Multiple sequence alignment - TraesCS6B01G221100

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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 TraesCS6B01G221100 chr6B 100.000 6766 0 0 1 6766 316610081 316603316 0.000000e+00 12495.0
1 TraesCS6B01G221100 chr6B 97.406 347 9 0 1 347 663567705 663568051 5.840000e-165 592.0
2 TraesCS6B01G221100 chr6B 90.625 256 12 10 382 626 663568050 663568304 5.060000e-86 329.0
3 TraesCS6B01G221100 chr6B 93.636 220 10 3 634 852 663568264 663568480 6.540000e-85 326.0
4 TraesCS6B01G221100 chr6B 79.952 414 57 20 2524 2918 31395472 31395878 1.440000e-71 281.0
5 TraesCS6B01G221100 chr6B 77.386 482 73 25 2467 2918 422401741 422402216 3.130000e-63 254.0
6 TraesCS6B01G221100 chr6B 92.308 143 1 2 1648 1780 316607306 316607164 1.930000e-45 195.0
7 TraesCS6B01G221100 chr6B 89.256 121 10 3 751 869 239326224 239326105 1.520000e-31 148.0
8 TraesCS6B01G221100 chr6B 90.291 103 9 1 761 862 17920635 17920737 4.260000e-27 134.0
9 TraesCS6B01G221100 chr6D 95.426 2099 77 12 2180 4268 164763694 164765783 0.000000e+00 3326.0
10 TraesCS6B01G221100 chr6D 96.572 1546 35 7 4263 5798 164766781 164768318 0.000000e+00 2545.0
11 TraesCS6B01G221100 chr6D 94.959 734 25 6 941 1663 164761915 164762647 0.000000e+00 1140.0
12 TraesCS6B01G221100 chr6D 85.831 981 114 15 5794 6766 164803009 164803972 0.000000e+00 1018.0
13 TraesCS6B01G221100 chr6D 88.386 508 25 11 1659 2135 164763192 164763696 1.260000e-161 580.0
14 TraesCS6B01G221100 chr6D 81.855 248 38 6 5902 6145 78360321 78360565 1.150000e-47 202.0
15 TraesCS6B01G221100 chr6D 77.297 185 29 11 2217 2397 199715640 199715465 5.590000e-16 97.1
16 TraesCS6B01G221100 chr6A 96.784 1679 35 9 3322 4998 259206195 259207856 0.000000e+00 2784.0
17 TraesCS6B01G221100 chr6A 92.017 1428 84 7 1938 3338 259204759 259206183 0.000000e+00 1978.0
18 TraesCS6B01G221100 chr6A 90.973 1274 83 19 5072 6321 259207856 259209121 0.000000e+00 1687.0
19 TraesCS6B01G221100 chr6A 94.851 874 26 4 910 1766 259203546 259204417 0.000000e+00 1347.0
20 TraesCS6B01G221100 chr6A 89.568 556 29 11 1 550 576235461 576235993 0.000000e+00 678.0
21 TraesCS6B01G221100 chr6A 88.000 425 42 4 6343 6766 259273021 259273437 1.700000e-135 494.0
22 TraesCS6B01G221100 chr6A 93.774 257 11 3 1 254 576403068 576403322 1.380000e-101 381.0
23 TraesCS6B01G221100 chr6A 93.191 235 13 2 319 550 576403598 576403832 6.500000e-90 342.0
24 TraesCS6B01G221100 chr6A 82.492 297 40 11 1635 1929 394887898 394888184 4.050000e-62 250.0
25 TraesCS6B01G221100 chr3B 81.735 876 107 30 1943 2775 159935636 159936501 0.000000e+00 682.0
26 TraesCS6B01G221100 chr3B 84.887 311 30 9 1635 1934 790618931 790618627 1.430000e-76 298.0
27 TraesCS6B01G221100 chr3B 77.984 486 65 29 2467 2919 210601862 210601386 4.020000e-67 267.0
28 TraesCS6B01G221100 chr3B 85.398 226 29 2 5922 6143 43488631 43488856 1.470000e-56 231.0
29 TraesCS6B01G221100 chr3B 82.105 285 36 11 2646 2918 465658873 465658592 5.280000e-56 230.0
30 TraesCS6B01G221100 chr3B 84.211 152 15 7 717 863 405242621 405242474 9.150000e-29 139.0
31 TraesCS6B01G221100 chr5D 83.140 605 86 11 6166 6766 467595214 467594622 7.720000e-149 538.0
32 TraesCS6B01G221100 chr5D 85.088 228 29 3 5922 6145 547504261 547504487 1.900000e-55 228.0
33 TraesCS6B01G221100 chr5D 80.968 310 38 8 1635 1932 329860603 329860903 6.830000e-55 226.0
34 TraesCS6B01G221100 chr5D 72.842 556 113 26 6216 6762 407925199 407925725 9.090000e-34 156.0
35 TraesCS6B01G221100 chr5D 93.878 98 4 2 1635 1732 499924023 499923928 5.470000e-31 147.0
36 TraesCS6B01G221100 chr3D 78.841 742 108 31 2140 2839 425076526 425075792 8.000000e-124 455.0
37 TraesCS6B01G221100 chr3D 80.920 587 96 13 6186 6766 373319177 373319753 3.720000e-122 449.0
38 TraesCS6B01G221100 chr3D 78.955 689 104 15 1943 2591 108379261 108379948 1.350000e-116 431.0
39 TraesCS6B01G221100 chr3D 86.817 311 30 6 1635 1935 81380835 81380526 3.020000e-88 337.0
40 TraesCS6B01G221100 chr3D 81.773 203 35 2 3831 4032 303580692 303580893 1.170000e-37 169.0
41 TraesCS6B01G221100 chr3D 85.321 109 16 0 3896 4004 32351364 32351472 5.550000e-21 113.0
42 TraesCS6B01G221100 chr4A 82.671 554 51 20 1 550 350882564 350883076 3.720000e-122 449.0
43 TraesCS6B01G221100 chr4A 78.758 612 97 23 6165 6766 430173324 430173912 4.950000e-101 379.0
44 TraesCS6B01G221100 chr4A 85.761 309 36 7 2470 2775 175759271 175758968 3.040000e-83 320.0
45 TraesCS6B01G221100 chr3A 80.479 584 80 14 2220 2775 563412917 563413494 3.770000e-112 416.0
46 TraesCS6B01G221100 chr2A 84.235 425 63 4 6344 6766 657091826 657091404 1.760000e-110 411.0
47 TraesCS6B01G221100 chr2A 84.665 313 25 7 1635 1929 39249272 39249579 2.390000e-74 291.0
48 TraesCS6B01G221100 chr2A 80.351 285 46 7 6409 6690 719294398 719294675 2.470000e-49 207.0
49 TraesCS6B01G221100 chr2A 83.981 206 15 11 1635 1826 648030796 648030997 1.500000e-41 182.0
