Multiple sequence alignment - TraesCS6D01G249800

Loading Multiple Alignment...

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 TraesCS6D01G249800 chr6D 100.000 2869 0 0 1 2869 353101384 353098516 0.000000e+00 5299.0
1 TraesCS6D01G249800 chr6D 78.818 694 77 34 117 763 254961536 254962206 1.240000e-108 403.0
2 TraesCS6D01G249800 chr6D 90.816 98 6 3 13 108 33892054 33892150 8.340000e-26 128.0
3 TraesCS6D01G249800 chr6B 89.187 2201 149 38 1 2140 525312578 525314750 0.000000e+00 2663.0
4 TraesCS6D01G249800 chr6B 84.692 601 91 1 1084 1684 79955401 79956000 1.470000e-167 599.0
5 TraesCS6D01G249800 chr6B 84.692 601 91 1 1084 1684 80007920 80008519 1.470000e-167 599.0
6 TraesCS6D01G249800 chr6A 93.250 1363 72 11 795 2140 489441322 489442681 0.000000e+00 1989.0
7 TraesCS6D01G249800 chr7D 80.246 896 129 35 842 1700 22650158 22651042 5.220000e-177 630.0
8 TraesCS6D01G249800 chrUn 85.442 577 84 0 1108 1684 27583017 27582441 4.090000e-168 601.0
9 TraesCS6D01G249800 chrUn 81.893 729 112 16 970 1684 27607480 27606758 5.290000e-167 597.0
10 TraesCS6D01G249800 chrUn 94.444 36 2 0 2058 2093 104682718 104682753 3.990000e-04 56.5
11 TraesCS6D01G249800 chr4A 84.330 619 85 11 1089 1700 705628192 705627579 1.900000e-166 595.0
12 TraesCS6D01G249800 chr7A 79.561 866 131 29 871 1700 23107934 23108789 6.890000e-161 577.0
13 TraesCS6D01G249800 chr3B 86.073 438 48 9 2442 2869 474362702 474363136 2.600000e-125 459.0
14 TraesCS6D01G249800 chr1B 85.747 435 50 11 2438 2865 192707305 192706876 1.570000e-122 449.0
15 TraesCS6D01G249800 chr1B 85.584 437 49 10 2442 2869 562660175 562660606 2.030000e-121 446.0
16 TraesCS6D01G249800 chr1B 84.510 439 53 10 2442 2869 562878970 562879404 1.230000e-113 420.0
17 TraesCS6D01G249800 chr1B 88.421 95 8 3 1 94 328816806 328816714 8.400000e-21 111.0
18 TraesCS6D01G249800 chr2B 79.823 679 82 27 144 775 786239203 786239873 7.290000e-121 444.0
19 TraesCS6D01G249800 chr2A 84.494 445 60 8 2429 2868 599791143 599790703 5.680000e-117 431.0
20 TraesCS6D01G249800 chr2A 86.071 280 28 11 498 773 587021118 587021390 1.010000e-74 291.0
21 TraesCS6D01G249800 chr1D 84.842 442 52 14 2438 2869 402938226 402937790 5.680000e-117 431.0
22 TraesCS6D01G249800 chr1D 83.746 283 38 7 498 776 493735234 493735512 7.880000e-66 261.0
23 TraesCS6D01G249800 chr1D 85.882 85 11 1 20 103 465706650 465706566 3.940000e-14 89.8
24 TraesCS6D01G249800 chr5B 85.023 434 52 11 2442 2869 680399278 680398852 2.040000e-116 429.0
25 TraesCS6D01G249800 chr5B 83.982 437 61 9 2438 2869 318869611 318869179 7.400000e-111 411.0
26 TraesCS6D01G249800 chr5B 84.507 284 34 10 498 774 608367256 608366976 3.640000e-69 272.0
27 TraesCS6D01G249800 chr5B 82.168 286 39 11 498 776 608216239 608215959 4.780000e-58 235.0
28 TraesCS6D01G249800 chr5B 77.429 350 36 19 452 774 697031263 697030930 4.920000e-38 169.0
29 TraesCS6D01G249800 chr2D 84.009 444 48 14 2438 2867 492535023 492534589 3.440000e-109 405.0
30 TraesCS6D01G249800 chr2D 80.068 592 73 21 2289 2869 161353869 161354426 5.760000e-107 398.0
31 TraesCS6D01G249800 chr2D 82.807 285 37 10 498 776 472480216 472479938 7.940000e-61 244.0
32 TraesCS6D01G249800 chr3D 86.429 280 32 6 498 774 580329465 580329741 4.650000e-78 302.0
33 TraesCS6D01G249800 chr3D 100.000 28 0 0 2062 2089 603138967 603138994 5.000000e-03 52.8
34 TraesCS6D01G249800 chr3A 87.097 248 26 6 498 741 343228296 343228541 2.820000e-70 276.0
35 TraesCS6D01G249800 chr1A 85.938 256 29 7 450 698 7081423 7081678 1.690000e-67 267.0
36 TraesCS6D01G249800 chr1A 80.172 232 41 3 198 426 244547934 244547705 4.920000e-38 169.0
37 TraesCS6D01G249800 chr1A 79.399 233 40 6 198 426 222373823 222373595 1.060000e-34 158.0
38 TraesCS6D01G249800 chr1A 89.423 104 10 1 3 105 536364775 536364672 2.320000e-26 130.0
39 TraesCS6D01G249800 chr7B 83.333 282 40 6 498 774 354699850 354699571 1.320000e-63 254.0
40 TraesCS6D01G249800 chr7B 90.244 41 4 0 2056 2096 717176281 717176241 1.000000e-03 54.7
41 TraesCS6D01G249800 chr7B 90.244 41 4 0 2056 2096 717250934 717250894 1.000000e-03 54.7
42 TraesCS6D01G249800 chr4D 84.553 123 16 2 1 120 20231796 20231674 5.020000e-23 119.0
43 TraesCS6D01G249800 chr5A 85.321 109 12 4 1 107 696741425 696741319 3.020000e-20 110.0
44 TraesCS6D01G249800 chr5A 100.000 30 0 0 2062 2091 632529260 632529231 3.990000e-04 56.5
45 TraesCS6D01G249800 chr4B 100.000 28 0 0 2065 2092 135587307 135587334 5.000000e-03 52.8


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 TraesCS6D01G249800 chr6D 353098516 353101384 2868 True 5299 5299 100.000 1 2869 1 chr6D.!!$R1 2868
1 TraesCS6D01G249800 chr6D 254961536 254962206 670 False 403 403 78.818 117 763 1 chr6D.!!$F2 646
2 TraesCS6D01G249800 chr6B 525312578 525314750 2172 False 2663 2663 89.187 1 2140 1 chr6B.!!$F3 2139
3 TraesCS6D01G249800 chr6B 79955401 79956000 599 False 599 599 84.692 1084 1684 1 chr6B.!!$F1 600
