Multiple sequence alignment - TraesCS3B01G202500

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 TraesCS3B01G202500 chr3B 100.000 4797 0 0 1 4797 236499136 236494340 0.000000e+00 8859.0
1 TraesCS3B01G202500 chr3B 95.109 184 9 0 4233 4416 161459629 161459446 1.690000e-74 291.0
2 TraesCS3B01G202500 chr3D 95.478 4268 111 36 1 4212 159789507 159785266 0.000000e+00 6737.0
3 TraesCS3B01G202500 chr3D 84.108 409 39 5 4411 4795 159785275 159784869 5.860000e-99 372.0
4 TraesCS3B01G202500 chr3D 83.978 362 31 9 4458 4797 120104399 120104755 5.990000e-84 322.0
5 TraesCS3B01G202500 chr3D 88.384 198 22 1 4458 4655 551004210 551004014 2.230000e-58 237.0
6 TraesCS3B01G202500 chr3A 95.418 3383 99 26 881 4230 186042974 186039615 0.000000e+00 5337.0
7 TraesCS3B01G202500 chr3A 96.798 812 24 2 1 811 186043914 186043104 0.000000e+00 1354.0
8 TraesCS3B01G202500 chr3A 81.694 366 39 10 4458 4797 682009056 682009419 3.660000e-71 279.0
9 TraesCS3B01G202500 chr3A 77.976 168 31 5 4050 4216 736946377 736946539 3.050000e-17 100.0
10 TraesCS3B01G202500 chr3A 78.947 95 18 2 4050 4143 40161228 40161321 4.010000e-06 63.9
11 TraesCS3B01G202500 chr4A 86.359 909 116 7 2674 3578 900639 901543 0.000000e+00 985.0
12 TraesCS3B01G202500 chr4D 80.742 1293 202 32 2316 3577 629733 631009 0.000000e+00 965.0
13 TraesCS3B01G202500 chr4D 73.767 953 227 21 1237 2179 628615 629554 2.120000e-93 353.0
14 TraesCS3B01G202500 chr4D 81.818 363 39 12 4458 4797 498691631 498691273 3.660000e-71 279.0
15 TraesCS3B01G202500 chr4B 85.557 907 122 7 2674 3577 1244614 1243714 0.000000e+00 941.0
16 TraesCS3B01G202500 chr4B 73.849 956 221 24 1237 2179 1246105 1245166 2.120000e-93 353.0
17 TraesCS3B01G202500 chr4B 96.685 181 6 0 4231 4411 666660338 666660158 7.800000e-78 302.0
18 TraesCS3B01G202500 chr4B 96.133 181 5 1 4231 4411 666696962 666696784 1.310000e-75 294.0
19 TraesCS3B01G202500 chr4B 80.541 370 37 15 4459 4797 595302156 595302521 7.970000e-63 252.0
20 TraesCS3B01G202500 chr4B 79.019 367 38 14 4456 4797 449195692 449195340 1.050000e-51 215.0
21 TraesCS3B01G202500 chr5D 81.747 893 145 17 2682 3568 425840488 425841368 0.000000e+00 730.0
22 TraesCS3B01G202500 chr5D 81.200 883 137 18 2698 3564 454977930 454978799 0.000000e+00 684.0
23 TraesCS3B01G202500 chr5D 81.200 883 137 18 2698 3564 455049178 455050047 0.000000e+00 684.0
24 TraesCS3B01G202500 chr5D 80.909 880 139 18 2698 3561 455221896 455222762 0.000000e+00 667.0
25 TraesCS3B01G202500 chr5D 80.990 768 122 15 2809 3564 455121047 455121802 5.350000e-164 588.0
26 TraesCS3B01G202500 chr5D 81.944 360 33 11 4460 4797 73814418 73814069 4.730000e-70 276.0
27 TraesCS3B01G202500 chr5A 81.594 891 150 13 2682 3568 540053546 540054426 0.000000e+00 725.0
28 TraesCS3B01G202500 chr5A 82.105 95 15 2 4050 4143 616368585 616368678 3.980000e-11 80.5
29 TraesCS3B01G202500 chr5A 79.070 129 9 7 4024 4143 546142411 546142292 6.660000e-09 73.1
30 TraesCS3B01G202500 chr5B 81.236 890 155 11 2682 3568 515185659 515186539 0.000000e+00 708.0
31 TraesCS3B01G202500 chr5B 96.629 178 4 1 4231 4408 532890293 532890468 1.310000e-75 294.0
32 TraesCS3B01G202500 chr2B 83.473 357 37 5 4462 4797 790774509 790774154 3.600000e-81 313.0
33 TraesCS3B01G202500 chr2B 95.722 187 7 1 4226 4411 64891780 64891594 2.810000e-77 300.0
34 TraesCS3B01G202500 chr2B 95.604 182 7 1 4230 4411 170394471 170394651 1.690000e-74 291.0
35 TraesCS3B01G202500 chr2B 95.580 181 7 1 4231 4411 405271695 405271874 6.070000e-74 289.0
36 TraesCS3B01G202500 chr2B 86.466 133 13 5 4050 4180 701766189 701766318 1.800000e-29 141.0
37 TraesCS3B01G202500 chr1B 94.030 201 9 3 4220 4418 583404531 583404332 7.800000e-78 302.0
38 TraesCS3B01G202500 chr1B 96.089 179 7 0 4231 4409 580537141 580537319 4.700000e-75 292.0
39 TraesCS3B01G202500 chr1B 88.356 146 16 1 4652 4797 354991460 354991316 1.770000e-39 174.0
40 TraesCS3B01G202500 chr6D 81.892 370 35 5 4459 4797 65107533 65107901 2.830000e-72 283.0
41 TraesCS3B01G202500 chr7D 81.492 362 41 8 4460 4797 461392218 461391859 1.700000e-69 274.0
42 TraesCS3B01G202500 chr7D 88.000 200 23 1 4457 4655 369779771 369779572 8.030000e-58 235.0
43 TraesCS3B01G202500 chr6B 80.769 364 44 6 4459 4797 514660423 514660061 1.320000e-65 261.0
44 TraesCS3B01G202500 chr6B 79.211 380 45 14 4446 4795 159697914 159697539 2.890000e-57 233.0
45 TraesCS3B01G202500 chr1D 90.395 177 17 0 4460 4636 27696031 27696207 2.890000e-57 233.0
46 TraesCS3B01G202500 chr1D 82.812 256 25 7 4561 4797 267759654 267759909 1.350000e-50 211.0
47 TraesCS3B01G202500 chr2D 85.294 136 15 5 4050 4183 582711673 582711805 8.370000e-28 135.0
48 TraesCS3B01G202500 chr6A 84.211 95 13 2 4050 4143 407158114 407158207 1.840000e-14 91.6
49 TraesCS3B01G202500 chr7B 89.286 56 5 1 4050 4104 530460654 530460709 8.610000e-08 69.4


