Multiple sequence alignment - TraesCS2D01G338000

Loading Multiple Alignment...

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 TraesCS2D01G338000 chr2D 100.000 5315 0 0 1 5315 431514319 431519633 0.000000e+00 9816.0
1 TraesCS2D01G338000 chr2B 92.907 4709 256 45 1 4671 510399179 510403847 0.000000e+00 6774.0
2 TraesCS2D01G338000 chr2A 92.809 4714 239 54 1 4671 554824887 554820231 0.000000e+00 6735.0
3 TraesCS2D01G338000 chr3D 99.307 577 4 0 4739 5315 141492938 141492362 0.000000e+00 1044.0
4 TraesCS2D01G338000 chr3D 98.960 577 6 0 4739 5315 351930738 351931314 0.000000e+00 1033.0
5 TraesCS2D01G338000 chr3D 91.525 59 5 0 5257 5315 74359468 74359526 1.230000e-11 82.4
6 TraesCS2D01G338000 chr1D 99.275 552 4 0 4739 5290 50885305 50884754 0.000000e+00 998.0
7 TraesCS2D01G338000 chr7D 96.379 580 17 3 4737 5315 324450289 324450865 0.000000e+00 952.0
8 TraesCS2D01G338000 chr1A 96.021 578 21 2 4738 5315 223823340 223823915 0.000000e+00 939.0
9 TraesCS2D01G338000 chr1A 89.073 302 28 2 4942 5240 162698274 162698573 2.340000e-98 370.0
10 TraesCS2D01G338000 chr1A 88.449 303 26 5 4942 5239 162647968 162648266 1.820000e-94 357.0
11 TraesCS2D01G338000 chr1A 87.459 303 32 3 4942 5240 166665094 166664794 1.420000e-90 344.0
12 TraesCS2D01G338000 chr1A 89.418 189 18 2 4737 4925 162698101 162698287 2.470000e-58 237.0
13 TraesCS2D01G338000 chr1A 89.785 186 15 4 4741 4925 185849607 185849425 8.900000e-58 235.0
14 TraesCS2D01G338000 chr1A 94.915 59 3 0 5257 5315 39438927 39438869 5.670000e-15 93.5
15 TraesCS2D01G338000 chr1A 92.982 57 4 0 5257 5313 39185640 39185696 3.410000e-12 84.2
16 TraesCS2D01G338000 chr3A 95.494 577 23 3 4739 5315 38988788 38989361 0.000000e+00 918.0
17 TraesCS2D01G338000 chr1B 88.945 199 20 1 4736 4934 17531468 17531272 1.480000e-60 244.0


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 TraesCS2D01G338000 chr2D 431514319 431519633 5314 False 9816 9816 100.000 1 5315 1 chr2D.!!$F1 5314
1 TraesCS2D01G338000 chr2B 510399179 510403847 4668 False 6774 6774 92.907 1 4671 1 chr2B.!!$F1 4670
2 TraesCS2D01G338000 chr2A 554820231 554824887 4656 True 6735 6735 92.809 1 4671 1 chr2A.!!$R1 4670
3 TraesCS2D01G338000 chr3D 141492362 141492938 576 True 1044 1044 99.307 4739 5315 1 chr3D.!!$R1 576
4 TraesCS2D01G338000 chr3D 351930738 351931314 576 False 1033 1033 98.960 4739 5315 1 chr3D.!!$F2 576
5 TraesCS2D01G338000 chr1D 50884754 50885305 551 True 998 998 99.275 4739 5290 1 chr1D.!!$R1 551
6 TraesCS2D01G338000 chr7D 324450289 324450865 576 False 952 952 96.379 4737 5315 1 chr7D.!!$F1 578
7 TraesCS2D01G338000 chr1A 223823340 223823915 575 False 939 939 96.021 4738 5315 1 chr1A.!!$F3 577
8 TraesCS2D01G338000 chr3A 38988788 38989361 573 False 918 918 95.494 4739 5315 1 chr3A.!!$F1 576

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
960 961 0.254178 ATCCAAGCAGCAACCGATCT 59.746 50.0 0.00 0.00 0.00 2.75 F
1836 1853 0.108396 TGTTGCTGCTAGAGTGCCAA 59.892 50.0 0.00 0.00 0.00 4.52 F
2213 2238 0.811219 TCAGGAAATGCCATCGCTCG 60.811 55.0 0.00 0.00 40.02 5.03 F
3858 3894 0.904865 CTGCAGGTCCTGGTCTACCA 60.905 60.0 20.72 7.64 45.30 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2534 2567 1.416243 TAGCCGGGTATTAGGTGTGG 58.584 55.000 9.87 0.0 0.00 4.17 R
3694 3729 1.519455 GTGCACCCTAGCAGCTACG 60.519 63.158 5.22 0.0 46.69 3.51 R
3909 3945 0.107643 TCGCAGATTCCACCAACACA 59.892 50.000 0.00 0.0 0.00 3.72 R
4696 4750 0.106149 AAACACTTCCCTTCGAGCGT 59.894 50.000 0.00 0.0 0.00 5.07 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
41 42 0.652592 CTCCGCGCCTTATCAAGTTG 59.347 55.000 0.00 0.00 0.00 3.16
118 119 3.066208 TCCCCTTCTCCTCTGCATAAT 57.934 47.619 0.00 0.00 0.00 1.28
264 265 4.350816 TCCTTCCAGTCTCCATTCTTGAAA 59.649 41.667 0.00 0.00 0.00 2.69
309 310 2.510382 TGTAACCACACCCTTTTCCTCA 59.490 45.455 0.00 0.00 0.00 3.86
483 484 1.990563 CAGGACTTTACGGTGTTAGCG 59.009 52.381 0.00 0.00 45.69 4.26
600 601 3.709653 AGAAGGCACGGATAAGGATGTTA 59.290 43.478 0.00 0.00 0.00 2.41
762 763 1.910772 ACCGGACTTGAGCAGAGCT 60.911 57.895 9.46 0.00 43.88 4.09
918 919 1.926511 CTTAAGCGCACCAGGCCAAG 61.927 60.000 11.47 0.00 40.31 3.61
960 961 0.254178 ATCCAAGCAGCAACCGATCT 59.746 50.000 0.00 0.00 0.00 2.75
962 963 1.651240 CCAAGCAGCAACCGATCTGG 61.651 60.000 0.00 2.55 46.41 3.86
1070 1078 4.956075 CCCAGTAATTACCATGGCTTCTTT 59.044 41.667 13.04 1.44 0.00 2.52
1082 1090 2.289072 TGGCTTCTTTCTCTCCAACTCG 60.289 50.000 0.00 0.00 0.00 4.18
