Multiple sequence alignment - TraesCS7D01G315100

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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 TraesCS7D01G315100 chr7D 100.000 4840 0 0 1 4840 401095141 401090302 0.000000e+00 8938.0
1 TraesCS7D01G315100 chr7B 92.998 2542 85 33 249 2758 410621818 410619338 0.000000e+00 3622.0
2 TraesCS7D01G315100 chr7B 93.956 1274 44 7 2852 4124 410619339 410618098 0.000000e+00 1895.0
3 TraesCS7D01G315100 chr7B 94.118 187 8 2 4545 4730 410615966 410615782 1.030000e-71 281.0
4 TraesCS7D01G315100 chr7B 89.498 219 13 3 4358 4566 410616222 410616004 7.980000e-68 268.0
5 TraesCS7D01G315100 chr7B 92.818 181 11 2 4194 4373 410616415 410616236 1.340000e-65 261.0
6 TraesCS7D01G315100 chr7B 93.805 113 7 0 4728 4840 410579979 410579867 2.320000e-38 171.0
7 TraesCS7D01G315100 chr7B 91.743 109 5 1 4106 4210 410617904 410617796 1.090000e-31 148.0
8 TraesCS7D01G315100 chr7A 94.212 2004 85 11 2852 4840 458933279 458931292 0.000000e+00 3029.0
9 TraesCS7D01G315100 chr7A 97.328 1160 24 2 714 1873 458935328 458934176 0.000000e+00 1964.0
10 TraesCS7D01G315100 chr7A 92.919 918 39 13 1843 2756 458934176 458933281 0.000000e+00 1312.0
11 TraesCS7D01G315100 chr7A 95.112 491 12 7 255 738 458935829 458935344 0.000000e+00 763.0
12 TraesCS7D01G315100 chr7A 95.781 237 10 0 1 237 469354460 469354224 2.730000e-102 383.0
13 TraesCS7D01G315100 chr1D 97.436 234 6 0 1 234 258334035 258333802 2.710000e-107 399.0
14 TraesCS7D01G315100 chr1D 88.400 250 26 2 1472 1721 355698589 355698343 1.020000e-76 298.0
15 TraesCS7D01G315100 chr1D 90.476 147 14 0 1120 1266 355698801 355698655 1.370000e-45 195.0
16 TraesCS7D01G315100 chr3D 97.034 236 7 0 1 236 104388383 104388148 9.760000e-107 398.0
17 TraesCS7D01G315100 chr3D 86.786 280 32 4 1474 1752 512707435 512707160 1.690000e-79 307.0
18 TraesCS7D01G315100 chr3D 89.634 164 13 4 1108 1268 512707685 512707523 6.350000e-49 206.0
19 TraesCS7D01G315100 chr3D 91.892 111 7 2 2745 2854 582796971 582796862 2.330000e-33 154.0
20 TraesCS7D01G315100 chrUn 96.624 237 8 0 1 237 91887195 91887431 1.260000e-105 394.0
21 TraesCS7D01G315100 chrUn 94.821 251 12 1 1 251 134458095 134458344 1.630000e-104 390.0
22 TraesCS7D01G315100 chr5D 96.610 236 8 0 1 236 460446797 460447032 4.540000e-105 392.0
23 TraesCS7D01G315100 chr5D 96.186 236 8 1 1 236 311612722 311612488 7.600000e-103 385.0
24 TraesCS7D01G315100 chr2D 96.581 234 8 0 1 234 107574553 107574786 5.870000e-104 388.0
25 TraesCS7D01G315100 chr2D 91.667 108 9 0 2757 2864 442441937 442441830 3.020000e-32 150.0
26 TraesCS7D01G315100 chr2D 89.565 115 10 2 2751 2864 371163951 371164064 1.400000e-30 145.0
27 TraesCS7D01G315100 chr4D 95.763 236 10 0 1 236 261260372 261260607 9.830000e-102 381.0
28 TraesCS7D01G315100 chr4D 91.304 115 8 1 2744 2856 54727339 54727225 6.490000e-34 156.0
29 TraesCS7D01G315100 chr4D 73.444 241 53 8 1488 1721 485764233 485763997 4.020000e-11 80.5
30 TraesCS7D01G315100 chr3A 86.102 295 33 7 1474 1764 648311910 648311620 1.310000e-80 311.0
31 TraesCS7D01G315100 chr3A 92.381 105 7 1 2750 2853 287684790 287684686 1.090000e-31 148.0
32 TraesCS7D01G315100 chr3B 86.429 280 33 4 1474 1752 675281921 675281646 7.870000e-78 302.0
33 TraesCS7D01G315100 chr3B 88.415 164 15 4 1108 1268 675282171 675282009 1.370000e-45 195.0
34 TraesCS7D01G315100 chr1B 88.400 250 26 2 1472 1721 478583494 478583248 1.020000e-76 298.0
35 TraesCS7D01G315100 chr1B 90.476 147 14 0 1120 1266 478583727 478583581 1.370000e-45 195.0
36 TraesCS7D01G315100 chr1A 88.400 250 26 2 1472 1721 456323328 456323082 1.020000e-76 298.0
37 TraesCS7D01G315100 chr1A 89.796 147 15 0 1120 1266 456323557 456323411 6.390000e-44 189.0
38 TraesCS7D01G315100 chr1A 92.453 106 6 2 2756 2860 423909781 423909885 3.020000e-32 150.0
39 TraesCS7D01G315100 chr5B 90.598 117 8 3 2738 2853 625959444 625959558 8.390000e-33 152.0
40 TraesCS7D01G315100 chr6D 91.667 108 7 2 2757 2862 389141616 389141723 1.090000e-31 148.0
41 TraesCS7D01G315100 chr6B 90.826 109 10 0 2757 2865 475446753 475446861 3.900000e-31 147.0


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 TraesCS7D01G315100 chr7D 401090302 401095141 4839 True 8938.000000 8938 100.000000 1 4840 1 chr7D.!!$R1 4839
1 TraesCS7D01G315100 chr7B 410615782 410621818 6036 True 1079.166667 3622 92.521833 249 4730 6 chr7B.!!$R2 4481
2 TraesCS7D01G315100 chr7A 458931292 458935829 4537 True 1767.000000 3029 94.892750 255 4840 4 chr7A.!!$R2 4585
3 TraesCS7D01G315100 chr3D 512707160 512707685 525 True 256.500000 307 88.210000 1108 1752 2 chr3D.!!$R3 644
4 TraesCS7D01G315100 chr3B 675281646 675282171 525 True 248.500000 302 87.422000 1108 1752 2 chr3B.!!$R1 644

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
244 245 0.035630 AGTTGCTCTTAGCTGGCTGG 60.036 55.0 5.25 0.0 42.97 4.85 F
395 402 0.328258 CCTTCAACCCCTCCATCGTT 59.672 55.0 0.00 0.0 0.00 3.85 F
1462 1535 1.164041 GGGTCGATTGTATTGCGGGG 61.164 60.0 0.00 0.0 0.00 5.73 F
2772 2889 0.337082 TCATACTCCCTCCGTCCCAA 59.663 55.0 0.00 0.0 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1105 1177 2.214181 ATCACCGTCTCCACGTGCTC 62.214 60.000 10.91 0.0 45.17 4.26 R
