Multiple sequence alignment - TraesCS4A01G231300

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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 TraesCS4A01G231300 chr4A 100.000 6146 0 0 1 6146 540605473 540599328 0.000000e+00 11350
1 TraesCS4A01G231300 chr4D 93.984 2643 135 16 1 2638 56031084 56028461 0.000000e+00 3978
2 TraesCS4A01G231300 chr4D 90.204 2154 130 25 3870 5963 56027146 56025014 0.000000e+00 2734
3 TraesCS4A01G231300 chr4D 94.529 658 30 3 2638 3292 56028319 56027665 0.000000e+00 1011
4 TraesCS4A01G231300 chr4D 94.326 282 9 1 3530 3804 56027436 56027155 5.690000e-115 425
5 TraesCS4A01G231300 chr4D 92.818 181 8 1 3365 3545 56027635 56027460 2.200000e-64 257
6 TraesCS4A01G231300 chr4D 86.170 188 14 5 5959 6146 56024943 56024768 6.290000e-45 193
7 TraesCS4A01G231300 chr4B 89.252 2540 159 52 3517 5975 83054625 83052119 0.000000e+00 3073
8 TraesCS4A01G231300 chr4B 95.087 1791 85 3 1 1789 83059777 83057988 0.000000e+00 2817
9 TraesCS4A01G231300 chr4B 90.856 853 62 12 1788 2638 83056468 83055630 0.000000e+00 1129
10 TraesCS4A01G231300 chr4B 89.853 887 56 18 2646 3532 83055503 83054651 0.000000e+00 1109
11 TraesCS4A01G231300 chr4B 92.553 188 14 0 5959 6146 83052058 83051871 2.820000e-68 270


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 TraesCS4A01G231300 chr4A 540599328 540605473 6145 True 11350.0 11350 100.000000 1 6146 1 chr4A.!!$R1 6145
1 TraesCS4A01G231300 chr4D 56024768 56031084 6316 True 1433.0 3978 92.005167 1 6146 6 chr4D.!!$R1 6145
2 TraesCS4A01G231300 chr4B 83051871 83059777 7906 True 1679.6 3073 91.520200 1 6146 5 chr4B.!!$R1 6145

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
961 965 0.250858 CCTGGTTGATCTGCACCACA 60.251 55.0 7.64 0.0 0.00 4.17 F
2209 3736 0.321122 GCATGATGAGATCGACCCCC 60.321 60.0 0.00 0.0 0.00 5.40 F
2796 4468 0.451783 GGTGTTCATTAAGCCGCTGG 59.548 55.0 0.00 0.0 0.00 4.85 F
4151 5895 0.179040 GGTGAGTCACGAAACCCCAA 60.179 55.0 16.89 0.0 34.83 4.12 F
4686 6445 0.041839 GCATTGTGATCGATCGCACC 60.042 55.0 34.83 23.4 45.92 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2813 4485 0.108804 CGTTCTCCATGTGTAGGCGT 60.109 55.0 0.00 0.00 0.00 5.68 R
3347 5022 0.036952 CAGCACAGGGACAAGTCGAT 60.037 55.0 0.00 0.00 0.00 3.59 R
4356 6115 0.034670 ATGCCCAGCTGGAAAGACTC 60.035 55.0 34.91 13.17 37.39 3.36 R
5030 6789 0.106967 GAGGTTCCCTCCAATCAGGC 60.107 60.0 0.00 0.00 44.36 4.85 R
5912 7716 0.524816 CTCATGCATGAAGCCGTTGC 60.525 55.0 28.39 0.00 44.83 4.17 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
38 39 1.065401 TGAAAGTGCACTTTTCCGCTG 59.935 47.619 37.78 0.00 45.37 5.18
198 199 3.724738 ACTGATAAGAGGAGCTAGGAGGA 59.275 47.826 0.00 0.00 0.00 3.71
200 201 5.144100 CTGATAAGAGGAGCTAGGAGGAAA 58.856 45.833 0.00 0.00 0.00 3.13
411 412 0.616891 AATTAAAGACCGCCCCGACT 59.383 50.000 0.00 0.00 0.00 4.18
415 417 2.047213 AAAGACCGCCCCGACTTGAA 62.047 55.000 0.00 0.00 0.00 2.69
432 434 1.798223 TGAATTGTCTTTCGGACTGCG 59.202 47.619 0.00 0.00 44.74 5.18
461 463 1.553690 ATGGACCCAACCTGACTCGG 61.554 60.000 0.00 0.00 0.00 4.63
463 465 2.526873 ACCCAACCTGACTCGGCT 60.527 61.111 0.00 0.00 0.00 5.52
467 469 0.970937 CCAACCTGACTCGGCTAGGA 60.971 60.000 0.00 0.00 35.55 2.94
495 497 2.291043 CGGACTAGGGCCAGGTTGT 61.291 63.158 6.18 0.00 0.00 3.32
513 516 5.417580 AGGTTGTGTATGTTGTGACACTTTT 59.582 36.000 7.20 0.00 45.08 2.27
896 900 0.526211 GGATGAAACGGCTTTGGACC 59.474 55.000 0.00 0.00 0.00 4.46
961 965 0.250858 CCTGGTTGATCTGCACCACA 60.251 55.000 7.64 0.00 0.00 4.17
991 995 1.069906 GGTTGCATTCGTATCGCCATC 60.070 52.381 0.00 0.00 0.00 3.51
1011 1015 7.459486 GCCATCTAGCTATAATGTTTTCATCG 58.541 38.462 12.70 0.00 39.94 3.84
1019 1023 8.677300 AGCTATAATGTTTTCATCGAATGTTGT 58.323 29.630 0.00 0.00 39.94 3.32
1048 1052 1.003233 AAGGAGAAGAACTGCCCGC 60.003 57.895 0.00 0.00 37.69 6.13
1085 1089 8.035394 TCCTACGGAATAGATCATTTAGCATTC 58.965 37.037 0.00 0.00 31.83 2.67
1136 1140 7.159322 AGATGTACAATGTCTAAAGTCGAGT 57.841 36.000 0.00 0.00 0.00 4.18
1259 1263 8.634444 TGTTTATTTGCTATTGGTAGTGTTGTT 58.366 29.630 0.00 0.00 0.00 2.83
1315 1319 8.674607 GTGTCCAAAATAATAAAGGTAGTCAGG 58.325 37.037 0.00 0.00 0.00 3.86
1351 1355 7.737972 TCGTTTAATTGAAGTCATTTCTCCA 57.262 32.000 0.00 0.00 36.71 3.86
