Multiple sequence alignment - TraesCS3A01G111900

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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 TraesCS3A01G111900 chr3A 100.000 8928 0 0 1 8928 79387769 79378842 0.000000e+00 16488
1 TraesCS3A01G111900 chr3A 78.302 424 64 16 4068 4482 79399151 79398747 1.920000e-61 248
2 TraesCS3A01G111900 chr3D 96.457 3980 81 20 940 4886 67681887 67677935 0.000000e+00 6514
3 TraesCS3A01G111900 chr3D 96.425 1818 55 5 5010 6821 67677936 67676123 0.000000e+00 2988
4 TraesCS3A01G111900 chr3D 95.682 440 16 2 6901 7337 67676126 67675687 0.000000e+00 704
5 TraesCS3A01G111900 chr3D 95.699 372 11 3 7344 7715 67675546 67675180 2.150000e-165 593
6 TraesCS3A01G111900 chr3D 90.854 164 15 0 7638 7801 67675214 67675051 4.200000e-53 220
7 TraesCS3A01G111900 chr3D 78.771 358 54 12 4102 4456 67696976 67696638 4.200000e-53 220
8 TraesCS3A01G111900 chr3D 94.853 136 7 0 4884 5019 84562737 84562602 7.020000e-51 213
9 TraesCS3A01G111900 chr3B 91.086 3231 162 53 1 3170 114193634 114196799 0.000000e+00 4255
10 TraesCS3A01G111900 chr3B 98.307 2304 20 8 2589 4886 114196810 114199100 0.000000e+00 4021
11 TraesCS3A01G111900 chr3B 96.099 1820 47 17 5010 6821 114199099 114200902 0.000000e+00 2946
12 TraesCS3A01G111900 chr3B 93.383 937 39 14 6928 7854 114200909 114201832 0.000000e+00 1365
13 TraesCS3A01G111900 chr3B 82.604 960 158 9 7974 8928 812783765 812784720 0.000000e+00 839
14 TraesCS3A01G111900 chr3B 77.712 507 81 16 3959 4456 114149282 114149765 1.900000e-71 281
15 TraesCS3A01G111900 chr3B 81.338 284 51 2 5339 5622 114150913 114151194 6.970000e-56 230
16 TraesCS3A01G111900 chr3B 88.462 104 8 3 6808 6907 62394181 62394284 1.220000e-23 122
17 TraesCS3A01G111900 chr3B 90.426 94 7 2 6641 6733 229298772 229298680 1.220000e-23 122
18 TraesCS3A01G111900 chr7A 97.672 1074 25 0 7855 8928 20430312 20429239 0.000000e+00 1845
19 TraesCS3A01G111900 chr7A 96.296 135 2 3 4878 5011 189327630 189327498 1.510000e-52 219
20 TraesCS3A01G111900 chr5A 97.240 1087 30 0 7842 8928 632193669 632192583 0.000000e+00 1842
21 TraesCS3A01G111900 chr5A 95.420 131 6 0 4882 5012 279670551 279670421 9.080000e-50 209
22 TraesCS3A01G111900 chr5A 86.667 105 11 3 6626 6729 496024640 496024742 7.330000e-21 113
23 TraesCS3A01G111900 chr1A 96.980 861 26 0 8068 8928 549552424 549551564 0.000000e+00 1447
24 TraesCS3A01G111900 chr1A 93.333 90 2 2 6817 6904 518662848 518662761 7.270000e-26 130
25 TraesCS3A01G111900 chr6D 89.739 1072 88 10 7857 8928 327608403 327609452 0.000000e+00 1351
26 TraesCS3A01G111900 chr6D 87.523 1074 129 5 7857 8928 378431866 378432936 0.000000e+00 1236
27 TraesCS3A01G111900 chr2A 87.832 904 106 4 7852 8754 86288399 86289299 0.000000e+00 1057
28 TraesCS3A01G111900 chr2A 80.924 671 61 25 696 1321 73691429 73692077 1.360000e-127 468
29 TraesCS3A01G111900 chr2A 93.056 144 8 2 4869 5012 708949031 708949172 9.080000e-50 209
30 TraesCS3A01G111900 chr2A 83.799 179 19 5 1366 1538 73692080 73692254 2.580000e-35 161
31 TraesCS3A01G111900 chr7B 82.665 1073 163 13 7857 8926 696889652 696890704 0.000000e+00 929
32 TraesCS3A01G111900 chr1D 95.387 542 25 0 7857 8398 307154224 307154765 0.000000e+00 863
33 TraesCS3A01G111900 chr1D 93.182 88 5 1 6645 6732 448689978 448689892 2.620000e-25 128
34 TraesCS3A01G111900 chr1D 93.023 86 5 1 6645 6730 472748767 472748683 3.380000e-24 124
35 TraesCS3A01G111900 chr4B 83.506 770 121 6 8162 8928 26234257 26235023 0.000000e+00 713
36 TraesCS3A01G111900 chr4B 82.727 770 127 6 8162 8928 26273310 26274076 0.000000e+00 680
37 TraesCS3A01G111900 chr4B 95.620 137 5 1 4885 5021 55926031 55925896 1.510000e-52 219
38 TraesCS3A01G111900 chr2D 83.677 533 41 17 1033 1538 74328365 74328878 2.270000e-125 460
39 TraesCS3A01G111900 chr2D 79.880 333 29 12 698 1006 74328050 74328368 9.080000e-50 209
40 TraesCS3A01G111900 chr2D 91.579 95 4 2 6812 6904 589522245 589522337 2.620000e-25 128
41 TraesCS3A01G111900 chr5B 94.928 138 5 2 4875 5011 383524643 383524779 1.950000e-51 215
42 TraesCS3A01G111900 chr5B 90.000 100 5 3 6817 6914 440023834 440023738 3.380000e-24 124
43 TraesCS3A01G111900 chrUn 94.815 135 7 0 4877 5011 322720544 322720410 2.530000e-50 211
44 TraesCS3A01G111900 chr4D 89.441 161 13 3 4855 5011 478510159 478509999 5.470000e-47 200
45 TraesCS3A01G111900 chr4D 89.474 95 8 2 6645 6738 492602153 492602246 1.570000e-22 119
46 TraesCS3A01G111900 chr2B 86.932 176 16 6 4854 5027 551567839 551568009 3.290000e-44 191
47 TraesCS3A01G111900 chr2B 91.489 94 4 2 6817 6908 166044481 166044572 9.410000e-25 126
48 TraesCS3A01G111900 chr2B 92.135 89 5 2 6645 6732 762802193 762802106 3.380000e-24 124
49 TraesCS3A01G111900 chr6A 92.473 93 3 2 6820 6910 93285788 93285698 7.270000e-26 130
50 TraesCS3A01G111900 chr7D 93.182 88 5 1 6645 6732 45403756 45403842 2.620000e-25 128
51 TraesCS3A01G111900 chr6B 92.308 91 3 2 6816 6904 13827614 13827526 9.410000e-25 126