2394 2509 1.203001 TCCTAAGTTTGTTGGGCAGGG 60.203 52.381 0.00 0.0 0.00 4.45 R
2864 2981 1.132657 TGGAACTGAAGGAGGTGGGTA 60.133 52.381 0.00 0.0 0.00 3.69 R
4766 6601 0.820871 GGGTGGAGCTAGAGACACTG 59.179 60.000 0.00 0.0 34.42 3.66 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
17 18 4.666105 GGGCTGAAATGTCCCTCC 57.334 61.111 0.00 0.00 37.08 4.30
18 19 1.076705 GGGCTGAAATGTCCCTCCC 60.077 63.158 0.00 0.00 37.08 4.30
19 20 1.452108 GGCTGAAATGTCCCTCCCG 60.452 63.158 0.00 0.00 0.00 5.14
20 21 2.115291 GCTGAAATGTCCCTCCCGC 61.115 63.158 0.00 0.00 0.00 6.13
21 22 1.452108 CTGAAATGTCCCTCCCGCC 60.452 63.158 0.00 0.00 0.00 6.13
22 23 2.196997 CTGAAATGTCCCTCCCGCCA 62.197 60.000 0.00 0.00 0.00 5.69
23 24 1.001393 GAAATGTCCCTCCCGCCAA 60.001 57.895 0.00 0.00 0.00 4.52
24 25 1.304134 AAATGTCCCTCCCGCCAAC 60.304 57.895 0.00 0.00 0.00 3.77
25 26 1.789576 AAATGTCCCTCCCGCCAACT 61.790 55.000 0.00 0.00 0.00 3.16
26 27 2.484287 AATGTCCCTCCCGCCAACTG 62.484 60.000 0.00 0.00 0.00 3.16
29 30 4.351054 CCCTCCCGCCAACTGCTT 62.351 66.667 0.00 0.00 38.05 3.91
30 31 2.747855 CCTCCCGCCAACTGCTTC 60.748 66.667 0.00 0.00 38.05 3.86
31 32 2.348998 CTCCCGCCAACTGCTTCT 59.651 61.111 0.00 0.00 38.05 2.85
32 33 1.743252 CTCCCGCCAACTGCTTCTC 60.743 63.158 0.00 0.00 38.05 2.87
33 34 2.177594 CTCCCGCCAACTGCTTCTCT 62.178 60.000 0.00 0.00 38.05 3.10
34 35 2.037136 CCCGCCAACTGCTTCTCTG 61.037 63.158 0.00 0.00 38.05 3.35
35 36 1.302033 CCGCCAACTGCTTCTCTGT 60.302 57.895 0.00 0.00 38.05 3.41
36 37 1.572085 CCGCCAACTGCTTCTCTGTG 61.572 60.000 0.00 0.00 38.05 3.66
37 38 0.601046 CGCCAACTGCTTCTCTGTGA 60.601 55.000 0.00 0.00 38.05 3.58
38 39 1.818642 GCCAACTGCTTCTCTGTGAT 58.181 50.000 0.00 0.00 36.87 3.06
39 40 1.467734 GCCAACTGCTTCTCTGTGATG 59.532 52.381 0.00 0.00 36.87 3.07
40 41 1.467734 CCAACTGCTTCTCTGTGATGC 59.532 52.381 9.77 9.77 43.58 3.91
43 44 3.545724 TGCTTCTCTGTGATGCAGG 57.454 52.632 13.97 0.00 46.47 4.85
44 45 0.035725 TGCTTCTCTGTGATGCAGGG 60.036 55.000 13.97 0.00 46.47 4.45
45 46 1.375098 GCTTCTCTGTGATGCAGGGC 61.375 60.000 11.31 0.00 45.27 5.19
46 47 0.035725 CTTCTCTGTGATGCAGGGCA 60.036 55.000 0.00 0.00 45.27 5.36
47 48 0.321919 TTCTCTGTGATGCAGGGCAC 60.322 55.000 9.46 9.46 45.27 5.01
79 80 2.646719 GGAAACCCGCGTTTTCCC 59.353 61.111 27.40 15.73 42.34 3.97
80 81 2.253154 GAAACCCGCGTTTTCCCG 59.747 61.111 15.95 0.00 42.34 5.14
81 82 2.516695 AAACCCGCGTTTTCCCGT 60.517 55.556 4.92 0.00 39.18 5.28
82 83 2.720561 GAAACCCGCGTTTTCCCGTG 62.721 60.000 15.95 0.00 42.34 4.94
83 84 4.550697 ACCCGCGTTTTCCCGTGT 62.551 61.111 4.92 0.00 36.65 4.49
84 85 3.281395 CCCGCGTTTTCCCGTGTT 61.281 61.111 4.92 0.00 36.65 3.32
85 86 2.051703 CCGCGTTTTCCCGTGTTG 60.052 61.111 4.92 0.00 36.65 3.33
86 87 2.051703 CGCGTTTTCCCGTGTTGG 60.052 61.111 0.00 0.00 33.84 3.77
95 96 4.958897 CCGTGTTGGGGCCGGAAA 62.959 66.667 5.05 0.00 44.41 3.13
96 97 2.675075 CGTGTTGGGGCCGGAAAT 60.675 61.111 5.05 0.00 0.00 2.17
97 98 2.272447 CGTGTTGGGGCCGGAAATT 61.272 57.895 5.05 0.00 0.00 1.82
98 99 1.811645 CGTGTTGGGGCCGGAAATTT 61.812 55.000 5.05 0.00 0.00 1.82
99 100 0.320334 GTGTTGGGGCCGGAAATTTG 60.320 55.000 5.05 0.00 0.00 2.32
100 101 1.375396 GTTGGGGCCGGAAATTTGC 60.375 57.895 5.05 0.00 0.00 3.68
101 102 2.588201 TTGGGGCCGGAAATTTGCC 61.588 57.895 5.05 9.07 44.59 4.52
102 103 4.141965 GGGGCCGGAAATTTGCCG 62.142 66.667 5.05 9.00 46.31 5.69
108 109 4.812476 GGAAATTTGCCGCGCCCC 62.812 66.667 0.00 0.00 0.00 5.80
109 110 4.812476 GAAATTTGCCGCGCCCCC 62.812 66.667 0.00 0.00 0.00 5.40
111 112 3.948004 AAATTTGCCGCGCCCCCTA 62.948 57.895 0.00 0.00 0.00 3.53
112 113 3.948004 AATTTGCCGCGCCCCCTAA 62.948 57.895 0.00 0.00 0.00 2.69
113 114 3.948004 ATTTGCCGCGCCCCCTAAA 62.948 57.895 0.00 0.00 0.00 1.85
114 115 3.948004 TTTGCCGCGCCCCCTAAAT 62.948 57.895 0.00 0.00 0.00 1.40
115 116 3.948004 TTGCCGCGCCCCCTAAATT 62.948 57.895 0.00 0.00 0.00 1.82
116 117 3.144871 GCCGCGCCCCCTAAATTT 61.145 61.111 0.00 0.00 0.00 1.82
117 118 2.717044 GCCGCGCCCCCTAAATTTT 61.717 57.895 0.00 0.00 0.00 1.82
118 119 1.894512 CCGCGCCCCCTAAATTTTT 59.105 52.632 0.00 0.00 0.00 1.94
150 151 4.176752 GGGATGCGGGGTCTGGTC 62.177 72.222 0.00 0.00 0.00 4.02
151 152 4.530857 GGATGCGGGGTCTGGTCG 62.531 72.222 0.00 0.00 0.00 4.79
152 153 4.530857 GATGCGGGGTCTGGTCGG 62.531 72.222 0.00 0.00 0.00 4.79
160 161 4.021925 GTCTGGTCGGGCAGGCTT 62.022 66.667 0.00 0.00 0.00 4.35
161 162 3.249189 TCTGGTCGGGCAGGCTTT 61.249 61.111 0.00 0.00 0.00 3.51
162 163 2.747855 CTGGTCGGGCAGGCTTTC 60.748 66.667 0.00 0.00 0.00 2.62
163 164 4.344865 TGGTCGGGCAGGCTTTCC 62.345 66.667 0.00 0.00 0.00 3.13
183 184 4.433877 CCCGCACCCGCATTTTGG 62.434 66.667 0.00 0.00 38.40 3.28
195 196 3.116063 GCATTTTGGCGGTTATTTTGC 57.884 42.857 0.00 0.00 0.00 3.68
196 197 2.473704 GCATTTTGGCGGTTATTTTGCG 60.474 45.455 0.00 0.00 0.00 4.85
197 198 1.784525 TTTTGGCGGTTATTTTGCGG 58.215 45.000 0.00 0.00 0.00 5.69
198 199 0.038159 TTTGGCGGTTATTTTGCGGG 60.038 50.000 0.00 0.00 0.00 6.13
199 200 2.202690 GGCGGTTATTTTGCGGGC 60.203 61.111 0.00 0.00 0.00 6.13
