Multiple sequence alignment - TraesCS5B01G181600

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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 TraesCS5B01G181600 chr5B 100.000 3200 0 0 1 3200 331252804 331249605 0.000000e+00 5910.0
1 TraesCS5B01G181600 chr5B 96.919 714 20 2 1 713 503788926 503789638 0.000000e+00 1195.0
2 TraesCS5B01G181600 chr5B 93.522 741 39 7 51 788 43890553 43891287 0.000000e+00 1094.0
3 TraesCS5B01G181600 chr5B 93.514 740 40 6 51 788 487182652 487183385 0.000000e+00 1094.0
4 TraesCS5B01G181600 chr5B 93.416 729 41 6 51 778 485881299 485882021 0.000000e+00 1074.0
5 TraesCS5B01G181600 chr5A 91.767 1919 113 23 827 2725 382782589 382780696 0.000000e+00 2627.0
6 TraesCS5B01G181600 chr5A 86.071 481 39 11 2723 3200 382780573 382780118 2.870000e-135 492.0
7 TraesCS5B01G181600 chr7B 97.462 788 19 1 1 788 116399702 116400488 0.000000e+00 1343.0
8 TraesCS5B01G181600 chr4B 96.705 789 22 3 1 788 672175360 672176145 0.000000e+00 1310.0
9 TraesCS5B01G181600 chr6B 96.862 701 20 2 1 701 275481411 275482109 0.000000e+00 1171.0
10 TraesCS5B01G181600 chr3B 93.378 740 43 5 51 788 123367524 123368259 0.000000e+00 1090.0
11 TraesCS5B01G181600 chr3B 91.781 73 6 0 1 73 7083369 7083441 5.650000e-18 102.0
12 TraesCS5B01G181600 chr4A 92.848 741 43 7 51 788 714267546 714268279 0.000000e+00 1066.0
13 TraesCS5B01G181600 chr3D 78.166 1232 196 46 976 2173 520708868 520707676 0.000000e+00 717.0
14 TraesCS5B01G181600 chr3D 88.406 69 4 3 2341 2406 520706281 520706214 2.650000e-11 80.5
15 TraesCS5B01G181600 chr5D 90.672 268 24 1 2931 3197 290396620 290396353 3.930000e-94 355.0
16 TraesCS5B01G181600 chr5D 88.158 152 18 0 2777 2928 438974709 438974558 7.050000e-42 182.0
17 TraesCS5B01G181600 chr2B 86.161 224 31 0 2934 3157 122450198 122450421 3.190000e-60 243.0
18 TraesCS5B01G181600 chr6D 80.503 159 29 2 2775 2932 416429997 416430154 1.560000e-23 121.0


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 TraesCS5B01G181600 chr5B 331249605 331252804 3199 True 5910.00 5910 100.000 1 3200 1 chr5B.!!$R1 3199
1 TraesCS5B01G181600 chr5B 503788926 503789638 712 False 1195.00 1195 96.919 1 713 1 chr5B.!!$F4 712
2 TraesCS5B01G181600 chr5B 43890553 43891287 734 False 1094.00 1094 93.522 51 788 1 chr5B.!!$F1 737
3 TraesCS5B01G181600 chr5B 487182652 487183385 733 False 1094.00 1094 93.514 51 788 1 chr5B.!!$F3 737
4 TraesCS5B01G181600 chr5B 485881299 485882021 722 False 1074.00 1074 93.416 51 778 1 chr5B.!!$F2 727
5 TraesCS5B01G181600 chr5A 382780118 382782589 2471 True 1559.50 2627 88.919 827 3200 2 chr5A.!!$R1 2373
6 TraesCS5B01G181600 chr7B 116399702 116400488 786 False 1343.00 1343 97.462 1 788 1 chr7B.!!$F1 787
7 TraesCS5B01G181600 chr4B 672175360 672176145 785 False 1310.00 1310 96.705 1 788 1 chr4B.!!$F1 787
8 TraesCS5B01G181600 chr6B 275481411 275482109 698 False 1171.00 1171 96.862 1 701 1 chr6B.!!$F1 700
9 TraesCS5B01G181600 chr3B 123367524 123368259 735 False 1090.00 1090 93.378 51 788 1 chr3B.!!$F2 737
10 TraesCS5B01G181600 chr4A 714267546 714268279 733 False 1066.00 1066 92.848 51 788 1 chr4A.!!$F1 737
11 TraesCS5B01G181600 chr3D 520706214 520708868 2654 True 398.75 717 83.286 976 2406 2 chr3D.!!$R1 1430

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
837 846 0.109532 TCGTGATGGGCTGGAAAACA 59.890 50.0 0.0 0.0 0.0 2.83 F
956 972 0.196118 TTCCAAGGGTTCCTCCTCCT 59.804 55.0 0.0 0.0 35.8 3.69 F
957 973 0.252742 TCCAAGGGTTCCTCCTCCTC 60.253 60.0 0.0 0.0 35.8 3.71 F
1339 1365 0.457851 CTCGCTCGACTTTCTCCCAT 59.542 55.0 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1828 1869 0.460311 ACCTCGAGCCTGAAATACCG 59.540 55.0 6.99 0.0 0.00 4.02 R
1950 1994 0.533755 ACTGCTGCAGTTGGACACTC 60.534 55.0 28.49 0.0 42.59 3.51 R
1992 2036 0.742505 TGTCGACGTTCAACTCACCT 59.257 50.0 11.62 0.0 0.00 4.00 R
3031 4465 0.472471 GGGTTTCCCGGATGATGCTA 59.528 55.0 0.73 0.0 32.13 3.49 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
368 374 8.317891 TCGCTTACAAATTTGTTCTCTGATTA 57.682 30.769 27.66 4.89 42.35 1.75
536 543 6.435428 TCTAAAATTTGGAAAGTGTTCGCTC 58.565 36.000 0.00 0.00 34.28 5.03
