Multiple sequence alignment - TraesCS2B01G477900

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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 TraesCS2B01G477900 chr2B 100.000 5548 0 0 1 5548 675349841 675344294 0 10246
1 TraesCS2B01G477900 chr2D 94.575 5585 213 39 1 5548 564089162 564083631 0 8552
2 TraesCS2B01G477900 chr2A 95.470 4040 151 19 1526 5548 704768994 704764970 0 6418
3 TraesCS2B01G477900 chr2A 94.865 1480 69 6 1 1476 704770484 704769008 0 2305


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 TraesCS2B01G477900 chr2B 675344294 675349841 5547 True 10246.0 10246 100.0000 1 5548 1 chr2B.!!$R1 5547
1 TraesCS2B01G477900 chr2D 564083631 564089162 5531 True 8552.0 8552 94.5750 1 5548 1 chr2D.!!$R1 5547
2 TraesCS2B01G477900 chr2A 704764970 704770484 5514 True 4361.5 6418 95.1675 1 5548 2 chr2A.!!$R1 5547

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
55 56 0.034186 TCAGGCATGCCCTCGAAAAT 60.034 50.000 33.14 9.27 44.09 1.82 F
375 376 0.103937 GAAGGTCTCCAGAGCATCCG 59.896 60.000 8.44 0.00 44.42 4.18 F
1524 1544 0.250234 TTCTTCTGTGATCGGCTGGG 59.750 55.000 0.00 0.00 0.00 4.45 F
1586 1606 0.999712 AGGGTTGATTGGGACGGAAT 59.000 50.000 0.00 0.00 0.00 3.01 F
2879 2903 1.326548 GCATGTATCGGAACCGTGTTC 59.673 52.381 12.93 7.90 40.74 3.18 F
3907 3933 2.359975 CGCCCAACCCTCTTCCAC 60.360 66.667 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1518 1528 0.034089 AACATAAGAGGTGCCCAGCC 60.034 55.000 0.00 0.00 0.00 4.85 R
2081 2105 0.035739 TACCAACCCAGTTTCGGAGC 59.964 55.000 0.00 0.00 0.00 4.70 R
2866 2890 0.032952 CTTCCTGAACACGGTTCCGA 59.967 55.000 18.28 6.84 0.00 4.55 R
3011 3035 5.380900 TGATCAACAGACCAATACCAACAA 58.619 37.500 0.00 0.00 0.00 2.83 R
4011 4037 1.079750 GTCAGTTCGCTGGTCCTCC 60.080 63.158 0.00 0.00 45.04 4.30 R
5375 5419 0.105593 CCACCAGATGTCGATCCAGG 59.894 60.000 0.00 0.00 32.79 4.45 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
46 47 0.745845 ACATCTCGTTCAGGCATGCC 60.746 55.000 30.12 30.12 0.00 4.40
55 56 0.034186 TCAGGCATGCCCTCGAAAAT 60.034 50.000 33.14 9.27 44.09 1.82
104 105 2.037136 GGCATAGCCCGCTAGCATG 61.037 63.158 16.45 11.33 44.06 4.06
140 141 4.871933 AACAGTTGGCCTTTTAATCTGG 57.128 40.909 3.32 0.00 0.00 3.86
