Multiple sequence alignment - TraesCS6A01G167300

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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 TraesCS6A01G167300 chr6A 100.000 8989 0 0 1 8989 170902625 170911613 0.000000e+00 16600.0
1 TraesCS6A01G167300 chr6D 96.217 4520 130 10 4007 8514 131944648 131949138 0.000000e+00 7361.0
2 TraesCS6A01G167300 chr6D 94.440 1367 48 12 371 1729 131942181 131943527 0.000000e+00 2078.0
3 TraesCS6A01G167300 chr6D 94.169 1149 32 4 2868 3988 131943525 131944666 0.000000e+00 1718.0
4 TraesCS6A01G167300 chr6D 92.946 482 28 3 8512 8988 131950479 131950959 0.000000e+00 697.0
5 TraesCS6A01G167300 chr6D 94.792 96 5 0 5189 5284 199210419 199210324 5.620000e-32 150.0
6 TraesCS6A01G167300 chr6D 92.929 99 5 2 5196 5294 20553669 20553765 9.410000e-30 143.0
7 TraesCS6A01G167300 chr6D 77.444 266 34 17 1 257 131941618 131941866 1.570000e-27 135.0
8 TraesCS6A01G167300 chr6B 96.150 4493 128 14 4358 8826 229526734 229531205 0.000000e+00 7297.0
9 TraesCS6A01G167300 chr6B 95.661 1521 38 2 2867 4360 229525101 229526620 0.000000e+00 2418.0
10 TraesCS6A01G167300 chr6B 92.017 1378 56 26 371 1729 229523762 229525104 0.000000e+00 1886.0
11 TraesCS6A01G167300 chr6B 80.745 322 43 11 6404 6723 701615009 701614705 5.430000e-57 233.0
12 TraesCS6A01G167300 chr6B 80.435 322 44 12 6404 6723 173811820 173812124 2.520000e-55 228.0
13 TraesCS6A01G167300 chr6B 79.167 264 36 13 1 257 229523133 229523384 2.010000e-36 165.0
14 TraesCS6A01G167300 chr6B 93.590 78 5 0 7028 7105 91069185 91069262 5.700000e-22 117.0
15 TraesCS6A01G167300 chr5A 98.338 1143 19 0 1728 2870 602839197 602838055 0.000000e+00 2006.0
16 TraesCS6A01G167300 chr5A 98.160 1141 21 0 1730 2870 483276582 483275442 0.000000e+00 1991.0
17 TraesCS6A01G167300 chr5A 87.847 288 33 1 8354 8641 582102387 582102672 4.020000e-88 337.0
18 TraesCS6A01G167300 chr5A 87.762 286 33 1 8356 8641 665818298 665818015 5.200000e-87 333.0
19 TraesCS6A01G167300 chr1D 98.335 1141 19 0 1730 2870 223524573 223523433 0.000000e+00 2002.0
20 TraesCS6A01G167300 chr1D 95.833 72 3 0 7028 7099 90555465 90555394 5.700000e-22 117.0
21 TraesCS6A01G167300 chr7D 98.330 1138 19 0 1733 2870 465340562 465339425 0.000000e+00 1997.0
22 TraesCS6A01G167300 chr3D 98.249 1142 19 1 1730 2870 422743146 422742005 0.000000e+00 1997.0
23 TraesCS6A01G167300 chr3D 89.233 743 59 11 991 1723 550516554 550517285 0.000000e+00 909.0
24 TraesCS6A01G167300 chr3D 89.271 727 59 9 1012 1729 274322348 274321632 0.000000e+00 893.0
25 TraesCS6A01G167300 chr3D 91.874 443 34 2 3522 3963 274320997 274320556 1.280000e-172 617.0
26 TraesCS6A01G167300 chr3D 89.157 498 46 4 2986 3482 550517336 550517826 1.660000e-171 614.0
27 TraesCS6A01G167300 chr3D 91.648 443 35 2 3522 3963 550517926 550518367 5.970000e-171 612.0
28 TraesCS6A01G167300 chr3D 88.956 498 47 4 2986 3482 274321587 274321097 7.720000e-170 608.0
29 TraesCS6A01G167300 chr3D 89.423 208 18 3 7231 7435 583144942 583144736 8.950000e-65 259.0
30 TraesCS6A01G167300 chr3D 95.833 72 3 0 7028 7099 583145078 583145007 5.700000e-22 117.0
31 TraesCS6A01G167300 chr3D 86.207 58 6 2 3467 3523 550517844 550517900 2.710000e-05 62.1
32 TraesCS6A01G167300 chr2D 98.244 1139 20 0 1732 2870 97865388 97866526 0.000000e+00 1993.0
33 TraesCS6A01G167300 chr2D 86.947 452 47 5 6581 7031 512808477 512808917 1.740000e-136 497.0
34 TraesCS6A01G167300 chr4D 98.072 1141 22 0 1730 2870 83146863 83145723 0.000000e+00 1986.0
35 TraesCS6A01G167300 chr4D 88.693 283 30 1 8359 8641 494264251 494263971 2.400000e-90 344.0
36 TraesCS6A01G167300 chr4D 92.500 160 11 1 8356 8515 435854912 435854754 2.520000e-55 228.0
37 TraesCS6A01G167300 chr7A 98.072 1141 21 1 1730 2870 109351957 109350818 0.000000e+00 1984.0
38 TraesCS6A01G167300 chr7A 84.800 250 32 3 7191 7435 54591702 54591454 6.970000e-61 246.0
39 TraesCS6A01G167300 chr7A 85.496 131 19 0 8511 8641 580274478 580274348 4.380000e-28 137.0
40 TraesCS6A01G167300 chr7A 91.026 78 7 0 7028 7105 54591807 54591730 1.230000e-18 106.0
41 TraesCS6A01G167300 chr1A 97.897 1141 23 1 1730 2870 420384903 420386042 0.000000e+00 1973.0
42 TraesCS6A01G167300 chr1A 96.667 90 3 0 5193 5282 209362157 209362068 5.620000e-32 150.0
43 TraesCS6A01G167300 chr5D 89.778 675 57 5 1012 1677 34070126 34069455 0.000000e+00 854.0
44 TraesCS6A01G167300 chr3B 88.938 452 39 4 6581 7031 62721312 62720871 1.710000e-151 547.0
45 TraesCS6A01G167300 chr3B 91.608 286 23 1 8356 8641 222823703 222823419 2.350000e-105 394.0
46 TraesCS6A01G167300 chr3B 83.663 202 27 5 6404 6604 706205386 706205582 1.540000e-42 185.0
47 TraesCS6A01G167300 chr3B 95.833 72 3 0 7028 7099 62718927 62718856 5.700000e-22 117.0
48 TraesCS6A01G167300 chr3B 81.752 137 17 5 8853 8988 822004377 822004506 3.430000e-19 108.0
49 TraesCS6A01G167300 chr3B 81.752 137 17 5 8853 8988 822019350 822019479 3.430000e-19 108.0
50 TraesCS6A01G167300 chr3B 81.752 137 17 5 8853 8988 822034811 822034940 3.430000e-19 108.0
51 TraesCS6A01G167300 chr5B 88.767 454 37 6 6581 7031 92207707 92207265 2.210000e-150 544.0
52 TraesCS6A01G167300 chr5B 96.667 90 3 0 5192 5281 432174790 432174701 5.620000e-32 150.0
53 TraesCS6A01G167300 chr5B 94.737 95 5 0 5196 5290 26770499 26770405 2.020000e-31 148.0
54 TraesCS6A01G167300 chr5B 94.444 72 4 0 7028 7099 92205371 92205300 2.650000e-20 111.0
