Multiple sequence alignment - TraesCS1A01G364900

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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 TraesCS1A01G364900 chr1A 100.000 5804 0 0 1 5804 544427031 544432834 0.000000e+00 10719
1 TraesCS1A01G364900 chr1D 94.535 4172 203 13 803 4957 449207224 449211387 0.000000e+00 6418
2 TraesCS1A01G364900 chr1D 88.360 189 10 5 5181 5357 449211473 449211661 3.520000e-52 217
3 TraesCS1A01G364900 chr1D 95.960 99 4 0 573 671 449206902 449207000 1.670000e-35 161
4 TraesCS1A01G364900 chr1D 92.929 99 7 0 5361 5459 449218691 449218789 1.690000e-30 145
5 TraesCS1A01G364900 chr1D 91.071 56 3 1 683 736 449207049 449207104 2.240000e-09 75
6 TraesCS1A01G364900 chr1B 94.027 4219 212 23 643 4833 614714933 614719139 0.000000e+00 6359
7 TraesCS1A01G364900 chr1B 89.583 576 48 6 1 569 410663271 410663841 0.000000e+00 721
8 TraesCS1A01G364900 chr1B 90.000 360 22 5 5091 5437 614719409 614719767 2.470000e-123 453
9 TraesCS1A01G364900 chr1B 80.625 320 55 5 218 536 429759374 429759687 2.090000e-59 241
10 TraesCS1A01G364900 chr3D 82.474 582 82 14 1 571 21923625 21923053 5.230000e-135 492
11 TraesCS1A01G364900 chr4B 82.504 583 61 14 1 571 507233564 507233011 1.890000e-129 473
12 TraesCS1A01G364900 chr2D 79.323 561 100 10 1 552 147354565 147354012 4.240000e-101 379
13 TraesCS1A01G364900 chr7D 76.401 589 115 18 1 576 33036071 33035494 4.400000e-76 296
14 TraesCS1A01G364900 chr6A 90.667 225 11 5 348 571 586829304 586829519 2.050000e-74 291
15 TraesCS1A01G364900 chr7B 83.333 162 19 7 411 571 115362026 115362180 6.060000e-30 143
16 TraesCS1A01G364900 chr7B 80.247 162 24 7 411 571 693157592 693157746 1.320000e-21 115
17 TraesCS1A01G364900 chr5D 81.818 165 19 9 411 572 463089784 463089628 1.700000e-25 128


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 TraesCS1A01G364900 chr1A 544427031 544432834 5803 False 10719.00 10719 100.0000 1 5804 1 chr1A.!!$F1 5803
1 TraesCS1A01G364900 chr1D 449206902 449211661 4759 False 1717.75 6418 92.4815 573 5357 4 chr1D.!!$F2 4784
2 TraesCS1A01G364900 chr1B 614714933 614719767 4834 False 3406.00 6359 92.0135 643 5437 2 chr1B.!!$F3 4794
3 TraesCS1A01G364900 chr1B 410663271 410663841 570 False 721.00 721 89.5830 1 569 1 chr1B.!!$F1 568
4 TraesCS1A01G364900 chr3D 21923053 21923625 572 True 492.00 492 82.4740 1 571 1 chr3D.!!$R1 570
5 TraesCS1A01G364900 chr4B 507233011 507233564 553 True 473.00 473 82.5040 1 571 1 chr4B.!!$R1 570
6 TraesCS1A01G364900 chr2D 147354012 147354565 553 True 379.00 379 79.3230 1 552 1 chr2D.!!$R1 551
7 TraesCS1A01G364900 chr7D 33035494 33036071 577 True 296.00 296 76.4010 1 576 1 chr7D.!!$R1 575

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
51 52 0.109532 TTGGTGCTGGACATCGGAAA 59.890 50.000 0.77 0.00 28.88 3.13 F
1459 1599 0.114954 TGGCAGCTCCCTTTGGAAAT 59.885 50.000 0.00 0.00 41.17 2.17 F
1617 1757 0.527113 TCGTCTCCGTAAAATCGCCA 59.473 50.000 0.00 0.00 35.01 5.69 F
1819 1959 1.032114 CATCAAGGCCGAGTTTCCCC 61.032 60.000 0.00 0.00 0.00 4.81 F
2272 2412 1.142465 AGCTATCACCCATGGAGCAAG 59.858 52.381 20.91 9.99 37.55 4.01 F
3449 3601 0.875059 GGAAGCAACGAGGTTTCAGG 59.125 55.000 0.00 0.00 38.24 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2125 1.579698 ATCGCTGACATCTGTGATGC 58.420 50.0 12.39 2.31 41.39 3.91 R
2613 2759 0.038251 AGCATCGTTCGACAAGCTCA 60.038 50.0 10.98 0.00 0.00 4.26 R
2856 3002 0.443869 CGAAGAACAGGATTGTGCGG 59.556 55.0 0.00 0.00 37.97 5.69 R
3111 3257 0.464452 CATTGGGAGGACGGAGGTAC 59.536 60.0 0.00 0.00 0.00 3.34 R
3868 4020 0.543277 ATGATCATGGTGGTGAGCGT 59.457 50.0 7.59 0.00 37.33 5.07 R
5015 5296 0.035915 GCTTGGGGGAGAGTTGACTC 60.036 60.0 2.93 2.93 43.17 3.36 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
33 34 0.392193 CTGGCTCGCACTCAAGGATT 60.392 55.000 0.00 0.00 0.00 3.01
50 51 0.327924 ATTGGTGCTGGACATCGGAA 59.672 50.000 0.77 0.00 28.88 4.30
51 52 0.109532 TTGGTGCTGGACATCGGAAA 59.890 50.000 0.77 0.00 28.88 3.13
85 90 2.753966 GCCGCATCAAGACGCATGT 61.754 57.895 0.00 0.00 0.00 3.21
107 115 2.548920 CCCTTATGCGAGGAGGATGAAC 60.549 54.545 2.42 0.00 39.25 3.18
290 299 8.418597 TCTCCACACTATCTTTGTACTAACTT 57.581 34.615 0.00 0.00 0.00 2.66
304 313 4.497291 ACTAACTTTGTGGGAGTTGTGA 57.503 40.909 0.09 0.00 37.84 3.58
317 326 1.880027 AGTTGTGAAAGCATCGGAACC 59.120 47.619 0.00 0.00 0.00 3.62
318 327 1.880027 GTTGTGAAAGCATCGGAACCT 59.120 47.619 0.00 0.00 0.00 3.50
337 346 3.099141 CCTTATTGTGTTTGATGGGGCT 58.901 45.455 0.00 0.00 0.00 5.19
371 380 1.043116 TGAGCTCATGGGTAGGGTCG 61.043 60.000 13.74 0.00 0.00 4.79
447 480 4.282496 CCCTTCTTCCTTAGACTAGAGCA 58.718 47.826 0.00 0.00 30.90 4.26
449 482 4.202111 CCTTCTTCCTTAGACTAGAGCAGC 60.202 50.000 0.00 0.00 30.90 5.25
450 483 2.946329 TCTTCCTTAGACTAGAGCAGCG 59.054 50.000 0.00 0.00 0.00 5.18
