Multiple sequence alignment - TraesCS3A01G262500

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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 TraesCS3A01G262500 chr3A 100.000 5011 0 0 1 5011 485520841 485525851 0.000000e+00 9254
1 TraesCS3A01G262500 chr3A 99.400 3836 20 3 1001 4834 485598480 485602314 0.000000e+00 6953
2 TraesCS3A01G262500 chr3A 85.039 508 73 2 410 915 720597394 720596888 9.620000e-142 514
3 TraesCS3A01G262500 chr3A 94.634 205 10 1 4808 5011 518488429 518488633 2.910000e-82 316
4 TraesCS3A01G262500 chr3A 72.400 500 124 13 423 916 215202152 215202643 4.040000e-31 147
5 TraesCS3A01G262500 chr3A 73.925 372 82 14 549 914 7364271 7363909 8.750000e-28 135
6 TraesCS3A01G262500 chr3D 93.839 3295 128 21 1547 4815 364232818 364236063 0.000000e+00 4891
7 TraesCS3A01G262500 chr3D 97.167 600 12 3 916 1512 364232225 364232822 0.000000e+00 1009
8 TraesCS3A01G262500 chr3B 94.852 1962 74 13 949 2904 474367045 474368985 0.000000e+00 3038
9 TraesCS3A01G262500 chr3B 92.941 1955 84 26 2891 4815 474370585 474372515 0.000000e+00 2796
10 TraesCS3A01G262500 chr3B 79.775 178 26 8 741 914 58460118 58459947 2.450000e-23 121
11 TraesCS3A01G262500 chr6A 94.360 922 50 2 1 921 716827 715907 0.000000e+00 1413
12 TraesCS3A01G262500 chr4A 94.581 203 10 1 4810 5011 47646371 47646573 3.770000e-81 313
13 TraesCS3A01G262500 chr4A 94.924 197 10 0 4815 5011 216440706 216440510 4.870000e-80 309
14 TraesCS3A01G262500 chr4A 94.949 198 9 1 4815 5011 219188145 219187948 4.870000e-80 309
15 TraesCS3A01G262500 chr2A 95.000 200 9 1 4813 5011 482409809 482410008 3.770000e-81 313
16 TraesCS3A01G262500 chr2A 93.627 204 12 1 4809 5011 639969098 639969301 2.270000e-78 303
17 TraesCS3A01G262500 chr2A 93.137 204 13 1 4809 5011 639976470 639976673 1.050000e-76 298
18 TraesCS3A01G262500 chr5A 94.527 201 11 0 4811 5011 646990211 646990011 1.350000e-80 311
19 TraesCS3A01G262500 chr5A 94.444 126 7 0 791 916 549379077 549378952 1.420000e-45 195
20 TraesCS3A01G262500 chr1A 93.659 205 11 2 4809 5011 572331704 572331500 6.300000e-79 305
21 TraesCS3A01G262500 chr1A 72.667 450 103 19 474 914 333142754 333143192 1.130000e-26 132
22 TraesCS3A01G262500 chr2B 72.464 483 119 12 441 916 24050469 24050944 5.230000e-30 143
23 TraesCS3A01G262500 chrUn 80.473 169 21 10 753 916 347830717 347830878 8.810000e-23 119


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 TraesCS3A01G262500 chr3A 485520841 485525851 5010 False 9254 9254 100.0000 1 5011 1 chr3A.!!$F2 5010
1 TraesCS3A01G262500 chr3A 485598480 485602314 3834 False 6953 6953 99.4000 1001 4834 1 chr3A.!!$F3 3833
2 TraesCS3A01G262500 chr3A 720596888 720597394 506 True 514 514 85.0390 410 915 1 chr3A.!!$R2 505
3 TraesCS3A01G262500 chr3D 364232225 364236063 3838 False 2950 4891 95.5030 916 4815 2 chr3D.!!$F1 3899
4 TraesCS3A01G262500 chr3B 474367045 474372515 5470 False 2917 3038 93.8965 949 4815 2 chr3B.!!$F1 3866
5 TraesCS3A01G262500 chr6A 715907 716827 920 True 1413 1413 94.3600 1 921 1 chr6A.!!$R1 920

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
860 862 0.107410 GCCCCATGACCATCGTTGTA 60.107 55.000 0.0 0.0 0.00 2.41 F
1062 1067 0.253044 CGAAGGGAAAGGAGGATGCA 59.747 55.000 0.0 0.0 0.00 3.96 F
1547 1593 2.095768 TGAAGCGTAGAAACATTGCTGC 60.096 45.455 0.0 0.0 35.77 5.25 F
2181 2229 5.011635 ACCCTGAATTAAACGGCAAATTTCT 59.988 36.000 0.0 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2628 2677 3.423206 GCAAAAGCAACAATCTTCACGAG 59.577 43.478 0.00 0.0 0.0 4.18 R
2808 2857 4.183865 CAACTGCAGAAATCGAGGTATCA 58.816 43.478 23.35 0.0 0.0 2.15 R
3448 5112 1.892474 TGGAAAACATAAGCTGCCACC 59.108 47.619 0.00 0.0 0.0 4.61 R
4125 5797 2.592861 CGCCCAGCTATTCTGCCC 60.593 66.667 0.00 0.0 41.5 5.36 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
22 23 3.866582 GGAGGATGTGAGGGCCCG 61.867 72.222 18.44 0.00 0.00 6.13
39 40 2.121786 CCCGTCGTAATATGTCAACGG 58.878 52.381 11.17 11.17 46.88 4.44
47 48 3.819564 AATATGTCAACGGCTAGCTCA 57.180 42.857 15.72 5.37 0.00 4.26
56 57 2.203126 GCTAGCTCATGCGGCCTT 60.203 61.111 7.70 0.00 45.42 4.35
78 79 1.303309 CGGTTCTCCTGATTCATGGC 58.697 55.000 0.00 0.00 0.00 4.40
93 94 0.982852 ATGGCGTCATTCCCTCCTGA 60.983 55.000 0.00 0.00 0.00 3.86
116 117 1.015109 GCACAGTCTCCAGATGCATG 58.985 55.000 2.46 0.00 36.30 4.06
137 138 0.759346 GGGCGTTGGTAGATGAGGAT 59.241 55.000 0.00 0.00 0.00 3.24
141 142 3.531538 GCGTTGGTAGATGAGGATTTGA 58.468 45.455 0.00 0.00 0.00 2.69
