Multiple sequence alignment - TraesCS2B01G358700

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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 TraesCS2B01G358700 chr2B 100.000 2657 0 0 1 2657 511280696 511278040 0.000000e+00 4907
1 TraesCS2B01G358700 chr2B 75.573 917 184 34 634 1533 245006021 245006914 1.470000e-112 416
2 TraesCS2B01G358700 chr2B 72.242 861 175 51 709 1531 39158900 39158066 9.640000e-50 207
3 TraesCS2B01G358700 chr2D 94.997 1539 55 4 240 1778 433510689 433509173 0.000000e+00 2396
4 TraesCS2B01G358700 chr2D 94.244 886 42 4 1778 2657 433509069 433508187 0.000000e+00 1345
5 TraesCS2B01G358700 chr2D 73.055 861 162 51 709 1531 22785842 22786670 9.500000e-60 241
6 TraesCS2B01G358700 chr2A 93.207 1369 73 8 414 1778 553482871 553484223 0.000000e+00 1995
7 TraesCS2B01G358700 chr2A 95.039 887 26 7 1777 2657 553484409 553485283 0.000000e+00 1378
8 TraesCS2B01G358700 chr2A 75.642 895 183 31 655 1533 203002057 203002932 1.900000e-111 412
9 TraesCS2B01G358700 chr2A 86.920 237 28 2 1 237 502325169 502324936 2.030000e-66 263
10 TraesCS2B01G358700 chr2A 76.077 418 80 17 1127 1534 24181447 24181040 1.610000e-47 200
11 TraesCS2B01G358700 chr2A 72.031 783 175 38 774 1534 24277509 24276749 2.700000e-45 193
12 TraesCS2B01G358700 chr2A 79.325 237 33 7 1 237 654868242 654868022 4.580000e-33 152
13 TraesCS2B01G358700 chr6B 92.405 237 18 0 1 237 281013918 281014154 3.280000e-89 339
14 TraesCS2B01G358700 chr7B 92.017 238 18 1 1 238 591470020 591470256 1.520000e-87 333
15 TraesCS2B01G358700 chr4D 79.318 440 67 12 2217 2650 94258544 94258965 1.200000e-73 287
16 TraesCS2B01G358700 chr6D 88.186 237 28 0 1 237 409495786 409496022 1.560000e-72 283
17 TraesCS2B01G358700 chr4B 79.091 440 68 14 2217 2650 132852864 132853285 5.600000e-72 281
18 TraesCS2B01G358700 chr5A 86.920 237 31 0 1 237 431027528 431027764 1.570000e-67 267
19 TraesCS2B01G358700 chr4A 86.777 242 29 1 2409 2650 486643214 486642976 1.570000e-67 267
20 TraesCS2B01G358700 chr3B 86.498 237 32 0 1 237 448590906 448591142 7.300000e-66 261
21 TraesCS2B01G358700 chr3B 89.944 179 13 1 1 179 534164446 534164273 2.660000e-55 226
22 TraesCS2B01G358700 chr6A 86.076 237 31 2 1 237 195132485 195132251 1.220000e-63 254


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 TraesCS2B01G358700 chr2B 511278040 511280696 2656 True 4907.0 4907 100.0000 1 2657 1 chr2B.!!$R2 2656
1 TraesCS2B01G358700 chr2B 245006021 245006914 893 False 416.0 416 75.5730 634 1533 1 chr2B.!!$F1 899
2 TraesCS2B01G358700 chr2B 39158066 39158900 834 True 207.0 207 72.2420 709 1531 1 chr2B.!!$R1 822
3 TraesCS2B01G358700 chr2D 433508187 433510689 2502 True 1870.5 2396 94.6205 240 2657 2 chr2D.!!$R1 2417
4 TraesCS2B01G358700 chr2D 22785842 22786670 828 False 241.0 241 73.0550 709 1531 1 chr2D.!!$F1 822
5 TraesCS2B01G358700 chr2A 553482871 553485283 2412 False 1686.5 1995 94.1230 414 2657 2 chr2A.!!$F2 2243
6 TraesCS2B01G358700 chr2A 203002057 203002932 875 False 412.0 412 75.6420 655 1533 1 chr2A.!!$F1 878

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
196 197 0.036671 GGCAAAGGTAGCGGTACTGT 60.037 55.0 22.84 9.24 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 2204 0.625316 TACATGGCCTGCACCTGAAT 59.375 50.0 3.32 0.0 0.0 2.57 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
18 19 2.859992 CTTAGCCACAGCAAGTCCC 58.140 57.895 0.00 0.00 43.56 4.46
19 20 0.678048 CTTAGCCACAGCAAGTCCCC 60.678 60.000 0.00 0.00 43.56 4.81
20 21 2.463589 TTAGCCACAGCAAGTCCCCG 62.464 60.000 0.00 0.00 43.56 5.73
22 23 4.335647 CCACAGCAAGTCCCCGCT 62.336 66.667 0.00 0.00 39.66 5.52
30 31 3.563512 AGTCCCCGCTGACTTTGT 58.436 55.556 0.00 0.00 42.92 2.83
31 32 1.371558 AGTCCCCGCTGACTTTGTC 59.628 57.895 0.00 0.00 42.92 3.18
32 33 2.027625 GTCCCCGCTGACTTTGTCG 61.028 63.158 0.00 0.00 34.95 4.35
33 34 2.030562 CCCCGCTGACTTTGTCGT 59.969 61.111 0.00 0.00 34.95 4.34
34 35 1.180456 TCCCCGCTGACTTTGTCGTA 61.180 55.000 0.00 0.00 34.95 3.43
35 36 0.736325 CCCCGCTGACTTTGTCGTAG 60.736 60.000 0.00 0.00 34.95 3.51
36 37 0.736325 CCCGCTGACTTTGTCGTAGG 60.736 60.000 0.00 0.00 34.95 3.18
37 38 0.242825 CCGCTGACTTTGTCGTAGGA 59.757 55.000 0.00 0.00 34.95 2.94
38 39 1.135083 CCGCTGACTTTGTCGTAGGAT 60.135 52.381 0.00 0.00 34.95 3.24
39 40 2.186076 CGCTGACTTTGTCGTAGGATC 58.814 52.381 0.00 0.00 34.95 3.36
40 41 2.415491 CGCTGACTTTGTCGTAGGATCA 60.415 50.000 0.00 0.00 34.95 2.92
41 42 3.585862 GCTGACTTTGTCGTAGGATCAA 58.414 45.455 0.00 0.00 34.95 2.57
42 43 3.614616 GCTGACTTTGTCGTAGGATCAAG 59.385 47.826 0.00 5.47 34.95 3.02
43 44 4.618460 GCTGACTTTGTCGTAGGATCAAGA 60.618 45.833 11.48 0.00 34.95 3.02
44 45 5.462530 TGACTTTGTCGTAGGATCAAGAA 57.537 39.130 11.48 0.86 34.95 2.52
