Multiple sequence alignment - TraesCS1A01G122700

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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 TraesCS1A01G122700 chr1A 100.000 5016 0 0 1 5016 139557176 139562191 0.000000e+00 9263.0
1 TraesCS1A01G122700 chr1A 96.914 162 5 0 2882 3043 534875785 534875946 6.400000e-69 272.0
2 TraesCS1A01G122700 chr1A 96.914 162 5 0 2882 3043 534894671 534894832 6.400000e-69 272.0
3 TraesCS1A01G122700 chr1A 96.914 162 5 0 2882 3043 534913758 534913919 6.400000e-69 272.0
4 TraesCS1A01G122700 chr1A 96.296 162 6 0 2882 3043 534918060 534918221 2.980000e-67 267.0
5 TraesCS1A01G122700 chr1D 96.085 1737 44 9 1101 2826 125829106 125830829 0.000000e+00 2809.0
6 TraesCS1A01G122700 chr1D 92.386 1274 50 17 3042 4311 125830868 125832098 0.000000e+00 1772.0
7 TraesCS1A01G122700 chr1D 87.481 647 78 2 4372 5016 267761697 267761052 0.000000e+00 743.0
8 TraesCS1A01G122700 chr1D 95.833 288 7 1 809 1091 125828489 125828776 1.270000e-125 460.0
9 TraesCS1A01G122700 chr1D 89.189 185 15 5 3101 3283 73725749 73725568 5.050000e-55 226.0
10 TraesCS1A01G122700 chr1B 92.639 1345 56 14 1565 2883 189703973 189705300 0.000000e+00 1895.0
11 TraesCS1A01G122700 chr1B 96.534 779 22 3 787 1560 189703142 189703920 0.000000e+00 1284.0
12 TraesCS1A01G122700 chr1B 94.286 735 34 6 3260 3993 189705358 189706085 0.000000e+00 1118.0
13 TraesCS1A01G122700 chr1B 88.976 635 65 5 4385 5015 345326191 345326824 0.000000e+00 780.0
14 TraesCS1A01G122700 chr1B 95.679 162 7 0 2882 3043 623195844 623195683 1.390000e-65 261.0
15 TraesCS1A01G122700 chr1B 93.443 61 4 0 3042 3102 189705299 189705359 1.920000e-14 91.6
16 TraesCS1A01G122700 chr3A 91.783 791 45 9 1 774 109144535 109145322 0.000000e+00 1083.0
17 TraesCS1A01G122700 chr3A 92.857 182 10 3 3094 3273 600920847 600921027 1.390000e-65 261.0
18 TraesCS1A01G122700 chr3A 95.152 165 8 0 2882 3046 648037286 648037450 1.390000e-65 261.0
19 TraesCS1A01G122700 chr2D 91.762 789 46 10 1 775 450874496 450875279 0.000000e+00 1079.0
20 TraesCS1A01G122700 chr2D 94.643 168 8 1 2876 3043 362930974 362930808 4.980000e-65 259.0
21 TraesCS1A01G122700 chr7D 91.614 787 50 10 1 774 506162656 506161873 0.000000e+00 1074.0
22 TraesCS1A01G122700 chr7D 91.105 787 53 12 1 774 71634355 71633573 0.000000e+00 1050.0
23 TraesCS1A01G122700 chr7D 84.818 685 80 17 4349 5016 38740121 38739444 0.000000e+00 667.0
24 TraesCS1A01G122700 chr7D 92.771 166 10 2 3101 3265 397555077 397554913 6.490000e-59 239.0
25 TraesCS1A01G122700 chr2A 91.403 791 48 11 1 776 699800361 699801146 0.000000e+00 1066.0
26 TraesCS1A01G122700 chr2A 90.561 784 57 11 1 774 603859907 603859131 0.000000e+00 1022.0
27 TraesCS1A01G122700 chr2A 89.186 786 64 14 1 774 38757076 38757852 0.000000e+00 961.0
28 TraesCS1A01G122700 chr2A 80.597 134 9 7 4349 4469 239372041 239372170 2.490000e-13 87.9
29 TraesCS1A01G122700 chr6A 90.152 792 51 18 1 774 597283110 597283892 0.000000e+00 1005.0
30 TraesCS1A01G122700 chr6A 90.909 176 11 4 3100 3273 91902568 91902396 1.090000e-56 231.0
31 TraesCS1A01G122700 chr5A 88.662 785 74 9 1 774 569652398 569653178 0.000000e+00 942.0
32 TraesCS1A01G122700 chr5A 95.092 163 8 0 2881 3043 19681306 19681144 1.790000e-64 257.0
33 TraesCS1A01G122700 chr5A 91.765 170 12 2 3098 3266 605231140 605231308 8.400000e-58 235.0
34 TraesCS1A01G122700 chr4B 88.707 673 70 5 4346 5016 481524827 481525495 0.000000e+00 817.0
35 TraesCS1A01G122700 chr6B 88.365 636 70 4 4385 5016 82405396 82406031 0.000000e+00 761.0
36 TraesCS1A01G122700 chr5D 88.365 636 66 7 4387 5016 477874565 477875198 0.000000e+00 758.0
37 TraesCS1A01G122700 chr5D 87.931 638 70 6 4385 5016 73811307 73811943 0.000000e+00 745.0
38 TraesCS1A01G122700 chr5D 94.578 166 9 0 2881 3046 53583076 53583241 1.790000e-64 257.0
39 TraesCS1A01G122700 chr5D 92.216 167 12 1 3101 3266 59947843 59947677 8.400000e-58 235.0
40 TraesCS1A01G122700 chr3D 87.832 641 68 10 4385 5016 520728017 520728656 0.000000e+00 743.0
41 TraesCS1A01G122700 chr2B 86.792 636 74 10 4388 5016 451814793 451815425 0.000000e+00 701.0
42 TraesCS1A01G122700 chr7A 92.899 169 10 2 3098 3265 451519808 451519975 1.390000e-60 244.0
43 TraesCS1A01G122700 chr7B 92.262 168 12 1 3097 3263 194607282 194607115 2.330000e-58 237.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G122700 chr1A 139557176 139562191 5015 False 9263.000000 9263 100.0000 1 5016 1 chr1A.!!$F1 5015
1 TraesCS1A01G122700 chr1D 125828489 125832098 3609 False 1680.333333 2809 94.7680 809 4311 3 chr1D.!!$F1 3502
2 TraesCS1A01G122700 chr1D 267761052 267761697 645 True 743.000000 743 87.4810 4372 5016 1 chr1D.!!$R2 644
3 TraesCS1A01G122700 chr1B 189703142 189706085 2943 False 1097.150000 1895 94.2255 787 3993 4 chr1B.!!$F2 3206
4 TraesCS1A01G122700 chr1B 345326191 345326824 633 False 780.000000 780 88.9760 4385 5015 1 chr1B.!!$F1 630
5 TraesCS1A01G122700 chr3A 109144535 109145322 787 False 1083.000000 1083 91.7830 1 774 1 chr3A.!!$F1 773
