Multiple sequence alignment - TraesCS7A01G167500

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 TraesCS7A01G167500 chr7A 100.000 4107 0 0 853 4959 122759312 122763418 0.000000e+00 7585.0
1 TraesCS7A01G167500 chr7A 100.000 292 0 0 1 292 122758460 122758751 1.570000e-149 540.0
2 TraesCS7A01G167500 chr7A 88.398 181 15 4 29 206 149258413 149258236 3.890000e-51 213.0
3 TraesCS7A01G167500 chr7D 92.350 3660 226 22 876 4496 118824237 118827881 0.000000e+00 5158.0
4 TraesCS7A01G167500 chr7D 90.104 192 15 4 4485 4675 118828020 118828208 3.830000e-61 246.0
5 TraesCS7A01G167500 chr7D 88.506 174 15 2 30 201 194092200 194092370 6.510000e-49 206.0
6 TraesCS7A01G167500 chr7D 90.278 144 12 1 4776 4917 118828239 118828382 2.360000e-43 187.0
7 TraesCS7A01G167500 chr7D 98.000 50 1 0 210 259 118824014 118824063 2.460000e-13 87.9
8 TraesCS7A01G167500 chr7D 96.970 33 1 0 260 292 118824078 118824110 6.930000e-04 56.5
9 TraesCS7A01G167500 chr7B 92.279 2422 142 11 873 3284 79386747 79389133 0.000000e+00 3395.0
10 TraesCS7A01G167500 chr7B 92.791 1082 40 11 3282 4333 79389214 79390287 0.000000e+00 1531.0
11 TraesCS7A01G167500 chr7B 89.432 511 33 11 4335 4828 79390356 79390862 4.210000e-175 625.0
12 TraesCS7A01G167500 chr4D 86.341 205 22 3 8 209 107740066 107739865 8.360000e-53 219.0
13 TraesCS7A01G167500 chr4D 88.764 178 13 4 30 204 366086711 366086538 1.400000e-50 211.0
14 TraesCS7A01G167500 chr4D 87.778 180 16 3 29 206 50931242 50931417 6.510000e-49 206.0
15 TraesCS7A01G167500 chr4D 87.778 180 16 2 30 206 216436317 216436141 6.510000e-49 206.0
16 TraesCS7A01G167500 chr2A 88.268 179 15 4 30 206 424647726 424647900 5.030000e-50 209.0
17 TraesCS7A01G167500 chr3D 87.640 178 18 2 30 206 110911522 110911696 2.340000e-48 204.0
18 TraesCS7A01G167500 chr1D 87.709 179 17 2 30 206 290499526 290499701 2.340000e-48 204.0
19 TraesCS7A01G167500 chr6B 81.643 207 38 0 2465 2671 619526983 619527189 6.600000e-39 172.0
20 TraesCS7A01G167500 chr6A 80.488 205 40 0 2467 2671 556741337 556741541 1.850000e-34 158.0


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 TraesCS7A01G167500 chr7A 122758460 122763418 4958 False 4062.500000 7585 100.000000 1 4959 2 chr7A.!!$F1 4958
1 TraesCS7A01G167500 chr7D 118824014 118828382 4368 False 1147.080000 5158 93.540400 210 4917 5 chr7D.!!$F2 4707
2 TraesCS7A01G167500 chr7B 79386747 79390862 4115 False 1850.333333 3395 91.500667 873 4828 3 chr7B.!!$F1 3955

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
883 898 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.0 0.0 0.0 0.00 3.71 F
1686 1701 0.036306 GTCGTGGTGAATCCCCAACT 59.964 55.0 0.0 0.0 32.72 3.16 F
1997 2015 0.110486 AAGGATTCAGTTGGTGCGGT 59.890 50.0 0.0 0.0 0.00 5.68 F
1998 2016 0.110486 AGGATTCAGTTGGTGCGGTT 59.890 50.0 0.0 0.0 0.00 4.44 F
2397 2415 0.943835 AAACAATCGCCGCAAAAGCC 60.944 50.0 0.0 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2332 2350 0.960861 GCACTAACCTGGGGAGTTGC 60.961 60.0 0.00 4.21 0.0 4.17 R
3346 3458 0.307760 CTTCCTGTGGCACGTTGAAC 59.692 55.0 13.77 0.00 0.0 3.18 R
3565 3677 0.400213 TTCGGTCAAGGGCAAGTCAT 59.600 50.0 0.00 0.00 0.0 3.06 R
3943 4057 4.281688 ACTTGCATTTACTGTTGGAGCATT 59.718 37.5 0.00 0.00 0.0 3.56 R
4182 4312 0.111061 ACATCCTTGAGCACAGCCAA 59.889 50.0 0.00 0.00 0.0 4.52 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
26 27 8.856490 ATGAAAACTATTCGGCATTATTCAAC 57.144 30.769 0.00 0.00 0.00 3.18
27 28 6.964370 TGAAAACTATTCGGCATTATTCAACG 59.036 34.615 0.00 0.00 0.00 4.10
28 29 4.468095 ACTATTCGGCATTATTCAACGC 57.532 40.909 0.00 0.00 0.00 4.84
29 30 4.127171 ACTATTCGGCATTATTCAACGCT 58.873 39.130 0.00 0.00 0.00 5.07
30 31 3.609103 ATTCGGCATTATTCAACGCTC 57.391 42.857 0.00 0.00 0.00 5.03
31 32 2.309528 TCGGCATTATTCAACGCTCT 57.690 45.000 0.00 0.00 0.00 4.09
32 33 2.627945 TCGGCATTATTCAACGCTCTT 58.372 42.857 0.00 0.00 0.00 2.85
33 34 3.006940 TCGGCATTATTCAACGCTCTTT 58.993 40.909 0.00 0.00 0.00 2.52
34 35 3.438781 TCGGCATTATTCAACGCTCTTTT 59.561 39.130 0.00 0.00 0.00 2.27
35 36 4.083003 TCGGCATTATTCAACGCTCTTTTT 60.083 37.500 0.00 0.00 0.00 1.94
36 37 4.262976 CGGCATTATTCAACGCTCTTTTTC 59.737 41.667 0.00 0.00 0.00 2.29
37 38 5.160641 GGCATTATTCAACGCTCTTTTTCA 58.839 37.500 0.00 0.00 0.00 2.69
38 39 5.807011 GGCATTATTCAACGCTCTTTTTCAT 59.193 36.000 0.00 0.00 0.00 2.57
39 40 6.972328 GGCATTATTCAACGCTCTTTTTCATA 59.028 34.615 0.00 0.00 0.00 2.15
40 41 7.166473 GGCATTATTCAACGCTCTTTTTCATAG 59.834 37.037 0.00 0.00 0.00 2.23
41 42 7.698130 GCATTATTCAACGCTCTTTTTCATAGT 59.302 33.333 0.00 0.00 0.00 2.12
42 43 9.559958 CATTATTCAACGCTCTTTTTCATAGTT 57.440 29.630 0.00 0.00 0.00 2.24
43 44 9.774742 ATTATTCAACGCTCTTTTTCATAGTTC 57.225 29.630 0.00 0.00 0.00 3.01
44 45 6.612247 TTCAACGCTCTTTTTCATAGTTCA 57.388 33.333 0.00 0.00 0.00 3.18
45 46 5.985781 TCAACGCTCTTTTTCATAGTTCAC 58.014 37.500 0.00 0.00 0.00 3.18
