Multiple sequence alignment - TraesCS6A01G273700

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 TraesCS6A01G273700 chr6A 100.000 3829 0 0 1 3829 499953215 499957043 0.000000e+00 7071.0
1 TraesCS6A01G273700 chr6A 90.860 186 7 5 2091 2276 74320417 74320592 1.370000e-59 241.0
2 TraesCS6A01G273700 chr6A 89.189 74 6 2 2343 2414 74320576 74320649 1.460000e-14 91.6
3 TraesCS6A01G273700 chr6A 91.489 47 3 1 1873 1918 74320375 74320421 3.190000e-06 63.9
4 TraesCS6A01G273700 chr6D 87.450 3753 207 123 151 3829 357594172 357590610 0.000000e+00 4078.0
5 TraesCS6A01G273700 chr6D 78.497 772 53 41 493 1224 357873382 357872684 5.960000e-108 401.0
6 TraesCS6A01G273700 chr6D 87.391 230 12 8 179 408 357596204 357595992 8.210000e-62 248.0
7 TraesCS6A01G273700 chr6B 86.405 3803 190 120 151 3827 539197346 539193745 0.000000e+00 3856.0
8 TraesCS6A01G273700 chr2A 88.682 698 63 11 1861 2550 228397083 228397772 0.000000e+00 837.0
9 TraesCS6A01G273700 chr2A 97.059 34 1 0 2647 2680 228397769 228397802 1.490000e-04 58.4
10 TraesCS6A01G273700 chr1B 87.895 727 64 14 2308 3027 185184936 185184227 0.000000e+00 833.0
11 TraesCS6A01G273700 chr1B 86.230 305 28 5 1532 1836 658480822 658481112 6.170000e-83 318.0
12 TraesCS6A01G273700 chr4B 84.379 717 76 10 1309 2025 141577866 141577186 0.000000e+00 671.0
13 TraesCS6A01G273700 chr2D 90.071 423 42 0 1732 2154 578229257 578229679 2.010000e-152 549.0
14 TraesCS6A01G273700 chr2D 91.111 225 14 4 2341 2559 578306521 578306745 2.240000e-77 300.0
15 TraesCS6A01G273700 chr2D 85.075 201 18 6 1538 1738 578203264 578203452 1.090000e-45 195.0
16 TraesCS6A01G273700 chr2D 78.378 148 19 6 1837 1982 388481929 388481793 2.450000e-12 84.2
17 TraesCS6A01G273700 chr1D 87.625 299 25 5 1538 1836 8012520 8012806 1.700000e-88 337.0
18 TraesCS6A01G273700 chr2B 86.913 298 26 8 1539 1836 682132819 682132535 4.770000e-84 322.0
19 TraesCS6A01G273700 chr5D 81.579 190 26 7 2258 2443 359475492 359475676 8.570000e-32 148.0
20 TraesCS6A01G273700 chr5B 81.579 190 26 7 2258 2443 425094284 425094468 8.570000e-32 148.0
21 TraesCS6A01G273700 chr3D 79.433 141 21 5 1844 1983 305622304 305622437 4.070000e-15 93.5
22 TraesCS6A01G273700 chr3B 78.621 145 21 6 1844 1986 416135821 416135685 1.890000e-13 87.9
23 TraesCS6A01G273700 chr3A 78.723 141 22 5 1844 1983 423671794 423671927 1.890000e-13 87.9


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 TraesCS6A01G273700 chr6A 499953215 499957043 3828 False 7071.0 7071 100.0000 1 3829 1 chr6A.!!$F1 3828
1 TraesCS6A01G273700 chr6D 357590610 357596204 5594 True 2163.0 4078 87.4205 151 3829 2 chr6D.!!$R2 3678
2 TraesCS6A01G273700 chr6D 357872684 357873382 698 True 401.0 401 78.4970 493 1224 1 chr6D.!!$R1 731
3 TraesCS6A01G273700 chr6B 539193745 539197346 3601 True 3856.0 3856 86.4050 151 3827 1 chr6B.!!$R1 3676
4 TraesCS6A01G273700 chr2A 228397083 228397802 719 False 447.7 837 92.8705 1861 2680 2 chr2A.!!$F1 819
5 TraesCS6A01G273700 chr1B 185184227 185184936 709 True 833.0 833 87.8950 2308 3027 1 chr1B.!!$R1 719
6 TraesCS6A01G273700 chr4B 141577186 141577866 680 True 671.0 671 84.3790 1309 2025 1 chr4B.!!$R1 716

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
387 2272 0.179012 GGTTTGGGTTCTGGGTTCGA 60.179 55.0 0.0 0.0 0.00 3.71 F
895 2881 0.639943 TGCCATACCACCCTCTAGGA 59.360 55.0 0.0 0.0 39.89 2.94 F
1355 3365 0.107703 CATCGCCACCACTACACCAT 60.108 55.0 0.0 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1249 3250 0.183971 TCCTCCTCATCGTCCTCCTC 59.816 60.0 0.00 0.00 0.0 3.71 R
2682 4768 0.782384 GCACGAGTTAACACCTGACG 59.218 55.0 8.61 6.16 0.0 4.35 R
3203 5356 0.107654 AAGTACATTCCGAGCCAGCC 60.108 55.0 0.00 0.00 0.0 4.85 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
32 33 4.318021 GCACAGTGCAGTGTGGCG 62.318 66.667 41.15 25.40 46.73 5.69
33 34 4.318021 CACAGTGCAGTGTGGCGC 62.318 66.667 36.71 0.00 43.56 6.53
39 40 4.996434 GCAGTGTGGCGCCTGACT 62.996 66.667 29.70 24.74 0.00 3.41
42 43 3.044305 GTGTGGCGCCTGACTGTC 61.044 66.667 29.70 9.40 0.00 3.51
43 44 4.662961 TGTGGCGCCTGACTGTCG 62.663 66.667 29.70 0.00 0.00 4.35
50 51 2.047844 CCTGACTGTCGGGCACTG 60.048 66.667 21.95 0.00 35.89 3.66
51 52 2.737180 CTGACTGTCGGGCACTGT 59.263 61.111 8.80 0.00 39.75 3.55
52 53 1.532604 CCTGACTGTCGGGCACTGTA 61.533 60.000 21.95 0.00 35.89 2.74
54 55 0.538746 TGACTGTCGGGCACTGTAGA 60.539 55.000 2.98 0.00 37.30 2.59
55 56 0.601558 GACTGTCGGGCACTGTAGAA 59.398 55.000 0.00 0.00 37.30 2.10
56 57 1.000506 GACTGTCGGGCACTGTAGAAA 59.999 52.381 0.00 0.00 37.30 2.52
57 58 1.414919 ACTGTCGGGCACTGTAGAAAA 59.585 47.619 0.00 0.00 35.50 2.29
