Multiple sequence alignment - TraesCS2D01G491700

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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 TraesCS2D01G491700 chr2D 100.000 3430 0 0 2116 5545 590068975 590072404 0.000000e+00 6335
1 TraesCS2D01G491700 chr2D 100.000 1869 0 0 1 1869 590066860 590068728 0.000000e+00 3452
2 TraesCS2D01G491700 chr2D 89.372 207 20 2 3641 3846 647674604 647674809 5.510000e-65 259
3 TraesCS2D01G491700 chr2D 83.065 124 18 3 1 123 646491503 646491624 5.870000e-20 110
4 TraesCS2D01G491700 chr2D 95.652 46 2 0 535 580 646499746 646499791 2.140000e-09 75
5 TraesCS2D01G491700 chr2B 93.982 2609 116 12 2268 4855 714498120 714500708 0.000000e+00 3910
6 TraesCS2D01G491700 chr2B 90.134 1348 70 25 535 1869 714496675 714497972 0.000000e+00 1694
7 TraesCS2D01G491700 chr2B 85.227 528 30 23 1 490 714495902 714496419 2.980000e-137 499
8 TraesCS2D01G491700 chr2B 87.791 172 21 0 5243 5414 714264725 714264554 9.420000e-48 202
9 TraesCS2D01G491700 chr2B 87.791 172 21 0 5243 5414 714319810 714319639 9.420000e-48 202
10 TraesCS2D01G491700 chr2B 91.026 78 5 2 2207 2284 714498032 714498107 2.730000e-18 104
11 TraesCS2D01G491700 chr2A 96.495 1455 44 4 2943 4391 724374708 724376161 0.000000e+00 2398
12 TraesCS2D01G491700 chr2A 92.301 1104 69 15 767 1869 724372663 724373751 0.000000e+00 1554
13 TraesCS2D01G491700 chr2A 95.814 645 21 6 4384 5024 724377029 724377671 0.000000e+00 1037
14 TraesCS2D01G491700 chr2A 93.686 681 26 6 2279 2944 724373948 724374626 0.000000e+00 1003
15 TraesCS2D01G491700 chr2A 92.757 497 26 4 5053 5545 724377662 724378152 0.000000e+00 710
16 TraesCS2D01G491700 chr2A 91.481 270 11 4 1 258 724371907 724372176 1.470000e-95 361
17 TraesCS2D01G491700 chr2A 90.977 266 20 2 4574 4838 724356796 724356534 6.830000e-94 355
18 TraesCS2D01G491700 chr2A 77.111 450 58 27 4970 5408 724353671 724353256 9.350000e-53 219
19 TraesCS2D01G491700 chr2A 88.344 163 16 2 984 1145 724367796 724367956 5.670000e-45 193
20 TraesCS2D01G491700 chr5D 93.939 198 12 0 3647 3844 468172228 468172031 3.250000e-77 300
21 TraesCS2D01G491700 chr5D 92.391 92 6 1 2116 2207 38319088 38319178 4.510000e-26 130
22 TraesCS2D01G491700 chr5B 93.434 198 13 0 3647 3844 574958083 574957886 1.510000e-75 294
23 TraesCS2D01G491700 chr5B 95.699 93 4 0 2116 2208 80200682 80200590 3.460000e-32 150
24 TraesCS2D01G491700 chr5B 95.699 93 4 0 2116 2208 80605163 80605071 3.460000e-32 150
25 TraesCS2D01G491700 chr7A 92.040 201 15 1 3644 3843 5651078 5650878 1.180000e-71 281
26 TraesCS2D01G491700 chr6B 91.133 203 16 2 3642 3843 347750844 347751045 1.970000e-69 274
27 TraesCS2D01G491700 chr6B 93.548 93 6 0 2116 2208 615646511 615646603 7.490000e-29 139
28 TraesCS2D01G491700 chr4D 91.133 203 17 1 3642 3843 258893655 258893453 1.970000e-69 274
29 TraesCS2D01G491700 chr1D 90.594 202 16 3 3644 3843 481698013 481697813 1.180000e-66 265
30 TraesCS2D01G491700 chr4B 98.925 93 1 0 2116 2208 459067662 459067754 3.440000e-37 167
31 TraesCS2D01G491700 chr4B 97.849 93 2 0 2116 2208 646867465 646867373 1.600000e-35 161
32 TraesCS2D01G491700 chr6D 97.849 93 2 0 2116 2208 6390262 6390354 1.600000e-35 161
33 TraesCS2D01G491700 chr3A 96.774 93 3 0 2116 2208 584293859 584293767 7.440000e-34 156
34 TraesCS2D01G491700 chr7D 91.398 93 7 1 2116 2208 453547011 453546920 5.830000e-25 126


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 TraesCS2D01G491700 chr2D 590066860 590072404 5544 False 4893.500000 6335 100.000000 1 5545 2 chr2D.!!$F4 5544
1 TraesCS2D01G491700 chr2B 714495902 714500708 4806 False 1551.750000 3910 90.092250 1 4855 4 chr2B.!!$F1 4854
2 TraesCS2D01G491700 chr2A 724367796 724378152 10356 False 1036.571429 2398 92.982571 1 5545 7 chr2A.!!$F1 5544
3 TraesCS2D01G491700 chr2A 724353256 724356796 3540 True 287.000000 355 84.044000 4574 5408 2 chr2A.!!$R1 834

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
693 5118 0.039437 CGTCCTCCGAATATCCCACG 60.039 60.0 0.00 0.0 39.56 4.94 F
971 5413 0.321653 GACATCTCACCACCACCACC 60.322 60.0 0.00 0.0 0.00 4.61 F
973 5415 0.606401 CATCTCACCACCACCACCAC 60.606 60.0 0.00 0.0 0.00 4.16 F
974 5416 1.779061 ATCTCACCACCACCACCACC 61.779 60.0 0.00 0.0 0.00 4.61 F
3084 7725 0.693049 ATGGAAAAGGTCTGAGCCGT 59.307 50.0 2.76 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2571 7114 0.969149 TCGGTGAGTTCTGACTGCAT 59.031 50.000 0.00 0.0 35.88 3.96 R
2965 7599 7.667219 ACAAGATCACCTGATAACAACTGAAAT 59.333 33.333 0.00 0.0 34.37 2.17 R
3084 7725 2.763448 CCCCTCAACACAAGACCAAAAA 59.237 45.455 0.00 0.0 0.00 1.94 R
3148 7789 4.818546 AGCATCAACATTATCACTACCAGC 59.181 41.667 0.00 0.0 0.00 4.85 R
4656 10181 0.899717 GCCTTGTCATCAAAGGGGCA 60.900 55.000 4.48 0.0 40.13 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
40 4152 0.524862 GACTGTTCGGCCGACTCTAA 59.475 55.000 31.19 10.55 0.00 2.10
