Multiple sequence alignment - TraesCS3B01G247300

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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 TraesCS3B01G247300 chr3B 100.000 2825 0 0 1 2825 393228972 393231796 0.000000e+00 5217.0
1 TraesCS3B01G247300 chr3A 89.883 1878 117 30 1 1855 395761019 395762846 0.000000e+00 2348.0
2 TraesCS3B01G247300 chr3D 88.479 1328 59 33 4 1325 298058882 298060121 0.000000e+00 1519.0
3 TraesCS3B01G247300 chr3D 91.250 640 44 8 1234 1865 298060134 298060769 0.000000e+00 861.0
4 TraesCS3B01G247300 chr7B 93.644 472 26 3 2356 2825 728138865 728138396 0.000000e+00 702.0
5 TraesCS3B01G247300 chr7B 92.647 272 19 1 1880 2150 728139125 728138854 9.490000e-105 390.0
6 TraesCS3B01G247300 chr7B 77.922 308 52 13 1846 2150 181043623 181043917 8.040000e-41 178.0
7 TraesCS3B01G247300 chr2B 93.817 469 26 2 2356 2822 92505605 92506072 0.000000e+00 702.0
8 TraesCS3B01G247300 chr2B 93.092 304 20 1 1848 2150 92505313 92505616 7.180000e-121 444.0
9 TraesCS3B01G247300 chr2B 91.429 70 5 1 1846 1914 195495390 195495459 8.330000e-16 95.3
10 TraesCS3B01G247300 chr4B 93.162 468 28 4 2356 2821 617759625 617759160 0.000000e+00 684.0
11 TraesCS3B01G247300 chr4B 92.926 311 16 2 1846 2150 617759924 617759614 5.550000e-122 448.0
12 TraesCS3B01G247300 chrUn 89.765 469 44 4 2356 2822 58868525 58868991 5.210000e-167 597.0
13 TraesCS3B01G247300 chrUn 83.062 307 38 7 1846 2150 58868242 58868536 1.670000e-67 267.0
14 TraesCS3B01G247300 chr5A 89.894 188 16 1 1846 2030 30912249 30912436 3.640000e-59 239.0
15 TraesCS3B01G247300 chr6A 81.311 305 43 8 1848 2150 6842673 6842381 4.700000e-58 235.0


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 TraesCS3B01G247300 chr3B 393228972 393231796 2824 False 5217 5217 100.0000 1 2825 1 chr3B.!!$F1 2824
1 TraesCS3B01G247300 chr3A 395761019 395762846 1827 False 2348 2348 89.8830 1 1855 1 chr3A.!!$F1 1854
2 TraesCS3B01G247300 chr3D 298058882 298060769 1887 False 1190 1519 89.8645 4 1865 2 chr3D.!!$F1 1861
3 TraesCS3B01G247300 chr7B 728138396 728139125 729 True 546 702 93.1455 1880 2825 2 chr7B.!!$R1 945
4 TraesCS3B01G247300 chr2B 92505313 92506072 759 False 573 702 93.4545 1848 2822 2 chr2B.!!$F2 974
5 TraesCS3B01G247300 chr4B 617759160 617759924 764 True 566 684 93.0440 1846 2821 2 chr4B.!!$R1 975
6 TraesCS3B01G247300 chrUn 58868242 58868991 749 False 432 597 86.4135 1846 2822 2 chrUn.!!$F1 976

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
996 1008 0.392461 GTTGGATTCACGGCCTGCTA 60.392 55.0 0.0 0.0 0.0 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2206 2359 0.031917 TACATTGGCCTCTACCCGGA 60.032 55.0 0.73 0.0 0.0 5.14 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
63 66 2.915869 CCCGTGTATTCCCTGGGG 59.084 66.667 14.00 2.42 36.16 4.96
81 84 1.685148 GGGAACTCCAATCCATGCTC 58.315 55.000 0.00 0.00 38.80 4.26
96 99 1.521457 GCTCGACGGGATGATGCAA 60.521 57.895 0.00 0.00 0.00 4.08
140 143 0.595095 CCACCAAGCAGCTTCTTCAC 59.405 55.000 4.07 0.00 0.00 3.18
148 151 1.302033 AGCTTCTTCACCAGCACCG 60.302 57.895 0.00 0.00 38.61 4.94
380 383 1.548357 TTGCAGAGACTGGGAGAGCC 61.548 60.000 0.00 0.00 31.21 4.70
390 393 0.547471 TGGGAGAGCCATTCACAGGA 60.547 55.000 0.00 0.00 35.15 3.86
392 395 1.680249 GGGAGAGCCATTCACAGGAAC 60.680 57.143 0.00 0.00 35.46 3.62
404 407 4.421479 AGGAACCGTCGAGCGCTG 62.421 66.667 18.48 7.71 39.71 5.18
483 486 9.205719 GGAATAAAGAAGACGGTAGATATTTCC 57.794 37.037 0.00 0.00 0.00 3.13
527 530 8.115490 AGGATCTCCATTGTTAGTTTTTCTTG 57.885 34.615 0.00 0.00 38.89 3.02
717 722 2.308866 CCCCCACTTGTTATCTGGTTCT 59.691 50.000 0.00 0.00 0.00 3.01
721 726 4.504864 CCCACTTGTTATCTGGTTCTGTCA 60.505 45.833 0.00 0.00 0.00 3.58
722 727 5.063204 CCACTTGTTATCTGGTTCTGTCAA 58.937 41.667 0.00 0.00 0.00 3.18
723 728 5.180117 CCACTTGTTATCTGGTTCTGTCAAG 59.820 44.000 0.00 0.00 37.58 3.02
726 731 5.290493 TGTTATCTGGTTCTGTCAAGTGT 57.710 39.130 0.00 0.00 0.00 3.55
730 735 3.531538 TCTGGTTCTGTCAAGTGTCAAC 58.468 45.455 0.00 0.00 0.00 3.18
786 794 4.012374 ACTTACAACGAGGACCGAATAGA 58.988 43.478 0.00 0.00 41.76 1.98
787 795 4.643784 ACTTACAACGAGGACCGAATAGAT 59.356 41.667 0.00 0.00 41.76 1.98
788 796 5.126707 ACTTACAACGAGGACCGAATAGATT 59.873 40.000 0.00 0.00 41.76 2.40
801 813 7.117379 GGACCGAATAGATTATTACCTTTTCCG 59.883 40.741 0.00 0.00 0.00 4.30
803 815 7.440255 ACCGAATAGATTATTACCTTTTCCGTG 59.560 37.037 0.00 0.00 0.00 4.94
824 836 8.020819 TCCGTGAAAAAGAAATTGCACTAATAG 58.979 33.333 0.00 0.00 0.00 1.73
919 931 2.348411 GCACCAGCATACCAATACCT 57.652 50.000 0.00 0.00 41.58 3.08
920 932 1.949525 GCACCAGCATACCAATACCTG 59.050 52.381 0.00 0.00 41.58 4.00
942 954 5.433526 TGTTTAGGATATGCACCAGTAACC 58.566 41.667 0.00 0.00 0.00 2.85
946 958 3.780294 AGGATATGCACCAGTAACCAAGA 59.220 43.478 0.00 0.00 0.00 3.02
975 987 6.761714 GGTTATCCAGTTCATATATAAGGCGG 59.238 42.308 0.00 0.00 0.00 6.13
993 1005 1.586154 GGTGTTGGATTCACGGCCTG 61.586 60.000 0.00 0.00 36.76 4.85
