Multiple sequence alignment - TraesCS2B01G497700

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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 TraesCS2B01G497700 chr2B 100.000 2965 0 0 1 2965 694265423 694268387 0.000000e+00 5476
1 TraesCS2B01G497700 chr2B 78.295 516 81 22 1475 1982 694541988 694541496 1.340000e-78 303
2 TraesCS2B01G497700 chr2B 97.590 166 4 0 2022 2187 182011109 182011274 4.840000e-73 285
3 TraesCS2B01G497700 chr2B 83.412 211 29 6 2023 2228 121270974 121270765 1.080000e-44 191
4 TraesCS2B01G497700 chr2B 94.000 100 5 1 2444 2543 127747510 127747412 1.840000e-32 150
5 TraesCS2B01G497700 chr2D 93.568 1928 77 12 4 1916 577326454 577328349 0.000000e+00 2830
6 TraesCS2B01G497700 chr2D 89.703 437 34 4 2539 2965 577328739 577329174 5.590000e-152 547
7 TraesCS2B01G497700 chr2D 91.954 261 21 0 2186 2446 577328482 577328742 1.680000e-97 366
8 TraesCS2B01G497700 chr2D 97.794 136 2 1 1890 2024 577328348 577328483 1.780000e-57 233
9 TraesCS2B01G497700 chr2D 84.762 210 28 4 2023 2228 182871849 182872058 1.080000e-49 207
10 TraesCS2B01G497700 chr2D 84.038 213 27 6 2023 2228 74361886 74362098 6.480000e-47 198
11 TraesCS2B01G497700 chr2A 93.089 1939 97 19 1 1916 715404623 715406547 0.000000e+00 2804
12 TraesCS2B01G497700 chr2A 88.409 440 37 5 2539 2965 715406939 715407377 4.380000e-143 518
13 TraesCS2B01G497700 chr2A 90.805 261 24 0 2186 2446 715406682 715406942 1.690000e-92 350
14 TraesCS2B01G497700 chr2A 78.740 508 79 20 1483 1982 715632887 715632401 2.220000e-81 313
15 TraesCS2B01G497700 chr2A 97.794 136 2 1 1890 2024 715406548 715406683 1.780000e-57 233
16 TraesCS2B01G497700 chr2A 89.542 153 14 2 69 220 57999164 57999315 3.020000e-45 193
17 TraesCS2B01G497700 chr3B 97.076 171 5 0 2018 2188 658491670 658491840 3.740000e-74 289
18 TraesCS2B01G497700 chr3B 97.059 170 4 1 2019 2188 261791682 261791514 4.840000e-73 285
19 TraesCS2B01G497700 chr3B 94.944 178 9 0 2022 2199 246304015 246303838 2.250000e-71 279
20 TraesCS2B01G497700 chr3B 92.453 106 7 1 2445 2550 362482033 362482137 1.840000e-32 150
21 TraesCS2B01G497700 chr4B 94.624 186 8 2 2004 2188 20487344 20487528 1.340000e-73 287
22 TraesCS2B01G497700 chr4B 95.954 173 7 0 2018 2190 1094144 1093972 6.260000e-72 281
23 TraesCS2B01G497700 chr1B 97.041 169 5 0 2020 2188 603523061 603523229 4.840000e-73 285
24 TraesCS2B01G497700 chr1B 94.000 100 5 1 2443 2542 156596561 156596659 1.840000e-32 150
25 TraesCS2B01G497700 chr1B 91.818 110 6 3 2441 2549 171887312 171887419 1.840000e-32 150
26 TraesCS2B01G497700 chr7B 97.576 165 4 0 2023 2187 707640027 707639863 1.740000e-72 283
27 TraesCS2B01G497700 chr7B 86.928 153 20 0 69 221 382331940 382332092 3.930000e-39 172
28 TraesCS2B01G497700 chr7B 84.066 182 20 7 71 244 627724908 627725088 1.830000e-37 167
29 TraesCS2B01G497700 chr6B 95.930 172 7 0 2016 2187 238152479 238152650 2.250000e-71 279
30 TraesCS2B01G497700 chr6B 93.878 98 5 1 2445 2542 336181217 336181313 2.380000e-31 147
31 TraesCS2B01G497700 chr3D 84.286 210 29 4 2023 2228 460988882 460988673 5.010000e-48 202
32 TraesCS2B01G497700 chr3D 84.211 209 29 4 2023 2227 338433236 338433028 1.800000e-47 200
33 TraesCS2B01G497700 chr5D 88.554 166 18 1 2023 2187 258573207 258573372 1.800000e-47 200
34 TraesCS2B01G497700 chr5D 86.335 161 22 0 69 229 129872941 129872781 3.040000e-40 176
35 TraesCS2B01G497700 chr5D 92.661 109 7 1 2442 2550 45212350 45212243 3.960000e-34 156
36 TraesCS2B01G497700 chr7D 83.810 210 30 4 2023 2228 549143958 549144167 2.330000e-46 196
37 TraesCS2B01G497700 chr5B 83.810 210 27 6 2023 2228 368387165 368386959 3.020000e-45 193
38 TraesCS2B01G497700 chr5B 88.158 152 18 0 69 220 144586323 144586474 6.530000e-42 182
39 TraesCS2B01G497700 chr5B 94.059 101 5 1 2442 2542 50175724 50175625 5.120000e-33 152
40 TraesCS2B01G497700 chr5B 92.523 107 5 3 2445 2550 91884530 91884426 1.840000e-32 150
41 TraesCS2B01G497700 chr4A 83.254 209 30 5 2023 2226 95308539 95308331 1.400000e-43 187
42 TraesCS2B01G497700 chr4D 87.975 158 17 2 70 226 16653010 16653166 5.050000e-43 185
43 TraesCS2B01G497700 chr4D 86.709 158 19 2 71 227 49508743 49508587 1.090000e-39 174
44 TraesCS2B01G497700 chr1D 92.381 105 7 1 2438 2542 315816900 315817003 6.620000e-32 148


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 TraesCS2B01G497700 chr2B 694265423 694268387 2964 False 5476.00 5476 100.00000 1 2965 1 chr2B.!!$F2 2964
1 TraesCS2B01G497700 chr2D 577326454 577329174 2720 False 994.00 2830 93.25475 4 2965 4 chr2D.!!$F3 2961
2 TraesCS2B01G497700 chr2A 715404623 715407377 2754 False 976.25 2804 92.52425 1 2965 4 chr2A.!!$F2 2964

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
790 811 1.366679 ATGCATGATGGCGATCGATC 58.633 50.0 21.57 15.68 36.28 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2526 2583 0.033405 CTTCTACTCCCTCCGTCCCA 60.033 60.0 0.0 0.0 0.0 4.37 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
125 142 4.098349 ACGGACTACATACGGAGCAAAATA 59.902 41.667 0.00 0.00 0.00 1.40
132 149 6.178239 ACATACGGAGCAAAATAAGTGAAC 57.822 37.500 0.00 0.00 0.00 3.18
233 251 7.563724 TGGAGGGAGTATTACTTTTTGTAGT 57.436 36.000 0.00 0.00 32.08 2.73