1371 1375 6.156775 TCTCCATAGGATCAAACATCACTTGA 59.843 38.462 0.00 0.00 37.22 3.02
1426 1430 9.781834 GATTTCAGTATCTAATGGAGTAGATCG 57.218 37.037 0.05 0.00 40.54 3.69
1608 1612 0.541998 TTCTCTCCTTCGACCCAGCA 60.542 55.000 0.00 0.00 0.00 4.41
1623 1627 4.097418 ACCCAGCACATATAGTATCCTCC 58.903 47.826 0.00 0.00 0.00 4.30
1626 1630 4.220821 CCAGCACATATAGTATCCTCCGTT 59.779 45.833 0.00 0.00 0.00 4.44
1682 1686 4.573607 GGTCCTCGAAGTTAGTTTTGTGTT 59.426 41.667 0.00 0.00 0.00 3.32
1778 1782 6.357367 TGGGATTTCAGTAAATTCTAGAGCC 58.643 40.000 0.00 0.00 35.41 4.70
1873 3400 5.929697 TGCTCTTTGTGAGTAGTCAATTG 57.070 39.130 0.69 0.00 44.41 2.32
1979 3506 9.357652 ACATAATTGTTAATCATGTGCAGTTTC 57.642 29.630 0.00 0.00 29.55 2.78
1985 3512 1.522668 TCATGTGCAGTTTCCCTTCG 58.477 50.000 0.00 0.00 0.00 3.79
2170 3697 1.685224 GCCATGGTTGGAGAGTGGA 59.315 57.895 14.67 0.00 46.92 4.02
2209 3736 0.321122 GCATGATGAGATCGACCCCC 60.321 60.000 0.00 0.00 0.00 5.40
2224 3751 2.813726 CCCCGCATCCCAACCGATA 61.814 63.158 0.00 0.00 0.00 2.92
2239 3766 5.163754 CCAACCGATAACAAAGACTTCATCC 60.164 44.000 0.00 0.00 0.00 3.51
2241 3768 3.001330 CCGATAACAAAGACTTCATCCGC 59.999 47.826 0.00 0.00 0.00 5.54
2271 3798 1.802960 GGCACGATGGATGATGATGAC 59.197 52.381 0.00 0.00 0.00 3.06
2294 3821 1.813753 TTGCTACCGCGGATGAAGC 60.814 57.895 35.90 30.38 39.65 3.86
2301 3828 1.270147 ACCGCGGATGAAGCTATTACC 60.270 52.381 35.90 0.00 0.00 2.85
2319 3846 4.840005 GGTGCCGGGAGTGCTAGC 62.840 72.222 8.10 8.10 0.00 3.42
2324 3851 1.741770 CCGGGAGTGCTAGCAACAC 60.742 63.158 21.29 16.50 38.35 3.32
2438 3965 5.104527 TCCAAAGACGATATGAACCAATCCT 60.105 40.000 0.00 0.00 0.00 3.24
2443 3970 5.010516 AGACGATATGAACCAATCCTCTCTG 59.989 44.000 0.00 0.00 0.00 3.35
2455 3982 0.743701 CCTCTCTGGTGATGTGCAGC 60.744 60.000 0.00 0.00 45.12 5.25
2467 3994 0.896479 TGTGCAGCATGTTCCAGCAT 60.896 50.000 0.00 0.00 39.31 3.79
2487 4014 2.041922 TCCCCACCCCGATGAGAG 60.042 66.667 0.00 0.00 0.00 3.20
2497 4024 2.484651 CCCCGATGAGAGTCTACGTATG 59.515 54.545 0.00 0.00 0.00 2.39
2504 4031 0.592148 GAGTCTACGTATGGCCCTCG 59.408 60.000 0.00 4.90 0.00 4.63
2579 4106 1.135402 GCAATGCAAAGAAGGTACGGG 60.135 52.381 0.00 0.00 0.00 5.28
2582 4109 2.396157 GCAAAGAAGGTACGGGCCG 61.396 63.158 27.06 27.06 0.00 6.13
2590 4117 1.153568 GGTACGGGCCGGTCTTAAC 60.154 63.158 31.78 12.50 0.00 2.01
2606 4133 6.519761 CGGTCTTAACTTTCGATTGATGTTTG 59.480 38.462 7.03 3.20 0.00 2.93
2634 4161 8.616076 CACAAGATTTGATCAAGTACTAATCCC 58.384 37.037 8.41 0.00 32.07 3.85
2643 4315 9.177608 TGATCAAGTACTAATCCCTTTGAAATG 57.822 33.333 13.04 0.00 0.00 2.32
2644 4316 7.938140 TCAAGTACTAATCCCTTTGAAATGG 57.062 36.000 0.00 0.00 0.00 3.16
2672 4344 1.998315 CAGAACCAGAATGAGCGTCAG 59.002 52.381 0.00 0.00 39.69 3.51
2753 4425 1.746727 CGGCGATGCTGAAGAAGACG 61.747 60.000 0.00 0.00 37.02 4.18
2796 4468 0.451783 GGTGTTCATTAAGCCGCTGG 59.548 55.000 0.00 0.00 0.00 4.85
2939 4611 2.209064 ATCTCAACGTCGACCCCGTG 62.209 60.000 10.58 3.11 38.77 4.94
3059 4734 3.782244 GCGCTTGAGAGGCACGTG 61.782 66.667 12.28 12.28 0.00 4.49
3171 4846 4.840288 TGTATCGCGCGACCACGG 62.840 66.667 37.37 1.23 40.15 4.94
3191 4866 1.038130 TCCCAGGCTTACTCGAGCTC 61.038 60.000 13.61 2.73 42.32 4.09
3252 4927 1.818060 GCATGGTTATGTGCACTGGAA 59.182 47.619 19.41 6.48 40.94 3.53
3289 4964 4.123497 TCTTCATGGACGAGGTAACATG 57.877 45.455 0.00 0.00 41.44 3.21
3292 4967 2.829120 TCATGGACGAGGTAACATGACA 59.171 45.455 0.00 0.00 43.23 3.58
3293 4968 2.736144 TGGACGAGGTAACATGACAC 57.264 50.000 0.00 0.00 41.41 3.67
3294 4969 1.964933 TGGACGAGGTAACATGACACA 59.035 47.619 0.00 0.00 41.41 3.72
3295 4970 2.288579 TGGACGAGGTAACATGACACAC 60.289 50.000 0.00 0.00 41.41 3.82
3296 4971 2.334838 GACGAGGTAACATGACACACC 58.665 52.381 0.00 0.52 41.41 4.16
3297 4972 1.968493 ACGAGGTAACATGACACACCT 59.032 47.619 0.00 5.86 44.11 4.00
3298 4973 3.159472 ACGAGGTAACATGACACACCTA 58.841 45.455 0.00 0.00 41.49 3.08
3299 4974 3.192844 ACGAGGTAACATGACACACCTAG 59.807 47.826 0.00 8.72 41.49 3.02
3300 4975 3.192844 CGAGGTAACATGACACACCTAGT 59.807 47.826 0.00 0.00 41.49 2.57
3301 4976 7.287397 ACGAGGTAACATGACACACCTAGTG 62.287 48.000 17.41 11.27 42.93 2.74
3330 5005 6.591834 CCATATGTCTCATCCCGTAATTTCTC 59.408 42.308 1.24 0.00 0.00 2.87
