Multiple sequence alignment - TraesCS3A01G232300

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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 TraesCS3A01G232300 chr3A 100.000 7169 0 0 1 7169 433994257 434001425 0.000000e+00 13239.0
1 TraesCS3A01G232300 chr3B 96.536 3378 103 6 3031 6405 419763373 419766739 0.000000e+00 5578.0
2 TraesCS3A01G232300 chr3B 90.672 2069 110 35 95 2114 419761346 419763380 0.000000e+00 2675.0
3 TraesCS3A01G232300 chr3B 89.586 893 85 7 2118 3006 739337244 739338132 0.000000e+00 1127.0
4 TraesCS3A01G232300 chr3B 91.221 786 67 2 2134 2919 508761540 508762323 0.000000e+00 1068.0
5 TraesCS3A01G232300 chr3B 95.652 575 21 3 6556 7128 419766950 419767522 0.000000e+00 920.0
6 TraesCS3A01G232300 chr3B 84.117 617 62 20 2440 3025 709291959 709292570 1.350000e-156 564.0
7 TraesCS3A01G232300 chr3B 86.863 373 46 3 2661 3031 284635923 284636294 1.440000e-111 414.0
8 TraesCS3A01G232300 chr3B 97.076 171 4 1 6402 6572 419766766 419766935 3.270000e-73 287.0
9 TraesCS3A01G232300 chr3B 96.491 57 2 0 7113 7169 419774596 419774652 2.130000e-15 95.3
10 TraesCS3A01G232300 chr3D 96.334 3382 109 10 3031 6405 301444031 301440658 0.000000e+00 5544.0
11 TraesCS3A01G232300 chr3D 93.493 1967 94 17 180 2114 301445988 301444024 0.000000e+00 2892.0
12 TraesCS3A01G232300 chr3D 95.067 750 19 6 6405 7152 301440628 301439895 0.000000e+00 1164.0
13 TraesCS3A01G232300 chr3D 94.186 86 4 1 6638 6723 565374416 565374332 5.840000e-26 130.0
14 TraesCS3A01G232300 chr3D 91.579 95 2 3 6638 6731 557459100 557459189 7.550000e-25 126.0
15 TraesCS3A01G232300 chr5B 87.935 2470 288 9 3580 6045 675080219 675082682 0.000000e+00 2902.0
16 TraesCS3A01G232300 chr5B 87.938 2454 290 6 3580 6030 674892250 674894700 0.000000e+00 2887.0
17 TraesCS3A01G232300 chr5B 93.103 87 4 2 6638 6723 279098264 279098349 7.550000e-25 126.0
18 TraesCS3A01G232300 chr7B 88.020 2454 290 4 3580 6031 624351127 624353578 0.000000e+00 2900.0
19 TraesCS3A01G232300 chr5D 87.912 2457 291 6 3580 6033 534856926 534859379 0.000000e+00 2887.0
20 TraesCS3A01G232300 chr5D 87.692 2470 294 9 3580 6045 534637033 534639496 0.000000e+00 2868.0
21 TraesCS3A01G232300 chr7D 87.770 2453 298 2 3580 6031 568598503 568600954 0.000000e+00 2867.0
22 TraesCS3A01G232300 chr7D 91.489 94 4 4 6638 6728 204247274 204247182 7.550000e-25 126.0
23 TraesCS3A01G232300 chr7D 92.135 89 5 2 6638 6726 119165943 119166029 2.720000e-24 124.0
24 TraesCS3A01G232300 chr7D 86.441 118 9 7 6601 6717 195653998 195654109 9.770000e-24 122.0
25 TraesCS3A01G232300 chr7A 87.648 2453 301 2 3580 6031 657353225 657355676 0.000000e+00 2850.0
26 TraesCS3A01G232300 chr7A 90.164 854 82 2 2116 2969 34136496 34135645 0.000000e+00 1110.0
27 TraesCS3A01G232300 chr1B 92.232 914 68 3 2118 3031 624823235 624822325 0.000000e+00 1291.0
28 TraesCS3A01G232300 chr6D 91.657 899 67 6 2136 3032 464401681 464400789 0.000000e+00 1238.0
29 TraesCS3A01G232300 chr6D 89.978 908 71 6 2124 3029 400087522 400088411 0.000000e+00 1155.0
30 TraesCS3A01G232300 chr2D 92.388 867 61 4 2166 3031 555161325 555160463 0.000000e+00 1230.0
31 TraesCS3A01G232300 chr2D 93.333 90 5 1 6634 6723 101695509 101695421 1.620000e-26 132.0
32 TraesCS3A01G232300 chr4D 91.600 881 53 12 2117 2994 381411427 381412289 0.000000e+00 1197.0
33 TraesCS3A01G232300 chr6B 89.227 919 73 11 2116 3032 698071404 698070510 0.000000e+00 1125.0
34 TraesCS3A01G232300 chr4A 84.354 147 20 3 1670 1815 636687839 636687695 2.700000e-29 141.0


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 TraesCS3A01G232300 chr3A 433994257 434001425 7168 False 13239 13239 100.000000 1 7169 1 chr3A.!!$F1 7168
1 TraesCS3A01G232300 chr3B 419761346 419767522 6176 False 2365 5578 94.984000 95 7128 4 chr3B.!!$F6 7033
2 TraesCS3A01G232300 chr3B 739337244 739338132 888 False 1127 1127 89.586000 2118 3006 1 chr3B.!!$F5 888
3 TraesCS3A01G232300 chr3B 508761540 508762323 783 False 1068 1068 91.221000 2134 2919 1 chr3B.!!$F3 785
4 TraesCS3A01G232300 chr3B 709291959 709292570 611 False 564 564 84.117000 2440 3025 1 chr3B.!!$F4 585
5 TraesCS3A01G232300 chr3D 301439895 301445988 6093 True 3200 5544 94.964667 180 7152 3 chr3D.!!$R2 6972
6 TraesCS3A01G232300 chr5B 675080219 675082682 2463 False 2902 2902 87.935000 3580 6045 1 chr5B.!!$F3 2465
7 TraesCS3A01G232300 chr5B 674892250 674894700 2450 False 2887 2887 87.938000 3580 6030 1 chr5B.!!$F2 2450
8 TraesCS3A01G232300 chr7B 624351127 624353578 2451 False 2900 2900 88.020000 3580 6031 1 chr7B.!!$F1 2451
9 TraesCS3A01G232300 chr5D 534856926 534859379 2453 False 2887 2887 87.912000 3580 6033 1 chr5D.!!$F2 2453
10 TraesCS3A01G232300 chr5D 534637033 534639496 2463 False 2868 2868 87.692000 3580 6045 1 chr5D.!!$F1 2465
