Multiple sequence alignment - TraesCS1B01G179600

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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 TraesCS1B01G179600 chr1B 100.000 2887 0 0 1 2887 325819650 325816764 0 5332
1 TraesCS1B01G179600 chr1A 88.813 1752 144 27 113 1846 292076101 292077818 0 2102
2 TraesCS1B01G179600 chr1A 97.639 847 10 4 2045 2887 292078162 292079002 0 1445
3 TraesCS1B01G179600 chr1D 86.000 1600 108 52 469 1993 225711598 225710040 0 1607
4 TraesCS1B01G179600 chr1D 94.784 901 23 8 2007 2887 225709935 225709039 0 1382
5 TraesCS1B01G179600 chr1D 92.308 741 45 9 6 744 225712334 225711604 0 1042


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 TraesCS1B01G179600 chr1B 325816764 325819650 2886 True 5332.000000 5332 100.000000 1 2887 1 chr1B.!!$R1 2886
1 TraesCS1B01G179600 chr1A 292076101 292079002 2901 False 1773.500000 2102 93.226000 113 2887 2 chr1A.!!$F1 2774
2 TraesCS1B01G179600 chr1D 225709039 225712334 3295 True 1343.666667 1607 91.030667 6 2887 3 chr1D.!!$R1 2881

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
846 1154 0.039798 TACAACAGACTCCACGACGC 60.040 55.0 0.0 0.0 0.00 5.19 F
1466 1818 0.181114 TCACTTGCTCAACAGCCTGT 59.819 50.0 0.0 0.0 46.26 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1661 2022 0.251474 TCCAAGCTTGCCATTCAGCT 60.251 50.0 21.43 0.0 39.55 4.24 R
2389 2983 0.391661 TGATCCTGAACAAGCTCGCC 60.392 55.0 0.00 0.0 0.00 5.54 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
22 23 3.855379 TGCTACACATACGAAAGCTTACG 59.145 43.478 0.00 0.00 34.28 3.18
67 68 1.076265 GGAGGTGGGTAATTGGGCC 60.076 63.158 0.00 0.00 0.00 5.80
175 178 5.602978 AGTAGGTGTAGGATTATTGGGACAG 59.397 44.000 0.00 0.00 42.39 3.51
339 342 2.249844 TTTGGAGGTTCCGAACAGAC 57.750 50.000 13.23 3.02 40.17 3.51
451 454 1.708551 CAAGACCCAAGACCCCCTTTA 59.291 52.381 0.00 0.00 31.42 1.85
453 456 1.709115 AGACCCAAGACCCCCTTTAAC 59.291 52.381 0.00 0.00 31.42 2.01
460 463 4.018779 CCAAGACCCCCTTTAACAGTATCA 60.019 45.833 0.00 0.00 31.42 2.15
470 473 6.929606 CCCTTTAACAGTATCAGCATACCTAC 59.070 42.308 0.00 0.00 36.26 3.18
504 507 3.966979 TCATGCCAAAGCTTGATCCTTA 58.033 40.909 0.00 0.00 45.37 2.69
521 524 2.500098 CCTTAGATTTCGAGGGGTCACA 59.500 50.000 0.00 0.00 0.00 3.58
583 586 8.043113 AGCTGATCAACACTATGAGAAATTGTA 58.957 33.333 0.00 0.00 31.76 2.41
611 614 7.004086 TCCCTTTATTCAGTCTTGTTGTCATT 58.996 34.615 0.00 0.00 0.00 2.57
669 952 1.961394 ACAGCTTGACTACTTCCACGA 59.039 47.619 0.00 0.00 0.00 4.35
670 953 2.288273 ACAGCTTGACTACTTCCACGAC 60.288 50.000 0.00 0.00 0.00 4.34
