Multiple sequence alignment - TraesCS4B01G058000

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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 TraesCS4B01G058000 chr4B 100.000 2261 0 0 1 2261 48644400 48646660 0.000000e+00 4176
1 TraesCS4B01G058000 chr4B 87.962 1354 148 11 1 1342 642421071 642422421 0.000000e+00 1583
2 TraesCS4B01G058000 chr1B 97.771 1570 28 4 1 1564 162001408 161999840 0.000000e+00 2699
3 TraesCS4B01G058000 chr1B 93.431 1568 87 11 1 1562 649685025 649686582 0.000000e+00 2311
4 TraesCS4B01G058000 chr1B 88.604 1246 131 8 27 1263 683124858 683123615 0.000000e+00 1504
5 TraesCS4B01G058000 chr3B 97.516 1570 22 4 1 1565 5420126 5421683 0.000000e+00 2667
6 TraesCS4B01G058000 chr3B 96.830 1041 17 3 529 1565 3296824 3295796 0.000000e+00 1725
7 TraesCS4B01G058000 chr3B 80.000 350 59 8 1914 2254 315388221 315387874 4.820000e-62 248
8 TraesCS4B01G058000 chrUn 97.452 1570 23 4 1 1565 299795448 299797005 0.000000e+00 2662
9 TraesCS4B01G058000 chrUn 82.683 1588 230 38 1 1565 246202280 246203845 0.000000e+00 1367
10 TraesCS4B01G058000 chrUn 77.778 315 52 12 1958 2261 81277392 81277699 6.420000e-41 178
11 TraesCS4B01G058000 chr6B 83.694 1570 230 20 4 1562 144732324 144730770 0.000000e+00 1458
12 TraesCS4B01G058000 chr6B 96.914 162 5 0 1402 1563 11385618 11385779 2.860000e-69 272
13 TraesCS4B01G058000 chr6B 96.914 162 4 1 1402 1563 11362444 11362604 1.030000e-68 270
14 TraesCS4B01G058000 chr6B 96.319 163 5 1 1402 1563 11346316 11346478 1.330000e-67 267
15 TraesCS4B01G058000 chr2B 85.094 1382 188 13 4 1373 599216481 599217856 0.000000e+00 1395
16 TraesCS4B01G058000 chr2B 77.376 442 73 15 1814 2237 182367513 182367945 1.040000e-58 237
17 TraesCS4B01G058000 chr7B 85.377 1354 186 9 1 1346 20091780 20093129 0.000000e+00 1393
18 TraesCS4B01G058000 chr4A 79.888 716 105 19 1568 2260 568872854 568872155 2.610000e-134 488
19 TraesCS4B01G058000 chr4D 91.940 335 20 5 1565 1897 33245578 33245907 1.580000e-126 462
20 TraesCS4B01G058000 chr3D 80.418 383 63 8 1880 2254 266666380 266666758 4.750000e-72 281
21 TraesCS4B01G058000 chr6D 78.571 434 77 8 1815 2237 326762787 326763215 2.860000e-69 272
22 TraesCS4B01G058000 chr1A 80.000 390 56 11 1869 2241 292883603 292883987 3.700000e-68 268
23 TraesCS4B01G058000 chr5A 78.409 440 69 18 1819 2237 117492423 117491989 1.720000e-66 263