52 TraesCS3A01G111900 chr6B 91.579 95 3 3 6813 6904 472612053 472612145 9.410000e-25 126
53 TraesCS3A01G111900 chr6B 88.119 101 9 3 6629 6729 22555586 22555683 5.660000e-22 117
54 TraesCS3A01G111900 chr5D 88.235 102 8 2 6808 6907 310705362 310705263 1.570000e-22 119
55 TraesCS3A01G111900 chr1B 88.660 97 9 2 6645 6740 572646693 572646598 5.660000e-22 117


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 TraesCS3A01G111900 chr3A 79378842 79387769 8927 True 16488.00 16488 100.00000 1 8928 1 chr3A.!!$R1 8927
1 TraesCS3A01G111900 chr3D 67675051 67681887 6836 True 2203.80 6514 95.02340 940 7801 5 chr3D.!!$R3 6861
2 TraesCS3A01G111900 chr3B 114193634 114201832 8198 False 3146.75 4255 94.71875 1 7854 4 chr3B.!!$F4 7853
3 TraesCS3A01G111900 chr3B 812783765 812784720 955 False 839.00 839 82.60400 7974 8928 1 chr3B.!!$F2 954
4 TraesCS3A01G111900 chr3B 114149282 114151194 1912 False 255.50 281 79.52500 3959 5622 2 chr3B.!!$F3 1663
5 TraesCS3A01G111900 chr7A 20429239 20430312 1073 True 1845.00 1845 97.67200 7855 8928 1 chr7A.!!$R1 1073
6 TraesCS3A01G111900 chr5A 632192583 632193669 1086 True 1842.00 1842 97.24000 7842 8928 1 chr5A.!!$R2 1086
7 TraesCS3A01G111900 chr1A 549551564 549552424 860 True 1447.00 1447 96.98000 8068 8928 1 chr1A.!!$R2 860
8 TraesCS3A01G111900 chr6D 327608403 327609452 1049 False 1351.00 1351 89.73900 7857 8928 1 chr6D.!!$F1 1071
9 TraesCS3A01G111900 chr6D 378431866 378432936 1070 False 1236.00 1236 87.52300 7857 8928 1 chr6D.!!$F2 1071
10 TraesCS3A01G111900 chr2A 86288399 86289299 900 False 1057.00 1057 87.83200 7852 8754 1 chr2A.!!$F1 902
11 TraesCS3A01G111900 chr2A 73691429 73692254 825 False 314.50 468 82.36150 696 1538 2 chr2A.!!$F3 842
12 TraesCS3A01G111900 chr7B 696889652 696890704 1052 False 929.00 929 82.66500 7857 8926 1 chr7B.!!$F1 1069
13 TraesCS3A01G111900 chr1D 307154224 307154765 541 False 863.00 863 95.38700 7857 8398 1 chr1D.!!$F1 541
14 TraesCS3A01G111900 chr4B 26234257 26235023 766 False 713.00 713 83.50600 8162 8928 1 chr4B.!!$F1 766
15 TraesCS3A01G111900 chr4B 26273310 26274076 766 False 680.00 680 82.72700 8162 8928 1 chr4B.!!$F2 766
16 TraesCS3A01G111900 chr2D 74328050 74328878 828 False 334.50 460 81.77850 698 1538 2 chr2D.!!$F2 840

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
828 865 0.174845 CCCCAACTCGCTCGATTACA 59.825 55.000 0.00 0.00 0.00 2.41 F
1540 1613 0.951558 CGCTGCTAAGTTGGGTTGTT 59.048 50.000 0.00 0.00 0.00 2.83 F
1582 1655 1.012841 CGCCTTCTCCTCTGAATTGC 58.987 55.000 0.00 0.00 0.00 3.56 F
2048 2136 4.006319 GCTGCAAGTTATGACTTCCTTCT 58.994 43.478 0.00 0.00 44.14 2.85 F
3565 4256 2.026169 AGACGTCTCACAGACCCAGATA 60.026 50.000 13.58 0.00 42.12 1.98 F
3853 4544 2.632228 CGATATGCAACATGAAGCACG 58.368 47.619 16.63 12.76 44.49 5.34 F
4522 5256 3.157881 TCTCTGACAGTTTGAGACGGAT 58.842 45.455 1.59 0.00 32.63 4.18 F
4899 5868 0.033796 TATATACTCCCTCCGCCCGG 60.034 60.000 0.00 0.00 0.00 5.73 F
4909 5878 0.107848 CTCCGCCCGGAAATACTTGT 60.108 55.000 0.73 0.00 44.66 3.16 F
4910 5879 0.108041 TCCGCCCGGAAATACTTGTC 60.108 55.000 0.73 0.00 42.05 3.18 F
5886 7034 0.329596 GGCTTCATCACCCCTCTTGT 59.670 55.000 0.00 0.00 0.00 3.16 F
7820 9158 0.160182 GGTCTTTGTGTACGCGTTCG 59.840 55.000 20.78 0.00 42.43 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 1765 0.107017 AATCCTGCCAACTCCCGATG 60.107 55.000 0.00 0.0 0.00 3.84 R
2383 2471 6.979465 TCAGATCTAGCATGTCATTACTCAG 58.021 40.000 0.00 0.0 0.00 3.35 R
3565 4256 4.210331 AGAGAACATCTGTTTTGCCTTGT 58.790 39.130 0.00 0.0 38.56 3.16 R
3820 4511 0.031314 CATATCGCGTCACCTGAGCT 59.969 55.000 5.77 0.0 0.00 4.09 R
4890 5859 0.107848 ACAAGTATTTCCGGGCGGAG 60.108 55.000 0.00 0.0 46.06 4.63 R
4891 5860 0.108041 GACAAGTATTTCCGGGCGGA 60.108 55.000 0.00 0.0 43.52 5.54 R
6396 7548 1.880646 GCTTTGAACTACGGGCTTCCA 60.881 52.381 0.00 0.0 0.00 3.53 R
6893 8049 1.000496 GCTACCGAATTACTCCCTCCG 60.000 57.143 0.00 0.0 0.00 4.63 R
6894 8050 2.037144 TGCTACCGAATTACTCCCTCC 58.963 52.381 0.00 0.0 0.00 4.30 R
6895 8051 2.429610 TGTGCTACCGAATTACTCCCTC 59.570 50.000 0.00 0.0 0.00 4.30 R
7836 9174 0.238289 AAACCGAATGCGCTCACTTG 59.762 50.000 9.73 0.0 35.83 3.16 R
8777 10117 0.106519 GCCAGGCACTCATTACCCAT 60.107 55.000 6.55 0.0 34.60 4.00 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
97 99 2.146920 TTTTTGGGAACGGGTGAAGT 57.853 45.000 0.00 0.00 0.00 3.01
196 198 6.796426 TGTGTAACATGTTTCGAAAATTCCA 58.204 32.000 17.78 6.77 45.67 3.53
201 203 5.047188 ACATGTTTCGAAAATTCCACAACC 58.953 37.500 13.10 0.00 0.00 3.77
202 204 4.993029 TGTTTCGAAAATTCCACAACCT 57.007 36.364 13.10 0.00 0.00 3.50
395 404 8.837099 AGAATATGTCCAAATTTATGGTGGAA 57.163 30.769 0.00 0.00 42.97 3.53
476 485 2.611971 CGAAAACTAGTGCAGGTGCCTA 60.612 50.000 0.00 0.37 41.18 3.93
477 486 2.474410 AAACTAGTGCAGGTGCCTAC 57.526 50.000 0.00 0.00 41.18 3.18
478 487 0.246635 AACTAGTGCAGGTGCCTACG 59.753 55.000 0.00 0.00 41.18 3.51
494 504 2.288457 CCTACGTCCATGCCTATGTGAG 60.288 54.545 0.00 0.00 32.21 3.51
