Multiple sequence alignment - TraesCS3D01G385800

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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 TraesCS3D01G385800 chr3D 100.000 4812 0 0 1 4812 501297323 501302134 0.000000e+00 8887.0
1 TraesCS3D01G385800 chr3D 89.504 343 28 6 2022 2358 501299282 501299622 1.240000e-115 427.0
2 TraesCS3D01G385800 chr3D 89.504 343 28 6 1960 2300 501299344 501299680 1.240000e-115 427.0
3 TraesCS3D01G385800 chr3A 95.367 2698 114 7 1960 4648 640766542 640769237 0.000000e+00 4279.0
4 TraesCS3D01G385800 chr3A 88.529 2162 131 55 256 2361 640764667 640766767 0.000000e+00 2510.0
5 TraesCS3D01G385800 chr3A 88.136 413 36 8 1960 2361 640766419 640766829 3.370000e-131 479.0
6 TraesCS3D01G385800 chr3A 88.148 405 41 5 1960 2358 640766480 640766883 4.360000e-130 475.0
7 TraesCS3D01G385800 chr3A 87.826 345 31 9 1960 2300 640766604 640766941 1.260000e-105 394.0
8 TraesCS3D01G385800 chr3A 88.673 309 23 7 2063 2361 640766399 640766705 2.740000e-97 366.0
9 TraesCS3D01G385800 chr3A 89.600 125 11 1 16 140 640764388 640764510 1.790000e-34 158.0
10 TraesCS3D01G385800 chr3B 92.319 2721 150 33 2063 4755 662976750 662979439 0.000000e+00 3812.0
11 TraesCS3D01G385800 chr3B 85.951 2356 171 77 15 2300 662974780 662977045 0.000000e+00 2370.0
12 TraesCS3D01G385800 chr3B 90.476 42 4 0 4748 4789 429338584 429338625 6.730000e-04 56.5
13 TraesCS3D01G385800 chr2D 80.153 393 48 21 798 1181 626865715 626866086 2.860000e-67 267.0
14 TraesCS3D01G385800 chr2A 87.629 194 20 4 4262 4453 24347999 24348190 6.270000e-54 222.0


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 TraesCS3D01G385800 chr3D 501297323 501302134 4811 False 3247.000000 8887 93.002667 1 4812 3 chr3D.!!$F1 4811
1 TraesCS3D01G385800 chr3A 640764388 640769237 4849 False 1237.285714 4279 89.468429 16 4648 7 chr3A.!!$F1 4632
2 TraesCS3D01G385800 chr3B 662974780 662979439 4659 False 3091.000000 3812 89.135000 15 4755 2 chr3B.!!$F2 4740

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
674 793 0.916358 CACCCACCTCCCTCTCCATT 60.916 60.000 0.00 0.0 0.0 3.16 F
745 874 1.228033 CGCTGCCATCATCCATCCA 60.228 57.895 0.00 0.0 0.0 3.41 F
2026 2236 0.240945 CGTGGGTTGCCATTTCTGAC 59.759 55.000 0.00 0.0 0.0 3.51 F
2628 3026 0.107214 ACCGTTGGCATGTGGATAGG 60.107 55.000 7.11 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 1953 0.107703 CCTATCGCTTGACTTGCCCA 60.108 55.000 0.00 0.0 0.00 5.36 R
2007 2217 0.240945 GTCAGAAATGGCAACCCACG 59.759 55.000 0.00 0.0 45.77 4.94 R
3556 3957 0.179119 GAGGCATGCATTTCAGTGGC 60.179 55.000 21.36 0.0 37.40 5.01 R
4556 4983 1.328374 CATGCTGATTTCGCATCGTCA 59.672 47.619 6.83 0.0 45.65 4.35 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
91 92 1.401905 GTTGCCATGGACGAGGATTTC 59.598 52.381 18.40 0.00 0.00 2.17
106 107 3.057734 GGATTTCTATACGTGCCTTCCG 58.942 50.000 0.00 0.00 0.00 4.30
119 120 1.587547 CCTTCCGGAAAGCTATCTGC 58.412 55.000 19.39 0.00 43.29 4.26
120 121 1.587547 CTTCCGGAAAGCTATCTGCC 58.412 55.000 19.39 0.00 44.23 4.85
130 131 1.761784 AGCTATCTGCCTCTGTTCCAG 59.238 52.381 0.00 0.00 44.23 3.86
132 133 1.761784 CTATCTGCCTCTGTTCCAGCT 59.238 52.381 0.00 0.00 0.00 4.24
141 142 2.818432 CTCTGTTCCAGCTGAATTGCTT 59.182 45.455 17.39 0.00 41.98 3.91
143 144 4.005650 TCTGTTCCAGCTGAATTGCTTAG 58.994 43.478 17.39 2.63 41.98 2.18
144 145 3.084039 TGTTCCAGCTGAATTGCTTAGG 58.916 45.455 17.39 0.00 41.98 2.69
148 149 3.054434 TCCAGCTGAATTGCTTAGGCTAA 60.054 43.478 17.39 6.80 41.98 3.09
152 153 6.039717 CCAGCTGAATTGCTTAGGCTAAATTA 59.960 38.462 17.39 0.00 41.98 1.40
178 181 2.422832 AGAAAACGGAGGCTACGACTAG 59.577 50.000 28.69 0.00 34.93 2.57
195 202 1.269723 CTAGCACCGACACAACAGAGA 59.730 52.381 0.00 0.00 0.00 3.10
200 207 1.341531 ACCGACACAACAGAGAAGGAG 59.658 52.381 0.00 0.00 0.00 3.69
205 212 4.752101 CGACACAACAGAGAAGGAGAAAAT 59.248 41.667 0.00 0.00 0.00 1.82
216 244 4.708909 AGAAGGAGAAAATGAAGGGCAATC 59.291 41.667 0.00 0.00 0.00 2.67
222 250 2.919666 AATGAAGGGCAATCGTTTCG 57.080 45.000 0.00 0.00 0.00 3.46
