Multiple sequence alignment - TraesCS2B01G060100

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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 TraesCS2B01G060100 chr2B 100.000 2681 0 0 1 2681 29024818 29027498 0.000000e+00 4951.0
1 TraesCS2B01G060100 chr4B 99.475 953 5 0 1 953 205445164 205446116 0.000000e+00 1733.0
2 TraesCS2B01G060100 chr4B 99.056 953 9 0 1 953 253380501 253379549 0.000000e+00 1711.0
3 TraesCS2B01G060100 chr7B 99.370 953 6 0 1 953 258526732 258525780 0.000000e+00 1727.0
4 TraesCS2B01G060100 chr1A 99.266 954 7 0 1 954 182675196 182676149 0.000000e+00 1724.0
5 TraesCS2B01G060100 chr1A 99.161 954 8 0 1 954 130377571 130376618 0.000000e+00 1718.0
6 TraesCS2B01G060100 chr1A 83.958 1627 211 33 957 2548 562616862 562615251 0.000000e+00 1513.0
7 TraesCS2B01G060100 chr1A 81.250 96 18 0 992 1087 551599259 551599354 7.960000e-11 78.7
8 TraesCS2B01G060100 chr5A 99.161 953 8 0 1 953 625277447 625278399 0.000000e+00 1716.0
9 TraesCS2B01G060100 chr5B 99.161 953 7 1 1 953 709212628 709211677 0.000000e+00 1714.0
10 TraesCS2B01G060100 chr5B 88.608 158 17 1 2517 2674 65246882 65246726 9.800000e-45 191.0
11 TraesCS2B01G060100 chr5B 89.313 131 13 1 1938 2068 65247008 65246879 2.140000e-36 163.0
12 TraesCS2B01G060100 chr5B 73.256 258 53 12 1013 1267 661872776 661872532 2.210000e-11 80.5
13 TraesCS2B01G060100 chr6A 99.057 954 9 0 1 954 181100082 181101035 0.000000e+00 1712.0
14 TraesCS2B01G060100 chr6A 99.057 954 9 0 1 954 439513105 439514058 0.000000e+00 1712.0
15 TraesCS2B01G060100 chr4D 82.639 1152 172 15 954 2080 151957628 151958776 0.000000e+00 994.0
16 TraesCS2B01G060100 chr1B 77.794 671 138 8 1353 2017 238765046 238764381 1.160000e-108 403.0
17 TraesCS2B01G060100 chr1B 85.131 343 50 1 1319 1660 51232783 51233125 1.530000e-92 350.0
18 TraesCS2B01G060100 chr1B 83.019 106 17 1 1877 1982 649981992 649982096 7.900000e-16 95.3
19 TraesCS2B01G060100 chr3D 77.645 671 135 11 1353 2017 191103696 191104357 6.960000e-106 394.0
20 TraesCS2B01G060100 chr3D 81.132 106 20 0 1877 1982 359635086 359634981 4.760000e-13 86.1
21 TraesCS2B01G060100 chr5D 76.648 698 142 15 1320 2004 444367608 444366919 1.520000e-97 366.0
22 TraesCS2B01G060100 chr7A 78.017 232 46 5 1783 2011 79119427 79119198 1.000000e-29 141.0
23 TraesCS2B01G060100 chr6B 79.104 134 27 1 1877 2009 628254363 628254230 1.020000e-14 91.6
24 TraesCS2B01G060100 chr3B 78.378 148 24 5 1837 1982 113982183 113982324 3.680000e-14 89.8


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 TraesCS2B01G060100 chr2B 29024818 29027498 2680 False 4951 4951 100.000 1 2681 1 chr2B.!!$F1 2680
1 TraesCS2B01G060100 chr4B 205445164 205446116 952 False 1733 1733 99.475 1 953 1 chr4B.!!$F1 952
2 TraesCS2B01G060100 chr4B 253379549 253380501 952 True 1711 1711 99.056 1 953 1 chr4B.!!$R1 952
3 TraesCS2B01G060100 chr7B 258525780 258526732 952 True 1727 1727 99.370 1 953 1 chr7B.!!$R1 952
4 TraesCS2B01G060100 chr1A 182675196 182676149 953 False 1724 1724 99.266 1 954 1 chr1A.!!$F1 953
5 TraesCS2B01G060100 chr1A 130376618 130377571 953 True 1718 1718 99.161 1 954 1 chr1A.!!$R1 953
6 TraesCS2B01G060100 chr1A 562615251 562616862 1611 True 1513 1513 83.958 957 2548 1 chr1A.!!$R2 1591
7 TraesCS2B01G060100 chr5A 625277447 625278399 952 False 1716 1716 99.161 1 953 1 chr5A.!!$F1 952
8 TraesCS2B01G060100 chr5B 709211677 709212628 951 True 1714 1714 99.161 1 953 1 chr5B.!!$R2 952
9 TraesCS2B01G060100 chr6A 181100082 181101035 953 False 1712 1712 99.057 1 954 1 chr6A.!!$F1 953
10 TraesCS2B01G060100 chr6A 439513105 439514058 953 False 1712 1712 99.057 1 954 1 chr6A.!!$F2 953
11 TraesCS2B01G060100 chr4D 151957628 151958776 1148 False 994 994 82.639 954 2080 1 chr4D.!!$F1 1126
12 TraesCS2B01G060100 chr1B 238764381 238765046 665 True 403 403 77.794 1353 2017 1 chr1B.!!$R1 664
13 TraesCS2B01G060100 chr3D 191103696 191104357 661 False 394 394 77.645 1353 2017 1 chr3D.!!$F1 664
14 TraesCS2B01G060100 chr5D 444366919 444367608 689 True 366 366 76.648 1320 2004 1 chr5D.!!$R1 684

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
987 988 0.403271 ATATGCATGGGAGGCCACTC 59.597 55.0 10.16 0.0 43.2 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2134 2173 0.037447 GGGAAGAAGCAGAGGCAAGT 59.963 55.0 0.0 0.0 44.61 3.16 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
814 815 4.522789 TCATATGGATGCTAGCGACACTAA 59.477 41.667 10.77 0.00 32.62 2.24
987 988 0.403271 ATATGCATGGGAGGCCACTC 59.597 55.000 10.16 0.00 43.20 3.51
989 990 0.695462 ATGCATGGGAGGCCACTCTA 60.695 55.000 5.01 0.00 43.46 2.43
990 991 1.147153 GCATGGGAGGCCACTCTAC 59.853 63.158 5.01 0.00 43.46 2.59
991 992 1.626356 GCATGGGAGGCCACTCTACA 61.626 60.000 5.01 0.00 43.46 2.74
1008 1009 2.867109 ACAGAGCAAACATGGCTACT 57.133 45.000 0.00 0.00 42.78 2.57
1014 1015 3.753272 GAGCAAACATGGCTACTGAAAGA 59.247 43.478 0.00 0.00 42.78 2.52
1026 1027 2.309613 ACTGAAAGACATGCTGGCAAA 58.690 42.857 0.00 0.00 37.43 3.68
1059 1060 2.557924 AGCAATGTTCGAGCAATTTGGA 59.442 40.909 5.91 0.00 0.00 3.53
