Multiple sequence alignment - TraesCS4A01G449400

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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 TraesCS4A01G449400 chr4A 100.000 2612 0 0 1 2612 715557821 715560432 0.000000e+00 4824.0
1 TraesCS4A01G449400 chr4A 96.429 1960 53 6 1 1957 715946499 715944554 0.000000e+00 3216.0
2 TraesCS4A01G449400 chr4A 80.091 1316 193 30 362 1655 716299732 716301000 0.000000e+00 915.0
3 TraesCS4A01G449400 chr4A 91.863 553 39 5 2065 2612 715944501 715943950 0.000000e+00 767.0
4 TraesCS4A01G449400 chr4A 77.114 402 83 7 1020 1416 715955077 715955474 9.410000e-55 224.0
5 TraesCS4A01G449400 chr4A 76.177 361 81 4 1098 1454 715931729 715931370 4.440000e-43 185.0
6 TraesCS4A01G449400 chr7D 76.581 1328 245 40 372 1655 17665371 17664066 0.000000e+00 669.0
7 TraesCS4A01G449400 chr7D 76.471 408 85 9 1017 1417 12070401 12070804 7.320000e-51 211.0
8 TraesCS4A01G449400 chr7D 76.152 369 83 5 1053 1417 49270817 49270450 3.430000e-44 189.0
9 TraesCS4A01G449400 chr7D 72.846 383 86 14 824 1191 12312729 12312350 5.910000e-22 115.0
10 TraesCS4A01G449400 chr7A 76.194 1319 256 36 372 1647 17162517 17161214 0.000000e+00 643.0
11 TraesCS4A01G449400 chr7A 80.921 152 27 2 1303 1454 11869520 11869371 4.570000e-23 119.0
12 TraesCS4A01G449400 chr7A 73.107 383 82 18 825 1191 11761901 11761524 1.640000e-22 117.0
13 TraesCS4A01G449400 chr5A 85.714 91 11 2 273 362 508533621 508533532 7.700000e-16 95.3
14 TraesCS4A01G449400 chr5A 84.783 92 12 2 273 363 508557150 508557060 9.950000e-15 91.6
15 TraesCS4A01G449400 chr2B 89.189 74 7 1 288 361 313701525 313701453 9.950000e-15 91.6
16 TraesCS4A01G449400 chr4B 85.393 89 8 5 283 370 239803309 239803393 1.290000e-13 87.9
17 TraesCS4A01G449400 chrUn 82.292 96 17 0 266 361 93192772 93192867 1.670000e-12 84.2
18 TraesCS4A01G449400 chr1D 86.486 74 10 0 288 361 424481644 424481571 5.990000e-12 82.4
19 TraesCS4A01G449400 chr2D 83.146 89 14 1 273 361 651065499 651065586 2.150000e-11 80.5
20 TraesCS4A01G449400 chr6B 75.912 137 29 4 228 362 78356430 78356296 1.680000e-07 67.6


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 TraesCS4A01G449400 chr4A 715557821 715560432 2611 False 4824.0 4824 100.000 1 2612 1 chr4A.!!$F1 2611
1 TraesCS4A01G449400 chr4A 715943950 715946499 2549 True 1991.5 3216 94.146 1 2612 2 chr4A.!!$R2 2611