61 62 1.349688 TCGGGCACTGTAGAAAATGGT 59.650 47.619 0.00 0.00 35.30 3.55
62 63 1.737793 CGGGCACTGTAGAAAATGGTC 59.262 52.381 0.00 0.00 0.00 4.02
63 64 2.615493 CGGGCACTGTAGAAAATGGTCT 60.615 50.000 0.00 0.00 0.00 3.85
65 66 3.559171 GGGCACTGTAGAAAATGGTCTGA 60.559 47.826 0.00 0.00 0.00 3.27
66 67 4.072131 GGCACTGTAGAAAATGGTCTGAA 58.928 43.478 0.00 0.00 0.00 3.02
67 68 4.702131 GGCACTGTAGAAAATGGTCTGAAT 59.298 41.667 0.00 0.00 0.00 2.57
68 69 5.183904 GGCACTGTAGAAAATGGTCTGAATT 59.816 40.000 0.00 0.00 0.00 2.17
69 70 6.294731 GGCACTGTAGAAAATGGTCTGAATTT 60.295 38.462 0.00 0.00 0.00 1.82
71 72 7.653311 GCACTGTAGAAAATGGTCTGAATTTTT 59.347 33.333 2.56 0.00 37.35 1.94
91 92 5.830900 TTTTTCAAACACGGTTCACTTTG 57.169 34.783 0.00 0.00 0.00 2.77
94 95 3.075148 TCAAACACGGTTCACTTTGTGA 58.925 40.909 0.00 0.00 41.09 3.58
107 108 6.721571 TCACTTTGTGAAATAGTTCCGATC 57.278 37.500 0.00 0.00 39.78 3.69
108 109 6.227522 TCACTTTGTGAAATAGTTCCGATCA 58.772 36.000 0.00 0.00 39.78 2.92
109 110 6.147164 TCACTTTGTGAAATAGTTCCGATCAC 59.853 38.462 0.00 0.00 39.78 3.06
112 113 5.400066 TGTGAAATAGTTCCGATCACAGA 57.600 39.130 0.00 0.00 43.79 3.41
113 114 5.977635 TGTGAAATAGTTCCGATCACAGAT 58.022 37.500 0.00 0.00 43.79 2.90
114 115 6.042777 TGTGAAATAGTTCCGATCACAGATC 58.957 40.000 0.00 0.00 43.79 2.75
115 116 6.042777 GTGAAATAGTTCCGATCACAGATCA 58.957 40.000 0.00 0.00 40.02 2.92
116 117 6.199908 GTGAAATAGTTCCGATCACAGATCAG 59.800 42.308 0.00 0.00 40.02 2.90
118 119 5.860941 ATAGTTCCGATCACAGATCAGTT 57.139 39.130 7.67 0.00 0.00 3.16
119 120 6.961360 ATAGTTCCGATCACAGATCAGTTA 57.039 37.500 7.67 0.00 0.00 2.24
120 121 5.860941 AGTTCCGATCACAGATCAGTTAT 57.139 39.130 7.67 0.00 0.00 1.89
121 122 5.595885 AGTTCCGATCACAGATCAGTTATG 58.404 41.667 7.67 0.00 0.00 1.90
122 123 5.127845 AGTTCCGATCACAGATCAGTTATGT 59.872 40.000 7.67 0.00 0.00 2.29
132 133 7.227314 TCACAGATCAGTTATGTGATATTTGCC 59.773 37.037 9.90 0.00 46.17 4.52
133 134 6.203530 ACAGATCAGTTATGTGATATTTGCCG 59.796 38.462 0.00 0.00 37.29 5.69
134 135 4.811555 TCAGTTATGTGATATTTGCCGC 57.188 40.909 0.00 0.00 0.00 6.53
135 136 4.195416 TCAGTTATGTGATATTTGCCGCA 58.805 39.130 0.00 0.00 0.00 5.69
136 137 4.035091 TCAGTTATGTGATATTTGCCGCAC 59.965 41.667 0.00 0.00 0.00 5.34
139 140 0.808125 TGTGATATTTGCCGCACCAC 59.192 50.000 0.00 0.00 0.00 4.16
140 141 0.248054 GTGATATTTGCCGCACCACG 60.248 55.000 0.00 0.00 43.15 4.94
141 142 1.298339 GATATTTGCCGCACCACGC 60.298 57.895 0.00 0.00 41.76 5.34
299 2184 1.811941 GCGCCATTAAGGAAGCTAGCT 60.812 52.381 12.68 12.68 41.22 3.32
300 2185 2.548067 GCGCCATTAAGGAAGCTAGCTA 60.548 50.000 19.70 0.40 41.22 3.32
301 2186 3.321497 CGCCATTAAGGAAGCTAGCTAG 58.679 50.000 19.70 16.84 41.22 3.42
302 2187 3.070748 GCCATTAAGGAAGCTAGCTAGC 58.929 50.000 33.96 33.96 44.78 3.42
334 2219 4.156622 CGCCATGCACGCACAGAG 62.157 66.667 8.23 0.00 0.00 3.35
335 2220 2.743538 GCCATGCACGCACAGAGA 60.744 61.111 2.77 0.00 0.00 3.10
336 2221 2.747822 GCCATGCACGCACAGAGAG 61.748 63.158 2.77 0.00 0.00 3.20
378 2263 2.299013 GGTTTGATCAGGGTTTGGGTTC 59.701 50.000 0.00 0.00 0.00 3.62
385 2270 0.187606 AGGGTTTGGGTTCTGGGTTC 59.812 55.000 0.00 0.00 0.00 3.62
387 2272 0.179012 GGTTTGGGTTCTGGGTTCGA 60.179 55.000 0.00 0.00 0.00 3.71
391 2276 0.765135 TGGGTTCTGGGTTCGAAGGA 60.765 55.000 0.00 0.00 0.00 3.36
393 2278 0.974383 GGTTCTGGGTTCGAAGGAGA 59.026 55.000 0.00 0.00 0.00 3.71
398 2285 1.079057 GGGTTCGAAGGAGAGGTGC 60.079 63.158 0.00 0.00 0.00 5.01
459 2354 3.379445 GTCTTCCCGTGGGAGCGA 61.379 66.667 7.85 6.34 46.06 4.93
460 2355 3.068691 TCTTCCCGTGGGAGCGAG 61.069 66.667 7.85 3.26 46.06 5.03
461 2356 3.068691 CTTCCCGTGGGAGCGAGA 61.069 66.667 7.85 0.00 46.06 4.04
462 2357 3.068691 TTCCCGTGGGAGCGAGAG 61.069 66.667 7.85 0.00 46.06 3.20
536 2431 1.153086 CATGGGCTTCTTCCTCCCG 60.153 63.158 0.00 0.00 42.98 5.14
559 2471 5.374071 GTCCAAACCTCTCTCTAAAAACCA 58.626 41.667 0.00 0.00 0.00 3.67
657 2590 1.018226 CAGCGGCCACTTTCTCTCTG 61.018 60.000 2.24 0.00 0.00 3.35
720 2688 4.036380 TCCGTTTCTTTCTTTTGAGAAGCC 59.964 41.667 0.00 0.00 33.77 4.35
721 2693 4.290969 CGTTTCTTTCTTTTGAGAAGCCC 58.709 43.478 0.00 0.00 33.77 5.19
724 2696 1.541588 CTTTCTTTTGAGAAGCCCGGG 59.458 52.381 19.09 19.09 0.00 5.73
744 2716 4.417437 GGGTAGATAAGATGGCCTAGTGA 58.583 47.826 3.32 0.00 0.00 3.41
745 2717 4.464597 GGGTAGATAAGATGGCCTAGTGAG 59.535 50.000 3.32 0.00 0.00 3.51
746 2718 5.326069 GGTAGATAAGATGGCCTAGTGAGA 58.674 45.833 3.32 0.00 0.00 3.27
747 2719 5.417580 GGTAGATAAGATGGCCTAGTGAGAG 59.582 48.000 3.32 0.00 0.00 3.20
748 2720 5.332106 AGATAAGATGGCCTAGTGAGAGA 57.668 43.478 3.32 0.00 0.00 3.10
749 2721 5.324409 AGATAAGATGGCCTAGTGAGAGAG 58.676 45.833 3.32 0.00 0.00 3.20
