Multiple sequence alignment - TraesCS5A01G076700

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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 TraesCS5A01G076700 chr5A 100.000 2288 0 0 1 2288 92207742 92210029 0.000000e+00 4226.0
1 TraesCS5A01G076700 chr1D 94.833 1316 64 4 1 1313 142662904 142664218 0.000000e+00 2050.0
2 TraesCS5A01G076700 chr1D 90.172 1282 103 12 1 1259 5420182 5418901 0.000000e+00 1648.0
3 TraesCS5A01G076700 chr2A 94.701 1321 65 5 1 1317 550181800 550183119 0.000000e+00 2047.0
4 TraesCS5A01G076700 chr2A 94.221 1315 72 4 2 1313 348049956 348051269 0.000000e+00 2004.0
5 TraesCS5A01G076700 chr6A 94.677 1315 66 4 1 1313 155747339 155746027 0.000000e+00 2037.0
6 TraesCS5A01G076700 chr5D 91.705 1314 94 11 1 1312 378150663 378151963 0.000000e+00 1808.0
7 TraesCS5A01G076700 chr5D 89.067 997 87 14 1308 2288 97059590 97060580 0.000000e+00 1218.0
8 TraesCS5A01G076700 chr5D 79.839 124 25 0 2165 2288 458002464 458002341 8.700000e-15 91.6
9 TraesCS5A01G076700 chr2D 91.420 1317 109 4 1 1313 460579484 460580800 0.000000e+00 1803.0
10 TraesCS5A01G076700 chr2D 83.698 1325 200 15 1 1318 313468493 313467178 0.000000e+00 1236.0
11 TraesCS5A01G076700 chr5B 91.850 1043 83 2 273 1313 642595752 642594710 0.000000e+00 1454.0
12 TraesCS5A01G076700 chr1B 91.353 532 44 2 1 531 57128803 57128273 0.000000e+00 726.0
13 TraesCS5A01G076700 chr3B 85.227 88 13 0 2201 2288 270871407 270871494 8.700000e-15 91.6


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 TraesCS5A01G076700 chr5A 92207742 92210029 2287 False 4226 4226 100.000 1 2288 1 chr5A.!!$F1 2287
1 TraesCS5A01G076700 chr1D 142662904 142664218 1314 False 2050 2050 94.833 1 1313 1 chr1D.!!$F1 1312
2 TraesCS5A01G076700 chr1D 5418901 5420182 1281 True 1648 1648 90.172 1 1259 1 chr1D.!!$R1 1258
3 TraesCS5A01G076700 chr2A 550181800 550183119 1319 False 2047 2047 94.701 1 1317 1 chr2A.!!$F2 1316
4 TraesCS5A01G076700 chr2A 348049956 348051269 1313 False 2004 2004 94.221 2 1313 1 chr2A.!!$F1 1311
5 TraesCS5A01G076700 chr6A 155746027 155747339 1312 True 2037 2037 94.677 1 1313 1 chr6A.!!$R1 1312
6 TraesCS5A01G076700 chr5D 378150663 378151963 1300 False 1808 1808 91.705 1 1312 1 chr5D.!!$F2 1311
7 TraesCS5A01G076700 chr5D 97059590 97060580 990 False 1218 1218 89.067 1308 2288 1 chr5D.!!$F1 980
8 TraesCS5A01G076700 chr2D 460579484 460580800 1316 False 1803 1803 91.420 1 1313 1 chr2D.!!$F1 1312
9 TraesCS5A01G076700 chr2D 313467178 313468493 1315 True 1236 1236 83.698 1 1318 1 chr2D.!!$R1 1317