50 TraesCS6B01G221100 chr2A 86.275 51 7 0 6712 6762 735749205 735749255 1.000000e-03 56.5
51 TraesCS6B01G221100 chr2B 76.999 813 105 43 1945 2679 23640075 23639267 2.290000e-104 390.0
52 TraesCS6B01G221100 chr2B 85.906 298 26 9 1646 1931 23932515 23932808 3.070000e-78 303.0
53 TraesCS6B01G221100 chr2B 77.984 486 66 28 2467 2918 359376893 359377371 4.020000e-67 267.0
54 TraesCS6B01G221100 chr2B 91.071 112 6 4 757 865 501792997 501792887 1.520000e-31 148.0
55 TraesCS6B01G221100 chr5A 78.702 601 97 14 6168 6766 19654602 19655173 8.290000e-99 372.0
56 TraesCS6B01G221100 chr5A 75.789 190 41 4 3897 4085 464169054 464168869 2.600000e-14 91.6
57 TraesCS6B01G221100 chr5B 92.469 239 14 2 1 236 237130175 237129938 8.410000e-89 339.0
58 TraesCS6B01G221100 chr5B 91.453 234 18 1 317 548 237129516 237129283 3.040000e-83 320.0
59 TraesCS6B01G221100 chr5B 82.609 230 35 4 5920 6145 345518606 345518378 1.490000e-46 198.0
60 TraesCS6B01G221100 chr5B 75.987 304 60 11 6166 6465 361012108 361012402 1.970000e-30 145.0
61 TraesCS6B01G221100 chr5B 87.069 116 9 5 1623 1736 547672477 547672366 7.120000e-25 126.0
62 TraesCS6B01G221100 chr7D 86.688 308 26 9 1636 1932 121739835 121740138 1.820000e-85 327.0
63 TraesCS6B01G221100 chr7D 84.711 242 32 3 5911 6147 580887676 580887435 3.150000e-58 237.0
64 TraesCS6B01G221100 chr4B 82.973 370 56 6 1944 2311 377969291 377969655 1.820000e-85 327.0
65 TraesCS6B01G221100 chr4B 83.284 335 38 11 1613 1935 255665063 255664735 6.640000e-75 292.0
66 TraesCS6B01G221100 chr4B 75.168 298 53 11 6172 6465 186602462 186602182 3.310000e-23 121.0
67 TraesCS6B01G221100 chr4B 84.810 79 11 1 4009 4087 608498179 608498102 2.020000e-10 78.7
68 TraesCS6B01G221100 chr1D 86.645 307 24 11 1635 1929 457163114 457163415 2.350000e-84 324.0
69 TraesCS6B01G221100 chr1D 78.014 564 83 23 2237 2775 490080586 490080039 3.940000e-82 316.0
70 TraesCS6B01G221100 chr1D 93.671 158 8 1 1 158 348662759 348662604 1.130000e-57 235.0
71 TraesCS6B01G221100 chr1D 81.724 290 46 4 6479 6766 463989842 463989558 1.130000e-57 235.0
72 TraesCS6B01G221100 chr1D 83.333 246 33 5 5906 6145 11804479 11804236 3.180000e-53 220.0
73 TraesCS6B01G221100 chr1A 84.665 313 29 11 1635 1935 588372772 588372467 1.850000e-75 294.0
74 TraesCS6B01G221100 chr1A 82.254 355 35 12 1947 2274 580624967 580624614 1.440000e-71 281.0
75 TraesCS6B01G221100 chr1A 93.038 158 8 2 1 158 449199987 449200141 1.900000e-55 228.0
76 TraesCS6B01G221100 chr4D 75.884 622 112 25 6168 6766 22231191 22230585 3.990000e-72 283.0
77 TraesCS6B01G221100 chr4D 82.427 239 37 3 5911 6145 421546586 421546349 3.200000e-48 204.0
78 TraesCS6B01G221100 chr2D 85.283 265 22 8 1686 1935 276923243 276922981 2.420000e-64 257.0
79 TraesCS6B01G221100 chr2D 77.002 487 67 31 2467 2918 515071959 515072435 3.150000e-58 237.0
80 TraesCS6B01G221100 chr2D 83.539 243 35 3 5908 6145 483172275 483172517 8.830000e-54 222.0
81 TraesCS6B01G221100 chr1B 94.304 158 7 1 1 158 470296660 470296505 2.440000e-59 241.0
82 TraesCS6B01G221100 chr1B 90.435 115 7 3 757 868 554649553 554649440 1.520000e-31 148.0
83 TraesCS6B01G221100 chr1B 90.826 109 8 2 751 858 124914707 124914814 1.970000e-30 145.0
84 TraesCS6B01G221100 chr7A 75.180 556 109 23 6217 6757 523950096 523950637 1.130000e-57 235.0
85 TraesCS6B01G221100 chr7A 84.232 241 32 4 5911 6145 41366573 41366813 5.280000e-56 230.0
86 TraesCS6B01G221100 chrUn 82.105 285 36 11 2646 2918 339540176 339539895 5.280000e-56 230.0
87 TraesCS6B01G221100 chrUn 83.673 147 15 6 717 858 283217131 283217273 5.510000e-26 130.0
88 TraesCS6B01G221100 chrUn 82.313 147 17 6 717 858 16484468 16484610 1.190000e-22 119.0
89 TraesCS6B01G221100 chrUn 92.208 77 6 0 474 550 477838036 477837960 7.170000e-20 110.0


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 TraesCS6B01G221100 chr6B 316603316 316610081 6765 True 6345.000000 12495 96.15400 1 6766 2 chr6B.!!$R2 6765
1 TraesCS6B01G221100 chr6B 663567705 663568480 775 False 415.666667 592 93.88900 1 852 3 chr6B.!!$F4 851
2 TraesCS6B01G221100 chr6D 164761915 164768318 6403 False 1897.750000 3326 93.83575 941 5798 4 chr6D.!!$F3 4857
3 TraesCS6B01G221100 chr6D 164803009 164803972 963 False 1018.000000 1018 85.83100 5794 6766 1 chr6D.!!$F2 972
4 TraesCS6B01G221100 chr6A 259203546 259209121 5575 False 1949.000000 2784 93.65625 910 6321 4 chr6A.!!$F4 5411
5 TraesCS6B01G221100 chr6A 576235461 576235993 532 False 678.000000 678 89.56800 1 550 1 chr6A.!!$F3 549
6 TraesCS6B01G221100 chr6A 576403068 576403832 764 False 361.500000 381 93.48250 1 550 2 chr6A.!!$F5 549
7 TraesCS6B01G221100 chr3B 159935636 159936501 865 False 682.000000 682 81.73500 1943 2775 1 chr3B.!!$F2 832
8 TraesCS6B01G221100 chr5D 467594622 467595214 592 True 538.000000 538 83.14000 6166 6766 1 chr5D.!!$R1 600
9 TraesCS6B01G221100 chr3D 425075792 425076526 734 True 455.000000 455 78.84100 2140 2839 1 chr3D.!!$R2 699