200 201 2.202690 GCGGTTATTTTGCGGGCC 60.203 61.111 0.00 0.00 0.00 5.80
201 202 2.101380 CGGTTATTTTGCGGGCCG 59.899 61.111 24.35 24.35 0.00 6.13
202 203 2.492560 GGTTATTTTGCGGGCCGG 59.507 61.111 29.48 9.71 0.00 6.13
203 204 2.492560 GTTATTTTGCGGGCCGGG 59.507 61.111 29.48 0.00 0.00 5.73
204 205 2.756283 TTATTTTGCGGGCCGGGG 60.756 61.111 29.48 0.00 0.00 5.73
205 206 4.824515 TATTTTGCGGGCCGGGGG 62.825 66.667 29.48 0.00 0.00 5.40
220 221 4.489771 GGGCGGATGTGGGGTCTG 62.490 72.222 0.00 0.00 0.00 3.51
222 223 4.101448 GCGGATGTGGGGTCTGCT 62.101 66.667 0.00 0.00 43.12 4.24
223 224 2.731571 GCGGATGTGGGGTCTGCTA 61.732 63.158 0.00 0.00 43.12 3.49
224 225 1.443407 CGGATGTGGGGTCTGCTAG 59.557 63.158 0.00 0.00 0.00 3.42
225 226 1.043116 CGGATGTGGGGTCTGCTAGA 61.043 60.000 0.00 0.00 0.00 2.43
226 227 0.755686 GGATGTGGGGTCTGCTAGAG 59.244 60.000 0.00 0.00 0.00 2.43
227 228 1.490574 GATGTGGGGTCTGCTAGAGT 58.509 55.000 0.00 0.00 0.00 3.24
228 229 1.834263 GATGTGGGGTCTGCTAGAGTT 59.166 52.381 0.00 0.00 0.00 3.01
229 230 0.976641 TGTGGGGTCTGCTAGAGTTG 59.023 55.000 0.00 0.00 0.00 3.16
230 231 0.391793 GTGGGGTCTGCTAGAGTTGC 60.392 60.000 0.00 0.00 0.00 4.17
231 232 0.545309 TGGGGTCTGCTAGAGTTGCT 60.545 55.000 0.00 0.00 0.00 3.91
232 233 0.176910 GGGGTCTGCTAGAGTTGCTC 59.823 60.000 0.00 0.00 0.00 4.26
233 234 1.190643 GGGTCTGCTAGAGTTGCTCT 58.809 55.000 4.02 4.02 43.83 4.09
234 235 1.552792 GGGTCTGCTAGAGTTGCTCTT 59.447 52.381 3.87 0.00 41.50 2.85
235 236 2.761208 GGGTCTGCTAGAGTTGCTCTTA 59.239 50.000 3.87 0.00 41.50 2.10
236 237 3.181480 GGGTCTGCTAGAGTTGCTCTTAG 60.181 52.174 3.87 2.21 41.50 2.18
237 238 3.443976 GTCTGCTAGAGTTGCTCTTAGC 58.556 50.000 3.87 10.83 41.50 3.09
238 239 3.130340 GTCTGCTAGAGTTGCTCTTAGCT 59.870 47.826 18.66 0.00 42.97 3.32
239 240 3.130164 TCTGCTAGAGTTGCTCTTAGCTG 59.870 47.826 18.66 18.02 42.97 4.24
240 241 2.167281 TGCTAGAGTTGCTCTTAGCTGG 59.833 50.000 18.66 0.00 42.97 4.85
241 242 2.820330 CTAGAGTTGCTCTTAGCTGGC 58.180 52.381 3.87 0.00 42.97 4.85
242 243 1.274712 AGAGTTGCTCTTAGCTGGCT 58.725 50.000 0.00 0.00 42.97 4.75
243 244 1.066286 AGAGTTGCTCTTAGCTGGCTG 60.066 52.381 5.25 0.00 42.97 4.85
244 245 0.035630 AGTTGCTCTTAGCTGGCTGG 60.036 55.000 5.25 0.00 42.97 4.85
245 246 1.377725 TTGCTCTTAGCTGGCTGGC 60.378 57.895 5.25 0.00 42.97 4.85
246 247 2.515757 GCTCTTAGCTGGCTGGCC 60.516 66.667 4.43 4.43 38.45 5.36
247 248 2.202987 CTCTTAGCTGGCTGGCCG 60.203 66.667 7.14 3.45 39.42 6.13
271 272 6.671616 CGACGTGTAGTGAAAATAACGATTTC 59.328 38.462 0.00 0.00 34.01 2.17
288 295 7.455641 ACGATTTCATCTCTCTATACCGATT 57.544 36.000 0.00 0.00 0.00 3.34
395 402 0.328258 CCTTCAACCCCTCCATCGTT 59.672 55.000 0.00 0.00 0.00 3.85
438 445 6.890268 TGTTCTAACTCTCCTCAGCTAATGTA 59.110 38.462 0.00 0.00 0.00 2.29
441 448 7.120051 TCTAACTCTCCTCAGCTAATGTAACT 58.880 38.462 0.00 0.00 0.00 2.24
483 490 3.254060 CAGAGCTAGTGCGTACAATGTT 58.746 45.455 6.38 0.00 45.42 2.71
484 491 3.061295 CAGAGCTAGTGCGTACAATGTTG 59.939 47.826 6.38 0.00 45.42 3.33
485 492 1.732259 AGCTAGTGCGTACAATGTTGC 59.268 47.619 6.38 0.00 45.42 4.17
486 493 1.463056 GCTAGTGCGTACAATGTTGCA 59.537 47.619 6.38 8.57 34.44 4.08
583 595 7.455641 AACGGTGATCGATATCTCTTATCTT 57.544 36.000 0.00 0.00 42.43 2.40
903 966 2.622436 GCCTTGTACAAGCTAGGACTG 58.378 52.381 27.05 13.53 37.11 3.51
967 1030 2.426023 CTATAAAGGGCGCCGGCT 59.574 61.111 26.68 10.33 39.81 5.52
1056 1125 1.292223 CGTACCAGACCACCACCAG 59.708 63.158 0.00 0.00 0.00 4.00
1274 1346 3.642503 CCCCGGTACTGCCCAACA 61.643 66.667 0.00 0.00 0.00 3.33
1346 1418 2.679336 TGATTTCATGCATGTGACTCGG 59.321 45.455 25.43 0.00 0.00 4.63
1462 1535 1.164041 GGGTCGATTGTATTGCGGGG 61.164 60.000 0.00 0.00 0.00 5.73
1514 1594 3.519913 GGGACAAGGAGTGGTTCTTCTAT 59.480 47.826 0.00 0.00 30.54 1.98
1928 2038 5.738619 ATTGGGTTTGATTAACTTGACCC 57.261 39.130 10.52 10.52 45.49 4.46
1958 2068 2.011617 AAGTTGCCCCCTTGAGCTGT 62.012 55.000 0.00 0.00 0.00 4.40
1959 2069 2.115910 TTGCCCCCTTGAGCTGTG 59.884 61.111 0.00 0.00 0.00 3.66
2225 2337 3.756933 AAAGGTGTAGAAGGTGCGTAA 57.243 42.857 0.00 0.00 0.00 3.18
2226 2338 3.975168 AAGGTGTAGAAGGTGCGTAAT 57.025 42.857 0.00 0.00 0.00 1.89
2227 2339 5.410355 AAAGGTGTAGAAGGTGCGTAATA 57.590 39.130 0.00 0.00 0.00 0.98
2228 2340 5.609533 AAGGTGTAGAAGGTGCGTAATAT 57.390 39.130 0.00 0.00 0.00 1.28
2229 2341 6.720112 AAGGTGTAGAAGGTGCGTAATATA 57.280 37.500 0.00 0.00 0.00 0.86
2230 2342 6.720112 AGGTGTAGAAGGTGCGTAATATAA 57.280 37.500 0.00 0.00 0.00 0.98
2291 2403 5.190528 TCTCAAATTCTCCATGGCTTCTACT 59.809 40.000 6.96 0.00 0.00 2.57
2292 2404 5.431765 TCAAATTCTCCATGGCTTCTACTC 58.568 41.667 6.96 0.00 0.00 2.59
2293 2405 5.190528 TCAAATTCTCCATGGCTTCTACTCT 59.809 40.000 6.96 0.00 0.00 3.24
2294 2406 6.384015 TCAAATTCTCCATGGCTTCTACTCTA 59.616 38.462 6.96 0.00 0.00 2.43
2295 2407 5.799827 ATTCTCCATGGCTTCTACTCTAC 57.200 43.478 6.96 0.00 0.00 2.59
2349 2464 7.201410 CGTGTACATCGCTCTTTGTAGTTTTAT 60.201 37.037 0.00 0.00 0.00 1.40
2350 2465 9.079833 GTGTACATCGCTCTTTGTAGTTTTATA 57.920 33.333 0.00 0.00 0.00 0.98
2381 2496 6.054295 TGCAAAATTTCTTTGTAGCCACAAT 58.946 32.000 0.00 0.00 44.01 2.71