4 TraesCS6D01G249800 chr6B 80007920 80008519 599 False 599 599 84.692 1084 1684 1 chr6B.!!$F2 600
5 TraesCS6D01G249800 chr6A 489441322 489442681 1359 False 1989 1989 93.250 795 2140 1 chr6A.!!$F1 1345
6 TraesCS6D01G249800 chr7D 22650158 22651042 884 False 630 630 80.246 842 1700 1 chr7D.!!$F1 858
7 TraesCS6D01G249800 chrUn 27582441 27583017 576 True 601 601 85.442 1108 1684 1 chrUn.!!$R1 576
8 TraesCS6D01G249800 chrUn 27606758 27607480 722 True 597 597 81.893 970 1684 1 chrUn.!!$R2 714
9 TraesCS6D01G249800 chr4A 705627579 705628192 613 True 595 595 84.330 1089 1700 1 chr4A.!!$R1 611
10 TraesCS6D01G249800 chr7A 23107934 23108789 855 False 577 577 79.561 871 1700 1 chr7A.!!$F1 829
11 TraesCS6D01G249800 chr2B 786239203 786239873 670 False 444 444 79.823 144 775 1 chr2B.!!$F1 631
12 TraesCS6D01G249800 chr2D 161353869 161354426 557 False 398 398 80.068 2289 2869 1 chr2D.!!$F1 580

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
860 946 1.796459 CTACGGACGTTCCTTGTTTGG 59.204 52.381 1.57 0.0 33.3 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2507 2662 0.03392 GCTTGAAACAAGCCAAGGGG 59.966 55.0 21.13 0.0 39.93 4.79 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
88 89 2.731571 GGCCGACCCATGCAGTAGA 61.732 63.158 0.00 0.00 0.00 2.59
106 107 2.883026 AGAGACCTCCTATAATGCGCT 58.117 47.619 9.73 0.00 0.00 5.92
108 109 1.896465 AGACCTCCTATAATGCGCTCC 59.104 52.381 9.73 0.00 0.00 4.70
110 111 2.234908 GACCTCCTATAATGCGCTCCAT 59.765 50.000 9.73 0.81 35.06 3.41
407 413 7.841956 TCCAAAAGATTCAAAAACTGTTGGTA 58.158 30.769 14.83 4.12 44.65 3.25
481 526 7.602517 TGTTCGTGGATTTCAAAAATTGTTT 57.397 28.000 0.00 0.00 0.00 2.83
642 715 7.578736 GCATTTGTAAAAGTGTTCACGAATTTG 59.421 33.333 0.00 0.00 0.00 2.32
652 725 6.196353 AGTGTTCACGAATTTGAAAATGTTCG 59.804 34.615 9.73 9.73 44.52 3.95
715 789 8.634335 TGATTTCATGAAATTGAGAGTGGTAA 57.366 30.769 29.44 2.40 40.77 2.85
768 843 9.453572 GGCATGACCATTAGAGATTATGAATTA 57.546 33.333 0.00 0.00 38.86 1.40
782 868 8.850156 AGATTATGAATTATTTTCTCCAACGGG 58.150 33.333 0.00 0.00 0.00 5.28
789 875 2.358322 TTTCTCCAACGGGCTCTTTT 57.642 45.000 0.00 0.00 0.00 2.27
810 896 8.259411 TCTTTTGCCCGTAACAGAAATATACTA 58.741 33.333 0.00 0.00 0.00 1.82
838 924 2.862780 ACCCAAGGTAGGTCTGCAA 58.137 52.632 0.00 0.00 32.11 4.08
860 946 1.796459 CTACGGACGTTCCTTGTTTGG 59.204 52.381 1.57 0.00 33.30 3.28
905 996 2.282674 TACGCACCCGGTCTCTGT 60.283 61.111 0.00 0.00 39.22 3.41
1095 1229 2.497173 ATCGAGGCGATCTGCTGCT 61.497 57.895 0.00 0.28 43.45 4.24
1746 1883 2.876645 GAACGTCGCCGAGAGCAG 60.877 66.667 0.00 0.00 44.04 4.24
1801 1938 4.573900 AGCTCATGACATTTCTTCTCGTT 58.426 39.130 0.00 0.00 0.00 3.85
1819 1956 2.541999 CGTTCTCGCCTCTAGGATTGTC 60.542 54.545 0.00 0.00 37.39 3.18
1830 1970 5.099042 TCTAGGATTGTCTTTTAGGTGCC 57.901 43.478 0.00 0.00 0.00 5.01
1852 1992 3.300388 TCTAGGATTCTGGTACTGCAGG 58.700 50.000 19.93 0.00 0.00 4.85
1877 2019 9.722056 GGTCAGATGTCATTACATTACATTTTC 57.278 33.333 0.00 0.00 46.49 2.29
1956 2098 5.273208 AGCTAGGACATGTCTCTTTTCCTA 58.727 41.667 24.50 14.87 37.82 2.94
1995 2137 1.154035 GGGCGAATTGGCTCAAACG 60.154 57.895 12.42 10.74 44.11 3.60
2001 2151 2.742774 GAATTGGCTCAAACGCAACTT 58.257 42.857 0.00 0.00 0.00 2.66
2004 2154 1.007387 GGCTCAAACGCAACTTGGG 60.007 57.895 4.34 4.34 36.28 4.12
2008 2158 1.591327 CAAACGCAACTTGGGTGGC 60.591 57.895 11.90 0.00 43.03 5.01
2018 2168 3.934457 ACTTGGGTGGCTTTATTTTCG 57.066 42.857 0.00 0.00 0.00 3.46
2022 2172 2.817258 TGGGTGGCTTTATTTTCGTCAG 59.183 45.455 0.00 0.00 0.00 3.51
2024 2174 2.415491 GGTGGCTTTATTTTCGTCAGGC 60.415 50.000 0.00 0.00 0.00 4.85
2026 2176 1.535088 GCTTTATTTTCGTCAGGCGC 58.465 50.000 0.00 0.00 41.07 6.53
2028 2178 2.774007 CTTTATTTTCGTCAGGCGCAG 58.226 47.619 10.83 0.00 41.07 5.18
2033 2183 2.309528 TTTCGTCAGGCGCAGAATAT 57.690 45.000 10.83 0.00 41.07 1.28
2034 2184 2.309528 TTCGTCAGGCGCAGAATATT 57.690 45.000 10.83 0.00 41.07 1.28
2036 2186 3.660501 TCGTCAGGCGCAGAATATTAT 57.339 42.857 10.83 0.00 41.07 1.28
2122 2275 2.026636 TCTTCAATTCCAGGTTACCCGG 60.027 50.000 0.00 0.00 35.12 5.73
2123 2277 1.659022 TCAATTCCAGGTTACCCGGA 58.341 50.000 0.73 1.50 35.12 5.14
2129 2283 3.076079 TCCAGGTTACCCGGATTTTTC 57.924 47.619 0.73 0.00 35.12 2.29
2140 2294 5.660460 ACCCGGATTTTTCATAAATTGCTC 58.340 37.500 0.73 0.00 0.00 4.26
2141 2295 5.422012 ACCCGGATTTTTCATAAATTGCTCT 59.578 36.000 0.73 0.00 0.00 4.09
2142 2296 5.979517 CCCGGATTTTTCATAAATTGCTCTC 59.020 40.000 0.73 0.00 0.00 3.20
2143 2297 5.682862 CCGGATTTTTCATAAATTGCTCTCG 59.317 40.000 0.00 0.00 0.00 4.04
2144 2298 5.682862 CGGATTTTTCATAAATTGCTCTCGG 59.317 40.000 0.00 0.00 0.00 4.63
2145 2299 5.460091 GGATTTTTCATAAATTGCTCTCGGC 59.540 40.000 0.00 0.00 42.22 5.54
2146 2300 4.370364 TTTTCATAAATTGCTCTCGGCC 57.630 40.909 0.00 0.00 40.92 6.13
2147 2301 2.708216 TCATAAATTGCTCTCGGCCA 57.292 45.000 2.24 0.00 40.92 5.36
2148 2302 2.564771 TCATAAATTGCTCTCGGCCAG 58.435 47.619 2.24 0.00 40.92 4.85