671 954 1.272769 AGCTTGACTACTTCCACGACC 59.727 52.381 0.00 0.00 0.00 4.79
672 955 1.672145 GCTTGACTACTTCCACGACCC 60.672 57.143 0.00 0.00 0.00 4.46
688 971 1.966451 CCCCCGCGATTGCTTATCC 60.966 63.158 8.23 0.00 39.65 2.59
692 975 1.676006 CCCGCGATTGCTTATCCTTTT 59.324 47.619 8.23 0.00 39.65 2.27
696 994 3.706698 GCGATTGCTTATCCTTTTTCCC 58.293 45.455 0.00 0.00 38.39 3.97
697 995 3.130340 GCGATTGCTTATCCTTTTTCCCA 59.870 43.478 0.00 0.00 38.39 4.37
698 996 4.672409 CGATTGCTTATCCTTTTTCCCAC 58.328 43.478 0.00 0.00 0.00 4.61
699 997 4.399303 CGATTGCTTATCCTTTTTCCCACT 59.601 41.667 0.00 0.00 0.00 4.00
707 1005 4.335400 TCCTTTTTCCCACTCAAATTGC 57.665 40.909 0.00 0.00 0.00 3.56
740 1038 3.213206 TGATATGGTTGAGGGCATGTC 57.787 47.619 0.00 0.00 0.00 3.06
751 1049 0.819582 GGGCATGTCAACCATCCAAG 59.180 55.000 0.00 0.00 0.00 3.61
757 1055 3.786368 TGTCAACCATCCAAGACATCA 57.214 42.857 0.00 0.00 36.20 3.07
773 1071 4.037208 AGACATCAATGCCGAAATTCATCC 59.963 41.667 0.00 0.00 0.00 3.51
774 1072 3.243168 ACATCAATGCCGAAATTCATCCG 60.243 43.478 0.00 0.00 0.00 4.18
818 1126 3.748083 AGTTCTGTTCAGACATGCATGT 58.252 40.909 31.82 31.82 45.16 3.21
834 1142 3.195610 TGCATGTCCTAGTCCTACAACAG 59.804 47.826 0.00 0.00 0.00 3.16
839 1147 3.695556 GTCCTAGTCCTACAACAGACTCC 59.304 52.174 0.00 0.00 42.31 3.85
840 1148 3.332783 TCCTAGTCCTACAACAGACTCCA 59.667 47.826 0.00 0.00 42.31 3.86
842 1150 1.887198 AGTCCTACAACAGACTCCACG 59.113 52.381 0.00 0.00 39.08 4.94
845 1153 1.401148 CCTACAACAGACTCCACGACG 60.401 57.143 0.00 0.00 0.00 5.12
846 1154 0.039798 TACAACAGACTCCACGACGC 60.040 55.000 0.00 0.00 0.00 5.19
848 1156 1.007271 AACAGACTCCACGACGCTG 60.007 57.895 0.00 0.00 0.00 5.18
859 1167 0.601558 ACGACGCTGTCACACCTATT 59.398 50.000 0.00 0.00 32.09 1.73
884 1192 5.753744 CATTTGCATGCAAACACAAAGATT 58.246 33.333 40.10 22.62 46.80 2.40
917 1225 0.817634 CCGTGGAACCAGCTCACAAA 60.818 55.000 3.70 0.00 0.00 2.83
1007 1315 2.697751 CCAGACCCTCTAGAACCATCAG 59.302 54.545 0.00 0.00 0.00 2.90
1085 1403 2.620459 CACGACACACACAGCACG 59.380 61.111 0.00 0.00 0.00 5.34
1435 1783 2.743928 CAACTGCGGAGGTGAGCC 60.744 66.667 18.26 0.00 39.56 4.70
1440 1788 3.461773 GCGGAGGTGAGCCAGCTA 61.462 66.667 6.85 0.00 42.53 3.32
1456 1804 0.726256 GCTAGCTGCTTCACTTGCTC 59.274 55.000 7.79 0.00 38.95 4.26
1466 1818 0.181114 TCACTTGCTCAACAGCCTGT 59.819 50.000 0.00 0.00 46.26 4.00
1473 1825 2.026915 TGCTCAACAGCCTGTACATGAT 60.027 45.455 0.00 0.00 46.26 2.45
1500 1852 0.537188 AGACTGACATGCTTACCCCG 59.463 55.000 0.00 0.00 0.00 5.73