1314 1322 2.828549 GCGGCGATGGGGTTCAAT 60.829 61.111 12.98 0.00 0.00 2.57
1495 1503 1.838077 GGGTAGGTGGTTGCTATCAGT 59.162 52.381 0.00 0.00 0.00 3.41
1509 1517 7.362574 GGTTGCTATCAGTGCTTTAAATAACCA 60.363 37.037 0.00 0.00 33.43 3.67
1530 1542 0.474614 GGTTATCCCCTGAGAAGCCC 59.525 60.000 0.00 0.00 34.87 5.19
1550 1562 4.571984 GCCCAGATTGCATTTGTTTATTCC 59.428 41.667 0.00 0.00 0.00 3.01
1554 1566 6.418819 CCAGATTGCATTTGTTTATTCCGATC 59.581 38.462 0.00 0.00 0.00 3.69
1561 1573 0.586802 GTTTATTCCGATCCCTGCGC 59.413 55.000 0.00 0.00 0.00 6.09
1599 1611 7.280205 GGACTTGATGTCGGTATTAATCAAACT 59.720 37.037 0.00 0.00 46.24 2.66
1697 1714 6.759497 ATCTTACTACCACCAAAGAATTGC 57.241 37.500 0.00 0.00 35.10 3.56
1707 1724 3.197549 ACCAAAGAATTGCCAAGTGTTGT 59.802 39.130 0.00 0.00 35.10 3.32
1722 1739 5.994887 AGTGTTGTTAGTGTTGCGAATTA 57.005 34.783 0.00 0.00 0.00 1.40
1724 1741 5.526111 AGTGTTGTTAGTGTTGCGAATTAGT 59.474 36.000 0.00 0.00 0.00 2.24
1726 1743 7.386848 AGTGTTGTTAGTGTTGCGAATTAGTAT 59.613 33.333 0.00 0.00 0.00 2.12
1727 1744 8.649841 GTGTTGTTAGTGTTGCGAATTAGTATA 58.350 33.333 0.00 0.00 0.00 1.47
1728 1745 9.205719 TGTTGTTAGTGTTGCGAATTAGTATAA 57.794 29.630 0.00 0.00 0.00 0.98
1729 1746 9.685005 GTTGTTAGTGTTGCGAATTAGTATAAG 57.315 33.333 0.00 0.00 0.00 1.73
1730 1747 8.415192 TGTTAGTGTTGCGAATTAGTATAAGG 57.585 34.615 0.00 0.00 0.00 2.69
1731 1748 8.036575 TGTTAGTGTTGCGAATTAGTATAAGGT 58.963 33.333 0.00 0.00 0.00 3.50
1732 1749 8.876790 GTTAGTGTTGCGAATTAGTATAAGGTT 58.123 33.333 0.00 0.00 0.00 3.50
1733 1750 7.535489 AGTGTTGCGAATTAGTATAAGGTTC 57.465 36.000 0.00 0.00 0.00 3.62
1836 1853 0.108396 TGTTGCTGCTAGAGTGCCAA 59.892 50.000 0.00 0.00 0.00 4.52
1848 1866 3.960571 AGAGTGCCAATTAGCAGTGAAT 58.039 40.909 11.08 0.00 46.36 2.57
1971 1995 9.230122 TCATGAATCAATTTGTCTGTAGCTAAA 57.770 29.630 0.00 0.00 0.00 1.85
2027 2051 3.378427 ACTTGCTTCAGAAGTCCAAACAC 59.622 43.478 11.94 0.00 0.00 3.32
2061 2085 7.779073 AGAGGAATTCTGAAGGCAAATAATTG 58.221 34.615 5.23 0.00 35.68 2.32
2081 2105 2.634453 TGATCAGAACTCACAAGGCTCA 59.366 45.455 0.00 0.00 0.00 4.26
2088 2112 1.242076 CTCACAAGGCTCACCAAAGG 58.758 55.000 0.00 0.00 39.06 3.11
2090 2114 1.425066 TCACAAGGCTCACCAAAGGAT 59.575 47.619 0.00 0.00 39.06 3.24
2091 2115 1.815003 CACAAGGCTCACCAAAGGATC 59.185 52.381 0.00 0.00 39.06 3.36
2092 2116 1.707427 ACAAGGCTCACCAAAGGATCT 59.293 47.619 0.00 0.00 39.06 2.75
2093 2117 2.290577 ACAAGGCTCACCAAAGGATCTC 60.291 50.000 0.00 0.00 39.06 2.75
2094 2118 1.661463 AGGCTCACCAAAGGATCTCA 58.339 50.000 0.00 0.00 39.06 3.27
2095 2119 1.280421 AGGCTCACCAAAGGATCTCAC 59.720 52.381 0.00 0.00 39.06 3.51
2096 2120 1.003580 GGCTCACCAAAGGATCTCACA 59.996 52.381 0.00 0.00 35.26 3.58
2097 2121 2.356535 GGCTCACCAAAGGATCTCACAT 60.357 50.000 0.00 0.00 35.26 3.21
2140 2164 7.496346 TCTCTTTATTAAGGACACCATCTGT 57.504 36.000 0.00 0.00 34.96 3.41
2146 2170 2.363306 AGGACACCATCTGTTGCAAA 57.637 45.000 0.00 0.00 31.03 3.68
2148 2172 2.362077 AGGACACCATCTGTTGCAAAAC 59.638 45.455 0.00 0.00 31.03 2.43
2162 2186 3.088532 TGCAAAACGAGGGATAAATGCT 58.911 40.909 0.00 0.00 33.87 3.79
2166 2190 5.687285 GCAAAACGAGGGATAAATGCTAATG 59.313 40.000 0.00 0.00 0.00 1.90
2213 2238 0.811219 TCAGGAAATGCCATCGCTCG 60.811 55.000 0.00 0.00 40.02 5.03
2224 2249 3.243101 TGCCATCGCTCGTTGTTTAAAAA 60.243 39.130 0.00 0.00 35.36 1.94
2250 2275 6.653320 ACTGTCTTTCATTTTATTCGCCACTA 59.347 34.615 0.00 0.00 0.00 2.74
2333 2358 2.703416 TGCAAGTCACAATGCTCTAGG 58.297 47.619 7.08 0.00 42.97 3.02
2360 2385 6.620678 GCACAAATCTTGCTTGTAGGATTTA 58.379 36.000 8.04 0.00 36.60 1.40
2388 2413 4.860802 TGATGGGGATACATGTCACTTT 57.139 40.909 0.00 0.00 39.74 2.66
2394 2419 4.764823 GGGGATACATGTCACTTTCAAACA 59.235 41.667 0.00 0.00 39.74 2.83
2420 2445 4.534500 TGGATTAGGTGAGCTGGTTCTTTA 59.466 41.667 0.00 0.00 0.00 1.85
2444 2469 4.078219 TCCATACCAGGTATCTAGTTGGGT 60.078 45.833 9.41 0.00 34.99 4.51
2448 2473 2.170607 CCAGGTATCTAGTTGGGTGTGG 59.829 54.545 0.00 0.00 0.00 4.17
2456 2481 2.856988 TTGGGTGTGGGGGTCTCC 60.857 66.667 0.00 0.00 0.00 3.71
2475 2500 5.182169 CTCCCGAGGAGGTATCTAGTTAT 57.818 47.826 11.05 0.00 45.43 1.89
2489 2514 9.862371 GGTATCTAGTTATCTGACATGGTAATG 57.138 37.037 0.00 0.00 39.89 1.90
2509 2542 9.046296 GGTAATGTAGGACAAATGATCTAGTTG 57.954 37.037 0.00 0.00 40.08 3.16
2534 2567 4.744631 CCAACCTGTATGTTTTTCTTGTGC 59.255 41.667 0.00 0.00 0.00 4.57
2543 2576 3.764434 TGTTTTTCTTGTGCCACACCTAA 59.236 39.130 0.00 0.00 32.73 2.69