3331 5006 5.878406 ATGTCTCATCCCGTAATTTCTCT 57.122 39.130 0.00 0.00 0.00 3.10
3332 5007 5.677319 TGTCTCATCCCGTAATTTCTCTT 57.323 39.130 0.00 0.00 0.00 2.85
3334 5009 6.472887 TGTCTCATCCCGTAATTTCTCTTTT 58.527 36.000 0.00 0.00 0.00 2.27
3335 5010 7.617225 TGTCTCATCCCGTAATTTCTCTTTTA 58.383 34.615 0.00 0.00 0.00 1.52
3336 5011 7.548075 TGTCTCATCCCGTAATTTCTCTTTTAC 59.452 37.037 0.00 0.00 0.00 2.01
3337 5012 7.764901 GTCTCATCCCGTAATTTCTCTTTTACT 59.235 37.037 0.00 0.00 0.00 2.24
3338 5013 7.764443 TCTCATCCCGTAATTTCTCTTTTACTG 59.236 37.037 0.00 0.00 0.00 2.74
3340 5015 8.533657 TCATCCCGTAATTTCTCTTTTACTGTA 58.466 33.333 0.00 0.00 0.00 2.74
3342 5017 7.669427 TCCCGTAATTTCTCTTTTACTGTACA 58.331 34.615 0.00 0.00 0.00 2.90
3343 5018 8.316214 TCCCGTAATTTCTCTTTTACTGTACAT 58.684 33.333 0.00 0.00 0.00 2.29
3344 5019 9.590451 CCCGTAATTTCTCTTTTACTGTACATA 57.410 33.333 0.00 0.00 0.00 2.29
3352 5027 9.731819 TTCTCTTTTACTGTACATATGATCGAC 57.268 33.333 10.38 2.60 0.00 4.20
3353 5028 9.121658 TCTCTTTTACTGTACATATGATCGACT 57.878 33.333 10.38 0.00 0.00 4.18
3354 5029 9.737427 CTCTTTTACTGTACATATGATCGACTT 57.263 33.333 10.38 0.00 0.00 3.01
3355 5030 9.516314 TCTTTTACTGTACATATGATCGACTTG 57.484 33.333 10.38 2.85 0.00 3.16
3356 5031 9.302345 CTTTTACTGTACATATGATCGACTTGT 57.698 33.333 10.38 7.62 0.00 3.16
3357 5032 8.851960 TTTACTGTACATATGATCGACTTGTC 57.148 34.615 10.38 0.00 0.00 3.18
3358 5033 5.833082 ACTGTACATATGATCGACTTGTCC 58.167 41.667 10.38 0.00 0.00 4.02
3359 5034 5.196341 TGTACATATGATCGACTTGTCCC 57.804 43.478 10.38 0.00 0.00 4.46
3360 5035 4.893524 TGTACATATGATCGACTTGTCCCT 59.106 41.667 10.38 0.00 0.00 4.20
3361 5036 4.327982 ACATATGATCGACTTGTCCCTG 57.672 45.455 10.38 0.00 0.00 4.45
3362 5037 3.706594 ACATATGATCGACTTGTCCCTGT 59.293 43.478 10.38 0.00 0.00 4.00
3363 5038 2.680312 ATGATCGACTTGTCCCTGTG 57.320 50.000 0.00 0.00 0.00 3.66
3375 5050 0.463654 TCCCTGTGCTGTGTGTGTTC 60.464 55.000 0.00 0.00 0.00 3.18
3468 5143 1.300311 CATCGGCCGCGGTTGTATA 60.300 57.895 28.70 7.12 0.00 1.47
3576 5298 0.373716 AAAATCCGTTCGATCGCAGC 59.626 50.000 11.09 1.74 0.00 5.25
3622 5344 1.961277 CAGGGGTGTCGAGTTGCAC 60.961 63.158 0.00 0.00 35.07 4.57
3634 5356 0.657840 AGTTGCACTGTGAAGTTCGC 59.342 50.000 12.86 9.55 0.00 4.70
3641 5363 1.621301 CTGTGAAGTTCGCGAGGCAG 61.621 60.000 9.59 8.81 0.00 4.85
3663 5385 1.202734 GCCAGATGATAGAGCAAGGCA 60.203 52.381 0.00 0.00 40.50 4.75
3723 5445 4.859400 CTGAGCTCAGAGCATGGG 57.141 61.111 35.69 9.43 45.56 4.00
3807 5536 1.938585 TGGCTACTGCAAGGTACTCT 58.061 50.000 0.00 0.00 41.91 3.24
3820 5549 3.207778 AGGTACTCTCATCTCTACACGC 58.792 50.000 0.00 0.00 0.00 5.34
3825 5554 3.127895 ACTCTCATCTCTACACGCACTTC 59.872 47.826 0.00 0.00 0.00 3.01
3837 5566 0.798776 CGCACTTCAGGAATGTGGAC 59.201 55.000 11.08 0.00 32.85 4.02
3838 5567 1.168714 GCACTTCAGGAATGTGGACC 58.831 55.000 11.08 0.00 32.85 4.46
3839 5568 1.545428 GCACTTCAGGAATGTGGACCA 60.545 52.381 0.00 0.00 32.85 4.02
3842 5571 3.941483 CACTTCAGGAATGTGGACCATAC 59.059 47.826 0.00 0.00 31.97 2.39
3843 5572 3.587061 ACTTCAGGAATGTGGACCATACA 59.413 43.478 0.00 0.00 31.97 2.29
3844 5573 4.228210 ACTTCAGGAATGTGGACCATACAT 59.772 41.667 0.00 0.00 40.30 2.29
3845 5574 5.428457 ACTTCAGGAATGTGGACCATACATA 59.572 40.000 0.00 0.00 37.77 2.29
3847 5576 6.114187 TCAGGAATGTGGACCATACATATC 57.886 41.667 0.00 0.00 37.77 1.63
3849 5578 6.329986 TCAGGAATGTGGACCATACATATCTT 59.670 38.462 0.00 0.00 37.77 2.40
3850 5579 6.429078 CAGGAATGTGGACCATACATATCTTG 59.571 42.308 0.00 2.22 37.77 3.02
3852 5581 7.292356 AGGAATGTGGACCATACATATCTTGTA 59.708 37.037 0.00 0.00 44.71 2.41
3853 5582 7.604164 GGAATGTGGACCATACATATCTTGTAG 59.396 40.741 0.00 0.00 43.87 2.74
3854 5583 7.618019 ATGTGGACCATACATATCTTGTAGT 57.382 36.000 0.00 0.00 43.87 2.73
3855 5584 8.721133 ATGTGGACCATACATATCTTGTAGTA 57.279 34.615 0.00 0.00 43.87 1.82
3857 5586 9.816787 TGTGGACCATACATATCTTGTAGTATA 57.183 33.333 0.00 0.00 43.87 1.47
3908 5637 4.801891 ACTGACATATTGCTGCAAACAAG 58.198 39.130 20.06 12.82 0.00 3.16
4029 5773 3.385384 CTCCACCCGCTGCTGAGA 61.385 66.667 0.00 0.00 0.00 3.27
4038 5782 1.148723 GCTGCTGAGATCAGGGCAT 59.851 57.895 11.63 0.00 43.94 4.40
4151 5895 0.179040 GGTGAGTCACGAAACCCCAA 60.179 55.000 16.89 0.00 34.83 4.12