55 TraesCS6A01G167300 chr1B 88.717 452 40 4 6581 7031 163698832 163698391 7.940000e-150 542.0
56 TraesCS6A01G167300 chr1B 87.611 452 45 6 6581 7031 133673976 133674417 1.730000e-141 514.0
57 TraesCS6A01G167300 chr1B 86.158 419 43 6 6619 7031 169953962 169953553 1.070000e-118 438.0
58 TraesCS6A01G167300 chr1B 88.153 287 31 2 8356 8641 520904157 520903873 1.120000e-88 339.0
59 TraesCS6A01G167300 chr1B 88.591 149 16 1 7287 7435 163696160 163696013 7.170000e-41 180.0
60 TraesCS6A01G167300 chr1B 87.500 152 18 1 7284 7435 133675132 133675282 3.340000e-39 174.0
61 TraesCS6A01G167300 chr1B 95.652 92 3 1 5192 5283 453136564 453136474 7.270000e-31 147.0
62 TraesCS6A01G167300 chr1B 84.564 149 15 6 7191 7333 102651921 102651775 3.380000e-29 141.0
63 TraesCS6A01G167300 chr1B 91.262 103 9 0 7228 7330 133675028 133675130 3.380000e-29 141.0
64 TraesCS6A01G167300 chr1B 84.564 149 15 6 7191 7333 163696308 163696162 3.380000e-29 141.0
65 TraesCS6A01G167300 chr4B 86.058 416 46 4 6619 7031 81933372 81932966 3.850000e-118 436.0
66 TraesCS6A01G167300 chr4B 79.814 322 46 12 6404 6723 399950320 399950016 5.470000e-52 217.0
67 TraesCS6A01G167300 chr7B 88.412 233 23 3 8409 8641 445655070 445654842 2.470000e-70 278.0
68 TraesCS6A01G167300 chr7B 80.435 322 44 11 6404 6723 68664313 68664617 2.520000e-55 228.0
69 TraesCS6A01G167300 chr4A 80.745 322 43 11 6404 6723 617015267 617015571 5.430000e-57 233.0
70 TraesCS6A01G167300 chr3A 80.435 322 44 11 6404 6723 61560144 61560448 2.520000e-55 228.0
71 TraesCS6A01G167300 chr2B 95.745 94 4 0 5189 5282 751183280 751183373 1.560000e-32 152.0
72 TraesCS6A01G167300 chrUn 97.222 72 2 0 7028 7099 41667394 41667465 1.230000e-23 122.0


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 TraesCS6A01G167300 chr6A 170902625 170911613 8988 False 16600.000000 16600 100.000000 1 8989 1 chr6A.!!$F1 8988
1 TraesCS6A01G167300 chr6D 131941618 131950959 9341 False 2397.800000 7361 91.043200 1 8988 5 chr6D.!!$F2 8987
2 TraesCS6A01G167300 chr6B 229523133 229531205 8072 False 2941.500000 7297 90.748750 1 8826 4 chr6B.!!$F3 8825
3 TraesCS6A01G167300 chr5A 602838055 602839197 1142 True 2006.000000 2006 98.338000 1728 2870 1 chr5A.!!$R2 1142
4 TraesCS6A01G167300 chr5A 483275442 483276582 1140 True 1991.000000 1991 98.160000 1730 2870 1 chr5A.!!$R1 1140
5 TraesCS6A01G167300 chr1D 223523433 223524573 1140 True 2002.000000 2002 98.335000 1730 2870 1 chr1D.!!$R2 1140
6 TraesCS6A01G167300 chr7D 465339425 465340562 1137 True 1997.000000 1997 98.330000 1733 2870 1 chr7D.!!$R1 1137
7 TraesCS6A01G167300 chr3D 422742005 422743146 1141 True 1997.000000 1997 98.249000 1730 2870 1 chr3D.!!$R1 1140
8 TraesCS6A01G167300 chr3D 274320556 274322348 1792 True 706.000000 893 90.033667 1012 3963 3 chr3D.!!$R2 2951
9 TraesCS6A01G167300 chr3D 550516554 550518367 1813 False 549.275000 909 89.061250 991 3963 4 chr3D.!!$F1 2972
10 TraesCS6A01G167300 chr2D 97865388 97866526 1138 False 1993.000000 1993 98.244000 1732 2870 1 chr2D.!!$F1 1138
11 TraesCS6A01G167300 chr4D 83145723 83146863 1140 True 1986.000000 1986 98.072000 1730 2870 1 chr4D.!!$R1 1140
12 TraesCS6A01G167300 chr7A 109350818 109351957 1139 True 1984.000000 1984 98.072000 1730 2870 1 chr7A.!!$R1 1140
13 TraesCS6A01G167300 chr1A 420384903 420386042 1139 False 1973.000000 1973 97.897000 1730 2870 1 chr1A.!!$F1 1140
14 TraesCS6A01G167300 chr5D 34069455 34070126 671 True 854.000000 854 89.778000 1012 1677 1 chr5D.!!$R1 665
15 TraesCS6A01G167300 chr3B 62718856 62721312 2456 True 332.000000 547 92.385500 6581 7099 2 chr3B.!!$R2 518
16 TraesCS6A01G167300 chr5B 92205300 92207707 2407 True 327.500000 544 91.605500 6581 7099 2 chr5B.!!$R3 518
17 TraesCS6A01G167300 chr1B 163696013 163698832 2819 True 287.666667 542 87.290667 6581 7435 3 chr1B.!!$R5 854
18 TraesCS6A01G167300 chr1B 133673976 133675282 1306 False 276.333333 514 88.791000 6581 7435 3 chr1B.!!$F1 854

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
323 354 0.114560 TCGGTGAGAGAAGGGGAGTT 59.885 55.000 0.00 0.00 0.00 3.01 F
1073 1359 0.246635 AGTCAATCCGTCAGAACCCG 59.753 55.000 0.00 0.00 0.00 5.28 F
2132 2440 0.253894 TGGCCACACATCCATCTCAG 59.746 55.000 0.00 0.00 0.00 3.35 F
2210 2518 0.675208 TCCGCGCCATACAACATTGT 60.675 50.000 0.00 2.32 44.86 2.71 F
2586 2894 0.729116 CATCGTCCGCAAAGAGCATT 59.271 50.000 0.00 0.00 46.13 3.56 F
3342 3650 1.238439 TTGCTCTGCTTTGTAGTGCC 58.762 50.000 7.11 0.00 34.78 5.01 F
4130 4500 1.003118 TCGATTGTTCCAGGTCCCTTG 59.997 52.381 0.00 0.00 0.00 3.61 F
4133 4503 1.217916 TTGTTCCAGGTCCCTTGTCA 58.782 50.000 0.00 0.00 0.00 3.58 F
5845 6345 1.971481 TCACTGCTGCTTGAATGTGT 58.029 45.000 0.00 0.00 0.00 3.72 F
6772 7284 1.669265 GCGGTGCTATTTACCCACTTC 59.331 52.381 0.00 0.00 34.66 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2213 2521 0.108329 CTACAGGACGGCGGTTCAAT 60.108 55.000 13.24 0.0 0.00 2.57 R
2571 2879 0.169009 GGTGAATGCTCTTTGCGGAC 59.831 55.000 0.00 0.0 46.63 4.79 R
3330 3638 0.527565 CACCCATGGCACTACAAAGC 59.472 55.000 6.09 0.0 0.00 3.51 R
4114 4484 1.133915 GTGACAAGGGACCTGGAACAA 60.134 52.381 0.00 0.0 38.70 2.83 R
4130 4500 1.137872 CTGATACTGAGCAGGGGTGAC 59.862 57.143 2.20 0.0 35.34 3.67 R
4276 4646 3.026694 CCCCTCAGCTTTTCCCATTAAG 58.973 50.000 0.00 0.0 0.00 1.85 R
5925 6428 2.107950 TCCTACAATTGGTGAAGCGG 57.892 50.000 10.83 0.0 0.00 5.52 R
