Multiple sequence alignment - TraesCS3D01G452200

Loading Multiple Alignment...

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 TraesCS3D01G452200 chr3D 100.000 4883 0 0 1 4883 560026983 560022101 0.000000e+00 9018.0
1 TraesCS3D01G452200 chr3D 85.069 288 39 4 1 285 577147600 577147886 1.720000e-74 291.0
2 TraesCS3D01G452200 chr3D 85.246 122 15 2 4764 4883 236639143 236639263 6.640000e-24 122.0
3 TraesCS3D01G452200 chr1B 92.216 2672 148 32 1707 4359 4519388 4516758 0.000000e+00 3727.0
4 TraesCS3D01G452200 chr1B 91.339 2725 205 15 1708 4417 4109787 4112495 0.000000e+00 3696.0
5 TraesCS3D01G452200 chr1B 92.509 2256 150 9 1707 3954 4144343 4146587 0.000000e+00 3212.0
6 TraesCS3D01G452200 chr1B 88.638 2526 225 34 2120 4603 4597569 4595064 0.000000e+00 3018.0
7 TraesCS3D01G452200 chr1B 87.481 2636 204 48 2076 4629 46830379 46827788 0.000000e+00 2924.0
8 TraesCS3D01G452200 chr1B 88.697 1734 80 38 1 1656 4521100 4519405 0.000000e+00 2010.0
9 TraesCS3D01G452200 chr1B 80.819 1319 134 58 486 1743 46690477 46691737 0.000000e+00 924.0
10 TraesCS3D01G452200 chr1B 92.269 401 20 5 1263 1656 538505114 538505510 4.270000e-155 558.0
11 TraesCS3D01G452200 chr1B 95.335 343 16 0 1711 2053 538505531 538505873 3.320000e-151 545.0
12 TraesCS3D01G452200 chr1B 82.971 552 56 25 3903 4440 46693721 46694248 9.570000e-127 464.0
13 TraesCS3D01G452200 chr1B 77.597 799 91 49 693 1456 46831142 46830397 2.120000e-108 403.0
14 TraesCS3D01G452200 chr1B 80.174 575 54 34 1111 1656 4143783 4144326 4.610000e-100 375.0
15 TraesCS3D01G452200 chr1B 94.819 193 8 1 293 483 46675040 46675232 2.860000e-77 300.0
16 TraesCS3D01G452200 chr1B 77.329 644 56 48 746 1328 4955744 4955130 1.030000e-76 298.0
17 TraesCS3D01G452200 chr1B 80.328 427 31 29 1323 1743 4543325 4542946 1.730000e-69 274.0
18 TraesCS3D01G452200 chr1B 82.935 293 42 7 1 289 53839786 53839498 1.740000e-64 257.0
19 TraesCS3D01G452200 chr1B 75.662 604 79 33 487 1041 4108680 4109264 6.320000e-59 239.0
20 TraesCS3D01G452200 chr1B 94.156 154 6 2 1579 1732 585356800 585356950 1.060000e-56 231.0
21 TraesCS3D01G452200 chr1B 85.778 225 15 12 1471 1683 4597980 4597761 6.360000e-54 222.0
22 TraesCS3D01G452200 chr1B 91.772 158 6 3 4603 4759 4797575 4797424 3.830000e-51 213.0
23 TraesCS3D01G452200 chr1B 78.158 380 42 26 1200 1550 4542982 4542615 2.300000e-48 204.0
24 TraesCS3D01G452200 chr1B 90.066 151 5 6 1323 1469 4597745 4597601 2.320000e-43 187.0
25 TraesCS3D01G452200 chr1B 88.024 167 5 8 1309 1470 4955100 4954944 3.000000e-42 183.0
26 TraesCS3D01G452200 chr1B 82.716 162 23 4 605 766 70231885 70232041 6.590000e-29 139.0
27 TraesCS3D01G452200 chr1B 77.778 252 22 18 1778 2013 4143927 4144160 1.850000e-24 124.0
28 TraesCS3D01G452200 chr1B 87.356 87 5 1 4624 4710 46694578 46694658 1.450000e-15 95.3
29 TraesCS3D01G452200 chr1B 95.918 49 2 0 4458 4506 4516590 4516542 4.050000e-11 80.5
30 TraesCS3D01G452200 chr1B 81.443 97 7 4 992 1077 4143670 4143766 8.770000e-08 69.4
31 TraesCS3D01G452200 chr1B 82.857 70 9 1 4563 4629 4516500 4516431 5.280000e-05 60.2
32 TraesCS3D01G452200 chr6A 88.479 2630 227 35 2014 4602 613493534 613496128 0.000000e+00 3109.0
33 TraesCS3D01G452200 chr6A 85.090 1442 143 39 3091 4499 64065208 64063806 0.000000e+00 1406.0
34 TraesCS3D01G452200 chr6A 77.320 1067 129 64 524 1550 613492098 613493091 4.330000e-145 525.0
35 TraesCS3D01G452200 chr6A 84.980 253 23 8 1465 1713 613493556 613493797 4.880000e-60 243.0
36 TraesCS3D01G452200 chr6A 82.818 291 29 7 1 287 48638076 48638349 1.760000e-59 241.0
37 TraesCS3D01G452200 chr6A 83.439 157 9 9 4603 4759 613496187 613496326 3.970000e-26 130.0
38 TraesCS3D01G452200 chr6A 92.982 57 1 3 4624 4680 64063480 64063427 4.050000e-11 80.5
39 TraesCS3D01G452200 chr5B 88.260 2649 221 43 1994 4583 60826101 60823484 0.000000e+00 3086.0
40 TraesCS3D01G452200 chr5B 81.282 390 52 13 524 894 60827176 60826789 3.700000e-76 296.0
41 TraesCS3D01G452200 chr5B 87.649 251 19 8 1465 1713 60826059 60825819 1.030000e-71 281.0
42 TraesCS3D01G452200 chr5D 89.225 2348 194 32 1994 4304 57819423 57821748 0.000000e+00 2880.0
43 TraesCS3D01G452200 chr5D 83.288 365 36 10 1319 1663 535497279 535496920 3.670000e-81 313.0
44 TraesCS3D01G452200 chr5D 86.296 270 30 5 524 787 57818291 57818559 2.220000e-73 287.0
45 TraesCS3D01G452200 chr5D 86.381 257 22 7 1458 1713 57819460 57819704 8.060000e-68 268.0
46 TraesCS3D01G452200 chr5D 83.065 124 11 2 4453 4567 497870071 497870193 2.400000e-18 104.0
47 TraesCS3D01G452200 chr1A 95.539 1771 78 1 2399 4168 3013317 3015087 0.000000e+00 2832.0
48 TraesCS3D01G452200 chr1A 89.553 2259 185 34 2155 4380 2943275 2945515 0.000000e+00 2817.0
49 TraesCS3D01G452200 chr1A 82.353 510 51 23 4118 4603 3015087 3015581 1.640000e-109 407.0
50 TraesCS3D01G452200 chr1A 95.495 111 5 0 1633 1743 2949333 2949443 1.400000e-40 178.0
51 TraesCS3D01G452200 chr1A 92.553 94 6 1 4668 4761 32548113 32548205 3.070000e-27 134.0
52 TraesCS3D01G452200 chr1A 81.657 169 10 11 1027 1177 2942228 2942393 2.390000e-23 121.0
53 TraesCS3D01G452200 chr6B 87.372 2534 235 48 2006 4499 120132994 120130506 0.000000e+00 2828.0
54 TraesCS3D01G452200 chr6B 85.587 2692 266 62 1772 4440 120355401 120352809 0.000000e+00 2710.0