41 4153 0.243095 ACTGTTCGGCCGACTCTAAC 59.757 55.000 31.19 23.47 0.00 2.34
44 4156 0.522915 GTTCGGCCGACTCTAACGAG 60.523 60.000 31.19 0.00 43.10 4.18
151 4266 0.656259 CAGCAGCATTGATCGGTCTG 59.344 55.000 0.00 0.00 0.00 3.51
219 4343 2.759191 TGATGCTGTGTGTCTTCAGTC 58.241 47.619 0.00 0.00 34.57 3.51
285 4409 1.830587 CTGGACCTGCCACTGCTGTA 61.831 60.000 0.00 0.00 43.33 2.74
312 4436 4.760530 ATCACCATCTAAAGCTGCAGTA 57.239 40.909 16.64 0.00 0.00 2.74
313 4437 4.551702 TCACCATCTAAAGCTGCAGTAA 57.448 40.909 16.64 0.00 0.00 2.24
314 4438 4.507710 TCACCATCTAAAGCTGCAGTAAG 58.492 43.478 16.64 7.89 0.00 2.34
361 4499 3.802948 AGTACCATTCATGAGACCGAC 57.197 47.619 0.00 0.00 0.00 4.79
363 4501 0.175760 ACCATTCATGAGACCGACGG 59.824 55.000 13.61 13.61 0.00 4.79
364 4502 1.154205 CCATTCATGAGACCGACGGC 61.154 60.000 15.39 7.02 0.00 5.68
365 4503 0.460109 CATTCATGAGACCGACGGCA 60.460 55.000 15.39 4.22 0.00 5.69
366 4504 0.179100 ATTCATGAGACCGACGGCAG 60.179 55.000 15.39 0.00 0.00 4.85
367 4505 1.532604 TTCATGAGACCGACGGCAGT 61.533 55.000 15.39 0.00 0.00 4.40
368 4506 0.678684 TCATGAGACCGACGGCAGTA 60.679 55.000 15.39 0.00 0.00 2.74
369 4507 0.525668 CATGAGACCGACGGCAGTAC 60.526 60.000 15.39 2.03 0.00 2.73
370 4508 0.963856 ATGAGACCGACGGCAGTACA 60.964 55.000 15.39 7.98 0.00 2.90
385 4523 3.364366 GCAGTACAGAACATCAAGTGCAC 60.364 47.826 9.40 9.40 36.68 4.57
386 4524 3.187227 CAGTACAGAACATCAAGTGCACC 59.813 47.826 14.63 0.00 0.00 5.01
390 4528 0.163788 GAACATCAAGTGCACCGTCG 59.836 55.000 14.63 0.98 0.00 5.12
437 4603 0.682209 CCTCATTGTCCCTGGCCTTG 60.682 60.000 3.32 0.00 0.00 3.61
454 4620 3.243636 GCCTTGTGAATATCTGCCCAATG 60.244 47.826 0.00 0.00 0.00 2.82
476 4643 4.096532 TGTTTTAGGAACAAACATGTGCGA 59.903 37.500 0.00 0.00 38.84 5.10
491 4658 1.929836 GTGCGACAGATTAGCCTCTTG 59.070 52.381 0.00 0.00 0.00 3.02
492 4659 0.933796 GCGACAGATTAGCCTCTTGC 59.066 55.000 0.00 0.00 41.71 4.01
493 4660 1.740380 GCGACAGATTAGCCTCTTGCA 60.740 52.381 0.00 0.00 44.83 4.08
496 4663 3.492309 CGACAGATTAGCCTCTTGCAGAT 60.492 47.826 0.00 0.00 44.83 2.90
497 4664 4.261783 CGACAGATTAGCCTCTTGCAGATA 60.262 45.833 0.00 0.00 44.83 1.98
498 4665 5.566429 CGACAGATTAGCCTCTTGCAGATAT 60.566 44.000 0.00 0.00 44.83 1.63
499 4666 5.549347 ACAGATTAGCCTCTTGCAGATATG 58.451 41.667 0.00 0.00 44.83 1.78
501 4668 5.638657 CAGATTAGCCTCTTGCAGATATGAC 59.361 44.000 0.00 0.00 44.83 3.06
505 4672 5.149973 AGCCTCTTGCAGATATGACTATG 57.850 43.478 0.00 0.00 44.83 2.23
506 4673 4.592351 AGCCTCTTGCAGATATGACTATGT 59.408 41.667 0.00 0.00 44.83 2.29
507 4674 5.071519 AGCCTCTTGCAGATATGACTATGTT 59.928 40.000 0.00 0.00 44.83 2.71
508 4675 5.762218 GCCTCTTGCAGATATGACTATGTTT 59.238 40.000 0.00 0.00 40.77 2.83
510 4677 7.201767 GCCTCTTGCAGATATGACTATGTTTTT 60.202 37.037 0.00 0.00 40.77 1.94
569 4989 5.978919 TGATCAGCAGAAAACATTTGAACAC 59.021 36.000 0.00 0.00 0.00 3.32
595 5015 2.159430 TCAACAGACCGCGATTGATTTG 59.841 45.455 8.23 3.75 0.00 2.32
597 5017 1.086696 CAGACCGCGATTGATTTGGT 58.913 50.000 8.23 0.00 35.14 3.67
599 5019 2.675844 CAGACCGCGATTGATTTGGTTA 59.324 45.455 8.23 0.00 31.86 2.85
600 5020 3.312421 CAGACCGCGATTGATTTGGTTAT 59.688 43.478 8.23 0.00 31.86 1.89
619 5044 5.858049 GGTTATTAACAAACTTGGTTACGCC 59.142 40.000 8.73 0.00 30.91 5.68
644 5069 1.206371 ACGAAGGCCAGCGTAAACTAT 59.794 47.619 19.49 0.00 39.21 2.12
662 5087 2.125773 ATAAGTCCACGTCTCCGTCT 57.874 50.000 0.00 0.00 46.28 4.18
680 5105 2.095692 GTCTTCTTCTACCGTCGTCCTC 59.904 54.545 0.00 0.00 0.00 3.71
683 5108 0.742281 CTTCTACCGTCGTCCTCCGA 60.742 60.000 0.00 0.00 45.00 4.55
691 5116 3.833729 TCGTCCTCCGAATATCCCA 57.166 52.632 0.00 0.00 44.03 4.37
692 5117 1.325355 TCGTCCTCCGAATATCCCAC 58.675 55.000 0.00 0.00 44.03 4.61
693 5118 0.039437 CGTCCTCCGAATATCCCACG 60.039 60.000 0.00 0.00 39.56 4.94
695 5120 0.469331 TCCTCCGAATATCCCACGCT 60.469 55.000 0.00 0.00 0.00 5.07
698 5123 2.022129 CCGAATATCCCACGCTCGC 61.022 63.158 0.00 0.00 0.00 5.03
721 5146 2.511600 GATCGTCGCCCCCACAAG 60.512 66.667 0.00 0.00 0.00 3.16
722 5147 4.096003 ATCGTCGCCCCCACAAGG 62.096 66.667 0.00 0.00 0.00 3.61
741 5166 2.664081 CCACAGCCTCTCCACCTCC 61.664 68.421 0.00 0.00 0.00 4.30
744 5169 0.768221 ACAGCCTCTCCACCTCCAAA 60.768 55.000 0.00 0.00 0.00 3.28
746 5171 0.474660 AGCCTCTCCACCTCCAAACT 60.475 55.000 0.00 0.00 0.00 2.66
747 5172 0.402121 GCCTCTCCACCTCCAAACTT 59.598 55.000 0.00 0.00 0.00 2.66
748 5173 1.611936 GCCTCTCCACCTCCAAACTTC 60.612 57.143 0.00 0.00 0.00 3.01
749 5174 1.003696 CCTCTCCACCTCCAAACTTCC 59.996 57.143 0.00 0.00 0.00 3.46
750 5175 1.699634 CTCTCCACCTCCAAACTTCCA 59.300 52.381 0.00 0.00 0.00 3.53
751 5176 2.106511 CTCTCCACCTCCAAACTTCCAA 59.893 50.000 0.00 0.00 0.00 3.53
752 5177 2.512056 TCTCCACCTCCAAACTTCCAAA 59.488 45.455 0.00 0.00 0.00 3.28
753 5178 2.623416 CTCCACCTCCAAACTTCCAAAC 59.377 50.000 0.00 0.00 0.00 2.93
754 5179 2.243736 TCCACCTCCAAACTTCCAAACT 59.756 45.455 0.00 0.00 0.00 2.66