4157 5901 0.748729 TCACGAAACCCCAACACCAC 60.749 55.000 0.00 0.00 0.00 4.16
4174 5918 2.441750 ACCACACCATCCACCCATATAC 59.558 50.000 0.00 0.00 0.00 1.47
4182 5926 3.719268 TCCACCCATATACATGCATCC 57.281 47.619 0.00 0.00 0.00 3.51
4193 5937 1.841919 ACATGCATCCAGTCCAGATGA 59.158 47.619 0.00 0.00 43.15 2.92
4294 6038 2.609244 GGATGACGGAGAGCTTCTATGC 60.609 54.545 0.00 0.00 0.00 3.14
4372 6131 0.390472 GACGAGTCTTTCCAGCTGGG 60.390 60.000 32.23 16.79 35.41 4.45
4388 6147 3.737172 GGCATGCACGTGGTGACC 61.737 66.667 21.36 0.00 35.23 4.02
4389 6148 2.977456 GCATGCACGTGGTGACCA 60.977 61.111 18.88 0.00 35.23 4.02
4564 6323 3.706373 GCAGGAGGACGCTTCCCA 61.706 66.667 5.45 0.00 44.10 4.37
4587 6346 4.148825 CGGCCCAGTTCCCTCTCG 62.149 72.222 0.00 0.00 0.00 4.04
4611 6370 3.154473 TCTCCATCCTTCGCCCCG 61.154 66.667 0.00 0.00 0.00 5.73
4630 6389 1.531677 CGCTGTAATGGTTTGCATCCG 60.532 52.381 0.00 0.00 0.00 4.18
4658 6417 6.569228 TCAAACATTCTTATCGCTACTTCG 57.431 37.500 0.00 0.00 0.00 3.79
4659 6418 6.327154 TCAAACATTCTTATCGCTACTTCGA 58.673 36.000 0.00 0.00 43.09 3.71
4661 6420 6.994868 AACATTCTTATCGCTACTTCGATC 57.005 37.500 1.73 0.00 44.97 3.69
4680 6439 0.875908 CGGTCCGCATTGTGATCGAT 60.876 55.000 0.00 0.00 37.28 3.59
4682 6441 0.504384 GTCCGCATTGTGATCGATCG 59.496 55.000 20.03 9.36 0.00 3.69
4683 6442 1.202568 CCGCATTGTGATCGATCGC 59.797 57.895 28.01 28.01 37.80 4.58
4685 6444 0.382272 CGCATTGTGATCGATCGCAC 60.382 55.000 34.83 24.10 45.92 5.34
4686 6445 0.041839 GCATTGTGATCGATCGCACC 60.042 55.000 34.83 23.40 45.92 5.01
4687 6446 1.289276 CATTGTGATCGATCGCACCA 58.711 50.000 34.83 24.34 45.92 4.17
4688 6447 1.665169 CATTGTGATCGATCGCACCAA 59.335 47.619 34.83 23.69 45.92 3.67
4689 6448 2.022764 TTGTGATCGATCGCACCAAT 57.977 45.000 34.83 4.87 45.92 3.16
4690 6449 1.289276 TGTGATCGATCGCACCAATG 58.711 50.000 32.19 0.00 41.89 2.82
4691 6450 1.290203 GTGATCGATCGCACCAATGT 58.710 50.000 29.31 0.00 37.27 2.71
4692 6451 1.004610 GTGATCGATCGCACCAATGTG 60.005 52.381 29.31 0.00 45.65 3.21
4693 6452 0.583438 GATCGATCGCACCAATGTGG 59.417 55.000 11.09 0.00 42.99 4.17
4694 6453 0.177836 ATCGATCGCACCAATGTGGA 59.822 50.000 11.09 0.00 40.96 4.02
4704 6463 3.504906 GCACCAATGTGGATGGATATCTG 59.495 47.826 2.05 0.00 40.96 2.90
4719 6478 0.107508 ATCTGACGGTTGGCCATCTG 60.108 55.000 19.29 19.29 34.09 2.90
4756 6515 1.505353 GGTCGTGGTCGTGGTAGAG 59.495 63.158 0.00 0.00 38.33 2.43
4757 6516 1.154073 GTCGTGGTCGTGGTAGAGC 60.154 63.158 0.00 0.00 38.95 4.09
4885 6644 4.828925 GCAGCCGTGCCTCTCTCC 62.829 72.222 0.00 0.00 44.72 3.71
4991 6750 1.580059 GACCCCATAGACCACCAGAA 58.420 55.000 0.00 0.00 0.00 3.02
4994 6753 2.196595 CCCCATAGACCACCAGAAGAA 58.803 52.381 0.00 0.00 0.00 2.52
5087 6846 4.675510 GACAACGTCGGGAATAATGTCTA 58.324 43.478 0.00 0.00 34.41 2.59
5112 6871 4.578105 GGTTCCATCATGAAGATCAAGGAC 59.422 45.833 0.00 0.00 33.72 3.85
5115 6874 2.315925 TCATGAAGATCAAGGACGCC 57.684 50.000 0.00 0.00 0.00 5.68
5136 6895 2.576615 GTCCATGCCAAGAGGGTTATC 58.423 52.381 0.00 0.00 39.65 1.75
5157 6916 0.032678 CCGTCTGATGCGCCTTCTAT 59.967 55.000 4.18 0.00 0.00 1.98
5166 6925 1.134521 TGCGCCTTCTATCATTTCCGT 60.135 47.619 4.18 0.00 0.00 4.69
5226 6985 9.226606 TGAGAATAAATTTGTGGACTTCGTTAT 57.773 29.630 0.00 0.00 0.00 1.89
5273 7037 2.412870 TGTAGACATTGAACTGCACCG 58.587 47.619 0.00 0.00 0.00 4.94
5338 7102 9.965824 TTGTTTTTCTCTGGATATTGTCTTTTC 57.034 29.630 0.00 0.00 0.00 2.29
5391 7155 7.750014 ACTTTTCATTGCATTTTTGTTGTTGTC 59.250 29.630 0.00 0.00 0.00 3.18
5392 7156 6.981762 TTCATTGCATTTTTGTTGTTGTCT 57.018 29.167 0.00 0.00 0.00 3.41
5393 7157 6.981762 TCATTGCATTTTTGTTGTTGTCTT 57.018 29.167 0.00 0.00 0.00 3.01
5394 7158 7.002816 TCATTGCATTTTTGTTGTTGTCTTC 57.997 32.000 0.00 0.00 0.00 2.87
5396 7160 3.305629 TGCATTTTTGTTGTTGTCTTCGC 59.694 39.130 0.00 0.00 0.00 4.70
5397 7161 3.551485 GCATTTTTGTTGTTGTCTTCGCT 59.449 39.130 0.00 0.00 0.00 4.93
5398 7162 4.317348 GCATTTTTGTTGTTGTCTTCGCTC 60.317 41.667 0.00 0.00 0.00 5.03
5399 7163 4.695217 TTTTTGTTGTTGTCTTCGCTCT 57.305 36.364 0.00 0.00 0.00 4.09
5400 7164 3.944422 TTTGTTGTTGTCTTCGCTCTC 57.056 42.857 0.00 0.00 0.00 3.20
5401 7165 1.865865 TGTTGTTGTCTTCGCTCTCC 58.134 50.000 0.00 0.00 0.00 3.71