24 TraesCS4B01G058000 chr1D 77.444 399 66 14 1856 2243 467128912 467128527 1.360000e-52 217
25 TraesCS4B01G058000 chr1D 76.790 405 76 13 1847 2237 15065072 15064672 6.330000e-51 211
26 TraesCS4B01G058000 chr2A 79.787 282 46 9 1814 2089 135483144 135483420 6.370000e-46 195
27 TraesCS4B01G058000 chr5D 79.327 208 29 4 2039 2237 525990079 525989877 1.410000e-27 134


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 TraesCS4B01G058000 chr4B 48644400 48646660 2260 False 4176 4176 100.000 1 2261 1 chr4B.!!$F1 2260
1 TraesCS4B01G058000 chr4B 642421071 642422421 1350 False 1583 1583 87.962 1 1342 1 chr4B.!!$F2 1341
2 TraesCS4B01G058000 chr1B 161999840 162001408 1568 True 2699 2699 97.771 1 1564 1 chr1B.!!$R1 1563
3 TraesCS4B01G058000 chr1B 649685025 649686582 1557 False 2311 2311 93.431 1 1562 1 chr1B.!!$F1 1561
4 TraesCS4B01G058000 chr1B 683123615 683124858 1243 True 1504 1504 88.604 27 1263 1 chr1B.!!$R2 1236
5 TraesCS4B01G058000 chr3B 5420126 5421683 1557 False 2667 2667 97.516 1 1565 1 chr3B.!!$F1 1564
6 TraesCS4B01G058000 chr3B 3295796 3296824 1028 True 1725 1725 96.830 529 1565 1 chr3B.!!$R1 1036
7 TraesCS4B01G058000 chrUn 299795448 299797005 1557 False 2662 2662 97.452 1 1565 1 chrUn.!!$F3 1564
8 TraesCS4B01G058000 chrUn 246202280 246203845 1565 False 1367 1367 82.683 1 1565 1 chrUn.!!$F2 1564
9 TraesCS4B01G058000 chr6B 144730770 144732324 1554 True 1458 1458 83.694 4 1562 1 chr6B.!!$R1 1558
10 TraesCS4B01G058000 chr2B 599216481 599217856 1375 False 1395 1395 85.094 4 1373 1 chr2B.!!$F2 1369
11 TraesCS4B01G058000 chr7B 20091780 20093129 1349 False 1393 1393 85.377 1 1346 1 chr7B.!!$F1 1345
12 TraesCS4B01G058000 chr4A 568872155 568872854 699 True 488 488 79.888 1568 2260 1 chr4A.!!$R1 692

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
899 912 1.801178 GCTCCACTGCTTCACTGTTAC 59.199 52.381 0.0 0.0 0.0 2.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 2074 0.107165 GGCCATGGGTGTAAGAGTCC 60.107 60.0 15.13 0.0 0.0 3.85 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
240 244 6.897706 ATGGTTTTGGAAAATGGAAAATGG 57.102 33.333 0.00 0.00 0.00 3.16
495 501 9.183368 TGATATATGCTTTGACCACAACATTAA 57.817 29.630 0.00 0.00 35.63 1.40
703 712 7.300658 AGGAAATTGATAGCAGTTGGGATAAT 58.699 34.615 0.00 0.00 0.00 1.28
899 912 1.801178 GCTCCACTGCTTCACTGTTAC 59.199 52.381 0.00 0.00 0.00 2.50