1090 1091 1.877443 ACGAATGTGGTGCTTACCAAC 59.123 47.619 0.00 0.00 42.10 3.77
1118 1119 6.901081 AGAGGTAGAAAAAGGGAAAACATG 57.099 37.500 0.00 0.00 0.00 3.21
1119 1120 5.243954 AGAGGTAGAAAAAGGGAAAACATGC 59.756 40.000 0.00 0.00 0.00 4.06
1123 1124 4.368315 AGAAAAAGGGAAAACATGCGTTC 58.632 39.130 0.00 0.00 32.91 3.95
1134 1135 1.939934 ACATGCGTTCCAATCCATACG 59.060 47.619 0.00 0.00 37.09 3.06
1136 1137 0.462937 TGCGTTCCAATCCATACGGG 60.463 55.000 0.00 0.00 34.76 5.28
1143 1144 0.464373 CAATCCATACGGGTGCAGCT 60.464 55.000 16.65 0.00 38.11 4.24
1185 1186 6.183360 GCAGGATTTCATACAAGGTTACTGTC 60.183 42.308 0.00 0.00 0.00 3.51
1188 1189 6.035758 GGATTTCATACAAGGTTACTGTCGTC 59.964 42.308 0.00 0.00 0.00 4.20
1200 1201 4.410743 GTCGTCGACGGTGGGGAC 62.411 72.222 35.05 21.77 40.29 4.46
1218 1219 2.159627 GGACGAATTTGACTGCGAATGT 59.840 45.455 0.00 0.00 0.00 2.71
1240 1241 3.181435 TGGACAATTCACTCACATGGGAA 60.181 43.478 0.00 0.00 0.00 3.97
1267 1268 4.199310 GTGCAGCCATATTCTGAAGGTAA 58.801 43.478 6.04 0.00 33.54 2.85
1274 1275 9.725019 CAGCCATATTCTGAAGGTAATAACATA 57.275 33.333 0.00 0.00 33.54 2.29
1276 1277 8.669243 GCCATATTCTGAAGGTAATAACATAGC 58.331 37.037 0.00 0.00 0.00 2.97
1277 1278 9.725019 CCATATTCTGAAGGTAATAACATAGCA 57.275 33.333 0.00 0.00 0.00 3.49
1299 1322 5.812127 GCATTGAAAAGGTGGTATTCAATCC 59.188 40.000 9.35 0.00 45.71 3.01
1300 1323 5.637006 TTGAAAAGGTGGTATTCAATCCG 57.363 39.130 0.00 0.00 37.95 4.18
1308 1331 4.117685 GTGGTATTCAATCCGGTACTGAC 58.882 47.826 2.31 0.00 0.00 3.51
1350 1373 2.186076 GTTCTAGACTTCATCCGCGTG 58.814 52.381 4.92 0.00 0.00 5.34
1351 1374 0.738975 TCTAGACTTCATCCGCGTGG 59.261 55.000 9.28 9.28 0.00 4.94
1371 1394 4.156008 GTGGCAGAAATACCGAAGAAACAT 59.844 41.667 0.00 0.00 0.00 2.71
1398 1421 0.534412 AGAGGTGGACAAGAGATGCG 59.466 55.000 0.00 0.00 0.00 4.73
1399 1422 0.532573 GAGGTGGACAAGAGATGCGA 59.467 55.000 0.00 0.00 0.00 5.10
1422 1445 1.136329 ACATCCTGCCTCCACACCTT 61.136 55.000 0.00 0.00 0.00 3.50
1423 1446 0.038744 CATCCTGCCTCCACACCTTT 59.961 55.000 0.00 0.00 0.00 3.11
1464 1487 1.269723 GCTAACAGCAACAACCCCTTC 59.730 52.381 0.00 0.00 41.89 3.46
1530 1553 0.819582 GAATGGGGGATGCAAGTGTG 59.180 55.000 0.00 0.00 0.00 3.82
1548 1571 0.815213 TGCAAGCATATGACCGCCTC 60.815 55.000 6.97 0.00 0.00 4.70
1589 1612 4.334552 TGTGCTGAAGAAATGAAGCCATA 58.665 39.130 0.00 0.00 34.70 2.74
1590 1613 4.156556 TGTGCTGAAGAAATGAAGCCATAC 59.843 41.667 0.00 0.00 34.70 2.39
1591 1614 4.156556 GTGCTGAAGAAATGAAGCCATACA 59.843 41.667 0.00 0.00 34.70 2.29
1626 1649 4.101448 CTTGGCCTGGAGGACCGG 62.101 72.222 3.32 0.00 44.80 5.28
1641 1665 0.923358 ACCGGATGGCTAAAATGGGA 59.077 50.000 9.46 0.00 39.70 4.37
1649 1673 4.799564 TGGCTAAAATGGGATTGTTGTC 57.200 40.909 0.00 0.00 0.00 3.18
1656 1680 5.365021 AAATGGGATTGTTGTCAACCAAA 57.635 34.783 13.13 2.27 34.77 3.28
1683 1707 2.099921 GCAGAAGCTGATCGACTAGGAA 59.900 50.000 0.00 0.00 37.91 3.36
1684 1708 3.701241 CAGAAGCTGATCGACTAGGAAC 58.299 50.000 0.00 0.00 32.44 3.62
1704 1734 2.146342 CTGATATGGCGACCAATGGAC 58.854 52.381 6.16 0.00 36.95 4.02
1764 1794 2.229784 GGTAATATGCTTGCAGGGATGC 59.770 50.000 13.24 2.28 0.00 3.91
1859 1897 6.874134 TGAGCAAGAGAACTAGATTTTGTACC 59.126 38.462 0.00 0.00 0.00 3.34
1869 1907 9.477484 GAACTAGATTTTGTACCATATGTCGAT 57.523 33.333 0.00 0.00 0.00 3.59
2026 2064 6.369890 AGGCTAAATATGTGATTGTATGAGCG 59.630 38.462 0.00 0.00 0.00 5.03
2028 2067 7.230222 GCTAAATATGTGATTGTATGAGCGTC 58.770 38.462 0.00 0.00 0.00 5.19
2033 2072 4.421058 TGTGATTGTATGAGCGTCTGTAC 58.579 43.478 0.00 0.00 0.00 2.90
2043 2082 3.679502 TGAGCGTCTGTACAATGTTGATG 59.320 43.478 0.00 0.00 0.00 3.07
2047 2086 4.032900 GCGTCTGTACAATGTTGATGTAGG 59.967 45.833 0.00 0.00 34.14 3.18
2051 2090 6.426937 GTCTGTACAATGTTGATGTAGGTGTT 59.573 38.462 0.00 0.00 34.14 3.32
2103 2142 9.744468 ACCAAAACTATTTAAGCTTTGTGTTAG 57.256 29.630 3.20 2.46 38.89 2.34
2118 2157 7.414098 GCTTTGTGTTAGTCAACTTCTCTGAAA 60.414 37.037 0.00 0.00 35.56 2.69
2123 2162 9.865484 GTGTTAGTCAACTTCTCTGAAAAATAC 57.135 33.333 0.00 0.00 35.56 1.89
2126 2165 7.971183 AGTCAACTTCTCTGAAAAATACCTC 57.029 36.000 0.00 0.00 0.00 3.85
2127 2166 6.937465 AGTCAACTTCTCTGAAAAATACCTCC 59.063 38.462 0.00 0.00 0.00 4.30
2128 2167 6.710744 GTCAACTTCTCTGAAAAATACCTCCA 59.289 38.462 0.00 0.00 0.00 3.86
2129 2168 6.936900 TCAACTTCTCTGAAAAATACCTCCAG 59.063 38.462 0.00 0.00 0.00 3.86
2130 2169 5.810095 ACTTCTCTGAAAAATACCTCCAGG 58.190 41.667 0.00 0.00 42.17 4.45
2131 2170 5.548056 ACTTCTCTGAAAAATACCTCCAGGA 59.452 40.000 0.00 0.00 38.94 3.86
2132 2171 5.422214 TCTCTGAAAAATACCTCCAGGAC 57.578 43.478 0.00 0.00 38.94 3.85
2133 2172 4.844085 TCTCTGAAAAATACCTCCAGGACA 59.156 41.667 0.00 0.00 38.94 4.02
2134 2173 5.309543 TCTCTGAAAAATACCTCCAGGACAA 59.690 40.000 0.00 0.00 38.94 3.18
2140 2179 0.690762 TACCTCCAGGACAACTTGCC 59.309 55.000 0.00 0.00 38.94 4.52
2144 2183 0.397941 TCCAGGACAACTTGCCTCTG 59.602 55.000 2.72 2.17 30.41 3.35
2146 2185 0.250640 CAGGACAACTTGCCTCTGCT 60.251 55.000 2.72 0.00 38.71 4.24
2148 2187 0.877743 GGACAACTTGCCTCTGCTTC 59.122 55.000 0.00 0.00 38.71 3.86
