Multiple sequence alignment - TraesCS4D01G008700

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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 TraesCS4D01G008700 chr4D 100.000 4364 0 0 1 4364 4275956 4271593 0.000000e+00 8059.0
1 TraesCS4D01G008700 chr4D 84.758 1299 150 19 2476 3754 4208988 4210258 0.000000e+00 1258.0
2 TraesCS4D01G008700 chr4D 79.325 1214 217 26 2617 3818 4248694 4249885 0.000000e+00 821.0
3 TraesCS4D01G008700 chr4D 89.313 655 66 2 985 1639 4321271 4320621 0.000000e+00 819.0
4 TraesCS4D01G008700 chr4D 79.630 540 72 23 2484 2998 4349359 4348833 1.930000e-93 353.0
5 TraesCS4D01G008700 chr4D 86.885 305 38 2 2165 2468 4208716 4209019 1.500000e-89 340.0
6 TraesCS4D01G008700 chr4D 72.900 893 163 40 1636 2468 4247728 4248601 7.300000e-58 235.0
7 TraesCS4D01G008700 chr4D 85.870 184 23 2 1636 1818 4320546 4320365 4.450000e-45 193.0
8 TraesCS4D01G008700 chr4D 84.615 182 24 3 2288 2468 4285583 4285405 1.250000e-40 178.0
9 TraesCS4D01G008700 chr4D 85.380 171 21 4 2300 2469 4526535 4526702 1.610000e-39 174.0
10 TraesCS4D01G008700 chr4D 80.690 145 26 2 3291 3434 4520321 4520464 1.280000e-20 111.0
11 TraesCS4D01G008700 chrUn 86.433 2742 290 35 1652 4364 47347318 47350006 0.000000e+00 2928.0
12 TraesCS4D01G008700 chrUn 92.542 952 41 13 1 944 47345662 47346591 0.000000e+00 1338.0
13 TraesCS4D01G008700 chrUn 91.551 651 53 2 990 1639 47346588 47347237 0.000000e+00 896.0
14 TraesCS4D01G008700 chrUn 81.564 179 29 3 2292 2469 476939206 476939381 1.260000e-30 145.0
15 TraesCS4D01G008700 chrUn 84.507 142 20 2 3294 3434 47331742 47331882 5.890000e-29 139.0
16 TraesCS4D01G008700 chrUn 79.310 145 28 2 3291 3434 47245531 47245388 2.780000e-17 100.0
17 TraesCS4D01G008700 chrUn 79.310 145 28 2 3291 3434 47251247 47251104 2.780000e-17 100.0
18 TraesCS4D01G008700 chr4A 86.433 2742 290 35 1652 4364 599628904 599631592 0.000000e+00 2928.0
19 TraesCS4D01G008700 chr4A 92.542 952 41 13 1 944 599627248 599628177 0.000000e+00 1338.0
20 TraesCS4D01G008700 chr4A 91.551 651 53 2 990 1639 599628174 599628823 0.000000e+00 896.0
21 TraesCS4D01G008700 chr4A 78.182 1265 210 41 2617 3840 599644514 599643275 0.000000e+00 747.0
22 TraesCS4D01G008700 chr4A 80.989 647 64 27 3209 3840 599354918 599355520 3.980000e-125 459.0
23 TraesCS4D01G008700 chr4A 80.157 509 82 17 2475 2971 599351342 599351843 3.210000e-96 363.0
24 TraesCS4D01G008700 chr4A 73.188 869 164 43 1649 2468 599645455 599644607 2.610000e-62 250.0
25 TraesCS4D01G008700 chr4B 77.141 1378 249 42 2480 3833 4300912 4299577 0.000000e+00 739.0
26 TraesCS4D01G008700 chr4B 77.458 1251 222 39 2617 3840 4331473 4330256 0.000000e+00 693.0
27 TraesCS4D01G008700 chr4B 73.493 879 154 52 1649 2468 4301743 4300885 4.330000e-65 259.0
28 TraesCS4D01G008700 chr4B 77.533 227 43 6 3210 3434 7502249 7502469 3.540000e-26 130.0
29 TraesCS4D01G008700 chr7A 80.112 538 82 17 979 1508 726137635 726137115 1.150000e-100 377.0
30 TraesCS4D01G008700 chr7A 84.533 375 49 5 1139 1512 726343808 726343442 3.210000e-96 363.0
31 TraesCS4D01G008700 chr7A 76.203 790 123 30 740 1512 726122588 726121847 1.490000e-94 357.0
32 TraesCS4D01G008700 chr7A 84.367 371 49 5 1139 1508 726273103 726272741 5.370000e-94 355.0
33 TraesCS4D01G008700 chr7A 76.178 785 123 33 740 1508 726363678 726362942 5.370000e-94 355.0
34 TraesCS4D01G008700 chr7A 76.178 785 123 33 740 1508 726366807 726366071 5.370000e-94 355.0
35 TraesCS4D01G008700 chr3D 87.313 134 14 2 603 736 542201742 542201872 2.720000e-32 150.0
36 TraesCS4D01G008700 chr3D 92.857 70 5 0 667 736 542132368 542132437 7.720000e-18 102.0
37 TraesCS4D01G008700 chr1B 83.803 142 21 2 3294 3434 46551273 46551413 2.740000e-27 134.0
38 TraesCS4D01G008700 chr3B 91.429 70 6 0 667 736 717692874 717692943 3.590000e-16 97.1
39 TraesCS4D01G008700 chr3B 91.429 70 6 0 667 736 717696607 717696676 3.590000e-16 97.1
40 TraesCS4D01G008700 chr3B 93.651 63 2 1 603 665 717689044 717689104 4.650000e-15 93.5
41 TraesCS4D01G008700 chr3B 86.765 68 9 0 667 734 717752589 717752656 4.680000e-10 76.8
42 TraesCS4D01G008700 chr3B 100.000 35 0 0 603 637 717696522 717696556 1.010000e-06 65.8
43 TraesCS4D01G008700 chr3B 100.000 32 0 0 603 634 717692789 717692820 4.710000e-05 60.2