198 199 3.058983 TCTCACGAACATGTCAACAATGC 60.059 43.478 0.00 0.00 0.00 3.56
375 376 0.103937 GAAGGTCTCCAGAGCATCCG 59.896 60.000 8.44 0.00 44.42 4.18
410 411 1.112113 GGAAGTAGCCGGACATGAGA 58.888 55.000 5.05 0.00 0.00 3.27
446 447 3.116746 TGACATCCCTCCTAGGCATTCTA 60.117 47.826 2.96 0.00 32.73 2.10
452 453 2.900546 CCTCCTAGGCATTCTACCGAAT 59.099 50.000 2.96 0.00 40.43 3.34
459 460 2.300437 GGCATTCTACCGAATAGCTCCT 59.700 50.000 0.00 0.00 37.77 3.69
461 462 3.827625 CATTCTACCGAATAGCTCCTCG 58.172 50.000 9.78 9.78 37.77 4.63
818 822 1.659233 CATTCAAACACAGGCCGCA 59.341 52.632 0.00 0.00 0.00 5.69
851 855 0.527817 GGACGTGAAGCGGAGTATGG 60.528 60.000 0.00 0.00 46.52 2.74
866 870 2.252072 TATGGCAAGTGGGACCGAGC 62.252 60.000 0.00 0.00 0.00 5.03
874 878 2.048127 GGGACCGAGCTGTGTGAC 60.048 66.667 0.00 0.00 0.00 3.67
876 880 2.574955 GGACCGAGCTGTGTGACCT 61.575 63.158 0.00 0.00 0.00 3.85
901 905 0.396417 TGGGTGTGGACCAAAAGGTG 60.396 55.000 0.00 0.00 45.25 4.00
906 914 0.467290 GTGGACCAAAAGGTGCTGGA 60.467 55.000 7.66 0.00 36.49 3.86
923 931 1.287425 GGAGCAGATACCGTTTTCCG 58.713 55.000 0.00 0.00 0.00 4.30
940 948 5.365403 TTTCCGAATGTGAAAGCGTAAAT 57.635 34.783 0.00 0.00 0.00 1.40
1018 1027 1.891811 CTCTGACTCTGTCCTTGCTCA 59.108 52.381 0.00 0.00 0.00 4.26
1237 1247 5.833667 CCCTCTTACATCTGTACATGTCCTA 59.166 44.000 0.00 0.00 38.07 2.94
1283 1293 2.519175 CCGCCGTTTCCCGATTACG 61.519 63.158 0.00 0.00 39.56 3.18
1302 1312 1.468224 CGTCGTGCTGCTAGTGAGAAT 60.468 52.381 0.00 0.00 0.00 2.40
1318 1328 6.231211 AGTGAGAATATTTCGTGGTCTGTTT 58.769 36.000 0.00 0.00 34.02 2.83
1319 1329 6.710744 AGTGAGAATATTTCGTGGTCTGTTTT 59.289 34.615 0.00 0.00 34.02 2.43
1320 1330 7.876068 AGTGAGAATATTTCGTGGTCTGTTTTA 59.124 33.333 0.00 0.00 34.02 1.52
1353 1363 8.430801 CTGATTTCAGTGGGAGAAATAGTTAG 57.569 38.462 0.00 0.00 43.60 2.34
1507 1517 5.067674 TGCTTTGGCACATCCTGTATATTTC 59.932 40.000 0.00 0.00 44.28 2.17
1511 1521 6.252599 TGGCACATCCTGTATATTTCTTCT 57.747 37.500 0.00 0.00 35.26 2.85
1512 1522 6.057533 TGGCACATCCTGTATATTTCTTCTG 58.942 40.000 0.00 0.00 35.26 3.02
1513 1523 6.058183 GGCACATCCTGTATATTTCTTCTGT 58.942 40.000 0.00 0.00 0.00 3.41
1514 1524 6.017605 GGCACATCCTGTATATTTCTTCTGTG 60.018 42.308 0.00 0.00 34.80 3.66
1515 1525 6.763135 GCACATCCTGTATATTTCTTCTGTGA 59.237 38.462 0.00 0.00 33.82 3.58
