Multiple sequence alignment - TraesCS1D01G357000

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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 TraesCS1D01G357000 chr1D 100.000 5429 0 0 1 5429 441080303 441074875 0.000000e+00 10026.0
1 TraesCS1D01G357000 chr1A 96.675 4511 104 15 1 4489 536934654 536939140 0.000000e+00 7457.0
2 TraesCS1D01G357000 chr1A 91.080 213 8 5 4553 4757 536939144 536939353 1.490000e-70 278.0
3 TraesCS1D01G357000 chr1A 92.814 167 12 0 4712 4878 536939352 536939518 5.430000e-60 243.0
4 TraesCS1D01G357000 chr1A 92.308 143 11 0 1 143 167219172 167219314 2.560000e-48 204.0
5 TraesCS1D01G357000 chr1A 93.023 86 6 0 4942 5027 536939519 536939604 5.710000e-25 126.0
6 TraesCS1D01G357000 chr1A 92.045 88 5 2 5340 5426 536958241 536958327 7.380000e-24 122.0
7 TraesCS1D01G357000 chr1A 97.619 42 1 0 4809 4850 536939409 536939450 7.540000e-09 73.1
8 TraesCS1D01G357000 chr1B 96.355 4554 127 16 7 4536 598905629 598901091 0.000000e+00 7454.0
9 TraesCS1D01G357000 chr1B 91.950 323 25 1 4846 5168 598900735 598900414 8.290000e-123 451.0
10 TraesCS1D01G357000 chr1B 91.085 258 13 6 4590 4839 598901093 598900838 1.870000e-89 340.0
11 TraesCS1D01G357000 chr1B 95.714 140 2 3 5220 5356 598885783 598885645 7.080000e-54 222.0
12 TraesCS1D01G357000 chr1B 96.825 126 2 2 5145 5269 598885720 598885596 5.510000e-50 209.0
13 TraesCS1D01G357000 chr1B 95.946 74 1 2 5355 5426 598884764 598884691 9.550000e-23 119.0
14 TraesCS1D01G357000 chr1B 95.349 43 1 1 4809 4850 598900910 598900868 3.510000e-07 67.6
15 TraesCS1D01G357000 chrUn 100.000 398 0 0 3015 3412 478968816 478968419 0.000000e+00 736.0
16 TraesCS1D01G357000 chr6A 75.958 574 115 21 1964 2526 187739319 187739880 1.930000e-69 274.0
17 TraesCS1D01G357000 chr6B 75.784 574 116 21 1964 2526 248354546 248355107 8.960000e-68 268.0
18 TraesCS1D01G357000 chr6D 75.652 575 115 23 1964 2526 142747621 142748182 4.170000e-66 263.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G357000 chr1D 441074875 441080303 5428 True 10026.00 10026 100.00000 1 5429 1 chr1D.!!$R1 5428
1 TraesCS1D01G357000 chr1A 536934654 536939604 4950 False 1635.42 7457 94.24220 1 5027 5 chr1A.!!$F3 5026
2 TraesCS1D01G357000 chr1B 598900414 598905629 5215 True 2078.15 7454 93.68475 7 5168 4 chr1B.!!$R2 5161
3 TraesCS1D01G357000 chr6A 187739319 187739880 561 False 274.00 274 75.95800 1964 2526 1 chr6A.!!$F1 562
4 TraesCS1D01G357000 chr6B 248354546 248355107 561 False 268.00 268 75.78400 1964 2526 1 chr6B.!!$F1 562
5 TraesCS1D01G357000 chr6D 142747621 142748182 561 False 263.00 263 75.65200 1964 2526 1 chr6D.!!$F1 562

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
822 825 0.459237 GGTCTGGTGAGATGCTGTCG 60.459 60.000 0.00 0.00 0.0 4.35 F
1408 1412 0.254178 ACCTGCAATTCTCCAGCGAT 59.746 50.000 0.00 0.00 0.0 4.58 F
2831 2842 2.843113 AGGTAAGCTGGCAATCTTCTCT 59.157 45.455 5.12 2.91 0.0 3.10 F
3621 3633 0.108329 CGCTTGTCAAGTCCGGGTAT 60.108 55.000 14.03 0.00 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2301 2308 1.002033 CGATGCAAAGGCCTTGATAGC 60.002 52.381 21.33 20.3 40.13 2.97 R
2907 2918 0.110486 TGGCCTGGTGTTTTCTCCTC 59.890 55.000 3.32 0.0 34.83 3.71 R
4131 4144 0.104855 TCCATCCGCCAAAGAGATCG 59.895 55.000 0.00 0.0 0.00 3.69 R
5238 5442 0.030638 CACGGCTCCAAACCAAACAG 59.969 55.000 0.00 0.0 0.00 3.16 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.768870 CTCCCCGTCCATCCATTACTT 59.231 52.381 0.00 0.00 0.00 2.24
52 53 4.243270 CATTACTTCCGTCGGAGAAAACT 58.757 43.478 14.79 0.00 39.69 2.66
57 58 4.946157 ACTTCCGTCGGAGAAAACTCTATA 59.054 41.667 14.79 0.00 39.69 1.31
173 174 4.627741 CGTCTCTAATTGGGGAAATGGGAA 60.628 45.833 0.00 0.00 0.00 3.97
283 285 3.911868 TGAATTAACCACTGCATTGTGC 58.088 40.909 3.14 0.00 45.29 4.57
306 308 8.697067 GTGCAATTTTCATCTCATATATGTTGC 58.303 33.333 18.00 18.00 35.14 4.17
307 309 7.868922 TGCAATTTTCATCTCATATATGTTGCC 59.131 33.333 20.26 9.74 34.35 4.52
324 326 1.922447 TGCCTCTGGTCCCATGTAATT 59.078 47.619 0.00 0.00 0.00 1.40
430 433 2.191400 CCTTGGATGGAGTTCCTCTGA 58.809 52.381 0.00 0.00 36.68 3.27
822 825 0.459237 GGTCTGGTGAGATGCTGTCG 60.459 60.000 0.00 0.00 0.00 4.35
888 891 8.390354 TGTGATTATTGTCTGAATTGATTCGTC 58.610 33.333 0.00 0.00 39.62 4.20
1036 1039 3.195825 TCCTCTCGTTTTCTTGATCCTCC 59.804 47.826 0.00 0.00 0.00 4.30
1039 1042 5.105310 CCTCTCGTTTTCTTGATCCTCCTAA 60.105 44.000 0.00 0.00 0.00 2.69
1063 1066 0.322816 TCATGGAACCAAGGCTGCTC 60.323 55.000 0.00 0.00 0.00 4.26
1238 1242 4.943705 CAGCCTACATTATGGTTTGTCTGT 59.056 41.667 0.00 0.00 0.00 3.41
1358 1362 1.611977 CATACAGCATGGCAATGGGAG 59.388 52.381 2.54 0.00 43.62 4.30
1408 1412 0.254178 ACCTGCAATTCTCCAGCGAT 59.746 50.000 0.00 0.00 0.00 4.58
1467 1471 7.325660 ACAATTCGTCAAATATTGCTGAGAT 57.674 32.000 0.00 0.00 33.61 2.75
1558 1562 7.423844 TTTCAAATCAGAGGAGCTACATAGA 57.576 36.000 0.00 0.00 0.00 1.98
1643 1647 6.471146 AGTACTTTATCCATGCTCCATGATC 58.529 40.000 6.77 0.00 43.81 2.92
1665 1669 3.708563 AGTTAGCAATTGCAAACGTGT 57.291 38.095 30.89 11.93 45.16 4.49
2360 2367 4.568956 AGCAATTTATTTGGCCACAGAAC 58.431 39.130 3.88 0.00 35.75 3.01