1504 1856 1.377987 GACATGCTTACCCCGCCAA 60.378 57.895 0.00 0.00 0.00 4.52
1506 1858 0.324275 ACATGCTTACCCCGCCAAAT 60.324 50.000 0.00 0.00 0.00 2.32
1508 1860 0.823460 ATGCTTACCCCGCCAAATTG 59.177 50.000 0.00 0.00 0.00 2.32
1509 1861 1.153647 GCTTACCCCGCCAAATTGC 60.154 57.895 0.00 0.00 0.00 3.56
1528 1880 1.666189 GCGCTAGTCCATTCAAACCTC 59.334 52.381 0.00 0.00 0.00 3.85
1531 1883 3.274288 GCTAGTCCATTCAAACCTCAGG 58.726 50.000 0.00 0.00 0.00 3.86
1541 1893 4.286297 TCAAACCTCAGGGAACTACATG 57.714 45.455 0.00 0.00 40.21 3.21
1543 1897 4.841813 TCAAACCTCAGGGAACTACATGTA 59.158 41.667 5.25 5.25 40.21 2.29
1547 1901 4.900054 ACCTCAGGGAACTACATGTATACC 59.100 45.833 5.91 9.79 40.21 2.73
1548 1902 4.899457 CCTCAGGGAACTACATGTATACCA 59.101 45.833 5.91 0.00 40.21 3.25
1551 1905 4.899457 CAGGGAACTACATGTATACCAGGA 59.101 45.833 5.91 0.00 40.21 3.86
1564 1918 9.823647 CATGTATACCAGGATTACTATTCATCC 57.176 37.037 0.00 0.00 39.59 3.51
1565 1919 8.966155 TGTATACCAGGATTACTATTCATCCA 57.034 34.615 0.00 0.00 41.51 3.41
1566 1920 9.387397 TGTATACCAGGATTACTATTCATCCAA 57.613 33.333 0.00 0.00 41.51 3.53
1572 1926 8.917088 CCAGGATTACTATTCATCCAAAAATGT 58.083 33.333 1.17 0.00 41.51 2.71
1581 1935 4.062293 TCATCCAAAAATGTCGTTCGAGT 58.938 39.130 0.00 0.00 0.00 4.18
1610 1968 9.886132 ATTATTCTAAGTAACAGTTGAACCGAT 57.114 29.630 0.00 0.00 0.00 4.18
1651 2012 1.480137 AGGATCGAAGGTCTGAAGCAG 59.520 52.381 0.00 0.00 0.00 4.24
1661 2022 1.073722 CTGAAGCAGGAACAGGCCA 59.926 57.895 5.01 0.00 0.00 5.36
1700 2061 1.065358 TAACGTAAGCAGCGCAGTTC 58.935 50.000 11.47 0.00 45.62 3.01
1744 2106 2.093447 GTCCTGGTCAACTCATAGGTGG 60.093 54.545 0.00 0.00 32.64 4.61
1768 2130 3.056313 GCCGGAGCACAAGGAATGC 62.056 63.158 5.05 0.00 43.74 3.56
1790 2152 1.702182 TGCCATTCAGTTGCTGGAAA 58.298 45.000 5.17 0.00 31.38 3.13
1825 2187 4.435425 TGTACTTTGACTACGTTGCAACT 58.565 39.130 26.09 15.70 0.00 3.16
1839 2201 2.566952 GCAACTTGTTGCAAGACTGT 57.433 45.000 27.19 0.00 46.60 3.55
1901 2263 2.301870 ACGTTGCAACTTCCCTGATAGA 59.698 45.455 26.09 0.00 0.00 1.98
1902 2264 2.932614 CGTTGCAACTTCCCTGATAGAG 59.067 50.000 26.09 3.12 0.00 2.43
1903 2265 3.617531 CGTTGCAACTTCCCTGATAGAGT 60.618 47.826 26.09 0.00 0.00 3.24
1904 2266 4.381612 CGTTGCAACTTCCCTGATAGAGTA 60.382 45.833 26.09 0.00 0.00 2.59
1905 2267 5.675538 GTTGCAACTTCCCTGATAGAGTAT 58.324 41.667 22.36 0.00 0.00 2.12
1907 2269 7.272978 GTTGCAACTTCCCTGATAGAGTATTA 58.727 38.462 22.36 0.00 0.00 0.98
1908 2270 6.817184 TGCAACTTCCCTGATAGAGTATTAC 58.183 40.000 0.00 0.00 0.00 1.89