755 5180 3.031013 CCACCTCCAAACTTCCAAACTT 58.969 45.455 0.00 0.00 0.00 2.66
756 5181 3.068165 CCACCTCCAAACTTCCAAACTTC 59.932 47.826 0.00 0.00 0.00 3.01
757 5182 3.068165 CACCTCCAAACTTCCAAACTTCC 59.932 47.826 0.00 0.00 0.00 3.46
758 5183 3.052869 ACCTCCAAACTTCCAAACTTCCT 60.053 43.478 0.00 0.00 0.00 3.36
759 5184 3.960755 CCTCCAAACTTCCAAACTTCCTT 59.039 43.478 0.00 0.00 0.00 3.36
760 5185 4.038042 CCTCCAAACTTCCAAACTTCCTTC 59.962 45.833 0.00 0.00 0.00 3.46
761 5186 4.867086 TCCAAACTTCCAAACTTCCTTCT 58.133 39.130 0.00 0.00 0.00 2.85
772 5197 5.312079 CAAACTTCCTTCTCAACTCCAGAT 58.688 41.667 0.00 0.00 0.00 2.90
773 5198 4.817318 ACTTCCTTCTCAACTCCAGATC 57.183 45.455 0.00 0.00 0.00 2.75
774 5199 4.163427 ACTTCCTTCTCAACTCCAGATCA 58.837 43.478 0.00 0.00 0.00 2.92
780 5211 3.184628 TCTCAACTCCAGATCACCCAAT 58.815 45.455 0.00 0.00 0.00 3.16
814 5245 1.812571 GTCGGCAATCCATCAAACACT 59.187 47.619 0.00 0.00 0.00 3.55
816 5247 2.228582 TCGGCAATCCATCAAACACTTG 59.771 45.455 0.00 0.00 0.00 3.16
819 5250 3.367703 GGCAATCCATCAAACACTTGGAG 60.368 47.826 0.00 0.00 42.53 3.86
900 5332 1.842381 CTTCGAACCCCCAAGAGCCT 61.842 60.000 0.00 0.00 0.00 4.58
912 5354 4.851214 GAGCCTCGCCCCTCTCCT 62.851 72.222 0.00 0.00 0.00 3.69
938 5380 2.614013 ATCCCCACTCCACCACCC 60.614 66.667 0.00 0.00 0.00 4.61
968 5410 0.389948 GACGACATCTCACCACCACC 60.390 60.000 0.00 0.00 0.00 4.61
969 5411 1.118965 ACGACATCTCACCACCACCA 61.119 55.000 0.00 0.00 0.00 4.17
970 5412 0.670546 CGACATCTCACCACCACCAC 60.671 60.000 0.00 0.00 0.00 4.16
971 5413 0.321653 GACATCTCACCACCACCACC 60.322 60.000 0.00 0.00 0.00 4.61
972 5414 1.059584 ACATCTCACCACCACCACCA 61.060 55.000 0.00 0.00 0.00 4.17
973 5415 0.606401 CATCTCACCACCACCACCAC 60.606 60.000 0.00 0.00 0.00 4.16
974 5416 1.779061 ATCTCACCACCACCACCACC 61.779 60.000 0.00 0.00 0.00 4.61
975 5417 2.692741 TCACCACCACCACCACCA 60.693 61.111 0.00 0.00 0.00 4.17
976 5418 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
982 5424 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
988 5430 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
991 5433 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
994 5436 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
1209 5651 1.831652 CGCACTTCCAGGACCTCCTT 61.832 60.000 0.00 0.00 46.09 3.36
1669 6111 2.941583 GGGGCTGGGAGGTTTCCT 60.942 66.667 0.00 0.00 43.49 3.36
1836 6278 6.205464 GCATTGCAGAATTAGTTGCTATCCTA 59.795 38.462 3.15 0.00 40.87 2.94
2141 6585 9.196552 GAATATATTTCAAAGTGGCCTTAATGC 57.803 33.333 3.32 0.00 0.00 3.56
2154 6598 5.056894 GCCTTAATGCCATGAGATTGATC 57.943 43.478 0.00 0.00 0.00 2.92
2155 6599 4.082354 GCCTTAATGCCATGAGATTGATCC 60.082 45.833 0.00 0.00 0.00 3.36
2156 6600 5.074804 CCTTAATGCCATGAGATTGATCCA 58.925 41.667 0.00 0.00 0.00 3.41
2157 6601 5.183331 CCTTAATGCCATGAGATTGATCCAG 59.817 44.000 0.00 0.00 0.00 3.86
2158 6602 3.878237 ATGCCATGAGATTGATCCAGT 57.122 42.857 0.00 0.00 0.00 4.00
2159 6603 3.657398 TGCCATGAGATTGATCCAGTT 57.343 42.857 0.00 0.00 0.00 3.16
2160 6604 3.972133 TGCCATGAGATTGATCCAGTTT 58.028 40.909 0.00 0.00 0.00 2.66
2161 6605 5.114764 TGCCATGAGATTGATCCAGTTTA 57.885 39.130 0.00 0.00 0.00 2.01
2162 6606 5.698104 TGCCATGAGATTGATCCAGTTTAT 58.302 37.500 0.00 0.00 0.00 1.40
2163 6607 6.840527 TGCCATGAGATTGATCCAGTTTATA 58.159 36.000 0.00 0.00 0.00 0.98
2164 6608 7.289310 TGCCATGAGATTGATCCAGTTTATAA 58.711 34.615 0.00 0.00 0.00 0.98
2165 6609 7.446319 TGCCATGAGATTGATCCAGTTTATAAG 59.554 37.037 0.00 0.00 0.00 1.73
2166 6610 7.094463 GCCATGAGATTGATCCAGTTTATAAGG 60.094 40.741 0.00 0.00 0.00 2.69
2167 6611 8.159447 CCATGAGATTGATCCAGTTTATAAGGA 58.841 37.037 0.00 0.00 35.59 3.36
2168 6612 9.565090 CATGAGATTGATCCAGTTTATAAGGAA 57.435 33.333 0.00 0.00 34.62 3.36
2170 6614 9.973661 TGAGATTGATCCAGTTTATAAGGAAAA 57.026 29.630 0.00 0.00 34.62 2.29
2172 6616 9.190317 AGATTGATCCAGTTTATAAGGAAAACC 57.810 33.333 0.00 0.00 37.51 3.27
2173 6617 6.995511 TGATCCAGTTTATAAGGAAAACCG 57.004 37.500 0.00 0.00 37.51 4.44
2174 6618 5.883673 TGATCCAGTTTATAAGGAAAACCGG 59.116 40.000 0.00 0.00 37.51 5.28
2175 6619 5.502089 TCCAGTTTATAAGGAAAACCGGA 57.498 39.130 9.46 0.63 39.79 5.14
2176 6620 6.069705 TCCAGTTTATAAGGAAAACCGGAT 57.930 37.500 9.46 0.00 38.09 4.18
2177 6621 6.117488 TCCAGTTTATAAGGAAAACCGGATC 58.883 40.000 9.46 2.88 38.09 3.36
2178 6622 5.007332 CCAGTTTATAAGGAAAACCGGATCG 59.993 44.000 9.46 0.00 36.79 3.69
2179 6623 5.813672 CAGTTTATAAGGAAAACCGGATCGA 59.186 40.000 9.46 0.00 37.51 3.59
2180 6624 6.314400 CAGTTTATAAGGAAAACCGGATCGAA 59.686 38.462 9.46 0.00 37.51 3.71
2181 6625 6.880529 AGTTTATAAGGAAAACCGGATCGAAA 59.119 34.615 9.46 0.00 37.51 3.46
2182 6626 7.391275 AGTTTATAAGGAAAACCGGATCGAAAA 59.609 33.333 9.46 0.00 37.51 2.29
2183 6627 3.909776 AAGGAAAACCGGATCGAAAAC 57.090 42.857 9.46 0.00 0.00 2.43
2184 6628 2.156917 AGGAAAACCGGATCGAAAACC 58.843 47.619 9.46 0.11 0.00 3.27
