Multiple sequence alignment - TraesCS2D01G208100

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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 TraesCS2D01G208100 chr2D 100.000 6263 0 0 1 6263 162161809 162155547 0.000000e+00 11566.0
1 TraesCS2D01G208100 chr2D 93.158 190 9 4 2039 2226 616648536 616648349 6.180000e-70 276.0
2 TraesCS2D01G208100 chr2B 93.932 2785 120 26 2715 5456 221488475 221485697 0.000000e+00 4161.0
3 TraesCS2D01G208100 chr2B 91.313 2095 91 18 1 2056 221491124 221489082 0.000000e+00 2776.0
4 TraesCS2D01G208100 chr2B 95.225 754 27 6 5516 6263 221484669 221483919 0.000000e+00 1184.0
5 TraesCS2D01G208100 chr2B 96.104 462 15 3 2257 2716 221489015 221488555 0.000000e+00 750.0
6 TraesCS2D01G208100 chr2A 94.588 2402 87 14 2241 4633 173130530 173128163 0.000000e+00 3675.0
7 TraesCS2D01G208100 chr2A 94.191 1446 58 10 625 2056 173131978 173130545 0.000000e+00 2182.0
8 TraesCS2D01G208100 chr2A 90.448 848 39 11 4643 5459 173128100 173127264 0.000000e+00 1079.0
9 TraesCS2D01G208100 chr2A 95.807 644 20 5 5626 6263 173126924 173126282 0.000000e+00 1033.0
10 TraesCS2D01G208100 chr2A 94.286 245 14 0 5459 5703 173127161 173126917 5.930000e-100 375.0
11 TraesCS2D01G208100 chr2A 91.971 274 10 2 335 602 173132323 173132056 2.130000e-99 374.0
12 TraesCS2D01G208100 chr2A 82.500 200 17 10 1 197 173137021 173136837 6.500000e-35 159.0
13 TraesCS2D01G208100 chr1D 96.512 172 6 0 2055 2226 238940380 238940209 1.030000e-72 285.0
14 TraesCS2D01G208100 chr6D 96.450 169 6 0 2055 2223 392896975 392897143 4.780000e-71 279.0
15 TraesCS2D01G208100 chr6D 93.923 181 10 1 2049 2228 406391352 406391532 8.000000e-69 272.0
16 TraesCS2D01G208100 chr3A 92.746 193 11 3 2040 2230 649812020 649811829 6.180000e-70 276.0
17 TraesCS2D01G208100 chr7D 93.514 185 11 1 2042 2226 39001461 39001278 2.220000e-69 274.0
18 TraesCS2D01G208100 chr7D 94.886 176 8 1 2047 2222 192936191 192936017 2.220000e-69 274.0
19 TraesCS2D01G208100 chr5A 93.989 183 7 4 2047 2225 290391686 290391868 2.220000e-69 274.0
20 TraesCS2D01G208100 chr5A 79.699 133 21 3 99 228 657375118 657375247 2.400000e-14 91.6
21 TraesCS2D01G208100 chr3D 93.011 186 10 3 2032 2216 355892331 355892514 1.030000e-67 268.0
22 TraesCS2D01G208100 chr5B 76.506 166 22 13 270 427 309685095 309685251 2.420000e-09 75.0


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 TraesCS2D01G208100 chr2D 162155547 162161809 6262 True 11566.00 11566 100.0000 1 6263 1 chr2D.!!$R1 6262
1 TraesCS2D01G208100 chr2B 221483919 221491124 7205 True 2217.75 4161 94.1435 1 6263 4 chr2B.!!$R1 6262
2 TraesCS2D01G208100 chr2A 173126282 173132323 6041 True 1453.00 3675 93.5485 335 6263 6 chr2A.!!$R2 5928

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
199 201 0.034186 TGGGAGGATTCATGTGTGCC 60.034 55.000 0.00 0.00 0.00 5.01 F
247 249 0.035152 GTGACATGGATGGTGCCTCA 60.035 55.000 0.00 0.00 0.00 3.86 F
1250 1336 0.442699 GTTCGACCGATTGGCTGAAC 59.557 55.000 16.92 16.92 42.12 3.18 F
3034 3235 0.722676 AACTGATAGGAGGGGGTGGA 59.277 55.000 0.00 0.00 0.00 4.02 F
3300 3501 0.602638 CCGCATAAGCCCGCTTCATA 60.603 55.000 4.96 0.00 37.47 2.15 F
3629 3830 1.408702 GTGTGGCATGACAACTTGGTT 59.591 47.619 0.58 0.00 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 1845 0.029035 CTCCGTCAGGTTACCGATCG 59.971 60.000 8.51 8.51 39.05 3.69 R
2236 2326 0.247458 GATCAGAACTGAAAGCGCGC 60.247 55.000 26.66 26.66 43.58 6.86 R
3159 3360 2.682856 TGGCACGATTTCTTTATGGAGC 59.317 45.455 0.00 0.00 0.00 4.70 R
4634 4850 0.790814 GCCTGCGTAACAACAGAGAC 59.209 55.000 0.00 0.00 35.90 3.36 R
5112 5396 3.384146 TCATGGCGTCTACGGGTATAAAA 59.616 43.478 4.49 0.00 40.23 1.52 R
5547 6827 3.128938 TGCGTCCTAGTTCTAGAGAAAGC 59.871 47.826 8.26 11.48 35.58 3.51 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
27 28 3.367630 GCAAAATCATACGTTGGGCTTTG 59.632 43.478 0.00 0.43 0.00 2.77
127 129 1.183676 GCATGGGAGGATTCATGGGC 61.184 60.000 0.00 0.00 40.59 5.36
195 197 1.325355 GGCATGGGAGGATTCATGTG 58.675 55.000 0.00 0.00 41.83 3.21
196 198 1.410648 GGCATGGGAGGATTCATGTGT 60.411 52.381 0.00 0.00 41.83 3.72
197 199 1.679680 GCATGGGAGGATTCATGTGTG 59.320 52.381 0.00 0.00 41.83 3.82
198 200 1.679680 CATGGGAGGATTCATGTGTGC 59.320 52.381 0.00 0.00 36.82 4.57
199 201 0.034186 TGGGAGGATTCATGTGTGCC 60.034 55.000 0.00 0.00 0.00 5.01
200 202 0.034186 GGGAGGATTCATGTGTGCCA 60.034 55.000 0.00 0.00 0.00 4.92
201 203 1.410648 GGGAGGATTCATGTGTGCCAT 60.411 52.381 0.00 0.00 0.00 4.40
247 249 0.035152 GTGACATGGATGGTGCCTCA 60.035 55.000 0.00 0.00 0.00 3.86