496 506 0.179076 CGTCCATGCCTATGTGAGCA 60.179 55.000 0.00 0.00 44.45 4.26
525 535 6.322201 GTGATCATGGACTAACCCATTTTGAT 59.678 38.462 0.00 0.00 44.11 2.57
526 536 6.896860 TGATCATGGACTAACCCATTTTGATT 59.103 34.615 0.00 0.00 44.11 2.57
604 617 8.958175 AAAACAGCATATTTTTCAAATGCATG 57.042 26.923 0.00 0.00 46.66 4.06
605 618 7.908827 AACAGCATATTTTTCAAATGCATGA 57.091 28.000 0.00 0.00 46.66 3.07
650 663 8.999431 ACATATTTACTCAAATATTGTAGGCGG 58.001 33.333 0.00 0.00 42.23 6.13
704 717 2.035066 GCTTCTCTGCAACAACCACAAT 59.965 45.455 0.00 0.00 0.00 2.71
705 718 3.635331 CTTCTCTGCAACAACCACAATG 58.365 45.455 0.00 0.00 0.00 2.82
761 774 1.129251 CGCAGTGAAGCACATTTCGAT 59.871 47.619 0.00 0.00 36.74 3.59
828 865 0.174845 CCCCAACTCGCTCGATTACA 59.825 55.000 0.00 0.00 0.00 2.41
876 913 4.982295 AGTACGTAACTGGAAACCGTTAAC 59.018 41.667 0.00 0.00 36.93 2.01
877 914 2.794350 ACGTAACTGGAAACCGTTAACG 59.206 45.455 20.99 20.99 39.44 3.18
924 961 9.064706 GGTGATAATCATCAACTCATCAATCTT 57.935 33.333 0.00 0.00 44.25 2.40
929 966 4.330894 TCATCAACTCATCAATCTTGCGAC 59.669 41.667 0.00 0.00 0.00 5.19
1070 1111 2.965147 TGTGAGCGATGATCTCCCAATA 59.035 45.455 0.00 0.00 0.00 1.90
1071 1112 3.006217 TGTGAGCGATGATCTCCCAATAG 59.994 47.826 0.00 0.00 0.00 1.73
1122 1165 4.054671 GCTTAAGATCAATCACCTCTCCG 58.945 47.826 6.67 0.00 0.00 4.63
1150 1193 2.617762 CGATCGAAGCAAGCGAGC 59.382 61.111 10.26 0.00 41.49 5.03
1151 1194 2.617762 GATCGAAGCAAGCGAGCG 59.382 61.111 0.00 0.00 41.49 5.03
1152 1195 1.874019 GATCGAAGCAAGCGAGCGA 60.874 57.895 8.73 8.73 41.49 4.93
1153 1196 1.806251 GATCGAAGCAAGCGAGCGAG 61.806 60.000 11.15 0.00 41.49 5.03
1179 1222 2.431942 GTTCGCTTCGCCGAGGAA 60.432 61.111 0.00 0.00 38.60 3.36
1180 1223 2.126071 TTCGCTTCGCCGAGGAAG 60.126 61.111 0.00 10.07 44.92 3.46
1181 1224 3.642778 TTCGCTTCGCCGAGGAAGG 62.643 63.158 0.00 7.26 42.88 3.46
1317 1381 4.416601 CCTCCCTCCGTTCCCCCT 62.417 72.222 0.00 0.00 0.00 4.79
1494 1567 2.719774 GGGTTTTCGCGTCGTACGG 61.720 63.158 16.52 0.69 42.82 4.02
1538 1611 1.210155 GCGCTGCTAAGTTGGGTTG 59.790 57.895 0.00 0.00 0.00 3.77
1539 1612 1.515521 GCGCTGCTAAGTTGGGTTGT 61.516 55.000 0.00 0.00 0.00 3.32
1540 1613 0.951558 CGCTGCTAAGTTGGGTTGTT 59.048 50.000 0.00 0.00 0.00 2.83
1541 1614 1.334960 CGCTGCTAAGTTGGGTTGTTG 60.335 52.381 0.00 0.00 0.00 3.33
1582 1655 1.012841 CGCCTTCTCCTCTGAATTGC 58.987 55.000 0.00 0.00 0.00 3.56
1805 1887 7.654520 TCGTGTACTTACTGCAAATTAGAAAGT 59.345 33.333 0.00 0.00 0.00 2.66
1897 1979 6.263344 TGATGTACAGCGTACTTATCTGAAC 58.737 40.000 6.63 2.54 0.00 3.18
2048 2136 4.006319 GCTGCAAGTTATGACTTCCTTCT 58.994 43.478 0.00 0.00 44.14 2.85
2083 2171 6.204688 TGAAGATGTTCACTGGTGTTTATGAC 59.795 38.462 0.23 0.00 37.79 3.06
2252 2340 9.255304 AGATCGATAAAGCTGATTTAACTTCTC 57.745 33.333 0.00 0.00 36.94 2.87
3565 4256 2.026169 AGACGTCTCACAGACCCAGATA 60.026 50.000 13.58 0.00 42.12 1.98
3659 4350 6.860539 CGTATCCACTCACTCTTTCTATCATG 59.139 42.308 0.00 0.00 0.00 3.07
3698 4389 5.102953 AGTTAGCACTTATTCCTCATGCA 57.897 39.130 0.00 0.00 38.79 3.96
3748 4439 4.602340 TCTCCTGTGGTTGTAGAAAGAC 57.398 45.455 0.00 0.00 0.00 3.01
3853 4544 2.632228 CGATATGCAACATGAAGCACG 58.368 47.619 16.63 12.76 44.49 5.34
3878 4569 7.201291 CGTTGAAATGTGAAATGCTGACTATTG 60.201 37.037 0.00 0.00 0.00 1.90
3879 4570 7.218228 TGAAATGTGAAATGCTGACTATTGT 57.782 32.000 0.00 0.00 0.00 2.71
4472 5169 7.382218 GGATGTTATGCTATGTTATGTTTTGGC 59.618 37.037 0.00 0.00 0.00 4.52
4522 5256 3.157881 TCTCTGACAGTTTGAGACGGAT 58.842 45.455 1.59 0.00 32.63 4.18
4871 5840 7.912949 TGTTTCGAAAAGAATGTCATTTGAG 57.087 32.000 13.10 0.00 38.86 3.02
4894 5863 8.582437 TGAGTAACAAATTATATACTCCCTCCG 58.418 37.037 15.97 0.00 42.18 4.63
4895 5864 7.384477 AGTAACAAATTATATACTCCCTCCGC 58.616 38.462 0.00 0.00 0.00 5.54
4896 5865 5.161943 ACAAATTATATACTCCCTCCGCC 57.838 43.478 0.00 0.00 0.00 6.13
4897 5866 4.019591 ACAAATTATATACTCCCTCCGCCC 60.020 45.833 0.00 0.00 0.00 6.13
4898 5867 1.843368 TTATATACTCCCTCCGCCCG 58.157 55.000 0.00 0.00 0.00 6.13
4899 5868 0.033796 TATATACTCCCTCCGCCCGG 60.034 60.000 0.00 0.00 0.00 5.73
4900 5869 1.797018 ATATACTCCCTCCGCCCGGA 61.797 60.000 0.73 9.31 42.90 5.14
4901 5870 2.010412 TATACTCCCTCCGCCCGGAA 62.010 60.000 0.73 0.00 44.66 4.30
4902 5871 2.884179 ATACTCCCTCCGCCCGGAAA 62.884 60.000 0.73 0.00 44.66 3.13
4903 5872 2.884179 TACTCCCTCCGCCCGGAAAT 62.884 60.000 0.73 0.00 44.66 2.17
4904 5873 2.041715 TCCCTCCGCCCGGAAATA 60.042 61.111 0.73 0.00 44.66 1.40
4905 5874 2.110420 CCCTCCGCCCGGAAATAC 59.890 66.667 0.73 0.00 44.66 1.89
4906 5875 2.440817 CCCTCCGCCCGGAAATACT 61.441 63.158 0.73 0.00 44.66 2.12
4907 5876 1.525442 CCTCCGCCCGGAAATACTT 59.475 57.895 0.73 0.00 44.66 2.24
4908 5877 0.814010 CCTCCGCCCGGAAATACTTG 60.814 60.000 0.73 0.00 44.66 3.16
4909 5878 0.107848 CTCCGCCCGGAAATACTTGT 60.108 55.000 0.73 0.00 44.66 3.16
4910 5879 0.108041 TCCGCCCGGAAATACTTGTC 60.108 55.000 0.73 0.00 42.05 3.18
4911 5880 0.391927 CCGCCCGGAAATACTTGTCA 60.392 55.000 0.73 0.00 37.50 3.58