546 553 6.262273 TGGAAAGTGTTCGCTCTTTAAGAAAT 59.738 34.615 0.00 0.00 39.94 2.17
616 623 4.065789 GCCTCCTTTACATTTATCTCCGG 58.934 47.826 0.00 0.00 0.00 5.14
629 636 0.673985 TCTCCGGACGCCATATCAAG 59.326 55.000 0.00 0.00 0.00 3.02
703 711 1.403687 CCCTGGTTCGATCCCTCTCC 61.404 65.000 10.02 0.00 0.00 3.71
788 797 4.700365 TGTGCGTCCGCTCGACAG 62.700 66.667 13.31 0.00 42.07 3.51
789 798 4.400109 GTGCGTCCGCTCGACAGA 62.400 66.667 13.31 0.00 42.07 3.41
800 809 3.770625 TCGACAGAGCTCTCGAGAT 57.229 52.632 20.47 0.92 34.09 2.75
801 810 1.294857 TCGACAGAGCTCTCGAGATG 58.705 55.000 20.47 13.73 34.09 2.90
802 811 1.134670 TCGACAGAGCTCTCGAGATGA 60.135 52.381 20.47 8.33 34.09 2.92
803 812 1.003972 CGACAGAGCTCTCGAGATGAC 60.004 57.143 17.03 10.53 34.09 3.06
804 813 1.333619 GACAGAGCTCTCGAGATGACC 59.666 57.143 17.03 5.91 34.09 4.02
805 814 1.064758 ACAGAGCTCTCGAGATGACCT 60.065 52.381 17.03 9.92 34.09 3.85
806 815 2.171659 ACAGAGCTCTCGAGATGACCTA 59.828 50.000 17.03 0.00 34.09 3.08
807 816 2.548057 CAGAGCTCTCGAGATGACCTAC 59.452 54.545 17.03 3.99 34.09 3.18
808 817 1.877443 GAGCTCTCGAGATGACCTACC 59.123 57.143 17.03 0.00 0.00 3.18
809 818 1.493022 AGCTCTCGAGATGACCTACCT 59.507 52.381 17.03 0.02 0.00 3.08
810 819 1.877443 GCTCTCGAGATGACCTACCTC 59.123 57.143 17.03 0.00 0.00 3.85
811 820 2.500229 CTCTCGAGATGACCTACCTCC 58.500 57.143 17.03 0.00 0.00 4.30
812 821 2.105821 CTCTCGAGATGACCTACCTCCT 59.894 54.545 17.03 0.00 0.00 3.69
813 822 3.315596 TCTCGAGATGACCTACCTCCTA 58.684 50.000 12.08 0.00 0.00 2.94
814 823 3.071312 TCTCGAGATGACCTACCTCCTAC 59.929 52.174 12.08 0.00 0.00 3.18
815 824 2.775960 TCGAGATGACCTACCTCCTACA 59.224 50.000 0.00 0.00 0.00 2.74
816 825 3.394940 TCGAGATGACCTACCTCCTACAT 59.605 47.826 0.00 0.00 0.00 2.29
817 826 4.141228 TCGAGATGACCTACCTCCTACATT 60.141 45.833 0.00 0.00 0.00 2.71
818 827 4.585162 CGAGATGACCTACCTCCTACATTT 59.415 45.833 0.00 0.00 0.00 2.32
819 828 5.278561 CGAGATGACCTACCTCCTACATTTC 60.279 48.000 0.00 0.00 0.00 2.17
820 829 4.585162 AGATGACCTACCTCCTACATTTCG 59.415 45.833 0.00 0.00 0.00 3.46
821 830 3.705051 TGACCTACCTCCTACATTTCGT 58.295 45.455 0.00 0.00 0.00 3.85
822 831 3.446161 TGACCTACCTCCTACATTTCGTG 59.554 47.826 0.00 0.00 0.00 4.35
823 832 3.698040 GACCTACCTCCTACATTTCGTGA 59.302 47.826 0.00 0.00 0.00 4.35
824 833 4.287552 ACCTACCTCCTACATTTCGTGAT 58.712 43.478 0.00 0.00 0.00 3.06
825 834 4.099573 ACCTACCTCCTACATTTCGTGATG 59.900 45.833 0.37 0.37 0.00 3.07
826 835 3.543680 ACCTCCTACATTTCGTGATGG 57.456 47.619 5.92 0.00 0.00 3.51
827 836 2.170607 ACCTCCTACATTTCGTGATGGG 59.829 50.000 5.92 0.00 0.00 4.00
828 837 2.213499 CTCCTACATTTCGTGATGGGC 58.787 52.381 5.92 0.00 0.00 5.36
829 838 1.837439 TCCTACATTTCGTGATGGGCT 59.163 47.619 5.92 0.00 0.00 5.19
830 839 1.942657 CCTACATTTCGTGATGGGCTG 59.057 52.381 5.92 0.00 0.00 4.85
831 840 1.942657 CTACATTTCGTGATGGGCTGG 59.057 52.381 5.92 0.00 0.00 4.85
835 844 1.988293 TTTCGTGATGGGCTGGAAAA 58.012 45.000 0.00 0.00 0.00 2.29
836 845 1.243902 TTCGTGATGGGCTGGAAAAC 58.756 50.000 0.00 0.00 0.00 2.43
837 846 0.109532 TCGTGATGGGCTGGAAAACA 59.890 50.000 0.00 0.00 0.00 2.83
844 853 3.182887 TGGGCTGGAAAACATGGTAAT 57.817 42.857 0.00 0.00 0.00 1.89
850 859 4.380867 GCTGGAAAACATGGTAATCACTGG 60.381 45.833 0.00 0.00 0.00 4.00
857 866 0.327924 TGGTAATCACTGGTGGGCTG 59.672 55.000 0.70 0.00 0.00 4.85
859 868 1.407437 GGTAATCACTGGTGGGCTGAG 60.407 57.143 0.70 0.00 0.00 3.35
891 900 4.141482 GGTGGGTCAGATCTTAAAGGCATA 60.141 45.833 0.00 0.00 0.00 3.14
893 902 6.064717 GTGGGTCAGATCTTAAAGGCATATT 58.935 40.000 0.00 0.00 0.00 1.28
913 929 9.261180 GCATATTGTGGCAATATATATAGTCGT 57.739 33.333 12.32 0.00 0.00 4.34
916 932 8.703604 ATTGTGGCAATATATATAGTCGTGAC 57.296 34.615 0.00 0.00 0.00 3.67
917 933 7.462571 TGTGGCAATATATATAGTCGTGACT 57.537 36.000 7.77 7.77 45.02 3.41
918 934 7.312899 TGTGGCAATATATATAGTCGTGACTG 58.687 38.462 12.66 0.00 42.52 3.51
919 935 6.253727 GTGGCAATATATATAGTCGTGACTGC 59.746 42.308 12.66 4.89 42.52 4.40
920 936 6.152831 TGGCAATATATATAGTCGTGACTGCT 59.847 38.462 12.66 2.93 42.52 4.24