248 250 0.921166 TGACATGGATGGTGCCTCAT 59.079 50.000 0.00 0.00 0.00 2.90
313 315 5.511202 GGAAGCAACCCATGAAGAATTGAAA 60.511 40.000 0.00 0.00 0.00 2.69
331 333 4.052608 TGAAAATGCAAGCACAAGTGATG 58.947 39.130 4.04 3.47 0.00 3.07
491 510 5.277825 TGTTGCAAAGTTTAAACTCCATCG 58.722 37.500 20.78 9.12 38.57 3.84
524 543 4.857509 TTTGTGGTGCCCTATTTTACAC 57.142 40.909 0.00 0.00 0.00 2.90
638 712 6.868339 CCCTTACATACAAAGAAAAGGCAAAG 59.132 38.462 0.00 0.00 33.63 2.77
655 729 4.376146 GCAAAGCCAATAAACAAGGAACA 58.624 39.130 0.00 0.00 0.00 3.18
656 730 4.813697 GCAAAGCCAATAAACAAGGAACAA 59.186 37.500 0.00 0.00 0.00 2.83
744 818 1.726791 CCGATGACGAACTCAAACAGG 59.273 52.381 0.00 0.00 42.66 4.00
1092 1172 2.606213 TCGCCCCATGGACTCACA 60.606 61.111 15.22 0.00 0.00 3.58
1126 1212 1.970114 CAGCACAGCCCCTGAACTG 60.970 63.158 0.00 2.71 39.86 3.16
1139 1225 2.104901 CTGAACTGTCGATCGATCACG 58.895 52.381 22.50 12.81 41.26 4.35
1146 1232 0.812549 TCGATCGATCACGGAACCAA 59.187 50.000 24.40 0.00 40.21 3.67
1147 1233 1.407618 TCGATCGATCACGGAACCAAT 59.592 47.619 24.40 0.00 40.21 3.16
1182 1268 4.714632 TCGGGACAGATTTTCAGTTCTTT 58.285 39.130 0.00 0.00 0.00 2.52
1186 1272 4.584743 GGACAGATTTTCAGTTCTTTGGGT 59.415 41.667 0.00 0.00 0.00 4.51
1250 1336 0.442699 GTTCGACCGATTGGCTGAAC 59.557 55.000 16.92 16.92 42.12 3.18
1332 1418 1.985473 TGCTGTTCACTGCCAAATCT 58.015 45.000 6.38 0.00 39.65 2.40
1340 1426 1.822990 CACTGCCAAATCTGATGCCTT 59.177 47.619 0.00 0.00 0.00 4.35
1421 1507 1.069978 GACTCAAGGAGGAGCTATGGC 59.930 57.143 0.00 0.00 38.50 4.40
1557 1643 1.678101 GCTGTAAGTGCCCATGGAATC 59.322 52.381 15.22 2.24 35.30 2.52
1558 1644 2.684927 GCTGTAAGTGCCCATGGAATCT 60.685 50.000 15.22 4.99 35.30 2.40
1567 1653 2.482490 GCCCATGGAATCTTGACAATGC 60.482 50.000 15.22 0.00 0.00 3.56
1574 1660 3.425359 GGAATCTTGACAATGCTCACACG 60.425 47.826 0.00 0.00 0.00 4.49
1575 1661 2.524569 TCTTGACAATGCTCACACGA 57.475 45.000 0.00 0.00 0.00 4.35
1577 1663 2.995939 TCTTGACAATGCTCACACGATC 59.004 45.455 0.00 0.00 0.00 3.69
1581 1667 2.349886 GACAATGCTCACACGATCCTTC 59.650 50.000 0.00 0.00 0.00 3.46
1583 1669 3.005554 CAATGCTCACACGATCCTTCTT 58.994 45.455 0.00 0.00 0.00 2.52
1584 1670 2.370281 TGCTCACACGATCCTTCTTC 57.630 50.000 0.00 0.00 0.00 2.87
1587 1673 3.244215 TGCTCACACGATCCTTCTTCTTT 60.244 43.478 0.00 0.00 0.00 2.52
1631 1720 7.399245 TGTGCCTCTGTTTATTATTTTACCC 57.601 36.000 0.00 0.00 0.00 3.69
1677 1766 1.004440 GTCTGAGAGGTGGTGTGCC 60.004 63.158 0.00 0.00 0.00 5.01
1698 1787 4.319766 GCCGTTGCAACCAATCTGATATAG 60.320 45.833 23.42 4.77 37.47 1.31
1710 1799 4.184649 TCTGATATAGGCTGGTGTCTGA 57.815 45.455 0.00 0.90 0.00 3.27
1711 1800 4.148079 TCTGATATAGGCTGGTGTCTGAG 58.852 47.826 0.00 0.00 0.00 3.35
1727 1816 4.214119 TGTCTGAGCAGGAATTTTTCTTCG 59.786 41.667 0.00 0.00 0.00 3.79
1736 1825 6.145535 CAGGAATTTTTCTTCGAAGGAACTG 58.854 40.000 24.37 19.22 40.86 3.16
1751 1840 1.194121 AACTGCAAGGGCCAATTCCC 61.194 55.000 6.18 0.00 46.93 3.97
1816 1906 4.107622 CAGTGCCTGTGTTTCTTTTTGAG 58.892 43.478 0.00 0.00 0.00 3.02
2054 2144 8.253113 CCTAGGCATCACTCAAATTAAAATGTT 58.747 33.333 0.00 0.00 0.00 2.71
2056 2146 8.986477 AGGCATCACTCAAATTAAAATGTTAC 57.014 30.769 0.00 0.00 0.00 2.50
2057 2147 8.806146 AGGCATCACTCAAATTAAAATGTTACT 58.194 29.630 0.00 0.00 0.00 2.24
2058 2148 9.076596 GGCATCACTCAAATTAAAATGTTACTC 57.923 33.333 0.00 0.00 0.00 2.59
2059 2149 9.076596 GCATCACTCAAATTAAAATGTTACTCC 57.923 33.333 0.00 0.00 0.00 3.85
2063 2153 9.626045 CACTCAAATTAAAATGTTACTCCTTCC 57.374 33.333 0.00 0.00 0.00 3.46
2064 2154 8.512138 ACTCAAATTAAAATGTTACTCCTTCCG 58.488 33.333 0.00 0.00 0.00 4.30
2065 2155 8.398878 TCAAATTAAAATGTTACTCCTTCCGT 57.601 30.769 0.00 0.00 0.00 4.69
2066 2156 8.852135 TCAAATTAAAATGTTACTCCTTCCGTT 58.148 29.630 0.00 0.00 0.00 4.44
2067 2157 9.124807 CAAATTAAAATGTTACTCCTTCCGTTC 57.875 33.333 0.00 0.00 0.00 3.95
2068 2158 6.806388 TTAAAATGTTACTCCTTCCGTTCC 57.194 37.500 0.00 0.00 0.00 3.62
2069 2159 4.635699 AAATGTTACTCCTTCCGTTCCT 57.364 40.909 0.00 0.00 0.00 3.36
2070 2160 5.750352 AAATGTTACTCCTTCCGTTCCTA 57.250 39.130 0.00 0.00 0.00 2.94
2071 2161 5.750352 AATGTTACTCCTTCCGTTCCTAA 57.250 39.130 0.00 0.00 0.00 2.69
2072 2162 5.750352 ATGTTACTCCTTCCGTTCCTAAA 57.250 39.130 0.00 0.00 0.00 1.85
2073 2163 5.750352 TGTTACTCCTTCCGTTCCTAAAT 57.250 39.130 0.00 0.00 0.00 1.40
2074 2164 6.855763 TGTTACTCCTTCCGTTCCTAAATA 57.144 37.500 0.00 0.00 0.00 1.40
2075 2165 7.243604 TGTTACTCCTTCCGTTCCTAAATAA 57.756 36.000 0.00 0.00 0.00 1.40
