Multiple sequence alignment - TraesCS5B01G075100

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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 TraesCS5B01G075100 chr5B 100.000 6463 0 0 1 6463 89633889 89627427 0.000000e+00 11936.0
1 TraesCS5B01G075100 chr5A 92.916 6183 228 79 105 6109 77091039 77084889 0.000000e+00 8798.0
2 TraesCS5B01G075100 chr5A 93.458 107 7 0 6107 6213 77084766 77084660 6.710000e-35 159.0
3 TraesCS5B01G075100 chr5D 94.221 5710 196 55 533 6148 80704538 80698869 0.000000e+00 8593.0
4 TraesCS5B01G075100 chr5D 90.572 297 18 7 178 469 80704970 80704679 1.020000e-102 385.0
5 TraesCS5B01G075100 chr5D 91.743 109 7 2 1 108 432989614 432989721 4.040000e-32 150.0
6 TraesCS5B01G075100 chr5D 83.951 162 10 2 6146 6294 80696759 80696601 2.430000e-29 141.0
7 TraesCS5B01G075100 chr6B 92.593 108 7 1 1 107 514727168 514727275 3.120000e-33 154.0
8 TraesCS5B01G075100 chr6B 92.771 83 6 0 6291 6373 690883911 690883993 3.170000e-23 121.0
9 TraesCS5B01G075100 chr6B 87.692 65 6 2 6308 6371 662098339 662098276 2.500000e-09 75.0
10 TraesCS5B01G075100 chr4B 93.333 105 6 1 1 104 135811685 135811581 3.120000e-33 154.0
11 TraesCS5B01G075100 chr4B 85.542 83 8 4 6292 6371 643790640 643790559 4.150000e-12 84.2
12 TraesCS5B01G075100 chr4A 81.868 182 33 0 4341 4522 38367601 38367782 3.120000e-33 154.0
13 TraesCS5B01G075100 chr3D 93.333 105 6 1 1 104 498881643 498881539 3.120000e-33 154.0
14 TraesCS5B01G075100 chr3D 85.965 57 6 2 6316 6371 597626404 597626459 7.000000e-05 60.2
15 TraesCS5B01G075100 chr2D 92.453 106 7 1 1 105 498258215 498258320 4.040000e-32 150.0
16 TraesCS5B01G075100 chr1D 91.743 109 7 2 1 107 280936825 280936933 4.040000e-32 150.0
17 TraesCS5B01G075100 chr4D 92.381 105 7 1 1 104 14854225 14854329 1.450000e-31 148.0
18 TraesCS5B01G075100 chrUn 90.909 110 8 2 1 108 334477920 334477811 5.220000e-31 147.0
19 TraesCS5B01G075100 chr3B 90.909 110 8 2 1 108 968129 968020 5.220000e-31 147.0
20 TraesCS5B01G075100 chr3B 92.000 50 2 2 6317 6365 671267940 671267892 1.160000e-07 69.4
21 TraesCS5B01G075100 chr3A 89.474 57 4 2 6316 6371 724396470 724396415 3.230000e-08 71.3
22 TraesCS5B01G075100 chr2B 87.037 54 5 2 6294 6347 226699676 226699625 7.000000e-05 60.2


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 TraesCS5B01G075100 chr5B 89627427 89633889 6462 True 11936.000000 11936 100.000000 1 6463 1 chr5B.!!$R1 6462
1 TraesCS5B01G075100 chr5A 77084660 77091039 6379 True 4478.500000 8798 93.187000 105 6213 2 chr5A.!!$R1 6108
2 TraesCS5B01G075100 chr5D 80696601 80704970 8369 True 3039.666667 8593 89.581333 178 6294 3 chr5D.!!$R1 6116

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
130 131 0.039035 ACAATAGGCGGCCCTTTCAA 59.961 50.000 17.02 0.0 42.87 2.69 F
886 1024 0.178891 ACACACACTCCCCATCCTCT 60.179 55.000 0.00 0.0 0.00 3.69 F
906 1065 1.227118 CACAAACCCAACCAACGCC 60.227 57.895 0.00 0.0 0.00 5.68 F
977 1136 1.772063 GAGCGAGCGAGAGAGGAGTC 61.772 65.000 0.00 0.0 0.00 3.36 F
1405 1599 1.927895 AGATTTAGCTTCGAGCACCG 58.072 50.000 0.00 0.0 45.56 4.94 F
3102 3343 2.428890 AGCTACTACCATCTGCAGTGAC 59.571 50.000 14.67 0.0 0.00 3.67 F
4609 4889 0.739462 TAGGAAATGCGCCACTGACG 60.739 55.000 4.18 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1405 1599 0.108233 AAGCTAGCAGCAGCACTCTC 60.108 55.000 18.83 0.00 45.56 3.20 R
2103 2344 0.314935 TTGCAAGCTTGGCTGCTAAC 59.685 50.000 27.10 8.86 43.24 2.34 R
2104 2345 0.314935 GTTGCAAGCTTGGCTGCTAA 59.685 50.000 27.10 8.41 43.24 3.09 R
3042 3283 0.166814 CAGCTAAGTTGCGAACCAGC 59.833 55.000 11.73 11.73 39.17 4.85 R
3453 3694 2.838202 ACAATGTGAACGGTATCCTCCT 59.162 45.455 0.00 0.00 0.00 3.69 R
5171 5465 0.033504 GTGAGAGTCCAAGTTCGCCA 59.966 55.000 0.00 0.00 0.00 5.69 R
5484 5778 0.181587 TTTTCGCCACACCTCCTTCA 59.818 50.000 0.00 0.00 0.00 3.02 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
21 22 4.489306 CTCCCTCCCTTCGAAATTACTT 57.511 45.455 0.00 0.00 0.00 2.24
22 23 4.192317 CTCCCTCCCTTCGAAATTACTTG 58.808 47.826 0.00 0.00 0.00 3.16
23 24 3.585732 TCCCTCCCTTCGAAATTACTTGT 59.414 43.478 0.00 0.00 0.00 3.16
24 25 3.939592 CCCTCCCTTCGAAATTACTTGTC 59.060 47.826 0.00 0.00 0.00 3.18
25 26 4.564821 CCCTCCCTTCGAAATTACTTGTCA 60.565 45.833 0.00 0.00 0.00 3.58
26 27 4.392138 CCTCCCTTCGAAATTACTTGTCAC 59.608 45.833 0.00 0.00 0.00 3.67
27 28 4.963373 TCCCTTCGAAATTACTTGTCACA 58.037 39.130 0.00 0.00 0.00 3.58
28 29 5.369833 TCCCTTCGAAATTACTTGTCACAA 58.630 37.500 0.00 0.00 0.00 3.33
29 30 5.823570 TCCCTTCGAAATTACTTGTCACAAA 59.176 36.000 0.00 0.00 0.00 2.83
