Multiple sequence alignment - TraesCS5B01G364800

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 TraesCS5B01G364800 chr5B 100.000 5980 0 0 1 5980 543301898 543295919 0.000000e+00 11044.0
1 TraesCS5B01G364800 chr5B 90.196 867 65 2 5114 5980 425359095 425359941 0.000000e+00 1112.0
2 TraesCS5B01G364800 chr5B 86.429 840 69 9 5146 5980 57988214 57989013 0.000000e+00 878.0
3 TraesCS5B01G364800 chr5B 84.923 650 89 5 3259 3905 543244966 543244323 0.000000e+00 649.0
4 TraesCS5B01G364800 chr5B 82.704 636 103 4 3248 3882 531193741 531194370 5.230000e-155 558.0
5 TraesCS5B01G364800 chr5B 82.287 446 68 7 2016 2460 531192588 531193023 5.660000e-100 375.0
6 TraesCS5B01G364800 chr5B 83.721 387 57 5 2019 2402 543275704 543275321 1.580000e-95 361.0
7 TraesCS5B01G364800 chr5B 87.943 282 31 1 4170 4451 543270162 543269884 4.470000e-86 329.0
8 TraesCS5B01G364800 chr5B 86.644 292 37 2 4161 4451 531194721 531195011 7.480000e-84 322.0
9 TraesCS5B01G364800 chr5B 84.146 328 46 6 4156 4482 531206714 531207036 4.500000e-81 313.0
10 TraesCS5B01G364800 chr5B 76.724 580 117 14 2461 3033 543274307 543273739 2.090000e-79 307.0
11 TraesCS5B01G364800 chr5B 83.333 114 13 2 4667 4774 542950439 542950326 3.810000e-17 100.0
12 TraesCS5B01G364800 chr5B 97.143 35 1 0 1215 1249 543283357 543283323 6.470000e-05 60.2
13 TraesCS5B01G364800 chr5D 93.636 1697 96 2 2461 4157 445491694 445490010 0.000000e+00 2525.0
14 TraesCS5B01G364800 chr5D 96.320 951 23 3 4152 5090 445489970 445489020 0.000000e+00 1552.0
15 TraesCS5B01G364800 chr5D 90.121 1073 47 22 965 2012 445493287 445492249 0.000000e+00 1339.0
16 TraesCS5B01G364800 chr5D 92.012 964 58 9 1 963 445494455 445493510 0.000000e+00 1336.0
17 TraesCS5B01G364800 chr5D 98.448 451 7 0 2010 2460 445492175 445491725 0.000000e+00 795.0
18 TraesCS5B01G364800 chr5D 84.462 650 92 5 3259 3905 445404374 445403731 3.040000e-177 632.0
19 TraesCS5B01G364800 chr5D 83.333 636 99 4 3248 3882 436982341 436982970 1.120000e-161 580.0
20 TraesCS5B01G364800 chr5D 83.857 446 61 9 2016 2460 436981188 436981623 1.200000e-111 414.0
21 TraesCS5B01G364800 chr5D 83.503 394 51 11 4087 4476 553912589 553912972 7.370000e-94 355.0
22 TraesCS5B01G364800 chr5D 89.179 268 23 5 4216 4482 445403495 445403233 4.470000e-86 329.0
23 TraesCS5B01G364800 chr5D 83.761 351 43 7 4101 4450 436983273 436983610 2.690000e-83 320.0
24 TraesCS5B01G364800 chr5D 83.871 341 48 7 4143 4482 437017230 437017564 9.670000e-83 318.0
25 TraesCS5B01G364800 chr5D 75.468 587 86 26 4224 4794 445317028 445316484 3.600000e-57 233.0
26 TraesCS5B01G364800 chr7B 90.899 868 55 8 5114 5980 586759588 586758744 0.000000e+00 1144.0
27 TraesCS5B01G364800 chr7B 89.920 873 60 7 5114 5980 586777539 586776689 0.000000e+00 1099.0
28 TraesCS5B01G364800 chr7B 89.528 869 64 6 5114 5980 112126899 112126056 0.000000e+00 1075.0
29 TraesCS5B01G364800 chr4A 89.885 870 66 4 5114 5980 729322882 729323732 0.000000e+00 1099.0
30 TraesCS5B01G364800 chr4A 93.333 45 2 1 647 691 642916401 642916444 1.390000e-06 65.8
31 TraesCS5B01G364800 chr3B 89.988 869 57 10 5114 5980 651731458 651730618 0.000000e+00 1096.0
32 TraesCS5B01G364800 chr2B 89.782 871 66 6 5114 5980 728584166 728583315 0.000000e+00 1094.0
33 TraesCS5B01G364800 chr2B 91.879 628 49 1 5114 5739 39330055 39330682 0.000000e+00 876.0
34 TraesCS5B01G364800 chr1B 89.323 871 66 9 5114 5980 465681402 465682249 0.000000e+00 1068.0
35 TraesCS5B01G364800 chr1B 84.047 771 78 13 5211 5980 658532510 658533236 0.000000e+00 701.0
36 TraesCS5B01G364800 chr1B 82.847 548 90 2 3336 3882 553014175 553013631 6.970000e-134 488.0
37 TraesCS5B01G364800 chr1B 85.194 439 65 0 2023 2461 553015496 553015058 9.140000e-123 451.0
38 TraesCS5B01G364800 chr1B 77.901 181 34 5 466 641 644268528 644268707 2.280000e-19 108.0
39 TraesCS5B01G364800 chr4B 86.636 868 62 19 5114 5980 587268985 587269799 0.000000e+00 911.0
40 TraesCS5B01G364800 chr4B 86.709 158 17 2 4869 5022 2207406 2207563 7.970000e-39 172.0
41 TraesCS5B01G364800 chr4B 86.709 158 17 2 4869 5022 2236837 2236994 7.970000e-39 172.0
42 TraesCS5B01G364800 chr2D 85.537 885 87 15 5114 5980 590329761 590328900 0.000000e+00 887.0
43 TraesCS5B01G364800 chr2D 74.802 504 80 29 130 594 4468936 4468441 3.680000e-42 183.0
