Multiple sequence alignment - TraesCS3D01G345900

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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 TraesCS3D01G345900 chr3D 100.000 5338 0 0 1 5338 457236696 457231359 0.000000e+00 9858.0
1 TraesCS3D01G345900 chr3D 87.879 165 19 1 307 470 500128852 500129016 5.460000e-45 193.0
2 TraesCS3D01G345900 chr3D 87.349 166 18 3 310 473 87926000 87926164 2.540000e-43 187.0
3 TraesCS3D01G345900 chr3B 94.057 3029 116 23 593 3598 604275072 604272085 0.000000e+00 4538.0
4 TraesCS3D01G345900 chr3B 90.988 1043 45 25 3639 4635 604272074 604271035 0.000000e+00 1360.0
5 TraesCS3D01G345900 chr3B 95.853 627 26 0 4712 5338 604271063 604270437 0.000000e+00 1014.0
6 TraesCS3D01G345900 chr3B 84.118 170 19 6 1 165 604275358 604275192 1.990000e-34 158.0
7 TraesCS3D01G345900 chr3A 92.567 2731 106 51 1972 4635 600026532 600023832 0.000000e+00 3829.0
8 TraesCS3D01G345900 chr3A 93.783 1528 77 11 458 1974 600028164 600026644 0.000000e+00 2279.0
9 TraesCS3D01G345900 chr3A 95.246 631 29 1 4709 5338 600023864 600023234 0.000000e+00 998.0
10 TraesCS3D01G345900 chr3A 88.150 481 43 7 1 469 600028724 600028246 1.300000e-155 560.0
11 TraesCS3D01G345900 chr3A 93.103 58 3 1 4637 4693 600024064 600024007 3.430000e-12 84.2
12 TraesCS3D01G345900 chr2A 89.103 156 16 1 319 473 135473380 135473225 5.460000e-45 193.0
13 TraesCS3D01G345900 chr1A 89.542 153 15 1 319 470 586049385 586049233 5.460000e-45 193.0
14 TraesCS3D01G345900 chr1A 85.227 176 21 5 310 483 10142154 10141982 5.490000e-40 176.0
15 TraesCS3D01G345900 chr7A 87.117 163 19 2 309 470 719012600 719012439 3.280000e-42 183.0
16 TraesCS3D01G345900 chr2B 86.747 166 20 2 307 470 331238588 331238753 3.280000e-42 183.0
17 TraesCS3D01G345900 chr4B 85.632 174 20 5 302 473 124750126 124750296 1.530000e-40 178.0
18 TraesCS3D01G345900 chr5D 87.342 158 12 6 5181 5338 524596978 524597127 1.980000e-39 174.0
19 TraesCS3D01G345900 chr4A 100.000 28 0 0 553 580 521895209 521895236 1.000000e-02 52.8


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 TraesCS3D01G345900 chr3D 457231359 457236696 5337 True 9858.00 9858 100.0000 1 5338 1 chr3D.!!$R1 5337
1 TraesCS3D01G345900 chr3B 604270437 604275358 4921 True 1767.50 4538 91.2540 1 5338 4 chr3B.!!$R1 5337
2 TraesCS3D01G345900 chr3A 600023234 600028724 5490 True 1550.04 3829 92.5698 1 5338 5 chr3A.!!$R1 5337

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
282 290 0.784778 GAAAGAAGCGTCGTCACCTG 59.215 55.000 0.0 0.0 0.00 4.00 F
2057 2291 0.875059 GGGAAACTTCTTGTCGCTGG 59.125 55.000 0.0 0.0 0.00 4.85 F
2062 2296 1.583054 ACTTCTTGTCGCTGGTGTTC 58.417 50.000 0.0 0.0 0.00 3.18 F
2944 3194 1.477700 ACATTGTGTTGCTGTTGCTGT 59.522 42.857 0.0 0.0 40.48 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 2322 1.656652 ATCACGCTGCCAGTATTGAC 58.343 50.0 0.00 0.0 0.0 3.18 R
2928 3178 0.458197 GCAACAGCAACAGCAACACA 60.458 50.0 0.00 0.0 0.0 3.72 R
3666 3935 0.958091 TTCCCTGAAATTGCACACCG 59.042 50.0 0.00 0.0 0.0 4.94 R
4568 4882 0.179001 TCACGTCCAGAGTCCAGACA 60.179 55.0 9.98 0.0 0.0 3.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.353030 GCACGTGCGGGTGAAAAC 60.353 61.111 26.77 0.00 40.38 2.43
34 35 4.546570 GGTGAAAACTTATGAAGGCACAC 58.453 43.478 0.00 0.00 0.00 3.82
36 37 5.278957 GGTGAAAACTTATGAAGGCACACAT 60.279 40.000 0.00 0.00 0.00 3.21
96 100 9.231297 CTCTATTTCTATGAACACCTCCAAAAA 57.769 33.333 0.00 0.00 0.00 1.94
221 229 2.493278 CCTGATGGGTTGATTTCACCAC 59.507 50.000 0.00 0.00 35.52 4.16
282 290 0.784778 GAAAGAAGCGTCGTCACCTG 59.215 55.000 0.00 0.00 0.00 4.00
333 347 7.871463 ACTACTCCGCATGTTCCTAAATATAAC 59.129 37.037 0.00 0.00 0.00 1.89
337 351 6.042781 TCCGCATGTTCCTAAATATAACTCCT 59.957 38.462 0.00 0.00 0.00 3.69
360 374 9.621239 TCCTTTTAGAGATTCCATATGGACTAT 57.379 33.333 24.47 16.36 45.39 2.12
383 397 9.638300 CTATATGTAAAGCAAAACGAGTGAATC 57.362 33.333 0.00 0.00 0.00 2.52
608 716 8.553085 TGGAGAAAGTATCTTAATCCTCATGA 57.447 34.615 0.00 0.00 38.96 3.07
660 768 6.761117 ACTTTTGAAATCAACGAAACTTTGC 58.239 32.000 0.00 0.00 35.28 3.68