750 2722 3.678965 AAGATGGCCTAGTGAGAGAGA 57.321 47.619 3.32 0.00 0.00 3.10
751 2723 3.901570 AGATGGCCTAGTGAGAGAGAT 57.098 47.619 3.32 0.00 0.00 2.75
752 2724 5.332106 AAGATGGCCTAGTGAGAGAGATA 57.668 43.478 3.32 0.00 0.00 1.98
753 2725 4.922206 AGATGGCCTAGTGAGAGAGATAG 58.078 47.826 3.32 0.00 0.00 2.08
754 2726 4.601420 AGATGGCCTAGTGAGAGAGATAGA 59.399 45.833 3.32 0.00 0.00 1.98
755 2727 5.253798 AGATGGCCTAGTGAGAGAGATAGAT 59.746 44.000 3.32 0.00 0.00 1.98
756 2728 4.661222 TGGCCTAGTGAGAGAGATAGATG 58.339 47.826 3.32 0.00 0.00 2.90
757 2729 3.443681 GGCCTAGTGAGAGAGATAGATGC 59.556 52.174 0.00 0.00 0.00 3.91
758 2730 4.078537 GCCTAGTGAGAGAGATAGATGCA 58.921 47.826 0.00 0.00 0.00 3.96
759 2731 4.156556 GCCTAGTGAGAGAGATAGATGCAG 59.843 50.000 0.00 0.00 0.00 4.41
760 2732 5.559770 CCTAGTGAGAGAGATAGATGCAGA 58.440 45.833 0.00 0.00 0.00 4.26
761 2733 6.182627 CCTAGTGAGAGAGATAGATGCAGAT 58.817 44.000 0.00 0.00 0.00 2.90
762 2734 7.337938 CCTAGTGAGAGAGATAGATGCAGATA 58.662 42.308 0.00 0.00 0.00 1.98
763 2735 7.496920 CCTAGTGAGAGAGATAGATGCAGATAG 59.503 44.444 0.00 0.00 0.00 2.08
764 2736 7.019656 AGTGAGAGAGATAGATGCAGATAGA 57.980 40.000 0.00 0.00 0.00 1.98
765 2737 7.636579 AGTGAGAGAGATAGATGCAGATAGAT 58.363 38.462 0.00 0.00 0.00 1.98
848 2833 1.289694 TGGTTACTGCCACCGTACG 59.710 57.895 8.69 8.69 37.07 3.67
849 2834 1.290009 GGTTACTGCCACCGTACGT 59.710 57.895 15.21 0.00 0.00 3.57
888 2874 1.829533 CAGCCATGCCATACCACCC 60.830 63.158 0.00 0.00 0.00 4.61
890 2876 1.529244 GCCATGCCATACCACCCTC 60.529 63.158 0.00 0.00 0.00 4.30
894 2880 1.349026 CATGCCATACCACCCTCTAGG 59.651 57.143 0.00 0.00 43.78 3.02
895 2881 0.639943 TGCCATACCACCCTCTAGGA 59.360 55.000 0.00 0.00 39.89 2.94
896 2882 1.343069 GCCATACCACCCTCTAGGAG 58.657 60.000 0.00 0.00 39.89 3.69
897 2883 1.413227 GCCATACCACCCTCTAGGAGT 60.413 57.143 0.00 0.00 39.89 3.85
898 2884 2.320781 CCATACCACCCTCTAGGAGTG 58.679 57.143 0.00 4.35 39.89 3.51
899 2885 2.359355 CCATACCACCCTCTAGGAGTGT 60.359 54.545 13.30 4.17 39.89 3.55
900 2886 3.375699 CATACCACCCTCTAGGAGTGTT 58.624 50.000 13.30 5.41 39.89 3.32
901 2887 1.939980 ACCACCCTCTAGGAGTGTTC 58.060 55.000 13.30 0.00 39.89 3.18
902 2888 1.196012 CCACCCTCTAGGAGTGTTCC 58.804 60.000 13.30 0.00 44.39 3.62
916 2902 0.979187 TGTTCCGGTGTATCCCTCCC 60.979 60.000 0.00 0.00 0.00 4.30
917 2903 1.759299 TTCCGGTGTATCCCTCCCG 60.759 63.158 0.00 0.00 40.12 5.14
918 2904 3.925090 CCGGTGTATCCCTCCCGC 61.925 72.222 0.00 0.00 39.12 6.13
919 2905 3.925090 CGGTGTATCCCTCCCGCC 61.925 72.222 0.00 0.00 33.20 6.13
920 2906 3.557290 GGTGTATCCCTCCCGCCC 61.557 72.222 0.00 0.00 0.00 6.13
921 2907 3.925090 GTGTATCCCTCCCGCCCG 61.925 72.222 0.00 0.00 0.00 6.13
964 2962 2.283173 CCTTGAGGCCAACACCCC 60.283 66.667 5.01 0.00 0.00 4.95
965 2963 2.283173 CTTGAGGCCAACACCCCC 60.283 66.667 5.01 0.00 0.00 5.40
1034 3032 5.634020 CCCACTTAGAAGTTAGAACAAGTCG 59.366 44.000 0.00 0.00 37.08 4.18
1104 3105 1.068250 GAGAAGAATCTCCGGCCCG 59.932 63.158 0.00 0.00 45.35 6.13
1105 3106 1.677637 GAGAAGAATCTCCGGCCCGT 61.678 60.000 0.85 0.00 45.35 5.28
1106 3107 1.227292 GAAGAATCTCCGGCCCGTC 60.227 63.158 0.85 0.00 0.00 4.79
1107 3108 2.646117 GAAGAATCTCCGGCCCGTCC 62.646 65.000 0.85 0.00 0.00 4.79
1108 3109 3.155167 GAATCTCCGGCCCGTCCT 61.155 66.667 0.85 0.00 0.00 3.85
1248 3249 1.289530 GAGGAGGAGGAGGAAGAGGAA 59.710 57.143 0.00 0.00 0.00 3.36
1249 3250 1.290732 AGGAGGAGGAGGAAGAGGAAG 59.709 57.143 0.00 0.00 0.00 3.46
1250 3251 1.289530 GGAGGAGGAGGAAGAGGAAGA 59.710 57.143 0.00 0.00 0.00 2.87
1355 3365 0.107703 CATCGCCACCACTACACCAT 60.108 55.000 0.00 0.00 0.00 3.55
1600 3610 2.606826 ACCGGAGAAGGGTGGACC 60.607 66.667 9.46 0.00 36.14 4.46
1602 3612 4.452733 CGGAGAAGGGTGGACCGC 62.453 72.222 0.00 0.00 46.96 5.68
1656 3666 4.767255 GAGGCCCACCGTCAGCAG 62.767 72.222 0.00 0.00 42.76 4.24
1710 3774 4.598894 CATCAGGAGCCGGCGAGG 62.599 72.222 23.20 10.30 44.97 4.63
1725 3789 3.056313 GAGGAATGGCGTGCTTGGC 62.056 63.158 0.00 0.00 0.00 4.52
2010 4074 4.787280 CTGGTCCCCTCGCCCTCT 62.787 72.222 0.00 0.00 0.00 3.69
2509 4573 2.283966 ACGACCCCAGTCCTCCTG 60.284 66.667 0.00 0.00 40.12 3.86
2511 4575 2.284995 GACCCCAGTCCTCCTGCT 60.285 66.667 0.00 0.00 40.06 4.24
2513 4577 3.086600 CCCCAGTCCTCCTGCTCC 61.087 72.222 0.00 0.00 40.06 4.70
2555 4634 4.746309 GCCCCACCATCAGCAGCA 62.746 66.667 0.00 0.00 0.00 4.41
2556 4635 2.439701 CCCCACCATCAGCAGCAG 60.440 66.667 0.00 0.00 0.00 4.24
2682 4768 2.884894 ATTCCCGTAACCTCATCGTC 57.115 50.000 0.00 0.00 0.00 4.20
2733 4823 3.053544 CACTTAGGAGGGAGTAGACCAGA 60.054 52.174 0.00 0.00 0.00 3.86
2734 4824 3.053470 ACTTAGGAGGGAGTAGACCAGAC 60.053 52.174 0.00 0.00 0.00 3.51