238 266 3.840763 CGTTTCGCATAAAGAAGTGCTTC 59.159 43.478 3.89 3.89 39.16 3.86
239 267 4.159120 GTTTCGCATAAAGAAGTGCTTCC 58.841 43.478 8.19 0.00 40.33 3.46
254 282 2.658679 CTTCCGCTGGGACACACACA 62.659 60.000 0.00 0.00 43.74 3.72
289 332 2.320781 ACGATGGAATCTGGGAGTAGG 58.679 52.381 0.00 0.00 42.58 3.18
328 378 2.570169 CGTTTAATGCACTCCACGTTG 58.430 47.619 0.00 0.00 0.00 4.10
330 380 3.547214 CGTTTAATGCACTCCACGTTGTT 60.547 43.478 0.00 0.00 0.00 2.83
362 413 5.479716 AAAAACCTGCCGAATTATACTCG 57.520 39.130 0.00 0.00 36.06 4.18
364 415 1.687123 ACCTGCCGAATTATACTCGCT 59.313 47.619 0.00 0.00 34.95 4.93
365 416 2.288273 ACCTGCCGAATTATACTCGCTC 60.288 50.000 0.00 0.00 34.95 5.03
366 417 2.329379 CTGCCGAATTATACTCGCTCC 58.671 52.381 0.00 0.00 34.95 4.70
367 418 1.684450 TGCCGAATTATACTCGCTCCA 59.316 47.619 0.00 0.00 34.95 3.86
369 420 2.673833 CCGAATTATACTCGCTCCACC 58.326 52.381 0.00 0.00 34.95 4.61
400 465 2.612212 GTGAGAACGGAAACTGCAAAGA 59.388 45.455 0.00 0.00 0.00 2.52
412 477 2.335712 GCAAAGAGCGAACCCCAGG 61.336 63.158 0.00 0.00 0.00 4.45
459 550 2.497675 GCAAGGAGGGGAAGAAAAATCC 59.502 50.000 0.00 0.00 36.16 3.01
460 551 3.778265 CAAGGAGGGGAAGAAAAATCCA 58.222 45.455 0.00 0.00 38.80 3.41
514 614 2.425773 CGAACGCACAGCAACAGC 60.426 61.111 0.00 0.00 0.00 4.40
515 615 2.715005 GAACGCACAGCAACAGCA 59.285 55.556 0.00 0.00 0.00 4.41
516 616 1.655350 GAACGCACAGCAACAGCAC 60.655 57.895 0.00 0.00 0.00 4.40
517 617 2.321668 GAACGCACAGCAACAGCACA 62.322 55.000 0.00 0.00 0.00 4.57
518 618 2.051614 CGCACAGCAACAGCACAG 60.052 61.111 0.00 0.00 0.00 3.66
519 619 2.333938 GCACAGCAACAGCACAGG 59.666 61.111 0.00 0.00 0.00 4.00
520 620 2.333938 CACAGCAACAGCACAGGC 59.666 61.111 0.00 0.00 41.61 4.85
590 701 4.845580 CGCCTGCCTGCCTGGTAG 62.846 72.222 4.63 4.63 46.45 3.18
592 703 3.720601 CCTGCCTGCCTGGTAGCA 61.721 66.667 6.24 6.75 45.67 3.49
593 704 2.352422 CTGCCTGCCTGGTAGCAA 59.648 61.111 6.24 0.00 43.52 3.91
608 719 3.769300 GGTAGCAACCATCCAAAAATCCT 59.231 43.478 0.00 0.00 45.98 3.24
636 747 1.441695 TCCCCGTCTTTTCCTTCCTT 58.558 50.000 0.00 0.00 0.00 3.36
641 752 2.338500 CGTCTTTTCCTTCCTTCCTCG 58.662 52.381 0.00 0.00 0.00 4.63
644 755 3.056035 GTCTTTTCCTTCCTTCCTCGCTA 60.056 47.826 0.00 0.00 0.00 4.26
663 782 1.920835 GCTTCTCCCTCACCCACCT 60.921 63.158 0.00 0.00 0.00 4.00
674 793 0.916358 CACCCACCTCCCTCTCCATT 60.916 60.000 0.00 0.00 0.00 3.16
725 854 4.175337 ACACCACACCACGCTGCT 62.175 61.111 0.00 0.00 0.00 4.24
741 870 2.515290 CTGCGCTGCCATCATCCA 60.515 61.111 9.73 0.00 0.00 3.41
745 874 1.228033 CGCTGCCATCATCCATCCA 60.228 57.895 0.00 0.00 0.00 3.41
893 1029 3.151022 CAGCTCCGACCTCCTCCC 61.151 72.222 0.00 0.00 0.00 4.30
1234 1380 4.821589 CCAACTCGGCGCTCTCCC 62.822 72.222 7.64 0.00 0.00 4.30
1471 1617 2.664851 CCAACGACGCCTTCTGCA 60.665 61.111 0.00 0.00 41.33 4.41
1707 1853 6.289834 TCCGGCAAGGTATAATTTAATTCGA 58.710 36.000 0.00 0.00 41.99 3.71
1712 1859 9.612620 GGCAAGGTATAATTTAATTCGATTCTG 57.387 33.333 0.00 0.00 0.00 3.02
1796 1945 5.997746 ACATAATACTGCAGTGTGAAGTTGT 59.002 36.000 29.57 14.01 37.46 3.32
1804 1953 3.119495 GCAGTGTGAAGTTGTCCAAAAGT 60.119 43.478 0.00 0.00 0.00 2.66
1831 1980 6.404293 GGCAAGTCAAGCGATAGGAATTTTTA 60.404 38.462 0.00 0.00 0.00 1.52
1888 2037 5.643379 TCACCAGCATTATTTCAGAAACC 57.357 39.130 0.00 0.00 0.00 3.27
1894 2043 5.577945 CAGCATTATTTCAGAAACCGCAAAT 59.422 36.000 0.00 0.00 0.00 2.32
1910 2059 3.357897 GCAAATGAGAATTGCGCTAGTC 58.642 45.455 11.27 11.27 43.14 2.59
1964 2113 9.969001 ATAGTTCCCTAGTCTATTAGATCTGAC 57.031 37.037 5.18 4.07 0.00 3.51
1965 2114 8.052621 AGTTCCCTAGTCTATTAGATCTGACT 57.947 38.462 15.46 15.46 41.81 3.41
1966 2115 9.173231 AGTTCCCTAGTCTATTAGATCTGACTA 57.827 37.037 15.92 15.92 39.94 2.59
1971 2120 6.817765 AGTCTATTAGATCTGACTAGCAGC 57.182 41.667 10.81 0.00 44.52 5.25
1972 2121 5.411361 AGTCTATTAGATCTGACTAGCAGCG 59.589 44.000 10.81 0.00 44.52 5.18
1973 2122 3.932545 ATTAGATCTGACTAGCAGCGG 57.067 47.619 5.18 0.00 44.52 5.52
