Multiple sequence alignment - TraesCS3D01G178000

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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 TraesCS3D01G178000 chr3D 100.000 3218 0 0 1 3218 159614955 159618172 0.000000e+00 5943.0
1 TraesCS3D01G178000 chr3B 88.375 2099 134 42 3 2047 236352259 236354301 0.000000e+00 2423.0
2 TraesCS3D01G178000 chr3B 90.815 1165 62 24 2085 3218 236354375 236355525 0.000000e+00 1517.0
3 TraesCS3D01G178000 chr3A 89.777 1702 65 49 959 2588 185173817 185175481 0.000000e+00 2078.0
4 TraesCS3D01G178000 chr3A 94.064 438 21 2 2782 3217 185175488 185175922 0.000000e+00 660.0
5 TraesCS3D01G178000 chr5A 79.036 477 66 16 49 495 37635708 37635236 2.430000e-76 296.0
6 TraesCS3D01G178000 chr2B 91.163 215 14 4 2705 2916 772141327 772141539 1.460000e-73 287.0
7 TraesCS3D01G178000 chr6A 76.628 522 81 13 2 487 199593248 199592732 1.920000e-62 250.0
8 TraesCS3D01G178000 chr6A 97.059 34 1 0 700 733 133794118 133794085 1.250000e-04 58.4
9 TraesCS3D01G178000 chr4B 100.000 31 0 0 700 730 190167822 190167852 1.250000e-04 58.4
10 TraesCS3D01G178000 chr4B 100.000 31 0 0 700 730 190169560 190169590 1.250000e-04 58.4
11 TraesCS3D01G178000 chr4B 97.059 34 1 0 700 733 622955181 622955148 1.250000e-04 58.4
12 TraesCS3D01G178000 chr4A 97.059 34 1 0 700 733 514807919 514807886 1.250000e-04 58.4
13 TraesCS3D01G178000 chr4A 97.059 34 1 0 700 733 604046358 604046325 1.250000e-04 58.4


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 TraesCS3D01G178000 chr3D 159614955 159618172 3217 False 5943 5943 100.0000 1 3218 1 chr3D.!!$F1 3217
1 TraesCS3D01G178000 chr3B 236352259 236355525 3266 False 1970 2423 89.5950 3 3218 2 chr3B.!!$F1 3215
2 TraesCS3D01G178000 chr3A 185173817 185175922 2105 False 1369 2078 91.9205 959 3217 2 chr3A.!!$F1 2258
3 TraesCS3D01G178000 chr6A 199592732 199593248 516 True 250 250 76.6280 2 487 1 chr6A.!!$R2 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
523 562 0.037697 AATGCTGCGACCTACAACGA 60.038 50.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2370 2524 0.174389 TGGCTCAAGATCAGCTCGTC 59.826 55.0 3.79 0.0 37.05 4.2 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
28 29 4.673298 TGCCACGTACCCGCACAG 62.673 66.667 0.00 0.00 37.70 3.66
32 33 2.028484 ACGTACCCGCACAGTGTG 59.972 61.111 19.27 19.27 37.70 3.82
53 54 1.550524 TGCCTTATCTGCTTGAGTCGT 59.449 47.619 0.00 0.00 0.00 4.34
108 122 0.620556 TCCTCTCCCAAATGAGCCAC 59.379 55.000 0.00 0.00 32.22 5.01
