Multiple sequence alignment - TraesCS5B01G539300

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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 TraesCS5B01G539300 chr5B 100.000 3028 0 0 1 3028 694204767 694201740 0.000000e+00 5592
1 TraesCS5B01G539300 chr5B 87.130 1453 110 37 628 2016 710314857 710313418 0.000000e+00 1576
2 TraesCS5B01G539300 chr5B 82.038 1119 121 28 1026 2101 710326012 710324931 0.000000e+00 880
3 TraesCS5B01G539300 chr5B 91.863 553 45 0 2297 2849 56578955 56579507 0.000000e+00 773
4 TraesCS5B01G539300 chr5B 78.090 1068 140 55 1026 2039 694289323 694288296 9.350000e-165 590
5 TraesCS5B01G539300 chr4A 85.669 1256 96 35 833 2013 604940439 604941685 0.000000e+00 1245
6 TraesCS5B01G539300 chr4A 85.011 894 80 30 1374 2249 604857093 604857950 0.000000e+00 859
7 TraesCS5B01G539300 chr4A 80.820 829 117 30 1026 1826 613544343 613543529 2.000000e-171 612
8 TraesCS5B01G539300 chr4A 86.726 226 23 5 628 851 604939755 604939975 8.390000e-61 244
9 TraesCS5B01G539300 chr4A 86.341 205 22 1 1 199 692452316 692452112 5.080000e-53 219
10 TraesCS5B01G539300 chr5D 91.880 665 52 2 2302 2965 497929865 497929202 0.000000e+00 928
11 TraesCS5B01G539300 chr5D 89.474 589 56 6 2264 2849 470045834 470046419 0.000000e+00 739
12 TraesCS5B01G539300 chr5D 79.245 1060 137 51 1026 2033 556423329 556424357 0.000000e+00 662
13 TraesCS5B01G539300 chr5D 84.932 584 51 14 1379 1931 559978688 559978111 9.480000e-155 556
14 TraesCS5B01G539300 chr5D 81.448 663 97 21 1173 1828 556449538 556450181 1.240000e-143 520
15 TraesCS5B01G539300 chr5D 92.771 83 3 3 2947 3026 384296616 384296534 1.910000e-22 117
16 TraesCS5B01G539300 chr5D 85.849 106 13 1 2923 3026 30509227 30509332 8.870000e-21 111
17 TraesCS5B01G539300 chr7D 92.960 554 36 3 2301 2852 562819408 562819960 0.000000e+00 804
18 TraesCS5B01G539300 chr4B 93.236 547 36 1 2303 2849 648823813 648824358 0.000000e+00 804
19 TraesCS5B01G539300 chr4B 88.837 215 17 6 2757 2964 648824437 648824651 1.080000e-64 257
20 TraesCS5B01G539300 chr6D 93.066 548 38 0 2305 2852 94778172 94777625 0.000000e+00 802
21 TraesCS5B01G539300 chr6D 89.352 216 16 3 2757 2965 453368085 453368300 6.440000e-67 265
22 TraesCS5B01G539300 chr2D 92.559 551 40 1 2303 2852 649514882 649514332 0.000000e+00 789
23 TraesCS5B01G539300 chr2D 88.991 218 15 5 2754 2964 635804854 635804639 8.330000e-66 261
24 TraesCS5B01G539300 chr5A 92.532 549 38 3 2302 2849 700212373 700212919 0.000000e+00 784
25 TraesCS5B01G539300 chr5A 98.571 70 1 0 2959 3028 487453056 487452987 1.140000e-24 124
26 TraesCS5B01G539300 chr5A 94.872 78 3 1 2952 3028 633656600 633656677 1.470000e-23 121
27 TraesCS5B01G539300 chr2B 90.576 573 51 3 2302 2873 747814285 747813715 0.000000e+00 756
28 TraesCS5B01G539300 chr2B 96.482 199 7 0 1 199 51071420 51071222 2.250000e-86 329
29 TraesCS5B01G539300 chr2B 91.463 82 4 3 259 339 799376352 799376273 3.190000e-20 110
30 TraesCS5B01G539300 chr3B 90.813 566 44 5 2289 2849 81531975 81532537 0.000000e+00 750
31 TraesCS5B01G539300 chr3B 89.179 268 25 3 367 631 444684245 444683979 6.260000e-87 331
32 TraesCS5B01G539300 chr3B 87.197 289 31 5 337 621 118577831 118577545 1.050000e-84 324
33 TraesCS5B01G539300 chr3B 88.722 266 26 3 367 629 252929069 252929333 3.770000e-84 322
34 TraesCS5B01G539300 chr1A 77.764 814 134 30 1046 1828 517519743 517520540 9.890000e-125 457
35 TraesCS5B01G539300 chr1A 91.089 202 15 1 1 199 514203860 514204061 1.380000e-68 270
36 TraesCS5B01G539300 chr7A 90.637 267 22 2 367 630 119299185 119298919 4.800000e-93 351
37 TraesCS5B01G539300 chr7A 90.226 266 23 2 367 629 119296240 119295975 8.040000e-91 344
38 TraesCS5B01G539300 chr7A 89.888 178 17 1 42 219 3213812 3213636 8.450000e-56 228
39 TraesCS5B01G539300 chr7A 98.571 70 1 0 2957 3026 711620733 711620802 1.140000e-24 124
40 TraesCS5B01G539300 chr1D 89.888 267 22 4 367 629 251792586 251792321 3.740000e-89 339
41 TraesCS5B01G539300 chr1D 89.767 215 15 3 2757 2964 491925431 491925217 4.980000e-68 268
42 TraesCS5B01G539300 chr1D 85.577 104 11 4 2926 3026 411426189 411426087 4.130000e-19 106
43 TraesCS5B01G539300 chr2A 85.809 303 35 5 334 629 757560464 757560765 6.300000e-82 315
44 TraesCS5B01G539300 chr2A 91.975 162 13 0 42 203 778633036 778632875 8.450000e-56 228
45 TraesCS5B01G539300 chr2A 91.765 85 4 3 2944 3028 38365974 38366055 6.860000e-22 115
46 TraesCS5B01G539300 chr2A 84.483 116 11 7 2915 3028 659099431 659099541 1.150000e-19 108
47 TraesCS5B01G539300 chr7B 94.975 199 10 0 1 199 702228354 702228552 2.270000e-81 313
48 TraesCS5B01G539300 chr7B 89.767 215 15 3 2757 2964 43761411 43761197 4.980000e-68 268
49 TraesCS5B01G539300 chr7B 86.207 203 25 1 1 200 715923067 715922865 1.830000e-52 217
50 TraesCS5B01G539300 chr7B 85.714 203 26 1 1 200 715958019 715957817 8.510000e-51 211
51 TraesCS5B01G539300 chr3D 88.837 215 17 3 2757 2964 590230181 590230395 1.080000e-64 257
52 TraesCS5B01G539300 chrUn 85.714 203 26 1 1 200 335665965 335666167 8.510000e-51 211
53 TraesCS5B01G539300 chr4D 96.000 75 3 0 2952 3026 19710357 19710431 4.100000e-24 122


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 TraesCS5B01G539300 chr5B 694201740 694204767 3027 True 5592.0 5592 100.0000 1 3028 1 chr5B.!!$R1 3027