2076 2166 7.854337 TGTTACTCCTTCCGTTCCTAAATAAT 58.146 34.615 0.00 0.00 0.00 1.28
2077 2167 8.323567 TGTTACTCCTTCCGTTCCTAAATAATT 58.676 33.333 0.00 0.00 0.00 1.40
2078 2168 8.610035 GTTACTCCTTCCGTTCCTAAATAATTG 58.390 37.037 0.00 0.00 0.00 2.32
2079 2169 6.718294 ACTCCTTCCGTTCCTAAATAATTGT 58.282 36.000 0.00 0.00 0.00 2.71
2080 2170 6.822170 ACTCCTTCCGTTCCTAAATAATTGTC 59.178 38.462 0.00 0.00 0.00 3.18
2081 2171 6.954232 TCCTTCCGTTCCTAAATAATTGTCT 58.046 36.000 0.00 0.00 0.00 3.41
2082 2172 7.399634 TCCTTCCGTTCCTAAATAATTGTCTT 58.600 34.615 0.00 0.00 0.00 3.01
2083 2173 7.886446 TCCTTCCGTTCCTAAATAATTGTCTTT 59.114 33.333 0.00 0.00 0.00 2.52
2084 2174 8.182227 CCTTCCGTTCCTAAATAATTGTCTTTC 58.818 37.037 0.00 0.00 0.00 2.62
2085 2175 8.857694 TTCCGTTCCTAAATAATTGTCTTTCT 57.142 30.769 0.00 0.00 0.00 2.52
2086 2176 9.947433 TTCCGTTCCTAAATAATTGTCTTTCTA 57.053 29.630 0.00 0.00 0.00 2.10
2087 2177 9.595823 TCCGTTCCTAAATAATTGTCTTTCTAG 57.404 33.333 0.00 0.00 0.00 2.43
2088 2178 9.595823 CCGTTCCTAAATAATTGTCTTTCTAGA 57.404 33.333 0.00 0.00 0.00 2.43
2101 2191 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2102 2192 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
2103 2193 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
2104 2194 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2105 2195 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
2106 2196 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
2107 2197 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
2108 2198 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
2109 2199 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
2110 2200 9.429359 CTAGAGATTTCAACAAGTGACTACATT 57.571 33.333 0.00 0.00 35.39 2.71
2111 2201 8.316640 AGAGATTTCAACAAGTGACTACATTC 57.683 34.615 0.00 0.00 35.39 2.67
2112 2202 7.116948 AGAGATTTCAACAAGTGACTACATTCG 59.883 37.037 0.00 0.00 35.39 3.34
2113 2203 5.666969 TTTCAACAAGTGACTACATTCGG 57.333 39.130 0.00 0.00 35.39 4.30
2114 2204 4.594123 TCAACAAGTGACTACATTCGGA 57.406 40.909 0.00 0.00 0.00 4.55
2115 2205 4.556233 TCAACAAGTGACTACATTCGGAG 58.444 43.478 0.00 0.00 0.00 4.63
2116 2206 2.960819 ACAAGTGACTACATTCGGAGC 58.039 47.619 0.00 0.00 0.00 4.70
2117 2207 2.299013 ACAAGTGACTACATTCGGAGCA 59.701 45.455 0.00 0.00 0.00 4.26
2118 2208 3.244078 ACAAGTGACTACATTCGGAGCAA 60.244 43.478 0.00 0.00 0.00 3.91
2119 2209 3.678056 AGTGACTACATTCGGAGCAAA 57.322 42.857 0.00 0.00 0.00 3.68
2120 2210 4.002906 AGTGACTACATTCGGAGCAAAA 57.997 40.909 0.00 0.00 0.00 2.44
2121 2211 4.579869 AGTGACTACATTCGGAGCAAAAT 58.420 39.130 0.00 0.00 0.00 1.82
2122 2212 4.393062 AGTGACTACATTCGGAGCAAAATG 59.607 41.667 0.00 0.00 38.54 2.32
2123 2213 4.391830 GTGACTACATTCGGAGCAAAATGA 59.608 41.667 2.36 0.00 36.57 2.57
2124 2214 4.631377 TGACTACATTCGGAGCAAAATGAG 59.369 41.667 2.36 0.00 36.57 2.90
2125 2215 4.579869 ACTACATTCGGAGCAAAATGAGT 58.420 39.130 2.36 0.09 36.57 3.41
2126 2216 3.837213 ACATTCGGAGCAAAATGAGTG 57.163 42.857 2.36 0.00 36.57 3.51
2127 2217 3.411446 ACATTCGGAGCAAAATGAGTGA 58.589 40.909 2.36 0.00 36.57 3.41
2128 2218 3.820467 ACATTCGGAGCAAAATGAGTGAA 59.180 39.130 2.36 0.00 36.57 3.18
2129 2219 4.460382 ACATTCGGAGCAAAATGAGTGAAT 59.540 37.500 2.36 0.00 36.57 2.57
2130 2220 4.685169 TTCGGAGCAAAATGAGTGAATC 57.315 40.909 0.00 0.00 0.00 2.52
2131 2221 3.942829 TCGGAGCAAAATGAGTGAATCT 58.057 40.909 0.00 0.00 0.00 2.40
2132 2222 5.084818 TCGGAGCAAAATGAGTGAATCTA 57.915 39.130 0.00 0.00 0.00 1.98
2133 2223 4.870426 TCGGAGCAAAATGAGTGAATCTAC 59.130 41.667 0.00 0.00 0.00 2.59
2134 2224 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2135 2225 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2167 2257 9.653287 AATATGTCTTTATACATCCGTATGTGG 57.347 33.333 3.56 0.00 45.99 4.17
2168 2258 6.474140 TGTCTTTATACATCCGTATGTGGT 57.526 37.500 3.56 0.00 45.99 4.16
2169 2259 7.585579 TGTCTTTATACATCCGTATGTGGTA 57.414 36.000 3.56 0.00 45.99 3.25
2170 2260 7.654568 TGTCTTTATACATCCGTATGTGGTAG 58.345 38.462 3.56 0.00 45.99 3.18
2171 2261 7.286087 TGTCTTTATACATCCGTATGTGGTAGT 59.714 37.037 3.56 0.00 45.99 2.73
2172 2262 7.806960 GTCTTTATACATCCGTATGTGGTAGTC 59.193 40.741 3.56 0.00 45.99 2.59
2173 2263 6.579666 TTATACATCCGTATGTGGTAGTCC 57.420 41.667 3.56 0.00 45.99 3.85
2174 2264 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
2175 2265 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
2176 2266 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
2177 2267 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