2149 2188 1.544314 GGACAACTTGCCTCTGCTTCT 60.544 52.381 0.00 0.00 38.71 2.85
2152 2191 1.538950 CAACTTGCCTCTGCTTCTTCC 59.461 52.381 0.00 0.00 38.71 3.46
2154 2193 0.679321 CTTGCCTCTGCTTCTTCCCC 60.679 60.000 0.00 0.00 38.71 4.81
2157 2196 2.586792 CTCTGCTTCTTCCCCGGG 59.413 66.667 15.80 15.80 0.00 5.73
2171 2210 0.109504 CCCGGGTGTATTTGTTTGCG 60.110 55.000 14.18 0.00 0.00 4.85
2172 2211 0.875728 CCGGGTGTATTTGTTTGCGA 59.124 50.000 0.00 0.00 0.00 5.10
2173 2212 1.267261 CCGGGTGTATTTGTTTGCGAA 59.733 47.619 0.00 0.00 0.00 4.70
2174 2213 2.312348 CGGGTGTATTTGTTTGCGAAC 58.688 47.619 10.09 10.09 36.29 3.95
2175 2214 2.287069 CGGGTGTATTTGTTTGCGAACA 60.287 45.455 15.77 15.77 43.73 3.18
2176 2215 3.610585 CGGGTGTATTTGTTTGCGAACAT 60.611 43.478 20.12 9.11 44.71 2.71
2177 2216 4.378563 CGGGTGTATTTGTTTGCGAACATA 60.379 41.667 20.12 15.69 44.71 2.29
2178 2217 5.646606 GGGTGTATTTGTTTGCGAACATAT 58.353 37.500 20.12 21.02 44.71 1.78
2179 2218 6.096695 GGGTGTATTTGTTTGCGAACATATT 58.903 36.000 22.73 12.83 44.71 1.28
2180 2219 7.251994 GGGTGTATTTGTTTGCGAACATATTA 58.748 34.615 22.73 12.81 44.71 0.98
2208 2247 5.212532 TGTTGACAAATATTTTGCTGGCT 57.787 34.783 0.00 0.00 0.00 4.75
2210 2249 6.389091 TGTTGACAAATATTTTGCTGGCTAG 58.611 36.000 0.00 0.00 0.00 3.42
2213 2252 6.620678 TGACAAATATTTTGCTGGCTAGAAC 58.379 36.000 0.00 0.00 0.00 3.01
2214 2253 6.434028 TGACAAATATTTTGCTGGCTAGAACT 59.566 34.615 0.00 0.00 0.00 3.01
2217 2256 7.599998 ACAAATATTTTGCTGGCTAGAACTTTG 59.400 33.333 0.00 3.85 0.00 2.77
2220 2259 6.648879 ATTTTGCTGGCTAGAACTTTGTTA 57.351 33.333 0.00 0.00 0.00 2.41
2222 2261 5.432885 TTGCTGGCTAGAACTTTGTTAAC 57.567 39.130 0.00 0.00 0.00 2.01
2232 2271 8.774586 GCTAGAACTTTGTTAACTGAATGAAGA 58.225 33.333 7.22 0.00 0.00 2.87
2241 2280 8.833231 TGTTAACTGAATGAAGACTTCTAAGG 57.167 34.615 16.02 5.71 0.00 2.69
2242 2281 8.647796 TGTTAACTGAATGAAGACTTCTAAGGA 58.352 33.333 16.02 0.00 0.00 3.36
2265 2305 8.052748 AGGATGTAGTTAGAATTATTGTTGGCA 58.947 33.333 0.00 0.00 0.00 4.92
2270 2310 9.646336 GTAGTTAGAATTATTGTTGGCAATACG 57.354 33.333 1.92 0.00 44.50 3.06
2281 2321 2.784596 CAATACGCCGTGGTGCAG 59.215 61.111 0.00 0.00 0.00 4.41
2283 2323 1.089481 CAATACGCCGTGGTGCAGAT 61.089 55.000 0.00 0.00 0.00 2.90
2284 2324 0.810031 AATACGCCGTGGTGCAGATC 60.810 55.000 0.00 0.00 0.00 2.75
2290 2332 0.812811 CCGTGGTGCAGATCATGGAG 60.813 60.000 14.42 0.00 41.50 3.86
2291 2333 0.176449 CGTGGTGCAGATCATGGAGA 59.824 55.000 0.00 0.00 0.00 3.71
2297 2339 4.001652 GGTGCAGATCATGGAGATGTATG 58.998 47.826 0.00 0.00 37.00 2.39
2298 2340 4.504514 GGTGCAGATCATGGAGATGTATGT 60.505 45.833 0.00 0.00 37.00 2.29
2300 2342 4.001652 GCAGATCATGGAGATGTATGTGG 58.998 47.826 0.00 0.00 37.00 4.17
2301 2343 4.001652 CAGATCATGGAGATGTATGTGGC 58.998 47.826 0.00 0.00 37.00 5.01
2311 2353 2.708216 TGTATGTGGCTGGTATGGTG 57.292 50.000 0.00 0.00 0.00 4.17
2317 2359 1.881973 GTGGCTGGTATGGTGCATATG 59.118 52.381 0.00 0.00 0.00 1.78
2347 2397 0.038599 AATGACACTGGCAGCATGGA 59.961 50.000 15.89 0.00 35.86 3.41
2349 2399 2.359107 ACACTGGCAGCATGGACG 60.359 61.111 15.89 0.00 35.86 4.79
2352 2402 2.046988 CTGGCAGCATGGACGTGA 60.047 61.111 0.00 0.00 35.86 4.35
2392 2442 4.487412 GTGCTGAGCGCCATTGCC 62.487 66.667 6.76 0.00 38.05 4.52
2400 2450 1.445926 GCGCCATTGCCGTTCAAAT 60.446 52.632 0.00 0.00 38.34 2.32
2422 2472 2.538512 TGAATCAGATGAGCGGGATG 57.461 50.000 0.00 0.00 0.00 3.51
2423 2473 1.071228 TGAATCAGATGAGCGGGATGG 59.929 52.381 0.00 0.00 0.00 3.51
2459 2509 2.127708 ACATAAAGGGGAGGTGCCTAG 58.872 52.381 0.00 0.00 36.66 3.02
2474 2524 1.466558 GCCTAGTGCAAGAAAGCAGAC 59.533 52.381 0.00 0.00 46.69 3.51
2478 2528 1.599542 AGTGCAAGAAAGCAGACGAAC 59.400 47.619 0.00 0.00 46.69 3.95
2481 2531 1.260561 GCAAGAAAGCAGACGAACGAA 59.739 47.619 0.14 0.00 0.00 3.85
2484 2534 2.128035 AGAAAGCAGACGAACGAACTG 58.872 47.619 15.88 15.88 35.14 3.16
2510 2560 4.153411 GGAGCAAGTAGGCTAAGATAGGA 58.847 47.826 0.00 0.00 45.99 2.94
2530 2580 3.618351 GAGGCCATATGGATCAGAATGG 58.382 50.000 26.47 12.70 41.55 3.16
2534 2584 4.219288 GGCCATATGGATCAGAATGGTTTC 59.781 45.833 26.47 1.86 40.86 2.78
2548 2598 3.726557 TGGTTTCTCCATCTCTGCATT 57.273 42.857 0.00 0.00 41.93 3.56
2549 2599 3.349927 TGGTTTCTCCATCTCTGCATTG 58.650 45.455 0.00 0.00 41.93 2.82
2550 2600 3.009363 TGGTTTCTCCATCTCTGCATTGA 59.991 43.478 0.00 0.00 41.93 2.57
2551 2601 3.376546 GGTTTCTCCATCTCTGCATTGAC 59.623 47.826 0.00 0.00 35.97 3.18
2552 2602 2.996249 TCTCCATCTCTGCATTGACC 57.004 50.000 0.00 0.00 0.00 4.02
2553 2603 2.190538 TCTCCATCTCTGCATTGACCA 58.809 47.619 0.00 0.00 0.00 4.02
2554 2604 2.169978 TCTCCATCTCTGCATTGACCAG 59.830 50.000 0.00 0.00 0.00 4.00
2555 2605 1.022735 CCATCTCTGCATTGACCAGC 58.977 55.000 0.00 0.00 0.00 4.85
2556 2606 1.408405 CCATCTCTGCATTGACCAGCT 60.408 52.381 0.00 0.00 0.00 4.24
2557 2607 1.941294 CATCTCTGCATTGACCAGCTC 59.059 52.381 0.00 0.00 0.00 4.09
2558 2608 1.273759 TCTCTGCATTGACCAGCTCT 58.726 50.000 0.00 0.00 0.00 4.09
2559 2609 2.460669 TCTCTGCATTGACCAGCTCTA 58.539 47.619 0.00 0.00 0.00 2.43