44 TraesCS5B01G364800 chr4D 78.869 1415 211 39 2461 3857 2974234 2975578 0.000000e+00 876.0
45 TraesCS5B01G364800 chr4D 89.888 445 45 0 2010 2454 2973750 2974194 1.870000e-159 573.0
46 TraesCS5B01G364800 chr4D 82.324 611 68 24 4157 4730 2975766 2976373 1.500000e-135 494.0
47 TraesCS5B01G364800 chr4D 79.073 626 108 16 3244 3868 1688855 1689458 5.580000e-110 409.0
48 TraesCS5B01G364800 chr4D 82.667 450 75 3 2015 2461 1687521 1687970 4.340000e-106 396.0
49 TraesCS5B01G364800 chr4D 88.667 300 34 0 4156 4455 1689605 1689904 3.410000e-97 366.0
50 TraesCS5B01G364800 chr4D 78.909 550 96 14 2494 3033 1688033 1688572 7.370000e-94 355.0
51 TraesCS5B01G364800 chr4D 87.879 297 32 3 4156 4451 1638532 1638825 4.440000e-91 346.0
52 TraesCS5B01G364800 chr4D 88.485 165 18 1 4830 4993 2976561 2976725 1.310000e-46 198.0
53 TraesCS5B01G364800 chr4D 82.540 126 16 6 122 243 382304292 382304169 8.200000e-19 106.0
54 TraesCS5B01G364800 chr7D 84.312 886 95 23 5114 5980 104359725 104360585 0.000000e+00 826.0
55 TraesCS5B01G364800 chr7D 74.303 502 80 34 172 634 101025778 101026269 3.710000e-37 167.0
56 TraesCS5B01G364800 chr7D 73.970 461 83 20 207 641 629494695 629494246 1.040000e-32 152.0
57 TraesCS5B01G364800 chrUn 90.517 580 44 5 313 891 433954845 433954276 0.000000e+00 756.0
58 TraesCS5B01G364800 chrUn 81.687 830 79 29 1202 2002 63573878 63573093 1.830000e-174 623.0
59 TraesCS5B01G364800 chrUn 83.560 663 67 16 1369 2002 411621315 411620666 3.110000e-162 582.0
60 TraesCS5B01G364800 chrUn 85.388 219 15 7 33 249 433955058 433954855 1.690000e-50 211.0
61 TraesCS5B01G364800 chrUn 86.709 158 17 2 4869 5022 51689915 51690072 7.970000e-39 172.0
62 TraesCS5B01G364800 chrUn 90.000 100 10 0 1202 1301 475131360 475131261 4.860000e-26 130.0
63 TraesCS5B01G364800 chrUn 76.577 222 44 7 3402 3619 310057855 310057638 1.360000e-21 115.0
64 TraesCS5B01G364800 chr5A 85.077 650 88 3 3259 3905 563255050 563254407 0.000000e+00 654.0
65 TraesCS5B01G364800 chr5A 83.176 636 100 4 3248 3882 552268791 552269420 5.200000e-160 575.0
66 TraesCS5B01G364800 chr5A 84.305 446 59 9 2016 2460 552267617 552268052 5.540000e-115 425.0
67 TraesCS5B01G364800 chr5A 77.875 574 116 9 2461 3033 552268083 552268646 4.440000e-91 346.0
68 TraesCS5B01G364800 chr5A 83.117 385 53 10 4099 4482 552300381 552300754 2.060000e-89 340.0
69 TraesCS5B01G364800 chr5A 84.328 134 14 3 4667 4794 562889479 562889347 2.260000e-24 124.0
70 TraesCS5B01G364800 chr5A 81.250 128 21 3 515 641 141558989 141559114 3.810000e-17 100.0
71 TraesCS5B01G364800 chr1D 82.683 589 89 8 3333 3911 410458608 410458023 1.490000e-140 510.0
72 TraesCS5B01G364800 chr1D 83.024 377 63 1 2023 2399 410460185 410459810 2.060000e-89 340.0
73 TraesCS5B01G364800 chr1D 80.444 225 34 7 149 369 485737653 485737871 4.800000e-36 163.0
74 TraesCS5B01G364800 chr1D 94.872 39 2 0 204 242 14517591 14517629 1.800000e-05 62.1
75 TraesCS5B01G364800 chr1D 94.872 39 2 0 204 242 14530587 14530625 1.800000e-05 62.1
76 TraesCS5B01G364800 chr1A 84.810 395 59 1 3370 3763 506278662 506278268 4.340000e-106 396.0
77 TraesCS5B01G364800 chr1A 84.589 292 40 3 4159 4449 506277699 506277412 9.810000e-73 285.0
78 TraesCS5B01G364800 chr1A 78.988 257 46 7 388 639 252276564 252276311 1.030000e-37 169.0
79 TraesCS5B01G364800 chr1A 84.874 119 11 7 129 243 15425966 15425851 4.900000e-21 113.0
80 TraesCS5B01G364800 chr1A 87.500 56 7 0 4211 4266 21616617 21616672 1.390000e-06 65.8
81 TraesCS5B01G364800 chr7A 83.692 325 46 6 4156 4478 7826586 7826905 3.500000e-77 300.0
82 TraesCS5B01G364800 chr3D 78.243 239 43 8 411 641 600494395 600494632 1.740000e-30 145.0
83 TraesCS5B01G364800 chr3D 93.333 45 2 1 647 691 523388520 523388563 1.390000e-06 65.8
84 TraesCS5B01G364800 chr2A 76.834 259 53 6 388 641 676375026 676375282 8.080000e-29 139.0
85 TraesCS5B01G364800 chr6A 75.676 222 47 5 3402 3619 614842902 614843120 2.950000e-18 104.0
86 TraesCS5B01G364800 chr6B 75.120 209 42 8 3402 3605 716264308 716264511 8.250000e-14 89.8


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 TraesCS5B01G364800 chr5B 543295919 543301898 5979 True 11044.000000 11044 100.000000 1 5980 1 chr5B.!!$R4 5979