150 151 2.574006 TGAGGATTTGAGCTGCAGTT 57.426 45.000 16.64 9.79 0.00 3.16
182 183 2.593956 GGAGACGGGGGCAAAGAGT 61.594 63.158 0.00 0.00 0.00 3.24
266 267 1.824329 GGCGATCTGGACCTCGAGA 60.824 63.158 15.71 0.00 37.05 4.04
267 268 1.357334 GCGATCTGGACCTCGAGAC 59.643 63.158 15.71 7.53 37.05 3.36
310 312 1.488705 TTCCAATCACCCAGGCGACT 61.489 55.000 0.00 0.00 46.44 4.18
325 327 5.048507 CAGGCGACTAAGGAGTTTATAACC 58.951 45.833 0.00 0.00 40.21 2.85
343 345 1.064758 ACCCGCTTCATGGCTGATTTA 60.065 47.619 0.00 0.00 0.00 1.40
358 360 5.590530 CTGATTTAGCTACTGTCTCACCT 57.409 43.478 0.00 0.00 0.00 4.00
377 379 2.932614 CCTCCTGCAAAGATCAACGTAG 59.067 50.000 0.00 0.00 0.00 3.51
382 384 2.734606 TGCAAAGATCAACGTAGGTTCG 59.265 45.455 0.00 0.00 32.98 3.95
389 391 1.374252 AACGTAGGTTCGGCAGCTG 60.374 57.895 10.11 10.11 34.13 4.24
406 408 2.047274 GCTGGCCACGCTTCTACA 60.047 61.111 16.95 0.00 0.00 2.74
408 410 1.293498 CTGGCCACGCTTCTACACT 59.707 57.895 0.00 0.00 0.00 3.55
483 485 4.472833 AGTAAGATTTCAGAGAGGTGGCAT 59.527 41.667 0.00 0.00 0.00 4.40
516 518 2.046507 CAGAGACAGCCAGGGTGC 60.047 66.667 19.14 11.36 34.04 5.01
562 564 4.699522 GCCGGAGTTTGCGACCCT 62.700 66.667 5.05 0.00 30.86 4.34
572 574 4.357947 GCGACCCTGCGACACTGA 62.358 66.667 0.00 0.00 0.00 3.41
658 660 1.065551 GCTTCGGACTGCAAACAAGTT 59.934 47.619 0.00 0.00 0.00 2.66
675 677 4.142687 ACAAGTTATTGGCGACATTGCTAC 60.143 41.667 0.00 0.00 42.32 3.58
690 692 0.393077 GCTACGGGTAGTCATGGCAT 59.607 55.000 0.00 0.00 35.65 4.40
765 767 4.608948 ATTTCACCTTTGAGAGTCGAGT 57.391 40.909 0.00 0.00 31.71 4.18
773 775 5.477291 ACCTTTGAGAGTCGAGTTCAGAATA 59.523 40.000 0.00 0.00 0.00 1.75
813 815 6.223351 AGCTAGGTTTTCTTTATCGCTACT 57.777 37.500 0.00 0.00 0.00 2.57
823 825 0.892358 TATCGCTACTACCAGGGCGG 60.892 60.000 7.13 0.00 46.31 6.13
860 862 0.107410 GCCCCATGACCATCGTTGTA 60.107 55.000 0.00 0.00 0.00 2.41
867 869 1.903183 TGACCATCGTTGTATCCCACA 59.097 47.619 0.00 0.00 34.51 4.17
870 872 2.238646 ACCATCGTTGTATCCCACACAT 59.761 45.455 0.00 0.00 36.69 3.21
944 946 1.071471 CCCAGGAAGCGACAACACT 59.929 57.895 0.00 0.00 0.00 3.55
1062 1067 0.253044 CGAAGGGAAAGGAGGATGCA 59.747 55.000 0.00 0.00 0.00 3.96
1509 1555 6.267471 AGGAATAGTTTCATTTGTTTCCAGCA 59.733 34.615 0.00 0.00 34.86 4.41
1510 1556 7.038799 AGGAATAGTTTCATTTGTTTCCAGCAT 60.039 33.333 0.00 0.00 34.86 3.79
1511 1557 8.250332 GGAATAGTTTCATTTGTTTCCAGCATA 58.750 33.333 0.00 0.00 33.10 3.14
1512 1558 9.807649 GAATAGTTTCATTTGTTTCCAGCATAT 57.192 29.630 0.00 0.00 0.00 1.78
1516 1562 9.995003 AGTTTCATTTGTTTCCAGCATATAAAA 57.005 25.926 0.00 0.00 0.00 1.52
1518 1564 9.995003 TTTCATTTGTTTCCAGCATATAAAACT 57.005 25.926 0.00 0.00 33.75 2.66
1519 1565 8.984891 TCATTTGTTTCCAGCATATAAAACTG 57.015 30.769 0.00 0.00 33.75 3.16
1529 1575 8.450578 CCAGCATATAAAACTGGTCTTATGAA 57.549 34.615 9.74 0.00 44.91 2.57
1530 1576 8.562892 CCAGCATATAAAACTGGTCTTATGAAG 58.437 37.037 9.74 0.00 44.91 3.02
1531 1577 8.072567 CAGCATATAAAACTGGTCTTATGAAGC 58.927 37.037 0.00 0.00 0.00 3.86
1532 1578 7.041780 AGCATATAAAACTGGTCTTATGAAGCG 60.042 37.037 0.00 0.00 0.00 4.68
1533 1579 7.254795 GCATATAAAACTGGTCTTATGAAGCGT 60.255 37.037 0.00 0.00 0.00 5.07
1534 1580 9.256477 CATATAAAACTGGTCTTATGAAGCGTA 57.744 33.333 0.00 0.00 0.00 4.42
1535 1581 7.772332 ATAAAACTGGTCTTATGAAGCGTAG 57.228 36.000 0.00 0.00 0.00 3.51
1536 1582 5.401531 AAACTGGTCTTATGAAGCGTAGA 57.598 39.130 0.00 0.00 0.00 2.59
1537 1583 5.401531 AACTGGTCTTATGAAGCGTAGAA 57.598 39.130 0.00 0.00 0.00 2.10
1538 1584 5.401531 ACTGGTCTTATGAAGCGTAGAAA 57.598 39.130 0.00 0.00 0.00 2.52
1539 1585 5.169295 ACTGGTCTTATGAAGCGTAGAAAC 58.831 41.667 0.00 0.00 0.00 2.78
1540 1586 5.142061 TGGTCTTATGAAGCGTAGAAACA 57.858 39.130 0.00 0.00 0.00 2.83
1541 1587 5.730550 TGGTCTTATGAAGCGTAGAAACAT 58.269 37.500 0.00 0.00 0.00 2.71
1542 1588 6.170506 TGGTCTTATGAAGCGTAGAAACATT 58.829 36.000 0.00 0.00 0.00 2.71
1543 1589 6.092122 TGGTCTTATGAAGCGTAGAAACATTG 59.908 38.462 0.00 0.00 0.00 2.82
1544 1590 5.960105 GTCTTATGAAGCGTAGAAACATTGC 59.040 40.000 0.00 0.00 0.00 3.56
1545 1591 5.874810 TCTTATGAAGCGTAGAAACATTGCT 59.125 36.000 0.00 0.00 37.53 3.91
1546 1592 3.811722 TGAAGCGTAGAAACATTGCTG 57.188 42.857 0.00 0.00 35.77 4.41
1547 1593 2.095768 TGAAGCGTAGAAACATTGCTGC 60.096 45.455 0.00 0.00 35.77 5.25
2181 2229 5.011635 ACCCTGAATTAAACGGCAAATTTCT 59.988 36.000 0.00 0.00 0.00 2.52
3186 4850 5.497474 ACCAGACTGAGTTAACTTTGTTGT 58.503 37.500 10.02 4.81 0.00 3.32