1 TraesCS5B01G539300 chr5B 710313418 710314857 1439 True 1576.0 1576 87.1300 628 2016 1 chr5B.!!$R3 1388
2 TraesCS5B01G539300 chr5B 710324931 710326012 1081 True 880.0 880 82.0380 1026 2101 1 chr5B.!!$R4 1075
3 TraesCS5B01G539300 chr5B 56578955 56579507 552 False 773.0 773 91.8630 2297 2849 1 chr5B.!!$F1 552
4 TraesCS5B01G539300 chr5B 694288296 694289323 1027 True 590.0 590 78.0900 1026 2039 1 chr5B.!!$R2 1013
5 TraesCS5B01G539300 chr4A 604857093 604857950 857 False 859.0 859 85.0110 1374 2249 1 chr4A.!!$F1 875
6 TraesCS5B01G539300 chr4A 604939755 604941685 1930 False 744.5 1245 86.1975 628 2013 2 chr4A.!!$F2 1385
7 TraesCS5B01G539300 chr4A 613543529 613544343 814 True 612.0 612 80.8200 1026 1826 1 chr4A.!!$R1 800
8 TraesCS5B01G539300 chr5D 497929202 497929865 663 True 928.0 928 91.8800 2302 2965 1 chr5D.!!$R2 663
9 TraesCS5B01G539300 chr5D 470045834 470046419 585 False 739.0 739 89.4740 2264 2849 1 chr5D.!!$F2 585
10 TraesCS5B01G539300 chr5D 556423329 556424357 1028 False 662.0 662 79.2450 1026 2033 1 chr5D.!!$F3 1007
11 TraesCS5B01G539300 chr5D 559978111 559978688 577 True 556.0 556 84.9320 1379 1931 1 chr5D.!!$R3 552
12 TraesCS5B01G539300 chr5D 556449538 556450181 643 False 520.0 520 81.4480 1173 1828 1 chr5D.!!$F4 655
13 TraesCS5B01G539300 chr7D 562819408 562819960 552 False 804.0 804 92.9600 2301 2852 1 chr7D.!!$F1 551
14 TraesCS5B01G539300 chr4B 648823813 648824651 838 False 530.5 804 91.0365 2303 2964 2 chr4B.!!$F1 661
15 TraesCS5B01G539300 chr6D 94777625 94778172 547 True 802.0 802 93.0660 2305 2852 1 chr6D.!!$R1 547
16 TraesCS5B01G539300 chr2D 649514332 649514882 550 True 789.0 789 92.5590 2303 2852 1 chr2D.!!$R2 549
17 TraesCS5B01G539300 chr5A 700212373 700212919 546 False 784.0 784 92.5320 2302 2849 1 chr5A.!!$F2 547
18 TraesCS5B01G539300 chr2B 747813715 747814285 570 True 756.0 756 90.5760 2302 2873 1 chr2B.!!$R2 571
19 TraesCS5B01G539300 chr3B 81531975 81532537 562 False 750.0 750 90.8130 2289 2849 1 chr3B.!!$F1 560
20 TraesCS5B01G539300 chr1A 517519743 517520540 797 False 457.0 457 77.7640 1046 1828 1 chr1A.!!$F2 782
21 TraesCS5B01G539300 chr7A 119295975 119299185 3210 True 347.5 351 90.4315 367 630 2 chr7A.!!$R2 263

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
103 104 0.036306 TCCAGAAAAAGAGGACCGCC 59.964 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 5680 0.620556 GACCTCAGGCTCCATTCCAA 59.379 55.0 0.0 0.0 0.0 3.53 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
27 28 3.896133 GCGGCTGCCATGGTCATG 61.896 66.667 20.29 4.09 38.51 3.07
28 29 2.124612 CGGCTGCCATGGTCATGA 60.125 61.111 20.29 0.00 41.20 3.07
29 30 2.475466 CGGCTGCCATGGTCATGAC 61.475 63.158 20.29 17.91 41.20 3.06
53 54 4.368543 GCCGTCGGTCCTTTCGGT 62.369 66.667 13.94 0.00 44.07 4.69
54 55 2.126189 CCGTCGGTCCTTTCGGTC 60.126 66.667 2.08 0.00 38.45 4.79
55 56 2.126189 CGTCGGTCCTTTCGGTCC 60.126 66.667 0.00 0.00 35.43 4.46
59 60 4.772687 GGTCCTTTCGGTCCGGCC 62.773 72.222 12.29 0.00 0.00 6.13
60 61 4.772687 GTCCTTTCGGTCCGGCCC 62.773 72.222 12.29 0.00 0.00 5.80
68 69 3.777910 GGTCCGGCCCGAGCTTTA 61.778 66.667 14.98 0.00 39.73 1.85
69 70 2.510918 GTCCGGCCCGAGCTTTAC 60.511 66.667 3.71 0.00 39.73 2.01
70 71 3.777910 TCCGGCCCGAGCTTTACC 61.778 66.667 3.71 0.00 39.73 2.85
71 72 3.782443 CCGGCCCGAGCTTTACCT 61.782 66.667 3.71 0.00 39.73 3.08
72 73 2.202892 CGGCCCGAGCTTTACCTC 60.203 66.667 0.00 0.00 39.73 3.85
73 74 2.189784 GGCCCGAGCTTTACCTCC 59.810 66.667 0.00 0.00 39.73 4.30
74 75 2.202892 GCCCGAGCTTTACCTCCG 60.203 66.667 0.00 0.00 35.50 4.63
75 76 2.202892 CCCGAGCTTTACCTCCGC 60.203 66.667 0.00 0.00 0.00 5.54
76 77 2.202892 CCGAGCTTTACCTCCGCC 60.203 66.667 0.00 0.00 0.00 6.13
77 78 2.577059 CGAGCTTTACCTCCGCCA 59.423 61.111 0.00 0.00 0.00 5.69
78 79 1.519455 CGAGCTTTACCTCCGCCAG 60.519 63.158 0.00 0.00 0.00 4.85
79 80 1.597461 GAGCTTTACCTCCGCCAGT 59.403 57.895 0.00 0.00 0.00 4.00
80 81 0.460459 GAGCTTTACCTCCGCCAGTC 60.460 60.000 0.00 0.00 0.00 3.51
81 82 1.449778 GCTTTACCTCCGCCAGTCC 60.450 63.158 0.00 0.00 0.00 3.85
82 83 1.153628 CTTTACCTCCGCCAGTCCG 60.154 63.158 0.00 0.00 0.00 4.79
90 91 3.691342 CGCCAGTCCGGTCCAGAA 61.691 66.667 0.00 0.00 36.97 3.02
91 92 2.747686 GCCAGTCCGGTCCAGAAA 59.252 61.111 0.00 0.00 36.97 2.52
92 93 1.072505 GCCAGTCCGGTCCAGAAAA 59.927 57.895 0.00 0.00 36.97 2.29
93 94 0.536460 GCCAGTCCGGTCCAGAAAAA 60.536 55.000 0.00 0.00 36.97 1.94
94 95 1.523758 CCAGTCCGGTCCAGAAAAAG 58.476 55.000 0.00 0.00 0.00 2.27
95 96 1.071699 CCAGTCCGGTCCAGAAAAAGA 59.928 52.381 0.00 0.00 0.00 2.52
96 97 2.417719 CAGTCCGGTCCAGAAAAAGAG 58.582 52.381 0.00 0.00 0.00 2.85
97 98 1.348036 AGTCCGGTCCAGAAAAAGAGG 59.652 52.381 0.00 0.00 0.00 3.69
98 99 1.346722 GTCCGGTCCAGAAAAAGAGGA 59.653 52.381 0.00 0.00 0.00 3.71
102 103 1.157585 GTCCAGAAAAAGAGGACCGC 58.842 55.000 0.00 0.00 44.72 5.68
103 104 0.036306 TCCAGAAAAAGAGGACCGCC 59.964 55.000 0.00 0.00 0.00 6.13
104 105 1.298859 CCAGAAAAAGAGGACCGCCG 61.299 60.000 0.00 0.00 39.96 6.46
105 106 1.671379 AGAAAAAGAGGACCGCCGC 60.671 57.895 0.00 0.00 39.96 6.53
107 108 1.636570 GAAAAAGAGGACCGCCGCTC 61.637 60.000 0.00 0.00 44.17 5.03
108 109 2.113243 AAAAAGAGGACCGCCGCTCT 62.113 55.000 0.00 0.00 44.17 4.09
109 110 2.113243 AAAAGAGGACCGCCGCTCTT 62.113 55.000 0.44 0.44 44.17 2.85
110 111 2.508586 AAAGAGGACCGCCGCTCTTC 62.509 60.000 6.04 0.00 44.17 2.87
