Multiple sequence alignment - TraesCS5A01G423800

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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 TraesCS5A01G423800 chr5A 100.000 4406 0 0 1 4406 609270748 609275153 0.000000e+00 8137
1 TraesCS5A01G423800 chr5B 90.365 3508 231 58 482 3928 601416131 601419592 0.000000e+00 4506
2 TraesCS5A01G423800 chr5B 84.797 296 33 8 54 339 601415320 601415613 2.010000e-73 287
3 TraesCS5A01G423800 chr5B 92.857 84 5 1 373 455 601415614 601415697 2.150000e-23 121
4 TraesCS5A01G423800 chr5D 92.330 2777 138 36 1 2739 488432237 488434976 0.000000e+00 3879
5 TraesCS5A01G423800 chr5D 92.457 464 27 5 2768 3224 488434969 488435431 0.000000e+00 656
6 TraesCS5A01G423800 chr5D 82.955 352 37 13 3315 3650 488435463 488435807 3.330000e-76 296
7 TraesCS5A01G423800 chr5D 80.510 431 45 13 3968 4392 488436104 488436501 1.200000e-75 294


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 TraesCS5A01G423800 chr5A 609270748 609275153 4405 False 8137.00 8137 100.000000 1 4406 1 chr5A.!!$F1 4405
1 TraesCS5A01G423800 chr5B 601415320 601419592 4272 False 1638.00 4506 89.339667 54 3928 3 chr5B.!!$F1 3874
2 TraesCS5A01G423800 chr5D 488432237 488436501 4264 False 1281.25 3879 87.063000 1 4392 4 chr5D.!!$F1 4391

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
642 1069 0.252467 TGGGGCGAAATGGGGAAATT 60.252 50.000 0.00 0.0 0.00 1.82 F
1128 1562 0.174389 CCGCTGATGAGCTGTGTACT 59.826 55.000 1.81 0.0 43.77 2.73 F
1132 1566 0.250234 TGATGAGCTGTGTACTGCCC 59.750 55.000 9.80 0.0 41.03 5.36 F
1417 1877 0.391528 TGCGCTATCAGCAAGCTTCA 60.392 50.000 9.73 0.0 42.58 3.02 F
2495 2961 2.225091 TGTTCCCTGTGGATTGATTGCT 60.225 45.455 0.00 0.0 41.40 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2570 3036 1.275291 TGTTCCCGATCACTTCTCCAC 59.725 52.381 0.0 0.0 0.00 4.02 R
2779 3245 0.396974 AGCTGGCAAAAGGACACCAA 60.397 50.000 0.0 0.0 0.00 3.67 R
2780 3246 0.476338 TAGCTGGCAAAAGGACACCA 59.524 50.000 0.0 0.0 0.00 4.17 R
2781 3247 1.541588 CTTAGCTGGCAAAAGGACACC 59.458 52.381 0.0 0.0 0.00 4.16 R
4253 4817 0.040336 GACGCACGACTGAAGACAGA 60.040 55.000 0.0 0.0 46.03 3.41 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
63 64 3.968227 TCGAGAGAAACTGCTAACGGCA 61.968 50.000 0.00 0.00 43.28 5.69
105 106 3.587506 TCCTTTTCCCTACTCCTTTCTGG 59.412 47.826 0.00 0.00 37.10 3.86
110 111 3.442076 TCCCTACTCCTTTCTGGACTTC 58.558 50.000 0.00 0.00 40.56 3.01
119 120 4.006319 CCTTTCTGGACTTCTTGGATGTC 58.994 47.826 5.39 5.39 38.35 3.06
135 136 8.222637 TCTTGGATGTCATTTCCTCATCATAAT 58.777 33.333 0.00 0.00 39.47 1.28
155 156 1.961793 TCGGTTGAGTGTTGAAAGGG 58.038 50.000 0.00 0.00 0.00 3.95
236 245 4.898829 TGAATTGAGCCACCAAATATCG 57.101 40.909 0.00 0.00 0.00 2.92
239 248 3.627395 TTGAGCCACCAAATATCGTCT 57.373 42.857 0.00 0.00 0.00 4.18
240 249 3.179443 TGAGCCACCAAATATCGTCTC 57.821 47.619 0.00 0.00 0.00 3.36
242 251 1.141053 AGCCACCAAATATCGTCTCCC 59.859 52.381 0.00 0.00 0.00 4.30
245 254 3.555168 GCCACCAAATATCGTCTCCCTAG 60.555 52.174 0.00 0.00 0.00 3.02
260 269 5.760743 GTCTCCCTAGACCTAAAAATGATGC 59.239 44.000 0.00 0.00 45.50 3.91
265 276 5.584649 CCTAGACCTAAAAATGATGCGTTCA 59.415 40.000 0.00 0.00 39.12 3.18
282 293 4.680708 GCGTTCAATCCATAGGAGAGTGAA 60.681 45.833 0.02 0.02 34.05 3.18
344 359 9.458374 CCAATGGTTTAATCGAACATTTATACC 57.542 33.333 8.39 8.39 32.95 2.73
352 367 5.670792 TCGAACATTTATACCCACTGTCT 57.329 39.130 0.00 0.00 0.00 3.41
366 381 4.530857 GTCTGCTGCCCCGCGTAT 62.531 66.667 4.92 0.00 0.00 3.06
374 389 2.522436 CCCCGCGTATCCCACCTA 60.522 66.667 4.92 0.00 0.00 3.08
393 408 3.843027 CCTACGATCCTACCCTAGGTCTA 59.157 52.174 8.29 0.00 46.32 2.59
396 411 2.038295 CGATCCTACCCTAGGTCTACGT 59.962 54.545 8.29 0.03 46.32 3.57
404 420 2.483491 CCCTAGGTCTACGTAGAATCGC 59.517 54.545 26.21 13.84 36.68 4.58
642 1069 0.252467 TGGGGCGAAATGGGGAAATT 60.252 50.000 0.00 0.00 0.00 1.82
750 1177 0.536460 AACCCAAAGCCCACACTACG 60.536 55.000 0.00 0.00 0.00 3.51
788 1215 1.069596 CACCTTTGCTGGCCCAAAC 59.930 57.895 0.00 0.00 31.85 2.93