996 1008 0.392461 GTTGGATTCACGGCCTGCTA 60.392 55.000 0.00 0.00 0.00 3.49
998 1010 0.392461 TGGATTCACGGCCTGCTAAC 60.392 55.000 0.00 0.00 0.00 2.34
999 1011 0.107654 GGATTCACGGCCTGCTAACT 60.108 55.000 0.00 0.00 0.00 2.24
1000 1012 1.138266 GGATTCACGGCCTGCTAACTA 59.862 52.381 0.00 0.00 0.00 2.24
1058 1071 0.984230 GCCCCTCCGGATGATGATAA 59.016 55.000 3.57 0.00 0.00 1.75
1059 1072 1.065854 GCCCCTCCGGATGATGATAAG 60.066 57.143 3.57 0.00 0.00 1.73
1072 1085 5.426689 TGATGATAAGCCTGGTATCCATC 57.573 43.478 0.00 0.00 30.82 3.51
1079 1092 2.158696 AGCCTGGTATCCATCTCTTTGC 60.159 50.000 0.00 0.00 30.82 3.68
1201 1214 3.252284 CACCACCCAGCACCTCCT 61.252 66.667 0.00 0.00 0.00 3.69
1202 1215 3.252284 ACCACCCAGCACCTCCTG 61.252 66.667 0.00 0.00 0.00 3.86
1203 1216 2.930019 CCACCCAGCACCTCCTGA 60.930 66.667 0.00 0.00 34.77 3.86
1204 1217 2.667418 CACCCAGCACCTCCTGAG 59.333 66.667 0.00 0.00 34.77 3.35
1205 1218 3.325753 ACCCAGCACCTCCTGAGC 61.326 66.667 0.00 0.00 34.77 4.26
1206 1219 3.324930 CCCAGCACCTCCTGAGCA 61.325 66.667 0.00 0.00 34.77 4.26
1207 1220 2.046507 CCAGCACCTCCTGAGCAC 60.047 66.667 0.00 0.00 34.77 4.40
1208 1221 2.433838 CAGCACCTCCTGAGCACG 60.434 66.667 0.00 0.00 34.77 5.34
1209 1222 2.601666 AGCACCTCCTGAGCACGA 60.602 61.111 0.00 0.00 0.00 4.35
1210 1223 2.210013 AGCACCTCCTGAGCACGAA 61.210 57.895 0.00 0.00 0.00 3.85
1211 1224 1.078848 GCACCTCCTGAGCACGAAT 60.079 57.895 0.00 0.00 0.00 3.34
1212 1225 0.175760 GCACCTCCTGAGCACGAATA 59.824 55.000 0.00 0.00 0.00 1.75
1213 1226 1.927895 CACCTCCTGAGCACGAATAC 58.072 55.000 0.00 0.00 0.00 1.89
1214 1227 1.204704 CACCTCCTGAGCACGAATACA 59.795 52.381 0.00 0.00 0.00 2.29
1215 1228 1.899814 ACCTCCTGAGCACGAATACAA 59.100 47.619 0.00 0.00 0.00 2.41
1216 1229 2.301870 ACCTCCTGAGCACGAATACAAA 59.698 45.455 0.00 0.00 0.00 2.83
1222 1235 4.442706 CTGAGCACGAATACAAATACCCT 58.557 43.478 0.00 0.00 0.00 4.34
1285 1424 2.229928 AAAGCCTGAGCCTGAGCCT 61.230 57.895 0.00 0.00 41.25 4.58
1286 1425 2.481307 AAAGCCTGAGCCTGAGCCTG 62.481 60.000 0.00 0.00 41.25 4.85
1291 1430 3.397439 GAGCCTGAGCCTGAGCCA 61.397 66.667 0.00 0.00 41.25 4.75
1292 1431 2.932194 AGCCTGAGCCTGAGCCAA 60.932 61.111 0.00 0.00 41.25 4.52
1339 1478 0.683504 CACAGTACTACCCGCCTCCT 60.684 60.000 0.00 0.00 0.00 3.69
1344 1483 4.835891 CTACCCGCCTCCTCCGGT 62.836 72.222 0.00 0.00 44.13 5.28
1456 1598 2.990395 TACCCGTACGTGCAGCCA 60.990 61.111 15.21 0.00 0.00 4.75
1507 1649 1.227263 GCAGATGTACCCGCGTGAT 60.227 57.895 4.92 0.00 0.00 3.06
1565 1707 2.233271 GTCGTGGGATATCCTCCGTAA 58.767 52.381 21.18 6.36 46.01 3.18
1616 1758 5.453339 GGGCTACTGTCACTGCTCATATAAA 60.453 44.000 0.00 0.00 0.00 1.40
1744 1889 9.390795 CTTCATTTCAAATGTGTAACTCTGAAG 57.609 33.333 9.98 0.00 38.04 3.02
1785 1930 6.153067 TGTTGAACTTTGAATTTGTTCGTGT 58.847 32.000 0.00 0.00 41.88 4.49
1790 1935 6.184580 ACTTTGAATTTGTTCGTGTGTGTA 57.815 33.333 0.00 0.00 0.00 2.90
1813 1958 3.693654 TGCAACTGCGCATATTTGTATG 58.306 40.909 12.24 7.44 45.83 2.39
1840 1985 7.746475 GTGAAAATAAATTCCAGTGAGTTCTCG 59.254 37.037 0.00 0.00 0.00 4.04
1841 1986 7.444183 TGAAAATAAATTCCAGTGAGTTCTCGT 59.556 33.333 0.00 0.00 0.00 4.18
1842 1987 6.969828 AATAAATTCCAGTGAGTTCTCGTC 57.030 37.500 0.00 0.00 0.00 4.20
1843 1988 4.608948 AAATTCCAGTGAGTTCTCGTCT 57.391 40.909 0.00 0.00 0.00 4.18
1844 1989 3.859411 ATTCCAGTGAGTTCTCGTCTC 57.141 47.619 0.00 0.00 0.00 3.36
1941 2092 9.113876 GTGATGTTACAAATTACAGTTTACAGC 57.886 33.333 0.00 0.00 0.00 4.40
2066 2218 1.392710 CGTCTCCCCGAAGCATACCT 61.393 60.000 0.00 0.00 0.00 3.08
2138 2291 1.377202 GGAAGGTGAAGCGCCATCA 60.377 57.895 2.29 6.59 33.98 3.07
2139 2292 0.960364 GGAAGGTGAAGCGCCATCAA 60.960 55.000 14.32 0.00 33.98 2.57
2140 2293 0.881118 GAAGGTGAAGCGCCATCAAA 59.119 50.000 14.32 0.00 36.32 2.69
2141 2294 0.883833 AAGGTGAAGCGCCATCAAAG 59.116 50.000 14.32 0.00 36.32 2.77
2142 2295 0.036732 AGGTGAAGCGCCATCAAAGA 59.963 50.000 14.32 0.00 36.32 2.52
2143 2296 0.169009 GGTGAAGCGCCATCAAAGAC 59.831 55.000 14.32 3.38 33.65 3.01
2144 2297 0.874390 GTGAAGCGCCATCAAAGACA 59.126 50.000 14.32 0.00 0.00 3.41
2145 2298 1.266718 GTGAAGCGCCATCAAAGACAA 59.733 47.619 14.32 0.00 0.00 3.18
2146 2299 2.095059 GTGAAGCGCCATCAAAGACAAT 60.095 45.455 14.32 0.00 0.00 2.71
2147 2300 2.095110 TGAAGCGCCATCAAAGACAATG 60.095 45.455 2.29 0.00 0.00 2.82
2148 2301 0.813184 AGCGCCATCAAAGACAATGG 59.187 50.000 2.29 0.00 44.42 3.16
2154 2307 4.627611 CCATCAAAGACAATGGCTAGTG 57.372 45.455 0.00 0.00 36.31 2.74
2155 2308 4.012374 CCATCAAAGACAATGGCTAGTGT 58.988 43.478 1.71 1.71 37.91 3.55
2156 2309 4.460382 CCATCAAAGACAATGGCTAGTGTT 59.540 41.667 4.21 0.00 34.87 3.32
2157 2310 5.392380 CCATCAAAGACAATGGCTAGTGTTC 60.392 44.000 4.21 0.00 34.87 3.18
2158 2311 4.072131 TCAAAGACAATGGCTAGTGTTCC 58.928 43.478 4.21 0.00 34.87 3.62
2159 2312 2.789409 AGACAATGGCTAGTGTTCCC 57.211 50.000 4.21 0.00 34.87 3.97
2160 2313 2.269940 AGACAATGGCTAGTGTTCCCT 58.730 47.619 4.21 0.00 34.87 4.20