1 TraesCS5B01G364800 chr5B 425359095 425359941 846 False 1112.000000 1112 90.196000 5114 5980 1 chr5B.!!$F2 866
2 TraesCS5B01G364800 chr5B 57988214 57989013 799 False 878.000000 878 86.429000 5146 5980 1 chr5B.!!$F1 834
3 TraesCS5B01G364800 chr5B 543244323 543244966 643 True 649.000000 649 84.923000 3259 3905 1 chr5B.!!$R2 646
4 TraesCS5B01G364800 chr5B 531192588 531195011 2423 False 418.333333 558 83.878333 2016 4451 3 chr5B.!!$F4 2435
5 TraesCS5B01G364800 chr5B 543269884 543275704 5820 True 332.333333 361 82.796000 2019 4451 3 chr5B.!!$R5 2432
6 TraesCS5B01G364800 chr5D 445489020 445494455 5435 True 1509.400000 2525 94.107400 1 5090 5 chr5D.!!$R3 5089
7 TraesCS5B01G364800 chr5D 445403233 445404374 1141 True 480.500000 632 86.820500 3259 4482 2 chr5D.!!$R2 1223
8 TraesCS5B01G364800 chr5D 436981188 436983610 2422 False 438.000000 580 83.650333 2016 4450 3 chr5D.!!$F3 2434
9 TraesCS5B01G364800 chr5D 445316484 445317028 544 True 233.000000 233 75.468000 4224 4794 1 chr5D.!!$R1 570
10 TraesCS5B01G364800 chr7B 586758744 586759588 844 True 1144.000000 1144 90.899000 5114 5980 1 chr7B.!!$R2 866
11 TraesCS5B01G364800 chr7B 586776689 586777539 850 True 1099.000000 1099 89.920000 5114 5980 1 chr7B.!!$R3 866
12 TraesCS5B01G364800 chr7B 112126056 112126899 843 True 1075.000000 1075 89.528000 5114 5980 1 chr7B.!!$R1 866
13 TraesCS5B01G364800 chr4A 729322882 729323732 850 False 1099.000000 1099 89.885000 5114 5980 1 chr4A.!!$F2 866
14 TraesCS5B01G364800 chr3B 651730618 651731458 840 True 1096.000000 1096 89.988000 5114 5980 1 chr3B.!!$R1 866
15 TraesCS5B01G364800 chr2B 728583315 728584166 851 True 1094.000000 1094 89.782000 5114 5980 1 chr2B.!!$R1 866
16 TraesCS5B01G364800 chr2B 39330055 39330682 627 False 876.000000 876 91.879000 5114 5739 1 chr2B.!!$F1 625
17 TraesCS5B01G364800 chr1B 465681402 465682249 847 False 1068.000000 1068 89.323000 5114 5980 1 chr1B.!!$F1 866
18 TraesCS5B01G364800 chr1B 658532510 658533236 726 False 701.000000 701 84.047000 5211 5980 1 chr1B.!!$F3 769
19 TraesCS5B01G364800 chr1B 553013631 553015496 1865 True 469.500000 488 84.020500 2023 3882 2 chr1B.!!$R1 1859
20 TraesCS5B01G364800 chr4B 587268985 587269799 814 False 911.000000 911 86.636000 5114 5980 1 chr4B.!!$F3 866
21 TraesCS5B01G364800 chr2D 590328900 590329761 861 True 887.000000 887 85.537000 5114 5980 1 chr2D.!!$R2 866
22 TraesCS5B01G364800 chr4D 2973750 2976725 2975 False 535.250000 876 84.891500 2010 4993 4 chr4D.!!$F3 2983
23 TraesCS5B01G364800 chr4D 1687521 1689904 2383 False 381.500000 409 82.329000 2015 4455 4 chr4D.!!$F2 2440
24 TraesCS5B01G364800 chr7D 104359725 104360585 860 False 826.000000 826 84.312000 5114 5980 1 chr7D.!!$F2 866
25 TraesCS5B01G364800 chrUn 63573093 63573878 785 True 623.000000 623 81.687000 1202 2002 1 chrUn.!!$R1 800
26 TraesCS5B01G364800 chrUn 411620666 411621315 649 True 582.000000 582 83.560000 1369 2002 1 chrUn.!!$R3 633
27 TraesCS5B01G364800 chrUn 433954276 433955058 782 True 483.500000 756 87.952500 33 891 2 chrUn.!!$R5 858
28 TraesCS5B01G364800 chr5A 563254407 563255050 643 True 654.000000 654 85.077000 3259 3905 1 chr5A.!!$R2 646
29 TraesCS5B01G364800 chr5A 552267617 552269420 1803 False 448.666667 575 81.785333 2016 3882 3 chr5A.!!$F3 1866
30 TraesCS5B01G364800 chr1D 410458023 410460185 2162 True 425.000000 510 82.853500 2023 3911 2 chr1D.!!$R1 1888
31 TraesCS5B01G364800 chr1A 506277412 506278662 1250 True 340.500000 396 84.699500 3370 4449 2 chr1A.!!$R3 1079

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
955 961 0.035915 GAGAGAGGGGTTGAACCAGC 60.036 60.0 17.27 4.51 41.02 4.85 F
2583 4230 0.247460 CTGTCCTCGAGCACATGGAA 59.753 55.0 10.17 0.00 0.00 3.53 F
3737 7999 0.674895 AGCCAATCGGTGCAGAGAAC 60.675 55.0 0.00 0.00 33.28 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2613 4263 0.308376 TTGTTTGTAACGGCGGCTTC 59.692 50.0 13.24 0.0 0.00 3.86 R
4089 8841 0.256752 TATGCATTCTGTGGGCTGCT 59.743 50.0 3.54 0.0 35.66 4.24 R
5107 10095 0.035152 TGTTGGAGATGCTCGGCAAT 60.035 50.0 2.68 0.0 43.62 3.56 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
31 32 1.479730 CTGCATCTGTGAGACTAGGCA 59.520 52.381 0.00 0.00 0.00 4.75
82 83 5.067273 TGGACGTTGGAAAGAATATGTTGT 58.933 37.500 0.00 0.00 0.00 3.32
