Multiple sequence alignment - TraesCS6A01G300000

Loading Multiple Alignment...

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 TraesCS6A01G300000 chr6A 100.000 2222 0 0 1 2222 532897301 532899522 0.000000e+00 4104.0
1 TraesCS6A01G300000 chr6A 75.549 319 47 15 4 298 533252433 533252744 6.440000e-26 128.0
2 TraesCS6A01G300000 chr6B 86.660 937 75 23 1 910 578949717 578950630 0.000000e+00 992.0
3 TraesCS6A01G300000 chr6B 92.760 442 30 2 1370 1810 578951389 578951829 2.410000e-179 638.0
4 TraesCS6A01G300000 chr6B 92.435 423 21 3 950 1368 578950615 578951030 5.280000e-166 593.0
5 TraesCS6A01G300000 chr6B 89.888 178 11 3 2049 2222 578951828 578952002 2.870000e-54 222.0
6 TraesCS6A01G300000 chr6B 81.223 229 26 9 694 906 579094126 579094353 3.790000e-38 169.0
7 TraesCS6A01G300000 chr6B 75.051 489 58 37 334 801 579102168 579102613 3.790000e-38 169.0
8 TraesCS6A01G300000 chr6B 85.897 156 20 2 953 1106 579214503 579214658 4.910000e-37 165.0
9 TraesCS6A01G300000 chr6B 76.994 326 37 18 5 298 579090937 579091256 3.820000e-33 152.0
10 TraesCS6A01G300000 chr6D 94.297 526 26 2 948 1470 387780767 387781291 0.000000e+00 802.0
11 TraesCS6A01G300000 chr6D 87.551 739 26 21 94 791 387766941 387767654 0.000000e+00 795.0
12 TraesCS6A01G300000 chr6D 90.751 346 22 3 1464 1809 387782322 387782657 9.350000e-124 453.0
13 TraesCS6A01G300000 chr6D 94.220 173 8 1 2050 2222 387782663 387782833 1.690000e-66 263.0
14 TraesCS6A01G300000 chr6D 95.495 111 4 1 1 110 387764061 387764171 2.270000e-40 176.0
15 TraesCS6A01G300000 chr6D 80.531 113 13 2 193 298 387880919 387881029 6.580000e-11 78.7
16 TraesCS6A01G300000 chr7A 94.262 244 13 1 1808 2051 664890473 664890715 2.690000e-99 372.0
17 TraesCS6A01G300000 chr7A 92.800 250 16 2 1802 2050 722869192 722869440 5.830000e-96 361.0
18 TraesCS6A01G300000 chr7A 97.778 45 1 0 1640 1684 124795738 124795694 6.580000e-11 78.7
19 TraesCS6A01G300000 chr5B 93.173 249 16 1 1803 2051 375130065 375130312 4.510000e-97 364.0
20 TraesCS6A01G300000 chr3A 92.578 256 16 3 1795 2050 123305511 123305763 4.510000e-97 364.0
21 TraesCS6A01G300000 chr5A 92.218 257 18 2 1801 2057 609286029 609286283 1.620000e-96 363.0
22 TraesCS6A01G300000 chr3B 93.496 246 13 3 1806 2050 497096331 497096574 1.620000e-96 363.0
23 TraesCS6A01G300000 chr2A 92.218 257 19 1 1807 2062 80822417 80822673 1.620000e-96 363.0
24 TraesCS6A01G300000 chr2A 92.188 256 18 2 1796 2050 752282681 752282935 5.830000e-96 361.0
25 TraesCS6A01G300000 chr2A 92.771 249 17 1 1809 2057 746964226 746963979 2.100000e-95 359.0
26 TraesCS6A01G300000 chr7B 97.727 44 1 0 1641 1684 472327472 472327515 2.370000e-10 76.8
27 TraesCS6A01G300000 chr7B 97.727 44 1 0 1641 1684 472394343 472394386 2.370000e-10 76.8
28 TraesCS6A01G300000 chr7B 95.745 47 2 0 1641 1687 651450550 651450504 2.370000e-10 76.8
29 TraesCS6A01G300000 chr7B 97.674 43 1 0 1642 1684 702453439 702453481 8.510000e-10 75.0
30 TraesCS6A01G300000 chr4D 95.556 45 2 0 1640 1684 370369252 370369296 3.060000e-09 73.1
31 TraesCS6A01G300000 chr5D 95.455 44 1 1 1641 1683 376654424 376654381 3.960000e-08 69.4


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 TraesCS6A01G300000 chr6A 532897301 532899522 2221 False 4104.00 4104 100.000000 1 2222 1 chr6A.!!$F1 2221
1 TraesCS6A01G300000 chr6B 578949717 578952002 2285 False 611.25 992 90.435750 1 2222 4 chr6B.!!$F3 2221
2 TraesCS6A01G300000 chr6D 387780767 387782833 2066 False 506.00 802 93.089333 948 2222 3 chr6D.!!$F3 1274
3 TraesCS6A01G300000 chr6D 387764061 387767654 3593 False 485.50 795 91.523000 1 791 2 chr6D.!!$F2 790

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
853 3702 0.530744 TACACACATCCGAGCTCCAC 59.469 55.0 8.47 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 6127 0.027194 CGCCGCAGTTGATCTCATTG 59.973 55.0 0.0 0.0 0.0 2.82 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
100 102 5.927954 AAAAAGAAATGTCTTACCGCGTA 57.072 34.783 4.92 0.00 43.59 4.42
103 105 4.184079 AGAAATGTCTTACCGCGTAAGT 57.816 40.909 20.28 9.35 43.95 2.24
135 2923 7.745972 TGTGGAGTAATACATATACGATCGAC 58.254 38.462 24.34 5.07 0.00 4.20
192 2980 3.939066 AGGGATCGTAAGTTTTCAGTGG 58.061 45.455 0.00 0.00 39.48 4.00
371 3177 4.324402 GCAAAGCATGTTGTCGAATAAAGG 59.676 41.667 0.00 0.00 0.00 3.11
385 3191 1.029408 TAAAGGGCATGCGACGCAAT 61.029 50.000 28.24 12.59 43.62 3.56
415 3225 3.003689 CCAGATTATTTGTGCGTCCCATC 59.996 47.826 0.00 0.00 0.00 3.51
494 3325 3.337358 GCAAAGCAAGCCATACCAAAAT 58.663 40.909 0.00 0.00 0.00 1.82
495 3326 4.502962 GCAAAGCAAGCCATACCAAAATA 58.497 39.130 0.00 0.00 0.00 1.40
542 3374 6.339587 AGAGGTTTCTCTCTTGACTACTTG 57.660 41.667 0.00 0.00 46.79 3.16
543 3375 6.071984 AGAGGTTTCTCTCTTGACTACTTGA 58.928 40.000 0.00 0.00 46.79 3.02
563 3395 3.069016 TGACTAAAACGACTTGGAGCTCA 59.931 43.478 17.19 0.00 0.00 4.26
598 3430 2.549349 GGGAGTACACGTTTCACATGGT 60.549 50.000 0.00 0.00 0.00 3.55
599 3431 2.478894 GGAGTACACGTTTCACATGGTG 59.521 50.000 0.00 0.00 36.50 4.17
