Multiple sequence alignment - TraesCS6B01G050100

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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 TraesCS6B01G050100 chr6B 100.000 2720 0 0 1 2720 29758460 29755741 0.000000e+00 5024
1 TraesCS6B01G050100 chr6B 94.971 696 31 3 96 790 29417794 29418486 0.000000e+00 1088
2 TraesCS6B01G050100 chr6B 86.583 954 88 9 777 1730 29418502 29419415 0.000000e+00 1016
3 TraesCS6B01G050100 chr6B 80.174 691 95 26 2066 2720 29856497 29857181 1.890000e-131 479
4 TraesCS6B01G050100 chr6B 79.335 692 99 25 2066 2720 29920633 29921317 1.920000e-121 446
5 TraesCS6B01G050100 chr6B 86.802 394 38 8 2012 2395 29426740 29427129 6.960000e-116 427
6 TraesCS6B01G050100 chr6B 91.573 178 12 2 1724 1901 29426378 29426552 2.710000e-60 243
7 TraesCS6B01G050100 chr6A 90.996 1366 101 5 556 1901 17601151 17602514 0.000000e+00 1821
8 TraesCS6B01G050100 chr6A 89.011 728 56 9 2012 2720 17602702 17603424 0.000000e+00 880
9 TraesCS6B01G050100 chr6A 79.624 692 98 18 2066 2720 17646763 17647448 8.880000e-125 457
10 TraesCS6B01G050100 chr6D 91.214 1343 101 7 570 1901 16771872 16773208 0.000000e+00 1810
11 TraesCS6B01G050100 chr6D 89.163 729 54 10 2012 2720 16773396 16774119 0.000000e+00 885
12 TraesCS6B01G050100 chr6D 93.590 390 17 3 1 382 16771485 16771874 2.350000e-160 575
13 TraesCS6B01G050100 chr2D 77.108 498 83 20 2243 2720 15518285 15517799 2.690000e-65 259
14 TraesCS6B01G050100 chr2D 75.977 512 88 24 2235 2720 15474081 15473579 5.860000e-57 231
15 TraesCS6B01G050100 chr7A 88.667 150 12 5 2012 2160 721828162 721828307 7.740000e-41 178
16 TraesCS6B01G050100 chr2A 74.031 516 88 32 2235 2720 17551350 17550851 4.660000e-38 169
17 TraesCS6B01G050100 chr2A 72.763 514 98 28 2235 2720 17536015 17535516 4.720000e-28 135
18 TraesCS6B01G050100 chr1D 95.312 64 3 0 1950 2013 493805101 493805164 4.790000e-18 102


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 TraesCS6B01G050100 chr6B 29755741 29758460 2719 True 5024.0 5024 100.000000 1 2720 1 chr6B.!!$R1 2719
1 TraesCS6B01G050100 chr6B 29417794 29419415 1621 False 1052.0 1088 90.777000 96 1730 2 chr6B.!!$F3 1634
2 TraesCS6B01G050100 chr6B 29856497 29857181 684 False 479.0 479 80.174000 2066 2720 1 chr6B.!!$F1 654
3 TraesCS6B01G050100 chr6B 29920633 29921317 684 False 446.0 446 79.335000 2066 2720 1 chr6B.!!$F2 654
4 TraesCS6B01G050100 chr6B 29426378 29427129 751 False 335.0 427 89.187500 1724 2395 2 chr6B.!!$F4 671
5 TraesCS6B01G050100 chr6A 17601151 17603424 2273 False 1350.5 1821 90.003500 556 2720 2 chr6A.!!$F2 2164
