Multiple sequence alignment - TraesCS3A01G156700

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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 TraesCS3A01G156700 chr3A 100.000 1456 0 0 692 2147 152001010 151999555 0.000000e+00 2689.0
1 TraesCS3A01G156700 chr3A 95.116 819 31 4 1336 2147 697840804 697841620 0.000000e+00 1282.0
2 TraesCS3A01G156700 chr3A 96.304 460 17 0 934 1393 570198475 570198016 0.000000e+00 756.0
3 TraesCS3A01G156700 chr3A 100.000 127 0 0 1 127 152001701 152001575 3.560000e-58 235.0
4 TraesCS3A01G156700 chr3A 95.604 91 4 0 2057 2147 11774630 11774540 1.720000e-31 147.0
5 TraesCS3A01G156700 chr3A 98.551 69 1 0 1269 1337 697840632 697840700 2.890000e-24 122.0
6 TraesCS3A01G156700 chr2D 96.381 1271 46 0 877 2147 407453569 407454839 0.000000e+00 2093.0
7 TraesCS3A01G156700 chr2D 94.704 642 25 2 877 1518 622711628 622712260 0.000000e+00 989.0
8 TraesCS3A01G156700 chr4A 94.256 1271 73 0 877 2147 407814942 407816212 0.000000e+00 1943.0
9 TraesCS3A01G156700 chr4A 93.804 581 34 1 933 1513 657666627 657666049 0.000000e+00 872.0
10 TraesCS3A01G156700 chr4D 95.921 760 29 1 1388 2147 328701246 328700489 0.000000e+00 1230.0
11 TraesCS3A01G156700 chr1A 95.332 707 32 1 1441 2147 16474745 16474040 0.000000e+00 1122.0
12 TraesCS3A01G156700 chr1A 95.643 459 20 0 935 1393 564808215 564807757 0.000000e+00 737.0
13 TraesCS3A01G156700 chr1A 95.082 61 3 0 1 61 88798612 88798552 1.750000e-16 97.1
14 TraesCS3A01G156700 chr6A 92.680 765 55 1 1383 2147 360195012 360195775 0.000000e+00 1101.0
15 TraesCS3A01G156700 chr7B 93.777 707 43 1 1441 2147 346799476 346800181 0.000000e+00 1061.0
16 TraesCS3A01G156700 chr7B 94.652 187 10 0 692 878 700395902 700395716 7.500000e-75 291.0
17 TraesCS3A01G156700 chr7B 88.601 193 16 1 692 878 701869231 701869423 1.660000e-56 230.0
18 TraesCS3A01G156700 chr2B 95.126 554 24 3 1513 2064 795317409 795316857 0.000000e+00 870.0
19 TraesCS3A01G156700 chr2B 95.604 91 4 0 2057 2147 795316572 795316482 1.720000e-31 147.0
20 TraesCS3A01G156700 chr2B 91.071 56 4 1 2 56 50223188 50223243 8.220000e-10 75.0
21 TraesCS3A01G156700 chr6B 94.575 553 28 2 1513 2064 310605584 310605033 0.000000e+00 854.0
22 TraesCS3A01G156700 chr7D 93.976 498 26 1 877 1374 475101049 475100556 0.000000e+00 750.0
23 TraesCS3A01G156700 chr7D 95.722 187 8 0 692 878 611235219 611235033 3.460000e-78 302.0
24 TraesCS3A01G156700 chr7D 88.601 193 16 5 692 878 612436653 612436845 1.660000e-56 230.0
