Multiple sequence alignment - TraesCS7A01G393600

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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 TraesCS7A01G393600 chr7A 100.000 6189 0 0 1 6189 571700457 571706645 0.000000e+00 11430.0
1 TraesCS7A01G393600 chr7A 95.968 620 23 2 5570 6188 7868316 7868934 0.000000e+00 1005.0
2 TraesCS7A01G393600 chr7A 88.136 59 7 0 1716 1774 665749028 665748970 3.100000e-08 71.3
3 TraesCS7A01G393600 chr7D 94.726 3280 120 26 2328 5566 504175741 504179008 0.000000e+00 5049.0
4 TraesCS7A01G393600 chr7D 94.812 1889 61 16 213 2083 504173769 504175638 0.000000e+00 2911.0
5 TraesCS7A01G393600 chr7D 91.628 215 14 1 1 211 504173515 504173729 1.690000e-75 294.0
6 TraesCS7A01G393600 chr7D 85.609 271 32 6 1264 1529 169915302 169915034 1.700000e-70 278.0
7 TraesCS7A01G393600 chr7D 89.286 168 11 1 2166 2326 504175637 504175804 2.920000e-48 204.0
8 TraesCS7A01G393600 chr7D 100.000 86 0 0 2082 2167 242790663 242790578 6.420000e-35 159.0
9 TraesCS7A01G393600 chr7D 88.136 59 7 0 1716 1774 575508214 575508156 3.100000e-08 71.3
10 TraesCS7A01G393600 chr7B 94.522 3231 128 26 2328 5525 532276688 532279902 0.000000e+00 4940.0
11 TraesCS7A01G393600 chr7B 91.848 1926 73 34 213 2083 532274688 532276584 0.000000e+00 2610.0
12 TraesCS7A01G393600 chr7B 94.313 211 12 0 1 211 532274438 532274648 2.150000e-84 324.0
13 TraesCS7A01G393600 chr7B 87.574 169 13 2 2166 2326 532276583 532276751 8.190000e-44 189.0
14 TraesCS7A01G393600 chr7B 88.136 59 7 0 1716 1774 637230925 637230867 3.100000e-08 71.3
15 TraesCS7A01G393600 chr3A 96.774 620 19 1 5570 6188 588518526 588519145 0.000000e+00 1033.0
16 TraesCS7A01G393600 chr3A 96.272 617 22 1 5573 6188 733028353 733028969 0.000000e+00 1011.0
17 TraesCS7A01G393600 chr3A 95.645 620 26 1 5570 6188 640674661 640675280 0.000000e+00 994.0
18 TraesCS7A01G393600 chr3A 95.645 620 26 1 5570 6188 640745762 640746381 0.000000e+00 994.0
19 TraesCS7A01G393600 chr3A 95.638 619 26 1 5570 6188 720874730 720875347 0.000000e+00 992.0
20 TraesCS7A01G393600 chr3A 95.638 619 25 2 5570 6188 720945458 720946074 0.000000e+00 992.0
21 TraesCS7A01G393600 chr6A 95.948 617 24 1 5573 6188 562244332 562244948 0.000000e+00 1000.0
22 TraesCS7A01G393600 chr6A 85.159 283 34 7 1264 1542 523949626 523949348 3.650000e-72 283.0
23 TraesCS7A01G393600 chr5A 95.793 618 23 3 5572 6188 539089085 539088470 0.000000e+00 994.0
24 TraesCS7A01G393600 chr2B 87.063 286 33 4 1246 1529 91257408 91257691 2.780000e-83 320.0
25 TraesCS7A01G393600 chr2B 92.453 53 4 0 1721 1773 91257832 91257884 6.650000e-10 76.8
26 TraesCS7A01G393600 chr2D 85.664 286 37 4 1246 1529 58777653 58777936 1.300000e-76 298.0
27 TraesCS7A01G393600 chr2D 91.228 57 5 0 1721 1777 58778077 58778133 1.850000e-10 78.7
28 TraesCS7A01G393600 chr2A 86.567 268 34 2 1246 1512 59557970 59557704 1.690000e-75 294.0
29 TraesCS7A01G393600 chr2A 92.453 53 4 0 1721 1773 59557546 59557494 6.650000e-10 76.8
30 TraesCS7A01G393600 chr2A 92.453 53 4 0 1721 1773 59568127 59568075 6.650000e-10 76.8
31 TraesCS7A01G393600 chr6D 85.507 276 34 5 1264 1534 381999832 381999558 3.650000e-72 283.0
32 TraesCS7A01G393600 chr6D 97.753 89 2 0 2082 2170 17299403 17299491 2.990000e-33 154.0
33 TraesCS7A01G393600 chr6D 92.523 107 3 5 2067 2170 68334487 68334383 1.390000e-31 148.0
34 TraesCS7A01G393600 chr6B 84.828 290 35 7 1264 1549 570982480 570982196 3.650000e-72 283.0
35 TraesCS7A01G393600 chr5D 98.864 88 1 0 2080 2167 492288320 492288233 2.310000e-34 158.0
36 TraesCS7A01G393600 chr5D 96.809 94 2 1 2074 2167 528755002 528755094 8.310000e-34 156.0
37 TraesCS7A01G393600 chr4D 95.745 94 2 2 2082 2175 293383757 293383848 3.860000e-32 150.0
38 TraesCS7A01G393600 chr4D 96.667 90 3 0 2082 2171 379169417 379169328 3.860000e-32 150.0
39 TraesCS7A01G393600 chr4D 94.792 96 4 1 2082 2177 293383841 293383747 1.390000e-31 148.0
40 TraesCS7A01G393600 chr4B 91.346 104 8 1 2066 2168 670190809 670190912 2.330000e-29 141.0


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 TraesCS7A01G393600 chr7A 571700457 571706645 6188 False 11430.00 11430 100.00000 1 6189 1 chr7A.!!$F2 6188
1 TraesCS7A01G393600 chr7A 7868316 7868934 618 False 1005.00 1005 95.96800 5570 6188 1 chr7A.!!$F1 618
2 TraesCS7A01G393600 chr7D 504173515 504179008 5493 False 2114.50 5049 92.61300 1 5566 4 chr7D.!!$F1 5565
3 TraesCS7A01G393600 chr7B 532274438 532279902 5464 False 2015.75 4940 92.06425 1 5525 4 chr7B.!!$F1 5524
4 TraesCS7A01G393600 chr3A 588518526 588519145 619 False 1033.00 1033 96.77400 5570 6188 1 chr3A.!!$F1 618
5 TraesCS7A01G393600 chr3A 733028353 733028969 616 False 1011.00 1011 96.27200 5573 6188 1 chr3A.!!$F6 615
6 TraesCS7A01G393600 chr3A 640674661 640675280 619 False 994.00 994 95.64500 5570 6188 1 chr3A.!!$F2 618