6 TraesCS6B01G050100 chr6A 17646763 17647448 685 False 457.0 457 79.624000 2066 2720 1 chr6A.!!$F1 654
7 TraesCS6B01G050100 chr6D 16771485 16774119 2634 False 1090.0 1810 91.322333 1 2720 3 chr6D.!!$F1 2719
8 TraesCS6B01G050100 chr2D 15473579 15474081 502 True 231.0 231 75.977000 2235 2720 1 chr2D.!!$R1 485

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
933 988 1.172812 AAGCAAAGGGAGAACACCGC 61.173 55.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2484 2698 0.251386 TCACCGACAGAGGAAGCTCT 60.251 55.0 0.0 0.0 34.73 4.09 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
29 35 2.551459 CAGCTAGCAGACAAGCACTTTT 59.449 45.455 18.83 0.00 41.32 2.27
87 93 2.810852 GGTATTGCAGCTCTAGGATTGC 59.189 50.000 0.00 6.39 37.09 3.56
160 169 3.245016 TGGCCATTGAAATCTCTGTCTGT 60.245 43.478 0.00 0.00 0.00 3.41
164 173 4.999311 CCATTGAAATCTCTGTCTGTCACA 59.001 41.667 0.00 0.00 0.00 3.58
165 174 5.646793 CCATTGAAATCTCTGTCTGTCACAT 59.353 40.000 0.00 0.00 33.23 3.21
171 180 6.611613 AATCTCTGTCTGTCACATTTAGGA 57.388 37.500 0.00 0.00 33.23 2.94
173 182 5.325239 TCTCTGTCTGTCACATTTAGGAGA 58.675 41.667 0.00 0.00 33.23 3.71
213 222 4.885907 GGATTTGATTGCATCTCTTCTCCA 59.114 41.667 0.00 0.00 0.00 3.86
215 224 5.633830 TTTGATTGCATCTCTTCTCCAAC 57.366 39.130 0.00 0.00 0.00 3.77
383 393 2.996631 ACAGCCAGATGATCAGAAACC 58.003 47.619 0.09 0.00 0.00 3.27
470 480 6.153340 ACAAATTCTACAATCCCTGAACCATG 59.847 38.462 0.00 0.00 0.00 3.66
537 547 5.832539 ATCTTCTTTCCTTCCAAGAGACA 57.167 39.130 0.00 0.00 31.84 3.41
538 548 5.630415 TCTTCTTTCCTTCCAAGAGACAA 57.370 39.130 0.00 0.00 31.84 3.18
554 564 4.837860 AGAGACAACACATTCTCTCCTCTT 59.162 41.667 0.00 0.00 44.40 2.85
558 568 3.064900 ACACATTCTCTCCTCTTTGCC 57.935 47.619 0.00 0.00 0.00 4.52
689 707 5.874810 TGGACTATGTTCACTGCTGATTAAC 59.125 40.000 0.00 0.00 0.00 2.01
732 750 3.525537 ACCTGCACTAATTCATCTCGTG 58.474 45.455 0.00 0.00 0.00 4.35
733 751 2.868583 CCTGCACTAATTCATCTCGTGG 59.131 50.000 0.00 0.00 0.00 4.94
752 770 5.305128 TCGTGGGTTATATTCTCCCGTTAAT 59.695 40.000 0.00 0.00 43.75 1.40
885 940 8.690680 TTAACGCAATAAAACACCATAAATCC 57.309 30.769 0.00 0.00 0.00 3.01
896 951 6.834168 ACACCATAAATCCCTTTGTTACAG 57.166 37.500 0.00 0.00 0.00 2.74
900 955 5.067805 CCATAAATCCCTTTGTTACAGCTCC 59.932 44.000 0.00 0.00 0.00 4.70
925 980 1.474077 AGCGCAATAAAGCAAAGGGAG 59.526 47.619 11.47 0.00 35.48 4.30
927 982 2.094752 GCGCAATAAAGCAAAGGGAGAA 60.095 45.455 0.30 0.00 0.00 2.87
932 987 1.318576 AAAGCAAAGGGAGAACACCG 58.681 50.000 0.00 0.00 0.00 4.94
933 988 1.172812 AAGCAAAGGGAGAACACCGC 61.173 55.000 0.00 0.00 0.00 5.68