25 TraesCS3A01G156700 chr2A 95.879 461 19 0 933 1393 121688158 121688618 0.000000e+00 747.0
26 TraesCS3A01G156700 chr2A 95.228 461 22 0 933 1393 736664475 736664935 0.000000e+00 730.0
27 TraesCS3A01G156700 chr2A 95.604 91 4 0 2057 2147 762080811 762080901 1.720000e-31 147.0
28 TraesCS3A01G156700 chr7A 94.652 187 10 0 692 878 701274569 701274383 7.500000e-75 291.0
29 TraesCS3A01G156700 chr7A 89.119 193 15 1 692 878 702978539 702978347 3.560000e-58 235.0


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 TraesCS3A01G156700 chr3A 151999555 152001701 2146 True 1462.0 2689 100.0000 1 2147 2 chr3A.!!$R3 2146
1 TraesCS3A01G156700 chr3A 697840632 697841620 988 False 702.0 1282 96.8335 1269 2147 2 chr3A.!!$F1 878
2 TraesCS3A01G156700 chr2D 407453569 407454839 1270 False 2093.0 2093 96.3810 877 2147 1 chr2D.!!$F1 1270
3 TraesCS3A01G156700 chr2D 622711628 622712260 632 False 989.0 989 94.7040 877 1518 1 chr2D.!!$F2 641
4 TraesCS3A01G156700 chr4A 407814942 407816212 1270 False 1943.0 1943 94.2560 877 2147 1 chr4A.!!$F1 1270
5 TraesCS3A01G156700 chr4A 657666049 657666627 578 True 872.0 872 93.8040 933 1513 1 chr4A.!!$R1 580
6 TraesCS3A01G156700 chr4D 328700489 328701246 757 True 1230.0 1230 95.9210 1388 2147 1 chr4D.!!$R1 759
7 TraesCS3A01G156700 chr1A 16474040 16474745 705 True 1122.0 1122 95.3320 1441 2147 1 chr1A.!!$R1 706
8 TraesCS3A01G156700 chr6A 360195012 360195775 763 False 1101.0 1101 92.6800 1383 2147 1 chr6A.!!$F1 764
9 TraesCS3A01G156700 chr7B 346799476 346800181 705 False 1061.0 1061 93.7770 1441 2147 1 chr7B.!!$F1 706
10 TraesCS3A01G156700 chr2B 795316482 795317409 927 True 508.5 870 95.3650 1513 2147 2 chr2B.!!$R1 634
11 TraesCS3A01G156700 chr6B 310605033 310605584 551 True 854.0 854 94.5750 1513 2064 1 chr6B.!!$R1 551

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
38 39 0.460987 CACAATCTCCTCGCCACCTC 60.461 60.0 0.0 0.0 0.0 3.85 F
764 765 0.462759 CTTCGCCATCTTCCACCTCC 60.463 60.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1119 1120 1.908483 GACGAAGGGGCCAATCTCT 59.092 57.895 4.39 0.0 0.00 3.10 R
2055 2169 1.266175 GTCGACGTTGACTCTCCAGAA 59.734 52.381 25.69 0.0 35.95 3.02 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
23 24 3.003173 CGGCTCCTCTCCCCACAA 61.003 66.667 0.00 0.00 0.00 3.33
24 25 2.370445 CGGCTCCTCTCCCCACAAT 61.370 63.158 0.00 0.00 0.00 2.71
25 26 1.529309 GGCTCCTCTCCCCACAATC 59.471 63.158 0.00 0.00 0.00 2.67
