Multiple sequence alignment - TraesCS7B01G184600

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 TraesCS7B01G184600 chr7B 100.000 3404 0 0 1 3404 297414102 297410699 0.000000e+00 6287.0
1 TraesCS7B01G184600 chr7B 86.716 271 27 8 2913 3181 677059638 677059901 3.320000e-75 292.0
2 TraesCS7B01G184600 chr7A 92.017 2330 127 32 355 2642 391894988 391897300 0.000000e+00 3217.0
3 TraesCS7B01G184600 chr7A 94.418 627 22 5 2789 3404 391897293 391897917 0.000000e+00 952.0
4 TraesCS7B01G184600 chr7A 92.857 98 7 0 1 98 68191061 68191158 3.540000e-30 143.0
5 TraesCS7B01G184600 chr7D 96.262 1926 45 10 736 2642 353912862 353914779 0.000000e+00 3133.0
6 TraesCS7B01G184600 chr7D 93.131 626 22 5 2789 3404 353914772 353915386 0.000000e+00 898.0
7 TraesCS7B01G184600 chr7D 88.667 300 23 10 2917 3213 554145806 554146097 4.180000e-94 355.0
8 TraesCS7B01G184600 chr7D 78.926 484 66 23 288 746 353911347 353911819 2.570000e-76 296.0
9 TraesCS7B01G184600 chr7D 97.080 137 4 0 2642 2778 76982552 76982688 7.350000e-57 231.0
10 TraesCS7B01G184600 chr7D 87.342 79 7 3 159 236 633356197 633356273 1.680000e-13 87.9
11 TraesCS7B01G184600 chr5A 91.096 292 21 5 2922 3211 329237090 329236802 1.150000e-104 390.0
12 TraesCS7B01G184600 chr5A 75.769 260 29 16 1 229 703191056 703191312 2.160000e-17 100.0
13 TraesCS7B01G184600 chr2A 90.572 297 21 6 2917 3211 604138520 604138229 1.480000e-103 387.0
14 TraesCS7B01G184600 chr2A 92.857 98 7 0 1 98 683569552 683569649 3.540000e-30 143.0
15 TraesCS7B01G184600 chr2D 87.960 299 27 8 2917 3213 85604762 85605053 9.040000e-91 344.0
16 TraesCS7B01G184600 chr2D 79.365 252 30 8 1 230 569260921 569261172 1.260000e-34 158.0
17 TraesCS7B01G184600 chr3A 87.970 266 24 7 2917 3180 102892357 102892098 1.190000e-79 307.0
18 TraesCS7B01G184600 chr3A 86.207 290 21 12 2917 3192 195173271 195173555 2.570000e-76 296.0
19 TraesCS7B01G184600 chr3A 82.609 253 17 8 2 230 10698334 10698583 7.450000e-47 198.0
20 TraesCS7B01G184600 chr3A 79.468 263 21 10 1 230 487651088 487651350 4.550000e-34 156.0
21 TraesCS7B01G184600 chrUn 97.080 137 4 0 2642 2778 20761972 20761836 7.350000e-57 231.0
22 TraesCS7B01G184600 chr5D 97.080 137 4 0 2642 2778 236022783 236022647 7.350000e-57 231.0
23 TraesCS7B01G184600 chr5D 97.080 137 4 0 2642 2778 290185551 290185415 7.350000e-57 231.0
24 TraesCS7B01G184600 chr5D 81.226 261 18 10 1 230 54690813 54690553 7.500000e-42 182.0
25 TraesCS7B01G184600 chr5D 80.162 247 25 4 6 230 421880758 421880514 2.720000e-36 163.0
26 TraesCS7B01G184600 chr5D 79.447 253 27 9 2 232 445208511 445208760 4.550000e-34 156.0
27 TraesCS7B01G184600 chr3D 97.080 137 4 0 2642 2778 29056598 29056734 7.350000e-57 231.0
28 TraesCS7B01G184600 chr3D 97.080 137 4 0 2642 2778 49676657 49676793 7.350000e-57 231.0
29 TraesCS7B01G184600 chr3D 97.080 137 4 0 2642 2778 307294181 307294317 7.350000e-57 231.0
30 TraesCS7B01G184600 chr3D 97.080 137 4 0 2642 2778 453270583 453270719 7.350000e-57 231.0
31 TraesCS7B01G184600 chr3D 80.451 266 16 11 1 232 299556870 299556607 1.620000e-38 171.0
32 TraesCS7B01G184600 chr1D 97.080 137 4 0 2642 2778 314177350 314177214 7.350000e-57 231.0
33 TraesCS7B01G184600 chr6D 80.682 264 17 9 1 230 36685983 36685720 1.260000e-39 174.0
34 TraesCS7B01G184600 chr6D 80.534 262 19 8 1 230 464852010 464852271 4.520000e-39 172.0
35 TraesCS7B01G184600 chr3B 80.237 253 25 6 1 230 592858811 592858561 2.100000e-37 167.0
36 TraesCS7B01G184600 chr5B 92.929 99 5 2 1 98 573864977 573864880 3.540000e-30 143.0
37 TraesCS7B01G184600 chr5B 79.638 221 20 12 34 230 591857788 591858007 5.930000e-28 135.0
38 TraesCS7B01G184600 chr5B 77.381 252 28 8 7 232 52643169 52642921 4.610000e-24 122.0
39 TraesCS7B01G184600 chr5B 90.588 85 8 0 2 86 528669482 528669566 2.780000e-21 113.0
40 TraesCS7B01G184600 chr4B 80.147 136 22 5 97 228 509586203 509586069 2.800000e-16 97.1
41 TraesCS7B01G184600 chr4D 79.021 143 16 8 102 230 324221574 324221432 6.050000e-13 86.1


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 TraesCS7B01G184600 chr7B 297410699 297414102 3403 True 6287.000000 6287 100.000000 1 3404 1 chr7B.!!$R1 3403
1 TraesCS7B01G184600 chr7A 391894988 391897917 2929 False 2084.500000 3217 93.217500 355 3404 2 chr7A.!!$F2 3049
2 TraesCS7B01G184600 chr7D 353911347 353915386 4039 False 1442.333333 3133 89.439667 288 3404 3 chr7D.!!$F4 3116

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
449 457 0.244721 CACAGTCGTGCCTCTCATGA 59.755 55.0 0.00 0.0 38.33 3.07 F
841 1921 0.472471 AAACCTTCAGGCAAGACGGA 59.528 50.0 9.02 0.0 39.32 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2045 3141 1.303309 AGGCATGCTCGATAGTTTGC 58.697 50.0 18.92 0.00 34.13 3.68 R
2674 3775 0.105862 TAGAGCCTAGGCCCGCTTAA 60.106 55.0 30.42 8.52 43.17 1.85 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
22 23 5.319140 CAAATCATTTGGACATCTGAGCA 57.681 39.130 1.73 0.00 37.01 4.26
23 24 5.340803 CAAATCATTTGGACATCTGAGCAG 58.659 41.667 1.73 0.00 37.01 4.24