2548 2581 2.026636 TCTTGTGCCACACCTAATACCC 60.027 50.000 0.00 0.00 32.73 3.69
2597 2630 6.945938 TTTTCGTTTTTGTCTATCAAGGGA 57.054 33.333 0.00 0.00 37.35 4.20
2641 2674 6.520021 TCATCCTTCTGATATGGGTCAAAT 57.480 37.500 0.00 0.00 30.56 2.32
2646 2679 8.519799 TCCTTCTGATATGGGTCAAATTTAAC 57.480 34.615 0.00 0.00 0.00 2.01
2788 2821 3.423539 TGACCCTGAAGAATGGTTGAG 57.576 47.619 0.00 0.00 30.97 3.02
2873 2906 1.056700 ATGAGCTTCGTGGCCCCTAT 61.057 55.000 0.00 0.00 0.00 2.57
2931 2964 1.588239 AAGGCCCTCATGAGTCATGA 58.412 50.000 29.39 29.39 46.84 3.07
3623 3658 4.096532 TCGTTTGCTGAACCAACACATAAA 59.903 37.500 0.00 0.00 34.67 1.40
3630 3665 5.523438 TGAACCAACACATAAACCTTTCC 57.477 39.130 0.00 0.00 0.00 3.13
3642 3677 6.833933 ACATAAACCTTTCCTGGGTATTCATC 59.166 38.462 0.00 0.00 35.83 2.92
3656 3691 9.587772 CTGGGTATTCATCTAGGATAATTTACG 57.412 37.037 0.00 0.00 0.00 3.18
3694 3729 9.696917 ATTGACCTTCAAAAGTGATTGTAAATC 57.303 29.630 0.00 0.00 40.12 2.17
3698 3733 8.504005 ACCTTCAAAAGTGATTGTAAATCGTAG 58.496 33.333 0.00 0.00 32.48 3.51
3767 3803 4.143618 GCAAGAAAAACTAAAATCCACGCG 60.144 41.667 3.53 3.53 0.00 6.01
3789 3825 4.723862 CGAAGTATAATGCGAACACTTTGC 59.276 41.667 0.00 0.00 40.58 3.68
3858 3894 0.904865 CTGCAGGTCCTGGTCTACCA 60.905 60.000 20.72 7.64 45.30 3.25
3909 3945 0.032017 ATCCTCTAACCGGGCTCTGT 60.032 55.000 6.32 0.00 0.00 3.41
3945 3981 0.099436 CGAATGTGCTTAAGCTGGGC 59.901 55.000 26.90 14.91 42.66 5.36
3981 4017 1.000506 GACGCTTGGAACTACACCTCA 59.999 52.381 0.00 0.00 0.00 3.86
3984 4020 1.270839 GCTTGGAACTACACCTCAGCA 60.271 52.381 0.00 0.00 35.76 4.41
4050 4086 3.146066 GTCTGTGGGTGATACTGCAAAA 58.854 45.455 0.00 0.00 0.00 2.44
4105 4141 5.933617 AGTGGCAGCTAATATCTGATTCAA 58.066 37.500 0.00 0.00 33.54 2.69
4119 4155 6.578163 TCTGATTCAAGAATGCATGTTTCA 57.422 33.333 0.00 0.00 0.00 2.69
4200 4236 2.555325 CACCACAGATCAATGCAAGTGT 59.445 45.455 0.00 0.00 31.21 3.55
4201 4237 3.005050 CACCACAGATCAATGCAAGTGTT 59.995 43.478 0.00 0.00 31.21 3.32
4318 4354 2.964209 CATCTCTTGGACCCTAGCCTA 58.036 52.381 0.00 0.00 0.00 3.93
4320 4356 1.033574 CTCTTGGACCCTAGCCTACG 58.966 60.000 0.00 0.00 0.00 3.51
4323 4359 0.040058 TTGGACCCTAGCCTACGACA 59.960 55.000 0.00 0.00 0.00 4.35
4332 4368 2.279582 AGCCTACGACATCAAGTTCG 57.720 50.000 0.00 0.00 0.00 3.95
4333 4369 0.645868 GCCTACGACATCAAGTTCGC 59.354 55.000 0.00 0.00 0.00 4.70
4335 4371 1.403647 CCTACGACATCAAGTTCGCCA 60.404 52.381 0.00 0.00 0.00 5.69
4342 4378 0.606604 ATCAAGTTCGCCACGGTAGT 59.393 50.000 0.00 0.00 0.00 2.73
4343 4379 1.246649 TCAAGTTCGCCACGGTAGTA 58.753 50.000 0.00 0.00 0.00 1.82
4345 4381 2.231964 TCAAGTTCGCCACGGTAGTAAT 59.768 45.455 0.00 0.00 0.00 1.89
4349 4385 2.012937 TCGCCACGGTAGTAATTTGG 57.987 50.000 0.00 0.00 0.00 3.28
4354 4390 3.666274 CCACGGTAGTAATTTGGACACA 58.334 45.455 0.00 0.00 0.00 3.72
4359 4395 4.032445 CGGTAGTAATTTGGACACACATCG 59.968 45.833 0.00 0.00 0.00 3.84
4369 4405 2.938403 CACACATCGTGCATGCATG 58.062 52.632 30.20 30.20 39.19 4.06
4372 4408 1.398041 ACACATCGTGCATGCATGTAC 59.602 47.619 33.08 31.04 39.57 2.90
4374 4410 1.935873 ACATCGTGCATGCATGTACTC 59.064 47.619 34.88 17.92 40.59 2.59
4401 4437 3.450457 ACAAAGTTGTTCAGGCCAATTCA 59.550 39.130 5.01 0.00 38.47 2.57
4420 4467 1.993370 CAACGACGATCTGGGAAGTTC 59.007 52.381 0.00 0.00 0.00 3.01
4430 4477 1.001378 CTGGGAAGTTCCACGCAAAAG 60.001 52.381 23.33 5.25 38.64 2.27
4472 4519 6.761242 GCTCAAGTGTGTATAATGTATCACCA 59.239 38.462 0.00 0.00 0.00 4.17
4474 4521 9.981114 CTCAAGTGTGTATAATGTATCACCATA 57.019 33.333 0.00 0.00 0.00 2.74
4486 4533 8.752005 AATGTATCACCATATAAGCACTTGTT 57.248 30.769 0.00 0.00 0.00 2.83
4489 4536 8.673711 TGTATCACCATATAAGCACTTGTTTTC 58.326 33.333 0.00 0.00 0.00 2.29
4532 4579 3.392769 TGTGTGTTGCTTACGTTGTTC 57.607 42.857 0.00 0.00 0.00 3.18
4533 4580 2.742589 TGTGTGTTGCTTACGTTGTTCA 59.257 40.909 0.00 0.00 0.00 3.18
4553 4600 8.378172 TGTTCAGTTCAGAATAAAACTACAGG 57.622 34.615 0.00 0.00 34.05 4.00
4554 4601 7.990886 TGTTCAGTTCAGAATAAAACTACAGGT 59.009 33.333 0.00 0.00 34.05 4.00
4555 4602 7.962964 TCAGTTCAGAATAAAACTACAGGTG 57.037 36.000 0.00 0.00 34.05 4.00
4556 4603 6.934645 TCAGTTCAGAATAAAACTACAGGTGG 59.065 38.462 0.00 0.00 34.05 4.61
4557 4604 6.934645 CAGTTCAGAATAAAACTACAGGTGGA 59.065 38.462 0.00 0.00 34.05 4.02
4558 4605 7.444183 CAGTTCAGAATAAAACTACAGGTGGAA 59.556 37.037 0.00 0.00 34.05 3.53
4559 4606 8.164070 AGTTCAGAATAAAACTACAGGTGGAAT 58.836 33.333 0.00 0.00 34.05 3.01
4560 4607 8.451748 GTTCAGAATAAAACTACAGGTGGAATC 58.548 37.037 0.00 0.00 0.00 2.52