7 TraesCS7A01G393600 chr3A 640745762 640746381 619 False 994.00 994 95.64500 5570 6188 1 chr3A.!!$F3 618
8 TraesCS7A01G393600 chr3A 720874730 720875347 617 False 992.00 992 95.63800 5570 6188 1 chr3A.!!$F4 618
9 TraesCS7A01G393600 chr3A 720945458 720946074 616 False 992.00 992 95.63800 5570 6188 1 chr3A.!!$F5 618
10 TraesCS7A01G393600 chr6A 562244332 562244948 616 False 1000.00 1000 95.94800 5573 6188 1 chr6A.!!$F1 615
11 TraesCS7A01G393600 chr5A 539088470 539089085 615 True 994.00 994 95.79300 5572 6188 1 chr5A.!!$R1 616

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
968 1061 0.319211 TCCGAGCGTGTACAAACAGG 60.319 55.000 0.0 1.12 42.96 4.00 F
1502 1596 0.106918 CGCTCTACTCCCTCCTCTGT 60.107 60.000 0.0 0.00 0.00 3.41 F
2092 2190 0.115745 TTCCCTGTTACTCCCTCCGT 59.884 55.000 0.0 0.00 0.00 4.69 F
2094 2192 0.535797 CCCTGTTACTCCCTCCGTTC 59.464 60.000 0.0 0.00 0.00 3.95 F
2347 2453 0.734889 GGCCGATGAAACAGTGGATG 59.265 55.000 0.0 0.00 0.00 3.51 F
2348 2454 0.734889 GCCGATGAAACAGTGGATGG 59.265 55.000 0.0 0.00 0.00 3.51 F
3544 3670 0.984230 TCCTCGGATCTTTTGCCAGT 59.016 50.000 0.0 0.00 0.00 4.00 F
3837 3963 2.091541 TGCTTAGCTGTAACCATTGGC 58.908 47.619 5.6 0.00 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2253 2359 0.036448 TCATTCGGCCGGTTTTACCA 59.964 50.000 27.83 0.00 38.47 3.25 R
2680 2794 0.391597 TGCCGTCGGTCTTTTCTTCT 59.608 50.000 13.94 0.00 0.00 2.85 R
2993 3118 1.181786 GGGCGAAAATGAATCCCACA 58.818 50.000 0.00 0.00 36.96 4.17 R
3301 3427 3.056821 TCTTCACCTGTATCGACAACTGG 60.057 47.826 18.57 18.57 40.66 4.00 R
3660 3786 4.043200 GCTTGGCTGCCGACAACC 62.043 66.667 14.98 0.00 31.83 3.77 R
3837 3963 4.201950 CCCAAGTGTTTTGTGTCTCTGAAG 60.202 45.833 0.00 0.00 0.00 3.02 R
4457 4587 0.678950 TGCTCGTCACCAACATCAGA 59.321 50.000 0.00 0.00 0.00 3.27 R
5566 5714 1.115930 GCCGGAGATGCCCTTAGAGA 61.116 60.000 5.05 0.00 0.00 3.10 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
56 57 4.729227 TTGCAGTATGATTGACCGTCTA 57.271 40.909 0.00 0.00 39.69 2.59
171 176 2.103373 TCTCTCATCTGGTGTAGGCAC 58.897 52.381 0.00 0.00 44.53 5.01
200 205 3.795623 AGTGAACTACCGTTATCGCAT 57.204 42.857 0.00 0.00 32.39 4.73
211 216 4.394920 ACCGTTATCGCATCACTCAAAATT 59.605 37.500 0.00 0.00 35.54 1.82
332 378 7.149973 CCCAATAAATGCTTATGGACATCTTG 58.850 38.462 0.00 0.00 0.00 3.02
391 450 3.942829 TGAACACATCTCCTGTCCATTC 58.057 45.455 0.00 0.00 35.29 2.67
393 452 4.042062 TGAACACATCTCCTGTCCATTCTT 59.958 41.667 0.00 0.00 35.29 2.52
423 482 0.669619 TGCAGCCACACTTGACATTG 59.330 50.000 0.00 0.00 0.00 2.82
676 750 1.330655 TGATCCCCTGCTTCTCGTCC 61.331 60.000 0.00 0.00 0.00 4.79
864 957 4.123545 CCACCCCCATTCCCGTCC 62.124 72.222 0.00 0.00 0.00 4.79
968 1061 0.319211 TCCGAGCGTGTACAAACAGG 60.319 55.000 0.00 1.12 42.96 4.00
969 1062 1.289109 CCGAGCGTGTACAAACAGGG 61.289 60.000 0.00 0.00 40.93 4.45
970 1063 1.866925 GAGCGTGTACAAACAGGGC 59.133 57.895 0.00 0.00 40.93 5.19
971 1064 1.574702 GAGCGTGTACAAACAGGGCC 61.575 60.000 0.00 0.00 40.93 5.80
997 1090 4.779733 GAGCGGTGGAGGGGGAGA 62.780 72.222 0.00 0.00 0.00 3.71
1039 1132 4.753662 ACCCTGAGACCGCGGCTA 62.754 66.667 28.58 8.15 0.00 3.93
1092 1185 1.302511 GCCGGAGTTGCCTTTCTGA 60.303 57.895 5.05 0.00 0.00 3.27
1105 1198 6.653526 TGCCTTTCTGATGATTCTTGAAAA 57.346 33.333 0.00 0.00 30.63 2.29
1107 1200 5.866092 GCCTTTCTGATGATTCTTGAAAACC 59.134 40.000 0.00 0.00 30.63 3.27
1197 1291 1.525197 TCTGATGTTTGTCACGCGTTC 59.475 47.619 10.22 6.64 0.00 3.95
1201 1295 1.368850 GTTTGTCACGCGTTCTGGC 60.369 57.895 10.22 0.00 0.00 4.85
1203 1297 1.771073 TTTGTCACGCGTTCTGGCTG 61.771 55.000 10.22 0.00 0.00 4.85
1322 1416 4.748679 ACGTCGCCGCTGTACGTC 62.749 66.667 8.94 0.00 46.04 4.34
1502 1596 0.106918 CGCTCTACTCCCTCCTCTGT 60.107 60.000 0.00 0.00 0.00 3.41
1712 1806 3.449227 CGGGTCCTGCTCGTGCTA 61.449 66.667 11.19 0.00 40.48 3.49
1715 1809 2.202810 GTCCTGCTCGTGCTAGCC 60.203 66.667 13.29 2.49 42.05 3.93
1795 1889 1.269448 GTCTTCTTGCCAAATCGCCAA 59.731 47.619 0.00 0.00 0.00 4.52
1806 1900 2.642139 AATCGCCAAACAAGATGCTG 57.358 45.000 0.00 0.00 0.00 4.41
1946 2040 3.318313 GGAGTTATCCATGGAGAAGGGA 58.682 50.000 21.98 0.00 45.87 4.20
2025 2122 4.462483 TGGATTTACAAGGCAGATTTGTCC 59.538 41.667 0.00 0.00 39.36 4.02
2086 2184 3.017442 GGAATTGCTTCCCTGTTACTCC 58.983 50.000 0.00 0.00 44.56 3.85
2087 2185 2.808906 ATTGCTTCCCTGTTACTCCC 57.191 50.000 0.00 0.00 0.00 4.30
2088 2186 1.742308 TTGCTTCCCTGTTACTCCCT 58.258 50.000 0.00 0.00 0.00 4.20
2089 2187 1.276622 TGCTTCCCTGTTACTCCCTC 58.723 55.000 0.00 0.00 0.00 4.30
2090 2188 0.542333 GCTTCCCTGTTACTCCCTCC 59.458 60.000 0.00 0.00 0.00 4.30
2091 2189 0.824759 CTTCCCTGTTACTCCCTCCG 59.175 60.000 0.00 0.00 0.00 4.63
2092 2190 0.115745 TTCCCTGTTACTCCCTCCGT 59.884 55.000 0.00 0.00 0.00 4.69
2093 2191 0.115745 TCCCTGTTACTCCCTCCGTT 59.884 55.000 0.00 0.00 0.00 4.44
2094 2192 0.535797 CCCTGTTACTCCCTCCGTTC 59.464 60.000 0.00 0.00 0.00 3.95