661 769 5.710613 TTTGAAATCAACGAAACTTTGCC 57.289 34.783 0.00 0.00 35.28 4.52
680 788 1.070175 CCGAGCAAACGAAATCAACGT 60.070 47.619 0.00 0.00 45.89 3.99
701 809 6.349300 ACGTAGCCTGATTGACTTGATTAAT 58.651 36.000 0.00 0.00 0.00 1.40
702 810 6.480320 ACGTAGCCTGATTGACTTGATTAATC 59.520 38.462 8.60 8.60 0.00 1.75
903 1015 2.109126 CAGCTCGCCAGTTTAGCCC 61.109 63.158 0.00 0.00 36.92 5.19
1329 1445 2.829003 CGCTACCCGCTCCTCTCA 60.829 66.667 0.00 0.00 36.13 3.27
1495 1612 3.366052 TTGGGTTCCTTGGAGCTATTC 57.634 47.619 3.65 0.00 0.00 1.75
1497 1614 1.475213 GGGTTCCTTGGAGCTATTCGG 60.475 57.143 3.65 0.00 0.00 4.30
1503 1620 2.093447 CCTTGGAGCTATTCGGTGTTCT 60.093 50.000 0.00 0.00 0.00 3.01
1505 1622 1.291132 GGAGCTATTCGGTGTTCTGC 58.709 55.000 0.00 0.00 0.00 4.26
1506 1623 0.924090 GAGCTATTCGGTGTTCTGCG 59.076 55.000 0.00 0.00 0.00 5.18
1533 1650 4.240323 GGGGGATAGATACTTTGGAAGGA 58.760 47.826 0.00 0.00 0.00 3.36
1536 1653 5.012251 GGGGATAGATACTTTGGAAGGAGAC 59.988 48.000 0.00 0.00 0.00 3.36
1548 1665 3.206964 GGAAGGAGACGGATTCCATTTC 58.793 50.000 3.09 0.00 41.78 2.17
1609 1726 1.671850 GCCGTCCATTTCTGTCTTCGA 60.672 52.381 0.00 0.00 0.00 3.71
1664 1781 4.321230 GGTTTGAGCTAATTGGGTGTTCTG 60.321 45.833 0.00 0.00 0.00 3.02
1729 1846 4.831107 TGCTGCTGAATTAGTATGTGTGA 58.169 39.130 0.00 0.00 0.00 3.58
1755 1872 2.046285 CAGGCCATTTCGGGGTGTC 61.046 63.158 5.01 0.00 34.06 3.67
1766 1883 1.687014 GGGGTGTCGGGTGGTAAAT 59.313 57.895 0.00 0.00 0.00 1.40
1771 1888 3.370739 GGGTGTCGGGTGGTAAATAATCA 60.371 47.826 0.00 0.00 0.00 2.57
1788 1905 1.452110 TCACCGTCTCCGATTACGAA 58.548 50.000 5.28 0.00 41.55 3.85
1852 1969 3.072211 GTTGGTGTTAGTAGCCACTTCC 58.928 50.000 0.00 0.00 36.14 3.46
1925 2042 2.180276 TCTCTAGACAAGGGCTGGTTC 58.820 52.381 0.00 0.00 0.00 3.62
1929 2046 1.140312 AGACAAGGGCTGGTTCAGAA 58.860 50.000 0.00 0.00 32.44 3.02
2057 2291 0.875059 GGGAAACTTCTTGTCGCTGG 59.125 55.000 0.00 0.00 0.00 4.85
2062 2296 1.583054 ACTTCTTGTCGCTGGTGTTC 58.417 50.000 0.00 0.00 0.00 3.18
2081 2315 7.038729 TGGTGTTCTTTGAGAAGATATCTGAGT 60.039 37.037 5.86 0.00 41.35 3.41
2088 2322 2.890311 AGAAGATATCTGAGTCTGCCCG 59.110 50.000 5.86 0.00 36.88 6.13
2139 2373 9.844790 ATGAATTATGATATTACGCATTTGGTG 57.155 29.630 0.00 0.00 0.00 4.17
2328 2563 3.681897 AGTCAGCTTTAACGATTCTGCTG 59.318 43.478 14.53 14.53 46.21 4.41
2364 2599 9.551734 TCATTATCTCTGAACAAATATGGACTG 57.448 33.333 0.00 0.00 0.00 3.51
2509 2746 6.765989 TGCATATCAACTGATAAGGTACCAAC 59.234 38.462 15.94 2.77 40.09 3.77
2626 2864 6.970484 ACAAAAGGTGAATCATGTTACTGTC 58.030 36.000 0.00 0.00 0.00 3.51
2701 2939 2.102588 TCTTATCCTCTTTACAGCGGGC 59.897 50.000 0.00 0.00 0.00 6.13
2742 2986 8.672815 GGCTGCTAATATTTTATTCATCTCTCC 58.327 37.037 0.00 0.00 0.00 3.71
2855 3099 4.755123 CACAATAGGTTCAAACTCCGTCTT 59.245 41.667 0.00 0.00 0.00 3.01
2912 3162 5.131142 ACAGAAACTTCCCCATAGGATACAG 59.869 44.000 0.00 0.00 46.94 2.74
2928 3178 9.920946 ATAGGATACAGGTGATTTTGTAACATT 57.079 29.630 0.00 0.00 41.41 2.71
2935 3185 5.752955 AGGTGATTTTGTAACATTGTGTTGC 59.247 36.000 5.64 4.94 41.30 4.17
2936 3186 5.752955 GGTGATTTTGTAACATTGTGTTGCT 59.247 36.000 11.20 0.00 42.31 3.91
2937 3187 6.292274 GGTGATTTTGTAACATTGTGTTGCTG 60.292 38.462 11.20 0.00 42.31 4.41
2938 3188 6.255453 GTGATTTTGTAACATTGTGTTGCTGT 59.745 34.615 11.20 0.00 42.31 4.40
2939 3189 6.815641 TGATTTTGTAACATTGTGTTGCTGTT 59.184 30.769 11.20 0.00 42.31 3.16
2940 3190 6.400579 TTTTGTAACATTGTGTTGCTGTTG 57.599 33.333 11.20 0.00 42.31 3.33
2941 3191 3.443037 TGTAACATTGTGTTGCTGTTGC 58.557 40.909 11.20 0.00 42.31 4.17
2942 3192 2.965572 AACATTGTGTTGCTGTTGCT 57.034 40.000 0.00 0.00 39.45 3.91
2943 3193 2.212869 ACATTGTGTTGCTGTTGCTG 57.787 45.000 0.00 0.00 40.48 4.41
2944 3194 1.477700 ACATTGTGTTGCTGTTGCTGT 59.522 42.857 0.00 0.00 40.48 4.40
2945 3195 2.094078 ACATTGTGTTGCTGTTGCTGTT 60.094 40.909 0.00 0.00 40.48 3.16
2946 3196 1.993542 TTGTGTTGCTGTTGCTGTTG 58.006 45.000 0.00 0.00 40.48 3.33
2987 3237 6.624352 TGATAGCCATCATTACTTTGCTTC 57.376 37.500 0.00 0.00 36.22 3.86
3167 3417 6.041979 ACACAATCCTTTCTTTTAAGGCATGT 59.958 34.615 0.00 0.00 43.62 3.21