625 3457 2.042831 CCGGGCCAAAAGCTCTCTG 61.043 63.158 4.39 0.00 41.26 3.35
655 3501 4.847365 GAGTACGTACATACTCGTGTCA 57.153 45.455 26.55 0.00 41.20 3.58
664 3510 4.185394 ACATACTCGTGTCACACAAAACA 58.815 39.130 9.06 0.00 33.40 2.83
672 3518 4.671508 CGTGTCACACAAAACATCACTGTT 60.672 41.667 9.06 0.00 39.69 3.16
673 3519 5.446607 CGTGTCACACAAAACATCACTGTTA 60.447 40.000 9.06 0.00 38.22 2.41
674 3520 6.494842 GTGTCACACAAAACATCACTGTTAT 58.505 36.000 2.00 0.00 38.22 1.89
675 3521 6.414694 GTGTCACACAAAACATCACTGTTATG 59.585 38.462 2.00 0.57 38.22 1.90
676 3522 6.094742 TGTCACACAAAACATCACTGTTATGT 59.905 34.615 1.87 1.87 44.83 2.29
677 3523 7.281100 TGTCACACAAAACATCACTGTTATGTA 59.719 33.333 7.94 0.00 44.83 2.29
678 3524 7.586300 GTCACACAAAACATCACTGTTATGTAC 59.414 37.037 7.94 0.00 44.83 2.90
679 3525 7.497579 TCACACAAAACATCACTGTTATGTACT 59.502 33.333 7.94 0.00 44.83 2.73
680 3526 8.769891 CACACAAAACATCACTGTTATGTACTA 58.230 33.333 7.94 0.00 44.83 1.82
681 3527 8.770828 ACACAAAACATCACTGTTATGTACTAC 58.229 33.333 7.94 0.00 44.83 2.73
682 3528 8.988934 CACAAAACATCACTGTTATGTACTACT 58.011 33.333 7.94 0.00 44.83 2.57
688 3534 8.824781 ACATCACTGTTATGTACTACTAGTACG 58.175 37.037 17.77 7.98 42.42 3.67
711 3557 5.229469 CGTACATTCGCTGTAAAGTTCCTAG 59.771 44.000 0.00 0.00 41.93 3.02
712 3558 3.933332 ACATTCGCTGTAAAGTTCCTAGC 59.067 43.478 0.00 0.00 35.91 3.42
760 3607 3.211963 GCCAAGCCGCCCATGTAG 61.212 66.667 0.00 0.00 0.00 2.74
769 3616 1.472552 CCGCCCATGTAGACGATGAAA 60.473 52.381 0.00 0.00 0.00 2.69
810 3657 3.131577 CGACGCAGGGCCCTTATATATAA 59.868 47.826 26.10 5.10 0.00 0.98
811 3658 4.439968 GACGCAGGGCCCTTATATATAAC 58.560 47.826 26.10 3.04 0.00 1.89
812 3659 3.118884 ACGCAGGGCCCTTATATATAACG 60.119 47.826 26.10 16.31 0.00 3.18
813 3660 3.118884 CGCAGGGCCCTTATATATAACGT 60.119 47.826 26.10 0.00 0.00 3.99
820 3667 5.636543 GGCCCTTATATATAACGTGTGTCAC 59.363 44.000 0.81 0.00 0.00 3.67
825 3672 7.652105 CCTTATATATAACGTGTGTCACAAGCT 59.348 37.037 17.45 9.16 33.40 3.74
826 3673 6.828502 ATATATAACGTGTGTCACAAGCTG 57.171 37.500 17.45 6.53 33.40 4.24
841 3688 3.832490 ACAAGCTGGTAGATCTACACACA 59.168 43.478 29.36 18.86 37.78 3.72
844 3691 3.639094 AGCTGGTAGATCTACACACATCC 59.361 47.826 29.36 14.17 37.78 3.51
845 3692 3.551046 GCTGGTAGATCTACACACATCCG 60.551 52.174 29.36 15.23 37.78 4.18
853 3702 0.530744 TACACACATCCGAGCTCCAC 59.469 55.000 8.47 0.00 0.00 4.02
903 3752 3.342377 TTCAGCGAGAAGAGAGAGAGA 57.658 47.619 0.00 0.00 0.00 3.10
904 3753 2.905075 TCAGCGAGAAGAGAGAGAGAG 58.095 52.381 0.00 0.00 0.00 3.20
905 3754 2.499693 TCAGCGAGAAGAGAGAGAGAGA 59.500 50.000 0.00 0.00 0.00 3.10
906 3755 2.868583 CAGCGAGAAGAGAGAGAGAGAG 59.131 54.545 0.00 0.00 0.00 3.20
907 3756 2.766263 AGCGAGAAGAGAGAGAGAGAGA 59.234 50.000 0.00 0.00 0.00 3.10
908 3757 3.126831 GCGAGAAGAGAGAGAGAGAGAG 58.873 54.545 0.00 0.00 0.00 3.20
909 3758 3.181475 GCGAGAAGAGAGAGAGAGAGAGA 60.181 52.174 0.00 0.00 0.00 3.10
910 3759 4.615949 CGAGAAGAGAGAGAGAGAGAGAG 58.384 52.174 0.00 0.00 0.00 3.20
911 3760 4.339530 CGAGAAGAGAGAGAGAGAGAGAGA 59.660 50.000 0.00 0.00 0.00 3.10
912 3761 5.507149 CGAGAAGAGAGAGAGAGAGAGAGAG 60.507 52.000 0.00 0.00 0.00 3.20
913 3762 5.523588 AGAAGAGAGAGAGAGAGAGAGAGA 58.476 45.833 0.00 0.00 0.00 3.10
914 3763 5.598005 AGAAGAGAGAGAGAGAGAGAGAGAG 59.402 48.000 0.00 0.00 0.00 3.20
915 3764 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
916 3765 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
917 3766 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
918 3767 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
919 3768 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
920 3769 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
921 3770 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
922 3771 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
923 3772 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
924 3773 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
925 3774 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
926 3775 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
927 3776 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
928 3777 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
929 3778 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
930 3779 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
931 3780 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
932 3781 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
933 3782 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
934 3783 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
935 3784 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
936 3785 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
937 3786 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
938 3787 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
939 3788 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