2178 2268 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
2179 2269 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
2180 2270 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
2181 2271 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
2182 2272 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
2183 2273 6.238374 CCGTATGTGGTAGTCCATTTGAAATC 60.238 42.308 0.00 0.00 46.20 2.17
2184 2274 6.538742 CGTATGTGGTAGTCCATTTGAAATCT 59.461 38.462 0.00 0.00 46.20 2.40
2185 2275 7.254455 CGTATGTGGTAGTCCATTTGAAATCTC 60.254 40.741 0.00 0.00 46.20 2.75
2186 2276 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
2187 2277 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
2188 2278 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
2189 2279 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
2190 2280 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
2191 2281 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
2195 2285 8.507249 AGTCCATTTGAAATCTCTAAAAAGACG 58.493 33.333 0.00 0.00 0.00 4.18
2196 2286 8.504005 GTCCATTTGAAATCTCTAAAAAGACGA 58.496 33.333 0.00 0.00 0.00 4.20
2197 2287 9.062524 TCCATTTGAAATCTCTAAAAAGACGAA 57.937 29.630 0.00 0.00 0.00 3.85
2198 2288 9.846248 CCATTTGAAATCTCTAAAAAGACGAAT 57.154 29.630 0.00 0.00 0.00 3.34
2210 2300 9.090692 TCTAAAAAGACGAATATTTAGGAACGG 57.909 33.333 0.00 0.00 36.48 4.44
2211 2301 7.910441 AAAAAGACGAATATTTAGGAACGGA 57.090 32.000 0.00 0.00 0.00 4.69
2212 2302 7.535489 AAAAGACGAATATTTAGGAACGGAG 57.465 36.000 0.00 0.00 0.00 4.63
2213 2303 5.197682 AGACGAATATTTAGGAACGGAGG 57.802 43.478 0.00 0.00 0.00 4.30
2214 2304 4.038883 AGACGAATATTTAGGAACGGAGGG 59.961 45.833 0.00 0.00 0.00 4.30
2215 2305 3.962718 ACGAATATTTAGGAACGGAGGGA 59.037 43.478 0.00 0.00 0.00 4.20
2216 2306 4.406649 ACGAATATTTAGGAACGGAGGGAA 59.593 41.667 0.00 0.00 0.00 3.97
2236 2326 8.263854 AGGGAATATTATATAGACCCAATCCG 57.736 38.462 17.49 0.00 38.42 4.18
2732 2933 6.994496 ACACAGCTATTAGATATTGTGCACAT 59.006 34.615 22.39 13.21 39.48 3.21
2737 2938 6.370994 GCTATTAGATATTGTGCACATCTGCT 59.629 38.462 24.96 19.55 44.57 4.24
2802 3003 5.678871 GCATCATTGAGTTCATCTGTGCATT 60.679 40.000 0.00 0.00 0.00 3.56
3034 3235 0.722676 AACTGATAGGAGGGGGTGGA 59.277 55.000 0.00 0.00 0.00 4.02
3180 3381 2.682856 GCTCCATAAAGAAATCGTGCCA 59.317 45.455 0.00 0.00 0.00 4.92
3255 3456 3.367646 ACACTCTTCTCTCCGGTGATA 57.632 47.619 6.68 0.00 0.00 2.15
3300 3501 0.602638 CCGCATAAGCCCGCTTCATA 60.603 55.000 4.96 0.00 37.47 2.15
3309 3510 2.170607 AGCCCGCTTCATACTGTATGTT 59.829 45.455 23.14 0.00 37.45 2.71
3320 3521 1.421410 CTGTATGTTGCCCGAGTCGC 61.421 60.000 7.12 0.00 0.00 5.19
3321 3522 2.171725 GTATGTTGCCCGAGTCGCC 61.172 63.158 7.12 0.39 0.00 5.54
3330 3531 2.885644 CGAGTCGCCCGTTGATGG 60.886 66.667 0.00 0.00 0.00 3.51
3350 3551 7.620880 TGATGGCATTTCAGTTACTTAGTACT 58.379 34.615 0.00 0.00 0.00 2.73
3447 3648 1.531149 CGCCCCTAACATAAATGCTCG 59.469 52.381 0.00 0.00 0.00 5.03
3629 3830 1.408702 GTGTGGCATGACAACTTGGTT 59.591 47.619 0.58 0.00 0.00 3.67
3716 3917 3.417101 CTCACTACAGGATCGCCTCTAT 58.583 50.000 0.00 0.00 44.80 1.98
3866 4067 4.627284 TGGTGCTGCTAAAGGTTAGTAA 57.373 40.909 0.00 0.00 0.00 2.24
3869 4070 4.201920 GGTGCTGCTAAAGGTTAGTAATGC 60.202 45.833 0.00 0.00 0.00 3.56
3949 4155 5.354792 TGTTCTTATGTAATTTACGGCCACC 59.645 40.000 2.24 0.00 0.00 4.61
4180 4394 3.492313 GTTTTCAAAGTATGCGCCTCAG 58.508 45.455 4.18 0.00 0.00 3.35
4253 4467 5.790593 TGGATCCTGAGTAAGTTTGTACAC 58.209 41.667 14.23 0.00 0.00 2.90
4258 4472 6.688578 TCCTGAGTAAGTTTGTACACTGATC 58.311 40.000 0.00 0.00 0.00 2.92
4263 4477 7.050970 AGTAAGTTTGTACACTGATCTCACA 57.949 36.000 0.00 0.00 0.00 3.58
4264 4478 7.671302 AGTAAGTTTGTACACTGATCTCACAT 58.329 34.615 0.00 0.00 0.00 3.21
4265 4479 6.791887 AAGTTTGTACACTGATCTCACATG 57.208 37.500 0.00 0.00 0.00 3.21
4266 4480 4.692625 AGTTTGTACACTGATCTCACATGC 59.307 41.667 0.00 0.00 0.00 4.06
4267 4481 2.879826 TGTACACTGATCTCACATGCG 58.120 47.619 0.00 0.00 0.00 4.73
4268 4482 2.491693 TGTACACTGATCTCACATGCGA 59.508 45.455 0.00 0.00 0.00 5.10
4269 4483 2.749280 ACACTGATCTCACATGCGAA 57.251 45.000 0.00 0.00 0.00 4.70
4327 4543 9.221775 GTAGTACTATTTTTGTGCATTGCATAC 57.778 33.333 15.49 9.52 41.91 2.39
4358 4574 5.423015 TCATTGCTTTACCATCTCTCTGAC 58.577 41.667 0.00 0.00 0.00 3.51
4582 4798 2.003301 GCTGCTGCTAGTTCTGGTTAC 58.997 52.381 8.53 0.00 36.03 2.50
4583 4799 2.612972 GCTGCTGCTAGTTCTGGTTACA 60.613 50.000 8.53 0.00 36.03 2.41
