Multiple sequence alignment - TraesCS4A01G227000

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 TraesCS4A01G227000 chr4A 100.000 5628 0 0 1 5628 535249317 535243690 0.000000e+00 10394.0
1 TraesCS4A01G227000 chr4A 92.683 41 3 0 770 810 444429062 444429022 6.090000e-05 60.2
2 TraesCS4A01G227000 chr4D 95.780 3460 118 20 2186 5628 61961062 61957614 0.000000e+00 5555.0
3 TraesCS4A01G227000 chr4D 93.453 947 37 9 810 1743 61971248 61970314 0.000000e+00 1382.0
4 TraesCS4A01G227000 chr4D 92.308 494 34 4 190 679 61972012 61971519 0.000000e+00 699.0
5 TraesCS4A01G227000 chr4D 91.257 366 20 4 1738 2103 61961621 61961268 6.550000e-134 488.0
6 TraesCS4A01G227000 chr4D 94.186 172 8 2 32 202 61985375 61985205 1.560000e-65 261.0
7 TraesCS4A01G227000 chr4D 94.382 89 5 0 2100 2188 61961188 61961100 2.730000e-28 137.0
8 TraesCS4A01G227000 chr4D 93.023 43 2 1 769 810 124929844 124929886 1.690000e-05 62.1
9 TraesCS4A01G227000 chr4D 90.698 43 3 1 769 810 319742571 319742613 7.880000e-04 56.5
10 TraesCS4A01G227000 chr4B 94.127 1941 78 22 2323 4255 90721808 90723720 0.000000e+00 2920.0
11 TraesCS4A01G227000 chr4B 95.204 1397 48 6 4238 5628 90726537 90727920 0.000000e+00 2191.0
12 TraesCS4A01G227000 chr4B 93.391 1392 51 23 751 2122 90720051 90721421 0.000000e+00 2023.0
13 TraesCS4A01G227000 chr4B 88.442 398 40 6 357 751 90719574 90719968 5.100000e-130 475.0
14 TraesCS4A01G227000 chr4B 98.701 77 1 0 2248 2324 90721573 90721649 2.730000e-28 137.0
15 TraesCS4A01G227000 chr4B 95.312 64 3 0 2186 2249 90721426 90721489 9.980000e-18 102.0
16 TraesCS4A01G227000 chr6D 95.122 41 2 0 770 810 100426021 100425981 1.310000e-06 65.8
17 TraesCS4A01G227000 chr2A 93.182 44 3 0 765 808 367157514 367157557 1.310000e-06 65.8
18 TraesCS4A01G227000 chr1B 95.122 41 2 0 770 810 228197471 228197511 1.310000e-06 65.8
19 TraesCS4A01G227000 chr7B 100.000 33 0 0 778 810 554736774 554736742 1.690000e-05 62.1
20 TraesCS4A01G227000 chr5B 92.683 41 3 0 770 810 198177084 198177124 6.090000e-05 60.2


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 TraesCS4A01G227000 chr4A 535243690 535249317 5627 True 10394.0 10394 100.000000 1 5628 1 chr4A.!!$R2 5627
1 TraesCS4A01G227000 chr4D 61957614 61961621 4007 True 2060.0 5555 93.806333 1738 5628 3 chr4D.!!$R2 3890
2 TraesCS4A01G227000 chr4D 61970314 61972012 1698 True 1040.5 1382 92.880500 190 1743 2 chr4D.!!$R3 1553
3 TraesCS4A01G227000 chr4B 90719574 90727920 8346 False 1308.0 2920 94.196167 357 5628 6 chr4B.!!$F1 5271

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
159 160 0.403271 ATGGAGCTTGGTGAAGTGCT 59.597 50.000 0.00 0.00 38.59 4.40 F
672 679 1.024579 GCCCCGTAGTGTGTGGATTG 61.025 60.000 0.00 0.00 0.00 2.67 F
1248 1520 2.100631 CGTTACCCTGCGCTCTTGG 61.101 63.158 9.73 6.23 0.00 3.61 F
2500 3145 1.439143 GGAATCTCCTCCCTCCCCTAT 59.561 57.143 0.00 0.00 32.53 2.57 F
3151 3801 2.554344 GCAGTTTGACTGGAATACCCCA 60.554 50.000 9.85 0.00 46.01 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1215 1487 0.034337 TAACGCGGAAACAAGGAGCT 59.966 50.000 12.47 0.0 0.00 4.09 R
1765 2040 1.768275 TCTCAGAGTTCAAGTGGCCAA 59.232 47.619 7.24 0.0 0.00 4.52 R
2913 3558 2.564947 TGTTTGTTTCAAGCCAGTTGGT 59.435 40.909 0.00 0.0 36.71 3.67 R
3708 4362 1.130561 GCCTTTCGGGATCGTTTTCAG 59.869 52.381 0.00 0.0 37.23 3.02 R
4942 8440 2.122989 ACACACACCCCCGAGAGT 60.123 61.111 0.00 0.0 0.00 3.24 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
28 29 6.826893 AATGTTTTTCTGGTTGATTGTTCG 57.173 33.333 0.00 0.00 0.00 3.95
29 30 5.317733 TGTTTTTCTGGTTGATTGTTCGT 57.682 34.783 0.00 0.00 0.00 3.85
30 31 6.438259 TGTTTTTCTGGTTGATTGTTCGTA 57.562 33.333 0.00 0.00 0.00 3.43
31 32 6.853720 TGTTTTTCTGGTTGATTGTTCGTAA 58.146 32.000 0.00 0.00 0.00 3.18
32 33 7.313646 TGTTTTTCTGGTTGATTGTTCGTAAA 58.686 30.769 0.00 0.00 0.00 2.01
33 34 7.813148 TGTTTTTCTGGTTGATTGTTCGTAAAA 59.187 29.630 0.00 0.00 0.00 1.52
34 35 7.979115 TTTTCTGGTTGATTGTTCGTAAAAG 57.021 32.000 0.00 0.00 0.00 2.27
35 36 6.928979 TTCTGGTTGATTGTTCGTAAAAGA 57.071 33.333 0.00 0.00 0.00 2.52
36 37 6.295039 TCTGGTTGATTGTTCGTAAAAGAC 57.705 37.500 0.00 0.00 0.00 3.01
37 38 5.818336 TCTGGTTGATTGTTCGTAAAAGACA 59.182 36.000 0.00 0.00 0.00 3.41
38 39 6.018262 TCTGGTTGATTGTTCGTAAAAGACAG 60.018 38.462 0.00 0.00 0.00 3.51
39 40 5.587043 TGGTTGATTGTTCGTAAAAGACAGT 59.413 36.000 0.00 0.00 0.00 3.55
40 41 6.094325 TGGTTGATTGTTCGTAAAAGACAGTT 59.906 34.615 0.00 0.00 0.00 3.16
41 42 6.970613 GGTTGATTGTTCGTAAAAGACAGTTT 59.029 34.615 0.00 0.00 0.00 2.66
42 43 8.124199 GGTTGATTGTTCGTAAAAGACAGTTTA 58.876 33.333 0.00 0.00 0.00 2.01
43 44 9.493206 GTTGATTGTTCGTAAAAGACAGTTTAA 57.507 29.630 0.00 0.00 0.00 1.52
45 46 9.872757 TGATTGTTCGTAAAAGACAGTTTAATC 57.127 29.630 0.00 0.00 0.00 1.75
46 47 9.872757 GATTGTTCGTAAAAGACAGTTTAATCA 57.127 29.630 0.00 0.00 0.00 2.57
52 53 9.724839 TCGTAAAAGACAGTTTAATCAAAAAGG 57.275 29.630 0.00 0.00 0.00 3.11
53 54 8.964150 CGTAAAAGACAGTTTAATCAAAAAGGG 58.036 33.333 0.00 0.00 0.00 3.95