2149 2303 2.092968 TCATAAATTGCTCTCGGCCAGT 60.093 45.455 2.24 0.00 40.92 4.00
2150 2304 2.024176 TAAATTGCTCTCGGCCAGTC 57.976 50.000 2.24 0.00 40.92 3.51
2151 2305 0.036732 AAATTGCTCTCGGCCAGTCA 59.963 50.000 2.24 0.26 40.92 3.41
2152 2306 0.674895 AATTGCTCTCGGCCAGTCAC 60.675 55.000 2.24 0.00 40.92 3.67
2153 2307 2.527951 ATTGCTCTCGGCCAGTCACC 62.528 60.000 2.24 0.00 40.92 4.02
2154 2308 4.459089 GCTCTCGGCCAGTCACCC 62.459 72.222 2.24 0.00 34.27 4.61
2155 2309 2.681778 CTCTCGGCCAGTCACCCT 60.682 66.667 2.24 0.00 0.00 4.34
2156 2310 2.203788 TCTCGGCCAGTCACCCTT 60.204 61.111 2.24 0.00 0.00 3.95
2157 2311 2.046892 CTCGGCCAGTCACCCTTG 60.047 66.667 2.24 0.00 0.00 3.61
2158 2312 4.329545 TCGGCCAGTCACCCTTGC 62.330 66.667 2.24 0.00 0.00 4.01
2159 2313 4.641645 CGGCCAGTCACCCTTGCA 62.642 66.667 2.24 0.00 33.53 4.08
2160 2314 2.985847 GGCCAGTCACCCTTGCAC 60.986 66.667 0.00 0.00 33.53 4.57
2161 2315 2.203337 GCCAGTCACCCTTGCACA 60.203 61.111 0.00 0.00 32.18 4.57
2162 2316 2.555547 GCCAGTCACCCTTGCACAC 61.556 63.158 0.00 0.00 32.18 3.82
2163 2317 1.149174 CCAGTCACCCTTGCACACT 59.851 57.895 0.00 0.00 0.00 3.55
2164 2318 0.886490 CCAGTCACCCTTGCACACTC 60.886 60.000 0.00 0.00 0.00 3.51
2165 2319 0.886490 CAGTCACCCTTGCACACTCC 60.886 60.000 0.00 0.00 0.00 3.85
2166 2320 1.148273 GTCACCCTTGCACACTCCA 59.852 57.895 0.00 0.00 0.00 3.86
2167 2321 0.250901 GTCACCCTTGCACACTCCAT 60.251 55.000 0.00 0.00 0.00 3.41
2168 2322 0.250858 TCACCCTTGCACACTCCATG 60.251 55.000 0.00 0.00 0.00 3.66
2169 2323 1.604593 ACCCTTGCACACTCCATGC 60.605 57.895 0.00 0.00 43.68 4.06
2170 2324 2.693762 CCCTTGCACACTCCATGCG 61.694 63.158 0.00 0.00 46.49 4.73
2171 2325 2.693762 CCTTGCACACTCCATGCGG 61.694 63.158 0.00 0.00 46.49 5.69
2172 2326 2.672651 TTGCACACTCCATGCGGG 60.673 61.111 0.00 0.00 46.49 6.13
2173 2327 4.720902 TGCACACTCCATGCGGGG 62.721 66.667 0.00 0.00 46.49 5.73
2174 2328 4.408821 GCACACTCCATGCGGGGA 62.409 66.667 0.00 0.00 35.64 4.81
2175 2329 2.350895 CACACTCCATGCGGGGAA 59.649 61.111 0.00 0.00 35.64 3.97
2176 2330 1.746615 CACACTCCATGCGGGGAAG 60.747 63.158 0.00 0.00 35.64 3.46
2177 2331 2.825836 CACTCCATGCGGGGAAGC 60.826 66.667 0.00 0.00 35.64 3.86
2178 2332 3.011517 ACTCCATGCGGGGAAGCT 61.012 61.111 0.00 0.00 35.64 3.74
2179 2333 2.515523 CTCCATGCGGGGAAGCTG 60.516 66.667 0.00 0.00 32.53 4.24
2180 2334 3.008517 TCCATGCGGGGAAGCTGA 61.009 61.111 0.00 0.00 38.13 4.26
2181 2335 2.825836 CCATGCGGGGAAGCTGAC 60.826 66.667 0.00 0.00 38.13 3.51
2182 2336 2.825836 CATGCGGGGAAGCTGACC 60.826 66.667 0.00 0.00 38.13 4.02
2183 2337 3.329889 ATGCGGGGAAGCTGACCA 61.330 61.111 11.49 0.00 38.13 4.02
2184 2338 3.628646 ATGCGGGGAAGCTGACCAC 62.629 63.158 11.49 7.35 38.13 4.16
2187 2341 2.358737 GGGGAAGCTGACCACGTG 60.359 66.667 9.08 9.08 0.00 4.49
2188 2342 3.050275 GGGAAGCTGACCACGTGC 61.050 66.667 10.91 0.00 0.00 5.34
2189 2343 3.050275 GGAAGCTGACCACGTGCC 61.050 66.667 10.91 4.54 0.00 5.01
2190 2344 2.031163 GAAGCTGACCACGTGCCT 59.969 61.111 10.91 0.00 0.00 4.75
2191 2345 2.029844 GAAGCTGACCACGTGCCTC 61.030 63.158 10.91 7.28 0.00 4.70
2192 2346 2.715532 GAAGCTGACCACGTGCCTCA 62.716 60.000 10.91 11.69 0.00 3.86
2193 2347 2.996168 AAGCTGACCACGTGCCTCAC 62.996 60.000 10.91 7.73 0.00 3.51
2194 2348 2.737180 CTGACCACGTGCCTCACT 59.263 61.111 10.91 0.00 31.34 3.41
2195 2349 1.373497 CTGACCACGTGCCTCACTC 60.373 63.158 10.91 0.00 31.34 3.51
2196 2350 2.430921 GACCACGTGCCTCACTCG 60.431 66.667 10.91 0.00 40.98 4.18
2197 2351 3.916392 GACCACGTGCCTCACTCGG 62.916 68.421 10.91 0.00 39.54 4.63
2198 2352 4.742201 CCACGTGCCTCACTCGGG 62.742 72.222 10.91 0.00 39.54 5.14
2204 2358 4.344865 GCCTCACTCGGGCCCAAA 62.345 66.667 24.92 8.34 43.49 3.28
2205 2359 2.677228 CCTCACTCGGGCCCAAAT 59.323 61.111 24.92 1.90 0.00 2.32
2206 2360 1.750399 CCTCACTCGGGCCCAAATG 60.750 63.158 24.92 16.19 0.00 2.32
2207 2361 1.299648 CTCACTCGGGCCCAAATGA 59.700 57.895 24.92 19.62 0.00 2.57
2208 2362 0.745845 CTCACTCGGGCCCAAATGAG 60.746 60.000 24.92 24.59 34.65 2.90
2209 2363 1.198094 TCACTCGGGCCCAAATGAGA 61.198 55.000 25.99 12.29 32.81 3.27
2210 2364 0.107017 CACTCGGGCCCAAATGAGAT 60.107 55.000 25.99 11.13 32.81 2.75
2211 2365 0.107017 ACTCGGGCCCAAATGAGATG 60.107 55.000 25.99 6.32 32.81 2.90
2212 2366 0.107017 CTCGGGCCCAAATGAGATGT 60.107 55.000 24.92 0.00 0.00 3.06
2213 2367 0.331278 TCGGGCCCAAATGAGATGTT 59.669 50.000 24.92 0.00 0.00 2.71
2214 2368 0.740737 CGGGCCCAAATGAGATGTTC 59.259 55.000 24.92 0.00 0.00 3.18
2215 2369 0.740737 GGGCCCAAATGAGATGTTCG 59.259 55.000 19.95 0.00 0.00 3.95
2216 2370 1.463674 GGCCCAAATGAGATGTTCGT 58.536 50.000 0.00 0.00 0.00 3.85
2217 2371 1.818674 GGCCCAAATGAGATGTTCGTT 59.181 47.619 0.00 0.00 36.58 3.85
2218 2372 2.159379 GGCCCAAATGAGATGTTCGTTC 60.159 50.000 0.00 0.00 33.89 3.95
2219 2373 2.159379 GCCCAAATGAGATGTTCGTTCC 60.159 50.000 0.00 0.00 33.89 3.62
2220 2374 3.347216 CCCAAATGAGATGTTCGTTCCT 58.653 45.455 0.00 0.00 33.89 3.36