10 TraesCS5A01G076700 chr5B 642594710 642595752 1042 True 1454 1454 91.850 273 1313 1 chr5B.!!$R1 1040
11 TraesCS5A01G076700 chr1B 57128273 57128803 530 True 726 726 91.353 1 531 1 chr1B.!!$R1 530

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
380 418 1.343465 GGCGTATACTGCATGGTACCT 59.657 52.381 14.36 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 2187 0.039035 GGGGTGTATGGTTTGCAGGA 59.961 55.0 0.0 0.0 0.0 3.86 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
74 75 4.392921 AGTCTGTGATCTTATTGACCCG 57.607 45.455 0.00 0.00 0.00 5.28
78 79 2.159156 TGTGATCTTATTGACCCGGTCG 60.159 50.000 13.02 0.00 34.95 4.79
93 94 1.537348 CGGTCGCGAATTCTTGGGATA 60.537 52.381 12.06 0.00 0.00 2.59
96 97 3.375922 GGTCGCGAATTCTTGGGATAAAA 59.624 43.478 12.06 0.00 0.00 1.52
106 107 8.846943 AATTCTTGGGATAAAAATTTGGTGAC 57.153 30.769 0.00 0.00 0.00 3.67
156 157 6.723977 TCAAAGGGTATTAGCAATTCCACTTT 59.276 34.615 6.79 9.15 33.48 2.66
157 158 7.234577 TCAAAGGGTATTAGCAATTCCACTTTT 59.765 33.333 12.34 6.64 32.26 2.27
184 185 5.238432 TGCGTAATATGCCTGACTTTATTGG 59.762 40.000 1.60 0.00 0.00 3.16
188 189 7.011950 CGTAATATGCCTGACTTTATTGGTTGA 59.988 37.037 0.00 0.00 0.00 3.18
221 237 6.937436 AAAAAGGTAAGTTCACTGTTCGAT 57.063 33.333 0.00 0.00 0.00 3.59
222 238 6.541111 AAAAGGTAAGTTCACTGTTCGATC 57.459 37.500 0.00 0.00 0.00 3.69
223 239 4.866508 AGGTAAGTTCACTGTTCGATCA 57.133 40.909 0.00 0.00 0.00 2.92
224 240 5.209818 AGGTAAGTTCACTGTTCGATCAA 57.790 39.130 0.00 0.00 0.00 2.57
225 241 4.989168 AGGTAAGTTCACTGTTCGATCAAC 59.011 41.667 0.00 0.00 35.28 3.18
226 242 4.989168 GGTAAGTTCACTGTTCGATCAACT 59.011 41.667 0.00 0.00 35.79 3.16
227 243 5.465724 GGTAAGTTCACTGTTCGATCAACTT 59.534 40.000 13.15 13.15 37.70 2.66
228 244 6.643770 GGTAAGTTCACTGTTCGATCAACTTA 59.356 38.462 11.70 11.70 35.99 2.24
229 245 7.331193 GGTAAGTTCACTGTTCGATCAACTTAT 59.669 37.037 16.02 1.10 38.15 1.73
230 246 7.730364 AAGTTCACTGTTCGATCAACTTATT 57.270 32.000 8.75 0.00 33.39 1.40
380 418 1.343465 GGCGTATACTGCATGGTACCT 59.657 52.381 14.36 0.00 0.00 3.08
433 471 9.088987 AGACATATAAAAGTTTCACCCATTTGT 57.911 29.630 0.00 0.00 0.00 2.83
439 477 4.184649 AGTTTCACCCATTTGTCCTTCT 57.815 40.909 0.00 0.00 0.00 2.85
575 615 3.227276 CGGGAGAGGCGGTGCTAT 61.227 66.667 0.00 0.00 0.00 2.97
724 764 6.265196 AGTTACAGGATGCAAATCAAACTTCA 59.735 34.615 0.00 0.00 42.53 3.02
833 873 5.884792 CCTAGAGGATTTGTCAAGCTGAATT 59.115 40.000 0.00 0.00 37.39 2.17
840 880 6.647895 GGATTTGTCAAGCTGAATTTTGATGT 59.352 34.615 0.00 0.00 35.91 3.06