1516 1526 7.443575 GCACATCCTGTATATTTCTTCTGTGAT 59.556 37.037 0.00 0.00 33.82 3.06
1517 1527 8.986847 CACATCCTGTATATTTCTTCTGTGATC 58.013 37.037 0.00 0.00 33.82 2.92
1518 1528 7.869937 ACATCCTGTATATTTCTTCTGTGATCG 59.130 37.037 0.00 0.00 0.00 3.69
1519 1529 6.749139 TCCTGTATATTTCTTCTGTGATCGG 58.251 40.000 0.00 0.00 0.00 4.18
1520 1530 5.406780 CCTGTATATTTCTTCTGTGATCGGC 59.593 44.000 0.00 0.00 0.00 5.54
1524 1544 0.250234 TTCTTCTGTGATCGGCTGGG 59.750 55.000 0.00 0.00 0.00 4.45
1586 1606 0.999712 AGGGTTGATTGGGACGGAAT 59.000 50.000 0.00 0.00 0.00 3.01
1588 1608 2.578940 AGGGTTGATTGGGACGGAATTA 59.421 45.455 0.00 0.00 0.00 1.40
1662 1682 4.104143 CCTACACGGCGAATCACC 57.896 61.111 16.62 0.00 0.00 4.02
1686 1708 2.542020 TGTGTATGAGTGGTGGTGTG 57.458 50.000 0.00 0.00 0.00 3.82
1699 1721 2.493278 GGTGGTGTGCTTGCAGAATTAT 59.507 45.455 0.00 0.00 0.00 1.28
1715 1737 7.615365 TGCAGAATTATTGGACCTAGTTTTCAT 59.385 33.333 0.00 0.00 0.00 2.57
1811 1835 5.951148 TCTGCTGATATTTCCATTTGGACAA 59.049 36.000 0.00 0.00 45.39 3.18
1861 1885 1.828768 GCTCCCTCATCTGGACCAG 59.171 63.158 15.99 15.99 0.00 4.00
1873 1897 1.376553 GGACCAGTTGGCTGCTCTC 60.377 63.158 0.00 0.00 41.26 3.20
1874 1898 1.372683 GACCAGTTGGCTGCTCTCA 59.627 57.895 0.00 0.00 41.26 3.27
1935 1959 4.935205 CCCGTCACACATTCTTTGATTCTA 59.065 41.667 0.00 0.00 0.00 2.10
2046 2070 5.357742 TCAATTCTGCAGTAGGCTAATCA 57.642 39.130 14.67 0.00 45.15 2.57
2470 2494 3.873910 ACCTTTTACCATCATCTCACCG 58.126 45.455 0.00 0.00 0.00 4.94
2497 2521 8.181904 ACCATGTGTTTTAAACTGAAGATCAT 57.818 30.769 9.33 0.00 0.00 2.45
2573 2597 6.859112 TGGCTCTCTTATGACTTCTTACTT 57.141 37.500 0.00 0.00 0.00 2.24
2660 2684 2.942804 TCAACCTGCTTTTCACCATCA 58.057 42.857 0.00 0.00 0.00 3.07
2810 2834 4.462508 TCTTAGTGAAGCTCTGGACATG 57.537 45.455 0.00 0.00 32.21 3.21
2841 2865 7.324178 TCTTAGTAGAAAAGGTCATGAAGCTC 58.676 38.462 0.00 0.00 33.60 4.09
2866 2890 8.579006 TCAAACTTCTCTGAAAAATGCATGTAT 58.421 29.630 0.00 0.00 0.00 2.29
2879 2903 1.326548 GCATGTATCGGAACCGTGTTC 59.673 52.381 12.93 7.90 40.74 3.18
2880 2904 2.612604 CATGTATCGGAACCGTGTTCA 58.387 47.619 12.93 7.84 40.74 3.18
3045 3069 6.990798 TGGTCTGTTGATCAAATTGCATTTA 58.009 32.000 10.35 0.00 29.04 1.40