3547 5211 6.621380 GCAGTTCATGTTCATCTTTTCATCGA 60.621 38.462 0.00 0.00 0.00 3.59
3630 5295 9.463443 CATATACATTGTACGACTGAATCTGAA 57.537 33.333 0.00 0.00 0.00 3.02
4066 5738 3.707316 CAAACCCTCCATGTAAATGGGA 58.293 45.455 12.25 0.00 41.95 4.37
4125 5797 7.909267 TGAATGTATTCATCTTTCTGTTAGCG 58.091 34.615 3.28 0.00 41.51 4.26
4400 6104 9.699703 TTTTACAGCAAATTATAAGTTTGTCCC 57.300 29.630 6.32 0.25 38.49 4.46
4401 6105 5.949735 ACAGCAAATTATAAGTTTGTCCCG 58.050 37.500 15.54 0.55 38.49 5.14
4402 6106 5.105917 ACAGCAAATTATAAGTTTGTCCCGG 60.106 40.000 15.54 0.00 38.49 5.73
4403 6107 5.014202 AGCAAATTATAAGTTTGTCCCGGT 58.986 37.500 0.00 1.79 38.49 5.28
4404 6108 5.479027 AGCAAATTATAAGTTTGTCCCGGTT 59.521 36.000 0.00 0.00 38.49 4.44
4405 6109 6.014925 AGCAAATTATAAGTTTGTCCCGGTTT 60.015 34.615 0.00 0.00 38.49 3.27
4406 6110 7.177041 AGCAAATTATAAGTTTGTCCCGGTTTA 59.823 33.333 0.00 0.00 38.49 2.01
4407 6111 7.977293 GCAAATTATAAGTTTGTCCCGGTTTAT 59.023 33.333 0.00 0.00 38.49 1.40
4408 6112 9.863845 CAAATTATAAGTTTGTCCCGGTTTATT 57.136 29.630 0.00 0.00 33.12 1.40
4413 6117 5.710513 AGTTTGTCCCGGTTTATTTTACC 57.289 39.130 0.00 0.00 0.00 2.85
4414 6118 5.387788 AGTTTGTCCCGGTTTATTTTACCT 58.612 37.500 0.00 0.00 33.35 3.08
4415 6119 5.474532 AGTTTGTCCCGGTTTATTTTACCTC 59.525 40.000 0.00 0.00 33.35 3.85
4416 6120 3.954200 TGTCCCGGTTTATTTTACCTCC 58.046 45.455 0.00 0.00 33.35 4.30
4417 6121 3.282021 GTCCCGGTTTATTTTACCTCCC 58.718 50.000 0.00 0.00 33.35 4.30
4418 6122 3.054139 GTCCCGGTTTATTTTACCTCCCT 60.054 47.826 0.00 0.00 33.35 4.20
4419 6123 3.054213 TCCCGGTTTATTTTACCTCCCTG 60.054 47.826 0.00 0.00 33.35 4.45
4420 6124 3.054213 CCCGGTTTATTTTACCTCCCTGA 60.054 47.826 0.00 0.00 33.35 3.86
4421 6125 4.196971 CCGGTTTATTTTACCTCCCTGAG 58.803 47.826 0.00 0.00 33.35 3.35
4647 6376 6.929049 CCTAATCTGAACGCTGAAATATACCA 59.071 38.462 0.00 0.00 0.00 3.25
4830 6567 5.195940 CAATCTTAGGGCCTCTTTGATTCA 58.804 41.667 10.74 0.00 29.93 2.57
4834 6571 3.872459 AGGGCCTCTTTGATTCATAGG 57.128 47.619 0.00 5.38 0.00 2.57
4835 6572 3.397527 AGGGCCTCTTTGATTCATAGGA 58.602 45.455 0.00 0.85 0.00 2.94
4836 6573 3.986134 AGGGCCTCTTTGATTCATAGGAT 59.014 43.478 0.00 0.00 0.00 3.24
4837 6574 4.418190 AGGGCCTCTTTGATTCATAGGATT 59.582 41.667 0.00 0.00 0.00 3.01
4838 6575 5.103344 AGGGCCTCTTTGATTCATAGGATTT 60.103 40.000 0.00 0.00 0.00 2.17
4839 6576 5.600069 GGGCCTCTTTGATTCATAGGATTTT 59.400 40.000 0.84 0.00 0.00 1.82
4840 6577 6.462067 GGGCCTCTTTGATTCATAGGATTTTG 60.462 42.308 0.84 0.00 0.00 2.44
4841 6578 6.322201 GGCCTCTTTGATTCATAGGATTTTGA 59.678 38.462 12.17 0.00 0.00 2.69
4842 6579 7.147846 GGCCTCTTTGATTCATAGGATTTTGAA 60.148 37.037 12.17 0.00 36.38 2.69
4843 6580 8.253113 GCCTCTTTGATTCATAGGATTTTGAAA 58.747 33.333 12.17 0.00 35.63 2.69
4858 6595 9.190317 AGGATTTTGAAAACATAGGAATAGGAC 57.810 33.333 0.00 0.00 0.00 3.85
4859 6596 8.966868 GGATTTTGAAAACATAGGAATAGGACA 58.033 33.333 0.00 0.00 0.00 4.02
4862 6599 8.934023 TTTGAAAACATAGGAATAGGACAAGT 57.066 30.769 0.00 0.00 0.00 3.16
4863 6600 7.921786 TGAAAACATAGGAATAGGACAAGTG 57.078 36.000 0.00 0.00 0.00 3.16
4864 6601 7.458397 TGAAAACATAGGAATAGGACAAGTGT 58.542 34.615 0.00 0.00 0.00 3.55
4865 6602 8.598916 TGAAAACATAGGAATAGGACAAGTGTA 58.401 33.333 0.00 0.00 0.00 2.90
4866 6603 9.099454 GAAAACATAGGAATAGGACAAGTGTAG 57.901 37.037 0.00 0.00 0.00 2.74
4867 6604 6.732896 ACATAGGAATAGGACAAGTGTAGG 57.267 41.667 0.00 0.00 0.00 3.18
4868 6605 5.602978 ACATAGGAATAGGACAAGTGTAGGG 59.397 44.000 0.00 0.00 0.00 3.53
4869 6606 4.076175 AGGAATAGGACAAGTGTAGGGT 57.924 45.455 0.00 0.00 0.00 4.34
4870 6607 4.436079 AGGAATAGGACAAGTGTAGGGTT 58.564 43.478 0.00 0.00 0.00 4.11
4871 6608 4.225267 AGGAATAGGACAAGTGTAGGGTTG 59.775 45.833 0.00 0.00 0.00 3.77
4872 6609 4.514401 GAATAGGACAAGTGTAGGGTTGG 58.486 47.826 0.00 0.00 0.00 3.77
4873 6610 2.112279 AGGACAAGTGTAGGGTTGGA 57.888 50.000 0.00 0.00 0.00 3.53
4874 6611 1.978580 AGGACAAGTGTAGGGTTGGAG 59.021 52.381 0.00 0.00 0.00 3.86
4875 6612 1.697982 GGACAAGTGTAGGGTTGGAGT 59.302 52.381 0.00 0.00 0.00 3.85
4876 6613 2.550208 GGACAAGTGTAGGGTTGGAGTG 60.550 54.545 0.00 0.00 0.00 3.51
4877 6614 1.420138 ACAAGTGTAGGGTTGGAGTGG 59.580 52.381 0.00 0.00 0.00 4.00
4878 6615 0.400594 AAGTGTAGGGTTGGAGTGGC 59.599 55.000 0.00 0.00 0.00 5.01
4879 6616 0.766674 AGTGTAGGGTTGGAGTGGCA 60.767 55.000 0.00 0.00 0.00 4.92
4880 6617 0.328258 GTGTAGGGTTGGAGTGGCAT 59.672 55.000 0.00 0.00 0.00 4.40
4881 6618 0.327924 TGTAGGGTTGGAGTGGCATG 59.672 55.000 0.00 0.00 0.00 4.06
