Multiple sequence alignment - TraesCS1D01G414200

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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 TraesCS1D01G414200 chr1D 100.000 4196 0 0 1 4196 474288169 474292364 0.000000e+00 7749.0
1 TraesCS1D01G414200 chr1D 78.348 1949 337 55 1444 3342 474266409 474268322 0.000000e+00 1182.0
2 TraesCS1D01G414200 chr1D 78.930 1215 206 37 850 2044 474128584 474129768 0.000000e+00 780.0
3 TraesCS1D01G414200 chr1D 78.947 1026 194 12 2179 3193 474129897 474130911 0.000000e+00 678.0
4 TraesCS1D01G414200 chr1D 78.723 611 109 10 1444 2042 474307719 474308320 5.090000e-104 388.0
5 TraesCS1D01G414200 chr1D 78.993 457 92 2 900 1353 474265838 474266293 4.070000e-80 309.0
6 TraesCS1D01G414200 chr1D 78.355 462 91 7 894 1352 474307142 474307597 1.480000e-74 291.0
7 TraesCS1D01G414200 chr1A 95.640 2569 92 4 821 3385 568644156 568646708 0.000000e+00 4106.0
8 TraesCS1D01G414200 chr1A 78.389 1217 205 40 850 2044 568550146 568551326 0.000000e+00 737.0
9 TraesCS1D01G414200 chr1A 78.468 1031 203 12 2180 3193 568551456 568552484 0.000000e+00 656.0
10 TraesCS1D01G414200 chr1A 78.925 930 160 19 1444 2361 568687347 568688252 2.160000e-167 599.0
11 TraesCS1D01G414200 chr1A 93.267 401 23 2 365 761 568643757 568644157 4.670000e-164 588.0
12 TraesCS1D01G414200 chr1A 100.000 38 0 0 13 50 568643622 568643659 2.090000e-08 71.3
13 TraesCS1D01G414200 chrUn 95.275 2582 87 12 821 3385 8470969 8473532 0.000000e+00 4060.0
14 TraesCS1D01G414200 chrUn 96.280 699 19 2 3505 4196 2009610 2008912 0.000000e+00 1140.0
15 TraesCS1D01G414200 chrUn 100.000 393 0 0 1723 2115 479608927 479608535 0.000000e+00 726.0
16 TraesCS1D01G414200 chrUn 88.562 577 50 10 94 657 8470086 8470659 0.000000e+00 686.0
17 TraesCS1D01G414200 chrUn 86.508 126 13 3 640 761 8470845 8470970 7.320000e-28 135.0
18 TraesCS1D01G414200 chrUn 89.231 65 3 3 760 822 337364454 337364392 1.250000e-10 78.7
19 TraesCS1D01G414200 chrUn 94.000 50 3 0 1 50 8469959 8470008 4.500000e-10 76.8
20 TraesCS1D01G414200 chr5B 96.700 697 16 2 3507 4196 63274843 63275539 0.000000e+00 1153.0
21 TraesCS1D01G414200 chr5B 96.557 697 17 2 3507 4196 362948331 362949027 0.000000e+00 1147.0
22 TraesCS1D01G414200 chr5B 86.022 93 9 3 347 435 554765738 554765646 3.450000e-16 97.1
23 TraesCS1D01G414200 chr2B 96.700 697 16 2 3507 4196 528837733 528837037 0.000000e+00 1153.0
24 TraesCS1D01G414200 chr2B 96.557 697 17 2 3507 4196 199159769 199160465 0.000000e+00 1147.0
25 TraesCS1D01G414200 chr2B 95.603 705 24 5 3499 4196 727722921 727723625 0.000000e+00 1123.0
26 TraesCS1D01G414200 chr2B 90.769 65 5 1 759 822 69685392 69685456 7.470000e-13 86.1
27 TraesCS1D01G414200 chr2B 79.825 114 20 1 2225 2335 28151169 28151282 3.480000e-11 80.5
28 TraesCS1D01G414200 chr2A 96.700 697 16 2 3507 4196 771611051 771611747 0.000000e+00 1153.0
29 TraesCS1D01G414200 chr7D 96.040 707 21 2 3497 4196 166480355 166479649 0.000000e+00 1144.0
30 TraesCS1D01G414200 chr7D 87.209 86 9 2 348 431 498243212 498243297 3.450000e-16 97.1
31 TraesCS1D01G414200 chr7D 88.889 54 5 1 383 435 136906274 136906327 9.740000e-07 65.8
32 TraesCS1D01G414200 chr7B 96.413 697 18 2 3507 4196 748190683 748189987 0.000000e+00 1142.0
33 TraesCS1D01G414200 chr1B 78.691 1192 213 30 850 2022 659571899 659570730 0.000000e+00 756.0
34 TraesCS1D01G414200 chr1B 77.507 1027 207 14 2179 3193 659570587 659569573 2.790000e-166 595.0
35 TraesCS1D01G414200 chr1B 92.188 64 4 1 760 822 411441446 411441383 5.780000e-14 89.8
36 TraesCS1D01G414200 chr4A 85.268 224 23 9 218 436 522166327 522166109 5.460000e-54 222.0
37 TraesCS1D01G414200 chr2D 91.304 69 4 2 760 826 367592367 367592299 4.470000e-15 93.5
38 TraesCS1D01G414200 chr2D 90.000 70 5 2 756 823 367592299 367592368 5.780000e-14 89.8
39 TraesCS1D01G414200 chr3B 83.838 99 12 4 336 431 482482206 482482109 1.610000e-14 91.6
40 TraesCS1D01G414200 chr3B 87.500 72 3 3 759 824 284425143 284425214 1.250000e-10 78.7
41 TraesCS1D01G414200 chr3D 76.836 177 26 8 262 433 19269148 19268982 7.470000e-13 86.1
42 TraesCS1D01G414200 chr7A 89.231 65 3 3 760 822 163076346 163076284 1.250000e-10 78.7
43 TraesCS1D01G414200 chr7A 88.889 63 4 2 760 822 579550021 579549962 1.620000e-09 75.0
44 TraesCS1D01G414200 chr6A 88.235 68 5 3 347 412 574375443 574375509 1.250000e-10 78.7
45 TraesCS1D01G414200 chr5D 89.231 65 4 3 760 822 281431045 281431108 1.250000e-10 78.7


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 TraesCS1D01G414200 chr1D 474288169 474292364 4195 False 7749.000000 7749 100.000000 1 4196 1 chr1D.!!$F1 4195
1 TraesCS1D01G414200 chr1D 474265838 474268322 2484 False 745.500000 1182 78.670500 900 3342 2 chr1D.!!$F3 2442