117 131 2.602878 CAAATGAGCCACAGTTCATGC 58.397 47.619 0.00 0.00 42.49 4.06
147 162 2.668212 CGAAAGGAGGCCGCAACA 60.668 61.111 9.31 0.00 0.00 3.33
155 170 2.904866 GGCCGCAACAGGTGTCAA 60.905 61.111 0.00 0.00 0.00 3.18
163 178 0.697854 AACAGGTGTCAAGGGGAGGT 60.698 55.000 0.00 0.00 0.00 3.85
170 185 2.742372 CAAGGGGAGGTTGCGACG 60.742 66.667 0.00 0.00 0.00 5.12
293 332 1.097547 ATCGCATGCTGCTACAACCC 61.098 55.000 17.13 0.00 42.25 4.11
324 363 1.153901 GCTGCAATGCACAATCGCT 60.154 52.632 2.72 0.00 33.79 4.93
327 366 0.314618 TGCAATGCACAATCGCTGTT 59.685 45.000 2.72 0.00 35.47 3.16
405 444 2.680312 TCCATTCACAGCTGAGCTAC 57.320 50.000 23.35 0.00 36.40 3.58
406 445 1.901833 TCCATTCACAGCTGAGCTACA 59.098 47.619 23.35 0.00 36.40 2.74
415 454 1.805945 CTGAGCTACAACCCGCGAC 60.806 63.158 8.23 0.00 0.00 5.19
419 458 2.256158 CTACAACCCGCGACGACA 59.744 61.111 8.23 0.00 0.00 4.35
421 460 2.467946 CTACAACCCGCGACGACAGT 62.468 60.000 8.23 0.43 0.00 3.55
427 466 0.248907 CCCGCGACGACAGTAATGAT 60.249 55.000 8.23 0.00 0.00 2.45
453 492 4.459390 TTGCCGCAACTGTAGTAGATTA 57.541 40.909 0.38 0.00 0.00 1.75
462 501 6.144080 GCAACTGTAGTAGATTATTGCTACGG 59.856 42.308 8.07 8.07 42.28 4.02
466 505 2.029290 AGTAGATTATTGCTACGGCCGG 60.029 50.000 31.76 14.21 42.28 6.13
499 538 6.603237 TTGCTACATCCATTCATTTAGACG 57.397 37.500 0.00 0.00 0.00 4.18
521 560 2.979813 CAAAAATGCTGCGACCTACAAC 59.020 45.455 0.00 0.00 0.00 3.32
523 562 0.037697 AATGCTGCGACCTACAACGA 60.038 50.000 0.00 0.00 0.00 3.85
556 595 4.164252 GGCGACGATGACGACTTT 57.836 55.556 0.00 0.00 42.66 2.66
588 628 6.095432 TGCAACCTTGTTTATGTTTGCTAT 57.905 33.333 5.77 0.00 0.00 2.97
590 630 7.087639 TGCAACCTTGTTTATGTTTGCTATAC 58.912 34.615 5.77 0.00 0.00 1.47
591 631 6.250527 GCAACCTTGTTTATGTTTGCTATACG 59.749 38.462 0.00 0.00 0.00 3.06
594 634 6.877322 ACCTTGTTTATGTTTGCTATACGACT 59.123 34.615 0.00 0.00 0.00 4.18
617 657 2.556622 ACAACGAAATTTGCTACCAGGG 59.443 45.455 0.00 0.00 0.00 4.45
627 667 1.980052 CTACCAGGGAAGGCGAACA 59.020 57.895 0.00 0.00 0.00 3.18
635 675 1.418373 GGAAGGCGAACATGTTTTGC 58.582 50.000 21.83 21.83 0.00 3.68
639 679 0.040425 GGCGAACATGTTTTGCGACT 60.040 50.000 22.57 0.00 0.00 4.18
659 699 3.391296 ACTATCCAAGGTATGTTCCGCAT 59.609 43.478 0.00 0.00 41.42 4.73
696 744 1.433879 CGAGCTTAGGTGGACGAGG 59.566 63.158 0.00 0.00 0.00 4.63
697 745 1.313812 CGAGCTTAGGTGGACGAGGT 61.314 60.000 0.00 0.00 0.00 3.85