24 25 2.362736 TCATTTGGACATCTGAGCAGC 58.637 47.619 0.00 0.00 0.00 5.25
25 26 2.026542 TCATTTGGACATCTGAGCAGCT 60.027 45.455 0.00 0.00 0.00 4.24
26 27 2.105006 TTTGGACATCTGAGCAGCTC 57.895 50.000 16.21 16.21 0.00 4.09
27 28 1.273759 TTGGACATCTGAGCAGCTCT 58.726 50.000 23.15 2.04 0.00 4.09
28 29 0.822811 TGGACATCTGAGCAGCTCTC 59.177 55.000 23.15 11.57 42.23 3.20
35 36 3.711937 TGAGCAGCTCTCAGCAAAA 57.288 47.368 23.15 0.00 46.34 2.44
36 37 1.971481 TGAGCAGCTCTCAGCAAAAA 58.029 45.000 23.15 0.00 46.34 1.94
87 88 8.512138 AGTTTACTATTCATGTACTGTTTTGGC 58.488 33.333 0.00 0.00 0.00 4.52
88 89 5.897377 ACTATTCATGTACTGTTTTGGCC 57.103 39.130 0.00 0.00 0.00 5.36
89 90 5.570320 ACTATTCATGTACTGTTTTGGCCT 58.430 37.500 3.32 0.00 0.00 5.19
90 91 4.789012 ATTCATGTACTGTTTTGGCCTG 57.211 40.909 3.32 0.00 0.00 4.85
91 92 3.500448 TCATGTACTGTTTTGGCCTGA 57.500 42.857 3.32 0.00 0.00 3.86
92 93 4.032960 TCATGTACTGTTTTGGCCTGAT 57.967 40.909 3.32 0.00 0.00 2.90
93 94 4.406456 TCATGTACTGTTTTGGCCTGATT 58.594 39.130 3.32 0.00 0.00 2.57
94 95 4.832266 TCATGTACTGTTTTGGCCTGATTT 59.168 37.500 3.32 0.00 0.00 2.17
95 96 4.582701 TGTACTGTTTTGGCCTGATTTG 57.417 40.909 3.32 0.00 0.00 2.32
96 97 3.957497 TGTACTGTTTTGGCCTGATTTGT 59.043 39.130 3.32 0.00 0.00 2.83
97 98 3.733443 ACTGTTTTGGCCTGATTTGTC 57.267 42.857 3.32 0.00 0.00 3.18
98 99 3.030291 ACTGTTTTGGCCTGATTTGTCA 58.970 40.909 3.32 0.00 0.00 3.58
99 100 3.068590 ACTGTTTTGGCCTGATTTGTCAG 59.931 43.478 3.32 4.73 37.48 3.51
100 101 3.295093 TGTTTTGGCCTGATTTGTCAGA 58.705 40.909 3.32 0.00 39.99 3.27
101 102 3.896888 TGTTTTGGCCTGATTTGTCAGAT 59.103 39.130 3.32 0.00 39.99 2.90
102 103 4.240096 GTTTTGGCCTGATTTGTCAGATG 58.760 43.478 3.32 0.00 39.99 2.90
103 104 2.885135 TGGCCTGATTTGTCAGATGT 57.115 45.000 3.32 0.00 39.99 3.06
104 105 2.715046 TGGCCTGATTTGTCAGATGTC 58.285 47.619 3.32 0.00 39.99 3.06
105 106 2.019984 GGCCTGATTTGTCAGATGTCC 58.980 52.381 6.99 0.18 39.99 4.02
106 107 2.618816 GGCCTGATTTGTCAGATGTCCA 60.619 50.000 6.99 0.00 39.99 4.02
107 108 3.084039 GCCTGATTTGTCAGATGTCCAA 58.916 45.455 6.99 0.00 39.99 3.53
108 109 3.507233 GCCTGATTTGTCAGATGTCCAAA 59.493 43.478 6.99 0.00 39.99 3.28
109 110 4.159135 GCCTGATTTGTCAGATGTCCAAAT 59.841 41.667 6.99 10.71 40.47 2.32
110 111 5.647589 CCTGATTTGTCAGATGTCCAAATG 58.352 41.667 6.99 5.34 38.53 2.32
111 112 5.416639 CCTGATTTGTCAGATGTCCAAATGA 59.583 40.000 6.99 8.01 38.53 2.57
112 113 6.096423 CCTGATTTGTCAGATGTCCAAATGAT 59.904 38.462 6.99 0.00 38.53 2.45
113 114 7.363530 CCTGATTTGTCAGATGTCCAAATGATT 60.364 37.037 6.99 0.00 38.53 2.57
114 115 7.898918 TGATTTGTCAGATGTCCAAATGATTT 58.101 30.769 13.82 0.00 38.53 2.17
115 116 7.815549 TGATTTGTCAGATGTCCAAATGATTTG 59.184 33.333 10.84 10.84 38.53 2.32
116 117 6.897706 TTGTCAGATGTCCAAATGATTTGA 57.102 33.333 18.82 0.00 43.26 2.69
117 118 6.897706 TGTCAGATGTCCAAATGATTTGAA 57.102 33.333 18.82 0.00 43.26 2.69
118 119 7.287512 TGTCAGATGTCCAAATGATTTGAAA 57.712 32.000 18.82 4.37 43.26 2.69
119 120 7.898918 TGTCAGATGTCCAAATGATTTGAAAT 58.101 30.769 18.82 9.08 43.26 2.17
120 121 8.369424 TGTCAGATGTCCAAATGATTTGAAATT 58.631 29.630 18.82 1.83 43.26 1.82
121 122 9.211485 GTCAGATGTCCAAATGATTTGAAATTT 57.789 29.630 18.82 0.00 43.26 1.82
122 123 9.781633 TCAGATGTCCAAATGATTTGAAATTTT 57.218 25.926 18.82 0.00 43.26 1.82
123 124 9.820229 CAGATGTCCAAATGATTTGAAATTTTG 57.180 29.630 18.82 7.68 43.26 2.44
124 125 9.781633 AGATGTCCAAATGATTTGAAATTTTGA 57.218 25.926 18.82 3.41 43.26 2.69
126 127 8.961294 TGTCCAAATGATTTGAAATTTTGAGT 57.039 26.923 18.82 0.00 43.26 3.41
127 128 8.828644 TGTCCAAATGATTTGAAATTTTGAGTG 58.171 29.630 18.82 0.00 43.26 3.51
128 129 8.284693 GTCCAAATGATTTGAAATTTTGAGTGG 58.715 33.333 18.82 7.79 43.26 4.00
129 130 7.444792 TCCAAATGATTTGAAATTTTGAGTGGG 59.555 33.333 18.82 0.00 43.26 4.61
130 131 6.806388 AATGATTTGAAATTTTGAGTGGGC 57.194 33.333 0.00 0.00 0.00 5.36
131 132 4.640364 TGATTTGAAATTTTGAGTGGGCC 58.360 39.130 0.00 0.00 0.00 5.80
132 133 4.347583 TGATTTGAAATTTTGAGTGGGCCT 59.652 37.500 4.53 0.00 0.00 5.19
133 134 4.335400 TTTGAAATTTTGAGTGGGCCTC 57.665 40.909 4.53 0.00 40.89 4.70
142 143 2.359850 GTGGGCCTCACGCATCAA 60.360 61.111 4.53 0.00 43.95 2.57
143 144 1.971167 GTGGGCCTCACGCATCAAA 60.971 57.895 4.53 0.00 43.95 2.69
144 145 1.001020 TGGGCCTCACGCATCAAAT 60.001 52.632 4.53 0.00 40.31 2.32
145 146 0.611618 TGGGCCTCACGCATCAAATT 60.612 50.000 4.53 0.00 40.31 1.82
146 147 0.532115 GGGCCTCACGCATCAAATTT 59.468 50.000 0.84 0.00 40.31 1.82
147 148 1.066929 GGGCCTCACGCATCAAATTTT 60.067 47.619 0.84 0.00 40.31 1.82
148 149 2.262211 GGCCTCACGCATCAAATTTTC 58.738 47.619 0.00 0.00 40.31 2.29
149 150 2.094545 GGCCTCACGCATCAAATTTTCT 60.095 45.455 0.00 0.00 40.31 2.52
150 151 3.128589 GGCCTCACGCATCAAATTTTCTA 59.871 43.478 0.00 0.00 40.31 2.10
151 152 4.098416 GCCTCACGCATCAAATTTTCTAC 58.902 43.478 0.00 0.00 37.47 2.59
152 153 4.662145 CCTCACGCATCAAATTTTCTACC 58.338 43.478 0.00 0.00 0.00 3.18
