Multiple sequence alignment - TraesCS4A01G188800

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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 TraesCS4A01G188800 chr4A 100.000 2604 0 0 1 2604 467540961 467538358 0.000000e+00 4809
1 TraesCS4A01G188800 chr4D 90.634 1719 70 48 1 1664 108850768 108852450 0.000000e+00 2198
2 TraesCS4A01G188800 chr4D 91.848 920 37 13 1717 2604 108852453 108853366 0.000000e+00 1249
3 TraesCS4A01G188800 chr4B 88.670 1880 93 36 1 1838 167943145 167941344 0.000000e+00 2182
4 TraesCS4A01G188800 chr4B 97.151 702 14 2 1909 2604 167941118 167940417 0.000000e+00 1181
5 TraesCS4A01G188800 chr5B 79.344 305 39 11 2282 2565 263524144 263523843 2.640000e-45 193


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 TraesCS4A01G188800 chr4A 467538358 467540961 2603 True 4809.0 4809 100.0000 1 2604 1 chr4A.!!$R1 2603
1 TraesCS4A01G188800 chr4D 108850768 108853366 2598 False 1723.5 2198 91.2410 1 2604 2 chr4D.!!$F1 2603
2 TraesCS4A01G188800 chr4B 167940417 167943145 2728 True 1681.5 2182 92.9105 1 2604 2 chr4B.!!$R1 2603

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
51 52 0.179009 AGGCACTGCATTGTGTCACT 60.179 50.0 12.58 4.44 44.21 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1720 1800 0.17902 TTGAGGTTGCACAGGTCAGG 60.179 55.0 0.0 0.0 0.0 3.86 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
48 49 4.963276 TTTATAGGCACTGCATTGTGTC 57.037 40.909 5.89 4.22 41.52 3.67
49 50 2.495155 ATAGGCACTGCATTGTGTCA 57.505 45.000 12.58 0.54 44.21 3.58
50 51 1.522668 TAGGCACTGCATTGTGTCAC 58.477 50.000 12.58 0.00 44.21 3.67
51 52 0.179009 AGGCACTGCATTGTGTCACT 60.179 50.000 12.58 4.44 44.21 3.41
52 53 0.239347 GGCACTGCATTGTGTCACTC 59.761 55.000 5.86 0.00 41.69 3.51
53 54 0.946528 GCACTGCATTGTGTCACTCA 59.053 50.000 5.89 0.00 39.89 3.41
54 55 1.538512 GCACTGCATTGTGTCACTCAT 59.461 47.619 5.89 0.00 39.89 2.90
55 56 2.030540 GCACTGCATTGTGTCACTCATT 60.031 45.455 5.89 0.00 39.89 2.57
56 57 3.189080 GCACTGCATTGTGTCACTCATTA 59.811 43.478 5.89 0.00 39.89 1.90
57 58 4.670992 GCACTGCATTGTGTCACTCATTAG 60.671 45.833 5.89 0.74 39.89 1.73
65 66 6.968131 TTGTGTCACTCATTAGTCATTAGC 57.032 37.500 4.27 0.00 31.97 3.09
136 139 6.574350 AGTAGATTAACTGTAGCACCATGTC 58.426 40.000 0.00 0.00 0.00 3.06
147 151 4.232188 AGCACCATGTCTGAGATGAATT 57.768 40.909 15.64 0.00 0.00 2.17