5402 7166 1.412710 TGTTGTTGTCTTCGCTCTCCT 59.587 47.619 0.00 0.00 0.00 3.69
5472 7270 6.127925 TGTGAAAATGCACATCTGAATCCTAC 60.128 38.462 0.00 0.00 43.35 3.18
5498 7296 3.402628 AATAAACTGTCCACTGCGAGT 57.597 42.857 0.00 0.00 0.00 4.18
5510 7308 1.066143 ACTGCGAGTCCTAATTGTGGG 60.066 52.381 0.00 0.00 0.00 4.61
5531 7329 0.321653 GACCAAGTCCAATGGCGACT 60.322 55.000 0.00 0.00 42.41 4.18
5575 7373 0.667184 CCGGTTTTGGCAGCAATGAC 60.667 55.000 0.00 0.00 0.00 3.06
5652 7450 2.124507 TTTGTTCCTCCTCCAGCCCG 62.125 60.000 0.00 0.00 0.00 6.13
5773 7571 5.118203 GTCACGACAACAATAAGGTCTACAC 59.882 44.000 0.00 0.00 0.00 2.90
5791 7589 6.595326 GTCTACACCAACATGATCATTGAGAA 59.405 38.462 5.16 0.00 0.00 2.87
5792 7590 5.892160 ACACCAACATGATCATTGAGAAG 57.108 39.130 5.16 0.00 0.00 2.85
5794 7596 6.005823 ACACCAACATGATCATTGAGAAGAA 58.994 36.000 5.16 0.00 0.00 2.52
5819 7622 8.186709 AGTCTACATCATCATGATCATACACA 57.813 34.615 8.15 0.00 34.28 3.72
5836 7639 9.725019 ATCATACACAAGTTTCTAACATCTCAA 57.275 29.630 0.00 0.00 0.00 3.02
5909 7713 5.437289 TCAAAGATGTGCAAGTAAACCAG 57.563 39.130 0.00 0.00 0.00 4.00
5912 7716 2.816087 AGATGTGCAAGTAAACCAGCAG 59.184 45.455 0.00 0.00 37.72 4.24
5949 7753 2.000447 GAGGTTTCGCTACACACATCC 59.000 52.381 0.00 0.00 0.00 3.51
5987 7867 6.289064 TCTCCTGTCCAAGTTACTTCTTTTC 58.711 40.000 0.00 0.00 0.00 2.29
6011 7891 1.354705 AGTACCCTTTGCCTTTCCCTC 59.645 52.381 0.00 0.00 0.00 4.30
6101 7981 3.869912 GCAATGAAGCTACACTCAGGGAA 60.870 47.826 0.00 0.00 0.00 3.97
6106 7986 0.253327 GCTACACTCAGGGAAAGGGG 59.747 60.000 0.00 0.00 0.00 4.79
6132 8012 4.593206 AGTGGAATCTGAGGTTGTTCTGTA 59.407 41.667 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 6.151817 AGACAAACATAGGCAGGAGAATTTTC 59.848 38.462 0.00 0.00 0.00 2.29
169 170 2.417379 GCTCCTCTTATCAGTCAACGCA 60.417 50.000 0.00 0.00 0.00 5.24
198 199 9.289782 GATTATGTAATCCTAGCTCCACATTTT 57.710 33.333 0.00 0.00 36.85 1.82
200 201 7.977818 TGATTATGTAATCCTAGCTCCACATT 58.022 34.615 9.59 0.00 40.98 2.71
297 298 7.847096 TGTAGGAGTGAAGATTGCATTACTAA 58.153 34.615 0.00 0.00 0.00 2.24
309 310 5.652891 GGAGTCATAGTTGTAGGAGTGAAGA 59.347 44.000 0.00 0.00 0.00 2.87
315 316 7.255660 GGACATTAGGAGTCATAGTTGTAGGAG 60.256 44.444 3.40 0.00 37.74 3.69
353 354 0.913934 TGGCCTGACCCAATGCTAGA 60.914 55.000 3.32 0.00 37.83 2.43
384 385 4.885325 GGGGCGGTCTTTAATTTTCAGATA 59.115 41.667 0.00 0.00 0.00 1.98
393 394 0.616891 AAGTCGGGGCGGTCTTTAAT 59.383 50.000 0.00 0.00 0.00 1.40
432 434 3.134127 GGGTCCATGCCTCGTTGC 61.134 66.667 0.00 0.00 0.00 4.17
461 463 2.014857 GTCCGACCCAAAAATCCTAGC 58.985 52.381 0.00 0.00 0.00 3.42
463 465 3.453353 CCTAGTCCGACCCAAAAATCCTA 59.547 47.826 0.00 0.00 0.00 2.94
467 469 1.340697 GCCCTAGTCCGACCCAAAAAT 60.341 52.381 0.00 0.00 0.00 1.82
513 516 7.930865 AGCTTGGCAAACATATTCTTGTTAAAA 59.069 29.630 0.00 0.00 38.85 1.52
529 532 2.791347 TCGGGTAATAGCTTGGCAAA 57.209 45.000 0.00 0.00 0.00 3.68
896 900 3.294943 GACCGACGGAAATGTCTATACG 58.705 50.000 23.38 0.00 36.71 3.06
961 965 1.429463 GAATGCAACCTCGACGTCTT 58.571 50.000 14.70 0.00 0.00 3.01
1116 1120 5.345202 CCACACTCGACTTTAGACATTGTAC 59.655 44.000 0.00 0.00 0.00 2.90
1136 1140 3.131933 CCAATTGTGTCAAAGAACCCACA 59.868 43.478 4.43 0.00 36.12 4.17
1351 1355 7.286316 GGGAAATCAAGTGATGTTTGATCCTAT 59.714 37.037 1.41 0.00 42.73 2.57
1371 1375 9.927081 ACAAGATCTTCAACTAATATGGGAAAT 57.073 29.630 4.57 0.00 0.00 2.17
1623 1627 7.621991 TGTTTTGTTAATAAAATGTGGCAACG 58.378 30.769 12.48 0.00 33.55 4.10
1721 1725 8.250143 AGGAACTGACAATAGTGGAAAATTTT 57.750 30.769 2.28 2.28 37.18 1.82
1725 1729 5.009610 GCAAGGAACTGACAATAGTGGAAAA 59.990 40.000 0.00 0.00 40.86 2.29
1778 1782 8.476657 TTGTTTACATTAATTGTGATGCCATG 57.523 30.769 0.00 0.00 39.48 3.66
1905 3432 9.603921 ATTGCATAAACTTCCCAAATAATTCTG 57.396 29.630 0.00 0.00 0.00 3.02
1955 3482 7.981225 GGGAAACTGCACATGATTAACAATTAT 59.019 33.333 0.00 0.00 0.00 1.28
1979 3506 8.784043 CAGAATATAAAAAGGGAATACGAAGGG 58.216 37.037 0.00 0.00 0.00 3.95
2095 3622 0.855349 GACGCACGGATCAATAGCTG 59.145 55.000 0.00 0.00 0.00 4.24
2170 3697 0.899019 ACTTGGCCGTTTTGTGGTTT 59.101 45.000 0.00 0.00 0.00 3.27
2209 3736 1.374560 TTGTTATCGGTTGGGATGCG 58.625 50.000 0.00 0.00 0.00 4.73