1140 1154 0.402887 TGACTGACTGGTCCGTCCTA 59.597 55.000 17.87 3.18 41.29 2.94
1344 1359 5.693555 CCTTTCTTGCTTCTTTTGCTTTAGG 59.306 40.000 0.00 0.00 0.00 2.69
1350 1365 6.458232 TGCTTCTTTTGCTTTAGGTGTAAA 57.542 33.333 0.00 0.00 0.00 2.01
1396 1435 6.707273 AGGGGTTAATTTGTACTCAGGTTA 57.293 37.500 0.00 0.00 0.00 2.85
1451 1509 1.073025 CTGGTGGTGTTGGCAGCTA 59.927 57.895 2.28 0.00 43.05 3.32
1473 1531 7.174080 AGCTATGTTCTTTTCTGTTCTTTCTCC 59.826 37.037 0.00 0.00 0.00 3.71
1588 1647 1.305930 GCGCGGGTTTCCTGAGAAAT 61.306 55.000 8.83 0.00 43.67 2.17
1590 1649 1.933853 CGCGGGTTTCCTGAGAAATAG 59.066 52.381 0.00 0.00 43.67 1.73
1635 1694 7.464358 AGTGATTGCAGTAATTCGAATACAAC 58.536 34.615 11.83 10.18 0.00 3.32
1640 1699 7.060600 TGCAGTAATTCGAATACAACTTGAG 57.939 36.000 11.83 5.61 0.00 3.02
1650 1709 5.118050 CGAATACAACTTGAGTTTACTCGCA 59.882 40.000 5.50 0.00 45.72 5.10
1651 1710 6.346279 CGAATACAACTTGAGTTTACTCGCAA 60.346 38.462 5.50 0.00 45.72 4.85
1655 1714 6.027749 ACAACTTGAGTTTACTCGCAAAAAG 58.972 36.000 5.50 5.64 45.72 2.27
1657 1716 6.431198 ACTTGAGTTTACTCGCAAAAAGAA 57.569 33.333 11.58 0.00 45.72 2.52
1658 1717 6.848451 ACTTGAGTTTACTCGCAAAAAGAAA 58.152 32.000 11.58 0.00 45.72 2.52
1664 1723 9.104126 GAGTTTACTCGCAAAAAGAAAGAATAC 57.896 33.333 0.00 0.00 32.78 1.89
1753 1833 9.886132 TCCAAGAAATACTAAGGAGTACAATTC 57.114 33.333 0.00 0.00 41.01 2.17
1763 1845 9.018582 ACTAAGGAGTACAATTCGTAGTAAACT 57.981 33.333 0.00 0.00 33.68 2.66
1767 1849 9.798994 AGGAGTACAATTCGTAGTAAACTAATG 57.201 33.333 0.00 0.00 33.68 1.90
1816 1898 9.139174 GGTGACCAATTTATGAAACATTGTAAG 57.861 33.333 0.00 0.00 0.00 2.34
1817 1899 8.647226 GTGACCAATTTATGAAACATTGTAAGC 58.353 33.333 0.00 0.00 0.00 3.09
1828 1910 4.970662 ACATTGTAAGCGCATCTTCAAT 57.029 36.364 11.47 10.03 35.20 2.57
1830 1912 2.830772 TGTAAGCGCATCTTCAATGC 57.169 45.000 11.47 0.00 41.35 3.56
1842 1924 2.094675 CTTCAATGCGGACCCTCAAAT 58.905 47.619 0.00 0.00 0.00 2.32
1843 1925 1.462616 TCAATGCGGACCCTCAAATG 58.537 50.000 0.00 0.00 0.00 2.32
1844 1926 0.457035 CAATGCGGACCCTCAAATGG 59.543 55.000 0.00 0.00 0.00 3.16
1848 1930 2.770130 GGACCCTCAAATGGCCCA 59.230 61.111 0.00 0.00 0.00 5.36
1854 1936 1.024271 CCTCAAATGGCCCACATACG 58.976 55.000 0.00 0.00 39.40 3.06
1856 1938 2.091541 CTCAAATGGCCCACATACGTT 58.908 47.619 0.00 0.00 39.40 3.99
1857 1939 2.088423 TCAAATGGCCCACATACGTTC 58.912 47.619 0.00 0.00 39.40 3.95