11 TraesCS3A01G232300 chr7D 568598503 568600954 2451 False 2867 2867 87.770000 3580 6031 1 chr7D.!!$F3 2451
12 TraesCS3A01G232300 chr7A 657353225 657355676 2451 False 2850 2850 87.648000 3580 6031 1 chr7A.!!$F1 2451
13 TraesCS3A01G232300 chr7A 34135645 34136496 851 True 1110 1110 90.164000 2116 2969 1 chr7A.!!$R1 853
14 TraesCS3A01G232300 chr1B 624822325 624823235 910 True 1291 1291 92.232000 2118 3031 1 chr1B.!!$R1 913
15 TraesCS3A01G232300 chr6D 464400789 464401681 892 True 1238 1238 91.657000 2136 3032 1 chr6D.!!$R1 896
16 TraesCS3A01G232300 chr6D 400087522 400088411 889 False 1155 1155 89.978000 2124 3029 1 chr6D.!!$F1 905
17 TraesCS3A01G232300 chr2D 555160463 555161325 862 True 1230 1230 92.388000 2166 3031 1 chr2D.!!$R2 865
18 TraesCS3A01G232300 chr4D 381411427 381412289 862 False 1197 1197 91.600000 2117 2994 1 chr4D.!!$F1 877
19 TraesCS3A01G232300 chr6B 698070510 698071404 894 True 1125 1125 89.227000 2116 3032 1 chr6B.!!$R1 916

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
778 794 0.103208 CCCTGTAGATCGTCCAGTGC 59.897 60.000 8.03 0.00 0.00 4.40 F
779 795 0.248661 CCTGTAGATCGTCCAGTGCG 60.249 60.000 8.03 0.00 0.00 5.34 F
781 797 0.450583 TGTAGATCGTCCAGTGCGTC 59.549 55.000 0.00 0.00 0.00 5.19 F
2755 2850 1.862201 TGCAGTTAAACGAACGTGGAG 59.138 47.619 0.00 0.00 43.37 3.86 F
2908 3047 0.250338 GGACCACGAGGCAAAAGACT 60.250 55.000 0.00 0.00 39.06 3.24 F
3950 4092 1.141858 CTTGGTGAGAGGATTAGGCCC 59.858 57.143 0.00 0.00 0.00 5.80 F
4970 5112 0.383002 CTGTTGTACGCGTTGCTGTG 60.383 55.000 20.78 0.23 0.00 3.66 F
5864 6006 1.264749 TTAGGGCTGCGACATCTGGT 61.265 55.000 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2368 2428 0.447801 GCGTGTGGGCAAACTGATAG 59.552 55.000 0.00 0.0 0.00 2.08 R
2734 2829 2.277969 TCCACGTTCGTTTAACTGCAA 58.722 42.857 0.00 0.0 35.81 4.08 R
2778 2873 2.966732 AATCACCACGCGTCCCCAT 61.967 57.895 9.86 0.0 0.00 4.00 R
3573 3715 1.470979 CGTAGACTTGCCTGCCGTAAT 60.471 52.381 0.00 0.0 0.00 1.89 R
4901 5043 1.188863 GGCATGCATCAACCTCCTTT 58.811 50.000 21.36 0.0 0.00 3.11 R
5354 5496 0.107831 TGTCCCAACCAAACTCCTCG 59.892 55.000 0.00 0.0 0.00 4.63 R
6108 6252 3.655615 ACAACACAACCCAAGGAACTA 57.344 42.857 0.00 0.0 38.49 2.24 R
7052 7260 3.209410 CCAGCCACATAGAAGACAATCC 58.791 50.000 0.00 0.0 0.00 3.01 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
19 20 3.138128 GCACCCGTGGGCCATAAC 61.138 66.667 10.70 0.00 39.32 1.89
20 21 2.353189 CACCCGTGGGCCATAACA 59.647 61.111 10.70 0.00 39.32 2.41
21 22 2.043980 CACCCGTGGGCCATAACAC 61.044 63.158 10.70 1.80 39.32 3.32
22 23 2.439519 CCCGTGGGCCATAACACC 60.440 66.667 10.70 0.00 34.18 4.16
23 24 2.822255 CCGTGGGCCATAACACCG 60.822 66.667 10.70 7.32 34.18 4.94
24 25 2.046700 CGTGGGCCATAACACCGT 60.047 61.111 10.70 0.00 34.18 4.83
25 26 1.673009 CGTGGGCCATAACACCGTT 60.673 57.895 10.70 0.00 34.18 4.44
26 27 0.391395 CGTGGGCCATAACACCGTTA 60.391 55.000 10.70 0.00 34.18 3.18
27 28 1.375551 GTGGGCCATAACACCGTTAG 58.624 55.000 10.70 0.00 0.00 2.34
28 29 0.985760 TGGGCCATAACACCGTTAGT 59.014 50.000 0.00 0.00 0.00 2.24
29 30 2.093553 GTGGGCCATAACACCGTTAGTA 60.094 50.000 10.70 0.00 0.00 1.82
30 31 2.773087 TGGGCCATAACACCGTTAGTAT 59.227 45.455 0.00 0.00 0.00 2.12
31 32 3.181463 TGGGCCATAACACCGTTAGTATC 60.181 47.826 0.00 0.00 0.00 2.24
32 33 3.396560 GGCCATAACACCGTTAGTATCC 58.603 50.000 0.00 0.00 0.00 2.59
33 34 3.396560 GCCATAACACCGTTAGTATCCC 58.603 50.000 0.00 0.00 0.00 3.85
34 35 3.181463 GCCATAACACCGTTAGTATCCCA 60.181 47.826 0.00 0.00 0.00 4.37
35 36 4.504340 GCCATAACACCGTTAGTATCCCAT 60.504 45.833 0.00 0.00 0.00 4.00
36 37 4.994852 CCATAACACCGTTAGTATCCCATG 59.005 45.833 0.00 0.00 0.00 3.66
37 38 5.221561 CCATAACACCGTTAGTATCCCATGA 60.222 44.000 0.00 0.00 0.00 3.07
38 39 4.829872 AACACCGTTAGTATCCCATGAA 57.170 40.909 0.00 0.00 0.00 2.57
39 40 4.133013 ACACCGTTAGTATCCCATGAAC 57.867 45.455 0.00 0.00 0.00 3.18
40 41 3.773119 ACACCGTTAGTATCCCATGAACT 59.227 43.478 0.00 0.00 0.00 3.01
41 42 4.119862 CACCGTTAGTATCCCATGAACTG 58.880 47.826 0.00 0.00 0.00 3.16
42 43 3.134081 ACCGTTAGTATCCCATGAACTGG 59.866 47.826 0.00 0.00 45.51 4.00
43 44 3.134081 CCGTTAGTATCCCATGAACTGGT 59.866 47.826 0.00 0.00 44.30 4.00
44 45 4.383770 CCGTTAGTATCCCATGAACTGGTT 60.384 45.833 0.00 0.00 44.30 3.67
45 46 5.163385 CCGTTAGTATCCCATGAACTGGTTA 60.163 44.000 0.00 0.00 44.30 2.85
46 47 6.463897 CCGTTAGTATCCCATGAACTGGTTAT 60.464 42.308 0.00 0.00 44.30 1.89
47 48 6.645415 CGTTAGTATCCCATGAACTGGTTATC 59.355 42.308 0.00 0.00 44.30 1.75
48 49 7.506114 GTTAGTATCCCATGAACTGGTTATCA 58.494 38.462 0.00 0.00 44.30 2.15
59 60 1.470098 CTGGTTATCAGGCTTGTGTGC 59.530 52.381 0.00 0.00 39.76 4.57