2513 2520 4.752101 GCGGAAATCTTGCAGTACATAGAT 59.248 41.667 0.00 0.00 31.54 1.98
2586 2593 3.719871 TCAGGAGCCATAGGTAAGAACA 58.280 45.455 0.00 0.00 0.00 3.18
2621 2628 3.072944 GCCATGCTGGAAGAAGCTATAG 58.927 50.000 6.40 0.00 40.96 1.31
2831 2842 2.843113 AGGTAAGCTGGCAATCTTCTCT 59.157 45.455 5.12 2.91 0.00 3.10
3013 3024 1.819632 GGTGAAAGATGGCGCGGAT 60.820 57.895 8.83 0.00 0.00 4.18
3473 3484 7.646922 GCATCCTACTTTTGACATGATTCATTC 59.353 37.037 0.00 0.00 0.00 2.67
3474 3485 8.900781 CATCCTACTTTTGACATGATTCATTCT 58.099 33.333 0.00 0.00 0.00 2.40
3475 3486 8.498054 TCCTACTTTTGACATGATTCATTCTC 57.502 34.615 0.00 0.00 0.00 2.87
3621 3633 0.108329 CGCTTGTCAAGTCCGGGTAT 60.108 55.000 14.03 0.00 0.00 2.73
3873 3885 3.857854 GTCGACAGGCTGCATGCG 61.858 66.667 15.89 17.65 44.05 4.73
4067 4079 2.156917 TCTGCTTTGCTTGATGGACAG 58.843 47.619 0.00 0.00 0.00 3.51
4112 4125 3.057969 TCTTCCTGACGCACAATGAAT 57.942 42.857 0.00 0.00 0.00 2.57
4113 4126 2.743664 TCTTCCTGACGCACAATGAATG 59.256 45.455 0.00 0.00 0.00 2.67
4114 4127 2.470983 TCCTGACGCACAATGAATGA 57.529 45.000 0.00 0.00 0.00 2.57
4115 4128 2.777094 TCCTGACGCACAATGAATGAA 58.223 42.857 0.00 0.00 0.00 2.57
4422 4435 5.413309 ACATCAATATGGCTAGCCTAGAC 57.587 43.478 33.07 8.17 37.43 2.59
4474 4523 0.036952 ACTTGACATGGGTGCTCTCG 60.037 55.000 0.00 0.00 0.00 4.04
4489 4538 0.240145 TCTCGTAGAAGGTGTGTGCG 59.760 55.000 0.00 0.00 34.09 5.34
4528 4577 3.908382 GCGTCTGCATTGTGTTTCTAAAG 59.092 43.478 0.00 0.00 42.15 1.85
4608 4661 1.064685 CAAATACCCCACCCCACTCTC 60.065 57.143 0.00 0.00 0.00 3.20
4670 4733 5.818136 ATGCGTTAGTTACCTAGTTACGA 57.182 39.130 0.00 0.00 30.18 3.43
4671 4734 5.818136 TGCGTTAGTTACCTAGTTACGAT 57.182 39.130 0.00 0.00 30.18 3.73
4672 4735 5.810525 TGCGTTAGTTACCTAGTTACGATC 58.189 41.667 0.00 0.00 30.18 3.69
4761 4867 3.181469 TGTTATGATCCAAGGTAGGCGTC 60.181 47.826 0.00 0.00 0.00 5.19
4782 4888 2.225019 CCTGCCGATGCTGATTTCATAC 59.775 50.000 0.00 0.00 38.61 2.39
4814 4921 5.108517 GGAGAAAATGCAAATAAATGCCGA 58.891 37.500 0.00 0.00 45.83 5.54
4859 5063 8.621286 AGAAAATGCTAATAAATACGAAGTGGG 58.379 33.333 0.00 0.00 45.73 4.61
4893 5097 4.100344 TGAGGAAAACTAAGGCAAAAACCC 59.900 41.667 0.00 0.00 0.00 4.11
4971 5175 4.767409 GGGGAGTAGTGAGCAAAATCTTTT 59.233 41.667 0.00 0.00 0.00 2.27
4990 5194 0.762418 TGAAAACGCCTCCAAGGAGA 59.238 50.000 17.57 0.00 44.53 3.71
5018 5222 1.260297 CGTCAGCAAACATTGTCGTCA 59.740 47.619 0.00 0.00 0.00 4.35
5023 5227 4.216042 TCAGCAAACATTGTCGTCATCAAT 59.784 37.500 0.00 0.00 36.16 2.57
5035 5239 4.876107 GTCGTCATCAATATTGACCCTGTT 59.124 41.667 20.19 0.64 40.29 3.16
5045 5249 8.656130 TCAATATTGACCCTGTTGAAGACCAAC 61.656 40.741 14.23 0.00 42.61 3.77
5064 5268 1.243902 CCTTCCGCCAAAAGCTACAA 58.756 50.000 0.00 0.00 40.39 2.41
5097 5301 2.784347 CCAAACCTTGAGGAAGAGTCC 58.216 52.381 3.59 0.00 45.35 3.85
5106 5310 2.741092 GAAGAGTCCGGCCACACA 59.259 61.111 2.24 0.00 0.00 3.72
5128 5332 0.611618 AAAAGCCGCCATGACATCCA 60.612 50.000 0.00 0.00 0.00 3.41
5130 5334 3.576356 GCCGCCATGACATCCACG 61.576 66.667 0.00 0.00 0.00 4.94
5153 5357 1.507141 CCGAGCAGACACAACCCAAC 61.507 60.000 0.00 0.00 0.00 3.77
5163 5367 2.443255 ACACAACCCAACAGAGAGGAAT 59.557 45.455 0.00 0.00 0.00 3.01
5168 5372 2.569404 ACCCAACAGAGAGGAATCACTC 59.431 50.000 0.00 0.00 37.77 3.51
5178 5382 4.753233 AGAGGAATCACTCTTCGACAATG 58.247 43.478 0.00 0.00 45.21 2.82
5179 5383 3.265791 AGGAATCACTCTTCGACAATGC 58.734 45.455 0.00 0.00 0.00 3.56
5180 5384 2.352960 GGAATCACTCTTCGACAATGCC 59.647 50.000 0.00 0.00 0.00 4.40
5181 5385 3.265791 GAATCACTCTTCGACAATGCCT 58.734 45.455 0.00 0.00 0.00 4.75
5182 5386 4.433615 GAATCACTCTTCGACAATGCCTA 58.566 43.478 0.00 0.00 0.00 3.93
5183 5387 3.953712 TCACTCTTCGACAATGCCTAA 57.046 42.857 0.00 0.00 0.00 2.69
5184 5388 4.265904 TCACTCTTCGACAATGCCTAAA 57.734 40.909 0.00 0.00 0.00 1.85
5185 5389 4.637276 TCACTCTTCGACAATGCCTAAAA 58.363 39.130 0.00 0.00 0.00 1.52
5186 5390 5.060506 TCACTCTTCGACAATGCCTAAAAA 58.939 37.500 0.00 0.00 0.00 1.94
5208 5412 4.655762 AAAGAGAAAAACACCCTCAAGC 57.344 40.909 0.00 0.00 0.00 4.01
5209 5413 2.587522 AGAGAAAAACACCCTCAAGCC 58.412 47.619 0.00 0.00 0.00 4.35
5210 5414 1.613925 GAGAAAAACACCCTCAAGCCC 59.386 52.381 0.00 0.00 0.00 5.19
5211 5415 0.679505 GAAAAACACCCTCAAGCCCC 59.320 55.000 0.00 0.00 0.00 5.80
5212 5416 0.031616 AAAAACACCCTCAAGCCCCA 60.032 50.000 0.00 0.00 0.00 4.96
5213 5417 0.190815 AAAACACCCTCAAGCCCCAT 59.809 50.000 0.00 0.00 0.00 4.00
5214 5418 0.251787 AAACACCCTCAAGCCCCATC 60.252 55.000 0.00 0.00 0.00 3.51
5215 5419 1.434513 AACACCCTCAAGCCCCATCA 61.435 55.000 0.00 0.00 0.00 3.07
5216 5420 1.217057 ACACCCTCAAGCCCCATCAT 61.217 55.000 0.00 0.00 0.00 2.45
5217 5421 0.466922 CACCCTCAAGCCCCATCATC 60.467 60.000 0.00 0.00 0.00 2.92
5218 5422 0.920763 ACCCTCAAGCCCCATCATCA 60.921 55.000 0.00 0.00 0.00 3.07
5219 5423 0.466922 CCCTCAAGCCCCATCATCAC 60.467 60.000 0.00 0.00 0.00 3.06
5220 5424 0.549950 CCTCAAGCCCCATCATCACT 59.450 55.000 0.00 0.00 0.00 3.41
5221 5425 1.476471 CCTCAAGCCCCATCATCACTC 60.476 57.143 0.00 0.00 0.00 3.51
