Multiple sequence alignment - TraesCS3D01G137400

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 TraesCS3D01G137400 chr3D 100.000 2643 0 0 1 2643 95959582 95956940 0.000000e+00 4881.0
1 TraesCS3D01G137400 chr3D 93.984 2111 84 21 1 2081 93187668 93189765 0.000000e+00 3155.0
2 TraesCS3D01G137400 chr3D 90.316 475 33 8 2170 2642 96124905 96124442 6.250000e-171 610.0
3 TraesCS3D01G137400 chr3D 82.597 385 44 18 1 371 516071125 516070750 4.250000e-83 318.0
4 TraesCS3D01G137400 chr7D 94.630 2123 63 17 1 2086 561525579 561523471 0.000000e+00 3241.0
5 TraesCS3D01G137400 chr7D 92.580 2116 89 15 1 2079 174131637 174133721 0.000000e+00 2976.0
6 TraesCS3D01G137400 chr7D 91.741 2143 100 36 1 2080 433075523 433077651 0.000000e+00 2905.0
7 TraesCS3D01G137400 chr7D 94.759 1679 70 10 410 2080 188556081 188554413 0.000000e+00 2597.0
8 TraesCS3D01G137400 chr1D 93.107 2118 79 17 1 2081 451193913 451191826 0.000000e+00 3040.0
9 TraesCS3D01G137400 chr1A 92.705 2111 100 19 1 2083 46268995 46266911 0.000000e+00 2996.0
10 TraesCS3D01G137400 chr1A 92.515 2111 104 18 1 2083 46225045 46222961 0.000000e+00 2974.0
11 TraesCS3D01G137400 chr7A 92.711 2099 86 26 1 2053 141058798 141056721 0.000000e+00 2966.0
12 TraesCS3D01G137400 chr7A 92.465 2097 90 21 1 2053 140769356 140767284 0.000000e+00 2935.0
13 TraesCS3D01G137400 chr3A 92.238 2087 124 19 16 2080 697689303 697687233 0.000000e+00 2922.0
14 TraesCS3D01G137400 chr3A 95.960 495 18 1 2149 2641 114048122 114047628 0.000000e+00 802.0
15 TraesCS3D01G137400 chr3A 89.641 473 40 1 2170 2642 114238859 114238396 6.300000e-166 593.0
16 TraesCS3D01G137400 chr3A 86.711 301 16 5 1785 2084 598684792 598684515 1.980000e-81 313.0
17 TraesCS3D01G137400 chr1B 91.412 2131 119 29 2 2078 584462057 584459937 0.000000e+00 2863.0
18 TraesCS3D01G137400 chr4D 93.939 1815 73 16 294 2083 15240513 15238711 0.000000e+00 2708.0
19 TraesCS3D01G137400 chr4D 93.151 1723 97 11 371 2083 490089233 490087522 0.000000e+00 2508.0
20 TraesCS3D01G137400 chr4A 86.994 2099 208 44 21 2080 327748724 327746652 0.000000e+00 2303.0
21 TraesCS3D01G137400 chr4A 90.579 1348 82 21 1 1320 571522689 571521359 0.000000e+00 1744.0
22 TraesCS3D01G137400 chr4A 86.409 802 60 12 1 760 63445722 63446516 0.000000e+00 832.0
23 TraesCS3D01G137400 chr2D 87.005 1339 126 30 1 1320 314352660 314351351 0.000000e+00 1465.0
24 TraesCS3D01G137400 chr3B 94.790 499 19 1 2145 2643 146891475 146890984 0.000000e+00 771.0
25 TraesCS3D01G137400 chr3B 88.936 470 39 4 2175 2642 147184231 147183773 3.820000e-158 568.0
26 TraesCS3D01G137400 chr6B 81.250 128 15 5 1956 2082 72402786 72402667 7.790000e-16 95.3


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 TraesCS3D01G137400 chr3D 95956940 95959582 2642 True 4881 4881 100.000 1 2643 1 chr3D.!!$R1 2642
1 TraesCS3D01G137400 chr3D 93187668 93189765 2097 False 3155 3155 93.984 1 2081 1 chr3D.!!$F1 2080
2 TraesCS3D01G137400 chr7D 561523471 561525579 2108 True 3241 3241 94.630 1 2086 1 chr7D.!!$R2 2085
3 TraesCS3D01G137400 chr7D 174131637 174133721 2084 False 2976 2976 92.580 1 2079 1 chr7D.!!$F1 2078
4 TraesCS3D01G137400 chr7D 433075523 433077651 2128 False 2905 2905 91.741 1 2080 1 chr7D.!!$F2 2079
5 TraesCS3D01G137400 chr7D 188554413 188556081 1668 True 2597 2597 94.759 410 2080 1 chr7D.!!$R1 1670
6 TraesCS3D01G137400 chr1D 451191826 451193913 2087 True 3040 3040 93.107 1 2081 1 chr1D.!!$R1 2080
7 TraesCS3D01G137400 chr1A 46266911 46268995 2084 True 2996 2996 92.705 1 2083 1 chr1A.!!$R2 2082
8 TraesCS3D01G137400 chr1A 46222961 46225045 2084 True 2974 2974 92.515 1 2083 1 chr1A.!!$R1 2082
9 TraesCS3D01G137400 chr7A 141056721 141058798 2077 True 2966 2966 92.711 1 2053 1 chr7A.!!$R2 2052
10 TraesCS3D01G137400 chr7A 140767284 140769356 2072 True 2935 2935 92.465 1 2053 1 chr7A.!!$R1 2052
11 TraesCS3D01G137400 chr3A 697687233 697689303 2070 True 2922 2922 92.238 16 2080 1 chr3A.!!$R4 2064
12 TraesCS3D01G137400 chr1B 584459937 584462057 2120 True 2863 2863 91.412 2 2078 1 chr1B.!!$R1 2076
13 TraesCS3D01G137400 chr4D 15238711 15240513 1802 True 2708 2708 93.939 294 2083 1 chr4D.!!$R1 1789
14 TraesCS3D01G137400 chr4D 490087522 490089233 1711 True 2508 2508 93.151 371 2083 1 chr4D.!!$R2 1712
15 TraesCS3D01G137400 chr4A 327746652 327748724 2072 True 2303 2303 86.994 21 2080 1 chr4A.!!$R1 2059
16 TraesCS3D01G137400 chr4A 571521359 571522689 1330 True 1744 1744 90.579 1 1320 1 chr4A.!!$R2 1319
17 TraesCS3D01G137400 chr4A 63445722 63446516 794 False 832 832 86.409 1 760 1 chr4A.!!$F1 759
18 TraesCS3D01G137400 chr2D 314351351 314352660 1309 True 1465 1465 87.005 1 1320 1 chr2D.!!$R1 1319

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
960 1147 0.252742 AGAGAGGGGGTGGGTAAGTG 60.253 60.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2255 2492 0.030297 AGATGAGGGATGGGCTGAGT 60.03 55.0 0.0 0.0 0.0 3.41 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
570 723 2.030412 CCAGTACACTGCGGCACA 59.970 61.111 0.00 0.00 42.47 4.57
588 741 2.280186 GCGGTCATTAGGAGCCCG 60.280 66.667 0.00 0.00 40.99 6.13
960 1147 0.252742 AGAGAGGGGGTGGGTAAGTG 60.253 60.000 0.00 0.00 0.00 3.16
