Multiple sequence alignment - TraesCS7D01G047000

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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 TraesCS7D01G047000 chr7D 100.000 3399 0 0 1 3399 24325379 24328777 0.000000e+00 6277
1 TraesCS7D01G047000 chr7D 84.634 1230 175 11 1035 2262 24021262 24020045 0.000000e+00 1212
2 TraesCS7D01G047000 chr7D 97.843 510 11 0 1 510 393026311 393026820 0.000000e+00 881
3 TraesCS7D01G047000 chr7D 97.847 511 10 1 1 510 420762631 420763141 0.000000e+00 881
4 TraesCS7D01G047000 chr7D 96.750 523 15 1 1 521 78600359 78599837 0.000000e+00 870
5 TraesCS7D01G047000 chr7D 90.625 224 20 1 776 998 592546466 592546243 2.560000e-76 296
6 TraesCS7D01G047000 chr7D 88.559 236 26 1 779 1013 385395313 385395548 5.550000e-73 285
7 TraesCS7D01G047000 chr7D 80.309 259 33 12 542 784 24021519 24021263 2.690000e-41 180
8 TraesCS7D01G047000 chr7D 90.698 129 11 1 542 669 24119097 24118969 1.620000e-38 171
9 TraesCS7D01G047000 chr4A 89.741 2125 159 31 1056 3133 707305506 707303394 0.000000e+00 2662
10 TraesCS7D01G047000 chr4A 82.987 1252 197 11 1014 2262 707674762 707676000 0.000000e+00 1118
11 TraesCS7D01G047000 chr4A 83.145 1240 187 14 1031 2262 707487548 707488773 0.000000e+00 1112
12 TraesCS7D01G047000 chr4A 82.827 1252 199 11 1014 2262 707702221 707703459 0.000000e+00 1107
13 TraesCS7D01G047000 chr4A 82.163 1239 201 12 1031 2262 706089818 706088593 0.000000e+00 1046
14 TraesCS7D01G047000 chr4A 81.987 1238 205 11 1031 2262 705953842 705952617 0.000000e+00 1035
15 TraesCS7D01G047000 chr4A 85.652 683 62 23 2745 3397 707514028 707514704 0.000000e+00 686
16 TraesCS7D01G047000 chr4A 75.604 828 172 18 1437 2262 707260630 707259831 1.910000e-102 383
17 TraesCS7D01G047000 chr4A 86.395 294 38 2 1557 1849 707513038 707513330 1.520000e-83 320
18 TraesCS7D01G047000 chr4A 95.722 187 6 2 1844 2029 707513846 707514031 1.980000e-77 300
19 TraesCS7D01G047000 chr4A 90.435 115 9 2 556 669 707487291 707487404 2.110000e-32 150
20 TraesCS7D01G047000 chr4A 92.308 104 7 1 567 669 707305624 707305521 2.730000e-31 147
21 TraesCS7D01G047000 chrUn 81.987 1238 205 11 1031 2262 220049480 220048255 0.000000e+00 1035
22 TraesCS7D01G047000 chr5D 98.434 511 8 0 1 511 57004868 57004358 0.000000e+00 900
23 TraesCS7D01G047000 chr5D 96.296 513 13 5 1 510 544198434 544197925 0.000000e+00 837
24 TraesCS7D01G047000 chr3D 97.652 511 12 0 1 511 44905635 44905125 0.000000e+00 878
25 TraesCS7D01G047000 chr3D 97.456 511 13 0 1 511 623688 623178 0.000000e+00 872
26 TraesCS7D01G047000 chr4D 97.451 510 13 0 1 510 497138289 497137780 0.000000e+00 870
27 TraesCS7D01G047000 chr2D 96.869 511 16 0 1 511 531995222 531994712 0.000000e+00 856
28 TraesCS7D01G047000 chr2D 90.351 228 22 0 777 1004 197540731 197540958 1.980000e-77 300
29 TraesCS7D01G047000 chr2D 90.435 230 18 3 775 1004 477630055 477629830 1.980000e-77 300
30 TraesCS7D01G047000 chr2D 89.030 237 24 2 779 1013 284559957 284560193 3.320000e-75 292
31 TraesCS7D01G047000 chr1B 91.781 219 18 0 779 997 455204878 455204660 4.260000e-79 305
32 TraesCS7D01G047000 chr3B 91.324 219 18 1 779 997 335696845 335697062 7.130000e-77 298
33 TraesCS7D01G047000 chr2A 91.589 214 18 0 779 992 11869051 11868838 2.560000e-76 296
34 TraesCS7D01G047000 chr1D 89.316 234 21 3 779 1012 2855855 2856084 1.190000e-74 291
35 TraesCS7D01G047000 chr6B 76.454 361 67 12 1391 1748 14126673 14127018 2.690000e-41 180


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 TraesCS7D01G047000 chr7D 24325379 24328777 3398 False 6277.000000 6277 100.000000 1 3399 1 chr7D.!!$F1 3398
1 TraesCS7D01G047000 chr7D 393026311 393026820 509 False 881.000000 881 97.843000 1 510 1 chr7D.!!$F3 509
2 TraesCS7D01G047000 chr7D 420762631 420763141 510 False 881.000000 881 97.847000 1 510 1 chr7D.!!$F4 509
3 TraesCS7D01G047000 chr7D 78599837 78600359 522 True 870.000000 870 96.750000 1 521 1 chr7D.!!$R2 520
4 TraesCS7D01G047000 chr7D 24020045 24021519 1474 True 696.000000 1212 82.471500 542 2262 2 chr7D.!!$R4 1720
5 TraesCS7D01G047000 chr4A 707303394 707305624 2230 True 1404.500000 2662 91.024500 567 3133 2 chr4A.!!$R4 2566
6 TraesCS7D01G047000 chr4A 707674762 707676000 1238 False 1118.000000 1118 82.987000 1014 2262 1 chr4A.!!$F1 1248
7 TraesCS7D01G047000 chr4A 707702221 707703459 1238 False 1107.000000 1107 82.827000 1014 2262 1 chr4A.!!$F2 1248
8 TraesCS7D01G047000 chr4A 706088593 706089818 1225 True 1046.000000 1046 82.163000 1031 2262 1 chr4A.!!$R2 1231
9 TraesCS7D01G047000 chr4A 705952617 705953842 1225 True 1035.000000 1035 81.987000 1031 2262 1 chr4A.!!$R1 1231
10 TraesCS7D01G047000 chr4A 707487291 707488773 1482 False 631.000000 1112 86.790000 556 2262 2 chr4A.!!$F3 1706
11 TraesCS7D01G047000 chr4A 707513038 707514704 1666 False 435.333333 686 89.256333 1557 3397 3 chr4A.!!$F4 1840
12 TraesCS7D01G047000 chr4A 707259831 707260630 799 True 383.000000 383 75.604000 1437 2262 1 chr4A.!!$R3 825
