Multiple sequence alignment - TraesCS1A01G310700

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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 TraesCS1A01G310700 chr1A 100.000 3781 0 0 1 3781 501701108 501704888 0.000000e+00 6983.0
1 TraesCS1A01G310700 chr1A 100.000 3367 0 0 4124 7490 501705231 501708597 0.000000e+00 6218.0
2 TraesCS1A01G310700 chr1A 87.611 226 23 5 36 261 581437327 581437107 2.680000e-64 257.0
3 TraesCS1A01G310700 chr1D 94.223 2839 94 32 4165 6957 406549135 406551949 0.000000e+00 4270.0
4 TraesCS1A01G310700 chr1D 95.022 2531 91 19 336 2857 406545312 406547816 0.000000e+00 3943.0
5 TraesCS1A01G310700 chr1D 94.954 872 26 7 2856 3721 406547878 406548737 0.000000e+00 1351.0
6 TraesCS1A01G310700 chr1D 95.955 445 12 3 6975 7415 406552063 406552505 0.000000e+00 717.0
7 TraesCS1A01G310700 chr1D 90.210 143 10 4 6817 6957 406551938 406552078 4.620000e-42 183.0
8 TraesCS1A01G310700 chr1D 91.566 83 4 3 6817 6897 406552002 406552083 2.210000e-20 111.0
9 TraesCS1A01G310700 chr1D 94.444 36 2 0 303 338 482895382 482895347 1.000000e-03 56.5
10 TraesCS1A01G310700 chr1B 93.171 2797 110 33 4737 7490 546532205 546534963 0.000000e+00 4032.0
11 TraesCS1A01G310700 chr1B 93.297 2536 127 19 336 2857 546528124 546530630 0.000000e+00 3701.0
12 TraesCS1A01G310700 chr1B 95.923 932 24 5 2856 3781 546530692 546531615 0.000000e+00 1498.0
13 TraesCS1A01G310700 chr1B 95.304 575 26 1 4126 4700 546531638 546532211 0.000000e+00 911.0
14 TraesCS1A01G310700 chr5B 86.463 229 27 4 33 260 536311661 536311436 1.610000e-61 248.0
15 TraesCS1A01G310700 chr5D 86.667 225 27 2 36 260 440780828 440780607 5.800000e-61 246.0
16 TraesCS1A01G310700 chr4D 86.222 225 28 2 36 260 22018349 22018570 2.700000e-59 241.0
17 TraesCS1A01G310700 chr4D 85.398 226 25 7 36 260 428936418 428936200 2.100000e-55 228.0
18 TraesCS1A01G310700 chr4A 85.333 225 29 3 36 260 579865446 579865226 5.850000e-56 230.0
19 TraesCS1A01G310700 chr5A 86.603 209 24 3 36 243 556778811 556778606 2.100000e-55 228.0
20 TraesCS1A01G310700 chr2A 84.444 225 31 4 36 260 637227818 637227598 1.270000e-52 219.0
21 TraesCS1A01G310700 chr3D 82.743 226 32 4 36 260 61698177 61698396 2.130000e-45 195.0


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 TraesCS1A01G310700 chr1A 501701108 501708597 7489 False 6600.5 6983 100.00000 1 7490 2 chr1A.!!$F1 7489
1 TraesCS1A01G310700 chr1D 406545312 406552505 7193 False 1762.5 4270 93.65500 336 7415 6 chr1D.!!$F1 7079
2 TraesCS1A01G310700 chr1B 546528124 546534963 6839 False 2535.5 4032 94.42375 336 7490 4 chr1B.!!$F1 7154

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
44 45 0.250513 GTCAAAGCATCTCCCTCCGT 59.749 55.000 0.00 0.00 0.00 4.69 F
48 49 0.253327 AAGCATCTCCCTCCGTTTCC 59.747 55.000 0.00 0.00 0.00 3.13 F
1160 1169 0.397564 TTTCCGGCGGTTAGGTTTCT 59.602 50.000 27.32 0.00 0.00 2.52 F
1797 1813 0.951040 CCAGGTCTTCTGCGGTGTTC 60.951 60.000 0.00 0.00 42.05 3.18 F
2912 2994 0.537143 AGAAATGGCAGCGTTGACCA 60.537 50.000 15.31 15.31 35.79 4.02 F
3777 3865 1.001706 GCGTACTCGATGACTATGGCA 60.002 52.381 0.00 0.00 39.71 4.92 F
4227 4315 1.137086 GAGAATTGGCACTCTAGCGGA 59.863 52.381 0.00 0.00 34.64 5.54 F
4468 4556 1.539065 CGGCCTCTTATAGTGCACCTG 60.539 57.143 14.63 0.00 0.00 4.00 F
6163 6273 1.657804 AGAGATTGGAGACGGGGTTT 58.342 50.000 0.00 0.00 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1215 1224 0.547553 TGCATCTATCAAGCCCAGCA 59.452 50.000 0.00 0.00 0.00 4.41 R
1320 1330 1.620822 ACATGAAACAAGCCCAGGAC 58.379 50.000 0.00 0.00 0.00 3.85 R
2241 2260 0.609131 AACACTTGCATCTTCCCCCG 60.609 55.000 0.00 0.00 0.00 5.73 R
3393 3481 1.153706 GGCAACTGTGGATGCATGC 60.154 57.895 11.82 11.82 42.01 4.06 R
4124 4212 0.889994 TCAACTCTTACCGCGGCTAA 59.110 50.000 28.58 20.64 0.00 3.09 R
5762 5870 2.488952 GATTCCTCCTCGCTTTCATCC 58.511 52.381 0.00 0.00 0.00 3.51 R
6189 6299 1.186917 TGGCATTGCTCAAAGGGGTG 61.187 55.000 8.82 0.00 0.00 4.61 R
6365 6484 3.175133 CCCAGGAAATCCTTGGTCG 57.825 57.895 10.72 0.00 46.09 4.79 R
7124 7414 0.552848 CTGGGGCCTATCCAACATGT 59.447 55.000 0.84 0.00 36.21 3.21 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
25 26 7.658179 TGTATTCTTAGCTCACAAAGACAAG 57.342 36.000 0.00 0.00 31.62 3.16
26 27 7.217200 TGTATTCTTAGCTCACAAAGACAAGT 58.783 34.615 0.00 0.00 31.62 3.16
27 28 6.793492 ATTCTTAGCTCACAAAGACAAGTC 57.207 37.500 0.00 0.00 31.62 3.01
28 29 5.276461 TCTTAGCTCACAAAGACAAGTCA 57.724 39.130 2.72 0.00 0.00 3.41