5999 6502 5.516339 CACAACTTTGCGAAGAACTGAATTT 59.484 36.000 20.86 0.0 36.69 1.82 R
7457 10134 1.454111 CTCGGTGAGGATCGGAGGT 60.454 63.158 0.00 0.0 38.61 3.85 R
8175 10852 1.090052 GCCCAAGCATCGTGTCCTAC 61.090 60.000 0.00 0.0 39.53 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
28 29 2.811317 CCGCAGCTTCCACGTCTC 60.811 66.667 0.00 0.00 0.00 3.36
36 37 2.364324 AGCTTCCACGTCTCTACACAAA 59.636 45.455 0.00 0.00 0.00 2.83
45 46 7.279536 TCCACGTCTCTACACAAATACTACTAG 59.720 40.741 0.00 0.00 0.00 2.57
62 63 5.727766 ACTACTAGTATAACCAAGCCCCAAA 59.272 40.000 2.33 0.00 0.00 3.28
63 64 5.523883 ACTAGTATAACCAAGCCCCAAAA 57.476 39.130 0.00 0.00 0.00 2.44
72 73 3.457749 ACCAAGCCCCAAAAGAAAATTCA 59.542 39.130 0.00 0.00 0.00 2.57
81 82 5.288804 CCAAAAGAAAATTCACGTGGTCAT 58.711 37.500 17.00 2.75 0.00 3.06
85 86 5.235305 AGAAAATTCACGTGGTCATATGC 57.765 39.130 17.00 0.00 0.00 3.14
86 87 4.096382 AGAAAATTCACGTGGTCATATGCC 59.904 41.667 17.00 3.57 0.00 4.40
87 88 3.281727 AATTCACGTGGTCATATGCCT 57.718 42.857 17.00 0.00 0.00 4.75
88 89 2.022764 TTCACGTGGTCATATGCCTG 57.977 50.000 17.00 10.60 0.00 4.85
89 90 0.177836 TCACGTGGTCATATGCCTGG 59.822 55.000 17.00 9.94 0.00 4.45
91 92 0.618458 ACGTGGTCATATGCCTGGTT 59.382 50.000 14.63 0.00 0.00 3.67
92 93 1.834896 ACGTGGTCATATGCCTGGTTA 59.165 47.619 14.63 0.00 0.00 2.85
93 94 2.158957 ACGTGGTCATATGCCTGGTTAG 60.159 50.000 14.63 5.35 0.00 2.34
95 96 1.774254 TGGTCATATGCCTGGTTAGGG 59.226 52.381 14.63 0.00 44.75 3.53
162 165 5.683876 ACTCTTCTATGCTAGGCTTTTCA 57.316 39.130 0.00 0.00 0.00 2.69
163 166 6.245890 ACTCTTCTATGCTAGGCTTTTCAT 57.754 37.500 0.00 0.00 0.00 2.57
164 167 6.287525 ACTCTTCTATGCTAGGCTTTTCATC 58.712 40.000 0.00 0.00 0.00 2.92
165 168 5.292765 TCTTCTATGCTAGGCTTTTCATCG 58.707 41.667 0.00 0.00 0.00 3.84
166 169 4.672587 TCTATGCTAGGCTTTTCATCGT 57.327 40.909 0.00 0.00 0.00 3.73
167 170 4.621991 TCTATGCTAGGCTTTTCATCGTC 58.378 43.478 0.00 0.00 0.00 4.20
168 171 1.640428 TGCTAGGCTTTTCATCGTCG 58.360 50.000 0.00 0.00 0.00 5.12
169 172 1.203758 TGCTAGGCTTTTCATCGTCGA 59.796 47.619 0.00 0.00 0.00 4.20
170 173 1.588861 GCTAGGCTTTTCATCGTCGAC 59.411 52.381 5.18 5.18 0.00 4.20
171 174 2.194271 CTAGGCTTTTCATCGTCGACC 58.806 52.381 10.58 0.00 0.00 4.79
172 175 0.391263 AGGCTTTTCATCGTCGACCC 60.391 55.000 10.58 1.56 0.00 4.46
173 176 0.391263 GGCTTTTCATCGTCGACCCT 60.391 55.000 10.58 0.00 0.00 4.34
174 177 1.439679 GCTTTTCATCGTCGACCCTT 58.560 50.000 10.58 0.00 0.00 3.95
175 178 2.613691 GCTTTTCATCGTCGACCCTTA 58.386 47.619 10.58 0.00 0.00 2.69
176 179 2.603560 GCTTTTCATCGTCGACCCTTAG 59.396 50.000 10.58 0.00 0.00 2.18
177 180 3.846360 CTTTTCATCGTCGACCCTTAGT 58.154 45.455 10.58 0.00 0.00 2.24
178 181 4.676196 GCTTTTCATCGTCGACCCTTAGTA 60.676 45.833 10.58 0.00 0.00 1.82
179 182 4.361451 TTTCATCGTCGACCCTTAGTAC 57.639 45.455 10.58 0.00 0.00 2.73
205 208 1.747355 GGAATGTGGATGCAGGTCTTG 59.253 52.381 0.00 0.00 0.00 3.02
207 210 0.994247 ATGTGGATGCAGGTCTTGGA 59.006 50.000 0.00 0.00 0.00 3.53
223 226 5.049405 GGTCTTGGAAAACTAGTCACACATG 60.049 44.000 0.00 0.00 0.00 3.21
231 234 8.391106 GGAAAACTAGTCACACATGAATGATAC 58.609 37.037 0.00 0.00 36.31 2.24
232 235 8.846943 AAAACTAGTCACACATGAATGATACA 57.153 30.769 0.00 0.00 36.31 2.29
233 236 9.453572 AAAACTAGTCACACATGAATGATACAT 57.546 29.630 0.00 0.00 36.31 2.29
236 239 6.915544 AGTCACACATGAATGATACATCAC 57.084 37.500 0.00 0.00 40.03 3.06
237 240 6.408869 AGTCACACATGAATGATACATCACA 58.591 36.000 0.00 0.00 40.03 3.58
238 241 6.314648 AGTCACACATGAATGATACATCACAC 59.685 38.462 0.00 0.00 40.03 3.82
239 242 5.585844 TCACACATGAATGATACATCACACC 59.414 40.000 0.00 0.00 40.03 4.16
240 243 4.883585 ACACATGAATGATACATCACACCC 59.116 41.667 0.00 0.00 40.03 4.61
242 245 3.192541 TGAATGATACATCACACCCGG 57.807 47.619 0.00 0.00 40.03 5.73
243 246 2.769095 TGAATGATACATCACACCCGGA 59.231 45.455 0.73 0.00 40.03 5.14
244 247 3.198853 TGAATGATACATCACACCCGGAA 59.801 43.478 0.73 0.00 40.03 4.30
246 249 2.184533 TGATACATCACACCCGGAAGT 58.815 47.619 0.73 0.00 0.00 3.01
286 317 3.607777 GAGAGGTCGACGATGACAC 57.392 57.895 9.92 0.00 40.72 3.67
306 337 6.470556 TGACACACACAAATACATTTTGTTCG 59.529 34.615 1.17 0.00 40.30 3.95
307 338 5.746245 ACACACACAAATACATTTTGTTCGG 59.254 36.000 1.17 0.00 40.30 4.30
308 339 5.746245 CACACACAAATACATTTTGTTCGGT 59.254 36.000 1.17 0.00 40.30 4.69
310 341 5.974158 CACACAAATACATTTTGTTCGGTGA 59.026 36.000 11.61 0.00 40.30 4.02
311 342 6.142161 CACACAAATACATTTTGTTCGGTGAG 59.858 38.462 11.61 0.00 40.30 3.51
312 343 6.038825 ACACAAATACATTTTGTTCGGTGAGA 59.961 34.615 1.17 0.00 40.30 3.27
313 344 6.578545 CACAAATACATTTTGTTCGGTGAGAG 59.421 38.462 1.17 0.00 40.30 3.20
314 345 6.485313 ACAAATACATTTTGTTCGGTGAGAGA 59.515 34.615 0.00 0.00 39.36 3.10
315 346 7.012894 ACAAATACATTTTGTTCGGTGAGAGAA 59.987 33.333 0.00 0.00 39.36 2.87
316 347 6.727824 ATACATTTTGTTCGGTGAGAGAAG 57.272 37.500 0.00 0.00 0.00 2.85
317 348 3.815401 ACATTTTGTTCGGTGAGAGAAGG 59.185 43.478 0.00 0.00 0.00 3.46
318 349 2.543777 TTTGTTCGGTGAGAGAAGGG 57.456 50.000 0.00 0.00 0.00 3.95
320 351 0.178944 TGTTCGGTGAGAGAAGGGGA 60.179 55.000 0.00 0.00 0.00 4.81
323 354 0.114560 TCGGTGAGAGAAGGGGAGTT 59.885 55.000 0.00 0.00 0.00 3.01
324 355 1.356738 TCGGTGAGAGAAGGGGAGTTA 59.643 52.381 0.00 0.00 0.00 2.24
325 356 2.024273 TCGGTGAGAGAAGGGGAGTTAT 60.024 50.000 0.00 0.00 0.00 1.89
326 357 2.766828 CGGTGAGAGAAGGGGAGTTATT 59.233 50.000 0.00 0.00 0.00 1.40