167 171 9.918630 ATGAATTAACTTTCCAAACTTGATCAG 57.081 29.630 0.00 0.00 0.00 2.90
178 182 7.097192 TCCAAACTTGATCAGTACACTATGTC 58.903 38.462 0.00 0.00 32.94 3.06
393 409 1.279271 CACTTTGCTAGCTACCCCAGT 59.721 52.381 17.23 5.86 0.00 4.00
407 423 1.539929 CCCCAGTCGATCTGAATCTGC 60.540 57.143 14.19 0.00 46.27 4.26
427 443 2.156917 CAGGATGCATTGTCACACTGT 58.843 47.619 0.00 0.00 0.00 3.55
513 529 4.090761 ACCAGTCAAAAAGATCAGCTCA 57.909 40.909 0.00 0.00 0.00 4.26
529 545 4.776837 TCAGCTCAGAAGAAGAGGAAGATT 59.223 41.667 0.00 0.00 33.72 2.40
531 547 3.622612 GCTCAGAAGAAGAGGAAGATTGC 59.377 47.826 0.00 0.00 33.72 3.56
540 556 6.488715 AGAAGAGGAAGATTGCAGGTATTTT 58.511 36.000 0.00 0.00 0.00 1.82
572 589 4.452455 GGCGGTGGATATTAGTCAAAGATG 59.548 45.833 0.00 0.00 0.00 2.90
575 593 4.762251 GGTGGATATTAGTCAAAGATGGCC 59.238 45.833 0.00 0.00 0.00 5.36
586 604 0.994247 AAGATGGCCTCACATGGTCA 59.006 50.000 3.32 0.00 46.55 4.02
596 619 3.818787 CATGGTCAGCCGCCAAGC 61.819 66.667 0.00 0.00 39.72 4.01
647 674 2.009774 GCCAGTGTAAACTCGATGCAT 58.990 47.619 0.00 0.00 0.00 3.96
648 675 2.223112 GCCAGTGTAAACTCGATGCATG 60.223 50.000 2.46 0.00 0.00 4.06
649 676 3.002791 CCAGTGTAAACTCGATGCATGT 58.997 45.455 2.46 0.00 0.00 3.21
650 677 4.180817 CCAGTGTAAACTCGATGCATGTA 58.819 43.478 2.46 0.00 0.00 2.29
651 678 4.629634 CCAGTGTAAACTCGATGCATGTAA 59.370 41.667 2.46 0.00 0.00 2.41
652 679 5.121611 CCAGTGTAAACTCGATGCATGTAAA 59.878 40.000 2.46 0.00 0.00 2.01
653 680 6.183360 CCAGTGTAAACTCGATGCATGTAAAT 60.183 38.462 2.46 0.00 0.00 1.40
727 754 6.079763 TGTAACGCTAGTGTTAGTTTCTACG 58.920 40.000 25.42 2.87 35.13 3.51
733 760 6.237490 CGCTAGTGTTAGTTTCTACGGAATTG 60.237 42.308 0.00 0.00 0.00 2.32
737 764 7.095270 AGTGTTAGTTTCTACGGAATTGGTAG 58.905 38.462 6.85 6.85 38.94 3.18
739 766 8.028938 GTGTTAGTTTCTACGGAATTGGTAGTA 58.971 37.037 11.18 2.32 38.74 1.82
740 767 8.584157 TGTTAGTTTCTACGGAATTGGTAGTAA 58.416 33.333 11.18 7.02 38.74 2.24
741 768 9.591792 GTTAGTTTCTACGGAATTGGTAGTAAT 57.408 33.333 11.18 5.44 38.74 1.89
744 771 8.975295 AGTTTCTACGGAATTGGTAGTAATAGT 58.025 33.333 11.18 0.00 38.74 2.12
748 775 9.797642 TCTACGGAATTGGTAGTAATAGTATGA 57.202 33.333 11.18 0.00 38.74 2.15
768 795 0.749454 ATGAATCGGCTGGCTGGAAC 60.749 55.000 0.00 0.00 0.00 3.62
908 940 1.305549 TTCCCACGTACTCCCTCCC 60.306 63.158 0.00 0.00 0.00 4.30
959 997 3.200593 CGCATGCTGCTGGTCTCC 61.201 66.667 17.13 0.00 42.25 3.71