29 30 5.670485 TCTTAGCTCACAAAGACAAGTCAA 58.330 37.500 2.72 0.00 0.00 3.18
30 31 6.112734 TCTTAGCTCACAAAGACAAGTCAAA 58.887 36.000 2.72 0.00 0.00 2.69
31 32 4.889832 AGCTCACAAAGACAAGTCAAAG 57.110 40.909 2.72 0.00 0.00 2.77
32 33 3.065925 AGCTCACAAAGACAAGTCAAAGC 59.934 43.478 2.72 2.58 0.00 3.51
33 34 3.181497 GCTCACAAAGACAAGTCAAAGCA 60.181 43.478 2.72 0.00 0.00 3.91
34 35 4.498682 GCTCACAAAGACAAGTCAAAGCAT 60.499 41.667 2.72 0.00 0.00 3.79
35 36 5.173774 TCACAAAGACAAGTCAAAGCATC 57.826 39.130 2.72 0.00 0.00 3.91
36 37 4.883585 TCACAAAGACAAGTCAAAGCATCT 59.116 37.500 2.72 0.00 0.00 2.90
37 38 5.008019 TCACAAAGACAAGTCAAAGCATCTC 59.992 40.000 2.72 0.00 0.00 2.75
38 39 4.276926 ACAAAGACAAGTCAAAGCATCTCC 59.723 41.667 2.72 0.00 0.00 3.71
39 40 3.064900 AGACAAGTCAAAGCATCTCCC 57.935 47.619 2.72 0.00 0.00 4.30
40 41 2.641815 AGACAAGTCAAAGCATCTCCCT 59.358 45.455 2.72 0.00 0.00 4.20
41 42 3.006247 GACAAGTCAAAGCATCTCCCTC 58.994 50.000 0.00 0.00 0.00 4.30
42 43 2.290577 ACAAGTCAAAGCATCTCCCTCC 60.291 50.000 0.00 0.00 0.00 4.30
43 44 0.539051 AGTCAAAGCATCTCCCTCCG 59.461 55.000 0.00 0.00 0.00 4.63
44 45 0.250513 GTCAAAGCATCTCCCTCCGT 59.749 55.000 0.00 0.00 0.00 4.69
45 46 0.984230 TCAAAGCATCTCCCTCCGTT 59.016 50.000 0.00 0.00 0.00 4.44
46 47 1.351017 TCAAAGCATCTCCCTCCGTTT 59.649 47.619 0.00 0.00 0.00 3.60
47 48 1.740025 CAAAGCATCTCCCTCCGTTTC 59.260 52.381 0.00 0.00 0.00 2.78
48 49 0.253327 AAGCATCTCCCTCCGTTTCC 59.747 55.000 0.00 0.00 0.00 3.13
49 50 0.618968 AGCATCTCCCTCCGTTTCCT 60.619 55.000 0.00 0.00 0.00 3.36
50 51 0.253327 GCATCTCCCTCCGTTTCCTT 59.747 55.000 0.00 0.00 0.00 3.36
51 52 1.340114 GCATCTCCCTCCGTTTCCTTT 60.340 52.381 0.00 0.00 0.00 3.11
52 53 2.880167 GCATCTCCCTCCGTTTCCTTTT 60.880 50.000 0.00 0.00 0.00 2.27
53 54 3.421844 CATCTCCCTCCGTTTCCTTTTT 58.578 45.455 0.00 0.00 0.00 1.94
96 97 9.868277 TTTGATCAAAGTCAAACTAAACAATGT 57.132 25.926 16.91 0.00 41.70 2.71
97 98 9.868277 TTGATCAAAGTCAAACTAAACAATGTT 57.132 25.926 5.45 0.00 35.31 2.71
98 99 9.868277 TGATCAAAGTCAAACTAAACAATGTTT 57.132 25.926 16.05 16.05 36.91 2.83
100 101 9.868277 ATCAAAGTCAAACTAAACAATGTTTCA 57.132 25.926 15.22 1.78 34.60 2.69
101 102 9.698309 TCAAAGTCAAACTAAACAATGTTTCAA 57.302 25.926 15.22 0.00 34.60 2.69
102 103 9.739786 CAAAGTCAAACTAAACAATGTTTCAAC 57.260 29.630 15.22 5.99 34.60 3.18
103 104 9.482627 AAAGTCAAACTAAACAATGTTTCAACA 57.517 25.926 15.22 0.00 44.06 3.33
104 105 9.482627 AAGTCAAACTAAACAATGTTTCAACAA 57.517 25.926 15.22 0.00 43.03 2.83
105 106 9.651913 AGTCAAACTAAACAATGTTTCAACAAT 57.348 25.926 15.22 0.00 43.03 2.71
257 258 9.878599 AGTCAAACATTATAAAGTTCGACTTTG 57.121 29.630 17.29 7.52 46.83 2.77
258 259 9.872757 GTCAAACATTATAAAGTTCGACTTTGA 57.127 29.630 14.42 7.87 46.83 2.69
259 260 9.872757 TCAAACATTATAAAGTTCGACTTTGAC 57.127 29.630 17.66 0.45 46.83 3.18
260 261 9.878599 CAAACATTATAAAGTTCGACTTTGACT 57.121 29.630 17.66 2.65 46.83 3.41
314 315 8.587952 AAGACAAACCAACTTTATATGCAAAC 57.412 30.769 0.00 0.00 0.00 2.93
315 316 7.951591 AGACAAACCAACTTTATATGCAAACT 58.048 30.769 0.00 0.00 0.00 2.66
316 317 9.073475 AGACAAACCAACTTTATATGCAAACTA 57.927 29.630 0.00 0.00 0.00 2.24
317 318 9.685828 GACAAACCAACTTTATATGCAAACTAA 57.314 29.630 0.00 0.00 0.00 2.24
330 331 8.742554 ATATGCAAACTAAAAAGAAAACGGAG 57.257 30.769 0.00 0.00 0.00 4.63
331 332 5.344884 TGCAAACTAAAAAGAAAACGGAGG 58.655 37.500 0.00 0.00 0.00 4.30
332 333 5.125739 TGCAAACTAAAAAGAAAACGGAGGA 59.874 36.000 0.00 0.00 0.00 3.71
333 334 6.037726 GCAAACTAAAAAGAAAACGGAGGAA 58.962 36.000 0.00 0.00 0.00 3.36
334 335 6.198403 GCAAACTAAAAAGAAAACGGAGGAAG 59.802 38.462 0.00 0.00 0.00 3.46
349 350 3.712218 GGAGGAAGTACCCAGATAAAGCT 59.288 47.826 0.00 0.00 40.05 3.74
399 400 2.342279 CCAAGGCCACGAACGAGA 59.658 61.111 5.01 0.00 0.00 4.04
473 482 0.817634 CCACGAACCAGCCAGAAACA 60.818 55.000 0.00 0.00 0.00 2.83
631 640 2.509336 GGTCCGTCGCATCCACAG 60.509 66.667 0.00 0.00 0.00 3.66
709 718 0.687757 TCCAGGAGCTTAGCGTCCAT 60.688 55.000 19.41 6.98 35.02 3.41
722 731 3.838271 TCCATGCGCCGGAGAGTC 61.838 66.667 10.31 0.00 0.00 3.36
1159 1168 0.518636 GTTTCCGGCGGTTAGGTTTC 59.481 55.000 27.32 5.45 0.00 2.78
1160 1169 0.397564 TTTCCGGCGGTTAGGTTTCT 59.602 50.000 27.32 0.00 0.00 2.52
1169 1178 4.456566 GGCGGTTAGGTTTCTGTAAATTGA 59.543 41.667 0.00 0.00 0.00 2.57
1212 1221 4.454678 TGCATGTTTGTCTGTTTCTCTCT 58.545 39.130 0.00 0.00 0.00 3.10
1215 1224 6.712095 TGCATGTTTGTCTGTTTCTCTCTATT 59.288 34.615 0.00 0.00 0.00 1.73