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 TraesCS3B01G202500 chr3B 236494340 236499136 4796 True 8859.0 8859 100.0000 1 4797 1 chr3B.!!$R2 4796
1 TraesCS3B01G202500 chr3D 159784869 159789507 4638 True 3554.5 6737 89.7930 1 4795 2 chr3D.!!$R2 4794
2 TraesCS3B01G202500 chr3A 186039615 186043914 4299 True 3345.5 5337 96.1080 1 4230 2 chr3A.!!$R1 4229
3 TraesCS3B01G202500 chr4A 900639 901543 904 False 985.0 985 86.3590 2674 3578 1 chr4A.!!$F1 904
4 TraesCS3B01G202500 chr4D 628615 631009 2394 False 659.0 965 77.2545 1237 3577 2 chr4D.!!$F1 2340
5 TraesCS3B01G202500 chr4B 1243714 1246105 2391 True 647.0 941 79.7030 1237 3577 2 chr4B.!!$R4 2340
6 TraesCS3B01G202500 chr5D 425840488 425841368 880 False 730.0 730 81.7470 2682 3568 1 chr5D.!!$F1 886
7 TraesCS3B01G202500 chr5D 454977930 454978799 869 False 684.0 684 81.2000 2698 3564 1 chr5D.!!$F2 866
8 TraesCS3B01G202500 chr5D 455049178 455050047 869 False 684.0 684 81.2000 2698 3564 1 chr5D.!!$F3 866
9 TraesCS3B01G202500 chr5D 455221896 455222762 866 False 667.0 667 80.9090 2698 3561 1 chr5D.!!$F5 863
10 TraesCS3B01G202500 chr5D 455121047 455121802 755 False 588.0 588 80.9900 2809 3564 1 chr5D.!!$F4 755
11 TraesCS3B01G202500 chr5A 540053546 540054426 880 False 725.0 725 81.5940 2682 3568 1 chr5A.!!$F1 886
12 TraesCS3B01G202500 chr5B 515185659 515186539 880 False 708.0 708 81.2360 2682 3568 1 chr5B.!!$F1 886

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
944 1030 0.108963 TCGACGTGGGGGATTTTTGT 59.891 50.000 0.0 0.0 0.00 2.83 F
945 1031 0.955905 CGACGTGGGGGATTTTTGTT 59.044 50.000 0.0 0.0 0.00 2.83 F
2251 2391 2.034879 CAAGGACTTCGCCGTGCAT 61.035 57.895 0.0 0.0 30.94 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2843 3019 1.825474 GATCTCCGTCTGGAACTCCAA 59.175 52.381 0.00 0.00 46.97 3.53 R
3187 3369 4.235762 ACGTGCGCCTGGTTCACT 62.236 61.111 4.18 3.98 0.00 3.41 R
4353 4562 0.242825 CACGCTCCTTCCGTCTAACA 59.757 55.000 0.00 0.00 36.69 2.41 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
48 49 5.277974 CCTTGTCCACAACACTGACAATTAG 60.278 44.000 4.93 0.00 45.10 1.73
141 143 9.556030 TTTGCGTATCTATAGAACTGATTATCG 57.444 33.333 6.52 2.51 0.00 2.92
223 228 2.357517 CCACAGACACGGCCAGTC 60.358 66.667 15.65 15.65 36.26 3.51
574 579 4.184629 CGGTTTTCTCGGAAGATCTTCAT 58.815 43.478 31.29 0.99 41.20 2.57
642 647 1.887707 GCCTCTAACCGCCCATTCG 60.888 63.158 0.00 0.00 0.00 3.34
669 674 0.949105 GTGGTGTTAGTGACCTGGCG 60.949 60.000 0.00 0.00 34.26 5.69
707 712 7.232534 AGCAGTACCTGTAAATTCCATTTTTCA 59.767 33.333 0.00 0.00 33.43 2.69
763 768 5.543507 ACATTTGATGGCTTTGTACCAAA 57.456 34.783 0.00 0.00 41.49 3.28
838 884 4.574599 ACTTTGAGTTGCAACAGGAATC 57.425 40.909 30.11 18.69 35.91 2.52
839 885 3.953612 ACTTTGAGTTGCAACAGGAATCA 59.046 39.130 30.11 20.95 35.91 2.57
840 886 4.402155 ACTTTGAGTTGCAACAGGAATCAA 59.598 37.500 30.11 24.88 35.91 2.57
884 930 1.152777 TGTTGCCTGTGTGGGGAAG 60.153 57.895 0.00 0.00 37.37 3.46
941 1027 1.002990 GGTCGACGTGGGGGATTTT 60.003 57.895 9.92 0.00 0.00 1.82
942 1028 0.607217 GGTCGACGTGGGGGATTTTT 60.607 55.000 9.92 0.00 0.00 1.94
943 1029 0.519961 GTCGACGTGGGGGATTTTTG 59.480 55.000 0.00 0.00 0.00 2.44
944 1030 0.108963 TCGACGTGGGGGATTTTTGT 59.891 50.000 0.00 0.00 0.00 2.83
945 1031 0.955905 CGACGTGGGGGATTTTTGTT 59.044 50.000 0.00 0.00 0.00 2.83
1038 1131 3.249189 GCTCCCACTCCCCACACA 61.249 66.667 0.00 0.00 0.00 3.72
1189 1287 2.807045 CTGCTCGCGCTTCTCGTT 60.807 61.111 5.56 0.00 41.07 3.85
1975 2079 2.203877 AAGTACCCCACCGAGGCA 60.204 61.111 0.00 0.00 35.39 4.75
1978 2082 2.064581 GTACCCCACCGAGGCATCT 61.065 63.158 0.00 0.00 35.39 2.90
2251 2391 2.034879 CAAGGACTTCGCCGTGCAT 61.035 57.895 0.00 0.00 30.94 3.96
2450 2596 2.507324 GCGACAGCGAGAAGGACC 60.507 66.667 0.00 0.00 40.82 4.46
2551 2697 4.830765 GCGGCCATCTGCGTGGTA 62.831 66.667 2.24 0.00 41.47 3.25
2659 2817 2.283388 AAGTCGTCCGGCCACCTA 60.283 61.111 2.24 0.00 0.00 3.08
3187 3369 2.915659 AAGTCCGGCTCGTCCACA 60.916 61.111 0.00 0.00 34.01 4.17
4006 4195 5.435820 AGCTAAGGTACTAGCGAATACAC 57.564 43.478 8.11 0.00 38.49 2.90
4037 4226 6.552008 TCACTGGAATTTAATCAAGGGTCTT 58.448 36.000 0.00 0.00 0.00 3.01
4050 4239 4.020218 TCAAGGGTCTTTCTAGGACACATG 60.020 45.833 3.18 1.70 39.36 3.21
4051 4240 3.791320 AGGGTCTTTCTAGGACACATGA 58.209 45.455 0.00 0.00 39.36 3.07
4052 4241 3.515901 AGGGTCTTTCTAGGACACATGAC 59.484 47.826 0.00 0.00 39.36 3.06
4053 4242 3.260884 GGGTCTTTCTAGGACACATGACA 59.739 47.826 0.00 0.00 37.11 3.58
4054 4243 4.080863 GGGTCTTTCTAGGACACATGACAT 60.081 45.833 0.00 0.00 37.11 3.06
4055 4244 5.128827 GGGTCTTTCTAGGACACATGACATA 59.871 44.000 0.00 0.00 37.11 2.29
4056 4245 6.351881 GGGTCTTTCTAGGACACATGACATAA 60.352 42.308 0.00 0.00 37.11 1.90