960 998 2.045634 GCATGCTGCTGGTCTCCA 60.046 61.111 11.37 0.00 40.96 3.86
996 1034 0.942410 GCGCCGTAGAAGACAACACA 60.942 55.000 0.00 0.00 0.00 3.72
997 1035 1.060713 CGCCGTAGAAGACAACACAG 58.939 55.000 0.00 0.00 0.00 3.66
1007 1045 0.590195 GACAACACAGCAGCTCCAAG 59.410 55.000 0.00 0.00 0.00 3.61
1008 1046 1.285023 CAACACAGCAGCTCCAAGC 59.715 57.895 0.00 0.00 42.84 4.01
1009 1047 1.900498 AACACAGCAGCTCCAAGCC 60.900 57.895 0.00 0.00 43.77 4.35
1010 1048 2.033757 CACAGCAGCTCCAAGCCT 59.966 61.111 0.00 0.00 43.77 4.58
1011 1049 2.039405 CACAGCAGCTCCAAGCCTC 61.039 63.158 0.00 0.00 43.77 4.70
1012 1050 2.438075 CAGCAGCTCCAAGCCTCC 60.438 66.667 0.00 0.00 43.77 4.30
1013 1051 2.932194 AGCAGCTCCAAGCCTCCA 60.932 61.111 0.00 0.00 43.77 3.86
1014 1052 2.034687 GCAGCTCCAAGCCTCCAA 59.965 61.111 0.00 0.00 43.77 3.53
1034 1072 2.057922 ACTCTTCAACTCCCACCACAT 58.942 47.619 0.00 0.00 0.00 3.21
1074 1113 1.398390 GGTTCGATCAAGTGCCATGAC 59.602 52.381 0.00 0.00 0.00 3.06
1180 1236 4.273257 TTGCTCACGCCGTCGACA 62.273 61.111 17.16 0.00 39.41 4.35
1181 1237 4.700365 TGCTCACGCCGTCGACAG 62.700 66.667 17.16 5.18 39.41 3.51
1330 1389 0.580104 CCAACGAGTTCCACGTCAAC 59.420 55.000 0.00 0.00 43.16 3.18
1337 1396 2.854401 TTCCACGTCAACGGCGGTA 61.854 57.895 13.24 0.00 44.95 4.02
1438 1497 9.860898 GGCTCAAACAAAAATCATAATTAGTCT 57.139 29.630 0.00 0.00 0.00 3.24
1465 1524 5.189934 GGAACTGAATCTCCTTCCTTCCTTA 59.810 44.000 0.00 0.00 37.05 2.69
1641 1716 0.397564 TGCTCCAGTGCTGATGTGAA 59.602 50.000 0.02 0.00 0.00 3.18
1671 1746 7.981102 ATAGATCATCTGTCCATGTCAATTG 57.019 36.000 0.00 0.00 0.00 2.32
1673 1748 5.821470 AGATCATCTGTCCATGTCAATTGAC 59.179 40.000 28.10 28.10 44.97 3.18
1674 1749 5.169992 TCATCTGTCCATGTCAATTGACT 57.830 39.130 32.57 18.91 44.99 3.41
1675 1750 6.298441 TCATCTGTCCATGTCAATTGACTA 57.702 37.500 32.57 21.73 44.99 2.59
1682 1757 7.377398 TGTCCATGTCAATTGACTATTTTTGG 58.623 34.615 32.57 26.09 44.99 3.28
1705 1780 5.507315 GGAAGTTTTACCACAACCATCACAG 60.507 44.000 0.00 0.00 0.00 3.66
1710 1785 3.243359 ACCACAACCATCACAGGAAAT 57.757 42.857 0.00 0.00 0.00 2.17
1715 1795 5.224888 CACAACCATCACAGGAAATTTCAG 58.775 41.667 19.49 13.27 0.00 3.02
1720 1800 5.010012 ACCATCACAGGAAATTTCAGTTCAC 59.990 40.000 19.49 1.43 0.00 3.18
1732 1812 0.179048 CAGTTCACCTGACCTGTGCA 60.179 55.000 0.00 0.00 44.49 4.57
1744 1824 1.145738 ACCTGTGCAACCTCAAATCCT 59.854 47.619 0.00 0.00 34.36 3.24