1262 1272 1.418373 GAATTTTTGGGTGCTGTCGC 58.582 50.000 0.00 0.00 0.00 5.19
1269 1279 2.772077 TGGGTGCTGTCGCTAAATAA 57.228 45.000 0.00 0.00 36.97 1.40
1293 1303 1.075542 TAGATTTCGCAGCACGGTTG 58.924 50.000 0.00 0.00 43.89 3.77
1295 1305 1.573829 GATTTCGCAGCACGGTTGGA 61.574 55.000 0.00 0.00 43.89 3.53
1493 1505 7.535489 AACGTTTCACTAGTATATGGCTTTC 57.465 36.000 0.00 0.00 0.00 2.62
1495 1507 5.175126 CGTTTCACTAGTATATGGCTTTCCG 59.825 44.000 0.00 0.00 34.14 4.30
1496 1508 4.252971 TCACTAGTATATGGCTTTCCGC 57.747 45.455 0.00 0.00 38.13 5.54
1497 1509 2.987149 CACTAGTATATGGCTTTCCGCG 59.013 50.000 0.00 0.00 40.44 6.46
1499 1511 1.045407 AGTATATGGCTTTCCGCGGA 58.955 50.000 27.28 27.28 40.44 5.54
1500 1512 1.145803 GTATATGGCTTTCCGCGGAC 58.854 55.000 31.19 17.58 40.44 4.79
1590 1605 7.287061 TCGTTATGATTAAATCCTTGGGTCAT 58.713 34.615 0.00 0.00 0.00 3.06
1746 1762 6.539103 GGAATGAGAGTTTAACTTAAGCGGAT 59.461 38.462 1.29 0.00 0.00 4.18
1797 1813 0.951040 CCAGGTCTTCTGCGGTGTTC 60.951 60.000 0.00 0.00 42.05 3.18
1910 1927 4.028993 TCCCAAATTAAAAGAGGAGCGT 57.971 40.909 0.00 0.00 0.00 5.07
2161 2180 3.558418 AGTGTTGGTTAAAGCTGTGTACG 59.442 43.478 0.00 0.00 0.00 3.67
2241 2260 4.142600 CCGATCTGTTTTTGGTCCATCTTC 60.143 45.833 0.00 0.00 0.00 2.87
2427 2446 4.621991 ACCACATGTGAATACTATCGCTC 58.378 43.478 27.46 0.00 0.00 5.03
2456 2475 3.191162 CCTTTTCCATCGAAGTTGCATCA 59.809 43.478 0.00 0.00 0.00 3.07
2492 2511 6.907212 GCACTGTAGTATGCAACAATCATAAC 59.093 38.462 0.00 0.00 41.65 1.89
2822 2841 4.274214 TCTGTTGTTAACGAGAGAGTTCGA 59.726 41.667 16.74 0.00 43.03 3.71
2829 2848 3.617540 ACGAGAGAGTTCGATAGCATG 57.382 47.619 2.12 0.00 43.03 4.06
2834 2853 4.930963 AGAGAGTTCGATAGCATGTCTTG 58.069 43.478 0.00 0.00 0.00 3.02
2904 2986 2.421399 GGGCTCCAGAAATGGCAGC 61.421 63.158 0.00 9.05 0.00 5.25
2912 2994 0.537143 AGAAATGGCAGCGTTGACCA 60.537 50.000 15.31 15.31 35.79 4.02
2970 3052 7.974675 TCTCATATTCAAACCGAAGCTAAAAG 58.025 34.615 0.00 0.00 36.95 2.27
3031 3113 9.262358 GGTGTAAACAAAACATAGGCAAAATTA 57.738 29.630 0.00 0.00 0.00 1.40
3284 3371 6.816140 GTCATCTTTCTTGTTAAGAGGAGGAG 59.184 42.308 0.00 0.00 41.43 3.69
3293 3380 2.246091 AAGAGGAGGAGCTTGCTACT 57.754 50.000 7.13 7.13 28.54 2.57
3301 3388 1.484240 GGAGCTTGCTACTGAGGTCAT 59.516 52.381 0.00 0.00 41.05 3.06
3322 3409 3.754965 TCAGAGCTAAGGTGCAAATGTT 58.245 40.909 0.00 0.00 34.99 2.71
3693 3781 1.414550 GAGAGGGCTAGACATGGGAAC 59.585 57.143 0.00 0.00 0.00 3.62
3750 3838 7.133891 CACAAAATTGAGTGGAGTACTTAGG 57.866 40.000 0.00 0.00 40.53 2.69
3751 3839 5.705905 ACAAAATTGAGTGGAGTACTTAGGC 59.294 40.000 0.00 0.00 40.53 3.93
3752 3840 3.802948 ATTGAGTGGAGTACTTAGGCG 57.197 47.619 0.00 0.00 40.53 5.52
3753 3841 2.211250 TGAGTGGAGTACTTAGGCGT 57.789 50.000 0.00 0.00 40.53 5.68
3756 3844 3.693085 TGAGTGGAGTACTTAGGCGTTAG 59.307 47.826 0.00 0.00 40.53 2.34
3777 3865 1.001706 GCGTACTCGATGACTATGGCA 60.002 52.381 0.00 0.00 39.71 4.92
4162 4250 2.154462 GATGTGTACCTGCTGTTTGCT 58.846 47.619 0.00 0.00 43.37 3.91
4189 4277 5.860941 AGGACCATACATTGAGTGAGTAG 57.139 43.478 0.00 0.00 0.00 2.57
4222 4310 6.798427 AGATACTTGAGAATTGGCACTCTA 57.202 37.500 5.36 0.00 34.65 2.43
4227 4315 1.137086 GAGAATTGGCACTCTAGCGGA 59.863 52.381 0.00 0.00 34.64 5.54
4282 4370 2.682836 GCATGTACAAAAATGCCGGTT 58.317 42.857 1.90 0.00 42.73 4.44
4287 4375 3.570125 TGTACAAAAATGCCGGTTCATCA 59.430 39.130 1.90 0.00 0.00 3.07
4348 4436 3.545703 ACATCAACAGCAAGGTATAGCC 58.454 45.455 0.00 0.00 37.58 3.93
4366 4454 6.906157 ATAGCCTAATTGCATGTGCTTATT 57.094 33.333 6.55 8.41 42.66 1.40
4373 4461 6.715344 AATTGCATGTGCTTATTTGAACTG 57.285 33.333 6.55 0.00 42.66 3.16
4468 4556 1.539065 CGGCCTCTTATAGTGCACCTG 60.539 57.143 14.63 0.00 0.00 4.00
4710 4798 5.675684 AACACCTTTTTGTTTGACTGGAT 57.324 34.783 0.00 0.00 36.22 3.41
4717 4805 9.533831 ACCTTTTTGTTTGACTGGATAGATAAT 57.466 29.630 0.00 0.00 0.00 1.28
4778 4866 5.405935 AACCTTGGAAGCATTACCATTTC 57.594 39.130 0.00 0.00 36.02 2.17
4805 4893 9.504708 TCATTTTGATTTTTCTTGGCAATACAT 57.495 25.926 0.00 0.00 0.00 2.29
4846 4935 6.994421 ACCCATAAATTGTTTCCTCAAGTT 57.006 33.333 0.00 0.00 38.71 2.66
4847 4936 6.993079 ACCCATAAATTGTTTCCTCAAGTTC 58.007 36.000 0.00 0.00 37.00 3.01
4848 4937 6.553100 ACCCATAAATTGTTTCCTCAAGTTCA 59.447 34.615 0.00 0.00 37.00 3.18
4849 4938 7.092716 CCCATAAATTGTTTCCTCAAGTTCAG 58.907 38.462 0.00 0.00 37.00 3.02
4850 4939 7.255942 CCCATAAATTGTTTCCTCAAGTTCAGT 60.256 37.037 0.00 0.00 37.00 3.41