921 937 6.473778 GGCAATATATATAGTCGTGACTGCTG 59.526 42.308 12.66 0.00 42.52 4.41
922 938 7.251281 GCAATATATATAGTCGTGACTGCTGA 58.749 38.462 12.66 0.00 42.52 4.26
923 939 7.430793 GCAATATATATAGTCGTGACTGCTGAG 59.569 40.741 12.66 0.00 42.52 3.35
924 940 8.669243 CAATATATATAGTCGTGACTGCTGAGA 58.331 37.037 12.66 0.00 42.52 3.27
925 941 8.972458 ATATATATAGTCGTGACTGCTGAGAT 57.028 34.615 12.66 0.00 42.52 2.75
926 942 3.706802 ATAGTCGTGACTGCTGAGATG 57.293 47.619 12.66 0.00 42.52 2.90
927 943 1.252175 AGTCGTGACTGCTGAGATGT 58.748 50.000 0.86 0.00 40.75 3.06
935 951 1.347707 ACTGCTGAGATGTCCCGAAAA 59.652 47.619 0.00 0.00 0.00 2.29
956 972 0.196118 TTCCAAGGGTTCCTCCTCCT 59.804 55.000 0.00 0.00 35.80 3.69
957 973 0.252742 TCCAAGGGTTCCTCCTCCTC 60.253 60.000 0.00 0.00 35.80 3.71
958 974 1.275421 CCAAGGGTTCCTCCTCCTCC 61.275 65.000 0.00 0.00 35.80 4.30
980 996 4.201122 CCAGAGCATCCCAGGCCC 62.201 72.222 0.00 0.00 33.66 5.80
1012 1028 1.428912 TGGCAAAAATGGAGGGAGACT 59.571 47.619 0.00 0.00 0.00 3.24
1033 1049 4.194720 GTGAGATCTCGGCGCCGT 62.195 66.667 44.16 29.14 40.74 5.68
1311 1337 4.129737 ACCGTCGACATGCTCCCG 62.130 66.667 17.16 0.00 0.00 5.14
1338 1364 0.608308 TCTCGCTCGACTTTCTCCCA 60.608 55.000 0.00 0.00 0.00 4.37
1339 1365 0.457851 CTCGCTCGACTTTCTCCCAT 59.542 55.000 0.00 0.00 0.00 4.00
1347 1373 2.223829 CGACTTTCTCCCATACTGCGAT 60.224 50.000 0.00 0.00 0.00 4.58
1408 1434 0.742281 CCTCCTGAATCAGTGCACGG 60.742 60.000 12.01 11.52 0.00 4.94
1581 1613 3.260483 GAGCGCATCAGCCTGTCG 61.260 66.667 11.47 0.00 37.52 4.35
1596 1628 7.272244 TCAGCCTGTCGAATTTCAGAATAATA 58.728 34.615 2.52 0.00 34.02 0.98
1674 1715 3.545124 TTTCTGGACCATGGCGCGT 62.545 57.895 13.04 0.00 0.00 6.01
1713 1754 4.093291 AGGCCCGAGAGCAGCTTG 62.093 66.667 0.00 0.00 0.00 4.01
1732 1773 3.306917 TGTACTTCGCTCGGAATTTCA 57.693 42.857 0.00 0.00 33.26 2.69
1737 1778 2.461110 CGCTCGGAATTTCACCCGG 61.461 63.158 0.00 0.00 45.36 5.73
1828 1869 0.804989 CTTGTTCCCGGAAGACATGC 59.195 55.000 0.73 0.00 0.00 4.06
1913 1957 2.626840 GAGCCATCTCAAGGTCTTCAC 58.373 52.381 0.00 0.00 39.16 3.18
1918 1962 4.330250 CCATCTCAAGGTCTTCACACAAT 58.670 43.478 0.00 0.00 0.00 2.71
1950 1994 2.295885 GATGAATGGGTGCTGGAGAAG 58.704 52.381 0.00 0.00 0.00 2.85
2017 2061 0.163788 GTTGAACGTCGACATGCTGG 59.836 55.000 17.16 0.00 31.07 4.85
2055 2099 1.752833 GGAGGGGTCTGTCGTGTTT 59.247 57.895 0.00 0.00 0.00 2.83
2067 2111 4.327898 TCTGTCGTGTTTTGTACAGACAAC 59.672 41.667 13.65 10.44 45.29 3.32
2068 2112 4.247258 TGTCGTGTTTTGTACAGACAACT 58.753 39.130 13.65 0.00 45.29 3.16
2116 2160 1.447838 ACCATGGAGTGTAAGCGCG 60.448 57.895 21.47 0.00 0.00 6.86
2152 2196 0.659957 GTACTACGGGCCAGAGTACG 59.340 60.000 22.28 11.21 37.05 3.67
2164 2208 1.810755 CAGAGTACGTGTACCAGCTGA 59.189 52.381 17.39 0.00 36.75 4.26
2211 3508 3.065925 GCTTACCATGAACCAGCAATCTC 59.934 47.826 0.00 0.00 0.00 2.75
2215 3512 1.709147 ATGAACCAGCAATCTCGCGC 61.709 55.000 0.00 0.00 36.85 6.86
2256 3553 9.856488 TCTCAAGTATGAACTGTATTAAGTGAC 57.144 33.333 0.00 0.00 35.62 3.67
2257 3554 9.639601 CTCAAGTATGAACTGTATTAAGTGACA 57.360 33.333 0.00 0.00 35.62 3.58
2268 3569 8.950210 ACTGTATTAAGTGACAATCAATCTTGG 58.050 33.333 0.00 0.00 0.00 3.61
2278 3579 4.529377 ACAATCAATCTTGGGCTGATTTGT 59.471 37.500 0.00 0.00 37.63 2.83
2290 3594 4.412207 GGCTGATTTGTATTTCGTTCCAC 58.588 43.478 0.00 0.00 0.00 4.02
2389 3693 8.523915 ACATTATCATTGTTGCATTCTCCTTA 57.476 30.769 0.00 0.00 0.00 2.69
2424 3728 1.469703 CTTGATTGATGGAAGCGTGCA 59.530 47.619 0.00 0.00 0.00 4.57
2425 3729 1.532523 TGATTGATGGAAGCGTGCAA 58.467 45.000 0.00 0.00 0.00 4.08
2448 3752 2.533266 TTCAGAAGCTGTCCACTGAC 57.467 50.000 0.00 0.00 38.77 3.51
2468 3772 5.371526 TGACTGCTGTTGAGATTTCTTCTT 58.628 37.500 0.00 0.00 33.74 2.52
2470 3774 6.017605 TGACTGCTGTTGAGATTTCTTCTTTC 60.018 38.462 0.00 0.00 33.74 2.62
2471 3775 6.060788 ACTGCTGTTGAGATTTCTTCTTTCT 58.939 36.000 0.00 0.00 33.74 2.52
2482 3786 7.210873 AGATTTCTTCTTTCTGTCGTGTTAGT 58.789 34.615 0.00 0.00 0.00 2.24
2488 3792 4.337274 TCTTTCTGTCGTGTTAGTCAGTCA 59.663 41.667 0.00 0.00 0.00 3.41