1865 1947 1.444724 CACATACGTTCGGACCGCA 60.445 57.895 9.66 0.00 0.00 5.69
1866 1948 1.444895 ACATACGTTCGGACCGCAC 60.445 57.895 9.66 8.01 0.00 5.34
1880 1962 3.998672 GCACGGTTCGGACCCAGA 61.999 66.667 7.48 0.00 43.42 3.86
1884 1966 2.943978 CGGTTCGGACCCAGAAGCT 61.944 63.158 7.48 0.00 43.42 3.74
1893 1975 2.173569 GGACCCAGAAGCTATCCAACAT 59.826 50.000 0.00 0.00 0.00 2.71
1898 1980 1.565759 AGAAGCTATCCAACATGGGCA 59.434 47.619 0.00 0.00 38.32 5.36
1911 1993 1.407656 ATGGGCATGTATCGGTCCGT 61.408 55.000 11.88 1.23 0.00 4.69
1917 1999 1.793134 ATGTATCGGTCCGTCGAGCC 61.793 60.000 11.88 0.00 42.69 4.70
1933 2015 1.969589 GCCGTCCGGACCATGTTTT 60.970 57.895 28.52 0.00 37.50 2.43
1943 2025 3.191791 CGGACCATGTTTTTCCCGTAAAT 59.808 43.478 0.00 0.00 33.02 1.40
1948 2030 5.167845 CCATGTTTTTCCCGTAAATTGGAG 58.832 41.667 0.00 0.00 30.91 3.86
1949 2031 4.245845 TGTTTTTCCCGTAAATTGGAGC 57.754 40.909 0.00 0.00 30.91 4.70
1953 2035 2.588464 TCCCGTAAATTGGAGCCAAA 57.412 45.000 5.98 0.00 39.55 3.28
1955 2037 4.237976 TCCCGTAAATTGGAGCCAAATA 57.762 40.909 5.98 0.51 39.55 1.40
1956 2038 3.949113 TCCCGTAAATTGGAGCCAAATAC 59.051 43.478 5.98 11.12 39.55 1.89
1965 2047 4.027884 GCCAAATACGGGGGCTTT 57.972 55.556 0.00 0.00 44.32 3.51
1968 2050 1.254284 CCAAATACGGGGGCTTTGCA 61.254 55.000 0.00 0.00 0.00 4.08
1971 2053 2.150014 AATACGGGGGCTTTGCAGGT 62.150 55.000 0.00 0.00 0.00 4.00
1978 2060 3.365265 GCTTTGCAGGTGTCCGGG 61.365 66.667 0.00 0.00 0.00 5.73
2003 2085 1.534595 AGACACGTCGGACTCTTACAC 59.465 52.381 6.57 0.00 34.09 2.90
2009 2091 1.134788 GTCGGACTCTTACACCCATGG 60.135 57.143 4.14 4.14 0.00 3.66
2031 2113 1.547372 CCAACCAAATGGAAGGCAGAG 59.453 52.381 6.42 0.00 43.54 3.35
2063 2145 2.950673 GCATCCCGCGTTGTTTCA 59.049 55.556 4.92 0.00 0.00 2.69
2064 2146 1.284408 GCATCCCGCGTTGTTTCAA 59.716 52.632 4.92 0.00 0.00 2.69
2075 2157 2.131972 GTTGTTTCAACGCCCAAATCC 58.868 47.619 0.00 0.00 0.00 3.01
2076 2158 0.676736 TGTTTCAACGCCCAAATCCC 59.323 50.000 0.00 0.00 0.00 3.85
2092 2174 2.723530 TCCCCCACTCTCTTCTCTTT 57.276 50.000 0.00 0.00 0.00 2.52
2098 2180 3.118445 CCCACTCTCTTCTCTTTCATCCC 60.118 52.174 0.00 0.00 0.00 3.85
2099 2181 3.517100 CCACTCTCTTCTCTTTCATCCCA 59.483 47.826 0.00 0.00 0.00 4.37
2112 2194 3.625632 ATCCCACCGCTCTCCACCT 62.626 63.158 0.00 0.00 0.00 4.00
2113 2195 2.238319 ATCCCACCGCTCTCCACCTA 62.238 60.000 0.00 0.00 0.00 3.08
