Multiple sequence alignment - TraesCS5B01G512600

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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 TraesCS5B01G512600 chr5B 100.000 4226 0 0 1 4226 677792576 677788351 0.000000e+00 7805.0
1 TraesCS5B01G512600 chr5B 94.320 581 32 1 1 581 252755932 252756511 0.000000e+00 889.0
2 TraesCS5B01G512600 chr5B 83.664 906 104 26 1933 2807 677754223 677753331 0.000000e+00 813.0
3 TraesCS5B01G512600 chr5B 86.258 604 77 3 1233 1836 677754818 677754221 0.000000e+00 651.0
4 TraesCS5B01G512600 chr5B 87.662 154 7 2 4085 4226 517851027 517851180 7.270000e-38 169.0
5 TraesCS5B01G512600 chr4A 90.254 3037 153 59 799 3779 632912656 632915605 0.000000e+00 3836.0
6 TraesCS5B01G512600 chr4A 83.219 1019 130 25 1225 2227 632918055 632919048 0.000000e+00 896.0
7 TraesCS5B01G512600 chr4A 93.976 581 33 2 1 580 716598457 716599036 0.000000e+00 878.0
8 TraesCS5B01G512600 chr4A 95.946 74 3 0 658 731 632912194 632912267 2.060000e-23 121.0
9 TraesCS5B01G512600 chr4A 92.683 41 2 1 663 703 632912166 632912205 1.640000e-04 58.4
10 TraesCS5B01G512600 chr5D 84.866 1381 173 24 1233 2598 537325244 537323885 0.000000e+00 1360.0
11 TraesCS5B01G512600 chr5D 95.533 582 24 2 1 581 420043422 420042842 0.000000e+00 929.0
12 TraesCS5B01G512600 chr5D 88.961 154 4 3 4085 4226 418284803 418284955 1.210000e-40 178.0
13 TraesCS5B01G512600 chr5D 84.874 119 6 5 4120 4226 482585758 482585640 4.470000e-20 110.0
14 TraesCS5B01G512600 chr5D 93.056 72 5 0 3514 3585 537326798 537326727 5.780000e-19 106.0
15 TraesCS5B01G512600 chr7B 93.966 580 35 0 1 580 719751765 719751186 0.000000e+00 878.0
16 TraesCS5B01G512600 chr7B 93.966 580 34 1 1 580 730656322 730655744 0.000000e+00 876.0
17 TraesCS5B01G512600 chr7B 91.837 49 4 0 3245 3293 55847014 55846966 7.580000e-08 69.4
18 TraesCS5B01G512600 chr1B 93.976 581 31 2 1 581 333745971 333746547 0.000000e+00 876.0
19 TraesCS5B01G512600 chr2D 93.836 584 31 4 1 582 610759434 610758854 0.000000e+00 874.0
20 TraesCS5B01G512600 chr2D 93.804 581 34 2 1 580 623715455 623714876 0.000000e+00 872.0
21 TraesCS5B01G512600 chr3B 93.793 580 34 2 8 586 226301143 226300565 0.000000e+00 870.0
22 TraesCS5B01G512600 chr7D 88.961 154 5 2 4085 4226 562636052 562636205 3.360000e-41 180.0
23 TraesCS5B01G512600 chr7D 91.837 49 4 0 3245 3293 100274373 100274325 7.580000e-08 69.4