1749 1829 5.393461 CCTGTGCAACCTCAAATCCTAATTC 60.393 44.000 0.00 0.00 34.36 2.17
1752 1832 5.185828 GTGCAACCTCAAATCCTAATTCCTT 59.814 40.000 0.00 0.00 0.00 3.36
1753 1833 5.418840 TGCAACCTCAAATCCTAATTCCTTC 59.581 40.000 0.00 0.00 0.00 3.46
1754 1834 5.163509 GCAACCTCAAATCCTAATTCCTTCC 60.164 44.000 0.00 0.00 0.00 3.46
1755 1835 5.796502 ACCTCAAATCCTAATTCCTTCCA 57.203 39.130 0.00 0.00 0.00 3.53
1765 1845 5.073144 TCCTAATTCCTTCCATGTATCCCAC 59.927 44.000 0.00 0.00 0.00 4.61
1778 1858 1.507140 ATCCCACTAGATTTCCGGCA 58.493 50.000 0.00 0.00 0.00 5.69
1781 1861 1.017387 CCACTAGATTTCCGGCAAGC 58.983 55.000 0.00 0.00 0.00 4.01
1804 1884 3.573538 CCCCACTTCATTGACACAATGAA 59.426 43.478 26.83 26.83 42.44 2.57
1806 1886 5.404946 CCCACTTCATTGACACAATGAATC 58.595 41.667 27.95 0.00 43.31 2.52
1815 1895 3.682377 TGACACAATGAATCGCGTGTAAT 59.318 39.130 5.77 0.00 42.42 1.89
1850 1953 3.542712 AATCAAACTAGCAGCAACACG 57.457 42.857 0.00 0.00 0.00 4.49
1852 1955 2.135139 TCAAACTAGCAGCAACACGAG 58.865 47.619 0.00 0.00 0.00 4.18
1872 1980 6.792250 CACGAGTCACAAGTAATCAAATGAAC 59.208 38.462 0.00 0.00 0.00 3.18
1878 1986 6.072728 TCACAAGTAATCAAATGAACGAAGGG 60.073 38.462 0.00 0.00 0.00 3.95
1879 1987 5.183140 ACAAGTAATCAAATGAACGAAGGGG 59.817 40.000 0.00 0.00 0.00 4.79
1880 1988 4.270008 AGTAATCAAATGAACGAAGGGGG 58.730 43.478 0.00 0.00 0.00 5.40
1895 2003 1.832167 GGGGGAAAGTTGCAGCACA 60.832 57.895 2.55 0.00 0.00 4.57
1903 2011 4.990426 GGAAAGTTGCAGCACAAACATTAT 59.010 37.500 2.55 0.00 40.82 1.28
1975 2211 6.472686 AGTTACAGTTCAGATCCCATCTAC 57.527 41.667 0.00 0.00 37.58 2.59
2038 2277 4.712476 TGGGCAACAACAATTTAAGCAAT 58.288 34.783 0.00 0.00 39.74 3.56
2469 2711 1.539124 GGAGGTGGAGGAGGTGGTT 60.539 63.158 0.00 0.00 0.00 3.67
2518 2760 0.706433 AATGGAAGTGGAGGTGGCAT 59.294 50.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 7.440255 TGTGATGATGCTAATGACTAATGAGTG 59.560 37.037 0.00 0.00 35.45 3.51
49 50 7.503549 TGTGATGATGCTAATGACTAATGAGT 58.496 34.615 0.00 0.00 39.20 3.41
50 51 7.958053 TGTGATGATGCTAATGACTAATGAG 57.042 36.000 0.00 0.00 0.00 2.90
51 52 8.913487 AATGTGATGATGCTAATGACTAATGA 57.087 30.769 0.00 0.00 0.00 2.57
52 53 9.961265 AAAATGTGATGATGCTAATGACTAATG 57.039 29.630 0.00 0.00 0.00 1.90
54 55 9.176460 TGAAAATGTGATGATGCTAATGACTAA 57.824 29.630 0.00 0.00 0.00 2.24
55 56 8.735692 TGAAAATGTGATGATGCTAATGACTA 57.264 30.769 0.00 0.00 0.00 2.59