13 TraesCS7D01G047000 chrUn 220048255 220049480 1225 True 1035.000000 1035 81.987000 1031 2262 1 chrUn.!!$R1 1231
14 TraesCS7D01G047000 chr5D 57004358 57004868 510 True 900.000000 900 98.434000 1 511 1 chr5D.!!$R1 510
15 TraesCS7D01G047000 chr5D 544197925 544198434 509 True 837.000000 837 96.296000 1 510 1 chr5D.!!$R2 509
16 TraesCS7D01G047000 chr3D 44905125 44905635 510 True 878.000000 878 97.652000 1 511 1 chr3D.!!$R2 510
17 TraesCS7D01G047000 chr3D 623178 623688 510 True 872.000000 872 97.456000 1 511 1 chr3D.!!$R1 510
18 TraesCS7D01G047000 chr4D 497137780 497138289 509 True 870.000000 870 97.451000 1 510 1 chr4D.!!$R1 509
19 TraesCS7D01G047000 chr2D 531994712 531995222 510 True 856.000000 856 96.869000 1 511 1 chr2D.!!$R2 510

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
811 857 0.163788 CAGTTTACAAGTCCTGCGCG 59.836 55.0 0.0 0.0 0.0 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2566 3177 0.594602 GTCAATTCACAGCAGCAGCA 59.405 50.0 3.17 0.0 45.49 4.41 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 179 4.066139 GGCCCTTGACCCATGCCT 62.066 66.667 0.00 0.00 39.05 4.75
213 214 2.203538 CCCAAGCAAGGCTGGTGT 60.204 61.111 0.00 0.00 39.62 4.16
338 341 1.219124 GAGGCACTGAAGCGATGGA 59.781 57.895 0.00 0.00 41.55 3.41
396 399 1.079197 TCTACACCGACCGTCGCTA 60.079 57.895 15.64 3.65 38.82 4.26
513 518 4.141228 TCGATCCAGTAAGTCTATCACCCT 60.141 45.833 0.00 0.00 0.00 4.34
515 520 3.031736 TCCAGTAAGTCTATCACCCTGC 58.968 50.000 0.00 0.00 0.00 4.85
518 523 3.068873 CAGTAAGTCTATCACCCTGCTCC 59.931 52.174 0.00 0.00 0.00 4.70
519 524 1.501582 AAGTCTATCACCCTGCTCCC 58.498 55.000 0.00 0.00 0.00 4.30
520 525 0.639392 AGTCTATCACCCTGCTCCCT 59.361 55.000 0.00 0.00 0.00 4.20
521 526 1.008938 AGTCTATCACCCTGCTCCCTT 59.991 52.381 0.00 0.00 0.00 3.95
522 527 1.840635 GTCTATCACCCTGCTCCCTTT 59.159 52.381 0.00 0.00 0.00 3.11
523 528 2.239907 GTCTATCACCCTGCTCCCTTTT 59.760 50.000 0.00 0.00 0.00 2.27
524 529 2.919602 TCTATCACCCTGCTCCCTTTTT 59.080 45.455 0.00 0.00 0.00 1.94
570 575 3.801997 CGGGGAGCATGAGCCCTT 61.802 66.667 19.19 0.00 44.10 3.95
572 577 2.381941 GGGGAGCATGAGCCCTTCT 61.382 63.158 19.19 0.00 44.10 2.85
599 605 2.536130 CGTCTTTAAATACTTGCCGCCG 60.536 50.000 2.68 0.00 0.00 6.46
657 663 1.912371 CTCTCGCCCCGTTTGCTTTC 61.912 60.000 0.00 0.00 0.00 2.62
669 675 3.483558 CGTTTGCTTTCTTCTTCACAAGC 59.516 43.478 0.00 0.00 41.75 4.01
670 676 3.715628 TTGCTTTCTTCTTCACAAGCC 57.284 42.857 0.00 0.00 40.86 4.35
671 677 1.956477 TGCTTTCTTCTTCACAAGCCC 59.044 47.619 0.00 0.00 40.86 5.19
675 681 0.472471 TCTTCTTCACAAGCCCCGTT 59.528 50.000 0.00 0.00 0.00 4.44
684 690 3.443588 AGCCCCGTTGCTTTGTTC 58.556 55.556 0.00 0.00 38.85 3.18
685 691 1.152756 AGCCCCGTTGCTTTGTTCT 60.153 52.632 0.00 0.00 38.85 3.01
706 751 2.577700 TCTCTCGGGTTCAGCTATCTC 58.422 52.381 0.00 0.00 0.00 2.75
717 762 4.691326 TCAGCTATCTCTCGAGTAGGAA 57.309 45.455 13.13 0.00 0.00 3.36
723 768 4.781775 ATCTCTCGAGTAGGAAAGGAGA 57.218 45.455 13.13 5.01 33.77 3.71
735 781 4.764491 AGGAAAGGAGAAGAAGGTAAGGA 58.236 43.478 0.00 0.00 0.00 3.36
741 787 8.410673 AAAGGAGAAGAAGGTAAGGATTTTTC 57.589 34.615 0.00 0.00 0.00 2.29
742 788 6.486056 AGGAGAAGAAGGTAAGGATTTTTCC 58.514 40.000 0.00 0.00 0.00 3.13
743 789 5.652891 GGAGAAGAAGGTAAGGATTTTTCCC 59.347 44.000 0.00 0.00 0.00 3.97
755 801 5.519808 AGGATTTTTCCCAACCTAAGATCC 58.480 41.667 0.00 0.00 0.00 3.36
777 823 4.082571 CCATCGCTTTTCAAGGAAACTGAT 60.083 41.667 0.00 0.00 42.68 2.90
778 824 5.464168 CATCGCTTTTCAAGGAAACTGATT 58.536 37.500 0.00 0.00 42.68 2.57
779 825 6.349280 CCATCGCTTTTCAAGGAAACTGATTA 60.349 38.462 0.00 0.00 42.68 1.75
780 826 5.997385 TCGCTTTTCAAGGAAACTGATTAC 58.003 37.500 0.00 0.00 42.68 1.89
781 827 5.763204 TCGCTTTTCAAGGAAACTGATTACT 59.237 36.000 0.00 0.00 42.68 2.24
782 828 6.932400 TCGCTTTTCAAGGAAACTGATTACTA 59.068 34.615 0.00 0.00 42.68 1.82
783 829 7.015877 CGCTTTTCAAGGAAACTGATTACTAC 58.984 38.462 0.00 0.00 42.68 2.73
784 830 7.306213 GCTTTTCAAGGAAACTGATTACTACC 58.694 38.462 0.00 0.00 42.68 3.18
785 831 7.175119 GCTTTTCAAGGAAACTGATTACTACCT 59.825 37.037 0.00 0.00 42.68 3.08
786 832 8.990163 TTTTCAAGGAAACTGATTACTACCTT 57.010 30.769 0.00 0.00 42.68 3.50
787 833 8.617290 TTTCAAGGAAACTGATTACTACCTTC 57.383 34.615 0.00 0.00 42.68 3.46
788 834 6.395629 TCAAGGAAACTGATTACTACCTTCG 58.604 40.000 0.00 0.00 42.68 3.79
789 835 5.997384 AGGAAACTGATTACTACCTTCGT 57.003 39.130 0.00 0.00 41.13 3.85
790 836 6.356186 AGGAAACTGATTACTACCTTCGTT 57.644 37.500 0.00 0.00 41.13 3.85
791 837 6.766429 AGGAAACTGATTACTACCTTCGTTT 58.234 36.000 0.00 0.00 41.13 3.60
792 838 6.872547 AGGAAACTGATTACTACCTTCGTTTC 59.127 38.462 0.00 0.00 41.13 2.78
793 839 6.647895 GGAAACTGATTACTACCTTCGTTTCA 59.352 38.462 0.00 0.00 40.17 2.69
794 840 7.148623 GGAAACTGATTACTACCTTCGTTTCAG 60.149 40.741 0.00 0.00 40.17 3.02
795 841 6.342338 ACTGATTACTACCTTCGTTTCAGT 57.658 37.500 0.00 0.00 38.12 3.41
796 842 6.756221 ACTGATTACTACCTTCGTTTCAGTT 58.244 36.000 0.00 0.00 39.47 3.16