4851 4940 8.143835 CCATAAATTGTTTCCTCAAGTTCAGTT 58.856 33.333 0.00 0.00 37.00 3.16
4852 4941 9.185192 CATAAATTGTTTCCTCAAGTTCAGTTC 57.815 33.333 0.00 0.00 37.00 3.01
4971 5067 4.934075 ACATCGTTTCACTGATGACATG 57.066 40.909 9.01 0.00 43.68 3.21
5021 5119 9.118300 TCACATTGGCTGTTATTTTTCAATTTT 57.882 25.926 0.00 0.00 35.29 1.82
5094 5192 4.566759 GCTTTGACGTACTGATATTGCTCA 59.433 41.667 0.00 0.00 0.00 4.26
5280 5387 4.349930 TGGAAGCTGTAAAAGTACCTTCCT 59.650 41.667 18.24 0.00 42.93 3.36
5290 5397 8.598916 TGTAAAAGTACCTTCCTTGATACATGA 58.401 33.333 0.00 0.00 0.00 3.07
5299 5406 7.121759 ACCTTCCTTGATACATGATTTGAACTG 59.878 37.037 0.00 0.00 0.00 3.16
5302 5409 8.634335 TCCTTGATACATGATTTGAACTGAAA 57.366 30.769 0.00 0.00 0.00 2.69
5424 5532 5.239087 GGTTGCATCATTTCAATTTGTGGTT 59.761 36.000 0.00 0.00 0.00 3.67
5452 5560 6.387192 TGGGACTTATTTTCTTGATCCTGA 57.613 37.500 0.00 0.00 0.00 3.86
5453 5561 6.973642 TGGGACTTATTTTCTTGATCCTGAT 58.026 36.000 0.00 0.00 0.00 2.90
5762 5870 3.678289 TGTCATCAGGAAACATGGTGAG 58.322 45.455 0.00 0.00 38.43 3.51
5801 5909 3.306917 TCGAAGCGGACAAGAAATGTA 57.693 42.857 0.00 0.00 44.12 2.29
5807 5915 4.642429 AGCGGACAAGAAATGTAAGTCTT 58.358 39.130 0.00 0.00 44.12 3.01
5883 5991 5.491982 ACAGTTTTTAGTATGAGCTCAGGG 58.508 41.667 22.96 2.93 0.00 4.45
5930 6040 4.091509 CCTGTAGCTTGTTTCGTATGACAC 59.908 45.833 0.00 0.00 0.00 3.67
5994 6104 6.991531 TCCTTTTGCTGATAAAAGTTTTGCAT 59.008 30.769 11.18 0.00 43.02 3.96
5998 6108 8.830201 TTTGCTGATAAAAGTTTTGCATATGT 57.170 26.923 11.18 0.00 0.00 2.29
6158 6268 3.024547 TGAAGGTAGAGATTGGAGACGG 58.975 50.000 0.00 0.00 0.00 4.79
6159 6269 2.074729 AGGTAGAGATTGGAGACGGG 57.925 55.000 0.00 0.00 0.00 5.28
6163 6273 1.657804 AGAGATTGGAGACGGGGTTT 58.342 50.000 0.00 0.00 0.00 3.27
6189 6299 3.119495 ACACAAGTGAAACCAAAGAGCAC 60.119 43.478 7.28 0.00 37.80 4.40
6365 6484 3.627577 TCACAGTTGAAAGAAGAAGTGGC 59.372 43.478 0.00 0.00 0.00 5.01
6501 6631 6.538021 ACAATGAAGAATGATGTGACTCTAGC 59.462 38.462 0.00 0.00 0.00 3.42
6502 6632 4.676546 TGAAGAATGATGTGACTCTAGCG 58.323 43.478 0.00 0.00 0.00 4.26
6503 6633 4.158579 TGAAGAATGATGTGACTCTAGCGT 59.841 41.667 0.00 0.00 0.00 5.07
6504 6634 4.039151 AGAATGATGTGACTCTAGCGTG 57.961 45.455 0.00 0.00 0.00 5.34
6505 6635 2.879002 ATGATGTGACTCTAGCGTGG 57.121 50.000 0.00 0.00 0.00 4.94
6506 6636 1.834188 TGATGTGACTCTAGCGTGGA 58.166 50.000 0.00 0.00 0.00 4.02
6507 6637 2.379005 TGATGTGACTCTAGCGTGGAT 58.621 47.619 0.00 0.00 0.00 3.41
6508 6638 2.760650 TGATGTGACTCTAGCGTGGATT 59.239 45.455 0.00 0.00 0.00 3.01
6509 6639 3.195610 TGATGTGACTCTAGCGTGGATTT 59.804 43.478 0.00 0.00 0.00 2.17
6510 6640 4.401202 TGATGTGACTCTAGCGTGGATTTA 59.599 41.667 0.00 0.00 0.00 1.40
6511 6641 4.371855 TGTGACTCTAGCGTGGATTTAG 57.628 45.455 0.00 0.00 0.00 1.85
6674 6804 7.414762 GCTCAATAGCCAGTAGTAGCTAGTATC 60.415 44.444 11.44 5.96 44.36 2.24
6700 6830 6.665465 TGTGTAGCAACTATATAGTGTAGCG 58.335 40.000 16.11 4.56 36.50 4.26
6866 7087 3.768757 CCAGGTGGGATTTTTATCTTGCA 59.231 43.478 0.00 0.00 40.01 4.08
6871 7092 6.324770 AGGTGGGATTTTTATCTTGCATTAGG 59.675 38.462 0.00 0.00 0.00 2.69
6875 7096 7.568366 TGGGATTTTTATCTTGCATTAGGGATT 59.432 33.333 0.00 0.00 0.00 3.01
6876 7097 8.432013 GGGATTTTTATCTTGCATTAGGGATTT 58.568 33.333 0.00 0.00 0.00 2.17
6985 7271 4.974368 TTTGAAACGGACAATCTTGTGT 57.026 36.364 0.00 0.00 42.43 3.72
6986 7272 4.974368 TTGAAACGGACAATCTTGTGTT 57.026 36.364 0.00 0.00 42.43 3.32
6987 7273 6.438259 TTTGAAACGGACAATCTTGTGTTA 57.562 33.333 0.00 0.00 42.43 2.41
6988 7274 6.627395 TTGAAACGGACAATCTTGTGTTAT 57.373 33.333 0.00 0.00 42.43 1.89
6989 7275 6.627395 TGAAACGGACAATCTTGTGTTATT 57.373 33.333 0.00 0.00 42.43 1.40
7035 7321 4.223953 GGAGATATGTGGGAGGTGAAGTA 58.776 47.826 0.00 0.00 0.00 2.24
7162 7455 0.318445 GCCACAAGCTTCAGCAGTTG 60.318 55.000 0.00 0.58 45.16 3.16
7425 7722 6.653320 CCAGCAGGTTAATCAGTTACAGTTAA 59.347 38.462 0.00 0.00 0.00 2.01
7426 7723 7.336931 CCAGCAGGTTAATCAGTTACAGTTAAT 59.663 37.037 0.00 0.00 0.00 1.40
7457 7754 2.118132 CAATTGGCTTGGGATCGGG 58.882 57.895 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.880195 ACTTGTCTTTGTGAGCTAAGAATACAT 59.120 33.333 0.00 0.00 37.98 2.29
1 2 7.217200 ACTTGTCTTTGTGAGCTAAGAATACA 58.783 34.615 0.00 0.00 37.98 2.29
2 3 7.385205 TGACTTGTCTTTGTGAGCTAAGAATAC 59.615 37.037 0.00 0.00 37.98 1.89
3 4 7.441836 TGACTTGTCTTTGTGAGCTAAGAATA 58.558 34.615 0.00 0.00 37.98 1.75