2495 3799 7.707464 TCTGTCGTGTTAGTCAGTCAATTTTAA 59.293 33.333 0.00 0.00 0.00 1.52
2553 3857 3.400054 GGGTTAGAGCCCGCCACT 61.400 66.667 0.00 0.00 39.17 4.00
2554 3858 2.187163 GGTTAGAGCCCGCCACTC 59.813 66.667 0.00 0.00 0.00 3.51
2555 3859 2.202756 GTTAGAGCCCGCCACTCG 60.203 66.667 0.00 0.00 39.23 4.18
2617 3921 8.282455 TGATGAAAATTTAGTTGCCGGTAATA 57.718 30.769 8.64 0.00 0.00 0.98
2625 3929 4.667519 AGTTGCCGGTAATACCTAGAAG 57.332 45.455 8.64 0.00 35.66 2.85
2626 3930 4.284178 AGTTGCCGGTAATACCTAGAAGA 58.716 43.478 8.64 0.00 35.66 2.87
2627 3931 4.341520 AGTTGCCGGTAATACCTAGAAGAG 59.658 45.833 8.64 0.00 35.66 2.85
2628 3932 3.907221 TGCCGGTAATACCTAGAAGAGT 58.093 45.455 7.95 0.00 35.66 3.24
2629 3933 4.284178 TGCCGGTAATACCTAGAAGAGTT 58.716 43.478 7.95 0.00 35.66 3.01
2630 3934 4.713321 TGCCGGTAATACCTAGAAGAGTTT 59.287 41.667 7.95 0.00 35.66 2.66
2631 3935 5.188359 TGCCGGTAATACCTAGAAGAGTTTT 59.812 40.000 7.95 0.00 35.66 2.43
2633 3937 6.047231 CCGGTAATACCTAGAAGAGTTTTGG 58.953 44.000 7.95 0.00 35.66 3.28
2636 3940 6.822170 GGTAATACCTAGAAGAGTTTTGGGTG 59.178 42.308 1.41 0.00 34.73 4.61
2671 3977 1.372087 GAATGGCGGCAGGAGTTCTG 61.372 60.000 19.29 0.00 46.03 3.02
2716 4025 6.876257 ACTAGAAAGAATACCAGAGTTTGCTG 59.124 38.462 0.00 0.00 35.66 4.41
2717 4026 5.869579 AGAAAGAATACCAGAGTTTGCTGA 58.130 37.500 0.00 0.00 38.14 4.26
2725 4034 3.515502 ACCAGAGTTTGCTGATAGCTACA 59.484 43.478 0.00 0.00 42.97 2.74
2726 4035 4.118410 CCAGAGTTTGCTGATAGCTACAG 58.882 47.826 15.08 15.08 42.97 2.74
2758 4192 4.212847 CCTGATGATTTAGACAATGCCTCG 59.787 45.833 0.00 0.00 0.00 4.63
2768 4202 0.950836 CAATGCCTCGACACCAAACA 59.049 50.000 0.00 0.00 0.00 2.83
2773 4207 0.179056 CCTCGACACCAAACACACCT 60.179 55.000 0.00 0.00 0.00 4.00
2774 4208 0.937304 CTCGACACCAAACACACCTG 59.063 55.000 0.00 0.00 0.00 4.00
2789 4223 4.400884 ACACACCTGAGTAAAATGCACAAA 59.599 37.500 0.00 0.00 0.00 2.83
2791 4225 5.231991 CACACCTGAGTAAAATGCACAAAAC 59.768 40.000 0.00 0.00 0.00 2.43
2798 4232 2.323968 AAATGCACAAAACCACCACC 57.676 45.000 0.00 0.00 0.00 4.61
2803 4237 2.028876 GCACAAAACCACCACCTTAGT 58.971 47.619 0.00 0.00 0.00 2.24
2804 4238 2.223711 GCACAAAACCACCACCTTAGTG 60.224 50.000 0.00 0.00 44.12 2.74
2815 4249 4.645136 CACCACCTTAGTGTCATAGCTCTA 59.355 45.833 0.00 0.00 42.88 2.43
2817 4251 5.133941 CCACCTTAGTGTCATAGCTCTAGA 58.866 45.833 0.00 0.00 42.88 2.43
2823 4257 7.492994 CCTTAGTGTCATAGCTCTAGAAAAACC 59.507 40.741 0.00 0.00 0.00 3.27
2825 4259 6.951971 AGTGTCATAGCTCTAGAAAAACCAT 58.048 36.000 0.00 0.00 0.00 3.55
2829 4263 6.818644 GTCATAGCTCTAGAAAAACCATCACA 59.181 38.462 0.00 0.00 0.00 3.58
2853 4287 3.380142 ACAAAATGTGACATTTCGCACC 58.620 40.909 22.29 0.00 45.01 5.01
2854 4288 2.330231 AAATGTGACATTTCGCACCG 57.670 45.000 17.19 0.00 45.01 4.94
2855 4289 1.518325 AATGTGACATTTCGCACCGA 58.482 45.000 4.72 0.00 45.01 4.69
2856 4290 1.518325 ATGTGACATTTCGCACCGAA 58.482 45.000 0.00 0.00 45.01 4.30
2857 4291 0.584396 TGTGACATTTCGCACCGAAC 59.416 50.000 0.00 0.00 45.64 3.95
2858 4292 0.110373 GTGACATTTCGCACCGAACC 60.110 55.000 0.00 0.00 45.64 3.62
2859 4293 0.533085 TGACATTTCGCACCGAACCA 60.533 50.000 0.00 0.00 45.64 3.67
2860 4294 0.589223 GACATTTCGCACCGAACCAA 59.411 50.000 0.00 0.00 45.64 3.67
2861 4295 1.002251 GACATTTCGCACCGAACCAAA 60.002 47.619 0.00 0.00 45.64 3.28
2862 4296 1.405821 ACATTTCGCACCGAACCAAAA 59.594 42.857 0.00 0.00 45.64 2.44
2863 4297 2.159226 ACATTTCGCACCGAACCAAAAA 60.159 40.909 0.00 0.00 45.64 1.94
2864 4298 2.873133 TTTCGCACCGAACCAAAAAT 57.127 40.000 0.00 0.00 45.64 1.82
2865 4299 2.873133 TTCGCACCGAACCAAAAATT 57.127 40.000 0.00 0.00 41.05 1.82
2866 4300 2.873133 TCGCACCGAACCAAAAATTT 57.127 40.000 0.00 0.00 31.06 1.82
2867 4301 2.464865 TCGCACCGAACCAAAAATTTG 58.535 42.857 0.00 0.00 33.67 2.32
2868 4302 2.099263 TCGCACCGAACCAAAAATTTGA 59.901 40.909 7.44 0.00 34.92 2.69
2869 4303 2.217620 CGCACCGAACCAAAAATTTGAC 59.782 45.455 7.44 0.00 40.55 3.18
2870 4304 3.190874 GCACCGAACCAAAAATTTGACA 58.809 40.909 7.44 0.00 40.55 3.58
2871 4305 3.245048 GCACCGAACCAAAAATTTGACAG 59.755 43.478 7.44 0.00 40.55 3.51