153 154 4.396166 CCTCACGCATCAAATTTTCTACCT 59.604 41.667 0.00 0.00 0.00 3.08
154 155 5.447818 CCTCACGCATCAAATTTTCTACCTC 60.448 44.000 0.00 0.00 0.00 3.85
155 156 5.000591 TCACGCATCAAATTTTCTACCTCA 58.999 37.500 0.00 0.00 0.00 3.86
156 157 5.647658 TCACGCATCAAATTTTCTACCTCAT 59.352 36.000 0.00 0.00 0.00 2.90
157 158 6.821160 TCACGCATCAAATTTTCTACCTCATA 59.179 34.615 0.00 0.00 0.00 2.15
158 159 7.335673 TCACGCATCAAATTTTCTACCTCATAA 59.664 33.333 0.00 0.00 0.00 1.90
159 160 8.131100 CACGCATCAAATTTTCTACCTCATAAT 58.869 33.333 0.00 0.00 0.00 1.28
160 161 8.686334 ACGCATCAAATTTTCTACCTCATAATT 58.314 29.630 0.00 0.00 0.00 1.40
161 162 9.520204 CGCATCAAATTTTCTACCTCATAATTT 57.480 29.630 0.00 0.00 0.00 1.82
214 215 4.365514 TTTTCTAACCAGGTGCAGATGA 57.634 40.909 0.00 0.00 0.00 2.92
215 216 3.616956 TTCTAACCAGGTGCAGATGAG 57.383 47.619 0.00 0.00 0.00 2.90
216 217 1.208052 TCTAACCAGGTGCAGATGAGC 59.792 52.381 0.00 0.00 0.00 4.26
217 218 0.253044 TAACCAGGTGCAGATGAGCC 59.747 55.000 0.00 0.00 0.00 4.70
218 219 1.495579 AACCAGGTGCAGATGAGCCT 61.496 55.000 0.00 0.00 0.00 4.58
219 220 1.451567 CCAGGTGCAGATGAGCCTG 60.452 63.158 10.99 10.99 45.86 4.85
220 221 1.451567 CAGGTGCAGATGAGCCTGG 60.452 63.158 10.25 0.00 43.39 4.45
221 222 2.124403 GGTGCAGATGAGCCTGGG 60.124 66.667 0.00 0.00 34.82 4.45
222 223 2.827642 GTGCAGATGAGCCTGGGC 60.828 66.667 3.00 3.00 42.33 5.36
223 224 3.332385 TGCAGATGAGCCTGGGCA 61.332 61.111 14.39 0.00 44.88 5.36
224 225 2.827642 GCAGATGAGCCTGGGCAC 60.828 66.667 14.39 8.23 44.88 5.01
236 237 2.126502 GGGCACCGAAATGTTGCG 60.127 61.111 0.00 0.00 40.86 4.85
237 238 2.642700 GGCACCGAAATGTTGCGT 59.357 55.556 0.00 0.00 0.00 5.24
238 239 1.007849 GGCACCGAAATGTTGCGTT 60.008 52.632 0.00 0.00 0.00 4.84
239 240 1.001745 GGCACCGAAATGTTGCGTTC 61.002 55.000 0.00 0.00 0.00 3.95
240 241 1.327292 GCACCGAAATGTTGCGTTCG 61.327 55.000 0.00 0.00 44.80 3.95
252 253 8.682128 AAATGTTGCGTTCGAAAAATATATGT 57.318 26.923 0.00 0.00 0.00 2.29
253 254 8.682128 AATGTTGCGTTCGAAAAATATATGTT 57.318 26.923 0.00 0.00 0.00 2.71
254 255 8.682128 ATGTTGCGTTCGAAAAATATATGTTT 57.318 26.923 0.00 0.17 0.00 2.83
255 256 8.508800 TGTTGCGTTCGAAAAATATATGTTTT 57.491 26.923 0.00 4.49 32.94 2.43
256 257 8.969267 TGTTGCGTTCGAAAAATATATGTTTTT 58.031 25.926 19.22 19.22 42.29 1.94
276 277 5.903764 TTTTTCATGGAAGCAAAATCGTG 57.096 34.783 0.00 0.00 0.00 4.35
277 278 4.582701 TTTCATGGAAGCAAAATCGTGT 57.417 36.364 0.00 0.00 0.00 4.49
278 279 3.829886 TCATGGAAGCAAAATCGTGTC 57.170 42.857 0.00 0.00 0.00 3.67
279 280 3.411446 TCATGGAAGCAAAATCGTGTCT 58.589 40.909 0.00 0.00 0.00 3.41
280 281 3.436704 TCATGGAAGCAAAATCGTGTCTC 59.563 43.478 0.00 0.00 0.00 3.36
281 282 3.126001 TGGAAGCAAAATCGTGTCTCT 57.874 42.857 0.00 0.00 0.00 3.10
282 283 3.067106 TGGAAGCAAAATCGTGTCTCTC 58.933 45.455 0.00 0.00 0.00 3.20
283 284 2.092838 GGAAGCAAAATCGTGTCTCTCG 59.907 50.000 0.00 0.00 0.00 4.04
284 285 1.071605 AGCAAAATCGTGTCTCTCGC 58.928 50.000 0.00 0.00 0.00 5.03
285 286 0.790207 GCAAAATCGTGTCTCTCGCA 59.210 50.000 0.00 0.00 0.00 5.10
286 287 1.194547 GCAAAATCGTGTCTCTCGCAA 59.805 47.619 0.00 0.00 0.00 4.85
294 295 2.644078 GTGTCTCTCGCAAAAGCAAAG 58.356 47.619 0.00 0.00 0.00 2.77
297 298 0.311790 CTCTCGCAAAAGCAAAGCCA 59.688 50.000 0.00 0.00 0.00 4.75
300 301 0.388659 TCGCAAAAGCAAAGCCATGT 59.611 45.000 0.00 0.00 0.00 3.21
308 309 1.712081 CAAAGCCATGTCTCTCGCG 59.288 57.895 0.00 0.00 0.00 5.87
309 310 0.737367 CAAAGCCATGTCTCTCGCGA 60.737 55.000 9.26 9.26 0.00 5.87
313 314 0.458543 GCCATGTCTCTCGCGAAAGA 60.459 55.000 8.35 8.35 0.00 2.52
378 380 1.611491 TGCCTTTCGCGGAAGAAAAAT 59.389 42.857 28.73 0.00 42.08 1.82
433 441 4.909696 TTTTTCATTTTCGAGAGCCACA 57.090 36.364 0.00 0.00 0.00 4.17
435 443 2.839486 TCATTTTCGAGAGCCACAGT 57.161 45.000 0.00 0.00 0.00 3.55
446 454 3.051210 CCACAGTCGTGCCTCTCA 58.949 61.111 0.00 0.00 42.17 3.27
447 455 1.593787 CCACAGTCGTGCCTCTCAT 59.406 57.895 0.00 0.00 42.17 2.90
449 457 0.244721 CACAGTCGTGCCTCTCATGA 59.755 55.000 0.00 0.00 38.33 3.07
462 470 5.065914 GCCTCTCATGATAGCAAAACCATA 58.934 41.667 0.00 0.00 0.00 2.74
540 548 9.705290 TTTTTGTCAAAAAGTTAAGAAAGAGCT 57.295 25.926 17.56 0.00 36.65 4.09
544 552 8.567948 TGTCAAAAAGTTAAGAAAGAGCTATGG 58.432 33.333 0.00 0.00 0.00 2.74
692 720 0.816018 TTGTTGCGAGGCTTCCGAAA 60.816 50.000 0.00 0.00 0.00 3.46
793 1873 1.066502 GCACGGGGCAAAACCATAATT 60.067 47.619 0.00 0.00 43.97 1.40
794 1874 2.166664 GCACGGGGCAAAACCATAATTA 59.833 45.455 0.00 0.00 43.97 1.40
837 1917 2.616842 GACGAAAAACCTTCAGGCAAGA 59.383 45.455 0.00 0.00 39.32 3.02
838 1918 2.357952 ACGAAAAACCTTCAGGCAAGAC 59.642 45.455 0.00 0.00 39.32 3.01
839 1919 2.602217 CGAAAAACCTTCAGGCAAGACG 60.602 50.000 0.00 0.00 39.32 4.18
840 1920 1.318576 AAAACCTTCAGGCAAGACGG 58.681 50.000 0.00 1.75 39.32 4.79
841 1921 0.472471 AAACCTTCAGGCAAGACGGA 59.528 50.000 9.02 0.00 39.32 4.69
918 2000 0.675837 GCTTAAACCCTCGGTCCACC 60.676 60.000 0.00 0.00 33.12 4.61
1119 2205 1.021390 CAAGGTAGCTCCCTGTTGCG 61.021 60.000 0.00 0.00 34.19 4.85