60 61 1.202867 TGGTTATCAGGCTTGTGTGCA 60.203 47.619 0.00 0.00 34.04 4.57
61 62 2.094675 GGTTATCAGGCTTGTGTGCAT 58.905 47.619 0.00 0.00 34.04 3.96
62 63 2.098117 GGTTATCAGGCTTGTGTGCATC 59.902 50.000 0.00 0.00 34.04 3.91
63 64 2.042686 TATCAGGCTTGTGTGCATCC 57.957 50.000 0.00 0.00 34.04 3.51
64 65 0.682209 ATCAGGCTTGTGTGCATCCC 60.682 55.000 0.00 0.00 34.04 3.85
65 66 2.360350 AGGCTTGTGTGCATCCCG 60.360 61.111 0.00 0.00 34.04 5.14
66 67 2.359850 GGCTTGTGTGCATCCCGA 60.360 61.111 0.00 0.00 34.04 5.14
67 68 2.690778 GGCTTGTGTGCATCCCGAC 61.691 63.158 0.00 0.00 34.04 4.79
68 69 2.690778 GCTTGTGTGCATCCCGACC 61.691 63.158 0.00 0.00 0.00 4.79
69 70 1.302431 CTTGTGTGCATCCCGACCA 60.302 57.895 0.00 0.00 0.00 4.02
70 71 0.888736 CTTGTGTGCATCCCGACCAA 60.889 55.000 0.00 0.00 0.00 3.67
71 72 1.169661 TTGTGTGCATCCCGACCAAC 61.170 55.000 0.00 0.00 0.00 3.77
72 73 1.599518 GTGTGCATCCCGACCAACA 60.600 57.895 0.00 0.00 0.00 3.33
73 74 0.960364 GTGTGCATCCCGACCAACAT 60.960 55.000 0.00 0.00 0.00 2.71
74 75 0.676466 TGTGCATCCCGACCAACATC 60.676 55.000 0.00 0.00 0.00 3.06
75 76 1.449423 TGCATCCCGACCAACATCG 60.449 57.895 0.00 0.00 41.89 3.84
76 77 1.153449 GCATCCCGACCAACATCGA 60.153 57.895 0.00 0.00 45.13 3.59
77 78 0.532862 GCATCCCGACCAACATCGAT 60.533 55.000 0.00 0.00 45.13 3.59
78 79 1.502231 CATCCCGACCAACATCGATC 58.498 55.000 0.00 0.00 45.13 3.69
79 80 0.393077 ATCCCGACCAACATCGATCC 59.607 55.000 0.00 0.00 45.13 3.36
80 81 0.973496 TCCCGACCAACATCGATCCA 60.973 55.000 0.00 0.00 45.13 3.41
81 82 0.810031 CCCGACCAACATCGATCCAC 60.810 60.000 0.00 0.00 45.13 4.02
82 83 0.810031 CCGACCAACATCGATCCACC 60.810 60.000 0.00 0.00 45.13 4.61
83 84 0.810031 CGACCAACATCGATCCACCC 60.810 60.000 0.00 0.00 45.13 4.61
84 85 0.251916 GACCAACATCGATCCACCCA 59.748 55.000 0.00 0.00 0.00 4.51
85 86 0.918983 ACCAACATCGATCCACCCAT 59.081 50.000 0.00 0.00 0.00 4.00
86 87 1.284785 ACCAACATCGATCCACCCATT 59.715 47.619 0.00 0.00 0.00 3.16
87 88 2.291540 ACCAACATCGATCCACCCATTT 60.292 45.455 0.00 0.00 0.00 2.32
88 89 2.358898 CCAACATCGATCCACCCATTTC 59.641 50.000 0.00 0.00 0.00 2.17
89 90 3.282021 CAACATCGATCCACCCATTTCT 58.718 45.455 0.00 0.00 0.00 2.52
90 91 3.199880 ACATCGATCCACCCATTTCTC 57.800 47.619 0.00 0.00 0.00 2.87
91 92 2.158755 ACATCGATCCACCCATTTCTCC 60.159 50.000 0.00 0.00 0.00 3.71
92 93 1.879575 TCGATCCACCCATTTCTCCT 58.120 50.000 0.00 0.00 0.00 3.69
93 94 1.762957 TCGATCCACCCATTTCTCCTC 59.237 52.381 0.00 0.00 0.00 3.71
94 95 1.765314 CGATCCACCCATTTCTCCTCT 59.235 52.381 0.00 0.00 0.00 3.69
95 96 2.484417 CGATCCACCCATTTCTCCTCTG 60.484 54.545 0.00 0.00 0.00 3.35
96 97 2.044793 TCCACCCATTTCTCCTCTGT 57.955 50.000 0.00 0.00 0.00 3.41
118 119 6.933130 TGTCGAACACGATCAATCAAATATC 58.067 36.000 0.00 0.00 38.30 1.63
119 120 6.533367 TGTCGAACACGATCAATCAAATATCA 59.467 34.615 0.00 0.00 38.30 2.15
128 129 9.590451 ACGATCAATCAAATATCAAAAGCAATT 57.410 25.926 0.00 0.00 0.00 2.32
147 148 9.801873 AAGCAATTCATTTTATACATACCACAC 57.198 29.630 0.00 0.00 0.00 3.82
153 154 6.759356 TCATTTTATACATACCACACTGGACG 59.241 38.462 0.00 0.00 40.96 4.79
154 155 4.659111 TTATACATACCACACTGGACGG 57.341 45.455 0.00 0.00 40.96 4.79
172 173 6.286758 TGGACGGTAAACACAAATACTTACA 58.713 36.000 0.00 0.00 0.00 2.41
173 174 6.765036 TGGACGGTAAACACAAATACTTACAA 59.235 34.615 0.00 0.00 0.00 2.41
176 177 7.134163 ACGGTAAACACAAATACTTACAAAGC 58.866 34.615 0.00 0.00 0.00 3.51
177 178 6.579666 CGGTAAACACAAATACTTACAAAGCC 59.420 38.462 0.00 0.00 0.00 4.35
201 202 5.460419 CGGTATCATTTAGAGCTTCTGTCAC 59.540 44.000 0.00 0.00 0.00 3.67
208 209 6.942532 TTTAGAGCTTCTGTCACAATGTTT 57.057 33.333 0.00 0.00 0.00 2.83
209 210 4.825546 AGAGCTTCTGTCACAATGTTTG 57.174 40.909 0.00 0.00 0.00 2.93
243 244 7.756722 GCAGATTTGTTGCTAGTATTCACATTT 59.243 33.333 0.00 0.00 38.51 2.32
319 320 4.044426 GGCTGCACAACAAGAAGTAAAAG 58.956 43.478 0.50 0.00 0.00 2.27
328 329 7.228706 CACAACAAGAAGTAAAAGTGGATACCT 59.771 37.037 0.00 0.00 0.00 3.08
329 330 8.434392 ACAACAAGAAGTAAAAGTGGATACCTA 58.566 33.333 0.00 0.00 0.00 3.08
443 446 1.748591 GCCCAGAAATCAGCTCGGAAT 60.749 52.381 0.00 0.00 0.00 3.01
472 475 1.600663 CGCGCATTCTCCGAACTATCT 60.601 52.381 8.75 0.00 0.00 1.98
475 478 3.560503 CGCATTCTCCGAACTATCTCTC 58.439 50.000 0.00 0.00 0.00 3.20
483 486 3.203710 TCCGAACTATCTCTCCCTTGGTA 59.796 47.826 0.00 0.00 0.00 3.25
497 500 1.252215 TTGGTACAGATCGGACGGCA 61.252 55.000 0.00 0.00 42.39 5.69
658 661 2.262915 CTTCTCCTGCGCCTTCGT 59.737 61.111 4.18 0.00 38.14 3.85
774 790 4.448720 TCTATTCCCTGTAGATCGTCCA 57.551 45.455 0.00 0.00 0.00 4.02
775 791 4.399219 TCTATTCCCTGTAGATCGTCCAG 58.601 47.826 3.25 3.25 0.00 3.86
776 792 2.526888 TTCCCTGTAGATCGTCCAGT 57.473 50.000 8.03 0.00 0.00 4.00