655 676 2.936498 GCTATCAGCGTACCACATTGTT 59.064 45.455 0.00 0.00 0.00 2.83
727 748 2.032981 CCGGCTATGCATTCCAACC 58.967 57.895 3.54 0.00 0.00 3.77
734 755 1.549203 ATGCATTCCAACCGCTTCTT 58.451 45.000 0.00 0.00 0.00 2.52
737 758 1.541588 GCATTCCAACCGCTTCTTCTT 59.458 47.619 0.00 0.00 0.00 2.52
790 811 1.366679 ATGCATGATGGCGATCGATC 58.633 50.000 21.57 15.68 36.28 3.69
827 848 2.986479 CACAATGATCGATCGCGGAATA 59.014 45.455 20.03 1.32 38.28 1.75
884 905 7.607607 AGATTCCTCCATTGCCAATTTTTAAAC 59.392 33.333 0.00 0.00 0.00 2.01
927 948 3.005897 ACAGTTCACGCTCATGTACTTCT 59.994 43.478 0.00 0.00 28.66 2.85
1022 1043 1.227853 AGAACACAACACCCGCCTC 60.228 57.895 0.00 0.00 0.00 4.70
1046 1068 1.202627 GCTTATCACTGCTGCTAGCCT 60.203 52.381 13.29 0.00 41.51 4.58
1082 1104 5.064452 GCAGTTTCTCATACACATGGAGAAG 59.936 44.000 10.12 3.20 33.64 2.85
1084 1106 7.046652 CAGTTTCTCATACACATGGAGAAGAT 58.953 38.462 10.12 3.17 33.64 2.40
1283 1308 3.445096 CCTCATTTGATTCCTTGGGTGAC 59.555 47.826 0.00 0.00 0.00 3.67
1463 1489 6.927294 ACAGCAGTACATATTTAGCCTTTC 57.073 37.500 0.00 0.00 0.00 2.62
1508 1534 6.062434 TGATTTTTGTTGTACAGGTAACCG 57.938 37.500 0.00 0.00 37.17 4.44
1568 1594 0.107643 TGCGAAGGACATGAACACCA 59.892 50.000 0.00 0.00 0.00 4.17
1596 1622 3.186909 TGGTATGTTCGAGAAGCAATCG 58.813 45.455 0.00 0.00 41.50 3.34
1622 1648 5.255710 TCATCTCTTTCTAGCTTCCTTCG 57.744 43.478 0.00 0.00 0.00 3.79
1678 1705 6.791303 TCTTACAATTGTGTGTTCCTGAAAC 58.209 36.000 21.42 0.00 38.82 2.78
1703 1730 2.280628 CAGGCCAAGTATTTCCTCGAC 58.719 52.381 5.01 0.00 0.00 4.20
1706 1733 2.004583 CCAAGTATTTCCTCGACGCA 57.995 50.000 0.00 0.00 0.00 5.24
1707 1734 1.659098 CCAAGTATTTCCTCGACGCAC 59.341 52.381 0.00 0.00 0.00 5.34
1738 1765 4.980805 GGCGACTGGTGCGGTTCA 62.981 66.667 0.00 0.00 0.00 3.18
1817 1844 1.966354 AGGAAGAAAGGGCTTTGCTTG 59.034 47.619 7.41 0.00 32.11 4.01
1952 2009 0.541392 TTGTGGACTGTGTCAGCTGT 59.459 50.000 14.67 0.00 34.37 4.40
2024 2081 9.908152 AACTAATAAAAACAGGCATTCAACTAC 57.092 29.630 0.00 0.00 0.00 2.73
2025 2082 9.297037 ACTAATAAAAACAGGCATTCAACTACT 57.703 29.630 0.00 0.00 0.00 2.57
2026 2083 9.774742 CTAATAAAAACAGGCATTCAACTACTC 57.225 33.333 0.00 0.00 0.00 2.59
2027 2084 5.453567 AAAAACAGGCATTCAACTACTCC 57.546 39.130 0.00 0.00 0.00 3.85
2028 2085 2.789409 ACAGGCATTCAACTACTCCC 57.211 50.000 0.00 0.00 0.00 4.30
2029 2086 2.269940 ACAGGCATTCAACTACTCCCT 58.730 47.619 0.00 0.00 0.00 4.20
2030 2087 2.237392 ACAGGCATTCAACTACTCCCTC 59.763 50.000 0.00 0.00 0.00 4.30
2031 2088 1.840635 AGGCATTCAACTACTCCCTCC 59.159 52.381 0.00 0.00 0.00 4.30
2032 2089 1.473434 GGCATTCAACTACTCCCTCCG 60.473 57.143 0.00 0.00 0.00 4.63
2033 2090 1.207329 GCATTCAACTACTCCCTCCGT 59.793 52.381 0.00 0.00 0.00 4.69
2034 2091 2.354805 GCATTCAACTACTCCCTCCGTT 60.355 50.000 0.00 0.00 0.00 4.44
2035 2092 3.522553 CATTCAACTACTCCCTCCGTTC 58.477 50.000 0.00 0.00 0.00 3.95
2036 2093 1.553706 TCAACTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 0.00 3.62
2037 2094 1.076677 TCAACTACTCCCTCCGTTCCT 59.923 52.381 0.00 0.00 0.00 3.36
2038 2095 2.309755 TCAACTACTCCCTCCGTTCCTA 59.690 50.000 0.00 0.00 0.00 2.94
2039 2096 3.094572 CAACTACTCCCTCCGTTCCTAA 58.905 50.000 0.00 0.00 0.00 2.69
2040 2097 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2041 2098 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2042 2099 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2043 2100 5.522641 ACTACTCCCTCCGTTCCTAAATAA 58.477 41.667 0.00 0.00 0.00 1.40
2044 2101 6.141790 ACTACTCCCTCCGTTCCTAAATAAT 58.858 40.000 0.00 0.00 0.00 1.28
2045 2102 5.970501 ACTCCCTCCGTTCCTAAATAATT 57.029 39.130 0.00 0.00 0.00 1.40
2046 2103 5.681639 ACTCCCTCCGTTCCTAAATAATTG 58.318 41.667 0.00 0.00 0.00 2.32
2047 2104 5.191124 ACTCCCTCCGTTCCTAAATAATTGT 59.809 40.000 0.00 0.00 0.00 2.71
2048 2105 5.677567 TCCCTCCGTTCCTAAATAATTGTC 58.322 41.667 0.00 0.00 0.00 3.18
2049 2106 5.427481 TCCCTCCGTTCCTAAATAATTGTCT 59.573 40.000 0.00 0.00 0.00 3.41
2050 2107 6.069847 TCCCTCCGTTCCTAAATAATTGTCTT 60.070 38.462 0.00 0.00 0.00 3.01
2051 2108 6.602009 CCCTCCGTTCCTAAATAATTGTCTTT 59.398 38.462 0.00 0.00 0.00 2.52
2052 2109 7.201705 CCCTCCGTTCCTAAATAATTGTCTTTC 60.202 40.741 0.00 0.00 0.00 2.62
2053 2110 7.553044 CCTCCGTTCCTAAATAATTGTCTTTCT 59.447 37.037 0.00 0.00 0.00 2.52
2054 2111 9.595823 CTCCGTTCCTAAATAATTGTCTTTCTA 57.404 33.333 0.00 0.00 0.00 2.10
2055 2112 9.595823 TCCGTTCCTAAATAATTGTCTTTCTAG 57.404 33.333 0.00 0.00 0.00 2.43
2056 2113 9.595823 CCGTTCCTAAATAATTGTCTTTCTAGA 57.404 33.333 0.00 0.00 0.00 2.43
2069 2126 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2070 2127 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
2071 2128 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
2072 2129 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2073 2130 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
2074 2131 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
2075 2132 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
2076 2133 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
2077 2134 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