4882 6619 1.032114 GTAGGGTTGGAGTGGCATGC 61.032 60.000 9.90 9.90 0.00 4.06
4883 6620 2.210144 TAGGGTTGGAGTGGCATGCC 62.210 60.000 30.54 30.54 0.00 4.40
4884 6621 3.070576 GGTTGGAGTGGCATGCCC 61.071 66.667 33.44 23.56 34.56 5.36
4885 6622 2.283101 GTTGGAGTGGCATGCCCA 60.283 61.111 33.44 20.96 42.79 5.36
4894 6631 0.831966 TGGCATGCCCATTTGAATCC 59.168 50.000 33.44 4.70 39.18 3.01
4895 6632 1.125633 GGCATGCCCATTTGAATCCT 58.874 50.000 27.24 0.00 0.00 3.24
4896 6633 2.318908 GGCATGCCCATTTGAATCCTA 58.681 47.619 27.24 0.00 0.00 2.94
4897 6634 2.901839 GGCATGCCCATTTGAATCCTAT 59.098 45.455 27.24 0.00 0.00 2.57
4898 6635 4.088634 GGCATGCCCATTTGAATCCTATA 58.911 43.478 27.24 0.00 0.00 1.31
4899 6636 4.159135 GGCATGCCCATTTGAATCCTATAG 59.841 45.833 27.24 0.00 0.00 1.31
4900 6637 5.012239 GCATGCCCATTTGAATCCTATAGA 58.988 41.667 6.36 0.00 0.00 1.98
4901 6638 5.477984 GCATGCCCATTTGAATCCTATAGAA 59.522 40.000 6.36 0.00 0.00 2.10
4902 6639 6.154021 GCATGCCCATTTGAATCCTATAGAAT 59.846 38.462 6.36 0.00 0.00 2.40
4903 6640 7.310237 GCATGCCCATTTGAATCCTATAGAATT 60.310 37.037 6.36 0.00 0.00 2.17
4904 6641 9.246670 CATGCCCATTTGAATCCTATAGAATTA 57.753 33.333 0.00 0.00 0.00 1.40
4905 6642 8.868522 TGCCCATTTGAATCCTATAGAATTAG 57.131 34.615 0.00 0.00 0.00 1.73
4906 6643 7.394359 TGCCCATTTGAATCCTATAGAATTAGC 59.606 37.037 0.00 0.00 0.00 3.09
4907 6644 7.394359 GCCCATTTGAATCCTATAGAATTAGCA 59.606 37.037 0.00 0.00 0.00 3.49
4908 6645 9.300681 CCCATTTGAATCCTATAGAATTAGCAA 57.699 33.333 0.00 0.00 0.00 3.91
4922 6659 7.766219 AGAATTAGCAATGATTGTTTGATGC 57.234 32.000 7.05 0.00 0.00 3.91
4923 6660 6.759827 AGAATTAGCAATGATTGTTTGATGCC 59.240 34.615 7.05 0.00 34.44 4.40
4924 6661 3.965379 AGCAATGATTGTTTGATGCCA 57.035 38.095 7.05 0.00 34.44 4.92
4925 6662 3.592059 AGCAATGATTGTTTGATGCCAC 58.408 40.909 7.05 0.00 34.44 5.01
4926 6663 3.007074 AGCAATGATTGTTTGATGCCACA 59.993 39.130 7.05 0.00 34.44 4.17
4927 6664 3.369756 GCAATGATTGTTTGATGCCACAG 59.630 43.478 7.05 0.00 0.00 3.66
4928 6665 3.880047 ATGATTGTTTGATGCCACAGG 57.120 42.857 0.00 0.00 0.00 4.00
4929 6666 2.874014 TGATTGTTTGATGCCACAGGA 58.126 42.857 0.00 0.00 0.00 3.86
4930 6667 3.229293 TGATTGTTTGATGCCACAGGAA 58.771 40.909 0.00 0.00 0.00 3.36
4931 6668 3.640498 TGATTGTTTGATGCCACAGGAAA 59.360 39.130 0.00 0.00 0.00 3.13
4932 6669 4.100653 TGATTGTTTGATGCCACAGGAAAA 59.899 37.500 0.00 0.00 0.00 2.29
4933 6670 4.478206 TTGTTTGATGCCACAGGAAAAA 57.522 36.364 0.00 0.00 0.00 1.94
4934 6671 3.791245 TGTTTGATGCCACAGGAAAAAC 58.209 40.909 0.00 0.00 0.00 2.43
4935 6672 3.196469 TGTTTGATGCCACAGGAAAAACA 59.804 39.130 0.00 0.00 34.62 2.83
4936 6673 4.187694 GTTTGATGCCACAGGAAAAACAA 58.812 39.130 0.00 0.00 0.00 2.83
4937 6674 4.478206 TTGATGCCACAGGAAAAACAAA 57.522 36.364 0.00 0.00 0.00 2.83
4938 6675 4.057406 TGATGCCACAGGAAAAACAAAG 57.943 40.909 0.00 0.00 0.00 2.77
4939 6676 3.703556 TGATGCCACAGGAAAAACAAAGA 59.296 39.130 0.00 0.00 0.00 2.52
4940 6677 4.161189 TGATGCCACAGGAAAAACAAAGAA 59.839 37.500 0.00 0.00 0.00 2.52
4941 6678 4.543590 TGCCACAGGAAAAACAAAGAAA 57.456 36.364 0.00 0.00 0.00 2.52
4942 6679 5.096443 TGCCACAGGAAAAACAAAGAAAT 57.904 34.783 0.00 0.00 0.00 2.17
4943 6680 5.495640 TGCCACAGGAAAAACAAAGAAATT 58.504 33.333 0.00 0.00 0.00 1.82
4944 6681 5.353678 TGCCACAGGAAAAACAAAGAAATTG 59.646 36.000 0.00 0.00 44.95 2.32
4959 6696 7.940850 CAAAGAAATTGTAGAAAGAGGTTGGA 58.059 34.615 0.00 0.00 34.16 3.53
4960 6697 7.751768 AAGAAATTGTAGAAAGAGGTTGGAG 57.248 36.000 0.00 0.00 0.00 3.86
4961 6698 6.842676 AGAAATTGTAGAAAGAGGTTGGAGT 58.157 36.000 0.00 0.00 0.00 3.85
4962 6699 6.712547 AGAAATTGTAGAAAGAGGTTGGAGTG 59.287 38.462 0.00 0.00 0.00 3.51
4963 6700 4.351874 TTGTAGAAAGAGGTTGGAGTGG 57.648 45.455 0.00 0.00 0.00 4.00
4964 6701 3.583228 TGTAGAAAGAGGTTGGAGTGGA 58.417 45.455 0.00 0.00 0.00 4.02
4965 6702 4.168101 TGTAGAAAGAGGTTGGAGTGGAT 58.832 43.478 0.00 0.00 0.00 3.41
4966 6703 3.710209 AGAAAGAGGTTGGAGTGGATG 57.290 47.619 0.00 0.00 0.00 3.51
4967 6704 2.982488 AGAAAGAGGTTGGAGTGGATGT 59.018 45.455 0.00 0.00 0.00 3.06
4968 6705 3.395941 AGAAAGAGGTTGGAGTGGATGTT 59.604 43.478 0.00 0.00 0.00 2.71
4969 6706 4.597507 AGAAAGAGGTTGGAGTGGATGTTA 59.402 41.667 0.00 0.00 0.00 2.41
4970 6707 4.993705 AAGAGGTTGGAGTGGATGTTAA 57.006 40.909 0.00 0.00 0.00 2.01
4971 6708 5.520748 AAGAGGTTGGAGTGGATGTTAAT 57.479 39.130 0.00 0.00 0.00 1.40
4972 6709 5.520748 AGAGGTTGGAGTGGATGTTAATT 57.479 39.130 0.00 0.00 0.00 1.40
4973 6710 5.892348 AGAGGTTGGAGTGGATGTTAATTT 58.108 37.500 0.00 0.00 0.00 1.82
