Multiple sequence alignment - TraesCS4D01G207500

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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 TraesCS4D01G207500 chr4D 100.000 4073 0 0 1 4073 355861561 355857489 0.000000e+00 7522.0
1 TraesCS4D01G207500 chr4D 87.069 1655 212 2 1327 2980 354136403 354138056 0.000000e+00 1869.0
2 TraesCS4D01G207500 chr4D 89.823 226 22 1 1001 1226 124263152 124262928 5.150000e-74 289.0
3 TraesCS4D01G207500 chr4D 85.606 132 11 4 3298 3428 10969931 10970055 9.190000e-27 132.0
4 TraesCS4D01G207500 chr4D 100.000 30 0 0 3369 3398 10968379 10968408 5.690000e-04 56.5
5 TraesCS4D01G207500 chr4B 96.454 3271 73 17 319 3563 439323045 439319792 0.000000e+00 5358.0
6 TraesCS4D01G207500 chr4B 86.949 1655 212 4 1328 2980 437949441 437951093 0.000000e+00 1857.0
7 TraesCS4D01G207500 chr4B 91.176 884 16 18 3146 4005 439319791 439318946 0.000000e+00 1144.0
8 TraesCS4D01G207500 chr4B 93.103 203 13 1 1019 1220 437949114 437949316 3.080000e-76 296.0
9 TraesCS4D01G207500 chr4B 82.051 234 20 9 3431 3650 20719033 20719258 3.230000e-41 180.0
10 TraesCS4D01G207500 chr4B 100.000 30 0 0 3369 3398 20717401 20717430 5.690000e-04 56.5
11 TraesCS4D01G207500 chr4A 96.784 2705 63 10 527 3227 109423277 109425961 0.000000e+00 4492.0
12 TraesCS4D01G207500 chr4A 85.739 1760 239 9 1327 3077 110638837 110637081 0.000000e+00 1849.0
13 TraesCS4D01G207500 chr4A 92.798 361 15 5 3220 3574 109426190 109426545 2.810000e-141 512.0
14 TraesCS4D01G207500 chr4A 92.033 364 11 10 3647 4005 109426540 109426890 2.830000e-136 496.0
15 TraesCS4D01G207500 chr4A 93.103 203 13 1 1019 1220 110639171 110638969 3.080000e-76 296.0
16 TraesCS4D01G207500 chr4A 89.730 185 9 6 3745 3920 591848667 591848850 1.140000e-55 228.0
17 TraesCS4D01G207500 chr4A 81.928 249 21 8 259 497 109420415 109420649 5.370000e-44 189.0
18 TraesCS4D01G207500 chr4A 86.364 132 10 4 3298 3428 591848032 591848156 1.970000e-28 137.0
19 TraesCS4D01G207500 chr4A 100.000 30 0 0 3369 3398 591846548 591846577 5.690000e-04 56.5
20 TraesCS4D01G207500 chr3D 86.310 1702 225 4 1326 3023 463191627 463189930 0.000000e+00 1845.0
21 TraesCS4D01G207500 chr3D 86.667 1665 220 2 1326 2989 462851023 462852686 0.000000e+00 1844.0
22 TraesCS4D01G207500 chr3A 85.698 1748 232 12 1328 3073 606436003 606434272 0.000000e+00 1827.0
23 TraesCS4D01G207500 chr3B 86.047 1677 226 6 1328 3002 615772845 615774515 0.000000e+00 1794.0
24 TraesCS4D01G207500 chr5B 97.044 203 6 0 1 203 663121937 663121735 3.900000e-90 342.0
25 TraesCS4D01G207500 chr5B 90.000 220 21 1 1010 1229 660365443 660365661 2.400000e-72 283.0
26 TraesCS4D01G207500 chr6A 97.030 202 6 0 1 202 600308521 600308722 1.400000e-89 340.0
27 TraesCS4D01G207500 chr1D 94.472 199 11 0 1019 1217 382237625 382237427 1.420000e-79 307.0
28 TraesCS4D01G207500 chr1B 94.472 199 11 0 1019 1217 512175815 512175617 1.420000e-79 307.0
29 TraesCS4D01G207500 chr1A 94.472 199 11 0 1019 1217 482338963 482338765 1.420000e-79 307.0
30 TraesCS4D01G207500 chr1A 97.436 39 1 0 4035 4073 544641143 544641105 2.630000e-07 67.6
31 TraesCS4D01G207500 chr7D 93.970 199 6 2 1 199 77030599 77030791 3.080000e-76 296.0
32 TraesCS4D01G207500 chr5A 90.506 158 6 5 3772 3920 622204582 622204425 2.480000e-47 200.0
33 TraesCS4D01G207500 chr5A 100.000 30 0 0 3369 3398 622206767 622206738 5.690000e-04 56.5
34 TraesCS4D01G207500 chr6D 96.667 60 1 1 4014 4073 14506986 14507044 9.320000e-17 99.0


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 TraesCS4D01G207500 chr4D 355857489 355861561 4072 True 7522.00 7522 100.00000 1 4073 1 chr4D.!!$R2 4072
1 TraesCS4D01G207500 chr4D 354136403 354138056 1653 False 1869.00 1869 87.06900 1327 2980 1 chr4D.!!$F1 1653
2 TraesCS4D01G207500 chr4B 439318946 439323045 4099 True 3251.00 5358 93.81500 319 4005 2 chr4B.!!$R1 3686
3 TraesCS4D01G207500 chr4B 437949114 437951093 1979 False 1076.50 1857 90.02600 1019 2980 2 chr4B.!!$F2 1961
4 TraesCS4D01G207500 chr4A 109420415 109426890 6475 False 1422.25 4492 90.88575 259 4005 4 chr4A.!!$F1 3746
5 TraesCS4D01G207500 chr4A 110637081 110639171 2090 True 1072.50 1849 89.42100 1019 3077 2 chr4A.!!$R1 2058
6 TraesCS4D01G207500 chr3D 463189930 463191627 1697 True 1845.00 1845 86.31000 1326 3023 1 chr3D.!!$R1 1697
7 TraesCS4D01G207500 chr3D 462851023 462852686 1663 False 1844.00 1844 86.66700 1326 2989 1 chr3D.!!$F1 1663
8 TraesCS4D01G207500 chr3A 606434272 606436003 1731 True 1827.00 1827 85.69800 1328 3073 1 chr3A.!!$R1 1745