26 27 0.985490 GGCTCCTCTCCCCACAATCT 60.985 60.000 0.00 0.00 0.00 2.40
27 28 0.467804 GCTCCTCTCCCCACAATCTC 59.532 60.000 0.00 0.00 0.00 2.75
28 29 1.127343 CTCCTCTCCCCACAATCTCC 58.873 60.000 0.00 0.00 0.00 3.71
29 30 0.719015 TCCTCTCCCCACAATCTCCT 59.281 55.000 0.00 0.00 0.00 3.69
30 31 1.127343 CCTCTCCCCACAATCTCCTC 58.873 60.000 0.00 0.00 0.00 3.71
31 32 0.749649 CTCTCCCCACAATCTCCTCG 59.250 60.000 0.00 0.00 0.00 4.63
32 33 1.144936 CTCCCCACAATCTCCTCGC 59.855 63.158 0.00 0.00 0.00 5.03
33 34 2.190578 CCCCACAATCTCCTCGCC 59.809 66.667 0.00 0.00 0.00 5.54
34 35 2.669133 CCCCACAATCTCCTCGCCA 61.669 63.158 0.00 0.00 0.00 5.69
35 36 1.450312 CCCACAATCTCCTCGCCAC 60.450 63.158 0.00 0.00 0.00 5.01
36 37 1.450312 CCACAATCTCCTCGCCACC 60.450 63.158 0.00 0.00 0.00 4.61
37 38 1.599047 CACAATCTCCTCGCCACCT 59.401 57.895 0.00 0.00 0.00 4.00
38 39 0.460987 CACAATCTCCTCGCCACCTC 60.461 60.000 0.00 0.00 0.00 3.85
39 40 1.144936 CAATCTCCTCGCCACCTCC 59.855 63.158 0.00 0.00 0.00 4.30
40 41 1.306141 AATCTCCTCGCCACCTCCA 60.306 57.895 0.00 0.00 0.00 3.86
41 42 1.617947 AATCTCCTCGCCACCTCCAC 61.618 60.000 0.00 0.00 0.00 4.02
42 43 3.775654 CTCCTCGCCACCTCCACC 61.776 72.222 0.00 0.00 0.00 4.61
43 44 4.631740 TCCTCGCCACCTCCACCA 62.632 66.667 0.00 0.00 0.00 4.17
44 45 4.394712 CCTCGCCACCTCCACCAC 62.395 72.222 0.00 0.00 0.00 4.16
45 46 4.394712 CTCGCCACCTCCACCACC 62.395 72.222 0.00 0.00 0.00 4.61
48 49 4.660938 GCCACCTCCACCACCCAC 62.661 72.222 0.00 0.00 0.00 4.61
49 50 4.329545 CCACCTCCACCACCCACG 62.330 72.222 0.00 0.00 0.00 4.94
73 74 4.341783 AGGTCACCCTGCTGCTGC 62.342 66.667 8.89 8.89 40.58 5.25
75 76 3.360340 GTCACCCTGCTGCTGCAC 61.360 66.667 14.93 0.00 45.31 4.57
76 77 4.648626 TCACCCTGCTGCTGCACC 62.649 66.667 14.93 0.00 45.31 5.01
710 711 1.212616 GATCTGCTACGACATGGTGC 58.787 55.000 0.00 0.00 0.00 5.01
711 712 0.528466 ATCTGCTACGACATGGTGCG 60.528 55.000 0.00 0.04 0.00 5.34
712 713 2.802667 CTGCTACGACATGGTGCGC 61.803 63.158 0.00 0.00 0.00 6.09
713 714 2.509336 GCTACGACATGGTGCGCT 60.509 61.111 9.73 0.00 0.00 5.92
714 715 2.802667 GCTACGACATGGTGCGCTG 61.803 63.158 9.73 0.00 0.00 5.18
715 716 2.802667 CTACGACATGGTGCGCTGC 61.803 63.158 9.73 0.69 0.00 5.25
716 717 3.295304 TACGACATGGTGCGCTGCT 62.295 57.895 9.73 0.00 0.00 4.24
717 718 3.857854 CGACATGGTGCGCTGCTC 61.858 66.667 9.73 0.00 0.00 4.26
718 719 3.503363 GACATGGTGCGCTGCTCC 61.503 66.667 9.73 12.62 41.88 4.70