222 225 6.037786 TCAAGATCTCAATAAGTCCACGTT 57.962 37.500 0.00 0.00 0.00 3.99
266 269 6.040955 TCTCATCTATGTTGTCGCTTATCCTT 59.959 38.462 0.00 0.00 0.00 3.36
272 275 2.937149 GTTGTCGCTTATCCTTCTTCCC 59.063 50.000 0.00 0.00 0.00 3.97
311 314 0.943673 TCAATGCTCACACAACCACG 59.056 50.000 0.00 0.00 0.00 4.94
320 323 3.532542 TCACACAACCACGACATGTTTA 58.467 40.909 0.00 0.00 0.00 2.01
373 376 9.591404 CTCGACATAAAATGAGAAATCTATTGC 57.409 33.333 0.00 0.00 0.00 3.56
393 396 4.985538 TGCTTTTCTCCTGTGAGGTTATT 58.014 39.130 0.00 0.00 39.23 1.40
435 438 4.083110 CGATCTGATTTTGCTGAGGTGTTT 60.083 41.667 0.00 0.00 0.00 2.83
483 486 1.071605 GAAAGACAGATCGTGCGCTT 58.928 50.000 9.73 0.00 0.00 4.68
678 683 3.191371 GTGGTCTTCAAAGCCTTGTATGG 59.809 47.826 0.00 0.00 33.94 2.74
733 738 8.763356 GTGCAATGTATTTTTCAATCTTCAACA 58.237 29.630 0.00 0.00 0.00 3.33
825 830 7.995289 TGTGTTTTGTTGTCTTCACATTCTAT 58.005 30.769 0.00 0.00 32.19 1.98
831 836 7.889589 TGTTGTCTTCACATTCTATGTACTG 57.110 36.000 0.00 0.00 42.70 2.74
908 914 1.995542 TCTCAGAAAATGGGGAAGCCT 59.004 47.619 0.00 0.00 0.00 4.58
909 915 2.379907 TCTCAGAAAATGGGGAAGCCTT 59.620 45.455 0.00 0.00 0.00 4.35
910 916 3.168292 CTCAGAAAATGGGGAAGCCTTT 58.832 45.455 0.00 0.00 0.00 3.11
911 917 3.165071 TCAGAAAATGGGGAAGCCTTTC 58.835 45.455 0.00 0.00 0.00 2.62
912 918 2.899256 CAGAAAATGGGGAAGCCTTTCA 59.101 45.455 0.00 0.00 34.90 2.69
913 919 3.056322 CAGAAAATGGGGAAGCCTTTCAG 60.056 47.826 0.00 0.00 34.90 3.02
914 920 1.942776 AAATGGGGAAGCCTTTCAGG 58.057 50.000 0.00 0.00 38.80 3.86
917 923 0.560688 TGGGGAAGCCTTTCAGGTTT 59.439 50.000 0.00 0.00 41.76 3.27
930 936 1.134220 TCAGGTTTCAGCCAAACGTCT 60.134 47.619 0.00 0.00 44.90 4.18
935 941 1.808411 TTCAGCCAAACGTCTGATCC 58.192 50.000 5.61 0.00 38.90 3.36
936 942 0.389817 TCAGCCAAACGTCTGATCCG 60.390 55.000 0.83 0.00 34.69 4.18
945 951 1.169661 CGTCTGATCCGAGAGAGGGG 61.170 65.000 0.00 0.00 0.00 4.79
947 953 0.631753 TCTGATCCGAGAGAGGGGTT 59.368 55.000 0.00 0.00 0.00 4.11
950 956 1.273041 TGATCCGAGAGAGGGGTTGAA 60.273 52.381 0.00 0.00 0.00 2.69
952 958 0.903454 TCCGAGAGAGGGGTTGAACC 60.903 60.000 5.62 5.62 37.60 3.62
953 959 1.192146 CCGAGAGAGGGGTTGAACCA 61.192 60.000 17.27 0.00 41.02 3.67
954 960 0.247736 CGAGAGAGGGGTTGAACCAG 59.752 60.000 17.27 0.00 41.02 4.00
955 961 0.035915 GAGAGAGGGGTTGAACCAGC 60.036 60.000 17.27 4.51 41.02 4.85
956 962 1.376037 GAGAGGGGTTGAACCAGCG 60.376 63.158 17.27 0.00 41.02 5.18
958 964 1.671379 GAGGGGTTGAACCAGCGTC 60.671 63.158 17.27 7.09 41.02 5.19
959 965 2.112297 GGGGTTGAACCAGCGTCA 59.888 61.111 17.27 0.00 41.02 4.35
961 967 1.966451 GGGTTGAACCAGCGTCAGG 60.966 63.158 17.27 0.00 41.02 3.86
962 968 2.617274 GGTTGAACCAGCGTCAGGC 61.617 63.158 9.98 0.00 38.42 4.85
963 969 2.281484 TTGAACCAGCGTCAGGCC 60.281 61.111 0.00 0.00 45.17 5.19
1007 1233 4.029186 CGCGCTTGAAGCCTTGCA 62.029 61.111 12.13 0.00 38.18 4.08
1174 1400 3.015312 GCCCTTTCCTCCGTACGCT 62.015 63.158 10.49 0.00 0.00 5.07
1293 1522 2.143925 GCTACCTGGTGTTCAACTGAC 58.856 52.381 10.23 0.00 0.00 3.51
1297 1526 1.597742 CTGGTGTTCAACTGACTGGG 58.402 55.000 0.00 0.00 0.00 4.45
1304 1533 4.681978 AACTGACTGGGGCGCGAC 62.682 66.667 12.10 6.99 0.00 5.19
1358 1587 2.496817 CCTCGACTGGCTACTGGC 59.503 66.667 0.00 0.00 40.90 4.85
1395 1624 4.131596 GGTACTCAGTCTCACTAGCTAGG 58.868 52.174 24.35 13.33 0.00 3.02
1402 1631 4.275689 CAGTCTCACTAGCTAGGTGATGAG 59.724 50.000 23.60 23.60 41.90 2.90
1412 1641 4.721776 AGCTAGGTGATGAGTATTTTGGGA 59.278 41.667 0.00 0.00 0.00 4.37
1469 1707 6.350445 GGTTGTGATTTTCTTGTATGCATCCT 60.350 38.462 0.19 0.00 0.00 3.24
1828 2096 6.289064 GTTCCGGTCATATCTTTGTTCCTAT 58.711 40.000 0.00 0.00 0.00 2.57
1829 2097 7.439381 GTTCCGGTCATATCTTTGTTCCTATA 58.561 38.462 0.00 0.00 0.00 1.31
1876 2145 2.978018 GCGGACGGGGAAGCAAAAG 61.978 63.158 0.00 0.00 0.00 2.27
1922 2191 0.962356 CTGTGCAATGGTGGGAGGAC 60.962 60.000 0.00 0.00 0.00 3.85
1935 2204 4.254709 AGGACTGGCAACTGCGCA 62.255 61.111 10.98 10.98 43.26 6.09
2236 2581 2.185867 GGCGGCGACATGAGGTTA 59.814 61.111 12.98 0.00 0.00 2.85
2349 3622 2.668120 GCTCTTCTGGCCCTGCTCT 61.668 63.158 0.00 0.00 0.00 4.09
2353 3626 1.229304 TTCTGGCCCTGCTCTGAGA 60.229 57.895 9.28 0.00 0.00 3.27