2 TraesCS4A01G449400 chr4A 716299732 716301000 1268 False 915.0 915 80.091 362 1655 1 chr4A.!!$F3 1293
3 TraesCS4A01G449400 chr7D 17664066 17665371 1305 True 669.0 669 76.581 372 1655 1 chr7D.!!$R2 1283
4 TraesCS4A01G449400 chr7A 17161214 17162517 1303 True 643.0 643 76.194 372 1647 1 chr7A.!!$R3 1275

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
127 128 0.029567 CCCGCGACTGCTAGAACTAG 59.97 60.0 8.23 4.67 39.65 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2062 0.032615 ACTCTGCTCCGAGGGATCTT 60.033 55.0 0.0 0.0 35.33 2.4 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
36 37 2.228138 TAAAGTTACTATGGCGGGCG 57.772 50.000 0.00 0.00 0.00 6.13
37 38 0.538118 AAAGTTACTATGGCGGGCGA 59.462 50.000 0.00 0.00 0.00 5.54
71 72 4.693566 CCGCCAGTTCTAACTTGTGAATAA 59.306 41.667 8.58 0.00 37.08 1.40
113 114 1.491563 GCGTAGATAATTGCCCGCG 59.508 57.895 0.00 0.00 0.00 6.46
119 120 1.153168 ATAATTGCCCGCGACTGCT 60.153 52.632 8.23 0.00 39.65 4.24
121 122 0.529773 TAATTGCCCGCGACTGCTAG 60.530 55.000 8.23 0.00 39.65 3.42
122 123 2.238847 AATTGCCCGCGACTGCTAGA 62.239 55.000 8.23 0.00 39.65 2.43
123 124 2.238847 ATTGCCCGCGACTGCTAGAA 62.239 55.000 8.23 0.00 39.65 2.10
124 125 2.886124 GCCCGCGACTGCTAGAAC 60.886 66.667 8.23 0.00 39.65 3.01
125 126 2.885861 CCCGCGACTGCTAGAACT 59.114 61.111 8.23 0.00 39.65 3.01
126 127 2.001361 GCCCGCGACTGCTAGAACTA 62.001 60.000 8.23 0.00 39.65 2.24
127 128 0.029567 CCCGCGACTGCTAGAACTAG 59.970 60.000 8.23 4.67 39.65 2.57
128 129 0.733729 CCGCGACTGCTAGAACTAGT 59.266 55.000 8.23 0.00 39.65 2.57
129 130 1.132643 CCGCGACTGCTAGAACTAGTT 59.867 52.381 8.23 8.13 39.65 2.24
130 131 2.177977 CGCGACTGCTAGAACTAGTTG 58.822 52.381 14.14 0.00 39.65 3.16
131 132 1.921230 GCGACTGCTAGAACTAGTTGC 59.079 52.381 14.14 11.08 42.60 4.17
132 133 2.671351 GCGACTGCTAGAACTAGTTGCA 60.671 50.000 14.14 15.18 46.32 4.08
296 297 7.305474 GCACTGCTACTTTTTGAAATTAGCTA 58.695 34.615 17.73 0.00 36.83 3.32
299 300 8.462016 ACTGCTACTTTTTGAAATTAGCTATGG 58.538 33.333 17.73 10.92 36.83 2.74
347 348 3.375647 TTTGGGTTCACCTATAAGCCC 57.624 47.619 0.00 0.00 42.57 5.19
351 352 3.053917 TGGGTTCACCTATAAGCCCTTTC 60.054 47.826 0.00 0.00 42.57 2.62
352 353 3.552875 GGTTCACCTATAAGCCCTTTCC 58.447 50.000 0.00 0.00 0.00 3.13
356 357 2.777692 CACCTATAAGCCCTTTCCCAGA 59.222 50.000 0.00 0.00 0.00 3.86
681 764 4.262377 CCAAACTGGGCATCAATGTGTTTA 60.262 41.667 0.00 0.00 32.67 2.01