777 793 1.763968 TCCCTGTAGATCGTCCAGTG 58.236 55.000 8.03 0.00 0.00 3.66
778 794 0.103208 CCCTGTAGATCGTCCAGTGC 59.897 60.000 8.03 0.00 0.00 4.40
779 795 0.248661 CCTGTAGATCGTCCAGTGCG 60.249 60.000 8.03 0.00 0.00 5.34
781 797 0.450583 TGTAGATCGTCCAGTGCGTC 59.549 55.000 0.00 0.00 0.00 5.19
830 852 2.778299 TCTTGTTCTTCCCGTGGAATG 58.222 47.619 5.92 2.25 41.23 2.67
831 853 2.370519 TCTTGTTCTTCCCGTGGAATGA 59.629 45.455 5.92 4.15 41.23 2.57
844 866 7.936584 TCCCGTGGAATGATTTAACATTATTC 58.063 34.615 0.00 0.00 40.03 1.75
888 910 2.288666 GGTGCTGAATGCCGATCTAAA 58.711 47.619 0.00 0.00 42.00 1.85
945 967 4.385754 GCCCTAGATTTTTCTCCCTGATGT 60.386 45.833 0.00 0.00 0.00 3.06
985 1007 5.670097 CGATATAAATGCCGTTCTGTTGAG 58.330 41.667 0.00 0.00 0.00 3.02
1004 1030 7.632721 TGTTGAGACGTTTTAGGTGTTATTTC 58.367 34.615 0.00 0.00 0.00 2.17
1012 1038 6.521821 CGTTTTAGGTGTTATTTCACATTCGG 59.478 38.462 0.00 0.00 39.76 4.30
1029 1055 5.124936 ACATTCGGTTTTATTTCCAGTAGCC 59.875 40.000 0.00 0.00 0.00 3.93
1049 1075 8.262933 AGTAGCCGAGTTTAAATTATGTTAGGT 58.737 33.333 0.00 0.00 0.00 3.08
1355 1383 9.778741 TTCTTGCTATGTAAATAGGGATAACAG 57.221 33.333 2.03 0.00 0.00 3.16
1356 1384 9.154632 TCTTGCTATGTAAATAGGGATAACAGA 57.845 33.333 2.03 0.00 0.00 3.41
1357 1385 9.778741 CTTGCTATGTAAATAGGGATAACAGAA 57.221 33.333 2.03 0.00 0.00 3.02
1359 1387 9.725019 TGCTATGTAAATAGGGATAACAGAATG 57.275 33.333 2.03 0.00 46.00 2.67
1416 1458 6.741992 TTACCTTAGTTGTCATGCAGAATG 57.258 37.500 0.00 0.00 40.87 2.67
1482 1524 4.707448 TCCTTGTTTTCAACCTGTGCTTTA 59.293 37.500 0.00 0.00 35.77 1.85
1519 1563 8.352942 GTGTCTACTGAATTTTGTCTTTCCATT 58.647 33.333 0.00 0.00 0.00 3.16
1531 1576 4.254492 GTCTTTCCATTCTCGCTTACCTT 58.746 43.478 0.00 0.00 0.00 3.50
1549 1594 7.466860 GCTTACCTTTGTGCACTTATGTATACC 60.467 40.741 19.41 3.39 0.00 2.73
1572 1617 5.431765 CAACATAGGAGCTACCAAATCTGT 58.568 41.667 0.00 0.00 42.04 3.41
1585 1634 5.690865 ACCAAATCTGTTTAGGACTGTCAA 58.309 37.500 10.38 0.00 0.00 3.18
1586 1635 6.306987 ACCAAATCTGTTTAGGACTGTCAAT 58.693 36.000 10.38 0.00 0.00 2.57
1587 1636 6.431234 ACCAAATCTGTTTAGGACTGTCAATC 59.569 38.462 10.38 0.00 0.00 2.67
1588 1637 6.430925 CCAAATCTGTTTAGGACTGTCAATCA 59.569 38.462 10.38 1.50 0.00 2.57
1681 1730 6.930667 TGGTTACTACTTTTGAACAGGAAC 57.069 37.500 0.00 0.00 32.12 3.62
2199 2256 4.275662 CGTTTGTGTTTGCACGAATCTTA 58.724 39.130 4.05 0.00 46.94 2.10
2201 2258 5.270853 GTTTGTGTTTGCACGAATCTTAGT 58.729 37.500 4.05 0.00 46.94 2.24
2594 2662 6.215845 AGTTTTCAAATCATGGCAACTGTAC 58.784 36.000 0.00 0.00 33.19 2.90
2734 2829 3.156293 TGTAGTTCAGCAACATGGCAAT 58.844 40.909 0.00 0.00 34.60 3.56
2750 2845 2.403698 GGCAATTGCAGTTAAACGAACG 59.596 45.455 30.32 0.00 44.36 3.95
2755 2850 1.862201 TGCAGTTAAACGAACGTGGAG 59.138 47.619 0.00 0.00 43.37 3.86
2778 2873 1.600107 GTCCGGACCATGGCAACTA 59.400 57.895 24.75 0.00 37.61 2.24
2795 2890 2.028125 CTATGGGGACGCGTGGTGAT 62.028 60.000 20.70 6.03 0.00 3.06
2831 2926 2.200052 GGAACGGTGAGGTAGGAGG 58.800 63.158 0.00 0.00 0.00 4.30
2832 2927 1.516423 GAACGGTGAGGTAGGAGGC 59.484 63.158 0.00 0.00 0.00 4.70
2833 2928 1.957765 GAACGGTGAGGTAGGAGGCC 61.958 65.000 0.00 0.00 0.00 5.19
2834 2929 3.528370 CGGTGAGGTAGGAGGCCG 61.528 72.222 0.00 0.00 0.00 6.13
2837 2947 2.043248 TGAGGTAGGAGGCCGGAC 60.043 66.667 5.05 0.00 0.00 4.79
2908 3047 0.250338 GGACCACGAGGCAAAAGACT 60.250 55.000 0.00 0.00 39.06 3.24
3178 3318 7.726291 TCAATGGATAACCTGTTTGTTCCTTTA 59.274 33.333 0.00 0.00 37.04 1.85
3214 3354 7.220030 TCTGATCATCCAGGATTTAAAGCTAC 58.780 38.462 0.00 0.00 34.99 3.58
3259 3399 8.891671 AAATGGGTGATTATTTCAATATGTGC 57.108 30.769 0.00 0.00 35.70 4.57
3272 3412 8.755696 TTTCAATATGTGCTGGTTGTATTTTC 57.244 30.769 0.00 0.00 0.00 2.29
3287 3428 9.158233 GGTTGTATTTTCTGTACTGCATAGTTA 57.842 33.333 0.00 0.00 38.36 2.24
3347 3489 7.134362 TCATCAAGCCATTTTCTATCTCTCT 57.866 36.000 0.00 0.00 0.00 3.10
3430 3572 5.665916 ATCCCTGAATTCCAACATTTGTC 57.334 39.130 2.27 0.00 0.00 3.18
3443 3585 6.486657 TCCAACATTTGTCTACTCTCCTTTTG 59.513 38.462 0.00 0.00 0.00 2.44
3452 3594 1.421646 ACTCTCCTTTTGGTGGGTCAG 59.578 52.381 0.00 0.00 42.67 3.51
3458 3600 2.499693 CCTTTTGGTGGGTCAGTGTTTT 59.500 45.455 0.00 0.00 34.07 2.43
3476 3618 6.017605 AGTGTTTTGACTGTGCTCTATCTTTG 60.018 38.462 0.00 0.00 0.00 2.77
3478 3620 6.989759 TGTTTTGACTGTGCTCTATCTTTGTA 59.010 34.615 0.00 0.00 0.00 2.41
3481 3623 4.220602 TGACTGTGCTCTATCTTTGTAGCA 59.779 41.667 0.00 0.00 42.41 3.49
3484 3626 5.814705 ACTGTGCTCTATCTTTGTAGCATTC 59.185 40.000 0.00 0.00 45.86 2.67
3508 3650 2.574322 CGCTCCGTTTCTTGTTCAATG 58.426 47.619 0.00 0.00 0.00 2.82
3522 3664 6.262944 TCTTGTTCAATGTTAAGAGTGTGCAT 59.737 34.615 0.00 0.00 0.00 3.96
3524 3666 6.207928 TGTTCAATGTTAAGAGTGTGCATTG 58.792 36.000 8.69 8.69 44.34 2.82