45 46 6.037786 TGACTTTGTCGTAGGATCAAGAAT 57.962 37.500 11.48 0.09 34.95 2.40
46 47 6.100004 TGACTTTGTCGTAGGATCAAGAATC 58.900 40.000 11.48 7.02 34.95 2.52
47 48 5.103000 ACTTTGTCGTAGGATCAAGAATCG 58.897 41.667 11.48 0.00 34.99 3.34
48 49 4.976224 TTGTCGTAGGATCAAGAATCGA 57.024 40.909 0.00 0.00 34.99 3.59
49 50 4.976224 TGTCGTAGGATCAAGAATCGAA 57.024 40.909 0.00 0.00 34.99 3.71
50 51 4.921547 TGTCGTAGGATCAAGAATCGAAG 58.078 43.478 0.00 0.00 34.99 3.79
51 52 4.202020 TGTCGTAGGATCAAGAATCGAAGG 60.202 45.833 0.00 0.00 34.99 3.46
52 53 3.053455 CGTAGGATCAAGAATCGAAGGC 58.947 50.000 0.00 0.00 34.99 4.35
53 54 3.243569 CGTAGGATCAAGAATCGAAGGCT 60.244 47.826 0.00 0.00 34.99 4.58
54 55 3.191078 AGGATCAAGAATCGAAGGCTG 57.809 47.619 0.00 0.00 34.99 4.85
55 56 2.768527 AGGATCAAGAATCGAAGGCTGA 59.231 45.455 0.00 0.00 34.99 4.26
56 57 3.129871 GGATCAAGAATCGAAGGCTGAG 58.870 50.000 0.00 0.00 34.99 3.35
57 58 3.181471 GGATCAAGAATCGAAGGCTGAGA 60.181 47.826 0.00 0.00 34.99 3.27
58 59 4.502950 GGATCAAGAATCGAAGGCTGAGAT 60.503 45.833 0.00 0.00 34.99 2.75
59 60 4.478206 TCAAGAATCGAAGGCTGAGATT 57.522 40.909 14.90 14.90 37.32 2.40
60 61 4.437239 TCAAGAATCGAAGGCTGAGATTC 58.563 43.478 25.35 25.35 46.24 2.52
62 63 2.815478 GAATCGAAGGCTGAGATTCGT 58.185 47.619 21.42 3.21 46.34 3.85
63 64 2.500509 ATCGAAGGCTGAGATTCGTC 57.499 50.000 16.23 0.00 46.34 4.20
64 65 1.173913 TCGAAGGCTGAGATTCGTCA 58.826 50.000 16.23 0.58 46.34 4.35
65 66 1.544246 TCGAAGGCTGAGATTCGTCAA 59.456 47.619 16.23 0.00 46.34 3.18
66 67 2.029380 TCGAAGGCTGAGATTCGTCAAA 60.029 45.455 16.23 0.00 46.34 2.69
67 68 2.932614 CGAAGGCTGAGATTCGTCAAAT 59.067 45.455 10.78 0.00 42.47 2.32
68 69 3.000724 CGAAGGCTGAGATTCGTCAAATC 59.999 47.826 10.78 0.00 42.47 2.17
69 70 3.616956 AGGCTGAGATTCGTCAAATCA 57.383 42.857 0.00 0.00 45.34 2.57
70 71 3.265791 AGGCTGAGATTCGTCAAATCAC 58.734 45.455 0.00 0.00 45.34 3.06
71 72 3.055530 AGGCTGAGATTCGTCAAATCACT 60.056 43.478 0.00 0.00 45.34 3.41
72 73 4.160439 AGGCTGAGATTCGTCAAATCACTA 59.840 41.667 0.00 0.00 45.34 2.74
73 74 5.053145 GGCTGAGATTCGTCAAATCACTAT 58.947 41.667 1.07 0.00 45.34 2.12
74 75 5.525378 GGCTGAGATTCGTCAAATCACTATT 59.475 40.000 1.07 0.00 45.34 1.73
75 76 6.292596 GGCTGAGATTCGTCAAATCACTATTC 60.293 42.308 1.07 0.00 45.34 1.75
76 77 6.478344 GCTGAGATTCGTCAAATCACTATTCT 59.522 38.462 1.07 0.00 45.34 2.40
77 78 7.306515 GCTGAGATTCGTCAAATCACTATTCTC 60.307 40.741 1.07 0.00 45.34 2.87
78 79 7.547227 TGAGATTCGTCAAATCACTATTCTCA 58.453 34.615 0.00 0.00 45.34 3.27
79 80 8.034804 TGAGATTCGTCAAATCACTATTCTCAA 58.965 33.333 0.00 0.00 45.34 3.02
80 81 8.777865 AGATTCGTCAAATCACTATTCTCAAA 57.222 30.769 1.07 0.00 45.34 2.69
81 82 8.660373 AGATTCGTCAAATCACTATTCTCAAAC 58.340 33.333 1.07 0.00 45.34 2.93
82 83 7.722795 TTCGTCAAATCACTATTCTCAAACA 57.277 32.000 0.00 0.00 0.00 2.83
83 84 7.117241 TCGTCAAATCACTATTCTCAAACAC 57.883 36.000 0.00 0.00 0.00 3.32
84 85 6.929049 TCGTCAAATCACTATTCTCAAACACT 59.071 34.615 0.00 0.00 0.00 3.55
85 86 8.085909 TCGTCAAATCACTATTCTCAAACACTA 58.914 33.333 0.00 0.00 0.00 2.74
86 87 8.873830 CGTCAAATCACTATTCTCAAACACTAT 58.126 33.333 0.00 0.00 0.00 2.12
91 92 9.725019 AATCACTATTCTCAAACACTATTCACA 57.275 29.630 0.00 0.00 0.00 3.58
92 93 9.896645 ATCACTATTCTCAAACACTATTCACAT 57.103 29.630 0.00 0.00 0.00 3.21
98 99 8.684386 TTCTCAAACACTATTCACATAAACCA 57.316 30.769 0.00 0.00 0.00 3.67
99 100 8.094798 TCTCAAACACTATTCACATAAACCAC 57.905 34.615 0.00 0.00 0.00 4.16
100 101 7.936847 TCTCAAACACTATTCACATAAACCACT 59.063 33.333 0.00 0.00 0.00 4.00
101 102 7.870826 TCAAACACTATTCACATAAACCACTG 58.129 34.615 0.00 0.00 0.00 3.66
102 103 7.500892 TCAAACACTATTCACATAAACCACTGT 59.499 33.333 0.00 0.00 0.00 3.55
103 104 7.817418 AACACTATTCACATAAACCACTGTT 57.183 32.000 0.00 0.00 35.82 3.16
104 105 7.435068 ACACTATTCACATAAACCACTGTTC 57.565 36.000 0.00 0.00 32.15 3.18
105 106 6.995686 ACACTATTCACATAAACCACTGTTCA 59.004 34.615 0.00 0.00 32.15 3.18
106 107 7.041372 ACACTATTCACATAAACCACTGTTCAC 60.041 37.037 0.00 0.00 32.15 3.18
107 108 4.804608 TTCACATAAACCACTGTTCACG 57.195 40.909 0.00 0.00 32.15 4.35
108 109 2.546368 TCACATAAACCACTGTTCACGC 59.454 45.455 0.00 0.00 32.15 5.34
109 110 2.289274 CACATAAACCACTGTTCACGCA 59.711 45.455 0.00 0.00 32.15 5.24
110 111 2.946329 ACATAAACCACTGTTCACGCAA 59.054 40.909 0.00 0.00 32.15 4.85
111 112 3.378742 ACATAAACCACTGTTCACGCAAA 59.621 39.130 0.00 0.00 32.15 3.68
112 113 4.037446 ACATAAACCACTGTTCACGCAAAT 59.963 37.500 0.00 0.00 32.15 2.32
113 114 2.774439 AACCACTGTTCACGCAAATC 57.226 45.000 0.00 0.00 0.00 2.17
114 115 1.674359 ACCACTGTTCACGCAAATCA 58.326 45.000 0.00 0.00 0.00 2.57
115 116 1.333619 ACCACTGTTCACGCAAATCAC 59.666 47.619 0.00 0.00 0.00 3.06