4 5 6.291377 TGACTTGTCTTTGTGAGCTAAGAAT 58.709 36.000 0.00 0.00 37.98 2.40
5 6 5.670485 TGACTTGTCTTTGTGAGCTAAGAA 58.330 37.500 0.00 0.00 37.98 2.52
6 7 5.276461 TGACTTGTCTTTGTGAGCTAAGA 57.724 39.130 2.35 0.00 34.90 2.10
7 8 5.991328 TTGACTTGTCTTTGTGAGCTAAG 57.009 39.130 2.35 0.00 0.00 2.18
8 9 5.220854 GCTTTGACTTGTCTTTGTGAGCTAA 60.221 40.000 2.35 0.00 0.00 3.09
9 10 4.273480 GCTTTGACTTGTCTTTGTGAGCTA 59.727 41.667 2.35 0.00 0.00 3.32
10 11 3.065925 GCTTTGACTTGTCTTTGTGAGCT 59.934 43.478 2.35 0.00 0.00 4.09
11 12 3.181497 TGCTTTGACTTGTCTTTGTGAGC 60.181 43.478 2.35 0.00 0.00 4.26
12 13 4.621068 TGCTTTGACTTGTCTTTGTGAG 57.379 40.909 2.35 0.00 0.00 3.51
13 14 4.883585 AGATGCTTTGACTTGTCTTTGTGA 59.116 37.500 2.35 0.00 0.00 3.58
14 15 5.179045 AGATGCTTTGACTTGTCTTTGTG 57.821 39.130 2.35 0.00 0.00 3.33
15 16 4.276926 GGAGATGCTTTGACTTGTCTTTGT 59.723 41.667 2.35 0.00 0.00 2.83
16 17 4.320788 GGGAGATGCTTTGACTTGTCTTTG 60.321 45.833 2.35 0.00 0.00 2.77
17 18 3.823304 GGGAGATGCTTTGACTTGTCTTT 59.177 43.478 2.35 0.00 0.00 2.52
18 19 3.073650 AGGGAGATGCTTTGACTTGTCTT 59.926 43.478 2.35 0.00 0.00 3.01
19 20 2.641815 AGGGAGATGCTTTGACTTGTCT 59.358 45.455 2.35 0.00 0.00 3.41
20 21 3.006247 GAGGGAGATGCTTTGACTTGTC 58.994 50.000 0.00 0.00 0.00 3.18
21 22 2.290577 GGAGGGAGATGCTTTGACTTGT 60.291 50.000 0.00 0.00 0.00 3.16
22 23 2.363683 GGAGGGAGATGCTTTGACTTG 58.636 52.381 0.00 0.00 0.00 3.16
23 24 1.065854 CGGAGGGAGATGCTTTGACTT 60.066 52.381 0.00 0.00 0.00 3.01
24 25 0.539051 CGGAGGGAGATGCTTTGACT 59.461 55.000 0.00 0.00 0.00 3.41
25 26 0.250513 ACGGAGGGAGATGCTTTGAC 59.749 55.000 0.00 0.00 0.00 3.18
26 27 0.984230 AACGGAGGGAGATGCTTTGA 59.016 50.000 0.00 0.00 0.00 2.69
27 28 1.740025 GAAACGGAGGGAGATGCTTTG 59.260 52.381 0.00 0.00 0.00 2.77
28 29 1.340114 GGAAACGGAGGGAGATGCTTT 60.340 52.381 0.00 0.00 0.00 3.51
29 30 0.253327 GGAAACGGAGGGAGATGCTT 59.747 55.000 0.00 0.00 0.00 3.91
30 31 0.618968 AGGAAACGGAGGGAGATGCT 60.619 55.000 0.00 0.00 0.00 3.79
31 32 0.253327 AAGGAAACGGAGGGAGATGC 59.747 55.000 0.00 0.00 0.00 3.91
32 33 2.789409 AAAGGAAACGGAGGGAGATG 57.211 50.000 0.00 0.00 0.00 2.90
33 34 3.808834 AAAAAGGAAACGGAGGGAGAT 57.191 42.857 0.00 0.00 0.00 2.75
70 71 9.868277 ACATTGTTTAGTTTGACTTTGATCAAA 57.132 25.926 19.45 19.45 44.40 2.69
71 72 9.868277 AACATTGTTTAGTTTGACTTTGATCAA 57.132 25.926 3.38 3.38 36.80 2.57
72 73 9.868277 AAACATTGTTTAGTTTGACTTTGATCA 57.132 25.926 12.98 0.00 36.65 2.92
74 75 9.868277 TGAAACATTGTTTAGTTTGACTTTGAT 57.132 25.926 14.49 0.00 38.01 2.57
75 76 9.698309 TTGAAACATTGTTTAGTTTGACTTTGA 57.302 25.926 14.49 0.00 38.01 2.69
76 77 9.739786 GTTGAAACATTGTTTAGTTTGACTTTG 57.260 29.630 14.49 0.00 38.01 2.77
77 78 9.482627 TGTTGAAACATTGTTTAGTTTGACTTT 57.517 25.926 14.49 0.00 38.01 2.66
78 79 9.482627 TTGTTGAAACATTGTTTAGTTTGACTT 57.517 25.926 14.49 0.00 38.01 3.01
79 80 9.651913 ATTGTTGAAACATTGTTTAGTTTGACT 57.348 25.926 14.49 0.00 38.01 3.41
232 233 9.872757 TCAAAGTCGAACTTTATAATGTTTGAC 57.127 29.630 33.01 33.01 45.84 3.18
233 234 9.872757 GTCAAAGTCGAACTTTATAATGTTTGA 57.127 29.630 21.73 21.73 45.84 2.69
234 235 9.878599 AGTCAAAGTCGAACTTTATAATGTTTG 57.121 29.630 18.89 18.89 45.84 2.93
288 289 9.685828 GTTTGCATATAAAGTTGGTTTGTCTTA 57.314 29.630 0.00 0.00 0.00 2.10
289 290 8.421002 AGTTTGCATATAAAGTTGGTTTGTCTT 58.579 29.630 0.00 0.00 0.00 3.01
290 291 7.951591 AGTTTGCATATAAAGTTGGTTTGTCT 58.048 30.769 0.00 0.00 0.00 3.41
291 292 9.685828 TTAGTTTGCATATAAAGTTGGTTTGTC 57.314 29.630 0.00 0.00 0.00 3.18
304 305 9.834628 CTCCGTTTTCTTTTTAGTTTGCATATA 57.165 29.630 0.00 0.00 0.00 0.86
305 306 7.812669 CCTCCGTTTTCTTTTTAGTTTGCATAT 59.187 33.333 0.00 0.00 0.00 1.78
306 307 7.013464 TCCTCCGTTTTCTTTTTAGTTTGCATA 59.987 33.333 0.00 0.00 0.00 3.14
307 308 5.983118 CCTCCGTTTTCTTTTTAGTTTGCAT 59.017 36.000 0.00 0.00 0.00 3.96
308 309 5.125739 TCCTCCGTTTTCTTTTTAGTTTGCA 59.874 36.000 0.00 0.00 0.00 4.08
309 310 5.584442 TCCTCCGTTTTCTTTTTAGTTTGC 58.416 37.500 0.00 0.00 0.00 3.68
310 311 7.255569 ACTTCCTCCGTTTTCTTTTTAGTTTG 58.744 34.615 0.00 0.00 0.00 2.93
311 312 7.400599 ACTTCCTCCGTTTTCTTTTTAGTTT 57.599 32.000 0.00 0.00 0.00 2.66
312 313 7.012704 GGTACTTCCTCCGTTTTCTTTTTAGTT 59.987 37.037 0.00 0.00 0.00 2.24
313 314 6.484643 GGTACTTCCTCCGTTTTCTTTTTAGT 59.515 38.462 0.00 0.00 0.00 2.24
314 315 6.072838 GGGTACTTCCTCCGTTTTCTTTTTAG 60.073 42.308 0.00 0.00 36.25 1.85
315 316 5.764686 GGGTACTTCCTCCGTTTTCTTTTTA 59.235 40.000 0.00 0.00 36.25 1.52