9 TraesCS4D01G207500 chr3B 615772845 615774515 1670 False 1794.00 1794 86.04700 1328 3002 1 chr3B.!!$F1 1674

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
256 257 0.035176 CCATTTGTTGGGGTTGCCTG 59.965 55.000 0.00 0.00 42.33 4.85 F
257 258 0.758123 CATTTGTTGGGGTTGCCTGT 59.242 50.000 0.00 0.00 0.00 4.00 F
1374 4048 0.454117 GTTTCTCGGACTCGTCGGTC 60.454 60.000 5.57 5.57 37.69 4.79 F
1416 4090 1.683441 GTTCAAGGTGATCCCCGGT 59.317 57.895 0.00 0.00 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1083 3706 0.460109 CGTTGGCGATGATCTCCACA 60.460 55.0 3.17 0.0 41.33 4.17 R
1569 4243 0.606604 GGGAGTCGTTGAAGTAGGCA 59.393 55.0 0.00 0.0 0.00 4.75 R
2892 5567 0.603707 CAAACTCTTCAGCCTCGGCA 60.604 55.0 11.02 0.0 44.88 5.69 R
3339 6699 5.408604 ACACTAGTTGCAATTAAACCTCTCG 59.591 40.0 0.59 0.0 0.00 4.04 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
23 24 6.252967 ACTCTATCATAGATGAGAGTTGCG 57.747 41.667 12.58 4.78 44.29 4.85
24 25 5.182950 ACTCTATCATAGATGAGAGTTGCGG 59.817 44.000 12.58 4.26 44.29 5.69
25 26 5.316987 TCTATCATAGATGAGAGTTGCGGA 58.683 41.667 12.58 0.00 44.29 5.54
26 27 3.717400 TCATAGATGAGAGTTGCGGAC 57.283 47.619 0.00 0.00 32.11 4.79
27 28 2.362397 TCATAGATGAGAGTTGCGGACC 59.638 50.000 0.00 0.00 32.11 4.46
28 29 0.738975 TAGATGAGAGTTGCGGACCG 59.261 55.000 10.29 10.29 0.00 4.79
29 30 0.965866 AGATGAGAGTTGCGGACCGA 60.966 55.000 20.50 0.00 0.00 4.69
30 31 0.526524 GATGAGAGTTGCGGACCGAG 60.527 60.000 20.50 0.00 0.00 4.63
31 32 2.507324 GAGAGTTGCGGACCGAGC 60.507 66.667 20.50 6.36 0.00 5.03
32 33 3.991536 GAGAGTTGCGGACCGAGCC 62.992 68.421 20.50 3.32 0.00 4.70
40 41 3.917760 GGACCGAGCCGATCAGGG 61.918 72.222 5.87 0.00 41.48 4.45
41 42 2.833582 GACCGAGCCGATCAGGGA 60.834 66.667 5.87 0.00 41.48 4.20
42 43 2.835431 ACCGAGCCGATCAGGGAG 60.835 66.667 5.87 0.00 41.48 4.30
43 44 2.835431 CCGAGCCGATCAGGGAGT 60.835 66.667 5.87 0.00 41.48 3.85
44 45 2.725008 CGAGCCGATCAGGGAGTC 59.275 66.667 5.87 0.00 41.48 3.36
45 46 2.851071 CGAGCCGATCAGGGAGTCC 61.851 68.421 0.00 0.00 41.48 3.85
46 47 2.444895 AGCCGATCAGGGAGTCCC 60.445 66.667 21.81 21.81 45.90 4.46
55 56 4.452733 GGGAGTCCCGACGGCAAG 62.453 72.222 13.89 0.00 32.13 4.01
87 88 4.540153 CGCAAGGTGTCCATAGGG 57.460 61.111 0.00 0.00 0.00 3.53
88 89 1.602237 CGCAAGGTGTCCATAGGGT 59.398 57.895 0.00 0.00 34.93 4.34
89 90 0.828022 CGCAAGGTGTCCATAGGGTA 59.172 55.000 0.00 0.00 34.93 3.69
90 91 1.202533 CGCAAGGTGTCCATAGGGTAG 60.203 57.143 0.00 0.00 34.93 3.18
91 92 2.116238 GCAAGGTGTCCATAGGGTAGA 58.884 52.381 0.00 0.00 34.93 2.59
92 93 2.158943 GCAAGGTGTCCATAGGGTAGAC 60.159 54.545 0.00 0.00 34.93 2.59
93 94 2.068834 AGGTGTCCATAGGGTAGACG 57.931 55.000 0.00 0.00 33.09 4.18
94 95 1.287146 AGGTGTCCATAGGGTAGACGT 59.713 52.381 0.00 0.00 33.09 4.34
95 96 1.680207 GGTGTCCATAGGGTAGACGTC 59.320 57.143 7.70 7.70 33.09 4.34
96 97 1.332997 GTGTCCATAGGGTAGACGTCG 59.667 57.143 10.46 0.00 33.09 5.12
97 98 1.065199 TGTCCATAGGGTAGACGTCGT 60.065 52.381 10.46 0.00 33.09 4.34
98 99 1.601430 GTCCATAGGGTAGACGTCGTC 59.399 57.143 17.70 17.70 34.93 4.20
99 100 1.487976 TCCATAGGGTAGACGTCGTCT 59.512 52.381 29.25 29.25 45.54 4.18
100 101 1.602851 CCATAGGGTAGACGTCGTCTG 59.397 57.143 32.86 17.50 43.30 3.51
101 102 1.002684 CATAGGGTAGACGTCGTCTGC 60.003 57.143 32.86 30.76 43.30 4.26
102 103 0.036105 TAGGGTAGACGTCGTCTGCA 60.036 55.000 34.28 18.45 44.86 4.41
103 104 1.154073 GGGTAGACGTCGTCTGCAC 60.154 63.158 34.28 30.68 44.86 4.57
104 105 1.577922 GGTAGACGTCGTCTGCACA 59.422 57.895 34.28 16.66 44.86 4.57
105 106 0.170561 GGTAGACGTCGTCTGCACAT 59.829 55.000 34.28 14.94 44.86 3.21
106 107 1.260206 GTAGACGTCGTCTGCACATG 58.740 55.000 32.86 0.00 43.30 3.21
107 108 0.170339 TAGACGTCGTCTGCACATGG 59.830 55.000 32.86 0.00 43.30 3.66
108 109 2.048222 ACGTCGTCTGCACATGGG 60.048 61.111 0.00 0.00 0.00 4.00
109 110 2.261361 CGTCGTCTGCACATGGGA 59.739 61.111 0.00 0.00 0.00 4.37
110 111 2.094659 CGTCGTCTGCACATGGGAC 61.095 63.158 0.00 0.00 0.00 4.46
112 113 2.815211 CGTCTGCACATGGGACGG 60.815 66.667 15.43 7.96 45.81 4.79
113 114 3.127533 GTCTGCACATGGGACGGC 61.128 66.667 0.00 0.00 0.00 5.68
114 115 3.635191 TCTGCACATGGGACGGCA 61.635 61.111 0.00 0.00 34.66 5.69
115 116 3.129502 CTGCACATGGGACGGCAG 61.130 66.667 0.00 5.17 46.47 4.85
145 146 3.423154 GAAGCCACGCCGGACAAG 61.423 66.667 5.05 0.00 36.56 3.16
185 186 2.745037 TGGTGTCGCCAGGGTTAC 59.255 61.111 0.00 0.00 43.61 2.50
186 187 2.046604 GGTGTCGCCAGGGTTACC 60.047 66.667 0.00 0.00 37.17 2.85