2 TraesCS1D01G414200 chr1D 474128584 474130911 2327 False 729.000000 780 78.938500 850 3193 2 chr1D.!!$F2 2343
3 TraesCS1D01G414200 chr1D 474307142 474308320 1178 False 339.500000 388 78.539000 894 2042 2 chr1D.!!$F4 1148
4 TraesCS1D01G414200 chr1A 568643622 568646708 3086 False 1588.433333 4106 96.302333 13 3385 3 chr1A.!!$F3 3372
5 TraesCS1D01G414200 chr1A 568550146 568552484 2338 False 696.500000 737 78.428500 850 3193 2 chr1A.!!$F2 2343
6 TraesCS1D01G414200 chr1A 568687347 568688252 905 False 599.000000 599 78.925000 1444 2361 1 chr1A.!!$F1 917
7 TraesCS1D01G414200 chrUn 8469959 8473532 3573 False 1239.450000 4060 91.086250 1 3385 4 chrUn.!!$F1 3384
8 TraesCS1D01G414200 chrUn 2008912 2009610 698 True 1140.000000 1140 96.280000 3505 4196 1 chrUn.!!$R1 691
9 TraesCS1D01G414200 chr5B 63274843 63275539 696 False 1153.000000 1153 96.700000 3507 4196 1 chr5B.!!$F1 689
10 TraesCS1D01G414200 chr5B 362948331 362949027 696 False 1147.000000 1147 96.557000 3507 4196 1 chr5B.!!$F2 689
11 TraesCS1D01G414200 chr2B 528837037 528837733 696 True 1153.000000 1153 96.700000 3507 4196 1 chr2B.!!$R1 689
12 TraesCS1D01G414200 chr2B 199159769 199160465 696 False 1147.000000 1147 96.557000 3507 4196 1 chr2B.!!$F3 689
13 TraesCS1D01G414200 chr2B 727722921 727723625 704 False 1123.000000 1123 95.603000 3499 4196 1 chr2B.!!$F4 697
14 TraesCS1D01G414200 chr2A 771611051 771611747 696 False 1153.000000 1153 96.700000 3507 4196 1 chr2A.!!$F1 689
15 TraesCS1D01G414200 chr7D 166479649 166480355 706 True 1144.000000 1144 96.040000 3497 4196 1 chr7D.!!$R1 699
16 TraesCS1D01G414200 chr7B 748189987 748190683 696 True 1142.000000 1142 96.413000 3507 4196 1 chr7B.!!$R1 689
17 TraesCS1D01G414200 chr1B 659569573 659571899 2326 True 675.500000 756 78.099000 850 3193 2 chr1B.!!$R2 2343

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
126 163 0.968405 GCAAATCTTGGTGCCCTCAA 59.032 50.0 0.00 0.0 34.58 3.02 F
1127 1387 0.105039 GATGTCGTCTCCACCATCCC 59.895 60.0 0.00 0.0 0.00 3.85 F
2486 2798 0.692419 ATCCTTCATCTGCCGGACCT 60.692 55.0 5.05 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 1890 4.023707 GGTACATCATGCTCACTTATTGCC 60.024 45.833 0.00 0.0 0.00 4.52 R
3055 3394 1.001745 TGCTCGTCGATGTTGTCACG 61.002 55.000 4.21 0.0 34.70 4.35 R
3486 3875 0.100682 CTCGTCATCACCTACCGTGG 59.899 60.000 0.00 0.0 43.23 4.94 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
50 51 4.689345 GCTAATTAAATATCCTCCGCACGT 59.311 41.667 0.00 0.00 0.00 4.49
78 96 6.939163 GTCATCTCAGCCAGGACATAAATATT 59.061 38.462 0.00 0.00 0.00 1.28
126 163 0.968405 GCAAATCTTGGTGCCCTCAA 59.032 50.000 0.00 0.00 34.58 3.02
150 187 2.542907 CGGCCGCTTGTGTGAGTTT 61.543 57.895 14.67 0.00 0.00 2.66
151 188 1.282875 GGCCGCTTGTGTGAGTTTC 59.717 57.895 0.00 0.00 0.00 2.78
152 189 1.166531 GGCCGCTTGTGTGAGTTTCT 61.167 55.000 0.00 0.00 0.00 2.52
154 191 1.871039 GCCGCTTGTGTGAGTTTCTAA 59.129 47.619 0.00 0.00 0.00 2.10
156 193 3.058224 GCCGCTTGTGTGAGTTTCTAAAT 60.058 43.478 0.00 0.00 0.00 1.40
159 196 4.452455 CGCTTGTGTGAGTTTCTAAATCCT 59.548 41.667 0.00 0.00 0.00 3.24
166 203 8.311836 TGTGTGAGTTTCTAAATCCTAACTAGG 58.688 37.037 0.00 0.00 45.02 3.02
230 271 1.065126 GGAGCTCTGCTTTGGGTACAT 60.065 52.381 14.64 0.00 39.88 2.29
232 273 1.630369 AGCTCTGCTTTGGGTACATCA 59.370 47.619 0.00 0.00 33.89 3.07
233 274 1.740025 GCTCTGCTTTGGGTACATCAC 59.260 52.381 0.00 0.00 0.00 3.06
234 275 5.757633 AGCTCTGCTTTGGGTACATCACC 62.758 52.174 0.00 0.00 40.85 4.02
253 294 6.947644 TCACCCTTAAAAGTTTACAGGAAC 57.052 37.500 12.67 0.00 0.00 3.62
254 295 5.829391 TCACCCTTAAAAGTTTACAGGAACC 59.171 40.000 12.67 0.00 0.00 3.62
275 320 9.991906 GGAACCTTAAAGTTATTTAAAAAGGCT 57.008 29.630 10.98 1.59 39.70 4.58
294 339 4.350816 AGGCTATCACCATATAAACCTGCA 59.649 41.667 0.00 0.00 0.00 4.41
302 347 7.062322 TCACCATATAAACCTGCAGATCAAAT 58.938 34.615 17.39 4.61 0.00 2.32
303 348 7.560991 TCACCATATAAACCTGCAGATCAAATT 59.439 33.333 17.39 3.28 0.00 1.82
356 401 9.927668 ACAAGACAATATTACCCTTTTTGATTG 57.072 29.630 0.00 0.00 0.00 2.67
499 547 5.623335 TGGTCTAAATTACGCAAAATCACG 58.377 37.500 0.00 0.00 0.00 4.35
512 560 1.156736 AATCACGCTTCACCCGAAAG 58.843 50.000 0.00 0.00 0.00 2.62
526 574 7.760131 TCACCCGAAAGTATAAATCGTTAAG 57.240 36.000 0.00 0.00 34.90 1.85
700 954 7.373778 ACTATGGTCAAATCCGTAAACTTTC 57.626 36.000 0.00 0.00 0.00 2.62
701 955 7.166167 ACTATGGTCAAATCCGTAAACTTTCT 58.834 34.615 0.00 0.00 0.00 2.52
707 961 8.508875 GGTCAAATCCGTAAACTTTCTTCATAA 58.491 33.333 0.00 0.00 0.00 1.90
759 1016 4.888823 TGCTGCATATTTGTGATGGTGTAT 59.111 37.500 0.00 0.00 0.00 2.29
760 1017 6.060788 TGCTGCATATTTGTGATGGTGTATA 58.939 36.000 0.00 0.00 0.00 1.47
