTTGCAGGCGATTTGTAA 60.050 36.000 21.60 0.74 45.67 2.41
113 114 5.525378 ACAAATTTTGCAGGCGATTTGTAAA 59.475 32.000 21.12 3.54 45.62 2.01
114 115 6.037610 ACAAATTTTGCAGGCGATTTGTAAAA 59.962 30.769 21.12 8.52 45.62 1.52
115 116 6.610741 AATTTTGCAGGCGATTTGTAAAAA 57.389 29.167 11.74 6.78 41.26 1.94
116 117 5.649602 TTTTGCAGGCGATTTGTAAAAAG 57.350 34.783 7.41 0.00 37.25 2.27
117 118 4.576216 TTGCAGGCGATTTGTAAAAAGA 57.424 36.364 0.00 0.00 0.00 2.52
118 119 4.576216 TGCAGGCGATTTGTAAAAAGAA 57.424 36.364 0.00 0.00 0.00 2.52
119 120 4.938080 TGCAGGCGATTTGTAAAAAGAAA 58.062 34.783 0.00 0.00 0.00 2.52
120 121 4.742659 TGCAGGCGATTTGTAAAAAGAAAC 59.257 37.500 0.00 0.00 0.00 2.78
121 122 4.742659 GCAGGCGATTTGTAAAAAGAAACA 59.257 37.500 0.00 0.00 0.00 2.83
122 123 5.405269 GCAGGCGATTTGTAAAAAGAAACAT 59.595 36.000 0.00 0.00 0.00 2.71
123 124 6.616260 GCAGGCGATTTGTAAAAAGAAACATG 60.616 38.462 0.00 0.00 0.00 3.21
124 125 6.420604 CAGGCGATTTGTAAAAAGAAACATGT 59.579 34.615 0.00 0.00 0.00 3.21
125 126 6.420604 AGGCGATTTGTAAAAAGAAACATGTG 59.579 34.615 0.00 0.00 0.00 3.21
126 127 6.200097 GGCGATTTGTAAAAAGAAACATGTGT 59.800 34.615 0.00 0.00 0.00 3.72
127 128 7.254286 GGCGATTTGTAAAAAGAAACATGTGTT 60.254 33.333 0.00 0.00 40.50 3.32
128 129 7.578736 GCGATTTGTAAAAAGAAACATGTGTTG 59.421 33.333 0.00 0.00 38.44 3.33
129 130 8.591312 CGATTTGTAAAAAGAAACATGTGTTGT 58.409 29.630 0.00 0.00 41.53 3.32
139 140 4.454728 AACATGTGTTGTTGAGCTTGTT 57.545 36.364 0.00 0.00 46.80 2.83
140 141 4.454728 ACATGTGTTGTTGAGCTTGTTT 57.545 36.364 0.00 0.00 33.74 2.83
141 142 4.819769 ACATGTGTTGTTGAGCTTGTTTT 58.180 34.783 0.00 0.00 33.74 2.43
142 143 5.237048 ACATGTGTTGTTGAGCTTGTTTTT 58.763 33.333 0.00 0.00 33.74 1.94
143 144 5.348451 ACATGTGTTGTTGAGCTTGTTTTTC 59.652 36.000 0.00 0.00 33.74 2.29
144 145 4.241681 TGTGTTGTTGAGCTTGTTTTTCC 58.758 39.130 0.00 0.00 0.00 3.13
145 146 4.241681 GTGTTGTTGAGCTTGTTTTTCCA 58.758 39.130 0.00 0.00 0.00 3.53
146 147 4.869861 GTGTTGTTGAGCTTGTTTTTCCAT 59.130 37.500 0.00 0.00 0.00 3.41
147 148 4.869297 TGTTGTTGAGCTTGTTTTTCCATG 59.131 37.500 0.00 0.00 0.00 3.66
148 149 3.456280 TGTTGAGCTTGTTTTTCCATGC 58.544 40.909 0.00 0.00 36.15 4.06
149 150 2.420628 TGAGCTTGTTTTTCCATGCG 57.579 45.000 0.00 0.00 39.67 4.73
150 151 1.952990 TGAGCTTGTTTTTCCATGCGA 59.047 42.857 0.00 0.00 39.67 5.10
151 152 2.030893 TGAGCTTGTTTTTCCATGCGAG 60.031 45.455 0.00 0.00 39.67 5.03
152 153 1.270550 AGCTTGTTTTTCCATGCGAGG 59.729 47.619 0.00 0.00 39.67 4.63
153 154 1.269448 GCTTGTTTTTCCATGCGAGGA 59.731 47.619 0.00 0.00 35.41 3.71
154 155 2.669391 GCTTGTTTTTCCATGCGAGGAG 60.669 50.000 0.00 0.00 39.25 3.69
165 166 2.721945 GCGAGGAGCTTAGCCTAGA 58.278 57.895 0.00 0.00 44.04 2.43
166 167 0.596082 GCGAGGAGCTTAGCCTAGAG 59.404 60.000 0.00 0.00 44.04 2.43
167 168 0.596082 CGAGGAGCTTAGCCTAGAGC 59.404 60.000 0.00 0.00 44.25 4.09
279 286 1.445582 CCAACGACTACGCTGTCCC 60.446 63.158 0.00 0.00 43.96 4.46
282 289 4.189188 CGACTACGCTGTCCCGGG 62.189 72.222 16.85 16.85 33.70 5.73
283 290 2.753043 GACTACGCTGTCCCGGGA 60.753 66.667 22.63 22.63 0.00 5.14
285 292 3.834799 CTACGCTGTCCCGGGACC 61.835 72.222 43.35 30.37 43.97 4.46
286 293 4.682334 TACGCTGTCCCGGGACCA 62.682 66.667 43.35 31.01 43.97 4.02
288 295 4.096003 CGCTGTCCCGGGACCAAT 62.096 66.667 43.35 0.00 43.97 3.16
289 296 2.727392 CGCTGTCCCGGGACCAATA 61.727 63.158 43.35 27.69 43.97 1.90
290 297 1.146263 GCTGTCCCGGGACCAATAG 59.854 63.158 43.35 34.60 43.97 1.73