3238 3489 3.308053 CGAAGATGGTAATCTGCAGTGTG 59.692 47.826 14.67 0.00 42.60 3.82
3239 3490 4.507710 GAAGATGGTAATCTGCAGTGTGA 58.492 43.478 14.67 0.00 42.60 3.58
3240 3491 4.134379 AGATGGTAATCTGCAGTGTGAG 57.866 45.455 14.67 0.00 41.80 3.51
3241 3492 3.771479 AGATGGTAATCTGCAGTGTGAGA 59.229 43.478 14.67 0.00 41.80 3.27
3242 3493 3.319137 TGGTAATCTGCAGTGTGAGAC 57.681 47.619 14.67 4.70 0.00 3.36
3271 3522 3.693085 AGTGTAAGGATTAGAGCGACGAA 59.307 43.478 0.00 0.00 0.00 3.85
3481 3734 1.749634 AGCTCATCAATTCTGCTTGCC 59.250 47.619 0.00 0.00 0.00 4.52
3599 3868 3.742433 AGACTGGCTGATAGTGCATAC 57.258 47.619 0.00 0.00 0.00 2.39
3607 3876 7.061566 TGGCTGATAGTGCATACAATACTTA 57.938 36.000 0.00 0.00 0.00 2.24
3627 3896 9.709387 ATACTTATTTGCCAATAACCTAAACCT 57.291 29.630 0.00 0.00 32.41 3.50
3628 3897 8.430573 ACTTATTTGCCAATAACCTAAACCTT 57.569 30.769 0.00 0.00 32.41 3.50
3642 3911 3.396260 AAACCTTTACAGTAGCGAGCA 57.604 42.857 0.00 0.00 0.00 4.26
3664 3933 6.376299 AGCAAGTTCATTTTCTGATATCAGCA 59.624 34.615 25.27 14.19 43.46 4.41
3666 3935 6.374565 AGTTCATTTTCTGATATCAGCAGC 57.625 37.500 25.27 10.48 43.46 5.25
3672 3941 1.202452 TCTGATATCAGCAGCGGTGTG 60.202 52.381 25.27 12.87 43.46 3.82
3796 4065 2.101415 GCAGCCTTTGAATGGAATACCC 59.899 50.000 0.70 0.00 34.81 3.69
4341 4618 6.711277 TCTAATGCACAGTTCAAGGTCTATT 58.289 36.000 0.00 0.00 0.00 1.73
4342 4619 7.847096 TCTAATGCACAGTTCAAGGTCTATTA 58.153 34.615 0.00 0.00 0.00 0.98
4343 4620 8.486210 TCTAATGCACAGTTCAAGGTCTATTAT 58.514 33.333 0.00 0.00 0.00 1.28
4344 4621 7.559590 AATGCACAGTTCAAGGTCTATTATC 57.440 36.000 0.00 0.00 0.00 1.75
4451 4738 6.368791 GTCCAGGGAATTTTAACAGCATTTTC 59.631 38.462 0.00 0.00 0.00 2.29
4461 4748 2.327568 ACAGCATTTTCGCCAAAATCG 58.672 42.857 0.00 0.00 39.75 3.34
4503 4790 8.600449 ACTATCTGATATTTAAGCTTGCTGAC 57.400 34.615 9.86 0.00 0.00 3.51
4504 4791 8.206867 ACTATCTGATATTTAAGCTTGCTGACA 58.793 33.333 9.86 1.90 0.00 3.58
4505 4792 9.217278 CTATCTGATATTTAAGCTTGCTGACAT 57.783 33.333 9.86 0.00 0.00 3.06
4506 4793 7.870509 TCTGATATTTAAGCTTGCTGACATT 57.129 32.000 9.86 0.00 0.00 2.71
4509 4796 9.443283 CTGATATTTAAGCTTGCTGACATTTAC 57.557 33.333 9.86 0.00 0.00 2.01
4510 4797 8.955388 TGATATTTAAGCTTGCTGACATTTACA 58.045 29.630 9.86 0.00 0.00 2.41
4513 4800 6.633500 TTAAGCTTGCTGACATTTACAAGT 57.367 33.333 9.86 0.00 41.22 3.16
4516 4803 4.023707 AGCTTGCTGACATTTACAAGTCAC 60.024 41.667 0.00 0.00 41.22 3.67
4518 4805 5.733091 GCTTGCTGACATTTACAAGTCACAA 60.733 40.000 0.00 0.00 41.22 3.33
4519 4806 5.422666 TGCTGACATTTACAAGTCACAAG 57.577 39.130 0.00 0.00 39.65 3.16
4521 4808 5.007626 TGCTGACATTTACAAGTCACAAGAC 59.992 40.000 0.00 0.00 45.31 3.01
4522 4809 5.560953 GCTGACATTTACAAGTCACAAGACC 60.561 44.000 0.00 0.00 46.15 3.85
4523 4810 5.680619 TGACATTTACAAGTCACAAGACCT 58.319 37.500 0.00 0.00 46.15 3.85
4524 4811 5.527214 TGACATTTACAAGTCACAAGACCTG 59.473 40.000 0.00 0.00 46.15 4.00
4525 4812 4.821805 ACATTTACAAGTCACAAGACCTGG 59.178 41.667 0.00 0.00 46.15 4.45
4526 4813 4.764050 TTTACAAGTCACAAGACCTGGA 57.236 40.909 0.00 0.00 46.15 3.86
4541 4855 2.827921 ACCTGGATTTTAAGCTTGCTGG 59.172 45.455 9.86 3.65 0.00 4.85
4547 4861 3.317603 TTTTAAGCTTGCTGGCATTCC 57.682 42.857 9.86 0.00 34.17 3.01
4568 4882 5.319453 TCCAATTTTGTCAGAATCTCTGCT 58.681 37.500 0.00 0.00 43.95 4.24
4570 4884 5.048224 CCAATTTTGTCAGAATCTCTGCTGT 60.048 40.000 0.00 0.00 43.95 4.40
4574 4888 2.233186 TGTCAGAATCTCTGCTGTCTGG 59.767 50.000 8.45 0.00 43.95 3.86
4584 4898 1.214062 GCTGTCTGGACTCTGGACG 59.786 63.158 2.38 0.00 33.21 4.79
4588 4902 1.178276 GTCTGGACTCTGGACGTGAT 58.822 55.000 0.00 0.00 0.00 3.06
4590 4904 2.753452 GTCTGGACTCTGGACGTGATAA 59.247 50.000 0.00 0.00 0.00 1.75
4595 4909 3.018149 GACTCTGGACGTGATAAGAGGT 58.982 50.000 14.40 4.40 40.41 3.85
4609 4923 7.415318 CGTGATAAGAGGTACTGAAGCTTCTTA 60.415 40.741 26.09 14.14 41.55 2.10
4610 4924 8.417884 GTGATAAGAGGTACTGAAGCTTCTTAT 58.582 37.037 26.09 17.84 41.55 1.73
4611 4925 8.982723 TGATAAGAGGTACTGAAGCTTCTTATT 58.017 33.333 26.09 10.72 41.55 1.40
4612 4926 9.825109 GATAAGAGGTACTGAAGCTTCTTATTT 57.175 33.333 26.09 12.12 41.55 1.40
