Multiple sequence alignment - TraesCS7B01G372000

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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 TraesCS7B01G372000 chr7B 100.000 3893 0 0 1 3893 637824661 637820769 0.000000e+00 7190.0
1 TraesCS7B01G372000 chr7B 90.193 622 43 7 2569 3173 637869183 637868563 0.000000e+00 795.0
2 TraesCS7B01G372000 chr7B 92.143 420 25 4 240 658 637880732 637880320 1.560000e-163 586.0
3 TraesCS7B01G372000 chr7B 90.943 265 17 4 3176 3440 637780796 637780539 2.230000e-92 350.0
4 TraesCS7B01G372000 chr7B 83.784 296 23 12 867 1145 637951217 637950930 1.390000e-64 257.0
5 TraesCS7B01G372000 chr7B 88.776 196 17 4 950 1143 637916367 637916175 6.500000e-58 235.0
6 TraesCS7B01G372000 chr7B 94.615 130 7 0 88 217 680907436 680907565 6.600000e-48 202.0
7 TraesCS7B01G372000 chr7B 75.565 487 72 31 1781 2254 637950432 637949980 3.070000e-46 196.0
8 TraesCS7B01G372000 chr7B 96.581 117 2 1 690 806 637880231 637880117 3.970000e-45 193.0
9 TraesCS7B01G372000 chr7B 81.383 188 21 9 366 545 637893293 637893112 1.460000e-29 141.0
10 TraesCS7B01G372000 chr7B 81.383 188 21 9 366 545 637917059 637916878 1.460000e-29 141.0
11 TraesCS7B01G372000 chr7B 75.099 253 34 18 2690 2937 552348139 552348367 1.490000e-14 91.6
12 TraesCS7B01G372000 chr7A 86.635 2095 134 67 1180 3173 666213309 666211260 0.000000e+00 2183.0
13 TraesCS7B01G372000 chr7A 78.785 971 105 46 1400 2322 666506722 666505805 3.400000e-155 558.0
14 TraesCS7B01G372000 chr7A 92.112 393 22 6 756 1144 666213686 666213299 2.640000e-151 545.0
15 TraesCS7B01G372000 chr7A 90.881 329 24 4 217 544 666227302 666226979 1.660000e-118 436.0
16 TraesCS7B01G372000 chr7A 80.769 468 50 25 217 654 666507886 666507429 2.900000e-86 329.0
17 TraesCS7B01G372000 chr7A 79.848 526 36 31 675 1140 666569075 666568560 1.750000e-83 320.0
18 TraesCS7B01G372000 chr7A 79.184 490 49 27 705 1143 666507420 666506933 1.370000e-74 291.0
19 TraesCS7B01G372000 chr7A 78.338 337 56 9 2610 2940 666588609 666588284 6.600000e-48 202.0
20 TraesCS7B01G372000 chr7A 80.723 249 39 7 298 545 666574680 666574440 6.640000e-43 185.0
21 TraesCS7B01G372000 chr7A 78.626 262 35 12 2613 2862 666519300 666519048 1.870000e-33 154.0
22 TraesCS7B01G372000 chr7A 73.931 491 76 35 1781 2254 666589899 666589444 2.420000e-32 150.0
23 TraesCS7B01G372000 chr7A 93.333 45 1 1 308 352 666591215 666591173 9.030000e-07 65.8
24 TraesCS7B01G372000 chr7D 89.111 900 55 17 1469 2328 575691924 575691028 0.000000e+00 1079.0
25 TraesCS7B01G372000 chr7D 92.609 663 42 6 2329 2985 575690999 575690338 0.000000e+00 946.0
26 TraesCS7B01G372000 chr7D 81.098 984 106 38 1399 2328 575743059 575742102 0.000000e+00 713.0
27 TraesCS7B01G372000 chr7D 93.987 449 19 4 217 658 575709006 575708559 0.000000e+00 673.0
28 TraesCS7B01G372000 chr7D 92.747 455 17 9 703 1143 575692551 575692099 0.000000e+00 643.0
29 TraesCS7B01G372000 chr7D 84.848 297 23 11 867 1143 575774759 575774465 2.960000e-71 279.0
30 TraesCS7B01G372000 chr7D 77.871 479 59 31 705 1145 575821517 575821048 1.800000e-63 254.0
31 TraesCS7B01G372000 chr7D 90.206 194 7 5 2991 3173 575689841 575689649 3.890000e-60 243.0
32 TraesCS7B01G372000 chr7D 92.105 152 12 0 992 1143 575743613 575743462 8.470000e-52 215.0
33 TraesCS7B01G372000 chr7D 80.268 299 37 13 366 658 575821804 575821522 5.100000e-49 206.0
34 TraesCS7B01G372000 chr7D 94.531 128 7 0 91 218 576290327 576290200 8.530000e-47 198.0
35 TraesCS7B01G372000 chr7D 85.405 185 12 3 1180 1349 575692108 575691924 1.110000e-40 178.0
36 TraesCS7B01G372000 chr7D 75.988 329 63 8 2618 2940 575819125 575818807 5.210000e-34 156.0
37 TraesCS7B01G372000 chr7D 74.249 466 72 33 1807 2254 575820459 575820024 6.740000e-33 152.0
38 TraesCS7B01G372000 chr7D 76.401 339 37 20 328 638 575757055 575756732 4.050000e-30 143.0
39 TraesCS7B01G372000 chr7D 93.023 86 6 0 8 93 575709098 575709013 4.080000e-25 126.0
40 TraesCS7B01G372000 chr7D 94.937 79 3 1 691 769 575756717 575756640 5.280000e-24 122.0
41 TraesCS7B01G372000 chr2B 88.920 722 49 12 3174 3891 417771256 417770562 0.000000e+00 861.0
42 TraesCS7B01G372000 chr2B 91.176 272 17 5 3174 3440 548631366 548631635 2.860000e-96 363.0
43 TraesCS7B01G372000 chr2B 90.406 271 20 3 3174 3440 417658382 417658114 6.190000e-93 351.0
44 TraesCS7B01G372000 chr2B 90.262 267 25 1 3174 3440 447903161 447903426 8.010000e-92 348.0
45 TraesCS7B01G372000 chr2B 89.781 274 21 5 3174 3440 635690177 635690450 1.040000e-90 344.0
46 TraesCS7B01G372000 chr2B 92.908 141 9 1 88 227 199013722 199013862 1.830000e-48 204.0
47 TraesCS7B01G372000 chr5B 93.797 403 25 0 3489 3891 539077991 539078393 1.200000e-169 606.0
48 TraesCS7B01G372000 chr5B 93.300 403 27 0 3489 3891 501420593 501420995 2.590000e-166 595.0
49 TraesCS7B01G372000 chr5B 95.276 127 6 0 91 217 431061997 431062123 6.600000e-48 202.0
50 TraesCS7B01G372000 chr5B 93.939 132 8 0 89 220 324497247 324497116 2.370000e-47 200.0