2221 2375 3.758554 CCCAAATGAGATGTTCGTTCCTT 59.241 43.478 0.00 0.00 33.89 3.36
2222 2376 4.941263 CCCAAATGAGATGTTCGTTCCTTA 59.059 41.667 0.00 0.00 33.89 2.69
2223 2377 5.590259 CCCAAATGAGATGTTCGTTCCTTAT 59.410 40.000 0.00 0.00 33.89 1.73
2224 2378 6.238484 CCCAAATGAGATGTTCGTTCCTTATC 60.238 42.308 0.00 0.00 33.89 1.75
2225 2379 6.540189 CCAAATGAGATGTTCGTTCCTTATCT 59.460 38.462 0.00 0.00 33.89 1.98
2226 2380 7.254590 CCAAATGAGATGTTCGTTCCTTATCTC 60.255 40.741 0.00 0.00 42.42 2.75
2227 2381 6.723298 ATGAGATGTTCGTTCCTTATCTCT 57.277 37.500 12.17 0.00 42.51 3.10
2228 2382 6.531503 TGAGATGTTCGTTCCTTATCTCTT 57.468 37.500 12.17 0.00 42.51 2.85
2229 2383 6.565234 TGAGATGTTCGTTCCTTATCTCTTC 58.435 40.000 12.17 0.00 42.51 2.87
2230 2384 5.583495 AGATGTTCGTTCCTTATCTCTTCG 58.417 41.667 0.00 0.00 0.00 3.79
2231 2385 3.508762 TGTTCGTTCCTTATCTCTTCGC 58.491 45.455 0.00 0.00 0.00 4.70
2232 2386 3.057104 TGTTCGTTCCTTATCTCTTCGCA 60.057 43.478 0.00 0.00 0.00 5.10
2233 2387 4.113354 GTTCGTTCCTTATCTCTTCGCAT 58.887 43.478 0.00 0.00 0.00 4.73
2234 2388 3.706698 TCGTTCCTTATCTCTTCGCATG 58.293 45.455 0.00 0.00 0.00 4.06
2235 2389 2.797156 CGTTCCTTATCTCTTCGCATGG 59.203 50.000 0.00 0.00 0.00 3.66
2236 2390 2.533266 TCCTTATCTCTTCGCATGGC 57.467 50.000 0.00 0.00 0.00 4.40
2247 2401 4.107051 GCATGGCGGTGTGTGAGC 62.107 66.667 0.00 0.00 0.00 4.26
2252 2406 2.591715 GCGGTGTGTGAGCCACTT 60.592 61.111 6.83 0.00 44.81 3.16
2253 2407 2.896801 GCGGTGTGTGAGCCACTTG 61.897 63.158 6.83 0.00 44.81 3.16
2254 2408 2.896801 CGGTGTGTGAGCCACTTGC 61.897 63.158 6.83 0.00 44.81 4.01
2263 2417 2.028043 GCCACTTGCTTGCACACC 59.972 61.111 0.00 0.00 36.87 4.16
2264 2418 2.784356 GCCACTTGCTTGCACACCA 61.784 57.895 0.00 0.00 36.87 4.17
2265 2419 2.043625 CCACTTGCTTGCACACCAT 58.956 52.632 0.00 0.00 0.00 3.55
2266 2420 0.038892 CCACTTGCTTGCACACCATC 60.039 55.000 0.00 0.00 0.00 3.51
2267 2421 0.956633 CACTTGCTTGCACACCATCT 59.043 50.000 0.00 0.00 0.00 2.90
2268 2422 1.338973 CACTTGCTTGCACACCATCTT 59.661 47.619 0.00 0.00 0.00 2.40
2269 2423 2.034124 ACTTGCTTGCACACCATCTTT 58.966 42.857 0.00 0.00 0.00 2.52
2270 2424 2.431782 ACTTGCTTGCACACCATCTTTT 59.568 40.909 0.00 0.00 0.00 2.27
2271 2425 3.118665 ACTTGCTTGCACACCATCTTTTT 60.119 39.130 0.00 0.00 0.00 1.94
2272 2426 3.096489 TGCTTGCACACCATCTTTTTC 57.904 42.857 0.00 0.00 0.00 2.29
2273 2427 2.694628 TGCTTGCACACCATCTTTTTCT 59.305 40.909 0.00 0.00 0.00 2.52
2274 2428 3.243501 TGCTTGCACACCATCTTTTTCTC 60.244 43.478 0.00 0.00 0.00 2.87
2275 2429 3.005155 GCTTGCACACCATCTTTTTCTCT 59.995 43.478 0.00 0.00 0.00 3.10
2276 2430 4.791974 CTTGCACACCATCTTTTTCTCTC 58.208 43.478 0.00 0.00 0.00 3.20
2277 2431 4.090761 TGCACACCATCTTTTTCTCTCT 57.909 40.909 0.00 0.00 0.00 3.10
2278 2432 4.067896 TGCACACCATCTTTTTCTCTCTC 58.932 43.478 0.00 0.00 0.00 3.20
2279 2433 3.124297 GCACACCATCTTTTTCTCTCTCG 59.876 47.826 0.00 0.00 0.00 4.04
2280 2434 3.124297 CACACCATCTTTTTCTCTCTCGC 59.876 47.826 0.00 0.00 0.00 5.03
2281 2435 3.244215 ACACCATCTTTTTCTCTCTCGCA 60.244 43.478 0.00 0.00 0.00 5.10
2282 2436 3.370366 CACCATCTTTTTCTCTCTCGCAG 59.630 47.826 0.00 0.00 0.00 5.18
2283 2437 2.351111 CCATCTTTTTCTCTCTCGCAGC 59.649 50.000 0.00 0.00 0.00 5.25
2284 2438 2.820059 TCTTTTTCTCTCTCGCAGCA 57.180 45.000 0.00 0.00 0.00 4.41
2285 2439 3.111853 TCTTTTTCTCTCTCGCAGCAA 57.888 42.857 0.00 0.00 0.00 3.91
2286 2440 3.466836 TCTTTTTCTCTCTCGCAGCAAA 58.533 40.909 0.00 0.00 0.00 3.68
2287 2441 3.876914 TCTTTTTCTCTCTCGCAGCAAAA 59.123 39.130 0.00 0.00 0.00 2.44
2311 2465 1.927051 ATCCTTGGGGCCCTAAGAAT 58.073 50.000 41.25 29.68 0.00 2.40
2317 2471 1.214424 TGGGGCCCTAAGAATAAGCAC 59.786 52.381 25.93 0.00 0.00 4.40
2319 2473 2.158460 GGGGCCCTAAGAATAAGCACAT 60.158 50.000 24.38 0.00 0.00 3.21
2320 2474 3.566351 GGGCCCTAAGAATAAGCACATT 58.434 45.455 17.04 0.00 0.00 2.71
2326 2480 5.183904 CCCTAAGAATAAGCACATTATGGCC 59.816 44.000 0.00 0.00 34.21 5.36
2327 2481 5.183904 CCTAAGAATAAGCACATTATGGCCC 59.816 44.000 0.00 0.00 34.21 5.80
2330 2484 4.586001 AGAATAAGCACATTATGGCCCAAG 59.414 41.667 0.00 0.00 34.21 3.61
2334 2488 2.024464 AGCACATTATGGCCCAAGGTTA 60.024 45.455 0.00 0.00 0.00 2.85
2338 2492 5.418676 CACATTATGGCCCAAGGTTAAAAG 58.581 41.667 0.00 0.00 0.00 2.27
2339 2493 5.186797 CACATTATGGCCCAAGGTTAAAAGA 59.813 40.000 0.00 0.00 0.00 2.52
2341 2495 5.731957 TTATGGCCCAAGGTTAAAAGAAC 57.268 39.130 0.00 0.00 0.00 3.01
2354 2508 5.283012 GGTTAAAAGAACGTTGCGATGATTC 59.717 40.000 5.00 0.77 0.00 2.52
2360 2514 2.549926 ACGTTGCGATGATTCAGCATA 58.450 42.857 0.00 0.00 40.83 3.14
2409 2563 7.222872 AGGGAGATCTTGCTAAACATCATAAG 58.777 38.462 0.00 0.00 0.00 1.73
2410 2564 7.071698 AGGGAGATCTTGCTAAACATCATAAGA 59.928 37.037 0.00 0.00 0.00 2.10
2416 2570 8.256611 TCTTGCTAAACATCATAAGAGACAAC 57.743 34.615 0.00 0.00 0.00 3.32
2417 2571 7.877612 TCTTGCTAAACATCATAAGAGACAACA 59.122 33.333 0.00 0.00 0.00 3.33
2418 2572 7.977789 TGCTAAACATCATAAGAGACAACAA 57.022 32.000 0.00 0.00 0.00 2.83