2185 6629 2.156917 GGAAAACCGGATCGAAAACCT 58.843 47.619 9.46 0.00 0.00 3.50
2186 6630 3.008266 AGGAAAACCGGATCGAAAACCTA 59.992 43.478 9.46 0.00 0.00 3.08
2187 6631 3.373130 GGAAAACCGGATCGAAAACCTAG 59.627 47.826 9.46 0.00 0.00 3.02
2188 6632 3.967332 AAACCGGATCGAAAACCTAGA 57.033 42.857 9.46 0.00 0.00 2.43
2189 6633 2.955477 ACCGGATCGAAAACCTAGAC 57.045 50.000 9.46 0.00 0.00 2.59
2190 6634 2.173519 ACCGGATCGAAAACCTAGACA 58.826 47.619 9.46 0.00 0.00 3.41
2191 6635 2.564062 ACCGGATCGAAAACCTAGACAA 59.436 45.455 9.46 0.00 0.00 3.18
2192 6636 3.197116 ACCGGATCGAAAACCTAGACAAT 59.803 43.478 9.46 0.00 0.00 2.71
2193 6637 4.189231 CCGGATCGAAAACCTAGACAATT 58.811 43.478 0.00 0.00 0.00 2.32
2194 6638 5.105228 ACCGGATCGAAAACCTAGACAATTA 60.105 40.000 9.46 0.00 0.00 1.40
2195 6639 5.462398 CCGGATCGAAAACCTAGACAATTAG 59.538 44.000 0.00 0.00 0.00 1.73
2196 6640 6.270815 CGGATCGAAAACCTAGACAATTAGA 58.729 40.000 0.00 0.00 0.00 2.10
2197 6641 6.198591 CGGATCGAAAACCTAGACAATTAGAC 59.801 42.308 0.00 0.00 0.00 2.59
2198 6642 6.479331 GGATCGAAAACCTAGACAATTAGACC 59.521 42.308 0.00 0.00 0.00 3.85
2199 6643 5.727434 TCGAAAACCTAGACAATTAGACCC 58.273 41.667 0.00 0.00 0.00 4.46
2200 6644 5.482878 TCGAAAACCTAGACAATTAGACCCT 59.517 40.000 0.00 0.00 0.00 4.34
2201 6645 5.581085 CGAAAACCTAGACAATTAGACCCTG 59.419 44.000 0.00 0.00 0.00 4.45
2202 6646 6.449830 AAAACCTAGACAATTAGACCCTGT 57.550 37.500 0.00 0.00 0.00 4.00
2203 6647 6.449830 AAACCTAGACAATTAGACCCTGTT 57.550 37.500 0.00 0.00 0.00 3.16
2204 6648 6.449830 AACCTAGACAATTAGACCCTGTTT 57.550 37.500 0.00 0.00 0.00 2.83
2205 6649 7.563724 AACCTAGACAATTAGACCCTGTTTA 57.436 36.000 0.00 0.00 0.00 2.01
2384 6921 4.065088 TCAGTGCTTGCTAGAAAATTCGT 58.935 39.130 0.00 0.00 0.00 3.85
2393 6930 8.388103 GCTTGCTAGAAAATTCGTATTGTTCTA 58.612 33.333 0.00 13.37 30.68 2.10
2527 7070 6.213677 GCTGGGAAAATCGTTTAGAAAAACT 58.786 36.000 0.14 0.00 42.39 2.66
2571 7114 8.615878 TTTTATTAGCACTAAACTGAAGCTCA 57.384 30.769 0.00 0.00 36.80 4.26
2579 7122 2.556144 AACTGAAGCTCATGCAGTCA 57.444 45.000 10.60 0.00 41.65 3.41
2588 7131 2.344950 CTCATGCAGTCAGAACTCACC 58.655 52.381 0.00 0.00 31.71 4.02
2614 7157 7.472334 AGTTCATGACCTCATTATTTTGCTT 57.528 32.000 0.00 0.00 33.61 3.91
2619 7162 6.899393 TGACCTCATTATTTTGCTTCAACT 57.101 33.333 0.00 0.00 0.00 3.16
2955 7589 7.492352 TCTTTGTAAGCTAGTTTTCTTGTCC 57.508 36.000 0.00 0.00 0.00 4.02
2965 7599 7.719633 AGCTAGTTTTCTTGTCCAGATTGTAAA 59.280 33.333 0.00 0.00 0.00 2.01
3004 7645 6.093219 CAGGTGATCTTGTAAAATCCTGTCAG 59.907 42.308 0.00 0.00 37.16 3.51
3026 7667 9.046296 GTCAGGACCTGATTACATTATAAGTTG 57.954 37.037 26.78 0.00 42.73 3.16
3084 7725 0.693049 ATGGAAAAGGTCTGAGCCGT 59.307 50.000 2.76 0.00 0.00 5.68
3148 7789 4.611943 TCTAATCTCGGCATTCTCGAAAG 58.388 43.478 0.00 0.00 36.15 2.62
3234 7875 8.787852 GGATTTGAGAACAAAGACACTTTCTAT 58.212 33.333 0.00 0.00 46.84 1.98
3308 7949 3.128589 CCATCGGGTATGACTTTTGTTGG 59.871 47.826 0.00 0.00 37.86 3.77
3339 7980 5.105797 CCTTTGCCACATTTGATTGTAGCTA 60.106 40.000 0.00 0.00 35.60 3.32
3569 8210 7.557719 TCTCTCATTCCCAATCAGGTTAAATTC 59.442 37.037 0.00 0.00 34.66 2.17
3578 8219 7.385267 CCAATCAGGTTAAATTCCACATTTGA 58.615 34.615 0.00 0.00 0.00 2.69
3733 8376 4.042934 ACTGGTGCTTATTTGTAGAGGGTT 59.957 41.667 0.00 0.00 0.00 4.11
3791 8434 0.821711 TGGTGCTTCAGGAAAACCCG 60.822 55.000 9.74 0.00 40.87 5.28
3937 8582 8.685838 AACTACAGGTTGTTTGAATTAGCTAA 57.314 30.769 8.99 8.99 36.70 3.09
3993 8638 7.170658 GTGCTTTTAAAATCCAAACATAGTGCA 59.829 33.333 0.09 0.21 0.00 4.57
4027 8672 5.227593 AGGGTAGATGGATGATAACCACTT 58.772 41.667 0.00 0.00 40.36 3.16
4111 8759 9.282247 CATAACTGCATATCACTGTTTTTCTTC 57.718 33.333 0.00 0.00 32.38 2.87
4258 8906 5.123979 GGTTATTTACCTGTTGAGGCTTCAG 59.876 44.000 0.00 0.00 44.33 3.02
4563 10086 6.015772 ACGTTGATTTAGTTTTATGGCCAAGT 60.016 34.615 10.96 0.00 0.00 3.16
4605 10129 2.295909 GCTGCCATACAAAAGTGGACAA 59.704 45.455 0.00 0.00 37.72 3.18
4647 10172 8.075761 ACTTTTGAGGTATATAGAGTTCGGTT 57.924 34.615 0.00 0.00 0.00 4.44
4656 10181 8.078596 GGTATATAGAGTTCGGTTCACGTATTT 58.921 37.037 0.00 0.00 44.69 1.40
4669 10194 2.752354 CACGTATTTGCCCCTTTGATGA 59.248 45.455 0.00 0.00 0.00 2.92
4670 10195 2.752903 ACGTATTTGCCCCTTTGATGAC 59.247 45.455 0.00 0.00 0.00 3.06
4769 10296 2.147150 GTGCCTGAGTTTCCTTCTCAC 58.853 52.381 0.00 0.00 37.07 3.51
4975 13303 2.095461 GAAAGTTGCCCATCTCCCTTC 58.905 52.381 0.00 0.00 0.00 3.46
4990 13318 2.362397 TCCCTTCGATGTCTGATAGTGC 59.638 50.000 0.00 0.00 0.00 4.40
5000 13328 3.072330 TGTCTGATAGTGCCACCTTTTGA 59.928 43.478 0.00 0.00 0.00 2.69
5015 13343 4.161333 CCTTTTGATTGACAGATTCGTGC 58.839 43.478 0.00 0.00 0.00 5.34
5022 13350 1.272212 TGACAGATTCGTGCTGCTGTA 59.728 47.619 0.00 0.00 41.30 2.74
5034 13362 2.036862 TGCTGCTGTATGGCTATCTCAG 59.963 50.000 0.00 9.64 0.00 3.35