327 358 3.430929 CGGTGAGAGAAGGGGAGTTATTG 60.431 52.174 0.00 0.00 0.00 1.90
328 359 3.775316 GGTGAGAGAAGGGGAGTTATTGA 59.225 47.826 0.00 0.00 0.00 2.57
330 361 5.104318 GGTGAGAGAAGGGGAGTTATTGAAT 60.104 44.000 0.00 0.00 0.00 2.57
331 362 6.052360 GTGAGAGAAGGGGAGTTATTGAATC 58.948 44.000 0.00 0.00 0.00 2.52
333 364 6.126940 TGAGAGAAGGGGAGTTATTGAATCTG 60.127 42.308 0.00 0.00 0.00 2.90
334 365 5.728741 AGAGAAGGGGAGTTATTGAATCTGT 59.271 40.000 0.00 0.00 0.00 3.41
335 366 5.995446 AGAAGGGGAGTTATTGAATCTGTC 58.005 41.667 0.00 0.00 0.00 3.51
339 605 3.871594 GGGAGTTATTGAATCTGTCCACG 59.128 47.826 3.07 0.00 0.00 4.94
348 614 5.152623 TGAATCTGTCCACGAGAAGAAAT 57.847 39.130 0.00 0.00 0.00 2.17
354 620 7.979444 TCTGTCCACGAGAAGAAATAAAAAT 57.021 32.000 0.00 0.00 0.00 1.82
386 658 3.013921 TGCAAAATAGACATTCCCGGTC 58.986 45.455 0.00 0.00 35.50 4.79
459 734 3.056328 AGGAAAAAGAGCCGGCGC 61.056 61.111 23.92 23.92 0.00 6.53
470 745 1.525306 GCCGGCGCTTTATTAGGGT 60.525 57.895 12.58 0.00 38.96 4.34
562 838 2.204306 CCACCTTCCCCTTCCCCT 60.204 66.667 0.00 0.00 0.00 4.79
563 839 1.857348 CCACCTTCCCCTTCCCCTT 60.857 63.158 0.00 0.00 0.00 3.95
564 840 1.691823 CACCTTCCCCTTCCCCTTC 59.308 63.158 0.00 0.00 0.00 3.46
565 841 1.544151 ACCTTCCCCTTCCCCTTCC 60.544 63.158 0.00 0.00 0.00 3.46
566 842 2.317378 CCTTCCCCTTCCCCTTCCC 61.317 68.421 0.00 0.00 0.00 3.97
567 843 2.204401 TTCCCCTTCCCCTTCCCC 60.204 66.667 0.00 0.00 0.00 4.81
590 866 1.187087 CGTAAGCCTCCCTGAACTCT 58.813 55.000 0.00 0.00 0.00 3.24
623 899 4.832608 AATTCGCCGCGTCCCTCC 62.833 66.667 13.39 0.00 0.00 4.30
693 969 1.364626 CTTGCAATCGCGGCTCTCTT 61.365 55.000 6.13 0.00 42.97 2.85
696 972 1.156645 GCAATCGCGGCTCTCTTGAT 61.157 55.000 6.13 0.00 0.00 2.57
766 1042 5.004440 GCTCCGTTCTTTTTCTGTGTTTTTC 59.996 40.000 0.00 0.00 0.00 2.29
778 1055 4.456911 TCTGTGTTTTTCTCTGATGGATGC 59.543 41.667 0.00 0.00 0.00 3.91
796 1073 0.248621 GCTGGAATTTTGGATCGGCG 60.249 55.000 0.00 0.00 0.00 6.46
952 1238 4.074627 GAGCCCTAGGGTCTGATTAAAC 57.925 50.000 28.96 8.12 45.63 2.01
953 1239 2.778270 AGCCCTAGGGTCTGATTAAACC 59.222 50.000 28.96 7.59 37.65 3.27
1073 1359 0.246635 AGTCAATCCGTCAGAACCCG 59.753 55.000 0.00 0.00 0.00 5.28
1245 1537 1.599071 CTGTTCTGTTCTGCGCTTGAA 59.401 47.619 9.73 10.69 0.00 2.69
1253 1545 4.475028 TGTTCTGCGCTTGAATTTGTATG 58.525 39.130 9.73 0.00 0.00 2.39
1446 1745 7.803659 GCATTCTCTTGTAAAGTTGGAAAGTAC 59.196 37.037 0.00 0.00 46.34 2.73
1453 1752 3.832615 AAGTTGGAAAGTACTCGTGGT 57.167 42.857 0.00 0.00 0.00 4.16
1560 1864 2.746362 ACAGCATGCTTAGTTTCTGCTC 59.254 45.455 19.98 0.00 41.01 4.26
1682 1990 6.649141 GCCTTTAAGGAACAAATTTACCTTGG 59.351 38.462 16.18 18.28 41.86 3.61
1704 2012 5.095490 GGTTCAAATATATTATGCCTGCGC 58.905 41.667 0.00 0.00 0.00 6.09
1726 2034 4.093556 GCTGCACTAGATTGTGTTACCTTC 59.906 45.833 0.00 0.00 39.89 3.46
1889 2197 5.359194 TCTTTGGTGATACTCCAATCCTC 57.641 43.478 6.20 0.00 43.25 3.71
1907 2215 1.751924 CTCCAGGTCTCTCTTAACGGG 59.248 57.143 0.00 0.00 0.00 5.28
2030 2338 0.770499 TGCCCAAACCATCTCAGACA 59.230 50.000 0.00 0.00 0.00 3.41
2132 2440 0.253894 TGGCCACACATCCATCTCAG 59.746 55.000 0.00 0.00 0.00 3.35
2210 2518 0.675208 TCCGCGCCATACAACATTGT 60.675 50.000 0.00 2.32 44.86 2.71
2213 2521 0.808125 GCGCCATACAACATTGTGGA 59.192 50.000 7.53 0.00 42.31 4.02
2215 2523 2.159254 GCGCCATACAACATTGTGGATT 60.159 45.455 7.53 0.00 42.31 3.01
2395 2703 2.772287 GAAAGGTGTCCTTCAGAGGTG 58.228 52.381 1.36 0.00 43.92 4.00
2571 2879 0.992072 CGTCAACTAGCACCACATCG 59.008 55.000 0.00 0.00 0.00 3.84
2586 2894 0.729116 CATCGTCCGCAAAGAGCATT 59.271 50.000 0.00 0.00 46.13 3.56
2719 3027 1.805120 CGGTGTCGACCTCACTTGTTT 60.805 52.381 14.12 0.00 40.58 2.83
2760 3068 8.435187 ACATTATCATACATGTCCTTGATGAGT 58.565 33.333 20.67 15.25 31.59 3.41
3018 3326 1.269166 CTTGGATTCGTCCGTCTTCG 58.731 55.000 0.00 0.00 0.00 3.79
3079 3387 7.012894 TCTGTCGGTTCAAAGTTATTTCATGTT 59.987 33.333 0.00 0.00 0.00 2.71
3330 3638 3.691609 GGAGGTGTCCTTTAATTGCTCTG 59.308 47.826 0.00 0.00 40.17 3.35
3342 3650 1.238439 TTGCTCTGCTTTGTAGTGCC 58.762 50.000 7.11 0.00 34.78 5.01
3459 3768 1.940613 AGTCAAGTTTCTGTGCCGAAC 59.059 47.619 0.00 0.00 0.00 3.95
3487 3829 5.931146 AGCTTAATCTATCACTGTATGCTGC 59.069 40.000 0.00 0.00 0.00 5.25
3539 3908 9.638300 CTATAGCACAAACTTGATTAATTCGTC 57.362 33.333 0.00 0.00 0.00 4.20
4114 4484 1.641577 GAGTTGCTTAGCCGTTCGAT 58.358 50.000 0.29 0.00 0.00 3.59
4130 4500 1.003118 TCGATTGTTCCAGGTCCCTTG 59.997 52.381 0.00 0.00 0.00 3.61
4133 4503 1.217916 TTGTTCCAGGTCCCTTGTCA 58.782 50.000 0.00 0.00 0.00 3.58
4276 4646 9.593134 CATCCTGAATTTCTGGTATAGTATAGC 57.407 37.037 18.52 11.67 36.89 2.97
4324 4694 5.888161 ACTTCCACTTTCTTTGTGAATCTGT 59.112 36.000 0.00 0.00 37.60 3.41
4368 4854 8.740123 TCTTTTGATGTTTGGTAGTAGTTTGA 57.260 30.769 0.00 0.00 0.00 2.69
4373 4859 7.925993 TGATGTTTGGTAGTAGTTTGAAAGTG 58.074 34.615 0.00 0.00 0.00 3.16
4427 4913 7.028361 AGCAGTCGAAAGTTAGTATACAAGAC 58.972 38.462 5.50 0.70 0.00 3.01
4838 5324 2.158682 TGCATTGGGTGTACTGAGTTGT 60.159 45.455 0.00 0.00 0.00 3.32
4902 5388 3.078837 TGTGCGGAATTCTTTTAGACCC 58.921 45.455 5.23 0.00 0.00 4.46
5028 5516 5.957798 TGAGCTCTAATGCCTTGAAATTTG 58.042 37.500 16.19 0.00 0.00 2.32
5191 5682 6.536582 GCTTTTCTTCTATCAGATGCACTGTA 59.463 38.462 13.59 7.06 45.86 2.74
5384 5884 8.593945 TTGAAATAATCCTATTGCTCTGGTTT 57.406 30.769 0.00 0.00 0.00 3.27