1167 2253 2.359230 GCCTGCCTGCTCGTTTCT 60.359 61.111 0.00 0.00 0.00 2.52
1223 2309 0.586319 CTTGTTGTTCGTGACCGCAT 59.414 50.000 0.00 0.00 0.00 4.73
1226 2312 1.000052 TGTTGTTCGTGACCGCATAGA 60.000 47.619 0.00 0.00 0.00 1.98
1275 2361 2.290367 GTGGCTATGTGATTATGCGCAA 59.710 45.455 17.11 0.00 0.00 4.85
1590 2686 8.821147 TGACAACTTATTAGTGTAATGTTCGT 57.179 30.769 0.00 0.00 34.01 3.85
1591 2687 9.263538 TGACAACTTATTAGTGTAATGTTCGTT 57.736 29.630 0.00 0.00 34.01 3.85
1803 2899 6.715280 TGAGAGCAGGAAGATGTTTTATCTT 58.285 36.000 2.05 2.05 40.72 2.40
1886 2982 7.890127 TGAAGATCTAAATCATGAACAACCCTT 59.110 33.333 0.00 0.00 34.07 3.95
2017 3113 2.267351 TTTGCCCATGCTGTGTCGG 61.267 57.895 0.00 0.00 38.71 4.79
2386 3482 0.950116 TGTTCATGCATGCGACACAA 59.050 45.000 22.25 6.98 0.00 3.33
2642 3743 1.200020 CCGTTGCCTCAAGAAATGGTC 59.800 52.381 0.00 0.00 0.00 4.02
2643 3744 1.879380 CGTTGCCTCAAGAAATGGTCA 59.121 47.619 0.00 0.00 0.00 4.02
2644 3745 2.489329 CGTTGCCTCAAGAAATGGTCAT 59.511 45.455 0.00 0.00 0.00 3.06
2645 3746 3.689161 CGTTGCCTCAAGAAATGGTCATA 59.311 43.478 0.00 0.00 0.00 2.15
2646 3747 4.201851 CGTTGCCTCAAGAAATGGTCATAG 60.202 45.833 0.00 0.00 0.00 2.23
2647 3748 4.842531 TGCCTCAAGAAATGGTCATAGA 57.157 40.909 0.00 0.00 0.00 1.98
2648 3749 5.378230 TGCCTCAAGAAATGGTCATAGAT 57.622 39.130 0.00 0.00 0.00 1.98
2649 3750 6.499106 TGCCTCAAGAAATGGTCATAGATA 57.501 37.500 0.00 0.00 0.00 1.98
2650 3751 6.899089 TGCCTCAAGAAATGGTCATAGATAA 58.101 36.000 0.00 0.00 0.00 1.75
2651 3752 7.345691 TGCCTCAAGAAATGGTCATAGATAAA 58.654 34.615 0.00 0.00 0.00 1.40
2652 3753 7.833682 TGCCTCAAGAAATGGTCATAGATAAAA 59.166 33.333 0.00 0.00 0.00 1.52
2653 3754 8.686334 GCCTCAAGAAATGGTCATAGATAAAAA 58.314 33.333 0.00 0.00 0.00 1.94
2689 3790 2.592001 GCTTAAGCGGGCCTAGGC 60.592 66.667 26.55 26.55 41.06 3.93
2690 3791 3.108288 GCTTAAGCGGGCCTAGGCT 62.108 63.158 32.18 15.49 42.33 4.58
2691 3792 1.069935 CTTAAGCGGGCCTAGGCTC 59.930 63.158 32.18 28.79 38.88 4.70
2692 3793 1.382695 TTAAGCGGGCCTAGGCTCT 60.383 57.895 30.77 21.84 39.97 4.09
2693 3794 0.105862 TTAAGCGGGCCTAGGCTCTA 60.106 55.000 30.77 14.38 39.97 2.43
2694 3795 0.539901 TAAGCGGGCCTAGGCTCTAG 60.540 60.000 30.77 17.66 39.97 2.43
2695 3796 3.307108 GCGGGCCTAGGCTCTAGG 61.307 72.222 30.77 16.90 39.97 3.02
2701 3802 1.742768 CCTAGGCTCTAGGCGTTGG 59.257 63.158 13.35 10.22 46.23 3.77
2702 3803 1.068250 CTAGGCTCTAGGCGTTGGC 59.932 63.158 0.00 0.00 46.23 4.52
2703 3804 1.676678 CTAGGCTCTAGGCGTTGGCA 61.677 60.000 0.00 0.00 46.23 4.92
2704 3805 1.261938 TAGGCTCTAGGCGTTGGCAA 61.262 55.000 0.00 0.00 46.23 4.52
2705 3806 1.674322 GGCTCTAGGCGTTGGCAAA 60.674 57.895 0.00 0.00 42.47 3.68
2706 3807 1.241315 GGCTCTAGGCGTTGGCAAAA 61.241 55.000 0.00 0.00 42.47 2.44
2707 3808 0.109735 GCTCTAGGCGTTGGCAAAAC 60.110 55.000 0.00 0.00 42.47 2.43
2708 3809 0.165944 CTCTAGGCGTTGGCAAAACG 59.834 55.000 16.88 16.88 45.56 3.60
2736 3837 4.994734 CGCATAACTACGCTTAATCTGTG 58.005 43.478 0.00 0.00 0.00 3.66
2737 3838 4.606232 CGCATAACTACGCTTAATCTGTGC 60.606 45.833 0.00 0.00 0.00 4.57
2738 3839 4.270084 GCATAACTACGCTTAATCTGTGCA 59.730 41.667 0.00 0.00 0.00 4.57
2739 3840 5.050091 GCATAACTACGCTTAATCTGTGCAT 60.050 40.000 0.00 0.00 0.00 3.96
2740 3841 6.145534 GCATAACTACGCTTAATCTGTGCATA 59.854 38.462 0.00 0.00 0.00 3.14
2741 3842 7.307160 GCATAACTACGCTTAATCTGTGCATAA 60.307 37.037 0.00 0.00 0.00 1.90
2742 3843 5.968387 ACTACGCTTAATCTGTGCATAAC 57.032 39.130 0.00 0.00 0.00 1.89
2743 3844 5.661458 ACTACGCTTAATCTGTGCATAACT 58.339 37.500 0.00 0.00 0.00 2.24
2744 3845 4.864916 ACGCTTAATCTGTGCATAACTG 57.135 40.909 0.00 0.00 0.00 3.16
2755 3856 2.693797 GCATAACTGCGCATAAGCAT 57.306 45.000 12.24 0.00 46.97 3.79
2756 3857 2.313234 GCATAACTGCGCATAAGCATG 58.687 47.619 12.24 11.51 46.97 4.06
2769 3870 2.956987 GCATGCGCTTTGGTCAGT 59.043 55.556 9.73 0.00 34.30 3.41
2770 3871 2.170738 GCATGCGCTTTGGTCAGTA 58.829 52.632 9.73 0.00 34.30 2.74
2771 3872 0.521291 GCATGCGCTTTGGTCAGTAA 59.479 50.000 9.73 0.00 34.30 2.24
2772 3873 1.068610 GCATGCGCTTTGGTCAGTAAA 60.069 47.619 9.73 0.00 34.30 2.01
2773 3874 2.855180 CATGCGCTTTGGTCAGTAAAG 58.145 47.619 9.73 0.00 38.00 1.85
2779 3880 3.559238 CTTTGGTCAGTAAAGCGCATT 57.441 42.857 11.47 6.65 0.00 3.56
2780 3881 2.987413 TTGGTCAGTAAAGCGCATTG 57.013 45.000 11.47 0.00 0.00 2.82
2781 3882 2.177394 TGGTCAGTAAAGCGCATTGA 57.823 45.000 11.47 0.00 0.00 2.57
2782 3883 2.499197 TGGTCAGTAAAGCGCATTGAA 58.501 42.857 11.47 0.00 0.00 2.69
2783 3884 2.225491 TGGTCAGTAAAGCGCATTGAAC 59.775 45.455 11.47 4.86 0.00 3.18
2784 3885 2.484264 GGTCAGTAAAGCGCATTGAACT 59.516 45.455 11.47 1.99 0.00 3.01
2785 3886 3.682858 GGTCAGTAAAGCGCATTGAACTA 59.317 43.478 11.47 0.00 0.00 2.24
2786 3887 4.332819 GGTCAGTAAAGCGCATTGAACTAT 59.667 41.667 11.47 0.00 0.00 2.12
2787 3888 5.258622 GTCAGTAAAGCGCATTGAACTATG 58.741 41.667 11.47 0.00 0.00 2.23
2788 3889 4.332543 TCAGTAAAGCGCATTGAACTATGG 59.667 41.667 11.47 0.00 0.00 2.74