2224 3751 1.537202 GCTGCGGATGAAGTCTTTGTT 59.463 47.619 0.00 0.00 0.00 2.83
2241 3768 3.049674 ATCGTGCCCGTGTTGCTG 61.050 61.111 0.00 0.00 35.01 4.41
2271 3798 1.591594 ATCCGCGGTAGCAACATCG 60.592 57.895 27.15 0.00 45.49 3.84
2301 3828 4.514577 CTAGCACTCCCGGCACCG 62.515 72.222 1.02 1.02 39.44 4.94
2319 3846 1.376037 GCCCCTCTTCCTCGTGTTG 60.376 63.158 0.00 0.00 0.00 3.33
2324 3851 4.168291 GCCTGCCCCTCTTCCTCG 62.168 72.222 0.00 0.00 0.00 4.63
2412 3939 6.073003 GGATTGGTTCATATCGTCTTTGGATC 60.073 42.308 0.00 0.00 0.00 3.36
2438 3965 0.616891 ATGCTGCACATCACCAGAGA 59.383 50.000 3.57 0.00 31.52 3.10
2443 3970 0.171903 GGAACATGCTGCACATCACC 59.828 55.000 3.57 1.64 36.64 4.02
2455 3982 0.819582 GGGGACAATGCTGGAACATG 59.180 55.000 0.00 0.00 38.20 3.21
2467 3994 2.204013 TCATCGGGGTGGGGACAA 60.204 61.111 0.00 0.00 46.06 3.18
2487 4014 1.658673 CCGAGGGCCATACGTAGAC 59.341 63.158 6.18 0.00 0.00 2.59
2504 4031 2.825836 CATGCCCACCTTCTCGCC 60.826 66.667 0.00 0.00 0.00 5.54
2507 4034 0.179006 GGATCCATGCCCACCTTCTC 60.179 60.000 6.95 0.00 0.00 2.87
2579 4106 2.997986 TCAATCGAAAGTTAAGACCGGC 59.002 45.455 0.00 0.00 0.00 6.13
2582 4109 6.305638 GCAAACATCAATCGAAAGTTAAGACC 59.694 38.462 0.00 0.00 0.00 3.85
2590 4117 3.899734 TGTGGCAAACATCAATCGAAAG 58.100 40.909 0.00 0.00 32.36 2.62
2606 4133 5.886960 AGTACTTGATCAAATCTTGTGGC 57.113 39.130 9.88 2.23 0.00 5.01
2634 4161 5.349543 GGTTCTGCATTTAGCCATTTCAAAG 59.650 40.000 0.00 0.00 44.83 2.77
2643 4315 3.696051 TCATTCTGGTTCTGCATTTAGCC 59.304 43.478 0.00 0.00 44.83 3.93
2644 4316 4.732938 GCTCATTCTGGTTCTGCATTTAGC 60.733 45.833 0.00 0.00 45.96 3.09
2672 4344 2.401766 CCGGAGCACCATGTTCTGC 61.402 63.158 0.00 0.00 33.33 4.26
2700 4372 5.767269 TCGATTCTCTTCTGCTAGCATAAG 58.233 41.667 28.18 28.18 33.26 1.73
2753 4425 2.658422 CCTTTGCATGTGGGGCAC 59.342 61.111 0.00 0.00 41.75 5.01
2812 4484 1.133598 CGTTCTCCATGTGTAGGCGTA 59.866 52.381 0.00 0.00 0.00 4.42
2813 4485 0.108804 CGTTCTCCATGTGTAGGCGT 60.109 55.000 0.00 0.00 0.00 5.68
2879 4551 2.125753 GCAGTCCCAGCAGAGACG 60.126 66.667 0.00 0.00 38.08 4.18
2982 4654 2.032681 GGGAGCACAGTGACCCAC 59.967 66.667 23.30 3.28 41.72 4.61
3071 4746 1.931906 TCAGCATCATGAGCTCGTTC 58.068 50.000 5.46 0.00 41.14 3.95
3143 4818 1.521681 GCGATACAGCTGGTGGTCC 60.522 63.158 19.93 0.00 0.00 4.46
3171 4846 1.142097 GCTCGAGTAAGCCTGGGAC 59.858 63.158 15.13 0.00 36.22 4.46
3252 4927 1.827399 AAGATGCGGACAAGGTCGGT 61.827 55.000 5.93 0.00 35.71 4.69
3292 4967 4.547671 AGACATATGGTAGCACTAGGTGT 58.452 43.478 7.80 0.00 35.75 4.16
3293 4968 4.584743 TGAGACATATGGTAGCACTAGGTG 59.415 45.833 7.80 0.00 36.51 4.00
3294 4969 4.804597 TGAGACATATGGTAGCACTAGGT 58.195 43.478 7.80 0.00 0.00 3.08
3295 4970 5.105554 GGATGAGACATATGGTAGCACTAGG 60.106 48.000 7.80 0.00 0.00 3.02
3296 4971 5.105554 GGGATGAGACATATGGTAGCACTAG 60.106 48.000 7.80 0.00 0.00 2.57
3297 4972 4.772624 GGGATGAGACATATGGTAGCACTA 59.227 45.833 7.80 0.00 0.00 2.74
3298 4973 3.580458 GGGATGAGACATATGGTAGCACT 59.420 47.826 7.80 0.00 0.00 4.40
3299 4974 3.615110 CGGGATGAGACATATGGTAGCAC 60.615 52.174 7.80 0.00 0.00 4.40
3300 4975 2.562738 CGGGATGAGACATATGGTAGCA 59.437 50.000 7.80 0.00 0.00 3.49
3301 4976 2.563179 ACGGGATGAGACATATGGTAGC 59.437 50.000 7.80 0.00 0.00 3.58
3307 4982 7.546250 AGAGAAATTACGGGATGAGACATAT 57.454 36.000 0.00 0.00 0.00 1.78
3311 4986 6.986904 AAAAGAGAAATTACGGGATGAGAC 57.013 37.500 0.00 0.00 0.00 3.36
3330 5005 9.302345 ACAAGTCGATCATATGTACAGTAAAAG 57.698 33.333 0.33 0.00 0.00 2.27
3331 5006 9.297586 GACAAGTCGATCATATGTACAGTAAAA 57.702 33.333 0.33 0.00 0.00 1.52
3332 5007 7.919091 GGACAAGTCGATCATATGTACAGTAAA 59.081 37.037 0.33 0.00 0.00 2.01
3334 5009 6.016527 GGGACAAGTCGATCATATGTACAGTA 60.017 42.308 0.33 0.00 0.00 2.74
3335 5010 5.221263 GGGACAAGTCGATCATATGTACAGT 60.221 44.000 0.33 0.00 0.00 3.55
3336 5011 5.010112 AGGGACAAGTCGATCATATGTACAG 59.990 44.000 0.33 0.00 0.00 2.74
3337 5012 4.893524 AGGGACAAGTCGATCATATGTACA 59.106 41.667 0.00 0.00 0.00 2.90
3338 5013 5.221263 ACAGGGACAAGTCGATCATATGTAC 60.221 44.000 1.90 0.00 0.00 2.90
3340 5015 3.706594 ACAGGGACAAGTCGATCATATGT 59.293 43.478 1.90 0.00 0.00 2.29
3342 5017 3.493350 GCACAGGGACAAGTCGATCATAT 60.493 47.826 0.00 0.00 0.00 1.78
3343 5018 2.159099 GCACAGGGACAAGTCGATCATA 60.159 50.000 0.00 0.00 0.00 2.15
