Multiple sequence alignment - TraesCS3B01G276800

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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 TraesCS3B01G276800 chr3B 100.000 2404 0 0 1 2404 447001886 447004289 0.000000e+00 4440.0
1 TraesCS3B01G276800 chr3B 100.000 2193 0 0 2727 4919 447004612 447006804 0.000000e+00 4050.0
2 TraesCS3B01G276800 chr3B 81.690 568 75 15 337 887 407205919 407205364 3.490000e-121 446.0
3 TraesCS3B01G276800 chr3B 76.765 680 96 35 327 959 790599151 790599815 1.710000e-84 324.0
4 TraesCS3B01G276800 chr3B 80.420 286 36 7 531 796 42728206 42727921 3.000000e-47 200.0
5 TraesCS3B01G276800 chr3D 97.994 2094 23 4 2832 4919 346974654 346976734 0.000000e+00 3616.0
6 TraesCS3B01G276800 chr3D 97.182 887 23 1 1078 1962 346973249 346974135 0.000000e+00 1498.0
7 TraesCS3B01G276800 chr3D 91.034 435 23 3 1979 2404 346974226 346974653 1.540000e-159 573.0
8 TraesCS3B01G276800 chr3D 79.467 638 92 17 326 936 16022136 16022761 2.740000e-112 416.0
9 TraesCS3B01G276800 chr3D 79.929 563 77 16 351 880 312885090 312885649 9.990000e-102 381.0
10 TraesCS3B01G276800 chr3D 89.524 105 10 1 2727 2830 467844365 467844469 1.110000e-26 132.0
11 TraesCS3B01G276800 chr3D 95.122 41 2 0 326 366 142639390 142639350 1.140000e-06 65.8
12 TraesCS3B01G276800 chr3A 96.408 2088 56 3 2832 4919 466108184 466110252 0.000000e+00 3422.0
13 TraesCS3B01G276800 chr3A 97.592 955 16 3 1014 1962 466106721 466107674 0.000000e+00 1629.0
14 TraesCS3B01G276800 chr3A 93.427 426 21 1 1979 2404 466107765 466108183 4.180000e-175 625.0
15 TraesCS3B01G276800 chr3A 85.103 631 68 15 386 995 466097832 466098457 5.410000e-174 621.0
16 TraesCS3B01G276800 chr3A 82.303 469 62 11 528 975 657227720 657227252 2.150000e-103 387.0
17 TraesCS3B01G276800 chr1D 83.058 667 77 12 326 959 341181327 341180664 1.540000e-159 573.0
18 TraesCS3B01G276800 chr1D 81.058 586 80 17 326 880 411398468 411399053 5.850000e-119 438.0
19 TraesCS3B01G276800 chr1A 81.431 657 76 25 326 942 549489715 549489065 3.420000e-136 496.0
20 TraesCS3B01G276800 chr6D 83.480 454 54 10 351 788 275942414 275941966 2.130000e-108 403.0
21 TraesCS3B01G276800 chr7B 78.906 640 96 17 361 964 532487139 532486503 9.920000e-107 398.0
22 TraesCS3B01G276800 chr7B 74.513 667 114 32 328 959 55057739 55057094 6.360000e-59 239.0
23 TraesCS3B01G276800 chr5D 82.255 479 49 19 530 975 106685427 106685902 9.990000e-102 381.0
24 TraesCS3B01G276800 chr5D 75.873 659 97 35 351 969 564447430 564448066 3.750000e-71 279.0
25 TraesCS3B01G276800 chr5D 79.880 333 36 14 660 978 361602979 361602664 1.070000e-51 215.0
26 TraesCS3B01G276800 chr5D 91.429 105 9 0 2727 2831 435347532 435347636 1.430000e-30 145.0
27 TraesCS3B01G276800 chr7D 78.404 639 93 29 351 978 172265318 172264714 1.670000e-99 374.0
28 TraesCS3B01G276800 chr7D 76.551 661 114 17 347 978 24160904 24160256 1.710000e-84 324.0
29 TraesCS3B01G276800 chr7D 76.149 348 50 13 619 934 109178195 109178541 8.530000e-33 152.0
30 TraesCS3B01G276800 chr5A 78.111 667 81 26 351 981 109939656 109939019 3.620000e-96 363.0
31 TraesCS3B01G276800 chr5A 96.190 105 4 0 2727 2831 607806544 607806648 6.550000e-39 172.0
32 TraesCS3B01G276800 chr4A 79.604 505 65 10 326 796 582429220 582428720 1.320000e-85 327.0
33 TraesCS3B01G276800 chr2A 76.696 575 79 25 326 871 604796578 604797126 8.120000e-68 268.0
34 TraesCS3B01G276800 chr2D 79.830 352 39 15 619 940 351047935 351048284 1.380000e-55 228.0
35 TraesCS3B01G276800 chr2D 82.707 133 20 3 100 232 535558993 535558864 1.120000e-21 115.0
36 TraesCS3B01G276800 chr4B 84.127 189 30 0 43 231 17465836 17465648 3.020000e-42 183.0
37 TraesCS3B01G276800 chr4B 73.701 616 89 42 373 937 560890646 560891239 6.550000e-39 172.0
38 TraesCS3B01G276800 chr5B 83.598 189 31 0 43 231 69543769 69543957 1.410000e-40 178.0
39 TraesCS3B01G276800 chr5B 80.717 223 32 9 751 969 470523423 470523208 3.940000e-36 163.0
40 TraesCS3B01G276800 chr6A 83.246 191 26 5 45 233 503841502 503841316 2.350000e-38 171.0
41 TraesCS3B01G276800 chr6A 81.250 144 19 7 580 717 531720743 531720602 5.210000e-20 110.0
42 TraesCS3B01G276800 chr2B 80.000 190 35 3 43 230 458617688 458617876 2.390000e-28 137.0
43 TraesCS3B01G276800 chr2B 77.536 138 26 5 96 232 783235789 783235922 1.470000e-10 78.7
44 TraesCS3B01G276800 chr1B 78.882 161 33 1 45 205 531635947 531635788 1.870000e-19 108.0


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 TraesCS3B01G276800 chr3B 447001886 447006804 4918 False 4245.000000 4440 100.000000 1 4919 2 chr3B.!!$F2 4918
1 TraesCS3B01G276800 chr3B 407205364 407205919 555 True 446.000000 446 81.690000 337 887 1 chr3B.!!$R2 550
2 TraesCS3B01G276800 chr3B 790599151 790599815 664 False 324.000000 324 76.765000 327 959 1 chr3B.!!$F1 632
3 TraesCS3B01G276800 chr3D 346973249 346976734 3485 False 1895.666667 3616 95.403333 1078 4919 3 chr3D.!!$F4 3841
4 TraesCS3B01G276800 chr3D 16022136 16022761 625 False 416.000000 416 79.467000 326 936 1 chr3D.!!$F1 610
5 TraesCS3B01G276800 chr3D 312885090 312885649 559 False 381.000000 381 79.929000 351 880 1 chr3D.!!$F2 529
6 TraesCS3B01G276800 chr3A 466106721 466110252 3531 False 1892.000000 3422 95.809000 1014 4919 3 chr3A.!!$F2 3905
7 TraesCS3B01G276800 chr3A 466097832 466098457 625 False 621.000000 621 85.103000 386 995 1 chr3A.!!$F1 609