2872 4306 4.429108 CACCGAACCAAAAATTTGACAGT 58.571 39.130 7.44 0.00 40.55 3.55
2873 4307 4.267452 CACCGAACCAAAAATTTGACAGTG 59.733 41.667 7.44 0.00 40.55 3.66
2874 4308 4.158764 ACCGAACCAAAAATTTGACAGTGA 59.841 37.500 7.44 0.00 40.55 3.41
2875 4309 4.502645 CCGAACCAAAAATTTGACAGTGAC 59.497 41.667 7.44 0.00 40.55 3.67
2876 4310 5.098893 CGAACCAAAAATTTGACAGTGACA 58.901 37.500 7.44 0.00 40.55 3.58
2877 4311 5.574830 CGAACCAAAAATTTGACAGTGACAA 59.425 36.000 7.44 3.83 40.55 3.18
2924 4358 4.555801 CGTTTTGATGACGTCACTAATCG 58.444 43.478 22.71 20.41 36.32 3.34
2945 4379 0.254747 CCGGGCTCAAGGTGGATTAA 59.745 55.000 0.00 0.00 0.00 1.40
2952 4386 3.620966 GCTCAAGGTGGATTAAGAGTGCT 60.621 47.826 0.00 0.00 0.00 4.40
2974 4408 5.574830 GCTAGATATCACCGCTCATAACAAG 59.425 44.000 5.32 0.00 0.00 3.16
3028 4462 8.737168 TTCTCAACAAGTATAATTCTCCATGG 57.263 34.615 4.97 4.97 0.00 3.66
3031 4465 7.410174 TCAACAAGTATAATTCTCCATGGGTT 58.590 34.615 13.02 4.97 0.00 4.11
3033 4467 8.840321 CAACAAGTATAATTCTCCATGGGTTAG 58.160 37.037 13.02 1.69 0.00 2.34
3041 4475 2.373169 TCTCCATGGGTTAGCATCATCC 59.627 50.000 13.02 0.00 0.00 3.51
3044 4478 0.401738 ATGGGTTAGCATCATCCGGG 59.598 55.000 0.00 0.00 0.00 5.73
3071 4505 4.382470 CCCACTATTCACACTCTCTTCCTG 60.382 50.000 0.00 0.00 0.00 3.86
3077 4511 4.047627 TCACACTCTCTTCCTGGTGATA 57.952 45.455 0.00 0.00 34.28 2.15
3087 4521 2.126882 TCCTGGTGATAGGATGGTTGG 58.873 52.381 0.00 0.00 41.85 3.77
3105 4539 3.611025 TGGATCCTTTTGGTGGAAAGT 57.389 42.857 14.23 0.00 41.38 2.66
3107 4541 5.068215 TGGATCCTTTTGGTGGAAAGTTA 57.932 39.130 14.23 0.00 41.38 2.24
3111 4545 6.437477 GGATCCTTTTGGTGGAAAGTTATTCT 59.563 38.462 3.84 0.00 41.38 2.40
3130 4567 9.691362 GTTATTCTGAGACTTCTATCCATCTTC 57.309 37.037 0.00 0.00 0.00 2.87
3137 4574 7.604164 TGAGACTTCTATCCATCTTCAAACAAC 59.396 37.037 0.00 0.00 0.00 3.32
3141 4578 9.136323 ACTTCTATCCATCTTCAAACAACTTTT 57.864 29.630 0.00 0.00 0.00 2.27
3148 4585 6.638468 CCATCTTCAAACAACTTTTAGTCTGC 59.362 38.462 0.00 0.00 0.00 4.26
3157 4594 3.222603 ACTTTTAGTCTGCAAACCTGGG 58.777 45.455 0.00 0.00 0.00 4.45
3197 4634 0.112218 TTGGACTGATGGTTGGTGGG 59.888 55.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
546 553 6.210078 ACGCGAAAATGATTTTGAAAAGGTA 58.790 32.000 15.93 0.00 32.49 3.08
560 567 5.627172 TCTGAAATTCCTAACGCGAAAATG 58.373 37.500 15.93 0.00 0.00 2.32
616 623 3.179443 TCCTTGACTTGATATGGCGTC 57.821 47.619 0.00 0.00 0.00 5.19
629 636 2.930682 GCGATAGACAACCTTCCTTGAC 59.069 50.000 0.00 0.00 39.76 3.18
703 711 2.169832 TCACAAAAAGCTCTCCTCGG 57.830 50.000 0.00 0.00 0.00 4.63
734 743 3.276091 CGGCCCATTCGCGCAATA 61.276 61.111 8.75 0.00 0.00 1.90
788 797 1.877443 GGTAGGTCATCTCGAGAGCTC 59.123 57.143 21.52 5.27 42.35 4.09
789 798 1.493022 AGGTAGGTCATCTCGAGAGCT 59.507 52.381 21.52 14.81 45.03 4.09
790 799 1.877443 GAGGTAGGTCATCTCGAGAGC 59.123 57.143 21.52 12.81 0.00 4.09
791 800 2.105821 AGGAGGTAGGTCATCTCGAGAG 59.894 54.545 21.52 12.70 0.00 3.20
792 801 2.128535 AGGAGGTAGGTCATCTCGAGA 58.871 52.381 19.19 19.19 0.00 4.04
793 802 2.649531 AGGAGGTAGGTCATCTCGAG 57.350 55.000 5.93 5.93 0.00 4.04
794 803 2.775960 TGTAGGAGGTAGGTCATCTCGA 59.224 50.000 0.00 0.00 0.00 4.04
795 804 3.210232 TGTAGGAGGTAGGTCATCTCG 57.790 52.381 0.00 0.00 0.00 4.04
796 805 5.278561 CGAAATGTAGGAGGTAGGTCATCTC 60.279 48.000 0.00 0.00 0.00 2.75
797 806 4.585162 CGAAATGTAGGAGGTAGGTCATCT 59.415 45.833 0.00 0.00 0.00 2.90
798 807 4.341520 ACGAAATGTAGGAGGTAGGTCATC 59.658 45.833 0.00 0.00 0.00 2.92
799 808 4.099573 CACGAAATGTAGGAGGTAGGTCAT 59.900 45.833 0.00 0.00 0.00 3.06
800 809 3.446161 CACGAAATGTAGGAGGTAGGTCA 59.554 47.826 0.00 0.00 0.00 4.02
801 810 3.698040 TCACGAAATGTAGGAGGTAGGTC 59.302 47.826 0.00 0.00 0.00 3.85
802 811 3.705051 TCACGAAATGTAGGAGGTAGGT 58.295 45.455 0.00 0.00 0.00 3.08
803 812 4.501571 CCATCACGAAATGTAGGAGGTAGG 60.502 50.000 0.00 0.00 0.00 3.18
804 813 4.501571 CCCATCACGAAATGTAGGAGGTAG 60.502 50.000 0.00 0.00 0.00 3.18
805 814 3.386726 CCCATCACGAAATGTAGGAGGTA 59.613 47.826 0.00 0.00 0.00 3.08
806 815 2.170607 CCCATCACGAAATGTAGGAGGT 59.829 50.000 0.00 0.00 0.00 3.85