941 996 1.471287 GGGAGAACACCGCAATTTACC 59.529 52.381 0.00 0.00 0.00 2.85
957 1012 1.807771 TACCCCTCTCGTCCCCAAGT 61.808 60.000 0.00 0.00 0.00 3.16
1032 1087 1.079543 GAAGAGAGCCAAGCTGCGA 60.080 57.895 0.00 0.00 39.88 5.10
1041 1096 1.750193 CCAAGCTGCGAAAATCCCTA 58.250 50.000 0.00 0.00 0.00 3.53
1054 1109 1.798626 ATCCCTACAGCTCTGCATCA 58.201 50.000 0.00 0.00 0.00 3.07
1056 1111 0.829333 CCCTACAGCTCTGCATCACT 59.171 55.000 0.00 0.00 0.00 3.41
1058 1113 2.035704 CCCTACAGCTCTGCATCACTAG 59.964 54.545 0.00 0.00 0.00 2.57
1062 1117 2.168106 ACAGCTCTGCATCACTAGGAAG 59.832 50.000 0.00 0.00 0.00 3.46
1081 1136 0.105778 GCTCAAGAAGATCCCTCCGG 59.894 60.000 0.00 0.00 0.00 5.14
1101 1156 1.191489 TTCACATCCCCAGCTCGACA 61.191 55.000 0.00 0.00 0.00 4.35
1107 1162 1.815421 CCCCAGCTCGACAATTCCG 60.815 63.158 0.00 0.00 0.00 4.30
1125 1180 3.818787 GCAACCATCGCCAGCAGG 61.819 66.667 0.00 0.00 38.23 4.85
1147 1202 4.154347 GGCTCCTCTCCACCTGCG 62.154 72.222 0.00 0.00 0.00 5.18
1214 1281 4.238514 GCTACCAACAACAACAACAACAA 58.761 39.130 0.00 0.00 0.00 2.83
1215 1282 4.090786 GCTACCAACAACAACAACAACAAC 59.909 41.667 0.00 0.00 0.00 3.32
1216 1283 3.053455 ACCAACAACAACAACAACAACG 58.947 40.909 0.00 0.00 0.00 4.10
1272 1339 1.721926 CGCTTCCTCTTCGACAACTTC 59.278 52.381 0.00 0.00 0.00 3.01
1284 1351 2.159544 CGACAACTTCCGGTCTCTCTAC 60.160 54.545 0.00 0.00 31.88 2.59
1287 1354 4.597004 ACAACTTCCGGTCTCTCTACATA 58.403 43.478 0.00 0.00 0.00 2.29
1296 1363 3.253677 GGTCTCTCTACATACATGACCGG 59.746 52.174 0.00 0.00 34.17 5.28
1323 1390 2.960129 GTGCGCCTCCCGTTATCG 60.960 66.667 4.18 0.00 39.71 2.92
1365 1450 4.400109 GTCGACGAGACGCAGGCA 62.400 66.667 0.00 0.00 40.43 4.75
1400 1485 2.743636 TCCTTGTCGGATTCAGTCAC 57.256 50.000 0.00 0.00 36.69 3.67
1489 1574 0.248565 GGACCCTTACACCGACTTCC 59.751 60.000 0.00 0.00 0.00 3.46
1527 1612 1.378531 TGATAAAGATGCACCACGGC 58.621 50.000 0.00 0.00 0.00 5.68
1538 1623 2.202932 CCACGGCCAGGAATCTCG 60.203 66.667 2.24 0.00 0.00 4.04
1540 1625 4.162690 ACGGCCAGGAATCTCGGC 62.163 66.667 2.24 5.15 45.47 5.54
1584 1669 5.300034 GGAGGAGCTACTCTTTTACTACCTC 59.700 48.000 25.23 12.65 39.26 3.85
1593 1678 5.485708 ACTCTTTTACTACCTCCAGCTCAAT 59.514 40.000 0.00 0.00 0.00 2.57
1629 1714 0.813821 GGCACATTCTCAAGGCCTTC 59.186 55.000 17.29 0.01 41.39 3.46
1653 1738 1.302832 CCTCACTGCTGGAACCCAC 60.303 63.158 0.00 0.00 0.00 4.61
1655 1740 0.179020 CTCACTGCTGGAACCCACAA 60.179 55.000 0.00 0.00 0.00 3.33
1662 1747 3.119319 TGCTGGAACCCACAAGGATATA 58.881 45.455 0.00 0.00 39.89 0.86