3525 3667 6.183360 TGTTCAATGTTAAGAGTGTGCATTGT 60.183 34.615 13.06 0.00 43.77 2.71
3526 3668 7.012799 TGTTCAATGTTAAGAGTGTGCATTGTA 59.987 33.333 13.06 3.90 43.77 2.41
3527 3669 7.503521 TCAATGTTAAGAGTGTGCATTGTAA 57.496 32.000 13.06 0.00 43.77 2.41
3528 3670 8.109705 TCAATGTTAAGAGTGTGCATTGTAAT 57.890 30.769 13.06 0.00 43.77 1.89
3558 3700 9.691362 ATGTTATTAACTCATGTTTTTGACCAC 57.309 29.630 7.99 0.00 37.59 4.16
3559 3701 8.687242 TGTTATTAACTCATGTTTTTGACCACA 58.313 29.630 7.99 0.00 37.59 4.17
3608 3750 6.458478 GCAAGTCTACGCTTACTGATTCTCTA 60.458 42.308 0.00 0.00 0.00 2.43
3753 3895 4.715792 AGATGACTGATGAATCACTCAGGT 59.284 41.667 19.27 10.17 42.56 4.00
3950 4092 1.141858 CTTGGTGAGAGGATTAGGCCC 59.858 57.143 0.00 0.00 0.00 5.80
4160 4302 2.092429 TGGATGGGCATTTACTCTCACC 60.092 50.000 0.00 0.00 0.00 4.02
4523 4665 1.657804 TCCACCTTCCTTCTCCTTCC 58.342 55.000 0.00 0.00 0.00 3.46
4535 4677 3.576078 TCTCCTTCCAAAGCACAGAAA 57.424 42.857 0.00 0.00 0.00 2.52
4901 5043 2.851263 ATGCTACCCTGACAAACGAA 57.149 45.000 0.00 0.00 0.00 3.85
4928 5070 1.752498 GTTGATGCATGCCCAATCAGA 59.248 47.619 20.62 10.04 0.00 3.27
4940 5082 4.020039 TGCCCAATCAGAGCAATGAAATTT 60.020 37.500 0.00 0.00 31.22 1.82
4970 5112 0.383002 CTGTTGTACGCGTTGCTGTG 60.383 55.000 20.78 0.23 0.00 3.66
5006 5148 4.006319 CCTCTGATCTTCCCAAACTTGTC 58.994 47.826 0.00 0.00 0.00 3.18
5160 5302 4.411869 TCATGGGTGGTGCTGAGATTATTA 59.588 41.667 0.00 0.00 0.00 0.98
5354 5496 2.266055 CGCTCCAAGGTCCTGTCC 59.734 66.667 0.00 0.00 0.00 4.02
5630 5772 2.356780 CCCGACGGCTAGAAGGGTT 61.357 63.158 8.86 0.00 36.10 4.11
5669 5811 3.072476 TCACAGCTAAGCCAAGGTTACTT 59.928 43.478 0.00 0.00 37.43 2.24
5684 5826 3.512724 GGTTACTTGAGCCTGTGTACCTA 59.487 47.826 0.00 0.00 0.00 3.08
5864 6006 1.264749 TTAGGGCTGCGACATCTGGT 61.265 55.000 0.00 0.00 0.00 4.00
5969 6111 3.054728 TGGTTTTGGATATCCGCAAGAGA 60.055 43.478 17.04 0.00 39.43 3.10
6056 6198 5.366477 TCCCATGTTATCTGTTATCTCAGCA 59.634 40.000 0.00 0.00 35.63 4.41
6153 6298 5.434352 TGAACCTATTTCGGTCTCTATCG 57.566 43.478 0.00 0.00 36.97 2.92
6349 6494 9.683069 AAACTTGAGCAGATTGTTGTAAATTAG 57.317 29.630 0.00 0.00 0.00 1.73
6350 6495 7.308435 ACTTGAGCAGATTGTTGTAAATTAGC 58.692 34.615 0.00 0.00 0.00 3.09
6378 6523 6.056884 TGCCATTTCTTTGCAAGAGATTTTT 58.943 32.000 0.00 0.00 39.03 1.94
6466 6641 9.772973 AGAAACACTGTACACTGTATTATTTCA 57.227 29.630 8.35 0.00 0.00 2.69
6600 6806 1.475280 CATTGTCCATTGTGCTCTGGG 59.525 52.381 0.00 0.00 33.13 4.45
6813 7019 6.414694 ACGTATGCAATTGAAATAGCAAATCG 59.585 34.615 10.34 7.78 40.76 3.34
6827 7033 2.817844 GCAAATCGTCTTAACCCTGGTT 59.182 45.455 6.81 6.81 41.65 3.67
6946 7154 8.718158 AAATGTGAGACTGATGGAGAGATATA 57.282 34.615 0.00 0.00 0.00 0.86
7051 7259 0.892358 CCCTGAAGCACATGCACACT 60.892 55.000 6.64 0.00 45.16 3.55
7052 7260 0.240145 CCTGAAGCACATGCACACTG 59.760 55.000 6.64 0.00 45.16 3.66
7065 7273 4.558226 TGCACACTGGATTGTCTTCTAT 57.442 40.909 0.00 0.00 0.00 1.98
7076 7284 3.057969 TGTCTTCTATGTGGCTGGTTG 57.942 47.619 0.00 0.00 0.00 3.77
7120 7328 5.466127 AATTTATCACCCTGCTCCCTTTA 57.534 39.130 0.00 0.00 0.00 1.85
7152 7360 8.201554 TGTGCATGAACTTGACTCTTATTATC 57.798 34.615 5.18 0.00 0.00 1.75
7153 7361 7.823799 TGTGCATGAACTTGACTCTTATTATCA 59.176 33.333 5.18 0.00 0.00 2.15
7154 7362 8.333908 GTGCATGAACTTGACTCTTATTATCAG 58.666 37.037 0.00 0.00 0.00 2.90
7155 7363 8.260114 TGCATGAACTTGACTCTTATTATCAGA 58.740 33.333 0.00 0.00 0.00 3.27
7156 7364 9.270640 GCATGAACTTGACTCTTATTATCAGAT 57.729 33.333 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.138128 GTTATGGCCCACGGGTGC 61.138 66.667 0.00 0.00 37.65 5.01
3 4 2.043980 GTGTTATGGCCCACGGGTG 61.044 63.158 0.00 0.00 37.65 4.61
5 6 2.439519 GGTGTTATGGCCCACGGG 60.440 66.667 0.00 0.00 38.57 5.28
6 7 2.822255 CGGTGTTATGGCCCACGG 60.822 66.667 0.00 1.25 32.30 4.94
8 9 1.339342 ACTAACGGTGTTATGGCCCAC 60.339 52.381 0.00 0.00 0.00 4.61
9 10 0.985760 ACTAACGGTGTTATGGCCCA 59.014 50.000 0.00 0.00 0.00 5.36
10 11 2.985957 TACTAACGGTGTTATGGCCC 57.014 50.000 0.00 0.00 0.00 5.80
11 12 3.396560 GGATACTAACGGTGTTATGGCC 58.603 50.000 0.00 0.00 0.00 5.36
12 13 3.181463 TGGGATACTAACGGTGTTATGGC 60.181 47.826 0.00 0.00 0.00 4.40
13 14 4.675976 TGGGATACTAACGGTGTTATGG 57.324 45.455 0.00 0.00 0.00 2.74
14 15 5.849510 TCATGGGATACTAACGGTGTTATG 58.150 41.667 0.00 0.00 0.00 1.90
15 16 6.099269 AGTTCATGGGATACTAACGGTGTTAT 59.901 38.462 0.00 0.00 0.00 1.89
16 17 5.422970 AGTTCATGGGATACTAACGGTGTTA 59.577 40.000 0.00 0.00 0.00 2.41
17 18 4.224370 AGTTCATGGGATACTAACGGTGTT 59.776 41.667 0.00 0.00 0.00 3.32
18 19 3.773119 AGTTCATGGGATACTAACGGTGT 59.227 43.478 0.00 0.00 0.00 4.16
19 20 4.119862 CAGTTCATGGGATACTAACGGTG 58.880 47.826 0.00 0.00 0.00 4.94