2560 2610 2.833943 TCTCTGCATTGACCAGCTCTAA 59.166 45.455 0.00 0.00 0.00 2.10
2561 2611 3.261643 TCTCTGCATTGACCAGCTCTAAA 59.738 43.478 0.00 0.00 0.00 1.85
2562 2612 3.603532 TCTGCATTGACCAGCTCTAAAG 58.396 45.455 0.00 0.00 0.00 1.85
2563 2613 3.261643 TCTGCATTGACCAGCTCTAAAGA 59.738 43.478 0.00 0.00 0.00 2.52
2564 2614 4.080695 TCTGCATTGACCAGCTCTAAAGAT 60.081 41.667 0.00 0.00 0.00 2.40
2565 2615 4.592942 TGCATTGACCAGCTCTAAAGATT 58.407 39.130 0.00 0.00 0.00 2.40
2566 2616 4.397103 TGCATTGACCAGCTCTAAAGATTG 59.603 41.667 0.00 0.00 0.00 2.67
2567 2617 4.732938 GCATTGACCAGCTCTAAAGATTGC 60.733 45.833 0.00 0.00 0.00 3.56
2568 2618 3.988976 TGACCAGCTCTAAAGATTGCT 57.011 42.857 0.00 0.00 36.04 3.91
2569 2619 3.866651 TGACCAGCTCTAAAGATTGCTC 58.133 45.455 0.00 0.00 33.03 4.26
2570 2620 3.517100 TGACCAGCTCTAAAGATTGCTCT 59.483 43.478 0.00 0.00 33.03 4.09
2571 2621 4.711846 TGACCAGCTCTAAAGATTGCTCTA 59.288 41.667 0.00 0.00 33.03 2.43
2572 2622 5.365025 TGACCAGCTCTAAAGATTGCTCTAT 59.635 40.000 0.00 0.00 33.03 1.98
2573 2623 6.126940 TGACCAGCTCTAAAGATTGCTCTATT 60.127 38.462 0.00 0.00 33.03 1.73
2574 2624 6.287525 ACCAGCTCTAAAGATTGCTCTATTC 58.712 40.000 0.00 0.00 33.03 1.75
2575 2625 5.700373 CCAGCTCTAAAGATTGCTCTATTCC 59.300 44.000 0.00 0.00 33.03 3.01
2576 2626 5.700373 CAGCTCTAAAGATTGCTCTATTCCC 59.300 44.000 0.00 0.00 33.03 3.97
2577 2627 5.606329 AGCTCTAAAGATTGCTCTATTCCCT 59.394 40.000 0.00 0.00 0.00 4.20
2578 2628 5.700373 GCTCTAAAGATTGCTCTATTCCCTG 59.300 44.000 0.00 0.00 0.00 4.45
2579 2629 6.179906 TCTAAAGATTGCTCTATTCCCTGG 57.820 41.667 0.00 0.00 0.00 4.45
2580 2630 3.872459 AAGATTGCTCTATTCCCTGGG 57.128 47.619 6.33 6.33 0.00 4.45
2581 2631 2.781667 AGATTGCTCTATTCCCTGGGT 58.218 47.619 13.56 0.00 0.00 4.51
2582 2632 2.708325 AGATTGCTCTATTCCCTGGGTC 59.292 50.000 13.56 0.00 0.00 4.46
2583 2633 0.830648 TTGCTCTATTCCCTGGGTCG 59.169 55.000 13.56 0.00 0.00 4.79
2584 2634 0.325296 TGCTCTATTCCCTGGGTCGT 60.325 55.000 13.56 2.61 0.00 4.34
2585 2635 0.831307 GCTCTATTCCCTGGGTCGTT 59.169 55.000 13.56 0.00 0.00 3.85
2586 2636 1.202545 GCTCTATTCCCTGGGTCGTTC 60.203 57.143 13.56 0.00 0.00 3.95
2587 2637 1.413077 CTCTATTCCCTGGGTCGTTCC 59.587 57.143 13.56 0.00 0.00 3.62
2588 2638 1.007963 TCTATTCCCTGGGTCGTTCCT 59.992 52.381 13.56 0.00 36.25 3.36
2589 2639 2.245546 TCTATTCCCTGGGTCGTTCCTA 59.754 50.000 13.56 0.00 36.25 2.94
2590 2640 2.191981 ATTCCCTGGGTCGTTCCTAT 57.808 50.000 13.56 0.00 36.25 2.57
2591 2641 1.961133 TTCCCTGGGTCGTTCCTATT 58.039 50.000 13.56 0.00 36.25 1.73
2592 2642 1.492764 TCCCTGGGTCGTTCCTATTC 58.507 55.000 13.56 0.00 36.25 1.75
2593 2643 1.200519 CCCTGGGTCGTTCCTATTCA 58.799 55.000 3.97 0.00 36.25 2.57
2594 2644 1.139058 CCCTGGGTCGTTCCTATTCAG 59.861 57.143 3.97 0.00 36.25 3.02
2595 2645 1.139058 CCTGGGTCGTTCCTATTCAGG 59.861 57.143 0.00 0.00 44.17 3.86
2596 2646 1.831736 CTGGGTCGTTCCTATTCAGGT 59.168 52.381 0.00 0.00 43.18 4.00
2597 2647 3.028850 CTGGGTCGTTCCTATTCAGGTA 58.971 50.000 0.00 0.00 43.18 3.08
2598 2648 3.443052 TGGGTCGTTCCTATTCAGGTAA 58.557 45.455 0.00 0.00 43.18 2.85
2599 2649 3.839490 TGGGTCGTTCCTATTCAGGTAAA 59.161 43.478 0.00 0.00 43.18 2.01
2600 2650 4.472108 TGGGTCGTTCCTATTCAGGTAAAT 59.528 41.667 0.00 0.00 43.18 1.40
2601 2651 5.055144 GGGTCGTTCCTATTCAGGTAAATC 58.945 45.833 0.00 0.00 43.18 2.17
2602 2652 5.163332 GGGTCGTTCCTATTCAGGTAAATCT 60.163 44.000 0.00 0.00 43.18 2.40
2603 2653 6.041296 GGGTCGTTCCTATTCAGGTAAATCTA 59.959 42.308 0.00 0.00 43.18 1.98
2604 2654 7.418254 GGGTCGTTCCTATTCAGGTAAATCTAA 60.418 40.741 0.00 0.00 43.18 2.10
2605 2655 7.652507 GGTCGTTCCTATTCAGGTAAATCTAAG 59.347 40.741 0.00 0.00 43.18 2.18
2606 2656 8.196103 GTCGTTCCTATTCAGGTAAATCTAAGT 58.804 37.037 0.00 0.00 43.18 2.24
2607 2657 8.755977 TCGTTCCTATTCAGGTAAATCTAAGTT 58.244 33.333 0.00 0.00 43.18 2.66
2608 2658 9.379791 CGTTCCTATTCAGGTAAATCTAAGTTT 57.620 33.333 0.00 0.00 43.18 2.66
2630 2680 9.239551 AGTTTATTGGTAAAGGATTGTAGAACC 57.760 33.333 0.00 0.00 30.76 3.62
2631 2681 9.016438 GTTTATTGGTAAAGGATTGTAGAACCA 57.984 33.333 0.00 0.00 33.87 3.67
2632 2682 8.801882 TTATTGGTAAAGGATTGTAGAACCAG 57.198 34.615 0.00 0.00 36.90 4.00
2633 2683 5.836024 TGGTAAAGGATTGTAGAACCAGT 57.164 39.130 0.00 0.00 32.07 4.00
2634 2684 6.938698 TGGTAAAGGATTGTAGAACCAGTA 57.061 37.500 0.00 0.00 32.07 2.74
2635 2685 6.704310 TGGTAAAGGATTGTAGAACCAGTAC 58.296 40.000 0.00 0.00 32.07 2.73
2636 2686 6.111382 GGTAAAGGATTGTAGAACCAGTACC 58.889 44.000 0.00 0.00 32.46 3.34
2637 2687 6.070366 GGTAAAGGATTGTAGAACCAGTACCT 60.070 42.308 0.00 0.00 34.95 3.08
2638 2688 5.678955 AAGGATTGTAGAACCAGTACCTC 57.321 43.478 0.00 0.00 0.00 3.85
2639 2689 4.684724 AGGATTGTAGAACCAGTACCTCA 58.315 43.478 0.00 0.00 0.00 3.86
2640 2690 5.281314 AGGATTGTAGAACCAGTACCTCAT 58.719 41.667 0.00 0.00 0.00 2.90
2641 2691 5.364157 AGGATTGTAGAACCAGTACCTCATC 59.636 44.000 0.00 0.00 0.00 2.92
2642 2692 4.713824 TTGTAGAACCAGTACCTCATCG 57.286 45.455 0.00 0.00 0.00 3.84
2643 2693 3.021695 TGTAGAACCAGTACCTCATCGG 58.978 50.000 0.00 0.00 39.35 4.18
