Multiple sequence alignment - TraesCS6B01G282500

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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 TraesCS6B01G282500 chr6B 100.000 4552 0 0 1 4552 508938484 508943035 0.000000e+00 8407.0
1 TraesCS6B01G282500 chr6D 93.587 2152 71 18 583 2691 315960128 315958001 0.000000e+00 3147.0
2 TraesCS6B01G282500 chr6D 93.917 1085 31 12 2771 3839 315958004 315956939 0.000000e+00 1605.0
3 TraesCS6B01G282500 chr6D 86.627 501 55 9 1 499 315967054 315966564 1.110000e-150 544.0
4 TraesCS6B01G282500 chr6D 93.646 362 20 2 4022 4381 315956674 315956314 5.180000e-149 538.0
5 TraesCS6B01G282500 chr6D 95.425 153 5 1 3841 3993 315956823 315956673 4.550000e-60 243.0
6 TraesCS6B01G282500 chr6D 93.651 63 4 0 532 594 315966567 315966505 1.350000e-15 95.3
7 TraesCS6B01G282500 chr6A 92.529 1874 108 18 1 1858 453828762 453826905 0.000000e+00 2656.0
8 TraesCS6B01G282500 chr6A 92.115 1636 60 17 2771 4381 453825688 453824097 0.000000e+00 2242.0
9 TraesCS6B01G282500 chr6A 90.625 544 23 13 2163 2691 453826215 453825685 0.000000e+00 697.0
10 TraesCS6B01G282500 chr6A 87.047 386 17 16 1822 2176 453826901 453826518 5.480000e-109 405.0
11 TraesCS6B01G282500 chr6A 90.805 87 8 0 2689 2775 610209064 610209150 2.880000e-22 117.0
12 TraesCS6B01G282500 chr2A 92.053 151 11 1 1618 1767 642227519 642227369 1.280000e-50 211.0
13 TraesCS6B01G282500 chr2D 91.391 151 12 1 1618 1767 497925691 497925541 5.970000e-49 206.0
14 TraesCS6B01G282500 chr2B 91.667 132 11 0 3382 3513 583788152 583788021 2.800000e-42 183.0
15 TraesCS6B01G282500 chr5D 89.888 89 8 1 2689 2776 551772444 551772356 3.720000e-21 113.0
16 TraesCS6B01G282500 chr3D 88.764 89 10 0 2688 2776 141424360 141424272 4.810000e-20 110.0
17 TraesCS6B01G282500 chr3D 88.372 86 10 0 2688 2773 565374417 565374332 2.240000e-18 104.0
18 TraesCS6B01G282500 chr3D 89.024 82 9 0 2689 2770 565374332 565374413 8.060000e-18 102.0
19 TraesCS6B01G282500 chr3A 90.123 81 8 0 2689 2769 434000894 434000974 6.230000e-19 106.0
20 TraesCS6B01G282500 chr5B 87.234 94 8 3 2678 2770 279098256 279098346 2.240000e-18 104.0
21 TraesCS6B01G282500 chr5B 87.640 89 9 2 2689 2776 684062705 684062618 8.060000e-18 102.0
22 TraesCS6B01G282500 chr7D 85.000 100 14 1 2689 2787 204247274 204247175 2.900000e-17 100.0
23 TraesCS6B01G282500 chr7A 97.368 38 1 0 58 95 29427522 29427485 1.060000e-06 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G282500 chr6B 508938484 508943035 4551 False 8407.00 8407 100.00000 1 4552 1 chr6B.!!$F1 4551
1 TraesCS6B01G282500 chr6D 315956314 315960128 3814 True 1383.25 3147 94.14375 583 4381 4 chr6D.!!$R1 3798
2 TraesCS6B01G282500 chr6D 315966505 315967054 549 True 319.65 544 90.13900 1 594 2 chr6D.!!$R2 593
3 TraesCS6B01G282500 chr6A 453824097 453828762 4665 True 1500.00 2656 90.57900 1 4381 4 chr6A.!!$R1 4380

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
354 356 0.179129 CAACATCTTTGCATCCGGCC 60.179 55.0 0.0 0.0 43.89 6.13 F
1283 1294 0.108329 ACGGTCGGTTTCATGCCTAG 60.108 55.0 0.0 0.0 0.00 3.02 F
1585 1600 0.592637 CATTGTGGTGTGCGTGTGAT 59.407 50.0 0.0 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 1418 1.598130 GCCAACTCTTGCCGTCACT 60.598 57.895 0.00 0.00 0.00 3.41 R
3275 3708 0.826062 GCCCCGCTTTAGGTAGTACA 59.174 55.000 2.06 0.00 0.00 2.90 R
3577 4010 2.370824 GATCGAGCACTTGCATGGCG 62.371 60.000 3.62 2.14 45.16 5.69 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
18 19 2.789873 AGGGTTAGCCGGGGTAAAA 58.210 52.632 19.45 0.00 34.97 1.52
19 20 1.074766 AGGGTTAGCCGGGGTAAAAA 58.925 50.000 19.45 0.00 34.97 1.94
20 21 1.176527 GGGTTAGCCGGGGTAAAAAC 58.823 55.000 19.45 10.59 34.97 2.43
75 76 2.579201 CGTGGGCGTCATCTCCTT 59.421 61.111 0.00 0.00 0.00 3.36
103 105 1.733389 GCACCGTCATGGCTTTCATTG 60.733 52.381 0.00 0.00 43.94 2.82
113 115 0.392998 GCTTTCATTGCCCTCCGAGA 60.393 55.000 0.00 0.00 0.00 4.04
114 116 1.373570 CTTTCATTGCCCTCCGAGAC 58.626 55.000 0.00 0.00 0.00 3.36
117 119 4.514577 ATTGCCCTCCGAGACGCG 62.515 66.667 3.53 3.53 40.47 6.01
141 143 3.118075 TGCGGATGAAAACCATGATCCTA 60.118 43.478 0.00 0.00 35.17 2.94
153 155 1.728323 TGATCCTATGGATTGGGCGA 58.272 50.000 0.26 0.00 43.27 5.54
177 179 2.251642 GCACTTCGGTGTGGTGTCC 61.252 63.158 9.90 0.00 46.81 4.02
189 191 0.843309 TGGTGTCCTTCTTGAAGGCA 59.157 50.000 21.16 18.61 39.80 4.75
192 194 0.843309 TGTCCTTCTTGAAGGCACCA 59.157 50.000 21.16 15.02 39.80 4.17
197 199 2.294512 CCTTCTTGAAGGCACCACTTTC 59.705 50.000 15.43 0.00 32.43 2.62
204 206 2.281484 GCACCACTTTCGAGGCCA 60.281 61.111 5.01 0.00 0.00 5.36
210 212 1.363744 CACTTTCGAGGCCATGTCTC 58.636 55.000 5.01 0.00 0.00 3.36
266 268 2.160721 TCATAGTCGAGGGCTCCTTT 57.839 50.000 0.00 0.00 31.76 3.11