10 TraesCS6B01G221100 chr3D 373319177 373319753 576 False 449.000000 449 80.92000 6186 6766 1 chr3D.!!$F4 580
11 TraesCS6B01G221100 chr3D 108379261 108379948 687 False 431.000000 431 78.95500 1943 2591 1 chr3D.!!$F2 648
12 TraesCS6B01G221100 chr4A 350882564 350883076 512 False 449.000000 449 82.67100 1 550 1 chr4A.!!$F1 549
13 TraesCS6B01G221100 chr4A 430173324 430173912 588 False 379.000000 379 78.75800 6165 6766 1 chr4A.!!$F2 601
14 TraesCS6B01G221100 chr3A 563412917 563413494 577 False 416.000000 416 80.47900 2220 2775 1 chr3A.!!$F1 555
15 TraesCS6B01G221100 chr2B 23639267 23640075 808 True 390.000000 390 76.99900 1945 2679 1 chr2B.!!$R1 734
16 TraesCS6B01G221100 chr5A 19654602 19655173 571 False 372.000000 372 78.70200 6168 6766 1 chr5A.!!$F1 598
17 TraesCS6B01G221100 chr5B 237129283 237130175 892 True 329.500000 339 91.96100 1 548 2 chr5B.!!$R3 547
18 TraesCS6B01G221100 chr1D 490080039 490080586 547 True 316.000000 316 78.01400 2237 2775 1 chr1D.!!$R4 538
19 TraesCS6B01G221100 chr4D 22230585 22231191 606 True 283.000000 283 75.88400 6168 6766 1 chr4D.!!$R1 598
20 TraesCS6B01G221100 chr7A 523950096 523950637 541 False 235.000000 235 75.18000 6217 6757 1 chr7A.!!$F2 540

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
711 1062 0.187606 TCGAGGAGGCTGGGCTATTA 59.812 55.0 0.00 0.00 0.00 0.98 F
745 1096 0.821517 TCTCATGCATACCGGTTCGT 59.178 50.0 15.04 0.59 0.00 3.85 F
1808 2741 0.318360 CAGTCACAACGGTAGCGACA 60.318 55.0 22.88 0.00 0.00 4.35 F
2598 3793 0.321996 GACCGGCAGAGAGAAAACCT 59.678 55.0 0.00 0.00 0.00 3.50 F
2644 3845 0.396139 GGCCAGCCCATCAAGAATCA 60.396 55.0 0.00 0.00 0.00 2.57 F
2748 3952 0.464452 GTGCGGTGGCTAGGTCTAAT 59.536 55.0 0.00 0.00 40.82 1.73 F
4008 5277 1.188219 GGAGGATATGAGGGCGCTCA 61.188 60.0 32.47 32.47 37.79 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 2741 0.110678 TCTCCAGTCTCACCGTCTGT 59.889 55.000 0.0 0.00 0.00 3.41 R
2229 3392 0.324368 TGCATCACCTACCGTCTCCT 60.324 55.000 0.0 0.00 0.00 3.69 R
2644 3845 0.460284 CATAGCAAGGTTCGTCCGCT 60.460 55.000 0.0 0.00 41.99 5.52 R
4110 5379 2.280628 CCGGACTGAGCTAATTTGACC 58.719 52.381 0.0 0.00 0.00 4.02 R
4227 5497 2.770164 ACCAGGATGTACTGTGCTTC 57.230 50.000 0.0 3.67 36.75 3.86 R
4433 6712 5.815581 TCCAGCAACACCTGAAAATAGTAT 58.184 37.500 0.0 0.00 34.77 2.12 R
6003 8292 0.386226 GCTGATAGTCGTCGCTAGGC 60.386 60.000 0.0 0.00 0.00 3.93 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
197 201 3.012959 TCACCTCCCTATCTCCTTTCTGT 59.987 47.826 0.00 0.00 0.00 3.41
293 297 4.640690 ACCAGCGACACCCCTCCT 62.641 66.667 0.00 0.00 0.00 3.69
300 304 4.026357 ACACCCCTCCTCCTCCCC 62.026 72.222 0.00 0.00 0.00 4.81
711 1062 0.187606 TCGAGGAGGCTGGGCTATTA 59.812 55.000 0.00 0.00 0.00 0.98
712 1063 1.203187 TCGAGGAGGCTGGGCTATTAT 60.203 52.381 0.00 0.00 0.00 1.28
713 1064 1.625818 CGAGGAGGCTGGGCTATTATT 59.374 52.381 0.00 0.00 0.00 1.40
714 1065 2.832129 CGAGGAGGCTGGGCTATTATTA 59.168 50.000 0.00 0.00 0.00 0.98
745 1096 0.821517 TCTCATGCATACCGGTTCGT 59.178 50.000 15.04 0.59 0.00 3.85
756 1107 1.820519 ACCGGTTCGTGCTGACTTATA 59.179 47.619 0.00 0.00 0.00 0.98
785 1136 8.301252 AGGACTGCGGGTTAATTTTTATAAAT 57.699 30.769 0.00 0.00 35.49 1.40
787 1138 8.410912 GGACTGCGGGTTAATTTTTATAAATCT 58.589 33.333 0.00 0.00 32.85 2.40
847 1198 5.105756 CGGCAGAAACCCAATTCTCTTTATT 60.106 40.000 0.00 0.00 37.56 1.40
848 1199 6.094881 CGGCAGAAACCCAATTCTCTTTATTA 59.905 38.462 0.00 0.00 37.56 0.98
849 1200 7.201821 CGGCAGAAACCCAATTCTCTTTATTAT 60.202 37.037 0.00 0.00 37.56 1.28
894 1245 7.855545 AGATAAAAATGATACACTGCTAAGCG 58.144 34.615 0.00 0.00 0.00 4.68
895 1246 5.880054 AAAAATGATACACTGCTAAGCGT 57.120 34.783 0.00 0.00 0.00 5.07
896 1247 6.978343 AAAAATGATACACTGCTAAGCGTA 57.022 33.333 0.00 0.00 0.00 4.42
897 1248 7.553881 AAAAATGATACACTGCTAAGCGTAT 57.446 32.000 0.00 0.00 34.95 3.06
898 1249 7.553881 AAAATGATACACTGCTAAGCGTATT 57.446 32.000 0.00 0.00 32.91 1.89
899 1250 6.771188 AATGATACACTGCTAAGCGTATTC 57.229 37.500 0.00 0.00 32.91 1.75
900 1251 5.257082 TGATACACTGCTAAGCGTATTCA 57.743 39.130 0.00 0.00 32.91 2.57
901 1252 5.041287 TGATACACTGCTAAGCGTATTCAC 58.959 41.667 0.00 0.00 32.91 3.18
902 1253 2.618053 ACACTGCTAAGCGTATTCACC 58.382 47.619 0.00 0.00 0.00 4.02
903 1254 2.028476 ACACTGCTAAGCGTATTCACCA 60.028 45.455 0.00 0.00 0.00 4.17
904 1255 3.000041 CACTGCTAAGCGTATTCACCAA 59.000 45.455 0.00 0.00 0.00 3.67
905 1256 3.435327 CACTGCTAAGCGTATTCACCAAA 59.565 43.478 0.00 0.00 0.00 3.28
906 1257 4.069304 ACTGCTAAGCGTATTCACCAAAA 58.931 39.130 0.00 0.00 0.00 2.44
907 1258 4.517453 ACTGCTAAGCGTATTCACCAAAAA 59.483 37.500 0.00 0.00 0.00 1.94
908 1259 5.183140 ACTGCTAAGCGTATTCACCAAAAAT 59.817 36.000 0.00 0.00 0.00 1.82
909 1260 6.373216 ACTGCTAAGCGTATTCACCAAAAATA 59.627 34.615 0.00 0.00 0.00 1.40
910 1261 7.094549 ACTGCTAAGCGTATTCACCAAAAATAA 60.095 33.333 0.00 0.00 0.00 1.40