202 203 4.603989 GTTACCTAACCCTAGAGCCATC 57.396 50.000 0.00 0.00 0.00 3.51
203 204 4.224762 GTTACCTAACCCTAGAGCCATCT 58.775 47.826 0.00 0.00 39.75 2.90
204 205 2.965562 ACCTAACCCTAGAGCCATCTC 58.034 52.381 0.00 0.00 36.96 2.75
205 206 1.889829 CCTAACCCTAGAGCCATCTCG 59.110 57.143 0.00 0.00 44.02 4.04
206 207 1.271102 CTAACCCTAGAGCCATCTCGC 59.729 57.143 0.00 0.00 44.02 5.03
207 208 0.687757 AACCCTAGAGCCATCTCGCA 60.688 55.000 0.00 0.00 44.02 5.10
208 209 0.470833 ACCCTAGAGCCATCTCGCAT 60.471 55.000 0.00 0.00 44.02 4.73
209 210 1.203063 ACCCTAGAGCCATCTCGCATA 60.203 52.381 0.00 0.00 44.02 3.14
210 211 1.476085 CCCTAGAGCCATCTCGCATAG 59.524 57.143 0.00 0.00 44.02 2.23
211 212 2.166829 CCTAGAGCCATCTCGCATAGT 58.833 52.381 0.00 0.00 44.02 2.12
212 213 2.560542 CCTAGAGCCATCTCGCATAGTT 59.439 50.000 0.00 0.00 44.02 2.24
213 214 3.006323 CCTAGAGCCATCTCGCATAGTTT 59.994 47.826 0.00 0.00 44.02 2.66
214 215 3.104843 AGAGCCATCTCGCATAGTTTC 57.895 47.619 0.00 0.00 44.02 2.78
215 216 2.432146 AGAGCCATCTCGCATAGTTTCA 59.568 45.455 0.00 0.00 44.02 2.69
216 217 2.541762 GAGCCATCTCGCATAGTTTCAC 59.458 50.000 0.00 0.00 0.00 3.18
217 218 1.599542 GCCATCTCGCATAGTTTCACC 59.400 52.381 0.00 0.00 0.00 4.02
218 219 1.860950 CCATCTCGCATAGTTTCACCG 59.139 52.381 0.00 0.00 0.00 4.94
219 220 2.481276 CCATCTCGCATAGTTTCACCGA 60.481 50.000 0.00 0.00 0.00 4.69
220 221 3.384668 CATCTCGCATAGTTTCACCGAT 58.615 45.455 0.00 0.00 0.00 4.18
221 222 3.520290 TCTCGCATAGTTTCACCGATT 57.480 42.857 0.00 0.00 0.00 3.34
222 223 3.186909 TCTCGCATAGTTTCACCGATTG 58.813 45.455 0.00 0.00 0.00 2.67
223 224 2.276201 TCGCATAGTTTCACCGATTGG 58.724 47.619 0.00 0.00 42.84 3.16
224 225 1.268032 CGCATAGTTTCACCGATTGGC 60.268 52.381 0.00 0.00 39.70 4.52
225 226 1.065551 GCATAGTTTCACCGATTGGCC 59.934 52.381 0.00 0.00 39.70 5.36
226 227 2.643551 CATAGTTTCACCGATTGGCCT 58.356 47.619 3.32 0.00 39.70 5.19
227 228 2.871096 TAGTTTCACCGATTGGCCTT 57.129 45.000 3.32 0.00 39.70 4.35
228 229 1.995376 AGTTTCACCGATTGGCCTTT 58.005 45.000 3.32 0.00 39.70 3.11
229 230 1.886542 AGTTTCACCGATTGGCCTTTC 59.113 47.619 3.32 0.00 39.70 2.62
230 231 1.886542 GTTTCACCGATTGGCCTTTCT 59.113 47.619 3.32 0.00 39.70 2.52
231 232 3.078837 GTTTCACCGATTGGCCTTTCTA 58.921 45.455 3.32 0.00 39.70 2.10
232 233 3.644966 TTCACCGATTGGCCTTTCTAT 57.355 42.857 3.32 0.00 39.70 1.98
233 234 3.194005 TCACCGATTGGCCTTTCTATC 57.806 47.619 3.32 0.00 39.70 2.08
234 235 1.867233 CACCGATTGGCCTTTCTATCG 59.133 52.381 3.32 10.55 39.70 2.92
235 236 1.760613 ACCGATTGGCCTTTCTATCGA 59.239 47.619 19.08 0.00 41.65 3.59
236 237 2.135933 CCGATTGGCCTTTCTATCGAC 58.864 52.381 19.08 0.00 41.65 4.20
237 238 2.135933 CGATTGGCCTTTCTATCGACC 58.864 52.381 3.32 0.00 41.65 4.79
238 239 2.495084 GATTGGCCTTTCTATCGACCC 58.505 52.381 3.32 0.00 0.00 4.46
239 240 1.281419 TTGGCCTTTCTATCGACCCA 58.719 50.000 3.32 0.00 0.00 4.51
240 241 1.507140 TGGCCTTTCTATCGACCCAT 58.493 50.000 3.32 0.00 0.00 4.00
241 242 1.843851 TGGCCTTTCTATCGACCCATT 59.156 47.619 3.32 0.00 0.00 3.16
242 243 2.241176 TGGCCTTTCTATCGACCCATTT 59.759 45.455 3.32 0.00 0.00 2.32
243 244 2.618709 GGCCTTTCTATCGACCCATTTG 59.381 50.000 0.00 0.00 0.00 2.32
244 245 3.279434 GCCTTTCTATCGACCCATTTGT 58.721 45.455 0.00 0.00 0.00 2.83
245 246 3.694566 GCCTTTCTATCGACCCATTTGTT 59.305 43.478 0.00 0.00 0.00 2.83
246 247 4.438744 GCCTTTCTATCGACCCATTTGTTG 60.439 45.833 0.00 0.00 0.00 3.33
247 248 4.096382 CCTTTCTATCGACCCATTTGTTGG 59.904 45.833 0.00 0.00 46.00 3.77
255 256 2.450992 CCATTTGTTGGGGTTGCCT 58.549 52.632 0.00 0.00 42.33 4.75
256 257 0.035176 CCATTTGTTGGGGTTGCCTG 59.965 55.000 0.00 0.00 42.33 4.85
257 258 0.758123 CATTTGTTGGGGTTGCCTGT 59.242 50.000 0.00 0.00 0.00 4.00
291 295 2.094675 CGAAGGACATGGGCAAAGATT 58.905 47.619 0.00 0.00 0.00 2.40
292 296 2.159338 CGAAGGACATGGGCAAAGATTG 60.159 50.000 0.00 0.00 0.00 2.67
295 299 1.133025 GGACATGGGCAAAGATTGTCG 59.867 52.381 0.00 0.00 38.02 4.35
296 300 1.812571 GACATGGGCAAAGATTGTCGT 59.187 47.619 0.00 0.00 35.72 4.34
307 311 3.585748 AGATTGTCGTTGTTTGTCGTG 57.414 42.857 0.00 0.00 0.00 4.35
311 315 1.921887 TGTCGTTGTTTGTCGTGAGTC 59.078 47.619 0.00 0.00 0.00 3.36
312 316 1.072348 GTCGTTGTTTGTCGTGAGTCG 60.072 52.381 0.00 0.00 41.41 4.18
313 317 0.918619 CGTTGTTTGTCGTGAGTCGT 59.081 50.000 0.00 0.00 40.80 4.34
314 318 1.322338 CGTTGTTTGTCGTGAGTCGTT 59.678 47.619 0.00 0.00 40.80 3.85
315 319 2.531103 CGTTGTTTGTCGTGAGTCGTTA 59.469 45.455 0.00 0.00 40.80 3.18