843 891 3.417275 CTGACGCGCGGAGATCCTT 62.417 63.158 35.22 10.37 0.00 3.36
887 935 2.569183 CGAAGGAGGAAGACGACCT 58.431 57.895 0.00 0.00 40.80 3.85
888 936 0.171455 CGAAGGAGGAAGACGACCTG 59.829 60.000 0.00 0.00 37.93 4.00
1050 1102 1.344953 TTGTGGTCCTGCACTCCTGT 61.345 55.000 0.00 0.00 0.00 4.00
1178 1230 0.969894 CTGTCCTCGTCCAAACCTCT 59.030 55.000 0.00 0.00 0.00 3.69
1218 1270 2.199535 GGCGGTAGTAGGCCCCTA 59.800 66.667 0.00 0.00 43.64 3.53
1410 1464 1.669440 CGTCGACCCTTTCCCTCAA 59.331 57.895 10.58 0.00 0.00 3.02
1413 1467 0.828762 TCGACCCTTTCCCTCAACGA 60.829 55.000 0.00 0.00 0.00 3.85
1617 1677 3.853330 CGGCGCGTCCATGTTCAG 61.853 66.667 17.57 0.00 34.01 3.02
1618 1678 4.166011 GGCGCGTCCATGTTCAGC 62.166 66.667 8.43 0.00 34.01 4.26
1620 1680 3.112075 CGCGTCCATGTTCAGCGT 61.112 61.111 0.00 0.00 44.96 5.07
1621 1681 2.476051 GCGTCCATGTTCAGCGTG 59.524 61.111 0.00 0.00 0.00 5.34
1663 1732 2.117423 TGGTCCGCAGAGTCCTCA 59.883 61.111 0.00 0.00 0.00 3.86
1666 1735 2.117423 TCCGCAGAGTCCTCACCA 59.883 61.111 0.00 0.00 0.00 4.17
1853 1922 2.152699 CGCTCGTCAGGTAACAGCG 61.153 63.158 0.00 0.00 46.11 5.18
1885 1959 4.216257 CCACTCTGTACAATTTTCACCCAG 59.784 45.833 0.00 0.00 0.00 4.45
1908 1982 3.031013 TCATTACTCGGCTCATCCTTCA 58.969 45.455 0.00 0.00 0.00 3.02
1910 1984 4.101585 TCATTACTCGGCTCATCCTTCAAT 59.898 41.667 0.00 0.00 0.00 2.57
1911 1985 2.611225 ACTCGGCTCATCCTTCAATC 57.389 50.000 0.00 0.00 0.00 2.67
1913 1987 0.469917 TCGGCTCATCCTTCAATCCC 59.530 55.000 0.00 0.00 0.00 3.85
1914 1988 0.181114 CGGCTCATCCTTCAATCCCA 59.819 55.000 0.00 0.00 0.00 4.37
1915 1989 1.685148 GGCTCATCCTTCAATCCCAC 58.315 55.000 0.00 0.00 0.00 4.61
1916 1990 1.213926 GGCTCATCCTTCAATCCCACT 59.786 52.381 0.00 0.00 0.00 4.00
1917 1991 2.570135 GCTCATCCTTCAATCCCACTC 58.430 52.381 0.00 0.00 0.00 3.51
1918 1992 2.172293 GCTCATCCTTCAATCCCACTCT 59.828 50.000 0.00 0.00 0.00 3.24
1919 1993 3.743899 GCTCATCCTTCAATCCCACTCTC 60.744 52.174 0.00 0.00 0.00 3.20
1920 1994 3.710677 CTCATCCTTCAATCCCACTCTCT 59.289 47.826 0.00 0.00 0.00 3.10
1921 1995 4.883759 TCATCCTTCAATCCCACTCTCTA 58.116 43.478 0.00 0.00 0.00 2.43
1922 1996 5.280499 TCATCCTTCAATCCCACTCTCTAA 58.720 41.667 0.00 0.00 0.00 2.10
1923 1997 5.365025 TCATCCTTCAATCCCACTCTCTAAG 59.635 44.000 0.00 0.00 0.00 2.18
1927 2001 2.768527 TCAATCCCACTCTCTAAGCCTG 59.231 50.000 0.00 0.00 0.00 4.85
1949 2037 1.426816 AACATCGATCGCTGCTGCTG 61.427 55.000 18.25 6.38 36.97 4.41
1950 2038 2.965999 ATCGATCGCTGCTGCTGC 60.966 61.111 19.94 19.94 36.97 5.25