275 277 2.344093 AGGGCTCCTTTGACCTCTAA 57.656 50.000 0.00 0.00 43.16 2.10
283 285 3.055094 TCCTTTGACCTCTAATGGTGCTC 60.055 47.826 0.00 0.00 41.00 4.26
301 303 6.092122 TGGTGCTCTATTTTCTATGTCGTTTG 59.908 38.462 0.00 0.00 0.00 2.93
303 305 5.874810 TGCTCTATTTTCTATGTCGTTTGCT 59.125 36.000 0.00 0.00 0.00 3.91
329 331 2.027192 GTCCTTTGGAGTGATGTAGGCA 60.027 50.000 0.00 0.00 29.39 4.75
337 339 4.019411 TGGAGTGATGTAGGCATTCTTCAA 60.019 41.667 0.00 0.00 35.07 2.69
340 342 5.503927 AGTGATGTAGGCATTCTTCAACAT 58.496 37.500 0.00 0.00 35.07 2.71
346 348 4.184079 AGGCATTCTTCAACATCTTTGC 57.816 40.909 0.00 0.00 0.00 3.68
354 356 0.179129 CAACATCTTTGCATCCGGCC 60.179 55.000 0.00 0.00 43.89 6.13
359 361 2.679642 TTTGCATCCGGCCTTGGG 60.680 61.111 0.00 0.00 43.89 4.12
363 365 2.438434 CATCCGGCCTTGGGTGTC 60.438 66.667 0.00 0.00 35.29 3.67
400 409 4.653868 TGTATCCGTTGGGTTGTATGTTT 58.346 39.130 0.00 0.00 33.83 2.83
401 410 5.802465 TGTATCCGTTGGGTTGTATGTTTA 58.198 37.500 0.00 0.00 33.83 2.01
408 417 5.107026 CGTTGGGTTGTATGTTTATCGTTGA 60.107 40.000 0.00 0.00 0.00 3.18
427 436 6.708949 TCGTTGATTTATCTATAAAGTGGGGC 59.291 38.462 2.00 0.00 35.88 5.80
432 441 7.444183 TGATTTATCTATAAAGTGGGGCGAAAG 59.556 37.037 2.00 0.00 35.88 2.62
473 484 6.321821 TGGATGGCTAGTTTAATGTAGGTT 57.678 37.500 0.00 0.00 0.00 3.50
474 485 6.354130 TGGATGGCTAGTTTAATGTAGGTTC 58.646 40.000 0.00 0.00 0.00 3.62
516 527 8.615878 TCTGTTTTTGTATGTACAGCTGTAAT 57.384 30.769 27.61 22.26 38.26 1.89
523 534 9.884636 TTTGTATGTACAGCTGTAATAGAACAT 57.115 29.630 27.61 26.52 37.52 2.71
579 590 9.301153 GGCCTATGTGACAAAACAAAATATAAG 57.699 33.333 0.00 0.00 32.81 1.73
584 595 7.500992 TGTGACAAAACAAAATATAAGGGCAA 58.499 30.769 0.00 0.00 0.00 4.52
616 627 4.901868 AGAATGCTACTGGTTTCCGTAAA 58.098 39.130 0.00 0.00 0.00 2.01
618 629 5.411669 AGAATGCTACTGGTTTCCGTAAAAG 59.588 40.000 0.00 0.00 0.00 2.27
622 633 5.237779 TGCTACTGGTTTCCGTAAAAGAAAG 59.762 40.000 0.00 0.00 34.04 2.62
683 694 1.957877 ACCCGACATCTAGCTAAGAGC 59.042 52.381 0.00 0.00 42.84 4.09
898 909 8.970859 AAAATAAGAGAGAGAGAGAGAGAGAG 57.029 38.462 0.00 0.00 0.00 3.20
899 910 7.921041 AATAAGAGAGAGAGAGAGAGAGAGA 57.079 40.000 0.00 0.00 0.00 3.10
900 911 5.867903 AAGAGAGAGAGAGAGAGAGAGAG 57.132 47.826 0.00 0.00 0.00 3.20
901 912 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
902 913 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
903 914 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
904 915 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
905 916 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
906 917 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1034 1045 2.442236 GATCAAGGGAGCCAATTGGA 57.558 50.000 29.02 4.56 37.39 3.53
1059 1070 3.908103 TGGCTTACTGTCTTCCTAACCTT 59.092 43.478 0.00 0.00 0.00 3.50
1283 1294 0.108329 ACGGTCGGTTTCATGCCTAG 60.108 55.000 0.00 0.00 0.00 3.02
1330 1341 8.176365 GCTCTTTGCTAGCTTCATAATCATATG 58.824 37.037 17.23 0.00 37.61 1.78
1407 1418 2.171209 CTGATCAGGTGGGCACGTCA 62.171 60.000 15.38 0.00 0.00 4.35
1585 1600 0.592637 CATTGTGGTGTGCGTGTGAT 59.407 50.000 0.00 0.00 0.00 3.06
1605 1620 1.612442 GTACAGGTGGAGGGGCTCA 60.612 63.158 0.00 0.00 31.08 4.26
1903 1967 7.707893 ACAGATTGTTTGAAAGGATCAGTTTTG 59.292 33.333 0.00 0.00 39.77 2.44
1904 1968 6.703165 AGATTGTTTGAAAGGATCAGTTTTGC 59.297 34.615 0.00 0.00 39.77 3.68
2063 2154 3.078097 TGCAACAATACCGCAGTTGTAT 58.922 40.909 0.00 0.00 43.31 2.29
2073 2164 1.464687 CGCAGTTGTATGTGCAAGCTC 60.465 52.381 0.00 0.00 39.83 4.09
2085 2176 3.005684 TGTGCAAGCTCTTTTTATGGGTG 59.994 43.478 0.00 0.00 0.00 4.61
2087 2178 2.867429 CAAGCTCTTTTTATGGGTGCG 58.133 47.619 0.00 0.00 0.00 5.34
2164 2255 5.053811 TGAAACACGCTCTCAACATAGAAA 58.946 37.500 0.00 0.00 0.00 2.52
2176 2586 8.824159 TCTCAACATAGAAAAGAAGTTCTCTG 57.176 34.615 5.70 0.77 38.75 3.35
2284 2700 4.253685 GTTTCGAAATCATCTGGGTCTCA 58.746 43.478 14.69 0.00 0.00 3.27
2318 2734 6.560003 TCTTCAGATAAATACAGAAGGCCA 57.440 37.500 5.01 0.00 37.04 5.36
2330 2746 3.137360 ACAGAAGGCCAAAGAGAGTTCTT 59.863 43.478 5.01 0.00 45.51 2.52
2427 2843 5.941555 AGAATGGGTGAACTAAGGAGTAG 57.058 43.478 0.00 0.00 33.58 2.57
2469 2885 4.447138 TTCTAAAAGAACAGAAGGGGCA 57.553 40.909 0.00 0.00 0.00 5.36
2512 2929 7.712639 GCATTATGACAGAGGAGATTGTAGAAA 59.287 37.037 0.00 0.00 0.00 2.52
2594 3011 2.753452 CGGATCACTAGCGGTGGTATAT 59.247 50.000 2.42 0.34 45.38 0.86
2595 3012 3.943381 CGGATCACTAGCGGTGGTATATA 59.057 47.826 2.42 0.00 45.38 0.86
2596 3013 4.035324 CGGATCACTAGCGGTGGTATATAG 59.965 50.000 2.42 0.00 45.38 1.31
2620 3037 7.677892 AGTATAATTTAGGCACCTTACCTAGC 58.322 38.462 0.00 0.00 40.80 3.42
2685 3111 5.733226 TGCATATACACGAGACAAAATGG 57.267 39.130 0.00 0.00 0.00 3.16
2687 3113 4.814234 GCATATACACGAGACAAAATGGGA 59.186 41.667 0.00 0.00 0.00 4.37