5222 5426 0.548031 TCAAGCCCCATCATCACTCC 59.452 55.000 0.00 0.00 0.00 3.85
5223 5427 0.466922 CAAGCCCCATCATCACTCCC 60.467 60.000 0.00 0.00 0.00 4.30
5224 5428 0.625683 AAGCCCCATCATCACTCCCT 60.626 55.000 0.00 0.00 0.00 4.20
5225 5429 0.625683 AGCCCCATCATCACTCCCTT 60.626 55.000 0.00 0.00 0.00 3.95
5226 5430 0.466922 GCCCCATCATCACTCCCTTG 60.467 60.000 0.00 0.00 0.00 3.61
5227 5431 1.216064 CCCCATCATCACTCCCTTGA 58.784 55.000 0.00 0.00 0.00 3.02
5228 5432 1.565759 CCCCATCATCACTCCCTTGAA 59.434 52.381 0.00 0.00 0.00 2.69
5229 5433 2.422519 CCCCATCATCACTCCCTTGAAG 60.423 54.545 0.00 0.00 0.00 3.02
5230 5434 2.507058 CCCATCATCACTCCCTTGAAGA 59.493 50.000 0.00 0.00 0.00 2.87
5231 5435 3.539604 CCATCATCACTCCCTTGAAGAC 58.460 50.000 0.00 0.00 0.00 3.01
5232 5436 3.199508 CCATCATCACTCCCTTGAAGACT 59.800 47.826 0.00 0.00 0.00 3.24
5233 5437 4.406972 CCATCATCACTCCCTTGAAGACTA 59.593 45.833 0.00 0.00 0.00 2.59
5234 5438 5.453057 CCATCATCACTCCCTTGAAGACTAG 60.453 48.000 0.00 0.00 0.00 2.57
5235 5439 4.026744 TCATCACTCCCTTGAAGACTAGG 58.973 47.826 0.00 0.00 38.43 3.02
5241 5445 1.280457 CCTTGAAGACTAGGGGCTGT 58.720 55.000 0.00 0.00 35.85 4.40
5242 5446 1.630878 CCTTGAAGACTAGGGGCTGTT 59.369 52.381 0.00 0.00 35.85 3.16
5243 5447 2.040412 CCTTGAAGACTAGGGGCTGTTT 59.960 50.000 0.00 0.00 35.85 2.83
5244 5448 2.859165 TGAAGACTAGGGGCTGTTTG 57.141 50.000 0.00 0.00 0.00 2.93
5245 5449 1.351017 TGAAGACTAGGGGCTGTTTGG 59.649 52.381 0.00 0.00 0.00 3.28
5246 5450 1.351350 GAAGACTAGGGGCTGTTTGGT 59.649 52.381 0.00 0.00 0.00 3.67
5247 5451 1.446016 AGACTAGGGGCTGTTTGGTT 58.554 50.000 0.00 0.00 0.00 3.67
5248 5452 1.780919 AGACTAGGGGCTGTTTGGTTT 59.219 47.619 0.00 0.00 0.00 3.27
5249 5453 1.886542 GACTAGGGGCTGTTTGGTTTG 59.113 52.381 0.00 0.00 0.00 2.93
5250 5454 1.256812 CTAGGGGCTGTTTGGTTTGG 58.743 55.000 0.00 0.00 0.00 3.28
5251 5455 0.854218 TAGGGGCTGTTTGGTTTGGA 59.146 50.000 0.00 0.00 0.00 3.53
5252 5456 0.469892 AGGGGCTGTTTGGTTTGGAG 60.470 55.000 0.00 0.00 0.00 3.86
5253 5457 1.367471 GGGCTGTTTGGTTTGGAGC 59.633 57.895 0.00 0.00 0.00 4.70
5254 5458 1.367471 GGCTGTTTGGTTTGGAGCC 59.633 57.895 0.00 0.00 42.37 4.70
5255 5459 1.007387 GCTGTTTGGTTTGGAGCCG 60.007 57.895 0.00 0.00 0.00 5.52
5256 5460 1.734388 GCTGTTTGGTTTGGAGCCGT 61.734 55.000 0.00 0.00 0.00 5.68
5257 5461 0.030638 CTGTTTGGTTTGGAGCCGTG 59.969 55.000 0.00 0.00 0.00 4.94
5258 5462 1.299850 GTTTGGTTTGGAGCCGTGC 60.300 57.895 0.00 0.00 0.00 5.34
5259 5463 2.494530 TTTGGTTTGGAGCCGTGCC 61.495 57.895 0.00 0.00 0.00 5.01
5260 5464 4.966787 TGGTTTGGAGCCGTGCCC 62.967 66.667 0.00 0.00 0.00 5.36
5261 5465 4.660938 GGTTTGGAGCCGTGCCCT 62.661 66.667 0.00 0.00 0.00 5.19
5262 5466 3.365265 GTTTGGAGCCGTGCCCTG 61.365 66.667 0.00 0.00 0.00 4.45
5275 5479 4.872574 CCCTGCCCTACGCCCCTA 62.873 72.222 0.00 0.00 36.24 3.53
5276 5480 3.547513 CCTGCCCTACGCCCCTAC 61.548 72.222 0.00 0.00 36.24 3.18
5277 5481 3.547513 CTGCCCTACGCCCCTACC 61.548 72.222 0.00 0.00 36.24 3.18
5280 5484 2.203596 CCCTACGCCCCTACCGAT 60.204 66.667 0.00 0.00 0.00 4.18
5281 5485 1.075482 CCCTACGCCCCTACCGATA 59.925 63.158 0.00 0.00 0.00 2.92
5282 5486 1.246737 CCCTACGCCCCTACCGATAC 61.247 65.000 0.00 0.00 0.00 2.24
5283 5487 0.538057 CCTACGCCCCTACCGATACA 60.538 60.000 0.00 0.00 0.00 2.29
5284 5488 1.321474 CTACGCCCCTACCGATACAA 58.679 55.000 0.00 0.00 0.00 2.41
5285 5489 1.000938 CTACGCCCCTACCGATACAAC 60.001 57.143 0.00 0.00 0.00 3.32
5286 5490 1.068585 CGCCCCTACCGATACAACC 59.931 63.158 0.00 0.00 0.00 3.77
5287 5491 1.448924 GCCCCTACCGATACAACCC 59.551 63.158 0.00 0.00 0.00 4.11
5288 5492 1.339644 GCCCCTACCGATACAACCCA 61.340 60.000 0.00 0.00 0.00 4.51
5289 5493 1.205966 CCCCTACCGATACAACCCAA 58.794 55.000 0.00 0.00 0.00 4.12
5290 5494 1.134310 CCCCTACCGATACAACCCAAC 60.134 57.143 0.00 0.00 0.00 3.77
5291 5495 1.555992 CCCTACCGATACAACCCAACA 59.444 52.381 0.00 0.00 0.00 3.33
5292 5496 2.419574 CCCTACCGATACAACCCAACAG 60.420 54.545 0.00 0.00 0.00 3.16
5293 5497 2.498481 CCTACCGATACAACCCAACAGA 59.502 50.000 0.00 0.00 0.00 3.41
5294 5498 2.762535 ACCGATACAACCCAACAGAG 57.237 50.000 0.00 0.00 0.00 3.35
5295 5499 1.278127 ACCGATACAACCCAACAGAGG 59.722 52.381 0.00 0.00 0.00 3.69
5296 5500 1.553248 CCGATACAACCCAACAGAGGA 59.447 52.381 0.00 0.00 0.00 3.71
5297 5501 2.027561 CCGATACAACCCAACAGAGGAA 60.028 50.000 0.00 0.00 0.00 3.36
5298 5502 3.370527 CCGATACAACCCAACAGAGGAAT 60.371 47.826 0.00 0.00 0.00 3.01
5299 5503 3.871594 CGATACAACCCAACAGAGGAATC 59.128 47.826 0.00 0.00 0.00 2.52
5300 5504 4.622933 CGATACAACCCAACAGAGGAATCA 60.623 45.833 0.00 0.00 0.00 2.57
5301 5505 2.863809 ACAACCCAACAGAGGAATCAC 58.136 47.619 0.00 0.00 0.00 3.06
5302 5506 2.443255 ACAACCCAACAGAGGAATCACT 59.557 45.455 0.00 0.00 0.00 3.41
5303 5507 3.077359 CAACCCAACAGAGGAATCACTC 58.923 50.000 0.00 0.00 37.77 3.51
5305 5509 2.982488 ACCCAACAGAGGAATCACTCTT 59.018 45.455 0.00 0.00 45.21 2.85
5306 5510 3.008485 ACCCAACAGAGGAATCACTCTTC 59.992 47.826 0.00 0.00 45.21 2.87
5307 5511 3.257393 CCAACAGAGGAATCACTCTTCG 58.743 50.000 0.00 0.00 45.21 3.79