1951 2039 3.442512 ATCGATCGCTGCTGCTGCT 62.443 57.895 25.43 10.95 40.48 4.24
1965 2053 1.642037 GCTGCTGCAGATTGCTCGAA 61.642 55.000 32.30 0.00 45.31 3.71
2048 2184 9.570488 CCACTGTCATCTTTTACTAGTTACTAC 57.430 37.037 0.00 0.00 0.00 2.73
2075 2211 4.359434 TCTCGCCTACTAGATCATCTGT 57.641 45.455 0.00 0.00 0.00 3.41
2076 2212 4.320023 TCTCGCCTACTAGATCATCTGTC 58.680 47.826 0.00 0.00 0.00 3.51
2124 2261 1.241315 TGATGAGCTGGACGACGACA 61.241 55.000 0.00 0.00 0.00 4.35
2205 2342 1.378882 CGGACGATAACACGGAGGGA 61.379 60.000 0.00 0.00 37.61 4.20
2319 2473 3.753797 GGGATCGATTCAGATTTTAGGGC 59.246 47.826 5.94 0.00 0.00 5.19
2370 2524 7.946655 TTATTGTCTTATGTAGCTTGATCCG 57.053 36.000 0.00 0.00 0.00 4.18
2452 2639 5.060662 TGCACTATAATGATCCTACTCGC 57.939 43.478 0.00 0.00 0.00 5.03
2645 2835 9.125026 AGTAACTTCCATATAGAGCCAATTTTG 57.875 33.333 0.00 0.00 0.00 2.44
2648 2838 8.000780 ACTTCCATATAGAGCCAATTTTGTTC 57.999 34.615 0.00 0.00 0.00 3.18
2652 2842 9.034800 TCCATATAGAGCCAATTTTGTTCTTTT 57.965 29.630 0.00 0.00 0.00 2.27
2676 2868 2.480416 CGCATAGAAGACCACAGGAGTC 60.480 54.545 0.00 0.00 34.31 3.36
2690 2882 1.281899 GGAGTCATTCCTTCGCGAAG 58.718 55.000 36.06 36.06 43.16 3.79
2722 2914 3.005472 TGAGTATAACGCTAGACCATGCC 59.995 47.826 0.00 0.00 0.00 4.40
2878 3073 5.396324 CCCTTTTTATCCCCAAGCAAATACC 60.396 44.000 0.00 0.00 0.00 2.73
2945 3140 1.228276 GCCAGGCCCTATGCTAACC 60.228 63.158 0.00 0.00 40.92 2.85
3042 3237 2.568623 AACCCTGGCAACTTGAGTAG 57.431 50.000 0.00 0.00 37.61 2.57
3104 3300 2.983166 ACAGCGAACACGTCTATATCG 58.017 47.619 0.00 0.00 36.64 2.92
3110 3306 5.049886 AGCGAACACGTCTATATCGTCATAA 60.050 40.000 0.00 0.00 39.55 1.90
3166 3362 3.495670 TTTGTACAGCAAACGCTTTGT 57.504 38.095 0.00 0.00 41.68 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.675029 ACTGTGCGGGTACGTGGC 62.675 66.667 0.00 0.00 43.45 5.01
28 29 2.417933 CTCAAGCAGATAAGGCACACAC 59.582 50.000 0.00 0.00 0.00 3.82
32 33 1.929836 CGACTCAAGCAGATAAGGCAC 59.070 52.381 0.00 0.00 0.00 5.01
53 54 1.887198 GAAGAAGACGTGTGGAGAGGA 59.113 52.381 0.00 0.00 0.00 3.71
132 146 2.282462 CCTGTTGCGGCCTCCTTT 60.282 61.111 0.00 0.00 0.00 3.11
147 162 2.069165 GCAACCTCCCCTTGACACCT 62.069 60.000 0.00 0.00 0.00 4.00
163 178 0.801872 CATTTCATGGTCCGTCGCAA 59.198 50.000 0.00 0.00 0.00 4.85
395 434 2.266055 GCGGGTTGTAGCTCAGCT 59.734 61.111 3.60 3.60 43.41 4.24
405 444 0.734942 ATTACTGTCGTCGCGGGTTG 60.735 55.000 6.13 0.00 0.00 3.77