991 1179 4.240323 CAGGGTGAGTAAATATAGGGGGT 58.760 47.826 0.00 0.00 0.00 4.95
993 1181 3.329814 GGGTGAGTAAATATAGGGGGTGG 59.670 52.174 0.00 0.00 0.00 4.61
994 1182 4.237018 GGTGAGTAAATATAGGGGGTGGA 58.763 47.826 0.00 0.00 0.00 4.02
1017 1212 3.505386 AGGAGAAGAGTGACAGTCATGT 58.495 45.455 6.51 0.00 44.31 3.21
1114 1309 1.880675 GAGAGCAATGAGATGGGCATG 59.119 52.381 0.00 0.00 0.00 4.06
1204 1412 3.470888 CCCACCGCCGAGGAAGAT 61.471 66.667 3.89 0.00 45.00 2.40
1217 1425 0.175989 GGAAGATCCGAAGACGCCTT 59.824 55.000 0.00 0.00 38.29 4.35
1225 1433 1.885163 CGAAGACGCCTTAGGGTGGT 61.885 60.000 9.51 0.00 46.67 4.16
1672 1892 6.432107 CCTAAGTACTATCGAGTCTGCTTTC 58.568 44.000 0.00 0.00 37.10 2.62
1718 1950 5.294356 TGCGTAGAACTGTTATGAAGTGTT 58.706 37.500 0.00 0.00 0.00 3.32
1778 2013 5.265191 TCCTCTGTTTATACTCTGCTCTGT 58.735 41.667 0.00 0.00 0.00 3.41
1976 2212 2.034878 TGCAGGCAACCAAACAACATA 58.965 42.857 0.00 0.00 37.17 2.29
2018 2255 2.170166 CATTTGCTTAGCCAGGTTGGA 58.830 47.619 0.29 0.00 40.96 3.53
2044 2281 3.315191 AGAAATGTATGCAATGCGGGTAC 59.685 43.478 0.00 4.65 0.00 3.34
2045 2282 2.638480 ATGTATGCAATGCGGGTACT 57.362 45.000 13.50 1.50 0.00 2.73
2046 2283 1.662517 TGTATGCAATGCGGGTACTG 58.337 50.000 13.50 0.00 38.10 2.74
2047 2284 1.065782 TGTATGCAATGCGGGTACTGT 60.066 47.619 13.50 0.00 36.83 3.55
2048 2285 2.168728 TGTATGCAATGCGGGTACTGTA 59.831 45.455 13.50 0.00 36.83 2.74
2049 2286 1.953559 ATGCAATGCGGGTACTGTAG 58.046 50.000 0.00 0.00 36.83 2.74
2050 2287 0.107897 TGCAATGCGGGTACTGTAGG 60.108 55.000 0.00 0.00 36.83 3.18
2086 2323 1.338769 ACCAAACACGCCCTATGAGAC 60.339 52.381 0.00 0.00 0.00 3.36
2087 2324 0.999406 CAAACACGCCCTATGAGACG 59.001 55.000 0.00 0.00 0.00 4.18
2088 2325 0.108329 AAACACGCCCTATGAGACGG 60.108 55.000 0.00 0.00 0.00 4.79
2089 2326 0.968901 AACACGCCCTATGAGACGGA 60.969 55.000 0.00 0.00 0.00 4.69
2090 2327 1.360551 CACGCCCTATGAGACGGAG 59.639 63.158 0.00 0.00 0.00 4.63
2091 2328 1.828660 ACGCCCTATGAGACGGAGG 60.829 63.158 0.00 0.00 0.00 4.30
2095 2332 3.831651 CCTATGAGACGGAGGGAGT 57.168 57.895 0.00 0.00 0.00 3.85
2096 2333 2.953284 CCTATGAGACGGAGGGAGTA 57.047 55.000 0.00 0.00 0.00 2.59
2097 2334 2.506444 CCTATGAGACGGAGGGAGTAC 58.494 57.143 0.00 0.00 0.00 2.73
2098 2335 2.106857 CCTATGAGACGGAGGGAGTACT 59.893 54.545 0.00 0.00 0.00 2.73
2099 2336 2.060050 ATGAGACGGAGGGAGTACTG 57.940 55.000 0.00 0.00 0.00 2.74
2100 2337 0.697079 TGAGACGGAGGGAGTACTGT 59.303 55.000 0.00 0.00 0.00 3.55
2101 2338 1.096416 GAGACGGAGGGAGTACTGTG 58.904 60.000 0.00 0.00 0.00 3.66
2102 2339 0.404812 AGACGGAGGGAGTACTGTGT 59.595 55.000 0.00 0.00 0.00 3.72
2103 2340 1.632409 AGACGGAGGGAGTACTGTGTA 59.368 52.381 0.00 0.00 0.00 2.90
2104 2341 2.241685 AGACGGAGGGAGTACTGTGTAT 59.758 50.000 0.00 0.00 0.00 2.29
2105 2342 3.457380 AGACGGAGGGAGTACTGTGTATA 59.543 47.826 0.00 0.00 0.00 1.47
2106 2343 3.549794 ACGGAGGGAGTACTGTGTATAC 58.450 50.000 0.00 0.00 0.00 1.47
2107 2344 3.054139 ACGGAGGGAGTACTGTGTATACA 60.054 47.826 0.00 0.08 35.08 2.29
2108 2345 3.314635 CGGAGGGAGTACTGTGTATACAC 59.685 52.174 25.99 25.99 46.59 2.90
2109 2346 3.635836 GGAGGGAGTACTGTGTATACACC 59.364 52.174 28.67 15.71 45.88 4.16
2110 2347 3.285484 AGGGAGTACTGTGTATACACCG 58.715 50.000 28.67 25.07 45.88 4.94
2111 2348 2.360165 GGGAGTACTGTGTATACACCGG 59.640 54.545 28.67 23.01 45.88 5.28
2112 2349 3.282021 GGAGTACTGTGTATACACCGGA 58.718 50.000 28.67 19.19 45.88 5.14
2113 2350 3.887716 GGAGTACTGTGTATACACCGGAT 59.112 47.826 28.67 14.87 45.88 4.18
2114 2351 4.261489 GGAGTACTGTGTATACACCGGATG 60.261 50.000 28.67 16.99 45.88 3.51
2115 2352 4.529897 AGTACTGTGTATACACCGGATGA 58.470 43.478 28.67 11.54 45.88 2.92
2116 2353 5.138276 AGTACTGTGTATACACCGGATGAT 58.862 41.667 28.67 11.82 45.88 2.45
2117 2354 4.322080 ACTGTGTATACACCGGATGATG 57.678 45.455 28.67 13.05 45.88 3.07
2118 2355 3.069586 ACTGTGTATACACCGGATGATGG 59.930 47.826 28.67 12.18 45.88 3.51
2119 2356 2.224185 TGTGTATACACCGGATGATGGC 60.224 50.000 28.67 4.43 45.88 4.40
2120 2357 1.346395 TGTATACACCGGATGATGGCC 59.654 52.381 9.46 0.00 0.00 5.36
2127 2364 3.070076 CGGATGATGGCCGGATATG 57.930 57.895 5.05 0.00 44.87 1.78
2128 2365 0.462581 CGGATGATGGCCGGATATGG 60.463 60.000 5.05 0.00 44.87 2.74
2129 2366 0.107017 GGATGATGGCCGGATATGGG 60.107 60.000 5.05 0.00 0.00 4.00
2130 2367 0.620556 GATGATGGCCGGATATGGGT 59.379 55.000 5.05 0.00 0.00 4.51
2131 2368 0.329261 ATGATGGCCGGATATGGGTG 59.671 55.000 5.05 0.00 0.00 4.61
2132 2369 1.059584 TGATGGCCGGATATGGGTGT 61.060 55.000 5.05 0.00 0.00 4.16
2133 2370 0.321653 GATGGCCGGATATGGGTGTC 60.322 60.000 5.05 0.00 0.00 3.67
2134 2371 0.768221 ATGGCCGGATATGGGTGTCT 60.768 55.000 5.05 0.00 0.00 3.41
2135 2372 0.986019 TGGCCGGATATGGGTGTCTT 60.986 55.000 5.05 0.00 0.00 3.01
2136 2373 1.053424 GGCCGGATATGGGTGTCTTA 58.947 55.000 5.05 0.00 0.00 2.10
2137 2374 1.418637 GGCCGGATATGGGTGTCTTAA 59.581 52.381 5.05 0.00 0.00 1.85
2138 2375 2.039879 GGCCGGATATGGGTGTCTTAAT 59.960 50.000 5.05 0.00 0.00 1.40
2139 2376 3.262405 GGCCGGATATGGGTGTCTTAATA 59.738 47.826 5.05 0.00 0.00 0.98