5531 6031 7.742963 ACATAACAATTCACACGTAATTTCGTC 59.257 33.333 7.18 0.00 42.27 4.20
5672 6172 7.255625 GGGCATCTGGTAATATTTTCTTCCTTC 60.256 40.741 0.00 0.00 0.00 3.46
5757 6257 2.761767 TGCTGGCTACAGTACGGAAATA 59.238 45.455 0.00 0.00 46.62 1.40
5845 6345 1.971481 TCACTGCTGCTTGAATGTGT 58.029 45.000 0.00 0.00 0.00 3.72
5859 6359 7.924947 TGCTTGAATGTGTTTGTGATTTATCAA 59.075 29.630 0.00 0.00 38.75 2.57
5916 6419 4.067972 TCCTAGACAAACACTTGTGACC 57.932 45.455 7.83 0.00 45.98 4.02
5948 6451 4.035208 CCGCTTCACCAATTGTAGGATAAC 59.965 45.833 4.43 0.00 0.00 1.89
5999 6502 8.058847 AGGAGTATAATTGGAAGCAATGGTTTA 58.941 33.333 0.00 0.00 0.00 2.01
6032 6535 3.206964 TCGCAAAGTTGTGGTATTGACA 58.793 40.909 4.85 0.00 39.10 3.58
6119 6626 6.817765 TTCTTCTGGATTATGTGTTGTTCC 57.182 37.500 0.00 0.00 0.00 3.62
6157 6665 8.851541 ATGTGTATTTTGAGGCAATGAAAATT 57.148 26.923 4.22 0.00 32.78 1.82
6176 6684 8.849168 TGAAAATTTATGATCTGTGTGTCTTGT 58.151 29.630 0.00 0.00 0.00 3.16
6194 6702 5.009610 GTCTTGTAGAGGCATTGGAAAACAA 59.990 40.000 0.00 0.00 44.54 2.83
6346 6854 4.957684 AGTTGTAGCCTACTTGAAGTGT 57.042 40.909 8.33 0.00 0.00 3.55
6356 6864 5.479306 CCTACTTGAAGTGTAGCAGCTTTA 58.521 41.667 8.33 0.00 36.86 1.85
6401 6909 3.951563 TTTGCTGTTCCATATAGGGCT 57.048 42.857 0.00 0.00 38.24 5.19
6677 7185 7.530426 TCTCTGCTATATCATGCTCAACTTA 57.470 36.000 0.00 0.00 0.00 2.24
6772 7284 1.669265 GCGGTGCTATTTACCCACTTC 59.331 52.381 0.00 0.00 34.66 3.01
6944 7456 3.930848 GGAGTAACATTACAACCGACCAG 59.069 47.826 4.67 0.00 36.12 4.00
7031 9654 7.978982 ACATCTATTCAATGAGCAAACACTAC 58.021 34.615 0.00 0.00 0.00 2.73
7363 10039 7.704899 CCACTTTTCCAACTGGTTAGTTAAAAG 59.295 37.037 17.82 17.82 46.16 2.27
7384 10060 2.615912 GCCTTGATCTAACTGCATGGTC 59.384 50.000 0.00 0.00 31.55 4.02
7457 10134 6.042781 AGGTCTCCAAGTTGTATGAAGTTGTA 59.957 38.462 1.45 0.00 0.00 2.41
7661 10338 8.589335 TGAAGCACGGTATATTAATTTCTCTC 57.411 34.615 0.00 0.00 0.00 3.20
7682 10359 8.612619 TCTCTCGCTTAAATTTATCAATTCACC 58.387 33.333 0.00 0.00 30.80 4.02
7685 10362 8.275015 TCGCTTAAATTTATCAATTCACCAGA 57.725 30.769 0.00 0.00 30.80 3.86
7840 10517 3.309410 CCTCCCCTTCAATTTCCAGATGT 60.309 47.826 0.00 0.00 0.00 3.06
7855 10532 7.411486 TTCCAGATGTTTCTTTGTTTGGTTA 57.589 32.000 0.00 0.00 0.00 2.85
8006 10683 4.380531 CTTGAAGCTACACCAGTTCTTCA 58.619 43.478 0.00 0.00 40.80 3.02
8062 10739 4.112716 TCGACGACATAAATTAGGCACA 57.887 40.909 0.00 0.00 0.00 4.57
8147 10824 5.240121 GGTAGAATTTTGTACCCAAGTCGA 58.760 41.667 5.54 0.00 40.24 4.20
8157 10834 3.208747 ACCCAAGTCGAACAATCTGTT 57.791 42.857 0.00 0.00 44.37 3.16
8162 10839 5.449304 CCAAGTCGAACAATCTGTTAAACC 58.551 41.667 0.00 0.00 41.28 3.27
8175 10852 4.761739 TCTGTTAAACCTGGCATGAAAGAG 59.238 41.667 0.00 0.00 0.00 2.85
8231 10908 7.224290 GGCAACGTTTTTGTACTTTATGTTT 57.776 32.000 0.00 0.00 0.00 2.83
8232 10909 7.677309 GGCAACGTTTTTGTACTTTATGTTTT 58.323 30.769 0.00 0.00 0.00 2.43
8257 10934 4.058817 GAGTTCTGAACCACACCAGTTAG 58.941 47.826 16.48 0.00 0.00 2.34
8306 10983 8.567948 CATTTCTACTGAGGTGTTTGTATTTGT 58.432 33.333 0.00 0.00 0.00 2.83
8316 10993 8.331730 AGGTGTTTGTATTTGTGAGTTATACC 57.668 34.615 0.00 0.00 0.00 2.73
8389 11066 1.228154 ACAGGGTTTGGGAAGCGTC 60.228 57.895 0.00 0.00 34.11 5.19
8401 11078 2.484947 GGGAAGCGTCGGAATAGGAAAT 60.485 50.000 0.00 0.00 0.00 2.17
8405 11082 4.602340 AGCGTCGGAATAGGAAATGTAT 57.398 40.909 0.00 0.00 0.00 2.29
8453 11130 1.067635 TCCTACGTCGGGTAGCAAAAC 60.068 52.381 6.24 0.00 46.03 2.43
8496 11173 3.706086 AGTCCAACCTCATGCTTGTTTTT 59.294 39.130 0.00 0.00 0.00 1.94
8599 12627 4.664688 AAATTCCAGAGGGTGTTGATCT 57.335 40.909 0.00 0.00 34.93 2.75
8609 12637 7.255942 CCAGAGGGTGTTGATCTTGTAAAATTT 60.256 37.037 0.00 0.00 0.00 1.82
8677 12705 6.017275 GCTAGATGTGCTTCTCAATTTGCTAT 60.017 38.462 0.00 0.00 0.00 2.97
8769 12797 9.625747 AAGTTGGAATGTTAAATGTTTTCCATT 57.374 25.926 3.74 0.00 43.82 3.16
8908 12941 8.178964 TGAACAAACATCTTACAAACAGTACAC 58.821 33.333 0.00 0.00 30.91 2.90
8909 12942 7.618502 ACAAACATCTTACAAACAGTACACA 57.381 32.000 0.00 0.00 30.91 3.72
8915 12948 5.676552 TCTTACAAACAGTACACATGTGGT 58.323 37.500 28.64 14.49 30.91 4.16
8928 12961 5.809001 ACACATGTGGTCATTACAAGAGAT 58.191 37.500 28.64 0.00 34.19 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 6.627209 TGGGGCTTGGTTATACTAGTAGTAT 58.373 40.000 23.09 23.09 43.36 2.12
45 46 5.731957 TTTCTTTTGGGGCTTGGTTATAC 57.268 39.130 0.00 0.00 0.00 1.47
55 56 2.799978 CACGTGAATTTTCTTTTGGGGC 59.200 45.455 10.90 0.00 0.00 5.80
62 63 5.393027 GGCATATGACCACGTGAATTTTCTT 60.393 40.000 19.30 6.02 0.00 2.52
63 64 4.096382 GGCATATGACCACGTGAATTTTCT 59.904 41.667 19.30 0.00 0.00 2.52
72 73 0.618458 AACCAGGCATATGACCACGT 59.382 50.000 4.47 4.03 0.00 4.49
85 86 2.372074 TTAGGCCGCCCTAACCAGG 61.372 63.158 5.55 0.00 46.32 4.45
86 87 3.316029 TTAGGCCGCCCTAACCAG 58.684 61.111 5.55 0.00 46.32 4.00
91 92 1.202769 ACAAAGGTTAGGCCGCCCTA 61.203 55.000 5.55 0.00 42.87 3.53
92 93 2.076597 AACAAAGGTTAGGCCGCCCT 62.077 55.000 5.55 7.63 45.61 5.19
93 94 1.183030 AAACAAAGGTTAGGCCGCCC 61.183 55.000 5.55 5.47 43.70 6.13
94 95 0.038618 CAAACAAAGGTTAGGCCGCC 60.039 55.000 0.00 0.00 43.70 6.13
95 96 0.038618 CCAAACAAAGGTTAGGCCGC 60.039 55.000 0.00 0.00 43.70 6.53
96 97 1.000717 CACCAAACAAAGGTTAGGCCG 60.001 52.381 0.00 0.00 43.70 6.13
98 99 1.270094 GCCACCAAACAAAGGTTAGGC 60.270 52.381 0.00 0.00 37.23 3.93