2161 2314 2.026822 AGACAATGGCTAGTGTTCCCTG 60.027 50.000 4.21 0.00 34.87 4.45
2162 2315 1.985159 ACAATGGCTAGTGTTCCCTGA 59.015 47.619 0.00 0.00 29.47 3.86
2163 2316 2.290323 ACAATGGCTAGTGTTCCCTGAC 60.290 50.000 0.00 0.00 29.47 3.51
2164 2317 0.912486 ATGGCTAGTGTTCCCTGACC 59.088 55.000 0.00 0.00 0.00 4.02
2165 2318 0.178903 TGGCTAGTGTTCCCTGACCT 60.179 55.000 0.00 0.00 0.00 3.85
2166 2319 0.984995 GGCTAGTGTTCCCTGACCTT 59.015 55.000 0.00 0.00 0.00 3.50
2167 2320 1.339151 GGCTAGTGTTCCCTGACCTTG 60.339 57.143 0.00 0.00 0.00 3.61
2168 2321 1.339151 GCTAGTGTTCCCTGACCTTGG 60.339 57.143 0.00 0.00 0.00 3.61
2169 2322 0.690762 TAGTGTTCCCTGACCTTGGC 59.309 55.000 0.00 0.00 0.00 4.52
2170 2323 1.062488 AGTGTTCCCTGACCTTGGCT 61.062 55.000 0.00 0.00 0.00 4.75
2171 2324 0.690762 GTGTTCCCTGACCTTGGCTA 59.309 55.000 0.00 0.00 0.00 3.93
2172 2325 0.984230 TGTTCCCTGACCTTGGCTAG 59.016 55.000 0.00 0.00 0.00 3.42
2173 2326 1.276622 GTTCCCTGACCTTGGCTAGA 58.723 55.000 0.00 0.00 0.00 2.43
2174 2327 1.208293 GTTCCCTGACCTTGGCTAGAG 59.792 57.143 0.00 0.00 0.00 2.43
2175 2328 0.325671 TCCCTGACCTTGGCTAGAGG 60.326 60.000 0.00 0.00 40.24 3.69
2176 2329 1.524482 CCTGACCTTGGCTAGAGGC 59.476 63.158 0.00 0.00 37.84 4.70
2188 2341 3.268023 GCTAGAGGCCAATGTAACTGT 57.732 47.619 5.01 0.00 34.27 3.55
2189 2342 4.402056 GCTAGAGGCCAATGTAACTGTA 57.598 45.455 5.01 0.00 34.27 2.74
2190 2343 4.120589 GCTAGAGGCCAATGTAACTGTAC 58.879 47.826 5.01 0.00 34.27 2.90
2191 2344 3.629142 AGAGGCCAATGTAACTGTACC 57.371 47.619 5.01 0.00 0.00 3.34
2192 2345 2.093658 AGAGGCCAATGTAACTGTACCG 60.094 50.000 5.01 0.00 0.00 4.02
2193 2346 1.626825 AGGCCAATGTAACTGTACCGT 59.373 47.619 5.01 0.00 0.00 4.83
2194 2347 2.004733 GGCCAATGTAACTGTACCGTC 58.995 52.381 0.00 0.00 0.00 4.79
2195 2348 2.004733 GCCAATGTAACTGTACCGTCC 58.995 52.381 0.00 0.00 0.00 4.79
2196 2349 2.624636 CCAATGTAACTGTACCGTCCC 58.375 52.381 0.00 0.00 0.00 4.46
2197 2350 2.235402 CCAATGTAACTGTACCGTCCCT 59.765 50.000 0.00 0.00 0.00 4.20
2198 2351 3.307199 CCAATGTAACTGTACCGTCCCTT 60.307 47.826 0.00 0.00 0.00 3.95
2199 2352 3.881937 ATGTAACTGTACCGTCCCTTC 57.118 47.619 0.00 0.00 0.00 3.46
2200 2353 1.895131 TGTAACTGTACCGTCCCTTCC 59.105 52.381 0.00 0.00 0.00 3.46
2201 2354 1.895131 GTAACTGTACCGTCCCTTCCA 59.105 52.381 0.00 0.00 0.00 3.53
2202 2355 1.652947 AACTGTACCGTCCCTTCCAT 58.347 50.000 0.00 0.00 0.00 3.41
2203 2356 0.902531 ACTGTACCGTCCCTTCCATG 59.097 55.000 0.00 0.00 0.00 3.66
2204 2357 1.191535 CTGTACCGTCCCTTCCATGA 58.808 55.000 0.00 0.00 0.00 3.07
2205 2358 1.762957 CTGTACCGTCCCTTCCATGAT 59.237 52.381 0.00 0.00 0.00 2.45
2206 2359 2.170607 CTGTACCGTCCCTTCCATGATT 59.829 50.000 0.00 0.00 0.00 2.57
2207 2360 2.169769 TGTACCGTCCCTTCCATGATTC 59.830 50.000 0.00 0.00 0.00 2.52
2208 2361 0.546598 ACCGTCCCTTCCATGATTCC 59.453 55.000 0.00 0.00 0.00 3.01
2209 2362 0.532862 CCGTCCCTTCCATGATTCCG 60.533 60.000 0.00 0.00 0.00 4.30
2210 2363 0.532862 CGTCCCTTCCATGATTCCGG 60.533 60.000 0.00 0.00 0.00 5.14
2211 2364 0.179018 GTCCCTTCCATGATTCCGGG 60.179 60.000 0.00 0.00 0.00 5.73
2212 2365 0.623324 TCCCTTCCATGATTCCGGGT 60.623 55.000 0.00 0.00 33.41 5.28
2213 2366 1.136828 CCCTTCCATGATTCCGGGTA 58.863 55.000 0.00 0.00 0.00 3.69
2214 2367 1.072331 CCCTTCCATGATTCCGGGTAG 59.928 57.143 0.00 0.00 0.00 3.18
2215 2368 2.047061 CCTTCCATGATTCCGGGTAGA 58.953 52.381 0.00 0.00 0.00 2.59
2216 2369 2.037772 CCTTCCATGATTCCGGGTAGAG 59.962 54.545 0.00 0.00 0.00 2.43
2217 2370 1.717032 TCCATGATTCCGGGTAGAGG 58.283 55.000 0.00 0.00 0.00 3.69
2218 2371 0.035458 CCATGATTCCGGGTAGAGGC 59.965 60.000 0.00 0.00 0.00 4.70
2219 2372 0.035458 CATGATTCCGGGTAGAGGCC 59.965 60.000 0.00 0.00 0.00 5.19
2220 2373 0.399949 ATGATTCCGGGTAGAGGCCA 60.400 55.000 5.01 0.00 0.00 5.36
2221 2374 0.619255 TGATTCCGGGTAGAGGCCAA 60.619 55.000 5.01 0.00 0.00 4.52
2222 2375 0.765510 GATTCCGGGTAGAGGCCAAT 59.234 55.000 5.01 0.00 0.00 3.16
2223 2376 0.474184 ATTCCGGGTAGAGGCCAATG 59.526 55.000 5.01 0.00 0.00 2.82
2224 2377 0.912487 TTCCGGGTAGAGGCCAATGT 60.912 55.000 5.01 0.00 0.00 2.71
2225 2378 0.031917 TCCGGGTAGAGGCCAATGTA 60.032 55.000 5.01 0.00 0.00 2.29
2226 2379 0.834612 CCGGGTAGAGGCCAATGTAA 59.165 55.000 5.01 0.00 0.00 2.41
2227 2380 1.420138 CCGGGTAGAGGCCAATGTAAT 59.580 52.381 5.01 0.00 0.00 1.89
2228 2381 2.158667 CCGGGTAGAGGCCAATGTAATT 60.159 50.000 5.01 0.00 36.63 1.40
2229 2382 3.071892 CCGGGTAGAGGCCAATGTAATTA 59.928 47.826 5.01 0.00 32.46 1.40
2230 2383 4.062991 CGGGTAGAGGCCAATGTAATTAC 58.937 47.826 5.01 8.75 32.46 1.89
2231 2384 4.062991 GGGTAGAGGCCAATGTAATTACG 58.937 47.826 5.01 0.00 32.46 3.18
2232 2385 3.497262 GGTAGAGGCCAATGTAATTACGC 59.503 47.826 5.01 7.73 32.46 4.42
2233 2386 2.210116 AGAGGCCAATGTAATTACGCG 58.790 47.619 5.01 3.53 32.46 6.01
2234 2387 1.263217 GAGGCCAATGTAATTACGCGG 59.737 52.381 12.47 11.26 32.46 6.46
2235 2388 0.309612 GGCCAATGTAATTACGCGGG 59.690 55.000 12.47 11.80 32.46 6.13