4613 4927 7.913674 AAGAGGTACTGAAGCTTCTTATTTG 57.086 36.000 26.09 11.85 41.55 2.32
4614 4928 7.246171 AGAGGTACTGAAGCTTCTTATTTGA 57.754 36.000 26.09 4.18 41.55 2.69
4615 4929 7.327214 AGAGGTACTGAAGCTTCTTATTTGAG 58.673 38.462 26.09 15.61 41.55 3.02
4616 4930 7.010339 AGGTACTGAAGCTTCTTATTTGAGT 57.990 36.000 26.09 20.01 37.18 3.41
4617 4931 7.454225 AGGTACTGAAGCTTCTTATTTGAGTT 58.546 34.615 26.09 3.34 37.18 3.01
4618 4932 7.939588 AGGTACTGAAGCTTCTTATTTGAGTTT 59.060 33.333 26.09 7.06 37.18 2.66
4619 4933 8.231161 GGTACTGAAGCTTCTTATTTGAGTTTC 58.769 37.037 26.09 14.38 0.00 2.78
4620 4934 8.994170 GTACTGAAGCTTCTTATTTGAGTTTCT 58.006 33.333 26.09 1.71 0.00 2.52
4621 4935 7.869800 ACTGAAGCTTCTTATTTGAGTTTCTG 58.130 34.615 26.09 3.15 0.00 3.02
4622 4936 7.040823 ACTGAAGCTTCTTATTTGAGTTTCTGG 60.041 37.037 26.09 0.00 0.00 3.86
4623 4937 6.998074 TGAAGCTTCTTATTTGAGTTTCTGGA 59.002 34.615 26.09 0.00 0.00 3.86
4624 4938 7.667219 TGAAGCTTCTTATTTGAGTTTCTGGAT 59.333 33.333 26.09 0.00 0.00 3.41
4625 4939 7.388460 AGCTTCTTATTTGAGTTTCTGGATG 57.612 36.000 0.00 0.00 0.00 3.51
4626 4940 6.032717 GCTTCTTATTTGAGTTTCTGGATGC 58.967 40.000 0.00 0.00 0.00 3.91
4627 4941 6.349611 GCTTCTTATTTGAGTTTCTGGATGCA 60.350 38.462 0.00 0.00 0.00 3.96
4628 4942 7.523293 TTCTTATTTGAGTTTCTGGATGCAA 57.477 32.000 0.00 0.00 0.00 4.08
4629 4943 7.523293 TCTTATTTGAGTTTCTGGATGCAAA 57.477 32.000 0.00 0.00 0.00 3.68
4630 4944 7.950512 TCTTATTTGAGTTTCTGGATGCAAAA 58.049 30.769 0.00 0.00 0.00 2.44
4631 4945 8.420222 TCTTATTTGAGTTTCTGGATGCAAAAA 58.580 29.630 0.00 0.00 0.00 1.94
4632 4946 9.211485 CTTATTTGAGTTTCTGGATGCAAAAAT 57.789 29.630 0.00 0.00 0.00 1.82
4633 4947 7.662604 ATTTGAGTTTCTGGATGCAAAAATC 57.337 32.000 12.02 12.02 0.00 2.17
4634 4948 4.797471 TGAGTTTCTGGATGCAAAAATCG 58.203 39.130 13.18 0.00 31.56 3.34
4635 4949 4.518590 TGAGTTTCTGGATGCAAAAATCGA 59.481 37.500 13.18 0.00 31.56 3.59
4636 4950 5.051891 AGTTTCTGGATGCAAAAATCGAG 57.948 39.130 0.00 0.00 34.65 4.04
4637 4951 4.082571 AGTTTCTGGATGCAAAAATCGAGG 60.083 41.667 0.00 0.00 34.26 4.63
4638 4952 3.348647 TCTGGATGCAAAAATCGAGGA 57.651 42.857 0.00 0.00 34.26 3.71
4639 4953 3.684908 TCTGGATGCAAAAATCGAGGAA 58.315 40.909 0.00 0.00 34.26 3.36
4640 4954 4.272489 TCTGGATGCAAAAATCGAGGAAT 58.728 39.130 0.00 0.00 34.26 3.01
4641 4955 4.096833 TCTGGATGCAAAAATCGAGGAATG 59.903 41.667 0.00 0.00 34.26 2.67
4642 4956 3.763360 TGGATGCAAAAATCGAGGAATGT 59.237 39.130 0.00 0.00 0.00 2.71
4643 4957 4.220382 TGGATGCAAAAATCGAGGAATGTT 59.780 37.500 0.00 0.00 0.00 2.71
4644 4958 5.417266 TGGATGCAAAAATCGAGGAATGTTA 59.583 36.000 0.00 0.00 0.00 2.41
4645 4959 5.743872 GGATGCAAAAATCGAGGAATGTTAC 59.256 40.000 0.00 0.00 0.00 2.50
4646 4960 5.054390 TGCAAAAATCGAGGAATGTTACC 57.946 39.130 0.00 0.00 0.00 2.85
4647 4961 4.520874 TGCAAAAATCGAGGAATGTTACCA 59.479 37.500 0.00 0.00 0.00 3.25
4648 4962 5.095490 GCAAAAATCGAGGAATGTTACCAG 58.905 41.667 0.00 0.00 0.00 4.00
4649 4963 4.965119 AAAATCGAGGAATGTTACCAGC 57.035 40.909 0.00 0.00 0.00 4.85
4650 4964 3.627395 AATCGAGGAATGTTACCAGCA 57.373 42.857 0.00 0.00 0.00 4.41
4651 4965 3.845781 ATCGAGGAATGTTACCAGCAT 57.154 42.857 0.00 0.00 0.00 3.79
4652 4966 3.627395 TCGAGGAATGTTACCAGCATT 57.373 42.857 0.00 0.00 39.04 3.56
4653 4967 3.950397 TCGAGGAATGTTACCAGCATTT 58.050 40.909 0.00 0.00 36.77 2.32
4654 4968 4.331968 TCGAGGAATGTTACCAGCATTTT 58.668 39.130 0.00 0.00 36.77 1.82
4655 4969 5.492895 TCGAGGAATGTTACCAGCATTTTA 58.507 37.500 0.00 0.00 36.77 1.52
4656 4970 5.353123 TCGAGGAATGTTACCAGCATTTTAC 59.647 40.000 0.00 0.00 36.77 2.01
4657 4971 5.448632 CGAGGAATGTTACCAGCATTTTACC 60.449 44.000 0.00 0.00 36.77 2.85
4658 4972 5.329399 AGGAATGTTACCAGCATTTTACCA 58.671 37.500 0.00 0.00 36.77 3.25
4659 4973 5.777732 AGGAATGTTACCAGCATTTTACCAA 59.222 36.000 0.00 0.00 36.77 3.67
4660 4974 6.268847 AGGAATGTTACCAGCATTTTACCAAA 59.731 34.615 0.00 0.00 36.77 3.28
4661 4975 6.931840 GGAATGTTACCAGCATTTTACCAAAA 59.068 34.615 0.00 0.00 36.77 2.44
4662 4976 7.606073 GGAATGTTACCAGCATTTTACCAAAAT 59.394 33.333 0.00 0.00 41.57 1.82
4663 4977 8.546597 AATGTTACCAGCATTTTACCAAAATC 57.453 30.769 0.00 0.00 38.97 2.17