8 TraesCS3B01G276800 chr1D 341180664 341181327 663 True 573.000000 573 83.058000 326 959 1 chr1D.!!$R1 633
9 TraesCS3B01G276800 chr1D 411398468 411399053 585 False 438.000000 438 81.058000 326 880 1 chr1D.!!$F1 554
10 TraesCS3B01G276800 chr1A 549489065 549489715 650 True 496.000000 496 81.431000 326 942 1 chr1A.!!$R1 616
11 TraesCS3B01G276800 chr7B 532486503 532487139 636 True 398.000000 398 78.906000 361 964 1 chr7B.!!$R2 603
12 TraesCS3B01G276800 chr7B 55057094 55057739 645 True 239.000000 239 74.513000 328 959 1 chr7B.!!$R1 631
13 TraesCS3B01G276800 chr5D 564447430 564448066 636 False 279.000000 279 75.873000 351 969 1 chr5D.!!$F3 618
14 TraesCS3B01G276800 chr7D 172264714 172265318 604 True 374.000000 374 78.404000 351 978 1 chr7D.!!$R2 627
15 TraesCS3B01G276800 chr7D 24160256 24160904 648 True 324.000000 324 76.551000 347 978 1 chr7D.!!$R1 631
16 TraesCS3B01G276800 chr5A 109939019 109939656 637 True 363.000000 363 78.111000 351 981 1 chr5A.!!$R1 630
17 TraesCS3B01G276800 chr4A 582428720 582429220 500 True 327.000000 327 79.604000 326 796 1 chr4A.!!$R1 470
18 TraesCS3B01G276800 chr2A 604796578 604797126 548 False 268.000000 268 76.696000 326 871 1 chr2A.!!$F1 545

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
64 65 0.034767 ACGTAGGACTGACGATGGGA 60.035 55.0 1.71 0.00 42.98 4.37 F
112 113 0.039764 TGGTCTGACGGACATCTCCT 59.960 55.0 16.20 0.00 46.16 3.69 F
225 226 0.105453 TAGCCCATCCACCTCCTCTC 60.105 60.0 0.00 0.00 0.00 3.20 F
1543 1728 0.169009 GTTCGGTGAAATGCCTGAGC 59.831 55.0 0.00 0.00 40.48 4.26 F
1787 1972 0.329261 TGCAAGGAAGGAGATGTGGG 59.671 55.0 0.00 0.00 0.00 4.61 F
2757 3027 0.880278 CGTTGGACCACTGACAGGTG 60.880 60.0 7.51 2.99 40.09 4.00 F
2794 3064 0.035152 GCCCATGTGTCAGTGATGGA 60.035 55.0 11.39 0.00 39.29 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1543 1728 1.008652 TGTACGACACCACGTTCCG 60.009 57.895 0.00 0.00 44.14 4.30 R
1787 1972 1.527433 AAAAAGCTTCCTGGCGCTCC 61.527 55.000 7.64 0.00 34.96 4.70 R
2054 2315 7.982354 GCTCACTAGAGGTATAAAATTGACACT 59.018 37.037 0.00 0.00 42.33 3.55 R
2775 3045 0.035152 TCCATCACTGACACATGGGC 60.035 55.000 0.00 0.00 38.13 5.36 R
2780 3050 0.602638 GCCGTTCCATCACTGACACA 60.603 55.000 0.00 0.00 0.00 3.72 R
3559 3829 1.065410 TGAGTCTTGGAAGCCCCCAA 61.065 55.000 7.14 7.14 43.42 4.12 R
4729 5001 2.417933 CAGCAGCTAGACCAATGTTGTC 59.582 50.000 0.00 0.00 0.00 3.18 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
25 26 4.556233 TCTAATCCAAATATGAGGCGTCG 58.444 43.478 1.39 0.00 0.00 5.12
26 27 2.169832 ATCCAAATATGAGGCGTCGG 57.830 50.000 1.39 0.00 0.00 4.79
27 28 0.105964 TCCAAATATGAGGCGTCGGG 59.894 55.000 1.39 0.00 0.00 5.14
28 29 0.884704 CCAAATATGAGGCGTCGGGG 60.885 60.000 1.39 0.00 0.00 5.73
29 30 1.227853 AAATATGAGGCGTCGGGGC 60.228 57.895 1.39 0.00 42.69 5.80
49 50 4.323477 GCCTGGGTGTGCCACGTA 62.323 66.667 0.00 0.00 34.83 3.57
50 51 2.047274 CCTGGGTGTGCCACGTAG 60.047 66.667 0.00 0.00 34.83 3.51
51 52 2.047274 CTGGGTGTGCCACGTAGG 60.047 66.667 0.00 0.00 41.84 3.18
52 53 2.524640 TGGGTGTGCCACGTAGGA 60.525 61.111 8.04 0.00 41.22 2.94
53 54 2.047560 GGGTGTGCCACGTAGGAC 60.048 66.667 0.00 0.00 41.22 3.85
54 55 2.580601 GGGTGTGCCACGTAGGACT 61.581 63.158 7.20 0.00 41.22 3.85
55 56 1.374252 GGTGTGCCACGTAGGACTG 60.374 63.158 7.20 0.00 41.22 3.51
56 57 1.663739 GTGTGCCACGTAGGACTGA 59.336 57.895 7.20 0.00 41.22 3.41
57 58 0.666577 GTGTGCCACGTAGGACTGAC 60.667 60.000 7.20 0.00 41.22 3.51
58 59 1.443872 GTGCCACGTAGGACTGACG 60.444 63.158 8.04 0.00 45.75 4.35
59 60 1.601477 TGCCACGTAGGACTGACGA 60.601 57.895 8.04 0.00 42.98 4.20
60 61 0.963856 TGCCACGTAGGACTGACGAT 60.964 55.000 8.04 0.00 42.98 3.73
61 62 0.525668 GCCACGTAGGACTGACGATG 60.526 60.000 8.04 0.00 42.98 3.84
62 63 0.100682 CCACGTAGGACTGACGATGG 59.899 60.000 1.71 2.86 42.98 3.51
63 64 0.100682 CACGTAGGACTGACGATGGG 59.899 60.000 1.71 0.00 42.98 4.00
64 65 0.034767 ACGTAGGACTGACGATGGGA 60.035 55.000 1.71 0.00 42.98 4.37
65 66 1.319541 CGTAGGACTGACGATGGGAT 58.680 55.000 0.00 0.00 42.98 3.85
66 67 1.267261 CGTAGGACTGACGATGGGATC 59.733 57.143 0.00 0.00 42.98 3.36
67 68 1.614413 GTAGGACTGACGATGGGATCC 59.386 57.143 1.92 1.92 0.00 3.36
68 69 0.760945 AGGACTGACGATGGGATCCC 60.761 60.000 25.22 25.22 0.00 3.85
82 83 3.000819 TCCCACGTGGAATCGCCT 61.001 61.111 36.07 0.00 41.40 5.52
83 84 1.683025 TCCCACGTGGAATCGCCTA 60.683 57.895 36.07 7.39 41.40 3.93
84 85 1.227263 CCCACGTGGAATCGCCTAG 60.227 63.158 36.07 11.77 37.39 3.02
85 86 1.672854 CCCACGTGGAATCGCCTAGA 61.673 60.000 36.07 0.00 37.39 2.43
86 87 0.174845 CCACGTGGAATCGCCTAGAA 59.825 55.000 31.31 0.00 37.39 2.10
87 88 1.404986 CCACGTGGAATCGCCTAGAAA 60.405 52.381 31.31 0.00 37.39 2.52
88 89 1.659098 CACGTGGAATCGCCTAGAAAC 59.341 52.381 7.95 0.00 37.63 2.78
89 90 1.287425 CGTGGAATCGCCTAGAAACC 58.713 55.000 0.00 0.00 37.63 3.27
90 91 1.134788 CGTGGAATCGCCTAGAAACCT 60.135 52.381 0.00 0.00 37.63 3.50
91 92 2.280628 GTGGAATCGCCTAGAAACCTG 58.719 52.381 0.00 0.00 37.63 4.00
92 93 2.093658 GTGGAATCGCCTAGAAACCTGA 60.094 50.000 0.00 0.00 37.63 3.86
93 94 2.771943 TGGAATCGCCTAGAAACCTGAT 59.228 45.455 0.00 0.00 37.63 2.90
94 95 3.134458 GGAATCGCCTAGAAACCTGATG 58.866 50.000 0.00 0.00 0.00 3.07
95 96 2.918712 ATCGCCTAGAAACCTGATGG 57.081 50.000 0.00 0.00 39.83 3.51
104 105 4.865629 ACCTGATGGTCTGACGGA 57.134 55.556 1.07 0.00 44.78 4.69
105 106 2.277858 ACCTGATGGTCTGACGGAC 58.722 57.895 5.81 5.81 44.78 4.79