4561 4608 7.918076 TCAGAATAAAACTACAGGTGGAATCT 58.082 34.615 0.00 0.00 0.00 2.40
4562 4609 9.042450 TCAGAATAAAACTACAGGTGGAATCTA 57.958 33.333 0.00 0.00 0.00 1.98
4563 4610 9.838339 CAGAATAAAACTACAGGTGGAATCTAT 57.162 33.333 0.00 0.00 0.00 1.98
4569 4616 9.838339 AAAACTACAGGTGGAATCTATAGAATG 57.162 33.333 6.52 0.75 0.00 2.67
4570 4617 6.998802 ACTACAGGTGGAATCTATAGAATGC 58.001 40.000 6.52 4.31 0.00 3.56
4574 4621 6.328672 ACAGGTGGAATCTATAGAATGCTCTT 59.671 38.462 6.52 0.00 32.70 2.85
4584 4631 3.911661 AGAATGCTCTTGTGCTTGTTC 57.088 42.857 0.00 0.00 0.00 3.18
4585 4632 3.484407 AGAATGCTCTTGTGCTTGTTCT 58.516 40.909 0.00 0.00 0.00 3.01
4588 4635 2.216046 TGCTCTTGTGCTTGTTCTCTG 58.784 47.619 0.00 0.00 0.00 3.35
4601 4648 1.602377 GTTCTCTGACCGTTGTTTGGG 59.398 52.381 0.00 0.00 0.00 4.12
4612 4663 1.544246 GTTGTTTGGGTGAGTATGCCC 59.456 52.381 0.00 0.00 45.04 5.36
4640 4694 1.631898 GCCAAGGTGGTCTAGGGTTTA 59.368 52.381 0.00 0.00 40.46 2.01
4654 4708 3.690460 AGGGTTTAATCTGAGGTTGCAG 58.310 45.455 0.00 0.00 37.24 4.41
4657 4711 4.327680 GGTTTAATCTGAGGTTGCAGTCT 58.672 43.478 0.00 0.00 37.20 3.24
4671 4725 1.471684 GCAGTCTTGCTCAAATGGAGG 59.528 52.381 0.00 0.00 46.95 4.30
4672 4726 1.471684 CAGTCTTGCTCAAATGGAGGC 59.528 52.381 0.00 0.00 44.22 4.70
4673 4727 0.813821 GTCTTGCTCAAATGGAGGCC 59.186 55.000 0.00 0.00 44.22 5.19
4674 4728 0.323725 TCTTGCTCAAATGGAGGCCC 60.324 55.000 0.00 0.00 44.22 5.80
4675 4729 1.305213 TTGCTCAAATGGAGGCCCC 60.305 57.895 0.00 0.03 44.22 5.80
4676 4730 2.830370 GCTCAAATGGAGGCCCCG 60.830 66.667 0.00 0.00 44.22 5.73
4677 4731 2.124151 CTCAAATGGAGGCCCCGG 60.124 66.667 0.00 0.00 40.13 5.73
4678 4732 2.612430 TCAAATGGAGGCCCCGGA 60.612 61.111 0.73 0.00 37.93 5.14
4679 4733 2.124151 CAAATGGAGGCCCCGGAG 60.124 66.667 0.73 0.00 37.93 4.63
4680 4734 4.129148 AAATGGAGGCCCCGGAGC 62.129 66.667 0.73 0.00 37.93 4.70
4691 4745 3.554342 CCGGAGCCATGAGGGGAG 61.554 72.222 0.00 0.00 37.04 4.30
4692 4746 2.444706 CGGAGCCATGAGGGGAGA 60.445 66.667 0.00 0.00 37.04 3.71
4693 4747 1.840650 CGGAGCCATGAGGGGAGAT 60.841 63.158 0.00 0.00 37.04 2.75
4694 4748 1.759881 GGAGCCATGAGGGGAGATG 59.240 63.158 0.00 0.00 37.04 2.90
4695 4749 1.759881 GAGCCATGAGGGGAGATGG 59.240 63.158 0.00 0.00 41.95 3.51
4696 4750 0.765903 GAGCCATGAGGGGAGATGGA 60.766 60.000 0.00 0.00 41.63 3.41
4697 4751 1.059006 AGCCATGAGGGGAGATGGAC 61.059 60.000 0.00 0.00 41.63 4.02
4698 4752 1.750930 CCATGAGGGGAGATGGACG 59.249 63.158 0.00 0.00 41.63 4.79
4699 4753 1.070445 CATGAGGGGAGATGGACGC 59.930 63.158 0.00 0.00 0.00 5.19
4700 4754 1.074926 ATGAGGGGAGATGGACGCT 60.075 57.895 0.00 0.00 0.00 5.07
4701 4755 1.118356 ATGAGGGGAGATGGACGCTC 61.118 60.000 0.00 0.00 44.22 5.03
4702 4756 2.835431 AGGGGAGATGGACGCTCG 60.835 66.667 0.00 0.00 33.19 5.03
4703 4757 2.833582 GGGGAGATGGACGCTCGA 60.834 66.667 0.00 0.00 33.19 4.04
4704 4758 2.423898 GGGGAGATGGACGCTCGAA 61.424 63.158 0.00 0.00 33.19 3.71
4705 4759 1.066587 GGGAGATGGACGCTCGAAG 59.933 63.158 0.00 0.00 33.19 3.79
4706 4760 1.066587 GGAGATGGACGCTCGAAGG 59.933 63.158 0.00 0.00 33.19 3.46
4707 4761 1.066587 GAGATGGACGCTCGAAGGG 59.933 63.158 0.00 0.00 0.00 3.95
4708 4762 1.379977 AGATGGACGCTCGAAGGGA 60.380 57.895 0.00 0.00 31.91 4.20
4709 4763 0.970937 AGATGGACGCTCGAAGGGAA 60.971 55.000 0.00 0.00 31.91 3.97
4710 4764 0.528684 GATGGACGCTCGAAGGGAAG 60.529 60.000 0.00 0.00 31.91 3.46
4711 4765 1.258445 ATGGACGCTCGAAGGGAAGT 61.258 55.000 0.00 0.00 31.91 3.01
4712 4766 1.446272 GGACGCTCGAAGGGAAGTG 60.446 63.158 0.00 0.00 31.91 3.16
4713 4767 1.289380 GACGCTCGAAGGGAAGTGT 59.711 57.895 0.00 0.00 31.91 3.55
4714 4768 0.319641 GACGCTCGAAGGGAAGTGTT 60.320 55.000 0.00 0.00 31.91 3.32
4715 4769 0.106149 ACGCTCGAAGGGAAGTGTTT 59.894 50.000 0.00 0.00 31.91 2.83
4716 4770 0.790814 CGCTCGAAGGGAAGTGTTTC 59.209 55.000 0.00 0.00 0.00 2.78
4717 4771 1.605712 CGCTCGAAGGGAAGTGTTTCT 60.606 52.381 0.00 0.00 33.68 2.52
4718 4772 1.801178 GCTCGAAGGGAAGTGTTTCTG 59.199 52.381 0.00 0.00 33.68 3.02
4719 4773 2.548067 GCTCGAAGGGAAGTGTTTCTGA 60.548 50.000 0.00 0.00 33.68 3.27
4720 4774 3.728845 CTCGAAGGGAAGTGTTTCTGAA 58.271 45.455 0.00 0.00 33.68 3.02
4721 4775 4.127171 CTCGAAGGGAAGTGTTTCTGAAA 58.873 43.478 0.00 0.00 33.68 2.69
4722 4776 4.714632 TCGAAGGGAAGTGTTTCTGAAAT 58.285 39.130 6.06 0.00 33.68 2.17
4723 4777 5.860611 TCGAAGGGAAGTGTTTCTGAAATA 58.139 37.500 6.06 0.30 33.68 1.40
4724 4778 5.699458 TCGAAGGGAAGTGTTTCTGAAATAC 59.301 40.000 18.70 18.70 33.68 1.89