291 298 1.335132 GCTGTCCCGGGACCAATAGA 61.335 60.000 43.35 26.63 43.97 1.98
408 416 3.136626 AGCCGCAAACCCTAATCTAATCT 59.863 43.478 0.00 0.00 0.00 2.40
410 418 5.061179 GCCGCAAACCCTAATCTAATCTAA 58.939 41.667 0.00 0.00 0.00 2.10
411 419 5.705905 GCCGCAAACCCTAATCTAATCTAAT 59.294 40.000 0.00 0.00 0.00 1.73
414 422 6.090898 CGCAAACCCTAATCTAATCTAATCCG 59.909 42.308 0.00 0.00 0.00 4.18
417 425 5.091552 ACCCTAATCTAATCTAATCCGCCA 58.908 41.667 0.00 0.00 0.00 5.69
422 430 1.978580 CTAATCTAATCCGCCACCCCT 59.021 52.381 0.00 0.00 0.00 4.79
424 432 0.104934 ATCTAATCCGCCACCCCTCT 60.105 55.000 0.00 0.00 0.00 3.69
425 433 0.759436 TCTAATCCGCCACCCCTCTC 60.759 60.000 0.00 0.00 0.00 3.20
426 434 1.759459 CTAATCCGCCACCCCTCTCC 61.759 65.000 0.00 0.00 0.00 3.71
439 447 2.610859 TCTCCCCCTGACCTTGGC 60.611 66.667 0.00 0.00 0.00 4.52
480 488 4.395080 CGTCAGCGCTAATCCGAA 57.605 55.556 10.99 0.00 0.00 4.30
481 489 1.917921 CGTCAGCGCTAATCCGAAC 59.082 57.895 10.99 0.00 0.00 3.95
482 490 1.480219 CGTCAGCGCTAATCCGAACC 61.480 60.000 10.99 0.00 0.00 3.62
485 493 2.188469 GCGCTAATCCGAACCCCA 59.812 61.111 0.00 0.00 0.00 4.96
487 495 1.027792 GCGCTAATCCGAACCCCAAA 61.028 55.000 0.00 0.00 0.00 3.28
494 502 0.756070 TCCGAACCCCAAACCCAAAC 60.756 55.000 0.00 0.00 0.00 2.93
496 504 0.757561 CGAACCCCAAACCCAAACCT 60.758 55.000 0.00 0.00 0.00 3.50
500 512 1.176619 CCCCAAACCCAAACCTCGTC 61.177 60.000 0.00 0.00 0.00 4.20
523 535 1.300388 CGAGTAATTACCCCCGCCG 60.300 63.158 12.05 3.49 0.00 6.46
570 582 2.245714 CTTTCCTTTCTCGCTGGCGC 62.246 60.000 10.28 0.00 39.59 6.53
571 583 4.760047 TCCTTTCTCGCTGGCGCC 62.760 66.667 22.73 22.73 39.59 6.53
573 585 3.494336 CTTTCTCGCTGGCGCCAG 61.494 66.667 45.07 45.07 46.15 4.85
574 586 4.314440 TTTCTCGCTGGCGCCAGT 62.314 61.111 46.58 0.00 45.24 4.00
575 587 4.742201 TTCTCGCTGGCGCCAGTC 62.742 66.667 46.58 37.51 45.24 3.51
669 695 3.717294 CCAACCCCCGAGGACCAG 61.717 72.222 0.00 0.00 39.89 4.00
705 731 2.072298 CGTCTTTTTGAGGAGCTGGAG 58.928 52.381 0.00 0.00 32.72 3.86
732 759 7.800155 ACAAAGGAAGAAGAAGAAGAAGAAG 57.200 36.000 0.00 0.00 0.00 2.85
733 760 6.262049 ACAAAGGAAGAAGAAGAAGAAGAAGC 59.738 38.462 0.00 0.00 0.00 3.86
734 761 4.905429 AGGAAGAAGAAGAAGAAGAAGCC 58.095 43.478 0.00 0.00 0.00 4.35
735 762 4.349342 AGGAAGAAGAAGAAGAAGAAGCCA 59.651 41.667 0.00 0.00 0.00 4.75
736 763 5.066593 GGAAGAAGAAGAAGAAGAAGCCAA 58.933 41.667 0.00 0.00 0.00 4.52
740 767 2.163509 GAAGAAGAAGAAGCCAACCCC 58.836 52.381 0.00 0.00 0.00 4.95
741 768 0.405973 AGAAGAAGAAGCCAACCCCC 59.594 55.000 0.00 0.00 0.00 5.40
742 769 0.112412 GAAGAAGAAGCCAACCCCCA 59.888 55.000 0.00 0.00 0.00 4.96
743 770 0.178961 AAGAAGAAGCCAACCCCCAC 60.179 55.000 0.00 0.00 0.00 4.61
776 902 4.368808 CTTCCACCGCGTGCGTTG 62.369 66.667 13.70 9.26 37.81 4.10
786 912 1.493311 CGTGCGTTGCTTTCCTCTC 59.507 57.895 0.00 0.00 0.00 3.20
787 913 1.869690 GTGCGTTGCTTTCCTCTCC 59.130 57.895 0.00 0.00 0.00 3.71
788 914 0.603975 GTGCGTTGCTTTCCTCTCCT 60.604 55.000 0.00 0.00 0.00 3.69
789 915 0.320771 TGCGTTGCTTTCCTCTCCTC 60.321 55.000 0.00 0.00 0.00 3.71
790 916 0.036858 GCGTTGCTTTCCTCTCCTCT 60.037 55.000 0.00 0.00 0.00 3.69
791 917 1.719600 CGTTGCTTTCCTCTCCTCTG 58.280 55.000 0.00 0.00 0.00 3.35
792 918 1.447945 GTTGCTTTCCTCTCCTCTGC 58.552 55.000 0.00 0.00 0.00 4.26
793 919 0.326264 TTGCTTTCCTCTCCTCTGCC 59.674 55.000 0.00 0.00 0.00 4.85
794 920 1.153469 GCTTTCCTCTCCTCTGCCG 60.153 63.158 0.00 0.00 0.00 5.69
795 921 1.893919 GCTTTCCTCTCCTCTGCCGT 61.894 60.000 0.00 0.00 0.00 5.68