54 55 9.256477 GTAAAAGACAGTTTAATCAAAAAGGGG 57.744 33.333 0.00 0.00 0.00 4.79
55 56 7.432148 AAAGACAGTTTAATCAAAAAGGGGT 57.568 32.000 0.00 0.00 0.00 4.95
56 57 6.405278 AGACAGTTTAATCAAAAAGGGGTG 57.595 37.500 0.00 0.00 0.00 4.61
57 58 5.304357 AGACAGTTTAATCAAAAAGGGGTGG 59.696 40.000 0.00 0.00 0.00 4.61
58 59 5.212745 ACAGTTTAATCAAAAAGGGGTGGA 58.787 37.500 0.00 0.00 0.00 4.02
59 60 5.663556 ACAGTTTAATCAAAAAGGGGTGGAA 59.336 36.000 0.00 0.00 0.00 3.53
60 61 6.157123 ACAGTTTAATCAAAAAGGGGTGGAAA 59.843 34.615 0.00 0.00 0.00 3.13
61 62 6.705825 CAGTTTAATCAAAAAGGGGTGGAAAG 59.294 38.462 0.00 0.00 0.00 2.62
62 63 3.769739 AATCAAAAAGGGGTGGAAAGC 57.230 42.857 0.00 0.00 0.00 3.51
63 64 2.166907 TCAAAAAGGGGTGGAAAGCA 57.833 45.000 0.00 0.00 0.00 3.91
64 65 2.472029 TCAAAAAGGGGTGGAAAGCAA 58.528 42.857 0.00 0.00 0.00 3.91
65 66 2.840651 TCAAAAAGGGGTGGAAAGCAAA 59.159 40.909 0.00 0.00 0.00 3.68
66 67 3.264450 TCAAAAAGGGGTGGAAAGCAAAA 59.736 39.130 0.00 0.00 0.00 2.44
67 68 4.013050 CAAAAAGGGGTGGAAAGCAAAAA 58.987 39.130 0.00 0.00 0.00 1.94
91 92 4.945246 GAGTGTGTTTACTCTGGACAAGA 58.055 43.478 0.00 0.00 42.93 3.02
92 93 5.542779 GAGTGTGTTTACTCTGGACAAGAT 58.457 41.667 0.00 0.00 42.93 2.40
93 94 5.300752 AGTGTGTTTACTCTGGACAAGATG 58.699 41.667 0.00 0.00 33.29 2.90
94 95 5.070446 AGTGTGTTTACTCTGGACAAGATGA 59.930 40.000 0.00 0.00 33.29 2.92
95 96 5.758296 GTGTGTTTACTCTGGACAAGATGAA 59.242 40.000 0.00 0.00 33.29 2.57
96 97 6.260050 GTGTGTTTACTCTGGACAAGATGAAA 59.740 38.462 0.00 0.00 33.29 2.69
97 98 6.483307 TGTGTTTACTCTGGACAAGATGAAAG 59.517 38.462 0.00 0.00 33.29 2.62
98 99 6.483640 GTGTTTACTCTGGACAAGATGAAAGT 59.516 38.462 0.00 0.00 33.29 2.66
99 100 7.656137 GTGTTTACTCTGGACAAGATGAAAGTA 59.344 37.037 0.00 0.00 33.29 2.24
100 101 8.375506 TGTTTACTCTGGACAAGATGAAAGTAT 58.624 33.333 0.00 0.00 33.29 2.12
101 102 9.871238 GTTTACTCTGGACAAGATGAAAGTATA 57.129 33.333 0.00 0.00 33.29 1.47
103 104 7.962995 ACTCTGGACAAGATGAAAGTATAGA 57.037 36.000 0.00 0.00 33.29 1.98
104 105 8.546083 ACTCTGGACAAGATGAAAGTATAGAT 57.454 34.615 0.00 0.00 33.29 1.98
105 106 8.637986 ACTCTGGACAAGATGAAAGTATAGATC 58.362 37.037 0.00 0.00 33.29 2.75
106 107 8.539117 TCTGGACAAGATGAAAGTATAGATCA 57.461 34.615 0.00 0.00 0.00 2.92
107 108 8.417106 TCTGGACAAGATGAAAGTATAGATCAC 58.583 37.037 0.00 0.00 0.00 3.06
108 109 7.500992 TGGACAAGATGAAAGTATAGATCACC 58.499 38.462 0.00 0.00 0.00 4.02
109 110 7.345653 TGGACAAGATGAAAGTATAGATCACCT 59.654 37.037 0.00 0.00 0.00 4.00
110 111 7.655328 GGACAAGATGAAAGTATAGATCACCTG 59.345 40.741 0.00 0.00 0.00 4.00
111 112 8.083828 ACAAGATGAAAGTATAGATCACCTGT 57.916 34.615 0.00 0.00 0.00 4.00
112 113 8.543774 ACAAGATGAAAGTATAGATCACCTGTT 58.456 33.333 0.00 0.00 0.00 3.16
113 114 9.039870 CAAGATGAAAGTATAGATCACCTGTTC 57.960 37.037 0.00 0.00 0.00 3.18
114 115 8.546083 AGATGAAAGTATAGATCACCTGTTCT 57.454 34.615 0.00 0.00 0.00 3.01
115 116 8.986991 AGATGAAAGTATAGATCACCTGTTCTT 58.013 33.333 0.00 0.00 0.00 2.52
116 117 9.606631 GATGAAAGTATAGATCACCTGTTCTTT 57.393 33.333 0.00 0.00 36.71 2.52
125 126 9.965902 ATAGATCACCTGTTCTTTAATTGTTCT 57.034 29.630 0.00 0.00 0.00 3.01
126 127 8.103948 AGATCACCTGTTCTTTAATTGTTCTG 57.896 34.615 0.00 0.00 0.00 3.02
127 128 6.072112 TCACCTGTTCTTTAATTGTTCTGC 57.928 37.500 0.00 0.00 0.00 4.26
128 129 5.827797 TCACCTGTTCTTTAATTGTTCTGCT 59.172 36.000 0.00 0.00 0.00 4.24
129 130 6.995686 TCACCTGTTCTTTAATTGTTCTGCTA 59.004 34.615 0.00 0.00 0.00 3.49
130 131 7.041372 TCACCTGTTCTTTAATTGTTCTGCTAC 60.041 37.037 0.00 0.00 0.00 3.58
131 132 6.206829 ACCTGTTCTTTAATTGTTCTGCTACC 59.793 38.462 0.00 0.00 0.00 3.18
132 133 6.206634 CCTGTTCTTTAATTGTTCTGCTACCA 59.793 38.462 0.00 0.00 0.00 3.25
133 134 7.202016 TGTTCTTTAATTGTTCTGCTACCAG 57.798 36.000 0.00 0.00 40.54 4.00
134 135 6.206634 TGTTCTTTAATTGTTCTGCTACCAGG 59.793 38.462 0.00 0.00 39.61 4.45
135 136 4.700213 TCTTTAATTGTTCTGCTACCAGGC 59.300 41.667 0.00 0.00 39.61 4.85
136 137 2.887151 AATTGTTCTGCTACCAGGCT 57.113 45.000 0.00 0.00 39.61 4.58
137 138 2.887151 ATTGTTCTGCTACCAGGCTT 57.113 45.000 0.00 0.00 39.61 4.35
138 139 4.301072 AATTGTTCTGCTACCAGGCTTA 57.699 40.909 0.00 0.00 39.61 3.09
139 140 4.510167 ATTGTTCTGCTACCAGGCTTAT 57.490 40.909 0.00 0.00 39.61 1.73
140 141 5.630415 ATTGTTCTGCTACCAGGCTTATA 57.370 39.130 0.00 0.00 39.61 0.98
141 142 5.630415 TTGTTCTGCTACCAGGCTTATAT 57.370 39.130 0.00 0.00 39.61 0.86
142 143 4.960938 TGTTCTGCTACCAGGCTTATATG 58.039 43.478 0.00 0.00 39.61 1.78
143 144 4.202357 TGTTCTGCTACCAGGCTTATATGG 60.202 45.833 0.00 0.00 42.60 2.74
144 145 3.856900 TCTGCTACCAGGCTTATATGGA 58.143 45.455 0.00 0.00 39.02 3.41
145 146 3.834813 TCTGCTACCAGGCTTATATGGAG 59.165 47.826 0.00 0.00 39.02 3.86
146 147 2.303022 TGCTACCAGGCTTATATGGAGC 59.697 50.000 0.00 4.76 39.02 4.70
147 148 2.569404 GCTACCAGGCTTATATGGAGCT 59.431 50.000 11.29 0.00 39.02 4.09
148 149 3.008485 GCTACCAGGCTTATATGGAGCTT 59.992 47.826 11.29 3.11 39.02 3.74
149 150 3.498774 ACCAGGCTTATATGGAGCTTG 57.501 47.619 14.30 14.30 44.16 4.01