106 107 0.541998 ACCTGATGGTCTGACGGACA 60.542 55.000 16.20 3.22 44.78 4.02
107 108 0.826715 CCTGATGGTCTGACGGACAT 59.173 55.000 16.20 7.73 46.16 3.06
108 109 1.202463 CCTGATGGTCTGACGGACATC 60.202 57.143 16.20 15.36 46.16 3.06
109 110 1.753649 CTGATGGTCTGACGGACATCT 59.246 52.381 16.20 0.00 46.16 2.90
110 111 1.751351 TGATGGTCTGACGGACATCTC 59.249 52.381 16.20 9.34 46.16 2.75
111 112 1.067821 GATGGTCTGACGGACATCTCC 59.932 57.143 16.20 0.00 46.16 3.71
112 113 0.039764 TGGTCTGACGGACATCTCCT 59.960 55.000 16.20 0.00 46.16 3.69
113 114 0.741915 GGTCTGACGGACATCTCCTC 59.258 60.000 16.20 0.00 46.16 3.71
114 115 0.741915 GTCTGACGGACATCTCCTCC 59.258 60.000 9.65 0.00 43.94 4.30
118 119 2.716244 CGGACATCTCCTCCGTCG 59.284 66.667 0.00 0.00 44.82 5.12
119 120 2.413765 GGACATCTCCTCCGTCGC 59.586 66.667 0.00 0.00 33.07 5.19
120 121 2.122167 GGACATCTCCTCCGTCGCT 61.122 63.158 0.00 0.00 33.07 4.93
121 122 1.064946 GACATCTCCTCCGTCGCTG 59.935 63.158 0.00 0.00 0.00 5.18
122 123 2.279120 CATCTCCTCCGTCGCTGC 60.279 66.667 0.00 0.00 0.00 5.25
123 124 3.893763 ATCTCCTCCGTCGCTGCG 61.894 66.667 17.25 17.25 0.00 5.18
131 132 4.059459 CGTCGCTGCGGTGTGAAC 62.059 66.667 23.03 10.61 0.00 3.18
132 133 4.059459 GTCGCTGCGGTGTGAACG 62.059 66.667 23.03 0.00 0.00 3.95
133 134 4.578898 TCGCTGCGGTGTGAACGT 62.579 61.111 23.03 0.00 0.00 3.99
134 135 4.059459 CGCTGCGGTGTGAACGTC 62.059 66.667 15.40 0.00 0.00 4.34
135 136 4.059459 GCTGCGGTGTGAACGTCG 62.059 66.667 0.00 0.00 0.00 5.12
139 140 4.042060 CGGTGTGAACGTCGCGTG 62.042 66.667 5.77 2.22 39.99 5.34
140 141 2.656007 GGTGTGAACGTCGCGTGA 60.656 61.111 5.77 0.00 39.99 4.35
141 142 2.538058 GTGTGAACGTCGCGTGAC 59.462 61.111 19.11 19.11 39.99 3.67
194 195 0.582005 GCTATTTAAGCCGGCAGACG 59.418 55.000 31.54 10.84 46.25 4.18
195 196 1.935933 CTATTTAAGCCGGCAGACGT 58.064 50.000 31.54 14.01 42.24 4.34
196 197 1.859080 CTATTTAAGCCGGCAGACGTC 59.141 52.381 31.54 7.70 42.24 4.34
197 198 0.743345 ATTTAAGCCGGCAGACGTCC 60.743 55.000 31.54 0.00 42.24 4.79
198 199 2.791501 TTTAAGCCGGCAGACGTCCC 62.792 60.000 31.54 6.34 42.24 4.46
204 205 4.717313 GGCAGACGTCCCCCAACC 62.717 72.222 13.01 1.07 0.00 3.77
205 206 3.637273 GCAGACGTCCCCCAACCT 61.637 66.667 13.01 0.00 0.00 3.50
206 207 3.157680 CAGACGTCCCCCAACCTT 58.842 61.111 13.01 0.00 0.00 3.50
207 208 1.833787 GCAGACGTCCCCCAACCTTA 61.834 60.000 13.01 0.00 0.00 2.69
208 209 0.249398 CAGACGTCCCCCAACCTTAG 59.751 60.000 13.01 0.00 0.00 2.18
209 210 1.078637 GACGTCCCCCAACCTTAGC 60.079 63.158 3.51 0.00 0.00 3.09
210 211 2.271173 CGTCCCCCAACCTTAGCC 59.729 66.667 0.00 0.00 0.00 3.93
211 212 2.681591 GTCCCCCAACCTTAGCCC 59.318 66.667 0.00 0.00 0.00 5.19
212 213 2.211575 TCCCCCAACCTTAGCCCA 59.788 61.111 0.00 0.00 0.00 5.36
213 214 1.230482 TCCCCCAACCTTAGCCCAT 60.230 57.895 0.00 0.00 0.00 4.00
214 215 1.230212 CCCCCAACCTTAGCCCATC 59.770 63.158 0.00 0.00 0.00 3.51
215 216 1.230212 CCCCAACCTTAGCCCATCC 59.770 63.158 0.00 0.00 0.00 3.51
216 217 1.580066 CCCCAACCTTAGCCCATCCA 61.580 60.000 0.00 0.00 0.00 3.41
217 218 0.395724 CCCAACCTTAGCCCATCCAC 60.396 60.000 0.00 0.00 0.00 4.02
218 219 0.395724 CCAACCTTAGCCCATCCACC 60.396 60.000 0.00 0.00 0.00 4.61
219 220 0.625849 CAACCTTAGCCCATCCACCT 59.374 55.000 0.00 0.00 0.00 4.00
220 221 0.919710 AACCTTAGCCCATCCACCTC 59.080 55.000 0.00 0.00 0.00 3.85
221 222 0.988678 ACCTTAGCCCATCCACCTCC 60.989 60.000 0.00 0.00 0.00 4.30
222 223 0.695803 CCTTAGCCCATCCACCTCCT 60.696 60.000 0.00 0.00 0.00 3.69
223 224 0.761802 CTTAGCCCATCCACCTCCTC 59.238 60.000 0.00 0.00 0.00 3.71
224 225 0.343372 TTAGCCCATCCACCTCCTCT 59.657 55.000 0.00 0.00 0.00 3.69
225 226 0.105453 TAGCCCATCCACCTCCTCTC 60.105 60.000 0.00 0.00 0.00 3.20
226 227 1.383803 GCCCATCCACCTCCTCTCT 60.384 63.158 0.00 0.00 0.00 3.10
227 228 1.406860 GCCCATCCACCTCCTCTCTC 61.407 65.000 0.00 0.00 0.00 3.20
228 229 0.264359 CCCATCCACCTCCTCTCTCT 59.736 60.000 0.00 0.00 0.00 3.10
229 230 1.703411 CCATCCACCTCCTCTCTCTC 58.297 60.000 0.00 0.00 0.00 3.20
230 231 1.217689 CCATCCACCTCCTCTCTCTCT 59.782 57.143 0.00 0.00 0.00 3.10
231 232 2.586425 CATCCACCTCCTCTCTCTCTC 58.414 57.143 0.00 0.00 0.00 3.20
232 233 1.979809 TCCACCTCCTCTCTCTCTCT 58.020 55.000 0.00 0.00 0.00 3.10
233 234 1.843851 TCCACCTCCTCTCTCTCTCTC 59.156 57.143 0.00 0.00 0.00 3.20
234 235 1.846439 CCACCTCCTCTCTCTCTCTCT 59.154 57.143 0.00 0.00 0.00 3.10
235 236 2.158755 CCACCTCCTCTCTCTCTCTCTC 60.159 59.091 0.00 0.00 0.00 3.20
236 237 2.774234 CACCTCCTCTCTCTCTCTCTCT 59.226 54.545 0.00 0.00 0.00 3.10
237 238 3.041946 ACCTCCTCTCTCTCTCTCTCTC 58.958 54.545 0.00 0.00 0.00 3.20
238 239 3.310954 ACCTCCTCTCTCTCTCTCTCTCT 60.311 52.174 0.00 0.00 0.00 3.10
239 240 3.323403 CCTCCTCTCTCTCTCTCTCTCTC 59.677 56.522 0.00 0.00 0.00 3.20
240 241 4.222336 CTCCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
241 242 4.219115 TCCTCTCTCTCTCTCTCTCTCTC 58.781 52.174 0.00 0.00 0.00 3.20
242 243 4.078922 TCCTCTCTCTCTCTCTCTCTCTCT 60.079 50.000 0.00 0.00 0.00 3.10
243 244 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
244 245 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
245 246 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
246 247 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
247 248 6.101881 TCTCTCTCTCTCTCTCTCTCTCTCTA 59.898 46.154 0.00 0.00 0.00 2.43
248 249 6.857848 TCTCTCTCTCTCTCTCTCTCTCTAT 58.142 44.000 0.00 0.00 0.00 1.98