2735 4825 0.632294 AGGAGGGAGTAGACCAGACC 59.368 60.000 0.00 0.00 0.00 3.85
2736 4826 0.335361 GGAGGGAGTAGACCAGACCA 59.665 60.000 0.00 0.00 0.00 4.02
2737 4827 1.686741 GGAGGGAGTAGACCAGACCAG 60.687 61.905 0.00 0.00 0.00 4.00
2747 4842 3.779444 AGACCAGACCAGTAATGTGAGA 58.221 45.455 0.00 0.00 0.00 3.27
2750 4845 4.096681 ACCAGACCAGTAATGTGAGATGA 58.903 43.478 0.00 0.00 0.00 2.92
2751 4846 4.161189 ACCAGACCAGTAATGTGAGATGAG 59.839 45.833 0.00 0.00 0.00 2.90
2752 4847 4.442612 CCAGACCAGTAATGTGAGATGAGG 60.443 50.000 0.00 0.00 0.00 3.86
2753 4848 3.133721 AGACCAGTAATGTGAGATGAGGC 59.866 47.826 0.00 0.00 0.00 4.70
2755 4850 3.118482 ACCAGTAATGTGAGATGAGGCAG 60.118 47.826 0.00 0.00 0.00 4.85
2756 4851 2.871022 CAGTAATGTGAGATGAGGCAGC 59.129 50.000 0.00 0.00 0.00 5.25
2757 4852 2.158842 AGTAATGTGAGATGAGGCAGCC 60.159 50.000 1.84 1.84 0.00 4.85
2758 4853 0.917533 AATGTGAGATGAGGCAGCCT 59.082 50.000 16.12 16.12 36.03 4.58
2769 4864 1.676967 GGCAGCCTTGAACCCTGAG 60.677 63.158 3.29 0.00 0.00 3.35
2770 4865 1.676967 GCAGCCTTGAACCCTGAGG 60.677 63.158 0.00 0.00 40.04 3.86
2806 4901 3.436243 TCACTCCTTCCTTCTTCCTCTC 58.564 50.000 0.00 0.00 0.00 3.20
2843 4938 6.204688 TCGTCTCATGGATAAATAACAATGGC 59.795 38.462 0.00 0.00 0.00 4.40
2863 4958 0.815734 TAGGTTAGCACGGTGAGAGC 59.184 55.000 13.29 6.15 36.67 4.09
2890 4985 5.163457 ACTGCTTCTTGCTTAGATCCTACTC 60.163 44.000 0.00 0.00 43.37 2.59
2930 5035 1.972872 CCTCTCTCTCTCTCTCTGCC 58.027 60.000 0.00 0.00 0.00 4.85
2933 5038 1.027357 CTCTCTCTCTCTCTGCCAGC 58.973 60.000 0.00 0.00 0.00 4.85
2971 5084 0.921347 CCGTGCTCGCTTGTATGTAC 59.079 55.000 1.89 0.00 35.54 2.90
2972 5085 0.566136 CGTGCTCGCTTGTATGTACG 59.434 55.000 0.00 0.00 33.07 3.67
2973 5086 1.625616 GTGCTCGCTTGTATGTACGT 58.374 50.000 0.00 0.00 0.00 3.57
2974 5087 2.788750 CGTGCTCGCTTGTATGTACGTA 60.789 50.000 0.00 0.00 34.75 3.57
2975 5088 2.529090 GTGCTCGCTTGTATGTACGTAC 59.471 50.000 18.90 18.90 0.00 3.67
2976 5089 1.771848 GCTCGCTTGTATGTACGTACG 59.228 52.381 20.18 15.01 0.00 3.67
2977 5090 1.771848 CTCGCTTGTATGTACGTACGC 59.228 52.381 20.18 14.63 0.00 4.42
2978 5091 1.130186 TCGCTTGTATGTACGTACGCA 59.870 47.619 20.18 15.42 0.00 5.24
2979 5092 1.511552 CGCTTGTATGTACGTACGCAG 59.488 52.381 20.18 16.62 0.00 5.18
2980 5093 1.254570 GCTTGTATGTACGTACGCAGC 59.745 52.381 23.34 23.34 0.00 5.25
2981 5094 2.793933 CTTGTATGTACGTACGCAGCT 58.206 47.619 20.18 0.00 0.00 4.24
2982 5095 2.182904 TGTATGTACGTACGCAGCTG 57.817 50.000 20.18 10.11 0.00 4.24
2983 5096 0.844503 GTATGTACGTACGCAGCTGC 59.155 55.000 29.12 29.12 37.78 5.25
2984 5097 0.452585 TATGTACGTACGCAGCTGCA 59.547 50.000 36.03 17.26 42.21 4.41
2985 5098 0.802222 ATGTACGTACGCAGCTGCAG 60.802 55.000 36.03 28.85 42.21 4.41
2986 5099 2.158959 GTACGTACGCAGCTGCAGG 61.159 63.158 36.03 24.86 42.21 4.85
2987 5100 3.982372 TACGTACGCAGCTGCAGGC 62.982 63.158 36.03 23.05 42.21 4.85
3080 5220 2.434331 CCCGTCTTGGCTTGGGAA 59.566 61.111 0.00 0.00 44.88 3.97
3110 5250 4.782533 CGTTGCTTTTTGACTTTGCTTTTG 59.217 37.500 0.00 0.00 0.00 2.44
3161 5314 0.100325 ATTGTGTTGTGGTGTGTGCG 59.900 50.000 0.00 0.00 0.00 5.34
3162 5315 1.237954 TTGTGTTGTGGTGTGTGCGT 61.238 50.000 0.00 0.00 0.00 5.24
3163 5316 1.237954 TGTGTTGTGGTGTGTGCGTT 61.238 50.000 0.00 0.00 0.00 4.84
3164 5317 0.796491 GTGTTGTGGTGTGTGCGTTG 60.796 55.000 0.00 0.00 0.00 4.10
3165 5318 1.871789 GTTGTGGTGTGTGCGTTGC 60.872 57.895 0.00 0.00 0.00 4.17
3166 5319 3.057547 TTGTGGTGTGTGCGTTGCC 62.058 57.895 0.00 0.00 0.00 4.52
3167 5320 4.605967 GTGGTGTGTGCGTTGCCG 62.606 66.667 0.00 0.00 37.07 5.69
3375 5534 0.603975 GTTGTCTCGGCAGCCTTTCT 60.604 55.000 10.54 0.00 0.00 2.52
3442 5607 1.748500 GCCTCCTGCCAAAGCTCTC 60.749 63.158 0.00 0.00 40.80 3.20
3474 5639 9.908152 TTTTCTTTCTTTTTCTTTCGTTCTTCT 57.092 25.926 0.00 0.00 0.00 2.85
3475 5640 9.556030 TTTCTTTCTTTTTCTTTCGTTCTTCTC 57.444 29.630 0.00 0.00 0.00 2.87
3476 5641 7.399523 TCTTTCTTTTTCTTTCGTTCTTCTCG 58.600 34.615 0.00 0.00 0.00 4.04
3477 5642 6.657836 TTCTTTTTCTTTCGTTCTTCTCGT 57.342 33.333 0.00 0.00 0.00 4.18
3478 5643 6.270096 TCTTTTTCTTTCGTTCTTCTCGTC 57.730 37.500 0.00 0.00 0.00 4.20
3479 5644 6.040878 TCTTTTTCTTTCGTTCTTCTCGTCT 58.959 36.000 0.00 0.00 0.00 4.18
3480 5645 5.885020 TTTTCTTTCGTTCTTCTCGTCTC 57.115 39.130 0.00 0.00 0.00 3.36
3481 5646 3.555917 TCTTTCGTTCTTCTCGTCTCC 57.444 47.619 0.00 0.00 0.00 3.71
3482 5647 2.228343 TCTTTCGTTCTTCTCGTCTCCC 59.772 50.000 0.00 0.00 0.00 4.30
3483 5648 1.906990 TTCGTTCTTCTCGTCTCCCT 58.093 50.000 0.00 0.00 0.00 4.20
3484 5649 1.451067 TCGTTCTTCTCGTCTCCCTC 58.549 55.000 0.00 0.00 0.00 4.30
3485 5650 1.003349 TCGTTCTTCTCGTCTCCCTCT 59.997 52.381 0.00 0.00 0.00 3.69