55 TraesCS3D01G452200 chr6B 92.982 57 1 3 4624 4680 120130177 120130124 4.050000e-11 80.5
56 TraesCS3D01G452200 chr6B 93.333 45 3 0 4553 4597 120217716 120217672 3.150000e-07 67.6
57 TraesCS3D01G452200 chr6D 85.891 2587 256 55 1977 4506 53144956 53142422 0.000000e+00 2654.0
58 TraesCS3D01G452200 chr6D 85.246 122 15 2 4764 4883 325339058 325338938 6.640000e-24 122.0
59 TraesCS3D01G452200 chr6D 95.556 45 2 0 4553 4597 51076572 51076616 6.780000e-09 73.1
60 TraesCS3D01G452200 chr6D 95.556 45 2 0 4553 4597 51351387 51351431 6.780000e-09 73.1
61 TraesCS3D01G452200 chr1D 83.903 702 66 16 3930 4602 387236 387919 1.150000e-175 627.0
62 TraesCS3D01G452200 chr1D 83.849 291 44 3 1 289 35596301 35596012 1.730000e-69 274.0
63 TraesCS3D01G452200 chr1D 81.659 229 34 8 1 226 260606527 260606750 3.000000e-42 183.0
64 TraesCS3D01G452200 chr1D 91.489 94 7 1 4668 4761 33988264 33988356 1.430000e-25 128.0
65 TraesCS3D01G452200 chr1D 85.246 122 15 2 4764 4883 90379774 90379894 6.640000e-24 122.0
66 TraesCS3D01G452200 chr2B 93.267 401 16 5 1263 1656 741895653 741896049 9.110000e-162 580.0
67 TraesCS3D01G452200 chr2B 92.711 343 13 1 1711 2053 741896070 741896400 7.350000e-133 484.0
68 TraesCS3D01G452200 chr4A 92.553 188 11 2 1558 1743 666694471 666694285 2.900000e-67 267.0
69 TraesCS3D01G452200 chr4A 93.443 122 8 0 4762 4883 234383177 234383056 1.080000e-41 182.0
70 TraesCS3D01G452200 chr4A 92.982 114 8 0 4770 4883 234372859 234372746 3.020000e-37 167.0
71 TraesCS3D01G452200 chr4A 81.818 187 25 5 105 289 133829997 133829818 1.100000e-31 148.0
72 TraesCS3D01G452200 chr4A 85.034 147 18 4 2142 2288 666694037 666693895 3.940000e-31 147.0
73 TraesCS3D01G452200 chr4A 79.268 246 18 11 1200 1432 666694321 666694096 1.830000e-29 141.0
74 TraesCS3D01G452200 chr4A 100.000 29 0 0 1781 1809 666694255 666694227 2.000000e-03 54.7
75 TraesCS3D01G452200 chr4D 83.219 292 39 9 1 289 483207895 483208179 4.850000e-65 259.0
76 TraesCS3D01G452200 chr4D 86.066 122 14 2 4764 4883 487699719 487699839 1.430000e-25 128.0
77 TraesCS3D01G452200 chr4D 85.246 122 15 2 4764 4883 178566843 178566723 6.640000e-24 122.0
78 TraesCS3D01G452200 chr4D 85.246 122 15 2 4764 4883 252474153 252474273 6.640000e-24 122.0
79 TraesCS3D01G452200 chr4D 85.246 122 15 2 4764 4883 298686526 298686646 6.640000e-24 122.0
80 TraesCS3D01G452200 chr5A 81.379 290 40 13 5 290 665890794 665891073 1.770000e-54 224.0
81 TraesCS3D01G452200 chr7B 82.716 243 35 6 51 289 714839686 714839447 4.950000e-50 209.0
82 TraesCS3D01G452200 chr7B 90.265 113 9 1 1990 2102 216661810 216661920 3.940000e-31 147.0
83 TraesCS3D01G452200 chr7D 81.928 249 23 17 1465 1713 548231014 548231240 1.790000e-44 191.0
84 TraesCS3D01G452200 chrUn 95.495 111 5 0 1633 1743 325465674 325465784 1.400000e-40 178.0


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 TraesCS3D01G452200 chr3D 560022101 560026983 4882 True 9018.000000 9018 100.000000 1 4883 1 chr3D.!!$R1 4882
1 TraesCS3D01G452200 chr1B 4108680 4112495 3815 False 1967.500000 3696 83.500500 487 4417 2 chr1B.!!$F4 3930
2 TraesCS3D01G452200 chr1B 46827788 46831142 3354 True 1663.500000 2924 82.539000 693 4629 2 chr1B.!!$R7 3936
3 TraesCS3D01G452200 chr1B 4516431 4521100 4669 True 1469.425000 3727 89.922000 1 4629 4 chr1B.!!$R3 4628
4 TraesCS3D01G452200 chr1B 4595064 4597980 2916 True 1142.333333 3018 88.160667 1323 4603 3 chr1B.!!$R5 3280
5 TraesCS3D01G452200 chr1B 4143670 4146587 2917 False 945.100000 3212 82.976000 992 3954 4 chr1B.!!$F5 2962
6 TraesCS3D01G452200 chr1B 538505114 538505873 759 False 551.500000 558 93.802000 1263 2053 2 chr1B.!!$F7 790
7 TraesCS3D01G452200 chr1B 46690477 46694658 4181 False 494.433333 924 83.715333 486 4710 3 chr1B.!!$F6 4224
8 TraesCS3D01G452200 chr1B 4954944 4955744 800 True 240.500000 298 82.676500 746 1470 2 chr1B.!!$R6 724
9 TraesCS3D01G452200 chr1B 4542615 4543325 710 True 239.000000 274 79.243000 1200 1743 2 chr1B.!!$R4 543
10 TraesCS3D01G452200 chr6A 613492098 613496326 4228 False 1001.750000 3109 83.554500 524 4759 4 chr6A.!!$F2 4235
11 TraesCS3D01G452200 chr6A 64063427 64065208 1781 True 743.250000 1406 89.036000 3091 4680 2 chr6A.!!$R1 1589
12 TraesCS3D01G452200 chr5B 60823484 60827176 3692 True 1221.000000 3086 85.730333 524 4583 3 chr5B.!!$R1 4059
13 TraesCS3D01G452200 chr5D 57818291 57821748 3457 False 1145.000000 2880 87.300667 524 4304 3 chr5D.!!$F2 3780
14 TraesCS3D01G452200 chr1A 3013317 3015581 2264 False 1619.500000 2832 88.946000 2399 4603 2 chr1A.!!$F3 2204
15 TraesCS3D01G452200 chr1A 2942228 2949443 7215 False 1038.666667 2817 88.901667 1027 4380 3 chr1A.!!$F2 3353
16 TraesCS3D01G452200 chr6B 120352809 120355401 2592 True 2710.000000 2710 85.587000 1772 4440 1 chr6B.!!$R2 2668
17 TraesCS3D01G452200 chr6B 120130124 120132994 2870 True 1454.250000 2828 90.177000 2006 4680 2 chr6B.!!$R3 2674
18 TraesCS3D01G452200 chr6D 53142422 53144956 2534 True 2654.000000 2654 85.891000 1977 4506 1 chr6D.!!$R1 2529
19 TraesCS3D01G452200 chr1D 387236 387919 683 False 627.000000 627 83.903000 3930 4602 1 chr1D.!!$F1 672
