Multiple sequence alignment - TraesCS6A01G403700

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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 TraesCS6A01G403700 chr6A 100.000 4899 0 0 715 5613 610902089 610906987 0.000000e+00 9047.0
1 TraesCS6A01G403700 chr6A 100.000 349 0 0 1 349 610901375 610901723 0.000000e+00 645.0
2 TraesCS6A01G403700 chr6A 80.272 147 20 3 1301 1438 610902627 610902773 9.950000e-18 102.0
3 TraesCS6A01G403700 chr6A 80.272 147 20 3 1253 1399 610902675 610902812 9.950000e-18 102.0
4 TraesCS6A01G403700 chr6D 90.121 2227 135 34 1245 3436 464264011 464266187 0.000000e+00 2815.0
5 TraesCS6A01G403700 chr6D 88.442 1393 98 32 3785 5143 464266653 464268016 0.000000e+00 1622.0
6 TraesCS6A01G403700 chr6D 87.386 769 43 11 715 1442 464263417 464264172 0.000000e+00 833.0
7 TraesCS6A01G403700 chr6D 87.209 344 18 6 1 319 464262044 464262386 8.880000e-98 368.0
8 TraesCS6A01G403700 chr6B 90.789 1813 101 16 1264 3050 708023977 708025749 0.000000e+00 2362.0
9 TraesCS6A01G403700 chr6B 90.562 1833 93 31 3785 5579 708026490 708028280 0.000000e+00 2353.0
10 TraesCS6A01G403700 chr6B 91.700 759 51 6 3018 3768 708025751 708026505 0.000000e+00 1042.0
11 TraesCS6A01G403700 chr6B 85.695 734 45 26 715 1421 708023398 708024098 0.000000e+00 719.0
12 TraesCS6A01G403700 chr4D 100.000 35 0 0 5425 5459 50147128 50147162 1.310000e-06 65.8
13 TraesCS6A01G403700 chr4A 100.000 31 0 0 5425 5455 546800670 546800640 2.180000e-04 58.4


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 TraesCS6A01G403700 chr6A 610901375 610906987 5612 False 4846.0 9047 100.0000 1 5613 2 chr6A.!!$F1 5612
1 TraesCS6A01G403700 chr6D 464262044 464268016 5972 False 1409.5 2815 88.2895 1 5143 4 chr6D.!!$F1 5142
2 TraesCS6A01G403700 chr6B 708023398 708028280 4882 False 1619.0 2362 89.6865 715 5579 4 chr6B.!!$F1 4864

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
925 1606 0.323178 CTCCATTGCCTGAAGCCAGT 60.323 55.000 0.00 0.00 42.71 4.00 F
972 1653 0.389687 GGCTGTGAGTGAGCTCTGTC 60.390 60.000 16.19 11.75 42.13 3.51 F
1713 2505 1.591703 CTCTGGTTCAGGCGCACTA 59.408 57.895 10.83 0.00 31.51 2.74 F
3169 4030 0.874390 TGCCTGTCAGTTTGCGATTC 59.126 50.000 0.00 0.00 0.00 2.52 F
4070 5083 0.036022 GCTCATCATGTAGGGAGCCC 59.964 60.000 15.02 0.00 45.31 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2476 3278 2.000447 GTAGCACCGCAAAAGGTCTAG 59.000 52.381 0.0 0.0 43.89 2.43 R
2865 3683 2.175878 ACAAGCAAGAGCCTGTACTG 57.824 50.000 0.0 0.0 43.36 2.74 R
3401 4262 1.326548 GTAATAAAGAGTGCGTGCGGG 59.673 52.381 0.0 0.0 0.00 6.13 R
4376 5389 0.175989 TTGTTTTTGTTGGACCCGCC 59.824 50.000 0.0 0.0 37.10 6.13 R
5144 6216 0.178992 TTGAACCAGCTTGAGTGGGG 60.179 55.000 0.0 0.0 39.65 4.96 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
20 21 1.080093 TTTGGCGAGGCTAGTCACG 60.080 57.895 9.96 9.96 0.00 4.35
35 36 1.393539 GTCACGACGCTATGCAAACAT 59.606 47.619 0.00 0.00 40.49 2.71
52 53 0.538516 CATCCCCAAACAACCCGTCA 60.539 55.000 0.00 0.00 0.00 4.35
68 69 2.546795 CCGTCAGCACAAGAAAGACTCT 60.547 50.000 0.00 0.00 35.13 3.24
81 82 5.626142 AGAAAGACTCTCACTCACTCACTA 58.374 41.667 0.00 0.00 0.00 2.74
97 98 4.141620 ACTCACTACCTGCCCATGATAAAG 60.142 45.833 0.00 0.00 0.00 1.85
103 104 1.600957 CTGCCCATGATAAAGCACTCG 59.399 52.381 0.00 0.00 0.00 4.18
116 117 8.194769 TGATAAAGCACTCGTGTTATAATGAGA 58.805 33.333 15.22 3.90 36.79 3.27
118 119 5.584253 AGCACTCGTGTTATAATGAGACT 57.416 39.130 15.22 10.58 36.79 3.24
121 122 6.095021 AGCACTCGTGTTATAATGAGACTACA 59.905 38.462 15.22 0.00 36.79 2.74
153 154 1.593933 GTGTACCAAAAAGTCGACGCA 59.406 47.619 10.46 0.00 0.00 5.24
227 253 0.861155 TACCCCAAACAACCACCCAT 59.139 50.000 0.00 0.00 0.00 4.00
242 268 1.398174 CCCATGGCAAACACACACCA 61.398 55.000 6.09 0.00 36.43 4.17
268 294 1.901591 AGGTTGATCTTGTGCCACAG 58.098 50.000 0.00 0.00 0.00 3.66
271 297 1.610522 GTTGATCTTGTGCCACAGCTT 59.389 47.619 0.00 0.00 40.80 3.74
289 315 2.449031 TTTGGCCGCACAGACGATCT 62.449 55.000 0.00 0.00 34.06 2.75
291 317 2.583593 GCCGCACAGACGATCTCC 60.584 66.667 0.00 0.00 34.06 3.71
344 932 0.631753 TCTTCCTCCTCCATCTCGGT 59.368 55.000 0.00 0.00 35.57 4.69
345 933 1.007238 TCTTCCTCCTCCATCTCGGTT 59.993 52.381 0.00 0.00 35.57 4.44
346 934 1.410882 CTTCCTCCTCCATCTCGGTTC 59.589 57.143 0.00 0.00 35.57 3.62
347 935 0.397254 TCCTCCTCCATCTCGGTTCC 60.397 60.000 0.00 0.00 35.57 3.62
348 936 0.397816 CCTCCTCCATCTCGGTTCCT 60.398 60.000 0.00 0.00 35.57 3.36