1681 1766 2.281208 CAGCCCGTGGAAAACCGA 60.281 61.111 0.00 0.00 0.00 4.69
1692 1777 1.534729 GAAAACCGAACTGGGCTGAT 58.465 50.000 0.00 0.00 44.64 2.90
1698 1783 1.482593 CCGAACTGGGCTGATAAGAGT 59.517 52.381 0.00 0.00 0.00 3.24
1745 1830 9.167311 GGACACAGATTCAAAGACTTATGTTAT 57.833 33.333 0.00 0.00 0.00 1.89
1765 1850 6.929049 TGTTATAGGATACATGTTGCTACTGC 59.071 38.462 2.30 2.50 41.41 4.40
1782 1867 4.226427 ACTGCACCATGTCATCTATTGT 57.774 40.909 0.00 0.00 0.00 2.71
1797 1882 9.764363 GTCATCTATTGTATAACCTGATTCACA 57.236 33.333 0.00 0.00 0.00 3.58
1845 1930 8.717717 AGAATACATCTTCCTGTATTGAATCCA 58.282 33.333 12.72 0.00 46.93 3.41
1910 2020 6.174720 AGAGTTTCTGACATGTCTAAACCA 57.825 37.500 31.67 14.74 37.12 3.67
1914 2024 6.042093 AGTTTCTGACATGTCTAAACCAGAGA 59.958 38.462 31.67 20.99 37.12 3.10
1920 2030 6.096987 TGACATGTCTAAACCAGAGATAGTCC 59.903 42.308 25.55 0.00 35.12 3.85
1934 2044 3.637229 AGATAGTCCATTACACACCTCGG 59.363 47.826 0.00 0.00 0.00 4.63
1935 2045 0.249398 AGTCCATTACACACCTCGGC 59.751 55.000 0.00 0.00 0.00 5.54
1936 2046 0.249398 GTCCATTACACACCTCGGCT 59.751 55.000 0.00 0.00 0.00 5.52
1938 2048 1.369091 CCATTACACACCTCGGCTGC 61.369 60.000 0.00 0.00 0.00 5.25
1941 2051 2.167398 TTACACACCTCGGCTGCCTC 62.167 60.000 17.92 0.00 0.00 4.70
1946 2056 3.080121 CCTCGGCTGCCTCCTCTT 61.080 66.667 17.92 0.00 0.00 2.85
1947 2057 2.498726 CTCGGCTGCCTCCTCTTC 59.501 66.667 17.92 0.00 0.00 2.87
1956 2089 0.915364 GCCTCCTCTTCCATTCACCT 59.085 55.000 0.00 0.00 0.00 4.00
1972 2105 2.300152 TCACCTTCGAGTCATCAAAGCT 59.700 45.455 0.00 0.00 0.00 3.74
1973 2106 2.414481 CACCTTCGAGTCATCAAAGCTG 59.586 50.000 0.00 0.00 0.00 4.24
1990 2123 3.604582 AGCTGTCAACTAATTCAGAGGC 58.395 45.455 0.00 0.00 0.00 4.70
2027 2190 1.674057 CCCTCTGTCTTTGGCGACT 59.326 57.895 0.00 0.00 35.00 4.18
2029 2192 1.275291 CCCTCTGTCTTTGGCGACTAA 59.725 52.381 0.00 0.00 35.00 2.24
2034 2197 3.558418 TCTGTCTTTGGCGACTAACAAAC 59.442 43.478 0.00 0.00 35.00 2.93
2035 2198 3.271729 TGTCTTTGGCGACTAACAAACA 58.728 40.909 0.00 0.00 35.00 2.83
2036 2199 3.690139 TGTCTTTGGCGACTAACAAACAA 59.310 39.130 0.00 0.00 35.00 2.83
2038 2201 4.497966 GTCTTTGGCGACTAACAAACAAAC 59.502 41.667 0.00 0.00 33.45 2.93
2039 2202 4.156190 TCTTTGGCGACTAACAAACAAACA 59.844 37.500 0.00 0.00 33.45 2.83
2041 2204 3.271729 TGGCGACTAACAAACAAACAGA 58.728 40.909 0.00 0.00 0.00 3.41
2042 2205 3.311322 TGGCGACTAACAAACAAACAGAG 59.689 43.478 0.00 0.00 0.00 3.35
2043 2206 3.303791 GGCGACTAACAAACAAACAGAGG 60.304 47.826 0.00 0.00 0.00 3.69
2044 2207 3.303791 GCGACTAACAAACAAACAGAGGG 60.304 47.826 0.00 0.00 0.00 4.30