116 117 1.603802 CCACTGTTCACGCAAATCACT 59.396 47.619 0.00 0.00 0.00 3.41
117 118 2.602933 CCACTGTTCACGCAAATCACTG 60.603 50.000 0.00 0.00 0.00 3.66
118 119 2.032054 CACTGTTCACGCAAATCACTGT 59.968 45.455 0.00 0.00 0.00 3.55
119 120 2.682856 ACTGTTCACGCAAATCACTGTT 59.317 40.909 0.00 0.00 0.00 3.16
120 121 3.038017 CTGTTCACGCAAATCACTGTTG 58.962 45.455 0.00 0.00 0.00 3.33
121 122 2.680339 TGTTCACGCAAATCACTGTTGA 59.320 40.909 0.00 0.00 35.73 3.18
122 123 3.035942 GTTCACGCAAATCACTGTTGAC 58.964 45.455 0.00 0.00 33.38 3.18
123 124 1.601903 TCACGCAAATCACTGTTGACC 59.398 47.619 0.00 0.00 33.38 4.02
124 125 1.333308 CACGCAAATCACTGTTGACCA 59.667 47.619 0.00 0.00 33.38 4.02
125 126 1.333619 ACGCAAATCACTGTTGACCAC 59.666 47.619 0.00 0.00 33.38 4.16
126 127 1.333308 CGCAAATCACTGTTGACCACA 59.667 47.619 0.00 0.00 33.38 4.17
127 128 2.731217 GCAAATCACTGTTGACCACAC 58.269 47.619 0.00 0.00 33.38 3.82
128 129 2.358898 GCAAATCACTGTTGACCACACT 59.641 45.455 0.00 0.00 33.38 3.55
129 130 3.563808 GCAAATCACTGTTGACCACACTA 59.436 43.478 0.00 0.00 33.38 2.74
130 131 4.216257 GCAAATCACTGTTGACCACACTAT 59.784 41.667 0.00 0.00 33.38 2.12
131 132 5.411361 GCAAATCACTGTTGACCACACTATA 59.589 40.000 0.00 0.00 33.38 1.31
132 133 6.402550 GCAAATCACTGTTGACCACACTATAG 60.403 42.308 0.00 0.00 33.38 1.31
133 134 4.188247 TCACTGTTGACCACACTATAGC 57.812 45.455 0.00 0.00 0.00 2.97
134 135 3.056107 TCACTGTTGACCACACTATAGCC 60.056 47.826 0.00 0.00 0.00 3.93
135 136 2.236395 ACTGTTGACCACACTATAGCCC 59.764 50.000 0.00 0.00 0.00 5.19
136 137 1.557832 TGTTGACCACACTATAGCCCC 59.442 52.381 0.00 0.00 0.00 5.80
137 138 1.838077 GTTGACCACACTATAGCCCCT 59.162 52.381 0.00 0.00 0.00 4.79
138 139 1.496060 TGACCACACTATAGCCCCTG 58.504 55.000 0.00 0.00 0.00 4.45
139 140 1.007842 TGACCACACTATAGCCCCTGA 59.992 52.381 0.00 0.00 0.00 3.86
140 141 2.330216 GACCACACTATAGCCCCTGAT 58.670 52.381 0.00 0.00 0.00 2.90
141 142 2.300437 GACCACACTATAGCCCCTGATC 59.700 54.545 0.00 0.00 0.00 2.92
142 143 2.090494 ACCACACTATAGCCCCTGATCT 60.090 50.000 0.00 0.00 0.00 2.75
143 144 3.142217 ACCACACTATAGCCCCTGATCTA 59.858 47.826 0.00 0.00 0.00 1.98
144 145 3.766591 CCACACTATAGCCCCTGATCTAG 59.233 52.174 0.00 0.00 0.00 2.43
145 146 4.411927 CACACTATAGCCCCTGATCTAGT 58.588 47.826 0.00 0.00 0.00 2.57
146 147 4.461081 CACACTATAGCCCCTGATCTAGTC 59.539 50.000 0.00 0.00 0.00 2.59
147 148 4.355588 ACACTATAGCCCCTGATCTAGTCT 59.644 45.833 0.00 0.00 0.00 3.24
148 149 4.704540 CACTATAGCCCCTGATCTAGTCTG 59.295 50.000 0.00 0.00 0.00 3.51
149 150 3.913370 ATAGCCCCTGATCTAGTCTGT 57.087 47.619 0.00 0.00 0.00 3.41
150 151 2.080654 AGCCCCTGATCTAGTCTGTC 57.919 55.000 0.00 0.00 0.00 3.51
151 152 0.671251 GCCCCTGATCTAGTCTGTCG 59.329 60.000 0.00 0.00 0.00 4.35
152 153 0.671251 CCCCTGATCTAGTCTGTCGC 59.329 60.000 0.00 0.00 0.00 5.19
153 154 1.686355 CCCTGATCTAGTCTGTCGCT 58.314 55.000 0.00 0.00 0.00 4.93
154 155 2.028130 CCCTGATCTAGTCTGTCGCTT 58.972 52.381 0.00 0.00 0.00 4.68
155 156 2.428890 CCCTGATCTAGTCTGTCGCTTT 59.571 50.000 0.00 0.00 0.00 3.51
156 157 3.118956 CCCTGATCTAGTCTGTCGCTTTT 60.119 47.826 0.00 0.00 0.00 2.27
157 158 4.109050 CCTGATCTAGTCTGTCGCTTTTC 58.891 47.826 0.00 0.00 0.00 2.29
158 159 4.380973 CCTGATCTAGTCTGTCGCTTTTCA 60.381 45.833 0.00 0.00 0.00 2.69
159 160 5.134202 TGATCTAGTCTGTCGCTTTTCAA 57.866 39.130 0.00 0.00 0.00 2.69
160 161 5.724328 TGATCTAGTCTGTCGCTTTTCAAT 58.276 37.500 0.00 0.00 0.00 2.57
161 162 5.807520 TGATCTAGTCTGTCGCTTTTCAATC 59.192 40.000 0.00 0.00 0.00 2.67
162 163 4.495422 TCTAGTCTGTCGCTTTTCAATCC 58.505 43.478 0.00 0.00 0.00 3.01
163 164 2.069273 AGTCTGTCGCTTTTCAATCCG 58.931 47.619 0.00 0.00 0.00 4.18
164 165 2.066262 GTCTGTCGCTTTTCAATCCGA 58.934 47.619 0.00 0.00 0.00 4.55
166 167 3.562869 GTCGCTTTTCAATCCGACG 57.437 52.632 0.00 0.00 40.27 5.12
167 168 0.094730 GTCGCTTTTCAATCCGACGG 59.905 55.000 7.84 7.84 40.27 4.79
168 169 0.038067 TCGCTTTTCAATCCGACGGA 60.038 50.000 20.85 20.85 35.55 4.69
169 170 0.094730 CGCTTTTCAATCCGACGGAC 59.905 55.000 21.02 2.48 32.98 4.79
170 171 0.094730 GCTTTTCAATCCGACGGACG 59.905 55.000 21.02 13.83 42.18 4.79
182 183 4.323477 CGGACGGGACTGGGCAAA 62.323 66.667 0.00 0.00 0.00 3.68
183 184 2.359975 GGACGGGACTGGGCAAAG 60.360 66.667 0.00 0.00 0.00 2.77
184 185 2.359975 GACGGGACTGGGCAAAGG 60.360 66.667 0.00 0.00 0.00 3.11
185 186 3.175710 ACGGGACTGGGCAAAGGT 61.176 61.111 0.00 0.00 0.00 3.50
186 187 1.833787 GACGGGACTGGGCAAAGGTA 61.834 60.000 0.00 0.00 0.00 3.08
187 188 1.078426 CGGGACTGGGCAAAGGTAG 60.078 63.158 0.00 0.00 0.00 3.18
188 189 1.378646 GGGACTGGGCAAAGGTAGC 60.379 63.158 0.00 0.00 0.00 3.58
189 190 1.745489 GGACTGGGCAAAGGTAGCG 60.745 63.158 0.00 0.00 0.00 4.26