44 TraesCS4D01G008700 chr3A 96.491 57 2 0 680 736 677882232 677882288 1.290000e-15 95.3
45 TraesCS4D01G008700 chr3A 94.915 59 3 0 678 736 677877440 677877498 4.650000e-15 93.5


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 TraesCS4D01G008700 chr4D 4271593 4275956 4363 True 8059.000000 8059 100.000000 1 4364 1 chr4D.!!$R1 4363
1 TraesCS4D01G008700 chr4D 4208716 4210258 1542 False 799.000000 1258 85.821500 2165 3754 2 chr4D.!!$F3 1589
2 TraesCS4D01G008700 chr4D 4247728 4249885 2157 False 528.000000 821 76.112500 1636 3818 2 chr4D.!!$F4 2182
3 TraesCS4D01G008700 chr4D 4320365 4321271 906 True 506.000000 819 87.591500 985 1818 2 chr4D.!!$R4 833
4 TraesCS4D01G008700 chr4D 4348833 4349359 526 True 353.000000 353 79.630000 2484 2998 1 chr4D.!!$R3 514
5 TraesCS4D01G008700 chrUn 47345662 47350006 4344 False 1720.666667 2928 90.175333 1 4364 3 chrUn.!!$F3 4363
6 TraesCS4D01G008700 chr4A 599627248 599631592 4344 False 1720.666667 2928 90.175333 1 4364 3 chr4A.!!$F2 4363
7 TraesCS4D01G008700 chr4A 599643275 599645455 2180 True 498.500000 747 75.685000 1649 3840 2 chr4A.!!$R1 2191
8 TraesCS4D01G008700 chr4A 599351342 599355520 4178 False 411.000000 459 80.573000 2475 3840 2 chr4A.!!$F1 1365
9 TraesCS4D01G008700 chr4B 4330256 4331473 1217 True 693.000000 693 77.458000 2617 3840 1 chr4B.!!$R1 1223
10 TraesCS4D01G008700 chr4B 4299577 4301743 2166 True 499.000000 739 75.317000 1649 3833 2 chr4B.!!$R2 2184
11 TraesCS4D01G008700 chr7A 726137115 726137635 520 True 377.000000 377 80.112000 979 1508 1 chr7A.!!$R2 529
12 TraesCS4D01G008700 chr7A 726121847 726122588 741 True 357.000000 357 76.203000 740 1512 1 chr7A.!!$R1 772
13 TraesCS4D01G008700 chr7A 726362942 726366807 3865 True 355.000000 355 76.178000 740 1508 2 chr7A.!!$R5 768

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
636 643 0.107945 GCCTCCTCAACCTGTAGCTG 60.108 60.000 0.00 0.0 0.00 4.24 F
637 644 1.270907 CCTCCTCAACCTGTAGCTGT 58.729 55.000 0.00 0.0 0.00 4.40 F
901 915 1.608283 CCGAAACACCCTCCAACTCTC 60.608 57.143 0.00 0.0 0.00 3.20 F
1647 2241 0.095935 GATATCCATGCATCACGCGC 59.904 55.000 5.73 0.0 46.97 6.86 F
1724 2319 1.447140 GCGGCTGTCGGATACACAA 60.447 57.895 3.02 0.0 39.69 3.33 F
2880 3665 1.398390 CATGGCGTTGGCTCTTCTTAC 59.602 52.381 0.00 0.0 39.81 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 1842 0.603439 TGCGCGTGATGCATGGATAT 60.603 50.000 2.46 0.00 46.97 1.63 R
1641 2235 0.796312 AGAAAACTACCATGCGCGTG 59.204 50.000 22.83 22.83 0.00 5.34 R
2037 2673 1.067060 ACAGCTATGCGATAGTGCGAA 59.933 47.619 0.00 0.00 37.81 4.70 R
2880 3665 1.267235 GCACATCGCAGAACTCATTCG 60.267 52.381 0.00 0.00 43.58 3.34 R
3205 7483 1.342174 TGGTCGGTATCTTATTCCGGC 59.658 52.381 0.00 3.46 45.48 6.13 R
4036 8933 0.111253 GATTCCCCCATGGCGATCTT 59.889 55.000 6.09 0.00 0.00 2.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.443016 CCTACAGAGCTCCGCCCT 60.443 66.667 10.93 0.00 0.00 5.19
29 30 2.060980 CCTACAGAGCTCCGCCCTT 61.061 63.158 10.93 0.00 0.00 3.95
30 31 1.617947 CCTACAGAGCTCCGCCCTTT 61.618 60.000 10.93 0.00 0.00 3.11
48 49 2.620251 TTGTCATAGCCTTGATCGGG 57.380 50.000 0.70 0.70 0.00 5.14
56 57 1.162800 GCCTTGATCGGGTGCTCATC 61.163 60.000 6.44 0.00 0.00 2.92
57 58 0.467384 CCTTGATCGGGTGCTCATCT 59.533 55.000 0.00 0.00 0.00 2.90
60 61 0.462581 TGATCGGGTGCTCATCTTGC 60.463 55.000 0.00 0.00 0.00 4.01
100 101 4.017126 GGCTAATCCCCTTGCCATTATAC 58.983 47.826 0.00 0.00 44.34 1.47
101 102 4.263949 GGCTAATCCCCTTGCCATTATACT 60.264 45.833 0.00 0.00 44.34 2.12
102 103 4.702131 GCTAATCCCCTTGCCATTATACTG 59.298 45.833 0.00 0.00 0.00 2.74
103 104 4.814224 AATCCCCTTGCCATTATACTGT 57.186 40.909 0.00 0.00 0.00 3.55
104 105 5.922960 AATCCCCTTGCCATTATACTGTA 57.077 39.130 0.00 0.00 0.00 2.74
105 106 6.468972 AATCCCCTTGCCATTATACTGTAT 57.531 37.500 5.53 5.53 0.00 2.29
106 107 7.582909 AATCCCCTTGCCATTATACTGTATA 57.417 36.000 3.44 3.44 0.00 1.47
107 108 7.771506 ATCCCCTTGCCATTATACTGTATAT 57.228 36.000 8.27 0.00 0.00 0.86
108 109 7.195374 TCCCCTTGCCATTATACTGTATATC 57.805 40.000 8.27 0.75 0.00 1.63
109 110 6.733334 TCCCCTTGCCATTATACTGTATATCA 59.267 38.462 8.27 2.96 0.00 2.15
110 111 7.405858 TCCCCTTGCCATTATACTGTATATCAT 59.594 37.037 8.27 0.00 0.00 2.45
132 133 4.946784 AACGAAAATACACAGCTGATCC 57.053 40.909 23.35 0.00 0.00 3.36