5035 13363 2.298446 GCTGCTGTATGGCTATCTCAGA 59.702 50.000 15.61 0.00 0.00 3.27
5036 13364 3.860378 GCTGCTGTATGGCTATCTCAGAC 60.860 52.174 15.61 9.43 0.00 3.51
5037 13365 3.570540 TGCTGTATGGCTATCTCAGACT 58.429 45.455 15.61 0.00 31.12 3.24
5038 13366 3.963374 TGCTGTATGGCTATCTCAGACTT 59.037 43.478 15.61 0.00 31.12 3.01
5039 13367 4.038522 TGCTGTATGGCTATCTCAGACTTC 59.961 45.833 15.61 3.05 31.12 3.01
5040 13368 4.280677 GCTGTATGGCTATCTCAGACTTCT 59.719 45.833 15.61 0.00 31.12 2.85
5041 13369 5.771469 CTGTATGGCTATCTCAGACTTCTG 58.229 45.833 8.71 0.00 45.08 3.02
5042 13370 5.204292 TGTATGGCTATCTCAGACTTCTGT 58.796 41.667 6.15 0.00 44.12 3.41
5043 13371 5.658634 TGTATGGCTATCTCAGACTTCTGTT 59.341 40.000 6.15 0.00 44.12 3.16
5122 13459 7.004086 ACAACAGAAGTTTCAATAGGGAATGA 58.996 34.615 0.00 0.00 35.28 2.57
5170 13513 9.590637 GTGTTTACACTAAGGGCATTCCTTGTG 62.591 44.444 17.41 17.41 46.85 3.33
5208 13552 1.846439 TGTGGGGAAGAGGATTCCATC 59.154 52.381 5.29 0.26 40.32 3.51
5241 13585 5.588958 TGATTCTGTCTCTGATACTGTGG 57.411 43.478 0.00 0.00 0.00 4.17
5247 13591 4.667573 TGTCTCTGATACTGTGGAGTTCT 58.332 43.478 0.00 0.00 33.21 3.01
5352 13696 5.119125 GCAAACTAATGCATTGTTCAACCTC 59.881 40.000 22.27 6.98 45.70 3.85
5420 13767 5.565439 CGATGATTTCTGAAAGCCCAAAGTT 60.565 40.000 15.02 0.00 0.00 2.66
5462 13809 1.081892 CTGTCAAGGAGGATGTTGCG 58.918 55.000 0.00 0.00 0.00 4.85
5481 13828 1.532505 CGAGGCTTCAAATCGCATTGG 60.533 52.381 0.00 0.00 0.00 3.16
5488 13835 5.008613 GGCTTCAAATCGCATTGGATTACTA 59.991 40.000 1.05 0.00 35.65 1.82
5494 13841 2.805671 TCGCATTGGATTACTAATGGCG 59.194 45.455 0.00 0.00 42.53 5.69
5502 13849 5.547465 TGGATTACTAATGGCGGACTATTG 58.453 41.667 0.00 0.00 0.00 1.90
5503 13850 4.392138 GGATTACTAATGGCGGACTATTGC 59.608 45.833 0.00 0.00 0.00 3.56
5513 13860 3.492656 GGCGGACTATTGCTGTGAAGATA 60.493 47.826 0.00 0.00 0.00 1.98
5518 13865 5.982516 GGACTATTGCTGTGAAGATAGTCTG 59.017 44.000 17.08 0.00 45.12 3.51
5528 13875 2.906691 AGATAGTCTGGTGCATCTGC 57.093 50.000 0.00 0.00 42.50 4.26
5539 13887 1.723870 GCATCTGCAACATCGACCC 59.276 57.895 0.00 0.00 41.59 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 4153 4.218578 ATGCTCGGCCTCTGCTCG 62.219 66.667 0.00 0.00 37.74 5.03
44 4156 2.588314 CTCATGCTCGGCCTCTGC 60.588 66.667 0.00 2.51 0.00 4.26
151 4266 4.351192 GAGAACAAAACACATCACCACAC 58.649 43.478 0.00 0.00 0.00 3.82
208 4323 5.638234 GGTAGGTACAATTGACTGAAGACAC 59.362 44.000 13.59 1.77 0.00 3.67
210 4325 5.176592 GGGTAGGTACAATTGACTGAAGAC 58.823 45.833 13.59 2.73 0.00 3.01
269 4393 2.691409 TATTACAGCAGTGGCAGGTC 57.309 50.000 0.00 0.00 44.61 3.85
285 4409 7.941238 ACTGCAGCTTTAGATGGTGATAATATT 59.059 33.333 15.27 0.00 35.20 1.28
304 4428 6.744537 CAGTGATTTGTATTTCTTACTGCAGC 59.255 38.462 15.27 0.00 0.00 5.25
342 4480 2.460918 CGTCGGTCTCATGAATGGTAC 58.539 52.381 0.00 0.00 0.00 3.34
343 4481 1.407618 CCGTCGGTCTCATGAATGGTA 59.592 52.381 2.08 0.00 0.00 3.25
344 4482 0.175760 CCGTCGGTCTCATGAATGGT 59.824 55.000 2.08 0.00 0.00 3.55
347 4485 0.179100 CTGCCGTCGGTCTCATGAAT 60.179 55.000 13.94 0.00 0.00 2.57
349 4487 0.678684 TACTGCCGTCGGTCTCATGA 60.679 55.000 13.94 0.00 33.08 3.07
361 4499 2.413112 CACTTGATGTTCTGTACTGCCG 59.587 50.000 0.00 0.00 0.00 5.69
363 4501 2.807967 TGCACTTGATGTTCTGTACTGC 59.192 45.455 0.00 0.00 0.00 4.40
364 4502 3.187227 GGTGCACTTGATGTTCTGTACTG 59.813 47.826 17.98 0.00 0.00 2.74
365 4503 3.403038 GGTGCACTTGATGTTCTGTACT 58.597 45.455 17.98 0.00 0.00 2.73
366 4504 2.157668 CGGTGCACTTGATGTTCTGTAC 59.842 50.000 17.98 0.00 0.00 2.90
367 4505 2.224185 ACGGTGCACTTGATGTTCTGTA 60.224 45.455 17.98 0.00 0.00 2.74
368 4506 1.229428 CGGTGCACTTGATGTTCTGT 58.771 50.000 17.98 0.00 0.00 3.41
369 4507 1.195448 GACGGTGCACTTGATGTTCTG 59.805 52.381 17.98 0.00 0.00 3.02
370 4508 1.512926 GACGGTGCACTTGATGTTCT 58.487 50.000 17.98 0.00 0.00 3.01
390 4528 0.733909 GCAAATGCTCTTCAACGCCC 60.734 55.000 0.00 0.00 38.21 6.13
422 4588 0.482446 TTCACAAGGCCAGGGACAAT 59.518 50.000 5.01 0.00 0.00 2.71
437 4603 6.321181 TCCTAAAACATTGGGCAGATATTCAC 59.679 38.462 0.00 0.00 0.00 3.18
454 4620 4.439776 GTCGCACATGTTTGTTCCTAAAAC 59.560 41.667 0.00 0.00 37.90 2.43
518 4685 9.750125 CACTAAAACATGCTGTAGTCATATCTA 57.250 33.333 0.00 0.00 0.00 1.98
519 4686 8.260818 ACACTAAAACATGCTGTAGTCATATCT 58.739 33.333 0.00 0.00 0.00 1.98
520 4687 8.331022 CACACTAAAACATGCTGTAGTCATATC 58.669 37.037 0.00 0.00 0.00 1.63
521 4688 8.040727 TCACACTAAAACATGCTGTAGTCATAT 58.959 33.333 0.00 0.00 0.00 1.78
524 4691 5.606505 TCACACTAAAACATGCTGTAGTCA 58.393 37.500 0.00 0.00 0.00 3.41
525 4692 6.368791 TGATCACACTAAAACATGCTGTAGTC 59.631 38.462 0.00 0.00 0.00 2.59
528 4695 5.122239 GCTGATCACACTAAAACATGCTGTA 59.878 40.000 0.00 0.00 0.00 2.74
532 4699 4.154737 TCTGCTGATCACACTAAAACATGC 59.845 41.667 0.00 0.00 0.00 4.06
533 4700 5.868043 TCTGCTGATCACACTAAAACATG 57.132 39.130 0.00 0.00 0.00 3.21