875 1024 3.911719 CTTCCTGGGATTGGGGAAG 57.088 57.895 6.58 6.58 46.36 3.46
876 1025 3.530685 TTCCTGGGATTGGGGAAGA 57.469 52.632 0.00 0.00 34.64 2.87
877 1026 1.766951 TTCCTGGGATTGGGGAAGAA 58.233 50.000 0.00 0.00 34.64 2.52
921 1074 1.146041 CTCCGCCGGATTGATTGGA 59.854 57.895 6.16 0.00 0.00 3.53
928 1081 2.294512 GCCGGATTGATTGGAGAATTCC 59.705 50.000 5.05 0.00 44.31 3.01
929 1082 3.825328 CCGGATTGATTGGAGAATTCCT 58.175 45.455 0.00 0.00 44.36 3.36
931 1084 4.276926 CCGGATTGATTGGAGAATTCCTTC 59.723 45.833 0.00 0.00 44.36 3.46
933 1086 5.453158 GGATTGATTGGAGAATTCCTTCCT 58.547 41.667 13.33 0.00 44.36 3.36
934 1087 5.301298 GGATTGATTGGAGAATTCCTTCCTG 59.699 44.000 13.33 0.00 44.36 3.86
978 1142 1.309950 GGCGGAGGATTTTAAGAGGC 58.690 55.000 0.00 0.00 0.00 4.70
979 1143 0.938008 GCGGAGGATTTTAAGAGGCG 59.062 55.000 0.00 0.00 0.00 5.52
980 1144 0.938008 CGGAGGATTTTAAGAGGCGC 59.062 55.000 0.00 0.00 0.00 6.53
989 1178 0.746563 TTAAGAGGCGCCGGATTTGG 60.747 55.000 23.20 0.00 0.00 3.28
1068 1272 4.759205 GACCACCACCATGGGGCC 62.759 72.222 18.09 0.00 40.43 5.80
1229 1433 0.526662 AACTACGAGAAGGCCGTCAG 59.473 55.000 21.26 15.80 40.95 3.51
1314 1518 0.108207 GCTACATGCAGATGAGCCCT 59.892 55.000 0.00 0.00 42.31 5.19
1542 1746 2.490902 GGAGAAGGGGTTTGTTGTGGAT 60.491 50.000 0.00 0.00 0.00 3.41
1956 2160 3.181467 GGCTCTATGTCACTGAAGCTGAT 60.181 47.826 0.00 0.00 0.00 2.90
2127 2331 1.864029 GCACGCCTTTTCAAGAACCAC 60.864 52.381 0.00 0.00 0.00 4.16
2244 2448 3.159984 GAGGTGTTTCAGCTCGCG 58.840 61.111 12.03 0.00 46.42 5.87
2256 2460 2.663196 CTCGCGGAGGGGAACTTT 59.337 61.111 6.13 0.00 42.39 2.66
2310 2514 3.596214 GGGTAATGTTCACATGTCTCGT 58.404 45.455 0.00 0.00 36.56 4.18
2956 3160 2.159379 GCCCAAGATGGTAAGAAAAGCG 60.159 50.000 0.00 0.00 35.17 4.68
2959 3163 4.399303 CCCAAGATGGTAAGAAAAGCGATT 59.601 41.667 0.00 0.00 35.17 3.34
3115 3328 3.181477 CCCTTCTCTAGAGATGCTGTGTG 60.181 52.174 22.93 10.80 37.29 3.82
3127 3340 2.023673 TGCTGTGTGTTTTTGCTAGCT 58.976 42.857 17.23 0.00 0.00 3.32
3280 3493 3.022607 ACAGAAAACCGGTCTCTTACG 57.977 47.619 8.04 4.33 0.00 3.18
3460 3677 5.334028 CGTGTAACTTTCATTGCATCACTCA 60.334 40.000 0.00 0.00 31.75 3.41
3640 3857 7.230108 GCATATGGCATTGGAGCATATATAGTT 59.770 37.037 4.78 0.00 43.97 2.24
3659 3876 5.633830 AGTTTGTATGAAGTTGCTCCATG 57.366 39.130 0.00 0.00 0.00 3.66
3932 4151 4.260139 TGTAGTTCTTCCAACGCACATA 57.740 40.909 0.00 0.00 0.00 2.29
3974 4193 9.959749 TTCATTTGTTTAGTTGTCCTTGTTATC 57.040 29.630 0.00 0.00 0.00 1.75
3994 4213 1.949525 CGGTCCATAGATGCCTTTTGG 59.050 52.381 0.00 0.00 44.18 3.28
3998 4217 4.466015 GGTCCATAGATGCCTTTTGGAAAA 59.534 41.667 0.00 0.00 44.07 2.29
4186 4405 3.055819 TCAGAAAGCATGGTAGGTGAGAC 60.056 47.826 0.00 0.00 0.00 3.36
4334 4553 7.114882 CATAGTCTGCACATGATAAGCTAAC 57.885 40.000 0.00 1.42 0.00 2.34
4454 4674 9.895138 CTTAAGGGTTTAATTTACTGTAGGCTA 57.105 33.333 0.00 0.00 0.00 3.93
4482 4702 7.998964 AGGACTTTGAAATAAACTCTTCCTGAA 59.001 33.333 0.00 0.00 0.00 3.02
4483 4703 8.797438 GGACTTTGAAATAAACTCTTCCTGAAT 58.203 33.333 0.00 0.00 0.00 2.57
4484 4704 9.833182 GACTTTGAAATAAACTCTTCCTGAATC 57.167 33.333 0.00 0.00 0.00 2.52
4485 4705 8.797438 ACTTTGAAATAAACTCTTCCTGAATCC 58.203 33.333 0.00 0.00 0.00 3.01
4486 4706 8.940397 TTTGAAATAAACTCTTCCTGAATCCT 57.060 30.769 0.00 0.00 0.00 3.24
4487 4707 7.928307 TGAAATAAACTCTTCCTGAATCCTG 57.072 36.000 0.00 0.00 0.00 3.86