451 484 1.681538 TCCTTAGACTAGAGCAGCGG 58.318 55.000 0.00 0.00 0.00 5.52
452 485 1.212195 TCCTTAGACTAGAGCAGCGGA 59.788 52.381 0.00 0.00 0.00 5.54
453 486 1.606668 CCTTAGACTAGAGCAGCGGAG 59.393 57.143 0.00 0.00 0.00 4.63
484 517 2.889045 AGTGAGGAGTAGCGTTGTAACA 59.111 45.455 0.00 0.00 0.00 2.41
587 624 2.690653 AAACACAGCCGGCTAGCCAA 62.691 55.000 32.30 0.00 35.37 4.52
593 630 0.546598 AGCCGGCTAGCCAACTAAAT 59.453 50.000 31.86 8.54 35.37 1.40
674 711 5.122239 GGTATTTTACACCCACGGACTAAAC 59.878 44.000 0.00 0.00 0.00 2.01
732 808 6.140303 ACTTTGCTATCAAACATAGCCATG 57.860 37.500 10.40 5.46 44.66 3.66
760 867 2.330231 TTTGCAGCGCACACTAATTC 57.670 45.000 11.47 0.00 38.71 2.17
771 878 3.810373 CACACTAATTCAAGAACCGTGC 58.190 45.455 7.45 0.00 0.00 5.34
772 879 2.478894 ACACTAATTCAAGAACCGTGCG 59.521 45.455 7.45 0.00 0.00 5.34
773 880 2.478894 CACTAATTCAAGAACCGTGCGT 59.521 45.455 0.00 0.00 0.00 5.24
774 881 3.676172 CACTAATTCAAGAACCGTGCGTA 59.324 43.478 0.00 0.00 0.00 4.42
870 1004 2.362169 TCGATGCACGACTTGATCAA 57.638 45.000 8.12 8.12 46.45 2.57
884 1018 0.441533 GATCAACAGCGCACAGTCAG 59.558 55.000 11.47 2.13 0.00 3.51
910 1044 2.730094 CAACCACAACAGCCAGCC 59.270 61.111 0.00 0.00 0.00 4.85
936 1070 3.511146 TCCATTTGCTTCTTCCATGGAAC 59.489 43.478 23.63 13.94 40.39 3.62
946 1080 5.641789 TCTTCCATGGAACTGATCATCAT 57.358 39.130 23.63 0.00 0.00 2.45
952 1086 5.510349 CCATGGAACTGATCATCATACGAGT 60.510 44.000 5.56 0.00 0.00 4.18
954 1088 5.351458 TGGAACTGATCATCATACGAGTTG 58.649 41.667 0.00 0.00 0.00 3.16
980 1114 0.539986 TGGTTATCCAGCTCCCGAAC 59.460 55.000 0.00 0.00 39.03 3.95
1295 1429 4.592936 CCTCGAGTACGCGCTCCG 62.593 72.222 14.59 5.11 44.21 4.63
1438 1572 1.466167 CACCAAGAACCGCTTCATCTG 59.534 52.381 0.00 0.00 33.60 2.90
1459 1599 0.114954 TGGCAGCTCCCTTTGGAAAT 59.885 50.000 0.00 0.00 41.17 2.17
1493 1633 4.527157 GAGCAGCGCCGTCAATGC 62.527 66.667 2.29 6.32 38.97 3.56
1617 1757 0.527113 TCGTCTCCGTAAAATCGCCA 59.473 50.000 0.00 0.00 35.01 5.69
1623 1763 1.093496 CCGTAAAATCGCCAGGGGAC 61.093 60.000 8.73 0.00 0.00 4.46
1815 1955 2.739932 CGAGATCATCAAGGCCGAGTTT 60.740 50.000 0.00 0.00 0.00 2.66
1819 1959 1.032114 CATCAAGGCCGAGTTTCCCC 61.032 60.000 0.00 0.00 0.00 4.81
1842 1982 3.695606 ATGTGGGCGCACGTCTCT 61.696 61.111 26.42 7.95 0.00 3.10
1905 2045 2.185310 ATCCGGTGGTTGCAGGAGAC 62.185 60.000 0.00 0.00 36.26 3.36
1918 2058 4.451150 GAGACGCCGGCCATGACA 62.451 66.667 23.46 0.00 0.00 3.58
1971 2111 2.436824 GCCGGCAAGAGGTTCCTC 60.437 66.667 24.80 10.57 0.00 3.71
1985 2125 4.180946 CCTCCTCGTGCTCGACCG 62.181 72.222 6.80 0.57 41.35 4.79
2272 2412 1.142465 AGCTATCACCCATGGAGCAAG 59.858 52.381 20.91 9.99 37.55 4.01
2278 2418 1.452651 CCCATGGAGCAAGTCGCAT 60.453 57.895 15.22 0.00 46.13 4.73
2279 2419 1.721664 CCCATGGAGCAAGTCGCATG 61.722 60.000 15.22 0.00 46.13 4.06
2281 2421 2.117156 ATGGAGCAAGTCGCATGCC 61.117 57.895 13.15 0.00 44.91 4.40
2283 2423 2.334946 GGAGCAAGTCGCATGCCAA 61.335 57.895 13.15 0.00 44.91 4.52
2286 2426 1.401552 GAGCAAGTCGCATGCCAAATA 59.598 47.619 13.15 0.00 44.91 1.40
2340 2480 2.750888 GGCAATCGGGCGTTCACTC 61.751 63.158 0.00 0.00 33.57 3.51
2379 2519 2.087646 GAAGGCCACTGGAAAGATGTC 58.912 52.381 5.01 0.00 0.00 3.06
2409 2549 3.506743 TTGTGGCAGCAGGGGGAA 61.507 61.111 0.00 0.00 0.00 3.97
2671 2817 1.933853 GGAACAGATACGTCATGCACC 59.066 52.381 0.00 0.00 0.00 5.01
2684 2830 1.668793 TGCACCACACGATGCAGAG 60.669 57.895 0.00 0.00 46.63 3.35
2688 2834 2.104859 CCACACGATGCAGAGGCTG 61.105 63.158 0.00 0.00 41.91 4.85
2689 2835 1.375140 CACACGATGCAGAGGCTGT 60.375 57.895 0.00 0.00 41.91 4.40
2691 2837 2.163390 CACGATGCAGAGGCTGTCG 61.163 63.158 0.00 2.27 46.63 4.35
2856 3002 1.452108 CCATTTCCTCCAGCGGGTC 60.452 63.158 1.81 0.00 34.93 4.46
3095 3241 2.343758 GCTGCAGGTCCTTGACGA 59.656 61.111 17.12 0.00 32.65 4.20
3341 3487 1.750399 GCGATGCCAGTGGGTTCAT 60.750 57.895 12.15 5.84 36.17 2.57
3412 3558 1.200020 GCAAACTACACCTGTCATGGC 59.800 52.381 0.00 0.00 0.00 4.40
3449 3601 0.875059 GGAAGCAACGAGGTTTCAGG 59.125 55.000 0.00 0.00 38.24 3.86
3573 3725 0.962356 CTTGCTCCCTGCCGAATGTT 60.962 55.000 0.00 0.00 42.00 2.71
3586 3738 3.809832 GCCGAATGTTACATCTATGTGCT 59.190 43.478 5.85 0.00 41.89 4.40
3594 3746 6.643388 TGTTACATCTATGTGCTTGACAGAT 58.357 36.000 5.85 0.00 41.89 2.90
3622 3774 3.726144 GGGAGAGCCTGCCTTGCT 61.726 66.667 5.65 0.00 38.98 3.91
3648 3800 1.817099 CATGCCTTGCCTCGAGGTC 60.817 63.158 31.43 23.14 37.36 3.85
3686 3838 0.947244 CACTCTGTCAACAAGGTGGC 59.053 55.000 7.05 0.00 0.00 5.01
3705 3857 5.128919 GTGGCCATTTCTCAACTATCAGAT 58.871 41.667 9.72 0.00 0.00 2.90
3712 3864 9.339850 CCATTTCTCAACTATCAGATCAAGAAT 57.660 33.333 0.00 0.00 0.00 2.40
3852 4004 1.841556 TCCCAGCCTGACGACCTTT 60.842 57.895 0.00 0.00 0.00 3.11
3855 4007 1.738099 CAGCCTGACGACCTTTCCG 60.738 63.158 0.00 0.00 0.00 4.30