1993 2448 8.523523 TGTGCAGATTCATCAAAACAATTTAG 57.476 30.769 0.00 0.00 0.00 1.85
1995 2450 9.362539 GTGCAGATTCATCAAAACAATTTAGAT 57.637 29.630 0.00 0.00 0.00 1.98
1996 2451 9.361315 TGCAGATTCATCAAAACAATTTAGATG 57.639 29.630 0.00 0.00 36.48 2.90
1997 2452 8.325997 GCAGATTCATCAAAACAATTTAGATGC 58.674 33.333 0.00 0.00 35.87 3.91
1998 2453 8.814235 CAGATTCATCAAAACAATTTAGATGCC 58.186 33.333 0.00 0.00 35.87 4.40
1999 2454 8.533657 AGATTCATCAAAACAATTTAGATGCCA 58.466 29.630 0.00 0.00 35.87 4.92
2000 2455 9.153721 GATTCATCAAAACAATTTAGATGCCAA 57.846 29.630 0.00 0.00 35.87 4.52
2001 2456 8.899427 TTCATCAAAACAATTTAGATGCCAAA 57.101 26.923 0.00 0.00 35.87 3.28
2002 2457 8.899427 TCATCAAAACAATTTAGATGCCAAAA 57.101 26.923 0.00 0.00 35.87 2.44
2003 2458 9.334947 TCATCAAAACAATTTAGATGCCAAAAA 57.665 25.926 0.00 0.00 35.87 1.94
2004 2459 9.384682 CATCAAAACAATTTAGATGCCAAAAAC 57.615 29.630 0.00 0.00 32.55 2.43
2017 2571 7.322664 AGATGCCAAAAACCTACAAACATATG 58.677 34.615 0.00 0.00 0.00 1.78
2043 2597 3.067180 ACACAGAAGACAAAATGGCACTG 59.933 43.478 0.00 8.23 37.80 3.66
2164 2738 4.166144 CCCCCAGTGGAAGAACTATACAAT 59.834 45.833 11.95 0.00 35.39 2.71
2184 2762 1.375396 CGCCCTCCACGAATCACAA 60.375 57.895 0.00 0.00 0.00 3.33
2302 2896 4.159506 TCACCATCATCATACACTCACGAA 59.840 41.667 0.00 0.00 0.00 3.85
2332 2926 3.267233 TTGAGCCTGCCCCACCAT 61.267 61.111 0.00 0.00 0.00 3.55
2371 2965 4.373116 GAGGACTCGTTGCCGCCA 62.373 66.667 0.00 0.00 0.00 5.69
2372 2966 4.681978 AGGACTCGTTGCCGCCAC 62.682 66.667 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.855379 CGTAAGCTTTCGTATGTGTAGCA 59.145 43.478 16.37 0.00 34.37 3.49
1 2 3.855950 ACGTAAGCTTTCGTATGTGTAGC 59.144 43.478 26.72 0.00 45.62 3.58
2 3 5.090757 TCACGTAAGCTTTCGTATGTGTAG 58.909 41.667 27.23 15.07 41.65 2.74
3 4 5.045668 TCACGTAAGCTTTCGTATGTGTA 57.954 39.130 27.23 9.11 41.65 2.90
4 5 3.904571 TCACGTAAGCTTTCGTATGTGT 58.095 40.909 27.23 4.64 41.65 3.72
8 9 2.165845 AGCCTCACGTAAGCTTTCGTAT 59.834 45.455 27.23 6.78 45.62 3.06
67 68 1.377994 GGCCCCATCTGCTATCCTG 59.622 63.158 0.00 0.00 0.00 3.86
185 188 1.167851 TACTCACGTTCGGTACCTGG 58.832 55.000 10.90 0.00 0.00 4.45
186 189 2.995466 TTACTCACGTTCGGTACCTG 57.005 50.000 10.90 3.80 0.00 4.00
226 229 4.202161 CCAAGCAAGGTGTCTCGTATATCT 60.202 45.833 0.00 0.00 0.00 1.98
265 268 9.690913 TCTAGATAGTTAGTTAGTTGCACCTTA 57.309 33.333 0.00 0.00 0.00 2.69
268 271 9.250624 CAATCTAGATAGTTAGTTAGTTGCACC 57.749 37.037 5.46 0.00 0.00 5.01
285 288 3.324556 GGAGCCTCTGAAGCAATCTAGAT 59.675 47.826 0.00 0.00 0.00 1.98