2079 2136 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2080 2137 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2081 2138 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
2082 2139 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2083 2140 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2084 2141 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2085 2142 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2086 2143 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2087 2144 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2088 2145 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2089 2146 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2090 2147 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2091 2148 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2092 2149 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
2093 2150 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2094 2151 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2095 2152 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2096 2153 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2097 2154 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2098 2155 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2099 2156 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2100 2157 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2101 2158 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2102 2159 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2103 2160 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2116 2173 8.764524 AGTGAATCTACACTCTAAAACATGTC 57.235 34.615 0.00 0.00 46.36 3.06
2117 2174 8.589338 AGTGAATCTACACTCTAAAACATGTCT 58.411 33.333 0.00 0.00 46.36 3.41
2118 2175 8.651588 GTGAATCTACACTCTAAAACATGTCTG 58.348 37.037 0.00 0.00 37.73 3.51
2119 2176 7.331934 TGAATCTACACTCTAAAACATGTCTGC 59.668 37.037 0.00 0.00 0.00 4.26
2120 2177 5.161358 TCTACACTCTAAAACATGTCTGCG 58.839 41.667 0.00 0.00 0.00 5.18
2121 2178 3.728845 ACACTCTAAAACATGTCTGCGT 58.271 40.909 0.00 0.00 0.00 5.24
2122 2179 4.878439 ACACTCTAAAACATGTCTGCGTA 58.122 39.130 0.00 0.00 0.00 4.42
2123 2180 4.684703 ACACTCTAAAACATGTCTGCGTAC 59.315 41.667 0.00 0.00 0.00 3.67
2124 2181 4.684242 CACTCTAAAACATGTCTGCGTACA 59.316 41.667 0.00 0.00 0.00 2.90
2125 2182 5.348724 CACTCTAAAACATGTCTGCGTACAT 59.651 40.000 0.00 0.00 40.75 2.29
2126 2183 5.577164 ACTCTAAAACATGTCTGCGTACATC 59.423 40.000 0.00 0.00 38.01 3.06
2127 2184 4.868171 TCTAAAACATGTCTGCGTACATCC 59.132 41.667 0.00 0.00 38.01 3.51
2128 2185 1.640428 AACATGTCTGCGTACATCCG 58.360 50.000 0.00 0.00 38.01 4.18
2129 2186 0.530744 ACATGTCTGCGTACATCCGT 59.469 50.000 0.00 0.00 38.01 4.69
2130 2187 1.746787 ACATGTCTGCGTACATCCGTA 59.253 47.619 0.00 0.00 38.01 4.02
2131 2188 2.361119 ACATGTCTGCGTACATCCGTAT 59.639 45.455 0.00 0.00 38.01 3.06
2132 2189 2.485266 TGTCTGCGTACATCCGTATG 57.515 50.000 0.00 0.00 37.62 2.39
2134 2191 2.164827 TGTCTGCGTACATCCGTATGTT 59.835 45.455 0.00 0.00 44.07 2.71
2135 2192 2.534349 GTCTGCGTACATCCGTATGTTG 59.466 50.000 0.00 0.00 44.07 3.33
2136 2193 2.164827 TCTGCGTACATCCGTATGTTGT 59.835 45.455 0.00 0.00 44.07 3.32
2137 2194 3.377798 TCTGCGTACATCCGTATGTTGTA 59.622 43.478 0.00 0.00 44.07 2.41
2138 2195 3.697982 TGCGTACATCCGTATGTTGTAG 58.302 45.455 0.00 0.00 44.07 2.74
2139 2196 3.129113 TGCGTACATCCGTATGTTGTAGT 59.871 43.478 0.00 0.00 44.07 2.73
2140 2197 3.727723 GCGTACATCCGTATGTTGTAGTC 59.272 47.826 0.00 0.00 44.07 2.59
2141 2198 4.497006 GCGTACATCCGTATGTTGTAGTCT 60.497 45.833 0.00 0.00 44.07 3.24
2142 2199 5.277490 GCGTACATCCGTATGTTGTAGTCTA 60.277 44.000 0.00 0.00 44.07 2.59
2143 2200 6.567321 GCGTACATCCGTATGTTGTAGTCTAT 60.567 42.308 0.00 0.00 44.07 1.98
2144 2201 7.358066 CGTACATCCGTATGTTGTAGTCTATT 58.642 38.462 0.00 0.00 44.07 1.73
2145 2202 7.859377 CGTACATCCGTATGTTGTAGTCTATTT 59.141 37.037 0.00 0.00 44.07 1.40
2146 2203 8.965172 GTACATCCGTATGTTGTAGTCTATTTG 58.035 37.037 0.00 0.00 44.07 2.32
2147 2204 7.778083 ACATCCGTATGTTGTAGTCTATTTGA 58.222 34.615 0.00 0.00 44.07 2.69
2148 2205 7.921214 ACATCCGTATGTTGTAGTCTATTTGAG 59.079 37.037 0.00 0.00 44.07 3.02
2149 2206 7.634671 TCCGTATGTTGTAGTCTATTTGAGA 57.365 36.000 0.00 0.00 0.00 3.27
2150 2207 8.234136 TCCGTATGTTGTAGTCTATTTGAGAT 57.766 34.615 0.00 0.00 36.29 2.75
2151 2208 8.135529 TCCGTATGTTGTAGTCTATTTGAGATG 58.864 37.037 0.00 0.00 36.29 2.90
2152 2209 8.135529 CCGTATGTTGTAGTCTATTTGAGATGA 58.864 37.037 0.00 0.00 36.29 2.92
2153 2210 8.959058 CGTATGTTGTAGTCTATTTGAGATGAC 58.041 37.037 0.00 0.00 36.29 3.06
2157 2214 9.462606 TGTTGTAGTCTATTTGAGATGACTAGA 57.537 33.333 0.00 0.00 41.03 2.43
2163 2220 9.249053 AGTCTATTTGAGATGACTAGAAAGACA 57.751 33.333 0.00 0.00 37.92 3.41
2164 2221 9.862371 GTCTATTTGAGATGACTAGAAAGACAA 57.138 33.333 0.00 0.00 36.29 3.18
2178 2235 9.379791 ACTAGAAAGACAATTATTTAGGAACGG 57.620 33.333 0.00 0.00 0.00 4.44