797 843 7.215085 ACTGATTACTACCTTCGTTTCAGTTT 58.785 34.615 0.00 0.00 39.47 2.66
798 844 8.362639 ACTGATTACTACCTTCGTTTCAGTTTA 58.637 33.333 0.00 0.00 39.47 2.01
799 845 8.524870 TGATTACTACCTTCGTTTCAGTTTAC 57.475 34.615 0.00 0.00 0.00 2.01
800 846 8.143193 TGATTACTACCTTCGTTTCAGTTTACA 58.857 33.333 0.00 0.00 0.00 2.41
801 847 8.891671 ATTACTACCTTCGTTTCAGTTTACAA 57.108 30.769 0.00 0.00 0.00 2.41
802 848 6.839820 ACTACCTTCGTTTCAGTTTACAAG 57.160 37.500 0.00 0.00 0.00 3.16
803 849 6.343703 ACTACCTTCGTTTCAGTTTACAAGT 58.656 36.000 0.00 0.00 0.00 3.16
804 850 5.729974 ACCTTCGTTTCAGTTTACAAGTC 57.270 39.130 0.00 0.00 0.00 3.01
805 851 4.573607 ACCTTCGTTTCAGTTTACAAGTCC 59.426 41.667 0.00 0.00 0.00 3.85
806 852 4.814771 CCTTCGTTTCAGTTTACAAGTCCT 59.185 41.667 0.00 0.00 0.00 3.85
807 853 5.277345 CCTTCGTTTCAGTTTACAAGTCCTG 60.277 44.000 0.00 0.00 0.00 3.86
808 854 3.558418 TCGTTTCAGTTTACAAGTCCTGC 59.442 43.478 0.00 0.00 0.00 4.85
809 855 3.603857 CGTTTCAGTTTACAAGTCCTGCG 60.604 47.826 0.00 0.00 0.00 5.18
810 856 1.508632 TCAGTTTACAAGTCCTGCGC 58.491 50.000 0.00 0.00 0.00 6.09
811 857 0.163788 CAGTTTACAAGTCCTGCGCG 59.836 55.000 0.00 0.00 0.00 6.86
812 858 0.249741 AGTTTACAAGTCCTGCGCGT 60.250 50.000 8.43 0.00 0.00 6.01
813 859 1.000060 AGTTTACAAGTCCTGCGCGTA 60.000 47.619 8.43 0.71 0.00 4.42
814 860 1.997606 GTTTACAAGTCCTGCGCGTAT 59.002 47.619 8.43 0.00 0.00 3.06
815 861 3.119388 AGTTTACAAGTCCTGCGCGTATA 60.119 43.478 8.43 0.00 0.00 1.47
816 862 3.720949 TTACAAGTCCTGCGCGTATAT 57.279 42.857 8.43 0.00 0.00 0.86
817 863 2.135664 ACAAGTCCTGCGCGTATATC 57.864 50.000 8.43 0.00 0.00 1.63
818 864 1.681793 ACAAGTCCTGCGCGTATATCT 59.318 47.619 8.43 0.00 0.00 1.98
819 865 2.882761 ACAAGTCCTGCGCGTATATCTA 59.117 45.455 8.43 0.00 0.00 1.98
820 866 3.058155 ACAAGTCCTGCGCGTATATCTAG 60.058 47.826 8.43 0.00 0.00 2.43
821 867 2.085320 AGTCCTGCGCGTATATCTAGG 58.915 52.381 8.43 0.52 0.00 3.02
822 868 1.811359 GTCCTGCGCGTATATCTAGGT 59.189 52.381 8.43 0.00 0.00 3.08
823 869 2.228343 GTCCTGCGCGTATATCTAGGTT 59.772 50.000 8.43 0.00 0.00 3.50
824 870 2.228103 TCCTGCGCGTATATCTAGGTTG 59.772 50.000 8.43 0.00 0.00 3.77
825 871 1.986378 CTGCGCGTATATCTAGGTTGC 59.014 52.381 8.43 0.00 0.00 4.17
826 872 1.336517 TGCGCGTATATCTAGGTTGCC 60.337 52.381 8.43 0.00 0.00 4.52
827 873 1.336517 GCGCGTATATCTAGGTTGCCA 60.337 52.381 8.43 0.00 0.00 4.92
828 874 2.864882 GCGCGTATATCTAGGTTGCCAA 60.865 50.000 8.43 0.00 0.00 4.52
829 875 3.585862 CGCGTATATCTAGGTTGCCAAT 58.414 45.455 0.00 0.00 0.00 3.16
830 876 3.994392 CGCGTATATCTAGGTTGCCAATT 59.006 43.478 0.00 0.00 0.00 2.32
831 877 4.451096 CGCGTATATCTAGGTTGCCAATTT 59.549 41.667 0.00 0.00 0.00 1.82
832 878 5.049680 CGCGTATATCTAGGTTGCCAATTTT 60.050 40.000 0.00 0.00 0.00 1.82
833 879 6.146510 CGCGTATATCTAGGTTGCCAATTTTA 59.853 38.462 0.00 0.00 0.00 1.52
834 880 7.148474 CGCGTATATCTAGGTTGCCAATTTTAT 60.148 37.037 0.00 0.00 0.00 1.40
835 881 8.175716 GCGTATATCTAGGTTGCCAATTTTATC 58.824 37.037 0.00 0.00 0.00 1.75
836 882 9.214957 CGTATATCTAGGTTGCCAATTTTATCA 57.785 33.333 0.00 0.00 0.00 2.15
838 884 6.715347 ATCTAGGTTGCCAATTTTATCACC 57.285 37.500 0.00 0.00 0.00 4.02
839 885 3.866883 AGGTTGCCAATTTTATCACCG 57.133 42.857 0.00 0.00 0.00 4.94
840 886 3.161866 AGGTTGCCAATTTTATCACCGT 58.838 40.909 0.00 0.00 0.00 4.83
841 887 4.337145 AGGTTGCCAATTTTATCACCGTA 58.663 39.130 0.00 0.00 0.00 4.02
842 888 4.767928 AGGTTGCCAATTTTATCACCGTAA 59.232 37.500 0.00 0.00 0.00 3.18
843 889 5.420739 AGGTTGCCAATTTTATCACCGTAAT 59.579 36.000 0.00 0.00 0.00 1.89
844 890 6.603997 AGGTTGCCAATTTTATCACCGTAATA 59.396 34.615 0.00 0.00 0.00 0.98
845 891 7.286775 AGGTTGCCAATTTTATCACCGTAATAT 59.713 33.333 0.00 0.00 0.00 1.28
846 892 8.569641 GGTTGCCAATTTTATCACCGTAATATA 58.430 33.333 0.00 0.00 0.00 0.86
847 893 9.953697 GTTGCCAATTTTATCACCGTAATATAA 57.046 29.630 0.00 0.00 0.00 0.98
849 895 9.953697 TGCCAATTTTATCACCGTAATATAAAC 57.046 29.630 0.00 0.00 0.00 2.01
895 941 9.136323 ACCTTTTGAAAATAGAACATCTGAAGT 57.864 29.630 0.00 0.00 0.00 3.01
896 942 9.971922 CCTTTTGAAAATAGAACATCTGAAGTT 57.028 29.630 0.00 0.00 0.00 2.66
948 994 8.335532 TGACTTCTATTAGGTTGGACAAATTG 57.664 34.615 0.00 0.00 0.00 2.32
949 995 8.160765 TGACTTCTATTAGGTTGGACAAATTGA 58.839 33.333 0.00 0.00 0.00 2.57
950 996 8.336801 ACTTCTATTAGGTTGGACAAATTGAC 57.663 34.615 0.00 0.00 0.00 3.18
951 997 7.942341 ACTTCTATTAGGTTGGACAAATTGACA 59.058 33.333 0.00 0.00 0.00 3.58
952 998 8.698973 TTCTATTAGGTTGGACAAATTGACAA 57.301 30.769 0.00 1.91 0.00 3.18
953 999 8.106247 TCTATTAGGTTGGACAAATTGACAAC 57.894 34.615 20.85 20.85 37.72 3.32
957 1003 5.523438 GGTTGGACAAATTGACAACCTAA 57.477 39.130 30.31 12.54 45.70 2.69
958 1004 5.908341 GGTTGGACAAATTGACAACCTAAA 58.092 37.500 30.31 9.32 45.70 1.85
959 1005 5.983118 GGTTGGACAAATTGACAACCTAAAG 59.017 40.000 30.31 0.00 45.70 1.85
960 1006 5.782893 TGGACAAATTGACAACCTAAAGG 57.217 39.130 0.00 0.00 42.17 3.11
972 1018 1.435577 CCTAAAGGTACACACACGCC 58.564 55.000 0.00 0.00 0.00 5.68
973 1019 1.001633 CCTAAAGGTACACACACGCCT 59.998 52.381 0.00 0.00 0.00 5.52
