Multiple sequence alignment - TraesCS3D01G412500

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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 TraesCS3D01G412500 chr3D 100.000 7025 0 0 961 7985 524864513 524871537 0.000000e+00 12973.0
1 TraesCS3D01G412500 chr3D 100.000 816 0 0 1 816 524863553 524864368 0.000000e+00 1507.0
2 TraesCS3D01G412500 chr3D 87.629 194 22 1 7581 7774 524870561 524870752 2.900000e-54 224.0
3 TraesCS3D01G412500 chr3D 87.629 194 22 1 7009 7200 524871133 524871326 2.900000e-54 224.0
4 TraesCS3D01G412500 chr3A 94.563 4764 176 26 961 5681 659392805 659397528 0.000000e+00 7286.0
5 TraesCS3D01G412500 chr3A 94.783 1725 72 12 5719 7433 659397525 659399241 0.000000e+00 2671.0
6 TraesCS3D01G412500 chr3A 93.483 491 24 6 329 815 659392322 659392808 0.000000e+00 723.0
7 TraesCS3D01G412500 chr3A 83.301 509 62 15 7478 7982 659399242 659399731 1.580000e-121 448.0
8 TraesCS3D01G412500 chr3A 89.728 331 30 3 1 327 659390526 659390856 3.450000e-113 420.0
9 TraesCS3D01G412500 chr3A 81.127 355 49 13 7201 7547 659399482 659399826 1.320000e-67 268.0
10 TraesCS3D01G412500 chr3A 86.449 214 24 5 6995 7207 659399324 659399533 6.230000e-56 230.0
11 TraesCS3D01G412500 chr3A 86.082 194 22 2 7581 7774 659398821 659399009 3.780000e-48 204.0
12 TraesCS3D01G412500 chr3A 89.431 123 11 2 13 134 532312171 532312292 3.860000e-33 154.0
13 TraesCS3D01G412500 chr3B 95.669 3025 103 11 1064 4081 692835249 692838252 0.000000e+00 4835.0
14 TraesCS3D01G412500 chr3B 93.121 2980 132 32 5027 7985 692839235 692842162 0.000000e+00 4300.0
15 TraesCS3D01G412500 chr3B 92.351 889 30 9 4079 4937 692838365 692839245 0.000000e+00 1230.0
16 TraesCS3D01G412500 chr3B 94.982 279 7 4 488 759 692834694 692834972 1.590000e-116 431.0
17 TraesCS3D01G412500 chr3B 87.681 276 30 3 1 273 692238201 692238475 1.290000e-82 318.0
18 TraesCS3D01G412500 chr3B 86.598 194 21 2 7581 7774 692841213 692841401 8.120000e-50 209.0
19 TraesCS3D01G412500 chr3B 90.476 63 5 1 266 327 692556219 692556281 1.850000e-11 82.4
20 TraesCS3D01G412500 chr3B 94.118 51 2 1 329 379 59894294 59894343 8.590000e-10 76.8
21 TraesCS3D01G412500 chr1D 85.827 127 17 1 13 138 380582421 380582547 5.030000e-27 134.0
22 TraesCS3D01G412500 chr1D 85.714 126 14 4 16 138 211492900 211492776 6.500000e-26 130.0
23 TraesCS3D01G412500 chr6B 85.714 126 12 2 16 137 422722614 422722491 2.340000e-25 128.0
24 TraesCS3D01G412500 chr5D 85.156 128 16 3 13 138 88138290 88138416 2.340000e-25 128.0
25 TraesCS3D01G412500 chr5D 84.956 113 14 2 329 441 423077214 423077105 2.360000e-20 111.0
26 TraesCS3D01G412500 chr2D 85.156 128 16 3 13 138 584893180 584893306 2.340000e-25 128.0
27 TraesCS3D01G412500 chr1A 85.039 127 18 1 13 138 433731107 433731233 2.340000e-25 128.0
28 TraesCS3D01G412500 chr1B 87.850 107 12 1 329 435 24636118 24636013 3.030000e-24 124.0
29 TraesCS3D01G412500 chr4A 86.364 110 14 1 329 438 735098471 735098579 1.410000e-22 119.0
30 TraesCS3D01G412500 chr4A 92.593 54 4 0 502 555 664059330 664059383 2.390000e-10 78.7
31 TraesCS3D01G412500 chr6A 85.455 110 13 2 329 438 325258325 325258431 2.360000e-20 111.0


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 TraesCS3D01G412500 chr3D 524863553 524871537 7984 False 3732.00 12973 93.8145 1 7985 4 chr3D.!!$F1 7984
1 TraesCS3D01G412500 chr3A 659390526 659399826 9300 False 1531.25 7286 88.6895 1 7982 8 chr3A.!!$F2 7981
2 TraesCS3D01G412500 chr3B 692834694 692842162 7468 False 2201.00 4835 92.5442 488 7985 5 chr3B.!!$F4 7497

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
812 2311 0.342313 TCCTAAACCCCTCTCCTCCC 59.658 60.000 0.00 0.00 0.00 4.30 F
1151 2650 0.172803 CCCGACGAGTAAGTTCCCTG 59.827 60.000 0.00 0.00 0.00 4.45 F
2077 3578 0.944386 TGTCTTGCGACCTTTTCTGC 59.056 50.000 0.00 0.00 39.47 4.26 F
2975 4481 1.528586 CGTCTTCTTTGTGCTCACTGG 59.471 52.381 1.47 0.00 0.00 4.00 F
3654 5160 1.807226 GATAAACTTGCGCCCCACC 59.193 57.895 4.18 0.00 0.00 4.61 F
4621 6274 2.556622 TGTTTTTGCCCTTCGATCTTCC 59.443 45.455 0.00 0.00 0.00 3.46 F
5610 7291 0.817229 GCAGGATTCTAGTGGCAGCC 60.817 60.000 3.66 3.66 0.00 4.85 F