4488 4708 7.689299 TGAAATAAACTCTTCCTGAATCCTGA 58.311 34.615 0.00 0.00 0.00 3.86
4554 4778 8.856103 ACTGTTATTGTAGGTTAATGCAACTTT 58.144 29.630 0.00 0.00 37.30 2.66
4627 4851 3.025322 TCCTCTGTTTTCTTTTGGGCA 57.975 42.857 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.188342 TGCAAGAAAGAAGGGCCCTT 59.812 50.000 37.85 37.85 39.23 3.95
2 3 0.411058 ATGCAAGAAAGAAGGGCCCT 59.589 50.000 22.28 22.28 0.00 5.19
3 4 1.751351 GTATGCAAGAAAGAAGGGCCC 59.249 52.381 16.46 16.46 0.00 5.80
4 5 1.401905 CGTATGCAAGAAAGAAGGGCC 59.598 52.381 0.00 0.00 0.00 5.80
5 6 1.202188 GCGTATGCAAGAAAGAAGGGC 60.202 52.381 0.89 0.00 42.15 5.19
6 7 1.401905 GGCGTATGCAAGAAAGAAGGG 59.598 52.381 9.59 0.00 45.35 3.95
7 8 1.062587 CGGCGTATGCAAGAAAGAAGG 59.937 52.381 9.59 0.00 45.35 3.46
8 9 1.062587 CCGGCGTATGCAAGAAAGAAG 59.937 52.381 9.59 0.00 45.35 2.85
9 10 1.083489 CCGGCGTATGCAAGAAAGAA 58.917 50.000 9.59 0.00 45.35 2.52
10 11 1.366111 GCCGGCGTATGCAAGAAAGA 61.366 55.000 12.58 0.00 45.35 2.52
11 12 1.062525 GCCGGCGTATGCAAGAAAG 59.937 57.895 12.58 0.00 45.35 2.62
12 13 2.745785 CGCCGGCGTATGCAAGAAA 61.746 57.895 39.71 0.00 45.35 2.52
13 14 3.192230 CGCCGGCGTATGCAAGAA 61.192 61.111 39.71 0.00 45.35 2.52
14 15 4.136511 TCGCCGGCGTATGCAAGA 62.137 61.111 44.16 23.32 45.35 3.02
15 16 3.925238 GTCGCCGGCGTATGCAAG 61.925 66.667 44.16 18.00 45.35 4.01
28 29 3.685214 ATGTCGAGACTGCCGTCGC 62.685 63.158 2.37 2.14 44.93 5.19
29 30 1.869574 CATGTCGAGACTGCCGTCG 60.870 63.158 2.37 0.00 44.93 5.12
30 31 1.517257 CCATGTCGAGACTGCCGTC 60.517 63.158 0.00 0.00 40.54 4.79
31 32 1.938657 CTCCATGTCGAGACTGCCGT 61.939 60.000 4.78 0.00 30.97 5.68
32 33 1.226802 CTCCATGTCGAGACTGCCG 60.227 63.158 4.78 0.00 30.97 5.69
33 34 1.520342 GCTCCATGTCGAGACTGCC 60.520 63.158 4.78 0.00 30.97 4.85
34 35 0.527385 GAGCTCCATGTCGAGACTGC 60.527 60.000 0.87 2.27 30.97 4.40
35 36 1.102154 AGAGCTCCATGTCGAGACTG 58.898 55.000 10.93 1.18 30.97 3.51
36 37 1.102154 CAGAGCTCCATGTCGAGACT 58.898 55.000 10.93 0.76 30.97 3.24
37 38 0.102120 CCAGAGCTCCATGTCGAGAC 59.898 60.000 10.93 0.00 30.97 3.36
38 39 1.039785 CCCAGAGCTCCATGTCGAGA 61.040 60.000 10.93 0.00 30.97 4.04
39 40 1.440893 CCCAGAGCTCCATGTCGAG 59.559 63.158 10.93 0.00 0.00 4.04
40 41 2.725312 GCCCAGAGCTCCATGTCGA 61.725 63.158 10.93 0.00 38.99 4.20
41 42 2.202987 GCCCAGAGCTCCATGTCG 60.203 66.667 10.93 0.00 38.99 4.35
42 43 1.028868 GTTGCCCAGAGCTCCATGTC 61.029 60.000 10.93 0.00 44.23 3.06
43 44 1.001641 GTTGCCCAGAGCTCCATGT 60.002 57.895 10.93 0.00 44.23 3.21
44 45 0.323178 AAGTTGCCCAGAGCTCCATG 60.323 55.000 10.93 2.65 44.23 3.66
45 46 0.034670 GAAGTTGCCCAGAGCTCCAT 60.035 55.000 10.93 0.00 44.23 3.41
46 47 1.376466 GAAGTTGCCCAGAGCTCCA 59.624 57.895 10.93 0.00 44.23 3.86
47 48 1.377856 GGAAGTTGCCCAGAGCTCC 60.378 63.158 10.93 0.00 44.23 4.70
48 49 0.037447 AAGGAAGTTGCCCAGAGCTC 59.963 55.000 5.27 5.27 44.23 4.09
49 50 0.480252 AAAGGAAGTTGCCCAGAGCT 59.520 50.000 0.00 0.00 44.23 4.09
50 51 2.200373 TAAAGGAAGTTGCCCAGAGC 57.800 50.000 0.00 0.00 44.14 4.09
51 52 3.441572 CACATAAAGGAAGTTGCCCAGAG 59.558 47.826 0.00 0.00 0.00 3.35
52 53 3.073798 TCACATAAAGGAAGTTGCCCAGA 59.926 43.478 0.00 0.00 0.00 3.86
53 54 3.420893 TCACATAAAGGAAGTTGCCCAG 58.579 45.455 0.00 0.00 0.00 4.45
54 55 3.517296 TCACATAAAGGAAGTTGCCCA 57.483 42.857 0.00 0.00 0.00 5.36
55 56 4.864704 TTTCACATAAAGGAAGTTGCCC 57.135 40.909 0.00 0.00 0.00 5.36
56 57 4.988540 GGTTTTCACATAAAGGAAGTTGCC 59.011 41.667 0.00 0.00 0.00 4.52