733 1394 0.515564 AAAGATCGGGTTTTGACGCG 59.484 50.000 3.53 3.53 45.50 6.01
852 1513 2.041405 GGGAGGGGTAGCTGCTCT 60.041 66.667 4.91 0.00 0.00 4.09
925 1606 0.323178 CTCCATTGCCTGAAGCCAGT 60.323 55.000 0.00 0.00 42.71 4.00
971 1652 1.670590 GGCTGTGAGTGAGCTCTGT 59.329 57.895 16.19 1.10 42.13 3.41
972 1653 0.389687 GGCTGTGAGTGAGCTCTGTC 60.390 60.000 16.19 11.75 42.13 3.51
1214 1895 2.283388 CCACATTGGCCAGCAGGT 60.283 61.111 5.11 0.00 37.19 4.00
1244 1940 2.969238 CCATGTCGAGATGGCGCC 60.969 66.667 26.71 22.73 36.69 6.53
1294 2035 1.708193 GCATATGACGCAGCACAGCA 61.708 55.000 6.97 0.00 0.00 4.41
1331 2072 2.108976 CGGGTCGCAGCATATGGT 59.891 61.111 0.40 0.40 0.00 3.55
1372 2113 2.711711 GGTGGCTCACAGCATATGG 58.288 57.895 4.56 0.00 44.75 2.74
1611 2403 2.329690 CTCTCGCCATCTCCGTCG 59.670 66.667 0.00 0.00 0.00 5.12
1695 2487 3.493303 GGGACAGGATCAGGGGGC 61.493 72.222 0.00 0.00 0.00 5.80
1713 2505 1.591703 CTCTGGTTCAGGCGCACTA 59.408 57.895 10.83 0.00 31.51 2.74
1909 2701 4.217550 ACAGCACCGTTATAAACATGCTTT 59.782 37.500 13.28 7.18 45.81 3.51
1916 2708 8.181573 CACCGTTATAAACATGCTTTGTAGATT 58.818 33.333 0.00 0.00 37.68 2.40
1917 2709 8.736244 ACCGTTATAAACATGCTTTGTAGATTT 58.264 29.630 0.00 0.00 37.68 2.17
1918 2710 9.221775 CCGTTATAAACATGCTTTGTAGATTTC 57.778 33.333 0.00 0.00 37.68 2.17
2189 2982 7.683578 TCTTTATCATCAGTTGGGAGATATGG 58.316 38.462 0.00 0.00 0.00 2.74
2407 3204 3.822594 ATTGACGAATTGCGCAAGTTA 57.177 38.095 28.62 14.58 46.04 2.24
2419 3216 5.621197 TGCGCAAGTTATATGTTGACTTT 57.379 34.783 8.16 0.00 41.68 2.66
2436 3233 7.013274 TGTTGACTTTATTCTGTTAAGCAAGCT 59.987 33.333 0.00 0.00 0.00 3.74
2446 3244 5.182001 TCTGTTAAGCAAGCTCTTTTCATCC 59.818 40.000 0.00 0.00 0.00 3.51
2447 3245 4.218417 TGTTAAGCAAGCTCTTTTCATCCC 59.782 41.667 0.00 0.00 0.00 3.85
2492 3294 3.564225 AGAAAACTAGACCTTTTGCGGTG 59.436 43.478 0.00 0.00 37.42 4.94
2515 3317 9.841880 GGTGCTACCTTTTTCTTCTTTTTATAG 57.158 33.333 0.00 0.00 34.73 1.31
2636 3438 8.910351 ATTATTATTTCAGCTGGAGAGGTAAC 57.090 34.615 15.13 0.00 0.00 2.50
2652 3454 7.172875 GGAGAGGTAACATGAGAATGATCAATG 59.827 40.741 0.00 0.64 41.41 2.82
2703 3509 7.744087 ATGTTGCTGACACACTATCTTTAAA 57.256 32.000 0.00 0.00 42.04 1.52
2707 3513 9.118236 GTTGCTGACACACTATCTTTAAATTTC 57.882 33.333 0.00 0.00 0.00 2.17
2722 3528 9.672086 TCTTTAAATTTCGGCATTATTATTCCG 57.328 29.630 0.00 0.00 41.21 4.30
2736 3542 5.813080 ATTATTCCGTAAAACTGCTGGAC 57.187 39.130 0.00 0.00 0.00 4.02
2742 3548 2.096218 CGTAAAACTGCTGGACTCTTGC 60.096 50.000 0.00 0.00 0.00 4.01
2756 3562 2.826128 ACTCTTGCTTCCGTGAGTGATA 59.174 45.455 0.00 0.00 38.22 2.15
2813 3619 6.790285 AATTGTTTCTTGATTTGCCATGTC 57.210 33.333 0.00 0.00 0.00 3.06
2817 3623 6.990798 TGTTTCTTGATTTGCCATGTCATAA 58.009 32.000 0.00 0.00 0.00 1.90
2818 3624 6.867816 TGTTTCTTGATTTGCCATGTCATAAC 59.132 34.615 0.00 0.00 0.00 1.89
2819 3625 6.587206 TTCTTGATTTGCCATGTCATAACA 57.413 33.333 0.00 0.00 40.38 2.41
2821 3627 7.878547 TCTTGATTTGCCATGTCATAACATA 57.121 32.000 0.00 0.00 44.41 2.29
2822 3628 8.291191 TCTTGATTTGCCATGTCATAACATAA 57.709 30.769 0.00 0.00 44.41 1.90
2823 3629 8.190122 TCTTGATTTGCCATGTCATAACATAAC 58.810 33.333 0.00 0.00 44.41 1.89
2824 3630 7.643569 TGATTTGCCATGTCATAACATAACT 57.356 32.000 0.00 0.00 44.41 2.24
2825 3631 7.482474 TGATTTGCCATGTCATAACATAACTG 58.518 34.615 0.00 0.00 44.41 3.16
2839 3657 9.853555 CATAACATAACTGGCATAACAGAAAAA 57.146 29.630 0.00 0.00 40.97 1.94
2865 3683 6.531594 GCAAAAGCTTCATTAACCAATAGACC 59.468 38.462 0.00 0.00 0.00 3.85
2869 3687 7.195374 AGCTTCATTAACCAATAGACCAGTA 57.805 36.000 0.00 0.00 0.00 2.74
2947 3765 3.412386 ACTCCATAGGCGGCATTTAATC 58.588 45.455 13.08 0.00 0.00 1.75
2968 3786 2.670229 CGATGCATGCATTAATCCCAGC 60.670 50.000 32.60 16.02 36.70 4.85
2983 3801 1.610522 CCCAGCCTTTTTGACAGACAG 59.389 52.381 0.00 0.00 0.00 3.51
2987 3805 4.338118 CCAGCCTTTTTGACAGACAGTTAA 59.662 41.667 0.00 0.00 0.00 2.01
3000 3818 6.237901 ACAGACAGTTAAATGCTGTGGAATA 58.762 36.000 22.83 0.00 45.99 1.75
3002 3820 7.230510 ACAGACAGTTAAATGCTGTGGAATAAA 59.769 33.333 22.83 0.00 45.99 1.40
3003 3821 8.081633 CAGACAGTTAAATGCTGTGGAATAAAA 58.918 33.333 14.88 0.00 45.99 1.52
3007 3825 9.906660 CAGTTAAATGCTGTGGAATAAAAGTTA 57.093 29.630 0.00 0.00 0.00 2.24
3126 3984 9.743057 TTTGTTTGTTTCTGGAAATACTACATG 57.257 29.630 0.00 0.00 32.36 3.21
3127 3985 7.881142 TGTTTGTTTCTGGAAATACTACATGG 58.119 34.615 0.00 0.00 32.36 3.66