2419 2573 8.032952 TGCTAAACATCATAAGAGACAACAAG 57.967 34.615 0.00 0.00 0.00 3.16
2420 2574 7.119699 TGCTAAACATCATAAGAGACAACAAGG 59.880 37.037 0.00 0.00 0.00 3.61
2421 2575 7.119846 GCTAAACATCATAAGAGACAACAAGGT 59.880 37.037 0.00 0.00 0.00 3.50
2422 2576 7.440523 AAACATCATAAGAGACAACAAGGTC 57.559 36.000 0.00 0.00 38.08 3.85
2423 2577 6.114187 ACATCATAAGAGACAACAAGGTCA 57.886 37.500 0.00 0.00 40.29 4.02
2424 2578 6.533730 ACATCATAAGAGACAACAAGGTCAA 58.466 36.000 0.00 0.00 40.29 3.18
2425 2579 6.998074 ACATCATAAGAGACAACAAGGTCAAA 59.002 34.615 0.00 0.00 40.29 2.69
2426 2580 7.502226 ACATCATAAGAGACAACAAGGTCAAAA 59.498 33.333 0.00 0.00 40.29 2.44
2427 2581 7.873719 TCATAAGAGACAACAAGGTCAAAAA 57.126 32.000 0.00 0.00 40.29 1.94
2455 2609 4.353777 TCATAAGAGACAAGCCTACCACT 58.646 43.478 0.00 0.00 0.00 4.00
2459 2613 2.300437 AGAGACAAGCCTACCACTTCAC 59.700 50.000 0.00 0.00 0.00 3.18
2461 2615 0.034896 ACAAGCCTACCACTTCACCG 59.965 55.000 0.00 0.00 0.00 4.94
2463 2617 2.436115 GCCTACCACTTCACCGCC 60.436 66.667 0.00 0.00 0.00 6.13
2467 2621 3.229156 TACCACTTCACCGCCACCG 62.229 63.158 0.00 0.00 0.00 4.94
2479 2633 2.345991 CCACCGCCTCCGAAGAAA 59.654 61.111 0.00 0.00 36.29 2.52
2490 2644 4.632153 CCTCCGAAGAAAGAAACTTGAGA 58.368 43.478 0.00 0.00 0.00 3.27
2491 2645 4.449405 CCTCCGAAGAAAGAAACTTGAGAC 59.551 45.833 0.00 0.00 0.00 3.36
2492 2646 5.018539 TCCGAAGAAAGAAACTTGAGACA 57.981 39.130 0.00 0.00 0.00 3.41
2493 2647 4.809426 TCCGAAGAAAGAAACTTGAGACAC 59.191 41.667 0.00 0.00 0.00 3.67
2494 2648 4.318121 CCGAAGAAAGAAACTTGAGACACG 60.318 45.833 0.00 0.00 0.00 4.49
2497 2651 3.118371 AGAAAGAAACTTGAGACACGGGT 60.118 43.478 0.00 0.00 0.00 5.28
2498 2652 4.100498 AGAAAGAAACTTGAGACACGGGTA 59.900 41.667 0.00 0.00 0.00 3.69
2499 2653 4.618920 AAGAAACTTGAGACACGGGTAT 57.381 40.909 0.00 0.00 0.00 2.73
2500 2654 3.926616 AGAAACTTGAGACACGGGTATG 58.073 45.455 0.00 0.00 0.00 2.39
2502 2656 0.249398 ACTTGAGACACGGGTATGGC 59.751 55.000 0.00 0.00 0.00 4.40
2527 2682 1.043022 CCCTTGGCTTGTTTCAAGCT 58.957 50.000 26.11 0.00 42.62 3.74
2568 2723 7.384115 CGGTATCGTATCACCATCACTTTTATT 59.616 37.037 0.00 0.00 34.25 1.40
2609 2765 9.638176 AGTTTGATCCTTAGCTATTTCATGATT 57.362 29.630 0.00 0.00 0.00 2.57
2654 2810 8.260818 AGTATGATGTAGTATTTGAGTGCTTGT 58.739 33.333 0.00 0.00 0.00 3.16
2658 2814 6.223138 TGTAGTATTTGAGTGCTTGTTTCG 57.777 37.500 0.00 0.00 0.00 3.46
2667 2823 4.864806 TGAGTGCTTGTTTCGTGATCTATC 59.135 41.667 0.00 0.00 0.00 2.08
2670 2826 6.810911 AGTGCTTGTTTCGTGATCTATCTAT 58.189 36.000 0.00 0.00 0.00 1.98
2671 2827 7.941919 AGTGCTTGTTTCGTGATCTATCTATA 58.058 34.615 0.00 0.00 0.00 1.31
2672 2828 8.580720 AGTGCTTGTTTCGTGATCTATCTATAT 58.419 33.333 0.00 0.00 0.00 0.86
2683 2839 9.804547 CGTGATCTATCTATATATGTGATCGTG 57.195 37.037 0.00 0.00 33.64 4.35
2694 2850 2.742774 TGTGATCGTGTGTGAGAGTTG 58.257 47.619 0.00 0.00 0.00 3.16
2706 2862 9.302345 CGTGTGTGAGAGTTGTATAATAAAGAT 57.698 33.333 0.00 0.00 0.00 2.40
2726 2884 8.862550 AAAGATTAGTTTGAGTCTTTGCTTTG 57.137 30.769 0.00 0.00 38.92 2.77
2731 2889 5.105063 AGTTTGAGTCTTTGCTTTGCTTTC 58.895 37.500 0.00 0.00 0.00 2.62
2733 2891 4.558538 TGAGTCTTTGCTTTGCTTTCTC 57.441 40.909 0.00 0.00 0.00 2.87
2743 2901 4.202000 TGCTTTGCTTTCTCGTTTCAATCA 60.202 37.500 0.00 0.00 0.00 2.57
2744 2902 4.739716 GCTTTGCTTTCTCGTTTCAATCAA 59.260 37.500 0.00 0.00 0.00 2.57
2749 2907 4.739716 GCTTTCTCGTTTCAATCAAAGCAA 59.260 37.500 8.88 0.00 43.35 3.91
2797 2962 7.290948 TCTGATGGGAGTAATGACTTCACATAT 59.709 37.037 0.00 0.00 35.45 1.78
2803 2968 9.482627 GGGAGTAATGACTTCACATATAAGAAG 57.517 37.037 12.41 12.41 45.14 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 2.302587 GGATTCCCCTGTTTGGAACA 57.697 50.000 0.00 0.00 44.30 3.18
71 72 1.227380 CTCTACTGCATGGGTCGGC 60.227 63.158 0.00 0.00 0.00 5.54
73 74 0.103208 GGTCTCTACTGCATGGGTCG 59.897 60.000 0.00 0.00 0.00 4.79
88 89 1.896465 GGAGCGCATTATAGGAGGTCT 59.104 52.381 11.47 0.00 33.85 3.85
108 109 0.597568 TTTTGAAGTCCCAGCGCATG 59.402 50.000 11.47 4.88 0.00 4.06
110 111 2.800516 TTTTTGAAGTCCCAGCGCA 58.199 47.368 11.47 0.00 0.00 6.09
389 395 9.575783 TTGTAAGTTACCAACAGTTTTTGAATC 57.424 29.630 10.51 0.00 0.00 2.52
600 673 9.906660 TTTACAAATGCTCGAACATTTTCTAAT 57.093 25.926 21.10 9.43 45.63 1.73
652 725 9.929722 TTAACTCGTGCATATATTTGAAATCAC 57.070 29.630 0.00 0.00 0.00 3.06
712 786 4.808895 TGTTGCATCACCGAGATACATTAC 59.191 41.667 0.00 0.00 34.43 1.89
715 789 3.541996 TGTTGCATCACCGAGATACAT 57.458 42.857 0.00 0.00 34.43 2.29
768 843 2.586648 AAGAGCCCGTTGGAGAAAAT 57.413 45.000 0.00 0.00 0.00 1.82
782 868 1.519408 TCTGTTACGGGCAAAAGAGC 58.481 50.000 0.00 0.00 0.00 4.09
789 875 6.762661 GGTTTAGTATATTTCTGTTACGGGCA 59.237 38.462 0.00 0.00 0.00 5.36
895 986 1.171308 TCGGAGTAAACAGAGACCGG 58.829 55.000 0.00 0.00 40.59 5.28
905 996 4.272504 GCAATGAAATCGGATCGGAGTAAA 59.727 41.667 9.03 0.00 0.00 2.01
1095 1229 3.067684 GAGGGAATCCACGAAAAAGGA 57.932 47.619 0.09 0.00 38.50 3.36
