Multiple sequence alignment - TraesCS4B01G012000

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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 TraesCS4B01G012000 chr4B 100.000 4995 0 0 1 4995 7812600 7807606 0.000000e+00 9225.0
1 TraesCS4B01G012000 chr4B 88.843 484 23 12 4319 4782 8411966 8412438 2.610000e-157 566.0
2 TraesCS4B01G012000 chr4D 94.028 4789 188 43 135 4863 4764306 4759556 0.000000e+00 7169.0
3 TraesCS4B01G012000 chr4D 92.000 200 13 1 3230 3429 5034844 5035040 1.370000e-70 278.0
4 TraesCS4B01G012000 chr4D 86.624 157 5 2 1 141 4764523 4764367 5.180000e-35 159.0
5 TraesCS4B01G012000 chr4A 94.769 4473 177 30 130 4577 598716428 598711988 0.000000e+00 6911.0
6 TraesCS4B01G012000 chr4A 84.848 165 7 3 1 147 598716638 598716474 3.110000e-32 150.0
7 TraesCS4B01G012000 chr7D 80.000 150 13 8 4819 4952 201196087 201196235 1.480000e-15 95.3
8 TraesCS4B01G012000 chr3D 92.188 64 3 1 4894 4957 410671270 410671331 6.890000e-14 89.8
9 TraesCS4B01G012000 chr2D 95.556 45 2 0 4819 4863 82395344 82395388 6.940000e-09 73.1
10 TraesCS4B01G012000 chr3A 100.000 36 0 0 4828 4863 117059163 117059128 3.230000e-07 67.6
11 TraesCS4B01G012000 chr2B 91.111 45 4 0 4819 4863 153584355 153584399 1.500000e-05 62.1


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 TraesCS4B01G012000 chr4B 7807606 7812600 4994 True 9225.0 9225 100.0000 1 4995 1 chr4B.!!$R1 4994
1 TraesCS4B01G012000 chr4D 4759556 4764523 4967 True 3664.0 7169 90.3260 1 4863 2 chr4D.!!$R1 4862
2 TraesCS4B01G012000 chr4A 598711988 598716638 4650 True 3530.5 6911 89.8085 1 4577 2 chr4A.!!$R1 4576

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
339 425 1.153549 CTTCTACAGAGGCACGGGC 60.154 63.158 0.00 0.00 40.13 6.13 F
1272 1363 0.462225 CCTGCTGATCAGTGAGCCAG 60.462 60.000 23.38 19.29 41.25 4.85 F
1646 1742 0.679505 TTACAGCGTGCTCAGAAGGT 59.320 50.000 0.00 0.00 0.00 3.50 F
3181 3291 0.169672 CTTTGAAGCCTCATGCACCG 59.830 55.000 0.00 0.00 44.83 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1313 1404 0.250858 AGCAGCTACAACACCATGCA 60.251 50.0 0.00 0.00 36.15 3.96 R
2974 3084 0.903942 CCTCTTCAGGCTGCTCTTCT 59.096 55.0 10.34 0.00 30.98 2.85 R
3321 3431 0.537828 TTTACCGGGGTTCCTTGCAC 60.538 55.0 6.32 0.00 0.00 4.57 R
4816 4964 0.323360 TTGAATCAAAGGGGCCCTCG 60.323 55.0 28.97 20.61 30.89 4.63 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
102 119 6.618287 TTATGAATGGAATGACGAATGGAC 57.382 37.500 0.00 0.00 0.00 4.02
133 150 8.548880 AACACTATACCTCTTTTATAGCTGGA 57.451 34.615 0.00 0.00 34.18 3.86
227 311 5.689068 CCATTTGTTGTTTGCTTCTTCTCTC 59.311 40.000 0.00 0.00 0.00 3.20
339 425 1.153549 CTTCTACAGAGGCACGGGC 60.154 63.158 0.00 0.00 40.13 6.13
441 532 6.016777 CCATTGGTTCCTTTGTCTAGCATATC 60.017 42.308 0.00 0.00 0.00 1.63
479 570 2.927477 TGCCGAAAGAATTAGTGTAGCG 59.073 45.455 0.00 0.00 0.00 4.26
511 602 6.483307 CCTCTGTTTGTTCTGTTGTCAATCTA 59.517 38.462 0.00 0.00 0.00 1.98
520 611 9.154847 TGTTCTGTTGTCAATCTATGATAGTTG 57.845 33.333 0.00 4.34 40.97 3.16
609 700 7.066307 ACCATTTCCTTGCTTCTGTTTTATT 57.934 32.000 0.00 0.00 0.00 1.40
612 703 7.442062 CCATTTCCTTGCTTCTGTTTTATTTGT 59.558 33.333 0.00 0.00 0.00 2.83
613 704 8.829612 CATTTCCTTGCTTCTGTTTTATTTGTT 58.170 29.630 0.00 0.00 0.00 2.83
614 705 7.769272 TTCCTTGCTTCTGTTTTATTTGTTG 57.231 32.000 0.00 0.00 0.00 3.33
617 708 5.964887 TGCTTCTGTTTTATTTGTTGTGC 57.035 34.783 0.00 0.00 0.00 4.57
672 763 1.234806 ATTATGGTGGAGGGGCATGT 58.765 50.000 0.00 0.00 0.00 3.21
681 772 2.972713 TGGAGGGGCATGTCTATCTTAC 59.027 50.000 0.00 0.00 0.00 2.34
688 779 4.999950 GGGCATGTCTATCTTACTTGATGG 59.000 45.833 0.00 0.00 0.00 3.51
816 907 9.720769 CTTCAAAATTACCTGAGGTTAGTCTTA 57.279 33.333 10.53 0.00 37.09 2.10
841 932 8.561738 AACCCTACATTTTGTACTTGACATAG 57.438 34.615 0.00 0.00 38.07 2.23
885 976 4.617253 AACCCCAGTTTCCTTTTTATGC 57.383 40.909 0.00 0.00 29.61 3.14
887 978 2.560981 CCCCAGTTTCCTTTTTATGCGT 59.439 45.455 0.00 0.00 0.00 5.24
891 982 5.469479 CCAGTTTCCTTTTTATGCGTTGAT 58.531 37.500 0.00 0.00 0.00 2.57
892 983 5.345741 CCAGTTTCCTTTTTATGCGTTGATG 59.654 40.000 0.00 0.00 0.00 3.07
893 984 6.148948 CAGTTTCCTTTTTATGCGTTGATGA 58.851 36.000 0.00 0.00 0.00 2.92
894 985 6.088085 CAGTTTCCTTTTTATGCGTTGATGAC 59.912 38.462 0.00 0.00 0.00 3.06
1261 1352 6.379133 TCTTTTGATATTTTCTGCCTGCTGAT 59.621 34.615 0.00 0.00 0.00 2.90