111 112 3.453679 GAGGACCGCCGCTCTTCT 61.454 66.667 0.00 0.00 39.96 2.85
112 113 3.418744 GAGGACCGCCGCTCTTCTC 62.419 68.421 0.00 0.00 39.96 2.87
113 114 4.856607 GGACCGCCGCTCTTCTCG 62.857 72.222 0.00 0.00 0.00 4.04
119 120 4.194720 CCGCTCTTCTCGGTCCGG 62.195 72.222 12.29 0.00 41.85 5.14
120 121 3.441290 CGCTCTTCTCGGTCCGGT 61.441 66.667 12.29 0.00 0.00 5.28
121 122 2.182030 GCTCTTCTCGGTCCGGTG 59.818 66.667 12.29 5.13 0.00 4.94
122 123 2.182030 CTCTTCTCGGTCCGGTGC 59.818 66.667 12.29 0.00 0.00 5.01
123 124 3.685214 CTCTTCTCGGTCCGGTGCG 62.685 68.421 12.29 0.00 0.00 5.34
163 164 3.039134 CCAAACGGTGGCTTGGTC 58.961 61.111 2.55 0.00 41.72 4.02
164 165 1.826054 CCAAACGGTGGCTTGGTCA 60.826 57.895 2.55 0.00 41.72 4.02
165 166 1.654220 CAAACGGTGGCTTGGTCAG 59.346 57.895 0.00 0.00 0.00 3.51
166 167 1.528309 AAACGGTGGCTTGGTCAGG 60.528 57.895 0.00 0.00 0.00 3.86
167 168 2.976494 AAACGGTGGCTTGGTCAGGG 62.976 60.000 0.00 0.00 0.00 4.45
168 169 3.636231 CGGTGGCTTGGTCAGGGA 61.636 66.667 0.00 0.00 0.00 4.20
169 170 2.034221 GGTGGCTTGGTCAGGGAC 59.966 66.667 0.00 0.00 0.00 4.46
199 200 2.342648 GACCGTGTCCACCCTGAC 59.657 66.667 0.00 0.00 35.77 3.51
200 201 3.236003 GACCGTGTCCACCCTGACC 62.236 68.421 0.00 0.00 34.25 4.02
201 202 4.016706 CCGTGTCCACCCTGACCC 62.017 72.222 0.00 0.00 34.25 4.46
202 203 3.238497 CGTGTCCACCCTGACCCA 61.238 66.667 0.00 0.00 34.25 4.51
203 204 2.592993 CGTGTCCACCCTGACCCAT 61.593 63.158 0.00 0.00 34.25 4.00
204 205 1.299976 GTGTCCACCCTGACCCATC 59.700 63.158 0.00 0.00 34.25 3.51
205 206 2.290287 TGTCCACCCTGACCCATCG 61.290 63.158 0.00 0.00 34.25 3.84
206 207 2.687200 TCCACCCTGACCCATCGG 60.687 66.667 0.00 0.00 0.00 4.18
207 208 4.489771 CCACCCTGACCCATCGGC 62.490 72.222 0.00 0.00 0.00 5.54
208 209 4.838152 CACCCTGACCCATCGGCG 62.838 72.222 0.00 0.00 0.00 6.46
210 211 4.530857 CCCTGACCCATCGGCGAC 62.531 72.222 13.76 0.00 0.00 5.19
211 212 4.530857 CCTGACCCATCGGCGACC 62.531 72.222 13.76 0.00 0.00 4.79
212 213 4.530857 CTGACCCATCGGCGACCC 62.531 72.222 13.76 0.00 0.00 4.46
231 232 2.844362 CTGCCCCAGCCGATCCTA 60.844 66.667 0.00 0.00 38.69 2.94
232 233 2.844362 TGCCCCAGCCGATCCTAG 60.844 66.667 0.00 0.00 38.69 3.02
233 234 3.631046 GCCCCAGCCGATCCTAGG 61.631 72.222 0.82 0.82 0.00 3.02
239 240 2.027751 GCCGATCCTAGGCGACAC 59.972 66.667 2.96 0.00 45.58 3.67
240 241 2.728817 CCGATCCTAGGCGACACC 59.271 66.667 2.96 0.00 39.61 4.16
241 242 2.728817 CGATCCTAGGCGACACCC 59.271 66.667 2.96 0.00 40.58 4.61
242 243 1.828660 CGATCCTAGGCGACACCCT 60.829 63.158 2.96 0.00 40.58 4.34
243 244 1.797211 CGATCCTAGGCGACACCCTC 61.797 65.000 2.96 0.00 40.58 4.30
244 245 1.797211 GATCCTAGGCGACACCCTCG 61.797 65.000 2.96 0.00 45.97 4.63
272 273 3.471806 GTCTCCCGGGCCCTTCTC 61.472 72.222 22.43 1.29 0.00 2.87
273 274 4.798682 TCTCCCGGGCCCTTCTCC 62.799 72.222 22.43 0.00 0.00 3.71
283 284 4.416601 CCTTCTCCCCCTCCCCGT 62.417 72.222 0.00 0.00 0.00 5.28
284 285 3.083997 CTTCTCCCCCTCCCCGTG 61.084 72.222 0.00 0.00 0.00 4.94
285 286 3.925914 CTTCTCCCCCTCCCCGTGT 62.926 68.421 0.00 0.00 0.00 4.49
286 287 3.918328 TTCTCCCCCTCCCCGTGTC 62.918 68.421 0.00 0.00 0.00 3.67
299 300 4.626081 GTGTCCGCAGCCACAGGT 62.626 66.667 0.00 0.00 0.00 4.00
300 301 4.314440 TGTCCGCAGCCACAGGTC 62.314 66.667 0.00 0.00 0.00 3.85
301 302 4.314440 GTCCGCAGCCACAGGTCA 62.314 66.667 0.00 0.00 0.00 4.02
302 303 4.314440 TCCGCAGCCACAGGTCAC 62.314 66.667 0.00 0.00 0.00 3.67
305 306 4.269523 GCAGCCACAGGTCACCCA 62.270 66.667 0.00 0.00 0.00 4.51
306 307 2.759114 CAGCCACAGGTCACCCAT 59.241 61.111 0.00 0.00 0.00 4.00
307 308 1.377725 CAGCCACAGGTCACCCATC 60.378 63.158 0.00 0.00 0.00 3.51
308 309 2.436646 GCCACAGGTCACCCATCG 60.437 66.667 0.00 0.00 0.00 3.84
309 310 2.268920 CCACAGGTCACCCATCGG 59.731 66.667 0.00 0.00 0.00 4.18
310 311 2.436646 CACAGGTCACCCATCGGC 60.437 66.667 0.00 0.00 0.00 5.54
311 312 4.082523 ACAGGTCACCCATCGGCG 62.083 66.667 0.00 0.00 0.00 6.46
312 313 3.770040 CAGGTCACCCATCGGCGA 61.770 66.667 13.87 13.87 0.00 5.54
313 314 3.771160 AGGTCACCCATCGGCGAC 61.771 66.667 13.76 0.00 0.00 5.19
314 315 4.832608 GGTCACCCATCGGCGACC 62.833 72.222 13.76 3.31 36.87 4.79
315 316 4.832608 GTCACCCATCGGCGACCC 62.833 72.222 13.76 0.00 0.00 4.46
345 346 4.389576 CCGCTGCTGGCAAACGAC 62.390 66.667 15.83 0.00 41.91 4.34
346 347 4.724697 CGCTGCTGGCAAACGACG 62.725 66.667 10.74 0.00 41.91 5.12
347 348 4.389576 GCTGCTGGCAAACGACGG 62.390 66.667 0.00 0.00 41.35 4.79
348 349 4.389576 CTGCTGGCAAACGACGGC 62.390 66.667 0.00 0.00 44.86 5.68
373 374 2.037136 GGCAGCAGCAACGTGAGAT 61.037 57.895 2.65 0.00 44.61 2.75
377 378 2.313234 CAGCAGCAACGTGAGATTTTG 58.687 47.619 0.00 0.00 0.00 2.44
389 390 5.010617 ACGTGAGATTTTGTTTTGCCCTAAT 59.989 36.000 0.00 0.00 0.00 1.73
504 508 0.104855 GCGCACACCATCTCAGGATA 59.895 55.000 0.30 0.00 0.00 2.59
505 509 1.473257 GCGCACACCATCTCAGGATAA 60.473 52.381 0.30 0.00 0.00 1.75
557 3506 3.327172 AGAGGGATGATCTAATGGTGCTG 59.673 47.826 0.00 0.00 0.00 4.41
587 3536 3.243704 TGTGTACGTTTACTGGGGTGTAC 60.244 47.826 0.00 0.00 34.32 2.90
783 3733 9.995003 TTATTTGGCTGTAATCACTTGAATTTT 57.005 25.926 0.00 0.00 0.00 1.82
796 3746 7.211573 TCACTTGAATTTTGCATCTCAATTGT 58.788 30.769 5.13 3.89 32.98 2.71
803 3753 3.084536 TGCATCTCAATTGTTAGCCCA 57.915 42.857 5.13 0.00 0.00 5.36
818 3768 7.658525 TGTTAGCCCAATCACATCATAAAAT 57.341 32.000 0.00 0.00 0.00 1.82