4912 5881 1.663695 CGCCCGGAAATACTTGTCAT 58.336 50.000 0.73 0.00 0.00 3.06
4913 5882 1.597663 CGCCCGGAAATACTTGTCATC 59.402 52.381 0.73 0.00 0.00 2.92
4914 5883 2.639065 GCCCGGAAATACTTGTCATCA 58.361 47.619 0.73 0.00 0.00 3.07
4915 5884 3.013921 GCCCGGAAATACTTGTCATCAA 58.986 45.455 0.73 0.00 0.00 2.57
4933 5902 7.828508 TCATCAAGATGAATAAAAGGGGATG 57.171 36.000 10.16 0.00 44.14 3.51
4934 5903 7.356680 TCATCAAGATGAATAAAAGGGGATGT 58.643 34.615 10.16 0.00 44.14 3.06
4935 5904 8.501904 TCATCAAGATGAATAAAAGGGGATGTA 58.498 33.333 10.16 0.00 44.14 2.29
4936 5905 9.305555 CATCAAGATGAATAAAAGGGGATGTAT 57.694 33.333 4.01 0.00 41.20 2.29
4937 5906 8.924511 TCAAGATGAATAAAAGGGGATGTATC 57.075 34.615 0.00 0.00 0.00 2.24
4938 5907 8.727149 TCAAGATGAATAAAAGGGGATGTATCT 58.273 33.333 0.00 0.00 0.00 1.98
4941 5910 9.621239 AGATGAATAAAAGGGGATGTATCTAGA 57.379 33.333 0.00 0.00 0.00 2.43
4942 5911 9.660180 GATGAATAAAAGGGGATGTATCTAGAC 57.340 37.037 0.00 0.00 0.00 2.59
4943 5912 8.561536 TGAATAAAAGGGGATGTATCTAGACA 57.438 34.615 0.00 0.00 0.00 3.41
4944 5913 9.170890 TGAATAAAAGGGGATGTATCTAGACAT 57.829 33.333 0.00 0.00 42.82 3.06
4952 5921 9.845214 AGGGGATGTATCTAGACATATTTTAGT 57.155 33.333 0.00 0.00 40.18 2.24
4976 5945 9.225682 AGTTCTAGATACATCCCTTTTTATCCA 57.774 33.333 0.00 0.00 0.00 3.41
4981 5950 8.930846 AGATACATCCCTTTTTATCCATTCTG 57.069 34.615 0.00 0.00 0.00 3.02
4982 5951 8.727149 AGATACATCCCTTTTTATCCATTCTGA 58.273 33.333 0.00 0.00 0.00 3.27
4983 5952 9.525826 GATACATCCCTTTTTATCCATTCTGAT 57.474 33.333 0.00 0.00 0.00 2.90
4984 5953 7.592885 ACATCCCTTTTTATCCATTCTGATG 57.407 36.000 0.00 0.00 33.80 3.07
4985 5954 7.356680 ACATCCCTTTTTATCCATTCTGATGA 58.643 34.615 0.00 0.00 35.16 2.92
4986 5955 7.286316 ACATCCCTTTTTATCCATTCTGATGAC 59.714 37.037 0.00 0.00 35.16 3.06
4987 5956 6.730447 TCCCTTTTTATCCATTCTGATGACA 58.270 36.000 0.00 0.00 35.16 3.58
4988 5957 7.181361 TCCCTTTTTATCCATTCTGATGACAA 58.819 34.615 0.00 0.00 35.16 3.18
4989 5958 7.340232 TCCCTTTTTATCCATTCTGATGACAAG 59.660 37.037 0.00 0.00 35.16 3.16
4990 5959 7.123247 CCCTTTTTATCCATTCTGATGACAAGT 59.877 37.037 0.00 0.00 35.16 3.16
4991 5960 9.177608 CCTTTTTATCCATTCTGATGACAAGTA 57.822 33.333 0.00 0.00 35.16 2.24
4997 5966 7.307493 TCCATTCTGATGACAAGTATTTTCG 57.693 36.000 0.00 0.00 35.16 3.46
4998 5967 6.316140 TCCATTCTGATGACAAGTATTTTCGG 59.684 38.462 0.00 0.00 35.16 4.30
4999 5968 6.316140 CCATTCTGATGACAAGTATTTTCGGA 59.684 38.462 0.00 0.00 35.16 4.55
5000 5969 6.721571 TTCTGATGACAAGTATTTTCGGAC 57.278 37.500 0.00 0.00 0.00 4.79
5001 5970 4.862574 TCTGATGACAAGTATTTTCGGACG 59.137 41.667 0.00 0.00 0.00 4.79
5002 5971 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
5003 5972 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
5004 5973 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
5005 5974 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
5006 5975 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
5007 5976 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
5008 5977 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
5009 5978 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
5025 5994 8.931568 ACGGAGGGAGTATAAAATTAACACTAT 58.068 33.333 0.00 0.00 0.00 2.12
5256 6401 9.730420 TCAAAACTAATTTGCAGTTCTTACTTC 57.270 29.630 0.00 0.00 46.53 3.01
5259 6404 6.888430 ACTAATTTGCAGTTCTTACTTCACG 58.112 36.000 0.00 0.00 30.26 4.35
5588 6736 7.979444 TGAAGAGGTGTTACTTTTTCCATAG 57.021 36.000 0.00 0.00 0.00 2.23
5648 6796 4.386867 ACAGTGTATCATAGTCCAACCG 57.613 45.455 0.00 0.00 0.00 4.44
5886 7034 0.329596 GGCTTCATCACCCCTCTTGT 59.670 55.000 0.00 0.00 0.00 3.16
6042 7190 2.012673 GATGTTGCTCCTGATCCACAC 58.987 52.381 0.00 0.00 0.00 3.82
6098 7246 2.755655 AGGACAGTGATGAAGAGGTACG 59.244 50.000 0.00 0.00 0.00 3.67
6124 7274 2.977772 TTTGTTGGCTTGTTCCTTGG 57.022 45.000 0.00 0.00 0.00 3.61
6156 7306 9.331282 ACTTGTGAATCTTATTACTAAGCCATC 57.669 33.333 0.00 0.00 35.32 3.51
6280 7430 1.298859 GCTAGTGAAAGTGGTGGCGG 61.299 60.000 0.00 0.00 0.00 6.13
6355 7505 5.523188 GTCAACTCTGCTAATGATCTCTTGG 59.477 44.000 0.00 0.00 0.00 3.61
6356 7506 5.188555 TCAACTCTGCTAATGATCTCTTGGT 59.811 40.000 0.00 0.00 0.00 3.67
6396 7548 7.895429 TCCTAATCTCCAAAAGTCATCCAAAAT 59.105 33.333 0.00 0.00 0.00 1.82
6669 7821 7.177921 CACTACCTCCGTCCCATAATATAAGAA 59.822 40.741 0.00 0.00 0.00 2.52
6670 7822 7.731688 ACTACCTCCGTCCCATAATATAAGAAA 59.268 37.037 0.00 0.00 0.00 2.52
6737 7889 4.262506 GGGACGGAGGGAGTAATTCATAAG 60.263 50.000 0.00 0.00 0.00 1.73
6743 7895 9.151177 ACGGAGGGAGTAATTCATAAGTTAATA 57.849 33.333 0.00 0.00 0.00 0.98
6785 7937 8.922058 TCTAGAGTTATTTCGCGTAAAGAATT 57.078 30.769 5.77 6.10 31.38 2.17
6810 7966 2.389715 ACTTCTCGGGATCGGAGATTT 58.610 47.619 13.84 4.08 45.12 2.17
6878 8034 9.733219 GATAACTAAAGTAGTGATCTAAACGCT 57.267 33.333 5.75 0.00 41.55 5.07
6879 8035 9.733219 ATAACTAAAGTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 39.39 5.03
6880 8036 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