2179 2236 9.595823 CTAGAAAGACAATTATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2180 2237 8.494016 AGAAAGACAATTATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2181 2238 7.553044 AGAAAGACAATTATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2182 2239 5.681639 AGACAATTATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2183 2240 5.427481 AGACAATTATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2184 2241 5.681639 ACAATTATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2185 2242 5.191124 ACAATTATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2186 2243 6.384886 ACAATTATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
2187 2244 7.072076 ACAATTATTTAGGAACGGAGGGAGTAT 59.928 37.037 0.00 0.00 0.00 2.12
2188 2245 6.661304 TTATTTAGGAACGGAGGGAGTATC 57.339 41.667 0.00 0.00 0.00 2.24
2189 2246 3.675348 TTAGGAACGGAGGGAGTATCA 57.325 47.619 0.00 0.00 36.25 2.15
2190 2247 2.544844 AGGAACGGAGGGAGTATCAA 57.455 50.000 0.00 0.00 36.25 2.57
2191 2248 2.389715 AGGAACGGAGGGAGTATCAAG 58.610 52.381 0.00 0.00 36.25 3.02
2192 2249 1.413077 GGAACGGAGGGAGTATCAAGG 59.587 57.143 0.00 0.00 36.25 3.61
2193 2250 2.385803 GAACGGAGGGAGTATCAAGGA 58.614 52.381 0.00 0.00 36.25 3.36
2194 2251 2.544844 ACGGAGGGAGTATCAAGGAA 57.455 50.000 0.00 0.00 36.25 3.36
2195 2252 2.108970 ACGGAGGGAGTATCAAGGAAC 58.891 52.381 0.00 0.00 36.25 3.62
2238 2295 3.473923 TTCAAGTGCATGACAGTGAGA 57.526 42.857 0.00 0.00 30.18 3.27
2287 2344 7.653647 ACATTGTATGTGTACCGAAACATTTT 58.346 30.769 2.28 0.00 43.01 1.82
2292 2349 9.613957 TGTATGTGTACCGAAACATTTTAAATG 57.386 29.630 15.25 15.25 38.05 2.32
2303 2360 9.232082 CGAAACATTTTAAATGTCAAGTTGAGA 57.768 29.630 21.50 5.30 0.00 3.27
2317 2374 5.013079 TCAAGTTGAGATACAATCCCAGTGT 59.987 40.000 0.08 0.00 40.76 3.55
2330 2387 2.905736 TCCCAGTGTGATTCATCAGTGA 59.094 45.455 18.00 0.00 37.51 3.41
2332 2389 2.669924 CCAGTGTGATTCATCAGTGACG 59.330 50.000 18.00 0.00 37.51 4.35
2334 2391 3.742882 CAGTGTGATTCATCAGTGACGTT 59.257 43.478 14.04 0.00 37.51 3.99
2398 2455 6.152379 CAGAAAGCTTGGGTCAGATTTTTAC 58.848 40.000 0.00 0.00 32.52 2.01
2404 2461 1.129811 GGGTCAGATTTTTACGCCGTG 59.870 52.381 0.00 0.00 0.00 4.94
2418 2475 0.109319 GCCGTGAACATTTTGCCGAT 60.109 50.000 0.00 0.00 0.00 4.18
2442 2499 5.991933 TGCAGGCATTTACCTTGAAATTA 57.008 34.783 0.00 0.00 38.26 1.40
2443 2500 5.964758 TGCAGGCATTTACCTTGAAATTAG 58.035 37.500 0.00 0.00 38.26 1.73
2444 2501 5.480073 TGCAGGCATTTACCTTGAAATTAGT 59.520 36.000 0.00 0.00 38.26 2.24
2445 2502 6.661377 TGCAGGCATTTACCTTGAAATTAGTA 59.339 34.615 0.00 0.00 38.26 1.82
2446 2503 6.972901 GCAGGCATTTACCTTGAAATTAGTAC 59.027 38.462 0.00 0.00 38.26 2.73
2447 2504 7.148069 GCAGGCATTTACCTTGAAATTAGTACT 60.148 37.037 0.00 0.00 38.26 2.73
2448 2505 8.398665 CAGGCATTTACCTTGAAATTAGTACTC 58.601 37.037 0.00 0.00 38.26 2.59
2449 2506 7.556635 AGGCATTTACCTTGAAATTAGTACTCC 59.443 37.037 0.00 0.00 36.28 3.85
2450 2507 7.201794 GGCATTTACCTTGAAATTAGTACTCCC 60.202 40.741 0.00 0.00 0.00 4.30
2451 2508 7.556635 GCATTTACCTTGAAATTAGTACTCCCT 59.443 37.037 0.00 0.00 0.00 4.20
2452 2509 9.462606 CATTTACCTTGAAATTAGTACTCCCTT 57.537 33.333 0.00 0.00 0.00 3.95
2453 2510 9.682465 ATTTACCTTGAAATTAGTACTCCCTTC 57.318 33.333 0.00 1.23 0.00 3.46
2454 2511 5.731591 ACCTTGAAATTAGTACTCCCTTCG 58.268 41.667 0.00 0.00 0.00 3.79
2455 2512 5.247792 ACCTTGAAATTAGTACTCCCTTCGT 59.752 40.000 0.00 0.00 0.00 3.85
2456 2513 5.811100 CCTTGAAATTAGTACTCCCTTCGTC 59.189 44.000 0.00 0.00 0.00 4.20
2457 2514 5.334724 TGAAATTAGTACTCCCTTCGTCC 57.665 43.478 0.00 0.00 0.00 4.79
2458 2515 4.161001 TGAAATTAGTACTCCCTTCGTCCC 59.839 45.833 0.00 0.00 0.00 4.46
2459 2516 2.905415 TTAGTACTCCCTTCGTCCCA 57.095 50.000 0.00 0.00 0.00 4.37
2460 2517 2.905415 TAGTACTCCCTTCGTCCCAA 57.095 50.000 0.00 0.00 0.00 4.12
2461 2518 2.019807 AGTACTCCCTTCGTCCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
2462 2519 2.332117 AGTACTCCCTTCGTCCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
2463 2520 2.910977 AGTACTCCCTTCGTCCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
2464 2521 4.098894 AGTACTCCCTTCGTCCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
2465 2522 4.533311 AGTACTCCCTTCGTCCCAAAATAA 59.467 41.667 0.00 0.00 0.00 1.40
2466 2523 4.376225 ACTCCCTTCGTCCCAAAATAAA 57.624 40.909 0.00 0.00 0.00 1.40
2467 2524 4.930696 ACTCCCTTCGTCCCAAAATAAAT 58.069 39.130 0.00 0.00 0.00 1.40
2468 2525 6.069705 ACTCCCTTCGTCCCAAAATAAATA 57.930 37.500 0.00 0.00 0.00 1.40
2469 2526 6.669631 ACTCCCTTCGTCCCAAAATAAATAT 58.330 36.000 0.00 0.00 0.00 1.28
2470 2527 7.123383 ACTCCCTTCGTCCCAAAATAAATATT 58.877 34.615 0.00 0.00 0.00 1.28
2471 2528 7.618117 ACTCCCTTCGTCCCAAAATAAATATTT 59.382 33.333 5.89 5.89 37.49 1.40
2472 2529 8.368962 TCCCTTCGTCCCAAAATAAATATTTT 57.631 30.769 5.91 5.52 44.27 1.82
2517 2574 7.622713 ACTAGAGCTAGTACAAAGTAGAGACA 58.377 38.462 8.35 0.00 43.98 3.41
2518 2575 6.746745 AGAGCTAGTACAAAGTAGAGACAC 57.253 41.667 0.00 0.00 31.18 3.67
2519 2576 6.478129 AGAGCTAGTACAAAGTAGAGACACT 58.522 40.000 0.00 0.00 31.18 3.55
2520 2577 6.943718 AGAGCTAGTACAAAGTAGAGACACTT 59.056 38.462 0.00 0.00 40.49 3.16
2521 2578 8.102047 AGAGCTAGTACAAAGTAGAGACACTTA 58.898 37.037 0.00 0.00 37.78 2.24
2522 2579 8.810990 AGCTAGTACAAAGTAGAGACACTTAT 57.189 34.615 0.00 0.00 37.78 1.73
2523 2580 9.245481 AGCTAGTACAAAGTAGAGACACTTATT 57.755 33.333 0.00 0.00 37.78 1.40
2524 2581 9.857957 GCTAGTACAAAGTAGAGACACTTATTT 57.142 33.333 0.00 0.00 37.78 1.40