2394 2509 6.919721 TGTAGCCACAATTTTTCCTTGTATC 58.080 36.000 0.00 0.00 35.15 2.24
2397 2512 4.222810 GCCACAATTTTTCCTTGTATCCCT 59.777 41.667 0.00 0.00 35.15 4.20
2440 2555 2.854522 GTCACTGGACCCGGAATTG 58.145 57.895 0.73 0.00 38.12 2.32
2458 2575 9.292195 CCGGAATTGTTTTTAGGGTATATACAT 57.708 33.333 14.70 5.30 0.00 2.29
2474 2591 7.817962 GGTATATACATGTTAGTTAGTGCCCAG 59.182 40.741 14.70 0.00 0.00 4.45
2482 2599 3.508845 AGTTAGTGCCCAGATTTGTGT 57.491 42.857 0.00 0.00 0.00 3.72
2520 2637 9.866655 TGAAGGAGTATGATATTTTGGCTTAAT 57.133 29.630 0.00 0.00 0.00 1.40
2552 2669 4.156556 GCTGTGACTTTGGCAATGAGATTA 59.843 41.667 18.73 0.00 0.00 1.75
2580 2697 6.001460 CCACCCTACTTACATTTCTTTCACA 58.999 40.000 0.00 0.00 0.00 3.58
2601 2718 4.402155 ACAGTTCTTGCCAGAATTTTGTCA 59.598 37.500 3.22 0.00 41.26 3.58
2740 2857 2.915738 AAGTACGTACAGCTCCTTCG 57.084 50.000 26.55 0.00 0.00 3.79
2756 2873 4.272489 TCCTTCGCATTTCCTTTGATCAT 58.728 39.130 0.00 0.00 0.00 2.45
2757 2874 5.436175 TCCTTCGCATTTCCTTTGATCATA 58.564 37.500 0.00 0.00 0.00 2.15
2758 2875 5.296780 TCCTTCGCATTTCCTTTGATCATAC 59.703 40.000 0.00 0.00 0.00 2.39
2759 2876 5.297776 CCTTCGCATTTCCTTTGATCATACT 59.702 40.000 0.00 0.00 0.00 2.12
2760 2877 5.991328 TCGCATTTCCTTTGATCATACTC 57.009 39.130 0.00 0.00 0.00 2.59
2761 2878 4.816385 TCGCATTTCCTTTGATCATACTCC 59.184 41.667 0.00 0.00 0.00 3.85
2762 2879 4.023707 CGCATTTCCTTTGATCATACTCCC 60.024 45.833 0.00 0.00 0.00 4.30
2763 2880 5.136105 GCATTTCCTTTGATCATACTCCCT 58.864 41.667 0.00 0.00 0.00 4.20
2764 2881 5.240403 GCATTTCCTTTGATCATACTCCCTC 59.760 44.000 0.00 0.00 0.00 4.30
2765 2882 5.373812 TTTCCTTTGATCATACTCCCTCC 57.626 43.478 0.00 0.00 0.00 4.30
2766 2883 2.965831 TCCTTTGATCATACTCCCTCCG 59.034 50.000 0.00 0.00 0.00 4.63
2767 2884 2.700897 CCTTTGATCATACTCCCTCCGT 59.299 50.000 0.00 0.00 0.00 4.69
2768 2885 3.243907 CCTTTGATCATACTCCCTCCGTC 60.244 52.174 0.00 0.00 0.00 4.79
2769 2886 1.996798 TGATCATACTCCCTCCGTCC 58.003 55.000 0.00 0.00 0.00 4.79
2770 2887 1.258676 GATCATACTCCCTCCGTCCC 58.741 60.000 0.00 0.00 0.00 4.46
2771 2888 0.561184 ATCATACTCCCTCCGTCCCA 59.439 55.000 0.00 0.00 0.00 4.37
2772 2889 0.337082 TCATACTCCCTCCGTCCCAA 59.663 55.000 0.00 0.00 0.00 4.12
2773 2890 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
2774 2891 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
2775 2892 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2776 2893 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2777 2894 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2778 2895 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2779 2896 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
2780 2897 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2781 2898 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
2782 2899 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
2783 2900 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
2784 2901 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
2785 2902 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
2786 2903 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
2787 2904 4.154195 CCGTCCCAAAATAAGTGACTCAAG 59.846 45.833 0.00 0.00 0.00 3.02
2788 2905 4.755123 CGTCCCAAAATAAGTGACTCAAGT 59.245 41.667 0.00 0.00 0.00 3.16
2789 2906 5.238650 CGTCCCAAAATAAGTGACTCAAGTT 59.761 40.000 0.00 0.00 0.00 2.66
2790 2907 6.238648 CGTCCCAAAATAAGTGACTCAAGTTT 60.239 38.462 0.00 0.00 0.00 2.66
2791 2908 6.918022 GTCCCAAAATAAGTGACTCAAGTTTG 59.082 38.462 11.50 11.50 0.00 2.93
2792 2909 6.605594 TCCCAAAATAAGTGACTCAAGTTTGT 59.394 34.615 15.07 0.00 0.00 2.83
2793 2910 7.776030 TCCCAAAATAAGTGACTCAAGTTTGTA 59.224 33.333 15.07 5.29 0.00 2.41
2794 2911 8.410141 CCCAAAATAAGTGACTCAAGTTTGTAA 58.590 33.333 15.07 0.00 0.00 2.41
2795 2912 9.965824 CCAAAATAAGTGACTCAAGTTTGTAAT 57.034 29.630 15.07 0.00 0.00 1.89
2803 2920 9.174166 AGTGACTCAAGTTTGTAATAACTTTGT 57.826 29.630 0.00 0.00 43.85 2.83
2804 2921 9.783256 GTGACTCAAGTTTGTAATAACTTTGTT 57.217 29.630 0.00 0.00 43.85 2.83
2805 2922 9.997482 TGACTCAAGTTTGTAATAACTTTGTTC 57.003 29.630 0.00 0.00 43.85 3.18
2827 2944 9.880157 TGTTCTAAAACTAGTACAAAGTTGAGT 57.120 29.630 12.72 6.13 37.26 3.41
2839 2956 9.778741 AGTACAAAGTTGAGTCATTTATCTTGA 57.221 29.630 0.00 0.00 0.00 3.02
2841 2958 8.908786 ACAAAGTTGAGTCATTTATCTTGAGA 57.091 30.769 0.00 0.00 0.00 3.27
2842 2959 8.778358 ACAAAGTTGAGTCATTTATCTTGAGAC 58.222 33.333 0.00 0.00 0.00 3.36
2843 2960 7.588143 AAGTTGAGTCATTTATCTTGAGACG 57.412 36.000 0.00 0.00 34.56 4.18
2844 2961 6.102663 AGTTGAGTCATTTATCTTGAGACGG 58.897 40.000 0.00 0.00 34.56 4.79
2845 2962 5.914898 TGAGTCATTTATCTTGAGACGGA 57.085 39.130 0.00 0.00 34.56 4.69
2846 2963 5.895928 TGAGTCATTTATCTTGAGACGGAG 58.104 41.667 0.00 0.00 34.56 4.63
2847 2964 5.163509 TGAGTCATTTATCTTGAGACGGAGG 60.164 44.000 0.00 0.00 34.56 4.30
2848 2965 4.100189 AGTCATTTATCTTGAGACGGAGGG 59.900 45.833 0.00 0.00 34.56 4.30
2849 2966 4.099573 GTCATTTATCTTGAGACGGAGGGA 59.900 45.833 0.00 0.00 0.00 4.20
2850 2967 4.342378 TCATTTATCTTGAGACGGAGGGAG 59.658 45.833 0.00 0.00 0.00 4.30
2864 2981 4.264442 ACGGAGGGAGTATATAGCAGGAAT 60.264 45.833 0.00 0.00 0.00 3.01