20 TraesCS3D01G452200 chr2B 741895653 741896400 747 False 532.000000 580 92.989000 1263 2053 2 chr2B.!!$F1 790

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
243 245 0.677842 GGTACGTTGAGGTGGACACT 59.322 55.000 0.00 0.0 0.00 3.55 F
1117 1425 0.887836 GTTGGTTCCCCGACTTGACC 60.888 60.000 0.00 0.0 41.39 4.02 F
1330 2203 0.321564 TTGGCCCTGTGAACTCATCG 60.322 55.000 0.00 0.0 0.00 3.84 F
1881 2998 1.689273 ACCCTATGAACTCATCGGCTC 59.311 52.381 5.01 0.0 37.74 4.70 F
2603 4359 0.179181 GCACTGACATCATTGTGCGG 60.179 55.000 9.63 0.0 44.60 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1325 2198 0.527113 CATTTTGCCACAGCCGATGA 59.473 50.000 0.00 0.00 38.69 2.92 R
2002 3177 1.557099 AGACCCACGTGCTGAATCTA 58.443 50.000 10.91 0.00 0.00 1.98 R
2603 4359 2.094066 CGCAAATTTGGGAAGCGGC 61.094 57.895 26.35 6.14 44.20 6.53 R
2934 4691 3.436180 GCTCTTCCAATGATCCATCCCTT 60.436 47.826 0.00 0.00 0.00 3.95 R
4320 6296 1.067283 CCATACCAAAATTGCCACGCA 60.067 47.619 0.00 0.00 36.47 5.24 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
90 92 5.710513 TTCAGACCAAAATGTGAAGGATG 57.289 39.130 0.00 0.00 29.23 3.51
134 136 5.923114 GTGGTAGCATGACATACATAGACTG 59.077 44.000 0.00 0.00 37.46 3.51
173 175 2.671130 TGCATGACTCGCTTATGTGA 57.329 45.000 0.00 0.00 0.00 3.58
203 205 2.911484 CATGGCTTAGTGGGAGAGAAC 58.089 52.381 0.00 0.00 0.00 3.01
226 228 3.828451 ACTTCAATGCATTGCTTAGTGGT 59.172 39.130 30.57 17.73 37.68 4.16
228 230 4.963276 TCAATGCATTGCTTAGTGGTAC 57.037 40.909 30.57 0.00 37.68 3.34
243 245 0.677842 GGTACGTTGAGGTGGACACT 59.322 55.000 0.00 0.00 0.00 3.55
250 252 4.039488 ACGTTGAGGTGGACACTTTACATA 59.961 41.667 2.13 0.00 0.00 2.29
277 279 7.741785 TGAGAGAATTGGTACCAACTTCTTAA 58.258 34.615 31.24 23.22 38.88 1.85
278 280 7.878127 TGAGAGAATTGGTACCAACTTCTTAAG 59.122 37.037 31.24 0.00 38.88 1.85
281 283 8.990163 AGAATTGGTACCAACTTCTTAAGAAA 57.010 30.769 29.35 2.74 38.88 2.52
315 317 8.669243 AGAGATTAATTAGAGAAAAAGTTGCCG 58.331 33.333 0.00 0.00 0.00 5.69
384 386 6.087820 GTCGAAAAGTGTCATGTCAGTAGTAC 59.912 42.308 0.54 0.00 0.00 2.73
517 519 7.278646 CCGAAATACTCATATGGATGTACATGG 59.721 40.741 14.43 0.00 34.41 3.66
520 522 3.652387 ACTCATATGGATGTACATGGGCA 59.348 43.478 14.43 0.00 34.41 5.36
521 523 4.290459 ACTCATATGGATGTACATGGGCAT 59.710 41.667 14.43 0.30 34.41 4.40
522 524 5.222192 ACTCATATGGATGTACATGGGCATT 60.222 40.000 14.43 0.00 34.41 3.56
619 636 5.878332 TTGATACATGTGAACATTTCGCT 57.122 34.783 9.11 0.00 40.72 4.93
1022 1302 2.362632 CTCCTCTCCCGGTCGGTT 60.363 66.667 8.67 0.00 0.00 4.44
1023 1303 2.362120 TCCTCTCCCGGTCGGTTC 60.362 66.667 8.67 0.00 0.00 3.62
1089 1391 2.364961 CCCTCCCTCCCTCTTCGT 59.635 66.667 0.00 0.00 0.00 3.85
1117 1425 0.887836 GTTGGTTCCCCGACTTGACC 60.888 60.000 0.00 0.00 41.39 4.02
1118 1426 2.047560 GGTTCCCCGACTTGACCG 60.048 66.667 0.00 0.00 0.00 4.79
1119 1427 2.741211 GTTCCCCGACTTGACCGC 60.741 66.667 0.00 0.00 0.00 5.68
1123 1431 4.675029 CCCGACTTGACCGCCGTT 62.675 66.667 0.00 0.00 0.00 4.44
1157 1482 6.467723 TTCGCTTTCTTGTTCTTGATAGAC 57.532 37.500 0.00 0.00 0.00 2.59
1183 1513 2.678471 AACCAAACCCGGTAGTATCG 57.322 50.000 0.00 0.00 38.76 2.92
1195 1530 2.496470 GGTAGTATCGTCCCCATCCATC 59.504 54.545 0.00 0.00 0.00 3.51
1196 1531 1.645710 AGTATCGTCCCCATCCATCC 58.354 55.000 0.00 0.00 0.00 3.51
1321 2194 4.978099 ACAGATATTAGATTGGCCCTGTG 58.022 43.478 0.00 0.00 33.05 3.66
1322 2195 4.660303 ACAGATATTAGATTGGCCCTGTGA 59.340 41.667 0.00 0.00 33.05 3.58
1324 2197 5.471456 CAGATATTAGATTGGCCCTGTGAAC 59.529 44.000 0.00 0.00 0.00 3.18
1325 2198 5.370880 AGATATTAGATTGGCCCTGTGAACT 59.629 40.000 0.00 0.00 0.00 3.01
1326 2199 3.350219 TTAGATTGGCCCTGTGAACTC 57.650 47.619 0.00 0.00 0.00 3.01
1329 2202 2.019984 GATTGGCCCTGTGAACTCATC 58.980 52.381 0.00 0.00 0.00 2.92
1330 2203 0.321564 TTGGCCCTGTGAACTCATCG 60.322 55.000 0.00 0.00 0.00 3.84
1352 2394 4.004982 GGCTGTGGCAAAATGATTGATTT 58.995 39.130 0.00 0.00 40.87 2.17
1353 2395 4.093850 GGCTGTGGCAAAATGATTGATTTC 59.906 41.667 0.00 0.00 40.87 2.17
1354 2396 4.093850 GCTGTGGCAAAATGATTGATTTCC 59.906 41.667 0.00 0.00 32.76 3.13
1355 2397 4.577875 TGTGGCAAAATGATTGATTTCCC 58.422 39.130 0.00 0.00 32.76 3.97
1358 2400 6.044682 GTGGCAAAATGATTGATTTCCCTAG 58.955 40.000 0.00 0.00 32.76 3.02
1376 2430 4.019231 CCCTAGTACTTTCTTTCTTGCCCT 60.019 45.833 0.00 0.00 0.00 5.19
1545 2627 5.945784 TCTGCTTGCTTCTTAATTATGGTGT 59.054 36.000 0.00 0.00 0.00 4.16
1551 2633 7.938140 TGCTTCTTAATTATGGTGTTAGCTT 57.062 32.000 0.00 0.00 0.00 3.74
1575 2657 9.590451 CTTGTTTAATTTAATGATGATGTGGCT 57.410 29.630 0.00 0.00 0.00 4.75
1629 2716 6.892658 ATCTAGACACAGATAAGGTGCTAG 57.107 41.667 0.00 13.13 40.41 3.42
1633 2720 4.582656 AGACACAGATAAGGTGCTAGCTAG 59.417 45.833 16.84 16.84 39.87 3.42
1656 2743 7.552050 AGCTACTCTAATAAATCTCCATGCT 57.448 36.000 0.00 0.00 0.00 3.79
1658 2745 9.094578 AGCTACTCTAATAAATCTCCATGCTTA 57.905 33.333 0.00 0.00 0.00 3.09
1659 2746 9.883142 GCTACTCTAATAAATCTCCATGCTTAT 57.117 33.333 0.00 0.00 0.00 1.73
1667 2754 6.839124 AAATCTCCATGCTTATGAACAACA 57.161 33.333 0.00 0.00 0.00 3.33
1668 2755 5.824904 ATCTCCATGCTTATGAACAACAC 57.175 39.130 0.00 0.00 0.00 3.32
1669 2756 4.650734 TCTCCATGCTTATGAACAACACA 58.349 39.130 0.00 0.00 0.00 3.72