2644 2694 0.824759 AGAACCAGTACCTCATCGGC 59.175 55.000 0.00 0.00 35.61 5.54
2645 2695 0.535335 GAACCAGTACCTCATCGGCA 59.465 55.000 0.00 0.00 35.61 5.69
2646 2696 0.249398 AACCAGTACCTCATCGGCAC 59.751 55.000 0.00 0.00 35.61 5.01
2647 2697 0.902984 ACCAGTACCTCATCGGCACA 60.903 55.000 0.00 0.00 35.61 4.57
2648 2698 0.460284 CCAGTACCTCATCGGCACAC 60.460 60.000 0.00 0.00 35.61 3.82
2649 2699 0.246360 CAGTACCTCATCGGCACACA 59.754 55.000 0.00 0.00 35.61 3.72
2650 2700 0.246635 AGTACCTCATCGGCACACAC 59.753 55.000 0.00 0.00 35.61 3.82
2651 2701 0.246635 GTACCTCATCGGCACACACT 59.753 55.000 0.00 0.00 35.61 3.55
2652 2702 0.530744 TACCTCATCGGCACACACTC 59.469 55.000 0.00 0.00 35.61 3.51
2653 2703 1.293179 CCTCATCGGCACACACTCA 59.707 57.895 0.00 0.00 0.00 3.41
2654 2704 0.107993 CCTCATCGGCACACACTCAT 60.108 55.000 0.00 0.00 0.00 2.90
2655 2705 1.004595 CTCATCGGCACACACTCATG 58.995 55.000 0.00 0.00 0.00 3.07
2656 2706 0.391528 TCATCGGCACACACTCATGG 60.392 55.000 0.00 0.00 0.00 3.66
2657 2707 1.746615 ATCGGCACACACTCATGGC 60.747 57.895 0.00 0.00 38.00 4.40
2658 2708 2.189191 ATCGGCACACACTCATGGCT 62.189 55.000 0.00 0.00 39.16 4.75
2659 2709 1.968017 CGGCACACACTCATGGCTT 60.968 57.895 0.00 0.00 39.16 4.35
2660 2710 1.878775 GGCACACACTCATGGCTTC 59.121 57.895 0.00 0.00 38.32 3.86
2661 2711 0.607489 GGCACACACTCATGGCTTCT 60.607 55.000 0.00 0.00 38.32 2.85
2662 2712 0.520404 GCACACACTCATGGCTTCTG 59.480 55.000 0.00 0.00 0.00 3.02
2663 2713 0.520404 CACACACTCATGGCTTCTGC 59.480 55.000 0.00 0.00 38.76 4.26
2664 2714 0.952497 ACACACTCATGGCTTCTGCG 60.952 55.000 0.00 0.00 40.82 5.18
2665 2715 0.952497 CACACTCATGGCTTCTGCGT 60.952 55.000 0.00 0.00 40.82 5.24
2666 2716 0.250467 ACACTCATGGCTTCTGCGTT 60.250 50.000 0.00 0.00 40.82 4.84
2667 2717 0.877071 CACTCATGGCTTCTGCGTTT 59.123 50.000 0.00 0.00 40.82 3.60
2668 2718 1.267806 CACTCATGGCTTCTGCGTTTT 59.732 47.619 0.00 0.00 40.82 2.43
2669 2719 1.956477 ACTCATGGCTTCTGCGTTTTT 59.044 42.857 0.00 0.00 40.82 1.94
2670 2720 2.030805 ACTCATGGCTTCTGCGTTTTTC 60.031 45.455 0.00 0.00 40.82 2.29
2671 2721 1.952990 TCATGGCTTCTGCGTTTTTCA 59.047 42.857 0.00 0.00 40.82 2.69
2672 2722 2.030893 TCATGGCTTCTGCGTTTTTCAG 60.031 45.455 0.00 0.00 40.82 3.02
2673 2723 0.667993 TGGCTTCTGCGTTTTTCAGG 59.332 50.000 0.00 0.00 40.82 3.86
2674 2724 0.039165 GGCTTCTGCGTTTTTCAGGG 60.039 55.000 0.00 0.00 40.82 4.45
2675 2725 0.039165 GCTTCTGCGTTTTTCAGGGG 60.039 55.000 0.00 0.00 32.63 4.79
2676 2726 0.598065 CTTCTGCGTTTTTCAGGGGG 59.402 55.000 0.00 0.00 32.63 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
955 956 7.177216 CCTCCCATGCATATACAAATGTATGTT 59.823 37.037 14.74 1.73 44.05 2.71
975 976 0.324738 CTCTGTAGAGTGGCCTCCCA 60.325 60.000 3.32 0.00 38.58 4.37
987 988 3.620374 CAGTAGCCATGTTTGCTCTGTAG 59.380 47.826 0.00 0.00 40.23 2.74
989 990 2.038952 TCAGTAGCCATGTTTGCTCTGT 59.961 45.455 14.86 0.00 40.23 3.41
990 991 2.703416 TCAGTAGCCATGTTTGCTCTG 58.297 47.619 0.00 6.82 40.23 3.35
991 992 3.423539 TTCAGTAGCCATGTTTGCTCT 57.576 42.857 0.00 0.00 40.23 4.09
1008 1009 5.664294 ATATTTTGCCAGCATGTCTTTCA 57.336 34.783 0.00 0.00 0.00 2.69
1014 1015 4.022603 TGGTGTATATTTTGCCAGCATGT 58.977 39.130 0.00 0.00 31.06 3.21
1026 1027 5.670485 TCGAACATTGCTCTGGTGTATATT 58.330 37.500 0.00 0.00 0.00 1.28
1040 1041 3.899734 TGTCCAAATTGCTCGAACATTG 58.100 40.909 0.00 0.00 0.00 2.82
1090 1091 7.937394 TGTTTTCCCTTTTTCTACCTCTTCTAG 59.063 37.037 0.00 0.00 0.00 2.43
1118 1119 0.463116 ACCCGTATGGATTGGAACGC 60.463 55.000 1.27 0.00 37.49 4.84
1119 1120 1.295792 CACCCGTATGGATTGGAACG 58.704 55.000 1.27 0.00 37.49 3.95
1123 1124 1.447317 GCTGCACCCGTATGGATTGG 61.447 60.000 1.27 0.00 37.49 3.16
1134 1135 3.071206 TCTCTCCGAGCTGCACCC 61.071 66.667 1.02 0.00 0.00 4.61
1136 1137 0.244994 TTTCTCTCTCCGAGCTGCAC 59.755 55.000 1.02 0.00 39.70 4.57
1143 1144 1.205655 CTGCACCATTTCTCTCTCCGA 59.794 52.381 0.00 0.00 0.00 4.55
1155 1156 3.956199 CCTTGTATGAAATCCTGCACCAT 59.044 43.478 0.00 0.00 0.00 3.55
1188 1189 1.375013 AAATTCGTCCCCACCGTCG 60.375 57.895 0.00 0.00 0.00 5.12
1197 1198 2.159627 ACATTCGCAGTCAAATTCGTCC 59.840 45.455 0.00 0.00 0.00 4.79
1200 1201 2.159430 TCCACATTCGCAGTCAAATTCG 59.841 45.455 0.00 0.00 0.00 3.34
1218 1219 2.374839 TCCCATGTGAGTGAATTGTCCA 59.625 45.455 0.00 0.00 0.00 4.02
1260 1261 9.736023 CCTTTTCAATGCTATGTTATTACCTTC 57.264 33.333 0.00 0.00 0.00 3.46
1267 1268 8.766994 ATACCACCTTTTCAATGCTATGTTAT 57.233 30.769 0.00 0.00 0.00 1.89
1274 1275 6.351286 GGATTGAATACCACCTTTTCAATGCT 60.351 38.462 16.72 0.00 46.19 3.79
1276 1277 6.035843 CGGATTGAATACCACCTTTTCAATG 58.964 40.000 13.16 0.00 45.35 2.82
1279 1302 4.013728 CCGGATTGAATACCACCTTTTCA 58.986 43.478 0.00 0.00 0.00 2.69
1299 1322 4.138817 CAAATTTCGTTTCGTCAGTACCG 58.861 43.478 0.00 0.00 0.00 4.02
1300 1323 4.901881 CACAAATTTCGTTTCGTCAGTACC 59.098 41.667 0.00 0.00 0.00 3.34
1308 1331 3.361644 CCTGCATCACAAATTTCGTTTCG 59.638 43.478 0.00 0.00 0.00 3.46
1350 1373 4.965119 ATGTTTCTTCGGTATTTCTGCC 57.035 40.909 0.00 0.00 0.00 4.85
1351 1374 8.276325 CACTATATGTTTCTTCGGTATTTCTGC 58.724 37.037 0.00 0.00 0.00 4.26