4584 4800 3.257393 CTGCTGCTAGTTCTGGTTACAG 58.743 50.000 0.00 0.00 46.30 2.74
4591 4807 6.395629 TGCTAGTTCTGGTTACAGTACATTC 58.604 40.000 7.14 0.00 44.59 2.67
4596 4812 3.827876 TCTGGTTACAGTACATTCCACGA 59.172 43.478 0.00 0.00 45.14 4.35
4602 4818 6.591062 GGTTACAGTACATTCCACGATTGTTA 59.409 38.462 0.00 0.00 30.45 2.41
4612 4828 4.963373 TCCACGATTGTTAGAGGAAAACA 58.037 39.130 0.00 0.00 35.12 2.83
4615 4831 5.120830 CCACGATTGTTAGAGGAAAACAGAG 59.879 44.000 0.00 0.00 38.05 3.35
4619 4835 6.400091 CGATTGTTAGAGGAAAACAGAGAACG 60.400 42.308 0.00 0.00 38.05 3.95
4629 4845 6.481313 AGGAAAACAGAGAACGGTAAACTTAC 59.519 38.462 0.00 0.00 0.00 2.34
4630 4846 6.258507 GGAAAACAGAGAACGGTAAACTTACA 59.741 38.462 2.25 0.00 35.37 2.41
4631 4847 6.839820 AAACAGAGAACGGTAAACTTACAG 57.160 37.500 2.25 0.65 35.37 2.74
4633 4849 5.287226 ACAGAGAACGGTAAACTTACAGTG 58.713 41.667 6.22 0.00 40.34 3.66
4634 4850 4.684703 CAGAGAACGGTAAACTTACAGTGG 59.315 45.833 6.22 0.00 40.34 4.00
4648 4915 3.093717 ACAGTGGTCTCTGTTGTTACG 57.906 47.619 0.00 0.00 44.92 3.18
4876 5143 2.202797 CGGTCCATGGAGAGCACG 60.203 66.667 16.81 11.20 33.83 5.34
4879 5146 3.083349 TCCATGGAGAGCACGGGG 61.083 66.667 11.44 0.00 0.00 5.73
5112 5396 1.534235 AGGAAGACACAGCCGGAGT 60.534 57.895 5.05 0.00 0.00 3.85
5372 5680 7.326063 GCATAAGTTCATTATTTCGGGCATTAC 59.674 37.037 0.00 0.00 31.40 1.89
5450 5762 3.853671 GCATCCACACGTTTCATGATTTC 59.146 43.478 0.00 0.00 0.00 2.17
5524 6804 3.900941 AGTTTTGCGACATAAAAGCAGG 58.099 40.909 0.00 0.00 42.19 4.85
5547 6827 5.535030 GGGCCAAAATACTCCTTAATGTAGG 59.465 44.000 4.39 0.00 36.59 3.18
5548 6828 5.009710 GGCCAAAATACTCCTTAATGTAGGC 59.990 44.000 0.00 0.00 35.15 3.93
5619 6899 1.614903 CCTCAGCCAACATTCAAAGCA 59.385 47.619 0.00 0.00 0.00 3.91
5628 6908 2.028130 ACATTCAAAGCACGGTTCCAA 58.972 42.857 0.00 0.00 0.00 3.53
5652 6932 8.730680 CAAAACTAGTAAATGTTACAGAGCCAT 58.269 33.333 0.00 0.00 0.00 4.40
5682 7034 3.244911 GGCTAAGCAAATCTAGCCCCATA 60.245 47.826 8.63 0.00 46.92 2.74
5683 7035 4.568592 GGCTAAGCAAATCTAGCCCCATAT 60.569 45.833 8.63 0.00 46.92 1.78
5724 7076 6.499172 ACTCAAACTAAAAGAGCAAAAGCTC 58.501 36.000 9.34 9.34 37.11 4.09
5734 7086 5.131594 AGAGCAAAAGCTCCAGAAATTTC 57.868 39.130 10.33 10.33 37.53 2.17
6147 7504 1.342819 CAAGCCCAAACATCCGGAAAA 59.657 47.619 9.01 0.00 0.00 2.29
6258 7615 5.570589 GCATCTGTGATGTTTTGCTTTCTAC 59.429 40.000 8.98 0.00 0.00 2.59
6260 7617 5.129634 TCTGTGATGTTTTGCTTTCTACCA 58.870 37.500 0.00 0.00 0.00 3.25
6261 7618 5.008613 TCTGTGATGTTTTGCTTTCTACCAC 59.991 40.000 0.00 0.00 0.00 4.16
6262 7619 4.642437 TGTGATGTTTTGCTTTCTACCACA 59.358 37.500 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.278637 GTCGTGACAAAGCCCAACG 59.721 57.895 0.00 0.00 0.00 4.10
127 129 1.820906 CATGCCACCTCCCATGACG 60.821 63.158 0.00 0.00 40.92 4.35
200 202 1.000739 CTTCCATGGCACCACCCAT 59.999 57.895 6.96 0.00 46.35 4.00
201 203 2.440147 CTTCCATGGCACCACCCA 59.560 61.111 6.96 0.00 39.65 4.51
202 204 2.362889 CCTTCCATGGCACCACCC 60.363 66.667 6.96 0.00 37.83 4.61
203 205 1.379044 CTCCTTCCATGGCACCACC 60.379 63.158 6.96 0.00 39.84 4.61
204 206 1.379044 CCTCCTTCCATGGCACCAC 60.379 63.158 6.96 0.00 0.00 4.16
205 207 3.089838 CCTCCTTCCATGGCACCA 58.910 61.111 6.96 0.00 0.00 4.17
206 208 2.440980 GCCTCCTTCCATGGCACC 60.441 66.667 6.96 0.00 45.46 5.01
247 249 6.127281 TGGCTTCATTGTCTTCATTTGCATAT 60.127 34.615 0.00 0.00 0.00 1.78
248 250 5.185442 TGGCTTCATTGTCTTCATTTGCATA 59.815 36.000 0.00 0.00 0.00 3.14
313 315 5.648178 TTATCATCACTTGTGCTTGCATT 57.352 34.783 0.00 0.00 0.00 3.56
331 333 5.603596 TCAAATGCCATTGCCTTCATTATC 58.396 37.500 0.00 0.00 36.33 1.75
491 510 2.351738 GCACCACAAAACATGAGCTACC 60.352 50.000 0.00 0.00 0.00 3.18
524 543 2.791383 TTTTCTGGCGTGTCAAATGG 57.209 45.000 0.00 0.00 0.00 3.16
638 712 6.481644 TCAACAATTGTTCCTTGTTTATTGGC 59.518 34.615 20.85 0.00 42.58 4.52
640 714 8.497554 CCATCAACAATTGTTCCTTGTTTATTG 58.502 33.333 20.85 6.51 42.58 1.90
655 729 6.404623 CGGTACATGATTGACCATCAACAATT 60.405 38.462 0.00 0.00 45.45 2.32
656 730 5.066375 CGGTACATGATTGACCATCAACAAT 59.934 40.000 0.00 0.00 45.45 2.71
754 828 1.785041 TTGCTCTGTTGTTGCGCTCC 61.785 55.000 9.73 0.00 0.00 4.70
1092 1172 2.100197 TGCTGCTCTCGTATACCTTGT 58.900 47.619 0.00 0.00 0.00 3.16
1126 1212 0.099968 TGGTTCCGTGATCGATCGAC 59.900 55.000 22.06 14.65 39.71 4.20
1139 1225 5.399013 CGAAATTGTAACTGGATTGGTTCC 58.601 41.667 0.00 0.00 45.69 3.62
1146 1232 4.019681 TCTGTCCCGAAATTGTAACTGGAT 60.020 41.667 0.00 0.00 0.00 3.41
1147 1233 3.325425 TCTGTCCCGAAATTGTAACTGGA 59.675 43.478 0.00 0.00 0.00 3.86