2688 3114 5.470098 GCATATACACGAGACAAAATGGGAT 59.530 40.000 0.00 0.00 0.00 3.85
2689 3115 6.649141 GCATATACACGAGACAAAATGGGATA 59.351 38.462 0.00 0.00 0.00 2.59
2690 3116 7.360101 GCATATACACGAGACAAAATGGGATAC 60.360 40.741 0.00 0.00 0.00 2.24
2715 3141 9.955102 ACCCCCTTCGTAAATTAATATAAGATC 57.045 33.333 0.00 0.00 0.00 2.75
2974 3401 5.874810 TGTTATCCTTTGATCACTGTAGCAC 59.125 40.000 0.00 0.00 32.18 4.40
3014 3441 5.975693 AAAAGATTCGTGATAGGGCAAAA 57.024 34.783 0.00 0.00 0.00 2.44
3115 3548 6.219473 TGATTGTGTTTCTTCAGAGAGTCTC 58.781 40.000 12.54 12.54 32.44 3.36
3274 3707 4.857679 AGTGGTTCTGGAGTAGTAGTAGG 58.142 47.826 0.00 0.00 0.00 3.18
3275 3708 4.291777 AGTGGTTCTGGAGTAGTAGTAGGT 59.708 45.833 0.00 0.00 0.00 3.08
3298 3731 0.180406 CTACCTAAAGCGGGGCACAT 59.820 55.000 0.00 0.00 0.00 3.21
3299 3732 1.414919 CTACCTAAAGCGGGGCACATA 59.585 52.381 0.00 0.00 0.00 2.29
3300 3733 0.843984 ACCTAAAGCGGGGCACATAT 59.156 50.000 0.00 0.00 0.00 1.78
3301 3734 2.051692 ACCTAAAGCGGGGCACATATA 58.948 47.619 0.00 0.00 0.00 0.86
3302 3735 2.642807 ACCTAAAGCGGGGCACATATAT 59.357 45.455 0.00 0.00 0.00 0.86
3303 3736 3.841845 ACCTAAAGCGGGGCACATATATA 59.158 43.478 0.00 0.00 0.00 0.86
3304 3737 4.473559 ACCTAAAGCGGGGCACATATATAT 59.526 41.667 0.00 0.00 0.00 0.86
3332 3765 4.940463 TCCCATAGTGTAAACATCGTAGC 58.060 43.478 0.00 0.00 0.00 3.58
3362 3795 6.662414 AACACATCATGGATACTGTAAACG 57.338 37.500 0.00 0.00 37.61 3.60
3563 3996 0.463474 GCTTCTGATCACCTGCTCCC 60.463 60.000 0.00 0.00 0.00 4.30
3564 3997 1.202330 CTTCTGATCACCTGCTCCCT 58.798 55.000 0.00 0.00 0.00 4.20
3577 4010 1.437986 CTCCCTTCCGTCCATCGTC 59.562 63.158 0.00 0.00 37.94 4.20
3631 4068 4.077184 GCATCCACCGACCCACGA 62.077 66.667 0.00 0.00 45.77 4.35
3659 4097 4.283678 CGATCGATCGGCTCCTTATATTC 58.716 47.826 34.54 0.67 45.93 1.75
3738 4177 7.661847 AGATATATATCACGCGATCTATCCACA 59.338 37.037 21.95 0.00 35.17 4.17
3819 4270 8.243961 ACTTTCTATGTATGAGTATCTGTGCT 57.756 34.615 0.00 0.00 34.92 4.40
3843 4408 5.262009 TGTGATGGACTAGCTACACTAACT 58.738 41.667 10.25 0.00 0.00 2.24
3922 4487 3.023949 GCAGGTGATCTGTCCGGCT 62.024 63.158 15.25 0.00 45.08 5.52
3923 4488 1.599047 CAGGTGATCTGTCCGGCTT 59.401 57.895 0.00 0.00 38.64 4.35
3999 4564 1.003118 GGGCCTGACAGAACATGTACA 59.997 52.381 0.84 0.00 44.17 2.90
4044 4609 3.280211 TGCACATCAGGCATGCAC 58.720 55.556 21.36 9.10 44.17 4.57
4121 4686 3.119637 CGACCAAAACCGCCATTAATTCT 60.120 43.478 0.00 0.00 0.00 2.40
4172 4737 4.339530 TGAGATTCAGAGGTTACTCCATCG 59.660 45.833 0.00 0.00 45.11 3.84
4177 4742 0.530870 GAGGTTACTCCATCGCAGGC 60.531 60.000 0.00 0.00 37.79 4.85
4221 4786 4.571984 GTGAATGGACAATGATCATCGTCA 59.428 41.667 24.45 13.24 0.00 4.35
4258 4823 2.299013 CGATGAGGTCCCGGAATCATTA 59.701 50.000 0.73 0.00 32.68 1.90
4274 4839 3.197265 TCATTACGAGATCGACCGTGTA 58.803 45.455 16.36 0.49 43.02 2.90
4275 4840 3.811497 TCATTACGAGATCGACCGTGTAT 59.189 43.478 16.36 8.96 43.02 2.29
4289 4854 2.199236 CGTGTATCCGGTTAAAGGAGC 58.801 52.381 0.00 3.86 41.66 4.70
4294 4859 3.864789 ATCCGGTTAAAGGAGCATCAT 57.135 42.857 0.00 0.00 41.66 2.45
4342 4909 0.412244 TAGTAGTGCACCAGTCCCCT 59.588 55.000 14.63 1.70 0.00 4.79
4346 4913 4.269523 TGCACCAGTCCCCTGCAC 62.270 66.667 0.00 0.00 36.00 4.57
4349 4916 2.448542 ACCAGTCCCCTGCACTGT 60.449 61.111 1.16 0.00 39.84 3.55
4355 4922 2.501723 CAGTCCCCTGCACTGTACTAAT 59.498 50.000 0.00 0.00 37.15 1.73
4381 4948 8.946085 TCTACCAGTTTAGCATTAAAATGTCTG 58.054 33.333 4.71 6.03 41.09 3.51
4382 4949 7.759489 ACCAGTTTAGCATTAAAATGTCTGA 57.241 32.000 4.71 0.00 41.09 3.27
4383 4950 8.177119 ACCAGTTTAGCATTAAAATGTCTGAA 57.823 30.769 4.71 3.42 41.09 3.02
4384 4951 8.637986 ACCAGTTTAGCATTAAAATGTCTGAAA 58.362 29.630 4.71 0.00 41.09 2.69
4385 4952 9.474920 CCAGTTTAGCATTAAAATGTCTGAAAA 57.525 29.630 4.71 0.15 41.09 2.29
4407 4974 3.996150 AAACCTTGACTTCGTACTCGA 57.004 42.857 0.00 0.00 44.66 4.04
4422 4989 6.088824 TCGTACTCGAAGTCTGAAATAAACC 58.911 40.000 0.00 0.00 43.34 3.27
4423 4990 5.287992 CGTACTCGAAGTCTGAAATAAACCC 59.712 44.000 0.00 0.00 39.71 4.11
4424 4991 5.485209 ACTCGAAGTCTGAAATAAACCCT 57.515 39.130 0.00 0.00 0.00 4.34
4425 4992 6.600882 ACTCGAAGTCTGAAATAAACCCTA 57.399 37.500 0.00 0.00 0.00 3.53
4426 4993 7.001099 ACTCGAAGTCTGAAATAAACCCTAA 57.999 36.000 0.00 0.00 0.00 2.69
4427 4994 7.447594 ACTCGAAGTCTGAAATAAACCCTAAA 58.552 34.615 0.00 0.00 0.00 1.85
4428 4995 7.387122 ACTCGAAGTCTGAAATAAACCCTAAAC 59.613 37.037 0.00 0.00 0.00 2.01
4429 4996 7.447594 TCGAAGTCTGAAATAAACCCTAAACT 58.552 34.615 0.00 0.00 0.00 2.66
4430 4997 7.935210 TCGAAGTCTGAAATAAACCCTAAACTT 59.065 33.333 0.00 0.00 0.00 2.66
4431 4998 8.228464 CGAAGTCTGAAATAAACCCTAAACTTC 58.772 37.037 0.00 0.00 36.92 3.01