873 1307 4.106925 GGCTCTCCCACCTGCAGG 62.107 72.222 31.60 31.60 42.17 4.85
874 1308 4.792804 GCTCTCCCACCTGCAGGC 62.793 72.222 33.06 12.19 39.32 4.85
875 1309 3.007920 CTCTCCCACCTGCAGGCT 61.008 66.667 33.06 16.98 39.32 4.58
876 1310 3.324930 TCTCCCACCTGCAGGCTG 61.325 66.667 33.06 26.25 39.32 4.85
901 1335 0.608640 TCTGTTCTTCTTCTCCGGCC 59.391 55.000 0.00 0.00 0.00 6.13
1083 1517 1.002011 GGGAGGTGAGCCAGGTTTC 60.002 63.158 0.00 0.00 37.19 2.78
1127 1561 1.424493 GCCGCTGATGAGCTGTGTAC 61.424 60.000 1.81 0.00 43.77 2.90
1128 1562 0.174389 CCGCTGATGAGCTGTGTACT 59.826 55.000 1.81 0.00 43.77 2.73
1131 1565 1.649664 CTGATGAGCTGTGTACTGCC 58.350 55.000 9.80 3.65 41.03 4.85
1132 1566 0.250234 TGATGAGCTGTGTACTGCCC 59.750 55.000 9.80 0.00 41.03 5.36
1135 1569 2.529136 AGCTGTGTACTGCCCCCA 60.529 61.111 9.80 0.00 41.03 4.96
1152 1586 0.532573 CCATCTGCGTGACTAGGTGT 59.467 55.000 0.00 0.00 0.00 4.16
1171 1605 1.741770 CTCCGTGTGCTAGGGTTGC 60.742 63.158 0.00 0.00 35.77 4.17
1179 1613 3.071580 GCTAGGGTTGCTAGCTGTG 57.928 57.895 17.23 0.63 44.49 3.66
1197 1631 4.104696 TGTGTGCGATCTCGAGAAATTA 57.895 40.909 20.91 3.94 43.02 1.40
1246 1680 8.684520 GCTATATATGGATTTACCTCTACGTGT 58.315 37.037 0.00 0.00 39.86 4.49
1253 1693 5.803967 GGATTTACCTCTACGTGTTAGTGTG 59.196 44.000 0.00 0.00 35.41 3.82
1256 1696 3.973657 ACCTCTACGTGTTAGTGTGTTG 58.026 45.455 0.00 0.00 0.00 3.33
1266 1706 3.382865 TGTTAGTGTGTTGTACGGTGGTA 59.617 43.478 0.00 0.00 0.00 3.25
1271 1711 1.796459 GTGTTGTACGGTGGTAGCTTG 59.204 52.381 0.00 0.00 0.00 4.01
1272 1712 1.687660 TGTTGTACGGTGGTAGCTTGA 59.312 47.619 0.00 0.00 0.00 3.02
1273 1713 2.064014 GTTGTACGGTGGTAGCTTGAC 58.936 52.381 0.00 0.00 0.00 3.18
1346 1799 3.050619 CGCATAGGGTTAATCGAGTGAC 58.949 50.000 0.00 0.00 0.00 3.67
1347 1800 3.490249 CGCATAGGGTTAATCGAGTGACA 60.490 47.826 10.02 0.00 0.00 3.58
1368 1821 7.867403 GTGACAAAATAAGTCATCCACAACATT 59.133 33.333 0.00 0.00 46.52 2.71
1417 1877 0.391528 TGCGCTATCAGCAAGCTTCA 60.392 50.000 9.73 0.00 42.58 3.02
1454 1916 8.903570 TTACTGAAATTGTTTGTTACACAGTG 57.096 30.769 10.02 0.00 39.39 3.66
1455 1917 7.151999 ACTGAAATTGTTTGTTACACAGTGA 57.848 32.000 7.81 0.00 38.32 3.41
1458 1920 7.471721 TGAAATTGTTTGTTACACAGTGAGAG 58.528 34.615 7.81 0.00 36.21 3.20
1460 1922 7.624360 AATTGTTTGTTACACAGTGAGAGAA 57.376 32.000 7.81 0.00 36.21 2.87
1475 1937 6.366061 CAGTGAGAGAATGAATGTCGTTTACA 59.634 38.462 0.00 0.00 43.86 2.41
1549 2011 7.931407 TCATGTCGGTTTTGCAGTATTCTATAT 59.069 33.333 0.00 0.00 0.00 0.86
1615 2077 2.361119 CAGGATACGTAAGCTGGCACTA 59.639 50.000 0.00 0.00 46.39 2.74
1667 2129 7.094762 GGCATTAAGTATTTGCATAGTACTCCC 60.095 40.741 0.00 0.00 38.12 4.30
1740 2203 8.982091 TGATAATTGGGATTATTTTCGTACCA 57.018 30.769 0.00 0.00 38.31 3.25
1781 2244 8.774586 TCTTCAAGCTTCAAACAGAGTAATAAC 58.225 33.333 0.00 0.00 0.00 1.89
1834 2297 4.517952 TGGCATTAGTTTGGTTGTCATG 57.482 40.909 0.00 0.00 0.00 3.07
2067 2530 7.553044 ACAGGCTGGACTATAATTTCTTTGTAC 59.447 37.037 20.34 0.00 0.00 2.90
2096 2559 2.687935 TGAGTTCAGTTTGGGACTTTGC 59.312 45.455 0.00 0.00 36.10 3.68
2144 2608 8.936864 CAGTTTTCTTGTCCTATCTTCGTAATT 58.063 33.333 0.00 0.00 0.00 1.40
2150 2614 9.151471 TCTTGTCCTATCTTCGTAATTTTTCTG 57.849 33.333 0.00 0.00 0.00 3.02
2312 2777 6.235664 ACAACTGATTAATTTACTGGTCGGT 58.764 36.000 0.00 0.00 0.00 4.69
2319 2784 7.546667 TGATTAATTTACTGGTCGGTGTCTTAC 59.453 37.037 0.00 0.00 0.00 2.34
2340 2805 7.872993 TCTTACAAGAAGAAACACTATGTCCTG 59.127 37.037 0.00 0.00 30.73 3.86
2450 2916 2.288640 TGATAGCTCATGCAGTCCGATG 60.289 50.000 0.00 0.00 42.74 3.84
2495 2961 2.225091 TGTTCCCTGTGGATTGATTGCT 60.225 45.455 0.00 0.00 41.40 3.91
2570 3036 7.312154 TGATGGTTGATAGGAAAAACATTTCG 58.688 34.615 0.00 0.00 33.89 3.46
2601 3067 2.922740 TCGGGAACATAAGTATGGCC 57.077 50.000 0.00 0.00 38.00 5.36
2753 3219 7.672983 TCCTTAAGAAGACAAGTTAATGCTG 57.327 36.000 3.36 0.00 0.00 4.41
2762 3228 7.112452 AGACAAGTTAATGCTGGTTTTCTTT 57.888 32.000 0.00 0.00 0.00 2.52
2763 3229 7.555965 AGACAAGTTAATGCTGGTTTTCTTTT 58.444 30.769 0.00 0.00 0.00 2.27