151 152 3.498774 CAGGCTTATATGGAGCTTGGT 57.501 47.619 13.74 0.00 41.79 3.67
152 153 3.144506 CAGGCTTATATGGAGCTTGGTG 58.855 50.000 13.74 4.88 41.79 4.17
153 154 3.048600 AGGCTTATATGGAGCTTGGTGA 58.951 45.455 11.29 0.00 40.01 4.02
154 155 3.459598 AGGCTTATATGGAGCTTGGTGAA 59.540 43.478 11.29 0.00 40.01 3.18
155 156 3.817647 GGCTTATATGGAGCTTGGTGAAG 59.182 47.826 11.29 0.00 40.01 3.02
156 157 4.455606 GCTTATATGGAGCTTGGTGAAGT 58.544 43.478 5.85 0.00 37.18 3.01
157 158 4.274459 GCTTATATGGAGCTTGGTGAAGTG 59.726 45.833 5.85 0.00 37.18 3.16
158 159 2.113860 TATGGAGCTTGGTGAAGTGC 57.886 50.000 0.00 0.00 0.00 4.40
159 160 0.403271 ATGGAGCTTGGTGAAGTGCT 59.597 50.000 0.00 0.00 38.59 4.40
161 162 3.621953 GAGCTTGGTGAAGTGCTCT 57.378 52.632 6.58 0.00 45.78 4.09
162 163 1.889545 GAGCTTGGTGAAGTGCTCTT 58.110 50.000 0.00 0.00 45.78 2.85
163 164 1.534595 GAGCTTGGTGAAGTGCTCTTG 59.465 52.381 5.61 0.00 45.78 3.02
164 165 1.133976 AGCTTGGTGAAGTGCTCTTGT 60.134 47.619 5.61 0.00 33.64 3.16
165 166 1.265365 GCTTGGTGAAGTGCTCTTGTC 59.735 52.381 5.61 0.00 33.64 3.18
166 167 2.564771 CTTGGTGAAGTGCTCTTGTCA 58.435 47.619 5.61 0.00 33.64 3.58
167 168 2.936919 TGGTGAAGTGCTCTTGTCAT 57.063 45.000 5.61 0.00 33.64 3.06
168 169 3.213206 TGGTGAAGTGCTCTTGTCATT 57.787 42.857 5.61 0.00 33.64 2.57
169 170 3.554934 TGGTGAAGTGCTCTTGTCATTT 58.445 40.909 5.61 0.00 33.64 2.32
170 171 3.316029 TGGTGAAGTGCTCTTGTCATTTG 59.684 43.478 5.61 0.00 33.64 2.32
171 172 3.304928 GGTGAAGTGCTCTTGTCATTTGG 60.305 47.826 5.61 0.00 33.64 3.28
172 173 2.886523 TGAAGTGCTCTTGTCATTTGGG 59.113 45.455 5.61 0.00 33.64 4.12
173 174 2.957402 AGTGCTCTTGTCATTTGGGA 57.043 45.000 0.00 0.00 0.00 4.37
174 175 3.446442 AGTGCTCTTGTCATTTGGGAT 57.554 42.857 0.00 0.00 0.00 3.85
175 176 3.350833 AGTGCTCTTGTCATTTGGGATC 58.649 45.455 0.00 0.00 0.00 3.36
176 177 3.084039 GTGCTCTTGTCATTTGGGATCA 58.916 45.455 0.00 0.00 0.00 2.92
177 178 3.128242 GTGCTCTTGTCATTTGGGATCAG 59.872 47.826 0.00 0.00 0.00 2.90
178 179 2.098770 GCTCTTGTCATTTGGGATCAGC 59.901 50.000 0.00 0.00 0.00 4.26
179 180 3.618351 CTCTTGTCATTTGGGATCAGCT 58.382 45.455 0.00 0.00 0.00 4.24
180 181 3.614092 TCTTGTCATTTGGGATCAGCTC 58.386 45.455 0.00 0.00 0.00 4.09
181 182 2.425143 TGTCATTTGGGATCAGCTCC 57.575 50.000 0.00 0.00 44.11 4.70
188 189 2.914289 GGATCAGCTCCCAGTGGG 59.086 66.667 23.57 23.57 46.11 4.61
213 215 4.341806 TGGATGATTGTTGAATGTATGGCC 59.658 41.667 0.00 0.00 0.00 5.36
214 216 4.341806 GGATGATTGTTGAATGTATGGCCA 59.658 41.667 8.56 8.56 0.00 5.36
231 233 5.109500 TGGCCAAAAACCTTTCAGAAATT 57.891 34.783 0.61 0.00 0.00 1.82
233 235 5.356470 TGGCCAAAAACCTTTCAGAAATTTG 59.644 36.000 0.61 10.77 0.00 2.32
236 238 7.362487 GGCCAAAAACCTTTCAGAAATTTGAAA 60.362 33.333 16.39 0.00 42.93 2.69
319 323 9.677567 GAATGCTATTGTCTTTAGAACAAAACA 57.322 29.630 0.00 0.00 0.00 2.83
399 403 8.593945 ATCTATTTTGCAGATAAAGAACCCAA 57.406 30.769 0.00 0.00 30.89 4.12
422 426 3.198635 AGCAAAAGCTACTGATGCTAGGA 59.801 43.478 9.13 0.00 44.92 2.94
444 448 2.096819 GCAAAAATAATCGAGCGGGTGA 59.903 45.455 0.00 0.00 0.00 4.02
461 465 4.570772 CGGGTGACAAATGAAATCTATCGT 59.429 41.667 0.00 0.00 0.00 3.73
476 480 4.700365 CGTGCGTCGCAGGACTGA 62.700 66.667 30.56 0.03 45.68 3.41
505 509 1.960689 GGTGCAAAGGCTGGAAAACTA 59.039 47.619 0.00 0.00 41.91 2.24
585 590 6.174720 ACCTGTGTATCTTGACTTCTTCAA 57.825 37.500 0.00 0.00 42.26 2.69
601 606 7.910304 ACTTCTTCAACGATTTATGTCTATGC 58.090 34.615 0.00 0.00 0.00 3.14
602 607 7.549134 ACTTCTTCAACGATTTATGTCTATGCA 59.451 33.333 0.00 0.00 0.00 3.96
603 608 8.437360 TTCTTCAACGATTTATGTCTATGCAT 57.563 30.769 3.79 3.79 0.00 3.96
604 609 9.541143 TTCTTCAACGATTTATGTCTATGCATA 57.459 29.630 6.20 6.20 0.00 3.14
672 679 1.024579 GCCCCGTAGTGTGTGGATTG 61.025 60.000 0.00 0.00 0.00 2.67
700 707 6.751157 TCTGTTATGTCGTCTAAACCTTTGA 58.249 36.000 0.00 0.00 0.00 2.69
705 712 5.728351 TGTCGTCTAAACCTTTGAACTTG 57.272 39.130 0.00 0.00 0.00 3.16
758 848 7.269522 TGGCCTGGATTTGTGATATATGATA 57.730 36.000 3.32 0.00 0.00 2.15
776 866 5.499139 TGATATCCTTTTGATGGTTTCGC 57.501 39.130 0.00 0.00 34.76 4.70
794 884 4.131649 TCGCTAATGAAATCGGAGGAAA 57.868 40.909 0.00 0.00 0.00 3.13
813 1073 7.821652 GAGGAAACCCTCTCTTTTGATAAAAG 58.178 38.462 7.53 7.53 45.36 2.27
925 1186 2.884639 CCCCTTTCAGTTCAACACGAAT 59.115 45.455 0.00 0.00 35.63 3.34
1019 1286 4.404098 GGGGGCGGCGAAGAGAAA 62.404 66.667 12.98 0.00 0.00 2.52
1198 1465 4.461198 CCTTCCTGTACAGTTCAACCTTT 58.539 43.478 21.18 0.00 0.00 3.11
1201 1468 5.617528 TCCTGTACAGTTCAACCTTTGTA 57.382 39.130 21.18 0.00 0.00 2.41
1202 1469 5.362263 TCCTGTACAGTTCAACCTTTGTAC 58.638 41.667 21.18 10.31 43.72 2.90
1204 1471 5.465724 CCTGTACAGTTCAACCTTTGTACTC 59.534 44.000 21.18 0.00 43.77 2.59
1205 1472 5.362263 TGTACAGTTCAACCTTTGTACTCC 58.638 41.667 15.73 0.00 43.77 3.85
1206 1473 4.772886 ACAGTTCAACCTTTGTACTCCT 57.227 40.909 0.00 0.00 38.94 3.69
1207 1474 5.112129 ACAGTTCAACCTTTGTACTCCTT 57.888 39.130 0.00 0.00 38.94 3.36
1210 1477 5.823045 CAGTTCAACCTTTGTACTCCTTTCT 59.177 40.000 0.00 0.00 38.94 2.52