4057 4246 7.275920 GGTCTTTCTAGGACACATGACATAAT 58.724 38.462 0.00 0.00 35.61 1.28
4058 4247 7.770897 GGTCTTTCTAGGACACATGACATAATT 59.229 37.037 0.00 0.00 35.61 1.40
4059 4248 9.817809 GTCTTTCTAGGACACATGACATAATTA 57.182 33.333 0.00 0.00 34.23 1.40
4093 4302 2.317530 TGACGTCACCATGTTTGTGA 57.682 45.000 15.76 0.00 40.28 3.58
4114 4323 1.757118 CCCTCCTGATCGCTCTGTTTA 59.243 52.381 0.00 0.00 0.00 2.01
4181 4390 4.441792 GGCACTCATCCTTTTTGTTTGTT 58.558 39.130 0.00 0.00 0.00 2.83
4220 4429 4.693915 CCCTCCCCCTCCCCAACA 62.694 72.222 0.00 0.00 0.00 3.33
4222 4431 3.339093 CTCCCCCTCCCCAACACC 61.339 72.222 0.00 0.00 0.00 4.16
4227 4436 3.979497 CCTCCCCAACACCCCCAC 61.979 72.222 0.00 0.00 0.00 4.61
4228 4437 3.979497 CTCCCCAACACCCCCACC 61.979 72.222 0.00 0.00 0.00 4.61
4240 4449 4.122149 CCCACCCCGGCAATGCTA 62.122 66.667 4.82 0.00 0.00 3.49
4241 4450 2.828549 CCACCCCGGCAATGCTAC 60.829 66.667 4.82 0.00 0.00 3.58
4242 4451 2.045438 CACCCCGGCAATGCTACA 60.045 61.111 4.82 0.00 0.00 2.74
4243 4452 2.045340 ACCCCGGCAATGCTACAC 60.045 61.111 4.82 0.00 0.00 2.90
4244 4453 3.202001 CCCCGGCAATGCTACACG 61.202 66.667 4.82 0.00 0.00 4.49
4245 4454 2.435938 CCCGGCAATGCTACACGT 60.436 61.111 4.82 0.00 0.00 4.49
4246 4455 1.153529 CCCGGCAATGCTACACGTA 60.154 57.895 4.82 0.00 0.00 3.57
4247 4456 1.426041 CCCGGCAATGCTACACGTAC 61.426 60.000 4.82 0.00 0.00 3.67
4248 4457 0.738063 CCGGCAATGCTACACGTACA 60.738 55.000 4.82 0.00 0.00 2.90
4249 4458 1.072391 CGGCAATGCTACACGTACAA 58.928 50.000 4.82 0.00 0.00 2.41
4250 4459 1.461512 CGGCAATGCTACACGTACAAA 59.538 47.619 4.82 0.00 0.00 2.83
4251 4460 2.723618 CGGCAATGCTACACGTACAAAC 60.724 50.000 4.82 0.00 0.00 2.93
4268 4477 7.771219 GTACAAACGATTTACAGGCTTTTAC 57.229 36.000 0.00 0.00 0.00 2.01
4269 4478 6.380095 ACAAACGATTTACAGGCTTTTACA 57.620 33.333 0.00 0.00 0.00 2.41
4270 4479 6.435428 ACAAACGATTTACAGGCTTTTACAG 58.565 36.000 0.00 0.00 0.00 2.74
4271 4480 5.622770 AACGATTTACAGGCTTTTACAGG 57.377 39.130 0.00 0.00 0.00 4.00
4272 4481 4.901868 ACGATTTACAGGCTTTTACAGGA 58.098 39.130 0.00 0.00 0.00 3.86
4273 4482 5.497474 ACGATTTACAGGCTTTTACAGGAT 58.503 37.500 0.00 0.00 0.00 3.24
4274 4483 5.354234 ACGATTTACAGGCTTTTACAGGATG 59.646 40.000 0.00 0.00 46.00 3.51
4275 4484 5.220854 CGATTTACAGGCTTTTACAGGATGG 60.221 44.000 0.00 0.00 43.62 3.51
4276 4485 4.650972 TTACAGGCTTTTACAGGATGGT 57.349 40.909 0.00 0.00 43.62 3.55
4277 4486 3.525800 ACAGGCTTTTACAGGATGGTT 57.474 42.857 0.00 0.00 43.62 3.67
4278 4487 4.650972 ACAGGCTTTTACAGGATGGTTA 57.349 40.909 0.00 0.00 43.62 2.85
4279 4488 4.993028 ACAGGCTTTTACAGGATGGTTAA 58.007 39.130 0.00 0.00 43.62 2.01
4280 4489 5.580022 ACAGGCTTTTACAGGATGGTTAAT 58.420 37.500 0.00 0.00 43.62 1.40
4281 4490 5.652452 ACAGGCTTTTACAGGATGGTTAATC 59.348 40.000 0.00 0.00 43.62 1.75
4282 4491 5.888161 CAGGCTTTTACAGGATGGTTAATCT 59.112 40.000 0.00 0.00 43.62 2.40
4283 4492 6.378280 CAGGCTTTTACAGGATGGTTAATCTT 59.622 38.462 0.00 0.00 43.62 2.40
4284 4493 6.378280 AGGCTTTTACAGGATGGTTAATCTTG 59.622 38.462 0.00 0.00 45.55 3.02
4285 4494 6.377146 GGCTTTTACAGGATGGTTAATCTTGA 59.623 38.462 4.67 0.00 43.40 3.02
4286 4495 7.068716 GGCTTTTACAGGATGGTTAATCTTGAT 59.931 37.037 4.67 0.00 43.40 2.57
4287 4496 8.470002 GCTTTTACAGGATGGTTAATCTTGATT 58.530 33.333 4.67 1.35 43.40 2.57
4288 4497 9.793252 CTTTTACAGGATGGTTAATCTTGATTG 57.207 33.333 6.15 0.00 43.40 2.67
4289 4498 7.880160 TTACAGGATGGTTAATCTTGATTGG 57.120 36.000 6.15 0.00 43.40 3.16
4290 4499 5.831103 ACAGGATGGTTAATCTTGATTGGT 58.169 37.500 6.15 0.00 43.40 3.67
4291 4500 5.888161 ACAGGATGGTTAATCTTGATTGGTC 59.112 40.000 6.15 0.00 43.40 4.02
4292 4501 5.887598 CAGGATGGTTAATCTTGATTGGTCA 59.112 40.000 6.15 2.60 43.40 4.02
4293 4502 6.377996 CAGGATGGTTAATCTTGATTGGTCAA 59.622 38.462 6.15 0.00 43.40 3.18
4294 4503 7.069085 CAGGATGGTTAATCTTGATTGGTCAAT 59.931 37.037 6.15 0.00 43.40 2.57
4295 4504 8.281531 AGGATGGTTAATCTTGATTGGTCAATA 58.718 33.333 6.15 0.00 43.08 1.90
4296 4505 8.571336 GGATGGTTAATCTTGATTGGTCAATAG 58.429 37.037 6.15 0.00 43.08 1.73
4297 4506 7.880160 TGGTTAATCTTGATTGGTCAATAGG 57.120 36.000 6.15 0.00 43.08 2.57
4298 4507 7.410174 TGGTTAATCTTGATTGGTCAATAGGT 58.590 34.615 6.15 0.00 43.08 3.08
4299 4508 7.339212 TGGTTAATCTTGATTGGTCAATAGGTG 59.661 37.037 6.15 0.00 43.08 4.00
4300 4509 7.556275 GGTTAATCTTGATTGGTCAATAGGTGA 59.444 37.037 6.15 0.00 43.08 4.02
4301 4510 8.616076 GTTAATCTTGATTGGTCAATAGGTGAG 58.384 37.037 6.15 0.00 43.08 3.51
4305 4514 4.857251 GGTCAATAGGTGAGCGGG 57.143 61.111 0.00 0.00 44.38 6.13
4306 4515 1.146263 GGTCAATAGGTGAGCGGGG 59.854 63.158 0.00 0.00 44.38 5.73
4307 4516 1.523938 GTCAATAGGTGAGCGGGGC 60.524 63.158 0.00 0.00 36.74 5.80
4308 4517 2.588877 CAATAGGTGAGCGGGGCG 60.589 66.667 0.00 0.00 0.00 6.13