2114 2196 1.987855 CCCACCGCTCTCCACCTAA 60.988 63.158 0.00 0.00 0.00 2.69
2115 2197 1.338136 CCCACCGCTCTCCACCTAAT 61.338 60.000 0.00 0.00 0.00 1.73
2116 2198 0.541863 CCACCGCTCTCCACCTAATT 59.458 55.000 0.00 0.00 0.00 1.40
2117 2199 1.473434 CCACCGCTCTCCACCTAATTC 60.473 57.143 0.00 0.00 0.00 2.17
2118 2200 0.831307 ACCGCTCTCCACCTAATTCC 59.169 55.000 0.00 0.00 0.00 3.01
2119 2201 0.106894 CCGCTCTCCACCTAATTCCC 59.893 60.000 0.00 0.00 0.00 3.97
2120 2202 0.249489 CGCTCTCCACCTAATTCCCG 60.249 60.000 0.00 0.00 0.00 5.14
2132 2214 1.485124 AATTCCCGCCATTTTCTCCC 58.515 50.000 0.00 0.00 0.00 4.30
2134 2216 0.610785 TTCCCGCCATTTTCTCCCAC 60.611 55.000 0.00 0.00 0.00 4.61
2150 2241 2.303022 TCCCACTTTCTTCTTCGCTGAT 59.697 45.455 0.00 0.00 0.00 2.90
2151 2242 2.417933 CCCACTTTCTTCTTCGCTGATG 59.582 50.000 0.00 0.00 0.00 3.07
2155 2246 3.126514 ACTTTCTTCTTCGCTGATGCATG 59.873 43.478 2.46 0.00 39.64 4.06
2169 2260 2.186903 CATGGAACCGGACGAGGG 59.813 66.667 9.46 0.00 35.02 4.30
2198 2289 1.774217 ATGGTGGTGGTGGAGGTGT 60.774 57.895 0.00 0.00 0.00 4.16
2208 2299 1.075536 GGTGGAGGTGTTGGAGGATTT 59.924 52.381 0.00 0.00 0.00 2.17
2226 2317 2.825836 GAGCATCACCCTTGCCCG 60.826 66.667 0.00 0.00 41.06 6.13
2229 2320 2.354729 CATCACCCTTGCCCGGAA 59.645 61.111 0.73 0.00 0.00 4.30
2242 2333 1.299648 CCGGAAGATCAACCTGGCA 59.700 57.895 0.00 0.00 0.00 4.92
2247 2338 0.537143 AAGATCAACCTGGCAACGCA 60.537 50.000 0.00 0.00 42.51 5.24
2248 2339 0.537143 AGATCAACCTGGCAACGCAA 60.537 50.000 0.00 0.00 42.51 4.85
2254 2345 0.247736 ACCTGGCAACGCAACAAAAA 59.752 45.000 0.00 0.00 42.51 1.94
2255 2346 1.134551 ACCTGGCAACGCAACAAAAAT 60.135 42.857 0.00 0.00 42.51 1.82
2256 2347 1.526464 CCTGGCAACGCAACAAAAATC 59.474 47.619 0.00 0.00 42.51 2.17
2257 2348 2.472816 CTGGCAACGCAACAAAAATCT 58.527 42.857 0.00 0.00 42.51 2.40
2259 2350 1.792367 GGCAACGCAACAAAAATCTCC 59.208 47.619 0.00 0.00 0.00 3.71
2260 2351 1.451651 GCAACGCAACAAAAATCTCCG 59.548 47.619 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
240 244 0.908198 ATCCTGCCACAGACCTCTTC 59.092 55.000 0.00 0.00 32.44 2.87
495 501 5.163258 CCTTTCTGTATAGCCTCTTCCACAT 60.163 44.000 0.00 0.00 0.00 3.21
703 712 6.884472 TCCATAAGTATTTCTGTGGGAAGA 57.116 37.500 0.00 0.00 35.08 2.87
775 788 6.814146 GCAGCACATCCCTAGTTAATATACTC 59.186 42.308 0.00 0.00 0.00 2.59
899 912 0.250727 ACACATCTGACCAAACCCCG 60.251 55.000 0.00 0.00 0.00 5.73