190 191 1.745489 GACTGGGCAAAGGTAGCGG 60.745 63.158 0.00 0.00 0.00 5.52
191 192 2.351276 CTGGGCAAAGGTAGCGGT 59.649 61.111 0.00 0.00 0.00 5.68
192 193 1.196104 ACTGGGCAAAGGTAGCGGTA 61.196 55.000 0.00 0.00 0.00 4.02
193 194 0.743345 CTGGGCAAAGGTAGCGGTAC 60.743 60.000 16.33 16.33 0.00 3.34
194 195 1.196104 TGGGCAAAGGTAGCGGTACT 61.196 55.000 22.84 7.69 0.00 2.73
195 196 0.743345 GGGCAAAGGTAGCGGTACTG 60.743 60.000 22.84 14.93 0.00 2.74
196 197 0.036671 GGCAAAGGTAGCGGTACTGT 60.037 55.000 22.84 9.24 0.00 3.55
197 198 1.205417 GGCAAAGGTAGCGGTACTGTA 59.795 52.381 22.84 0.00 0.00 2.74
198 199 2.537401 GCAAAGGTAGCGGTACTGTAG 58.463 52.381 22.84 12.56 0.00 2.74
199 200 2.537401 CAAAGGTAGCGGTACTGTAGC 58.463 52.381 22.84 6.94 0.00 3.58
205 206 2.789917 CGGTACTGTAGCGTCGCT 59.210 61.111 25.08 25.08 43.94 4.93
206 207 2.009108 CGGTACTGTAGCGTCGCTA 58.991 57.895 26.13 22.68 43.94 4.26
213 214 4.489249 TAGCGTCGCTACCTTTGC 57.511 55.556 22.68 0.00 40.44 3.68
214 215 1.153706 TAGCGTCGCTACCTTTGCC 60.154 57.895 22.68 0.00 40.44 4.52
215 216 1.879737 TAGCGTCGCTACCTTTGCCA 61.880 55.000 22.68 0.00 40.44 4.92
216 217 3.023591 GCGTCGCTACCTTTGCCAC 62.024 63.158 10.68 0.00 0.00 5.01
217 218 1.666553 CGTCGCTACCTTTGCCACA 60.667 57.895 0.00 0.00 0.00 4.17
218 219 1.626654 CGTCGCTACCTTTGCCACAG 61.627 60.000 0.00 0.00 0.00 3.66
219 220 1.671054 TCGCTACCTTTGCCACAGC 60.671 57.895 0.00 0.00 40.48 4.40
229 230 3.966215 GCCACAGCAAGTTAGCGA 58.034 55.556 0.00 0.00 40.15 4.93
230 231 2.244000 GCCACAGCAAGTTAGCGAA 58.756 52.632 0.00 0.00 40.15 4.70
231 232 0.804989 GCCACAGCAAGTTAGCGAAT 59.195 50.000 0.00 0.00 40.15 3.34
232 233 1.202076 GCCACAGCAAGTTAGCGAATC 60.202 52.381 0.00 0.00 40.15 2.52
233 234 2.350522 CCACAGCAAGTTAGCGAATCT 58.649 47.619 0.00 0.00 40.15 2.40
234 235 2.094894 CCACAGCAAGTTAGCGAATCTG 59.905 50.000 0.00 0.00 40.15 2.90
235 236 2.995939 CACAGCAAGTTAGCGAATCTGA 59.004 45.455 0.00 0.00 40.15 3.27
236 237 3.433274 CACAGCAAGTTAGCGAATCTGAA 59.567 43.478 0.00 0.00 40.15 3.02
237 238 3.433615 ACAGCAAGTTAGCGAATCTGAAC 59.566 43.478 0.00 0.00 40.15 3.18
238 239 3.433274 CAGCAAGTTAGCGAATCTGAACA 59.567 43.478 0.00 0.00 40.15 3.18
382 383 6.074463 GCTACTAATATGTTTCCCTTTCGACG 60.074 42.308 0.00 0.00 0.00 5.12
385 386 5.952526 AATATGTTTCCCTTTCGACGTTT 57.047 34.783 0.00 0.00 0.00 3.60
386 387 3.619233 ATGTTTCCCTTTCGACGTTTG 57.381 42.857 0.00 0.00 0.00 2.93
387 388 1.671845 TGTTTCCCTTTCGACGTTTGG 59.328 47.619 0.00 0.00 0.00 3.28
389 390 2.041251 TTCCCTTTCGACGTTTGGTT 57.959 45.000 0.00 0.00 0.00 3.67
390 391 1.585297 TCCCTTTCGACGTTTGGTTC 58.415 50.000 0.00 0.00 0.00 3.62
391 392 0.589708 CCCTTTCGACGTTTGGTTCC 59.410 55.000 0.00 0.00 0.00 3.62
393 394 0.233848 CTTTCGACGTTTGGTTCCGG 59.766 55.000 0.00 0.00 0.00 5.14
394 395 1.774046 TTTCGACGTTTGGTTCCGGC 61.774 55.000 0.00 0.00 0.00 6.13
395 396 3.719144 CGACGTTTGGTTCCGGCC 61.719 66.667 0.00 0.00 0.00 6.13
396 397 2.592287 GACGTTTGGTTCCGGCCA 60.592 61.111 2.24 0.00 36.62 5.36
397 398 2.124236 ACGTTTGGTTCCGGCCAA 60.124 55.556 9.28 9.28 45.83 4.52
409 410 2.822255 GGCCAAGCCGCGACATTA 60.822 61.111 8.23 0.00 39.62 1.90
410 411 2.186826 GGCCAAGCCGCGACATTAT 61.187 57.895 8.23 0.00 39.62 1.28
411 412 0.882927 GGCCAAGCCGCGACATTATA 60.883 55.000 8.23 0.00 39.62 0.98
412 413 1.156736 GCCAAGCCGCGACATTATAT 58.843 50.000 8.23 0.00 0.00 0.86
557 562 3.138884 TGCTCCTGCATCTTGTAAACA 57.861 42.857 0.00 0.00 45.31 2.83
562 567 5.586243 GCTCCTGCATCTTGTAAACATCTAA 59.414 40.000 0.00 0.00 39.41 2.10
785 790 3.009115 CCTCCCCTTCGCCTTCCA 61.009 66.667 0.00 0.00 0.00 3.53
828 836 2.646175 CGGGTTCTTCCTCGCCTGA 61.646 63.158 0.00 0.00 36.25 3.86
909 917 3.383681 TTCCCCGGATTCGTCGCA 61.384 61.111 0.73 0.00 33.95 5.10
1215 1251 2.998097 CTGCGGGATTTCTGGGGA 59.002 61.111 0.00 0.00 0.00 4.81
1771 1819 6.793203 GCTGTCGATTTGTTACGAAAATGTAA 59.207 34.615 0.00 0.00 40.12 2.41
1772 1820 7.006210 GCTGTCGATTTGTTACGAAAATGTAAG 59.994 37.037 0.00 0.00 40.12 2.34
1795 2030 5.347907 AGGAAACTCGTTTATTACTCGCTTG 59.652 40.000 0.00 0.00 32.90 4.01
1829 2064 5.048013 TGAACTGACGATGATTGACAGTACT 60.048 40.000 16.12 4.16 40.51 2.73
1945 2180 4.696402 TCCAAATTTGCTTCAAATCCATGC 59.304 37.500 12.92 0.00 42.32 4.06
1987 2222 0.968901 CATTCAGGTGCAGGCCATGT 60.969 55.000 5.01 0.00 0.00 3.21
2011 2246 3.491792 GCCTCTTTCCTATCGTTCCTCAG 60.492 52.174 0.00 0.00 0.00 3.35
2091 2332 7.946043 AGTTACGTACAGTACATTTCAAATCG 58.054 34.615 11.37 0.00 34.56 3.34
2180 2421 4.446371 CTCAAAACACCAGTTCTCAGTCT 58.554 43.478 0.00 0.00 36.84 3.24
2193 2434 0.969149 TCAGTCTGTCACCGCTGATT 59.031 50.000 0.00 0.00 33.62 2.57
2194 2435 1.073964 CAGTCTGTCACCGCTGATTG 58.926 55.000 0.00 0.00 0.00 2.67