761 1018 6.017192 TGCTGCATATTTGTGATGGTGTATAC 60.017 38.462 0.00 0.00 0.00 1.47
762 1019 6.205464 GCTGCATATTTGTGATGGTGTATACT 59.795 38.462 4.17 0.00 0.00 2.12
763 1020 7.571983 GCTGCATATTTGTGATGGTGTATACTC 60.572 40.741 4.17 0.00 0.00 2.59
764 1021 6.710295 TGCATATTTGTGATGGTGTATACTCC 59.290 38.462 15.67 15.67 0.00 3.85
765 1022 6.149474 GCATATTTGTGATGGTGTATACTCCC 59.851 42.308 18.90 12.09 0.00 4.30
766 1023 5.975988 ATTTGTGATGGTGTATACTCCCT 57.024 39.130 18.90 10.86 0.00 4.20
767 1024 5.353394 TTTGTGATGGTGTATACTCCCTC 57.647 43.478 18.90 18.15 0.00 4.30
768 1025 3.305720 TGTGATGGTGTATACTCCCTCC 58.694 50.000 18.90 13.11 0.00 4.30
769 1026 3.305720 GTGATGGTGTATACTCCCTCCA 58.694 50.000 18.90 11.90 0.00 3.86
770 1027 3.904339 GTGATGGTGTATACTCCCTCCAT 59.096 47.826 18.90 15.43 38.21 3.41
771 1028 4.348168 GTGATGGTGTATACTCCCTCCATT 59.652 45.833 18.90 0.46 36.07 3.16
772 1029 4.593206 TGATGGTGTATACTCCCTCCATTC 59.407 45.833 18.90 8.53 36.07 2.67
773 1030 3.314693 TGGTGTATACTCCCTCCATTCC 58.685 50.000 18.90 1.62 0.00 3.01
774 1031 3.311028 TGGTGTATACTCCCTCCATTCCA 60.311 47.826 18.90 0.00 0.00 3.53
775 1032 3.714798 GGTGTATACTCCCTCCATTCCAA 59.285 47.826 12.17 0.00 0.00 3.53
776 1033 4.165372 GGTGTATACTCCCTCCATTCCAAA 59.835 45.833 12.17 0.00 0.00 3.28
777 1034 5.339695 GGTGTATACTCCCTCCATTCCAAAA 60.340 44.000 12.17 0.00 0.00 2.44
778 1035 6.365520 GTGTATACTCCCTCCATTCCAAAAT 58.634 40.000 4.17 0.00 0.00 1.82
779 1036 7.420913 GGTGTATACTCCCTCCATTCCAAAATA 60.421 40.741 12.17 0.00 0.00 1.40
780 1037 7.996644 GTGTATACTCCCTCCATTCCAAAATAA 59.003 37.037 4.17 0.00 0.00 1.40
781 1038 8.561769 TGTATACTCCCTCCATTCCAAAATAAA 58.438 33.333 4.17 0.00 0.00 1.40
782 1039 9.588096 GTATACTCCCTCCATTCCAAAATAAAT 57.412 33.333 0.00 0.00 0.00 1.40
783 1040 6.796785 ACTCCCTCCATTCCAAAATAAATG 57.203 37.500 0.00 0.00 33.57 2.32
784 1041 6.502138 ACTCCCTCCATTCCAAAATAAATGA 58.498 36.000 0.00 0.00 35.35 2.57
785 1042 6.381133 ACTCCCTCCATTCCAAAATAAATGAC 59.619 38.462 0.00 0.00 35.35 3.06
786 1043 6.502138 TCCCTCCATTCCAAAATAAATGACT 58.498 36.000 0.00 0.00 35.35 3.41
787 1044 6.607198 TCCCTCCATTCCAAAATAAATGACTC 59.393 38.462 0.00 0.00 35.35 3.36
788 1045 6.380846 CCCTCCATTCCAAAATAAATGACTCA 59.619 38.462 0.00 0.00 35.35 3.41
789 1046 7.093377 CCCTCCATTCCAAAATAAATGACTCAA 60.093 37.037 0.00 0.00 35.35 3.02
790 1047 7.761249 CCTCCATTCCAAAATAAATGACTCAAC 59.239 37.037 0.00 0.00 35.35 3.18
791 1048 8.421249 TCCATTCCAAAATAAATGACTCAACT 57.579 30.769 0.00 0.00 35.35 3.16
792 1049 8.869109 TCCATTCCAAAATAAATGACTCAACTT 58.131 29.630 0.00 0.00 35.35 2.66
793 1050 8.928733 CCATTCCAAAATAAATGACTCAACTTG 58.071 33.333 0.00 0.00 35.35 3.16
794 1051 8.928733 CATTCCAAAATAAATGACTCAACTTGG 58.071 33.333 0.00 0.00 35.35 3.61
795 1052 6.991938 TCCAAAATAAATGACTCAACTTGGG 58.008 36.000 0.00 0.00 33.23 4.12
796 1053 6.553100 TCCAAAATAAATGACTCAACTTGGGT 59.447 34.615 0.00 0.00 30.71 4.51
807 1064 6.824305 ACTCAACTTGGGTCATCTATTTTG 57.176 37.500 0.00 0.00 0.00 2.44
808 1065 6.542821 ACTCAACTTGGGTCATCTATTTTGA 58.457 36.000 0.00 0.00 0.00 2.69
809 1066 7.004086 ACTCAACTTGGGTCATCTATTTTGAA 58.996 34.615 0.00 0.00 0.00 2.69
810 1067 7.505585 ACTCAACTTGGGTCATCTATTTTGAAA 59.494 33.333 0.00 0.00 0.00 2.69
811 1068 7.657336 TCAACTTGGGTCATCTATTTTGAAAC 58.343 34.615 0.00 0.00 0.00 2.78
812 1069 6.254281 ACTTGGGTCATCTATTTTGAAACG 57.746 37.500 0.00 0.00 0.00 3.60
813 1070 5.183140 ACTTGGGTCATCTATTTTGAAACGG 59.817 40.000 0.00 0.00 0.00 4.44
814 1071 4.912586 TGGGTCATCTATTTTGAAACGGA 58.087 39.130 0.00 0.00 0.00 4.69
815 1072 4.941263 TGGGTCATCTATTTTGAAACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
816 1073 4.335594 GGGTCATCTATTTTGAAACGGAGG 59.664 45.833 0.00 0.00 0.00 4.30
817 1074 4.335594 GGTCATCTATTTTGAAACGGAGGG 59.664 45.833 0.00 0.00 0.00 4.30
818 1075 5.183228 GTCATCTATTTTGAAACGGAGGGA 58.817 41.667 0.00 0.00 0.00 4.20
819 1076 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
1127 1387 0.105039 GATGTCGTCTCCACCATCCC 59.895 60.000 0.00 0.00 0.00 3.85
1368 1632 4.874966 GCCTACATGATGATAGAATCAGGC 59.125 45.833 0.00 0.00 41.03 4.85
1465 1762 6.828273 TGCACTACCATATGCTCTTATTTTGT 59.172 34.615 0.00 0.00 42.55 2.83
1590 1890 3.624777 AGGAACCCATTATGCTGAGTTG 58.375 45.455 0.00 0.00 0.00 3.16
2197 2509 6.935167 AGTTTTGGAAGATTGTTGTTTGACT 58.065 32.000 0.00 0.00 0.00 3.41
2427 2739 3.838317 TGTACCAGTGCTCAATCCTAGTT 59.162 43.478 0.00 0.00 0.00 2.24
2486 2798 0.692419 ATCCTTCATCTGCCGGACCT 60.692 55.000 5.05 0.00 0.00 3.85
2514 2826 4.569943 TGAAGATACCAAGAGCAGTGAAC 58.430 43.478 0.00 0.00 0.00 3.18
2835 3168 5.086104 TGTATAAGGCTGTCAAGAAGGAC 57.914 43.478 0.00 0.00 38.29 3.85
3081 3420 4.111016 ATCGACGAGCACGCGGAA 62.111 61.111 12.47 3.38 43.96 4.30