316 320 3.360384 CGTTGTTTGTCGTGAGTCGTTAG 60.360 47.826 0.00 0.00 40.80 2.34
393 397 5.535043 TCACGAGAAACATCATTCACATG 57.465 39.130 0.00 0.00 0.00 3.21
400 404 7.063898 CGAGAAACATCATTCACATGTAGTTCT 59.936 37.037 0.00 0.00 33.12 3.01
409 413 9.739276 TCATTCACATGTAGTTCTCCTAAATTT 57.261 29.630 0.00 0.00 0.00 1.82
419 423 9.827411 GTAGTTCTCCTAAATTTTTAGTTGCAG 57.173 33.333 0.00 1.36 38.73 4.41
428 432 4.985044 TTTTTAGTTGCAGTAGTCGCTC 57.015 40.909 0.00 0.00 0.00 5.03
439 443 2.093447 AGTAGTCGCTCCATTTCTTGGG 60.093 50.000 0.00 0.00 46.45 4.12
462 473 5.065474 GGTGCAATTAGTCTTTACGCCAATA 59.935 40.000 0.00 0.00 0.00 1.90
469 480 9.620660 AATTAGTCTTTACGCCAATAACAAAAG 57.379 29.630 0.00 0.00 0.00 2.27
544 3162 1.535204 CCAGGTCAAAATTGGCGGCT 61.535 55.000 11.43 0.00 32.44 5.52
601 3219 1.289109 CCGTTGTAGCCACGAACCAG 61.289 60.000 0.00 0.00 0.00 4.00
618 3236 1.079127 AGTCGATGGCTTCCAACCG 60.079 57.895 0.00 5.17 36.95 4.44
619 3237 2.106683 GTCGATGGCTTCCAACCGG 61.107 63.158 0.00 0.00 36.95 5.28
830 3453 3.181465 GCCATCCGAGGAACATTCTAGAA 60.181 47.826 7.82 7.82 0.00 2.10
839 3462 3.118371 GGAACATTCTAGAACCCATCCGT 60.118 47.826 7.48 0.00 0.00 4.69
916 3539 1.369983 ACCACCTATTCTCCCTCCCTT 59.630 52.381 0.00 0.00 0.00 3.95
974 3597 3.243737 GCAATTCCCTTCGAGGTTGTTTT 60.244 43.478 0.00 0.00 31.93 2.43
975 3598 4.739436 GCAATTCCCTTCGAGGTTGTTTTT 60.739 41.667 0.00 0.00 31.93 1.94
1322 3993 2.030562 CGAGCCCGTGTCCTGTTT 59.969 61.111 0.00 0.00 0.00 2.83
1323 3994 2.317609 CGAGCCCGTGTCCTGTTTG 61.318 63.158 0.00 0.00 0.00 2.93
1324 3995 2.594592 AGCCCGTGTCCTGTTTGC 60.595 61.111 0.00 0.00 0.00 3.68
1374 4048 0.454117 GTTTCTCGGACTCGTCGGTC 60.454 60.000 5.57 5.57 37.69 4.79
1416 4090 1.683441 GTTCAAGGTGATCCCCGGT 59.317 57.895 0.00 0.00 0.00 5.28
1569 4243 3.681835 GCAGTCGTCACCGTCCCT 61.682 66.667 0.00 0.00 35.01 4.20
2460 5134 2.900273 GGCGTGCTCATCCAGGTA 59.100 61.111 0.00 0.00 0.00 3.08
2583 5258 3.007074 TGTGCTTTGACATTGATGCCAAT 59.993 39.130 0.00 0.00 43.37 3.16
2601 5276 3.133003 CCAATGGTATCCTGAACGTCTCT 59.867 47.826 0.00 0.00 0.00 3.10
2851 5526 4.276183 CCGACAAGAAGAAGATCGAGGATA 59.724 45.833 0.00 0.00 34.77 2.59
2892 5567 1.166531 GGCTCGACAACAACCAGCTT 61.167 55.000 0.00 0.00 0.00 3.74
3118 5802 8.430801 ACTATTCTGCTTGAATAATGTGTCTC 57.569 34.615 11.72 0.00 44.30 3.36
3139 5823 5.833667 TCTCTCATTGTACGGTGGATTCTAT 59.166 40.000 0.00 0.00 0.00 1.98
3304 6663 5.008613 TGAATGTCTGGTTGCTCAACTTAAC 59.991 40.000 11.91 8.25 40.94 2.01
3305 6664 4.150897 TGTCTGGTTGCTCAACTTAACT 57.849 40.909 11.91 0.00 40.94 2.24
3339 6699 6.034591 TCTCTAGTTGCTACAATCGCTTTAC 58.965 40.000 0.13 0.00 0.00 2.01
3429 6789 3.054287 TGAAACATTCGGGCTGGGTATTA 60.054 43.478 0.00 0.00 0.00 0.98
3430 6790 3.876309 AACATTCGGGCTGGGTATTAT 57.124 42.857 0.00 0.00 0.00 1.28
3431 6791 3.876309 ACATTCGGGCTGGGTATTATT 57.124 42.857 0.00 0.00 0.00 1.40
3565 6940 3.594603 AGTTTAGCTCAGCACGTACAT 57.405 42.857 0.00 0.00 0.00 2.29
3573 6948 3.780902 CTCAGCACGTACATGATTACCA 58.219 45.455 0.00 0.00 0.00 3.25
3613 6988 9.979578 TTGATGTTCTTTATTAATTTGTGCACT 57.020 25.926 19.41 0.00 0.00 4.40
3614 6989 9.979578 TGATGTTCTTTATTAATTTGTGCACTT 57.020 25.926 19.41 6.73 0.00 3.16
3617 6992 9.593134 TGTTCTTTATTAATTTGTGCACTTTGT 57.407 25.926 19.41 3.69 0.00 2.83
3623 6998 9.988815 TTATTAATTTGTGCACTTTGTATTGGT 57.011 25.926 19.41 6.37 0.00 3.67
3624 6999 7.938563 TTAATTTGTGCACTTTGTATTGGTC 57.061 32.000 19.41 0.00 0.00 4.02
3625 7000 4.991153 TTTGTGCACTTTGTATTGGTCA 57.009 36.364 19.41 0.00 0.00 4.02
3626 7001 4.566545 TTGTGCACTTTGTATTGGTCAG 57.433 40.909 19.41 0.00 0.00 3.51
3821 7200 5.928839 GCAGACAATGAGAACTGAGAAGTTA 59.071 40.000 0.00 0.00 32.90 2.24
3824 7203 9.299963 CAGACAATGAGAACTGAGAAGTTATAG 57.700 37.037 0.00 0.00 32.90 1.31
4006 7387 8.737168 TTACCTGATGAAATTCTATCAAGTGG 57.263 34.615 14.26 11.53 32.10 4.00
4007 7388 5.591877 ACCTGATGAAATTCTATCAAGTGGC 59.408 40.000 8.05 0.00 33.30 5.01
4008 7389 5.277683 CCTGATGAAATTCTATCAAGTGGCG 60.278 44.000 8.59 0.00 33.30 5.69
4009 7390 4.576053 TGATGAAATTCTATCAAGTGGCGG 59.424 41.667 5.91 0.00 30.84 6.13
4010 7391 2.682856 TGAAATTCTATCAAGTGGCGGC 59.317 45.455 0.00 0.00 0.00 6.53
4011 7392 2.717639 AATTCTATCAAGTGGCGGCT 57.282 45.000 11.43 0.00 0.00 5.52
4012 7393 2.246719 ATTCTATCAAGTGGCGGCTC 57.753 50.000 11.43 6.75 0.00 4.70
4013 7394 0.178068 TTCTATCAAGTGGCGGCTCC 59.822 55.000 11.43 0.09 0.00 4.70
4014 7395 1.227674 CTATCAAGTGGCGGCTCCC 60.228 63.158 11.43 0.00 0.00 4.30