2789 3890 4.332543 CAGTAAAGCGCATTGAACTATGGA 59.667 41.667 11.47 0.00 0.00 3.41
2790 3891 4.941263 AGTAAAGCGCATTGAACTATGGAA 59.059 37.500 11.47 0.00 0.00 3.53
2791 3892 4.782019 AAAGCGCATTGAACTATGGAAA 57.218 36.364 11.47 0.00 0.00 3.13
2792 3893 4.989279 AAGCGCATTGAACTATGGAAAT 57.011 36.364 11.47 0.00 0.00 2.17
2793 3894 4.297299 AGCGCATTGAACTATGGAAATG 57.703 40.909 11.47 0.00 33.98 2.32
2794 3895 3.067180 AGCGCATTGAACTATGGAAATGG 59.933 43.478 11.47 0.00 31.97 3.16
2795 3896 3.181487 GCGCATTGAACTATGGAAATGGT 60.181 43.478 0.30 0.00 31.97 3.55
2830 3931 6.528537 TTGTGTCCCTCCATTATGAATTTG 57.471 37.500 0.00 0.00 0.00 2.32
2834 3935 4.279420 GTCCCTCCATTATGAATTTGAGCC 59.721 45.833 0.00 0.00 0.00 4.70
2918 4031 2.224843 TGGATTCTCATGTTGCAGGTGT 60.225 45.455 0.00 0.00 0.00 4.16
2919 4032 2.821969 GGATTCTCATGTTGCAGGTGTT 59.178 45.455 0.00 0.00 0.00 3.32
2920 4033 4.009675 GGATTCTCATGTTGCAGGTGTTA 58.990 43.478 0.00 0.00 0.00 2.41
2921 4034 4.458989 GGATTCTCATGTTGCAGGTGTTAA 59.541 41.667 0.00 0.00 0.00 2.01
2922 4035 5.392380 GGATTCTCATGTTGCAGGTGTTAAG 60.392 44.000 0.00 0.00 0.00 1.85
3102 4217 1.226435 TTTTTCGCACGCGCAACTT 60.226 47.368 5.73 0.00 38.40 2.66
3120 4235 4.851639 ACTTGTGCTAAGATCCAATCCT 57.148 40.909 8.05 0.00 0.00 3.24
3272 4387 0.539669 GCTGCCACTTTTACCCACCT 60.540 55.000 0.00 0.00 0.00 4.00
3275 4390 2.039879 CTGCCACTTTTACCCACCTAGT 59.960 50.000 0.00 0.00 0.00 2.57
3395 4510 0.389948 GCTTCATCCGACCACGACTT 60.390 55.000 0.00 0.00 42.66 3.01
3397 4512 0.963225 TTCATCCGACCACGACTTGA 59.037 50.000 0.00 0.00 42.66 3.02
3400 4515 1.135139 CATCCGACCACGACTTGAGAT 59.865 52.381 0.00 0.00 42.66 2.75
3401 4516 0.809385 TCCGACCACGACTTGAGATC 59.191 55.000 0.00 0.00 42.66 2.75
3402 4517 0.526211 CCGACCACGACTTGAGATCA 59.474 55.000 0.00 0.00 42.66 2.92
3403 4518 1.468224 CCGACCACGACTTGAGATCAG 60.468 57.143 0.00 0.00 42.66 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.319140 TGCTCAGATGTCCAAATGATTTG 57.681 39.130 10.84 10.84 40.32 2.32
1 2 4.142227 GCTGCTCAGATGTCCAAATGATTT 60.142 41.667 0.29 0.00 0.00 2.17
2 3 3.380637 GCTGCTCAGATGTCCAAATGATT 59.619 43.478 0.29 0.00 0.00 2.57
3 4 2.950309 GCTGCTCAGATGTCCAAATGAT 59.050 45.455 0.29 0.00 0.00 2.45
4 5 2.026542 AGCTGCTCAGATGTCCAAATGA 60.027 45.455 0.00 0.00 0.00 2.57
5 6 2.355132 GAGCTGCTCAGATGTCCAAATG 59.645 50.000 24.02 0.00 0.00 2.32
6 7 2.239150 AGAGCTGCTCAGATGTCCAAAT 59.761 45.455 29.49 3.19 32.06 2.32
7 8 1.627329 AGAGCTGCTCAGATGTCCAAA 59.373 47.619 29.49 0.00 32.06 3.28
8 9 1.206610 GAGAGCTGCTCAGATGTCCAA 59.793 52.381 29.49 0.00 43.38 3.53
9 10 0.822811 GAGAGCTGCTCAGATGTCCA 59.177 55.000 29.49 0.00 43.38 4.02
10 11 3.665544 GAGAGCTGCTCAGATGTCC 57.334 57.895 29.49 2.47 43.38 4.02
61 62 8.512138 GCCAAAACAGTACATGAATAGTAAACT 58.488 33.333 0.00 0.00 0.00 2.66
62 63 7.753580 GGCCAAAACAGTACATGAATAGTAAAC 59.246 37.037 0.00 0.00 0.00 2.01
63 64 7.668052 AGGCCAAAACAGTACATGAATAGTAAA 59.332 33.333 5.01 0.00 0.00 2.01
64 65 7.120579 CAGGCCAAAACAGTACATGAATAGTAA 59.879 37.037 5.01 0.00 0.00 2.24
65 66 6.597672 CAGGCCAAAACAGTACATGAATAGTA 59.402 38.462 5.01 0.00 0.00 1.82
66 67 5.415701 CAGGCCAAAACAGTACATGAATAGT 59.584 40.000 5.01 0.00 0.00 2.12
67 68 5.647658 TCAGGCCAAAACAGTACATGAATAG 59.352 40.000 5.01 0.00 0.00 1.73
68 69 5.565509 TCAGGCCAAAACAGTACATGAATA 58.434 37.500 5.01 0.00 0.00 1.75
69 70 4.406456 TCAGGCCAAAACAGTACATGAAT 58.594 39.130 5.01 0.00 0.00 2.57
70 71 3.826524 TCAGGCCAAAACAGTACATGAA 58.173 40.909 5.01 0.00 0.00 2.57
71 72 3.500448 TCAGGCCAAAACAGTACATGA 57.500 42.857 5.01 0.00 0.00 3.07
72 73 4.789012 AATCAGGCCAAAACAGTACATG 57.211 40.909 5.01 0.00 0.00 3.21
73 74 4.588528 ACAAATCAGGCCAAAACAGTACAT 59.411 37.500 5.01 0.00 0.00 2.29
74 75 3.957497 ACAAATCAGGCCAAAACAGTACA 59.043 39.130 5.01 0.00 0.00 2.90
75 76 4.037446 TGACAAATCAGGCCAAAACAGTAC 59.963 41.667 5.01 0.00 0.00 2.73
76 77 4.211125 TGACAAATCAGGCCAAAACAGTA 58.789 39.130 5.01 0.00 0.00 2.74
77 78 3.030291 TGACAAATCAGGCCAAAACAGT 58.970 40.909 5.01 0.00 0.00 3.55
78 79 3.731652 TGACAAATCAGGCCAAAACAG 57.268 42.857 5.01 0.00 0.00 3.16
89 90 7.470935 AATCATTTGGACATCTGACAAATCA 57.529 32.000 11.67 4.09 41.41 2.57
90 91 8.030692 TCAAATCATTTGGACATCTGACAAATC 58.969 33.333 10.30 0.00 41.41 2.17
91 92 7.898918 TCAAATCATTTGGACATCTGACAAAT 58.101 30.769 10.30 9.90 43.40 2.32
92 93 7.287512 TCAAATCATTTGGACATCTGACAAA 57.712 32.000 10.30 0.00 40.98 2.83
93 94 6.897706 TCAAATCATTTGGACATCTGACAA 57.102 33.333 10.30 0.00 40.98 3.18
94 95 6.897706 TTCAAATCATTTGGACATCTGACA 57.102 33.333 10.30 0.00 40.98 3.58
95 96 8.767478 AATTTCAAATCATTTGGACATCTGAC 57.233 30.769 10.30 0.00 40.98 3.51
96 97 9.781633 AAAATTTCAAATCATTTGGACATCTGA 57.218 25.926 10.30 0.00 40.98 3.27
97 98 9.820229 CAAAATTTCAAATCATTTGGACATCTG 57.180 29.630 10.30 0.00 40.98 2.90
98 99 9.781633 TCAAAATTTCAAATCATTTGGACATCT 57.218 25.926 10.30 0.00 40.98 2.90
100 101 9.563748 ACTCAAAATTTCAAATCATTTGGACAT 57.436 25.926 10.30 0.00 40.98 3.06