911 1262 7.594714 TGCTAAGCGTATTCACCAAAAATAAA 58.405 30.769 0.00 0.00 0.00 1.40
912 1263 8.082852 TGCTAAGCGTATTCACCAAAAATAAAA 58.917 29.630 0.00 0.00 0.00 1.52
913 1264 8.583765 GCTAAGCGTATTCACCAAAAATAAAAG 58.416 33.333 0.00 0.00 0.00 2.27
984 1341 2.632377 CATACAAAGTGTGCCCTCGAT 58.368 47.619 0.00 0.00 0.00 3.59
997 1354 3.321111 TGCCCTCGATGAATAGGTTCTAC 59.679 47.826 0.00 0.00 35.33 2.59
1020 1386 2.826488 AGATAGATCTAAGCGGCCCAT 58.174 47.619 6.52 0.00 34.85 4.00
1164 1530 1.578206 GCACCAAGGTCTTCGCCTTC 61.578 60.000 0.00 0.00 46.33 3.46
1201 1567 6.267242 TCACTGGATTTGATTGATTGGTTTGA 59.733 34.615 0.00 0.00 0.00 2.69
1445 1811 5.587844 AGATTGATTCTGTACATGGAGTTGC 59.412 40.000 0.00 0.00 31.79 4.17
1532 1898 9.559732 CTCCATAAGTGATGTATAATTGGAACA 57.440 33.333 0.00 0.00 33.19 3.18
1551 1917 6.126940 TGGAACAATGTTTCTTGGGATTCAAA 60.127 34.615 5.94 0.00 31.73 2.69
1580 1946 0.961019 ACTTGACGTTACGTAGCCCA 59.039 50.000 11.32 1.08 41.37 5.36
1611 1977 2.229302 ACTTCAGAGCTCGTTGTAGGTC 59.771 50.000 8.37 0.00 42.94 3.85
1688 2603 3.138884 TGTTGTATTGCTTGAGCCTCA 57.861 42.857 0.00 0.00 41.18 3.86
1690 2605 3.441222 TGTTGTATTGCTTGAGCCTCATG 59.559 43.478 0.00 0.00 41.18 3.07
1691 2606 2.646930 TGTATTGCTTGAGCCTCATGG 58.353 47.619 9.39 0.96 41.18 3.66
1713 2628 7.855784 TGGGCATATATATAGGAGTACATGG 57.144 40.000 8.56 0.00 0.00 3.66
1804 2737 2.380410 CCGCAGTCACAACGGTAGC 61.380 63.158 0.43 0.00 42.01 3.58
1808 2741 0.318360 CAGTCACAACGGTAGCGACA 60.318 55.000 22.88 0.00 0.00 4.35
1814 2747 1.081641 AACGGTAGCGACACAGACG 60.082 57.895 22.88 0.00 0.00 4.18
1825 2758 4.923068 ACAGACGGTGAGACTGGA 57.077 55.556 0.00 0.00 44.83 3.86
1882 2815 1.922570 AGTCGTAATGGTCGATGCAC 58.077 50.000 0.00 0.00 39.45 4.57
2009 3105 1.144057 GCGGGTGATCAATCCGACT 59.856 57.895 30.93 0.00 45.96 4.18
2017 3113 1.361668 ATCAATCCGACTGCACACGC 61.362 55.000 2.74 0.00 39.24 5.34
2052 3161 2.610694 CGGTGATGATGATGGCGGC 61.611 63.158 0.00 0.00 0.00 6.53
2454 3624 2.124612 CATGACAGGCCGGCATGA 60.125 61.111 44.23 25.94 41.35 3.07
2598 3793 0.321996 GACCGGCAGAGAGAAAACCT 59.678 55.000 0.00 0.00 0.00 3.50
2599 3794 0.765510 ACCGGCAGAGAGAAAACCTT 59.234 50.000 0.00 0.00 0.00 3.50
2627 3826 1.468914 GATCGGAAAAACTCACCAGGC 59.531 52.381 0.00 0.00 0.00 4.85
2633 3832 3.513750 AAACTCACCAGGCCAGCCC 62.514 63.158 5.01 0.00 36.58 5.19
2639 3838 2.441532 CCAGGCCAGCCCATCAAG 60.442 66.667 5.01 0.00 36.58 3.02
2644 3845 0.396139 GGCCAGCCCATCAAGAATCA 60.396 55.000 0.00 0.00 0.00 2.57
2748 3952 0.464452 GTGCGGTGGCTAGGTCTAAT 59.536 55.000 0.00 0.00 40.82 1.73
2755 3959 4.142004 CGGTGGCTAGGTCTAATAACTTGT 60.142 45.833 0.00 0.00 0.00 3.16
3051 4288 6.217294 GCTAGGTATCCTGTACAGATTTGTC 58.783 44.000 24.68 8.85 35.46 3.18
3248 4485 6.861065 AATGTACAGTTGTGTTAAGGACAG 57.139 37.500 0.33 0.00 39.39 3.51
3593 4859 5.690464 ATCCTCTCTGATGTTGCTAACTT 57.310 39.130 0.00 0.00 0.00 2.66
3636 4902 6.449635 TGTCCATTTGTGTTATATGCTTCC 57.550 37.500 0.00 0.00 0.00 3.46
3696 4962 4.447724 CGTGTTCTAATGTAACAGTGTGCT 59.552 41.667 0.00 0.00 37.51 4.40
3698 4964 5.465390 GTGTTCTAATGTAACAGTGTGCTGA 59.535 40.000 0.00 0.00 45.28 4.26
3875 5141 3.181433 CCCAACTTTCCCCCTATATGTCC 60.181 52.174 0.00 0.00 0.00 4.02
3925 5194 3.907458 AAAAAGTCACCCAACCGGA 57.093 47.368 9.46 0.00 34.64 5.14
4008 5277 1.188219 GGAGGATATGAGGGCGCTCA 61.188 60.000 32.47 32.47 37.79 4.26
4061 5330 1.792118 GCCCACCACGTTCCACTTTC 61.792 60.000 0.00 0.00 0.00 2.62
4110 5379 1.664306 GTCCGCGGAAGTATAGGGG 59.336 63.158 32.93 0.00 39.06 4.79
4227 5497 6.205270 TGCCAATGATAGTGCACATATAAGTG 59.795 38.462 21.04 14.75 42.37 3.16
4265 5535 5.242838 CCTGGTATTGCAAAGGTTTGACTTA 59.757 40.000 1.71 0.00 40.55 2.24
4266 5536 6.325919 TGGTATTGCAAAGGTTTGACTTAG 57.674 37.500 1.71 0.00 40.55 2.18
4317 6592 6.051717 CCATACTAGTAAAGCATCAGCAACT 58.948 40.000 6.70 0.00 45.49 3.16
4318 6593 6.540189 CCATACTAGTAAAGCATCAGCAACTT 59.460 38.462 6.70 0.00 45.49 2.66
4319 6594 7.710907 CCATACTAGTAAAGCATCAGCAACTTA 59.289 37.037 6.70 0.00 45.49 2.24
4320 6595 8.759641 CATACTAGTAAAGCATCAGCAACTTAG 58.240 37.037 6.70 0.00 45.49 2.18
4396 6675 2.371841 ACAAGCACTGGTGGACAATCTA 59.628 45.455 2.84 0.00 0.00 1.98
4433 6712 5.532032 TGTCAGAATGCTTTGAGATGTTTCA 59.468 36.000 0.00 0.00 34.76 2.69
4682 6961 8.741841 GGAGGTATTAGCATAGTAGAGTTTAGG 58.258 40.741 0.00 0.00 0.00 2.69
5116 7395 1.101331 GGAATGCAGAGAGGCCTTTG 58.899 55.000 6.77 7.65 0.00 2.77
5150 7429 8.383175 TGAAGACTAGGGTGAAGAAACAATATT 58.617 33.333 0.00 0.00 0.00 1.28
5410 7697 8.231692 TCTTATGTGGTCATCTTTTTGTTTCA 57.768 30.769 0.00 0.00 35.70 2.69
5526 7813 1.028905 CAAACTGGCCGGAGAACAAA 58.971 50.000 21.41 0.00 0.00 2.83
5602 7889 3.442273 TGGGATTTCGATACTTGTTTGGC 59.558 43.478 0.00 0.00 0.00 4.52
5622 7909 3.676646 GGCATCAAGTTGCAGATTTGTTC 59.323 43.478 0.00 0.00 44.59 3.18
5627 7914 3.885484 AGTTGCAGATTTGTTCGTCAG 57.115 42.857 0.00 0.00 0.00 3.51