46 47 5.525745 TCAACGCTCTTTTTCATAGTTCACA 59.474 36.000 0.00 0.00 0.00 3.58
47 48 6.204688 TCAACGCTCTTTTTCATAGTTCACAT 59.795 34.615 0.00 0.00 0.00 3.21
48 49 6.170675 ACGCTCTTTTTCATAGTTCACATC 57.829 37.500 0.00 0.00 0.00 3.06
49 50 5.934625 ACGCTCTTTTTCATAGTTCACATCT 59.065 36.000 0.00 0.00 0.00 2.90
50 51 6.091441 ACGCTCTTTTTCATAGTTCACATCTC 59.909 38.462 0.00 0.00 0.00 2.75
51 52 6.473521 GCTCTTTTTCATAGTTCACATCTCG 58.526 40.000 0.00 0.00 0.00 4.04
52 53 6.091441 GCTCTTTTTCATAGTTCACATCTCGT 59.909 38.462 0.00 0.00 0.00 4.18
53 54 7.275779 GCTCTTTTTCATAGTTCACATCTCGTA 59.724 37.037 0.00 0.00 0.00 3.43
54 55 9.140286 CTCTTTTTCATAGTTCACATCTCGTAA 57.860 33.333 0.00 0.00 0.00 3.18
55 56 9.653287 TCTTTTTCATAGTTCACATCTCGTAAT 57.347 29.630 0.00 0.00 0.00 1.89
56 57 9.694520 CTTTTTCATAGTTCACATCTCGTAATG 57.305 33.333 0.00 0.00 0.00 1.90
57 58 8.771920 TTTTCATAGTTCACATCTCGTAATGT 57.228 30.769 0.53 0.53 40.49 2.71
67 68 6.861065 ACATCTCGTAATGTGTTTCAACTT 57.139 33.333 4.93 0.00 38.43 2.66
68 69 6.658831 ACATCTCGTAATGTGTTTCAACTTG 58.341 36.000 4.93 0.00 38.43 3.16
69 70 6.481976 ACATCTCGTAATGTGTTTCAACTTGA 59.518 34.615 4.93 0.00 38.43 3.02
70 71 6.912203 TCTCGTAATGTGTTTCAACTTGAA 57.088 33.333 0.00 0.00 34.03 2.69
71 72 7.310072 TCTCGTAATGTGTTTCAACTTGAAA 57.690 32.000 12.12 12.12 43.37 2.69
72 73 7.925993 TCTCGTAATGTGTTTCAACTTGAAAT 58.074 30.769 17.84 6.42 46.55 2.17
73 74 8.402472 TCTCGTAATGTGTTTCAACTTGAAATT 58.598 29.630 17.84 11.48 46.55 1.82
74 75 8.918961 TCGTAATGTGTTTCAACTTGAAATTT 57.081 26.923 17.84 12.29 46.55 1.82
75 76 9.360093 TCGTAATGTGTTTCAACTTGAAATTTT 57.640 25.926 17.84 12.03 46.55 1.82
76 77 9.407514 CGTAATGTGTTTCAACTTGAAATTTTG 57.592 29.630 17.84 3.81 46.55 2.44
79 80 7.721286 TGTGTTTCAACTTGAAATTTTGTGT 57.279 28.000 17.84 0.00 46.55 3.72
80 81 7.571026 TGTGTTTCAACTTGAAATTTTGTGTG 58.429 30.769 17.84 0.00 46.55 3.82
81 82 7.014702 GTGTTTCAACTTGAAATTTTGTGTGG 58.985 34.615 17.84 0.00 46.55 4.17
82 83 5.793026 TTCAACTTGAAATTTTGTGTGGC 57.207 34.783 1.47 0.00 32.71 5.01
83 84 3.862267 TCAACTTGAAATTTTGTGTGGCG 59.138 39.130 0.00 0.00 0.00 5.69
84 85 3.791973 ACTTGAAATTTTGTGTGGCGA 57.208 38.095 0.00 0.00 0.00 5.54
85 86 4.320608 ACTTGAAATTTTGTGTGGCGAT 57.679 36.364 0.00 0.00 0.00 4.58
86 87 5.446143 ACTTGAAATTTTGTGTGGCGATA 57.554 34.783 0.00 0.00 0.00 2.92
87 88 5.837437 ACTTGAAATTTTGTGTGGCGATAA 58.163 33.333 0.00 0.00 0.00 1.75
88 89 6.276847 ACTTGAAATTTTGTGTGGCGATAAA 58.723 32.000 0.00 0.00 0.00 1.40
89 90 6.758886 ACTTGAAATTTTGTGTGGCGATAAAA 59.241 30.769 0.00 0.00 0.00 1.52
90 91 6.517914 TGAAATTTTGTGTGGCGATAAAAC 57.482 33.333 0.00 0.00 0.00 2.43
91 92 6.042777 TGAAATTTTGTGTGGCGATAAAACA 58.957 32.000 0.00 0.00 0.00 2.83
92 93 6.703607 TGAAATTTTGTGTGGCGATAAAACAT 59.296 30.769 0.00 0.00 0.00 2.71
93 94 6.704512 AATTTTGTGTGGCGATAAAACATC 57.295 33.333 0.00 0.00 0.00 3.06
94 95 4.837896 TTTGTGTGGCGATAAAACATCA 57.162 36.364 0.00 0.00 0.00 3.07
95 96 5.384063 TTTGTGTGGCGATAAAACATCAT 57.616 34.783 0.00 0.00 0.00 2.45
96 97 4.614555 TGTGTGGCGATAAAACATCATC 57.385 40.909 0.00 0.00 0.00 2.92
97 98 3.376859 TGTGTGGCGATAAAACATCATCC 59.623 43.478 0.00 0.00 0.00 3.51
98 99 3.627577 GTGTGGCGATAAAACATCATCCT 59.372 43.478 0.00 0.00 0.00 3.24
99 100 3.876914 TGTGGCGATAAAACATCATCCTC 59.123 43.478 0.00 0.00 0.00 3.71
100 101 4.130118 GTGGCGATAAAACATCATCCTCT 58.870 43.478 0.00 0.00 0.00 3.69
101 102 4.576463 GTGGCGATAAAACATCATCCTCTT 59.424 41.667 0.00 0.00 0.00 2.85
102 103 5.758296 GTGGCGATAAAACATCATCCTCTTA 59.242 40.000 0.00 0.00 0.00 2.10
103 104 5.758296 TGGCGATAAAACATCATCCTCTTAC 59.242 40.000 0.00 0.00 0.00 2.34
104 105 5.179555 GGCGATAAAACATCATCCTCTTACC 59.820 44.000 0.00 0.00 0.00 2.85
105 106 5.758296 GCGATAAAACATCATCCTCTTACCA 59.242 40.000 0.00 0.00 0.00 3.25
106 107 6.428159 GCGATAAAACATCATCCTCTTACCAT 59.572 38.462 0.00 0.00 0.00 3.55
107 108 7.360438 GCGATAAAACATCATCCTCTTACCATC 60.360 40.741 0.00 0.00 0.00 3.51
108 109 7.118390 CGATAAAACATCATCCTCTTACCATCC 59.882 40.741 0.00 0.00 0.00 3.51
109 110 4.713792 AACATCATCCTCTTACCATCCC 57.286 45.455 0.00 0.00 0.00 3.85
110 111 3.946824 ACATCATCCTCTTACCATCCCT 58.053 45.455 0.00 0.00 0.00 4.20
111 112 4.310740 ACATCATCCTCTTACCATCCCTT 58.689 43.478 0.00 0.00 0.00 3.95
112 113 4.728860 ACATCATCCTCTTACCATCCCTTT 59.271 41.667 0.00 0.00 0.00 3.11
113 114 5.194537 ACATCATCCTCTTACCATCCCTTTT 59.805 40.000 0.00 0.00 0.00 2.27
114 115 5.796502 TCATCCTCTTACCATCCCTTTTT 57.203 39.130 0.00 0.00 0.00 1.94
153 154 9.520204 TTGAAACTTCAAAACATCATCTTCTTC 57.480 29.630 2.38 0.00 43.62 2.87
154 155 8.906867 TGAAACTTCAAAACATCATCTTCTTCT 58.093 29.630 0.00 0.00 33.55 2.85
155 156 9.178427 GAAACTTCAAAACATCATCTTCTTCTG 57.822 33.333 0.00 0.00 0.00 3.02
156 157 7.211966 ACTTCAAAACATCATCTTCTTCTGG 57.788 36.000 0.00 0.00 0.00 3.86
157 158 6.774656 ACTTCAAAACATCATCTTCTTCTGGT 59.225 34.615 0.00 0.00 0.00 4.00
158 159 7.286316 ACTTCAAAACATCATCTTCTTCTGGTT 59.714 33.333 0.00 0.00 0.00 3.67