843 883 4.275689 TGTCAAGCTGAATTTTGATGTCGT 59.724 37.500 0.00 0.00 35.91 4.34
863 903 4.954092 GTTTTCGAGCATGATCTCCTTT 57.046 40.909 9.64 0.00 0.00 3.11
864 904 4.656041 GTTTTCGAGCATGATCTCCTTTG 58.344 43.478 9.64 0.00 0.00 2.77
873 913 4.383552 GCATGATCTCCTTTGAGGTACAGT 60.384 45.833 0.00 0.00 39.23 3.55
874 914 4.808414 TGATCTCCTTTGAGGTACAGTG 57.192 45.455 0.00 0.00 39.23 3.66
875 915 3.055819 TGATCTCCTTTGAGGTACAGTGC 60.056 47.826 0.00 0.00 39.23 4.40
910 951 5.907662 AGAGATGATAAGGGAAGGTTCATCA 59.092 40.000 12.26 0.00 43.19 3.07
937 978 2.087646 GAAACTGGAGGATTGACTGGC 58.912 52.381 0.00 0.00 0.00 4.85
1000 1041 5.755409 TGGTTTATTCCTAGCACAGAAGA 57.245 39.130 0.00 0.00 0.00 2.87
1001 1042 6.313519 TGGTTTATTCCTAGCACAGAAGAT 57.686 37.500 0.00 0.00 0.00 2.40
1008 1050 2.026822 CCTAGCACAGAAGATGGGTTGT 60.027 50.000 0.00 0.00 33.46 3.32
1171 1213 7.630082 ACACTGTAATAGGGAAGCAAATAGAA 58.370 34.615 0.00 0.00 32.67 2.10
1346 1390 0.389948 GATCTCACACGGTCACACCC 60.390 60.000 0.00 0.00 33.75 4.61
1348 1392 1.046472 TCTCACACGGTCACACCCTT 61.046 55.000 0.00 0.00 33.75 3.95
1349 1393 0.880278 CTCACACGGTCACACCCTTG 60.880 60.000 0.00 0.00 33.75 3.61
1350 1394 1.145156 CACACGGTCACACCCTTGA 59.855 57.895 0.00 0.00 33.75 3.02
1351 1395 1.145377 ACACGGTCACACCCTTGAC 59.855 57.895 0.00 0.00 44.53 3.18
1353 1397 0.462937 CACGGTCACACCCTTGACAA 60.463 55.000 5.67 0.00 46.68 3.18
1354 1398 0.253610 ACGGTCACACCCTTGACAAA 59.746 50.000 5.67 0.00 46.68 2.83
1356 1400 1.953686 CGGTCACACCCTTGACAAATT 59.046 47.619 5.67 0.00 46.68 1.82
1414 1458 3.279434 GTTGGGAAATCTAACTCGCCAT 58.721 45.455 0.00 0.00 0.00 4.40
1415 1459 3.644966 TGGGAAATCTAACTCGCCATT 57.355 42.857 0.00 0.00 0.00 3.16
1416 1460 3.963129 TGGGAAATCTAACTCGCCATTT 58.037 40.909 0.00 0.00 0.00 2.32
1417 1461 4.340617 TGGGAAATCTAACTCGCCATTTT 58.659 39.130 0.00 0.00 0.00 1.82
1418 1462 4.770010 TGGGAAATCTAACTCGCCATTTTT 59.230 37.500 0.00 0.00 0.00 1.94
1484 1536 4.646492 AGGGAATGGACATTTATCAGCAAC 59.354 41.667 0.00 0.00 0.00 4.17
1489 1541 4.650734 TGGACATTTATCAGCAACAGACA 58.349 39.130 0.00 0.00 0.00 3.41
1554 1606 1.470805 CCATGTTATCGCGGTGAGTCA 60.471 52.381 6.13 0.00 0.00 3.41
1561 1613 2.034879 CGCGGTGAGTCAAGGCAAT 61.035 57.895 14.80 0.00 0.00 3.56
1566 1618 1.003580 GGTGAGTCAAGGCAATCAGGA 59.996 52.381 0.00 0.00 0.00 3.86
1588 1640 3.298958 GGTGGTCAGCTCCATCGA 58.701 61.111 0.00 0.00 39.81 3.59
1618 1670 2.046292 TCCATATGACGGCAATGGAGA 58.954 47.619 23.25 9.35 43.27 3.71