3455 3481 7.161773 TGGAATGATTCTGAAATCTGGAAAC 57.838 36.000 5.03 0.00 41.63 2.78
3464 3490 9.710900 ATTCTGAAATCTGGAAACAAAATTACC 57.289 29.630 0.00 0.00 42.06 2.85
3498 3524 5.369833 TGGTCGAAAAAGATGGTGAGTTAA 58.630 37.500 0.00 0.00 0.00 2.01
3644 3670 8.839745 TGATAATTAGAATATCTTGCCCTCCAT 58.160 33.333 0.00 0.00 0.00 3.41
3645 3671 9.692325 GATAATTAGAATATCTTGCCCTCCATT 57.308 33.333 0.00 0.00 0.00 3.16
3648 3674 9.471702 AATTAGAATATCTTGCCCTCCATTATG 57.528 33.333 0.00 0.00 0.00 1.90
3690 3716 5.422012 AGAACCCTGTATTTGGCCTTAATTG 59.578 40.000 3.32 0.00 0.00 2.32
3702 3728 6.478512 TGGCCTTAATTGTTCTGTTTTCTT 57.521 33.333 3.32 0.00 0.00 2.52
3707 3733 8.084684 GCCTTAATTGTTCTGTTTTCTTCTGAT 58.915 33.333 0.00 0.00 0.00 2.90
3887 3913 3.058224 GTGAACGGCAATGCTAGTTCTTT 60.058 43.478 30.06 8.61 41.98 2.52
3907 3933 2.359975 CGCCCAACCCTCTTCCAC 60.360 66.667 0.00 0.00 0.00 4.02
3930 3956 2.497675 TGACAGATCTACAGAACCTGCC 59.502 50.000 0.00 3.09 34.37 4.85
3931 3957 2.497675 GACAGATCTACAGAACCTGCCA 59.502 50.000 0.00 0.00 34.37 4.92
3974 4000 7.230712 TCAGAGTCACACAACTGAAGATAGTAA 59.769 37.037 0.00 0.00 36.63 2.24
4065 4091 6.108687 TGATACACTGTTTGAGGATGATCAC 58.891 40.000 0.00 0.00 0.00 3.06
4209 4235 4.191544 CCATGTTTGGTGATAGTGACGAT 58.808 43.478 0.00 0.00 38.30 3.73
4365 4393 5.394663 CCACCAACACAAATTTTGTACCTCA 60.395 40.000 14.13 0.00 43.23 3.86
4538 4567 7.617533 ATGTTACTGTTGAATTACGCAAAAC 57.382 32.000 0.00 0.00 0.00 2.43
4622 4651 2.190538 TGGTGCATCTGGAGATCTTCA 58.809 47.619 3.02 3.02 31.21 3.02
4660 4689 8.599055 ATCAGATATACAACAGCACATAACAG 57.401 34.615 0.00 0.00 0.00 3.16
4696 4725 7.704899 TCCATATCATGTGTTCAGTACGTAAAG 59.295 37.037 0.00 0.00 0.00 1.85
4708 4737 7.218228 TCAGTACGTAAAGTCTATTGTTCCA 57.782 36.000 0.00 0.00 0.00 3.53
4788 4817 5.478679 CCAAGGGGTTTATACAATTCACACA 59.521 40.000 0.00 0.00 0.00 3.72
4793 4822 8.113462 AGGGGTTTATACAATTCACACAGTTAT 58.887 33.333 0.00 0.00 0.00 1.89
4968 5009 2.192175 GCATACCCCTTGGACCGG 59.808 66.667 0.00 0.00 34.81 5.28
4969 5010 2.372074 GCATACCCCTTGGACCGGA 61.372 63.158 9.46 0.00 34.81 5.14
5007 5048 4.375272 CTGCGAAACATGGTAGAGATCAT 58.625 43.478 0.00 0.00 0.00 2.45
5042 5085 5.762045 CCAGACAGTGGTAAAACAAATCAG 58.238 41.667 0.00 0.00 42.17 2.90