1272 1363 0.462225 CCTGCTGATCAGTGAGCCAG 60.462 60.000 23.38 19.29 41.25 4.85
1283 1374 2.095364 CAGTGAGCCAGATTCAAACAGC 60.095 50.000 0.00 0.00 0.00 4.40
1285 1376 2.095364 GTGAGCCAGATTCAAACAGCTG 60.095 50.000 13.48 13.48 0.00 4.24
1298 1389 7.561021 TTCAAACAGCTGTACATTTCTTGTA 57.439 32.000 22.01 9.89 39.87 2.41
1299 1390 7.561021 TCAAACAGCTGTACATTTCTTGTAA 57.439 32.000 22.01 1.31 42.37 2.41
1372 1464 3.005554 ACCGTGCAATCTTTCTCTGATG 58.994 45.455 0.00 0.00 0.00 3.07
1581 1677 5.468540 AATTACTTGCCCTCCTTTGTTTC 57.531 39.130 0.00 0.00 0.00 2.78
1587 1683 3.642141 TGCCCTCCTTTGTTTCTCTTTT 58.358 40.909 0.00 0.00 0.00 2.27
1646 1742 0.679505 TTACAGCGTGCTCAGAAGGT 59.320 50.000 0.00 0.00 0.00 3.50
1656 1752 4.143094 CGTGCTCAGAAGGTTACTTTTAGC 60.143 45.833 0.00 0.00 36.97 3.09
1688 1784 2.983229 TGAAAAGCCAGAGAGAGATGC 58.017 47.619 0.00 0.00 0.00 3.91
1827 1923 1.991965 CGCAACCATTTGTATGCAACC 59.008 47.619 0.00 0.00 38.69 3.77
1976 2072 2.957006 AGTACATCTGGGACGACATACC 59.043 50.000 0.00 0.00 0.00 2.73
2040 2136 1.680249 GGAGAACCCTTGGCTGATGAC 60.680 57.143 0.00 0.00 0.00 3.06
2042 2138 1.002134 AACCCTTGGCTGATGACGG 60.002 57.895 0.00 0.00 0.00 4.79
2231 2327 3.582208 AGTGCTATTTTTGCCATGGGAAA 59.418 39.130 25.85 25.85 33.75 3.13
2293 2390 5.016173 TGCCTTCAACTTTGCAACCTATAT 58.984 37.500 0.00 0.00 0.00 0.86
2362 2460 8.718102 TCTCTTCATACATGCCTTTAAACTAC 57.282 34.615 0.00 0.00 0.00 2.73
2434 2532 3.239449 TCATAGTAAGCGTGATGGGGAT 58.761 45.455 0.00 0.00 0.00 3.85
2524 2622 4.202482 TGGTTATCCCAGGAAAAACTTCGA 60.202 41.667 12.45 0.00 38.72 3.71
2617 2715 2.441750 TGTTGGATTATCAGGGGCCTAC 59.558 50.000 0.84 0.00 0.00 3.18
2662 2760 4.213059 AGTGCAAAACAAAAATATTGGCCG 59.787 37.500 0.00 0.00 0.00 6.13
2770 2880 3.019564 CCAGGAAGAGCATAACCAAAGG 58.980 50.000 0.00 0.00 0.00 3.11
2771 2881 3.308402 CCAGGAAGAGCATAACCAAAGGA 60.308 47.826 0.00 0.00 0.00 3.36
2783 2893 1.145738 ACCAAAGGACTCATGCCTTGT 59.854 47.619 4.11 0.00 44.72 3.16
2796 2906 2.582052 TGCCTTGTCTCAAAATTCCGT 58.418 42.857 0.00 0.00 0.00 4.69
2912 3022 4.498241 GAAGCCATTTCATCAACCCTTTC 58.502 43.478 0.00 0.00 35.78 2.62
2974 3084 2.092049 TCTGCCTCTGTCTACCGGAATA 60.092 50.000 9.46 0.00 0.00 1.75
3145 3255 2.437281 GGCATCTCTTCCATCTTCCTCA 59.563 50.000 0.00 0.00 0.00 3.86
3181 3291 0.169672 CTTTGAAGCCTCATGCACCG 59.830 55.000 0.00 0.00 44.83 4.94
3259 3369 2.126417 CTGCTGCACCACTGTCAAGC 62.126 60.000 0.00 0.00 32.83 4.01
3321 3431 1.811266 CCACCGATTCGTCTGCTGG 60.811 63.158 5.20 0.00 0.00 4.85
3367 3477 0.928922 CGAGCACATCAGATGTCAGC 59.071 55.000 13.53 14.47 42.70 4.26
3389 3499 4.463879 CAGCTCCACCTCCGCCAG 62.464 72.222 0.00 0.00 0.00 4.85
3429 3539 3.310652 GGAGACACCTGCCCCTAC 58.689 66.667 0.00 0.00 35.41 3.18
3460 3570 0.178992 TGCCCAAACCTCCTGAAGTG 60.179 55.000 0.00 0.00 0.00 3.16
3478 3588 3.118531 AGTGGAGATGGCTGACCTAATT 58.881 45.455 0.00 0.00 36.63 1.40
3644 3754 2.103941 GGACCAGAGGAGGCTAGAAATG 59.896 54.545 0.00 0.00 0.00 2.32
3691 3801 1.576356 CTAGCAAGAGCCGTTGGATC 58.424 55.000 0.00 0.00 43.56 3.36
3740 3850 3.319031 TCCTGGACTCTGCATCTGATA 57.681 47.619 0.00 0.00 0.00 2.15
3741 3851 3.646534 TCCTGGACTCTGCATCTGATAA 58.353 45.455 0.00 0.00 0.00 1.75
3845 3955 4.333649 AGCAGTTTGATGACATGTATTCCG 59.666 41.667 0.00 0.00 0.00 4.30
3901 4011 4.065088 TGTATTATGATCGCTCAAAGGCC 58.935 43.478 0.00 0.00 34.37 5.19
3940 4059 1.355720 AGTAAAGAGCTGGCACCCATT 59.644 47.619 0.00 0.00 30.82 3.16
3961 4080 1.265095 GTCCATGCAAGATGTATGCCG 59.735 52.381 0.00 0.00 43.16 5.69
3973 4092 3.576078 TGTATGCCGGGAATCTCAAAT 57.424 42.857 0.00 0.00 0.00 2.32
3999 4118 3.327757 GGCATGGAGGTGGATTAGTATGA 59.672 47.826 0.00 0.00 0.00 2.15
4068 4188 4.665451 TGACATTGAGGTGGATTGTCAAT 58.335 39.130 0.00 0.00 42.53 2.57
4103 4223 1.284198 AGCAGAGCCTCAAATGATGGT 59.716 47.619 0.00 0.00 0.00 3.55
4104 4224 1.404391 GCAGAGCCTCAAATGATGGTG 59.596 52.381 0.00 0.00 0.00 4.17
4105 4225 2.022195 CAGAGCCTCAAATGATGGTGG 58.978 52.381 0.00 0.00 0.00 4.61
4106 4226 0.743097 GAGCCTCAAATGATGGTGGC 59.257 55.000 3.83 3.83 44.13 5.01
4107 4227 0.040058 AGCCTCAAATGATGGTGGCA 59.960 50.000 12.29 0.00 45.30 4.92
4108 4228 1.117150 GCCTCAAATGATGGTGGCAT 58.883 50.000 6.55 0.00 43.64 4.40
4111 4231 2.380941 CTCAAATGATGGTGGCATGGA 58.619 47.619 0.00 0.00 0.00 3.41