1155 1241 5.376854 ACTGAAAATCTGTCCCGAAATTG 57.623 39.130 0.00 0.00 0.00 2.32
1250 1336 1.571215 GGCACCGAAGTTTACACCGG 61.571 60.000 0.00 0.00 46.65 5.28
1421 1507 2.040278 TCTCATGTCCTGGGTTCCTTTG 59.960 50.000 0.00 0.00 0.00 2.77
1557 1643 2.094894 GGATCGTGTGAGCATTGTCAAG 59.905 50.000 0.00 0.00 30.14 3.02
1558 1644 2.076100 GGATCGTGTGAGCATTGTCAA 58.924 47.619 0.00 0.00 30.14 3.18
1567 1653 3.929610 GGAAAGAAGAAGGATCGTGTGAG 59.070 47.826 0.00 0.00 0.00 3.51
1631 1720 9.421806 CAATGTCTCTAGGCTCTTAATTCATAG 57.578 37.037 0.00 0.00 0.00 2.23
1677 1766 4.319766 GCCTATATCAGATTGGTTGCAACG 60.320 45.833 22.67 8.42 0.00 4.10
1698 1787 2.046507 CCTGCTCAGACACCAGCC 60.047 66.667 0.00 0.00 34.47 4.85
1710 1799 4.398319 TCCTTCGAAGAAAAATTCCTGCT 58.602 39.130 26.61 0.00 45.90 4.24
1711 1800 4.766404 TCCTTCGAAGAAAAATTCCTGC 57.234 40.909 26.61 0.00 45.90 4.85
1718 1807 4.202010 CCTTGCAGTTCCTTCGAAGAAAAA 60.202 41.667 26.61 14.00 45.90 1.94
1727 1816 0.827507 TTGGCCCTTGCAGTTCCTTC 60.828 55.000 0.00 0.00 40.13 3.46
1736 1825 4.147449 GCGGGAATTGGCCCTTGC 62.147 66.667 0.00 0.00 46.44 4.01
1756 1845 0.029035 CTCCGTCAGGTTACCGATCG 59.971 60.000 8.51 8.51 39.05 3.69
1816 1906 4.997395 TCTCTAGAACAAGGCATTGAACAC 59.003 41.667 19.41 5.87 38.83 3.32
2054 2144 7.854337 ACAATTATTTAGGAACGGAAGGAGTA 58.146 34.615 0.00 0.00 0.00 2.59
2055 2145 6.718294 ACAATTATTTAGGAACGGAAGGAGT 58.282 36.000 0.00 0.00 0.00 3.85
2056 2146 7.048512 AGACAATTATTTAGGAACGGAAGGAG 58.951 38.462 0.00 0.00 0.00 3.69
2057 2147 6.954232 AGACAATTATTTAGGAACGGAAGGA 58.046 36.000 0.00 0.00 0.00 3.36
2058 2148 7.625828 AAGACAATTATTTAGGAACGGAAGG 57.374 36.000 0.00 0.00 0.00 3.46
2059 2149 8.947115 AGAAAGACAATTATTTAGGAACGGAAG 58.053 33.333 0.00 0.00 0.00 3.46
2060 2150 8.857694 AGAAAGACAATTATTTAGGAACGGAA 57.142 30.769 0.00 0.00 0.00 4.30
2061 2151 9.595823 CTAGAAAGACAATTATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2062 2152 9.595823 TCTAGAAAGACAATTATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2075 2165 9.566432 ACTTGTTGAAATCTCTAGAAAGACAAT 57.434 29.630 0.00 0.00 0.00 2.71
2076 2166 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
2077 2167 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
2078 2168 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
2079 2169 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
2080 2170 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
2081 2171 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
2082 2172 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
2083 2173 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
2084 2174 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
2085 2175 9.424319 GAATGTAGTCACTTGTTGAAATCTCTA 57.576 33.333 0.00 0.00 35.39 2.43
2086 2176 7.116948 CGAATGTAGTCACTTGTTGAAATCTCT 59.883 37.037 0.00 0.00 35.39 3.10
2087 2177 7.230222 CGAATGTAGTCACTTGTTGAAATCTC 58.770 38.462 0.00 0.00 35.39 2.75
2088 2178 6.147821 CCGAATGTAGTCACTTGTTGAAATCT 59.852 38.462 0.00 0.00 35.39 2.40
2089 2179 6.147164 TCCGAATGTAGTCACTTGTTGAAATC 59.853 38.462 0.00 0.00 35.39 2.17
2090 2180 5.995282 TCCGAATGTAGTCACTTGTTGAAAT 59.005 36.000 0.00 0.00 35.39 2.17
2091 2181 5.361427 TCCGAATGTAGTCACTTGTTGAAA 58.639 37.500 0.00 0.00 35.39 2.69
2092 2182 4.951254 TCCGAATGTAGTCACTTGTTGAA 58.049 39.130 0.00 0.00 35.39 2.69
2093 2183 4.556233 CTCCGAATGTAGTCACTTGTTGA 58.444 43.478 0.00 0.00 0.00 3.18
2094 2184 3.123621 GCTCCGAATGTAGTCACTTGTTG 59.876 47.826 0.00 0.00 0.00 3.33
2095 2185 3.244078 TGCTCCGAATGTAGTCACTTGTT 60.244 43.478 0.00 0.00 0.00 2.83
2096 2186 2.299013 TGCTCCGAATGTAGTCACTTGT 59.701 45.455 0.00 0.00 0.00 3.16
2097 2187 2.959516 TGCTCCGAATGTAGTCACTTG 58.040 47.619 0.00 0.00 0.00 3.16
2098 2188 3.678056 TTGCTCCGAATGTAGTCACTT 57.322 42.857 0.00 0.00 0.00 3.16
2099 2189 3.678056 TTTGCTCCGAATGTAGTCACT 57.322 42.857 0.00 0.00 0.00 3.41
2100 2190 4.391830 TCATTTTGCTCCGAATGTAGTCAC 59.608 41.667 0.00 0.00 35.35 3.67
2101 2191 4.574892 TCATTTTGCTCCGAATGTAGTCA 58.425 39.130 0.00 0.00 35.35 3.41
2102 2192 4.631813 ACTCATTTTGCTCCGAATGTAGTC 59.368 41.667 0.00 0.00 35.35 2.59
2103 2193 4.393062 CACTCATTTTGCTCCGAATGTAGT 59.607 41.667 0.00 0.00 35.35 2.73
2104 2194 4.631377 TCACTCATTTTGCTCCGAATGTAG 59.369 41.667 0.00 0.00 35.35 2.74
2105 2195 4.574892 TCACTCATTTTGCTCCGAATGTA 58.425 39.130 0.00 0.00 35.35 2.29
2106 2196 3.411446 TCACTCATTTTGCTCCGAATGT 58.589 40.909 0.00 0.00 35.35 2.71
2107 2197 4.424061 TTCACTCATTTTGCTCCGAATG 57.576 40.909 0.00 0.00 35.18 2.67