4725 4779 5.701290 CGAAGGGAAGTGTTTCTGAAATACT 59.299 40.000 22.00 22.00 43.48 2.12
4726 4780 6.128526 CGAAGGGAAGTGTTTCTGAAATACTC 60.129 42.308 25.94 19.64 41.22 2.59
4727 4781 6.441088 AGGGAAGTGTTTCTGAAATACTCT 57.559 37.500 25.94 18.28 41.22 3.24
4728 4782 6.468543 AGGGAAGTGTTTCTGAAATACTCTC 58.531 40.000 25.94 22.71 41.22 3.20
4729 4783 5.644206 GGGAAGTGTTTCTGAAATACTCTCC 59.356 44.000 28.27 28.27 41.22 3.71
4730 4784 6.468543 GGAAGTGTTTCTGAAATACTCTCCT 58.531 40.000 28.52 18.88 41.22 3.69
4731 4785 6.937465 GGAAGTGTTTCTGAAATACTCTCCTT 59.063 38.462 28.52 18.64 41.22 3.36
4732 4786 8.095169 GGAAGTGTTTCTGAAATACTCTCCTTA 58.905 37.037 28.52 1.88 41.22 2.69
4733 4787 8.834749 AAGTGTTTCTGAAATACTCTCCTTAC 57.165 34.615 25.94 3.80 41.22 2.34
4734 4788 7.387643 AGTGTTTCTGAAATACTCTCCTTACC 58.612 38.462 22.00 0.37 38.25 2.85
4735 4789 7.235812 AGTGTTTCTGAAATACTCTCCTTACCT 59.764 37.037 22.00 2.10 38.25 3.08
4990 5044 1.276989 GTCATTCGTAACCCTCCCACA 59.723 52.381 0.00 0.00 0.00 4.17
5290 5346 8.981724 TCTAAAATATGTCTACATACATCCGC 57.018 34.615 4.98 0.00 41.15 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.698040 GGAGATTGTTTGACAGGATGCAT 59.302 43.478 0.00 0.00 42.53 3.96
118 119 4.207281 CGGCGAGCGGATTGGAGA 62.207 66.667 0.00 0.00 0.00 3.71
264 265 0.826715 ATGCGATGATAGCGGGCTAT 59.173 50.000 12.74 12.74 41.48 2.97
438 439 3.525537 CAGGATATATGCCTTGGCTACG 58.474 50.000 13.18 0.00 32.12 3.51
483 484 2.436646 CCCGACCAGCACACCATC 60.437 66.667 0.00 0.00 0.00 3.51
581 582 4.321750 CGTATAACATCCTTATCCGTGCCT 60.322 45.833 0.00 0.00 0.00 4.75
600 601 3.950254 CTCTCCGCGCGGTCGTAT 61.950 66.667 44.16 0.00 38.14 3.06
762 763 4.687215 GTGCCTCAGCTCCACGCA 62.687 66.667 0.00 0.00 42.61 5.24
923 924 4.151883 TGGATAAGCAAAGAAAGGCAAGT 58.848 39.130 0.00 0.00 0.00 3.16
1070 1078 1.599606 GAGCAGCCGAGTTGGAGAGA 61.600 60.000 0.00 0.00 42.00 3.10
1102 1110 2.821688 CGGACGCTAGGAGGACGAC 61.822 68.421 0.00 0.00 0.00 4.34
1495 1503 6.381707 GGGGATAACCTTGGTTATTTAAAGCA 59.618 38.462 21.62 0.00 40.03 3.91
1509 1517 1.847088 GGCTTCTCAGGGGATAACCTT 59.153 52.381 0.00 0.00 39.34 3.50
1530 1542 6.418819 GGATCGGAATAAACAAATGCAATCTG 59.581 38.462 0.00 0.00 0.00 2.90
1550 1562 0.596083 CTAGAACAGCGCAGGGATCG 60.596 60.000 11.47 0.00 0.00 3.69
1554 1566 0.798776 CAAACTAGAACAGCGCAGGG 59.201 55.000 11.47 0.14 0.00 4.45
1561 1573 5.119279 CGACATCAAGTCCAAACTAGAACAG 59.881 44.000 0.00 0.00 44.66 3.16
1602 1614 9.362539 CTTGCACTTTTGAATAGCTAAATGAAT 57.637 29.630 0.00 0.00 0.00 2.57
1697 1714 2.353269 TCGCAACACTAACAACACTTGG 59.647 45.455 0.00 0.00 34.12 3.61
1707 1724 9.090692 GAACCTTATACTAATTCGCAACACTAA 57.909 33.333 0.00 0.00 0.00 2.24
1722 1739 8.644374 TTTTGGCATAACTTGAACCTTATACT 57.356 30.769 0.00 0.00 0.00 2.12
1724 1741 9.868277 CAATTTTGGCATAACTTGAACCTTATA 57.132 29.630 0.00 0.00 0.00 0.98
1726 1743 7.957002 TCAATTTTGGCATAACTTGAACCTTA 58.043 30.769 10.43 0.00 0.00 2.69
1727 1744 6.825610 TCAATTTTGGCATAACTTGAACCTT 58.174 32.000 10.43 0.00 0.00 3.50
1728 1745 6.418057 TCAATTTTGGCATAACTTGAACCT 57.582 33.333 10.43 0.00 0.00 3.50
1729 1746 7.671495 ATTCAATTTTGGCATAACTTGAACC 57.329 32.000 19.52 0.00 35.97 3.62
1731 1748 9.941325 ACATATTCAATTTTGGCATAACTTGAA 57.059 25.926 19.46 19.46 37.12 2.69
1732 1749 9.585099 GACATATTCAATTTTGGCATAACTTGA 57.415 29.630 9.43 9.43 0.00 3.02
1733 1750 9.590451 AGACATATTCAATTTTGGCATAACTTG 57.410 29.630 0.00 0.00 0.00 3.16
1804 1821 9.661187 CTCTAGCAGCAACAAATATATTCAAAG 57.339 33.333 0.00 0.00 0.00 2.77
1848 1866 4.193090 ACATACGGTGTTGTGAAGTTCAA 58.807 39.130 7.25 0.00 38.01 2.69
1927 1950 9.559958 GATTCATGACATACAAATTTTTCGACT 57.440 29.630 0.00 0.00 0.00 4.18
1937 1960 9.628746 CAGACAAATTGATTCATGACATACAAA 57.371 29.630 0.00 0.00 0.00 2.83
1938 1961 8.795513 ACAGACAAATTGATTCATGACATACAA 58.204 29.630 0.00 0.26 0.00 2.41
1971 1995 5.067674 TCAAAACAGTGCTAATTTCAGCTGT 59.932 36.000 14.67 0.00 42.30 4.40
2027 2051 6.149142 GCCTTCAGAATTCCTCTAATATGCAG 59.851 42.308 0.65 0.00 31.12 4.41
2061 2085 2.999355 GTGAGCCTTGTGAGTTCTGATC 59.001 50.000 0.00 0.00 0.00 2.92
2081 2105 3.199508 CCTGAGATGTGAGATCCTTTGGT 59.800 47.826 0.00 0.00 0.00 3.67
2088 2112 4.415596 AGGATACCCTGAGATGTGAGATC 58.584 47.826 0.00 0.00 42.42 2.75
2090 2114 3.981516 AGGATACCCTGAGATGTGAGA 57.018 47.619 0.00 0.00 42.42 3.27
2091 2115 4.222336 AGAAGGATACCCTGAGATGTGAG 58.778 47.826 0.00 0.00 43.48 3.51
2092 2116 4.271807 AGAAGGATACCCTGAGATGTGA 57.728 45.455 0.00 0.00 43.48 3.58