320 323 1.539496 CGTCTGTTCGGAACCTCCAAA 60.539 52.381 17.62 0.00 35.91 3.28
339 342 5.317733 AGTCCTAACTCTCTTCACATTCG 57.682 43.478 0.00 0.00 0.00 3.34
427 430 0.250770 GGGGTCTTGGGTCTTGTGAC 60.251 60.000 0.00 0.00 42.22 3.67
451 454 4.888239 AGTCGTAGGTATGCTGATACTGTT 59.112 41.667 0.00 0.00 35.63 3.16
453 456 4.377533 CGAGTCGTAGGTATGCTGATACTG 60.378 50.000 3.82 0.00 35.63 2.74
460 463 2.355132 CACTTCGAGTCGTAGGTATGCT 59.645 50.000 21.16 0.00 0.00 3.79
470 473 1.203928 GGCATGATCACTTCGAGTCG 58.796 55.000 6.09 6.09 0.00 4.18
504 507 2.552373 GGTTTGTGACCCCTCGAAATCT 60.552 50.000 0.00 0.00 43.06 2.40
521 524 5.835280 AGATGTTGAGTTTGGAAGATGGTTT 59.165 36.000 0.00 0.00 0.00 3.27
669 952 1.227853 GATAAGCAATCGCGGGGGT 60.228 57.895 6.13 0.00 45.49 4.95
670 953 1.966451 GGATAAGCAATCGCGGGGG 60.966 63.158 6.13 0.00 45.49 5.40
671 954 0.535102 AAGGATAAGCAATCGCGGGG 60.535 55.000 6.13 0.00 45.49 5.73
672 955 1.308998 AAAGGATAAGCAATCGCGGG 58.691 50.000 6.13 0.00 45.49 6.13
688 971 2.476241 GCGCAATTTGAGTGGGAAAAAG 59.524 45.455 0.30 0.00 0.00 2.27
692 975 1.035923 TTGCGCAATTTGAGTGGGAA 58.964 45.000 21.02 0.00 0.00 3.97
696 994 8.593842 TCATTATTTATTTGCGCAATTTGAGTG 58.406 29.630 25.64 15.40 0.00 3.51
697 995 8.700722 TCATTATTTATTTGCGCAATTTGAGT 57.299 26.923 25.64 10.63 0.00 3.41
707 1005 9.345517 CCTCAACCATATCATTATTTATTTGCG 57.654 33.333 0.00 0.00 0.00 4.85
740 1038 3.429822 GGCATTGATGTCTTGGATGGTTG 60.430 47.826 0.00 0.00 0.00 3.77
743 1041 1.335810 CGGCATTGATGTCTTGGATGG 59.664 52.381 0.00 0.00 0.00 3.51
751 1049 4.293415 GGATGAATTTCGGCATTGATGTC 58.707 43.478 0.00 0.00 0.00 3.06
809 1107 3.374764 TGTAGGACTAGGACATGCATGT 58.625 45.455 31.82 31.82 45.16 3.21
818 1126 3.332783 TGGAGTCTGTTGTAGGACTAGGA 59.667 47.826 0.00 0.00 42.06 2.94
819 1127 3.444388 GTGGAGTCTGTTGTAGGACTAGG 59.556 52.174 0.00 0.00 42.06 3.02
821 1129 3.079578 CGTGGAGTCTGTTGTAGGACTA 58.920 50.000 0.00 0.00 42.06 2.59
822 1130 1.887198 CGTGGAGTCTGTTGTAGGACT 59.113 52.381 0.00 0.00 44.29 3.85
824 1132 1.884579 GTCGTGGAGTCTGTTGTAGGA 59.115 52.381 0.00 0.00 0.00 2.94
825 1133 1.401148 CGTCGTGGAGTCTGTTGTAGG 60.401 57.143 0.00 0.00 0.00 3.18
834 1142 1.729838 GTGACAGCGTCGTGGAGTC 60.730 63.158 0.00 0.00 34.95 3.36
839 1147 0.109272 ATAGGTGTGACAGCGTCGTG 60.109 55.000 9.30 0.00 36.92 4.35
840 1148 0.601558 AATAGGTGTGACAGCGTCGT 59.398 50.000 9.30 0.00 36.92 4.34
842 1150 0.721718 GCAATAGGTGTGACAGCGTC 59.278 55.000 9.30 2.32 36.92 5.19
845 1153 3.504863 CAAATGCAATAGGTGTGACAGC 58.495 45.455 6.68 6.68 0.00 4.40
846 1154 3.504863 GCAAATGCAATAGGTGTGACAG 58.495 45.455 0.00 0.00 41.59 3.51