3868 4020 1.229145 TTTCCGGACGTCCCCCTTA 60.229 57.895 28.52 7.93 0.00 2.69
3870 4022 3.830192 CCGGACGTCCCCCTTACG 61.830 72.222 28.52 14.46 45.64 3.18
3894 4046 5.394883 GCTCACCACCATGATCATTGAAAAT 60.395 40.000 13.42 0.00 0.00 1.82
3915 4067 4.074526 GGTCTCGAGCTGCTGCCA 62.075 66.667 7.01 0.00 40.80 4.92
3924 4076 1.681793 GAGCTGCTGCCAATGATTCAT 59.318 47.619 7.01 0.00 40.80 2.57
3948 4100 4.903054 ACAAGCAGTCATCATCAGAAGAA 58.097 39.130 0.00 0.00 0.00 2.52
4104 4256 2.937469 CTCTGTCGATCAAGAGCTGT 57.063 50.000 9.07 0.00 0.00 4.40
4110 4262 1.745653 TCGATCAAGAGCTGTGACGAT 59.254 47.619 0.00 0.00 0.00 3.73
4167 4319 3.071206 GCGCTGAGGGACCTCTCA 61.071 66.667 18.48 13.98 43.12 3.27
4331 4483 4.103103 CTCGCACGTGAGCTCCGA 62.103 66.667 22.23 16.84 0.00 4.55
4421 4573 1.257155 GGAGAACACGTCGTTTGTGAC 59.743 52.381 0.00 5.40 38.19 3.67
4448 4600 4.942761 ACATGTTTGACAAGCTCCATTT 57.057 36.364 3.59 0.00 0.00 2.32
4452 4604 5.186996 TGTTTGACAAGCTCCATTTTCTC 57.813 39.130 3.59 0.00 0.00 2.87
4716 4868 4.852962 GAGCTGATCCAGAGGTGC 57.147 61.111 0.00 0.00 32.44 5.01
4719 4871 1.145819 GCTGATCCAGAGGTGCCTC 59.854 63.158 10.12 10.12 43.03 4.70
4779 4931 3.128589 GTGTCGTTTACATTGATGGGCAT 59.871 43.478 0.00 0.00 41.10 4.40
4828 4980 2.952310 GGCATTCTTGTTCCCCTGTATC 59.048 50.000 0.00 0.00 0.00 2.24
4897 5176 6.513180 TCCATCTGAATCGTATGAAACCTAC 58.487 40.000 0.00 0.00 0.00 3.18
4898 5177 6.323996 TCCATCTGAATCGTATGAAACCTACT 59.676 38.462 0.00 0.00 0.00 2.57
4899 5178 6.422100 CCATCTGAATCGTATGAAACCTACTG 59.578 42.308 0.00 0.00 0.00 2.74
4914 5193 9.256477 TGAAACCTACTGTATTATATTGCTTCG 57.744 33.333 0.00 0.00 0.00 3.79
4915 5194 8.603242 AAACCTACTGTATTATATTGCTTCGG 57.397 34.615 0.00 0.00 0.00 4.30
4917 5196 7.376615 ACCTACTGTATTATATTGCTTCGGAC 58.623 38.462 0.00 0.00 0.00 4.79
4925 5204 0.537143 ATTGCTTCGGACTGTTGGCA 60.537 50.000 0.00 0.00 0.00 4.92
4929 5210 1.405526 GCTTCGGACTGTTGGCATAGA 60.406 52.381 6.31 0.00 0.00 1.98
4936 5217 4.125703 GGACTGTTGGCATAGAGATTGAG 58.874 47.826 6.31 0.00 0.00 3.02
4940 5221 4.711399 TGTTGGCATAGAGATTGAGATGG 58.289 43.478 0.00 0.00 0.00 3.51
4960 5241 2.159198 GGCATTGGTACCTGCAATTCAG 60.159 50.000 23.31 2.67 42.49 3.02
4961 5242 2.493278 GCATTGGTACCTGCAATTCAGT 59.507 45.455 18.65 0.00 41.25 3.41
4963 5244 4.561326 GCATTGGTACCTGCAATTCAGTTT 60.561 41.667 18.65 0.00 41.25 2.66
4965 5246 5.606348 TTGGTACCTGCAATTCAGTTTTT 57.394 34.783 14.36 0.00 41.25 1.94
4966 5247 4.942852 TGGTACCTGCAATTCAGTTTTTG 58.057 39.130 14.36 0.00 41.25 2.44
4967 5248 3.740832 GGTACCTGCAATTCAGTTTTTGC 59.259 43.478 4.06 0.88 46.53 3.68
4995 5276 4.871933 GTGAACTCCACATTTTCCCATT 57.128 40.909 0.00 0.00 45.03 3.16
4996 5277 5.213891 GTGAACTCCACATTTTCCCATTT 57.786 39.130 0.00 0.00 45.03 2.32
4997 5278 4.990426 GTGAACTCCACATTTTCCCATTTG 59.010 41.667 0.00 0.00 45.03 2.32
4998 5279 3.683365 ACTCCACATTTTCCCATTTGC 57.317 42.857 0.00 0.00 0.00 3.68
4999 5280 2.971330 ACTCCACATTTTCCCATTTGCA 59.029 40.909 0.00 0.00 0.00 4.08
5000 5281 3.244181 ACTCCACATTTTCCCATTTGCAC 60.244 43.478 0.00 0.00 0.00 4.57
5001 5282 2.067766 CCACATTTTCCCATTTGCACG 58.932 47.619 0.00 0.00 0.00 5.34
5002 5283 1.460359 CACATTTTCCCATTTGCACGC 59.540 47.619 0.00 0.00 0.00 5.34
5003 5284 1.069823 ACATTTTCCCATTTGCACGCA 59.930 42.857 0.00 0.00 0.00 5.24
5004 5285 1.460359 CATTTTCCCATTTGCACGCAC 59.540 47.619 0.00 0.00 0.00 5.34
5005 5286 0.461548 TTTTCCCATTTGCACGCACA 59.538 45.000 0.00 0.00 0.00 4.57
5006 5287 0.249238 TTTCCCATTTGCACGCACAC 60.249 50.000 0.00 0.00 0.00 3.82
5007 5288 1.106351 TTCCCATTTGCACGCACACT 61.106 50.000 0.00 0.00 0.00 3.55
5008 5289 1.106351 TCCCATTTGCACGCACACTT 61.106 50.000 0.00 0.00 0.00 3.16
5009 5290 0.249405 CCCATTTGCACGCACACTTT 60.249 50.000 0.00 0.00 0.00 2.66
5010 5291 0.854062 CCATTTGCACGCACACTTTG 59.146 50.000 0.00 0.00 0.00 2.77
5011 5292 1.558741 CATTTGCACGCACACTTTGT 58.441 45.000 0.00 0.00 0.00 2.83
5012 5293 1.518102 CATTTGCACGCACACTTTGTC 59.482 47.619 0.00 0.00 0.00 3.18
5013 5294 0.808125 TTTGCACGCACACTTTGTCT 59.192 45.000 0.00 0.00 0.00 3.41
5014 5295 0.376852 TTGCACGCACACTTTGTCTC 59.623 50.000 0.00 0.00 0.00 3.36
5015 5296 1.083401 GCACGCACACTTTGTCTCG 60.083 57.895 0.00 0.00 32.13 4.04
5016 5297 1.487452 GCACGCACACTTTGTCTCGA 61.487 55.000 4.97 0.00 30.95 4.04
5017 5298 0.504384 CACGCACACTTTGTCTCGAG 59.496 55.000 5.93 5.93 30.95 4.04
5018 5299 0.102481 ACGCACACTTTGTCTCGAGT 59.898 50.000 13.13 0.00 30.95 4.18
5028 5309 1.535833 TGTCTCGAGTCAACTCTCCC 58.464 55.000 13.13 0.00 40.75 4.30
5031 5312 0.612174 CTCGAGTCAACTCTCCCCCA 60.612 60.000 3.62 0.00 40.75 4.96
5033 5314 0.247736 CGAGTCAACTCTCCCCCAAG 59.752 60.000 8.43 0.00 40.75 3.61
5044 5325 4.722700 CCCCAAGCCCCGTGTCTG 62.723 72.222 0.00 0.00 0.00 3.51