316 317 4.581824 GGGTACTTCCTCCGTTTTCTTTTT 59.418 41.667 0.00 0.00 36.25 1.94
317 318 4.139786 GGGTACTTCCTCCGTTTTCTTTT 58.860 43.478 0.00 0.00 36.25 2.27
318 319 3.136992 TGGGTACTTCCTCCGTTTTCTTT 59.863 43.478 0.00 0.00 36.25 2.52
319 320 2.707257 TGGGTACTTCCTCCGTTTTCTT 59.293 45.455 0.00 0.00 36.25 2.52
320 321 2.302157 CTGGGTACTTCCTCCGTTTTCT 59.698 50.000 0.00 0.00 36.25 2.52
321 322 2.301009 TCTGGGTACTTCCTCCGTTTTC 59.699 50.000 0.00 0.00 36.25 2.29
322 323 2.332117 TCTGGGTACTTCCTCCGTTTT 58.668 47.619 0.00 0.00 36.25 2.43
323 324 2.019807 TCTGGGTACTTCCTCCGTTT 57.980 50.000 0.00 0.00 36.25 3.60
324 325 2.249309 ATCTGGGTACTTCCTCCGTT 57.751 50.000 0.00 0.00 36.25 4.44
325 326 3.393426 TTATCTGGGTACTTCCTCCGT 57.607 47.619 0.00 0.00 36.25 4.69
326 327 3.492829 GCTTTATCTGGGTACTTCCTCCG 60.493 52.174 0.00 0.00 36.25 4.63
327 328 3.712218 AGCTTTATCTGGGTACTTCCTCC 59.288 47.826 0.00 0.00 36.25 4.30
328 329 5.834204 TCTAGCTTTATCTGGGTACTTCCTC 59.166 44.000 0.00 0.00 36.25 3.71
329 330 5.778542 TCTAGCTTTATCTGGGTACTTCCT 58.221 41.667 0.00 0.00 36.25 3.36
330 331 5.510009 GCTCTAGCTTTATCTGGGTACTTCC 60.510 48.000 0.00 0.00 38.21 3.46
331 332 5.510009 GGCTCTAGCTTTATCTGGGTACTTC 60.510 48.000 0.00 0.00 41.70 3.01
332 333 4.345547 GGCTCTAGCTTTATCTGGGTACTT 59.654 45.833 0.00 0.00 41.70 2.24
333 334 3.898741 GGCTCTAGCTTTATCTGGGTACT 59.101 47.826 0.00 0.00 41.70 2.73
334 335 3.007074 GGGCTCTAGCTTTATCTGGGTAC 59.993 52.174 0.00 0.00 41.70 3.34
349 350 1.860641 TCGTCCATTCTTGGGCTCTA 58.139 50.000 0.00 0.00 46.04 2.43
426 435 4.183686 GTCCGCCGTCCGATTCGA 62.184 66.667 7.83 0.00 40.02 3.71
463 472 2.037847 GGCCCCATGTTTCTGGCT 59.962 61.111 0.00 0.00 43.50 4.75
473 482 3.105928 GGATGAGGTGGGCCCCAT 61.106 66.667 22.27 15.74 35.28 4.00
537 546 2.354199 CGTAGTTAGACCTCTCCCGAAC 59.646 54.545 0.00 0.00 0.00 3.95
538 547 2.636830 CGTAGTTAGACCTCTCCCGAA 58.363 52.381 0.00 0.00 0.00 4.30
539 548 1.745141 GCGTAGTTAGACCTCTCCCGA 60.745 57.143 0.00 0.00 0.00 5.14
540 549 0.662085 GCGTAGTTAGACCTCTCCCG 59.338 60.000 0.00 0.00 0.00 5.14
628 637 2.362397 CGTAGTAGATGGTCCATGCTGT 59.638 50.000 9.76 2.07 0.00 4.40
631 640 1.687123 ACCGTAGTAGATGGTCCATGC 59.313 52.381 9.76 1.08 44.99 4.06
639 648 2.350580 GGCGCTAAGACCGTAGTAGATG 60.351 54.545 7.64 0.00 0.00 2.90
640 649 1.878734 GGCGCTAAGACCGTAGTAGAT 59.121 52.381 7.64 0.00 0.00 1.98
641 650 1.303309 GGCGCTAAGACCGTAGTAGA 58.697 55.000 7.64 0.00 0.00 2.59
642 651 0.041488 CGGCGCTAAGACCGTAGTAG 60.041 60.000 7.64 0.00 44.46 2.57
643 652 2.016961 CGGCGCTAAGACCGTAGTA 58.983 57.895 7.64 0.00 44.46 1.82
644 653 2.796651 CGGCGCTAAGACCGTAGT 59.203 61.111 7.64 0.00 44.46 2.73
898 907 4.664677 CGGGGGACATCGGATCGC 62.665 72.222 0.00 0.00 0.00 4.58
1118 1127 2.440539 AACCTAGACGAAGCACACAG 57.559 50.000 0.00 0.00 0.00 3.66
1159 1168 2.752354 TCCATTGGCCGTCAATTTACAG 59.248 45.455 0.00 0.00 43.04 2.74
1160 1169 2.490115 GTCCATTGGCCGTCAATTTACA 59.510 45.455 0.00 0.00 43.04 2.41
1199 1208 4.187694 CCCAGCAATAGAGAGAAACAGAC 58.812 47.826 0.00 0.00 0.00 3.51
1200 1209 3.369892 GCCCAGCAATAGAGAGAAACAGA 60.370 47.826 0.00 0.00 0.00 3.41
1212 1221 3.181441 TGCATCTATCAAGCCCAGCAATA 60.181 43.478 0.00 0.00 0.00 1.90
1215 1224 0.547553 TGCATCTATCAAGCCCAGCA 59.452 50.000 0.00 0.00 0.00 4.41
1262 1272 9.746711 GTGCTGCGAAATCTACATATTATTTAG 57.253 33.333 0.00 0.00 0.00 1.85
1269 1279 3.059884 CCGTGCTGCGAAATCTACATAT 58.940 45.455 2.97 0.00 44.77 1.78
1293 1303 2.007608 ACGCGAGAGGCTAAAAATTCC 58.992 47.619 15.93 0.00 40.44 3.01
1295 1305 2.159627 CACACGCGAGAGGCTAAAAATT 59.840 45.455 15.93 0.00 40.44 1.82
1320 1330 1.620822 ACATGAAACAAGCCCAGGAC 58.379 50.000 0.00 0.00 0.00 3.85
1493 1505 2.884087 AATAGCACACTCGTCCGCGG 62.884 60.000 22.12 22.12 38.89 6.46
1495 1507 1.917273 TTAATAGCACACTCGTCCGC 58.083 50.000 0.00 0.00 0.00 5.54
1496 1508 3.966154 AGATTAATAGCACACTCGTCCG 58.034 45.455 0.00 0.00 0.00 4.79
1497 1509 6.074544 AGTAGATTAATAGCACACTCGTCC 57.925 41.667 0.00 0.00 0.00 4.79
1590 1605 3.084039 CCTAGCAATTGAAGCACAAGGA 58.916 45.455 10.34 0.00 42.02 3.36
1746 1762 5.227569 TCTCTTGAGACAATTAAGCCACA 57.772 39.130 0.00 0.00 0.00 4.17
1797 1813 3.251004 GCAAGCTACCGATCAAAATAGGG 59.749 47.826 0.00 0.00 32.26 3.53
1892 1909 6.381801 ACAATCACGCTCCTCTTTTAATTTG 58.618 36.000 0.00 0.00 0.00 2.32
1910 1927 5.825679 AGTTAGCACTTTGTACCAACAATCA 59.174 36.000 0.00 0.00 44.85 2.57
2045 2062 9.208022 CAAAATCTGAACAGTACTAACTCATCA 57.792 33.333 0.00 0.00 31.97 3.07