754 755 3.885521 GGCAGCTGCTTCGCCATC 61.886 66.667 35.82 14.76 45.52 3.51
755 756 2.823147 GCAGCTGCTTCGCCATCT 60.823 61.111 31.33 0.00 38.21 2.90
756 757 2.404995 GCAGCTGCTTCGCCATCTT 61.405 57.895 31.33 0.00 38.21 2.40
757 758 1.720301 CAGCTGCTTCGCCATCTTC 59.280 57.895 0.00 0.00 0.00 2.87
758 759 1.451028 AGCTGCTTCGCCATCTTCC 60.451 57.895 0.00 0.00 0.00 3.46
759 760 1.746615 GCTGCTTCGCCATCTTCCA 60.747 57.895 0.00 0.00 0.00 3.53
760 761 1.986575 GCTGCTTCGCCATCTTCCAC 61.987 60.000 0.00 0.00 0.00 4.02
761 762 1.372087 CTGCTTCGCCATCTTCCACC 61.372 60.000 0.00 0.00 0.00 4.61
762 763 1.078143 GCTTCGCCATCTTCCACCT 60.078 57.895 0.00 0.00 0.00 4.00
763 764 1.092345 GCTTCGCCATCTTCCACCTC 61.092 60.000 0.00 0.00 0.00 3.85
764 765 0.462759 CTTCGCCATCTTCCACCTCC 60.463 60.000 0.00 0.00 0.00 4.30
765 766 1.910580 TTCGCCATCTTCCACCTCCC 61.911 60.000 0.00 0.00 0.00 4.30
766 767 2.597903 GCCATCTTCCACCTCCCC 59.402 66.667 0.00 0.00 0.00 4.81
767 768 2.003548 GCCATCTTCCACCTCCCCT 61.004 63.158 0.00 0.00 0.00 4.79
768 769 0.694444 GCCATCTTCCACCTCCCCTA 60.694 60.000 0.00 0.00 0.00 3.53
769 770 1.132500 CCATCTTCCACCTCCCCTAC 58.868 60.000 0.00 0.00 0.00 3.18
770 771 1.625228 CCATCTTCCACCTCCCCTACA 60.625 57.143 0.00 0.00 0.00 2.74
771 772 2.412591 CATCTTCCACCTCCCCTACAT 58.587 52.381 0.00 0.00 0.00 2.29
772 773 2.176247 TCTTCCACCTCCCCTACATC 57.824 55.000 0.00 0.00 0.00 3.06
773 774 1.132500 CTTCCACCTCCCCTACATCC 58.868 60.000 0.00 0.00 0.00 3.51
774 775 0.689745 TTCCACCTCCCCTACATCCG 60.690 60.000 0.00 0.00 0.00 4.18
775 776 2.808206 CCACCTCCCCTACATCCGC 61.808 68.421 0.00 0.00 0.00 5.54
776 777 2.063979 CACCTCCCCTACATCCGCA 61.064 63.158 0.00 0.00 0.00 5.69
777 778 1.762460 ACCTCCCCTACATCCGCAG 60.762 63.158 0.00 0.00 0.00 5.18
823 824 4.131088 GACGACCCGGCCTCTGAC 62.131 72.222 0.00 0.00 0.00 3.51
824 825 4.680537 ACGACCCGGCCTCTGACT 62.681 66.667 0.00 0.00 0.00 3.41
825 826 3.827898 CGACCCGGCCTCTGACTC 61.828 72.222 0.00 0.00 0.00 3.36
826 827 2.680352 GACCCGGCCTCTGACTCA 60.680 66.667 0.00 0.00 0.00 3.41
827 828 2.039624 ACCCGGCCTCTGACTCAT 59.960 61.111 0.00 0.00 0.00 2.90
828 829 2.303549 GACCCGGCCTCTGACTCATG 62.304 65.000 0.00 0.00 0.00 3.07
829 830 2.503061 CCGGCCTCTGACTCATGG 59.497 66.667 0.00 0.00 0.00 3.66
830 831 2.202987 CGGCCTCTGACTCATGGC 60.203 66.667 0.00 12.42 44.22 4.40
831 832 2.202987 GGCCTCTGACTCATGGCG 60.203 66.667 13.74 0.00 45.75 5.69
832 833 2.894387 GCCTCTGACTCATGGCGC 60.894 66.667 0.00 0.00 35.79 6.53