249 250 7.990055 TCTCTCTCTCTCTCTCTCTCTCTATA 58.010 42.308 0.00 0.00 0.00 1.31
250 251 7.885922 TCTCTCTCTCTCTCTCTCTCTCTATAC 59.114 44.444 0.00 0.00 0.00 1.47
251 252 7.526918 TCTCTCTCTCTCTCTCTCTCTATACA 58.473 42.308 0.00 0.00 0.00 2.29
252 253 8.173412 TCTCTCTCTCTCTCTCTCTCTATACAT 58.827 40.741 0.00 0.00 0.00 2.29
253 254 9.467796 CTCTCTCTCTCTCTCTCTCTATACATA 57.532 40.741 0.00 0.00 0.00 2.29
254 255 9.244292 TCTCTCTCTCTCTCTCTCTATACATAC 57.756 40.741 0.00 0.00 0.00 2.39
255 256 8.950007 TCTCTCTCTCTCTCTCTATACATACA 57.050 38.462 0.00 0.00 0.00 2.29
256 257 9.547279 TCTCTCTCTCTCTCTCTATACATACAT 57.453 37.037 0.00 0.00 0.00 2.29
847 1019 4.576463 GGCACGGAGATAATTGACATCTTT 59.424 41.667 0.00 0.00 32.86 2.52
848 1020 5.758296 GGCACGGAGATAATTGACATCTTTA 59.242 40.000 0.00 0.00 32.86 1.85
859 1031 5.462530 TTGACATCTTTAACGAGGAGTGA 57.537 39.130 0.21 0.00 0.00 3.41
905 1085 7.327275 CGTAGGTTATTTTGTTTGCATGCTTTA 59.673 33.333 20.33 1.11 0.00 1.85
959 1140 5.019498 CGGACGTAATTGTGCTAATTTGAC 58.981 41.667 0.00 0.00 0.00 3.18
971 1152 4.759693 TGCTAATTTGACAAGTGTCCGATT 59.240 37.500 8.91 10.56 44.15 3.34
980 1161 3.176708 CAAGTGTCCGATTACTACCACG 58.823 50.000 0.00 0.00 0.00 4.94
983 1164 1.402968 TGTCCGATTACTACCACGAGC 59.597 52.381 0.00 0.00 0.00 5.03
988 1169 3.005050 CCGATTACTACCACGAGCCATAA 59.995 47.826 0.00 0.00 0.00 1.90
991 1172 5.694910 CGATTACTACCACGAGCCATAATTT 59.305 40.000 0.00 0.00 0.00 1.82
992 1173 6.864685 CGATTACTACCACGAGCCATAATTTA 59.135 38.462 0.00 0.00 0.00 1.40
993 1174 7.544566 CGATTACTACCACGAGCCATAATTTAT 59.455 37.037 0.00 0.00 0.00 1.40
994 1175 8.773404 ATTACTACCACGAGCCATAATTTATC 57.227 34.615 0.00 0.00 0.00 1.75
995 1176 6.420913 ACTACCACGAGCCATAATTTATCT 57.579 37.500 0.00 0.00 0.00 1.98
996 1177 6.223852 ACTACCACGAGCCATAATTTATCTG 58.776 40.000 0.00 0.00 0.00 2.90
997 1178 5.036117 ACCACGAGCCATAATTTATCTGT 57.964 39.130 0.00 0.00 0.00 3.41
998 1179 6.169557 ACCACGAGCCATAATTTATCTGTA 57.830 37.500 0.00 0.00 0.00 2.74
999 1180 6.223852 ACCACGAGCCATAATTTATCTGTAG 58.776 40.000 0.00 0.00 0.00 2.74
1000 1181 6.041637 ACCACGAGCCATAATTTATCTGTAGA 59.958 38.462 0.00 0.00 0.00 2.59
1001 1182 7.099764 CCACGAGCCATAATTTATCTGTAGAT 58.900 38.462 0.00 0.00 38.51 1.98
1002 1183 7.063898 CCACGAGCCATAATTTATCTGTAGATG 59.936 40.741 4.67 0.00 36.05 2.90
1003 1184 6.591834 ACGAGCCATAATTTATCTGTAGATGC 59.408 38.462 4.67 0.00 36.05 3.91
1004 1185 6.815641 CGAGCCATAATTTATCTGTAGATGCT 59.184 38.462 4.67 2.34 36.05 3.79
1005 1186 7.009999 CGAGCCATAATTTATCTGTAGATGCTC 59.990 40.741 12.72 12.72 36.04 4.26
1006 1187 7.915930 AGCCATAATTTATCTGTAGATGCTCT 58.084 34.615 4.67 0.00 36.05 4.09
1007 1188 8.381636 AGCCATAATTTATCTGTAGATGCTCTT 58.618 33.333 4.67 0.00 36.05 2.85
1008 1189 9.658799 GCCATAATTTATCTGTAGATGCTCTTA 57.341 33.333 4.67 0.00 36.05 2.10
1013 1194 8.910351 ATTTATCTGTAGATGCTCTTAAACCC 57.090 34.615 4.67 0.00 36.05 4.11
1014 1195 4.755266 TCTGTAGATGCTCTTAAACCCC 57.245 45.455 0.00 0.00 0.00 4.95
1015 1196 3.454812 TCTGTAGATGCTCTTAAACCCCC 59.545 47.826 0.00 0.00 0.00 5.40
1016 1197 3.456277 CTGTAGATGCTCTTAAACCCCCT 59.544 47.826 0.00 0.00 0.00 4.79
1017 1198 3.850173 TGTAGATGCTCTTAAACCCCCTT 59.150 43.478 0.00 0.00 0.00 3.95
1018 1199 4.291249 TGTAGATGCTCTTAAACCCCCTTT 59.709 41.667 0.00 0.00 0.00 3.11
1389 1574 3.263503 CTGGAACTCCGTCGTCGCA 62.264 63.158 0.00 0.00 39.43 5.10
1543 1728 0.169009 GTTCGGTGAAATGCCTGAGC 59.831 55.000 0.00 0.00 40.48 4.26
1632 1817 0.591170 CGGTGTTTGACGAAATGCCT 59.409 50.000 0.00 0.00 0.00 4.75
1787 1972 0.329261 TGCAAGGAAGGAGATGTGGG 59.671 55.000 0.00 0.00 0.00 4.61
1881 2066 7.416664 GGTTGCTATTCCTTTCTCATTATGCAA 60.417 37.037 0.00 0.00 33.96 4.08
1939 2124 7.251704 AGAATTCTTATGTTGCTTGGATACG 57.748 36.000 0.88 0.00 42.51 3.06
1955 2140 6.718522 TGGATACGTCTATTGGATGTTGTA 57.281 37.500 0.00 0.00 43.26 2.41
1957 2142 7.732025 TGGATACGTCTATTGGATGTTGTATT 58.268 34.615 0.00 0.00 43.26 1.89
1959 2144 9.701098 GGATACGTCTATTGGATGTTGTATTTA 57.299 33.333 0.00 0.00 43.26 1.40
1961 2146 7.781548 ACGTCTATTGGATGTTGTATTTACC 57.218 36.000 0.00 0.00 40.95 2.85
2054 2315 6.528423 CCGTTTCAAACAATTGACAGTGTTTA 59.472 34.615 13.59 3.40 46.78 2.01
2135 2396 5.528043 TTCTTGCTTGGCATGAACTAAAA 57.472 34.783 14.01 0.00 44.00 1.52
2136 2397 5.125100 TCTTGCTTGGCATGAACTAAAAG 57.875 39.130 4.32 0.00 39.22 2.27
2137 2398 4.826733 TCTTGCTTGGCATGAACTAAAAGA 59.173 37.500 4.32 0.00 39.22 2.52
2138 2399 5.477984 TCTTGCTTGGCATGAACTAAAAGAT 59.522 36.000 4.32 0.00 39.22 2.40
2139 2400 5.063180 TGCTTGGCATGAACTAAAAGATG 57.937 39.130 4.32 0.00 31.71 2.90
2140 2401 4.523943 TGCTTGGCATGAACTAAAAGATGT 59.476 37.500 4.32 0.00 31.71 3.06
2141 2402 5.709631 TGCTTGGCATGAACTAAAAGATGTA 59.290 36.000 4.32 0.00 31.71 2.29
2170 2431 8.094798 TGGTTGTAATACTCTGAATCAACAAC 57.905 34.615 13.43 13.43 42.80 3.32
2176 2437 6.712241 ATACTCTGAATCAACAACGTTCTG 57.288 37.500 0.00 0.00 0.00 3.02
2178 2439 4.508124 ACTCTGAATCAACAACGTTCTGTC 59.492 41.667 0.00 0.00 0.00 3.51
2182 2443 5.056480 TGAATCAACAACGTTCTGTCAGAT 58.944 37.500 2.68 0.31 0.00 2.90
2183 2444 5.527214 TGAATCAACAACGTTCTGTCAGATT 59.473 36.000 15.30 15.30 37.00 2.40
2184 2445 6.038161 TGAATCAACAACGTTCTGTCAGATTT 59.962 34.615 15.97 0.00 35.67 2.17
2185 2446 5.811399 TCAACAACGTTCTGTCAGATTTT 57.189 34.783 2.68 0.00 0.00 1.82