1673 2760 4.022935 CCATGCTTATGAACAACACACAGT 60.023 41.667 0.00 0.00 0.00 3.55
1675 2762 6.293900 CCATGCTTATGAACAACACACAGTTA 60.294 38.462 0.00 0.00 38.74 2.24
1676 2763 6.685527 TGCTTATGAACAACACACAGTTAA 57.314 33.333 0.00 0.00 38.74 2.01
1677 2764 6.724263 TGCTTATGAACAACACACAGTTAAG 58.276 36.000 0.00 0.00 38.74 1.85
1680 2767 7.700656 GCTTATGAACAACACACAGTTAAGTTT 59.299 33.333 0.00 0.00 38.74 2.66
1681 2768 9.567848 CTTATGAACAACACACAGTTAAGTTTT 57.432 29.630 0.00 0.00 38.74 2.43
1682 2769 7.810766 ATGAACAACACACAGTTAAGTTTTG 57.189 32.000 0.00 0.00 38.74 2.44
1683 2770 6.153067 TGAACAACACACAGTTAAGTTTTGG 58.847 36.000 0.00 0.00 38.74 3.28
1684 2771 5.968528 ACAACACACAGTTAAGTTTTGGA 57.031 34.783 0.00 0.00 38.74 3.53
1685 2772 5.705902 ACAACACACAGTTAAGTTTTGGAC 58.294 37.500 0.00 0.00 38.74 4.02
1687 2774 5.560966 ACACACAGTTAAGTTTTGGACAG 57.439 39.130 0.00 0.00 0.00 3.51
1688 2775 5.250200 ACACACAGTTAAGTTTTGGACAGA 58.750 37.500 0.00 0.00 0.00 3.41
1689 2776 5.885912 ACACACAGTTAAGTTTTGGACAGAT 59.114 36.000 0.00 0.00 0.00 2.90
1690 2777 7.051623 ACACACAGTTAAGTTTTGGACAGATA 58.948 34.615 0.00 0.00 0.00 1.98
1691 2778 7.012044 ACACACAGTTAAGTTTTGGACAGATAC 59.988 37.037 0.00 0.00 0.00 2.24
1692 2779 7.011950 CACACAGTTAAGTTTTGGACAGATACA 59.988 37.037 0.00 0.00 0.00 2.29
1693 2780 7.226720 ACACAGTTAAGTTTTGGACAGATACAG 59.773 37.037 0.00 0.00 0.00 2.74
1694 2781 6.204882 ACAGTTAAGTTTTGGACAGATACAGC 59.795 38.462 0.00 0.00 0.00 4.40
1695 2782 6.204688 CAGTTAAGTTTTGGACAGATACAGCA 59.795 38.462 0.00 0.00 0.00 4.41
1696 2783 6.428159 AGTTAAGTTTTGGACAGATACAGCAG 59.572 38.462 0.00 0.00 0.00 4.24
1697 2784 4.623932 AGTTTTGGACAGATACAGCAGA 57.376 40.909 0.00 0.00 0.00 4.26
1698 2785 4.973168 AGTTTTGGACAGATACAGCAGAA 58.027 39.130 0.00 0.00 0.00 3.02
1700 2787 5.471456 AGTTTTGGACAGATACAGCAGAAAG 59.529 40.000 0.00 0.00 0.00 2.62
1701 2788 4.623932 TTGGACAGATACAGCAGAAAGT 57.376 40.909 0.00 0.00 0.00 2.66
1702 2789 3.930336 TGGACAGATACAGCAGAAAGTG 58.070 45.455 0.00 0.00 0.00 3.16
1744 2849 4.407945 TGTAAAGCCATTCTCCTAGGTACC 59.592 45.833 9.08 2.73 0.00 3.34
1746 2857 3.352611 AGCCATTCTCCTAGGTACCAT 57.647 47.619 15.94 1.66 0.00 3.55
1750 2861 5.852250 AGCCATTCTCCTAGGTACCATAAAT 59.148 40.000 15.94 2.20 0.00 1.40
1769 2881 8.223100 CCATAAATTAAGCTTTTTGCAACTGAC 58.777 33.333 3.20 0.00 45.94 3.51
1802 2914 3.877508 CCTAGGGTTGCAGCAAATACTAC 59.122 47.826 10.11 0.00 0.00 2.73
1803 2915 3.721087 AGGGTTGCAGCAAATACTACT 57.279 42.857 10.11 0.00 0.00 2.57
1804 2916 3.347216 AGGGTTGCAGCAAATACTACTG 58.653 45.455 10.11 0.00 34.48 2.74
1806 2918 4.019681 AGGGTTGCAGCAAATACTACTGTA 60.020 41.667 10.11 0.00 33.87 2.74
1881 2998 1.689273 ACCCTATGAACTCATCGGCTC 59.311 52.381 5.01 0.00 37.74 4.70
1895 3012 5.427378 TCATCGGCTCTGTCAAAATGATTA 58.573 37.500 0.00 0.00 0.00 1.75
1906 3023 8.966868 TCTGTCAAAATGATTAATTTCCCTACC 58.033 33.333 0.00 0.00 37.51 3.18
1916 3033 9.822727 TGATTAATTTCCCTACCTTCTTTCTTT 57.177 29.630 0.00 0.00 0.00 2.52
1960 3079 8.526147 AGTACTAATTTCAATTTGCATGCTCTT 58.474 29.630 20.33 6.69 0.00 2.85
2118 3404 7.014326 TCTGCTACTTTATGGTGGTATCTAGTG 59.986 40.741 0.00 0.00 0.00 2.74
2325 4045 6.647334 TCTGATCTCCATCTATCTTCACAC 57.353 41.667 0.00 0.00 0.00 3.82
2359 4094 7.972277 TCTGATGTATCGTAAGTTTTAGTCCAC 59.028 37.037 0.00 0.00 39.48 4.02
2522 4276 2.759191 TGTGTCAAAGCAGCTCTACAG 58.241 47.619 0.00 0.00 0.00 2.74
2603 4359 0.179181 GCACTGACATCATTGTGCGG 60.179 55.000 9.63 0.00 44.60 5.69
2634 4390 4.514816 CCAAATTTGCGGAAAGTGGAAATT 59.485 37.500 22.81 3.21 45.42 1.82
2676 4432 1.684248 GGACATGGAAAGCAGCTGGAT 60.684 52.381 17.12 0.00 0.00 3.41
2777 4533 0.771127 TCTGGGCTTGGTTGCTTAGT 59.229 50.000 0.00 0.00 0.00 2.24
2934 4691 1.559682 GAGTGGCTGGAATACCTTGGA 59.440 52.381 0.00 0.00 37.04 3.53
2998 4755 7.629866 GCAAAGGAATCAATCATCATGACTTCA 60.630 37.037 0.00 0.00 0.00 3.02
3057 4815 5.373812 TTGAGTTTGAGAGGAAAAGAGGT 57.626 39.130 0.00 0.00 0.00 3.85
3116 4886 2.760650 ACTCCTCGTATGATGCTCACAA 59.239 45.455 0.00 0.00 0.00 3.33
3213 4983 2.577105 AGGACTTCGAGTTCTCCTAGGA 59.423 50.000 11.98 11.98 23.20 2.94
3375 5145 3.901222 TCAACTATTGTGAGACCAGGACA 59.099 43.478 0.00 0.00 0.00 4.02
3390 5160 7.504403 AGACCAGGACATCATTTACTGATAAG 58.496 38.462 0.00 0.00 42.91 1.73
3593 5363 1.773653 GATGAAGGCCCTCTCATCCTT 59.226 52.381 21.52 0.00 42.47 3.36
3744 5514 0.694771 TGGCTGAACTGGAAGATGCT 59.305 50.000 0.00 0.00 37.43 3.79
4320 6296 7.013823 ACATATATCTCTGCCTGCTATGTTT 57.986 36.000 0.00 0.00 0.00 2.83
4345 6321 4.202141 CGTGGCAATTTTGGTATGGATCAT 60.202 41.667 0.00 0.00 0.00 2.45
4346 6322 5.673514 GTGGCAATTTTGGTATGGATCATT 58.326 37.500 0.00 0.00 0.00 2.57
4442 6427 5.087323 ACTCTACTGGAGGATGTCTTTCAA 58.913 41.667 0.00 0.00 45.83 2.69
4443 6428 5.544176 ACTCTACTGGAGGATGTCTTTCAAA 59.456 40.000 0.00 0.00 45.83 2.69
4444 6429 6.043243 ACTCTACTGGAGGATGTCTTTCAAAA 59.957 38.462 0.00 0.00 45.83 2.44
4445 6430 7.020827 TCTACTGGAGGATGTCTTTCAAAAT 57.979 36.000 0.00 0.00 0.00 1.82
4446 6431 8.146053 TCTACTGGAGGATGTCTTTCAAAATA 57.854 34.615 0.00 0.00 0.00 1.40
4447 6432 8.602424 TCTACTGGAGGATGTCTTTCAAAATAA 58.398 33.333 0.00 0.00 0.00 1.40
4448 6433 9.401058 CTACTGGAGGATGTCTTTCAAAATAAT 57.599 33.333 0.00 0.00 0.00 1.28