20 21 3.134081 CCAGTTCATGGGATACTAACGGT 59.866 47.826 0.00 0.00 46.36 4.83
21 22 3.728845 CCAGTTCATGGGATACTAACGG 58.271 50.000 0.00 0.00 46.36 4.44
33 34 4.012374 ACAAGCCTGATAACCAGTTCATG 58.988 43.478 0.00 0.00 41.33 3.07
34 35 4.012374 CACAAGCCTGATAACCAGTTCAT 58.988 43.478 0.00 0.00 41.33 2.57
35 36 3.181445 ACACAAGCCTGATAACCAGTTCA 60.181 43.478 0.00 0.00 41.33 3.18
36 37 3.189287 CACACAAGCCTGATAACCAGTTC 59.811 47.826 0.00 0.00 41.33 3.01
37 38 3.149196 CACACAAGCCTGATAACCAGTT 58.851 45.455 0.00 0.00 41.33 3.16
38 39 2.783135 CACACAAGCCTGATAACCAGT 58.217 47.619 0.00 0.00 41.33 4.00
39 40 1.470098 GCACACAAGCCTGATAACCAG 59.530 52.381 0.00 0.00 42.55 4.00
40 41 1.202867 TGCACACAAGCCTGATAACCA 60.203 47.619 0.00 0.00 0.00 3.67
41 42 1.533625 TGCACACAAGCCTGATAACC 58.466 50.000 0.00 0.00 0.00 2.85
42 43 2.098117 GGATGCACACAAGCCTGATAAC 59.902 50.000 0.00 0.00 0.00 1.89
43 44 2.368439 GGATGCACACAAGCCTGATAA 58.632 47.619 0.00 0.00 0.00 1.75
44 45 1.408683 GGGATGCACACAAGCCTGATA 60.409 52.381 0.00 0.00 0.00 2.15
45 46 0.682209 GGGATGCACACAAGCCTGAT 60.682 55.000 0.00 0.00 0.00 2.90
46 47 1.303561 GGGATGCACACAAGCCTGA 60.304 57.895 0.00 0.00 0.00 3.86
47 48 2.693762 CGGGATGCACACAAGCCTG 61.694 63.158 0.00 0.00 0.00 4.85
48 49 2.360350 CGGGATGCACACAAGCCT 60.360 61.111 0.00 0.00 0.00 4.58
49 50 2.359850 TCGGGATGCACACAAGCC 60.360 61.111 0.00 0.00 0.00 4.35
50 51 2.690778 GGTCGGGATGCACACAAGC 61.691 63.158 0.00 0.00 0.00 4.01
51 52 0.888736 TTGGTCGGGATGCACACAAG 60.889 55.000 0.00 0.00 0.00 3.16
52 53 1.149401 TTGGTCGGGATGCACACAA 59.851 52.632 0.00 0.00 0.00 3.33
53 54 1.599518 GTTGGTCGGGATGCACACA 60.600 57.895 0.00 0.00 0.00 3.72
54 55 0.960364 ATGTTGGTCGGGATGCACAC 60.960 55.000 0.00 0.00 0.00 3.82
55 56 0.676466 GATGTTGGTCGGGATGCACA 60.676 55.000 0.00 0.00 0.00 4.57
56 57 1.705337 CGATGTTGGTCGGGATGCAC 61.705 60.000 0.00 0.00 37.94 4.57
57 58 1.449423 CGATGTTGGTCGGGATGCA 60.449 57.895 0.00 0.00 37.94 3.96
58 59 0.532862 ATCGATGTTGGTCGGGATGC 60.533 55.000 0.00 0.00 41.74 3.91
59 60 1.502231 GATCGATGTTGGTCGGGATG 58.498 55.000 0.54 0.00 41.74 3.51
60 61 0.393077 GGATCGATGTTGGTCGGGAT 59.607 55.000 0.54 0.00 41.74 3.85
61 62 0.973496 TGGATCGATGTTGGTCGGGA 60.973 55.000 0.54 0.00 41.74 5.14
62 63 0.810031 GTGGATCGATGTTGGTCGGG 60.810 60.000 0.54 0.00 41.74 5.14
63 64 0.810031 GGTGGATCGATGTTGGTCGG 60.810 60.000 0.54 0.00 41.74 4.79
64 65 0.810031 GGGTGGATCGATGTTGGTCG 60.810 60.000 0.54 0.00 42.74 4.79
65 66 0.251916 TGGGTGGATCGATGTTGGTC 59.748 55.000 0.54 0.00 0.00 4.02
66 67 0.918983 ATGGGTGGATCGATGTTGGT 59.081 50.000 0.54 0.00 0.00 3.67
67 68 2.057137 AATGGGTGGATCGATGTTGG 57.943 50.000 0.54 0.00 0.00 3.77
68 69 3.282021 AGAAATGGGTGGATCGATGTTG 58.718 45.455 0.54 0.00 0.00 3.33
69 70 3.545703 GAGAAATGGGTGGATCGATGTT 58.454 45.455 0.54 0.00 0.00 2.71
70 71 2.158755 GGAGAAATGGGTGGATCGATGT 60.159 50.000 0.54 0.00 0.00 3.06
71 72 2.105477 AGGAGAAATGGGTGGATCGATG 59.895 50.000 0.54 0.00 0.00 3.84
72 73 2.370189 GAGGAGAAATGGGTGGATCGAT 59.630 50.000 0.00 0.00 0.00 3.59
73 74 1.762957 GAGGAGAAATGGGTGGATCGA 59.237 52.381 0.00 0.00 0.00 3.59
74 75 1.765314 AGAGGAGAAATGGGTGGATCG 59.235 52.381 0.00 0.00 0.00 3.69
75 76 2.507471 ACAGAGGAGAAATGGGTGGATC 59.493 50.000 0.00 0.00 0.00 3.36
76 77 2.507471 GACAGAGGAGAAATGGGTGGAT 59.493 50.000 0.00 0.00 0.00 3.41
77 78 1.909302 GACAGAGGAGAAATGGGTGGA 59.091 52.381 0.00 0.00 0.00 4.02
78 79 1.406069 CGACAGAGGAGAAATGGGTGG 60.406 57.143 0.00 0.00 0.00 4.61
79 80 1.550524 TCGACAGAGGAGAAATGGGTG 59.449 52.381 0.00 0.00 0.00 4.61
80 81 1.938585 TCGACAGAGGAGAAATGGGT 58.061 50.000 0.00 0.00 0.00 4.51
81 82 2.028112 TGTTCGACAGAGGAGAAATGGG 60.028 50.000 0.00 0.00 0.00 4.00
82 83 2.996621 GTGTTCGACAGAGGAGAAATGG 59.003 50.000 0.00 0.00 0.00 3.16
83 84 2.663602 CGTGTTCGACAGAGGAGAAATG 59.336 50.000 0.00 0.00 39.71 2.32
84 85 2.557056 TCGTGTTCGACAGAGGAGAAAT 59.443 45.455 0.00 0.00 41.35 2.17
85 86 1.951602 TCGTGTTCGACAGAGGAGAAA 59.048 47.619 0.00 0.00 41.35 2.52
86 87 1.601166 TCGTGTTCGACAGAGGAGAA 58.399 50.000 0.00 0.00 41.35 2.87
87 88 3.317449 TCGTGTTCGACAGAGGAGA 57.683 52.632 0.00 0.00 41.35 3.71
128 129 6.759356 CGTCCAGTGTGGTATGTATAAAATGA 59.241 38.462 0.00 0.00 39.03 2.57
129 130 6.018262 CCGTCCAGTGTGGTATGTATAAAATG 60.018 42.308 0.00 0.00 39.03 2.32
135 136 2.463752 ACCGTCCAGTGTGGTATGTAT 58.536 47.619 0.00 0.00 39.03 2.29
137 138 1.927487 TACCGTCCAGTGTGGTATGT 58.073 50.000 2.88 0.00 39.03 2.29
147 148 5.934935 AAGTATTTGTGTTTACCGTCCAG 57.065 39.130 0.00 0.00 0.00 3.86
153 154 6.579666 CGGCTTTGTAAGTATTTGTGTTTACC 59.420 38.462 0.00 0.00 0.00 2.85
154 155 6.579666 CCGGCTTTGTAAGTATTTGTGTTTAC 59.420 38.462 0.00 0.00 0.00 2.01