4015 7396 2.666596 CTATCAAGTGGCGGCTCCCC 62.667 65.000 11.43 0.00 0.00 4.81
4034 7415 3.129502 CTCCCGTGTCGCTCCGTA 61.130 66.667 0.00 0.00 0.00 4.02
4035 7416 3.109612 CTCCCGTGTCGCTCCGTAG 62.110 68.421 0.00 0.00 0.00 3.51
4048 7429 2.575461 CGTAGGTCGACCCCAACC 59.425 66.667 30.82 12.98 42.86 3.77
4049 7430 2.984623 GTAGGTCGACCCCAACCC 59.015 66.667 30.82 8.82 36.11 4.11
4050 7431 1.611556 GTAGGTCGACCCCAACCCT 60.612 63.158 30.82 13.15 36.11 4.34
4051 7432 0.324645 GTAGGTCGACCCCAACCCTA 60.325 60.000 30.82 12.06 36.11 3.53
4052 7433 0.032813 TAGGTCGACCCCAACCCTAG 60.033 60.000 30.82 0.00 36.11 3.02
4053 7434 2.582978 GTCGACCCCAACCCTAGC 59.417 66.667 3.51 0.00 0.00 3.42
4054 7435 2.686106 TCGACCCCAACCCTAGCC 60.686 66.667 0.00 0.00 0.00 3.93
4055 7436 4.157120 CGACCCCAACCCTAGCCG 62.157 72.222 0.00 0.00 0.00 5.52
4056 7437 4.484872 GACCCCAACCCTAGCCGC 62.485 72.222 0.00 0.00 0.00 6.53
4059 7440 4.489771 CCCAACCCTAGCCGCCAG 62.490 72.222 0.00 0.00 0.00 4.85
4060 7441 3.399181 CCAACCCTAGCCGCCAGA 61.399 66.667 0.00 0.00 0.00 3.86
4061 7442 2.746375 CCAACCCTAGCCGCCAGAT 61.746 63.158 0.00 0.00 0.00 2.90
4062 7443 1.227674 CAACCCTAGCCGCCAGATC 60.228 63.158 0.00 0.00 0.00 2.75
4063 7444 2.444256 AACCCTAGCCGCCAGATCC 61.444 63.158 0.00 0.00 0.00 3.36
4064 7445 2.844362 CCCTAGCCGCCAGATCCA 60.844 66.667 0.00 0.00 0.00 3.41
4065 7446 2.423446 CCTAGCCGCCAGATCCAC 59.577 66.667 0.00 0.00 0.00 4.02
4066 7447 2.423446 CTAGCCGCCAGATCCACC 59.577 66.667 0.00 0.00 0.00 4.61
4067 7448 2.041922 TAGCCGCCAGATCCACCT 60.042 61.111 0.00 0.00 0.00 4.00
4068 7449 2.093537 CTAGCCGCCAGATCCACCTC 62.094 65.000 0.00 0.00 0.00 3.85
4069 7450 4.554036 GCCGCCAGATCCACCTCC 62.554 72.222 0.00 0.00 0.00 4.30
4070 7451 3.083349 CCGCCAGATCCACCTCCA 61.083 66.667 0.00 0.00 0.00 3.86
4071 7452 2.187946 CGCCAGATCCACCTCCAC 59.812 66.667 0.00 0.00 0.00 4.02
4072 7453 2.592308 GCCAGATCCACCTCCACC 59.408 66.667 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.182950 CCGCAACTCTCATCTATGATAGAGT 59.817 44.000 8.30 9.68 41.34 3.24
1 2 5.414144 TCCGCAACTCTCATCTATGATAGAG 59.586 44.000 8.30 9.16 38.38 2.43
2 3 5.182190 GTCCGCAACTCTCATCTATGATAGA 59.818 44.000 4.40 4.40 35.36 1.98
4 5 4.218635 GGTCCGCAACTCTCATCTATGATA 59.781 45.833 0.00 0.00 36.02 2.15
5 6 3.006323 GGTCCGCAACTCTCATCTATGAT 59.994 47.826 0.00 0.00 36.02 2.45
7 8 2.748605 GGTCCGCAACTCTCATCTATG 58.251 52.381 0.00 0.00 0.00 2.23
8 9 1.338337 CGGTCCGCAACTCTCATCTAT 59.662 52.381 0.00 0.00 0.00 1.98
9 10 0.738975 CGGTCCGCAACTCTCATCTA 59.261 55.000 0.00 0.00 0.00 1.98
10 11 0.965866 TCGGTCCGCAACTCTCATCT 60.966 55.000 6.34 0.00 0.00 2.90
11 12 0.526524 CTCGGTCCGCAACTCTCATC 60.527 60.000 6.34 0.00 0.00 2.92
12 13 1.513158 CTCGGTCCGCAACTCTCAT 59.487 57.895 6.34 0.00 0.00 2.90
13 14 2.962569 CTCGGTCCGCAACTCTCA 59.037 61.111 6.34 0.00 0.00 3.27
14 15 2.507324 GCTCGGTCCGCAACTCTC 60.507 66.667 6.34 0.00 0.00 3.20
15 16 4.070552 GGCTCGGTCCGCAACTCT 62.071 66.667 6.34 0.00 0.00 3.24
23 24 3.917760 CCCTGATCGGCTCGGTCC 61.918 72.222 0.00 0.00 35.99 4.46
24 25 2.833582 TCCCTGATCGGCTCGGTC 60.834 66.667 0.00 1.43 37.52 4.79
25 26 2.835431 CTCCCTGATCGGCTCGGT 60.835 66.667 0.00 0.00 0.00 4.69
26 27 2.835431 ACTCCCTGATCGGCTCGG 60.835 66.667 0.00 0.00 0.00 4.63
27 28 2.725008 GACTCCCTGATCGGCTCG 59.275 66.667 0.00 0.00 0.00 5.03
28 29 2.503382 GGGACTCCCTGATCGGCTC 61.503 68.421 6.90 0.00 41.34 4.70
29 30 2.444895 GGGACTCCCTGATCGGCT 60.445 66.667 6.90 0.00 41.34 5.52
30 31 3.917760 CGGGACTCCCTGATCGGC 61.918 72.222 12.62 0.00 42.67 5.54
31 32 2.123854 TCGGGACTCCCTGATCGG 60.124 66.667 12.62 0.00 42.79 4.18
38 39 4.452733 CTTGCCGTCGGGACTCCC 62.453 72.222 14.38 3.63 41.09 4.30
66 67 3.338275 TATGGACACCTTGCGGCCC 62.338 63.158 0.00 0.00 0.00 5.80
67 68 1.819632 CTATGGACACCTTGCGGCC 60.820 63.158 0.00 0.00 0.00 6.13
68 69 1.819632 CCTATGGACACCTTGCGGC 60.820 63.158 0.00 0.00 0.00 6.53
69 70 1.153168 CCCTATGGACACCTTGCGG 60.153 63.158 0.00 0.00 0.00 5.69
70 71 0.828022 TACCCTATGGACACCTTGCG 59.172 55.000 0.00 0.00 34.81 4.85
71 72 2.116238 TCTACCCTATGGACACCTTGC 58.884 52.381 0.00 0.00 34.81 4.01
72 73 2.100916 CGTCTACCCTATGGACACCTTG 59.899 54.545 0.00 0.00 38.71 3.61
73 74 2.292061 ACGTCTACCCTATGGACACCTT 60.292 50.000 0.00 0.00 38.71 3.50
74 75 1.287146 ACGTCTACCCTATGGACACCT 59.713 52.381 0.00 0.00 38.71 4.00
75 76 1.680207 GACGTCTACCCTATGGACACC 59.320 57.143 8.70 0.00 38.71 4.16
76 77 1.332997 CGACGTCTACCCTATGGACAC 59.667 57.143 14.70 0.00 38.71 3.67