2045 2208 3.303791 CGACTAACAAACAAACAGAGGGC 60.304 47.826 0.00 0.00 0.00 5.19
2046 2209 3.883489 GACTAACAAACAAACAGAGGGCT 59.117 43.478 0.00 0.00 0.00 5.19
2047 2210 5.043737 ACTAACAAACAAACAGAGGGCTA 57.956 39.130 0.00 0.00 0.00 3.93
2051 2214 5.006153 ACAAACAAACAGAGGGCTAAAAC 57.994 39.130 0.00 0.00 0.00 2.43
2060 2224 4.254492 CAGAGGGCTAAAACCTGTAGTTC 58.746 47.826 0.00 0.00 37.88 3.01
2073 2237 5.300752 ACCTGTAGTTCTGAACAGTGATTG 58.699 41.667 21.50 7.03 41.25 2.67
2180 2364 2.823984 TCGTTTTTAGTCGCCTTGTCA 58.176 42.857 0.00 0.00 0.00 3.58
2192 2377 4.618489 GTCGCCTTGTCATTTGAAATGAAG 59.382 41.667 20.94 15.41 0.00 3.02
2267 2460 6.261603 TGAACATTGCAGAATATCAGGATCAC 59.738 38.462 0.00 0.00 0.00 3.06
2352 2549 1.314730 ATCTGGTTTTCGCGGTTTGT 58.685 45.000 6.13 0.00 0.00 2.83
2356 2553 1.948145 TGGTTTTCGCGGTTTGTATGT 59.052 42.857 6.13 0.00 0.00 2.29
2371 2568 4.518278 TGTATGTATTTGGGGCATCAGT 57.482 40.909 0.00 0.00 0.00 3.41
2388 2585 1.344438 CAGTGGTACTCAAGGCAGTGA 59.656 52.381 0.00 0.00 0.00 3.41
2390 2587 1.070134 GTGGTACTCAAGGCAGTGACA 59.930 52.381 0.00 0.00 0.00 3.58
2530 2744 2.083774 TCTTCAATTGGTGCGATGACC 58.916 47.619 5.42 0.00 36.43 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 135 1.866483 AATGGCCAGGGATGTGCAGA 61.866 55.000 13.05 0.00 0.00 4.26
160 169 2.421952 GGCCTGCATCTCCTAAATGTGA 60.422 50.000 0.00 0.00 0.00 3.58
164 173 0.109342 CCGGCCTGCATCTCCTAAAT 59.891 55.000 0.00 0.00 0.00 1.40
165 174 1.526887 CCGGCCTGCATCTCCTAAA 59.473 57.895 0.00 0.00 0.00 1.85
213 222 3.897239 TCAAGTTGGTGGATGAAGTGTT 58.103 40.909 2.34 0.00 0.00 3.32
215 224 4.330250 AGATCAAGTTGGTGGATGAAGTG 58.670 43.478 2.34 0.00 0.00 3.16
359 369 4.498894 TTCTGATCATCTGGCTGTTGAT 57.501 40.909 15.22 15.22 37.69 2.57
383 393 2.957491 TCCCTTTTGTGTTGCACTTG 57.043 45.000 0.00 0.00 35.11 3.16
520 530 4.199310 TGTGTTGTCTCTTGGAAGGAAAG 58.801 43.478 0.00 0.00 0.00 2.62
537 547 3.416156 GGCAAAGAGGAGAGAATGTGTT 58.584 45.455 0.00 0.00 0.00 3.32
538 548 2.290577 GGGCAAAGAGGAGAGAATGTGT 60.291 50.000 0.00 0.00 0.00 3.72
548 558 1.210204 ATGCTCCAGGGCAAAGAGGA 61.210 55.000 0.00 0.00 45.68 3.71
554 564 3.953612 CTGTATTTAATGCTCCAGGGCAA 59.046 43.478 0.00 0.00 45.68 4.52
558 568 4.202441 AGTGCTGTATTTAATGCTCCAGG 58.798 43.478 0.00 0.00 0.00 4.45
607 617 7.403312 TGGGAATTTGGTCTATACATGTTTG 57.597 36.000 2.30 0.00 0.00 2.93
689 707 6.375455 AGGTAAGGCTCATAAACATTTGACTG 59.625 38.462 0.00 0.00 0.00 3.51
732 750 8.512138 CAATTGATTAACGGGAGAATATAACCC 58.488 37.037 0.00 0.00 40.17 4.11
733 751 8.021396 GCAATTGATTAACGGGAGAATATAACC 58.979 37.037 10.34 0.00 0.00 2.85