1974 2123 1.610363 TAGATCTGACTAGCAGCGGG 58.390 55.000 5.18 0.00 44.52 6.13
1975 2124 0.396417 AGATCTGACTAGCAGCGGGT 60.396 55.000 0.00 0.00 44.52 5.28
1977 2126 0.905357 ATCTGACTAGCAGCGGGTTT 59.095 50.000 8.72 0.00 44.52 3.27
1978 2127 1.552578 TCTGACTAGCAGCGGGTTTA 58.447 50.000 8.72 0.00 44.52 2.01
1980 2129 1.476891 CTGACTAGCAGCGGGTTTAGA 59.523 52.381 0.00 0.00 37.90 2.10
1981 2130 1.476891 TGACTAGCAGCGGGTTTAGAG 59.523 52.381 0.00 0.00 0.00 2.43
1982 2131 1.749634 GACTAGCAGCGGGTTTAGAGA 59.250 52.381 0.00 0.00 0.00 3.10
1983 2132 1.751924 ACTAGCAGCGGGTTTAGAGAG 59.248 52.381 0.00 0.00 0.00 3.20
1984 2133 2.025155 CTAGCAGCGGGTTTAGAGAGA 58.975 52.381 0.00 0.00 0.00 3.10
1986 2135 0.808060 GCAGCGGGTTTAGAGAGAGC 60.808 60.000 0.00 0.00 0.00 4.09
1988 2137 1.107945 AGCGGGTTTAGAGAGAGCTC 58.892 55.000 5.27 5.27 41.62 4.09
1989 2138 0.818296 GCGGGTTTAGAGAGAGCTCA 59.182 55.000 17.77 0.00 43.81 4.26
1990 2139 1.470112 GCGGGTTTAGAGAGAGCTCAC 60.470 57.143 17.77 10.21 43.81 3.51
1991 2140 1.202200 CGGGTTTAGAGAGAGCTCACG 60.202 57.143 17.77 0.00 43.81 4.35
1992 2141 2.093106 GGGTTTAGAGAGAGCTCACGA 58.907 52.381 17.77 0.40 43.81 4.35
1993 2142 2.492484 GGGTTTAGAGAGAGCTCACGAA 59.508 50.000 17.77 6.75 43.81 3.85
1994 2143 3.131400 GGGTTTAGAGAGAGCTCACGAAT 59.869 47.826 17.77 3.88 43.81 3.34
1995 2144 4.338682 GGGTTTAGAGAGAGCTCACGAATA 59.661 45.833 17.77 2.90 43.81 1.75
1996 2145 5.010213 GGGTTTAGAGAGAGCTCACGAATAT 59.990 44.000 17.77 0.00 43.81 1.28
1997 2146 6.207025 GGGTTTAGAGAGAGCTCACGAATATA 59.793 42.308 17.77 0.00 43.81 0.86
1998 2147 7.094118 GGGTTTAGAGAGAGCTCACGAATATAT 60.094 40.741 17.77 0.00 43.81 0.86
1999 2148 7.966204 GGTTTAGAGAGAGCTCACGAATATATC 59.034 40.741 17.77 0.76 43.81 1.63
2007 2217 5.491982 AGCTCACGAATATATCATTTCCCC 58.508 41.667 0.00 0.00 0.00 4.81
2011 2221 4.391830 CACGAATATATCATTTCCCCGTGG 59.608 45.833 0.00 0.00 40.46 4.94
2013 2223 4.564821 CGAATATATCATTTCCCCGTGGGT 60.565 45.833 3.83 0.00 44.74 4.51
2021 2231 2.603171 CCCCGTGGGTTGCCATTT 60.603 61.111 3.83 0.00 38.25 2.32
2022 2232 2.645192 CCCCGTGGGTTGCCATTTC 61.645 63.158 3.83 0.00 38.25 2.17
2023 2233 1.606313 CCCGTGGGTTGCCATTTCT 60.606 57.895 0.00 0.00 0.00 2.52
2024 2234 1.586028 CCGTGGGTTGCCATTTCTG 59.414 57.895 0.00 0.00 0.00 3.02
2025 2235 0.893270 CCGTGGGTTGCCATTTCTGA 60.893 55.000 0.00 0.00 0.00 3.27
2026 2236 0.240945 CGTGGGTTGCCATTTCTGAC 59.759 55.000 0.00 0.00 0.00 3.51
2027 2237 1.620822 GTGGGTTGCCATTTCTGACT 58.379 50.000 0.00 0.00 0.00 3.41
2028 2238 2.790433 GTGGGTTGCCATTTCTGACTA 58.210 47.619 0.00 0.00 0.00 2.59
2029 2239 2.749621 GTGGGTTGCCATTTCTGACTAG 59.250 50.000 0.00 0.00 0.00 2.57
2030 2240 1.745653 GGGTTGCCATTTCTGACTAGC 59.254 52.381 0.00 0.00 0.00 3.42
2031 2241 2.436417 GGTTGCCATTTCTGACTAGCA 58.564 47.619 0.00 0.00 0.00 3.49
2032 2242 2.421424 GGTTGCCATTTCTGACTAGCAG 59.579 50.000 7.59 7.59 46.31 4.24
2033 2243 1.742761 TGCCATTTCTGACTAGCAGC 58.257 50.000 8.72 0.00 44.52 5.25
2034 2244 0.654683 GCCATTTCTGACTAGCAGCG 59.345 55.000 8.72 0.00 44.52 5.18
2035 2245 1.293924 CCATTTCTGACTAGCAGCGG 58.706 55.000 8.72 4.36 44.52 5.52
2036 2246 1.293924 CATTTCTGACTAGCAGCGGG 58.706 55.000 8.72 0.00 44.52 6.13
2037 2247 0.905357 ATTTCTGACTAGCAGCGGGT 59.095 50.000 8.72 0.00 44.52 5.28
2038 2248 0.685097 TTTCTGACTAGCAGCGGGTT 59.315 50.000 8.72 0.00 44.52 4.11
2039 2249 0.685097 TTCTGACTAGCAGCGGGTTT 59.315 50.000 8.72 0.00 44.52 3.27
2040 2250 1.552578 TCTGACTAGCAGCGGGTTTA 58.447 50.000 8.72 0.00 44.52 2.01
2041 2251 1.476891 TCTGACTAGCAGCGGGTTTAG 59.523 52.381 8.72 0.00 44.52 1.85
2042 2252 1.204941 CTGACTAGCAGCGGGTTTAGT 59.795 52.381 0.00 0.00 37.90 2.24
2043 2253 1.067142 TGACTAGCAGCGGGTTTAGTG 60.067 52.381 0.00 0.00 0.00 2.74
2044 2254 1.203994 GACTAGCAGCGGGTTTAGTGA 59.796 52.381 0.00 0.00 0.00 3.41
2045 2255 1.204941 ACTAGCAGCGGGTTTAGTGAG 59.795 52.381 0.00 0.00 0.00 3.51
2046 2256 1.476891 CTAGCAGCGGGTTTAGTGAGA 59.523 52.381 0.00 0.00 0.00 3.27
2047 2257 0.247736 AGCAGCGGGTTTAGTGAGAG 59.752 55.000 0.00 0.00 0.00 3.20