1627 1679 1.519455 GCAATGGAGAGGGTCGTCG 60.519 63.158 0.00 0.00 0.00 5.12
1652 1704 2.400399 TGTCGCTTCTCGTCGAATTTT 58.600 42.857 0.00 0.00 39.67 1.82
1697 1749 3.178046 GAGAAGGGAAGGAAGGAGAGTT 58.822 50.000 0.00 0.00 0.00 3.01
1703 1755 0.402121 AAGGAAGGAGAGTTGTGGGC 59.598 55.000 0.00 0.00 0.00 5.36
1714 1766 3.008049 AGAGTTGTGGGCTCGAGTAATTT 59.992 43.478 15.13 0.00 37.99 1.82
1716 1768 2.107950 TGTGGGCTCGAGTAATTTGG 57.892 50.000 15.13 0.00 0.00 3.28
1718 1770 0.988832 TGGGCTCGAGTAATTTGGGT 59.011 50.000 15.13 0.00 0.00 4.51
1720 1772 1.339727 GGGCTCGAGTAATTTGGGTGT 60.340 52.381 15.13 0.00 0.00 4.16
1743 1795 0.035881 TCAACAGAGAGCCCAGCAAG 59.964 55.000 0.00 0.00 0.00 4.01
1748 1800 2.124819 AGAGCCCAGCAAGCATCG 60.125 61.111 0.00 0.00 0.00 3.84
1749 1801 3.207669 GAGCCCAGCAAGCATCGG 61.208 66.667 0.00 0.00 0.00 4.18
1750 1802 3.984193 GAGCCCAGCAAGCATCGGT 62.984 63.158 0.00 0.00 0.00 4.69
1757 1809 2.032634 GCAAGCATCGGTTCGACCA 61.033 57.895 5.15 0.00 39.18 4.02
1777 1829 0.318360 CGACACACACACCTCGCTAA 60.318 55.000 0.00 0.00 0.00 3.09
1796 1848 3.644884 AAAGTCGAGAAAAGAGAGCGA 57.355 42.857 0.00 0.00 0.00 4.93
1812 1864 4.274147 AGAGCGACTCTAGAGAAATTGGA 58.726 43.478 26.57 0.00 39.28 3.53
1878 1930 2.612672 TCGATCATAGTCGGCCGATATC 59.387 50.000 33.58 24.27 41.74 1.63
1892 1944 2.548920 CCGATATCTGGGGAAGACAAGC 60.549 54.545 0.34 0.00 37.88 4.01
1911 1963 1.572085 CTCGCAAGTGGCTGAGGTTG 61.572 60.000 4.10 0.00 41.67 3.77
1918 1970 0.249911 GTGGCTGAGGTTGACGAGTT 60.250 55.000 0.00 0.00 0.00 3.01
1920 1972 0.951040 GGCTGAGGTTGACGAGTTGG 60.951 60.000 0.00 0.00 0.00 3.77
1926 1978 3.576982 TGAGGTTGACGAGTTGGTTAGAT 59.423 43.478 0.00 0.00 0.00 1.98
1931 1983 4.611310 TGACGAGTTGGTTAGATAGTCG 57.389 45.455 0.00 0.00 39.83 4.18
1932 1984 3.181503 TGACGAGTTGGTTAGATAGTCGC 60.182 47.826 0.00 0.00 38.06 5.19
1948 2000 4.197498 GCATGGTGCCGATGGTGC 62.197 66.667 0.00 0.00 37.42 5.01
1977 2029 0.381089 AGGTCGCGGAAAGTCGATAG 59.619 55.000 6.13 0.00 37.06 2.08
1998 2050 7.759433 CGATAGCCACAAATTTAGGAACAAATT 59.241 33.333 11.86 0.00 39.26 1.82
2006 2058 5.598416 ATTTAGGAACAAATTAGGCAGCC 57.402 39.130 1.84 1.84 0.00 4.85
2008 2060 1.004277 AGGAACAAATTAGGCAGCCGA 59.996 47.619 5.55 0.00 0.00 5.54
2011 2063 3.501950 GAACAAATTAGGCAGCCGAAAG 58.498 45.455 11.45 7.08 0.00 2.62
2020 2072 1.586541 CAGCCGAAAGAAAAGGGGC 59.413 57.895 0.00 0.00 44.07 5.80
2055 2107 1.749063 CGAGCATCTGTGTGGGTACTA 59.251 52.381 0.00 0.00 0.00 1.82