77 78 1.065199 ACGACGTCTACCCTATGGACA 60.065 52.381 14.70 0.00 38.71 4.02
78 79 1.601430 GACGACGTCTACCCTATGGAC 59.399 57.143 20.52 0.00 35.49 4.02
79 80 1.487976 AGACGACGTCTACCCTATGGA 59.512 52.381 28.28 0.00 41.51 3.41
80 81 1.602851 CAGACGACGTCTACCCTATGG 59.397 57.143 28.78 11.31 41.37 2.74
81 82 1.002684 GCAGACGACGTCTACCCTATG 60.003 57.143 28.78 16.86 41.37 2.23
82 83 1.307097 GCAGACGACGTCTACCCTAT 58.693 55.000 28.78 3.93 41.37 2.57
83 84 0.036105 TGCAGACGACGTCTACCCTA 60.036 55.000 28.78 11.54 41.37 3.53
84 85 1.303074 TGCAGACGACGTCTACCCT 60.303 57.895 28.78 5.49 41.37 4.34
85 86 1.154073 GTGCAGACGACGTCTACCC 60.154 63.158 28.78 19.55 41.37 3.69
86 87 0.170561 ATGTGCAGACGACGTCTACC 59.829 55.000 28.78 21.79 41.37 3.18
87 88 1.260206 CATGTGCAGACGACGTCTAC 58.740 55.000 28.78 23.82 41.37 2.59
88 89 0.170339 CCATGTGCAGACGACGTCTA 59.830 55.000 28.78 14.93 41.37 2.59
89 90 1.080501 CCATGTGCAGACGACGTCT 60.081 57.895 24.44 24.44 44.44 4.18
90 91 2.094659 CCCATGTGCAGACGACGTC 61.095 63.158 20.25 20.25 0.00 4.34
91 92 2.048222 CCCATGTGCAGACGACGT 60.048 61.111 0.00 0.00 0.00 4.34
92 93 2.094659 GTCCCATGTGCAGACGACG 61.095 63.158 0.00 0.00 0.00 5.12
93 94 3.876300 GTCCCATGTGCAGACGAC 58.124 61.111 0.00 0.00 0.00 4.34
96 97 3.127533 GCCGTCCCATGTGCAGAC 61.128 66.667 0.00 0.00 0.00 3.51
97 98 3.635191 TGCCGTCCCATGTGCAGA 61.635 61.111 0.00 0.00 0.00 4.26
98 99 3.129502 CTGCCGTCCCATGTGCAG 61.130 66.667 0.00 0.00 44.43 4.41
128 129 3.423154 CTTGTCCGGCGTGGCTTC 61.423 66.667 6.01 0.00 37.80 3.86
168 169 3.916632 TAGGTAACCCTGGCGACACCA 62.917 57.143 0.00 0.00 42.67 4.17
169 170 1.259840 TAGGTAACCCTGGCGACACC 61.260 60.000 0.00 0.00 42.67 4.16
170 171 0.609662 TTAGGTAACCCTGGCGACAC 59.390 55.000 0.00 0.00 42.67 3.67
171 172 0.609662 GTTAGGTAACCCTGGCGACA 59.390 55.000 0.00 0.00 42.67 4.35
172 173 3.448267 GTTAGGTAACCCTGGCGAC 57.552 57.895 0.00 0.00 42.67 5.19
180 181 6.737225 GAGATGGCTCTAGGGTTAGGTAACC 61.737 52.000 10.06 10.06 44.51 2.85
181 182 4.224762 AGATGGCTCTAGGGTTAGGTAAC 58.775 47.826 0.00 0.00 35.50 2.50
182 183 4.481072 GAGATGGCTCTAGGGTTAGGTAA 58.519 47.826 0.00 0.00 38.16 2.85
183 184 3.498121 CGAGATGGCTCTAGGGTTAGGTA 60.498 52.174 0.00 0.00 39.06 3.08
184 185 2.753507 CGAGATGGCTCTAGGGTTAGGT 60.754 54.545 0.00 0.00 39.06 3.08
185 186 1.889829 CGAGATGGCTCTAGGGTTAGG 59.110 57.143 0.00 0.00 39.06 2.69
186 187 1.271102 GCGAGATGGCTCTAGGGTTAG 59.729 57.143 0.00 0.00 39.06 2.34
187 188 1.329256 GCGAGATGGCTCTAGGGTTA 58.671 55.000 0.00 0.00 39.06 2.85
188 189 0.687757 TGCGAGATGGCTCTAGGGTT 60.688 55.000 0.00 0.00 39.06 4.11
189 190 0.470833 ATGCGAGATGGCTCTAGGGT 60.471 55.000 0.00 0.00 39.06 4.34
190 191 1.476085 CTATGCGAGATGGCTCTAGGG 59.524 57.143 0.00 0.00 39.06 3.53
191 192 2.166829 ACTATGCGAGATGGCTCTAGG 58.833 52.381 0.00 0.00 39.06 3.02
192 193 3.932545 AACTATGCGAGATGGCTCTAG 57.067 47.619 0.00 0.00 39.06 2.43
193 194 3.636764 TGAAACTATGCGAGATGGCTCTA 59.363 43.478 0.00 0.00 39.06 2.43
194 195 2.432146 TGAAACTATGCGAGATGGCTCT 59.568 45.455 0.00 0.00 39.06 4.09
195 196 2.541762 GTGAAACTATGCGAGATGGCTC 59.458 50.000 0.00 0.00 37.81 4.70
196 197 2.555199 GTGAAACTATGCGAGATGGCT 58.445 47.619 0.00 0.00 0.00 4.75
197 198 1.599542 GGTGAAACTATGCGAGATGGC 59.400 52.381 0.00 0.00 36.74 4.40
198 199 1.860950 CGGTGAAACTATGCGAGATGG 59.139 52.381 0.00 0.00 36.74 3.51
199 200 2.809446 TCGGTGAAACTATGCGAGATG 58.191 47.619 0.00 0.00 36.74 2.90
200 201 3.735237 ATCGGTGAAACTATGCGAGAT 57.265 42.857 0.00 0.00 36.74 2.75
201 202 3.186909 CAATCGGTGAAACTATGCGAGA 58.813 45.455 0.00 0.00 36.74 4.04
202 203 2.285220 CCAATCGGTGAAACTATGCGAG 59.715 50.000 0.00 0.00 36.74 5.03
203 204 2.276201 CCAATCGGTGAAACTATGCGA 58.724 47.619 0.00 0.00 36.74 5.10
204 205 1.268032 GCCAATCGGTGAAACTATGCG 60.268 52.381 0.00 0.00 36.74 4.73
205 206 1.065551 GGCCAATCGGTGAAACTATGC 59.934 52.381 0.00 0.00 36.74 3.14
206 207 2.643551 AGGCCAATCGGTGAAACTATG 58.356 47.619 5.01 0.00 36.74 2.23
207 208 3.366052 AAGGCCAATCGGTGAAACTAT 57.634 42.857 5.01 0.00 36.74 2.12
208 209 2.871096 AAGGCCAATCGGTGAAACTA 57.129 45.000 5.01 0.00 36.74 2.24
209 210 1.886542 GAAAGGCCAATCGGTGAAACT 59.113 47.619 5.01 0.00 36.74 2.66
210 211 1.886542 AGAAAGGCCAATCGGTGAAAC 59.113 47.619 5.01 0.00 33.28 2.78
211 212 2.286365 AGAAAGGCCAATCGGTGAAA 57.714 45.000 5.01 0.00 33.28 2.69
212 213 3.541632 GATAGAAAGGCCAATCGGTGAA 58.458 45.455 5.01 0.00 33.28 3.18
213 214 2.483013 CGATAGAAAGGCCAATCGGTGA 60.483 50.000 5.01 0.00 38.01 4.02