6 TraesCS1A01G122700 chr2D 450874496 450875279 783 False 1079.000000 1079 91.7620 1 775 1 chr2D.!!$F1 774
7 TraesCS1A01G122700 chr7D 506161873 506162656 783 True 1074.000000 1074 91.6140 1 774 1 chr7D.!!$R4 773
8 TraesCS1A01G122700 chr7D 71633573 71634355 782 True 1050.000000 1050 91.1050 1 774 1 chr7D.!!$R2 773
9 TraesCS1A01G122700 chr7D 38739444 38740121 677 True 667.000000 667 84.8180 4349 5016 1 chr7D.!!$R1 667
10 TraesCS1A01G122700 chr2A 699800361 699801146 785 False 1066.000000 1066 91.4030 1 776 1 chr2A.!!$F3 775
11 TraesCS1A01G122700 chr2A 603859131 603859907 776 True 1022.000000 1022 90.5610 1 774 1 chr2A.!!$R1 773
12 TraesCS1A01G122700 chr2A 38757076 38757852 776 False 961.000000 961 89.1860 1 774 1 chr2A.!!$F1 773
13 TraesCS1A01G122700 chr6A 597283110 597283892 782 False 1005.000000 1005 90.1520 1 774 1 chr6A.!!$F1 773
14 TraesCS1A01G122700 chr5A 569652398 569653178 780 False 942.000000 942 88.6620 1 774 1 chr5A.!!$F1 773
15 TraesCS1A01G122700 chr4B 481524827 481525495 668 False 817.000000 817 88.7070 4346 5016 1 chr4B.!!$F1 670
16 TraesCS1A01G122700 chr6B 82405396 82406031 635 False 761.000000 761 88.3650 4385 5016 1 chr6B.!!$F1 631
17 TraesCS1A01G122700 chr5D 477874565 477875198 633 False 758.000000 758 88.3650 4387 5016 1 chr5D.!!$F3 629
18 TraesCS1A01G122700 chr5D 73811307 73811943 636 False 745.000000 745 87.9310 4385 5016 1 chr5D.!!$F2 631
19 TraesCS1A01G122700 chr3D 520728017 520728656 639 False 743.000000 743 87.8320 4385 5016 1 chr3D.!!$F1 631
20 TraesCS1A01G122700 chr2B 451814793 451815425 632 False 701.000000 701 86.7920 4388 5016 1 chr2B.!!$F1 628

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
784 829 0.247695 GTGATTTCGCTTACTGCCGC 60.248 55.0 0.00 0.0 38.78 6.53 F
1275 1651 0.666577 GACTGTGGCGGTAGTGTGAC 60.667 60.0 0.00 0.0 0.00 3.67 F
1794 2239 0.467384 ATGCCAATCTCTGACCCTCG 59.533 55.0 0.00 0.0 0.00 4.63 F
2299 2744 1.357907 GTCATGTCAGTGCTGCTCTC 58.642 55.0 0.47 0.0 0.00 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 2199 0.815095 CAGAGATTGGCATGCAAGCA 59.185 50.000 21.36 5.42 35.83 3.91 R
2299 2744 1.135083 ACATCTACTCCGCCAAGAACG 60.135 52.381 0.00 0.00 0.00 3.95 R
2840 3293 1.243902 ACATCGAACATTTTGGCCGT 58.756 45.000 0.00 0.00 0.00 5.68 R
4261 4722 1.556911 CACCCCAGATGCTAAGACAGT 59.443 52.381 0.00 0.00 0.00 3.55 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
165 179 3.796717 CGTGCCTCTTGAAAAGGAAAAAC 59.203 43.478 0.00 0.00 46.24 2.43
166 180 4.676723 CGTGCCTCTTGAAAAGGAAAAACA 60.677 41.667 0.00 0.00 46.24 2.83
170 184 6.148645 TGCCTCTTGAAAAGGAAAAACAAAAC 59.851 34.615 0.00 0.00 46.24 2.43
171 185 6.672118 GCCTCTTGAAAAGGAAAAACAAAACG 60.672 38.462 0.00 0.00 46.24 3.60
172 186 6.159419 TCTTGAAAAGGAAAAACAAAACGC 57.841 33.333 0.00 0.00 46.24 4.84
173 187 4.569801 TGAAAAGGAAAAACAAAACGCG 57.430 36.364 3.53 3.53 0.00 6.01
174 188 3.988517 TGAAAAGGAAAAACAAAACGCGT 59.011 34.783 5.58 5.58 0.00 6.01
578 623 5.624344 TCTAGTTTTGAAGATCTCGACGT 57.376 39.130 0.00 0.00 0.00 4.34
776 821 8.258708 AGTACTCCTTAATTAGTGATTTCGCTT 58.741 33.333 0.00 0.00 37.87 4.68
777 822 9.525409 GTACTCCTTAATTAGTGATTTCGCTTA 57.475 33.333 0.00 0.00 37.87 3.09
778 823 8.421673 ACTCCTTAATTAGTGATTTCGCTTAC 57.578 34.615 0.00 0.00 37.87 2.34
779 824 8.258708 ACTCCTTAATTAGTGATTTCGCTTACT 58.741 33.333 0.00 0.00 37.87 2.24
780 825 8.420374 TCCTTAATTAGTGATTTCGCTTACTG 57.580 34.615 0.00 0.00 37.87 2.74
781 826 7.011109 TCCTTAATTAGTGATTTCGCTTACTGC 59.989 37.037 0.00 0.00 37.87 4.40
782 827 5.485662 AATTAGTGATTTCGCTTACTGCC 57.514 39.130 0.00 0.00 37.87 4.85
783 828 1.359848 AGTGATTTCGCTTACTGCCG 58.640 50.000 0.00 0.00 38.78 5.69
784 829 0.247695 GTGATTTCGCTTACTGCCGC 60.248 55.000 0.00 0.00 38.78 6.53
785 830 0.672091 TGATTTCGCTTACTGCCGCA 60.672 50.000 0.00 0.00 38.78 5.69
800 845 3.288092 TGCCGCACTCTCTTATCTCTAA 58.712 45.455 0.00 0.00 0.00 2.10
841 886 2.457743 ATAAAGGCCCACGTGCGACA 62.458 55.000 10.91 0.00 0.00 4.35
879 924 2.452600 ACATGGGCCGGACATTTATT 57.547 45.000 11.00 0.00 0.00 1.40
1068 1121 1.062685 CGACTCACTCACGATCCGG 59.937 63.158 0.00 0.00 0.00 5.14
1275 1651 0.666577 GACTGTGGCGGTAGTGTGAC 60.667 60.000 0.00 0.00 0.00 3.67
1397 1774 2.029666 CAGGATGGCCGGATCGAC 59.970 66.667 5.05 0.00 39.96 4.20
1671 2096 4.081642 CGGACTCTGGGAGAAATTACTTCA 60.082 45.833 1.31 0.00 36.40 3.02
1753 2184 6.573725 CGTTTGAGTAAGTGAGTATGTTTTGC 59.426 38.462 0.00 0.00 0.00 3.68
1755 2186 5.616270 TGAGTAAGTGAGTATGTTTTGCCA 58.384 37.500 0.00 0.00 0.00 4.92
1768 2199 9.737844 AGTATGTTTTGCCAAAAATTAATGGAT 57.262 25.926 3.79 0.71 39.12 3.41
1794 2239 0.467384 ATGCCAATCTCTGACCCTCG 59.533 55.000 0.00 0.00 0.00 4.63
1831 2276 4.849813 ACTGACAATGGATGGAGAATCA 57.150 40.909 0.00 0.00 36.98 2.57
2028 2473 3.181477 TGGCACCAAACATATATTGCTGC 60.181 43.478 10.24 10.24 38.20 5.25
2120 2565 9.696917 ACCAAATCAATCTTCATTTGTTTACTC 57.303 29.630 0.00 0.00 38.02 2.59
2134 2579 9.329913 CATTTGTTTACTCGTATTTTTCTCAGG 57.670 33.333 0.00 0.00 0.00 3.86