4432 4999 8.990163 AAGTCTGAAATAAACCCTAAACTTCA 57.010 30.769 0.00 0.00 0.00 3.02
4433 5000 8.990163 AGTCTGAAATAAACCCTAAACTTCAA 57.010 30.769 0.00 0.00 0.00 2.69
4434 5001 9.416284 AGTCTGAAATAAACCCTAAACTTCAAA 57.584 29.630 0.00 0.00 0.00 2.69
4437 5004 9.639601 CTGAAATAAACCCTAAACTTCAAATCC 57.360 33.333 0.00 0.00 0.00 3.01
4438 5005 9.374711 TGAAATAAACCCTAAACTTCAAATCCT 57.625 29.630 0.00 0.00 0.00 3.24
4446 5013 9.374711 ACCCTAAACTTCAAATCCTTAAAATCA 57.625 29.630 0.00 0.00 0.00 2.57
4447 5014 9.860898 CCCTAAACTTCAAATCCTTAAAATCAG 57.139 33.333 0.00 0.00 0.00 2.90
4448 5015 9.358872 CCTAAACTTCAAATCCTTAAAATCAGC 57.641 33.333 0.00 0.00 0.00 4.26
4449 5016 9.912634 CTAAACTTCAAATCCTTAAAATCAGCA 57.087 29.630 0.00 0.00 0.00 4.41
4450 5017 8.593492 AAACTTCAAATCCTTAAAATCAGCAC 57.407 30.769 0.00 0.00 0.00 4.40
4451 5018 7.530426 ACTTCAAATCCTTAAAATCAGCACT 57.470 32.000 0.00 0.00 0.00 4.40
4452 5019 7.597386 ACTTCAAATCCTTAAAATCAGCACTC 58.403 34.615 0.00 0.00 0.00 3.51
4453 5020 7.449704 ACTTCAAATCCTTAAAATCAGCACTCT 59.550 33.333 0.00 0.00 0.00 3.24
4454 5021 7.149569 TCAAATCCTTAAAATCAGCACTCTG 57.850 36.000 0.00 0.00 41.67 3.35
4455 5022 6.716628 TCAAATCCTTAAAATCAGCACTCTGT 59.283 34.615 0.00 0.00 41.10 3.41
4456 5023 6.749923 AATCCTTAAAATCAGCACTCTGTC 57.250 37.500 0.00 0.00 41.10 3.51
4457 5024 5.489792 TCCTTAAAATCAGCACTCTGTCT 57.510 39.130 0.00 0.00 41.10 3.41
4458 5025 5.869579 TCCTTAAAATCAGCACTCTGTCTT 58.130 37.500 0.00 0.00 41.10 3.01
4459 5026 7.004555 TCCTTAAAATCAGCACTCTGTCTTA 57.995 36.000 0.00 0.00 41.10 2.10
4460 5027 7.624549 TCCTTAAAATCAGCACTCTGTCTTAT 58.375 34.615 0.00 0.00 41.10 1.73
4461 5028 7.766278 TCCTTAAAATCAGCACTCTGTCTTATC 59.234 37.037 0.00 0.00 41.10 1.75
4462 5029 7.768120 CCTTAAAATCAGCACTCTGTCTTATCT 59.232 37.037 0.00 0.00 41.10 1.98
4463 5030 9.809096 CTTAAAATCAGCACTCTGTCTTATCTA 57.191 33.333 0.00 0.00 41.10 1.98
4466 5033 8.885494 AAATCAGCACTCTGTCTTATCTAATC 57.115 34.615 0.00 0.00 41.10 1.75
4467 5034 6.398234 TCAGCACTCTGTCTTATCTAATCC 57.602 41.667 0.00 0.00 41.10 3.01
4468 5035 5.303078 TCAGCACTCTGTCTTATCTAATCCC 59.697 44.000 0.00 0.00 41.10 3.85
4469 5036 4.279671 AGCACTCTGTCTTATCTAATCCCG 59.720 45.833 0.00 0.00 0.00 5.14
4470 5037 4.559704 GCACTCTGTCTTATCTAATCCCGG 60.560 50.000 0.00 0.00 0.00 5.73
4471 5038 4.585162 CACTCTGTCTTATCTAATCCCGGT 59.415 45.833 0.00 0.00 0.00 5.28
4472 5039 5.069251 CACTCTGTCTTATCTAATCCCGGTT 59.931 44.000 0.00 0.00 0.00 4.44
4473 5040 5.661759 ACTCTGTCTTATCTAATCCCGGTTT 59.338 40.000 0.00 0.00 0.00 3.27
4474 5041 6.837568 ACTCTGTCTTATCTAATCCCGGTTTA 59.162 38.462 0.00 0.00 0.00 2.01
4475 5042 7.509659 ACTCTGTCTTATCTAATCCCGGTTTAT 59.490 37.037 0.00 0.00 0.00 1.40
4476 5043 7.893658 TCTGTCTTATCTAATCCCGGTTTATC 58.106 38.462 0.00 0.00 0.00 1.75
4477 5044 7.001099 TGTCTTATCTAATCCCGGTTTATCC 57.999 40.000 0.00 0.00 0.00 2.59
4478 5045 6.013984 TGTCTTATCTAATCCCGGTTTATCCC 60.014 42.308 0.00 0.00 0.00 3.85
4485 5052 2.593420 CGGTTTATCCCGGCCCTT 59.407 61.111 0.00 0.00 44.32 3.95
4486 5053 1.525306 CGGTTTATCCCGGCCCTTC 60.525 63.158 0.00 0.00 44.32 3.46
4487 5054 1.920532 GGTTTATCCCGGCCCTTCT 59.079 57.895 0.00 0.00 0.00 2.85
4488 5055 0.257905 GGTTTATCCCGGCCCTTCTT 59.742 55.000 0.00 0.00 0.00 2.52
4489 5056 1.389555 GTTTATCCCGGCCCTTCTTG 58.610 55.000 0.00 0.00 0.00 3.02
4490 5057 0.257616 TTTATCCCGGCCCTTCTTGG 59.742 55.000 0.00 0.00 0.00 3.61
4497 5064 2.351276 GCCCTTCTTGGCCGAGAA 59.649 61.111 29.90 29.90 46.11 2.87
4502 5069 1.884235 CTTCTTGGCCGAGAAGTTGT 58.116 50.000 39.17 0.00 44.82 3.32
4503 5070 2.222027 CTTCTTGGCCGAGAAGTTGTT 58.778 47.619 39.17 0.00 44.82 2.83
4504 5071 2.341846 TCTTGGCCGAGAAGTTGTTT 57.658 45.000 21.16 0.00 0.00 2.83
4505 5072 1.946768 TCTTGGCCGAGAAGTTGTTTG 59.053 47.619 21.16 0.00 0.00 2.93
4506 5073 1.676006 CTTGGCCGAGAAGTTGTTTGT 59.324 47.619 15.76 0.00 0.00 2.83
4507 5074 1.305201 TGGCCGAGAAGTTGTTTGTC 58.695 50.000 0.00 0.00 0.00 3.18
4508 5075 1.134220 TGGCCGAGAAGTTGTTTGTCT 60.134 47.619 0.00 0.00 0.00 3.41
4509 5076 1.531578 GGCCGAGAAGTTGTTTGTCTC 59.468 52.381 0.00 0.00 35.47 3.36
4510 5077 2.484889 GCCGAGAAGTTGTTTGTCTCT 58.515 47.619 0.00 0.00 36.46 3.10
4511 5078 2.221981 GCCGAGAAGTTGTTTGTCTCTG 59.778 50.000 0.00 0.00 36.46 3.35
4512 5079 2.221981 CCGAGAAGTTGTTTGTCTCTGC 59.778 50.000 0.00 0.00 36.46 4.26
4513 5080 2.221981 CGAGAAGTTGTTTGTCTCTGCC 59.778 50.000 0.00 0.00 36.46 4.85
4514 5081 2.213499 AGAAGTTGTTTGTCTCTGCCG 58.787 47.619 0.00 0.00 0.00 5.69
4515 5082 1.264288 GAAGTTGTTTGTCTCTGCCGG 59.736 52.381 0.00 0.00 0.00 6.13
4516 5083 0.535102 AGTTGTTTGTCTCTGCCGGG 60.535 55.000 2.18 0.00 0.00 5.73
4517 5084 0.534203 GTTGTTTGTCTCTGCCGGGA 60.534 55.000 2.18 0.00 0.00 5.14
4518 5085 0.400213 TTGTTTGTCTCTGCCGGGAT 59.600 50.000 2.18 0.00 0.00 3.85