3128 3986 7.504238 TGTTTGTTTCTGGAAATACTACATGGT 59.496 33.333 0.00 0.00 32.36 3.55
3169 4030 0.874390 TGCCTGTCAGTTTGCGATTC 59.126 50.000 0.00 0.00 0.00 2.52
3185 4046 9.210426 GTTTGCGATTCTTATAAGTTGTGTATG 57.790 33.333 12.19 0.00 0.00 2.39
3201 4062 2.086869 GTATGTGTGCAGGATGTTGCT 58.913 47.619 0.00 0.00 44.38 3.91
3340 4201 4.606210 TGAGGTATCTTGCTGTAGGTGTA 58.394 43.478 0.00 0.00 0.00 2.90
3372 4233 8.882415 TTCGTTTCATTGTAGTAGAAAGACTT 57.118 30.769 0.00 0.00 32.48 3.01
3401 4262 6.851609 TGTATGACATGCATCCTTTTGTTAC 58.148 36.000 1.64 0.00 38.44 2.50
3402 4263 4.782019 TGACATGCATCCTTTTGTTACC 57.218 40.909 0.00 0.00 0.00 2.85
3407 4268 1.402325 GCATCCTTTTGTTACCCGCAC 60.402 52.381 0.00 0.00 0.00 5.34
3465 4421 2.294512 GTGCTTCTTCAGTGAAAAGGGG 59.705 50.000 20.01 6.40 0.00 4.79
3546 4504 6.588719 TTATCAAAATGCTTTACTGCTGGT 57.411 33.333 0.00 0.00 0.00 4.00
3547 4505 4.935352 TCAAAATGCTTTACTGCTGGTT 57.065 36.364 0.00 0.00 0.00 3.67
3568 4526 3.930336 TGCTTCAGTAACCTGTCATCTG 58.070 45.455 0.00 0.00 39.82 2.90
3578 4536 4.657814 ACCTGTCATCTGGTGGTAAAAT 57.342 40.909 0.00 0.00 42.81 1.82
3587 4545 7.012421 GTCATCTGGTGGTAAAATTATCCTGAC 59.988 40.741 0.00 0.00 0.00 3.51
3607 4566 8.988060 TCCTGACTAACCACTGATTTATTGATA 58.012 33.333 0.00 0.00 0.00 2.15
3654 4660 6.826893 TCATGAGTTTGCTTTAACTTTTGC 57.173 33.333 0.00 0.00 38.43 3.68
3660 4666 5.812127 AGTTTGCTTTAACTTTTGCTCCAAG 59.188 36.000 0.00 0.00 34.81 3.61
3666 4672 7.283580 TGCTTTAACTTTTGCTCCAAGTTAGTA 59.716 33.333 12.46 5.01 43.98 1.82
3719 4726 6.912203 TTTTTGTCATCGAACAGTTCACTA 57.088 33.333 13.82 0.00 0.00 2.74
3720 4727 5.900339 TTTGTCATCGAACAGTTCACTAC 57.100 39.130 13.82 6.19 0.00 2.73
3751 4764 4.651503 CCCTTGAGCCTGAGAAGAACTATA 59.348 45.833 0.00 0.00 0.00 1.31
3794 4807 5.794687 TTTTGCGAGTACTTGTCCATATG 57.205 39.130 11.83 0.00 0.00 1.78
3795 4808 4.465632 TTGCGAGTACTTGTCCATATGT 57.534 40.909 11.83 0.00 0.00 2.29
3796 4809 5.585820 TTGCGAGTACTTGTCCATATGTA 57.414 39.130 11.83 0.00 0.00 2.29
3797 4810 5.183014 TGCGAGTACTTGTCCATATGTAG 57.817 43.478 11.83 0.00 0.00 2.74
3798 4811 4.643334 TGCGAGTACTTGTCCATATGTAGT 59.357 41.667 11.83 2.67 0.00 2.73
3799 4812 5.126545 TGCGAGTACTTGTCCATATGTAGTT 59.873 40.000 11.83 0.00 0.00 2.24
3800 4813 5.686397 GCGAGTACTTGTCCATATGTAGTTC 59.314 44.000 11.83 0.00 0.00 3.01
3801 4814 6.679638 GCGAGTACTTGTCCATATGTAGTTCA 60.680 42.308 11.83 0.00 0.00 3.18
3802 4815 7.426410 CGAGTACTTGTCCATATGTAGTTCAT 58.574 38.462 0.00 0.00 40.25 2.57
3803 4816 7.379797 CGAGTACTTGTCCATATGTAGTTCATG 59.620 40.741 0.00 0.00 37.91 3.07
3804 4817 6.986817 AGTACTTGTCCATATGTAGTTCATGC 59.013 38.462 1.24 0.00 37.91 4.06
3805 4818 5.994250 ACTTGTCCATATGTAGTTCATGCT 58.006 37.500 1.24 0.00 37.91 3.79
3806 4819 6.051717 ACTTGTCCATATGTAGTTCATGCTC 58.948 40.000 1.24 0.00 37.91 4.26
3807 4820 5.876651 TGTCCATATGTAGTTCATGCTCT 57.123 39.130 1.24 0.00 37.91 4.09
3808 4821 6.239217 TGTCCATATGTAGTTCATGCTCTT 57.761 37.500 1.24 0.00 37.91 2.85
3809 4822 7.360113 TGTCCATATGTAGTTCATGCTCTTA 57.640 36.000 1.24 0.00 37.91 2.10
3810 4823 7.966812 TGTCCATATGTAGTTCATGCTCTTAT 58.033 34.615 1.24 0.00 37.91 1.73
3811 4824 7.874528 TGTCCATATGTAGTTCATGCTCTTATG 59.125 37.037 1.24 0.00 37.91 1.90
3812 4825 7.875041 GTCCATATGTAGTTCATGCTCTTATGT 59.125 37.037 1.24 0.00 37.91 2.29
3813 4826 9.088987 TCCATATGTAGTTCATGCTCTTATGTA 57.911 33.333 1.24 0.00 37.91 2.29
3814 4827 9.881649 CCATATGTAGTTCATGCTCTTATGTAT 57.118 33.333 1.24 0.00 37.91 2.29
3889 4902 5.437060 TCATATTTGGTGGTAGAAGAAGGC 58.563 41.667 0.00 0.00 0.00 4.35
4031 5044 5.901552 TCAGAATTTTGGGTGTTGTCTTTC 58.098 37.500 0.00 0.00 0.00 2.62
4040 5053 2.041216 GGTGTTGTCTTTCCCCCTGTAT 59.959 50.000 0.00 0.00 0.00 2.29
4051 5064 2.094675 CCCCCTGTATCAGTTGCTTTG 58.905 52.381 0.00 0.00 0.00 2.77
4052 5065 1.474077 CCCCTGTATCAGTTGCTTTGC 59.526 52.381 0.00 0.00 0.00 3.68
4053 5066 2.440409 CCCTGTATCAGTTGCTTTGCT 58.560 47.619 0.00 0.00 0.00 3.91
4054 5067 2.421424 CCCTGTATCAGTTGCTTTGCTC 59.579 50.000 0.00 0.00 0.00 4.26
4055 5068 3.076621 CCTGTATCAGTTGCTTTGCTCA 58.923 45.455 0.00 0.00 0.00 4.26
4056 5069 3.693085 CCTGTATCAGTTGCTTTGCTCAT 59.307 43.478 0.00 0.00 0.00 2.90
4061 5074 3.151554 TCAGTTGCTTTGCTCATCATGT 58.848 40.909 0.00 0.00 0.00 3.21
4070 5083 0.036022 GCTCATCATGTAGGGAGCCC 59.964 60.000 15.02 0.00 45.31 5.19
4165 5178 1.874129 TACACCAGGTGATAGTGGGG 58.126 55.000 27.39 0.00 43.57 4.96