2299 2744 1.357907 GTCATGTCAGTGCTGCTCTC 58.642 55.000 0.47 0.00 0.00 3.20
2551 2998 2.486203 AGTGAACAAACGCAACAGTTCA 59.514 40.909 0.00 0.00 45.57 3.18
2703 3153 2.619074 GGAGGGAATTGCACTTGTAGCT 60.619 50.000 0.00 0.00 0.00 3.32
2866 3319 6.142161 CGGCCAAAATGTTCGATGTTTATATG 59.858 38.462 2.24 0.00 0.00 1.78
2881 3334 6.662755 TGTTTATATGATGAGCTTCCAACCT 58.337 36.000 0.00 0.00 0.00 3.50
2882 3335 7.801104 TGTTTATATGATGAGCTTCCAACCTA 58.199 34.615 0.00 0.00 0.00 3.08
2883 3336 7.715249 TGTTTATATGATGAGCTTCCAACCTAC 59.285 37.037 0.00 0.00 0.00 3.18
2884 3337 7.618019 TTATATGATGAGCTTCCAACCTACT 57.382 36.000 0.00 0.00 0.00 2.57
2885 3338 3.895232 TGATGAGCTTCCAACCTACTC 57.105 47.619 0.00 0.00 0.00 2.59
2886 3339 2.501723 TGATGAGCTTCCAACCTACTCC 59.498 50.000 0.00 0.00 0.00 3.85
2887 3340 1.276622 TGAGCTTCCAACCTACTCCC 58.723 55.000 0.00 0.00 0.00 4.30
2888 3341 1.203313 TGAGCTTCCAACCTACTCCCT 60.203 52.381 0.00 0.00 0.00 4.20
2889 3342 1.483004 GAGCTTCCAACCTACTCCCTC 59.517 57.143 0.00 0.00 0.00 4.30
2890 3343 0.542333 GCTTCCAACCTACTCCCTCC 59.458 60.000 0.00 0.00 0.00 4.30
2891 3344 0.824759 CTTCCAACCTACTCCCTCCG 59.175 60.000 0.00 0.00 0.00 4.63
2892 3345 0.115745 TTCCAACCTACTCCCTCCGT 59.884 55.000 0.00 0.00 0.00 4.69
2893 3346 0.115745 TCCAACCTACTCCCTCCGTT 59.884 55.000 0.00 0.00 0.00 4.44
2894 3347 0.535797 CCAACCTACTCCCTCCGTTC 59.464 60.000 0.00 0.00 0.00 3.95
2895 3348 0.535797 CAACCTACTCCCTCCGTTCC 59.464 60.000 0.00 0.00 0.00 3.62
2896 3349 0.412640 AACCTACTCCCTCCGTTCCT 59.587 55.000 0.00 0.00 0.00 3.36
2897 3350 1.302907 ACCTACTCCCTCCGTTCCTA 58.697 55.000 0.00 0.00 0.00 2.94
2898 3351 1.642762 ACCTACTCCCTCCGTTCCTAA 59.357 52.381 0.00 0.00 0.00 2.69
2899 3352 2.043526 ACCTACTCCCTCCGTTCCTAAA 59.956 50.000 0.00 0.00 0.00 1.85
2900 3353 3.306613 CCTACTCCCTCCGTTCCTAAAT 58.693 50.000 0.00 0.00 0.00 1.40
2901 3354 4.078980 ACCTACTCCCTCCGTTCCTAAATA 60.079 45.833 0.00 0.00 0.00 1.40
2902 3355 4.280425 CCTACTCCCTCCGTTCCTAAATAC 59.720 50.000 0.00 0.00 0.00 1.89
2903 3356 3.716431 ACTCCCTCCGTTCCTAAATACA 58.284 45.455 0.00 0.00 0.00 2.29
2904 3357 4.098894 ACTCCCTCCGTTCCTAAATACAA 58.901 43.478 0.00 0.00 0.00 2.41
2905 3358 4.161754 ACTCCCTCCGTTCCTAAATACAAG 59.838 45.833 0.00 0.00 0.00 3.16
2906 3359 4.098894 TCCCTCCGTTCCTAAATACAAGT 58.901 43.478 0.00 0.00 0.00 3.16
2907 3360 4.161001 TCCCTCCGTTCCTAAATACAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
2908 3361 4.161754 CCCTCCGTTCCTAAATACAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
2909 3362 5.338137 CCCTCCGTTCCTAAATACAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
2910 3363 6.171213 CCTCCGTTCCTAAATACAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
2911 3364 6.653740 CCTCCGTTCCTAAATACAAGTCTTTT 59.346 38.462 0.00 0.00 0.00 2.27
2912 3365 7.174426 CCTCCGTTCCTAAATACAAGTCTTTTT 59.826 37.037 0.00 0.00 0.00 1.94
2913 3366 9.211485 CTCCGTTCCTAAATACAAGTCTTTTTA 57.789 33.333 0.00 0.00 0.00 1.52
2914 3367 9.558396 TCCGTTCCTAAATACAAGTCTTTTTAA 57.442 29.630 0.00 0.00 0.00 1.52
2939 3392 8.475331 AAGATTTCACTACAAACTACATACGG 57.525 34.615 0.00 0.00 0.00 4.02
2940 3393 7.833786 AGATTTCACTACAAACTACATACGGA 58.166 34.615 0.00 0.00 0.00 4.69
2941 3394 8.475639 AGATTTCACTACAAACTACATACGGAT 58.524 33.333 0.00 0.00 0.00 4.18
2942 3395 7.821595 TTTCACTACAAACTACATACGGATG 57.178 36.000 5.94 5.94 39.16 3.51
2944 3397 7.628769 TCACTACAAACTACATACGGATGTA 57.371 36.000 19.32 19.32 44.77 2.29
2945 3398 8.229253 TCACTACAAACTACATACGGATGTAT 57.771 34.615 20.64 8.38 45.42 2.29
2946 3399 9.341078 TCACTACAAACTACATACGGATGTATA 57.659 33.333 20.64 9.08 45.42 1.47
2983 3436 7.934855 AGAGTGTAGATTCATTCATTTTGCT 57.065 32.000 0.00 0.00 0.00 3.91
2984 3437 7.983307 AGAGTGTAGATTCATTCATTTTGCTC 58.017 34.615 0.00 0.00 0.00 4.26
2985 3438 7.066766 AGAGTGTAGATTCATTCATTTTGCTCC 59.933 37.037 0.00 0.00 0.00 4.70
2986 3439 5.967674 GTGTAGATTCATTCATTTTGCTCCG 59.032 40.000 0.00 0.00 0.00 4.63
2987 3440 5.647658 TGTAGATTCATTCATTTTGCTCCGT 59.352 36.000 0.00 0.00 0.00 4.69
2988 3441 6.821160 TGTAGATTCATTCATTTTGCTCCGTA 59.179 34.615 0.00 0.00 0.00 4.02
2989 3442 6.949352 AGATTCATTCATTTTGCTCCGTAT 57.051 33.333 0.00 0.00 0.00 3.06
2990 3443 6.732154 AGATTCATTCATTTTGCTCCGTATG 58.268 36.000 0.00 0.00 0.00 2.39
2991 3444 5.895636 TTCATTCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
2992 3445 6.993786 TTCATTCATTTTGCTCCGTATGTA 57.006 33.333 0.00 0.00 0.00 2.29
2993 3446 6.603237 TCATTCATTTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
2994 3447 6.112734 TCATTCATTTTGCTCCGTATGTAGT 58.887 36.000 0.00 0.00 0.00 2.73
2995 3448 6.257849 TCATTCATTTTGCTCCGTATGTAGTC 59.742 38.462 0.00 0.00 0.00 2.59
2996 3449 5.339008 TCATTTTGCTCCGTATGTAGTCT 57.661 39.130 0.00 0.00 0.00 3.24
2997 3450 6.459670 TCATTTTGCTCCGTATGTAGTCTA 57.540 37.500 0.00 0.00 0.00 2.59
2998 3451 7.050970 TCATTTTGCTCCGTATGTAGTCTAT 57.949 36.000 0.00 0.00 0.00 1.98