884 1192 2.280524 ACGGTGCGTGCTTGCTTA 60.281 55.556 2.56 0.00 39.18 3.09
917 1225 0.176219 CGGCCATGGAAATGCAATGT 59.824 50.000 18.40 0.00 0.00 2.71
1007 1315 3.827722 TGCCTTGGGTATTTATAGTGCC 58.172 45.455 0.00 0.00 0.00 5.01
1085 1403 4.770874 TCCCTTTACGCCGCTGCC 62.771 66.667 0.00 0.00 0.00 4.85
1136 1454 4.082523 GCCACCGCAGTCAGGCTA 62.083 66.667 0.00 0.00 43.70 3.93
1440 1788 0.950116 GTTGAGCAAGTGAAGCAGCT 59.050 50.000 0.00 0.00 40.60 4.24
1454 1802 4.256110 TCAATCATGTACAGGCTGTTGAG 58.744 43.478 27.24 12.27 0.00 3.02
1456 1804 4.456911 AGTTCAATCATGTACAGGCTGTTG 59.543 41.667 27.24 18.07 29.93 3.33
1466 1818 6.345096 TGTCAGTCTCAGTTCAATCATGTA 57.655 37.500 0.00 0.00 0.00 2.29
1473 1825 3.758755 AGCATGTCAGTCTCAGTTCAA 57.241 42.857 0.00 0.00 0.00 2.69
1500 1852 0.740737 ATGGACTAGCGCAATTTGGC 59.259 50.000 11.47 0.00 0.00 4.52
1504 1856 3.119495 GGTTTGAATGGACTAGCGCAATT 60.119 43.478 11.47 0.00 0.00 2.32
1506 1858 1.810151 GGTTTGAATGGACTAGCGCAA 59.190 47.619 11.47 0.00 0.00 4.85
1508 1860 1.666189 GAGGTTTGAATGGACTAGCGC 59.334 52.381 0.00 0.00 0.00 5.92
1509 1861 2.932614 CTGAGGTTTGAATGGACTAGCG 59.067 50.000 0.00 0.00 0.00 4.26
1516 1868 3.160679 AGTTCCCTGAGGTTTGAATGG 57.839 47.619 0.00 0.00 0.00 3.16
1528 1880 4.899457 TCCTGGTATACATGTAGTTCCCTG 59.101 45.833 11.91 10.92 0.00 4.45
1531 1883 8.191534 AGTAATCCTGGTATACATGTAGTTCC 57.808 38.462 11.91 12.85 0.00 3.62
1547 1901 9.956720 GACATTTTTGGATGAATAGTAATCCTG 57.043 33.333 8.05 0.35 42.51 3.86
1548 1902 8.840321 CGACATTTTTGGATGAATAGTAATCCT 58.160 33.333 8.05 0.00 42.51 3.24
1558 1912 4.513692 ACTCGAACGACATTTTTGGATGAA 59.486 37.500 0.00 0.00 0.00 2.57
1564 1918 8.434870 AATAATGAACTCGAACGACATTTTTG 57.565 30.769 13.55 0.00 33.99 2.44
1565 1919 8.504005 AGAATAATGAACTCGAACGACATTTTT 58.496 29.630 13.55 12.28 33.99 1.94
1566 1920 8.029642 AGAATAATGAACTCGAACGACATTTT 57.970 30.769 13.55 6.54 33.99 1.82
1567 1921 7.596749 AGAATAATGAACTCGAACGACATTT 57.403 32.000 13.55 1.89 33.99 2.32
1568 1922 8.697846 TTAGAATAATGAACTCGAACGACATT 57.302 30.769 13.11 13.11 35.73 2.71
1572 1926 9.282247 GTTACTTAGAATAATGAACTCGAACGA 57.718 33.333 0.00 0.00 0.00 3.85
1600 1958 3.553917 CCCAAAACACAAATCGGTTCAAC 59.446 43.478 0.00 0.00 0.00 3.18
1607 1965 7.115663 CCTGTAATAAACCCAAAACACAAATCG 59.884 37.037 0.00 0.00 0.00 3.34
1610 1968 7.419711 TCCTGTAATAAACCCAAAACACAAA 57.580 32.000 0.00 0.00 0.00 2.83
1651 2012 1.318158 CCATTCAGCTGGCCTGTTCC 61.318 60.000 15.13 0.00 42.38 3.62
1661 2022 0.251474 TCCAAGCTTGCCATTCAGCT 60.251 50.000 21.43 0.00 39.55 4.24