4112 4232 2.361119 CTCAAATGATGGTGGCATGGAG 59.639 50.000 0.00 0.00 0.00 3.86
4113 4233 1.411246 CAAATGATGGTGGCATGGAGG 59.589 52.381 0.00 0.00 0.00 4.30
4114 4234 0.757935 AATGATGGTGGCATGGAGGC 60.758 55.000 0.00 0.00 44.50 4.70
4149 4269 2.086426 GTGCACAGCGACGATCGAA 61.086 57.895 24.34 0.00 43.74 3.71
4225 4345 5.491070 TCTCCACCATTTGTCATGTAGAAG 58.509 41.667 0.00 0.00 0.00 2.85
4268 4388 7.839200 AGAATAAACATACCCAGCCAATTAGTT 59.161 33.333 0.00 0.00 0.00 2.24
4285 4406 2.836667 AGTTGGCCATTTTGATCCCAT 58.163 42.857 6.09 0.00 0.00 4.00
4303 4424 2.819608 CCATCGAGTCAACATTTTGGGT 59.180 45.455 0.00 0.00 33.06 4.51
4305 4426 2.226330 TCGAGTCAACATTTTGGGTGG 58.774 47.619 0.00 0.00 33.06 4.61
4355 4476 3.350219 TTCTGTTGTTCATAGGAGGCC 57.650 47.619 0.00 0.00 0.00 5.19
4356 4477 2.265367 TCTGTTGTTCATAGGAGGCCA 58.735 47.619 5.01 0.00 0.00 5.36
4357 4478 2.846206 TCTGTTGTTCATAGGAGGCCAT 59.154 45.455 5.01 0.00 0.00 4.40
4358 4479 2.947652 CTGTTGTTCATAGGAGGCCATG 59.052 50.000 5.01 0.00 0.00 3.66
4415 4536 1.153353 CTTAACCAGGCGAGCGAAAA 58.847 50.000 0.00 0.00 0.00 2.29
4502 4624 6.098017 AGATGTAGTAGCGGTTTTTGTACTC 58.902 40.000 0.00 0.00 0.00 2.59
4552 4674 5.144832 TCATGGATGGATGCAGATTTGAAT 58.855 37.500 0.00 0.00 0.00 2.57
4553 4675 5.243060 TCATGGATGGATGCAGATTTGAATC 59.757 40.000 0.00 0.00 38.48 2.52
4597 4720 6.533723 TGCTTTGTATCTACCTGTGTTATTCG 59.466 38.462 0.00 0.00 0.00 3.34
4606 4729 2.083774 CTGTGTTATTCGGCCATGTGT 58.916 47.619 2.24 0.00 0.00 3.72
4607 4730 2.487762 CTGTGTTATTCGGCCATGTGTT 59.512 45.455 2.24 0.00 0.00 3.32
4618 4741 4.814234 TCGGCCATGTGTTATTCTGTTATC 59.186 41.667 2.24 0.00 0.00 1.75
4620 4743 5.277490 CGGCCATGTGTTATTCTGTTATCTG 60.277 44.000 2.24 0.00 0.00 2.90
4621 4744 5.506317 GGCCATGTGTTATTCTGTTATCTGC 60.506 44.000 0.00 0.00 0.00 4.26
4622 4745 5.066375 GCCATGTGTTATTCTGTTATCTGCA 59.934 40.000 0.00 0.00 0.00 4.41
4645 4775 4.997395 ACACAGTTGAATGTACACAGGATC 59.003 41.667 0.00 0.00 0.00 3.36
4679 4809 3.374220 TGTTCTCTTTTGCAAGGCATG 57.626 42.857 0.00 0.00 38.76 4.06
4680 4810 2.694628 TGTTCTCTTTTGCAAGGCATGT 59.305 40.909 0.00 0.00 38.76 3.21
4688 4818 1.126488 TGCAAGGCATGTTTTTCCCA 58.874 45.000 0.00 0.00 31.71 4.37
4715 4845 9.995003 TTATATTTTGTTTGATTTGAAGGCAGT 57.005 25.926 0.00 0.00 0.00 4.40
4719 4849 3.870419 TGTTTGATTTGAAGGCAGTTTGC 59.130 39.130 0.00 0.00 44.08 3.68
4720 4850 4.122046 GTTTGATTTGAAGGCAGTTTGCT 58.878 39.130 0.67 0.00 44.28 3.91
4722 4852 3.719924 TGATTTGAAGGCAGTTTGCTTG 58.280 40.909 0.67 0.00 44.28 4.01
4724 4854 1.774110 TTGAAGGCAGTTTGCTTGGA 58.226 45.000 0.67 0.00 44.28 3.53
4725 4855 1.999648 TGAAGGCAGTTTGCTTGGAT 58.000 45.000 0.67 0.00 44.28 3.41
4727 4857 2.297033 TGAAGGCAGTTTGCTTGGATTC 59.703 45.455 0.67 0.44 44.28 2.52
4729 4859 1.891150 AGGCAGTTTGCTTGGATTCTG 59.109 47.619 0.67 0.00 44.28 3.02
4730 4860 1.615392 GGCAGTTTGCTTGGATTCTGT 59.385 47.619 0.67 0.00 44.28 3.41
4731 4861 2.036346 GGCAGTTTGCTTGGATTCTGTT 59.964 45.455 0.67 0.00 44.28 3.16
4732 4862 3.054878 GCAGTTTGCTTGGATTCTGTTG 58.945 45.455 0.00 0.00 40.96 3.33
4734 4864 4.261572 GCAGTTTGCTTGGATTCTGTTGTA 60.262 41.667 0.00 0.00 40.96 2.41
4735 4865 5.735922 GCAGTTTGCTTGGATTCTGTTGTAA 60.736 40.000 0.00 0.00 40.96 2.41
4736 4866 6.449698 CAGTTTGCTTGGATTCTGTTGTAAT 58.550 36.000 0.00 0.00 0.00 1.89
4738 4868 6.040842 AGTTTGCTTGGATTCTGTTGTAATGT 59.959 34.615 0.00 0.00 0.00 2.71
4739 4869 7.230510 AGTTTGCTTGGATTCTGTTGTAATGTA 59.769 33.333 0.00 0.00 0.00 2.29
4740 4870 7.701539 TTGCTTGGATTCTGTTGTAATGTAT 57.298 32.000 0.00 0.00 0.00 2.29
4757 4901 8.356657 TGTAATGTATTTTCCTTTTGTGTGGAG 58.643 33.333 0.00 0.00 33.46 3.86
4798 4943 3.199946 TCCCTTTCTGGACATGTATCACC 59.800 47.826 0.00 0.00 38.35 4.02
4816 4964 3.010138 TCACCCTATTATTGCCCATAGCC 59.990 47.826 0.00 0.00 42.71 3.93
4820 4968 2.496899 ATTATTGCCCATAGCCGAGG 57.503 50.000 0.00 0.00 42.71 4.63
4865 5013 6.354130 TCCTAAAGGAATTTTGGAGGATACG 58.646 40.000 0.00 0.00 42.18 3.06
4866 5014 6.157297 TCCTAAAGGAATTTTGGAGGATACGA 59.843 38.462 0.00 0.00 42.18 3.43
4867 5015 6.260271 CCTAAAGGAATTTTGGAGGATACGAC 59.740 42.308 0.00 0.00 38.90 4.34
4868 5016 4.837093 AGGAATTTTGGAGGATACGACA 57.163 40.909 0.00 0.00 46.39 4.35
4869 5017 5.373812 AGGAATTTTGGAGGATACGACAT 57.626 39.130 0.00 0.00 46.39 3.06