2492 4088 1.375908 GAAGACGCTGCCATGGACA 60.376 57.895 18.40 12.31 0.00 4.02
2567 4214 1.557269 GCCTGACCACCATCCTCTGT 61.557 60.000 0.00 0.00 0.00 3.41
2583 4230 0.247460 CTGTCCTCGAGCACATGGAA 59.753 55.000 10.17 0.00 0.00 3.53
2604 4254 5.414789 AAAAGCCGCCTAAACCAAATAAT 57.585 34.783 0.00 0.00 0.00 1.28
2609 4259 5.531287 AGCCGCCTAAACCAAATAATAGAAG 59.469 40.000 0.00 0.00 0.00 2.85
2613 4263 8.129211 CCGCCTAAACCAAATAATAGAAGAAAG 58.871 37.037 0.00 0.00 0.00 2.62
2655 4311 8.491134 ACAAAGGGTAAAAGAAATAAAAAGCCT 58.509 29.630 0.00 0.00 34.99 4.58
2874 4531 3.692791 AAGACGCAAGGAAAACTCAAC 57.307 42.857 0.00 0.00 46.39 3.18
3261 5107 6.094186 AAGGCACTCTTAAATAGCTTTGTAGC 59.906 38.462 0.00 0.00 43.77 3.58
3303 5149 3.637432 TCTTTGCATGTAACAAAAGGCG 58.363 40.909 0.00 0.00 36.63 5.52
3304 5150 2.430546 TTGCATGTAACAAAAGGCGG 57.569 45.000 0.00 0.00 0.00 6.13
3321 5167 1.617018 CGGTCCTCCTGGAAGATGCA 61.617 60.000 0.00 0.00 45.18 3.96
3367 5214 5.048846 AGGACTTTGTTGACCAGTATTGT 57.951 39.130 0.00 0.00 0.00 2.71
3378 5225 1.284785 CCAGTATTGTGGGTCCATGGT 59.715 52.381 12.58 0.00 33.46 3.55
3436 5283 5.280011 GGTTCTGGAGTATGTGAAGAAAGGA 60.280 44.000 0.00 0.00 0.00 3.36
3529 7737 1.261619 GTCAACAAGTGCGACCAAGAG 59.738 52.381 0.00 0.00 0.00 2.85
3737 7999 0.674895 AGCCAATCGGTGCAGAGAAC 60.675 55.000 0.00 0.00 33.28 3.01
3912 8421 2.507058 CACTCATGGAGATCTTGGGGAA 59.493 50.000 0.00 0.00 33.32 3.97
3951 8526 6.552008 TCTGGATTATTTGGAAGGTCTTGTT 58.448 36.000 0.00 0.00 0.00 2.83
3964 8608 1.595794 GTCTTGTTCGACGCCAAAAGA 59.404 47.619 0.00 0.00 0.00 2.52
3981 8733 2.100605 AGAAAATGGCGTGAGGAGAC 57.899 50.000 0.00 0.00 0.00 3.36
4089 8841 4.564782 ATGCAGAGACAATCTCCAAGAA 57.435 40.909 2.18 0.00 44.42 2.52
4093 8845 3.933955 CAGAGACAATCTCCAAGAAGCAG 59.066 47.826 2.18 0.00 44.42 4.24
4136 8897 2.884012 CCGTCAGATGCAGAGATACTCT 59.116 50.000 0.00 0.00 42.11 3.24
4500 9324 6.922957 TGAAAAACCATTTGTACTCTGCATTC 59.077 34.615 0.00 0.00 0.00 2.67
4563 9387 3.374988 GTGTCATCCTTTCATTGCGATGA 59.625 43.478 12.88 12.88 40.46 2.92
4565 9389 4.641541 TGTCATCCTTTCATTGCGATGATT 59.358 37.500 17.46 0.00 42.15 2.57
4771 9758 1.630369 AGTTTGATGCCTGGCAGACTA 59.370 47.619 27.20 16.40 43.65 2.59
4821 9808 9.920946 TGCCAGATTAATTACCTTTTATCTCTT 57.079 29.630 0.00 0.00 0.00 2.85
5002 9990 4.572985 TTGTCAGAAATTGAAGTGCTGG 57.427 40.909 0.19 0.00 37.61 4.85
5024 10012 4.263771 GGTTTTCTCCCTCAACCTCCAATA 60.264 45.833 0.00 0.00 37.56 1.90
5025 10013 4.569719 TTTCTCCCTCAACCTCCAATAC 57.430 45.455 0.00 0.00 0.00 1.89
5071 10059 1.153147 GGAGGGGATGGAAAGACGC 60.153 63.158 0.00 0.00 0.00 5.19
5090 10078 1.061711 GCTACTGCTGCTGACGAAATG 59.938 52.381 13.69 0.00 36.03 2.32
5091 10079 2.610433 CTACTGCTGCTGACGAAATGA 58.390 47.619 13.69 0.00 0.00 2.57
5092 10080 1.436600 ACTGCTGCTGACGAAATGAG 58.563 50.000 13.69 0.00 0.00 2.90
5093 10081 1.270518 ACTGCTGCTGACGAAATGAGT 60.271 47.619 13.69 0.00 0.00 3.41
5094 10082 2.029020 ACTGCTGCTGACGAAATGAGTA 60.029 45.455 13.69 0.00 0.00 2.59
5095 10083 2.995939 CTGCTGCTGACGAAATGAGTAA 59.004 45.455 0.00 0.00 0.00 2.24
5096 10084 2.736721 TGCTGCTGACGAAATGAGTAAC 59.263 45.455 0.00 0.00 0.00 2.50
5097 10085 2.094417 GCTGCTGACGAAATGAGTAACC 59.906 50.000 0.00 0.00 0.00 2.85
5098 10086 3.589988 CTGCTGACGAAATGAGTAACCT 58.410 45.455 0.00 0.00 0.00 3.50
5099 10087 3.325870 TGCTGACGAAATGAGTAACCTG 58.674 45.455 0.00 0.00 0.00 4.00
5100 10088 3.006430 TGCTGACGAAATGAGTAACCTGA 59.994 43.478 0.00 0.00 0.00 3.86
5101 10089 4.184629 GCTGACGAAATGAGTAACCTGAT 58.815 43.478 0.00 0.00 0.00 2.90
5102 10090 5.105513 TGCTGACGAAATGAGTAACCTGATA 60.106 40.000 0.00 0.00 0.00 2.15
5103 10091 5.810587 GCTGACGAAATGAGTAACCTGATAA 59.189 40.000 0.00 0.00 0.00 1.75
5104 10092 6.312918 GCTGACGAAATGAGTAACCTGATAAA 59.687 38.462 0.00 0.00 0.00 1.40
5105 10093 7.011482 GCTGACGAAATGAGTAACCTGATAAAT 59.989 37.037 0.00 0.00 0.00 1.40
5106 10094 8.786826 TGACGAAATGAGTAACCTGATAAATT 57.213 30.769 0.00 0.00 0.00 1.82
5107 10095 9.878667 TGACGAAATGAGTAACCTGATAAATTA 57.121 29.630 0.00 0.00 0.00 1.40
5277 10271 1.226379 CGTGCCGCTTATTTGCTGG 60.226 57.895 0.00 0.00 0.00 4.85
5407 10408 0.463833 GGCACTTCCCCGGTATCTTG 60.464 60.000 0.00 0.00 0.00 3.02