57 58 5.596845 TGGTTTTCACATAAAGGAAGTTGC 58.403 37.500 0.00 0.00 0.00 4.17
58 59 6.478673 GGTTGGTTTTCACATAAAGGAAGTTG 59.521 38.462 0.00 0.00 0.00 3.16
59 60 6.382859 AGGTTGGTTTTCACATAAAGGAAGTT 59.617 34.615 0.00 0.00 0.00 2.66
60 61 5.897250 AGGTTGGTTTTCACATAAAGGAAGT 59.103 36.000 0.00 0.00 0.00 3.01
61 62 6.405278 AGGTTGGTTTTCACATAAAGGAAG 57.595 37.500 0.00 0.00 0.00 3.46
62 63 7.470841 GCTTAGGTTGGTTTTCACATAAAGGAA 60.471 37.037 0.00 0.00 0.00 3.36
63 64 6.015772 GCTTAGGTTGGTTTTCACATAAAGGA 60.016 38.462 0.00 0.00 0.00 3.36
64 65 6.156519 GCTTAGGTTGGTTTTCACATAAAGG 58.843 40.000 0.00 0.00 0.00 3.11
65 66 6.640907 GTGCTTAGGTTGGTTTTCACATAAAG 59.359 38.462 0.00 0.00 0.00 1.85
66 67 6.096987 TGTGCTTAGGTTGGTTTTCACATAAA 59.903 34.615 0.00 0.00 0.00 1.40
67 68 5.594725 TGTGCTTAGGTTGGTTTTCACATAA 59.405 36.000 0.00 0.00 0.00 1.90
68 69 5.133941 TGTGCTTAGGTTGGTTTTCACATA 58.866 37.500 0.00 0.00 0.00 2.29
69 70 3.957497 TGTGCTTAGGTTGGTTTTCACAT 59.043 39.130 0.00 0.00 0.00 3.21
70 71 3.357203 TGTGCTTAGGTTGGTTTTCACA 58.643 40.909 0.00 0.00 0.00 3.58
71 72 4.379339 TTGTGCTTAGGTTGGTTTTCAC 57.621 40.909 0.00 0.00 0.00 3.18
72 73 5.606348 ATTTGTGCTTAGGTTGGTTTTCA 57.394 34.783 0.00 0.00 0.00 2.69
73 74 6.918892 AAATTTGTGCTTAGGTTGGTTTTC 57.081 33.333 0.00 0.00 0.00 2.29
74 75 6.404184 GCAAAATTTGTGCTTAGGTTGGTTTT 60.404 34.615 7.60 0.00 39.00 2.43
75 76 5.065859 GCAAAATTTGTGCTTAGGTTGGTTT 59.934 36.000 7.60 0.00 39.00 3.27
76 77 4.574421 GCAAAATTTGTGCTTAGGTTGGTT 59.426 37.500 7.60 0.00 39.00 3.67
77 78 4.126437 GCAAAATTTGTGCTTAGGTTGGT 58.874 39.130 7.60 0.00 39.00 3.67
78 79 4.125703 TGCAAAATTTGTGCTTAGGTTGG 58.874 39.130 12.62 0.00 42.69 3.77
79 80 4.211794 CCTGCAAAATTTGTGCTTAGGTTG 59.788 41.667 12.62 2.16 42.69 3.77
80 81 4.379652 CCTGCAAAATTTGTGCTTAGGTT 58.620 39.130 12.62 0.00 42.69 3.50
81 82 3.803368 GCCTGCAAAATTTGTGCTTAGGT 60.803 43.478 15.69 0.00 42.69 3.08
82 83 2.738314 GCCTGCAAAATTTGTGCTTAGG 59.262 45.455 12.62 12.16 42.69 2.69
83 84 2.409378 CGCCTGCAAAATTTGTGCTTAG 59.591 45.455 12.62 2.95 42.69 2.18
84 85 2.035193 TCGCCTGCAAAATTTGTGCTTA 59.965 40.909 12.62 0.00 42.69 3.09
85 86 1.202510 TCGCCTGCAAAATTTGTGCTT 60.203 42.857 12.62 0.00 42.69 3.91
86 87 0.388659 TCGCCTGCAAAATTTGTGCT 59.611 45.000 12.62 0.00 42.69 4.40
87 88 1.431496 ATCGCCTGCAAAATTTGTGC 58.569 45.000 7.60 4.51 42.55 4.57
88 89 3.248125 ACAAATCGCCTGCAAAATTTGTG 59.752 39.130 19.34 1.31 45.62 3.33
89 90 3.465871 ACAAATCGCCTGCAAAATTTGT 58.534 36.364 16.47 16.47 43.73 2.83
90 91 5.588568 TTACAAATCGCCTGCAAAATTTG 57.411 34.783 15.58 15.58 42.20 2.32
91 92 6.610741 TTTTACAAATCGCCTGCAAAATTT 57.389 29.167 0.00 0.00 0.00 1.82
92 93 6.481644 TCTTTTTACAAATCGCCTGCAAAATT 59.518 30.769 0.00 0.00 0.00 1.82
93 94 5.988561 TCTTTTTACAAATCGCCTGCAAAAT 59.011 32.000 0.00 0.00 0.00 1.82
94 95 5.352284 TCTTTTTACAAATCGCCTGCAAAA 58.648 33.333 0.00 0.00 0.00 2.44
95 96 4.938080 TCTTTTTACAAATCGCCTGCAAA 58.062 34.783 0.00 0.00 0.00 3.68
96 97 4.576216 TCTTTTTACAAATCGCCTGCAA 57.424 36.364 0.00 0.00 0.00 4.08
97 98 4.576216 TTCTTTTTACAAATCGCCTGCA 57.424 36.364 0.00 0.00 0.00 4.41
98 99 4.742659 TGTTTCTTTTTACAAATCGCCTGC 59.257 37.500 0.00 0.00 0.00 4.85
99 100 6.420604 ACATGTTTCTTTTTACAAATCGCCTG 59.579 34.615 0.00 0.00 0.00 4.85
100 101 6.420604 CACATGTTTCTTTTTACAAATCGCCT 59.579 34.615 0.00 0.00 0.00 5.52
101 102 6.200097 ACACATGTTTCTTTTTACAAATCGCC 59.800 34.615 0.00 0.00 0.00 5.54
102 103 7.160633 ACACATGTTTCTTTTTACAAATCGC 57.839 32.000 0.00 0.00 0.00 4.58