4870 5018 5.755849 AGGAATTTTGGAGGATACGACATT 58.244 37.500 0.00 0.00 46.39 2.71
4871 5019 6.187682 AGGAATTTTGGAGGATACGACATTT 58.812 36.000 0.00 0.00 46.39 2.32
4872 5020 6.663523 AGGAATTTTGGAGGATACGACATTTT 59.336 34.615 0.00 0.00 46.39 1.82
4873 5021 6.972901 GGAATTTTGGAGGATACGACATTTTC 59.027 38.462 0.00 0.00 46.39 2.29
4874 5022 5.890424 TTTTGGAGGATACGACATTTTCC 57.110 39.130 0.00 0.00 46.39 3.13
4875 5023 4.837093 TTGGAGGATACGACATTTTCCT 57.163 40.909 0.00 0.00 41.29 3.36
4876 5024 5.943349 TTGGAGGATACGACATTTTCCTA 57.057 39.130 0.00 0.00 38.71 2.94
4877 5025 6.494666 TTGGAGGATACGACATTTTCCTAT 57.505 37.500 0.00 0.00 38.71 2.57
4878 5026 5.853936 TGGAGGATACGACATTTTCCTATG 58.146 41.667 0.00 0.00 38.71 2.23
4879 5027 5.365605 TGGAGGATACGACATTTTCCTATGT 59.634 40.000 0.00 0.00 38.71 2.29
4880 5028 5.696724 GGAGGATACGACATTTTCCTATGTG 59.303 44.000 0.00 0.00 38.71 3.21
4881 5029 6.235231 AGGATACGACATTTTCCTATGTGT 57.765 37.500 0.00 0.00 38.80 3.72
4882 5030 6.049149 AGGATACGACATTTTCCTATGTGTG 58.951 40.000 0.00 0.00 38.80 3.82
4883 5031 5.236478 GGATACGACATTTTCCTATGTGTGG 59.764 44.000 0.00 0.00 38.80 4.17
4884 5032 2.747446 ACGACATTTTCCTATGTGTGGC 59.253 45.455 0.00 0.00 38.80 5.01
4885 5033 3.009723 CGACATTTTCCTATGTGTGGCT 58.990 45.455 0.00 0.00 38.80 4.75
4886 5034 3.440173 CGACATTTTCCTATGTGTGGCTT 59.560 43.478 0.00 0.00 38.80 4.35
4887 5035 4.672542 CGACATTTTCCTATGTGTGGCTTG 60.673 45.833 0.00 0.00 38.80 4.01
4888 5036 4.151883 ACATTTTCCTATGTGTGGCTTGT 58.848 39.130 0.00 0.00 37.36 3.16
4889 5037 4.588528 ACATTTTCCTATGTGTGGCTTGTT 59.411 37.500 0.00 0.00 37.36 2.83
4890 5038 5.070313 ACATTTTCCTATGTGTGGCTTGTTT 59.930 36.000 0.00 0.00 37.36 2.83
4891 5039 4.582701 TTTCCTATGTGTGGCTTGTTTG 57.417 40.909 0.00 0.00 0.00 2.93
4892 5040 1.885887 TCCTATGTGTGGCTTGTTTGC 59.114 47.619 0.00 0.00 0.00 3.68
4893 5041 1.612950 CCTATGTGTGGCTTGTTTGCA 59.387 47.619 0.00 0.00 34.04 4.08
4894 5042 2.352030 CCTATGTGTGGCTTGTTTGCAG 60.352 50.000 0.00 0.00 34.04 4.41
4895 5043 0.390124 ATGTGTGGCTTGTTTGCAGG 59.610 50.000 0.00 0.00 34.04 4.85
4896 5044 0.682532 TGTGTGGCTTGTTTGCAGGA 60.683 50.000 0.00 0.00 34.04 3.86
4897 5045 0.675633 GTGTGGCTTGTTTGCAGGAT 59.324 50.000 0.00 0.00 34.04 3.24
4898 5046 1.069049 GTGTGGCTTGTTTGCAGGATT 59.931 47.619 0.00 0.00 34.04 3.01
4899 5047 1.761784 TGTGGCTTGTTTGCAGGATTT 59.238 42.857 0.00 0.00 34.04 2.17
4900 5048 2.170187 TGTGGCTTGTTTGCAGGATTTT 59.830 40.909 0.00 0.00 34.04 1.82
4901 5049 3.205338 GTGGCTTGTTTGCAGGATTTTT 58.795 40.909 0.00 0.00 34.04 1.94
4924 5072 8.893563 TTTTTCCCATAGGATTCATTTGTAGT 57.106 30.769 0.00 0.00 43.54 2.73
4925 5073 9.983024 TTTTTCCCATAGGATTCATTTGTAGTA 57.017 29.630 0.00 0.00 43.54 1.82
4926 5074 9.627123 TTTTCCCATAGGATTCATTTGTAGTAG 57.373 33.333 0.00 0.00 43.54 2.57
4927 5075 7.931015 TCCCATAGGATTCATTTGTAGTAGT 57.069 36.000 0.00 0.00 37.19 2.73
4928 5076 8.331931 TCCCATAGGATTCATTTGTAGTAGTT 57.668 34.615 0.00 0.00 37.19 2.24
4929 5077 8.778059 TCCCATAGGATTCATTTGTAGTAGTTT 58.222 33.333 0.00 0.00 37.19 2.66
4930 5078 9.408648 CCCATAGGATTCATTTGTAGTAGTTTT 57.591 33.333 0.00 0.00 33.47 2.43
4936 5084 9.626045 GGATTCATTTGTAGTAGTTTTCAAAGG 57.374 33.333 0.00 0.00 34.17 3.11
4957 5105 4.632327 GAAAATTTCCATCCACCCCAAA 57.368 40.909 0.00 0.00 0.00 3.28
4958 5106 4.979335 GAAAATTTCCATCCACCCCAAAA 58.021 39.130 0.00 0.00 0.00 2.44
4959 5107 4.639078 AAATTTCCATCCACCCCAAAAG 57.361 40.909 0.00 0.00 0.00 2.27
4960 5108 3.558608 ATTTCCATCCACCCCAAAAGA 57.441 42.857 0.00 0.00 0.00 2.52
4961 5109 3.336509 TTTCCATCCACCCCAAAAGAA 57.663 42.857 0.00 0.00 0.00 2.52
4962 5110 3.558608 TTCCATCCACCCCAAAAGAAT 57.441 42.857 0.00 0.00 0.00 2.40
4963 5111 3.100207 TCCATCCACCCCAAAAGAATC 57.900 47.619 0.00 0.00 0.00 2.52
4964 5112 2.110578 CCATCCACCCCAAAAGAATCC 58.889 52.381 0.00 0.00 0.00 3.01
4965 5113 2.292455 CCATCCACCCCAAAAGAATCCT 60.292 50.000 0.00 0.00 0.00 3.24
4966 5114 3.052944 CCATCCACCCCAAAAGAATCCTA 60.053 47.826 0.00 0.00 0.00 2.94
4967 5115 3.732048 TCCACCCCAAAAGAATCCTAC 57.268 47.619 0.00 0.00 0.00 3.18
4968 5116 2.026636 TCCACCCCAAAAGAATCCTACG 60.027 50.000 0.00 0.00 0.00 3.51
4969 5117 2.290705 CCACCCCAAAAGAATCCTACGT 60.291 50.000 0.00 0.00 0.00 3.57
4970 5118 3.418047 CACCCCAAAAGAATCCTACGTT 58.582 45.455 0.00 0.00 0.00 3.99