742 825 5.618056 AGCATCAATGTATTTGCGGATAG 57.382 39.130 0.00 0.00 40.00 2.08
935 1018 3.016736 CTGCCCGACACATTTTCCTATT 58.983 45.455 0.00 0.00 0.00 1.73
1338 1436 1.552226 CGATGCGCGTCCTTACTTTA 58.448 50.000 23.36 0.00 34.64 1.85
1605 1703 5.164620 TCACATTGCCAGAAGAGATGTTA 57.835 39.130 0.00 0.00 0.00 2.41
1694 1792 0.901827 ATGCTGTGTACATCCGGTGA 59.098 50.000 0.00 0.00 0.00 4.02
1780 1878 6.152932 TCATTTTACTACTCCCGTCATACC 57.847 41.667 0.00 0.00 0.00 2.73
1792 1890 7.893658 ACTCCCGTCATACCTAAATATAAGTG 58.106 38.462 0.00 0.00 0.00 3.16
1821 1919 7.348080 TGGTAGGATAGCAGTATATATGCAC 57.652 40.000 13.48 3.94 45.27 4.57
1844 1942 2.888534 CCGCCACGTACATTCGGG 60.889 66.667 0.00 0.00 36.73 5.14
1845 1943 3.560278 CGCCACGTACATTCGGGC 61.560 66.667 0.90 0.90 40.75 6.13
1846 1944 2.125269 GCCACGTACATTCGGGCT 60.125 61.111 3.72 0.00 40.87 5.19
1847 1945 2.461110 GCCACGTACATTCGGGCTG 61.461 63.158 3.72 0.00 40.87 4.85
1848 1946 1.216977 CCACGTACATTCGGGCTGA 59.783 57.895 0.00 0.00 32.43 4.26
1849 1947 1.082117 CCACGTACATTCGGGCTGAC 61.082 60.000 0.00 0.00 32.43 3.51
1850 1948 1.153901 ACGTACATTCGGGCTGACG 60.154 57.895 0.00 0.00 36.42 4.35
1909 2009 1.679944 CGGATCAGCCCATCAACAACT 60.680 52.381 0.00 0.00 0.00 3.16
1927 2027 1.066430 ACTAACACGGACGCATCCAAT 60.066 47.619 0.00 0.00 46.67 3.16
1935 2035 0.462047 GACGCATCCAATCCCTCGTT 60.462 55.000 0.00 0.00 0.00 3.85
1957 2057 7.553044 TCGTTTCTCATAGTCTCATCTGTCTAA 59.447 37.037 0.00 0.00 0.00 2.10
1958 2058 8.184848 CGTTTCTCATAGTCTCATCTGTCTAAA 58.815 37.037 0.00 0.00 0.00 1.85
1959 2059 9.862371 GTTTCTCATAGTCTCATCTGTCTAAAA 57.138 33.333 0.00 0.00 0.00 1.52
1978 2078 2.409948 AAAAAGATCCCTCGGAGCAG 57.590 50.000 0.00 0.00 41.08 4.24
1979 2079 1.573108 AAAAGATCCCTCGGAGCAGA 58.427 50.000 0.00 0.00 41.08 4.26
1980 2080 1.118838 AAAGATCCCTCGGAGCAGAG 58.881 55.000 0.00 0.00 41.08 3.35
1981 2081 0.032615 AAGATCCCTCGGAGCAGAGT 60.033 55.000 0.00 0.00 41.08 3.24
1982 2082 0.847373 AGATCCCTCGGAGCAGAGTA 59.153 55.000 0.00 0.00 41.08 2.59
1983 2083 1.215673 AGATCCCTCGGAGCAGAGTAA 59.784 52.381 0.00 0.00 41.08 2.24
1984 2084 1.611491 GATCCCTCGGAGCAGAGTAAG 59.389 57.143 0.00 0.00 38.12 2.34
1985 2085 1.038130 TCCCTCGGAGCAGAGTAAGC 61.038 60.000 0.00 0.00 36.56 3.09
1986 2086 1.040339 CCCTCGGAGCAGAGTAAGCT 61.040 60.000 0.00 0.00 46.82 3.74