2048 2258 1.362406 GCAGCGGGTTTAGTGAGAGC 61.362 60.000 0.00 0.00 0.00 4.09
2049 2259 0.247736 CAGCGGGTTTAGTGAGAGCT 59.752 55.000 0.00 0.00 0.00 4.09
2050 2260 0.533032 AGCGGGTTTAGTGAGAGCTC 59.467 55.000 5.27 5.27 0.00 4.09
2051 2261 0.246635 GCGGGTTTAGTGAGAGCTCA 59.753 55.000 17.77 0.00 37.24 4.26
2067 2277 7.093354 TGAGAGCTCACGAATATATCATTTCC 58.907 38.462 17.77 0.00 34.14 3.13
2068 2278 6.402222 AGAGCTCACGAATATATCATTTCCC 58.598 40.000 17.77 0.00 0.00 3.97
2069 2279 5.491982 AGCTCACGAATATATCATTTCCCC 58.508 41.667 0.00 0.00 0.00 4.81
2070 2280 4.330074 GCTCACGAATATATCATTTCCCCG 59.670 45.833 0.00 0.00 0.00 5.73
2071 2281 5.477607 TCACGAATATATCATTTCCCCGT 57.522 39.130 0.00 0.00 0.00 5.28
2072 2282 5.234752 TCACGAATATATCATTTCCCCGTG 58.765 41.667 0.00 0.00 43.96 4.94
2073 2283 4.391830 CACGAATATATCATTTCCCCGTGG 59.608 45.833 0.00 0.00 40.46 4.94
2074 2284 3.938963 CGAATATATCATTTCCCCGTGGG 59.061 47.826 0.00 0.00 46.11 4.61
2075 2285 4.564821 CGAATATATCATTTCCCCGTGGGT 60.565 45.833 3.83 0.00 44.74 4.51
2076 2286 5.321927 GAATATATCATTTCCCCGTGGGTT 58.678 41.667 3.83 0.00 44.74 4.11
2077 2287 2.428544 TATCATTTCCCCGTGGGTTG 57.571 50.000 3.83 6.10 44.74 3.77
2078 2288 0.970427 ATCATTTCCCCGTGGGTTGC 60.970 55.000 3.83 0.00 44.74 4.17
2079 2289 2.283604 ATTTCCCCGTGGGTTGCC 60.284 61.111 3.83 0.00 44.74 4.52
2080 2290 3.153629 ATTTCCCCGTGGGTTGCCA 62.154 57.895 3.83 0.00 44.74 4.92
2081 2291 2.454459 ATTTCCCCGTGGGTTGCCAT 62.454 55.000 3.83 0.00 44.74 4.40
2082 2292 2.664835 TTTCCCCGTGGGTTGCCATT 62.665 55.000 3.83 0.00 44.74 3.16
2083 2293 2.603171 CCCCGTGGGTTGCCATTT 60.603 61.111 3.83 0.00 38.25 2.32
2135 2345 2.835156 TGAGTATGTCATTTCCCCGTGA 59.165 45.455 0.00 0.00 0.00 4.35
2145 2355 0.608035 TTCCCCGTGAGTTGCCATTC 60.608 55.000 0.00 0.00 0.00 2.67
2146 2356 1.002134 CCCCGTGAGTTGCCATTCT 60.002 57.895 0.00 0.00 0.00 2.40
2175 2386 2.495669 AGCAGGTTTAGAGAGAGCTCAC 59.504 50.000 17.77 10.21 43.81 3.51
2214 2487 2.488153 GTGGGTTGCCATTTCTGACTAC 59.512 50.000 0.00 0.00 0.00 2.73
2255 2528 4.445448 GCTCATGAGTATGTCATTTCCCCT 60.445 45.833 23.38 0.00 44.05 4.79
2279 2676 3.944015 GAGTTGCCATTTCTGACTAGCAT 59.056 43.478 0.00 0.00 0.00 3.79
2352 2749 1.367659 GCAGCAGGTTTAGAGCTCAG 58.632 55.000 17.77 0.00 36.26 3.35
2365 2762 3.707316 AGAGCTCAGGAGTATGTTGACT 58.293 45.455 17.77 0.00 0.00 3.41
2386 2783 5.016831 ACTGGGGAAGATTCAATGTTTACC 58.983 41.667 0.00 0.00 0.00 2.85
2406 2803 4.090090 ACCAGCTGACAGTTATACTCACT 58.910 43.478 17.39 0.00 0.00 3.41
2470 2868 2.127251 GCACCTTAGCTTTTTGTGTGC 58.873 47.619 0.00 0.00 40.49 4.57
2628 3026 0.107214 ACCGTTGGCATGTGGATAGG 60.107 55.000 7.11 0.00 0.00 2.57
2638 3036 3.181483 GCATGTGGATAGGCCTTTTCTTG 60.181 47.826 12.58 7.83 37.63 3.02
2808 3206 8.112822 TCTGGGATTCTTTATTGGTCATGTTTA 58.887 33.333 0.00 0.00 0.00 2.01
2850 3248 5.978919 TGAAATTGAATTGCACTGAACTGTC 59.021 36.000 0.00 0.00 0.00 3.51
2889 3287 6.483640 CAGTTAAAACTTACTCTGGTCTGCTT 59.516 38.462 0.00 0.00 37.08 3.91
2960 3358 8.040716 ACCTGATGAAATTAGTACCTTTTTCG 57.959 34.615 0.00 0.00 32.13 3.46
3001 3399 6.978659 TCCGTGATCTCTTAAATGTGATGTAC 59.021 38.462 0.00 0.00 0.00 2.90
3128 3526 9.970395 TTTCAAATAGAATAGCTGCATATTTGG 57.030 29.630 22.05 12.19 41.15 3.28
3355 3756 4.387862 GTGGAAGATGCAAAGCAATTTGAG 59.612 41.667 0.00 0.00 43.62 3.02
3370 3771 0.468226 TTGAGCCAGTCAAGGTCGTT 59.532 50.000 0.00 0.00 40.45 3.85
3574 3975 1.895238 GCCACTGAAATGCATGCCT 59.105 52.632 16.68 1.31 0.00 4.75
3709 4110 1.873591 GTCCATGAGTTCGCAACACTT 59.126 47.619 0.00 0.00 0.00 3.16
3931 4332 4.025360 TGAGGAACCAGTTAGGCGTAATA 58.975 43.478 1.65 0.00 43.14 0.98
3933 4334 4.957296 AGGAACCAGTTAGGCGTAATATG 58.043 43.478 1.65 5.00 43.14 1.78
3934 4335 4.652421 AGGAACCAGTTAGGCGTAATATGA 59.348 41.667 13.03 0.00 43.14 2.15
4228 4640 6.418057 ACTTGGTTTGCCTTGAAATATCAA 57.582 33.333 0.00 0.00 43.18 2.57
4258 4670 9.722056 GTTTGACTTTGTAGCATAATTATCTGG 57.278 33.333 0.00 0.00 0.00 3.86
4265 4683 7.136822 TGTAGCATAATTATCTGGGTTCTGT 57.863 36.000 0.00 0.00 0.00 3.41