2114 2166 5.477984 TGTAGAAAAATGGCTTGAGATGCTT 59.522 36.000 0.00 0.00 0.00 3.91
2134 2186 2.425143 TAAGGGCATCTTCAAGGCAG 57.575 50.000 0.00 0.00 36.93 4.85
2135 2187 0.407139 AAGGGCATCTTCAAGGCAGT 59.593 50.000 0.00 0.00 0.00 4.40
2152 2204 1.812571 CAGTCCTGCAAACCATACACC 59.187 52.381 0.00 0.00 0.00 4.16
2153 2205 1.173913 GTCCTGCAAACCATACACCC 58.826 55.000 0.00 0.00 0.00 4.61
2154 2206 0.039035 TCCTGCAAACCATACACCCC 59.961 55.000 0.00 0.00 0.00 4.95
2155 2207 1.312371 CCTGCAAACCATACACCCCG 61.312 60.000 0.00 0.00 0.00 5.73
2156 2208 1.303724 TGCAAACCATACACCCCGG 60.304 57.895 0.00 0.00 0.00 5.73
2159 2211 2.540021 AAACCATACACCCCGGCCA 61.540 57.895 2.24 0.00 0.00 5.36
2160 2212 1.869824 AAACCATACACCCCGGCCAT 61.870 55.000 2.24 0.00 0.00 4.40
2161 2213 0.989212 AACCATACACCCCGGCCATA 60.989 55.000 2.24 0.00 0.00 2.74
2176 2234 2.590821 GCCATAGAAGCCATCCAATGT 58.409 47.619 0.00 0.00 0.00 2.71
2191 2249 1.670811 CAATGTGGCCTTGTATCGGTC 59.329 52.381 3.32 0.00 0.00 4.79
2198 2256 3.709880 CTTGTATCGGTCCGCGGCA 62.710 63.158 23.51 7.94 0.00 5.69
2221 2279 2.235402 GGTCTGGACGTATTTTCTCCCA 59.765 50.000 0.00 0.00 0.00 4.37
2226 2284 4.069304 TGGACGTATTTTCTCCCACAAAG 58.931 43.478 0.00 0.00 0.00 2.77
2227 2285 4.202377 TGGACGTATTTTCTCCCACAAAGA 60.202 41.667 0.00 0.00 0.00 2.52
2244 2302 4.263949 ACAAAGAGGAGATAAAAGTGGGGG 60.264 45.833 0.00 0.00 0.00 5.40
2259 2317 2.034221 GGGAGCTTTGCGGGAGTT 59.966 61.111 0.00 0.00 0.00 3.01
2267 2325 0.534203 TTTGCGGGAGTTCAGACACC 60.534 55.000 0.00 0.00 35.96 4.16
2271 2329 0.898320 CGGGAGTTCAGACACCAGAT 59.102 55.000 0.00 0.00 38.17 2.90
2275 2333 2.159226 GGAGTTCAGACACCAGATACGG 60.159 54.545 0.00 0.00 36.62 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 7.793036 AGTATTTGTCCCCTTCTATGAGTAAC 58.207 38.462 0.00 0.00 0.00 2.50
74 75 2.234300 TATCCCAAGAATTCGCGACC 57.766 50.000 9.15 0.40 0.00 4.79
78 79 6.593770 ACCAAATTTTTATCCCAAGAATTCGC 59.406 34.615 0.00 0.00 0.00 4.70
93 94 7.201565 CCATAACGTTTGTGTCACCAAATTTTT 60.202 33.333 5.91 0.70 36.75 1.94
96 97 5.285651 CCATAACGTTTGTGTCACCAAATT 58.714 37.500 5.91 0.00 36.75 1.82
106 107 3.906998 TCAATTGGCCATAACGTTTGTG 58.093 40.909 6.09 6.24 0.00 3.33
157 158 3.751479 AGTCAGGCATATTACGCATGA 57.249 42.857 0.00 0.00 46.85 3.07
215 231 8.007716 TCGTTCTTTCAAATAAGTTGATCGAAC 58.992 33.333 15.25 15.25 45.71 3.95
218 234 8.618952 GTTTCGTTCTTTCAAATAAGTTGATCG 58.381 33.333 0.00 0.00 45.71 3.69
219 235 8.902735 GGTTTCGTTCTTTCAAATAAGTTGATC 58.097 33.333 0.00 0.00 45.71 2.92