2867 2984 5.599242 GGAGGGAGTATATAGCAGGAATACC 59.401 48.000 0.00 0.00 0.00 2.73
2882 2999 3.370633 GGAATACCCACCTCCTTCAGTTC 60.371 52.174 0.00 0.00 34.14 3.01
2902 3019 2.097629 TCCAACTCTTCGCAGTCGATAG 59.902 50.000 0.00 0.00 45.04 2.08
2931 3048 6.525629 AGCCATTTTGCTGTACTACTATAGG 58.474 40.000 4.43 0.00 40.90 2.57
3279 3396 1.299089 GGCACAACAACAAGGTCGC 60.299 57.895 0.00 0.00 0.00 5.19
3344 3461 0.320771 GGACGTCAGTGGCAACTCAT 60.321 55.000 18.91 0.00 32.98 2.90
3374 3491 1.227853 GCCAGTGTTTGTCGAGGGT 60.228 57.895 0.00 0.00 0.00 4.34
3410 3527 2.034878 TCATCTGCTCTCAAGGCGTAT 58.965 47.619 0.00 0.00 0.00 3.06
3444 3561 0.388907 CCAAGGAACAAATGCAGCCG 60.389 55.000 0.00 0.00 0.00 5.52
3468 3585 4.758251 TGGCATCACTGTCGGCGG 62.758 66.667 7.21 0.00 0.00 6.13
3471 3588 3.190849 CATCACTGTCGGCGGCAG 61.191 66.667 36.97 36.97 39.67 4.85
3507 3624 2.030401 CCGGCAATGTTTCGGTCGA 61.030 57.895 0.00 0.00 39.04 4.20
3680 3797 2.651361 GCGACCATCCCGATCGAT 59.349 61.111 18.66 0.00 38.10 3.59
3870 3987 2.101750 TGCATGAATGGATCAATGCACC 59.898 45.455 12.39 0.98 42.40 5.01
4080 4199 4.933134 TGTGATCCAATCATTTCCCTTCA 58.067 39.130 0.00 0.00 42.04 3.02
4120 4452 9.811995 TTAAATTAAGTATGCACAGATAGACGT 57.188 29.630 0.00 0.00 0.00 4.34
4142 4474 5.560148 GTGTACATAGTTTTTCAGGATGCG 58.440 41.667 0.00 0.00 34.76 4.73
4143 4475 4.634004 TGTACATAGTTTTTCAGGATGCGG 59.366 41.667 0.00 0.00 34.76 5.69
4163 4495 4.037446 GCGGCCATGAAAGTATCCAATTTA 59.963 41.667 2.24 0.00 0.00 1.40
4210 5943 1.899814 TCTAGGTTGACCGAGTTGCAT 59.100 47.619 9.64 0.00 39.42 3.96
4291 6025 4.447724 TGTAGTTGACGAGTTGAGCATTTC 59.552 41.667 0.00 0.00 0.00 2.17
4295 6029 5.934625 AGTTGACGAGTTGAGCATTTCTAAT 59.065 36.000 0.00 0.00 0.00 1.73
4332 6066 2.411748 TCGTTTCTAGCACGAGCAATTG 59.588 45.455 7.77 0.00 41.66 2.32
4371 6133 6.563010 CGATCAAGAACCTATCGCTCAAATTC 60.563 42.308 0.00 0.00 36.46 2.17
4419 6181 2.304470 TCATCCGAATTTGACACTCCCA 59.696 45.455 0.00 0.00 0.00 4.37
4481 6246 9.758651 AAAAGTGTGTATATGATCGTATGCTTA 57.241 29.630 19.74 9.16 0.00 3.09
4537 6311 9.104965 TGAAAACAGTACTAATTATTCCCATCG 57.895 33.333 0.00 0.00 0.00 3.84
4578 6412 9.621629 CTTTCTATACCTCGATATATCTGGACT 57.378 37.037 21.18 13.07 0.00 3.85
4579 6413 9.976776 TTTCTATACCTCGATATATCTGGACTT 57.023 33.333 21.18 11.54 0.00 3.01
4646 6480 1.491670 CAATATCCGCTCGGTGTCTG 58.508 55.000 8.28 0.00 36.47 3.51
4758 6593 7.611213 ACTAGTTTCCTGATAAAATGTTCCG 57.389 36.000 0.00 0.00 0.00 4.30
4763 6598 4.780815 TCCTGATAAAATGTTCCGAGCAT 58.219 39.130 0.00 0.00 0.00 3.79
4765 6600 4.576053 CCTGATAAAATGTTCCGAGCATGA 59.424 41.667 0.00 0.00 0.00 3.07
4766 6601 5.484173 TGATAAAATGTTCCGAGCATGAC 57.516 39.130 0.00 0.00 0.00 3.06
4790 6625 1.834263 GTCTCTAGCTCCACCCACATT 59.166 52.381 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.115291 GCGGGAGGGACATTTCAGC 61.115 63.158 0.00 0.00 0.00 4.26
4 5 1.784301 TTGGCGGGAGGGACATTTCA 61.784 55.000 0.00 0.00 0.00 2.69
5 6 1.001393 TTGGCGGGAGGGACATTTC 60.001 57.895 0.00 0.00 0.00 2.17
6 7 1.304134 GTTGGCGGGAGGGACATTT 60.304 57.895 0.00 0.00 0.00 2.32
7 8 2.231380 AGTTGGCGGGAGGGACATT 61.231 57.895 0.00 0.00 0.00 2.71
9 10 3.636231 CAGTTGGCGGGAGGGACA 61.636 66.667 0.00 0.00 0.00 4.02
19 20 1.467734 CATCACAGAGAAGCAGTTGGC 59.532 52.381 0.00 0.00 45.30 4.52
20 21 1.467734 GCATCACAGAGAAGCAGTTGG 59.532 52.381 0.00 0.00 40.56 3.77
21 22 2.148768 TGCATCACAGAGAAGCAGTTG 58.851 47.619 0.00 0.00 45.18 3.16
22 23 2.556144 TGCATCACAGAGAAGCAGTT 57.444 45.000 0.00 0.00 45.18 3.16
32 33 3.129502 CGGTGCCCTGCATCACAG 61.130 66.667 13.50 7.59 40.05 3.66
60 61 2.646719 GAAAACGCGGGTTTCCCC 59.353 61.111 27.90 17.09 45.35 4.81
61 62 2.646719 GGAAAACGCGGGTTTCCC 59.353 61.111 31.21 22.83 45.35 3.97
62 63 2.646719 GGGAAAACGCGGGTTTCC 59.353 61.111 32.45 32.45 45.35 3.13
63 64 2.253154 CGGGAAAACGCGGGTTTC 59.747 61.111 27.90 22.28 45.35 2.78
65 66 3.281395 CACGGGAAAACGCGGGTT 61.281 61.111 12.67 12.67 38.22 4.11
66 67 4.550697 ACACGGGAAAACGCGGGT 62.551 61.111 12.47 8.60 37.37 5.28
67 68 3.281395 AACACGGGAAAACGCGGG 61.281 61.111 12.47 7.33 37.37 6.13
68 69 2.051703 CAACACGGGAAAACGCGG 60.052 61.111 12.47 0.00 37.37 6.46
69 70 2.051703 CCAACACGGGAAAACGCG 60.052 61.111 3.53 3.53 37.37 6.01
79 80 1.811645 AAATTTCCGGCCCCAACACG 61.812 55.000 0.00 0.00 0.00 4.49
80 81 0.320334 CAAATTTCCGGCCCCAACAC 60.320 55.000 0.00 0.00 0.00 3.32
81 82 2.053618 CAAATTTCCGGCCCCAACA 58.946 52.632 0.00 0.00 0.00 3.33
82 83 1.375396 GCAAATTTCCGGCCCCAAC 60.375 57.895 0.00 0.00 0.00 3.77
83 84 2.588201 GGCAAATTTCCGGCCCCAA 61.588 57.895 6.74 0.00 41.90 4.12
84 85 3.000233 GGCAAATTTCCGGCCCCA 61.000 61.111 6.74 0.00 41.90 4.96
85 86 4.141965 CGGCAAATTTCCGGCCCC 62.142 66.667 16.57 0.00 44.90 5.80
86 87 4.812476 GCGGCAAATTTCCGGCCC 62.812 66.667 22.16 9.58 46.51 5.80
91 92 4.812476 GGGGCGCGGCAAATTTCC 62.812 66.667 34.30 20.66 0.00 3.13
92 93 4.812476 GGGGGCGCGGCAAATTTC 62.812 66.667 34.30 15.35 0.00 2.17
93 94 3.948004 TAGGGGGCGCGGCAAATTT 62.948 57.895 34.30 16.18 0.00 1.82
94 95 3.948004 TTAGGGGGCGCGGCAAATT 62.948 57.895 34.30 17.95 0.00 1.82