1427 1564 0.535553 TGTTCCCCGGTTGTACAAGC 60.536 55.000 24.53 24.53 35.61 4.01
1801 1938 2.738587 AGACAATCCTAGAGGCGAGA 57.261 50.000 0.00 0.00 34.44 4.04
1819 1956 5.363939 CAGAATCCTAGAGGCACCTAAAAG 58.636 45.833 0.00 0.00 34.44 2.27
1830 1970 3.320541 CCTGCAGTACCAGAATCCTAGAG 59.679 52.174 13.81 0.00 34.77 2.43
1852 1992 9.722056 GGAAAATGTAATGTAATGACATCTGAC 57.278 33.333 0.00 0.00 45.93 3.51
1910 2052 3.126831 GCCCATCTGATCGTTCTACAAG 58.873 50.000 0.00 0.00 0.00 3.16
1969 2111 3.259374 TGAGCCAATTCGCCCAAAATTAA 59.741 39.130 0.00 0.00 0.00 1.40
1971 2113 1.622811 TGAGCCAATTCGCCCAAAATT 59.377 42.857 0.00 0.00 0.00 1.82
1972 2114 1.265236 TGAGCCAATTCGCCCAAAAT 58.735 45.000 0.00 0.00 0.00 1.82
1976 2118 1.861542 CGTTTGAGCCAATTCGCCCA 61.862 55.000 0.00 0.00 0.00 5.36
1995 2137 3.401033 AAATAAAGCCACCCAAGTTGC 57.599 42.857 0.00 0.00 34.89 4.17
2001 2151 2.817258 CTGACGAAAATAAAGCCACCCA 59.183 45.455 0.00 0.00 0.00 4.51
2004 2154 2.863739 GCCTGACGAAAATAAAGCCAC 58.136 47.619 0.00 0.00 0.00 5.01
2018 2168 5.931441 AAAGATAATATTCTGCGCCTGAC 57.069 39.130 4.18 0.00 0.00 3.51
2022 2172 9.922305 GTGAATATAAAGATAATATTCTGCGCC 57.078 33.333 4.18 0.00 42.74 6.53
2052 2202 7.881232 ACGACACTTATTTTAGGATGGAAGAAA 59.119 33.333 0.00 0.00 0.00 2.52
2054 2204 6.942976 ACGACACTTATTTTAGGATGGAAGA 58.057 36.000 0.00 0.00 0.00 2.87
2056 2206 7.162761 TCAACGACACTTATTTTAGGATGGAA 58.837 34.615 0.00 0.00 0.00 3.53
2093 2243 8.749354 GGTAACCTGGAATTGAAGAAATGTAAT 58.251 33.333 0.00 0.00 0.00 1.89
2118 2271 5.906073 AGAGCAATTTATGAAAAATCCGGG 58.094 37.500 0.00 0.00 0.00 5.73
2122 2275 5.460091 GGCCGAGAGCAATTTATGAAAAATC 59.540 40.000 0.00 0.00 46.50 2.17
2123 2277 5.105392 TGGCCGAGAGCAATTTATGAAAAAT 60.105 36.000 0.00 0.00 46.50 1.82
2129 2283 2.289002 GACTGGCCGAGAGCAATTTATG 59.711 50.000 8.91 0.00 46.50 1.90
2140 2294 2.046892 CAAGGGTGACTGGCCGAG 60.047 66.667 0.00 0.00 0.00 4.63
2141 2295 4.329545 GCAAGGGTGACTGGCCGA 62.330 66.667 0.00 0.00 40.50 5.54
2142 2296 4.641645 TGCAAGGGTGACTGGCCG 62.642 66.667 0.00 0.00 46.19 6.13
2143 2297 2.985847 GTGCAAGGGTGACTGGCC 60.986 66.667 0.00 0.00 46.19 5.36
2144 2298 2.203337 TGTGCAAGGGTGACTGGC 60.203 61.111 0.00 0.00 46.97 4.85
2145 2299 0.886490 GAGTGTGCAAGGGTGACTGG 60.886 60.000 0.00 0.00 0.00 4.00
2146 2300 0.886490 GGAGTGTGCAAGGGTGACTG 60.886 60.000 0.00 0.00 0.00 3.51
2147 2301 1.344953 TGGAGTGTGCAAGGGTGACT 61.345 55.000 0.00 0.00 0.00 3.41
2148 2302 0.250901 ATGGAGTGTGCAAGGGTGAC 60.251 55.000 0.00 0.00 0.00 3.67
2149 2303 0.250858 CATGGAGTGTGCAAGGGTGA 60.251 55.000 0.00 0.00 0.00 4.02
2150 2304 1.870055 GCATGGAGTGTGCAAGGGTG 61.870 60.000 0.00 0.00 42.08 4.61
2151 2305 1.604593 GCATGGAGTGTGCAAGGGT 60.605 57.895 0.00 0.00 42.08 4.34
2152 2306 2.693762 CGCATGGAGTGTGCAAGGG 61.694 63.158 0.00 0.00 42.62 3.95
2153 2307 2.693762 CCGCATGGAGTGTGCAAGG 61.694 63.158 0.00 0.00 42.62 3.61
2154 2308 2.693762 CCCGCATGGAGTGTGCAAG 61.694 63.158 0.00 0.00 42.62 4.01
2155 2309 2.672651 CCCGCATGGAGTGTGCAA 60.673 61.111 0.00 0.00 42.62 4.08
2156 2310 4.720902 CCCCGCATGGAGTGTGCA 62.721 66.667 0.00 0.00 42.62 4.57
2157 2311 3.918253 TTCCCCGCATGGAGTGTGC 62.918 63.158 0.00 0.00 37.00 4.57
2158 2312 1.746615 CTTCCCCGCATGGAGTGTG 60.747 63.158 0.00 0.00 37.49 3.82
2159 2313 2.671070 CTTCCCCGCATGGAGTGT 59.329 61.111 0.00 0.00 37.49 3.55
2160 2314 2.825836 GCTTCCCCGCATGGAGTG 60.826 66.667 0.00 0.00 37.49 3.51
2161 2315 3.011517 AGCTTCCCCGCATGGAGT 61.012 61.111 0.00 0.00 37.49 3.85
2162 2316 2.515523 CAGCTTCCCCGCATGGAG 60.516 66.667 0.00 0.00 37.49 3.86
2163 2317 3.008517 TCAGCTTCCCCGCATGGA 61.009 61.111 0.00 0.00 37.49 3.41
2164 2318 2.825836 GTCAGCTTCCCCGCATGG 60.826 66.667 0.00 0.00 0.00 3.66
2165 2319 2.825836 GGTCAGCTTCCCCGCATG 60.826 66.667 0.00 0.00 0.00 4.06
2166 2320 3.329889 TGGTCAGCTTCCCCGCAT 61.330 61.111 2.68 0.00 0.00 4.73
2167 2321 4.329545 GTGGTCAGCTTCCCCGCA 62.330 66.667 2.68 0.00 0.00 5.69
2169 2323 4.003788 ACGTGGTCAGCTTCCCCG 62.004 66.667 7.75 7.75 0.00 5.73
2170 2324 2.358737 CACGTGGTCAGCTTCCCC 60.359 66.667 7.95 0.00 0.00 4.81
2171 2325 3.050275 GCACGTGGTCAGCTTCCC 61.050 66.667 18.88 0.00 0.00 3.97
2172 2326 3.050275 GGCACGTGGTCAGCTTCC 61.050 66.667 18.88 3.03 0.00 3.46
2173 2327 2.029844 GAGGCACGTGGTCAGCTTC 61.030 63.158 18.88 4.32 0.00 3.86
2174 2328 2.031163 GAGGCACGTGGTCAGCTT 59.969 61.111 18.88 0.00 0.00 3.74
2175 2329 3.233980 TGAGGCACGTGGTCAGCT 61.234 61.111 18.88 0.00 0.00 4.24
2176 2330 3.044305 GTGAGGCACGTGGTCAGC 61.044 66.667 18.88 1.27 0.00 4.26
2177 2331 1.373497 GAGTGAGGCACGTGGTCAG 60.373 63.158 18.88 0.00 39.64 3.51
2178 2332 2.734591 GAGTGAGGCACGTGGTCA 59.265 61.111 18.88 0.00 39.64 4.02
2179 2333 2.430921 CGAGTGAGGCACGTGGTC 60.431 66.667 18.88 0.44 39.64 4.02
2180 2334 3.991051 CCGAGTGAGGCACGTGGT 61.991 66.667 18.88 0.00 39.64 4.16
2181 2335 4.742201 CCCGAGTGAGGCACGTGG 62.742 72.222 18.88 0.00 39.64 4.94
2188 2342 1.750399 CATTTGGGCCCGAGTGAGG 60.750 63.158 27.03 3.91 0.00 3.86