24 TraesCS5B01G512600 chr3D 88.961 154 5 3 4085 4226 17766903 17767056 3.360000e-41 180.0
25 TraesCS5B01G512600 chr3D 88.961 154 5 2 4085 4226 354651990 354651837 3.360000e-41 180.0
26 TraesCS5B01G512600 chr4D 88.312 154 6 3 4085 4226 477501985 477501832 1.560000e-39 174.0
27 TraesCS5B01G512600 chr2B 88.312 154 6 2 4085 4226 560176832 560176679 1.560000e-39 174.0
28 TraesCS5B01G512600 chr2B 86.364 154 9 2 4085 4226 711708352 711708199 1.570000e-34 158.0
29 TraesCS5B01G512600 chr1D 88.312 154 6 2 4085 4226 208180175 208180022 1.560000e-39 174.0
30 TraesCS5B01G512600 chr1D 86.364 154 9 2 4085 4226 468710820 468710667 1.570000e-34 158.0
31 TraesCS5B01G512600 chr6D 87.662 154 7 2 4085 4226 465681757 465681604 7.270000e-38 169.0
32 TraesCS5B01G512600 chr2A 86.364 154 9 1 4085 4226 221302879 221302726 1.570000e-34 158.0
33 TraesCS5B01G512600 chrUn 95.181 83 4 0 4085 4167 477306064 477305982 9.530000e-27 132.0
34 TraesCS5B01G512600 chr7A 97.436 39 1 0 3245 3283 102531413 102531375 2.730000e-07 67.6


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 TraesCS5B01G512600 chr5B 677788351 677792576 4225 True 7805.00 7805 100.0000 1 4226 1 chr5B.!!$R1 4225
1 TraesCS5B01G512600 chr5B 252755932 252756511 579 False 889.00 889 94.3200 1 581 1 chr5B.!!$F1 580
2 TraesCS5B01G512600 chr5B 677753331 677754818 1487 True 732.00 813 84.9610 1233 2807 2 chr5B.!!$R2 1574
3 TraesCS5B01G512600 chr4A 632912166 632919048 6882 False 1227.85 3836 90.5255 658 3779 4 chr4A.!!$F2 3121
4 TraesCS5B01G512600 chr4A 716598457 716599036 579 False 878.00 878 93.9760 1 580 1 chr4A.!!$F1 579
5 TraesCS5B01G512600 chr5D 420042842 420043422 580 True 929.00 929 95.5330 1 581 1 chr5D.!!$R1 580
6 TraesCS5B01G512600 chr5D 537323885 537326798 2913 True 733.00 1360 88.9610 1233 3585 2 chr5D.!!$R3 2352
7 TraesCS5B01G512600 chr7B 719751186 719751765 579 True 878.00 878 93.9660 1 580 1 chr7B.!!$R2 579
8 TraesCS5B01G512600 chr7B 730655744 730656322 578 True 876.00 876 93.9660 1 580 1 chr7B.!!$R3 579
9 TraesCS5B01G512600 chr1B 333745971 333746547 576 False 876.00 876 93.9760 1 581 1 chr1B.!!$F1 580
10 TraesCS5B01G512600 chr2D 610758854 610759434 580 True 874.00 874 93.8360 1 582 1 chr2D.!!$R1 581
11 TraesCS5B01G512600 chr2D 623714876 623715455 579 True 872.00 872 93.8040 1 580 1 chr2D.!!$R2 579