4450 6435 9.753674 ACTGGAGGATGTCTTTCAAAATAATTA 57.246 29.630 0.00 0.00 0.00 1.40
4452 6437 9.753674 TGGAGGATGTCTTTCAAAATAATTACT 57.246 29.630 0.00 0.00 0.00 2.24
4502 6592 5.047566 TCCAAAATGACCTGAAGTTGAGA 57.952 39.130 0.00 0.00 0.00 3.27
4506 6596 6.183360 CCAAAATGACCTGAAGTTGAGAAACT 60.183 38.462 0.00 0.00 33.76 2.66
4507 6597 7.260603 CAAAATGACCTGAAGTTGAGAAACTT 58.739 34.615 3.61 3.61 44.95 2.66
4509 6599 5.097742 TGACCTGAAGTTGAGAAACTTGA 57.902 39.130 8.49 0.00 42.57 3.02
4511 6601 5.104259 ACCTGAAGTTGAGAAACTTGAGT 57.896 39.130 14.04 5.01 40.74 3.41
4603 6783 3.826524 TGGACATCCAGCACTAAACAAA 58.173 40.909 0.00 0.00 42.01 2.83
4605 6785 4.278170 TGGACATCCAGCACTAAACAAAAG 59.722 41.667 0.00 0.00 42.01 2.27
4727 8926 5.371115 TTTGCCTTGTATTTGTAGCTCAC 57.629 39.130 0.00 0.00 0.00 3.51
4730 8929 3.375299 GCCTTGTATTTGTAGCTCACCAG 59.625 47.826 0.00 0.00 0.00 4.00
4743 8942 1.542915 CTCACCAGGATGCCAACTTTG 59.457 52.381 0.00 0.00 31.97 2.77
4753 8952 0.179076 GCCAACTTTGCTTTGCTGGT 60.179 50.000 0.00 0.00 0.00 4.00
4759 8958 4.670896 ACTTTGCTTTGCTGGTTATGTT 57.329 36.364 0.00 0.00 0.00 2.71
4763 8962 7.891561 ACTTTGCTTTGCTGGTTATGTTATAA 58.108 30.769 0.00 0.00 0.00 0.98
4764 8963 7.812669 ACTTTGCTTTGCTGGTTATGTTATAAC 59.187 33.333 8.75 8.75 0.00 1.89
4765 8964 5.874831 TGCTTTGCTGGTTATGTTATAACG 58.125 37.500 10.92 0.00 0.00 3.18
4766 8965 4.733405 GCTTTGCTGGTTATGTTATAACGC 59.267 41.667 10.92 6.76 0.00 4.84
4767 8966 4.886247 TTGCTGGTTATGTTATAACGCC 57.114 40.909 10.92 10.27 0.00 5.68
4768 8967 3.207778 TGCTGGTTATGTTATAACGCCC 58.792 45.455 10.92 8.08 0.00 6.13
4769 8968 2.222445 GCTGGTTATGTTATAACGCCCG 59.778 50.000 10.92 7.86 0.00 6.13
4770 8969 2.803956 CTGGTTATGTTATAACGCCCGG 59.196 50.000 10.92 0.00 0.00 5.73
4772 8971 3.071312 TGGTTATGTTATAACGCCCGGAT 59.929 43.478 0.73 0.76 0.00 4.18
4773 8972 4.282957 TGGTTATGTTATAACGCCCGGATA 59.717 41.667 0.73 0.00 0.00 2.59
4776 8975 6.372381 GGTTATGTTATAACGCCCGGATAATT 59.628 38.462 0.73 0.00 0.00 1.40
4777 8976 7.548780 GGTTATGTTATAACGCCCGGATAATTA 59.451 37.037 0.73 0.00 0.00 1.40
4778 8977 8.934825 GTTATGTTATAACGCCCGGATAATTAA 58.065 33.333 0.73 0.00 0.00 1.40
4779 8978 7.605410 ATGTTATAACGCCCGGATAATTAAG 57.395 36.000 0.73 0.00 0.00 1.85
4780 8979 5.409214 TGTTATAACGCCCGGATAATTAAGC 59.591 40.000 0.73 0.00 0.00 3.09
4782 8981 3.756933 AACGCCCGGATAATTAAGCTA 57.243 42.857 0.73 0.00 0.00 3.32
4783 8982 3.036075 ACGCCCGGATAATTAAGCTAC 57.964 47.619 0.73 0.00 0.00 3.58
4785 8984 2.993899 CGCCCGGATAATTAAGCTACAG 59.006 50.000 0.73 0.00 0.00 2.74
4786 8985 3.554337 CGCCCGGATAATTAAGCTACAGT 60.554 47.826 0.73 0.00 0.00 3.55
4788 8987 5.544650 GCCCGGATAATTAAGCTACAGTAA 58.455 41.667 0.73 0.00 0.00 2.24
4789 8988 5.407691 GCCCGGATAATTAAGCTACAGTAAC 59.592 44.000 0.73 0.00 0.00 2.50
4790 8989 5.930569 CCCGGATAATTAAGCTACAGTAACC 59.069 44.000 0.73 0.00 0.00 2.85
4791 8990 5.930569 CCGGATAATTAAGCTACAGTAACCC 59.069 44.000 0.00 0.00 0.00 4.11
4792 8991 6.239515 CCGGATAATTAAGCTACAGTAACCCT 60.240 42.308 0.00 0.00 0.00 4.34
4793 8992 6.867293 CGGATAATTAAGCTACAGTAACCCTC 59.133 42.308 0.00 0.00 0.00 4.30
4794 8993 7.255871 CGGATAATTAAGCTACAGTAACCCTCT 60.256 40.741 0.00 0.00 0.00 3.69
4802 9001 8.548880 AAGCTACAGTAACCCTCTATTAATGA 57.451 34.615 0.00 0.00 33.11 2.57
4803 9002 8.728596 AGCTACAGTAACCCTCTATTAATGAT 57.271 34.615 0.00 0.00 33.11 2.45
4804 9003 8.589338 AGCTACAGTAACCCTCTATTAATGATG 58.411 37.037 0.00 0.00 33.11 3.07
4805 9004 7.332182 GCTACAGTAACCCTCTATTAATGATGC 59.668 40.741 0.00 0.72 33.11 3.91
4806 9005 6.534634 ACAGTAACCCTCTATTAATGATGCC 58.465 40.000 0.00 0.00 33.11 4.40
4810 9009 5.589367 ACCCTCTATTAATGATGCCACAT 57.411 39.130 0.00 0.00 0.00 3.21
4811 9010 5.564550 ACCCTCTATTAATGATGCCACATC 58.435 41.667 0.00 0.55 0.00 3.06
4812 9011 5.073554 ACCCTCTATTAATGATGCCACATCA 59.926 40.000 12.30 12.30 0.00 3.07
4813 9012 5.413833 CCCTCTATTAATGATGCCACATCAC 59.586 44.000 12.18 0.00 0.00 3.06
4814 9013 5.413833 CCTCTATTAATGATGCCACATCACC 59.586 44.000 12.18 0.00 0.00 4.02
4815 9014 5.939447 TCTATTAATGATGCCACATCACCA 58.061 37.500 12.18 1.26 0.00 4.17
4816 9015 4.924305 ATTAATGATGCCACATCACCAC 57.076 40.909 12.18 0.00 0.00 4.16
4818 9017 1.758936 ATGATGCCACATCACCACTG 58.241 50.000 12.18 0.00 0.00 3.66
4820 9019 1.202915 TGATGCCACATCACCACTGTT 60.203 47.619 6.17 0.00 0.00 3.16
4821 9020 2.039613 TGATGCCACATCACCACTGTTA 59.960 45.455 6.17 0.00 0.00 2.41
4822 9021 1.890876 TGCCACATCACCACTGTTAC 58.109 50.000 0.00 0.00 0.00 2.50
4824 9023 1.806542 GCCACATCACCACTGTTACTG 59.193 52.381 0.00 0.00 0.00 2.74
4827 9026 3.250762 CCACATCACCACTGTTACTGTTG 59.749 47.826 0.00 0.00 0.00 3.33
4828 9027 2.878406 ACATCACCACTGTTACTGTTGC 59.122 45.455 0.00 0.00 0.00 4.17
4829 9028 3.141398 CATCACCACTGTTACTGTTGCT 58.859 45.455 0.00 0.00 0.00 3.91
4830 9029 4.202315 ACATCACCACTGTTACTGTTGCTA 60.202 41.667 0.00 0.00 0.00 3.49
4831 9030 4.409718 TCACCACTGTTACTGTTGCTAA 57.590 40.909 0.00 0.00 0.00 3.09
4832 9031 4.771903 TCACCACTGTTACTGTTGCTAAA 58.228 39.130 0.00 0.00 0.00 1.85
4833 9032 4.814234 TCACCACTGTTACTGTTGCTAAAG 59.186 41.667 0.00 0.00 0.00 1.85
4834 9033 4.574828 CACCACTGTTACTGTTGCTAAAGT 59.425 41.667 0.00 0.00 0.00 2.66