4180 5193 0.183492 TGGGGAGCTTCATGTATGGC 59.817 55.000 0.00 0.00 0.00 4.40
4210 5223 4.081752 TCAAAGAAGAACAAAGGCAAAGCA 60.082 37.500 0.00 0.00 0.00 3.91
4219 5232 0.407139 AAGGCAAAGCAGACCAGGAT 59.593 50.000 0.00 0.00 0.00 3.24
4276 5289 3.948719 GAGACCCCCACGTTGGCA 61.949 66.667 0.00 0.00 35.79 4.92
4376 5389 2.071844 ATCGTCTCCCATGTACGGCG 62.072 60.000 4.80 4.80 37.24 6.46
4405 5421 3.999663 CCAACAAAAACAAGACCAAAGCA 59.000 39.130 0.00 0.00 0.00 3.91
4414 5430 1.889545 AGACCAAAGCAGAGCAAGAC 58.110 50.000 0.00 0.00 0.00 3.01
4423 5439 1.134159 GCAGAGCAAGACATGGAGGAT 60.134 52.381 0.00 0.00 0.00 3.24
4484 5503 3.957535 CAATGGCGCATCCCGAGC 61.958 66.667 10.83 0.00 40.02 5.03
4493 5512 1.026182 GCATCCCGAGCACAACATGA 61.026 55.000 0.00 0.00 0.00 3.07
4616 5635 1.227586 TCGATCCGCGAGTAGCTCT 60.228 57.895 8.23 0.00 45.59 4.09
4617 5636 1.082431 CGATCCGCGAGTAGCTCTG 60.082 63.158 8.23 0.00 45.59 3.35
4619 5638 0.382515 GATCCGCGAGTAGCTCTGTT 59.617 55.000 8.23 0.00 45.59 3.16
4800 5824 6.244552 ACCCTGCATATCGATTGATCATAT 57.755 37.500 1.71 0.00 35.99 1.78
4928 5962 6.764085 TGGAATAATGTTGGGAATGTACTACG 59.236 38.462 0.00 0.00 0.00 3.51
4931 5965 1.283736 GTTGGGAATGTACTACGCCG 58.716 55.000 0.00 0.00 0.00 6.46
4966 6000 3.386402 AGCTTCATCCACCTAGCTAGTTC 59.614 47.826 19.31 0.00 41.87 3.01
4971 6005 5.978814 TCATCCACCTAGCTAGTTCTTTTC 58.021 41.667 19.31 0.00 0.00 2.29
4984 6018 7.067494 AGCTAGTTCTTTTCTTTTTGAGCTTCA 59.933 33.333 0.00 0.00 32.85 3.02
4991 6025 3.157087 TCTTTTTGAGCTTCATCCACCC 58.843 45.455 0.00 0.00 0.00 4.61
4992 6026 2.673775 TTTTGAGCTTCATCCACCCA 57.326 45.000 0.00 0.00 0.00 4.51
5010 6044 2.374504 CCCATAGCTTCTCCATCCATGT 59.625 50.000 0.00 0.00 0.00 3.21
5089 6160 2.628657 CCTATACTCCCTCCGTTCCAAG 59.371 54.545 0.00 0.00 0.00 3.61
5095 6166 2.766828 CTCCCTCCGTTCCAAGATACTT 59.233 50.000 0.00 0.00 0.00 2.24
5143 6215 1.463674 GGATGGTTTCATGAGCGGTT 58.536 50.000 0.00 0.00 32.98 4.44
5144 6216 1.401905 GGATGGTTTCATGAGCGGTTC 59.598 52.381 0.00 0.00 32.98 3.62
5145 6217 1.401905 GATGGTTTCATGAGCGGTTCC 59.598 52.381 0.00 0.00 32.98 3.62
5146 6218 0.608035 TGGTTTCATGAGCGGTTCCC 60.608 55.000 0.00 0.00 0.00 3.97
5147 6219 1.313091 GGTTTCATGAGCGGTTCCCC 61.313 60.000 0.00 0.00 0.00 4.81
5148 6220 0.608035 GTTTCATGAGCGGTTCCCCA 60.608 55.000 0.00 0.00 0.00 4.96
5149 6221 0.608035 TTTCATGAGCGGTTCCCCAC 60.608 55.000 0.00 0.00 0.00 4.61
5150 6222 1.488705 TTCATGAGCGGTTCCCCACT 61.489 55.000 0.00 0.00 0.00 4.00
5151 6223 1.450312 CATGAGCGGTTCCCCACTC 60.450 63.158 0.00 0.00 39.87 3.51
5152 6224 2.525629 TGAGCGGTTCCCCACTCA 60.526 61.111 0.00 0.00 45.48 3.41
5153 6225 2.144078 TGAGCGGTTCCCCACTCAA 61.144 57.895 0.00 0.00 44.87 3.02
5154 6226 1.376037 GAGCGGTTCCCCACTCAAG 60.376 63.158 0.00 0.00 39.34 3.02
5155 6227 3.056328 GCGGTTCCCCACTCAAGC 61.056 66.667 0.00 0.00 0.00 4.01
5156 6228 2.750350 CGGTTCCCCACTCAAGCT 59.250 61.111 0.00 0.00 0.00 3.74
5157 6229 1.672356 CGGTTCCCCACTCAAGCTG 60.672 63.158 0.00 0.00 0.00 4.24
5164 6236 0.954452 CCCACTCAAGCTGGTTCAAC 59.046 55.000 0.00 0.00 0.00 3.18
5222 6294 5.242838 CCACTAAAACACTAGCCCATTTTCA 59.757 40.000 0.00 0.00 0.00 2.69
5268 6341 5.872617 TCGTCATTCCAGTGGTTATTTGTAG 59.127 40.000 9.54 0.00 0.00 2.74
5306 6380 8.700644 CACGGTTTCTAGTTTCTATGTATATGC 58.299 37.037 0.00 0.00 0.00 3.14
5318 6392 3.574354 TGTATATGCAGGCACAATCCA 57.426 42.857 0.00 0.00 0.00 3.41
5363 6437 7.508977 TCCATTGTTCTGTTTCCTATCCTTTTT 59.491 33.333 0.00 0.00 0.00 1.94
5413 6487 3.118261 TGAGCCAAGTTTCAGAGACAACT 60.118 43.478 0.00 0.00 34.58 3.16
5419 6493 5.355596 CAAGTTTCAGAGACAACTGAGAGT 58.644 41.667 0.00 0.00 45.63 3.24
5424 6498 5.598416 TCAGAGACAACTGAGAGTTTTCA 57.402 39.130 5.64 0.00 41.21 2.69
5436 6510 7.171447 CTGAGAGTTTTCAGTAACAACTCAG 57.829 40.000 18.85 18.85 46.03 3.35
5462 6536 6.027749 GCTATCAAAAGGTTCAATGGTTACG 58.972 40.000 0.00 0.00 0.00 3.18
5470 6544 4.947388 AGGTTCAATGGTTACGTATGCATT 59.053 37.500 3.54 0.00 0.00 3.56
5551 6625 7.594758 GCAAAAGTGATATTGACTTGTTTGCTA 59.405 33.333 19.12 0.00 40.65 3.49
5584 6658 3.591979 GCATTGCCTTGCTGTCAAA 57.408 47.368 0.00 0.00 39.57 2.69
5585 6659 1.868469 GCATTGCCTTGCTGTCAAAA 58.132 45.000 0.00 0.00 39.57 2.44
5586 6660 2.211806 GCATTGCCTTGCTGTCAAAAA 58.788 42.857 0.00 0.00 39.57 1.94
5587 6661 2.222445 GCATTGCCTTGCTGTCAAAAAG 59.778 45.455 0.00 0.00 39.57 2.27
5588 6662 3.460103 CATTGCCTTGCTGTCAAAAAGT 58.540 40.909 0.00 0.00 0.00 2.66