819 3769 7.715657 TGTTAGCCCAATCACATCATAAAATC 58.284 34.615 0.00 0.00 0.00 2.17
899 4329 1.911293 GCACATCGCCATCACACGTT 61.911 55.000 0.00 0.00 32.94 3.99
945 4375 7.343357 TCCAGAAACAGTTAAGAAAAGAAGGA 58.657 34.615 0.00 0.00 0.00 3.36
987 4418 7.520614 GCATTTTTCCTATAAATCCCGACTCTG 60.521 40.741 0.00 0.00 0.00 3.35
1007 4438 0.106819 CCCTCCCCTGCTTCATCTTG 60.107 60.000 0.00 0.00 0.00 3.02
1041 4472 4.821589 GGCACGGCCTCTTCCTCG 62.822 72.222 0.00 0.00 46.69 4.63
1053 4510 2.600122 CTTCCTCGCCGTCCTCTTCG 62.600 65.000 0.00 0.00 0.00 3.79
1054 4511 4.856607 CCTCGCCGTCCTCTTCGC 62.857 72.222 0.00 0.00 0.00 4.70
1100 4557 2.746269 CGTCGTTAACTTCTTGACCCA 58.254 47.619 3.71 0.00 0.00 4.51
1128 4593 1.891919 GACCACGCAGCAGAACCAA 60.892 57.895 0.00 0.00 0.00 3.67
1132 4597 2.249309 CGCAGCAGAACCAACACG 59.751 61.111 0.00 0.00 0.00 4.49
1134 4599 2.249309 CAGCAGAACCAACACGCG 59.751 61.111 3.53 3.53 0.00 6.01
1136 4601 2.970324 GCAGAACCAACACGCGGA 60.970 61.111 12.47 0.00 0.00 5.54
1156 4621 4.431131 CAGCATCCCGCCAACCCT 62.431 66.667 0.00 0.00 44.04 4.34
1275 4758 1.680522 ATGCCGACGAGATGCTCCTT 61.681 55.000 0.00 0.00 0.00 3.36
1291 4774 1.829849 TCCTTCTCCACATGCTCTCAG 59.170 52.381 0.00 0.00 0.00 3.35
1431 4949 1.978712 GAGATCCGTGACTCGACGCA 61.979 60.000 0.00 0.00 42.86 5.24
1543 5061 2.032681 GCCGTGCTCAACTTCCCT 59.967 61.111 0.00 0.00 0.00 4.20
1782 5311 4.504916 CGGCGCCTCAGAGGACAG 62.505 72.222 26.68 11.30 37.67 3.51
1783 5312 4.828925 GGCGCCTCAGAGGACAGC 62.829 72.222 22.15 19.83 37.67 4.40
1786 5315 4.828925 GCCTCAGAGGACAGCGCC 62.829 72.222 21.89 0.00 37.67 6.53
1787 5316 3.385384 CCTCAGAGGACAGCGCCA 61.385 66.667 11.62 0.00 37.67 5.69
1791 5320 3.005539 AGAGGACAGCGCCACCAT 61.006 61.111 2.29 0.00 0.00 3.55
1843 5402 5.425630 CACTCCATGACTTGAAGATGATGA 58.574 41.667 0.00 0.00 0.00 2.92
1905 5479 9.462174 CAGTCTTGTTCTAGCTAGATAGAATTG 57.538 37.037 28.04 20.78 42.25 2.32
1969 5543 0.175531 GCTGTGCAGGTTTGGTTTGT 59.824 50.000 1.11 0.00 0.00 2.83
1971 5545 2.798145 GCTGTGCAGGTTTGGTTTGTAC 60.798 50.000 1.11 0.00 0.00 2.90
2016 5603 7.231115 TGAATCAAGTCAGGTCAAAATGAATGA 59.769 33.333 0.00 0.00 31.84 2.57
2036 5626 8.956426 TGAATGATTTTGGATAGTTCACCTAAC 58.044 33.333 0.00 0.00 38.46 2.34
2043 5633 3.118884 GGATAGTTCACCTAACGCTTGGA 60.119 47.826 0.00 0.00 43.29 3.53
2089 5680 5.650543 GAATTTTATGGTTGACGGCTGAAT 58.349 37.500 0.00 0.00 0.00 2.57
2101 5692 0.749049 GGCTGAATTGGAATGGAGCC 59.251 55.000 0.00 0.00 36.81 4.70
2103 5694 1.407979 GCTGAATTGGAATGGAGCCTG 59.592 52.381 0.00 0.00 0.00 4.85
2104 5695 2.947243 GCTGAATTGGAATGGAGCCTGA 60.947 50.000 0.00 0.00 0.00 3.86
2105 5696 2.950309 CTGAATTGGAATGGAGCCTGAG 59.050 50.000 0.00 0.00 0.00 3.35
2106 5697 2.305009 GAATTGGAATGGAGCCTGAGG 58.695 52.381 0.00 0.00 0.00 3.86
2107 5698 1.302907 ATTGGAATGGAGCCTGAGGT 58.697 50.000 0.00 0.00 0.00 3.85
2109 5700 0.547471 TGGAATGGAGCCTGAGGTCA 60.547 55.000 0.00 0.00 42.52 4.02
2110 5701 0.620556 GGAATGGAGCCTGAGGTCAA 59.379 55.000 0.00 0.00 42.52 3.18
2112 5703 1.556911 GAATGGAGCCTGAGGTCAAGA 59.443 52.381 0.00 0.00 42.52 3.02
2114 5705 1.220477 GGAGCCTGAGGTCAAGAGC 59.780 63.158 0.00 0.00 42.52 4.09
2115 5706 1.220477 GAGCCTGAGGTCAAGAGCC 59.780 63.158 0.00 0.00 40.37 4.70
2179 5781 1.483415 GAGCCCAAACATGCATCCATT 59.517 47.619 0.00 0.00 0.00 3.16
2180 5782 2.694628 GAGCCCAAACATGCATCCATTA 59.305 45.455 0.00 0.00 0.00 1.90
2181 5783 2.431782 AGCCCAAACATGCATCCATTAC 59.568 45.455 0.00 0.00 0.00 1.89
2182 5784 2.168106 GCCCAAACATGCATCCATTACA 59.832 45.455 0.00 0.00 0.00 2.41
2183 5785 3.181463 GCCCAAACATGCATCCATTACAT 60.181 43.478 0.00 0.00 0.00 2.29
2201 5803 1.129251 CATGCAAGTTGGTAGCACTCG 59.871 52.381 4.75 0.00 41.60 4.18
2213 5815 2.546321 CACTCGCTCACGTGCAAC 59.454 61.111 11.67 1.15 41.18 4.17
2216 5818 0.663568 ACTCGCTCACGTGCAACTAC 60.664 55.000 11.67 0.00 41.18 2.73
2228 5830 3.783943 CGTGCAACTACAAACACAAGAAC 59.216 43.478 0.00 0.00 33.23 3.01
2230 5832 5.157781 GTGCAACTACAAACACAAGAACAA 58.842 37.500 0.00 0.00 33.23 2.83
2231 5833 5.286082 GTGCAACTACAAACACAAGAACAAG 59.714 40.000 0.00 0.00 33.23 3.16
2232 5834 4.798387 GCAACTACAAACACAAGAACAAGG 59.202 41.667 0.00 0.00 0.00 3.61
2239 5841 5.245075 ACAAACACAAGAACAAGGAAAGGAA 59.755 36.000 0.00 0.00 0.00 3.36
2271 5873 3.602390 TTTCACGGAAAAGCTTCTTCG 57.398 42.857 0.00 0.00 0.00 3.79
2276 5878 0.166161 GGAAAAGCTTCTTCGCGTCC 59.834 55.000 5.77 0.00 34.40 4.79
2279 5881 3.575351 AAGCTTCTTCGCGTCCGCT 62.575 57.895 5.77 5.66 39.32 5.52
2280 5882 3.546397 GCTTCTTCGCGTCCGCTC 61.546 66.667 5.77 0.00 39.32 5.03
2281 5883 3.241059 CTTCTTCGCGTCCGCTCG 61.241 66.667 5.77 0.00 39.32 5.03
2282 5884 3.948086 CTTCTTCGCGTCCGCTCGT 62.948 63.158 5.77 0.00 39.32 4.18
2283 5885 3.547249 TTCTTCGCGTCCGCTCGTT 62.547 57.895 5.77 0.00 39.32 3.85
2284 5886 3.827784 CTTCGCGTCCGCTCGTTG 61.828 66.667 5.77 0.00 39.32 4.10
2295 5897 4.889427 CTCGTTGGAGCGATCACA 57.111 55.556 1.84 0.00 40.29 3.58
2334 5936 2.811431 GGTTGCTGTGTGCTACAATACA 59.189 45.455 4.87 0.00 46.50 2.29
2340 5942 3.851098 TGTGTGCTACAATACATGCGTA 58.149 40.909 0.00 0.00 36.06 4.42
2362 5964 1.833630 CATACCCTTCTCCACTCAGCA 59.166 52.381 0.00 0.00 0.00 4.41
2467 6069 3.269178 CTTTGGCATGTTGTTTGGTTGT 58.731 40.909 0.00 0.00 0.00 3.32
2477 6079 3.883830 TGTTTGGTTGTCTGCATTGTT 57.116 38.095 0.00 0.00 0.00 2.83