2186 2447 6.189677 TCAACAACGTTCTGTCAGATTTTT 57.810 33.333 2.68 0.00 0.00 1.94
2262 2523 5.324409 AGGAACTCATGCCTTAATTGTTGA 58.676 37.500 0.00 0.00 0.00 3.18
2747 3017 4.947147 GCACCTGCCGTTGGACCA 62.947 66.667 0.00 0.00 34.31 4.02
2748 3018 2.978010 CACCTGCCGTTGGACCAC 60.978 66.667 0.00 0.00 0.00 4.16
2749 3019 3.168528 ACCTGCCGTTGGACCACT 61.169 61.111 0.00 0.00 0.00 4.00
2750 3020 2.669569 CCTGCCGTTGGACCACTG 60.670 66.667 0.00 0.00 0.00 3.66
2751 3021 2.425592 CTGCCGTTGGACCACTGA 59.574 61.111 0.00 0.00 0.00 3.41
2752 3022 1.961277 CTGCCGTTGGACCACTGAC 60.961 63.158 0.00 0.00 0.00 3.51
2753 3023 2.110213 GCCGTTGGACCACTGACA 59.890 61.111 0.00 0.00 0.00 3.58
2754 3024 1.961277 GCCGTTGGACCACTGACAG 60.961 63.158 0.00 0.00 0.00 3.51
2755 3025 1.301716 CCGTTGGACCACTGACAGG 60.302 63.158 7.51 0.00 0.00 4.00
2756 3026 1.445942 CGTTGGACCACTGACAGGT 59.554 57.895 7.51 0.00 43.46 4.00
2757 3027 0.880278 CGTTGGACCACTGACAGGTG 60.880 60.000 7.51 2.99 40.09 4.00
2763 3033 2.759114 CACTGACAGGTGGGCCAT 59.241 61.111 10.70 0.00 37.19 4.40
2764 3034 1.676635 CACTGACAGGTGGGCCATG 60.677 63.158 10.70 7.70 37.19 3.66
2765 3035 2.156098 ACTGACAGGTGGGCCATGT 61.156 57.895 10.70 11.73 37.19 3.21
2766 3036 1.075482 CTGACAGGTGGGCCATGTT 59.925 57.895 10.70 0.00 37.19 2.71
2767 3037 0.962356 CTGACAGGTGGGCCATGTTC 60.962 60.000 10.70 4.92 37.19 3.18
2768 3038 1.678970 GACAGGTGGGCCATGTTCC 60.679 63.158 10.70 6.06 37.19 3.62
2769 3039 2.424842 GACAGGTGGGCCATGTTCCA 62.425 60.000 10.70 0.66 37.19 3.53
2770 3040 1.679977 CAGGTGGGCCATGTTCCAG 60.680 63.158 10.70 0.00 37.19 3.86
2771 3041 3.070576 GGTGGGCCATGTTCCAGC 61.071 66.667 10.70 14.98 43.04 4.85
2772 3042 3.070576 GTGGGCCATGTTCCAGCC 61.071 66.667 10.70 3.18 46.37 4.85
2788 3058 4.033776 CCGGGCCCATGTGTCAGT 62.034 66.667 24.92 0.00 0.00 3.41
2789 3059 2.747460 CGGGCCCATGTGTCAGTG 60.747 66.667 24.92 0.00 0.00 3.66
2790 3060 2.756400 GGGCCCATGTGTCAGTGA 59.244 61.111 19.95 0.00 0.00 3.41
2791 3061 1.304282 GGGCCCATGTGTCAGTGAT 59.696 57.895 19.95 0.00 0.00 3.06
2792 3062 1.033746 GGGCCCATGTGTCAGTGATG 61.034 60.000 19.95 0.00 0.00 3.07
2793 3063 1.033746 GGCCCATGTGTCAGTGATGG 61.034 60.000 0.00 0.00 37.05 3.51
2794 3064 0.035152 GCCCATGTGTCAGTGATGGA 60.035 55.000 11.39 0.00 39.29 3.41
2795 3065 1.614051 GCCCATGTGTCAGTGATGGAA 60.614 52.381 11.39 0.00 39.29 3.53
2796 3066 2.086869 CCCATGTGTCAGTGATGGAAC 58.913 52.381 11.39 2.45 39.29 3.62
2797 3067 1.733912 CCATGTGTCAGTGATGGAACG 59.266 52.381 4.71 0.00 39.29 3.95
2798 3068 1.733912 CATGTGTCAGTGATGGAACGG 59.266 52.381 0.00 0.00 0.00 4.44
2799 3069 0.602638 TGTGTCAGTGATGGAACGGC 60.603 55.000 0.00 0.00 0.00 5.68
2800 3070 0.602638 GTGTCAGTGATGGAACGGCA 60.603 55.000 0.00 0.00 0.00 5.69
2801 3071 0.602638 TGTCAGTGATGGAACGGCAC 60.603 55.000 0.00 0.00 35.67 5.01
2802 3072 1.003839 TCAGTGATGGAACGGCACC 60.004 57.895 0.00 0.00 35.98 5.01
2803 3073 2.040544 CAGTGATGGAACGGCACCC 61.041 63.158 0.00 0.00 35.98 4.61
2804 3074 2.224159 AGTGATGGAACGGCACCCT 61.224 57.895 0.00 0.00 35.98 4.34
2805 3075 2.040544 GTGATGGAACGGCACCCTG 61.041 63.158 0.00 0.00 0.00 4.45
2806 3076 3.134127 GATGGAACGGCACCCTGC 61.134 66.667 0.00 0.00 44.08 4.85
2823 3093 3.925090 CCGTACGGCAGGGGATCC 61.925 72.222 23.44 1.92 0.00 3.36
2824 3094 2.838225 CGTACGGCAGGGGATCCT 60.838 66.667 12.58 0.00 46.26 3.24
2825 3095 2.857744 CGTACGGCAGGGGATCCTC 61.858 68.421 12.58 7.90 42.67 3.71
2826 3096 2.520982 TACGGCAGGGGATCCTCG 60.521 66.667 12.58 5.37 42.67 4.63
2827 3097 3.369410 TACGGCAGGGGATCCTCGT 62.369 63.158 12.58 15.21 42.67 4.18
2828 3098 3.917760 CGGCAGGGGATCCTCGTC 61.918 72.222 12.58 4.80 42.67 4.20
2829 3099 3.551407 GGCAGGGGATCCTCGTCC 61.551 72.222 12.58 10.58 42.67 4.79
2830 3100 3.917760 GCAGGGGATCCTCGTCCG 61.918 72.222 12.58 0.08 42.67 4.79
2891 3161 9.696572 AAAAACTCTACCTAGGTCTTTTTCTTT 57.303 29.630 20.32 8.58 0.00 2.52
2892 3162 8.905660 AAACTCTACCTAGGTCTTTTTCTTTC 57.094 34.615 20.32 0.00 0.00 2.62
3213 3483 6.146347 GTGAGTCAGAGTTGGTCTTCATAAAC 59.854 42.308 0.00 0.00 30.64 2.01
3333 3603 1.283736 CACGTGGGCTAATACCGAAC 58.716 55.000 7.95 0.00 0.00 3.95
3397 3667 0.679002 CAGGGTGGATGACAGCTTGG 60.679 60.000 1.39 0.00 46.98 3.61
3492 3762 1.079750 GGGACGAGCAGGACAGTTC 60.080 63.158 0.00 0.00 0.00 3.01
3501 3771 1.606737 GCAGGACAGTTCGAGAAAGCT 60.607 52.381 0.00 0.00 0.00 3.74
3559 3829 2.328319 AGAATGTTTGGGGTGCATTGT 58.672 42.857 0.00 0.00 33.56 2.71
3933 4203 8.734593 AATCTAGATAGGGCTTTTCATACTCT 57.265 34.615 5.46 0.00 0.00 3.24
3934 4204 8.734593 ATCTAGATAGGGCTTTTCATACTCTT 57.265 34.615 2.53 0.00 0.00 2.85
3935 4205 8.184304 TCTAGATAGGGCTTTTCATACTCTTC 57.816 38.462 0.00 0.00 0.00 2.87
3936 4206 6.814954 AGATAGGGCTTTTCATACTCTTCA 57.185 37.500 0.00 0.00 0.00 3.02
3937 4207 7.385894 AGATAGGGCTTTTCATACTCTTCAT 57.614 36.000 0.00 0.00 0.00 2.57
3938 4208 7.222872 AGATAGGGCTTTTCATACTCTTCATG 58.777 38.462 0.00 0.00 0.00 3.07
3939 4209 3.950395 AGGGCTTTTCATACTCTTCATGC 59.050 43.478 0.00 0.00 0.00 4.06
3940 4210 3.696051 GGGCTTTTCATACTCTTCATGCA 59.304 43.478 0.00 0.00 0.00 3.96
3941 4211 4.439289 GGGCTTTTCATACTCTTCATGCAC 60.439 45.833 0.00 0.00 0.00 4.57
4155 4425 6.149129 CCCCCTGCTGTTTATAAAGAAATC 57.851 41.667 0.00 0.00 0.00 2.17
4706 4978 8.433421 AGTCACTTGTATATTTTGGTAATCCG 57.567 34.615 0.00 0.00 36.30 4.18