103 104 8.591312 ACAACACATGTTTCTTTTTACAAATCG 58.409 29.630 0.00 0.00 40.06 3.34
119 120 4.454728 AAACAAGCTCAACAACACATGT 57.545 36.364 0.00 0.00 46.82 3.21
120 121 5.220453 GGAAAAACAAGCTCAACAACACATG 60.220 40.000 0.00 0.00 0.00 3.21
121 122 4.869861 GGAAAAACAAGCTCAACAACACAT 59.130 37.500 0.00 0.00 0.00 3.21
122 123 4.241681 GGAAAAACAAGCTCAACAACACA 58.758 39.130 0.00 0.00 0.00 3.72
123 124 4.241681 TGGAAAAACAAGCTCAACAACAC 58.758 39.130 0.00 0.00 0.00 3.32
124 125 4.527509 TGGAAAAACAAGCTCAACAACA 57.472 36.364 0.00 0.00 0.00 3.33
125 126 4.260334 GCATGGAAAAACAAGCTCAACAAC 60.260 41.667 0.00 0.00 32.72 3.32
126 127 3.870419 GCATGGAAAAACAAGCTCAACAA 59.130 39.130 0.00 0.00 32.72 2.83
127 128 3.456280 GCATGGAAAAACAAGCTCAACA 58.544 40.909 0.00 0.00 32.72 3.33
128 129 2.472488 CGCATGGAAAAACAAGCTCAAC 59.528 45.455 0.00 0.00 33.25 3.18
129 130 2.360483 TCGCATGGAAAAACAAGCTCAA 59.640 40.909 0.00 0.00 33.25 3.02
130 131 1.952990 TCGCATGGAAAAACAAGCTCA 59.047 42.857 0.00 0.00 33.25 4.26
131 132 2.589014 CTCGCATGGAAAAACAAGCTC 58.411 47.619 0.00 0.00 33.25 4.09
132 133 1.270550 CCTCGCATGGAAAAACAAGCT 59.729 47.619 0.00 0.00 33.25 3.74
133 134 1.269448 TCCTCGCATGGAAAAACAAGC 59.731 47.619 0.00 0.00 32.39 4.01
134 135 2.669391 GCTCCTCGCATGGAAAAACAAG 60.669 50.000 0.00 0.00 38.92 3.16
135 136 1.269448 GCTCCTCGCATGGAAAAACAA 59.731 47.619 0.00 0.00 38.92 2.83
136 137 0.881118 GCTCCTCGCATGGAAAAACA 59.119 50.000 0.00 0.00 38.92 2.83
137 138 1.168714 AGCTCCTCGCATGGAAAAAC 58.831 50.000 0.00 0.00 42.61 2.43
138 139 1.909700 AAGCTCCTCGCATGGAAAAA 58.090 45.000 0.00 0.00 42.61 1.94
139 140 2.632377 CTAAGCTCCTCGCATGGAAAA 58.368 47.619 0.00 0.00 42.61 2.29
140 141 1.743772 GCTAAGCTCCTCGCATGGAAA 60.744 52.381 0.00 0.00 42.61 3.13
141 142 0.179073 GCTAAGCTCCTCGCATGGAA 60.179 55.000 0.00 0.00 42.61 3.53
142 143 1.443407 GCTAAGCTCCTCGCATGGA 59.557 57.895 0.00 0.00 42.61 3.41
143 144 1.596477 GGCTAAGCTCCTCGCATGG 60.596 63.158 0.00 0.00 42.61 3.66
144 145 0.676184 TAGGCTAAGCTCCTCGCATG 59.324 55.000 0.00 0.00 42.61 4.06
145 146 0.965439 CTAGGCTAAGCTCCTCGCAT 59.035 55.000 0.00 0.00 42.61 4.73
146 147 0.106669 TCTAGGCTAAGCTCCTCGCA 60.107 55.000 0.00 0.00 42.61 5.10
147 148 0.596082 CTCTAGGCTAAGCTCCTCGC 59.404 60.000 0.00 0.00 35.21 5.03
148 149 0.596082 GCTCTAGGCTAAGCTCCTCG 59.404 60.000 16.44 0.00 38.06 4.63
149 150 0.596082 CGCTCTAGGCTAAGCTCCTC 59.404 60.000 19.36 0.00 39.13 3.71
150 151 1.460273 GCGCTCTAGGCTAAGCTCCT 61.460 60.000 19.36 0.00 39.13 3.69
151 152 1.006688 GCGCTCTAGGCTAAGCTCC 60.007 63.158 19.36 11.01 39.13 4.70
152 153 0.316841 ATGCGCTCTAGGCTAAGCTC 59.683 55.000 9.73 14.83 39.13 4.09
153 154 0.033228 CATGCGCTCTAGGCTAAGCT 59.967 55.000 9.73 0.00 39.13 3.74
154 155 1.564295 GCATGCGCTCTAGGCTAAGC 61.564 60.000 9.73 14.71 39.13 3.09
155 156 1.280886 CGCATGCGCTCTAGGCTAAG 61.281 60.000 29.09 0.00 39.13 2.18
156 157 1.300156 CGCATGCGCTCTAGGCTAA 60.300 57.895 29.09 0.00 39.13 3.09
157 158 2.336448 CGCATGCGCTCTAGGCTA 59.664 61.111 29.09 0.00 39.13 3.93
158 159 4.598894 CCGCATGCGCTCTAGGCT 62.599 66.667 34.00 0.00 39.13 4.58
177 178 4.477975 GTCTCGACTGGCCGACCG 62.478 72.222 0.00 0.49 39.70 4.79
178 179 2.430382 TTTGTCTCGACTGGCCGACC 62.430 60.000 0.00 0.00 34.56 4.79
179 180 0.389948 ATTTGTCTCGACTGGCCGAC 60.390 55.000 0.00 0.00 34.56 4.79
185 186 1.879380 TGCCCAAATTTGTCTCGACTG 59.121 47.619 16.73 0.00 0.00 3.51
189 190 1.001815 ACGTTGCCCAAATTTGTCTCG 60.002 47.619 16.73 14.44 0.00 4.04