2496 6098 1.024046 TTCGGCGCATGCAACTACAT 61.024 50.000 19.57 0.00 45.35 2.29
2852 6461 3.194542 ACGACTCTAGTGTAGTAGGACGT 59.805 47.826 8.67 4.72 0.00 4.34
2895 6681 0.249657 GCTTCGGCATCGAGAGGAAT 60.250 55.000 0.00 0.00 46.75 3.01
2931 6717 2.310349 TGAGTAGAGGACAGAGGAGCTT 59.690 50.000 0.00 0.00 0.00 3.74
2945 6731 1.975363 GAGCTTGACATGGCAGCGTC 61.975 60.000 14.69 11.76 0.00 5.19
2960 6746 0.039074 GCGTCAGTGCAGTAGACTGT 60.039 55.000 11.19 0.00 45.45 3.55
2961 6747 1.691127 CGTCAGTGCAGTAGACTGTG 58.309 55.000 11.19 2.48 45.45 3.66
2962 6748 1.001268 CGTCAGTGCAGTAGACTGTGT 60.001 52.381 11.19 0.00 45.45 3.72
2964 6750 2.797156 GTCAGTGCAGTAGACTGTGTTG 59.203 50.000 11.19 7.17 45.45 3.33
2966 6752 1.070758 AGTGCAGTAGACTGTGTTGGG 59.929 52.381 11.19 0.00 45.45 4.12
2967 6753 1.128200 TGCAGTAGACTGTGTTGGGT 58.872 50.000 11.19 0.00 45.45 4.51
2968 6754 2.036733 GTGCAGTAGACTGTGTTGGGTA 59.963 50.000 11.19 0.00 45.45 3.69
2969 6755 2.701423 TGCAGTAGACTGTGTTGGGTAA 59.299 45.455 11.19 0.00 45.45 2.85
2970 6756 3.064931 GCAGTAGACTGTGTTGGGTAAC 58.935 50.000 11.19 0.00 45.45 2.50
2971 6757 3.314553 CAGTAGACTGTGTTGGGTAACG 58.685 50.000 1.28 0.00 39.09 3.18
2972 6758 2.961062 AGTAGACTGTGTTGGGTAACGT 59.039 45.455 0.00 0.00 39.71 3.99
2973 6759 4.022935 CAGTAGACTGTGTTGGGTAACGTA 60.023 45.833 1.28 0.00 39.09 3.57
2974 6760 3.655276 AGACTGTGTTGGGTAACGTAG 57.345 47.619 0.00 0.00 39.71 3.51
2975 6761 8.173410 CAGTAGACTGTGTTGGGTAACGTAGT 62.173 46.154 1.28 0.00 40.43 2.73
2976 6762 4.144297 AGACTGTGTTGGGTAACGTAGTA 58.856 43.478 0.00 0.00 45.00 1.82
2977 6763 4.584325 AGACTGTGTTGGGTAACGTAGTAA 59.416 41.667 0.00 0.00 45.00 2.24
2978 6764 5.244626 AGACTGTGTTGGGTAACGTAGTAAT 59.755 40.000 0.00 0.00 45.00 1.89
2979 6765 5.857268 ACTGTGTTGGGTAACGTAGTAATT 58.143 37.500 0.00 0.00 45.00 1.40
2980 6766 6.290605 ACTGTGTTGGGTAACGTAGTAATTT 58.709 36.000 0.00 0.00 45.00 1.82
2981 6767 6.424812 ACTGTGTTGGGTAACGTAGTAATTTC 59.575 38.462 0.00 0.00 45.00 2.17
2982 6768 6.286758 TGTGTTGGGTAACGTAGTAATTTCA 58.713 36.000 0.00 0.00 45.00 2.69
2983 6769 6.765036 TGTGTTGGGTAACGTAGTAATTTCAA 59.235 34.615 0.00 0.00 45.00 2.69
2984 6770 7.281774 TGTGTTGGGTAACGTAGTAATTTCAAA 59.718 33.333 0.00 0.00 45.00 2.69
2985 6771 8.291740 GTGTTGGGTAACGTAGTAATTTCAAAT 58.708 33.333 0.00 0.00 45.00 2.32
2986 6772 8.848182 TGTTGGGTAACGTAGTAATTTCAAATT 58.152 29.630 0.02 0.02 45.00 1.82
2987 6773 9.681692 GTTGGGTAACGTAGTAATTTCAAATTT 57.318 29.630 0.00 0.00 45.00 1.82
2995 6781 9.815936 ACGTAGTAATTTCAAATTTTTCCTACG 57.184 29.630 24.33 24.33 45.52 3.51
2996 6782 8.782327 CGTAGTAATTTCAAATTTTTCCTACGC 58.218 33.333 19.64 5.61 38.04 4.42
2997 6783 9.615295 GTAGTAATTTCAAATTTTTCCTACGCA 57.385 29.630 0.00 0.00 0.00 5.24
2998 6784 8.515473 AGTAATTTCAAATTTTTCCTACGCAC 57.485 30.769 0.00 0.00 0.00 5.34
2999 6785 8.138712 AGTAATTTCAAATTTTTCCTACGCACA 58.861 29.630 0.00 0.00 0.00 4.57
3000 6786 6.763303 ATTTCAAATTTTTCCTACGCACAC 57.237 33.333 0.00 0.00 0.00 3.82
3002 6788 2.325509 AATTTTTCCTACGCACACGC 57.674 45.000 0.00 0.00 45.53 5.34
3003 6789 1.231221 ATTTTTCCTACGCACACGCA 58.769 45.000 0.00 0.00 45.53 5.24
3004 6790 1.015109 TTTTTCCTACGCACACGCAA 58.985 45.000 0.00 0.00 45.53 4.85
3005 6791 0.584396 TTTTCCTACGCACACGCAAG 59.416 50.000 0.00 0.00 45.53 4.01
3006 6792 0.249531 TTTCCTACGCACACGCAAGA 60.250 50.000 0.00 0.00 45.53 3.02
3007 6793 0.037697 TTCCTACGCACACGCAAGAT 60.038 50.000 0.00 0.00 45.53 2.40
3008 6794 0.457853 TCCTACGCACACGCAAGATC 60.458 55.000 0.00 0.00 45.53 2.75
3009 6795 0.735978 CCTACGCACACGCAAGATCA 60.736 55.000 0.00 0.00 45.53 2.92
3010 6796 1.280982 CTACGCACACGCAAGATCAT 58.719 50.000 0.00 0.00 45.53 2.45
3011 6797 0.998669 TACGCACACGCAAGATCATG 59.001 50.000 0.00 0.00 45.53 3.07
3012 6798 1.061411 CGCACACGCAAGATCATGG 59.939 57.895 0.00 0.00 43.62 3.66
3013 6799 1.638388 CGCACACGCAAGATCATGGT 61.638 55.000 0.00 0.00 43.62 3.55
3014 6800 0.179181 GCACACGCAAGATCATGGTG 60.179 55.000 14.17 14.17 43.62 4.17
3015 6801 1.441738 CACACGCAAGATCATGGTGA 58.558 50.000 19.56 0.00 43.62 4.02
3016 6802 2.011947 CACACGCAAGATCATGGTGAT 58.988 47.619 19.56 0.00 40.34 3.06
3017 6803 2.011947 ACACGCAAGATCATGGTGATG 58.988 47.619 19.56 8.58 37.20 3.07
3018 6804 1.019673 ACGCAAGATCATGGTGATGC 58.980 50.000 0.00 3.06 37.20 3.91
3019 6805 1.018910 CGCAAGATCATGGTGATGCA 58.981 50.000 11.83 0.00 37.20 3.96
3020 6806 1.607148 CGCAAGATCATGGTGATGCAT 59.393 47.619 0.00 0.00 37.20 3.96
3021 6807 2.809696 CGCAAGATCATGGTGATGCATA 59.190 45.455 0.00 0.00 37.20 3.14
3022 6808 3.120304 CGCAAGATCATGGTGATGCATAG 60.120 47.826 0.00 0.00 37.20 2.23
3023 6809 3.366070 GCAAGATCATGGTGATGCATAGC 60.366 47.826 0.00 0.00 37.20 2.97
3024 6810 3.782656 AGATCATGGTGATGCATAGCA 57.217 42.857 0.00 4.86 44.86 3.49
3025 6811 4.094830 AGATCATGGTGATGCATAGCAA 57.905 40.909 0.00 0.00 43.62 3.91
3026 6812 4.663334 AGATCATGGTGATGCATAGCAAT 58.337 39.130 0.00 0.00 43.62 3.56
3027 6813 4.459337 AGATCATGGTGATGCATAGCAATG 59.541 41.667 0.00 5.10 43.62 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.124612 TCATGACCATGGCAGCCG 60.125 61.111 13.04 4.45 39.24 5.52
12 13 3.518003 GTCATGACCATGGCAGCC 58.482 61.111 15.31 3.66 42.66 4.85
51 52 3.777910 TAAAGCTCGGGCCGGACC 61.778 66.667 27.98 19.81 39.73 4.46
52 53 2.510918 GTAAAGCTCGGGCCGGAC 60.511 66.667 27.98 18.43 39.73 4.79