5050 5093 8.567948 CAGTGGTAAAACAAATCAGACTATTGT 58.432 33.333 0.00 0.00 38.85 2.71
5075 5118 6.981762 AGTTCAGTTATCAGATTGAGCTTG 57.018 37.500 0.00 0.00 28.50 4.01
5082 5125 8.295288 CAGTTATCAGATTGAGCTTGAAACTTT 58.705 33.333 0.00 0.00 0.00 2.66
5110 5153 3.370840 ACTCATTTATCCTGCCTGCAA 57.629 42.857 0.00 0.00 0.00 4.08
5177 5220 1.825191 CTGGATTGTGGCATCGGGG 60.825 63.158 0.00 0.00 0.00 5.73
5178 5221 3.219198 GGATTGTGGCATCGGGGC 61.219 66.667 0.00 0.00 43.73 5.80
5185 5228 4.329831 GGCATCGGGGCAAGTTAA 57.670 55.556 1.84 0.00 42.77 2.01
5186 5229 2.573920 GGCATCGGGGCAAGTTAAA 58.426 52.632 1.84 0.00 42.77 1.52
5187 5230 0.455815 GGCATCGGGGCAAGTTAAAG 59.544 55.000 1.84 0.00 42.77 1.85
5188 5231 1.459450 GCATCGGGGCAAGTTAAAGA 58.541 50.000 0.00 0.00 0.00 2.52
5192 5235 4.278419 GCATCGGGGCAAGTTAAAGAATAT 59.722 41.667 0.00 0.00 0.00 1.28
5195 5239 5.690865 TCGGGGCAAGTTAAAGAATATCAT 58.309 37.500 0.00 0.00 0.00 2.45
5241 5285 1.617839 AAGCCTCTAGCCTTGCCCT 60.618 57.895 0.00 0.00 45.47 5.19
5375 5419 4.762289 ACTGGAATCCATCTAACTGTCC 57.238 45.455 0.87 0.00 30.82 4.02
5470 5514 4.638865 TGTGATCTCCTTTTCTGATGCATG 59.361 41.667 2.46 0.00 0.00 4.06
5471 5515 4.880120 GTGATCTCCTTTTCTGATGCATGA 59.120 41.667 2.46 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 4.186926 TCATGCTCTTGAGATTTTCGAGG 58.813 43.478 1.30 0.00 37.82 4.63
55 56 3.603532 GGTGTTGATCATGCTCTTGAGA 58.396 45.455 0.00 0.00 0.00 3.27
198 199 2.738521 CCCTGACGTTGCGACTGG 60.739 66.667 1.84 9.10 39.31 4.00
339 340 1.643868 TTCATGTCCATGCGCCGAAC 61.644 55.000 4.18 0.00 38.65 3.95
375 376 2.731691 TTCCAGAGCGGCCAGTTCAC 62.732 60.000 2.24 0.00 31.99 3.18
410 411 1.625818 GATGTCACCTCCTGGAACACT 59.374 52.381 0.00 0.00 36.17 3.55
437 438 2.300437 GGAGCTATTCGGTAGAATGCCT 59.700 50.000 4.20 0.88 45.86 4.75
452 453 2.519541 AGCGATGCCGAGGAGCTA 60.520 61.111 0.00 0.00 36.28 3.32
459 460 4.519437 CAGCCTGAGCGATGCCGA 62.519 66.667 0.00 0.00 46.67 5.54
485 486 4.973168 ACATAATGATGAATGGGTACGCT 58.027 39.130 11.59 0.00 36.48 5.07
759 760 4.779733 GCCGTCTCCTCCCCCTCA 62.780 72.222 0.00 0.00 0.00 3.86
826 830 2.805353 CGCTTCACGTCCACCTCG 60.805 66.667 0.00 0.00 36.87 4.63
851 855 2.743928 CAGCTCGGTCCCACTTGC 60.744 66.667 0.00 0.00 0.00 4.01
866 870 1.174712 CCCAGGCAAAGGTCACACAG 61.175 60.000 0.00 0.00 0.00 3.66