172 173 4.423625 AGCTCTAAATGATACCGGCTTT 57.576 40.909 0.00 0.00 0.00 3.51
173 174 4.101741 AGAAGCTCTAAATGATACCGGCTT 59.898 41.667 0.00 0.00 40.71 4.35
176 177 4.950050 ACAGAAGCTCTAAATGATACCGG 58.050 43.478 0.00 0.00 0.00 5.28
177 178 5.460419 GTGACAGAAGCTCTAAATGATACCG 59.540 44.000 0.00 0.00 0.00 4.02
201 202 7.810658 ACAAATCTGCTCTACTACAAACATTG 58.189 34.615 0.00 0.00 0.00 2.82
243 244 5.293079 GTGCAACTTTTTCAGCCAAAATACA 59.707 36.000 0.00 0.00 33.82 2.29
335 336 5.222254 TGGCCCTTACTCTTCCATTTTTACT 60.222 40.000 0.00 0.00 0.00 2.24
414 417 1.339055 TGATTTCTGGGCCACTCTTCG 60.339 52.381 0.00 0.00 0.00 3.79
443 446 0.459585 GAGAATGCGCGGTGGACTTA 60.460 55.000 8.83 0.00 0.00 2.24
472 475 1.286849 TCCGATCTGTACCAAGGGAGA 59.713 52.381 0.00 0.00 0.00 3.71
475 478 0.102481 CGTCCGATCTGTACCAAGGG 59.898 60.000 0.00 0.00 0.00 3.95
483 486 2.413351 CGATGCCGTCCGATCTGT 59.587 61.111 0.00 0.00 0.00 3.41
497 500 4.521062 GGCTGTGAGGCGAGCGAT 62.521 66.667 0.00 0.00 35.95 4.58
507 510 4.662961 CTGTCCGTGCGGCTGTGA 62.663 66.667 5.64 0.00 34.68 3.58
614 617 4.512914 GATCCCCCAGTGGCCTGC 62.513 72.222 3.32 0.00 37.38 4.85
623 626 2.122989 GACCTAGGCGATCCCCCA 60.123 66.667 9.30 0.00 0.00 4.96
774 790 1.157870 CCAAAACCACTCGACGCACT 61.158 55.000 0.00 0.00 0.00 4.40
775 791 1.278637 CCAAAACCACTCGACGCAC 59.721 57.895 0.00 0.00 0.00 5.34
776 792 1.153329 ACCAAAACCACTCGACGCA 60.153 52.632 0.00 0.00 0.00 5.24
777 793 1.568025 GACCAAAACCACTCGACGC 59.432 57.895 0.00 0.00 0.00 5.19
778 794 0.531090 TGGACCAAAACCACTCGACG 60.531 55.000 0.00 0.00 32.03 5.12
779 795 1.226746 CTGGACCAAAACCACTCGAC 58.773 55.000 0.00 0.00 33.57 4.20
781 797 0.535102 AGCTGGACCAAAACCACTCG 60.535 55.000 0.00 0.00 33.57 4.18
830 852 9.316730 TGTACCCACTACGAATAATGTTAAATC 57.683 33.333 0.00 0.00 0.00 2.17
831 853 9.669887 TTGTACCCACTACGAATAATGTTAAAT 57.330 29.630 0.00 0.00 0.00 1.40
844 866 4.159135 AGACCATTACTTGTACCCACTACG 59.841 45.833 0.00 0.00 0.00 3.51
888 910 9.988815 GTGATACAAAAGATACATCTACCAGAT 57.011 33.333 0.00 0.00 35.76 2.90
945 967 9.647797 ATTTATATCGCATCAGACGGTAAAATA 57.352 29.630 0.00 0.00 28.55 1.40
985 1007 7.267600 CGAATGTGAAATAACACCTAAAACGTC 59.732 37.037 0.00 0.00 39.69 4.34
1004 1030 6.027749 GCTACTGGAAATAAAACCGAATGTG 58.972 40.000 0.00 0.00 0.00 3.21
1012 1038 5.874895 AACTCGGCTACTGGAAATAAAAC 57.125 39.130 0.00 0.00 0.00 2.43
1075 1101 5.458015 GCCCTGCGGAAACAATATATTTAC 58.542 41.667 0.00 0.00 0.00 2.01
1081 1107 0.033601 TGGCCCTGCGGAAACAATAT 60.034 50.000 0.00 0.00 0.00 1.28
1288 1316 7.939588 AGTAGAGATAACAGAAAACAAAGCCTT 59.060 33.333 0.00 0.00 0.00 4.35
1329 1357 9.778741 CTGTTATCCCTATTTACATAGCAAGAA 57.221 33.333 0.00 0.00 32.17 2.52
1366 1394 8.458573 TGTTGTACCATTAAACATTTCAGTCT 57.541 30.769 0.00 0.00 0.00 3.24
1367 1395 9.691362 AATGTTGTACCATTAAACATTTCAGTC 57.309 29.630 12.89 0.00 46.91 3.51
1416 1458 8.030106 GCCAGGTGATACTTCAGTCTATATTAC 58.970 40.741 0.00 0.00 30.85 1.89
1433 1475 5.387788 TCAATATAATGCAAGCCAGGTGAT 58.612 37.500 0.00 0.00 0.00 3.06
1493 1537 7.259290 TGGAAAGACAAAATTCAGTAGACAC 57.741 36.000 0.00 0.00 0.00 3.67
1499 1543 6.672147 CGAGAATGGAAAGACAAAATTCAGT 58.328 36.000 0.00 0.00 31.15 3.41
1501 1545 5.241506 AGCGAGAATGGAAAGACAAAATTCA 59.758 36.000 0.00 0.00 31.15 2.57
1519 1563 1.070134 AGTGCACAAAGGTAAGCGAGA 59.930 47.619 21.04 0.00 0.00 4.04
1531 1576 7.497579 CCTATGTTGGTATACATAAGTGCACAA 59.502 37.037 21.04 7.03 39.72 3.33
1549 1594 5.431765 ACAGATTTGGTAGCTCCTATGTTG 58.568 41.667 0.00 0.00 37.07 3.33
1572 1617 7.918076 AGGTAGAAATGATTGACAGTCCTAAA 58.082 34.615 0.00 0.00 0.00 1.85
2108 2165 4.642437 TGGGCGTTATCTTTTTCATATGCA 59.358 37.500 0.00 0.00 0.00 3.96
2109 2166 4.976116 GTGGGCGTTATCTTTTTCATATGC 59.024 41.667 0.00 0.00 0.00 3.14
2110 2167 5.971202 GTGTGGGCGTTATCTTTTTCATATG 59.029 40.000 0.00 0.00 0.00 1.78
2111 2168 5.220777 CGTGTGGGCGTTATCTTTTTCATAT 60.221 40.000 0.00 0.00 0.00 1.78
2112 2169 4.093703 CGTGTGGGCGTTATCTTTTTCATA 59.906 41.667 0.00 0.00 0.00 2.15
2113 2170 3.119990 CGTGTGGGCGTTATCTTTTTCAT 60.120 43.478 0.00 0.00 0.00 2.57
2114 2171 2.224549 CGTGTGGGCGTTATCTTTTTCA 59.775 45.455 0.00 0.00 0.00 2.69
2368 2428 0.447801 GCGTGTGGGCAAACTGATAG 59.552 55.000 0.00 0.00 0.00 2.08
2734 2829 2.277969 TCCACGTTCGTTTAACTGCAA 58.722 42.857 0.00 0.00 35.81 4.08
2750 2845 3.075641 GTCCGGACCCTCCTCCAC 61.076 72.222 24.75 0.00 33.30 4.02
2778 2873 2.966732 AATCACCACGCGTCCCCAT 61.967 57.895 9.86 0.00 0.00 4.00
2818 2913 3.155167 CCGGCCTCCTACCTCACC 61.155 72.222 0.00 0.00 0.00 4.02
2821 2916 2.615227 TACGTCCGGCCTCCTACCTC 62.615 65.000 0.00 0.00 0.00 3.85
2822 2917 2.683465 TACGTCCGGCCTCCTACCT 61.683 63.158 0.00 0.00 0.00 3.08