2999 3452 8.173542 TCATTTTGCTCCGTATGTAGTCTATA 57.826 34.615 0.00 0.00 0.00 1.31
3000 3453 8.297426 TCATTTTGCTCCGTATGTAGTCTATAG 58.703 37.037 0.00 0.00 0.00 1.31
3001 3454 7.578310 TTTTGCTCCGTATGTAGTCTATAGT 57.422 36.000 0.00 0.00 0.00 2.12
3002 3455 6.555812 TTGCTCCGTATGTAGTCTATAGTG 57.444 41.667 0.00 0.00 0.00 2.74
3003 3456 5.618236 TGCTCCGTATGTAGTCTATAGTGT 58.382 41.667 0.00 0.00 0.00 3.55
3004 3457 6.762333 TGCTCCGTATGTAGTCTATAGTGTA 58.238 40.000 0.00 0.00 0.00 2.90
3005 3458 7.219322 TGCTCCGTATGTAGTCTATAGTGTAA 58.781 38.462 0.00 0.00 0.00 2.41
3006 3459 7.881751 TGCTCCGTATGTAGTCTATAGTGTAAT 59.118 37.037 0.00 0.00 0.00 1.89
3007 3460 8.389603 GCTCCGTATGTAGTCTATAGTGTAATC 58.610 40.741 0.00 0.00 0.00 1.75
3008 3461 9.656040 CTCCGTATGTAGTCTATAGTGTAATCT 57.344 37.037 0.00 0.00 0.00 2.40
3009 3462 9.650539 TCCGTATGTAGTCTATAGTGTAATCTC 57.349 37.037 0.00 0.00 0.00 2.75
3010 3463 9.656040 CCGTATGTAGTCTATAGTGTAATCTCT 57.344 37.037 0.00 0.00 0.00 3.10
3037 3490 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
3038 3491 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
3039 3492 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
3040 3493 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
3089 3542 3.873361 ACATGGCTGACATACATTTCTCG 59.127 43.478 0.00 0.00 37.84 4.04
3100 3553 9.214957 TGACATACATTTCTCGTTGTAAATTCT 57.785 29.630 0.00 0.00 32.46 2.40
3221 3674 3.196901 TGCTCCGTATGTAGTCCATGTTT 59.803 43.478 0.00 0.00 34.86 2.83
3317 3771 4.878397 ACTGCATAGTTTCTTCTACCATGC 59.122 41.667 0.00 0.00 31.66 4.06
3380 3839 1.137086 CTAGCAGGGATACGCAGTTGT 59.863 52.381 0.00 0.00 37.78 3.32
3384 3843 1.393539 CAGGGATACGCAGTTGTTTCG 59.606 52.381 0.00 0.00 37.78 3.46
3385 3844 1.001633 AGGGATACGCAGTTGTTTCGT 59.998 47.619 0.00 0.00 37.78 3.85
3469 3928 9.305555 AGCATTGATTAAAGTGCTGGAATATAT 57.694 29.630 0.00 0.00 45.44 0.86
3539 3998 6.467677 TCACTGCTTTGCTAATCTAGTTTCT 58.532 36.000 0.00 0.00 0.00 2.52
3704 4164 1.532437 TGATGCTTGAGCGTTGTGAAG 59.468 47.619 0.00 0.00 45.83 3.02
3705 4165 1.532868 GATGCTTGAGCGTTGTGAAGT 59.467 47.619 0.00 0.00 45.83 3.01
3822 4282 2.069273 AGTGATCTTGTGTGCTTACGC 58.931 47.619 0.00 0.00 0.00 4.42
3827 4287 0.944311 CTTGTGTGCTTACGCTCGGT 60.944 55.000 0.00 0.00 36.97 4.69
3832 4292 0.666577 GTGCTTACGCTCGGTCAAGT 60.667 55.000 0.00 0.00 36.97 3.16
3844 4304 4.744570 CTCGGTCAAGTAGTCATGCTAAA 58.255 43.478 0.00 0.00 0.00 1.85
3926 4386 9.029243 TGTATTTTGTTGTACTTGCTGAATTTG 57.971 29.630 0.00 0.00 0.00 2.32
3960 4420 3.126001 TGTTAAACTGTCTCTGGGCTG 57.874 47.619 0.00 0.00 0.00 4.85
4021 4481 4.617298 CGGTTAACTATGGCAACCAAAAGG 60.617 45.833 5.42 0.00 41.52 3.11
4023 4483 5.227152 GTTAACTATGGCAACCAAAAGGTG 58.773 41.667 0.00 0.00 36.95 4.00
4064 4524 6.817765 TGATTTCAAATCACCAAGTAGTCC 57.182 37.500 8.85 0.00 0.00 3.85
4068 4528 4.894784 TCAAATCACCAAGTAGTCCAGTC 58.105 43.478 0.00 0.00 0.00 3.51
4094 4554 2.024414 GTGTGGGAGGTTCATAATGCC 58.976 52.381 0.00 0.00 0.00 4.40
4103 4563 4.517285 AGGTTCATAATGCCAGTGTACTG 58.483 43.478 5.05 5.05 43.40 2.74
4105 4565 5.188948 AGGTTCATAATGCCAGTGTACTGTA 59.811 40.000 10.80 0.77 42.27 2.74
4110 4570 2.717580 TGCCAGTGTACTGTAACTCG 57.282 50.000 10.80 0.00 42.27 4.18
4112 4572 1.271656 GCCAGTGTACTGTAACTCGGT 59.728 52.381 10.80 0.00 42.27 4.69
4133 4593 5.059833 GGTTCCTGAAGATTGGCTAGTATG 58.940 45.833 0.00 0.00 0.00 2.39
4134 4594 4.963318 TCCTGAAGATTGGCTAGTATGG 57.037 45.455 0.00 0.00 0.00 2.74
4135 4595 3.648067 TCCTGAAGATTGGCTAGTATGGG 59.352 47.826 0.00 0.00 0.00 4.00
4136 4596 3.244700 CCTGAAGATTGGCTAGTATGGGG 60.245 52.174 0.00 0.00 0.00 4.96
4137 4597 3.392616 CTGAAGATTGGCTAGTATGGGGT 59.607 47.826 0.00 0.00 0.00 4.95
4138 4598 3.391296 TGAAGATTGGCTAGTATGGGGTC 59.609 47.826 0.00 0.00 0.00 4.46
4139 4599 1.971357 AGATTGGCTAGTATGGGGTCG 59.029 52.381 0.00 0.00 0.00 4.79
4140 4600 1.692519 GATTGGCTAGTATGGGGTCGT 59.307 52.381 0.00 0.00 0.00 4.34
4141 4601 2.457813 TTGGCTAGTATGGGGTCGTA 57.542 50.000 0.00 0.00 0.00 3.43
4142 4602 2.688902 TGGCTAGTATGGGGTCGTAT 57.311 50.000 0.00 0.00 0.00 3.06
4154 4614 5.787953 TGGGGTCGTATAATCGATTGTTA 57.212 39.130 20.87 9.39 41.78 2.41
4170 4630 2.546778 TGTTAATGCGCTAGGTGCTAC 58.453 47.619 9.73 0.00 40.03 3.58
4193 4653 9.773328 CTACATATAACACCTGAAAAACATGTG 57.227 33.333 0.00 0.00 45.81 3.21
4200 4660 3.957497 ACCTGAAAAACATGTGGCAGTAA 59.043 39.130 0.00 0.00 0.00 2.24
4201 4661 4.202111 ACCTGAAAAACATGTGGCAGTAAC 60.202 41.667 0.00 0.00 0.00 2.50
4202 4662 4.298332 CTGAAAAACATGTGGCAGTAACC 58.702 43.478 0.00 0.00 0.00 2.85
4203 4663 3.701542 TGAAAAACATGTGGCAGTAACCA 59.298 39.130 0.00 0.00 37.38 3.67
4204 4664 4.202101 TGAAAAACATGTGGCAGTAACCAG 60.202 41.667 0.00 0.00 41.46 4.00
4213 4673 1.443802 GCAGTAACCAGGACTTCTGC 58.556 55.000 12.18 12.18 42.05 4.26
4214 4674 1.714794 CAGTAACCAGGACTTCTGCG 58.285 55.000 0.00 0.00 42.05 5.18
4235 4695 4.894896 GGGCGGGCGAAATGGGAT 62.895 66.667 0.00 0.00 0.00 3.85
4249 4710 6.092533 GCGAAATGGGATGTTGAAATTGATTT 59.907 34.615 0.00 0.00 0.00 2.17