2314 2555 0.685097 CCTTCCTCTTCCGGTTGTCA 59.315 55.000 0.00 0.00 0.00 3.58
2365 2606 2.355193 GGACAGCTCGCCCTCTTCT 61.355 63.158 0.00 0.00 0.00 2.85
2407 2648 0.252057 TGTTCTGGTGATCCTCCCGA 60.252 55.000 0.00 0.00 34.23 5.14
2497 2738 1.988107 TGTTCCAGCTCCCTCTCAATT 59.012 47.619 0.00 0.00 0.00 2.32
2518 2759 6.699242 ATTAGGTCATCATCATCCATGACT 57.301 37.500 10.92 2.16 44.70 3.41
2557 2798 2.101233 GCCTTTCGACTTCCTCCGC 61.101 63.158 0.00 0.00 0.00 5.54
2587 2828 2.096496 CGCAGCTTTCACCTTATCCTTG 59.904 50.000 0.00 0.00 0.00 3.61
2629 2870 7.628580 GCATCCATCATTGATGAGGACATATTG 60.629 40.741 24.93 11.84 42.09 1.90
2649 2890 0.668401 GTGCCTTCATTGCTGTTGGC 60.668 55.000 0.00 0.00 40.02 4.52
2650 2891 0.828762 TGCCTTCATTGCTGTTGGCT 60.829 50.000 0.00 0.00 40.16 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.378762 GGGGACTTGCTGTGGCTAA 59.621 57.895 0.00 0.00 39.59 3.09
2 3 2.954684 CGGGGACTTGCTGTGGCTA 61.955 63.158 0.00 0.00 39.59 3.93
3 4 4.335647 CGGGGACTTGCTGTGGCT 62.336 66.667 0.00 0.00 39.59 4.75
5 6 4.335647 AGCGGGGACTTGCTGTGG 62.336 66.667 0.00 0.00 38.44 4.17
6 7 3.052082 CAGCGGGGACTTGCTGTG 61.052 66.667 6.07 0.00 46.71 3.66
9 10 2.925170 AGTCAGCGGGGACTTGCT 60.925 61.111 3.34 0.00 45.59 3.91
14 15 2.027625 CGACAAAGTCAGCGGGGAC 61.028 63.158 0.00 0.00 38.08 4.46
15 16 1.180456 TACGACAAAGTCAGCGGGGA 61.180 55.000 0.00 0.00 32.09 4.81
16 17 0.736325 CTACGACAAAGTCAGCGGGG 60.736 60.000 0.00 0.00 32.09 5.73
17 18 0.736325 CCTACGACAAAGTCAGCGGG 60.736 60.000 0.00 0.00 32.09 6.13
18 19 0.242825 TCCTACGACAAAGTCAGCGG 59.757 55.000 0.00 0.00 32.09 5.52
19 20 2.186076 GATCCTACGACAAAGTCAGCG 58.814 52.381 0.00 0.00 32.09 5.18
20 21 3.232213 TGATCCTACGACAAAGTCAGC 57.768 47.619 0.00 0.00 32.09 4.26
21 22 5.060662 TCTTGATCCTACGACAAAGTCAG 57.939 43.478 0.00 0.00 32.09 3.51
22 23 5.462530 TTCTTGATCCTACGACAAAGTCA 57.537 39.130 0.00 0.00 32.09 3.41
23 24 5.230306 CGATTCTTGATCCTACGACAAAGTC 59.770 44.000 0.00 0.00 0.00 3.01
24 25 5.103000 CGATTCTTGATCCTACGACAAAGT 58.897 41.667 0.00 0.00 0.00 2.66
25 26 5.340803 TCGATTCTTGATCCTACGACAAAG 58.659 41.667 0.00 0.00 0.00 2.77
26 27 5.319140 TCGATTCTTGATCCTACGACAAA 57.681 39.130 0.00 0.00 0.00 2.83
27 28 4.976224 TCGATTCTTGATCCTACGACAA 57.024 40.909 0.00 0.00 0.00 3.18
28 29 4.202020 CCTTCGATTCTTGATCCTACGACA 60.202 45.833 0.00 0.00 0.00 4.35
29 30 4.291783 CCTTCGATTCTTGATCCTACGAC 58.708 47.826 0.00 0.00 0.00 4.34
30 31 3.243434 GCCTTCGATTCTTGATCCTACGA 60.243 47.826 0.00 0.00 0.00 3.43
31 32 3.053455 GCCTTCGATTCTTGATCCTACG 58.947 50.000 0.00 0.00 0.00 3.51
32 33 4.054671 CAGCCTTCGATTCTTGATCCTAC 58.945 47.826 0.00 0.00 0.00 3.18
33 34 3.960755 TCAGCCTTCGATTCTTGATCCTA 59.039 43.478 0.00 0.00 0.00 2.94
34 35 2.768527 TCAGCCTTCGATTCTTGATCCT 59.231 45.455 0.00 0.00 0.00 3.24
35 36 3.129871 CTCAGCCTTCGATTCTTGATCC 58.870 50.000 0.00 0.00 0.00 3.36
36 37 4.052159 TCTCAGCCTTCGATTCTTGATC 57.948 45.455 0.00 0.00 0.00 2.92
37 38 4.686191 ATCTCAGCCTTCGATTCTTGAT 57.314 40.909 0.00 0.00 0.00 2.57
38 39 4.437239 GAATCTCAGCCTTCGATTCTTGA 58.563 43.478 0.00 0.00 39.73 3.02
39 40 3.244814 CGAATCTCAGCCTTCGATTCTTG 59.755 47.826 3.79 0.00 45.31 3.02
40 41 3.118956 ACGAATCTCAGCCTTCGATTCTT 60.119 43.478 14.02 0.69 45.31 2.52
41 42 2.428890 ACGAATCTCAGCCTTCGATTCT 59.571 45.455 14.02 0.00 45.31 2.40
42 43 2.792116 GACGAATCTCAGCCTTCGATTC 59.208 50.000 14.02 0.00 45.31 2.52
43 44 2.166459 TGACGAATCTCAGCCTTCGATT 59.834 45.455 14.02 0.00 45.31 3.34
44 45 1.751351 TGACGAATCTCAGCCTTCGAT 59.249 47.619 14.02 1.74 45.31 3.59
45 46 1.173913 TGACGAATCTCAGCCTTCGA 58.826 50.000 14.02 0.00 45.31 3.71
47 48 3.935203 TGATTTGACGAATCTCAGCCTTC 59.065 43.478 15.09 0.00 43.74 3.46
48 49 3.686726 GTGATTTGACGAATCTCAGCCTT 59.313 43.478 15.09 0.00 43.74 4.35
49 50 3.055530 AGTGATTTGACGAATCTCAGCCT 60.056 43.478 15.09 2.92 43.74 4.58
50 51 3.265791 AGTGATTTGACGAATCTCAGCC 58.734 45.455 15.09 1.06 43.74 4.85
51 52 6.478344 AGAATAGTGATTTGACGAATCTCAGC 59.522 38.462 15.09 4.95 43.74 4.26
52 53 7.704047 TGAGAATAGTGATTTGACGAATCTCAG 59.296 37.037 15.09 0.00 43.74 3.35
53 54 7.547227 TGAGAATAGTGATTTGACGAATCTCA 58.453 34.615 15.09 7.52 43.74 3.27
54 55 7.993821 TGAGAATAGTGATTTGACGAATCTC 57.006 36.000 15.09 11.87 43.74 2.75
55 56 8.660373 GTTTGAGAATAGTGATTTGACGAATCT 58.340 33.333 15.09 0.69 43.74 2.40
56 57 8.443160 TGTTTGAGAATAGTGATTTGACGAATC 58.557 33.333 8.31 8.31 43.67 2.52
57 58 8.230486 GTGTTTGAGAATAGTGATTTGACGAAT 58.770 33.333 0.00 0.00 0.00 3.34
58 59 7.441157 AGTGTTTGAGAATAGTGATTTGACGAA 59.559 33.333 0.00 0.00 0.00 3.85
59 60 6.929049 AGTGTTTGAGAATAGTGATTTGACGA 59.071 34.615 0.00 0.00 0.00 4.20
60 61 7.121974 AGTGTTTGAGAATAGTGATTTGACG 57.878 36.000 0.00 0.00 0.00 4.35