2048 2065 9.692749 CTACAAAATCTGAACAGTACTAACTCA 57.307 33.333 0.00 0.00 31.97 3.41
2202 2221 5.247110 ACAGATCGGAGAATATACCATGCTT 59.753 40.000 0.00 0.00 43.58 3.91
2241 2260 0.609131 AACACTTGCATCTTCCCCCG 60.609 55.000 0.00 0.00 0.00 5.73
2427 2446 4.256920 ACTTCGATGGAAAAGGACATGAG 58.743 43.478 0.00 0.00 0.00 2.90
2456 2475 2.528564 ACTACAGTGCAAATGGCCAAT 58.471 42.857 10.96 0.00 43.89 3.16
2536 2555 7.631717 AAAGTAGTAGGAATCTGCCATTTTC 57.368 36.000 0.00 0.00 0.00 2.29
2822 2841 2.507058 TGGCCTCTTCAAGACATGCTAT 59.493 45.455 3.32 0.00 0.00 2.97
2829 2848 3.895232 TGTCTATGGCCTCTTCAAGAC 57.105 47.619 3.32 8.35 35.13 3.01
2834 2853 4.550076 AGCATATGTCTATGGCCTCTTC 57.450 45.455 3.32 0.00 36.11 2.87
2904 2986 2.093306 TCCTATTGCAGTGGTCAACG 57.907 50.000 0.00 0.00 0.00 4.10
2912 2994 7.951347 AGAAAGATGAAATTCCTATTGCAGT 57.049 32.000 0.00 0.00 32.76 4.40
3284 3371 2.548875 CTGATGACCTCAGTAGCAAGC 58.451 52.381 0.00 0.00 45.42 4.01
3293 3380 2.762887 CACCTTAGCTCTGATGACCTCA 59.237 50.000 0.00 0.00 0.00 3.86
3301 3388 3.423539 ACATTTGCACCTTAGCTCTGA 57.576 42.857 0.00 0.00 34.99 3.27
3322 3409 1.388174 TTCCCTGGCCCAAAGGATTA 58.612 50.000 9.21 0.00 36.91 1.75
3393 3481 1.153706 GGCAACTGTGGATGCATGC 60.154 57.895 11.82 11.82 42.01 4.06
3523 3611 4.178540 CCAAATCATCAAGACATGTTGGC 58.821 43.478 0.00 0.00 31.00 4.52
3693 3781 6.000891 ACTGTGCAATGTATACACAAGTTG 57.999 37.500 7.96 9.89 43.25 3.16
3752 3840 4.465016 CATAGTCATCGAGTACGCCTAAC 58.535 47.826 0.00 0.00 39.58 2.34
3753 3841 3.501062 CCATAGTCATCGAGTACGCCTAA 59.499 47.826 0.00 0.00 39.58 2.69
3756 3844 1.666311 GCCATAGTCATCGAGTACGCC 60.666 57.143 0.00 0.00 39.58 5.68
4123 4211 1.273048 TCAACTCTTACCGCGGCTAAA 59.727 47.619 28.58 16.47 0.00 1.85
4124 4212 0.889994 TCAACTCTTACCGCGGCTAA 59.110 50.000 28.58 20.64 0.00 3.09
4210 4298 1.486310 TGATCCGCTAGAGTGCCAATT 59.514 47.619 0.00 0.00 0.00 2.32
4222 4310 3.735237 ACATTCGAAGTATGATCCGCT 57.265 42.857 3.35 0.00 0.00 5.52
4282 4370 3.330701 AGGGGTTTGCTTTCTACTGATGA 59.669 43.478 0.00 0.00 0.00 2.92
4287 4375 4.995624 AAGTAGGGGTTTGCTTTCTACT 57.004 40.909 0.00 0.00 41.38 2.57
4348 4436 7.543172 ACAGTTCAAATAAGCACATGCAATTAG 59.457 33.333 6.64 0.00 45.16 1.73
4730 4818 8.810652 TTGCCATACTAATCAAAAAGTTCAAC 57.189 30.769 0.00 0.00 0.00 3.18
4732 4820 9.255304 GTTTTGCCATACTAATCAAAAAGTTCA 57.745 29.630 0.00 0.00 39.26 3.18
4733 4821 8.708742 GGTTTTGCCATACTAATCAAAAAGTTC 58.291 33.333 0.00 0.00 39.26 3.01
4739 4827 6.495181 TCCAAGGTTTTGCCATACTAATCAAA 59.505 34.615 0.00 0.00 40.61 2.69
4778 4866 8.991026 TGTATTGCCAAGAAAAATCAAAATGAG 58.009 29.630 0.00 0.00 0.00 2.90
4805 4893 5.344743 TGGGTACAAAATTGCAAGAACAA 57.655 34.783 4.94 0.00 0.00 2.83
4848 4937 5.358442 AGCGACAGAATATGACAGTAGAACT 59.642 40.000 0.00 0.00 0.00 3.01
4849 4938 5.583495 AGCGACAGAATATGACAGTAGAAC 58.417 41.667 0.00 0.00 0.00 3.01
4850 4939 5.836821 AGCGACAGAATATGACAGTAGAA 57.163 39.130 0.00 0.00 0.00 2.10
4851 4940 5.125578 ACAAGCGACAGAATATGACAGTAGA 59.874 40.000 0.00 0.00 0.00 2.59
4852 4941 5.230936 CACAAGCGACAGAATATGACAGTAG 59.769 44.000 0.00 0.00 0.00 2.57
4980 5076 4.549458 CAATGTGACAATGAAAGGTGGAC 58.451 43.478 0.00 0.00 0.00 4.02
5021 5119 8.682710 ACAACTGAATTTGTTTAGTAAAGCTGA 58.317 29.630 0.00 0.00 36.22 4.26
5043 5141 9.944663 TTTCACTTCTGATGTTTGTTATACAAC 57.055 29.630 0.00 0.00 37.90 3.32
5094 5192 8.902806 TGAAAATGTCATTGTGAAAGAGTACTT 58.097 29.630 0.00 0.00 38.05 2.24
5132 5237 2.639839 TCAGTTCAAAAGGAGCTAGCCT 59.360 45.455 12.13 0.00 40.93 4.58
5280 5387 9.506018 TCTCTTTCAGTTCAAATCATGTATCAA 57.494 29.630 0.00 0.00 0.00 2.57
5290 5397 7.546250 TCTACCTCTCTCTTTCAGTTCAAAT 57.454 36.000 0.00 0.00 0.00 2.32
5299 5406 6.922957 CACATGCTTATCTACCTCTCTCTTTC 59.077 42.308 0.00 0.00 0.00 2.62
5302 5409 5.454062 ACACATGCTTATCTACCTCTCTCT 58.546 41.667 0.00 0.00 0.00 3.10
5424 5532 7.895429 AGGATCAAGAAAATAAGTCCCATTTCA 59.105 33.333 0.00 0.00 34.91 2.69
5493 5601 6.101588 TGAATGAGATAATGGGACCATCAGAA 59.898 38.462 3.98 0.00 35.31 3.02
5494 5602 5.608015 TGAATGAGATAATGGGACCATCAGA 59.392 40.000 3.98 0.00 35.31 3.27
5499 5607 7.392766 AATACTGAATGAGATAATGGGACCA 57.607 36.000 0.00 0.00 0.00 4.02
5762 5870 2.488952 GATTCCTCCTCGCTTTCATCC 58.511 52.381 0.00 0.00 0.00 3.51
5801 5909 5.632034 AAAGGTACAGGTCAGAAAGACTT 57.368 39.130 0.00 0.00 46.72 3.01
5807 5915 6.681729 ATACAGAAAAGGTACAGGTCAGAA 57.318 37.500 0.00 0.00 0.00 3.02
5848 5956 9.848172 CATACTAAAAACTGTTCACAAAAATGC 57.152 29.630 0.00 0.00 0.00 3.56