5047 5328 4.988598 CAAGCCCCGTGTCTGCGT 62.989 66.667 0.00 0.00 0.00 5.24
5048 5329 4.681978 AAGCCCCGTGTCTGCGTC 62.682 66.667 0.00 0.00 0.00 5.19
5077 5358 4.688966 GGGAGGCGCATCCGGATC 62.689 72.222 32.41 16.60 40.56 3.36
5078 5359 4.688966 GGAGGCGCATCCGGATCC 62.689 72.222 26.96 13.52 40.77 3.36
5111 5392 1.606313 CCACATCCCCACCAACCAC 60.606 63.158 0.00 0.00 0.00 4.16
5257 5588 4.525949 GGAGGGTCGCGGCCTTAC 62.526 72.222 31.31 21.30 0.00 2.34
5376 5719 4.530857 CCGTCCCTCGCCATGTCC 62.531 72.222 0.00 0.00 38.35 4.02
5389 5732 3.958147 ATGTCCGGCGTGCAAGGAG 62.958 63.158 6.01 0.00 34.29 3.69
5409 5752 4.832608 GGCTAGGCCGTCGGGTTG 62.833 72.222 14.38 0.00 39.62 3.77
5412 5755 2.362760 TAGGCCGTCGGGTTGCTA 60.363 61.111 14.38 0.00 34.97 3.49
5415 5758 2.713967 GGCCGTCGGGTTGCTACTA 61.714 63.158 14.38 0.00 34.97 1.82
5422 5765 0.036765 CGGGTTGCTACTACTGGCAA 60.037 55.000 0.00 0.00 44.64 4.52
5426 5769 1.003233 GTTGCTACTACTGGCAAGGGT 59.997 52.381 0.00 0.00 46.87 4.34
5428 5771 0.107654 GCTACTACTGGCAAGGGTGG 60.108 60.000 0.00 0.00 0.00 4.61
5429 5772 1.568504 CTACTACTGGCAAGGGTGGA 58.431 55.000 0.00 0.00 0.00 4.02
5431 5774 1.201429 ACTACTGGCAAGGGTGGAGG 61.201 60.000 0.00 0.00 0.00 4.30
5432 5775 1.151899 TACTGGCAAGGGTGGAGGT 60.152 57.895 0.00 0.00 0.00 3.85
5433 5776 1.488705 TACTGGCAAGGGTGGAGGTG 61.489 60.000 0.00 0.00 0.00 4.00
5434 5777 4.284550 TGGCAAGGGTGGAGGTGC 62.285 66.667 0.00 0.00 36.24 5.01
5435 5778 4.284550 GGCAAGGGTGGAGGTGCA 62.285 66.667 0.00 0.00 38.78 4.57
5436 5779 2.674380 GCAAGGGTGGAGGTGCAG 60.674 66.667 0.00 0.00 36.97 4.41
5437 5780 2.674380 CAAGGGTGGAGGTGCAGC 60.674 66.667 8.11 8.11 0.00 5.25
5438 5781 4.335647 AAGGGTGGAGGTGCAGCG 62.336 66.667 10.78 0.00 0.00 5.18
5463 5806 3.599602 TTGGCCACAAGGGATGGA 58.400 55.556 3.88 0.00 39.87 3.41
5464 5807 1.857049 TTGGCCACAAGGGATGGAA 59.143 52.632 3.88 0.00 39.87 3.53
5465 5808 0.413037 TTGGCCACAAGGGATGGAAT 59.587 50.000 3.88 0.00 39.87 3.01
5466 5809 0.413037 TGGCCACAAGGGATGGAATT 59.587 50.000 0.00 0.00 39.87 2.17
5467 5810 1.203288 TGGCCACAAGGGATGGAATTT 60.203 47.619 0.00 0.00 39.87 1.82
5468 5811 1.908619 GGCCACAAGGGATGGAATTTT 59.091 47.619 0.00 0.00 39.87 1.82
5469 5812 2.305635 GGCCACAAGGGATGGAATTTTT 59.694 45.455 0.00 0.00 39.87 1.94
5517 5860 8.908172 TTTTGCAAAAAGAAATCCAAATTCAC 57.092 26.923 21.94 0.00 0.00 3.18
5518 5861 6.284475 TGCAAAAAGAAATCCAAATTCACG 57.716 33.333 0.00 0.00 0.00 4.35
5519 5862 6.045318 TGCAAAAAGAAATCCAAATTCACGA 58.955 32.000 0.00 0.00 0.00 4.35
5520 5863 6.536582 TGCAAAAAGAAATCCAAATTCACGAA 59.463 30.769 0.00 0.00 0.00 3.85
5521 5864 7.065283 GCAAAAAGAAATCCAAATTCACGAAG 58.935 34.615 0.00 0.00 0.00 3.79
5523 5866 8.603181 CAAAAAGAAATCCAAATTCACGAAGTT 58.397 29.630 0.00 0.00 41.61 2.66
5524 5867 8.716646 AAAAGAAATCCAAATTCACGAAGTTT 57.283 26.923 0.00 0.00 41.61 2.66
5525 5868 8.716646 AAAGAAATCCAAATTCACGAAGTTTT 57.283 26.923 0.00 0.00 41.61 2.43
5526 5869 8.716646 AAGAAATCCAAATTCACGAAGTTTTT 57.283 26.923 0.00 0.00 41.61 1.94
5560 5903 9.938670 CAAATTCAAAAATGTTCATCAATGTGT 57.061 25.926 0.00 0.00 0.00 3.72
5571 5914 9.761504 ATGTTCATCAATGTGTAAAAATGTTCA 57.238 25.926 0.00 0.00 0.00 3.18
5572 5915 9.761504 TGTTCATCAATGTGTAAAAATGTTCAT 57.238 25.926 0.00 0.00 0.00 2.57
5633 5976 9.170734 TGTTCATCCAAATTCAAAATTTGTTCA 57.829 25.926 18.67 7.40 37.32 3.18
5636 5979 8.710551 TCATCCAAATTCAAAATTTGTTCATCG 58.289 29.630 18.67 7.18 37.32 3.84
5637 5980 8.710551 CATCCAAATTCAAAATTTGTTCATCGA 58.289 29.630 18.67 10.95 37.32 3.59
5638 5981 8.654230 TCCAAATTCAAAATTTGTTCATCGAA 57.346 26.923 18.67 0.00 37.32 3.71
5639 5982 9.270640 TCCAAATTCAAAATTTGTTCATCGAAT 57.729 25.926 18.67 0.00 37.32 3.34
5640 5983 9.881529 CCAAATTCAAAATTTGTTCATCGAATT 57.118 25.926 18.67 0.36 40.65 2.17
5675 6018 7.849496 TCATCAAATTCCAAATTTGTTCAACG 58.151 30.769 16.73 0.81 39.36 4.10
5676 6019 7.708322 TCATCAAATTCCAAATTTGTTCAACGA 59.292 29.630 16.73 7.12 39.36 3.85
5677 6020 8.497554 CATCAAATTCCAAATTTGTTCAACGAT 58.502 29.630 16.73 8.90 39.36 3.73
5678 6021 8.430801 TCAAATTCCAAATTTGTTCAACGATT 57.569 26.923 16.73 3.98 39.36 3.34
5679 6022 8.887717 TCAAATTCCAAATTTGTTCAACGATTT 58.112 25.926 16.73 8.78 39.36 2.17
5680 6023 9.157259 CAAATTCCAAATTTGTTCAACGATTTC 57.843 29.630 16.73 0.00 35.07 2.17
5681 6024 8.430801 AATTCCAAATTTGTTCAACGATTTCA 57.569 26.923 16.73 0.00 0.00 2.69
5682 6025 7.834068 TTCCAAATTTGTTCAACGATTTCAA 57.166 28.000 16.73 0.00 0.00 2.69
5683 6026 7.834068 TCCAAATTTGTTCAACGATTTCAAA 57.166 28.000 16.73 0.00 33.61 2.69
5684 6027 8.256611 TCCAAATTTGTTCAACGATTTCAAAA 57.743 26.923 16.73 0.00 32.99 2.44
5685 6028 8.721478 TCCAAATTTGTTCAACGATTTCAAAAA 58.279 25.926 16.73 0.00 32.99 1.94
5711 6054 9.881529 AAATGTGCATCAAATACAAAATTTGTC 57.118 25.926 15.22 0.00 44.12 3.18
5712 6055 7.418840 TGTGCATCAAATACAAAATTTGTCC 57.581 32.000 15.22 0.00 44.12 4.02