134 135 2.614057 CGAAAATACACAGCTGATCCCC 59.386 50.000 23.35 0.64 0.00 4.81
168 169 1.175983 TCCACCATGGTGCGAAAACC 61.176 55.000 35.34 0.00 44.16 3.27
184 185 4.063967 CCGAGCGGCACCACACTA 62.064 66.667 1.45 0.00 0.00 2.74
263 264 5.057149 GCGGATTCAAGGTACAGATACAAT 58.943 41.667 0.00 0.00 32.40 2.71
269 270 8.954950 ATTCAAGGTACAGATACAATCTCAAG 57.045 34.615 0.00 0.00 37.58 3.02
271 272 4.938080 AGGTACAGATACAATCTCAAGCG 58.062 43.478 0.00 0.00 37.58 4.68
299 300 4.341366 AAATCAAACAGCAAGAAAGGGG 57.659 40.909 0.00 0.00 0.00 4.79
327 328 0.248843 CTGAGCAGGAGGTGGAGAAC 59.751 60.000 0.00 0.00 0.00 3.01
365 367 2.579201 CGTGGCCGTGATCCTTCT 59.421 61.111 0.00 0.00 0.00 2.85
380 382 2.781757 TCCTTCTGGATGCCTGATCAAT 59.218 45.455 0.00 0.00 37.46 2.57
382 384 2.945080 TCTGGATGCCTGATCAATCC 57.055 50.000 15.37 15.37 31.91 3.01
396 398 1.134699 TCAATCCATGGCTCTCGTGAC 60.135 52.381 6.96 0.00 34.35 3.67
427 429 2.289444 TGTTGAGAAATCCTCCCGTCAC 60.289 50.000 0.00 0.00 41.25 3.67
432 434 1.131303 AAATCCTCCCGTCACCCACA 61.131 55.000 0.00 0.00 0.00 4.17
522 524 1.068588 CGAGAACCAGACACCAGTTCA 59.931 52.381 5.07 0.00 41.86 3.18
528 530 0.930310 CAGACACCAGTTCACACACG 59.070 55.000 0.00 0.00 0.00 4.49
576 578 4.568592 GGGACAGAACCATCCAAAGAAGAT 60.569 45.833 0.00 0.00 36.65 2.40
579 581 3.760151 CAGAACCATCCAAAGAAGATGCA 59.240 43.478 0.00 0.00 39.87 3.96
591 593 4.935352 AGAAGATGCACTACTCCATCTC 57.065 45.455 3.88 0.00 45.40 2.75
619 626 2.194212 CATCTGGATGCAGCTGGCC 61.194 63.158 17.12 0.00 43.89 5.36
636 643 0.107945 GCCTCCTCAACCTGTAGCTG 60.108 60.000 0.00 0.00 0.00 4.24
637 644 1.270907 CCTCCTCAACCTGTAGCTGT 58.729 55.000 0.00 0.00 0.00 4.40
638 645 2.457598 CCTCCTCAACCTGTAGCTGTA 58.542 52.381 0.00 0.00 0.00 2.74
639 646 2.428890 CCTCCTCAACCTGTAGCTGTAG 59.571 54.545 0.00 0.00 0.00 2.74
640 647 1.825474 TCCTCAACCTGTAGCTGTAGC 59.175 52.381 0.00 0.00 42.49 3.58
731 738 4.419939 GCCAAAAGCTTCCGCGGG 62.420 66.667 27.83 11.74 42.32 6.13
835 848 2.742372 CCCAGCCAAACGTCTCCG 60.742 66.667 0.00 0.00 40.83 4.63
836 849 3.423154 CCAGCCAAACGTCTCCGC 61.423 66.667 0.00 0.00 37.70 5.54
837 850 3.777925 CAGCCAAACGTCTCCGCG 61.778 66.667 0.00 0.00 37.70 6.46
888 902 2.646719 CTCCGTCGACCCGAAACA 59.353 61.111 10.58 0.00 37.72 2.83
901 915 1.608283 CCGAAACACCCTCCAACTCTC 60.608 57.143 0.00 0.00 0.00 3.20
965 980 3.710722 CCCTTCGCCACCTGCTCT 61.711 66.667 0.00 0.00 38.05 4.09
966 981 2.125350 CCTTCGCCACCTGCTCTC 60.125 66.667 0.00 0.00 38.05 3.20
968 983 3.672295 CTTCGCCACCTGCTCTCCC 62.672 68.421 0.00 0.00 38.05 4.30
1146 1173 6.051074 GTGATGTGATGTGATTCATGTAGGA 58.949 40.000 0.00 0.00 36.83 2.94
1285 1312 3.397439 ATCGCCAGCCTGCTGTCT 61.397 61.111 17.23 0.00 42.15 3.41
1294 1321 2.357836 CTGCTGTCTGCCCCCAAT 59.642 61.111 0.00 0.00 42.00 3.16
1318 1346 2.765135 CTCCTCTCTCCATCTGCTTTCA 59.235 50.000 0.00 0.00 0.00 2.69
1336 1364 6.002704 GCTTTCATCATCTCATCTTGGGTAT 58.997 40.000 0.00 0.00 0.00 2.73
1344 1372 7.576403 TCATCTCATCTTGGGTATTGATTTCA 58.424 34.615 0.00 0.00 0.00 2.69
1349 1377 5.366482 TCTTGGGTATTGATTTCATCCGA 57.634 39.130 0.00 0.00 0.00 4.55
1376 1404 4.910956 CGATTCGCAGGAACCAGA 57.089 55.556 0.00 0.00 34.37 3.86
1559 1772 2.295909 TGGGCAAGCAGTTTATGTTGTC 59.704 45.455 0.00 0.00 0.00 3.18
1560 1773 2.295909 GGGCAAGCAGTTTATGTTGTCA 59.704 45.455 0.00 0.00 30.74 3.58
1571 1784 8.690840 GCAGTTTATGTTGTCATTTAAGTTGTC 58.309 33.333 0.00 0.00 35.70 3.18
1572 1785 9.729023 CAGTTTATGTTGTCATTTAAGTTGTCA 57.271 29.630 0.00 0.00 35.70 3.58
1601 1814 5.800941 GTCATAGGTAGAAGTGTCGAGTTTG 59.199 44.000 0.00 0.00 0.00 2.93
1605 1818 3.808174 GGTAGAAGTGTCGAGTTTGCTTT 59.192 43.478 0.00 0.00 0.00 3.51
1618 1831 7.167468 GTCGAGTTTGCTTTTGTTTCATGTAAT 59.833 33.333 0.00 0.00 0.00 1.89
1641 2235 5.798132 TGGAAGTACAGATATCCATGCATC 58.202 41.667 0.00 0.00 37.05 3.91
1646 2240 1.392510 CAGATATCCATGCATCACGCG 59.607 52.381 3.53 3.53 46.97 6.01
1647 2241 0.095935 GATATCCATGCATCACGCGC 59.904 55.000 5.73 0.00 46.97 6.86
1699 2294 2.574929 GGATGTGTCGGCGTGGTA 59.425 61.111 6.85 0.00 0.00 3.25
1724 2319 1.447140 GCGGCTGTCGGATACACAA 60.447 57.895 3.02 0.00 39.69 3.33
1769 2367 7.750458 CAGTTGTGTTACACATGGAATTATCAC 59.250 37.037 19.32 9.87 44.16 3.06
1782 2381 6.764379 TGGAATTATCACTATTCGTGCCATA 58.236 36.000 0.00 0.00 43.46 2.74