51 TraesCS7B01G372000 chr2D 93.300 403 27 0 3489 3891 40911283 40911685 2.590000e-166 595.0
52 TraesCS7B01G372000 chr2D 93.103 406 25 2 3489 3891 38792465 38792870 3.350000e-165 592.0
53 TraesCS7B01G372000 chr2D 92.193 269 15 3 3174 3440 40915855 40916119 3.670000e-100 375.0
54 TraesCS7B01G372000 chr2D 88.158 304 21 10 3174 3463 50243802 50244104 8.010000e-92 348.0
55 TraesCS7B01G372000 chr2D 90.840 262 18 4 3175 3434 40910873 40911130 2.880000e-91 346.0
56 TraesCS7B01G372000 chr1B 93.300 403 26 1 3489 3891 577877435 577877836 9.310000e-166 593.0
57 TraesCS7B01G372000 chr1B 93.052 403 28 0 3489 3891 656784316 656784718 1.200000e-164 590.0
58 TraesCS7B01G372000 chr1B 92.857 406 29 0 3486 3891 656789823 656790228 1.200000e-164 590.0
59 TraesCS7B01G372000 chr3B 93.267 401 27 0 3491 3891 62306360 62305960 3.350000e-165 592.0
60 TraesCS7B01G372000 chr3B 93.939 132 8 0 89 220 515351078 515351209 2.370000e-47 200.0
61 TraesCS7B01G372000 chr3B 94.595 37 2 0 1149 1185 828528791 828528755 1.510000e-04 58.4
62 TraesCS7B01G372000 chr3D 91.760 267 17 3 3174 3440 110284048 110283787 2.210000e-97 366.0
63 TraesCS7B01G372000 chr3D 89.865 148 14 1 91 237 496172882 496172735 5.130000e-44 189.0
64 TraesCS7B01G372000 chr3D 97.368 38 0 1 1145 1182 608773988 608774024 3.250000e-06 63.9
65 TraesCS7B01G372000 chrUn 76.984 756 90 32 1399 2121 86902016 86902720 4.780000e-94 355.0
66 TraesCS7B01G372000 chrUn 85.116 215 23 8 2117 2324 86902748 86902960 1.100000e-50 211.0
67 TraesCS7B01G372000 chrUn 93.893 131 7 1 91 221 66416535 66416406 3.070000e-46 196.0
68 TraesCS7B01G372000 chrUn 93.182 132 9 0 89 220 274213497 274213366 1.100000e-45 195.0
69 TraesCS7B01G372000 chrUn 93.182 132 9 0 89 220 324918604 324918735 1.100000e-45 195.0
70 TraesCS7B01G372000 chrUn 93.182 132 9 0 89 220 343584860 343584729 1.100000e-45 195.0
71 TraesCS7B01G372000 chrUn 93.182 132 9 0 89 220 370371247 370371378 1.100000e-45 195.0
72 TraesCS7B01G372000 chrUn 93.182 132 9 0 89 220 418858314 418858183 1.100000e-45 195.0
73 TraesCS7B01G372000 chrUn 93.130 131 9 0 91 221 27078762 27078892 3.970000e-45 193.0
74 TraesCS7B01G372000 chrUn 92.424 132 10 0 89 220 4978168 4978299 5.130000e-44 189.0
75 TraesCS7B01G372000 chrUn 92.424 132 10 0 89 220 118818253 118818122 5.130000e-44 189.0
76 TraesCS7B01G372000 chrUn 91.304 138 10 2 87 224 396963132 396962997 1.850000e-43 187.0
77 TraesCS7B01G372000 chr6B 94.853 136 7 0 82 217 644370904 644370769 3.050000e-51 213.0
78 TraesCS7B01G372000 chr6B 93.939 132 8 0 89 220 244146251 244146382 2.370000e-47 200.0
79 TraesCS7B01G372000 chr6B 92.754 138 9 1 88 225 160666283 160666147 8.530000e-47 198.0
80 TraesCS7B01G372000 chr6B 86.275 102 7 6 2841 2937 364933472 364933571 1.910000e-18 104.0
81 TraesCS7B01G372000 chr6B 86.905 84 10 1 2820 2902 636374660 636374743 4.140000e-15 93.5
82 TraesCS7B01G372000 chr5D 95.276 127 6 0 91 217 558898540 558898414 6.600000e-48 202.0
83 TraesCS7B01G372000 chr5D 94.488 127 7 0 91 217 241844078 241844204 3.070000e-46 196.0
84 TraesCS7B01G372000 chr5D 97.436 39 1 0 1144 1182 398638862 398638900 2.510000e-07 67.6
85 TraesCS7B01G372000 chr2A 92.199 141 9 1 85 223 773183321 773183461 8.530000e-47 198.0
86 TraesCS7B01G372000 chr2A 92.701 137 9 1 84 220 140276700 140276835 3.070000e-46 196.0
87 TraesCS7B01G372000 chr2A 93.233 133 9 0 91 223 158594142 158594010 3.070000e-46 196.0
88 TraesCS7B01G372000 chr2A 83.051 59 10 0 1829 1887 656967813 656967755 2.000000e-03 54.7
89 TraesCS7B01G372000 chr5A 92.647 136 10 0 89 224 309945722 309945587 3.070000e-46 196.0
90 TraesCS7B01G372000 chr4B 94.488 127 7 0 91 217 11930370 11930244 3.070000e-46 196.0
91 TraesCS7B01G372000 chr4B 95.000 40 2 0 1146 1185 518140319 518140280 3.250000e-06 63.9
92 TraesCS7B01G372000 chr4B 95.000 40 2 0 1146 1185 550472211 550472172 3.250000e-06 63.9
93 TraesCS7B01G372000 chr1A 94.488 127 7 0 91 217 12099253 12099127 3.070000e-46 196.0
94 TraesCS7B01G372000 chr1A 75.107 233 31 19 2672 2902 18151992 18151785 2.490000e-12 84.2
95 TraesCS7B01G372000 chr6D 92.086 139 10 1 86 224 95895966 95896103 1.100000e-45 195.0
96 TraesCS7B01G372000 chr6D 93.798 129 8 0 89 217 126631751 126631879 1.100000e-45 195.0
97 TraesCS7B01G372000 chr1D 93.182 132 9 0 89 220 469018556 469018687 1.100000e-45 195.0
98 TraesCS7B01G372000 chr1D 97.222 36 0 1 1147 1182 345404397 345404363 4.200000e-05 60.2


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 TraesCS7B01G372000 chr7B 637820769 637824661 3892 True 7190.000000 7190 100.000000 1 3893 1 chr7B.!!$R2 3892
1 TraesCS7B01G372000 chr7B 637868563 637869183 620 True 795.000000 795 90.193000 2569 3173 1 chr7B.!!$R3 604
2 TraesCS7B01G372000 chr7B 637880117 637880732 615 True 389.500000 586 94.362000 240 806 2 chr7B.!!$R5 566
3 TraesCS7B01G372000 chr7B 637949980 637951217 1237 True 226.500000 257 79.674500 867 2254 2 chr7B.!!$R7 1387