53 54 3.777910 GGTAAAGCTCGGGCCGGA 61.778 66.667 27.98 13.04 39.73 5.14
54 55 3.735037 GAGGTAAAGCTCGGGCCGG 62.735 68.421 27.98 17.85 39.73 6.13
55 56 2.202892 GAGGTAAAGCTCGGGCCG 60.203 66.667 22.51 22.51 39.73 6.13
56 57 2.189784 GGAGGTAAAGCTCGGGCC 59.810 66.667 2.00 0.00 39.73 5.80
57 58 2.202892 CGGAGGTAAAGCTCGGGC 60.203 66.667 0.00 0.00 39.06 6.13
58 59 2.202892 GCGGAGGTAAAGCTCGGG 60.203 66.667 15.64 6.67 0.00 5.14
59 60 2.202892 GGCGGAGGTAAAGCTCGG 60.203 66.667 11.17 11.17 0.00 4.63
60 61 1.519455 CTGGCGGAGGTAAAGCTCG 60.519 63.158 3.29 1.01 0.00 5.03
61 62 0.460459 GACTGGCGGAGGTAAAGCTC 60.460 60.000 0.00 0.46 0.00 4.09
62 63 1.597461 GACTGGCGGAGGTAAAGCT 59.403 57.895 0.00 0.00 0.00 3.74
63 64 1.449778 GGACTGGCGGAGGTAAAGC 60.450 63.158 0.00 0.00 0.00 3.51
64 65 1.153628 CGGACTGGCGGAGGTAAAG 60.154 63.158 0.00 0.00 0.00 1.85
65 66 2.652095 CCGGACTGGCGGAGGTAAA 61.652 63.158 0.00 0.00 0.00 2.01
66 67 3.072468 CCGGACTGGCGGAGGTAA 61.072 66.667 0.00 0.00 0.00 2.85
67 68 4.371417 ACCGGACTGGCGGAGGTA 62.371 66.667 9.46 0.00 43.94 3.08
73 74 2.725203 TTTTCTGGACCGGACTGGCG 62.725 60.000 9.46 0.00 43.94 5.69
74 75 0.536460 TTTTTCTGGACCGGACTGGC 60.536 55.000 9.46 0.00 43.94 4.85
75 76 1.071699 TCTTTTTCTGGACCGGACTGG 59.928 52.381 9.46 0.00 46.41 4.00
76 77 2.417719 CTCTTTTTCTGGACCGGACTG 58.582 52.381 9.46 4.84 0.00 3.51
77 78 1.348036 CCTCTTTTTCTGGACCGGACT 59.652 52.381 9.46 0.00 0.00 3.85
78 79 1.346722 TCCTCTTTTTCTGGACCGGAC 59.653 52.381 9.46 0.00 0.00 4.79
79 80 1.346722 GTCCTCTTTTTCTGGACCGGA 59.653 52.381 9.46 0.00 43.10 5.14
80 81 1.809684 GTCCTCTTTTTCTGGACCGG 58.190 55.000 0.00 0.00 43.10 5.28
83 84 1.157585 GCGGTCCTCTTTTTCTGGAC 58.842 55.000 0.00 0.00 46.83 4.02
84 85 0.036306 GGCGGTCCTCTTTTTCTGGA 59.964 55.000 0.00 0.00 0.00 3.86
85 86 1.298859 CGGCGGTCCTCTTTTTCTGG 61.299 60.000 0.00 0.00 0.00 3.86
86 87 1.912371 GCGGCGGTCCTCTTTTTCTG 61.912 60.000 9.78 0.00 0.00 3.02
87 88 1.671379 GCGGCGGTCCTCTTTTTCT 60.671 57.895 9.78 0.00 0.00 2.52
88 89 1.636570 GAGCGGCGGTCCTCTTTTTC 61.637 60.000 27.28 0.00 0.00 2.29
89 90 1.671379 GAGCGGCGGTCCTCTTTTT 60.671 57.895 27.28 0.00 0.00 1.94
90 91 2.047179 GAGCGGCGGTCCTCTTTT 60.047 61.111 27.28 0.00 0.00 2.27
91 92 2.508586 GAAGAGCGGCGGTCCTCTTT 62.509 60.000 32.58 21.34 45.64 2.52
92 93 2.997897 AAGAGCGGCGGTCCTCTT 60.998 61.111 32.58 24.87 42.07 2.85
93 94 3.453679 GAAGAGCGGCGGTCCTCT 61.454 66.667 32.58 20.79 40.00 3.69
94 95 3.418744 GAGAAGAGCGGCGGTCCTC 62.419 68.421 32.58 28.91 0.00 3.71
95 96 3.453679 GAGAAGAGCGGCGGTCCT 61.454 66.667 32.58 23.93 0.00 3.85
96 97 4.856607 CGAGAAGAGCGGCGGTCC 62.857 72.222 32.58 19.75 0.00 4.46
97 98 4.856607 CCGAGAAGAGCGGCGGTC 62.857 72.222 29.85 29.85 42.55 4.79
103 104 3.441290 ACCGGACCGAGAAGAGCG 61.441 66.667 17.49 0.00 0.00 5.03
104 105 2.182030 CACCGGACCGAGAAGAGC 59.818 66.667 17.49 0.00 0.00 4.09
105 106 2.182030 GCACCGGACCGAGAAGAG 59.818 66.667 17.49 0.00 0.00 2.85
106 107 3.744719 CGCACCGGACCGAGAAGA 61.745 66.667 17.49 0.00 0.00 2.87
147 148 1.654220 CTGACCAAGCCACCGTTTG 59.346 57.895 0.00 0.00 0.00 2.93
148 149 1.528309 CCTGACCAAGCCACCGTTT 60.528 57.895 0.00 0.00 0.00 3.60
149 150 2.113139 CCTGACCAAGCCACCGTT 59.887 61.111 0.00 0.00 0.00 4.44
150 151 3.953775 CCCTGACCAAGCCACCGT 61.954 66.667 0.00 0.00 0.00 4.83
151 152 3.636231 TCCCTGACCAAGCCACCG 61.636 66.667 0.00 0.00 0.00 4.94
152 153 2.034221 GTCCCTGACCAAGCCACC 59.966 66.667 0.00 0.00 0.00 4.61
182 183 2.342648 GTCAGGGTGGACACGGTC 59.657 66.667 0.00 0.00 37.73 4.79
183 184 3.239253 GGTCAGGGTGGACACGGT 61.239 66.667 0.00 0.00 39.59 4.83
184 185 4.016706 GGGTCAGGGTGGACACGG 62.017 72.222 0.00 0.00 39.59 4.94
185 186 2.521958 GATGGGTCAGGGTGGACACG 62.522 65.000 0.00 0.00 44.26 4.49
186 187 1.299976 GATGGGTCAGGGTGGACAC 59.700 63.158 0.00 0.00 41.65 3.67
187 188 2.290287 CGATGGGTCAGGGTGGACA 61.290 63.158 0.00 0.00 39.59 4.02
188 189 2.584608 CGATGGGTCAGGGTGGAC 59.415 66.667 0.00 0.00 37.06 4.02
189 190 2.687200 CCGATGGGTCAGGGTGGA 60.687 66.667 0.00 0.00 0.00 4.02
190 191 4.489771 GCCGATGGGTCAGGGTGG 62.490 72.222 0.00 0.00 34.97 4.61
191 192 4.838152 CGCCGATGGGTCAGGGTG 62.838 72.222 0.00 0.00 34.97 4.61
193 194 4.530857 GTCGCCGATGGGTCAGGG 62.531 72.222 0.00 0.00 34.97 4.45
194 195 4.530857 GGTCGCCGATGGGTCAGG 62.531 72.222 0.00 0.00 34.97 3.86
195 196 4.530857 GGGTCGCCGATGGGTCAG 62.531 72.222 0.00 0.00 34.97 3.51
214 215 2.844362 TAGGATCGGCTGGGGCAG 60.844 66.667 0.00 0.00 40.87 4.85
215 216 2.844362 CTAGGATCGGCTGGGGCA 60.844 66.667 0.00 0.00 40.87 5.36
216 217 3.631046 CCTAGGATCGGCTGGGGC 61.631 72.222 1.05 0.00 37.82 5.80
217 218 3.631046 GCCTAGGATCGGCTGGGG 61.631 72.222 14.75 0.00 44.17 4.96
218 219 3.996124 CGCCTAGGATCGGCTGGG 61.996 72.222 14.75 3.24 45.37 4.45
219 220 2.912542 TCGCCTAGGATCGGCTGG 60.913 66.667 14.75 0.00 45.37 4.85
220 221 2.336809 GTCGCCTAGGATCGGCTG 59.663 66.667 14.75 3.04 45.37 4.85
221 222 2.123854 TGTCGCCTAGGATCGGCT 60.124 61.111 14.75 0.00 45.37 5.52
222 223 2.027751 GTGTCGCCTAGGATCGGC 59.972 66.667 14.75 9.92 44.11 5.54
223 224 2.728817 GGTGTCGCCTAGGATCGG 59.271 66.667 14.75 0.00 0.00 4.18
224 225 1.797211 GAGGGTGTCGCCTAGGATCG 61.797 65.000 14.75 7.82 37.43 3.69
225 226 1.797211 CGAGGGTGTCGCCTAGGATC 61.797 65.000 14.75 1.97 43.03 3.36