833 834 2.898738 CCTCTGACTCATGGCGCT 59.101 61.111 7.64 0.00 0.00 5.92
834 835 1.521010 CCTCTGACTCATGGCGCTG 60.521 63.158 7.64 0.00 0.00 5.18
835 836 2.125391 TCTGACTCATGGCGCTGC 60.125 61.111 7.64 0.00 0.00 5.25
855 856 4.648626 GGGCTGCCAGTCTGTGCA 62.649 66.667 22.05 13.30 35.86 4.57
859 860 2.427320 TGCCAGTCTGTGCAGGAC 59.573 61.111 10.78 10.69 32.77 3.85
860 861 2.740055 GCCAGTCTGTGCAGGACG 60.740 66.667 12.28 8.49 38.58 4.79
861 862 2.737180 CCAGTCTGTGCAGGACGT 59.263 61.111 12.28 0.00 38.58 4.34
862 863 1.373497 CCAGTCTGTGCAGGACGTC 60.373 63.158 7.13 7.13 38.58 4.34
863 864 1.373497 CAGTCTGTGCAGGACGTCC 60.373 63.158 27.67 27.67 38.58 4.79
864 865 2.048127 GTCTGTGCAGGACGTCCC 60.048 66.667 30.82 17.09 36.42 4.46
865 866 3.311110 TCTGTGCAGGACGTCCCC 61.311 66.667 30.82 21.75 36.42 4.81
866 867 4.742201 CTGTGCAGGACGTCCCCG 62.742 72.222 30.82 22.63 40.83 5.73
885 886 1.149361 GCCCGCGACATCATTTCGTA 61.149 55.000 8.23 0.00 38.77 3.43
968 969 2.356665 TGCCAGCAAAGTAAGGAACA 57.643 45.000 0.00 0.00 0.00 3.18
977 978 4.519350 GCAAAGTAAGGAACACTAAGGCTT 59.481 41.667 4.58 4.58 0.00 4.35
1305 1306 0.249322 ATACACGCCGGCTATGTGTC 60.249 55.000 32.80 1.69 45.04 3.67
1351 1457 8.709646 GTTTGCCAAATATATTCGAGTACCTAG 58.290 37.037 0.00 0.00 0.00 3.02
1456 1562 9.465199 TTTCCAAGTCATTTCTATCATGATTGA 57.535 29.630 14.65 14.70 33.22 2.57
1653 1760 6.096001 GGCTAATGATGATTCTTTGTGTTCCT 59.904 38.462 0.00 0.00 0.00 3.36
1891 2005 4.215742 CATGCCTTGGCCGCCATG 62.216 66.667 14.30 15.69 31.53 3.66
1922 2036 2.671070 CTGGTGGCCAACGGAGAT 59.329 61.111 26.57 0.00 30.80 2.75
1928 2042 1.207329 GTGGCCAACGGAGATAGAGTT 59.793 52.381 7.24 0.00 0.00 3.01
1988 2102 0.536687 ATCATCAAGCGAGCATGGGG 60.537 55.000 0.00 0.00 0.00 4.96
2055 2169 7.768120 TCTGAACCACACTTGCATTTTTAAATT 59.232 29.630 0.00 0.00 0.00 1.82
2079 2485 1.521450 GAGAGTCAACGTCGACCCCA 61.521 60.000 10.58 0.00 36.52 4.96
2112 2518 1.901464 GGTGTCCATGGGCAACGTT 60.901 57.895 23.33 0.00 37.60 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.317149 GATTGTGGGGAGAGGAGCCG 62.317 65.000 0.00 0.00 0.00 5.52
7 8 0.985490 AGATTGTGGGGAGAGGAGCC 60.985 60.000 0.00 0.00 0.00 4.70
8 9 0.467804 GAGATTGTGGGGAGAGGAGC 59.532 60.000 0.00 0.00 0.00 4.70
9 10 1.127343 GGAGATTGTGGGGAGAGGAG 58.873 60.000 0.00 0.00 0.00 3.69
10 11 0.719015 AGGAGATTGTGGGGAGAGGA 59.281 55.000 0.00 0.00 0.00 3.71
11 12 1.127343 GAGGAGATTGTGGGGAGAGG 58.873 60.000 0.00 0.00 0.00 3.69