3486 5651 1.399089 CGTTCTTCTCGTCTCCCTCTC 59.601 57.143 0.00 0.00 0.00 3.20
3487 5652 1.746787 GTTCTTCTCGTCTCCCTCTCC 59.253 57.143 0.00 0.00 0.00 3.71
3488 5653 0.256464 TCTTCTCGTCTCCCTCTCCC 59.744 60.000 0.00 0.00 0.00 4.30
3496 5661 0.996762 TCTCCCTCTCCCCTCCTCTC 60.997 65.000 0.00 0.00 0.00 3.20
3501 5673 1.550374 TCTCCCCTCCTCTCCCCTT 60.550 63.158 0.00 0.00 0.00 3.95
3580 5771 1.079543 ATGTGAGAGCGGACTGTGC 60.080 57.895 0.00 0.00 0.00 4.57
3589 5780 1.730902 CGGACTGTGCGTGTCAGAG 60.731 63.158 13.79 0.00 41.48 3.35
3603 5794 0.914644 TCAGAGGCTGATCAAAGGGG 59.085 55.000 0.00 0.00 35.39 4.79
3604 5795 0.106819 CAGAGGCTGATCAAAGGGGG 60.107 60.000 0.00 0.00 32.44 5.40
3636 5827 2.250939 CGGCCTGCGTTTTGAGTGA 61.251 57.895 0.00 0.00 0.00 3.41
3642 5833 1.933181 CTGCGTTTTGAGTGAGTGTGA 59.067 47.619 0.00 0.00 0.00 3.58
3648 5839 3.610040 TTTGAGTGAGTGTGAGTGTGT 57.390 42.857 0.00 0.00 0.00 3.72
3649 5840 2.584492 TGAGTGAGTGTGAGTGTGTG 57.416 50.000 0.00 0.00 0.00 3.82
3650 5841 1.212616 GAGTGAGTGTGAGTGTGTGC 58.787 55.000 0.00 0.00 0.00 4.57
3651 5842 0.528466 AGTGAGTGTGAGTGTGTGCG 60.528 55.000 0.00 0.00 0.00 5.34
3652 5843 0.806102 GTGAGTGTGAGTGTGTGCGT 60.806 55.000 0.00 0.00 0.00 5.24
3692 5883 6.429078 AGCGCAAAGTGAATGATGATATGTAT 59.571 34.615 11.47 0.00 0.00 2.29
3722 5913 3.120442 GCAAAATTGAAGGCTTGCATCAC 60.120 43.478 3.46 0.00 42.91 3.06
3755 5946 0.248215 CCTGCGATTTGGTGCGATTC 60.248 55.000 0.00 0.00 0.00 2.52
3756 5947 0.248215 CTGCGATTTGGTGCGATTCC 60.248 55.000 0.00 0.00 0.00 3.01
3827 6023 1.235724 CCAGCGTGATGATGATGCAT 58.764 50.000 0.00 0.00 35.47 3.96
3828 6024 2.419667 CCAGCGTGATGATGATGCATA 58.580 47.619 0.00 0.00 35.47 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.349006 GCACTGTGCACCGTCTGG 61.349 66.667 26.70 3.58 44.26 3.86
16 17 4.318021 GCGCCACACTGCACTGTG 62.318 66.667 16.85 16.85 41.19 3.66
25 26 3.044305 GACAGTCAGGCGCCACAC 61.044 66.667 31.54 23.80 0.00 3.82
26 27 4.662961 CGACAGTCAGGCGCCACA 62.663 66.667 31.54 11.93 45.03 4.17
33 34 1.532604 TACAGTGCCCGACAGTCAGG 61.533 60.000 0.41 0.00 0.00 3.86
35 36 0.538746 TCTACAGTGCCCGACAGTCA 60.539 55.000 0.41 0.00 0.00 3.41
37 38 1.045407 TTTCTACAGTGCCCGACAGT 58.955 50.000 0.00 0.00 0.00 3.55
38 39 2.163818 TTTTCTACAGTGCCCGACAG 57.836 50.000 0.00 0.00 0.00 3.51
39 40 2.422597 CATTTTCTACAGTGCCCGACA 58.577 47.619 0.00 0.00 0.00 4.35
42 43 1.737793 GACCATTTTCTACAGTGCCCG 59.262 52.381 0.00 0.00 0.00 6.13
43 44 2.749621 CAGACCATTTTCTACAGTGCCC 59.250 50.000 0.00 0.00 0.00 5.36
44 45 3.674997 TCAGACCATTTTCTACAGTGCC 58.325 45.455 0.00 0.00 0.00 5.01
69 70 5.175856 CACAAAGTGAACCGTGTTTGAAAAA 59.824 36.000 0.00 0.00 35.23 1.94
71 72 4.023107 TCACAAAGTGAACCGTGTTTGAAA 60.023 37.500 0.00 0.00 39.78 2.69
72 73 3.502595 TCACAAAGTGAACCGTGTTTGAA 59.497 39.130 0.00 0.00 39.78 2.69
73 74 3.075148 TCACAAAGTGAACCGTGTTTGA 58.925 40.909 0.00 0.00 39.78 2.69
74 75 3.479505 TCACAAAGTGAACCGTGTTTG 57.520 42.857 0.00 0.00 39.78 2.93
84 85 6.147164 GTGATCGGAACTATTTCACAAAGTGA 59.853 38.462 0.00 0.00 41.09 3.41
85 86 6.073276 TGTGATCGGAACTATTTCACAAAGTG 60.073 38.462 7.25 0.00 42.53 3.16
86 87 5.995282 TGTGATCGGAACTATTTCACAAAGT 59.005 36.000 7.25 0.00 42.53 2.66
87 88 6.368791 TCTGTGATCGGAACTATTTCACAAAG 59.631 38.462 10.14 2.27 44.19 2.77
88 89 6.227522 TCTGTGATCGGAACTATTTCACAAA 58.772 36.000 10.14 0.00 44.19 2.83
89 90 5.789521 TCTGTGATCGGAACTATTTCACAA 58.210 37.500 10.14 1.71 44.19 3.33
90 91 5.400066 TCTGTGATCGGAACTATTTCACA 57.600 39.130 8.93 8.93 43.07 3.58
91 92 6.042777 TGATCTGTGATCGGAACTATTTCAC 58.957 40.000 0.00 1.25 37.73 3.18
94 95 6.227298 ACTGATCTGTGATCGGAACTATTT 57.773 37.500 19.52 0.00 32.29 1.40
96 97 5.860941 AACTGATCTGTGATCGGAACTAT 57.139 39.130 19.52 0.00 32.29 2.12
97 98 6.321435 ACATAACTGATCTGTGATCGGAACTA 59.679 38.462 19.52 10.07 32.29 2.24
98 99 5.127845 ACATAACTGATCTGTGATCGGAACT 59.872 40.000 19.52 8.62 32.29 3.01
100 101 5.127031 TCACATAACTGATCTGTGATCGGAA 59.873 40.000 19.52 9.79 43.10 4.30
101 102 4.644685 TCACATAACTGATCTGTGATCGGA 59.355 41.667 19.52 4.12 43.10 4.55
107 108 7.358066 GGCAAATATCACATAACTGATCTGTG 58.642 38.462 5.96 5.89 41.24 3.66
108 109 6.203530 CGGCAAATATCACATAACTGATCTGT 59.796 38.462 0.00 0.00 32.86 3.41
109 110 6.596703 CGGCAAATATCACATAACTGATCTG 58.403 40.000 0.00 0.00 32.86 2.90
112 113 4.821260 TGCGGCAAATATCACATAACTGAT 59.179 37.500 0.00 0.00 35.05 2.90
113 114 4.035091 GTGCGGCAAATATCACATAACTGA 59.965 41.667 3.23 0.00 0.00 3.41
114 115 4.282068 GTGCGGCAAATATCACATAACTG 58.718 43.478 3.23 0.00 0.00 3.16
115 116 3.315191 GGTGCGGCAAATATCACATAACT 59.685 43.478 3.23 0.00 0.00 2.24