4664 4978 7.055667 TGTTACCAGCATTTTACCAAAATCA 57.944 32.000 0.00 0.00 38.97 2.57
4665 4979 7.675062 TGTTACCAGCATTTTACCAAAATCAT 58.325 30.769 0.00 0.00 38.97 2.45
4666 4980 7.601886 TGTTACCAGCATTTTACCAAAATCATG 59.398 33.333 0.00 0.00 38.97 3.07
4667 4981 6.112927 ACCAGCATTTTACCAAAATCATGT 57.887 33.333 0.00 0.00 38.97 3.21
4668 4982 5.933463 ACCAGCATTTTACCAAAATCATGTG 59.067 36.000 0.00 0.00 38.97 3.21
4669 4983 5.933463 CCAGCATTTTACCAAAATCATGTGT 59.067 36.000 0.00 0.00 38.97 3.72
4670 4984 6.427547 CCAGCATTTTACCAAAATCATGTGTT 59.572 34.615 0.00 0.00 38.97 3.32
4671 4985 7.041235 CCAGCATTTTACCAAAATCATGTGTTT 60.041 33.333 0.00 0.00 38.97 2.83
4672 4986 8.986847 CAGCATTTTACCAAAATCATGTGTTTA 58.013 29.630 0.00 0.00 38.97 2.01
4673 4987 9.723601 AGCATTTTACCAAAATCATGTGTTTAT 57.276 25.926 0.00 0.00 38.97 1.40
4687 5001 9.632638 ATCATGTGTTTATAAATCTAACCAGCT 57.367 29.630 0.31 0.00 0.00 4.24
4688 5002 8.892723 TCATGTGTTTATAAATCTAACCAGCTG 58.107 33.333 6.78 6.78 0.00 4.24
4689 5003 8.892723 CATGTGTTTATAAATCTAACCAGCTGA 58.107 33.333 17.39 0.00 0.00 4.26
4690 5004 9.632638 ATGTGTTTATAAATCTAACCAGCTGAT 57.367 29.630 17.39 6.23 0.00 2.90
4707 5021 9.935241 ACCAGCTGATATAGTGATATTTACAAG 57.065 33.333 17.39 0.00 0.00 3.16
4708 5022 8.877779 CCAGCTGATATAGTGATATTTACAAGC 58.122 37.037 17.39 0.00 0.00 4.01
4709 5023 9.650539 CAGCTGATATAGTGATATTTACAAGCT 57.349 33.333 8.42 0.00 0.00 3.74
4739 5053 2.478894 GAGTTTCTGGACGCGAAAATCA 59.521 45.455 15.93 2.16 42.06 2.57
4740 5054 3.074412 AGTTTCTGGACGCGAAAATCAT 58.926 40.909 15.93 0.00 32.71 2.45
4778 5092 0.829990 TGATAATCTGTGCCGCCTCA 59.170 50.000 0.00 0.00 0.00 3.86
4790 5104 1.369625 CCGCCTCATCAAACCTGTAC 58.630 55.000 0.00 0.00 0.00 2.90
4855 5169 2.520260 GATGCTGGGGTCATGGCC 60.520 66.667 8.19 8.19 0.00 5.36
5027 5341 1.082117 CGTAGGCGTTCATGGTGACC 61.082 60.000 0.00 0.00 0.00 4.02
5093 5407 1.961277 GAACACCTCCACCACGCTG 60.961 63.158 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.037446 TGTGTGCCTTCATAAGTTTTCACC 59.963 41.667 0.00 0.00 0.00 4.02
16 17 5.789643 ACATGTGTGCCTTCATAAGTTTT 57.210 34.783 0.00 0.00 0.00 2.43
20 21 6.291377 AGGTATACATGTGTGCCTTCATAAG 58.709 40.000 23.48 0.00 0.00 1.73
34 35 5.463392 GCGTGCATATGGATAGGTATACATG 59.537 44.000 4.56 0.00 37.77 3.21
36 37 4.464597 TGCGTGCATATGGATAGGTATACA 59.535 41.667 4.56 0.00 0.00 2.29
122 126 8.564574 CGAGACTTCTCTATGCTATCTTTTAGT 58.435 37.037 4.76 0.00 40.75 2.24
123 127 8.779303 TCGAGACTTCTCTATGCTATCTTTTAG 58.221 37.037 4.76 0.00 40.75 1.85
124 128 8.678593 TCGAGACTTCTCTATGCTATCTTTTA 57.321 34.615 4.76 0.00 40.75 1.52
128 136 8.856153 TTATTCGAGACTTCTCTATGCTATCT 57.144 34.615 4.76 0.00 40.75 1.98
135 143 7.747155 TCGGATTTATTCGAGACTTCTCTAT 57.253 36.000 4.76 1.40 40.75 1.98
175 183 7.148306 GGTTTGAAGTGTTAGACTTGACAAAGA 60.148 37.037 0.00 0.00 45.48 2.52
216 224 3.146104 AGGGTCAGATTTCTTGTGGTG 57.854 47.619 0.00 0.00 0.00 4.17
221 229 5.238214 GCATAGCTTAGGGTCAGATTTCTTG 59.762 44.000 0.00 0.00 0.00 3.02
344 358 9.890629 TGCTTTACATATAGTCCATATGGAATC 57.109 33.333 27.07 15.37 45.76 2.52
353 367 7.064134 CACTCGTTTTGCTTTACATATAGTCCA 59.936 37.037 0.00 0.00 0.00 4.02
354 368 7.277098 TCACTCGTTTTGCTTTACATATAGTCC 59.723 37.037 0.00 0.00 0.00 3.85
355 369 8.181487 TCACTCGTTTTGCTTTACATATAGTC 57.819 34.615 0.00 0.00 0.00 2.59
360 374 7.667043 AGATTCACTCGTTTTGCTTTACATA 57.333 32.000 0.00 0.00 0.00 2.29
364 378 6.704493 AGTGTAGATTCACTCGTTTTGCTTTA 59.296 34.615 0.00 0.00 44.07 1.85
579 687 7.016661 TGAGGATTAAGATACTTTCTCCATCCC 59.983 40.741 0.00 0.00 40.67 3.85
580 688 7.967908 TGAGGATTAAGATACTTTCTCCATCC 58.032 38.462 0.00 0.00 40.38 3.51
581 689 9.434420 CATGAGGATTAAGATACTTTCTCCATC 57.566 37.037 0.00 0.00 31.78 3.51
583 691 8.553085 TCATGAGGATTAAGATACTTTCTCCA 57.447 34.615 0.00 0.00 31.78 3.86
660 768 1.070175 ACGTTGATTTCGTTTGCTCGG 60.070 47.619 0.00 0.00 38.38 4.63
661 769 2.294479 ACGTTGATTTCGTTTGCTCG 57.706 45.000 0.00 0.00 38.38 5.03
680 788 7.568349 ACAGATTAATCAAGTCAATCAGGCTA 58.432 34.615 17.56 0.00 32.27 3.93
701 809 3.138304 GTGGTGCAGTAATGTTGACAGA 58.862 45.455 0.00 0.00 0.00 3.41