5561 10568 5.815581 AGGTATGTATTGCTTCCAACTTCA 58.184 37.500 0.00 0.00 32.95 3.02
5591 10598 4.891260 TGCATGAAATTTGGTGCATGTTA 58.109 34.783 18.22 7.41 42.13 2.41
5643 10663 3.371965 AGTTCGGGCTATAACTCTTCCA 58.628 45.455 0.00 0.00 30.08 3.53
5680 10700 2.045047 TGGAAGAGGAGGAGGATCTTGT 59.955 50.000 0.00 0.00 33.53 3.16
5807 10829 2.874014 TGCCCACAACAGATTGATGAA 58.126 42.857 0.00 0.00 39.30 2.57
5916 10939 2.697751 AGAGAAACTAGCGAGCCATGAT 59.302 45.455 0.00 0.00 0.00 2.45
5922 10946 3.017323 GCGAGCCATGATCGGTTG 58.983 61.111 18.10 3.19 41.94 3.77
5956 10980 0.452184 GAATGTCGTCGGAGAGCTCA 59.548 55.000 17.77 0.00 36.95 4.26
5962 10986 1.144565 CGTCGGAGAGCTCAAGCATG 61.145 60.000 17.77 0.00 45.16 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.139654 TGGATGCATGCCTAGTCTCAC 59.860 52.381 16.68 0.00 0.00 3.51
82 83 3.065233 GCAGATGCCGTATGATTTGTTCA 59.935 43.478 0.00 0.00 35.12 3.18
168 171 8.613034 TGGTTATTAGGTTAGGGATGTGTTTAA 58.387 33.333 0.00 0.00 0.00 1.52
169 172 8.160434 TGGTTATTAGGTTAGGGATGTGTTTA 57.840 34.615 0.00 0.00 0.00 2.01
222 225 9.676861 AGATGAGATGTCATGTTGAAATAAAGA 57.323 29.630 10.56 0.00 43.92 2.52
249 252 4.192317 GGAAGAAGGATAAGCGACAACAT 58.808 43.478 0.00 0.00 0.00 2.71
266 269 1.550524 CCGTCTGTGAAGATGGGAAGA 59.449 52.381 6.14 0.00 40.41 2.87
289 292 1.133823 TGGTTGTGTGAGCATTGAGGT 60.134 47.619 0.00 0.00 0.00 3.85
311 314 9.853555 TTATGATTGACCACATTTAAACATGTC 57.146 29.630 0.00 0.00 35.03 3.06
320 323 4.016444 ACGCCTTATGATTGACCACATTT 58.984 39.130 0.00 0.00 0.00 2.32
373 376 6.094603 CCATCAATAACCTCACAGGAGAAAAG 59.905 42.308 0.00 0.00 44.26 2.27
413 416 5.382618 AAACACCTCAGCAAAATCAGATC 57.617 39.130 0.00 0.00 0.00 2.75
435 438 1.000618 TGGCGCTGATTCAAATTGCAA 59.999 42.857 7.64 0.00 0.00 4.08
618 623 9.185680 ACGGCAAATACTTTTCTAAAATATCCT 57.814 29.630 0.00 0.00 0.00 3.24
642 647 1.066858 AGACCACAATAGCCACTGACG 60.067 52.381 0.00 0.00 0.00 4.35
647 652 3.366374 GCTTTGAAGACCACAATAGCCAC 60.366 47.826 0.00 0.00 31.80 5.01
695 700 5.720371 ATACATTGCACCAAAAGTAAGCA 57.280 34.783 0.00 0.00 0.00 3.91
703 708 8.674263 AAGATTGAAAAATACATTGCACCAAA 57.326 26.923 0.00 0.00 0.00 3.28
709 714 8.437742 CCTGTTGAAGATTGAAAAATACATTGC 58.562 33.333 0.00 0.00 0.00 3.56
712 717 7.235399 ACCCCTGTTGAAGATTGAAAAATACAT 59.765 33.333 0.00 0.00 0.00 2.29
733 738 1.831736 CTCCTTCGATTGTACACCCCT 59.168 52.381 0.00 0.00 0.00 4.79
785 790 7.023197 ACAAAACACAAGACAACCACTATAC 57.977 36.000 0.00 0.00 0.00 1.47
786 791 7.121463 ACAACAAAACACAAGACAACCACTATA 59.879 33.333 0.00 0.00 0.00 1.31
825 830 8.043113 TCGAGGAAAATAGTAGTAGACAGTACA 58.957 37.037 0.00 0.00 33.62 2.90
908 914 2.096248 ACGTTTGGCTGAAACCTGAAA 58.904 42.857 6.38 0.00 40.94 2.69
909 915 1.673920 GACGTTTGGCTGAAACCTGAA 59.326 47.619 0.00 0.00 40.94 3.02
910 916 1.134220 AGACGTTTGGCTGAAACCTGA 60.134 47.619 0.00 0.00 40.94 3.86
911 917 1.002468 CAGACGTTTGGCTGAAACCTG 60.002 52.381 0.00 5.53 40.94 4.00
912 918 1.134220 TCAGACGTTTGGCTGAAACCT 60.134 47.619 6.21 0.00 40.94 3.50
913 919 1.305201 TCAGACGTTTGGCTGAAACC 58.695 50.000 6.21 0.00 40.94 3.27
914 920 2.095718 GGATCAGACGTTTGGCTGAAAC 60.096 50.000 4.73 2.96 43.63 2.78
917 923 0.389817 CGGATCAGACGTTTGGCTGA 60.390 55.000 6.21 2.88 44.43 4.26
930 936 0.335019 TCAACCCCTCTCTCGGATCA 59.665 55.000 0.00 0.00 0.00 2.92
935 941 0.247736 CTGGTTCAACCCCTCTCTCG 59.752 60.000 3.42 0.00 37.50 4.04
936 942 0.035915 GCTGGTTCAACCCCTCTCTC 60.036 60.000 3.42 0.00 37.50 3.20
945 951 2.617274 GGCCTGACGCTGGTTCAAC 61.617 63.158 0.00 0.00 37.74 3.18
947 953 2.410322 AATGGCCTGACGCTGGTTCA 62.410 55.000 3.32 4.84 37.74 3.18
950 956 2.045926 GAATGGCCTGACGCTGGT 60.046 61.111 3.32 0.00 37.74 4.00
952 958 1.522355 ATCGAATGGCCTGACGCTG 60.522 57.895 3.32 0.00 37.74 5.18
953 959 1.522355 CATCGAATGGCCTGACGCT 60.522 57.895 3.32 0.00 37.74 5.07
954 960 3.017323 CATCGAATGGCCTGACGC 58.983 61.111 3.32 0.00 0.00 5.19
955 961 3.017323 GCATCGAATGGCCTGACG 58.983 61.111 3.32 7.01 0.00 4.35
962 968 2.537560 GCTCGTGGGCATCGAATGG 61.538 63.158 0.00 0.00 36.89 3.16
963 969 2.537560 GGCTCGTGGGCATCGAATG 61.538 63.158 0.00 0.00 40.53 2.67
1028 1254 0.331954 TCTCCTGTAGTCGCCCTCTT 59.668 55.000 0.00 0.00 0.00 2.85
1060 1286 1.167155 ATCGACGAGGTGGATCTCCG 61.167 60.000 3.01 0.00 39.43 4.63