4974 6711 6.314917 AGAGGTTGGAGTGGATGTTAATTTT 58.685 36.000 0.00 0.00 0.00 1.82
4975 6712 6.434340 AGAGGTTGGAGTGGATGTTAATTTTC 59.566 38.462 0.00 0.00 0.00 2.29
4976 6713 5.480422 AGGTTGGAGTGGATGTTAATTTTCC 59.520 40.000 0.00 0.00 0.00 3.13
4977 6714 5.480422 GGTTGGAGTGGATGTTAATTTTCCT 59.520 40.000 0.00 0.00 0.00 3.36
4978 6715 6.661805 GGTTGGAGTGGATGTTAATTTTCCTA 59.338 38.462 0.00 0.00 0.00 2.94
4979 6716 7.342026 GGTTGGAGTGGATGTTAATTTTCCTAT 59.658 37.037 0.00 0.00 0.00 2.57
4980 6717 7.880160 TGGAGTGGATGTTAATTTTCCTATG 57.120 36.000 0.00 0.00 0.00 2.23
4981 6718 7.638444 TGGAGTGGATGTTAATTTTCCTATGA 58.362 34.615 0.00 0.00 0.00 2.15
4982 6719 8.112822 TGGAGTGGATGTTAATTTTCCTATGAA 58.887 33.333 0.00 0.00 0.00 2.57
4983 6720 8.966868 GGAGTGGATGTTAATTTTCCTATGAAA 58.033 33.333 0.00 0.00 38.69 2.69
4984 6721 9.788960 GAGTGGATGTTAATTTTCCTATGAAAC 57.211 33.333 0.00 0.00 40.12 2.78
4985 6722 8.458843 AGTGGATGTTAATTTTCCTATGAAACG 58.541 33.333 0.00 0.00 40.12 3.60
4986 6723 8.241367 GTGGATGTTAATTTTCCTATGAAACGT 58.759 33.333 0.00 0.00 40.12 3.99
4987 6724 9.451002 TGGATGTTAATTTTCCTATGAAACGTA 57.549 29.630 0.00 0.00 40.12 3.57
4988 6725 9.931210 GGATGTTAATTTTCCTATGAAACGTAG 57.069 33.333 0.00 0.00 40.12 3.51
5001 6738 9.843334 CCTATGAAACGTAGTATAGAAGATTCC 57.157 37.037 12.03 0.00 45.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.424529 GCTAGCCGTTGACATATTACGAC 59.575 47.826 2.29 0.00 37.47 4.34
39 40 1.821332 AAAGGCCGCATGAGCTAGC 60.821 57.895 6.62 6.62 39.10 3.42
47 48 3.747976 GAACCGCAAAGGCCGCAT 61.748 61.111 0.00 0.00 46.52 4.73
56 57 2.358957 CATGAATCAGGAGAACCGCAA 58.641 47.619 0.00 0.00 41.83 4.85
78 79 2.009042 GCACTTCAGGAGGGAATGACG 61.009 57.143 0.00 0.00 0.00 4.35
93 94 1.610102 GCATCTGGAGACTGTGCACTT 60.610 52.381 19.41 4.64 36.80 3.16
116 117 0.462047 CCTCATCTACCAACGCCCAC 60.462 60.000 0.00 0.00 0.00 4.61
137 138 0.662619 CGACCAAACTGCAGCTCAAA 59.337 50.000 15.27 0.00 0.00 2.69
141 142 1.580845 GATGCGACCAAACTGCAGCT 61.581 55.000 15.27 0.00 42.65 4.24
150 151 0.669318 GTCTCCGTTGATGCGACCAA 60.669 55.000 0.00 0.00 0.00 3.67
171 172 3.686760 GAGCCAACTCTTTGCCCC 58.313 61.111 0.00 0.00 40.03 5.80
182 183 6.015180 GCATATCCATTAATCCAAAGAGCCAA 60.015 38.462 0.00 0.00 0.00 4.52
266 267 6.949352 ATTGATTCATGGATAGCTTTTCGT 57.051 33.333 0.00 0.00 0.00 3.85
267 268 9.552114 GAATATTGATTCATGGATAGCTTTTCG 57.448 33.333 0.00 0.00 41.12 3.46
310 312 5.680594 TGAAGCGGGTTATAAACTCCTTA 57.319 39.130 0.00 0.00 0.00 2.69
325 327 1.002033 GCTAAATCAGCCATGAAGCGG 60.002 52.381 0.00 0.00 45.23 5.52
343 345 1.846007 CAGGAGGTGAGACAGTAGCT 58.154 55.000 0.00 0.00 0.00 3.32
351 353 2.259917 TGATCTTTGCAGGAGGTGAGA 58.740 47.619 0.00 0.00 0.00 3.27
357 359 2.932614 CCTACGTTGATCTTTGCAGGAG 59.067 50.000 0.00 0.00 0.00 3.69
358 360 2.301870 ACCTACGTTGATCTTTGCAGGA 59.698 45.455 0.00 0.00 0.00 3.86
389 391 2.047274 TGTAGAAGCGTGGCCAGC 60.047 61.111 5.11 12.81 0.00 4.85
483 485 3.881952 CTGCATATAGCCGCGGCCA 62.882 63.158 44.47 34.90 44.83 5.36
493 495 1.973515 CCCTGGCTGTCTCTGCATATA 59.026 52.381 0.00 0.00 0.00 0.86
516 518 3.448934 AGTGATGAGCTCCCCATATAGG 58.551 50.000 12.15 0.00 37.03 2.57
562 564 0.108186 CTATGGCCTTCAGTGTCGCA 60.108 55.000 3.32 0.00 0.00 5.10
572 574 1.149174 CCCGACATGCTATGGCCTT 59.851 57.895 3.32 0.00 33.66 4.35
627 629 0.958822 GTCCGAAGCCACCACAAAAT 59.041 50.000 0.00 0.00 0.00 1.82
658 660 1.577468 CCGTAGCAATGTCGCCAATA 58.423 50.000 0.00 0.00 0.00 1.90
675 677 2.813754 CCATAAATGCCATGACTACCCG 59.186 50.000 0.00 0.00 0.00 5.28
773 775 4.099266 CCTAGCTATCTTGTGAGCTTCAGT 59.901 45.833 1.16 0.00 46.99 3.41
785 787 7.501844 AGCGATAAAGAAAACCTAGCTATCTT 58.498 34.615 0.00 0.00 31.98 2.40
813 815 3.326578 ACACATGCCGCCCTGGTA 61.327 61.111 0.00 0.00 41.21 3.25
870 872 9.213799 GCCAACTTTATTAATCAAAATCCACAA 57.786 29.630 0.00 0.00 0.00 3.33
915 917 4.753662 TCCTGGGCGCTCGTACCT 62.754 66.667 7.64 0.00 0.00 3.08
917 919 2.202756 CTTCCTGGGCGCTCGTAC 60.203 66.667 7.64 0.00 0.00 3.67
918 920 4.143333 GCTTCCTGGGCGCTCGTA 62.143 66.667 7.64 0.00 0.00 3.43
944 946 5.652014 TCTTTCTTTTTCTGTCTTCCTTGCA 59.348 36.000 0.00 0.00 0.00 4.08
1062 1067 1.819229 CAGCCTACTGGATGCGAGT 59.181 57.895 0.00 0.00 43.22 4.18
1509 1555 9.477484 CTACGCTTCATAAGACCAGTTTTATAT 57.523 33.333 0.00 0.00 0.00 0.86
1510 1556 8.689061 TCTACGCTTCATAAGACCAGTTTTATA 58.311 33.333 0.00 0.00 0.00 0.98
1511 1557 7.553334 TCTACGCTTCATAAGACCAGTTTTAT 58.447 34.615 0.00 0.00 0.00 1.40