2823 2918 2.124151 TACGTCCGGCCTCCTACC 60.124 66.667 0.00 0.00 0.00 3.18
2824 2919 2.828128 CGTACGTCCGGCCTCCTAC 61.828 68.421 7.22 0.00 0.00 3.18
2825 2920 2.514592 CGTACGTCCGGCCTCCTA 60.515 66.667 7.22 0.00 0.00 2.94
2908 3047 0.036164 AAGTAATGCCCACACGCTCA 59.964 50.000 0.00 0.00 0.00 4.26
2957 3096 6.034591 CGTTTCGTGTGGTATCTAAGAGAAT 58.965 40.000 0.00 0.00 0.00 2.40
3178 3318 7.819500 TCCTGGATGATCAGATCCTTAAAATT 58.180 34.615 14.93 0.00 42.36 1.82
3214 3354 8.028938 CCCATTTACTTCAGGACAATACAAAAG 58.971 37.037 0.00 0.00 0.00 2.27
3259 3399 5.940192 TGCAGTACAGAAAATACAACCAG 57.060 39.130 0.00 0.00 0.00 4.00
3430 3572 2.637872 TGACCCACCAAAAGGAGAGTAG 59.362 50.000 0.00 0.00 0.00 2.57
3443 3585 1.676006 CAGTCAAAACACTGACCCACC 59.324 52.381 0.24 0.00 45.92 4.61
3452 3594 5.931441 AAGATAGAGCACAGTCAAAACAC 57.069 39.130 0.00 0.00 0.00 3.32
3458 3600 4.220602 TGCTACAAAGATAGAGCACAGTCA 59.779 41.667 0.00 0.00 39.93 3.41
3476 3618 0.030908 ACGGAGCGCTAGAATGCTAC 59.969 55.000 11.50 4.70 42.60 3.58
3478 3620 0.108138 AAACGGAGCGCTAGAATGCT 60.108 50.000 11.50 4.48 45.90 3.79
3481 3623 2.271800 CAAGAAACGGAGCGCTAGAAT 58.728 47.619 11.50 2.02 0.00 2.40
3484 3626 1.390463 GAACAAGAAACGGAGCGCTAG 59.610 52.381 11.50 10.82 0.00 3.42
3532 3674 9.691362 GTGGTCAAAAACATGAGTTAATAACAT 57.309 29.630 0.00 0.00 36.84 2.71
3534 3676 9.691362 ATGTGGTCAAAAACATGAGTTAATAAC 57.309 29.630 0.00 0.00 36.84 1.89
3536 3678 9.906660 GAATGTGGTCAAAAACATGAGTTAATA 57.093 29.630 0.00 0.00 37.11 0.98
3537 3679 8.420222 TGAATGTGGTCAAAAACATGAGTTAAT 58.580 29.630 0.00 0.00 37.11 1.40
3539 3681 7.340122 TGAATGTGGTCAAAAACATGAGTTA 57.660 32.000 0.00 0.00 37.11 2.24
3540 3682 6.219417 TGAATGTGGTCAAAAACATGAGTT 57.781 33.333 0.00 0.00 37.11 3.01
3541 3683 5.850557 TGAATGTGGTCAAAAACATGAGT 57.149 34.783 0.00 0.00 37.11 3.41
3542 3684 5.636121 CCATGAATGTGGTCAAAAACATGAG 59.364 40.000 0.00 0.00 37.11 2.90
3558 3700 6.255453 CCTGCCGTAATTAAAAACCATGAATG 59.745 38.462 0.00 0.00 0.00 2.67
3559 3701 6.337356 CCTGCCGTAATTAAAAACCATGAAT 58.663 36.000 0.00 0.00 0.00 2.57
3573 3715 1.470979 CGTAGACTTGCCTGCCGTAAT 60.471 52.381 0.00 0.00 0.00 1.89
3608 3750 1.565390 TAATCCCAGCAGCTGCCACT 61.565 55.000 34.39 14.59 43.38 4.00
3753 3895 4.082845 CCATCTCTCTCGCCCTTATAAGA 58.917 47.826 14.28 0.00 0.00 2.10
3950 4092 3.679980 CCATCTTGTTCACAGTAAGGACG 59.320 47.826 0.00 0.00 0.00 4.79
4160 4302 5.220931 GGAGGCATACATCTTAGCAAAGTTG 60.221 44.000 0.00 0.00 38.07 3.16
4523 4665 6.531594 TCTCTACACGATATTTCTGTGCTTTG 59.468 38.462 0.00 0.00 37.11 2.77
4535 4677 7.040340 CCCTCATACAAGTTCTCTACACGATAT 60.040 40.741 0.00 0.00 0.00 1.63
4901 5043 1.188863 GGCATGCATCAACCTCCTTT 58.811 50.000 21.36 0.00 0.00 3.11
4928 5070 5.960202 AGGGGATACAGAAAATTTCATTGCT 59.040 36.000 8.55 0.00 39.74 3.91
4940 5082 2.093869 GCGTACAACAGGGGATACAGAA 60.094 50.000 0.00 0.00 39.74 3.02
5160 5302 2.637165 AGAGACAACAGGAGGGGAAAT 58.363 47.619 0.00 0.00 0.00 2.17
5307 5449 4.094646 ATCACGTGGGCCGATGCA 62.095 61.111 17.00 0.00 40.13 3.96
5354 5496 0.107831 TGTCCCAACCAAACTCCTCG 59.892 55.000 0.00 0.00 0.00 4.63
5630 5772 4.813161 GCTGTGAGCTGAGAAGCATAAATA 59.187 41.667 0.00 0.00 38.45 1.40
5669 5811 1.076513 TCCACTAGGTACACAGGCTCA 59.923 52.381 0.00 0.00 35.89 4.26
5684 5826 1.081833 AGGTGCCTGGATCTCCACT 59.918 57.895 0.00 0.00 42.01 4.00
5699 5841 1.546323 CCACCAAGTGCATTCTCAGGT 60.546 52.381 0.00 0.00 31.34 4.00
5864 6006 4.020617 CACTGCGGGAAGGCCTGA 62.021 66.667 5.69 0.00 43.76 3.86
5969 6111 5.069119 GGTCATCTGTTCTTTCAACCCTTTT 59.931 40.000 0.00 0.00 0.00 2.27
6056 6198 7.816031 CACAGACCAAGCATAGATCAAAAATTT 59.184 33.333 0.00 0.00 0.00 1.82
6108 6252 3.655615 ACAACACAACCCAAGGAACTA 57.344 42.857 0.00 0.00 38.49 2.24
6185 6330 8.186821 GCTAAAATCAACTACTCAATCAAGCAT 58.813 33.333 0.00 0.00 0.00 3.79
6186 6331 7.174772 TGCTAAAATCAACTACTCAATCAAGCA 59.825 33.333 0.00 0.00 0.00 3.91
6387 6532 4.991776 AGCTCTGAGCATAGTCCTACATA 58.008 43.478 29.49 0.00 45.56 2.29
6399 6544 4.541973 TTCACATTAGAAGCTCTGAGCA 57.458 40.909 29.49 10.61 45.56 4.26
6466 6641 9.113838 AGTTAAATGCAAGAGAATTATCGTCAT 57.886 29.630 0.00 0.00 0.00 3.06
6480 6655 6.645003 GGGGTGTTTCTTAAGTTAAATGCAAG 59.355 38.462 1.63 0.00 0.00 4.01
6600 6806 8.213518 TCAAGAGTGAACTTCCATTTATATGC 57.786 34.615 0.00 0.00 0.00 3.14
6813 7019 7.520451 AAACAGAAATAACCAGGGTTAAGAC 57.480 36.000 14.42 8.75 42.82 3.01
6946 7154 5.277828 GGTGACAACTCGAAGCAAAGTAATT 60.278 40.000 0.00 0.00 0.00 1.40
7051 7259 3.370846 CCAGCCACATAGAAGACAATCCA 60.371 47.826 0.00 0.00 0.00 3.41
7052 7260 3.209410 CCAGCCACATAGAAGACAATCC 58.791 50.000 0.00 0.00 0.00 3.01
7076 7284 7.889589 ATTTGGTAAGAAAATGCAGTTAAGC 57.110 32.000 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.