5308 5512 3.056536 CCAACAGAGGAATCACTCTTCGA 60.057 47.826 0.00 0.00 45.21 3.71
5309 5513 3.859411 ACAGAGGAATCACTCTTCGAC 57.141 47.619 0.00 0.00 45.21 4.20
5310 5514 3.157881 ACAGAGGAATCACTCTTCGACA 58.842 45.455 0.00 0.00 45.21 4.35
5311 5515 3.574396 ACAGAGGAATCACTCTTCGACAA 59.426 43.478 0.00 0.00 45.21 3.18
5312 5516 4.221703 ACAGAGGAATCACTCTTCGACAAT 59.778 41.667 0.00 0.00 45.21 2.71
5313 5517 4.565962 CAGAGGAATCACTCTTCGACAATG 59.434 45.833 0.00 0.00 45.21 2.82
5314 5518 3.265791 AGGAATCACTCTTCGACAATGC 58.734 45.455 0.00 0.00 0.00 3.56
5315 5519 2.352960 GGAATCACTCTTCGACAATGCC 59.647 50.000 0.00 0.00 0.00 4.40
5316 5520 3.265791 GAATCACTCTTCGACAATGCCT 58.734 45.455 0.00 0.00 0.00 4.75
5317 5521 2.370281 TCACTCTTCGACAATGCCTC 57.630 50.000 0.00 0.00 0.00 4.70
5318 5522 1.618343 TCACTCTTCGACAATGCCTCA 59.382 47.619 0.00 0.00 0.00 3.86
5319 5523 2.037121 TCACTCTTCGACAATGCCTCAA 59.963 45.455 0.00 0.00 0.00 3.02
5320 5524 2.807967 CACTCTTCGACAATGCCTCAAA 59.192 45.455 0.00 0.00 0.00 2.69
5321 5525 3.070018 ACTCTTCGACAATGCCTCAAAG 58.930 45.455 0.00 0.00 0.00 2.77
5322 5526 3.244215 ACTCTTCGACAATGCCTCAAAGA 60.244 43.478 0.00 0.00 0.00 2.52
5323 5527 3.738982 TCTTCGACAATGCCTCAAAGAA 58.261 40.909 0.00 0.00 0.00 2.52
5324 5528 4.133820 TCTTCGACAATGCCTCAAAGAAA 58.866 39.130 0.00 0.00 0.00 2.52
5325 5529 4.214119 TCTTCGACAATGCCTCAAAGAAAG 59.786 41.667 0.00 0.00 0.00 2.62
5326 5530 3.738982 TCGACAATGCCTCAAAGAAAGA 58.261 40.909 0.00 0.00 0.00 2.52
5327 5531 3.748048 TCGACAATGCCTCAAAGAAAGAG 59.252 43.478 0.00 0.00 0.00 2.85
5328 5532 3.748048 CGACAATGCCTCAAAGAAAGAGA 59.252 43.478 0.00 0.00 35.09 3.10
5329 5533 4.214119 CGACAATGCCTCAAAGAAAGAGAA 59.786 41.667 0.00 0.00 35.09 2.87
5330 5534 5.277974 CGACAATGCCTCAAAGAAAGAGAAA 60.278 40.000 0.00 0.00 35.09 2.52
5331 5535 6.469782 ACAATGCCTCAAAGAAAGAGAAAA 57.530 33.333 0.00 0.00 35.09 2.29
5332 5536 6.877236 ACAATGCCTCAAAGAAAGAGAAAAA 58.123 32.000 0.00 0.00 35.09 1.94
5333 5537 6.758416 ACAATGCCTCAAAGAAAGAGAAAAAC 59.242 34.615 0.00 0.00 35.09 2.43
5334 5538 5.913137 TGCCTCAAAGAAAGAGAAAAACA 57.087 34.783 0.00 0.00 35.09 2.83
5335 5539 5.650543 TGCCTCAAAGAAAGAGAAAAACAC 58.349 37.500 0.00 0.00 35.09 3.32
5336 5540 5.043903 GCCTCAAAGAAAGAGAAAAACACC 58.956 41.667 0.00 0.00 35.09 4.16
5337 5541 5.592054 CCTCAAAGAAAGAGAAAAACACCC 58.408 41.667 0.00 0.00 35.09 4.61
5338 5542 5.360999 CCTCAAAGAAAGAGAAAAACACCCT 59.639 40.000 0.00 0.00 35.09 4.34
5339 5543 6.451064 TCAAAGAAAGAGAAAAACACCCTC 57.549 37.500 0.00 0.00 0.00 4.30
5340 5544 5.949354 TCAAAGAAAGAGAAAAACACCCTCA 59.051 36.000 0.00 0.00 0.00 3.86
5341 5545 6.435904 TCAAAGAAAGAGAAAAACACCCTCAA 59.564 34.615 0.00 0.00 0.00 3.02
5342 5546 6.456795 AAGAAAGAGAAAAACACCCTCAAG 57.543 37.500 0.00 0.00 0.00 3.02
5343 5547 4.339530 AGAAAGAGAAAAACACCCTCAAGC 59.660 41.667 0.00 0.00 0.00 4.01
5344 5548 3.297134 AGAGAAAAACACCCTCAAGCA 57.703 42.857 0.00 0.00 0.00 3.91
5345 5549 2.952310 AGAGAAAAACACCCTCAAGCAC 59.048 45.455 0.00 0.00 0.00 4.40
5346 5550 2.031870 AGAAAAACACCCTCAAGCACC 58.968 47.619 0.00 0.00 0.00 5.01
5347 5551 1.754226 GAAAAACACCCTCAAGCACCA 59.246 47.619 0.00 0.00 0.00 4.17
5348 5552 2.086610 AAAACACCCTCAAGCACCAT 57.913 45.000 0.00 0.00 0.00 3.55
5349 5553 1.620822 AAACACCCTCAAGCACCATC 58.379 50.000 0.00 0.00 0.00 3.51
5350 5554 0.478072 AACACCCTCAAGCACCATCA 59.522 50.000 0.00 0.00 0.00 3.07
5351 5555 0.700564 ACACCCTCAAGCACCATCAT 59.299 50.000 0.00 0.00 0.00 2.45
5352 5556 1.340405 ACACCCTCAAGCACCATCATC 60.340 52.381 0.00 0.00 0.00 2.92
5353 5557 0.994247 ACCCTCAAGCACCATCATCA 59.006 50.000 0.00 0.00 0.00 3.07
5354 5558 1.340405 ACCCTCAAGCACCATCATCAC 60.340 52.381 0.00 0.00 0.00 3.06
5355 5559 1.064906 CCCTCAAGCACCATCATCACT 60.065 52.381 0.00 0.00 0.00 3.41
5356 5560 2.619849 CCCTCAAGCACCATCATCACTT 60.620 50.000 0.00 0.00 0.00 3.16
5357 5561 3.087031 CCTCAAGCACCATCATCACTTT 58.913 45.455 0.00 0.00 0.00 2.66
5358 5562 3.128242 CCTCAAGCACCATCATCACTTTC 59.872 47.826 0.00 0.00 0.00 2.62
5359 5563 2.743664 TCAAGCACCATCATCACTTTCG 59.256 45.455 0.00 0.00 0.00 3.46
5360 5564 1.089920 AGCACCATCATCACTTTCGC 58.910 50.000 0.00 0.00 0.00 4.70
5361 5565 1.089920 GCACCATCATCACTTTCGCT 58.910 50.000 0.00 0.00 0.00 4.93
5362 5566 2.093500 AGCACCATCATCACTTTCGCTA 60.093 45.455 0.00 0.00 0.00 4.26
5363 5567 2.286294 GCACCATCATCACTTTCGCTAG 59.714 50.000 0.00 0.00 0.00 3.42
5364 5568 3.785486 CACCATCATCACTTTCGCTAGA 58.215 45.455 0.00 0.00 0.00 2.43
5365 5569 3.801050 CACCATCATCACTTTCGCTAGAG 59.199 47.826 0.00 0.00 0.00 2.43
5366 5570 2.799412 CCATCATCACTTTCGCTAGAGC 59.201 50.000 0.00 0.00 37.78 4.09
5367 5571 2.586258 TCATCACTTTCGCTAGAGCC 57.414 50.000 0.00 0.00 37.91 4.70
5368 5572 2.103373 TCATCACTTTCGCTAGAGCCT 58.897 47.619 0.00 0.00 37.91 4.58
5369 5573 2.497675 TCATCACTTTCGCTAGAGCCTT 59.502 45.455 0.00 0.00 37.91 4.35
5370 5574 2.370281 TCACTTTCGCTAGAGCCTTG 57.630 50.000 0.00 0.00 37.91 3.61
5371 5575 1.893137 TCACTTTCGCTAGAGCCTTGA 59.107 47.619 0.00 0.00 37.91 3.02
5372 5576 2.094494 TCACTTTCGCTAGAGCCTTGAG 60.094 50.000 0.00 0.00 37.91 3.02