6881 8037 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
6882 8038 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
6883 8039 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
6895 8051 9.241317 TCTAAACGCTCTTATATTTCTTTACGG 57.759 33.333 0.00 0.00 0.00 4.02
6896 8052 9.241317 CTAAACGCTCTTATATTTCTTTACGGA 57.759 33.333 0.00 0.00 0.00 4.69
6897 8053 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
6898 8054 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
6899 8055 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
6917 8073 2.835764 AGGGAGTAATTCGGTAGCACAA 59.164 45.455 0.00 0.00 0.00 3.33
7071 8228 4.130857 ACGACAAATGAACCATGTACACA 58.869 39.130 0.00 0.00 0.00 3.72
7094 8251 6.693978 ACAAAGAGTTTAATGTTTAACCGCAC 59.306 34.615 0.00 0.00 0.00 5.34
7155 8317 8.093927 CCTTTTTGGTTAAGCATTATTCCTTGA 58.906 33.333 8.40 0.00 0.00 3.02
7251 8413 2.067932 TTGGCTCAGGGTGTGAAGGG 62.068 60.000 0.00 0.00 33.60 3.95
7391 8686 1.746322 TTCCTCCCGCACGTGTAACA 61.746 55.000 18.38 0.00 35.74 2.41
7392 8687 1.079405 CCTCCCGCACGTGTAACAT 60.079 57.895 18.38 0.00 35.74 2.71
7461 8756 1.406614 CCTTGCTCTCCCTGTCATGAC 60.407 57.143 19.27 19.27 0.00 3.06
7597 8892 3.369892 GGCAATGGCTCTGACTAGAAGAA 60.370 47.826 0.00 0.00 40.87 2.52
7671 8966 3.074412 CGTAGGGCAGTTTGAACAAGAT 58.926 45.455 0.00 0.00 0.00 2.40
7717 9012 4.096732 AGTGCAGTTTGAACAAGAACAC 57.903 40.909 0.00 0.00 0.00 3.32
7747 9085 1.935873 CATGAACCTGCATACCGTGAG 59.064 52.381 0.00 0.00 0.00 3.51
7780 9118 4.519906 TGGGTCTTTTCTTTTGAGAGGT 57.480 40.909 0.00 0.00 0.00 3.85
7782 9120 6.008696 TGGGTCTTTTCTTTTGAGAGGTAA 57.991 37.500 0.00 0.00 0.00 2.85
7792 9130 1.573108 TGAGAGGTAAAGGGAGGCTG 58.427 55.000 0.00 0.00 0.00 4.85
7807 9145 3.200165 GGAGGCTGTACTTATGGGTCTTT 59.800 47.826 0.00 0.00 0.00 2.52
7811 9149 4.324267 GCTGTACTTATGGGTCTTTGTGT 58.676 43.478 0.00 0.00 0.00 3.72
7819 9157 0.509929 GGGTCTTTGTGTACGCGTTC 59.490 55.000 20.78 14.31 0.00 3.95
7820 9158 0.160182 GGTCTTTGTGTACGCGTTCG 59.840 55.000 20.78 0.00 42.43 3.95
7847 9185 3.137687 TGGAGACAAGTGAGCGCA 58.862 55.556 11.47 0.00 37.44 6.09
8008 9346 2.810780 TGAGCATCTCCGTTCGAACGA 61.811 52.381 43.01 29.27 45.92 3.85
8206 9544 4.643463 TGCATGCCAAACATTCAAGAATT 58.357 34.783 16.68 0.00 36.64 2.17
8270 9608 4.207165 CAAATAGTTTCCCCGGTCATCAT 58.793 43.478 0.00 0.00 0.00 2.45
8470 9809 0.673333 AGCGGTTGATGAATGCGTGA 60.673 50.000 0.00 0.00 0.00 4.35
8700 10040 2.163509 AGAGCAGTCAAGAAGCGAGTA 58.836 47.619 0.00 0.00 0.00 2.59
8777 10117 2.029020 CGGTGTTCTCTGACATCTTCCA 60.029 50.000 0.00 0.00 0.00 3.53
8889 10229 8.842358 TTTTCTTGTTGTATATTCGAAGTCCT 57.158 30.769 3.35 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
182 184 6.656314 AAAAGGTTGTGGAATTTTCGAAAC 57.344 33.333 10.79 0.00 0.00 2.78
271 275 5.995282 ACGAGTTCAAGAAAATGTATGTGGA 59.005 36.000 0.00 0.00 0.00 4.02
282 286 6.315144 TGAAAGATGTTCACGAGTTCAAGAAA 59.685 34.615 0.00 0.00 0.00 2.52
286 290 6.618287 ATTGAAAGATGTTCACGAGTTCAA 57.382 33.333 0.00 0.00 37.75 2.69
456 465 1.897560 AGGCACCTGCACTAGTTTTC 58.102 50.000 0.00 0.00 44.36 2.29
476 485 0.179073 GCTCACATAGGCATGGACGT 60.179 55.000 0.00 0.00 36.39 4.34
477 486 0.179076 TGCTCACATAGGCATGGACG 60.179 55.000 0.00 0.00 36.39 4.79
478 487 2.267174 ATGCTCACATAGGCATGGAC 57.733 50.000 0.00 0.00 45.81 4.02
494 504 3.313526 GGTTAGTCCATGATCACACATGC 59.686 47.826 0.00 0.00 44.11 4.06
496 506 3.523157 TGGGTTAGTCCATGATCACACAT 59.477 43.478 0.00 0.00 38.11 3.21
625 638 8.999431 ACCGCCTACAATATTTGAGTAAATATG 58.001 33.333 6.15 4.41 44.64 1.78
627 640 8.967664 AACCGCCTACAATATTTGAGTAAATA 57.032 30.769 0.00 0.00 41.56 1.40
628 641 7.875327 AACCGCCTACAATATTTGAGTAAAT 57.125 32.000 0.00 0.00 39.69 1.40
629 642 8.967664 ATAACCGCCTACAATATTTGAGTAAA 57.032 30.769 0.00 0.00 0.00 2.01
632 645 8.833493 GTTTATAACCGCCTACAATATTTGAGT 58.167 33.333 0.00 0.00 0.00 3.41
633 646 8.007716 CGTTTATAACCGCCTACAATATTTGAG 58.992 37.037 0.00 0.00 0.00 3.02
634 647 7.518689 GCGTTTATAACCGCCTACAATATTTGA 60.519 37.037 15.70 0.00 43.96 2.69
643 656 0.854705 CCGCGTTTATAACCGCCTAC 59.145 55.000 19.86 0.00 46.83 3.18
646 659 0.302589 CTTCCGCGTTTATAACCGCC 59.697 55.000 19.86 4.63 46.83 6.13
648 661 0.302589 GGCTTCCGCGTTTATAACCG 59.697 55.000 4.92 0.00 36.88 4.44
650 663 3.474693 TTTGGCTTCCGCGTTTATAAC 57.525 42.857 4.92 0.00 36.88 1.89
656 669 1.067821 TCAAATTTTGGCTTCCGCGTT 59.932 42.857 4.92 0.00 36.88 4.84
661 674 5.066375 AGCTTGTTTTCAAATTTTGGCTTCC 59.934 36.000 9.18 0.00 39.47 3.46
675 688 4.032703 TGTTGCAGAGAAGCTTGTTTTC 57.967 40.909 2.10 0.00 34.99 2.29
680 693 1.677576 TGGTTGTTGCAGAGAAGCTTG 59.322 47.619 2.10 0.00 34.99 4.01
704 717 1.917495 CATCCTCTCCCCACATGCA 59.083 57.895 0.00 0.00 0.00 3.96
705 718 1.527844 GCATCCTCTCCCCACATGC 60.528 63.158 0.00 0.00 33.57 4.06
746 759 3.305267 CCAAACCATCGAAATGTGCTTCA 60.305 43.478 0.00 0.00 0.00 3.02
761 774 2.596923 TGCGCTGCATCCAAACCA 60.597 55.556 9.73 0.00 31.71 3.67