2093 2117 5.365021 AAAGAAGGATACCCTGAGATGTG 57.635 43.478 0.00 0.00 43.48 3.21
2094 2118 5.728741 AGAAAAGAAGGATACCCTGAGATGT 59.271 40.000 0.00 0.00 43.48 3.06
2095 2119 6.099557 AGAGAAAAGAAGGATACCCTGAGATG 59.900 42.308 0.00 0.00 43.48 2.90
2096 2120 6.209026 AGAGAAAAGAAGGATACCCTGAGAT 58.791 40.000 0.00 0.00 43.48 2.75
2097 2121 5.594777 AGAGAAAAGAAGGATACCCTGAGA 58.405 41.667 0.00 0.00 43.48 3.27
2140 2164 3.509575 AGCATTTATCCCTCGTTTTGCAA 59.490 39.130 0.00 0.00 0.00 4.08
2146 2170 7.062749 TCTACATTAGCATTTATCCCTCGTT 57.937 36.000 0.00 0.00 0.00 3.85
2148 2172 7.962964 TTTCTACATTAGCATTTATCCCTCG 57.037 36.000 0.00 0.00 0.00 4.63
2175 2199 7.523293 TCCTGAAATAGCAAAAACAATCAGA 57.477 32.000 0.00 0.00 36.11 3.27
2176 2200 8.592105 TTTCCTGAAATAGCAAAAACAATCAG 57.408 30.769 0.00 0.00 34.33 2.90
2181 2205 5.700373 GGCATTTCCTGAAATAGCAAAAACA 59.300 36.000 19.19 0.00 38.84 2.83
2182 2206 5.700373 TGGCATTTCCTGAAATAGCAAAAAC 59.300 36.000 19.19 9.23 38.84 2.43
2224 2249 6.016276 AGTGGCGAATAAAATGAAAGACAGTT 60.016 34.615 0.00 0.00 38.47 3.16
2226 2251 5.942872 AGTGGCGAATAAAATGAAAGACAG 58.057 37.500 0.00 0.00 0.00 3.51
2233 2258 8.402472 CAACCTAAATAGTGGCGAATAAAATGA 58.598 33.333 0.00 0.00 0.00 2.57
2250 2275 7.750947 AGGTATACCTCTGTTCAACCTAAAT 57.249 36.000 19.27 0.00 44.77 1.40
2285 2310 6.306199 CACCCTCATATTGGACCATCAATTA 58.694 40.000 0.00 0.00 38.24 1.40
2344 2369 7.999679 TCATCCAAATAAATCCTACAAGCAAG 58.000 34.615 0.00 0.00 0.00 4.01
2360 2385 5.162958 TGACATGTATCCCCATCATCCAAAT 60.163 40.000 0.00 0.00 0.00 2.32
2388 2413 5.183713 CAGCTCACCTAATCCATTTGTTTGA 59.816 40.000 0.00 0.00 0.00 2.69
2394 2419 4.018050 AGAACCAGCTCACCTAATCCATTT 60.018 41.667 0.00 0.00 0.00 2.32
2420 2445 5.094387 CCCAACTAGATACCTGGTATGGAT 58.906 45.833 23.51 11.60 35.83 3.41
2431 2456 1.489230 CCCCCACACCCAACTAGATAC 59.511 57.143 0.00 0.00 0.00 2.24
2456 2481 5.644636 GTCAGATAACTAGATACCTCCTCGG 59.355 48.000 0.00 0.00 39.35 4.63
2459 2484 6.951198 CCATGTCAGATAACTAGATACCTCCT 59.049 42.308 0.00 0.00 0.00 3.69
2475 2500 6.367374 TTTGTCCTACATTACCATGTCAGA 57.633 37.500 0.00 0.00 43.06 3.27
2489 2514 4.816925 GGGCAACTAGATCATTTGTCCTAC 59.183 45.833 14.26 0.00 41.08 3.18
2493 2518 4.142381 GGTTGGGCAACTAGATCATTTGTC 60.142 45.833 0.00 0.00 40.94 3.18
2509 2542 4.202212 ACAAGAAAAACATACAGGTTGGGC 60.202 41.667 0.00 0.00 0.00 5.36
2534 2567 1.416243 TAGCCGGGTATTAGGTGTGG 58.584 55.000 9.87 0.00 0.00 4.17
2543 2576 3.199071 TCACTTCATGTTTAGCCGGGTAT 59.801 43.478 15.31 0.00 0.00 2.73
2548 2581 4.854399 TGTTTTCACTTCATGTTTAGCCG 58.146 39.130 0.00 0.00 0.00 5.52
2578 2611 8.673711 TCATTTATCCCTTGATAGACAAAAACG 58.326 33.333 0.00 0.00 38.08 3.60
2615 2648 4.221482 TGACCCATATCAGAAGGATGATCG 59.779 45.833 0.00 0.00 40.40 3.69
2641 2674 3.118038 AGCTGACACCACTTCCTGTTAAA 60.118 43.478 0.00 0.00 0.00 1.52
2646 2679 1.605710 CAAAGCTGACACCACTTCCTG 59.394 52.381 0.00 0.00 0.00 3.86
2735 2768 2.304761 TCCAAAGAAGCCATTACCGTCT 59.695 45.455 0.00 0.00 0.00 4.18
2788 2821 2.757099 CCATTGCACTGAGGCCCC 60.757 66.667 5.49 0.00 0.00 5.80
2828 2861 1.538047 AGCTCATGCCGACAACATTT 58.462 45.000 0.00 0.00 40.80 2.32
2873 2906 6.603997 ACCTGTACCACAAACTAACATTTTGA 59.396 34.615 1.97 0.00 37.39 2.69
3547 3580 3.687212 ACAAAATGTGTCTGACAACGTCA 59.313 39.130 12.81 6.68 36.52 4.35
3623 3658 4.660771 CCTAGATGAATACCCAGGAAAGGT 59.339 45.833 0.00 0.00 41.64 3.50
3630 3665 9.587772 CGTAAATTATCCTAGATGAATACCCAG 57.412 37.037 0.00 0.00 0.00 4.45
3656 3691 9.294030 CTTTTGAAGGTCAATAAATGCATACTC 57.706 33.333 0.00 0.00 36.11 2.59
3674 3709 8.230486 AGCTACGATTTACAATCACTTTTGAAG 58.770 33.333 0.00 0.00 34.61 3.02
3694 3729 1.519455 GTGCACCCTAGCAGCTACG 60.519 63.158 5.22 0.00 46.69 3.51
3698 3733 2.103042 CGAAGTGCACCCTAGCAGC 61.103 63.158 14.63 0.00 46.69 5.25
3767 3803 5.869350 AGCAAAGTGTTCGCATTATACTTC 58.131 37.500 0.00 0.00 31.71 3.01
3831 3867 3.895656 GACCAGGACCTGCAGTATATACA 59.104 47.826 16.72 0.00 0.00 2.29
3832 3868 4.153411 AGACCAGGACCTGCAGTATATAC 58.847 47.826 16.72 4.60 0.00 1.47
3858 3894 3.569701 CCTTGTATGGTTTGTGACTGCTT 59.430 43.478 0.00 0.00 0.00 3.91
3909 3945 0.107643 TCGCAGATTCCACCAACACA 59.892 50.000 0.00 0.00 0.00 3.72
3961 3997 1.000506 TGAGGTGTAGTTCCAAGCGTC 59.999 52.381 0.00 0.00 0.00 5.19
4050 4086 2.433446 CTGCAGCCAGTCCCAAGT 59.567 61.111 0.00 0.00 34.31 3.16
4105 4141 1.825090 TCGGCTGAAACATGCATTCT 58.175 45.000 0.00 0.00 0.00 2.40
4119 4155 2.093447 CCCATTCTTAGTGAGTTCGGCT 60.093 50.000 0.00 0.00 0.00 5.52