3159 3513 1.857853 CAGCGTCGACGACTACACG 60.858 63.158 39.74 19.24 43.02 4.49
3208 3562 5.933187 TGTTGTTTAATCGTGCTATGTGT 57.067 34.783 0.00 0.00 0.00 3.72
3209 3563 5.684850 TGTTGTTTAATCGTGCTATGTGTG 58.315 37.500 0.00 0.00 0.00 3.82
3210 3564 4.335082 TGTTTAATCGTGCTATGTGTGC 57.665 40.909 0.00 0.00 0.00 4.57
3211 3565 3.748568 TGTTTAATCGTGCTATGTGTGCA 59.251 39.130 0.00 0.00 38.19 4.57
3238 3592 4.821260 TGCTGTACTTGCTCTTCATTTCAA 59.179 37.500 11.48 0.00 0.00 2.69
3254 3608 3.320610 TTCAATTGGTTGGGACCTTGA 57.679 42.857 5.42 0.00 46.66 3.02
3268 3622 1.802365 ACCTTGAAATCCGTTACGTGC 59.198 47.619 3.52 0.00 0.00 5.34
3276 3658 0.037697 TCCGTTACGTGCAATGCTCT 60.038 50.000 6.82 0.00 0.00 4.09
3277 3659 0.796312 CCGTTACGTGCAATGCTCTT 59.204 50.000 6.82 0.00 0.00 2.85
3280 3662 3.296628 CGTTACGTGCAATGCTCTTTTT 58.703 40.909 6.82 0.00 0.00 1.94
3282 3664 4.549599 CGTTACGTGCAATGCTCTTTTTAG 59.450 41.667 6.82 0.00 0.00 1.85
3287 3669 4.739716 CGTGCAATGCTCTTTTTAGTGTTT 59.260 37.500 6.82 0.00 0.00 2.83
3288 3670 5.231991 CGTGCAATGCTCTTTTTAGTGTTTT 59.768 36.000 6.82 0.00 0.00 2.43
3289 3671 6.560251 CGTGCAATGCTCTTTTTAGTGTTTTC 60.560 38.462 6.82 0.00 0.00 2.29
3290 3672 6.476706 GTGCAATGCTCTTTTTAGTGTTTTCT 59.523 34.615 6.82 0.00 0.00 2.52
3291 3673 7.647715 GTGCAATGCTCTTTTTAGTGTTTTCTA 59.352 33.333 6.82 0.00 0.00 2.10
3296 3678 8.276252 TGCTCTTTTTAGTGTTTTCTAAGTGT 57.724 30.769 0.00 0.00 32.55 3.55
3297 3679 8.736244 TGCTCTTTTTAGTGTTTTCTAAGTGTT 58.264 29.630 0.00 0.00 32.55 3.32
3298 3680 9.222916 GCTCTTTTTAGTGTTTTCTAAGTGTTC 57.777 33.333 0.00 0.00 32.55 3.18
3299 3681 9.717892 CTCTTTTTAGTGTTTTCTAAGTGTTCC 57.282 33.333 0.00 0.00 32.55 3.62
3337 3719 3.831333 TGATCTCCTGGATGAGCAGTATC 59.169 47.826 0.00 0.00 34.33 2.24
3357 3746 3.259064 TCCAAAATCCGTCGATGACTTC 58.741 45.455 6.11 0.00 0.00 3.01
3385 3774 2.715046 TGCTCATGATCCCACTTGTTC 58.285 47.619 0.00 0.00 0.00 3.18
3386 3775 2.019984 GCTCATGATCCCACTTGTTCC 58.980 52.381 0.00 0.00 0.00 3.62
3387 3776 2.356535 GCTCATGATCCCACTTGTTCCT 60.357 50.000 0.00 0.00 0.00 3.36
3388 3777 3.875369 GCTCATGATCCCACTTGTTCCTT 60.875 47.826 0.00 0.00 0.00 3.36
3389 3778 4.338879 CTCATGATCCCACTTGTTCCTTT 58.661 43.478 0.00 0.00 0.00 3.11
3390 3779 4.739793 TCATGATCCCACTTGTTCCTTTT 58.260 39.130 0.00 0.00 0.00 2.27
3391 3780 4.766891 TCATGATCCCACTTGTTCCTTTTC 59.233 41.667 0.00 0.00 0.00 2.29
3392 3781 4.453480 TGATCCCACTTGTTCCTTTTCT 57.547 40.909 0.00 0.00 0.00 2.52
3393 3782 5.576563 TGATCCCACTTGTTCCTTTTCTA 57.423 39.130 0.00 0.00 0.00 2.10
3394 3783 5.947663 TGATCCCACTTGTTCCTTTTCTAA 58.052 37.500 0.00 0.00 0.00 2.10
3395 3784 6.369629 TGATCCCACTTGTTCCTTTTCTAAA 58.630 36.000 0.00 0.00 0.00 1.85
3396 3785 6.836527 TGATCCCACTTGTTCCTTTTCTAAAA 59.163 34.615 0.00 0.00 0.00 1.52
3397 3786 7.343316 TGATCCCACTTGTTCCTTTTCTAAAAA 59.657 33.333 0.00 0.00 0.00 1.94
3420 3809 6.976934 AAATGATCCCACTTGTTGTTAAGT 57.023 33.333 0.00 0.00 41.37 2.24
3421 3810 6.976934 AATGATCCCACTTGTTGTTAAGTT 57.023 33.333 0.00 0.00 38.78 2.66
3422 3811 6.976934 ATGATCCCACTTGTTGTTAAGTTT 57.023 33.333 0.00 0.00 38.78 2.66
3423 3812 6.142818 TGATCCCACTTGTTGTTAAGTTTG 57.857 37.500 0.00 0.00 38.78 2.93
3424 3813 5.654650 TGATCCCACTTGTTGTTAAGTTTGT 59.345 36.000 0.00 0.00 38.78 2.83
3425 3814 6.829298 TGATCCCACTTGTTGTTAAGTTTGTA 59.171 34.615 0.00 0.00 38.78 2.41
3426 3815 6.439675 TCCCACTTGTTGTTAAGTTTGTAC 57.560 37.500 0.00 0.00 38.78 2.90
3427 3816 5.064962 TCCCACTTGTTGTTAAGTTTGTACG 59.935 40.000 0.00 0.00 38.78 3.67
3428 3817 5.267776 CCACTTGTTGTTAAGTTTGTACGG 58.732 41.667 0.00 0.00 38.78 4.02
3429 3818 5.163733 CCACTTGTTGTTAAGTTTGTACGGT 60.164 40.000 0.00 0.00 38.78 4.83
3430 3819 6.036953 CCACTTGTTGTTAAGTTTGTACGGTA 59.963 38.462 0.00 0.00 38.78 4.02
3431 3820 7.413877 CCACTTGTTGTTAAGTTTGTACGGTAA 60.414 37.037 0.00 0.00 38.78 2.85
3432 3821 8.124199 CACTTGTTGTTAAGTTTGTACGGTAAT 58.876 33.333 0.00 0.00 38.78 1.89
3433 3822 8.124199 ACTTGTTGTTAAGTTTGTACGGTAATG 58.876 33.333 0.00 0.00 37.62 1.90
3434 3823 7.783090 TGTTGTTAAGTTTGTACGGTAATGA 57.217 32.000 0.00 0.00 0.00 2.57
3435 3824 8.206325 TGTTGTTAAGTTTGTACGGTAATGAA 57.794 30.769 0.00 0.00 0.00 2.57
3436 3825 8.671921 TGTTGTTAAGTTTGTACGGTAATGAAA 58.328 29.630 0.00 0.00 0.00 2.69
3437 3826 9.667989 GTTGTTAAGTTTGTACGGTAATGAAAT 57.332 29.630 0.00 0.00 0.00 2.17
3438 3827 9.666626 TTGTTAAGTTTGTACGGTAATGAAATG 57.333 29.630 0.00 0.00 0.00 2.32
3439 3828 9.053840 TGTTAAGTTTGTACGGTAATGAAATGA 57.946 29.630 0.00 0.00 0.00 2.57
3442 3831 8.964420 AAGTTTGTACGGTAATGAAATGATTG 57.036 30.769 0.00 0.00 0.00 2.67
3443 3832 8.106247 AGTTTGTACGGTAATGAAATGATTGT 57.894 30.769 0.00 0.00 0.00 2.71