95 96 3.948004 TTTAGGGGGCGCGGCAAAT 62.948 57.895 34.30 20.22 0.00 2.32
96 97 3.948004 ATTTAGGGGGCGCGGCAAA 62.948 57.895 34.30 24.48 0.00 3.68
97 98 3.948004 AATTTAGGGGGCGCGGCAA 62.948 57.895 34.30 19.56 0.00 4.52
98 99 3.948004 AAATTTAGGGGGCGCGGCA 62.948 57.895 34.30 13.23 0.00 5.69
99 100 2.233605 AAAAATTTAGGGGGCGCGGC 62.234 55.000 26.39 26.39 0.00 6.53
100 101 1.894512 AAAAATTTAGGGGGCGCGG 59.105 52.632 8.83 0.00 0.00 6.46
133 134 4.176752 GACCAGACCCCGCATCCC 62.177 72.222 0.00 0.00 0.00 3.85
134 135 4.530857 CGACCAGACCCCGCATCC 62.531 72.222 0.00 0.00 0.00 3.51
135 136 4.530857 CCGACCAGACCCCGCATC 62.531 72.222 0.00 0.00 0.00 3.91
143 144 3.553095 AAAGCCTGCCCGACCAGAC 62.553 63.158 4.17 0.00 34.77 3.51
144 145 3.249189 AAAGCCTGCCCGACCAGA 61.249 61.111 4.17 0.00 34.77 3.86
145 146 2.747855 GAAAGCCTGCCCGACCAG 60.748 66.667 0.00 0.00 0.00 4.00
146 147 4.344865 GGAAAGCCTGCCCGACCA 62.345 66.667 0.00 0.00 0.00 4.02
175 176 2.473704 CGCAAAATAACCGCCAAAATGC 60.474 45.455 0.00 0.00 0.00 3.56
176 177 2.093467 CCGCAAAATAACCGCCAAAATG 59.907 45.455 0.00 0.00 0.00 2.32
177 178 2.342179 CCGCAAAATAACCGCCAAAAT 58.658 42.857 0.00 0.00 0.00 1.82
178 179 1.605712 CCCGCAAAATAACCGCCAAAA 60.606 47.619 0.00 0.00 0.00 2.44
179 180 0.038159 CCCGCAAAATAACCGCCAAA 60.038 50.000 0.00 0.00 0.00 3.28
180 181 1.587054 CCCGCAAAATAACCGCCAA 59.413 52.632 0.00 0.00 0.00 4.52
181 182 2.995872 GCCCGCAAAATAACCGCCA 61.996 57.895 0.00 0.00 0.00 5.69
182 183 2.202690 GCCCGCAAAATAACCGCC 60.203 61.111 0.00 0.00 0.00 6.13
183 184 2.202690 GGCCCGCAAAATAACCGC 60.203 61.111 0.00 0.00 0.00 5.68
184 185 2.101380 CGGCCCGCAAAATAACCG 59.899 61.111 0.00 0.00 0.00 4.44
185 186 2.492560 CCGGCCCGCAAAATAACC 59.507 61.111 0.00 0.00 0.00 2.85
186 187 2.492560 CCCGGCCCGCAAAATAAC 59.507 61.111 0.00 0.00 0.00 1.89
187 188 2.756283 CCCCGGCCCGCAAAATAA 60.756 61.111 0.00 0.00 0.00 1.40
188 189 4.824515 CCCCCGGCCCGCAAAATA 62.825 66.667 0.00 0.00 0.00 1.40
203 204 4.489771 CAGACCCCACATCCGCCC 62.490 72.222 0.00 0.00 0.00 6.13
205 206 2.650813 CTAGCAGACCCCACATCCGC 62.651 65.000 0.00 0.00 0.00 5.54
206 207 1.043116 TCTAGCAGACCCCACATCCG 61.043 60.000 0.00 0.00 0.00 4.18
207 208 0.755686 CTCTAGCAGACCCCACATCC 59.244 60.000 0.00 0.00 0.00 3.51
208 209 1.490574 ACTCTAGCAGACCCCACATC 58.509 55.000 0.00 0.00 0.00 3.06
209 210 1.556911 CAACTCTAGCAGACCCCACAT 59.443 52.381 0.00 0.00 0.00 3.21
210 211 0.976641 CAACTCTAGCAGACCCCACA 59.023 55.000 0.00 0.00 0.00 4.17
211 212 0.391793 GCAACTCTAGCAGACCCCAC 60.392 60.000 0.00 0.00 0.00 4.61
212 213 0.545309 AGCAACTCTAGCAGACCCCA 60.545 55.000 0.00 0.00 0.00 4.96
213 214 0.176910 GAGCAACTCTAGCAGACCCC 59.823 60.000 0.00 0.00 0.00 4.95
214 215 1.190643 AGAGCAACTCTAGCAGACCC 58.809 55.000 0.00 0.00 39.28 4.46
215 216 3.736740 GCTAAGAGCAACTCTAGCAGACC 60.737 52.174 15.23 0.00 40.28 3.85
216 217 3.130340 AGCTAAGAGCAACTCTAGCAGAC 59.870 47.826 19.12 7.40 45.56 3.51
217 218 3.130164 CAGCTAAGAGCAACTCTAGCAGA 59.870 47.826 19.12 0.00 45.56 4.26
218 219 3.446799 CAGCTAAGAGCAACTCTAGCAG 58.553 50.000 19.12 12.39 45.56 4.24
219 220 2.167281 CCAGCTAAGAGCAACTCTAGCA 59.833 50.000 19.12 2.81 45.56 3.49
220 221 2.820330 CCAGCTAAGAGCAACTCTAGC 58.180 52.381 13.54 13.54 45.56 3.42
221 222 2.430332 AGCCAGCTAAGAGCAACTCTAG 59.570 50.000 0.64 0.00 45.56 2.43
222 223 2.167281 CAGCCAGCTAAGAGCAACTCTA 59.833 50.000 0.64 0.00 45.56 2.43
223 224 1.066286 CAGCCAGCTAAGAGCAACTCT 60.066 52.381 0.64 0.00 45.56 3.24
224 225 1.367659 CAGCCAGCTAAGAGCAACTC 58.632 55.000 0.64 0.00 45.56 3.01
225 226 0.035630 CCAGCCAGCTAAGAGCAACT 60.036 55.000 0.64 0.00 45.56 3.16
226 227 1.652167 GCCAGCCAGCTAAGAGCAAC 61.652 60.000 0.64 0.00 45.56 4.17
227 228 1.377725 GCCAGCCAGCTAAGAGCAA 60.378 57.895 0.64 0.00 45.56 3.91
228 229 2.270205 GCCAGCCAGCTAAGAGCA 59.730 61.111 0.64 0.00 45.56 4.26
229 230 2.515757 GGCCAGCCAGCTAAGAGC 60.516 66.667 3.12 0.00 42.84 4.09
230 231 2.202987 CGGCCAGCCAGCTAAGAG 60.203 66.667 9.78 0.00 35.37 2.85
231 232 2.683572 TCGGCCAGCCAGCTAAGA 60.684 61.111 9.78 0.00 35.37 2.10
232 233 2.512515 GTCGGCCAGCCAGCTAAG 60.513 66.667 9.78 0.00 35.37 2.18
233 234 4.451150 CGTCGGCCAGCCAGCTAA 62.451 66.667 9.78 0.00 35.37 3.09
237 238 3.989698 CTACACGTCGGCCAGCCAG 62.990 68.421 9.78 1.86 35.37 4.85
238 239 4.063967 CTACACGTCGGCCAGCCA 62.064 66.667 9.78 0.00 35.37 4.75
239 240 4.065281 ACTACACGTCGGCCAGCC 62.065 66.667 2.24 0.00 0.00 4.85
240 241 2.758770 TTCACTACACGTCGGCCAGC 62.759 60.000 2.24 0.00 0.00 4.85
241 242 0.319211 TTTCACTACACGTCGGCCAG 60.319 55.000 2.24 0.00 0.00 4.85
242 243 0.104487 TTTTCACTACACGTCGGCCA 59.896 50.000 2.24 0.00 0.00 5.36
243 244 1.435577 ATTTTCACTACACGTCGGCC 58.564 50.000 0.00 0.00 0.00 6.13
244 245 3.480825 CGTTATTTTCACTACACGTCGGC 60.481 47.826 0.00 0.00 0.00 5.54
245 246 3.913763 TCGTTATTTTCACTACACGTCGG 59.086 43.478 0.00 0.00 0.00 4.79
246 247 5.675778 ATCGTTATTTTCACTACACGTCG 57.324 39.130 0.00 0.00 0.00 5.12
247 248 7.503991 TGAAATCGTTATTTTCACTACACGTC 58.496 34.615 0.00 0.00 37.97 4.34
271 272 7.068103 AGCTTGGATAATCGGTATAGAGAGATG 59.932 40.741 0.00 0.00 0.00 2.90