1140 1154 5.723672 TTCTTGACGACTCCTTTATCTGT 57.276 39.130 0.00 0.00 0.00 3.41
1344 1359 6.446318 TCAAACTGCCAAATCATCTTTACAC 58.554 36.000 0.00 0.00 0.00 2.90
1350 1365 5.796424 AAGTTCAAACTGCCAAATCATCT 57.204 34.783 0.00 0.00 39.66 2.90
1396 1435 1.125633 GGCCAGCCATGAATTCCAAT 58.874 50.000 3.12 0.00 35.81 3.16
1451 1509 7.888250 AAGGAGAAAGAACAGAAAAGAACAT 57.112 32.000 0.00 0.00 0.00 2.71
1482 1540 5.749109 CGAGTTCTACAGGCGAGATAAAAAT 59.251 40.000 0.00 0.00 0.00 1.82
1565 1624 0.742990 CTCAGGAAACCCGCGCATTA 60.743 55.000 8.75 0.00 0.00 1.90
1566 1625 2.033448 TCAGGAAACCCGCGCATT 59.967 55.556 8.75 0.00 0.00 3.56
1570 1629 1.933853 CTATTTCTCAGGAAACCCGCG 59.066 52.381 0.00 0.00 43.16 6.46
1604 1663 8.437360 TTCGAATTACTGCAATCACTTCATAT 57.563 30.769 0.00 0.00 0.00 1.78
1605 1664 7.841915 TTCGAATTACTGCAATCACTTCATA 57.158 32.000 0.00 0.00 0.00 2.15
1606 1665 6.741992 TTCGAATTACTGCAATCACTTCAT 57.258 33.333 0.00 0.00 0.00 2.57
1614 1673 8.039603 TCAAGTTGTATTCGAATTACTGCAAT 57.960 30.769 17.19 0.81 0.00 3.56
1635 1694 7.186804 TCTTTCTTTTTGCGAGTAAACTCAAG 58.813 34.615 10.55 6.01 43.00 3.02
1640 1699 8.776680 TGTATTCTTTCTTTTTGCGAGTAAAC 57.223 30.769 0.00 0.00 0.00 2.01
1689 1749 6.200097 CCTCAAACTTTTCCAACAAATTACCG 59.800 38.462 0.00 0.00 0.00 4.02
1776 1858 8.650143 AAATTGGTCACCATACTGTTAATTCT 57.350 30.769 0.00 0.00 31.53 2.40
1779 1861 9.693739 TCATAAATTGGTCACCATACTGTTAAT 57.306 29.630 0.00 0.00 31.53 1.40
1780 1862 9.521841 TTCATAAATTGGTCACCATACTGTTAA 57.478 29.630 0.00 0.00 31.53 2.01
1781 1863 9.521841 TTTCATAAATTGGTCACCATACTGTTA 57.478 29.630 0.00 0.00 31.53 2.41
1782 1864 8.303876 GTTTCATAAATTGGTCACCATACTGTT 58.696 33.333 0.00 0.00 31.53 3.16
1783 1865 7.450014 TGTTTCATAAATTGGTCACCATACTGT 59.550 33.333 0.00 0.00 31.53 3.55
1784 1866 7.825681 TGTTTCATAAATTGGTCACCATACTG 58.174 34.615 0.00 0.00 31.53 2.74
1785 1867 8.593945 ATGTTTCATAAATTGGTCACCATACT 57.406 30.769 0.00 0.00 31.53 2.12
1786 1868 9.086336 CAATGTTTCATAAATTGGTCACCATAC 57.914 33.333 0.00 0.00 31.53 2.39
1787 1869 8.811017 ACAATGTTTCATAAATTGGTCACCATA 58.189 29.630 0.00 0.00 35.95 2.74
1788 1870 7.678837 ACAATGTTTCATAAATTGGTCACCAT 58.321 30.769 0.00 0.00 35.95 3.55
1789 1871 7.060383 ACAATGTTTCATAAATTGGTCACCA 57.940 32.000 0.00 0.00 35.95 4.17
1790 1872 9.139174 CTTACAATGTTTCATAAATTGGTCACC 57.861 33.333 0.00 0.00 35.95 4.02