2140 2377 4.504858 GCCGGATATGGGTGTCTTAATAG 58.495 47.826 5.05 0.00 0.00 1.73
2141 2378 4.222145 GCCGGATATGGGTGTCTTAATAGA 59.778 45.833 5.05 0.00 0.00 1.98
2142 2379 5.279809 GCCGGATATGGGTGTCTTAATAGAA 60.280 44.000 5.05 0.00 30.65 2.10
2143 2380 6.743208 GCCGGATATGGGTGTCTTAATAGAAA 60.743 42.308 5.05 0.00 30.65 2.52
2144 2381 6.649557 CCGGATATGGGTGTCTTAATAGAAAC 59.350 42.308 0.00 0.00 37.82 2.78
2145 2382 7.442656 CGGATATGGGTGTCTTAATAGAAACT 58.557 38.462 0.00 0.00 38.48 2.66
2146 2383 7.599245 CGGATATGGGTGTCTTAATAGAAACTC 59.401 40.741 0.00 0.00 39.28 3.01
2147 2384 7.599245 GGATATGGGTGTCTTAATAGAAACTCG 59.401 40.741 0.00 0.00 41.39 4.18
2148 2385 5.988310 TGGGTGTCTTAATAGAAACTCGA 57.012 39.130 0.00 0.00 41.39 4.04
2149 2386 6.540438 TGGGTGTCTTAATAGAAACTCGAT 57.460 37.500 0.00 0.00 41.39 3.59
2150 2387 6.570692 TGGGTGTCTTAATAGAAACTCGATC 58.429 40.000 0.00 0.00 41.39 3.69
2151 2388 6.153851 TGGGTGTCTTAATAGAAACTCGATCA 59.846 38.462 0.00 0.00 41.39 2.92
2152 2389 6.476053 GGGTGTCTTAATAGAAACTCGATCAC 59.524 42.308 0.00 0.00 38.48 3.06
2153 2390 6.476053 GGTGTCTTAATAGAAACTCGATCACC 59.524 42.308 0.00 0.00 38.48 4.02
2154 2391 7.259161 GTGTCTTAATAGAAACTCGATCACCT 58.741 38.462 0.00 0.00 35.97 4.00
2155 2392 7.432838 GTGTCTTAATAGAAACTCGATCACCTC 59.567 40.741 0.00 0.00 35.97 3.85
2156 2393 6.633634 GTCTTAATAGAAACTCGATCACCTCG 59.366 42.308 0.00 0.00 39.39 4.63
2157 2394 8.666378 GTCTTAATAGAAACTCGATCACCTCGC 61.666 44.444 0.00 0.00 38.55 5.03
2163 2400 2.049985 CGATCACCTCGCGATCCC 60.050 66.667 10.36 0.00 41.14 3.85
2164 2401 2.340443 GATCACCTCGCGATCCCC 59.660 66.667 10.36 0.00 34.42 4.81
2165 2402 2.443952 ATCACCTCGCGATCCCCA 60.444 61.111 10.36 0.00 0.00 4.96
2166 2403 2.028125 GATCACCTCGCGATCCCCAA 62.028 60.000 10.36 0.00 34.42 4.12
2167 2404 1.622607 ATCACCTCGCGATCCCCAAA 61.623 55.000 10.36 0.00 0.00 3.28
2168 2405 1.153168 CACCTCGCGATCCCCAAAT 60.153 57.895 10.36 0.00 0.00 2.32
2169 2406 1.146263 ACCTCGCGATCCCCAAATC 59.854 57.895 10.36 0.00 0.00 2.17
2170 2407 1.598130 CCTCGCGATCCCCAAATCC 60.598 63.158 10.36 0.00 0.00 3.01
2171 2408 1.598130 CTCGCGATCCCCAAATCCC 60.598 63.158 10.36 0.00 0.00 3.85
2172 2409 2.594592 CGCGATCCCCAAATCCCC 60.595 66.667 0.00 0.00 0.00 4.81
2173 2410 2.594592 GCGATCCCCAAATCCCCG 60.595 66.667 0.00 0.00 0.00 5.73
2174 2411 3.114825 GCGATCCCCAAATCCCCGA 62.115 63.158 0.00 0.00 0.00 5.14
2175 2412 1.529796 CGATCCCCAAATCCCCGAA 59.470 57.895 0.00 0.00 0.00 4.30
2176 2413 0.110486 CGATCCCCAAATCCCCGAAT 59.890 55.000 0.00 0.00 0.00 3.34
2177 2414 1.620822 GATCCCCAAATCCCCGAATG 58.379 55.000 0.00 0.00 0.00 2.67
2178 2415 0.188342 ATCCCCAAATCCCCGAATGG 59.812 55.000 0.00 0.00 0.00 3.16
2179 2416 0.921749 TCCCCAAATCCCCGAATGGA 60.922 55.000 0.00 0.00 39.18 3.41
2180 2417 0.755327 CCCCAAATCCCCGAATGGAC 60.755 60.000 0.00 0.00 37.20 4.02
2181 2418 0.033601 CCCAAATCCCCGAATGGACA 60.034 55.000 0.00 0.00 37.20 4.02
2182 2419 1.618345 CCCAAATCCCCGAATGGACAA 60.618 52.381 0.00 0.00 37.20 3.18
2183 2420 1.750778 CCAAATCCCCGAATGGACAAG 59.249 52.381 0.00 0.00 37.20 3.16
2184 2421 1.134946 CAAATCCCCGAATGGACAAGC 59.865 52.381 0.00 0.00 37.20 4.01
2185 2422 0.748005 AATCCCCGAATGGACAAGCG 60.748 55.000 0.00 0.00 37.20 4.68
2186 2423 1.622607 ATCCCCGAATGGACAAGCGA 61.623 55.000 0.00 0.00 37.20 4.93
2187 2424 1.376683 CCCCGAATGGACAAGCGAA 60.377 57.895 0.00 0.00 37.49 4.70
2188 2425 1.644786 CCCCGAATGGACAAGCGAAC 61.645 60.000 0.00 0.00 37.49 3.95
2189 2426 1.644786 CCCGAATGGACAAGCGAACC 61.645 60.000 0.00 0.00 37.49 3.62
2190 2427 0.953471 CCGAATGGACAAGCGAACCA 60.953 55.000 0.00 0.00 37.49 3.67
2191 2428 1.086696 CGAATGGACAAGCGAACCAT 58.913 50.000 0.00 0.00 44.87 3.55
2192 2429 1.202065 CGAATGGACAAGCGAACCATG 60.202 52.381 0.00 0.00 42.59 3.66
2193 2430 1.812571 GAATGGACAAGCGAACCATGT 59.187 47.619 0.00 0.00 42.59 3.21
2194 2431 1.167851 ATGGACAAGCGAACCATGTG 58.832 50.000 0.00 0.00 41.96 3.21
2195 2432 1.210155 GGACAAGCGAACCATGTGC 59.790 57.895 0.00 0.00 0.00 4.57
2196 2433 1.514678 GGACAAGCGAACCATGTGCA 61.515 55.000 0.00 0.00 35.73 4.57
2197 2434 0.385974 GACAAGCGAACCATGTGCAC 60.386 55.000 10.75 10.75 0.00 4.57
2198 2435 1.100463 ACAAGCGAACCATGTGCACA 61.100 50.000 24.08 24.08 0.00 4.57
2199 2436 0.386352 CAAGCGAACCATGTGCACAG 60.386 55.000 25.84 14.95 0.00 3.66
2200 2437 0.819259 AAGCGAACCATGTGCACAGT 60.819 50.000 25.84 15.66 0.00 3.55
2201 2438 1.081906 GCGAACCATGTGCACAGTG 60.082 57.895 25.84 20.74 0.00 3.66
2202 2439 1.575922 CGAACCATGTGCACAGTGG 59.424 57.895 30.51 30.51 38.96 4.00
2203 2440 0.884259 CGAACCATGTGCACAGTGGA 60.884 55.000 35.04 14.16 36.82 4.02
2204 2441 0.877071 GAACCATGTGCACAGTGGAG 59.123 55.000 35.04 21.63 36.82 3.86
2205 2442 0.473755 AACCATGTGCACAGTGGAGA 59.526 50.000 35.04 12.88 36.82 3.71
2206 2443 0.473755 ACCATGTGCACAGTGGAGAA 59.526 50.000 35.04 12.24 36.82 2.87
2207 2444 1.162698 CCATGTGCACAGTGGAGAAG 58.837 55.000 29.47 12.70 34.94 2.85
2208 2445 0.520404 CATGTGCACAGTGGAGAAGC 59.480 55.000 25.84 0.00 0.00 3.86
2209 2446 0.952497 ATGTGCACAGTGGAGAAGCG 60.952 55.000 25.84 0.00 0.00 4.68
2210 2447 2.666190 TGCACAGTGGAGAAGCGC 60.666 61.111 0.00 0.00 0.00 5.92