116 117 3.066064 TGGTGCGGCAAATATCACATAAC 59.934 43.478 3.23 0.00 0.00 1.89
118 119 2.616376 GTGGTGCGGCAAATATCACATA 59.384 45.455 3.23 0.00 0.00 2.29
119 120 1.405105 GTGGTGCGGCAAATATCACAT 59.595 47.619 3.23 0.00 0.00 3.21
120 121 0.808125 GTGGTGCGGCAAATATCACA 59.192 50.000 3.23 0.00 0.00 3.58
121 122 0.248054 CGTGGTGCGGCAAATATCAC 60.248 55.000 3.23 7.78 36.85 3.06
122 123 1.987704 GCGTGGTGCGGCAAATATCA 61.988 55.000 3.23 0.00 41.69 2.15
124 125 2.798009 GCGTGGTGCGGCAAATAT 59.202 55.556 3.23 0.00 41.69 1.28
134 135 4.081030 CTCTTGCGCTGCGTGGTG 62.081 66.667 24.04 11.39 0.00 4.17
135 136 3.596066 ATCTCTTGCGCTGCGTGGT 62.596 57.895 24.04 2.73 0.00 4.16
136 137 2.816958 ATCTCTTGCGCTGCGTGG 60.817 61.111 24.04 13.41 0.00 4.94
139 140 3.570638 CCCATCTCTTGCGCTGCG 61.571 66.667 19.17 19.17 0.00 5.18
140 141 3.885521 GCCCATCTCTTGCGCTGC 61.886 66.667 9.73 0.00 0.00 5.25
141 142 3.570638 CGCCCATCTCTTGCGCTG 61.571 66.667 9.73 1.08 41.95 5.18
146 147 1.746615 CACCCACGCCCATCTCTTG 60.747 63.158 0.00 0.00 0.00 3.02
149 150 4.489771 CCCACCCACGCCCATCTC 62.490 72.222 0.00 0.00 0.00 2.75
159 2042 2.391130 GCCCATGTATCCCCACCCA 61.391 63.158 0.00 0.00 0.00 4.51
169 2053 0.910566 ACCCCAAGTACGCCCATGTA 60.911 55.000 0.00 0.00 0.00 2.29
301 2186 1.592939 GCGTGCCCTAGCTAGAAGC 60.593 63.158 22.70 22.32 42.84 3.86
302 2187 1.068250 GGCGTGCCCTAGCTAGAAG 59.932 63.158 22.70 13.65 40.80 2.85
303 2188 1.048724 ATGGCGTGCCCTAGCTAGAA 61.049 55.000 22.70 4.53 40.80 2.10
304 2189 1.457643 ATGGCGTGCCCTAGCTAGA 60.458 57.895 22.70 0.00 40.80 2.43
305 2190 1.301244 CATGGCGTGCCCTAGCTAG 60.301 63.158 14.20 14.20 40.80 3.42
306 2191 2.821685 CATGGCGTGCCCTAGCTA 59.178 61.111 8.69 0.00 40.80 3.32
327 2212 1.011451 GCCGTGTTCTCTCTCTGTGC 61.011 60.000 0.00 0.00 0.00 4.57
330 2215 0.735632 GCTGCCGTGTTCTCTCTCTG 60.736 60.000 0.00 0.00 0.00 3.35
334 2219 0.445436 CATTGCTGCCGTGTTCTCTC 59.555 55.000 0.00 0.00 0.00 3.20
335 2220 0.957395 CCATTGCTGCCGTGTTCTCT 60.957 55.000 0.00 0.00 0.00 3.10
336 2221 1.503542 CCATTGCTGCCGTGTTCTC 59.496 57.895 0.00 0.00 0.00 2.87
358 2243 3.005791 CAGAACCCAAACCCTGATCAAAC 59.994 47.826 0.00 0.00 0.00 2.93
378 2263 0.247736 CACCTCTCCTTCGAACCCAG 59.752 60.000 0.00 0.00 0.00 4.45
385 2270 2.005960 CTACCGGCACCTCTCCTTCG 62.006 65.000 0.00 0.00 0.00 3.79
387 2272 2.359967 GCTACCGGCACCTCTCCTT 61.360 63.158 0.00 0.00 41.35 3.36
398 2285 1.735360 CCATTGCCATTGCTACCGG 59.265 57.895 0.00 0.00 38.71 5.28
459 2354 0.687354 ATGTTTCACCACCTCGCTCT 59.313 50.000 0.00 0.00 0.00 4.09
460 2355 0.798776 CATGTTTCACCACCTCGCTC 59.201 55.000 0.00 0.00 0.00 5.03
461 2356 0.606401 CCATGTTTCACCACCTCGCT 60.606 55.000 0.00 0.00 0.00 4.93
462 2357 1.875963 CCATGTTTCACCACCTCGC 59.124 57.895 0.00 0.00 0.00 5.03
463 2358 1.586154 GGCCATGTTTCACCACCTCG 61.586 60.000 0.00 0.00 0.00 4.63
464 2359 1.250840 GGGCCATGTTTCACCACCTC 61.251 60.000 4.39 0.00 0.00 3.85
465 2360 1.228862 GGGCCATGTTTCACCACCT 60.229 57.895 4.39 0.00 0.00 4.00
536 2431 5.238868 GTGGTTTTTAGAGAGAGGTTTGGAC 59.761 44.000 0.00 0.00 0.00 4.02
609 2528 1.856265 CGGCTTGCTTGAACCAGTCC 61.856 60.000 0.00 0.00 0.00 3.85
693 2661 3.219281 TCAAAAGAAAGAAACGGAGGGG 58.781 45.455 0.00 0.00 0.00 4.79
694 2662 4.134563 TCTCAAAAGAAAGAAACGGAGGG 58.865 43.478 0.00 0.00 0.00 4.30
695 2663 5.751243 TTCTCAAAAGAAAGAAACGGAGG 57.249 39.130 0.00 0.00 38.58 4.30
696 2664 5.208503 GCTTCTCAAAAGAAAGAAACGGAG 58.791 41.667 0.00 0.00 40.95 4.63
697 2665 4.036380 GGCTTCTCAAAAGAAAGAAACGGA 59.964 41.667 0.00 0.00 40.95 4.69
720 2688 1.645710 AGGCCATCTTATCTACCCGG 58.354 55.000 5.01 0.00 0.00 5.73
721 2693 3.193691 CACTAGGCCATCTTATCTACCCG 59.806 52.174 5.01 0.00 0.00 5.28
724 2696 6.242396 TCTCTCACTAGGCCATCTTATCTAC 58.758 44.000 5.01 0.00 0.00 2.59
769 2741 9.090103 GAGAGAGCTAGCTATCCTATCTATCTA 57.910 40.741 30.68 0.00 39.59 1.98
846 2831 3.814005 AGCGATGGTTATTAAGGACGT 57.186 42.857 0.00 0.00 0.00 4.34
847 2832 4.446719 GGTTAGCGATGGTTATTAAGGACG 59.553 45.833 0.00 0.00 0.00 4.79
848 2833 5.362263 TGGTTAGCGATGGTTATTAAGGAC 58.638 41.667 0.00 0.00 0.00 3.85
849 2834 5.607477 CTGGTTAGCGATGGTTATTAAGGA 58.393 41.667 0.00 0.00 0.00 3.36
888 2874 1.546961 ACACCGGAACACTCCTAGAG 58.453 55.000 9.46 0.00 39.93 2.43
890 2876 2.361438 GGATACACCGGAACACTCCTAG 59.639 54.545 9.46 0.00 39.93 3.02
894 2880 1.136500 GAGGGATACACCGGAACACTC 59.864 57.143 9.46 6.54 40.11 3.51
895 2881 1.192428 GAGGGATACACCGGAACACT 58.808 55.000 9.46 0.00 40.11 3.55
896 2882 0.177373 GGAGGGATACACCGGAACAC 59.823 60.000 9.46 0.00 40.11 3.32
897 2883 0.979187 GGGAGGGATACACCGGAACA 60.979 60.000 9.46 0.00 40.11 3.18
898 2884 1.828081 GGGAGGGATACACCGGAAC 59.172 63.158 9.46 0.00 40.11 3.62