2005 2105 8.213679 AGTAAGCTCTTGCCTATCAATAAATGA 58.786 33.333 0.00 0.00 40.61 2.57
2008 2108 8.558973 AGCTCTTGCCTATCAATAAATGATAC 57.441 34.615 0.00 0.00 42.87 2.24
2053 2153 5.956068 AAAAAGAGGAAGCTCTTCACATC 57.044 39.130 11.27 6.36 42.26 3.06
2054 2154 4.906747 AAAGAGGAAGCTCTTCACATCT 57.093 40.909 11.27 8.19 42.26 2.90
2055 2155 4.906747 AAGAGGAAGCTCTTCACATCTT 57.093 40.909 11.27 12.59 39.24 2.40
2056 2156 6.365970 AAAGAGGAAGCTCTTCACATCTTA 57.634 37.500 16.89 0.00 42.26 2.10
2057 2157 6.558488 AAGAGGAAGCTCTTCACATCTTAT 57.442 37.500 15.86 2.18 39.24 1.73
2058 2158 5.916318 AGAGGAAGCTCTTCACATCTTATG 58.084 41.667 11.27 0.00 41.20 1.90
2059 2159 5.033589 AGGAAGCTCTTCACATCTTATGG 57.966 43.478 11.27 0.00 41.20 2.74
2060 2160 4.472833 AGGAAGCTCTTCACATCTTATGGT 59.527 41.667 11.27 0.00 41.20 3.55
2061 2161 4.574013 GGAAGCTCTTCACATCTTATGGTG 59.426 45.833 11.27 0.00 41.20 4.17
2062 2162 3.539604 AGCTCTTCACATCTTATGGTGC 58.460 45.455 0.00 0.00 35.04 5.01
2063 2163 2.615912 GCTCTTCACATCTTATGGTGCC 59.384 50.000 0.00 0.00 35.04 5.01
2099 2199 4.950050 AGCTTGGTAGTATGCAGATGTAC 58.050 43.478 0.00 0.00 0.00 2.90
2100 2200 3.736252 GCTTGGTAGTATGCAGATGTACG 59.264 47.826 0.00 0.00 0.00 3.67
2101 2201 4.736759 GCTTGGTAGTATGCAGATGTACGT 60.737 45.833 0.00 0.00 0.00 3.57
2102 2202 4.994907 TGGTAGTATGCAGATGTACGTT 57.005 40.909 0.00 0.00 0.00 3.99
2103 2203 4.678622 TGGTAGTATGCAGATGTACGTTG 58.321 43.478 0.00 0.00 0.00 4.10
2104 2204 4.049186 GGTAGTATGCAGATGTACGTTGG 58.951 47.826 0.00 0.00 0.00 3.77
2105 2205 4.202080 GGTAGTATGCAGATGTACGTTGGA 60.202 45.833 0.00 0.00 0.00 3.53
2106 2206 4.672587 AGTATGCAGATGTACGTTGGAT 57.327 40.909 0.00 0.00 0.00 3.41
2107 2207 4.371786 AGTATGCAGATGTACGTTGGATG 58.628 43.478 0.00 0.00 0.00 3.51
2108 2208 2.022764 TGCAGATGTACGTTGGATGG 57.977 50.000 0.00 0.00 0.00 3.51
2121 2223 1.889105 GGATGGACGTGATGCGCAT 60.889 57.895 25.66 25.66 46.11 4.73
2135 2237 1.132834 TGCGCATGCCAACTAGAAATG 59.867 47.619 13.15 0.00 41.78 2.32
2147 2249 7.286087 TGCCAACTAGAAATGCATAATCAGAAT 59.714 33.333 0.00 0.00 0.00 2.40
2148 2250 7.806960 GCCAACTAGAAATGCATAATCAGAATC 59.193 37.037 0.00 0.00 0.00 2.52
2167 2269 3.717400 TCAACCATATCAGCGTCTCTC 57.283 47.619 0.00 0.00 0.00 3.20
2173 2275 1.584175 TATCAGCGTCTCTCGTCTCC 58.416 55.000 0.00 0.00 42.13 3.71
2205 2307 1.206745 ATAATTCTGCGACGACGGCG 61.207 55.000 21.02 21.02 44.79 6.46