214 215 1.867233 CGATAGAAAGGCCAATCGGTG 59.133 52.381 5.01 0.00 38.01 4.94
215 216 1.760613 TCGATAGAAAGGCCAATCGGT 59.239 47.619 5.01 0.00 46.15 4.69
216 217 2.526304 TCGATAGAAAGGCCAATCGG 57.474 50.000 5.01 0.00 46.15 4.18
223 224 7.391547 CCAACAAATGGGTCGATAGAAAGGC 62.392 48.000 0.00 0.00 44.50 4.35
224 225 4.096382 CCAACAAATGGGTCGATAGAAAGG 59.904 45.833 0.00 0.00 44.50 3.11
225 226 5.235305 CCAACAAATGGGTCGATAGAAAG 57.765 43.478 0.00 0.00 44.50 2.62
238 239 0.758123 ACAGGCAACCCCAACAAATG 59.242 50.000 0.00 0.00 35.39 2.32
239 240 1.140652 CAACAGGCAACCCCAACAAAT 59.859 47.619 0.00 0.00 35.39 2.32
240 241 0.539051 CAACAGGCAACCCCAACAAA 59.461 50.000 0.00 0.00 35.39 2.83
241 242 1.965754 GCAACAGGCAACCCCAACAA 61.966 55.000 0.00 0.00 43.97 2.83
242 243 2.430610 GCAACAGGCAACCCCAACA 61.431 57.895 0.00 0.00 43.97 3.33
243 244 2.421314 GCAACAGGCAACCCCAAC 59.579 61.111 0.00 0.00 43.97 3.77
253 254 2.361610 ATCGGCAAGGGCAACAGG 60.362 61.111 0.00 0.00 43.71 4.00
254 255 2.753966 CGATCGGCAAGGGCAACAG 61.754 63.158 7.38 0.00 43.71 3.16
255 256 2.739849 TTCGATCGGCAAGGGCAACA 62.740 55.000 16.41 0.00 43.71 3.33
256 257 1.982073 CTTCGATCGGCAAGGGCAAC 61.982 60.000 16.41 0.00 43.71 4.17
257 258 1.745115 CTTCGATCGGCAAGGGCAA 60.745 57.895 16.41 0.00 43.71 4.52
291 295 1.921887 GACTCACGACAAACAACGACA 59.078 47.619 0.00 0.00 0.00 4.35
292 296 1.072348 CGACTCACGACAAACAACGAC 60.072 52.381 0.00 0.00 45.77 4.34
295 299 3.549070 ACTAACGACTCACGACAAACAAC 59.451 43.478 0.00 0.00 45.77 3.32
296 300 3.772932 ACTAACGACTCACGACAAACAA 58.227 40.909 0.00 0.00 45.77 2.83
393 397 9.827411 CTGCAACTAAAAATTTAGGAGAACTAC 57.173 33.333 15.32 0.00 43.38 2.73
400 404 7.360607 GCGACTACTGCAACTAAAAATTTAGGA 60.361 37.037 15.32 0.00 43.38 2.94
409 413 2.297880 TGGAGCGACTACTGCAACTAAA 59.702 45.455 0.00 0.00 34.81 1.85
439 443 4.413495 TTGGCGTAAAGACTAATTGCAC 57.587 40.909 0.00 0.00 0.00 4.57
462 473 6.726764 ACTCCTACTAGATGACTCCTTTTGTT 59.273 38.462 0.00 0.00 0.00 2.83
469 480 8.644374 ATTTATCACTCCTACTAGATGACTCC 57.356 38.462 0.00 0.00 0.00 3.85
601 3219 2.106683 CCGGTTGGAAGCCATCGAC 61.107 63.158 0.00 0.00 37.49 4.20
618 3236 0.606673 GTTCCAGACTTGTGGCCTCC 60.607 60.000 3.32 0.00 37.53 4.30
619 3237 0.108585 TGTTCCAGACTTGTGGCCTC 59.891 55.000 3.32 0.00 37.53 4.70
763 3386 4.699522 ACAGGAGGAAACCGCGGC 62.700 66.667 28.58 9.25 34.73 6.53
815 3438 4.709250 GGATGGGTTCTAGAATGTTCCTC 58.291 47.826 8.75 0.00 0.00 3.71
855 3478 1.897133 ACGGGGTTGGATTTAAAAGGC 59.103 47.619 0.00 0.00 0.00 4.35
937 3560 1.864669 ATTGCGGGATTGGTTGGATT 58.135 45.000 0.00 0.00 0.00 3.01
974 3597 0.662374 GTCGACTTGTCGAGCGGAAA 60.662 55.000 23.55 0.65 43.18 3.13
975 3598 1.081641 GTCGACTTGTCGAGCGGAA 60.082 57.895 23.55 1.35 43.18 4.30
986 3609 0.103208 GGCCATGATCTCGTCGACTT 59.897 55.000 14.70 0.00 0.00 3.01
987 3610 1.736586 GGCCATGATCTCGTCGACT 59.263 57.895 14.70 0.00 0.00 4.18
1083 3706 0.460109 CGTTGGCGATGATCTCCACA 60.460 55.000 3.17 0.00 41.33 4.17
1322 3993 2.872557 GCTTCGCATCTGCAAGCA 59.127 55.556 22.71 0.00 45.50 3.91
1323 3994 2.277120 CGCTTCGCATCTGCAAGC 60.277 61.111 20.01 20.01 44.19 4.01
1324 3995 2.402388 CCGCTTCGCATCTGCAAG 59.598 61.111 2.72 6.51 42.21 4.01
1374 4048 4.749310 AGCTTGGCGTCGCTCTGG 62.749 66.667 18.11 6.44 0.00 3.86
1536 4210 3.064207 GACTGCGTTCTTGATGGTTGTA 58.936 45.455 0.00 0.00 0.00 2.41
1569 4243 0.606604 GGGAGTCGTTGAAGTAGGCA 59.393 55.000 0.00 0.00 0.00 4.75
1677 4351 1.340248 GTGGACTTCTTGTCGAGACCA 59.660 52.381 0.34 0.00 46.24 4.02
2460 5134 2.279069 CGCCCTCTCGCCCTCATAT 61.279 63.158 0.00 0.00 0.00 1.78
2583 5258 1.476891 GCAGAGACGTTCAGGATACCA 59.523 52.381 0.00 0.00 37.17 3.25
2601 5276 2.741092 GTGGTCTTGTCCTCCGCA 59.259 61.111 0.00 0.00 0.00 5.69
2802 5477 0.753262 GGAGCTTGGAGGCGATCTTA 59.247 55.000 0.00 0.00 37.29 2.10
2892 5567 0.603707 CAAACTCTTCAGCCTCGGCA 60.604 55.000 11.02 0.00 44.88 5.69
3118 5802 7.273598 CGATAATAGAATCCACCGTACAATGAG 59.726 40.741 0.00 0.00 0.00 2.90
3139 5823 5.412526 AACGAAAAACTGCAGAACGATAA 57.587 34.783 23.35 0.00 0.00 1.75
3304 6663 7.038048 TGTAGCAACTAGAGATTCATGACAAG 58.962 38.462 0.00 0.00 0.00 3.16
3305 6664 6.935167 TGTAGCAACTAGAGATTCATGACAA 58.065 36.000 0.00 0.00 0.00 3.18
3339 6699 5.408604 ACACTAGTTGCAATTAAACCTCTCG 59.591 40.000 0.59 0.00 0.00 4.04
3467 6837 5.007724 GCTAGAATAATAAACAGCTTGCGGT 59.992 40.000 0.00 0.00 0.00 5.68
3471 6841 7.916977 TGCAATGCTAGAATAATAAACAGCTTG 59.083 33.333 6.82 0.00 0.00 4.01
3587 6962 9.979578 AGTGCACAAATTAATAAAGAACATCAA 57.020 25.926 21.04 0.00 0.00 2.57