406 445 0.734942 CATTACTGTCGTCGCGGGTT 60.735 55.000 6.13 0.00 0.00 4.11
436 475 6.129431 CGTAGCAATAATCTACTACAGTTGCG 60.129 42.308 0.00 0.00 43.63 4.85
499 538 1.068610 TGTAGGTCGCAGCATTTTTGC 60.069 47.619 0.00 0.00 38.18 3.68
521 560 4.883300 GCCGGTCGTAGCTCGTCG 62.883 72.222 1.90 3.62 40.80 5.12
556 595 6.428159 ACATAAACAAGGTTGCAACACAAAAA 59.572 30.769 29.55 10.48 40.82 1.94
564 603 4.764172 AGCAAACATAAACAAGGTTGCAA 58.236 34.783 16.27 0.00 31.16 4.08
576 616 6.034150 CGTTGTCAGTCGTATAGCAAACATAA 59.966 38.462 0.00 0.00 0.00 1.90
588 628 3.805422 AGCAAATTTCGTTGTCAGTCGTA 59.195 39.130 0.00 0.00 0.00 3.43
590 630 3.253371 AGCAAATTTCGTTGTCAGTCG 57.747 42.857 0.00 0.00 0.00 4.18
591 631 4.024387 TGGTAGCAAATTTCGTTGTCAGTC 60.024 41.667 0.00 0.00 0.00 3.51
594 634 3.252215 CCTGGTAGCAAATTTCGTTGTCA 59.748 43.478 0.00 0.00 0.00 3.58
617 657 1.052287 CGCAAAACATGTTCGCCTTC 58.948 50.000 21.02 5.62 0.00 3.46
627 667 3.686016 ACCTTGGATAGTCGCAAAACAT 58.314 40.909 0.00 0.00 0.00 2.71
635 675 3.639538 CGGAACATACCTTGGATAGTCG 58.360 50.000 0.00 0.00 0.00 4.18
639 679 4.133820 CAATGCGGAACATACCTTGGATA 58.866 43.478 0.00 0.00 38.34 2.59
676 724 2.005960 CTCGTCCACCTAAGCTCGGG 62.006 65.000 6.92 5.32 0.00 5.14
677 725 1.433879 CTCGTCCACCTAAGCTCGG 59.566 63.158 0.00 0.00 0.00 4.63
683 731 0.541063 TGCTCACCTCGTCCACCTAA 60.541 55.000 0.00 0.00 0.00 2.69
809 857 4.218578 AGCCGCCTCATGCTCGAG 62.219 66.667 8.45 8.45 38.05 4.04
871 919 1.545706 GCCAGGTCGTCTTCCTCCTT 61.546 60.000 0.00 0.00 32.37 3.36
872 920 1.985116 GCCAGGTCGTCTTCCTCCT 60.985 63.158 0.00 0.00 32.37 3.69
873 921 2.579738 GCCAGGTCGTCTTCCTCC 59.420 66.667 0.00 0.00 32.37 4.30
874 922 2.579738 GGCCAGGTCGTCTTCCTC 59.420 66.667 0.00 0.00 32.37 3.71
875 923 3.382832 CGGCCAGGTCGTCTTCCT 61.383 66.667 4.87 0.00 35.45 3.36
946 994 2.642700 CGGCCGGTCCAACTTTTG 59.357 61.111 20.10 0.00 34.01 2.44
947 995 2.596338 CCGGCCGGTCCAACTTTT 60.596 61.111 36.64 0.00 34.01 2.27
969 1017 0.039035 AAAAAGGGCGATGGTAGGCA 59.961 50.000 0.00 0.00 35.71 4.75
1030 1082 0.179020 CAGGAGTGCAGGACCACAAA 60.179 55.000 0.00 0.00 38.18 2.83
1178 1230 3.535629 CTGTTCTGCAGGGCACGGA 62.536 63.158 15.13 0.00 41.42 4.69
1381 1433 3.097728 GTCGACGCACTGGACACG 61.098 66.667 0.00 0.00 0.00 4.49
1382 1434 2.733593 GGTCGACGCACTGGACAC 60.734 66.667 9.92 0.00 32.39 3.67
1388 1440 2.342648 GGAAAGGGTCGACGCACT 59.657 61.111 31.03 18.85 0.00 4.40
1410 1464 1.403814 ACACCCGATCAGATCATCGT 58.596 50.000 11.12 0.21 43.53 3.73