2095 2193 0.535797 CCTGTTACTCCCTCCGTTCC 59.464 60.000 0.00 0.00 0.00 3.62
2096 2194 1.263356 CTGTTACTCCCTCCGTTCCA 58.737 55.000 0.00 0.00 0.00 3.53
2097 2195 1.831736 CTGTTACTCCCTCCGTTCCAT 59.168 52.381 0.00 0.00 0.00 3.41
2098 2196 3.028850 CTGTTACTCCCTCCGTTCCATA 58.971 50.000 0.00 0.00 0.00 2.74
2099 2197 3.641906 CTGTTACTCCCTCCGTTCCATAT 59.358 47.826 0.00 0.00 0.00 1.78
2100 2198 4.035112 TGTTACTCCCTCCGTTCCATATT 58.965 43.478 0.00 0.00 0.00 1.28
2101 2199 5.210430 TGTTACTCCCTCCGTTCCATATTA 58.790 41.667 0.00 0.00 0.00 0.98
2102 2200 5.069516 TGTTACTCCCTCCGTTCCATATTAC 59.930 44.000 0.00 0.00 0.00 1.89
2103 2201 3.924922 ACTCCCTCCGTTCCATATTACT 58.075 45.455 0.00 0.00 0.00 2.24
2104 2202 4.296056 ACTCCCTCCGTTCCATATTACTT 58.704 43.478 0.00 0.00 0.00 2.24
2105 2203 4.101119 ACTCCCTCCGTTCCATATTACTTG 59.899 45.833 0.00 0.00 0.00 3.16
2106 2204 4.035112 TCCCTCCGTTCCATATTACTTGT 58.965 43.478 0.00 0.00 0.00 3.16
2107 2205 4.100498 TCCCTCCGTTCCATATTACTTGTC 59.900 45.833 0.00 0.00 0.00 3.18
2108 2206 4.377897 CCTCCGTTCCATATTACTTGTCC 58.622 47.826 0.00 0.00 0.00 4.02
2109 2207 4.377897 CTCCGTTCCATATTACTTGTCCC 58.622 47.826 0.00 0.00 0.00 4.46
2110 2208 4.035112 TCCGTTCCATATTACTTGTCCCT 58.965 43.478 0.00 0.00 0.00 4.20
2111 2209 4.127171 CCGTTCCATATTACTTGTCCCTG 58.873 47.826 0.00 0.00 0.00 4.45
2112 2210 4.141801 CCGTTCCATATTACTTGTCCCTGA 60.142 45.833 0.00 0.00 0.00 3.86
2113 2211 5.454755 CCGTTCCATATTACTTGTCCCTGAT 60.455 44.000 0.00 0.00 0.00 2.90
2114 2212 6.055588 CGTTCCATATTACTTGTCCCTGATT 58.944 40.000 0.00 0.00 0.00 2.57
2115 2213 6.542370 CGTTCCATATTACTTGTCCCTGATTT 59.458 38.462 0.00 0.00 0.00 2.17
2116 2214 7.713507 CGTTCCATATTACTTGTCCCTGATTTA 59.286 37.037 0.00 0.00 0.00 1.40
2117 2215 9.057089 GTTCCATATTACTTGTCCCTGATTTAG 57.943 37.037 0.00 0.00 0.00 1.85
2118 2216 8.331931 TCCATATTACTTGTCCCTGATTTAGT 57.668 34.615 0.00 0.00 0.00 2.24
2119 2217 9.442062 TCCATATTACTTGTCCCTGATTTAGTA 57.558 33.333 0.00 0.00 0.00 1.82
2120 2218 9.490379 CCATATTACTTGTCCCTGATTTAGTAC 57.510 37.037 0.00 0.00 0.00 2.73
2124 2222 8.842358 TTACTTGTCCCTGATTTAGTACAAAG 57.158 34.615 0.00 0.00 32.96 2.77
2125 2223 6.838382 ACTTGTCCCTGATTTAGTACAAAGT 58.162 36.000 0.00 0.00 32.96 2.66
2126 2224 7.287810 ACTTGTCCCTGATTTAGTACAAAGTT 58.712 34.615 0.00 0.00 32.96 2.66
2127 2225 7.228706 ACTTGTCCCTGATTTAGTACAAAGTTG 59.771 37.037 0.00 0.00 32.96 3.16
2128 2226 6.597562 TGTCCCTGATTTAGTACAAAGTTGT 58.402 36.000 1.75 1.75 44.86 3.32
2129 2227 7.737869 TGTCCCTGATTTAGTACAAAGTTGTA 58.262 34.615 0.00 0.00 42.35 2.41
2142 2240 6.224420 ACAAAGTTGTACTAAATCAGCGAC 57.776 37.500 0.00 0.00 40.16 5.19
2143 2241 5.756347 ACAAAGTTGTACTAAATCAGCGACA 59.244 36.000 0.00 0.00 40.16 4.35
2144 2242 6.259167 ACAAAGTTGTACTAAATCAGCGACAA 59.741 34.615 0.00 0.00 40.16 3.18
2145 2243 6.467723 AAGTTGTACTAAATCAGCGACAAG 57.532 37.500 0.00 0.00 35.28 3.16
2146 2244 5.539048 AGTTGTACTAAATCAGCGACAAGT 58.461 37.500 0.00 0.00 35.28 3.16
2147 2245 6.684686 AGTTGTACTAAATCAGCGACAAGTA 58.315 36.000 0.00 0.00 36.22 2.24
2148 2246 7.149973 AGTTGTACTAAATCAGCGACAAGTAA 58.850 34.615 0.00 0.00 36.22 2.24
2149 2247 7.817962 AGTTGTACTAAATCAGCGACAAGTAAT 59.182 33.333 0.00 0.00 36.22 1.89
2150 2248 9.079833 GTTGTACTAAATCAGCGACAAGTAATA 57.920 33.333 0.00 0.00 35.28 0.98
2151 2249 9.811995 TTGTACTAAATCAGCGACAAGTAATAT 57.188 29.630 0.00 0.00 31.65 1.28
2152 2250 9.244799 TGTACTAAATCAGCGACAAGTAATATG 57.755 33.333 0.00 0.00 0.00 1.78
2153 2251 7.715265 ACTAAATCAGCGACAAGTAATATGG 57.285 36.000 0.00 0.00 0.00 2.74
2154 2252 7.497595 ACTAAATCAGCGACAAGTAATATGGA 58.502 34.615 0.00 0.00 0.00 3.41
2155 2253 7.985184 ACTAAATCAGCGACAAGTAATATGGAA 59.015 33.333 0.00 0.00 0.00 3.53
2156 2254 6.604735 AATCAGCGACAAGTAATATGGAAC 57.395 37.500 0.00 0.00 0.00 3.62
2157 2255 4.109766 TCAGCGACAAGTAATATGGAACG 58.890 43.478 0.00 0.00 0.00 3.95
2158 2256 3.245284 CAGCGACAAGTAATATGGAACGG 59.755 47.826 0.00 0.00 0.00 4.44
2159 2257 3.131577 AGCGACAAGTAATATGGAACGGA 59.868 43.478 0.00 0.00 0.00 4.69
2160 2258 3.489785 GCGACAAGTAATATGGAACGGAG 59.510 47.826 0.00 0.00 0.00 4.63
2161 2259 4.049186 CGACAAGTAATATGGAACGGAGG 58.951 47.826 0.00 0.00 0.00 4.30
2162 2260 4.377897 GACAAGTAATATGGAACGGAGGG 58.622 47.826 0.00 0.00 0.00 4.30
2163 2261 4.035112 ACAAGTAATATGGAACGGAGGGA 58.965 43.478 0.00 0.00 0.00 4.20
2164 2262 4.101119 ACAAGTAATATGGAACGGAGGGAG 59.899 45.833 0.00 0.00 0.00 4.30
2179 2278 5.069251 ACGGAGGGAGTAGATCACTAATTTG 59.931 44.000 0.00 0.00 43.76 2.32
2182 2281 7.158021 GGAGGGAGTAGATCACTAATTTGATG 58.842 42.308 0.00 0.00 43.76 3.07
2185 2284 6.465035 GGGAGTAGATCACTAATTTGATGCCT 60.465 42.308 0.00 0.00 37.72 4.75
2192 2291 5.815581 TCACTAATTTGATGCCTACCACTT 58.184 37.500 0.00 0.00 0.00 3.16
2281 2387 1.883021 GGCCGAATGAAACAGTGGG 59.117 57.895 0.00 0.00 30.88 4.61