30 31 6.319152 TCCCTTCGAAATTACTTGTCACAAAA 59.681 34.615 0.00 0.00 0.00 2.44
31 32 6.975772 CCCTTCGAAATTACTTGTCACAAAAA 59.024 34.615 0.00 0.00 0.00 1.94
32 33 7.651704 CCCTTCGAAATTACTTGTCACAAAAAT 59.348 33.333 0.00 0.00 0.00 1.82
33 34 9.672086 CCTTCGAAATTACTTGTCACAAAAATA 57.328 29.630 0.00 0.00 0.00 1.40
94 95 5.844301 TTTTTGGACGAGTAATTCCGTAC 57.156 39.130 0.00 0.00 39.30 3.67
95 96 4.517952 TTTGGACGAGTAATTCCGTACA 57.482 40.909 8.28 8.28 46.52 2.90
96 97 3.770263 TGGACGAGTAATTCCGTACAG 57.230 47.619 8.28 0.00 43.77 2.74
97 98 2.424601 TGGACGAGTAATTCCGTACAGG 59.575 50.000 8.28 0.00 43.77 4.00
98 99 2.223665 GGACGAGTAATTCCGTACAGGG 60.224 54.545 0.00 0.00 39.29 4.45
99 100 1.753073 ACGAGTAATTCCGTACAGGGG 59.247 52.381 0.00 0.00 41.52 4.79
100 101 2.026641 CGAGTAATTCCGTACAGGGGA 58.973 52.381 0.00 0.00 41.52 4.81
101 102 2.034305 CGAGTAATTCCGTACAGGGGAG 59.966 54.545 0.00 0.00 41.52 4.30
102 103 3.029570 GAGTAATTCCGTACAGGGGAGT 58.970 50.000 0.00 0.00 41.52 3.85
103 104 4.210331 GAGTAATTCCGTACAGGGGAGTA 58.790 47.826 0.00 0.00 41.52 2.59
114 115 3.233507 ACAGGGGAGTAGTAACGAACAA 58.766 45.455 0.00 0.00 0.00 2.83
121 122 4.037858 AGTAGTAACGAACAATAGGCGG 57.962 45.455 0.00 0.00 0.00 6.13
130 131 0.039035 ACAATAGGCGGCCCTTTCAA 59.961 50.000 17.02 0.00 42.87 2.69
134 135 0.963225 TAGGCGGCCCTTTCAAAAAC 59.037 50.000 17.02 0.00 42.87 2.43
145 146 7.414436 GGCCCTTTCAAAAACAAACTAAAATC 58.586 34.615 0.00 0.00 0.00 2.17
162 163 6.929606 ACTAAAATCAATACGATAGGTGGAGC 59.070 38.462 0.00 0.00 43.77 4.70
164 165 2.578786 TCAATACGATAGGTGGAGCGA 58.421 47.619 0.00 0.00 43.77 4.93
165 166 3.154710 TCAATACGATAGGTGGAGCGAT 58.845 45.455 0.00 0.00 43.77 4.58
166 167 3.190744 TCAATACGATAGGTGGAGCGATC 59.809 47.826 0.00 0.00 43.77 3.69
168 169 1.693627 ACGATAGGTGGAGCGATCTT 58.306 50.000 0.00 0.00 43.77 2.40
171 172 3.053455 CGATAGGTGGAGCGATCTTTTC 58.947 50.000 0.00 0.00 0.00 2.29
172 173 6.792311 ACGATAGGTGGAGCGATCTTTTCG 62.792 50.000 0.00 4.29 46.71 3.46
191 195 8.311836 TCTTTTCGTTTATTGAGACTGATAGGT 58.688 33.333 0.00 0.00 0.00 3.08
198 202 2.103373 TGAGACTGATAGGTGGAGTGC 58.897 52.381 0.00 0.00 0.00 4.40
202 206 2.032860 CTGATAGGTGGAGTGCCCCG 62.033 65.000 0.00 0.00 31.83 5.73
249 264 5.426689 AGAGGTTAAGCATGTGATTCTCA 57.573 39.130 7.52 0.00 0.00 3.27
265 280 0.531532 CTCACGATCCCATCAGTGCC 60.532 60.000 0.00 0.00 35.39 5.01
299 314 0.235665 CGTGTAAAGTGTGCAGCAGG 59.764 55.000 0.00 0.00 0.00 4.85
407 447 9.056005 CAAAATATACTTCCTGTTGCTATGCTA 57.944 33.333 0.00 0.00 0.00 3.49
415 455 0.938008 GTTGCTATGCTACCTTCGCC 59.062 55.000 0.00 0.00 0.00 5.54
416 456 0.830648 TTGCTATGCTACCTTCGCCT 59.169 50.000 0.00 0.00 0.00 5.52
417 457 0.830648 TGCTATGCTACCTTCGCCTT 59.169 50.000 0.00 0.00 0.00 4.35
418 458 1.209504 TGCTATGCTACCTTCGCCTTT 59.790 47.619 0.00 0.00 0.00 3.11
419 459 2.289565 GCTATGCTACCTTCGCCTTTT 58.710 47.619 0.00 0.00 0.00 2.27
420 460 2.288186 GCTATGCTACCTTCGCCTTTTC 59.712 50.000 0.00 0.00 0.00 2.29
455 498 4.925054 GCCAAACACATTCTACGTACTACA 59.075 41.667 0.00 0.00 0.00 2.74
465 508 7.484007 ACATTCTACGTACTACAACGAGATTTG 59.516 37.037 3.10 5.90 45.68 2.32
556 676 5.078153 ACAGTATTTATACACGCGCATTG 57.922 39.130 5.73 6.30 35.74 2.82
560 680 6.850823 CAGTATTTATACACGCGCATTGATTT 59.149 34.615 5.73 0.00 35.74 2.17
561 681 7.375808 CAGTATTTATACACGCGCATTGATTTT 59.624 33.333 5.73 0.00 35.74 1.82
562 682 8.552865 AGTATTTATACACGCGCATTGATTTTA 58.447 29.630 5.73 0.00 35.74 1.52
625 751 6.636850 CCTTCCTTGTATCTTCGTTTTTGTTG 59.363 38.462 0.00 0.00 0.00 3.33
628 754 6.540914 TCCTTGTATCTTCGTTTTTGTTGTCT 59.459 34.615 0.00 0.00 0.00 3.41
663 792 0.736325 CTAGTGACGTTGCCGGGAAG 60.736 60.000 9.39 6.11 38.78 3.46
744 877 5.814188 GAAAAAGATTTCCCTCGGTACGTAT 59.186 40.000 0.00 0.00 45.26 3.06
746 879 9.511590 GAAAAAGATTTCCCTCGGTACGTATGC 62.512 44.444 0.00 0.00 45.26 3.14
758 894 1.153449 CGTATGCTTTGGCCGGAGA 60.153 57.895 5.05 0.00 37.74 3.71
811 949 2.719426 ACTTCTACTCGTTTGACCCG 57.281 50.000 0.00 0.00 0.00 5.28
886 1024 0.178891 ACACACACTCCCCATCCTCT 60.179 55.000 0.00 0.00 0.00 3.69
906 1065 1.227118 CACAAACCCAACCAACGCC 60.227 57.895 0.00 0.00 0.00 5.68
920 1079 4.161295 CGCCTCAATCCCGGCTCA 62.161 66.667 0.00 0.00 44.11 4.26
973 1132 4.605967 GCGAGCGAGCGAGAGAGG 62.606 72.222 1.41 0.00 0.00 3.69
974 1133 2.892914 CGAGCGAGCGAGAGAGGA 60.893 66.667 0.00 0.00 0.00 3.71
975 1134 2.881266 CGAGCGAGCGAGAGAGGAG 61.881 68.421 0.00 0.00 0.00 3.69
976 1135 1.817941 GAGCGAGCGAGAGAGGAGT 60.818 63.158 0.00 0.00 0.00 3.85