874 878 1.903404 GTCCACACCCAGGCAAAGG 60.903 63.158 0.00 0.00 0.00 3.11
876 880 2.197324 GGTCCACACCCAGGCAAA 59.803 61.111 0.00 0.00 36.54 3.68
901 905 1.666189 GAAAACGGTATCTGCTCCAGC 59.334 52.381 0.00 0.00 42.50 4.85
906 914 2.754946 TTCGGAAAACGGTATCTGCT 57.245 45.000 0.00 0.00 44.45 4.24
923 931 6.149633 AGGAACAATTTACGCTTTCACATTC 58.850 36.000 0.00 0.00 0.00 2.67
940 948 1.600636 CAGGCAAGGCGAGGAACAA 60.601 57.895 0.00 0.00 0.00 2.83
1047 1056 4.882396 GCTCCTCTTCCTCGCCGC 62.882 72.222 0.00 0.00 0.00 6.53
1237 1247 2.508300 ACCCTAAGCACGTATCCCAATT 59.492 45.455 0.00 0.00 0.00 2.32
1283 1293 2.285827 ATTCTCACTAGCAGCACGAC 57.714 50.000 0.00 0.00 0.00 4.34
1302 1312 7.972832 AATCACTAAAACAGACCACGAAATA 57.027 32.000 0.00 0.00 0.00 1.40
1353 1363 1.134491 CCTTCCCCGTCAACTCCATAC 60.134 57.143 0.00 0.00 0.00 2.39
1501 1511 4.384056 CCAGCCGATCACAGAAGAAATAT 58.616 43.478 0.00 0.00 0.00 1.28
1507 1517 1.817099 GCCCAGCCGATCACAGAAG 60.817 63.158 0.00 0.00 0.00 2.85
1511 1521 4.408821 GGTGCCCAGCCGATCACA 62.409 66.667 0.00 0.00 0.00 3.58
1512 1522 4.101448 AGGTGCCCAGCCGATCAC 62.101 66.667 0.00 0.00 0.00 3.06
1513 1523 3.785859 GAGGTGCCCAGCCGATCA 61.786 66.667 0.00 0.00 0.00 2.92
1514 1524 1.686325 TAAGAGGTGCCCAGCCGATC 61.686 60.000 0.00 0.00 0.00 3.69
1515 1525 1.056700 ATAAGAGGTGCCCAGCCGAT 61.057 55.000 0.00 0.00 0.00 4.18
1516 1526 1.689233 ATAAGAGGTGCCCAGCCGA 60.689 57.895 0.00 0.00 0.00 5.54
1517 1527 1.524621 CATAAGAGGTGCCCAGCCG 60.525 63.158 0.00 0.00 0.00 5.52
1518 1528 0.034089 AACATAAGAGGTGCCCAGCC 60.034 55.000 0.00 0.00 0.00 4.85
1519 1529 1.065126 AGAACATAAGAGGTGCCCAGC 60.065 52.381 0.00 0.00 0.00 4.85
1520 1530 3.356529 AAGAACATAAGAGGTGCCCAG 57.643 47.619 0.00 0.00 0.00 4.45
1524 1544 7.283127 TGGAAATGATAAGAACATAAGAGGTGC 59.717 37.037 0.00 0.00 0.00 5.01
1662 1682 1.798223 CCACCACTCATACACAACACG 59.202 52.381 0.00 0.00 0.00 4.49
1686 1708 4.884164 ACTAGGTCCAATAATTCTGCAAGC 59.116 41.667 0.00 0.00 0.00 4.01
1715 1737 7.786030 CAGAGGTTCTGTCAGATATCCTTAAA 58.214 38.462 17.22 0.00 39.58 1.52
1811 1835 3.884037 AAACCCTTCCTCAAGATGTGT 57.116 42.857 0.00 0.00 0.00 3.72
1861 1885 2.615912 GACCATAATGAGAGCAGCCAAC 59.384 50.000 0.00 0.00 0.00 3.77