5653 7940 1.423395 CGAGGCCGCTTATCTGATTC 58.577 55.000 4.53 0.00 0.00 2.52
5654 7941 1.000283 CGAGGCCGCTTATCTGATTCT 60.000 52.381 4.53 0.00 0.00 2.40
5655 7942 2.682836 GAGGCCGCTTATCTGATTCTC 58.317 52.381 0.00 0.00 0.00 2.87
5656 7943 2.298729 GAGGCCGCTTATCTGATTCTCT 59.701 50.000 0.00 0.00 0.00 3.10
5657 7944 2.036992 AGGCCGCTTATCTGATTCTCTG 59.963 50.000 0.00 0.00 0.00 3.35
5658 7945 2.224161 GGCCGCTTATCTGATTCTCTGT 60.224 50.000 0.00 0.00 0.00 3.41
5661 7948 3.806521 CCGCTTATCTGATTCTCTGTTGG 59.193 47.826 0.00 0.00 0.00 3.77
5663 7950 5.451937 CCGCTTATCTGATTCTCTGTTGGTA 60.452 44.000 0.00 0.00 0.00 3.25
5669 7956 6.516739 TCTGATTCTCTGTTGGTAGTACTG 57.483 41.667 5.39 0.00 0.00 2.74
5680 7967 8.423349 TCTGTTGGTAGTACTGTTTAAGCTTTA 58.577 33.333 3.20 0.00 0.00 1.85
5733 8020 9.160412 AGCTATGGATATACTTGGTCTACTTTT 57.840 33.333 0.00 0.00 0.00 2.27
5749 8036 8.515414 GGTCTACTTTTGAGAGCAAATAATTGT 58.485 33.333 0.00 0.00 43.07 2.71
5788 8076 4.411256 AGTTCTGGTCGTTCCAAGTTTA 57.589 40.909 4.04 0.00 46.59 2.01
5825 8113 5.711506 TGGCATGTAAATCTCATGTTTGACT 59.288 36.000 7.55 0.00 42.94 3.41
5847 8135 5.637810 ACTACATGTACTTCGTTGGTCAATG 59.362 40.000 0.08 0.00 0.00 2.82
5877 8165 5.751586 TGGTTAAGGCTTTACTATTCCAGG 58.248 41.667 15.17 0.00 0.00 4.45
5903 8191 2.026262 ACATGCTCCAAGGAACCGTTAT 60.026 45.455 0.00 0.00 0.00 1.89
5904 8192 2.396590 TGCTCCAAGGAACCGTTATC 57.603 50.000 0.00 0.00 0.00 1.75
5905 8193 1.065709 TGCTCCAAGGAACCGTTATCC 60.066 52.381 0.00 0.00 37.22 2.59
5917 8206 5.242171 GGAACCGTTATCCTTTCTTTTTGGA 59.758 40.000 0.00 0.00 33.98 3.53
5918 8207 6.239092 GGAACCGTTATCCTTTCTTTTTGGAA 60.239 38.462 0.00 0.00 33.98 3.53
5961 8250 7.543756 TCATCTTCAATCATCGTAGTACAACA 58.456 34.615 0.38 0.00 0.00 3.33
6003 8292 0.597637 GCATCCACATCCGTAGACCG 60.598 60.000 0.00 0.00 0.00 4.79
6005 8294 1.745320 ATCCACATCCGTAGACCGCC 61.745 60.000 0.00 0.00 34.38 6.13
6025 8314 0.661552 TAGCGACGACTATCAGCACC 59.338 55.000 0.00 0.00 0.00 5.01
6034 8323 0.101399 CTATCAGCACCGAAGCGAGT 59.899 55.000 0.00 0.00 40.15 4.18
6041 8330 2.881352 CCGAAGCGAGTCGAAGGC 60.881 66.667 18.61 0.00 43.86 4.35
6065 8354 4.899239 CTGTCATCGCCCCTCGCC 62.899 72.222 0.00 0.00 38.27 5.54
6094 8383 7.339466 AGCCGGACAAATCTTATTTTTGTAGAT 59.661 33.333 5.05 0.00 44.90 1.98
6118 8407 1.139095 GGGAGTCGTCGTGCTAAGG 59.861 63.158 0.00 0.00 0.00 2.69
6119 8408 1.593296 GGGAGTCGTCGTGCTAAGGT 61.593 60.000 0.00 0.00 0.00 3.50
6126 8415 1.340248 CGTCGTGCTAAGGTCCCATAT 59.660 52.381 0.00 0.00 0.00 1.78
6147 8436 0.951558 ACCAACGCATCAGAACAACC 59.048 50.000 0.00 0.00 0.00 3.77
6148 8437 0.110238 CCAACGCATCAGAACAACCG 60.110 55.000 0.00 0.00 0.00 4.44
6149 8438 0.586319 CAACGCATCAGAACAACCGT 59.414 50.000 0.00 0.00 0.00 4.83
6150 8439 1.002900 CAACGCATCAGAACAACCGTT 60.003 47.619 0.00 0.00 39.17 4.44
6151 8440 0.586319 ACGCATCAGAACAACCGTTG 59.414 50.000 9.80 9.80 34.75 4.10
6152 8441 5.613268 CAACGCATCAGAACAACCGTTGT 62.613 47.826 11.24 11.24 45.87 3.32
6176 8479 2.266279 TGGAGTAGCTTAGGGCAACTT 58.734 47.619 0.00 0.00 44.79 2.66
6209 8513 3.636929 AAATGGTCCGGCCGCATCA 62.637 57.895 22.85 13.98 41.21 3.07
6212 8516 3.845259 GGTCCGGCCGCATCAGTA 61.845 66.667 22.85 0.00 0.00 2.74
6214 8518 1.663739 GTCCGGCCGCATCAGTATA 59.336 57.895 22.85 0.00 0.00 1.47
6273 8577 1.470285 GCAAACGGACCAGCGTCTATA 60.470 52.381 0.00 0.00 39.15 1.31
6301 8605 0.463833 GCTTTCGACCCATTCCCGAT 60.464 55.000 0.00 0.00 32.07 4.18
6307 8611 0.254747 GACCCATTCCCGATCCAACA 59.745 55.000 0.00 0.00 0.00 3.33
6309 8613 1.321474 CCCATTCCCGATCCAACATG 58.679 55.000 0.00 0.00 0.00 3.21
6312 8616 0.468029 ATTCCCGATCCAACATGGGC 60.468 55.000 0.00 0.00 41.65 5.36
6313 8617 2.519302 CCCGATCCAACATGGGCC 60.519 66.667 0.00 0.00 38.32 5.80
6314 8618 2.901840 CCGATCCAACATGGGCCG 60.902 66.667 0.00 1.12 38.32 6.13
6315 8619 2.189257 CGATCCAACATGGGCCGA 59.811 61.111 0.00 0.00 38.32 5.54
6316 8620 1.889105 CGATCCAACATGGGCCGAG 60.889 63.158 0.00 0.00 38.32 4.63
6317 8621 1.224592 GATCCAACATGGGCCGAGT 59.775 57.895 0.00 0.00 38.32 4.18
6318 8622 0.394352 GATCCAACATGGGCCGAGTT 60.394 55.000 7.51 7.51 38.32 3.01
6319 8623 0.039618 ATCCAACATGGGCCGAGTTT 59.960 50.000 10.31 0.00 38.32 2.66
6320 8624 0.893270 TCCAACATGGGCCGAGTTTG 60.893 55.000 10.31 7.91 38.32 2.93
6321 8625 1.586028 CAACATGGGCCGAGTTTGG 59.414 57.895 10.31 0.00 0.00 3.28
6322 8626 0.893270 CAACATGGGCCGAGTTTGGA 60.893 55.000 10.31 0.00 0.00 3.53
6323 8627 0.039618 AACATGGGCCGAGTTTGGAT 59.960 50.000 7.51 0.00 0.00 3.41
6324 8628 0.394352 ACATGGGCCGAGTTTGGATC 60.394 55.000 0.00 0.00 0.00 3.36
6328 8632 2.435938 GCCGAGTTTGGATCGCCA 60.436 61.111 0.00 0.00 44.17 5.69
6335 8639 0.386731 GTTTGGATCGCCACGTTTGG 60.387 55.000 0.00 0.00 45.94 3.28
6349 8663 0.179233 GTTTGGATCGAAACGGACGC 60.179 55.000 16.17 0.00 0.00 5.19
6382 8698 1.306997 CTTGTCCTCCCCTGGCCTA 60.307 63.158 3.32 0.00 0.00 3.93