12 TraesCS5B01G512600 chr3B 226300565 226301143 578 True 870.00 870 93.7930 8 586 1 chr3B.!!$R1 578

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
738 740 0.034477 AGCCCCACCCGTCAATTTAG 60.034 55.0 0.00 0.0 0.0 1.85 F
758 760 0.116541 ATAGATACGTGGGGGAGGGG 59.883 60.0 0.00 0.0 0.0 4.79 F
1662 2019 0.175989 GACCTGATCCCGGACTTCAC 59.824 60.0 0.73 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2304 2667 0.033011 TCCTAGCTGAGGGGAGACAC 60.033 60.0 0.0 0.0 46.7 3.67 R
2691 3071 0.250727 AGTTTCGTGGGGTGTGATGG 60.251 55.0 0.0 0.0 0.0 3.51 R
3559 3963 0.313672 GCAGGTCCATGTCGCAAAAA 59.686 50.0 0.0 0.0 0.0 1.94 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
27 28 3.162858 TCACCCGGGACCGTGTTT 61.163 61.111 32.02 0.00 37.81 2.83
429 431 8.030913 AGTCGGTTACAAGGAAGGAAATATAT 57.969 34.615 0.00 0.00 0.00 0.86
586 588 0.244994 CAGGACTCCCTCACTTGTCG 59.755 60.000 0.00 0.00 42.02 4.35
588 590 1.444553 GACTCCCTCACTTGTCGCG 60.445 63.158 0.00 0.00 0.00 5.87
589 591 1.863662 GACTCCCTCACTTGTCGCGA 61.864 60.000 3.71 3.71 0.00 5.87
590 592 1.289066 CTCCCTCACTTGTCGCGAA 59.711 57.895 12.06 0.00 0.00 4.70
591 593 0.108615 CTCCCTCACTTGTCGCGAAT 60.109 55.000 12.06 0.00 0.00 3.34
592 594 0.389817 TCCCTCACTTGTCGCGAATG 60.390 55.000 12.06 7.53 0.00 2.67
593 595 0.670546 CCCTCACTTGTCGCGAATGT 60.671 55.000 12.06 7.28 0.00 2.71
595 597 1.531149 CCTCACTTGTCGCGAATGTTT 59.469 47.619 12.06 0.00 0.00 2.83
596 598 2.411547 CCTCACTTGTCGCGAATGTTTC 60.412 50.000 12.06 0.00 0.00 2.78
598 600 2.033236 TCACTTGTCGCGAATGTTTCAC 60.033 45.455 12.06 0.00 0.00 3.18
600 602 0.589223 TTGTCGCGAATGTTTCACCC 59.411 50.000 12.06 0.00 0.00 4.61
601 603 0.250124 TGTCGCGAATGTTTCACCCT 60.250 50.000 12.06 0.00 0.00 4.34
602 604 0.165944 GTCGCGAATGTTTCACCCTG 59.834 55.000 12.06 0.00 0.00 4.45
604 606 1.212751 GCGAATGTTTCACCCTGGC 59.787 57.895 0.00 0.00 0.00 4.85
605 607 1.883021 CGAATGTTTCACCCTGGCC 59.117 57.895 0.00 0.00 0.00 5.36
606 608 1.595093 CGAATGTTTCACCCTGGCCC 61.595 60.000 0.00 0.00 0.00 5.80
607 609 0.541764 GAATGTTTCACCCTGGCCCA 60.542 55.000 0.00 0.00 0.00 5.36
608 610 0.116940 AATGTTTCACCCTGGCCCAT 59.883 50.000 0.00 0.00 0.00 4.00
609 611 0.615544 ATGTTTCACCCTGGCCCATG 60.616 55.000 0.00 0.00 0.00 3.66
610 612 1.228862 GTTTCACCCTGGCCCATGT 60.229 57.895 0.00 0.00 0.00 3.21
611 613 0.831711 GTTTCACCCTGGCCCATGTT 60.832 55.000 0.00 0.00 0.00 2.71