2529 2586 8.166422 ACAAAGTAGAGACACTTATTTTTGGG 57.834 34.615 0.00 0.00 37.78 4.12
2530 2587 7.996644 ACAAAGTAGAGACACTTATTTTTGGGA 59.003 33.333 0.00 0.00 37.78 4.37
2531 2588 7.981102 AAGTAGAGACACTTATTTTTGGGAC 57.019 36.000 0.00 0.00 36.99 4.46
2532 2589 6.164176 AGTAGAGACACTTATTTTTGGGACG 58.836 40.000 0.00 0.00 0.00 4.79
2533 2590 4.324267 AGAGACACTTATTTTTGGGACGG 58.676 43.478 0.00 0.00 0.00 4.79
2534 2591 4.041198 AGAGACACTTATTTTTGGGACGGA 59.959 41.667 0.00 0.00 0.00 4.69
2535 2592 4.324267 AGACACTTATTTTTGGGACGGAG 58.676 43.478 0.00 0.00 0.00 4.63
2536 2593 3.418047 ACACTTATTTTTGGGACGGAGG 58.582 45.455 0.00 0.00 0.00 4.30
2537 2594 2.752903 CACTTATTTTTGGGACGGAGGG 59.247 50.000 0.00 0.00 0.00 4.30
2558 2615 7.169287 AGGGAGTAGAAGATATCAGGTTAGT 57.831 40.000 5.32 0.00 0.00 2.24
2641 2698 0.888285 AGCTGGCTCACTCAGTTTGC 60.888 55.000 0.00 0.00 34.89 3.68
2642 2699 1.860484 GCTGGCTCACTCAGTTTGCC 61.860 60.000 10.22 10.22 43.49 4.52
2654 2711 3.554934 TCAGTTTGCCATCTGAGTTTGT 58.445 40.909 0.00 0.00 36.04 2.83
2655 2712 4.713553 TCAGTTTGCCATCTGAGTTTGTA 58.286 39.130 0.00 0.00 36.04 2.41
2657 2714 5.239306 TCAGTTTGCCATCTGAGTTTGTAAG 59.761 40.000 0.00 0.00 36.04 2.34
2665 2722 5.934043 CCATCTGAGTTTGTAAGTCACATGA 59.066 40.000 0.00 2.30 38.66 3.07
2690 2747 9.220767 GATCAAAAGATTCCGTTAAGCCTATAT 57.779 33.333 0.00 0.00 0.00 0.86
2774 2841 9.077885 ACACAAAGGCTAATCTTTCTTTAATCA 57.922 29.630 0.00 0.00 35.04 2.57
2777 2844 9.565213 CAAAGGCTAATCTTTCTTTAATCACTG 57.435 33.333 0.00 0.00 35.04 3.66
2797 2864 4.218852 ACTGCTCACTAGAAAGTACCAGAC 59.781 45.833 0.00 0.00 33.48 3.51
2804 2871 1.352156 GAAAGTACCAGACGCCTGCG 61.352 60.000 10.40 10.40 46.03 5.18
2805 2872 3.934391 AAGTACCAGACGCCTGCGC 62.934 63.158 12.03 0.00 44.19 6.09
2807 2874 3.770040 TACCAGACGCCTGCGCAT 61.770 61.111 12.24 0.00 44.19 4.73
2817 2884 1.063912 CGCCTGCGCATTTAATCAGAA 59.936 47.619 12.24 0.00 34.03 3.02
2843 2910 3.181470 GCAGAAGGGGTATCTCTGACTTC 60.181 52.174 2.57 0.00 35.72 3.01
2847 2914 4.901785 AGGGGTATCTCTGACTTCCTAA 57.098 45.455 0.00 0.00 0.00 2.69
2850 2917 6.030082 AGGGGTATCTCTGACTTCCTAAAAA 58.970 40.000 0.00 0.00 0.00 1.94
2860 2927 9.883142 CTCTGACTTCCTAAAAATATCAGAACT 57.117 33.333 0.00 0.00 40.27 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 98 5.713389 TCCGTACTGGAATCTCTAAACAGAA 59.287 40.000 4.28 0.00 46.38 3.02
149 166 9.696572 ATGAACTACATACGGGTGTATATAGAT 57.303 33.333 7.52 0.00 39.42 1.98
192 209 3.181483 CCTCCATTCCTAAATGCAAGTGC 60.181 47.826 0.00 0.00 40.85 4.40
193 210 3.382546 CCCTCCATTCCTAAATGCAAGTG 59.617 47.826 0.00 0.00 40.85 3.16
206 224 7.939784 ACAAAAAGTAATACTCCCTCCATTC 57.060 36.000 0.00 0.00 0.00 2.67
210 228 7.392418 ACACTACAAAAAGTAATACTCCCTCC 58.608 38.462 0.00 0.00 30.92 4.30
263 281 9.838339 ATAAGGGACACTTGTATTTCTAGATTG 57.162 33.333 0.00 0.00 40.37 2.67
278 296 5.422214 CCTGTCAGTTTATAAGGGACACT 57.578 43.478 10.21 0.00 34.97 3.55
357 375 9.388506 ACACTATGAATCTATCAAGTTTTCTGG 57.611 33.333 0.00 0.00 42.54 3.86
450 468 4.681781 CGAGCTCAAGTGGTCTCCATATTT 60.682 45.833 15.40 0.00 35.28 1.40
457 475 1.216710 CCCGAGCTCAAGTGGTCTC 59.783 63.158 15.40 0.00 32.83 3.36
655 676 3.519510 ACTGTAAGCCTCTCTTGCCAATA 59.480 43.478 0.00 0.00 37.60 1.90
727 748 0.443088 CAGCAGCAGAAGAAGAAGCG 59.557 55.000 0.00 0.00 0.00 4.68
734 755 1.303074 CCCAAGCAGCAGCAGAAGA 60.303 57.895 3.17 0.00 45.49 2.87
737 758 2.033141 GACCCAAGCAGCAGCAGA 59.967 61.111 3.17 0.00 45.49 4.26
796 817 4.058721 TCGATCATTGTGACCGATTGAT 57.941 40.909 0.00 0.00 0.00 2.57
797 818 3.518634 TCGATCATTGTGACCGATTGA 57.481 42.857 0.00 0.00 0.00 2.57
798 819 3.121227 CGATCGATCATTGTGACCGATTG 60.121 47.826 24.40 9.60 39.65 2.67
799 820 3.052745 CGATCGATCATTGTGACCGATT 58.947 45.455 24.40 0.00 39.65 3.34
800 821 2.666026 CGATCGATCATTGTGACCGAT 58.334 47.619 24.40 8.83 41.85 4.18
801 822 1.864029 GCGATCGATCATTGTGACCGA 60.864 52.381 24.40 0.00 0.00 4.69
802 823 0.504384 GCGATCGATCATTGTGACCG 59.496 55.000 24.40 9.35 0.00 4.79
803 824 0.504384 CGCGATCGATCATTGTGACC 59.496 55.000 24.40 0.00 38.10 4.02
827 848 6.878317 TGTAATGGTCTCTTGATCGAGAATT 58.122 36.000 13.77 12.12 41.38 2.17
957 978 4.398358 GTGCTGACCGTATATATAGCTCCA 59.602 45.833 0.00 0.00 32.66 3.86
1022 1043 1.649664 AGCAGCAGTGATAAGCTTCG 58.350 50.000 0.00 0.00 39.50 3.79
1046 1068 2.026641 AGAAACTGCAAGCAGAAGCAA 58.973 42.857 27.17 0.00 46.30 3.91
1082 1104 5.505286 CAAGAAGATTGTGGCGATGTTATC 58.495 41.667 0.00 0.00 0.00 1.75
1084 1106 3.126858 GCAAGAAGATTGTGGCGATGTTA 59.873 43.478 0.00 0.00 0.00 2.41
1209 1234 2.119495 GGCTTCTCCTCCTTGGTGATA 58.881 52.381 0.00 0.00 38.05 2.15
1596 1622 6.345096 AGGAAGCTAGAAAGAGATGATAGC 57.655 41.667 0.00 0.00 39.28 2.97
1678 1705 2.762327 AGGAAATACTTGGCCTGCAATG 59.238 45.455 3.32 0.00 0.00 2.82
1703 1730 3.584250 CTGCTGCCTTGAACGTGCG 62.584 63.158 0.00 0.00 0.00 5.34
1706 1733 2.980233 GCCTGCTGCCTTGAACGT 60.980 61.111 0.00 0.00 0.00 3.99
1707 1734 4.093952 CGCCTGCTGCCTTGAACG 62.094 66.667 0.00 0.00 36.24 3.95
1738 1765 0.976641 TCCACCGCTGATCACTTCTT 59.023 50.000 0.00 0.00 0.00 2.52
1817 1844 1.573108 TCAACATGGAGAGAGGGACC 58.427 55.000 0.00 0.00 0.00 4.46
1952 2009 3.609853 GGCATGATGGAAGTAGTGTTCA 58.390 45.455 0.00 0.00 0.00 3.18