857 894 3.422890 CGTTAACGGTTTCCAGTTACG 57.577 47.619 20.24 0.00 33.18 3.18
943 980 3.939592 GCTTACTCGCTAGATTGGGTTTT 59.060 43.478 0.00 0.00 0.00 2.43
944 981 3.197983 AGCTTACTCGCTAGATTGGGTTT 59.802 43.478 0.00 0.00 38.76 3.27
946 983 2.362717 GAGCTTACTCGCTAGATTGGGT 59.637 50.000 0.00 0.00 41.08 4.51
947 984 2.362397 TGAGCTTACTCGCTAGATTGGG 59.638 50.000 0.00 0.00 46.69 4.12
948 985 3.717400 TGAGCTTACTCGCTAGATTGG 57.283 47.619 0.00 0.00 46.69 3.16
1052 1093 3.675775 GCTCTATTGGGAGATCATCGCTC 60.676 52.174 0.00 0.00 41.37 5.03
1070 1111 4.731612 CGCAGTGGCACTCGCTCT 62.732 66.667 27.29 5.01 41.24 4.09
1122 1165 0.041135 CTTCGATCGGCTCTACGGAC 60.041 60.000 16.41 0.00 0.00 4.79
1151 1194 4.681978 AGCGAACACGGGTGCCTC 62.682 66.667 0.00 0.00 0.00 4.70
1152 1195 4.250305 AAGCGAACACGGGTGCCT 62.250 61.111 0.00 0.00 0.00 4.75
1153 1196 3.723348 GAAGCGAACACGGGTGCC 61.723 66.667 0.00 0.00 0.00 5.01
1310 1374 0.253207 GAGGAAGAGGGAAGGGGGAA 60.253 60.000 0.00 0.00 0.00 3.97
1311 1375 1.396594 GAGGAAGAGGGAAGGGGGA 59.603 63.158 0.00 0.00 0.00 4.81
1315 1379 2.736826 GCGGGAGGAAGAGGGAAGG 61.737 68.421 0.00 0.00 0.00 3.46
1317 1381 3.075005 CGCGGGAGGAAGAGGGAA 61.075 66.667 0.00 0.00 0.00 3.97
1494 1567 1.065273 CAGAGCGCAAATGCATCCC 59.935 57.895 11.47 0.00 42.21 3.85
1538 1611 0.320421 TACCAAGCACTCGCCTCAAC 60.320 55.000 0.00 0.00 39.83 3.18
1539 1612 0.037326 CTACCAAGCACTCGCCTCAA 60.037 55.000 0.00 0.00 39.83 3.02
1540 1613 1.591703 CTACCAAGCACTCGCCTCA 59.408 57.895 0.00 0.00 39.83 3.86
1541 1614 1.153549 CCTACCAAGCACTCGCCTC 60.154 63.158 0.00 0.00 39.83 4.70
1570 1643 3.157087 GGAAACCAAGCAATTCAGAGGA 58.843 45.455 0.00 0.00 0.00 3.71
1575 1648 3.511146 GGATCAGGAAACCAAGCAATTCA 59.489 43.478 0.00 0.00 0.00 2.57
1582 1655 1.467920 GGCAGGATCAGGAAACCAAG 58.532 55.000 0.00 0.00 0.00 3.61
1683 1765 0.107017 AATCCTGCCAACTCCCGATG 60.107 55.000 0.00 0.00 0.00 3.84
1849 1931 0.397187 AAACATTTGCAGCCATGGCA 59.603 45.000 37.18 18.00 44.88 4.92
1897 1979 7.489757 GGTCAGAGAAAGCTTAAGTGTACATAG 59.510 40.741 0.00 0.00 0.00 2.23
2048 2136 7.556275 ACCAGTGAACATCTTCAAAGAGTAAAA 59.444 33.333 0.00 0.00 38.17 1.52
2115 2203 7.968246 AGTAATGAAACATGACAAGATTCTCG 58.032 34.615 0.00 0.00 0.00 4.04
2252 2340 2.025981 TGGGGACTTTCATCCATGTCAG 60.026 50.000 0.00 0.00 40.96 3.51
2383 2471 6.979465 TCAGATCTAGCATGTCATTACTCAG 58.021 40.000 0.00 0.00 0.00 3.35
3565 4256 4.210331 AGAGAACATCTGTTTTGCCTTGT 58.790 39.130 0.00 0.00 38.56 3.16
3659 4350 8.943002 AGTGCTAACTAATACCATAAACAACAC 58.057 33.333 0.00 0.00 33.79 3.32
3820 4511 0.031314 CATATCGCGTCACCTGAGCT 59.969 55.000 5.77 0.00 0.00 4.09
3853 4544 7.596248 ACAATAGTCAGCATTTCACATTTCAAC 59.404 33.333 0.00 0.00 0.00 3.18
4472 5169 8.147642 AGAGAAACAGTCAAACAATCAAGTAG 57.852 34.615 0.00 0.00 0.00 2.57
4871 5840 6.592994 GGCGGAGGGAGTATATAATTTGTTAC 59.407 42.308 0.00 0.00 0.00 2.50
4886 5855 2.138179 TATTTCCGGGCGGAGGGAG 61.138 63.158 0.00 0.00 46.06 4.30
4887 5856 2.041715 TATTTCCGGGCGGAGGGA 60.042 61.111 0.00 0.00 46.06 4.20
4888 5857 1.979619 AAGTATTTCCGGGCGGAGGG 61.980 60.000 0.00 0.00 46.06 4.30
4889 5858 0.814010 CAAGTATTTCCGGGCGGAGG 60.814 60.000 0.00 0.00 46.06 4.30
4890 5859 0.107848 ACAAGTATTTCCGGGCGGAG 60.108 55.000 0.00 0.00 46.06 4.63
4891 5860 0.108041 GACAAGTATTTCCGGGCGGA 60.108 55.000 0.00 0.00 43.52 5.54
4892 5861 0.391927 TGACAAGTATTTCCGGGCGG 60.392 55.000 0.00 0.00 0.00 6.13
4893 5862 1.597663 GATGACAAGTATTTCCGGGCG 59.402 52.381 0.00 0.00 0.00 6.13
4894 5863 2.639065 TGATGACAAGTATTTCCGGGC 58.361 47.619 0.00 0.00 0.00 6.13
4895 5864 4.882671 CTTGATGACAAGTATTTCCGGG 57.117 45.455 0.00 0.00 45.73 5.73
4906 5875 7.181361 TCCCCTTTTATTCATCTTGATGACAA 58.819 34.615 12.28 7.53 34.65 3.18
4907 5876 6.730447 TCCCCTTTTATTCATCTTGATGACA 58.270 36.000 12.28 5.64 0.00 3.58
4908 5877 7.286316 ACATCCCCTTTTATTCATCTTGATGAC 59.714 37.037 12.28 0.00 32.39 3.06
4909 5878 7.356680 ACATCCCCTTTTATTCATCTTGATGA 58.643 34.615 9.02 9.02 32.39 2.92
4910 5879 7.592885 ACATCCCCTTTTATTCATCTTGATG 57.407 36.000 4.35 4.35 33.80 3.07
4911 5880 9.525826 GATACATCCCCTTTTATTCATCTTGAT 57.474 33.333 0.00 0.00 0.00 2.57
4912 5881 8.727149 AGATACATCCCCTTTTATTCATCTTGA 58.273 33.333 0.00 0.00 0.00 3.02
4913 5882 8.930846 AGATACATCCCCTTTTATTCATCTTG 57.069 34.615 0.00 0.00 0.00 3.02
4915 5884 9.621239 TCTAGATACATCCCCTTTTATTCATCT 57.379 33.333 0.00 0.00 0.00 2.90
4916 5885 9.660180 GTCTAGATACATCCCCTTTTATTCATC 57.340 37.037 0.00 0.00 0.00 2.92
4917 5886 9.170890 TGTCTAGATACATCCCCTTTTATTCAT 57.829 33.333 0.00 0.00 0.00 2.57
4918 5887 8.561536 TGTCTAGATACATCCCCTTTTATTCA 57.438 34.615 0.00 0.00 0.00 2.57
4926 5895 9.845214 ACTAAAATATGTCTAGATACATCCCCT 57.155 33.333 0.00 0.00 40.52 4.79
4950 5919 9.225682 TGGATAAAAAGGGATGTATCTAGAACT 57.774 33.333 0.00 0.00 0.00 3.01
4956 5925 8.727149 TCAGAATGGATAAAAAGGGATGTATCT 58.273 33.333 0.00 0.00 36.16 1.98
4957 5926 8.924511 TCAGAATGGATAAAAAGGGATGTATC 57.075 34.615 0.00 0.00 36.16 2.24