612 614 0.541764 TTTCACCCTGGCCCATGTTC 60.542 55.000 0.00 0.00 0.00 3.18
614 616 3.256960 ACCCTGGCCCATGTTCGT 61.257 61.111 0.00 0.00 0.00 3.85
615 617 2.751436 CCCTGGCCCATGTTCGTG 60.751 66.667 0.00 0.00 0.00 4.35
616 618 2.350895 CCTGGCCCATGTTCGTGA 59.649 61.111 0.00 0.00 0.00 4.35
617 619 1.077501 CCTGGCCCATGTTCGTGAT 60.078 57.895 0.00 0.00 0.00 3.06
621 623 0.392998 GGCCCATGTTCGTGATGTCT 60.393 55.000 0.00 0.00 0.00 3.41
622 624 1.134521 GGCCCATGTTCGTGATGTCTA 60.135 52.381 0.00 0.00 0.00 2.59
623 625 2.627945 GCCCATGTTCGTGATGTCTAA 58.372 47.619 0.00 0.00 0.00 2.10
626 628 4.679639 GCCCATGTTCGTGATGTCTAAGTA 60.680 45.833 0.00 0.00 0.00 2.24
627 629 5.043903 CCCATGTTCGTGATGTCTAAGTAG 58.956 45.833 0.00 0.00 0.00 2.57
628 630 5.163550 CCCATGTTCGTGATGTCTAAGTAGA 60.164 44.000 0.00 0.00 0.00 2.59
629 631 6.461648 CCCATGTTCGTGATGTCTAAGTAGAT 60.462 42.308 0.00 0.00 34.39 1.98
630 632 7.255486 CCCATGTTCGTGATGTCTAAGTAGATA 60.255 40.741 0.00 0.00 34.39 1.98
631 633 8.135529 CCATGTTCGTGATGTCTAAGTAGATAA 58.864 37.037 0.00 0.00 34.39 1.75
632 634 8.959058 CATGTTCGTGATGTCTAAGTAGATAAC 58.041 37.037 0.00 0.00 34.39 1.89
633 635 8.047413 TGTTCGTGATGTCTAAGTAGATAACA 57.953 34.615 0.00 0.00 34.39 2.41
634 636 7.966753 TGTTCGTGATGTCTAAGTAGATAACAC 59.033 37.037 12.53 12.53 40.90 3.32
635 637 7.024340 TCGTGATGTCTAAGTAGATAACACC 57.976 40.000 15.18 3.93 41.09 4.16
636 638 6.827251 TCGTGATGTCTAAGTAGATAACACCT 59.173 38.462 15.18 0.00 41.09 4.00
637 639 7.338703 TCGTGATGTCTAAGTAGATAACACCTT 59.661 37.037 15.18 0.00 41.09 3.50
638 640 8.618677 CGTGATGTCTAAGTAGATAACACCTTA 58.381 37.037 15.18 0.00 41.09 2.69
639 641 9.733219 GTGATGTCTAAGTAGATAACACCTTAC 57.267 37.037 11.86 0.00 39.54 2.34
640 642 9.470399 TGATGTCTAAGTAGATAACACCTTACA 57.530 33.333 0.00 0.00 34.39 2.41
649 651 8.915036 AGTAGATAACACCTTACATCCTACTTG 58.085 37.037 0.00 0.00 0.00 3.16
650 652 7.735326 AGATAACACCTTACATCCTACTTGT 57.265 36.000 0.00 0.00 0.00 3.16
652 654 5.562298 AACACCTTACATCCTACTTGTGT 57.438 39.130 0.00 0.00 37.30 3.72
653 655 5.562298 ACACCTTACATCCTACTTGTGTT 57.438 39.130 0.00 0.00 32.19 3.32
654 656 6.675413 ACACCTTACATCCTACTTGTGTTA 57.325 37.500 0.00 0.00 32.19 2.41
655 657 7.069877 ACACCTTACATCCTACTTGTGTTAA 57.930 36.000 0.00 0.00 32.19 2.01
656 658 7.686434 ACACCTTACATCCTACTTGTGTTAAT 58.314 34.615 0.00 0.00 32.19 1.40