899 2885 1.759299 CGGGAGGGATACACCGGAA 60.759 63.158 9.46 0.00 43.41 4.30
900 2886 2.123597 CGGGAGGGATACACCGGA 60.124 66.667 9.46 0.00 43.41 5.14
901 2887 3.925090 GCGGGAGGGATACACCGG 61.925 72.222 0.00 0.00 46.02 5.28
917 2903 4.468689 AGCTTAACGGAGGCGGGC 62.469 66.667 0.00 0.00 0.00 6.13
918 2904 2.202892 GAGCTTAACGGAGGCGGG 60.203 66.667 0.00 0.00 0.00 6.13
919 2905 2.202892 GGAGCTTAACGGAGGCGG 60.203 66.667 0.00 0.00 0.00 6.13
920 2906 2.202892 GGGAGCTTAACGGAGGCG 60.203 66.667 0.00 0.00 0.00 5.52
921 2907 2.189784 GGGGAGCTTAACGGAGGC 59.810 66.667 0.00 0.00 0.00 4.70
922 2908 0.688087 AGAGGGGAGCTTAACGGAGG 60.688 60.000 0.00 0.00 0.00 4.30
923 2909 1.196012 AAGAGGGGAGCTTAACGGAG 58.804 55.000 0.00 0.00 0.00 4.63
964 2962 4.421554 TGGAGCTGGGAGGGAGGG 62.422 72.222 0.00 0.00 0.00 4.30
965 2963 3.086600 GTGGAGCTGGGAGGGAGG 61.087 72.222 0.00 0.00 0.00 4.30
966 2964 3.086600 GGTGGAGCTGGGAGGGAG 61.087 72.222 0.00 0.00 0.00 4.30
967 2965 3.940480 TGGTGGAGCTGGGAGGGA 61.940 66.667 0.00 0.00 0.00 4.20
1098 3099 2.365095 GATTAGGACAGGACGGGCCG 62.365 65.000 27.06 27.06 43.43 6.13
1104 3105 0.527817 CGGTGCGATTAGGACAGGAC 60.528 60.000 0.00 0.00 43.57 3.85
1105 3106 1.813859 CGGTGCGATTAGGACAGGA 59.186 57.895 0.00 0.00 43.57 3.86
1106 3107 4.420143 CGGTGCGATTAGGACAGG 57.580 61.111 0.00 0.00 43.57 4.00
1107 3108 1.883084 GCCGGTGCGATTAGGACAG 60.883 63.158 1.90 0.00 43.57 3.51
1108 3109 2.185867 GCCGGTGCGATTAGGACA 59.814 61.111 1.90 0.00 43.57 4.02
1248 3249 0.184933 CCTCCTCATCGTCCTCCTCT 59.815 60.000 0.00 0.00 0.00 3.69
1249 3250 0.183971 TCCTCCTCATCGTCCTCCTC 59.816 60.000 0.00 0.00 0.00 3.71
1250 3251 0.184933 CTCCTCCTCATCGTCCTCCT 59.815 60.000 0.00 0.00 0.00 3.69
1320 3330 4.720902 TGATGGTGCGGGTGCTGG 62.721 66.667 0.00 0.00 43.34 4.85
1410 3420 3.435186 GGCGAGCCAAGAACCTGC 61.435 66.667 9.58 0.00 35.81 4.85
1566 3576 4.051167 TGGGGATGCTGGTGCTGG 62.051 66.667 0.00 0.00 40.48 4.85
1602 3612 2.904866 CTCTCCCGCTCCCTCTCG 60.905 72.222 0.00 0.00 0.00 4.04
1612 3622 3.141488 CTCCACCGTCCTCTCCCG 61.141 72.222 0.00 0.00 0.00 5.14
1710 3774 4.481112 CCGCCAAGCACGCCATTC 62.481 66.667 0.00 0.00 0.00 2.67
2538 4614 4.746309 TGCTGCTGATGGTGGGGC 62.746 66.667 0.00 0.00 0.00 5.80
2540 4616 3.138798 GCTGCTGCTGATGGTGGG 61.139 66.667 10.92 0.00 36.03 4.61
2545 4624 2.794621 CTGCTGCTGCTGCTGATG 59.205 61.111 27.67 13.98 40.01 3.07
2594 4673 2.050351 GTTGTGCTGCTGCTGCTG 60.050 61.111 27.67 16.73 40.48 4.41
2595 4674 3.657059 CGTTGTGCTGCTGCTGCT 61.657 61.111 27.67 0.00 40.48 4.24
2638 4724 5.167845 ACACGGGACAAATGATAAAAATGC 58.832 37.500 0.00 0.00 0.00 3.56
2639 4725 8.925161 ATTACACGGGACAAATGATAAAAATG 57.075 30.769 0.00 0.00 0.00 2.32
2640 4726 9.581099 GAATTACACGGGACAAATGATAAAAAT 57.419 29.630 0.00 0.00 0.00 1.82
2682 4768 0.782384 GCACGAGTTAACACCTGACG 59.218 55.000 8.61 6.16 0.00 4.35
2733 4823 2.840038 TGCCTCATCTCACATTACTGGT 59.160 45.455 0.00 0.00 0.00 4.00
2734 4824 3.464907 CTGCCTCATCTCACATTACTGG 58.535 50.000 0.00 0.00 0.00 4.00
2735 4825 2.871022 GCTGCCTCATCTCACATTACTG 59.129 50.000 0.00 0.00 0.00 2.74
2736 4826 2.158842 GGCTGCCTCATCTCACATTACT 60.159 50.000 12.43 0.00 0.00 2.24
2737 4827 2.158842 AGGCTGCCTCATCTCACATTAC 60.159 50.000 17.22 0.00 0.00 1.89
2747 4842 1.000396 GGGTTCAAGGCTGCCTCAT 60.000 57.895 23.61 3.93 30.89 2.90
2750 4845 2.134630 CTCAGGGTTCAAGGCTGCCT 62.135 60.000 17.22 17.22 33.87 4.75
2751 4846 1.676967 CTCAGGGTTCAAGGCTGCC 60.677 63.158 11.65 11.65 0.00 4.85
2752 4847 1.676967 CCTCAGGGTTCAAGGCTGC 60.677 63.158 0.00 0.00 0.00 5.25
2753 4848 4.730487 CCTCAGGGTTCAAGGCTG 57.270 61.111 0.00 0.00 0.00 4.85
2756 4851 2.045926 CCGCCTCAGGGTTCAAGG 60.046 66.667 0.00 0.00 34.45 3.61
2757 4852 2.747855 GCCGCCTCAGGGTTCAAG 60.748 66.667 0.00 0.00 34.45 3.02
2758 4853 2.905996 ATGCCGCCTCAGGGTTCAA 61.906 57.895 0.00 0.00 34.45 2.69
2788 4883 1.136110 GCGAGAGGAAGAAGGAAGGAG 59.864 57.143 0.00 0.00 0.00 3.69
2791 4886 1.821753 TGAGCGAGAGGAAGAAGGAAG 59.178 52.381 0.00 0.00 0.00 3.46
2843 4938 1.202313 GCTCTCACCGTGCTAACCTAG 60.202 57.143 0.00 0.00 0.00 3.02
2890 4985 3.132824 GGCCCTAAAATCTTCAATGTGGG 59.867 47.826 0.00 0.00 35.47 4.61
2959 5064 1.511552 CTGCGTACGTACATACAAGCG 59.488 52.381 24.50 9.75 0.00 4.68
2995 5122 0.526954 CATCAAGAAATGCCGCTGCC 60.527 55.000 0.00 0.00 36.33 4.85
3032 5172 1.641123 GCATTTGGCAATGGCACTGC 61.641 55.000 21.58 21.58 43.71 4.40
3033 5173 2.462503 GCATTTGGCAATGGCACTG 58.537 52.632 9.62 11.33 43.71 3.66
3066 5206 1.228552 TGCCTTCCCAAGCCAAGAC 60.229 57.895 0.00 0.00 0.00 3.01
3110 5250 0.252239 AAGGGAATCCAACAAGCCCC 60.252 55.000 0.09 0.00 39.68 5.80