4309 4518 3.861797 AATAGGTGAGCGGGGCGG 61.862 66.667 0.00 0.00 0.00 6.13
4340 4549 4.935352 CTGTAAATCAGGAGAGGAGAGG 57.065 50.000 0.00 0.00 40.23 3.69
4341 4550 4.285863 CTGTAAATCAGGAGAGGAGAGGT 58.714 47.826 0.00 0.00 40.23 3.85
4342 4551 4.689062 TGTAAATCAGGAGAGGAGAGGTT 58.311 43.478 0.00 0.00 0.00 3.50
4343 4552 5.094387 TGTAAATCAGGAGAGGAGAGGTTT 58.906 41.667 0.00 0.00 0.00 3.27
4344 4553 4.566426 AAATCAGGAGAGGAGAGGTTTG 57.434 45.455 0.00 0.00 0.00 2.93
4345 4554 2.704190 TCAGGAGAGGAGAGGTTTGT 57.296 50.000 0.00 0.00 0.00 2.83
4346 4555 2.251818 TCAGGAGAGGAGAGGTTTGTG 58.748 52.381 0.00 0.00 0.00 3.33
4347 4556 2.158310 TCAGGAGAGGAGAGGTTTGTGA 60.158 50.000 0.00 0.00 0.00 3.58
4348 4557 2.836981 CAGGAGAGGAGAGGTTTGTGAT 59.163 50.000 0.00 0.00 0.00 3.06
4349 4558 3.262915 CAGGAGAGGAGAGGTTTGTGATT 59.737 47.826 0.00 0.00 0.00 2.57
4350 4559 3.262915 AGGAGAGGAGAGGTTTGTGATTG 59.737 47.826 0.00 0.00 0.00 2.67
4351 4560 3.604582 GAGAGGAGAGGTTTGTGATTGG 58.395 50.000 0.00 0.00 0.00 3.16
4352 4561 2.982488 AGAGGAGAGGTTTGTGATTGGT 59.018 45.455 0.00 0.00 0.00 3.67
4353 4562 3.395941 AGAGGAGAGGTTTGTGATTGGTT 59.604 43.478 0.00 0.00 0.00 3.67
4354 4563 3.490348 AGGAGAGGTTTGTGATTGGTTG 58.510 45.455 0.00 0.00 0.00 3.77
4355 4564 3.117512 AGGAGAGGTTTGTGATTGGTTGT 60.118 43.478 0.00 0.00 0.00 3.32
4356 4565 3.636764 GGAGAGGTTTGTGATTGGTTGTT 59.363 43.478 0.00 0.00 0.00 2.83
4357 4566 4.825085 GGAGAGGTTTGTGATTGGTTGTTA 59.175 41.667 0.00 0.00 0.00 2.41
4358 4567 5.048713 GGAGAGGTTTGTGATTGGTTGTTAG 60.049 44.000 0.00 0.00 0.00 2.34
4359 4568 5.690865 AGAGGTTTGTGATTGGTTGTTAGA 58.309 37.500 0.00 0.00 0.00 2.10
4360 4569 5.531287 AGAGGTTTGTGATTGGTTGTTAGAC 59.469 40.000 0.00 0.00 0.00 2.59
4361 4570 4.274950 AGGTTTGTGATTGGTTGTTAGACG 59.725 41.667 0.00 0.00 0.00 4.18
4362 4571 4.533222 GTTTGTGATTGGTTGTTAGACGG 58.467 43.478 0.00 0.00 0.00 4.79
4363 4572 3.755112 TGTGATTGGTTGTTAGACGGA 57.245 42.857 0.00 0.00 0.00 4.69
4364 4573 4.074627 TGTGATTGGTTGTTAGACGGAA 57.925 40.909 0.00 0.00 0.00 4.30
4365 4574 4.062293 TGTGATTGGTTGTTAGACGGAAG 58.938 43.478 0.00 0.00 0.00 3.46
4366 4575 3.435671 GTGATTGGTTGTTAGACGGAAGG 59.564 47.826 0.00 0.00 0.00 3.46
4367 4576 3.325425 TGATTGGTTGTTAGACGGAAGGA 59.675 43.478 0.00 0.00 0.00 3.36
4368 4577 3.396260 TTGGTTGTTAGACGGAAGGAG 57.604 47.619 0.00 0.00 0.00 3.69
4369 4578 1.001633 TGGTTGTTAGACGGAAGGAGC 59.998 52.381 0.00 0.00 0.00 4.70
4370 4579 1.347320 GTTGTTAGACGGAAGGAGCG 58.653 55.000 0.00 0.00 0.00 5.03
4371 4580 0.963962 TTGTTAGACGGAAGGAGCGT 59.036 50.000 0.00 0.00 0.00 5.07
4372 4581 0.242825 TGTTAGACGGAAGGAGCGTG 59.757 55.000 0.00 0.00 0.00 5.34
4373 4582 0.243095 GTTAGACGGAAGGAGCGTGT 59.757 55.000 0.00 0.00 0.00 4.49
4374 4583 1.470098 GTTAGACGGAAGGAGCGTGTA 59.530 52.381 0.00 0.00 0.00 2.90
4375 4584 1.825090 TAGACGGAAGGAGCGTGTAA 58.175 50.000 0.00 0.00 0.00 2.41
4376 4585 0.963962 AGACGGAAGGAGCGTGTAAA 59.036 50.000 0.00 0.00 0.00 2.01
4377 4586 1.342174 AGACGGAAGGAGCGTGTAAAA 59.658 47.619 0.00 0.00 0.00 1.52
4378 4587 1.725164 GACGGAAGGAGCGTGTAAAAG 59.275 52.381 0.00 0.00 0.00 2.27
4379 4588 0.442699 CGGAAGGAGCGTGTAAAAGC 59.557 55.000 0.00 0.00 0.00 3.51
4380 4589 0.442699 GGAAGGAGCGTGTAAAAGCG 59.557 55.000 0.00 0.00 38.61 4.68
4381 4590 1.145803 GAAGGAGCGTGTAAAAGCGT 58.854 50.000 0.00 0.00 38.61 5.07
4382 4591 0.865769 AAGGAGCGTGTAAAAGCGTG 59.134 50.000 0.00 0.00 38.61 5.34
4383 4592 0.249741 AGGAGCGTGTAAAAGCGTGT 60.250 50.000 0.00 0.00 38.61 4.49
4384 4593 1.000060 AGGAGCGTGTAAAAGCGTGTA 60.000 47.619 0.00 0.00 38.61 2.90
4385 4594 1.794116 GGAGCGTGTAAAAGCGTGTAA 59.206 47.619 0.00 0.00 38.61 2.41
4386 4595 2.159881 GGAGCGTGTAAAAGCGTGTAAG 60.160 50.000 0.00 0.00 38.61 2.34
4387 4596 2.473984 GAGCGTGTAAAAGCGTGTAAGT 59.526 45.455 0.00 0.00 38.61 2.24
4388 4597 2.473984 AGCGTGTAAAAGCGTGTAAGTC 59.526 45.455 0.00 0.00 38.61 3.01
4389 4598 2.473984 GCGTGTAAAAGCGTGTAAGTCT 59.526 45.455 0.00 0.00 0.00 3.24
4390 4599 3.060070 GCGTGTAAAAGCGTGTAAGTCTT 60.060 43.478 0.00 0.00 0.00 3.01
4391 4600 4.551410 GCGTGTAAAAGCGTGTAAGTCTTT 60.551 41.667 0.00 0.00 0.00 2.52
4392 4601 4.896238 CGTGTAAAAGCGTGTAAGTCTTTG 59.104 41.667 0.00 0.00 31.21 2.77
4393 4602 5.501252 CGTGTAAAAGCGTGTAAGTCTTTGT 60.501 40.000 0.00 0.00 31.21 2.83
4394 4603 6.291743 CGTGTAAAAGCGTGTAAGTCTTTGTA 60.292 38.462 0.00 0.00 31.21 2.41
4395 4604 7.568134 CGTGTAAAAGCGTGTAAGTCTTTGTAT 60.568 37.037 0.00 0.00 31.21 2.29
4396 4605 7.529519 GTGTAAAAGCGTGTAAGTCTTTGTATG 59.470 37.037 0.00 0.00 31.21 2.39
4397 4606 6.613755 AAAAGCGTGTAAGTCTTTGTATGT 57.386 33.333 0.00 0.00 31.21 2.29
4398 4607 5.840940 AAGCGTGTAAGTCTTTGTATGTC 57.159 39.130 0.00 0.00 0.00 3.06
4399 4608 5.135508 AGCGTGTAAGTCTTTGTATGTCT 57.864 39.130 0.00 0.00 0.00 3.41