2236 2389 0.309612 GCCAATGTAATTACGCGGGG 59.690 55.000 12.47 10.22 32.46 5.73
2237 2390 0.309612 CCAATGTAATTACGCGGGGC 59.690 55.000 12.47 0.00 32.46 5.80
2238 2391 1.305201 CAATGTAATTACGCGGGGCT 58.695 50.000 12.47 0.00 32.46 5.19
2239 2392 1.002900 CAATGTAATTACGCGGGGCTG 60.003 52.381 12.47 0.00 32.46 4.85
2240 2393 1.164041 ATGTAATTACGCGGGGCTGC 61.164 55.000 12.47 0.00 0.00 5.25
2241 2394 1.523032 GTAATTACGCGGGGCTGCT 60.523 57.895 12.47 0.00 0.00 4.24
2242 2395 1.522806 TAATTACGCGGGGCTGCTG 60.523 57.895 12.47 0.00 0.00 4.41
2243 2396 2.933878 TAATTACGCGGGGCTGCTGG 62.934 60.000 12.47 0.00 0.00 4.85
2253 2406 4.415150 GCTGCTGGCACCTGGCTA 62.415 66.667 0.00 0.00 44.01 3.93
2266 2419 4.995594 GGCTAGGCCTGATTTGCT 57.004 55.556 17.99 0.00 46.69 3.91
2268 2421 1.889545 GGCTAGGCCTGATTTGCTAG 58.110 55.000 17.99 2.45 46.69 3.42
2269 2422 1.141858 GGCTAGGCCTGATTTGCTAGT 59.858 52.381 17.99 0.00 46.69 2.57
2270 2423 2.216898 GCTAGGCCTGATTTGCTAGTG 58.783 52.381 17.99 0.00 0.00 2.74
2271 2424 2.420687 GCTAGGCCTGATTTGCTAGTGT 60.421 50.000 17.99 0.00 0.00 3.55
2272 2425 2.887151 AGGCCTGATTTGCTAGTGTT 57.113 45.000 3.11 0.00 0.00 3.32
2273 2426 2.716217 AGGCCTGATTTGCTAGTGTTC 58.284 47.619 3.11 0.00 0.00 3.18
2274 2427 1.745653 GGCCTGATTTGCTAGTGTTCC 59.254 52.381 0.00 0.00 0.00 3.62
2275 2428 1.745653 GCCTGATTTGCTAGTGTTCCC 59.254 52.381 0.00 0.00 0.00 3.97
2276 2429 2.619074 GCCTGATTTGCTAGTGTTCCCT 60.619 50.000 0.00 0.00 0.00 4.20
2277 2430 3.012518 CCTGATTTGCTAGTGTTCCCTG 58.987 50.000 0.00 0.00 0.00 4.45
2278 2431 3.307691 CCTGATTTGCTAGTGTTCCCTGA 60.308 47.826 0.00 0.00 0.00 3.86
2279 2432 3.674997 TGATTTGCTAGTGTTCCCTGAC 58.325 45.455 0.00 0.00 0.00 3.51
2280 2433 2.561478 TTTGCTAGTGTTCCCTGACC 57.439 50.000 0.00 0.00 0.00 4.02
2281 2434 0.690762 TTGCTAGTGTTCCCTGACCC 59.309 55.000 0.00 0.00 0.00 4.46
2282 2435 0.178903 TGCTAGTGTTCCCTGACCCT 60.179 55.000 0.00 0.00 0.00 4.34
2283 2436 0.537653 GCTAGTGTTCCCTGACCCTC 59.462 60.000 0.00 0.00 0.00 4.30
2284 2437 1.897647 GCTAGTGTTCCCTGACCCTCT 60.898 57.143 0.00 0.00 0.00 3.69
2285 2438 2.104170 CTAGTGTTCCCTGACCCTCTC 58.896 57.143 0.00 0.00 0.00 3.20
2286 2439 0.489567 AGTGTTCCCTGACCCTCTCT 59.510 55.000 0.00 0.00 0.00 3.10
2287 2440 1.132689 AGTGTTCCCTGACCCTCTCTT 60.133 52.381 0.00 0.00 0.00 2.85
2288 2441 1.002544 GTGTTCCCTGACCCTCTCTTG 59.997 57.143 0.00 0.00 0.00 3.02
2289 2442 1.353091 GTTCCCTGACCCTCTCTTGT 58.647 55.000 0.00 0.00 0.00 3.16
2290 2443 2.158219 TGTTCCCTGACCCTCTCTTGTA 60.158 50.000 0.00 0.00 0.00 2.41
2291 2444 2.904434 GTTCCCTGACCCTCTCTTGTAA 59.096 50.000 0.00 0.00 0.00 2.41
2292 2445 2.537143 TCCCTGACCCTCTCTTGTAAC 58.463 52.381 0.00 0.00 0.00 2.50
2293 2446 2.111972 TCCCTGACCCTCTCTTGTAACT 59.888 50.000 0.00 0.00 0.00 2.24
2294 2447 2.234908 CCCTGACCCTCTCTTGTAACTG 59.765 54.545 0.00 0.00 0.00 3.16
2295 2448 2.900546 CCTGACCCTCTCTTGTAACTGT 59.099 50.000 0.00 0.00 0.00 3.55
2296 2449 4.087182 CCTGACCCTCTCTTGTAACTGTA 58.913 47.826 0.00 0.00 0.00 2.74
2297 2450 4.082136 CCTGACCCTCTCTTGTAACTGTAC 60.082 50.000 0.00 0.00 0.00 2.90
2298 2451 3.830755 TGACCCTCTCTTGTAACTGTACC 59.169 47.826 0.00 0.00 0.00 3.34
2299 2452 2.824341 ACCCTCTCTTGTAACTGTACCG 59.176 50.000 0.00 0.00 0.00 4.02
2300 2453 2.824341 CCCTCTCTTGTAACTGTACCGT 59.176 50.000 0.00 0.00 0.00 4.83
2301 2454 3.119566 CCCTCTCTTGTAACTGTACCGTC 60.120 52.174 0.00 0.00 0.00 4.79
2302 2455 3.119566 CCTCTCTTGTAACTGTACCGTCC 60.120 52.174 0.00 0.00 0.00 4.79
2303 2456 2.821969 TCTCTTGTAACTGTACCGTCCC 59.178 50.000 0.00 0.00 0.00 4.46
2304 2457 2.824341 CTCTTGTAACTGTACCGTCCCT 59.176 50.000 0.00 0.00 0.00 4.20
2305 2458 3.233507 TCTTGTAACTGTACCGTCCCTT 58.766 45.455 0.00 0.00 0.00 3.95
2306 2459 3.642848 TCTTGTAACTGTACCGTCCCTTT 59.357 43.478 0.00 0.00 0.00 3.11
2307 2460 3.665745 TGTAACTGTACCGTCCCTTTC 57.334 47.619 0.00 0.00 0.00 2.62
2308 2461 2.964464 TGTAACTGTACCGTCCCTTTCA 59.036 45.455 0.00 0.00 0.00 2.69
2309 2462 2.538512 AACTGTACCGTCCCTTTCAC 57.461 50.000 0.00 0.00 0.00 3.18
2310 2463 1.713297 ACTGTACCGTCCCTTTCACT 58.287 50.000 0.00 0.00 0.00 3.41
2311 2464 2.880443 ACTGTACCGTCCCTTTCACTA 58.120 47.619 0.00 0.00 0.00 2.74
2312 2465 3.438183 ACTGTACCGTCCCTTTCACTAT 58.562 45.455 0.00 0.00 0.00 2.12
2313 2466 4.603131 ACTGTACCGTCCCTTTCACTATA 58.397 43.478 0.00 0.00 0.00 1.31
2314 2467 5.206587 ACTGTACCGTCCCTTTCACTATAT 58.793 41.667 0.00 0.00 0.00 0.86
2315 2468 5.301298 ACTGTACCGTCCCTTTCACTATATC 59.699 44.000 0.00 0.00 0.00 1.63
2316 2469 5.202765 TGTACCGTCCCTTTCACTATATCA 58.797 41.667 0.00 0.00 0.00 2.15
2317 2470 5.657745 TGTACCGTCCCTTTCACTATATCAA 59.342 40.000 0.00 0.00 0.00 2.57
2318 2471 5.888982 ACCGTCCCTTTCACTATATCAAT 57.111 39.130 0.00 0.00 0.00 2.57
2319 2472 5.611374 ACCGTCCCTTTCACTATATCAATG 58.389 41.667 0.00 0.00 0.00 2.82
2320 2473 5.365605 ACCGTCCCTTTCACTATATCAATGA 59.634 40.000 0.00 0.00 0.00 2.57
2321 2474 6.126883 ACCGTCCCTTTCACTATATCAATGAA 60.127 38.462 0.00 0.00 0.00 2.57