3203 5356 0.107654 AAGTACATTCCGAGCCAGCC 60.108 55.000 0.00 0.00 0.00 4.85
3207 5364 1.867166 GCCTAAGTACATTCCGAGCC 58.133 55.000 0.00 0.00 0.00 4.70
3211 5368 1.567504 CCACGCCTAAGTACATTCCG 58.432 55.000 0.00 0.00 0.00 4.30
3306 5463 1.203994 CCAATCAAGGGCAGAAAGCTG 59.796 52.381 0.00 0.00 44.79 4.24
3339 5497 4.288887 AGACAACTTAGGAAAGGGGGTTAG 59.711 45.833 0.00 0.00 37.01 2.34
3404 5563 1.455217 ATCCATGGAAGCAGCAGCC 60.455 57.895 20.67 0.00 43.56 4.85
3452 5617 7.180748 ACGAGAAGAACGAAAGAAAAAGAAAG 58.819 34.615 0.00 0.00 34.70 2.62
3453 5618 7.064253 AGACGAGAAGAACGAAAGAAAAAGAAA 59.936 33.333 0.00 0.00 34.70 2.52
3454 5619 6.534079 AGACGAGAAGAACGAAAGAAAAAGAA 59.466 34.615 0.00 0.00 34.70 2.52
3455 5620 6.040878 AGACGAGAAGAACGAAAGAAAAAGA 58.959 36.000 0.00 0.00 34.70 2.52
3456 5621 6.275305 AGACGAGAAGAACGAAAGAAAAAG 57.725 37.500 0.00 0.00 34.70 2.27
3457 5622 5.233689 GGAGACGAGAAGAACGAAAGAAAAA 59.766 40.000 0.00 0.00 34.70 1.94
3458 5623 4.743644 GGAGACGAGAAGAACGAAAGAAAA 59.256 41.667 0.00 0.00 34.70 2.29
3459 5624 4.296690 GGAGACGAGAAGAACGAAAGAAA 58.703 43.478 0.00 0.00 34.70 2.52
3460 5625 3.305199 GGGAGACGAGAAGAACGAAAGAA 60.305 47.826 0.00 0.00 34.70 2.52
3461 5626 2.228343 GGGAGACGAGAAGAACGAAAGA 59.772 50.000 0.00 0.00 34.70 2.52
3462 5627 2.229302 AGGGAGACGAGAAGAACGAAAG 59.771 50.000 0.00 0.00 34.70 2.62
3463 5628 2.228343 GAGGGAGACGAGAAGAACGAAA 59.772 50.000 0.00 0.00 34.70 3.46
3464 5629 1.811359 GAGGGAGACGAGAAGAACGAA 59.189 52.381 0.00 0.00 34.70 3.85
3465 5630 1.003349 AGAGGGAGACGAGAAGAACGA 59.997 52.381 0.00 0.00 34.70 3.85
3466 5631 1.399089 GAGAGGGAGACGAGAAGAACG 59.601 57.143 0.00 0.00 0.00 3.95
3467 5632 1.746787 GGAGAGGGAGACGAGAAGAAC 59.253 57.143 0.00 0.00 0.00 3.01
3468 5633 1.341187 GGGAGAGGGAGACGAGAAGAA 60.341 57.143 0.00 0.00 0.00 2.52
3469 5634 0.256464 GGGAGAGGGAGACGAGAAGA 59.744 60.000 0.00 0.00 0.00 2.87
3470 5635 0.753848 GGGGAGAGGGAGACGAGAAG 60.754 65.000 0.00 0.00 0.00 2.85
3471 5636 1.215679 AGGGGAGAGGGAGACGAGAA 61.216 60.000 0.00 0.00 0.00 2.87
3472 5637 1.619975 AGGGGAGAGGGAGACGAGA 60.620 63.158 0.00 0.00 0.00 4.04
3473 5638 1.152839 GAGGGGAGAGGGAGACGAG 60.153 68.421 0.00 0.00 0.00 4.18
3474 5639 2.691779 GGAGGGGAGAGGGAGACGA 61.692 68.421 0.00 0.00 0.00 4.20
3475 5640 2.123640 GGAGGGGAGAGGGAGACG 60.124 72.222 0.00 0.00 0.00 4.18
3476 5641 1.231928 GAGGAGGGGAGAGGGAGAC 59.768 68.421 0.00 0.00 0.00 3.36
3477 5642 0.996762 GAGAGGAGGGGAGAGGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
3478 5643 1.541672 GAGAGGAGGGGAGAGGGAG 59.458 68.421 0.00 0.00 0.00 4.30
3479 5644 2.015726 GGAGAGGAGGGGAGAGGGA 61.016 68.421 0.00 0.00 0.00 4.20
3480 5645 2.612251 GGAGAGGAGGGGAGAGGG 59.388 72.222 0.00 0.00 0.00 4.30
3481 5646 2.612251 GGGAGAGGAGGGGAGAGG 59.388 72.222 0.00 0.00 0.00 3.69
3482 5647 1.598856 AAGGGGAGAGGAGGGGAGAG 61.599 65.000 0.00 0.00 0.00 3.20
3483 5648 1.550374 AAGGGGAGAGGAGGGGAGA 60.550 63.158 0.00 0.00 0.00 3.71
3484 5649 1.074850 GAAGGGGAGAGGAGGGGAG 60.075 68.421 0.00 0.00 0.00 4.30
3485 5650 2.647949 GGAAGGGGAGAGGAGGGGA 61.648 68.421 0.00 0.00 0.00 4.81
3486 5651 2.040359 GGAAGGGGAGAGGAGGGG 60.040 72.222 0.00 0.00 0.00 4.79
3487 5652 1.383803 CAGGAAGGGGAGAGGAGGG 60.384 68.421 0.00 0.00 0.00 4.30
3488 5653 0.267356 ATCAGGAAGGGGAGAGGAGG 59.733 60.000 0.00 0.00 0.00 4.30
3496 5661 0.394352 CACCGGAAATCAGGAAGGGG 60.394 60.000 9.46 0.00 35.12 4.79
3501 5673 1.131303 ACCACCACCGGAAATCAGGA 61.131 55.000 9.46 0.00 35.12 3.86
3580 5771 1.998315 CTTTGATCAGCCTCTGACACG 59.002 52.381 0.00 0.00 43.63 4.49
3616 5807 4.404654 CTCAAAACGCAGGCCGGC 62.405 66.667 21.18 21.18 42.52 6.13
3636 5827 0.391130 AACACGCACACACTCACACT 60.391 50.000 0.00 0.00 0.00 3.55
3642 5833 2.112198 CACCCAACACGCACACACT 61.112 57.895 0.00 0.00 0.00 3.55
3648 5839 2.282110 CCATCCACCCAACACGCA 60.282 61.111 0.00 0.00 0.00 5.24
3649 5840 3.747976 GCCATCCACCCAACACGC 61.748 66.667 0.00 0.00 0.00 5.34
3650 5841 2.282110 TGCCATCCACCCAACACG 60.282 61.111 0.00 0.00 0.00 4.49
3651 5842 2.639327 GCTGCCATCCACCCAACAC 61.639 63.158 0.00 0.00 0.00 3.32
3652 5843 2.283101 GCTGCCATCCACCCAACA 60.283 61.111 0.00 0.00 0.00 3.33
3692 5883 3.509575 AGCCTTCAATTTTGCCGACAATA 59.490 39.130 0.00 0.00 35.21 1.90
3722 5913 2.441532 CAGGGCTGGATGGGCTTG 60.442 66.667 0.00 0.00 33.25 4.01
3741 5932 1.064134 GCCGGAATCGCACCAAATC 59.936 57.895 5.05 0.00 34.56 2.17
3755 5946 1.067516 GGGATGAAATGTCATTGCCGG 59.932 52.381 0.00 0.00 44.83 6.13
3756 5947 1.268692 CGGGATGAAATGTCATTGCCG 60.269 52.381 11.69 11.69 44.83 5.69


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

AutoCloner maintained by Alex Coulton.