5713 6056 6.988580 TGTGCATCAAATACAAAATTTGTCCA 59.011 30.769 15.22 0.00 44.12 4.02
5714 6057 7.660617 TGTGCATCAAATACAAAATTTGTCCAT 59.339 29.630 15.22 1.38 44.12 3.41
5715 6058 8.170553 GTGCATCAAATACAAAATTTGTCCATC 58.829 33.333 15.22 0.00 44.12 3.51
5716 6059 7.063191 TGCATCAAATACAAAATTTGTCCATCG 59.937 33.333 15.22 2.24 44.12 3.84
5717 6060 7.275341 GCATCAAATACAAAATTTGTCCATCGA 59.725 33.333 15.22 7.38 44.12 3.59
5718 6061 9.138062 CATCAAATACAAAATTTGTCCATCGAA 57.862 29.630 15.22 0.00 44.12 3.71
5719 6062 9.874205 ATCAAATACAAAATTTGTCCATCGAAT 57.126 25.926 15.22 0.00 44.12 3.34
5720 6063 9.138062 TCAAATACAAAATTTGTCCATCGAATG 57.862 29.630 15.22 5.14 44.12 2.67
5721 6064 8.924691 CAAATACAAAATTTGTCCATCGAATGT 58.075 29.630 15.22 0.00 44.12 2.71
5722 6065 8.464770 AATACAAAATTTGTCCATCGAATGTG 57.535 30.769 15.22 0.00 44.12 3.21
5723 6066 5.841810 ACAAAATTTGTCCATCGAATGTGT 58.158 33.333 5.41 0.00 40.56 3.72
5724 6067 6.279882 ACAAAATTTGTCCATCGAATGTGTT 58.720 32.000 5.41 0.00 40.56 3.32
5725 6068 6.420604 ACAAAATTTGTCCATCGAATGTGTTC 59.579 34.615 5.41 0.00 40.56 3.18
5726 6069 5.703978 AATTTGTCCATCGAATGTGTTCA 57.296 34.783 0.00 0.00 33.86 3.18
5727 6070 5.902613 ATTTGTCCATCGAATGTGTTCAT 57.097 34.783 0.00 0.00 33.86 2.57
5728 6071 4.944962 TTGTCCATCGAATGTGTTCATC 57.055 40.909 0.00 0.00 33.86 2.92
5729 6072 3.270027 TGTCCATCGAATGTGTTCATCC 58.730 45.455 0.00 0.00 33.86 3.51
5730 6073 3.270027 GTCCATCGAATGTGTTCATCCA 58.730 45.455 0.00 0.00 33.86 3.41
5731 6074 3.879295 GTCCATCGAATGTGTTCATCCAT 59.121 43.478 0.00 0.00 33.86 3.41
5732 6075 4.336433 GTCCATCGAATGTGTTCATCCATT 59.664 41.667 0.00 0.00 33.86 3.16
5733 6076 5.527214 GTCCATCGAATGTGTTCATCCATTA 59.473 40.000 0.00 0.00 33.86 1.90
5734 6077 6.205464 GTCCATCGAATGTGTTCATCCATTAT 59.795 38.462 0.00 0.00 33.86 1.28
5735 6078 6.772233 TCCATCGAATGTGTTCATCCATTATT 59.228 34.615 0.00 0.00 33.86 1.40
5736 6079 7.041167 TCCATCGAATGTGTTCATCCATTATTC 60.041 37.037 0.00 0.00 33.86 1.75
5737 6080 7.255208 CCATCGAATGTGTTCATCCATTATTCA 60.255 37.037 0.00 0.00 33.86 2.57
5738 6081 7.622893 TCGAATGTGTTCATCCATTATTCAA 57.377 32.000 0.00 0.00 33.86 2.69
5739 6082 8.049655 TCGAATGTGTTCATCCATTATTCAAA 57.950 30.769 0.00 0.00 33.86 2.69
5740 6083 8.518702 TCGAATGTGTTCATCCATTATTCAAAA 58.481 29.630 0.00 0.00 33.86 2.44
5741 6084 9.138062 CGAATGTGTTCATCCATTATTCAAAAA 57.862 29.630 0.00 0.00 33.86 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 0.321564 CTTTCCGATGTCCAGCACCA 60.322 55.000 0.00 0.00 0.00 4.17
85 90 1.133167 TCATCCTCCTCGCATAAGGGA 60.133 52.381 0.00 0.00 37.02 4.20
181 190 2.264794 GTCGGCGTCCAATCCAGT 59.735 61.111 6.85 0.00 0.00 4.00
290 299 2.136298 TGCTTTCACAACTCCCACAA 57.864 45.000 0.00 0.00 0.00 3.33
304 313 4.079253 ACACAATAAGGTTCCGATGCTTT 58.921 39.130 0.00 0.00 0.00 3.51
317 326 4.675146 CGAAGCCCCATCAAACACAATAAG 60.675 45.833 0.00 0.00 0.00 1.73
318 327 3.192422 CGAAGCCCCATCAAACACAATAA 59.808 43.478 0.00 0.00 0.00 1.40
346 355 0.839277 TACCCATGAGCTCACCCATG 59.161 55.000 20.97 13.41 39.72 3.66
361 370 1.305549 TTCAGACCCGACCCTACCC 60.306 63.158 0.00 0.00 0.00 3.69
371 380 2.576648 ACCATAACCTTCCTTCAGACCC 59.423 50.000 0.00 0.00 0.00 4.46
447 480 3.203412 CTACTCGTCCGCTCCGCT 61.203 66.667 0.00 0.00 0.00 5.52
449 482 2.037913 CTCACTACTCGTCCGCTCCG 62.038 65.000 0.00 0.00 0.00 4.63
450 483 1.716826 CCTCACTACTCGTCCGCTCC 61.717 65.000 0.00 0.00 0.00 4.70
451 484 0.743701 TCCTCACTACTCGTCCGCTC 60.744 60.000 0.00 0.00 0.00 5.03
452 485 0.745128 CTCCTCACTACTCGTCCGCT 60.745 60.000 0.00 0.00 0.00 5.52
453 486 1.025647 ACTCCTCACTACTCGTCCGC 61.026 60.000 0.00 0.00 0.00 5.54
454 487 2.203401 CTACTCCTCACTACTCGTCCG 58.797 57.143 0.00 0.00 0.00 4.79
484 517 4.343814 CCACCACCAATTTACAAAGGTCTT 59.656 41.667 0.00 0.00 30.44 3.01
571 608 2.238847 TAGTTGGCTAGCCGGCTGTG 62.239 60.000 38.98 29.37 39.42 3.66
574 611 0.546598 ATTTAGTTGGCTAGCCGGCT 59.453 50.000 34.85 34.85 39.42 5.52
587 624 3.057806 GTGGGCAGCGTTGTAAATTTAGT 60.058 43.478 0.00 0.00 0.00 2.24
593 630 2.255172 CCGTGGGCAGCGTTGTAAA 61.255 57.895 0.00 0.00 0.00 2.01
620 657 5.060662 TGACATAATACAGAGCGCCTATC 57.939 43.478 2.29 0.00 0.00 2.08
674 711 9.950680 AAACAATGTATCAACAAACTACAGAAG 57.049 29.630 0.00 0.00 39.58 2.85
703 779 8.072567 GGCTATGTTTGATAGCAAAGTATTGAG 58.927 37.037 6.36 2.11 46.47 3.02
732 808 1.387756 GTGCGCTGCAAATTCAACATC 59.612 47.619 9.73 0.00 41.47 3.06
906 1040 0.457337 GAAGCAAATGGAAGCGGCTG 60.457 55.000 1.81 0.00 34.56 4.85
910 1044 1.541147 TGGAAGAAGCAAATGGAAGCG 59.459 47.619 0.00 0.00 35.48 4.68
936 1070 3.721035 TGCCAACTCGTATGATGATCAG 58.279 45.455 0.09 0.00 0.00 2.90
946 1080 2.851263 AACCAATCTGCCAACTCGTA 57.149 45.000 0.00 0.00 0.00 3.43
952 1086 2.025037 AGCTGGATAACCAATCTGCCAA 60.025 45.455 0.00 0.00 46.32 4.52