2766 3232 9.260002 ACAAGTTAATGCTGGTTTTCTTTTATG 57.740 29.630 0.00 0.00 0.00 1.90
2865 3331 1.804748 CCCCAGTTTCGAAAGCTGTAC 59.195 52.381 25.21 11.67 0.00 2.90
2979 3445 3.568007 GCCTGGTTCTTACAACATCAACA 59.432 43.478 0.00 0.00 0.00 3.33
3092 3558 6.022315 TCCATGTGAAAATCCCAAGGTAATT 58.978 36.000 0.00 0.00 0.00 1.40
3109 3575 9.927668 CAAGGTAATTGATAAGGTGAATGTTTT 57.072 29.630 0.00 0.00 41.83 2.43
3140 3608 4.223923 CCCTTGTGACCATCTTCTACTTCT 59.776 45.833 0.00 0.00 0.00 2.85
3143 3611 6.295575 CCTTGTGACCATCTTCTACTTCTTCT 60.296 42.308 0.00 0.00 0.00 2.85
3178 3646 1.202110 GCATGTTGTCTGAAGGCGATG 60.202 52.381 0.00 0.00 0.00 3.84
3202 3674 6.553852 TGATACTACTAGTCTTTGATTCCCCC 59.446 42.308 0.00 0.00 0.00 5.40
3257 3730 4.320275 GCAGTAAACAAAACCTCCTAGTGC 60.320 45.833 0.00 0.00 0.00 4.40
3258 3731 5.063880 CAGTAAACAAAACCTCCTAGTGCT 58.936 41.667 0.00 0.00 0.00 4.40
3266 3739 3.340814 ACCTCCTAGTGCTGATTGTTG 57.659 47.619 0.00 0.00 0.00 3.33
3278 3751 5.808540 GTGCTGATTGTTGAATTGCATGTAT 59.191 36.000 0.00 0.00 35.35 2.29
3292 3765 8.546597 AATTGCATGTATATTCACATACGCTA 57.453 30.769 0.00 0.00 37.02 4.26
3295 3768 9.816354 TTGCATGTATATTCACATACGCTATAT 57.184 29.630 0.00 0.00 37.02 0.86
3428 3904 5.766222 AGCTTCTGTGCATAGTTCTTTTTG 58.234 37.500 10.52 0.00 34.99 2.44
3554 4037 2.184322 TGCCGTGCAGCTAGTAGC 59.816 61.111 14.62 14.62 42.84 3.58
3579 4062 4.101448 CCTGGCCAGAGGTTCCCG 62.101 72.222 34.91 10.80 0.00 5.14
3601 4091 4.351938 CGTTCCGTCTCCGCACCA 62.352 66.667 0.00 0.00 0.00 4.17
3648 4138 3.503748 GCAGCTTCAGGTTTCATACACTT 59.496 43.478 0.00 0.00 0.00 3.16
3715 4205 7.056006 TCATACACATACTTGGAGCATGAAAT 58.944 34.615 0.00 0.00 0.00 2.17
3803 4324 6.466885 ACTAGAGCCGTGTAAAACTGATAT 57.533 37.500 0.00 0.00 0.00 1.63
3804 4325 7.578310 ACTAGAGCCGTGTAAAACTGATATA 57.422 36.000 0.00 0.00 0.00 0.86
3805 4326 8.179509 ACTAGAGCCGTGTAAAACTGATATAT 57.820 34.615 0.00 0.00 0.00 0.86
3806 4327 9.293404 ACTAGAGCCGTGTAAAACTGATATATA 57.707 33.333 0.00 0.00 0.00 0.86
3807 4328 9.557338 CTAGAGCCGTGTAAAACTGATATATAC 57.443 37.037 0.00 0.00 0.00 1.47
3808 4329 8.179509 AGAGCCGTGTAAAACTGATATATACT 57.820 34.615 0.00 0.00 0.00 2.12
3809 4330 8.639761 AGAGCCGTGTAAAACTGATATATACTT 58.360 33.333 0.00 0.00 0.00 2.24
3810 4331 8.589335 AGCCGTGTAAAACTGATATATACTTG 57.411 34.615 0.00 0.00 0.00 3.16
3811 4332 7.656137 AGCCGTGTAAAACTGATATATACTTGG 59.344 37.037 0.00 0.00 0.00 3.61
3812 4333 7.654520 GCCGTGTAAAACTGATATATACTTGGA 59.345 37.037 0.00 0.00 0.00 3.53
3813 4334 9.193133 CCGTGTAAAACTGATATATACTTGGAG 57.807 37.037 0.00 0.00 0.00 3.86
3912 4451 1.512694 GAAGCATGCTTTTCCCCCG 59.487 57.895 32.36 0.00 36.26 5.73
3916 4455 1.512694 CATGCTTTTCCCCCGCTTC 59.487 57.895 0.00 0.00 0.00 3.86
3930 4469 2.547007 CCCGCTTCAAAAATCCGGTTTT 60.547 45.455 0.00 2.22 41.69 2.43
3944 4483 1.976045 CGGTTTTGCGTGCATTTCTAC 59.024 47.619 0.00 0.00 0.00 2.59
3945 4484 2.603412 CGGTTTTGCGTGCATTTCTACA 60.603 45.455 0.00 0.00 0.00 2.74
3946 4485 3.574614 GGTTTTGCGTGCATTTCTACAT 58.425 40.909 0.00 0.00 0.00 2.29
3947 4486 4.670478 CGGTTTTGCGTGCATTTCTACATA 60.670 41.667 0.00 0.00 0.00 2.29
3948 4487 4.793216 GGTTTTGCGTGCATTTCTACATAG 59.207 41.667 0.00 0.00 0.00 2.23
3949 4488 3.673746 TTGCGTGCATTTCTACATAGC 57.326 42.857 0.00 0.00 0.00 2.97
3950 4489 2.626840 TGCGTGCATTTCTACATAGCA 58.373 42.857 0.00 0.00 32.50 3.49
3951 4490 3.205338 TGCGTGCATTTCTACATAGCAT 58.795 40.909 0.00 0.00 37.56 3.79
3952 4491 3.248363 TGCGTGCATTTCTACATAGCATC 59.752 43.478 0.00 0.00 37.56 3.91
3953 4492 3.248363 GCGTGCATTTCTACATAGCATCA 59.752 43.478 0.00 0.00 37.56 3.07
3954 4493 4.260743 GCGTGCATTTCTACATAGCATCAA 60.261 41.667 0.00 0.00 37.56 2.57
3955 4494 5.200454 CGTGCATTTCTACATAGCATCAAC 58.800 41.667 0.00 0.00 37.56 3.18
3956 4495 5.220643 CGTGCATTTCTACATAGCATCAACA 60.221 40.000 0.00 0.00 37.56 3.33
3957 4496 6.512253 CGTGCATTTCTACATAGCATCAACAT 60.512 38.462 0.00 0.00 37.56 2.71
3958 4497 6.854892 GTGCATTTCTACATAGCATCAACATC 59.145 38.462 0.00 0.00 37.56 3.06