1371 1394 5.827756 TCTCTTGTCCACCTCTTCACTATA 58.172 41.667 0.00 0.00 0.00 1.31
1398 1421 1.690633 TGGAGGCAGGATGTCCCTC 60.691 63.158 0.00 0.00 46.31 4.30
1399 1422 1.997874 GTGGAGGCAGGATGTCCCT 60.998 63.158 0.00 0.00 46.31 4.20
1422 1445 1.429930 TGTCCTTCTGGTACTGGCAA 58.570 50.000 0.00 0.00 34.23 4.52
1423 1446 1.429930 TTGTCCTTCTGGTACTGGCA 58.570 50.000 0.00 0.00 34.23 4.92
1464 1487 7.984391 TGTACATATTGAAATGCCTGTAACTG 58.016 34.615 0.00 0.00 0.00 3.16
1506 1529 1.570857 TTGCATCCCCCATTCGGACT 61.571 55.000 0.00 0.00 30.39 3.85
1530 1553 1.835483 CGAGGCGGTCATATGCTTGC 61.835 60.000 0.00 1.17 0.00 4.01
1542 1565 2.954753 GAACAGTGCAACGAGGCGG 61.955 63.158 0.00 0.00 45.86 6.13
1548 1571 1.782569 CAATGCTTGAACAGTGCAACG 59.217 47.619 0.00 0.00 45.86 4.10
1589 1612 0.739561 GCCGTCTCTAATCTCCGTGT 59.260 55.000 0.00 0.00 0.00 4.49
1590 1613 0.030908 GGCCGTCTCTAATCTCCGTG 59.969 60.000 0.00 0.00 0.00 4.94
1591 1614 0.106619 AGGCCGTCTCTAATCTCCGT 60.107 55.000 0.00 0.00 0.00 4.69
1626 1649 5.105392 TGACAACAATCCCATTTTAGCCATC 60.105 40.000 0.00 0.00 0.00 3.51
1641 1665 3.801983 GCCGGATTTTGGTTGACAACAAT 60.802 43.478 19.58 10.76 39.19 2.71
1649 1673 1.669795 GCTTCTGCCGGATTTTGGTTG 60.670 52.381 5.05 0.00 0.00 3.77
1656 1680 0.531532 CGATCAGCTTCTGCCGGATT 60.532 55.000 5.05 0.00 40.80 3.01
1675 1699 3.305471 GGTCGCCATATCAGTTCCTAGTC 60.305 52.174 0.00 0.00 0.00 2.59
1683 1707 1.768275 TCCATTGGTCGCCATATCAGT 59.232 47.619 1.86 0.00 31.53 3.41
1684 1708 2.146342 GTCCATTGGTCGCCATATCAG 58.854 52.381 1.86 0.00 31.53 2.90
1704 1734 7.172019 TGAGTTGATATCATCGTTCATCAATGG 59.828 37.037 6.17 0.00 33.32 3.16
1710 1740 5.305386 TCCCTGAGTTGATATCATCGTTCAT 59.695 40.000 6.17 0.00 0.00 2.57
1814 1852 3.716353 TCAGCCCTTCATATGGAGCTTTA 59.284 43.478 5.37 0.00 31.83 1.85
1817 1855 1.698532 CTCAGCCCTTCATATGGAGCT 59.301 52.381 5.37 0.00 33.51 4.09
1859 1897 6.309980 GCTTATGTCCTTCTCATCGACATATG 59.690 42.308 9.29 0.00 44.65 1.78
1869 1907 4.461431 TGTAGTTCGCTTATGTCCTTCTCA 59.539 41.667 0.00 0.00 0.00 3.27
2006 2044 6.763135 ACAGACGCTCATACAATCACATATTT 59.237 34.615 0.00 0.00 0.00 1.40
2012 2050 4.421058 TGTACAGACGCTCATACAATCAC 58.579 43.478 0.00 0.00 0.00 3.06
2017 2055 4.450082 ACATTGTACAGACGCTCATACA 57.550 40.909 0.00 0.00 0.00 2.29
2026 2064 5.932303 ACACCTACATCAACATTGTACAGAC 59.068 40.000 0.00 0.00 0.00 3.51
2028 2067 6.650807 AGAACACCTACATCAACATTGTACAG 59.349 38.462 0.00 0.00 0.00 2.74
2033 2072 6.205464 ACAGAAGAACACCTACATCAACATTG 59.795 38.462 0.00 0.00 0.00 2.82
2086 2125 8.903820 AGAAGTTGACTAACACAAAGCTTAAAT 58.096 29.630 0.00 0.00 39.30 1.40
2091 2130 5.525378 CAGAGAAGTTGACTAACACAAAGCT 59.475 40.000 0.00 0.00 39.30 3.74
2094 2133 7.915293 TTTCAGAGAAGTTGACTAACACAAA 57.085 32.000 0.00 0.00 39.30 2.83
2103 2142 6.710744 TGGAGGTATTTTTCAGAGAAGTTGAC 59.289 38.462 0.00 0.00 0.00 3.18
2105 2144 6.150140 CCTGGAGGTATTTTTCAGAGAAGTTG 59.850 42.308 0.00 0.00 0.00 3.16
2118 2157 3.421844 GCAAGTTGTCCTGGAGGTATTT 58.578 45.455 4.48 0.00 36.34 1.40
2123 2162 0.322008 GAGGCAAGTTGTCCTGGAGG 60.322 60.000 19.49 0.00 31.71 4.30
2126 2165 1.239968 GCAGAGGCAAGTTGTCCTGG 61.240 60.000 19.49 13.54 40.72 4.45
2127 2166 0.250640 AGCAGAGGCAAGTTGTCCTG 60.251 55.000 19.49 18.12 44.61 3.86
2128 2167 0.475906 AAGCAGAGGCAAGTTGTCCT 59.524 50.000 15.89 15.89 44.61 3.85
2129 2168 0.877743 GAAGCAGAGGCAAGTTGTCC 59.122 55.000 3.25 6.05 44.61 4.02
2130 2169 1.889545 AGAAGCAGAGGCAAGTTGTC 58.110 50.000 0.00 0.00 44.61 3.18
2131 2170 2.225467 GAAGAAGCAGAGGCAAGTTGT 58.775 47.619 4.48 0.00 44.61 3.32
2132 2171 1.538950 GGAAGAAGCAGAGGCAAGTTG 59.461 52.381 0.00 0.00 44.61 3.16
2133 2172 1.546548 GGGAAGAAGCAGAGGCAAGTT 60.547 52.381 0.00 0.00 44.61 2.66
2134 2173 0.037447 GGGAAGAAGCAGAGGCAAGT 59.963 55.000 0.00 0.00 44.61 3.16
2140 2179 2.294078 ACCCGGGGAAGAAGCAGAG 61.294 63.158 27.92 0.00 0.00 3.35
2144 2183 0.255033 AATACACCCGGGGAAGAAGC 59.745 55.000 27.92 0.00 0.00 3.86
2146 2185 1.706305 ACAAATACACCCGGGGAAGAA 59.294 47.619 27.92 5.50 0.00 2.52
2148 2187 2.209690 AACAAATACACCCGGGGAAG 57.790 50.000 27.92 16.98 0.00 3.46
2149 2188 2.240279 CAAACAAATACACCCGGGGAA 58.760 47.619 27.92 10.13 0.00 3.97
2152 2191 0.109504 CGCAAACAAATACACCCGGG 60.110 55.000 22.25 22.25 0.00 5.73
2154 2193 2.287069 TGTTCGCAAACAAATACACCCG 60.287 45.455 0.00 0.00 42.34 5.28
2183 2222 7.385267 AGCCAGCAAAATATTTGTCAACAATA 58.615 30.769 0.39 0.00 35.55 1.90
2184 2223 6.232692 AGCCAGCAAAATATTTGTCAACAAT 58.767 32.000 0.39 0.00 35.55 2.71
2185 2224 5.609423 AGCCAGCAAAATATTTGTCAACAA 58.391 33.333 0.39 0.00 0.00 2.83
2187 2226 6.620678 TCTAGCCAGCAAAATATTTGTCAAC 58.379 36.000 0.39 0.00 0.00 3.18
2188 2227 6.832520 TCTAGCCAGCAAAATATTTGTCAA 57.167 33.333 0.39 0.00 0.00 3.18
2189 2228 6.434028 AGTTCTAGCCAGCAAAATATTTGTCA 59.566 34.615 0.39 0.00 0.00 3.58
2190 2229 6.856895 AGTTCTAGCCAGCAAAATATTTGTC 58.143 36.000 0.39 0.00 0.00 3.18
2191 2230 6.840780 AGTTCTAGCCAGCAAAATATTTGT 57.159 33.333 0.39 0.00 0.00 2.83
2192 2231 7.599998 ACAAAGTTCTAGCCAGCAAAATATTTG 59.400 33.333 0.39 0.00 0.00 2.32