1215 1487 5.382664 ACCTTTGTACTCCTTTCTTTCCA 57.617 39.130 0.00 0.00 0.00 3.53
1248 1520 2.100631 CGTTACCCTGCGCTCTTGG 61.101 63.158 9.73 6.23 0.00 3.61
1307 1580 2.383245 ATATCGCTTCCGTGCCCTGG 62.383 60.000 0.00 0.00 35.54 4.45
1382 1656 4.698304 GTCCTCCACGGTTCAAAATATTGA 59.302 41.667 0.00 0.00 43.70 2.57
1414 1688 7.148722 GCTAGTAGTTCTTGTTCAGATTGTGAC 60.149 40.741 0.00 0.00 33.71 3.67
1416 1690 7.275920 AGTAGTTCTTGTTCAGATTGTGACTT 58.724 34.615 0.00 0.00 33.71 3.01
1433 1707 7.624360 TGTGACTTGTTTTGAAGTTAGTCAT 57.376 32.000 0.00 0.00 42.51 3.06
1523 1797 4.408921 GGGAGGCATACATGTATATAGGCA 59.591 45.833 22.30 0.00 0.00 4.75
1524 1798 5.072329 GGGAGGCATACATGTATATAGGCAT 59.928 44.000 22.30 17.42 0.00 4.40
1584 1858 9.382275 ACAGATTGGGATAATTTTGTTTAATGC 57.618 29.630 0.00 0.00 0.00 3.56
1585 1859 8.542132 CAGATTGGGATAATTTTGTTTAATGCG 58.458 33.333 0.00 0.00 0.00 4.73
1638 1913 3.067461 GCAAGTGGTGTAACAACATTGGA 59.933 43.478 5.99 0.00 45.64 3.53
2153 2511 5.594317 GTGCCCCTATACAAATTGAGACAAT 59.406 40.000 0.00 0.00 0.00 2.71
2168 2526 5.928976 TGAGACAATGTTTCTTCTCTCCAA 58.071 37.500 5.52 0.00 36.29 3.53
2170 2528 6.260936 TGAGACAATGTTTCTTCTCTCCAAAC 59.739 38.462 5.52 0.00 36.29 2.93
2315 2798 6.118852 AGATCTATTCTTTTGCTCCCTTGTC 58.881 40.000 0.00 0.00 0.00 3.18
2373 3016 8.605746 GCTTGCATATTTATTTTCTTGCATTGA 58.394 29.630 0.00 0.00 39.56 2.57
2406 3050 4.079253 AGATGGCATACCGACAAGTTTTT 58.921 39.130 0.00 0.00 34.96 1.94
2500 3145 1.439143 GGAATCTCCTCCCTCCCCTAT 59.561 57.143 0.00 0.00 32.53 2.57
2510 3155 2.844348 TCCCTCCCCTATTGTTTGTCTC 59.156 50.000 0.00 0.00 0.00 3.36
2512 3157 3.203040 CCCTCCCCTATTGTTTGTCTCAT 59.797 47.826 0.00 0.00 0.00 2.90
2706 3351 9.804758 AAAAGACATTCAAACGTTGGTAAAATA 57.195 25.926 0.00 0.00 0.00 1.40
2744 3389 7.398047 TCCAAATCTGCCTAAGTAAGTACTGTA 59.602 37.037 0.00 0.00 36.50 2.74
2913 3558 7.947782 ATCTGGAGGGTAAAGTGGAATTATA 57.052 36.000 0.00 0.00 0.00 0.98
2914 3559 7.133133 TCTGGAGGGTAAAGTGGAATTATAC 57.867 40.000 0.00 0.00 0.00 1.47
2948 3594 2.572290 ACAAACACTCCCAGTAGTTGC 58.428 47.619 0.00 0.00 29.23 4.17
2955 3601 4.347000 ACACTCCCAGTAGTTGCTAAAAGA 59.653 41.667 0.00 0.00 0.00 2.52
2960 3606 5.529800 TCCCAGTAGTTGCTAAAAGAACAAC 59.470 40.000 0.00 0.00 43.12 3.32
2981 3627 8.225603 ACAACAGAAAATTGACTTGTGTATCT 57.774 30.769 0.00 0.00 30.72 1.98
3057 3705 5.445964 TGGAGAAAGAACCTTAAACAAGCT 58.554 37.500 0.00 0.00 0.00 3.74
3147 3797 4.458989 TGATTGGCAGTTTGACTGGAATAC 59.541 41.667 9.85 0.00 46.01 1.89
3151 3801 2.554344 GCAGTTTGACTGGAATACCCCA 60.554 50.000 9.85 0.00 46.01 4.96
3166 3816 3.141767 ACCCCAGAACAAGAGCTTTAC 57.858 47.619 0.00 0.00 0.00 2.01
3187 3837 4.960938 ACTCAGTATTGCAGTGTGAAAGA 58.039 39.130 0.00 0.00 0.00 2.52
3261 3912 8.964476 TCTATTTTAACTTAAGCTCCATCCTG 57.036 34.615 1.29 0.00 0.00 3.86
3328 3980 9.835389 ATTTTACCGTAACATATTAGCACCTAA 57.165 29.630 0.00 0.00 0.00 2.69
3342 3994 5.746990 AGCACCTAAGAGTGTTCAAGTAT 57.253 39.130 0.00 0.00 40.04 2.12
3345 3997 5.568825 GCACCTAAGAGTGTTCAAGTATGGA 60.569 44.000 0.00 0.00 40.04 3.41
3357 4009 5.449297 TCAAGTATGGATTGATCCCAACA 57.551 39.130 7.53 0.00 46.59 3.33
3559 4213 6.720112 ATTATAGGCATGCAACACTTGATT 57.280 33.333 21.36 0.00 0.00 2.57
3671 4325 8.721019 AACATTGTAAAATGGCATTTCTATGG 57.279 30.769 24.51 14.95 34.56 2.74
3708 4362 3.542712 AATGATTGTGTCGTGTCTTGC 57.457 42.857 0.00 0.00 0.00 4.01
3715 4369 2.095213 TGTGTCGTGTCTTGCTGAAAAC 59.905 45.455 0.00 0.00 0.00 2.43
3721 4375 2.095718 GTGTCTTGCTGAAAACGATCCC 60.096 50.000 0.00 0.00 0.00 3.85
3818 4472 3.620966 GCTTTTAGAGGACCAGTGCAGAT 60.621 47.826 0.00 0.00 0.00 2.90
3950 4604 7.801547 ACAAACAAAAATAGCATCTCATTCG 57.198 32.000 0.00 0.00 0.00 3.34
3956 4610 6.992063 AAAATAGCATCTCATTCGTGACTT 57.008 33.333 0.00 0.00 0.00 3.01
4017 4672 2.957402 TCTGACAGCATGAGGGTTTT 57.043 45.000 0.00 0.00 39.69 2.43
4037 4692 7.284716 GGGTTTTGAATAAATAGACCTGGTAGG 59.715 40.741 0.00 0.00 42.49 3.18
4110 4765 8.976986 ATTTCAGCACTAATTGTTTGAGATTC 57.023 30.769 0.00 0.00 0.00 2.52
4251 7742 3.077229 TGCACATGTGTTTTACTGCAC 57.923 42.857 26.01 6.75 34.32 4.57
4263 7754 6.526674 GTGTTTTACTGCACTAATATGCCAAC 59.473 38.462 0.00 0.00 45.50 3.77
4282 7779 6.922957 TGCCAACATTTCTGAAAATTGTAGTC 59.077 34.615 20.19 10.10 32.69 2.59
4352 7849 2.945008 TCTGTGCAAGTTCTCTGTTTGG 59.055 45.455 0.00 0.00 0.00 3.28
4391 7888 9.251440 ACTAAGTATTATATCACCCTCGCATAA 57.749 33.333 0.00 0.00 0.00 1.90
4693 8190 6.550108 TGGTGATTAGTTGGATAGAGACTACC 59.450 42.308 0.00 0.00 0.00 3.18
4772 8269 5.248477 GGGTTCTGACATTATGCTATAGGGA 59.752 44.000 1.04 0.00 0.00 4.20
4835 8332 9.458374 GTTAAGAAAGAAAATTCAAACCGATGA 57.542 29.630 0.00 0.00 0.00 2.92
4837 8334 8.579682 AAGAAAGAAAATTCAAACCGATGAAG 57.420 30.769 4.92 0.00 42.21 3.02
4838 8335 7.940850 AGAAAGAAAATTCAAACCGATGAAGA 58.059 30.769 4.92 0.00 42.21 2.87
4900 8398 2.751259 TGGTTTTGCTCATCTCATCTGC 59.249 45.455 0.00 0.00 0.00 4.26
4942 8440 3.005684 GGTGCTGTCAAATTGTGATGGAA 59.994 43.478 0.00 0.00 38.90 3.53