159 160 7.587037 TCAAAACATCATCTTCTTCTGGTTT 57.413 32.000 0.00 0.00 0.00 3.27
160 161 8.010733 TCAAAACATCATCTTCTTCTGGTTTT 57.989 30.769 0.00 0.00 37.60 2.43
161 162 8.477256 TCAAAACATCATCTTCTTCTGGTTTTT 58.523 29.630 0.00 0.00 35.68 1.94
162 163 9.748708 CAAAACATCATCTTCTTCTGGTTTTTA 57.251 29.630 0.00 0.00 35.68 1.52
165 166 9.918630 AACATCATCTTCTTCTGGTTTTTATTG 57.081 29.630 0.00 0.00 0.00 1.90
166 167 8.526147 ACATCATCTTCTTCTGGTTTTTATTGG 58.474 33.333 0.00 0.00 0.00 3.16
167 168 8.526147 CATCATCTTCTTCTGGTTTTTATTGGT 58.474 33.333 0.00 0.00 0.00 3.67
168 169 8.477419 TCATCTTCTTCTGGTTTTTATTGGTT 57.523 30.769 0.00 0.00 0.00 3.67
169 170 8.923270 TCATCTTCTTCTGGTTTTTATTGGTTT 58.077 29.630 0.00 0.00 0.00 3.27
170 171 9.546428 CATCTTCTTCTGGTTTTTATTGGTTTT 57.454 29.630 0.00 0.00 0.00 2.43
171 172 9.764363 ATCTTCTTCTGGTTTTTATTGGTTTTC 57.236 29.630 0.00 0.00 0.00 2.29
172 173 8.754080 TCTTCTTCTGGTTTTTATTGGTTTTCA 58.246 29.630 0.00 0.00 0.00 2.69
173 174 8.710835 TTCTTCTGGTTTTTATTGGTTTTCAC 57.289 30.769 0.00 0.00 0.00 3.18
174 175 7.269316 TCTTCTGGTTTTTATTGGTTTTCACC 58.731 34.615 0.00 0.00 44.56 4.02
188 189 6.096673 GGTTTTCACCACTGAATATTGGTT 57.903 37.500 0.00 0.00 44.06 3.67
189 190 6.521162 GGTTTTCACCACTGAATATTGGTTT 58.479 36.000 0.00 0.00 44.06 3.27
190 191 6.645003 GGTTTTCACCACTGAATATTGGTTTC 59.355 38.462 0.00 0.00 44.06 2.78
191 192 7.433680 GTTTTCACCACTGAATATTGGTTTCT 58.566 34.615 0.00 0.00 44.06 2.52
192 193 8.573035 GTTTTCACCACTGAATATTGGTTTCTA 58.427 33.333 0.00 0.00 44.06 2.10
193 194 8.877864 TTTCACCACTGAATATTGGTTTCTAT 57.122 30.769 0.00 0.00 44.06 1.98
194 195 9.967451 TTTCACCACTGAATATTGGTTTCTATA 57.033 29.630 0.00 0.00 44.06 1.31
196 197 9.559732 TCACCACTGAATATTGGTTTCTATATG 57.440 33.333 0.00 0.00 44.06 1.78
197 198 9.559732 CACCACTGAATATTGGTTTCTATATGA 57.440 33.333 0.00 0.00 44.06 2.15
250 251 1.889170 GCTTTGACCCTCCCAAGAAAG 59.111 52.381 0.00 0.00 0.00 2.62
883 898 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
916 931 3.316573 CTTCCTCACCGCCTCCACC 62.317 68.421 0.00 0.00 0.00 4.61
1269 1284 2.508439 CCGTACCGCTCGCATGTT 60.508 61.111 0.00 0.00 0.00 2.71
1296 1311 0.705253 TCTTCTCCTCCGTCTTCCCT 59.295 55.000 0.00 0.00 0.00 4.20
1297 1312 0.820871 CTTCTCCTCCGTCTTCCCTG 59.179 60.000 0.00 0.00 0.00 4.45
1400 1415 1.478137 GTGAGTCGCGATGTGGATAC 58.522 55.000 14.06 0.00 0.00 2.24
1419 1434 1.079405 TAAGCAAGTCGGAAGCGGG 60.079 57.895 0.00 0.00 0.00 6.13
1470 1485 1.228245 TGACAAGCAGTTGGGGAGC 60.228 57.895 0.00 0.00 38.07 4.70
1669 1684 2.891307 TAGTAGCCAGGCAGGGGGTC 62.891 65.000 15.80 0.00 37.34 4.46
1686 1701 0.036306 GTCGTGGTGAATCCCCAACT 59.964 55.000 0.00 0.00 32.72 3.16
1695 1710 4.080299 GGTGAATCCCCAACTAGTGATTCT 60.080 45.833 23.56 0.00 42.17 2.40
1708 1723 2.093764 AGTGATTCTGCCGGAGAAAGAG 60.094 50.000 5.05 0.00 44.11 2.85
1714 1729 2.815647 CCGGAGAAAGAGCCGTGC 60.816 66.667 0.00 0.00 45.85 5.34
1849 1864 2.479750 GGAGTCTCCGGCGGTAGTC 61.480 68.421 27.32 24.21 0.00 2.59
1892 1907 4.217550 GGTGAAGTCCGATTCCAAAATTGA 59.782 41.667 0.00 0.00 0.00 2.57
1894 1909 4.082787 TGAAGTCCGATTCCAAAATTGAGC 60.083 41.667 0.00 0.00 0.00 4.26
1955 1973 3.019564 GTGGTTCTGCTGCTGGAAATAT 58.980 45.455 6.69 0.00 0.00 1.28
1997 2015 0.110486 AAGGATTCAGTTGGTGCGGT 59.890 50.000 0.00 0.00 0.00 5.68
1998 2016 0.110486 AGGATTCAGTTGGTGCGGTT 59.890 50.000 0.00 0.00 0.00 4.44
2000 2018 2.156098 GGATTCAGTTGGTGCGGTTAA 58.844 47.619 0.00 0.00 0.00 2.01
2022 2040 4.821589 GGCTCGGCCGGAAGTGAG 62.822 72.222 27.83 15.46 39.62 3.51
2034 2052 3.194861 CGGAAGTGAGACAGTTGTGAAA 58.805 45.455 0.00 0.00 0.00 2.69
2035 2053 3.809832 CGGAAGTGAGACAGTTGTGAAAT 59.190 43.478 0.00 0.00 0.00 2.17
2095 2113 5.653769 AGTGGAAATGTAGATGAAACCCATG 59.346 40.000 0.00 0.00 35.17 3.66
2139 2157 1.396301 GTGAAGAGCAATGCCGAAGAG 59.604 52.381 0.00 0.00 0.00 2.85
2153 2171 1.208052 CGAAGAGGGAGGAATTCAGCA 59.792 52.381 7.93 0.00 0.00 4.41
2177 2195 2.879103 AAATCGAGTGGGAATGTGGT 57.121 45.000 0.00 0.00 0.00 4.16
2205 2223 1.065854 AGTAATCAGACTGCAGTGGCC 60.066 52.381 27.27 10.34 40.13 5.36
2207 2225 1.830587 AATCAGACTGCAGTGGCCGA 61.831 55.000 27.27 14.83 40.13 5.54
2222 2240 1.482593 GGCCGAGGAGAAAGAAGATGA 59.517 52.381 0.00 0.00 0.00 2.92
2268 2286 3.609853 TGTAGCATCTCCAATTGTGACC 58.390 45.455 4.43 0.00 0.00 4.02
2332 2350 3.600388 AGTGCGGTGAATAAGAAGGAAG 58.400 45.455 0.00 0.00 0.00 3.46
2353 2371 1.145571 AACTCCCCAGGTTAGTGCAA 58.854 50.000 0.00 0.00 0.00 4.08
2397 2415 0.943835 AAACAATCGCCGCAAAAGCC 60.944 50.000 0.00 0.00 0.00 4.35
2403 2421 4.717629 GCCGCAAAAGCCGGGAAC 62.718 66.667 2.18 0.00 45.66 3.62
2574 2598 1.534175 GGATCGTGTCCTCACATCGAC 60.534 57.143 0.00 0.00 44.16 4.20
2668 2692 1.826385 CAACATCCCAAGGTGAGGAC 58.174 55.000 0.00 0.00 34.20 3.85
2687 2711 3.634448 GGACAGCTCATTAGACTAGCTCA 59.366 47.826 0.00 0.00 44.58 4.26