2189 2343 0.745845 CTCATTTGGGCCCGAGTGAG 60.746 60.000 37.15 37.15 37.67 3.51
2190 2344 1.198094 TCTCATTTGGGCCCGAGTGA 61.198 55.000 30.14 30.14 0.00 3.41
2191 2345 0.107017 ATCTCATTTGGGCCCGAGTG 60.107 55.000 25.53 25.53 0.00 3.51
2192 2346 0.107017 CATCTCATTTGGGCCCGAGT 60.107 55.000 19.37 9.86 0.00 4.18
2193 2347 0.107017 ACATCTCATTTGGGCCCGAG 60.107 55.000 19.37 17.51 0.00 4.63
2194 2348 0.331278 AACATCTCATTTGGGCCCGA 59.669 50.000 19.37 14.11 0.00 5.14
2195 2349 0.740737 GAACATCTCATTTGGGCCCG 59.259 55.000 19.37 1.86 0.00 6.13
2196 2350 0.740737 CGAACATCTCATTTGGGCCC 59.259 55.000 17.59 17.59 0.00 5.80
2197 2351 1.463674 ACGAACATCTCATTTGGGCC 58.536 50.000 0.00 0.00 0.00 5.80
2198 2352 2.159379 GGAACGAACATCTCATTTGGGC 60.159 50.000 0.00 0.00 0.00 5.36
2199 2353 3.347216 AGGAACGAACATCTCATTTGGG 58.653 45.455 0.00 0.00 0.00 4.12
2200 2354 6.540189 AGATAAGGAACGAACATCTCATTTGG 59.460 38.462 0.00 0.00 0.00 3.28
2201 2355 7.493971 AGAGATAAGGAACGAACATCTCATTTG 59.506 37.037 11.31 0.00 42.59 2.32
2202 2356 7.560368 AGAGATAAGGAACGAACATCTCATTT 58.440 34.615 11.31 0.00 42.59 2.32
2203 2357 7.118496 AGAGATAAGGAACGAACATCTCATT 57.882 36.000 11.31 0.00 42.59 2.57
2204 2358 6.723298 AGAGATAAGGAACGAACATCTCAT 57.277 37.500 11.31 0.00 42.59 2.90
2205 2359 6.531503 AAGAGATAAGGAACGAACATCTCA 57.468 37.500 11.31 0.00 42.59 3.27
2206 2360 5.683743 CGAAGAGATAAGGAACGAACATCTC 59.316 44.000 0.00 0.00 41.17 2.75
2207 2361 5.583495 CGAAGAGATAAGGAACGAACATCT 58.417 41.667 0.00 0.00 0.00 2.90
2208 2362 4.207429 GCGAAGAGATAAGGAACGAACATC 59.793 45.833 0.00 0.00 0.00 3.06
2209 2363 4.113354 GCGAAGAGATAAGGAACGAACAT 58.887 43.478 0.00 0.00 0.00 2.71
2210 2364 3.057104 TGCGAAGAGATAAGGAACGAACA 60.057 43.478 0.00 0.00 0.00 3.18
2211 2365 3.508762 TGCGAAGAGATAAGGAACGAAC 58.491 45.455 0.00 0.00 0.00 3.95
2212 2366 3.861276 TGCGAAGAGATAAGGAACGAA 57.139 42.857 0.00 0.00 0.00 3.85
2213 2367 3.490933 CCATGCGAAGAGATAAGGAACGA 60.491 47.826 0.00 0.00 0.00 3.85
2214 2368 2.797156 CCATGCGAAGAGATAAGGAACG 59.203 50.000 0.00 0.00 0.00 3.95
2215 2369 2.545946 GCCATGCGAAGAGATAAGGAAC 59.454 50.000 0.00 0.00 0.00 3.62
2216 2370 2.838736 GCCATGCGAAGAGATAAGGAA 58.161 47.619 0.00 0.00 0.00 3.36
2217 2371 2.533266 GCCATGCGAAGAGATAAGGA 57.467 50.000 0.00 0.00 0.00 3.36
2230 2384 4.107051 GCTCACACACCGCCATGC 62.107 66.667 0.00 0.00 0.00 4.06
2231 2385 3.434319 GGCTCACACACCGCCATG 61.434 66.667 0.00 0.00 43.25 3.66
2246 2400 2.028043 GGTGTGCAAGCAAGTGGC 59.972 61.111 0.00 0.00 45.30 5.01
2247 2401 0.038892 GATGGTGTGCAAGCAAGTGG 60.039 55.000 0.00 0.00 40.33 4.00
2248 2402 0.956633 AGATGGTGTGCAAGCAAGTG 59.043 50.000 0.00 0.00 40.33 3.16
2249 2403 1.696063 AAGATGGTGTGCAAGCAAGT 58.304 45.000 0.00 0.00 40.33 3.16
2250 2404 2.806608 AAAGATGGTGTGCAAGCAAG 57.193 45.000 0.00 0.00 40.33 4.01
2251 2405 3.132646 AGAAAAAGATGGTGTGCAAGCAA 59.867 39.130 0.00 0.00 40.33 3.91
2252 2406 2.694628 AGAAAAAGATGGTGTGCAAGCA 59.305 40.909 0.00 0.00 41.41 3.91
2253 2407 3.005155 AGAGAAAAAGATGGTGTGCAAGC 59.995 43.478 0.00 0.00 0.00 4.01
2254 2408 4.518211 AGAGAGAAAAAGATGGTGTGCAAG 59.482 41.667 0.00 0.00 0.00 4.01
2255 2409 4.464008 AGAGAGAAAAAGATGGTGTGCAA 58.536 39.130 0.00 0.00 0.00 4.08
2256 2410 4.067896 GAGAGAGAAAAAGATGGTGTGCA 58.932 43.478 0.00 0.00 0.00 4.57
2257 2411 3.124297 CGAGAGAGAAAAAGATGGTGTGC 59.876 47.826 0.00 0.00 0.00 4.57
2258 2412 3.124297 GCGAGAGAGAAAAAGATGGTGTG 59.876 47.826 0.00 0.00 0.00 3.82
2259 2413 3.244215 TGCGAGAGAGAAAAAGATGGTGT 60.244 43.478 0.00 0.00 0.00 4.16
2260 2414 3.329386 TGCGAGAGAGAAAAAGATGGTG 58.671 45.455 0.00 0.00 0.00 4.17
2261 2415 3.594134 CTGCGAGAGAGAAAAAGATGGT 58.406 45.455 0.00 0.00 0.00 3.55
2262 2416 2.351111 GCTGCGAGAGAGAAAAAGATGG 59.649 50.000 0.00 0.00 0.00 3.51
2263 2417 2.998670 TGCTGCGAGAGAGAAAAAGATG 59.001 45.455 0.00 0.00 0.00 2.90
2264 2418 3.325293 TGCTGCGAGAGAGAAAAAGAT 57.675 42.857 0.00 0.00 0.00 2.40
2265 2419 2.820059 TGCTGCGAGAGAGAAAAAGA 57.180 45.000 0.00 0.00 0.00 2.52
2266 2420 3.885484 TTTGCTGCGAGAGAGAAAAAG 57.115 42.857 0.00 0.00 0.00 2.27
2267 2421 4.630894 TTTTTGCTGCGAGAGAGAAAAA 57.369 36.364 0.00 0.00 29.71 1.94
2290 2444 1.693799 TCTTAGGGCCCCAAGGATTT 58.306 50.000 27.24 5.60 33.47 2.17
2299 2453 2.729028 TGTGCTTATTCTTAGGGCCC 57.271 50.000 16.46 16.46 0.00 5.80
2302 2456 5.183904 GGCCATAATGTGCTTATTCTTAGGG 59.816 44.000 0.00 0.00 0.00 3.53
2306 2460 4.545678 TGGGCCATAATGTGCTTATTCTT 58.454 39.130 0.00 0.00 0.00 2.52
2311 2465 2.024464 ACCTTGGGCCATAATGTGCTTA 60.024 45.455 7.26 0.00 0.00 3.09
2317 2471 5.930837 TCTTTTAACCTTGGGCCATAATG 57.069 39.130 7.26 0.00 0.00 1.90
2319 2473 4.218852 CGTTCTTTTAACCTTGGGCCATAA 59.781 41.667 7.26 0.00 0.00 1.90
2320 2474 3.759618 CGTTCTTTTAACCTTGGGCCATA 59.240 43.478 7.26 0.00 0.00 2.74
2326 2480 3.040099 CGCAACGTTCTTTTAACCTTGG 58.960 45.455 0.00 0.00 0.00 3.61
2327 2481 3.942739 TCGCAACGTTCTTTTAACCTTG 58.057 40.909 0.00 0.00 0.00 3.61