4947 8445 5.618640 GCTGTCAAATTGTGATGGAACTCTC 60.619 44.000 0.00 0.00 38.90 3.20
5065 8563 4.855715 TGGCTCCTGATAAACGAGATAG 57.144 45.455 0.00 0.00 0.00 2.08
5118 8616 1.003928 TCATCTGCCAAGTCAGCACAT 59.996 47.619 0.00 0.00 36.01 3.21
5119 8617 2.236893 TCATCTGCCAAGTCAGCACATA 59.763 45.455 0.00 0.00 36.01 2.29
5194 8692 1.538666 CCCCCTTGGCCTATCCTTG 59.461 63.158 3.32 0.00 35.26 3.61
5310 8809 3.672295 CTGAGCACGCCCCTTCTCC 62.672 68.421 0.00 0.00 0.00 3.71
5567 9066 2.039084 ACAAAGAAATCTGACGGGCTCT 59.961 45.455 0.00 0.00 0.00 4.09
5592 9091 6.379417 TCAGCTGAGATTTCACTCTTATCAGA 59.621 38.462 13.74 0.00 37.73 3.27
5619 9118 7.121974 ACTTGTTCAGTTCTGAATATTCGTG 57.878 36.000 16.55 6.47 27.32 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.812329 CGAACAATCAACCAGAAAAACATTTAA 58.188 29.630 0.00 0.00 0.00 1.52
3 4 7.976734 ACGAACAATCAACCAGAAAAACATTTA 59.023 29.630 0.00 0.00 0.00 1.40
4 5 6.816140 ACGAACAATCAACCAGAAAAACATTT 59.184 30.769 0.00 0.00 0.00 2.32
5 6 6.337356 ACGAACAATCAACCAGAAAAACATT 58.663 32.000 0.00 0.00 0.00 2.71
6 7 5.901552 ACGAACAATCAACCAGAAAAACAT 58.098 33.333 0.00 0.00 0.00 2.71
7 8 5.317733 ACGAACAATCAACCAGAAAAACA 57.682 34.783 0.00 0.00 0.00 2.83
8 9 7.743520 TTTACGAACAATCAACCAGAAAAAC 57.256 32.000 0.00 0.00 0.00 2.43
9 10 8.244802 TCTTTTACGAACAATCAACCAGAAAAA 58.755 29.630 0.00 0.00 0.00 1.94
10 11 7.698970 GTCTTTTACGAACAATCAACCAGAAAA 59.301 33.333 0.00 0.00 0.00 2.29
11 12 7.148222 TGTCTTTTACGAACAATCAACCAGAAA 60.148 33.333 0.00 0.00 0.00 2.52
12 13 6.316640 TGTCTTTTACGAACAATCAACCAGAA 59.683 34.615 0.00 0.00 0.00 3.02
13 14 5.818336 TGTCTTTTACGAACAATCAACCAGA 59.182 36.000 0.00 0.00 0.00 3.86
14 15 6.055231 TGTCTTTTACGAACAATCAACCAG 57.945 37.500 0.00 0.00 0.00 4.00
15 16 5.587043 ACTGTCTTTTACGAACAATCAACCA 59.413 36.000 0.00 0.00 0.00 3.67
16 17 6.056428 ACTGTCTTTTACGAACAATCAACC 57.944 37.500 0.00 0.00 0.00 3.77
17 18 7.964545 AAACTGTCTTTTACGAACAATCAAC 57.035 32.000 0.00 0.00 0.00 3.18
19 20 9.872757 GATTAAACTGTCTTTTACGAACAATCA 57.127 29.630 0.00 0.00 0.00 2.57
20 21 9.872757 TGATTAAACTGTCTTTTACGAACAATC 57.127 29.630 0.00 0.00 0.00 2.67
26 27 9.724839 CCTTTTTGATTAAACTGTCTTTTACGA 57.275 29.630 0.00 0.00 0.00 3.43
27 28 8.964150 CCCTTTTTGATTAAACTGTCTTTTACG 58.036 33.333 0.00 0.00 0.00 3.18
28 29 9.256477 CCCCTTTTTGATTAAACTGTCTTTTAC 57.744 33.333 0.00 0.00 0.00 2.01
29 30 8.983789 ACCCCTTTTTGATTAAACTGTCTTTTA 58.016 29.630 0.00 0.00 0.00 1.52
30 31 7.768582 CACCCCTTTTTGATTAAACTGTCTTTT 59.231 33.333 0.00 0.00 0.00 2.27
31 32 7.272244 CACCCCTTTTTGATTAAACTGTCTTT 58.728 34.615 0.00 0.00 0.00 2.52
32 33 6.183360 CCACCCCTTTTTGATTAAACTGTCTT 60.183 38.462 0.00 0.00 0.00 3.01
33 34 5.304357 CCACCCCTTTTTGATTAAACTGTCT 59.696 40.000 0.00 0.00 0.00 3.41
34 35 5.303333 TCCACCCCTTTTTGATTAAACTGTC 59.697 40.000 0.00 0.00 0.00 3.51
35 36 5.212745 TCCACCCCTTTTTGATTAAACTGT 58.787 37.500 0.00 0.00 0.00 3.55
36 37 5.799827 TCCACCCCTTTTTGATTAAACTG 57.200 39.130 0.00 0.00 0.00 3.16
37 38 6.687901 GCTTTCCACCCCTTTTTGATTAAACT 60.688 38.462 0.00 0.00 0.00 2.66
38 39 5.468746 GCTTTCCACCCCTTTTTGATTAAAC 59.531 40.000 0.00 0.00 0.00 2.01
39 40 5.131142 TGCTTTCCACCCCTTTTTGATTAAA 59.869 36.000 0.00 0.00 0.00 1.52
40 41 4.656112 TGCTTTCCACCCCTTTTTGATTAA 59.344 37.500 0.00 0.00 0.00 1.40
41 42 4.227197 TGCTTTCCACCCCTTTTTGATTA 58.773 39.130 0.00 0.00 0.00 1.75
42 43 3.044894 TGCTTTCCACCCCTTTTTGATT 58.955 40.909 0.00 0.00 0.00 2.57
43 44 2.688477 TGCTTTCCACCCCTTTTTGAT 58.312 42.857 0.00 0.00 0.00 2.57
44 45 2.166907 TGCTTTCCACCCCTTTTTGA 57.833 45.000 0.00 0.00 0.00 2.69
45 46 2.998316 TTGCTTTCCACCCCTTTTTG 57.002 45.000 0.00 0.00 0.00 2.44
46 47 4.308526 TTTTTGCTTTCCACCCCTTTTT 57.691 36.364 0.00 0.00 0.00 1.94
69 70 4.945246 TCTTGTCCAGAGTAAACACACTC 58.055 43.478 0.00 0.00 44.44 3.51
70 71 5.070446 TCATCTTGTCCAGAGTAAACACACT 59.930 40.000 0.00 0.00 33.87 3.55
71 72 5.297547 TCATCTTGTCCAGAGTAAACACAC 58.702 41.667 0.00 0.00 33.87 3.82
72 73 5.545063 TCATCTTGTCCAGAGTAAACACA 57.455 39.130 0.00 0.00 33.87 3.72
73 74 6.483640 ACTTTCATCTTGTCCAGAGTAAACAC 59.516 38.462 0.00 0.00 33.87 3.32
74 75 6.591935 ACTTTCATCTTGTCCAGAGTAAACA 58.408 36.000 0.00 0.00 33.87 2.83
75 76 8.779354 ATACTTTCATCTTGTCCAGAGTAAAC 57.221 34.615 0.00 0.00 33.87 2.01
77 78 9.475620 TCTATACTTTCATCTTGTCCAGAGTAA 57.524 33.333 0.00 0.00 33.87 2.24
78 79 9.647918 ATCTATACTTTCATCTTGTCCAGAGTA 57.352 33.333 0.00 0.00 33.87 2.59
79 80 7.962995 TCTATACTTTCATCTTGTCCAGAGT 57.037 36.000 0.00 0.00 33.87 3.24
80 81 8.637099 TGATCTATACTTTCATCTTGTCCAGAG 58.363 37.037 0.00 0.00 33.87 3.35
81 82 8.417106 GTGATCTATACTTTCATCTTGTCCAGA 58.583 37.037 0.00 0.00 35.33 3.86
82 83 7.655328 GGTGATCTATACTTTCATCTTGTCCAG 59.345 40.741 0.00 0.00 0.00 3.86
83 84 7.345653 AGGTGATCTATACTTTCATCTTGTCCA 59.654 37.037 0.00 0.00 26.15 4.02
84 85 7.655328 CAGGTGATCTATACTTTCATCTTGTCC 59.345 40.741 0.00 0.00 28.42 4.02
85 86 8.200792 ACAGGTGATCTATACTTTCATCTTGTC 58.799 37.037 0.00 0.00 28.42 3.18