2108 2198 4.946157 AGATTCACTCATTTTGCTCCGAAT 59.054 37.500 0.00 0.00 0.00 3.34
2109 2199 4.326826 AGATTCACTCATTTTGCTCCGAA 58.673 39.130 0.00 0.00 0.00 4.30
2110 2200 3.942829 AGATTCACTCATTTTGCTCCGA 58.057 40.909 0.00 0.00 0.00 4.55
2111 2201 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2112 2202 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2113 2203 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2141 2231 9.653287 CCACATACGGATGTATAAAGACATATT 57.347 33.333 14.23 0.00 44.82 1.28
2142 2232 8.812972 ACCACATACGGATGTATAAAGACATAT 58.187 33.333 14.23 0.00 44.82 1.78
2143 2233 8.185506 ACCACATACGGATGTATAAAGACATA 57.814 34.615 14.23 0.00 44.82 2.29
2144 2234 7.062749 ACCACATACGGATGTATAAAGACAT 57.937 36.000 14.23 0.00 44.82 3.06
2145 2235 6.474140 ACCACATACGGATGTATAAAGACA 57.526 37.500 14.23 0.00 44.82 3.41
2146 2236 7.655490 ACTACCACATACGGATGTATAAAGAC 58.345 38.462 14.23 0.00 44.82 3.01
2147 2237 7.040201 GGACTACCACATACGGATGTATAAAGA 60.040 40.741 14.23 0.00 44.82 2.52
2148 2238 7.088905 GGACTACCACATACGGATGTATAAAG 58.911 42.308 14.23 10.96 44.82 1.85
2149 2239 6.550481 TGGACTACCACATACGGATGTATAAA 59.450 38.462 14.23 0.00 44.82 1.40
2150 2240 6.069994 TGGACTACCACATACGGATGTATAA 58.930 40.000 14.23 0.29 44.82 0.98
2151 2241 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
2152 2242 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
2153 2243 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
2169 2259 8.507249 CGTCTTTTTAGAGATTTCAAATGGACT 58.493 33.333 0.00 0.00 0.00 3.85
2170 2260 8.504005 TCGTCTTTTTAGAGATTTCAAATGGAC 58.496 33.333 0.00 0.00 0.00 4.02
2171 2261 8.615878 TCGTCTTTTTAGAGATTTCAAATGGA 57.384 30.769 0.00 0.00 0.00 3.41
2172 2262 9.846248 ATTCGTCTTTTTAGAGATTTCAAATGG 57.154 29.630 0.00 0.00 0.00 3.16
2184 2274 9.090692 CCGTTCCTAAATATTCGTCTTTTTAGA 57.909 33.333 0.00 0.00 34.90 2.10
2185 2275 9.090692 TCCGTTCCTAAATATTCGTCTTTTTAG 57.909 33.333 0.00 0.00 33.47 1.85
2186 2276 9.090692 CTCCGTTCCTAAATATTCGTCTTTTTA 57.909 33.333 0.00 0.00 0.00 1.52
2187 2277 7.065443 CCTCCGTTCCTAAATATTCGTCTTTTT 59.935 37.037 0.00 0.00 0.00 1.94
2188 2278 6.537660 CCTCCGTTCCTAAATATTCGTCTTTT 59.462 38.462 0.00 0.00 0.00 2.27
2189 2279 6.047231 CCTCCGTTCCTAAATATTCGTCTTT 58.953 40.000 0.00 0.00 0.00 2.52
2190 2280 5.452917 CCCTCCGTTCCTAAATATTCGTCTT 60.453 44.000 0.00 0.00 0.00 3.01
2191 2281 4.038883 CCCTCCGTTCCTAAATATTCGTCT 59.961 45.833 0.00 0.00 0.00 4.18
2192 2282 4.038402 TCCCTCCGTTCCTAAATATTCGTC 59.962 45.833 0.00 0.00 0.00 4.20
2193 2283 3.962718 TCCCTCCGTTCCTAAATATTCGT 59.037 43.478 0.00 0.00 0.00 3.85
2194 2284 4.595762 TCCCTCCGTTCCTAAATATTCG 57.404 45.455 0.00 0.00 0.00 3.34
2202 2292 9.638176 GTCTATATAATATTCCCTCCGTTCCTA 57.362 37.037 0.00 0.00 0.00 2.94
2203 2293 7.564292 GGTCTATATAATATTCCCTCCGTTCCT 59.436 40.741 0.00 0.00 0.00 3.36
2204 2294 7.201983 GGGTCTATATAATATTCCCTCCGTTCC 60.202 44.444 0.00 0.00 0.00 3.62
2205 2295 7.343833 TGGGTCTATATAATATTCCCTCCGTTC 59.656 40.741 7.45 0.00 35.00 3.95
2206 2296 7.194050 TGGGTCTATATAATATTCCCTCCGTT 58.806 38.462 7.45 0.00 35.00 4.44
2207 2297 6.748969 TGGGTCTATATAATATTCCCTCCGT 58.251 40.000 7.45 0.00 35.00 4.69
2208 2298 7.670605 TTGGGTCTATATAATATTCCCTCCG 57.329 40.000 7.45 0.00 35.00 4.63
2209 2299 8.661345 GGATTGGGTCTATATAATATTCCCTCC 58.339 40.741 7.45 4.08 35.00 4.30
2210 2300 8.368668 CGGATTGGGTCTATATAATATTCCCTC 58.631 40.741 7.45 0.00 35.00 4.30
2211 2301 7.202102 GCGGATTGGGTCTATATAATATTCCCT 60.202 40.741 7.45 0.00 35.00 4.20
2212 2302 6.935208 GCGGATTGGGTCTATATAATATTCCC 59.065 42.308 0.00 0.00 0.00 3.97
2213 2303 6.645415 CGCGGATTGGGTCTATATAATATTCC 59.355 42.308 0.00 0.00 0.00 3.01
2214 2304 6.145696 GCGCGGATTGGGTCTATATAATATTC 59.854 42.308 8.83 0.00 0.00 1.75
2215 2305 5.989777 GCGCGGATTGGGTCTATATAATATT 59.010 40.000 8.83 0.00 0.00 1.28
2216 2306 5.539048 GCGCGGATTGGGTCTATATAATAT 58.461 41.667 8.83 0.00 0.00 1.28
2236 2326 0.247458 GATCAGAACTGAAAGCGCGC 60.247 55.000 26.66 26.66 43.58 6.86
2732 2933 5.853936 ACATGAACTAACTACACAAGCAGA 58.146 37.500 0.00 0.00 0.00 4.26
2737 2938 4.319190 GCGCAACATGAACTAACTACACAA 60.319 41.667 0.30 0.00 0.00 3.33
2802 3003 7.716799 AATAAAGGTTTCTGATACCATGCAA 57.283 32.000 17.71 1.46 38.16 4.08
3034 3235 6.485171 AGTACCTTGATAAACAGCTCCAAAT 58.515 36.000 0.00 0.00 0.00 2.32
3159 3360 2.682856 TGGCACGATTTCTTTATGGAGC 59.317 45.455 0.00 0.00 0.00 4.70
3300 3501 0.108804 CGACTCGGGCAACATACAGT 60.109 55.000 0.00 0.00 39.74 3.55