99 100 2.035632 TGCCACCAAACAAAGGTTAGG 58.964 47.619 0.00 0.00 37.23 2.69
100 101 3.810310 TTGCCACCAAACAAAGGTTAG 57.190 42.857 0.00 0.00 37.23 2.34
101 102 4.508662 CTTTTGCCACCAAACAAAGGTTA 58.491 39.130 0.00 0.00 40.45 2.85
136 139 9.094578 TGAAAAGCCTAGCATAGAAGAGTATAT 57.905 33.333 0.00 0.00 42.77 0.86
137 140 8.478775 TGAAAAGCCTAGCATAGAAGAGTATA 57.521 34.615 0.00 0.00 42.77 1.47
148 151 2.159099 TCGACGATGAAAAGCCTAGCAT 60.159 45.455 0.00 0.00 0.00 3.79
149 152 1.203758 TCGACGATGAAAAGCCTAGCA 59.796 47.619 0.00 0.00 0.00 3.49
150 153 1.588861 GTCGACGATGAAAAGCCTAGC 59.411 52.381 0.00 0.00 0.00 3.42
151 154 2.194271 GGTCGACGATGAAAAGCCTAG 58.806 52.381 9.92 0.00 0.00 3.02
152 155 1.134907 GGGTCGACGATGAAAAGCCTA 60.135 52.381 9.92 0.00 0.00 3.93
154 157 0.391263 AGGGTCGACGATGAAAAGCC 60.391 55.000 9.92 1.34 0.00 4.35
155 158 1.439679 AAGGGTCGACGATGAAAAGC 58.560 50.000 9.92 0.00 0.00 3.51
156 159 3.846360 ACTAAGGGTCGACGATGAAAAG 58.154 45.455 9.92 3.20 0.00 2.27
159 162 3.346315 TGTACTAAGGGTCGACGATGAA 58.654 45.455 9.92 0.00 0.00 2.57
160 163 2.989909 TGTACTAAGGGTCGACGATGA 58.010 47.619 9.92 0.00 0.00 2.92
162 165 5.048224 CCATATTGTACTAAGGGTCGACGAT 60.048 44.000 9.92 0.32 0.00 3.73
163 166 4.276678 CCATATTGTACTAAGGGTCGACGA 59.723 45.833 9.92 0.00 0.00 4.20
164 167 4.276678 TCCATATTGTACTAAGGGTCGACG 59.723 45.833 9.92 0.00 0.00 5.12
165 168 5.779529 TCCATATTGTACTAAGGGTCGAC 57.220 43.478 7.13 7.13 0.00 4.20
166 169 6.325545 ACATTCCATATTGTACTAAGGGTCGA 59.674 38.462 0.00 0.00 0.00 4.20
167 170 6.423905 CACATTCCATATTGTACTAAGGGTCG 59.576 42.308 0.00 0.00 0.00 4.79
168 171 6.710744 CCACATTCCATATTGTACTAAGGGTC 59.289 42.308 0.00 0.00 0.00 4.46
169 172 6.388689 TCCACATTCCATATTGTACTAAGGGT 59.611 38.462 0.00 0.00 0.00 4.34
170 173 6.837312 TCCACATTCCATATTGTACTAAGGG 58.163 40.000 0.00 0.00 0.00 3.95
171 174 7.094634 GCATCCACATTCCATATTGTACTAAGG 60.095 40.741 0.00 0.00 0.00 2.69
172 175 7.445096 TGCATCCACATTCCATATTGTACTAAG 59.555 37.037 0.00 0.00 0.00 2.18
173 176 7.286313 TGCATCCACATTCCATATTGTACTAA 58.714 34.615 0.00 0.00 0.00 2.24
174 177 6.836242 TGCATCCACATTCCATATTGTACTA 58.164 36.000 0.00 0.00 0.00 1.82
175 178 5.693961 TGCATCCACATTCCATATTGTACT 58.306 37.500 0.00 0.00 0.00 2.73
176 179 5.048504 CCTGCATCCACATTCCATATTGTAC 60.049 44.000 0.00 0.00 0.00 2.90
177 180 5.072055 CCTGCATCCACATTCCATATTGTA 58.928 41.667 0.00 0.00 0.00 2.41
178 181 3.893200 CCTGCATCCACATTCCATATTGT 59.107 43.478 0.00 0.00 0.00 2.71
179 182 3.893200 ACCTGCATCCACATTCCATATTG 59.107 43.478 0.00 0.00 0.00 1.90
205 208 6.801539 TCATTCATGTGTGACTAGTTTTCC 57.198 37.500 0.00 0.00 33.11 3.13
207 210 8.846943 TGTATCATTCATGTGTGACTAGTTTT 57.153 30.769 0.00 0.00 33.11 2.43
223 226 3.469008 TCCGGGTGTGATGTATCATTC 57.531 47.619 0.00 0.00 39.30 2.67
236 239 1.226746 GTCTTTGACACTTCCGGGTG 58.773 55.000 0.00 5.29 42.34 4.61
237 240 0.249741 CGTCTTTGACACTTCCGGGT 60.250 55.000 0.00 0.00 32.09 5.28
238 241 1.566018 GCGTCTTTGACACTTCCGGG 61.566 60.000 0.00 0.00 32.09 5.73
239 242 0.600255 AGCGTCTTTGACACTTCCGG 60.600 55.000 0.00 0.00 32.09 5.14
240 243 1.192534 GAAGCGTCTTTGACACTTCCG 59.807 52.381 14.11 0.00 42.42 4.30
242 245 2.866762 ACAGAAGCGTCTTTGACACTTC 59.133 45.455 16.20 16.20 46.06 3.01
243 246 2.906354 ACAGAAGCGTCTTTGACACTT 58.094 42.857 0.00 1.28 37.59 3.16
244 247 2.604046 ACAGAAGCGTCTTTGACACT 57.396 45.000 0.00 0.00 32.09 3.55
246 249 2.607635 GTGAACAGAAGCGTCTTTGACA 59.392 45.455 0.00 0.00 32.09 3.58
252 283 0.952280 TCTCGTGAACAGAAGCGTCT 59.048 50.000 0.00 0.00 32.85 4.18
263 294 0.446616 CATCGTCGACCTCTCGTGAA 59.553 55.000 10.58 0.00 41.02 3.18
277 308 5.940192 AATGTATTTGTGTGTGTCATCGT 57.060 34.783 0.00 0.00 0.00 3.73
284 315 5.746245 ACCGAACAAAATGTATTTGTGTGTG 59.254 36.000 7.27 1.06 41.30 3.82
286 317 5.974158 TCACCGAACAAAATGTATTTGTGTG 59.026 36.000 7.27 10.61 41.30 3.82
306 337 3.775316 TCAATAACTCCCCTTCTCTCACC 59.225 47.826 0.00 0.00 0.00 4.02
307 338 5.422214 TTCAATAACTCCCCTTCTCTCAC 57.578 43.478 0.00 0.00 0.00 3.51
308 339 5.966935 AGATTCAATAACTCCCCTTCTCTCA 59.033 40.000 0.00 0.00 0.00 3.27
310 341 5.728741 ACAGATTCAATAACTCCCCTTCTCT 59.271 40.000 0.00 0.00 0.00 3.10
311 342 5.995446 ACAGATTCAATAACTCCCCTTCTC 58.005 41.667 0.00 0.00 0.00 2.87
312 343 5.104318 GGACAGATTCAATAACTCCCCTTCT 60.104 44.000 0.00 0.00 0.00 2.85
313 344 5.126779 GGACAGATTCAATAACTCCCCTTC 58.873 45.833 0.00 0.00 0.00 3.46
314 345 4.540099 TGGACAGATTCAATAACTCCCCTT 59.460 41.667 0.00 0.00 0.00 3.95
315 346 4.080299 GTGGACAGATTCAATAACTCCCCT 60.080 45.833 0.00 0.00 0.00 4.79
316 347 4.200092 GTGGACAGATTCAATAACTCCCC 58.800 47.826 0.00 0.00 0.00 4.81
317 348 3.871594 CGTGGACAGATTCAATAACTCCC 59.128 47.826 0.00 0.00 0.00 4.30
318 349 4.755411 TCGTGGACAGATTCAATAACTCC 58.245 43.478 0.00 0.00 0.00 3.85
320 351 5.661056 TCTCGTGGACAGATTCAATAACT 57.339 39.130 0.00 0.00 0.00 2.24
323 354 5.914898 TCTTCTCGTGGACAGATTCAATA 57.085 39.130 0.00 0.00 0.00 1.90
324 355 4.808414 TCTTCTCGTGGACAGATTCAAT 57.192 40.909 0.00 0.00 0.00 2.57
325 356 4.600692 TTCTTCTCGTGGACAGATTCAA 57.399 40.909 0.00 0.00 0.00 2.69
326 357 4.600692 TTTCTTCTCGTGGACAGATTCA 57.399 40.909 0.00 0.00 0.00 2.57
327 358 7.596749 TTTATTTCTTCTCGTGGACAGATTC 57.403 36.000 0.00 0.00 0.00 2.52
328 359 7.979444 TTTTATTTCTTCTCGTGGACAGATT 57.021 32.000 0.00 0.00 0.00 2.40
330 361 7.979444 ATTTTTATTTCTTCTCGTGGACAGA 57.021 32.000 0.00 0.00 0.00 3.41