1822 2421 5.849510 TCAAGGAATACTTTGTCGTCTTGA 58.150 37.500 0.00 0.00 37.29 3.02
1840 2439 6.578023 GTCTTGAGGACATTTCTAGTGCTAT 58.422 40.000 0.00 0.00 43.94 2.97
1844 2450 8.635765 TTGAGGACATTTCTAGTGCTATTTTT 57.364 30.769 0.00 0.00 37.81 1.94
1877 2483 4.082081 TGGCAATTTTCTAGACTGGCAATG 60.082 41.667 13.81 1.19 39.33 2.82
1880 2486 5.803967 GCAATTTTCTAGACTGGCAATGAAG 59.196 40.000 0.00 0.00 0.00 3.02
1882 2488 6.749923 ATTTTCTAGACTGGCAATGAAGAC 57.250 37.500 0.00 0.00 0.00 3.01
1885 2496 6.605471 TTCTAGACTGGCAATGAAGACTTA 57.395 37.500 0.00 0.00 0.00 2.24
1887 2498 7.187824 TCTAGACTGGCAATGAAGACTTATT 57.812 36.000 0.00 0.00 0.00 1.40
1888 2499 7.044181 TCTAGACTGGCAATGAAGACTTATTG 58.956 38.462 10.56 10.56 37.35 1.90
1891 2502 6.491403 AGACTGGCAATGAAGACTTATTGTTT 59.509 34.615 13.89 3.15 36.81 2.83
1894 2505 6.815089 TGGCAATGAAGACTTATTGTTTTGT 58.185 32.000 13.89 0.00 36.81 2.83
1957 2570 4.454728 TGCCAATGGTCATTTTTCTAGC 57.545 40.909 0.00 0.00 0.00 3.42
1967 2603 5.241728 GGTCATTTTTCTAGCTTGTCCACTT 59.758 40.000 0.00 0.00 0.00 3.16
2025 2661 2.099098 GGTGTGTACTTTATGGGCATGC 59.901 50.000 9.90 9.90 0.00 4.06
2049 2685 1.624323 GTGTCGTTCGCACTATCGC 59.376 57.895 10.58 0.00 34.30 4.58
2069 2705 9.411801 CTATCGCATAGCTGTAATTAGAAAAGA 57.588 33.333 0.00 0.00 0.00 2.52
2125 2761 7.520119 TCATCGATAGTCACACAAATGTTAC 57.480 36.000 0.00 0.00 34.98 2.50
2126 2762 7.320399 TCATCGATAGTCACACAAATGTTACT 58.680 34.615 0.00 0.46 43.95 2.24
2252 2888 8.970691 ATTTATTGTGCTGACAAACATTAGAC 57.029 30.769 0.00 0.00 45.23 2.59
2277 2914 7.038799 ACAAATGGCTCCTTGAGAACATTATTT 60.039 33.333 11.98 0.00 37.60 1.40
2279 2916 6.916360 TGGCTCCTTGAGAACATTATTTTT 57.084 33.333 0.00 0.00 0.00 1.94
2285 2922 7.826690 TCCTTGAGAACATTATTTTTACAGCC 58.173 34.615 0.00 0.00 0.00 4.85
2297 2972 4.388189 TTTTACAGCCGTAGCGTTTAAC 57.612 40.909 0.00 0.00 46.67 2.01
2298 2973 1.616620 TACAGCCGTAGCGTTTAACG 58.383 50.000 13.57 13.57 46.67 3.18
2304 2979 2.661195 GCCGTAGCGTTTAACGAGTTTA 59.339 45.455 22.15 4.73 46.05 2.01
2433 3108 6.668283 AGAAGCAAAGAAGGGTCAGTATACTA 59.332 38.462 4.74 0.00 0.00 1.82
2434 3109 6.869206 AGCAAAGAAGGGTCAGTATACTAA 57.131 37.500 4.74 0.00 0.00 2.24
2439 3114 8.968969 CAAAGAAGGGTCAGTATACTAAGTACT 58.031 37.037 4.74 0.00 32.80 2.73
2519 3198 7.412853 CACAATAATTATTCTCCACACTCTGC 58.587 38.462 7.76 0.00 0.00 4.26
2523 3202 6.690194 AATTATTCTCCACACTCTGCATTC 57.310 37.500 0.00 0.00 0.00 2.67
2534 3216 4.454847 ACACTCTGCATTCTTCACATTCTG 59.545 41.667 0.00 0.00 0.00 3.02
2692 3466 6.956202 ATGCCTCTTTGATTATTCTCTTGG 57.044 37.500 0.00 0.00 0.00 3.61
2693 3467 5.819991 TGCCTCTTTGATTATTCTCTTGGT 58.180 37.500 0.00 0.00 0.00 3.67
2789 3572 3.486875 GGCTTACGATTTTCGAACCATGG 60.487 47.826 11.19 11.19 43.74 3.66
2880 3665 1.398390 CATGGCGTTGGCTCTTCTTAC 59.602 52.381 0.00 0.00 39.81 2.34
3004 3789 5.079689 TGCTCTACAAATCGGTCATGTAA 57.920 39.130 0.00 0.00 0.00 2.41
3018 6790 9.787532 ATCGGTCATGTAATGTTTAATTTGAAG 57.212 29.630 0.00 0.00 46.80 3.02
3104 7382 9.129209 GTTTGGTTTCTTAAGTATCTGAAATGC 57.871 33.333 1.63 0.00 32.22 3.56
3113 7391 5.573337 AGTATCTGAAATGCTTTTGCCTC 57.427 39.130 1.76 0.00 46.87 4.70
3120 7398 6.203338 TCTGAAATGCTTTTGCCTCAATTTTC 59.797 34.615 1.76 0.00 46.87 2.29
3150 7428 7.346471 ACACATTTCTGTAGCTATATTGGGTT 58.654 34.615 0.00 0.00 33.14 4.11
3205 7483 3.486875 CGTAAAATTAGCTTGGCGAAGGG 60.487 47.826 10.68 0.00 0.00 3.95
3246 7524 4.981674 CCACGTTGTAACATTGCTGATTTT 59.018 37.500 0.00 0.00 0.00 1.82
3370 7648 4.796038 TGTGGTCCTAAGTAGTAGCAAC 57.204 45.455 0.00 0.00 0.00 4.17
3394 7679 0.101219 GCAAAAAGAGCATAGCCCCG 59.899 55.000 0.00 0.00 0.00 5.73
3484 7776 6.183360 TGGCTTTCAGGCGGTTATAAAATAAG 60.183 38.462 0.00 0.00 44.78 1.73
3489 7781 8.918202 TTCAGGCGGTTATAAAATAAGATGAT 57.082 30.769 0.00 0.00 0.00 2.45
3530 7842 6.772716 ACTCTAGTCTGGCAAATCTTCAAAAA 59.227 34.615 0.00 0.00 0.00 1.94
3656 7985 4.923281 GGTTAATGGTGTCTTCATTGTTGC 59.077 41.667 0.00 0.00 36.40 4.17
3666 7995 3.509967 TCTTCATTGTTGCCTCTCTCGTA 59.490 43.478 0.00 0.00 0.00 3.43
3800 8216 3.610040 TGGCTAGTACAATGTGAGTGG 57.390 47.619 0.00 0.00 0.00 4.00
3833 8723 3.772025 CCTCCACAACTATCAGAACCTCT 59.228 47.826 0.00 0.00 0.00 3.69
3840 8730 6.486657 CACAACTATCAGAACCTCTGGAAAAA 59.513 38.462 3.92 0.00 44.39 1.94