5589 6663 4.619973 CATTGCCTTGCTGTCAAAAAGTA 58.380 39.130 0.00 0.00 0.00 2.24
5590 6664 4.727507 TTGCCTTGCTGTCAAAAAGTAA 57.272 36.364 0.00 0.00 0.00 2.24
5591 6665 4.305989 TGCCTTGCTGTCAAAAAGTAAG 57.694 40.909 0.00 0.00 37.18 2.34
5593 6667 4.918810 CCTTGCTGTCAAAAAGTAAGGT 57.081 40.909 10.95 0.00 46.57 3.50
5594 6668 5.262588 CCTTGCTGTCAAAAAGTAAGGTT 57.737 39.130 10.95 0.00 46.57 3.50
5595 6669 5.660460 CCTTGCTGTCAAAAAGTAAGGTTT 58.340 37.500 10.95 0.00 46.57 3.27
5596 6670 6.106003 CCTTGCTGTCAAAAAGTAAGGTTTT 58.894 36.000 10.95 0.00 46.57 2.43
5597 6671 6.255670 CCTTGCTGTCAAAAAGTAAGGTTTTC 59.744 38.462 10.95 0.00 46.57 2.29
5598 6672 6.524101 TGCTGTCAAAAAGTAAGGTTTTCT 57.476 33.333 0.00 0.00 0.00 2.52
5599 6673 6.329496 TGCTGTCAAAAAGTAAGGTTTTCTG 58.671 36.000 0.00 0.00 0.00 3.02
5600 6674 5.748630 GCTGTCAAAAAGTAAGGTTTTCTGG 59.251 40.000 0.00 0.00 0.00 3.86
5601 6675 6.627287 GCTGTCAAAAAGTAAGGTTTTCTGGT 60.627 38.462 0.00 0.00 0.00 4.00
5602 6676 7.234661 TGTCAAAAAGTAAGGTTTTCTGGTT 57.765 32.000 0.00 0.00 0.00 3.67
5603 6677 7.672240 TGTCAAAAAGTAAGGTTTTCTGGTTT 58.328 30.769 0.00 0.00 0.00 3.27
5604 6678 7.815549 TGTCAAAAAGTAAGGTTTTCTGGTTTC 59.184 33.333 0.00 0.00 0.00 2.78
5605 6679 7.277098 GTCAAAAAGTAAGGTTTTCTGGTTTCC 59.723 37.037 0.00 0.00 0.00 3.13
5606 6680 6.860790 AAAAGTAAGGTTTTCTGGTTTCCA 57.139 33.333 0.00 0.00 0.00 3.53
5607 6681 6.860790 AAAGTAAGGTTTTCTGGTTTCCAA 57.139 33.333 0.00 0.00 30.80 3.53
5608 6682 5.847111 AGTAAGGTTTTCTGGTTTCCAAC 57.153 39.130 0.00 0.00 30.80 3.77
5609 6683 5.516044 AGTAAGGTTTTCTGGTTTCCAACT 58.484 37.500 0.00 0.00 30.80 3.16
5610 6684 4.736126 AAGGTTTTCTGGTTTCCAACTG 57.264 40.909 0.00 0.00 30.80 3.16
5611 6685 3.976015 AGGTTTTCTGGTTTCCAACTGA 58.024 40.909 0.00 0.00 30.80 3.41
5612 6686 4.349365 AGGTTTTCTGGTTTCCAACTGAA 58.651 39.130 0.00 0.00 30.80 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.426816 TAGCGTCGTGACTAGCCTCG 61.427 60.000 0.00 0.00 0.00 4.63
20 21 0.663153 GGGGATGTTTGCATAGCGTC 59.337 55.000 0.00 0.00 35.07 5.19
35 36 1.149627 CTGACGGGTTGTTTGGGGA 59.850 57.895 0.00 0.00 0.00 4.81
52 53 3.386078 TGAGTGAGAGTCTTTCTTGTGCT 59.614 43.478 0.00 0.00 35.87 4.40
68 69 1.257743 GGCAGGTAGTGAGTGAGTGA 58.742 55.000 0.00 0.00 0.00 3.41
81 82 1.285962 AGTGCTTTATCATGGGCAGGT 59.714 47.619 0.00 0.00 35.29 4.00
97 98 6.263344 TGTAGTCTCATTATAACACGAGTGC 58.737 40.000 2.76 3.45 0.00 4.40
103 104 6.810182 ACACCGTTGTAGTCTCATTATAACAC 59.190 38.462 0.00 0.00 32.60 3.32
116 117 3.163630 ACACGTTTACACCGTTGTAGT 57.836 42.857 0.00 0.00 39.44 2.73
118 119 3.181486 TGGTACACGTTTACACCGTTGTA 60.181 43.478 13.49 0.00 36.17 2.41
121 122 2.593346 TGGTACACGTTTACACCGTT 57.407 45.000 13.49 0.00 36.17 4.44
227 253 2.839486 TTTTTGGTGTGTGTTTGCCA 57.161 40.000 0.00 0.00 0.00 4.92
249 275 1.901591 CTGTGGCACAAGATCAACCT 58.098 50.000 22.31 0.00 44.16 3.50
268 294 4.389576 CGTCTGTGCGGCCAAAGC 62.390 66.667 2.24 0.00 38.76 3.51
271 297 2.434185 GATCGTCTGTGCGGCCAA 60.434 61.111 2.24 0.00 0.00 4.52
320 908 3.686978 CGAGATGGAGGAGGAAGAAGAGA 60.687 52.174 0.00 0.00 0.00 3.10
775 1436 0.323629 CTTGCCGAGTAAACAGGGGA 59.676 55.000 0.00 0.00 0.00 4.81
953 1634 0.389687 GACAGAGCTCACTCACAGCC 60.390 60.000 17.77 0.00 46.09 4.85
954 1635 0.602562 AGACAGAGCTCACTCACAGC 59.397 55.000 17.77 0.00 46.09 4.40
955 1636 1.612950 ACAGACAGAGCTCACTCACAG 59.387 52.381 17.77 6.40 46.09 3.66
956 1637 1.611006 GACAGACAGAGCTCACTCACA 59.389 52.381 17.77 0.00 46.09 3.58
960 1641 1.612950 CACAGACAGACAGAGCTCACT 59.387 52.381 17.77 9.29 0.00 3.41
971 1652 4.687215 GCGGCAGCCACAGACAGA 62.687 66.667 13.30 0.00 37.42 3.41
1165 1846 4.778143 GGGCGGCTGATGGAACGT 62.778 66.667 9.56 0.00 0.00 3.99
1214 1895 1.001520 CGACATGGTTCTGGTGGTACA 59.998 52.381 0.00 0.00 0.00 2.90
1262 1958 3.814615 ATATGCTGTGAGCCGCCGG 62.815 63.158 0.00 0.00 41.51 6.13
1272 1968 0.391528 TGTGCTGCGTCATATGCTGT 60.392 50.000 0.00 0.00 32.51 4.40
1421 2171 4.935495 CGCCACCAGCACCAGTGT 62.935 66.667 0.00 0.00 44.04 3.55
1443 2235 2.611505 AATGTCCATGCCCCCGTCA 61.612 57.895 0.00 0.00 0.00 4.35
1608 2400 3.676742 GACGAATGAGGCGTCGAC 58.323 61.111 5.18 5.18 46.85 4.20
1642 2434 0.323629 CCAGGTGTGGTAACCATCGT 59.676 55.000 0.00 0.00 43.20 3.73
1677 2469 3.164269 CCCCCTGATCCTGTCCCG 61.164 72.222 0.00 0.00 0.00 5.14
1686 2478 1.229951 TGAACCAGAGCCCCCTGAT 60.230 57.895 0.00 0.00 36.29 2.90
1695 2487 0.037326 TTAGTGCGCCTGAACCAGAG 60.037 55.000 4.18 0.00 32.44 3.35