2211 2448 3.782244 GCACAGTGGAGAAGCGCG 61.782 66.667 0.00 0.00 0.00 6.86
2212 2449 3.114616 CACAGTGGAGAAGCGCGG 61.115 66.667 8.83 0.00 0.00 6.46
2229 2466 4.451150 GCCGCGTCCACCTCATCA 62.451 66.667 4.92 0.00 0.00 3.07
2230 2467 2.509336 CCGCGTCCACCTCATCAC 60.509 66.667 4.92 0.00 0.00 3.06
2231 2468 2.509336 CGCGTCCACCTCATCACC 60.509 66.667 0.00 0.00 0.00 4.02
2232 2469 2.125106 GCGTCCACCTCATCACCC 60.125 66.667 0.00 0.00 0.00 4.61
2233 2470 2.660064 GCGTCCACCTCATCACCCT 61.660 63.158 0.00 0.00 0.00 4.34
2234 2471 1.517832 CGTCCACCTCATCACCCTC 59.482 63.158 0.00 0.00 0.00 4.30
2235 2472 1.257750 CGTCCACCTCATCACCCTCA 61.258 60.000 0.00 0.00 0.00 3.86
2236 2473 0.250513 GTCCACCTCATCACCCTCAC 59.749 60.000 0.00 0.00 0.00 3.51
2237 2474 0.909610 TCCACCTCATCACCCTCACC 60.910 60.000 0.00 0.00 0.00 4.02
2238 2475 1.219124 CACCTCATCACCCTCACCG 59.781 63.158 0.00 0.00 0.00 4.94
2239 2476 1.990060 ACCTCATCACCCTCACCGG 60.990 63.158 0.00 0.00 0.00 5.28
2240 2477 2.187946 CTCATCACCCTCACCGGC 59.812 66.667 0.00 0.00 0.00 6.13
2241 2478 3.723235 CTCATCACCCTCACCGGCG 62.723 68.421 0.00 0.00 0.00 6.46
2263 2500 4.803426 CGAGCACCGACTCAGCCC 62.803 72.222 0.00 0.00 41.76 5.19
2264 2501 3.695606 GAGCACCGACTCAGCCCA 61.696 66.667 0.00 0.00 36.65 5.36
2265 2502 3.005539 AGCACCGACTCAGCCCAT 61.006 61.111 0.00 0.00 0.00 4.00
2266 2503 2.512515 GCACCGACTCAGCCCATC 60.513 66.667 0.00 0.00 0.00 3.51
2267 2504 2.187946 CACCGACTCAGCCCATCC 59.812 66.667 0.00 0.00 0.00 3.51
2268 2505 3.083997 ACCGACTCAGCCCATCCC 61.084 66.667 0.00 0.00 0.00 3.85
2269 2506 2.765807 CCGACTCAGCCCATCCCT 60.766 66.667 0.00 0.00 0.00 4.20
2270 2507 2.801631 CCGACTCAGCCCATCCCTC 61.802 68.421 0.00 0.00 0.00 4.30
2271 2508 2.060383 CGACTCAGCCCATCCCTCA 61.060 63.158 0.00 0.00 0.00 3.86
2272 2509 1.406065 CGACTCAGCCCATCCCTCAT 61.406 60.000 0.00 0.00 0.00 2.90
2273 2510 0.396060 GACTCAGCCCATCCCTCATC 59.604 60.000 0.00 0.00 0.00 2.92
2274 2511 0.030297 ACTCAGCCCATCCCTCATCT 60.030 55.000 0.00 0.00 0.00 2.90
2275 2512 0.686224 CTCAGCCCATCCCTCATCTC 59.314 60.000 0.00 0.00 0.00 2.75
2276 2513 1.117749 TCAGCCCATCCCTCATCTCG 61.118 60.000 0.00 0.00 0.00 4.04
2277 2514 1.840650 AGCCCATCCCTCATCTCGG 60.841 63.158 0.00 0.00 0.00 4.63
2278 2515 2.746359 CCCATCCCTCATCTCGGC 59.254 66.667 0.00 0.00 0.00 5.54
2279 2516 2.746359 CCATCCCTCATCTCGGCC 59.254 66.667 0.00 0.00 0.00 6.13
2280 2517 2.746359 CATCCCTCATCTCGGCCC 59.254 66.667 0.00 0.00 0.00 5.80
2281 2518 1.840650 CATCCCTCATCTCGGCCCT 60.841 63.158 0.00 0.00 0.00 5.19
2282 2519 1.535202 ATCCCTCATCTCGGCCCTC 60.535 63.158 0.00 0.00 0.00 4.30
2283 2520 3.237741 CCCTCATCTCGGCCCTCC 61.238 72.222 0.00 0.00 0.00 4.30
2355 2592 3.771160 CCGCGGAGGGCAAGTACT 61.771 66.667 24.07 0.00 43.84 2.73
2356 2593 2.264794 CGCGGAGGGCAAGTACTT 59.735 61.111 1.12 1.12 43.84 2.24
2357 2594 1.810030 CGCGGAGGGCAAGTACTTC 60.810 63.158 4.77 0.93 43.84 3.01
2358 2595 1.597461 GCGGAGGGCAAGTACTTCT 59.403 57.895 4.77 0.00 42.87 2.85
2359 2596 0.460459 GCGGAGGGCAAGTACTTCTC 60.460 60.000 4.77 9.50 42.87 2.87
2360 2597 0.175989 CGGAGGGCAAGTACTTCTCC 59.824 60.000 23.08 23.08 40.28 3.71
2361 2598 1.276622 GGAGGGCAAGTACTTCTCCA 58.723 55.000 25.99 0.00 42.49 3.86
2362 2599 1.628846 GGAGGGCAAGTACTTCTCCAA 59.371 52.381 25.99 0.00 42.49 3.53
2363 2600 2.615747 GGAGGGCAAGTACTTCTCCAAC 60.616 54.545 25.99 17.54 42.49 3.77
2364 2601 1.002087 AGGGCAAGTACTTCTCCAACG 59.998 52.381 19.96 4.93 0.00 4.10
2365 2602 1.439679 GGCAAGTACTTCTCCAACGG 58.560 55.000 4.77 0.00 0.00 4.44
2366 2603 0.796927 GCAAGTACTTCTCCAACGGC 59.203 55.000 4.77 0.00 0.00 5.68
2367 2604 1.608283 GCAAGTACTTCTCCAACGGCT 60.608 52.381 4.77 0.00 0.00 5.52
2368 2605 2.767505 CAAGTACTTCTCCAACGGCTT 58.232 47.619 4.77 0.00 0.00 4.35
2369 2606 2.737252 CAAGTACTTCTCCAACGGCTTC 59.263 50.000 4.77 0.00 0.00 3.86
2370 2607 1.067776 AGTACTTCTCCAACGGCTTCG 60.068 52.381 0.00 0.00 40.22 3.79
2371 2608 1.068055 GTACTTCTCCAACGGCTTCGA 60.068 52.381 0.00 0.00 37.63 3.71
2372 2609 0.319641 ACTTCTCCAACGGCTTCGAC 60.320 55.000 0.00 0.00 37.63 4.20
2373 2610 1.005394 TTCTCCAACGGCTTCGACC 60.005 57.895 0.00 0.00 37.63 4.79
2374 2611 1.750341 TTCTCCAACGGCTTCGACCA 61.750 55.000 0.00 0.00 37.63 4.02
2375 2612 1.738099 CTCCAACGGCTTCGACCAG 60.738 63.158 0.00 0.00 37.63 4.00
2376 2613 2.742372 CCAACGGCTTCGACCAGG 60.742 66.667 0.00 0.00 37.63 4.45
2377 2614 3.423154 CAACGGCTTCGACCAGGC 61.423 66.667 0.69 0.69 37.63 4.85
2378 2615 4.699522 AACGGCTTCGACCAGGCC 62.700 66.667 0.00 0.00 42.18 5.19
2413 2650 4.083862 GCCCCACCTCCACGACTC 62.084 72.222 0.00 0.00 0.00 3.36
2414 2651 3.391382 CCCCACCTCCACGACTCC 61.391 72.222 0.00 0.00 0.00 3.85
2415 2652 2.603473 CCCACCTCCACGACTCCA 60.603 66.667 0.00 0.00 0.00 3.86
2416 2653 1.990060 CCCACCTCCACGACTCCAT 60.990 63.158 0.00 0.00 0.00 3.41
2417 2654 1.219124 CCACCTCCACGACTCCATG 59.781 63.158 0.00 0.00 0.00 3.66
2418 2655 1.257750 CCACCTCCACGACTCCATGA 61.258 60.000 0.00 0.00 0.00 3.07
2419 2656 0.174389 CACCTCCACGACTCCATGAG 59.826 60.000 0.00 0.00 35.52 2.90
2420 2657 0.039764 ACCTCCACGACTCCATGAGA 59.960 55.000 0.00 0.00 33.32 3.27