331 362 9.151471 TCTATTTTTATTTCTTCTCGTGGACAG 57.849 33.333 0.00 0.00 0.00 3.51
360 626 5.530915 CCGGGAATGTCTATTTTGCATTCTA 59.469 40.000 13.75 0.00 44.50 2.10
362 628 4.097892 ACCGGGAATGTCTATTTTGCATTC 59.902 41.667 6.32 7.68 44.41 2.67
365 631 3.013921 GACCGGGAATGTCTATTTTGCA 58.986 45.455 6.32 0.00 0.00 4.08
366 632 2.357952 GGACCGGGAATGTCTATTTTGC 59.642 50.000 6.32 0.00 33.22 3.68
367 633 2.949644 GGGACCGGGAATGTCTATTTTG 59.050 50.000 6.32 0.00 33.22 2.44
368 634 2.420967 CGGGACCGGGAATGTCTATTTT 60.421 50.000 6.32 0.00 35.56 1.82
374 646 0.033090 GTATCGGGACCGGGAATGTC 59.967 60.000 6.32 0.00 40.25 3.06
386 658 2.278596 CACTCCGCACGTATCGGG 60.279 66.667 22.84 17.03 46.43 5.14
459 734 5.751586 TGGAGTTGCCTTACCCTAATAAAG 58.248 41.667 0.00 0.00 37.63 1.85
562 838 3.305177 GAGGCTTACGCGTGGGGAA 62.305 63.158 24.59 7.05 36.88 3.97
563 839 3.766691 GAGGCTTACGCGTGGGGA 61.767 66.667 24.59 0.00 36.88 4.81
564 840 4.832608 GGAGGCTTACGCGTGGGG 62.833 72.222 24.59 12.61 36.88 4.96
565 841 4.832608 GGGAGGCTTACGCGTGGG 62.833 72.222 24.59 15.28 36.88 4.61
566 842 3.771160 AGGGAGGCTTACGCGTGG 61.771 66.667 24.59 15.67 36.88 4.94
567 843 2.501223 TTCAGGGAGGCTTACGCGTG 62.501 60.000 24.59 7.20 36.88 5.34
583 859 3.492656 CGACAGGGAAGTTTCAGAGTTCA 60.493 47.826 0.00 0.00 39.10 3.18
585 861 2.698797 TCGACAGGGAAGTTTCAGAGTT 59.301 45.455 0.00 0.00 0.00 3.01
590 866 3.064207 CGAATTCGACAGGGAAGTTTCA 58.936 45.455 23.29 0.00 43.02 2.69
623 899 3.707156 CTGGCAGATCAAACGCGCG 62.707 63.158 30.96 30.96 0.00 6.86
749 1025 7.339212 TCCATCAGAGAAAAACACAGAAAAAGA 59.661 33.333 0.00 0.00 0.00 2.52
766 1042 4.202121 CCAAAATTCCAGCATCCATCAGAG 60.202 45.833 0.00 0.00 0.00 3.35
778 1055 0.248621 GCGCCGATCCAAAATTCCAG 60.249 55.000 0.00 0.00 0.00 3.86
948 1234 3.745975 CAGAGCACGAACAAGATGGTTTA 59.254 43.478 0.00 0.00 0.00 2.01
949 1235 2.549754 CAGAGCACGAACAAGATGGTTT 59.450 45.455 0.00 0.00 0.00 3.27
951 1237 1.070758 ACAGAGCACGAACAAGATGGT 59.929 47.619 0.00 0.00 0.00 3.55
952 1238 1.462283 CACAGAGCACGAACAAGATGG 59.538 52.381 0.00 0.00 0.00 3.51
953 1239 1.136141 GCACAGAGCACGAACAAGATG 60.136 52.381 0.00 0.00 44.79 2.90
997 1283 2.267642 CCGGAAGAACGCCATGGA 59.732 61.111 18.40 0.00 0.00 3.41
1102 1388 6.927933 AAATCAGCATTAACAAACGCTTAC 57.072 33.333 0.00 0.00 30.72 2.34
1245 1537 6.910191 TCCAATCACAGTATCCCATACAAAT 58.090 36.000 0.00 0.00 38.21 2.32
1253 1545 3.378427 GCAGTTTCCAATCACAGTATCCC 59.622 47.826 0.00 0.00 0.00 3.85
1323 1616 1.792367 CGTCAGCGTCATGTTCAGAAA 59.208 47.619 0.00 0.00 0.00 2.52
1446 1745 6.582677 AGATAAGGAATCAGATACCACGAG 57.417 41.667 0.00 0.00 37.03 4.18
1580 1884 4.121317 CACCATGGCATTTGCGAATAAAT 58.879 39.130 13.04 0.00 43.26 1.40
1635 1940 7.729116 AGGCGTTAAGGTATTAAATGCTACTA 58.271 34.615 0.00 0.00 35.97 1.82
1636 1941 6.589135 AGGCGTTAAGGTATTAAATGCTACT 58.411 36.000 0.00 0.00 35.97 2.57
1637 1942 6.856135 AGGCGTTAAGGTATTAAATGCTAC 57.144 37.500 0.00 0.00 35.97 3.58
1682 1990 5.796935 CAGCGCAGGCATAATATATTTGAAC 59.203 40.000 11.47 0.62 43.41 3.18
1704 2012 4.631813 GGAAGGTAACACAATCTAGTGCAG 59.368 45.833 0.00 0.00 43.23 4.41
1726 2034 5.164002 GCTTTGTTGTTGTTGTTGTTGTAGG 60.164 40.000 0.00 0.00 0.00 3.18
1889 2197 0.175989 GCCCGTTAAGAGAGACCTGG 59.824 60.000 0.00 0.00 0.00 4.45
1907 2215 1.672881 CGAATTTGACATGGGAGGAGC 59.327 52.381 0.00 0.00 0.00 4.70
2030 2338 3.181440 TGAGGAGAAGCTTGTCCAACATT 60.181 43.478 36.25 20.54 42.72 2.71
2132 2440 2.280119 TGGCGGAGATGCGTATGC 60.280 61.111 0.00 0.00 43.20 3.14
2210 2518 2.046700 GGACGGCGGTTCAATCCA 60.047 61.111 13.24 0.00 0.00 3.41
2213 2521 0.108329 CTACAGGACGGCGGTTCAAT 60.108 55.000 13.24 0.00 0.00 2.57
2215 2523 1.180456 TTCTACAGGACGGCGGTTCA 61.180 55.000 13.24 0.00 0.00 3.18
2571 2879 0.169009 GGTGAATGCTCTTTGCGGAC 59.831 55.000 0.00 0.00 46.63 4.79
2586 2894 3.668821 ACAAGGAGATATCCCATGGTGA 58.331 45.455 11.73 8.21 0.00 4.02
2709 3017 5.088739 GTGACAAGTGTTCAAACAAGTGAG 58.911 41.667 11.82 0.00 41.21 3.51
2719 3027 6.934048 TGATAATGTTGTGACAAGTGTTCA 57.066 33.333 0.00 0.00 39.66 3.18
2760 3068 4.634012 AGTCCCAGCAAAGTACATTACA 57.366 40.909 0.00 0.00 0.00 2.41
3018 3326 1.235724 AAACAAGTGGTTAGAGCGGC 58.764 50.000 0.00 0.00 39.29 6.53
3079 3387 4.320861 CGGTCCTGTAACAAAATGCAATCA 60.321 41.667 0.00 0.00 0.00 2.57
3314 3622 5.126396 ACAAAGCAGAGCAATTAAAGGAC 57.874 39.130 0.00 0.00 0.00 3.85
3321 3629 2.229784 GGCACTACAAAGCAGAGCAATT 59.770 45.455 0.00 0.00 32.03 2.32
3330 3638 0.527565 CACCCATGGCACTACAAAGC 59.472 55.000 6.09 0.00 0.00 3.51
3421 3730 7.725251 ACTTGACTGGAGATCTCAAGATAATC 58.275 38.462 30.30 18.42 42.36 1.75
3459 3768 6.589523 GCATACAGTGATAGATTAAGCTCAGG 59.410 42.308 0.00 0.00 0.00 3.86
3487 3829 9.941664 GTCAATTCTGGAAAGTGATACATATTG 57.058 33.333 0.00 0.00 0.00 1.90
3539 3908 6.726258 TGTAGTCAAGCAAGTTGATGTATG 57.274 37.500 7.16 0.00 46.99 2.39
3656 4025 9.836864 AACAGAGATATACAGTGATGCATAAAA 57.163 29.630 0.00 0.00 0.00 1.52
3909 4279 8.883954 ATGTCATCTACTACATCAATGAACAG 57.116 34.615 0.00 0.00 30.54 3.16
4114 4484 1.133915 GTGACAAGGGACCTGGAACAA 60.134 52.381 0.00 0.00 38.70 2.83
4130 4500 1.137872 CTGATACTGAGCAGGGGTGAC 59.862 57.143 2.20 0.00 35.34 3.67
4133 4503 1.198713 CACTGATACTGAGCAGGGGT 58.801 55.000 2.20 0.00 43.70 4.95
4232 4602 7.267857 TCAGGATGATGTTTATGTGTACTCAG 58.732 38.462 3.75 0.00 42.56 3.35