2215 2317 4.111016 CGACGGCGACCTACAGCA 62.111 66.667 16.62 0.00 40.82 4.41
2229 2332 4.336993 ACCTACAGCATCTCTCGTCTAAAG 59.663 45.833 0.00 0.00 0.00 1.85
2233 2336 5.406649 ACAGCATCTCTCGTCTAAAGAAAG 58.593 41.667 0.00 0.00 0.00 2.62
2249 2352 1.605232 GAAAGAAAAACCTCGGCCGAA 59.395 47.619 30.53 13.22 0.00 4.30
2279 2382 4.858850 TGGATGGTTGATAATTCTGCAGT 58.141 39.130 14.67 0.00 0.00 4.40
2290 2393 0.764271 TTCTGCAGTCCCATGTGACA 59.236 50.000 14.67 0.00 37.73 3.58
2331 2435 7.129457 TCAGCCTATTATATCCAAGCCATAG 57.871 40.000 0.00 0.00 0.00 2.23
2367 2471 6.042552 CCATGACTGTCATCCTCCTACTATTT 59.957 42.308 19.89 0.00 34.28 1.40
2382 2486 9.908152 CTCCTACTATTTGTTTTAACTTTTGGG 57.092 33.333 0.00 0.00 0.00 4.12
2406 2510 0.036875 CCTCTTCTCCACACAACCCC 59.963 60.000 0.00 0.00 0.00 4.95
2430 2534 1.202533 CCTTACATACAGCCGACCAGG 60.203 57.143 0.00 0.00 44.97 4.45
2462 2566 2.030551 CTATCTACGGACCGCAGCA 58.969 57.895 15.39 1.14 0.00 4.41
2486 2590 3.723348 GTTCCCGTGCGTGGCTTC 61.723 66.667 0.00 0.00 0.00 3.86
2487 2591 4.243008 TTCCCGTGCGTGGCTTCA 62.243 61.111 0.00 0.00 0.00 3.02
2488 2592 3.545124 TTCCCGTGCGTGGCTTCAT 62.545 57.895 0.00 0.00 0.00 2.57
2490 2594 1.743623 CCCGTGCGTGGCTTCATAA 60.744 57.895 0.00 0.00 0.00 1.90
2494 2598 1.377987 TGCGTGGCTTCATAACCCC 60.378 57.895 0.00 0.00 0.00 4.95
2513 2617 3.487120 CCCCCTTCTAAACCTTATCGG 57.513 52.381 0.00 0.00 39.35 4.18
2524 2628 4.497291 AACCTTATCGGCCACAAGATTA 57.503 40.909 2.24 0.00 35.61 1.75
2528 2632 5.163195 ACCTTATCGGCCACAAGATTATCTT 60.163 40.000 2.24 0.99 34.59 2.40
2539 2643 3.853355 AGATTATCTTGGTGAGCCTGG 57.147 47.619 0.00 0.00 35.27 4.45
2540 2644 2.158696 AGATTATCTTGGTGAGCCTGGC 60.159 50.000 11.65 11.65 35.27 4.85
2552 2656 2.955881 GCCTGGCTCGTACCACCTT 61.956 63.158 12.43 0.00 35.33 3.50
2562 2666 1.274167 CGTACCACCTTAACCAGCAGA 59.726 52.381 0.00 0.00 0.00 4.26
2563 2667 2.674177 CGTACCACCTTAACCAGCAGAG 60.674 54.545 0.00 0.00 0.00 3.35
2589 2693 3.421844 GCCCAGGAATTTAAGACTGTGT 58.578 45.455 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 1.741770 CTGGCGGGTGCTAAGTGTC 60.742 63.158 0.00 0.00 42.25 3.67
37 38 2.052047 AACTGGCGGGTGCTAAGTGT 62.052 55.000 0.00 0.00 42.25 3.55
71 72 7.148188 CGCCAGCCACAAGATCATATATTTATT 60.148 37.037 0.00 0.00 0.00 1.40
119 120 0.457853 CGCCGCTGCAACTAGTTCTA 60.458 55.000 4.77 0.00 37.32 2.10
121 122 2.740714 CCGCCGCTGCAACTAGTTC 61.741 63.158 4.77 1.77 37.32 3.01