4729 5001 6.086222 CGGATAAACTGACATTTTCCTTGTG 58.914 40.000 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.980978 CGACGCCTCATATTTGGATTAGATAT 59.019 38.462 0.00 0.00 0.00 1.63
4 5 3.679980 CCGACGCCTCATATTTGGATTAG 59.320 47.826 0.00 0.00 0.00 1.73
5 6 3.556213 CCCGACGCCTCATATTTGGATTA 60.556 47.826 0.00 0.00 0.00 1.75
6 7 2.494059 CCGACGCCTCATATTTGGATT 58.506 47.619 0.00 0.00 0.00 3.01
7 8 1.270839 CCCGACGCCTCATATTTGGAT 60.271 52.381 0.00 0.00 0.00 3.41
8 9 0.105964 CCCGACGCCTCATATTTGGA 59.894 55.000 0.00 0.00 0.00 3.53
9 10 0.884704 CCCCGACGCCTCATATTTGG 60.885 60.000 0.00 0.00 0.00 3.28
10 11 1.507141 GCCCCGACGCCTCATATTTG 61.507 60.000 0.00 0.00 0.00 2.32
11 12 1.227853 GCCCCGACGCCTCATATTT 60.228 57.895 0.00 0.00 0.00 1.40
12 13 2.426023 GCCCCGACGCCTCATATT 59.574 61.111 0.00 0.00 0.00 1.28
13 14 3.991051 CGCCCCGACGCCTCATAT 61.991 66.667 0.00 0.00 0.00 1.78
39 40 1.663739 GTCAGTCCTACGTGGCACA 59.336 57.895 19.09 0.00 35.26 4.57
40 41 1.443872 CGTCAGTCCTACGTGGCAC 60.444 63.158 7.79 7.79 35.66 5.01
41 42 0.963856 ATCGTCAGTCCTACGTGGCA 60.964 55.000 0.00 0.00 41.08 4.92
42 43 0.525668 CATCGTCAGTCCTACGTGGC 60.526 60.000 0.00 0.00 41.08 5.01
43 44 0.100682 CCATCGTCAGTCCTACGTGG 59.899 60.000 0.00 0.00 41.08 4.94
44 45 0.100682 CCCATCGTCAGTCCTACGTG 59.899 60.000 0.00 0.00 41.08 4.49
45 46 0.034767 TCCCATCGTCAGTCCTACGT 60.035 55.000 0.00 0.00 41.08 3.57
46 47 1.267261 GATCCCATCGTCAGTCCTACG 59.733 57.143 0.00 0.00 41.64 3.51
47 48 1.614413 GGATCCCATCGTCAGTCCTAC 59.386 57.143 0.00 0.00 0.00 3.18
48 49 1.480683 GGGATCCCATCGTCAGTCCTA 60.481 57.143 26.95 0.00 35.81 2.94
49 50 0.760945 GGGATCCCATCGTCAGTCCT 60.761 60.000 26.95 0.00 35.81 3.85
50 51 1.048724 TGGGATCCCATCGTCAGTCC 61.049 60.000 30.62 0.00 41.89 3.85
51 52 2.516448 TGGGATCCCATCGTCAGTC 58.484 57.895 30.62 0.00 41.89 3.51
52 53 4.807321 TGGGATCCCATCGTCAGT 57.193 55.556 30.62 0.00 41.89 3.41
59 60 3.255387 CGATTCCACGTGGGATCCCAT 62.255 57.143 38.69 19.26 45.62 4.00
60 61 1.966901 CGATTCCACGTGGGATCCCA 61.967 60.000 38.69 30.62 45.62 4.37
61 62 1.227556 CGATTCCACGTGGGATCCC 60.228 63.158 38.69 25.22 45.62 3.85
62 63 1.887707 GCGATTCCACGTGGGATCC 60.888 63.158 38.69 29.71 45.62 3.36
65 66 1.672854 CTAGGCGATTCCACGTGGGA 61.673 60.000 33.40 27.63 46.61 4.37
66 67 1.227263 CTAGGCGATTCCACGTGGG 60.227 63.158 33.40 18.72 37.29 4.61
67 68 0.174845 TTCTAGGCGATTCCACGTGG 59.825 55.000 29.26 29.26 37.29 4.94
68 69 1.659098 GTTTCTAGGCGATTCCACGTG 59.341 52.381 9.08 9.08 37.29 4.49
69 70 1.405121 GGTTTCTAGGCGATTCCACGT 60.405 52.381 0.00 0.00 37.29 4.49
70 71 1.134788 AGGTTTCTAGGCGATTCCACG 60.135 52.381 0.00 0.00 37.29 4.94
71 72 2.093658 TCAGGTTTCTAGGCGATTCCAC 60.094 50.000 0.00 0.00 37.29 4.02
72 73 2.184533 TCAGGTTTCTAGGCGATTCCA 58.815 47.619 0.00 0.00 37.29 3.53
73 74 2.981859 TCAGGTTTCTAGGCGATTCC 57.018 50.000 0.00 0.00 0.00 3.01
74 75 3.134458 CCATCAGGTTTCTAGGCGATTC 58.866 50.000 0.00 0.00 0.00 2.52
75 76 3.199880 CCATCAGGTTTCTAGGCGATT 57.800 47.619 0.00 0.00 0.00 3.34
76 77 2.918712 CCATCAGGTTTCTAGGCGAT 57.081 50.000 0.00 0.00 0.00 4.58
88 89 0.826715 ATGTCCGTCAGACCATCAGG 59.173 55.000 0.00 0.00 45.68 3.86
89 90 1.753649 AGATGTCCGTCAGACCATCAG 59.246 52.381 16.30 0.00 45.68 2.90
90 91 1.751351 GAGATGTCCGTCAGACCATCA 59.249 52.381 16.30 5.29 45.68 3.07
91 92 1.067821 GGAGATGTCCGTCAGACCATC 59.932 57.143 9.25 9.25 45.68 3.51
92 93 1.115467 GGAGATGTCCGTCAGACCAT 58.885 55.000 0.00 0.00 45.68 3.55
93 94 2.579878 GGAGATGTCCGTCAGACCA 58.420 57.895 0.00 0.00 45.68 4.02
102 103 2.122167 AGCGACGGAGGAGATGTCC 61.122 63.158 0.00 0.00 44.33 4.02
103 104 1.064946 CAGCGACGGAGGAGATGTC 59.935 63.158 0.00 0.00 0.00 3.06
104 105 3.069980 GCAGCGACGGAGGAGATGT 62.070 63.158 0.00 0.00 0.00 3.06
105 106 2.279120 GCAGCGACGGAGGAGATG 60.279 66.667 0.00 0.00 0.00 2.90
106 107 3.893763 CGCAGCGACGGAGGAGAT 61.894 66.667 9.98 0.00 0.00 2.75
114 115 4.059459 GTTCACACCGCAGCGACG 62.059 66.667 18.75 9.28 0.00 5.12
115 116 4.059459 CGTTCACACCGCAGCGAC 62.059 66.667 18.75 3.92 0.00 5.19
116 117 4.578898 ACGTTCACACCGCAGCGA 62.579 61.111 18.75 0.00 0.00 4.93
117 118 4.059459 GACGTTCACACCGCAGCG 62.059 66.667 8.18 8.18 0.00 5.18
118 119 4.059459 CGACGTTCACACCGCAGC 62.059 66.667 0.00 0.00 0.00 5.25
119 120 4.059459 GCGACGTTCACACCGCAG 62.059 66.667 11.58 0.00 46.04 5.18
122 123 4.042060 CACGCGACGTTCACACCG 62.042 66.667 15.93 0.00 38.32 4.94
123 124 2.656007 TCACGCGACGTTCACACC 60.656 61.111 15.93 0.00 38.32 4.16
124 125 2.538058 GTCACGCGACGTTCACAC 59.462 61.111 15.93 0.00 38.32 3.82
176 177 1.859080 GACGTCTGCCGGCTTAAATAG 59.141 52.381 29.70 15.77 43.06 1.73
177 178 1.472026 GGACGTCTGCCGGCTTAAATA 60.472 52.381 29.70 4.55 46.68 1.40
178 179 0.743345 GGACGTCTGCCGGCTTAAAT 60.743 55.000 29.70 10.64 46.68 1.40
179 180 1.375013 GGACGTCTGCCGGCTTAAA 60.375 57.895 29.70 5.90 46.68 1.52
180 181 2.263540 GGACGTCTGCCGGCTTAA 59.736 61.111 29.70 10.16 46.68 1.85
181 182 3.766691 GGGACGTCTGCCGGCTTA 61.767 66.667 29.70 13.08 46.68 3.09
187 188 4.717313 GGTTGGGGGACGTCTGCC 62.717 72.222 16.46 8.98 0.00 4.85
188 189 1.833787 TAAGGTTGGGGGACGTCTGC 61.834 60.000 16.46 0.00 0.00 4.26
189 190 0.249398 CTAAGGTTGGGGGACGTCTG 59.751 60.000 16.46 0.00 0.00 3.51
190 191 1.551019 GCTAAGGTTGGGGGACGTCT 61.551 60.000 16.46 0.00 0.00 4.18
191 192 1.078637 GCTAAGGTTGGGGGACGTC 60.079 63.158 7.13 7.13 0.00 4.34
192 193 2.599757 GGCTAAGGTTGGGGGACGT 61.600 63.158 0.00 0.00 0.00 4.34