1713 2505 0.600255 CTCTGCCACGTTTCTCCGTT 60.600 55.000 0.00 0.00 39.45 4.44
1909 2701 6.716628 AGAAAACATGCCAGAAGAAATCTACA 59.283 34.615 0.00 0.00 36.32 2.74
1916 2708 3.565307 ACCAGAAAACATGCCAGAAGAA 58.435 40.909 0.00 0.00 0.00 2.52
1917 2709 3.228188 ACCAGAAAACATGCCAGAAGA 57.772 42.857 0.00 0.00 0.00 2.87
1918 2710 4.074970 ACTACCAGAAAACATGCCAGAAG 58.925 43.478 0.00 0.00 0.00 2.85
2189 2982 7.761249 GGGAATTATATTTGGCATGATAACAGC 59.239 37.037 0.00 0.00 0.00 4.40
2210 3003 9.533831 AGAACACATTAAAAGAATGTAGGGAAT 57.466 29.630 2.78 0.00 38.69 3.01
2419 3216 7.744087 TGAAAAGAGCTTGCTTAACAGAATA 57.256 32.000 0.00 0.00 0.00 1.75
2476 3278 2.000447 GTAGCACCGCAAAAGGTCTAG 59.000 52.381 0.00 0.00 43.89 2.43
2515 3317 4.931002 ACACCAATAGCAAATGCATCAAAC 59.069 37.500 8.28 0.00 45.16 2.93
2636 3438 8.951243 AGCTATCATTCATTGATCATTCTCATG 58.049 33.333 0.00 0.00 44.13 3.07
2652 3454 8.129840 TCGTAGAAAGAAGTACAGCTATCATTC 58.870 37.037 0.00 0.00 0.00 2.67
2722 3528 3.142174 AGCAAGAGTCCAGCAGTTTTAC 58.858 45.455 7.11 0.00 0.00 2.01
2736 3542 2.376808 ATCACTCACGGAAGCAAGAG 57.623 50.000 0.00 0.00 35.00 2.85
2756 3562 9.950496 AATTCGGTGCATTAGATAGAATATTCT 57.050 29.630 21.28 21.28 41.24 2.40
2813 3619 9.853555 TTTTTCTGTTATGCCAGTTATGTTATG 57.146 29.630 0.00 0.00 34.02 1.90
2817 3623 6.015519 TGCTTTTTCTGTTATGCCAGTTATGT 60.016 34.615 0.00 0.00 34.02 2.29
2818 3624 6.389091 TGCTTTTTCTGTTATGCCAGTTATG 58.611 36.000 0.00 0.00 34.02 1.90
2819 3625 6.588719 TGCTTTTTCTGTTATGCCAGTTAT 57.411 33.333 0.00 0.00 34.02 1.89
2820 3626 6.398234 TTGCTTTTTCTGTTATGCCAGTTA 57.602 33.333 0.00 0.00 34.02 2.24
2821 3627 4.935352 TGCTTTTTCTGTTATGCCAGTT 57.065 36.364 0.00 0.00 34.02 3.16
2822 3628 4.935352 TTGCTTTTTCTGTTATGCCAGT 57.065 36.364 0.00 0.00 34.02 4.00
2823 3629 5.333568 GCTTTTGCTTTTTCTGTTATGCCAG 60.334 40.000 0.00 0.00 43.35 4.85
2824 3630 4.511082 GCTTTTGCTTTTTCTGTTATGCCA 59.489 37.500 0.00 0.00 43.35 4.92
2825 3631 5.022335 GCTTTTGCTTTTTCTGTTATGCC 57.978 39.130 0.00 0.00 43.35 4.40
2865 3683 2.175878 ACAAGCAAGAGCCTGTACTG 57.824 50.000 0.00 0.00 43.36 2.74
2869 3687 2.370189 AGACTAACAAGCAAGAGCCTGT 59.630 45.455 0.00 0.00 46.99 4.00
2914 3732 6.650120 CCGCCTATGGAGTTAATTATATGGT 58.350 40.000 0.00 0.00 0.00 3.55
2915 3733 5.527582 GCCGCCTATGGAGTTAATTATATGG 59.472 44.000 0.00 0.00 0.00 2.74
2947 3765 2.670229 GCTGGGATTAATGCATGCATCG 60.670 50.000 32.25 15.29 35.31 3.84
2952 3770 4.411256 AAAAGGCTGGGATTAATGCATG 57.589 40.909 9.34 2.10 0.00 4.06
2968 3786 6.418819 CAGCATTTAACTGTCTGTCAAAAAGG 59.581 38.462 8.22 0.00 0.00 3.11
2987 3805 9.830975 AAGTTTTAACTTTTATTCCACAGCATT 57.169 25.926 2.10 0.00 46.52 3.56
3029 3887 8.362464 TGATGGTACTGTAGTTGATAGTTTCT 57.638 34.615 0.00 0.00 31.01 2.52
3032 3890 7.178628 ACACTGATGGTACTGTAGTTGATAGTT 59.821 37.037 0.00 0.00 31.01 2.24
3063 3921 5.929697 TTATCCAGATAATTCAGCTTGCG 57.070 39.130 0.00 0.00 0.00 4.85
3078 3936 9.976511 ACAAAATATTCAGATGCAATTATCCAG 57.023 29.630 0.00 0.00 0.00 3.86
3089 3947 9.695526 TCCAGAAACAAACAAAATATTCAGATG 57.304 29.630 0.00 0.00 0.00 2.90
3156 4016 7.172532 ACACAACTTATAAGAATCGCAAACTGA 59.827 33.333 19.38 0.00 0.00 3.41
3169 4030 6.593770 TCCTGCACACATACACAACTTATAAG 59.406 38.462 11.05 11.05 0.00 1.73
3201 4062 4.019411 TGTGAGAAGGACATTATTCTGGCA 60.019 41.667 0.00 0.00 35.93 4.92
3364 4225 6.037500 TGCATGTCATACATAGCAAGTCTTTC 59.962 38.462 11.87 0.00 38.60 2.62
3372 4233 4.628963 AGGATGCATGTCATACATAGCA 57.371 40.909 2.46 14.79 42.31 3.49
3401 4262 1.326548 GTAATAAAGAGTGCGTGCGGG 59.673 52.381 0.00 0.00 0.00 6.13
3402 4263 1.996898 TGTAATAAAGAGTGCGTGCGG 59.003 47.619 0.00 0.00 0.00 5.69
3407 4268 5.927030 TCTTTTGCTGTAATAAAGAGTGCG 58.073 37.500 0.00 0.00 34.07 5.34
3436 4297 6.545504 TTCACTGAAGAAGCACTACATTTC 57.454 37.500 0.00 0.00 0.00 2.17
3441 4397 4.214332 CCCTTTTCACTGAAGAAGCACTAC 59.786 45.833 0.00 0.00 0.00 2.73
3465 4421 4.816925 GGTGCAGGACAGAGGTATATTTTC 59.183 45.833 0.00 0.00 0.00 2.29
3568 4526 7.066645 GTGGTTAGTCAGGATAATTTTACCACC 59.933 40.741 0.00 0.00 43.60 4.61
3578 4536 9.613428 CAATAAATCAGTGGTTAGTCAGGATAA 57.387 33.333 0.00 0.00 0.00 1.75
3632 4591 6.074142 GGAGCAAAAGTTAAAGCAAACTCATG 60.074 38.462 0.34 0.00 38.76 3.07
3639 4598 5.337578 ACTTGGAGCAAAAGTTAAAGCAA 57.662 34.783 0.00 0.00 34.16 3.91
3646 4652 9.740710 ATAGAATACTAACTTGGAGCAAAAGTT 57.259 29.630 13.67 13.67 46.72 2.66