5373 5577 1.285578 CTTTCGCTAGAGCCTTGAGC 58.714 55.000 0.00 0.00 44.25 4.26
5374 5578 0.108138 TTTCGCTAGAGCCTTGAGCC 60.108 55.000 0.00 0.00 45.47 4.70
5375 5579 0.972983 TTCGCTAGAGCCTTGAGCCT 60.973 55.000 0.00 0.00 45.47 4.58
5376 5580 1.067250 CGCTAGAGCCTTGAGCCTC 59.933 63.158 0.00 0.00 45.47 4.70
5377 5581 1.391157 CGCTAGAGCCTTGAGCCTCT 61.391 60.000 0.00 0.00 45.47 3.69
5378 5582 0.389025 GCTAGAGCCTTGAGCCTCTC 59.611 60.000 0.00 0.00 45.47 3.20
5379 5583 1.039856 CTAGAGCCTTGAGCCTCTCC 58.960 60.000 0.00 0.00 45.47 3.71
5380 5584 0.753479 TAGAGCCTTGAGCCTCTCCG 60.753 60.000 0.00 0.00 45.47 4.63
5381 5585 3.731653 GAGCCTTGAGCCTCTCCGC 62.732 68.421 0.00 0.00 45.47 5.54
5382 5586 4.847444 GCCTTGAGCCTCTCCGCC 62.847 72.222 0.00 0.00 34.35 6.13
5383 5587 3.080121 CCTTGAGCCTCTCCGCCT 61.080 66.667 0.00 0.00 0.00 5.52
5384 5588 1.758514 CCTTGAGCCTCTCCGCCTA 60.759 63.158 0.00 0.00 0.00 3.93
5385 5589 1.330655 CCTTGAGCCTCTCCGCCTAA 61.331 60.000 0.00 0.00 0.00 2.69
5386 5590 0.179097 CTTGAGCCTCTCCGCCTAAC 60.179 60.000 0.00 0.00 0.00 2.34
5387 5591 1.945354 TTGAGCCTCTCCGCCTAACG 61.945 60.000 0.00 0.00 43.15 3.18
5398 5602 3.093835 CCTAACGGGCCCATGGGA 61.094 66.667 36.00 11.51 37.50 4.37
5399 5603 2.685534 CCTAACGGGCCCATGGGAA 61.686 63.158 36.00 10.31 37.50 3.97
5400 5604 1.152963 CTAACGGGCCCATGGGAAG 60.153 63.158 36.00 24.56 37.50 3.46
5401 5605 2.624674 CTAACGGGCCCATGGGAAGG 62.625 65.000 36.00 22.62 37.50 3.46
5403 5607 4.195334 CGGGCCCATGGGAAGGAG 62.195 72.222 36.00 15.66 37.50 3.69
5404 5608 4.529731 GGGCCCATGGGAAGGAGC 62.530 72.222 36.00 17.36 37.50 4.70
5405 5609 4.529731 GGCCCATGGGAAGGAGCC 62.530 72.222 36.00 22.60 37.50 4.70
5413 5617 3.334054 GGAAGGAGCCCAGCCACT 61.334 66.667 0.00 0.00 0.00 4.00
5414 5618 2.045536 GAAGGAGCCCAGCCACTG 60.046 66.667 0.00 0.00 0.00 3.66
5425 5629 2.827642 GCCACTGGCTCCATCTGC 60.828 66.667 13.28 0.00 46.69 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 5.879223 GGAGGAATAACGACGAGGATATAGA 59.121 44.000 0.00 0.00 0.00 1.98
57 58 1.962100 GGGAGGAATAACGACGAGGAT 59.038 52.381 0.00 0.00 0.00 3.24
173 174 3.507622 GGCTTTGACCTCTGTATGCTTTT 59.492 43.478 0.00 0.00 0.00 2.27
283 285 9.622004 GAGGCAACATATATGAGATGAAAATTG 57.378 33.333 19.63 10.37 41.41 2.32
295 297 3.072915 TGGGACCAGAGGCAACATATATG 59.927 47.826 11.29 11.29 41.41 1.78
306 308 6.000219 CAGATAAATTACATGGGACCAGAGG 59.000 44.000 0.00 0.00 0.00 3.69
307 309 6.830912 TCAGATAAATTACATGGGACCAGAG 58.169 40.000 0.00 0.00 0.00 3.35
324 326 9.346005 ACATGCATATGTTCAGAATTCAGATAA 57.654 29.630 8.44 0.00 45.01 1.75
430 433 0.537143 TTTCGTGCCATTGCTGGAGT 60.537 50.000 0.00 0.00 46.37 3.85
494 497 3.856206 AGCCAGAAAAACCTCCCCTTATA 59.144 43.478 0.00 0.00 0.00 0.98
495 498 2.654896 AGCCAGAAAAACCTCCCCTTAT 59.345 45.455 0.00 0.00 0.00 1.73
496 499 2.070573 AGCCAGAAAAACCTCCCCTTA 58.929 47.619 0.00 0.00 0.00 2.69
822 825 4.767409 AGTTGCAGAATTAAGGGAAAGGAC 59.233 41.667 0.00 0.00 0.00 3.85
1036 1039 4.952335 AGCCTTGGTTCCATGAAGAATTAG 59.048 41.667 0.00 0.00 0.00 1.73
1039 1042 3.094572 CAGCCTTGGTTCCATGAAGAAT 58.905 45.455 0.00 0.00 0.00 2.40
1063 1066 1.115930 CCCGGTACTGGAGGATCAGG 61.116 65.000 23.08 0.00 38.98 3.86
1065 1068 0.561184 ATCCCGGTACTGGAGGATCA 59.439 55.000 23.08 0.00 46.96 2.92
1163 1167 6.650239 TCTATACAAAATACGCGCTTTTCA 57.350 33.333 5.73 3.62 0.00 2.69
1238 1242 4.720649 ACTAGAAAGATTAGCAGCACGA 57.279 40.909 0.00 0.00 0.00 4.35
1358 1362 0.396811 ACCACCTCACACAAGCTACC 59.603 55.000 0.00 0.00 0.00 3.18
1467 1471 3.240134 GAGCCCCTGTCAGCGAACA 62.240 63.158 0.00 0.00 0.00 3.18
1685 1689 9.527157 TTTGAACCTTATTCACTCCAAATATGA 57.473 29.630 0.00 0.00 0.00 2.15
1805 1809 5.695851 AGTCAATACTTTGCAACAGGAAG 57.304 39.130 0.00 0.00 29.00 3.46
2301 2308 1.002033 CGATGCAAAGGCCTTGATAGC 60.002 52.381 21.33 20.30 40.13 2.97
2360 2367 3.181465 ACGGCTCCAAGTACATATCCTTG 60.181 47.826 0.00 0.00 38.21 3.61
2513 2520 3.181513 CGTCGACCGAGAAGTCTGAATTA 60.182 47.826 10.58 0.00 39.56 1.40
2621 2628 7.605410 AATTTTCATCAACATCCATTTCAGC 57.395 32.000 0.00 0.00 0.00 4.26
2831 2842 2.288948 GCAAAGCAACACCATGGATCAA 60.289 45.455 21.47 0.00 0.00 2.57
2907 2918 0.110486 TGGCCTGGTGTTTTCTCCTC 59.890 55.000 3.32 0.00 34.83 3.71
3013 3024 4.422057 TCCGGACCCAGCAATCTATTATA 58.578 43.478 0.00 0.00 0.00 0.98
3412 3423 4.944317 TCTACCTCTATGCCGATCAGTATG 59.056 45.833 0.00 0.00 37.54 2.39
3473 3484 1.226717 GGTAACAGGAGCGAGCGAG 60.227 63.158 0.00 0.00 0.00 5.03
3474 3485 0.393402 TAGGTAACAGGAGCGAGCGA 60.393 55.000 0.00 0.00 41.41 4.93
3475 3486 0.669077 ATAGGTAACAGGAGCGAGCG 59.331 55.000 0.00 0.00 41.41 5.03
3621 3633 2.300152 CTGCTTACAGGTCTCCTTGTCA 59.700 50.000 0.00 0.00 40.48 3.58
3816 3828 1.291877 CCAGGAAGAAGCCGTTGACG 61.292 60.000 0.00 0.00 39.44 4.35
3873 3885 1.067915 ACATACACGTGCAAATTGCCC 60.068 47.619 17.22 2.41 44.23 5.36
4024 4036 8.841300 CAGATACTGCTACTTACTGAAGTATGA 58.159 37.037 9.61 0.00 45.12 2.15
4067 4079 2.423538 AGATTTAACCAAGCGTCCATGC 59.576 45.455 0.00 0.00 0.00 4.06
4112 4125 9.952030 AGAGATCGAGTCAGACTATATATTTCA 57.048 33.333 2.00 0.00 0.00 2.69