702 810 2.226437 GGTGGTGCAGTAATGTTGACAG 59.774 50.000 0.00 0.00 0.00 3.51
816 928 3.071167 GGTCACCAGTAGAAGTGGAGTTT 59.929 47.826 7.77 0.00 41.28 2.66
817 929 2.633481 GGTCACCAGTAGAAGTGGAGTT 59.367 50.000 7.77 0.00 41.28 3.01
821 933 2.632996 TCTTGGTCACCAGTAGAAGTGG 59.367 50.000 0.00 0.00 44.34 4.00
822 934 3.574396 TCTCTTGGTCACCAGTAGAAGTG 59.426 47.826 7.57 0.00 33.81 3.16
1512 1629 5.012251 GTCTCCTTCCAAAGTATCTATCCCC 59.988 48.000 0.00 0.00 0.00 4.81
1514 1631 5.279056 CCGTCTCCTTCCAAAGTATCTATCC 60.279 48.000 0.00 0.00 0.00 2.59
1515 1632 5.535406 TCCGTCTCCTTCCAAAGTATCTATC 59.465 44.000 0.00 0.00 0.00 2.08
1548 1665 3.497332 TCCTACATCCACTTCCTATCGG 58.503 50.000 0.00 0.00 0.00 4.18
1609 1726 3.635591 CCTAATCCCAAATTCACCAGCT 58.364 45.455 0.00 0.00 0.00 4.24
1664 1781 5.183140 TCAAAGCTAACTGAATTAACCAGGC 59.817 40.000 10.38 5.46 36.03 4.85
1729 1846 2.026822 CCCGAAATGGCCTGCTCTATAT 60.027 50.000 3.32 0.00 35.87 0.86
1755 1872 2.867975 GACGGTGATTATTTACCACCCG 59.132 50.000 0.00 0.00 45.58 5.28
1788 1905 3.741388 GCAACACAAGTGACTCTAGGTGT 60.741 47.826 7.28 8.34 42.50 4.16
1925 2042 5.711976 ACACCAGGATCCTGTAAATTTTCTG 59.288 40.000 34.49 19.94 42.15 3.02
1929 2046 4.220602 GCAACACCAGGATCCTGTAAATTT 59.779 41.667 34.49 19.32 42.15 1.82
1980 2211 7.229306 TCAGTGATCAGAAACAATATATTGCCC 59.771 37.037 22.66 12.96 41.38 5.36
2057 2291 8.250332 AGACTCAGATATCTTCTCAAAGAACAC 58.750 37.037 1.33 0.00 44.49 3.32
2062 2296 5.984926 GGCAGACTCAGATATCTTCTCAAAG 59.015 44.000 1.33 0.00 29.93 2.77
2088 2322 1.656652 ATCACGCTGCCAGTATTGAC 58.343 50.000 0.00 0.00 0.00 3.18
2139 2373 4.934001 ACACATGCCGATTCATCTATCATC 59.066 41.667 0.00 0.00 0.00 2.92
2514 2751 5.629079 AACACAATAAAGTAGCAAGAGCC 57.371 39.130 0.00 0.00 43.56 4.70
2571 2808 2.906389 ACATCCTTTACAGCTCACCAGA 59.094 45.455 0.00 0.00 0.00 3.86
2572 2809 3.340814 ACATCCTTTACAGCTCACCAG 57.659 47.619 0.00 0.00 0.00 4.00
2626 2864 0.868406 GCAGACCAGGACGTTCAAAG 59.132 55.000 0.00 0.00 0.00 2.77
2701 2939 1.755179 CAGCCACCATACCTTCCAAG 58.245 55.000 0.00 0.00 0.00 3.61
2742 2986 0.536724 TGACTGGGATCATGTGACGG 59.463 55.000 0.00 0.00 0.00 4.79
2855 3099 6.127925 ACGTAGTAACAGTTGATGGACGATAA 60.128 38.462 12.25 0.00 41.94 1.75
2912 3162 5.752955 AGCAACACAATGTTACAAAATCACC 59.247 36.000 0.00 0.00 38.77 4.02
2928 3178 0.458197 GCAACAGCAACAGCAACACA 60.458 50.000 0.00 0.00 0.00 3.72
2935 3185 1.660575 GCAGCAGCAACAGCAACAG 60.661 57.895 0.00 0.00 41.58 3.16
2936 3186 2.122797 AGCAGCAGCAACAGCAACA 61.123 52.632 3.17 0.00 45.49 3.33
2937 3187 1.660575 CAGCAGCAGCAACAGCAAC 60.661 57.895 3.17 0.00 45.49 4.17
2938 3188 2.725641 CAGCAGCAGCAACAGCAA 59.274 55.556 3.17 0.00 45.49 3.91
2939 3189 3.973516 GCAGCAGCAGCAACAGCA 61.974 61.111 4.63 0.00 45.49 4.41
2987 3237 5.931724 TGATTAGTTGTGTACACATCACAGG 59.068 40.000 29.52 0.00 44.71 4.00
3238 3489 8.508883 TCTAATCCTTACACTACTCAAGTCTC 57.491 38.462 0.00 0.00 35.76 3.36
3239 3490 7.067737 GCTCTAATCCTTACACTACTCAAGTCT 59.932 40.741 0.00 0.00 35.76 3.24
3240 3491 7.197703 GCTCTAATCCTTACACTACTCAAGTC 58.802 42.308 0.00 0.00 35.76 3.01
3241 3492 6.183360 CGCTCTAATCCTTACACTACTCAAGT 60.183 42.308 0.00 0.00 39.81 3.16
3242 3493 6.038382 TCGCTCTAATCCTTACACTACTCAAG 59.962 42.308 0.00 0.00 0.00 3.02
3299 3552 1.142748 CAGAGATCCAGGGTCACGC 59.857 63.158 1.43 0.00 0.00 5.34
3363 3616 6.659242 ACAATAAATCCCTTATATTCTGGCCG 59.341 38.462 0.00 0.00 29.59 6.13
3416 3669 1.291877 GGCGCTATAAGGCATGACGG 61.292 60.000 7.64 0.00 0.00 4.79
3607 3876 8.196378 TGTAAAGGTTTAGGTTATTGGCAAAT 57.804 30.769 3.01 0.00 0.00 2.32
3624 3893 2.299297 ACTTGCTCGCTACTGTAAAGGT 59.701 45.455 0.00 0.00 0.00 3.50
3625 3894 2.960819 ACTTGCTCGCTACTGTAAAGG 58.039 47.619 0.00 0.00 0.00 3.11
3627 3896 3.985008 TGAACTTGCTCGCTACTGTAAA 58.015 40.909 0.00 0.00 0.00 2.01
3628 3897 3.653539 TGAACTTGCTCGCTACTGTAA 57.346 42.857 0.00 0.00 0.00 2.41
3642 3911 6.457934 CGCTGCTGATATCAGAAAATGAACTT 60.458 38.462 32.38 0.00 46.59 2.66
3664 3933 1.526575 CCCTGAAATTGCACACCGCT 61.527 55.000 0.00 0.00 43.06 5.52
3666 3935 0.958091 TTCCCTGAAATTGCACACCG 59.042 50.000 0.00 0.00 0.00 4.94