4400 4609 6.263516 AGCGTGTAAGTCTTTGTATGTCTA 57.736 37.500 0.00 0.00 0.00 2.59
4401 4610 6.323266 AGCGTGTAAGTCTTTGTATGTCTAG 58.677 40.000 0.00 0.00 0.00 2.43
4402 4611 5.004535 GCGTGTAAGTCTTTGTATGTCTAGC 59.995 44.000 0.00 0.00 0.00 3.42
4403 4612 6.090783 CGTGTAAGTCTTTGTATGTCTAGCA 58.909 40.000 0.00 0.00 0.00 3.49
4404 4613 6.752351 CGTGTAAGTCTTTGTATGTCTAGCAT 59.248 38.462 0.00 5.25 41.42 3.79
4405 4614 7.275779 CGTGTAAGTCTTTGTATGTCTAGCATT 59.724 37.037 5.22 0.00 38.94 3.56
4406 4615 8.936864 GTGTAAGTCTTTGTATGTCTAGCATTT 58.063 33.333 5.22 0.00 38.94 2.32
4407 4616 9.502091 TGTAAGTCTTTGTATGTCTAGCATTTT 57.498 29.630 5.22 0.00 38.94 1.82
4410 4619 7.308435 AGTCTTTGTATGTCTAGCATTTTTGC 58.692 34.615 5.22 0.00 38.94 3.68
4415 4624 1.203112 TGTCTAGCATTTTTGCCCCCA 60.203 47.619 0.00 0.00 34.90 4.96
4417 4626 0.536724 CTAGCATTTTTGCCCCCACC 59.463 55.000 0.00 0.00 34.90 4.61
4422 4631 3.783239 TTTTTGCCCCCACCCCCAG 62.783 63.158 0.00 0.00 0.00 4.45
4439 4648 2.037367 GGAACTTTCCCAGGCCCC 59.963 66.667 0.00 0.00 41.62 5.80
4479 4688 4.090057 GAGCAACTCCAACGCGGC 62.090 66.667 12.47 0.36 33.14 6.53
4493 4702 3.192922 CGGCGACCCATTTCGTCC 61.193 66.667 0.00 0.00 40.60 4.79
4528 4737 1.493311 GTCGGCGCAGACAGAAAAG 59.507 57.895 31.48 0.22 40.65 2.27
4538 4747 0.875059 GACAGAAAAGTCGGCCCAAG 59.125 55.000 0.00 0.00 0.00 3.61
4560 4769 3.326109 CGACCCAAACGGACACAC 58.674 61.111 0.00 0.00 34.64 3.82
4574 4783 1.085501 ACACACGTCCGCTTTTCGTT 61.086 50.000 0.00 0.00 35.62 3.85
4575 4784 0.382636 CACACGTCCGCTTTTCGTTC 60.383 55.000 0.00 0.00 35.62 3.95
4579 4788 3.045492 TCCGCTTTTCGTTCGCCC 61.045 61.111 0.00 0.00 36.19 6.13
4583 4792 2.548295 GCTTTTCGTTCGCCCACCA 61.548 57.895 0.00 0.00 0.00 4.17
4591 4800 1.152440 TTCGCCCACCAACCCATTT 60.152 52.632 0.00 0.00 0.00 2.32
4638 4847 4.796231 GGCGCGGACATGAGACGT 62.796 66.667 8.83 0.00 0.00 4.34
4640 4849 1.515519 GCGCGGACATGAGACGTAA 60.516 57.895 8.83 0.00 0.00 3.18
4648 4857 3.678717 ATGAGACGTAAGCGCGCGT 62.679 57.895 32.35 26.23 44.50 6.01
4691 4921 0.552848 GCCATCCTCTCCCATTCCAA 59.447 55.000 0.00 0.00 0.00 3.53
4692 4922 1.063717 GCCATCCTCTCCCATTCCAAA 60.064 52.381 0.00 0.00 0.00 3.28
4694 4924 3.711863 CCATCCTCTCCCATTCCAAAAA 58.288 45.455 0.00 0.00 0.00 1.94
4706 4936 0.747852 TCCAAAAACAAACCCTCGCC 59.252 50.000 0.00 0.00 0.00 5.54
4707 4937 0.249699 CCAAAAACAAACCCTCGCCC 60.250 55.000 0.00 0.00 0.00 6.13
4751 4984 0.389426 CATTTTGCCAGTGCCTCTGC 60.389 55.000 1.15 0.00 42.38 4.26
4778 5011 3.747976 GTGCCGCAACATCCACCC 61.748 66.667 0.00 0.00 0.00 4.61
4779 5012 3.965258 TGCCGCAACATCCACCCT 61.965 61.111 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 85 5.156523 GTTTAATGAACTAGCCTCCTGCGT 61.157 45.833 0.00 0.00 39.08 5.24
277 282 6.238484 CCCTCACAAAATCATCTTTCGGATAC 60.238 42.308 0.00 0.00 32.64 2.24
463 468 5.944599 GGATGAAGTGCCATCAGATTCATAT 59.055 40.000 0.00 0.00 43.49 1.78
574 579 1.486310 CCCCAAGATCATCGACCTTCA 59.514 52.381 0.00 0.00 0.00 3.02
642 647 1.071699 TCACTAACACCACCAGCCTTC 59.928 52.381 0.00 0.00 0.00 3.46
669 674 0.179081 GTACTGCTTCCCGATGACCC 60.179 60.000 0.00 0.00 0.00 4.46
707 712 2.664402 AGTCTTTTGCAGGTGGTGAT 57.336 45.000 0.00 0.00 0.00 3.06
763 768 5.474876 AGAAACCTCGAGCAAAATCATTTCT 59.525 36.000 6.99 8.24 0.00 2.52
837 883 2.159043 GCTGCAGATAGCTACCACTTGA 60.159 50.000 20.43 0.00 45.94 3.02
838 884 2.208431 GCTGCAGATAGCTACCACTTG 58.792 52.381 20.43 0.00 45.94 3.16
839 885 1.833630 TGCTGCAGATAGCTACCACTT 59.166 47.619 20.43 0.00 45.94 3.16
840 886 1.411977 CTGCTGCAGATAGCTACCACT 59.588 52.381 24.88 0.00 45.94 4.00
872 918 1.002868 CAGAGGCTTCCCCACACAG 60.003 63.158 0.00 0.00 35.39 3.66
938 1024 7.264373 TCCTTTTGCTTTCACAAAACAAAAA 57.736 28.000 10.08 0.00 42.88 1.94
941 1027 7.361628 GGAAATCCTTTTGCTTTCACAAAACAA 60.362 33.333 0.00 0.00 42.88 2.83
942 1028 6.093357 GGAAATCCTTTTGCTTTCACAAAACA 59.907 34.615 0.00 0.00 42.88 2.83
943 1029 6.316140 AGGAAATCCTTTTGCTTTCACAAAAC 59.684 34.615 0.00 0.00 46.09 2.43
944 1030 6.315891 CAGGAAATCCTTTTGCTTTCACAAAA 59.684 34.615 0.00 2.80 46.09 2.44
945 1031 5.816777 CAGGAAATCCTTTTGCTTTCACAAA 59.183 36.000 0.00 0.00 46.09 2.83
994 1087 1.530891 GGAGCCATGGCATGCATCT 60.531 57.895 37.18 16.13 44.88 2.90
1038 1131 4.070552 GGGGCGCTGAAGACGAGT 62.071 66.667 7.64 0.00 0.00 4.18
1654 1752 0.249120 TGAAGGTGACGGCGATGAAT 59.751 50.000 16.62 0.00 0.00 2.57
1678 1776 2.358247 ACGTTGGTCATGGGCGTC 60.358 61.111 0.00 0.00 0.00 5.19
1738 1842 1.038130 CGGGGTCCTCGAAGATGTCT 61.038 60.000 4.69 0.00 33.89 3.41
1975 2079 3.537874 GGGGCGGCGTACTCAGAT 61.538 66.667 9.37 0.00 0.00 2.90
2450 2596 2.084546 GTCCTTGGATTTCTTGGACCG 58.915 52.381 0.00 0.00 40.74 4.79
2551 2697 5.353394 TGTTCTTCTTGTTGTGGTAGACT 57.647 39.130 0.00 0.00 0.00 3.24
2843 3019 1.825474 GATCTCCGTCTGGAACTCCAA 59.175 52.381 0.00 0.00 46.97 3.53