12 13 0.749649 CGAGGAGATTGTGGGGAGAG 59.250 60.000 0.00 0.00 0.00 3.20
13 14 1.330655 GCGAGGAGATTGTGGGGAGA 61.331 60.000 0.00 0.00 0.00 3.71
14 15 1.144936 GCGAGGAGATTGTGGGGAG 59.855 63.158 0.00 0.00 0.00 4.30
15 16 2.367202 GGCGAGGAGATTGTGGGGA 61.367 63.158 0.00 0.00 0.00 4.81
16 17 2.190578 GGCGAGGAGATTGTGGGG 59.809 66.667 0.00 0.00 0.00 4.96
17 18 1.450312 GTGGCGAGGAGATTGTGGG 60.450 63.158 0.00 0.00 0.00 4.61
18 19 1.450312 GGTGGCGAGGAGATTGTGG 60.450 63.158 0.00 0.00 0.00 4.17
19 20 0.460987 GAGGTGGCGAGGAGATTGTG 60.461 60.000 0.00 0.00 0.00 3.33
20 21 1.617947 GGAGGTGGCGAGGAGATTGT 61.618 60.000 0.00 0.00 0.00 2.71
21 22 1.144936 GGAGGTGGCGAGGAGATTG 59.855 63.158 0.00 0.00 0.00 2.67
22 23 1.306141 TGGAGGTGGCGAGGAGATT 60.306 57.895 0.00 0.00 0.00 2.40
23 24 2.060980 GTGGAGGTGGCGAGGAGAT 61.061 63.158 0.00 0.00 0.00 2.75
24 25 2.680352 GTGGAGGTGGCGAGGAGA 60.680 66.667 0.00 0.00 0.00 3.71
25 26 3.775654 GGTGGAGGTGGCGAGGAG 61.776 72.222 0.00 0.00 0.00 3.69
26 27 4.631740 TGGTGGAGGTGGCGAGGA 62.632 66.667 0.00 0.00 0.00 3.71
27 28 4.394712 GTGGTGGAGGTGGCGAGG 62.395 72.222 0.00 0.00 0.00 4.63
28 29 4.394712 GGTGGTGGAGGTGGCGAG 62.395 72.222 0.00 0.00 0.00 5.03
31 32 4.660938 GTGGGTGGTGGAGGTGGC 62.661 72.222 0.00 0.00 0.00 5.01
32 33 4.329545 CGTGGGTGGTGGAGGTGG 62.330 72.222 0.00 0.00 0.00 4.61
691 692 1.212616 GCACCATGTCGTAGCAGATC 58.787 55.000 0.00 0.00 0.00 2.75
692 693 0.528466 CGCACCATGTCGTAGCAGAT 60.528 55.000 0.00 0.00 0.00 2.90
693 694 1.153842 CGCACCATGTCGTAGCAGA 60.154 57.895 0.00 0.00 0.00 4.26
694 695 2.802667 GCGCACCATGTCGTAGCAG 61.803 63.158 0.30 0.00 0.00 4.24
695 696 2.813474 GCGCACCATGTCGTAGCA 60.813 61.111 0.30 0.00 0.00 3.49
696 697 2.509336 AGCGCACCATGTCGTAGC 60.509 61.111 11.47 0.00 0.00 3.58
697 698 2.802667 GCAGCGCACCATGTCGTAG 61.803 63.158 11.47 0.00 0.00 3.51
698 699 2.813474 GCAGCGCACCATGTCGTA 60.813 61.111 11.47 0.00 0.00 3.43
699 700 4.687215 AGCAGCGCACCATGTCGT 62.687 61.111 11.47 0.00 0.00 4.34
700 701 3.857854 GAGCAGCGCACCATGTCG 61.858 66.667 11.47 0.00 0.00 4.35
701 702 3.503363 GGAGCAGCGCACCATGTC 61.503 66.667 11.47 0.00 39.08 3.06
745 746 0.462759 GGAGGTGGAAGATGGCGAAG 60.463 60.000 0.00 0.00 0.00 3.79
746 747 1.602237 GGAGGTGGAAGATGGCGAA 59.398 57.895 0.00 0.00 0.00 4.70
747 748 2.367202 GGGAGGTGGAAGATGGCGA 61.367 63.158 0.00 0.00 0.00 5.54
748 749 2.190578 GGGAGGTGGAAGATGGCG 59.809 66.667 0.00 0.00 0.00 5.69
749 750 0.694444 TAGGGGAGGTGGAAGATGGC 60.694 60.000 0.00 0.00 0.00 4.40