534 4701 6.882610 TTTCTGCTGATCACACTAAAACAT 57.117 33.333 0.00 0.00 0.00 2.71
536 4703 6.494842 TGTTTTCTGCTGATCACACTAAAAC 58.505 36.000 20.47 20.47 36.56 2.43
569 4989 1.695893 ATCGCGGTCTGTTGATTGCG 61.696 55.000 6.13 0.00 44.36 4.85
595 5015 5.858049 GGCGTAACCAAGTTTGTTAATAACC 59.142 40.000 1.36 0.00 38.86 2.85
597 5017 6.072563 GGAGGCGTAACCAAGTTTGTTAATAA 60.073 38.462 1.36 0.00 43.14 1.40
599 5019 4.216902 GGAGGCGTAACCAAGTTTGTTAAT 59.783 41.667 1.36 0.00 43.14 1.40
600 5020 3.565063 GGAGGCGTAACCAAGTTTGTTAA 59.435 43.478 1.36 0.00 43.14 2.01
662 5087 1.457346 GGAGGACGACGGTAGAAGAA 58.543 55.000 0.00 0.00 0.00 2.52
680 5105 2.022129 GCGAGCGTGGGATATTCGG 61.022 63.158 0.00 0.00 0.00 4.30
683 5108 2.029073 CGGCGAGCGTGGGATATT 59.971 61.111 0.00 0.00 0.00 1.28
685 5110 3.896133 GTCGGCGAGCGTGGGATA 61.896 66.667 11.20 0.00 0.00 2.59
722 5147 3.322318 GAGGTGGAGAGGCTGTGGC 62.322 68.421 0.00 0.00 37.82 5.01
723 5148 2.664081 GGAGGTGGAGAGGCTGTGG 61.664 68.421 0.00 0.00 0.00 4.17
724 5149 1.483595 TTGGAGGTGGAGAGGCTGTG 61.484 60.000 0.00 0.00 0.00 3.66
725 5150 0.768221 TTTGGAGGTGGAGAGGCTGT 60.768 55.000 0.00 0.00 0.00 4.40
726 5151 0.322008 GTTTGGAGGTGGAGAGGCTG 60.322 60.000 0.00 0.00 0.00 4.85
727 5152 0.474660 AGTTTGGAGGTGGAGAGGCT 60.475 55.000 0.00 0.00 0.00 4.58
728 5153 0.402121 AAGTTTGGAGGTGGAGAGGC 59.598 55.000 0.00 0.00 0.00 4.70
737 5162 3.566351 AGGAAGTTTGGAAGTTTGGAGG 58.434 45.455 0.00 0.00 0.00 4.30
741 5166 5.835113 TGAGAAGGAAGTTTGGAAGTTTG 57.165 39.130 0.00 0.00 0.00 2.93
744 5169 5.117406 AGTTGAGAAGGAAGTTTGGAAGT 57.883 39.130 0.00 0.00 0.00 3.01
746 5171 4.080015 TGGAGTTGAGAAGGAAGTTTGGAA 60.080 41.667 0.00 0.00 0.00 3.53
747 5172 3.458118 TGGAGTTGAGAAGGAAGTTTGGA 59.542 43.478 0.00 0.00 0.00 3.53
748 5173 3.817647 CTGGAGTTGAGAAGGAAGTTTGG 59.182 47.826 0.00 0.00 0.00 3.28
749 5174 4.708177 TCTGGAGTTGAGAAGGAAGTTTG 58.292 43.478 0.00 0.00 0.00 2.93
750 5175 5.072329 TGATCTGGAGTTGAGAAGGAAGTTT 59.928 40.000 0.00 0.00 0.00 2.66
751 5176 4.594920 TGATCTGGAGTTGAGAAGGAAGTT 59.405 41.667 0.00 0.00 0.00 2.66
752 5177 4.020662 GTGATCTGGAGTTGAGAAGGAAGT 60.021 45.833 0.00 0.00 0.00 3.01
753 5178 4.502962 GTGATCTGGAGTTGAGAAGGAAG 58.497 47.826 0.00 0.00 0.00 3.46
754 5179 3.261897 GGTGATCTGGAGTTGAGAAGGAA 59.738 47.826 0.00 0.00 0.00 3.36
755 5180 2.834549 GGTGATCTGGAGTTGAGAAGGA 59.165 50.000 0.00 0.00 0.00 3.36
756 5181 2.093235 GGGTGATCTGGAGTTGAGAAGG 60.093 54.545 0.00 0.00 0.00 3.46
757 5182 2.568956 TGGGTGATCTGGAGTTGAGAAG 59.431 50.000 0.00 0.00 0.00 2.85
758 5183 2.619931 TGGGTGATCTGGAGTTGAGAA 58.380 47.619 0.00 0.00 0.00 2.87
759 5184 2.325661 TGGGTGATCTGGAGTTGAGA 57.674 50.000 0.00 0.00 0.00 3.27
760 5185 3.641434 ATTGGGTGATCTGGAGTTGAG 57.359 47.619 0.00 0.00 0.00 3.02
761 5186 4.387026 AAATTGGGTGATCTGGAGTTGA 57.613 40.909 0.00 0.00 0.00 3.18
772 5197 2.554893 GCGGTAACTCAAAATTGGGTGA 59.445 45.455 0.00 0.00 42.06 4.02
773 5198 2.667171 CGCGGTAACTCAAAATTGGGTG 60.667 50.000 0.00 0.00 42.06 4.61
774 5199 1.538075 CGCGGTAACTCAAAATTGGGT 59.462 47.619 0.00 0.00 45.58 4.51
780 5211 2.519826 CCGACGCGGTAACTCAAAA 58.480 52.632 12.47 0.00 42.73 2.44
814 5245 3.711814 TTGGATCGCGGGCTCCAA 61.712 61.111 27.80 27.80 46.63 3.53
859 5290 2.454941 GGAGAGGGGAGGGTGGAA 59.545 66.667 0.00 0.00 0.00 3.53
900 5332 2.042843 GGAAGAGGAGAGGGGCGA 60.043 66.667 0.00 0.00 0.00 5.54
912 5354 1.382695 GAGTGGGGATCGGGGAAGA 60.383 63.158 0.00 0.00 0.00 2.87
968 5410 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
969 5411 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
970 5412 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
971 5413 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
972 5414 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
973 5415 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
974 5416 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
975 5417 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
976 5418 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
982 5424 4.974721 GGCTGGTGGTGGTGGTGG 62.975 72.222 0.00 0.00 0.00 4.61
1171 5613 1.838073 GCCGGAGTTTCAAGAGGGGA 61.838 60.000 5.05 0.00 0.00 4.81
1348 5790 3.181967 GTACACGCGCAGGAGCAG 61.182 66.667 5.73 0.00 42.27 4.24
1669 6111 4.995058 AACCCCCTTCCCGGCAGA 62.995 66.667 0.00 0.00 0.00 4.26
1803 6245 4.881273 ACTAATTCTGCAATGCATAACCGA 59.119 37.500 8.91 0.00 38.13 4.69
1806 6248 6.038356 AGCAACTAATTCTGCAATGCATAAC 58.962 36.000 8.91 0.00 41.17 1.89
2115 6559 9.196552 GCATTAAGGCCACTTTGAAATATATTC 57.803 33.333 5.01 0.00 38.14 1.75
2132 6576 4.082354 GGATCAATCTCATGGCATTAAGGC 60.082 45.833 2.86 2.86 44.50 4.35
2133 6577 5.074804 TGGATCAATCTCATGGCATTAAGG 58.925 41.667 0.00 0.00 0.00 2.69
2134 6578 5.768662 ACTGGATCAATCTCATGGCATTAAG 59.231 40.000 0.00 0.00 0.00 1.85
2135 6579 5.698104 ACTGGATCAATCTCATGGCATTAA 58.302 37.500 0.00 0.00 0.00 1.40