4251 4621 9.554053 AGCTATACTATACCAGAAATTCAGGAT 57.446 33.333 11.51 3.58 0.00 3.24
4276 4646 3.026694 CCCCTCAGCTTTTCCCATTAAG 58.973 50.000 0.00 0.00 0.00 1.85
4324 4694 9.884636 TCAAAAGAGTTAGCAACAGCTTATATA 57.115 29.630 0.00 0.00 39.77 0.86
4368 4854 7.937394 AGTGGAGTTAATAACAGCTTACACTTT 59.063 33.333 5.89 0.00 30.80 2.66
4373 4859 7.900782 TTCAGTGGAGTTAATAACAGCTTAC 57.099 36.000 5.89 2.25 0.00 2.34
4427 4913 6.869695 TCAATGGATCTGGAACAAATGAATG 58.130 36.000 0.00 0.00 38.70 2.67
4838 5324 8.862325 TCTTATTTCTTTCTAATGGCACTTCA 57.138 30.769 0.00 0.00 0.00 3.02
4902 5388 4.218417 CAGACCAAATTAACTCACTTGGGG 59.782 45.833 4.82 0.00 42.23 4.96
4941 5429 7.587037 TTGAAATTCACTCTCAACCTGAAAT 57.413 32.000 0.00 0.00 0.00 2.17
4942 5430 7.403312 TTTGAAATTCACTCTCAACCTGAAA 57.597 32.000 0.00 0.00 0.00 2.69
5028 5516 4.197750 AGATCACCATTGAGCAGATGAAC 58.802 43.478 0.00 0.00 40.89 3.18
5350 5850 7.306983 GCAATAGGATTATTTCAATTGCAGCAC 60.307 37.037 11.73 0.00 45.45 4.40
5352 5852 6.927381 AGCAATAGGATTATTTCAATTGCAGC 59.073 34.615 17.17 0.00 46.90 5.25
5384 5884 5.018809 CCCATCCTTGAAAATCCTTCAGAA 58.981 41.667 0.00 0.00 0.00 3.02
5744 6244 5.296780 CAGCCAAATCATATTTCCGTACTGT 59.703 40.000 0.00 0.00 0.00 3.55
5757 6257 3.196901 ACACAATGATGCAGCCAAATCAT 59.803 39.130 0.00 0.00 43.69 2.45
5845 6345 5.048434 TGCGTCATGGTTGATAAATCACAAA 60.048 36.000 0.00 0.00 36.36 2.83
5859 6359 3.541996 TTATCAGACATGCGTCATGGT 57.458 42.857 19.30 8.75 45.16 3.55
5916 6419 2.125350 GTGAAGCGGCCCTCTCTG 60.125 66.667 0.00 0.00 0.00 3.35
5925 6428 2.107950 TCCTACAATTGGTGAAGCGG 57.892 50.000 10.83 0.00 0.00 5.52
5999 6502 5.516339 CACAACTTTGCGAAGAACTGAATTT 59.484 36.000 20.86 0.00 36.69 1.82
6157 6665 6.628175 GCCTCTACAAGACACACAGATCATAA 60.628 42.308 0.00 0.00 0.00 1.90
6176 6684 7.531857 TGTATTTTGTTTTCCAATGCCTCTA 57.468 32.000 0.00 0.00 31.81 2.43
6212 6720 9.823647 CTTTAGATGATCTCCTTTAAGCTAACA 57.176 33.333 0.00 0.00 0.00 2.41
6233 6741 6.657875 AGATCAATTCCACCCTTCTCTTTAG 58.342 40.000 0.00 0.00 0.00 1.85
6299 6807 2.955660 CCACTACAAGTTTGGAGGCAAA 59.044 45.455 8.84 0.00 43.61 3.68
6401 6909 5.581126 ACAGCAACACAGAGAATTGAAAA 57.419 34.783 0.00 0.00 0.00 2.29
6677 7185 5.068636 CCAGTAGATCCATTTAGCAAGCAT 58.931 41.667 0.00 0.00 0.00 3.79
6772 7284 9.512435 CTTCTTCTTAACATCATATGCAAAAGG 57.488 33.333 0.00 0.00 0.00 3.11
6944 7456 7.934120 AGTGTCTTCCATACATATTCCTTAAGC 59.066 37.037 0.00 0.00 0.00 3.09
7031 9654 7.542130 GCAAACTTCCCATAAACTCATAAACAG 59.458 37.037 0.00 0.00 0.00 3.16
7363 10039 2.615912 GACCATGCAGTTAGATCAAGGC 59.384 50.000 0.00 0.00 0.00 4.35
7384 10060 5.193663 TGAGACTGTTGAACTGAAGAGAG 57.806 43.478 9.24 0.00 0.00 3.20
7457 10134 1.454111 CTCGGTGAGGATCGGAGGT 60.454 63.158 0.00 0.00 38.61 3.85
7661 10338 7.967854 TGTCTGGTGAATTGATAAATTTAAGCG 59.032 33.333 1.21 0.00 0.00 4.68
7682 10359 8.677871 TGTACTGTACGTTAAACATATGTCTG 57.322 34.615 9.23 0.98 0.00 3.51
7855 10532 9.976776 ATAATTGATCAAGATTAGCAGATGGAT 57.023 29.630 14.54 0.00 0.00 3.41
8062 10739 4.821532 AGATGGGGAAATGAGGCTAAAT 57.178 40.909 0.00 0.00 0.00 1.40
8076 10753 2.603075 TGGACAGGAAAAAGATGGGG 57.397 50.000 0.00 0.00 0.00 4.96
8147 10824 4.832266 TCATGCCAGGTTTAACAGATTGTT 59.168 37.500 0.00 0.00 43.88 2.83
8157 10834 4.534500 TCCTACTCTTTCATGCCAGGTTTA 59.466 41.667 0.00 0.00 0.00 2.01
8162 10839 3.265791 GTGTCCTACTCTTTCATGCCAG 58.734 50.000 0.00 0.00 0.00 4.85
8175 10852 1.090052 GCCCAAGCATCGTGTCCTAC 61.090 60.000 0.00 0.00 39.53 3.18
8231 10908 2.093394 TGGTGTGGTTCAGAACTCGAAA 60.093 45.455 13.13 0.00 0.00 3.46
8232 10909 1.483004 TGGTGTGGTTCAGAACTCGAA 59.517 47.619 13.13 0.00 0.00 3.71
8240 10917 1.697432 TCCCTAACTGGTGTGGTTCAG 59.303 52.381 0.00 0.00 37.07 3.02
8289 10966 8.995220 GTATAACTCACAAATACAAACACCTCA 58.005 33.333 0.00 0.00 0.00 3.86
8306 10983 7.618502 AAACGTAATTGCATGGTATAACTCA 57.381 32.000 0.00 0.00 0.00 3.41
8316 10993 3.735240 AGCACACAAAACGTAATTGCATG 59.265 39.130 12.46 11.64 32.15 4.06
8389 11066 8.978472 TCCTATTCCTATACATTTCCTATTCCG 58.022 37.037 0.00 0.00 0.00 4.30
8401 11078 9.696572 GTGGACAGTATATCCTATTCCTATACA 57.303 37.037 0.00 0.00 37.13 2.29
8405 11082 7.996788 TCAGTGGACAGTATATCCTATTCCTA 58.003 38.462 0.00 0.00 37.13 2.94
8417 11094 4.710375 ACGTAGGATTTCAGTGGACAGTAT 59.290 41.667 0.00 0.00 0.00 2.12
8521 12541 7.946219 TGCATTCCTCAGAAACCAATCATATAT 59.054 33.333 0.00 0.00 35.09 0.86
8526 12546 3.765381 TGCATTCCTCAGAAACCAATCA 58.235 40.909 0.00 0.00 35.09 2.57
8609 12637 9.187996 TCATTTGATTTACAGGATTTGCATAGA 57.812 29.630 0.00 0.00 0.00 1.98
8677 12705 9.761504 TTCAATTGAATTTTGAATAAGTGCTCA 57.238 25.926 16.91 0.00 37.97 4.26
8813 12841 6.644181 CACACACAAAATACCATTAATGTGCA 59.356 34.615 14.25 0.00 41.28 4.57
8880 12913 9.730420 GTACTGTTTGTAAGATGTTTGTTCAAT 57.270 29.630 0.00 0.00 32.25 2.57
8881 12914 8.731605 TGTACTGTTTGTAAGATGTTTGTTCAA 58.268 29.630 0.00 0.00 32.25 2.69
8882 12915 8.178964 GTGTACTGTTTGTAAGATGTTTGTTCA 58.821 33.333 0.00 0.00 32.25 3.18
8888 12921 7.255104 CCACATGTGTACTGTTTGTAAGATGTT 60.255 37.037 23.79 0.00 31.17 2.71
8897 12930 5.437289 AATGACCACATGTGTACTGTTTG 57.563 39.130 23.79 8.80 36.79 2.93
8903 12936 6.163476 TCTCTTGTAATGACCACATGTGTAC 58.837 40.000 23.79 18.14 36.79 2.90
8908 12941 9.716531 ATGTATATCTCTTGTAATGACCACATG 57.283 33.333 0.00 0.00 36.79 3.21


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

AutoCloner maintained by Alex Coulton.