56 57 7.634671 TGAAAATGTGATGATGCTAATGACT 57.365 32.000 0.00 0.00 0.00 3.41
57 58 8.867112 ATTGAAAATGTGATGATGCTAATGAC 57.133 30.769 0.00 0.00 0.00 3.06
136 139 9.403110 CAAGTTTGGAAAGTTAATTCATCTCAG 57.597 33.333 0.00 0.00 30.74 3.35
147 151 7.990886 AGTGTACTGATCAAGTTTGGAAAGTTA 59.009 33.333 0.00 0.00 40.56 2.24
167 171 8.784043 AGAAACAATGGAAAAGACATAGTGTAC 58.216 33.333 0.00 0.00 0.00 2.90
239 251 5.965033 ATGGTCTGGACTCATCAAACTAT 57.035 39.130 0.67 0.00 0.00 2.12
393 409 2.547430 GCATCCTGCAGATTCAGATCGA 60.547 50.000 17.39 0.00 44.26 3.59
407 423 2.095415 CACAGTGTGACAATGCATCCTG 60.095 50.000 18.83 4.31 35.23 3.86
427 443 4.260743 GCACGCAGAGCATAATATCAAACA 60.261 41.667 0.00 0.00 45.32 2.83
513 529 3.586618 ACCTGCAATCTTCCTCTTCTTCT 59.413 43.478 0.00 0.00 0.00 2.85
529 545 0.963355 GTCCGGCCAAAATACCTGCA 60.963 55.000 2.24 0.00 0.00 4.41
531 547 1.373590 CCGTCCGGCCAAAATACCTG 61.374 60.000 2.24 0.00 0.00 4.00
572 589 2.439156 GGCTGACCATGTGAGGCC 60.439 66.667 0.00 0.00 36.47 5.19
575 593 2.821366 GGCGGCTGACCATGTGAG 60.821 66.667 0.00 0.00 34.57 3.51
596 619 3.719144 GGGCGTTGTTCGTTCGGG 61.719 66.667 0.00 0.00 42.13 5.14
647 674 5.502153 ACGTTGCCACTTTACAATTTACA 57.498 34.783 0.00 0.00 0.00 2.41
648 675 6.575942 CAGTACGTTGCCACTTTACAATTTAC 59.424 38.462 0.00 0.00 0.00 2.01
649 676 6.293516 CCAGTACGTTGCCACTTTACAATTTA 60.294 38.462 0.00 0.00 0.00 1.40
650 677 5.506649 CCAGTACGTTGCCACTTTACAATTT 60.507 40.000 0.00 0.00 0.00 1.82
651 678 4.023536 CCAGTACGTTGCCACTTTACAATT 60.024 41.667 0.00 0.00 0.00 2.32
652 679 3.500680 CCAGTACGTTGCCACTTTACAAT 59.499 43.478 0.00 0.00 0.00 2.71
653 680 2.873472 CCAGTACGTTGCCACTTTACAA 59.127 45.455 0.00 0.00 0.00 2.41
733 760 8.251721 AGCCGATTCATTCATACTATTACTACC 58.748 37.037 0.00 0.00 0.00 3.18
737 764 6.183360 GCCAGCCGATTCATTCATACTATTAC 60.183 42.308 0.00 0.00 0.00 1.89
739 766 4.697352 GCCAGCCGATTCATTCATACTATT 59.303 41.667 0.00 0.00 0.00 1.73
740 767 4.019860 AGCCAGCCGATTCATTCATACTAT 60.020 41.667 0.00 0.00 0.00 2.12
741 768 3.324846 AGCCAGCCGATTCATTCATACTA 59.675 43.478 0.00 0.00 0.00 1.82
742 769 2.105477 AGCCAGCCGATTCATTCATACT 59.895 45.455 0.00 0.00 0.00 2.12
743 770 2.225019 CAGCCAGCCGATTCATTCATAC 59.775 50.000 0.00 0.00 0.00 2.39
744 771 2.497138 CAGCCAGCCGATTCATTCATA 58.503 47.619 0.00 0.00 0.00 2.15
745 772 1.315690 CAGCCAGCCGATTCATTCAT 58.684 50.000 0.00 0.00 0.00 2.57