4 TraesCS7B01G372000 chr7A 666211260 666213686 2426 True 1364.000000 2183 89.373500 756 3173 2 chr7A.!!$R5 2417
5 TraesCS7B01G372000 chr7A 666505805 666507886 2081 True 392.666667 558 79.579333 217 2322 3 chr7A.!!$R6 2105
6 TraesCS7B01G372000 chr7A 666568560 666569075 515 True 320.000000 320 79.848000 675 1140 1 chr7A.!!$R3 465
7 TraesCS7B01G372000 chr7D 575689649 575692551 2902 True 617.800000 1079 90.015600 703 3173 5 chr7D.!!$R3 2470
8 TraesCS7B01G372000 chr7D 575742102 575743613 1511 True 464.000000 713 86.601500 992 2328 2 chr7D.!!$R5 1336
9 TraesCS7B01G372000 chr7D 575708559 575709098 539 True 399.500000 673 93.505000 8 658 2 chr7D.!!$R4 650
10 TraesCS7B01G372000 chr2B 417770562 417771256 694 True 861.000000 861 88.920000 3174 3891 1 chr2B.!!$R2 717
11 TraesCS7B01G372000 chr2D 40910873 40911685 812 False 470.500000 595 92.070000 3175 3891 2 chr2D.!!$F4 716
12 TraesCS7B01G372000 chrUn 86902016 86902960 944 False 283.000000 355 81.050000 1399 2324 2 chrUn.!!$F5 925

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
100 101 0.105039 GGCTTGATGTACTCCCTCGG 59.895 60.0 0.00 0.0 0.0 4.63 F
650 683 0.108424 CTTCCGGCCTCTGTTCTCTG 60.108 60.0 0.00 0.0 0.0 3.35 F
1704 2199 0.039437 AGCGCGTGTATCCTTATCCG 60.039 55.0 8.43 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1447 1859 0.179936 TGCATGCATATCACGTGGGA 59.820 50.0 18.46 4.05 0.0 4.37 R
1752 2306 0.241749 CAGGTCAGCCGTACGTGTAA 59.758 55.0 15.21 0.00 40.5 2.41 R
3361 4577 0.323908 CGGAGGAGGAGGAAGAGTGT 60.324 60.0 0.00 0.00 0.0 3.55 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
37 38 5.103940 CCCATTTCCTTGGAGAAATCCTAGA 60.104 44.000 7.23 0.00 43.06 2.43
57 58 2.191128 ACTTCATGCAGAGGGTTGAC 57.809 50.000 0.00 0.00 0.00 3.18
74 75 7.514721 AGGGTTGACTTGACTCTAAACATTTA 58.485 34.615 0.00 0.00 0.00 1.40
82 83 9.167311 ACTTGACTCTAAACATTTAAGCTATGG 57.833 33.333 0.27 0.00 0.00 2.74
99 100 0.824109 TGGCTTGATGTACTCCCTCG 59.176 55.000 0.00 0.00 0.00 4.63
100 101 0.105039 GGCTTGATGTACTCCCTCGG 59.895 60.000 0.00 0.00 0.00 4.63
102 103 1.202428 GCTTGATGTACTCCCTCGGTC 60.202 57.143 0.00 0.00 0.00 4.79
103 104 1.409427 CTTGATGTACTCCCTCGGTCC 59.591 57.143 0.00 0.00 0.00 4.46
104 105 0.629596 TGATGTACTCCCTCGGTCCT 59.370 55.000 0.00 0.00 0.00 3.85
105 106 1.848388 TGATGTACTCCCTCGGTCCTA 59.152 52.381 0.00 0.00 0.00 2.94
106 107 2.242965 TGATGTACTCCCTCGGTCCTAA 59.757 50.000 0.00 0.00 0.00 2.69
107 108 2.905415 TGTACTCCCTCGGTCCTAAA 57.095 50.000 0.00 0.00 0.00 1.85
108 109 3.173953 TGTACTCCCTCGGTCCTAAAA 57.826 47.619 0.00 0.00 0.00 1.52
109 110 3.716431 TGTACTCCCTCGGTCCTAAAAT 58.284 45.455 0.00 0.00 0.00 1.82
110 111 4.098894 TGTACTCCCTCGGTCCTAAAATT 58.901 43.478 0.00 0.00 0.00 1.82
111 112 3.908643 ACTCCCTCGGTCCTAAAATTC 57.091 47.619 0.00 0.00 0.00 2.17
112 113 3.451890 ACTCCCTCGGTCCTAAAATTCT 58.548 45.455 0.00 0.00 0.00 2.40
113 114 3.844804 ACTCCCTCGGTCCTAAAATTCTT 59.155 43.478 0.00 0.00 0.00 2.52
114 115 4.192317 CTCCCTCGGTCCTAAAATTCTTG 58.808 47.826 0.00 0.00 0.00 3.02
115 116 3.585732 TCCCTCGGTCCTAAAATTCTTGT 59.414 43.478 0.00 0.00 0.00 3.16
116 117 3.939592 CCCTCGGTCCTAAAATTCTTGTC 59.060 47.826 0.00 0.00 0.00 3.18
117 118 4.323562 CCCTCGGTCCTAAAATTCTTGTCT 60.324 45.833 0.00 0.00 0.00 3.41
118 119 5.246307 CCTCGGTCCTAAAATTCTTGTCTT 58.754 41.667 0.00 0.00 0.00 3.01
119 120 6.403878 CCTCGGTCCTAAAATTCTTGTCTTA 58.596 40.000 0.00 0.00 0.00 2.10
120 121 6.535508 CCTCGGTCCTAAAATTCTTGTCTTAG 59.464 42.308 0.00 0.00 0.00 2.18
121 122 7.235935 TCGGTCCTAAAATTCTTGTCTTAGA 57.764 36.000 0.00 0.00 0.00 2.10
122 123 7.848128 TCGGTCCTAAAATTCTTGTCTTAGAT 58.152 34.615 0.00 0.00 0.00 1.98
123 124 8.319146 TCGGTCCTAAAATTCTTGTCTTAGATT 58.681 33.333 0.00 0.00 0.00 2.40
124 125 8.947115 CGGTCCTAAAATTCTTGTCTTAGATTT 58.053 33.333 0.00 0.00 0.00 2.17
136 137 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
137 138 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
139 140 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
140 141 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
159 160 9.745880 ACGGATGTATCTAGTTACATTTTAGTG 57.254 33.333 21.77 13.11 41.67 2.74
160 161 9.745880 CGGATGTATCTAGTTACATTTTAGTGT 57.254 33.333 21.77 4.20 41.67 3.55
182 183 9.128404 AGTGTTAAATACATCCGTATCTAGACA 57.872 33.333 0.00 0.00 37.34 3.41
183 184 9.740239 GTGTTAAATACATCCGTATCTAGACAA 57.260 33.333 0.00 0.00 37.34 3.18
190 191 9.698309 ATACATCCGTATCTAGACAAATTCAAG 57.302 33.333 0.00 0.00 32.66 3.02
191 192 7.782049 ACATCCGTATCTAGACAAATTCAAGA 58.218 34.615 0.00 0.00 0.00 3.02
192 193 7.707035 ACATCCGTATCTAGACAAATTCAAGAC 59.293 37.037 0.00 0.00 0.00 3.01
193 194 7.165460 TCCGTATCTAGACAAATTCAAGACA 57.835 36.000 0.00 0.00 0.00 3.41
194 195 7.608153 TCCGTATCTAGACAAATTCAAGACAA 58.392 34.615 0.00 0.00 0.00 3.18
195 196 7.759886 TCCGTATCTAGACAAATTCAAGACAAG 59.240 37.037 0.00 0.00 0.00 3.16
196 197 7.759886 CCGTATCTAGACAAATTCAAGACAAGA 59.240 37.037 0.00 0.00 0.00 3.02
197 198 9.140286 CGTATCTAGACAAATTCAAGACAAGAA 57.860 33.333 0.00 0.00 0.00 2.52