122 123 2.742372 CCGCCGCTGCAACTAGTT 60.742 61.111 1.12 1.12 37.32 2.24
123 124 4.760047 CCCGCCGCTGCAACTAGT 62.760 66.667 0.00 0.00 37.32 2.57
149 150 2.770164 AGTGATTAGTGGCAGGTCAC 57.230 50.000 11.36 11.36 39.47 3.67
319 320 3.593442 AGGTGAACCCAAATGAGTGAA 57.407 42.857 0.00 0.00 36.42 3.18
347 348 3.503748 CCTTTAGTGCACTTCTGGGAAAG 59.496 47.826 27.06 24.07 0.00 2.62
351 352 2.859165 TCCTTTAGTGCACTTCTGGG 57.141 50.000 27.06 20.43 0.00 4.45
352 353 5.514274 TTTTTCCTTTAGTGCACTTCTGG 57.486 39.130 27.06 22.24 0.00 3.86
356 357 6.761242 GGAACAATTTTTCCTTTAGTGCACTT 59.239 34.615 27.06 9.41 41.80 3.16
637 660 5.891451 TGGATCTTGTAGTATTGACACTCG 58.109 41.667 0.00 0.00 0.00 4.18
742 825 4.965200 ATCTTGGTATTAGTGCCCTCTC 57.035 45.455 0.00 0.00 0.00 3.20
935 1018 5.250543 TCAAGAGTGGTGGAGATAATTGGAA 59.749 40.000 0.00 0.00 0.00 3.53
1062 1160 2.664081 GCCACTACCAGAGCTGCCT 61.664 63.158 0.00 0.00 0.00 4.75
1191 1289 1.374252 CTTAGCGTTGGTGCTCCGT 60.374 57.895 0.00 0.00 45.87 4.69
1227 1325 2.620115 GGTGATGTCGATGGCAATGAAT 59.380 45.455 0.00 0.00 0.00 2.57
1338 1436 1.831106 TGTTCATAGTCCACCTCGCAT 59.169 47.619 0.00 0.00 0.00 4.73
1660 1758 9.225436 TGTACACAGCATCTCAAACATAATAAA 57.775 29.630 0.00 0.00 0.00 1.40
1792 1890 8.634444 CATATATACTGCTATCCTACCAAGACC 58.366 40.741 0.00 0.00 0.00 3.85
1815 1913 1.963855 GTGGCGGTGTGTGTGCATA 60.964 57.895 0.00 0.00 0.00 3.14
1821 1919 1.225376 AATGTACGTGGCGGTGTGTG 61.225 55.000 0.00 0.00 0.00 3.82
1927 2027 3.964411 TGAGACTATGAGAAACGAGGGA 58.036 45.455 0.00 0.00 0.00 4.20
1959 2059 1.909302 TCTGCTCCGAGGGATCTTTTT 59.091 47.619 0.00 0.00 0.00 1.94
1960 2060 1.484240 CTCTGCTCCGAGGGATCTTTT 59.516 52.381 0.00 0.00 0.00 2.27
1961 2061 1.118838 CTCTGCTCCGAGGGATCTTT 58.881 55.000 0.00 0.00 0.00 2.52
1962 2062 0.032615 ACTCTGCTCCGAGGGATCTT 60.033 55.000 0.00 0.00 35.33 2.40
1963 2063 0.847373 TACTCTGCTCCGAGGGATCT 59.153 55.000 0.00 0.00 35.33 2.75
1964 2064 1.611491 CTTACTCTGCTCCGAGGGATC 59.389 57.143 0.00 0.00 35.33 3.36
1965 2065 1.698506 CTTACTCTGCTCCGAGGGAT 58.301 55.000 0.00 0.00 35.33 3.85
1966 2066 1.038130 GCTTACTCTGCTCCGAGGGA 61.038 60.000 0.00 0.00 35.33 4.20
1967 2067 1.040339 AGCTTACTCTGCTCCGAGGG 61.040 60.000 0.00 0.00 35.67 4.30
1968 2068 2.499214 AGCTTACTCTGCTCCGAGG 58.501 57.895 0.00 0.00 35.67 4.63
1978 2078 8.502387 CATTTATTGATAGGCAAGAGCTTACTC 58.498 37.037 0.00 0.00 40.42 2.59