2136 6580 5.314718 ACTGGATCAATCTCATGGCATTA 57.685 39.130 0.00 0.00 0.00 1.90
2137 6581 4.180377 ACTGGATCAATCTCATGGCATT 57.820 40.909 0.00 0.00 0.00 3.56
2138 6582 3.878237 ACTGGATCAATCTCATGGCAT 57.122 42.857 0.00 0.00 0.00 4.40
2139 6583 3.657398 AACTGGATCAATCTCATGGCA 57.343 42.857 0.00 0.00 0.00 4.92
2140 6584 7.094463 CCTTATAAACTGGATCAATCTCATGGC 60.094 40.741 0.00 0.00 0.00 4.40
2141 6585 8.159447 TCCTTATAAACTGGATCAATCTCATGG 58.841 37.037 0.00 0.00 0.00 3.66
2142 6586 9.565090 TTCCTTATAAACTGGATCAATCTCATG 57.435 33.333 0.00 0.00 0.00 3.07
2144 6588 9.973661 TTTTCCTTATAAACTGGATCAATCTCA 57.026 29.630 0.00 0.00 0.00 3.27
2146 6590 9.190317 GGTTTTCCTTATAAACTGGATCAATCT 57.810 33.333 0.00 0.00 36.12 2.40
2147 6591 8.129211 CGGTTTTCCTTATAAACTGGATCAATC 58.871 37.037 0.00 0.00 37.92 2.67
2148 6592 7.996385 CGGTTTTCCTTATAAACTGGATCAAT 58.004 34.615 0.00 0.00 37.92 2.57
2149 6593 7.385778 CGGTTTTCCTTATAAACTGGATCAA 57.614 36.000 0.00 0.00 37.92 2.57
2150 6594 6.995511 CGGTTTTCCTTATAAACTGGATCA 57.004 37.500 0.00 0.00 37.92 2.92
2155 6599 5.813672 TCGATCCGGTTTTCCTTATAAACTG 59.186 40.000 0.00 0.00 40.12 3.16
2156 6600 5.981174 TCGATCCGGTTTTCCTTATAAACT 58.019 37.500 0.00 0.00 36.12 2.66
2157 6601 6.667007 TTCGATCCGGTTTTCCTTATAAAC 57.333 37.500 0.00 0.00 37.95 2.01
2158 6602 7.361971 GGTTTTCGATCCGGTTTTCCTTATAAA 60.362 37.037 0.00 0.00 37.95 1.40
2159 6603 6.093909 GGTTTTCGATCCGGTTTTCCTTATAA 59.906 38.462 0.00 0.00 37.95 0.98
2160 6604 5.585844 GGTTTTCGATCCGGTTTTCCTTATA 59.414 40.000 0.00 0.00 37.95 0.98
2161 6605 4.397103 GGTTTTCGATCCGGTTTTCCTTAT 59.603 41.667 0.00 0.00 37.95 1.73
2162 6606 3.752747 GGTTTTCGATCCGGTTTTCCTTA 59.247 43.478 0.00 0.00 37.95 2.69
2163 6607 2.555325 GGTTTTCGATCCGGTTTTCCTT 59.445 45.455 0.00 0.00 37.95 3.36
2164 6608 2.156917 GGTTTTCGATCCGGTTTTCCT 58.843 47.619 0.00 0.00 37.95 3.36
2165 6609 2.156917 AGGTTTTCGATCCGGTTTTCC 58.843 47.619 0.00 0.00 0.00 3.13
2166 6610 4.092529 GTCTAGGTTTTCGATCCGGTTTTC 59.907 45.833 0.00 0.00 0.00 2.29
2167 6611 3.999001 GTCTAGGTTTTCGATCCGGTTTT 59.001 43.478 0.00 0.00 0.00 2.43
2168 6612 3.007182 TGTCTAGGTTTTCGATCCGGTTT 59.993 43.478 0.00 0.00 0.00 3.27
2169 6613 2.564062 TGTCTAGGTTTTCGATCCGGTT 59.436 45.455 0.00 0.00 0.00 4.44
2170 6614 2.173519 TGTCTAGGTTTTCGATCCGGT 58.826 47.619 0.00 0.00 0.00 5.28
2171 6615 2.953466 TGTCTAGGTTTTCGATCCGG 57.047 50.000 0.00 0.00 0.00 5.14
2172 6616 6.198591 GTCTAATTGTCTAGGTTTTCGATCCG 59.801 42.308 0.00 0.00 0.00 4.18
2173 6617 6.479331 GGTCTAATTGTCTAGGTTTTCGATCC 59.521 42.308 0.00 0.00 0.00 3.36
2174 6618 6.479331 GGGTCTAATTGTCTAGGTTTTCGATC 59.521 42.308 0.00 0.00 0.00 3.69
2175 6619 6.156429 AGGGTCTAATTGTCTAGGTTTTCGAT 59.844 38.462 0.00 0.00 0.00 3.59
2176 6620 5.482878 AGGGTCTAATTGTCTAGGTTTTCGA 59.517 40.000 0.00 0.00 0.00 3.71
2177 6621 5.581085 CAGGGTCTAATTGTCTAGGTTTTCG 59.419 44.000 0.00 0.00 0.00 3.46
2178 6622 6.473758 ACAGGGTCTAATTGTCTAGGTTTTC 58.526 40.000 0.00 0.00 0.00 2.29
2179 6623 6.449830 ACAGGGTCTAATTGTCTAGGTTTT 57.550 37.500 0.00 0.00 0.00 2.43
2180 6624 6.449830 AACAGGGTCTAATTGTCTAGGTTT 57.550 37.500 0.00 0.00 0.00 3.27
2181 6625 6.449830 AAACAGGGTCTAATTGTCTAGGTT 57.550 37.500 0.00 0.00 0.00 3.50
2182 6626 7.565680 CATAAACAGGGTCTAATTGTCTAGGT 58.434 38.462 0.00 0.00 0.00 3.08
2183 6627 6.483640 GCATAAACAGGGTCTAATTGTCTAGG 59.516 42.308 0.00 0.00 0.00 3.02
2184 6628 7.047891 TGCATAAACAGGGTCTAATTGTCTAG 58.952 38.462 0.00 0.00 0.00 2.43
2185 6629 6.953101 TGCATAAACAGGGTCTAATTGTCTA 58.047 36.000 0.00 0.00 0.00 2.59
2186 6630 5.815581 TGCATAAACAGGGTCTAATTGTCT 58.184 37.500 0.00 0.00 0.00 3.41
2187 6631 6.509418 TTGCATAAACAGGGTCTAATTGTC 57.491 37.500 0.00 0.00 0.00 3.18
2188 6632 6.909550 TTTGCATAAACAGGGTCTAATTGT 57.090 33.333 0.00 0.00 0.00 2.71
2189 6633 8.034215 TCATTTTGCATAAACAGGGTCTAATTG 58.966 33.333 0.00 0.00 0.00 2.32
2190 6634 8.133024 TCATTTTGCATAAACAGGGTCTAATT 57.867 30.769 0.00 0.00 0.00 1.40
2191 6635 7.716799 TCATTTTGCATAAACAGGGTCTAAT 57.283 32.000 0.00 0.00 0.00 1.73
2192 6636 7.363705 CCATCATTTTGCATAAACAGGGTCTAA 60.364 37.037 0.00 0.00 0.00 2.10
2193 6637 6.096705 CCATCATTTTGCATAAACAGGGTCTA 59.903 38.462 0.00 0.00 0.00 2.59
2194 6638 5.105228 CCATCATTTTGCATAAACAGGGTCT 60.105 40.000 0.00 0.00 0.00 3.85
2195 6639 5.111293 CCATCATTTTGCATAAACAGGGTC 58.889 41.667 0.00 0.00 0.00 4.46
2196 6640 4.080975 CCCATCATTTTGCATAAACAGGGT 60.081 41.667 10.04 0.00 0.00 4.34
2197 6641 4.161942 TCCCATCATTTTGCATAAACAGGG 59.838 41.667 11.28 11.28 0.00 4.45
2198 6642 5.341872 TCCCATCATTTTGCATAAACAGG 57.658 39.130 0.00 0.00 0.00 4.00
2199 6643 7.670009 TTTTCCCATCATTTTGCATAAACAG 57.330 32.000 0.00 0.00 0.00 3.16
2200 6644 8.632906 AATTTTCCCATCATTTTGCATAAACA 57.367 26.923 0.00 0.00 0.00 2.83
2201 6645 9.558648 GAAATTTTCCCATCATTTTGCATAAAC 57.441 29.630 0.00 0.00 0.00 2.01