4131 4144 0.104855 TCCATCCGCCAAAGAGATCG 59.895 55.000 0.00 0.00 0.00 3.69
4196 4209 4.444838 CGGCGGGGTTGATCGTGA 62.445 66.667 0.00 0.00 0.00 4.35
4474 4523 1.663702 ACGCGCACACACCTTCTAC 60.664 57.895 5.73 0.00 0.00 2.59
4489 4538 2.546321 CAGACGCTCACAACACGC 59.454 61.111 0.00 0.00 0.00 5.34
4535 4584 0.107703 TCGATCGGCAGCCAGATTTT 60.108 50.000 16.41 0.00 0.00 1.82
4536 4585 0.811616 GTCGATCGGCAGCCAGATTT 60.812 55.000 16.20 0.00 0.00 2.17
4537 4586 1.227380 GTCGATCGGCAGCCAGATT 60.227 57.895 16.20 0.75 0.00 2.40
4538 4587 2.419198 GTCGATCGGCAGCCAGAT 59.581 61.111 16.20 14.88 0.00 2.90
4539 4588 4.193334 CGTCGATCGGCAGCCAGA 62.193 66.667 21.12 10.36 35.71 3.86
4548 4597 1.588404 CATTTCTTCACCCGTCGATCG 59.412 52.381 9.36 9.36 39.52 3.69
4549 4598 1.327764 GCATTTCTTCACCCGTCGATC 59.672 52.381 0.00 0.00 0.00 3.69
4550 4599 1.369625 GCATTTCTTCACCCGTCGAT 58.630 50.000 0.00 0.00 0.00 3.59
4551 4600 0.672401 GGCATTTCTTCACCCGTCGA 60.672 55.000 0.00 0.00 0.00 4.20
4670 4733 4.515191 ACACAAATGTTGTTCTAGTGCGAT 59.485 37.500 0.00 0.00 43.23 4.58
4671 4734 3.874543 ACACAAATGTTGTTCTAGTGCGA 59.125 39.130 0.00 0.00 43.23 5.10
4672 4735 4.209452 ACACAAATGTTGTTCTAGTGCG 57.791 40.909 0.00 0.00 43.23 5.34
4761 4867 1.315690 ATGAAATCAGCATCGGCAGG 58.684 50.000 0.00 0.00 44.61 4.85
4840 4948 3.185797 CGGCCCACTTCGTATTTATTAGC 59.814 47.826 0.00 0.00 0.00 3.09
4842 4950 4.669206 TCGGCCCACTTCGTATTTATTA 57.331 40.909 0.00 0.00 0.00 0.98
4859 5063 6.972901 CCTTAGTTTTCCTCATAAAAATCGGC 59.027 38.462 0.00 0.00 30.19 5.54
4893 5097 7.333174 GGTAGATGTTTCTCTTTCTCCTTCTTG 59.667 40.741 0.00 0.00 33.17 3.02
4971 5175 0.762418 TCTCCTTGGAGGCGTTTTCA 59.238 50.000 15.81 0.00 34.61 2.69
4990 5194 1.317613 TGTTTGCTGACGCCATCTTT 58.682 45.000 0.00 0.00 34.43 2.52
5009 5213 5.528690 CAGGGTCAATATTGATGACGACAAT 59.471 40.000 20.65 0.00 46.41 2.71
5018 5222 5.888161 GGTCTTCAACAGGGTCAATATTGAT 59.112 40.000 20.65 2.83 39.73 2.57
5023 5227 4.715534 TTGGTCTTCAACAGGGTCAATA 57.284 40.909 0.00 0.00 0.00 1.90
5035 5239 1.072505 GGCGGAAGGTTGGTCTTCA 59.927 57.895 6.88 0.00 43.52 3.02
5064 5268 3.525800 AGGTTTGGCAGGATAGTTGTT 57.474 42.857 0.00 0.00 0.00 2.83
5126 5330 4.803426 GTCTGCTCGGAGCCGTGG 62.803 72.222 26.00 13.73 41.51 4.94
5128 5332 4.057428 GTGTCTGCTCGGAGCCGT 62.057 66.667 26.00 0.00 41.51 5.68
5130 5334 2.029844 GTTGTGTCTGCTCGGAGCC 61.030 63.158 26.00 12.15 41.51 4.70
5153 5357 3.441922 TGTCGAAGAGTGATTCCTCTCTG 59.558 47.826 8.54 4.38 40.93 3.35
5163 5367 3.953712 TTAGGCATTGTCGAAGAGTGA 57.046 42.857 0.00 0.00 36.95 3.41
5185 5389 5.419542 GCTTGAGGGTGTTTTTCTCTTTTT 58.580 37.500 0.00 0.00 0.00 1.94
5186 5390 4.141937 GGCTTGAGGGTGTTTTTCTCTTTT 60.142 41.667 0.00 0.00 0.00 2.27
5187 5391 3.384789 GGCTTGAGGGTGTTTTTCTCTTT 59.615 43.478 0.00 0.00 0.00 2.52
5188 5392 2.959030 GGCTTGAGGGTGTTTTTCTCTT 59.041 45.455 0.00 0.00 0.00 2.85
5189 5393 2.587522 GGCTTGAGGGTGTTTTTCTCT 58.412 47.619 0.00 0.00 0.00 3.10
5190 5394 1.613925 GGGCTTGAGGGTGTTTTTCTC 59.386 52.381 0.00 0.00 0.00 2.87
5191 5395 1.704641 GGGCTTGAGGGTGTTTTTCT 58.295 50.000 0.00 0.00 0.00 2.52
5192 5396 0.679505 GGGGCTTGAGGGTGTTTTTC 59.320 55.000 0.00 0.00 0.00 2.29
5193 5397 0.031616 TGGGGCTTGAGGGTGTTTTT 60.032 50.000 0.00 0.00 0.00 1.94
5194 5398 0.190815 ATGGGGCTTGAGGGTGTTTT 59.809 50.000 0.00 0.00 0.00 2.43
5195 5399 0.251787 GATGGGGCTTGAGGGTGTTT 60.252 55.000 0.00 0.00 0.00 2.83
5196 5400 1.384191 GATGGGGCTTGAGGGTGTT 59.616 57.895 0.00 0.00 0.00 3.32
5197 5401 1.217057 ATGATGGGGCTTGAGGGTGT 61.217 55.000 0.00 0.00 0.00 4.16
5198 5402 0.466922 GATGATGGGGCTTGAGGGTG 60.467 60.000 0.00 0.00 0.00 4.61
5199 5403 0.920763 TGATGATGGGGCTTGAGGGT 60.921 55.000 0.00 0.00 0.00 4.34
5200 5404 0.466922 GTGATGATGGGGCTTGAGGG 60.467 60.000 0.00 0.00 0.00 4.30
5201 5405 0.549950 AGTGATGATGGGGCTTGAGG 59.450 55.000 0.00 0.00 0.00 3.86
5202 5406 1.476471 GGAGTGATGATGGGGCTTGAG 60.476 57.143 0.00 0.00 0.00 3.02
5203 5407 0.548031 GGAGTGATGATGGGGCTTGA 59.452 55.000 0.00 0.00 0.00 3.02
5204 5408 0.466922 GGGAGTGATGATGGGGCTTG 60.467 60.000 0.00 0.00 0.00 4.01
5205 5409 0.625683 AGGGAGTGATGATGGGGCTT 60.626 55.000 0.00 0.00 0.00 4.35
5206 5410 0.625683 AAGGGAGTGATGATGGGGCT 60.626 55.000 0.00 0.00 0.00 5.19
5207 5411 0.466922 CAAGGGAGTGATGATGGGGC 60.467 60.000 0.00 0.00 0.00 5.80
5208 5412 1.216064 TCAAGGGAGTGATGATGGGG 58.784 55.000 0.00 0.00 0.00 4.96
5209 5413 2.507058 TCTTCAAGGGAGTGATGATGGG 59.493 50.000 0.00 0.00 29.42 4.00
5210 5414 3.199508 AGTCTTCAAGGGAGTGATGATGG 59.800 47.826 0.00 0.00 35.07 3.51
5211 5415 4.484537 AGTCTTCAAGGGAGTGATGATG 57.515 45.455 0.00 0.00 35.07 3.07
5212 5416 4.653341 CCTAGTCTTCAAGGGAGTGATGAT 59.347 45.833 0.00 0.00 35.07 2.45
5213 5417 4.026744 CCTAGTCTTCAAGGGAGTGATGA 58.973 47.826 0.00 0.00 31.32 2.92
5214 5418 4.399004 CCTAGTCTTCAAGGGAGTGATG 57.601 50.000 0.00 0.00 0.00 3.07
5222 5426 1.280457 ACAGCCCCTAGTCTTCAAGG 58.720 55.000 0.00 0.00 0.00 3.61
5223 5427 3.077359 CAAACAGCCCCTAGTCTTCAAG 58.923 50.000 0.00 0.00 0.00 3.02
5224 5428 2.224769 CCAAACAGCCCCTAGTCTTCAA 60.225 50.000 0.00 0.00 0.00 2.69