2024 2081 5.681639 ACAATTATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2025 2082 5.427481 AGACAATTATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2026 2083 5.681639 AGACAATTATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2027 2084 7.553044 AGAAAGACAATTATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2028 2085 8.494016 AGAAAGACAATTATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2029 2086 9.595823 CTAGAAAGACAATTATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2030 2087 9.595823 TCTAGAAAGACAATTATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2043 2100 9.566432 ACTTGTTGAAATCTCTAGAAAGACAAT 57.434 29.630 0.00 0.00 0.00 2.71
2044 2101 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
2045 2102 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
2046 2103 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
2047 2104 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
2048 2105 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
2049 2106 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
2050 2107 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
2051 2108 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
2052 2109 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
2053 2110 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
2054 2111 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
2055 2112 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
2056 2113 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
2057 2114 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
2058 2115 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
2059 2116 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2060 2117 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
2061 2118 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
2062 2119 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
2063 2120 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2064 2121 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
2065 2122 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2066 2123 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2067 2124 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
2068 2125 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2069 2126 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2070 2127 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2071 2128 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2072 2129 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2073 2130 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2074 2131 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2075 2132 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2076 2133 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2077 2134 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2078 2135 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2079 2136 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2080 2137 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2081 2138 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2092 2149 8.651588 CAGACATGTTTTAGAGTGTAGATTCAC 58.348 37.037 0.00 0.00 38.46 3.18
2093 2150 7.331934 GCAGACATGTTTTAGAGTGTAGATTCA 59.668 37.037 0.00 0.00 0.00 2.57
2094 2151 7.463383 CGCAGACATGTTTTAGAGTGTAGATTC 60.463 40.741 0.00 0.00 0.00 2.52
2095 2152 6.311445 CGCAGACATGTTTTAGAGTGTAGATT 59.689 38.462 0.00 0.00 0.00 2.40
2096 2153 5.807520 CGCAGACATGTTTTAGAGTGTAGAT 59.192 40.000 0.00 0.00 0.00 1.98
2097 2154 5.161358 CGCAGACATGTTTTAGAGTGTAGA 58.839 41.667 0.00 0.00 0.00 2.59
2098 2155 4.923871 ACGCAGACATGTTTTAGAGTGTAG 59.076 41.667 0.00 0.00 0.00 2.74
2099 2156 4.878439 ACGCAGACATGTTTTAGAGTGTA 58.122 39.130 0.00 0.00 0.00 2.90
2100 2157 3.728845 ACGCAGACATGTTTTAGAGTGT 58.271 40.909 0.00 0.00 0.00 3.55
2101 2158 4.684242 TGTACGCAGACATGTTTTAGAGTG 59.316 41.667 0.00 0.00 0.00 3.51
2102 2159 4.878439 TGTACGCAGACATGTTTTAGAGT 58.122 39.130 0.00 1.34 0.00 3.24
2103 2160 5.005779 GGATGTACGCAGACATGTTTTAGAG 59.994 44.000 0.00 0.00 40.18 2.43
2104 2161 4.868171 GGATGTACGCAGACATGTTTTAGA 59.132 41.667 0.00 0.00 40.18 2.10
2105 2162 4.259810 CGGATGTACGCAGACATGTTTTAG 60.260 45.833 0.00 0.00 40.18 1.85
2106 2163 3.615056 CGGATGTACGCAGACATGTTTTA 59.385 43.478 0.00 0.00 40.18 1.52
2107 2164 2.415168 CGGATGTACGCAGACATGTTTT 59.585 45.455 0.00 0.00 40.18 2.43
2108 2165 1.999735 CGGATGTACGCAGACATGTTT 59.000 47.619 0.00 0.00 40.18 2.83
2109 2166 1.067142 ACGGATGTACGCAGACATGTT 60.067 47.619 0.00 0.00 40.18 2.71
2110 2167 0.530744 ACGGATGTACGCAGACATGT 59.469 50.000 0.00 0.00 40.18 3.21
2111 2168 2.485266 TACGGATGTACGCAGACATG 57.515 50.000 5.25 0.00 40.18 3.21
2112 2169 2.361119 ACATACGGATGTACGCAGACAT 59.639 45.455 12.79 0.21 44.77 3.06
2113 2170 1.746787 ACATACGGATGTACGCAGACA 59.253 47.619 12.79 0.00 44.77 3.41
2114 2171 2.486951 ACATACGGATGTACGCAGAC 57.513 50.000 12.79 0.00 44.77 3.51
2115 2172 2.164827 ACAACATACGGATGTACGCAGA 59.835 45.455 15.10 0.00 45.93 4.26
2116 2173 2.536365 ACAACATACGGATGTACGCAG 58.464 47.619 15.10 4.73 45.93 5.18