3187 3369 4.235762 ACGTGCGCCTGGTTCACT 62.236 61.111 4.18 3.98 0.00 3.41
3427 3612 1.945387 CGATCTGGTCCTTGATGGTG 58.055 55.000 3.25 0.00 37.07 4.17
3727 3912 1.376942 GTCGTCGTCCTCCTCCTCA 60.377 63.158 0.00 0.00 0.00 3.86
3762 3947 2.126307 GCACGAGCTGCGAGAAGA 60.126 61.111 11.64 0.00 44.57 2.87
3833 4018 2.985809 CTCTCTTCACTCTTGACGCTTG 59.014 50.000 0.00 0.00 0.00 4.01
3840 4025 3.383620 AGCACACTCTCTTCACTCTTG 57.616 47.619 0.00 0.00 0.00 3.02
3972 4161 7.711339 GCTAGTACCTTAGCTACATGAACATTT 59.289 37.037 0.00 0.00 42.18 2.32
3974 4163 6.515200 CGCTAGTACCTTAGCTACATGAACAT 60.515 42.308 0.00 0.00 43.05 2.71
4006 4195 7.546667 CCTTGATTAAATTCCAGTGAAACCATG 59.453 37.037 0.00 0.00 37.80 3.66
4054 4243 9.678941 GACGTCATCTTAGATGTGACATAATTA 57.321 33.333 20.09 0.00 41.69 1.40
4055 4244 8.197439 TGACGTCATCTTAGATGTGACATAATT 58.803 33.333 15.76 0.00 41.69 1.40
4056 4245 7.649705 GTGACGTCATCTTAGATGTGACATAAT 59.350 37.037 23.12 0.00 40.12 1.28
4057 4246 6.972901 GTGACGTCATCTTAGATGTGACATAA 59.027 38.462 23.12 0.00 40.12 1.90
4058 4247 6.459710 GGTGACGTCATCTTAGATGTGACATA 60.460 42.308 23.12 0.00 41.50 2.29
4059 4248 5.344066 GTGACGTCATCTTAGATGTGACAT 58.656 41.667 23.12 0.00 40.12 3.06
4060 4249 4.380550 GGTGACGTCATCTTAGATGTGACA 60.381 45.833 23.12 16.44 41.50 3.58
4061 4250 4.106197 GGTGACGTCATCTTAGATGTGAC 58.894 47.826 23.12 12.83 39.80 3.67
4062 4251 3.761752 TGGTGACGTCATCTTAGATGTGA 59.238 43.478 27.93 2.96 37.85 3.58
4063 4252 4.110036 TGGTGACGTCATCTTAGATGTG 57.890 45.455 27.93 16.06 37.85 3.21
4064 4253 4.160439 ACATGGTGACGTCATCTTAGATGT 59.840 41.667 27.93 23.91 40.31 3.06
4065 4254 4.686972 ACATGGTGACGTCATCTTAGATG 58.313 43.478 27.93 23.32 0.00 2.90
4066 4255 5.344743 AACATGGTGACGTCATCTTAGAT 57.655 39.130 27.93 11.61 0.00 1.98
4067 4256 4.801330 AACATGGTGACGTCATCTTAGA 57.199 40.909 27.93 9.66 0.00 2.10
4068 4257 4.690748 ACAAACATGGTGACGTCATCTTAG 59.309 41.667 27.93 19.21 0.00 2.18
4069 4258 4.450757 CACAAACATGGTGACGTCATCTTA 59.549 41.667 27.93 10.80 38.54 2.10
4070 4259 3.250762 CACAAACATGGTGACGTCATCTT 59.749 43.478 27.93 19.84 38.54 2.40
4093 4302 0.616111 AACAGAGCGATCAGGAGGGT 60.616 55.000 2.38 0.00 0.00 4.34
4114 4323 3.560068 ACAAACAAGCGAACGAGAGAAAT 59.440 39.130 0.00 0.00 0.00 2.17
4181 4390 3.411517 GGCCCAGCCCTAGAAGCA 61.412 66.667 7.37 0.00 44.06 3.91
4226 4435 2.045340 GTGTAGCATTGCCGGGGT 60.045 61.111 2.18 0.00 0.00 4.95
4227 4436 2.581208 TACGTGTAGCATTGCCGGGG 62.581 60.000 2.18 0.00 0.00 5.73
4228 4437 1.153529 TACGTGTAGCATTGCCGGG 60.154 57.895 2.18 0.00 0.00 5.73
4231 4440 2.723618 CGTTTGTACGTGTAGCATTGCC 60.724 50.000 4.70 0.00 42.72 4.52
4232 4441 2.492001 CGTTTGTACGTGTAGCATTGC 58.508 47.619 0.00 0.00 42.72 3.56
4244 4453 7.354257 TGTAAAAGCCTGTAAATCGTTTGTAC 58.646 34.615 0.00 0.00 0.00 2.90
4245 4454 7.308109 CCTGTAAAAGCCTGTAAATCGTTTGTA 60.308 37.037 0.00 0.00 0.00 2.41
4246 4455 6.380095 TGTAAAAGCCTGTAAATCGTTTGT 57.620 33.333 0.00 0.00 0.00 2.83
4247 4456 5.856455 CCTGTAAAAGCCTGTAAATCGTTTG 59.144 40.000 0.00 0.00 0.00 2.93
4248 4457 5.766174 TCCTGTAAAAGCCTGTAAATCGTTT 59.234 36.000 0.00 0.00 0.00 3.60
4249 4458 5.310451 TCCTGTAAAAGCCTGTAAATCGTT 58.690 37.500 0.00 0.00 0.00 3.85
4250 4459 4.901868 TCCTGTAAAAGCCTGTAAATCGT 58.098 39.130 0.00 0.00 0.00 3.73
4251 4460 5.220854 CCATCCTGTAAAAGCCTGTAAATCG 60.221 44.000 0.00 0.00 0.00 3.34
4252 4461 5.652452 ACCATCCTGTAAAAGCCTGTAAATC 59.348 40.000 0.00 0.00 0.00 2.17
4253 4462 5.580022 ACCATCCTGTAAAAGCCTGTAAAT 58.420 37.500 0.00 0.00 0.00 1.40
4254 4463 4.993028 ACCATCCTGTAAAAGCCTGTAAA 58.007 39.130 0.00 0.00 0.00 2.01
4255 4464 4.650972 ACCATCCTGTAAAAGCCTGTAA 57.349 40.909 0.00 0.00 0.00 2.41
4256 4465 4.650972 AACCATCCTGTAAAAGCCTGTA 57.349 40.909 0.00 0.00 0.00 2.74
4257 4466 3.525800 AACCATCCTGTAAAAGCCTGT 57.474 42.857 0.00 0.00 0.00 4.00
4258 4467 5.888161 AGATTAACCATCCTGTAAAAGCCTG 59.112 40.000 0.00 0.00 31.20 4.85
4259 4468 6.079712 AGATTAACCATCCTGTAAAAGCCT 57.920 37.500 0.00 0.00 31.20 4.58
4260 4469 6.377146 TCAAGATTAACCATCCTGTAAAAGCC 59.623 38.462 0.00 0.00 31.20 4.35
4261 4470 7.391148 TCAAGATTAACCATCCTGTAAAAGC 57.609 36.000 0.00 0.00 31.20 3.51
4262 4471 9.793252 CAATCAAGATTAACCATCCTGTAAAAG 57.207 33.333 0.00 0.00 31.20 2.27
4263 4472 8.748412 CCAATCAAGATTAACCATCCTGTAAAA 58.252 33.333 0.00 0.00 31.20 1.52
4264 4473 7.893302 ACCAATCAAGATTAACCATCCTGTAAA 59.107 33.333 0.00 0.00 31.20 2.01
4265 4474 7.410174 ACCAATCAAGATTAACCATCCTGTAA 58.590 34.615 0.00 0.00 31.20 2.41
4266 4475 6.969043 ACCAATCAAGATTAACCATCCTGTA 58.031 36.000 0.00 0.00 31.20 2.74
4267 4476 5.831103 ACCAATCAAGATTAACCATCCTGT 58.169 37.500 0.00 0.00 31.20 4.00
4268 4477 5.887598 TGACCAATCAAGATTAACCATCCTG 59.112 40.000 0.00 0.00 31.20 3.86