807 816 2.838736 CCCATCACGAAATGTAGGAGG 58.161 52.381 0.00 0.00 0.00 4.30
808 817 2.158900 AGCCCATCACGAAATGTAGGAG 60.159 50.000 0.00 0.00 0.00 3.69
809 818 1.837439 AGCCCATCACGAAATGTAGGA 59.163 47.619 0.00 0.00 0.00 2.94
810 819 1.942657 CAGCCCATCACGAAATGTAGG 59.057 52.381 0.00 0.00 0.00 3.18
811 820 1.942657 CCAGCCCATCACGAAATGTAG 59.057 52.381 0.00 0.00 0.00 2.74
812 821 1.557371 TCCAGCCCATCACGAAATGTA 59.443 47.619 0.00 0.00 0.00 2.29
813 822 0.327924 TCCAGCCCATCACGAAATGT 59.672 50.000 0.00 0.00 0.00 2.71
814 823 1.462616 TTCCAGCCCATCACGAAATG 58.537 50.000 0.00 0.00 0.00 2.32
815 824 2.214376 TTTCCAGCCCATCACGAAAT 57.786 45.000 0.00 0.00 0.00 2.17
816 825 1.611491 GTTTTCCAGCCCATCACGAAA 59.389 47.619 0.00 0.00 0.00 3.46
817 826 1.243902 GTTTTCCAGCCCATCACGAA 58.756 50.000 0.00 0.00 0.00 3.85
818 827 0.109532 TGTTTTCCAGCCCATCACGA 59.890 50.000 0.00 0.00 0.00 4.35
819 828 1.135315 CATGTTTTCCAGCCCATCACG 60.135 52.381 0.00 0.00 0.00 4.35
820 829 1.205417 CCATGTTTTCCAGCCCATCAC 59.795 52.381 0.00 0.00 0.00 3.06
821 830 1.203162 ACCATGTTTTCCAGCCCATCA 60.203 47.619 0.00 0.00 0.00 3.07
822 831 1.560505 ACCATGTTTTCCAGCCCATC 58.439 50.000 0.00 0.00 0.00 3.51
823 832 2.917713 TACCATGTTTTCCAGCCCAT 57.082 45.000 0.00 0.00 0.00 4.00
824 833 2.685106 TTACCATGTTTTCCAGCCCA 57.315 45.000 0.00 0.00 0.00 5.36
825 834 3.096092 TGATTACCATGTTTTCCAGCCC 58.904 45.455 0.00 0.00 0.00 5.19
826 835 3.763897 AGTGATTACCATGTTTTCCAGCC 59.236 43.478 0.00 0.00 0.00 4.85
827 836 4.380867 CCAGTGATTACCATGTTTTCCAGC 60.381 45.833 0.00 0.00 0.00 4.85
828 837 4.766891 ACCAGTGATTACCATGTTTTCCAG 59.233 41.667 0.00 0.00 0.00 3.86
829 838 4.522405 CACCAGTGATTACCATGTTTTCCA 59.478 41.667 0.00 0.00 0.00 3.53
830 839 4.082245 CCACCAGTGATTACCATGTTTTCC 60.082 45.833 0.00 0.00 0.00 3.13
831 840 4.082245 CCCACCAGTGATTACCATGTTTTC 60.082 45.833 0.00 0.00 0.00 2.29
835 844 1.340991 GCCCACCAGTGATTACCATGT 60.341 52.381 0.00 0.00 0.00 3.21
836 845 1.064463 AGCCCACCAGTGATTACCATG 60.064 52.381 0.00 0.00 0.00 3.66
837 846 1.064463 CAGCCCACCAGTGATTACCAT 60.064 52.381 0.00 0.00 0.00 3.55
844 853 1.483595 CCTTCTCAGCCCACCAGTGA 61.484 60.000 0.00 0.00 0.00 3.41
857 866 1.077429 GACCCACCATGGCCTTCTC 60.077 63.158 13.04 0.00 35.79 2.87
859 868 1.379044 CTGACCCACCATGGCCTTC 60.379 63.158 13.04 3.90 35.79 3.46
891 900 8.531982 AGTCACGACTATATATATTGCCACAAT 58.468 33.333 0.00 0.00 40.43 2.71
893 902 7.312899 CAGTCACGACTATATATATTGCCACA 58.687 38.462 0.00 0.00 40.20 4.17
898 907 8.669243 TCTCAGCAGTCACGACTATATATATTG 58.331 37.037 0.00 1.45 40.20 1.90
900 909 8.835439 CATCTCAGCAGTCACGACTATATATAT 58.165 37.037 0.00 0.00 40.20 0.86
902 911 6.657117 ACATCTCAGCAGTCACGACTATATAT 59.343 38.462 0.00 0.00 40.20 0.86
913 929 0.611896 TCGGGACATCTCAGCAGTCA 60.612 55.000 0.00 0.00 34.04 3.41
914 930 0.532573 TTCGGGACATCTCAGCAGTC 59.467 55.000 0.00 0.00 0.00 3.51
915 931 0.976641 TTTCGGGACATCTCAGCAGT 59.023 50.000 0.00 0.00 0.00 4.40
916 932 1.734465 GTTTTCGGGACATCTCAGCAG 59.266 52.381 0.00 0.00 0.00 4.24
917 933 1.347707 AGTTTTCGGGACATCTCAGCA 59.652 47.619 0.00 0.00 0.00 4.41
918 934 2.100605 AGTTTTCGGGACATCTCAGC 57.899 50.000 0.00 0.00 0.00 4.26
919 935 3.003480 GGAAGTTTTCGGGACATCTCAG 58.997 50.000 0.00 0.00 0.00 3.35
920 936 2.370519 TGGAAGTTTTCGGGACATCTCA 59.629 45.455 0.00 0.00 0.00 3.27
921 937 3.053831 TGGAAGTTTTCGGGACATCTC 57.946 47.619 0.00 0.00 0.00 2.75
922 938 3.412386 CTTGGAAGTTTTCGGGACATCT 58.588 45.455 0.00 0.00 0.00 2.90
923 939 2.488153 CCTTGGAAGTTTTCGGGACATC 59.512 50.000 0.00 0.00 0.00 3.06
924 940 2.514803 CCTTGGAAGTTTTCGGGACAT 58.485 47.619 0.00 0.00 0.00 3.06
925 941 1.477923 CCCTTGGAAGTTTTCGGGACA 60.478 52.381 0.00 0.00 31.64 4.02
926 942 1.244816 CCCTTGGAAGTTTTCGGGAC 58.755 55.000 0.00 0.00 31.64 4.46
927 943 0.848053 ACCCTTGGAAGTTTTCGGGA 59.152 50.000 0.00 0.00 33.55 5.14
935 951 1.363246 GAGGAGGAACCCTTGGAAGT 58.637 55.000 0.00 0.00 40.05 3.01
1012 1028 2.491621 CGCCGAGATCTCACTGCA 59.508 61.111 22.31 0.00 0.00 4.41
1122 1138 2.603247 CCAGCGCTTGCACGTACAA 61.603 57.895 7.50 0.45 42.66 2.41
1254 1277 0.252197 AGAAGACGGGGTTGCATACC 59.748 55.000 8.94 8.94 46.99 2.73