1413 1467 3.634397 AACAACACCCGATCAGATCAT 57.366 42.857 11.12 0.00 0.00 2.45
1618 1678 2.811317 GAGTCAGAAGGCGCCACG 60.811 66.667 31.54 13.77 0.00 4.94
1620 1680 3.303135 ACGAGTCAGAAGGCGCCA 61.303 61.111 31.54 3.61 0.00 5.69
1621 1681 2.811317 CACGAGTCAGAAGGCGCC 60.811 66.667 21.89 21.89 0.00 6.53
1623 1683 2.811317 GCCACGAGTCAGAAGGCG 60.811 66.667 0.00 0.00 35.42 5.52
1624 1684 1.739562 CAGCCACGAGTCAGAAGGC 60.740 63.158 0.00 0.00 45.54 4.35
1625 1685 1.739562 GCAGCCACGAGTCAGAAGG 60.740 63.158 0.00 0.00 0.00 3.46
1626 1686 1.013005 CAGCAGCCACGAGTCAGAAG 61.013 60.000 0.00 0.00 0.00 2.85
1627 1687 1.005748 CAGCAGCCACGAGTCAGAA 60.006 57.895 0.00 0.00 0.00 3.02
1628 1688 2.203082 ACAGCAGCCACGAGTCAGA 61.203 57.895 0.00 0.00 0.00 3.27
1663 1732 1.741732 GCTCAGCTCGATGAACATGGT 60.742 52.381 0.00 0.00 0.00 3.55
1666 1735 1.150567 GCGCTCAGCTCGATGAACAT 61.151 55.000 0.00 0.00 44.04 2.71
1718 1787 3.909258 AACAGCACGTACGCCTCCG 62.909 63.158 16.72 2.88 41.14 4.63
1853 1922 2.646175 TACAGAGTGGAGTGGCGGC 61.646 63.158 0.00 0.00 0.00 6.53
1885 1959 3.951775 AGGATGAGCCGAGTAATGATC 57.048 47.619 0.00 0.00 43.43 2.92
1908 1982 1.488393 GCAGGCTTAGAGAGTGGGATT 59.512 52.381 0.00 0.00 0.00 3.01
1910 1984 0.252239 TGCAGGCTTAGAGAGTGGGA 60.252 55.000 0.00 0.00 0.00 4.37
1911 1985 0.615331 TTGCAGGCTTAGAGAGTGGG 59.385 55.000 0.00 0.00 0.00 4.61
1913 1987 2.771089 TGTTTGCAGGCTTAGAGAGTG 58.229 47.619 0.00 0.00 0.00 3.51
1914 1988 3.604582 GATGTTTGCAGGCTTAGAGAGT 58.395 45.455 0.00 0.00 0.00 3.24
1915 1989 2.606725 CGATGTTTGCAGGCTTAGAGAG 59.393 50.000 0.00 0.00 0.00 3.20
1916 1990 2.233676 TCGATGTTTGCAGGCTTAGAGA 59.766 45.455 0.00 0.00 0.00 3.10
1917 1991 2.621338 TCGATGTTTGCAGGCTTAGAG 58.379 47.619 0.00 0.00 0.00 2.43
1918 1992 2.760634 TCGATGTTTGCAGGCTTAGA 57.239 45.000 0.00 0.00 0.00 2.10
1919 1993 2.033407 CGATCGATGTTTGCAGGCTTAG 60.033 50.000 10.26 0.00 0.00 2.18
1920 1994 1.933181 CGATCGATGTTTGCAGGCTTA 59.067 47.619 10.26 0.00 0.00 3.09
1921 1995 0.729116 CGATCGATGTTTGCAGGCTT 59.271 50.000 10.26 0.00 0.00 4.35
1922 1996 1.709147 GCGATCGATGTTTGCAGGCT 61.709 55.000 21.57 0.00 0.00 4.58
1923 1997 1.297893 GCGATCGATGTTTGCAGGC 60.298 57.895 21.57 0.00 0.00 4.85
1927 2001 0.588233 CAGCAGCGATCGATGTTTGC 60.588 55.000 31.33 22.64 33.56 3.68
1965 2053 1.547223 GCATTGGGATAGCTCCAGCAT 60.547 52.381 0.48 0.00 44.08 3.79
2048 2184 5.635417 TGATCTAGTAGGCGAGATGAATG 57.365 43.478 0.00 0.00 37.23 2.67