3886 8776 1.302511 GTGGCCATCACAGACGGTT 60.303 57.895 9.72 0.00 45.39 4.44
3905 8795 1.760479 TTGTTGATGACGGACCGGGT 61.760 55.000 20.00 0.00 0.00 5.28
3910 8800 3.291101 ATGACGGACCGGGTGAACG 62.291 63.158 20.00 9.23 0.00 3.95
3919 8809 2.585698 GGGTGAACGGGGCGATTA 59.414 61.111 0.00 0.00 0.00 1.75
3962 8852 3.402681 CTCCCCGGCACCACTCAT 61.403 66.667 0.00 0.00 0.00 2.90
3986 8883 1.269998 GTGCCTATAGTACCGGAGCTG 59.730 57.143 9.46 0.00 0.00 4.24
4005 8902 1.375908 GTTGAGCTGATGCGGTGGA 60.376 57.895 0.00 0.00 45.42 4.02
4023 8920 1.443802 GAAGGCCTTGTTCTCCTTCG 58.556 55.000 26.25 0.00 44.19 3.79
4036 8933 3.376078 CTTCGTCGGGGGAACGGA 61.376 66.667 0.00 0.00 40.45 4.69
4045 8942 2.582436 GGGAACGGAAGATCGCCA 59.418 61.111 8.16 0.00 39.42 5.69
4046 8943 1.146263 GGGAACGGAAGATCGCCAT 59.854 57.895 8.16 0.00 39.42 4.40
4047 8944 1.160329 GGGAACGGAAGATCGCCATG 61.160 60.000 8.16 0.00 39.42 3.66
4071 8968 3.434310 GGGAATCCTCAATCTTCACCCTC 60.434 52.174 0.00 0.00 32.93 4.30
4076 8973 0.530744 TCAATCTTCACCCTCCGTCG 59.469 55.000 0.00 0.00 0.00 5.12
4098 8995 2.287668 CGGTGGATTACGGTGAGAGATC 60.288 54.545 0.00 0.00 0.00 2.75
4099 8996 2.959707 GGTGGATTACGGTGAGAGATCT 59.040 50.000 0.00 0.00 0.00 2.75
4101 8998 4.767928 GGTGGATTACGGTGAGAGATCTAT 59.232 45.833 0.00 0.00 0.00 1.98
4117 9014 4.947388 AGATCTATAGGAGGACATTCTCGC 59.053 45.833 0.00 0.00 34.74 5.03
4123 9020 4.467084 GGACATTCTCGCGGGGCA 62.467 66.667 5.94 0.00 0.00 5.36
4130 9027 4.514577 CTCGCGGGGCAGTACCTG 62.515 72.222 6.13 0.00 39.10 4.00
4139 9036 0.983378 GGCAGTACCTGTGGGGAGAT 60.983 60.000 0.00 0.00 38.76 2.75
4143 9040 1.123928 GTACCTGTGGGGAGATGAGG 58.876 60.000 0.00 0.00 38.76 3.86
4144 9041 0.031111 TACCTGTGGGGAGATGAGGG 60.031 60.000 0.00 0.00 38.76 4.30
4154 9051 0.177604 GAGATGAGGGTGTGCTGGAG 59.822 60.000 0.00 0.00 0.00 3.86
4155 9052 0.252421 AGATGAGGGTGTGCTGGAGA 60.252 55.000 0.00 0.00 0.00 3.71
4166 9063 1.816537 GCTGGAGAGCGGACACATA 59.183 57.895 0.00 0.00 34.87 2.29
4172 9069 2.287909 GGAGAGCGGACACATAGTGATC 60.288 54.545 3.88 0.00 36.96 2.92
4181 9078 4.031426 GGACACATAGTGATCGACGTTTTC 59.969 45.833 3.88 0.00 36.96 2.29
4200 9097 6.635239 CGTTTTCGTGATCTTTATTGGTTGTT 59.365 34.615 0.00 0.00 38.65 2.83
4206 9103 6.185399 GTGATCTTTATTGGTTGTTCGATCG 58.815 40.000 9.36 9.36 31.22 3.69
4209 9106 1.999048 TATTGGTTGTTCGATCGCGT 58.001 45.000 11.09 0.00 38.98 6.01
4213 9110 0.179156 GGTTGTTCGATCGCGTAGGA 60.179 55.000 11.09 0.00 38.98 2.94
4238 9135 1.512996 GGCGTGAGTCCGATCCGATA 61.513 60.000 5.36 0.00 0.00 2.92
4244 9141 4.025563 CGTGAGTCCGATCCGATAGATATC 60.026 50.000 0.00 0.00 34.42 1.63
4272 9169 0.668535 TCATACGACATCTCCGGCAG 59.331 55.000 0.00 0.00 0.00 4.85
4273 9170 0.941463 CATACGACATCTCCGGCAGC 60.941 60.000 0.00 0.00 0.00 5.25
4285 9182 2.764314 CGGCAGCGGAATTGAAGGG 61.764 63.158 0.00 0.00 0.00 3.95
4329 9226 1.598130 GATCCAAATCCCGAGCCCG 60.598 63.158 0.00 0.00 0.00 6.13
4335 9232 1.759459 AAATCCCGAGCCCGATCTCC 61.759 60.000 0.00 0.00 38.22 3.71
4359 9256 2.983725 GATCGGGGGCCATTTCTGGG 62.984 65.000 4.39 0.00 43.36 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.238646 ACCCGATCAAGGCTATGACAAA 59.761 45.455 0.00 0.00 30.82 2.83
29 30 1.837439 ACCCGATCAAGGCTATGACAA 59.163 47.619 0.00 0.00 30.82 3.18
30 31 1.138859 CACCCGATCAAGGCTATGACA 59.861 52.381 0.00 0.00 30.82 3.58
48 49 1.136984 GCTGCAGCAAGATGAGCAC 59.863 57.895 33.36 0.00 41.59 4.40
56 57 1.862827 GGTTCAAAAAGCTGCAGCAAG 59.137 47.619 38.24 22.29 45.16 4.01
57 58 1.802136 CGGTTCAAAAAGCTGCAGCAA 60.802 47.619 38.24 21.00 45.16 3.91
60 61 0.318955 CCCGGTTCAAAAAGCTGCAG 60.319 55.000 10.11 10.11 0.00 4.41
101 102 9.758651 AGCTGTGTATTTTCGTTATGATATACA 57.241 29.630 0.00 6.08 34.60 2.29
103 104 9.974980 TCAGCTGTGTATTTTCGTTATGATATA 57.025 29.630 14.67 0.00 0.00 0.86
104 105 8.887036 TCAGCTGTGTATTTTCGTTATGATAT 57.113 30.769 14.67 0.00 0.00 1.63
105 106 8.887036 ATCAGCTGTGTATTTTCGTTATGATA 57.113 30.769 14.67 0.00 0.00 2.15
106 107 7.041780 GGATCAGCTGTGTATTTTCGTTATGAT 60.042 37.037 14.67 0.00 0.00 2.45
107 108 6.257849 GGATCAGCTGTGTATTTTCGTTATGA 59.742 38.462 14.67 0.00 0.00 2.15
108 109 6.422223 GGATCAGCTGTGTATTTTCGTTATG 58.578 40.000 14.67 0.00 0.00 1.90