220 236 8.410141 TGGTTTCGTTCTTTCAAATAAGTTGAT 58.590 29.630 0.00 0.00 45.71 2.57
221 237 7.763356 TGGTTTCGTTCTTTCAAATAAGTTGA 58.237 30.769 0.00 0.00 44.74 3.18
222 238 7.979115 TGGTTTCGTTCTTTCAAATAAGTTG 57.021 32.000 0.00 0.00 38.71 3.16
223 239 8.030106 TGTTGGTTTCGTTCTTTCAAATAAGTT 58.970 29.630 0.00 0.00 0.00 2.66
224 240 7.540299 TGTTGGTTTCGTTCTTTCAAATAAGT 58.460 30.769 0.00 0.00 0.00 2.24
225 241 7.979115 TGTTGGTTTCGTTCTTTCAAATAAG 57.021 32.000 0.00 0.00 0.00 1.73
226 242 7.813148 TGTTGTTGGTTTCGTTCTTTCAAATAA 59.187 29.630 0.00 0.00 0.00 1.40
227 243 7.313646 TGTTGTTGGTTTCGTTCTTTCAAATA 58.686 30.769 0.00 0.00 0.00 1.40
228 244 6.159988 TGTTGTTGGTTTCGTTCTTTCAAAT 58.840 32.000 0.00 0.00 0.00 2.32
229 245 5.529791 TGTTGTTGGTTTCGTTCTTTCAAA 58.470 33.333 0.00 0.00 0.00 2.69
230 246 5.122512 TGTTGTTGGTTTCGTTCTTTCAA 57.877 34.783 0.00 0.00 0.00 2.69
239 255 3.444703 TTTCCCATGTTGTTGGTTTCG 57.555 42.857 0.00 0.00 34.77 3.46
366 403 1.959710 TGGGAAGGTACCATGCAGTA 58.040 50.000 15.94 0.00 31.83 2.74
380 418 3.543884 GTGTAACTCGGCATGGGAA 57.456 52.632 0.00 0.00 0.00 3.97
433 471 2.795329 GGTCCATTTGAGCAAGAAGGA 58.205 47.619 0.00 0.00 41.24 3.36
439 477 0.322456 CCTCCGGTCCATTTGAGCAA 60.322 55.000 0.00 0.00 41.69 3.91
724 764 1.136828 TTATAGCACGAGCCCCCATT 58.863 50.000 0.00 0.00 43.56 3.16
814 854 6.409524 TCAAAATTCAGCTTGACAAATCCT 57.590 33.333 0.00 0.00 0.00 3.24
823 863 6.515043 AAAACGACATCAAAATTCAGCTTG 57.485 33.333 0.00 0.00 0.00 4.01
833 873 3.496507 TCATGCTCGAAAACGACATCAAA 59.503 39.130 0.00 0.00 0.00 2.69
840 880 2.166459 AGGAGATCATGCTCGAAAACGA 59.834 45.455 0.00 0.00 35.74 3.85
843 883 4.578871 TCAAAGGAGATCATGCTCGAAAA 58.421 39.130 0.00 0.00 35.74 2.29
850 890 4.125703 CTGTACCTCAAAGGAGATCATGC 58.874 47.826 0.00 0.00 44.26 4.06
863 903 2.154798 GACCGCAGCACTGTACCTCA 62.155 60.000 0.00 0.00 0.00 3.86
864 904 1.446272 GACCGCAGCACTGTACCTC 60.446 63.158 0.00 0.00 0.00 3.85
873 913 1.683707 ATCTCTCAGGACCGCAGCA 60.684 57.895 0.00 0.00 0.00 4.41
874 914 1.227205 CATCTCTCAGGACCGCAGC 60.227 63.158 0.00 0.00 0.00 5.25
875 915 1.039068 ATCATCTCTCAGGACCGCAG 58.961 55.000 0.00 0.00 0.00 5.18
910 951 3.593328 TCAATCCTCCAGTTTCCTCCAAT 59.407 43.478 0.00 0.00 0.00 3.16
1000 1041 2.491693 CAACAAGGCGATTACAACCCAT 59.508 45.455 0.00 0.00 0.00 4.00
1001 1042 1.883275 CAACAAGGCGATTACAACCCA 59.117 47.619 0.00 0.00 0.00 4.51
1008 1050 5.543714 TCTGAGTTTACAACAAGGCGATTA 58.456 37.500 0.00 0.00 0.00 1.75
1171 1213 2.718609 ACCTAGCTATTTCATGGGCCAT 59.281 45.455 14.78 14.78 0.00 4.40