2202 6646 9.517868 AGAAATTTTCCCATCATTTTGCATAAA 57.482 25.926 5.52 0.00 0.00 1.40
2235 6686 9.077885 ACAATATAGTCAAAGGAAAACATGTGT 57.922 29.630 0.00 0.00 0.00 3.72
2361 6898 4.083802 ACGAATTTTCTAGCAAGCACTGAC 60.084 41.667 0.00 0.00 0.00 3.51
2384 6921 9.710900 CTGAACAGCCACATATATAGAACAATA 57.289 33.333 0.00 0.00 0.00 1.90
2393 6930 6.051717 GTGAGTTCTGAACAGCCACATATAT 58.948 40.000 21.50 0.00 32.55 0.86
2402 6942 6.128418 GGATTCTTAAGTGAGTTCTGAACAGC 60.128 42.308 21.50 13.45 0.00 4.40
2561 7104 1.622312 TCTGACTGCATGAGCTTCAGT 59.378 47.619 8.72 9.56 44.81 3.41
2571 7114 0.969149 TCGGTGAGTTCTGACTGCAT 59.031 50.000 0.00 0.00 35.88 3.96
2965 7599 7.667219 ACAAGATCACCTGATAACAACTGAAAT 59.333 33.333 0.00 0.00 34.37 2.17
3084 7725 2.763448 CCCCTCAACACAAGACCAAAAA 59.237 45.455 0.00 0.00 0.00 1.94
3148 7789 4.818546 AGCATCAACATTATCACTACCAGC 59.181 41.667 0.00 0.00 0.00 4.85
3234 7875 2.292918 ACATAGGAACCCAGAGCTACCA 60.293 50.000 0.00 0.00 0.00 3.25
3308 7949 5.132897 TCAAATGTGGCAAAGGACATAAC 57.867 39.130 0.00 0.00 32.08 1.89
3339 7980 6.115448 ACCTGCTAGATTAGACAAACAGTT 57.885 37.500 0.00 0.00 0.00 3.16
3401 8042 2.281762 CGTTGCCTCATACGTCTTTAGC 59.718 50.000 0.00 0.00 33.33 3.09
3712 8355 4.042311 TCAACCCTCTACAAATAAGCACCA 59.958 41.667 0.00 0.00 0.00 4.17
3791 8434 7.215719 AGTGAGGTGCTTAGAAAAATAAACC 57.784 36.000 0.00 0.00 0.00 3.27
3937 8582 8.098286 GGTTTTGCTACTTTGGGGTAAATAAAT 58.902 33.333 0.00 0.00 0.00 1.40
3993 8638 3.165071 CCATCTACCCTTGTTGCCTTTT 58.835 45.455 0.00 0.00 0.00 2.27
4111 8759 2.288579 TGCCAAAGCTTGCAGATTTCAG 60.289 45.455 7.34 0.00 40.80 3.02
4258 8906 4.159135 TCCCCATACTTCGAAGTCAAGTAC 59.841 45.833 32.86 0.00 38.79 2.73
4647 10172 2.570415 TCAAAGGGGCAAATACGTGA 57.430 45.000 0.00 0.00 0.00 4.35
4656 10181 0.899717 GCCTTGTCATCAAAGGGGCA 60.900 55.000 4.48 0.00 40.13 5.36
4669 10194 1.187567 GGTCCTGCCAAATGCCTTGT 61.188 55.000 0.00 0.00 40.16 3.16
4670 10195 1.186917 TGGTCCTGCCAAATGCCTTG 61.187 55.000 0.00 0.00 45.94 3.61
4975 13303 1.410517 AGGTGGCACTATCAGACATCG 59.589 52.381 18.45 0.00 0.00 3.84
4990 13318 4.216257 ACGAATCTGTCAATCAAAAGGTGG 59.784 41.667 0.00 0.00 0.00 4.61
5000 13328 1.736126 CAGCAGCACGAATCTGTCAAT 59.264 47.619 0.00 0.00 34.21 2.57
5015 13343 3.573538 AGTCTGAGATAGCCATACAGCAG 59.426 47.826 0.00 0.00 34.23 4.24
5022 13350 5.304101 CCTAACAGAAGTCTGAGATAGCCAT 59.696 44.000 15.15 0.00 46.59 4.40
5034 13362 3.491267 GCATCGCATACCTAACAGAAGTC 59.509 47.826 0.00 0.00 0.00 3.01
5035 13363 3.133003 AGCATCGCATACCTAACAGAAGT 59.867 43.478 0.00 0.00 0.00 3.01
5036 13364 3.492383 CAGCATCGCATACCTAACAGAAG 59.508 47.826 0.00 0.00 0.00 2.85
5037 13365 3.118775 ACAGCATCGCATACCTAACAGAA 60.119 43.478 0.00 0.00 0.00 3.02
5038 13366 2.430694 ACAGCATCGCATACCTAACAGA 59.569 45.455 0.00 0.00 0.00 3.41
5039 13367 2.826428 ACAGCATCGCATACCTAACAG 58.174 47.619 0.00 0.00 0.00 3.16
5040 13368 2.979814 ACAGCATCGCATACCTAACA 57.020 45.000 0.00 0.00 0.00 2.41
5041 13369 5.924475 AAATACAGCATCGCATACCTAAC 57.076 39.130 0.00 0.00 0.00 2.34
5042 13370 6.765989 AGAAAAATACAGCATCGCATACCTAA 59.234 34.615 0.00 0.00 0.00 2.69
5043 13371 6.288294 AGAAAAATACAGCATCGCATACCTA 58.712 36.000 0.00 0.00 0.00 3.08
5092 13429 8.092687 TCCCTATTGAAACTTCTGTTGTACTAC 58.907 37.037 0.05 0.05 36.39 2.73
5116 13453 8.658840 AGTATCCTTCTTCTATAGGTCATTCC 57.341 38.462 0.00 0.00 33.15 3.01
5122 13459 7.133483 ACACCAAGTATCCTTCTTCTATAGGT 58.867 38.462 0.00 0.00 33.15 3.08
5170 13513 5.482006 CCCACAAAAGAAAATGGAATCCTC 58.518 41.667 0.00 0.00 33.80 3.71
5179 13523 4.814967 TCCTCTTCCCCACAAAAGAAAAT 58.185 39.130 0.00 0.00 31.45 1.82
5184 13528 3.092301 GGAATCCTCTTCCCCACAAAAG 58.908 50.000 0.00 0.00 32.48 2.27
5185 13529 2.448961 TGGAATCCTCTTCCCCACAAAA 59.551 45.455 0.00 0.00 37.79 2.44
5208 13552 1.135315 CAGAATCAAAGGTGCGGCG 59.865 57.895 0.51 0.51 0.00 6.46
5241 13585 3.126858 TGAAATATGTTGCCGCAGAACTC 59.873 43.478 0.00 0.00 0.00 3.01
5247 13591 3.192212 TGAACATGAAATATGTTGCCGCA 59.808 39.130 9.73 0.00 41.76 5.69
5314 13658 3.632855 AGTTTGCTTAGCTTCTGTTGC 57.367 42.857 5.60 0.00 0.00 4.17
5352 13696 2.846550 GCCATACGACGATGATGATACG 59.153 50.000 0.00 0.00 0.00 3.06
5430 13777 2.497138 CTTGACAGTGATTGGACTGCA 58.503 47.619 0.00 0.00 46.28 4.41
5439 13786 3.871463 GCAACATCCTCCTTGACAGTGAT 60.871 47.826 0.00 0.00 0.00 3.06
5462 13809 1.745087 TCCAATGCGATTTGAAGCCTC 59.255 47.619 0.00 0.00 0.00 4.70
5478 13825 5.818678 ATAGTCCGCCATTAGTAATCCAA 57.181 39.130 0.00 0.00 0.00 3.53
5481 13828 5.120830 CAGCAATAGTCCGCCATTAGTAATC 59.879 44.000 0.00 0.00 0.00 1.75
5488 13835 1.065491 TCACAGCAATAGTCCGCCATT 60.065 47.619 0.00 0.00 0.00 3.16
5494 13841 5.982516 CAGACTATCTTCACAGCAATAGTCC 59.017 44.000 14.54 2.14 46.08 3.85
5502 13849 2.275318 GCACCAGACTATCTTCACAGC 58.725 52.381 0.00 0.00 0.00 4.40
5503 13850 3.599730 TGCACCAGACTATCTTCACAG 57.400 47.619 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.