940 3789 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
941 3790 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
942 3791 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
943 3792 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
944 3793 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
945 3794 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
946 3795 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
947 3796 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
948 3797 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
949 3798 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
950 3799 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
951 3800 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
952 3801 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
953 3802 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
954 3803 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
955 3804 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
956 3805 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
957 3806 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
960 3809 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
966 3815 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1045 3894 1.153647 GTGCCGGTGATCGTGATGA 60.154 57.895 1.90 0.00 37.11 2.92
1062 3911 0.460109 TGATCATGGTGTTCTCGGCG 60.460 55.000 0.00 0.00 0.00 6.46
1065 3914 1.671054 CATGGTGTTCTCGGCGGTT 60.671 57.895 7.21 0.00 0.00 4.44
1342 4198 7.341917 AAACAGCAAACTGATGCCGTTAAAAA 61.342 34.615 10.50 0.00 44.01 1.94
1420 4633 2.110011 AGGCCCCTTGTTGAAAGTGTAT 59.890 45.455 0.00 0.00 0.00 2.29
1591 5842 6.211587 TGAATTGCCATTTCTCCAGTATTG 57.788 37.500 1.51 0.00 0.00 1.90
1639 5890 4.549458 CAAACCAACTGGAAATGCTACTG 58.451 43.478 1.86 0.00 38.94 2.74
1684 5935 6.015519 CACAACACTTATTTTGGAATGGAGGA 60.016 38.462 0.00 0.00 0.00 3.71
1704 5955 4.283467 AGGAAGACCTTTTATGCCCAAAAC 59.717 41.667 0.00 0.00 45.36 2.43
1747 5998 5.416947 ACTAAGCAAATAAGGAGTACCGTG 58.583 41.667 0.00 0.00 41.83 4.94
1765 6016 5.496556 ACCGTGAATTGACTTGATGGATTA 58.503 37.500 0.00 0.00 32.00 1.75
1796 6047 6.538742 TCAACAGAAACTCAAAAGTCACTAGG 59.461 38.462 0.00 0.00 33.48 3.02
1809 6060 9.268268 CAAAAGTCACTAGGTGAGTAAAACATA 57.732 33.333 8.20 0.00 44.28 2.29
1810 6061 8.828688 AAAGTCACTAGGTGAGTAAAACATAC 57.171 34.615 8.20 0.00 44.28 2.39
1811 6062 7.778185 AGTCACTAGGTGAGTAAAACATACT 57.222 36.000 6.26 0.00 43.39 2.12
1812 6063 7.828712 AGTCACTAGGTGAGTAAAACATACTC 58.171 38.462 6.26 8.35 43.39 2.59
1813 6064 7.034397 GTCACTAGGTGAGTAAAACATACTCC 58.966 42.308 11.85 4.94 43.57 3.85
1814 6065 6.034591 CACTAGGTGAGTAAAACATACTCCG 58.965 44.000 11.85 1.00 42.32 4.63
1815 6066 5.713861 ACTAGGTGAGTAAAACATACTCCGT 59.286 40.000 11.85 8.14 42.32 4.69
1816 6067 5.069501 AGGTGAGTAAAACATACTCCGTC 57.930 43.478 11.85 4.44 42.32 4.79
1817 6068 4.081807 AGGTGAGTAAAACATACTCCGTCC 60.082 45.833 11.85 11.16 42.32 4.79
1818 6069 4.322198 GGTGAGTAAAACATACTCCGTCCA 60.322 45.833 11.85 0.00 42.32 4.02
1819 6070 5.416947 GTGAGTAAAACATACTCCGTCCAT 58.583 41.667 11.85 0.00 42.32 3.41
1820 6071 5.873164 GTGAGTAAAACATACTCCGTCCATT 59.127 40.000 11.85 0.00 42.32 3.16
1821 6072 6.035758 GTGAGTAAAACATACTCCGTCCATTC 59.964 42.308 11.85 0.00 42.32 2.67
1822 6073 5.425630 AGTAAAACATACTCCGTCCATTCC 58.574 41.667 0.00 0.00 0.00 3.01
1823 6074 3.992943 AAACATACTCCGTCCATTCCA 57.007 42.857 0.00 0.00 0.00 3.53
1824 6075 3.992943 AACATACTCCGTCCATTCCAA 57.007 42.857 0.00 0.00 0.00 3.53
1825 6076 3.992943 ACATACTCCGTCCATTCCAAA 57.007 42.857 0.00 0.00 0.00 3.28
1826 6077 4.295141 ACATACTCCGTCCATTCCAAAA 57.705 40.909 0.00 0.00 0.00 2.44
1827 6078 4.855340 ACATACTCCGTCCATTCCAAAAT 58.145 39.130 0.00 0.00 0.00 1.82
1828 6079 5.996644 ACATACTCCGTCCATTCCAAAATA 58.003 37.500 0.00 0.00 0.00 1.40
1829 6080 6.601332 ACATACTCCGTCCATTCCAAAATAT 58.399 36.000 0.00 0.00 0.00 1.28
1830 6081 7.741785 ACATACTCCGTCCATTCCAAAATATA 58.258 34.615 0.00 0.00 0.00 0.86
1831 6082 7.878127 ACATACTCCGTCCATTCCAAAATATAG 59.122 37.037 0.00 0.00 0.00 1.31
1832 6083 6.248569 ACTCCGTCCATTCCAAAATATAGT 57.751 37.500 0.00 0.00 0.00 2.12
1833 6084 6.055588 ACTCCGTCCATTCCAAAATATAGTG 58.944 40.000 0.00 0.00 0.00 2.74
1834 6085 4.819630 TCCGTCCATTCCAAAATATAGTGC 59.180 41.667 0.00 0.00 0.00 4.40
1835 6086 4.319477 CCGTCCATTCCAAAATATAGTGCG 60.319 45.833 0.00 0.00 0.00 5.34
1836 6087 4.537015 GTCCATTCCAAAATATAGTGCGC 58.463 43.478 0.00 0.00 0.00 6.09
1837 6088 3.568007 TCCATTCCAAAATATAGTGCGCC 59.432 43.478 4.18 0.00 0.00 6.53
1838 6089 3.305335 CCATTCCAAAATATAGTGCGCCC 60.305 47.826 4.18 0.00 0.00 6.13
1839 6090 2.719531 TCCAAAATATAGTGCGCCCA 57.280 45.000 4.18 0.00 0.00 5.36
1840 6091 2.294074 TCCAAAATATAGTGCGCCCAC 58.706 47.619 4.18 0.00 42.39 4.61
1841 6092 1.002900 CCAAAATATAGTGCGCCCACG 60.003 52.381 4.18 0.00 46.62 4.94
1842 6093 1.668751 CAAAATATAGTGCGCCCACGT 59.331 47.619 4.18 0.00 46.62 4.49