4261 4722 5.829986 TGAAATTGATTTCCTGGAGATGGA 58.170 37.500 4.19 0.00 44.16 3.41
4282 4743 1.833630 CTGTCTTAGCATCTGGGGTGA 59.166 52.381 0.00 0.00 0.00 4.02
4302 4764 5.163814 GGTGATTCAGAACTGTGTGAATAGC 60.164 44.000 15.06 11.64 45.22 2.97
4305 4767 7.331934 GTGATTCAGAACTGTGTGAATAGCTTA 59.668 37.037 15.06 2.68 45.22 3.09
4311 4773 8.935844 CAGAACTGTGTGAATAGCTTATACAAA 58.064 33.333 0.00 0.00 0.00 2.83
4312 4774 9.155975 AGAACTGTGTGAATAGCTTATACAAAG 57.844 33.333 0.00 0.00 33.78 2.77
4313 4775 8.848474 AACTGTGTGAATAGCTTATACAAAGT 57.152 30.769 0.00 0.63 40.53 2.66
4314 4776 9.938280 AACTGTGTGAATAGCTTATACAAAGTA 57.062 29.630 13.10 0.00 38.51 2.24
4315 4777 9.938280 ACTGTGTGAATAGCTTATACAAAGTAA 57.062 29.630 11.78 0.00 37.89 2.24
4317 4779 9.713713 TGTGTGAATAGCTTATACAAAGTAACA 57.286 29.630 0.00 0.00 0.00 2.41
4320 4782 9.685005 GTGAATAGCTTATACAAAGTAACAACG 57.315 33.333 0.00 0.00 0.00 4.10
4321 4783 9.426837 TGAATAGCTTATACAAAGTAACAACGT 57.573 29.630 0.00 0.00 0.00 3.99
4324 4786 6.814343 AGCTTATACAAAGTAACAACGTTCG 58.186 36.000 0.00 0.00 0.00 3.95
4325 4787 6.421801 AGCTTATACAAAGTAACAACGTTCGT 59.578 34.615 0.00 0.00 0.00 3.85
4326 4788 7.594758 AGCTTATACAAAGTAACAACGTTCGTA 59.405 33.333 0.00 0.00 0.00 3.43
4327 4789 8.375465 GCTTATACAAAGTAACAACGTTCGTAT 58.625 33.333 0.00 0.00 0.00 3.06
4328 4790 9.877096 CTTATACAAAGTAACAACGTTCGTATC 57.123 33.333 0.00 0.00 0.00 2.24
4329 4791 5.580911 ACAAAGTAACAACGTTCGTATCC 57.419 39.130 0.00 0.00 0.00 2.59
4330 4792 5.049167 ACAAAGTAACAACGTTCGTATCCA 58.951 37.500 0.00 0.00 0.00 3.41
4331 4793 5.697633 ACAAAGTAACAACGTTCGTATCCAT 59.302 36.000 0.00 0.00 0.00 3.41
4332 4794 6.203338 ACAAAGTAACAACGTTCGTATCCATT 59.797 34.615 0.00 0.00 0.00 3.16
4333 4795 5.773239 AGTAACAACGTTCGTATCCATTG 57.227 39.130 0.00 0.00 0.00 2.82
4334 4796 3.465122 AACAACGTTCGTATCCATTGC 57.535 42.857 0.00 0.00 0.00 3.56
4335 4797 1.735571 ACAACGTTCGTATCCATTGCC 59.264 47.619 0.00 0.00 0.00 4.52
4336 4798 1.063469 CAACGTTCGTATCCATTGCCC 59.937 52.381 0.00 0.00 0.00 5.36
4337 4799 0.250793 ACGTTCGTATCCATTGCCCA 59.749 50.000 0.00 0.00 0.00 5.36
4338 4800 1.339247 ACGTTCGTATCCATTGCCCAA 60.339 47.619 0.00 0.00 0.00 4.12
4339 4801 1.330521 CGTTCGTATCCATTGCCCAAG 59.669 52.381 0.00 0.00 0.00 3.61
4340 4802 2.639065 GTTCGTATCCATTGCCCAAGA 58.361 47.619 0.00 0.00 0.00 3.02
4341 4803 2.614057 GTTCGTATCCATTGCCCAAGAG 59.386 50.000 0.00 0.00 0.00 2.85
4342 4804 1.837439 TCGTATCCATTGCCCAAGAGT 59.163 47.619 0.00 0.00 0.00 3.24
4343 4805 3.035363 TCGTATCCATTGCCCAAGAGTA 58.965 45.455 0.00 0.00 0.00 2.59
4344 4806 3.069586 TCGTATCCATTGCCCAAGAGTAG 59.930 47.826 0.00 0.00 0.00 2.57
4347 4809 1.992557 TCCATTGCCCAAGAGTAGGTT 59.007 47.619 0.00 0.00 0.00 3.50
4358 4820 4.464597 CCAAGAGTAGGTTAGAGCAACTCT 59.535 45.833 2.23 2.23 46.69 3.24
4366 4828 0.822164 TAGAGCAACTCTAACGGGGC 59.178 55.000 1.85 0.00 39.74 5.80
4377 4839 1.958902 TAACGGGGCGCGACCTAAAT 61.959 55.000 33.64 17.35 39.10 1.40
4458 4936 0.106708 ATCGGCAGTGCGTCCAATAT 59.893 50.000 9.45 0.00 0.00 1.28
4473 4951 6.460537 GCGTCCAATATGTCGACCCATATATA 60.461 42.308 14.12 3.23 37.10 0.86
4517 4995 4.208253 CCGTTTTCCAACAAATAGCACAAC 59.792 41.667 0.00 0.00 32.54 3.32
4581 5066 7.119262 ACAAGCAAACATATAGTCCACAACTAC 59.881 37.037 0.00 0.00 43.21 2.73
4711 5199 8.608317 CATATGCTCAATCAAATCATTTTGCAA 58.392 29.630 0.00 0.00 41.66 4.08
4738 5226 5.688823 CATGTGAGTTTTCTAATCACGCAA 58.311 37.500 0.00 0.00 45.00 4.85
4789 5279 3.272364 TTGCCGCTCCTCCATGCTT 62.272 57.895 0.00 0.00 0.00 3.91
4812 5302 2.821969 GGCACAACATTCTCACCTTGAT 59.178 45.455 0.00 0.00 0.00 2.57
4915 5405 0.392461 TCCCATAGTTTCTGCGTGCC 60.392 55.000 0.00 0.00 0.00 5.01
4920 5410 0.179015 TAGTTTCTGCGTGCCCCAAA 60.179 50.000 0.00 0.00 0.00 3.28
4974 5464 2.706339 TTGCAAAACACCAAAGGCAT 57.294 40.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 166 3.988517 ACGCGTTTTGTTTTTCCTTTTCA 59.011 34.783 5.58 0.00 0.00 2.69
384 421 2.325583 AAGCAAAACCGTGACTCTCA 57.674 45.000 0.00 0.00 0.00 3.27
463 501 1.067846 GGACCGGAAGCATGGTTTTTC 60.068 52.381 9.46 5.99 38.99 2.29
578 623 2.882137 GTTTTCACCGTTGGATTCCTCA 59.118 45.455 3.95 0.00 0.00 3.86
776 821 2.619177 GAGATAAGAGAGTGCGGCAGTA 59.381 50.000 10.86 0.00 0.00 2.74
777 822 1.407258 GAGATAAGAGAGTGCGGCAGT 59.593 52.381 10.66 10.66 0.00 4.40
778 823 1.680735 AGAGATAAGAGAGTGCGGCAG 59.319 52.381 1.18 0.00 0.00 4.85
779 824 1.769026 AGAGATAAGAGAGTGCGGCA 58.231 50.000 0.00 0.00 0.00 5.69
780 825 3.992260 TTAGAGATAAGAGAGTGCGGC 57.008 47.619 0.00 0.00 0.00 6.53
800 845 2.882761 GAGAGGGCGGTAGTTTGTTTTT 59.117 45.455 0.00 0.00 0.00 1.94
841 886 2.769663 TGTAATGTCGGCCTAATGGACT 59.230 45.455 0.00 0.00 39.94 3.85
879 924 5.600898 TGGAGATGGAATTGTTATCGGAGTA 59.399 40.000 0.00 0.00 0.00 2.59
1046 1099 0.378962 GATCGTGAGTGAGTCGGAGG 59.621 60.000 0.00 0.00 0.00 4.30
1068 1121 3.126528 CGGGGTCGTACCTGATCC 58.873 66.667 1.41 0.00 39.34 3.36