4519 5086 0.400213 TGTTTGTCTCTGCCGGGATT 59.600 50.000 2.18 0.00 0.00 3.01
4520 5087 0.804989 GTTTGTCTCTGCCGGGATTG 59.195 55.000 2.18 0.00 0.00 2.67
4521 5088 0.960364 TTTGTCTCTGCCGGGATTGC 60.960 55.000 2.18 0.00 0.00 3.56
4522 5089 2.123248 TTGTCTCTGCCGGGATTGCA 62.123 55.000 2.18 0.00 37.17 4.08
4523 5090 2.109126 GTCTCTGCCGGGATTGCAC 61.109 63.158 2.18 0.00 34.46 4.57
4524 5091 2.270205 CTCTGCCGGGATTGCACT 59.730 61.111 2.18 0.00 34.46 4.40
4525 5092 1.817099 CTCTGCCGGGATTGCACTC 60.817 63.158 2.18 0.00 34.46 3.51
4526 5093 3.197790 CTGCCGGGATTGCACTCG 61.198 66.667 2.18 0.00 34.46 4.18
4527 5094 3.958147 CTGCCGGGATTGCACTCGT 62.958 63.158 2.18 0.00 34.46 4.18
4528 5095 3.499737 GCCGGGATTGCACTCGTG 61.500 66.667 2.18 0.00 31.23 4.35
4529 5096 2.819595 CCGGGATTGCACTCGTGG 60.820 66.667 0.00 0.00 31.23 4.94
4530 5097 3.499737 CGGGATTGCACTCGTGGC 61.500 66.667 0.00 0.00 0.00 5.01
4531 5098 2.359850 GGGATTGCACTCGTGGCA 60.360 61.111 0.00 0.00 40.00 4.92
4532 5099 2.401766 GGGATTGCACTCGTGGCAG 61.402 63.158 0.00 0.00 43.05 4.85
4533 5100 1.375908 GGATTGCACTCGTGGCAGA 60.376 57.895 0.00 0.00 43.05 4.26
4534 5101 1.364626 GGATTGCACTCGTGGCAGAG 61.365 60.000 10.98 10.98 43.05 3.35
4535 5102 0.390340 GATTGCACTCGTGGCAGAGA 60.390 55.000 17.16 6.68 43.05 3.10
4536 5103 0.251354 ATTGCACTCGTGGCAGAGAT 59.749 50.000 17.16 2.08 43.05 2.75
4537 5104 0.671472 TTGCACTCGTGGCAGAGATG 60.671 55.000 17.16 12.91 43.05 2.90
4538 5105 1.079543 GCACTCGTGGCAGAGATGT 60.080 57.895 17.16 5.49 40.57 3.06
4539 5106 1.357258 GCACTCGTGGCAGAGATGTG 61.357 60.000 17.16 14.90 40.57 3.21
4540 5107 0.738762 CACTCGTGGCAGAGATGTGG 60.739 60.000 17.16 0.00 40.57 4.17
4541 5108 1.812922 CTCGTGGCAGAGATGTGGC 60.813 63.158 7.85 0.00 40.57 5.01
4546 5113 3.179925 GGCAGAGATGTGGCAATCA 57.820 52.632 10.74 0.00 42.50 2.57
4547 5114 0.737219 GGCAGAGATGTGGCAATCAC 59.263 55.000 10.74 5.97 46.23 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 0.321564 CCATGACGGTGCCTTCAAGA 60.322 55.000 1.51 0.00 0.00 3.02
97 98 1.218047 CGTCTCGGAGGGCAATGAA 59.782 57.895 4.96 0.00 0.00 2.57
117 119 0.810648 TCATGGTTTTCATCCGCAGC 59.189 50.000 0.00 0.00 32.92 5.25
120 122 2.301346 AGGATCATGGTTTTCATCCGC 58.699 47.619 0.00 0.00 39.98 5.54
124 126 6.495872 CCAATCCATAGGATCATGGTTTTCAT 59.504 38.462 10.92 0.00 42.27 2.57
141 143 2.595463 CGCCATCGCCCAATCCAT 60.595 61.111 0.00 0.00 0.00 3.41
161 163 0.106149 GAAGGACACCACACCGAAGT 59.894 55.000 0.00 0.00 0.00 3.01
177 179 2.031682 CGAAAGTGGTGCCTTCAAGAAG 60.032 50.000 2.83 2.83 38.14 2.85
189 191 0.321653 GACATGGCCTCGAAAGTGGT 60.322 55.000 3.32 0.00 46.17 4.16
192 194 3.842869 GAGACATGGCCTCGAAAGT 57.157 52.632 3.32 0.00 0.00 2.66
204 206 0.525668 GCCGAACATCGACGAGACAT 60.526 55.000 3.01 0.00 43.74 3.06
210 212 0.572590 GATGAAGCCGAACATCGACG 59.427 55.000 0.58 0.00 43.74 5.12
266 268 5.957771 AAATAGAGCACCATTAGAGGTCA 57.042 39.130 0.00 0.00 40.77 4.02
275 277 5.918608 ACGACATAGAAAATAGAGCACCAT 58.081 37.500 0.00 0.00 0.00 3.55
283 285 7.072177 TCCAAGCAAACGACATAGAAAATAG 57.928 36.000 0.00 0.00 0.00 1.73
301 303 1.072331 TCACTCCAAAGGACTCCAAGC 59.928 52.381 0.00 0.00 0.00 4.01
303 305 2.711009 ACATCACTCCAAAGGACTCCAA 59.289 45.455 0.00 0.00 0.00 3.53
329 331 4.142315 CCGGATGCAAAGATGTTGAAGAAT 60.142 41.667 0.00 0.00 0.00 2.40
337 339 0.323725 AAGGCCGGATGCAAAGATGT 60.324 50.000 5.05 0.00 43.89 3.06
340 342 1.678635 CCAAGGCCGGATGCAAAGA 60.679 57.895 5.05 0.00 43.89 2.52
346 348 2.438434 GACACCCAAGGCCGGATG 60.438 66.667 5.05 0.00 0.00 3.51
354 356 0.664761 CAACAGCACAGACACCCAAG 59.335 55.000 0.00 0.00 0.00 3.61
359 361 2.095263 ACAAACACAACAGCACAGACAC 60.095 45.455 0.00 0.00 0.00 3.67
363 365 3.606846 CGGATACAAACACAACAGCACAG 60.607 47.826 0.00 0.00 0.00 3.66
400 409 9.938280 CCCCACTTTATAGATAAATCAACGATA 57.062 33.333 0.00 0.00 32.36 2.92
401 410 7.390718 GCCCCACTTTATAGATAAATCAACGAT 59.609 37.037 0.00 0.00 32.36 3.73
408 417 6.206829 GCTTTCGCCCCACTTTATAGATAAAT 59.793 38.462 0.00 0.00 32.36 1.40
427 436 0.882927 TTGGAAGTCGGTGGCTTTCG 60.883 55.000 0.00 0.00 0.00 3.46
432 441 0.734889 CATGATTGGAAGTCGGTGGC 59.265 55.000 0.00 0.00 0.00 5.01
457 466 9.179909 TCTCAGAGAGAACCTACATTAAACTAG 57.820 37.037 0.00 0.00 35.59 2.57
464 473 7.732222 AGAAATCTCAGAGAGAACCTACATT 57.268 36.000 6.24 0.00 42.27 2.71
541 552 4.101741 GTCACATAGGCCAGAGTTATCCTT 59.898 45.833 5.01 0.00 0.00 3.36
550 561 3.500448 TGTTTTGTCACATAGGCCAGA 57.500 42.857 5.01 0.00 0.00 3.86
606 617 9.505995 TTGATTGTTACTTTCTTTTACGGAAAC 57.494 29.630 0.00 0.00 0.00 2.78
610 621 7.114388 GCCTTTGATTGTTACTTTCTTTTACGG 59.886 37.037 0.00 0.00 0.00 4.02
616 627 7.014615 ACAGATGCCTTTGATTGTTACTTTCTT 59.985 33.333 0.00 0.00 0.00 2.52
618 629 6.583806 CACAGATGCCTTTGATTGTTACTTTC 59.416 38.462 0.00 0.00 0.00 2.62