5225 5429 1.351017 CCAAACAGCCCCTAGTCTTCA 59.649 52.381 0.00 0.00 0.00 3.02
5226 5430 1.351350 ACCAAACAGCCCCTAGTCTTC 59.649 52.381 0.00 0.00 0.00 2.87
5227 5431 1.446016 ACCAAACAGCCCCTAGTCTT 58.554 50.000 0.00 0.00 0.00 3.01
5228 5432 1.446016 AACCAAACAGCCCCTAGTCT 58.554 50.000 0.00 0.00 0.00 3.24
5229 5433 1.886542 CAAACCAAACAGCCCCTAGTC 59.113 52.381 0.00 0.00 0.00 2.59
5230 5434 1.480498 CCAAACCAAACAGCCCCTAGT 60.480 52.381 0.00 0.00 0.00 2.57
5231 5435 1.203001 TCCAAACCAAACAGCCCCTAG 60.203 52.381 0.00 0.00 0.00 3.02
5232 5436 0.854218 TCCAAACCAAACAGCCCCTA 59.146 50.000 0.00 0.00 0.00 3.53
5233 5437 0.469892 CTCCAAACCAAACAGCCCCT 60.470 55.000 0.00 0.00 0.00 4.79
5234 5438 2.049435 CTCCAAACCAAACAGCCCC 58.951 57.895 0.00 0.00 0.00 5.80
5235 5439 1.367471 GCTCCAAACCAAACAGCCC 59.633 57.895 0.00 0.00 0.00 5.19
5236 5440 1.367471 GGCTCCAAACCAAACAGCC 59.633 57.895 0.00 0.00 42.87 4.85
5237 5441 1.007387 CGGCTCCAAACCAAACAGC 60.007 57.895 0.00 0.00 0.00 4.40
5238 5442 0.030638 CACGGCTCCAAACCAAACAG 59.969 55.000 0.00 0.00 0.00 3.16
5239 5443 2.010582 GCACGGCTCCAAACCAAACA 62.011 55.000 0.00 0.00 0.00 2.83
5240 5444 1.299850 GCACGGCTCCAAACCAAAC 60.300 57.895 0.00 0.00 0.00 2.93
5241 5445 2.494530 GGCACGGCTCCAAACCAAA 61.495 57.895 0.00 0.00 0.00 3.28
5242 5446 2.909965 GGCACGGCTCCAAACCAA 60.910 61.111 0.00 0.00 0.00 3.67
5243 5447 4.966787 GGGCACGGCTCCAAACCA 62.967 66.667 0.00 0.00 0.00 3.67
5244 5448 4.660938 AGGGCACGGCTCCAAACC 62.661 66.667 0.00 0.00 0.00 3.27
5245 5449 3.365265 CAGGGCACGGCTCCAAAC 61.365 66.667 0.00 0.00 0.00 2.93
5258 5462 4.872574 TAGGGGCGTAGGGCAGGG 62.873 72.222 11.36 0.00 46.16 4.45
5259 5463 3.547513 GTAGGGGCGTAGGGCAGG 61.548 72.222 11.36 0.00 46.16 4.85
5260 5464 3.547513 GGTAGGGGCGTAGGGCAG 61.548 72.222 11.36 0.00 46.16 4.85
5263 5467 1.075482 TATCGGTAGGGGCGTAGGG 59.925 63.158 0.00 0.00 0.00 3.53
5264 5468 0.538057 TGTATCGGTAGGGGCGTAGG 60.538 60.000 0.00 0.00 0.00 3.18
5265 5469 1.000938 GTTGTATCGGTAGGGGCGTAG 60.001 57.143 0.00 0.00 0.00 3.51
5266 5470 1.032014 GTTGTATCGGTAGGGGCGTA 58.968 55.000 0.00 0.00 0.00 4.42
5267 5471 1.679559 GGTTGTATCGGTAGGGGCGT 61.680 60.000 0.00 0.00 0.00 5.68
5268 5472 1.068585 GGTTGTATCGGTAGGGGCG 59.931 63.158 0.00 0.00 0.00 6.13
5269 5473 1.339644 TGGGTTGTATCGGTAGGGGC 61.340 60.000 0.00 0.00 0.00 5.80
5270 5474 1.134310 GTTGGGTTGTATCGGTAGGGG 60.134 57.143 0.00 0.00 0.00 4.79
5271 5475 1.555992 TGTTGGGTTGTATCGGTAGGG 59.444 52.381 0.00 0.00 0.00 3.53
5272 5476 2.498481 TCTGTTGGGTTGTATCGGTAGG 59.502 50.000 0.00 0.00 0.00 3.18
5273 5477 3.430374 CCTCTGTTGGGTTGTATCGGTAG 60.430 52.174 0.00 0.00 0.00 3.18
5274 5478 2.498481 CCTCTGTTGGGTTGTATCGGTA 59.502 50.000 0.00 0.00 0.00 4.02
5275 5479 1.278127 CCTCTGTTGGGTTGTATCGGT 59.722 52.381 0.00 0.00 0.00 4.69
5276 5480 1.553248 TCCTCTGTTGGGTTGTATCGG 59.447 52.381 0.00 0.00 0.00 4.18
5277 5481 3.328382 TTCCTCTGTTGGGTTGTATCG 57.672 47.619 0.00 0.00 0.00 2.92
5278 5482 4.636206 GTGATTCCTCTGTTGGGTTGTATC 59.364 45.833 0.00 0.00 0.00 2.24
5279 5483 4.289672 AGTGATTCCTCTGTTGGGTTGTAT 59.710 41.667 0.00 0.00 0.00 2.29
5280 5484 3.650942 AGTGATTCCTCTGTTGGGTTGTA 59.349 43.478 0.00 0.00 0.00 2.41
5281 5485 2.443255 AGTGATTCCTCTGTTGGGTTGT 59.557 45.455 0.00 0.00 0.00 3.32
5282 5486 3.077359 GAGTGATTCCTCTGTTGGGTTG 58.923 50.000 0.00 0.00 0.00 3.77
5283 5487 2.982488 AGAGTGATTCCTCTGTTGGGTT 59.018 45.455 4.48 0.00 40.30 4.11
5284 5488 2.625639 AGAGTGATTCCTCTGTTGGGT 58.374 47.619 4.48 0.00 40.30 4.51
5285 5489 3.604582 GAAGAGTGATTCCTCTGTTGGG 58.395 50.000 5.71 0.00 40.93 4.12
5286 5490 3.056536 TCGAAGAGTGATTCCTCTGTTGG 60.057 47.826 5.71 0.69 40.93 3.77
5287 5491 3.923461 GTCGAAGAGTGATTCCTCTGTTG 59.077 47.826 5.71 1.34 40.93 3.33
5288 5492 3.574396 TGTCGAAGAGTGATTCCTCTGTT 59.426 43.478 5.71 0.00 40.93 3.16
5289 5493 3.157881 TGTCGAAGAGTGATTCCTCTGT 58.842 45.455 5.71 0.00 40.93 3.41
5290 5494 3.857549 TGTCGAAGAGTGATTCCTCTG 57.142 47.619 5.71 0.00 40.93 3.35
5291 5495 4.753233 CATTGTCGAAGAGTGATTCCTCT 58.247 43.478 0.00 0.00 43.65 3.69
5292 5496 3.308323 GCATTGTCGAAGAGTGATTCCTC 59.692 47.826 0.00 0.00 36.95 3.71
5293 5497 3.265791 GCATTGTCGAAGAGTGATTCCT 58.734 45.455 0.00 0.00 36.95 3.36
5294 5498 2.352960 GGCATTGTCGAAGAGTGATTCC 59.647 50.000 0.00 0.00 36.95 3.01
5295 5499 3.265791 AGGCATTGTCGAAGAGTGATTC 58.734 45.455 0.00 0.00 36.95 2.52
5296 5500 3.265791 GAGGCATTGTCGAAGAGTGATT 58.734 45.455 0.00 0.00 36.95 2.57
5297 5501 2.234661 TGAGGCATTGTCGAAGAGTGAT 59.765 45.455 0.00 0.00 36.95 3.06
5298 5502 1.618343 TGAGGCATTGTCGAAGAGTGA 59.382 47.619 0.00 0.00 36.95 3.41
5299 5503 2.084610 TGAGGCATTGTCGAAGAGTG 57.915 50.000 0.00 0.00 36.95 3.51
5300 5504 2.839486 TTGAGGCATTGTCGAAGAGT 57.161 45.000 0.00 0.00 36.95 3.24
5301 5505 3.329386 TCTTTGAGGCATTGTCGAAGAG 58.671 45.455 0.00 0.00 38.85 2.85
5302 5506 3.401033 TCTTTGAGGCATTGTCGAAGA 57.599 42.857 0.00 3.84 40.64 2.87
5303 5507 4.214119 TCTTTCTTTGAGGCATTGTCGAAG 59.786 41.667 0.00 0.00 36.94 3.79
5304 5508 4.133820 TCTTTCTTTGAGGCATTGTCGAA 58.866 39.130 0.00 0.00 0.00 3.71