3344 5019 1.406069 GCACAGGGACAAGTCGATCAT 60.406 52.381 0.00 0.00 0.00 2.45
3345 5020 0.037326 GCACAGGGACAAGTCGATCA 60.037 55.000 0.00 0.00 0.00 2.92
3346 5021 0.247736 AGCACAGGGACAAGTCGATC 59.752 55.000 0.00 0.00 0.00 3.69
3347 5022 0.036952 CAGCACAGGGACAAGTCGAT 60.037 55.000 0.00 0.00 0.00 3.59
3348 5023 1.367471 CAGCACAGGGACAAGTCGA 59.633 57.895 0.00 0.00 0.00 4.20
3349 5024 1.069765 ACAGCACAGGGACAAGTCG 59.930 57.895 0.00 0.00 0.00 4.18
3350 5025 0.179045 ACACAGCACAGGGACAAGTC 60.179 55.000 0.00 0.00 0.00 3.01
3351 5026 0.464373 CACACAGCACAGGGACAAGT 60.464 55.000 0.00 0.00 0.00 3.16
3352 5027 0.464373 ACACACAGCACAGGGACAAG 60.464 55.000 0.00 0.00 0.00 3.16
3353 5028 0.747644 CACACACAGCACAGGGACAA 60.748 55.000 0.00 0.00 0.00 3.18
3354 5029 1.153188 CACACACAGCACAGGGACA 60.153 57.895 0.00 0.00 0.00 4.02
3355 5030 0.748005 AACACACACAGCACAGGGAC 60.748 55.000 0.00 0.00 0.00 4.46
3356 5031 0.463654 GAACACACACAGCACAGGGA 60.464 55.000 0.00 0.00 0.00 4.20
3357 5032 0.464373 AGAACACACACAGCACAGGG 60.464 55.000 0.00 0.00 0.00 4.45
3358 5033 0.659427 CAGAACACACACAGCACAGG 59.341 55.000 0.00 0.00 0.00 4.00
3359 5034 1.328680 GTCAGAACACACACAGCACAG 59.671 52.381 0.00 0.00 0.00 3.66
3360 5035 1.066215 AGTCAGAACACACACAGCACA 60.066 47.619 0.00 0.00 0.00 4.57
3361 5036 1.656652 AGTCAGAACACACACAGCAC 58.343 50.000 0.00 0.00 0.00 4.40
3362 5037 2.401583 AAGTCAGAACACACACAGCA 57.598 45.000 0.00 0.00 0.00 4.41
3363 5038 3.126858 TCAAAAGTCAGAACACACACAGC 59.873 43.478 0.00 0.00 0.00 4.40
3375 5050 1.677576 TGCCAACAGCTCAAAAGTCAG 59.322 47.619 0.00 0.00 44.23 3.51
3458 5133 0.951558 CCCTTGGCATATACAACCGC 59.048 55.000 0.00 0.00 0.00 5.68
3480 5155 2.167900 AGCGGAACTTACCAGTATGACC 59.832 50.000 0.00 0.00 39.69 4.02
3483 5158 1.933853 GCAGCGGAACTTACCAGTATG 59.066 52.381 0.00 0.00 30.68 2.39
3576 5298 0.257039 ACCCTAAGGCCTGCATTCAG 59.743 55.000 5.69 0.00 36.99 3.02
3622 5344 1.621301 CTGCCTCGCGAACTTCACAG 61.621 60.000 11.33 7.71 0.00 3.66
3641 5363 2.492012 CCTTGCTCTATCATCTGGCAC 58.508 52.381 0.00 0.00 32.47 5.01
3663 5385 2.282887 GTCCACCACGGCCCAAAT 60.283 61.111 0.00 0.00 33.14 2.32
3807 5536 2.164422 CCTGAAGTGCGTGTAGAGATGA 59.836 50.000 0.00 0.00 0.00 2.92
3820 5549 2.566833 TGGTCCACATTCCTGAAGTG 57.433 50.000 0.00 0.00 0.00 3.16
3825 5554 6.119240 AGATATGTATGGTCCACATTCCTG 57.881 41.667 0.00 0.00 41.03 3.86
3864 5593 9.667107 TCAGTAGGAATTACGAAAATTCTCAAT 57.333 29.630 19.78 10.00 37.35 2.57
3865 5594 8.932791 GTCAGTAGGAATTACGAAAATTCTCAA 58.067 33.333 19.78 9.07 37.35 3.02
3866 5595 8.092068 TGTCAGTAGGAATTACGAAAATTCTCA 58.908 33.333 19.78 10.49 37.35 3.27
3867 5596 8.475331 TGTCAGTAGGAATTACGAAAATTCTC 57.525 34.615 19.78 13.43 37.35 2.87
3874 5603 7.438160 CAGCAATATGTCAGTAGGAATTACGAA 59.562 37.037 0.00 0.00 37.35 3.85
3877 5606 6.483307 TGCAGCAATATGTCAGTAGGAATTAC 59.517 38.462 0.00 0.00 0.00 1.89
3883 5612 4.395854 TGTTTGCAGCAATATGTCAGTAGG 59.604 41.667 9.12 0.00 0.00 3.18
3917 5648 9.783081 GGCACAATGTATATGATATATCCATCA 57.217 33.333 10.25 3.61 39.20 3.07
4029 5773 0.107456 CGCTGAAGGTATGCCCTGAT 59.893 55.000 0.00 0.00 45.47 2.90
4151 5895 1.434513 ATGGGTGGATGGTGTGGTGT 61.435 55.000 0.00 0.00 0.00 4.16
4157 5901 3.084039 GCATGTATATGGGTGGATGGTG 58.916 50.000 1.33 0.00 34.79 4.17
4174 5918 2.632987 TCATCTGGACTGGATGCATG 57.367 50.000 2.46 0.00 40.02 4.06
4182 5926 4.822350 AGAATTGCATGATCATCTGGACTG 59.178 41.667 4.86 0.00 0.00 3.51
4193 5937 5.803461 CGTGAATGTTTCAGAATTGCATGAT 59.197 36.000 0.00 0.00 41.01 2.45
4355 6114 1.743252 GCCCAGCTGGAAAGACTCG 60.743 63.158 34.91 15.45 37.39 4.18
4356 6115 0.034670 ATGCCCAGCTGGAAAGACTC 60.035 55.000 34.91 13.17 37.39 3.36
4357 6116 0.323178 CATGCCCAGCTGGAAAGACT 60.323 55.000 34.91 9.24 37.39 3.24
4358 6117 1.941999 GCATGCCCAGCTGGAAAGAC 61.942 60.000 34.91 16.16 37.39 3.01
4359 6118 1.679977 GCATGCCCAGCTGGAAAGA 60.680 57.895 34.91 14.46 37.39 2.52
4360 6119 1.980232 TGCATGCCCAGCTGGAAAG 60.980 57.895 34.91 18.56 37.39 2.62
4361 6120 2.117858 TGCATGCCCAGCTGGAAA 59.882 55.556 34.91 21.36 37.39 3.13
4372 6131 2.977456 TGGTCACCACGTGCATGC 60.977 61.111 11.82 11.82 32.98 4.06
4439 6198 4.736896 GGGAGCCACACCGTCGTC 62.737 72.222 0.00 0.00 0.00 4.20