974 1020 2.549349 CCTAAAGGTACACACACGCCTT 60.549 50.000 0.00 0.00 42.54 4.35
975 1021 1.305201 AAAGGTACACACACGCCTTG 58.695 50.000 0.00 0.00 40.78 3.61
976 1022 0.179468 AAGGTACACACACGCCTTGT 59.821 50.000 0.00 0.00 39.60 3.16
977 1023 1.042229 AGGTACACACACGCCTTGTA 58.958 50.000 0.00 0.00 35.67 2.41
978 1024 1.413445 AGGTACACACACGCCTTGTAA 59.587 47.619 0.00 0.00 35.67 2.41
979 1025 2.158928 AGGTACACACACGCCTTGTAAA 60.159 45.455 0.00 0.00 35.67 2.01
980 1026 2.032636 GGTACACACACGCCTTGTAAAC 60.033 50.000 0.00 0.00 35.67 2.01
981 1027 2.032680 ACACACACGCCTTGTAAACT 57.967 45.000 0.00 0.00 35.67 2.66
982 1028 1.668751 ACACACACGCCTTGTAAACTG 59.331 47.619 0.00 0.00 35.67 3.16
983 1029 1.937223 CACACACGCCTTGTAAACTGA 59.063 47.619 0.00 0.00 35.67 3.41
984 1030 2.032894 CACACACGCCTTGTAAACTGAG 60.033 50.000 0.00 0.00 35.67 3.35
985 1031 2.159014 ACACACGCCTTGTAAACTGAGA 60.159 45.455 0.00 0.00 35.67 3.27
986 1032 2.476619 CACACGCCTTGTAAACTGAGAG 59.523 50.000 0.00 0.00 35.67 3.20
987 1033 2.364324 ACACGCCTTGTAAACTGAGAGA 59.636 45.455 0.00 0.00 36.32 3.10
988 1034 3.181469 ACACGCCTTGTAAACTGAGAGAA 60.181 43.478 0.00 0.00 36.32 2.87
989 1035 3.807622 CACGCCTTGTAAACTGAGAGAAA 59.192 43.478 0.00 0.00 0.00 2.52
990 1036 4.058817 ACGCCTTGTAAACTGAGAGAAAG 58.941 43.478 0.00 0.00 0.00 2.62
991 1037 3.433615 CGCCTTGTAAACTGAGAGAAAGG 59.566 47.826 0.00 0.00 36.58 3.11
992 1038 3.753797 GCCTTGTAAACTGAGAGAAAGGG 59.246 47.826 0.00 0.00 34.55 3.95
993 1039 4.327680 CCTTGTAAACTGAGAGAAAGGGG 58.672 47.826 0.00 0.00 31.12 4.79
994 1040 4.327680 CTTGTAAACTGAGAGAAAGGGGG 58.672 47.826 0.00 0.00 0.00 5.40
995 1041 3.323775 TGTAAACTGAGAGAAAGGGGGT 58.676 45.455 0.00 0.00 0.00 4.95
996 1042 4.495565 TGTAAACTGAGAGAAAGGGGGTA 58.504 43.478 0.00 0.00 0.00 3.69
997 1043 4.285260 TGTAAACTGAGAGAAAGGGGGTAC 59.715 45.833 0.00 0.00 0.00 3.34
998 1044 3.277416 AACTGAGAGAAAGGGGGTACT 57.723 47.619 0.00 0.00 0.00 2.73
999 1045 4.415224 AACTGAGAGAAAGGGGGTACTA 57.585 45.455 0.00 0.00 0.00 1.82
1000 1046 3.983821 ACTGAGAGAAAGGGGGTACTAG 58.016 50.000 0.00 0.00 0.00 2.57
1001 1047 3.337301 ACTGAGAGAAAGGGGGTACTAGT 59.663 47.826 0.00 0.00 0.00 2.57
1002 1048 4.543337 ACTGAGAGAAAGGGGGTACTAGTA 59.457 45.833 0.00 0.00 0.00 1.82
1003 1049 5.196165 ACTGAGAGAAAGGGGGTACTAGTAT 59.804 44.000 5.75 0.00 0.00 2.12
1004 1050 6.392245 ACTGAGAGAAAGGGGGTACTAGTATA 59.608 42.308 5.75 0.00 0.00 1.47
1005 1051 7.075267 ACTGAGAGAAAGGGGGTACTAGTATAT 59.925 40.741 5.75 0.00 0.00 0.86
1006 1052 8.529952 TGAGAGAAAGGGGGTACTAGTATATA 57.470 38.462 5.75 0.00 0.00 0.86
1007 1053 9.136828 TGAGAGAAAGGGGGTACTAGTATATAT 57.863 37.037 5.75 0.00 0.00 0.86
1010 1056 9.353431 GAGAAAGGGGGTACTAGTATATATAGC 57.647 40.741 5.75 0.00 0.00 2.97
1011 1057 9.082644 AGAAAGGGGGTACTAGTATATATAGCT 57.917 37.037 5.75 0.00 0.00 3.32
1014 1060 7.987820 AGGGGGTACTAGTATATATAGCTAGC 58.012 42.308 6.62 6.62 36.57 3.42
1015 1061 7.800569 AGGGGGTACTAGTATATATAGCTAGCT 59.199 40.741 23.12 23.12 36.57 3.32
1016 1062 8.102676 GGGGGTACTAGTATATATAGCTAGCTC 58.897 44.444 23.26 4.70 36.57 4.09
1093 1143 1.930133 ATCATCCCAGCCACCACCA 60.930 57.895 0.00 0.00 0.00 4.17
1266 1316 3.173390 CTTCGCCAAGCTATGCCGC 62.173 63.158 2.11 0.00 0.00 6.53
1527 1577 3.041940 GGTCTCCGCCACAACGTG 61.042 66.667 0.00 0.00 0.00 4.49
1869 2440 1.144969 GCATCGACTGGAACGTTTCA 58.855 50.000 9.39 9.39 0.00 2.69
1928 2499 2.629656 GCTTGCTGGATGCGTTGGT 61.630 57.895 0.00 0.00 46.63 3.67
2262 2839 1.223763 GGCTGCCACCTAGGGTAAC 59.776 63.158 15.17 0.00 38.09 2.50
2278 2855 3.568443 GGTAACCCCAAGAAAAGAACCA 58.432 45.455 0.00 0.00 0.00 3.67
2356 2933 6.281848 CATGCAATGCAACCTTTGATATTC 57.718 37.500 13.45 0.00 43.62 1.75
2387 2990 9.645128 ATCCAATATGTCACTTTGATATTTCCA 57.355 29.630 0.00 0.00 30.70 3.53
2396 2999 7.335422 GTCACTTTGATATTTCCATCTGTCACT 59.665 37.037 0.00 0.00 0.00 3.41
2399 3002 9.739276 ACTTTGATATTTCCATCTGTCACTTAA 57.261 29.630 0.00 0.00 0.00 1.85
2415 3018 6.649141 TGTCACTTAATTAAGCGATGTGAACT 59.351 34.615 22.45 0.00 36.79 3.01
2431 3034 3.990469 GTGAACTATGTGTGGTGTGAGAG 59.010 47.826 0.00 0.00 0.00 3.20
2436 3039 0.464036 TGTGTGGTGTGAGAGTGGTC 59.536 55.000 0.00 0.00 0.00 4.02
2449 3052 3.467803 AGAGTGGTCTTGTAAGTTGTGC 58.532 45.455 0.00 0.00 0.00 4.57
2462 3065 6.110033 TGTAAGTTGTGCAAGAGTGAGTTTA 58.890 36.000 0.00 0.00 0.00 2.01
2463 3066 6.596106 TGTAAGTTGTGCAAGAGTGAGTTTAA 59.404 34.615 0.00 0.00 0.00 1.52
2490 3093 4.992381 AAGTTGTGTAAGAGCGATCAAC 57.008 40.909 2.38 0.84 36.46 3.18
2495 3098 6.311445 AGTTGTGTAAGAGCGATCAACATTAG 59.689 38.462 11.30 0.00 37.97 1.73
2500 3103 3.397482 AGAGCGATCAACATTAGATGGC 58.603 45.455 2.38 0.00 44.42 4.40
2506 3109 5.124457 GCGATCAACATTAGATGGCCATAAT 59.876 40.000 20.84 13.29 40.12 1.28
2507 3110 6.316140 GCGATCAACATTAGATGGCCATAATA 59.684 38.462 20.84 12.22 40.12 0.98
2508 3111 7.012704 GCGATCAACATTAGATGGCCATAATAT 59.987 37.037 20.84 9.15 40.12 1.28
2509 3112 9.546428 CGATCAACATTAGATGGCCATAATATA 57.454 33.333 20.84 6.78 33.60 0.86