3712 4719 5.049612 GCTCAAGGGTAAAACAGTAGTGAAC 60.050 44.000 4.09 0.00 0.00 3.18
3719 4726 2.441750 TCAGGCTCAAGGGTAAAACAGT 59.558 45.455 0.00 0.00 0.00 3.55
3720 4727 3.077359 CTCAGGCTCAAGGGTAAAACAG 58.923 50.000 0.00 0.00 0.00 3.16
3722 4729 3.418684 TCTCAGGCTCAAGGGTAAAAC 57.581 47.619 0.00 0.00 0.00 2.43
3723 4730 3.650942 TCTTCTCAGGCTCAAGGGTAAAA 59.349 43.478 0.00 0.00 0.00 1.52
3725 4732 2.902608 TCTTCTCAGGCTCAAGGGTAA 58.097 47.619 0.00 0.00 0.00 2.85
3727 4734 1.349357 GTTCTTCTCAGGCTCAAGGGT 59.651 52.381 0.00 0.00 0.00 4.34
3771 4784 5.703592 ACATATGGACAAGTACTCGCAAAAA 59.296 36.000 7.80 0.00 0.00 1.94
3772 4785 5.242434 ACATATGGACAAGTACTCGCAAAA 58.758 37.500 7.80 0.00 0.00 2.44
3773 4786 4.827692 ACATATGGACAAGTACTCGCAAA 58.172 39.130 7.80 0.00 0.00 3.68
3774 4787 4.465632 ACATATGGACAAGTACTCGCAA 57.534 40.909 7.80 0.00 0.00 4.85
3776 4789 5.184340 ACTACATATGGACAAGTACTCGC 57.816 43.478 7.80 0.00 0.00 5.03
3777 4790 6.792326 TGAACTACATATGGACAAGTACTCG 58.208 40.000 7.80 0.00 0.00 4.18
3778 4791 7.169982 GCATGAACTACATATGGACAAGTACTC 59.830 40.741 7.80 2.16 37.46 2.59
3779 4792 6.986817 GCATGAACTACATATGGACAAGTACT 59.013 38.462 7.80 0.00 37.46 2.73
3780 4793 6.986817 AGCATGAACTACATATGGACAAGTAC 59.013 38.462 7.80 0.00 37.46 2.73
3781 4794 7.069950 AGAGCATGAACTACATATGGACAAGTA 59.930 37.037 7.80 0.00 37.46 2.24
3782 4795 5.994250 AGCATGAACTACATATGGACAAGT 58.006 37.500 7.80 2.37 37.46 3.16
3783 4796 6.286758 AGAGCATGAACTACATATGGACAAG 58.713 40.000 7.80 1.75 37.46 3.16
3784 4797 6.239217 AGAGCATGAACTACATATGGACAA 57.761 37.500 7.80 0.00 37.46 3.18
3785 4798 5.876651 AGAGCATGAACTACATATGGACA 57.123 39.130 7.80 0.00 37.46 4.02
3786 4799 7.875041 ACATAAGAGCATGAACTACATATGGAC 59.125 37.037 7.80 0.00 37.46 4.02
3787 4800 7.966812 ACATAAGAGCATGAACTACATATGGA 58.033 34.615 7.80 0.00 37.46 3.41
3788 4801 9.881649 ATACATAAGAGCATGAACTACATATGG 57.118 33.333 7.80 0.00 37.46 2.74
3952 4965 1.348064 CTCCACTAACACTCCCACCA 58.652 55.000 0.00 0.00 0.00 4.17
4025 5038 3.610911 CAACTGATACAGGGGGAAAGAC 58.389 50.000 0.00 0.00 35.51 3.01
4031 5044 2.094675 CAAAGCAACTGATACAGGGGG 58.905 52.381 0.00 0.00 35.51 5.40
4040 5053 3.151554 ACATGATGAGCAAAGCAACTGA 58.848 40.909 0.00 0.00 0.00 3.41
4052 5065 0.319728 CGGGCTCCCTACATGATGAG 59.680 60.000 0.00 0.46 0.00 2.90
4053 5066 1.121407 CCGGGCTCCCTACATGATGA 61.121 60.000 0.00 0.00 0.00 2.92
4054 5067 1.372683 CCGGGCTCCCTACATGATG 59.627 63.158 0.00 0.00 0.00 3.07
4055 5068 0.190069 TACCGGGCTCCCTACATGAT 59.810 55.000 6.32 0.00 0.00 2.45
4056 5069 0.190069 ATACCGGGCTCCCTACATGA 59.810 55.000 6.32 0.00 0.00 3.07
4061 5074 1.151760 TACTCATACCGGGCTCCCTA 58.848 55.000 6.32 0.00 0.00 3.53
4070 5083 9.093970 TCAGAATGTAAAACAATACTCATACCG 57.906 33.333 0.00 0.00 37.40 4.02
4103 5116 4.993705 ACCAGAGGAATGACTTAACCAA 57.006 40.909 0.00 0.00 0.00 3.67
4165 5178 1.835483 CGCCGCCATACATGAAGCTC 61.835 60.000 0.00 0.00 0.00 4.09
4180 5193 0.882927 TGTTCTTCTTTGACCCGCCG 60.883 55.000 0.00 0.00 0.00 6.46
4210 5223 0.898320 CGTTCTCCACATCCTGGTCT 59.102 55.000 0.00 0.00 41.52 3.85
4219 5232 1.328279 TCTGCTCTTCGTTCTCCACA 58.672 50.000 0.00 0.00 0.00 4.17
4341 5354 1.369321 GATCTCGGGTCCATCTGGC 59.631 63.158 0.00 0.00 34.44 4.85
4376 5389 0.175989 TTGTTTTTGTTGGACCCGCC 59.824 50.000 0.00 0.00 37.10 6.13
4379 5392 2.498078 TGGTCTTGTTTTTGTTGGACCC 59.502 45.455 0.00 0.00 41.53 4.46
4384 5397 4.928615 TCTGCTTTGGTCTTGTTTTTGTTG 59.071 37.500 0.00 0.00 0.00 3.33
4387 5403 3.553105 GCTCTGCTTTGGTCTTGTTTTTG 59.447 43.478 0.00 0.00 0.00 2.44
4388 5404 3.195396 TGCTCTGCTTTGGTCTTGTTTTT 59.805 39.130 0.00 0.00 0.00 1.94
4405 5421 2.475155 TCATCCTCCATGTCTTGCTCT 58.525 47.619 0.00 0.00 33.66 4.09
4414 5430 0.179065 TGCGCTCTTCATCCTCCATG 60.179 55.000 9.73 0.00 0.00 3.66
4484 5503 0.888736 TGCTCGGGGTTCATGTTGTG 60.889 55.000 0.00 0.00 0.00 3.33
4493 5512 2.290641 TGTTCATGTTATGCTCGGGGTT 60.291 45.455 0.00 0.00 0.00 4.11
4553 5572 0.462581 GAGTCCATCTGCCGCATCAA 60.463 55.000 0.00 0.00 0.00 2.57
4800 5824 5.182487 ACATCGCAGTACAATGACCAATAA 58.818 37.500 0.00 0.00 0.00 1.40
4926 5960 1.809651 GCTAGGTAGAGTACTCGGCGT 60.810 57.143 17.07 16.06 34.09 5.68
4928 5962 2.259266 AGCTAGGTAGAGTACTCGGC 57.741 55.000 17.07 13.15 34.09 5.54
4931 5965 5.239963 GTGGATGAAGCTAGGTAGAGTACTC 59.760 48.000 15.41 15.41 0.00 2.59
4966 6000 5.693555 GGTGGATGAAGCTCAAAAAGAAAAG 59.306 40.000 0.00 0.00 0.00 2.27
4971 6005 2.892852 TGGGTGGATGAAGCTCAAAAAG 59.107 45.455 0.00 0.00 0.00 2.27