109 110 5.527582 GGGATCAGCTGTGTATTTTCGTTAT 59.472 40.000 14.67 0.00 0.00 1.89
110 111 4.873827 GGGATCAGCTGTGTATTTTCGTTA 59.126 41.667 14.67 0.00 0.00 3.18
119 120 0.253044 GCAAGGGGATCAGCTGTGTA 59.747 55.000 14.67 0.00 0.00 2.90
125 126 1.407979 CTCAATTGCAAGGGGATCAGC 59.592 52.381 4.94 0.00 0.00 4.26
132 133 2.165030 GTGGATGTCTCAATTGCAAGGG 59.835 50.000 4.94 0.00 0.00 3.95
134 135 2.821378 TGGTGGATGTCTCAATTGCAAG 59.179 45.455 4.94 0.00 0.00 4.01
168 169 1.878522 GATAGTGTGGTGCCGCTCG 60.879 63.158 3.31 0.00 0.00 5.03
184 185 6.496565 AGGTAGCTAGCAGATTCTGTTATGAT 59.503 38.462 24.01 8.61 33.43 2.45
263 264 5.212194 GTTTGATTTTTAGCACGCTTGAGA 58.788 37.500 0.00 0.00 0.00 3.27
269 270 3.049206 TGCTGTTTGATTTTTAGCACGC 58.951 40.909 0.00 0.00 39.26 5.34
271 272 6.826893 TTCTTGCTGTTTGATTTTTAGCAC 57.173 33.333 0.00 0.00 43.32 4.40
299 300 1.206849 CCTCCTGCTCAGAACTCCTTC 59.793 57.143 0.00 0.00 0.00 3.46
365 367 2.490168 CCATGGATTGATCAGGCATCCA 60.490 50.000 23.58 23.58 44.44 3.41
380 382 0.904865 AAGGTCACGAGAGCCATGGA 60.905 55.000 18.40 0.00 43.21 3.41
382 384 1.813513 AAAAGGTCACGAGAGCCATG 58.186 50.000 8.47 0.00 43.21 3.66
427 429 3.136123 CGGCCTTGCATCTGTGGG 61.136 66.667 0.00 0.00 0.00 4.61
432 434 0.250209 CTATGAGCGGCCTTGCATCT 60.250 55.000 0.00 0.00 37.31 2.90
489 491 2.334946 TTCTCGTGCATGCTTGGCC 61.335 57.895 20.33 0.00 0.00 5.36
490 492 1.154150 GTTCTCGTGCATGCTTGGC 60.154 57.895 20.33 5.71 0.00 4.52
491 493 1.236616 TGGTTCTCGTGCATGCTTGG 61.237 55.000 20.33 8.03 0.00 3.61
492 494 0.167470 CTGGTTCTCGTGCATGCTTG 59.833 55.000 20.33 11.29 0.00 4.01
493 495 0.035317 TCTGGTTCTCGTGCATGCTT 59.965 50.000 20.33 0.00 0.00 3.91
494 496 0.671781 GTCTGGTTCTCGTGCATGCT 60.672 55.000 20.33 0.00 0.00 3.79
495 497 0.950555 TGTCTGGTTCTCGTGCATGC 60.951 55.000 11.82 11.82 0.00 4.06
498 500 1.069090 GGTGTCTGGTTCTCGTGCA 59.931 57.895 0.00 0.00 0.00 4.57
522 524 5.776519 TGTTTTTACGTACTTTCGTGTGT 57.223 34.783 0.00 0.00 43.93 3.72
528 530 6.788930 CGATGGTCTTGTTTTTACGTACTTTC 59.211 38.462 0.00 0.00 0.00 2.62
545 547 0.544357 TGGTTCTGTCCCGATGGTCT 60.544 55.000 0.00 0.00 0.00 3.85
576 578 1.937191 TGTGGAGATGGAGTAGTGCA 58.063 50.000 0.00 0.00 0.00 4.57
579 581 3.298686 TCGATGTGGAGATGGAGTAGT 57.701 47.619 0.00 0.00 0.00 2.73
591 593 2.074576 GCATCCAGATGATCGATGTGG 58.925 52.381 11.81 12.32 45.34 4.17
619 626 2.159170 GCTACAGCTACAGGTTGAGGAG 60.159 54.545 0.00 0.00 38.21 3.69
636 643 1.332997 GCAGTGCATGAATGGAGCTAC 59.667 52.381 11.09 0.00 0.00 3.58
637 644 1.065272 TGCAGTGCATGAATGGAGCTA 60.065 47.619 15.37 0.00 31.71 3.32
638 645 0.323087 TGCAGTGCATGAATGGAGCT 60.323 50.000 15.37 0.00 31.71 4.09
639 646 0.179145 GTGCAGTGCATGAATGGAGC 60.179 55.000 22.87 0.39 41.91 4.70
731 738 2.280052 GCAGCCAGATCGCCTCTC 60.280 66.667 0.00 0.00 29.16 3.20
736 743 3.344215 CGGATGCAGCCAGATCGC 61.344 66.667 22.95 0.00 0.00 4.58
883 897 1.271434 GGGAGAGTTGGAGGGTGTTTC 60.271 57.143 0.00 0.00 0.00 2.78
888 902 1.305381 CGAGGGAGAGTTGGAGGGT 60.305 63.158 0.00 0.00 0.00 4.34
983 998 1.840650 ATGGCGAGAGATCTGGGGG 60.841 63.158 0.00 0.00 0.00 5.40
988 1003 2.037053 CCGACATGGCGAGAGATCT 58.963 57.895 25.84 0.00 0.00 2.75
989 1004 4.643733 CCGACATGGCGAGAGATC 57.356 61.111 25.84 0.00 0.00 2.75
1108 1135 0.390866 CATCACGAGAAGGCACAGCT 60.391 55.000 0.00 0.00 0.00 4.24
1146 1173 3.025978 TGGAAATACTCGTCCACCGTAT 58.974 45.455 0.00 0.00 39.04 3.06
1285 1312 2.696125 GAGGAGGGATTGGGGGCA 60.696 66.667 0.00 0.00 0.00 5.36
1294 1321 0.105760 GCAGATGGAGAGAGGAGGGA 60.106 60.000 0.00 0.00 0.00 4.20
1318 1346 8.222637 TGAAATCAATACCCAAGATGAGATGAT 58.777 33.333 0.00 0.00 0.00 2.45
1344 1372 1.869767 GAATCGCAAAGCAGATCGGAT 59.130 47.619 0.00 0.00 0.00 4.18
1376 1404 4.998051 ACCTTGTTGAAATCTACCATGGT 58.002 39.130 23.55 23.55 0.00 3.55
1559 1772 9.383519 ACCTATGACTACATGACAACTTAAATG 57.616 33.333 0.00 0.00 37.87 2.32
1571 1784 6.260271 TCGACACTTCTACCTATGACTACATG 59.740 42.308 0.00 0.00 37.87 3.21
1572 1785 6.354938 TCGACACTTCTACCTATGACTACAT 58.645 40.000 0.00 0.00 40.16 2.29
1601 1814 7.865385 TGTACTTCCATTACATGAAACAAAAGC 59.135 33.333 0.00 0.00 0.00 3.51
1605 1818 8.862325 ATCTGTACTTCCATTACATGAAACAA 57.138 30.769 0.00 0.00 0.00 2.83
1618 1831 5.307716 TGATGCATGGATATCTGTACTTCCA 59.692 40.000 2.46 0.00 42.18 3.53