6927 8617 0.375803 GCGTGTTCCTTGTGTTCGTT 59.624 50.000 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 3338 0.043053 CGTGAAATGTGCTATCCGCG 60.043 55.000 0.00 0.00 43.27 6.46 R
3058 4564 0.534873 GACTCCTGGAGAACTCTGGC 59.465 60.000 29.71 0.00 33.32 4.85 R
3127 4633 1.341209 TGCGACTCAGTATGCCATAGG 59.659 52.381 0.00 0.00 34.76 2.57 R
4381 6034 1.892474 GGGAATGGCAGCTAAAACACA 59.108 47.619 0.00 0.00 0.00 3.72 R
5500 7180 1.597027 AAAAGCCTCCGTCGGTGTG 60.597 57.895 11.88 4.46 0.00 3.82 R
6428 8115 0.036483 TGCAAGCGATACTTCCTGCA 60.036 50.000 0.00 0.00 36.04 4.41 R
6961 8651 0.663153 GCAGTCTTCTGTTTTGCCGT 59.337 50.000 0.00 0.00 43.05 5.68 R
7728 9420 1.592223 GGAGAGGTCCGTCCACTTG 59.408 63.158 8.16 0.00 37.26 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
89 92 2.171448 CAGGGTCATCTCTCGGGAAAAT 59.829 50.000 0.00 0.00 0.00 1.82
93 96 3.369471 GGTCATCTCTCGGGAAAATGACA 60.369 47.826 28.32 4.45 45.04 3.58
95 98 4.878397 GTCATCTCTCGGGAAAATGACAAT 59.122 41.667 25.02 0.00 43.53 2.71
103 106 9.884465 CTCTCGGGAAAATGACAATAATTATTC 57.116 33.333 7.76 0.00 0.00 1.75
134 138 3.297736 ACCGGATCACTAAAGGGACTAG 58.702 50.000 9.46 0.00 38.49 2.57
138 142 4.202030 CGGATCACTAAAGGGACTAGTCAC 60.202 50.000 23.91 21.11 38.49 3.67
143 147 0.896226 AAAGGGACTAGTCACGCTCC 59.104 55.000 23.91 14.97 38.49 4.70
149 153 2.223618 GGACTAGTCACGCTCCAGATTC 60.224 54.545 23.91 0.00 0.00 2.52
157 161 1.287730 CGCTCCAGATTCGGCTATGC 61.288 60.000 0.00 0.00 0.00 3.14
171 175 0.600557 CTATGCTGGCCTCTAGGTCG 59.399 60.000 3.32 0.00 44.44 4.79
185 189 1.153229 GGTCGTTGGGCCTGGATAC 60.153 63.158 4.53 0.00 0.00 2.24
195 199 2.814023 CCTGGATACGGCTCTCTGT 58.186 57.895 0.00 0.00 43.74 3.41
198 202 1.268352 CTGGATACGGCTCTCTGTAGC 59.732 57.143 0.00 0.00 39.18 3.58
213 217 1.676529 TGTAGCGAGGTGATAGTCTGC 59.323 52.381 0.00 0.00 0.00 4.26
222 226 1.136305 GTGATAGTCTGCGGTGGCTTA 59.864 52.381 0.00 0.00 40.82 3.09
242 246 5.674569 GCTTACTTCATCGTCGGTGTTAGTA 60.675 44.000 14.77 14.77 0.00 1.82
256 260 3.435671 GTGTTAGTATGTGTTGCCACTCC 59.564 47.826 0.00 0.00 42.34 3.85
299 303 4.750098 ACTATGGATTGCGGTTATCGAAAG 59.250 41.667 0.00 0.00 40.16 2.62
315 319 5.432885 TCGAAAGATTTTTGTGAGGGTTC 57.567 39.130 0.00 0.00 33.31 3.62
317 321 5.238650 TCGAAAGATTTTTGTGAGGGTTCTC 59.761 40.000 0.00 0.00 36.38 2.87
318 322 5.239525 CGAAAGATTTTTGTGAGGGTTCTCT 59.760 40.000 0.00 0.00 40.58 3.10
320 324 7.423844 AAAGATTTTTGTGAGGGTTCTCTTT 57.576 32.000 0.00 0.00 40.58 2.52
321 325 6.641169 AGATTTTTGTGAGGGTTCTCTTTC 57.359 37.500 0.00 0.00 40.58 2.62
323 327 3.943671 TTTGTGAGGGTTCTCTTTCCA 57.056 42.857 0.00 0.00 40.58 3.53
324 328 3.492102 TTGTGAGGGTTCTCTTTCCAG 57.508 47.619 0.00 0.00 40.58 3.86
325 329 2.689658 TGTGAGGGTTCTCTTTCCAGA 58.310 47.619 0.00 0.00 40.58 3.86
326 330 3.251484 TGTGAGGGTTCTCTTTCCAGAT 58.749 45.455 0.00 0.00 40.58 2.90
343 1812 5.790593 TCCAGATTTGTTTAGTCGCTTACT 58.209 37.500 0.00 0.00 42.62 2.24
376 1845 0.737019 GGACGGTTGGATTAACGCGA 60.737 55.000 15.93 0.00 40.28 5.87
385 1854 1.283736 GATTAACGCGAACGGATGGT 58.716 50.000 15.93 0.00 46.04 3.55
387 1856 1.072116 TTAACGCGAACGGATGGTCG 61.072 55.000 15.93 0.00 46.04 4.79
806 2305 1.273896 CCCAGTCTCCTAAACCCCTCT 60.274 57.143 0.00 0.00 0.00 3.69
811 2310 1.291335 TCTCCTAAACCCCTCTCCTCC 59.709 57.143 0.00 0.00 0.00 4.30
812 2311 0.342313 TCCTAAACCCCTCTCCTCCC 59.658 60.000 0.00 0.00 0.00 4.30
813 2312 0.694783 CCTAAACCCCTCTCCTCCCC 60.695 65.000 0.00 0.00 0.00 4.81
814 2313 0.694783 CTAAACCCCTCTCCTCCCCC 60.695 65.000 0.00 0.00 0.00 5.40
1035 2534 4.475444 CCCCTGGCCGTCCTCCTA 62.475 72.222 0.00 0.00 0.00 2.94
1038 2537 2.128507 CCTGGCCGTCCTCCTACTC 61.129 68.421 0.00 0.00 0.00 2.59
1149 2648 1.514553 CCCCGACGAGTAAGTTCCC 59.485 63.158 0.00 0.00 0.00 3.97
1151 2650 0.172803 CCCGACGAGTAAGTTCCCTG 59.827 60.000 0.00 0.00 0.00 4.45
1157 2656 2.437895 GTAAGTTCCCTGGCCGCC 60.438 66.667 1.04 1.04 0.00 6.13
1241 2741 3.034878 CGGCTCAGATCGATCCGT 58.965 61.111 21.66 1.12 46.18 4.69
1357 2857 1.350193 CGGTCAGGACGTTCAAGATG 58.650 55.000 0.00 0.00 0.00 2.90
1558 3058 2.093711 TGCTTCTGCTGGTATTCGCTTA 60.094 45.455 0.00 0.00 40.48 3.09
1633 3133 1.021390 GGCTGTGATCAAGGACACCG 61.021 60.000 0.00 0.00 36.35 4.94
1668 3168 3.633065 AGTTCTACTATTCTGTCGGAGGC 59.367 47.826 0.00 0.00 0.00 4.70