1311 1337 2.126307 TCGAGCGAGAAGTGCTGC 60.126 61.111 0.00 0.00 44.18 5.25
1338 1364 2.029666 GAGCCGCCATCGCAGTAT 59.970 61.111 0.00 0.00 34.03 2.12
1339 1365 4.221422 GGAGCCGCCATCGCAGTA 62.221 66.667 0.00 0.00 36.34 2.74
1387 1413 1.731720 GTGCACTGATTCAGGAGGAC 58.268 55.000 17.66 15.59 35.51 3.85
1408 1434 3.878519 CTCCTCGTCCTCGGCGTC 61.879 72.222 6.85 0.00 37.69 5.19
1560 1592 4.479993 AGGCTGATGCGCTCACCC 62.480 66.667 9.73 10.68 40.82 4.61
1581 1613 6.216750 AGCGCGACTATTATTCTGAAATTC 57.783 37.500 12.10 0.00 0.00 2.17
1713 1754 2.347755 GGTGAAATTCCGAGCGAAGTAC 59.652 50.000 0.00 0.00 32.78 2.73
1732 1773 1.411216 CCTCCAGTAGACATACCGGGT 60.411 57.143 6.32 4.46 31.29 5.28
1737 1778 2.652590 ACGGTCCTCCAGTAGACATAC 58.347 52.381 0.00 0.00 34.58 2.39
1828 1869 0.460311 ACCTCGAGCCTGAAATACCG 59.540 55.000 6.99 0.00 0.00 4.02
1833 1874 1.275291 CCTACAACCTCGAGCCTGAAA 59.725 52.381 16.31 5.67 0.00 2.69
1892 1936 1.205655 TGAAGACCTTGAGATGGCTCG 59.794 52.381 0.00 0.00 44.33 5.03
1893 1937 2.027745 TGTGAAGACCTTGAGATGGCTC 60.028 50.000 0.00 0.00 41.67 4.70
1913 1957 0.549950 ATCCCTGCCCTCTGATTGTG 59.450 55.000 0.00 0.00 0.00 3.33
1918 1962 0.841961 CATTCATCCCTGCCCTCTGA 59.158 55.000 0.00 0.00 0.00 3.27
1950 1994 0.533755 ACTGCTGCAGTTGGACACTC 60.534 55.000 28.49 0.00 42.59 3.51
1992 2036 0.742505 TGTCGACGTTCAACTCACCT 59.257 50.000 11.62 0.00 0.00 4.00
2017 2061 1.646189 GCCACCGAGACAATCTTCTC 58.354 55.000 0.00 0.00 39.01 2.87
2055 2099 1.577468 CCACGCAGTTGTCTGTACAA 58.423 50.000 0.00 0.00 41.61 2.41
2067 2111 2.202987 GAGATGAGCCCCACGCAG 60.203 66.667 0.00 0.00 41.38 5.18
2068 2112 3.785859 GGAGATGAGCCCCACGCA 61.786 66.667 0.00 0.00 41.38 5.24
2116 2160 3.625938 AGTACTTGTTCTCGTCGTGAAC 58.374 45.455 25.65 25.65 42.77 3.18
2152 2196 1.026718 GGCCATGTCAGCTGGTACAC 61.027 60.000 15.13 4.99 36.10 2.90
2164 2208 2.746375 GGATCGTGGGAGGCCATGT 61.746 63.158 5.01 0.00 0.00 3.21
2211 3508 3.810373 AGAACAAAATAAACAGAGCGCG 58.190 40.909 0.00 0.00 0.00 6.86
2256 3553 5.080969 ACAAATCAGCCCAAGATTGATTG 57.919 39.130 0.26 0.00 39.82 2.67
2257 3554 7.427989 AATACAAATCAGCCCAAGATTGATT 57.572 32.000 0.00 0.00 41.84 2.57
2268 3569 4.412207 GTGGAACGAAATACAAATCAGCC 58.588 43.478 0.00 0.00 0.00 4.85
2323 3627 9.063615 GGAACTGAAATACTTGAAAGTTTCCTA 57.936 33.333 13.01 0.72 40.37 2.94
2324 3628 7.780271 AGGAACTGAAATACTTGAAAGTTTCCT 59.220 33.333 13.01 13.58 39.57 3.36
2325 3629 7.941919 AGGAACTGAAATACTTGAAAGTTTCC 58.058 34.615 13.01 6.72 37.68 3.13
2331 3635 7.889873 TTCCAAGGAACTGAAATACTTGAAA 57.110 32.000 0.00 0.00 40.86 2.69
2389 3693 7.892241 CCATCAATCAAGATATTTCCCCTACAT 59.108 37.037 0.00 0.00 0.00 2.29
2424 3728 4.889409 TCAGTGGACAGCTTCTGAAAAATT 59.111 37.500 0.29 0.00 34.61 1.82
2425 3729 4.276926 GTCAGTGGACAGCTTCTGAAAAAT 59.723 41.667 0.29 0.00 43.73 1.82
2448 3752 6.017275 ACAGAAAGAAGAAATCTCAACAGCAG 60.017 38.462 0.00 0.00 37.42 4.24
2468 3772 4.642445 TTGACTGACTAACACGACAGAA 57.358 40.909 0.00 0.00 34.88 3.02
2470 3774 5.907197 AAATTGACTGACTAACACGACAG 57.093 39.130 0.00 0.00 36.58 3.51
2471 3775 7.773864 TTAAAATTGACTGACTAACACGACA 57.226 32.000 0.00 0.00 0.00 4.35
2482 3786 8.886719 CATAGCTCTCACATTAAAATTGACTGA 58.113 33.333 0.00 0.00 0.00 3.41
2495 3799 5.600069 TGTGAAGGTATCATAGCTCTCACAT 59.400 40.000 23.56 1.88 42.33 3.21
2549 3853 4.988598 ACAAGTGGCGGCGAGTGG 62.989 66.667 12.98 0.00 0.00 4.00
2550 3854 2.972505 AACAAGTGGCGGCGAGTG 60.973 61.111 12.98 4.17 0.00 3.51
2551 3855 2.972505 CAACAAGTGGCGGCGAGT 60.973 61.111 12.98 0.00 0.00 4.18
2552 3856 4.389576 GCAACAAGTGGCGGCGAG 62.390 66.667 12.98 0.00 0.00 5.03
2554 3858 4.263209 TTGCAACAAGTGGCGGCG 62.263 61.111 0.51 0.51 0.00 6.46
2555 3859 2.355009 CTTGCAACAAGTGGCGGC 60.355 61.111 0.00 0.00 0.00 6.53
2565 3869 6.919721 TGGATTATAAAGTTGGTCTTGCAAC 58.080 36.000 0.00 0.00 36.40 4.17
2617 3921 4.790718 AACACCCAAAACTCTTCTAGGT 57.209 40.909 0.00 0.00 0.00 3.08
2651 3957 1.377202 GAACTCCTGCCGCCATTCA 60.377 57.895 0.00 0.00 0.00 2.57
2652 3958 1.078143 AGAACTCCTGCCGCCATTC 60.078 57.895 0.00 0.00 0.00 2.67