2430 2667 2.922162 TCCATGAGAGGAGCCTTCC 58.078 57.895 0.00 0.00 44.39 3.46
2453 2690 3.827898 CTCGTGGCCGACCTCCTC 61.828 72.222 0.00 0.00 38.40 3.71
2546 2783 3.248171 GACTCCGTCGTCATGCGC 61.248 66.667 0.00 0.00 41.07 6.09
2566 2803 3.072468 CTCCCGCGGGTTCCTGTA 61.072 66.667 41.57 21.40 36.47 2.74
2567 2804 3.366739 CTCCCGCGGGTTCCTGTAC 62.367 68.421 41.57 0.00 36.47 2.90
2568 2805 3.697747 CCCGCGGGTTCCTGTACA 61.698 66.667 36.64 0.00 0.00 2.90
2569 2806 2.582436 CCGCGGGTTCCTGTACAT 59.418 61.111 20.10 0.00 0.00 2.29
2570 2807 1.813753 CCGCGGGTTCCTGTACATG 60.814 63.158 20.10 0.00 0.00 3.21
2571 2808 1.216977 CGCGGGTTCCTGTACATGA 59.783 57.895 0.00 0.00 0.00 3.07
2572 2809 0.806102 CGCGGGTTCCTGTACATGAG 60.806 60.000 0.00 0.00 0.00 2.90
2573 2810 1.090052 GCGGGTTCCTGTACATGAGC 61.090 60.000 0.00 6.47 0.00 4.26
2574 2811 0.806102 CGGGTTCCTGTACATGAGCG 60.806 60.000 0.00 0.00 0.00 5.03
2575 2812 0.535335 GGGTTCCTGTACATGAGCGA 59.465 55.000 0.00 0.00 0.00 4.93
2576 2813 1.471676 GGGTTCCTGTACATGAGCGAG 60.472 57.143 0.00 0.00 0.00 5.03
2577 2814 1.471676 GGTTCCTGTACATGAGCGAGG 60.472 57.143 0.00 0.00 0.00 4.63
2578 2815 1.204941 GTTCCTGTACATGAGCGAGGT 59.795 52.381 0.00 0.00 0.00 3.85
2579 2816 1.103803 TCCTGTACATGAGCGAGGTC 58.896 55.000 0.00 0.00 0.00 3.85
2580 2817 0.248661 CCTGTACATGAGCGAGGTCG 60.249 60.000 0.00 0.00 43.27 4.79
2581 2818 0.733150 CTGTACATGAGCGAGGTCGA 59.267 55.000 0.00 0.00 43.02 4.20
2582 2819 0.450583 TGTACATGAGCGAGGTCGAC 59.549 55.000 7.13 7.13 43.02 4.20
2583 2820 0.589229 GTACATGAGCGAGGTCGACG 60.589 60.000 9.92 0.00 43.02 5.12
2584 2821 1.022982 TACATGAGCGAGGTCGACGT 61.023 55.000 11.12 11.12 43.02 4.34
2585 2822 1.583967 CATGAGCGAGGTCGACGTC 60.584 63.158 24.67 24.67 43.02 4.34
2594 2831 2.504244 GTCGACGTCGGCCTCAAG 60.504 66.667 35.05 7.30 38.15 3.02
2595 2832 2.981909 TCGACGTCGGCCTCAAGT 60.982 61.111 35.05 0.00 40.29 3.16
2596 2833 2.049433 CGACGTCGGCCTCAAGTT 60.049 61.111 29.70 0.00 35.37 2.66
2597 2834 2.087009 CGACGTCGGCCTCAAGTTC 61.087 63.158 29.70 0.00 35.37 3.01
2598 2835 2.049433 ACGTCGGCCTCAAGTTCG 60.049 61.111 0.00 0.00 0.00 3.95
2599 2836 3.479269 CGTCGGCCTCAAGTTCGC 61.479 66.667 0.00 0.00 0.00 4.70
2600 2837 3.119096 GTCGGCCTCAAGTTCGCC 61.119 66.667 0.00 0.00 39.41 5.54
2603 2840 3.119096 GGCCTCAAGTTCGCCGAC 61.119 66.667 0.00 0.00 31.92 4.79
2604 2841 2.048127 GCCTCAAGTTCGCCGACT 60.048 61.111 0.00 0.00 0.00 4.18
2605 2842 1.214589 GCCTCAAGTTCGCCGACTA 59.785 57.895 0.00 0.00 0.00 2.59
2606 2843 1.077089 GCCTCAAGTTCGCCGACTAC 61.077 60.000 0.00 0.00 0.00 2.73
2607 2844 0.526662 CCTCAAGTTCGCCGACTACT 59.473 55.000 0.00 0.00 0.00 2.57
2608 2845 1.067776 CCTCAAGTTCGCCGACTACTT 60.068 52.381 0.00 0.00 32.60 2.24
2609 2846 2.251893 CTCAAGTTCGCCGACTACTTC 58.748 52.381 1.36 0.00 30.08 3.01
2617 2854 3.921521 CGACTACTTCGGGGAGCT 58.078 61.111 0.00 0.00 44.60 4.09
2618 2855 1.433879 CGACTACTTCGGGGAGCTG 59.566 63.158 0.00 0.00 44.60 4.24
2619 2856 1.142097 GACTACTTCGGGGAGCTGC 59.858 63.158 0.00 0.00 0.00 5.25
2620 2857 1.305381 ACTACTTCGGGGAGCTGCT 60.305 57.895 0.00 0.00 0.00 4.24
2621 2858 1.324005 ACTACTTCGGGGAGCTGCTC 61.324 60.000 21.17 21.17 0.00 4.26
2634 2871 3.706373 TGCTCCGGCAGAAGGTCC 61.706 66.667 0.00 0.00 44.28 4.46
2635 2872 4.475135 GCTCCGGCAGAAGGTCCC 62.475 72.222 0.00 0.00 38.54 4.46
2636 2873 3.787001 CTCCGGCAGAAGGTCCCC 61.787 72.222 0.00 0.00 0.00 4.81
2639 2876 4.452733 CGGCAGAAGGTCCCCGAC 62.453 72.222 0.00 0.00 43.20 4.79
2640 2877 4.452733 GGCAGAAGGTCCCCGACG 62.453 72.222 0.00 0.00 32.65 5.12
2642 2879 3.691342 CAGAAGGTCCCCGACGCA 61.691 66.667 0.00 0.00 32.65 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 131 0.247736 AGAGAAGTGCTTACCGCCAG 59.752 55.000 0.00 0.00 38.05 4.85
570 723 2.797278 CGGGCTCCTAATGACCGCT 61.797 63.158 0.00 0.00 37.93 5.52
588 741 2.038033 TGGTGCAAGTACAAGACCTACC 59.962 50.000 0.00 0.00 0.00 3.18
960 1147 4.351054 CTCACCCTGCCCACCACC 62.351 72.222 0.00 0.00 0.00 4.61
991 1179 2.109128 ACTGTCACTCTTCTCCTCTCCA 59.891 50.000 0.00 0.00 0.00 3.86
993 1181 3.417101 TGACTGTCACTCTTCTCCTCTC 58.583 50.000 6.36 0.00 0.00 3.20
994 1182 3.517296 TGACTGTCACTCTTCTCCTCT 57.483 47.619 6.36 0.00 0.00 3.69
1204 1412 1.304713 ACCCTAAGGCGTCTTCGGA 60.305 57.895 21.03 0.00 37.87 4.55
1217 1425 1.676635 CCTCGTCGTCACCACCCTA 60.677 63.158 0.00 0.00 0.00 3.53
1225 1433 2.678580 TCCATGCCCTCGTCGTCA 60.679 61.111 0.00 0.00 0.00 4.35
1354 1568 1.604278 GAAGTGCTTGGTGAAGTCCAC 59.396 52.381 0.00 0.00 44.95 4.02
1434 1648 0.035317 TGCCGTTCATCAGCTTCACT 59.965 50.000 0.00 0.00 0.00 3.41
1672 1892 8.582930 CGCATAAACCATAAACATAAACAGTTG 58.417 33.333 0.00 0.00 0.00 3.16
1718 1950 7.730084 AGAGCATATTTCAGATAAGCAGTACA 58.270 34.615 0.00 0.00 0.00 2.90
1778 2013 5.181056 CACAACCAGTAGCACACATCATAAA 59.819 40.000 0.00 0.00 0.00 1.40
1833 2069 2.506231 TGGTGTGTGGTAACCTCTTTGA 59.494 45.455 0.00 0.00 37.36 2.69
1976 2212 2.688446 CAGCCTCAAATGCATCATCTGT 59.312 45.455 0.00 0.00 0.00 3.41
2018 2255 3.005050 CCGCATTGCATACATTTCTCCAT 59.995 43.478 9.69 0.00 0.00 3.41
2044 2281 1.874019 CGTGCGCTACAGCCTACAG 60.874 63.158 9.73 0.00 37.91 2.74