750 751 1.132500 GTAGGGGAGGTGGAAGATGG 58.868 60.000 0.00 0.00 0.00 3.51
751 752 1.879575 TGTAGGGGAGGTGGAAGATG 58.120 55.000 0.00 0.00 0.00 2.90
752 753 2.695585 GATGTAGGGGAGGTGGAAGAT 58.304 52.381 0.00 0.00 0.00 2.40
753 754 1.344087 GGATGTAGGGGAGGTGGAAGA 60.344 57.143 0.00 0.00 0.00 2.87
754 755 1.132500 GGATGTAGGGGAGGTGGAAG 58.868 60.000 0.00 0.00 0.00 3.46
755 756 0.689745 CGGATGTAGGGGAGGTGGAA 60.690 60.000 0.00 0.00 0.00 3.53
756 757 1.075525 CGGATGTAGGGGAGGTGGA 60.076 63.158 0.00 0.00 0.00 4.02
757 758 2.808206 GCGGATGTAGGGGAGGTGG 61.808 68.421 0.00 0.00 0.00 4.61
758 759 2.032860 CTGCGGATGTAGGGGAGGTG 62.033 65.000 0.00 0.00 0.00 4.00
759 760 1.762460 CTGCGGATGTAGGGGAGGT 60.762 63.158 0.00 0.00 0.00 3.85
760 761 2.511452 CCTGCGGATGTAGGGGAGG 61.511 68.421 0.00 0.00 43.67 4.30
761 762 3.142393 CCTGCGGATGTAGGGGAG 58.858 66.667 0.00 0.00 43.67 4.30
766 767 1.144057 GGTCCACCTGCGGATGTAG 59.856 63.158 0.00 0.00 37.41 2.74
767 768 2.363975 GGGTCCACCTGCGGATGTA 61.364 63.158 0.00 0.00 37.41 2.29
768 769 3.717294 GGGTCCACCTGCGGATGT 61.717 66.667 0.00 0.00 37.41 3.06
769 770 4.838152 CGGGTCCACCTGCGGATG 62.838 72.222 0.00 0.00 37.41 3.51
806 807 4.131088 GTCAGAGGCCGGGTCGTC 62.131 72.222 2.18 0.00 0.00 4.20
807 808 4.680537 AGTCAGAGGCCGGGTCGT 62.681 66.667 2.18 0.00 0.00 4.34
808 809 3.827898 GAGTCAGAGGCCGGGTCG 61.828 72.222 2.18 0.00 0.00 4.79
809 810 2.060980 ATGAGTCAGAGGCCGGGTC 61.061 63.158 2.18 0.00 0.00 4.46
810 811 2.039624 ATGAGTCAGAGGCCGGGT 59.960 61.111 2.18 0.00 0.00 5.28
811 812 2.503061 CATGAGTCAGAGGCCGGG 59.497 66.667 2.18 0.00 0.00 5.73
812 813 2.503061 CCATGAGTCAGAGGCCGG 59.497 66.667 0.00 0.00 0.00 6.13
813 814 2.202987 GCCATGAGTCAGAGGCCG 60.203 66.667 22.62 0.00 41.25 6.13
814 815 2.202987 CGCCATGAGTCAGAGGCC 60.203 66.667 25.44 13.20 44.18 5.19
815 816 2.894387 GCGCCATGAGTCAGAGGC 60.894 66.667 23.04 23.04 43.61 4.70
816 817 1.521010 CAGCGCCATGAGTCAGAGG 60.521 63.158 2.29 9.50 0.00 3.69
817 818 2.172372 GCAGCGCCATGAGTCAGAG 61.172 63.158 2.29 0.00 0.00 3.35
818 819 2.125391 GCAGCGCCATGAGTCAGA 60.125 61.111 2.29 0.00 0.00 3.27
838 839 4.648626 TGCACAGACTGGCAGCCC 62.649 66.667 15.89 6.92 34.58 5.19
842 843 2.427320 GTCCTGCACAGACTGGCA 59.573 61.111 15.12 15.12 38.52 4.92
843 844 2.740055 CGTCCTGCACAGACTGGC 60.740 66.667 7.51 8.09 0.00 4.85
844 845 1.373497 GACGTCCTGCACAGACTGG 60.373 63.158 3.51 0.00 0.00 4.00