2318 2424 2.867429 CAAGGACATGAACGAATTGGC 58.133 47.619 0.00 0.00 0.00 4.52
2319 2425 2.198827 AGGACATGAACGAATTGGCA 57.801 45.000 0.00 0.00 0.00 4.92
2320 2426 2.726821 AGGACATGAACGAATTGGCAT 58.273 42.857 0.00 0.00 0.00 4.40
2321 2427 3.884895 AGGACATGAACGAATTGGCATA 58.115 40.909 0.00 0.00 0.00 3.14
2322 2428 3.879295 AGGACATGAACGAATTGGCATAG 59.121 43.478 0.00 0.00 0.00 2.23
2323 2429 3.548818 GGACATGAACGAATTGGCATAGC 60.549 47.826 0.00 0.00 0.00 2.97
2339 2445 4.179579 GCCAGCGGCCGATGAAAC 62.180 66.667 42.61 27.16 44.06 2.78
2340 2446 2.745884 CCAGCGGCCGATGAAACA 60.746 61.111 42.61 0.00 32.62 2.83
2341 2447 2.753966 CCAGCGGCCGATGAAACAG 61.754 63.158 42.61 22.88 32.62 3.16
2342 2448 2.034879 CAGCGGCCGATGAAACAGT 61.035 57.895 38.89 1.33 32.62 3.55
2343 2449 2.034879 AGCGGCCGATGAAACAGTG 61.035 57.895 33.48 0.00 0.00 3.66
2344 2450 3.039202 GCGGCCGATGAAACAGTGG 62.039 63.158 33.48 0.00 0.00 4.00
2345 2451 1.375396 CGGCCGATGAAACAGTGGA 60.375 57.895 24.07 0.00 0.00 4.02
2346 2452 0.744414 CGGCCGATGAAACAGTGGAT 60.744 55.000 24.07 0.00 0.00 3.41
2347 2453 0.734889 GGCCGATGAAACAGTGGATG 59.265 55.000 0.00 0.00 0.00 3.51
2348 2454 0.734889 GCCGATGAAACAGTGGATGG 59.265 55.000 0.00 0.00 0.00 3.51
2349 2455 1.950484 GCCGATGAAACAGTGGATGGT 60.950 52.381 0.00 0.00 0.00 3.55
2350 2456 1.739466 CCGATGAAACAGTGGATGGTG 59.261 52.381 0.00 0.00 0.00 4.17
2351 2457 2.615240 CCGATGAAACAGTGGATGGTGA 60.615 50.000 0.00 0.00 0.00 4.02
2352 2458 3.073678 CGATGAAACAGTGGATGGTGAA 58.926 45.455 0.00 0.00 0.00 3.18
2353 2459 3.501828 CGATGAAACAGTGGATGGTGAAA 59.498 43.478 0.00 0.00 0.00 2.69
2354 2460 4.378770 CGATGAAACAGTGGATGGTGAAAG 60.379 45.833 0.00 0.00 0.00 2.62
2355 2461 3.897239 TGAAACAGTGGATGGTGAAAGT 58.103 40.909 0.00 0.00 0.00 2.66
2356 2462 4.277476 TGAAACAGTGGATGGTGAAAGTT 58.723 39.130 0.00 0.00 0.00 2.66
2357 2463 5.441500 TGAAACAGTGGATGGTGAAAGTTA 58.558 37.500 0.00 0.00 0.00 2.24
2358 2464 5.888724 TGAAACAGTGGATGGTGAAAGTTAA 59.111 36.000 0.00 0.00 0.00 2.01
2359 2465 5.767816 AACAGTGGATGGTGAAAGTTAAC 57.232 39.130 0.00 0.00 0.00 2.01
2360 2466 5.048846 ACAGTGGATGGTGAAAGTTAACT 57.951 39.130 1.12 1.12 0.00 2.24
2361 2467 4.821805 ACAGTGGATGGTGAAAGTTAACTG 59.178 41.667 9.34 0.00 38.70 3.16
2362 2468 3.821033 AGTGGATGGTGAAAGTTAACTGC 59.179 43.478 9.34 5.36 0.00 4.40
2363 2469 3.568007 GTGGATGGTGAAAGTTAACTGCA 59.432 43.478 9.34 8.06 0.00 4.41
2364 2470 4.037446 GTGGATGGTGAAAGTTAACTGCAA 59.963 41.667 9.34 0.00 0.00 4.08
2365 2471 4.037446 TGGATGGTGAAAGTTAACTGCAAC 59.963 41.667 9.34 13.54 0.00 4.17
2366 2472 3.684103 TGGTGAAAGTTAACTGCAACG 57.316 42.857 9.34 0.00 33.50 4.10
2367 2473 3.271729 TGGTGAAAGTTAACTGCAACGA 58.728 40.909 9.34 2.45 33.50 3.85
2368 2474 3.690139 TGGTGAAAGTTAACTGCAACGAA 59.310 39.130 9.34 0.00 33.50 3.85
2369 2475 4.156190 TGGTGAAAGTTAACTGCAACGAAA 59.844 37.500 9.34 0.00 33.50 3.46
2370 2476 5.163602 TGGTGAAAGTTAACTGCAACGAAAT 60.164 36.000 9.34 0.00 33.50 2.17
2371 2477 5.746721 GGTGAAAGTTAACTGCAACGAAATT 59.253 36.000 9.34 0.00 33.50 1.82
2372 2478 6.291585 GGTGAAAGTTAACTGCAACGAAATTG 60.292 38.462 9.34 0.00 41.69 2.32
2413 2519 1.739466 CAGTTGCGTGCCAAGATGTAT 59.261 47.619 0.00 0.00 33.21 2.29
2505 2611 3.054361 ACCAAATAAGGGACTACTGCCAG 60.054 47.826 0.00 0.00 38.49 4.85
2639 2753 4.098654 AGTTGGAGTTAGAGATGACCATCG 59.901 45.833 4.54 0.00 42.48 3.84
2649 2763 4.646945 AGAGATGACCATCGTCTACAATGT 59.353 41.667 0.54 0.00 42.42 2.71
2673 2787 4.916983 TGCTTGTTTAGTTCAATGTGCT 57.083 36.364 0.00 0.00 0.00 4.40
2677 2791 5.051508 GCTTGTTTAGTTCAATGTGCTGTTG 60.052 40.000 0.00 0.00 0.00 3.33
2680 2794 6.625362 TGTTTAGTTCAATGTGCTGTTGAAA 58.375 32.000 11.43 0.00 44.46 2.69
2691 2805 5.640732 TGTGCTGTTGAAAGAAGAAAAGAC 58.359 37.500 0.00 0.00 0.00 3.01
2694 2808 4.035208 GCTGTTGAAAGAAGAAAAGACCGA 59.965 41.667 0.00 0.00 0.00 4.69
2717 2831 4.574828 ACGGCACAAATATGGTATCTTGAC 59.425 41.667 0.00 0.00 0.00 3.18
2739 2853 3.266510 AGCGGAACATATGCTGAAGAA 57.733 42.857 1.58 0.00 37.62 2.52
2746 2860 6.183360 CGGAACATATGCTGAAGAAAATTCCT 60.183 38.462 1.58 0.00 31.63 3.36
2747 2861 7.550712 GGAACATATGCTGAAGAAAATTCCTT 58.449 34.615 1.58 0.00 31.22 3.36
2773 2887 4.495422 TCAGAGCATAGGAACTTCGTTTC 58.505 43.478 0.00 0.00 41.75 2.78
2804 2918 8.232913 TCCATACCAATAATTTAGCCTTTGTC 57.767 34.615 0.00 0.00 0.00 3.18
2845 2959 3.753272 ACATGTGTGCACTGTCCTTTATC 59.247 43.478 19.41 0.00 0.00 1.75
2930 3055 3.421919 TGTGATTCTGCAGATGTGGAA 57.578 42.857 19.04 0.75 0.00 3.53
2952 3077 3.008835 TGCCTCTTGCTTGCTTCATAT 57.991 42.857 0.00 0.00 42.00 1.78
2969 3094 1.697284 TATTGGTGTGCCTGTTTGCA 58.303 45.000 0.00 0.00 39.37 4.08
2984 3109 1.979855 TTGCACTGCAACACTATGGT 58.020 45.000 12.59 0.00 43.99 3.55
3062 3187 6.757947 GCATAAGCATGATTGGTGTTTACAAT 59.242 34.615 6.43 0.00 39.84 2.71