223 228 1.743394 CTTGTCCCATTTCGGCCTAAC 59.257 52.381 0.00 0.00 0.00 2.34
264 269 3.437795 CCGGGACAGCGTAGTCGT 61.438 66.667 0.00 0.00 39.42 4.34
279 286 0.179119 GTGGTCGTCTATTGGTCCCG 60.179 60.000 0.00 0.00 0.00 5.14
282 289 0.529378 ACCGTGGTCGTCTATTGGTC 59.471 55.000 0.00 0.00 35.01 4.02
283 290 0.529378 GACCGTGGTCGTCTATTGGT 59.471 55.000 2.78 0.00 35.30 3.67
285 292 0.179119 GGGACCGTGGTCGTCTATTG 60.179 60.000 12.65 0.00 45.41 1.90
286 293 0.612732 TGGGACCGTGGTCGTCTATT 60.613 55.000 12.65 0.00 45.41 1.73
287 294 1.000521 TGGGACCGTGGTCGTCTAT 60.001 57.895 12.65 0.00 45.41 1.98
288 295 1.676635 CTGGGACCGTGGTCGTCTA 60.677 63.158 12.65 0.00 45.41 2.59
289 296 2.989824 CTGGGACCGTGGTCGTCT 60.990 66.667 12.65 0.00 45.41 4.18
290 297 4.065281 CCTGGGACCGTGGTCGTC 62.065 72.222 12.65 8.23 45.41 4.20
370 378 4.766088 CTTTGCTTGCGCCGCCTC 62.766 66.667 6.63 0.00 34.43 4.70
408 416 1.764854 GGAGAGGGGTGGCGGATTA 60.765 63.158 0.00 0.00 0.00 1.75
417 425 4.026357 GGTCAGGGGGAGAGGGGT 62.026 72.222 0.00 0.00 0.00 4.95
422 430 2.610859 GCCAAGGTCAGGGGGAGA 60.611 66.667 0.00 0.00 0.00 3.71
424 432 2.935481 CAGCCAAGGTCAGGGGGA 60.935 66.667 0.00 0.00 0.00 4.81
425 433 4.052518 CCAGCCAAGGTCAGGGGG 62.053 72.222 0.00 0.00 0.00 5.40
426 434 4.052518 CCCAGCCAAGGTCAGGGG 62.053 72.222 0.00 0.00 35.83 4.79
427 435 4.052518 CCCCAGCCAAGGTCAGGG 62.053 72.222 0.00 0.00 39.29 4.45
463 471 1.480219 GGTTCGGATTAGCGCTGACG 61.480 60.000 22.90 18.30 44.07 4.35
464 472 1.152383 GGGTTCGGATTAGCGCTGAC 61.152 60.000 22.90 10.93 0.00 3.51
465 473 1.143183 GGGTTCGGATTAGCGCTGA 59.857 57.895 22.90 13.69 0.00 4.26
466 474 1.887707 GGGGTTCGGATTAGCGCTG 60.888 63.158 22.90 1.96 0.00 5.18
467 475 1.906105 TTGGGGTTCGGATTAGCGCT 61.906 55.000 17.26 17.26 0.00 5.92
468 476 1.027792 TTTGGGGTTCGGATTAGCGC 61.028 55.000 0.00 0.00 0.00 5.92
469 477 0.730840 GTTTGGGGTTCGGATTAGCG 59.269 55.000 0.00 0.00 0.00 4.26
470 478 1.100510 GGTTTGGGGTTCGGATTAGC 58.899 55.000 0.00 0.00 0.00 3.09
471 479 1.004979 TGGGTTTGGGGTTCGGATTAG 59.995 52.381 0.00 0.00 0.00 1.73
472 480 1.073931 TGGGTTTGGGGTTCGGATTA 58.926 50.000 0.00 0.00 0.00 1.75
473 481 0.188834 TTGGGTTTGGGGTTCGGATT 59.811 50.000 0.00 0.00 0.00 3.01
474 482 0.188834 TTTGGGTTTGGGGTTCGGAT 59.811 50.000 0.00 0.00 0.00 4.18
475 483 0.756070 GTTTGGGTTTGGGGTTCGGA 60.756 55.000 0.00 0.00 0.00 4.55
476 484 1.743391 GTTTGGGTTTGGGGTTCGG 59.257 57.895 0.00 0.00 0.00 4.30
477 485 0.757561 AGGTTTGGGTTTGGGGTTCG 60.758 55.000 0.00 0.00 0.00 3.95
478 486 1.045407 GAGGTTTGGGTTTGGGGTTC 58.955 55.000 0.00 0.00 0.00 3.62
479 487 0.757561 CGAGGTTTGGGTTTGGGGTT 60.758 55.000 0.00 0.00 0.00 4.11
480 488 1.152631 CGAGGTTTGGGTTTGGGGT 60.153 57.895 0.00 0.00 0.00 4.95
481 489 1.152631 ACGAGGTTTGGGTTTGGGG 60.153 57.895 0.00 0.00 0.00 4.96
482 490 1.176619 GGACGAGGTTTGGGTTTGGG 61.177 60.000 0.00 0.00 0.00 4.12
485 493 1.228033 CCGGACGAGGTTTGGGTTT 60.228 57.895 0.00 0.00 0.00 3.27
487 495 3.633116 CCCGGACGAGGTTTGGGT 61.633 66.667 0.73 0.00 35.05 4.51
496 504 0.381801 GTAATTACTCGCCCGGACGA 59.618 55.000 13.61 13.61 40.36 4.20
500 512 1.070275 GGGGTAATTACTCGCCCGG 59.930 63.158 15.05 0.00 41.95 5.73
506 518 0.249615 GTCGGCGGGGGTAATTACTC 60.250 60.000 15.05 11.30 0.00 2.59
669 695 0.454452 GACGAGATTTTTGCCCGTGC 60.454 55.000 0.00 0.00 33.32 5.34
705 731 6.768381 TCTTCTTCTTCTTCTTCCTTTGTTCC 59.232 38.462 0.00 0.00 0.00 3.62