1843 6094 2.032680 AAATATAGTGCGCCCACGTT 57.967 45.000 4.18 0.00 46.62 3.99
1844 6095 2.032680 AATATAGTGCGCCCACGTTT 57.967 45.000 4.18 0.00 46.62 3.60
1845 6096 1.578583 ATATAGTGCGCCCACGTTTC 58.421 50.000 4.18 0.00 46.62 2.78
1846 6097 0.460635 TATAGTGCGCCCACGTTTCC 60.461 55.000 4.18 0.00 46.62 3.13
1847 6098 3.765660 TATAGTGCGCCCACGTTTCCC 62.766 57.143 4.18 0.00 46.62 3.97
1852 6103 4.324991 GCCCACGTTTCCCGAGGT 62.325 66.667 0.00 0.00 44.75 3.85
1853 6104 2.047560 CCCACGTTTCCCGAGGTC 60.048 66.667 0.00 0.00 44.75 3.85
1854 6105 2.047560 CCACGTTTCCCGAGGTCC 60.048 66.667 0.00 0.00 41.74 4.46
1855 6106 2.738480 CACGTTTCCCGAGGTCCA 59.262 61.111 0.00 0.00 40.70 4.02
1856 6107 1.070105 CACGTTTCCCGAGGTCCAA 59.930 57.895 0.00 0.00 40.70 3.53
1857 6108 1.070275 ACGTTTCCCGAGGTCCAAC 59.930 57.895 0.00 0.00 40.70 3.77
1858 6109 1.370064 CGTTTCCCGAGGTCCAACT 59.630 57.895 0.00 0.00 39.56 3.16
1859 6110 0.250166 CGTTTCCCGAGGTCCAACTT 60.250 55.000 0.00 0.00 39.56 2.66
1860 6111 1.812708 CGTTTCCCGAGGTCCAACTTT 60.813 52.381 0.00 0.00 39.56 2.66
1861 6112 1.607148 GTTTCCCGAGGTCCAACTTTG 59.393 52.381 0.00 0.00 0.00 2.77
1862 6113 1.133363 TTCCCGAGGTCCAACTTTGA 58.867 50.000 0.00 0.00 0.00 2.69
1863 6114 0.395312 TCCCGAGGTCCAACTTTGAC 59.605 55.000 0.00 0.00 0.00 3.18
1864 6115 0.605589 CCCGAGGTCCAACTTTGACC 60.606 60.000 4.16 4.16 39.18 4.02
1865 6116 0.107831 CCGAGGTCCAACTTTGACCA 59.892 55.000 13.24 0.00 41.22 4.02
1866 6117 1.271379 CCGAGGTCCAACTTTGACCAT 60.271 52.381 13.24 0.72 41.22 3.55
1867 6118 2.027561 CCGAGGTCCAACTTTGACCATA 60.028 50.000 13.24 0.00 41.22 2.74
1868 6119 3.558321 CCGAGGTCCAACTTTGACCATAA 60.558 47.826 13.24 0.00 41.22 1.90
1869 6120 4.069304 CGAGGTCCAACTTTGACCATAAA 58.931 43.478 13.24 0.00 41.22 1.40
1870 6121 4.700213 CGAGGTCCAACTTTGACCATAAAT 59.300 41.667 13.24 0.00 41.22 1.40
1871 6122 5.183140 CGAGGTCCAACTTTGACCATAAATT 59.817 40.000 13.24 0.00 41.22 1.82
1872 6123 6.294508 CGAGGTCCAACTTTGACCATAAATTT 60.295 38.462 13.24 0.00 41.22 1.82
1873 6124 7.094549 CGAGGTCCAACTTTGACCATAAATTTA 60.095 37.037 13.24 0.00 41.22 1.40
1874 6125 8.485578 AGGTCCAACTTTGACCATAAATTTAA 57.514 30.769 13.24 0.00 41.22 1.52
1875 6126 8.364894 AGGTCCAACTTTGACCATAAATTTAAC 58.635 33.333 13.24 0.00 41.22 2.01
1876 6127 7.601130 GGTCCAACTTTGACCATAAATTTAACC 59.399 37.037 1.21 0.00 38.76 2.85
1877 6128 8.145122 GTCCAACTTTGACCATAAATTTAACCA 58.855 33.333 1.21 0.00 0.00 3.67
1878 6129 8.705594 TCCAACTTTGACCATAAATTTAACCAA 58.294 29.630 1.21 2.19 0.00 3.67
1879 6130 9.500785 CCAACTTTGACCATAAATTTAACCAAT 57.499 29.630 1.21 0.00 0.00 3.16
1882 6133 9.927668 ACTTTGACCATAAATTTAACCAATGAG 57.072 29.630 1.21 3.35 0.00 2.90
1886 6137 9.473007 TGACCATAAATTTAACCAATGAGATCA 57.527 29.630 1.21 0.18 0.00 2.92
1891 6142 9.807649 ATAAATTTAACCAATGAGATCAACTGC 57.192 29.630 1.21 0.00 0.00 4.40
1892 6143 4.944962 TTAACCAATGAGATCAACTGCG 57.055 40.909 0.00 0.00 0.00 5.18
1893 6144 1.742761 ACCAATGAGATCAACTGCGG 58.257 50.000 0.00 0.00 0.00 5.69
1894 6145 0.379669 CCAATGAGATCAACTGCGGC 59.620 55.000 0.00 0.00 0.00 6.53
1895 6146 0.027194 CAATGAGATCAACTGCGGCG 59.973 55.000 0.51 0.51 0.00 6.46
1896 6147 1.091771 AATGAGATCAACTGCGGCGG 61.092 55.000 9.78 7.39 0.00 6.13
1897 6148 2.892425 GAGATCAACTGCGGCGGG 60.892 66.667 14.26 2.36 0.00 6.13
1898 6149 3.371097 GAGATCAACTGCGGCGGGA 62.371 63.158 14.26 1.78 0.00 5.14
1899 6150 2.892425 GATCAACTGCGGCGGGAG 60.892 66.667 14.26 11.31 37.67 4.30
1900 6151 3.371097 GATCAACTGCGGCGGGAGA 62.371 63.158 19.55 10.60 35.29 3.71
1901 6152 2.852495 GATCAACTGCGGCGGGAGAA 62.852 60.000 19.55 4.96 35.29 2.87
1902 6153 2.463589 ATCAACTGCGGCGGGAGAAA 62.464 55.000 19.55 4.62 35.29 2.52
1903 6154 2.112297 AACTGCGGCGGGAGAAAA 59.888 55.556 19.55 0.00 35.29 2.29
1904 6155 1.527380 AACTGCGGCGGGAGAAAAA 60.527 52.632 19.55 0.00 35.29 1.94
1963 6214 9.480053 AATTCATTGATATAATTTTTGCTCCCG 57.520 29.630 0.00 0.00 0.00 5.14
1964 6215 6.446318 TCATTGATATAATTTTTGCTCCCGC 58.554 36.000 0.00 0.00 0.00 6.13
1965 6216 4.846779 TGATATAATTTTTGCTCCCGCC 57.153 40.909 0.00 0.00 34.43 6.13
1966 6217 3.252215 TGATATAATTTTTGCTCCCGCCG 59.748 43.478 0.00 0.00 34.43 6.46
1967 6218 0.102300 ATAATTTTTGCTCCCGCCGC 59.898 50.000 0.00 0.00 34.43 6.53
1968 6219 1.244697 TAATTTTTGCTCCCGCCGCA 61.245 50.000 0.00 0.00 35.22 5.69
1969 6220 2.093537 AATTTTTGCTCCCGCCGCAA 62.094 50.000 0.00 0.00 44.83 4.85
1970 6221 1.887344 ATTTTTGCTCCCGCCGCAAT 61.887 50.000 5.33 0.00 45.67 3.56
1971 6222 2.485188 TTTTTGCTCCCGCCGCAATC 62.485 55.000 5.33 0.00 45.67 2.67
1987 6238 5.712217 CGCAATCGGTCTTGATAGTTAAA 57.288 39.130 0.00 0.00 0.00 1.52
1988 6239 6.287107 CGCAATCGGTCTTGATAGTTAAAT 57.713 37.500 0.00 0.00 0.00 1.40
1989 6240 6.715464 CGCAATCGGTCTTGATAGTTAAATT 58.285 36.000 0.00 0.00 0.00 1.82
1990 6241 7.186804 CGCAATCGGTCTTGATAGTTAAATTT 58.813 34.615 0.00 0.00 0.00 1.82
1991 6242 8.332464 CGCAATCGGTCTTGATAGTTAAATTTA 58.668 33.333 0.00 0.00 0.00 1.40