622 633 5.376854 ACACAGATGCCTTTGATTGTTAC 57.623 39.130 0.00 0.00 0.00 2.50
891 902 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
892 903 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
893 904 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
894 905 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
895 906 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
896 907 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
897 908 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
898 909 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
899 910 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
900 911 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
901 912 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
902 913 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
903 914 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
904 915 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
905 916 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
906 917 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1034 1045 4.162509 GGTTAGGAAGACAGTAAGCCATCT 59.837 45.833 0.00 0.00 0.00 2.90
1059 1070 4.398358 GTGTAGTAGTGATCTGGCACACTA 59.602 45.833 11.21 11.21 44.06 2.74
1257 1268 2.593436 AAACCGACCGTGGGCTTG 60.593 61.111 0.00 0.00 0.00 4.01
1283 1294 1.802553 TACCTCCTCAGCCCCAATAC 58.197 55.000 0.00 0.00 0.00 1.89
1348 1359 9.671279 ATCAAAGGCATCGATATGTAATTGATA 57.329 29.630 15.64 0.00 37.96 2.15
1407 1418 1.598130 GCCAACTCTTGCCGTCACT 60.598 57.895 0.00 0.00 0.00 3.41
1585 1600 2.609610 GCCCCTCCACCTGTACCA 60.610 66.667 0.00 0.00 0.00 3.25
1605 1620 3.622060 CTCCCCCGCCAACATCGTT 62.622 63.158 0.00 0.00 0.00 3.85
1903 1967 3.131755 AGATTAACCTACCACTACCACGC 59.868 47.826 0.00 0.00 0.00 5.34
1904 1968 4.996788 AGATTAACCTACCACTACCACG 57.003 45.455 0.00 0.00 0.00 4.94
2024 2111 6.620678 TGTTGCAGGCTAATTAATCTCAAAC 58.379 36.000 0.00 0.00 0.00 2.93
2063 2154 3.005684 CACCCATAAAAAGAGCTTGCACA 59.994 43.478 0.00 0.00 0.00 4.57
2073 2164 4.635765 TCTCAGATTCGCACCCATAAAAAG 59.364 41.667 0.00 0.00 0.00 2.27
2085 2176 7.062839 CAGGCTATTAAGTATTCTCAGATTCGC 59.937 40.741 0.00 0.00 0.00 4.70
2164 2255 7.410120 AAACCACAAATTCAGAGAACTTCTT 57.590 32.000 0.00 0.00 32.41 2.52
2224 2638 6.677781 TGTATGGATTAGTTAAGCTTGTGC 57.322 37.500 9.86 0.00 40.05 4.57
2256 2672 5.476599 ACCCAGATGATTTCGAAACAAATGA 59.523 36.000 13.81 0.00 0.00 2.57
2257 2673 5.713025 ACCCAGATGATTTCGAAACAAATG 58.287 37.500 13.81 14.17 0.00 2.32
2258 2674 5.711976 AGACCCAGATGATTTCGAAACAAAT 59.288 36.000 13.81 7.10 0.00 2.32
2260 2676 4.651778 AGACCCAGATGATTTCGAAACAA 58.348 39.130 13.81 4.69 0.00 2.83
2262 2678 4.253685 TGAGACCCAGATGATTTCGAAAC 58.746 43.478 13.81 8.03 0.00 2.78
2264 2680 4.551702 TTGAGACCCAGATGATTTCGAA 57.448 40.909 0.00 0.00 0.00 3.71
2265 2681 4.697514 GATTGAGACCCAGATGATTTCGA 58.302 43.478 0.00 0.00 0.00 3.71
2266 2682 3.492383 CGATTGAGACCCAGATGATTTCG 59.508 47.826 0.00 0.00 0.00 3.46
2267 2683 4.272018 CACGATTGAGACCCAGATGATTTC 59.728 45.833 0.00 0.00 0.00 2.17
2268 2684 4.194640 CACGATTGAGACCCAGATGATTT 58.805 43.478 0.00 0.00 0.00 2.17
2284 2700 6.992063 ATTTATCTGAAGAAGCACACGATT 57.008 33.333 0.00 0.00 0.00 3.34
2409 2825 6.499350 ACAATAACTACTCCTTAGTTCACCCA 59.501 38.462 0.00 0.00 46.44 4.51
2469 2885 1.529244 GCCACTGCCTTTCCACACT 60.529 57.895 0.00 0.00 0.00 3.55
2512 2929 4.122776 GTTCGTGTGCAAGATGATATCCT 58.877 43.478 0.00 0.00 0.00 3.24
2594 3011 8.810041 GCTAGGTAAGGTGCCTAAATTATACTA 58.190 37.037 0.00 0.00 38.05 1.82
2595 3012 7.513091 AGCTAGGTAAGGTGCCTAAATTATACT 59.487 37.037 0.00 0.00 38.05 2.12
2596 3013 7.677892 AGCTAGGTAAGGTGCCTAAATTATAC 58.322 38.462 0.00 0.00 38.05 1.47
2689 3115 9.955102 GATCTTATATTAATTTACGAAGGGGGT 57.045 33.333 0.00 0.00 0.00 4.95
2754 3180 9.667107 CAATGAAGTATTCCCTCTGTAAACTAA 57.333 33.333 0.00 0.00 46.93 2.24
2755 3181 8.822805 ACAATGAAGTATTCCCTCTGTAAACTA 58.177 33.333 0.00 0.00 46.93 2.24
2756 3182 7.690256 ACAATGAAGTATTCCCTCTGTAAACT 58.310 34.615 0.00 0.00 46.93 2.66
2757 3183 7.923414 ACAATGAAGTATTCCCTCTGTAAAC 57.077 36.000 0.00 0.00 46.93 2.01
2758 3184 9.832445 GATACAATGAAGTATTCCCTCTGTAAA 57.168 33.333 0.00 0.00 46.93 2.01
2759 3185 9.213777 AGATACAATGAAGTATTCCCTCTGTAA 57.786 33.333 0.00 0.00 46.93 2.41
2760 3186 8.783660 AGATACAATGAAGTATTCCCTCTGTA 57.216 34.615 0.00 0.00 46.93 2.74
2761 3187 7.682787 AGATACAATGAAGTATTCCCTCTGT 57.317 36.000 0.00 0.00 46.93 3.41
2762 3188 9.650539 CATAGATACAATGAAGTATTCCCTCTG 57.349 37.037 0.00 0.00 46.93 3.35
2763 3189 9.386122 ACATAGATACAATGAAGTATTCCCTCT 57.614 33.333 0.00 0.00 46.93 3.69
3014 3441 5.262009 TGCATAGGCGTCTACTATATCCTT 58.738 41.667 0.00 0.00 45.35 3.36