2603 3214 7.337689 TGAATTGACATGTTTCCTCTGGAATAG 59.662 37.037 0.00 0.00 41.71 1.73
2618 3229 6.544650 TCTGGAATAGAGGCCTAACTAGTAG 58.455 44.000 4.42 0.00 0.00 2.57
2666 3277 8.833231 ATTACCATAGTAACTGATTTCATCCG 57.167 34.615 0.00 0.00 41.19 4.18
2668 3279 6.516718 ACCATAGTAACTGATTTCATCCGAG 58.483 40.000 0.00 0.00 0.00 4.63
2671 3282 5.677319 AGTAACTGATTTCATCCGAGGAA 57.323 39.130 0.00 0.00 0.00 3.36
2686 3297 2.917971 CGAGGAAGAAGTACAAGCGAAG 59.082 50.000 0.00 0.00 0.00 3.79
2690 3301 3.619038 GGAAGAAGTACAAGCGAAGATGG 59.381 47.826 0.00 0.00 0.00 3.51
2694 3305 5.112686 AGAAGTACAAGCGAAGATGGAATC 58.887 41.667 0.00 0.00 46.04 2.52
2716 3328 4.039124 TCGCACAAGCATATTCTCCTCATA 59.961 41.667 0.00 0.00 42.27 2.15
2781 3398 2.162754 CCGCGACATTGTACCGACC 61.163 63.158 8.23 0.00 0.00 4.79
2783 3400 1.153978 GCGACATTGTACCGACCGA 60.154 57.895 2.41 0.00 0.00 4.69
2795 3412 1.736645 CGACCGATTTGCCGAGTGT 60.737 57.895 0.00 0.00 0.00 3.55
2803 3420 4.360563 CGATTTGCCGAGTGTATAGAGTT 58.639 43.478 0.00 0.00 0.00 3.01
2874 3493 6.815089 ACAAACAATTCTTTATTGAGTGCCA 58.185 32.000 4.64 0.00 45.35 4.92
2875 3494 6.701400 ACAAACAATTCTTTATTGAGTGCCAC 59.299 34.615 4.64 0.00 45.35 5.01
2882 3501 5.348986 TCTTTATTGAGTGCCACGAGTATC 58.651 41.667 0.00 0.00 0.00 2.24
3033 3658 7.557719 TCATTGTCTTTTCATCCTCCCTATTTC 59.442 37.037 0.00 0.00 0.00 2.17
3034 3659 6.642733 TGTCTTTTCATCCTCCCTATTTCT 57.357 37.500 0.00 0.00 0.00 2.52
3038 3663 9.462606 GTCTTTTCATCCTCCCTATTTCTTTTA 57.537 33.333 0.00 0.00 0.00 1.52
3043 3668 9.520515 TTCATCCTCCCTATTTCTTTTATATGC 57.479 33.333 0.00 0.00 0.00 3.14
3044 3669 8.668653 TCATCCTCCCTATTTCTTTTATATGCA 58.331 33.333 0.00 0.00 0.00 3.96
3124 3752 9.907229 AAATGGAAAATTGTTAAAGTTGGGTTA 57.093 25.926 0.00 0.00 0.00 2.85
3141 3769 9.856162 AGTTGGGTTAAAAAGTCTATGTTTAGA 57.144 29.630 0.00 0.00 31.89 2.10
3204 3847 1.611977 AGACTCACGTCGAACATGGAA 59.388 47.619 0.00 0.00 44.93 3.53
3210 3853 7.174426 AGACTCACGTCGAACATGGAATATATA 59.826 37.037 0.00 0.00 44.93 0.86
3244 3887 6.206438 AGTTTTGAAAATGGCAAACAAAGTGT 59.794 30.769 0.00 0.00 35.20 3.55
3268 3911 2.460757 AACATGAAAGTTGGCATGCC 57.539 45.000 30.54 30.54 44.30 4.40
3270 3913 1.903860 ACATGAAAGTTGGCATGCCAT 59.096 42.857 38.78 25.02 46.64 4.40
3284 3927 4.262721 GGCATGCCATTGGTCATGATAAAT 60.263 41.667 32.08 0.00 38.51 1.40
3290 3934 8.247666 TGCCATTGGTCATGATAAATATTGAA 57.752 30.769 0.00 0.00 34.31 2.69
3315 3959 6.287107 AGATTTTGTAGAAGTTGTGACACG 57.713 37.500 0.22 0.00 0.00 4.49
3324 3969 1.867233 AGTTGTGACACGCAAGCTTAG 59.133 47.619 0.00 0.00 45.62 2.18
3352 3997 1.683917 ACCATCTCCGAGGAAGAATCG 59.316 52.381 0.00 0.00 39.86 3.34
3359 4004 3.323243 TCCGAGGAAGAATCGTTGTTTC 58.677 45.455 0.00 0.00 38.50 2.78
3361 4006 2.984471 CGAGGAAGAATCGTTGTTTCGA 59.016 45.455 0.00 0.00 43.86 3.71
3366 4011 5.120830 AGGAAGAATCGTTGTTTCGAGATTG 59.879 40.000 0.56 0.00 43.00 2.67
3369 4014 5.916969 AGAATCGTTGTTTCGAGATTGAAC 58.083 37.500 0.56 0.00 43.00 3.18
3370 4015 5.465390 AGAATCGTTGTTTCGAGATTGAACA 59.535 36.000 0.56 0.00 43.00 3.18
3372 4017 3.059868 TCGTTGTTTCGAGATTGAACAGC 60.060 43.478 4.30 4.30 34.85 4.40
3383 4028 4.464008 AGATTGAACAGCTCAGGTTTGAA 58.536 39.130 0.00 0.00 34.81 2.69
3388 4033 0.603707 CAGCTCAGGTTTGAAGGCGA 60.604 55.000 0.00 0.00 31.69 5.54
3397 4042 2.076863 GTTTGAAGGCGATGCTACTGT 58.923 47.619 0.00 0.00 0.00 3.55
3398 4043 2.472695 TTGAAGGCGATGCTACTGTT 57.527 45.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 147 2.676471 GCCCAATGAGCCGTTGGT 60.676 61.111 18.94 0.00 45.97 3.67
178 179 3.781307 CTGGACGCCCCCGATCAA 61.781 66.667 0.00 0.00 38.29 2.57
338 341 4.269523 TGGCAGCGGTGGAGCTTT 62.270 61.111 17.54 0.00 46.80 3.51
554 559 2.194326 GAAGGGCTCATGCTCCCC 59.806 66.667 15.79 11.50 43.67 4.81
559 564 2.899339 GCGGAGAAGGGCTCATGC 60.899 66.667 0.00 0.00 45.81 4.06
570 575 4.445452 AGTATTTAAAGACGTGCGGAGA 57.555 40.909 7.29 0.00 0.00 3.71
572 577 3.123959 GCAAGTATTTAAAGACGTGCGGA 59.876 43.478 28.81 0.00 43.30 5.54
599 605 2.190578 CGTTGGGAGATGGGAGGC 59.809 66.667 0.00 0.00 0.00 4.70
657 663 0.593128 CAACGGGGCTTGTGAAGAAG 59.407 55.000 0.00 0.00 0.00 2.85
669 675 1.266989 GAGAAGAACAAAGCAACGGGG 59.733 52.381 0.00 0.00 0.00 5.73
670 676 2.222027 AGAGAAGAACAAAGCAACGGG 58.778 47.619 0.00 0.00 0.00 5.28
671 677 2.096713 CGAGAGAAGAACAAAGCAACGG 60.097 50.000 0.00 0.00 0.00 4.44
675 681 1.416401 ACCCGAGAGAAGAACAAAGCA 59.584 47.619 0.00 0.00 0.00 3.91
679 685 2.548067 GCTGAACCCGAGAGAAGAACAA 60.548 50.000 0.00 0.00 0.00 2.83
680 686 1.000955 GCTGAACCCGAGAGAAGAACA 59.999 52.381 0.00 0.00 0.00 3.18
681 687 1.273886 AGCTGAACCCGAGAGAAGAAC 59.726 52.381 0.00 0.00 0.00 3.01
683 689 2.509166 TAGCTGAACCCGAGAGAAGA 57.491 50.000 0.00 0.00 0.00 2.87
684 690 2.955660 AGATAGCTGAACCCGAGAGAAG 59.044 50.000 0.00 0.00 0.00 2.85
685 691 2.952978 GAGATAGCTGAACCCGAGAGAA 59.047 50.000 0.00 0.00 0.00 2.87
706 751 4.097286 CCTTCTTCTCCTTTCCTACTCGAG 59.903 50.000 11.84 11.84 0.00 4.04