1164 1538 3.718210 AACCCTTCTCGCGGCGATC 62.718 63.158 26.60 0.00 34.61 3.69
1204 1578 2.102757 GAGACTAATCGGGAGGGGAAAC 59.897 54.545 0.00 0.00 0.00 2.78
1213 1587 1.836383 CCGAAACGAGACTAATCGGG 58.164 55.000 4.67 0.00 46.97 5.14
1275 1651 2.427245 CGCTCCCCTGACCTAGGTG 61.427 68.421 22.10 5.59 45.80 4.00
1379 1756 2.443952 TCGATCCGGCCATCCTGT 60.444 61.111 2.24 0.00 0.00 4.00
1671 2096 9.113838 CTGCAACATAAGGTAAACAGATAATCT 57.886 33.333 0.00 0.00 0.00 2.40
1753 2184 6.491394 CATGCAAGCATCCATTAATTTTTGG 58.509 36.000 4.24 0.92 33.90 3.28
1755 2186 5.066764 GGCATGCAAGCATCCATTAATTTTT 59.933 36.000 21.36 0.00 33.90 1.94
1768 2199 0.815095 CAGAGATTGGCATGCAAGCA 59.185 50.000 21.36 5.42 35.83 3.91
1794 2239 7.360438 CCATTGTCAGTTAGAAAGAACTACTGC 60.360 40.741 0.00 0.00 37.57 4.40
2028 2473 3.730761 GCAGCAGTTCCAGCACCG 61.731 66.667 0.00 0.00 0.00 4.94
2117 2562 8.138712 GTGATAGATCCTGAGAAAAATACGAGT 58.861 37.037 0.00 0.00 0.00 4.18
2120 2565 7.706607 TGTGTGATAGATCCTGAGAAAAATACG 59.293 37.037 0.00 0.00 0.00 3.06
2134 2579 6.834959 ATCATGACGTTTGTGTGATAGATC 57.165 37.500 0.00 0.00 31.71 2.75
2299 2744 1.135083 ACATCTACTCCGCCAAGAACG 60.135 52.381 0.00 0.00 0.00 3.95
2368 2813 7.334090 CCTGAATTTCTCTTATCAGAAGACCA 58.666 38.462 3.34 0.00 41.38 4.02
2551 2998 6.430962 AGATATCCACATAGTCAAGTGCAT 57.569 37.500 0.00 0.00 34.48 3.96
2840 3293 1.243902 ACATCGAACATTTTGGCCGT 58.756 45.000 0.00 0.00 0.00 5.68
2866 3319 2.158885 GGGAGTAGGTTGGAAGCTCATC 60.159 54.545 0.00 0.00 37.92 2.92
2881 3334 4.870636 TGTATTTAGGAACGGAGGGAGTA 58.129 43.478 0.00 0.00 0.00 2.59
2882 3335 3.716431 TGTATTTAGGAACGGAGGGAGT 58.284 45.455 0.00 0.00 0.00 3.85
2883 3336 4.161754 ACTTGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
2884 3337 4.098894 ACTTGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2885 3338 4.161754 AGACTTGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
2886 3339 5.340439 AGACTTGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
2887 3340 7.668525 AAAAGACTTGTATTTAGGAACGGAG 57.331 36.000 0.00 0.00 0.00 4.63
2888 3341 9.558396 TTAAAAAGACTTGTATTTAGGAACGGA 57.442 29.630 0.00 0.00 0.00 4.69
2913 3366 8.932791 CCGTATGTAGTTTGTAGTGAAATCTTT 58.067 33.333 0.00 0.00 0.00 2.52
2914 3367 8.308931 TCCGTATGTAGTTTGTAGTGAAATCTT 58.691 33.333 0.00 0.00 0.00 2.40
2915 3368 7.833786 TCCGTATGTAGTTTGTAGTGAAATCT 58.166 34.615 0.00 0.00 0.00 2.40
2916 3369 8.540492 CATCCGTATGTAGTTTGTAGTGAAATC 58.460 37.037 0.00 0.00 0.00 2.17
2917 3370 8.038944 ACATCCGTATGTAGTTTGTAGTGAAAT 58.961 33.333 0.00 0.00 44.66 2.17
2918 3371 7.380536 ACATCCGTATGTAGTTTGTAGTGAAA 58.619 34.615 0.00 0.00 44.66 2.69
2919 3372 6.927416 ACATCCGTATGTAGTTTGTAGTGAA 58.073 36.000 0.00 0.00 44.66 3.18
2920 3373 6.519679 ACATCCGTATGTAGTTTGTAGTGA 57.480 37.500 0.00 0.00 44.66 3.41
2957 3410 9.453572 AGCAAAATGAATGAATCTACACTCTAA 57.546 29.630 0.00 0.00 0.00 2.10
2958 3411 9.102757 GAGCAAAATGAATGAATCTACACTCTA 57.897 33.333 0.00 0.00 0.00 2.43
2959 3412 7.066766 GGAGCAAAATGAATGAATCTACACTCT 59.933 37.037 0.00 0.00 0.00 3.24
2960 3413 7.192232 GGAGCAAAATGAATGAATCTACACTC 58.808 38.462 0.00 0.00 0.00 3.51
2961 3414 6.183360 CGGAGCAAAATGAATGAATCTACACT 60.183 38.462 0.00 0.00 0.00 3.55
2962 3415 5.967674 CGGAGCAAAATGAATGAATCTACAC 59.032 40.000 0.00 0.00 0.00 2.90
2963 3416 5.647658 ACGGAGCAAAATGAATGAATCTACA 59.352 36.000 0.00 0.00 0.00 2.74
2964 3417 6.124088 ACGGAGCAAAATGAATGAATCTAC 57.876 37.500 0.00 0.00 0.00 2.59
2965 3418 7.498900 ACATACGGAGCAAAATGAATGAATCTA 59.501 33.333 0.00 0.00 0.00 1.98
2966 3419 6.319658 ACATACGGAGCAAAATGAATGAATCT 59.680 34.615 0.00 0.00 0.00 2.40
2967 3420 6.498304 ACATACGGAGCAAAATGAATGAATC 58.502 36.000 0.00 0.00 0.00 2.52
2968 3421 6.455360 ACATACGGAGCAAAATGAATGAAT 57.545 33.333 0.00 0.00 0.00 2.57
2969 3422 5.895636 ACATACGGAGCAAAATGAATGAA 57.104 34.783 0.00 0.00 0.00 2.57
2970 3423 6.112734 ACTACATACGGAGCAAAATGAATGA 58.887 36.000 0.00 0.00 0.00 2.57
2971 3424 6.258727 AGACTACATACGGAGCAAAATGAATG 59.741 38.462 0.00 0.00 0.00 2.67
2972 3425 6.349300 AGACTACATACGGAGCAAAATGAAT 58.651 36.000 0.00 0.00 0.00 2.57
2973 3426 5.730550 AGACTACATACGGAGCAAAATGAA 58.269 37.500 0.00 0.00 0.00 2.57
2974 3427 5.339008 AGACTACATACGGAGCAAAATGA 57.661 39.130 0.00 0.00 0.00 2.57
2975 3428 8.082852 ACTATAGACTACATACGGAGCAAAATG 58.917 37.037 6.78 0.00 0.00 2.32
2976 3429 8.082852 CACTATAGACTACATACGGAGCAAAAT 58.917 37.037 6.78 0.00 0.00 1.82
2977 3430 7.067859 ACACTATAGACTACATACGGAGCAAAA 59.932 37.037 6.78 0.00 0.00 2.44
2978 3431 6.544931 ACACTATAGACTACATACGGAGCAAA 59.455 38.462 6.78 0.00 0.00 3.68
2979 3432 6.060136 ACACTATAGACTACATACGGAGCAA 58.940 40.000 6.78 0.00 0.00 3.91
2980 3433 5.618236 ACACTATAGACTACATACGGAGCA 58.382 41.667 6.78 0.00 0.00 4.26
2981 3434 7.664082 TTACACTATAGACTACATACGGAGC 57.336 40.000 6.78 0.00 0.00 4.70
2982 3435 9.656040 AGATTACACTATAGACTACATACGGAG 57.344 37.037 6.78 0.00 0.00 4.63
2983 3436 9.650539 GAGATTACACTATAGACTACATACGGA 57.349 37.037 6.78 0.00 0.00 4.69