4835 9034 4.814771 ACCACTGTTACTGTTGCTAAAGTC 59.185 41.667 0.00 0.00 0.00 3.01
4836 9035 4.814234 CCACTGTTACTGTTGCTAAAGTCA 59.186 41.667 0.00 0.00 0.00 3.41
4837 9036 5.277345 CCACTGTTACTGTTGCTAAAGTCAC 60.277 44.000 0.00 0.00 0.00 3.67
4838 9037 5.523916 CACTGTTACTGTTGCTAAAGTCACT 59.476 40.000 0.00 0.00 0.00 3.41
4839 9038 5.753921 ACTGTTACTGTTGCTAAAGTCACTC 59.246 40.000 0.00 0.00 0.00 3.51
4841 9040 5.753438 TGTTACTGTTGCTAAAGTCACTCTG 59.247 40.000 0.00 0.00 0.00 3.35
4842 9041 4.672587 ACTGTTGCTAAAGTCACTCTGA 57.327 40.909 0.00 0.00 0.00 3.27
4845 10126 6.759272 ACTGTTGCTAAAGTCACTCTGATAA 58.241 36.000 0.00 0.00 0.00 1.75
4849 10130 9.066892 TGTTGCTAAAGTCACTCTGATAAAAAT 57.933 29.630 0.00 0.00 0.00 1.82
4850 10131 9.548208 GTTGCTAAAGTCACTCTGATAAAAATC 57.452 33.333 0.00 0.00 0.00 2.17
4852 10133 9.283768 TGCTAAAGTCACTCTGATAAAAATCAA 57.716 29.630 0.00 0.00 0.00 2.57
4869 10150 8.845413 AAAAATCAAATCCAAATTCCATTCGA 57.155 26.923 0.00 0.00 0.00 3.71
4874 10155 8.925161 TCAAATCCAAATTCCATTCGAAATAC 57.075 30.769 0.00 0.00 33.08 1.89
4878 10159 9.889128 AATCCAAATTCCATTCGAAATACAAAT 57.111 25.926 0.00 0.00 33.08 2.32
4879 10160 8.925161 TCCAAATTCCATTCGAAATACAAATC 57.075 30.769 0.00 0.00 33.08 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 74 6.206634 TGTTAGTCATCCTTCACATTTTGGTC 59.793 38.462 0.00 0.00 0.00 4.02
158 160 4.456280 AATCTGTCACATAAGCGAGTCA 57.544 40.909 0.00 0.00 0.00 3.41
173 175 3.194116 CCACTAAGCCATGCAAAATCTGT 59.806 43.478 0.00 0.00 0.00 3.41
203 205 4.171005 CCACTAAGCAATGCATTGAAGTG 58.829 43.478 34.77 34.77 40.41 3.16
226 228 3.384146 TGTAAAGTGTCCACCTCAACGTA 59.616 43.478 0.00 0.00 0.00 3.57
228 230 2.828877 TGTAAAGTGTCCACCTCAACG 58.171 47.619 0.00 0.00 0.00 4.10
243 245 9.967451 TTGGTACCAATTCTCTCAATATGTAAA 57.033 29.630 23.69 0.00 0.00 2.01
250 252 6.784031 AGAAGTTGGTACCAATTCTCTCAAT 58.216 36.000 29.40 9.16 38.28 2.57
290 292 7.910683 CCGGCAACTTTTTCTCTAATTAATCTC 59.089 37.037 0.00 0.00 0.00 2.75
294 296 6.674066 CACCGGCAACTTTTTCTCTAATTAA 58.326 36.000 0.00 0.00 0.00 1.40
354 356 3.738982 ACATGACACTTTTCGACCATGA 58.261 40.909 0.00 0.00 36.29 3.07
356 358 3.738982 TGACATGACACTTTTCGACCAT 58.261 40.909 0.00 0.00 0.00 3.55
399 401 1.079405 CGTTGCCCACCATACTCGT 60.079 57.895 0.00 0.00 0.00 4.18
425 427 6.754209 ACTAAATGCAAGAGATACGTTCTGAG 59.246 38.462 0.00 0.00 33.74 3.35
428 430 9.250624 GATAACTAAATGCAAGAGATACGTTCT 57.749 33.333 0.00 0.00 37.41 3.01
1022 1302 1.337823 GCGGTACCTTCTTTGAGCAGA 60.338 52.381 10.90 0.00 0.00 4.26
1023 1303 1.079503 GCGGTACCTTCTTTGAGCAG 58.920 55.000 10.90 0.00 0.00 4.24
1089 1391 2.409651 GGAACCAACGCAACGCAA 59.590 55.556 0.00 0.00 0.00 4.85
1117 1425 2.495939 CGAATCAGAAGAAAAACGGCG 58.504 47.619 4.80 4.80 0.00 6.46
1118 1426 2.095718 AGCGAATCAGAAGAAAAACGGC 60.096 45.455 0.00 0.00 0.00 5.68
1119 1427 3.813529 AGCGAATCAGAAGAAAAACGG 57.186 42.857 0.00 0.00 0.00 4.44
1121 1429 6.693113 ACAAGAAAGCGAATCAGAAGAAAAAC 59.307 34.615 0.00 0.00 0.00 2.43
1122 1430 6.795399 ACAAGAAAGCGAATCAGAAGAAAAA 58.205 32.000 0.00 0.00 0.00 1.94
1123 1431 6.377327 ACAAGAAAGCGAATCAGAAGAAAA 57.623 33.333 0.00 0.00 0.00 2.29
1157 1482 1.906333 CCGGGTTTGGTTTCCCCTG 60.906 63.158 0.00 0.00 40.54 4.45
1183 1513 3.884037 AGTTTATGGATGGATGGGGAC 57.116 47.619 0.00 0.00 0.00 4.46
1321 2194 0.955428 TTGCCACAGCCGATGAGTTC 60.955 55.000 0.00 0.00 38.69 3.01
1322 2195 0.537143 TTTGCCACAGCCGATGAGTT 60.537 50.000 0.00 0.00 38.69 3.01
1324 2197 0.813184 ATTTTGCCACAGCCGATGAG 59.187 50.000 0.00 0.00 38.69 2.90
1325 2198 0.527113 CATTTTGCCACAGCCGATGA 59.473 50.000 0.00 0.00 38.69 2.92
1326 2199 0.527113 TCATTTTGCCACAGCCGATG 59.473 50.000 0.00 0.00 38.69 3.84
1329 2202 1.067706 TCAATCATTTTGCCACAGCCG 60.068 47.619 0.00 0.00 38.69 5.52
1330 2203 2.747396 TCAATCATTTTGCCACAGCC 57.253 45.000 0.00 0.00 38.69 4.85
1352 2394 4.019591 GGGCAAGAAAGAAAGTACTAGGGA 60.020 45.833 0.00 0.00 0.00 4.20
1353 2395 4.019231 AGGGCAAGAAAGAAAGTACTAGGG 60.019 45.833 0.00 0.00 0.00 3.53
1354 2396 5.167303 AGGGCAAGAAAGAAAGTACTAGG 57.833 43.478 0.00 0.00 0.00 3.02
1355 2397 6.107343 GGTAGGGCAAGAAAGAAAGTACTAG 58.893 44.000 0.00 0.00 0.00 2.57
1358 2400 4.648651 TGGTAGGGCAAGAAAGAAAGTAC 58.351 43.478 0.00 0.00 0.00 2.73
1376 2430 5.560724 AGTACGTACTTGTAGGTCTTGGTA 58.439 41.667 22.45 0.00 31.13 3.25
1551 2633 7.914871 CGAGCCACATCATCATTAAATTAAACA 59.085 33.333 0.00 0.00 0.00 2.83
1629 2716 7.491048 GCATGGAGATTTATTAGAGTAGCTAGC 59.509 40.741 6.62 6.62 0.00 3.42
1633 2720 9.883142 ATAAGCATGGAGATTTATTAGAGTAGC 57.117 33.333 0.00 0.00 0.00 3.58
1656 2743 9.347934 CAAAACTTAACTGTGTGTTGTTCATAA 57.652 29.630 0.00 0.00 39.55 1.90
1658 2745 6.811170 CCAAAACTTAACTGTGTGTTGTTCAT 59.189 34.615 0.00 0.00 39.55 2.57
1659 2746 6.016192 TCCAAAACTTAACTGTGTGTTGTTCA 60.016 34.615 0.00 0.00 39.55 3.18
1660 2747 6.307077 GTCCAAAACTTAACTGTGTGTTGTTC 59.693 38.462 0.00 0.00 39.55 3.18
1661 2748 6.153756 GTCCAAAACTTAACTGTGTGTTGTT 58.846 36.000 0.00 0.00 39.55 2.83
1662 2749 5.241949 TGTCCAAAACTTAACTGTGTGTTGT 59.758 36.000 0.00 0.00 39.55 3.32
1663 2750 5.704888 TGTCCAAAACTTAACTGTGTGTTG 58.295 37.500 0.00 0.00 39.55 3.33
1664 2751 5.708230 TCTGTCCAAAACTTAACTGTGTGTT 59.292 36.000 0.00 0.00 42.31 3.32