2117 2174 2.658373 ACAACATACGGATGTACGCA 57.342 45.000 15.10 0.00 45.93 5.24
2118 2175 3.699067 ACTACAACATACGGATGTACGC 58.301 45.455 15.10 0.00 45.93 4.42
2119 2176 5.165911 AGACTACAACATACGGATGTACG 57.834 43.478 15.10 11.07 45.93 3.67
2120 2177 8.965172 CAAATAGACTACAACATACGGATGTAC 58.035 37.037 15.10 2.18 45.93 2.90
2121 2178 8.905850 TCAAATAGACTACAACATACGGATGTA 58.094 33.333 15.10 0.00 45.93 2.29
2123 2180 8.135529 TCTCAAATAGACTACAACATACGGATG 58.864 37.037 5.94 5.94 39.16 3.51
2124 2181 8.234136 TCTCAAATAGACTACAACATACGGAT 57.766 34.615 0.00 0.00 0.00 4.18
2125 2182 7.634671 TCTCAAATAGACTACAACATACGGA 57.365 36.000 0.00 0.00 0.00 4.69
2126 2183 8.135529 TCATCTCAAATAGACTACAACATACGG 58.864 37.037 0.00 0.00 36.93 4.02
2127 2184 8.959058 GTCATCTCAAATAGACTACAACATACG 58.041 37.037 0.00 0.00 36.93 3.06
2131 2188 9.462606 TCTAGTCATCTCAAATAGACTACAACA 57.537 33.333 0.00 0.00 41.27 3.33
2137 2194 9.249053 TGTCTTTCTAGTCATCTCAAATAGACT 57.751 33.333 0.00 0.00 43.25 3.24
2138 2195 9.862371 TTGTCTTTCTAGTCATCTCAAATAGAC 57.138 33.333 0.00 0.00 36.93 2.59
2152 2209 9.379791 CCGTTCCTAAATAATTGTCTTTCTAGT 57.620 33.333 0.00 0.00 0.00 2.57
2153 2210 9.595823 TCCGTTCCTAAATAATTGTCTTTCTAG 57.404 33.333 0.00 0.00 0.00 2.43
2154 2211 9.595823 CTCCGTTCCTAAATAATTGTCTTTCTA 57.404 33.333 0.00 0.00 0.00 2.10
2155 2212 7.553044 CCTCCGTTCCTAAATAATTGTCTTTCT 59.447 37.037 0.00 0.00 0.00 2.52
2156 2213 7.201705 CCCTCCGTTCCTAAATAATTGTCTTTC 60.202 40.741 0.00 0.00 0.00 2.62
2157 2214 6.602009 CCCTCCGTTCCTAAATAATTGTCTTT 59.398 38.462 0.00 0.00 0.00 2.52
2158 2215 6.069847 TCCCTCCGTTCCTAAATAATTGTCTT 60.070 38.462 0.00 0.00 0.00 3.01
2159 2216 5.427481 TCCCTCCGTTCCTAAATAATTGTCT 59.573 40.000 0.00 0.00 0.00 3.41
2160 2217 5.677567 TCCCTCCGTTCCTAAATAATTGTC 58.322 41.667 0.00 0.00 0.00 3.18
2161 2218 5.191124 ACTCCCTCCGTTCCTAAATAATTGT 59.809 40.000 0.00 0.00 0.00 2.71
2162 2219 5.681639 ACTCCCTCCGTTCCTAAATAATTG 58.318 41.667 0.00 0.00 0.00 2.32
2163 2220 5.970501 ACTCCCTCCGTTCCTAAATAATT 57.029 39.130 0.00 0.00 0.00 1.40
2164 2221 6.785963 TGATACTCCCTCCGTTCCTAAATAAT 59.214 38.462 0.00 0.00 0.00 1.28
2165 2222 6.138263 TGATACTCCCTCCGTTCCTAAATAA 58.862 40.000 0.00 0.00 0.00 1.40
2166 2223 5.708544 TGATACTCCCTCCGTTCCTAAATA 58.291 41.667 0.00 0.00 0.00 1.40
2167 2224 4.553678 TGATACTCCCTCCGTTCCTAAAT 58.446 43.478 0.00 0.00 0.00 1.40
2168 2225 3.985127 TGATACTCCCTCCGTTCCTAAA 58.015 45.455 0.00 0.00 0.00 1.85
2169 2226 3.675348 TGATACTCCCTCCGTTCCTAA 57.325 47.619 0.00 0.00 0.00 2.69
2170 2227 3.563223 CTTGATACTCCCTCCGTTCCTA 58.437 50.000 0.00 0.00 0.00 2.94
2171 2228 2.389715 CTTGATACTCCCTCCGTTCCT 58.610 52.381 0.00 0.00 0.00 3.36
2172 2229 1.413077 CCTTGATACTCCCTCCGTTCC 59.587 57.143 0.00 0.00 0.00 3.62
2173 2230 2.385803 TCCTTGATACTCCCTCCGTTC 58.614 52.381 0.00 0.00 0.00 3.95
2174 2231 2.500504 GTTCCTTGATACTCCCTCCGTT 59.499 50.000 0.00 0.00 0.00 4.44
2175 2232 2.108970 GTTCCTTGATACTCCCTCCGT 58.891 52.381 0.00 0.00 0.00 4.69
2176 2233 2.108168 TGTTCCTTGATACTCCCTCCG 58.892 52.381 0.00 0.00 0.00 4.63
2177 2234 4.779993 ATTGTTCCTTGATACTCCCTCC 57.220 45.455 0.00 0.00 0.00 4.30
2178 2235 7.110155 TGTTTATTGTTCCTTGATACTCCCTC 58.890 38.462 0.00 0.00 0.00 4.30
2179 2236 7.027874 TGTTTATTGTTCCTTGATACTCCCT 57.972 36.000 0.00 0.00 0.00 4.20
2180 2237 7.610305 TCTTGTTTATTGTTCCTTGATACTCCC 59.390 37.037 0.00 0.00 0.00 4.30
2181 2238 8.561738 TCTTGTTTATTGTTCCTTGATACTCC 57.438 34.615 0.00 0.00 0.00 3.85
2183 2240 9.574516 ACTTCTTGTTTATTGTTCCTTGATACT 57.425 29.630 0.00 0.00 0.00 2.12
2187 2244 9.621629 TCTTACTTCTTGTTTATTGTTCCTTGA 57.378 29.630 0.00 0.00 0.00 3.02
2287 2344 8.106462 TGGGATTGTATCTCAACTTGACATTTA 58.894 33.333 0.00 0.00 36.68 1.40
2292 2349 5.352569 CACTGGGATTGTATCTCAACTTGAC 59.647 44.000 0.00 0.00 39.74 3.18
2303 2360 6.005066 TGATGAATCACACTGGGATTGTAT 57.995 37.500 11.42 5.78 35.23 2.29
2306 2363 4.095932 CACTGATGAATCACACTGGGATTG 59.904 45.833 11.42 0.00 35.23 2.67
2309 2366 2.905736 TCACTGATGAATCACACTGGGA 59.094 45.455 0.00 0.00 32.50 4.37
2311 2368 2.669924 CGTCACTGATGAATCACACTGG 59.330 50.000 0.00 0.00 36.31 4.00
2317 2374 4.631131 ACTTGAACGTCACTGATGAATCA 58.369 39.130 5.20 6.38 36.31 2.57
2384 2441 1.129811 CACGGCGTAAAAATCTGACCC 59.870 52.381 14.22 0.00 0.00 4.46
2398 2455 2.080062 CGGCAAAATGTTCACGGCG 61.080 57.895 4.80 4.80 39.29 6.46
2404 2461 3.374745 CCTGCATATCGGCAAAATGTTC 58.625 45.455 0.00 0.00 44.40 3.18
2418 2475 6.543430 AATTTCAAGGTAAATGCCTGCATA 57.457 33.333 4.84 0.00 39.17 3.14
2442 2499 2.019807 TTTGGGACGAAGGGAGTACT 57.980 50.000 0.00 0.00 0.00 2.73
2443 2500 2.845363 TTTTGGGACGAAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
2444 2501 5.502089 TTTATTTTGGGACGAAGGGAGTA 57.498 39.130 0.00 0.00 0.00 2.59
2445 2502 4.376225 TTTATTTTGGGACGAAGGGAGT 57.624 40.909 0.00 0.00 0.00 3.85
2446 2503 7.582667 AATATTTATTTTGGGACGAAGGGAG 57.417 36.000 0.00 0.00 0.00 4.30
2447 2504 7.964666 AAATATTTATTTTGGGACGAAGGGA 57.035 32.000 0.00 0.00 32.28 4.20
2490 2547 9.768662 GTCTCTACTTTGTACTAGCTCTAGTAT 57.231 37.037 16.96 6.31 46.57 2.12
2491 2548 8.756927 TGTCTCTACTTTGTACTAGCTCTAGTA 58.243 37.037 11.59 11.59 43.98 1.82
2493 2550 7.767198 AGTGTCTCTACTTTGTACTAGCTCTAG 59.233 40.741 0.00 2.55 39.04 2.43