193 194 2.271173 GGCTAAGGTTGGGGGACG 59.729 66.667 0.00 0.00 0.00 4.79
194 195 1.580994 ATGGGCTAAGGTTGGGGGAC 61.581 60.000 0.00 0.00 0.00 4.46
195 196 1.230482 ATGGGCTAAGGTTGGGGGA 60.230 57.895 0.00 0.00 0.00 4.81
196 197 1.230212 GATGGGCTAAGGTTGGGGG 59.770 63.158 0.00 0.00 0.00 5.40
197 198 1.230212 GGATGGGCTAAGGTTGGGG 59.770 63.158 0.00 0.00 0.00 4.96
198 199 0.395724 GTGGATGGGCTAAGGTTGGG 60.396 60.000 0.00 0.00 0.00 4.12
199 200 0.395724 GGTGGATGGGCTAAGGTTGG 60.396 60.000 0.00 0.00 0.00 3.77
200 201 0.625849 AGGTGGATGGGCTAAGGTTG 59.374 55.000 0.00 0.00 0.00 3.77
201 202 0.919710 GAGGTGGATGGGCTAAGGTT 59.080 55.000 0.00 0.00 0.00 3.50
202 203 0.988678 GGAGGTGGATGGGCTAAGGT 60.989 60.000 0.00 0.00 0.00 3.50
203 204 0.695803 AGGAGGTGGATGGGCTAAGG 60.696 60.000 0.00 0.00 0.00 2.69
204 205 0.761802 GAGGAGGTGGATGGGCTAAG 59.238 60.000 0.00 0.00 0.00 2.18
205 206 0.343372 AGAGGAGGTGGATGGGCTAA 59.657 55.000 0.00 0.00 0.00 3.09
206 207 0.105453 GAGAGGAGGTGGATGGGCTA 60.105 60.000 0.00 0.00 0.00 3.93
207 208 1.383803 GAGAGGAGGTGGATGGGCT 60.384 63.158 0.00 0.00 0.00 5.19
208 209 1.383803 AGAGAGGAGGTGGATGGGC 60.384 63.158 0.00 0.00 0.00 5.36
209 210 0.264359 AGAGAGAGGAGGTGGATGGG 59.736 60.000 0.00 0.00 0.00 4.00
210 211 1.217689 AGAGAGAGAGGAGGTGGATGG 59.782 57.143 0.00 0.00 0.00 3.51
211 212 2.175499 AGAGAGAGAGAGGAGGTGGATG 59.825 54.545 0.00 0.00 0.00 3.51
212 213 2.443255 GAGAGAGAGAGAGGAGGTGGAT 59.557 54.545 0.00 0.00 0.00 3.41
213 214 1.843851 GAGAGAGAGAGAGGAGGTGGA 59.156 57.143 0.00 0.00 0.00 4.02
214 215 1.846439 AGAGAGAGAGAGAGGAGGTGG 59.154 57.143 0.00 0.00 0.00 4.61
215 216 2.774234 AGAGAGAGAGAGAGAGGAGGTG 59.226 54.545 0.00 0.00 0.00 4.00
216 217 3.041946 GAGAGAGAGAGAGAGAGGAGGT 58.958 54.545 0.00 0.00 0.00 3.85
217 218 3.312890 AGAGAGAGAGAGAGAGAGGAGG 58.687 54.545 0.00 0.00 0.00 4.30
218 219 4.222336 AGAGAGAGAGAGAGAGAGAGGAG 58.778 52.174 0.00 0.00 0.00 3.69
219 220 4.078922 AGAGAGAGAGAGAGAGAGAGAGGA 60.079 50.000 0.00 0.00 0.00 3.71
220 221 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
221 222 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
222 223 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
223 224 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
224 225 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
225 226 7.667635 TGTATAGAGAGAGAGAGAGAGAGAGAG 59.332 44.444 0.00 0.00 0.00 3.20
226 227 7.526918 TGTATAGAGAGAGAGAGAGAGAGAGA 58.473 42.308 0.00 0.00 0.00 3.10
227 228 7.767250 TGTATAGAGAGAGAGAGAGAGAGAG 57.233 44.000 0.00 0.00 0.00 3.20
228 229 9.244292 GTATGTATAGAGAGAGAGAGAGAGAGA 57.756 40.741 0.00 0.00 0.00 3.10
229 230 9.025041 TGTATGTATAGAGAGAGAGAGAGAGAG 57.975 40.741 0.00 0.00 0.00 3.20
230 231 8.950007 TGTATGTATAGAGAGAGAGAGAGAGA 57.050 38.462 0.00 0.00 0.00 3.10
310 311 9.841295 TCGAGTGGCGGCATATATATATATATA 57.159 33.333 17.19 19.97 41.33 0.86
311 312 8.747538 TCGAGTGGCGGCATATATATATATAT 57.252 34.615 17.19 16.45 41.33 0.86
312 313 7.201705 GCTCGAGTGGCGGCATATATATATATA 60.202 40.741 17.19 13.60 41.33 0.86
313 314 6.404844 GCTCGAGTGGCGGCATATATATATAT 60.405 42.308 17.19 9.12 41.33 0.86
314 315 5.106277 GCTCGAGTGGCGGCATATATATATA 60.106 44.000 17.19 4.92 41.33 0.86
315 316 4.321304 GCTCGAGTGGCGGCATATATATAT 60.321 45.833 17.19 0.00 41.33 0.86
316 317 3.004419 GCTCGAGTGGCGGCATATATATA 59.996 47.826 17.19 0.00 41.33 0.86
317 318 2.223829 GCTCGAGTGGCGGCATATATAT 60.224 50.000 17.19 0.00 41.33 0.86
318 319 1.134367 GCTCGAGTGGCGGCATATATA 59.866 52.381 17.19 0.00 41.33 0.86
319 320 0.108615 GCTCGAGTGGCGGCATATAT 60.109 55.000 17.19 1.20 41.33 0.86
320 321 1.289066 GCTCGAGTGGCGGCATATA 59.711 57.895 17.19 0.13 41.33 0.86
321 322 2.029666 GCTCGAGTGGCGGCATAT 59.970 61.111 17.19 7.23 41.33 1.78
322 323 4.221422 GGCTCGAGTGGCGGCATA 62.221 66.667 17.19 0.13 41.33 3.14
605 661 2.359354 CCGCCATGTTGAACCCGA 60.359 61.111 0.00 0.00 0.00 5.14
651 764 2.021068 GCCTGCTGCTCCGTCATCTA 62.021 60.000 0.00 0.00 36.87 1.98
847 1019 5.931294 AGATGATCTAGTCACTCCTCGTTA 58.069 41.667 0.00 0.00 40.28 3.18
848 1020 4.787551 AGATGATCTAGTCACTCCTCGTT 58.212 43.478 0.00 0.00 40.28 3.85
859 1031 8.814931 ACCTACGTACTACATAGATGATCTAGT 58.185 37.037 8.30 4.74 31.67 2.57
959 1140 3.119743 TCGTGGTAGTAATCGGACACTTG 60.120 47.826 0.00 0.00 0.00 3.16
971 1152 7.014905 ACAGATAAATTATGGCTCGTGGTAGTA 59.985 37.037 0.00 0.00 0.00 1.82
980 1161 8.195617 GAGCATCTACAGATAAATTATGGCTC 57.804 38.462 0.00 0.00 33.85 4.70
1543 1728 1.008652 TGTACGACACCACGTTCCG 60.009 57.895 0.00 0.00 44.14 4.30
1632 1817 2.557056 CCACGACACTAAGTTCCTCTCA 59.443 50.000 0.00 0.00 0.00 3.27
1787 1972 1.527433 AAAAAGCTTCCTGGCGCTCC 61.527 55.000 7.64 0.00 34.96 4.70
1939 2124 9.561069 AGATGGTAAATACAACATCCAATAGAC 57.439 33.333 0.00 0.00 40.33 2.59
2054 2315 7.982354 GCTCACTAGAGGTATAAAATTGACACT 59.018 37.037 0.00 0.00 42.33 3.55
2079 2340 8.227791 TGACTATTTGTTTCTTAATCGTGAAGC 58.772 33.333 0.00 0.00 0.00 3.86
2135 2396 8.758829 TCAGAGTATTACAACCAACATACATCT 58.241 33.333 0.00 0.00 0.00 2.90
2136 2397 8.942338 TCAGAGTATTACAACCAACATACATC 57.058 34.615 0.00 0.00 0.00 3.06
2137 2398 9.905713 ATTCAGAGTATTACAACCAACATACAT 57.094 29.630 0.00 0.00 0.00 2.29
2138 2399 9.378551 GATTCAGAGTATTACAACCAACATACA 57.621 33.333 0.00 0.00 0.00 2.29
2139 2400 9.378551 TGATTCAGAGTATTACAACCAACATAC 57.621 33.333 0.00 0.00 0.00 2.39