1791 1873 8.647226 GCTTACAATGTTTCATAAATTGGTCAC 58.353 33.333 0.00 0.00 35.95 3.67
1828 1910 2.361104 GCCATTTGAGGGTCCGCA 60.361 61.111 0.00 0.00 0.00 5.69
1830 1912 2.440247 GGGCCATTTGAGGGTCCG 60.440 66.667 4.39 0.00 41.05 4.79
1834 1916 1.402787 GTATGTGGGCCATTTGAGGG 58.597 55.000 10.70 0.00 34.86 4.30
1842 1924 2.266372 CCGAACGTATGTGGGCCA 59.734 61.111 0.00 0.00 0.00 5.36
1843 1925 1.812507 GTCCGAACGTATGTGGGCC 60.813 63.158 0.00 0.00 0.00 5.80
1844 1926 1.812507 GGTCCGAACGTATGTGGGC 60.813 63.158 0.00 0.00 0.00 5.36
1848 1930 1.444895 GTGCGGTCCGAACGTATGT 60.445 57.895 17.49 0.00 0.00 2.29
1867 1949 0.831307 ATAGCTTCTGGGTCCGAACC 59.169 55.000 0.00 0.00 45.65 3.62
1878 1960 1.565759 TGCCCATGTTGGATAGCTTCT 59.434 47.619 0.00 0.00 40.96 2.85
1880 1962 2.313317 CATGCCCATGTTGGATAGCTT 58.687 47.619 0.00 0.00 40.96 3.74
1893 1975 2.023414 GACGGACCGATACATGCCCA 62.023 60.000 23.38 0.00 0.00 5.36
1898 1980 1.653115 GCTCGACGGACCGATACAT 59.347 57.895 23.38 0.00 37.96 2.29
1917 1999 0.519961 GGAAAAACATGGTCCGGACG 59.480 55.000 27.68 16.79 0.00 4.79
1921 2003 1.810959 TACGGGAAAAACATGGTCCG 58.189 50.000 7.04 7.04 42.69 4.79
1923 2005 4.926832 CCAATTTACGGGAAAAACATGGTC 59.073 41.667 0.00 0.00 0.00 4.02
1928 2010 3.006003 GGCTCCAATTTACGGGAAAAACA 59.994 43.478 0.00 0.00 31.58 2.83
1933 2015 2.588464 TTGGCTCCAATTTACGGGAA 57.412 45.000 0.00 0.00 31.58 3.97
1943 2025 1.304952 CCCCCGTATTTGGCTCCAA 59.695 57.895 0.00 0.00 0.00 3.53
1948 2030 1.515487 CAAAGCCCCCGTATTTGGC 59.485 57.895 0.00 0.00 45.70 4.52
1949 2031 1.254284 TGCAAAGCCCCCGTATTTGG 61.254 55.000 0.00 0.00 35.07 3.28
1953 2035 2.275418 CCTGCAAAGCCCCCGTAT 59.725 61.111 0.00 0.00 0.00 3.06
1955 2037 4.974721 CACCTGCAAAGCCCCCGT 62.975 66.667 0.00 0.00 0.00 5.28
1956 2038 4.974721 ACACCTGCAAAGCCCCCG 62.975 66.667 0.00 0.00 0.00 5.73
1980 2062 2.185103 AAGAGTCCGACGTGTCTCGC 62.185 60.000 0.00 0.00 44.19 5.03
1989 2071 1.134788 CCATGGGTGTAAGAGTCCGAC 60.135 57.143 2.85 0.00 0.00 4.79
1991 2073 0.462047 GCCATGGGTGTAAGAGTCCG 60.462 60.000 15.13 0.00 0.00 4.79
1992 2074 0.107165 GGCCATGGGTGTAAGAGTCC 60.107 60.000 15.13 0.00 0.00 3.85
1993 2075 0.107165 GGGCCATGGGTGTAAGAGTC 60.107 60.000 15.13 0.00 0.00 3.36
1995 2077 0.331278 TTGGGCCATGGGTGTAAGAG 59.669 55.000 15.13 0.00 0.00 2.85
2009 2091 1.296392 GCCTTCCATTTGGTTGGGC 59.704 57.895 11.84 11.84 37.37 5.36