2322 2475 6.765989 CCGTCCCTTTCACTATATCAATGAAA 59.234 38.462 8.07 8.07 39.42 2.69
2323 2476 7.282224 CCGTCCCTTTCACTATATCAATGAAAA 59.718 37.037 9.15 0.00 40.74 2.29
2324 2477 8.840321 CGTCCCTTTCACTATATCAATGAAAAT 58.160 33.333 9.15 0.00 40.74 1.82
2326 2479 9.919416 TCCCTTTCACTATATCAATGAAAATCA 57.081 29.630 9.15 0.00 40.74 2.57
2328 2481 9.674824 CCTTTCACTATATCAATGAAAATCAGC 57.325 33.333 9.15 0.00 40.74 4.26
2332 2485 9.006839 TCACTATATCAATGAAAATCAGCATCC 57.993 33.333 0.00 0.00 0.00 3.51
2333 2486 9.011095 CACTATATCAATGAAAATCAGCATCCT 57.989 33.333 0.00 0.00 0.00 3.24
2334 2487 9.011095 ACTATATCAATGAAAATCAGCATCCTG 57.989 33.333 0.00 0.00 40.54 3.86
2335 2488 4.380841 TCAATGAAAATCAGCATCCTGC 57.619 40.909 0.00 0.00 45.46 4.85
2345 2498 3.025866 GCATCCTGCTGCTTTTTCG 57.974 52.632 0.00 0.00 40.96 3.46
2346 2499 0.242017 GCATCCTGCTGCTTTTTCGT 59.758 50.000 0.00 0.00 40.96 3.85
2347 2500 1.730446 GCATCCTGCTGCTTTTTCGTC 60.730 52.381 0.00 0.00 40.96 4.20
2348 2501 1.536766 CATCCTGCTGCTTTTTCGTCA 59.463 47.619 0.00 0.00 0.00 4.35
2349 2502 1.674359 TCCTGCTGCTTTTTCGTCAA 58.326 45.000 0.00 0.00 0.00 3.18
2350 2503 2.020720 TCCTGCTGCTTTTTCGTCAAA 58.979 42.857 0.00 0.00 0.00 2.69
2351 2504 2.425312 TCCTGCTGCTTTTTCGTCAAAA 59.575 40.909 0.00 0.00 33.12 2.44
2352 2505 3.119316 TCCTGCTGCTTTTTCGTCAAAAA 60.119 39.130 0.00 0.00 38.84 1.94
2437 2590 1.613630 TCCTTGCACTCCCTCCCTC 60.614 63.158 0.00 0.00 0.00 4.30
2483 2636 1.376609 CTTATGTTGTCCCCTGCCGC 61.377 60.000 0.00 0.00 0.00 6.53
2536 2689 1.899437 GACGATGGCCCAGACCTCAA 61.899 60.000 0.00 0.00 0.00 3.02
2719 2874 2.432146 CCTCGATCTCCAGGTGAAATCA 59.568 50.000 0.00 0.00 0.00 2.57
2726 2881 1.837439 TCCAGGTGAAATCAGCCGTAT 59.163 47.619 8.87 0.00 44.82 3.06
2741 2896 2.748605 CCGTATGGATCACTTCTCTGC 58.251 52.381 0.00 0.00 37.49 4.26
2822 2977 4.338012 ACCATGAGAATGAATCACTTGCA 58.662 39.130 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 66 1.134401 TCGAGCATGGATTGGAGTTCC 60.134 52.381 0.00 0.00 0.00 3.62
81 84 1.586422 AATCTTGCATCATCCCGTCG 58.414 50.000 0.00 0.00 0.00 5.12
140 143 4.351938 TCGACGAACCGGTGCTGG 62.352 66.667 8.52 0.00 0.00 4.85
148 151 3.464545 GAACCGCGTCGACGAACC 61.465 66.667 39.74 21.68 43.02 3.62
213 216 3.007323 AACCCCTGAGGCCGTACC 61.007 66.667 0.00 0.00 40.58 3.34
380 383 1.350193 CTCGACGGTTCCTGTGAATG 58.650 55.000 0.00 0.00 31.98 2.67
527 530 9.244292 TCATCTATGTACACCTACAATCTATCC 57.756 37.037 0.00 0.00 36.43 2.59
535 538 7.998964 TCTGATTCTCATCTATGTACACCTACA 59.001 37.037 0.00 0.00 37.28 2.74
666 671 5.560953 GCAGCTTCTAGATGAAAAACACGTT 60.561 40.000 9.72 0.00 32.38 3.99
667 672 4.083802 GCAGCTTCTAGATGAAAAACACGT 60.084 41.667 9.72 0.00 32.38 4.49
668 673 4.153117 AGCAGCTTCTAGATGAAAAACACG 59.847 41.667 9.72 0.00 32.38 4.49
669 674 5.619625 AGCAGCTTCTAGATGAAAAACAC 57.380 39.130 9.72 0.00 32.38 3.32
670 675 5.532406 ACAAGCAGCTTCTAGATGAAAAACA 59.468 36.000 4.07 0.00 32.38 2.83
671 676 6.006759 ACAAGCAGCTTCTAGATGAAAAAC 57.993 37.500 4.07 0.00 32.38 2.43
672 677 5.182001 GGACAAGCAGCTTCTAGATGAAAAA 59.818 40.000 4.07 0.00 32.38 1.94
717 722 2.158885 TCATTCGGGTTGACACTTGACA 60.159 45.455 0.00 0.00 0.00 3.58
721 726 1.812571 GCATCATTCGGGTTGACACTT 59.187 47.619 0.00 0.00 0.00 3.16
722 727 1.453155 GCATCATTCGGGTTGACACT 58.547 50.000 0.00 0.00 0.00 3.55
723 728 0.096976 CGCATCATTCGGGTTGACAC 59.903 55.000 0.00 0.00 0.00 3.67
726 731 0.036858 TCACGCATCATTCGGGTTGA 60.037 50.000 0.00 0.00 0.00 3.18
730 735 1.348250 CGTTCACGCATCATTCGGG 59.652 57.895 0.00 0.00 0.00 5.14
757 762 0.872388 CCTCGTTGTAAGTTGCCACC 59.128 55.000 0.00 0.00 0.00 4.61
801 813 8.915654 CACCTATTAGTGCAATTTCTTTTTCAC 58.084 33.333 0.00 0.00 0.00 3.18
803 815 8.088365 ACCACCTATTAGTGCAATTTCTTTTTC 58.912 33.333 0.00 0.00 36.38 2.29
814 826 1.903860 ACCGAACCACCTATTAGTGCA 59.096 47.619 0.00 0.00 36.38 4.57
824 836 3.292159 GCACCCAACCGAACCACC 61.292 66.667 0.00 0.00 0.00 4.61
919 931 5.045505 TGGTTACTGGTGCATATCCTAAACA 60.046 40.000 0.00 0.00 0.00 2.83
920 932 5.433526 TGGTTACTGGTGCATATCCTAAAC 58.566 41.667 0.00 0.00 0.00 2.01
942 954 9.784531 ATATATGAACTGGATAACCAAGTCTTG 57.215 33.333 5.53 5.53 46.32 3.02
975 987 1.875963 CAGGCCGTGAATCCAACAC 59.124 57.895 0.00 0.00 35.26 3.32
993 1005 6.155827 CAGGCAGATCTCAACTATAGTTAGC 58.844 44.000 17.62 5.96 36.32 3.09
996 1008 6.552445 AACAGGCAGATCTCAACTATAGTT 57.448 37.500 12.50 12.50 39.12 2.24
998 1010 6.155827 GCTAACAGGCAGATCTCAACTATAG 58.844 44.000 0.00 0.00 0.00 1.31
999 1011 5.598417 TGCTAACAGGCAGATCTCAACTATA 59.402 40.000 0.00 0.00 37.29 1.31
1000 1012 4.406972 TGCTAACAGGCAGATCTCAACTAT 59.593 41.667 0.00 0.00 37.29 2.12
1058 1071 2.158696 GCAAAGAGATGGATACCAGGCT 60.159 50.000 0.00 0.00 36.75 4.58
1059 1072 2.158696 AGCAAAGAGATGGATACCAGGC 60.159 50.000 0.00 0.00 36.75 4.85
1072 1085 1.338020 GGGGACACAACAAGCAAAGAG 59.662 52.381 0.00 0.00 0.00 2.85
1079 1092 1.000060 CATTGCAGGGGACACAACAAG 60.000 52.381 0.00 0.00 32.44 3.16