65 66 9.725019 TGTGAATAGTGTTTGAGAATAGTGATT 57.275 29.630 0.00 0.00 0.00 2.57
66 67 9.896645 ATGTGAATAGTGTTTGAGAATAGTGAT 57.103 29.630 0.00 0.00 0.00 3.06
72 73 9.295825 TGGTTTATGTGAATAGTGTTTGAGAAT 57.704 29.630 0.00 0.00 0.00 2.40
73 74 8.564574 GTGGTTTATGTGAATAGTGTTTGAGAA 58.435 33.333 0.00 0.00 0.00 2.87
74 75 7.936847 AGTGGTTTATGTGAATAGTGTTTGAGA 59.063 33.333 0.00 0.00 0.00 3.27
75 76 8.017373 CAGTGGTTTATGTGAATAGTGTTTGAG 58.983 37.037 0.00 0.00 0.00 3.02
76 77 7.500892 ACAGTGGTTTATGTGAATAGTGTTTGA 59.499 33.333 0.00 0.00 0.00 2.69
77 78 7.648142 ACAGTGGTTTATGTGAATAGTGTTTG 58.352 34.615 0.00 0.00 0.00 2.93
78 79 7.817418 ACAGTGGTTTATGTGAATAGTGTTT 57.183 32.000 0.00 0.00 0.00 2.83
79 80 7.500892 TGAACAGTGGTTTATGTGAATAGTGTT 59.499 33.333 0.00 0.00 37.36 3.32
80 81 6.995686 TGAACAGTGGTTTATGTGAATAGTGT 59.004 34.615 0.00 0.00 37.36 3.55
81 82 7.298122 GTGAACAGTGGTTTATGTGAATAGTG 58.702 38.462 0.00 0.00 37.36 2.74
82 83 6.147164 CGTGAACAGTGGTTTATGTGAATAGT 59.853 38.462 0.00 0.00 37.36 2.12
83 84 6.534059 CGTGAACAGTGGTTTATGTGAATAG 58.466 40.000 0.00 0.00 37.36 1.73
84 85 5.106869 GCGTGAACAGTGGTTTATGTGAATA 60.107 40.000 0.00 0.00 37.36 1.75
85 86 4.320202 GCGTGAACAGTGGTTTATGTGAAT 60.320 41.667 0.00 0.00 37.36 2.57
86 87 3.002862 GCGTGAACAGTGGTTTATGTGAA 59.997 43.478 0.00 0.00 37.36 3.18
87 88 2.546368 GCGTGAACAGTGGTTTATGTGA 59.454 45.455 0.00 0.00 37.36 3.58
88 89 2.289274 TGCGTGAACAGTGGTTTATGTG 59.711 45.455 0.00 0.00 37.36 3.21
89 90 2.566913 TGCGTGAACAGTGGTTTATGT 58.433 42.857 0.00 0.00 37.36 2.29
90 91 3.617540 TTGCGTGAACAGTGGTTTATG 57.382 42.857 0.00 0.00 37.36 1.90
91 92 4.277174 TGATTTGCGTGAACAGTGGTTTAT 59.723 37.500 0.00 0.00 37.36 1.40
92 93 3.628032 TGATTTGCGTGAACAGTGGTTTA 59.372 39.130 0.00 0.00 37.36 2.01
93 94 2.425312 TGATTTGCGTGAACAGTGGTTT 59.575 40.909 0.00 0.00 37.36 3.27
94 95 2.020720 TGATTTGCGTGAACAGTGGTT 58.979 42.857 0.00 0.00 40.76 3.67
95 96 1.333619 GTGATTTGCGTGAACAGTGGT 59.666 47.619 0.00 0.00 0.00 4.16
96 97 1.603802 AGTGATTTGCGTGAACAGTGG 59.396 47.619 0.00 0.00 0.00 4.00
97 98 2.032054 ACAGTGATTTGCGTGAACAGTG 59.968 45.455 0.00 0.00 37.74 3.66
98 99 2.288666 ACAGTGATTTGCGTGAACAGT 58.711 42.857 0.00 0.00 0.00 3.55
99 100 3.038017 CAACAGTGATTTGCGTGAACAG 58.962 45.455 0.00 0.00 0.00 3.16
100 101 2.680339 TCAACAGTGATTTGCGTGAACA 59.320 40.909 0.00 0.00 0.00 3.18
101 102 3.035942 GTCAACAGTGATTTGCGTGAAC 58.964 45.455 0.00 0.00 35.80 3.18
102 103 2.032799 GGTCAACAGTGATTTGCGTGAA 59.967 45.455 0.00 0.00 35.80 3.18
103 104 1.601903 GGTCAACAGTGATTTGCGTGA 59.398 47.619 0.00 0.00 35.80 4.35
104 105 1.333308 TGGTCAACAGTGATTTGCGTG 59.667 47.619 0.00 0.00 35.80 5.34
105 106 1.333619 GTGGTCAACAGTGATTTGCGT 59.666 47.619 0.00 0.00 35.80 5.24
106 107 1.333308 TGTGGTCAACAGTGATTTGCG 59.667 47.619 0.00 0.00 35.80 4.85
107 108 2.358898 AGTGTGGTCAACAGTGATTTGC 59.641 45.455 0.00 0.00 41.10 3.68
108 109 5.947228 ATAGTGTGGTCAACAGTGATTTG 57.053 39.130 0.00 0.00 42.63 2.32
109 110 5.643777 GCTATAGTGTGGTCAACAGTGATTT 59.356 40.000 0.00 0.00 42.63 2.17
110 111 5.178797 GCTATAGTGTGGTCAACAGTGATT 58.821 41.667 0.00 0.00 42.63 2.57
111 112 4.383118 GGCTATAGTGTGGTCAACAGTGAT 60.383 45.833 0.00 0.00 42.63 3.06
112 113 3.056107 GGCTATAGTGTGGTCAACAGTGA 60.056 47.826 0.00 0.00 42.63 3.41
113 114 3.262420 GGCTATAGTGTGGTCAACAGTG 58.738 50.000 0.84 0.00 42.63 3.66
114 115 2.236395 GGGCTATAGTGTGGTCAACAGT 59.764 50.000 0.84 0.00 44.84 3.55
115 116 2.420129 GGGGCTATAGTGTGGTCAACAG 60.420 54.545 0.84 0.00 40.26 3.16
116 117 1.557832 GGGGCTATAGTGTGGTCAACA 59.442 52.381 0.84 0.00 36.04 3.33
117 118 1.838077 AGGGGCTATAGTGTGGTCAAC 59.162 52.381 0.84 0.00 0.00 3.18
118 119 1.837439 CAGGGGCTATAGTGTGGTCAA 59.163 52.381 0.84 0.00 0.00 3.18
119 120 1.007842 TCAGGGGCTATAGTGTGGTCA 59.992 52.381 0.84 0.00 0.00 4.02
120 121 1.789523 TCAGGGGCTATAGTGTGGTC 58.210 55.000 0.84 0.00 0.00 4.02
121 122 2.090494 AGATCAGGGGCTATAGTGTGGT 60.090 50.000 0.84 0.00 0.00 4.16
122 123 2.614259 AGATCAGGGGCTATAGTGTGG 58.386 52.381 0.84 0.00 0.00 4.17
123 124 4.411927 ACTAGATCAGGGGCTATAGTGTG 58.588 47.826 0.00 0.00 0.00 3.82
124 125 4.355588 AGACTAGATCAGGGGCTATAGTGT 59.644 45.833 0.00 0.00 0.00 3.55
125 126 4.704540 CAGACTAGATCAGGGGCTATAGTG 59.295 50.000 0.00 0.00 0.00 2.74
126 127 4.355588 ACAGACTAGATCAGGGGCTATAGT 59.644 45.833 0.00 0.00 0.00 2.12
127 128 4.929479 ACAGACTAGATCAGGGGCTATAG 58.071 47.826 0.00 0.00 0.00 1.31
128 129 4.565861 CGACAGACTAGATCAGGGGCTATA 60.566 50.000 0.00 0.00 0.00 1.31
129 130 3.773560 GACAGACTAGATCAGGGGCTAT 58.226 50.000 0.00 0.00 0.00 2.97
130 131 2.487445 CGACAGACTAGATCAGGGGCTA 60.487 54.545 0.00 0.00 0.00 3.93
131 132 1.752436 CGACAGACTAGATCAGGGGCT 60.752 57.143 0.00 0.00 0.00 5.19