207 208 4.829064 TCAAGACAAGAATTTTGGGACG 57.171 40.909 5.68 0.00 0.00 4.79
208 209 3.568007 TCAAGACAAGAATTTTGGGACGG 59.432 43.478 0.00 0.00 0.00 4.79
209 210 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
210 211 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
211 212 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
212 213 2.107552 ACAAGAATTTTGGGACGGAGGA 59.892 45.455 0.00 0.00 0.00 3.71
213 214 3.153919 CAAGAATTTTGGGACGGAGGAA 58.846 45.455 0.00 0.00 0.00 3.36
214 215 3.073274 AGAATTTTGGGACGGAGGAAG 57.927 47.619 0.00 0.00 0.00 3.46
215 216 2.375509 AGAATTTTGGGACGGAGGAAGT 59.624 45.455 0.00 0.00 0.00 3.01
216 217 3.585732 AGAATTTTGGGACGGAGGAAGTA 59.414 43.478 0.00 0.00 0.00 2.24
217 218 2.845363 TTTTGGGACGGAGGAAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
218 219 2.019807 TTTGGGACGGAGGAAGTACT 57.980 50.000 0.00 0.00 0.00 2.73
228 229 6.096001 GGACGGAGGAAGTACTAATTAAGTCA 59.904 42.308 15.43 0.00 39.80 3.41
229 230 7.098074 ACGGAGGAAGTACTAATTAAGTCAG 57.902 40.000 0.00 0.00 39.80 3.51
234 235 8.235359 AGGAAGTACTAATTAAGTCAGCGTAT 57.765 34.615 0.00 0.00 39.80 3.06
336 340 5.630896 TTCTCGAGTAAGTTTGTCAAACG 57.369 39.130 20.04 9.51 45.88 3.60
354 358 1.226435 GTAGCGACACGGAGAGCTG 60.226 63.158 0.00 0.00 40.51 4.24
462 468 4.164030 TGGGTGACTGTTCATATGTATGCT 59.836 41.667 1.90 0.00 33.11 3.79
546 558 9.816354 TCGACCCATATGTATGTGATAAATATG 57.184 33.333 1.24 6.73 40.66 1.78
586 615 0.461548 GGATGTCTCTCGTGGATGCA 59.538 55.000 0.00 0.00 0.00 3.96
650 683 0.108424 CTTCCGGCCTCTGTTCTCTG 60.108 60.000 0.00 0.00 0.00 3.35
658 691 2.769095 GCCTCTGTTCTCTGGGTATCTT 59.231 50.000 0.00 0.00 0.00 2.40
659 692 3.198853 GCCTCTGTTCTCTGGGTATCTTT 59.801 47.826 0.00 0.00 0.00 2.52
661 694 5.804771 GCCTCTGTTCTCTGGGTATCTTTTT 60.805 44.000 0.00 0.00 0.00 1.94
686 719 4.764050 TTTGAACACTGTTCTCTGGGTA 57.236 40.909 20.18 0.00 0.00 3.69
687 720 4.974645 TTGAACACTGTTCTCTGGGTAT 57.025 40.909 20.18 0.00 0.00 2.73
718 812 4.060900 CTGAGAGCAAGTTAAGTGAGCAA 58.939 43.478 9.78 0.00 0.00 3.91
989 1167 0.825425 TAGCAGCAGGGAGAGATCGG 60.825 60.000 0.00 0.00 0.00 4.18
1134 1312 0.606604 GCCAGGACGGTCAGTTCTTA 59.393 55.000 10.76 0.00 36.25 2.10
1145 1323 4.511826 CGGTCAGTTCTTACTTCTTGCTTT 59.488 41.667 0.00 0.00 30.26 3.51
1147 1325 6.458342 CGGTCAGTTCTTACTTCTTGCTTTTT 60.458 38.462 0.00 0.00 30.26 1.94
1178 1356 3.723245 AGGTTTACCTCCGGCCTC 58.277 61.111 0.00 0.00 44.77 4.70
1179 1357 1.080538 AGGTTTACCTCCGGCCTCT 59.919 57.895 0.00 0.00 44.77 3.69
1180 1358 1.221021 GGTTTACCTCCGGCCTCTG 59.779 63.158 0.00 0.00 0.00 3.35
1181 1359 1.449778 GTTTACCTCCGGCCTCTGC 60.450 63.158 0.00 0.00 0.00 4.26
1182 1360 1.612442 TTTACCTCCGGCCTCTGCT 60.612 57.895 0.00 0.00 37.74 4.24
1183 1361 1.198759 TTTACCTCCGGCCTCTGCTT 61.199 55.000 0.00 0.00 37.74 3.91
1184 1362 1.614241 TTACCTCCGGCCTCTGCTTC 61.614 60.000 0.00 0.00 37.74 3.86
1185 1363 2.516048 TACCTCCGGCCTCTGCTTCT 62.516 60.000 0.00 0.00 37.74 2.85
1186 1364 2.664081 CCTCCGGCCTCTGCTTCTT 61.664 63.158 0.00 0.00 37.74 2.52
1187 1365 1.449246 CTCCGGCCTCTGCTTCTTG 60.449 63.158 0.00 0.00 37.74 3.02
1188 1366 3.130160 CCGGCCTCTGCTTCTTGC 61.130 66.667 0.00 0.00 43.25 4.01
1189 1367 2.046507 CGGCCTCTGCTTCTTGCT 60.047 61.111 0.00 0.00 43.37 3.91
1190 1368 2.396955 CGGCCTCTGCTTCTTGCTG 61.397 63.158 0.00 0.00 43.37 4.41
1256 1434 3.814615 ATGCATGGCGACCGGCTAG 62.815 63.158 16.54 10.00 42.94 3.42
1278 1666 7.864379 GCTAGTTGCACATTTTATAGCATGAAT 59.136 33.333 0.00 0.00 42.31 2.57
1282 1684 7.773864 TGCACATTTTATAGCATGAATTTGG 57.226 32.000 0.00 0.00 31.05 3.28
1302 1704 2.546789 GGTTTTTCACTGTCGGACGATT 59.453 45.455 3.34 0.00 0.00 3.34
1350 1754 2.380941 TCGGTGTGGATCGATTAAGGA 58.619 47.619 0.00 0.00 26.62 3.36
1355 1759 5.230942 GGTGTGGATCGATTAAGGATAGTG 58.769 45.833 0.00 0.00 0.00 2.74
1357 1761 5.692204 GTGTGGATCGATTAAGGATAGTGTG 59.308 44.000 0.00 0.00 0.00 3.82
1362 1766 5.440234 TCGATTAAGGATAGTGTGCTCTC 57.560 43.478 0.00 0.00 0.00 3.20
1376 1784 5.246203 AGTGTGCTCTCCATTTAGTACTTGA 59.754 40.000 0.00 0.00 30.61 3.02
1393 1801 7.506114 AGTACTTGATTTAGTCTTGTGGTTGA 58.494 34.615 0.00 0.00 0.00 3.18
1429 1837 5.011023 GGAATTGGTTCAAGTTCATGGAAGT 59.989 40.000 0.00 0.00 36.01 3.01
1442 1854 8.980481 AGTTCATGGAAGTAAAGAAAAGAGAA 57.020 30.769 0.00 0.00 0.00 2.87
1490 1902 5.195940 TGATGAACAAGATGAGATTTCCCC 58.804 41.667 0.00 0.00 0.00 4.81
1491 1903 3.968265 TGAACAAGATGAGATTTCCCCC 58.032 45.455 0.00 0.00 0.00 5.40
1518 1941 4.693283 TCTACCTCATTTATTGGCTGACG 58.307 43.478 0.00 0.00 0.00 4.35
1538 1961 5.297527 TGACGATGAATTATTTGCTGCTCAT 59.702 36.000 0.00 0.00 0.00 2.90
1611 2061 5.420104 ACTTTAGCAATAAATGGCAGCTCTT 59.580 36.000 0.00 0.00 36.80 2.85
1662 2157 4.018779 TGGGTTAACCTTTCCTCACCTATG 60.019 45.833 23.69 0.00 41.11 2.23
1701 2196 2.124903 CGAAAGCGCGTGTATCCTTAT 58.875 47.619 8.43 0.00 0.00 1.73
1702 2197 2.153247 CGAAAGCGCGTGTATCCTTATC 59.847 50.000 8.43 1.82 0.00 1.75