3320 3521 1.176527 ACTGAAATGCCATCAACGGG 58.823 50.000 0.00 0.00 0.00 5.28
3321 3522 3.440173 AGTAACTGAAATGCCATCAACGG 59.560 43.478 0.00 0.00 0.00 4.44
3350 3551 7.690952 AAACCTCACGGCAGTTATAAAAATA 57.309 32.000 0.00 0.00 0.00 1.40
3355 3556 3.189702 GCAAAACCTCACGGCAGTTATAA 59.810 43.478 0.00 0.00 0.00 0.98
3360 3561 2.542907 CGCAAAACCTCACGGCAGT 61.543 57.895 0.00 0.00 0.00 4.40
3407 3608 2.159435 CGCTGGCCAAATTACAGGTTAC 60.159 50.000 7.01 0.00 32.98 2.50
3447 3648 7.755373 GGAATAAACAAACTAACTGGAGCAATC 59.245 37.037 0.00 0.00 0.00 2.67
3481 3682 8.523464 GCGTGCAAAATGATTATTTTAGTACAG 58.477 33.333 7.77 9.21 42.92 2.74
3536 3737 0.179176 TGTGCGCAAACTGTGTCAAC 60.179 50.000 14.00 0.00 0.00 3.18
3629 3830 4.164030 TCACAGCAATAGCCAATTAGAGGA 59.836 41.667 0.00 0.00 43.56 3.71
3716 3917 8.458843 GCTAAATCTTCACAAAGCTTTATACCA 58.541 33.333 12.25 0.00 34.37 3.25
3780 3981 5.902613 TTTGATGCCTCACCTAAATGAAG 57.097 39.130 0.00 0.00 0.00 3.02
3949 4155 9.727627 GGAAGAATGAAGATAAAGTAGCATTTG 57.272 33.333 0.00 0.00 0.00 2.32
3990 4196 8.611654 AACTCAAAAGAAGCATTTGCAATATT 57.388 26.923 0.00 0.00 45.16 1.28
4035 4249 4.264460 ACTAGTCCTGAGCAAGAAACAG 57.736 45.455 0.00 0.00 0.00 3.16
4180 4394 1.237285 ATGCAACACTGTCGCCTTCC 61.237 55.000 0.00 0.00 0.00 3.46
4253 4467 6.635641 CCAATATTTTTCGCATGTGAGATCAG 59.364 38.462 9.26 0.00 0.00 2.90
4258 4472 6.550843 TGTACCAATATTTTTCGCATGTGAG 58.449 36.000 9.26 0.00 0.00 3.51
4263 4477 8.250332 ACAGATTTGTACCAATATTTTTCGCAT 58.750 29.630 0.00 0.00 35.25 4.73
4264 4478 7.598278 ACAGATTTGTACCAATATTTTTCGCA 58.402 30.769 0.00 0.00 35.25 5.10
4265 4479 7.968405 AGACAGATTTGTACCAATATTTTTCGC 59.032 33.333 0.00 0.00 37.76 4.70
4266 4480 9.277565 CAGACAGATTTGTACCAATATTTTTCG 57.722 33.333 0.00 0.00 37.76 3.46
4268 4482 9.912634 CACAGACAGATTTGTACCAATATTTTT 57.087 29.630 0.00 0.00 37.76 1.94
4269 4483 9.077885 ACACAGACAGATTTGTACCAATATTTT 57.922 29.630 0.00 0.00 37.76 1.82
4327 4543 9.499479 AGAGATGGTAAAGCAATGAATACATAG 57.501 33.333 0.00 0.00 35.50 2.23
4358 4574 8.618702 ATCTAAAAGATATGGAGCATTCACAG 57.381 34.615 0.00 0.00 32.12 3.66
4577 4793 4.933400 ACAATCGTGGAATGTACTGTAACC 59.067 41.667 0.00 0.00 0.00 2.85
4582 4798 5.520288 CCTCTAACAATCGTGGAATGTACTG 59.480 44.000 0.00 0.00 0.00 2.74
4583 4799 5.421056 TCCTCTAACAATCGTGGAATGTACT 59.579 40.000 0.00 0.00 0.00 2.73
4584 4800 5.657474 TCCTCTAACAATCGTGGAATGTAC 58.343 41.667 0.00 0.00 0.00 2.90
4591 4807 4.994852 TCTGTTTTCCTCTAACAATCGTGG 59.005 41.667 0.00 0.00 35.28 4.94
4596 4812 5.701290 CCGTTCTCTGTTTTCCTCTAACAAT 59.299 40.000 0.00 0.00 35.28 2.71
4602 4818 4.950205 TTACCGTTCTCTGTTTTCCTCT 57.050 40.909 0.00 0.00 0.00 3.69
4629 4845 1.792949 GCGTAACAACAGAGACCACTG 59.207 52.381 0.00 0.00 42.78 3.66
4630 4846 1.411246 TGCGTAACAACAGAGACCACT 59.589 47.619 0.00 0.00 0.00 4.00
4631 4847 1.792949 CTGCGTAACAACAGAGACCAC 59.207 52.381 0.00 0.00 35.90 4.16
4633 4849 1.429463 CCTGCGTAACAACAGAGACC 58.571 55.000 0.00 0.00 35.90 3.85
4634 4850 0.790814 GCCTGCGTAACAACAGAGAC 59.209 55.000 0.00 0.00 35.90 3.36
5112 5396 3.384146 TCATGGCGTCTACGGGTATAAAA 59.616 43.478 4.49 0.00 40.23 1.52
5341 5649 5.215160 CGAAATAATGAACTTATGCTGCCC 58.785 41.667 0.00 0.00 30.26 5.36
5494 6634 7.861176 TTTATGTCGCAAAACTTATGTTTCC 57.139 32.000 7.15 2.15 44.70 3.13
5503 6643 3.305335 CCCTGCTTTTATGTCGCAAAACT 60.305 43.478 0.00 0.00 32.66 2.66
5524 6804 5.009710 GCCTACATTAAGGAGTATTTTGGCC 59.990 44.000 0.00 0.00 39.15 5.36
5547 6827 3.128938 TGCGTCCTAGTTCTAGAGAAAGC 59.871 47.826 8.26 11.48 35.58 3.51
5548 6828 4.966965 TGCGTCCTAGTTCTAGAGAAAG 57.033 45.455 8.26 0.00 35.58 2.62
5619 6899 6.947644 AACATTTACTAGTTTTGGAACCGT 57.052 33.333 0.00 0.00 36.39 4.83
5628 6908 9.953565 TTATGGCTCTGTAACATTTACTAGTTT 57.046 29.630 0.00 0.00 0.00 2.66
5652 6932 4.351874 AGATTTGCTTAGCCGGCTATTA 57.648 40.909 35.60 21.45 0.00 0.98
5682 7034 7.232941 AGTTTGAGTTGTAGGTAGTGACAGTAT 59.767 37.037 0.00 0.00 0.00 2.12
5683 7035 6.548622 AGTTTGAGTTGTAGGTAGTGACAGTA 59.451 38.462 0.00 0.00 0.00 2.74
5724 7076 5.982516 TGTTCCAAATGTTCGAAATTTCTGG 59.017 36.000 15.92 13.77 0.00 3.86
5734 7086 2.033299 AGTGCTGTGTTCCAAATGTTCG 59.967 45.455 0.00 0.00 0.00 3.95
5797 7149 5.966636 AATTCAAAAGGAGAACGCAAAAC 57.033 34.783 0.00 0.00 0.00 2.43
6053 7410 4.036262 CGTCATTCCTTTTGACACCAGAAA 59.964 41.667 4.86 0.00 42.90 2.52
6061 7418 3.049912 GTTTGCCGTCATTCCTTTTGAC 58.950 45.455 0.00 0.00 40.06 3.18
6147 7504 0.679505 TTCAGCTGTAGTTCGGTGCT 59.320 50.000 14.67 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.