1627 1840 1.718396 CGCGTGATGCATGGATATCT 58.282 50.000 2.46 0.00 46.97 1.98
1629 1842 0.603439 TGCGCGTGATGCATGGATAT 60.603 50.000 2.46 0.00 46.97 1.63
1639 2233 1.396996 GAAAACTACCATGCGCGTGAT 59.603 47.619 30.68 17.70 0.00 3.06
1641 2235 0.796312 AGAAAACTACCATGCGCGTG 59.204 50.000 22.83 22.83 0.00 5.34
1646 2240 2.884639 ACACACCAGAAAACTACCATGC 59.115 45.455 0.00 0.00 0.00 4.06
1647 2241 3.502211 GGACACACCAGAAAACTACCATG 59.498 47.826 0.00 0.00 38.79 3.66
1699 2294 2.852495 ATCCGACAGCCGCAAACGAT 62.852 55.000 0.00 0.00 43.93 3.73
1724 2319 9.429359 CACAACTGAACTCAGATCTTATACTTT 57.571 33.333 13.61 0.00 46.59 2.66
1769 2367 1.391485 GCATCGCTATGGCACGAATAG 59.609 52.381 0.74 0.00 42.31 1.73
1782 2381 3.305950 CCTTGAAGAGCTATAGCATCGCT 60.306 47.826 26.07 14.15 45.16 4.93
1799 2398 5.849510 TCAAGACGACAAAGTATTCCTTGA 58.150 37.500 0.00 0.00 37.15 3.02
1844 2450 9.243105 AGTCTAGAAAATTGCCATTAGCTAAAA 57.757 29.630 10.85 0.15 44.23 1.52
1849 2455 5.734503 GCCAGTCTAGAAAATTGCCATTAGC 60.735 44.000 0.00 0.00 44.14 3.09
1861 2467 5.489792 AGTCTTCATTGCCAGTCTAGAAA 57.510 39.130 0.00 0.00 0.00 2.52
1868 2474 6.655078 AAACAATAAGTCTTCATTGCCAGT 57.345 33.333 11.53 0.00 35.91 4.00
1903 2514 8.700051 AGAATAGCCGCTCATTGATACTATAAT 58.300 33.333 0.00 0.00 0.00 1.28
1905 2516 7.646548 AGAATAGCCGCTCATTGATACTATA 57.353 36.000 0.00 0.00 0.00 1.31
1906 2517 6.537453 AGAATAGCCGCTCATTGATACTAT 57.463 37.500 0.00 0.00 0.00 2.12
1907 2518 5.984695 AGAATAGCCGCTCATTGATACTA 57.015 39.130 0.00 0.00 0.00 1.82
1908 2519 4.881019 AGAATAGCCGCTCATTGATACT 57.119 40.909 0.00 0.00 0.00 2.12
1919 2530 1.725164 GGCATTACGTAGAATAGCCGC 59.275 52.381 9.11 0.00 0.00 6.53
1957 2570 8.647143 AAAACAACATCAATAAAGTGGACAAG 57.353 30.769 0.00 0.00 0.00 3.16
1988 2624 2.438434 CCCCGTGCCAACTCATCC 60.438 66.667 0.00 0.00 0.00 3.51
2013 2649 2.186160 CGAGCCGCATGCCCATAAA 61.186 57.895 13.15 0.00 42.71 1.40
2015 2651 3.860605 ACGAGCCGCATGCCCATA 61.861 61.111 13.15 0.00 42.71 2.74
2037 2673 1.067060 ACAGCTATGCGATAGTGCGAA 59.933 47.619 0.00 0.00 37.81 4.70
2114 2750 5.676744 CACTTGTCGAACAGTAACATTTGTG 59.323 40.000 0.00 0.00 0.00 3.33
2115 2751 5.583061 TCACTTGTCGAACAGTAACATTTGT 59.417 36.000 0.00 0.00 0.00 2.83
2125 2761 6.685403 ACGTTAAAATTTCACTTGTCGAACAG 59.315 34.615 0.00 0.00 0.00 3.16
2126 2762 6.466413 CACGTTAAAATTTCACTTGTCGAACA 59.534 34.615 0.00 0.00 0.00 3.18
2237 2873 6.017400 AGCCATTTGTCTAATGTTTGTCAG 57.983 37.500 6.31 0.00 41.74 3.51
2244 2880 4.922206 TCAAGGAGCCATTTGTCTAATGT 58.078 39.130 6.31 0.00 41.74 2.71
2246 2882 5.441718 TCTCAAGGAGCCATTTGTCTAAT 57.558 39.130 0.00 0.00 0.00 1.73
2252 2888 4.796038 AATGTTCTCAAGGAGCCATTTG 57.204 40.909 0.00 0.00 31.77 2.32
2277 2914 2.408032 CGTTAAACGCTACGGCTGTAAA 59.592 45.455 6.88 0.00 33.65 2.01
2279 2916 1.198867 TCGTTAAACGCTACGGCTGTA 59.801 47.619 5.05 5.05 42.21 2.74
2285 2922 5.729665 TCTTAAACTCGTTAAACGCTACG 57.270 39.130 0.00 0.00 42.21 3.51
2318 2993 4.525487 TGCCAAAAAGAGCAAGATCAGAAT 59.475 37.500 0.00 0.00 35.69 2.40
2320 2995 3.489355 TGCCAAAAAGAGCAAGATCAGA 58.511 40.909 0.00 0.00 35.69 3.27
2454 3129 9.533253 AAGCTACCAAATGAATAATTATTGTGC 57.467 29.630 15.39 11.01 0.00 4.57
2470 3145 9.268268 GTGCAACATATATAGTAAGCTACCAAA 57.732 33.333 0.00 0.00 36.32 3.28
2601 3361 9.880157 ATAAAGTGAACGCTAGTCCTTATAAAA 57.120 29.630 0.00 0.00 0.00 1.52
2604 3364 9.309516 CAAATAAAGTGAACGCTAGTCCTTATA 57.690 33.333 0.00 0.00 0.00 0.98
2605 3365 7.201617 GCAAATAAAGTGAACGCTAGTCCTTAT 60.202 37.037 0.00 0.00 0.00 1.73
2765 3546 2.739913 TGGTTCGAAAATCGTAAGCCTG 59.260 45.455 0.00 0.00 41.35 4.85
2789 3572 8.239998 AGAGAATAATTAAGCAAACTGAACTGC 58.760 33.333 0.00 0.00 38.91 4.40
2880 3665 1.267235 GCACATCGCAGAACTCATTCG 60.267 52.381 0.00 0.00 43.58 3.34
2903 3688 2.421424 GCATCATGGTCTGGAACTTGTC 59.579 50.000 0.00 0.00 0.00 3.18
3104 7382 4.803088 TGTTGACGAAAATTGAGGCAAAAG 59.197 37.500 0.00 0.00 0.00 2.27
3113 7391 6.810888 ACAGAAATGTGTTGACGAAAATTG 57.189 33.333 0.00 0.00 0.00 2.32
3120 7398 7.700322 ATATAGCTACAGAAATGTGTTGACG 57.300 36.000 0.00 0.00 31.46 4.35
3205 7483 1.342174 TGGTCGGTATCTTATTCCGGC 59.658 52.381 0.00 3.46 45.48 6.13
3227 7505 8.223100 GGATTCAAAAATCAGCAATGTTACAAC 58.777 33.333 0.00 0.00 42.66 3.32
3246 7524 5.417266 TGTTTGTCAAGTCACAAGGATTCAA 59.583 36.000 0.00 0.00 37.57 2.69