2663 3969 9.606631 CTAATATAATAGAATGGGCAGAACTCC 57.393 37.037 0.00 0.00 0.00 3.85
2716 4025 2.966516 AGGTTGTAGGCCTGTAGCTATC 59.033 50.000 17.99 0.33 43.05 2.08
2717 4026 2.700897 CAGGTTGTAGGCCTGTAGCTAT 59.299 50.000 17.99 0.00 46.22 2.97
2725 4034 4.721776 TCTAAATCATCAGGTTGTAGGCCT 59.278 41.667 11.78 11.78 36.66 5.19
2726 4035 4.816925 GTCTAAATCATCAGGTTGTAGGCC 59.183 45.833 0.00 0.00 0.00 5.19
2758 4192 2.038387 ACTCAGGTGTGTTTGGTGTC 57.962 50.000 0.00 0.00 0.00 3.67
2768 4202 5.348164 GTTTTGTGCATTTTACTCAGGTGT 58.652 37.500 0.00 0.00 0.00 4.16
2773 4207 4.160439 TGGTGGTTTTGTGCATTTTACTCA 59.840 37.500 0.00 0.00 0.00 3.41
2774 4208 4.506288 GTGGTGGTTTTGTGCATTTTACTC 59.494 41.667 0.00 0.00 0.00 2.59
2789 4223 3.307480 GCTATGACACTAAGGTGGTGGTT 60.307 47.826 1.29 0.00 46.85 3.67
2791 4225 2.501723 AGCTATGACACTAAGGTGGTGG 59.498 50.000 0.00 0.00 46.85 4.61
2798 4232 8.035394 TGGTTTTTCTAGAGCTATGACACTAAG 58.965 37.037 0.00 0.00 0.00 2.18
2803 4237 6.818644 GTGATGGTTTTTCTAGAGCTATGACA 59.181 38.462 0.00 0.00 0.00 3.58
2804 4238 6.818644 TGTGATGGTTTTTCTAGAGCTATGAC 59.181 38.462 0.00 0.00 0.00 3.06
2829 4263 5.633182 GGTGCGAAATGTCACATTTTGTAAT 59.367 36.000 25.27 1.43 35.04 1.89
2853 4287 5.098893 TGTCACTGTCAAATTTTTGGTTCG 58.901 37.500 3.38 0.00 38.66 3.95
2854 4288 6.959671 TTGTCACTGTCAAATTTTTGGTTC 57.040 33.333 3.38 0.00 38.66 3.62
2855 4289 7.158021 TCTTTGTCACTGTCAAATTTTTGGTT 58.842 30.769 3.38 0.00 38.66 3.67
2856 4290 6.696411 TCTTTGTCACTGTCAAATTTTTGGT 58.304 32.000 3.38 0.00 38.66 3.67
2857 4291 7.117523 TGTTCTTTGTCACTGTCAAATTTTTGG 59.882 33.333 3.38 0.00 38.66 3.28
2858 4292 7.951565 GTGTTCTTTGTCACTGTCAAATTTTTG 59.048 33.333 2.50 0.00 39.48 2.44
2859 4293 7.872483 AGTGTTCTTTGTCACTGTCAAATTTTT 59.128 29.630 2.50 0.00 42.30 1.94
2860 4294 7.378181 AGTGTTCTTTGTCACTGTCAAATTTT 58.622 30.769 2.50 0.00 42.30 1.82
2861 4295 6.924111 AGTGTTCTTTGTCACTGTCAAATTT 58.076 32.000 2.50 0.00 42.30 1.82
2862 4296 6.515272 AGTGTTCTTTGTCACTGTCAAATT 57.485 33.333 2.50 0.00 42.30 1.82
2870 4304 2.093658 ACCGTCAGTGTTCTTTGTCACT 60.094 45.455 0.00 0.00 44.32 3.41
2871 4305 2.030457 CACCGTCAGTGTTCTTTGTCAC 59.970 50.000 0.00 0.00 41.93 3.67
2872 4306 2.276201 CACCGTCAGTGTTCTTTGTCA 58.724 47.619 0.00 0.00 41.93 3.58
2873 4307 1.597663 CCACCGTCAGTGTTCTTTGTC 59.402 52.381 0.00 0.00 45.74 3.18
2874 4308 1.208535 TCCACCGTCAGTGTTCTTTGT 59.791 47.619 0.00 0.00 45.74 2.83
2875 4309 1.948104 TCCACCGTCAGTGTTCTTTG 58.052 50.000 0.00 0.00 45.74 2.77
2876 4310 2.494059 CATCCACCGTCAGTGTTCTTT 58.506 47.619 0.00 0.00 45.74 2.52
2877 4311 1.878102 GCATCCACCGTCAGTGTTCTT 60.878 52.381 0.00 0.00 45.74 2.52
2889 4323 1.810151 TCAAAACGCTTAGCATCCACC 59.190 47.619 4.70 0.00 0.00 4.61
2945 4379 2.817258 GAGCGGTGATATCTAGCACTCT 59.183 50.000 15.95 3.82 41.94 3.24
2952 4386 5.566826 GCCTTGTTATGAGCGGTGATATCTA 60.567 44.000 3.98 0.00 0.00 1.98
2974 4408 3.863142 ATGAACTTCATGAGCAAAGCC 57.137 42.857 3.32 0.00 35.43 4.35
3028 4462 1.947456 GTTTCCCGGATGATGCTAACC 59.053 52.381 0.73 0.00 0.00 2.85
3031 4465 0.472471 GGGTTTCCCGGATGATGCTA 59.528 55.000 0.73 0.00 32.13 3.49
3033 4467 3.841870 GGGTTTCCCGGATGATGC 58.158 61.111 0.73 0.00 32.13 3.91
3044 4478 5.153950 AGAGAGTGTGAATAGTGGGTTTC 57.846 43.478 0.00 0.00 0.00 2.78
3071 4505 3.425162 GGATCCAACCATCCTATCACC 57.575 52.381 6.95 0.00 39.59 4.02
3087 4521 7.176690 TCAGAATAACTTTCCACCAAAAGGATC 59.823 37.037 1.90 0.00 39.96 3.36
3105 4539 9.426534 TGAAGATGGATAGAAGTCTCAGAATAA 57.573 33.333 0.00 0.00 0.00 1.40
3107 4541 7.911130 TGAAGATGGATAGAAGTCTCAGAAT 57.089 36.000 0.00 0.00 0.00 2.40
3111 4545 7.244886 TGTTTGAAGATGGATAGAAGTCTCA 57.755 36.000 0.00 0.00 0.00 3.27
3130 4567 6.034898 CAGGTTTGCAGACTAAAAGTTGTTTG 59.965 38.462 7.38 0.00 0.00 2.93
3137 4574 2.558359 CCCCAGGTTTGCAGACTAAAAG 59.442 50.000 7.38 0.00 0.00 2.27
3141 4578 1.133809 AGCCCCAGGTTTGCAGACTA 61.134 55.000 7.38 0.00 0.00 2.59
3145 4582 2.993264 CCAGCCCCAGGTTTGCAG 60.993 66.667 0.00 0.00 0.00 4.41
3148 4585 2.523902 TTGCCAGCCCCAGGTTTG 60.524 61.111 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.