1796 3296 6.237901 TGGTAGCTGATAAAGTTGTGTTGAT 58.762 36.000 0.00 0.00 0.00 2.57
1797 3297 6.714810 TGGTAGCTGATAAAGTTGTGTTGATT 59.285 34.615 0.00 0.00 0.00 2.57
1837 3338 4.537015 GCCACAGTGTTGTTTTATCTGAC 58.463 43.478 0.00 0.00 34.62 3.51
1861 3362 3.247411 CGGATAGCACATTTCACGCAATA 59.753 43.478 0.00 0.00 0.00 1.90
1957 3458 8.648968 GCTGTTTAAACTAGAGTTGTCTGATAC 58.351 37.037 18.72 0.00 38.44 2.24
2032 3533 1.143684 ACCAACAGTGCTGAATCCAGT 59.856 47.619 6.17 0.00 42.35 4.00
2077 3578 0.944386 TGTCTTGCGACCTTTTCTGC 59.056 50.000 0.00 0.00 39.47 4.26
2082 3583 2.774439 TGCGACCTTTTCTGCTTTTC 57.226 45.000 0.00 0.00 0.00 2.29
2311 3812 9.781834 GAGATGAAGAAGTCGGATAACTATATG 57.218 37.037 0.00 0.00 0.00 1.78
2340 3841 5.164954 TGTTGTGTCACAAAGCCTTTTAAC 58.835 37.500 19.77 5.19 40.15 2.01
2377 3878 3.645884 CTGAATGCCAGTGAAAACCTTG 58.354 45.455 0.00 0.00 38.10 3.61
2383 3884 2.949644 GCCAGTGAAAACCTTGTACACT 59.050 45.455 0.00 0.00 41.52 3.55
2515 4016 8.728833 AGAGCTTGATTTCAATACAAAAGAGAG 58.271 33.333 0.00 0.00 35.02 3.20
2516 4017 8.401490 AGCTTGATTTCAATACAAAAGAGAGT 57.599 30.769 0.00 0.00 35.02 3.24
2517 4018 8.295288 AGCTTGATTTCAATACAAAAGAGAGTG 58.705 33.333 0.00 0.00 35.02 3.51
2522 4025 9.994432 GATTTCAATACAAAAGAGAGTGGTATG 57.006 33.333 0.00 0.00 0.00 2.39
2619 4124 6.110411 TGCACATGACATGATCTATCATCT 57.890 37.500 22.19 0.00 45.23 2.90
2733 4239 3.990092 TGTGTACGATGTTCTGCTTTCT 58.010 40.909 0.00 0.00 0.00 2.52
2785 4291 4.889409 TGCTTCTTCCAAGTTTCAGTCAAT 59.111 37.500 0.00 0.00 0.00 2.57
2810 4316 8.994429 TTGTGTTTGTTCTGAATTTGTTATGT 57.006 26.923 0.00 0.00 0.00 2.29
2975 4481 1.528586 CGTCTTCTTTGTGCTCACTGG 59.471 52.381 1.47 0.00 0.00 4.00
3127 4633 8.573885 AGGAACTTAGTTACCAAATTGCTAAAC 58.426 33.333 3.33 0.00 27.25 2.01
3183 4689 8.373220 AGTTAGCAGTACTATTTAGTTGGTGTT 58.627 33.333 0.00 0.00 37.73 3.32
3190 4696 9.841295 AGTACTATTTAGTTGGTGTTCTTTGAA 57.159 29.630 0.00 0.00 37.73 2.69
3203 4709 7.505585 TGGTGTTCTTTGAAACTTCTCCATTAT 59.494 33.333 0.00 0.00 0.00 1.28
3240 4746 5.343307 ACTTGCAAGTGAAAATGTTCCTT 57.657 34.783 30.66 0.66 37.98 3.36
3476 4982 2.158385 AGCACCTCCCATAACCAACAAA 60.158 45.455 0.00 0.00 0.00 2.83
3629 5135 7.347252 AGGTAAGTTTTCCTCTCTTTTTCAGT 58.653 34.615 0.00 0.00 0.00 3.41
3654 5160 1.807226 GATAAACTTGCGCCCCACC 59.193 57.895 4.18 0.00 0.00 4.61
3781 5287 3.263425 CCTCCAAAGACCAGCTTAAGGTA 59.737 47.826 6.90 0.00 40.09 3.08
3919 5425 5.643348 TGCACTAATGATTGTTACTGTGAGG 59.357 40.000 0.00 0.00 0.00 3.86
3929 5435 7.706607 TGATTGTTACTGTGAGGAATTCTATCG 59.293 37.037 5.23 0.00 0.00 2.92
3999 5505 4.346734 CTTGTTTCGATACAAGCATGCT 57.653 40.909 27.92 16.30 45.85 3.79
4000 5506 5.469373 CTTGTTTCGATACAAGCATGCTA 57.531 39.130 27.92 5.74 45.85 3.49
4001 5507 6.052840 CTTGTTTCGATACAAGCATGCTAT 57.947 37.500 27.92 15.07 45.85 2.97
4002 5508 7.177498 CTTGTTTCGATACAAGCATGCTATA 57.823 36.000 27.92 16.86 45.85 1.31
4003 5509 7.546778 TTGTTTCGATACAAGCATGCTATAA 57.453 32.000 23.00 9.51 33.31 0.98
4004 5510 7.728847 TGTTTCGATACAAGCATGCTATAAT 57.271 32.000 23.00 14.15 0.00 1.28
4005 5511 8.153479 TGTTTCGATACAAGCATGCTATAATT 57.847 30.769 23.00 0.76 0.00 1.40
4006 5512 8.620416 TGTTTCGATACAAGCATGCTATAATTT 58.380 29.630 23.00 0.00 0.00 1.82
4007 5513 9.107367 GTTTCGATACAAGCATGCTATAATTTC 57.893 33.333 23.00 12.16 0.00 2.17
4008 5514 8.607441 TTCGATACAAGCATGCTATAATTTCT 57.393 30.769 23.00 0.00 0.00 2.52
4009 5515 9.705290 TTCGATACAAGCATGCTATAATTTCTA 57.295 29.630 23.00 3.30 0.00 2.10
4010 5516 9.705290 TCGATACAAGCATGCTATAATTTCTAA 57.295 29.630 23.00 0.00 0.00 2.10
4011 5517 9.746711 CGATACAAGCATGCTATAATTTCTAAC 57.253 33.333 23.00 3.24 0.00 2.34
4013 5519 9.799106 ATACAAGCATGCTATAATTTCTAACCT 57.201 29.630 23.00 0.00 0.00 3.50
4014 5520 8.525290 ACAAGCATGCTATAATTTCTAACCTT 57.475 30.769 23.00 0.00 0.00 3.50
4050 5575 6.500041 TGTGGTACTTTTGTAGTTGCAATTC 58.500 36.000 0.59 0.00 38.33 2.17
4101 5743 6.385843 TGTATATGGTGTGTGTGAAAATTGC 58.614 36.000 0.00 0.00 0.00 3.56
4157 5806 4.624336 TTTGACGCATGTTGTGTTTAGT 57.376 36.364 0.00 0.00 41.77 2.24
4264 5916 2.834549 TCCCCTCAGAGTGAATCTTGTC 59.165 50.000 0.00 0.00 35.47 3.18
4285 5937 3.347077 CAAGTCTTGGGCTCTGATTCT 57.653 47.619 4.52 0.00 0.00 2.40