2718 2742 8.697846 ATGTCAGTGAATTTATTTCATGCTTG 57.302 30.769 0.00 0.00 45.77 4.01
2769 2793 8.918202 TTTGTTACACTAGATTGAATCCAACT 57.082 30.769 0.75 0.00 34.72 3.16
2772 2796 8.321353 TGTTACACTAGATTGAATCCAACTGAT 58.679 33.333 0.75 0.00 34.72 2.90
2797 2821 1.604915 GAGAGGCTGAGGGGGAAAC 59.395 63.158 0.00 0.00 0.00 2.78
2877 2901 3.726557 TTGAGGCATTCTGTCAAGGAT 57.273 42.857 0.00 0.00 0.00 3.24
2879 2903 4.142609 TGAGGCATTCTGTCAAGGATAC 57.857 45.455 0.00 0.00 0.00 2.24
2943 2967 2.652590 GAGGGCTCGTACTCTTTCCTA 58.347 52.381 0.00 0.00 0.00 2.94
2955 2979 4.694339 ACTCTTTCCTATTCACGGTATGC 58.306 43.478 0.00 0.00 0.00 3.14
2958 2982 5.056480 TCTTTCCTATTCACGGTATGCATG 58.944 41.667 10.16 0.00 0.00 4.06
2959 2983 4.681074 TTCCTATTCACGGTATGCATGA 57.319 40.909 10.16 0.00 0.00 3.07
2960 2984 4.890158 TCCTATTCACGGTATGCATGAT 57.110 40.909 10.16 0.00 0.00 2.45
2991 3018 3.825014 GGACTGGTTCTACACTACTGTGA 59.175 47.826 3.03 0.00 46.55 3.58
2992 3019 4.463186 GGACTGGTTCTACACTACTGTGAT 59.537 45.833 3.03 0.00 46.55 3.06
2993 3020 5.651139 GGACTGGTTCTACACTACTGTGATA 59.349 44.000 3.03 0.00 46.55 2.15
2994 3021 6.404513 GGACTGGTTCTACACTACTGTGATAC 60.405 46.154 3.03 0.00 46.55 2.24
2995 3022 6.246919 ACTGGTTCTACACTACTGTGATACT 58.753 40.000 3.03 0.00 46.55 2.12
3003 3030 6.042638 ACACTACTGTGATACTTTGCATCT 57.957 37.500 3.03 0.00 46.55 2.90
3004 3031 6.467677 ACACTACTGTGATACTTTGCATCTT 58.532 36.000 3.03 0.00 46.55 2.40
3010 3037 6.265196 ACTGTGATACTTTGCATCTTTTTCCA 59.735 34.615 0.00 0.00 0.00 3.53
3093 3121 1.765230 TCCGCTCTCCTTTCCTAGTC 58.235 55.000 0.00 0.00 0.00 2.59
3186 3214 2.422597 TCACCAAAGTACAAGGATGCG 58.577 47.619 0.00 0.00 0.00 4.73
3303 3414 7.615582 TCTACATTTCATTCTTGTTGCCTAG 57.384 36.000 0.00 0.00 0.00 3.02
3304 3415 5.064441 ACATTTCATTCTTGTTGCCTAGC 57.936 39.130 0.00 0.00 0.00 3.42
3305 3416 4.523943 ACATTTCATTCTTGTTGCCTAGCA 59.476 37.500 0.00 0.00 36.47 3.49
3306 3417 5.186409 ACATTTCATTCTTGTTGCCTAGCAT 59.814 36.000 0.00 0.00 38.76 3.79
3307 3418 5.726980 TTTCATTCTTGTTGCCTAGCATT 57.273 34.783 0.00 0.00 38.76 3.56
3309 3420 5.314923 TCATTCTTGTTGCCTAGCATTTC 57.685 39.130 0.00 0.00 38.76 2.17
3346 3458 6.479990 TCGAATGCCTAAACACTGAAGATATG 59.520 38.462 0.00 0.00 0.00 1.78
3352 3464 7.094805 TGCCTAAACACTGAAGATATGTTCAAC 60.095 37.037 15.42 0.00 36.01 3.18
3398 3510 6.868622 CCAGGAAGGTAGTCACATATATAGC 58.131 44.000 0.00 0.00 0.00 2.97
3530 3642 6.539826 CAGCATCTCATTTCAGGTGTGTATAA 59.460 38.462 0.00 0.00 0.00 0.98
3536 3648 7.606456 TCTCATTTCAGGTGTGTATAACCTTTC 59.394 37.037 0.00 0.00 46.14 2.62
3554 3666 4.323485 CCTTTCCTGTGAACTGCCTACATA 60.323 45.833 0.00 0.00 0.00 2.29
3590 3703 2.107950 TGCCCTTGACCGAACTAATG 57.892 50.000 0.00 0.00 0.00 1.90
3592 3705 2.568062 TGCCCTTGACCGAACTAATGTA 59.432 45.455 0.00 0.00 0.00 2.29
3943 4057 5.278610 CCAACTTTTGATCAGTCAGCATCAA 60.279 40.000 0.00 0.00 37.26 2.57
3984 4098 4.439289 GCAAGTATGAGTTTTCTGGATGCC 60.439 45.833 0.00 0.00 0.00 4.40
4136 4263 3.982475 TCATGCCTACGCTAATCAGAAG 58.018 45.455 0.00 0.00 35.36 2.85
4143 4270 5.232414 GCCTACGCTAATCAGAAGTAAACAG 59.768 44.000 0.00 0.00 0.00 3.16
4250 4404 9.781834 TTTTGTATAAGCTGGAAAATACGAATG 57.218 29.630 0.00 0.00 31.50 2.67
4252 4406 3.782889 AAGCTGGAAAATACGAATGGC 57.217 42.857 0.00 0.00 0.00 4.40
4256 4410 3.796504 GCTGGAAAATACGAATGGCATGG 60.797 47.826 0.00 0.00 0.00 3.66
4280 4435 5.005740 TGCATAACAAAAGAGCTGTCTGAT 58.994 37.500 0.00 0.00 31.37 2.90
4281 4436 5.106436 TGCATAACAAAAGAGCTGTCTGATG 60.106 40.000 0.00 0.00 31.37 3.07
4284 4439 2.107204 ACAAAAGAGCTGTCTGATGGGT 59.893 45.455 0.00 0.00 31.37 4.51
4286 4441 0.617413 AAGAGCTGTCTGATGGGTGG 59.383 55.000 0.00 0.00 31.37 4.61
4291 4446 0.675837 CTGTCTGATGGGTGGCACTG 60.676 60.000 18.45 1.76 0.00 3.66
4333 4488 2.398588 TCAGTTGGTCTATAGGGCCTG 58.601 52.381 18.53 0.00 0.00 4.85
4489 4724 3.439476 GCCTTCATATGCTGCTATCCTTG 59.561 47.826 0.00 0.00 0.00 3.61
4569 4958 5.627499 ACGATGTGTTTACGAAGTACCTA 57.373 39.130 0.00 0.00 45.76 3.08
4592 4981 6.676990 ACATGAGCAAGATATATGTCCTGA 57.323 37.500 0.00 0.00 0.00 3.86
4719 5108 4.720649 TTGATCCTGAGACTTTACGAGG 57.279 45.455 0.00 0.00 0.00 4.63
4723 5112 3.015327 TCCTGAGACTTTACGAGGCTAC 58.985 50.000 0.00 0.00 46.50 3.58
4828 5225 1.509923 GTTGCAAGGCCTGAGATGC 59.490 57.895 18.48 18.48 39.22 3.91
4832 5229 1.144716 CAAGGCCTGAGATGCGCTA 59.855 57.895 5.69 0.00 0.00 4.26
4860 5257 1.891919 GACGCTGTGGCCTGTTTGA 60.892 57.895 3.32 0.00 34.44 2.69
4889 5286 2.619013 GCAGGTGCACATTTCTGTAC 57.381 50.000 20.43 1.32 41.59 2.90
4898 5295 5.458779 GTGCACATTTCTGTACCAAAACTTC 59.541 40.000 13.17 0.00 33.14 3.01
4923 5322 5.804944 TTTTCAATTTTCAGATGGGAGCA 57.195 34.783 0.00 0.00 0.00 4.26
4924 5323 5.804944 TTTCAATTTTCAGATGGGAGCAA 57.195 34.783 0.00 0.00 0.00 3.91
4925 5324 6.363167 TTTCAATTTTCAGATGGGAGCAAT 57.637 33.333 0.00 0.00 0.00 3.56
4926 5325 7.479352 TTTCAATTTTCAGATGGGAGCAATA 57.521 32.000 0.00 0.00 0.00 1.90