3962 4501 3.641436 TCTACATAGCATCAACATCCGGT 59.359 43.478 0.00 0.00 0.00 5.28
3996 4560 2.034685 GGATCACTACAGCTGCATACGA 59.965 50.000 15.27 4.70 0.00 3.43
4002 4566 4.386954 CACTACAGCTGCATACGATAATGG 59.613 45.833 15.27 0.00 0.00 3.16
4031 4595 1.731093 CGGAAGCGGGTTTGTTTGT 59.269 52.632 0.00 0.00 0.00 2.83
4035 4599 0.463620 AAGCGGGTTTGTTTGTGCAT 59.536 45.000 0.00 0.00 0.00 3.96
4037 4601 0.529555 GCGGGTTTGTTTGTGCATGT 60.530 50.000 0.00 0.00 0.00 3.21
4049 4613 1.340889 TGTGCATGTTTTTCTCTGGCC 59.659 47.619 0.00 0.00 0.00 5.36
4083 4647 2.125552 TGCTTCCTCCATCGCGTG 60.126 61.111 5.77 3.64 0.00 5.34
4085 4649 2.125552 CTTCCTCCATCGCGTGCA 60.126 61.111 5.77 0.00 0.00 4.57
4088 4652 1.960040 TTCCTCCATCGCGTGCAGAT 61.960 55.000 5.77 0.00 0.00 2.90
4091 4655 0.599466 CTCCATCGCGTGCAGATCAT 60.599 55.000 5.77 0.00 0.00 2.45
4093 4657 0.877213 CCATCGCGTGCAGATCATCA 60.877 55.000 5.77 0.00 0.00 3.07
4094 4658 0.231534 CATCGCGTGCAGATCATCAC 59.768 55.000 5.77 1.25 0.00 3.06
4095 4659 0.877649 ATCGCGTGCAGATCATCACC 60.878 55.000 5.77 4.64 0.00 4.02
4096 4660 1.520120 CGCGTGCAGATCATCACCT 60.520 57.895 0.00 0.00 0.00 4.00
4098 4662 0.179089 GCGTGCAGATCATCACCTCT 60.179 55.000 10.51 0.00 0.00 3.69
4099 4663 1.850377 CGTGCAGATCATCACCTCTC 58.150 55.000 10.51 0.00 0.00 3.20
4100 4664 1.135721 CGTGCAGATCATCACCTCTCA 59.864 52.381 10.51 0.00 0.00 3.27
4101 4665 2.223994 CGTGCAGATCATCACCTCTCAT 60.224 50.000 10.51 0.00 0.00 2.90
4102 4666 3.391965 GTGCAGATCATCACCTCTCATC 58.608 50.000 0.00 0.00 0.00 2.92
4103 4667 2.035576 TGCAGATCATCACCTCTCATCG 59.964 50.000 0.00 0.00 0.00 3.84
4104 4668 2.674954 CAGATCATCACCTCTCATCGC 58.325 52.381 0.00 0.00 0.00 4.58
4105 4669 1.269174 AGATCATCACCTCTCATCGCG 59.731 52.381 0.00 0.00 0.00 5.87
4106 4670 0.319383 ATCATCACCTCTCATCGCGC 60.319 55.000 0.00 0.00 0.00 6.86
4107 4671 2.026734 ATCACCTCTCATCGCGCG 59.973 61.111 26.76 26.76 0.00 6.86
4108 4672 4.854784 TCACCTCTCATCGCGCGC 62.855 66.667 27.95 23.91 0.00 6.86
4131 4695 1.302192 TCCGGCACTAGCAACCAAC 60.302 57.895 0.00 0.00 44.61 3.77
4134 4698 1.228429 GGCACTAGCAACCAACCCA 60.228 57.895 0.00 0.00 44.61 4.51
4153 4717 2.880879 CCGCGACGTGACCATCTG 60.881 66.667 8.23 0.00 0.00 2.90
4174 4738 2.520982 CCCCGATAGTCTCCGGCA 60.521 66.667 0.00 0.00 44.07 5.69
4203 4767 1.364626 CCATTGCCTCAGACGACAGC 61.365 60.000 0.00 0.00 0.00 4.40
4207 4771 4.135153 CCTCAGACGACAGCCCCG 62.135 72.222 0.00 0.00 0.00 5.73
4217 4781 2.180159 GACAGCCCCGCCTGAACTTA 62.180 60.000 3.46 0.00 36.67 2.24
4221 4785 1.900545 GCCCCGCCTGAACTTACTCT 61.901 60.000 0.00 0.00 0.00 3.24
4228 4792 3.736433 CGCCTGAACTTACTCTCAGATGG 60.736 52.174 0.68 0.00 41.38 3.51
4231 4795 4.441356 CCTGAACTTACTCTCAGATGGCTC 60.441 50.000 0.68 0.00 41.38 4.70
4248 4812 3.857854 CGCCAGCGCAGACATGAC 61.858 66.667 11.47 0.00 34.03 3.06
4250 4814 3.857854 CCAGCGCAGACATGACGC 61.858 66.667 11.47 15.58 45.82 5.19
4253 4817 2.507992 GCGCAGACATGACGCTCT 60.508 61.111 0.30 0.00 43.72 4.09
4254 4818 2.512301 GCGCAGACATGACGCTCTC 61.512 63.158 0.30 0.00 43.72 3.20
4255 4819 1.138459 CGCAGACATGACGCTCTCT 59.862 57.895 0.00 0.00 0.00 3.10
4257 4821 0.108898 GCAGACATGACGCTCTCTGT 60.109 55.000 0.00 0.00 33.92 3.41
4260 4824 2.094803 CAGACATGACGCTCTCTGTCTT 60.095 50.000 0.00 0.00 44.39 3.01
4261 4825 2.163412 AGACATGACGCTCTCTGTCTTC 59.837 50.000 0.00 0.00 44.39 2.87
4262 4826 1.889170 ACATGACGCTCTCTGTCTTCA 59.111 47.619 0.00 0.00 37.26 3.02
4305 4875 1.065926 GGAGGCTCACATCACATCACA 60.066 52.381 17.69 0.00 0.00 3.58
4306 4876 2.421107 GGAGGCTCACATCACATCACAT 60.421 50.000 17.69 0.00 0.00 3.21
4307 4877 2.871022 GAGGCTCACATCACATCACATC 59.129 50.000 10.25 0.00 0.00 3.06
4308 4878 2.237893 AGGCTCACATCACATCACATCA 59.762 45.455 0.00 0.00 0.00 3.07
4309 4879 2.353889 GGCTCACATCACATCACATCAC 59.646 50.000 0.00 0.00 0.00 3.06
4311 4881 2.941064 CTCACATCACATCACATCACCC 59.059 50.000 0.00 0.00 0.00 4.61
4312 4882 2.305343 TCACATCACATCACATCACCCA 59.695 45.455 0.00 0.00 0.00 4.51
4320 4890 4.415150 ACATCACCCAGCGCCCTG 62.415 66.667 2.29 0.00 38.85 4.45