4289 5941 4.357325 AGTCTTGGGCTCTGATTCTAAGA 58.643 43.478 0.00 3.39 0.00 2.10
4351 6004 8.080417 GGTGTTTACCTCTTGGAACTTATTTTC 58.920 37.037 0.00 0.00 43.97 2.29
4393 6046 6.019640 CCATTGTTTTGTCTGTGTTTTAGCTG 60.020 38.462 0.00 0.00 0.00 4.24
4395 6048 3.708563 TTTGTCTGTGTTTTAGCTGCC 57.291 42.857 0.00 0.00 0.00 4.85
4621 6274 2.556622 TGTTTTTGCCCTTCGATCTTCC 59.443 45.455 0.00 0.00 0.00 3.46
4845 6511 6.919775 ACAGATAAACTAACTCTGACACCT 57.080 37.500 5.84 0.00 38.96 4.00
4865 6531 4.079253 CCTACACCCAAGTAATTGCAACT 58.921 43.478 0.00 0.00 0.00 3.16
4948 6621 7.162082 CCTGTTAGTATGTGGTTCTTCTCTTT 58.838 38.462 0.00 0.00 0.00 2.52
4996 6669 2.821378 TCCTGCATTGTTTCAGTCATGG 59.179 45.455 0.00 0.00 0.00 3.66
4998 6671 3.256383 CCTGCATTGTTTCAGTCATGGAA 59.744 43.478 0.00 0.00 0.00 3.53
5002 6675 4.801891 CATTGTTTCAGTCATGGAACTGG 58.198 43.478 13.06 0.00 44.21 4.00
5160 6839 6.763355 AGATACAAAAGTTTCTCTCTCTGCA 58.237 36.000 0.00 0.00 0.00 4.41
5434 7113 5.444663 ACTCCAGAATTTGTTTTGCTCTC 57.555 39.130 0.00 0.00 0.00 3.20
5463 7142 5.007034 TCTCTCGGCAAATGTTTCCATTAA 58.993 37.500 0.00 0.00 40.42 1.40
5509 7189 1.003851 AGAAAACACACACACCGACG 58.996 50.000 0.00 0.00 0.00 5.12
5563 7243 6.599638 AGGTTATGTATCTTGTTTTCAGGAGC 59.400 38.462 0.00 0.00 39.21 4.70
5584 7265 6.095160 GGAGCTCTTTGATTCACATGATTCTT 59.905 38.462 14.64 0.00 0.00 2.52
5609 7290 1.156645 CGCAGGATTCTAGTGGCAGC 61.157 60.000 0.00 0.00 0.00 5.25
5610 7291 0.817229 GCAGGATTCTAGTGGCAGCC 60.817 60.000 3.66 3.66 0.00 4.85
5627 7308 3.251484 CAGCCCCCTAGAATATCCTTCA 58.749 50.000 0.00 0.00 0.00 3.02
5631 7312 4.043435 GCCCCCTAGAATATCCTTCAATGT 59.957 45.833 0.00 0.00 0.00 2.71
5636 7317 7.290061 CCCTAGAATATCCTTCAATGTTGGAA 58.710 38.462 0.00 0.00 33.20 3.53
5734 7416 3.853831 TTCAAGAGGTTACGCGTGATA 57.146 42.857 24.59 3.96 35.26 2.15
5831 7513 8.387039 AGCTTTAAGAAACTCTAGGAAGGAAAT 58.613 33.333 0.00 0.00 0.00 2.17
5839 7521 5.953571 ACTCTAGGAAGGAAATTTGTTGGT 58.046 37.500 0.00 0.00 0.00 3.67
5861 7544 2.977772 TTTTTGGCCAAGTGAGGTTG 57.022 45.000 19.48 0.00 0.00 3.77
5862 7545 2.151502 TTTTGGCCAAGTGAGGTTGA 57.848 45.000 19.48 0.00 0.00 3.18
5866 7549 1.064017 TGGCCAAGTGAGGTTGAAACT 60.064 47.619 0.61 0.00 0.00 2.66
5892 7575 3.683365 ATCCAGGTGCCAAAACATTTC 57.317 42.857 0.00 0.00 0.00 2.17
5975 7658 7.062605 CCTGTTGTGCTTGAATTTTATGATGTC 59.937 37.037 0.00 0.00 0.00 3.06
5995 7680 3.055530 GTCACTGGTCAGATGTGGAGATT 60.056 47.826 4.84 0.00 33.04 2.40
6015 7700 7.708752 GGAGATTAAGTACCAGAAGATCACTTG 59.291 40.741 0.00 0.00 36.39 3.16
6016 7701 7.560368 AGATTAAGTACCAGAAGATCACTTGG 58.440 38.462 0.00 1.55 36.39 3.61
6168 7855 5.520748 ACCTTTCTGGAACATATGACCTT 57.479 39.130 10.38 0.00 38.20 3.50
6177 7864 5.189180 GGAACATATGACCTTGAGCTTTCT 58.811 41.667 10.38 0.00 0.00 2.52
6211 7898 2.942376 TCAATGGTATGTCGCCACATTC 59.058 45.455 1.22 0.00 40.66 2.67
6384 8071 3.003897 CGTTAGCAAAGTTTAGGCCACAA 59.996 43.478 5.01 0.00 0.00 3.33
6396 8083 3.922171 AGGCCACAAAAGGAGATAGAG 57.078 47.619 5.01 0.00 0.00 2.43
6428 8115 3.397906 GCCAGAGAAGAGGCCACT 58.602 61.111 5.01 0.00 45.18 4.00
6438 8125 0.545309 AGAGGCCACTGCAGGAAGTA 60.545 55.000 19.93 0.00 40.13 2.24
6526 8213 8.056407 ACAATTCCTACTCTTGCTTTATTTCC 57.944 34.615 0.00 0.00 0.00 3.13
6747 8434 0.538584 TCGCATCACTCTTCCATGCT 59.461 50.000 0.00 0.00 40.73 3.79
6927 8617 0.375803 GCGTGTTCCTTGTGTTCGTT 59.624 50.000 0.00 0.00 0.00 3.85
6961 8651 4.141937 CCCTATCTCATCTTTCCAACACGA 60.142 45.833 0.00 0.00 0.00 4.35
7082 8772 2.755655 TGAGATCCTGACCGAGTTCTTC 59.244 50.000 0.00 0.00 0.00 2.87
7083 8773 3.020984 GAGATCCTGACCGAGTTCTTCT 58.979 50.000 0.00 0.00 0.00 2.85
7084 8774 3.436243 AGATCCTGACCGAGTTCTTCTT 58.564 45.455 0.00 0.00 0.00 2.52
7136 8826 1.199097 GTCATTTTGTAGTGGGTGCCG 59.801 52.381 0.00 0.00 0.00 5.69
7222 8912 0.903236 GTGGTAGGACCTCACCTTCC 59.097 60.000 16.47 0.00 44.36 3.46
7259 8949 7.552687 CACTGATGTTTACTAAATAGGCTGGAA 59.447 37.037 0.00 0.00 0.00 3.53
7262 8952 9.474313 TGATGTTTACTAAATAGGCTGGAATTT 57.526 29.630 0.00 0.00 0.00 1.82
7355 9047 7.605691 ACAAACTCACAAAACCAAATTCATTCA 59.394 29.630 0.00 0.00 0.00 2.57
7382 9074 3.495434 ACTCCCCAACGAATTGTAACA 57.505 42.857 0.00 0.00 33.60 2.41