86 87 8.083828 ACAGGTGATCTATACTTTCATCTTGT 57.916 34.615 0.00 0.00 28.42 3.16
87 88 8.954950 AACAGGTGATCTATACTTTCATCTTG 57.045 34.615 0.00 0.00 28.42 3.02
88 89 8.986991 AGAACAGGTGATCTATACTTTCATCTT 58.013 33.333 0.00 0.00 28.42 2.40
89 90 8.546083 AGAACAGGTGATCTATACTTTCATCT 57.454 34.615 0.00 0.00 31.04 2.90
90 91 9.606631 AAAGAACAGGTGATCTATACTTTCATC 57.393 33.333 0.00 0.00 0.00 2.92
99 100 9.965902 AGAACAATTAAAGAACAGGTGATCTAT 57.034 29.630 0.00 0.00 0.00 1.98
100 101 9.219603 CAGAACAATTAAAGAACAGGTGATCTA 57.780 33.333 0.00 0.00 0.00 1.98
101 102 7.308830 GCAGAACAATTAAAGAACAGGTGATCT 60.309 37.037 0.00 0.00 0.00 2.75
102 103 6.803807 GCAGAACAATTAAAGAACAGGTGATC 59.196 38.462 0.00 0.00 0.00 2.92
103 104 6.491403 AGCAGAACAATTAAAGAACAGGTGAT 59.509 34.615 0.00 0.00 0.00 3.06
104 105 5.827797 AGCAGAACAATTAAAGAACAGGTGA 59.172 36.000 0.00 0.00 0.00 4.02
105 106 6.076981 AGCAGAACAATTAAAGAACAGGTG 57.923 37.500 0.00 0.00 0.00 4.00
106 107 6.206829 GGTAGCAGAACAATTAAAGAACAGGT 59.793 38.462 0.00 0.00 0.00 4.00
107 108 6.206634 TGGTAGCAGAACAATTAAAGAACAGG 59.793 38.462 0.00 0.00 0.00 4.00
108 109 7.202016 TGGTAGCAGAACAATTAAAGAACAG 57.798 36.000 0.00 0.00 0.00 3.16
109 110 6.206634 CCTGGTAGCAGAACAATTAAAGAACA 59.793 38.462 23.31 0.00 0.00 3.18
110 111 6.612306 CCTGGTAGCAGAACAATTAAAGAAC 58.388 40.000 23.31 0.00 0.00 3.01
111 112 5.183140 GCCTGGTAGCAGAACAATTAAAGAA 59.817 40.000 23.31 0.00 0.00 2.52
112 113 4.700213 GCCTGGTAGCAGAACAATTAAAGA 59.300 41.667 23.31 0.00 0.00 2.52
113 114 4.702131 AGCCTGGTAGCAGAACAATTAAAG 59.298 41.667 23.31 3.51 34.23 1.85
114 115 4.662278 AGCCTGGTAGCAGAACAATTAAA 58.338 39.130 23.31 0.00 34.23 1.52
115 116 4.301072 AGCCTGGTAGCAGAACAATTAA 57.699 40.909 23.31 0.00 34.23 1.40
116 117 4.301072 AAGCCTGGTAGCAGAACAATTA 57.699 40.909 23.31 0.00 34.23 1.40
117 118 2.887151 AGCCTGGTAGCAGAACAATT 57.113 45.000 23.31 0.00 34.23 2.32
118 119 2.887151 AAGCCTGGTAGCAGAACAAT 57.113 45.000 23.31 5.64 34.23 2.71
119 120 5.368145 CATATAAGCCTGGTAGCAGAACAA 58.632 41.667 23.31 6.49 34.23 2.83
120 121 4.202357 CCATATAAGCCTGGTAGCAGAACA 60.202 45.833 23.31 5.80 34.23 3.18
121 122 4.040461 TCCATATAAGCCTGGTAGCAGAAC 59.960 45.833 23.31 14.22 34.03 3.01
122 123 4.231273 TCCATATAAGCCTGGTAGCAGAA 58.769 43.478 23.31 6.15 34.03 3.02
123 124 3.834813 CTCCATATAAGCCTGGTAGCAGA 59.165 47.826 23.31 3.38 34.03 4.26
124 125 3.618507 GCTCCATATAAGCCTGGTAGCAG 60.619 52.174 15.13 15.13 36.52 4.24
125 126 2.303022 GCTCCATATAAGCCTGGTAGCA 59.697 50.000 0.00 0.00 36.52 3.49
126 127 2.569404 AGCTCCATATAAGCCTGGTAGC 59.431 50.000 5.81 0.00 40.75 3.58
127 128 4.564406 CCAAGCTCCATATAAGCCTGGTAG 60.564 50.000 14.65 0.00 43.46 3.18
128 129 3.327757 CCAAGCTCCATATAAGCCTGGTA 59.672 47.826 14.65 0.00 43.46 3.25
129 130 2.107204 CCAAGCTCCATATAAGCCTGGT 59.893 50.000 14.65 0.00 43.46 4.00
130 131 2.787994 CCAAGCTCCATATAAGCCTGG 58.212 52.381 10.83 10.83 43.07 4.45
131 132 3.144506 CACCAAGCTCCATATAAGCCTG 58.855 50.000 5.81 3.98 40.75 4.85
132 133 3.048600 TCACCAAGCTCCATATAAGCCT 58.951 45.455 5.81 0.00 40.75 4.58
133 134 3.492102 TCACCAAGCTCCATATAAGCC 57.508 47.619 5.81 0.00 40.75 4.35
134 135 4.274459 CACTTCACCAAGCTCCATATAAGC 59.726 45.833 0.00 1.83 40.14 3.09
135 136 4.274459 GCACTTCACCAAGCTCCATATAAG 59.726 45.833 0.00 0.00 32.09 1.73
136 137 4.080356 AGCACTTCACCAAGCTCCATATAA 60.080 41.667 0.00 0.00 32.09 0.98
137 138 3.455910 AGCACTTCACCAAGCTCCATATA 59.544 43.478 0.00 0.00 32.09 0.86
138 139 2.240667 AGCACTTCACCAAGCTCCATAT 59.759 45.455 0.00 0.00 32.09 1.78
139 140 1.630369 AGCACTTCACCAAGCTCCATA 59.370 47.619 0.00 0.00 32.09 2.74
140 141 0.403271 AGCACTTCACCAAGCTCCAT 59.597 50.000 0.00 0.00 32.09 3.41
141 142 0.250467 GAGCACTTCACCAAGCTCCA 60.250 55.000 0.00 0.00 45.79 3.86
142 143 2.549332 GAGCACTTCACCAAGCTCC 58.451 57.895 0.00 0.00 45.79 4.70
144 145 1.133976 ACAAGAGCACTTCACCAAGCT 60.134 47.619 0.00 0.00 40.60 3.74
145 146 1.265365 GACAAGAGCACTTCACCAAGC 59.735 52.381 0.00 0.00 33.70 4.01
146 147 2.564771 TGACAAGAGCACTTCACCAAG 58.435 47.619 0.00 0.00 33.70 3.61
147 148 2.708216 TGACAAGAGCACTTCACCAA 57.292 45.000 0.00 0.00 33.70 3.67
148 149 2.936919 ATGACAAGAGCACTTCACCA 57.063 45.000 0.00 0.00 33.70 4.17
149 150 3.304928 CCAAATGACAAGAGCACTTCACC 60.305 47.826 0.00 0.00 33.70 4.02
150 151 3.304928 CCCAAATGACAAGAGCACTTCAC 60.305 47.826 0.00 0.00 33.70 3.18
151 152 2.886523 CCCAAATGACAAGAGCACTTCA 59.113 45.455 0.00 0.00 33.70 3.02
152 153 3.149196 TCCCAAATGACAAGAGCACTTC 58.851 45.455 0.00 0.00 33.70 3.01
153 154 3.228188 TCCCAAATGACAAGAGCACTT 57.772 42.857 0.00 0.00 36.73 3.16
154 155 2.957402 TCCCAAATGACAAGAGCACT 57.043 45.000 0.00 0.00 0.00 4.40
155 156 3.084039 TGATCCCAAATGACAAGAGCAC 58.916 45.455 0.00 0.00 0.00 4.40
156 157 3.349927 CTGATCCCAAATGACAAGAGCA 58.650 45.455 0.00 0.00 0.00 4.26
157 158 2.098770 GCTGATCCCAAATGACAAGAGC 59.901 50.000 0.00 0.00 0.00 4.09
158 159 3.618351 AGCTGATCCCAAATGACAAGAG 58.382 45.455 0.00 0.00 0.00 2.85
159 160 3.614092 GAGCTGATCCCAAATGACAAGA 58.386 45.455 0.00 0.00 0.00 3.02