977 1136 1.772063 GAGCGAGCGAGAGAGGAGTC 61.772 65.000 0.00 0.00 0.00 3.36
1191 1368 2.341101 CCACGTACGCACCTCCTCT 61.341 63.158 16.72 0.00 0.00 3.69
1194 1371 2.799371 GTACGCACCTCCTCTCCG 59.201 66.667 0.00 0.00 0.00 4.63
1231 1423 3.244561 ACTTCTGCTGCTGGCTAACTAAA 60.245 43.478 6.69 0.00 42.39 1.85
1264 1456 3.134127 GCATCGCCTGGTGGGTTC 61.134 66.667 7.51 0.00 37.43 3.62
1309 1501 2.670148 GGCGGTTCTGGGATCTGGT 61.670 63.158 0.00 0.00 0.00 4.00
1353 1547 2.099831 CGTGACCGGAGCTCGTAC 59.900 66.667 9.46 1.33 37.11 3.67
1405 1599 1.927895 AGATTTAGCTTCGAGCACCG 58.072 50.000 0.00 0.00 45.56 4.94
1520 1720 9.567776 TTCTCAAGTGAATTAACCAATTCTACA 57.432 29.630 10.49 0.00 46.87 2.74
1806 2030 4.318332 TGAGGTTACTGAAGTTCATGCTG 58.682 43.478 5.91 0.00 0.00 4.41
3042 3283 4.990257 AGAAAATGATGAATGACAAGGCG 58.010 39.130 0.00 0.00 0.00 5.52
3102 3343 2.428890 AGCTACTACCATCTGCAGTGAC 59.571 50.000 14.67 0.00 0.00 3.67
3369 3610 5.475564 GTCAATAGGTGGAAACTTTAAGGCA 59.524 40.000 0.00 0.00 0.00 4.75
3453 3694 2.158769 TGTCCTTCTTGAGCTTGCTGAA 60.159 45.455 0.00 0.00 0.00 3.02
3466 3707 1.568504 TGCTGAAGGAGGATACCGTT 58.431 50.000 0.00 0.00 34.73 4.44
3837 4078 3.454375 CCGTGAATGTGGTATACTCACC 58.546 50.000 16.86 0.00 39.20 4.02
3984 4243 3.244491 ACCATCTATCTGCAAGCTCATCC 60.244 47.826 0.00 0.00 0.00 3.51
4115 4374 0.815734 GCACAAATGATGCTCCTGCT 59.184 50.000 0.00 0.00 40.08 4.24
4196 4455 5.449725 GCTTGATCATTAAAGAGACCAAGCC 60.450 44.000 21.63 11.95 36.35 4.35
4197 4456 5.178096 TGATCATTAAAGAGACCAAGCCA 57.822 39.130 0.00 0.00 0.00 4.75
4198 4457 5.569355 TGATCATTAAAGAGACCAAGCCAA 58.431 37.500 0.00 0.00 0.00 4.52
4199 4458 6.189859 TGATCATTAAAGAGACCAAGCCAAT 58.810 36.000 0.00 0.00 0.00 3.16
4200 4459 5.902613 TCATTAAAGAGACCAAGCCAATG 57.097 39.130 0.00 0.00 0.00 2.82
4201 4460 5.569355 TCATTAAAGAGACCAAGCCAATGA 58.431 37.500 0.00 0.00 0.00 2.57
4202 4461 6.009589 TCATTAAAGAGACCAAGCCAATGAA 58.990 36.000 0.00 0.00 30.50 2.57
4203 4462 6.664816 TCATTAAAGAGACCAAGCCAATGAAT 59.335 34.615 0.00 0.00 30.50 2.57
4204 4463 4.796038 AAAGAGACCAAGCCAATGAATG 57.204 40.909 0.00 0.00 0.00 2.67
4220 4479 7.875041 GCCAATGAATGCTAATCTACTAGAAGA 59.125 37.037 0.00 0.00 0.00 2.87
4277 4553 4.517285 TCAGGACCTGAATATTGCAAGTC 58.483 43.478 22.30 4.74 37.57 3.01
4288 4564 7.706159 TGAATATTGCAAGTCCACATTGTATC 58.294 34.615 4.94 0.00 0.00 2.24
4298 4578 4.335594 GTCCACATTGTATCCTGGCTTAAC 59.664 45.833 0.00 0.00 0.00 2.01
4302 4582 6.404734 CCACATTGTATCCTGGCTTAACTTTC 60.405 42.308 0.00 0.00 0.00 2.62
4476 4756 9.009327 CAGTTTCAGTTAACTGTTAATGTTGTG 57.991 33.333 29.83 14.70 46.27 3.33
4609 4889 0.739462 TAGGAAATGCGCCACTGACG 60.739 55.000 4.18 0.00 0.00 4.35
4666 4946 1.007038 ACTTGGCGCACTTGCATTG 60.007 52.632 10.83 0.00 42.21 2.82
4741 5021 4.279169 ACAGGGAAGTTCATCACAAATGTG 59.721 41.667 7.22 7.22 46.91 3.21
4942 5222 1.804151 CCACTGGTGATGTGTTTACCG 59.196 52.381 1.93 0.00 37.29 4.02
5082 5368 1.900486 ACACAGCTGGTAGAGGGTTAC 59.100 52.381 19.93 0.00 0.00 2.50
5096 5382 6.636454 AGAGGGTTACTATGAATTTGGTGA 57.364 37.500 0.00 0.00 0.00 4.02
5163 5457 9.768662 AAAGTTCTGAAATAAGATTGCACATTT 57.231 25.926 0.00 0.00 0.00 2.32
5309 5603 1.963338 GTGTGTCCTCAGCAGCACC 60.963 63.158 0.00 0.00 0.00 5.01
5312 5606 2.031163 GTCCTCAGCAGCACCGTT 59.969 61.111 0.00 0.00 0.00 4.44
5336 5630 3.330405 TCTTCCAGTTCATCATGGTCCAA 59.670 43.478 0.00 0.00 37.84 3.53
5387 5681 0.114364 TCACCAGTCTCCAGTGGCTA 59.886 55.000 3.51 0.00 46.27 3.93
5414 5708 4.148825 CTCCTTGGCCTCGTCGGG 62.149 72.222 3.32 0.00 0.00 5.14
5429 5723 4.910585 GGGATGCCGATCGCCGTT 62.911 66.667 10.32 0.00 35.88 4.44
5517 5811 2.940410 GGCGAAAAGACCGATTCCATAA 59.060 45.455 0.00 0.00 0.00 1.90
5615 5909 5.007332 ACAAGTTTTAAAGCCTACGAGTGTG 59.993 40.000 0.00 0.00 0.00 3.82
5669 5964 3.694043 TTTGTATCTGGTGCTGTGCTA 57.306 42.857 0.00 0.00 0.00 3.49
5795 6090 4.161942 TCATTTCGACCCCTTTATTCCGTA 59.838 41.667 0.00 0.00 0.00 4.02
5829 6124 1.636003 GAGACTTTCCAGGAATGGGGT 59.364 52.381 17.36 8.25 0.00 4.95
5952 6261 9.693739 ATGTTATATCCTGTGATTAACCAACAA 57.306 29.630 0.00 0.00 31.09 2.83
6076 6385 8.831715 ATTACCATTGATCAACCAAAAGTTTC 57.168 30.769 11.07 0.00 36.18 2.78
6080 6389 4.829064 TGATCAACCAAAAGTTTCGAGG 57.171 40.909 0.00 0.00 36.18 4.63
6083 6392 4.893424 TCAACCAAAAGTTTCGAGGAAG 57.107 40.909 8.26 2.14 36.18 3.46
6101 6410 3.262151 GGAAGCACTCCTCTTACCTCTTT 59.738 47.826 0.00 0.00 41.61 2.52
6128 6562 6.373759 AGGTAAAAGGGAGTGTCTTGAAAAT 58.626 36.000 0.00 0.00 0.00 1.82