308 315 0.663568 AGCAGCGACGTGTACTTGTC 60.664 55.000 0.00 7.69 0.00 3.18
395 402 2.054799 ACACTTGTAAGAAGGGAGGCA 58.945 47.619 0.00 0.00 0.00 4.75
438 445 6.148264 GCTACAGTTGTCGTACTAGAAAGTT 58.852 40.000 0.00 0.00 37.15 2.66
441 448 5.471116 TCTGCTACAGTTGTCGTACTAGAAA 59.529 40.000 0.00 0.00 32.61 2.52
483 490 2.170166 CAGGTAAAAAGGAGGCATGCA 58.830 47.619 21.36 0.00 0.00 3.96
484 491 1.478105 CCAGGTAAAAAGGAGGCATGC 59.522 52.381 9.90 9.90 0.00 4.06
485 492 2.102578 CCCAGGTAAAAAGGAGGCATG 58.897 52.381 0.00 0.00 0.00 4.06
486 493 1.007118 CCCCAGGTAAAAAGGAGGCAT 59.993 52.381 0.00 0.00 0.00 4.40
560 572 7.362229 GGAAAGATAAGAGATATCGATCACCGT 60.362 40.741 0.00 0.00 44.37 4.83
620 635 3.206964 TGTTGATGTGTACTTGCCGAAA 58.793 40.909 0.00 0.00 0.00 3.46
903 966 0.907230 AGGAGGACTGGAGAAGCACC 60.907 60.000 0.00 0.00 0.00 5.01
967 1030 2.248248 CCTATCGATTACCCTGCCTCA 58.752 52.381 1.71 0.00 0.00 3.86
1038 1107 1.292223 CTGGTGGTGGTCTGGTACG 59.708 63.158 0.00 0.00 0.00 3.67
1104 1176 4.039357 ACCGTCTCCACGTGCTCG 62.039 66.667 10.91 6.63 45.17 5.03
1105 1177 2.214181 ATCACCGTCTCCACGTGCTC 62.214 60.000 10.91 0.00 45.17 4.26
1274 1346 9.231297 CCATGATTATAATTAGGTGGATTCGTT 57.769 33.333 0.00 0.00 0.00 3.85
1346 1418 5.690857 CGAGACGAGTTAATTAAAGGGATCC 59.309 44.000 1.92 1.92 0.00 3.36
1462 1535 2.288030 GCCAGTGCTGCCATGATTTATC 60.288 50.000 0.00 0.00 33.53 1.75
1928 2038 3.006430 AGGGGGCAACTTAATTTTGTTCG 59.994 43.478 0.00 0.00 0.00 3.95
1958 2068 3.958147 TCGGTTGCTCAGATTACCTATCA 59.042 43.478 0.00 0.00 35.59 2.15
1959 2069 4.585955 TCGGTTGCTCAGATTACCTATC 57.414 45.455 0.00 0.00 0.00 2.08
2228 2340 9.719355 TCTTGCTCATGTAATTTTCACTACTTA 57.281 29.630 0.00 0.00 0.00 2.24
2229 2341 8.621532 TCTTGCTCATGTAATTTTCACTACTT 57.378 30.769 0.00 0.00 0.00 2.24
2230 2342 8.621532 TTCTTGCTCATGTAATTTTCACTACT 57.378 30.769 0.00 0.00 0.00 2.57
2293 2405 9.537192 GCATGTGTGTATAACTGTTTATAGGTA 57.463 33.333 0.00 0.00 31.92 3.08
2294 2406 8.044309 TGCATGTGTGTATAACTGTTTATAGGT 58.956 33.333 0.00 0.00 31.92 3.08
2295 2407 8.335356 GTGCATGTGTGTATAACTGTTTATAGG 58.665 37.037 0.00 0.00 31.92 2.57
2317 2432 3.474904 GCGATGTACACGCGTGCA 61.475 61.111 37.35 27.82 46.05 4.57
2349 2464 5.669477 ACAAAGAAATTTTGCAAGCACCTA 58.331 33.333 0.00 0.00 32.93 3.08
2350 2465 4.516323 ACAAAGAAATTTTGCAAGCACCT 58.484 34.783 0.00 0.00 32.93 4.00
2381 2496 2.110899 TGGGCAGGGATACAAGGAAAAA 59.889 45.455 0.00 0.00 39.74 1.94
2394 2509 1.203001 TCCTAAGTTTGTTGGGCAGGG 60.203 52.381 0.00 0.00 0.00 4.45
2397 2512 3.330701 AGATCTCCTAAGTTTGTTGGGCA 59.669 43.478 0.00 0.00 0.00 5.36
2458 2575 4.759693 CACAAATCTGGGCACTAACTAACA 59.240 41.667 0.00 0.00 0.00 2.41
2520 2637 2.093764 CCAAAGTCACAGCCAACCAAAA 60.094 45.455 0.00 0.00 0.00 2.44
2552 2669 3.527665 AGAAATGTAAGTAGGGTGGGCAT 59.472 43.478 0.00 0.00 0.00 4.40
2580 2697 5.596836 TTGACAAAATTCTGGCAAGAACT 57.403 34.783 5.44 0.00 45.12 3.01
2601 2718 6.739565 GCAAGAGATTCCTTGAACCAACATTT 60.740 38.462 15.05 0.00 44.66 2.32
2660 2777 6.098409 CGTTGGAACCTATATATGCCCTAGAT 59.902 42.308 0.00 0.00 0.00 1.98
2661 2778 5.421056 CGTTGGAACCTATATATGCCCTAGA 59.579 44.000 0.00 0.00 0.00 2.43
2662 2779 5.187186 ACGTTGGAACCTATATATGCCCTAG 59.813 44.000 0.00 0.00 0.00 3.02
2740 2857 5.136105 AGGGAGTATGATCAAAGGAAATGC 58.864 41.667 0.00 0.00 0.00 3.56
2756 2873 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2757 2874 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
2758 2875 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
2759 2876 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2760 2877 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
2761 2878 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2762 2879 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
2763 2880 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
2764 2881 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
2765 2882 4.755123 ACTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
2766 2883 6.635030 AACTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 0.00 4.46
2767 2884 6.605594 ACAAACTTGAGTCACTTATTTTGGGA 59.394 34.615 9.57 0.00 0.00 4.37
2768 2885 6.805713 ACAAACTTGAGTCACTTATTTTGGG 58.194 36.000 9.57 0.00 0.00 4.12
2769 2886 9.965824 ATTACAAACTTGAGTCACTTATTTTGG 57.034 29.630 9.57 0.00 0.00 3.28
2777 2894 9.174166 ACAAAGTTATTACAAACTTGAGTCACT 57.826 29.630 2.97 0.00 46.40 3.41
2778 2895 9.783256 AACAAAGTTATTACAAACTTGAGTCAC 57.217 29.630 2.97 0.00 46.40 3.67
2779 2896 9.997482 GAACAAAGTTATTACAAACTTGAGTCA 57.003 29.630 2.97 0.00 46.40 3.41
2801 2918 9.880157 ACTCAACTTTGTACTAGTTTTAGAACA 57.120 29.630 0.00 0.00 38.26 3.18
2813 2930 9.778741 TCAAGATAAATGACTCAACTTTGTACT 57.221 29.630 0.00 0.00 0.00 2.73
2815 2932 9.996554 TCTCAAGATAAATGACTCAACTTTGTA 57.003 29.630 0.00 0.00 0.00 2.41
2816 2933 8.778358 GTCTCAAGATAAATGACTCAACTTTGT 58.222 33.333 0.00 0.00 0.00 2.83
2817 2934 7.954248 CGTCTCAAGATAAATGACTCAACTTTG 59.046 37.037 0.00 0.00 0.00 2.77
2818 2935 7.118390 CCGTCTCAAGATAAATGACTCAACTTT 59.882 37.037 0.00 0.00 0.00 2.66
2819 2936 6.591834 CCGTCTCAAGATAAATGACTCAACTT 59.408 38.462 0.00 0.00 0.00 2.66