160 161 2.686915 GGAGCTGATCCCAAATGACAAG 59.313 50.000 0.00 0.00 43.01 3.16
161 162 2.726821 GGAGCTGATCCCAAATGACAA 58.273 47.619 0.00 0.00 43.01 3.18
162 163 2.425143 GGAGCTGATCCCAAATGACA 57.575 50.000 0.00 0.00 43.01 3.58
181 182 2.220653 ACAATCATCCAACCCACTGG 57.779 50.000 0.00 0.00 37.87 4.00
182 183 3.156293 TCAACAATCATCCAACCCACTG 58.844 45.455 0.00 0.00 0.00 3.66
183 184 3.524095 TCAACAATCATCCAACCCACT 57.476 42.857 0.00 0.00 0.00 4.00
184 185 4.021192 ACATTCAACAATCATCCAACCCAC 60.021 41.667 0.00 0.00 0.00 4.61
185 186 4.158786 ACATTCAACAATCATCCAACCCA 58.841 39.130 0.00 0.00 0.00 4.51
186 187 4.806640 ACATTCAACAATCATCCAACCC 57.193 40.909 0.00 0.00 0.00 4.11
187 188 6.275335 CCATACATTCAACAATCATCCAACC 58.725 40.000 0.00 0.00 0.00 3.77
188 189 5.750067 GCCATACATTCAACAATCATCCAAC 59.250 40.000 0.00 0.00 0.00 3.77
248 252 8.180267 CAGAACATAGCAGAAATTCCAACTAAG 58.820 37.037 0.00 0.00 0.00 2.18
319 323 6.780457 AAAGAATCATGGGATCGTGAATTT 57.220 33.333 0.00 0.00 41.66 1.82
326 330 3.004106 GCCTCAAAAGAATCATGGGATCG 59.996 47.826 0.00 0.00 31.88 3.69
422 426 2.097466 CACCCGCTCGATTATTTTTGCT 59.903 45.455 0.00 0.00 0.00 3.91
444 448 4.259810 CGACGCACGATAGATTTCATTTGT 60.260 41.667 0.00 0.00 45.77 2.83
461 465 2.049156 CTTCAGTCCTGCGACGCA 60.049 61.111 22.99 22.99 44.28 5.24
472 476 1.352622 TTGCACCCCTGGTCTTCAGT 61.353 55.000 0.00 0.00 41.83 3.41
476 480 1.153756 CCTTTGCACCCCTGGTCTT 59.846 57.895 0.00 0.00 31.02 3.01
513 517 3.332034 ACGAAGGAAAGATAACCCAACG 58.668 45.455 0.00 0.00 0.00 4.10
514 518 4.576879 AGACGAAGGAAAGATAACCCAAC 58.423 43.478 0.00 0.00 0.00 3.77
515 519 4.903045 AGACGAAGGAAAGATAACCCAA 57.097 40.909 0.00 0.00 0.00 4.12
516 520 5.221185 CGATAGACGAAGGAAAGATAACCCA 60.221 44.000 0.00 0.00 45.77 4.51
517 521 5.221130 CGATAGACGAAGGAAAGATAACCC 58.779 45.833 0.00 0.00 45.77 4.11
521 526 4.261489 GCCACGATAGACGAAGGAAAGATA 60.261 45.833 0.00 0.00 45.77 1.98
585 590 7.299787 CAGCATATGCATAGACATAAATCGT 57.700 36.000 28.62 0.00 45.16 3.73
601 606 4.615949 AGTCTAGACGAAAGCAGCATATG 58.384 43.478 17.07 0.00 36.20 1.78
602 607 4.927978 AGTCTAGACGAAAGCAGCATAT 57.072 40.909 17.07 0.00 36.20 1.78
603 608 4.720649 AAGTCTAGACGAAAGCAGCATA 57.279 40.909 17.07 0.00 36.20 3.14
604 609 3.601443 AAGTCTAGACGAAAGCAGCAT 57.399 42.857 17.07 0.00 36.20 3.79
660 667 3.281727 ACAGAACACAATCCACACACT 57.718 42.857 0.00 0.00 0.00 3.55
672 679 5.924825 AGGTTTAGACGACATAACAGAACAC 59.075 40.000 0.00 0.00 0.00 3.32
700 707 6.613153 AATCTACCAGAAGCTAGACAAGTT 57.387 37.500 0.00 0.00 0.00 2.66
726 733 6.204852 TCACAAATCCAGGCCATAATCTAT 57.795 37.500 5.01 0.00 0.00 1.98
730 737 8.338493 TCATATATCACAAATCCAGGCCATAAT 58.662 33.333 5.01 0.00 0.00 1.28
733 740 6.143551 TCATATATCACAAATCCAGGCCAT 57.856 37.500 5.01 0.00 0.00 4.40
735 742 7.446625 GGATATCATATATCACAAATCCAGGCC 59.553 40.741 4.83 0.00 33.39 5.19
758 848 5.652014 TCATTAGCGAAACCATCAAAAGGAT 59.348 36.000 0.00 0.00 36.39 3.24
776 866 4.781934 AGGGTTTCCTCCGATTTCATTAG 58.218 43.478 0.00 0.00 39.80 1.73
855 1115 0.903454 CCGTTGGGGACTCTGGTAGT 60.903 60.000 0.00 0.00 42.80 2.73
856 1116 1.898154 CCGTTGGGGACTCTGGTAG 59.102 63.158 0.00 0.00 38.47 3.18
857 1117 4.123571 CCGTTGGGGACTCTGGTA 57.876 61.111 0.00 0.00 38.47 3.25
901 1161 2.650322 GTGTTGAACTGAAAGGGGTCA 58.350 47.619 0.00 0.00 39.30 4.02
925 1186 2.652095 CCCCTCCCTGTCGCGTTTA 61.652 63.158 5.77 0.00 0.00 2.01
1198 1465 3.008049 GGAGCTGGAAAGAAAGGAGTACA 59.992 47.826 0.00 0.00 0.00 2.90
1201 1468 2.343625 AGGAGCTGGAAAGAAAGGAGT 58.656 47.619 0.00 0.00 0.00 3.85
1202 1469 3.080319 CAAGGAGCTGGAAAGAAAGGAG 58.920 50.000 0.00 0.00 0.00 3.69
1204 1471 2.868899 ACAAGGAGCTGGAAAGAAAGG 58.131 47.619 0.00 0.00 0.00 3.11
1205 1472 4.261783 GGAAACAAGGAGCTGGAAAGAAAG 60.262 45.833 0.00 0.00 0.00 2.62
1206 1473 3.636764 GGAAACAAGGAGCTGGAAAGAAA 59.363 43.478 0.00 0.00 0.00 2.52
1207 1474 3.222603 GGAAACAAGGAGCTGGAAAGAA 58.777 45.455 0.00 0.00 0.00 2.52
1210 1477 1.604604 CGGAAACAAGGAGCTGGAAA 58.395 50.000 0.00 0.00 0.00 3.13
1215 1487 0.034337 TAACGCGGAAACAAGGAGCT 59.966 50.000 12.47 0.00 0.00 4.09
1248 1520 3.025619 CCGAATCAATCAGCCCGC 58.974 61.111 0.00 0.00 0.00 6.13
1307 1580 4.527564 CAATCAACCAACGAGACAGAAAC 58.472 43.478 0.00 0.00 0.00 2.78
1414 1688 7.086376 CCCATCATGACTAACTTCAAAACAAG 58.914 38.462 0.00 0.00 0.00 3.16
1416 1690 5.476599 CCCCATCATGACTAACTTCAAAACA 59.523 40.000 0.00 0.00 0.00 2.83
1433 1707 3.138283 CCCTGCTCTATTAAACCCCATCA 59.862 47.826 0.00 0.00 0.00 3.07
1524 1798 9.928618 TCCCCATTAAGAAATTTGTGTCATATA 57.071 29.630 0.00 0.00 0.00 0.86
1580 1854 3.936453 TCTAAAATTACTGCCGACGCATT 59.064 39.130 0.00 0.00 46.11 3.56
1582 1856 2.962125 TCTAAAATTACTGCCGACGCA 58.038 42.857 0.00 0.00 44.78 5.24
1583 1857 4.743644 AGTATCTAAAATTACTGCCGACGC 59.256 41.667 0.00 0.00 0.00 5.19
1584 1858 6.823678 AAGTATCTAAAATTACTGCCGACG 57.176 37.500 0.00 0.00 0.00 5.12
1585 1859 8.709646 CCATAAGTATCTAAAATTACTGCCGAC 58.290 37.037 0.00 0.00 0.00 4.79