2010 6261 8.728088 AAATTTATAGTCAAAGTTGAAGCACG 57.272 30.769 0.00 0.00 39.21 5.34
2011 6262 7.667043 ATTTATAGTCAAAGTTGAAGCACGA 57.333 32.000 0.00 0.00 39.21 4.35
2012 6263 6.706055 TTATAGTCAAAGTTGAAGCACGAG 57.294 37.500 0.00 0.00 39.21 4.18
2013 6264 3.179443 AGTCAAAGTTGAAGCACGAGA 57.821 42.857 0.00 0.00 39.21 4.04
2014 6265 3.531538 AGTCAAAGTTGAAGCACGAGAA 58.468 40.909 0.00 0.00 39.21 2.87
2015 6266 4.130118 AGTCAAAGTTGAAGCACGAGAAT 58.870 39.130 0.00 0.00 39.21 2.40
2016 6267 5.297547 AGTCAAAGTTGAAGCACGAGAATA 58.702 37.500 0.00 0.00 39.21 1.75
2017 6268 5.406780 AGTCAAAGTTGAAGCACGAGAATAG 59.593 40.000 0.00 0.00 39.21 1.73
2018 6269 5.405571 GTCAAAGTTGAAGCACGAGAATAGA 59.594 40.000 0.00 0.00 39.21 1.98
2019 6270 5.635280 TCAAAGTTGAAGCACGAGAATAGAG 59.365 40.000 0.00 0.00 33.55 2.43
2020 6271 5.392767 AAGTTGAAGCACGAGAATAGAGA 57.607 39.130 0.00 0.00 0.00 3.10
2021 6272 5.392767 AGTTGAAGCACGAGAATAGAGAA 57.607 39.130 0.00 0.00 0.00 2.87
2022 6273 5.784177 AGTTGAAGCACGAGAATAGAGAAA 58.216 37.500 0.00 0.00 0.00 2.52
2023 6274 5.866633 AGTTGAAGCACGAGAATAGAGAAAG 59.133 40.000 0.00 0.00 0.00 2.62
2024 6275 4.177026 TGAAGCACGAGAATAGAGAAAGC 58.823 43.478 0.00 0.00 0.00 3.51
2025 6276 3.876274 AGCACGAGAATAGAGAAAGCA 57.124 42.857 0.00 0.00 0.00 3.91
2026 6277 4.399004 AGCACGAGAATAGAGAAAGCAT 57.601 40.909 0.00 0.00 0.00 3.79
2027 6278 4.764172 AGCACGAGAATAGAGAAAGCATT 58.236 39.130 0.00 0.00 0.00 3.56
2028 6279 5.907207 AGCACGAGAATAGAGAAAGCATTA 58.093 37.500 0.00 0.00 0.00 1.90
2029 6280 6.520272 AGCACGAGAATAGAGAAAGCATTAT 58.480 36.000 0.00 0.00 0.00 1.28
2030 6281 7.661968 AGCACGAGAATAGAGAAAGCATTATA 58.338 34.615 0.00 0.00 0.00 0.98
2031 6282 8.310382 AGCACGAGAATAGAGAAAGCATTATAT 58.690 33.333 0.00 0.00 0.00 0.86
2032 6283 8.930760 GCACGAGAATAGAGAAAGCATTATATT 58.069 33.333 0.00 0.00 0.00 1.28
2034 6285 9.988815 ACGAGAATAGAGAAAGCATTATATTGT 57.011 29.630 0.00 0.00 0.00 2.71
2041 6292 8.985315 AGAGAAAGCATTATATTGTGGAATGA 57.015 30.769 0.28 0.00 33.28 2.57
2042 6293 9.412460 AGAGAAAGCATTATATTGTGGAATGAA 57.588 29.630 0.28 0.00 33.28 2.57
2043 6294 9.674824 GAGAAAGCATTATATTGTGGAATGAAG 57.325 33.333 0.28 0.00 33.28 3.02
2044 6295 8.636213 AGAAAGCATTATATTGTGGAATGAAGG 58.364 33.333 0.28 0.00 33.28 3.46
2045 6296 6.906157 AGCATTATATTGTGGAATGAAGGG 57.094 37.500 0.28 0.00 33.28 3.95
2046 6297 6.613699 AGCATTATATTGTGGAATGAAGGGA 58.386 36.000 0.28 0.00 33.28 4.20
2047 6298 6.718454 AGCATTATATTGTGGAATGAAGGGAG 59.282 38.462 0.28 0.00 33.28 4.30
2115 6366 0.977395 GGCCTGTTAGGTCTCACACT 59.023 55.000 0.00 0.00 36.93 3.55
2116 6367 2.176889 GGCCTGTTAGGTCTCACACTA 58.823 52.381 0.00 0.00 36.93 2.74
2136 6387 1.125633 TAAGGATTACCCGTGGCCTC 58.874 55.000 3.32 0.00 40.87 4.70
2145 6396 0.178958 CCCGTGGCCTCTCTATAGGT 60.179 60.000 3.32 0.00 39.02 3.08
2168 6419 4.035324 TCAAATTTGTTTCTAACGACGCCA 59.965 37.500 17.47 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.519408 GCGCTTGGAAGTTGGACTTA 58.481 50.000 0.00 0.00 38.80 2.24
100 102 4.781087 TGTATTACTCCACAGCCCTAACTT 59.219 41.667 0.00 0.00 0.00 2.66
103 105 7.094075 CGTATATGTATTACTCCACAGCCCTAA 60.094 40.741 0.00 0.00 0.00 2.69
371 3177 3.761445 ATGCATTGCGTCGCATGCC 62.761 57.895 32.27 20.83 46.78 4.40
385 3191 4.674885 CGCACAAATAATCTGGTCAATGCA 60.675 41.667 0.00 0.00 0.00 3.96
415 3225 0.958091 TCCGGTTTCAGTTTGCATGG 59.042 50.000 0.00 0.00 0.00 3.66
489 3320 7.559590 TGGACCCAAAAATGTGTTTATTTTG 57.440 32.000 0.00 0.00 39.48 2.44
490 3321 8.759481 ATTGGACCCAAAAATGTGTTTATTTT 57.241 26.923 5.49 0.00 40.84 1.82
491 3322 8.759481 AATTGGACCCAAAAATGTGTTTATTT 57.241 26.923 5.49 0.00 39.55 1.40
494 3325 9.331282 CTTAAATTGGACCCAAAAATGTGTTTA 57.669 29.630 5.49 2.23 39.55 2.01
495 3326 8.049721 TCTTAAATTGGACCCAAAAATGTGTTT 58.950 29.630 5.49 3.11 39.55 2.83
536 3368 5.118817 GCTCCAAGTCGTTTTAGTCAAGTAG 59.881 44.000 0.00 0.00 0.00 2.57
537 3369 4.986659 GCTCCAAGTCGTTTTAGTCAAGTA 59.013 41.667 0.00 0.00 0.00 2.24
538 3370 3.808174 GCTCCAAGTCGTTTTAGTCAAGT 59.192 43.478 0.00 0.00 0.00 3.16
539 3371 4.058817 AGCTCCAAGTCGTTTTAGTCAAG 58.941 43.478 0.00 0.00 0.00 3.02
540 3372 4.056050 GAGCTCCAAGTCGTTTTAGTCAA 58.944 43.478 0.87 0.00 0.00 3.18
541 3373 3.069016 TGAGCTCCAAGTCGTTTTAGTCA 59.931 43.478 12.15 0.00 0.00 3.41
542 3374 3.650139 TGAGCTCCAAGTCGTTTTAGTC 58.350 45.455 12.15 0.00 0.00 2.59
543 3375 3.746045 TGAGCTCCAAGTCGTTTTAGT 57.254 42.857 12.15 0.00 0.00 2.24
655 3501 7.801716 AGTACATAACAGTGATGTTTTGTGT 57.198 32.000 20.26 14.75 41.53 3.72
675 3521 6.019479 ACAGCGAATGTACGTACTAGTAGTAC 60.019 42.308 24.79 24.79 42.97 2.73
676 3522 6.042777 ACAGCGAATGTACGTACTAGTAGTA 58.957 40.000 25.12 5.90 41.60 1.82
677 3523 4.872691 ACAGCGAATGTACGTACTAGTAGT 59.127 41.667 25.12 8.14 41.60 2.73
678 3524 5.401033 ACAGCGAATGTACGTACTAGTAG 57.599 43.478 25.12 13.91 41.60 2.57
679 3525 6.902224 TTACAGCGAATGTACGTACTAGTA 57.098 37.500 25.12 13.72 44.14 1.82
680 3526 5.801350 TTACAGCGAATGTACGTACTAGT 57.199 39.130 25.12 11.78 44.14 2.57