4958 5927 9.305555 CATCAGAATGGATAAAAAGGGATGTAT 57.694 33.333 0.00 0.00 36.16 2.29
4959 5928 8.501904 TCATCAGAATGGATAAAAAGGGATGTA 58.498 33.333 0.00 0.00 36.16 2.29
4960 5929 7.286316 GTCATCAGAATGGATAAAAAGGGATGT 59.714 37.037 0.00 0.00 36.16 3.06
4961 5930 7.286087 TGTCATCAGAATGGATAAAAAGGGATG 59.714 37.037 0.00 0.00 36.16 3.51
4962 5931 7.356680 TGTCATCAGAATGGATAAAAAGGGAT 58.643 34.615 0.00 0.00 36.16 3.85
4963 5932 6.730447 TGTCATCAGAATGGATAAAAAGGGA 58.270 36.000 0.00 0.00 36.16 4.20
4964 5933 7.123247 ACTTGTCATCAGAATGGATAAAAAGGG 59.877 37.037 0.00 0.00 36.16 3.95
4965 5934 8.059798 ACTTGTCATCAGAATGGATAAAAAGG 57.940 34.615 0.00 0.00 36.16 3.11
4971 5940 9.045223 CGAAAATACTTGTCATCAGAATGGATA 57.955 33.333 0.00 0.00 36.16 2.59
4972 5941 7.012704 CCGAAAATACTTGTCATCAGAATGGAT 59.987 37.037 0.00 0.00 36.16 3.41
4973 5942 6.316140 CCGAAAATACTTGTCATCAGAATGGA 59.684 38.462 0.00 0.00 36.16 3.41
4974 5943 6.316140 TCCGAAAATACTTGTCATCAGAATGG 59.684 38.462 0.00 0.00 36.16 3.16
4975 5944 7.182761 GTCCGAAAATACTTGTCATCAGAATG 58.817 38.462 0.00 0.00 37.54 2.67
4976 5945 6.036083 CGTCCGAAAATACTTGTCATCAGAAT 59.964 38.462 0.00 0.00 0.00 2.40
4977 5946 5.347635 CGTCCGAAAATACTTGTCATCAGAA 59.652 40.000 0.00 0.00 0.00 3.02
4978 5947 4.862574 CGTCCGAAAATACTTGTCATCAGA 59.137 41.667 0.00 0.00 0.00 3.27
4979 5948 4.032900 CCGTCCGAAAATACTTGTCATCAG 59.967 45.833 0.00 0.00 0.00 2.90
4980 5949 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
4981 5950 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
4982 5951 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
4983 5952 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
4984 5953 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
4985 5954 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
4986 5955 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
4987 5956 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
4988 5957 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
4989 5958 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
4990 5959 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
4991 5960 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
4992 5961 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
4993 5962 2.734755 TATACTCCCTCCGTCCGAAA 57.265 50.000 0.00 0.00 0.00 3.46
4994 5963 2.734755 TTATACTCCCTCCGTCCGAA 57.265 50.000 0.00 0.00 0.00 4.30
4995 5964 2.734755 TTTATACTCCCTCCGTCCGA 57.265 50.000 0.00 0.00 0.00 4.55
4996 5965 4.332428 AATTTTATACTCCCTCCGTCCG 57.668 45.455 0.00 0.00 0.00 4.79
4997 5966 6.481313 GTGTTAATTTTATACTCCCTCCGTCC 59.519 42.308 0.00 0.00 0.00 4.79
4998 5967 7.270779 AGTGTTAATTTTATACTCCCTCCGTC 58.729 38.462 0.00 0.00 0.00 4.79
4999 5968 7.191593 AGTGTTAATTTTATACTCCCTCCGT 57.808 36.000 0.00 0.00 0.00 4.69
5025 5994 6.183361 ACCATATGATCTGTCCGAAAACCATA 60.183 38.462 3.65 0.00 0.00 2.74
5211 6356 9.736023 AGTTTTGAAAATCAAACATCACTCTAC 57.264 29.630 5.09 0.00 45.03 2.59
5256 6401 7.772332 AACTGCTAATAAAGGAGAATACGTG 57.228 36.000 0.00 0.00 46.18 4.49
5648 6796 5.936956 TGGGCATTGTGATTAAAATTCCAAC 59.063 36.000 0.00 0.00 0.00 3.77
6068 7216 3.010420 TCATCACTGTCCTCACTACTCG 58.990 50.000 0.00 0.00 0.00 4.18
6124 7274 7.602517 AGTAATAAGATTCACAAGTCAGCAC 57.397 36.000 0.00 0.00 0.00 4.40
6156 7306 9.537192 TGAAATGGTAAAGGACAAGTATATACG 57.463 33.333 7.23 0.00 0.00 3.06
6169 7319 3.364549 TCCTGGCATGAAATGGTAAAGG 58.635 45.455 0.00 0.00 46.86 3.11
6396 7548 1.880646 GCTTTGAACTACGGGCTTCCA 60.881 52.381 0.00 0.00 0.00 3.53
6643 7795 6.662234 TCTTATATTATGGGACGGAGGTAGTG 59.338 42.308 0.00 0.00 0.00 2.74
6644 7796 6.797707 TCTTATATTATGGGACGGAGGTAGT 58.202 40.000 0.00 0.00 0.00 2.73
6645 7797 7.713734 TTCTTATATTATGGGACGGAGGTAG 57.286 40.000 0.00 0.00 0.00 3.18
6680 7832 6.856426 AGAACGTTTTTCAAGCTAAACATAGC 59.144 34.615 0.46 0.00 43.12 2.97
6690 7842 9.233232 CCCATAATATAAGAACGTTTTTCAAGC 57.767 33.333 7.42 0.00 0.00 4.01
6693 7845 8.605746 CGTCCCATAATATAAGAACGTTTTTCA 58.394 33.333 7.42 0.00 0.00 2.69
6694 7846 8.066000 CCGTCCCATAATATAAGAACGTTTTTC 58.934 37.037 7.42 0.00 0.00 2.29
6760 7912 8.922058 AATTCTTTACGCGAAATAACTCTAGA 57.078 30.769 15.93 0.00 0.00 2.43
6785 7937 1.103803 CCGATCCCGAGAAGTTCAGA 58.896 55.000 5.50 0.00 38.22 3.27
6851 8007 9.733219 GCGTTTAGATCACTACTTTAGTTATCT 57.267 33.333 12.46 12.46 46.18 1.98
6852 8008 9.733219 AGCGTTTAGATCACTACTTTAGTTATC 57.267 33.333 0.00 0.95 38.88 1.75
6853 8009 9.733219 GAGCGTTTAGATCACTACTTTAGTTAT 57.267 33.333 0.00 0.00 36.76 1.89
6854 8010 8.954350 AGAGCGTTTAGATCACTACTTTAGTTA 58.046 33.333 0.00 0.00 37.82 2.24
6855 8011 7.828712 AGAGCGTTTAGATCACTACTTTAGTT 58.171 34.615 0.00 0.00 37.82 2.24
6856 8012 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
6857 8013 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
6869 8025 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
6870 8026 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
6871 8027 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