4269 4478 6.078456 TGACCAATCAAGATTAACCATCCT 57.922 37.500 0.00 0.00 31.20 3.24
4270 4479 6.773976 TTGACCAATCAAGATTAACCATCC 57.226 37.500 0.00 0.00 40.01 3.51
4283 4492 2.419990 CCGCTCACCTATTGACCAATCA 60.420 50.000 0.00 0.00 32.50 2.57
4284 4493 2.213499 CCGCTCACCTATTGACCAATC 58.787 52.381 0.00 0.00 32.50 2.67
4285 4494 1.134098 CCCGCTCACCTATTGACCAAT 60.134 52.381 0.64 0.64 34.93 3.16
4286 4495 0.251916 CCCGCTCACCTATTGACCAA 59.748 55.000 0.00 0.00 0.00 3.67
4287 4496 1.622607 CCCCGCTCACCTATTGACCA 61.623 60.000 0.00 0.00 0.00 4.02
4288 4497 1.146263 CCCCGCTCACCTATTGACC 59.854 63.158 0.00 0.00 0.00 4.02
4289 4498 1.523938 GCCCCGCTCACCTATTGAC 60.524 63.158 0.00 0.00 0.00 3.18
4290 4499 2.908015 GCCCCGCTCACCTATTGA 59.092 61.111 0.00 0.00 0.00 2.57
4291 4500 2.588877 CGCCCCGCTCACCTATTG 60.589 66.667 0.00 0.00 0.00 1.90
4292 4501 3.861797 CCGCCCCGCTCACCTATT 61.862 66.667 0.00 0.00 0.00 1.73
4319 4528 4.285863 ACCTCTCCTCTCCTGATTTACAG 58.714 47.826 0.00 0.00 45.36 2.74
4320 4529 4.338795 ACCTCTCCTCTCCTGATTTACA 57.661 45.455 0.00 0.00 0.00 2.41
4321 4530 5.046231 ACAAACCTCTCCTCTCCTGATTTAC 60.046 44.000 0.00 0.00 0.00 2.01
4322 4531 5.046304 CACAAACCTCTCCTCTCCTGATTTA 60.046 44.000 0.00 0.00 0.00 1.40
4323 4532 3.913163 ACAAACCTCTCCTCTCCTGATTT 59.087 43.478 0.00 0.00 0.00 2.17
4324 4533 3.262915 CACAAACCTCTCCTCTCCTGATT 59.737 47.826 0.00 0.00 0.00 2.57
4325 4534 2.836981 CACAAACCTCTCCTCTCCTGAT 59.163 50.000 0.00 0.00 0.00 2.90
4326 4535 2.158310 TCACAAACCTCTCCTCTCCTGA 60.158 50.000 0.00 0.00 0.00 3.86
4327 4536 2.251818 TCACAAACCTCTCCTCTCCTG 58.748 52.381 0.00 0.00 0.00 3.86
4328 4537 2.704190 TCACAAACCTCTCCTCTCCT 57.296 50.000 0.00 0.00 0.00 3.69
4329 4538 3.604582 CAATCACAAACCTCTCCTCTCC 58.395 50.000 0.00 0.00 0.00 3.71
4330 4539 3.008485 ACCAATCACAAACCTCTCCTCTC 59.992 47.826 0.00 0.00 0.00 3.20
4331 4540 2.982488 ACCAATCACAAACCTCTCCTCT 59.018 45.455 0.00 0.00 0.00 3.69
4332 4541 3.425162 ACCAATCACAAACCTCTCCTC 57.575 47.619 0.00 0.00 0.00 3.71
4333 4542 3.117512 ACAACCAATCACAAACCTCTCCT 60.118 43.478 0.00 0.00 0.00 3.69
4334 4543 3.222603 ACAACCAATCACAAACCTCTCC 58.777 45.455 0.00 0.00 0.00 3.71
4335 4544 4.918810 AACAACCAATCACAAACCTCTC 57.081 40.909 0.00 0.00 0.00 3.20
4336 4545 5.531287 GTCTAACAACCAATCACAAACCTCT 59.469 40.000 0.00 0.00 0.00 3.69
4337 4546 5.560183 CGTCTAACAACCAATCACAAACCTC 60.560 44.000 0.00 0.00 0.00 3.85
4338 4547 4.274950 CGTCTAACAACCAATCACAAACCT 59.725 41.667 0.00 0.00 0.00 3.50
4339 4548 4.533222 CGTCTAACAACCAATCACAAACC 58.467 43.478 0.00 0.00 0.00 3.27
4340 4549 4.273969 TCCGTCTAACAACCAATCACAAAC 59.726 41.667 0.00 0.00 0.00 2.93
4341 4550 4.452825 TCCGTCTAACAACCAATCACAAA 58.547 39.130 0.00 0.00 0.00 2.83
4342 4551 4.074627 TCCGTCTAACAACCAATCACAA 57.925 40.909 0.00 0.00 0.00 3.33
4343 4552 3.755112 TCCGTCTAACAACCAATCACA 57.245 42.857 0.00 0.00 0.00 3.58
4344 4553 3.435671 CCTTCCGTCTAACAACCAATCAC 59.564 47.826 0.00 0.00 0.00 3.06
4345 4554 3.325425 TCCTTCCGTCTAACAACCAATCA 59.675 43.478 0.00 0.00 0.00 2.57
4346 4555 3.933332 CTCCTTCCGTCTAACAACCAATC 59.067 47.826 0.00 0.00 0.00 2.67
4347 4556 3.868754 GCTCCTTCCGTCTAACAACCAAT 60.869 47.826 0.00 0.00 0.00 3.16
4348 4557 2.549349 GCTCCTTCCGTCTAACAACCAA 60.549 50.000 0.00 0.00 0.00 3.67
4349 4558 1.001633 GCTCCTTCCGTCTAACAACCA 59.998 52.381 0.00 0.00 0.00 3.67
4350 4559 1.723220 GCTCCTTCCGTCTAACAACC 58.277 55.000 0.00 0.00 0.00 3.77
4351 4560 1.336609 ACGCTCCTTCCGTCTAACAAC 60.337 52.381 0.00 0.00 32.83 3.32
4352 4561 0.963962 ACGCTCCTTCCGTCTAACAA 59.036 50.000 0.00 0.00 32.83 2.83
4353 4562 0.242825 CACGCTCCTTCCGTCTAACA 59.757 55.000 0.00 0.00 36.69 2.41
4354 4563 0.243095 ACACGCTCCTTCCGTCTAAC 59.757 55.000 0.00 0.00 36.69 2.34
4355 4564 1.825090 TACACGCTCCTTCCGTCTAA 58.175 50.000 0.00 0.00 36.69 2.10
4356 4565 1.825090 TTACACGCTCCTTCCGTCTA 58.175 50.000 0.00 0.00 36.69 2.59
4357 4566 0.963962 TTTACACGCTCCTTCCGTCT 59.036 50.000 0.00 0.00 36.69 4.18
4358 4567 1.725164 CTTTTACACGCTCCTTCCGTC 59.275 52.381 0.00 0.00 36.69 4.79
4359 4568 1.792006 CTTTTACACGCTCCTTCCGT 58.208 50.000 0.00 0.00 39.91 4.69
4360 4569 0.442699 GCTTTTACACGCTCCTTCCG 59.557 55.000 0.00 0.00 0.00 4.30
4361 4570 0.442699 CGCTTTTACACGCTCCTTCC 59.557 55.000 0.00 0.00 0.00 3.46
4362 4571 1.136336 CACGCTTTTACACGCTCCTTC 60.136 52.381 0.00 0.00 0.00 3.46
4363 4572 0.865769 CACGCTTTTACACGCTCCTT 59.134 50.000 0.00 0.00 0.00 3.36
4364 4573 0.249741 ACACGCTTTTACACGCTCCT 60.250 50.000 0.00 0.00 0.00 3.69
4365 4574 1.421382 TACACGCTTTTACACGCTCC 58.579 50.000 0.00 0.00 0.00 4.70
4366 4575 2.473984 ACTTACACGCTTTTACACGCTC 59.526 45.455 0.00 0.00 0.00 5.03
4367 4576 2.473984 GACTTACACGCTTTTACACGCT 59.526 45.455 0.00 0.00 0.00 5.07
4368 4577 2.473984 AGACTTACACGCTTTTACACGC 59.526 45.455 0.00 0.00 0.00 5.34