6423 8744 1.074566 CCCTTTTCTCTTCCACTGCCT 59.925 52.381 0.00 0.00 0.00 4.75
6425 8746 2.816672 CCTTTTCTCTTCCACTGCCTTC 59.183 50.000 0.00 0.00 0.00 3.46
6426 8747 2.568623 TTTCTCTTCCACTGCCTTCC 57.431 50.000 0.00 0.00 0.00 3.46
6427 8748 0.693049 TTCTCTTCCACTGCCTTCCC 59.307 55.000 0.00 0.00 0.00 3.97
6428 8749 0.178891 TCTCTTCCACTGCCTTCCCT 60.179 55.000 0.00 0.00 0.00 4.20
6429 8750 0.251634 CTCTTCCACTGCCTTCCCTC 59.748 60.000 0.00 0.00 0.00 4.30
6430 8751 0.178891 TCTTCCACTGCCTTCCCTCT 60.179 55.000 0.00 0.00 0.00 3.69
6431 8752 0.035630 CTTCCACTGCCTTCCCTCTG 60.036 60.000 0.00 0.00 0.00 3.35
6500 8835 3.172106 TTCCACCAAGGCCGTCCA 61.172 61.111 0.00 0.00 37.29 4.02
6536 8888 1.152963 GCCATAACCGTCCCATGCT 60.153 57.895 0.00 0.00 0.00 3.79
6537 8889 0.751643 GCCATAACCGTCCCATGCTT 60.752 55.000 0.00 0.00 0.00 3.91
6569 8923 0.100503 GCTTTTGCCAGTGTTCGTGT 59.899 50.000 0.00 0.00 40.15 4.49
6606 8960 4.143333 GAGAAGCTACGGCCGCCA 62.143 66.667 28.58 13.13 39.73 5.69
6608 8962 4.143333 GAAGCTACGGCCGCCAGA 62.143 66.667 28.58 7.33 39.73 3.86
6640 8998 0.688487 CCCTTACAACTTCCGGTGGA 59.312 55.000 0.00 0.00 0.00 4.02
6701 9066 1.134729 CAACCTTGCTTTGTTGCCTGT 60.135 47.619 0.00 0.00 35.87 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 6.712547 GCACCTGGTATAAGCTTATCATTTCT 59.287 38.462 22.09 0.36 0.00 2.52
117 118 2.438392 GGTTAGGCACCTGGTATAAGCT 59.562 50.000 0.00 0.00 43.29 3.74
285 289 2.370257 TTTTGGGGAGGAGGAGGGGT 62.370 60.000 0.00 0.00 0.00 4.95
293 297 1.001393 GTGGCGATTTTGGGGAGGA 60.001 57.895 0.00 0.00 0.00 3.71
300 304 1.003851 ATCCGTACGTGGCGATTTTG 58.996 50.000 15.21 0.00 0.00 2.44
677 1028 1.903890 TCGATCCCATCTCGAGCCC 60.904 63.158 7.81 0.00 40.01 5.19
713 1064 8.397906 CGGTATGCATGAGAGAAAAGAAAAATA 58.602 33.333 10.16 0.00 0.00 1.40
714 1065 7.253422 CGGTATGCATGAGAGAAAAGAAAAAT 58.747 34.615 10.16 0.00 0.00 1.82
730 1081 1.089481 CAGCACGAACCGGTATGCAT 61.089 55.000 29.56 17.36 40.63 3.96
732 1083 1.447140 TCAGCACGAACCGGTATGC 60.447 57.895 23.95 23.95 38.39 3.14
745 1096 2.688446 CAGTCCTCGGTATAAGTCAGCA 59.312 50.000 0.00 0.00 0.00 4.41
756 1107 1.262640 ATTAACCCGCAGTCCTCGGT 61.263 55.000 0.66 0.00 45.09 4.69
785 1136 4.338118 CGATTTTGCATAAAAGCCCCTAGA 59.662 41.667 0.00 0.00 38.59 2.43
787 1138 3.181480 GCGATTTTGCATAAAAGCCCCTA 60.181 43.478 8.13 0.00 38.59 3.53
818 1169 0.675522 ATTGGGTTTCTGCCGTACGG 60.676 55.000 30.06 30.06 38.57 4.02
868 1219 8.338259 CGCTTAGCAGTGTATCATTTTTATCTT 58.662 33.333 4.70 0.00 0.00 2.40
869 1220 7.495934 ACGCTTAGCAGTGTATCATTTTTATCT 59.504 33.333 4.70 0.00 42.25 1.98
870 1221 7.630924 ACGCTTAGCAGTGTATCATTTTTATC 58.369 34.615 4.70 0.00 42.25 1.75
871 1222 7.553881 ACGCTTAGCAGTGTATCATTTTTAT 57.446 32.000 4.70 0.00 42.25 1.40
872 1223 6.978343 ACGCTTAGCAGTGTATCATTTTTA 57.022 33.333 4.70 0.00 42.25 1.52
873 1224 5.880054 ACGCTTAGCAGTGTATCATTTTT 57.120 34.783 4.70 0.00 42.25 1.94
882 1233 2.028476 TGGTGAATACGCTTAGCAGTGT 60.028 45.455 4.70 0.00 46.01 3.55
883 1234 2.616960 TGGTGAATACGCTTAGCAGTG 58.383 47.619 4.70 0.00 36.50 3.66
884 1235 3.328382 TTGGTGAATACGCTTAGCAGT 57.672 42.857 4.70 6.00 0.00 4.40
885 1236 4.678509 TTTTGGTGAATACGCTTAGCAG 57.321 40.909 4.70 0.00 0.00 4.24
886 1237 5.637006 ATTTTTGGTGAATACGCTTAGCA 57.363 34.783 4.70 0.00 0.00 3.49
887 1238 8.455598 TTTTATTTTTGGTGAATACGCTTAGC 57.544 30.769 0.00 0.00 0.00 3.09
888 1239 9.072294 CCTTTTATTTTTGGTGAATACGCTTAG 57.928 33.333 0.00 0.00 0.00 2.18
889 1240 8.794553 TCCTTTTATTTTTGGTGAATACGCTTA 58.205 29.630 0.00 0.00 0.00 3.09
890 1241 7.597369 GTCCTTTTATTTTTGGTGAATACGCTT 59.403 33.333 0.00 0.00 0.00 4.68
891 1242 7.039993 AGTCCTTTTATTTTTGGTGAATACGCT 60.040 33.333 0.00 0.00 0.00 5.07
892 1243 7.088272 AGTCCTTTTATTTTTGGTGAATACGC 58.912 34.615 0.00 0.00 0.00 4.42
904 1255 9.921637 TGCGAATTCATTTAGTCCTTTTATTTT 57.078 25.926 6.22 0.00 0.00 1.82
906 1257 9.736023 GATGCGAATTCATTTAGTCCTTTTATT 57.264 29.630 6.22 0.00 0.00 1.40
907 1258 9.125026 AGATGCGAATTCATTTAGTCCTTTTAT 57.875 29.630 6.22 0.00 0.00 1.40
908 1259 8.506168 AGATGCGAATTCATTTAGTCCTTTTA 57.494 30.769 6.22 0.00 0.00 1.52
909 1260 7.396540 AGATGCGAATTCATTTAGTCCTTTT 57.603 32.000 6.22 0.00 0.00 2.27
910 1261 7.337942 AGAAGATGCGAATTCATTTAGTCCTTT 59.662 33.333 6.22 0.00 0.00 3.11
911 1262 6.825721 AGAAGATGCGAATTCATTTAGTCCTT 59.174 34.615 6.22 0.00 0.00 3.36
912 1263 6.352516 AGAAGATGCGAATTCATTTAGTCCT 58.647 36.000 6.22 0.00 0.00 3.85
913 1264 6.610741 AGAAGATGCGAATTCATTTAGTCC 57.389 37.500 6.22 0.00 0.00 3.85
997 1354 2.097791 GGGCCGCTTAGATCTATCTACG 59.902 54.545 2.58 5.41 39.00 3.51
1020 1386 4.082523 GCAGCTGGTGTCGGGCTA 62.083 66.667 17.12 0.00 34.71 3.93
1164 1530 3.996150 ATCCAGTGAAAACTGCAACAG 57.004 42.857 0.22 0.00 36.46 3.16
1201 1567 4.404185 AACCCAGGCTTAGAAAATTCCT 57.596 40.909 0.00 0.00 0.00 3.36
1271 1637 3.573772 CTTCTGCGCCACGGAGTCA 62.574 63.158 4.18 0.00 45.16 3.41