717 762 6.948886 GGAAAAATCCTTACCTTCTTCTCCTT 59.051 38.462 0.00 0.00 0.00 3.36
723 768 5.542635 GGTTGGGAAAAATCCTTACCTTCTT 59.457 40.000 9.96 0.00 33.50 2.52
735 781 5.594317 CGATGGATCTTAGGTTGGGAAAAAT 59.406 40.000 0.00 0.00 0.00 1.82
741 787 1.417890 AGCGATGGATCTTAGGTTGGG 59.582 52.381 0.00 0.00 0.00 4.12
742 788 2.918712 AGCGATGGATCTTAGGTTGG 57.081 50.000 0.00 0.00 0.00 3.77
743 789 4.635765 TGAAAAGCGATGGATCTTAGGTTG 59.364 41.667 0.00 0.00 0.00 3.77
755 801 4.488126 TCAGTTTCCTTGAAAAGCGATG 57.512 40.909 0.00 0.00 44.44 3.84
777 823 7.981225 ACTTGTAAACTGAAACGAAGGTAGTAA 59.019 33.333 0.00 0.00 0.00 2.24
778 824 7.491682 ACTTGTAAACTGAAACGAAGGTAGTA 58.508 34.615 0.00 0.00 0.00 1.82
779 825 6.343703 ACTTGTAAACTGAAACGAAGGTAGT 58.656 36.000 0.00 0.00 0.00 2.73
780 826 6.073927 GGACTTGTAAACTGAAACGAAGGTAG 60.074 42.308 0.00 0.00 0.00 3.18
781 827 5.754890 GGACTTGTAAACTGAAACGAAGGTA 59.245 40.000 0.00 0.00 0.00 3.08
782 828 4.573607 GGACTTGTAAACTGAAACGAAGGT 59.426 41.667 0.00 0.00 0.00 3.50
783 829 4.814771 AGGACTTGTAAACTGAAACGAAGG 59.185 41.667 0.00 0.00 0.00 3.46
784 830 5.738370 CAGGACTTGTAAACTGAAACGAAG 58.262 41.667 0.00 0.00 32.86 3.79
785 831 4.034742 GCAGGACTTGTAAACTGAAACGAA 59.965 41.667 0.00 0.00 32.86 3.85
786 832 3.558418 GCAGGACTTGTAAACTGAAACGA 59.442 43.478 0.00 0.00 32.86 3.85
787 833 3.603857 CGCAGGACTTGTAAACTGAAACG 60.604 47.826 0.00 0.00 32.86 3.60
788 834 3.848554 GCGCAGGACTTGTAAACTGAAAC 60.849 47.826 0.30 0.00 32.86 2.78
789 835 2.289547 GCGCAGGACTTGTAAACTGAAA 59.710 45.455 0.30 0.00 32.86 2.69
790 836 1.871039 GCGCAGGACTTGTAAACTGAA 59.129 47.619 0.30 0.00 32.86 3.02
791 837 1.508632 GCGCAGGACTTGTAAACTGA 58.491 50.000 0.30 0.00 32.86 3.41
792 838 0.163788 CGCGCAGGACTTGTAAACTG 59.836 55.000 8.75 0.00 0.00 3.16
793 839 0.249741 ACGCGCAGGACTTGTAAACT 60.250 50.000 5.73 0.00 0.00 2.66
794 840 1.421382 TACGCGCAGGACTTGTAAAC 58.579 50.000 5.73 0.00 0.00 2.01
795 841 2.373540 ATACGCGCAGGACTTGTAAA 57.626 45.000 5.73 0.00 0.00 2.01
796 842 3.317149 AGATATACGCGCAGGACTTGTAA 59.683 43.478 5.73 0.00 0.00 2.41
797 843 2.882761 AGATATACGCGCAGGACTTGTA 59.117 45.455 5.73 0.00 0.00 2.41
798 844 1.681793 AGATATACGCGCAGGACTTGT 59.318 47.619 5.73 0.00 0.00 3.16
799 845 2.423926 AGATATACGCGCAGGACTTG 57.576 50.000 5.73 0.00 0.00 3.16
800 846 2.488545 CCTAGATATACGCGCAGGACTT 59.511 50.000 5.73 0.00 0.00 3.01
801 847 2.085320 CCTAGATATACGCGCAGGACT 58.915 52.381 5.73 3.27 0.00 3.85
802 848 1.811359 ACCTAGATATACGCGCAGGAC 59.189 52.381 5.73 0.00 0.00 3.85
803 849 2.195741 ACCTAGATATACGCGCAGGA 57.804 50.000 5.73 0.00 0.00 3.86
804 850 2.596452 CAACCTAGATATACGCGCAGG 58.404 52.381 5.73 6.39 0.00 4.85
805 851 1.986378 GCAACCTAGATATACGCGCAG 59.014 52.381 5.73 2.42 0.00 5.18
806 852 1.336517 GGCAACCTAGATATACGCGCA 60.337 52.381 5.73 0.00 0.00 6.09
807 853 1.336517 TGGCAACCTAGATATACGCGC 60.337 52.381 5.73 0.00 0.00 6.86
808 854 2.717580 TGGCAACCTAGATATACGCG 57.282 50.000 3.53 3.53 0.00 6.01
809 855 5.941948 AAATTGGCAACCTAGATATACGC 57.058 39.130 0.00 0.00 0.00 4.42
810 856 9.214957 TGATAAAATTGGCAACCTAGATATACG 57.785 33.333 0.00 0.00 0.00 3.06
812 858 9.515226 GGTGATAAAATTGGCAACCTAGATATA 57.485 33.333 0.00 0.00 0.00 0.86
813 859 7.174946 CGGTGATAAAATTGGCAACCTAGATAT 59.825 37.037 0.00 0.00 0.00 1.63
814 860 6.485313 CGGTGATAAAATTGGCAACCTAGATA 59.515 38.462 0.00 0.00 0.00 1.98
815 861 5.299279 CGGTGATAAAATTGGCAACCTAGAT 59.701 40.000 0.00 0.00 0.00 1.98
816 862 4.638421 CGGTGATAAAATTGGCAACCTAGA 59.362 41.667 0.00 0.00 0.00 2.43
817 863 4.398044 ACGGTGATAAAATTGGCAACCTAG 59.602 41.667 0.00 0.00 0.00 3.02
818 864 4.337145 ACGGTGATAAAATTGGCAACCTA 58.663 39.130 0.00 0.00 0.00 3.08
819 865 3.161866 ACGGTGATAAAATTGGCAACCT 58.838 40.909 0.00 0.00 0.00 3.50
820 866 3.586100 ACGGTGATAAAATTGGCAACC 57.414 42.857 0.00 0.00 0.00 3.77
821 867 9.953697 TTATATTACGGTGATAAAATTGGCAAC 57.046 29.630 0.00 0.00 0.00 4.17
823 869 9.953697 GTTTATATTACGGTGATAAAATTGGCA 57.046 29.630 0.00 0.00 29.33 4.92
869 915 9.136323 ACTTCAGATGTTCTATTTTCAAAAGGT 57.864 29.630 0.00 0.00 0.00 3.50
870 916 9.971922 AACTTCAGATGTTCTATTTTCAAAAGG 57.028 29.630 0.00 0.00 0.00 3.11
922 968 8.960591 CAATTTGTCCAACCTAATAGAAGTCAT 58.039 33.333 0.00 0.00 0.00 3.06
923 969 8.160765 TCAATTTGTCCAACCTAATAGAAGTCA 58.839 33.333 0.00 0.00 0.00 3.41
924 970 8.451748 GTCAATTTGTCCAACCTAATAGAAGTC 58.548 37.037 0.00 0.00 0.00 3.01
925 971 7.942341 TGTCAATTTGTCCAACCTAATAGAAGT 59.058 33.333 0.00 0.00 0.00 3.01
926 972 8.335532 TGTCAATTTGTCCAACCTAATAGAAG 57.664 34.615 0.00 0.00 0.00 2.85
927 973 8.573035 GTTGTCAATTTGTCCAACCTAATAGAA 58.427 33.333 16.74 0.00 32.91 2.10
928 974 8.106247 GTTGTCAATTTGTCCAACCTAATAGA 57.894 34.615 16.74 0.00 32.91 1.98
936 982 5.983118 CCTTTAGGTTGTCAATTTGTCCAAC 59.017 40.000 18.17 18.17 37.14 3.77
937 983 6.155475 CCTTTAGGTTGTCAATTTGTCCAA 57.845 37.500 0.00 0.00 0.00 3.53
938 984 5.782893 CCTTTAGGTTGTCAATTTGTCCA 57.217 39.130 0.00 0.00 0.00 4.02
953 999 1.001633 AGGCGTGTGTGTACCTTTAGG 59.998 52.381 0.00 0.00 42.17 2.69