2193 2232 7.670364 ACAAAGTTCTAGCCAGCAAAATATTT 58.330 30.769 0.00 0.00 0.00 1.40
2198 2237 6.096282 AGTTAACAAAGTTCTAGCCAGCAAAA 59.904 34.615 8.61 0.00 0.00 2.44
2208 2247 9.832445 AGTCTTCATTCAGTTAACAAAGTTCTA 57.168 29.630 8.61 0.00 0.00 2.10
2210 2249 9.439537 GAAGTCTTCATTCAGTTAACAAAGTTC 57.560 33.333 8.61 0.00 0.00 3.01
2217 2256 9.660180 ATCCTTAGAAGTCTTCATTCAGTTAAC 57.340 33.333 14.97 0.00 0.00 2.01
2220 2259 7.684529 ACATCCTTAGAAGTCTTCATTCAGTT 58.315 34.615 14.97 0.00 0.00 3.16
2222 2261 8.474025 ACTACATCCTTAGAAGTCTTCATTCAG 58.526 37.037 14.97 4.74 0.00 3.02
2239 2278 8.052748 TGCCAACAATAATTCTAACTACATCCT 58.947 33.333 0.00 0.00 0.00 3.24
2240 2279 8.220755 TGCCAACAATAATTCTAACTACATCC 57.779 34.615 0.00 0.00 0.00 3.51
2265 2305 0.810031 GATCTGCACCACGGCGTATT 60.810 55.000 14.22 0.00 36.28 1.89
2269 2309 2.512286 ATGATCTGCACCACGGCG 60.512 61.111 4.80 4.80 36.28 6.46
2270 2310 2.475466 CCATGATCTGCACCACGGC 61.475 63.158 0.00 0.00 0.00 5.68
2275 2315 2.634815 ACATCTCCATGATCTGCACC 57.365 50.000 0.00 0.00 33.72 5.01
2281 2321 4.001652 CAGCCACATACATCTCCATGATC 58.998 47.826 0.00 0.00 33.72 2.92
2283 2323 2.105306 CCAGCCACATACATCTCCATGA 59.895 50.000 0.00 0.00 33.72 3.07
2284 2324 2.158711 ACCAGCCACATACATCTCCATG 60.159 50.000 0.00 0.00 35.92 3.66
2290 2332 3.141398 CACCATACCAGCCACATACATC 58.859 50.000 0.00 0.00 0.00 3.06
2291 2333 2.749466 GCACCATACCAGCCACATACAT 60.749 50.000 0.00 0.00 0.00 2.29
2297 2339 1.881973 CATATGCACCATACCAGCCAC 59.118 52.381 0.00 0.00 0.00 5.01
2298 2340 1.494296 ACATATGCACCATACCAGCCA 59.506 47.619 1.58 0.00 0.00 4.75
2300 2342 4.761739 ACATTACATATGCACCATACCAGC 59.238 41.667 1.58 0.00 0.00 4.85
2301 2343 7.977789 TTACATTACATATGCACCATACCAG 57.022 36.000 1.58 0.00 0.00 4.00
2317 2359 6.912591 GCTGCCAGTGTCATTAATTACATTAC 59.087 38.462 5.79 0.00 0.00 1.89
2332 2382 2.359107 CGTCCATGCTGCCAGTGT 60.359 61.111 0.00 0.00 0.00 3.55
2333 2383 2.359107 ACGTCCATGCTGCCAGTG 60.359 61.111 0.00 0.00 0.00 3.66
2334 2384 2.189191 ATCACGTCCATGCTGCCAGT 62.189 55.000 0.00 0.00 0.00 4.00
2336 2386 0.608856 AAATCACGTCCATGCTGCCA 60.609 50.000 0.00 0.00 0.00 4.92
2337 2387 0.527565 AAAATCACGTCCATGCTGCC 59.472 50.000 0.00 0.00 0.00 4.85
2338 2388 3.365832 CATAAAATCACGTCCATGCTGC 58.634 45.455 0.00 0.00 0.00 5.25
2400 2450 3.348647 TCCCGCTCATCTGATTCAAAA 57.651 42.857 0.00 0.00 0.00 2.44
2408 2458 2.664185 CGCCATCCCGCTCATCTG 60.664 66.667 0.00 0.00 0.00 2.90
2411 2461 4.241555 GGACGCCATCCCGCTCAT 62.242 66.667 0.00 0.00 42.46 2.90
2431 2481 2.158755 CCTCCCCTTTATGTACAGCCTG 60.159 54.545 0.33 0.00 0.00 4.85
2437 2487 1.844497 AGGCACCTCCCCTTTATGTAC 59.156 52.381 0.00 0.00 34.51 2.90
2459 2509 1.657538 CGTTCGTCTGCTTTCTTGCAC 60.658 52.381 0.00 0.00 38.12 4.57
2465 2515 2.561976 CAGTTCGTTCGTCTGCTTTC 57.438 50.000 0.00 0.00 0.00 2.62
2471 2521 0.387929 TCCAAGCAGTTCGTTCGTCT 59.612 50.000 0.00 0.00 0.00 4.18
2474 2524 1.493311 GCTCCAAGCAGTTCGTTCG 59.507 57.895 0.00 0.00 41.89 3.95
2484 2534 2.093447 TCTTAGCCTACTTGCTCCAAGC 60.093 50.000 4.96 0.00 44.43 4.01
2488 2538 4.153411 TCCTATCTTAGCCTACTTGCTCC 58.847 47.826 0.00 0.00 41.68 4.70
2499 2549 4.033709 TCCATATGGCCTCCTATCTTAGC 58.966 47.826 17.58 0.00 34.44 3.09
2500 2550 5.901853 TGATCCATATGGCCTCCTATCTTAG 59.098 44.000 17.58 0.00 34.44 2.18
2502 2552 4.703299 TGATCCATATGGCCTCCTATCTT 58.297 43.478 17.58 0.00 34.44 2.40
2510 2560 2.991713 ACCATTCTGATCCATATGGCCT 59.008 45.455 17.58 6.62 40.96 5.19
2530 2580 3.376546 GGTCAATGCAGAGATGGAGAAAC 59.623 47.826 0.00 0.00 0.00 2.78
2534 2584 2.562635 CTGGTCAATGCAGAGATGGAG 58.437 52.381 0.00 0.00 0.00 3.86
2543 2593 3.701205 TCTTTAGAGCTGGTCAATGCA 57.299 42.857 9.78 0.00 0.00 3.96
2548 2598 3.517100 AGAGCAATCTTTAGAGCTGGTCA 59.483 43.478 18.34 0.00 39.14 4.02
2549 2599 4.135747 AGAGCAATCTTTAGAGCTGGTC 57.864 45.455 0.00 12.43 37.48 4.02
2550 2600 5.885449 ATAGAGCAATCTTTAGAGCTGGT 57.115 39.130 0.00 0.00 37.48 4.00
2551 2601 5.700373 GGAATAGAGCAATCTTTAGAGCTGG 59.300 44.000 0.00 0.00 37.48 4.85
2552 2602 5.700373 GGGAATAGAGCAATCTTTAGAGCTG 59.300 44.000 0.00 0.00 37.48 4.24
2553 2603 5.606329 AGGGAATAGAGCAATCTTTAGAGCT 59.394 40.000 0.00 0.00 40.60 4.09
2554 2604 5.700373 CAGGGAATAGAGCAATCTTTAGAGC 59.300 44.000 0.00 0.00 0.00 4.09
2555 2605 6.229733 CCAGGGAATAGAGCAATCTTTAGAG 58.770 44.000 0.00 0.00 0.00 2.43
2556 2606 5.072329 CCCAGGGAATAGAGCAATCTTTAGA 59.928 44.000 0.00 0.00 0.00 2.10
2557 2607 5.163152 ACCCAGGGAATAGAGCAATCTTTAG 60.163 44.000 14.54 0.00 0.00 1.85
2558 2608 4.726825 ACCCAGGGAATAGAGCAATCTTTA 59.273 41.667 14.54 0.00 0.00 1.85
2559 2609 3.529319 ACCCAGGGAATAGAGCAATCTTT 59.471 43.478 14.54 0.00 0.00 2.52
2560 2610 3.126453 ACCCAGGGAATAGAGCAATCTT 58.874 45.455 14.54 0.00 0.00 2.40
2561 2611 2.708325 GACCCAGGGAATAGAGCAATCT 59.292 50.000 14.54 0.00 0.00 2.40
2562 2612 2.548920 CGACCCAGGGAATAGAGCAATC 60.549 54.545 14.54 0.00 0.00 2.67
2563 2613 1.417890 CGACCCAGGGAATAGAGCAAT 59.582 52.381 14.54 0.00 0.00 3.56
2564 2614 0.830648 CGACCCAGGGAATAGAGCAA 59.169 55.000 14.54 0.00 0.00 3.91