1638 1913 5.018809 AGCCAAATTGTCATACATCCAAGT 58.981 37.500 0.00 0.00 0.00 3.16
1765 2040 1.768275 TCTCAGAGTTCAAGTGGCCAA 59.232 47.619 7.24 0.00 0.00 4.52
2013 2288 8.269424 CACACTACATCGACAATTATCTAAAGC 58.731 37.037 0.00 0.00 0.00 3.51
2028 2303 8.289440 TGTTTACTTCTTTACACACTACATCG 57.711 34.615 0.00 0.00 0.00 3.84
2122 2480 7.221450 TCAATTTGTATAGGGGCACACTATAC 58.779 38.462 19.68 19.68 46.87 1.47
2153 2511 7.387948 GCAACTATAGTTTGGAGAGAAGAAACA 59.612 37.037 15.60 0.00 35.83 2.83
2245 2643 9.729023 CAATGATCACACTTTTAACAACTACAA 57.271 29.630 0.00 0.00 0.00 2.41
2315 2798 9.692749 TCTACCTTATATTTCTGATAGCAAACG 57.307 33.333 0.00 0.00 0.00 3.60
2363 3006 8.192774 CCATCTTAAGCTTATTTCAATGCAAGA 58.807 33.333 7.08 5.28 0.00 3.02
2373 3016 6.204882 GTCGGTATGCCATCTTAAGCTTATTT 59.795 38.462 7.08 0.00 34.09 1.40
2379 3022 2.833794 TGTCGGTATGCCATCTTAAGC 58.166 47.619 0.00 0.00 34.09 3.09
2380 3023 4.442706 ACTTGTCGGTATGCCATCTTAAG 58.557 43.478 0.00 0.00 34.09 1.85
2406 3050 6.908825 AGAGCTCAACATTTTTACGCATTAA 58.091 32.000 17.77 0.00 0.00 1.40
2669 3314 8.261908 CGTTTGAATGTCTTTTCTTTTCATCAC 58.738 33.333 0.00 0.00 0.00 3.06
2706 3351 3.766051 GCAGATTTGGAGTTTCCTGGAAT 59.234 43.478 10.45 0.00 37.46 3.01
2744 3389 6.218195 TCCCTCTAAATATTTCATGCCCAT 57.782 37.500 3.39 0.00 0.00 4.00
2785 3430 3.386768 ACAAGGCATAGCACGTATAGG 57.613 47.619 0.00 0.00 0.00 2.57
2913 3558 2.564947 TGTTTGTTTCAAGCCAGTTGGT 59.435 40.909 0.00 0.00 36.71 3.67
2914 3559 2.929398 GTGTTTGTTTCAAGCCAGTTGG 59.071 45.455 0.00 0.00 36.71 3.77
2955 3601 8.686334 AGATACACAAGTCAATTTTCTGTTGTT 58.314 29.630 0.00 0.00 0.00 2.83
2995 3641 8.998558 AGCTACGTATTTTAAGTTCAAACAAC 57.001 30.769 0.00 0.00 0.00 3.32
3057 3705 8.659925 TCTTTTCATTTCAAAGCATAAGCAAA 57.340 26.923 0.00 0.00 45.49 3.68
3095 3743 7.777910 CCAGTTTGGATAACTATTATGTGGGAA 59.222 37.037 0.00 0.00 40.96 3.97
3147 3797 3.244561 TGAGTAAAGCTCTTGTTCTGGGG 60.245 47.826 0.00 0.00 44.41 4.96
3151 3801 6.370166 GCAATACTGAGTAAAGCTCTTGTTCT 59.630 38.462 11.01 0.00 44.41 3.01
3166 3816 4.751600 TGTCTTTCACACTGCAATACTGAG 59.248 41.667 0.00 0.00 0.00 3.35
3187 3837 7.260603 CACTCTGTTCATTTTCTTCCTTTTGT 58.739 34.615 0.00 0.00 0.00 2.83
3305 3957 8.236585 TCTTAGGTGCTAATATGTTACGGTAA 57.763 34.615 0.00 0.00 0.00 2.85
3328 3980 6.352516 GGATCAATCCATACTTGAACACTCT 58.647 40.000 4.09 0.00 46.38 3.24
3345 3997 2.577606 TTGGACGTGTTGGGATCAAT 57.422 45.000 0.00 0.00 35.10 2.57
3357 4009 2.184167 CACAGCCGGTTTTGGACGT 61.184 57.895 1.90 0.00 0.00 4.34
3559 4213 5.180492 CCACTTCATTTTAGGCGTTCAAGTA 59.820 40.000 0.00 0.00 0.00 2.24
3645 4299 9.165035 CCATAGAAATGCCATTTTACAATGTTT 57.835 29.630 3.82 0.00 38.58 2.83
3671 4325 9.722056 CACAATCATTAAGTTAGCATTAGTTCC 57.278 33.333 0.00 0.00 0.00 3.62
3708 4362 1.130561 GCCTTTCGGGATCGTTTTCAG 59.869 52.381 0.00 0.00 37.23 3.02
3715 4369 1.448893 TTTCGGCCTTTCGGGATCG 60.449 57.895 0.00 0.00 37.23 3.69
3739 4393 5.595542 TGATTAGATTCCTCCAGGCAATTTG 59.404 40.000 0.00 0.00 34.44 2.32
3818 4472 8.202811 CCTGATAGAGAATGAGATTGTGAAGAA 58.797 37.037 0.00 0.00 0.00 2.52
3978 4632 8.531982 TGTCAGAAATAGAGTAATAGCACAGTT 58.468 33.333 0.00 0.00 0.00 3.16
3982 4636 6.980978 TGCTGTCAGAAATAGAGTAATAGCAC 59.019 38.462 3.32 0.00 32.09 4.40
4017 4672 7.931015 ACATCCTACCAGGTCTATTTATTCA 57.069 36.000 0.00 0.00 36.53 2.57
4086 4741 8.077991 CAGAATCTCAAACAATTAGTGCTGAAA 58.922 33.333 0.00 0.00 0.00 2.69
4377 7874 5.552870 AGATTAAGTTATGCGAGGGTGAT 57.447 39.130 0.00 0.00 0.00 3.06
4391 7888 8.463930 TCAACCATGAGAAACAAAGATTAAGT 57.536 30.769 0.00 0.00 0.00 2.24
4456 7953 6.101332 TGCATGCAAATTGAAGTTATCTTCC 58.899 36.000 20.30 0.00 46.66 3.46
4693 8190 7.702386 TCAAAATGGGATATTAATGTGACACG 58.298 34.615 0.22 0.00 0.00 4.49
4772 8269 8.961294 TCAACATTTCCAGAATTTCAAACAAT 57.039 26.923 0.00 0.00 0.00 2.71
4826 8323 7.985476 ACGATCATAAAAATCTTCATCGGTTT 58.015 30.769 0.00 0.00 36.76 3.27
4835 8332 9.988350 GACATGTACAACGATCATAAAAATCTT 57.012 29.630 0.00 0.00 0.00 2.40
4837 8334 7.582679 CCGACATGTACAACGATCATAAAAATC 59.417 37.037 17.50 0.00 0.00 2.17
4838 8335 7.406553 CCGACATGTACAACGATCATAAAAAT 58.593 34.615 17.50 0.00 0.00 1.82
4900 8398 5.464168 CACCAAATCAGGCTCAAGTTTTAG 58.536 41.667 0.00 0.00 0.00 1.85
4942 8440 2.122989 ACACACACCCCCGAGAGT 60.123 61.111 0.00 0.00 0.00 3.24
4947 8445 3.556306 AGACCACACACACCCCCG 61.556 66.667 0.00 0.00 0.00 5.73
5065 8563 2.440247 ACCATTAGGGCCGCTTGC 60.440 61.111 0.00 0.00 42.05 4.01
5194 8692 0.753111 GAGGATGTTGTGGGCCCATC 60.753 60.000 31.45 21.16 35.37 3.51
5310 8809 0.674895 CCTCGAGCCCAAAGTTGAGG 60.675 60.000 6.99 0.00 37.29 3.86
5508 9007 4.194720 AGCTCGTCGTCGATGCCC 62.195 66.667 9.67 3.20 45.21 5.36
5549 9048 1.902508 TGAGAGCCCGTCAGATTTCTT 59.097 47.619 0.00 0.00 0.00 2.52
5567 9066 6.379417 TCTGATAAGAGTGAAATCTCAGCTGA 59.621 38.462 17.19 17.19 36.97 4.26
5579 9078 8.807118 ACTGAACAAGTTATCTGATAAGAGTGA 58.193 33.333 10.26 1.42 34.57 3.41


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

AutoCloner maintained by Alex Coulton.