1704 2199 0.039437 AGCGCGTGTATCCTTATCCG 60.039 55.000 8.43 0.00 0.00 4.18
1706 2201 1.007336 CGCGTGTATCCTTATCCGGC 61.007 60.000 0.00 0.00 0.00 6.13
1710 2210 2.674177 CGTGTATCCTTATCCGGCATCC 60.674 54.545 0.00 0.00 0.00 3.51
1726 2226 2.975266 CATCCATCATGCTAGCTCTCC 58.025 52.381 17.23 0.00 0.00 3.71
1749 2303 4.495844 CCGATCCGAATTTTAACCAAGAGC 60.496 45.833 0.00 0.00 0.00 4.09
1751 2305 5.391523 CGATCCGAATTTTAACCAAGAGCAA 60.392 40.000 0.00 0.00 0.00 3.91
1752 2306 5.975693 TCCGAATTTTAACCAAGAGCAAT 57.024 34.783 0.00 0.00 0.00 3.56
1753 2307 6.339587 TCCGAATTTTAACCAAGAGCAATT 57.660 33.333 0.00 0.00 0.00 2.32
1767 2336 1.067425 AGCAATTACACGTACGGCTGA 60.067 47.619 21.06 3.11 0.00 4.26
1768 2337 1.060122 GCAATTACACGTACGGCTGAC 59.940 52.381 21.06 0.00 0.00 3.51
1853 2433 4.431131 CTGATGGGCGCCAAGGGT 62.431 66.667 30.85 0.34 36.95 4.34
2089 2687 2.682876 CGCCGCCGTACCAAATGTT 61.683 57.895 0.00 0.00 0.00 2.71
2181 2821 6.292488 CGAGTTGTTAATCAAACGTACTGGTT 60.292 38.462 0.00 0.00 41.30 3.67
2182 2822 6.721321 AGTTGTTAATCAAACGTACTGGTTG 58.279 36.000 6.37 8.57 41.30 3.77
2200 2840 1.805945 GTGTGCAGACCGTCGATCC 60.806 63.158 1.72 0.00 0.00 3.36
2325 2968 6.787085 TTTTGTCTAGCTAGAGAAAAGCAC 57.213 37.500 36.50 20.66 45.06 4.40
2351 3022 3.837355 ACAAATCCAGAGGAAGCAAAGT 58.163 40.909 0.00 0.00 34.34 2.66
2503 3187 3.640407 TGGCAGGCACCAGACTCC 61.640 66.667 0.00 0.00 33.75 3.85
2554 3241 2.461110 CGTGTATTGACCGCCCAGC 61.461 63.158 0.00 0.00 0.00 4.85
2611 3299 2.550830 AATCCGCCTGACATGGATAC 57.449 50.000 0.00 0.00 41.58 2.24
2862 3550 2.104792 TCTGAACCTTGACCTGAACCTG 59.895 50.000 0.00 0.00 0.00 4.00
2872 3560 2.525629 TGAACCTGGACCTCGCCA 60.526 61.111 0.00 0.00 36.30 5.69
2906 3594 1.270199 GCTCTGATGTGATCGATGGCT 60.270 52.381 0.54 0.00 0.00 4.75
2916 3604 1.000283 GATCGATGGCTCCCTGTGTAG 60.000 57.143 0.54 0.00 0.00 2.74
2961 3655 4.267349 TGTAAAGTTACTCACAGCTCCC 57.733 45.455 3.07 0.00 34.77 4.30
3062 4248 3.118261 TGAGTTTCCTTTGACAGACTGCT 60.118 43.478 1.25 0.00 0.00 4.24
3072 4258 2.765699 TGACAGACTGCTATACCATGCA 59.234 45.455 1.25 0.00 37.63 3.96
3121 4337 4.980573 TGGTTTGAGCCTTTGTATGTACT 58.019 39.130 0.00 0.00 0.00 2.73
3133 4349 8.765219 GCCTTTGTATGTACTTACATCACATAG 58.235 37.037 19.04 11.29 45.11 2.23
3185 4401 9.471084 CAATATGCACATTATGTTGAATCATGT 57.529 29.630 0.00 0.00 30.90 3.21
3231 4447 9.396022 GGACAATGATTCCTAGTTAATCTTGAA 57.604 33.333 19.75 5.72 34.95 2.69
3248 4464 4.411869 TCTTGAAGCCCATGTATGGTATGA 59.588 41.667 9.87 0.00 46.65 2.15
3270 4486 2.372172 CAGGTGGTGGGAAGTTTAGTCT 59.628 50.000 0.00 0.00 0.00 3.24
3278 4494 3.971305 TGGGAAGTTTAGTCTCACCTTGA 59.029 43.478 0.00 0.00 0.00 3.02
3321 4537 4.965200 CCTTTATAAGGGCTGCTCTACT 57.035 45.455 0.60 0.00 45.27 2.57
3383 4599 2.364317 CTTCCTCCTCCTCCGCCA 60.364 66.667 0.00 0.00 0.00 5.69
3440 4663 3.854669 CGGGAATGAGCCGAGCCT 61.855 66.667 0.00 0.00 0.00 4.58
3442 4665 1.821332 GGGAATGAGCCGAGCCTTG 60.821 63.158 0.00 0.00 0.00 3.61
3443 4666 2.476320 GGAATGAGCCGAGCCTTGC 61.476 63.158 0.00 0.00 0.00 4.01
3473 4807 4.254709 TTGCCGGCTCTGTGCTGT 62.255 61.111 29.70 0.00 46.27 4.40
3474 4808 4.687215 TGCCGGCTCTGTGCTGTC 62.687 66.667 29.70 0.00 46.27 3.51
3475 4809 4.385405 GCCGGCTCTGTGCTGTCT 62.385 66.667 22.15 0.00 46.27 3.41
3476 4810 2.125753 CCGGCTCTGTGCTGTCTC 60.126 66.667 9.43 0.00 46.27 3.36
3477 4811 2.125753 CGGCTCTGTGCTGTCTCC 60.126 66.667 2.46 0.00 42.87 3.71
3478 4812 2.125753 GGCTCTGTGCTGTCTCCG 60.126 66.667 1.44 0.00 42.39 4.63
3479 4813 2.125753 GCTCTGTGCTGTCTCCGG 60.126 66.667 0.00 0.00 38.95 5.14
3480 4814 2.575993 CTCTGTGCTGTCTCCGGG 59.424 66.667 0.00 0.00 0.00 5.73
3481 4815 2.997315 TCTGTGCTGTCTCCGGGG 60.997 66.667 0.00 0.00 0.00 5.73
3482 4816 2.997315 CTGTGCTGTCTCCGGGGA 60.997 66.667 0.00 0.00 0.00 4.81
3483 4817 3.302347 CTGTGCTGTCTCCGGGGAC 62.302 68.421 28.37 28.37 36.81 4.46
3511 4845 6.355397 TCTATGTTCTGTACGTGCTAGTAC 57.645 41.667 4.97 13.05 45.22 2.73
3531 4865 6.363065 AGTACAGTTAGGAATCGGTATGAGA 58.637 40.000 0.00 0.00 0.00 3.27
3537 4871 3.935315 AGGAATCGGTATGAGATGCATG 58.065 45.455 2.46 0.00 37.87 4.06
3556 4890 1.274728 TGCCGTTTTTGCCATGCTTAT 59.725 42.857 0.00 0.00 0.00 1.73
3560 4894 4.209080 GCCGTTTTTGCCATGCTTATTATC 59.791 41.667 0.00 0.00 0.00 1.75
3665 4999 0.746204 TTGCTGCGACACTGAAACCA 60.746 50.000 0.00 0.00 0.00 3.67
3735 5069 0.953727 GTGGCTCACAGCAATGAACA 59.046 50.000 0.00 0.00 44.75 3.18
3876 5210 4.040339 TGGTTGACGCATATCTCCATATGT 59.960 41.667 1.24 0.00 42.84 2.29
3891 5225 4.100035 TCCATATGTGTGTTGCCAAAAACA 59.900 37.500 1.24 0.00 37.71 2.83
3892 5226 4.996122 CCATATGTGTGTTGCCAAAAACAT 59.004 37.500 1.24 6.26 41.81 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 2.107204 AGTCAACCCTCTGCATGAAGTT 59.893 45.455 0.00 0.00 0.00 2.66
57 58 8.125448 GCCATAGCTTAAATGTTTAGAGTCAAG 58.875 37.037 0.00 0.00 35.50 3.02
81 82 0.105039 CCGAGGGAGTACATCAAGCC 59.895 60.000 0.00 0.00 0.00 4.35