7434 9126 1.965414 TGGGAGCAGAACCAATCCTA 58.035 50.000 0.00 0.00 32.89 2.94
7435 9127 1.839994 TGGGAGCAGAACCAATCCTAG 59.160 52.381 0.00 0.00 32.89 3.02
7451 9143 7.500559 ACCAATCCTAGCATTTCATTCTACTTC 59.499 37.037 0.00 0.00 0.00 3.01
7456 9148 6.535150 CCTAGCATTTCATTCTACTTCGTTCA 59.465 38.462 0.00 0.00 0.00 3.18
7460 9152 6.855914 GCATTTCATTCTACTTCGTTCACAAA 59.144 34.615 0.00 0.00 0.00 2.83
7464 9156 5.818336 TCATTCTACTTCGTTCACAAACCAA 59.182 36.000 0.00 0.00 31.27 3.67
7475 9167 2.632996 TCACAAACCAAACACACCCAAA 59.367 40.909 0.00 0.00 0.00 3.28
7476 9168 2.999355 CACAAACCAAACACACCCAAAG 59.001 45.455 0.00 0.00 0.00 2.77
7478 9170 3.517500 ACAAACCAAACACACCCAAAGAT 59.482 39.130 0.00 0.00 0.00 2.40
7479 9171 4.712337 ACAAACCAAACACACCCAAAGATA 59.288 37.500 0.00 0.00 0.00 1.98
7480 9172 5.187967 ACAAACCAAACACACCCAAAGATAA 59.812 36.000 0.00 0.00 0.00 1.75
7481 9173 6.126911 ACAAACCAAACACACCCAAAGATAAT 60.127 34.615 0.00 0.00 0.00 1.28
7482 9174 6.493189 AACCAAACACACCCAAAGATAATT 57.507 33.333 0.00 0.00 0.00 1.40
7492 9184 7.818930 CACACCCAAAGATAATTAAAGTGCATT 59.181 33.333 0.00 0.00 0.00 3.56
7518 9210 5.616204 GCTGCGTTTTAGTACAAACCTAAGG 60.616 44.000 0.00 0.00 33.71 2.69
7547 9239 8.696175 GGTTTAAATGTATTTTCAGGACAAACG 58.304 33.333 0.00 0.00 0.00 3.60
7556 9248 2.589442 GGACAAACGTGGCCGACA 60.589 61.111 0.00 0.00 45.39 4.35
7578 9270 9.191995 CGACATATACATGTGAGCTAACAATTA 57.808 33.333 8.32 2.77 45.58 1.40
7610 9302 2.345991 GGGCGGTCACAGTTGCTA 59.654 61.111 0.00 0.00 0.00 3.49
7701 9393 7.878495 AGGGACATAAGGGTATCATTTTGTAA 58.122 34.615 0.00 0.00 31.21 2.41
7728 9420 3.451178 TGCCAAGAATCCTGGTACTAGAC 59.549 47.826 7.98 0.00 0.00 2.59
7735 9427 3.820195 TCCTGGTACTAGACAAGTGGA 57.180 47.619 7.98 0.00 39.39 4.02
7736 9428 3.428532 TCCTGGTACTAGACAAGTGGAC 58.571 50.000 7.98 0.00 39.39 4.02
7744 9436 0.178958 AGACAAGTGGACGGACCTCT 60.179 55.000 0.00 0.00 43.32 3.69
7751 9443 0.041238 TGGACGGACCTCTCCTTCAT 59.959 55.000 6.62 0.00 36.69 2.57
7898 9590 7.967890 AACCAAATTCATTCCATTTCAACTC 57.032 32.000 0.00 0.00 0.00 3.01
7902 9594 3.824001 TCATTCCATTTCAACTCCCCA 57.176 42.857 0.00 0.00 0.00 4.96
7936 9628 4.529769 TGAATTGCAACCATTACATCCCAA 59.470 37.500 0.00 0.00 0.00 4.12
7937 9629 5.012458 TGAATTGCAACCATTACATCCCAAA 59.988 36.000 0.00 0.00 0.00 3.28
7938 9630 3.951775 TGCAACCATTACATCCCAAAC 57.048 42.857 0.00 0.00 0.00 2.93
7941 9633 4.101585 TGCAACCATTACATCCCAAACAAA 59.898 37.500 0.00 0.00 0.00 2.83
7942 9634 4.450757 GCAACCATTACATCCCAAACAAAC 59.549 41.667 0.00 0.00 0.00 2.93
7943 9635 4.513198 ACCATTACATCCCAAACAAACG 57.487 40.909 0.00 0.00 0.00 3.60
7961 9666 4.477302 AACGTAGGAACAAAACCAATCG 57.523 40.909 0.00 0.00 0.00 3.34
7963 9668 4.630111 ACGTAGGAACAAAACCAATCGTA 58.370 39.130 0.00 0.00 32.54 3.43
7969 9674 6.811954 AGGAACAAAACCAATCGTAACATTT 58.188 32.000 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 48 2.959707 GTTATCAGATCCACGAGAGGGT 59.040 50.000 0.00 0.00 0.00 4.34
60 63 3.885901 CGAGAGATGACCCTGAGTTATCA 59.114 47.826 0.00 0.00 42.53 2.15
76 79 9.627123 AATAATTATTGTCATTTTCCCGAGAGA 57.373 29.630 9.93 0.00 0.00 3.10
89 92 9.120538 GGTAAAGGAGCAGAATAATTATTGTCA 57.879 33.333 15.39 0.00 0.00 3.58
93 96 7.514721 TCCGGTAAAGGAGCAGAATAATTATT 58.485 34.615 10.51 10.51 34.92 1.40
95 98 6.488769 TCCGGTAAAGGAGCAGAATAATTA 57.511 37.500 0.00 0.00 34.92 1.40
134 138 2.167861 GCCGAATCTGGAGCGTGAC 61.168 63.158 0.00 0.00 0.00 3.67
138 142 1.287730 GCATAGCCGAATCTGGAGCG 61.288 60.000 0.00 0.00 0.00 5.03
143 147 1.233285 GGCCAGCATAGCCGAATCTG 61.233 60.000 0.00 0.00 41.41 2.90
157 161 1.517832 CCAACGACCTAGAGGCCAG 59.482 63.158 5.01 0.00 39.32 4.85
185 189 2.115911 ACCTCGCTACAGAGAGCCG 61.116 63.158 4.61 0.00 40.07 5.52
194 198 1.334239 CGCAGACTATCACCTCGCTAC 60.334 57.143 0.00 0.00 0.00 3.58
195 199 0.945099 CGCAGACTATCACCTCGCTA 59.055 55.000 0.00 0.00 0.00 4.26
198 202 0.248661 CACCGCAGACTATCACCTCG 60.249 60.000 0.00 0.00 0.00 4.63
213 217 1.278238 GACGATGAAGTAAGCCACCG 58.722 55.000 0.00 0.00 0.00 4.94
222 226 4.157289 ACATACTAACACCGACGATGAAGT 59.843 41.667 0.00 1.54 0.00 3.01
263 267 1.298413 CATAGTGAGGACGTCGCCG 60.298 63.158 9.92 0.00 36.18 6.46
266 270 2.732366 CAATCCATAGTGAGGACGTCG 58.268 52.381 9.92 0.00 38.13 5.12