1665 2752 5.250200 TCTGTCCAAAACTTAACTGTGTGT 58.750 37.500 0.00 0.00 0.00 3.72
1666 2753 5.811399 TCTGTCCAAAACTTAACTGTGTG 57.189 39.130 0.00 0.00 0.00 3.82
1667 2754 7.051623 TGTATCTGTCCAAAACTTAACTGTGT 58.948 34.615 0.00 0.00 0.00 3.72
1668 2755 7.490962 TGTATCTGTCCAAAACTTAACTGTG 57.509 36.000 0.00 0.00 0.00 3.66
1669 2756 6.204882 GCTGTATCTGTCCAAAACTTAACTGT 59.795 38.462 0.00 0.00 0.00 3.55
1673 2760 6.530120 TCTGCTGTATCTGTCCAAAACTTAA 58.470 36.000 0.00 0.00 0.00 1.85
1675 2762 4.973168 TCTGCTGTATCTGTCCAAAACTT 58.027 39.130 0.00 0.00 0.00 2.66
1676 2763 4.623932 TCTGCTGTATCTGTCCAAAACT 57.376 40.909 0.00 0.00 0.00 2.66
1677 2764 5.239525 ACTTTCTGCTGTATCTGTCCAAAAC 59.760 40.000 0.00 0.00 0.00 2.43
1680 2767 4.318332 CACTTTCTGCTGTATCTGTCCAA 58.682 43.478 0.00 0.00 0.00 3.53
1681 2768 3.866066 GCACTTTCTGCTGTATCTGTCCA 60.866 47.826 0.00 0.00 43.33 4.02
1682 2769 2.675348 GCACTTTCTGCTGTATCTGTCC 59.325 50.000 0.00 0.00 43.33 4.02
1694 2781 3.951979 ACGAACTTTGAGCACTTTCTG 57.048 42.857 0.00 0.00 0.00 3.02
1695 2782 6.038271 ACATTAACGAACTTTGAGCACTTTCT 59.962 34.615 0.00 0.00 0.00 2.52
1696 2783 6.199393 ACATTAACGAACTTTGAGCACTTTC 58.801 36.000 0.00 0.00 0.00 2.62
1697 2784 6.131544 ACATTAACGAACTTTGAGCACTTT 57.868 33.333 0.00 0.00 0.00 2.66
1698 2785 5.751243 ACATTAACGAACTTTGAGCACTT 57.249 34.783 0.00 0.00 0.00 3.16
1700 2787 5.270853 ACAACATTAACGAACTTTGAGCAC 58.729 37.500 0.00 0.00 0.00 4.40
1701 2788 5.493133 ACAACATTAACGAACTTTGAGCA 57.507 34.783 0.00 0.00 0.00 4.26
1702 2789 7.357287 GCTTTACAACATTAACGAACTTTGAGC 60.357 37.037 0.00 0.00 0.00 4.26
1703 2790 7.112984 GGCTTTACAACATTAACGAACTTTGAG 59.887 37.037 0.00 0.00 0.00 3.02
1704 2791 6.913673 GGCTTTACAACATTAACGAACTTTGA 59.086 34.615 0.00 0.00 0.00 2.69
1705 2792 6.693545 TGGCTTTACAACATTAACGAACTTTG 59.306 34.615 0.00 0.00 0.00 2.77
1744 2849 8.223100 GGTCAGTTGCAAAAAGCTTAATTTATG 58.777 33.333 0.00 0.00 45.94 1.90
1746 2857 6.419413 CGGTCAGTTGCAAAAAGCTTAATTTA 59.581 34.615 0.00 0.00 45.94 1.40
1750 2861 3.378742 TCGGTCAGTTGCAAAAAGCTTAA 59.621 39.130 0.00 0.00 45.94 1.85
1769 2881 1.134788 CAACCCTAGGCAAGTACTCGG 60.135 57.143 2.05 0.00 0.00 4.63
1837 2949 9.252962 GGTGCAGTTAGTATTAATACATAACGT 57.747 33.333 24.05 15.28 35.05 3.99
1844 2956 9.991906 TTCATAGGGTGCAGTTAGTATTAATAC 57.008 33.333 16.44 16.44 0.00 1.89
1853 2965 4.471904 TGAGTTCATAGGGTGCAGTTAG 57.528 45.455 0.00 0.00 0.00 2.34
1881 2998 8.971073 AGGTAGGGAAATTAATCATTTTGACAG 58.029 33.333 0.00 0.00 35.02 3.51
1895 3012 6.017192 GGGAAAGAAAGAAGGTAGGGAAATT 58.983 40.000 0.00 0.00 0.00 1.82
1906 3023 3.490348 TCTTGCCTGGGAAAGAAAGAAG 58.510 45.455 7.56 0.00 36.88 2.85
1916 3033 0.615331 CTTGTAGCTCTTGCCTGGGA 59.385 55.000 0.00 0.00 40.80 4.37
1960 3079 7.668052 AGGCACCTAATTAGTAACATGAAAACA 59.332 33.333 11.50 0.00 0.00 2.83
2002 3177 1.557099 AGACCCACGTGCTGAATCTA 58.443 50.000 10.91 0.00 0.00 1.98
2118 3404 3.552068 GGCGGGCCACATCATTAAATTAC 60.552 47.826 4.39 0.00 35.81 1.89
2325 4045 7.568267 ACTTACGATACATCAGAATAATGCG 57.432 36.000 0.00 0.00 0.00 4.73
2359 4094 4.497507 GGTTCAGAAAACAACGGAAAGAGG 60.498 45.833 0.00 0.00 0.00 3.69
2522 4276 3.327439 TCCCTTTGATTCCCCTCTATCC 58.673 50.000 0.00 0.00 0.00 2.59
2603 4359 2.094066 CGCAAATTTGGGAAGCGGC 61.094 57.895 26.35 6.14 44.20 6.53
2676 4432 5.186021 TGAAAACACAGAAAGGCCTTTGTTA 59.814 36.000 35.05 15.15 36.41 2.41
2777 4533 5.302568 AGAGACACCAATTTCTTGCAATTCA 59.697 36.000 0.00 0.00 0.00 2.57
2934 4691 3.436180 GCTCTTCCAATGATCCATCCCTT 60.436 47.826 0.00 0.00 0.00 3.95
2998 4755 6.493166 TCATCCATCCTGAACCAAACTTTAT 58.507 36.000 0.00 0.00 0.00 1.40
3116 4886 9.392259 CACAGCAGAAATCATATATATCCATGT 57.608 33.333 0.00 0.00 0.00 3.21
3213 4983 4.829492 AGCTTCTCCAATGCTTTACACTTT 59.171 37.500 0.00 0.00 32.61 2.66
3744 5514 6.570571 CGATGACCAAAGACTCTAACTTCTGA 60.571 42.308 0.00 0.00 0.00 3.27
4058 5857 1.831106 TCATTCACCAGATGCCGTACT 59.169 47.619 0.00 0.00 0.00 2.73
4060 5859 3.006940 GTTTCATTCACCAGATGCCGTA 58.993 45.455 0.00 0.00 0.00 4.02
4116 5950 8.997621 AATTAAGCAAGAGAATTACGTACAGA 57.002 30.769 0.00 0.00 0.00 3.41
4320 6296 1.067283 CCATACCAAAATTGCCACGCA 60.067 47.619 0.00 0.00 36.47 5.24
4446 6431 9.071276 CATCCACAATTATGCTTCCTAGTAATT 57.929 33.333 0.00 0.00 0.00 1.40
4447 6432 8.220559 ACATCCACAATTATGCTTCCTAGTAAT 58.779 33.333 0.00 0.00 0.00 1.89
4448 6433 7.573710 ACATCCACAATTATGCTTCCTAGTAA 58.426 34.615 0.00 0.00 0.00 2.24
4450 6435 6.006275 ACATCCACAATTATGCTTCCTAGT 57.994 37.500 0.00 0.00 0.00 2.57
4451 6436 6.949352 AACATCCACAATTATGCTTCCTAG 57.051 37.500 0.00 0.00 0.00 3.02
4452 6437 8.271458 TCTAAACATCCACAATTATGCTTCCTA 58.729 33.333 0.00 0.00 0.00 2.94
4454 6439 7.333528 TCTAAACATCCACAATTATGCTTCC 57.666 36.000 0.00 0.00 0.00 3.46
4509 6599 7.646548 TGCTATTATGTCTTGAGTAGTCACT 57.353 36.000 0.00 0.00 37.87 3.41
4511 6601 8.300286 GCTATGCTATTATGTCTTGAGTAGTCA 58.700 37.037 0.00 0.00 0.00 3.41
4550 6728 3.979101 TGATGTGACTACCTGCAATGA 57.021 42.857 0.00 0.00 0.00 2.57
4554 6732 2.833943 AGACATGATGTGACTACCTGCA 59.166 45.455 1.23 0.00 31.00 4.41
4555 6733 3.533606 AGACATGATGTGACTACCTGC 57.466 47.619 1.23 0.00 31.00 4.85
4556 6734 4.093998 GCAAAGACATGATGTGACTACCTG 59.906 45.833 1.23 0.00 32.50 4.00