4971 5119 3.824443 CACCCCAAAAGAATCCTACGTTT 59.176 43.478 0.00 0.00 0.00 3.60
4972 5120 4.279922 CACCCCAAAAGAATCCTACGTTTT 59.720 41.667 0.00 0.00 0.00 2.43
4973 5121 4.897076 ACCCCAAAAGAATCCTACGTTTTT 59.103 37.500 0.00 0.00 0.00 1.94
4974 5122 5.010314 ACCCCAAAAGAATCCTACGTTTTTC 59.990 40.000 0.00 0.00 0.00 2.29
4975 5123 5.466819 CCCAAAAGAATCCTACGTTTTTCC 58.533 41.667 0.00 0.00 0.00 3.13
4976 5124 5.243060 CCCAAAAGAATCCTACGTTTTTCCT 59.757 40.000 0.00 0.00 0.00 3.36
4977 5125 6.149633 CCAAAAGAATCCTACGTTTTTCCTG 58.850 40.000 0.00 0.00 0.00 3.86
4978 5126 6.238925 CCAAAAGAATCCTACGTTTTTCCTGT 60.239 38.462 0.00 0.00 0.00 4.00
4979 5127 5.941948 AAGAATCCTACGTTTTTCCTGTG 57.058 39.130 0.00 0.00 0.00 3.66
4980 5128 3.751698 AGAATCCTACGTTTTTCCTGTGC 59.248 43.478 0.00 0.00 0.00 4.57
4981 5129 2.623878 TCCTACGTTTTTCCTGTGCA 57.376 45.000 0.00 0.00 0.00 4.57
4982 5130 2.215196 TCCTACGTTTTTCCTGTGCAC 58.785 47.619 10.75 10.75 0.00 4.57
4983 5131 1.944024 CCTACGTTTTTCCTGTGCACA 59.056 47.619 20.37 20.37 0.00 4.57
4984 5132 2.356382 CCTACGTTTTTCCTGTGCACAA 59.644 45.455 21.98 3.65 0.00 3.33
4985 5133 3.004315 CCTACGTTTTTCCTGTGCACAAT 59.996 43.478 21.98 0.79 0.00 2.71
4986 5134 4.214545 CCTACGTTTTTCCTGTGCACAATA 59.785 41.667 21.98 8.91 0.00 1.90
4987 5135 3.959943 ACGTTTTTCCTGTGCACAATAC 58.040 40.909 21.98 10.05 0.00 1.89
4988 5136 3.378742 ACGTTTTTCCTGTGCACAATACA 59.621 39.130 21.98 2.54 0.00 2.29
4989 5137 4.142359 ACGTTTTTCCTGTGCACAATACAA 60.142 37.500 21.98 8.90 0.00 2.41
4990 5138 4.800993 CGTTTTTCCTGTGCACAATACAAA 59.199 37.500 21.98 14.19 0.00 2.83
4991 5139 5.276161 CGTTTTTCCTGTGCACAATACAAAC 60.276 40.000 21.98 22.33 0.00 2.93
4992 5140 4.991153 TTTCCTGTGCACAATACAAACA 57.009 36.364 21.98 0.00 0.00 2.83
4993 5141 4.991153 TTCCTGTGCACAATACAAACAA 57.009 36.364 21.98 2.07 0.00 2.83
4994 5142 4.300189 TCCTGTGCACAATACAAACAAC 57.700 40.909 21.98 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 108 1.341852 TGTTTCCTCGTCCATTCGTCA 59.658 47.619 0.00 0.00 0.00 4.35
133 150 2.549563 CCAGTGTCTGCAACATCAGAGT 60.550 50.000 5.26 0.00 43.10 3.24
380 468 0.250467 CCCCACTCTGGACACAACAG 60.250 60.000 0.00 0.00 40.96 3.16
417 505 6.769822 AGATATGCTAGACAAAGGAACCAATG 59.230 38.462 0.00 0.00 0.00 2.82
441 532 2.094894 CGGCAAGAGTAATCAACAGCAG 59.905 50.000 0.00 0.00 0.00 4.24
479 570 2.229784 CAGAACAAACAGAGGGCAATCC 59.770 50.000 0.00 0.00 0.00 3.01
567 658 7.719633 GGAAATGGTATCATAAGGAAACAGCTA 59.280 37.037 0.00 0.00 32.44 3.32
609 700 3.277715 TCACAGATTGACAGCACAACAA 58.722 40.909 0.00 0.00 32.50 2.83
612 703 4.898320 ACTATCACAGATTGACAGCACAA 58.102 39.130 0.00 0.00 36.92 3.33
613 704 4.541973 ACTATCACAGATTGACAGCACA 57.458 40.909 0.00 0.00 36.92 4.57
614 705 4.692625 ACAACTATCACAGATTGACAGCAC 59.307 41.667 0.00 0.00 36.92 4.40
617 708 8.939929 ACATTAACAACTATCACAGATTGACAG 58.060 33.333 0.00 0.00 36.92 3.51
672 763 5.189736 ACAGGCAACCATCAAGTAAGATAGA 59.810 40.000 0.00 0.00 37.17 1.98
681 772 2.559668 ACAATCACAGGCAACCATCAAG 59.440 45.455 0.00 0.00 37.17 3.02
688 779 2.488153 GGAACCTACAATCACAGGCAAC 59.512 50.000 0.00 0.00 35.14 4.17
816 907 7.120726 GCTATGTCAAGTACAAAATGTAGGGTT 59.879 37.037 0.00 0.00 42.70 4.11
829 920 6.201806 GTCATGAAGATGGCTATGTCAAGTAC 59.798 42.308 0.00 0.00 30.89 2.73
841 932 6.942532 TTATTAGGTTGTCATGAAGATGGC 57.057 37.500 0.00 0.00 34.50 4.40
885 976 4.051237 TGTCAAAGTCAGAGTCATCAACG 58.949 43.478 0.00 0.00 0.00 4.10
887 978 5.012458 AGGATGTCAAAGTCAGAGTCATCAA 59.988 40.000 0.00 0.00 34.01 2.57
891 982 6.211384 TCATTAGGATGTCAAAGTCAGAGTCA 59.789 38.462 0.00 0.00 34.77 3.41
892 983 6.533367 GTCATTAGGATGTCAAAGTCAGAGTC 59.467 42.308 0.00 0.00 34.77 3.36
893 984 6.402222 GTCATTAGGATGTCAAAGTCAGAGT 58.598 40.000 0.00 0.00 34.77 3.24
894 985 5.518128 CGTCATTAGGATGTCAAAGTCAGAG 59.482 44.000 0.00 0.00 34.77 3.35
1261 1352 3.405831 CTGTTTGAATCTGGCTCACTGA 58.594 45.455 0.00 0.00 0.00 3.41
1272 1363 7.141363 ACAAGAAATGTACAGCTGTTTGAATC 58.859 34.615 27.06 17.46 41.63 2.52
1311 1402 1.237533 CAGCTACAACACCATGCACA 58.762 50.000 0.00 0.00 0.00 4.57
1313 1404 0.250858 AGCAGCTACAACACCATGCA 60.251 50.000 0.00 0.00 36.15 3.96
1372 1464 1.895131 TCCAAATTGAAGGGAAGCAGC 59.105 47.619 0.00 0.00 0.00 5.25
1560 1656 4.740902 AGAAACAAAGGAGGGCAAGTAAT 58.259 39.130 0.00 0.00 0.00 1.89
1646 1742 6.013379 TCATGAATGGGGTTGCTAAAAGTAA 58.987 36.000 0.00 0.00 0.00 2.24