4927 5326 7.664552 TTCAATTTTCAGATGGGAGCAATAT 57.335 32.000 0.00 0.00 0.00 1.28
4928 5327 7.046292 TCAATTTTCAGATGGGAGCAATATG 57.954 36.000 0.00 0.00 0.00 1.78
4929 5328 6.608405 TCAATTTTCAGATGGGAGCAATATGT 59.392 34.615 0.00 0.00 0.00 2.29
4930 5329 7.124599 TCAATTTTCAGATGGGAGCAATATGTT 59.875 33.333 0.00 0.00 0.00 2.71
4931 5330 6.855763 TTTTCAGATGGGAGCAATATGTTT 57.144 33.333 0.00 0.00 0.00 2.83
4932 5331 6.855763 TTTCAGATGGGAGCAATATGTTTT 57.144 33.333 0.00 0.00 0.00 2.43
4933 5332 6.855763 TTCAGATGGGAGCAATATGTTTTT 57.144 33.333 0.00 0.00 0.00 1.94
4934 5333 6.211587 TCAGATGGGAGCAATATGTTTTTG 57.788 37.500 0.00 0.00 0.00 2.44
4946 5345 8.737770 GCAATATGTTTTTGCGTCATTTTATC 57.262 30.769 0.00 0.00 39.98 1.75
4947 5346 7.575186 GCAATATGTTTTTGCGTCATTTTATCG 59.425 33.333 0.00 0.00 39.98 2.92
4948 5347 8.793472 CAATATGTTTTTGCGTCATTTTATCGA 58.207 29.630 0.00 0.00 0.00 3.59
4949 5348 8.903570 ATATGTTTTTGCGTCATTTTATCGAA 57.096 26.923 0.00 0.00 0.00 3.71
4950 5349 7.630470 ATGTTTTTGCGTCATTTTATCGAAA 57.370 28.000 0.00 0.00 0.00 3.46
4951 5350 6.858057 TGTTTTTGCGTCATTTTATCGAAAC 58.142 32.000 0.00 0.00 0.00 2.78
4952 5351 6.074782 TGTTTTTGCGTCATTTTATCGAAACC 60.075 34.615 0.00 0.00 0.00 3.27
4953 5352 4.750952 TTGCGTCATTTTATCGAAACCA 57.249 36.364 0.00 0.00 0.00 3.67
4954 5353 4.750952 TGCGTCATTTTATCGAAACCAA 57.249 36.364 0.00 0.00 0.00 3.67
4955 5354 5.109662 TGCGTCATTTTATCGAAACCAAA 57.890 34.783 0.00 0.00 0.00 3.28
4956 5355 4.912766 TGCGTCATTTTATCGAAACCAAAC 59.087 37.500 0.00 0.00 0.00 2.93
4957 5356 4.912766 GCGTCATTTTATCGAAACCAAACA 59.087 37.500 0.00 0.00 0.00 2.83
4958 5357 5.059221 GCGTCATTTTATCGAAACCAAACAG 59.941 40.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.944663 GTTGAATAATGCCGAATAGTTTTCATA 57.055 29.630 0.00 0.00 0.00 2.15
1 2 7.643764 CGTTGAATAATGCCGAATAGTTTTCAT 59.356 33.333 0.00 0.00 0.00 2.57
2 3 6.964370 CGTTGAATAATGCCGAATAGTTTTCA 59.036 34.615 0.00 0.00 0.00 2.69
3 4 6.075572 GCGTTGAATAATGCCGAATAGTTTTC 60.076 38.462 0.00 0.00 41.85 2.29
4 5 5.741982 GCGTTGAATAATGCCGAATAGTTTT 59.258 36.000 0.00 0.00 41.85 2.43
5 6 5.270853 GCGTTGAATAATGCCGAATAGTTT 58.729 37.500 0.00 0.00 41.85 2.66
6 7 4.844267 GCGTTGAATAATGCCGAATAGTT 58.156 39.130 0.00 0.00 41.85 2.24
7 8 4.468095 GCGTTGAATAATGCCGAATAGT 57.532 40.909 0.00 0.00 41.85 2.12
15 16 6.875926 ATGAAAAAGAGCGTTGAATAATGC 57.124 33.333 0.00 0.00 46.77 3.56
16 17 9.559958 AACTATGAAAAAGAGCGTTGAATAATG 57.440 29.630 0.00 0.00 0.00 1.90
17 18 9.774742 GAACTATGAAAAAGAGCGTTGAATAAT 57.225 29.630 0.00 0.00 0.00 1.28
18 19 8.779303 TGAACTATGAAAAAGAGCGTTGAATAA 58.221 29.630 0.00 0.00 0.00 1.40
19 20 8.227791 GTGAACTATGAAAAAGAGCGTTGAATA 58.772 33.333 0.00 0.00 0.00 1.75
20 21 7.078228 GTGAACTATGAAAAAGAGCGTTGAAT 58.922 34.615 0.00 0.00 0.00 2.57
21 22 6.037720 TGTGAACTATGAAAAAGAGCGTTGAA 59.962 34.615 0.00 0.00 0.00 2.69
22 23 5.525745 TGTGAACTATGAAAAAGAGCGTTGA 59.474 36.000 0.00 0.00 0.00 3.18
23 24 5.747565 TGTGAACTATGAAAAAGAGCGTTG 58.252 37.500 0.00 0.00 0.00 4.10
24 25 6.428159 AGATGTGAACTATGAAAAAGAGCGTT 59.572 34.615 0.00 0.00 0.00 4.84
25 26 5.934625 AGATGTGAACTATGAAAAAGAGCGT 59.065 36.000 0.00 0.00 0.00 5.07
26 27 6.414408 AGATGTGAACTATGAAAAAGAGCG 57.586 37.500 0.00 0.00 0.00 5.03
27 28 6.091441 ACGAGATGTGAACTATGAAAAAGAGC 59.909 38.462 0.00 0.00 0.00 4.09
28 29 7.588143 ACGAGATGTGAACTATGAAAAAGAG 57.412 36.000 0.00 0.00 0.00 2.85
29 30 9.653287 ATTACGAGATGTGAACTATGAAAAAGA 57.347 29.630 0.00 0.00 0.00 2.52
30 31 9.694520 CATTACGAGATGTGAACTATGAAAAAG 57.305 33.333 0.00 0.00 0.00 2.27
31 32 9.214957 ACATTACGAGATGTGAACTATGAAAAA 57.785 29.630 7.44 0.00 38.75 1.94
32 33 8.771920 ACATTACGAGATGTGAACTATGAAAA 57.228 30.769 7.44 0.00 38.75 2.29
44 45 6.481976 TCAAGTTGAAACACATTACGAGATGT 59.518 34.615 2.20 0.00 40.76 3.06
45 46 6.887368 TCAAGTTGAAACACATTACGAGATG 58.113 36.000 2.20 0.00 0.00 2.90
46 47 7.490962 TTCAAGTTGAAACACATTACGAGAT 57.509 32.000 15.92 0.00 32.71 2.75
47 48 6.912203 TTCAAGTTGAAACACATTACGAGA 57.088 33.333 15.92 0.00 32.71 4.04
60 61 4.328440 CGCCACACAAAATTTCAAGTTGAA 59.672 37.500 14.35 14.35 34.03 2.69
61 62 3.862267 CGCCACACAAAATTTCAAGTTGA 59.138 39.130 0.08 0.08 0.00 3.18
62 63 3.862267 TCGCCACACAAAATTTCAAGTTG 59.138 39.130 0.00 0.00 0.00 3.16
63 64 4.116747 TCGCCACACAAAATTTCAAGTT 57.883 36.364 0.00 0.00 0.00 2.66
64 65 3.791973 TCGCCACACAAAATTTCAAGT 57.208 38.095 0.00 0.00 0.00 3.16
65 66 6.761731 TTTATCGCCACACAAAATTTCAAG 57.238 33.333 0.00 0.00 0.00 3.02
66 67 6.535150 TGTTTTATCGCCACACAAAATTTCAA 59.465 30.769 0.00 0.00 0.00 2.69
67 68 6.042777 TGTTTTATCGCCACACAAAATTTCA 58.957 32.000 0.00 0.00 0.00 2.69
68 69 6.517914 TGTTTTATCGCCACACAAAATTTC 57.482 33.333 0.00 0.00 0.00 2.17
69 70 6.703607 TGATGTTTTATCGCCACACAAAATTT 59.296 30.769 0.00 0.00 0.00 1.82
70 71 6.219473 TGATGTTTTATCGCCACACAAAATT 58.781 32.000 0.00 0.00 0.00 1.82