2565 2615 0.325296 ACGACCCAGGGAATAGAGCA 60.325 55.000 14.54 0.00 0.00 4.26
2566 2616 0.831307 AACGACCCAGGGAATAGAGC 59.169 55.000 14.54 0.00 0.00 4.09
2567 2617 1.413077 GGAACGACCCAGGGAATAGAG 59.587 57.143 14.54 0.00 0.00 2.43
2568 2618 1.007963 AGGAACGACCCAGGGAATAGA 59.992 52.381 14.54 0.00 40.05 1.98
2569 2619 1.497161 AGGAACGACCCAGGGAATAG 58.503 55.000 14.54 2.43 40.05 1.73
2570 2620 2.852714 TAGGAACGACCCAGGGAATA 57.147 50.000 14.54 0.00 40.05 1.75
2571 2621 2.191981 ATAGGAACGACCCAGGGAAT 57.808 50.000 14.54 0.00 40.05 3.01
2572 2622 1.835531 GAATAGGAACGACCCAGGGAA 59.164 52.381 14.54 0.00 40.05 3.97
2573 2623 1.273381 TGAATAGGAACGACCCAGGGA 60.273 52.381 14.54 0.00 40.05 4.20
2574 2624 1.139058 CTGAATAGGAACGACCCAGGG 59.861 57.143 2.85 2.85 40.05 4.45
2575 2625 2.604046 CTGAATAGGAACGACCCAGG 57.396 55.000 0.00 0.00 40.05 4.45
2604 2654 9.239551 GGTTCTACAATCCTTTACCAATAAACT 57.760 33.333 0.00 0.00 0.00 2.66
2605 2655 9.016438 TGGTTCTACAATCCTTTACCAATAAAC 57.984 33.333 0.00 0.00 31.71 2.01
2606 2656 9.238368 CTGGTTCTACAATCCTTTACCAATAAA 57.762 33.333 0.00 0.00 34.12 1.40
2607 2657 8.387813 ACTGGTTCTACAATCCTTTACCAATAA 58.612 33.333 0.00 0.00 34.12 1.40
2608 2658 7.924541 ACTGGTTCTACAATCCTTTACCAATA 58.075 34.615 0.00 0.00 34.12 1.90
2609 2659 6.790319 ACTGGTTCTACAATCCTTTACCAAT 58.210 36.000 0.00 0.00 34.12 3.16
2610 2660 6.195600 ACTGGTTCTACAATCCTTTACCAA 57.804 37.500 0.00 0.00 34.12 3.67
2611 2661 5.836024 ACTGGTTCTACAATCCTTTACCA 57.164 39.130 0.00 0.00 33.50 3.25
2612 2662 6.070366 AGGTACTGGTTCTACAATCCTTTACC 60.070 42.308 0.00 0.00 37.18 2.85
2613 2663 6.944096 AGGTACTGGTTCTACAATCCTTTAC 58.056 40.000 0.00 0.00 37.18 2.01
2614 2664 6.727231 TGAGGTACTGGTTCTACAATCCTTTA 59.273 38.462 0.00 0.00 41.55 1.85
2615 2665 5.546499 TGAGGTACTGGTTCTACAATCCTTT 59.454 40.000 0.00 0.00 41.55 3.11
2616 2666 5.091552 TGAGGTACTGGTTCTACAATCCTT 58.908 41.667 0.00 0.00 41.55 3.36
2617 2667 4.684724 TGAGGTACTGGTTCTACAATCCT 58.315 43.478 0.00 0.00 41.55 3.24
2618 2668 5.602628 GATGAGGTACTGGTTCTACAATCC 58.397 45.833 0.00 0.00 41.55 3.01
2619 2669 5.282510 CGATGAGGTACTGGTTCTACAATC 58.717 45.833 0.00 0.00 41.55 2.67
2620 2670 4.099573 CCGATGAGGTACTGGTTCTACAAT 59.900 45.833 0.00 0.00 41.55 2.71
2621 2671 3.446161 CCGATGAGGTACTGGTTCTACAA 59.554 47.826 0.00 0.00 41.55 2.41
2622 2672 3.021695 CCGATGAGGTACTGGTTCTACA 58.978 50.000 0.00 0.00 41.55 2.74
2623 2673 2.223758 GCCGATGAGGTACTGGTTCTAC 60.224 54.545 0.00 0.00 41.55 2.59
2624 2674 2.029623 GCCGATGAGGTACTGGTTCTA 58.970 52.381 0.00 0.00 41.55 2.10
2625 2675 0.824759 GCCGATGAGGTACTGGTTCT 59.175 55.000 0.00 0.00 41.55 3.01
2626 2676 0.535335 TGCCGATGAGGTACTGGTTC 59.465 55.000 0.00 0.00 41.55 3.62
2627 2677 2.678786 TGCCGATGAGGTACTGGTT 58.321 52.632 0.00 0.00 41.55 3.67
2628 2678 4.453454 TGCCGATGAGGTACTGGT 57.547 55.556 0.00 0.00 41.55 4.00
2633 2683 0.530744 GAGTGTGTGCCGATGAGGTA 59.469 55.000 0.00 0.00 43.70 3.08
2634 2684 1.293498 GAGTGTGTGCCGATGAGGT 59.707 57.895 0.00 0.00 43.70 3.85
2635 2685 0.107993 ATGAGTGTGTGCCGATGAGG 60.108 55.000 0.00 0.00 44.97 3.86
2636 2686 1.004595 CATGAGTGTGTGCCGATGAG 58.995 55.000 0.00 0.00 0.00 2.90
2637 2687 0.391528 CCATGAGTGTGTGCCGATGA 60.392 55.000 0.00 0.00 0.00 2.92
2638 2688 1.985447 GCCATGAGTGTGTGCCGATG 61.985 60.000 0.00 0.00 0.00 3.84
2639 2689 1.746615 GCCATGAGTGTGTGCCGAT 60.747 57.895 0.00 0.00 0.00 4.18
2640 2690 2.358615 GCCATGAGTGTGTGCCGA 60.359 61.111 0.00 0.00 0.00 5.54
2641 2691 1.915614 GAAGCCATGAGTGTGTGCCG 61.916 60.000 0.00 0.00 0.00 5.69
2642 2692 0.607489 AGAAGCCATGAGTGTGTGCC 60.607 55.000 0.00 0.00 0.00 5.01
2643 2693 0.520404 CAGAAGCCATGAGTGTGTGC 59.480 55.000 0.00 0.00 0.00 4.57
2644 2694 0.520404 GCAGAAGCCATGAGTGTGTG 59.480 55.000 0.00 0.00 33.58 3.82
2645 2695 0.952497 CGCAGAAGCCATGAGTGTGT 60.952 55.000 0.00 0.00 37.52 3.72
2646 2696 0.952497 ACGCAGAAGCCATGAGTGTG 60.952 55.000 0.00 0.00 37.52 3.82
2647 2697 0.250467 AACGCAGAAGCCATGAGTGT 60.250 50.000 0.00 0.00 37.52 3.55
2648 2698 0.877071 AAACGCAGAAGCCATGAGTG 59.123 50.000 0.00 0.00 37.52 3.51
2649 2699 1.609208 AAAACGCAGAAGCCATGAGT 58.391 45.000 0.00 0.00 37.52 3.41
2650 2700 2.030893 TGAAAAACGCAGAAGCCATGAG 60.031 45.455 0.00 0.00 37.52 2.90
2651 2701 1.952990 TGAAAAACGCAGAAGCCATGA 59.047 42.857 0.00 0.00 37.52 3.07
2652 2702 2.322161 CTGAAAAACGCAGAAGCCATG 58.678 47.619 0.00 0.00 37.52 3.66
2653 2703 1.270550 CCTGAAAAACGCAGAAGCCAT 59.729 47.619 0.00 0.00 37.52 4.40
2654 2704 0.667993 CCTGAAAAACGCAGAAGCCA 59.332 50.000 0.00 0.00 37.52 4.75
2655 2705 0.039165 CCCTGAAAAACGCAGAAGCC 60.039 55.000 0.00 0.00 37.52 4.35
2656 2706 0.039165 CCCCTGAAAAACGCAGAAGC 60.039 55.000 0.00 0.00 35.39 3.86
2657 2707 0.598065 CCCCCTGAAAAACGCAGAAG 59.402 55.000 0.00 0.00 35.39 2.85
2658 2708 2.727103 CCCCCTGAAAAACGCAGAA 58.273 52.632 0.00 0.00 35.39 3.02
2659 2709 4.492604 CCCCCTGAAAAACGCAGA 57.507 55.556 0.00 0.00 35.39 4.26


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

AutoCloner maintained by Alex Coulton.