772 798 3.003480 GGCCTCTGCAGTAACTTTGTAG 58.997 50.000 14.67 0.00 40.13 2.74
885 940 1.892209 AACGGGAGCTGTAACAAAGG 58.108 50.000 0.00 0.00 0.00 3.11
896 951 1.003866 CTTTATTGCGCTAACGGGAGC 60.004 52.381 9.73 0.93 40.57 4.70
900 955 2.535934 TTGCTTTATTGCGCTAACGG 57.464 45.000 9.73 0.00 40.57 4.44
908 963 4.237724 GTGTTCTCCCTTTGCTTTATTGC 58.762 43.478 0.00 0.00 0.00 3.56
925 980 1.471287 GAGGGGTAAATTGCGGTGTTC 59.529 52.381 0.00 0.00 0.00 3.18
927 982 0.696501 AGAGGGGTAAATTGCGGTGT 59.303 50.000 0.00 0.00 0.00 4.16
932 987 1.664873 GGACGAGAGGGGTAAATTGC 58.335 55.000 0.00 0.00 0.00 3.56
933 988 1.134189 GGGGACGAGAGGGGTAAATTG 60.134 57.143 0.00 0.00 0.00 2.32
941 996 1.192146 TGAACTTGGGGACGAGAGGG 61.192 60.000 0.00 0.00 45.46 4.30
985 1040 6.270927 TCATCTTCCATCTCTTTTCCCGATAT 59.729 38.462 0.00 0.00 0.00 1.63
1032 1087 3.054139 TGATGCAGAGCTGTAGGGATTTT 60.054 43.478 0.00 0.00 0.00 1.82
1041 1096 1.857965 TCCTAGTGATGCAGAGCTGT 58.142 50.000 0.00 0.00 0.00 4.40
1054 1109 3.709141 GGGATCTTCTTGAGCTTCCTAGT 59.291 47.826 0.00 0.00 31.59 2.57
1056 1111 3.964031 GAGGGATCTTCTTGAGCTTCCTA 59.036 47.826 0.00 0.00 31.59 2.94
1058 1113 2.158827 GGAGGGATCTTCTTGAGCTTCC 60.159 54.545 0.00 0.00 31.66 3.46
1062 1117 3.677002 CGGAGGGATCTTCTTGAGC 57.323 57.895 0.00 0.00 0.00 4.26
1081 1136 0.741221 GTCGAGCTGGGGATGTGAAC 60.741 60.000 0.00 0.00 0.00 3.18
1101 1156 2.414785 GGCGATGGTTGCCGGAATT 61.415 57.895 5.05 0.00 43.70 2.17
1158 1213 1.073216 CGATGTCCAGCGACTGTGTC 61.073 60.000 0.00 0.00 43.75 3.67
1249 1316 0.391597 TTGTCGAAGAGGAAGCGGTT 59.608 50.000 0.00 0.00 36.95 4.44
1272 1339 3.253677 GGTCATGTATGTAGAGAGACCGG 59.746 52.174 0.00 0.00 35.29 5.28
1284 1351 0.458260 TGTCGTCCCGGTCATGTATG 59.542 55.000 0.00 0.00 0.00 2.39
1287 1354 1.005394 GTTGTCGTCCCGGTCATGT 60.005 57.895 0.00 0.00 0.00 3.21
1306 1373 2.960129 CGATAACGGGAGGCGCAC 60.960 66.667 10.83 1.82 35.72 5.34
1307 1374 4.884257 GCGATAACGGGAGGCGCA 62.884 66.667 10.83 0.00 46.19 6.09
1316 1383 4.197498 ACGTCCCCGGCGATAACG 62.197 66.667 20.43 20.43 38.78 3.18
1317 1384 2.279054 GACGTCCCCGGCGATAAC 60.279 66.667 9.30 1.54 38.78 1.89
1363 1448 0.099436 GATGATGTTCCTGCGGTTGC 59.901 55.000 0.00 0.00 43.20 4.17
1364 1449 0.734889 GGATGATGTTCCTGCGGTTG 59.265 55.000 0.00 0.00 32.68 3.77
1365 1450 0.620556 AGGATGATGTTCCTGCGGTT 59.379 50.000 0.00 0.00 44.63 4.44
1390 1475 2.338500 GGTGTCTTCCGTGACTGAATC 58.662 52.381 0.00 0.00 37.79 2.52
1392 1477 0.031585 CGGTGTCTTCCGTGACTGAA 59.968 55.000 0.00 0.00 44.77 3.02
1414 1499 1.002134 CATCACCTGACCCGGCTTT 60.002 57.895 0.00 0.00 0.00 3.51