268 272 1.202417 CGCAATCCATAGTGAGGACGT 60.202 52.381 0.00 0.00 38.13 4.34
270 274 1.139058 ACCGCAATCCATAGTGAGGAC 59.861 52.381 2.69 0.00 42.48 3.85
279 283 3.804036 TCTTTCGATAACCGCAATCCAT 58.196 40.909 0.00 0.00 38.37 3.41
299 303 5.301805 TGGAAAGAGAACCCTCACAAAAATC 59.698 40.000 0.00 0.00 41.87 2.17
302 306 4.080015 TCTGGAAAGAGAACCCTCACAAAA 60.080 41.667 0.00 0.00 41.87 2.44
315 319 5.409826 AGCGACTAAACAAATCTGGAAAGAG 59.590 40.000 0.00 0.00 0.00 2.85
317 321 5.613358 AGCGACTAAACAAATCTGGAAAG 57.387 39.130 0.00 0.00 0.00 2.62
318 322 6.708949 AGTAAGCGACTAAACAAATCTGGAAA 59.291 34.615 0.00 0.00 36.27 3.13
320 324 5.790593 AGTAAGCGACTAAACAAATCTGGA 58.209 37.500 0.00 0.00 36.27 3.86
321 325 7.772332 ATAGTAAGCGACTAAACAAATCTGG 57.228 36.000 5.74 0.00 43.96 3.86
323 327 9.530633 CCTAATAGTAAGCGACTAAACAAATCT 57.469 33.333 5.74 0.00 43.96 2.40
324 328 9.525409 TCCTAATAGTAAGCGACTAAACAAATC 57.475 33.333 5.74 0.00 43.96 2.17
325 329 9.310716 GTCCTAATAGTAAGCGACTAAACAAAT 57.689 33.333 5.74 0.00 43.96 2.32
326 330 8.306038 TGTCCTAATAGTAAGCGACTAAACAAA 58.694 33.333 5.74 0.00 43.96 2.83
343 1812 5.662208 TCCAACCGTCCTTATTGTCCTAATA 59.338 40.000 0.00 0.00 0.00 0.98
376 1845 3.005897 CCAATAGATCTCGACCATCCGTT 59.994 47.826 0.00 0.00 0.00 4.44
483 1975 9.415544 GCACTGAATTTTCAATAAAGAGTGAAT 57.584 29.630 0.00 0.00 39.27 2.57
484 1976 7.591057 CGCACTGAATTTTCAATAAAGAGTGAA 59.409 33.333 0.00 0.00 37.86 3.18
485 1977 7.077605 CGCACTGAATTTTCAATAAAGAGTGA 58.922 34.615 0.00 0.00 36.64 3.41
1477 2977 3.490793 ATCGACGCTGCATCCGAGG 62.491 63.158 13.01 5.18 34.40 4.63
1558 3058 4.248859 CGAATCTCAGAACACCATCAAGT 58.751 43.478 0.00 0.00 0.00 3.16
1633 3133 2.159170 AGTAGAACTCCAGCAGCGAATC 60.159 50.000 0.00 0.00 0.00 2.52
1668 3168 1.078567 GACCTTCAGGCTGAGCAGG 60.079 63.158 26.52 26.52 39.32 4.85
1837 3338 0.043053 CGTGAAATGTGCTATCCGCG 60.043 55.000 0.00 0.00 43.27 6.46
1861 3362 4.096984 GCATATTGCACTGCTCTAACCTTT 59.903 41.667 1.98 0.00 44.26 3.11
2077 3578 4.977741 ACATTTGATTTGCAGCGAAAAG 57.022 36.364 0.00 0.00 0.00 2.27
2082 3583 4.039703 CCTGATACATTTGATTTGCAGCG 58.960 43.478 0.00 0.00 0.00 5.18
2311 3812 3.550030 GGCTTTGTGACACAACATGTACC 60.550 47.826 20.46 11.46 43.56 3.34
2340 3841 1.192146 TCAGTTCAACCCTCTCCCCG 61.192 60.000 0.00 0.00 0.00 5.73
2477 3978 3.131709 TCAAGCTCTTCCTGTTTCCAG 57.868 47.619 0.00 0.00 38.50 3.86
2480 3981 5.695851 TGAAATCAAGCTCTTCCTGTTTC 57.304 39.130 0.00 0.00 0.00 2.78
2515 4016 7.392393 AGGGATAAACAACTTGTTACATACCAC 59.608 37.037 21.77 3.10 40.14 4.16
2516 4017 7.463431 AGGGATAAACAACTTGTTACATACCA 58.537 34.615 21.77 2.54 40.14 3.25
2517 4018 7.608761 TGAGGGATAAACAACTTGTTACATACC 59.391 37.037 16.34 16.34 40.14 2.73
2522 4025 5.705905 AGCTGAGGGATAAACAACTTGTTAC 59.294 40.000 7.59 3.43 40.14 2.50
2569 4072 4.996788 AATTCAGATGAATGGAGGTTGC 57.003 40.909 8.76 0.00 43.41 4.17
2619 4124 4.144297 AGACATGGCTGCAACTCTTTTAA 58.856 39.130 0.00 0.00 0.00 1.52
2733 4239 5.695816 GCAACAAATTGTATGAGCCAAGAAA 59.304 36.000 0.00 0.00 38.17 2.52
2785 4291 8.867935 CACATAACAAATTCAGAACAAACACAA 58.132 29.630 0.00 0.00 0.00 3.33
2846 4352 1.496060 ATCAGGACCGCCAATAGTGA 58.504 50.000 0.00 0.00 36.29 3.41
3040 4546 7.630082 ACTCTGGCCAAGTTTAAGTTGATATA 58.370 34.615 7.01 0.00 30.18 0.86
3041 4547 6.485171 ACTCTGGCCAAGTTTAAGTTGATAT 58.515 36.000 7.01 0.00 30.18 1.63
3056 4562 0.906756 CTCCTGGAGAACTCTGGCCA 60.907 60.000 19.13 4.71 0.00 5.36
3058 4564 0.534873 GACTCCTGGAGAACTCTGGC 59.465 60.000 29.71 0.00 33.32 4.85
3127 4633 1.341209 TGCGACTCAGTATGCCATAGG 59.659 52.381 0.00 0.00 34.76 2.57
3183 4689 9.098355 CGTATCATAATGGAGAAGTTTCAAAGA 57.902 33.333 0.00 0.00 0.00 2.52
3190 4696 9.099454 GTTTCTTCGTATCATAATGGAGAAGTT 57.901 33.333 2.84 0.00 36.14 2.66
3203 4709 3.734463 TGCAAGTGGTTTCTTCGTATCA 58.266 40.909 0.00 0.00 0.00 2.15
3476 4982 1.352352 CAGGGATCTGTGGGTTGAGTT 59.648 52.381 0.00 0.00 36.30 3.01
3626 5132 4.318121 GGCGCAAGTTTATCGAGAATACTG 60.318 45.833 10.83 0.00 41.68 2.74
3629 5135 3.128349 GGGCGCAAGTTTATCGAGAATA 58.872 45.455 10.83 0.00 41.68 1.75
3654 5160 7.225538 CACAGGGCAACAGAGACTAATAATAAG 59.774 40.741 0.00 0.00 39.74 1.73
4002 5508 9.646522 ACATAGGATGCATAAAGGTTAGAAATT 57.353 29.630 0.00 0.00 0.00 1.82