101 102 8.828644 CACTCAAAATTTCAAATCATTTGGACA 58.171 29.630 10.30 0.00 40.98 4.02
102 103 8.284693 CCACTCAAAATTTCAAATCATTTGGAC 58.715 33.333 10.30 0.00 40.98 4.02
103 104 7.444792 CCCACTCAAAATTTCAAATCATTTGGA 59.555 33.333 10.30 0.00 40.98 3.53
104 105 7.586747 CCCACTCAAAATTTCAAATCATTTGG 58.413 34.615 10.30 0.00 40.98 3.28
105 106 7.079475 GCCCACTCAAAATTTCAAATCATTTG 58.921 34.615 3.46 3.46 41.96 2.32
106 107 6.207221 GGCCCACTCAAAATTTCAAATCATTT 59.793 34.615 0.00 0.00 0.00 2.32
107 108 5.706833 GGCCCACTCAAAATTTCAAATCATT 59.293 36.000 0.00 0.00 0.00 2.57
108 109 5.013391 AGGCCCACTCAAAATTTCAAATCAT 59.987 36.000 0.00 0.00 0.00 2.45
109 110 4.347583 AGGCCCACTCAAAATTTCAAATCA 59.652 37.500 0.00 0.00 0.00 2.57
110 111 4.898320 AGGCCCACTCAAAATTTCAAATC 58.102 39.130 0.00 0.00 0.00 2.17
111 112 4.898320 GAGGCCCACTCAAAATTTCAAAT 58.102 39.130 0.00 0.00 45.85 2.32
112 113 4.335400 GAGGCCCACTCAAAATTTCAAA 57.665 40.909 0.00 0.00 45.85 2.69
123 124 2.512515 GATGCGTGAGGCCCACTC 60.513 66.667 18.49 13.07 46.78 3.51
124 125 2.410322 TTTGATGCGTGAGGCCCACT 62.410 55.000 18.49 4.15 43.53 4.00
125 126 1.315257 ATTTGATGCGTGAGGCCCAC 61.315 55.000 12.83 12.83 42.61 4.61
126 127 0.611618 AATTTGATGCGTGAGGCCCA 60.612 50.000 0.00 0.00 42.61 5.36
127 128 0.532115 AAATTTGATGCGTGAGGCCC 59.468 50.000 0.00 0.00 42.61 5.80
128 129 2.094545 AGAAAATTTGATGCGTGAGGCC 60.095 45.455 0.00 0.00 42.61 5.19
129 130 3.221964 AGAAAATTTGATGCGTGAGGC 57.778 42.857 0.00 0.00 43.96 4.70
130 131 4.396166 AGGTAGAAAATTTGATGCGTGAGG 59.604 41.667 0.00 0.00 0.00 3.86
131 132 5.122239 TGAGGTAGAAAATTTGATGCGTGAG 59.878 40.000 0.00 0.00 0.00 3.51
132 133 5.000591 TGAGGTAGAAAATTTGATGCGTGA 58.999 37.500 0.00 0.00 0.00 4.35
133 134 5.295431 TGAGGTAGAAAATTTGATGCGTG 57.705 39.130 0.00 0.00 0.00 5.34
134 135 7.624360 TTATGAGGTAGAAAATTTGATGCGT 57.376 32.000 0.00 0.00 0.00 5.24
135 136 9.520204 AAATTATGAGGTAGAAAATTTGATGCG 57.480 29.630 0.00 0.00 30.69 4.73
192 193 4.724399 TCATCTGCACCTGGTTAGAAAAA 58.276 39.130 12.91 2.04 0.00 1.94
193 194 4.326826 CTCATCTGCACCTGGTTAGAAAA 58.673 43.478 12.91 5.48 0.00 2.29
194 195 3.869912 GCTCATCTGCACCTGGTTAGAAA 60.870 47.826 12.91 5.75 0.00 2.52
195 196 2.355108 GCTCATCTGCACCTGGTTAGAA 60.355 50.000 12.91 0.16 0.00 2.10
196 197 1.208052 GCTCATCTGCACCTGGTTAGA 59.792 52.381 11.67 11.67 0.00 2.10
197 198 1.661341 GCTCATCTGCACCTGGTTAG 58.339 55.000 0.00 0.00 0.00 2.34
198 199 0.253044 GGCTCATCTGCACCTGGTTA 59.747 55.000 0.00 0.00 34.04 2.85
199 200 1.001641 GGCTCATCTGCACCTGGTT 60.002 57.895 0.00 0.00 34.04 3.67
200 201 1.922369 AGGCTCATCTGCACCTGGT 60.922 57.895 0.00 0.00 34.04 4.00
201 202 1.451567 CAGGCTCATCTGCACCTGG 60.452 63.158 10.25 0.00 44.90 4.45
202 203 4.220413 CAGGCTCATCTGCACCTG 57.780 61.111 4.56 4.56 43.45 4.00
203 204 2.677289 CCCAGGCTCATCTGCACCT 61.677 63.158 0.00 0.00 33.64 4.00
204 205 2.124403 CCCAGGCTCATCTGCACC 60.124 66.667 0.00 0.00 33.64 5.01
205 206 2.827642 GCCCAGGCTCATCTGCAC 60.828 66.667 0.08 0.00 38.26 4.57
206 207 3.332385 TGCCCAGGCTCATCTGCA 61.332 61.111 10.58 0.00 42.51 4.41
207 208 2.827642 GTGCCCAGGCTCATCTGC 60.828 66.667 10.58 0.00 42.51 4.26
208 209 2.124403 GGTGCCCAGGCTCATCTG 60.124 66.667 10.58 0.00 42.51 2.90
209 210 3.790437 CGGTGCCCAGGCTCATCT 61.790 66.667 10.58 0.00 42.51 2.90
210 211 2.819984 TTTCGGTGCCCAGGCTCATC 62.820 60.000 10.58 0.00 42.51 2.92
211 212 2.215451 ATTTCGGTGCCCAGGCTCAT 62.215 55.000 10.58 0.00 42.51 2.90
212 213 2.905996 ATTTCGGTGCCCAGGCTCA 61.906 57.895 10.58 0.00 42.51 4.26
213 214 2.044946 ATTTCGGTGCCCAGGCTC 60.045 61.111 10.58 6.18 42.51 4.70
214 215 2.361610 CATTTCGGTGCCCAGGCT 60.362 61.111 10.58 0.00 42.51 4.58
215 216 2.275380 AACATTTCGGTGCCCAGGC 61.275 57.895 0.38 0.38 42.35 4.85
216 217 1.586028 CAACATTTCGGTGCCCAGG 59.414 57.895 0.00 0.00 0.00 4.45
217 218 1.080569 GCAACATTTCGGTGCCCAG 60.081 57.895 0.00 0.00 0.00 4.45
218 219 2.913765 CGCAACATTTCGGTGCCCA 61.914 57.895 0.00 0.00 0.00 5.36
219 220 2.126502 CGCAACATTTCGGTGCCC 60.127 61.111 0.00 0.00 0.00 5.36
220 221 1.001745 GAACGCAACATTTCGGTGCC 61.002 55.000 0.00 0.00 0.00 5.01
221 222 1.327292 CGAACGCAACATTTCGGTGC 61.327 55.000 0.00 0.00 40.73 5.01
222 223 0.233590 TCGAACGCAACATTTCGGTG 59.766 50.000 4.09 0.00 43.82 4.94
223 224 0.938713 TTCGAACGCAACATTTCGGT 59.061 45.000 0.00 0.00 43.82 4.69
224 225 2.025544 TTTCGAACGCAACATTTCGG 57.974 45.000 0.00 0.00 43.82 4.30
225 226 4.607238 ATTTTTCGAACGCAACATTTCG 57.393 36.364 0.00 0.00 44.79 3.46
226 227 8.794406 ACATATATTTTTCGAACGCAACATTTC 58.206 29.630 0.00 0.00 0.00 2.17
227 228 8.682128 ACATATATTTTTCGAACGCAACATTT 57.318 26.923 0.00 0.00 0.00 2.32
228 229 8.682128 AACATATATTTTTCGAACGCAACATT 57.318 26.923 0.00 0.00 0.00 2.71
229 230 8.682128 AAACATATATTTTTCGAACGCAACAT 57.318 26.923 0.00 0.00 0.00 2.71
230 231 8.508800 AAAACATATATTTTTCGAACGCAACA 57.491 26.923 0.00 0.00 0.00 3.33
254 255 5.355596 ACACGATTTTGCTTCCATGAAAAA 58.644 33.333 0.00 0.00 0.00 1.94