1201 1243 2.025887 ACCAATCCCTAGTGGCAGAAAG 60.026 50.000 0.00 0.00 44.95 2.62
1320 1363 2.283298 GACCGTGTGAGATCATTGCAT 58.717 47.619 0.00 0.00 0.00 3.96
1325 1369 1.066858 GGTGTGACCGTGTGAGATCAT 60.067 52.381 0.00 0.00 0.00 2.45
1416 1460 4.543590 TGACAAGTTGGCAAAGGAAAAA 57.456 36.364 9.57 0.00 28.38 1.94
1417 1461 4.543590 TTGACAAGTTGGCAAAGGAAAA 57.456 36.364 21.95 0.00 43.46 2.29
1460 1512 4.464008 TGCTGATAAATGTCCATTCCCTC 58.536 43.478 0.00 0.00 0.00 4.30
1484 1536 0.251341 CCCACCCCCTCTTTTGTCTG 60.251 60.000 0.00 0.00 0.00 3.51
1489 1541 1.857348 CTCCCCCACCCCCTCTTTT 60.857 63.158 0.00 0.00 0.00 2.27
1528 1580 1.134521 ACCGCGATAACATGGTCACAT 60.135 47.619 8.23 0.00 37.99 3.21
1529 1581 0.248012 ACCGCGATAACATGGTCACA 59.752 50.000 8.23 0.00 0.00 3.58
1554 1606 0.620556 ACCGTCATCCTGATTGCCTT 59.379 50.000 0.00 0.00 0.00 4.35
1561 1613 4.531351 TGACCACCGTCATCCTGA 57.469 55.556 0.00 0.00 44.20 3.86
1570 1622 2.202797 CGATGGAGCTGACCACCG 60.203 66.667 0.00 0.00 40.68 4.94
1604 1656 1.899437 GACCCTCTCCATTGCCGTCA 61.899 60.000 0.00 0.00 0.00 4.35
1607 1659 2.202932 CGACCCTCTCCATTGCCG 60.203 66.667 0.00 0.00 0.00 5.69
1618 1670 2.758737 GACATCCCCGACGACCCT 60.759 66.667 0.00 0.00 0.00 4.34
1627 1679 1.227002 GACGAGAAGCGACATCCCC 60.227 63.158 0.00 0.00 44.57 4.81
1652 1704 2.295909 CGAGTCCCTTGGCATTTTCAAA 59.704 45.455 0.00 0.00 0.00 2.69
1654 1706 1.533625 CGAGTCCCTTGGCATTTTCA 58.466 50.000 0.00 0.00 0.00 2.69
1697 1749 1.339631 CCCAAATTACTCGAGCCCACA 60.340 52.381 13.61 0.00 0.00 4.17
1703 1755 3.074412 AGCAACACCCAAATTACTCGAG 58.926 45.455 11.84 11.84 0.00 4.04
1714 1766 0.836606 TCTCTGTTGAGCAACACCCA 59.163 50.000 11.70 0.00 45.42 4.51
1736 1788 1.741401 TCGAACCGATGCTTGCTGG 60.741 57.895 0.00 0.00 0.00 4.85
1743 1795 2.126228 TCGTGGTCGAACCGATGC 60.126 61.111 9.53 0.00 42.58 3.91
1757 1809 1.449726 TAGCGAGGTGTGTGTGTCGT 61.450 55.000 0.00 0.00 34.87 4.34
1777 1829 2.936316 GTCGCTCTCTTTTCTCGACTT 58.064 47.619 5.92 0.00 44.06 3.01
1796 1848 6.305272 TCTGCATTCCAATTTCTCTAGAGT 57.695 37.500 19.21 0.00 0.00 3.24
1800 1852 5.426509 TCTCCTCTGCATTCCAATTTCTCTA 59.573 40.000 0.00 0.00 0.00 2.43
1805 1857 6.323225 CCTTATTCTCCTCTGCATTCCAATTT 59.677 38.462 0.00 0.00 0.00 1.82
1812 1864 3.950395 GCAACCTTATTCTCCTCTGCATT 59.050 43.478 0.00 0.00 0.00 3.56
1846 1898 1.001268 CTATGATCGACACCACTCGGG 60.001 57.143 0.00 0.00 44.81 5.14
1857 1909 2.103537 TATCGGCCGACTATGATCGA 57.896 50.000 33.75 3.58 45.13 3.59
1878 1930 1.743252 GCGAGCTTGTCTTCCCCAG 60.743 63.158 2.14 0.00 0.00 4.45