71 72 5.777802 TGATGTTTTATCGCCACACAAAAT 58.222 33.333 0.00 0.00 0.00 1.82
72 73 5.188327 TGATGTTTTATCGCCACACAAAA 57.812 34.783 0.00 0.00 0.00 2.44
73 74 4.837896 TGATGTTTTATCGCCACACAAA 57.162 36.364 0.00 0.00 0.00 2.83
74 75 4.142491 GGATGATGTTTTATCGCCACACAA 60.142 41.667 0.00 0.00 0.00 3.33
75 76 3.376859 GGATGATGTTTTATCGCCACACA 59.623 43.478 0.00 0.00 0.00 3.72
76 77 3.627577 AGGATGATGTTTTATCGCCACAC 59.372 43.478 0.00 0.00 0.00 3.82
77 78 3.876914 GAGGATGATGTTTTATCGCCACA 59.123 43.478 0.00 0.00 0.00 4.17
78 79 4.130118 AGAGGATGATGTTTTATCGCCAC 58.870 43.478 0.00 0.00 0.00 5.01
79 80 4.422073 AGAGGATGATGTTTTATCGCCA 57.578 40.909 0.00 0.00 0.00 5.69
80 81 5.179555 GGTAAGAGGATGATGTTTTATCGCC 59.820 44.000 0.00 0.00 0.00 5.54
81 82 5.758296 TGGTAAGAGGATGATGTTTTATCGC 59.242 40.000 0.00 0.00 0.00 4.58
82 83 7.118390 GGATGGTAAGAGGATGATGTTTTATCG 59.882 40.741 0.00 0.00 0.00 2.92
83 84 7.391833 GGGATGGTAAGAGGATGATGTTTTATC 59.608 40.741 0.00 0.00 0.00 1.75
84 85 7.074237 AGGGATGGTAAGAGGATGATGTTTTAT 59.926 37.037 0.00 0.00 0.00 1.40
85 86 6.389869 AGGGATGGTAAGAGGATGATGTTTTA 59.610 38.462 0.00 0.00 0.00 1.52
86 87 5.194537 AGGGATGGTAAGAGGATGATGTTTT 59.805 40.000 0.00 0.00 0.00 2.43
87 88 4.728860 AGGGATGGTAAGAGGATGATGTTT 59.271 41.667 0.00 0.00 0.00 2.83
88 89 4.310740 AGGGATGGTAAGAGGATGATGTT 58.689 43.478 0.00 0.00 0.00 2.71
89 90 3.946824 AGGGATGGTAAGAGGATGATGT 58.053 45.455 0.00 0.00 0.00 3.06
90 91 4.989875 AAGGGATGGTAAGAGGATGATG 57.010 45.455 0.00 0.00 0.00 3.07
91 92 6.347061 AAAAAGGGATGGTAAGAGGATGAT 57.653 37.500 0.00 0.00 0.00 2.45
92 93 5.796502 AAAAAGGGATGGTAAGAGGATGA 57.203 39.130 0.00 0.00 0.00 2.92
127 128 9.520204 GAAGAAGATGATGTTTTGAAGTTTCAA 57.480 29.630 3.28 3.28 44.78 2.69
128 129 8.906867 AGAAGAAGATGATGTTTTGAAGTTTCA 58.093 29.630 0.00 0.00 34.92 2.69
129 130 9.178427 CAGAAGAAGATGATGTTTTGAAGTTTC 57.822 33.333 0.00 0.00 0.00 2.78
130 131 8.139989 CCAGAAGAAGATGATGTTTTGAAGTTT 58.860 33.333 0.00 0.00 0.00 2.66
131 132 7.286316 ACCAGAAGAAGATGATGTTTTGAAGTT 59.714 33.333 0.00 0.00 0.00 2.66
132 133 6.774656 ACCAGAAGAAGATGATGTTTTGAAGT 59.225 34.615 0.00 0.00 0.00 3.01
133 134 7.211966 ACCAGAAGAAGATGATGTTTTGAAG 57.788 36.000 0.00 0.00 0.00 3.02
134 135 7.587037 AACCAGAAGAAGATGATGTTTTGAA 57.413 32.000 0.00 0.00 0.00 2.69
135 136 7.587037 AAACCAGAAGAAGATGATGTTTTGA 57.413 32.000 0.00 0.00 0.00 2.69
136 137 8.652810 AAAAACCAGAAGAAGATGATGTTTTG 57.347 30.769 0.00 0.00 35.54 2.44
139 140 9.918630 CAATAAAAACCAGAAGAAGATGATGTT 57.081 29.630 0.00 0.00 0.00 2.71
140 141 8.526147 CCAATAAAAACCAGAAGAAGATGATGT 58.474 33.333 0.00 0.00 0.00 3.06
141 142 8.526147 ACCAATAAAAACCAGAAGAAGATGATG 58.474 33.333 0.00 0.00 0.00 3.07
142 143 8.655935 ACCAATAAAAACCAGAAGAAGATGAT 57.344 30.769 0.00 0.00 0.00 2.45
143 144 8.477419 AACCAATAAAAACCAGAAGAAGATGA 57.523 30.769 0.00 0.00 0.00 2.92
144 145 9.546428 AAAACCAATAAAAACCAGAAGAAGATG 57.454 29.630 0.00 0.00 0.00 2.90
145 146 9.764363 GAAAACCAATAAAAACCAGAAGAAGAT 57.236 29.630 0.00 0.00 0.00 2.40
146 147 8.754080 TGAAAACCAATAAAAACCAGAAGAAGA 58.246 29.630 0.00 0.00 0.00 2.87
147 148 8.817100 GTGAAAACCAATAAAAACCAGAAGAAG 58.183 33.333 0.00 0.00 0.00 2.85
148 149 7.766738 GGTGAAAACCAATAAAAACCAGAAGAA 59.233 33.333 0.00 0.00 0.00 2.52
149 150 7.093289 TGGTGAAAACCAATAAAAACCAGAAGA 60.093 33.333 0.00 0.00 36.74 2.87
150 151 7.011016 GTGGTGAAAACCAATAAAAACCAGAAG 59.989 37.037 0.00 0.00 42.10 2.85
151 152 6.819146 GTGGTGAAAACCAATAAAAACCAGAA 59.181 34.615 0.00 0.00 42.10 3.02
152 153 6.155393 AGTGGTGAAAACCAATAAAAACCAGA 59.845 34.615 0.00 0.00 42.10 3.86
153 154 6.257630 CAGTGGTGAAAACCAATAAAAACCAG 59.742 38.462 0.00 0.00 42.10 4.00
154 155 6.070767 TCAGTGGTGAAAACCAATAAAAACCA 60.071 34.615 0.00 0.00 42.10 3.67
155 156 6.342111 TCAGTGGTGAAAACCAATAAAAACC 58.658 36.000 0.00 0.00 42.10 3.27
156 157 7.835634 TTCAGTGGTGAAAACCAATAAAAAC 57.164 32.000 0.00 0.00 39.85 2.43
159 160 9.703892 CAATATTCAGTGGTGAAAACCAATAAA 57.296 29.630 0.00 0.00 45.88 1.40
160 161 8.310382 CCAATATTCAGTGGTGAAAACCAATAA 58.690 33.333 0.00 0.00 45.88 1.40
161 162 7.835822 CCAATATTCAGTGGTGAAAACCAATA 58.164 34.615 0.00 0.00 45.88 1.90
162 163 6.700352 CCAATATTCAGTGGTGAAAACCAAT 58.300 36.000 0.00 0.00 45.88 3.16
163 164 6.095432 CCAATATTCAGTGGTGAAAACCAA 57.905 37.500 0.00 0.00 45.88 3.67
164 165 5.720371 CCAATATTCAGTGGTGAAAACCA 57.280 39.130 0.00 0.00 45.88 3.67
194 195 8.743714 GGAGTGTTTGAAAAAGGAGAATATCAT 58.256 33.333 0.00 0.00 0.00 2.45
195 196 7.944554 AGGAGTGTTTGAAAAAGGAGAATATCA 59.055 33.333 0.00 0.00 0.00 2.15
196 197 8.341892 AGGAGTGTTTGAAAAAGGAGAATATC 57.658 34.615 0.00 0.00 0.00 1.63
197 198 8.712228 AAGGAGTGTTTGAAAAAGGAGAATAT 57.288 30.769 0.00 0.00 0.00 1.28
198 199 8.533569 AAAGGAGTGTTTGAAAAAGGAGAATA 57.466 30.769 0.00 0.00 0.00 1.75
199 200 7.423844 AAAGGAGTGTTTGAAAAAGGAGAAT 57.576 32.000 0.00 0.00 0.00 2.40
200 201 6.850752 AAAGGAGTGTTTGAAAAAGGAGAA 57.149 33.333 0.00 0.00 0.00 2.87