6160 8706 9.846248 GTTCTTAGTTATTACTTCCGTTCACTA 57.154 33.333 0.00 0.00 35.78 2.74
6175 8721 7.478322 TCCGTTCACTACTATAAGATGTTCAC 58.522 38.462 0.00 0.00 0.00 3.18
6202 8748 7.618019 ATTTCAGTCTCTATGTAGCCCATAA 57.382 36.000 0.00 0.00 35.62 1.90
6230 8789 3.312736 TCCTTCCCTTGCAAAAGAAGT 57.687 42.857 25.22 0.00 35.57 3.01
6233 8792 4.469586 TCCTTCCCTTGCAAAAGAAGTTTT 59.530 37.500 25.22 0.00 35.57 2.43
6237 8796 6.391227 TCCCTTGCAAAAGAAGTTTTCTAG 57.609 37.500 0.00 0.00 39.61 2.43
6238 8797 5.891551 TCCCTTGCAAAAGAAGTTTTCTAGT 59.108 36.000 0.00 0.00 39.61 2.57
6239 8798 5.979517 CCCTTGCAAAAGAAGTTTTCTAGTG 59.020 40.000 0.00 0.00 39.61 2.74
6281 8840 9.950680 AAACAATTGCATAAGAAGATATTACGG 57.049 29.630 5.05 0.00 0.00 4.02
6291 8850 4.348168 AGAAGATATTACGGCTGTCCCAAT 59.652 41.667 0.00 0.00 0.00 3.16
6294 8853 5.445964 AGATATTACGGCTGTCCCAATTTT 58.554 37.500 0.00 0.00 0.00 1.82
6295 8854 5.891551 AGATATTACGGCTGTCCCAATTTTT 59.108 36.000 0.00 0.00 0.00 1.94
6337 8896 8.614469 AAAACCTTTGTGTTTCTTTTCATTGA 57.386 26.923 0.00 0.00 37.46 2.57
6338 8897 8.614469 AAACCTTTGTGTTTCTTTTCATTGAA 57.386 26.923 0.00 0.00 33.24 2.69
6339 8898 8.614469 AACCTTTGTGTTTCTTTTCATTGAAA 57.386 26.923 7.74 7.74 0.00 2.69
6340 8899 8.614469 ACCTTTGTGTTTCTTTTCATTGAAAA 57.386 26.923 20.33 20.33 38.90 2.29
6352 8911 7.889873 TTTTCATTGAAAAGGTAGGAAGTCA 57.110 32.000 18.29 0.00 36.73 3.41
6353 8912 7.510549 TTTCATTGAAAAGGTAGGAAGTCAG 57.489 36.000 9.36 0.00 0.00 3.51
6354 8913 6.187727 TCATTGAAAAGGTAGGAAGTCAGT 57.812 37.500 0.00 0.00 0.00 3.41
6355 8914 6.601332 TCATTGAAAAGGTAGGAAGTCAGTT 58.399 36.000 0.00 0.00 0.00 3.16
6356 8915 7.741785 TCATTGAAAAGGTAGGAAGTCAGTTA 58.258 34.615 0.00 0.00 0.00 2.24
6357 8916 7.660208 TCATTGAAAAGGTAGGAAGTCAGTTAC 59.340 37.037 0.00 0.00 0.00 2.50
6358 8917 6.488769 TGAAAAGGTAGGAAGTCAGTTACA 57.511 37.500 0.00 0.00 0.00 2.41
6359 8918 6.285990 TGAAAAGGTAGGAAGTCAGTTACAC 58.714 40.000 0.00 0.00 0.00 2.90
6360 8919 6.099269 TGAAAAGGTAGGAAGTCAGTTACACT 59.901 38.462 0.00 0.00 0.00 3.55
6361 8920 5.725325 AAGGTAGGAAGTCAGTTACACTC 57.275 43.478 0.00 0.00 0.00 3.51
6362 8921 3.757493 AGGTAGGAAGTCAGTTACACTCG 59.243 47.826 0.00 0.00 0.00 4.18
6363 8922 3.505293 GGTAGGAAGTCAGTTACACTCGT 59.495 47.826 0.00 0.00 0.00 4.18
6364 8923 3.919223 AGGAAGTCAGTTACACTCGTC 57.081 47.619 0.00 0.00 0.00 4.20
6365 8924 2.557490 AGGAAGTCAGTTACACTCGTCC 59.443 50.000 0.00 0.00 0.00 4.79
6366 8925 2.557490 GGAAGTCAGTTACACTCGTCCT 59.443 50.000 0.00 0.00 0.00 3.85
6367 8926 3.755378 GGAAGTCAGTTACACTCGTCCTA 59.245 47.826 0.00 0.00 0.00 2.94
6368 8927 4.142643 GGAAGTCAGTTACACTCGTCCTAG 60.143 50.000 0.00 0.00 0.00 3.02
6369 8928 3.345414 AGTCAGTTACACTCGTCCTAGG 58.655 50.000 0.82 0.82 0.00 3.02
6370 8929 3.008813 AGTCAGTTACACTCGTCCTAGGA 59.991 47.826 7.62 7.62 0.00 2.94
6371 8930 3.126686 GTCAGTTACACTCGTCCTAGGAC 59.873 52.174 29.18 29.18 41.40 3.85
6404 8963 5.488645 AAAAACGGGTACAACACTTAGTG 57.511 39.130 11.21 11.21 39.75 2.74
6405 8964 4.405116 AAACGGGTACAACACTTAGTGA 57.595 40.909 20.07 0.00 36.96 3.41
6406 8965 4.405116 AACGGGTACAACACTTAGTGAA 57.595 40.909 20.07 0.00 36.96 3.18
6407 8966 3.721035 ACGGGTACAACACTTAGTGAAC 58.279 45.455 20.07 10.59 36.96 3.18
6408 8967 3.132646 ACGGGTACAACACTTAGTGAACA 59.867 43.478 20.07 0.00 36.96 3.18
6409 8968 4.202284 ACGGGTACAACACTTAGTGAACAT 60.202 41.667 20.07 4.13 36.96 2.71
6410 8969 4.387862 CGGGTACAACACTTAGTGAACATC 59.612 45.833 20.07 6.27 36.96 3.06
6411 8970 4.694037 GGGTACAACACTTAGTGAACATCC 59.306 45.833 20.07 13.93 36.96 3.51
6412 8971 4.694037 GGTACAACACTTAGTGAACATCCC 59.306 45.833 20.07 7.53 36.96 3.85
6413 8972 4.431416 ACAACACTTAGTGAACATCCCA 57.569 40.909 20.07 0.00 36.96 4.37
6414 8973 4.985538 ACAACACTTAGTGAACATCCCAT 58.014 39.130 20.07 0.00 36.96 4.00
6415 8974 4.761739 ACAACACTTAGTGAACATCCCATG 59.238 41.667 20.07 6.01 36.96 3.66
6416 8975 4.908601 ACACTTAGTGAACATCCCATGA 57.091 40.909 20.07 0.00 36.96 3.07
6417 8976 4.836825 ACACTTAGTGAACATCCCATGAG 58.163 43.478 20.07 0.00 36.96 2.90
6418 8977 4.194640 CACTTAGTGAACATCCCATGAGG 58.805 47.826 6.50 0.00 35.23 3.86
6419 8978 4.080919 CACTTAGTGAACATCCCATGAGGA 60.081 45.833 6.50 5.52 42.25 3.71
6420 8979 5.571454 CACTTAGTGAACATCCCATGAGGAA 60.571 44.000 6.50 0.00 41.66 3.36
6421 8980 7.349444 CACTTAGTGAACATCCCATGAGGAAG 61.349 46.154 6.50 5.66 41.66 3.46
6428 8987 2.940514 TCCCATGAGGAAGGTAGTGA 57.059 50.000 0.00 0.00 43.78 3.41
6429 8988 3.421394 TCCCATGAGGAAGGTAGTGAT 57.579 47.619 0.00 0.00 43.78 3.06
6430 8989 3.041211 TCCCATGAGGAAGGTAGTGATG 58.959 50.000 0.00 0.00 43.78 3.07