1406 1772 9.334947 CAGAATCAATCTAGTATCCACAAACAT 57.665 33.333 0.00 0.00 36.32 2.71
1445 1811 5.826737 TCTACCCTACTAAGAGGATGAAACG 59.173 44.000 0.00 0.00 39.15 3.60
1532 1898 7.507829 TGTTCATTTGAATCCCAAGAAACATT 58.492 30.769 0.00 0.00 36.33 2.71
1542 1908 6.587608 GTCAAGTCATTGTTCATTTGAATCCC 59.412 38.462 0.00 0.00 37.68 3.85
1551 1917 4.748102 ACGTAACGTCAAGTCATTGTTCAT 59.252 37.500 0.00 0.00 33.69 2.57
1580 1946 3.931468 CGAGCTCTGAAGTGTGAAATCAT 59.069 43.478 12.85 0.00 0.00 2.45
1611 1977 3.087031 ACACTGATCCAAATTGCCTCAG 58.913 45.455 16.36 16.36 39.35 3.35
1688 2603 8.019050 ACCATGTACTCCTATATATATGCCCAT 58.981 37.037 5.44 0.00 0.00 4.00
1690 2605 7.509318 TGACCATGTACTCCTATATATATGCCC 59.491 40.741 5.44 0.00 0.00 5.36
1691 2606 8.478775 TGACCATGTACTCCTATATATATGCC 57.521 38.462 5.44 0.00 0.00 4.40
1799 2732 1.443872 CACCGTCTGTGTCGCTACC 60.444 63.158 0.00 0.00 40.26 3.18
1804 2737 0.386100 CAGTCTCACCGTCTGTGTCG 60.386 60.000 0.00 0.00 45.61 4.35
1808 2741 0.110678 TCTCCAGTCTCACCGTCTGT 59.889 55.000 0.00 0.00 0.00 3.41
1814 2747 2.169561 GGGATTCTTCTCCAGTCTCACC 59.830 54.545 0.00 0.00 37.01 4.02
1821 2754 4.775236 CTTACCTTGGGATTCTTCTCCAG 58.225 47.826 0.00 0.00 37.01 3.86
1825 2758 2.092914 CGGCTTACCTTGGGATTCTTCT 60.093 50.000 0.00 0.00 0.00 2.85
1888 2821 1.967319 TTTCACTCCAGCCACAACTC 58.033 50.000 0.00 0.00 0.00 3.01
1990 3086 1.153449 GTCGGATTGATCACCCGCA 60.153 57.895 23.73 13.84 42.70 5.69
2052 3161 3.175240 CTCGCTTCACTGTCCGCG 61.175 66.667 0.00 0.00 46.28 6.46
2101 3210 4.376176 CCGTACGCCGTTCCCCAA 62.376 66.667 10.49 0.00 33.66 4.12
2115 3224 3.950254 CGCTATCCGCTCGTCCGT 61.950 66.667 0.00 0.00 36.13 4.69
2229 3392 0.324368 TGCATCACCTACCGTCTCCT 60.324 55.000 0.00 0.00 0.00 3.69
2279 3442 2.980233 GCTGGTCGCTTTGTGCCT 60.980 61.111 0.00 0.00 38.78 4.75
2301 3464 2.355837 GCTGTCCTTCGCGTGTCA 60.356 61.111 5.77 0.00 0.00 3.58
2519 3707 1.048601 ATCGGATTATGTCGCCCACT 58.951 50.000 0.00 0.00 0.00 4.00
2598 3793 6.594159 GGTGAGTTTTTCCGATCTCTTGATAA 59.406 38.462 0.00 0.00 32.19 1.75
2599 3794 6.106673 GGTGAGTTTTTCCGATCTCTTGATA 58.893 40.000 0.00 0.00 32.19 2.15
2627 3826 1.030457 GCTGATTCTTGATGGGCTGG 58.970 55.000 0.00 0.00 0.00 4.85
2633 3832 1.926561 TCGTCCGCTGATTCTTGATG 58.073 50.000 0.00 0.00 0.00 3.07
2639 3838 0.721718 CAAGGTTCGTCCGCTGATTC 59.278 55.000 0.00 0.00 41.99 2.52
2644 3845 0.460284 CATAGCAAGGTTCGTCCGCT 60.460 55.000 0.00 0.00 41.99 5.52
2723 3927 3.649277 CTAGCCACCGCACGCTTCT 62.649 63.158 0.00 0.00 36.53 2.85
2748 3952 4.568072 ACATGGTATCAGCCACAAGTTA 57.432 40.909 0.00 0.00 41.94 2.24
2755 3959 5.396772 CCTCTTTCTAACATGGTATCAGCCA 60.397 44.000 0.00 0.00 43.48 4.75
3183 4420 5.122519 TGACGCAATTGTATATCACACCAT 58.877 37.500 7.40 0.00 36.69 3.55
3184 4421 4.508662 TGACGCAATTGTATATCACACCA 58.491 39.130 7.40 0.00 36.69 4.17
3287 4524 1.703411 CCCAAAAGCCAAGGACAAGA 58.297 50.000 0.00 0.00 0.00 3.02
3432 4697 5.940595 TCTAAAGTCTTAGAAGCGTCAGTC 58.059 41.667 1.61 0.00 40.48 3.51
3636 4902 6.449698 AGAAAGCATCATAAACAACACAAGG 58.550 36.000 0.00 0.00 0.00 3.61
3925 5194 2.379907 ACATGAGGACAATTTGAGGGGT 59.620 45.455 0.00 0.00 0.00 4.95
4028 5297 3.451894 GGGCCAAATCCAGCGTGG 61.452 66.667 4.39 0.00 39.43 4.94
4052 5321 8.980481 AGAATAAACAAAGAGAGAAAGTGGAA 57.020 30.769 0.00 0.00 0.00 3.53
4053 5322 8.980481 AAGAATAAACAAAGAGAGAAAGTGGA 57.020 30.769 0.00 0.00 0.00 4.02
4110 5379 2.280628 CCGGACTGAGCTAATTTGACC 58.719 52.381 0.00 0.00 0.00 4.02
4227 5497 2.770164 ACCAGGATGTACTGTGCTTC 57.230 50.000 0.00 3.67 36.75 3.86
4317 6592 9.143155 TGGCAACAGATATCATAGACTAACTAA 57.857 33.333 5.32 0.00 46.17 2.24
4318 6593 8.706322 TGGCAACAGATATCATAGACTAACTA 57.294 34.615 5.32 0.00 46.17 2.24
4319 6594 7.603180 TGGCAACAGATATCATAGACTAACT 57.397 36.000 5.32 0.00 46.17 2.24
4396 6675 6.835174 AGCATTCTGACATACCATCAAGTAT 58.165 36.000 0.00 0.00 33.10 2.12
4433 6712 5.815581 TCCAGCAACACCTGAAAATAGTAT 58.184 37.500 0.00 0.00 34.77 2.12
4682 6961 8.617761 TTATGTTTTGTTCAGTAAACGGTTTC 57.382 30.769 9.78 2.49 41.02 2.78
4821 7100 5.850046 ATGACCTCCAATATTAAGGGGAG 57.150 43.478 16.54 13.92 45.20 4.30
4866 7145 6.321435 TCGGTCACACAGAGATATAAGTGATT 59.679 38.462 0.00 0.00 38.16 2.57
5018 7297 4.019860 ACGTAGTGGAGTAGACTAACCAGA 60.020 45.833 9.16 0.78 42.51 3.86
5116 7395 2.498078 CACCCTAGTCTTCACCTCCTTC 59.502 54.545 0.00 0.00 0.00 3.46
5150 7429 2.300433 AGCAGACAATTGCACTGACAA 58.700 42.857 26.57 0.00 46.47 3.18
5410 7697 4.733988 AGGTTGAGAAATATCCCCCTTCAT 59.266 41.667 0.00 0.00 0.00 2.57
5581 7868 3.442273 TGCCAAACAAGTATCGAAATCCC 59.558 43.478 0.00 0.00 0.00 3.85
5602 7889 4.539870 ACGAACAAATCTGCAACTTGATG 58.460 39.130 8.60 0.00 0.00 3.07
5653 7940 6.456501 AGCTTAAACAGTACTACCAACAGAG 58.543 40.000 0.00 0.00 0.00 3.35
5654 7941 6.415206 AGCTTAAACAGTACTACCAACAGA 57.585 37.500 0.00 0.00 0.00 3.41
5655 7942 7.492352 AAAGCTTAAACAGTACTACCAACAG 57.508 36.000 0.00 0.00 0.00 3.16