201 202 6.435904 TCAAAAGGAGTGTTTGAAAAAGGAGA 59.564 34.615 0.00 0.00 40.96 3.71
202 203 6.531594 GTCAAAAGGAGTGTTTGAAAAAGGAG 59.468 38.462 1.42 0.00 44.35 3.69
203 204 6.210584 AGTCAAAAGGAGTGTTTGAAAAAGGA 59.789 34.615 1.42 0.00 44.35 3.36
204 205 6.398095 AGTCAAAAGGAGTGTTTGAAAAAGG 58.602 36.000 1.42 0.00 44.35 3.11
205 206 7.622048 GCAAGTCAAAAGGAGTGTTTGAAAAAG 60.622 37.037 1.42 0.00 44.35 2.27
206 207 6.147000 GCAAGTCAAAAGGAGTGTTTGAAAAA 59.853 34.615 1.42 0.00 44.35 1.94
207 208 5.637387 GCAAGTCAAAAGGAGTGTTTGAAAA 59.363 36.000 1.42 0.00 44.35 2.29
208 209 5.047377 AGCAAGTCAAAAGGAGTGTTTGAAA 60.047 36.000 1.42 0.00 44.35 2.69
250 251 8.622157 GTTTAGATTTCTCTTATTAGGTTGCCC 58.378 37.037 0.00 0.00 32.66 5.36
258 273 9.601217 GCTGGTCTGTTTAGATTTCTCTTATTA 57.399 33.333 0.00 0.00 34.94 0.98
261 276 7.004555 TGCTGGTCTGTTTAGATTTCTCTTA 57.995 36.000 0.00 0.00 34.94 2.10
883 898 0.946221 GGAAGCGACAGTGACAGTGG 60.946 60.000 14.70 0.00 0.00 4.00
1140 1155 0.530650 CGATGTAGGCCGTCAATGCT 60.531 55.000 0.00 0.00 0.00 3.79
1266 1281 2.299297 GGAGGAGAAGAAGGTCGAAACA 59.701 50.000 0.00 0.00 0.00 2.83
1269 1284 1.174783 CGGAGGAGAAGAAGGTCGAA 58.825 55.000 0.00 0.00 0.00 3.71
1380 1395 0.028902 TATCCACATCGCGACTCACG 59.971 55.000 12.93 0.00 45.66 4.35
1385 1400 2.052157 GCTTAGTATCCACATCGCGAC 58.948 52.381 12.93 0.00 0.00 5.19
1400 1415 1.084370 CCCGCTTCCGACTTGCTTAG 61.084 60.000 0.00 0.00 36.29 2.18
1419 1434 1.526225 GGAATTACCGCTCCCTGCC 60.526 63.158 0.00 0.00 38.78 4.85
1440 1455 1.669115 CTTGTCAGACCCAGCCGTG 60.669 63.158 0.00 0.00 0.00 4.94
1470 1485 2.509336 CTTGGCGCACTACCTCCG 60.509 66.667 10.83 0.00 0.00 4.63
1604 1619 2.802787 ATTCCGATCTGCCGAACTAG 57.197 50.000 0.00 0.00 0.00 2.57
1669 1684 1.278127 ACTAGTTGGGGATTCACCACG 59.722 52.381 7.28 0.00 47.00 4.94
1686 1701 3.096852 TCTTTCTCCGGCAGAATCACTA 58.903 45.455 14.49 2.47 41.02 2.74
1730 1745 2.435805 TGCTTACTGGATCCATCACTCC 59.564 50.000 16.63 3.32 0.00 3.85
1869 1884 4.217550 TCAATTTTGGAATCGGACTTCACC 59.782 41.667 0.00 0.00 0.00 4.02
1871 1886 4.082787 GCTCAATTTTGGAATCGGACTTCA 60.083 41.667 0.00 0.00 0.00 3.02
1955 1973 1.782201 ATCAGCCTTGGCTGTGGTGA 61.782 55.000 32.60 18.95 38.77 4.02
2018 2036 5.931146 AGATCAGATTTCACAACTGTCTCAC 59.069 40.000 0.00 0.00 33.93 3.51
2022 2040 6.791887 TTCAGATCAGATTTCACAACTGTC 57.208 37.500 0.00 0.00 33.93 3.51
2034 2052 8.315482 CCATCAGACTCATTATTCAGATCAGAT 58.685 37.037 0.00 0.00 0.00 2.90
2035 2053 7.289549 ACCATCAGACTCATTATTCAGATCAGA 59.710 37.037 0.00 0.00 0.00 3.27
2139 2157 2.910688 TATCGTGCTGAATTCCTCCC 57.089 50.000 2.27 0.00 0.00 4.30
2177 2195 6.646653 CACTGCAGTCTGATTACTAGTTGAAA 59.353 38.462 18.64 0.00 0.00 2.69
2222 2240 4.145052 GGTCTGGTTCTTGGTTGAAGATT 58.855 43.478 0.00 0.00 40.53 2.40
2268 2286 1.867233 CCACTCGTCTGGTTCTGTTTG 59.133 52.381 0.00 0.00 0.00 2.93
2309 2327 5.353394 TTCCTTCTTATTCACCGCACTAT 57.647 39.130 0.00 0.00 0.00 2.12
2332 2350 0.960861 GCACTAACCTGGGGAGTTGC 60.961 60.000 0.00 4.21 0.00 4.17
2353 2371 5.435291 GGATGAATGATCCTTCAGTGAACT 58.565 41.667 16.91 1.62 46.77 3.01
2397 2415 1.566018 GAACTTCGCTGTGGTTCCCG 61.566 60.000 0.00 0.00 34.90 5.14
2403 2421 2.328099 GGCCAGAACTTCGCTGTGG 61.328 63.158 0.00 0.00 0.00 4.17
2619 2643 3.589654 TTGCCACCGGAGCTTCTCG 62.590 63.158 9.46 0.00 0.00 4.04
2668 2692 5.840715 TGATTGAGCTAGTCTAATGAGCTG 58.159 41.667 0.00 0.00 46.42 4.24
2673 2697 8.429493 TGACATTTGATTGAGCTAGTCTAATG 57.571 34.615 18.74 18.74 40.96 1.90
2674 2698 8.263640 ACTGACATTTGATTGAGCTAGTCTAAT 58.736 33.333 0.00 0.00 0.00 1.73
2718 2742 4.518970 ACAGAAATGGTCATGTTACACACC 59.481 41.667 8.05 8.05 0.00 4.16
2731 2755 9.787435 TCTAGTGTAACAAATAACAGAAATGGT 57.213 29.630 0.00 0.00 41.43 3.55
2769 2793 2.702478 CCTCAGCCTCTCCAACATATCA 59.298 50.000 0.00 0.00 0.00 2.15
2772 2796 1.500474 CCCTCAGCCTCTCCAACATA 58.500 55.000 0.00 0.00 0.00 2.29
2797 2821 3.806316 ATCGCCAACAAAAACTAGTCG 57.194 42.857 0.00 0.00 0.00 4.18
2877 2901 2.370849 AGCCTCAAAAACCTTCCTCGTA 59.629 45.455 0.00 0.00 0.00 3.43
2879 2903 1.897560 AGCCTCAAAAACCTTCCTCG 58.102 50.000 0.00 0.00 0.00 4.63
2931 2955 5.690857 GCATACCGTGAATAGGAAAGAGTAC 59.309 44.000 0.00 0.00 0.00 2.73
2943 2967 3.817084 CTGGAATCATGCATACCGTGAAT 59.183 43.478 0.00 0.00 42.45 2.57
2979 3006 7.170393 AGATGCAAAGTATCACAGTAGTGTA 57.830 36.000 2.08 0.00 46.01 2.90
3035 3062 8.904834 TGCAGTTATAGTCCTAAACAACAAAAA 58.095 29.630 0.00 0.00 0.00 1.94
3093 3121 2.125912 CGCGTCTCCCACTCTTGG 60.126 66.667 0.00 0.00 43.50 3.61
3138 3166 3.849911 CTCGACAATGTCAAGCCTAAGA 58.150 45.455 14.24 0.00 32.09 2.10
3186 3214 7.121168 TGTCCAGTATTGAAAATGATGAAGTCC 59.879 37.037 0.00 0.00 0.00 3.85
3246 3274 5.175090 ACAAGAGAGCAGTAAAAACAAGC 57.825 39.130 0.00 0.00 0.00 4.01
3304 3415 4.898829 TTCGAATGTATGGCAGGAAATG 57.101 40.909 0.00 0.00 0.00 2.32
3305 3416 4.261741 GCATTCGAATGTATGGCAGGAAAT 60.262 41.667 32.52 0.00 38.65 2.17