132 133 0.671251 CGACAGACTAGATCAGGGGC 59.329 60.000 0.00 0.00 0.00 5.80
133 134 0.671251 GCGACAGACTAGATCAGGGG 59.329 60.000 0.00 0.00 0.00 4.79
134 135 1.686355 AGCGACAGACTAGATCAGGG 58.314 55.000 0.00 0.00 0.00 4.45
135 136 3.791973 AAAGCGACAGACTAGATCAGG 57.208 47.619 0.00 0.00 0.00 3.86
136 137 4.738124 TGAAAAGCGACAGACTAGATCAG 58.262 43.478 0.00 0.00 0.00 2.90
137 138 4.783764 TGAAAAGCGACAGACTAGATCA 57.216 40.909 0.00 0.00 0.00 2.92
138 139 5.233263 GGATTGAAAAGCGACAGACTAGATC 59.767 44.000 0.00 0.00 28.98 2.75
139 140 5.112686 GGATTGAAAAGCGACAGACTAGAT 58.887 41.667 0.00 0.00 28.98 1.98
140 141 4.495422 GGATTGAAAAGCGACAGACTAGA 58.505 43.478 0.00 0.00 28.98 2.43
141 142 3.304559 CGGATTGAAAAGCGACAGACTAG 59.695 47.826 0.00 0.00 28.98 2.57
142 143 3.057104 TCGGATTGAAAAGCGACAGACTA 60.057 43.478 0.00 0.00 28.98 2.59
143 144 2.069273 CGGATTGAAAAGCGACAGACT 58.931 47.619 0.00 0.00 28.98 3.24
144 145 2.066262 TCGGATTGAAAAGCGACAGAC 58.934 47.619 0.00 0.00 28.98 3.51
145 146 2.066262 GTCGGATTGAAAAGCGACAGA 58.934 47.619 0.00 0.00 36.38 3.41
146 147 1.201812 CGTCGGATTGAAAAGCGACAG 60.202 52.381 0.00 0.00 36.22 3.51
147 148 0.787787 CGTCGGATTGAAAAGCGACA 59.212 50.000 0.00 0.00 36.22 4.35
148 149 0.094730 CCGTCGGATTGAAAAGCGAC 59.905 55.000 4.91 0.00 34.29 5.19
149 150 0.038067 TCCGTCGGATTGAAAAGCGA 60.038 50.000 10.71 0.00 28.98 4.93
150 151 0.094730 GTCCGTCGGATTGAAAAGCG 59.905 55.000 18.75 0.00 32.73 4.68
151 152 0.094730 CGTCCGTCGGATTGAAAAGC 59.905 55.000 18.75 0.36 32.73 3.51
165 166 4.323477 TTTGCCCAGTCCCGTCCG 62.323 66.667 0.00 0.00 0.00 4.79
166 167 2.359975 CTTTGCCCAGTCCCGTCC 60.360 66.667 0.00 0.00 0.00 4.79
167 168 1.833787 TACCTTTGCCCAGTCCCGTC 61.834 60.000 0.00 0.00 0.00 4.79
168 169 1.838073 CTACCTTTGCCCAGTCCCGT 61.838 60.000 0.00 0.00 0.00 5.28
169 170 1.078426 CTACCTTTGCCCAGTCCCG 60.078 63.158 0.00 0.00 0.00 5.14
170 171 1.378646 GCTACCTTTGCCCAGTCCC 60.379 63.158 0.00 0.00 0.00 4.46
171 172 1.745489 CGCTACCTTTGCCCAGTCC 60.745 63.158 0.00 0.00 0.00 3.85
172 173 1.745489 CCGCTACCTTTGCCCAGTC 60.745 63.158 0.00 0.00 0.00 3.51
173 174 1.196104 TACCGCTACCTTTGCCCAGT 61.196 55.000 0.00 0.00 0.00 4.00
174 175 0.743345 GTACCGCTACCTTTGCCCAG 60.743 60.000 0.00 0.00 0.00 4.45
175 176 1.196104 AGTACCGCTACCTTTGCCCA 61.196 55.000 0.00 0.00 0.00 5.36
176 177 0.743345 CAGTACCGCTACCTTTGCCC 60.743 60.000 0.00 0.00 0.00 5.36
177 178 0.036671 ACAGTACCGCTACCTTTGCC 60.037 55.000 0.00 0.00 0.00 4.52
178 179 2.537401 CTACAGTACCGCTACCTTTGC 58.463 52.381 0.00 0.00 0.00 3.68
179 180 2.537401 GCTACAGTACCGCTACCTTTG 58.463 52.381 0.00 0.00 0.00 2.77
180 181 1.133790 CGCTACAGTACCGCTACCTTT 59.866 52.381 0.00 0.00 0.00 3.11
181 182 0.737219 CGCTACAGTACCGCTACCTT 59.263 55.000 0.00 0.00 0.00 3.50
182 183 0.393537 ACGCTACAGTACCGCTACCT 60.394 55.000 0.00 0.00 0.00 3.08
183 184 0.028637 GACGCTACAGTACCGCTACC 59.971 60.000 0.00 0.00 0.00 3.18
184 185 0.315706 CGACGCTACAGTACCGCTAC 60.316 60.000 0.00 0.00 0.00 3.58
185 186 2.009108 CGACGCTACAGTACCGCTA 58.991 57.895 0.00 0.00 0.00 4.26
186 187 2.789917 CGACGCTACAGTACCGCT 59.210 61.111 0.00 0.00 0.00 5.52
187 188 2.040213 TAGCGACGCTACAGTACCGC 62.040 60.000 25.04 0.00 40.44 5.68
188 189 2.009108 TAGCGACGCTACAGTACCG 58.991 57.895 25.04 0.00 40.44 4.02
196 197 1.153706 GGCAAAGGTAGCGACGCTA 60.154 57.895 25.04 25.04 40.44 4.26
197 198 2.434359 GGCAAAGGTAGCGACGCT 60.434 61.111 27.45 27.45 43.41 5.07
198 199 2.740826 TGGCAAAGGTAGCGACGC 60.741 61.111 13.03 13.03 0.00 5.19
199 200 1.626654 CTGTGGCAAAGGTAGCGACG 61.627 60.000 0.00 0.00 42.63 5.12
200 201 1.912371 GCTGTGGCAAAGGTAGCGAC 61.912 60.000 6.84 0.00 40.53 5.19
201 202 1.671054 GCTGTGGCAAAGGTAGCGA 60.671 57.895 6.84 0.00 38.54 4.93
202 203 1.965930 TGCTGTGGCAAAGGTAGCG 60.966 57.895 6.84 0.00 46.36 4.26
203 204 4.079446 TGCTGTGGCAAAGGTAGC 57.921 55.556 6.84 4.59 46.36 3.58
212 213 0.804989 ATTCGCTAACTTGCTGTGGC 59.195 50.000 0.00 0.00 39.26 5.01
213 214 2.094894 CAGATTCGCTAACTTGCTGTGG 59.905 50.000 0.00 0.00 0.00 4.17
214 215 2.995939 TCAGATTCGCTAACTTGCTGTG 59.004 45.455 0.00 0.00 0.00 3.66
215 216 3.319137 TCAGATTCGCTAACTTGCTGT 57.681 42.857 0.00 0.00 0.00 4.40
216 217 3.433274 TGTTCAGATTCGCTAACTTGCTG 59.567 43.478 0.00 0.00 0.00 4.41
217 218 3.433615 GTGTTCAGATTCGCTAACTTGCT 59.566 43.478 0.00 0.00 0.00 3.91
218 219 3.424962 GGTGTTCAGATTCGCTAACTTGC 60.425 47.826 0.00 0.00 0.00 4.01
219 220 3.997021 AGGTGTTCAGATTCGCTAACTTG 59.003 43.478 0.00 0.00 0.00 3.16
220 221 4.246458 GAGGTGTTCAGATTCGCTAACTT 58.754 43.478 0.00 0.00 0.00 2.66
221 222 3.258372 TGAGGTGTTCAGATTCGCTAACT 59.742 43.478 0.00 0.00 0.00 2.24
222 223 3.585862 TGAGGTGTTCAGATTCGCTAAC 58.414 45.455 0.00 0.00 0.00 2.34