226 227 1.828660 CGAGGGTGTCGCCTAGGAT 60.829 63.158 14.75 0.00 43.03 3.24
227 228 2.439701 CGAGGGTGTCGCCTAGGA 60.440 66.667 14.75 0.00 43.03 2.94
255 256 3.471806 GAGAAGGGCCCGGGAGAC 61.472 72.222 29.31 13.76 0.00 3.36
256 257 4.798682 GGAGAAGGGCCCGGGAGA 62.799 72.222 29.31 0.00 0.00 3.71
266 267 4.416601 ACGGGGAGGGGGAGAAGG 62.417 72.222 0.00 0.00 0.00 3.46
267 268 3.083997 CACGGGGAGGGGGAGAAG 61.084 72.222 0.00 0.00 0.00 2.85
268 269 3.918328 GACACGGGGAGGGGGAGAA 62.918 68.421 0.00 0.00 0.00 2.87
269 270 4.393778 GACACGGGGAGGGGGAGA 62.394 72.222 0.00 0.00 0.00 3.71
283 284 4.314440 GACCTGTGGCTGCGGACA 62.314 66.667 0.00 0.00 0.00 4.02
284 285 4.314440 TGACCTGTGGCTGCGGAC 62.314 66.667 0.00 0.00 0.00 4.79
285 286 4.314440 GTGACCTGTGGCTGCGGA 62.314 66.667 0.00 0.00 0.00 5.54
330 331 4.389576 CCGTCGTTTGCCAGCAGC 62.390 66.667 0.00 0.00 44.14 5.25
331 332 4.389576 GCCGTCGTTTGCCAGCAG 62.390 66.667 0.00 0.00 0.00 4.24
354 355 4.081030 CTCACGTTGCTGCTGCCG 62.081 66.667 13.47 12.37 38.71 5.69
355 356 1.580845 AATCTCACGTTGCTGCTGCC 61.581 55.000 13.47 0.00 38.71 4.85
356 357 0.239347 AAATCTCACGTTGCTGCTGC 59.761 50.000 8.89 8.89 40.20 5.25
357 358 2.287188 ACAAAATCTCACGTTGCTGCTG 60.287 45.455 0.00 0.00 0.00 4.41
358 359 1.949525 ACAAAATCTCACGTTGCTGCT 59.050 42.857 0.00 0.00 0.00 4.24
359 360 2.405892 ACAAAATCTCACGTTGCTGC 57.594 45.000 0.00 0.00 0.00 5.25
360 361 4.548726 GCAAAACAAAATCTCACGTTGCTG 60.549 41.667 0.00 0.00 37.67 4.41
361 362 3.551485 GCAAAACAAAATCTCACGTTGCT 59.449 39.130 0.00 0.00 37.67 3.91
362 363 3.302415 GGCAAAACAAAATCTCACGTTGC 60.302 43.478 0.00 0.00 39.44 4.17
363 364 3.245048 GGGCAAAACAAAATCTCACGTTG 59.755 43.478 0.00 0.00 0.00 4.10
364 365 3.132111 AGGGCAAAACAAAATCTCACGTT 59.868 39.130 0.00 0.00 0.00 3.99
365 366 2.693074 AGGGCAAAACAAAATCTCACGT 59.307 40.909 0.00 0.00 0.00 4.49
400 401 2.751436 GCTCAGCGCCAAATCCCA 60.751 61.111 2.29 0.00 0.00 4.37
424 427 3.744660 AGAAATATCCCATCCTGCGTTC 58.255 45.455 0.00 0.00 0.00 3.95
425 428 3.864789 AGAAATATCCCATCCTGCGTT 57.135 42.857 0.00 0.00 0.00 4.84
429 432 4.401925 GGGTGAAGAAATATCCCATCCTG 58.598 47.826 0.00 0.00 38.15 3.86
431 434 3.412386 CGGGTGAAGAAATATCCCATCC 58.588 50.000 0.00 0.00 38.15 3.51
434 437 2.092646 CACCGGGTGAAGAAATATCCCA 60.093 50.000 22.77 0.00 38.15 4.37
486 490 2.101415 TCTTATCCTGAGATGGTGTGCG 59.899 50.000 0.00 0.00 33.67 5.34
505 509 9.543783 GTAAATCTTAACCGTCAGGATTAATCT 57.456 33.333 14.95 0.00 41.02 2.40
557 3506 5.035443 CCAGTAAACGTACACAGCTAGATC 58.965 45.833 0.00 0.00 32.12 2.75
576 3525 5.899631 TTCTTTCTTAAGTACACCCCAGT 57.100 39.130 1.63 0.00 32.98 4.00
752 3702 7.870445 TCAAGTGATTACAGCCAAATAAAAACC 59.130 33.333 0.00 0.00 0.00 3.27
783 3733 3.084536 TGGGCTAACAATTGAGATGCA 57.915 42.857 13.59 0.00 0.00 3.96
796 3746 9.066892 GTAGATTTTATGATGTGATTGGGCTAA 57.933 33.333 0.00 0.00 0.00 3.09
819 3769 9.680315 GCATGTTCTAAGTAATGGTAGTAGTAG 57.320 37.037 0.00 0.00 0.00 2.57
858 4288 7.552330 TGTGCTCTTGTATTTGTGATGCTATTA 59.448 33.333 0.00 0.00 0.00 0.98
945 4375 2.299326 ATGCTTTGCTTCCTGGTCTT 57.701 45.000 0.00 0.00 0.00 3.01
987 4418 1.931007 AAGATGAAGCAGGGGAGGGC 61.931 60.000 0.00 0.00 0.00 5.19
1007 4438 1.303643 CCAGGGGTTGGTTGAGCTC 60.304 63.158 6.82 6.82 42.41 4.09
1038 4469 4.856607 GGCGAAGAGGACGGCGAG 62.857 72.222 16.62 0.00 45.03 5.03
1128 4593 3.121030 GATGCTGCTTCCGCGTGT 61.121 61.111 4.92 0.00 39.65 4.49
1134 4599 4.802051 TGGCGGGATGCTGCTTCC 62.802 66.667 22.55 22.55 45.43 3.46
1136 4601 3.064324 GTTGGCGGGATGCTGCTT 61.064 61.111 18.22 0.00 45.43 3.91
1291 4774 2.740055 CGTGTCCTGCTGGTGCTC 60.740 66.667 9.73 4.63 40.48 4.26
1493 5011 3.660111 GGCGAACGCAGCTTGGTT 61.660 61.111 20.16 0.00 44.11 3.67
1774 5303 3.005539 ATGGTGGCGCTGTCCTCT 61.006 61.111 7.64 0.00 0.00 3.69
1782 5311 3.520862 CCATGGTGATGGTGGCGC 61.521 66.667 2.57 0.00 43.98 6.53
1843 5402 0.949105 AAAACAGCGAGCGATCCGTT 60.949 50.000 0.00 0.00 0.00 4.44
1905 5479 4.054671 CTCAATCCCAACGAAGCTATCTC 58.945 47.826 0.00 0.00 0.00 2.75
1969 5543 8.594881 ATTCAAACCAAAATAATTTGCACGTA 57.405 26.923 0.00 0.00 43.73 3.57
1971 5545 7.571026 TGATTCAAACCAAAATAATTTGCACG 58.429 30.769 0.00 0.00 43.73 5.34
2016 5603 5.497474 AGCGTTAGGTGAACTATCCAAAAT 58.503 37.500 0.00 0.00 35.74 1.82
2089 5680 0.620556 GACCTCAGGCTCCATTCCAA 59.379 55.000 0.00 0.00 0.00 3.53
2101 5692 2.276732 TTTTGGGCTCTTGACCTCAG 57.723 50.000 0.00 0.00 43.49 3.35
2103 5694 1.889170 CCTTTTTGGGCTCTTGACCTC 59.111 52.381 0.00 0.00 43.49 3.85
2104 5695 1.499007 TCCTTTTTGGGCTCTTGACCT 59.501 47.619 0.00 0.00 43.49 3.85
2105 5696 1.995376 TCCTTTTTGGGCTCTTGACC 58.005 50.000 0.00 0.00 43.36 4.02
2106 5697 3.157087 TCATCCTTTTTGGGCTCTTGAC 58.843 45.455 0.00 0.00 36.20 3.18
2107 5698 3.524095 TCATCCTTTTTGGGCTCTTGA 57.476 42.857 0.00 0.00 36.20 3.02
2109 5700 4.564199 GCATTTCATCCTTTTTGGGCTCTT 60.564 41.667 0.00 0.00 36.20 2.85
2110 5701 3.055602 GCATTTCATCCTTTTTGGGCTCT 60.056 43.478 0.00 0.00 36.20 4.09
2112 5703 2.638855 TGCATTTCATCCTTTTTGGGCT 59.361 40.909 0.00 0.00 36.20 5.19
2114 5705 5.732633 TGTATGCATTTCATCCTTTTTGGG 58.267 37.500 3.54 0.00 36.63 4.12
2115 5706 6.819649 ACATGTATGCATTTCATCCTTTTTGG 59.180 34.615 3.54 0.00 36.63 3.28
2179 5781 3.334691 GAGTGCTACCAACTTGCATGTA 58.665 45.455 5.56 0.00 39.00 2.29
2180 5782 2.154462 GAGTGCTACCAACTTGCATGT 58.846 47.619 0.00 0.00 39.00 3.21