82 83 0.824759 ACCGAGGGAGTACATCAAGC 59.175 55.000 0.00 0.00 0.00 4.01
87 88 3.393426 TTTAGGACCGAGGGAGTACAT 57.607 47.619 0.00 0.00 0.00 2.29
93 94 3.585732 ACAAGAATTTTAGGACCGAGGGA 59.414 43.478 0.00 0.00 0.00 4.20
94 95 3.939592 GACAAGAATTTTAGGACCGAGGG 59.060 47.826 0.00 0.00 0.00 4.30
95 96 4.833390 AGACAAGAATTTTAGGACCGAGG 58.167 43.478 0.00 0.00 0.00 4.63
110 111 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
111 112 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
113 114 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
114 115 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
133 134 9.745880 CACTAAAATGTAACTAGATACATCCGT 57.254 33.333 21.77 14.49 43.83 4.69
134 135 9.745880 ACACTAAAATGTAACTAGATACATCCG 57.254 33.333 21.77 14.02 43.83 4.18
156 157 9.128404 TGTCTAGATACGGATGTATTTAACACT 57.872 33.333 0.00 0.00 41.37 3.55
157 158 9.740239 TTGTCTAGATACGGATGTATTTAACAC 57.260 33.333 0.00 0.00 41.37 3.32
164 165 9.698309 CTTGAATTTGTCTAGATACGGATGTAT 57.302 33.333 0.00 0.00 43.97 2.29
165 166 8.909923 TCTTGAATTTGTCTAGATACGGATGTA 58.090 33.333 0.00 0.00 33.79 2.29
166 167 7.707035 GTCTTGAATTTGTCTAGATACGGATGT 59.293 37.037 0.00 0.00 39.77 3.06
167 168 7.706607 TGTCTTGAATTTGTCTAGATACGGATG 59.293 37.037 0.00 0.00 39.77 3.51
168 169 7.782049 TGTCTTGAATTTGTCTAGATACGGAT 58.218 34.615 0.00 0.00 39.77 4.18
169 170 7.165460 TGTCTTGAATTTGTCTAGATACGGA 57.835 36.000 0.00 0.00 39.77 4.69
170 171 7.759886 TCTTGTCTTGAATTTGTCTAGATACGG 59.240 37.037 0.00 0.00 39.77 4.02
171 172 8.689251 TCTTGTCTTGAATTTGTCTAGATACG 57.311 34.615 0.00 0.00 39.77 3.06
177 178 9.748708 CCAAAATTCTTGTCTTGAATTTGTCTA 57.251 29.630 13.02 0.00 46.81 2.59
178 179 7.712205 CCCAAAATTCTTGTCTTGAATTTGTCT 59.288 33.333 13.02 0.00 46.81 3.41
179 180 7.710475 TCCCAAAATTCTTGTCTTGAATTTGTC 59.290 33.333 13.02 0.00 46.81 3.18
180 181 7.495606 GTCCCAAAATTCTTGTCTTGAATTTGT 59.504 33.333 13.02 4.15 46.81 2.83
181 182 7.306749 CGTCCCAAAATTCTTGTCTTGAATTTG 60.307 37.037 13.02 8.67 46.81 2.32
183 184 6.215845 CGTCCCAAAATTCTTGTCTTGAATT 58.784 36.000 0.00 0.00 43.44 2.17
184 185 5.278957 CCGTCCCAAAATTCTTGTCTTGAAT 60.279 40.000 0.00 0.00 35.88 2.57
185 186 4.037446 CCGTCCCAAAATTCTTGTCTTGAA 59.963 41.667 0.00 0.00 0.00 2.69
186 187 3.568007 CCGTCCCAAAATTCTTGTCTTGA 59.432 43.478 0.00 0.00 0.00 3.02
187 188 3.568007 TCCGTCCCAAAATTCTTGTCTTG 59.432 43.478 0.00 0.00 0.00 3.02
188 189 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
189 190 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
190 191 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
191 192 2.107552 TCCTCCGTCCCAAAATTCTTGT 59.892 45.455 0.00 0.00 0.00 3.16
192 193 2.790433 TCCTCCGTCCCAAAATTCTTG 58.210 47.619 0.00 0.00 0.00 3.02
193 194 3.181433 ACTTCCTCCGTCCCAAAATTCTT 60.181 43.478 0.00 0.00 0.00 2.52
194 195 2.375509 ACTTCCTCCGTCCCAAAATTCT 59.624 45.455 0.00 0.00 0.00 2.40
195 196 2.791655 ACTTCCTCCGTCCCAAAATTC 58.208 47.619 0.00 0.00 0.00 2.17
196 197 2.971901 ACTTCCTCCGTCCCAAAATT 57.028 45.000 0.00 0.00 0.00 1.82
197 198 2.910977 AGTACTTCCTCCGTCCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
198 199 2.332117 AGTACTTCCTCCGTCCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
199 200 2.019807 AGTACTTCCTCCGTCCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
200 201 2.905415 TAGTACTTCCTCCGTCCCAA 57.095 50.000 0.00 0.00 0.00 4.12
201 202 2.905415 TTAGTACTTCCTCCGTCCCA 57.095 50.000 0.00 0.00 0.00 4.37
202 203 5.362143 ACTTAATTAGTACTTCCTCCGTCCC 59.638 44.000 0.00 0.00 34.56 4.46
203 204 6.096001 TGACTTAATTAGTACTTCCTCCGTCC 59.904 42.308 0.00 0.00 37.17 4.79
204 205 7.093322 TGACTTAATTAGTACTTCCTCCGTC 57.907 40.000 0.00 3.12 37.17 4.79
205 206 6.405619 GCTGACTTAATTAGTACTTCCTCCGT 60.406 42.308 0.00 0.00 37.17 4.69
206 207 5.978322 GCTGACTTAATTAGTACTTCCTCCG 59.022 44.000 0.00 0.00 37.17 4.63
207 208 5.978322 CGCTGACTTAATTAGTACTTCCTCC 59.022 44.000 0.00 0.00 37.17 4.30
208 209 6.562518 ACGCTGACTTAATTAGTACTTCCTC 58.437 40.000 0.00 0.00 37.17 3.71
209 210 6.527057 ACGCTGACTTAATTAGTACTTCCT 57.473 37.500 0.00 0.00 37.17 3.36
210 211 7.096147 GCATACGCTGACTTAATTAGTACTTCC 60.096 40.741 0.00 0.00 34.00 3.46
211 212 7.434307 TGCATACGCTGACTTAATTAGTACTTC 59.566 37.037 0.00 0.00 36.66 3.01
212 213 7.262772 TGCATACGCTGACTTAATTAGTACTT 58.737 34.615 0.00 0.00 36.66 2.24
213 214 6.802608 TGCATACGCTGACTTAATTAGTACT 58.197 36.000 0.00 0.00 36.66 2.73
214 215 6.696148 ACTGCATACGCTGACTTAATTAGTAC 59.304 38.462 0.00 0.00 40.13 2.73
215 216 6.802608 ACTGCATACGCTGACTTAATTAGTA 58.197 36.000 0.00 0.00 40.13 1.82
216 217 5.661458 ACTGCATACGCTGACTTAATTAGT 58.339 37.500 0.00 0.00 40.13 2.24
217 218 5.980116 AGACTGCATACGCTGACTTAATTAG 59.020 40.000 0.00 0.00 38.52 1.73
218 219 5.748630 CAGACTGCATACGCTGACTTAATTA 59.251 40.000 0.00 0.00 39.34 1.40
336 340 1.226435 CAGCTCTCCGTGTCGCTAC 60.226 63.158 0.00 0.00 0.00 3.58
354 358 4.929198 CGGCATTGATGATTCCGC 57.071 55.556 0.00 0.00 33.36 5.54