4337 4907 2.099652 CTGTCAGCGACCCAACCAGA 62.100 60.000 6.30 0.00 0.00 3.86
4353 4923 1.002888 CCAGAGCAGCTCTCCTTTTCA 59.997 52.381 22.91 0.00 42.90 2.69
4354 4924 2.348660 CAGAGCAGCTCTCCTTTTCAG 58.651 52.381 22.91 4.83 42.90 3.02
4355 4925 1.085893 GAGCAGCTCTCCTTTTCAGC 58.914 55.000 15.78 0.00 35.77 4.26
4356 4926 0.691904 AGCAGCTCTCCTTTTCAGCT 59.308 50.000 0.00 0.00 44.59 4.24
4357 4927 1.905215 AGCAGCTCTCCTTTTCAGCTA 59.095 47.619 0.00 0.00 41.73 3.32
4358 4928 2.093553 AGCAGCTCTCCTTTTCAGCTAG 60.094 50.000 0.00 0.00 41.73 3.42
4384 4954 4.374702 CAGCTGCAACACGTCGCC 62.375 66.667 0.00 0.00 0.00 5.54
4385 4955 4.609018 AGCTGCAACACGTCGCCT 62.609 61.111 1.02 0.00 0.00 5.52
4392 4962 2.877974 AACACGTCGCCTCGTTTGC 61.878 57.895 0.00 0.00 42.27 3.68
4393 4963 4.072088 CACGTCGCCTCGTTTGCC 62.072 66.667 0.00 0.00 42.27 4.52
4400 4970 3.726517 CCTCGTTTGCCGCACCTG 61.727 66.667 0.00 0.00 36.19 4.00
4401 4971 4.389576 CTCGTTTGCCGCACCTGC 62.390 66.667 0.00 0.00 36.19 4.85
4403 4973 4.041917 CGTTTGCCGCACCTGCAT 62.042 61.111 0.00 0.00 42.21 3.96
4404 4974 2.126346 GTTTGCCGCACCTGCATC 60.126 61.111 0.00 0.00 42.21 3.91
4405 4975 2.282391 TTTGCCGCACCTGCATCT 60.282 55.556 0.00 0.00 42.21 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 5.014858 TCTCTCGATTACAAACTACAGGGT 58.985 41.667 0.00 0.00 0.00 4.34
60 61 3.077359 AGCTGAGTTTGACTTATGTGCC 58.923 45.455 0.00 0.00 0.00 5.01
63 64 6.552445 AGGATAGCTGAGTTTGACTTATGT 57.448 37.500 0.00 0.00 0.00 2.29
105 106 5.248640 TGAGGAAATGACATCCAAGAAGTC 58.751 41.667 0.00 0.00 39.55 3.01
110 111 7.812690 TTATGATGAGGAAATGACATCCAAG 57.187 36.000 0.00 0.00 39.55 3.61
119 120 7.012704 ACTCAACCGAATTATGATGAGGAAATG 59.987 37.037 14.49 0.00 38.81 2.32
135 136 2.092861 TCCCTTTCAACACTCAACCGAA 60.093 45.455 0.00 0.00 0.00 4.30
180 188 6.106003 GTGAAAAATATAGGGGGTTTTGCTG 58.894 40.000 0.00 0.00 0.00 4.41
239 248 4.163458 ACGCATCATTTTTAGGTCTAGGGA 59.837 41.667 0.00 0.00 0.00 4.20
240 249 4.451900 ACGCATCATTTTTAGGTCTAGGG 58.548 43.478 0.00 0.00 0.00 3.53
242 251 6.662414 TGAACGCATCATTTTTAGGTCTAG 57.338 37.500 0.00 0.00 31.50 2.43
245 254 5.743872 GGATTGAACGCATCATTTTTAGGTC 59.256 40.000 0.00 0.00 38.03 3.85
259 268 3.126831 CACTCTCCTATGGATTGAACGC 58.873 50.000 0.00 0.00 0.00 4.84
260 269 4.655762 TCACTCTCCTATGGATTGAACG 57.344 45.455 0.00 0.00 0.00 3.95
265 276 3.452627 ACGCTTTCACTCTCCTATGGATT 59.547 43.478 0.00 0.00 0.00 3.01
282 293 1.482182 TGATCTACAGCCATCACGCTT 59.518 47.619 0.00 0.00 36.82 4.68
364 379 2.042162 GGGTAGGATCGTAGGTGGGATA 59.958 54.545 0.00 0.00 0.00 2.59
366 381 0.186873 GGGTAGGATCGTAGGTGGGA 59.813 60.000 0.00 0.00 0.00 4.37
393 408 0.671163 TTTTGGGCGCGATTCTACGT 60.671 50.000 12.10 0.00 35.59 3.57
396 411 4.023536 GGATTTATTTTGGGCGCGATTCTA 60.024 41.667 12.10 0.00 0.00 2.10
404 420 3.525268 AAGCTGGATTTATTTTGGGCG 57.475 42.857 0.00 0.00 0.00 6.13
485 908 4.791069 ACCCCGGTCGCCAGGTAT 62.791 66.667 0.00 0.00 29.36 2.73
642 1069 3.506096 CGTCGCGGTCAGGAGCTA 61.506 66.667 6.13 0.00 0.00 3.32
788 1215 2.584391 GCTAGGCCCGGTGGATAGG 61.584 68.421 0.00 0.00 0.00 2.57
816 1247 0.396417 AGAGAGTGACGAGGGGGATG 60.396 60.000 0.00 0.00 0.00 3.51
822 1253 1.797441 CACGGAGAGAGTGACGAGG 59.203 63.158 0.00 0.00 41.83 4.63
824 1255 1.302591 AGCACGGAGAGAGTGACGA 60.303 57.895 0.07 0.00 41.83 4.20
825 1256 1.154131 CAGCACGGAGAGAGTGACG 60.154 63.158 0.07 0.00 41.83 4.35
826 1257 0.109504 GTCAGCACGGAGAGAGTGAC 60.110 60.000 0.07 0.00 41.83 3.67
827 1258 1.244697 GGTCAGCACGGAGAGAGTGA 61.245 60.000 0.07 0.00 41.83 3.41
829 1260 1.075836 AGGTCAGCACGGAGAGAGT 59.924 57.895 0.00 0.00 0.00 3.24
873 1307 1.451067 AGAAGAACAGATGCTGCAGC 58.549 50.000 31.89 31.89 42.50 5.25
874 1308 3.336468 AGAAGAAGAACAGATGCTGCAG 58.664 45.455 10.11 10.11 34.37 4.41
875 1309 3.332919 GAGAAGAAGAACAGATGCTGCA 58.667 45.455 4.13 4.13 34.37 4.41
876 1310 2.677337 GGAGAAGAAGAACAGATGCTGC 59.323 50.000 0.00 0.00 34.37 5.25
877 1311 2.928757 CGGAGAAGAAGAACAGATGCTG 59.071 50.000 0.00 0.00 37.52 4.41
878 1312 2.093764 CCGGAGAAGAAGAACAGATGCT 60.094 50.000 0.00 0.00 0.00 3.79