681 3527 6.253746 ACTTTACAGCGAATGTACGTACTAG 58.746 40.000 25.12 14.53 44.14 2.57
682 3528 6.182039 ACTTTACAGCGAATGTACGTACTA 57.818 37.500 25.12 12.85 44.14 1.82
683 3529 5.051891 ACTTTACAGCGAATGTACGTACT 57.948 39.130 25.12 7.23 44.14 2.73
684 3530 5.220098 GGAACTTTACAGCGAATGTACGTAC 60.220 44.000 18.90 18.90 44.14 3.67
685 3531 4.858692 GGAACTTTACAGCGAATGTACGTA 59.141 41.667 0.00 0.00 44.14 3.57
686 3532 3.676646 GGAACTTTACAGCGAATGTACGT 59.323 43.478 0.00 0.00 44.14 3.57
687 3533 3.924686 AGGAACTTTACAGCGAATGTACG 59.075 43.478 0.86 0.00 44.14 3.67
688 3534 5.005490 GCTAGGAACTTTACAGCGAATGTAC 59.995 44.000 0.86 0.00 41.60 2.90
689 3535 5.105473 AGCTAGGAACTTTACAGCGAATGTA 60.105 40.000 0.00 0.00 41.23 2.29
690 3536 3.933332 GCTAGGAACTTTACAGCGAATGT 59.067 43.478 0.00 0.00 42.94 2.71
711 3557 5.897377 TGAACTTTGAAAATAGCCCTAGC 57.103 39.130 0.00 0.00 40.32 3.42
712 3558 7.657336 TGTTTGAACTTTGAAAATAGCCCTAG 58.343 34.615 0.00 0.00 0.00 3.02
760 3607 0.721718 CCGGAAGCTGTTTCATCGTC 59.278 55.000 0.00 0.00 37.54 4.20
769 3616 4.035102 GGGAAGGCCGGAAGCTGT 62.035 66.667 5.05 0.00 43.05 4.40
791 3638 3.118884 ACGTTATATATAAGGGCCCTGCG 60.119 47.826 29.50 19.26 33.67 5.18
793 3640 5.175859 CACACGTTATATATAAGGGCCCTG 58.824 45.833 29.50 11.38 33.67 4.45
797 3644 6.218019 TGTGACACACGTTATATATAAGGGC 58.782 40.000 22.65 11.11 37.14 5.19
801 3648 7.436970 CCAGCTTGTGACACACGTTATATATAA 59.563 37.037 8.05 0.81 37.14 0.98
810 3657 0.462375 TACCAGCTTGTGACACACGT 59.538 50.000 8.05 2.60 37.14 4.49
811 3658 1.139989 CTACCAGCTTGTGACACACG 58.860 55.000 8.05 7.84 37.14 4.49
812 3659 2.526304 TCTACCAGCTTGTGACACAC 57.474 50.000 8.05 0.00 34.56 3.82
813 3660 2.899900 AGATCTACCAGCTTGTGACACA 59.100 45.455 3.56 3.56 0.00 3.72
820 3667 4.456280 TGTGTGTAGATCTACCAGCTTG 57.544 45.455 26.37 0.00 35.26 4.01
825 3672 3.883489 CTCGGATGTGTGTAGATCTACCA 59.117 47.826 26.37 20.62 35.26 3.25
826 3673 3.304794 GCTCGGATGTGTGTAGATCTACC 60.305 52.174 26.37 18.63 35.26 3.18
853 3702 4.470334 AGCTAGGAAGAAGAAGAAGCTG 57.530 45.455 0.00 0.00 37.44 4.24
883 3732 3.055458 TCTCTCTCTCTCTTCTCGCTGAA 60.055 47.826 0.00 0.00 0.00 3.02
884 3733 2.499693 TCTCTCTCTCTCTTCTCGCTGA 59.500 50.000 0.00 0.00 0.00 4.26
889 3738 5.596361 TCTCTCTCTCTCTCTCTCTCTTCTC 59.404 48.000 0.00 0.00 0.00 2.87
890 3739 5.523588 TCTCTCTCTCTCTCTCTCTCTTCT 58.476 45.833 0.00 0.00 0.00 2.85
901 3750 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
902 3751 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
903 3752 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
904 3753 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
905 3754 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
906 3755 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
907 3756 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
908 3757 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
909 3758 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
910 3759 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
911 3760 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
912 3761 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
913 3762 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
914 3763 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
915 3764 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
916 3765 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
917 3766 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
918 3767 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
919 3768 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
920 3769 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
921 3770 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
922 3771 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
923 3772 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
924 3773 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
925 3774 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
926 3775 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
927 3776 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
928 3777 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
929 3778 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
930 3779 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
931 3780 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
932 3781 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
933 3782 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
934 3783 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
935 3784 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
936 3785 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
937 3786 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
938 3787 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
939 3788 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
940 3789 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