255 256 4.942852 ACACGATTTTGCTTCCATGAAAA 58.057 34.783 0.00 0.00 0.00 2.29
256 257 4.278170 AGACACGATTTTGCTTCCATGAAA 59.722 37.500 0.00 0.00 0.00 2.69
257 258 3.820467 AGACACGATTTTGCTTCCATGAA 59.180 39.130 0.00 0.00 0.00 2.57
258 259 3.411446 AGACACGATTTTGCTTCCATGA 58.589 40.909 0.00 0.00 0.00 3.07
259 260 3.438087 AGAGACACGATTTTGCTTCCATG 59.562 43.478 0.00 0.00 0.00 3.66
260 261 3.679389 AGAGACACGATTTTGCTTCCAT 58.321 40.909 0.00 0.00 0.00 3.41
261 262 3.067106 GAGAGACACGATTTTGCTTCCA 58.933 45.455 0.00 0.00 0.00 3.53
262 263 2.092838 CGAGAGACACGATTTTGCTTCC 59.907 50.000 0.00 0.00 0.00 3.46
263 264 2.473049 GCGAGAGACACGATTTTGCTTC 60.473 50.000 0.00 0.00 0.00 3.86
264 265 1.461127 GCGAGAGACACGATTTTGCTT 59.539 47.619 0.00 0.00 0.00 3.91
265 266 1.071605 GCGAGAGACACGATTTTGCT 58.928 50.000 0.00 0.00 0.00 3.91
266 267 0.790207 TGCGAGAGACACGATTTTGC 59.210 50.000 0.00 0.00 0.00 3.68
267 268 3.519908 TTTGCGAGAGACACGATTTTG 57.480 42.857 0.00 0.00 0.00 2.44
268 269 3.607078 GCTTTTGCGAGAGACACGATTTT 60.607 43.478 0.00 0.00 34.86 1.82
269 270 2.096218 GCTTTTGCGAGAGACACGATTT 60.096 45.455 0.00 0.00 34.86 2.17
270 271 1.461127 GCTTTTGCGAGAGACACGATT 59.539 47.619 0.00 0.00 34.86 3.34
271 272 1.071605 GCTTTTGCGAGAGACACGAT 58.928 50.000 0.00 0.00 34.86 3.73
272 273 2.517598 GCTTTTGCGAGAGACACGA 58.482 52.632 0.00 0.00 34.86 4.35
284 285 3.572584 GAGAGACATGGCTTTGCTTTTG 58.427 45.455 0.41 0.00 0.00 2.44
285 286 2.227388 CGAGAGACATGGCTTTGCTTTT 59.773 45.455 0.41 0.00 0.00 2.27
286 287 1.808945 CGAGAGACATGGCTTTGCTTT 59.191 47.619 0.41 0.00 0.00 3.51
294 295 0.458543 TCTTTCGCGAGAGACATGGC 60.459 55.000 23.95 0.00 43.69 4.40
338 339 2.668280 GGTCGTGCCGCTTGAAGAC 61.668 63.158 0.00 0.00 0.00 3.01
340 341 2.034879 ATGGTCGTGCCGCTTGAAG 61.035 57.895 0.00 0.00 41.21 3.02
415 423 3.067106 GACTGTGGCTCTCGAAAATGAA 58.933 45.455 0.00 0.00 0.00 2.57
416 424 2.688507 GACTGTGGCTCTCGAAAATGA 58.311 47.619 0.00 0.00 0.00 2.57
418 426 1.000955 ACGACTGTGGCTCTCGAAAAT 59.999 47.619 5.41 0.00 0.00 1.82
433 441 1.339610 GCTATCATGAGAGGCACGACT 59.660 52.381 18.59 0.00 0.00 4.18
435 443 1.402787 TGCTATCATGAGAGGCACGA 58.597 50.000 18.59 0.00 33.55 4.35
446 454 5.163301 ACGAGAGGTATGGTTTTGCTATCAT 60.163 40.000 0.00 0.00 0.00 2.45
447 455 4.161565 ACGAGAGGTATGGTTTTGCTATCA 59.838 41.667 0.00 0.00 0.00 2.15
449 457 4.442706 CACGAGAGGTATGGTTTTGCTAT 58.557 43.478 0.00 0.00 0.00 2.97
657 685 1.726853 ACAATGTAGGCTGAGAACGC 58.273 50.000 0.00 0.00 0.00 4.84
660 688 2.076100 CGCAACAATGTAGGCTGAGAA 58.924 47.619 0.00 0.00 0.00 2.87
692 720 5.105997 GGAGCAACTAGTTGATGAGCATTTT 60.106 40.000 34.43 6.89 42.93 1.82
696 724 2.355108 GGGAGCAACTAGTTGATGAGCA 60.355 50.000 34.43 0.00 42.93 4.26
778 1858 2.223947 CCGGCTAATTATGGTTTTGCCC 60.224 50.000 0.00 0.00 35.89 5.36
779 1859 2.801699 GCCGGCTAATTATGGTTTTGCC 60.802 50.000 22.15 0.00 35.94 4.52
793 1873 3.524606 GCGTCACTAGGCCGGCTA 61.525 66.667 28.56 15.41 0.00 3.93
837 1917 4.712425 CGCTCCGTTCCGTTCCGT 62.712 66.667 0.00 0.00 0.00 4.69
838 1918 4.712425 ACGCTCCGTTCCGTTCCG 62.712 66.667 0.00 0.00 36.35 4.30
839 1919 2.808321 GACGCTCCGTTCCGTTCC 60.808 66.667 0.00 0.00 41.37 3.62
840 1920 3.170585 CGACGCTCCGTTCCGTTC 61.171 66.667 0.00 0.00 41.37 3.95
1094 2180 0.544595 AGGGAGCTACCTTGTTCGGT 60.545 55.000 13.46 0.00 37.69 4.69
1119 2205 4.983671 AAGCGAAAACCTCATTAATCCC 57.016 40.909 0.00 0.00 0.00 3.85
1204 2290 0.586319 ATGCGGTCACGAACAACAAG 59.414 50.000 0.00 0.00 44.60 3.16
1223 2309 7.040478 CCATGAACCAAAGAAAACATCACTCTA 60.040 37.037 0.00 0.00 0.00 2.43
1226 2312 5.221501 CCCATGAACCAAAGAAAACATCACT 60.222 40.000 0.00 0.00 0.00 3.41
1340 2428 6.127535 GGTTCATCATCATGGGGCTTTATATG 60.128 42.308 0.00 0.00 0.00 1.78
1553 2642 8.466798 ACTAATAAGTTGTCAAATGGGCATTAC 58.533 33.333 0.00 0.00 29.00 1.89
1849 2945 6.841229 TGATTTAGATCTTCAGCCCTTAGAGA 59.159 38.462 0.00 0.00 33.28 3.10
1886 2982 2.638325 TGGAAGGATAGGTTGAACCCA 58.362 47.619 11.41 0.00 39.75 4.51
2045 3141 1.303309 AGGCATGCTCGATAGTTTGC 58.697 50.000 18.92 0.00 34.13 3.68
2672 3773 2.592001 GCCTAGGCCCGCTTAAGC 60.592 66.667 24.19 17.83 34.56 3.09
2673 3774 1.069935 GAGCCTAGGCCCGCTTAAG 59.930 63.158 30.42 0.00 43.17 1.85
2674 3775 0.105862 TAGAGCCTAGGCCCGCTTAA 60.106 55.000 30.42 8.52 43.17 1.85
2675 3776 0.539901 CTAGAGCCTAGGCCCGCTTA 60.540 60.000 30.42 13.87 43.17 3.09
2676 3777 1.834822 CTAGAGCCTAGGCCCGCTT 60.835 63.158 30.42 11.60 43.17 4.68
2677 3778 2.203567 CTAGAGCCTAGGCCCGCT 60.204 66.667 30.42 24.84 43.17 5.52
2678 3779 3.307108 CCTAGAGCCTAGGCCCGC 61.307 72.222 30.42 19.32 43.17 6.13
2683 3784 1.742768 CCAACGCCTAGAGCCTAGG 59.257 63.158 18.85 18.85 38.78 3.02
2684 3785 1.068250 GCCAACGCCTAGAGCCTAG 59.932 63.158 0.00 3.06 38.78 3.02
2685 3786 1.261938 TTGCCAACGCCTAGAGCCTA 61.262 55.000 0.00 0.00 38.78 3.93
2686 3787 2.124507 TTTGCCAACGCCTAGAGCCT 62.125 55.000 0.00 0.00 38.78 4.58
2687 3788 1.241315 TTTTGCCAACGCCTAGAGCC 61.241 55.000 0.00 0.00 38.78 4.70