879 1313 2.275318 CCGGAGAAGAAGAACAGATGC 58.725 52.381 0.00 0.00 0.00 3.91
885 1319 1.078356 GGGGCCGGAGAAGAAGAAC 60.078 63.158 5.05 0.00 0.00 3.01
901 1335 1.228737 GAGAGATCGGGGGAGAGGG 60.229 68.421 0.00 0.00 0.00 4.30
1127 1561 4.100084 TCACGCAGATGGGGGCAG 62.100 66.667 1.78 0.00 0.00 4.85
1128 1562 4.408821 GTCACGCAGATGGGGGCA 62.409 66.667 1.78 0.00 0.00 5.36
1131 1565 1.330655 ACCTAGTCACGCAGATGGGG 61.331 60.000 1.78 0.00 0.00 4.96
1132 1566 0.179100 CACCTAGTCACGCAGATGGG 60.179 60.000 0.00 0.00 0.00 4.00
1152 1586 1.972198 CAACCCTAGCACACGGAGA 59.028 57.895 0.00 0.00 0.00 3.71
1171 1605 0.378610 TCGAGATCGCACACAGCTAG 59.621 55.000 0.00 0.00 42.61 3.42
1179 1613 3.060873 GCACTAATTTCTCGAGATCGCAC 60.061 47.826 17.44 0.00 39.60 5.34
1197 1631 2.350522 CTAAGAGGCATTTGTCGCACT 58.649 47.619 0.00 0.00 0.00 4.40
1246 1680 3.552684 GCTACCACCGTACAACACACTAA 60.553 47.826 0.00 0.00 0.00 2.24
1253 1693 2.064014 GTCAAGCTACCACCGTACAAC 58.936 52.381 0.00 0.00 0.00 3.32
1256 1696 0.523072 TCGTCAAGCTACCACCGTAC 59.477 55.000 0.00 0.00 0.00 3.67
1266 1706 2.093973 CCACACCTAAGATCGTCAAGCT 60.094 50.000 0.00 0.00 0.00 3.74
1271 1711 0.535335 TGCCCACACCTAAGATCGTC 59.465 55.000 0.00 0.00 0.00 4.20
1272 1712 1.134401 CATGCCCACACCTAAGATCGT 60.134 52.381 0.00 0.00 0.00 3.73
1273 1713 1.586422 CATGCCCACACCTAAGATCG 58.414 55.000 0.00 0.00 0.00 3.69
1368 1821 7.016957 ACATTTGCATCTCCCTCAATCTAGATA 59.983 37.037 5.46 0.00 0.00 1.98
1377 1830 1.554617 TCGACATTTGCATCTCCCTCA 59.445 47.619 0.00 0.00 0.00 3.86
1444 1906 6.183360 CGACATTCATTCTCTCACTGTGTAAC 60.183 42.308 7.79 0.00 37.35 2.50
1447 1909 4.240888 CGACATTCATTCTCTCACTGTGT 58.759 43.478 7.79 0.00 0.00 3.72
1454 1916 6.366332 AGTGTGTAAACGACATTCATTCTCTC 59.634 38.462 0.00 0.00 41.14 3.20
1455 1917 6.223852 AGTGTGTAAACGACATTCATTCTCT 58.776 36.000 0.00 0.00 41.14 3.10
1458 1920 7.569297 TGTAAGTGTGTAAACGACATTCATTC 58.431 34.615 0.00 0.00 41.14 2.67
1460 1922 6.926826 TCTGTAAGTGTGTAAACGACATTCAT 59.073 34.615 0.00 0.00 36.17 2.57
1475 1937 8.312564 GGGAAGAAACTTATAGTCTGTAAGTGT 58.687 37.037 19.29 15.27 40.49 3.55
1549 2011 2.439507 GGAAGATCCTGCTGGGTGAATA 59.560 50.000 10.07 0.00 36.25 1.75
1667 2129 5.305585 ACGGAAGTAATGCCATATAAGGTG 58.694 41.667 0.00 0.00 46.88 4.00
1734 2197 3.078837 ACAAATTAGCCCAACTGGTACG 58.921 45.455 0.00 0.00 36.04 3.67
1740 2203 4.021981 GCTTGAAGACAAATTAGCCCAACT 60.022 41.667 0.00 0.00 35.49 3.16
1781 2244 7.473366 CATCCATCAGACAGAAAAGAAATCAG 58.527 38.462 0.00 0.00 0.00 2.90
2184 2648 9.036980 ACCTGTAAATATACACTCTCAAGTCTT 57.963 33.333 0.00 0.00 37.11 3.01
2295 2759 7.388437 TGTAAGACACCGACCAGTAAATTAAT 58.612 34.615 0.00 0.00 0.00 1.40
2310 2775 7.441458 ACATAGTGTTTCTTCTTGTAAGACACC 59.559 37.037 8.86 0.00 34.13 4.16
2312 2777 7.656137 GGACATAGTGTTTCTTCTTGTAAGACA 59.344 37.037 0.00 0.00 34.13 3.41
2319 2784 6.226787 AGACAGGACATAGTGTTTCTTCTTG 58.773 40.000 0.00 0.00 0.00 3.02
2340 2805 5.218139 CAGATTCCTTTTGTTCAGCAAGAC 58.782 41.667 0.00 0.00 38.47 3.01
2450 2916 1.587043 GAAGGCCGTTGCTCCTTTCC 61.587 60.000 0.00 0.00 42.37 3.13
2495 2961 7.828717 TCATAAGTATCATTGAACAAGCTCCAA 59.171 33.333 0.00 0.00 0.00 3.53
2570 3036 1.275291 TGTTCCCGATCACTTCTCCAC 59.725 52.381 0.00 0.00 0.00 4.02
2694 3160 2.443887 GCATGAGCAACCAACAACAT 57.556 45.000 0.00 0.00 41.58 2.71
2720 3186 8.519799 ACTTGTCTTCTTAAGGAAAAATGTGA 57.480 30.769 1.85 0.00 33.07 3.58
2766 3232 5.767816 AGGACACCAATTGTTCAGTTAAC 57.232 39.130 4.43 0.00 39.17 2.01
2779 3245 0.396974 AGCTGGCAAAAGGACACCAA 60.397 50.000 0.00 0.00 0.00 3.67
2780 3246 0.476338 TAGCTGGCAAAAGGACACCA 59.524 50.000 0.00 0.00 0.00 4.17
2781 3247 1.541588 CTTAGCTGGCAAAAGGACACC 59.458 52.381 0.00 0.00 0.00 4.16
2865 3331 5.842907 TGTATATCCTCTTCAATGACACCG 58.157 41.667 0.00 0.00 0.00 4.94
2979 3445 1.565759 TCATTCTTGCCACCTAGCCAT 59.434 47.619 0.00 0.00 0.00 4.40
3109 3575 5.715439 AGATGGTCACAAGGGATAATTCA 57.285 39.130 0.00 0.00 0.00 2.57
3140 3608 9.360901 ACAACATGCTCTAAGAGAGATATAGAA 57.639 33.333 8.67 0.00 45.07 2.10