4003 5509 9.071276 CACATAGGATGCATAAAGGTTAGAAAT 57.929 33.333 0.00 0.00 0.00 2.17
4004 5510 7.502226 CCACATAGGATGCATAAAGGTTAGAAA 59.498 37.037 0.00 0.00 41.22 2.52
4005 5511 6.998074 CCACATAGGATGCATAAAGGTTAGAA 59.002 38.462 0.00 0.00 41.22 2.10
4006 5512 6.101150 ACCACATAGGATGCATAAAGGTTAGA 59.899 38.462 0.00 0.00 41.22 2.10
4007 5513 6.299141 ACCACATAGGATGCATAAAGGTTAG 58.701 40.000 0.00 0.00 41.22 2.34
4008 5514 6.260700 ACCACATAGGATGCATAAAGGTTA 57.739 37.500 0.00 0.00 41.22 2.85
4009 5515 5.129368 ACCACATAGGATGCATAAAGGTT 57.871 39.130 0.00 0.00 41.22 3.50
4010 5516 4.796110 ACCACATAGGATGCATAAAGGT 57.204 40.909 0.00 0.00 41.22 3.50
4011 5517 5.869579 AGTACCACATAGGATGCATAAAGG 58.130 41.667 0.00 0.00 41.22 3.11
4012 5518 7.807977 AAAGTACCACATAGGATGCATAAAG 57.192 36.000 0.00 0.00 41.22 1.85
4013 5519 7.613801 ACAAAAGTACCACATAGGATGCATAAA 59.386 33.333 0.00 0.00 41.22 1.40
4014 5520 7.116075 ACAAAAGTACCACATAGGATGCATAA 58.884 34.615 0.00 0.00 41.22 1.90
4075 5600 8.187480 GCAATTTTCACACACACCATATACATA 58.813 33.333 0.00 0.00 0.00 2.29
4101 5743 4.171005 CAAGATTGCAGCTAAATGTGGTG 58.829 43.478 0.00 0.00 36.18 4.17
4157 5806 6.422701 CACGAGTTGGAGTTAATTACACTGAA 59.577 38.462 0.00 0.00 0.00 3.02
4246 5898 3.969287 TGGACAAGATTCACTCTGAGG 57.031 47.619 9.85 0.00 33.29 3.86
4285 5937 3.515104 TGCTGTCAGTGGTGATGATCTTA 59.485 43.478 0.93 0.00 34.36 2.10
4289 5941 2.617276 CCTTGCTGTCAGTGGTGATGAT 60.617 50.000 0.93 0.00 34.36 2.45
4381 6034 1.892474 GGGAATGGCAGCTAAAACACA 59.108 47.619 0.00 0.00 0.00 3.72
4393 6046 3.321968 GGAAATGGATGTTAGGGAATGGC 59.678 47.826 0.00 0.00 0.00 4.40
4395 6048 6.040166 CAGAAGGAAATGGATGTTAGGGAATG 59.960 42.308 0.00 0.00 0.00 2.67
4493 6146 2.935481 AAACTAGCGAGTACTTCCCG 57.065 50.000 0.00 0.00 33.58 5.14
4621 6274 7.326454 TGTTCTGAATCCTGAAGAGTAATCTG 58.674 38.462 0.00 0.00 32.11 2.90
4845 6511 5.381757 AGAAGTTGCAATTACTTGGGTGTA 58.618 37.500 6.99 0.00 36.04 2.90
4948 6621 7.800155 TGTTCTCAAACAAATGTCAGATGTA 57.200 32.000 0.00 0.00 42.34 2.29
4996 6669 9.174166 ACTAATATATTGTTCAACACCCAGTTC 57.826 33.333 8.28 0.00 38.74 3.01
4998 6671 8.956426 CAACTAATATATTGTTCAACACCCAGT 58.044 33.333 8.28 0.00 0.00 4.00
5032 6711 8.096414 CCTAAACTTCCATTCCAATTTTCACAT 58.904 33.333 0.00 0.00 0.00 3.21
5033 6712 7.070571 ACCTAAACTTCCATTCCAATTTTCACA 59.929 33.333 0.00 0.00 0.00 3.58
5034 6713 7.441836 ACCTAAACTTCCATTCCAATTTTCAC 58.558 34.615 0.00 0.00 0.00 3.18
5035 6714 7.610580 ACCTAAACTTCCATTCCAATTTTCA 57.389 32.000 0.00 0.00 0.00 2.69
5036 6715 8.367911 AGAACCTAAACTTCCATTCCAATTTTC 58.632 33.333 0.00 0.00 0.00 2.29
5160 6839 3.740115 ACGTAACTTCTGCAGATGGTTT 58.260 40.909 28.24 19.37 0.00 3.27
5407 7086 6.303839 AGCAAAACAAATTCTGGAGTAGGTA 58.696 36.000 0.00 0.00 0.00 3.08
5420 7099 5.471456 AGAGAATGACGAGAGCAAAACAAAT 59.529 36.000 0.00 0.00 0.00 2.32
5434 7113 2.002586 ACATTTGCCGAGAGAATGACG 58.997 47.619 2.66 0.00 35.36 4.35
5500 7180 1.597027 AAAAGCCTCCGTCGGTGTG 60.597 57.895 11.88 4.46 0.00 3.82
5509 7189 3.956744 ACCTTCTATGTCAAAAGCCTCC 58.043 45.455 0.00 0.00 0.00 4.30
5548 7228 4.780815 TCAAAGAGCTCCTGAAAACAAGA 58.219 39.130 10.93 0.00 0.00 3.02
5584 7265 3.687698 GCCACTAGAATCCTGCGTTTTTA 59.312 43.478 0.00 0.00 0.00 1.52
5609 7290 5.850046 ACATTGAAGGATATTCTAGGGGG 57.150 43.478 0.00 0.00 0.00 5.40
5610 7291 6.006449 CCAACATTGAAGGATATTCTAGGGG 58.994 44.000 0.00 0.00 0.00 4.79
5627 7308 6.015856 TGTCAATTCATACGGTTTCCAACATT 60.016 34.615 0.00 0.00 0.00 2.71
5631 7312 4.216687 GGTGTCAATTCATACGGTTTCCAA 59.783 41.667 0.00 0.00 0.00 3.53
5636 7317 4.825085 ACTTTGGTGTCAATTCATACGGTT 59.175 37.500 0.00 0.00 32.28 4.44
5665 7346 9.154632 TCTTATGCTTTCCCTATAATGTAGTCA 57.845 33.333 0.00 0.00 0.00 3.41
5766 7448 8.934023 TGTTTGATTTGTAGGAATAGAAAGGT 57.066 30.769 0.00 0.00 0.00 3.50
5846 7528 1.064017 AGTTTCAACCTCACTTGGCCA 60.064 47.619 0.00 0.00 0.00 5.36
5847 7529 1.692411 AGTTTCAACCTCACTTGGCC 58.308 50.000 0.00 0.00 0.00 5.36
5861 7544 5.036117 TGGCACCTGGATAATCTAGTTTC 57.964 43.478 0.00 0.00 0.00 2.78
5862 7545 5.450818 TTGGCACCTGGATAATCTAGTTT 57.549 39.130 0.00 0.00 0.00 2.66
5866 7549 5.186256 TGTTTTGGCACCTGGATAATCTA 57.814 39.130 0.00 0.00 0.00 1.98