3146 3271 3.711704 TGAAGAAAACACAGAGAGGAGGT 59.288 43.478 0.00 0.00 0.00 3.85
3197 3322 5.373222 TGTGTTACAGGTAAAATGCTCAGT 58.627 37.500 0.00 0.00 0.00 3.41
3249 3375 9.379770 TGGATCATGACCTCTAATATAAAGTGA 57.620 33.333 0.00 0.00 0.00 3.41
3301 3427 1.135721 GCAGATCTGGGGCATTTCAAC 59.864 52.381 23.89 0.00 0.00 3.18
3530 3656 1.081892 CAGGCAAGTCATGTTCCTCG 58.918 55.000 0.00 0.00 0.00 4.63
3544 3670 0.984230 TCCTCGGATCTTTTGCCAGT 59.016 50.000 0.00 0.00 0.00 4.00
3837 3963 2.091541 TGCTTAGCTGTAACCATTGGC 58.908 47.619 5.60 0.00 0.00 4.52
3890 4016 8.436778 TGCATCAGGTATACCATGTTAATAAGT 58.563 33.333 23.87 0.00 38.89 2.24
3917 4043 6.980577 TGAATCACCTTATCCCCTGTTAAAT 58.019 36.000 0.00 0.00 0.00 1.40
3922 4048 6.011981 TCACCTTATCCCCTGTTAAATTGACT 60.012 38.462 0.00 0.00 0.00 3.41
4382 4509 3.382227 TGCATTCCATCAGGTATTTGCAG 59.618 43.478 0.00 0.00 34.24 4.41
4400 4527 5.432680 TGCAGATTCCTCTTCTTCTGAAT 57.567 39.130 3.11 0.00 38.25 2.57
4445 4575 5.824624 AGACATTCAGAAGTGTGTTGACATT 59.175 36.000 3.73 0.00 33.63 2.71
4448 4578 5.484173 TTCAGAAGTGTGTTGACATTCAC 57.516 39.130 4.87 4.87 33.63 3.18
4449 4579 4.512484 TCAGAAGTGTGTTGACATTCACA 58.488 39.130 9.07 9.07 41.37 3.58
4457 4587 5.728471 TGTGTTGACATTCACACCATTTTT 58.272 33.333 6.46 0.00 39.23 1.94
4471 4601 5.200368 ACCATTTTTCTGATGTTGGTGAC 57.800 39.130 0.00 0.00 36.18 3.67
4672 4803 1.874019 CGTCGCTGAGTTCATCCGG 60.874 63.158 0.00 0.00 0.00 5.14
4886 5023 4.368808 CAACGCCAACGCCGACAG 62.369 66.667 0.00 0.00 45.53 3.51
5052 5189 0.394938 TGCTACGTCAAGGCCAAGAA 59.605 50.000 5.01 0.00 0.00 2.52
5176 5313 1.006805 CCTCGAGGTCGGCATGATC 60.007 63.158 24.04 0.00 40.29 2.92
5189 5326 5.012893 TCGGCATGATCTACTATGTCTGAT 58.987 41.667 0.00 0.00 0.00 2.90
5200 5340 7.521669 TCTACTATGTCTGATCTCTGATGGAA 58.478 38.462 0.00 0.00 0.00 3.53
5333 5476 3.486383 CCTTGGTTTTCTTGTGCCTCTA 58.514 45.455 0.00 0.00 0.00 2.43
5406 5554 1.270839 GGCCAGAGAAGTTGTACTGCA 60.271 52.381 0.00 0.00 0.00 4.41
5410 5558 4.180057 CCAGAGAAGTTGTACTGCAGATC 58.820 47.826 23.35 13.02 0.00 2.75
5419 5567 3.242518 TGTACTGCAGATCGAAAAGACG 58.757 45.455 23.35 0.00 0.00 4.18
5496 5644 1.210722 GACCTCTGAATCTTGGTCCCC 59.789 57.143 0.00 0.00 42.11 4.81
5530 5678 5.532025 AAATCTTCAGTTAAGCTGCGTAC 57.468 39.130 0.00 0.00 44.66 3.67
5534 5682 1.082117 CAGTTAAGCTGCGTACCGGG 61.082 60.000 6.32 0.00 38.52 5.73
5536 5684 0.671472 GTTAAGCTGCGTACCGGGTT 60.671 55.000 4.31 10.92 42.78 4.11
5543 5691 3.107661 CGTACCGGGTTGTCGTGC 61.108 66.667 4.31 0.00 0.00 5.34
5546 5694 0.174162 GTACCGGGTTGTCGTGCTAT 59.826 55.000 4.31 0.00 0.00 2.97
5555 5703 3.751698 GGTTGTCGTGCTATTTTCTTCCT 59.248 43.478 0.00 0.00 0.00 3.36
5566 5714 3.685139 TTTTCTTCCTCAGCACTCGAT 57.315 42.857 0.00 0.00 0.00 3.59
5567 5715 2.949451 TTCTTCCTCAGCACTCGATC 57.051 50.000 0.00 0.00 0.00 3.69
5568 5716 2.136298 TCTTCCTCAGCACTCGATCT 57.864 50.000 0.00 0.00 0.00 2.75
5583 5731 1.201181 CGATCTCTAAGGGCATCTCCG 59.799 57.143 0.00 0.00 34.94 4.63
5622 5770 0.601558 CGCCTAAATAGAGCGGCCTA 59.398 55.000 0.00 0.00 45.88 3.93
5833 5983 1.910580 ATGATTCACTCGGCGGGGTT 61.911 55.000 13.20 0.00 0.00 4.11
5848 5998 2.281484 GTTGGCTCCAGGCGTTGA 60.281 61.111 0.00 0.00 44.42 3.18
5907 6057 4.624364 CGGTGCTGGGCTGTGTCA 62.624 66.667 0.00 0.00 0.00 3.58
6003 6153 2.354188 CTTGCGTCGTCGGTGTCA 60.354 61.111 3.90 0.00 37.56 3.58
6031 6181 0.745845 GCCGTCTGCATCTGGTTCAT 60.746 55.000 0.00 0.00 40.77 2.57
6073 6223 4.711949 CCACGCCCTGAGCTGCTT 62.712 66.667 2.53 0.00 40.39 3.91
6188 6338 1.825090 TGATGGCGCTGTTCTTCATT 58.175 45.000 7.64 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
171 176 2.287427 ACGGTAGTTCACTTCACTCACG 60.287 50.000 0.00 0.00 32.67 4.35
181 186 3.242248 GTGATGCGATAACGGTAGTTCAC 59.758 47.826 0.00 0.00 41.49 3.18
185 190 2.686405 TGAGTGATGCGATAACGGTAGT 59.314 45.455 0.00 0.00 40.15 2.73
200 205 5.450592 TGCTTATGTGCAATTTTGAGTGA 57.549 34.783 0.00 0.00 40.29 3.41
332 378 8.051901 ACTGTAACTTTGGCAGGAATTTATAC 57.948 34.615 0.00 0.00 34.79 1.47
423 482 9.190858 TGTGAAAATGTTAAGCATTGTAACATC 57.809 29.630 11.10 4.01 46.50 3.06
457 521 3.776969 TGTGGCATACTGAGGATTCTTCT 59.223 43.478 0.00 0.00 0.00 2.85
676 750 2.359975 GGCGGAACTGTGGAAGGG 60.360 66.667 0.00 0.00 0.00 3.95
780 861 0.955919 GGTCAAAGGAGCAGGTTCGG 60.956 60.000 0.00 0.00 41.19 4.30
864 957 3.365265 GTGCAGAAACCGGCAGGG 61.365 66.667 8.08 0.00 41.35 4.45
997 1090 1.075226 TAGGGGCGCTCTTCATCCT 60.075 57.895 7.48 5.87 0.00 3.24
1085 1178 7.020010 CGAGGTTTTCAAGAATCATCAGAAAG 58.980 38.462 0.00 0.00 35.05 2.62
1086 1179 6.710295 TCGAGGTTTTCAAGAATCATCAGAAA 59.290 34.615 0.00 0.00 33.09 2.52
1092 1185 5.419542 TCGATCGAGGTTTTCAAGAATCAT 58.580 37.500 15.15 0.00 0.00 2.45
1107 1200 4.292178 GCCTGGCCCTCGATCGAG 62.292 72.222 33.32 33.32 41.63 4.04
1139 1233 0.166814 GCACATTCAGCCAAGACGAC 59.833 55.000 0.00 0.00 0.00 4.34