6431 8990 2.774234 CCCATGAGGAAGGTAGTGATGT 59.226 50.000 0.00 0.00 38.24 3.06
6432 8991 3.432749 CCCATGAGGAAGGTAGTGATGTG 60.433 52.174 0.00 0.00 38.24 3.21
6433 8992 3.452264 CCATGAGGAAGGTAGTGATGTGA 59.548 47.826 0.00 0.00 36.89 3.58
6434 8993 4.102210 CCATGAGGAAGGTAGTGATGTGAT 59.898 45.833 0.00 0.00 36.89 3.06
6435 8994 5.295950 CATGAGGAAGGTAGTGATGTGATC 58.704 45.833 0.00 0.00 0.00 2.92
6436 8995 3.706594 TGAGGAAGGTAGTGATGTGATCC 59.293 47.826 0.00 0.00 0.00 3.36
6437 8996 2.695666 AGGAAGGTAGTGATGTGATCCG 59.304 50.000 0.00 0.00 0.00 4.18
6438 8997 2.693591 GGAAGGTAGTGATGTGATCCGA 59.306 50.000 0.00 0.00 0.00 4.55
6439 8998 3.491104 GGAAGGTAGTGATGTGATCCGAC 60.491 52.174 0.00 0.00 0.00 4.79
6440 8999 3.019799 AGGTAGTGATGTGATCCGACT 57.980 47.619 0.00 0.00 0.00 4.18
6441 9000 4.166246 AGGTAGTGATGTGATCCGACTA 57.834 45.455 0.00 0.00 0.00 2.59
6442 9001 4.138290 AGGTAGTGATGTGATCCGACTAG 58.862 47.826 0.00 0.00 0.00 2.57
6443 9002 4.135306 GGTAGTGATGTGATCCGACTAGA 58.865 47.826 0.00 0.00 0.00 2.43
6444 9003 4.023878 GGTAGTGATGTGATCCGACTAGAC 60.024 50.000 0.00 0.00 0.00 2.59
6445 9004 2.614520 AGTGATGTGATCCGACTAGACG 59.385 50.000 7.66 7.66 0.00 4.18
6460 9019 2.856089 GACGGCGAGTCGTTCATAG 58.144 57.895 16.62 2.36 43.96 2.23
6461 9020 0.591741 GACGGCGAGTCGTTCATAGG 60.592 60.000 16.62 0.00 43.96 2.57
6462 9021 1.310933 ACGGCGAGTCGTTCATAGGT 61.311 55.000 16.62 0.00 40.85 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.192317 CAAGTAATTTCGAAGGGAGGGAG 58.808 47.826 0.00 0.00 0.00 4.30
1 2 3.585732 ACAAGTAATTTCGAAGGGAGGGA 59.414 43.478 0.00 0.00 0.00 4.20
2 3 3.939592 GACAAGTAATTTCGAAGGGAGGG 59.060 47.826 0.00 0.00 0.00 4.30
3 4 4.392138 GTGACAAGTAATTTCGAAGGGAGG 59.608 45.833 0.00 0.00 0.00 4.30
4 5 4.994852 TGTGACAAGTAATTTCGAAGGGAG 59.005 41.667 0.00 0.00 0.00 4.30
5 6 4.963373 TGTGACAAGTAATTTCGAAGGGA 58.037 39.130 0.00 0.00 0.00 4.20
6 7 5.682943 TTGTGACAAGTAATTTCGAAGGG 57.317 39.130 0.00 0.00 0.00 3.95
7 8 7.979115 TTTTTGTGACAAGTAATTTCGAAGG 57.021 32.000 0.00 0.00 0.00 3.46
72 73 5.295950 TGTACGGAATTACTCGTCCAAAAA 58.704 37.500 4.59 0.00 40.31 1.94
73 74 4.880759 TGTACGGAATTACTCGTCCAAAA 58.119 39.130 4.59 0.00 40.31 2.44
74 75 4.487948 CTGTACGGAATTACTCGTCCAAA 58.512 43.478 0.00 0.00 40.31 3.28
75 76 3.119388 CCTGTACGGAATTACTCGTCCAA 60.119 47.826 2.31 0.00 40.31 3.53
76 77 2.424601 CCTGTACGGAATTACTCGTCCA 59.575 50.000 2.31 0.42 40.31 4.02
77 78 2.223665 CCCTGTACGGAATTACTCGTCC 60.224 54.545 2.31 0.00 40.31 4.79
78 79 2.223665 CCCCTGTACGGAATTACTCGTC 60.224 54.545 2.31 0.12 40.31 4.20
79 80 1.753073 CCCCTGTACGGAATTACTCGT 59.247 52.381 2.31 6.29 42.55 4.18
80 81 2.026641 TCCCCTGTACGGAATTACTCG 58.973 52.381 2.31 0.00 33.16 4.18
81 82 3.029570 ACTCCCCTGTACGGAATTACTC 58.970 50.000 2.31 0.00 33.16 2.59
82 83 3.111741 ACTCCCCTGTACGGAATTACT 57.888 47.619 2.31 0.00 33.16 2.24
83 84 3.956848 ACTACTCCCCTGTACGGAATTAC 59.043 47.826 2.31 0.00 33.16 1.89
84 85 4.255510 ACTACTCCCCTGTACGGAATTA 57.744 45.455 2.31 0.00 33.16 1.40
85 86 3.111741 ACTACTCCCCTGTACGGAATT 57.888 47.619 2.31 0.00 33.16 2.17
86 87 2.842645 ACTACTCCCCTGTACGGAAT 57.157 50.000 2.31 0.00 33.16 3.01
87 88 3.356290 GTTACTACTCCCCTGTACGGAA 58.644 50.000 2.31 0.00 33.16 4.30
88 89 2.680805 CGTTACTACTCCCCTGTACGGA 60.681 54.545 2.31 0.00 33.16 4.69
89 90 1.672881 CGTTACTACTCCCCTGTACGG 59.327 57.143 0.00 0.00 0.00 4.02
90 91 2.632377 TCGTTACTACTCCCCTGTACG 58.368 52.381 0.00 0.00 0.00 3.67
91 92 3.758554 TGTTCGTTACTACTCCCCTGTAC 59.241 47.826 0.00 0.00 0.00 2.90
92 93 4.032960 TGTTCGTTACTACTCCCCTGTA 57.967 45.455 0.00 0.00 0.00 2.74
93 94 2.880443 TGTTCGTTACTACTCCCCTGT 58.120 47.619 0.00 0.00 0.00 4.00
94 95 3.947910 TTGTTCGTTACTACTCCCCTG 57.052 47.619 0.00 0.00 0.00 4.45
95 96 4.648307 CCTATTGTTCGTTACTACTCCCCT 59.352 45.833 0.00 0.00 0.00 4.79
96 97 4.738839 GCCTATTGTTCGTTACTACTCCCC 60.739 50.000 0.00 0.00 0.00 4.81
97 98 4.366586 GCCTATTGTTCGTTACTACTCCC 58.633 47.826 0.00 0.00 0.00 4.30
98 99 4.040376 CGCCTATTGTTCGTTACTACTCC 58.960 47.826 0.00 0.00 0.00 3.85
99 100 4.040376 CCGCCTATTGTTCGTTACTACTC 58.960 47.826 0.00 0.00 0.00 2.59
100 101 3.736126 GCCGCCTATTGTTCGTTACTACT 60.736 47.826 0.00 0.00 0.00 2.57
101 102 2.537214 GCCGCCTATTGTTCGTTACTAC 59.463 50.000 0.00 0.00 0.00 2.73
102 103 2.481795 GGCCGCCTATTGTTCGTTACTA 60.482 50.000 0.71 0.00 0.00 1.82
103 104 1.648504 GCCGCCTATTGTTCGTTACT 58.351 50.000 0.00 0.00 0.00 2.24
114 115 1.548719 GTTTTTGAAAGGGCCGCCTAT 59.451 47.619 9.86 0.00 0.00 2.57