941 3790 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
942 3791 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
943 3792 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
944 3793 5.009610 GTCTCTCTCTCTCTCTCTCTCTCTC 59.990 52.000 0.00 0.00 0.00 3.20
945 3794 4.892934 GTCTCTCTCTCTCTCTCTCTCTCT 59.107 50.000 0.00 0.00 0.00 3.10
946 3795 4.261405 CGTCTCTCTCTCTCTCTCTCTCTC 60.261 54.167 0.00 0.00 0.00 3.20
947 3796 3.634448 CGTCTCTCTCTCTCTCTCTCTCT 59.366 52.174 0.00 0.00 0.00 3.10
948 3797 3.797184 GCGTCTCTCTCTCTCTCTCTCTC 60.797 56.522 0.00 0.00 0.00 3.20
949 3798 2.101582 GCGTCTCTCTCTCTCTCTCTCT 59.898 54.545 0.00 0.00 0.00 3.10
950 3799 2.159099 TGCGTCTCTCTCTCTCTCTCTC 60.159 54.545 0.00 0.00 0.00 3.20
951 3800 1.831106 TGCGTCTCTCTCTCTCTCTCT 59.169 52.381 0.00 0.00 0.00 3.10
952 3801 2.205074 CTGCGTCTCTCTCTCTCTCTC 58.795 57.143 0.00 0.00 0.00 3.20
953 3802 1.555075 ACTGCGTCTCTCTCTCTCTCT 59.445 52.381 0.00 0.00 0.00 3.10
954 3803 1.665679 CACTGCGTCTCTCTCTCTCTC 59.334 57.143 0.00 0.00 0.00 3.20
955 3804 1.003118 ACACTGCGTCTCTCTCTCTCT 59.997 52.381 0.00 0.00 0.00 3.10
956 3805 1.396996 GACACTGCGTCTCTCTCTCTC 59.603 57.143 0.00 0.00 41.81 3.20
957 3806 1.448985 GACACTGCGTCTCTCTCTCT 58.551 55.000 0.00 0.00 41.81 3.10
966 3815 1.015109 TATCTCCGAGACACTGCGTC 58.985 55.000 0.00 0.00 45.77 5.19
1045 3894 1.153369 CCGCCGAGAACACCATGAT 60.153 57.895 0.00 0.00 0.00 2.45
1251 4103 3.499737 GGCCACGCCGTTGATCAG 61.500 66.667 0.00 0.00 39.62 2.90
1384 4597 3.138468 AGGGGCCTTTAACTATGCCTTAG 59.862 47.826 0.84 0.00 43.50 2.18
1591 5842 3.879892 ACTTGAACTGAAGTCAAAGCCTC 59.120 43.478 5.45 0.00 29.85 4.70
1624 5875 6.655078 AATTTGAACAGTAGCATTTCCAGT 57.345 33.333 0.00 0.00 0.00 4.00
1654 5905 7.042119 CCATTCCAAAATAAGTGTTGTGGTTTC 60.042 37.037 0.00 0.00 0.00 2.78
1684 5935 5.622346 TTGTTTTGGGCATAAAAGGTCTT 57.378 34.783 0.00 0.00 30.79 3.01
1734 5985 5.244402 TCAAGTCAATTCACGGTACTCCTTA 59.756 40.000 0.00 0.00 0.00 2.69
1747 5998 7.554118 TGACTTCCTAATCCATCAAGTCAATTC 59.446 37.037 9.75 0.00 46.23 2.17
1765 6016 5.946377 ACTTTTGAGTTTCTGTTGACTTCCT 59.054 36.000 0.00 0.00 0.00 3.36
1810 6061 5.049405 GCACTATATTTTGGAATGGACGGAG 60.049 44.000 0.00 0.00 0.00 4.63
1811 6062 4.819630 GCACTATATTTTGGAATGGACGGA 59.180 41.667 0.00 0.00 0.00 4.69
1812 6063 4.319477 CGCACTATATTTTGGAATGGACGG 60.319 45.833 0.00 0.00 0.00 4.79
1813 6064 4.772434 CGCACTATATTTTGGAATGGACG 58.228 43.478 0.00 0.00 0.00 4.79
1814 6065 4.537015 GCGCACTATATTTTGGAATGGAC 58.463 43.478 0.30 0.00 0.00 4.02
1815 6066 3.568007 GGCGCACTATATTTTGGAATGGA 59.432 43.478 10.83 0.00 0.00 3.41
1816 6067 3.305335 GGGCGCACTATATTTTGGAATGG 60.305 47.826 10.83 0.00 0.00 3.16
1817 6068 3.317711 TGGGCGCACTATATTTTGGAATG 59.682 43.478 12.74 0.00 0.00 2.67
1818 6069 3.317993 GTGGGCGCACTATATTTTGGAAT 59.682 43.478 25.28 0.00 0.00 3.01
1819 6070 2.685897 GTGGGCGCACTATATTTTGGAA 59.314 45.455 25.28 0.00 0.00 3.53
1820 6071 2.294074 GTGGGCGCACTATATTTTGGA 58.706 47.619 25.28 0.00 0.00 3.53
1821 6072 1.002900 CGTGGGCGCACTATATTTTGG 60.003 52.381 28.52 8.56 0.00 3.28
1822 6073 1.668751 ACGTGGGCGCACTATATTTTG 59.331 47.619 28.52 14.49 42.83 2.44
1823 6074 2.032680 ACGTGGGCGCACTATATTTT 57.967 45.000 28.52 4.27 42.83 1.82
1824 6075 2.032680 AACGTGGGCGCACTATATTT 57.967 45.000 28.52 12.51 42.83 1.40
1825 6076 1.937899 GAAACGTGGGCGCACTATATT 59.062 47.619 28.52 17.97 42.83 1.28
1826 6077 1.578583 GAAACGTGGGCGCACTATAT 58.421 50.000 28.52 13.86 42.83 0.86
1827 6078 0.460635 GGAAACGTGGGCGCACTATA 60.461 55.000 28.52 0.00 42.83 1.31
1828 6079 1.743995 GGAAACGTGGGCGCACTAT 60.744 57.895 28.52 15.73 42.83 2.12
1829 6080 2.357760 GGAAACGTGGGCGCACTA 60.358 61.111 28.52 0.00 42.83 2.74
1838 6089 1.070105 TTGGACCTCGGGAAACGTG 59.930 57.895 0.00 0.00 44.69 4.49
1839 6090 1.070275 GTTGGACCTCGGGAAACGT 59.930 57.895 0.00 0.00 44.69 3.99
1840 6091 0.250166 AAGTTGGACCTCGGGAAACG 60.250 55.000 0.00 0.00 46.11 3.60
1841 6092 1.607148 CAAAGTTGGACCTCGGGAAAC 59.393 52.381 0.00 0.00 0.00 2.78
1842 6093 1.491332 TCAAAGTTGGACCTCGGGAAA 59.509 47.619 0.00 0.00 0.00 3.13
1843 6094 1.133363 TCAAAGTTGGACCTCGGGAA 58.867 50.000 0.00 0.00 0.00 3.97
1844 6095 0.395312 GTCAAAGTTGGACCTCGGGA 59.605 55.000 0.00 0.00 0.00 5.14
1845 6096 2.928416 GTCAAAGTTGGACCTCGGG 58.072 57.895 0.00 0.00 0.00 5.14
1851 6102 8.145122 TGGTTAAATTTATGGTCAAAGTTGGAC 58.855 33.333 1.31 1.31 29.44 4.02
1852 6103 8.251383 TGGTTAAATTTATGGTCAAAGTTGGA 57.749 30.769 0.00 0.00 29.44 3.53
1853 6104 8.894768 TTGGTTAAATTTATGGTCAAAGTTGG 57.105 30.769 0.00 0.00 29.44 3.77
1856 6107 9.927668 CTCATTGGTTAAATTTATGGTCAAAGT 57.072 29.630 0.00 0.00 0.00 2.66
1860 6111 9.473007 TGATCTCATTGGTTAAATTTATGGTCA 57.527 29.630 0.00 0.00 0.00 4.02
1865 6116 9.807649 GCAGTTGATCTCATTGGTTAAATTTAT 57.192 29.630 0.00 0.00 0.00 1.40
1866 6117 7.967854 CGCAGTTGATCTCATTGGTTAAATTTA 59.032 33.333 0.00 0.00 0.00 1.40
1867 6118 6.808212 CGCAGTTGATCTCATTGGTTAAATTT 59.192 34.615 0.00 0.00 0.00 1.82