5656 7943 8.995220 CATAAAGCTTAAACAGTACTACCAACA 58.005 33.333 0.00 0.00 0.00 3.33
5657 7944 9.211485 TCATAAAGCTTAAACAGTACTACCAAC 57.789 33.333 0.00 0.00 0.00 3.77
5658 7945 9.211485 GTCATAAAGCTTAAACAGTACTACCAA 57.789 33.333 0.00 0.00 0.00 3.67
5661 7948 9.635520 TCAGTCATAAAGCTTAAACAGTACTAC 57.364 33.333 0.00 0.00 0.00 2.73
5663 7950 9.555727 TTTCAGTCATAAAGCTTAAACAGTACT 57.444 29.630 0.00 0.00 0.00 2.73
5669 7956 9.821662 ATTACGTTTCAGTCATAAAGCTTAAAC 57.178 29.630 0.00 3.26 0.00 2.01
5720 8007 6.566197 ATTTGCTCTCAAAAGTAGACCAAG 57.434 37.500 0.00 0.00 44.44 3.61
5722 8009 8.514594 CAATTATTTGCTCTCAAAAGTAGACCA 58.485 33.333 0.00 0.00 44.44 4.02
5788 8076 7.831193 AGATTTACATGCCAGAACTTAGAACAT 59.169 33.333 0.00 0.00 0.00 2.71
5825 8113 4.390603 GCATTGACCAACGAAGTACATGTA 59.609 41.667 0.08 0.08 45.00 2.29
5847 8135 8.622948 AATAGTAAAGCCTTAACCATCTATGC 57.377 34.615 0.00 0.00 0.00 3.14
5877 8165 2.084546 GTTCCTTGGAGCATGTGGTAC 58.915 52.381 0.00 0.00 0.00 3.34
5991 8280 1.286260 GCTAGGCGGTCTACGGATG 59.714 63.158 0.00 0.00 44.51 3.51
6003 8292 0.386226 GCTGATAGTCGTCGCTAGGC 60.386 60.000 0.00 0.00 0.00 3.93
6005 8294 1.334239 GGTGCTGATAGTCGTCGCTAG 60.334 57.143 0.00 0.00 0.00 3.42
6018 8307 2.258591 GACTCGCTTCGGTGCTGA 59.741 61.111 0.00 0.00 0.00 4.26
6025 8314 3.241059 CGCCTTCGACTCGCTTCG 61.241 66.667 0.00 0.00 40.53 3.79
6065 8354 1.299541 ATAAGATTTGTCCGGCTGCG 58.700 50.000 0.00 0.00 0.00 5.18
6094 8383 1.742880 CACGACGACTCCCCGACTA 60.743 63.158 0.00 0.00 0.00 2.59
6099 8388 1.139095 CTTAGCACGACGACTCCCC 59.861 63.158 0.00 0.00 0.00 4.81
6118 8407 1.873591 GATGCGTTGGTCATATGGGAC 59.126 52.381 2.13 0.00 37.06 4.46
6119 8408 1.488393 TGATGCGTTGGTCATATGGGA 59.512 47.619 2.13 0.00 0.00 4.37
6126 8415 1.601903 GTTGTTCTGATGCGTTGGTCA 59.398 47.619 0.00 0.00 0.00 4.02
6132 8421 0.586319 CAACGGTTGTTCTGATGCGT 59.414 50.000 12.66 0.00 35.72 5.24
6147 8436 3.865745 CCTAAGCTACTCCATCAACAACG 59.134 47.826 0.00 0.00 0.00 4.10
6148 8437 4.192317 CCCTAAGCTACTCCATCAACAAC 58.808 47.826 0.00 0.00 0.00 3.32
6149 8438 3.370527 GCCCTAAGCTACTCCATCAACAA 60.371 47.826 0.00 0.00 38.99 2.83
6150 8439 2.170607 GCCCTAAGCTACTCCATCAACA 59.829 50.000 0.00 0.00 38.99 3.33
6151 8440 2.170607 TGCCCTAAGCTACTCCATCAAC 59.829 50.000 0.00 0.00 44.23 3.18
6152 8441 2.477245 TGCCCTAAGCTACTCCATCAA 58.523 47.619 0.00 0.00 44.23 2.57
6153 8442 2.170607 GTTGCCCTAAGCTACTCCATCA 59.829 50.000 0.00 0.00 43.00 3.07
6154 8443 2.839975 GTTGCCCTAAGCTACTCCATC 58.160 52.381 0.00 0.00 43.00 3.51
6176 8479 1.832366 CCATTTGGGGTCATGCATTGA 59.168 47.619 0.00 0.00 0.00 2.57
6209 8513 4.255510 TCTGTCCGTTTACCCCTATACT 57.744 45.455 0.00 0.00 0.00 2.12
6212 8516 4.041938 TGTTTTCTGTCCGTTTACCCCTAT 59.958 41.667 0.00 0.00 0.00 2.57
6214 8518 2.173143 TGTTTTCTGTCCGTTTACCCCT 59.827 45.455 0.00 0.00 0.00 4.79
6273 8577 0.958876 GGGTCGAAAGCGGACCAAAT 60.959 55.000 17.10 0.00 38.56 2.32
6301 8605 0.893270 CAAACTCGGCCCATGTTGGA 60.893 55.000 0.00 0.00 40.96 3.53
6307 8611 1.153168 CGATCCAAACTCGGCCCAT 60.153 57.895 0.00 0.00 32.58 4.00
6309 8613 3.202706 GCGATCCAAACTCGGCCC 61.203 66.667 0.00 0.00 36.65 5.80
6312 8616 2.452813 CGTGGCGATCCAAACTCGG 61.453 63.158 0.00 0.00 45.53 4.63
6313 8617 1.289109 AACGTGGCGATCCAAACTCG 61.289 55.000 0.00 0.00 45.53 4.18
6314 8618 0.872388 AAACGTGGCGATCCAAACTC 59.128 50.000 0.00 0.00 45.53 3.01
6315 8619 0.591170 CAAACGTGGCGATCCAAACT 59.409 50.000 0.00 0.00 45.53 2.66
6316 8620 0.386731 CCAAACGTGGCGATCCAAAC 60.387 55.000 0.00 0.00 45.53 2.93
6317 8621 0.535328 TCCAAACGTGGCGATCCAAA 60.535 50.000 0.00 0.00 45.53 3.28
6318 8622 0.322098 ATCCAAACGTGGCGATCCAA 60.322 50.000 0.00 0.00 45.53 3.53
6319 8623 0.742990 GATCCAAACGTGGCGATCCA 60.743 55.000 0.00 0.00 45.54 3.41
6320 8624 1.762222 CGATCCAAACGTGGCGATCC 61.762 60.000 11.35 0.00 45.54 3.36
6321 8625 0.804544 TCGATCCAAACGTGGCGATC 60.805 55.000 0.00 0.00 45.54 3.69
6322 8626 0.390603 TTCGATCCAAACGTGGCGAT 60.391 50.000 0.00 0.00 45.54 4.58
6323 8627 0.600518 TTTCGATCCAAACGTGGCGA 60.601 50.000 0.00 0.00 45.54 5.54
6324 8628 0.452122 GTTTCGATCCAAACGTGGCG 60.452 55.000 0.00 0.00 45.54 5.69
6335 8639 4.247828 CGCGCGTCCGTTTCGATC 62.248 66.667 24.19 0.00 36.67 3.69
6382 8698 4.555709 TTTGTGCCAGCGACGGGT 62.556 61.111 0.00 0.00 0.00 5.28
6500 8835 2.112297 ATGGCGTGGTCGTGGTTT 59.888 55.556 0.00 0.00 39.49 3.27
6536 8888 2.808244 CAAAAGCTTTCCAGAACGCAA 58.192 42.857 13.10 0.00 37.94 4.85
6537 8889 1.535860 GCAAAAGCTTTCCAGAACGCA 60.536 47.619 13.10 0.00 37.94 5.24
6624 8979 0.600782 GCGTCCACCGGAAGTTGTAA 60.601 55.000 9.46 0.00 33.83 2.41
6640 8998 2.819595 CCTACGGCAATGCAGCGT 60.820 61.111 13.38 13.38 34.64 5.07
6654 9012 2.589540 CTGGTCATTGGCGCCCTA 59.410 61.111 26.77 13.06 0.00 3.53
6701 9066 3.062466 CACGTCGAGCTCCCCTCA 61.062 66.667 8.47 0.00 40.78 3.86


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

AutoCloner maintained by Alex Coulton.