4564 6323 4.740822 GGAACTGGGCCGTGGCAT 62.741 66.667 13.76 0.00 44.11 4.40
4587 6346 4.162690 AAGGATGGAGACGCCGCC 62.163 66.667 0.00 0.00 40.66 6.13
4611 6370 1.742831 TCGGATGCAAACCATTACAGC 59.257 47.619 12.59 0.00 33.29 4.40
4630 6389 5.476752 AGCGATAAGAATGTTTGAAGCTC 57.523 39.130 0.00 0.00 0.00 4.09
4658 6417 0.861837 GATCACAATGCGGACCGATC 59.138 55.000 20.50 5.87 0.00 3.69
4659 6418 0.875908 CGATCACAATGCGGACCGAT 60.876 55.000 20.50 5.50 0.00 4.18
4660 6419 1.518352 CGATCACAATGCGGACCGA 60.518 57.895 20.50 2.93 0.00 4.69
4661 6420 0.875908 ATCGATCACAATGCGGACCG 60.876 55.000 10.29 10.29 0.00 4.79
4680 6439 0.255604 ATCCATCCACATTGGTGCGA 59.744 50.000 0.00 0.00 43.88 5.10
4682 6441 3.504906 CAGATATCCATCCACATTGGTGC 59.495 47.826 0.00 0.00 43.88 5.01
4683 6442 4.758674 GTCAGATATCCATCCACATTGGTG 59.241 45.833 0.00 0.00 44.85 4.17
4685 6444 3.999001 CGTCAGATATCCATCCACATTGG 59.001 47.826 0.00 0.00 39.43 3.16
4686 6445 3.999001 CCGTCAGATATCCATCCACATTG 59.001 47.826 0.00 0.00 0.00 2.82
4687 6446 3.648067 ACCGTCAGATATCCATCCACATT 59.352 43.478 0.00 0.00 0.00 2.71
4688 6447 3.242867 ACCGTCAGATATCCATCCACAT 58.757 45.455 0.00 0.00 0.00 3.21
4689 6448 2.677914 ACCGTCAGATATCCATCCACA 58.322 47.619 0.00 0.00 0.00 4.17
4690 6449 3.393800 CAACCGTCAGATATCCATCCAC 58.606 50.000 0.00 0.00 0.00 4.02
4691 6450 2.368548 CCAACCGTCAGATATCCATCCA 59.631 50.000 0.00 0.00 0.00 3.41
4692 6451 2.872038 GCCAACCGTCAGATATCCATCC 60.872 54.545 0.00 0.00 0.00 3.51
4693 6452 2.417719 GCCAACCGTCAGATATCCATC 58.582 52.381 0.00 0.00 0.00 3.51
4694 6453 1.072331 GGCCAACCGTCAGATATCCAT 59.928 52.381 0.00 0.00 0.00 3.41
4719 6478 0.179189 CCTGCGGCAATTCGAAGAAC 60.179 55.000 3.44 0.00 45.90 3.01
4756 6515 1.372623 GCTTCTTGTTGCAGCTGGC 60.373 57.895 17.12 8.54 45.13 4.85
4757 6516 0.240411 GAGCTTCTTGTTGCAGCTGG 59.760 55.000 17.12 0.00 44.92 4.85
4970 6729 1.686325 CTGGTGGTCTATGGGGTCGG 61.686 65.000 0.00 0.00 0.00 4.79
4991 6750 1.716826 GACGAGAGATCCGCGGTTCT 61.717 60.000 33.25 33.25 42.49 3.01
4994 6753 2.124653 AGACGAGAGATCCGCGGT 60.125 61.111 27.15 12.96 42.49 5.68
5030 6789 0.106967 GAGGTTCCCTCCAATCAGGC 60.107 60.000 0.00 0.00 44.36 4.85
5087 6846 3.912496 TGATCTTCATGATGGAACCGT 57.088 42.857 8.60 0.00 35.14 4.83
5112 6871 3.197790 CTCTTGGCATGGACGGCG 61.198 66.667 4.80 4.80 0.00 6.46
5115 6874 0.251916 TAACCCTCTTGGCATGGACG 59.748 55.000 0.00 0.00 37.83 4.79
5136 6895 2.434884 AAGGCGCATCAGACGGTG 60.435 61.111 10.83 0.00 0.00 4.94
5273 7037 3.336138 TTGGAAAACAAACAACCCACC 57.664 42.857 0.00 0.00 35.79 4.61
5330 7094 6.034470 GCATTTTGTCAACGAAAGAAAAGACA 59.966 34.615 0.00 0.00 33.16 3.41
5472 7270 5.178623 TCGCAGTGGACAGTTTATTTAGTTG 59.821 40.000 0.00 0.00 0.00 3.16
5498 7296 2.714250 ACTTGGTCACCCACAATTAGGA 59.286 45.455 0.00 0.00 41.67 2.94
5510 7308 0.605319 TCGCCATTGGACTTGGTCAC 60.605 55.000 6.95 0.00 36.57 3.67
5545 7343 1.234821 CAAAACCGGCTCTGCTTACA 58.765 50.000 0.00 0.00 0.00 2.41
5575 7373 2.034687 CAACAGCTCTGGGTGGGG 59.965 66.667 1.66 0.00 44.34 4.96
5652 7450 4.671766 GCGAGAGAAGAGTTGAGAAGAGAC 60.672 50.000 0.00 0.00 0.00 3.36
5713 7511 6.376299 TGCTCTCAATGTTCTGCATCTATTTT 59.624 34.615 0.00 0.00 36.67 1.82
5749 7547 5.118203 GTGTAGACCTTATTGTTGTCGTGAC 59.882 44.000 0.00 0.00 34.24 3.67
5773 7571 6.598457 AGACTTCTTCTCAATGATCATGTTGG 59.402 38.462 9.46 0.00 0.00 3.77
5791 7589 9.086758 TGTATGATCATGATGATGTAGACTTCT 57.913 33.333 18.72 0.00 37.20 2.85
5792 7590 9.138062 GTGTATGATCATGATGATGTAGACTTC 57.862 37.037 18.72 0.00 37.20 3.01
5794 7596 8.186709 TGTGTATGATCATGATGATGTAGACT 57.813 34.615 18.72 0.00 37.20 3.24
5879 7682 8.578308 TTACTTGCACATCTTTGATCTTTTTG 57.422 30.769 0.00 0.00 0.00 2.44
5912 7716 0.524816 CTCATGCATGAAGCCGTTGC 60.525 55.000 28.39 0.00 44.83 4.17
5949 7753 2.896685 ACAGGAGAAGGTGAGAAGACAG 59.103 50.000 0.00 0.00 0.00 3.51
5987 7867 1.541588 GAAAGGCAAAGGGTACTGCAG 59.458 52.381 13.48 13.48 40.46 4.41
6011 7891 0.890996 ACCAGCAAAGAAGAAGGCGG 60.891 55.000 0.00 0.00 0.00 6.13
6101 7981 2.122768 CTCAGATTCCACTAGCCCCTT 58.877 52.381 0.00 0.00 0.00 3.95
6106 7986 3.618690 ACAACCTCAGATTCCACTAGC 57.381 47.619 0.00 0.00 0.00 3.42


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

AutoCloner maintained by Alex Coulton.