1868 6119 6.324819 CGCAGTTGATCTCATTGGTTAAATT 58.675 36.000 0.00 0.00 0.00 1.82
1869 6120 5.163622 CCGCAGTTGATCTCATTGGTTAAAT 60.164 40.000 0.00 0.00 0.00 1.40
1870 6121 4.155826 CCGCAGTTGATCTCATTGGTTAAA 59.844 41.667 0.00 0.00 0.00 1.52
1871 6122 3.689161 CCGCAGTTGATCTCATTGGTTAA 59.311 43.478 0.00 0.00 0.00 2.01
1872 6123 3.270027 CCGCAGTTGATCTCATTGGTTA 58.730 45.455 0.00 0.00 0.00 2.85
1873 6124 2.086869 CCGCAGTTGATCTCATTGGTT 58.913 47.619 0.00 0.00 0.00 3.67
1874 6125 1.742761 CCGCAGTTGATCTCATTGGT 58.257 50.000 0.00 0.00 0.00 3.67
1875 6126 0.379669 GCCGCAGTTGATCTCATTGG 59.620 55.000 0.00 0.00 0.00 3.16
1876 6127 0.027194 CGCCGCAGTTGATCTCATTG 59.973 55.000 0.00 0.00 0.00 2.82
1877 6128 1.091771 CCGCCGCAGTTGATCTCATT 61.092 55.000 0.00 0.00 0.00 2.57
1878 6129 1.522355 CCGCCGCAGTTGATCTCAT 60.522 57.895 0.00 0.00 0.00 2.90
1879 6130 2.125552 CCGCCGCAGTTGATCTCA 60.126 61.111 0.00 0.00 0.00 3.27
1880 6131 2.892425 CCCGCCGCAGTTGATCTC 60.892 66.667 0.00 0.00 0.00 2.75
1881 6132 3.376935 CTCCCGCCGCAGTTGATCT 62.377 63.158 0.00 0.00 0.00 2.75
1882 6133 2.852495 TTCTCCCGCCGCAGTTGATC 62.852 60.000 0.00 0.00 0.00 2.92
1883 6134 2.463589 TTTCTCCCGCCGCAGTTGAT 62.464 55.000 0.00 0.00 0.00 2.57
1884 6135 2.668185 TTTTCTCCCGCCGCAGTTGA 62.668 55.000 0.00 0.00 0.00 3.18
1885 6136 1.791103 TTTTTCTCCCGCCGCAGTTG 61.791 55.000 0.00 0.00 0.00 3.16
1886 6137 1.527380 TTTTTCTCCCGCCGCAGTT 60.527 52.632 0.00 0.00 0.00 3.16
1887 6138 2.112297 TTTTTCTCCCGCCGCAGT 59.888 55.556 0.00 0.00 0.00 4.40
1937 6188 9.480053 CGGGAGCAAAAATTATATCAATGAATT 57.520 29.630 0.00 0.00 0.00 2.17
1965 6216 5.712217 TTTAACTATCAAGACCGATTGCG 57.288 39.130 0.00 0.00 37.24 4.85
1984 6235 9.820229 CGTGCTTCAACTTTGACTATAAATTTA 57.180 29.630 0.00 0.00 36.83 1.40
1985 6236 8.564574 TCGTGCTTCAACTTTGACTATAAATTT 58.435 29.630 0.00 0.00 36.83 1.82
1986 6237 8.094798 TCGTGCTTCAACTTTGACTATAAATT 57.905 30.769 0.00 0.00 36.83 1.82
1987 6238 7.602644 TCTCGTGCTTCAACTTTGACTATAAAT 59.397 33.333 0.00 0.00 36.83 1.40
1988 6239 6.926826 TCTCGTGCTTCAACTTTGACTATAAA 59.073 34.615 0.00 0.00 36.83 1.40
1989 6240 6.452242 TCTCGTGCTTCAACTTTGACTATAA 58.548 36.000 0.00 0.00 36.83 0.98
1990 6241 6.020971 TCTCGTGCTTCAACTTTGACTATA 57.979 37.500 0.00 0.00 36.83 1.31
1991 6242 4.883083 TCTCGTGCTTCAACTTTGACTAT 58.117 39.130 0.00 0.00 36.83 2.12
1992 6243 4.316205 TCTCGTGCTTCAACTTTGACTA 57.684 40.909 0.00 0.00 36.83 2.59
1993 6244 3.179443 TCTCGTGCTTCAACTTTGACT 57.821 42.857 0.00 0.00 36.83 3.41
1994 6245 3.944422 TTCTCGTGCTTCAACTTTGAC 57.056 42.857 0.00 0.00 36.83 3.18
1995 6246 5.538118 TCTATTCTCGTGCTTCAACTTTGA 58.462 37.500 0.00 0.00 34.92 2.69
1996 6247 5.635280 TCTCTATTCTCGTGCTTCAACTTTG 59.365 40.000 0.00 0.00 0.00 2.77
1997 6248 5.784177 TCTCTATTCTCGTGCTTCAACTTT 58.216 37.500 0.00 0.00 0.00 2.66
1998 6249 5.392767 TCTCTATTCTCGTGCTTCAACTT 57.607 39.130 0.00 0.00 0.00 2.66
1999 6250 5.392767 TTCTCTATTCTCGTGCTTCAACT 57.607 39.130 0.00 0.00 0.00 3.16
2000 6251 5.445275 GCTTTCTCTATTCTCGTGCTTCAAC 60.445 44.000 0.00 0.00 0.00 3.18
2001 6252 4.627467 GCTTTCTCTATTCTCGTGCTTCAA 59.373 41.667 0.00 0.00 0.00 2.69
2002 6253 4.177026 GCTTTCTCTATTCTCGTGCTTCA 58.823 43.478 0.00 0.00 0.00 3.02
2003 6254 4.177026 TGCTTTCTCTATTCTCGTGCTTC 58.823 43.478 0.00 0.00 0.00 3.86
2004 6255 4.193826 TGCTTTCTCTATTCTCGTGCTT 57.806 40.909 0.00 0.00 0.00 3.91
2005 6256 3.876274 TGCTTTCTCTATTCTCGTGCT 57.124 42.857 0.00 0.00 0.00 4.40
2006 6257 6.777526 ATAATGCTTTCTCTATTCTCGTGC 57.222 37.500 0.00 0.00 0.00 5.34
2008 6259 9.988815 ACAATATAATGCTTTCTCTATTCTCGT 57.011 29.630 0.00 0.00 0.00 4.18
2016 6267 8.985315 TCATTCCACAATATAATGCTTTCTCT 57.015 30.769 0.00 0.00 31.98 3.10
2017 6268 9.674824 CTTCATTCCACAATATAATGCTTTCTC 57.325 33.333 0.00 0.00 31.98 2.87
2018 6269 8.636213 CCTTCATTCCACAATATAATGCTTTCT 58.364 33.333 0.00 0.00 31.98 2.52
2019 6270 7.869429 CCCTTCATTCCACAATATAATGCTTTC 59.131 37.037 0.00 0.00 31.98 2.62
2020 6271 7.564660 TCCCTTCATTCCACAATATAATGCTTT 59.435 33.333 0.00 0.00 31.98 3.51
2021 6272 7.068702 TCCCTTCATTCCACAATATAATGCTT 58.931 34.615 0.00 0.00 31.98 3.91
2022 6273 6.613699 TCCCTTCATTCCACAATATAATGCT 58.386 36.000 0.00 0.00 31.98 3.79
2023 6274 6.491403 ACTCCCTTCATTCCACAATATAATGC 59.509 38.462 0.00 0.00 31.98 3.56
2024 6275 9.573166 TTACTCCCTTCATTCCACAATATAATG 57.427 33.333 0.00 0.00 32.96 1.90
2026 6277 9.983024 TTTTACTCCCTTCATTCCACAATATAA 57.017 29.630 0.00 0.00 0.00 0.98
2027 6278 9.983024 TTTTTACTCCCTTCATTCCACAATATA 57.017 29.630 0.00 0.00 0.00 0.86
2028 6279 8.893563 TTTTTACTCCCTTCATTCCACAATAT 57.106 30.769 0.00 0.00 0.00 1.28
2115 6366 2.901839 GAGGCCACGGGTAATCCTTATA 59.098 50.000 5.01 0.00 0.00 0.98
2116 6367 1.697982 GAGGCCACGGGTAATCCTTAT 59.302 52.381 5.01 0.00 0.00 1.73
2145 6396 4.035324 TGGCGTCGTTAGAAACAAATTTGA 59.965 37.500 24.64 0.00 0.00 2.69
2168 6419 6.961360 TGAGATGATGAAGGACGTTATACT 57.039 37.500 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.