1512 1558 6.927416 TCTACGCTTCATAAGACCAGTTTTA 58.073 36.000 0.00 0.00 0.00 1.52
1513 1559 5.790593 TCTACGCTTCATAAGACCAGTTTT 58.209 37.500 0.00 0.00 0.00 2.43
1514 1560 5.401531 TCTACGCTTCATAAGACCAGTTT 57.598 39.130 0.00 0.00 0.00 2.66
1515 1561 5.401531 TTCTACGCTTCATAAGACCAGTT 57.598 39.130 0.00 0.00 0.00 3.16
1516 1562 5.169295 GTTTCTACGCTTCATAAGACCAGT 58.831 41.667 0.00 0.00 0.00 4.00
1517 1563 5.168569 TGTTTCTACGCTTCATAAGACCAG 58.831 41.667 0.00 0.00 0.00 4.00
1518 1564 5.142061 TGTTTCTACGCTTCATAAGACCA 57.858 39.130 0.00 0.00 0.00 4.02
1519 1565 6.478588 CAATGTTTCTACGCTTCATAAGACC 58.521 40.000 0.00 0.00 0.00 3.85
1520 1566 5.960105 GCAATGTTTCTACGCTTCATAAGAC 59.040 40.000 0.00 0.00 0.00 3.01
1521 1567 5.874810 AGCAATGTTTCTACGCTTCATAAGA 59.125 36.000 0.00 0.00 0.00 2.10
1522 1568 5.961843 CAGCAATGTTTCTACGCTTCATAAG 59.038 40.000 0.00 0.00 0.00 1.73
1523 1569 5.673568 GCAGCAATGTTTCTACGCTTCATAA 60.674 40.000 0.00 0.00 0.00 1.90
1524 1570 4.201812 GCAGCAATGTTTCTACGCTTCATA 60.202 41.667 0.00 0.00 0.00 2.15
1525 1571 3.426695 GCAGCAATGTTTCTACGCTTCAT 60.427 43.478 0.00 0.00 0.00 2.57
1526 1572 2.095768 GCAGCAATGTTTCTACGCTTCA 60.096 45.455 0.00 0.00 0.00 3.02
1527 1573 2.095768 TGCAGCAATGTTTCTACGCTTC 60.096 45.455 0.00 0.00 0.00 3.86
1528 1574 1.879380 TGCAGCAATGTTTCTACGCTT 59.121 42.857 0.00 0.00 0.00 4.68
1529 1575 1.522668 TGCAGCAATGTTTCTACGCT 58.477 45.000 0.00 0.00 0.00 5.07
1530 1576 2.549633 ATGCAGCAATGTTTCTACGC 57.450 45.000 0.00 0.00 0.00 4.42
1531 1577 4.329801 TGTCTATGCAGCAATGTTTCTACG 59.670 41.667 0.00 0.00 0.00 3.51
1532 1578 5.801350 TGTCTATGCAGCAATGTTTCTAC 57.199 39.130 0.00 0.00 0.00 2.59
1533 1579 8.152898 AGATATGTCTATGCAGCAATGTTTCTA 58.847 33.333 0.00 0.00 31.36 2.10
1534 1580 6.996879 AGATATGTCTATGCAGCAATGTTTCT 59.003 34.615 0.00 0.00 31.36 2.52
1535 1581 7.199541 AGATATGTCTATGCAGCAATGTTTC 57.800 36.000 0.00 0.00 31.36 2.78
1536 1582 7.283807 TGAAGATATGTCTATGCAGCAATGTTT 59.716 33.333 0.00 0.00 33.30 2.83
1537 1583 6.769341 TGAAGATATGTCTATGCAGCAATGTT 59.231 34.615 0.00 0.00 33.30 2.71
1538 1584 6.293698 TGAAGATATGTCTATGCAGCAATGT 58.706 36.000 0.00 0.00 33.30 2.71
1539 1585 6.620949 GCTGAAGATATGTCTATGCAGCAATG 60.621 42.308 24.13 0.00 44.72 2.82
1540 1586 5.411977 GCTGAAGATATGTCTATGCAGCAAT 59.588 40.000 24.13 0.00 44.72 3.56
1541 1587 4.753610 GCTGAAGATATGTCTATGCAGCAA 59.246 41.667 24.13 0.00 44.72 3.91
1542 1588 4.040095 AGCTGAAGATATGTCTATGCAGCA 59.960 41.667 27.51 0.00 46.09 4.41
1543 1589 4.567971 AGCTGAAGATATGTCTATGCAGC 58.432 43.478 22.78 22.78 45.16 5.25
1544 1590 6.366604 CAGAAGCTGAAGATATGTCTATGCAG 59.633 42.308 11.59 11.07 33.30 4.41
1545 1591 6.041296 TCAGAAGCTGAAGATATGTCTATGCA 59.959 38.462 11.59 0.00 37.57 3.96
1546 1592 6.453943 TCAGAAGCTGAAGATATGTCTATGC 58.546 40.000 0.00 0.00 37.57 3.14
2181 2229 4.873827 AGAAGCACTCTGAACAAACGTTTA 59.126 37.500 14.20 0.00 31.12 2.01
2628 2677 3.423206 GCAAAAGCAACAATCTTCACGAG 59.577 43.478 0.00 0.00 0.00 4.18
2808 2857 4.183865 CAACTGCAGAAATCGAGGTATCA 58.816 43.478 23.35 0.00 0.00 2.15
2879 2928 7.387265 AAAACCAGAACCCTTATTTTGGAAT 57.613 32.000 2.37 0.00 36.20 3.01
3186 4850 8.780846 ATGTATCTTGTATTACAACCGAACAA 57.219 30.769 5.14 0.00 33.96 2.83
3448 5112 1.892474 TGGAAAACATAAGCTGCCACC 59.108 47.619 0.00 0.00 0.00 4.61
3547 5211 8.704668 AGGGAATTCAGTGTTAATGAAGTTTTT 58.295 29.630 7.93 0.00 39.86 1.94
3580 5245 5.972107 ACTTCTTGAATGATGAAAGGTGG 57.028 39.130 0.00 0.00 0.00 4.61
3630 5295 5.127682 AGCAAGTCAAATGGTGTCTTCTTTT 59.872 36.000 0.00 0.00 33.94 2.27
4125 5797 2.592861 CGCCCAGCTATTCTGCCC 60.593 66.667 0.00 0.00 41.50 5.36
4399 6103 4.196971 CTCAGGGAGGTAAAATAAACCGG 58.803 47.826 0.00 0.00 42.15 5.28
4400 6104 3.626217 GCTCAGGGAGGTAAAATAAACCG 59.374 47.826 0.00 0.00 42.15 4.44
4401 6105 3.952323 GGCTCAGGGAGGTAAAATAAACC 59.048 47.826 0.00 0.00 37.27 3.27
4402 6106 3.952323 GGGCTCAGGGAGGTAAAATAAAC 59.048 47.826 0.00 0.00 0.00 2.01
4403 6107 3.856206 AGGGCTCAGGGAGGTAAAATAAA 59.144 43.478 0.00 0.00 0.00 1.40
4404 6108 3.470868 AGGGCTCAGGGAGGTAAAATAA 58.529 45.455 0.00 0.00 0.00 1.40
4405 6109 3.145559 AGGGCTCAGGGAGGTAAAATA 57.854 47.619 0.00 0.00 0.00 1.40
4406 6110 1.987080 AGGGCTCAGGGAGGTAAAAT 58.013 50.000 0.00 0.00 0.00 1.82
4407 6111 1.354368 CAAGGGCTCAGGGAGGTAAAA 59.646 52.381 0.00 0.00 0.00 1.52
4408 6112 0.991920 CAAGGGCTCAGGGAGGTAAA 59.008 55.000 0.00 0.00 0.00 2.01
4409 6113 0.178873 ACAAGGGCTCAGGGAGGTAA 60.179 55.000 0.00 0.00 0.00 2.85