746 773 0.884514 GTGGAAGAAAAGCAGGGAGC 59.115 55.000 0.00 0.00 46.19 4.70
751 877 1.207593 CGCGGTGGAAGAAAAGCAG 59.792 57.895 0.00 0.00 0.00 4.24
755 881 2.887889 CGCACGCGGTGGAAGAAAA 61.888 57.895 12.47 0.00 33.64 2.29
776 902 1.153469 CGGCAGAGGAGAGGAAAGC 60.153 63.158 0.00 0.00 0.00 3.51
787 913 4.477975 GACGGACGGACGGCAGAG 62.478 72.222 4.41 0.00 42.70 3.35
794 920 4.112341 CAGGGTCGACGGACGGAC 62.112 72.222 9.92 0.00 44.39 4.79
838 965 1.203364 AGGAAGGAAGGAAGGCAGAGA 60.203 52.381 0.00 0.00 0.00 3.10
843 992 0.995803 AGGAAGGAAGGAAGGAAGGC 59.004 55.000 0.00 0.00 0.00 4.35
907 1056 2.294512 GGAATTCTCCAATCAATCCGGC 59.705 50.000 5.23 0.00 41.96 6.13
921 1074 1.286257 GGGAAGGCAGGAAGGAATTCT 59.714 52.381 5.23 0.00 0.00 2.40
928 1081 0.914644 TCAGATGGGAAGGCAGGAAG 59.085 55.000 0.00 0.00 0.00 3.46
929 1082 0.914644 CTCAGATGGGAAGGCAGGAA 59.085 55.000 0.00 0.00 0.00 3.36
931 1084 1.530771 CCTCAGATGGGAAGGCAGG 59.469 63.158 0.00 0.00 0.00 4.85
978 1142 2.123897 AATCCCCCAAATCCGGCG 60.124 61.111 0.00 0.00 0.00 6.46
979 1143 1.832608 GGAATCCCCCAAATCCGGC 60.833 63.158 0.00 0.00 0.00 6.13
980 1144 4.599036 GGAATCCCCCAAATCCGG 57.401 61.111 0.00 0.00 0.00 5.14
989 1178 2.069165 CTTCCCCATCCGGAATCCCC 62.069 65.000 9.01 0.00 41.12 4.81
1125 1329 0.378257 CCATCTCCGCGAAAATGGTG 59.622 55.000 8.23 0.00 35.08 4.17
1368 1572 1.362406 GCAGCGCCTTGGAGTACTTC 61.362 60.000 2.29 0.00 0.00 3.01
1818 2022 1.151668 CAAGAACAGCCTTGAGTCCG 58.848 55.000 0.00 0.00 44.66 4.79
1956 2160 0.394192 CATAAGGCTCATGCTCCGGA 59.606 55.000 2.93 2.93 39.59 5.14
2109 2313 0.661020 CGTGGTTCTTGAAAAGGCGT 59.339 50.000 0.00 0.00 46.24 5.68
2187 2391 2.470983 TCGTGTCTTCAATGGCATCA 57.529 45.000 0.00 0.00 0.00 3.07
2241 2445 1.741770 CTGAAAGTTCCCCTCCGCG 60.742 63.158 0.00 0.00 0.00 6.46
2244 2448 1.657804 TCTCCTGAAAGTTCCCCTCC 58.342 55.000 0.00 0.00 0.00 4.30
2256 2460 2.663075 AAGCGCTGCCATCTCCTGA 61.663 57.895 12.58 0.00 0.00 3.86
2310 2514 0.325110 AGAGCAGCCTCTTCCTAGCA 60.325 55.000 0.00 0.00 46.16 3.49
2775 2979 3.144506 CTCATAAAGCAGCATACCCCAG 58.855 50.000 0.00 0.00 0.00 4.45
2921 3125 2.036217 TCTTGGGCAGTTTCATTTGCAG 59.964 45.455 0.00 0.00 42.02 4.41
2956 3160 8.352942 AGAACATGGTGAACTAGAACAAAAATC 58.647 33.333 0.00 0.00 0.00 2.17
2959 3163 7.639113 AAGAACATGGTGAACTAGAACAAAA 57.361 32.000 0.00 0.00 0.00 2.44
3115 3328 2.226674 GAGGACCACAGCTAGCAAAAAC 59.773 50.000 18.83 3.52 0.00 2.43
3127 3340 5.560722 TTAAAGTGATCAAGAGGACCACA 57.439 39.130 0.00 0.00 0.00 4.17
3460 3677 8.907885 GGAAGCAAACAGGATATTCTTAGAAAT 58.092 33.333 0.00 0.00 0.00 2.17
3658 3875 4.341806 CAGTGCCCCAGAATTTAATATGCA 59.658 41.667 0.00 0.00 0.00 3.96
3659 3876 4.342092 ACAGTGCCCCAGAATTTAATATGC 59.658 41.667 0.00 0.00 0.00 3.14
3974 4193 1.949525 CCAAAAGGCATCTATGGACCG 59.050 52.381 0.00 0.00 34.05 4.79
3998 4217 3.244561 TGAGAGAGACGAAGGGCATTTTT 60.245 43.478 0.00 0.00 0.00 1.94
4220 4439 8.569641 AGTATCTCCATTAAAAGCTACTCTACG 58.430 37.037 0.00 0.00 0.00 3.51
4224 4443 8.639761 TGGTAGTATCTCCATTAAAAGCTACTC 58.360 37.037 0.00 0.00 29.79 2.59
4253 4472 8.459635 CCATGCAAAGATCTATTATCTTCATGG 58.540 37.037 21.65 21.65 44.63 3.66
4334 4553 0.987294 ATTGTGGGACAGAGGGAGTG 59.013 55.000 0.00 0.00 41.80 3.51
4454 4674 8.633561 CAGGAAGAGTTTATTTCAAAGTCCTTT 58.366 33.333 0.00 0.00 31.61 3.11
4554 4778 6.013206 TGCCCAAGGAACTAAGTTTATGTCTA 60.013 38.462 0.00 0.00 38.49 2.59


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

AutoCloner maintained by Alex Coulton.