1873 1897 9.159364 ACATCATTCATATCGAAGACCATAATG 57.841 33.333 0.00 0.00 42.51 1.90
1874 1898 9.376075 GACATCATTCATATCGAAGACCATAAT 57.624 33.333 0.00 0.00 42.51 1.28
2067 2091 0.248377 CGGAGCGTAAGTAAGGACGG 60.248 60.000 0.00 0.00 39.46 4.79
2081 2105 0.035739 TACCAACCCAGTTTCGGAGC 59.964 55.000 0.00 0.00 0.00 4.70
2366 2390 1.536766 TCAAAGTCAGCATTGGAAGCG 59.463 47.619 0.00 0.00 37.01 4.68
2470 2494 8.564574 TGATCTTCAGTTTAAAACACATGGTAC 58.435 33.333 0.00 0.00 0.00 3.34
2543 2567 4.437239 AGTCATAAGAGAGCCAATTGACG 58.563 43.478 7.12 0.00 37.62 4.35
2681 2705 6.147821 ACAGTGCTAAGTGAATCATACACAAC 59.852 38.462 0.00 0.00 40.25 3.32
2810 2834 6.038997 TGACCTTTTCTACTAAGAAGCTCC 57.961 41.667 0.00 0.00 42.60 4.70
2841 2865 8.752766 ATACATGCATTTTTCAGAGAAGTTTG 57.247 30.769 0.00 0.00 0.00 2.93
2866 2890 0.032952 CTTCCTGAACACGGTTCCGA 59.967 55.000 18.28 6.84 0.00 4.55
2879 2903 7.886338 AGCTTACAAAGGTTTAAATCTTCCTG 58.114 34.615 14.00 11.83 35.27 3.86
2880 2904 8.478775 AAGCTTACAAAGGTTTAAATCTTCCT 57.521 30.769 14.00 1.76 46.23 3.36
3011 3035 5.380900 TGATCAACAGACCAATACCAACAA 58.619 37.500 0.00 0.00 0.00 2.83
3053 3077 7.998383 TGCAGGTTCAGACATAAATTACCATAT 59.002 33.333 0.00 0.00 0.00 1.78
3054 3078 7.342581 TGCAGGTTCAGACATAAATTACCATA 58.657 34.615 0.00 0.00 0.00 2.74
3646 3672 8.704668 GGGTTCTAAATTCAATAATGGAACCAT 58.295 33.333 22.44 0.00 43.16 3.55
3647 3673 7.898636 AGGGTTCTAAATTCAATAATGGAACCA 59.101 33.333 22.44 0.00 43.16 3.67
3648 3674 8.197439 CAGGGTTCTAAATTCAATAATGGAACC 58.803 37.037 16.93 16.93 42.15 3.62
3887 3913 4.344865 GAAGAGGGTTGGGCGCCA 62.345 66.667 30.85 12.04 0.00 5.69
3907 3933 4.118410 GCAGGTTCTGTAGATCTGTCATG 58.882 47.826 5.18 1.46 33.43 3.07
3930 3956 7.442364 TGACTCTGAGTTACAGGATTTTCTTTG 59.558 37.037 12.27 0.00 45.76 2.77
3931 3957 7.442666 GTGACTCTGAGTTACAGGATTTTCTTT 59.557 37.037 23.11 0.00 45.76 2.52
4009 4035 1.216710 CAGTTCGCTGGTCCTCCTC 59.783 63.158 0.00 0.00 41.40 3.71
4010 4036 1.228894 TCAGTTCGCTGGTCCTCCT 60.229 57.895 0.00 0.00 45.04 3.69
4011 4037 1.079750 GTCAGTTCGCTGGTCCTCC 60.080 63.158 0.00 0.00 45.04 4.30
4041 4067 6.070596 AGTGATCATCCTCAAACAGTGTATCA 60.071 38.462 0.00 0.00 0.00 2.15
4042 4068 6.344500 AGTGATCATCCTCAAACAGTGTATC 58.656 40.000 0.00 0.00 0.00 2.24