2330 2484 4.136517 TCATCGCAACGTTCTTTTAACC 57.863 40.909 0.00 0.00 0.00 2.85
2334 2488 4.466828 CTGAATCATCGCAACGTTCTTTT 58.533 39.130 0.00 0.00 0.00 2.27
2338 2492 1.128507 TGCTGAATCATCGCAACGTTC 59.871 47.619 0.00 0.00 34.03 3.95
2339 2493 1.155889 TGCTGAATCATCGCAACGTT 58.844 45.000 0.00 0.00 34.03 3.99
2341 2495 3.476181 CATATGCTGAATCATCGCAACG 58.524 45.455 1.31 0.00 38.14 4.10
2366 2520 5.485353 TCTCCCTTAAGCTCTGAATTTCTCA 59.515 40.000 0.00 0.00 0.00 3.27
2368 2522 6.386635 AGATCTCCCTTAAGCTCTGAATTTCT 59.613 38.462 0.00 0.00 0.00 2.52
2377 2531 3.836365 AGCAAGATCTCCCTTAAGCTC 57.164 47.619 0.00 0.00 0.00 4.09
2426 2580 7.121315 GGTAGGCTTGTCTCTTATGATGTTTTT 59.879 37.037 0.00 0.00 0.00 1.94
2427 2581 6.599638 GGTAGGCTTGTCTCTTATGATGTTTT 59.400 38.462 0.00 0.00 0.00 2.43
2428 2582 6.116126 GGTAGGCTTGTCTCTTATGATGTTT 58.884 40.000 0.00 0.00 0.00 2.83
2429 2583 5.189736 TGGTAGGCTTGTCTCTTATGATGTT 59.810 40.000 0.00 0.00 0.00 2.71
2430 2584 4.716784 TGGTAGGCTTGTCTCTTATGATGT 59.283 41.667 0.00 0.00 0.00 3.06
2431 2585 5.053145 GTGGTAGGCTTGTCTCTTATGATG 58.947 45.833 0.00 0.00 0.00 3.07
2432 2586 4.965532 AGTGGTAGGCTTGTCTCTTATGAT 59.034 41.667 0.00 0.00 0.00 2.45
2433 2587 4.353777 AGTGGTAGGCTTGTCTCTTATGA 58.646 43.478 0.00 0.00 0.00 2.15
2434 2588 4.744795 AGTGGTAGGCTTGTCTCTTATG 57.255 45.455 0.00 0.00 0.00 1.90
2435 2589 4.777896 TGAAGTGGTAGGCTTGTCTCTTAT 59.222 41.667 0.00 0.00 0.00 1.73
2436 2590 4.021368 GTGAAGTGGTAGGCTTGTCTCTTA 60.021 45.833 0.00 0.00 0.00 2.10
2437 2591 2.972713 TGAAGTGGTAGGCTTGTCTCTT 59.027 45.455 0.00 0.00 0.00 2.85
2438 2592 2.300437 GTGAAGTGGTAGGCTTGTCTCT 59.700 50.000 0.00 0.00 0.00 3.10
2439 2593 2.613223 GGTGAAGTGGTAGGCTTGTCTC 60.613 54.545 0.00 0.00 0.00 3.36
2440 2594 1.348036 GGTGAAGTGGTAGGCTTGTCT 59.652 52.381 0.00 0.00 0.00 3.41
2441 2595 1.809684 GGTGAAGTGGTAGGCTTGTC 58.190 55.000 0.00 0.00 0.00 3.18
2442 2596 0.034896 CGGTGAAGTGGTAGGCTTGT 59.965 55.000 0.00 0.00 0.00 3.16
2443 2597 1.298859 GCGGTGAAGTGGTAGGCTTG 61.299 60.000 0.00 0.00 0.00 4.01
2444 2598 1.003718 GCGGTGAAGTGGTAGGCTT 60.004 57.895 0.00 0.00 0.00 4.35
2445 2599 2.663196 GCGGTGAAGTGGTAGGCT 59.337 61.111 0.00 0.00 0.00 4.58
2446 2600 2.436115 GGCGGTGAAGTGGTAGGC 60.436 66.667 0.00 0.00 0.00 3.93
2447 2601 1.375523 GTGGCGGTGAAGTGGTAGG 60.376 63.158 0.00 0.00 0.00 3.18
2448 2602 1.375523 GGTGGCGGTGAAGTGGTAG 60.376 63.158 0.00 0.00 0.00 3.18
2449 2603 2.745037 GGTGGCGGTGAAGTGGTA 59.255 61.111 0.00 0.00 0.00 3.25
2461 2615 3.894547 TTTCTTCGGAGGCGGTGGC 62.895 63.158 0.00 0.00 38.90 5.01
2463 2617 0.320421 TTCTTTCTTCGGAGGCGGTG 60.320 55.000 0.00 0.00 0.00 4.94
2467 2621 3.139077 TCAAGTTTCTTTCTTCGGAGGC 58.861 45.455 0.00 0.00 0.00 4.70
2468 2622 4.449405 GTCTCAAGTTTCTTTCTTCGGAGG 59.551 45.833 0.00 0.00 0.00 4.30
2470 2624 4.809426 GTGTCTCAAGTTTCTTTCTTCGGA 59.191 41.667 0.00 0.00 0.00 4.55
2479 2633 3.306780 CCATACCCGTGTCTCAAGTTTCT 60.307 47.826 0.00 0.00 0.00 2.52
2507 2662 0.033920 GCTTGAAACAAGCCAAGGGG 59.966 55.000 21.13 0.00 39.93 4.79
2521 2676 3.170362 CACCTCCCCCAAGCTTGA 58.830 61.111 28.05 6.71 0.00 3.02
2543 2698 8.603242 AATAAAAGTGATGGTGATACGATACC 57.397 34.615 0.00 0.00 37.48 2.73
2635 2791 5.756347 ACGAAACAAGCACTCAAATACTACA 59.244 36.000 0.00 0.00 0.00 2.74
2636 2792 6.071463 CACGAAACAAGCACTCAAATACTAC 58.929 40.000 0.00 0.00 0.00 2.73
2641 2797 4.516698 AGATCACGAAACAAGCACTCAAAT 59.483 37.500 0.00 0.00 0.00 2.32
2667 2823 7.811653 ACTCTCACACACGATCACATATATAG 58.188 38.462 0.00 0.00 0.00 1.31
2670 2826 6.127730 ACAACTCTCACACACGATCACATATA 60.128 38.462 0.00 0.00 0.00 0.86
2671 2827 4.991153 ACTCTCACACACGATCACATAT 57.009 40.909 0.00 0.00 0.00 1.78
2672 2828 4.022329 ACAACTCTCACACACGATCACATA 60.022 41.667 0.00 0.00 0.00 2.29
2677 2833 8.851960 TTATTATACAACTCTCACACACGATC 57.148 34.615 0.00 0.00 0.00 3.69
2706 2862 5.835113 AGCAAAGCAAAGACTCAAACTAA 57.165 34.783 0.00 0.00 0.00 2.24
2717 2873 4.104776 TGAAACGAGAAAGCAAAGCAAAG 58.895 39.130 0.00 0.00 0.00 2.77
2726 2884 4.290155 TGCTTTGATTGAAACGAGAAAGC 58.710 39.130 0.00 0.00 43.53 3.51
2767 2931 7.655328 GTGAAGTCATTACTCCCATCAGATTAG 59.345 40.741 0.00 0.00 33.75 1.73
2768 2932 7.125659 TGTGAAGTCATTACTCCCATCAGATTA 59.874 37.037 0.00 0.00 33.75 1.75
2773 2937 5.698741 ATGTGAAGTCATTACTCCCATCA 57.301 39.130 0.00 0.00 33.75 3.07
2774 2938 9.429359 CTTATATGTGAAGTCATTACTCCCATC 57.571 37.037 0.00 0.00 33.75 3.51
2829 2994 8.673711 TCCATGACAAACACTATATTTGCTAAC 58.326 33.333 0.00 0.00 40.10 2.34
2833 2998 6.418819 GCATCCATGACAAACACTATATTTGC 59.581 38.462 0.00 0.00 40.10 3.68
2838 3003 7.338957 TGAATTGCATCCATGACAAACACTATA 59.661 33.333 0.00 0.00 31.35 1.31
2843 3008 4.868314 TGAATTGCATCCATGACAAACA 57.132 36.364 0.00 0.00 31.35 2.83
2844 3009 5.412640 TCATGAATTGCATCCATGACAAAC 58.587 37.500 17.02 0.00 40.96 2.93


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

AutoCloner maintained by Alex Coulton.