2820 2937 6.071334 TCCGTCTCAAGATAAATGACTCAACT 60.071 38.462 0.00 0.00 0.00 3.16
2821 2938 6.100004 TCCGTCTCAAGATAAATGACTCAAC 58.900 40.000 0.00 0.00 0.00 3.18
2822 2939 6.280855 TCCGTCTCAAGATAAATGACTCAA 57.719 37.500 0.00 0.00 0.00 3.02
2823 2940 5.163509 CCTCCGTCTCAAGATAAATGACTCA 60.164 44.000 0.00 0.00 0.00 3.41
2824 2941 5.285651 CCTCCGTCTCAAGATAAATGACTC 58.714 45.833 0.00 0.00 0.00 3.36
2825 2942 4.100189 CCCTCCGTCTCAAGATAAATGACT 59.900 45.833 0.00 0.00 0.00 3.41
2826 2943 4.099573 TCCCTCCGTCTCAAGATAAATGAC 59.900 45.833 0.00 0.00 0.00 3.06
2827 2944 4.286707 TCCCTCCGTCTCAAGATAAATGA 58.713 43.478 0.00 0.00 0.00 2.57
2828 2945 4.100189 ACTCCCTCCGTCTCAAGATAAATG 59.900 45.833 0.00 0.00 0.00 2.32
2829 2946 4.290942 ACTCCCTCCGTCTCAAGATAAAT 58.709 43.478 0.00 0.00 0.00 1.40
2830 2947 3.709587 ACTCCCTCCGTCTCAAGATAAA 58.290 45.455 0.00 0.00 0.00 1.40
2831 2948 3.383698 ACTCCCTCCGTCTCAAGATAA 57.616 47.619 0.00 0.00 0.00 1.75
2832 2949 4.726035 ATACTCCCTCCGTCTCAAGATA 57.274 45.455 0.00 0.00 0.00 1.98
2833 2950 3.603965 ATACTCCCTCCGTCTCAAGAT 57.396 47.619 0.00 0.00 0.00 2.40
2834 2951 4.726035 ATATACTCCCTCCGTCTCAAGA 57.274 45.455 0.00 0.00 0.00 3.02
2835 2952 4.396790 GCTATATACTCCCTCCGTCTCAAG 59.603 50.000 0.00 0.00 0.00 3.02
2836 2953 4.202535 TGCTATATACTCCCTCCGTCTCAA 60.203 45.833 0.00 0.00 0.00 3.02
2837 2954 3.329814 TGCTATATACTCCCTCCGTCTCA 59.670 47.826 0.00 0.00 0.00 3.27
2838 2955 3.942748 CTGCTATATACTCCCTCCGTCTC 59.057 52.174 0.00 0.00 0.00 3.36
2839 2956 3.308545 CCTGCTATATACTCCCTCCGTCT 60.309 52.174 0.00 0.00 0.00 4.18
2840 2957 3.018149 CCTGCTATATACTCCCTCCGTC 58.982 54.545 0.00 0.00 0.00 4.79
2841 2958 2.648304 TCCTGCTATATACTCCCTCCGT 59.352 50.000 0.00 0.00 0.00 4.69
2842 2959 3.367646 TCCTGCTATATACTCCCTCCG 57.632 52.381 0.00 0.00 0.00 4.63
2843 2960 5.599242 GGTATTCCTGCTATATACTCCCTCC 59.401 48.000 0.00 0.00 0.00 4.30
2844 2961 5.599242 GGGTATTCCTGCTATATACTCCCTC 59.401 48.000 0.00 0.00 0.00 4.30
2845 2962 5.017431 TGGGTATTCCTGCTATATACTCCCT 59.983 44.000 0.00 0.00 36.20 4.20
2846 2963 5.128991 GTGGGTATTCCTGCTATATACTCCC 59.871 48.000 0.00 0.00 36.20 4.30
2847 2964 5.128991 GGTGGGTATTCCTGCTATATACTCC 59.871 48.000 0.00 0.00 36.20 3.85
2848 2965 5.958987 AGGTGGGTATTCCTGCTATATACTC 59.041 44.000 0.00 0.00 36.20 2.59
2849 2966 5.916806 AGGTGGGTATTCCTGCTATATACT 58.083 41.667 0.00 0.00 36.20 2.12
2850 2967 5.128991 GGAGGTGGGTATTCCTGCTATATAC 59.871 48.000 0.00 0.00 38.76 1.47
2864 2981 1.132657 TGGAACTGAAGGAGGTGGGTA 60.133 52.381 0.00 0.00 0.00 3.69
2867 2984 1.421646 AGTTGGAACTGAAGGAGGTGG 59.578 52.381 0.00 0.00 37.98 4.61
2882 2999 4.966005 TCGACTGCGAAGAGTTGG 57.034 55.556 0.00 0.00 44.78 3.77
2902 3019 4.783764 AGTACAGCAAAATGGCTTTACC 57.216 40.909 7.60 0.00 44.30 2.85
2931 3048 4.252073 CAGCCATCAGAGGTCATATAAGC 58.748 47.826 0.00 0.00 0.00 3.09
3033 3150 6.483687 GTTCAGTGTCACGTGAACTAAAAAT 58.516 36.000 21.95 1.60 46.04 1.82
3374 3491 1.552799 ATGATGAGTGGTGACCGCCA 61.553 55.000 12.26 10.03 33.99 5.69
3410 3527 3.786901 TTGGGTCGTGTGCGCGTTA 62.787 57.895 8.43 0.00 38.14 3.18
3444 3561 1.660560 GACAGTGATGCCATGGTGCC 61.661 60.000 14.67 3.03 0.00 5.01
3494 3611 2.030958 GGCCGTCGACCGAAACATT 61.031 57.895 10.58 0.00 39.56 2.71
3500 3617 3.610619 TACAGAGGCCGTCGACCGA 62.611 63.158 10.58 0.00 39.56 4.69
3560 3677 1.614241 GGTGGTGGTGGTAGAGCGAT 61.614 60.000 0.00 0.00 0.00 4.58
3680 3797 2.351244 AATCGCCCGACTCAGCTCA 61.351 57.895 0.00 0.00 0.00 4.26
3755 3872 4.079253 CCAAGCTAGGGAAGTTAAGCAAA 58.921 43.478 0.00 0.00 37.44 3.68
4120 4452 4.634004 CCGCATCCTGAAAAACTATGTACA 59.366 41.667 0.00 0.00 0.00 2.90
4142 4474 6.715347 AGTAAATTGGATACTTTCATGGCC 57.285 37.500 0.00 0.00 29.38 5.36
4143 4475 9.289782 AGATAGTAAATTGGATACTTTCATGGC 57.710 33.333 8.18 0.00 35.24 4.40
4163 4495 6.893005 AGAACTACACTTGCCTTAGAGATAGT 59.107 38.462 0.00 0.00 0.00 2.12
4276 6009 5.091261 AGGATTAGAAATGCTCAACTCGT 57.909 39.130 0.00 0.00 0.00 4.18
4291 6025 9.651718 GAAACGATGTTGCTATTTAAGGATTAG 57.348 33.333 0.00 0.00 0.00 1.73
4295 6029 7.011109 GCTAGAAACGATGTTGCTATTTAAGGA 59.989 37.037 0.00 0.00 0.00 3.36
4304 6038 1.726791 CGTGCTAGAAACGATGTTGCT 59.273 47.619 11.72 0.00 43.68 3.91
4312 6046 2.157668 ACAATTGCTCGTGCTAGAAACG 59.842 45.455 11.19 11.07 42.36 3.60
4332 6066 7.711339 AGGTTCTTGATCGAATGGTAATAGAAC 59.289 37.037 0.00 0.00 38.64 3.01
4371 6133 9.350357 CCAAGATTATGTTGAATTGAAGTCAAG 57.650 33.333 8.43 0.00 39.47 3.02
4454 6219 8.662781 AGCATACGATCATATACACACTTTTT 57.337 30.769 0.00 0.00 0.00 1.94
4508 6279 9.967451 TGGGAATAATTAGTACTGTTTTCATCA 57.033 29.630 5.39 7.05 0.00 3.07
4525 6299 7.890127 ACATGTTTGGATATCGATGGGAATAAT 59.110 33.333 8.54 0.00 0.00 1.28
4758 6593 2.426738 AGCTAGAGACACTGTCATGCTC 59.573 50.000 11.80 0.45 34.60 4.26
4763 6598 2.163509 GTGGAGCTAGAGACACTGTCA 58.836 52.381 11.80 0.00 34.60 3.58
4765 6600 1.551452 GGTGGAGCTAGAGACACTGT 58.449 55.000 0.00 0.00 34.42 3.55
4766 6601 0.820871 GGGTGGAGCTAGAGACACTG 59.179 60.000 0.00 0.00 34.42 3.66
4790 6625 2.112297 GGTTGGAGGGACGTTGCA 59.888 61.111 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.