954 1000 2.450609 AGGCGTGTGTGTACCTTTAG 57.549 50.000 0.00 0.00 0.00 1.85
955 1001 2.158928 ACAAGGCGTGTGTGTACCTTTA 60.159 45.455 4.97 0.00 40.54 1.85
956 1002 1.305201 CAAGGCGTGTGTGTACCTTT 58.695 50.000 0.00 0.00 40.54 3.11
957 1003 0.179468 ACAAGGCGTGTGTGTACCTT 59.821 50.000 4.97 0.00 43.28 3.50
958 1004 1.042229 TACAAGGCGTGTGTGTACCT 58.958 50.000 16.47 0.00 41.89 3.08
959 1005 1.868469 TTACAAGGCGTGTGTGTACC 58.132 50.000 16.47 0.00 41.89 3.34
960 1006 2.867975 AGTTTACAAGGCGTGTGTGTAC 59.132 45.455 16.47 8.34 41.89 2.90
961 1007 2.867368 CAGTTTACAAGGCGTGTGTGTA 59.133 45.455 16.47 0.58 41.89 2.90
962 1008 1.668751 CAGTTTACAAGGCGTGTGTGT 59.331 47.619 16.47 1.52 41.89 3.72
963 1009 1.937223 TCAGTTTACAAGGCGTGTGTG 59.063 47.619 16.47 8.22 41.89 3.82
964 1010 2.159014 TCTCAGTTTACAAGGCGTGTGT 60.159 45.455 16.47 6.54 41.89 3.72
965 1011 2.476619 CTCTCAGTTTACAAGGCGTGTG 59.523 50.000 16.47 0.11 41.89 3.82
966 1012 2.364324 TCTCTCAGTTTACAAGGCGTGT 59.636 45.455 11.52 11.52 44.82 4.49
967 1013 3.026630 TCTCTCAGTTTACAAGGCGTG 57.973 47.619 0.00 0.00 0.00 5.34
968 1014 3.746045 TTCTCTCAGTTTACAAGGCGT 57.254 42.857 0.00 0.00 0.00 5.68
969 1015 3.433615 CCTTTCTCTCAGTTTACAAGGCG 59.566 47.826 0.00 0.00 0.00 5.52
970 1016 3.753797 CCCTTTCTCTCAGTTTACAAGGC 59.246 47.826 0.00 0.00 0.00 4.35
971 1017 4.327680 CCCCTTTCTCTCAGTTTACAAGG 58.672 47.826 0.00 0.00 0.00 3.61
972 1018 4.202472 ACCCCCTTTCTCTCAGTTTACAAG 60.202 45.833 0.00 0.00 0.00 3.16
973 1019 3.720002 ACCCCCTTTCTCTCAGTTTACAA 59.280 43.478 0.00 0.00 0.00 2.41
974 1020 3.323775 ACCCCCTTTCTCTCAGTTTACA 58.676 45.455 0.00 0.00 0.00 2.41
975 1021 4.531339 AGTACCCCCTTTCTCTCAGTTTAC 59.469 45.833 0.00 0.00 0.00 2.01
976 1022 4.759953 AGTACCCCCTTTCTCTCAGTTTA 58.240 43.478 0.00 0.00 0.00 2.01
977 1023 3.599348 AGTACCCCCTTTCTCTCAGTTT 58.401 45.455 0.00 0.00 0.00 2.66
978 1024 3.277416 AGTACCCCCTTTCTCTCAGTT 57.723 47.619 0.00 0.00 0.00 3.16
979 1025 3.337301 ACTAGTACCCCCTTTCTCTCAGT 59.663 47.826 0.00 0.00 0.00 3.41
980 1026 3.983821 ACTAGTACCCCCTTTCTCTCAG 58.016 50.000 0.00 0.00 0.00 3.35
981 1027 5.745988 ATACTAGTACCCCCTTTCTCTCA 57.254 43.478 4.31 0.00 0.00 3.27
984 1030 9.353431 GCTATATATACTAGTACCCCCTTTCTC 57.647 40.741 4.31 0.00 0.00 2.87
985 1031 9.082644 AGCTATATATACTAGTACCCCCTTTCT 57.917 37.037 4.31 0.00 0.00 2.52
988 1034 8.447200 GCTAGCTATATATACTAGTACCCCCTT 58.553 40.741 7.70 0.00 36.57 3.95
989 1035 7.800569 AGCTAGCTATATATACTAGTACCCCCT 59.199 40.741 17.69 11.11 36.57 4.79
990 1036 7.987820 AGCTAGCTATATATACTAGTACCCCC 58.012 42.308 17.69 9.88 36.57 5.40
991 1037 8.883302 AGAGCTAGCTATATATACTAGTACCCC 58.117 40.741 19.38 0.00 36.57 4.95
1002 1048 9.362151 GGAGGAATGTTAGAGCTAGCTATATAT 57.638 37.037 19.38 13.20 0.00 0.86
1003 1049 8.561769 AGGAGGAATGTTAGAGCTAGCTATATA 58.438 37.037 19.38 11.44 0.00 0.86
1004 1050 7.418378 AGGAGGAATGTTAGAGCTAGCTATAT 58.582 38.462 19.38 9.52 0.00 0.86
1005 1051 6.795590 AGGAGGAATGTTAGAGCTAGCTATA 58.204 40.000 19.38 17.00 0.00 1.31
1006 1052 5.650283 AGGAGGAATGTTAGAGCTAGCTAT 58.350 41.667 19.38 18.26 0.00 2.97
1007 1053 5.068215 AGGAGGAATGTTAGAGCTAGCTA 57.932 43.478 19.38 0.97 0.00 3.32
1008 1054 3.895041 GAGGAGGAATGTTAGAGCTAGCT 59.105 47.826 19.45 19.45 0.00 3.32
1009 1055 3.895041 AGAGGAGGAATGTTAGAGCTAGC 59.105 47.826 6.62 6.62 0.00 3.42
1010 1056 5.385198 AGAGAGGAGGAATGTTAGAGCTAG 58.615 45.833 0.00 0.00 0.00 3.42
1011 1057 5.396057 AGAGAGGAGGAATGTTAGAGCTA 57.604 43.478 0.00 0.00 0.00 3.32
1012 1058 4.264373 AGAGAGGAGGAATGTTAGAGCT 57.736 45.455 0.00 0.00 0.00 4.09
1013 1059 5.351948 AAAGAGAGGAGGAATGTTAGAGC 57.648 43.478 0.00 0.00 0.00 4.09
1076 1126 1.930133 ATGGTGGTGGCTGGGATGA 60.930 57.895 0.00 0.00 0.00 2.92
1093 1143 1.452651 CAGCACGGATCTTGCCCAT 60.453 57.895 14.06 0.00 41.18 4.00
1099 1149 2.270205 CTGGGCAGCACGGATCTT 59.730 61.111 0.00 0.00 0.00 2.40
1118 1168 3.962421 CCGCTAGCCCGTCCGTAG 61.962 72.222 9.66 0.00 0.00 3.51
1191 1241 1.091771 CGCGGAAGTAGTAGTCGGGA 61.092 60.000 0.00 0.00 36.18 5.14
1266 1316 1.226802 CCTCTCGACGCCTGTGATG 60.227 63.158 0.00 0.00 0.00 3.07
1491 1541 3.700831 GAGGAGGGAGACGAGGCGA 62.701 68.421 0.00 0.00 0.00 5.54
1675 1725 2.273912 GGGTGTCGAAGGAGTCCGT 61.274 63.158 2.76 0.00 0.00 4.69
1869 2440 1.898574 CAGCCTTGGCAGTCCGTTT 60.899 57.895 14.54 0.00 34.14 3.60
1954 2525 1.244816 TCATTCCAGTCGACGACACT 58.755 50.000 28.31 7.36 34.60 3.55
2046 2617 3.494336 CTTGCCGCCAGCTTCTCG 61.494 66.667 0.00 0.00 44.23 4.04
2169 2746 3.054802 CCCACTCTTCATTAAGGTCAGCT 60.055 47.826 0.00 0.00 33.22 4.24
2244 2821 1.223763 GTTACCCTAGGTGGCAGCC 59.776 63.158 13.95 3.66 36.19 4.85
2262 2839 4.275689 GCATTTTTGGTTCTTTTCTTGGGG 59.724 41.667 0.00 0.00 0.00 4.96
2273 2850 2.492012 TGTGCCATGCATTTTTGGTTC 58.508 42.857 0.00 0.00 41.91 3.62
2274 2851 2.634815 TGTGCCATGCATTTTTGGTT 57.365 40.000 0.00 0.00 41.91 3.67
2276 2853 3.597255 TGTATGTGCCATGCATTTTTGG 58.403 40.909 0.00 0.00 41.91 3.28
2278 2855 4.221262 ACTCTGTATGTGCCATGCATTTTT 59.779 37.500 0.00 0.00 41.91 1.94