845 846 1.373497 GGACGTCCTGCACAGACTG 60.373 63.158 27.64 0.00 0.00 3.51
846 847 2.574955 GGGACGTCCTGCACAGACT 61.575 63.158 32.52 0.00 35.95 3.24
847 848 2.048127 GGGACGTCCTGCACAGAC 60.048 66.667 32.52 10.90 35.95 3.51
848 849 3.311110 GGGGACGTCCTGCACAGA 61.311 66.667 32.52 0.00 35.95 3.41
864 865 3.168237 GAAATGATGTCGCGGGCGG 62.168 63.158 13.60 0.00 40.25 6.13
865 866 2.324477 GAAATGATGTCGCGGGCG 59.676 61.111 6.13 6.74 41.35 6.13
866 867 1.149361 TACGAAATGATGTCGCGGGC 61.149 55.000 6.13 0.00 42.27 6.13
867 868 1.455786 GATACGAAATGATGTCGCGGG 59.544 52.381 6.13 0.00 42.27 6.13
868 869 2.394708 AGATACGAAATGATGTCGCGG 58.605 47.619 6.13 0.00 42.27 6.46
869 870 3.485743 TGAAGATACGAAATGATGTCGCG 59.514 43.478 4.66 0.00 42.27 5.87
870 871 5.389642 TTGAAGATACGAAATGATGTCGC 57.610 39.130 4.66 0.00 42.27 5.19
871 872 7.423598 CAGTTTTGAAGATACGAAATGATGTCG 59.576 37.037 2.98 2.98 44.10 4.35
872 873 7.217070 GCAGTTTTGAAGATACGAAATGATGTC 59.783 37.037 0.00 0.00 0.00 3.06
873 874 7.023575 GCAGTTTTGAAGATACGAAATGATGT 58.976 34.615 0.00 0.00 0.00 3.06
874 875 7.022979 TGCAGTTTTGAAGATACGAAATGATG 58.977 34.615 0.00 0.00 0.00 3.07
875 876 7.144722 TGCAGTTTTGAAGATACGAAATGAT 57.855 32.000 0.00 0.00 0.00 2.45
885 886 3.245052 ACCTAGCCTGCAGTTTTGAAGAT 60.245 43.478 13.81 0.00 30.76 2.40
949 950 1.953686 GTGTTCCTTACTTTGCTGGCA 59.046 47.619 0.00 0.00 0.00 4.92
968 969 0.401738 TTGCTCTGCCAAGCCTTAGT 59.598 50.000 5.10 0.00 41.77 2.24
977 978 2.759114 CCCTTCCTTGCTCTGCCA 59.241 61.111 0.00 0.00 0.00 4.92
1119 1120 1.908483 GACGAAGGGGCCAATCTCT 59.092 57.895 4.39 0.00 0.00 3.10
1305 1306 4.778534 ACACAAATCTCAGAGCCAATTG 57.221 40.909 0.00 0.00 0.00 2.32
1351 1457 3.817709 AGTCTCTCATTAGCCTCTTGC 57.182 47.619 0.00 0.00 41.71 4.01
1398 1504 8.345724 TCAGTTCTCCCTAATATACGATAACC 57.654 38.462 0.00 0.00 0.00 2.85
1446 1552 6.718912 TCCGAAGTCTCTATCTCAATCATGAT 59.281 38.462 1.18 1.18 34.37 2.45
1574 1680 4.653868 AGAGAAGACGTCTTGGTCTCTTA 58.346 43.478 34.23 0.00 46.21 2.10
1653 1760 6.823689 TGCAAAATGGTTGCCTTTTAAACTAA 59.176 30.769 8.47 0.00 44.32 2.24
1750 1857 2.702270 AAATGGGCAAAAGGAGGAGT 57.298 45.000 0.00 0.00 0.00 3.85
1919 2033 1.944024 CGCTGAGACGGAACTCTATCT 59.056 52.381 0.00 0.00 37.73 1.98
1988 2102 2.602257 ACTTGCTTGCAGGAAAAACC 57.398 45.000 11.60 0.00 39.35 3.27
2055 2169 1.266175 GTCGACGTTGACTCTCCAGAA 59.734 52.381 25.69 0.00 35.95 3.02


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

AutoCloner maintained by Alex Coulton.