954 1088 2.225467 GAGCTGGATAACCAATCTGCC 58.775 52.381 0.00 0.00 46.32 4.85
1012 1146 2.591715 GAGCTTGTGCGGTGGTGT 60.592 61.111 0.00 0.00 45.42 4.16
1438 1572 3.066814 CCAAAGGGAGCTGCCAGC 61.067 66.667 27.56 9.13 42.84 4.85
1493 1633 3.024547 TCTCTTAGTCCGTCCAGATTGG 58.975 50.000 0.00 0.00 39.43 3.16
1905 2045 4.854924 TGGATGTCATGGCCGGCG 62.855 66.667 22.54 6.96 0.00 6.46
1918 2058 3.036429 GCTCCCTGGCGTCTTGGAT 62.036 63.158 1.31 0.00 0.00 3.41
1985 2125 1.579698 ATCGCTGACATCTGTGATGC 58.420 50.000 12.39 2.31 41.39 3.91
1987 2127 1.579698 GCATCGCTGACATCTGTGAT 58.420 50.000 8.52 8.52 42.93 3.06
2106 2246 1.832912 GAGGATCAGCGGGGTCATT 59.167 57.895 0.00 0.00 33.17 2.57
2244 2384 0.105453 TGGGTGATAGCTCCTCCTCC 60.105 60.000 0.00 0.00 0.00 4.30
2272 2412 2.105984 TGGCTATTTGGCATGCGAC 58.894 52.632 12.44 0.00 46.76 5.19
2279 2419 2.159057 CCCATGTTCTTGGCTATTTGGC 60.159 50.000 0.00 0.00 42.18 4.52
2281 2421 3.169355 GCCCATGTTCTTGGCTATTTG 57.831 47.619 2.95 0.00 42.01 2.32
2340 2480 2.609183 CTTCGTCCCGCCGGAAGTAG 62.609 65.000 5.05 3.56 40.92 2.57
2379 2519 0.883833 GCCACAAGTTGTCATCCAGG 59.116 55.000 5.27 4.47 0.00 4.45
2613 2759 0.038251 AGCATCGTTCGACAAGCTCA 60.038 50.000 10.98 0.00 0.00 4.26
2671 2817 1.357258 GACAGCCTCTGCATCGTGTG 61.357 60.000 0.00 0.00 41.13 3.82
2684 2830 4.427661 AGACTGCTCGCGACAGCC 62.428 66.667 27.32 20.96 38.80 4.85
2688 2834 2.202544 CCTGAGACTGCTCGCGAC 60.203 66.667 3.71 2.83 44.33 5.19
2689 2835 3.443925 CCCTGAGACTGCTCGCGA 61.444 66.667 9.26 9.26 44.33 5.87
2691 2837 2.493973 CTCCCTGAGACTGCTCGC 59.506 66.667 0.00 0.00 44.33 5.03
2856 3002 0.443869 CGAAGAACAGGATTGTGCGG 59.556 55.000 0.00 0.00 37.97 5.69
3090 3236 1.538204 GGAGAGTTGCACTTGTCGTCA 60.538 52.381 0.00 0.00 0.00 4.35
3095 3241 1.270147 GGTACGGAGAGTTGCACTTGT 60.270 52.381 0.00 0.00 0.00 3.16
3111 3257 0.464452 CATTGGGAGGACGGAGGTAC 59.536 60.000 0.00 0.00 0.00 3.34
3114 3260 2.911143 CCATTGGGAGGACGGAGG 59.089 66.667 0.00 0.00 35.59 4.30
3341 3487 2.844348 GTTCCCTTCAGGATACCCTTCA 59.156 50.000 0.00 0.00 46.94 3.02
3412 3558 1.524621 CGGCCATGGAACTGCTAGG 60.525 63.158 18.40 0.00 0.00 3.02
3449 3601 2.415857 CACTCAAGCAGCTCTTCATCAC 59.584 50.000 0.00 0.00 31.27 3.06
3573 3725 5.525012 GCAATCTGTCAAGCACATAGATGTA 59.475 40.000 0.00 0.00 39.39 2.29
3586 3738 2.507484 CCAGTTCAGGCAATCTGTCAA 58.493 47.619 0.00 0.00 43.76 3.18
3594 3746 1.376466 GCTCTCCCAGTTCAGGCAA 59.624 57.895 0.00 0.00 0.00 4.52
3686 3838 8.728337 TTCTTGATCTGATAGTTGAGAAATGG 57.272 34.615 0.00 0.00 0.00 3.16
3705 3857 3.074412 GAGCTTCGGGAACAATTCTTGA 58.926 45.455 0.00 0.00 0.00 3.02
3712 3864 1.953686 CCTTTTGAGCTTCGGGAACAA 59.046 47.619 0.00 0.00 0.00 2.83
3852 4004 2.362889 GTAAGGGGGACGTCCGGA 60.363 66.667 27.68 0.00 36.71 5.14
3855 4007 3.073101 AGCGTAAGGGGGACGTCC 61.073 66.667 27.04 27.04 42.31 4.79
3868 4020 0.543277 ATGATCATGGTGGTGAGCGT 59.457 50.000 7.59 0.00 37.33 5.07
3870 4022 2.646930 TCAATGATCATGGTGGTGAGC 58.353 47.619 9.46 0.00 35.18 4.26
3894 4046 1.005748 CAGCAGCTCGAGACCAACA 60.006 57.895 18.75 0.00 0.00 3.33
4167 4319 1.585006 CTTCGGGCAGTCGTACAGT 59.415 57.895 0.00 0.00 0.00 3.55
4315 4467 3.396911 GATCGGAGCTCACGTGCGA 62.397 63.158 17.19 14.91 42.22 5.10
4331 4483 3.607163 CAACCTTGCCGCCATGAT 58.393 55.556 0.00 0.00 0.00 2.45
4354 4506 0.969917 GAGCTCAGCCAGTCCAGAGA 60.970 60.000 9.40 0.00 0.00 3.10
4421 4573 2.624838 AGCTTGTCAAACATGTTCAGGG 59.375 45.455 12.39 2.52 0.00 4.45
4479 4631 3.342627 CCGTCAAAGAACGCGCCA 61.343 61.111 5.73 0.00 41.26 5.69
4491 4643 0.107831 CAAACTCCCAGGAACCGTCA 59.892 55.000 0.00 0.00 0.00 4.35
4546 4698 2.031163 ACTCAGTTCACCGCAGCC 59.969 61.111 0.00 0.00 0.00 4.85
4611 4763 4.947147 GCCGGGCAGTTGTCCACA 62.947 66.667 15.62 0.00 40.62 4.17
4716 4868 1.536149 GATCAAGTTCGTCGTCGAGG 58.464 55.000 8.62 8.62 46.81 4.63
4719 4871 1.730593 GCCGATCAAGTTCGTCGTCG 61.731 60.000 0.00 0.00 37.42 5.12
4761 4913 7.062138 GCAATATTATGCCCATCAATGTAAACG 59.938 37.037 0.00 0.00 40.49 3.60
4897 5176 7.307396 CCAACAGTCCGAAGCAATATAATACAG 60.307 40.741 0.00 0.00 0.00 2.74
4898 5177 6.481976 CCAACAGTCCGAAGCAATATAATACA 59.518 38.462 0.00 0.00 0.00 2.29
4899 5178 6.565999 GCCAACAGTCCGAAGCAATATAATAC 60.566 42.308 0.00 0.00 0.00 1.89
4907 5186 0.537143 ATGCCAACAGTCCGAAGCAA 60.537 50.000 0.00 0.00 33.35 3.91
4914 5193 4.125703 CTCAATCTCTATGCCAACAGTCC 58.874 47.826 0.00 0.00 0.00 3.85
4915 5194 5.016051 TCTCAATCTCTATGCCAACAGTC 57.984 43.478 0.00 0.00 0.00 3.51
4917 5196 4.755629 CCATCTCAATCTCTATGCCAACAG 59.244 45.833 0.00 0.00 0.00 3.16
4925 5204 5.579753 ACCAATGCCATCTCAATCTCTAT 57.420 39.130 0.00 0.00 0.00 1.98
4929 5210 3.461085 AGGTACCAATGCCATCTCAATCT 59.539 43.478 15.94 0.00 31.71 2.40
4936 5217 1.473258 TTGCAGGTACCAATGCCATC 58.527 50.000 20.19 0.00 41.85 3.51