4299 4717 1.155889 TCTTTGTGTGCATGCTACGG 58.844 50.000 20.33 11.58 0.00 4.02
4308 4726 2.016318 TGCATGCTACGGATTTCCTTG 58.984 47.619 20.33 0.00 0.00 3.61
4449 4873 5.782047 TGTTCAATCATTGTTCATGTTCCC 58.218 37.500 0.00 0.00 34.06 3.97
4521 4948 5.014123 TGAAATCCTGAGAGTGGGTTAACAT 59.986 40.000 8.10 0.00 0.00 2.71
4590 5017 3.405831 TCAGCATGAACTGTTTCTCTGG 58.594 45.455 0.00 0.00 45.97 3.86
4657 5090 8.244802 GCAGTTGTCTTCTTAGAATAGTCAGTA 58.755 37.037 0.00 0.00 30.65 2.74
4701 5134 2.305343 GAGCATCCTGGAGCCAATATCT 59.695 50.000 1.52 0.00 0.00 1.98
4731 5164 4.082245 ACGCAAAGGCATTATTAAACAGCT 60.082 37.500 0.00 0.00 41.24 4.24
4740 5173 7.775093 AGGCATTATTAAACAGCTGTCATAAGA 59.225 33.333 21.95 16.31 0.00 2.10
4751 5184 5.932883 CAGCTGTCATAAGATATGCAGTCAT 59.067 40.000 5.25 0.00 36.73 3.06
4755 5188 9.761504 GCTGTCATAAGATATGCAGTCATATAT 57.238 33.333 16.07 0.00 43.84 0.86
4769 5202 9.023962 TGCAGTCATATATGATACACATACTCA 57.976 33.333 18.18 6.77 43.12 3.41
4773 5206 8.962111 GTCATATATGATACACATACTCATGCG 58.038 37.037 18.18 0.00 43.12 4.73
4774 5207 8.686334 TCATATATGATACACATACTCATGCGT 58.314 33.333 11.49 0.00 43.12 5.24
4775 5208 9.950680 CATATATGATACACATACTCATGCGTA 57.049 33.333 6.92 0.00 43.12 4.42
4778 5211 7.818493 ATGATACACATACTCATGCGTATTC 57.182 36.000 5.60 2.25 39.42 1.75
4779 5212 6.981722 TGATACACATACTCATGCGTATTCT 58.018 36.000 5.60 0.00 39.42 2.40
4780 5213 8.106247 TGATACACATACTCATGCGTATTCTA 57.894 34.615 5.60 0.00 39.42 2.10
4781 5214 8.237267 TGATACACATACTCATGCGTATTCTAG 58.763 37.037 5.60 0.00 39.42 2.43
4782 5215 6.635030 ACACATACTCATGCGTATTCTAGA 57.365 37.500 5.60 0.00 35.39 2.43
4783 5216 7.039313 ACACATACTCATGCGTATTCTAGAA 57.961 36.000 7.82 7.82 35.39 2.10
4784 5217 7.489160 ACACATACTCATGCGTATTCTAGAAA 58.511 34.615 9.71 0.00 35.39 2.52
4785 5218 7.979537 ACACATACTCATGCGTATTCTAGAAAA 59.020 33.333 9.71 0.00 35.39 2.29
4786 5219 8.817100 CACATACTCATGCGTATTCTAGAAAAA 58.183 33.333 9.71 0.00 35.39 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.357314 CCAGATATGTATTATCCGTCTCCGT 59.643 44.000 0.00 0.00 37.96 4.69
1 2 5.357314 ACCAGATATGTATTATCCGTCTCCG 59.643 44.000 0.00 0.00 37.96 4.63
2 3 6.777213 ACCAGATATGTATTATCCGTCTCC 57.223 41.667 0.00 0.00 37.96 3.71
3 4 7.603651 ACAACCAGATATGTATTATCCGTCTC 58.396 38.462 0.00 0.00 37.96 3.36
4 5 7.540474 ACAACCAGATATGTATTATCCGTCT 57.460 36.000 0.00 0.00 37.96 4.18
5 6 8.088981 AGAACAACCAGATATGTATTATCCGTC 58.911 37.037 0.00 0.00 37.96 4.79
6 7 7.963532 AGAACAACCAGATATGTATTATCCGT 58.036 34.615 0.00 0.00 37.96 4.69
7 8 8.088365 TGAGAACAACCAGATATGTATTATCCG 58.912 37.037 0.00 0.00 37.96 4.18
8 9 9.429359 CTGAGAACAACCAGATATGTATTATCC 57.571 37.037 0.00 0.00 37.96 2.59
9 10 8.930760 GCTGAGAACAACCAGATATGTATTATC 58.069 37.037 0.00 0.00 37.55 1.75
10 11 8.654997 AGCTGAGAACAACCAGATATGTATTAT 58.345 33.333 0.00 0.00 32.37 1.28
11 12 7.928167 CAGCTGAGAACAACCAGATATGTATTA 59.072 37.037 8.42 0.00 32.37 0.98
12 13 6.765036 CAGCTGAGAACAACCAGATATGTATT 59.235 38.462 8.42 0.00 32.37 1.89
13 14 6.098838 TCAGCTGAGAACAACCAGATATGTAT 59.901 38.462 13.74 0.00 32.37 2.29
106 107 2.998316 ACAGAGGCAGATAGCTTTCC 57.002 50.000 0.00 0.00 44.79 3.13
130 131 5.917447 GCTAATTTAGCCTAAGCAATTCAGC 59.083 40.000 16.10 0.00 45.95 4.26
148 149 4.781934 AGCCTCCGTTTTCTATGCTAATT 58.218 39.130 0.00 0.00 0.00 1.40
152 153 2.481449 CGTAGCCTCCGTTTTCTATGCT 60.481 50.000 0.00 0.00 0.00 3.79
178 181 0.861837 CTTCTCTGTTGTGTCGGTGC 59.138 55.000 0.00 0.00 0.00 5.01
195 202 3.445096 CGATTGCCCTTCATTTTCTCCTT 59.555 43.478 0.00 0.00 0.00 3.36
200 207 3.608073 CGAAACGATTGCCCTTCATTTTC 59.392 43.478 0.00 0.00 0.00 2.29
205 212 0.886938 TGCGAAACGATTGCCCTTCA 60.887 50.000 0.00 0.00 0.00 3.02
216 244 3.455619 AGCACTTCTTTATGCGAAACG 57.544 42.857 0.00 0.00 46.74 3.60
238 266 2.972505 GTGTGTGTGTCCCAGCGG 60.973 66.667 0.00 0.00 0.00 5.52
239 267 3.337889 CGTGTGTGTGTCCCAGCG 61.338 66.667 0.00 0.00 0.00 5.18
254 282 1.070843 CATCGTTTCACGTGAAAGCGT 60.071 47.619 36.05 28.21 43.82 5.07