2984 3437 9.656040 AGAGATTACACTATAGACTACATACGG 57.344 37.037 6.78 0.00 0.00 4.02
3011 3464 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
3012 3465 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
3013 3466 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3014 3467 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3015 3468 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3016 3469 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3017 3470 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3018 3471 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3019 3472 8.731591 AATACTCCCTCCGTTCCTAAATATAA 57.268 34.615 0.00 0.00 0.00 0.98
3020 3473 8.731591 AAATACTCCCTCCGTTCCTAAATATA 57.268 34.615 0.00 0.00 0.00 0.86
3021 3474 7.256583 GGAAATACTCCCTCCGTTCCTAAATAT 60.257 40.741 0.00 0.00 38.44 1.28
3022 3475 6.042437 GGAAATACTCCCTCCGTTCCTAAATA 59.958 42.308 0.00 0.00 38.44 1.40
3023 3476 5.163227 GGAAATACTCCCTCCGTTCCTAAAT 60.163 44.000 0.00 0.00 38.44 1.40
3024 3477 4.162888 GGAAATACTCCCTCCGTTCCTAAA 59.837 45.833 0.00 0.00 38.44 1.85
3025 3478 3.708121 GGAAATACTCCCTCCGTTCCTAA 59.292 47.826 0.00 0.00 38.44 2.69
3026 3479 3.052338 AGGAAATACTCCCTCCGTTCCTA 60.052 47.826 0.95 0.00 46.81 2.94
3027 3480 2.117051 GGAAATACTCCCTCCGTTCCT 58.883 52.381 0.00 0.00 38.44 3.36
3028 3481 2.117051 AGGAAATACTCCCTCCGTTCC 58.883 52.381 0.00 0.00 46.81 3.62
3029 3482 2.500504 ACAGGAAATACTCCCTCCGTTC 59.499 50.000 0.00 0.00 46.81 3.95
3030 3483 2.547990 ACAGGAAATACTCCCTCCGTT 58.452 47.619 0.00 0.00 46.81 4.44
3031 3484 2.249309 ACAGGAAATACTCCCTCCGT 57.751 50.000 0.00 0.00 46.81 4.69
3032 3485 3.629142 AAACAGGAAATACTCCCTCCG 57.371 47.619 0.00 0.00 46.81 4.63
3033 3486 4.017126 CCAAAACAGGAAATACTCCCTCC 58.983 47.826 0.00 0.00 46.81 4.30
3034 3487 4.663334 ACCAAAACAGGAAATACTCCCTC 58.337 43.478 0.00 0.00 46.81 4.30
3035 3488 4.508584 GGACCAAAACAGGAAATACTCCCT 60.509 45.833 0.00 0.00 46.81 4.20
3036 3489 3.762288 GGACCAAAACAGGAAATACTCCC 59.238 47.826 0.00 0.00 46.81 4.30
3037 3490 4.663334 AGGACCAAAACAGGAAATACTCC 58.337 43.478 0.00 0.00 45.81 3.85
3038 3491 5.768164 TGAAGGACCAAAACAGGAAATACTC 59.232 40.000 0.00 0.00 0.00 2.59
3039 3492 5.701224 TGAAGGACCAAAACAGGAAATACT 58.299 37.500 0.00 0.00 0.00 2.12
3040 3493 6.590234 ATGAAGGACCAAAACAGGAAATAC 57.410 37.500 0.00 0.00 0.00 1.89
3089 3542 6.594547 GGAACAGAGGGAGTAGAATTTACAAC 59.405 42.308 0.00 0.00 0.00 3.32
3100 3553 9.364653 GACTTATATTTAGGAACAGAGGGAGTA 57.635 37.037 0.00 0.00 0.00 2.59
3101 3554 8.068733 AGACTTATATTTAGGAACAGAGGGAGT 58.931 37.037 0.00 0.00 0.00 3.85
3102 3555 8.485578 AGACTTATATTTAGGAACAGAGGGAG 57.514 38.462 0.00 0.00 0.00 4.30
3103 3556 8.855804 AAGACTTATATTTAGGAACAGAGGGA 57.144 34.615 0.00 0.00 0.00 4.20
3250 3704 7.400339 TGAGAATTTGACTTACTACTCCATCCT 59.600 37.037 0.00 0.00 0.00 3.24
3254 3708 7.732025 TGTTGAGAATTTGACTTACTACTCCA 58.268 34.615 0.00 0.00 0.00 3.86
3317 3771 9.503427 CTTATAATTTTCCCAAAAACTCTAGCG 57.497 33.333 0.00 0.00 37.20 4.26
3380 3839 4.400120 ACACCTGCCCTTAATTAACGAAA 58.600 39.130 0.00 0.00 0.00 3.46
3384 3843 2.096980 GCGACACCTGCCCTTAATTAAC 59.903 50.000 0.00 0.00 0.00 2.01
3385 3844 2.026636 AGCGACACCTGCCCTTAATTAA 60.027 45.455 0.00 0.00 0.00 1.40
3539 3998 6.782988 TGTGTTCCCCTGGAATTATTAACAAA 59.217 34.615 0.00 0.00 44.04 2.83
3704 4164 7.329471 GCAAACAAGAGAAGGGATATCAAAAAC 59.671 37.037 4.83 0.00 0.00 2.43
3705 4165 7.015098 TGCAAACAAGAGAAGGGATATCAAAAA 59.985 33.333 4.83 0.00 0.00 1.94
3822 4282 2.949451 AGCATGACTACTTGACCGAG 57.051 50.000 0.00 0.00 0.00 4.63
3827 4287 6.801377 CGCAAATTTTTAGCATGACTACTTGA 59.199 34.615 0.00 0.00 0.00 3.02
3832 4292 4.082517 TGGCGCAAATTTTTAGCATGACTA 60.083 37.500 10.83 0.00 0.00 2.59
3844 4304 6.375945 AAAAAGAAGAAATGGCGCAAATTT 57.624 29.167 17.23 17.23 0.00 1.82
3926 4386 7.119846 AGACAGTTTAACATAAAGGTCTGCATC 59.880 37.037 12.58 0.00 33.48 3.91
3960 4420 8.867112 TTAGATTCATAGACGATAACACCAAC 57.133 34.615 0.00 0.00 0.00 3.77
4064 4524 2.586425 ACCTCCCACACAATTTGACTG 58.414 47.619 2.79 0.00 0.00 3.51
4068 4528 5.720371 TTATGAACCTCCCACACAATTTG 57.280 39.130 0.00 0.00 0.00 2.32
4103 4563 3.933332 CCAATCTTCAGGAACCGAGTTAC 59.067 47.826 0.00 0.00 0.00 2.50
4105 4565 2.876079 GCCAATCTTCAGGAACCGAGTT 60.876 50.000 0.00 0.00 0.00 3.01
4110 4570 3.636153 ACTAGCCAATCTTCAGGAACC 57.364 47.619 0.00 0.00 0.00 3.62
4112 4572 4.103153 CCCATACTAGCCAATCTTCAGGAA 59.897 45.833 0.00 0.00 0.00 3.36
4133 4593 6.401796 GCATTAACAATCGATTATACGACCCC 60.402 42.308 10.97 0.00 44.84 4.95
4134 4594 6.531439 GCATTAACAATCGATTATACGACCC 58.469 40.000 10.97 0.00 44.84 4.46
4135 4595 6.231365 CGCATTAACAATCGATTATACGACC 58.769 40.000 10.97 0.00 44.84 4.79
4136 4596 5.722141 GCGCATTAACAATCGATTATACGAC 59.278 40.000 10.97 1.20 44.84 4.34
4137 4597 5.631929 AGCGCATTAACAATCGATTATACGA 59.368 36.000 11.47 0.00 46.04 3.43
4138 4598 5.843442 AGCGCATTAACAATCGATTATACG 58.157 37.500 11.47 8.43 0.00 3.06