5305 5509 3.738982 TCTTTCTTTGAGGCATTGTCGA 58.261 40.909 0.00 0.00 0.00 4.20
5306 5510 3.748048 TCTCTTTCTTTGAGGCATTGTCG 59.252 43.478 0.00 0.00 32.78 4.35
5307 5511 5.695851 TTCTCTTTCTTTGAGGCATTGTC 57.304 39.130 0.00 0.00 32.78 3.18
5308 5512 6.469782 TTTTCTCTTTCTTTGAGGCATTGT 57.530 33.333 0.00 0.00 32.78 2.71
5309 5513 6.757947 TGTTTTTCTCTTTCTTTGAGGCATTG 59.242 34.615 0.00 0.00 32.78 2.82
5310 5514 6.758416 GTGTTTTTCTCTTTCTTTGAGGCATT 59.242 34.615 0.00 0.00 32.78 3.56
5311 5515 6.276091 GTGTTTTTCTCTTTCTTTGAGGCAT 58.724 36.000 0.00 0.00 32.78 4.40
5312 5516 5.394115 GGTGTTTTTCTCTTTCTTTGAGGCA 60.394 40.000 0.00 0.00 32.78 4.75
5313 5517 5.043903 GGTGTTTTTCTCTTTCTTTGAGGC 58.956 41.667 0.00 0.00 32.78 4.70
5314 5518 5.360999 AGGGTGTTTTTCTCTTTCTTTGAGG 59.639 40.000 0.00 0.00 32.78 3.86
5315 5519 6.095440 TGAGGGTGTTTTTCTCTTTCTTTGAG 59.905 38.462 0.00 0.00 0.00 3.02
5316 5520 5.949354 TGAGGGTGTTTTTCTCTTTCTTTGA 59.051 36.000 0.00 0.00 0.00 2.69
5317 5521 6.207691 TGAGGGTGTTTTTCTCTTTCTTTG 57.792 37.500 0.00 0.00 0.00 2.77
5318 5522 6.628175 GCTTGAGGGTGTTTTTCTCTTTCTTT 60.628 38.462 0.00 0.00 0.00 2.52
5319 5523 5.163509 GCTTGAGGGTGTTTTTCTCTTTCTT 60.164 40.000 0.00 0.00 0.00 2.52
5320 5524 4.339530 GCTTGAGGGTGTTTTTCTCTTTCT 59.660 41.667 0.00 0.00 0.00 2.52
5321 5525 4.097892 TGCTTGAGGGTGTTTTTCTCTTTC 59.902 41.667 0.00 0.00 0.00 2.62
5322 5526 4.023291 TGCTTGAGGGTGTTTTTCTCTTT 58.977 39.130 0.00 0.00 0.00 2.52
5323 5527 3.381590 GTGCTTGAGGGTGTTTTTCTCTT 59.618 43.478 0.00 0.00 0.00 2.85
5324 5528 2.952310 GTGCTTGAGGGTGTTTTTCTCT 59.048 45.455 0.00 0.00 0.00 3.10
5325 5529 2.034685 GGTGCTTGAGGGTGTTTTTCTC 59.965 50.000 0.00 0.00 0.00 2.87
5326 5530 2.031870 GGTGCTTGAGGGTGTTTTTCT 58.968 47.619 0.00 0.00 0.00 2.52
5327 5531 1.754226 TGGTGCTTGAGGGTGTTTTTC 59.246 47.619 0.00 0.00 0.00 2.29
5328 5532 1.859302 TGGTGCTTGAGGGTGTTTTT 58.141 45.000 0.00 0.00 0.00 1.94
5329 5533 1.963515 GATGGTGCTTGAGGGTGTTTT 59.036 47.619 0.00 0.00 0.00 2.43
5330 5534 1.133513 TGATGGTGCTTGAGGGTGTTT 60.134 47.619 0.00 0.00 0.00 2.83
5331 5535 0.478072 TGATGGTGCTTGAGGGTGTT 59.522 50.000 0.00 0.00 0.00 3.32
5332 5536 0.700564 ATGATGGTGCTTGAGGGTGT 59.299 50.000 0.00 0.00 0.00 4.16
5333 5537 1.340308 TGATGATGGTGCTTGAGGGTG 60.340 52.381 0.00 0.00 0.00 4.61
5334 5538 0.994247 TGATGATGGTGCTTGAGGGT 59.006 50.000 0.00 0.00 0.00 4.34
5335 5539 1.064906 AGTGATGATGGTGCTTGAGGG 60.065 52.381 0.00 0.00 0.00 4.30
5336 5540 2.414994 AGTGATGATGGTGCTTGAGG 57.585 50.000 0.00 0.00 0.00 3.86
5337 5541 3.181513 CGAAAGTGATGATGGTGCTTGAG 60.182 47.826 0.00 0.00 0.00 3.02
5338 5542 2.743664 CGAAAGTGATGATGGTGCTTGA 59.256 45.455 0.00 0.00 0.00 3.02
5339 5543 2.730090 GCGAAAGTGATGATGGTGCTTG 60.730 50.000 0.00 0.00 0.00 4.01
5340 5544 1.470098 GCGAAAGTGATGATGGTGCTT 59.530 47.619 0.00 0.00 0.00 3.91
5341 5545 1.089920 GCGAAAGTGATGATGGTGCT 58.910 50.000 0.00 0.00 0.00 4.40
5342 5546 1.089920 AGCGAAAGTGATGATGGTGC 58.910 50.000 0.00 0.00 0.00 5.01
5343 5547 3.785486 TCTAGCGAAAGTGATGATGGTG 58.215 45.455 0.00 0.00 0.00 4.17
5344 5548 3.739519 GCTCTAGCGAAAGTGATGATGGT 60.740 47.826 0.00 0.00 0.00 3.55
5345 5549 2.799412 GCTCTAGCGAAAGTGATGATGG 59.201 50.000 0.00 0.00 0.00 3.51
5346 5550 2.799412 GGCTCTAGCGAAAGTGATGATG 59.201 50.000 0.00 0.00 43.26 3.07
5347 5551 2.697751 AGGCTCTAGCGAAAGTGATGAT 59.302 45.455 0.00 0.00 43.26 2.45
5348 5552 2.103373 AGGCTCTAGCGAAAGTGATGA 58.897 47.619 0.00 0.00 43.26 2.92
5349 5553 2.593346 AGGCTCTAGCGAAAGTGATG 57.407 50.000 0.00 0.00 43.26 3.07
5350 5554 2.497675 TCAAGGCTCTAGCGAAAGTGAT 59.502 45.455 0.00 0.00 43.26 3.06
5351 5555 1.893137 TCAAGGCTCTAGCGAAAGTGA 59.107 47.619 0.00 0.00 43.26 3.41
5352 5556 2.266554 CTCAAGGCTCTAGCGAAAGTG 58.733 52.381 0.00 0.00 43.26 3.16
5353 5557 1.404851 GCTCAAGGCTCTAGCGAAAGT 60.405 52.381 5.42 0.00 43.26 2.66
5354 5558 1.285578 GCTCAAGGCTCTAGCGAAAG 58.714 55.000 5.42 0.00 43.26 2.62
5355 5559 0.108138 GGCTCAAGGCTCTAGCGAAA 60.108 55.000 13.08 0.00 43.26 3.46
5356 5560 1.517832 GGCTCAAGGCTCTAGCGAA 59.482 57.895 13.08 0.00 43.26 4.70
5357 5561 3.211288 GGCTCAAGGCTCTAGCGA 58.789 61.111 13.08 0.00 43.26 4.93
5365 5569 4.847444 GGCGGAGAGGCTCAAGGC 62.847 72.222 18.26 15.30 42.90 4.35
5381 5585 2.624674 CTTCCCATGGGCCCGTTAGG 62.625 65.000 27.41 18.66 39.47 2.69
5382 5586 1.152963 CTTCCCATGGGCCCGTTAG 60.153 63.158 27.41 8.93 34.68 2.34
5383 5587 2.685534 CCTTCCCATGGGCCCGTTA 61.686 63.158 27.41 4.40 34.68 3.18
5384 5588 4.060667 CCTTCCCATGGGCCCGTT 62.061 66.667 27.41 1.35 34.68 4.44
5386 5590 4.195334 CTCCTTCCCATGGGCCCG 62.195 72.222 27.41 15.58 34.68 6.13
5387 5591 4.529731 GCTCCTTCCCATGGGCCC 62.530 72.222 27.41 17.59 34.68 5.80
5388 5592 4.529731 GGCTCCTTCCCATGGGCC 62.530 72.222 27.41 18.48 35.13 5.80
5389 5593 4.529731 GGGCTCCTTCCCATGGGC 62.530 72.222 27.41 12.97 45.82 5.36
5395 5599 4.432741 GTGGCTGGGCTCCTTCCC 62.433 72.222 0.00 0.00 46.73 3.97
5396 5600 3.334054 AGTGGCTGGGCTCCTTCC 61.334 66.667 0.00 0.00 0.00 3.46
5397 5601 2.045536 CAGTGGCTGGGCTCCTTC 60.046 66.667 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.