1195 1208 1.557099 TGTATTCGTGCTCAGGAGGT 58.443 50.000 0.00 0.00 0.00 3.85
1199 1212 3.560068 GGGTATTTGTATTCGTGCTCAGG 59.440 47.826 0.00 0.00 0.00 3.86
1200 1213 4.442706 AGGGTATTTGTATTCGTGCTCAG 58.557 43.478 0.00 0.00 0.00 3.35
1201 1214 4.439057 GAGGGTATTTGTATTCGTGCTCA 58.561 43.478 0.00 0.00 0.00 4.26
1202 1215 3.808174 GGAGGGTATTTGTATTCGTGCTC 59.192 47.826 0.00 0.00 0.00 4.26
1203 1216 3.199071 TGGAGGGTATTTGTATTCGTGCT 59.801 43.478 0.00 0.00 0.00 4.40
1204 1217 3.311596 GTGGAGGGTATTTGTATTCGTGC 59.688 47.826 0.00 0.00 0.00 5.34
1205 1218 3.875134 GGTGGAGGGTATTTGTATTCGTG 59.125 47.826 0.00 0.00 0.00 4.35
1206 1219 3.431207 CGGTGGAGGGTATTTGTATTCGT 60.431 47.826 0.00 0.00 0.00 3.85
1207 1220 3.128349 CGGTGGAGGGTATTTGTATTCG 58.872 50.000 0.00 0.00 0.00 3.34
1208 1221 4.124970 GACGGTGGAGGGTATTTGTATTC 58.875 47.826 0.00 0.00 0.00 1.75
1209 1222 3.431207 CGACGGTGGAGGGTATTTGTATT 60.431 47.826 0.00 0.00 0.00 1.89
1210 1223 2.101917 CGACGGTGGAGGGTATTTGTAT 59.898 50.000 0.00 0.00 0.00 2.29
1211 1224 1.477700 CGACGGTGGAGGGTATTTGTA 59.522 52.381 0.00 0.00 0.00 2.41
1212 1225 0.248289 CGACGGTGGAGGGTATTTGT 59.752 55.000 0.00 0.00 0.00 2.83
1213 1226 0.461339 CCGACGGTGGAGGGTATTTG 60.461 60.000 5.48 0.00 0.00 2.32
1214 1227 0.615544 TCCGACGGTGGAGGGTATTT 60.616 55.000 14.79 0.00 33.05 1.40
1215 1228 1.000739 TCCGACGGTGGAGGGTATT 59.999 57.895 14.79 0.00 33.05 1.89
1216 1229 2.685366 TCCGACGGTGGAGGGTAT 59.315 61.111 14.79 0.00 33.05 2.73
1285 1424 4.722700 GGCTCCGGCTTTGGCTCA 62.723 66.667 0.00 0.00 38.73 4.26
1317 1456 2.202703 GCGGGTAGTACTGTGCCG 60.203 66.667 5.39 10.36 0.00 5.69
1319 1458 1.141234 GAGGCGGGTAGTACTGTGC 59.859 63.158 5.39 3.85 0.00 4.57
1325 1464 2.194056 CGGAGGAGGCGGGTAGTA 59.806 66.667 0.00 0.00 0.00 1.82
1507 1649 0.687920 TGGACGGGTTGAACATGCTA 59.312 50.000 0.00 0.00 0.00 3.49
1565 1707 0.820074 ACGATCGAGGAGGCGAGAAT 60.820 55.000 24.34 0.00 44.26 2.40
1616 1758 8.758829 TGTTGACTGAATGTATTCTAGGTACAT 58.241 33.333 12.92 12.92 42.83 2.29
1639 1781 2.369860 TGCTGATCAGGTTCAGTCTGTT 59.630 45.455 23.89 0.00 44.10 3.16
1751 1896 5.375417 TCAAAGTTCAACATCATTCGCAT 57.625 34.783 0.00 0.00 0.00 4.73
1785 1930 1.522580 TGCGCAGTTGCACTACACA 60.523 52.632 5.66 0.00 40.62 3.72
1813 1958 7.886338 AGAACTCACTGGAATTTATTTTCACC 58.114 34.615 0.00 0.00 0.00 4.02
1840 1985 2.507866 GTGCGTACTCGAGAAAGAGAC 58.492 52.381 21.68 4.55 40.57 3.36
1841 1986 1.128136 CGTGCGTACTCGAGAAAGAGA 59.872 52.381 21.68 0.00 40.57 3.10
1842 1987 1.128136 TCGTGCGTACTCGAGAAAGAG 59.872 52.381 21.68 6.61 43.56 2.85
1843 1988 1.150827 TCGTGCGTACTCGAGAAAGA 58.849 50.000 21.68 5.50 36.92 2.52
1844 1989 3.670500 TCGTGCGTACTCGAGAAAG 57.330 52.632 21.68 10.26 36.92 2.62
1899 2044 0.768221 TCACTGTGGAGGGGCTCTTT 60.768 55.000 8.11 0.00 0.00 2.52
1952 2103 0.676736 GAGTGGATTAGGAGGGAGCG 59.323 60.000 0.00 0.00 0.00 5.03
1962 2113 3.322541 TGAACGTTGAGTGGAGTGGATTA 59.677 43.478 5.00 0.00 0.00 1.75
2066 2218 3.936203 ACGGCGTGAAGGAAGGCA 61.936 61.111 13.76 0.00 32.60 4.75
2138 2291 3.074538 AGGGAACACTAGCCATTGTCTTT 59.925 43.478 0.00 0.00 0.00 2.52
2139 2292 2.644798 AGGGAACACTAGCCATTGTCTT 59.355 45.455 0.00 0.00 0.00 3.01
2140 2293 2.026822 CAGGGAACACTAGCCATTGTCT 60.027 50.000 0.00 0.00 0.00 3.41
2141 2294 2.027192 TCAGGGAACACTAGCCATTGTC 60.027 50.000 0.00 0.00 0.00 3.18
2142 2295 1.985159 TCAGGGAACACTAGCCATTGT 59.015 47.619 0.00 0.00 0.00 2.71
2143 2296 2.359900 GTCAGGGAACACTAGCCATTG 58.640 52.381 0.00 0.00 0.00 2.82
2144 2297 1.282157 GGTCAGGGAACACTAGCCATT 59.718 52.381 0.00 0.00 0.00 3.16
2145 2298 0.912486 GGTCAGGGAACACTAGCCAT 59.088 55.000 0.00 0.00 0.00 4.40
2146 2299 0.178903 AGGTCAGGGAACACTAGCCA 60.179 55.000 0.00 0.00 0.00 4.75
2147 2300 0.984995 AAGGTCAGGGAACACTAGCC 59.015 55.000 0.00 0.00 0.00 3.93
2148 2301 1.339151 CCAAGGTCAGGGAACACTAGC 60.339 57.143 0.00 0.00 0.00 3.42
2149 2302 1.339151 GCCAAGGTCAGGGAACACTAG 60.339 57.143 0.00 0.00 0.00 2.57
2150 2303 0.690762 GCCAAGGTCAGGGAACACTA 59.309 55.000 0.00 0.00 0.00 2.74
2151 2304 1.062488 AGCCAAGGTCAGGGAACACT 61.062 55.000 0.00 0.00 0.00 3.55
2152 2305 0.690762 TAGCCAAGGTCAGGGAACAC 59.309 55.000 0.00 0.00 0.00 3.32
2153 2306 0.984230 CTAGCCAAGGTCAGGGAACA 59.016 55.000 0.00 0.00 0.00 3.18
2154 2307 1.208293 CTCTAGCCAAGGTCAGGGAAC 59.792 57.143 0.00 0.00 0.00 3.62
2155 2308 1.573108 CTCTAGCCAAGGTCAGGGAA 58.427 55.000 0.00 0.00 0.00 3.97
2156 2309 0.325671 CCTCTAGCCAAGGTCAGGGA 60.326 60.000 0.00 0.00 0.00 4.20
2157 2310 1.977293 GCCTCTAGCCAAGGTCAGGG 61.977 65.000 0.00 0.00 36.21 4.45
2158 2311 1.524482 GCCTCTAGCCAAGGTCAGG 59.476 63.158 0.00 0.00 36.21 3.86
2168 2321 3.268023 ACAGTTACATTGGCCTCTAGC 57.732 47.619 3.32 0.00 42.60 3.42
2169 2322 4.694339 GGTACAGTTACATTGGCCTCTAG 58.306 47.826 3.32 0.00 0.00 2.43
2170 2323 3.131577 CGGTACAGTTACATTGGCCTCTA 59.868 47.826 3.32 0.00 0.00 2.43
2171 2324 2.093658 CGGTACAGTTACATTGGCCTCT 60.094 50.000 3.32 0.00 0.00 3.69