3444 3833 8.234546 AGTTTGTACGGTAATGAAATGATTGTC 58.765 33.333 0.00 0.00 0.00 3.18
3445 3834 6.671614 TGTACGGTAATGAAATGATTGTCC 57.328 37.500 0.00 0.00 0.00 4.02
3446 3835 6.411376 TGTACGGTAATGAAATGATTGTCCT 58.589 36.000 0.00 0.00 0.00 3.85
3447 3836 7.557724 TGTACGGTAATGAAATGATTGTCCTA 58.442 34.615 0.00 0.00 0.00 2.94
3448 3837 8.208224 TGTACGGTAATGAAATGATTGTCCTAT 58.792 33.333 0.00 0.00 0.00 2.57
3449 3838 7.730364 ACGGTAATGAAATGATTGTCCTATC 57.270 36.000 0.00 0.00 0.00 2.08
3450 3839 6.710744 ACGGTAATGAAATGATTGTCCTATCC 59.289 38.462 0.00 0.00 0.00 2.59
3451 3840 6.710295 CGGTAATGAAATGATTGTCCTATCCA 59.290 38.462 0.00 0.00 0.00 3.41
3452 3841 7.391554 CGGTAATGAAATGATTGTCCTATCCAT 59.608 37.037 0.00 0.00 0.00 3.41
3453 3842 9.739276 GGTAATGAAATGATTGTCCTATCCATA 57.261 33.333 0.00 0.00 0.00 2.74
3457 3846 9.872684 ATGAAATGATTGTCCTATCCATAAAGT 57.127 29.630 0.00 0.00 0.00 2.66
3463 3852 8.816894 TGATTGTCCTATCCATAAAGTATCTCC 58.183 37.037 0.00 0.00 0.00 3.71
3464 3853 7.554959 TTGTCCTATCCATAAAGTATCTCCC 57.445 40.000 0.00 0.00 0.00 4.30
3465 3854 6.875469 TGTCCTATCCATAAAGTATCTCCCT 58.125 40.000 0.00 0.00 0.00 4.20
3466 3855 6.726299 TGTCCTATCCATAAAGTATCTCCCTG 59.274 42.308 0.00 0.00 0.00 4.45
3467 3856 5.721960 TCCTATCCATAAAGTATCTCCCTGC 59.278 44.000 0.00 0.00 0.00 4.85
3468 3857 4.543590 ATCCATAAAGTATCTCCCTGCG 57.456 45.455 0.00 0.00 0.00 5.18
3469 3858 2.632996 TCCATAAAGTATCTCCCTGCGG 59.367 50.000 0.00 0.00 0.00 5.69
3470 3859 2.368875 CCATAAAGTATCTCCCTGCGGT 59.631 50.000 0.00 0.00 0.00 5.68
3471 3860 3.393800 CATAAAGTATCTCCCTGCGGTG 58.606 50.000 0.00 0.00 0.00 4.94
3472 3861 0.107654 AAAGTATCTCCCTGCGGTGC 60.108 55.000 0.00 0.00 0.00 5.01
3473 3862 1.264749 AAGTATCTCCCTGCGGTGCA 61.265 55.000 0.00 0.00 36.92 4.57
3474 3863 1.521681 GTATCTCCCTGCGGTGCAC 60.522 63.158 8.80 8.80 33.79 4.57
3475 3864 1.987306 TATCTCCCTGCGGTGCACA 60.987 57.895 20.43 0.00 33.79 4.57
3476 3865 1.549243 TATCTCCCTGCGGTGCACAA 61.549 55.000 20.43 2.32 33.79 3.33
3477 3866 3.357079 CTCCCTGCGGTGCACAAC 61.357 66.667 20.43 10.38 33.79 3.32
3478 3867 3.832237 CTCCCTGCGGTGCACAACT 62.832 63.158 20.43 0.00 33.79 3.16
3479 3868 3.357079 CCCTGCGGTGCACAACTC 61.357 66.667 20.43 4.59 33.79 3.01
3480 3869 3.357079 CCTGCGGTGCACAACTCC 61.357 66.667 20.43 0.00 33.79 3.85
3481 3870 2.591429 CTGCGGTGCACAACTCCA 60.591 61.111 20.43 6.57 33.79 3.86
3482 3871 2.591429 TGCGGTGCACAACTCCAG 60.591 61.111 20.43 1.60 31.71 3.86
3483 3872 2.591715 GCGGTGCACAACTCCAGT 60.592 61.111 20.43 0.00 31.85 4.00
3484 3873 1.301401 GCGGTGCACAACTCCAGTA 60.301 57.895 20.43 0.00 31.85 2.74
3485 3874 0.673644 GCGGTGCACAACTCCAGTAT 60.674 55.000 20.43 0.00 31.85 2.12
3486 3875 1.359848 CGGTGCACAACTCCAGTATC 58.640 55.000 20.43 0.00 31.85 2.24
3487 3876 1.739067 GGTGCACAACTCCAGTATCC 58.261 55.000 20.43 0.00 31.85 2.59
3488 3877 1.003118 GGTGCACAACTCCAGTATCCA 59.997 52.381 20.43 0.00 31.85 3.41
3489 3878 2.076863 GTGCACAACTCCAGTATCCAC 58.923 52.381 13.17 0.00 0.00 4.02
3490 3879 1.337728 TGCACAACTCCAGTATCCACG 60.338 52.381 0.00 0.00 0.00 4.94
3491 3880 2.007049 GCACAACTCCAGTATCCACGG 61.007 57.143 0.00 0.00 0.00 4.94
3492 3881 1.275291 CACAACTCCAGTATCCACGGT 59.725 52.381 0.00 0.00 0.00 4.83
3493 3882 2.494471 CACAACTCCAGTATCCACGGTA 59.506 50.000 0.00 0.00 0.00 4.02
3494 3883 2.758979 ACAACTCCAGTATCCACGGTAG 59.241 50.000 0.00 0.00 0.00 3.18
3495 3884 2.068834 ACTCCAGTATCCACGGTAGG 57.931 55.000 0.00 0.00 0.00 3.18
3664 4055 4.446023 GGGAAGATCGTAGAGGGAAGACTA 60.446 50.000 0.00 0.00 43.63 2.59
3730 4121 2.456119 GGACTGCCTCATTCGCGTG 61.456 63.158 5.77 0.00 0.00 5.34
3798 4189 1.696336 GGCCATTGATCCTAGCTCTGA 59.304 52.381 0.00 0.00 0.00 3.27
3840 4231 2.387445 CGGGATCGCGTTTTGAGCA 61.387 57.895 22.77 0.00 34.19 4.26
3926 4323 8.512956 CAAATATGGTCCTTTCAGATCATGATC 58.487 37.037 25.42 25.42 38.10 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 1.007118 TGTCCTGGCTGAGATGACCTA 59.993 52.381 0.00 0.00 0.00 3.08
98 135 1.213537 CAAGATTTGCAGCCCCGTG 59.786 57.895 0.00 0.00 0.00 4.94
134 171 1.508632 TAGAAACTCACACAAGCGGC 58.491 50.000 0.00 0.00 0.00 6.53
194 235 7.997803 AGCAGAGCTCCATCTAGAAAAATTATT 59.002 33.333 10.93 0.00 30.62 1.40
200 241 4.833478 AAGCAGAGCTCCATCTAGAAAA 57.167 40.909 10.93 0.00 38.25 2.29
203 244 2.433604 CCAAAGCAGAGCTCCATCTAGA 59.566 50.000 10.93 0.00 38.25 2.43
214 255 2.359900 GGTGATGTACCCAAAGCAGAG 58.640 52.381 0.00 0.00 44.15 3.35
230 271 5.829391 GGTTCCTGTAAACTTTTAAGGGTGA 59.171 40.000 8.72 0.00 0.00 4.02
232 273 6.022107 AGGTTCCTGTAAACTTTTAAGGGT 57.978 37.500 0.00 0.00 27.28 4.34
233 274 6.971726 AAGGTTCCTGTAAACTTTTAAGGG 57.028 37.500 0.00 3.92 42.71 3.95
234 275 9.961265 CTTTAAGGTTCCTGTAAACTTTTAAGG 57.039 33.333 0.00 0.00 42.71 2.69