4410 6114 0.909610 CACAAGGGCTCAGGGAGGTA 60.910 60.000 0.00 0.00 0.00 3.08
4411 6115 2.208349 ACAAGGGCTCAGGGAGGT 59.792 61.111 0.00 0.00 0.00 3.85
4412 6116 2.673523 CACAAGGGCTCAGGGAGG 59.326 66.667 0.00 0.00 0.00 4.30
4413 6117 2.673523 CCACAAGGGCTCAGGGAG 59.326 66.667 0.00 0.00 0.00 4.30
4836 6573 9.362151 ACTTGTCCTATTCCTATGTTTTCAAAA 57.638 29.630 0.00 0.00 0.00 2.44
4837 6574 8.792633 CACTTGTCCTATTCCTATGTTTTCAAA 58.207 33.333 0.00 0.00 0.00 2.69
4838 6575 7.942341 ACACTTGTCCTATTCCTATGTTTTCAA 59.058 33.333 0.00 0.00 0.00 2.69
4839 6576 7.458397 ACACTTGTCCTATTCCTATGTTTTCA 58.542 34.615 0.00 0.00 0.00 2.69
4840 6577 7.923414 ACACTTGTCCTATTCCTATGTTTTC 57.077 36.000 0.00 0.00 0.00 2.29
4841 6578 8.047310 CCTACACTTGTCCTATTCCTATGTTTT 58.953 37.037 0.00 0.00 0.00 2.43
4842 6579 7.365652 CCCTACACTTGTCCTATTCCTATGTTT 60.366 40.741 0.00 0.00 0.00 2.83
4843 6580 6.099845 CCCTACACTTGTCCTATTCCTATGTT 59.900 42.308 0.00 0.00 0.00 2.71
4844 6581 5.602978 CCCTACACTTGTCCTATTCCTATGT 59.397 44.000 0.00 0.00 0.00 2.29
4845 6582 5.602978 ACCCTACACTTGTCCTATTCCTATG 59.397 44.000 0.00 0.00 0.00 2.23
4846 6583 5.789535 ACCCTACACTTGTCCTATTCCTAT 58.210 41.667 0.00 0.00 0.00 2.57
4847 6584 5.216665 ACCCTACACTTGTCCTATTCCTA 57.783 43.478 0.00 0.00 0.00 2.94
4848 6585 4.076175 ACCCTACACTTGTCCTATTCCT 57.924 45.455 0.00 0.00 0.00 3.36
4849 6586 4.514401 CAACCCTACACTTGTCCTATTCC 58.486 47.826 0.00 0.00 0.00 3.01
4850 6587 4.224370 TCCAACCCTACACTTGTCCTATTC 59.776 45.833 0.00 0.00 0.00 1.75
4851 6588 4.172807 TCCAACCCTACACTTGTCCTATT 58.827 43.478 0.00 0.00 0.00 1.73
4852 6589 3.775316 CTCCAACCCTACACTTGTCCTAT 59.225 47.826 0.00 0.00 0.00 2.57
4853 6590 3.170717 CTCCAACCCTACACTTGTCCTA 58.829 50.000 0.00 0.00 0.00 2.94
4854 6591 1.978580 CTCCAACCCTACACTTGTCCT 59.021 52.381 0.00 0.00 0.00 3.85
4855 6592 1.697982 ACTCCAACCCTACACTTGTCC 59.302 52.381 0.00 0.00 0.00 4.02
4856 6593 2.550208 CCACTCCAACCCTACACTTGTC 60.550 54.545 0.00 0.00 0.00 3.18
4857 6594 1.420138 CCACTCCAACCCTACACTTGT 59.580 52.381 0.00 0.00 0.00 3.16
4858 6595 1.882352 GCCACTCCAACCCTACACTTG 60.882 57.143 0.00 0.00 0.00 3.16
4859 6596 0.400594 GCCACTCCAACCCTACACTT 59.599 55.000 0.00 0.00 0.00 3.16
4860 6597 0.766674 TGCCACTCCAACCCTACACT 60.767 55.000 0.00 0.00 0.00 3.55
4861 6598 0.328258 ATGCCACTCCAACCCTACAC 59.672 55.000 0.00 0.00 0.00 2.90
4862 6599 0.327924 CATGCCACTCCAACCCTACA 59.672 55.000 0.00 0.00 0.00 2.74
4863 6600 1.032114 GCATGCCACTCCAACCCTAC 61.032 60.000 6.36 0.00 0.00 3.18
4864 6601 1.302949 GCATGCCACTCCAACCCTA 59.697 57.895 6.36 0.00 0.00 3.53
4865 6602 2.036256 GCATGCCACTCCAACCCT 59.964 61.111 6.36 0.00 0.00 4.34
4866 6603 3.070576 GGCATGCCACTCCAACCC 61.071 66.667 32.08 0.00 35.81 4.11
4867 6604 3.070576 GGGCATGCCACTCCAACC 61.071 66.667 36.56 14.15 37.98 3.77
4868 6605 1.259840 AATGGGCATGCCACTCCAAC 61.260 55.000 36.56 18.56 37.98 3.77
4869 6606 0.544833 AAATGGGCATGCCACTCCAA 60.545 50.000 36.56 15.42 37.98 3.53
4870 6607 1.078891 AAATGGGCATGCCACTCCA 59.921 52.632 36.56 25.30 37.98 3.86
4871 6608 0.971959 TCAAATGGGCATGCCACTCC 60.972 55.000 36.56 20.41 37.98 3.85
4872 6609 0.896923 TTCAAATGGGCATGCCACTC 59.103 50.000 36.56 20.78 37.98 3.51
4873 6610 1.483415 GATTCAAATGGGCATGCCACT 59.517 47.619 36.56 20.94 37.98 4.00
4874 6611 1.473788 GGATTCAAATGGGCATGCCAC 60.474 52.381 36.56 25.50 37.98 5.01
4875 6612 0.831966 GGATTCAAATGGGCATGCCA 59.168 50.000 36.56 23.14 37.98 4.92
4876 6613 1.125633 AGGATTCAAATGGGCATGCC 58.874 50.000 29.47 29.47 0.00 4.40
4877 6614 5.012239 TCTATAGGATTCAAATGGGCATGC 58.988 41.667 9.90 9.90 0.00 4.06
4878 6615 7.713734 ATTCTATAGGATTCAAATGGGCATG 57.286 36.000 0.00 0.00 0.00 4.06
4879 6616 9.471702 CTAATTCTATAGGATTCAAATGGGCAT 57.528 33.333 9.67 0.00 0.00 4.40
4880 6617 7.394359 GCTAATTCTATAGGATTCAAATGGGCA 59.606 37.037 9.67 0.00 0.00 5.36
4881 6618 7.394359 TGCTAATTCTATAGGATTCAAATGGGC 59.606 37.037 9.67 5.60 0.00 5.36
4882 6619 8.868522 TGCTAATTCTATAGGATTCAAATGGG 57.131 34.615 9.67 0.00 0.00 4.00
4896 6633 9.472361 GCATCAAACAATCATTGCTAATTCTAT 57.528 29.630 0.00 0.00 0.00 1.98
4897 6634 7.922278 GGCATCAAACAATCATTGCTAATTCTA 59.078 33.333 0.00 0.00 0.00 2.10
4898 6635 6.759827 GGCATCAAACAATCATTGCTAATTCT 59.240 34.615 0.00 0.00 0.00 2.40
4899 6636 6.535865 TGGCATCAAACAATCATTGCTAATTC 59.464 34.615 0.00 0.00 0.00 2.17
4900 6637 6.314400 GTGGCATCAAACAATCATTGCTAATT 59.686 34.615 0.00 0.00 0.00 1.40
4901 6638 5.813672 GTGGCATCAAACAATCATTGCTAAT 59.186 36.000 0.00 0.00 0.00 1.73