1700 2061 4.550831 CGTCTTATTTATTCCAGCAGTGCG 60.551 45.833 10.00 4.69 0.00 5.34
1768 2130 1.546923 TCCAGCAACTGAATGGCAATG 59.453 47.619 0.00 0.00 32.44 2.82
1799 2161 7.386848 AGTTGCAACGTAGTCAAAGTACAATAT 59.613 33.333 23.21 0.00 45.00 1.28
1825 2187 4.358851 GCAATACAACAGTCTTGCAACAA 58.641 39.130 12.06 0.00 41.94 2.83
1836 2198 3.922240 GCAACTGAATGGCAATACAACAG 59.078 43.478 0.00 0.00 36.04 3.16
1837 2199 3.573538 AGCAACTGAATGGCAATACAACA 59.426 39.130 0.00 0.00 0.00 3.33
1838 2200 4.178545 AGCAACTGAATGGCAATACAAC 57.821 40.909 0.00 0.00 0.00 3.32
1839 2201 5.973899 TTAGCAACTGAATGGCAATACAA 57.026 34.783 0.00 0.00 0.00 2.41
1907 2269 9.813446 CTTCACCGGTAAACTTTAGATAATAGT 57.187 33.333 6.87 0.00 0.00 2.12
1919 2374 6.070424 TCCAGAATTATCTTCACCGGTAAACT 60.070 38.462 6.87 0.00 32.03 2.66
1920 2375 6.110707 TCCAGAATTATCTTCACCGGTAAAC 58.889 40.000 6.87 0.00 32.03 2.01
1923 2378 5.600898 TCATCCAGAATTATCTTCACCGGTA 59.399 40.000 6.87 0.00 32.03 4.02
1927 2382 6.586344 TCAGTCATCCAGAATTATCTTCACC 58.414 40.000 0.00 0.00 32.03 4.02
1936 2391 5.474876 GGTTTCAGTTCAGTCATCCAGAATT 59.525 40.000 0.00 0.00 0.00 2.17
1993 2448 6.035975 GCATATGTTTGTAGGTTTTTGGCATC 59.964 38.462 4.29 0.00 0.00 3.91
1995 2450 5.221521 TGCATATGTTTGTAGGTTTTTGGCA 60.222 36.000 4.29 0.00 0.00 4.92
1996 2451 5.233988 TGCATATGTTTGTAGGTTTTTGGC 58.766 37.500 4.29 0.00 0.00 4.52
1997 2452 8.031864 TGTATGCATATGTTTGTAGGTTTTTGG 58.968 33.333 10.16 0.00 0.00 3.28
1998 2453 8.859156 GTGTATGCATATGTTTGTAGGTTTTTG 58.141 33.333 10.16 0.00 0.00 2.44
1999 2454 8.580720 TGTGTATGCATATGTTTGTAGGTTTTT 58.419 29.630 10.16 0.00 0.00 1.94
2000 2455 8.116651 TGTGTATGCATATGTTTGTAGGTTTT 57.883 30.769 10.16 0.00 0.00 2.43
2001 2456 7.609918 TCTGTGTATGCATATGTTTGTAGGTTT 59.390 33.333 10.16 0.00 0.00 3.27
2002 2457 7.109501 TCTGTGTATGCATATGTTTGTAGGTT 58.890 34.615 10.16 0.00 0.00 3.50
2003 2458 6.649155 TCTGTGTATGCATATGTTTGTAGGT 58.351 36.000 10.16 0.00 0.00 3.08
2004 2459 7.495606 TCTTCTGTGTATGCATATGTTTGTAGG 59.504 37.037 10.16 0.00 0.00 3.18
2017 2571 4.168760 GCCATTTTGTCTTCTGTGTATGC 58.831 43.478 0.00 0.00 0.00 3.14
2043 2597 2.040947 GGGGAGAGATTGGGGATTGATC 59.959 54.545 0.00 0.00 0.00 2.92
2184 2762 1.963515 GTGTTTTGGGCTGGATGAGTT 59.036 47.619 0.00 0.00 0.00 3.01
2302 2896 1.215423 AGGCTCAACACCTCCAAGTTT 59.785 47.619 0.00 0.00 28.76 2.66
2332 2926 2.112297 AACTCGGCCAAGCGGAAA 59.888 55.556 2.24 0.00 37.43 3.13
2389 2983 0.391661 TGATCCTGAACAAGCTCGCC 60.392 55.000 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.