275 320 7.315066 TGATCTGCAGGTTTATATGGTGATA 57.685 36.000 15.13 0.00 0.00 2.15
279 324 7.902920 AATTTGATCTGCAGGTTTATATGGT 57.097 32.000 15.13 0.00 0.00 3.55
313 358 6.774673 TGTCTTGTGTATCCAAATCAACCTA 58.225 36.000 0.00 0.00 0.00 3.08
315 360 5.957842 TGTCTTGTGTATCCAAATCAACC 57.042 39.130 0.00 0.00 0.00 3.77
356 401 8.315482 AGAGGTGAAGATTAGAAGTTACCTTTC 58.685 37.037 0.00 0.00 37.42 2.62
489 537 0.729140 CGGGTGAAGCGTGATTTTGC 60.729 55.000 0.00 0.00 0.00 3.68
499 547 4.569564 ACGATTTATACTTTCGGGTGAAGC 59.430 41.667 0.00 0.00 37.20 3.86
526 574 7.805071 CCATGTTCTATGAAGAAACTTGAACAC 59.195 37.037 13.29 0.00 43.30 3.32
564 612 8.458843 AGAAAATCTGGTATGTAACAAATTCGG 58.541 33.333 0.00 0.00 0.00 4.30
565 613 9.840427 AAGAAAATCTGGTATGTAACAAATTCG 57.160 29.630 0.00 0.00 0.00 3.34
707 961 6.910259 AACCAGGGTAAGAGGATTTCTTAT 57.090 37.500 0.00 0.00 46.99 1.73
711 965 3.939592 CGAAACCAGGGTAAGAGGATTTC 59.060 47.826 0.00 0.00 0.00 2.17
714 968 2.829023 TCGAAACCAGGGTAAGAGGAT 58.171 47.619 0.00 0.00 0.00 3.24
715 969 2.314071 TCGAAACCAGGGTAAGAGGA 57.686 50.000 0.00 0.00 0.00 3.71
759 1016 7.559897 GTCATTTATTTTGGAATGGAGGGAGTA 59.440 37.037 0.00 0.00 34.74 2.59
760 1017 6.381133 GTCATTTATTTTGGAATGGAGGGAGT 59.619 38.462 0.00 0.00 34.74 3.85
761 1018 6.608808 AGTCATTTATTTTGGAATGGAGGGAG 59.391 38.462 0.00 0.00 34.74 4.30
762 1019 6.502138 AGTCATTTATTTTGGAATGGAGGGA 58.498 36.000 0.00 0.00 34.74 4.20
763 1020 6.380846 TGAGTCATTTATTTTGGAATGGAGGG 59.619 38.462 0.00 0.00 34.74 4.30
764 1021 7.408756 TGAGTCATTTATTTTGGAATGGAGG 57.591 36.000 0.00 0.00 34.74 4.30
765 1022 8.526147 AGTTGAGTCATTTATTTTGGAATGGAG 58.474 33.333 0.00 0.00 34.74 3.86
766 1023 8.421249 AGTTGAGTCATTTATTTTGGAATGGA 57.579 30.769 0.00 0.00 34.74 3.41
767 1024 8.928733 CAAGTTGAGTCATTTATTTTGGAATGG 58.071 33.333 0.00 0.00 34.74 3.16
768 1025 8.928733 CCAAGTTGAGTCATTTATTTTGGAATG 58.071 33.333 3.87 0.00 35.69 2.67
769 1026 8.096414 CCCAAGTTGAGTCATTTATTTTGGAAT 58.904 33.333 3.87 0.00 35.69 3.01
770 1027 7.070571 ACCCAAGTTGAGTCATTTATTTTGGAA 59.929 33.333 3.87 0.00 35.69 3.53
771 1028 6.553100 ACCCAAGTTGAGTCATTTATTTTGGA 59.447 34.615 3.87 0.00 35.69 3.53
772 1029 6.758254 ACCCAAGTTGAGTCATTTATTTTGG 58.242 36.000 3.87 2.77 33.95 3.28
773 1030 7.432869 TGACCCAAGTTGAGTCATTTATTTTG 58.567 34.615 15.48 0.00 35.67 2.44
774 1031 7.595819 TGACCCAAGTTGAGTCATTTATTTT 57.404 32.000 15.48 0.00 35.67 1.82
775 1032 7.781324 ATGACCCAAGTTGAGTCATTTATTT 57.219 32.000 23.07 5.40 46.42 1.40
782 1039 5.762179 AATAGATGACCCAAGTTGAGTCA 57.238 39.130 20.75 20.75 44.11 3.41
783 1040 6.655003 TCAAAATAGATGACCCAAGTTGAGTC 59.345 38.462 10.39 10.39 0.00 3.36
784 1041 6.542821 TCAAAATAGATGACCCAAGTTGAGT 58.457 36.000 3.87 0.00 0.00 3.41
785 1042 7.452880 TTCAAAATAGATGACCCAAGTTGAG 57.547 36.000 3.87 0.00 0.00 3.02
786 1043 7.521423 CGTTTCAAAATAGATGACCCAAGTTGA 60.521 37.037 3.87 0.00 0.00 3.18
787 1044 6.582295 CGTTTCAAAATAGATGACCCAAGTTG 59.418 38.462 0.00 0.00 0.00 3.16
788 1045 6.294508 CCGTTTCAAAATAGATGACCCAAGTT 60.295 38.462 0.00 0.00 0.00 2.66
789 1046 5.183140 CCGTTTCAAAATAGATGACCCAAGT 59.817 40.000 0.00 0.00 0.00 3.16
790 1047 5.414454 TCCGTTTCAAAATAGATGACCCAAG 59.586 40.000 0.00 0.00 0.00 3.61
791 1048 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
792 1049 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
793 1050 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
794 1051 4.335594 CCCTCCGTTTCAAAATAGATGACC 59.664 45.833 0.00 0.00 0.00 4.02
795 1052 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
796 1053 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
797 1054 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
798 1055 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
799 1056 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
800 1057 5.811100 GTCTACTCCCTCCGTTTCAAAATAG 59.189 44.000 0.00 0.00 0.00 1.73
801 1058 5.246656 TGTCTACTCCCTCCGTTTCAAAATA 59.753 40.000 0.00 0.00 0.00 1.40
802 1059 4.041198 TGTCTACTCCCTCCGTTTCAAAAT 59.959 41.667 0.00 0.00 0.00 1.82
803 1060 3.388676 TGTCTACTCCCTCCGTTTCAAAA 59.611 43.478 0.00 0.00 0.00 2.44
804 1061 2.967201 TGTCTACTCCCTCCGTTTCAAA 59.033 45.455 0.00 0.00 0.00 2.69
805 1062 2.600790 TGTCTACTCCCTCCGTTTCAA 58.399 47.619 0.00 0.00 0.00 2.69
806 1063 2.297698 TGTCTACTCCCTCCGTTTCA 57.702 50.000 0.00 0.00 0.00 2.69
807 1064 3.889520 ATTGTCTACTCCCTCCGTTTC 57.110 47.619 0.00 0.00 0.00 2.78
808 1065 3.868754 GCAATTGTCTACTCCCTCCGTTT 60.869 47.826 7.40 0.00 0.00 3.60
809 1066 2.354805 GCAATTGTCTACTCCCTCCGTT 60.355 50.000 7.40 0.00 0.00 4.44
810 1067 1.207329 GCAATTGTCTACTCCCTCCGT 59.793 52.381 7.40 0.00 0.00 4.69