358 362 0.039798 GCATCGCGGCATTGATGATT 60.040 50.000 17.04 0.00 43.68 2.57
462 468 0.836606 TCTTCCCTGCACAGTGACAA 59.163 50.000 4.15 0.00 0.00 3.18
546 558 6.455360 TCCAAATTCTTTCACATATGAGCC 57.545 37.500 10.38 0.00 35.83 4.70
550 562 8.900781 AGAGACATCCAAATTCTTTCACATATG 58.099 33.333 0.00 0.00 0.00 1.78
586 615 1.594331 GAGAAAACGTTGGCCTGTCT 58.406 50.000 3.32 0.00 0.00 3.41
663 696 4.340617 ACCCAGAGAACAGTGTTCAAAAA 58.659 39.130 32.02 0.00 0.00 1.94
665 698 3.644966 ACCCAGAGAACAGTGTTCAAA 57.355 42.857 32.02 0.00 0.00 2.69
666 699 4.593206 AGATACCCAGAGAACAGTGTTCAA 59.407 41.667 32.02 12.43 0.00 2.69
667 700 4.160329 AGATACCCAGAGAACAGTGTTCA 58.840 43.478 32.02 14.22 0.00 3.18
668 701 4.810191 AGATACCCAGAGAACAGTGTTC 57.190 45.455 25.51 25.51 0.00 3.18
669 702 4.466726 GGTAGATACCCAGAGAACAGTGTT 59.533 45.833 8.61 8.61 40.53 3.32
670 703 4.024670 GGTAGATACCCAGAGAACAGTGT 58.975 47.826 0.00 0.00 40.53 3.55
686 719 5.753721 AACTTGCTCTCAGAAAGGTAGAT 57.246 39.130 0.00 0.00 35.08 1.98
687 720 6.267928 ACTTAACTTGCTCTCAGAAAGGTAGA 59.732 38.462 0.00 0.00 34.63 2.59
718 812 3.515901 GACCTAGTCCAGTCAAACATCCT 59.484 47.826 0.00 0.00 33.08 3.24
953 1129 3.161067 TGCTAGAGCTATAGCCCTTCAG 58.839 50.000 31.69 10.98 46.27 3.02
989 1167 3.460857 ACCCTCTCATGCTTTATCGAC 57.539 47.619 0.00 0.00 0.00 4.20
1169 1347 1.449246 CAAGAAGCAGAGGCCGGAG 60.449 63.158 5.05 0.00 42.56 4.63
1170 1348 2.665000 CAAGAAGCAGAGGCCGGA 59.335 61.111 5.05 0.00 42.56 5.14
1171 1349 3.130160 GCAAGAAGCAGAGGCCGG 61.130 66.667 0.00 0.00 44.79 6.13
1180 1358 2.625737 TGTATCTGAGCAGCAAGAAGC 58.374 47.619 0.00 0.00 46.19 3.86
1181 1359 4.439968 TCATGTATCTGAGCAGCAAGAAG 58.560 43.478 0.00 0.00 0.00 2.85
1182 1360 4.476628 TCATGTATCTGAGCAGCAAGAA 57.523 40.909 0.00 0.00 0.00 2.52
1183 1361 4.684484 ATCATGTATCTGAGCAGCAAGA 57.316 40.909 0.00 0.00 0.00 3.02
1184 1362 7.545489 TCTATATCATGTATCTGAGCAGCAAG 58.455 38.462 0.00 0.00 0.00 4.01
1185 1363 7.472334 TCTATATCATGTATCTGAGCAGCAA 57.528 36.000 0.00 0.00 0.00 3.91
1186 1364 7.560626 AGATCTATATCATGTATCTGAGCAGCA 59.439 37.037 0.00 0.00 34.28 4.41
1187 1365 7.944061 AGATCTATATCATGTATCTGAGCAGC 58.056 38.462 0.00 0.00 34.28 5.25
1188 1366 9.346005 AGAGATCTATATCATGTATCTGAGCAG 57.654 37.037 0.00 0.00 34.28 4.24
1189 1367 9.341078 GAGAGATCTATATCATGTATCTGAGCA 57.659 37.037 0.00 0.00 34.28 4.26
1190 1368 9.565090 AGAGAGATCTATATCATGTATCTGAGC 57.435 37.037 0.00 0.00 34.28 4.26
1256 1434 8.117988 CCAAATTCATGCTATAAAATGTGCAAC 58.882 33.333 0.00 0.00 38.96 4.17
1278 1666 2.096174 CGTCCGACAGTGAAAAACCAAA 59.904 45.455 0.00 0.00 0.00 3.28
1282 1684 3.246699 TCAATCGTCCGACAGTGAAAAAC 59.753 43.478 0.00 0.00 0.00 2.43
1302 1704 9.434420 AGAAAAACACAAAAATTGAACAGATCA 57.566 25.926 0.00 0.00 35.85 2.92
1314 1716 5.177696 CCACACCGAAAGAAAAACACAAAAA 59.822 36.000 0.00 0.00 0.00 1.94
1327 1730 3.555956 CCTTAATCGATCCACACCGAAAG 59.444 47.826 0.00 0.00 38.36 2.62
1350 1754 7.124298 TCAAGTACTAAATGGAGAGCACACTAT 59.876 37.037 0.00 0.00 0.00 2.12
1355 1759 7.617041 AAATCAAGTACTAAATGGAGAGCAC 57.383 36.000 0.00 0.00 0.00 4.40
1357 1761 8.950208 ACTAAATCAAGTACTAAATGGAGAGC 57.050 34.615 0.00 0.00 0.00 4.09
1393 1801 5.205056 TGAACCAATTCCGGCCTAATTAAT 58.795 37.500 11.37 2.53 33.49 1.40
1442 1854 4.737352 GCATGCATATCACGTGGGATTTTT 60.737 41.667 17.00 0.00 0.00 1.94
1447 1859 0.179936 TGCATGCATATCACGTGGGA 59.820 50.000 18.46 4.05 0.00 4.37
1490 1902 4.505742 GCCAATAAATGAGGTAGAGAGGGG 60.506 50.000 0.00 0.00 0.00 4.79
1491 1903 4.349342 AGCCAATAAATGAGGTAGAGAGGG 59.651 45.833 0.00 0.00 0.00 4.30
1495 1907 4.747108 CGTCAGCCAATAAATGAGGTAGAG 59.253 45.833 0.00 0.00 0.00 2.43
1496 1908 4.404394 TCGTCAGCCAATAAATGAGGTAGA 59.596 41.667 0.00 0.00 32.24 2.59
1498 1910 4.746535 TCGTCAGCCAATAAATGAGGTA 57.253 40.909 0.00 0.00 32.24 3.08
1499 1911 3.627395 TCGTCAGCCAATAAATGAGGT 57.373 42.857 0.00 0.00 32.24 3.85
1504 1916 9.467258 CAAATAATTCATCGTCAGCCAATAAAT 57.533 29.630 0.00 0.00 0.00 1.40
1518 1941 5.919141 GTCCATGAGCAGCAAATAATTCATC 59.081 40.000 0.00 0.00 0.00 2.92
1538 1961 3.057876 GCACAATTAATTGGTGACGTCCA 60.058 43.478 27.43 1.75 41.96 4.02
1611 2061 6.443934 TTTTTCTTTGGACGAAATGACAGA 57.556 33.333 0.00 0.00 31.17 3.41
1662 2157 4.530710 TCGGATTATACTATGGTGTGCC 57.469 45.455 0.00 0.00 0.00 5.01
1680 2175 1.082117 AAGGATACACGCGCTTTCGG 61.082 55.000 5.73 0.00 41.41 4.30
1706 2201 2.354906 GGGAGAGCTAGCATGATGGATG 60.355 54.545 18.83 0.00 34.84 3.51
1710 2210 0.964700 TCGGGAGAGCTAGCATGATG 59.035 55.000 18.83 1.95 0.00 3.07
1726 2226 4.495844 GCTCTTGGTTAAAATTCGGATCGG 60.496 45.833 0.00 0.00 0.00 4.18
1749 2303 1.657094 GGTCAGCCGTACGTGTAATTG 59.343 52.381 15.21 3.40 0.00 2.32
1751 2305 1.135199 CAGGTCAGCCGTACGTGTAAT 60.135 52.381 15.21 0.00 40.50 1.89
1752 2306 0.241749 CAGGTCAGCCGTACGTGTAA 59.758 55.000 15.21 0.00 40.50 2.41
1753 2307 1.588824 CCAGGTCAGCCGTACGTGTA 61.589 60.000 15.21 0.00 40.50 2.90
1767 2336 3.136443 TGAAGAGAATGTCAACACCAGGT 59.864 43.478 0.00 0.00 0.00 4.00