3306 3417 3.066621 GCATTCGAATGTATGGCAGGAAA 59.933 43.478 32.52 0.00 38.65 3.13
3307 3418 2.618241 GCATTCGAATGTATGGCAGGAA 59.382 45.455 32.52 0.00 38.65 3.36
3309 3420 1.267806 GGCATTCGAATGTATGGCAGG 59.732 52.381 32.52 10.37 44.48 4.85
3314 3426 6.037062 TCAGTGTTTAGGCATTCGAATGTATG 59.963 38.462 32.52 14.96 38.65 2.39
3346 3458 0.307760 CTTCCTGTGGCACGTTGAAC 59.692 55.000 13.77 0.00 0.00 3.18
3352 3464 0.537188 ATAGTCCTTCCTGTGGCACG 59.463 55.000 13.77 7.78 0.00 5.34
3398 3510 1.058695 GCGTCCACGACATTTAACTCG 59.941 52.381 2.58 0.00 43.02 4.18
3530 3642 0.846693 AGGCAGTTCACAGGAAAGGT 59.153 50.000 0.00 0.00 34.13 3.50
3536 3648 3.895232 AGTATGTAGGCAGTTCACAGG 57.105 47.619 0.00 0.00 0.00 4.00
3554 3666 3.523564 AGGGCAAGTCATACCAACATAGT 59.476 43.478 0.00 0.00 0.00 2.12
3565 3677 0.400213 TTCGGTCAAGGGCAAGTCAT 59.600 50.000 0.00 0.00 0.00 3.06
3590 3703 7.012704 ACTGCATATTGAGATCCACAACAATAC 59.987 37.037 0.00 0.41 37.80 1.89
3592 3705 5.889853 ACTGCATATTGAGATCCACAACAAT 59.110 36.000 5.30 0.00 36.94 2.71
3943 4057 4.281688 ACTTGCATTTACTGTTGGAGCATT 59.718 37.500 0.00 0.00 0.00 3.56
3984 4098 9.498176 TGATGATCATTATCCTTGACAATACAG 57.502 33.333 10.14 0.00 0.00 2.74
4182 4312 0.111061 ACATCCTTGAGCACAGCCAA 59.889 50.000 0.00 0.00 0.00 4.52
4250 4404 3.514645 CTCTTTTGTTATGCACCATGCC 58.485 45.455 0.00 0.00 44.23 4.40
4252 4406 4.171005 CAGCTCTTTTGTTATGCACCATG 58.829 43.478 0.00 0.00 0.00 3.66
4256 4410 4.214119 TCAGACAGCTCTTTTGTTATGCAC 59.786 41.667 0.00 0.00 0.00 4.57
4280 4435 0.251297 CAGGATTTCAGTGCCACCCA 60.251 55.000 0.00 0.00 0.00 4.51
4281 4436 0.251341 ACAGGATTTCAGTGCCACCC 60.251 55.000 0.00 0.00 0.00 4.61
4284 4439 2.308570 ACCATACAGGATTTCAGTGCCA 59.691 45.455 0.00 0.00 41.22 4.92
4286 4441 5.163513 CAAAACCATACAGGATTTCAGTGC 58.836 41.667 0.00 0.00 40.07 4.40
4291 4446 7.926018 ACTGAAAACAAAACCATACAGGATTTC 59.074 33.333 0.00 0.00 40.07 2.17
4333 4488 9.334693 CAATTTTTCAGTCATAGACTAGCAAAC 57.665 33.333 0.00 0.00 41.37 2.93
4374 4596 4.072131 GGCTTCATGTGAGGTCAGTAAAA 58.928 43.478 0.00 0.00 0.00 1.52
4447 4682 4.339814 AGGCACTGTATTTTTCGGTTTTGA 59.660 37.500 0.00 0.00 37.18 2.69
4448 4683 4.616953 AGGCACTGTATTTTTCGGTTTTG 58.383 39.130 0.00 0.00 37.18 2.44
4452 4687 3.482436 TGAAGGCACTGTATTTTTCGGT 58.518 40.909 0.00 0.00 40.86 4.69
4453 4688 4.701956 ATGAAGGCACTGTATTTTTCGG 57.298 40.909 0.00 0.00 40.86 4.30
4454 4689 5.682862 GCATATGAAGGCACTGTATTTTTCG 59.317 40.000 6.97 0.00 40.86 3.46
4465 4700 2.746362 GGATAGCAGCATATGAAGGCAC 59.254 50.000 6.97 2.80 33.96 5.01
4534 4920 4.868450 ACACATCGTTTTCGTTCTTTCA 57.132 36.364 0.00 0.00 44.46 2.69
4561 4950 9.094578 ACATATATCTTGCTCATGTAGGTACTT 57.905 33.333 0.00 0.00 41.75 2.24
4569 4958 6.676990 TCAGGACATATATCTTGCTCATGT 57.323 37.500 0.00 0.00 32.70 3.21
4679 5068 2.119801 AACAGCCAGGCTCATTACAG 57.880 50.000 12.53 0.15 36.40 2.74
4682 5071 2.877097 TCAAACAGCCAGGCTCATTA 57.123 45.000 12.53 0.00 36.40 1.90
4685 5074 0.322816 GGATCAAACAGCCAGGCTCA 60.323 55.000 12.53 0.00 36.40 4.26
4719 5108 0.585357 CATGCAGGCTCGAATGTAGC 59.415 55.000 0.00 0.00 39.33 3.58
4721 5110 1.153597 CGCATGCAGGCTCGAATGTA 61.154 55.000 22.31 0.00 0.00 2.29
4723 5112 2.326897 CGCATGCAGGCTCGAATG 59.673 61.111 22.31 0.00 0.00 2.67
4828 5225 3.630148 CGTCTGCCGGCAATAGCG 61.630 66.667 32.09 25.42 43.41 4.26
4832 5229 4.704833 ACAGCGTCTGCCGGCAAT 62.705 61.111 32.09 11.25 44.31 3.56
4875 5272 5.359576 AGAAGTTTTGGTACAGAAATGTGCA 59.640 36.000 0.00 0.00 42.39 4.57
4876 5273 5.831997 AGAAGTTTTGGTACAGAAATGTGC 58.168 37.500 0.00 0.00 42.39 4.57
4877 5274 8.702163 AAAAGAAGTTTTGGTACAGAAATGTG 57.298 30.769 0.00 0.00 42.39 3.21
4907 5306 7.427989 AAACATATTGCTCCCATCTGAAAAT 57.572 32.000 0.00 0.00 0.00 1.82
4922 5321 8.793472 TCGATAAAATGACGCAAAAACATATTG 58.207 29.630 0.00 0.00 0.00 1.90
4923 5322 8.903570 TCGATAAAATGACGCAAAAACATATT 57.096 26.923 0.00 0.00 0.00 1.28
4924 5323 8.903570 TTCGATAAAATGACGCAAAAACATAT 57.096 26.923 0.00 0.00 0.00 1.78
4925 5324 8.631695 GTTTCGATAAAATGACGCAAAAACATA 58.368 29.630 0.00 0.00 0.00 2.29
4926 5325 7.358848 GGTTTCGATAAAATGACGCAAAAACAT 60.359 33.333 0.00 0.00 0.00 2.71
4927 5326 6.074782 GGTTTCGATAAAATGACGCAAAAACA 60.075 34.615 0.00 0.00 0.00 2.83
4928 5327 6.074782 TGGTTTCGATAAAATGACGCAAAAAC 60.075 34.615 0.00 0.00 0.00 2.43
4929 5328 5.977725 TGGTTTCGATAAAATGACGCAAAAA 59.022 32.000 0.00 0.00 0.00 1.94
4930 5329 5.520632 TGGTTTCGATAAAATGACGCAAAA 58.479 33.333 0.00 0.00 0.00 2.44
4931 5330 5.109662 TGGTTTCGATAAAATGACGCAAA 57.890 34.783 0.00 0.00 0.00 3.68
4932 5331 4.750952 TGGTTTCGATAAAATGACGCAA 57.249 36.364 0.00 0.00 0.00 4.85
4933 5332 4.750952 TTGGTTTCGATAAAATGACGCA 57.249 36.364 0.00 0.00 0.00 5.24
4934 5333 4.912766 TGTTTGGTTTCGATAAAATGACGC 59.087 37.500 0.00 0.00 0.00 5.19
4935 5334 6.596717 CTGTTTGGTTTCGATAAAATGACG 57.403 37.500 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.