811 1068 1.473434 GGCAATTGTCTACTCCCTCCG 60.473 57.143 7.40 0.00 0.00 4.63
812 1069 1.840635 AGGCAATTGTCTACTCCCTCC 59.159 52.381 11.74 0.00 0.00 4.30
813 1070 2.482142 CGAGGCAATTGTCTACTCCCTC 60.482 54.545 13.63 13.36 35.27 4.30
814 1071 1.482593 CGAGGCAATTGTCTACTCCCT 59.517 52.381 13.63 5.34 0.00 4.20
815 1072 1.480954 TCGAGGCAATTGTCTACTCCC 59.519 52.381 13.63 0.00 0.00 4.30
816 1073 2.094182 TGTCGAGGCAATTGTCTACTCC 60.094 50.000 13.63 0.57 0.00 3.85
817 1074 3.232213 TGTCGAGGCAATTGTCTACTC 57.768 47.619 13.63 11.22 0.00 2.59
818 1075 3.326747 GTTGTCGAGGCAATTGTCTACT 58.673 45.455 13.63 3.20 0.00 2.57
819 1076 2.415512 GGTTGTCGAGGCAATTGTCTAC 59.584 50.000 13.63 9.30 0.00 2.59
878 1135 7.228706 GGGTAGAATTTCCGCCCATTATATATG 59.771 40.741 16.62 0.00 39.13 1.78
1127 1387 5.964958 AACAGTGATGGTGTAAGGATTTG 57.035 39.130 0.00 0.00 0.00 2.32
1368 1632 8.255111 TGACATTATATCCATATGGCTCTAGG 57.745 38.462 17.58 6.23 34.44 3.02
1465 1762 7.090173 GCATAGTACTTCAAAAGCAATTTGGA 58.910 34.615 0.00 5.69 46.85 3.53
1590 1890 4.023707 GGTACATCATGCTCACTTATTGCC 60.024 45.833 0.00 0.00 0.00 4.52
2197 2509 3.380004 CCAAGTAGACACACTGGCAAAAA 59.620 43.478 0.00 0.00 0.00 1.94
2427 2739 3.526899 TGGATTTCTACTTGGGTGGAGA 58.473 45.455 0.00 0.00 34.54 3.71
2486 2798 5.188555 ACTGCTCTTGGTATCTTCATCTTCA 59.811 40.000 0.00 0.00 0.00 3.02
2681 3008 4.718940 TGCTCTCGTGATCTTGTCATTA 57.281 40.909 0.00 0.00 39.48 1.90
2970 3309 4.399395 CCTTCCGGCAGCTCAGCA 62.399 66.667 0.00 0.00 35.83 4.41
3055 3394 1.001745 TGCTCGTCGATGTTGTCACG 61.002 55.000 4.21 0.00 34.70 4.35
3209 3563 2.898705 AGAGCAAGTACAGCATAGTGC 58.101 47.619 12.08 0.00 45.46 4.40
3210 3564 4.498241 TGAAGAGCAAGTACAGCATAGTG 58.502 43.478 12.08 0.00 0.00 2.74
3211 3565 4.808414 TGAAGAGCAAGTACAGCATAGT 57.192 40.909 12.08 0.00 0.00 2.12
3212 3566 6.314648 TGAAATGAAGAGCAAGTACAGCATAG 59.685 38.462 12.08 0.00 0.00 2.23
3254 3608 1.810151 AGCATTGCACGTAACGGATTT 59.190 42.857 11.91 0.00 0.00 2.17
3268 3622 9.736023 ACTTAGAAAACACTAAAAAGAGCATTG 57.264 29.630 0.00 0.00 32.95 2.82
3282 3664 9.612620 CAATGAATAGGAACACTTAGAAAACAC 57.387 33.333 0.00 0.00 0.00 3.32
3287 3669 9.739276 AATCACAATGAATAGGAACACTTAGAA 57.261 29.630 0.00 0.00 0.00 2.10
3288 3670 9.166173 CAATCACAATGAATAGGAACACTTAGA 57.834 33.333 0.00 0.00 0.00 2.10
3289 3671 8.950210 ACAATCACAATGAATAGGAACACTTAG 58.050 33.333 0.00 0.00 0.00 2.18
3290 3672 8.729756 CACAATCACAATGAATAGGAACACTTA 58.270 33.333 0.00 0.00 0.00 2.24
3291 3673 7.448161 TCACAATCACAATGAATAGGAACACTT 59.552 33.333 0.00 0.00 0.00 3.16
3296 3678 7.500227 GGAGATCACAATCACAATGAATAGGAA 59.500 37.037 0.00 0.00 34.07 3.36
3297 3679 6.994496 GGAGATCACAATCACAATGAATAGGA 59.006 38.462 0.00 0.00 34.07 2.94
3298 3680 6.996879 AGGAGATCACAATCACAATGAATAGG 59.003 38.462 0.00 0.00 34.07 2.57
3299 3681 7.041303 CCAGGAGATCACAATCACAATGAATAG 60.041 40.741 0.00 0.00 34.07 1.73
3301 3683 5.593095 CCAGGAGATCACAATCACAATGAAT 59.407 40.000 0.00 0.00 34.07 2.57
3302 3684 4.945543 CCAGGAGATCACAATCACAATGAA 59.054 41.667 0.00 0.00 34.07 2.57
3337 3719 3.262420 AGAAGTCATCGACGGATTTTGG 58.738 45.455 0.00 0.00 37.67 3.28
3357 3746 4.021719 AGTGGGATCATGAGCAAAACAAAG 60.022 41.667 13.85 0.00 0.00 2.77
3395 3784 7.791029 ACTTAACAACAAGTGGGATCATTTTT 58.209 30.769 0.00 0.00 37.37 1.94
3396 3785 7.360113 ACTTAACAACAAGTGGGATCATTTT 57.640 32.000 0.00 0.00 37.37 1.82
3397 3786 6.976934 ACTTAACAACAAGTGGGATCATTT 57.023 33.333 0.00 0.00 37.37 2.32
3398 3787 6.976934 AACTTAACAACAAGTGGGATCATT 57.023 33.333 0.00 0.00 38.74 2.57
3399 3788 6.323739 ACAAACTTAACAACAAGTGGGATCAT 59.676 34.615 0.00 0.00 38.74 2.45
3400 3789 5.654650 ACAAACTTAACAACAAGTGGGATCA 59.345 36.000 0.00 0.00 38.74 2.92
3401 3790 6.144078 ACAAACTTAACAACAAGTGGGATC 57.856 37.500 0.00 0.00 38.74 3.36
3402 3791 6.238538 CGTACAAACTTAACAACAAGTGGGAT 60.239 38.462 0.00 0.00 38.74 3.85
3403 3792 5.064962 CGTACAAACTTAACAACAAGTGGGA 59.935 40.000 0.00 0.00 38.74 4.37
3404 3793 5.267776 CGTACAAACTTAACAACAAGTGGG 58.732 41.667 0.00 0.00 38.74 4.61
3405 3794 5.163733 ACCGTACAAACTTAACAACAAGTGG 60.164 40.000 0.00 0.00 38.74 4.00
3406 3795 5.871539 ACCGTACAAACTTAACAACAAGTG 58.128 37.500 0.00 0.00 38.74 3.16
3407 3796 7.608308 TTACCGTACAAACTTAACAACAAGT 57.392 32.000 0.00 0.00 40.49 3.16
3408 3797 8.336806 TCATTACCGTACAAACTTAACAACAAG 58.663 33.333 0.00 0.00 0.00 3.16
3409 3798 8.206325 TCATTACCGTACAAACTTAACAACAA 57.794 30.769 0.00 0.00 0.00 2.83
3410 3799 7.783090 TCATTACCGTACAAACTTAACAACA 57.217 32.000 0.00 0.00 0.00 3.33
3411 3800 9.667989 ATTTCATTACCGTACAAACTTAACAAC 57.332 29.630 0.00 0.00 0.00 3.32
3412 3801 9.666626 CATTTCATTACCGTACAAACTTAACAA 57.333 29.630 0.00 0.00 0.00 2.83
3413 3802 9.053840 TCATTTCATTACCGTACAAACTTAACA 57.946 29.630 0.00 0.00 0.00 2.41