3672 3941 4.036144 GCTCTCTGTATTCCCTGAAATTGC 59.964 45.833 0.00 0.00 0.00 3.56
3796 4065 3.304928 GTCCAGCTGAAAATGGAACACAG 60.305 47.826 17.39 0.00 46.87 3.66
4341 4618 3.135167 TGCAGCCTCTTGACATCATGATA 59.865 43.478 8.15 0.00 31.01 2.15
4342 4619 2.092592 TGCAGCCTCTTGACATCATGAT 60.093 45.455 1.18 1.18 31.01 2.45
4343 4620 1.279846 TGCAGCCTCTTGACATCATGA 59.720 47.619 0.00 0.00 0.00 3.07
4344 4621 1.746470 TGCAGCCTCTTGACATCATG 58.254 50.000 0.00 0.00 0.00 3.07
4388 4669 9.914923 GTTTGTGAATTTTACCAAACATTTCTC 57.085 29.630 8.71 0.00 43.70 2.87
4419 4706 7.189079 TGTTAAAATTCCCTGGACAAGTTTT 57.811 32.000 8.43 5.93 0.00 2.43
4423 4710 4.280677 TGCTGTTAAAATTCCCTGGACAAG 59.719 41.667 0.00 0.00 0.00 3.16
4428 4715 5.348451 CGAAAATGCTGTTAAAATTCCCTGG 59.652 40.000 0.00 0.00 0.00 4.45
4441 4728 2.288152 ACGATTTTGGCGAAAATGCTGT 60.288 40.909 22.08 14.63 41.06 4.40
4451 4738 6.745450 AGATTTATAAACACACGATTTTGGCG 59.255 34.615 0.00 0.00 0.00 5.69
4480 4767 9.565090 AATGTCAGCAAGCTTAAATATCAGATA 57.435 29.630 0.00 0.00 0.00 1.98
4493 4780 4.023707 GTGACTTGTAAATGTCAGCAAGCT 60.024 41.667 1.92 0.00 42.84 3.74
4494 4781 4.222114 GTGACTTGTAAATGTCAGCAAGC 58.778 43.478 1.92 0.00 42.84 4.01
4495 4782 5.422666 TGTGACTTGTAAATGTCAGCAAG 57.577 39.130 1.92 0.00 42.84 4.01
4496 4783 5.588246 TCTTGTGACTTGTAAATGTCAGCAA 59.412 36.000 1.92 8.54 42.84 3.91
4497 4784 5.007626 GTCTTGTGACTTGTAAATGTCAGCA 59.992 40.000 1.92 2.12 42.84 4.41
4500 4787 5.527214 CAGGTCTTGTGACTTGTAAATGTCA 59.473 40.000 0.00 0.00 42.88 3.58
4501 4788 5.049405 CCAGGTCTTGTGACTTGTAAATGTC 60.049 44.000 7.35 0.00 45.31 3.06
4503 4790 5.063204 TCCAGGTCTTGTGACTTGTAAATG 58.937 41.667 7.35 0.00 45.31 2.32
4504 4791 5.304686 TCCAGGTCTTGTGACTTGTAAAT 57.695 39.130 7.35 0.00 45.31 1.40
4505 4792 4.764050 TCCAGGTCTTGTGACTTGTAAA 57.236 40.909 7.35 0.00 45.31 2.01
4506 4793 4.974645 ATCCAGGTCTTGTGACTTGTAA 57.025 40.909 7.35 0.00 45.31 2.41
4509 4796 6.633500 TTAAAATCCAGGTCTTGTGACTTG 57.367 37.500 2.00 2.00 46.03 3.16
4510 4797 5.241728 GCTTAAAATCCAGGTCTTGTGACTT 59.758 40.000 0.00 0.00 42.54 3.01
4513 4800 4.985538 AGCTTAAAATCCAGGTCTTGTGA 58.014 39.130 0.00 0.00 0.00 3.58
4516 4803 4.219288 AGCAAGCTTAAAATCCAGGTCTTG 59.781 41.667 0.00 0.00 34.48 3.02
4518 4805 3.760684 CAGCAAGCTTAAAATCCAGGTCT 59.239 43.478 0.00 0.00 0.00 3.85
4519 4806 3.119352 CCAGCAAGCTTAAAATCCAGGTC 60.119 47.826 0.00 0.00 0.00 3.85
4521 4808 2.417787 GCCAGCAAGCTTAAAATCCAGG 60.418 50.000 0.00 0.00 0.00 4.45
4522 4809 2.231964 TGCCAGCAAGCTTAAAATCCAG 59.768 45.455 0.00 0.00 0.00 3.86
4523 4810 2.246469 TGCCAGCAAGCTTAAAATCCA 58.754 42.857 0.00 0.00 0.00 3.41
4524 4811 3.531934 ATGCCAGCAAGCTTAAAATCC 57.468 42.857 0.00 0.00 0.00 3.01
4525 4812 3.867493 GGAATGCCAGCAAGCTTAAAATC 59.133 43.478 0.00 0.00 0.00 2.17
4526 4813 3.261390 TGGAATGCCAGCAAGCTTAAAAT 59.739 39.130 0.00 0.00 39.92 1.82
4541 4855 6.628185 AGAGATTCTGACAAAATTGGAATGC 58.372 36.000 0.00 0.00 0.00 3.56
4568 4882 0.179001 TCACGTCCAGAGTCCAGACA 60.179 55.000 9.98 0.00 0.00 3.41
4570 4884 2.801077 TATCACGTCCAGAGTCCAGA 57.199 50.000 0.00 0.00 0.00 3.86
4574 4888 3.018149 ACCTCTTATCACGTCCAGAGTC 58.982 50.000 8.33 0.00 32.31 3.36
4584 4898 6.215495 AGAAGCTTCAGTACCTCTTATCAC 57.785 41.667 27.57 0.00 0.00 3.06
4588 4902 8.812972 TCAAATAAGAAGCTTCAGTACCTCTTA 58.187 33.333 27.57 14.73 0.00 2.10
4590 4904 7.038658 ACTCAAATAAGAAGCTTCAGTACCTCT 60.039 37.037 27.57 1.49 0.00 3.69
4595 4909 8.993121 CAGAAACTCAAATAAGAAGCTTCAGTA 58.007 33.333 27.57 18.65 0.00 2.74
4609 4923 6.366877 CGATTTTTGCATCCAGAAACTCAAAT 59.633 34.615 0.00 0.00 29.19 2.32
4610 4924 5.691305 CGATTTTTGCATCCAGAAACTCAAA 59.309 36.000 0.00 0.00 29.19 2.69
4611 4925 5.009510 TCGATTTTTGCATCCAGAAACTCAA 59.990 36.000 0.00 0.00 29.19 3.02
4612 4926 4.518590 TCGATTTTTGCATCCAGAAACTCA 59.481 37.500 0.00 0.00 29.19 3.41
4613 4927 5.046910 TCGATTTTTGCATCCAGAAACTC 57.953 39.130 0.00 0.00 29.19 3.01
4614 4928 4.082571 CCTCGATTTTTGCATCCAGAAACT 60.083 41.667 0.00 0.00 29.19 2.66
4615 4929 4.082787 TCCTCGATTTTTGCATCCAGAAAC 60.083 41.667 0.00 0.00 29.19 2.78