4139 4599 7.063074 ACCTAGCGCATTAACAATCGATTATAC 59.937 37.037 11.47 0.00 0.00 1.47
4140 4600 7.062956 CACCTAGCGCATTAACAATCGATTATA 59.937 37.037 11.47 4.59 0.00 0.98
4141 4601 5.932303 ACCTAGCGCATTAACAATCGATTAT 59.068 36.000 11.47 5.61 0.00 1.28
4142 4602 5.176774 CACCTAGCGCATTAACAATCGATTA 59.823 40.000 11.47 0.00 0.00 1.75
4180 4640 4.202101 TGGTTACTGCCACATGTTTTTCAG 60.202 41.667 0.00 3.83 32.81 3.02
4181 4641 3.701542 TGGTTACTGCCACATGTTTTTCA 59.298 39.130 0.00 0.00 32.81 2.69
4182 4642 4.298332 CTGGTTACTGCCACATGTTTTTC 58.702 43.478 0.00 0.00 34.36 2.29
4193 4653 1.946283 GCAGAAGTCCTGGTTACTGCC 60.946 57.143 18.72 4.38 42.91 4.85
4200 4660 4.021925 GCCCGCAGAAGTCCTGGT 62.022 66.667 0.00 0.00 43.13 4.00
4234 4694 7.364408 CCATCTCCAGGAAATCAATTTCAACAT 60.364 37.037 15.35 0.00 46.03 2.71
4235 4695 6.071221 CCATCTCCAGGAAATCAATTTCAACA 60.071 38.462 15.35 0.00 46.03 3.33
4249 4710 2.630889 AAGACAGTCCATCTCCAGGA 57.369 50.000 0.00 0.00 0.00 3.86
4261 4722 1.556911 CACCCCAGATGCTAAGACAGT 59.443 52.381 0.00 0.00 0.00 3.55
4282 4743 9.319143 GTATAAGCTATTCACACAGTTCTGAAT 57.681 33.333 6.83 7.93 39.79 2.57
4302 4764 9.877096 GATACGAACGTTGTTACTTTGTATAAG 57.123 33.333 5.00 0.00 30.54 1.73
4305 4767 6.867816 TGGATACGAACGTTGTTACTTTGTAT 59.132 34.615 5.00 0.00 42.51 2.29
4311 4773 4.092383 GCAATGGATACGAACGTTGTTACT 59.908 41.667 5.00 0.00 42.51 2.24
4312 4774 4.328667 GCAATGGATACGAACGTTGTTAC 58.671 43.478 5.00 2.62 42.51 2.50
4313 4775 3.371591 GGCAATGGATACGAACGTTGTTA 59.628 43.478 5.00 0.00 42.51 2.41
4314 4776 2.160813 GGCAATGGATACGAACGTTGTT 59.839 45.455 5.00 0.00 42.51 2.83
4315 4777 1.735571 GGCAATGGATACGAACGTTGT 59.264 47.619 5.00 7.08 42.51 3.32
4316 4778 1.063469 GGGCAATGGATACGAACGTTG 59.937 52.381 5.00 0.24 42.51 4.10
4317 4779 1.339247 TGGGCAATGGATACGAACGTT 60.339 47.619 0.00 0.00 42.51 3.99
4318 4780 0.250793 TGGGCAATGGATACGAACGT 59.749 50.000 5.03 5.03 42.51 3.99
4319 4781 1.330521 CTTGGGCAATGGATACGAACG 59.669 52.381 0.00 0.00 42.51 3.95
4320 4782 2.614057 CTCTTGGGCAATGGATACGAAC 59.386 50.000 0.00 0.00 42.51 3.95
4321 4783 2.238646 ACTCTTGGGCAATGGATACGAA 59.761 45.455 0.00 0.00 42.51 3.85
4322 4784 1.837439 ACTCTTGGGCAATGGATACGA 59.163 47.619 0.00 0.00 42.51 3.43
4323 4785 2.332063 ACTCTTGGGCAATGGATACG 57.668 50.000 0.00 0.00 42.51 3.06
4324 4786 3.136626 ACCTACTCTTGGGCAATGGATAC 59.863 47.826 0.00 0.00 0.00 2.24
4325 4787 3.393687 ACCTACTCTTGGGCAATGGATA 58.606 45.455 0.00 0.00 0.00 2.59
4326 4788 2.208872 ACCTACTCTTGGGCAATGGAT 58.791 47.619 0.00 0.00 0.00 3.41
4327 4789 1.668826 ACCTACTCTTGGGCAATGGA 58.331 50.000 0.00 0.00 0.00 3.41
4328 4790 2.514458 AACCTACTCTTGGGCAATGG 57.486 50.000 0.00 0.00 0.00 3.16
4329 4791 4.446371 CTCTAACCTACTCTTGGGCAATG 58.554 47.826 0.00 0.00 0.00 2.82
4330 4792 3.118223 GCTCTAACCTACTCTTGGGCAAT 60.118 47.826 0.00 0.00 0.00 3.56
4331 4793 2.236395 GCTCTAACCTACTCTTGGGCAA 59.764 50.000 0.00 0.00 0.00 4.52
4332 4794 1.831736 GCTCTAACCTACTCTTGGGCA 59.168 52.381 0.00 0.00 0.00 5.36
4333 4795 1.831736 TGCTCTAACCTACTCTTGGGC 59.168 52.381 0.00 0.00 0.00 5.36
4334 4796 3.515901 AGTTGCTCTAACCTACTCTTGGG 59.484 47.826 0.00 0.00 40.24 4.12
4335 4797 4.464597 AGAGTTGCTCTAACCTACTCTTGG 59.535 45.833 0.00 0.00 40.70 3.61
4336 4798 5.652994 AGAGTTGCTCTAACCTACTCTTG 57.347 43.478 0.00 0.00 40.70 3.02
4347 4809 0.822164 GCCCCGTTAGAGTTGCTCTA 59.178 55.000 2.07 2.07 41.50 2.43
4358 4820 1.958902 ATTTAGGTCGCGCCCCGTTA 61.959 55.000 0.72 0.00 38.26 3.18
4365 4827 2.522638 CCGTCCATTTAGGTCGCGC 61.523 63.158 0.00 0.00 45.75 6.86
4366 4828 2.522638 GCCGTCCATTTAGGTCGCG 61.523 63.158 0.00 0.00 45.75 5.87
4377 4839 2.975799 GGACAAAAGCGCCGTCCA 60.976 61.111 23.43 0.00 46.98 4.02
4420 4898 3.947834 CGATCCAAATCTTAAACAGGGCT 59.052 43.478 0.00 0.00 0.00 5.19
4430 4908 1.098050 GCACTGCCGATCCAAATCTT 58.902 50.000 0.00 0.00 0.00 2.40
4458 4936 2.821378 CACCGGTATATATGGGTCGACA 59.179 50.000 18.91 0.00 0.00 4.35
4489 4967 1.668101 TTTGTTGGAAAACGGCGGCT 61.668 50.000 13.24 0.00 0.00 5.52
4496 4974 6.902224 AAGTTGTGCTATTTGTTGGAAAAC 57.098 33.333 0.00 0.00 0.00 2.43
4501 4979 4.569966 TGCAAAAGTTGTGCTATTTGTTGG 59.430 37.500 18.72 0.00 42.69 3.77
4517 4995 7.467557 AGTTGTGTGTGAAATAATGCAAAAG 57.532 32.000 0.00 0.00 0.00 2.27
4670 5158 2.889045 GCATATGTGGGCTCATGTTGAT 59.111 45.455 4.29 0.00 0.00 2.57
4711 5199 6.317088 CGTGATTAGAAAACTCACATGCAAT 58.683 36.000 0.00 0.00 39.36 3.56
4738 5226 8.585471 ACAATTCACCTAATTTCATCATGACT 57.415 30.769 0.00 0.00 35.54 3.41
4789 5279 3.072330 TCAAGGTGAGAATGTTGTGCCTA 59.928 43.478 0.00 0.00 0.00 3.93
4812 5302 5.125097 GTCTCTACGATCAAGGGTTTCAGTA 59.875 44.000 0.00 0.00 0.00 2.74
4915 5405 5.160607 TCGGTATCCTGCTAATATTTGGG 57.839 43.478 0.00 0.00 0.00 4.12
4920 5410 3.353557 TCGCTCGGTATCCTGCTAATAT 58.646 45.455 0.00 0.00 0.00 1.28
4974 5464 1.654954 GCTAGGAAGGACGTCGAGCA 61.655 60.000 9.92 0.00 31.03 4.26


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

AutoCloner maintained by Alex Coulton.