4940 5221 3.056607 AACTGAATTGCAGGTACCAATGC 60.057 43.478 15.94 16.64 44.54 3.56
4960 5241 2.783832 GAGTTCACAGCTTCGCAAAAAC 59.216 45.455 0.00 0.00 0.00 2.43
4961 5242 2.223479 GGAGTTCACAGCTTCGCAAAAA 60.223 45.455 0.00 0.00 0.00 1.94
4963 5244 0.944386 GGAGTTCACAGCTTCGCAAA 59.056 50.000 0.00 0.00 0.00 3.68
4965 5246 0.880278 GTGGAGTTCACAGCTTCGCA 60.880 55.000 0.00 0.00 45.39 5.10
4966 5247 1.862806 GTGGAGTTCACAGCTTCGC 59.137 57.895 0.00 0.00 45.39 4.70
4974 5255 4.871933 AATGGGAAAATGTGGAGTTCAC 57.128 40.909 0.00 0.00 46.23 3.18
4976 5257 3.996363 GCAAATGGGAAAATGTGGAGTTC 59.004 43.478 0.00 0.00 0.00 3.01
4977 5258 3.390639 TGCAAATGGGAAAATGTGGAGTT 59.609 39.130 0.00 0.00 0.00 3.01
4978 5259 2.971330 TGCAAATGGGAAAATGTGGAGT 59.029 40.909 0.00 0.00 0.00 3.85
4979 5260 3.328505 GTGCAAATGGGAAAATGTGGAG 58.671 45.455 0.00 0.00 0.00 3.86
4980 5261 2.288702 CGTGCAAATGGGAAAATGTGGA 60.289 45.455 0.00 0.00 0.00 4.02
4981 5262 2.067766 CGTGCAAATGGGAAAATGTGG 58.932 47.619 0.00 0.00 0.00 4.17
4982 5263 1.460359 GCGTGCAAATGGGAAAATGTG 59.540 47.619 0.00 0.00 0.00 3.21
4983 5264 1.069823 TGCGTGCAAATGGGAAAATGT 59.930 42.857 0.00 0.00 0.00 2.71
4984 5265 1.460359 GTGCGTGCAAATGGGAAAATG 59.540 47.619 0.00 0.00 0.00 2.32
4985 5266 1.069823 TGTGCGTGCAAATGGGAAAAT 59.930 42.857 0.00 0.00 0.00 1.82
4986 5267 0.461548 TGTGCGTGCAAATGGGAAAA 59.538 45.000 0.00 0.00 0.00 2.29
4987 5268 0.249238 GTGTGCGTGCAAATGGGAAA 60.249 50.000 0.00 0.00 0.00 3.13
4988 5269 1.106351 AGTGTGCGTGCAAATGGGAA 61.106 50.000 0.00 0.00 0.00 3.97
4989 5270 1.106351 AAGTGTGCGTGCAAATGGGA 61.106 50.000 0.00 0.00 0.00 4.37
4990 5271 0.249405 AAAGTGTGCGTGCAAATGGG 60.249 50.000 0.00 0.00 0.00 4.00
4991 5272 0.854062 CAAAGTGTGCGTGCAAATGG 59.146 50.000 0.00 0.00 0.00 3.16
4992 5273 1.518102 GACAAAGTGTGCGTGCAAATG 59.482 47.619 0.00 0.00 0.00 2.32
4993 5274 1.405105 AGACAAAGTGTGCGTGCAAAT 59.595 42.857 0.00 0.00 0.00 2.32
4994 5275 0.808125 AGACAAAGTGTGCGTGCAAA 59.192 45.000 0.00 0.00 0.00 3.68
4995 5276 0.376852 GAGACAAAGTGTGCGTGCAA 59.623 50.000 0.00 0.00 0.00 4.08
4996 5277 1.761244 CGAGACAAAGTGTGCGTGCA 61.761 55.000 0.00 0.00 0.00 4.57
4997 5278 1.083401 CGAGACAAAGTGTGCGTGC 60.083 57.895 0.00 0.00 0.00 5.34
4998 5279 0.504384 CTCGAGACAAAGTGTGCGTG 59.496 55.000 6.58 0.00 0.00 5.34
4999 5280 0.102481 ACTCGAGACAAAGTGTGCGT 59.898 50.000 21.68 0.00 0.00 5.24
5000 5281 0.778815 GACTCGAGACAAAGTGTGCG 59.221 55.000 21.68 0.00 0.00 5.34
5001 5282 1.852942 TGACTCGAGACAAAGTGTGC 58.147 50.000 21.68 0.00 0.00 4.57
5002 5283 3.448686 AGTTGACTCGAGACAAAGTGTG 58.551 45.455 27.42 0.00 32.18 3.82
5003 5284 3.707793 GAGTTGACTCGAGACAAAGTGT 58.292 45.455 27.42 14.85 32.18 3.55
5015 5296 0.035915 GCTTGGGGGAGAGTTGACTC 60.036 60.000 2.93 2.93 43.17 3.36
5016 5297 1.492993 GGCTTGGGGGAGAGTTGACT 61.493 60.000 0.00 0.00 0.00 3.41
5017 5298 1.002011 GGCTTGGGGGAGAGTTGAC 60.002 63.158 0.00 0.00 0.00 3.18
5018 5299 2.231380 GGGCTTGGGGGAGAGTTGA 61.231 63.158 0.00 0.00 0.00 3.18
5031 5312 4.681978 GACGCAGACACGGGGCTT 62.682 66.667 0.00 0.00 37.37 4.35
5060 5341 4.688966 GATCCGGATGCGCCTCCC 62.689 72.222 24.82 12.30 31.04 4.30
5061 5342 4.688966 GGATCCGGATGCGCCTCC 62.689 72.222 24.82 20.63 0.00 4.30
5081 5362 4.157120 ATGTGGTACTCGGCGGCC 62.157 66.667 9.54 9.54 0.00 6.13
5086 5367 1.520666 GTGGGGATGTGGTACTCGG 59.479 63.158 0.00 0.00 0.00 4.63
5159 5440 3.787001 CTCCCTCCCGGCACCTTC 61.787 72.222 0.00 0.00 0.00 3.46
5370 5713 3.803082 CCTTGCACGCCGGACATG 61.803 66.667 5.05 0.00 0.00 3.21
5371 5714 3.958147 CTCCTTGCACGCCGGACAT 62.958 63.158 5.05 0.00 0.00 3.06
5409 5752 0.107654 CCACCCTTGCCAGTAGTAGC 60.108 60.000 0.00 0.00 0.00 3.58
5412 5755 1.201429 CCTCCACCCTTGCCAGTAGT 61.201 60.000 0.00 0.00 0.00 2.73
5415 5758 2.450502 ACCTCCACCCTTGCCAGT 60.451 61.111 0.00 0.00 0.00 4.00
5431 5774 3.730761 CAAGAGGCACCGCTGCAC 61.731 66.667 4.88 0.00 46.28 4.57
5445 5788 0.251742 TTCCATCCCTTGTGGCCAAG 60.252 55.000 7.24 0.96 46.33 3.61
5446 5789 0.413037 ATTCCATCCCTTGTGGCCAA 59.587 50.000 7.24 0.00 36.66 4.52
5447 5790 0.413037 AATTCCATCCCTTGTGGCCA 59.587 50.000 0.00 0.00 36.66 5.36
5448 5791 1.571955 AAATTCCATCCCTTGTGGCC 58.428 50.000 0.00 0.00 36.66 5.36
5449 5792 3.701205 AAAAATTCCATCCCTTGTGGC 57.299 42.857 0.00 0.00 36.66 5.01
5491 5834 9.351570 GTGAATTTGGATTTCTTTTTGCAAAAA 57.648 25.926 29.97 29.97 36.86 1.94
5492 5835 7.695618 CGTGAATTTGGATTTCTTTTTGCAAAA 59.304 29.630 20.46 20.46 36.86 2.44
5493 5836 7.065085 TCGTGAATTTGGATTTCTTTTTGCAAA 59.935 29.630 8.05 8.05 37.53 3.68
5494 5837 6.536582 TCGTGAATTTGGATTTCTTTTTGCAA 59.463 30.769 0.00 0.00 0.00 4.08
5495 5838 6.045318 TCGTGAATTTGGATTTCTTTTTGCA 58.955 32.000 0.00 0.00 0.00 4.08
5496 5839 6.523676 TCGTGAATTTGGATTTCTTTTTGC 57.476 33.333 0.00 0.00 0.00 3.68