4616 4930 4.078537 TCCTCGATTTTTGCATCCAGAAA 58.921 39.130 0.00 0.00 30.77 2.52
4617 4931 3.684908 TCCTCGATTTTTGCATCCAGAA 58.315 40.909 0.00 0.00 0.00 3.02
4618 4932 3.348647 TCCTCGATTTTTGCATCCAGA 57.651 42.857 0.00 0.00 0.00 3.86
4619 4933 4.142315 ACATTCCTCGATTTTTGCATCCAG 60.142 41.667 0.00 0.00 0.00 3.86
4620 4934 3.763360 ACATTCCTCGATTTTTGCATCCA 59.237 39.130 0.00 0.00 0.00 3.41
4621 4935 4.376340 ACATTCCTCGATTTTTGCATCC 57.624 40.909 0.00 0.00 0.00 3.51
4622 4936 5.743872 GGTAACATTCCTCGATTTTTGCATC 59.256 40.000 0.00 0.00 0.00 3.91
4623 4937 5.184864 TGGTAACATTCCTCGATTTTTGCAT 59.815 36.000 0.00 0.00 46.17 3.96
4624 4938 4.520874 TGGTAACATTCCTCGATTTTTGCA 59.479 37.500 0.00 0.00 46.17 4.08
4625 4939 5.054390 TGGTAACATTCCTCGATTTTTGC 57.946 39.130 0.00 0.00 46.17 3.68
4636 4950 7.606073 ATTTTGGTAAAATGCTGGTAACATTCC 59.394 33.333 0.00 0.00 42.37 3.01
4637 4951 8.546597 ATTTTGGTAAAATGCTGGTAACATTC 57.453 30.769 0.00 0.00 42.37 2.67
4638 4952 8.153550 TGATTTTGGTAAAATGCTGGTAACATT 58.846 29.630 4.42 0.00 43.36 2.71
4639 4953 7.675062 TGATTTTGGTAAAATGCTGGTAACAT 58.325 30.769 4.42 0.00 43.36 2.71
4640 4954 7.055667 TGATTTTGGTAAAATGCTGGTAACA 57.944 32.000 4.42 0.00 42.60 2.41
4641 4955 7.602265 ACATGATTTTGGTAAAATGCTGGTAAC 59.398 33.333 0.00 0.00 40.97 2.50
4642 4956 7.601886 CACATGATTTTGGTAAAATGCTGGTAA 59.398 33.333 0.00 0.00 40.97 2.85
4643 4957 7.095910 CACATGATTTTGGTAAAATGCTGGTA 58.904 34.615 0.00 0.00 40.97 3.25
4644 4958 5.933463 CACATGATTTTGGTAAAATGCTGGT 59.067 36.000 0.00 0.00 40.97 4.00
4645 4959 5.933463 ACACATGATTTTGGTAAAATGCTGG 59.067 36.000 0.00 1.01 40.97 4.85
4646 4960 7.424227 AACACATGATTTTGGTAAAATGCTG 57.576 32.000 0.00 4.71 40.97 4.41
4647 4961 9.723601 ATAAACACATGATTTTGGTAAAATGCT 57.276 25.926 0.00 0.00 40.97 3.79
4661 4975 9.632638 AGCTGGTTAGATTTATAAACACATGAT 57.367 29.630 0.00 0.00 29.48 2.45
4662 4976 8.892723 CAGCTGGTTAGATTTATAAACACATGA 58.107 33.333 5.57 0.00 29.48 3.07
4663 4977 8.892723 TCAGCTGGTTAGATTTATAAACACATG 58.107 33.333 15.13 0.00 29.48 3.21
4664 4978 9.632638 ATCAGCTGGTTAGATTTATAAACACAT 57.367 29.630 15.13 0.00 29.48 3.21
4681 4995 9.935241 CTTGTAAATATCACTATATCAGCTGGT 57.065 33.333 15.13 9.93 0.00 4.00
4682 4996 8.877779 GCTTGTAAATATCACTATATCAGCTGG 58.122 37.037 15.13 0.00 0.00 4.85
4683 4997 9.650539 AGCTTGTAAATATCACTATATCAGCTG 57.349 33.333 7.63 7.63 0.00 4.24
4699 5013 9.732130 AGAAACTCAGATAAGAAGCTTGTAAAT 57.268 29.630 2.10 0.00 0.00 1.40
4700 5014 8.993121 CAGAAACTCAGATAAGAAGCTTGTAAA 58.007 33.333 2.10 0.00 0.00 2.01
4701 5015 7.604164 CCAGAAACTCAGATAAGAAGCTTGTAA 59.396 37.037 2.10 0.00 0.00 2.41
4702 5016 7.039011 TCCAGAAACTCAGATAAGAAGCTTGTA 60.039 37.037 2.10 0.00 0.00 2.41
4703 5017 5.936956 CCAGAAACTCAGATAAGAAGCTTGT 59.063 40.000 2.10 0.00 0.00 3.16
4704 5018 6.091986 GTCCAGAAACTCAGATAAGAAGCTTG 59.908 42.308 2.10 0.00 0.00 4.01
4705 5019 6.169800 GTCCAGAAACTCAGATAAGAAGCTT 58.830 40.000 0.00 0.00 0.00 3.74
4706 5020 5.623368 CGTCCAGAAACTCAGATAAGAAGCT 60.623 44.000 0.00 0.00 0.00 3.74
4707 5021 4.564769 CGTCCAGAAACTCAGATAAGAAGC 59.435 45.833 0.00 0.00 0.00 3.86
4708 5022 4.564769 GCGTCCAGAAACTCAGATAAGAAG 59.435 45.833 0.00 0.00 0.00 2.85
4709 5023 4.495422 GCGTCCAGAAACTCAGATAAGAA 58.505 43.478 0.00 0.00 0.00 2.52
4710 5024 3.427638 CGCGTCCAGAAACTCAGATAAGA 60.428 47.826 0.00 0.00 0.00 2.10
4739 5053 3.197766 TCAGCCAGATACGAAGTTCCAAT 59.802 43.478 0.00 0.00 37.78 3.16
4740 5054 2.565391 TCAGCCAGATACGAAGTTCCAA 59.435 45.455 0.00 0.00 37.78 3.53
4778 5092 2.159366 CGAGAGAGCGTACAGGTTTGAT 60.159 50.000 0.00 0.00 0.00 2.57
4790 5104 2.325166 GGCGTCTACGAGAGAGCG 59.675 66.667 6.71 0.02 43.02 5.03
5061 5375 1.201647 GGTGTTCGACGAGATGAGGAA 59.798 52.381 0.00 0.00 0.00 3.36
5120 5434 2.903855 CACAGGGCGATGATGGGC 60.904 66.667 0.00 0.00 0.00 5.36
5121 5435 2.903855 GCACAGGGCGATGATGGG 60.904 66.667 0.00 0.00 0.00 4.00
5210 5524 3.397613 GAAGATCCTGGCCAGCGCT 62.398 63.158 28.39 19.43 34.44 5.92
5318 5632 2.261361 CAGACGATGGTGGTCGCA 59.739 61.111 0.00 0.00 45.12 5.10


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

AutoCloner maintained by Alex Coulton.