3306 7584 4.215827 AGCTGCATCAAAAGAAGAACAGAG 59.784 41.667 1.02 0.00 0.00 3.35
3370 7648 2.478539 GGCTATGCTCTTTTTGCTTCGG 60.479 50.000 0.00 0.00 0.00 4.30
3484 7776 7.271511 AGAGTTCCTACACAAGATTCATCATC 58.728 38.462 0.00 0.00 0.00 2.92
3489 7781 6.948886 AGACTAGAGTTCCTACACAAGATTCA 59.051 38.462 0.00 0.00 0.00 2.57
3530 7842 6.650807 AGACATAGACACATGACAACGATTTT 59.349 34.615 0.00 0.00 0.00 1.82
3656 7985 5.821516 AGACAGTAAACATACGAGAGAGG 57.178 43.478 0.00 0.00 0.00 3.69
3666 7995 3.689649 GCATCCCGAAAGACAGTAAACAT 59.310 43.478 0.00 0.00 0.00 2.71
3714 8130 9.616156 TGTAGTTTTAGAGAACCAACAAACATA 57.384 29.630 0.00 0.00 0.00 2.29
3757 8173 7.633772 GCCAACATAGGACTTCTAATCTCAAGA 60.634 40.741 0.00 0.00 0.00 3.02
3840 8730 5.032327 AGGGAACTGTAACGAGTCTTTTT 57.968 39.130 0.00 0.00 41.13 1.94
3841 8731 4.502777 GGAGGGAACTGTAACGAGTCTTTT 60.503 45.833 0.00 0.00 44.43 2.27
3842 8732 3.006644 GGAGGGAACTGTAACGAGTCTTT 59.993 47.826 0.00 0.00 44.43 2.52
3886 8776 1.004320 CCCGGTCCGTCATCAACAA 60.004 57.895 11.06 0.00 0.00 2.83
3957 8847 5.185249 CCGGTACTATAGGCACATAATGAGT 59.815 44.000 4.43 0.00 0.00 3.41
3958 8848 5.417894 TCCGGTACTATAGGCACATAATGAG 59.582 44.000 0.00 0.00 0.00 2.90
3959 8849 5.326900 TCCGGTACTATAGGCACATAATGA 58.673 41.667 0.00 0.00 0.00 2.57
3960 8850 5.651530 CTCCGGTACTATAGGCACATAATG 58.348 45.833 0.00 0.00 0.00 1.90
3961 8851 4.159879 GCTCCGGTACTATAGGCACATAAT 59.840 45.833 0.00 0.00 0.00 1.28
3962 8852 3.508793 GCTCCGGTACTATAGGCACATAA 59.491 47.826 0.00 0.00 0.00 1.90
3986 8883 2.401766 CCACCGCATCAGCTCAACC 61.402 63.158 0.00 0.00 39.10 3.77
3994 8891 2.905996 AAGGCCTTCCACCGCATCA 61.906 57.895 13.78 0.00 33.74 3.07
3999 8896 0.955919 GAGAACAAGGCCTTCCACCG 60.956 60.000 17.29 6.63 33.74 4.94
4005 8902 0.765510 ACGAAGGAGAACAAGGCCTT 59.234 50.000 13.78 13.78 44.32 4.35
4023 8920 1.143401 GATCTTCCGTTCCCCCGAC 59.857 63.158 0.00 0.00 0.00 4.79
4036 8933 0.111253 GATTCCCCCATGGCGATCTT 59.889 55.000 6.09 0.00 0.00 2.40
4044 8941 3.117398 TGAAGATTGAGGATTCCCCCATG 60.117 47.826 0.00 0.00 34.66 3.66
4045 8942 3.117360 GTGAAGATTGAGGATTCCCCCAT 60.117 47.826 0.00 0.00 34.66 4.00
4046 8943 2.242196 GTGAAGATTGAGGATTCCCCCA 59.758 50.000 0.00 0.00 34.66 4.96
4047 8944 2.423517 GGTGAAGATTGAGGATTCCCCC 60.424 54.545 0.00 0.00 34.66 5.40
4076 8973 0.527817 CTCTCACCGTAATCCACCGC 60.528 60.000 0.00 0.00 0.00 5.68
4079 8976 5.968528 ATAGATCTCTCACCGTAATCCAC 57.031 43.478 0.00 0.00 0.00 4.02
4098 8995 2.162608 CCGCGAGAATGTCCTCCTATAG 59.837 54.545 8.23 0.00 0.00 1.31
4099 8996 2.160205 CCGCGAGAATGTCCTCCTATA 58.840 52.381 8.23 0.00 0.00 1.31
4101 8998 1.107538 CCCGCGAGAATGTCCTCCTA 61.108 60.000 8.23 0.00 0.00 2.94
4123 9020 1.343478 CCTCATCTCCCCACAGGTACT 60.343 57.143 0.00 0.00 43.88 2.73
4130 9027 1.604378 CACACCCTCATCTCCCCAC 59.396 63.158 0.00 0.00 0.00 4.61
4131 9028 2.300967 GCACACCCTCATCTCCCCA 61.301 63.158 0.00 0.00 0.00 4.96
4139 9036 2.587247 GCTCTCCAGCACACCCTCA 61.587 63.158 0.00 0.00 46.06 3.86
4154 9051 1.333931 TCGATCACTATGTGTCCGCTC 59.666 52.381 0.00 0.00 34.79 5.03
4155 9052 1.065701 GTCGATCACTATGTGTCCGCT 59.934 52.381 0.00 0.00 34.79 5.52
4159 9056 5.114804 GAAAACGTCGATCACTATGTGTC 57.885 43.478 0.00 0.00 34.79 3.67
4181 9078 5.524511 TCGAACAACCAATAAAGATCACG 57.475 39.130 0.00 0.00 0.00 4.35
4183 9080 5.220586 GCGATCGAACAACCAATAAAGATCA 60.221 40.000 21.57 0.00 34.58 2.92
4189 9086 2.339418 ACGCGATCGAACAACCAATAA 58.661 42.857 21.57 0.00 39.41 1.40
4219 9116 1.512996 TATCGGATCGGACTCACGCC 61.513 60.000 4.94 0.00 0.00 5.68
4238 9135 5.705905 TGTCGTATGAAGATCCACGATATCT 59.294 40.000 0.34 0.00 44.29 1.98
4244 9141 4.222886 GAGATGTCGTATGAAGATCCACG 58.777 47.826 0.00 0.00 35.78 4.94
4254 9151 0.941463 GCTGCCGGAGATGTCGTATG 60.941 60.000 5.05 0.00 0.00 2.39
4255 9152 1.364171 GCTGCCGGAGATGTCGTAT 59.636 57.895 5.05 0.00 0.00 3.06
4272 9169 1.474330 ACCATTCCCTTCAATTCCGC 58.526 50.000 0.00 0.00 0.00 5.54
4273 9170 3.763897 AGAAACCATTCCCTTCAATTCCG 59.236 43.478 0.00 0.00 36.12 4.30
4285 9182 0.168128 CGCCAACCGAGAAACCATTC 59.832 55.000 0.00 0.00 40.02 2.67
4314 9211 1.598130 GATCGGGCTCGGGATTTGG 60.598 63.158 5.94 0.00 36.95 3.28
4339 9236 1.533711 CAGAAATGGCCCCCGATCT 59.466 57.895 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.