657 659 8.161425 ACACCTTACATCCTACTTGTGTTAATT 58.839 33.333 0.00 0.00 32.19 1.40
658 660 9.661563 CACCTTACATCCTACTTGTGTTAATTA 57.338 33.333 0.00 0.00 0.00 1.40
659 661 9.662947 ACCTTACATCCTACTTGTGTTAATTAC 57.337 33.333 0.00 0.00 0.00 1.89
660 662 9.886132 CCTTACATCCTACTTGTGTTAATTACT 57.114 33.333 0.00 0.00 0.00 2.24
694 696 9.194271 GGAGTAAAAAGTACGGATGATCTATTC 57.806 37.037 0.00 0.00 0.00 1.75
707 709 7.095732 CGGATGATCTATTCTGAGATTGTTGTG 60.096 40.741 0.00 0.00 36.27 3.33
712 714 8.627208 ATCTATTCTGAGATTGTTGTGTGTTT 57.373 30.769 0.00 0.00 31.92 2.83
731 733 1.335132 TTCTATGAGCCCCACCCGTC 61.335 60.000 0.00 0.00 0.00 4.79
732 734 2.039787 TATGAGCCCCACCCGTCA 59.960 61.111 0.00 0.00 0.00 4.35
733 735 1.613928 TATGAGCCCCACCCGTCAA 60.614 57.895 0.00 0.00 0.00 3.18
735 737 1.863155 ATGAGCCCCACCCGTCAATT 61.863 55.000 0.00 0.00 0.00 2.32
736 738 1.304134 GAGCCCCACCCGTCAATTT 60.304 57.895 0.00 0.00 0.00 1.82
738 740 0.034477 AGCCCCACCCGTCAATTTAG 60.034 55.000 0.00 0.00 0.00 1.85
740 742 1.409661 GCCCCACCCGTCAATTTAGAT 60.410 52.381 0.00 0.00 0.00 1.98
741 743 2.158726 GCCCCACCCGTCAATTTAGATA 60.159 50.000 0.00 0.00 0.00 1.98
742 744 3.740115 CCCCACCCGTCAATTTAGATAG 58.260 50.000 0.00 0.00 0.00 2.08
743 745 3.389983 CCCCACCCGTCAATTTAGATAGA 59.610 47.826 0.00 0.00 0.00 1.98
744 746 4.041691 CCCCACCCGTCAATTTAGATAGAT 59.958 45.833 0.00 0.00 0.00 1.98
745 747 5.247564 CCCCACCCGTCAATTTAGATAGATA 59.752 44.000 0.00 0.00 0.00 1.98
746 748 6.164176 CCCACCCGTCAATTTAGATAGATAC 58.836 44.000 0.00 0.00 0.00 2.24
752 754 5.862323 CGTCAATTTAGATAGATACGTGGGG 59.138 44.000 0.00 0.00 0.00 4.96
753 755 6.164176 GTCAATTTAGATAGATACGTGGGGG 58.836 44.000 0.00 0.00 0.00 5.40
754 756 6.014840 GTCAATTTAGATAGATACGTGGGGGA 60.015 42.308 0.00 0.00 0.00 4.81
757 759 1.077334 AGATAGATACGTGGGGGAGGG 59.923 57.143 0.00 0.00 0.00 4.30
758 760 0.116541 ATAGATACGTGGGGGAGGGG 59.883 60.000 0.00 0.00 0.00 4.79
759 761 2.027434 TAGATACGTGGGGGAGGGGG 62.027 65.000 0.00 0.00 0.00 5.40
773 775 4.494201 GGGGGTAGGGCTACTTGT 57.506 61.111 0.00 0.00 36.36 3.16
775 777 0.912968 GGGGGTAGGGCTACTTGTGT 60.913 60.000 0.00 0.00 36.36 3.72
776 778 0.989602 GGGGTAGGGCTACTTGTGTT 59.010 55.000 0.00 0.00 36.36 3.32
777 779 1.353358 GGGGTAGGGCTACTTGTGTTT 59.647 52.381 0.00 0.00 36.36 2.83