121 122 7.980062 TGATTTTAGTTTGTTTTTGAAAGGGC 58.020 30.769 0.00 0.00 0.00 5.19
134 135 9.104965 TCCACCTATCGTATTGATTTTAGTTTG 57.895 33.333 0.00 0.00 38.57 2.93
145 146 3.191581 AGATCGCTCCACCTATCGTATTG 59.808 47.826 0.00 0.00 0.00 1.90
164 165 9.319143 CCTATCAGTCTCAATAAACGAAAAGAT 57.681 33.333 0.00 0.00 0.00 2.40
165 166 8.311836 ACCTATCAGTCTCAATAAACGAAAAGA 58.688 33.333 0.00 0.00 0.00 2.52
166 167 8.383619 CACCTATCAGTCTCAATAAACGAAAAG 58.616 37.037 0.00 0.00 0.00 2.27
168 169 6.816640 CCACCTATCAGTCTCAATAAACGAAA 59.183 38.462 0.00 0.00 0.00 3.46
171 172 5.902681 TCCACCTATCAGTCTCAATAAACG 58.097 41.667 0.00 0.00 0.00 3.60
172 173 6.758886 CACTCCACCTATCAGTCTCAATAAAC 59.241 42.308 0.00 0.00 0.00 2.01
176 177 3.133721 GCACTCCACCTATCAGTCTCAAT 59.866 47.826 0.00 0.00 0.00 2.57
191 195 2.002018 AAAAACTCCGGGGCACTCCA 62.002 55.000 0.00 0.00 37.22 3.86
226 241 5.809001 TGAGAATCACATGCTTAACCTCTT 58.191 37.500 0.00 0.00 42.56 2.85
249 264 1.690219 GGAGGCACTGATGGGATCGT 61.690 60.000 0.00 0.00 41.55 3.73
254 269 2.124983 CACGGAGGCACTGATGGG 60.125 66.667 0.00 0.00 41.55 4.00
299 314 6.599638 ACAAAAATACAGAGGAGGAGCATAAC 59.400 38.462 0.00 0.00 0.00 1.89
407 447 4.620982 CATGAAAAAGAAAAGGCGAAGGT 58.379 39.130 0.00 0.00 0.00 3.50
415 455 5.064962 TGTTTGGCAGCATGAAAAAGAAAAG 59.935 36.000 0.00 0.00 39.69 2.27
416 456 4.940046 TGTTTGGCAGCATGAAAAAGAAAA 59.060 33.333 0.00 0.00 39.69 2.29
417 457 4.332268 GTGTTTGGCAGCATGAAAAAGAAA 59.668 37.500 0.00 0.00 39.69 2.52
418 458 3.870419 GTGTTTGGCAGCATGAAAAAGAA 59.130 39.130 0.00 0.00 39.69 2.52
419 459 3.118847 TGTGTTTGGCAGCATGAAAAAGA 60.119 39.130 0.00 0.00 39.69 2.52
420 460 3.196463 TGTGTTTGGCAGCATGAAAAAG 58.804 40.909 0.00 0.00 39.69 2.27
497 567 7.983166 AGATATATACCTAGAGAGAGACGGT 57.017 40.000 0.00 0.00 0.00 4.83
531 629 5.172460 TGCGCGTGTATAAATACTGTAGA 57.828 39.130 8.43 0.00 34.41 2.59
598 724 6.993902 ACAAAAACGAAGATACAAGGAAGGTA 59.006 34.615 0.00 0.00 0.00 3.08
625 751 2.154462 AGTGCTGCCAATGTAACAGAC 58.846 47.619 0.00 0.00 33.10 3.51
628 754 3.073678 CACTAGTGCTGCCAATGTAACA 58.926 45.455 10.54 0.00 0.00 2.41
663 792 1.419374 ACGTCACTGATGCGTTTCTC 58.581 50.000 0.00 0.00 35.85 2.87
732 865 1.567504 CCAAAGCATACGTACCGAGG 58.432 55.000 0.00 0.00 0.00 4.63
744 877 3.589654 CTCGTCTCCGGCCAAAGCA 62.590 63.158 2.24 0.00 42.56 3.91
746 879 1.153745 CTCTCGTCTCCGGCCAAAG 60.154 63.158 2.24 0.00 33.95 2.77
747 880 2.970639 CTCTCGTCTCCGGCCAAA 59.029 61.111 2.24 0.00 33.95 3.28
776 912 1.812686 AAGTACCCGAAGTCGCTGCA 61.813 55.000 0.00 0.00 38.18 4.41
777 913 1.077089 GAAGTACCCGAAGTCGCTGC 61.077 60.000 0.00 0.00 38.18 5.25
781 917 2.030213 CGAGTAGAAGTACCCGAAGTCG 59.970 54.545 0.00 0.00 32.38 4.18
811 949 4.872485 CTCGCTCGCGGAGTCGTC 62.872 72.222 6.13 0.00 40.25 4.20
886 1024 1.668101 GCGTTGGTTGGGTTTGTGGA 61.668 55.000 0.00 0.00 0.00 4.02
906 1065 2.249535 CGCATGAGCCGGGATTGAG 61.250 63.158 2.18 0.00 37.52 3.02
991 1168 1.133325 GTAGCTCTCCATCCTCCCTCA 60.133 57.143 0.00 0.00 0.00 3.86
1197 1374 1.621672 GCAGAAGTGGGAGAGAGGGG 61.622 65.000 0.00 0.00 0.00 4.79
1203 1380 1.675801 CAGCAGCAGAAGTGGGAGA 59.324 57.895 0.00 0.00 0.00 3.71
1249 1441 4.096003 CCGAACCCACCAGGCGAT 62.096 66.667 0.00 0.00 40.58 4.58
1309 1501 4.020617 CCGACCCAGCTCCAGCAA 62.021 66.667 0.48 0.00 45.16 3.91
1383 1577 3.262420 GGTGCTCGAAGCTAAATCTTGA 58.738 45.455 8.07 0.00 42.97 3.02
1405 1599 0.108233 AAGCTAGCAGCAGCACTCTC 60.108 55.000 18.83 0.00 45.56 3.20
1430 1629 0.837940 CCTACCAACCCTCCTAAGCC 59.162 60.000 0.00 0.00 0.00 4.35
1483 1683 0.318762 ACTTGAGAACTCCACGAGGC 59.681 55.000 0.00 0.00 33.35 4.70
1520 1720 4.190772 CCAAAATGCTCCAACAAAACACT 58.809 39.130 0.00 0.00 0.00 3.55
1780 2004 5.064452 GCATGAACTTCAGTAACCTCATGAG 59.936 44.000 16.24 16.24 41.63 2.90
1806 2030 2.481952 GCTTCTCCTGTCACACATCAAC 59.518 50.000 0.00 0.00 0.00 3.18
2103 2344 0.314935 TTGCAAGCTTGGCTGCTAAC 59.685 50.000 27.10 8.86 43.24 2.34
2104 2345 0.314935 GTTGCAAGCTTGGCTGCTAA 59.685 50.000 27.10 8.41 43.24 3.09
3042 3283 0.166814 CAGCTAAGTTGCGAACCAGC 59.833 55.000 11.73 11.73 39.17 4.85
3102 3343 4.073293 AGTTGTTAGTGTCCCTGTCTTG 57.927 45.455 0.00 0.00 0.00 3.02
3267 3508 6.011981 TCCCATCTTGGTTAATAACAACCTCT 60.012 38.462 5.45 0.00 46.85 3.69
3369 3610 4.787598 CAATCTTAGTTTCAGCACGCTTT 58.212 39.130 0.00 0.00 0.00 3.51
3453 3694 2.838202 ACAATGTGAACGGTATCCTCCT 59.162 45.455 0.00 0.00 0.00 3.69
3466 3707 4.713553 TCTGAAGCACCTTTACAATGTGA 58.286 39.130 0.00 0.00 31.66 3.58
3852 4093 0.464036 TGAAATCCGGTCCCTCGATG 59.536 55.000 0.00 0.00 0.00 3.84