1174 1400 4.373116 GACCTGTCGGCGCTTCCA 62.373 66.667 7.64 0.00 34.01 3.53
1187 1413 1.022451 GTCGAGTCGAGAGCTGACCT 61.022 60.000 17.12 0.00 36.23 3.85
1195 1421 2.033602 TGGGCAGTCGAGTCGAGA 59.966 61.111 17.12 0.00 36.23 4.04
1306 1535 1.004277 GAATATCGTGGGCTCTCGCG 61.004 60.000 2.47 0.00 41.41 5.87
1307 1536 0.315568 AGAATATCGTGGGCTCTCGC 59.684 55.000 2.47 0.00 0.00 5.03
1308 1537 1.068194 GGAGAATATCGTGGGCTCTCG 60.068 57.143 0.55 0.55 34.58 4.04
1309 1538 1.964223 TGGAGAATATCGTGGGCTCTC 59.036 52.381 0.00 0.00 33.28 3.20
1310 1539 1.689273 GTGGAGAATATCGTGGGCTCT 59.311 52.381 0.00 0.00 0.00 4.09
1311 1540 1.603172 CGTGGAGAATATCGTGGGCTC 60.603 57.143 0.00 0.00 0.00 4.70
1312 1541 0.389391 CGTGGAGAATATCGTGGGCT 59.611 55.000 0.00 0.00 0.00 5.19
1313 1542 0.600255 CCGTGGAGAATATCGTGGGC 60.600 60.000 0.00 0.00 0.00 5.36
1314 1543 0.750850 ACCGTGGAGAATATCGTGGG 59.249 55.000 0.00 0.00 0.00 4.61
1315 1544 2.201732 CAACCGTGGAGAATATCGTGG 58.798 52.381 0.00 0.00 0.00 4.94
1316 1545 1.593006 GCAACCGTGGAGAATATCGTG 59.407 52.381 0.00 0.00 0.00 4.35
1351 1580 1.203523 GAGACCACAGACAGCCAGTAG 59.796 57.143 0.00 0.00 0.00 2.57
1357 1586 1.248785 TACCCGAGACCACAGACAGC 61.249 60.000 0.00 0.00 0.00 4.40
1358 1587 0.526662 GTACCCGAGACCACAGACAG 59.473 60.000 0.00 0.00 0.00 3.51
1395 1624 5.473504 ACACTTGTCCCAAAATACTCATCAC 59.526 40.000 0.00 0.00 0.00 3.06
1402 1631 8.788325 ATTCTAGTACACTTGTCCCAAAATAC 57.212 34.615 0.00 0.00 0.00 1.89
1492 1730 4.803613 GGTTGCCTTAGACAAACAGTTTTG 59.196 41.667 0.00 0.00 46.61 2.44
1493 1731 4.142026 GGGTTGCCTTAGACAAACAGTTTT 60.142 41.667 0.00 0.00 36.41 2.43
1494 1732 3.383505 GGGTTGCCTTAGACAAACAGTTT 59.616 43.478 0.00 0.00 36.41 2.66
1564 1809 8.840321 CCGATTCCTTAAACTCATATGTGAATT 58.160 33.333 11.60 8.32 33.05 2.17
1571 1816 6.289064 GTCACCCGATTCCTTAAACTCATAT 58.711 40.000 0.00 0.00 0.00 1.78
1574 1819 3.307199 GGTCACCCGATTCCTTAAACTCA 60.307 47.826 0.00 0.00 0.00 3.41
1657 1906 3.643199 TCCCTTTTGCCTTTTGCTTTT 57.357 38.095 0.00 0.00 42.00 2.27
1676 1925 2.333014 CTCACGTGCTCCTCTTCTTTC 58.667 52.381 11.67 0.00 0.00 2.62
1677 1926 1.001406 CCTCACGTGCTCCTCTTCTTT 59.999 52.381 11.67 0.00 0.00 2.52
1828 2096 8.089597 TGGTCGTGAGTATTGTTTATTTGTCTA 58.910 33.333 0.00 0.00 0.00 2.59
1829 2097 6.932400 TGGTCGTGAGTATTGTTTATTTGTCT 59.068 34.615 0.00 0.00 0.00 3.41
1876 2145 1.134159 AGAGGCTCATGAATGGAGTGC 60.134 52.381 18.26 0.00 34.83 4.40
1922 2191 2.749044 AGGATGCGCAGTTGCCAG 60.749 61.111 18.32 0.00 37.91 4.85
1935 2204 2.496817 GCTGCCGAGAACGAGGAT 59.503 61.111 0.00 0.00 42.66 3.24
2006 2275 2.755469 CCCCTGGCGGTTGAATGG 60.755 66.667 0.00 0.00 0.00 3.16
2008 2277 2.677228 CTCCCCTGGCGGTTGAAT 59.323 61.111 0.00 0.00 0.00 2.57
2236 2581 5.864418 ATAAACAGATTGATGCCAGCAAT 57.136 34.783 8.09 8.09 38.58 3.56
2290 2635 2.040278 CTCCTGAGAGCCTGGGGT 59.960 66.667 0.00 0.00 34.88 4.95
2349 3622 1.613925 CTCCGTCTGTGTTCCTTCTCA 59.386 52.381 0.00 0.00 0.00 3.27
2353 3626 1.344763 CCTTCTCCGTCTGTGTTCCTT 59.655 52.381 0.00 0.00 0.00 3.36
2492 4088 3.997672 GCTGATAGTCGGCCTCAAT 57.002 52.632 0.00 0.00 42.80 2.57
2567 4214 1.945819 GCTTTTCCATGTGCTCGAGGA 60.946 52.381 15.58 9.02 0.00 3.71
2583 4230 5.889289 TCTATTATTTGGTTTAGGCGGCTTT 59.111 36.000 19.76 0.00 0.00 3.51
2604 4254 0.606604 ACGGCGGCTTCTTTCTTCTA 59.393 50.000 13.24 0.00 0.00 2.10
2609 4259 0.869730 TTGTAACGGCGGCTTCTTTC 59.130 50.000 13.24 0.00 0.00 2.62
2613 4263 0.308376 TTGTTTGTAACGGCGGCTTC 59.692 50.000 13.24 0.00 0.00 3.86
2874 4531 6.211515 CAGTCAGAAAGAAAAACCCAGATTG 58.788 40.000 0.00 0.00 0.00 2.67
3261 5107 8.796475 CAAAGAACCATACCAGATTATATTGGG 58.204 37.037 0.00 0.00 38.82 4.12
3303 5149 0.107459 GTGCATCTTCCAGGAGGACC 60.107 60.000 2.71 0.00 45.73 4.46
3304 5150 0.615331 TGTGCATCTTCCAGGAGGAC 59.385 55.000 2.71 0.00 45.73 3.85
3321 5167 4.083537 TGCAGTTAAAGAATTTCGCGATGT 60.084 37.500 10.88 0.00 40.09 3.06
3378 5225 2.594303 CGGTTGAGTTGCAGGGCA 60.594 61.111 0.00 0.00 36.47 5.36
3436 5283 7.562454 TCAGCATCTTTTATTTGATCTTCCCAT 59.438 33.333 0.00 0.00 0.00 4.00
3537 7745 2.832129 TCGAATGGTCTCCTTAAGCTGT 59.168 45.455 0.00 0.00 0.00 4.40
3737 7999 5.860941 AGGTAGATCATGTAGTTGGACAG 57.139 43.478 0.00 0.00 31.51 3.51