2045 2282 2.180769 CGTGCGCTACAGCCTACA 59.819 61.111 9.73 0.00 37.91 2.74
2046 2283 2.582498 CCGTGCGCTACAGCCTAC 60.582 66.667 9.73 0.00 37.91 3.18
2047 2284 4.508128 GCCGTGCGCTACAGCCTA 62.508 66.667 9.73 0.00 37.91 3.93
2050 2287 4.445545 GTTGCCGTGCGCTACAGC 62.446 66.667 9.73 9.98 42.09 4.40
2086 2323 3.314635 GTGTATACACAGTACTCCCTCCG 59.685 52.174 27.37 0.00 45.75 4.63
2087 2324 4.915158 GTGTATACACAGTACTCCCTCC 57.085 50.000 27.37 0.00 45.75 4.30
2099 2336 2.413837 GCCATCATCCGGTGTATACAC 58.586 52.381 25.00 25.00 45.72 2.90
2100 2337 1.346395 GGCCATCATCCGGTGTATACA 59.654 52.381 0.08 0.08 0.00 2.29
2101 2338 1.671850 CGGCCATCATCCGGTGTATAC 60.672 57.143 2.24 0.00 42.99 1.47
2102 2339 0.606096 CGGCCATCATCCGGTGTATA 59.394 55.000 2.24 0.00 42.99 1.47
2103 2340 1.371183 CGGCCATCATCCGGTGTAT 59.629 57.895 2.24 0.00 42.99 2.29
2104 2341 2.818841 CGGCCATCATCCGGTGTA 59.181 61.111 2.24 0.00 42.99 2.90
2109 2346 0.462581 CCATATCCGGCCATCATCCG 60.463 60.000 2.24 0.00 46.05 4.18
2110 2347 0.107017 CCCATATCCGGCCATCATCC 60.107 60.000 2.24 0.00 0.00 3.51
2111 2348 0.620556 ACCCATATCCGGCCATCATC 59.379 55.000 2.24 0.00 0.00 2.92
2112 2349 0.329261 CACCCATATCCGGCCATCAT 59.671 55.000 2.24 0.00 0.00 2.45
2113 2350 1.059584 ACACCCATATCCGGCCATCA 61.060 55.000 2.24 0.00 0.00 3.07
2114 2351 0.321653 GACACCCATATCCGGCCATC 60.322 60.000 2.24 0.00 0.00 3.51
2115 2352 0.768221 AGACACCCATATCCGGCCAT 60.768 55.000 2.24 0.00 0.00 4.40
2116 2353 0.986019 AAGACACCCATATCCGGCCA 60.986 55.000 2.24 0.00 0.00 5.36
2117 2354 1.053424 TAAGACACCCATATCCGGCC 58.947 55.000 0.00 0.00 0.00 6.13
2118 2355 2.922740 TTAAGACACCCATATCCGGC 57.077 50.000 0.00 0.00 0.00 6.13
2119 2356 5.995565 TCTATTAAGACACCCATATCCGG 57.004 43.478 0.00 0.00 0.00 5.14
2120 2357 7.442656 AGTTTCTATTAAGACACCCATATCCG 58.557 38.462 0.00 0.00 33.64 4.18
2121 2358 7.599245 CGAGTTTCTATTAAGACACCCATATCC 59.401 40.741 0.00 0.00 33.64 2.59
2122 2359 8.358148 TCGAGTTTCTATTAAGACACCCATATC 58.642 37.037 0.00 0.00 33.64 1.63
2123 2360 8.246430 TCGAGTTTCTATTAAGACACCCATAT 57.754 34.615 0.00 0.00 33.64 1.78
2124 2361 7.649533 TCGAGTTTCTATTAAGACACCCATA 57.350 36.000 0.00 0.00 33.64 2.74
2125 2362 6.540438 TCGAGTTTCTATTAAGACACCCAT 57.460 37.500 0.00 0.00 33.64 4.00
2126 2363 5.988310 TCGAGTTTCTATTAAGACACCCA 57.012 39.130 0.00 0.00 33.64 4.51
2127 2364 6.476053 GTGATCGAGTTTCTATTAAGACACCC 59.524 42.308 0.00 0.00 33.64 4.61
2128 2365 6.476053 GGTGATCGAGTTTCTATTAAGACACC 59.524 42.308 0.00 0.00 33.64 4.16
2129 2366 7.259161 AGGTGATCGAGTTTCTATTAAGACAC 58.741 38.462 0.00 0.00 33.39 3.67
2130 2367 7.406031 AGGTGATCGAGTTTCTATTAAGACA 57.594 36.000 0.00 0.00 0.00 3.41
2131 2368 7.917720 GAGGTGATCGAGTTTCTATTAAGAC 57.082 40.000 0.00 0.00 0.00 3.01
2147 2384 2.028125 TTGGGGATCGCGAGGTGATC 62.028 60.000 16.66 6.53 45.50 2.92
2148 2385 1.622607 TTTGGGGATCGCGAGGTGAT 61.623 55.000 16.66 0.00 35.33 3.06
2149 2386 1.622607 ATTTGGGGATCGCGAGGTGA 61.623 55.000 16.66 0.00 0.00 4.02
2150 2387 1.153168 ATTTGGGGATCGCGAGGTG 60.153 57.895 16.66 0.00 0.00 4.00
2151 2388 1.146263 GATTTGGGGATCGCGAGGT 59.854 57.895 16.66 0.00 0.00 3.85
2152 2389 1.598130 GGATTTGGGGATCGCGAGG 60.598 63.158 16.66 0.00 0.00 4.63
2153 2390 1.598130 GGGATTTGGGGATCGCGAG 60.598 63.158 16.66 0.00 30.75 5.03
2154 2391 2.508928 GGGATTTGGGGATCGCGA 59.491 61.111 13.09 13.09 30.75 5.87
2155 2392 2.594592 GGGGATTTGGGGATCGCG 60.595 66.667 0.00 0.00 39.21 5.87
2156 2393 2.594592 CGGGGATTTGGGGATCGC 60.595 66.667 0.06 0.06 38.02 4.58
2157 2394 0.110486 ATTCGGGGATTTGGGGATCG 59.890 55.000 0.00 0.00 0.00 3.69
2158 2395 1.620822 CATTCGGGGATTTGGGGATC 58.379 55.000 0.00 0.00 0.00 3.36
2159 2396 0.188342 CCATTCGGGGATTTGGGGAT 59.812 55.000 0.00 0.00 0.00 3.85
2160 2397 0.921749 TCCATTCGGGGATTTGGGGA 60.922 55.000 0.00 0.00 37.22 4.81
2161 2398 0.755327 GTCCATTCGGGGATTTGGGG 60.755 60.000 0.00 0.00 39.62 4.96
2162 2399 0.033601 TGTCCATTCGGGGATTTGGG 60.034 55.000 0.00 0.00 39.62 4.12
2163 2400 1.750778 CTTGTCCATTCGGGGATTTGG 59.249 52.381 0.00 0.00 39.62 3.28
2164 2401 1.134946 GCTTGTCCATTCGGGGATTTG 59.865 52.381 0.00 0.00 39.62 2.32
2165 2402 1.474330 GCTTGTCCATTCGGGGATTT 58.526 50.000 0.00 0.00 39.62 2.17
2166 2403 0.748005 CGCTTGTCCATTCGGGGATT 60.748 55.000 0.00 0.00 39.62 3.01
2167 2404 1.153168 CGCTTGTCCATTCGGGGAT 60.153 57.895 0.00 0.00 39.62 3.85
2168 2405 1.832719 TTCGCTTGTCCATTCGGGGA 61.833 55.000 0.00 0.00 37.22 4.81
2169 2406 1.376683 TTCGCTTGTCCATTCGGGG 60.377 57.895 0.00 0.00 37.22 5.73
2170 2407 1.644786 GGTTCGCTTGTCCATTCGGG 61.645 60.000 0.00 0.00 38.37 5.14
2171 2408 0.953471 TGGTTCGCTTGTCCATTCGG 60.953 55.000 0.00 0.00 0.00 4.30
2172 2409 1.086696 ATGGTTCGCTTGTCCATTCG 58.913 50.000 0.00 0.00 38.61 3.34
2173 2410 1.812571 ACATGGTTCGCTTGTCCATTC 59.187 47.619 0.00 0.00 39.57 2.67
2174 2411 1.541147 CACATGGTTCGCTTGTCCATT 59.459 47.619 0.00 0.00 39.57 3.16
2175 2412 1.167851 CACATGGTTCGCTTGTCCAT 58.832 50.000 0.00 0.00 41.88 3.41
2176 2413 1.514678 GCACATGGTTCGCTTGTCCA 61.515 55.000 0.00 0.00 35.64 4.02
2177 2414 1.210155 GCACATGGTTCGCTTGTCC 59.790 57.895 0.00 0.00 0.00 4.02