5975 7658 3.623906 AATCTCCACATCTGACCAGTG 57.376 47.619 0.00 0.00 0.00 3.66
5995 7680 5.187186 GTCCCAAGTGATCTTCTGGTACTTA 59.813 44.000 0.00 0.00 31.01 2.24
6015 7700 8.947055 AAAACATGCAAATTAAGATATGTCCC 57.053 30.769 0.00 0.00 0.00 4.46
6168 7855 1.881973 GCATCACCAACAGAAAGCTCA 59.118 47.619 0.00 0.00 0.00 4.26
6177 7864 2.596346 ACCATTGAAGCATCACCAACA 58.404 42.857 0.00 0.00 34.61 3.33
6384 8071 5.305644 ACGGAATATGTGCTCTATCTCCTTT 59.694 40.000 0.00 0.00 0.00 3.11
6428 8115 0.036483 TGCAAGCGATACTTCCTGCA 60.036 50.000 0.00 0.00 36.04 4.41
6438 8125 0.740737 GGCCAGTAAATGCAAGCGAT 59.259 50.000 0.00 0.00 0.00 4.58
6526 8213 6.815641 AGTACAGAAGTGTGATAGCAATTGAG 59.184 38.462 10.34 0.00 37.52 3.02
6604 8291 9.013229 TGTTGAATAAGCATATTCTCAACAACT 57.987 29.630 19.41 0.00 45.11 3.16
6634 8321 3.252701 CCAGAAGCACATTATCAGCATCC 59.747 47.826 0.00 0.00 0.00 3.51
6664 8351 1.409064 TCCCAGACGCATAAGCTACAG 59.591 52.381 0.00 0.00 39.10 2.74
6747 8434 3.441244 CAGTACTGCTGCGATTCCA 57.559 52.632 10.54 0.00 38.52 3.53
6927 8617 1.507742 TGAGATAGGGTCCTATGGCCA 59.492 52.381 8.56 8.56 39.15 5.36
6961 8651 0.663153 GCAGTCTTCTGTTTTGCCGT 59.337 50.000 0.00 0.00 43.05 5.68
7082 8772 2.785477 CTCAAAACTCAAGTTGCGCAAG 59.215 45.455 25.78 14.27 38.44 4.01
7083 8773 2.479389 CCTCAAAACTCAAGTTGCGCAA 60.479 45.455 21.02 21.02 38.44 4.85
7084 8774 1.065401 CCTCAAAACTCAAGTTGCGCA 59.935 47.619 5.66 5.66 38.44 6.09
7136 8826 5.300792 CCACTTCTCTAGTACCAGGATTCTC 59.699 48.000 0.00 0.00 34.56 2.87
7222 8912 4.604843 AAACATCAGTGCGTCATACATG 57.395 40.909 0.00 0.00 0.00 3.21
7355 9047 4.343814 ACAATTCGTTGGGGAGTTCAAATT 59.656 37.500 0.00 0.00 0.00 1.82
7434 9126 5.700832 TGTGAACGAAGTAGAATGAAATGCT 59.299 36.000 0.00 0.00 45.00 3.79
7435 9127 5.927030 TGTGAACGAAGTAGAATGAAATGC 58.073 37.500 0.00 0.00 45.00 3.56
7451 9143 2.255316 GGTGTGTTTGGTTTGTGAACG 58.745 47.619 0.00 0.00 36.61 3.95
7456 9148 2.900546 TCTTTGGGTGTGTTTGGTTTGT 59.099 40.909 0.00 0.00 0.00 2.83
7460 9152 7.604657 TTAATTATCTTTGGGTGTGTTTGGT 57.395 32.000 0.00 0.00 0.00 3.67
7464 9156 7.151976 GCACTTTAATTATCTTTGGGTGTGTT 58.848 34.615 0.00 0.00 0.00 3.32
7492 9184 2.291190 GGTTTGTACTAAAACGCAGCCA 59.709 45.455 0.00 0.00 40.29 4.75
7518 9210 7.662897 TGTCCTGAAAATACATTTAAACCACC 58.337 34.615 0.00 0.00 0.00 4.61
7547 9239 3.059884 CTCACATGTATATGTCGGCCAC 58.940 50.000 2.24 0.25 45.53 5.01
7578 9270 3.486383 ACCGCCCGAAAATTGATGATAT 58.514 40.909 0.00 0.00 0.00 1.63
7631 9323 0.895530 CTCGGTTAGGGTCTCAAGCA 59.104 55.000 0.00 0.00 0.00 3.91
7644 9336 0.736053 TGCGCAAGAAAAACTCGGTT 59.264 45.000 8.16 0.00 43.02 4.44
7701 9393 1.637553 ACCAGGATTCTTGGCACTCAT 59.362 47.619 14.35 0.00 0.00 2.90
7704 9396 2.269940 AGTACCAGGATTCTTGGCACT 58.730 47.619 13.53 13.53 0.00 4.40
7728 9420 1.592223 GGAGAGGTCCGTCCACTTG 59.408 63.158 8.16 0.00 37.26 3.16
7735 9427 4.937612 ATCATACATGAAGGAGAGGTCCGT 60.938 45.833 0.00 0.00 42.48 4.69
7736 9428 3.576118 ATCATACATGAAGGAGAGGTCCG 59.424 47.826 0.00 0.00 42.48 4.79
7744 9436 4.277423 CAGCAATGCATCATACATGAAGGA 59.723 41.667 8.35 0.00 40.69 3.36
7751 9443 7.622893 TTAGTAAACAGCAATGCATCATACA 57.377 32.000 8.35 0.00 0.00 2.29
7803 9495 8.772705 CAGCAAGAATCTGATCTTACTAATTCC 58.227 37.037 0.00 0.00 37.56 3.01
7810 9502 6.038050 CCTTTCCAGCAAGAATCTGATCTTAC 59.962 42.308 0.00 0.00 37.56 2.34
7816 9508 3.795688 ACCTTTCCAGCAAGAATCTGA 57.204 42.857 0.00 0.00 33.54 3.27
7821 9513 4.953579 ACAAGTTAACCTTTCCAGCAAGAA 59.046 37.500 0.88 0.00 0.00 2.52
7826 9518 4.649088 AACACAAGTTAACCTTTCCAGC 57.351 40.909 0.88 0.00 35.85 4.85
7898 9590 3.465871 CAATTCAGTGTTTGGTTTGGGG 58.534 45.455 0.00 0.00 0.00 4.96
7902 9594 3.938334 GGTTGCAATTCAGTGTTTGGTTT 59.062 39.130 0.59 0.00 0.00 3.27
7936 9628 5.388408 TTGGTTTTGTTCCTACGTTTGTT 57.612 34.783 0.00 0.00 0.00 2.83
7937 9629 5.584442 GATTGGTTTTGTTCCTACGTTTGT 58.416 37.500 0.00 0.00 0.00 2.83
7938 9630 4.673311 CGATTGGTTTTGTTCCTACGTTTG 59.327 41.667 0.00 0.00 0.00 2.93
7941 9633 3.469739 ACGATTGGTTTTGTTCCTACGT 58.530 40.909 0.00 0.00 0.00 3.57
7942 9634 5.050227 TGTTACGATTGGTTTTGTTCCTACG 60.050 40.000 0.00 0.00 0.00 3.51
7943 9635 6.303021 TGTTACGATTGGTTTTGTTCCTAC 57.697 37.500 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.