3857 8363 5.106396 CCTTGAGAATCTTTTTGAGCGATGT 60.106 40.000 0.00 0.00 34.92 3.06
3926 8501 6.735556 ACAAGACCTTCCAAATAATCCAGAT 58.264 36.000 0.00 0.00 0.00 2.90
3933 8508 4.449743 CGTCGAACAAGACCTTCCAAATAA 59.550 41.667 0.00 0.00 37.85 1.40
3939 8514 1.289800 GGCGTCGAACAAGACCTTCC 61.290 60.000 0.00 0.00 37.85 3.46
3951 8526 2.697431 CCATTTTCTTTTGGCGTCGA 57.303 45.000 0.00 0.00 0.00 4.20
3964 8608 0.400213 TGGTCTCCTCACGCCATTTT 59.600 50.000 0.00 0.00 0.00 1.82
3981 8733 3.119173 TGTTTGCACAAGTCCTCTTTTGG 60.119 43.478 0.00 0.00 33.48 3.28
4036 8788 1.020437 TTGTGCATGCGACAACTTCA 58.980 45.000 23.13 8.70 0.00 3.02
4089 8841 0.256752 TATGCATTCTGTGGGCTGCT 59.743 50.000 3.54 0.00 35.66 4.24
4093 8845 3.797865 GCAATTCTATGCATTCTGTGGGC 60.798 47.826 3.54 0.00 45.70 5.36
4136 8897 3.497115 TGTGGGCTGCACCTTGGA 61.497 61.111 0.00 0.00 39.10 3.53
4198 9010 7.120873 CACATCTTCTTCTCATCACCAAAATCT 59.879 37.037 0.00 0.00 0.00 2.40
4500 9324 7.702348 GGTAAGCAAATAAGCAACTAAGATTGG 59.298 37.037 0.00 0.00 36.85 3.16
4656 9518 1.377536 GCTTCATGAGCCCTTGAGTC 58.622 55.000 0.00 0.00 46.01 3.36
4681 9543 0.525668 CCGAGACGTAGATGCACCAC 60.526 60.000 0.00 0.00 0.00 4.16
4734 9605 5.057149 TCAAACTGGACTAGTGCTTTTCTC 58.943 41.667 15.92 0.00 40.26 2.87
4771 9758 8.121708 GCAATTCAAATAACACAACACACAAAT 58.878 29.630 0.00 0.00 0.00 2.32
4821 9808 5.291971 CCATACGACAGACATGATCATTGA 58.708 41.667 5.16 0.00 0.00 2.57
5002 9990 2.951229 TGGAGGTTGAGGGAGAAAAC 57.049 50.000 0.00 0.00 0.00 2.43
5024 10012 7.558081 AGCATGTATCTATCTGGTATATCACGT 59.442 37.037 0.00 0.00 0.00 4.49
5025 10013 7.935520 AGCATGTATCTATCTGGTATATCACG 58.064 38.462 0.00 0.00 0.00 4.35
5071 10059 2.602211 CTCATTTCGTCAGCAGCAGTAG 59.398 50.000 0.00 0.00 0.00 2.57
5090 10078 7.571428 GCTCGGCAATAATTTATCAGGTTACTC 60.571 40.741 0.00 0.00 0.00 2.59
5091 10079 6.204882 GCTCGGCAATAATTTATCAGGTTACT 59.795 38.462 0.00 0.00 0.00 2.24
5092 10080 6.017440 TGCTCGGCAATAATTTATCAGGTTAC 60.017 38.462 0.00 0.00 34.76 2.50
5093 10081 6.058833 TGCTCGGCAATAATTTATCAGGTTA 58.941 36.000 0.00 0.00 34.76 2.85
5094 10082 4.887071 TGCTCGGCAATAATTTATCAGGTT 59.113 37.500 0.00 0.00 34.76 3.50
5095 10083 4.460263 TGCTCGGCAATAATTTATCAGGT 58.540 39.130 0.00 0.00 34.76 4.00
5096 10084 5.413833 AGATGCTCGGCAATAATTTATCAGG 59.586 40.000 2.68 0.00 43.62 3.86
5097 10085 6.402983 GGAGATGCTCGGCAATAATTTATCAG 60.403 42.308 2.68 0.00 43.62 2.90
5098 10086 5.412594 GGAGATGCTCGGCAATAATTTATCA 59.587 40.000 2.68 0.00 43.62 2.15
5099 10087 5.412594 TGGAGATGCTCGGCAATAATTTATC 59.587 40.000 2.68 0.00 43.62 1.75
5100 10088 5.316167 TGGAGATGCTCGGCAATAATTTAT 58.684 37.500 2.68 0.00 43.62 1.40
5101 10089 4.713553 TGGAGATGCTCGGCAATAATTTA 58.286 39.130 2.68 0.00 43.62 1.40
5102 10090 3.554934 TGGAGATGCTCGGCAATAATTT 58.445 40.909 2.68 0.00 43.62 1.82
5103 10091 3.213206 TGGAGATGCTCGGCAATAATT 57.787 42.857 2.68 0.00 43.62 1.40
5104 10092 2.880890 GTTGGAGATGCTCGGCAATAAT 59.119 45.455 2.68 0.00 43.62 1.28
5105 10093 2.288666 GTTGGAGATGCTCGGCAATAA 58.711 47.619 2.68 0.00 43.62 1.40
5106 10094 1.209261 TGTTGGAGATGCTCGGCAATA 59.791 47.619 2.68 0.00 43.62 1.90
5107 10095 0.035152 TGTTGGAGATGCTCGGCAAT 60.035 50.000 2.68 0.00 43.62 3.56
5108 10096 0.674581 CTGTTGGAGATGCTCGGCAA 60.675 55.000 2.68 0.00 43.62 4.52
5109 10097 1.078918 CTGTTGGAGATGCTCGGCA 60.079 57.895 1.01 1.01 44.86 5.69
5110 10098 1.817099 CCTGTTGGAGATGCTCGGC 60.817 63.158 0.00 0.00 34.57 5.54
5111 10099 1.817099 GCCTGTTGGAGATGCTCGG 60.817 63.158 0.00 0.00 34.57 4.63
5112 10100 2.169789 CGCCTGTTGGAGATGCTCG 61.170 63.158 0.00 0.00 34.95 5.03
5305 10299 2.673341 TGGAGTGAGAGCGAGCGT 60.673 61.111 0.00 0.00 0.00 5.07
5391 10392 1.912971 GGCAAGATACCGGGGAAGT 59.087 57.895 6.32 0.00 0.00 3.01
5643 10663 9.406113 CTCCTCTTCCATATCAAATTCTTCTTT 57.594 33.333 0.00 0.00 0.00 2.52
5692 10712 7.222611 GCTTCGGTTTTTAATTGATGTGCATAT 59.777 33.333 0.00 0.00 0.00 1.78
5807 10829 4.263905 TGGGATTCTCCACAAAATAGTGCT 60.264 41.667 0.00 0.00 38.64 4.40
5916 10939 0.756294 TCCTCTGCTGAAACAACCGA 59.244 50.000 0.00 0.00 0.00 4.69
5922 10946 3.006247 GACATTCCTCCTCTGCTGAAAC 58.994 50.000 0.00 0.00 0.00 2.78
5956 10980 1.891150 CTTCTGAAAGGTGCCATGCTT 59.109 47.619 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.