269 312 2.320781 CCTACTCCCAGATTCCATCGT 58.679 52.381 0.00 0.00 0.00 3.73
355 406 2.426651 GCCTGGTGGAGCGAGTATA 58.573 57.895 0.00 0.00 34.57 1.47
362 413 1.675641 ACATTTCGCCTGGTGGAGC 60.676 57.895 7.51 0.00 34.57 4.70
364 415 0.321564 CTCACATTTCGCCTGGTGGA 60.322 55.000 7.51 0.00 34.57 4.02
365 416 0.321564 TCTCACATTTCGCCTGGTGG 60.322 55.000 7.51 0.00 32.29 4.61
366 417 1.197721 GTTCTCACATTTCGCCTGGTG 59.802 52.381 0.00 0.00 0.00 4.17
367 418 1.523758 GTTCTCACATTTCGCCTGGT 58.476 50.000 0.00 0.00 0.00 4.00
369 420 0.443869 CCGTTCTCACATTTCGCCTG 59.556 55.000 0.00 0.00 0.00 4.85
400 465 1.001248 TACTAGCCTGGGGTTCGCT 59.999 57.895 0.00 0.00 36.63 4.93
403 468 3.029483 ACTAGTACTAGCCTGGGGTTC 57.971 52.381 26.54 0.00 36.66 3.62
409 474 3.631227 GTGGTGGTACTAGTACTAGCCTG 59.369 52.174 32.64 7.50 42.07 4.85
410 475 3.372458 GGTGGTGGTACTAGTACTAGCCT 60.372 52.174 32.64 13.01 42.07 4.58
412 477 3.379688 GTGGTGGTGGTACTAGTACTAGC 59.620 52.174 30.68 30.68 42.74 3.42
459 550 0.108804 CGCCTGGTGGTACAGTAGTG 60.109 60.000 0.00 0.00 41.80 2.74
460 551 1.255667 CCGCCTGGTGGTACAGTAGT 61.256 60.000 18.33 0.00 41.80 2.73
586 697 3.769300 AGGATTTTTGGATGGTTGCTACC 59.231 43.478 10.70 10.70 45.26 3.18
587 698 4.142160 GGAGGATTTTTGGATGGTTGCTAC 60.142 45.833 0.00 0.00 0.00 3.58
588 699 4.023291 GGAGGATTTTTGGATGGTTGCTA 58.977 43.478 0.00 0.00 0.00 3.49
589 700 2.833943 GGAGGATTTTTGGATGGTTGCT 59.166 45.455 0.00 0.00 0.00 3.91
590 701 2.566724 TGGAGGATTTTTGGATGGTTGC 59.433 45.455 0.00 0.00 0.00 4.17
591 702 4.440525 CGATGGAGGATTTTTGGATGGTTG 60.441 45.833 0.00 0.00 0.00 3.77
592 703 3.701040 CGATGGAGGATTTTTGGATGGTT 59.299 43.478 0.00 0.00 0.00 3.67
593 704 3.290710 CGATGGAGGATTTTTGGATGGT 58.709 45.455 0.00 0.00 0.00 3.55
608 719 1.550130 AAAGACGGGGAAGCGATGGA 61.550 55.000 0.00 0.00 0.00 3.41
636 747 0.466555 GAGGGAGAAGCTAGCGAGGA 60.467 60.000 9.55 0.00 0.00 3.71
641 752 0.978146 TGGGTGAGGGAGAAGCTAGC 60.978 60.000 6.62 6.62 0.00 3.42
644 755 1.920835 GGTGGGTGAGGGAGAAGCT 60.921 63.158 0.00 0.00 0.00 3.74
663 782 2.046447 AGGAAGGAAGAATGGAGAGGGA 59.954 50.000 0.00 0.00 0.00 4.20
674 793 1.985895 GGGAAACAGGAGGAAGGAAGA 59.014 52.381 0.00 0.00 0.00 2.87
725 854 1.895231 GATGGATGATGGCAGCGCA 60.895 57.895 11.47 0.00 0.00 6.09
741 870 1.223077 TGGTAGGGTGGCTATCTGGAT 59.777 52.381 0.00 0.00 0.00 3.41
745 874 1.971357 CGATTGGTAGGGTGGCTATCT 59.029 52.381 0.00 0.00 0.00 1.98
907 1043 4.654412 ATCTGCTCGATCGCCGCC 62.654 66.667 21.07 6.90 38.37 6.13
941 1077 0.387202 CGCATCACAGGGAGAGGTAG 59.613 60.000 0.00 0.00 0.00 3.18
1234 1380 2.066393 TGGGGAGGAAGATGCGGAG 61.066 63.158 0.00 0.00 0.00 4.63
1474 1620 3.423154 GCAGAACTTGGCGACCCG 61.423 66.667 0.00 0.00 0.00 5.28
1647 1793 3.691342 CAGGGCTCGACGGTGGAA 61.691 66.667 0.00 0.00 0.00 3.53
1712 1859 9.860898 AAATGCAATTACAAAAGGAGAGATTAC 57.139 29.630 0.00 0.00 33.67 1.89
1714 1861 8.810041 AGAAATGCAATTACAAAAGGAGAGATT 58.190 29.630 0.00 0.00 33.67 2.40
1804 1953 0.107703 CCTATCGCTTGACTTGCCCA 60.108 55.000 0.00 0.00 0.00 5.36
1894 2043 2.995939 CACTTGACTAGCGCAATTCTCA 59.004 45.455 11.47 0.00 0.00 3.27
1910 2059 5.509771 TCATCGTTTTGACATGTTCACTTG 58.490 37.500 0.00 0.00 32.26 3.16
1956 2105 0.396417 ACCCGCTGCTAGTCAGATCT 60.396 55.000 15.59 0.00 45.72 2.75
1963 2112 1.751924 CTCTCTAAACCCGCTGCTAGT 59.248 52.381 0.00 0.00 0.00 2.57
1964 2113 2.025155 TCTCTCTAAACCCGCTGCTAG 58.975 52.381 0.00 0.00 0.00 3.42
1965 2114 2.025155 CTCTCTCTAAACCCGCTGCTA 58.975 52.381 0.00 0.00 0.00 3.49
1966 2115 0.820871 CTCTCTCTAAACCCGCTGCT 59.179 55.000 0.00 0.00 0.00 4.24
1967 2116 0.808060 GCTCTCTCTAAACCCGCTGC 60.808 60.000 0.00 0.00 0.00 5.25
1968 2117 0.820871 AGCTCTCTCTAAACCCGCTG 59.179 55.000 0.00 0.00 0.00 5.18
1969 2118 1.107945 GAGCTCTCTCTAAACCCGCT 58.892 55.000 6.43 0.00 36.42 5.52
1970 2119 0.818296 TGAGCTCTCTCTAAACCCGC 59.182 55.000 16.19 0.00 40.03 6.13
1971 2120 1.202200 CGTGAGCTCTCTCTAAACCCG 60.202 57.143 16.19 0.00 40.03 5.28
1972 2121 2.093106 TCGTGAGCTCTCTCTAAACCC 58.907 52.381 16.19 0.00 40.03 4.11