4984 6018 2.196742 TGGAGAAGCTATGGGTGGAT 57.803 50.000 0.00 0.00 0.00 3.41
5010 6044 5.104151 TGAATCATGGGTTGAAGCTACCATA 60.104 40.000 6.49 0.00 41.56 2.74
5014 6048 4.439289 GCTTGAATCATGGGTTGAAGCTAC 60.439 45.833 20.11 0.00 40.89 3.58
5020 6054 2.827322 CCAAGCTTGAATCATGGGTTGA 59.173 45.455 28.05 0.00 38.82 3.18
5064 6119 3.902467 GGAACGGAGGGAGTATAGGAAAT 59.098 47.826 0.00 0.00 0.00 2.17
5065 6120 3.303049 GGAACGGAGGGAGTATAGGAAA 58.697 50.000 0.00 0.00 0.00 3.13
5068 6123 2.376695 TGGAACGGAGGGAGTATAGG 57.623 55.000 0.00 0.00 0.00 2.57
5069 6124 3.563223 TCTTGGAACGGAGGGAGTATAG 58.437 50.000 0.00 0.00 0.00 1.31
5116 6188 2.582172 TCATGAAACCATCCCATCAGGT 59.418 45.455 0.00 0.00 37.20 4.00
5143 6215 1.059584 TGAACCAGCTTGAGTGGGGA 61.060 55.000 0.00 0.00 39.65 4.81
5144 6216 0.178992 TTGAACCAGCTTGAGTGGGG 60.179 55.000 0.00 0.00 39.65 4.96
5145 6217 0.954452 GTTGAACCAGCTTGAGTGGG 59.046 55.000 0.00 0.00 39.65 4.61
5146 6218 1.972872 AGTTGAACCAGCTTGAGTGG 58.027 50.000 0.00 0.00 41.30 4.00
5147 6219 2.291741 GGAAGTTGAACCAGCTTGAGTG 59.708 50.000 0.90 0.00 35.20 3.51
5148 6220 2.173569 AGGAAGTTGAACCAGCTTGAGT 59.826 45.455 0.90 0.00 35.20 3.41
5149 6221 2.810852 GAGGAAGTTGAACCAGCTTGAG 59.189 50.000 0.90 0.00 35.20 3.02
5150 6222 2.172505 TGAGGAAGTTGAACCAGCTTGA 59.827 45.455 0.90 0.00 35.20 3.02
5151 6223 2.575532 TGAGGAAGTTGAACCAGCTTG 58.424 47.619 0.90 0.00 35.20 4.01
5152 6224 3.515602 ATGAGGAAGTTGAACCAGCTT 57.484 42.857 0.00 0.00 37.60 3.74
5153 6225 4.042187 AGTTATGAGGAAGTTGAACCAGCT 59.958 41.667 0.00 0.00 0.00 4.24
5154 6226 4.327680 AGTTATGAGGAAGTTGAACCAGC 58.672 43.478 0.00 0.00 0.00 4.85
5155 6227 7.162082 ACTAAGTTATGAGGAAGTTGAACCAG 58.838 38.462 0.00 0.00 0.00 4.00
5156 6228 7.074653 ACTAAGTTATGAGGAAGTTGAACCA 57.925 36.000 0.00 0.00 0.00 3.67
5157 6229 7.660208 TGAACTAAGTTATGAGGAAGTTGAACC 59.340 37.037 0.00 0.00 0.00 3.62
5164 6236 6.540189 CCCATGTGAACTAAGTTATGAGGAAG 59.460 42.308 0.00 0.00 0.00 3.46
5222 6294 6.766467 ACGAAGACCTATTCAAGTTTTCACTT 59.234 34.615 0.00 0.00 44.72 3.16
5240 6312 2.457366 ACCACTGGAATGACGAAGAC 57.543 50.000 0.71 0.00 0.00 3.01
5241 6313 4.819105 ATAACCACTGGAATGACGAAGA 57.181 40.909 0.71 0.00 0.00 2.87
5242 6314 5.181245 ACAAATAACCACTGGAATGACGAAG 59.819 40.000 0.71 0.00 0.00 3.79
5243 6315 5.067273 ACAAATAACCACTGGAATGACGAA 58.933 37.500 0.71 0.00 0.00 3.85
5244 6316 4.647611 ACAAATAACCACTGGAATGACGA 58.352 39.130 0.71 0.00 0.00 4.20
5245 6317 5.872617 TCTACAAATAACCACTGGAATGACG 59.127 40.000 0.71 0.00 0.00 4.35
5268 6341 5.930569 ACTAGAAACCGTGAATAACCTGTTC 59.069 40.000 0.00 0.00 0.00 3.18
5306 6380 3.803082 CGCCGTGGATTGTGCCTG 61.803 66.667 0.00 0.00 0.00 4.85
5318 6392 2.819984 ATTCATGACAAGGGCGCCGT 62.820 55.000 22.54 20.09 0.00 5.68
5391 6465 3.118261 AGTTGTCTCTGAAACTTGGCTCA 60.118 43.478 0.00 0.00 32.75 4.26
5394 6468 3.206150 TCAGTTGTCTCTGAAACTTGGC 58.794 45.455 0.00 0.00 40.82 4.52
5413 6487 5.523916 GCTGAGTTGTTACTGAAAACTCTCA 59.476 40.000 13.98 14.70 46.44 3.27
5419 6493 3.202906 AGCGCTGAGTTGTTACTGAAAA 58.797 40.909 10.39 0.00 33.84 2.29
5424 6498 3.868757 TGATAGCGCTGAGTTGTTACT 57.131 42.857 22.90 0.00 37.31 2.24
5436 6510 3.119495 ACCATTGAACCTTTTGATAGCGC 60.119 43.478 0.00 0.00 0.00 5.92
5470 6544 5.070180 TCCCATGTTTTTGAGAAGCATGAAA 59.930 36.000 12.85 0.03 39.21 2.69
5478 6552 5.738909 TGCTTTTTCCCATGTTTTTGAGAA 58.261 33.333 0.00 0.00 0.00 2.87
5481 6555 5.248640 TGTTGCTTTTTCCCATGTTTTTGA 58.751 33.333 0.00 0.00 0.00 2.69
5537 6611 8.445275 TTCTTGATAAGTAGCAAACAAGTCAA 57.555 30.769 0.00 0.00 36.91 3.18
5551 6625 5.749462 AGGCAATGCTACTTCTTGATAAGT 58.251 37.500 4.82 0.00 42.31 2.24
5579 6653 7.277098 GGAAACCAGAAAACCTTACTTTTTGAC 59.723 37.037 0.00 0.00 0.00 3.18
5580 6654 7.038941 TGGAAACCAGAAAACCTTACTTTTTGA 60.039 33.333 0.00 0.00 0.00 2.69
5581 6655 7.100409 TGGAAACCAGAAAACCTTACTTTTTG 58.900 34.615 0.00 0.00 0.00 2.44
5582 6656 7.247456 TGGAAACCAGAAAACCTTACTTTTT 57.753 32.000 0.00 0.00 0.00 1.94
5583 6657 6.860790 TGGAAACCAGAAAACCTTACTTTT 57.139 33.333 0.00 0.00 0.00 2.27
5584 6658 6.636705 GTTGGAAACCAGAAAACCTTACTTT 58.363 36.000 0.00 0.00 42.21 2.66
5585 6659 6.216801 GTTGGAAACCAGAAAACCTTACTT 57.783 37.500 0.00 0.00 42.21 2.24
5586 6660 5.847111 GTTGGAAACCAGAAAACCTTACT 57.153 39.130 0.00 0.00 42.21 2.24


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

AutoCloner maintained by Alex Coulton.