4200 4236 3.250762 CGCAAGTTGGATCTTCAGTCAAA 59.749 43.478 4.75 0.00 0.00 2.69
4201 4237 2.807967 CGCAAGTTGGATCTTCAGTCAA 59.192 45.455 4.75 0.00 0.00 3.18
4313 4349 1.736032 GCGAACTTGATGTCGTAGGCT 60.736 52.381 0.00 0.00 0.00 4.58
4318 4354 1.282248 CGTGGCGAACTTGATGTCGT 61.282 55.000 0.00 0.00 0.00 4.34
4320 4356 0.949105 ACCGTGGCGAACTTGATGTC 60.949 55.000 0.00 0.00 0.00 3.06
4323 4359 0.606604 ACTACCGTGGCGAACTTGAT 59.393 50.000 0.00 0.00 0.00 2.57
4332 4368 2.417586 GTGTCCAAATTACTACCGTGGC 59.582 50.000 0.00 0.00 0.00 5.01
4333 4369 3.434299 GTGTGTCCAAATTACTACCGTGG 59.566 47.826 0.00 0.00 0.00 4.94
4335 4371 4.339872 TGTGTGTCCAAATTACTACCGT 57.660 40.909 0.00 0.00 0.00 4.83
4354 4390 1.935873 GAGTACATGCATGCACGATGT 59.064 47.619 25.37 24.76 34.14 3.06
4359 4395 0.933097 CCTCGAGTACATGCATGCAC 59.067 55.000 25.37 23.34 0.00 4.57
4366 4402 4.307432 ACAACTTTGTCCTCGAGTACATG 58.693 43.478 11.95 9.48 36.50 3.21
4369 4405 4.365723 TGAACAACTTTGTCCTCGAGTAC 58.634 43.478 12.31 6.42 41.31 2.73
4372 4408 2.802816 CCTGAACAACTTTGTCCTCGAG 59.197 50.000 5.13 5.13 41.31 4.04
4374 4410 1.264288 GCCTGAACAACTTTGTCCTCG 59.736 52.381 0.00 0.00 41.31 4.63
4401 4437 1.067071 GGAACTTCCCAGATCGTCGTT 60.067 52.381 0.00 0.00 0.00 3.85
4420 4467 0.318107 CTTGCAGACCTTTTGCGTGG 60.318 55.000 0.00 0.00 44.40 4.94
4447 4494 6.761242 TGGTGATACATTATACACACTTGAGC 59.239 38.462 0.00 0.00 35.33 4.26
4466 4513 7.944729 AGAAAACAAGTGCTTATATGGTGAT 57.055 32.000 0.00 0.00 0.00 3.06
4472 4519 9.899226 GACAGAAAAGAAAACAAGTGCTTATAT 57.101 29.630 0.00 0.00 0.00 0.86
4474 4521 7.771183 TGACAGAAAAGAAAACAAGTGCTTAT 58.229 30.769 0.00 0.00 0.00 1.73
4484 4531 9.528847 GTGATTTGTTTTGACAGAAAAGAAAAC 57.471 29.630 0.00 0.00 36.45 2.43
4486 4533 9.487790 AAGTGATTTGTTTTGACAGAAAAGAAA 57.512 25.926 0.00 0.00 37.00 2.52
4507 4554 2.623535 ACGTAAGCAACACACAAGTGA 58.376 42.857 7.28 0.00 45.97 3.41
4515 4562 3.668596 ACTGAACAACGTAAGCAACAC 57.331 42.857 0.00 0.00 45.62 3.32
4532 4579 6.934645 TCCACCTGTAGTTTTATTCTGAACTG 59.065 38.462 0.00 0.00 36.79 3.16
4533 4580 7.074653 TCCACCTGTAGTTTTATTCTGAACT 57.925 36.000 0.00 0.00 39.32 3.01
4553 4600 6.073331 GCACAAGAGCATTCTATAGATTCCAC 60.073 42.308 2.58 0.00 31.96 4.02
4554 4601 5.994054 GCACAAGAGCATTCTATAGATTCCA 59.006 40.000 2.58 0.00 31.96 3.53
4555 4602 6.229733 AGCACAAGAGCATTCTATAGATTCC 58.770 40.000 2.58 0.00 36.85 3.01
4556 4603 7.226325 ACAAGCACAAGAGCATTCTATAGATTC 59.774 37.037 2.58 0.26 36.85 2.52
4557 4604 7.052873 ACAAGCACAAGAGCATTCTATAGATT 58.947 34.615 2.58 0.00 36.85 2.40
4558 4605 6.590068 ACAAGCACAAGAGCATTCTATAGAT 58.410 36.000 2.58 0.00 36.85 1.98
4559 4606 5.982356 ACAAGCACAAGAGCATTCTATAGA 58.018 37.500 0.00 0.00 36.85 1.98
4560 4607 6.538021 AGAACAAGCACAAGAGCATTCTATAG 59.462 38.462 0.00 0.00 34.09 1.31
4561 4608 6.409704 AGAACAAGCACAAGAGCATTCTATA 58.590 36.000 0.00 0.00 34.09 1.31
4562 4609 5.251764 AGAACAAGCACAAGAGCATTCTAT 58.748 37.500 0.00 0.00 34.09 1.98
4563 4610 4.645535 AGAACAAGCACAAGAGCATTCTA 58.354 39.130 0.00 0.00 34.09 2.10
4564 4611 3.484407 AGAACAAGCACAAGAGCATTCT 58.516 40.909 0.00 0.00 36.85 2.40
4565 4612 3.501445 AGAGAACAAGCACAAGAGCATTC 59.499 43.478 0.00 0.00 36.85 2.67
4566 4613 3.252701 CAGAGAACAAGCACAAGAGCATT 59.747 43.478 0.00 0.00 36.85 3.56
4567 4614 2.812591 CAGAGAACAAGCACAAGAGCAT 59.187 45.455 0.00 0.00 36.85 3.79
4568 4615 2.158914 TCAGAGAACAAGCACAAGAGCA 60.159 45.455 0.00 0.00 36.85 4.26
4569 4616 2.222911 GTCAGAGAACAAGCACAAGAGC 59.777 50.000 0.00 0.00 0.00 4.09
4570 4617 2.805099 GGTCAGAGAACAAGCACAAGAG 59.195 50.000 0.00 0.00 0.00 2.85
4574 4621 0.464036 ACGGTCAGAGAACAAGCACA 59.536 50.000 0.00 0.00 0.00 4.57
4584 4631 0.944386 CACCCAAACAACGGTCAGAG 59.056 55.000 0.00 0.00 0.00 3.35
4585 4632 0.542333 TCACCCAAACAACGGTCAGA 59.458 50.000 0.00 0.00 0.00 3.27
4588 4635 2.243602 TACTCACCCAAACAACGGTC 57.756 50.000 0.00 0.00 0.00 4.79
4601 4648 1.463674 CCAACAAGGGGCATACTCAC 58.536 55.000 0.00 0.00 0.00 3.51
4624 4675 4.695606 TCAGATTAAACCCTAGACCACCT 58.304 43.478 0.00 0.00 0.00 4.00
4625 4676 4.141688 CCTCAGATTAAACCCTAGACCACC 60.142 50.000 0.00 0.00 0.00 4.61
4627 4678 4.695606 ACCTCAGATTAAACCCTAGACCA 58.304 43.478 0.00 0.00 0.00 4.02
4654 4708 0.813821 GGCCTCCATTTGAGCAAGAC 59.186 55.000 0.00 0.00 39.98 3.01
4657 4711 1.305213 GGGGCCTCCATTTGAGCAA 60.305 57.895 0.84 0.00 39.98 3.91
4674 4728 3.554342 CTCCCCTCATGGCTCCGG 61.554 72.222 0.00 0.00 0.00 5.14