1149 1243 9.139174 ACGAAAATAAATAAAAGGCACATTCAG 57.861 29.630 0.00 0.00 0.00 3.02
1168 1262 5.681105 CGTGACAAACATCAGAAACGAAAAT 59.319 36.000 0.00 0.00 0.00 1.82
1715 1809 4.457496 ATGCAGGTGCCGACGAGG 62.457 66.667 0.00 0.00 44.97 4.63
1795 1889 5.066505 GGATCCGAATTAACAGCATCTTGTT 59.933 40.000 0.00 0.00 43.34 2.83
1829 1923 7.668525 AACAGTCCAAAAATAGTAGTAGCAC 57.331 36.000 0.00 0.00 0.00 4.40
1830 1924 9.953565 ATAAACAGTCCAAAAATAGTAGTAGCA 57.046 29.630 0.00 0.00 0.00 3.49
1931 2025 2.441001 GTGATGTCCCTTCTCCATGGAT 59.559 50.000 16.63 0.00 0.00 3.41
1946 2040 6.891361 TGATTGGATCCTTACATTTGTGATGT 59.109 34.615 14.23 0.00 36.13 3.06
2010 2104 1.467920 GGGAGGACAAATCTGCCTTG 58.532 55.000 0.00 0.00 39.30 3.61
2025 2122 7.119846 CCTTGACTCAAAAACAGTAATAGGGAG 59.880 40.741 0.00 0.00 0.00 4.30
2081 2179 5.070823 AGTAATATGGAACGGAGGGAGTA 57.929 43.478 0.00 0.00 0.00 2.59
2082 2180 3.924922 AGTAATATGGAACGGAGGGAGT 58.075 45.455 0.00 0.00 0.00 3.85
2083 2181 4.101119 ACAAGTAATATGGAACGGAGGGAG 59.899 45.833 0.00 0.00 0.00 4.30
2084 2182 4.035112 ACAAGTAATATGGAACGGAGGGA 58.965 43.478 0.00 0.00 0.00 4.20
2085 2183 4.377897 GACAAGTAATATGGAACGGAGGG 58.622 47.826 0.00 0.00 0.00 4.30
2086 2184 4.377897 GGACAAGTAATATGGAACGGAGG 58.622 47.826 0.00 0.00 0.00 4.30
2087 2185 4.101119 AGGGACAAGTAATATGGAACGGAG 59.899 45.833 0.00 0.00 0.00 4.63
2088 2186 4.035112 AGGGACAAGTAATATGGAACGGA 58.965 43.478 0.00 0.00 0.00 4.69
2089 2187 4.127171 CAGGGACAAGTAATATGGAACGG 58.873 47.826 0.00 0.00 0.00 4.44
2090 2188 5.018539 TCAGGGACAAGTAATATGGAACG 57.981 43.478 0.00 0.00 0.00 3.95
2091 2189 7.881775 AAATCAGGGACAAGTAATATGGAAC 57.118 36.000 0.00 0.00 0.00 3.62
2092 2190 8.778059 ACTAAATCAGGGACAAGTAATATGGAA 58.222 33.333 0.00 0.00 0.00 3.53
2093 2191 8.331931 ACTAAATCAGGGACAAGTAATATGGA 57.668 34.615 0.00 0.00 0.00 3.41
2094 2192 9.490379 GTACTAAATCAGGGACAAGTAATATGG 57.510 37.037 0.00 0.00 0.00 2.74
2098 2196 9.449719 CTTTGTACTAAATCAGGGACAAGTAAT 57.550 33.333 0.00 0.00 36.29 1.89
2099 2197 8.434392 ACTTTGTACTAAATCAGGGACAAGTAA 58.566 33.333 0.00 0.00 36.29 2.24
2100 2198 7.970102 ACTTTGTACTAAATCAGGGACAAGTA 58.030 34.615 0.00 0.00 36.29 2.24
2101 2199 6.838382 ACTTTGTACTAAATCAGGGACAAGT 58.162 36.000 0.00 0.00 36.29 3.16
2102 2200 7.228706 ACAACTTTGTACTAAATCAGGGACAAG 59.771 37.037 0.00 0.00 40.16 3.16
2103 2201 7.057894 ACAACTTTGTACTAAATCAGGGACAA 58.942 34.615 0.00 0.00 40.16 3.18
2104 2202 6.597562 ACAACTTTGTACTAAATCAGGGACA 58.402 36.000 0.00 0.00 40.16 4.02
2118 2216 6.924612 TGTCGCTGATTTAGTACAACTTTGTA 59.075 34.615 0.00 0.00 42.35 2.41
2119 2217 5.756347 TGTCGCTGATTTAGTACAACTTTGT 59.244 36.000 0.00 0.00 44.86 2.83
2120 2218 6.223138 TGTCGCTGATTTAGTACAACTTTG 57.777 37.500 0.00 0.00 0.00 2.77
2121 2219 6.482308 ACTTGTCGCTGATTTAGTACAACTTT 59.518 34.615 0.00 0.00 33.64 2.66
2122 2220 5.989777 ACTTGTCGCTGATTTAGTACAACTT 59.010 36.000 0.00 0.00 33.64 2.66
2123 2221 5.539048 ACTTGTCGCTGATTTAGTACAACT 58.461 37.500 0.00 0.00 33.64 3.16
2124 2222 5.840940 ACTTGTCGCTGATTTAGTACAAC 57.159 39.130 0.00 0.00 33.64 3.32
2125 2223 9.811995 ATATTACTTGTCGCTGATTTAGTACAA 57.188 29.630 0.00 0.00 34.99 2.41
2126 2224 9.244799 CATATTACTTGTCGCTGATTTAGTACA 57.755 33.333 0.00 0.00 0.00 2.90
2127 2225 8.700644 CCATATTACTTGTCGCTGATTTAGTAC 58.299 37.037 0.00 0.00 0.00 2.73
2128 2226 8.635328 TCCATATTACTTGTCGCTGATTTAGTA 58.365 33.333 0.00 0.00 0.00 1.82
2129 2227 7.497595 TCCATATTACTTGTCGCTGATTTAGT 58.502 34.615 0.00 0.00 0.00 2.24
2130 2228 7.946655 TCCATATTACTTGTCGCTGATTTAG 57.053 36.000 0.00 0.00 0.00 1.85
2131 2229 7.042992 CGTTCCATATTACTTGTCGCTGATTTA 60.043 37.037 0.00 0.00 0.00 1.40
2132 2230 6.238103 CGTTCCATATTACTTGTCGCTGATTT 60.238 38.462 0.00 0.00 0.00 2.17
2133 2231 5.234329 CGTTCCATATTACTTGTCGCTGATT 59.766 40.000 0.00 0.00 0.00 2.57
2134 2232 4.745125 CGTTCCATATTACTTGTCGCTGAT 59.255 41.667 0.00 0.00 0.00 2.90
2135 2233 4.109766 CGTTCCATATTACTTGTCGCTGA 58.890 43.478 0.00 0.00 0.00 4.26
2136 2234 3.245284 CCGTTCCATATTACTTGTCGCTG 59.755 47.826 0.00 0.00 0.00 5.18
2137 2235 3.131577 TCCGTTCCATATTACTTGTCGCT 59.868 43.478 0.00 0.00 0.00 4.93
2138 2236 3.450578 TCCGTTCCATATTACTTGTCGC 58.549 45.455 0.00 0.00 0.00 5.19
2139 2237 4.049186 CCTCCGTTCCATATTACTTGTCG 58.951 47.826 0.00 0.00 0.00 4.35
2140 2238 4.100498 TCCCTCCGTTCCATATTACTTGTC 59.900 45.833 0.00 0.00 0.00 3.18
2141 2239 4.035112 TCCCTCCGTTCCATATTACTTGT 58.965 43.478 0.00 0.00 0.00 3.16
2142 2240 4.101119 ACTCCCTCCGTTCCATATTACTTG 59.899 45.833 0.00 0.00 0.00 3.16
2143 2241 4.296056 ACTCCCTCCGTTCCATATTACTT 58.704 43.478 0.00 0.00 0.00 2.24
2144 2242 3.924922 ACTCCCTCCGTTCCATATTACT 58.075 45.455 0.00 0.00 0.00 2.24
2145 2243 5.075493 TCTACTCCCTCCGTTCCATATTAC 58.925 45.833 0.00 0.00 0.00 1.89
2146 2244 5.329191 TCTACTCCCTCCGTTCCATATTA 57.671 43.478 0.00 0.00 0.00 0.98