2043 2125 0.800012 GAAACAACGCGGGATGCTAA 59.200 50.000 12.47 0.00 43.27 3.09
2055 2137 2.131972 GGATTTGGGCGTTGAAACAAC 58.868 47.619 0.00 0.00 0.00 3.32
2056 2138 1.069358 GGGATTTGGGCGTTGAAACAA 59.931 47.619 0.00 0.00 0.00 2.83
2062 2144 2.283532 TGGGGGATTTGGGCGTTG 60.284 61.111 0.00 0.00 0.00 4.10
2063 2145 2.283604 GTGGGGGATTTGGGCGTT 60.284 61.111 0.00 0.00 0.00 4.84
2064 2146 3.264845 AGTGGGGGATTTGGGCGT 61.265 61.111 0.00 0.00 0.00 5.68
2069 2151 2.843113 AGAGAAGAGAGTGGGGGATTTG 59.157 50.000 0.00 0.00 0.00 2.32
2075 2157 3.118445 GGATGAAAGAGAAGAGAGTGGGG 60.118 52.174 0.00 0.00 0.00 4.96
2076 2158 3.118445 GGGATGAAAGAGAAGAGAGTGGG 60.118 52.174 0.00 0.00 0.00 4.61
2092 2174 2.038813 TGGAGAGCGGTGGGATGA 59.961 61.111 0.00 0.00 0.00 2.92
2098 2180 1.473434 GGAATTAGGTGGAGAGCGGTG 60.473 57.143 0.00 0.00 0.00 4.94
2099 2181 0.831307 GGAATTAGGTGGAGAGCGGT 59.169 55.000 0.00 0.00 0.00 5.68
2112 2194 2.024846 TGGGAGAAAATGGCGGGAATTA 60.025 45.455 0.00 0.00 0.00 1.40
2113 2195 1.272985 TGGGAGAAAATGGCGGGAATT 60.273 47.619 0.00 0.00 0.00 2.17
2114 2196 0.334676 TGGGAGAAAATGGCGGGAAT 59.665 50.000 0.00 0.00 0.00 3.01
2115 2197 0.610785 GTGGGAGAAAATGGCGGGAA 60.611 55.000 0.00 0.00 0.00 3.97
2116 2198 1.001393 GTGGGAGAAAATGGCGGGA 60.001 57.895 0.00 0.00 0.00 5.14
2117 2199 0.611896 AAGTGGGAGAAAATGGCGGG 60.612 55.000 0.00 0.00 0.00 6.13
2118 2200 1.202348 GAAAGTGGGAGAAAATGGCGG 59.798 52.381 0.00 0.00 0.00 6.13
2119 2201 2.162681 AGAAAGTGGGAGAAAATGGCG 58.837 47.619 0.00 0.00 0.00 5.69
2120 2202 3.829026 AGAAGAAAGTGGGAGAAAATGGC 59.171 43.478 0.00 0.00 0.00 4.40
2132 2214 2.481568 TGCATCAGCGAAGAAGAAAGTG 59.518 45.455 0.00 0.00 46.23 3.16
2134 2216 3.487042 CCATGCATCAGCGAAGAAGAAAG 60.487 47.826 0.00 0.00 46.23 2.62
2150 2241 2.264480 CTCGTCCGGTTCCATGCA 59.736 61.111 0.00 0.00 0.00 3.96
2151 2242 2.511600 CCTCGTCCGGTTCCATGC 60.512 66.667 0.00 0.00 0.00 4.06
2176 2267 0.405585 CCTCCACCACCACCATCTTT 59.594 55.000 0.00 0.00 0.00 2.52
2184 2275 1.694525 TCCAACACCTCCACCACCA 60.695 57.895 0.00 0.00 0.00 4.17
2198 2289 2.621407 GGGTGATGCTCAAATCCTCCAA 60.621 50.000 0.00 0.00 0.00 3.53
2208 2299 2.356278 GGGCAAGGGTGATGCTCA 59.644 61.111 0.00 0.00 43.87 4.26
2226 2317 0.804989 CGTTGCCAGGTTGATCTTCC 59.195 55.000 0.00 0.00 0.00 3.46
2229 2320 0.537143 TTGCGTTGCCAGGTTGATCT 60.537 50.000 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.