3417 3806 8.573035 ACAATCATTTCATTACCGTACAAACTT 58.427 29.630 0.00 0.00 0.00 2.66
3418 3807 8.106247 ACAATCATTTCATTACCGTACAAACT 57.894 30.769 0.00 0.00 0.00 2.66
3419 3808 7.483691 GGACAATCATTTCATTACCGTACAAAC 59.516 37.037 0.00 0.00 0.00 2.93
3420 3809 7.392113 AGGACAATCATTTCATTACCGTACAAA 59.608 33.333 0.00 0.00 0.00 2.83
3421 3810 6.882140 AGGACAATCATTTCATTACCGTACAA 59.118 34.615 0.00 0.00 0.00 2.41
3422 3811 6.411376 AGGACAATCATTTCATTACCGTACA 58.589 36.000 0.00 0.00 0.00 2.90
3423 3812 6.920569 AGGACAATCATTTCATTACCGTAC 57.079 37.500 0.00 0.00 0.00 3.67
3424 3813 7.876068 GGATAGGACAATCATTTCATTACCGTA 59.124 37.037 0.00 0.00 0.00 4.02
3425 3814 6.710744 GGATAGGACAATCATTTCATTACCGT 59.289 38.462 0.00 0.00 0.00 4.83
3426 3815 6.710295 TGGATAGGACAATCATTTCATTACCG 59.290 38.462 0.00 0.00 0.00 4.02
3427 3816 8.641498 ATGGATAGGACAATCATTTCATTACC 57.359 34.615 0.00 0.00 0.00 2.85
3431 3820 9.872684 ACTTTATGGATAGGACAATCATTTCAT 57.127 29.630 0.00 0.00 0.00 2.57
3437 3826 8.816894 GGAGATACTTTATGGATAGGACAATCA 58.183 37.037 0.00 0.00 0.00 2.57
3438 3827 8.261522 GGGAGATACTTTATGGATAGGACAATC 58.738 40.741 0.00 0.00 0.00 2.67
3439 3828 7.964293 AGGGAGATACTTTATGGATAGGACAAT 59.036 37.037 0.00 0.00 0.00 2.71
3440 3829 7.235606 CAGGGAGATACTTTATGGATAGGACAA 59.764 40.741 0.00 0.00 0.00 3.18
3441 3830 6.726299 CAGGGAGATACTTTATGGATAGGACA 59.274 42.308 0.00 0.00 0.00 4.02
3442 3831 6.351456 GCAGGGAGATACTTTATGGATAGGAC 60.351 46.154 0.00 0.00 0.00 3.85
3443 3832 5.721960 GCAGGGAGATACTTTATGGATAGGA 59.278 44.000 0.00 0.00 0.00 2.94
3444 3833 5.394663 CGCAGGGAGATACTTTATGGATAGG 60.395 48.000 0.00 0.00 0.00 2.57
3445 3834 5.655488 CGCAGGGAGATACTTTATGGATAG 58.345 45.833 0.00 0.00 0.00 2.08
3446 3835 5.661056 CGCAGGGAGATACTTTATGGATA 57.339 43.478 0.00 0.00 0.00 2.59
3447 3836 4.543590 CGCAGGGAGATACTTTATGGAT 57.456 45.455 0.00 0.00 0.00 3.41
3464 3853 2.591429 TGGAGTTGTGCACCGCAG 60.591 61.111 15.69 0.00 40.08 5.18
3465 3854 2.034048 TACTGGAGTTGTGCACCGCA 62.034 55.000 15.69 0.00 35.60 5.69
3466 3855 0.673644 ATACTGGAGTTGTGCACCGC 60.674 55.000 15.69 7.03 0.00 5.68
3467 3856 1.359848 GATACTGGAGTTGTGCACCG 58.640 55.000 15.69 0.00 0.00 4.94
3468 3857 1.003118 TGGATACTGGAGTTGTGCACC 59.997 52.381 15.69 0.00 37.61 5.01
3469 3858 2.076863 GTGGATACTGGAGTTGTGCAC 58.923 52.381 10.75 10.75 37.61 4.57
3470 3859 1.337728 CGTGGATACTGGAGTTGTGCA 60.338 52.381 0.00 0.00 37.61 4.57
3471 3860 1.359848 CGTGGATACTGGAGTTGTGC 58.640 55.000 0.00 0.00 37.61 4.57
3472 3861 1.275291 ACCGTGGATACTGGAGTTGTG 59.725 52.381 0.00 0.00 37.61 3.33
3473 3862 1.640917 ACCGTGGATACTGGAGTTGT 58.359 50.000 0.00 0.00 37.61 3.32
3474 3863 2.100916 CCTACCGTGGATACTGGAGTTG 59.899 54.545 0.00 0.00 37.61 3.16
3475 3864 2.292061 ACCTACCGTGGATACTGGAGTT 60.292 50.000 0.00 0.00 37.61 3.01
3476 3865 1.287146 ACCTACCGTGGATACTGGAGT 59.713 52.381 0.00 0.00 37.61 3.85
3477 3866 1.681793 CACCTACCGTGGATACTGGAG 59.318 57.143 0.00 0.00 38.96 3.86
3478 3867 1.285667 TCACCTACCGTGGATACTGGA 59.714 52.381 0.00 0.00 43.23 3.86
3479 3868 1.771565 TCACCTACCGTGGATACTGG 58.228 55.000 0.00 0.00 43.23 4.00
3480 3869 2.956333 TCATCACCTACCGTGGATACTG 59.044 50.000 0.00 0.00 43.23 2.74
3481 3870 2.957006 GTCATCACCTACCGTGGATACT 59.043 50.000 0.00 0.00 43.23 2.12
3482 3871 2.287427 CGTCATCACCTACCGTGGATAC 60.287 54.545 0.00 0.00 43.23 2.24
3483 3872 1.951602 CGTCATCACCTACCGTGGATA 59.048 52.381 0.00 0.00 43.23 2.59
3484 3873 0.744874 CGTCATCACCTACCGTGGAT 59.255 55.000 0.00 0.00 43.23 3.41
3485 3874 0.322726 TCGTCATCACCTACCGTGGA 60.323 55.000 0.00 0.00 43.23 4.02
3486 3875 0.100682 CTCGTCATCACCTACCGTGG 59.899 60.000 0.00 0.00 43.23 4.94
3487 3876 1.092348 TCTCGTCATCACCTACCGTG 58.908 55.000 0.00 0.00 44.50 4.94
3488 3877 1.093159 GTCTCGTCATCACCTACCGT 58.907 55.000 0.00 0.00 0.00 4.83
3489 3878 0.381089 GGTCTCGTCATCACCTACCG 59.619 60.000 0.00 0.00 0.00 4.02
3490 3879 0.745468 GGGTCTCGTCATCACCTACC 59.255 60.000 0.00 0.00 0.00 3.18
3491 3880 0.745468 GGGGTCTCGTCATCACCTAC 59.255 60.000 0.00 0.00 0.00 3.18
3492 3881 0.396695 GGGGGTCTCGTCATCACCTA 60.397 60.000 0.00 0.00 0.00 3.08
3493 3882 1.686110 GGGGGTCTCGTCATCACCT 60.686 63.158 0.00 0.00 0.00 4.00
3494 3883 2.901042 GGGGGTCTCGTCATCACC 59.099 66.667 0.00 0.00 0.00 4.02
3495 3884 2.494918 CGGGGGTCTCGTCATCAC 59.505 66.667 0.00 0.00 0.00 3.06
3664 4055 1.561643 TCCATTCCTTCTCTCGCAGT 58.438 50.000 0.00 0.00 0.00 4.40
3798 4189 3.799755 GCGACTTTGCCGCCGAAT 61.800 61.111 0.00 0.00 46.22 3.34
3840 4231 2.185310 GACTTCGTCCATGGCCAGGT 62.185 60.000 17.55 0.00 0.00 4.00
4087 4484 4.094684 GGCTCATGAGACGAACCG 57.905 61.111 27.04 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.