2688 3789 0.109735 GTTTTGCCAACGCCTAGAGC 60.110 55.000 0.00 0.00 38.52 4.09
2689 3790 0.165944 CGTTTTGCCAACGCCTAGAG 59.834 55.000 5.44 0.00 36.82 2.43
2690 3791 2.240230 CGTTTTGCCAACGCCTAGA 58.760 52.632 5.44 0.00 36.82 2.43
2691 3792 4.838959 CGTTTTGCCAACGCCTAG 57.161 55.556 5.44 0.00 36.82 3.02
2714 3815 4.606232 GCACAGATTAAGCGTAGTTATGCG 60.606 45.833 0.00 0.00 42.84 4.73
2715 3816 4.270084 TGCACAGATTAAGCGTAGTTATGC 59.730 41.667 0.00 0.00 38.47 3.14
2716 3817 5.966636 TGCACAGATTAAGCGTAGTTATG 57.033 39.130 0.00 0.00 0.00 1.90
2717 3818 7.926555 AGTTATGCACAGATTAAGCGTAGTTAT 59.073 33.333 0.00 0.00 32.03 1.89
2718 3819 7.222031 CAGTTATGCACAGATTAAGCGTAGTTA 59.778 37.037 0.00 0.00 32.03 2.24
2719 3820 6.036083 CAGTTATGCACAGATTAAGCGTAGTT 59.964 38.462 0.00 0.00 32.03 2.24
2720 3821 5.520288 CAGTTATGCACAGATTAAGCGTAGT 59.480 40.000 0.00 0.00 32.03 2.73
2721 3822 5.967469 CAGTTATGCACAGATTAAGCGTAG 58.033 41.667 0.00 0.00 32.03 3.51
2722 3823 5.966636 CAGTTATGCACAGATTAAGCGTA 57.033 39.130 0.00 0.00 0.00 4.42
2723 3824 4.864916 CAGTTATGCACAGATTAAGCGT 57.135 40.909 0.00 0.00 0.00 5.07
2737 3838 2.313234 GCATGCTTATGCGCAGTTATG 58.687 47.619 18.32 15.92 44.10 1.90
2738 3839 2.693797 GCATGCTTATGCGCAGTTAT 57.306 45.000 18.32 0.10 44.10 1.89
2752 3853 0.521291 TTACTGACCAAAGCGCATGC 59.479 50.000 11.47 7.91 43.24 4.06
2753 3854 2.855180 CTTTACTGACCAAAGCGCATG 58.145 47.619 11.47 8.38 0.00 4.06
2754 3855 1.200020 GCTTTACTGACCAAAGCGCAT 59.800 47.619 11.47 0.00 45.88 4.73
2755 3856 0.591170 GCTTTACTGACCAAAGCGCA 59.409 50.000 11.47 0.00 45.88 6.09
2756 3857 3.384702 GCTTTACTGACCAAAGCGC 57.615 52.632 0.00 0.00 45.88 5.92
2759 3860 3.058293 TCAATGCGCTTTACTGACCAAAG 60.058 43.478 9.73 0.00 36.32 2.77
2760 3861 2.881513 TCAATGCGCTTTACTGACCAAA 59.118 40.909 9.73 0.00 0.00 3.28
2761 3862 2.499197 TCAATGCGCTTTACTGACCAA 58.501 42.857 9.73 0.00 0.00 3.67
2762 3863 2.177394 TCAATGCGCTTTACTGACCA 57.823 45.000 9.73 0.00 0.00 4.02
2763 3864 2.484264 AGTTCAATGCGCTTTACTGACC 59.516 45.455 9.73 0.00 0.00 4.02
2764 3865 3.813529 AGTTCAATGCGCTTTACTGAC 57.186 42.857 9.73 5.66 0.00 3.51
2765 3866 4.332543 CCATAGTTCAATGCGCTTTACTGA 59.667 41.667 17.24 6.83 0.00 3.41
2766 3867 4.332543 TCCATAGTTCAATGCGCTTTACTG 59.667 41.667 17.24 4.80 0.00 2.74
2767 3868 4.513442 TCCATAGTTCAATGCGCTTTACT 58.487 39.130 9.73 12.41 0.00 2.24
2768 3869 4.875544 TCCATAGTTCAATGCGCTTTAC 57.124 40.909 9.73 4.83 0.00 2.01
2769 3870 5.888691 TTTCCATAGTTCAATGCGCTTTA 57.111 34.783 9.73 0.00 0.00 1.85
2770 3871 4.782019 TTTCCATAGTTCAATGCGCTTT 57.218 36.364 9.73 5.65 0.00 3.51
2771 3872 4.440525 CCATTTCCATAGTTCAATGCGCTT 60.441 41.667 9.73 0.00 0.00 4.68
2772 3873 3.067180 CCATTTCCATAGTTCAATGCGCT 59.933 43.478 9.73 0.00 0.00 5.92
2773 3874 3.181487 ACCATTTCCATAGTTCAATGCGC 60.181 43.478 0.00 0.00 0.00 6.09
2774 3875 4.637483 ACCATTTCCATAGTTCAATGCG 57.363 40.909 0.00 0.00 0.00 4.73
2775 3876 5.964758 TCAACCATTTCCATAGTTCAATGC 58.035 37.500 0.00 0.00 0.00 3.56
2776 3877 7.549839 ACATCAACCATTTCCATAGTTCAATG 58.450 34.615 0.00 0.00 0.00 2.82
2777 3878 7.722949 ACATCAACCATTTCCATAGTTCAAT 57.277 32.000 0.00 0.00 0.00 2.57
2778 3879 7.537596 AACATCAACCATTTCCATAGTTCAA 57.462 32.000 0.00 0.00 0.00 2.69
2779 3880 7.377398 CAAACATCAACCATTTCCATAGTTCA 58.623 34.615 0.00 0.00 0.00 3.18
2780 3881 6.813152 CCAAACATCAACCATTTCCATAGTTC 59.187 38.462 0.00 0.00 0.00 3.01
2781 3882 6.269769 ACCAAACATCAACCATTTCCATAGTT 59.730 34.615 0.00 0.00 0.00 2.24
2782 3883 5.779771 ACCAAACATCAACCATTTCCATAGT 59.220 36.000 0.00 0.00 0.00 2.12
2783 3884 6.284891 ACCAAACATCAACCATTTCCATAG 57.715 37.500 0.00 0.00 0.00 2.23
2784 3885 6.678568 AACCAAACATCAACCATTTCCATA 57.321 33.333 0.00 0.00 0.00 2.74
2785 3886 5.565455 AACCAAACATCAACCATTTCCAT 57.435 34.783 0.00 0.00 0.00 3.41
2786 3887 5.121811 CAAACCAAACATCAACCATTTCCA 58.878 37.500 0.00 0.00 0.00 3.53
2787 3888 5.007528 CACAAACCAAACATCAACCATTTCC 59.992 40.000 0.00 0.00 0.00 3.13
2788 3889 5.584251 ACACAAACCAAACATCAACCATTTC 59.416 36.000 0.00 0.00 0.00 2.17
2789 3890 5.495640 ACACAAACCAAACATCAACCATTT 58.504 33.333 0.00 0.00 0.00 2.32
2790 3891 5.096443 ACACAAACCAAACATCAACCATT 57.904 34.783 0.00 0.00 0.00 3.16
2791 3892 4.442753 GGACACAAACCAAACATCAACCAT 60.443 41.667 0.00 0.00 0.00 3.55
2792 3893 3.118956 GGACACAAACCAAACATCAACCA 60.119 43.478 0.00 0.00 0.00 3.67
2793 3894 3.453424 GGACACAAACCAAACATCAACC 58.547 45.455 0.00 0.00 0.00 3.77
2794 3895 3.132111 AGGGACACAAACCAAACATCAAC 59.868 43.478 0.00 0.00 0.00 3.18
2795 3896 3.370104 AGGGACACAAACCAAACATCAA 58.630 40.909 0.00 0.00 0.00 2.57
2830 3931 1.198713 TGGAGGAGATGACTTGGCTC 58.801 55.000 0.00 0.00 0.00 4.70
2834 3935 6.825213 TCATAACATTTGGAGGAGATGACTTG 59.175 38.462 0.00 0.00 0.00 3.16
3102 4217 2.421952 GGCAGGATTGGATCTTAGCACA 60.422 50.000 0.00 0.00 0.00 4.57
3272 4387 3.755628 GACCTGCGGGCGTGACTA 61.756 66.667 12.89 0.00 35.63 2.59


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

AutoCloner maintained by Alex Coulton.