2178 2415 0.385974 GTGCACATGGTTCGCTTGTC 60.386 55.000 13.17 0.00 0.00 3.18
2179 2416 1.100463 TGTGCACATGGTTCGCTTGT 61.100 50.000 17.42 0.00 0.00 3.16
2180 2417 0.386352 CTGTGCACATGGTTCGCTTG 60.386 55.000 22.00 0.00 0.00 4.01
2181 2418 0.819259 ACTGTGCACATGGTTCGCTT 60.819 50.000 22.00 0.00 0.00 4.68
2182 2419 1.227943 ACTGTGCACATGGTTCGCT 60.228 52.632 22.00 0.00 0.00 4.93
2183 2420 1.081906 CACTGTGCACATGGTTCGC 60.082 57.895 22.00 0.00 0.00 4.70
2184 2421 0.884259 TCCACTGTGCACATGGTTCG 60.884 55.000 30.53 19.09 34.89 3.95
2185 2422 0.877071 CTCCACTGTGCACATGGTTC 59.123 55.000 30.53 5.04 34.89 3.62
2186 2423 0.473755 TCTCCACTGTGCACATGGTT 59.526 50.000 30.53 13.69 34.89 3.67
2187 2424 0.473755 TTCTCCACTGTGCACATGGT 59.526 50.000 30.53 21.34 34.89 3.55
2188 2425 1.162698 CTTCTCCACTGTGCACATGG 58.837 55.000 28.34 28.34 34.58 3.66
2189 2426 0.520404 GCTTCTCCACTGTGCACATG 59.480 55.000 22.00 19.05 0.00 3.21
2190 2427 0.952497 CGCTTCTCCACTGTGCACAT 60.952 55.000 22.00 7.99 0.00 3.21
2191 2428 1.595109 CGCTTCTCCACTGTGCACA 60.595 57.895 20.37 20.37 0.00 4.57
2192 2429 2.959357 GCGCTTCTCCACTGTGCAC 61.959 63.158 10.75 10.75 37.20 4.57
2193 2430 2.666190 GCGCTTCTCCACTGTGCA 60.666 61.111 0.00 0.00 37.20 4.57
2194 2431 3.782244 CGCGCTTCTCCACTGTGC 61.782 66.667 5.56 0.00 0.00 4.57
2195 2432 3.114616 CCGCGCTTCTCCACTGTG 61.115 66.667 5.56 0.00 0.00 3.66
2212 2449 4.451150 TGATGAGGTGGACGCGGC 62.451 66.667 12.47 7.53 0.00 6.53
2213 2450 2.509336 GTGATGAGGTGGACGCGG 60.509 66.667 12.47 0.00 0.00 6.46
2214 2451 2.509336 GGTGATGAGGTGGACGCG 60.509 66.667 3.53 3.53 0.00 6.01
2215 2452 2.125106 GGGTGATGAGGTGGACGC 60.125 66.667 0.00 0.00 0.00 5.19
2216 2453 1.257750 TGAGGGTGATGAGGTGGACG 61.258 60.000 0.00 0.00 0.00 4.79
2217 2454 0.250513 GTGAGGGTGATGAGGTGGAC 59.749 60.000 0.00 0.00 0.00 4.02
2218 2455 0.909610 GGTGAGGGTGATGAGGTGGA 60.910 60.000 0.00 0.00 0.00 4.02
2219 2456 1.604378 GGTGAGGGTGATGAGGTGG 59.396 63.158 0.00 0.00 0.00 4.61
2220 2457 1.219124 CGGTGAGGGTGATGAGGTG 59.781 63.158 0.00 0.00 0.00 4.00
2221 2458 1.990060 CCGGTGAGGGTGATGAGGT 60.990 63.158 0.00 0.00 35.97 3.85
2222 2459 2.903357 CCGGTGAGGGTGATGAGG 59.097 66.667 0.00 0.00 35.97 3.86
2223 2460 2.187946 GCCGGTGAGGGTGATGAG 59.812 66.667 1.90 0.00 41.48 2.90
2224 2461 3.770040 CGCCGGTGAGGGTGATGA 61.770 66.667 10.20 0.00 40.04 2.92
2246 2483 4.803426 GGGCTGAGTCGGTGCTCG 62.803 72.222 0.00 0.00 38.28 5.03
2247 2484 2.914777 GATGGGCTGAGTCGGTGCTC 62.915 65.000 0.00 0.00 36.12 4.26
2248 2485 3.005539 ATGGGCTGAGTCGGTGCT 61.006 61.111 0.00 0.00 0.00 4.40
2249 2486 2.512515 GATGGGCTGAGTCGGTGC 60.513 66.667 0.00 0.00 0.00 5.01
2250 2487 2.187946 GGATGGGCTGAGTCGGTG 59.812 66.667 0.00 0.00 0.00 4.94
2251 2488 3.083997 GGGATGGGCTGAGTCGGT 61.084 66.667 0.00 0.00 0.00 4.69
2252 2489 2.765807 AGGGATGGGCTGAGTCGG 60.766 66.667 0.00 0.00 0.00 4.79
2253 2490 1.406065 ATGAGGGATGGGCTGAGTCG 61.406 60.000 0.00 0.00 0.00 4.18
2254 2491 0.396060 GATGAGGGATGGGCTGAGTC 59.604 60.000 0.00 0.00 0.00 3.36
2255 2492 0.030297 AGATGAGGGATGGGCTGAGT 60.030 55.000 0.00 0.00 0.00 3.41
2256 2493 0.686224 GAGATGAGGGATGGGCTGAG 59.314 60.000 0.00 0.00 0.00 3.35
2257 2494 1.117749 CGAGATGAGGGATGGGCTGA 61.118 60.000 0.00 0.00 0.00 4.26
2258 2495 1.370437 CGAGATGAGGGATGGGCTG 59.630 63.158 0.00 0.00 0.00 4.85
2259 2496 1.840650 CCGAGATGAGGGATGGGCT 60.841 63.158 0.00 0.00 0.00 5.19
2260 2497 2.746359 CCGAGATGAGGGATGGGC 59.254 66.667 0.00 0.00 0.00 5.36
2261 2498 2.746359 GCCGAGATGAGGGATGGG 59.254 66.667 0.00 0.00 0.00 4.00
2262 2499 2.746359 GGCCGAGATGAGGGATGG 59.254 66.667 0.00 0.00 0.00 3.51
2263 2500 1.825281 GAGGGCCGAGATGAGGGATG 61.825 65.000 0.00 0.00 0.00 3.51
2264 2501 1.535202 GAGGGCCGAGATGAGGGAT 60.535 63.158 0.00 0.00 0.00 3.85
2265 2502 2.123251 GAGGGCCGAGATGAGGGA 60.123 66.667 0.00 0.00 0.00 4.20
2266 2503 3.237741 GGAGGGCCGAGATGAGGG 61.238 72.222 0.00 0.00 0.00 4.30
2338 2575 3.310860 AAGTACTTGCCCTCCGCGG 62.311 63.158 22.12 22.12 42.08 6.46
2339 2576 1.810030 GAAGTACTTGCCCTCCGCG 60.810 63.158 14.14 0.00 42.08 6.46
2340 2577 0.460459 GAGAAGTACTTGCCCTCCGC 60.460 60.000 14.14 0.00 38.31 5.54
2341 2578 0.175989 GGAGAAGTACTTGCCCTCCG 59.824 60.000 20.26 0.00 34.75 4.63
2342 2579 1.276622 TGGAGAAGTACTTGCCCTCC 58.723 55.000 24.93 24.93 42.72 4.30
2343 2580 2.701107 GTTGGAGAAGTACTTGCCCTC 58.299 52.381 14.14 13.00 0.00 4.30
2344 2581 1.002087 CGTTGGAGAAGTACTTGCCCT 59.998 52.381 14.14 3.70 0.00 5.19
2345 2582 1.439679 CGTTGGAGAAGTACTTGCCC 58.560 55.000 14.14 13.66 0.00 5.36
2346 2583 1.439679 CCGTTGGAGAAGTACTTGCC 58.560 55.000 14.14 14.31 0.00 4.52
2347 2584 0.796927 GCCGTTGGAGAAGTACTTGC 59.203 55.000 14.14 3.60 0.00 4.01
2348 2585 2.457366 AGCCGTTGGAGAAGTACTTG 57.543 50.000 14.14 0.00 0.00 3.16
2349 2586 2.609737 CGAAGCCGTTGGAGAAGTACTT 60.610 50.000 8.13 8.13 0.00 2.24
2350 2587 1.067776 CGAAGCCGTTGGAGAAGTACT 60.068 52.381 0.00 0.00 0.00 2.73
2351 2588 1.068055 TCGAAGCCGTTGGAGAAGTAC 60.068 52.381 0.00 0.00 37.05 2.73
2352 2589 1.068055 GTCGAAGCCGTTGGAGAAGTA 60.068 52.381 0.00 0.00 37.05 2.24
2353 2590 0.319641 GTCGAAGCCGTTGGAGAAGT 60.320 55.000 0.00 0.00 37.05 3.01