2350 2927 9.911788 AAGTGACATATTGGATATGGGAATATC 57.088 33.333 11.42 0.00 45.36 1.63
2356 2933 9.690913 ATATCAAAGTGACATATTGGATATGGG 57.309 33.333 11.42 0.00 45.36 4.00
2396 2999 8.387354 CACACATAGTTCACATCGCTTAATTAA 58.613 33.333 0.00 0.00 0.00 1.40
2399 3002 5.294306 CCACACATAGTTCACATCGCTTAAT 59.706 40.000 0.00 0.00 0.00 1.40
2400 3003 4.629634 CCACACATAGTTCACATCGCTTAA 59.370 41.667 0.00 0.00 0.00 1.85
2401 3004 4.180817 CCACACATAGTTCACATCGCTTA 58.819 43.478 0.00 0.00 0.00 3.09
2402 3005 3.002791 CCACACATAGTTCACATCGCTT 58.997 45.455 0.00 0.00 0.00 4.68
2415 3018 2.299013 GACCACTCTCACACCACACATA 59.701 50.000 0.00 0.00 0.00 2.29
2431 3034 3.625764 TCTTGCACAACTTACAAGACCAC 59.374 43.478 0.75 0.00 43.55 4.16
2436 3039 4.572389 ACTCACTCTTGCACAACTTACAAG 59.428 41.667 0.00 0.00 41.70 3.16
2482 3085 2.221169 TGGCCATCTAATGTTGATCGC 58.779 47.619 0.00 0.00 0.00 4.58
2546 3157 4.346418 AGCATCCCCAAATTAAACAACACA 59.654 37.500 0.00 0.00 0.00 3.72
2547 3158 4.690280 CAGCATCCCCAAATTAAACAACAC 59.310 41.667 0.00 0.00 0.00 3.32
2555 3166 1.113788 GCAGCAGCATCCCCAAATTA 58.886 50.000 0.00 0.00 41.58 1.40
2566 3177 0.594602 GTCAATTCACAGCAGCAGCA 59.405 50.000 3.17 0.00 45.49 4.41
2603 3214 5.538849 AATTCAGCTACTAGTTAGGCCTC 57.461 43.478 9.68 0.00 0.00 4.70
2618 3229 7.662604 ATTTTGAATTCCAGTGAAATTCAGC 57.337 32.000 15.88 0.00 33.57 4.26
2665 3276 2.631418 TCGCTTGTACTTCTTCCTCG 57.369 50.000 0.00 0.00 0.00 4.63
2666 3277 4.175787 TCTTCGCTTGTACTTCTTCCTC 57.824 45.455 0.00 0.00 0.00 3.71
2668 3279 3.619038 CCATCTTCGCTTGTACTTCTTCC 59.381 47.826 0.00 0.00 0.00 3.46
2671 3282 4.537135 TTCCATCTTCGCTTGTACTTCT 57.463 40.909 0.00 0.00 0.00 2.85
2686 3297 4.214971 AGAATATGCTTGTGCGATTCCATC 59.785 41.667 10.03 0.00 41.32 3.51
2690 3301 3.812053 AGGAGAATATGCTTGTGCGATTC 59.188 43.478 0.00 0.00 43.34 2.52
2694 3305 2.554142 TGAGGAGAATATGCTTGTGCG 58.446 47.619 0.00 0.00 43.34 5.34
2746 3358 1.965083 CGGATTCAGGTAGCGATACG 58.035 55.000 4.52 0.00 0.00 3.06
2781 3398 3.966154 ACTCTATACACTCGGCAAATCG 58.034 45.455 0.00 0.00 0.00 3.34
2783 3400 4.442706 CCAACTCTATACACTCGGCAAAT 58.557 43.478 0.00 0.00 0.00 2.32
2803 3420 2.974692 AATTGTGTGCCGAGTGCCCA 62.975 55.000 0.00 0.00 40.16 5.36
2844 3461 8.981647 ACTCAATAAAGAATTGTTTGTCAATGC 58.018 29.630 10.65 0.00 44.85 3.56
2864 3483 3.895232 AAGATACTCGTGGCACTCAAT 57.105 42.857 16.72 3.78 0.00 2.57
2874 3493 7.564044 CGAGTGTAAAAGAAAAGATACTCGT 57.436 36.000 13.40 0.00 46.40 4.18
2882 3501 7.241376 AGTGTTTGTCGAGTGTAAAAGAAAAG 58.759 34.615 0.00 0.00 0.00 2.27
2922 3541 6.591313 AAGAAACAAGAGAAAGACGAAGAC 57.409 37.500 0.00 0.00 0.00 3.01
3012 3637 7.946381 AAAGAAATAGGGAGGATGAAAAGAC 57.054 36.000 0.00 0.00 0.00 3.01
3086 3712 8.177119 ACAATTTTCCATTTACTAGCACTTCA 57.823 30.769 0.00 0.00 0.00 3.02
3096 3722 9.332502 ACCCAACTTTAACAATTTTCCATTTAC 57.667 29.630 0.00 0.00 0.00 2.01
3097 3723 9.907229 AACCCAACTTTAACAATTTTCCATTTA 57.093 25.926 0.00 0.00 0.00 1.40
3098 3724 8.815565 AACCCAACTTTAACAATTTTCCATTT 57.184 26.923 0.00 0.00 0.00 2.32
3100 3726 9.907229 TTTAACCCAACTTTAACAATTTTCCAT 57.093 25.926 0.00 0.00 0.00 3.41
3101 3727 9.734984 TTTTAACCCAACTTTAACAATTTTCCA 57.265 25.926 0.00 0.00 0.00 3.53
3116 3744 9.888878 GTCTAAACATAGACTTTTTAACCCAAC 57.111 33.333 8.40 0.00 42.29 3.77
3124 3752 8.832735 TGGATAGGGTCTAAACATAGACTTTTT 58.167 33.333 13.86 3.12 44.35 1.94
3171 3812 3.185330 CGTGAGTCTTGTCATCCTGATG 58.815 50.000 0.55 0.55 40.09 3.07
3220 3863 6.305160 CACACTTTGTTTGCCATTTTCAAAAC 59.695 34.615 0.00 0.00 35.49 2.43
3230 3873 4.380531 TGTTTTTCACACTTTGTTTGCCA 58.619 34.783 0.00 0.00 0.00 4.92
3232 3875 6.163159 TCATGTTTTTCACACTTTGTTTGC 57.837 33.333 0.00 0.00 38.61 3.68
3233 3876 8.281893 ACTTTCATGTTTTTCACACTTTGTTTG 58.718 29.630 0.00 0.00 38.61 2.93
3234 3877 8.376889 ACTTTCATGTTTTTCACACTTTGTTT 57.623 26.923 0.00 0.00 38.61 2.83
3237 3880 7.235777 CCAACTTTCATGTTTTTCACACTTTG 58.764 34.615 0.00 0.00 38.61 2.77
3244 3887 4.272991 GCATGCCAACTTTCATGTTTTTCA 59.727 37.500 6.36 0.00 41.44 2.69
3290 3934 7.186804 CGTGTCACAACTTCTACAAAATCTTT 58.813 34.615 3.42 0.00 0.00 2.52
3300 3944 1.864711 GCTTGCGTGTCACAACTTCTA 59.135 47.619 3.42 0.00 0.00 2.10
3301 3945 0.657840 GCTTGCGTGTCACAACTTCT 59.342 50.000 3.42 0.00 0.00 2.85
3315 3959 4.400567 AGATGGTCCAATTTCTAAGCTTGC 59.599 41.667 9.86 0.00 0.00 4.01
3352 3997 4.024893 TGAGCTGTTCAATCTCGAAACAAC 60.025 41.667 0.00 0.00 31.34 3.32
3359 4004 2.376808 ACCTGAGCTGTTCAATCTCG 57.623 50.000 0.00 0.00 34.81 4.04
3361 4006 4.090761 TCAAACCTGAGCTGTTCAATCT 57.909 40.909 0.00 0.00 34.81 2.40
3366 4011 1.268079 GCCTTCAAACCTGAGCTGTTC 59.732 52.381 0.00 0.00 31.69 3.18
3369 4014 0.603707 TCGCCTTCAAACCTGAGCTG 60.604 55.000 0.00 0.00 31.69 4.24
3370 4015 0.326264 ATCGCCTTCAAACCTGAGCT 59.674 50.000 0.00 0.00 31.69 4.09
3372 4017 0.449388 GCATCGCCTTCAAACCTGAG 59.551 55.000 0.00 0.00 31.69 3.35


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

AutoCloner maintained by Alex Coulton.