1973 2122 3.851976 TTCGTGAGCTCTCTCTAAACC 57.148 47.619 16.19 0.00 40.03 3.27
1974 2123 8.508062 TGATATATTCGTGAGCTCTCTCTAAAC 58.492 37.037 16.19 1.42 40.03 2.01
1975 2124 8.622948 TGATATATTCGTGAGCTCTCTCTAAA 57.377 34.615 16.19 4.09 40.03 1.85
1977 2126 8.800370 AATGATATATTCGTGAGCTCTCTCTA 57.200 34.615 16.19 3.63 40.03 2.43
1978 2127 7.701539 AATGATATATTCGTGAGCTCTCTCT 57.298 36.000 16.19 1.46 40.03 3.10
1980 2129 7.319646 GGAAATGATATATTCGTGAGCTCTCT 58.680 38.462 16.19 0.00 0.00 3.10
1981 2130 6.533367 GGGAAATGATATATTCGTGAGCTCTC 59.467 42.308 16.19 10.75 0.00 3.20
1982 2131 6.402222 GGGAAATGATATATTCGTGAGCTCT 58.598 40.000 16.19 0.00 0.00 4.09
1983 2132 5.582665 GGGGAAATGATATATTCGTGAGCTC 59.417 44.000 6.82 6.82 0.00 4.09
1984 2133 5.491982 GGGGAAATGATATATTCGTGAGCT 58.508 41.667 0.00 0.00 0.00 4.09
1986 2135 5.348724 CACGGGGAAATGATATATTCGTGAG 59.651 44.000 0.00 0.00 45.25 3.51
1988 2137 4.391830 CCACGGGGAAATGATATATTCGTG 59.608 45.833 0.00 0.00 43.08 4.35
1989 2138 4.575885 CCACGGGGAAATGATATATTCGT 58.424 43.478 0.00 0.00 35.59 3.85
2007 2217 0.240945 GTCAGAAATGGCAACCCACG 59.759 55.000 0.00 0.00 45.77 4.94
2011 2221 2.421424 CTGCTAGTCAGAAATGGCAACC 59.579 50.000 8.06 0.00 45.72 3.77
2013 2223 2.086869 GCTGCTAGTCAGAAATGGCAA 58.913 47.619 15.59 0.00 45.72 4.52
2021 2231 1.476891 CTAAACCCGCTGCTAGTCAGA 59.523 52.381 15.59 0.00 45.72 3.27
2022 2232 1.204941 ACTAAACCCGCTGCTAGTCAG 59.795 52.381 9.12 9.12 45.62 3.51
2023 2233 1.067142 CACTAAACCCGCTGCTAGTCA 60.067 52.381 0.00 0.00 0.00 3.41
2024 2234 1.203994 TCACTAAACCCGCTGCTAGTC 59.796 52.381 0.00 0.00 0.00 2.59
2025 2235 1.204941 CTCACTAAACCCGCTGCTAGT 59.795 52.381 0.00 0.00 0.00 2.57
2026 2236 1.476891 TCTCACTAAACCCGCTGCTAG 59.523 52.381 0.00 0.00 0.00 3.42
2027 2237 1.476891 CTCTCACTAAACCCGCTGCTA 59.523 52.381 0.00 0.00 0.00 3.49
2028 2238 0.247736 CTCTCACTAAACCCGCTGCT 59.752 55.000 0.00 0.00 0.00 4.24
2029 2239 1.362406 GCTCTCACTAAACCCGCTGC 61.362 60.000 0.00 0.00 0.00 5.25
2030 2240 0.247736 AGCTCTCACTAAACCCGCTG 59.752 55.000 0.00 0.00 0.00 5.18
2031 2241 0.533032 GAGCTCTCACTAAACCCGCT 59.467 55.000 6.43 0.00 0.00 5.52
2032 2242 0.246635 TGAGCTCTCACTAAACCCGC 59.753 55.000 16.19 0.00 34.14 6.13
2042 2252 7.093354 GGAAATGATATATTCGTGAGCTCTCA 58.907 38.462 16.19 7.12 37.24 3.27
2043 2253 6.533367 GGGAAATGATATATTCGTGAGCTCTC 59.467 42.308 16.19 10.75 0.00 3.20
2044 2254 6.402222 GGGAAATGATATATTCGTGAGCTCT 58.598 40.000 16.19 0.00 0.00 4.09
2045 2255 5.582665 GGGGAAATGATATATTCGTGAGCTC 59.417 44.000 6.82 6.82 0.00 4.09
2046 2256 5.491982 GGGGAAATGATATATTCGTGAGCT 58.508 41.667 0.00 0.00 0.00 4.09
2047 2257 4.330074 CGGGGAAATGATATATTCGTGAGC 59.670 45.833 0.00 0.00 0.00 4.26
2048 2258 5.348724 CACGGGGAAATGATATATTCGTGAG 59.651 44.000 0.00 0.00 45.25 3.51
2049 2259 5.234752 CACGGGGAAATGATATATTCGTGA 58.765 41.667 0.00 0.00 45.25 4.35
2050 2260 4.391830 CCACGGGGAAATGATATATTCGTG 59.608 45.833 0.00 0.00 43.08 4.35
2051 2261 4.575885 CCACGGGGAAATGATATATTCGT 58.424 43.478 0.00 0.00 35.59 3.85
2067 2277 1.606313 AGAAATGGCAACCCACGGG 60.606 57.895 0.00 0.00 45.77 5.28
2068 2278 0.893270 TCAGAAATGGCAACCCACGG 60.893 55.000 0.00 0.00 45.77 4.94
2069 2279 0.240945 GTCAGAAATGGCAACCCACG 59.759 55.000 0.00 0.00 45.77 4.94
2070 2280 1.620822 AGTCAGAAATGGCAACCCAC 58.379 50.000 0.00 0.00 45.77 4.61
2072 2282 1.745653 GCTAGTCAGAAATGGCAACCC 59.254 52.381 0.00 0.00 0.00 4.11
2073 2283 2.421424 CTGCTAGTCAGAAATGGCAACC 59.579 50.000 8.06 0.00 45.72 3.77
2074 2284 2.159462 GCTGCTAGTCAGAAATGGCAAC 60.159 50.000 15.59 0.00 45.72 4.17
2075 2285 2.086869 GCTGCTAGTCAGAAATGGCAA 58.913 47.619 15.59 0.00 45.72 4.52
2076 2286 1.003464 TGCTGCTAGTCAGAAATGGCA 59.997 47.619 15.59 0.00 45.72 4.92
2077 2287 1.669779 CTGCTGCTAGTCAGAAATGGC 59.330 52.381 15.59 3.60 45.72 4.40
2078 2288 2.286872 CCTGCTGCTAGTCAGAAATGG 58.713 52.381 15.59 8.57 45.72 3.16
2079 2289 2.983229 ACCTGCTGCTAGTCAGAAATG 58.017 47.619 15.59 4.78 45.72 2.32
2080 2290 3.710209 AACCTGCTGCTAGTCAGAAAT 57.290 42.857 15.59 0.00 45.72 2.17