223 224 3.953712 TGAGGTGTTCAGATTCGCTAA 57.046 42.857 0.00 0.00 0.00 3.09
224 225 3.585862 GTTGAGGTGTTCAGATTCGCTA 58.414 45.455 0.00 0.00 37.07 4.26
225 226 2.417719 GTTGAGGTGTTCAGATTCGCT 58.582 47.619 0.00 0.00 37.07 4.93
226 227 1.464997 GGTTGAGGTGTTCAGATTCGC 59.535 52.381 0.00 0.00 37.07 4.70
227 228 2.766313 TGGTTGAGGTGTTCAGATTCG 58.234 47.619 0.00 0.00 37.07 3.34
228 229 4.394300 CAGATGGTTGAGGTGTTCAGATTC 59.606 45.833 0.00 0.00 37.07 2.52
229 230 4.330250 CAGATGGTTGAGGTGTTCAGATT 58.670 43.478 0.00 0.00 37.07 2.40
230 231 3.871463 GCAGATGGTTGAGGTGTTCAGAT 60.871 47.826 0.00 0.00 37.07 2.90
231 232 2.550855 GCAGATGGTTGAGGTGTTCAGA 60.551 50.000 0.00 0.00 37.07 3.27
232 233 1.808945 GCAGATGGTTGAGGTGTTCAG 59.191 52.381 0.00 0.00 37.07 3.02
233 234 1.421268 AGCAGATGGTTGAGGTGTTCA 59.579 47.619 0.00 0.00 0.00 3.18
234 235 2.191128 AGCAGATGGTTGAGGTGTTC 57.809 50.000 0.00 0.00 0.00 3.18
235 236 2.158623 TGAAGCAGATGGTTGAGGTGTT 60.159 45.455 1.35 0.00 35.69 3.32
236 237 1.421268 TGAAGCAGATGGTTGAGGTGT 59.579 47.619 1.35 0.00 35.69 4.16
237 238 2.189594 TGAAGCAGATGGTTGAGGTG 57.810 50.000 1.35 0.00 35.69 4.00
238 239 2.957402 TTGAAGCAGATGGTTGAGGT 57.043 45.000 1.35 0.00 35.69 3.85
274 275 5.406477 GGATTGAAACAAACAAGAATGGAGC 59.594 40.000 0.00 0.00 0.00 4.70
393 394 1.156736 ATATAATGTCGCGGCTTGGC 58.843 50.000 13.81 0.00 0.00 4.52
394 395 4.629634 TCATTATATAATGTCGCGGCTTGG 59.370 41.667 27.01 5.37 42.70 3.61
395 396 5.778161 TCATTATATAATGTCGCGGCTTG 57.222 39.130 27.01 7.08 42.70 4.01
396 397 6.036083 GTCATCATTATATAATGTCGCGGCTT 59.964 38.462 27.01 1.49 42.70 4.35
397 398 5.520288 GTCATCATTATATAATGTCGCGGCT 59.480 40.000 27.01 0.00 42.70 5.52
398 399 5.290885 TGTCATCATTATATAATGTCGCGGC 59.709 40.000 27.01 18.12 42.70 6.53
399 400 6.508563 GCTGTCATCATTATATAATGTCGCGG 60.509 42.308 27.01 21.09 42.70 6.46
400 401 6.406018 GCTGTCATCATTATATAATGTCGCG 58.594 40.000 27.01 17.00 42.70 5.87
401 402 6.406018 CGCTGTCATCATTATATAATGTCGC 58.594 40.000 27.01 20.11 42.70 5.19
402 403 6.019559 CCCGCTGTCATCATTATATAATGTCG 60.020 42.308 27.01 20.65 42.70 4.35
403 404 6.258727 CCCCGCTGTCATCATTATATAATGTC 59.741 42.308 27.01 18.34 42.70 3.06
404 405 6.115446 CCCCGCTGTCATCATTATATAATGT 58.885 40.000 27.01 16.00 42.70 2.71
405 406 5.008019 GCCCCGCTGTCATCATTATATAATG 59.992 44.000 23.96 23.96 43.32 1.90
406 407 5.126067 GCCCCGCTGTCATCATTATATAAT 58.874 41.667 1.91 1.91 0.00 1.28
407 408 4.019771 TGCCCCGCTGTCATCATTATATAA 60.020 41.667 0.00 0.00 0.00 0.98
408 409 3.517500 TGCCCCGCTGTCATCATTATATA 59.482 43.478 0.00 0.00 0.00 0.86
409 410 2.305635 TGCCCCGCTGTCATCATTATAT 59.694 45.455 0.00 0.00 0.00 0.86
410 411 1.696884 TGCCCCGCTGTCATCATTATA 59.303 47.619 0.00 0.00 0.00 0.98
411 412 0.473755 TGCCCCGCTGTCATCATTAT 59.526 50.000 0.00 0.00 0.00 1.28
412 413 0.179048 CTGCCCCGCTGTCATCATTA 60.179 55.000 0.00 0.00 0.00 1.90
451 455 3.728845 TGGAAGCACGATAATTAGCTCC 58.271 45.455 0.00 0.00 36.07 4.70
456 461 4.065088 GGCAGATGGAAGCACGATAATTA 58.935 43.478 0.00 0.00 0.00 1.40
545 550 7.693951 CGCCTTCTTTTAGATGTTTACAAGATG 59.306 37.037 0.00 0.00 0.00 2.90
557 562 1.429148 CGCGCCGCCTTCTTTTAGAT 61.429 55.000 2.28 0.00 0.00 1.98
562 567 2.775032 TTACTCGCGCCGCCTTCTTT 62.775 55.000 2.28 0.00 0.00 2.52
828 836 1.080434 GAGCTTGAACTCGGCGAGT 60.080 57.895 34.91 34.91 45.64 4.18
1206 1242 4.697756 CAGCGCCGTCCCCAGAAA 62.698 66.667 2.29 0.00 0.00 2.52
1215 1251 4.681978 GACAGGTTCCAGCGCCGT 62.682 66.667 2.29 0.00 0.00 5.68
1771 1819 5.069501 AGCGAGTAATAAACGAGTTTCCT 57.930 39.130 4.32 0.00 34.23 3.36
1772 1820 5.119743 ACAAGCGAGTAATAAACGAGTTTCC 59.880 40.000 4.32 0.00 34.23 3.13
1795 2030 2.479837 TCGTCAGTTCATTGGTGTGAC 58.520 47.619 0.00 0.00 35.26 3.67
1829 2064 2.755655 CCGTATTTTGGGTGTGCCATTA 59.244 45.455 0.00 0.00 36.17 1.90
1882 2117 6.489361 TGGATTTGAAACAAATTTGATTGGGG 59.511 34.615 24.64 0.00 34.56 4.96
1969 2204 0.625316 TACATGGCCTGCACCTGAAT 59.375 50.000 3.32 0.00 0.00 2.57
1973 2208 2.273449 GCTACATGGCCTGCACCT 59.727 61.111 3.32 0.00 0.00 4.00
1987 2222 3.890147 GAGGAACGATAGGAAAGAGGCTA 59.110 47.826 0.00 0.00 43.77 3.93
2314 2555 2.898472 AATACCGCTCTCCTGGCCCT 62.898 60.000 0.00 0.00 0.00 5.19
2341 2582 4.459089 GGCGAGCTGTCCCTGGAC 62.459 72.222 9.44 9.44 44.77 4.02
2497 2738 5.012458 GGAAGTCATGGATGATGATGACCTA 59.988 44.000 0.00 0.00 46.54 3.08
2518 2759 2.354704 CGATGCTGGTAGGAAAGTGGAA 60.355 50.000 0.00 0.00 0.00 3.53
2557 2798 0.952497 TGAAAGCTGCGCTGGAGAAG 60.952 55.000 16.47 0.66 39.62 2.85
2587 2828 5.991328 TGGATGCGATGAAAAAGATAGAC 57.009 39.130 0.00 0.00 0.00 2.59
2629 2870 0.037975 CCAACAGCAATGAAGGCACC 60.038 55.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.