3984 4243 4.186159 ACCTTCAATACACGGAATTACGG 58.814 43.478 15.86 6.02 38.39 4.02
4277 4553 4.526970 AGTTAAGCCAGGATACAATGTGG 58.473 43.478 0.00 0.00 41.41 4.17
4288 4564 3.140325 TGAGTGGAAAGTTAAGCCAGG 57.860 47.619 0.00 0.00 31.18 4.45
4298 4578 6.037610 GGCTAGTGAATAACATGAGTGGAAAG 59.962 42.308 0.00 0.00 0.00 2.62
4302 4582 5.028549 AGGCTAGTGAATAACATGAGTGG 57.971 43.478 0.00 0.00 0.00 4.00
4476 4756 6.932947 TGAGGAGAAGTTAACTAGTAAAGCC 58.067 40.000 8.92 4.30 0.00 4.35
4553 4833 8.004215 TGCAAATTATCAATAGGAGGGTATGTT 58.996 33.333 0.00 0.00 0.00 2.71
4609 4889 2.031870 ACCCAAAGAAGTTGAACAGCC 58.968 47.619 0.00 0.00 39.87 4.85
4666 4946 1.228862 ATTGGGTGGTTCAGTGGCC 60.229 57.895 0.00 0.00 0.00 5.36
4741 5021 3.617288 GCCCAAAAATGTTCCTCCACATC 60.617 47.826 0.00 0.00 36.30 3.06
5082 5368 6.366877 CACCTTTGCTTTCACCAAATTCATAG 59.633 38.462 0.00 0.00 32.34 2.23
5171 5465 0.033504 GTGAGAGTCCAAGTTCGCCA 59.966 55.000 0.00 0.00 0.00 5.69
5309 5603 3.125829 CCATGATGAACTGGAAGACAACG 59.874 47.826 0.00 0.00 37.43 4.10
5312 5606 3.307691 GGACCATGATGAACTGGAAGACA 60.308 47.826 0.00 0.00 37.43 3.41
5336 5630 1.745489 GGCAAACTCGCCGAGGAAT 60.745 57.895 19.61 1.01 43.52 3.01
5414 5708 2.871427 GACAACGGCGATCGGCATC 61.871 63.158 36.24 24.23 46.16 3.91
5429 5723 1.344438 ACAGGAATGAGCTTGACGACA 59.656 47.619 0.00 0.00 0.00 4.35
5484 5778 0.181587 TTTTCGCCACACCTCCTTCA 59.818 50.000 0.00 0.00 0.00 3.02
5517 5811 1.561542 GGAGGATTCAGGTCCACACAT 59.438 52.381 0.00 0.00 40.90 3.21
5687 5982 4.193826 TCAATCTTACAGGTCTGCTGAC 57.806 45.455 14.87 14.87 42.22 3.51
5696 5991 3.875727 CAGCCAGACATCAATCTTACAGG 59.124 47.826 0.00 0.00 0.00 4.00
5730 6025 7.015195 TCGATCCACAGAATATACATCCTTTCA 59.985 37.037 0.00 0.00 0.00 2.69
5735 6030 9.088512 GTTTATCGATCCACAGAATATACATCC 57.911 37.037 0.00 0.00 0.00 3.51
5814 6109 0.413037 ATGCACCCCATTCCTGGAAA 59.587 50.000 14.03 0.00 46.37 3.13
5829 6124 2.529632 AGTCTGTCTGGACTACATGCA 58.470 47.619 0.00 0.00 43.76 3.96
5935 6244 4.789012 ATGCTTGTTGGTTAATCACAGG 57.211 40.909 0.00 0.00 0.00 4.00
5970 6279 8.499162 ACATATTTAATGCTCGCTTCTTACATC 58.501 33.333 0.00 0.00 0.00 3.06
6080 6389 4.021016 TCAAAGAGGTAAGAGGAGTGCTTC 60.021 45.833 0.00 0.00 0.00 3.86
6083 6392 3.963428 TCAAAGAGGTAAGAGGAGTGC 57.037 47.619 0.00 0.00 0.00 4.40
6101 6410 4.410883 TCAAGACACTCCCTTTTACCTTCA 59.589 41.667 0.00 0.00 0.00 3.02
6128 6562 9.328845 ACGGAAGTAATAACTAAGAACACAAAA 57.671 29.630 0.00 0.00 46.88 2.44
6175 8721 7.055667 TGGGCTACATAGAGACTGAAATAAG 57.944 40.000 0.00 0.00 0.00 1.73
6188 8734 9.911788 AAGGATATTTCATTATGGGCTACATAG 57.088 33.333 0.00 0.00 42.69 2.23
6202 8748 6.669154 TCTTTTGCAAGGGAAGGATATTTCAT 59.331 34.615 9.01 0.00 0.00 2.57
6230 8789 6.844097 AGAACCAAACCAAACACTAGAAAA 57.156 33.333 0.00 0.00 0.00 2.29
6233 8792 7.393796 TGTTTAAGAACCAAACCAAACACTAGA 59.606 33.333 0.00 0.00 35.46 2.43
6237 8796 7.603963 ATTGTTTAAGAACCAAACCAAACAC 57.396 32.000 0.00 0.00 36.07 3.32
6238 8797 7.361286 GCAATTGTTTAAGAACCAAACCAAACA 60.361 33.333 7.40 0.00 35.46 2.83
6239 8798 6.964370 GCAATTGTTTAAGAACCAAACCAAAC 59.036 34.615 7.40 0.00 35.46 2.93
6311 8870 9.061435 TCAATGAAAAGAAACACAAAGGTTTTT 57.939 25.926 0.00 0.00 40.85 1.94
6312 8871 8.614469 TCAATGAAAAGAAACACAAAGGTTTT 57.386 26.923 0.00 0.00 40.85 2.43
6313 8872 8.614469 TTCAATGAAAAGAAACACAAAGGTTT 57.386 26.923 0.00 0.00 43.30 3.27
6314 8873 8.614469 TTTCAATGAAAAGAAACACAAAGGTT 57.386 26.923 5.87 0.00 0.00 3.50
6315 8874 8.614469 TTTTCAATGAAAAGAAACACAAAGGT 57.386 26.923 16.28 0.00 36.73 3.50
6328 8887 7.559897 ACTGACTTCCTACCTTTTCAATGAAAA 59.440 33.333 18.68 18.68 38.90 2.29
6329 8888 7.060421 ACTGACTTCCTACCTTTTCAATGAAA 58.940 34.615 4.03 4.03 0.00 2.69
6330 8889 6.601332 ACTGACTTCCTACCTTTTCAATGAA 58.399 36.000 0.00 0.00 0.00 2.57
6331 8890 6.187727 ACTGACTTCCTACCTTTTCAATGA 57.812 37.500 0.00 0.00 0.00 2.57
6332 8891 6.884280 AACTGACTTCCTACCTTTTCAATG 57.116 37.500 0.00 0.00 0.00 2.82
6333 8892 7.444487 GTGTAACTGACTTCCTACCTTTTCAAT 59.556 37.037 0.00 0.00 0.00 2.57
6334 8893 6.764560 GTGTAACTGACTTCCTACCTTTTCAA 59.235 38.462 0.00 0.00 0.00 2.69
6335 8894 6.285990 GTGTAACTGACTTCCTACCTTTTCA 58.714 40.000 0.00 0.00 0.00 2.69
6336 8895 6.782298 GTGTAACTGACTTCCTACCTTTTC 57.218 41.667 0.00 0.00 0.00 2.29
6346 8905 8.266008 GTCCTAGGACGAGTGTAACTGACTTC 62.266 50.000 25.83 0.00 40.93 3.01
6347 8906 6.546615 GTCCTAGGACGAGTGTAACTGACTT 61.547 48.000 25.83 0.00 40.93 3.01
6348 8907 5.102130 GTCCTAGGACGAGTGTAACTGACT 61.102 50.000 25.83 0.00 40.93 3.41