2494 2551 7.622713 AGTGTCTCTACTTTGTACTAGCTCTA 58.377 38.462 0.00 0.00 0.00 2.43
2495 2552 6.478129 AGTGTCTCTACTTTGTACTAGCTCT 58.522 40.000 0.00 0.00 0.00 4.09
2496 2553 6.746745 AGTGTCTCTACTTTGTACTAGCTC 57.253 41.667 0.00 0.00 0.00 4.09
2497 2554 8.810990 ATAAGTGTCTCTACTTTGTACTAGCT 57.189 34.615 0.00 0.00 41.01 3.32
2498 2555 9.857957 AAATAAGTGTCTCTACTTTGTACTAGC 57.142 33.333 0.00 0.00 41.01 3.42
2503 2560 9.280174 CCCAAAAATAAGTGTCTCTACTTTGTA 57.720 33.333 0.00 0.00 41.01 2.41
2504 2561 7.996644 TCCCAAAAATAAGTGTCTCTACTTTGT 59.003 33.333 0.00 0.00 41.01 2.83
2505 2562 8.290325 GTCCCAAAAATAAGTGTCTCTACTTTG 58.710 37.037 0.00 0.00 41.01 2.77
2506 2563 7.172703 CGTCCCAAAAATAAGTGTCTCTACTTT 59.827 37.037 0.00 0.00 41.01 2.66
2507 2564 6.649557 CGTCCCAAAAATAAGTGTCTCTACTT 59.350 38.462 0.00 0.00 43.03 2.24
2508 2565 6.164176 CGTCCCAAAAATAAGTGTCTCTACT 58.836 40.000 0.00 0.00 0.00 2.57
2509 2566 5.350640 CCGTCCCAAAAATAAGTGTCTCTAC 59.649 44.000 0.00 0.00 0.00 2.59
2510 2567 5.246656 TCCGTCCCAAAAATAAGTGTCTCTA 59.753 40.000 0.00 0.00 0.00 2.43
2511 2568 4.041198 TCCGTCCCAAAAATAAGTGTCTCT 59.959 41.667 0.00 0.00 0.00 3.10
2512 2569 4.320870 TCCGTCCCAAAAATAAGTGTCTC 58.679 43.478 0.00 0.00 0.00 3.36
2513 2570 4.324267 CTCCGTCCCAAAAATAAGTGTCT 58.676 43.478 0.00 0.00 0.00 3.41
2514 2571 3.439129 CCTCCGTCCCAAAAATAAGTGTC 59.561 47.826 0.00 0.00 0.00 3.67
2515 2572 3.418047 CCTCCGTCCCAAAAATAAGTGT 58.582 45.455 0.00 0.00 0.00 3.55
2516 2573 2.752903 CCCTCCGTCCCAAAAATAAGTG 59.247 50.000 0.00 0.00 0.00 3.16
2517 2574 2.645797 TCCCTCCGTCCCAAAAATAAGT 59.354 45.455 0.00 0.00 0.00 2.24
2518 2575 3.279434 CTCCCTCCGTCCCAAAAATAAG 58.721 50.000 0.00 0.00 0.00 1.73
2519 2576 2.645797 ACTCCCTCCGTCCCAAAAATAA 59.354 45.455 0.00 0.00 0.00 1.40
2520 2577 2.271777 ACTCCCTCCGTCCCAAAAATA 58.728 47.619 0.00 0.00 0.00 1.40
2521 2578 1.073098 ACTCCCTCCGTCCCAAAAAT 58.927 50.000 0.00 0.00 0.00 1.82
2522 2579 1.626825 CTACTCCCTCCGTCCCAAAAA 59.373 52.381 0.00 0.00 0.00 1.94
2523 2580 1.203212 TCTACTCCCTCCGTCCCAAAA 60.203 52.381 0.00 0.00 0.00 2.44
2524 2581 0.410663 TCTACTCCCTCCGTCCCAAA 59.589 55.000 0.00 0.00 0.00 3.28
2525 2582 0.410663 TTCTACTCCCTCCGTCCCAA 59.589 55.000 0.00 0.00 0.00 4.12
2526 2583 0.033405 CTTCTACTCCCTCCGTCCCA 60.033 60.000 0.00 0.00 0.00 4.37
2527 2584 0.258194 TCTTCTACTCCCTCCGTCCC 59.742 60.000 0.00 0.00 0.00 4.46
2528 2585 2.368311 ATCTTCTACTCCCTCCGTCC 57.632 55.000 0.00 0.00 0.00 4.79
2529 2586 4.653868 TGATATCTTCTACTCCCTCCGTC 58.346 47.826 3.98 0.00 0.00 4.79
2530 2587 4.507691 CCTGATATCTTCTACTCCCTCCGT 60.508 50.000 3.98 0.00 0.00 4.69
2531 2588 4.013728 CCTGATATCTTCTACTCCCTCCG 58.986 52.174 3.98 0.00 0.00 4.63
2532 2589 5.005628 ACCTGATATCTTCTACTCCCTCC 57.994 47.826 3.98 0.00 0.00 4.30
2533 2590 7.235804 ACTAACCTGATATCTTCTACTCCCTC 58.764 42.308 3.98 0.00 0.00 4.30
2534 2591 7.169287 ACTAACCTGATATCTTCTACTCCCT 57.831 40.000 3.98 0.00 0.00 4.20
2535 2592 8.165397 AGTACTAACCTGATATCTTCTACTCCC 58.835 40.741 3.98 0.00 0.00 4.30
2605 2662 8.953313 TGAGCCAGCTCATTAATGATTATATTG 58.047 33.333 18.14 6.44 46.80 1.90
2641 2698 5.934043 TCATGTGACTTACAAACTCAGATGG 59.066 40.000 0.00 0.00 43.77 3.51
2642 2699 7.332678 TGATCATGTGACTTACAAACTCAGATG 59.667 37.037 0.00 0.00 43.77 2.90
2654 2711 6.878923 ACGGAATCTTTTGATCATGTGACTTA 59.121 34.615 0.00 0.00 38.40 2.24
2655 2712 5.707298 ACGGAATCTTTTGATCATGTGACTT 59.293 36.000 0.00 0.00 38.40 3.01
2657 2714 5.551760 ACGGAATCTTTTGATCATGTGAC 57.448 39.130 0.00 0.00 38.40 3.67
2665 2722 9.003658 CATATAGGCTTAACGGAATCTTTTGAT 57.996 33.333 0.00 0.00 41.73 2.57
2690 2747 1.530720 GTCACATCATTGACGTGTGCA 59.469 47.619 12.15 1.95 42.16 4.57
2721 2778 7.640630 CAGAAGAGTATTACAGCGTACTTGTAG 59.359 40.741 7.04 0.00 33.00 2.74
2722 2779 7.335171 TCAGAAGAGTATTACAGCGTACTTGTA 59.665 37.037 3.73 3.73 31.61 2.41
2723 2780 6.150641 TCAGAAGAGTATTACAGCGTACTTGT 59.849 38.462 5.40 5.40 31.61 3.16
2724 2781 6.469595 GTCAGAAGAGTATTACAGCGTACTTG 59.530 42.308 0.00 0.00 31.61 3.16
2726 2783 5.646793 TGTCAGAAGAGTATTACAGCGTACT 59.353 40.000 0.00 0.00 34.02 2.73
2727 2784 5.738225 GTGTCAGAAGAGTATTACAGCGTAC 59.262 44.000 0.00 0.00 0.00 3.67
2728 2785 5.413523 TGTGTCAGAAGAGTATTACAGCGTA 59.586 40.000 0.00 0.00 0.00 4.42
2729 2786 4.217767 TGTGTCAGAAGAGTATTACAGCGT 59.782 41.667 0.00 0.00 0.00 5.07
2730 2787 4.733850 TGTGTCAGAAGAGTATTACAGCG 58.266 43.478 0.00 0.00 0.00 5.18
2774 2841 4.218852 GTCTGGTACTTTCTAGTGAGCAGT 59.781 45.833 0.00 0.00 36.28 4.40
2777 2844 3.760537 CGTCTGGTACTTTCTAGTGAGC 58.239 50.000 0.00 0.00 35.78 4.26
2797 2864 0.657312 TCTGATTAAATGCGCAGGCG 59.343 50.000 18.32 9.68 44.10 5.52
2804 2871 7.144000 CCCTTCTGCTTATTCTGATTAAATGC 58.856 38.462 0.00 0.00 0.00 3.56
2805 2872 7.286316 ACCCCTTCTGCTTATTCTGATTAAATG 59.714 37.037 0.00 0.00 0.00 2.32
2807 2874 6.731467 ACCCCTTCTGCTTATTCTGATTAAA 58.269 36.000 0.00 0.00 0.00 1.52
2817 2884 4.591072 GTCAGAGATACCCCTTCTGCTTAT 59.409 45.833 0.00 0.00 0.00 1.73
2856 2923 8.926715 AGAACTTGTTTTGATTTGGTAAGTTC 57.073 30.769 15.34 15.34 46.24 3.01


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

AutoCloner maintained by Alex Coulton.