1656 1752 2.302445 TGGCTTTTCATGAATGGGGTTG 59.698 45.455 9.40 0.00 0.00 3.77
1688 1784 2.124151 CAATTCCAGGGCCCCTCG 60.124 66.667 21.43 7.43 0.00 4.63
1780 1876 6.552008 TGTCAAATATTTCTTCAGGGGAACT 58.448 36.000 0.00 0.00 0.00 3.01
1827 1923 1.288350 CAGAAGAGCGAGCATCCTTG 58.712 55.000 0.00 0.00 0.00 3.61
1976 2072 5.287674 TCCATAATCTGCTCCTTGAGAAG 57.712 43.478 0.00 0.00 36.69 2.85
2040 2136 5.352569 CCTATGGAAGCTTCTAATATTGCCG 59.647 44.000 25.05 11.02 0.00 5.69
2042 2138 5.124617 GCCCTATGGAAGCTTCTAATATTGC 59.875 44.000 25.05 20.11 0.00 3.56
2208 2304 3.172339 TCCCATGGCAAAAATAGCACTT 58.828 40.909 6.09 0.00 0.00 3.16
2302 2399 4.881920 ACATGGCAAATCACAAGGTTTAC 58.118 39.130 0.00 0.00 0.00 2.01
2387 2485 4.232188 ACTCTGCATGATCCTGAACAAT 57.768 40.909 0.00 0.00 0.00 2.71
2428 2526 3.398967 CCCTATCAATTCTTGGATCCCCA 59.601 47.826 9.90 0.00 41.64 4.96
2434 2532 5.893255 CCACATTTCCCTATCAATTCTTGGA 59.107 40.000 0.00 0.00 0.00 3.53
2520 2618 4.713946 GCCCAATGTCTGGTCGAA 57.286 55.556 0.00 0.00 44.76 3.71
2524 2622 2.270874 GATCCCGCCCAATGTCTGGT 62.271 60.000 0.00 0.00 44.76 4.00
2617 2715 1.448540 AAGGCTTGATCGTCCAGCG 60.449 57.895 0.00 0.00 43.01 5.18
2662 2760 2.762043 AGAGGAGGCGAGGAAGGC 60.762 66.667 0.00 0.00 0.00 4.35
2674 2772 3.965026 CTCACGGGCCTGGAGAGGA 62.965 68.421 22.28 9.36 42.93 3.71
2686 2784 1.831652 AACTTGGGGAGCTCTCACGG 61.832 60.000 17.22 6.65 32.67 4.94
2770 2880 5.382618 AATTTTGAGACAAGGCATGAGTC 57.617 39.130 0.00 0.00 0.00 3.36
2771 2881 4.219288 GGAATTTTGAGACAAGGCATGAGT 59.781 41.667 0.00 0.00 0.00 3.41
2783 2893 5.412594 CCTGAGAATTCACGGAATTTTGAGA 59.587 40.000 12.73 0.00 41.56 3.27
2796 2906 0.909610 AGGCCGACCCTGAGAATTCA 60.910 55.000 8.44 0.00 44.28 2.57
2852 2962 1.140312 ACAGGAGGGTGCTTTTGAGA 58.860 50.000 0.00 0.00 0.00 3.27
2912 3022 4.855388 CAGCGATGAAGAATTTTCTTGTGG 59.145 41.667 10.16 2.53 46.84 4.17
2974 3084 0.903942 CCTCTTCAGGCTGCTCTTCT 59.096 55.000 10.34 0.00 30.98 2.85
3145 3255 3.070576 GGGGCATTTTCGCTGGCT 61.071 61.111 0.00 0.00 39.05 4.75
3181 3291 1.545706 AAGGTGGGCGGAGAGAGTTC 61.546 60.000 0.00 0.00 0.00 3.01
3259 3369 2.224378 TGCAACCAGAGAACTGAGAAGG 60.224 50.000 0.00 0.00 46.03 3.46
3321 3431 0.537828 TTTACCGGGGTTCCTTGCAC 60.538 55.000 6.32 0.00 0.00 4.57
3328 3438 2.362736 GGACTTGATTTACCGGGGTTC 58.637 52.381 6.32 0.00 0.00 3.62
3331 3441 0.538118 TCGGACTTGATTTACCGGGG 59.462 55.000 6.32 0.00 44.57 5.73
3389 3499 1.569479 GCAACTGAAGGCTGGACGAC 61.569 60.000 0.00 0.00 0.00 4.34
3460 3570 2.856222 CCAATTAGGTCAGCCATCTCC 58.144 52.381 0.00 0.00 37.19 3.71
3646 3756 1.091771 ATCTTTCAGGTGCGATGCCG 61.092 55.000 0.00 0.00 39.16 5.69
3691 3801 1.278238 GCGGTTCAGGTAATCTGTCG 58.722 55.000 0.00 0.00 43.76 4.35
3740 3850 1.073199 CTGCGGTTCCCAGGTCTTT 59.927 57.895 0.00 0.00 0.00 2.52
3741 3851 1.831652 CTCTGCGGTTCCCAGGTCTT 61.832 60.000 0.00 0.00 0.00 3.01
3845 3955 1.068885 CATCCACTCGCTCCTATCGAC 60.069 57.143 0.00 0.00 32.08 4.20
3901 4011 3.965539 CTGGGAGCTGCCACCTTCG 62.966 68.421 24.87 9.65 38.95 3.79
3940 4059 2.300433 GGCATACATCTTGCATGGACA 58.700 47.619 0.00 0.00 41.95 4.02
3961 4080 3.006537 CCATGCCATCATTTGAGATTCCC 59.993 47.826 0.00 0.00 0.00 3.97
3973 4092 0.928505 AATCCACCTCCATGCCATCA 59.071 50.000 0.00 0.00 0.00 3.07
3999 4118 5.861727 TCTGCTGCTATATGACATGACAAT 58.138 37.500 0.00 0.00 0.00 2.71
4103 4223 1.380246 GGAATGTGCCTCCATGCCA 60.380 57.895 1.22 0.00 39.96 4.92
4104 4224 2.484062 CGGAATGTGCCTCCATGCC 61.484 63.158 0.00 0.00 37.20 4.40
4105 4225 1.750399 ACGGAATGTGCCTCCATGC 60.750 57.895 0.00 0.00 32.77 4.06
4106 4226 2.100846 CACGGAATGTGCCTCCATG 58.899 57.895 0.00 0.00 42.70 3.66
4107 4227 4.643795 CACGGAATGTGCCTCCAT 57.356 55.556 0.00 0.00 42.70 3.41
4146 4266 2.878406 CCCCACCTGCAGTATATTTTCG 59.122 50.000 13.81 0.00 0.00 3.46
4149 4269 2.849943 TCACCCCACCTGCAGTATATTT 59.150 45.455 13.81 0.00 0.00 1.40
4268 4388 1.064091 TCGATGGGATCAAAATGGCCA 60.064 47.619 8.56 8.56 0.00 5.36
4285 4406 2.226330 CCACCCAAAATGTTGACTCGA 58.774 47.619 0.00 0.00 36.83 4.04
4303 4424 1.923395 GTCATCTGACCCCACCCCA 60.923 63.158 0.00 0.00 39.07 4.96
4305 4426 1.507140 TATGTCATCTGACCCCACCC 58.493 55.000 7.81 0.00 44.15 4.61
4432 4553 3.299340 AAACAGCAGTAACTCGACGAT 57.701 42.857 0.00 0.00 0.00 3.73