2181 5783 1.129251 CGAGTGCTACCAACTTGCATG 59.871 52.381 0.00 0.00 39.00 4.06
2182 5784 1.442769 CGAGTGCTACCAACTTGCAT 58.557 50.000 0.00 0.00 39.00 3.96
2183 5785 1.227999 GCGAGTGCTACCAACTTGCA 61.228 55.000 10.25 0.00 39.86 4.08
2201 5803 1.329292 TGTTTGTAGTTGCACGTGAGC 59.671 47.619 22.23 5.09 0.00 4.26
2213 5815 6.094881 TCCTTTCCTTGTTCTTGTGTTTGTAG 59.905 38.462 0.00 0.00 0.00 2.74
2216 5818 5.323371 TCCTTTCCTTGTTCTTGTGTTTG 57.677 39.130 0.00 0.00 0.00 2.93
2239 5841 9.758651 AGCTTTTCCGTGAAAAATATACTTTTT 57.241 25.926 11.31 0.48 40.34 1.94
2243 5845 8.336801 AGAAGCTTTTCCGTGAAAAATATACT 57.663 30.769 0.00 6.52 40.34 2.12
2249 5851 4.347813 CGAAGAAGCTTTTCCGTGAAAAA 58.652 39.130 0.00 1.77 40.34 1.94
2250 5852 3.790789 GCGAAGAAGCTTTTCCGTGAAAA 60.791 43.478 0.00 10.18 38.90 2.29
2251 5853 2.286772 GCGAAGAAGCTTTTCCGTGAAA 60.287 45.455 0.00 0.00 0.00 2.69
2252 5854 1.263217 GCGAAGAAGCTTTTCCGTGAA 59.737 47.619 0.00 0.00 0.00 3.18
2253 5855 0.865769 GCGAAGAAGCTTTTCCGTGA 59.134 50.000 0.00 0.00 0.00 4.35
2254 5856 0.451135 CGCGAAGAAGCTTTTCCGTG 60.451 55.000 0.00 7.40 34.40 4.94
2255 5857 0.878961 ACGCGAAGAAGCTTTTCCGT 60.879 50.000 15.93 19.29 34.40 4.69
2256 5858 0.179248 GACGCGAAGAAGCTTTTCCG 60.179 55.000 15.93 13.24 34.40 4.30
2257 5859 0.166161 GGACGCGAAGAAGCTTTTCC 59.834 55.000 15.93 0.07 34.40 3.13
2258 5860 0.179248 CGGACGCGAAGAAGCTTTTC 60.179 55.000 15.93 5.91 34.40 2.29
2259 5861 1.860078 CGGACGCGAAGAAGCTTTT 59.140 52.632 15.93 0.00 34.40 2.27
2260 5862 2.668280 GCGGACGCGAAGAAGCTTT 61.668 57.895 15.93 0.00 34.40 3.51
2261 5863 3.112709 GCGGACGCGAAGAAGCTT 61.113 61.111 15.93 0.00 34.40 3.74
2279 5881 0.525455 CGATGTGATCGCTCCAACGA 60.525 55.000 7.94 0.00 46.55 3.85
2280 5882 1.920051 CGATGTGATCGCTCCAACG 59.080 57.895 7.94 2.86 46.55 4.10
2289 5891 3.668447 ACATGCCCTTATCGATGTGATC 58.332 45.455 8.54 0.00 38.57 2.92
2290 5892 3.777106 ACATGCCCTTATCGATGTGAT 57.223 42.857 8.54 0.00 41.30 3.06
2292 5894 3.243168 CCAAACATGCCCTTATCGATGTG 60.243 47.826 8.54 0.07 0.00 3.21
2293 5895 2.951642 CCAAACATGCCCTTATCGATGT 59.048 45.455 8.54 0.00 0.00 3.06
2294 5896 2.951642 ACCAAACATGCCCTTATCGATG 59.048 45.455 8.54 0.00 0.00 3.84
2295 5897 3.297134 ACCAAACATGCCCTTATCGAT 57.703 42.857 2.16 2.16 0.00 3.59
2298 5900 2.497273 AGCAACCAAACATGCCCTTATC 59.503 45.455 0.00 0.00 43.57 1.75
2307 5909 3.665544 GCACACAGCAACCAAACAT 57.334 47.368 0.00 0.00 44.79 2.71
2340 5942 2.114616 CTGAGTGGAGAAGGGTATGCT 58.885 52.381 0.00 0.00 0.00 3.79
2467 6069 1.585267 ATGCGCCGAAACAATGCAGA 61.585 50.000 4.18 0.00 39.17 4.26
2477 6079 1.024046 ATGTAGTTGCATGCGCCGAA 61.024 50.000 14.09 0.00 37.32 4.30
2852 6461 1.574526 CCCCTTGATCTCCTTGCCCA 61.575 60.000 0.00 0.00 0.00 5.36
2884 6670 4.462483 GCTCTCCTATTCATTCCTCTCGAT 59.538 45.833 0.00 0.00 0.00 3.59
2895 6681 5.456042 CCTCTACTCAGAGCTCTCCTATTCA 60.456 48.000 14.96 0.00 46.08 2.57
2931 6717 1.668793 CACTGACGCTGCCATGTCA 60.669 57.895 8.26 8.26 42.49 3.58
2960 6746 7.798596 TTTGAAATTACTACGTTACCCAACA 57.201 32.000 0.00 0.00 34.05 3.33
2961 6747 9.681692 AAATTTGAAATTACTACGTTACCCAAC 57.318 29.630 3.26 0.00 0.00 3.77
2969 6755 9.815936 CGTAGGAAAAATTTGAAATTACTACGT 57.184 29.630 24.37 15.52 42.70 3.57
2971 6757 9.615295 TGCGTAGGAAAAATTTGAAATTACTAC 57.385 29.630 3.26 12.03 0.00 2.73
2972 6758 9.615295 GTGCGTAGGAAAAATTTGAAATTACTA 57.385 29.630 3.26 2.70 0.00 1.82
2973 6759 8.138712 TGTGCGTAGGAAAAATTTGAAATTACT 58.861 29.630 3.26 3.55 0.00 2.24
2974 6760 8.211838 GTGTGCGTAGGAAAAATTTGAAATTAC 58.788 33.333 3.26 0.00 0.00 1.89
2975 6761 7.113684 CGTGTGCGTAGGAAAAATTTGAAATTA 59.886 33.333 3.26 0.00 0.00 1.40
2976 6762 6.074569 CGTGTGCGTAGGAAAAATTTGAAATT 60.075 34.615 0.00 0.00 0.00 1.82
2977 6763 5.401079 CGTGTGCGTAGGAAAAATTTGAAAT 59.599 36.000 0.00 0.00 0.00 2.17
2978 6764 4.735822 CGTGTGCGTAGGAAAAATTTGAAA 59.264 37.500 0.00 0.00 0.00 2.69
2979 6765 4.283678 CGTGTGCGTAGGAAAAATTTGAA 58.716 39.130 0.00 0.00 0.00 2.69
2980 6766 3.850374 GCGTGTGCGTAGGAAAAATTTGA 60.850 43.478 0.00 0.00 40.81 2.69
2981 6767 2.403698 GCGTGTGCGTAGGAAAAATTTG 59.596 45.455 0.00 0.00 40.81 2.32
2982 6768 2.657184 GCGTGTGCGTAGGAAAAATTT 58.343 42.857 0.00 0.00 40.81 1.82
2983 6769 2.325509 GCGTGTGCGTAGGAAAAATT 57.674 45.000 0.00 0.00 40.81 1.82
2995 6781 0.179181 CACCATGATCTTGCGTGTGC 60.179 55.000 15.81 0.00 43.20 4.57
2996 6782 1.441738 TCACCATGATCTTGCGTGTG 58.558 50.000 19.89 14.96 0.00 3.82
2997 6783 2.011947 CATCACCATGATCTTGCGTGT 58.988 47.619 19.89 6.63 34.28 4.49
2998 6784 1.268386 GCATCACCATGATCTTGCGTG 60.268 52.381 17.02 17.02 34.28 5.34
2999 6785 1.019673 GCATCACCATGATCTTGCGT 58.980 50.000 3.07 0.87 34.28 5.24
3000 6786 1.018910 TGCATCACCATGATCTTGCG 58.981 50.000 3.07 0.30 34.28 4.85
3001 6787 3.366070 GCTATGCATCACCATGATCTTGC 60.366 47.826 0.19 0.00 34.28 4.01
3002 6788 3.818773 TGCTATGCATCACCATGATCTTG 59.181 43.478 0.19 1.60 34.28 3.02
3003 6789 4.094830 TGCTATGCATCACCATGATCTT 57.905 40.909 0.19 0.00 34.28 2.40
3004 6790 3.782656 TGCTATGCATCACCATGATCT 57.217 42.857 0.19 0.00 34.28 2.75
3005 6791 4.733850 CATTGCTATGCATCACCATGATC 58.266 43.478 0.19 0.00 38.76 2.92
3006 6792 4.783764 CATTGCTATGCATCACCATGAT 57.216 40.909 0.19 0.00 38.76 2.45


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

AutoCloner maintained by Alex Coulton.