2081 2291 3.492102 AAACCTGCTGCTAGTCAGAAA 57.508 42.857 15.59 4.78 45.72 2.52
2082 2292 3.832490 TCTAAACCTGCTGCTAGTCAGAA 59.168 43.478 15.59 6.54 45.72 3.02
2083 2293 3.431415 TCTAAACCTGCTGCTAGTCAGA 58.569 45.455 15.59 2.63 45.72 3.27
2145 2355 1.208052 TCTAAACCTGCTGCTAGCCAG 59.792 52.381 13.29 12.87 41.51 4.85
2146 2356 1.208052 CTCTAAACCTGCTGCTAGCCA 59.792 52.381 13.29 2.57 41.51 4.75
2175 2386 2.201732 CACGGGGAAATGACATACTCG 58.798 52.381 5.68 5.68 0.00 4.18
2214 2487 1.830477 AGCTCTCTCTAAACCTGCTGG 59.170 52.381 8.29 8.29 39.83 4.85
2255 2528 2.839486 AGTCAGAAATGGCAACTCGA 57.161 45.000 0.00 0.00 37.61 4.04
2352 2749 2.838202 TCTTCCCCAGTCAACATACTCC 59.162 50.000 0.00 0.00 0.00 3.85
2365 2762 5.004361 TGGTAAACATTGAATCTTCCCCA 57.996 39.130 0.00 0.00 0.00 4.96
2386 2783 7.090808 TGTTAAGTGAGTATAACTGTCAGCTG 58.909 38.462 7.63 7.63 34.02 4.24
2406 2803 5.767665 ACAGAAAGTGCACACCATATGTTAA 59.232 36.000 21.04 0.00 40.64 2.01
2470 2868 1.135139 CCTGTGTACCCGATCAGAGTG 59.865 57.143 0.00 0.00 0.00 3.51
2535 2933 4.870636 TGGAGAATGTAATCCTGGCAAAT 58.129 39.130 0.00 0.00 36.50 2.32
2538 2936 4.314522 TTTGGAGAATGTAATCCTGGCA 57.685 40.909 0.00 0.00 36.50 4.92
2539 2937 4.889409 TCATTTGGAGAATGTAATCCTGGC 59.111 41.667 0.00 0.00 36.50 4.85
2638 3036 4.220602 ACATGTGCCCTAGAAAATTTCACC 59.779 41.667 8.55 0.00 0.00 4.02
2833 3231 2.143122 TCCGACAGTTCAGTGCAATTC 58.857 47.619 0.00 0.00 0.00 2.17
2850 3248 7.932120 AGTTTTAACTGATCTATTCGATCCG 57.068 36.000 0.00 0.00 46.52 4.18
2878 3276 2.327325 AGGTAAGGAAGCAGACCAGA 57.673 50.000 0.00 0.00 34.18 3.86
2940 3338 6.433093 AGGCACGAAAAAGGTACTAATTTCAT 59.567 34.615 13.94 1.64 41.49 2.57
2957 3355 4.696402 ACGGACATAATAAAAAGGCACGAA 59.304 37.500 0.00 0.00 0.00 3.85
2960 3358 5.554822 TCACGGACATAATAAAAAGGCAC 57.445 39.130 0.00 0.00 0.00 5.01
3125 3523 7.816995 GCAAGAACCATTTAATGATGTTACCAA 59.183 33.333 6.50 0.00 0.00 3.67
3128 3526 7.547227 AGGCAAGAACCATTTAATGATGTTAC 58.453 34.615 6.50 0.00 0.00 2.50
3355 3756 1.891919 TGCAACGACCTTGACTGGC 60.892 57.895 0.00 0.00 30.42 4.85
3370 3771 2.092968 GGGATACATCAGAACCTGTGCA 60.093 50.000 0.00 0.00 39.74 4.57
3556 3957 0.179119 GAGGCATGCATTTCAGTGGC 60.179 55.000 21.36 0.00 37.40 5.01
3574 3975 1.606668 GCAACGATTGTCAAGGTTGGA 59.393 47.619 23.21 0.00 39.97 3.53
3709 4110 1.608025 GGCGTCTTGAGGAACACATCA 60.608 52.381 0.00 0.00 0.00 3.07
3909 4310 1.927487 TACGCCTAACTGGTTCCTCA 58.073 50.000 0.00 0.00 38.35 3.86
3931 4332 3.196685 GGAAAGGTACTCAGCACTCTCAT 59.803 47.826 0.00 0.00 38.49 2.90
3933 4334 2.093921 GGGAAAGGTACTCAGCACTCTC 60.094 54.545 0.00 0.00 38.49 3.20
3934 4335 1.903183 GGGAAAGGTACTCAGCACTCT 59.097 52.381 0.00 0.00 38.49 3.24
4145 4550 8.616942 TGGATGGTATAAATTATTCACGTGTTG 58.383 33.333 16.51 0.00 0.00 3.33
4242 4654 8.451908 AAACAGAACCCAGATAATTATGCTAC 57.548 34.615 1.78 0.00 0.00 3.58
4265 4683 8.845227 TGCACACAAAGATAACTCTCATTTAAA 58.155 29.630 0.00 0.00 0.00 1.52
4543 4970 4.033932 TCGCATCGTCATTTTCTAACATGG 59.966 41.667 0.00 0.00 0.00 3.66
4549 4976 5.502382 GCTGATTTCGCATCGTCATTTTCTA 60.502 40.000 0.00 0.00 0.00 2.10
4551 4978 3.479949 GCTGATTTCGCATCGTCATTTTC 59.520 43.478 0.00 0.00 0.00 2.29
4556 4983 1.328374 CATGCTGATTTCGCATCGTCA 59.672 47.619 6.83 0.00 45.65 4.35
4590 5017 2.533266 TGCTGTGGAGAGTGTTCTTC 57.467 50.000 0.00 0.00 32.53 2.87
4657 5090 7.309073 GCTCAAAAGTTCCTCTTTGAGATCATT 60.309 37.037 22.36 0.00 44.50 2.57
4666 5099 4.522022 CAGGATGCTCAAAAGTTCCTCTTT 59.478 41.667 0.00 0.00 46.86 2.52
4701 5134 1.255882 AATGCCTTTGCGTCATTCCA 58.744 45.000 0.00 0.00 41.78 3.53
4709 5142 4.266029 CAGCTGTTTAATAATGCCTTTGCG 59.734 41.667 5.25 0.00 41.78 4.85
4721 5154 8.681486 TGCATATCTTATGACAGCTGTTTAAT 57.319 30.769 22.65 16.86 0.00 1.40
4724 5157 6.118170 ACTGCATATCTTATGACAGCTGTTT 58.882 36.000 22.65 14.28 30.69 2.83
4761 5194 8.942338 TTTTTCTAGAATACGCATGAGTATGT 57.058 30.769 20.85 14.23 37.39 2.29


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

AutoCloner maintained by Alex Coulton.