4502 4624 7.973388 TGAAGTTCTATTGTCAGTTTGGTTTTG 59.027 33.333 4.17 0.00 0.00 2.44
4552 4674 3.466836 CAAGAGCTAACAACACTGGTGA 58.533 45.455 0.00 0.00 0.00 4.02
4553 4675 2.031682 GCAAGAGCTAACAACACTGGTG 60.032 50.000 0.00 0.00 37.91 4.17
4577 4699 4.202182 GGCCGAATAACACAGGTAGATACA 60.202 45.833 0.00 0.00 0.00 2.29
4578 4700 4.202182 TGGCCGAATAACACAGGTAGATAC 60.202 45.833 0.00 0.00 0.00 2.24
4580 4702 2.769663 TGGCCGAATAACACAGGTAGAT 59.230 45.455 0.00 0.00 0.00 1.98
4584 4707 1.004277 ACATGGCCGAATAACACAGGT 59.996 47.619 0.00 0.00 0.00 4.00
4587 4710 2.192664 ACACATGGCCGAATAACACA 57.807 45.000 0.00 0.00 0.00 3.72
4588 4711 4.893424 ATAACACATGGCCGAATAACAC 57.107 40.909 0.00 0.00 0.00 3.32
4597 4720 5.506317 GCAGATAACAGAATAACACATGGCC 60.506 44.000 0.00 0.00 0.00 5.36
4606 4729 6.934083 TCAACTGTGTGCAGATAACAGAATAA 59.066 34.615 19.89 5.41 45.28 1.40
4607 4730 6.463360 TCAACTGTGTGCAGATAACAGAATA 58.537 36.000 19.89 6.66 45.28 1.75
4620 4743 3.303990 CCTGTGTACATTCAACTGTGTGC 60.304 47.826 0.00 0.00 0.00 4.57
4621 4744 4.126437 TCCTGTGTACATTCAACTGTGTG 58.874 43.478 0.00 0.00 0.00 3.82
4622 4745 4.415881 TCCTGTGTACATTCAACTGTGT 57.584 40.909 0.00 0.00 0.00 3.72
4645 4775 2.301296 AGAGAACATGTCCAGACACAGG 59.699 50.000 1.88 0.00 45.05 4.00
4657 4787 3.374220 TGCCTTGCAAAAGAGAACATG 57.626 42.857 0.00 0.00 34.76 3.21
4704 4834 2.106566 TCCAAGCAAACTGCCTTCAAA 58.893 42.857 0.00 0.00 46.52 2.69
4705 4835 1.774110 TCCAAGCAAACTGCCTTCAA 58.226 45.000 0.00 0.00 46.52 2.69
4706 4836 1.999648 ATCCAAGCAAACTGCCTTCA 58.000 45.000 0.00 0.00 46.52 3.02
4707 4837 2.560105 AGAATCCAAGCAAACTGCCTTC 59.440 45.455 0.00 0.00 46.52 3.46
4709 4839 1.891150 CAGAATCCAAGCAAACTGCCT 59.109 47.619 0.00 0.00 46.52 4.75
4710 4840 1.615392 ACAGAATCCAAGCAAACTGCC 59.385 47.619 0.00 0.00 46.52 4.85
4711 4841 3.054878 CAACAGAATCCAAGCAAACTGC 58.945 45.455 0.00 0.00 45.46 4.40
4712 4842 4.311816 ACAACAGAATCCAAGCAAACTG 57.688 40.909 0.00 0.00 0.00 3.16
4713 4843 6.040842 ACATTACAACAGAATCCAAGCAAACT 59.959 34.615 0.00 0.00 0.00 2.66
4715 4845 6.403866 ACATTACAACAGAATCCAAGCAAA 57.596 33.333 0.00 0.00 0.00 3.68
4719 4849 9.573133 GGAAAATACATTACAACAGAATCCAAG 57.427 33.333 0.00 0.00 0.00 3.61
4720 4850 9.308000 AGGAAAATACATTACAACAGAATCCAA 57.692 29.630 0.00 0.00 0.00 3.53
4727 4857 9.528018 ACACAAAAGGAAAATACATTACAACAG 57.472 29.630 0.00 0.00 0.00 3.16
4729 4859 8.760569 CCACACAAAAGGAAAATACATTACAAC 58.239 33.333 0.00 0.00 0.00 3.32
4730 4860 8.696374 TCCACACAAAAGGAAAATACATTACAA 58.304 29.630 0.00 0.00 0.00 2.41
4731 4861 8.239038 TCCACACAAAAGGAAAATACATTACA 57.761 30.769 0.00 0.00 0.00 2.41
4732 4862 7.812669 CCTCCACACAAAAGGAAAATACATTAC 59.187 37.037 0.00 0.00 32.57 1.89
4734 4864 6.741240 GCCTCCACACAAAAGGAAAATACATT 60.741 38.462 0.00 0.00 32.57 2.71
4735 4865 5.279456 GCCTCCACACAAAAGGAAAATACAT 60.279 40.000 0.00 0.00 32.57 2.29
4736 4866 4.038642 GCCTCCACACAAAAGGAAAATACA 59.961 41.667 0.00 0.00 32.57 2.29
4738 4868 4.219115 TGCCTCCACACAAAAGGAAAATA 58.781 39.130 0.00 0.00 32.57 1.40
4739 4869 3.037549 TGCCTCCACACAAAAGGAAAAT 58.962 40.909 0.00 0.00 32.57 1.82
4740 4870 2.430332 CTGCCTCCACACAAAAGGAAAA 59.570 45.455 0.00 0.00 32.57 2.29
4757 4901 2.533266 GAAATACATTGCACAGCTGCC 58.467 47.619 15.27 5.76 43.51 4.85
4798 4943 3.535561 CTCGGCTATGGGCAATAATAGG 58.464 50.000 2.96 0.00 44.01 2.57
4816 4964 0.323360 TTGAATCAAAGGGGCCCTCG 60.323 55.000 28.97 20.61 30.89 4.63
4855 5003 5.365605 ACATAGGAAAATGTCGTATCCTCCA 59.634 40.000 0.00 0.00 41.33 3.86
4863 5011 2.747446 GCCACACATAGGAAAATGTCGT 59.253 45.455 0.00 0.00 38.01 4.34
4864 5012 3.009723 AGCCACACATAGGAAAATGTCG 58.990 45.455 0.00 0.00 38.01 4.35
4865 5013 4.218417 ACAAGCCACACATAGGAAAATGTC 59.782 41.667 0.00 0.00 38.01 3.06
4866 5014 4.151883 ACAAGCCACACATAGGAAAATGT 58.848 39.130 0.00 0.00 40.75 2.71
4867 5015 4.789012 ACAAGCCACACATAGGAAAATG 57.211 40.909 0.00 0.00 0.00 2.32
4868 5016 5.540911 CAAACAAGCCACACATAGGAAAAT 58.459 37.500 0.00 0.00 0.00 1.82
4869 5017 4.739137 GCAAACAAGCCACACATAGGAAAA 60.739 41.667 0.00 0.00 0.00 2.29
4870 5018 3.243704 GCAAACAAGCCACACATAGGAAA 60.244 43.478 0.00 0.00 0.00 3.13
4871 5019 2.295909 GCAAACAAGCCACACATAGGAA 59.704 45.455 0.00 0.00 0.00 3.36
4872 5020 1.885887 GCAAACAAGCCACACATAGGA 59.114 47.619 0.00 0.00 0.00 2.94
4873 5021 1.612950 TGCAAACAAGCCACACATAGG 59.387 47.619 0.00 0.00 0.00 2.57