1438 1523 4.961511 TATGGCCGCATCGTCGCC 62.962 66.667 0.00 0.00 0.00 5.54
1443 1528 0.532573 ATAGGACTATGGCCGCATCG 59.467 55.000 0.00 0.00 0.00 3.84
1489 1574 0.107508 ATGTTCTGCATGGACCTCCG 60.108 55.000 0.00 0.00 39.43 4.63
1527 1612 3.854669 AGCGGCCGAGATTCCTGG 61.855 66.667 33.48 0.00 0.00 4.45
1540 1625 1.831652 AAGAAGTCCCAGTCCAGCGG 61.832 60.000 0.00 0.00 0.00 5.52
1542 1627 0.322008 CCAAGAAGTCCCAGTCCAGC 60.322 60.000 0.00 0.00 0.00 4.85
1584 1669 3.672511 GCACACTTTGATCATTGAGCTGG 60.673 47.826 3.27 0.00 0.00 4.85
1593 1678 0.953727 GCCTGTGCACACTTTGATCA 59.046 50.000 17.42 0.00 37.47 2.92
1632 1717 1.374758 GGTTCCAGCAGTGAGGTCG 60.375 63.158 0.00 0.00 0.00 4.79
1653 1738 1.270839 CCACGGGCTGGTATATCCTTG 60.271 57.143 0.00 0.00 34.90 3.61
1655 1740 0.190069 TCCACGGGCTGGTATATCCT 59.810 55.000 0.00 0.00 41.52 3.24
1662 1747 2.203437 GGTTTTCCACGGGCTGGT 60.203 61.111 0.00 0.00 41.52 4.00
1681 1766 4.080863 CCTAACACTCTTATCAGCCCAGTT 60.081 45.833 0.00 0.00 0.00 3.16
1698 1783 8.921205 GTGTCCTAATATTTCCTACTCCTAACA 58.079 37.037 0.00 0.00 0.00 2.41
1716 1801 8.375506 ACATAAGTCTTTGAATCTGTGTCCTAA 58.624 33.333 0.00 0.00 0.00 2.69
1765 1850 8.150296 TCAGGTTATACAATAGATGACATGGTG 58.850 37.037 0.00 0.00 28.85 4.17
1845 1930 8.099537 CCCATATATCTGTCTACAGCATTCTTT 58.900 37.037 5.21 0.00 43.46 2.52
1910 2020 4.580995 CGAGGTGTGTAATGGACTATCTCT 59.419 45.833 0.00 0.00 0.00 3.10
1914 2024 2.102588 GCCGAGGTGTGTAATGGACTAT 59.897 50.000 0.00 0.00 0.00 2.12
1920 2030 1.369091 GGCAGCCGAGGTGTGTAATG 61.369 60.000 0.00 0.00 33.19 1.90
1934 2044 0.254178 TGAATGGAAGAGGAGGCAGC 59.746 55.000 0.00 0.00 0.00 5.25
1935 2045 1.407989 GGTGAATGGAAGAGGAGGCAG 60.408 57.143 0.00 0.00 0.00 4.85
1936 2046 0.620556 GGTGAATGGAAGAGGAGGCA 59.379 55.000 0.00 0.00 0.00 4.75
1938 2048 2.419297 CGAAGGTGAATGGAAGAGGAGG 60.419 54.545 0.00 0.00 0.00 4.30
1941 2051 2.234908 ACTCGAAGGTGAATGGAAGAGG 59.765 50.000 0.00 0.00 0.00 3.69
1943 2053 2.897326 TGACTCGAAGGTGAATGGAAGA 59.103 45.455 0.00 0.00 0.00 2.87
1946 2056 2.831526 TGATGACTCGAAGGTGAATGGA 59.168 45.455 0.00 0.00 0.00 3.41
1947 2057 3.251479 TGATGACTCGAAGGTGAATGG 57.749 47.619 0.00 0.00 0.00 3.16
1956 2089 3.385193 TGACAGCTTTGATGACTCGAA 57.615 42.857 0.00 0.00 0.00 3.71
1972 2105 2.028112 AGCGCCTCTGAATTAGTTGACA 60.028 45.455 2.29 0.00 0.00 3.58
1973 2106 2.605366 GAGCGCCTCTGAATTAGTTGAC 59.395 50.000 2.29 0.00 0.00 3.18
2013 2146 3.311322 TGTTTGTTAGTCGCCAAAGACAG 59.689 43.478 0.00 0.00 43.24 3.51
2014 2147 3.271729 TGTTTGTTAGTCGCCAAAGACA 58.728 40.909 0.00 0.00 43.24 3.41