4902 6639 5.170021 GTGGCATCAAACAATCATTGCTAA 58.830 37.500 0.00 0.00 0.00 3.09
4903 6640 4.220163 TGTGGCATCAAACAATCATTGCTA 59.780 37.500 0.00 0.00 0.00 3.49
4904 6641 3.007074 TGTGGCATCAAACAATCATTGCT 59.993 39.130 0.00 0.00 0.00 3.91
4905 6642 3.327626 TGTGGCATCAAACAATCATTGC 58.672 40.909 0.00 0.00 0.00 3.56
4906 6643 3.930229 CCTGTGGCATCAAACAATCATTG 59.070 43.478 0.00 0.00 0.00 2.82
4907 6644 3.833650 TCCTGTGGCATCAAACAATCATT 59.166 39.130 0.00 0.00 0.00 2.57
4908 6645 3.433343 TCCTGTGGCATCAAACAATCAT 58.567 40.909 0.00 0.00 0.00 2.45
4909 6646 2.874014 TCCTGTGGCATCAAACAATCA 58.126 42.857 0.00 0.00 0.00 2.57
4910 6647 3.940209 TTCCTGTGGCATCAAACAATC 57.060 42.857 0.00 0.00 0.00 2.67
4911 6648 4.686191 TTTTCCTGTGGCATCAAACAAT 57.314 36.364 0.00 0.00 0.00 2.71
4912 6649 4.187694 GTTTTTCCTGTGGCATCAAACAA 58.812 39.130 0.00 0.00 0.00 2.83
4913 6650 3.196469 TGTTTTTCCTGTGGCATCAAACA 59.804 39.130 0.00 0.00 31.84 2.83
4914 6651 3.791245 TGTTTTTCCTGTGGCATCAAAC 58.209 40.909 0.00 0.00 0.00 2.93
4915 6652 4.478206 TTGTTTTTCCTGTGGCATCAAA 57.522 36.364 0.00 0.00 0.00 2.69
4916 6653 4.161189 TCTTTGTTTTTCCTGTGGCATCAA 59.839 37.500 0.00 0.00 0.00 2.57
4917 6654 3.703556 TCTTTGTTTTTCCTGTGGCATCA 59.296 39.130 0.00 0.00 0.00 3.07
4918 6655 4.320608 TCTTTGTTTTTCCTGTGGCATC 57.679 40.909 0.00 0.00 0.00 3.91
4919 6656 4.751767 TTCTTTGTTTTTCCTGTGGCAT 57.248 36.364 0.00 0.00 0.00 4.40
4920 6657 4.543590 TTTCTTTGTTTTTCCTGTGGCA 57.456 36.364 0.00 0.00 0.00 4.92
4921 6658 5.353956 ACAATTTCTTTGTTTTTCCTGTGGC 59.646 36.000 0.00 0.00 46.51 5.01
4922 6659 6.983474 ACAATTTCTTTGTTTTTCCTGTGG 57.017 33.333 0.00 0.00 46.51 4.17
4923 6660 8.925161 TCTACAATTTCTTTGTTTTTCCTGTG 57.075 30.769 0.00 0.00 46.51 3.66
4924 6661 9.936759 TTTCTACAATTTCTTTGTTTTTCCTGT 57.063 25.926 0.00 0.00 46.51 4.00
4931 6668 9.586435 CAACCTCTTTCTACAATTTCTTTGTTT 57.414 29.630 0.00 0.00 46.51 2.83
4932 6669 8.197439 CCAACCTCTTTCTACAATTTCTTTGTT 58.803 33.333 0.00 0.00 46.51 2.83
4934 6671 7.940850 TCCAACCTCTTTCTACAATTTCTTTG 58.059 34.615 0.00 0.00 41.36 2.77
4935 6672 7.780271 ACTCCAACCTCTTTCTACAATTTCTTT 59.220 33.333 0.00 0.00 0.00 2.52
4936 6673 7.229506 CACTCCAACCTCTTTCTACAATTTCTT 59.770 37.037 0.00 0.00 0.00 2.52
4937 6674 6.712547 CACTCCAACCTCTTTCTACAATTTCT 59.287 38.462 0.00 0.00 0.00 2.52
4938 6675 6.072452 CCACTCCAACCTCTTTCTACAATTTC 60.072 42.308 0.00 0.00 0.00 2.17
4939 6676 5.770162 CCACTCCAACCTCTTTCTACAATTT 59.230 40.000 0.00 0.00 0.00 1.82
4940 6677 5.073144 TCCACTCCAACCTCTTTCTACAATT 59.927 40.000 0.00 0.00 0.00 2.32
4941 6678 4.597507 TCCACTCCAACCTCTTTCTACAAT 59.402 41.667 0.00 0.00 0.00 2.71
4942 6679 3.971305 TCCACTCCAACCTCTTTCTACAA 59.029 43.478 0.00 0.00 0.00 2.41
4943 6680 3.583228 TCCACTCCAACCTCTTTCTACA 58.417 45.455 0.00 0.00 0.00 2.74
4944 6681 4.020128 ACATCCACTCCAACCTCTTTCTAC 60.020 45.833 0.00 0.00 0.00 2.59
4945 6682 4.168101 ACATCCACTCCAACCTCTTTCTA 58.832 43.478 0.00 0.00 0.00 2.10
4946 6683 2.982488 ACATCCACTCCAACCTCTTTCT 59.018 45.455 0.00 0.00 0.00 2.52
4947 6684 3.425162 ACATCCACTCCAACCTCTTTC 57.575 47.619 0.00 0.00 0.00 2.62
4948 6685 3.884037 AACATCCACTCCAACCTCTTT 57.116 42.857 0.00 0.00 0.00 2.52
4949 6686 4.993705 TTAACATCCACTCCAACCTCTT 57.006 40.909 0.00 0.00 0.00 2.85
4950 6687 5.520748 AATTAACATCCACTCCAACCTCT 57.479 39.130 0.00 0.00 0.00 3.69
4951 6688 6.350194 GGAAAATTAACATCCACTCCAACCTC 60.350 42.308 0.00 0.00 33.30 3.85
4952 6689 5.480422 GGAAAATTAACATCCACTCCAACCT 59.520 40.000 0.00 0.00 33.30 3.50
4953 6690 5.480422 AGGAAAATTAACATCCACTCCAACC 59.520 40.000 5.97 0.00 35.62 3.77
4954 6691 6.590234 AGGAAAATTAACATCCACTCCAAC 57.410 37.500 5.97 0.00 35.62 3.77
4955 6692 8.112822 TCATAGGAAAATTAACATCCACTCCAA 58.887 33.333 5.97 0.00 35.62 3.53
4956 6693 7.638444 TCATAGGAAAATTAACATCCACTCCA 58.362 34.615 5.97 0.00 35.62 3.86
4957 6694 8.519799 TTCATAGGAAAATTAACATCCACTCC 57.480 34.615 5.97 0.00 35.62 3.85
4958 6695 9.788960 GTTTCATAGGAAAATTAACATCCACTC 57.211 33.333 3.78 0.00 44.18 3.51
4959 6696 8.458843 CGTTTCATAGGAAAATTAACATCCACT 58.541 33.333 3.78 0.00 44.18 4.00
4960 6697 8.241367 ACGTTTCATAGGAAAATTAACATCCAC 58.759 33.333 3.78 0.00 44.18 4.02
4961 6698 8.343168 ACGTTTCATAGGAAAATTAACATCCA 57.657 30.769 3.78 0.00 44.18 3.41
4962 6699 9.931210 CTACGTTTCATAGGAAAATTAACATCC 57.069 33.333 3.78 0.00 44.18 3.51
4975 6712 9.843334 GGAATCTTCTATACTACGTTTCATAGG 57.157 37.037 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.