4874 5022 2.352030 CCTGCAAACAAGCCACACATAG 60.352 50.000 0.00 0.00 0.00 2.23
4875 5023 1.612950 CCTGCAAACAAGCCACACATA 59.387 47.619 0.00 0.00 0.00 2.29
4876 5024 0.390124 CCTGCAAACAAGCCACACAT 59.610 50.000 0.00 0.00 0.00 3.21
4877 5025 0.682532 TCCTGCAAACAAGCCACACA 60.683 50.000 0.00 0.00 0.00 3.72
4878 5026 0.675633 ATCCTGCAAACAAGCCACAC 59.324 50.000 0.00 0.00 0.00 3.82
4879 5027 1.412079 AATCCTGCAAACAAGCCACA 58.588 45.000 0.00 0.00 0.00 4.17
4880 5028 2.531522 AAATCCTGCAAACAAGCCAC 57.468 45.000 0.00 0.00 0.00 5.01
4881 5029 3.557228 AAAAATCCTGCAAACAAGCCA 57.443 38.095 0.00 0.00 0.00 4.75
4899 5047 8.893563 ACTACAAATGAATCCTATGGGAAAAA 57.106 30.769 0.22 0.00 45.78 1.94
4900 5048 9.627123 CTACTACAAATGAATCCTATGGGAAAA 57.373 33.333 0.22 0.00 45.78 2.29
4901 5049 8.778059 ACTACTACAAATGAATCCTATGGGAAA 58.222 33.333 0.22 0.00 45.78 3.13
4902 5050 8.331931 ACTACTACAAATGAATCCTATGGGAA 57.668 34.615 0.22 0.00 45.78 3.97
4903 5051 7.931015 ACTACTACAAATGAATCCTATGGGA 57.069 36.000 0.00 0.00 46.81 4.37
4904 5052 8.980481 AAACTACTACAAATGAATCCTATGGG 57.020 34.615 0.00 0.00 0.00 4.00
4910 5058 9.626045 CCTTTGAAAACTACTACAAATGAATCC 57.374 33.333 0.00 0.00 33.01 3.01
4936 5084 4.632327 TTTGGGGTGGATGGAAATTTTC 57.368 40.909 0.24 0.24 0.00 2.29
4937 5085 4.662650 TCTTTTGGGGTGGATGGAAATTTT 59.337 37.500 0.00 0.00 0.00 1.82
4938 5086 4.238669 TCTTTTGGGGTGGATGGAAATTT 58.761 39.130 0.00 0.00 0.00 1.82
4939 5087 3.868062 TCTTTTGGGGTGGATGGAAATT 58.132 40.909 0.00 0.00 0.00 1.82
4940 5088 3.558608 TCTTTTGGGGTGGATGGAAAT 57.441 42.857 0.00 0.00 0.00 2.17
4941 5089 3.336509 TTCTTTTGGGGTGGATGGAAA 57.663 42.857 0.00 0.00 0.00 3.13
4942 5090 3.440127 GATTCTTTTGGGGTGGATGGAA 58.560 45.455 0.00 0.00 0.00 3.53
4943 5091 2.292192 GGATTCTTTTGGGGTGGATGGA 60.292 50.000 0.00 0.00 0.00 3.41
4944 5092 2.110578 GGATTCTTTTGGGGTGGATGG 58.889 52.381 0.00 0.00 0.00 3.51
4945 5093 3.105959 AGGATTCTTTTGGGGTGGATG 57.894 47.619 0.00 0.00 0.00 3.51
4946 5094 3.371595 CGTAGGATTCTTTTGGGGTGGAT 60.372 47.826 0.00 0.00 0.00 3.41
4947 5095 2.026636 CGTAGGATTCTTTTGGGGTGGA 60.027 50.000 0.00 0.00 0.00 4.02
4948 5096 2.290705 ACGTAGGATTCTTTTGGGGTGG 60.291 50.000 0.00 0.00 0.00 4.61
4949 5097 3.067684 ACGTAGGATTCTTTTGGGGTG 57.932 47.619 0.00 0.00 0.00 4.61
4950 5098 3.801307 AACGTAGGATTCTTTTGGGGT 57.199 42.857 0.00 0.00 0.00 4.95
4951 5099 5.462530 AAAAACGTAGGATTCTTTTGGGG 57.537 39.130 0.00 0.00 0.00 4.96
4952 5100 5.243060 AGGAAAAACGTAGGATTCTTTTGGG 59.757 40.000 0.00 0.00 0.00 4.12
4953 5101 6.149633 CAGGAAAAACGTAGGATTCTTTTGG 58.850 40.000 0.00 0.00 0.00 3.28
4954 5102 6.636850 CACAGGAAAAACGTAGGATTCTTTTG 59.363 38.462 0.00 0.00 0.00 2.44
4955 5103 6.734871 GCACAGGAAAAACGTAGGATTCTTTT 60.735 38.462 0.00 0.00 0.00 2.27
4956 5104 5.278315 GCACAGGAAAAACGTAGGATTCTTT 60.278 40.000 0.00 0.00 0.00 2.52
4957 5105 4.215613 GCACAGGAAAAACGTAGGATTCTT 59.784 41.667 0.00 0.00 0.00 2.52
4958 5106 3.751698 GCACAGGAAAAACGTAGGATTCT 59.248 43.478 0.00 0.00 0.00 2.40
4959 5107 3.500680 TGCACAGGAAAAACGTAGGATTC 59.499 43.478 0.00 0.00 0.00 2.52
4960 5108 3.252458 GTGCACAGGAAAAACGTAGGATT 59.748 43.478 13.17 0.00 0.00 3.01
4961 5109 2.812011 GTGCACAGGAAAAACGTAGGAT 59.188 45.455 13.17 0.00 0.00 3.24
4962 5110 2.215196 GTGCACAGGAAAAACGTAGGA 58.785 47.619 13.17 0.00 0.00 2.94
4963 5111 1.944024 TGTGCACAGGAAAAACGTAGG 59.056 47.619 17.42 0.00 0.00 3.18
4964 5112 3.684103 TTGTGCACAGGAAAAACGTAG 57.316 42.857 20.59 0.00 0.00 3.51
4965 5113 4.575236 TGTATTGTGCACAGGAAAAACGTA 59.425 37.500 20.59 0.79 0.00 3.57
4966 5114 3.378742 TGTATTGTGCACAGGAAAAACGT 59.621 39.130 20.59 1.96 0.00 3.99
4967 5115 3.958704 TGTATTGTGCACAGGAAAAACG 58.041 40.909 20.59 0.00 0.00 3.60
4968 5116 5.578727 TGTTTGTATTGTGCACAGGAAAAAC 59.421 36.000 26.72 26.72 0.00 2.43
4969 5117 5.724328 TGTTTGTATTGTGCACAGGAAAAA 58.276 33.333 20.59 15.56 0.00 1.94
4970 5118 5.330455 TGTTTGTATTGTGCACAGGAAAA 57.670 34.783 20.59 15.53 0.00 2.29
4971 5119 4.991153 TGTTTGTATTGTGCACAGGAAA 57.009 36.364 20.59 13.75 0.00 3.13
4972 5120 4.677584 GTTGTTTGTATTGTGCACAGGAA 58.322 39.130 20.59 5.82 0.00 3.36
4973 5121 4.300189 GTTGTTTGTATTGTGCACAGGA 57.700 40.909 20.59 6.67 0.00 3.86


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

AutoCloner maintained by Alex Coulton.