2147 2245 4.194678 TCTACTCCCTCCGTTCCATATT 57.805 45.455 0.00 0.00 0.00 1.28
2148 2246 3.897657 TCTACTCCCTCCGTTCCATAT 57.102 47.619 0.00 0.00 0.00 1.78
2149 2247 3.139584 TGATCTACTCCCTCCGTTCCATA 59.860 47.826 0.00 0.00 0.00 2.74
2150 2248 2.091278 TGATCTACTCCCTCCGTTCCAT 60.091 50.000 0.00 0.00 0.00 3.41
2151 2249 1.286849 TGATCTACTCCCTCCGTTCCA 59.713 52.381 0.00 0.00 0.00 3.53
2152 2250 1.682323 GTGATCTACTCCCTCCGTTCC 59.318 57.143 0.00 0.00 0.00 3.62
2153 2251 2.657143 AGTGATCTACTCCCTCCGTTC 58.343 52.381 0.00 0.00 33.17 3.95
2154 2252 2.830651 AGTGATCTACTCCCTCCGTT 57.169 50.000 0.00 0.00 33.17 4.44
2155 2253 3.947612 TTAGTGATCTACTCCCTCCGT 57.052 47.619 0.00 0.00 40.89 4.69
2156 2254 5.302059 TCAAATTAGTGATCTACTCCCTCCG 59.698 44.000 0.00 0.00 40.89 4.63
2157 2255 6.732896 TCAAATTAGTGATCTACTCCCTCC 57.267 41.667 0.00 0.00 40.89 4.30
2158 2256 6.648725 GCATCAAATTAGTGATCTACTCCCTC 59.351 42.308 0.00 0.00 40.89 4.30
2159 2257 6.465035 GGCATCAAATTAGTGATCTACTCCCT 60.465 42.308 0.00 0.00 40.89 4.20
2160 2258 5.703130 GGCATCAAATTAGTGATCTACTCCC 59.297 44.000 0.00 0.00 40.89 4.30
2161 2259 6.529220 AGGCATCAAATTAGTGATCTACTCC 58.471 40.000 0.00 0.00 40.89 3.85
2162 2260 7.600752 GGTAGGCATCAAATTAGTGATCTACTC 59.399 40.741 13.43 5.92 40.89 2.59
2163 2261 7.071196 TGGTAGGCATCAAATTAGTGATCTACT 59.929 37.037 13.43 0.00 43.56 2.57
2164 2262 7.171678 GTGGTAGGCATCAAATTAGTGATCTAC 59.828 40.741 8.89 8.89 36.04 2.59
2179 2278 5.123979 CAGGTAAAAAGAAGTGGTAGGCATC 59.876 44.000 0.00 0.00 0.00 3.91
2182 2281 4.648651 TCAGGTAAAAAGAAGTGGTAGGC 58.351 43.478 0.00 0.00 0.00 3.93
2185 2284 8.584063 AAACTTTCAGGTAAAAAGAAGTGGTA 57.416 30.769 2.84 0.00 37.22 3.25
2192 2291 8.843262 GCTAGGTAAAACTTTCAGGTAAAAAGA 58.157 33.333 2.84 0.00 37.22 2.52
2253 2359 0.036448 TCATTCGGCCGGTTTTACCA 59.964 50.000 27.83 0.00 38.47 3.25
2281 2387 3.630312 TCCTTGCAGTTAACTTTCACCAC 59.370 43.478 5.07 0.00 0.00 4.16
2323 2429 2.745884 TGTTTCATCGGCCGCTGG 60.746 61.111 27.25 15.77 0.00 4.85
2324 2430 2.034879 ACTGTTTCATCGGCCGCTG 61.035 57.895 22.70 22.70 0.00 5.18
2325 2431 2.034879 CACTGTTTCATCGGCCGCT 61.035 57.895 23.51 8.48 0.00 5.52
2326 2432 2.480555 CACTGTTTCATCGGCCGC 59.519 61.111 23.51 5.62 0.00 6.53
2327 2433 0.744414 ATCCACTGTTTCATCGGCCG 60.744 55.000 22.12 22.12 0.00 6.13
2328 2434 0.734889 CATCCACTGTTTCATCGGCC 59.265 55.000 0.00 0.00 0.00 6.13
2329 2435 0.734889 CCATCCACTGTTTCATCGGC 59.265 55.000 0.00 0.00 0.00 5.54
2330 2436 1.739466 CACCATCCACTGTTTCATCGG 59.261 52.381 0.00 0.00 0.00 4.18
2331 2437 2.698803 TCACCATCCACTGTTTCATCG 58.301 47.619 0.00 0.00 0.00 3.84
2332 2438 4.520492 ACTTTCACCATCCACTGTTTCATC 59.480 41.667 0.00 0.00 0.00 2.92
2333 2439 4.473444 ACTTTCACCATCCACTGTTTCAT 58.527 39.130 0.00 0.00 0.00 2.57
2334 2440 3.897239 ACTTTCACCATCCACTGTTTCA 58.103 40.909 0.00 0.00 0.00 2.69
2335 2441 4.918810 AACTTTCACCATCCACTGTTTC 57.081 40.909 0.00 0.00 0.00 2.78
2336 2442 5.891551 AGTTAACTTTCACCATCCACTGTTT 59.108 36.000 1.12 0.00 0.00 2.83
2337 2443 5.299279 CAGTTAACTTTCACCATCCACTGTT 59.701 40.000 5.07 0.00 0.00 3.16
2338 2444 4.821805 CAGTTAACTTTCACCATCCACTGT 59.178 41.667 5.07 0.00 0.00 3.55
2339 2445 4.320494 GCAGTTAACTTTCACCATCCACTG 60.320 45.833 5.07 0.00 33.69 3.66
2340 2446 3.821033 GCAGTTAACTTTCACCATCCACT 59.179 43.478 5.07 0.00 0.00 4.00
2341 2447 3.568007 TGCAGTTAACTTTCACCATCCAC 59.432 43.478 5.07 0.00 0.00 4.02
2342 2448 3.826524 TGCAGTTAACTTTCACCATCCA 58.173 40.909 5.07 0.00 0.00 3.41
2343 2449 4.546570 GTTGCAGTTAACTTTCACCATCC 58.453 43.478 5.07 0.00 0.00 3.51
2344 2450 4.024387 TCGTTGCAGTTAACTTTCACCATC 60.024 41.667 5.07 0.00 0.00 3.51
2345 2451 3.880490 TCGTTGCAGTTAACTTTCACCAT 59.120 39.130 5.07 0.00 0.00 3.55
2346 2452 3.271729 TCGTTGCAGTTAACTTTCACCA 58.728 40.909 5.07 0.00 0.00 4.17
2347 2453 3.955771 TCGTTGCAGTTAACTTTCACC 57.044 42.857 5.07 0.00 0.00 4.02
2348 2454 6.627274 CAATTTCGTTGCAGTTAACTTTCAC 58.373 36.000 5.07 1.76 0.00 3.18
2349 2455 6.804534 CAATTTCGTTGCAGTTAACTTTCA 57.195 33.333 5.07 4.31 0.00 2.69
2362 2468 3.296322 TTGGCTAAGGCAATTTCGTTG 57.704 42.857 2.04 0.00 42.98 4.10
2370 2476 2.305635 TCATCTGAGTTGGCTAAGGCAA 59.694 45.455 2.04 2.04 45.54 4.52
2371 2477 1.908619 TCATCTGAGTTGGCTAAGGCA 59.091 47.619 0.00 0.00 40.87 4.75
2372 2478 2.698855 TCATCTGAGTTGGCTAAGGC 57.301 50.000 0.00 0.00 37.82 4.35
2373 2479 4.141756 ACTGATCATCTGAGTTGGCTAAGG 60.142 45.833 0.00 0.00 0.00 2.69
2413 2519 2.167487 TGAAGTACTGCACACACACTGA 59.833 45.455 0.00 0.00 0.00 3.41
2597 2711 6.951198 TCCAACTACATTTCCAACACCATTAT 59.049 34.615 0.00 0.00 0.00 1.28
2639 2753 9.543018 GAACTAAACAAGCATAACATTGTAGAC 57.457 33.333 0.00 0.00 38.66 2.59
2649 2763 6.862608 CAGCACATTGAACTAAACAAGCATAA 59.137 34.615 0.00 0.00 0.00 1.90
2673 2787 4.033587 CGTCGGTCTTTTCTTCTTTCAACA 59.966 41.667 0.00 0.00 0.00 3.33
2677 2791 2.096367 GCCGTCGGTCTTTTCTTCTTTC 60.096 50.000 13.94 0.00 0.00 2.62