6872 8028 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
6873 8029 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
6874 8030 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
6875 8031 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
6876 8032 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
6877 8033 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
6878 8034 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
6882 8038 7.871463 CGAATTACTCCCTCCGTAAAGAAATAT 59.129 37.037 0.00 0.00 31.36 1.28
6883 8039 7.205297 CGAATTACTCCCTCCGTAAAGAAATA 58.795 38.462 0.00 0.00 31.36 1.40
6884 8040 6.047231 CGAATTACTCCCTCCGTAAAGAAAT 58.953 40.000 0.00 0.00 31.36 2.17
6885 8041 5.413499 CGAATTACTCCCTCCGTAAAGAAA 58.587 41.667 0.00 0.00 31.36 2.52
6886 8042 4.142093 CCGAATTACTCCCTCCGTAAAGAA 60.142 45.833 0.00 0.00 31.36 2.52
6887 8043 3.382546 CCGAATTACTCCCTCCGTAAAGA 59.617 47.826 0.00 0.00 31.36 2.52
6888 8044 3.131755 ACCGAATTACTCCCTCCGTAAAG 59.868 47.826 0.00 0.00 31.36 1.85
6889 8045 3.099141 ACCGAATTACTCCCTCCGTAAA 58.901 45.455 0.00 0.00 31.36 2.01
6890 8046 2.738743 ACCGAATTACTCCCTCCGTAA 58.261 47.619 0.00 0.00 0.00 3.18
6891 8047 2.442236 ACCGAATTACTCCCTCCGTA 57.558 50.000 0.00 0.00 0.00 4.02
6892 8048 2.305009 CTACCGAATTACTCCCTCCGT 58.695 52.381 0.00 0.00 0.00 4.69
6893 8049 1.000496 GCTACCGAATTACTCCCTCCG 60.000 57.143 0.00 0.00 0.00 4.63
6894 8050 2.037144 TGCTACCGAATTACTCCCTCC 58.963 52.381 0.00 0.00 0.00 4.30
6895 8051 2.429610 TGTGCTACCGAATTACTCCCTC 59.570 50.000 0.00 0.00 0.00 4.30
6896 8052 2.463752 TGTGCTACCGAATTACTCCCT 58.536 47.619 0.00 0.00 0.00 4.20
6897 8053 2.973694 TGTGCTACCGAATTACTCCC 57.026 50.000 0.00 0.00 0.00 4.30
6898 8054 4.933400 TCTTTTGTGCTACCGAATTACTCC 59.067 41.667 0.00 0.00 0.00 3.85
6899 8055 5.638234 AGTCTTTTGTGCTACCGAATTACTC 59.362 40.000 0.00 0.00 0.00 2.59
6938 8094 6.087159 CGAAAATTCATGACCAATGATATGCG 59.913 38.462 0.00 0.00 44.84 4.73
7023 8179 5.711976 CCCTCCCTAGTGCCATAATTTATTG 59.288 44.000 0.00 0.00 0.00 1.90
7071 8228 7.034685 AGTGCGGTTAAACATTAAACTCTTT 57.965 32.000 0.00 0.00 0.00 2.52
7155 8317 6.139679 TCCAGAAAGAATTCAGTTACCCAT 57.860 37.500 8.44 0.00 38.06 4.00
7251 8413 0.822164 AGCCAAATCTGGATTGCTGC 59.178 50.000 7.16 0.00 46.92 5.25
7337 8499 7.618512 AGGGCACATAACGGAGTAATATATACT 59.381 37.037 0.00 0.00 45.00 2.12
7338 8500 7.779073 AGGGCACATAACGGAGTAATATATAC 58.221 38.462 0.00 0.00 45.00 1.47
7339 8501 7.966339 AGGGCACATAACGGAGTAATATATA 57.034 36.000 0.00 0.00 45.00 0.86
7340 8502 6.869206 AGGGCACATAACGGAGTAATATAT 57.131 37.500 0.00 0.00 45.00 0.86
7341 8503 7.779754 TTAGGGCACATAACGGAGTAATATA 57.220 36.000 0.00 0.00 45.00 0.86
7342 8504 6.675413 TTAGGGCACATAACGGAGTAATAT 57.325 37.500 0.00 0.00 45.00 1.28
7343 8505 6.460781 CATTAGGGCACATAACGGAGTAATA 58.539 40.000 0.00 0.00 45.00 0.98
7344 8506 5.305585 CATTAGGGCACATAACGGAGTAAT 58.694 41.667 0.00 0.00 45.00 1.89
7345 8507 4.699637 CATTAGGGCACATAACGGAGTAA 58.300 43.478 0.00 0.00 45.00 2.24
7346 8508 3.493699 GCATTAGGGCACATAACGGAGTA 60.494 47.826 0.00 0.00 45.00 2.59
7347 8509 5.263593 TGCATTAGGGCACATAACGGAGT 62.264 47.826 0.00 0.00 40.87 3.85
7391 8686 6.542852 GTGTTTGTGAACGCAACTGATATAT 58.457 36.000 0.14 0.00 43.92 0.86
7392 8687 5.922546 GTGTTTGTGAACGCAACTGATATA 58.077 37.500 0.14 0.00 43.92 0.86
7461 8756 1.576421 GTTGCTTGTCTTCGGCTGG 59.424 57.895 0.00 0.00 0.00 4.85
7634 8929 4.682320 GCCCTACGGTGATTTACAGATTCA 60.682 45.833 0.00 0.00 0.00 2.57
7671 8966 1.604278 CGATCTACAGATGCTCGGTCA 59.396 52.381 0.00 0.00 34.37 4.02
7747 9085 1.519498 AAGACCCATAAGTAGCCCCC 58.481 55.000 0.00 0.00 0.00 5.40
7780 9118 3.714798 CCCATAAGTACAGCCTCCCTTTA 59.285 47.826 0.00 0.00 0.00 1.85
7782 9120 2.127708 CCCATAAGTACAGCCTCCCTT 58.872 52.381 0.00 0.00 0.00 3.95
7792 9130 4.328169 GCGTACACAAAGACCCATAAGTAC 59.672 45.833 0.00 0.00 0.00 2.73
7832 9170 0.368227 CGAATGCGCTCACTTGTCTC 59.632 55.000 9.73 0.00 0.00 3.36
7833 9171 1.016130 CCGAATGCGCTCACTTGTCT 61.016 55.000 9.73 0.00 35.83 3.41
7834 9172 1.291877 ACCGAATGCGCTCACTTGTC 61.292 55.000 9.73 0.00 35.83 3.18
7835 9173 0.884704 AACCGAATGCGCTCACTTGT 60.885 50.000 9.73 0.00 35.83 3.16
7836 9174 0.238289 AAACCGAATGCGCTCACTTG 59.762 50.000 9.73 0.00 35.83 3.16
7979 9317 5.593010 GAACGGAGATGCTCATAGTTTAGT 58.407 41.667 0.00 0.00 31.08 2.24
8008 9346 3.314357 GTCAGTTAGTTTTTGAAGGGCGT 59.686 43.478 0.00 0.00 0.00 5.68
8283 9621 1.001764 CATGGGAGAGGTGCAGCAA 60.002 57.895 19.63 0.00 0.00 3.91
8287 9625 4.100084 CGCCATGGGAGAGGTGCA 62.100 66.667 15.13 0.00 0.00 4.57
8470 9809 0.323816 TCCAGAGTCCTCATGCGACT 60.324 55.000 13.30 13.30 43.28 4.18
8700 10040 2.508526 GTGCACAAGATTCTTGGAGGT 58.491 47.619 25.94 6.42 0.00 3.85
8777 10117 0.106519 GCCAGGCACTCATTACCCAT 60.107 55.000 6.55 0.00 34.60 4.00
8889 10229 2.884639 GCTTGGTTAGAAGGAACAGCAA 59.115 45.455 0.00 0.00 31.77 3.91


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

AutoCloner maintained by Alex Coulton.