2172 2325 2.277084 CGGTACAGTTACATTGGCCTC 58.723 52.381 3.32 0.00 0.00 4.70
2173 2326 1.626825 ACGGTACAGTTACATTGGCCT 59.373 47.619 3.32 0.00 0.00 5.19
2174 2327 2.004733 GACGGTACAGTTACATTGGCC 58.995 52.381 0.00 0.00 0.00 5.36
2175 2328 2.004733 GGACGGTACAGTTACATTGGC 58.995 52.381 0.00 0.00 0.00 4.52
2176 2329 2.235402 AGGGACGGTACAGTTACATTGG 59.765 50.000 0.00 0.00 0.00 3.16
2177 2330 3.604875 AGGGACGGTACAGTTACATTG 57.395 47.619 0.00 0.00 0.00 2.82
2178 2331 3.055602 GGAAGGGACGGTACAGTTACATT 60.056 47.826 0.00 1.02 0.00 2.71
2179 2332 2.498885 GGAAGGGACGGTACAGTTACAT 59.501 50.000 0.00 0.00 0.00 2.29
2180 2333 1.895131 GGAAGGGACGGTACAGTTACA 59.105 52.381 0.00 0.00 0.00 2.41
2181 2334 1.895131 TGGAAGGGACGGTACAGTTAC 59.105 52.381 0.00 0.00 0.00 2.50
2182 2335 2.307496 TGGAAGGGACGGTACAGTTA 57.693 50.000 0.00 0.00 0.00 2.24
2183 2336 1.278127 CATGGAAGGGACGGTACAGTT 59.722 52.381 0.00 0.00 0.00 3.16
2184 2337 0.902531 CATGGAAGGGACGGTACAGT 59.097 55.000 0.00 0.00 0.00 3.55
2185 2338 1.191535 TCATGGAAGGGACGGTACAG 58.808 55.000 0.00 0.00 0.00 2.74
2186 2339 1.874129 ATCATGGAAGGGACGGTACA 58.126 50.000 0.00 0.00 0.00 2.90
2187 2340 2.484947 GGAATCATGGAAGGGACGGTAC 60.485 54.545 0.00 0.00 0.00 3.34
2188 2341 1.766496 GGAATCATGGAAGGGACGGTA 59.234 52.381 0.00 0.00 0.00 4.02
2189 2342 0.546598 GGAATCATGGAAGGGACGGT 59.453 55.000 0.00 0.00 0.00 4.83
2190 2343 0.532862 CGGAATCATGGAAGGGACGG 60.533 60.000 0.00 0.00 0.00 4.79
2191 2344 0.532862 CCGGAATCATGGAAGGGACG 60.533 60.000 0.00 0.00 0.00 4.79
2192 2345 0.179018 CCCGGAATCATGGAAGGGAC 60.179 60.000 0.73 0.00 41.26 4.46
2193 2346 0.623324 ACCCGGAATCATGGAAGGGA 60.623 55.000 0.73 0.00 41.26 4.20
2194 2347 1.072331 CTACCCGGAATCATGGAAGGG 59.928 57.143 0.73 9.87 44.17 3.95
2195 2348 2.037772 CTCTACCCGGAATCATGGAAGG 59.962 54.545 0.73 0.00 0.00 3.46
2196 2349 2.037772 CCTCTACCCGGAATCATGGAAG 59.962 54.545 0.73 0.00 0.00 3.46
2197 2350 2.047061 CCTCTACCCGGAATCATGGAA 58.953 52.381 0.73 0.00 0.00 3.53
2198 2351 1.717032 CCTCTACCCGGAATCATGGA 58.283 55.000 0.73 0.00 0.00 3.41
2199 2352 0.035458 GCCTCTACCCGGAATCATGG 59.965 60.000 0.73 0.00 0.00 3.66
2200 2353 0.035458 GGCCTCTACCCGGAATCATG 59.965 60.000 0.73 0.00 0.00 3.07
2201 2354 0.399949 TGGCCTCTACCCGGAATCAT 60.400 55.000 0.73 0.00 0.00 2.45
2202 2355 0.619255 TTGGCCTCTACCCGGAATCA 60.619 55.000 0.73 0.00 0.00 2.57
2203 2356 0.765510 ATTGGCCTCTACCCGGAATC 59.234 55.000 0.73 0.00 0.00 2.52
2204 2357 0.474184 CATTGGCCTCTACCCGGAAT 59.526 55.000 0.73 0.00 0.00 3.01
2205 2358 0.912487 ACATTGGCCTCTACCCGGAA 60.912 55.000 0.73 0.00 0.00 4.30
2206 2359 0.031917 TACATTGGCCTCTACCCGGA 60.032 55.000 0.73 0.00 0.00 5.14
2207 2360 0.834612 TTACATTGGCCTCTACCCGG 59.165 55.000 3.32 0.00 0.00 5.73
2208 2361 2.930826 ATTACATTGGCCTCTACCCG 57.069 50.000 3.32 0.00 0.00 5.28
2209 2362 4.062991 CGTAATTACATTGGCCTCTACCC 58.937 47.826 15.67 0.00 0.00 3.69
2210 2363 3.497262 GCGTAATTACATTGGCCTCTACC 59.503 47.826 15.67 0.00 0.00 3.18
2211 2364 3.183775 CGCGTAATTACATTGGCCTCTAC 59.816 47.826 15.67 0.00 0.00 2.59
2212 2365 3.386486 CGCGTAATTACATTGGCCTCTA 58.614 45.455 15.67 0.00 0.00 2.43
2213 2366 2.210116 CGCGTAATTACATTGGCCTCT 58.790 47.619 15.67 0.00 0.00 3.69
2214 2367 1.263217 CCGCGTAATTACATTGGCCTC 59.737 52.381 15.67 0.00 0.00 4.70
2215 2368 1.305201 CCGCGTAATTACATTGGCCT 58.695 50.000 15.67 0.00 0.00 5.19
2216 2369 0.309612 CCCGCGTAATTACATTGGCC 59.690 55.000 15.67 0.00 0.00 5.36
2217 2370 0.309612 CCCCGCGTAATTACATTGGC 59.690 55.000 15.67 9.33 0.00 4.52
2218 2371 0.309612 GCCCCGCGTAATTACATTGG 59.690 55.000 15.67 12.31 0.00 3.16
2219 2372 1.002900 CAGCCCCGCGTAATTACATTG 60.003 52.381 15.67 4.40 0.00 2.82
2220 2373 1.305201 CAGCCCCGCGTAATTACATT 58.695 50.000 15.67 0.00 0.00 2.71
2221 2374 1.164041 GCAGCCCCGCGTAATTACAT 61.164 55.000 15.67 0.00 0.00 2.29
2222 2375 1.816259 GCAGCCCCGCGTAATTACA 60.816 57.895 15.67 0.00 0.00 2.41
2223 2376 1.523032 AGCAGCCCCGCGTAATTAC 60.523 57.895 4.92 5.47 36.85 1.89
2224 2377 1.522806 CAGCAGCCCCGCGTAATTA 60.523 57.895 4.92 0.00 36.85 1.40
2225 2378 2.824041 CAGCAGCCCCGCGTAATT 60.824 61.111 4.92 0.00 36.85 1.40
2226 2379 4.856801 CCAGCAGCCCCGCGTAAT 62.857 66.667 4.92 0.00 36.85 1.89
2236 2389 4.415150 TAGCCAGGTGCCAGCAGC 62.415 66.667 13.75 13.75 42.71 5.25
2237 2390 2.124819 CTAGCCAGGTGCCAGCAG 60.125 66.667 0.00 0.00 42.71 4.24
2238 2391 3.720601 CCTAGCCAGGTGCCAGCA 61.721 66.667 0.00 0.00 42.71 4.41
2250 2403 2.216898 CACTAGCAAATCAGGCCTAGC 58.783 52.381 3.98 4.97 0.00 3.42
2251 2404 3.550437 ACACTAGCAAATCAGGCCTAG 57.450 47.619 3.98 0.00 0.00 3.02
2252 2405 3.370527 GGAACACTAGCAAATCAGGCCTA 60.371 47.826 3.98 0.00 0.00 3.93
2253 2406 2.619074 GGAACACTAGCAAATCAGGCCT 60.619 50.000 0.00 0.00 0.00 5.19
2254 2407 1.745653 GGAACACTAGCAAATCAGGCC 59.254 52.381 0.00 0.00 0.00 5.19
2255 2408 1.745653 GGGAACACTAGCAAATCAGGC 59.254 52.381 0.00 0.00 0.00 4.85