6158 6268 3.517602 GTTTCACTTGTGTCCAAAACCC 58.482 45.455 0.46 0.00 0.00 4.11
6159 6269 3.056465 TGGTTTCACTTGTGTCCAAAACC 60.056 43.478 19.31 19.31 37.86 3.27
6163 6273 4.082845 TCTTTGGTTTCACTTGTGTCCAA 58.917 39.130 16.37 16.37 33.90 3.53
6189 6299 1.186917 TGGCATTGCTCAAAGGGGTG 61.187 55.000 8.82 0.00 0.00 4.61
6365 6484 3.175133 CCCAGGAAATCCTTGGTCG 57.825 57.895 10.72 0.00 46.09 4.79
6501 6631 4.690748 TCAGCTTCTCAAACTAAATCCACG 59.309 41.667 0.00 0.00 0.00 4.94
6502 6632 6.749923 ATCAGCTTCTCAAACTAAATCCAC 57.250 37.500 0.00 0.00 0.00 4.02
6503 6633 7.050377 CCTATCAGCTTCTCAAACTAAATCCA 58.950 38.462 0.00 0.00 0.00 3.41
6504 6634 7.051000 ACCTATCAGCTTCTCAAACTAAATCC 58.949 38.462 0.00 0.00 0.00 3.01
6505 6635 9.255304 CTACCTATCAGCTTCTCAAACTAAATC 57.745 37.037 0.00 0.00 0.00 2.17
6506 6636 8.982723 TCTACCTATCAGCTTCTCAAACTAAAT 58.017 33.333 0.00 0.00 0.00 1.40
6507 6637 8.251721 GTCTACCTATCAGCTTCTCAAACTAAA 58.748 37.037 0.00 0.00 0.00 1.85
6508 6638 7.396339 TGTCTACCTATCAGCTTCTCAAACTAA 59.604 37.037 0.00 0.00 0.00 2.24
6509 6639 6.890268 TGTCTACCTATCAGCTTCTCAAACTA 59.110 38.462 0.00 0.00 0.00 2.24
6510 6640 5.717178 TGTCTACCTATCAGCTTCTCAAACT 59.283 40.000 0.00 0.00 0.00 2.66
6511 6641 5.967088 TGTCTACCTATCAGCTTCTCAAAC 58.033 41.667 0.00 0.00 0.00 2.93
6674 6804 7.323895 CGCTACACTATATAGTTGCTACACAAG 59.676 40.741 12.87 0.87 39.50 3.16
6700 6830 6.741811 CGGCGAACATGTCTAGTTATATAGTC 59.258 42.308 0.00 0.00 0.00 2.59
6717 6847 1.880271 TGATTTACAACCGGCGAACA 58.120 45.000 9.30 0.00 0.00 3.18
6859 7080 8.773033 AGATTGTTAAATCCCTAATGCAAGAT 57.227 30.769 0.00 0.00 42.84 2.40
6860 7081 8.469200 CAAGATTGTTAAATCCCTAATGCAAGA 58.531 33.333 0.00 0.00 42.84 3.02
6878 7099 7.981225 AGCAAACTTCACAAATAACAAGATTGT 59.019 29.630 0.00 0.00 44.72 2.71
6879 7100 8.356533 AGCAAACTTCACAAATAACAAGATTG 57.643 30.769 0.00 0.00 33.84 2.67
6881 7102 7.945134 AGAGCAAACTTCACAAATAACAAGAT 58.055 30.769 0.00 0.00 0.00 2.40
6882 7103 7.333528 AGAGCAAACTTCACAAATAACAAGA 57.666 32.000 0.00 0.00 0.00 3.02
6883 7104 7.168135 GGAAGAGCAAACTTCACAAATAACAAG 59.832 37.037 16.04 0.00 45.39 3.16
6898 7184 0.110486 TCCCACCTGGAAGAGCAAAC 59.890 55.000 0.00 0.00 41.40 2.93
6962 7248 5.715070 ACACAAGATTGTCCGTTTCAAAAA 58.285 33.333 0.00 0.00 39.91 1.94
6963 7249 5.317733 ACACAAGATTGTCCGTTTCAAAA 57.682 34.783 0.00 0.00 39.91 2.44
6964 7250 4.974368 ACACAAGATTGTCCGTTTCAAA 57.026 36.364 0.00 0.00 39.91 2.69
6965 7251 4.974368 AACACAAGATTGTCCGTTTCAA 57.026 36.364 0.00 0.00 39.91 2.69
6966 7252 6.627395 AATAACACAAGATTGTCCGTTTCA 57.373 33.333 6.71 0.00 39.91 2.69
6967 7253 6.915843 ACAAATAACACAAGATTGTCCGTTTC 59.084 34.615 6.71 0.00 39.91 2.78
6968 7254 6.695278 CACAAATAACACAAGATTGTCCGTTT 59.305 34.615 6.71 0.23 39.91 3.60
6969 7255 6.038825 TCACAAATAACACAAGATTGTCCGTT 59.961 34.615 0.00 1.49 39.91 4.44
6970 7256 5.529430 TCACAAATAACACAAGATTGTCCGT 59.471 36.000 0.00 0.00 39.91 4.69
6971 7257 5.996219 TCACAAATAACACAAGATTGTCCG 58.004 37.500 0.00 0.00 39.91 4.79
6972 7258 6.308766 GCATCACAAATAACACAAGATTGTCC 59.691 38.462 0.00 0.00 39.91 4.02
6973 7259 6.862608 TGCATCACAAATAACACAAGATTGTC 59.137 34.615 0.00 0.00 39.91 3.18
6974 7260 6.747125 TGCATCACAAATAACACAAGATTGT 58.253 32.000 0.00 0.00 43.36 2.71
6975 7261 7.595875 TCTTGCATCACAAATAACACAAGATTG 59.404 33.333 0.00 0.00 37.83 2.67
6976 7262 7.596248 GTCTTGCATCACAAATAACACAAGATT 59.404 33.333 0.00 0.00 42.77 2.40
6977 7263 7.086376 GTCTTGCATCACAAATAACACAAGAT 58.914 34.615 0.00 0.00 42.77 2.40
6978 7264 6.039159 TGTCTTGCATCACAAATAACACAAGA 59.961 34.615 0.00 0.00 39.77 3.02
6979 7265 6.207928 TGTCTTGCATCACAAATAACACAAG 58.792 36.000 0.00 0.00 37.96 3.16
6980 7266 6.141560 TGTCTTGCATCACAAATAACACAA 57.858 33.333 0.00 0.00 37.96 3.33
6981 7267 5.764487 TGTCTTGCATCACAAATAACACA 57.236 34.783 0.00 0.00 37.96 3.72
7124 7414 0.552848 CTGGGGCCTATCCAACATGT 59.447 55.000 0.84 0.00 36.21 3.21
7382 7675 1.543802 TGGATCGGTGGTGAATTTTGC 59.456 47.619 0.00 0.00 0.00 3.68
7441 7738 1.227383 GACCCGATCCCAAGCCAAT 59.773 57.895 0.00 0.00 0.00 3.16
7442 7739 2.674754 GACCCGATCCCAAGCCAA 59.325 61.111 0.00 0.00 0.00 4.52
7452 7749 4.492303 ATCCCCACCCGACCCGAT 62.492 66.667 0.00 0.00 0.00 4.18
7455 7752 2.772622 ATCATCCCCACCCGACCC 60.773 66.667 0.00 0.00 0.00 4.46
7456 7753 1.345715 AAGATCATCCCCACCCGACC 61.346 60.000 0.00 0.00 0.00 4.79
7457 7754 1.070289 GTAAGATCATCCCCACCCGAC 59.930 57.143 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.