4619 8818 3.334583 TCAGAAAATCAGAACCCCTCG 57.665 47.619 0.00 0.00 0.00 4.63
4655 8854 3.643763 ACGAGCTGTCTTGTTACTTGAG 58.356 45.455 0.00 0.00 33.10 3.02
4658 8857 2.544267 GCAACGAGCTGTCTTGTTACTT 59.456 45.455 0.00 0.00 43.35 2.24
4659 8858 2.135933 GCAACGAGCTGTCTTGTTACT 58.864 47.619 0.00 0.00 43.35 2.24
4660 8859 1.864711 TGCAACGAGCTGTCTTGTTAC 59.135 47.619 0.00 1.84 43.35 2.50
4727 8926 0.971386 AAGCAAAGTTGGCATCCTGG 59.029 50.000 4.74 0.00 0.00 4.45
4730 8929 1.150827 GCAAAGCAAAGTTGGCATCC 58.849 50.000 4.74 0.00 0.00 3.51
4743 8942 4.733405 GCGTTATAACATAACCAGCAAAGC 59.267 41.667 15.67 2.52 0.00 3.51
4753 8952 9.153721 CTTAATTATCCGGGCGTTATAACATAA 57.846 33.333 15.67 10.35 0.00 1.90
4759 8958 5.410355 AGCTTAATTATCCGGGCGTTATA 57.590 39.130 0.00 0.00 0.00 0.98
4763 8962 2.366266 TGTAGCTTAATTATCCGGGCGT 59.634 45.455 0.00 0.00 0.00 5.68
4764 8963 2.993899 CTGTAGCTTAATTATCCGGGCG 59.006 50.000 0.00 0.00 0.00 6.13
4765 8964 4.004196 ACTGTAGCTTAATTATCCGGGC 57.996 45.455 0.00 0.00 0.00 6.13
4766 8965 5.930569 GGTTACTGTAGCTTAATTATCCGGG 59.069 44.000 0.00 0.00 0.00 5.73
4767 8966 5.930569 GGGTTACTGTAGCTTAATTATCCGG 59.069 44.000 0.00 0.00 0.00 5.14
4768 8967 6.756221 AGGGTTACTGTAGCTTAATTATCCG 58.244 40.000 0.00 0.00 0.00 4.18
4769 8968 7.964624 AGAGGGTTACTGTAGCTTAATTATCC 58.035 38.462 0.00 0.00 0.00 2.59
4776 8975 9.650714 TCATTAATAGAGGGTTACTGTAGCTTA 57.349 33.333 0.00 0.00 0.00 3.09
4777 8976 8.548880 TCATTAATAGAGGGTTACTGTAGCTT 57.451 34.615 0.00 0.00 0.00 3.74
4778 8977 8.589338 CATCATTAATAGAGGGTTACTGTAGCT 58.411 37.037 1.71 0.00 0.00 3.32
4779 8978 7.332182 GCATCATTAATAGAGGGTTACTGTAGC 59.668 40.741 0.00 0.00 0.00 3.58
4780 8979 7.819900 GGCATCATTAATAGAGGGTTACTGTAG 59.180 40.741 0.00 0.00 0.00 2.74
4782 8981 6.101150 TGGCATCATTAATAGAGGGTTACTGT 59.899 38.462 0.00 0.00 0.00 3.55
4783 8982 6.428159 GTGGCATCATTAATAGAGGGTTACTG 59.572 42.308 0.00 0.00 0.00 2.74
4785 8984 6.296026 TGTGGCATCATTAATAGAGGGTTAC 58.704 40.000 0.00 0.00 0.00 2.50
4786 8985 6.508030 TGTGGCATCATTAATAGAGGGTTA 57.492 37.500 0.00 0.00 0.00 2.85
4788 8987 5.073554 TGATGTGGCATCATTAATAGAGGGT 59.926 40.000 7.63 0.00 0.00 4.34
4789 8988 5.413833 GTGATGTGGCATCATTAATAGAGGG 59.586 44.000 13.88 0.00 0.00 4.30
4790 8989 5.413833 GGTGATGTGGCATCATTAATAGAGG 59.586 44.000 13.88 0.00 0.00 3.69
4791 8990 5.999600 TGGTGATGTGGCATCATTAATAGAG 59.000 40.000 13.88 0.00 0.00 2.43
4792 8991 5.764686 GTGGTGATGTGGCATCATTAATAGA 59.235 40.000 13.88 0.00 30.53 1.98
4793 8992 5.766670 AGTGGTGATGTGGCATCATTAATAG 59.233 40.000 13.88 0.00 30.53 1.73
4794 8993 5.532032 CAGTGGTGATGTGGCATCATTAATA 59.468 40.000 13.88 0.00 30.53 0.98
4796 8995 3.695556 CAGTGGTGATGTGGCATCATTAA 59.304 43.478 13.88 2.26 30.53 1.40
4797 8996 3.281158 CAGTGGTGATGTGGCATCATTA 58.719 45.455 13.88 5.04 30.53 1.90
4798 8997 2.097036 CAGTGGTGATGTGGCATCATT 58.903 47.619 13.88 0.49 30.53 2.57
4799 8998 1.005097 ACAGTGGTGATGTGGCATCAT 59.995 47.619 13.88 0.00 30.53 2.45
4801 9000 1.538047 AACAGTGGTGATGTGGCATC 58.462 50.000 0.00 2.44 0.00 3.91
4802 9001 2.040278 AGTAACAGTGGTGATGTGGCAT 59.960 45.455 0.00 0.00 0.00 4.40
4803 9002 1.419762 AGTAACAGTGGTGATGTGGCA 59.580 47.619 0.00 0.00 0.00 4.92
4804 9003 1.806542 CAGTAACAGTGGTGATGTGGC 59.193 52.381 0.00 0.00 0.00 5.01
4805 9004 3.126001 ACAGTAACAGTGGTGATGTGG 57.874 47.619 0.00 0.00 0.00 4.17
4806 9005 3.303990 GCAACAGTAACAGTGGTGATGTG 60.304 47.826 3.23 0.00 38.50 3.21
4810 9009 4.409718 TTAGCAACAGTAACAGTGGTGA 57.590 40.909 3.23 0.00 38.50 4.02
4811 9010 4.574828 ACTTTAGCAACAGTAACAGTGGTG 59.425 41.667 0.00 0.00 39.21 4.17
4812 9011 4.777463 ACTTTAGCAACAGTAACAGTGGT 58.223 39.130 0.00 0.00 0.00 4.16
4813 9012 4.814234 TGACTTTAGCAACAGTAACAGTGG 59.186 41.667 0.00 0.00 0.00 4.00
4814 9013 5.523916 AGTGACTTTAGCAACAGTAACAGTG 59.476 40.000 0.00 0.00 27.58 3.66
4815 9014 5.671493 AGTGACTTTAGCAACAGTAACAGT 58.329 37.500 0.00 0.00 27.58 3.55
4816 9015 5.986135 AGAGTGACTTTAGCAACAGTAACAG 59.014 40.000 0.00 0.00 27.58 3.16
4818 9017 5.983720 TCAGAGTGACTTTAGCAACAGTAAC 59.016 40.000 0.00 0.00 0.00 2.50
4820 9019 5.784578 TCAGAGTGACTTTAGCAACAGTA 57.215 39.130 0.00 0.00 0.00 2.74
4821 9020 4.672587 TCAGAGTGACTTTAGCAACAGT 57.327 40.909 0.00 0.00 0.00 3.55
4822 9021 7.658179 TTTATCAGAGTGACTTTAGCAACAG 57.342 36.000 0.00 0.00 0.00 3.16
4824 9023 9.548208 GATTTTTATCAGAGTGACTTTAGCAAC 57.452 33.333 0.00 0.00 0.00 4.17
4831 9030 9.300681 TGGATTTGATTTTTATCAGAGTGACTT 57.699 29.630 0.00 0.00 31.46 3.01
4832 9031 8.868522 TGGATTTGATTTTTATCAGAGTGACT 57.131 30.769 0.00 0.00 31.46 3.41
4833 9032 9.912634 TTTGGATTTGATTTTTATCAGAGTGAC 57.087 29.630 0.00 0.00 31.46 3.67
4845 10126 8.845413 TTCGAATGGAATTTGGATTTGATTTT 57.155 26.923 0.00 0.00 38.29 1.82
4849 10130 8.526978 TGTATTTCGAATGGAATTTGGATTTGA 58.473 29.630 0.00 0.00 38.29 2.69
4850 10131 8.700722 TGTATTTCGAATGGAATTTGGATTTG 57.299 30.769 0.00 0.00 38.29 2.32
4852 10133 9.889128 ATTTGTATTTCGAATGGAATTTGGATT 57.111 25.926 0.00 0.00 38.29 3.01
4855 10136 8.700722 TGATTTGTATTTCGAATGGAATTTGG 57.299 30.769 0.00 0.00 38.29 3.28


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

AutoCloner maintained by Alex Coulton.