2256 2409 3.012518 CAGGGAACACTAGCAAATCAGG 58.987 50.000 0.00 0.00 0.00 3.86
2257 2410 3.686726 GTCAGGGAACACTAGCAAATCAG 59.313 47.826 0.00 0.00 0.00 2.90
2258 2411 3.559171 GGTCAGGGAACACTAGCAAATCA 60.559 47.826 0.00 0.00 0.00 2.57
2259 2412 3.010420 GGTCAGGGAACACTAGCAAATC 58.990 50.000 0.00 0.00 0.00 2.17
2260 2413 2.290960 GGGTCAGGGAACACTAGCAAAT 60.291 50.000 0.00 0.00 0.00 2.32
2261 2414 1.073284 GGGTCAGGGAACACTAGCAAA 59.927 52.381 0.00 0.00 0.00 3.68
2262 2415 0.690762 GGGTCAGGGAACACTAGCAA 59.309 55.000 0.00 0.00 0.00 3.91
2263 2416 0.178903 AGGGTCAGGGAACACTAGCA 60.179 55.000 0.00 0.00 28.80 3.49
2264 2417 0.537653 GAGGGTCAGGGAACACTAGC 59.462 60.000 0.00 0.00 31.49 3.42
2265 2418 2.104170 GAGAGGGTCAGGGAACACTAG 58.896 57.143 0.00 0.00 31.49 2.57
2266 2419 1.717077 AGAGAGGGTCAGGGAACACTA 59.283 52.381 0.00 0.00 31.49 2.74
2267 2420 0.489567 AGAGAGGGTCAGGGAACACT 59.510 55.000 0.00 0.00 34.96 3.55
2268 2421 1.002544 CAAGAGAGGGTCAGGGAACAC 59.997 57.143 0.00 0.00 0.00 3.32
2269 2422 1.352083 CAAGAGAGGGTCAGGGAACA 58.648 55.000 0.00 0.00 0.00 3.18
2270 2423 1.353091 ACAAGAGAGGGTCAGGGAAC 58.647 55.000 0.00 0.00 0.00 3.62
2271 2424 2.904434 GTTACAAGAGAGGGTCAGGGAA 59.096 50.000 0.00 0.00 0.00 3.97
2272 2425 2.111972 AGTTACAAGAGAGGGTCAGGGA 59.888 50.000 0.00 0.00 0.00 4.20
2273 2426 2.234908 CAGTTACAAGAGAGGGTCAGGG 59.765 54.545 0.00 0.00 0.00 4.45
2274 2427 2.900546 ACAGTTACAAGAGAGGGTCAGG 59.099 50.000 0.00 0.00 0.00 3.86
2275 2428 4.082136 GGTACAGTTACAAGAGAGGGTCAG 60.082 50.000 0.00 0.00 0.00 3.51
2276 2429 3.830755 GGTACAGTTACAAGAGAGGGTCA 59.169 47.826 0.00 0.00 0.00 4.02
2277 2430 3.119566 CGGTACAGTTACAAGAGAGGGTC 60.120 52.174 0.00 0.00 0.00 4.46
2278 2431 2.824341 CGGTACAGTTACAAGAGAGGGT 59.176 50.000 0.00 0.00 0.00 4.34
2279 2432 2.824341 ACGGTACAGTTACAAGAGAGGG 59.176 50.000 0.00 0.00 0.00 4.30
2280 2433 3.119566 GGACGGTACAGTTACAAGAGAGG 60.120 52.174 0.00 0.00 0.00 3.69
2281 2434 3.119566 GGGACGGTACAGTTACAAGAGAG 60.120 52.174 0.00 0.00 0.00 3.20
2282 2435 2.821969 GGGACGGTACAGTTACAAGAGA 59.178 50.000 0.00 0.00 0.00 3.10
2283 2436 2.824341 AGGGACGGTACAGTTACAAGAG 59.176 50.000 0.00 0.00 0.00 2.85
2284 2437 2.880443 AGGGACGGTACAGTTACAAGA 58.120 47.619 0.00 0.00 0.00 3.02
2285 2438 3.672767 AAGGGACGGTACAGTTACAAG 57.327 47.619 0.00 0.00 0.00 3.16
2286 2439 3.387374 TGAAAGGGACGGTACAGTTACAA 59.613 43.478 0.00 0.00 0.00 2.41
2287 2440 2.964464 TGAAAGGGACGGTACAGTTACA 59.036 45.455 0.00 0.00 0.00 2.41
2288 2441 3.006217 AGTGAAAGGGACGGTACAGTTAC 59.994 47.826 0.00 0.00 0.00 2.50
2289 2442 3.233507 AGTGAAAGGGACGGTACAGTTA 58.766 45.455 0.00 0.00 0.00 2.24
2290 2443 2.044758 AGTGAAAGGGACGGTACAGTT 58.955 47.619 0.00 0.00 0.00 3.16
2291 2444 1.713297 AGTGAAAGGGACGGTACAGT 58.287 50.000 0.00 0.00 0.00 3.55
2292 2445 5.301045 TGATATAGTGAAAGGGACGGTACAG 59.699 44.000 0.00 0.00 0.00 2.74
2293 2446 5.202765 TGATATAGTGAAAGGGACGGTACA 58.797 41.667 0.00 0.00 0.00 2.90
2294 2447 5.779529 TGATATAGTGAAAGGGACGGTAC 57.220 43.478 0.00 0.00 0.00 3.34
2295 2448 6.551975 TCATTGATATAGTGAAAGGGACGGTA 59.448 38.462 0.00 0.00 0.00 4.02
2296 2449 5.365605 TCATTGATATAGTGAAAGGGACGGT 59.634 40.000 0.00 0.00 0.00 4.83
2297 2450 5.853936 TCATTGATATAGTGAAAGGGACGG 58.146 41.667 0.00 0.00 0.00 4.79
2298 2451 7.786178 TTTCATTGATATAGTGAAAGGGACG 57.214 36.000 5.85 0.00 39.27 4.79
2300 2453 9.919416 TGATTTTCATTGATATAGTGAAAGGGA 57.081 29.630 8.66 0.00 43.19 4.20
2302 2455 9.674824 GCTGATTTTCATTGATATAGTGAAAGG 57.325 33.333 8.66 4.73 43.19 3.11
2306 2459 9.006839 GGATGCTGATTTTCATTGATATAGTGA 57.993 33.333 0.00 0.00 0.00 3.41
2307 2460 9.011095 AGGATGCTGATTTTCATTGATATAGTG 57.989 33.333 0.00 0.00 0.00 2.74
2308 2461 9.011095 CAGGATGCTGATTTTCATTGATATAGT 57.989 33.333 8.85 0.00 0.00 2.12
2328 2481 1.536766 TGACGAAAAAGCAGCAGGATG 59.463 47.619 0.00 0.00 40.87 3.51
2329 2482 1.896220 TGACGAAAAAGCAGCAGGAT 58.104 45.000 0.00 0.00 0.00 3.24
2330 2483 1.674359 TTGACGAAAAAGCAGCAGGA 58.326 45.000 0.00 0.00 0.00 3.86
2331 2484 2.490328 TTTGACGAAAAAGCAGCAGG 57.510 45.000 0.00 0.00 0.00 4.85
2353 2506 3.383620 TCGCAATGCCATTGTCTTTTT 57.616 38.095 18.10 0.00 42.20 1.94
2354 2507 3.255725 CATCGCAATGCCATTGTCTTTT 58.744 40.909 18.10 0.00 42.20 2.27
2417 2570 2.266055 GGAGGGAGTGCAAGGACG 59.734 66.667 0.00 0.00 0.00 4.79
2437 2590 2.546795 GGTGTGCGAAGATAGGAGGATG 60.547 54.545 0.00 0.00 0.00 3.51
2488 2641 1.404047 CGCAAATAAACCAAGCTGGGG 60.404 52.381 13.11 7.69 43.37 4.96
2536 2689 0.464870 TGCTTGCTTGTGTTTGCCAT 59.535 45.000 0.00 0.00 0.00 4.40
2634 2789 4.309950 GGTGTTGGACGGCGGACT 62.310 66.667 13.24 0.00 0.00 3.85
2695 2850 2.444895 ACCTGGAGATCGAGGGCC 60.445 66.667 14.47 0.00 44.92 5.80
2719 2874 2.363680 CAGAGAAGTGATCCATACGGCT 59.636 50.000 0.00 0.00 0.00 5.52
2726 2881 1.274703 GGGGGCAGAGAAGTGATCCA 61.275 60.000 0.00 0.00 0.00 3.41
2741 2896 1.616091 ATGCGGCAAAATTCTGGGGG 61.616 55.000 6.82 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.