4369 4578 4.703899 AAGACTTACACGCTTTTACACG 57.296 40.909 0.00 0.00 0.00 4.49
4370 4579 5.803118 ACAAAGACTTACACGCTTTTACAC 58.197 37.500 0.00 0.00 30.00 2.90
4371 4580 7.225145 ACATACAAAGACTTACACGCTTTTACA 59.775 33.333 0.00 0.00 30.00 2.41
4372 4581 7.570161 ACATACAAAGACTTACACGCTTTTAC 58.430 34.615 0.00 0.00 30.00 2.01
4373 4582 7.654520 AGACATACAAAGACTTACACGCTTTTA 59.345 33.333 0.00 0.00 30.00 1.52
4374 4583 6.482308 AGACATACAAAGACTTACACGCTTTT 59.518 34.615 0.00 0.00 30.00 2.27
4375 4584 5.989777 AGACATACAAAGACTTACACGCTTT 59.010 36.000 0.00 0.00 32.46 3.51
4376 4585 5.539048 AGACATACAAAGACTTACACGCTT 58.461 37.500 0.00 0.00 0.00 4.68
4377 4586 5.135508 AGACATACAAAGACTTACACGCT 57.864 39.130 0.00 0.00 0.00 5.07
4378 4587 5.004535 GCTAGACATACAAAGACTTACACGC 59.995 44.000 0.00 0.00 0.00 5.34
4379 4588 6.090783 TGCTAGACATACAAAGACTTACACG 58.909 40.000 0.00 0.00 0.00 4.49
4380 4589 8.480643 AATGCTAGACATACAAAGACTTACAC 57.519 34.615 0.00 0.00 38.34 2.90
4381 4590 9.502091 AAAATGCTAGACATACAAAGACTTACA 57.498 29.630 0.00 0.00 38.34 2.41
4384 4593 7.809806 GCAAAAATGCTAGACATACAAAGACTT 59.190 33.333 0.00 0.00 38.34 3.01
4385 4594 7.308435 GCAAAAATGCTAGACATACAAAGACT 58.692 34.615 0.00 0.00 38.34 3.24
4386 4595 6.528072 GGCAAAAATGCTAGACATACAAAGAC 59.472 38.462 0.00 0.00 38.34 3.01
4387 4596 6.350110 GGGCAAAAATGCTAGACATACAAAGA 60.350 38.462 0.00 0.00 38.34 2.52
4388 4597 5.807011 GGGCAAAAATGCTAGACATACAAAG 59.193 40.000 0.00 0.00 38.34 2.77
4389 4598 5.337169 GGGGCAAAAATGCTAGACATACAAA 60.337 40.000 0.00 0.00 38.34 2.83
4390 4599 4.159506 GGGGCAAAAATGCTAGACATACAA 59.840 41.667 0.00 0.00 38.34 2.41
4391 4600 3.699038 GGGGCAAAAATGCTAGACATACA 59.301 43.478 0.00 0.00 38.34 2.29
4392 4601 3.068165 GGGGGCAAAAATGCTAGACATAC 59.932 47.826 0.00 0.00 38.34 2.39
4393 4602 3.295973 GGGGGCAAAAATGCTAGACATA 58.704 45.455 0.00 0.00 38.34 2.29
4394 4603 2.110578 GGGGGCAAAAATGCTAGACAT 58.889 47.619 0.00 0.00 42.30 3.06
4395 4604 1.203112 TGGGGGCAAAAATGCTAGACA 60.203 47.619 0.00 0.00 34.73 3.41
4396 4605 1.204704 GTGGGGGCAAAAATGCTAGAC 59.795 52.381 0.00 0.00 34.73 2.59
4397 4606 1.555967 GTGGGGGCAAAAATGCTAGA 58.444 50.000 0.00 0.00 34.73 2.43
4398 4607 0.536724 GGTGGGGGCAAAAATGCTAG 59.463 55.000 0.40 0.00 34.73 3.42
4399 4608 0.907230 GGGTGGGGGCAAAAATGCTA 60.907 55.000 0.40 0.00 34.73 3.49
4400 4609 2.223443 GGGTGGGGGCAAAAATGCT 61.223 57.895 0.40 0.00 34.73 3.79
4401 4610 2.350895 GGGTGGGGGCAAAAATGC 59.649 61.111 0.00 0.00 0.00 3.56
4402 4611 2.601702 GGGGGTGGGGGCAAAAATG 61.602 63.158 0.00 0.00 0.00 2.32
4403 4612 2.204074 GGGGGTGGGGGCAAAAAT 60.204 61.111 0.00 0.00 0.00 1.82
4404 4613 3.779083 TGGGGGTGGGGGCAAAAA 61.779 61.111 0.00 0.00 0.00 1.94
4405 4614 4.247130 CTGGGGGTGGGGGCAAAA 62.247 66.667 0.00 0.00 0.00 2.44
4415 4624 1.388217 TGGGAAAGTTCCTGGGGGT 60.388 57.895 9.88 0.00 46.72 4.95
4417 4626 1.384191 CCTGGGAAAGTTCCTGGGG 59.616 63.158 9.88 6.19 46.72 4.96
4422 4631 2.037367 GGGGCCTGGGAAAGTTCC 59.963 66.667 0.84 1.10 46.82 3.62
4439 4648 2.727544 CCCACAAACACAAGGCCG 59.272 61.111 0.00 0.00 0.00 6.13
4479 4688 3.550992 CGCGGACGAAATGGGTCG 61.551 66.667 0.00 0.00 46.54 4.79
4518 4727 0.472471 TTGGGCCGACTTTTCTGTCT 59.528 50.000 0.00 0.00 35.00 3.41
4556 4765 0.382636 GAACGAAAAGCGGACGTGTG 60.383 55.000 0.00 0.00 46.49 3.82
4557 4766 1.814211 CGAACGAAAAGCGGACGTGT 61.814 55.000 0.00 0.00 46.49 4.49
4560 4769 2.202008 GCGAACGAAAAGCGGACG 60.202 61.111 0.00 0.00 46.49 4.79
4574 4783 1.605165 GAAATGGGTTGGTGGGCGA 60.605 57.895 0.00 0.00 0.00 5.54
4575 4784 2.645192 GGAAATGGGTTGGTGGGCG 61.645 63.158 0.00 0.00 0.00 6.13
4579 4788 2.645192 GGCCGGAAATGGGTTGGTG 61.645 63.158 5.05 0.00 0.00 4.17
4583 4792 0.546507 AAATGGGCCGGAAATGGGTT 60.547 50.000 5.05 0.00 0.00 4.11
4605 4814 1.159713 CGCCGATGCAAATCTGGCTA 61.160 55.000 15.97 0.00 43.54 3.93
4606 4815 2.475466 CGCCGATGCAAATCTGGCT 61.475 57.895 15.97 0.00 43.54 4.75
4607 4816 2.025156 CGCCGATGCAAATCTGGC 59.975 61.111 11.01 11.01 42.29 4.85
4609 4818 2.351548 CGCGCCGATGCAAATCTG 60.352 61.111 0.00 0.00 37.32 2.90
4610 4819 3.576356 CCGCGCCGATGCAAATCT 61.576 61.111 0.00 0.00 37.32 2.40
4612 4821 3.876198 GTCCGCGCCGATGCAAAT 61.876 61.111 0.00 0.00 37.32 2.32
4618 4827 3.527427 TCTCATGTCCGCGCCGAT 61.527 61.111 0.00 0.00 0.00 4.18
4631 4840 4.394078 ACGCGCGCTTACGTCTCA 62.394 61.111 32.58 0.00 38.28 3.27
4691 4921 2.852180 GCGGGCGAGGGTTTGTTTT 61.852 57.895 0.00 0.00 0.00 2.43
4692 4922 3.292159 GCGGGCGAGGGTTTGTTT 61.292 61.111 0.00 0.00 0.00 2.83
4706 4936 4.831307 CGACGTCGAAGGAGGCGG 62.831 72.222 33.35 0.00 44.42 6.13
4741 4974 4.719106 GCAGCTGGCAGAGGCACT 62.719 66.667 20.86 1.64 43.22 4.40


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

AutoCloner maintained by Alex Coulton.