3143 3611 8.791675 CAGACAACATGCTCTAAGAGAGATATA 58.208 37.037 8.67 0.00 45.07 0.86
3178 3646 6.995364 GGGGGAATCAAAGACTAGTAGTATC 58.005 44.000 1.88 0.00 0.00 2.24
3202 3674 3.055094 ACAGTGTTAGGCTGTTATGAGGG 60.055 47.826 0.00 0.00 43.87 4.30
3203 3675 4.207891 ACAGTGTTAGGCTGTTATGAGG 57.792 45.455 0.00 0.00 43.87 3.86
3204 3676 7.849804 AAATACAGTGTTAGGCTGTTATGAG 57.150 36.000 0.00 0.00 43.87 2.90
3226 3699 4.096682 AGGTTTTGTTTACTGCTGCGTAAA 59.903 37.500 18.69 18.69 37.10 2.01
3257 3730 9.738832 TGAATATACATGCAATTCAACAATCAG 57.261 29.630 8.04 0.00 36.85 2.90
3258 3731 9.518906 GTGAATATACATGCAATTCAACAATCA 57.481 29.630 11.36 0.00 40.32 2.57
3266 3739 7.521529 AGCGTATGTGAATATACATGCAATTC 58.478 34.615 0.00 0.00 41.78 2.17
3292 3765 6.426937 GCCAATCCACAAACTACATCGTATAT 59.573 38.462 0.00 0.00 0.00 0.86
3295 3768 3.936453 GCCAATCCACAAACTACATCGTA 59.064 43.478 0.00 0.00 0.00 3.43
3298 3771 5.428253 TCTAGCCAATCCACAAACTACATC 58.572 41.667 0.00 0.00 0.00 3.06
3299 3772 5.435686 TCTAGCCAATCCACAAACTACAT 57.564 39.130 0.00 0.00 0.00 2.29
3428 3904 1.596464 CGATCGAGCGTGTACCTTACC 60.596 57.143 16.15 0.00 0.00 2.85
3554 4037 1.147824 CTCTGGCCAGGGTGCTATG 59.852 63.158 32.23 4.54 0.00 2.23
3594 4084 2.202797 CCTCGAGACATGGTGCGG 60.203 66.667 15.71 0.00 0.00 5.69
3601 4091 0.911769 TGCCATTTCCCTCGAGACAT 59.088 50.000 15.71 0.00 0.00 3.06
3648 4138 0.320683 CATGCTCCGTCCAAGTGTCA 60.321 55.000 0.00 0.00 0.00 3.58
3715 4205 0.978907 TCCTCAGCAGTCATCAAGCA 59.021 50.000 0.00 0.00 0.00 3.91
3804 4325 9.042008 CGCTTTTTACATACATACTCCAAGTAT 57.958 33.333 0.00 0.00 41.82 2.12
3805 4326 7.010738 GCGCTTTTTACATACATACTCCAAGTA 59.989 37.037 0.00 0.00 34.82 2.24
3806 4327 6.183360 GCGCTTTTTACATACATACTCCAAGT 60.183 38.462 0.00 0.00 0.00 3.16
3807 4328 6.192360 GCGCTTTTTACATACATACTCCAAG 58.808 40.000 0.00 0.00 0.00 3.61
3808 4329 5.065474 GGCGCTTTTTACATACATACTCCAA 59.935 40.000 7.64 0.00 0.00 3.53
3809 4330 4.573201 GGCGCTTTTTACATACATACTCCA 59.427 41.667 7.64 0.00 0.00 3.86
3810 4331 4.573201 TGGCGCTTTTTACATACATACTCC 59.427 41.667 7.64 0.00 0.00 3.85
3811 4332 5.728351 TGGCGCTTTTTACATACATACTC 57.272 39.130 7.64 0.00 0.00 2.59
3812 4333 6.204108 GGTATGGCGCTTTTTACATACATACT 59.796 38.462 24.09 0.00 44.51 2.12
3813 4334 6.017770 TGGTATGGCGCTTTTTACATACATAC 60.018 38.462 24.09 19.24 44.51 2.39
3912 4451 2.096958 CGCAAAACCGGATTTTTGAAGC 60.097 45.455 26.12 16.80 45.54 3.86
3916 4455 1.070909 GCACGCAAAACCGGATTTTTG 60.071 47.619 20.45 20.45 45.48 2.44
3930 4469 2.626840 TGCTATGTAGAAATGCACGCA 58.373 42.857 0.00 0.00 0.00 5.24
3944 4483 2.804527 CTCACCGGATGTTGATGCTATG 59.195 50.000 9.46 0.00 0.00 2.23
3945 4484 2.700371 TCTCACCGGATGTTGATGCTAT 59.300 45.455 9.46 0.00 0.00 2.97
3946 4485 2.101415 CTCTCACCGGATGTTGATGCTA 59.899 50.000 9.46 0.00 0.00 3.49
3947 4486 0.904649 TCTCACCGGATGTTGATGCT 59.095 50.000 9.46 0.00 0.00 3.79
3948 4487 1.293924 CTCTCACCGGATGTTGATGC 58.706 55.000 9.46 0.00 0.00 3.91
3949 4488 2.094026 TCACTCTCACCGGATGTTGATG 60.094 50.000 9.46 0.00 0.00 3.07
3950 4489 2.093973 GTCACTCTCACCGGATGTTGAT 60.094 50.000 9.46 0.00 0.00 2.57
3951 4490 1.272490 GTCACTCTCACCGGATGTTGA 59.728 52.381 9.46 0.00 0.00 3.18
3952 4491 1.714794 GTCACTCTCACCGGATGTTG 58.285 55.000 9.46 0.00 0.00 3.33
3953 4492 0.243907 CGTCACTCTCACCGGATGTT 59.756 55.000 9.46 0.00 0.00 2.71
3954 4493 0.894184 ACGTCACTCTCACCGGATGT 60.894 55.000 9.46 0.00 0.00 3.06
3955 4494 0.243907 AACGTCACTCTCACCGGATG 59.756 55.000 9.46 2.48 0.00 3.51
3956 4495 0.243907 CAACGTCACTCTCACCGGAT 59.756 55.000 9.46 0.00 0.00 4.18
3957 4496 1.658114 CAACGTCACTCTCACCGGA 59.342 57.895 9.46 0.00 0.00 5.14
3958 4497 1.372997 CCAACGTCACTCTCACCGG 60.373 63.158 0.00 0.00 0.00 5.28
3962 4501 2.724977 GTGATCCAACGTCACTCTCA 57.275 50.000 0.00 0.00 42.04 3.27
3982 4546 3.325870 GCCATTATCGTATGCAGCTGTA 58.674 45.455 16.64 12.13 0.00 2.74
3996 4560 3.276846 GCGTTCGCGGGCCATTAT 61.277 61.111 6.13 0.00 41.67 1.28
4020 4584 4.394610 AGAAAAACATGCACAAACAAACCC 59.605 37.500 0.00 0.00 0.00 4.11