2140 2401 9.952030 TTGATTCAGAGTATTACAACCAACATA 57.048 29.630 0.00 0.00 0.00 2.29
2141 2402 8.730680 GTTGATTCAGAGTATTACAACCAACAT 58.269 33.333 0.00 0.00 32.82 2.71
2276 2537 2.495409 CCATCCTGCGGCATTGCAT 61.495 57.895 11.39 0.00 45.26 3.96
2347 2608 0.107606 ACAACAACGTAGGGTGCACA 60.108 50.000 20.43 0.00 0.00 4.57
2730 3000 4.947147 TGGTCCAACGGCAGGTGC 62.947 66.667 0.00 0.00 41.14 5.01
2731 3001 2.978010 GTGGTCCAACGGCAGGTG 60.978 66.667 0.00 0.00 34.07 4.00
2732 3002 3.168528 AGTGGTCCAACGGCAGGT 61.169 61.111 0.00 0.00 0.00 4.00
2733 3003 2.669569 CAGTGGTCCAACGGCAGG 60.670 66.667 0.00 0.00 0.00 4.85
2734 3004 1.961277 GTCAGTGGTCCAACGGCAG 60.961 63.158 0.00 0.00 0.00 4.85
2735 3005 2.110213 GTCAGTGGTCCAACGGCA 59.890 61.111 0.00 0.00 0.00 5.69
2736 3006 1.961277 CTGTCAGTGGTCCAACGGC 60.961 63.158 0.00 0.00 0.00 5.68
2737 3007 1.301716 CCTGTCAGTGGTCCAACGG 60.302 63.158 0.00 0.00 0.00 4.44
2738 3008 0.880278 CACCTGTCAGTGGTCCAACG 60.880 60.000 0.00 0.00 35.28 4.10
2739 3009 3.006672 CACCTGTCAGTGGTCCAAC 57.993 57.895 0.00 0.00 35.28 3.77
2746 3016 1.676635 CATGGCCCACCTGTCAGTG 60.677 63.158 0.00 0.00 36.63 3.66
2747 3017 1.719063 AACATGGCCCACCTGTCAGT 61.719 55.000 0.00 0.00 36.63 3.41
2748 3018 0.962356 GAACATGGCCCACCTGTCAG 60.962 60.000 0.00 0.00 36.63 3.51
2749 3019 1.074775 GAACATGGCCCACCTGTCA 59.925 57.895 0.00 0.00 36.63 3.58
2750 3020 1.678970 GGAACATGGCCCACCTGTC 60.679 63.158 0.00 0.00 36.63 3.51
2751 3021 2.430704 CTGGAACATGGCCCACCTGT 62.431 60.000 0.00 0.00 38.20 4.00
2752 3022 1.679977 CTGGAACATGGCCCACCTG 60.680 63.158 0.00 0.00 38.20 4.00
2753 3023 2.765969 CTGGAACATGGCCCACCT 59.234 61.111 0.00 0.00 38.20 4.00
2754 3024 3.070576 GCTGGAACATGGCCCACC 61.071 66.667 0.00 0.00 38.20 4.61
2755 3025 3.070576 GGCTGGAACATGGCCCAC 61.071 66.667 0.00 0.00 42.95 4.61
2756 3026 4.738998 CGGCTGGAACATGGCCCA 62.739 66.667 0.00 7.89 45.52 5.36
2771 3041 4.033776 ACTGACACATGGGCCCGG 62.034 66.667 19.37 15.04 0.00 5.73
2772 3042 2.541547 ATCACTGACACATGGGCCCG 62.542 60.000 19.37 6.14 0.00 6.13
2773 3043 1.033746 CATCACTGACACATGGGCCC 61.034 60.000 17.59 17.59 0.00 5.80
2774 3044 1.033746 CCATCACTGACACATGGGCC 61.034 60.000 0.00 0.00 34.47 5.80
2775 3045 0.035152 TCCATCACTGACACATGGGC 60.035 55.000 0.00 0.00 38.13 5.36
2776 3046 2.086869 GTTCCATCACTGACACATGGG 58.913 52.381 0.00 0.00 38.13 4.00
2777 3047 1.733912 CGTTCCATCACTGACACATGG 59.266 52.381 0.00 0.00 38.83 3.66
2778 3048 1.733912 CCGTTCCATCACTGACACATG 59.266 52.381 0.00 0.00 0.00 3.21
2779 3049 1.945819 GCCGTTCCATCACTGACACAT 60.946 52.381 0.00 0.00 0.00 3.21
2780 3050 0.602638 GCCGTTCCATCACTGACACA 60.603 55.000 0.00 0.00 0.00 3.72
2781 3051 0.602638 TGCCGTTCCATCACTGACAC 60.603 55.000 0.00 0.00 0.00 3.67
2782 3052 0.602638 GTGCCGTTCCATCACTGACA 60.603 55.000 0.00 0.00 0.00 3.58
2783 3053 1.298859 GGTGCCGTTCCATCACTGAC 61.299 60.000 0.00 0.00 0.00 3.51
2784 3054 1.003839 GGTGCCGTTCCATCACTGA 60.004 57.895 0.00 0.00 0.00 3.41
2785 3055 2.040544 GGGTGCCGTTCCATCACTG 61.041 63.158 0.00 0.00 0.00 3.66
2786 3056 2.224159 AGGGTGCCGTTCCATCACT 61.224 57.895 0.00 0.00 0.00 3.41
2787 3057 2.040544 CAGGGTGCCGTTCCATCAC 61.041 63.158 0.00 0.00 0.00 3.06
2788 3058 2.350895 CAGGGTGCCGTTCCATCA 59.649 61.111 0.00 0.00 0.00 3.07
2789 3059 3.134127 GCAGGGTGCCGTTCCATC 61.134 66.667 0.00 0.00 37.42 3.51
2806 3076 3.925090 GGATCCCCTGCCGTACGG 61.925 72.222 30.06 30.06 38.57 4.02
2807 3077 2.838225 AGGATCCCCTGCCGTACG 60.838 66.667 8.55 8.69 42.42 3.67
2808 3078 2.857744 CGAGGATCCCCTGCCGTAC 61.858 68.421 8.55 0.00 44.53 3.67
2809 3079 2.520982 CGAGGATCCCCTGCCGTA 60.521 66.667 8.55 0.00 44.53 4.02
2810 3080 4.779733 ACGAGGATCCCCTGCCGT 62.780 66.667 8.55 7.95 44.53 5.68
2811 3081 3.917760 GACGAGGATCCCCTGCCG 61.918 72.222 8.55 7.30 44.53 5.69
2812 3082 3.551407 GGACGAGGATCCCCTGCC 61.551 72.222 8.55 1.52 44.53 4.85
2813 3083 3.917760 CGGACGAGGATCCCCTGC 61.918 72.222 8.55 0.00 44.53 4.85
2814 3084 3.227276 CCGGACGAGGATCCCCTG 61.227 72.222 8.55 0.45 44.53 4.45
2839 3109 9.528489 TTCTTTTATTATGATTGCTATACCCCC 57.472 33.333 0.00 0.00 0.00 5.40
2889 3159 5.528043 TCAGTGGCAGCATTAAAAAGAAA 57.472 34.783 0.00 0.00 0.00 2.52
2890 3160 5.068987 AGTTCAGTGGCAGCATTAAAAAGAA 59.931 36.000 0.00 0.00 0.00 2.52
2891 3161 4.584325 AGTTCAGTGGCAGCATTAAAAAGA 59.416 37.500 0.00 0.00 0.00 2.52
2892 3162 4.874970 AGTTCAGTGGCAGCATTAAAAAG 58.125 39.130 0.00 0.00 0.00 2.27
3111 3381 7.478667 GTGCTAGATTCTAACATTGTTTTGACG 59.521 37.037 7.45 0.00 0.00 4.35
3213 3483 4.871933 AACAATGTCCTGGCTTTTAAGG 57.128 40.909 0.00 0.00 34.65 2.69
3252 3522 0.931202 CATGTTGTGCATATGCCGCG 60.931 55.000 24.54 0.00 41.18 6.46
3324 3594 6.600882 AGGATGGTAATATCGTTCGGTATT 57.399 37.500 13.79 13.79 0.00 1.89
3333 3603 5.784177 AGCACACTAAGGATGGTAATATCG 58.216 41.667 0.00 0.00 0.00 2.92
3477 3747 0.889638 TCTCGAACTGTCCTGCTCGT 60.890 55.000 0.00 0.00 33.15 4.18
3492 3762 8.922676 TCTTTTATGTAACTACAAGCTTTCTCG 58.077 33.333 0.00 0.00 39.99 4.04
3501 3771 7.987750 TGGCATGTCTTTTATGTAACTACAA 57.012 32.000 0.00 0.00 39.99 2.41
3559 3829 1.065410 TGAGTCTTGGAAGCCCCCAA 61.065 55.000 7.14 7.14 43.42 4.12
4155 4425 8.576936 ACTGTTTCTTCTACTTTCTAGTTTCG 57.423 34.615 0.00 0.00 35.78 3.46
4706 4978 7.084486 GTCACAAGGAAAATGTCAGTTTATCC 58.916 38.462 0.00 0.00 0.00 2.59
4729 5001 2.417933 CAGCAGCTAGACCAATGTTGTC 59.582 50.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.