1911 1963 3.181503 TGCGACTATCTAACCAACTCGTC 60.182 47.826 0.00 0.00 0.00 4.20
1918 1970 2.483013 GCACCATGCGACTATCTAACCA 60.483 50.000 0.00 0.00 31.71 3.67
1920 1972 2.135933 GGCACCATGCGACTATCTAAC 58.864 52.381 0.00 0.00 46.21 2.34
1926 1978 1.227234 CATCGGCACCATGCGACTA 60.227 57.895 0.00 0.00 46.21 2.59
1931 1983 4.197498 GCACCATCGGCACCATGC 62.197 66.667 0.00 0.00 44.08 4.06
1932 1984 3.879682 CGCACCATCGGCACCATG 61.880 66.667 0.00 0.00 0.00 3.66
1977 2029 6.092122 GCCTAATTTGTTCCTAAATTTGTGGC 59.908 38.462 0.00 13.71 39.96 5.01
1998 2050 1.613255 CCCTTTTCTTTCGGCTGCCTA 60.613 52.381 17.92 2.11 0.00 3.93
2006 2058 2.747989 GGTTCTAGCCCCTTTTCTTTCG 59.252 50.000 0.00 0.00 0.00 3.46
2008 2060 3.170991 GGGTTCTAGCCCCTTTTCTTT 57.829 47.619 9.46 0.00 42.89 2.52
2020 2072 6.153067 CAGATGCTCGTATAAAGGGTTCTAG 58.847 44.000 0.00 0.00 0.00 2.43
2091 2143 5.573337 AGCATCTCAAGCCATTTTTCTAC 57.427 39.130 0.00 0.00 0.00 2.59
2114 2166 2.041620 ACTGCCTTGAAGATGCCCTTAA 59.958 45.455 0.00 0.00 34.68 1.85
2134 2186 1.173913 GGGTGTATGGTTTGCAGGAC 58.826 55.000 0.00 0.00 0.00 3.85
2135 2187 0.039035 GGGGTGTATGGTTTGCAGGA 59.961 55.000 0.00 0.00 0.00 3.86
2138 2190 1.303724 CCGGGGTGTATGGTTTGCA 60.304 57.895 0.00 0.00 0.00 4.08
2147 2199 1.692173 GCTTCTATGGCCGGGGTGTA 61.692 60.000 2.18 0.00 0.00 2.90
2150 2202 3.489513 GGCTTCTATGGCCGGGGT 61.490 66.667 2.18 0.00 40.19 4.95
2156 2208 2.295349 CACATTGGATGGCTTCTATGGC 59.705 50.000 15.11 0.00 33.60 4.40
2167 2225 2.291465 CGATACAAGGCCACATTGGATG 59.709 50.000 5.01 0.00 40.96 3.51
2171 2229 1.670811 GACCGATACAAGGCCACATTG 59.329 52.381 5.01 3.08 0.00 2.82
2176 2234 2.897207 CGGACCGATACAAGGCCA 59.103 61.111 8.64 0.00 0.00 5.36
2179 2237 2.279252 CCGCGGACCGATACAAGG 60.279 66.667 24.07 6.32 40.02 3.61
2181 2239 3.761140 TGCCGCGGACCGATACAA 61.761 61.111 33.48 0.00 40.02 2.41
2198 2256 2.094338 GGAGAAAATACGTCCAGACCGT 60.094 50.000 0.00 0.00 42.06 4.83
2203 2261 3.328382 TGTGGGAGAAAATACGTCCAG 57.672 47.619 0.00 0.00 31.31 3.86
2204 2262 3.773418 TTGTGGGAGAAAATACGTCCA 57.227 42.857 0.00 0.00 31.31 4.02
2221 2279 4.263949 CCCCCACTTTTATCTCCTCTTTGT 60.264 45.833 0.00 0.00 0.00 2.83
2226 2284 2.158740 GCTCCCCCACTTTTATCTCCTC 60.159 54.545 0.00 0.00 0.00 3.71
2227 2285 1.847088 GCTCCCCCACTTTTATCTCCT 59.153 52.381 0.00 0.00 0.00 3.69
2244 2302 0.320771 TCTGAACTCCCGCAAAGCTC 60.321 55.000 0.00 0.00 0.00 4.09
2259 2317 1.283905 TCCTCCGTATCTGGTGTCTGA 59.716 52.381 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.