6349 8908 3.126686 GTCCTAGGACGAGTGTAACTGAC 59.873 52.174 25.83 0.00 40.93 3.51
6350 8909 3.341823 GTCCTAGGACGAGTGTAACTGA 58.658 50.000 25.83 0.00 40.93 3.41
6351 8910 3.761311 GTCCTAGGACGAGTGTAACTG 57.239 52.381 25.83 0.00 40.93 3.16
6362 8921 3.498927 TTCGATTGTTCGTCCTAGGAC 57.501 47.619 29.18 29.18 45.65 3.85
6363 8922 4.524316 TTTTCGATTGTTCGTCCTAGGA 57.476 40.909 7.62 7.62 45.65 2.94
6382 8941 5.184711 TCACTAAGTGTTGTACCCGTTTTT 58.815 37.500 0.00 0.00 34.79 1.94
6383 8942 4.768583 TCACTAAGTGTTGTACCCGTTTT 58.231 39.130 0.00 0.00 34.79 2.43
6384 8943 4.405116 TCACTAAGTGTTGTACCCGTTT 57.595 40.909 0.00 0.00 34.79 3.60
6385 8944 4.122046 GTTCACTAAGTGTTGTACCCGTT 58.878 43.478 0.00 0.00 34.79 4.44
6386 8945 3.132646 TGTTCACTAAGTGTTGTACCCGT 59.867 43.478 0.00 0.00 34.79 5.28
6387 8946 3.719924 TGTTCACTAAGTGTTGTACCCG 58.280 45.455 0.00 0.00 34.79 5.28
6388 8947 4.694037 GGATGTTCACTAAGTGTTGTACCC 59.306 45.833 0.00 0.00 34.79 3.69
6389 8948 4.694037 GGGATGTTCACTAAGTGTTGTACC 59.306 45.833 0.00 0.00 34.79 3.34
6390 8949 5.302360 TGGGATGTTCACTAAGTGTTGTAC 58.698 41.667 0.00 0.00 34.79 2.90
6391 8950 5.554437 TGGGATGTTCACTAAGTGTTGTA 57.446 39.130 0.00 0.00 34.79 2.41
6392 8951 4.431416 TGGGATGTTCACTAAGTGTTGT 57.569 40.909 0.00 0.00 34.79 3.32
6393 8952 5.003160 TCATGGGATGTTCACTAAGTGTTG 58.997 41.667 0.00 0.00 34.79 3.33
6394 8953 5.241403 TCATGGGATGTTCACTAAGTGTT 57.759 39.130 0.00 0.00 34.79 3.32
6395 8954 4.323792 CCTCATGGGATGTTCACTAAGTGT 60.324 45.833 0.00 0.00 37.23 3.55
6396 8955 4.080919 TCCTCATGGGATGTTCACTAAGTG 60.081 45.833 0.00 0.00 39.58 3.16
6397 8956 4.104086 TCCTCATGGGATGTTCACTAAGT 58.896 43.478 0.00 0.00 39.58 2.24
6398 8957 4.760530 TCCTCATGGGATGTTCACTAAG 57.239 45.455 0.00 0.00 39.58 2.18
6399 8958 4.080356 CCTTCCTCATGGGATGTTCACTAA 60.080 45.833 0.00 0.00 44.66 2.24
6400 8959 3.455910 CCTTCCTCATGGGATGTTCACTA 59.544 47.826 0.00 0.00 44.66 2.74
6401 8960 2.240667 CCTTCCTCATGGGATGTTCACT 59.759 50.000 0.00 0.00 44.66 3.41
6402 8961 2.025887 ACCTTCCTCATGGGATGTTCAC 60.026 50.000 0.00 0.00 44.66 3.18
6403 8962 2.278245 ACCTTCCTCATGGGATGTTCA 58.722 47.619 0.00 0.00 44.66 3.18
6404 8963 3.456277 ACTACCTTCCTCATGGGATGTTC 59.544 47.826 0.00 0.00 44.66 3.18
6405 8964 3.200825 CACTACCTTCCTCATGGGATGTT 59.799 47.826 0.00 0.00 44.66 2.71
6406 8965 2.774234 CACTACCTTCCTCATGGGATGT 59.226 50.000 0.00 3.07 44.66 3.06
6407 8966 3.041211 TCACTACCTTCCTCATGGGATG 58.959 50.000 0.00 1.75 44.66 3.51
6408 8967 3.421394 TCACTACCTTCCTCATGGGAT 57.579 47.619 0.00 0.00 44.66 3.85
6409 8968 2.940514 TCACTACCTTCCTCATGGGA 57.059 50.000 0.00 0.00 43.41 4.37
6410 8969 2.774234 ACATCACTACCTTCCTCATGGG 59.226 50.000 0.00 0.00 0.00 4.00
6411 8970 3.452264 TCACATCACTACCTTCCTCATGG 59.548 47.826 0.00 0.00 0.00 3.66
6412 8971 4.743057 TCACATCACTACCTTCCTCATG 57.257 45.455 0.00 0.00 0.00 3.07
6413 8972 4.346418 GGATCACATCACTACCTTCCTCAT 59.654 45.833 0.00 0.00 0.00 2.90
6414 8973 3.706594 GGATCACATCACTACCTTCCTCA 59.293 47.826 0.00 0.00 0.00 3.86
6415 8974 3.243569 CGGATCACATCACTACCTTCCTC 60.244 52.174 0.00 0.00 0.00 3.71
6416 8975 2.695666 CGGATCACATCACTACCTTCCT 59.304 50.000 0.00 0.00 0.00 3.36
6417 8976 2.693591 TCGGATCACATCACTACCTTCC 59.306 50.000 0.00 0.00 0.00 3.46
6418 8977 3.381908 AGTCGGATCACATCACTACCTTC 59.618 47.826 0.00 0.00 0.00 3.46
6419 8978 3.366396 AGTCGGATCACATCACTACCTT 58.634 45.455 0.00 0.00 0.00 3.50
6420 8979 3.019799 AGTCGGATCACATCACTACCT 57.980 47.619 0.00 0.00 0.00 3.08
6421 8980 4.023878 GTCTAGTCGGATCACATCACTACC 60.024 50.000 0.00 0.00 0.00 3.18
6422 8981 4.318903 CGTCTAGTCGGATCACATCACTAC 60.319 50.000 1.12 0.00 0.00 2.73
6423 8982 3.808174 CGTCTAGTCGGATCACATCACTA 59.192 47.826 1.12 0.00 0.00 2.74
6424 8983 2.614520 CGTCTAGTCGGATCACATCACT 59.385 50.000 1.12 0.00 0.00 3.41
6425 8984 2.988343 CGTCTAGTCGGATCACATCAC 58.012 52.381 1.12 0.00 0.00 3.06
6437 8996 0.247616 GAACGACTCGCCGTCTAGTC 60.248 60.000 0.00 0.00 42.54 2.59
6438 8997 0.952497 TGAACGACTCGCCGTCTAGT 60.952 55.000 0.00 0.00 42.54 2.57
6439 8998 0.377554 ATGAACGACTCGCCGTCTAG 59.622 55.000 0.00 0.00 42.54 2.43
6440 8999 1.596260 CTATGAACGACTCGCCGTCTA 59.404 52.381 0.00 0.00 42.54 2.59
6441 9000 0.377554 CTATGAACGACTCGCCGTCT 59.622 55.000 0.00 0.00 42.54 4.18
6442 9001 0.591741 CCTATGAACGACTCGCCGTC 60.592 60.000 0.00 0.00 42.54 4.79
6443 9002 1.310933 ACCTATGAACGACTCGCCGT 61.311 55.000 0.00 0.00 45.64 5.68
6444 9003 1.432251 ACCTATGAACGACTCGCCG 59.568 57.895 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.