3115 3548 2.730715 GCTAGCTGTCGTCTGAAGTCTG 60.731 54.545 7.70 0.00 0.00 3.51
3274 3707 1.472201 GCCCCGCTTTAGGTAGTACAC 60.472 57.143 2.06 0.00 0.00 2.90
3275 3708 0.826062 GCCCCGCTTTAGGTAGTACA 59.174 55.000 2.06 0.00 0.00 2.90
3310 3743 4.498513 CGCTACGATGTTTACACTATGGGA 60.499 45.833 0.00 0.00 0.00 4.37
3350 3783 4.913345 GGCCAACAAAACGTTTACAGTATC 59.087 41.667 15.03 6.40 34.86 2.24
3577 4010 2.370824 GATCGAGCACTTGCATGGCG 62.371 60.000 3.62 2.14 45.16 5.69
3659 4097 2.611518 GTCTCATCGTTCACCCTTCAG 58.388 52.381 0.00 0.00 0.00 3.02
3806 4257 3.515104 TCCATCACAAGCACAGATACTCA 59.485 43.478 0.00 0.00 0.00 3.41
3819 4270 5.715279 AGTTAGTGTAGCTAGTCCATCACAA 59.285 40.000 11.23 3.15 0.00 3.33
3843 4408 2.262603 CTGCTGCTGCTACCACGA 59.737 61.111 17.00 0.00 40.48 4.35
3870 4435 0.250166 GGCACCGGTTTGAGTAGTGT 60.250 55.000 2.97 0.00 0.00 3.55
3871 4436 0.953960 GGGCACCGGTTTGAGTAGTG 60.954 60.000 2.97 0.00 40.86 2.74
3999 4564 1.199558 GTCTCTGTAACTCCTTCGCGT 59.800 52.381 5.77 0.00 0.00 6.01
4121 4686 1.220749 GCCTGAGGATACAACGCCA 59.779 57.895 0.65 0.00 41.41 5.69
4258 4823 0.942962 GGATACACGGTCGATCTCGT 59.057 55.000 5.77 5.77 40.80 4.18
4274 4839 3.480470 CATGATGCTCCTTTAACCGGAT 58.520 45.455 9.46 0.00 0.00 4.18
4275 4840 2.421388 CCATGATGCTCCTTTAACCGGA 60.421 50.000 9.46 0.00 0.00 5.14
4289 4854 1.475280 CAAAGCTCACACCCCATGATG 59.525 52.381 0.00 0.00 0.00 3.07
4294 4859 2.391130 ACCCAAAGCTCACACCCCA 61.391 57.895 0.00 0.00 0.00 4.96
4342 4909 5.995565 AACTGGTAGATTAGTACAGTGCA 57.004 39.130 0.00 0.00 0.00 4.57
4355 4922 8.946085 CAGACATTTTAATGCTAAACTGGTAGA 58.054 33.333 2.46 0.00 40.04 2.59
4385 4952 4.685924 TCGAGTACGAAGTCAAGGTTTTT 58.314 39.130 0.00 0.00 45.74 1.94
4386 4953 4.311816 TCGAGTACGAAGTCAAGGTTTT 57.688 40.909 0.00 0.00 45.74 2.43
4387 4954 3.996150 TCGAGTACGAAGTCAAGGTTT 57.004 42.857 0.00 0.00 45.74 3.27
4399 4966 5.287992 GGGTTTATTTCAGACTTCGAGTACG 59.712 44.000 0.00 0.00 41.26 3.67
4400 4967 6.396450 AGGGTTTATTTCAGACTTCGAGTAC 58.604 40.000 0.00 0.00 0.00 2.73
4401 4968 6.600882 AGGGTTTATTTCAGACTTCGAGTA 57.399 37.500 0.00 0.00 0.00 2.59
4402 4969 5.485209 AGGGTTTATTTCAGACTTCGAGT 57.515 39.130 0.00 0.00 0.00 4.18
4403 4970 7.603024 AGTTTAGGGTTTATTTCAGACTTCGAG 59.397 37.037 0.00 0.00 0.00 4.04
4404 4971 7.447594 AGTTTAGGGTTTATTTCAGACTTCGA 58.552 34.615 0.00 0.00 0.00 3.71
4405 4972 7.668525 AGTTTAGGGTTTATTTCAGACTTCG 57.331 36.000 0.00 0.00 0.00 3.79
4406 4973 9.063615 TGAAGTTTAGGGTTTATTTCAGACTTC 57.936 33.333 0.00 0.00 39.55 3.01
4407 4974 8.990163 TGAAGTTTAGGGTTTATTTCAGACTT 57.010 30.769 0.00 0.00 0.00 3.01
4408 4975 8.990163 TTGAAGTTTAGGGTTTATTTCAGACT 57.010 30.769 0.00 0.00 0.00 3.24
4411 4978 9.639601 GGATTTGAAGTTTAGGGTTTATTTCAG 57.360 33.333 0.00 0.00 0.00 3.02
4412 4979 9.374711 AGGATTTGAAGTTTAGGGTTTATTTCA 57.625 29.630 0.00 0.00 0.00 2.69
4420 4987 9.374711 TGATTTTAAGGATTTGAAGTTTAGGGT 57.625 29.630 0.00 0.00 0.00 4.34
4421 4988 9.860898 CTGATTTTAAGGATTTGAAGTTTAGGG 57.139 33.333 0.00 0.00 0.00 3.53
4422 4989 9.358872 GCTGATTTTAAGGATTTGAAGTTTAGG 57.641 33.333 0.00 0.00 0.00 2.69
4423 4990 9.912634 TGCTGATTTTAAGGATTTGAAGTTTAG 57.087 29.630 0.00 0.00 0.00 1.85
4424 4991 9.691362 GTGCTGATTTTAAGGATTTGAAGTTTA 57.309 29.630 0.00 0.00 0.00 2.01
4425 4992 8.424133 AGTGCTGATTTTAAGGATTTGAAGTTT 58.576 29.630 0.00 0.00 0.00 2.66
4426 4993 7.955918 AGTGCTGATTTTAAGGATTTGAAGTT 58.044 30.769 0.00 0.00 0.00 2.66
4427 4994 7.449704 AGAGTGCTGATTTTAAGGATTTGAAGT 59.550 33.333 0.00 0.00 0.00 3.01
4428 4995 7.754027 CAGAGTGCTGATTTTAAGGATTTGAAG 59.246 37.037 0.00 0.00 45.17 3.02
4429 4996 7.231317 ACAGAGTGCTGATTTTAAGGATTTGAA 59.769 33.333 0.00 0.00 45.17 2.69
4430 4997 6.716628 ACAGAGTGCTGATTTTAAGGATTTGA 59.283 34.615 0.00 0.00 45.17 2.69
4431 4998 6.917533 ACAGAGTGCTGATTTTAAGGATTTG 58.082 36.000 0.00 0.00 45.17 2.32
4432 4999 6.944862 AGACAGAGTGCTGATTTTAAGGATTT 59.055 34.615 0.00 0.00 45.17 2.17
4433 5000 6.479884 AGACAGAGTGCTGATTTTAAGGATT 58.520 36.000 0.00 0.00 45.17 3.01
4434 5001 6.059787 AGACAGAGTGCTGATTTTAAGGAT 57.940 37.500 0.00 0.00 45.17 3.24
4435 5002 5.489792 AGACAGAGTGCTGATTTTAAGGA 57.510 39.130 0.00 0.00 45.17 3.36
4436 5003 7.768120 AGATAAGACAGAGTGCTGATTTTAAGG 59.232 37.037 0.00 0.00 45.17 2.69
4437 5004 8.715191 AGATAAGACAGAGTGCTGATTTTAAG 57.285 34.615 0.00 0.00 45.17 1.85
4440 5007 9.323985 GATTAGATAAGACAGAGTGCTGATTTT 57.676 33.333 0.00 0.00 45.17 1.82
4441 5008 7.930865 GGATTAGATAAGACAGAGTGCTGATTT 59.069 37.037 0.00 0.00 45.17 2.17
4442 5009 7.441017 GGATTAGATAAGACAGAGTGCTGATT 58.559 38.462 0.00 0.00 45.17 2.57
4443 5010 6.014669 GGGATTAGATAAGACAGAGTGCTGAT 60.015 42.308 0.00 0.00 45.17 2.90
4444 5011 5.303078 GGGATTAGATAAGACAGAGTGCTGA 59.697 44.000 0.00 0.00 45.17 4.26