2354 2591 1.014564 GGTCGAAGCCGTTGGAGAAG 61.015 60.000 0.00 0.00 37.05 2.85
2355 2592 1.005394 GGTCGAAGCCGTTGGAGAA 60.005 57.895 0.00 0.00 37.05 2.87
2356 2593 2.154798 CTGGTCGAAGCCGTTGGAGA 62.155 60.000 0.00 0.00 37.05 3.71
2357 2594 1.738099 CTGGTCGAAGCCGTTGGAG 60.738 63.158 0.00 0.00 37.05 3.86
2358 2595 2.342279 CTGGTCGAAGCCGTTGGA 59.658 61.111 0.00 0.00 37.05 3.53
2359 2596 2.742372 CCTGGTCGAAGCCGTTGG 60.742 66.667 0.00 0.00 37.05 3.77
2360 2597 3.423154 GCCTGGTCGAAGCCGTTG 61.423 66.667 0.00 0.00 37.05 4.10
2361 2598 4.699522 GGCCTGGTCGAAGCCGTT 62.700 66.667 0.00 0.00 36.84 4.44
2364 2601 4.785453 CCAGGCCTGGTCGAAGCC 62.785 72.222 39.52 8.55 45.53 4.35
2396 2633 4.083862 GAGTCGTGGAGGTGGGGC 62.084 72.222 0.00 0.00 0.00 5.80
2397 2634 3.391382 GGAGTCGTGGAGGTGGGG 61.391 72.222 0.00 0.00 0.00 4.96
2398 2635 1.990060 ATGGAGTCGTGGAGGTGGG 60.990 63.158 0.00 0.00 0.00 4.61
2399 2636 1.219124 CATGGAGTCGTGGAGGTGG 59.781 63.158 0.00 0.00 0.00 4.61
2400 2637 0.174389 CTCATGGAGTCGTGGAGGTG 59.826 60.000 0.00 0.00 0.00 4.00
2401 2638 0.039764 TCTCATGGAGTCGTGGAGGT 59.960 55.000 0.00 0.00 0.00 3.85
2402 2639 0.743688 CTCTCATGGAGTCGTGGAGG 59.256 60.000 0.00 0.00 37.30 4.30
2403 2640 0.743688 CCTCTCATGGAGTCGTGGAG 59.256 60.000 9.47 0.00 40.30 3.86
2404 2641 0.331616 TCCTCTCATGGAGTCGTGGA 59.668 55.000 9.47 0.00 40.30 4.02
2405 2642 0.743688 CTCCTCTCATGGAGTCGTGG 59.256 60.000 9.47 0.00 46.33 4.94
2412 2649 1.045350 CGGAAGGCTCCTCTCATGGA 61.045 60.000 0.00 0.00 39.93 3.41
2413 2650 1.445095 CGGAAGGCTCCTCTCATGG 59.555 63.158 0.00 0.00 39.93 3.66
2414 2651 1.227497 GCGGAAGGCTCCTCTCATG 60.227 63.158 0.00 0.00 39.93 3.07
2415 2652 2.790791 CGCGGAAGGCTCCTCTCAT 61.791 63.158 0.00 0.00 39.93 2.90
2416 2653 3.452786 CGCGGAAGGCTCCTCTCA 61.453 66.667 0.00 0.00 39.93 3.27
2417 2654 4.882396 GCGCGGAAGGCTCCTCTC 62.882 72.222 8.83 0.00 39.93 3.20
2551 2788 3.026431 ATGTACAGGAACCCGCGGG 62.026 63.158 42.17 42.17 42.03 6.13
2552 2789 1.813753 CATGTACAGGAACCCGCGG 60.814 63.158 21.04 21.04 0.00 6.46
2553 2790 0.806102 CTCATGTACAGGAACCCGCG 60.806 60.000 11.87 0.00 0.00 6.46
2554 2791 1.090052 GCTCATGTACAGGAACCCGC 61.090 60.000 11.87 7.64 0.00 6.13
2555 2792 0.806102 CGCTCATGTACAGGAACCCG 60.806 60.000 11.87 10.43 0.00 5.28
2556 2793 0.535335 TCGCTCATGTACAGGAACCC 59.465 55.000 11.87 2.48 0.00 4.11
2557 2794 1.471676 CCTCGCTCATGTACAGGAACC 60.472 57.143 11.87 4.89 0.00 3.62
2558 2795 1.204941 ACCTCGCTCATGTACAGGAAC 59.795 52.381 11.87 6.26 0.00 3.62
2559 2796 1.476891 GACCTCGCTCATGTACAGGAA 59.523 52.381 11.87 0.00 0.00 3.36
2560 2797 1.103803 GACCTCGCTCATGTACAGGA 58.896 55.000 10.21 10.21 0.00 3.86
2561 2798 0.248661 CGACCTCGCTCATGTACAGG 60.249 60.000 0.00 0.00 0.00 4.00
2562 2799 0.733150 TCGACCTCGCTCATGTACAG 59.267 55.000 0.33 0.00 39.60 2.74
2563 2800 0.450583 GTCGACCTCGCTCATGTACA 59.549 55.000 3.51 0.00 39.60 2.90
2564 2801 0.589229 CGTCGACCTCGCTCATGTAC 60.589 60.000 10.58 0.00 39.60 2.90
2565 2802 1.022982 ACGTCGACCTCGCTCATGTA 61.023 55.000 10.58 0.00 39.60 2.29
2566 2803 2.254703 GACGTCGACCTCGCTCATGT 62.255 60.000 10.58 0.00 39.60 3.21
2567 2804 1.583967 GACGTCGACCTCGCTCATG 60.584 63.158 10.58 0.00 39.60 3.07
2568 2805 2.792599 GACGTCGACCTCGCTCAT 59.207 61.111 10.58 0.00 39.60 2.90
2569 2806 3.785499 CGACGTCGACCTCGCTCA 61.785 66.667 33.35 0.00 43.02 4.26
2570 2807 4.517703 CCGACGTCGACCTCGCTC 62.518 72.222 37.65 8.34 43.02 5.03
2576 2813 3.966026 CTTGAGGCCGACGTCGACC 62.966 68.421 37.65 35.11 42.45 4.79
2577 2814 2.504244 CTTGAGGCCGACGTCGAC 60.504 66.667 37.65 27.72 43.02 4.20
2578 2815 2.467946 GAACTTGAGGCCGACGTCGA 62.468 60.000 37.65 16.05 43.02 4.20
2579 2816 2.049433 AACTTGAGGCCGACGTCG 60.049 61.111 30.33 30.33 39.44 5.12
2580 2817 2.087009 CGAACTTGAGGCCGACGTC 61.087 63.158 5.18 5.18 0.00 4.34
2581 2818 2.049433 CGAACTTGAGGCCGACGT 60.049 61.111 0.00 0.00 0.00 4.34
2582 2819 3.479269 GCGAACTTGAGGCCGACG 61.479 66.667 0.00 0.00 0.00 5.12
2583 2820 3.119096 GGCGAACTTGAGGCCGAC 61.119 66.667 0.00 0.00 37.06 4.79
2586 2823 2.221906 TAGTCGGCGAACTTGAGGCC 62.222 60.000 12.92 0.00 43.42 5.19
2587 2824 1.077089 GTAGTCGGCGAACTTGAGGC 61.077 60.000 12.92 0.00 0.00 4.70
2588 2825 0.526662 AGTAGTCGGCGAACTTGAGG 59.473 55.000 12.92 0.00 0.00 3.86
2589 2826 2.251893 GAAGTAGTCGGCGAACTTGAG 58.748 52.381 26.37 0.00 33.72 3.02
2590 2827 1.400629 CGAAGTAGTCGGCGAACTTGA 60.401 52.381 26.37 5.10 46.45 3.02
2591 2828 0.982673 CGAAGTAGTCGGCGAACTTG 59.017 55.000 26.37 16.39 46.45 3.16
2592 2829 3.396491 CGAAGTAGTCGGCGAACTT 57.604 52.632 22.80 22.80 46.45 2.66
2601 2838 1.142097 GCAGCTCCCCGAAGTAGTC 59.858 63.158 0.00 0.00 0.00 2.59
2602 2839 1.305381 AGCAGCTCCCCGAAGTAGT 60.305 57.895 0.00 0.00 0.00 2.73
2603 2840 1.439644 GAGCAGCTCCCCGAAGTAG 59.560 63.158 11.84 0.00 0.00 2.57
2604 2841 2.058595 GGAGCAGCTCCCCGAAGTA 61.059 63.158 29.22 0.00 44.36 2.24
2605 2842 3.394836 GGAGCAGCTCCCCGAAGT 61.395 66.667 29.22 0.00 44.36 3.01
2618 2855 4.475135 GGGACCTTCTGCCGGAGC 62.475 72.222 5.05 0.00 40.48 4.70


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

AutoCloner maintained by Alex Coulton.