5497 5840 8.130307 ACTTCGTGAATTTGGATTTCTTTTTG 57.870 30.769 0.00 0.00 0.00 2.44
5498 5841 8.716646 AACTTCGTGAATTTGGATTTCTTTTT 57.283 26.923 0.00 0.00 0.00 1.94
5499 5842 8.716646 AAACTTCGTGAATTTGGATTTCTTTT 57.283 26.923 0.00 0.00 0.00 2.27
5500 5843 8.716646 AAAACTTCGTGAATTTGGATTTCTTT 57.283 26.923 0.00 0.00 0.00 2.52
5501 5844 8.716646 AAAAACTTCGTGAATTTGGATTTCTT 57.283 26.923 0.00 0.00 0.00 2.52
5534 5877 9.938670 ACACATTGATGAACATTTTTGAATTTG 57.061 25.926 0.00 0.00 0.00 2.32
5545 5888 9.761504 TGAACATTTTTACACATTGATGAACAT 57.238 25.926 0.00 0.00 0.00 2.71
5546 5889 9.761504 ATGAACATTTTTACACATTGATGAACA 57.238 25.926 0.00 0.00 0.00 3.18
5607 5950 9.170734 TGAACAAATTTTGAATTTGGATGAACA 57.829 25.926 22.70 13.36 41.80 3.18
5610 5953 8.710551 CGATGAACAAATTTTGAATTTGGATGA 58.289 29.630 22.70 11.14 41.80 2.92
5611 5954 8.710551 TCGATGAACAAATTTTGAATTTGGATG 58.289 29.630 22.70 11.12 41.80 3.51
5612 5955 8.830201 TCGATGAACAAATTTTGAATTTGGAT 57.170 26.923 22.70 14.64 41.80 3.41
5613 5956 8.654230 TTCGATGAACAAATTTTGAATTTGGA 57.346 26.923 22.70 11.31 41.80 3.53
5614 5957 9.881529 AATTCGATGAACAAATTTTGAATTTGG 57.118 25.926 22.70 9.73 41.80 3.28
5649 5992 8.333908 CGTTGAACAAATTTGGAATTTGATGAA 58.666 29.630 24.79 14.94 40.42 2.57
5650 5993 7.708322 TCGTTGAACAAATTTGGAATTTGATGA 59.292 29.630 24.79 14.16 40.42 2.92
5651 5994 7.849496 TCGTTGAACAAATTTGGAATTTGATG 58.151 30.769 24.79 12.64 40.42 3.07
5652 5995 8.606040 ATCGTTGAACAAATTTGGAATTTGAT 57.394 26.923 24.79 16.91 40.42 2.57
5653 5996 8.430801 AATCGTTGAACAAATTTGGAATTTGA 57.569 26.923 24.79 12.60 40.42 2.69
5654 5997 9.157259 GAAATCGTTGAACAAATTTGGAATTTG 57.843 29.630 21.74 19.22 42.81 2.32
5655 5998 8.887717 TGAAATCGTTGAACAAATTTGGAATTT 58.112 25.926 21.74 14.20 0.00 1.82
5656 5999 8.430801 TGAAATCGTTGAACAAATTTGGAATT 57.569 26.923 21.74 7.62 0.00 2.17
5657 6000 8.430801 TTGAAATCGTTGAACAAATTTGGAAT 57.569 26.923 21.74 7.99 0.00 3.01
5658 6001 7.834068 TTGAAATCGTTGAACAAATTTGGAA 57.166 28.000 21.74 8.92 0.00 3.53
5659 6002 7.834068 TTTGAAATCGTTGAACAAATTTGGA 57.166 28.000 21.74 8.81 0.00 3.53
5660 6003 8.886816 TTTTTGAAATCGTTGAACAAATTTGG 57.113 26.923 21.74 3.54 32.05 3.28
5685 6028 9.881529 GACAAATTTTGTATTTGATGCACATTT 57.118 25.926 14.49 0.00 45.52 2.32
5686 6029 8.505625 GGACAAATTTTGTATTTGATGCACATT 58.494 29.630 14.49 0.00 45.52 2.71
5687 6030 7.660617 TGGACAAATTTTGTATTTGATGCACAT 59.339 29.630 14.49 0.00 45.52 3.21
5688 6031 6.988580 TGGACAAATTTTGTATTTGATGCACA 59.011 30.769 14.49 5.59 45.52 4.57
5689 6032 7.418840 TGGACAAATTTTGTATTTGATGCAC 57.581 32.000 14.49 0.00 45.52 4.57
5690 6033 7.063191 CGATGGACAAATTTTGTATTTGATGCA 59.937 33.333 14.49 11.15 45.52 3.96
5691 6034 7.275341 TCGATGGACAAATTTTGTATTTGATGC 59.725 33.333 14.49 0.49 45.52 3.91
5692 6035 8.686397 TCGATGGACAAATTTTGTATTTGATG 57.314 30.769 14.49 3.20 45.52 3.07
5693 6036 9.874205 ATTCGATGGACAAATTTTGTATTTGAT 57.126 25.926 14.49 3.42 45.52 2.57
5694 6037 9.138062 CATTCGATGGACAAATTTTGTATTTGA 57.862 29.630 14.49 8.91 45.52 2.69
5695 6038 8.924691 ACATTCGATGGACAAATTTTGTATTTG 58.075 29.630 14.49 3.79 45.52 2.32
5696 6039 8.924691 CACATTCGATGGACAAATTTTGTATTT 58.075 29.630 14.49 2.88 45.52 1.40
5697 6040 8.087750 ACACATTCGATGGACAAATTTTGTATT 58.912 29.630 14.49 3.22 45.52 1.89
5698 6041 7.601856 ACACATTCGATGGACAAATTTTGTAT 58.398 30.769 14.49 6.05 45.52 2.29
5699 6042 6.976088 ACACATTCGATGGACAAATTTTGTA 58.024 32.000 14.49 1.15 45.52 2.41
5700 6043 7.896645 TGAACACATTCGATGGACAAATTTTGT 60.897 33.333 14.42 14.42 41.47 2.83
5701 6044 6.420306 TGAACACATTCGATGGACAAATTTTG 59.580 34.615 7.59 7.59 37.69 2.44
5702 6045 6.511416 TGAACACATTCGATGGACAAATTTT 58.489 32.000 0.00 0.00 37.69 1.82
5703 6046 6.083098 TGAACACATTCGATGGACAAATTT 57.917 33.333 0.00 0.00 37.69 1.82
5704 6047 5.703978 TGAACACATTCGATGGACAAATT 57.296 34.783 0.00 0.00 37.69 1.82
5705 6048 5.163622 GGATGAACACATTCGATGGACAAAT 60.164 40.000 0.00 0.00 37.69 2.32
5706 6049 4.155826 GGATGAACACATTCGATGGACAAA 59.844 41.667 0.00 0.00 37.69 2.83
5707 6050 3.689161 GGATGAACACATTCGATGGACAA 59.311 43.478 0.00 0.00 37.69 3.18
5708 6051 3.270027 GGATGAACACATTCGATGGACA 58.730 45.455 0.00 0.00 37.69 4.02
5709 6052 3.270027 TGGATGAACACATTCGATGGAC 58.730 45.455 0.00 0.00 37.69 4.02
5710 6053 3.625649 TGGATGAACACATTCGATGGA 57.374 42.857 0.00 0.00 37.69 3.41
5711 6054 4.906065 AATGGATGAACACATTCGATGG 57.094 40.909 0.00 0.00 37.69 3.51
5712 6055 7.641760 TGAATAATGGATGAACACATTCGATG 58.358 34.615 0.00 0.00 38.24 3.84
5713 6056 7.806409 TGAATAATGGATGAACACATTCGAT 57.194 32.000 0.00 0.00 38.24 3.59
5714 6057 7.622893 TTGAATAATGGATGAACACATTCGA 57.377 32.000 0.00 0.00 38.24 3.71
5715 6058 8.686397 TTTTGAATAATGGATGAACACATTCG 57.314 30.769 0.00 0.00 38.24 3.34


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

AutoCloner maintained by Alex Coulton.