1979 2079 8.213679 TCATTTATTGATAGGCAAGAGCTTACT 58.786 33.333 0.00 0.00 40.42 2.24
1980 2080 8.383318 TCATTTATTGATAGGCAAGAGCTTAC 57.617 34.615 0.00 0.00 40.42 2.34
1982 2082 9.007901 GTATCATTTATTGATAGGCAAGAGCTT 57.992 33.333 0.00 0.00 45.74 3.74
1983 2083 7.332926 CGTATCATTTATTGATAGGCAAGAGCT 59.667 37.037 0.00 0.00 45.74 4.09
1984 2084 7.459486 CGTATCATTTATTGATAGGCAAGAGC 58.541 38.462 4.60 0.00 45.74 4.09
2005 2105 5.232626 TCGCGAGTATGTAAAATTTGCGTAT 59.767 36.000 3.71 0.09 41.22 3.06
2008 2108 3.918635 TCGCGAGTATGTAAAATTTGCG 58.081 40.909 3.71 7.25 41.67 4.85
2036 2136 5.055812 CCATAAGATGTGAAGAGCTTCCTC 58.944 45.833 7.69 2.99 38.77 3.71
2042 2142 2.615912 GGCACCATAAGATGTGAAGAGC 59.384 50.000 0.00 0.00 0.00 4.09
2044 2144 3.519107 TGAGGCACCATAAGATGTGAAGA 59.481 43.478 0.00 0.00 0.00 2.87
2047 2147 2.571202 TGTGAGGCACCATAAGATGTGA 59.429 45.455 0.00 0.00 32.73 3.58
2048 2148 2.989909 TGTGAGGCACCATAAGATGTG 58.010 47.619 0.00 0.00 32.73 3.21
2049 2149 3.457380 AGATGTGAGGCACCATAAGATGT 59.543 43.478 0.00 0.00 32.73 3.06
2050 2150 4.082665 AGATGTGAGGCACCATAAGATG 57.917 45.455 0.00 0.00 32.73 2.90
2051 2151 4.445448 GGAAGATGTGAGGCACCATAAGAT 60.445 45.833 0.00 0.00 32.73 2.40
2052 2152 3.118261 GGAAGATGTGAGGCACCATAAGA 60.118 47.826 0.00 0.00 32.73 2.10
2053 2153 3.209410 GGAAGATGTGAGGCACCATAAG 58.791 50.000 0.00 0.00 32.73 1.73
2054 2154 2.092429 GGGAAGATGTGAGGCACCATAA 60.092 50.000 0.00 0.00 32.73 1.90
2055 2155 1.490490 GGGAAGATGTGAGGCACCATA 59.510 52.381 0.00 0.00 32.73 2.74
2056 2156 0.257039 GGGAAGATGTGAGGCACCAT 59.743 55.000 0.00 0.00 32.73 3.55
2057 2157 0.842030 AGGGAAGATGTGAGGCACCA 60.842 55.000 0.00 0.00 32.73 4.17
2058 2158 1.139853 CTAGGGAAGATGTGAGGCACC 59.860 57.143 0.00 0.00 32.73 5.01
2059 2159 1.474143 GCTAGGGAAGATGTGAGGCAC 60.474 57.143 0.00 0.00 34.56 5.01
2060 2160 0.833287 GCTAGGGAAGATGTGAGGCA 59.167 55.000 0.00 0.00 0.00 4.75
2061 2161 1.127343 AGCTAGGGAAGATGTGAGGC 58.873 55.000 0.00 0.00 0.00 4.70
2062 2162 2.158842 CCAAGCTAGGGAAGATGTGAGG 60.159 54.545 0.00 0.00 0.00 3.86
2063 2163 2.503356 ACCAAGCTAGGGAAGATGTGAG 59.497 50.000 11.10 0.00 0.00 3.51
2099 2199 1.715585 GCATCACGTCCATCCAACG 59.284 57.895 0.00 0.00 45.37 4.10
2100 2200 1.715585 CGCATCACGTCCATCCAAC 59.284 57.895 0.00 0.00 36.87 3.77
2101 2201 2.106074 GCGCATCACGTCCATCCAA 61.106 57.895 0.30 0.00 46.11 3.53