1768 2337 3.499918 GTGAAGAGAATGTCAACACCAGG 59.500 47.826 0.00 0.00 31.51 4.45
1853 2433 3.443681 TCTTGACGTGAGATATGCTGACA 59.556 43.478 0.00 0.00 29.11 3.58
2008 2597 0.391661 GATTCTGTCTGAAGCCGCCA 60.392 55.000 0.00 0.00 38.18 5.69
2181 2821 1.080772 GATCGACGGTCTGCACACA 60.081 57.895 6.57 0.00 0.00 3.72
2182 2822 1.805945 GGATCGACGGTCTGCACAC 60.806 63.158 8.23 0.00 0.00 3.82
2200 2840 2.157738 CCAGCTCCTGAAAACCTCTTG 58.842 52.381 0.00 0.00 32.44 3.02
2261 2901 7.803131 TGCTAGTACTTCTACCTTCTCTGATA 58.197 38.462 0.00 0.00 0.00 2.15
2325 2968 2.675348 GCTTCCTCTGGATTTGTTCTCG 59.325 50.000 0.00 0.00 0.00 4.04
2351 3022 9.968870 AAAAATGGAGTAGTTTATTTGCGTAAA 57.031 25.926 0.00 0.00 0.00 2.01
2386 3057 5.692115 TGGCTTGATGAACATACTCCTAA 57.308 39.130 0.00 0.00 0.00 2.69
2395 3066 2.884012 ACGTTTGATGGCTTGATGAACA 59.116 40.909 0.00 0.00 0.00 3.18
2396 3067 3.559238 ACGTTTGATGGCTTGATGAAC 57.441 42.857 0.00 0.00 0.00 3.18
2397 3068 3.567585 TGAACGTTTGATGGCTTGATGAA 59.432 39.130 0.46 0.00 0.00 2.57
2398 3069 3.145286 TGAACGTTTGATGGCTTGATGA 58.855 40.909 0.46 0.00 0.00 2.92
2399 3070 3.557577 TGAACGTTTGATGGCTTGATG 57.442 42.857 0.46 0.00 0.00 3.07
2400 3071 4.699735 TGTATGAACGTTTGATGGCTTGAT 59.300 37.500 0.46 0.00 0.00 2.57
2401 3072 4.068599 TGTATGAACGTTTGATGGCTTGA 58.931 39.130 0.46 0.00 0.00 3.02
2402 3073 4.418013 TGTATGAACGTTTGATGGCTTG 57.582 40.909 0.46 0.00 0.00 4.01
2403 3074 4.675146 GCATGTATGAACGTTTGATGGCTT 60.675 41.667 0.46 0.00 0.00 4.35
2404 3075 3.181497 GCATGTATGAACGTTTGATGGCT 60.181 43.478 0.46 0.00 0.00 4.75
2405 3076 3.108144 GCATGTATGAACGTTTGATGGC 58.892 45.455 0.46 0.00 0.00 4.40
2459 3142 9.508567 CCTAACGAACTATACTTACTAACAACC 57.491 37.037 0.00 0.00 0.00 3.77
2503 3187 1.813753 CCATGGTGGTAGTTCGGCG 60.814 63.158 2.57 0.00 31.35 6.46
2507 3191 4.013728 TGTTTATGCCATGGTGGTAGTTC 58.986 43.478 14.67 0.00 40.46 3.01
2554 3241 4.641396 TGATGTTACAACAGAACTGGAGG 58.359 43.478 6.76 0.00 43.04 4.30
2611 3299 1.705337 CCGGTCGCCTGCAATAACAG 61.705 60.000 0.00 0.00 37.42 3.16
2862 3550 0.755686 AAGATGAGATGGCGAGGTCC 59.244 55.000 0.00 0.00 0.00 4.46
2872 3560 4.409574 ACATCAGAGCCAAGAAGATGAGAT 59.590 41.667 7.62 0.00 38.62 2.75
2906 3594 7.643123 TGCATCTCTATATATCTACACAGGGA 58.357 38.462 0.00 0.00 0.00 4.20
3015 4201 2.494059 GCTAGCAAGAAACCTCACACA 58.506 47.619 10.63 0.00 0.00 3.72
3016 4202 1.807142 GGCTAGCAAGAAACCTCACAC 59.193 52.381 18.24 0.00 0.00 3.82
3062 4248 5.595542 AGAAACCGTACTACTGCATGGTATA 59.404 40.000 0.00 0.00 0.00 1.47
3072 4258 6.735145 GCATGCATAGTAGAAACCGTACTACT 60.735 42.308 14.21 16.94 46.92 2.57
3073 4259 5.401674 GCATGCATAGTAGAAACCGTACTAC 59.598 44.000 14.21 0.00 36.13 2.73
3074 4260 5.068067 TGCATGCATAGTAGAAACCGTACTA 59.932 40.000 18.46 0.00 37.38 1.82
3248 4464 2.105993 GACTAAACTTCCCACCACCTGT 59.894 50.000 0.00 0.00 0.00 4.00
3278 4494 4.027437 GGGTCTCAACTCTCCTCAACTAT 58.973 47.826 0.00 0.00 0.00 2.12
3321 4537 1.616725 CCAAGCTCCCAATGGCAAGTA 60.617 52.381 0.00 0.00 0.00 2.24
3361 4577 0.323908 CGGAGGAGGAGGAAGAGTGT 60.324 60.000 0.00 0.00 0.00 3.55
3363 4579 1.380650 GCGGAGGAGGAGGAAGAGT 60.381 63.158 0.00 0.00 0.00 3.24
3365 4581 2.042843 GGCGGAGGAGGAGGAAGA 60.043 66.667 0.00 0.00 0.00 2.87
3366 4582 2.364317 TGGCGGAGGAGGAGGAAG 60.364 66.667 0.00 0.00 0.00 3.46
3367 4583 2.683933 GTGGCGGAGGAGGAGGAA 60.684 66.667 0.00 0.00 0.00 3.36
3478 4812 1.421646 CAGAACATAGATGGGGTCCCC 59.578 57.143 21.64 21.64 45.71 4.81
3479 4813 2.127708 ACAGAACATAGATGGGGTCCC 58.872 52.381 0.00 0.00 0.00 4.46
3480 4814 3.243771 CGTACAGAACATAGATGGGGTCC 60.244 52.174 0.00 0.00 0.00 4.46
3481 4815 3.383825 ACGTACAGAACATAGATGGGGTC 59.616 47.826 0.00 0.00 0.00 4.46
3482 4816 3.132289 CACGTACAGAACATAGATGGGGT 59.868 47.826 0.00 0.00 0.00 4.95
3483 4817 3.717707 CACGTACAGAACATAGATGGGG 58.282 50.000 0.00 0.00 0.00 4.96
3484 4818 3.123804 GCACGTACAGAACATAGATGGG 58.876 50.000 0.00 0.00 0.00 4.00
3485 4819 4.046938 AGCACGTACAGAACATAGATGG 57.953 45.455 0.00 0.00 0.00 3.51
3486 4820 5.822278 ACTAGCACGTACAGAACATAGATG 58.178 41.667 0.00 0.00 0.00 2.90
3487 4821 6.541278 TGTACTAGCACGTACAGAACATAGAT 59.459 38.462 12.48 0.00 43.36 1.98
3511 4845 4.926238 GCATCTCATACCGATTCCTAACTG 59.074 45.833 0.00 0.00 0.00 3.16
3512 4846 4.588951 TGCATCTCATACCGATTCCTAACT 59.411 41.667 0.00 0.00 0.00 2.24
3513 4847 4.883083 TGCATCTCATACCGATTCCTAAC 58.117 43.478 0.00 0.00 0.00 2.34
3531 4865 1.370437 TGGCAAAAACGGCATGCAT 59.630 47.368 21.36 3.56 41.80 3.96
3537 4871 2.008752 ATAAGCATGGCAAAAACGGC 57.991 45.000 0.00 0.00 0.00 5.68
3560 4894 7.273320 TCCAATTAGACTAATCCACGAGTAG 57.727 40.000 8.17 0.00 36.47 2.57
3735 5069 0.185901 ACAGCACCAACCCAGAACAT 59.814 50.000 0.00 0.00 0.00 2.71
3786 5120 1.254026 GCCTCCCTAAACGCCTTTTT 58.746 50.000 0.00 0.00 0.00 1.94
3823 5157 3.958147 TCCGATCACAGTAAGAATGGCTA 59.042 43.478 0.00 0.00 0.00 3.93
3828 5162 5.186021 ACTTGTCTCCGATCACAGTAAGAAT 59.814 40.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.