2057 2193 2.413502 GCGACAGATGATCTAGTAGGCG 60.414 54.545 1.78 1.78 0.00 5.52
2075 2211 1.080501 CAACCAAGAGCTCTCGCGA 60.081 57.895 18.55 9.26 42.32 5.87
2076 2212 0.459237 ATCAACCAAGAGCTCTCGCG 60.459 55.000 18.55 9.81 42.32 5.87
2086 2223 2.353610 GCCCCTGCCATCAACCAAG 61.354 63.158 0.00 0.00 0.00 3.61
2205 2342 2.087646 GAGCCGCTTCATTCTTCCTTT 58.912 47.619 0.00 0.00 0.00 3.11
2319 2473 1.601663 GCTCAGTCGATCTTGATCCGG 60.602 57.143 0.00 0.00 0.00 5.14
2365 2519 1.335182 TCAAGATCAGCTCGTCGGATC 59.665 52.381 3.38 3.38 43.76 3.36
2366 2520 1.336440 CTCAAGATCAGCTCGTCGGAT 59.664 52.381 0.00 0.00 32.20 4.18
2367 2521 0.735471 CTCAAGATCAGCTCGTCGGA 59.265 55.000 0.00 0.00 0.00 4.55
2369 2523 0.869454 GGCTCAAGATCAGCTCGTCG 60.869 60.000 3.79 0.00 37.05 5.12
2370 2524 0.174389 TGGCTCAAGATCAGCTCGTC 59.826 55.000 3.79 0.00 37.05 4.20
2426 2613 7.380870 GCGAGTAGGATCATTATAGTGCATATG 59.619 40.741 0.00 0.00 0.00 1.78
2498 2687 5.034152 CACGTGCACTACAAAAATGTTTCT 58.966 37.500 16.19 0.00 0.00 2.52
2514 2703 2.512745 AACGCTTGACCACGTGCA 60.513 55.556 10.91 0.00 42.68 4.57
2613 2803 8.585881 TGGCTCTATATGGAAGTTACTATTGAC 58.414 37.037 0.00 0.00 0.00 3.18
2627 2817 9.657419 AAAAAGAACAAAATTGGCTCTATATGG 57.343 29.630 0.00 0.00 0.00 2.74
2652 2842 2.565391 TCCTGTGGTCTTCTATGCGAAA 59.435 45.455 0.00 0.00 0.00 3.46
2676 2868 2.415168 TGTAAAGCTTCGCGAAGGAATG 59.585 45.455 40.64 22.85 38.80 2.67
2685 2877 1.137513 ACTCACGTGTAAAGCTTCGC 58.862 50.000 16.51 0.00 0.00 4.70
2686 2878 5.275142 CGTTATACTCACGTGTAAAGCTTCG 60.275 44.000 16.51 0.82 30.09 3.79
2690 2882 3.855950 AGCGTTATACTCACGTGTAAAGC 59.144 43.478 19.52 19.52 45.38 3.51
2695 2887 3.064545 GGTCTAGCGTTATACTCACGTGT 59.935 47.826 16.51 0.00 39.92 4.49
2696 2888 3.064408 TGGTCTAGCGTTATACTCACGTG 59.936 47.826 9.94 9.94 39.92 4.49
2700 2892 3.005472 GGCATGGTCTAGCGTTATACTCA 59.995 47.826 0.00 0.00 0.00 3.41
2710 2902 2.691409 TGTAACAGGCATGGTCTAGC 57.309 50.000 2.31 0.00 0.00 3.42
2785 2978 1.384502 CCTGGGTCTAGGGGCATCA 60.385 63.158 0.00 0.00 34.06 3.07
2907 3102 2.486592 GCCACGTACCATATTAATGCCC 59.513 50.000 0.00 0.00 0.00 5.36
2945 3140 2.743664 TCTTTGAGCCGACAACATGATG 59.256 45.455 0.00 0.00 0.00 3.07
3042 3237 4.628074 TCGCTGTATAGGTTGGCTAAATC 58.372 43.478 0.00 0.00 0.00 2.17
3104 3300 9.095065 AGATTTATACACCAACGTCTTTATGAC 57.905 33.333 0.00 0.00 42.06 3.06
3110 3306 9.095065 GTTATGAGATTTATACACCAACGTCTT 57.905 33.333 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.