2680 2794 0.391597 TGCCGTCGGTCTTTTCTTCT 59.608 50.000 13.94 0.00 0.00 2.85
2691 2805 1.942677 TACCATATTTGTGCCGTCGG 58.057 50.000 6.99 6.99 0.00 4.79
2694 2808 4.574828 GTCAAGATACCATATTTGTGCCGT 59.425 41.667 0.00 0.00 0.00 5.68
2717 2831 2.938451 TCTTCAGCATATGTTCCGCTTG 59.062 45.455 4.29 0.00 32.48 4.01
2739 2853 8.907885 GTTCCTATGCTCTGAATTAAGGAATTT 58.092 33.333 11.87 0.00 42.05 1.82
2746 2860 6.640518 ACGAAGTTCCTATGCTCTGAATTAA 58.359 36.000 0.00 0.00 37.78 1.40
2747 2861 6.222038 ACGAAGTTCCTATGCTCTGAATTA 57.778 37.500 0.00 0.00 37.78 1.40
2773 2887 8.160106 AGGCTAAATTATTGGTATGGAGAAGAG 58.840 37.037 0.00 0.00 0.00 2.85
2804 2918 2.419673 TGTGCAGGCATAAATCAAGTCG 59.580 45.455 0.00 0.00 0.00 4.18
2845 2959 6.826893 ACAAATCCACAACAAAAAGAATCG 57.173 33.333 0.00 0.00 0.00 3.34
2904 3029 4.395231 CACATCTGCAGAATCACAATGACT 59.605 41.667 22.50 0.00 0.00 3.41
2906 3031 3.692593 CCACATCTGCAGAATCACAATGA 59.307 43.478 22.50 0.00 0.00 2.57
2952 3077 4.024717 TGCAAACAGGCACACCAA 57.975 50.000 0.00 0.00 39.25 3.67
2969 3094 3.306780 GGTGAGTACCATAGTGTTGCAGT 60.307 47.826 0.00 0.00 46.71 4.40
2984 3109 1.634960 TGAATCCCACACGGTGAGTA 58.365 50.000 16.29 0.00 35.23 2.59
2993 3118 1.181786 GGGCGAAAATGAATCCCACA 58.818 50.000 0.00 0.00 36.96 4.17
3062 3187 4.209538 CATGAGGCTCCCATTTCACAATA 58.790 43.478 12.86 0.00 0.00 1.90
3173 3298 5.470098 ACTGAGCATTTTACCTGTAACACAG 59.530 40.000 0.00 0.00 45.53 3.66
3197 3322 5.774690 AGATCAAGGCACTGAAAAATGGTTA 59.225 36.000 0.00 0.00 40.86 2.85
3301 3427 3.056821 TCTTCACCTGTATCGACAACTGG 60.057 47.826 18.57 18.57 40.66 4.00
3607 3733 6.442112 GCCATCTAATTACCTCTGAAAATGC 58.558 40.000 0.00 0.00 0.00 3.56
3660 3786 4.043200 GCTTGGCTGCCGACAACC 62.043 66.667 14.98 0.00 31.83 3.77
3837 3963 4.201950 CCCAAGTGTTTTGTGTCTCTGAAG 60.202 45.833 0.00 0.00 0.00 3.02
3890 4016 5.269554 ACAGGGGATAAGGTGATTCAAAA 57.730 39.130 0.00 0.00 0.00 2.44
3922 4048 9.880157 CACCACATCATCATTCATATGTATAGA 57.120 33.333 1.90 0.58 31.55 1.98
3940 4066 6.734137 TGTTTTACAGAAACATCACCACATC 58.266 36.000 0.55 0.00 35.45 3.06
4382 4509 6.538381 GGTCAAGATTCAGAAGAAGAGGAATC 59.462 42.308 0.00 0.00 43.64 2.52
4400 4527 1.001633 GACAAGGTAAGCCGGTCAAGA 59.998 52.381 1.90 0.00 40.92 3.02
4445 4575 4.648762 ACCAACATCAGAAAAATGGTGTGA 59.351 37.500 0.00 0.00 43.71 3.58
4449 4579 4.261572 CGTCACCAACATCAGAAAAATGGT 60.262 41.667 0.00 0.00 41.65 3.55
4450 4580 4.023279 TCGTCACCAACATCAGAAAAATGG 60.023 41.667 0.00 0.00 0.00 3.16
4451 4581 5.107109 TCGTCACCAACATCAGAAAAATG 57.893 39.130 0.00 0.00 0.00 2.32
4452 4582 4.320494 GCTCGTCACCAACATCAGAAAAAT 60.320 41.667 0.00 0.00 0.00 1.82
4453 4583 3.003275 GCTCGTCACCAACATCAGAAAAA 59.997 43.478 0.00 0.00 0.00 1.94
4457 4587 0.678950 TGCTCGTCACCAACATCAGA 59.321 50.000 0.00 0.00 0.00 3.27
4660 4791 1.264749 CCCCTGACCGGATGAACTCA 61.265 60.000 9.46 0.00 33.16 3.41
5052 5189 3.003763 GGAGGAAGCTGGACCCGT 61.004 66.667 0.00 0.00 0.00 5.28
5176 5313 7.448161 AGTTCCATCAGAGATCAGACATAGTAG 59.552 40.741 0.00 0.00 0.00 2.57
5189 5326 2.755655 GTCTTCGGAGTTCCATCAGAGA 59.244 50.000 0.00 0.00 35.14 3.10
5200 5340 6.003859 TCTTCTTCCTATAGTCTTCGGAGT 57.996 41.667 0.00 0.00 0.00 3.85
5333 5476 6.295180 GCTACTACTTACAGGTTGAAGAAGGT 60.295 42.308 0.00 0.00 0.00 3.50
5382 5530 1.623811 GTACAACTTCTCTGGCCCTCA 59.376 52.381 0.00 0.00 0.00 3.86
5406 5554 1.819288 TCTGCTCCGTCTTTTCGATCT 59.181 47.619 0.00 0.00 0.00 2.75
5410 5558 2.094417 GGATTTCTGCTCCGTCTTTTCG 59.906 50.000 0.00 0.00 0.00 3.46
5419 5567 2.015587 CAGCTTCTGGATTTCTGCTCC 58.984 52.381 0.00 0.00 0.00 4.70
5463 5611 2.175202 CAGAGGTCTTGACAGCTACCT 58.825 52.381 3.18 3.18 45.02 3.08
5464 5612 2.171840 TCAGAGGTCTTGACAGCTACC 58.828 52.381 3.08 0.00 0.00 3.18
5496 5644 5.597813 ACTGAAGATTTTAGACACTTGCG 57.402 39.130 0.00 0.00 0.00 4.85
5530 5678 1.129811 GAAAATAGCACGACAACCCGG 59.870 52.381 0.00 0.00 0.00 5.73
5534 5682 4.451096 TGAGGAAGAAAATAGCACGACAAC 59.549 41.667 0.00 0.00 0.00 3.32
5536 5684 4.245660 CTGAGGAAGAAAATAGCACGACA 58.754 43.478 0.00 0.00 0.00 4.35
5543 5691 4.748892 TCGAGTGCTGAGGAAGAAAATAG 58.251 43.478 0.00 0.00 0.00 1.73
5546 5694 3.259374 AGATCGAGTGCTGAGGAAGAAAA 59.741 43.478 0.00 0.00 0.00 2.29
5555 5703 2.302260 CCCTTAGAGATCGAGTGCTGA 58.698 52.381 0.00 0.00 0.00 4.26
5561 5709 2.491693 GGAGATGCCCTTAGAGATCGAG 59.508 54.545 0.00 0.00 0.00 4.04
5566 5714 1.115930 GCCGGAGATGCCCTTAGAGA 61.116 60.000 5.05 0.00 0.00 3.10
5567 5715 1.369321 GCCGGAGATGCCCTTAGAG 59.631 63.158 5.05 0.00 0.00 2.43
5568 5716 2.140792 GGCCGGAGATGCCCTTAGA 61.141 63.158 5.05 0.00 43.33 2.10
5700 5849 5.224888 GGAACGACCAAGTTTAAATTTCCC 58.775 41.667 0.00 0.00 38.79 3.97
5833 5983 4.680237 CGTCAACGCCTGGAGCCA 62.680 66.667 0.00 0.00 38.78 4.75


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

AutoCloner maintained by Alex Coulton.