4045 4071 4.630644 AGTGATCATCCTCAAACAGTGT 57.369 40.909 0.00 0.00 0.00 3.55
4065 4091 3.428725 GCTCCAGATCATCTACGCCATAG 60.429 52.174 0.00 0.00 0.00 2.23
4209 4235 1.203441 AGACAGCATGGAAGCCCTCA 61.203 55.000 0.00 0.00 43.62 3.86
4423 4451 6.477253 TGATACAGCACAAACCCTATAACAA 58.523 36.000 0.00 0.00 0.00 2.83
4511 4539 9.900710 TTTTGCGTAATTCAACAGTAACATAAT 57.099 25.926 0.00 0.00 0.00 1.28
4530 4558 6.149308 TCTCATTTATCACTCATGTTTTGCGT 59.851 34.615 0.00 0.00 0.00 5.24
4538 4567 6.231951 AGGATGCTCTCATTTATCACTCATG 58.768 40.000 0.00 0.00 31.96 3.07
4660 4689 5.118990 ACACATGATATGGAGCACTGTTAC 58.881 41.667 0.00 0.00 33.60 2.50
4708 4737 9.438228 GTTTTAGCTGTAGATAGAGGAGTTTTT 57.562 33.333 0.00 0.00 0.00 1.94
4788 4817 6.323739 TCAAAAAGCTTGGAAGGACAATAACT 59.676 34.615 0.00 0.00 0.00 2.24
4793 4822 5.833131 ACTATCAAAAAGCTTGGAAGGACAA 59.167 36.000 0.00 0.00 0.00 3.18
4968 5009 2.673368 CGCAGGTAACACCATTCTCTTC 59.327 50.000 0.00 0.00 41.95 2.87
4969 5010 2.301870 TCGCAGGTAACACCATTCTCTT 59.698 45.455 0.00 0.00 41.95 2.85
5007 5048 3.515502 CCACTGTCTGGAATAACTCTCCA 59.484 47.826 0.00 0.00 43.95 3.86
5050 5093 8.314021 TCAAGCTCAATCTGATAACTGAACTAA 58.686 33.333 0.00 0.00 0.00 2.24
5082 5125 7.601856 CAGGCAGGATAAATGAGTTGTTTTAA 58.398 34.615 0.00 0.00 0.00 1.52
5185 5228 8.472413 AGTGCTTGCAATTAACATGATATTCTT 58.528 29.630 0.00 0.00 0.00 2.52
5186 5229 8.004087 AGTGCTTGCAATTAACATGATATTCT 57.996 30.769 0.00 0.00 0.00 2.40
5187 5230 7.916977 TGAGTGCTTGCAATTAACATGATATTC 59.083 33.333 0.00 0.00 0.00 1.75
5188 5231 7.703621 GTGAGTGCTTGCAATTAACATGATATT 59.296 33.333 0.00 0.00 0.00 1.28
5192 5235 4.277921 TGTGAGTGCTTGCAATTAACATGA 59.722 37.500 0.00 0.00 0.00 3.07
5195 5239 4.277921 TGATGTGAGTGCTTGCAATTAACA 59.722 37.500 0.00 12.34 0.00 2.41
5207 5251 2.490903 AGGCTTCAAATGATGTGAGTGC 59.509 45.455 4.71 4.71 0.00 4.40
5241 5285 1.896220 AGCCGAACATGAAGCTTTGA 58.104 45.000 0.00 0.00 29.27 2.69
5278 5322 7.797121 AAGGAATGTTTATCAAAAGGATGGT 57.203 32.000 0.00 0.00 36.72 3.55
5375 5419 0.105593 CCACCAGATGTCGATCCAGG 59.894 60.000 0.00 0.00 32.79 4.45
5470 5514 4.546570 GGCTTACAAATGAACAACAGGTC 58.453 43.478 0.00 0.00 0.00 3.85
5471 5515 3.004315 CGGCTTACAAATGAACAACAGGT 59.996 43.478 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.