2102 2202 2.511373 GCGCATCACGTCCATCCA 60.511 61.111 0.30 0.00 46.11 3.41
2103 2203 1.889105 ATGCGCATCACGTCCATCC 60.889 57.895 19.28 0.00 46.11 3.51
2104 2204 1.277739 CATGCGCATCACGTCCATC 59.722 57.895 22.51 0.00 46.11 3.51
2105 2205 2.827051 GCATGCGCATCACGTCCAT 61.827 57.895 22.51 0.00 46.11 3.41
2106 2206 3.498834 GCATGCGCATCACGTCCA 61.499 61.111 22.51 0.00 46.11 4.02
2107 2207 4.241999 GGCATGCGCATCACGTCC 62.242 66.667 22.51 12.62 46.11 4.79
2108 2208 3.037992 TTGGCATGCGCATCACGTC 62.038 57.895 22.51 12.19 46.11 4.34
2121 2223 6.121590 TCTGATTATGCATTTCTAGTTGGCA 58.878 36.000 3.54 0.00 39.03 4.92
2135 2237 7.249147 GCTGATATGGTTGATTCTGATTATGC 58.751 38.462 0.00 0.00 0.00 3.14
2147 2249 2.033424 CGAGAGACGCTGATATGGTTGA 59.967 50.000 0.00 0.00 34.51 3.18
2148 2250 2.223595 ACGAGAGACGCTGATATGGTTG 60.224 50.000 0.00 0.00 46.94 3.77
2173 2275 6.455646 GTCGCAGAATTATGGAACAGTTGTAG 60.456 42.308 1.67 0.00 40.69 2.74
2205 2307 2.294074 AGACGAGAGATGCTGTAGGTC 58.706 52.381 0.00 0.00 0.00 3.85
2215 2317 8.151596 AGGTTTTTCTTTCTTTAGACGAGAGAT 58.848 33.333 0.00 0.00 0.00 2.75
2229 2332 1.232119 TCGGCCGAGGTTTTTCTTTC 58.768 50.000 27.28 0.00 0.00 2.62
2233 2336 0.887836 ACCTTCGGCCGAGGTTTTTC 60.888 55.000 31.31 0.00 30.72 2.29
2331 2435 2.289002 GACAGTCATGGGATTCGCATTC 59.711 50.000 13.07 9.67 34.83 2.67
2367 2471 2.701423 GGAGGCCCCAAAAGTTAAAACA 59.299 45.455 0.00 0.00 34.14 2.83
2382 2486 1.194781 TGTGTGGAGAAGAGGAGGCC 61.195 60.000 0.00 0.00 0.00 5.19
2406 2510 2.277084 GTCGGCTGTATGTAAGGGTTG 58.723 52.381 0.00 0.00 0.00 3.77
2442 2546 1.286260 CTGCGGTCCGTAGATAGCC 59.714 63.158 23.49 0.00 41.80 3.93
2494 2598 2.486727 GGCCGATAAGGTTTAGAAGGGG 60.487 54.545 0.00 0.00 43.70 4.79
2524 2628 3.832175 AGCCAGGCTCACCAAGAT 58.168 55.556 8.70 0.00 39.06 2.40
2537 2641 0.609662 GGTTAAGGTGGTACGAGCCA 59.390 55.000 3.25 0.00 35.93 4.75
2539 2643 2.005560 GCTGGTTAAGGTGGTACGAGC 61.006 57.143 0.00 0.00 36.68 5.03
2540 2644 1.274167 TGCTGGTTAAGGTGGTACGAG 59.726 52.381 0.00 0.00 0.00 4.18
2543 2647 2.354805 CCTCTGCTGGTTAAGGTGGTAC 60.355 54.545 0.00 0.00 0.00 3.34
2552 2656 4.096003 GCCCGCCTCTGCTGGTTA 62.096 66.667 0.00 0.00 43.29 2.85
2562 2666 1.869824 TTAAATTCCTGGGCCCGCCT 61.870 55.000 19.37 0.00 36.10 5.52
2563 2667 1.380650 TTAAATTCCTGGGCCCGCC 60.381 57.895 19.37 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.