3588 6963 9.979578 AAGTGCACAAATTAATAAAGAACATCA 57.020 25.926 21.04 0.00 0.00 3.07
3607 6982 3.563808 TGTCTGACCAATACAAAGTGCAC 59.436 43.478 9.40 9.40 0.00 4.57
3609 6984 4.275936 AGTTGTCTGACCAATACAAAGTGC 59.724 41.667 5.17 0.00 35.08 4.40
3610 6985 6.201517 CAAGTTGTCTGACCAATACAAAGTG 58.798 40.000 5.17 0.00 35.08 3.16
3611 6986 5.221048 GCAAGTTGTCTGACCAATACAAAGT 60.221 40.000 5.17 0.00 35.08 2.66
3612 6987 5.215160 GCAAGTTGTCTGACCAATACAAAG 58.785 41.667 5.17 0.00 35.08 2.77
3613 6988 4.037446 GGCAAGTTGTCTGACCAATACAAA 59.963 41.667 5.17 0.00 35.08 2.83
3614 6989 3.568007 GGCAAGTTGTCTGACCAATACAA 59.432 43.478 5.17 0.00 0.00 2.41
3615 6990 3.146066 GGCAAGTTGTCTGACCAATACA 58.854 45.455 5.17 0.00 0.00 2.29
3616 6991 2.488153 GGGCAAGTTGTCTGACCAATAC 59.512 50.000 7.52 0.00 0.00 1.89
3617 6992 2.107378 TGGGCAAGTTGTCTGACCAATA 59.893 45.455 7.52 0.00 0.00 1.90
3618 6993 1.133513 TGGGCAAGTTGTCTGACCAAT 60.134 47.619 7.52 0.00 0.00 3.16
3619 6994 0.257328 TGGGCAAGTTGTCTGACCAA 59.743 50.000 7.52 0.00 0.00 3.67
3620 6995 0.478072 ATGGGCAAGTTGTCTGACCA 59.522 50.000 7.52 0.00 0.00 4.02
3621 6996 1.541588 GAATGGGCAAGTTGTCTGACC 59.458 52.381 7.52 0.00 0.00 4.02
3622 6997 2.229792 TGAATGGGCAAGTTGTCTGAC 58.770 47.619 7.52 0.00 0.00 3.51
3623 6998 2.655090 TGAATGGGCAAGTTGTCTGA 57.345 45.000 7.52 0.00 0.00 3.27
3624 6999 3.947910 ATTGAATGGGCAAGTTGTCTG 57.052 42.857 7.52 0.00 0.00 3.51
3625 7000 4.961438 AAATTGAATGGGCAAGTTGTCT 57.039 36.364 7.52 0.00 35.10 3.41
3626 7001 5.408299 GGTAAAATTGAATGGGCAAGTTGTC 59.592 40.000 4.48 0.81 36.35 3.18
3872 7251 5.394738 TCCAACTATCTCGGGATGTAAGAT 58.605 41.667 8.42 0.00 33.71 2.40
4017 7398 3.109612 CTACGGAGCGACACGGGAG 62.110 68.421 0.00 0.00 0.00 4.30
4018 7399 3.129502 CTACGGAGCGACACGGGA 61.130 66.667 0.00 0.00 0.00 5.14
4019 7400 4.189188 CCTACGGAGCGACACGGG 62.189 72.222 0.00 0.00 0.00 5.28
4020 7401 3.392595 GACCTACGGAGCGACACGG 62.393 68.421 0.00 0.00 0.00 4.94
4021 7402 2.099831 GACCTACGGAGCGACACG 59.900 66.667 0.00 0.00 0.00 4.49
4022 7403 2.099831 CGACCTACGGAGCGACAC 59.900 66.667 0.00 0.00 38.46 3.67
4023 7404 2.046988 TCGACCTACGGAGCGACA 60.047 61.111 0.00 0.00 42.82 4.35
4024 7405 2.402787 GTCGACCTACGGAGCGAC 59.597 66.667 11.30 11.30 42.42 5.19
4025 7406 2.821366 GGTCGACCTACGGAGCGA 60.821 66.667 27.64 0.00 42.82 4.93
4026 7407 3.885521 GGGTCGACCTACGGAGCG 61.886 72.222 32.52 0.00 42.82 5.03
4027 7408 3.525545 GGGGTCGACCTACGGAGC 61.526 72.222 32.52 14.82 42.82 4.70
4028 7409 1.679977 TTGGGGTCGACCTACGGAG 60.680 63.158 32.52 0.00 42.82 4.63
4029 7410 1.978617 GTTGGGGTCGACCTACGGA 60.979 63.158 32.52 15.81 42.82 4.69
4030 7411 2.575461 GTTGGGGTCGACCTACGG 59.425 66.667 32.52 0.00 42.82 4.02
4031 7412 2.575461 GGTTGGGGTCGACCTACG 59.425 66.667 32.52 0.00 42.86 3.51
4032 7413 0.324645 TAGGGTTGGGGTCGACCTAC 60.325 60.000 32.52 25.15 45.02 3.18
4033 7414 0.032813 CTAGGGTTGGGGTCGACCTA 60.033 60.000 32.52 19.78 45.02 3.08
4034 7415 1.305887 CTAGGGTTGGGGTCGACCT 60.306 63.158 32.52 14.63 45.02 3.85
4035 7416 3.027675 GCTAGGGTTGGGGTCGACC 62.028 68.421 27.04 27.04 44.95 4.79
4036 7417 2.582978 GCTAGGGTTGGGGTCGAC 59.417 66.667 7.13 7.13 0.00 4.20
4037 7418 2.686106 GGCTAGGGTTGGGGTCGA 60.686 66.667 0.00 0.00 0.00 4.20
4038 7419 4.157120 CGGCTAGGGTTGGGGTCG 62.157 72.222 0.00 0.00 0.00 4.79
4039 7420 4.484872 GCGGCTAGGGTTGGGGTC 62.485 72.222 0.00 0.00 0.00 4.46
4042 7423 4.489771 CTGGCGGCTAGGGTTGGG 62.490 72.222 11.43 0.00 0.00 4.12
4043 7424 2.666596 GATCTGGCGGCTAGGGTTGG 62.667 65.000 13.65 0.00 0.00 3.77
4044 7425 1.227674 GATCTGGCGGCTAGGGTTG 60.228 63.158 13.65 0.00 0.00 3.77
4045 7426 2.444256 GGATCTGGCGGCTAGGGTT 61.444 63.158 13.65 0.00 0.00 4.11
4046 7427 2.844839 GGATCTGGCGGCTAGGGT 60.845 66.667 13.65 2.78 0.00 4.34
4047 7428 2.844362 TGGATCTGGCGGCTAGGG 60.844 66.667 13.65 0.00 0.00 3.53
4048 7429 2.423446 GTGGATCTGGCGGCTAGG 59.577 66.667 13.65 0.36 0.00 3.02
4049 7430 2.093537 GAGGTGGATCTGGCGGCTAG 62.094 65.000 11.43 7.07 0.00 3.42
4050 7431 2.041922 AGGTGGATCTGGCGGCTA 60.042 61.111 11.43 0.00 0.00 3.93
4051 7432 3.474570 GAGGTGGATCTGGCGGCT 61.475 66.667 11.43 0.00 0.00 5.52
4052 7433 4.554036 GGAGGTGGATCTGGCGGC 62.554 72.222 0.00 0.00 0.00 6.53
4053 7434 3.083349 TGGAGGTGGATCTGGCGG 61.083 66.667 0.00 0.00 0.00 6.13
4054 7435 2.187946 GTGGAGGTGGATCTGGCG 59.812 66.667 0.00 0.00 0.00 5.69
4055 7436 2.592308 GGTGGAGGTGGATCTGGC 59.408 66.667 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.