2024 2187 3.883489 AGCCCTCTGTTTGTTTGTTAGTC 59.117 43.478 0.00 0.00 0.00 2.59
2027 2190 6.406065 GGTTTTAGCCCTCTGTTTGTTTGTTA 60.406 38.462 0.00 0.00 0.00 2.41
2029 2192 4.142026 GGTTTTAGCCCTCTGTTTGTTTGT 60.142 41.667 0.00 0.00 0.00 2.83
2034 2197 3.222603 ACAGGTTTTAGCCCTCTGTTTG 58.777 45.455 0.00 0.00 35.44 2.93
2035 2198 3.595190 ACAGGTTTTAGCCCTCTGTTT 57.405 42.857 0.00 0.00 35.44 2.83
2036 2199 3.651423 ACTACAGGTTTTAGCCCTCTGTT 59.349 43.478 0.00 0.00 39.16 3.16
2038 2201 3.983044 ACTACAGGTTTTAGCCCTCTG 57.017 47.619 0.00 0.00 0.00 3.35
2039 2202 4.020128 CAGAACTACAGGTTTTAGCCCTCT 60.020 45.833 0.00 0.00 38.41 3.69
2041 2204 3.908103 TCAGAACTACAGGTTTTAGCCCT 59.092 43.478 0.00 0.00 38.41 5.19
2042 2205 4.281898 TCAGAACTACAGGTTTTAGCCC 57.718 45.455 0.00 0.00 38.41 5.19
2043 2206 5.061179 TGTTCAGAACTACAGGTTTTAGCC 58.939 41.667 14.51 0.00 38.41 3.93
2044 2207 5.758784 ACTGTTCAGAACTACAGGTTTTAGC 59.241 40.000 14.51 0.00 44.68 3.09
2045 2208 6.984474 TCACTGTTCAGAACTACAGGTTTTAG 59.016 38.462 14.51 2.15 44.68 1.85
2046 2209 6.880484 TCACTGTTCAGAACTACAGGTTTTA 58.120 36.000 14.51 0.00 44.68 1.52
2047 2210 5.741011 TCACTGTTCAGAACTACAGGTTTT 58.259 37.500 14.51 0.00 44.68 2.43
2051 2214 5.541845 TCAATCACTGTTCAGAACTACAGG 58.458 41.667 14.51 2.88 44.68 4.00
2060 2224 3.340928 TGGAGCATCAATCACTGTTCAG 58.659 45.455 0.00 0.00 36.25 3.02
2073 2237 6.690194 ATTAAGACACAAATCTGGAGCATC 57.310 37.500 0.00 0.00 0.00 3.91
2161 2344 3.806316 ATGACAAGGCGACTAAAAACG 57.194 42.857 0.00 0.00 42.68 3.60
2241 2434 7.002276 TGATCCTGATATTCTGCAATGTTCAT 58.998 34.615 0.00 0.00 0.00 2.57
2352 2549 3.204158 ACCACTGATGCCCCAAATACATA 59.796 43.478 0.00 0.00 0.00 2.29
2356 2553 2.849943 AGTACCACTGATGCCCCAAATA 59.150 45.455 0.00 0.00 0.00 1.40
2371 2568 1.419381 TGTCACTGCCTTGAGTACCA 58.581 50.000 0.00 0.00 0.00 3.25
2388 2585 9.603921 ACTTTGATTTTGATTCAGATGTTTTGT 57.396 25.926 0.00 0.00 0.00 2.83
2484 2698 0.251386 TCACCGACAGAGGAAGCTCT 60.251 55.000 0.00 0.00 34.73 4.09
2530 2744 2.604914 CCACAAATCATCTTCCTCGTCG 59.395 50.000 0.00 0.00 0.00 5.12
2563 2779 1.360551 GCTATCGCCGCTGAAGAGA 59.639 57.895 0.00 0.00 0.00 3.10
2572 2788 2.929531 ACTGATATCTGCTATCGCCG 57.070 50.000 9.35 0.00 39.36 6.46
2598 2814 4.683320 ACCGTTAACGAGCTTTCTTAAGAC 59.317 41.667 28.79 0.00 43.02 3.01
2646 2862 6.299141 ACAGATCAATGTGTTTGTAACTCCT 58.701 36.000 0.00 0.00 36.65 3.69
2658 2874 3.181517 CCGCACTTGTACAGATCAATGTG 60.182 47.826 0.00 0.29 34.56 3.21


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

AutoCloner maintained by Alex Coulton.