4675 4729 1.840650 ATCTCCCCTCATGGCTCCG 60.841 63.158 0.00 0.00 0.00 4.63
4676 4730 1.759881 CATCTCCCCTCATGGCTCC 59.240 63.158 0.00 0.00 0.00 4.70
4677 4731 0.765903 TCCATCTCCCCTCATGGCTC 60.766 60.000 0.00 0.00 39.69 4.70
4678 4732 1.059006 GTCCATCTCCCCTCATGGCT 61.059 60.000 0.00 0.00 39.69 4.75
4679 4733 1.453669 GTCCATCTCCCCTCATGGC 59.546 63.158 0.00 0.00 39.69 4.40
4680 4734 1.750930 CGTCCATCTCCCCTCATGG 59.249 63.158 0.00 0.00 41.04 3.66
4681 4735 1.070445 GCGTCCATCTCCCCTCATG 59.930 63.158 0.00 0.00 0.00 3.07
4682 4736 1.074926 AGCGTCCATCTCCCCTCAT 60.075 57.895 0.00 0.00 0.00 2.90
4683 4737 1.758514 GAGCGTCCATCTCCCCTCA 60.759 63.158 0.00 0.00 0.00 3.86
4684 4738 2.851071 CGAGCGTCCATCTCCCCTC 61.851 68.421 0.00 0.00 0.00 4.30
4685 4739 2.835431 CGAGCGTCCATCTCCCCT 60.835 66.667 0.00 0.00 0.00 4.79
4686 4740 2.356818 CTTCGAGCGTCCATCTCCCC 62.357 65.000 0.00 0.00 0.00 4.81
4687 4741 1.066587 CTTCGAGCGTCCATCTCCC 59.933 63.158 0.00 0.00 0.00 4.30
4688 4742 1.066587 CCTTCGAGCGTCCATCTCC 59.933 63.158 0.00 0.00 0.00 3.71
4689 4743 1.066587 CCCTTCGAGCGTCCATCTC 59.933 63.158 0.00 0.00 0.00 2.75
4690 4744 0.970937 TTCCCTTCGAGCGTCCATCT 60.971 55.000 0.00 0.00 0.00 2.90
4691 4745 0.528684 CTTCCCTTCGAGCGTCCATC 60.529 60.000 0.00 0.00 0.00 3.51
4692 4746 1.258445 ACTTCCCTTCGAGCGTCCAT 61.258 55.000 0.00 0.00 0.00 3.41
4693 4747 1.906824 ACTTCCCTTCGAGCGTCCA 60.907 57.895 0.00 0.00 0.00 4.02
4694 4748 1.446272 CACTTCCCTTCGAGCGTCC 60.446 63.158 0.00 0.00 0.00 4.79
4695 4749 0.319641 AACACTTCCCTTCGAGCGTC 60.320 55.000 0.00 0.00 0.00 5.19
4696 4750 0.106149 AAACACTTCCCTTCGAGCGT 59.894 50.000 0.00 0.00 0.00 5.07
4697 4751 0.790814 GAAACACTTCCCTTCGAGCG 59.209 55.000 0.00 0.00 0.00 5.03
4698 4752 1.801178 CAGAAACACTTCCCTTCGAGC 59.199 52.381 0.00 0.00 31.28 5.03
4699 4753 3.386768 TCAGAAACACTTCCCTTCGAG 57.613 47.619 0.00 0.00 31.28 4.04
4700 4754 3.830744 TTCAGAAACACTTCCCTTCGA 57.169 42.857 0.00 0.00 31.28 3.71
4701 4755 5.701290 AGTATTTCAGAAACACTTCCCTTCG 59.299 40.000 0.59 0.00 31.28 3.79
4702 4756 6.937465 AGAGTATTTCAGAAACACTTCCCTTC 59.063 38.462 8.25 0.00 31.28 3.46
4703 4757 6.842676 AGAGTATTTCAGAAACACTTCCCTT 58.157 36.000 8.25 0.00 31.28 3.95
4704 4758 6.441088 AGAGTATTTCAGAAACACTTCCCT 57.559 37.500 8.25 0.00 31.28 4.20
4705 4759 5.644206 GGAGAGTATTTCAGAAACACTTCCC 59.356 44.000 8.25 8.72 31.28 3.97
4706 4760 6.468543 AGGAGAGTATTTCAGAAACACTTCC 58.531 40.000 18.53 18.53 31.28 3.46
4707 4761 7.971183 AAGGAGAGTATTTCAGAAACACTTC 57.029 36.000 8.25 7.77 0.00 3.01
4708 4762 7.878644 GGTAAGGAGAGTATTTCAGAAACACTT 59.121 37.037 8.25 0.00 0.00 3.16
4709 4763 7.235812 AGGTAAGGAGAGTATTTCAGAAACACT 59.764 37.037 6.53 6.53 0.00 3.55
4710 4764 7.387643 AGGTAAGGAGAGTATTTCAGAAACAC 58.612 38.462 0.00 0.00 0.00 3.32
4711 4765 7.554959 AGGTAAGGAGAGTATTTCAGAAACA 57.445 36.000 0.00 0.00 0.00 2.83
4712 4766 8.850007 AAAGGTAAGGAGAGTATTTCAGAAAC 57.150 34.615 0.00 0.00 0.00 2.78
4713 4767 9.939802 GTAAAGGTAAGGAGAGTATTTCAGAAA 57.060 33.333 0.00 0.00 0.00 2.52
4714 4768 9.322769 AGTAAAGGTAAGGAGAGTATTTCAGAA 57.677 33.333 0.00 0.00 0.00 3.02
4715 4769 8.896722 AGTAAAGGTAAGGAGAGTATTTCAGA 57.103 34.615 0.00 0.00 0.00 3.27
4717 4771 9.765295 ACTAGTAAAGGTAAGGAGAGTATTTCA 57.235 33.333 0.00 0.00 0.00 2.69
4723 4777 8.946797 TTTGTACTAGTAAAGGTAAGGAGAGT 57.053 34.615 3.61 0.00 0.00 3.24
4724 4778 9.804758 CATTTGTACTAGTAAAGGTAAGGAGAG 57.195 37.037 3.61 0.00 0.00 3.20
4725 4779 8.255905 GCATTTGTACTAGTAAAGGTAAGGAGA 58.744 37.037 3.61 0.00 0.00 3.71
4726 4780 7.494952 GGCATTTGTACTAGTAAAGGTAAGGAG 59.505 40.741 3.61 0.00 0.00 3.69
4727 4781 7.333323 GGCATTTGTACTAGTAAAGGTAAGGA 58.667 38.462 3.61 0.00 0.00 3.36
4728 4782 6.541278 GGGCATTTGTACTAGTAAAGGTAAGG 59.459 42.308 3.61 0.00 0.00 2.69
4729 4783 6.257193 CGGGCATTTGTACTAGTAAAGGTAAG 59.743 42.308 3.61 0.00 0.00 2.34
4730 4784 6.108015 CGGGCATTTGTACTAGTAAAGGTAA 58.892 40.000 3.61 0.00 0.00 2.85
4731 4785 5.187576 ACGGGCATTTGTACTAGTAAAGGTA 59.812 40.000 3.61 0.00 0.00 3.08
4732 4786 4.019950 ACGGGCATTTGTACTAGTAAAGGT 60.020 41.667 3.61 0.00 0.00 3.50
4733 4787 4.331717 CACGGGCATTTGTACTAGTAAAGG 59.668 45.833 3.61 1.25 0.00 3.11
4734 4788 4.201783 GCACGGGCATTTGTACTAGTAAAG 60.202 45.833 3.77 0.00 40.72 1.85
4735 4789 3.685756 GCACGGGCATTTGTACTAGTAAA 59.314 43.478 3.77 0.00 40.72 2.01
4990 5044 4.810491 GTGTTTGGAATTCAAAGTGTGCAT 59.190 37.500 7.93 0.00 45.00 3.96


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

AutoCloner maintained by Alex Coulton.