748 775 0.034186 TTCCAGCCAGCCGATTCATT 60.034 50.000 0.00 0.00 0.00 2.57
756 783 4.785453 CTCCCGTTCCAGCCAGCC 62.785 72.222 0.00 0.00 0.00 4.85
768 795 2.636893 AGATCTGGATCCATTTCTCCCG 59.363 50.000 16.63 0.36 38.58 5.14
771 798 3.306641 CCCGAGATCTGGATCCATTTCTC 60.307 52.174 28.39 28.39 38.58 2.87
772 799 2.636893 CCCGAGATCTGGATCCATTTCT 59.363 50.000 16.63 19.30 38.58 2.52
955 993 3.571571 GCGTATATAATGCGTGTGGAGA 58.428 45.455 0.00 0.00 40.59 3.71
996 1034 2.532532 TTGGAGGCTTGGAGCTGCT 61.533 57.895 6.82 0.00 41.99 4.24
997 1035 2.034687 TTGGAGGCTTGGAGCTGC 59.965 61.111 0.00 0.00 41.99 5.25
1007 1045 1.611936 GGGAGTTGAAGAGTTGGAGGC 60.612 57.143 0.00 0.00 0.00 4.70
1008 1046 1.699634 TGGGAGTTGAAGAGTTGGAGG 59.300 52.381 0.00 0.00 0.00 4.30
1009 1047 2.551071 GGTGGGAGTTGAAGAGTTGGAG 60.551 54.545 0.00 0.00 0.00 3.86
1010 1048 1.420138 GGTGGGAGTTGAAGAGTTGGA 59.580 52.381 0.00 0.00 0.00 3.53
1011 1049 1.142870 TGGTGGGAGTTGAAGAGTTGG 59.857 52.381 0.00 0.00 0.00 3.77
1012 1050 2.222027 GTGGTGGGAGTTGAAGAGTTG 58.778 52.381 0.00 0.00 0.00 3.16
1013 1051 1.843851 TGTGGTGGGAGTTGAAGAGTT 59.156 47.619 0.00 0.00 0.00 3.01
1014 1052 1.507140 TGTGGTGGGAGTTGAAGAGT 58.493 50.000 0.00 0.00 0.00 3.24
1034 1072 3.396260 CGTAAGGTTGGAGACTTGGAA 57.604 47.619 0.00 0.00 0.00 3.53
1204 1263 4.704833 AGCCACGGCGATGCTGTT 62.705 61.111 22.63 3.97 46.97 3.16
1301 1360 2.432628 CTCGTTGGTCTCCGTGCC 60.433 66.667 0.00 0.00 0.00 5.01
1302 1361 1.282930 GAACTCGTTGGTCTCCGTGC 61.283 60.000 0.00 0.00 0.00 5.34
1303 1362 0.666577 GGAACTCGTTGGTCTCCGTG 60.667 60.000 0.00 0.00 31.77 4.94
1304 1363 1.111116 TGGAACTCGTTGGTCTCCGT 61.111 55.000 0.00 0.00 31.77 4.69
1305 1364 0.666577 GTGGAACTCGTTGGTCTCCG 60.667 60.000 0.00 0.00 31.77 4.63
1438 1497 1.916181 GGAAGGAGATTCAGTTCCCCA 59.084 52.381 0.00 0.00 39.91 4.96
1465 1524 4.888326 ACAGCTGATCAAAGAGAGAAGT 57.112 40.909 23.35 0.00 0.00 3.01
1631 1706 1.412710 TCTATCCGGGTTCACATCAGC 59.587 52.381 0.00 0.00 0.00 4.26
1641 1716 2.158310 TGGACAGATGATCTATCCGGGT 60.158 50.000 14.54 0.00 42.94 5.28
1670 1745 8.294954 TGTGGTAAAACTTCCAAAAATAGTCA 57.705 30.769 0.00 0.00 35.38 3.41
1671 1746 9.027129 GTTGTGGTAAAACTTCCAAAAATAGTC 57.973 33.333 0.00 0.00 33.42 2.59
1673 1748 7.982354 TGGTTGTGGTAAAACTTCCAAAAATAG 59.018 33.333 0.00 0.00 33.42 1.73
1674 1749 7.848128 TGGTTGTGGTAAAACTTCCAAAAATA 58.152 30.769 0.00 0.00 33.42 1.40