4031 4595 1.614903 CAGGCCAGAGAAAAACATGCA 59.385 47.619 5.01 0.00 0.00 3.96
4035 4599 3.214328 GAAGACAGGCCAGAGAAAAACA 58.786 45.455 5.01 0.00 0.00 2.83
4037 4601 3.576078 TGAAGACAGGCCAGAGAAAAA 57.424 42.857 5.01 0.00 0.00 1.94
4049 4613 1.558756 AGCAGGGGAAGATGAAGACAG 59.441 52.381 0.00 0.00 0.00 3.51
4083 4647 2.674954 CGATGAGAGGTGATGATCTGC 58.325 52.381 0.00 0.00 0.00 4.26
4085 4649 1.269174 CGCGATGAGAGGTGATGATCT 59.731 52.381 0.00 0.00 0.00 2.75
4088 4652 1.066422 GCGCGATGAGAGGTGATGA 59.934 57.895 12.10 0.00 0.00 2.92
4091 4655 4.854784 GCGCGCGATGAGAGGTGA 62.855 66.667 37.18 0.00 0.00 4.02
4108 4672 3.001902 TTGCTAGTGCCGGACGAGG 62.002 63.158 5.05 0.00 38.71 4.63
4109 4673 1.805945 GTTGCTAGTGCCGGACGAG 60.806 63.158 5.05 7.72 38.71 4.18
4110 4674 2.260434 GTTGCTAGTGCCGGACGA 59.740 61.111 5.05 0.00 38.71 4.20
4111 4675 2.813908 GGTTGCTAGTGCCGGACG 60.814 66.667 5.05 0.00 38.71 4.79
4112 4676 1.302192 TTGGTTGCTAGTGCCGGAC 60.302 57.895 5.05 0.00 38.71 4.79
4113 4677 1.302192 GTTGGTTGCTAGTGCCGGA 60.302 57.895 5.05 0.00 38.71 5.14
4114 4678 2.332654 GGTTGGTTGCTAGTGCCGG 61.333 63.158 0.00 0.00 38.71 6.13
4115 4679 2.332654 GGGTTGGTTGCTAGTGCCG 61.333 63.158 0.00 0.00 38.71 5.69
4116 4680 0.825840 TTGGGTTGGTTGCTAGTGCC 60.826 55.000 0.00 0.00 38.71 5.01
4117 4681 0.313987 GTTGGGTTGGTTGCTAGTGC 59.686 55.000 0.00 0.00 40.20 4.40
4118 4682 0.958822 GGTTGGGTTGGTTGCTAGTG 59.041 55.000 0.00 0.00 0.00 2.74
4119 4683 0.536460 CGGTTGGGTTGGTTGCTAGT 60.536 55.000 0.00 0.00 0.00 2.57
4120 4684 1.862602 GCGGTTGGGTTGGTTGCTAG 61.863 60.000 0.00 0.00 0.00 3.42
4121 4685 1.899534 GCGGTTGGGTTGGTTGCTA 60.900 57.895 0.00 0.00 0.00 3.49
4122 4686 3.223589 GCGGTTGGGTTGGTTGCT 61.224 61.111 0.00 0.00 0.00 3.91
4123 4687 4.639171 CGCGGTTGGGTTGGTTGC 62.639 66.667 0.00 0.00 0.00 4.17
4124 4688 2.902846 TCGCGGTTGGGTTGGTTG 60.903 61.111 6.13 0.00 0.00 3.77
4134 4698 2.431942 GATGGTCACGTCGCGGTT 60.432 61.111 6.13 0.00 0.00 4.44
4153 4717 1.461911 CCGGAGACTATCGGGGGAAC 61.462 65.000 0.00 0.00 43.14 3.62
4179 4743 1.442526 CGTCTGAGGCAATGGGATGC 61.443 60.000 0.00 0.00 45.67 3.91
4181 4745 0.179000 GTCGTCTGAGGCAATGGGAT 59.821 55.000 0.00 0.00 0.00 3.85
4203 4767 0.175989 GAGAGTAAGTTCAGGCGGGG 59.824 60.000 0.00 0.00 0.00 5.73
4207 4771 3.791245 CCATCTGAGAGTAAGTTCAGGC 58.209 50.000 2.07 0.00 40.89 4.85
4210 4774 3.129462 CGAGCCATCTGAGAGTAAGTTCA 59.871 47.826 0.00 0.00 0.00 3.18
4213 4777 1.407258 GCGAGCCATCTGAGAGTAAGT 59.593 52.381 0.00 0.00 0.00 2.24
4217 4781 1.674764 CTGGCGAGCCATCTGAGAGT 61.675 60.000 17.94 0.00 46.15 3.24
4221 4785 4.519437 CGCTGGCGAGCCATCTGA 62.519 66.667 17.94 0.00 46.15 3.27
4231 4795 3.857854 GTCATGTCTGCGCTGGCG 61.858 66.667 14.34 10.80 44.10 5.69
4242 4806 1.889170 TGAAGACAGAGAGCGTCATGT 59.111 47.619 0.00 0.00 35.77 3.21
4248 4812 0.519519 ACGACTGAAGACAGAGAGCG 59.480 55.000 0.00 0.00 46.03 5.03
4250 4814 1.727535 CGCACGACTGAAGACAGAGAG 60.728 57.143 0.00 0.00 46.03 3.20
4253 4817 0.040336 GACGCACGACTGAAGACAGA 60.040 55.000 0.00 0.00 46.03 3.41
4255 4819 1.370051 CGACGCACGACTGAAGACA 60.370 57.895 0.00 0.00 45.77 3.41
4257 4821 2.428569 GCGACGCACGACTGAAGA 60.429 61.111 16.42 0.00 45.77 2.87
4260 4824 2.472232 ATCTTGCGACGCACGACTGA 62.472 55.000 28.29 17.97 39.49 3.41
4261 4825 2.002963 GATCTTGCGACGCACGACTG 62.003 60.000 28.29 13.78 39.49 3.51
4262 4826 1.801913 GATCTTGCGACGCACGACT 60.802 57.895 28.29 18.02 39.49 4.18
4305 4875 4.101448 GACAGGGCGCTGGGTGAT 62.101 66.667 31.41 12.82 0.00 3.06
4320 4890 1.374758 CTCTGGTTGGGTCGCTGAC 60.375 63.158 0.79 0.79 0.00 3.51
4324 4894 2.743928 CTGCTCTGGTTGGGTCGC 60.744 66.667 0.00 0.00 0.00 5.19
4327 4897 1.835927 GAGAGCTGCTCTGGTTGGGT 61.836 60.000 34.84 10.22 41.35 4.51
4337 4907 0.691904 AGCTGAAAAGGAGAGCTGCT 59.308 50.000 0.00 0.00 41.56 4.24
4362 4932 0.319555 GACGTGTTGCAGCTGTCCTA 60.320 55.000 16.64 0.00 0.00 2.94
4371 4941 4.578898 ACGAGGCGACGTGTTGCA 62.579 61.111 13.87 0.00 44.84 4.08


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

AutoCloner maintained by Alex Coulton.