4446 5013 4.279671 CGGGATTAGATAAGACAGAGTGCT 59.720 45.833 0.00 0.00 0.00 4.40
4447 5014 4.551388 CGGGATTAGATAAGACAGAGTGC 58.449 47.826 0.00 0.00 0.00 4.40
4448 5015 4.585162 ACCGGGATTAGATAAGACAGAGTG 59.415 45.833 6.32 0.00 0.00 3.51
4449 5016 4.805744 ACCGGGATTAGATAAGACAGAGT 58.194 43.478 6.32 0.00 0.00 3.24
4450 5017 5.793030 AACCGGGATTAGATAAGACAGAG 57.207 43.478 6.32 0.00 0.00 3.35
4451 5018 7.039223 GGATAAACCGGGATTAGATAAGACAGA 60.039 40.741 6.32 0.00 0.00 3.41
4452 5019 7.097834 GGATAAACCGGGATTAGATAAGACAG 58.902 42.308 6.32 0.00 0.00 3.51
4453 5020 6.013984 GGGATAAACCGGGATTAGATAAGACA 60.014 42.308 6.32 0.00 40.11 3.41
4454 5021 6.404708 GGGATAAACCGGGATTAGATAAGAC 58.595 44.000 6.32 0.00 40.11 3.01
4455 5022 6.616237 GGGATAAACCGGGATTAGATAAGA 57.384 41.667 6.32 0.00 40.11 2.10
4469 5036 0.257905 AAGAAGGGCCGGGATAAACC 59.742 55.000 2.18 0.00 38.08 3.27
4470 5037 1.389555 CAAGAAGGGCCGGGATAAAC 58.610 55.000 2.18 0.00 0.00 2.01
4471 5038 0.257616 CCAAGAAGGGCCGGGATAAA 59.742 55.000 2.18 0.00 0.00 1.40
4472 5039 1.919771 CCAAGAAGGGCCGGGATAA 59.080 57.895 2.18 0.00 0.00 1.75
4473 5040 3.655358 CCAAGAAGGGCCGGGATA 58.345 61.111 2.18 0.00 0.00 2.59
4481 5048 4.625800 CTTCTCGGCCAAGAAGGG 57.374 61.111 23.67 1.85 45.61 3.95
4484 5051 2.341846 AACAACTTCTCGGCCAAGAA 57.658 45.000 5.87 5.87 34.22 2.52
4485 5052 1.946768 CAAACAACTTCTCGGCCAAGA 59.053 47.619 2.24 0.00 0.00 3.02
4486 5053 1.676006 ACAAACAACTTCTCGGCCAAG 59.324 47.619 2.24 0.82 0.00 3.61
4487 5054 1.673920 GACAAACAACTTCTCGGCCAA 59.326 47.619 2.24 0.00 0.00 4.52
4488 5055 1.134220 AGACAAACAACTTCTCGGCCA 60.134 47.619 2.24 0.00 0.00 5.36
4489 5056 1.531578 GAGACAAACAACTTCTCGGCC 59.468 52.381 0.00 0.00 0.00 6.13
4490 5057 2.221981 CAGAGACAAACAACTTCTCGGC 59.778 50.000 0.00 0.00 40.68 5.54
4491 5058 2.221981 GCAGAGACAAACAACTTCTCGG 59.778 50.000 0.00 0.00 40.68 4.63
4492 5059 2.221981 GGCAGAGACAAACAACTTCTCG 59.778 50.000 0.00 0.00 40.68 4.04
4493 5060 2.221981 CGGCAGAGACAAACAACTTCTC 59.778 50.000 0.00 0.00 36.76 2.87
4494 5061 2.213499 CGGCAGAGACAAACAACTTCT 58.787 47.619 0.00 0.00 0.00 2.85
4495 5062 1.264288 CCGGCAGAGACAAACAACTTC 59.736 52.381 0.00 0.00 0.00 3.01
4496 5063 1.308998 CCGGCAGAGACAAACAACTT 58.691 50.000 0.00 0.00 0.00 2.66
4497 5064 0.535102 CCCGGCAGAGACAAACAACT 60.535 55.000 0.00 0.00 0.00 3.16
4498 5065 0.534203 TCCCGGCAGAGACAAACAAC 60.534 55.000 0.00 0.00 0.00 3.32
4499 5066 0.400213 ATCCCGGCAGAGACAAACAA 59.600 50.000 0.00 0.00 0.00 2.83
4500 5067 0.400213 AATCCCGGCAGAGACAAACA 59.600 50.000 0.00 0.00 0.00 2.83
4501 5068 0.804989 CAATCCCGGCAGAGACAAAC 59.195 55.000 0.00 0.00 0.00 2.93
4502 5069 0.960364 GCAATCCCGGCAGAGACAAA 60.960 55.000 0.00 0.00 0.00 2.83
4503 5070 1.377202 GCAATCCCGGCAGAGACAA 60.377 57.895 0.00 0.00 0.00 3.18
4504 5071 2.268920 GCAATCCCGGCAGAGACA 59.731 61.111 0.00 0.00 0.00 3.41
4505 5072 2.109126 GTGCAATCCCGGCAGAGAC 61.109 63.158 0.00 0.00 42.85 3.36
4506 5073 2.244117 GAGTGCAATCCCGGCAGAGA 62.244 60.000 1.86 0.00 42.85 3.10
4507 5074 1.817099 GAGTGCAATCCCGGCAGAG 60.817 63.158 1.86 0.00 42.85 3.35
4508 5075 2.268920 GAGTGCAATCCCGGCAGA 59.731 61.111 1.86 0.00 42.85 4.26
4509 5076 3.197790 CGAGTGCAATCCCGGCAG 61.198 66.667 8.83 0.00 42.85 4.85
4510 5077 4.015406 ACGAGTGCAATCCCGGCA 62.015 61.111 8.83 0.00 39.32 5.69
4511 5078 3.499737 CACGAGTGCAATCCCGGC 61.500 66.667 8.83 0.00 0.00 6.13
4512 5079 2.819595 CCACGAGTGCAATCCCGG 60.820 66.667 8.83 5.33 0.00 5.73
4513 5080 3.499737 GCCACGAGTGCAATCCCG 61.500 66.667 8.83 0.59 0.00 5.14
4514 5081 2.359850 TGCCACGAGTGCAATCCC 60.360 61.111 8.83 0.00 35.40 3.85
4515 5082 1.364626 CTCTGCCACGAGTGCAATCC 61.365 60.000 8.83 0.00 38.46 3.01
4516 5083 0.390340 TCTCTGCCACGAGTGCAATC 60.390 55.000 3.54 3.54 38.46 2.67
4517 5084 0.251354 ATCTCTGCCACGAGTGCAAT 59.749 50.000 0.00 0.00 38.46 3.56
4518 5085 0.671472 CATCTCTGCCACGAGTGCAA 60.671 55.000 0.00 0.00 38.46 4.08
4519 5086 1.079612 CATCTCTGCCACGAGTGCA 60.080 57.895 0.00 0.00 37.17 4.57
4520 5087 1.079543 ACATCTCTGCCACGAGTGC 60.080 57.895 0.00 0.00 32.83 4.40
4521 5088 0.738762 CCACATCTCTGCCACGAGTG 60.739 60.000 0.00 0.00 32.83 3.51
4522 5089 1.593787 CCACATCTCTGCCACGAGT 59.406 57.895 0.00 0.00 32.83 4.18
4523 5090 1.812922 GCCACATCTCTGCCACGAG 60.813 63.158 0.00 0.00 0.00 4.18
4524 5091 2.110757 TTGCCACATCTCTGCCACGA 62.111 55.000 0.00 0.00 0.00 4.35
4525 5092 1.028330 ATTGCCACATCTCTGCCACG 61.028 55.000 0.00 0.00 0.00 4.94
4526 5093 0.737219 GATTGCCACATCTCTGCCAC 59.263 55.000 0.00 0.00 0.00 5.01
4527 5094 0.328926 TGATTGCCACATCTCTGCCA 59.671 50.000 0.00 0.00 0.00 4.92
4528 5095 0.737219 GTGATTGCCACATCTCTGCC 59.263 55.000 0.00 0.00 45.03 4.85


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

AutoCloner maintained by Alex Coulton.