1675 1750 6.712276 TGGTTGTGGTAAAACTTCCAAAAAT 58.288 32.000 0.00 0.00 33.42 1.82
1682 1757 5.507315 CCTGTGATGGTTGTGGTAAAACTTC 60.507 44.000 0.00 0.00 0.00 3.01
1690 1765 2.746279 TTTCCTGTGATGGTTGTGGT 57.254 45.000 0.00 0.00 0.00 4.16
1715 1795 0.663153 GTTGCACAGGTCAGGTGAAC 59.337 55.000 0.00 0.00 38.54 3.18
1720 1800 0.179020 TTGAGGTTGCACAGGTCAGG 60.179 55.000 0.00 0.00 0.00 3.86
1730 1810 5.163509 GGAAGGAATTAGGATTTGAGGTTGC 60.164 44.000 0.00 0.00 0.00 4.17
1732 1812 6.152638 TGGAAGGAATTAGGATTTGAGGTT 57.847 37.500 0.00 0.00 0.00 3.50
1744 1824 7.079700 TCTAGTGGGATACATGGAAGGAATTA 58.920 38.462 0.00 0.00 39.74 1.40
1749 1829 5.832539 AATCTAGTGGGATACATGGAAGG 57.167 43.478 0.00 0.00 39.74 3.46
1752 1832 4.283467 CGGAAATCTAGTGGGATACATGGA 59.717 45.833 0.00 0.00 39.74 3.41
1753 1833 4.563580 CCGGAAATCTAGTGGGATACATGG 60.564 50.000 0.00 0.00 39.74 3.66
1754 1834 4.569943 CCGGAAATCTAGTGGGATACATG 58.430 47.826 0.00 0.00 39.74 3.21
1755 1835 3.008049 GCCGGAAATCTAGTGGGATACAT 59.992 47.826 5.05 0.00 39.74 2.29
1765 1845 0.819666 GGGGCTTGCCGGAAATCTAG 60.820 60.000 5.05 0.00 0.00 2.43
1778 1858 0.482446 TGTCAATGAAGTGGGGGCTT 59.518 50.000 0.00 0.00 0.00 4.35
1781 1861 1.993956 TTGTGTCAATGAAGTGGGGG 58.006 50.000 0.00 0.00 0.00 5.40
1804 1884 2.268298 GTGGTGAAGATTACACGCGAT 58.732 47.619 15.93 2.23 38.90 4.58
1806 1886 1.390123 CTGTGGTGAAGATTACACGCG 59.610 52.381 3.53 3.53 38.90 6.01
1815 1895 7.041372 GCTAGTTTGATTTAACTGTGGTGAAGA 60.041 37.037 0.00 0.00 38.72 2.87
1850 1953 7.117241 TCGTTCATTTGATTACTTGTGACTC 57.883 36.000 0.00 0.00 0.00 3.36
1852 1955 6.797033 CCTTCGTTCATTTGATTACTTGTGAC 59.203 38.462 0.00 0.00 0.00 3.67
1878 1986 0.463620 TTTGTGCTGCAACTTTCCCC 59.536 50.000 2.77 0.00 36.72 4.81
1879 1987 1.134848 TGTTTGTGCTGCAACTTTCCC 60.135 47.619 2.77 0.00 36.72 3.97
1880 1988 2.292103 TGTTTGTGCTGCAACTTTCC 57.708 45.000 2.77 0.00 36.72 3.13
1881 1989 7.636259 TTATAATGTTTGTGCTGCAACTTTC 57.364 32.000 2.77 0.00 36.72 2.62
1975 2211 2.477525 GCTCAGTCGTAGAACTTACCGG 60.478 54.545 0.00 0.00 39.69 5.28
2038 2277 6.878923 CAGAGACAAACAAATGGGTGATACTA 59.121 38.462 0.00 0.00 0.00 1.82
2286 2525 6.205853 TGATGTTATATTACAAATGTCGGGGC 59.794 38.462 0.00 0.00 0.00 5.80
2469 2711 3.139850 CAGGTTTTGCAATGCCAAATGA 58.860 40.909 18.26 0.00 34.92 2.57
2518 2760 0.400381 TGGGATGATGGCTGGCTCTA 60.400 55.000 2.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.