779 781 3.493334 GGGTAGGGCTACTTGTGTTTTT 58.507 45.455 0.00 0.00 36.36 1.94
802 1125 1.135333 TGTGTGTGTCTTCGTGCACTA 59.865 47.619 16.19 0.00 36.63 2.74
831 1157 7.728847 ACATTTTCCCTTCAATTTTTGCTAC 57.271 32.000 0.00 0.00 0.00 3.58
863 1189 2.211353 TACGTTGCCTTGGCAAAAAC 57.789 45.000 26.12 15.23 0.00 2.43
866 1192 1.734465 CGTTGCCTTGGCAAAAACAAA 59.266 42.857 26.12 2.28 0.00 2.83
867 1193 2.160417 CGTTGCCTTGGCAAAAACAAAA 59.840 40.909 26.12 1.53 0.00 2.44
868 1194 3.365364 CGTTGCCTTGGCAAAAACAAAAA 60.365 39.130 26.12 0.80 0.00 1.94
869 1195 4.673841 CGTTGCCTTGGCAAAAACAAAAAT 60.674 37.500 26.12 0.00 0.00 1.82
870 1196 4.367386 TGCCTTGGCAAAAACAAAAATG 57.633 36.364 12.40 0.00 0.00 2.32
872 1198 4.142513 TGCCTTGGCAAAAACAAAAATGTC 60.143 37.500 12.40 0.00 0.00 3.06
873 1199 4.142513 GCCTTGGCAAAAACAAAAATGTCA 60.143 37.500 6.79 0.00 0.00 3.58
876 1202 5.542616 TGGCAAAAACAAAAATGTCACAG 57.457 34.783 0.00 0.00 0.00 3.66
877 1203 4.142730 TGGCAAAAACAAAAATGTCACAGC 60.143 37.500 0.00 0.00 0.00 4.40
878 1204 4.142730 GGCAAAAACAAAAATGTCACAGCA 60.143 37.500 0.00 0.00 0.00 4.41
879 1205 5.448904 GGCAAAAACAAAAATGTCACAGCAT 60.449 36.000 0.00 0.00 0.00 3.79
1037 1392 6.708502 TGTACTAGTTGAGCAGTGCAATTTTA 59.291 34.615 19.20 3.36 34.95 1.52
1133 1490 6.867662 TTTTTGAGGTGTTTTTGCTTTTCA 57.132 29.167 0.00 0.00 0.00 2.69
1134 1491 7.446001 TTTTTGAGGTGTTTTTGCTTTTCAT 57.554 28.000 0.00 0.00 0.00 2.57
1191 1548 2.434774 GAAAACCCGAGGCCCACT 59.565 61.111 0.00 0.00 0.00 4.00
1241 1598 1.212375 CCCCCAAAATCCAAATCCCC 58.788 55.000 0.00 0.00 0.00 4.81
1242 1599 1.556713 CCCCCAAAATCCAAATCCCCA 60.557 52.381 0.00 0.00 0.00 4.96
1243 1600 2.273619 CCCCAAAATCCAAATCCCCAA 58.726 47.619 0.00 0.00 0.00 4.12
1244 1601 2.026356 CCCCAAAATCCAAATCCCCAAC 60.026 50.000 0.00 0.00 0.00 3.77
1245 1602 2.026356 CCCAAAATCCAAATCCCCAACC 60.026 50.000 0.00 0.00 0.00 3.77
1246 1603 2.912295 CCAAAATCCAAATCCCCAACCT 59.088 45.455 0.00 0.00 0.00 3.50
1247 1604 3.055167 CCAAAATCCAAATCCCCAACCTC 60.055 47.826 0.00 0.00 0.00 3.85
1248 1605 2.143876 AATCCAAATCCCCAACCTCG 57.856 50.000 0.00 0.00 0.00 4.63
1249 1606 1.295020 ATCCAAATCCCCAACCTCGA 58.705 50.000 0.00 0.00 0.00 4.04
1250 1607 1.295020 TCCAAATCCCCAACCTCGAT 58.705 50.000 0.00 0.00 0.00 3.59
1251 1608 1.211949 TCCAAATCCCCAACCTCGATC 59.788 52.381 0.00 0.00 0.00 3.69
1252 1609 1.299541 CAAATCCCCAACCTCGATCG 58.700 55.000 9.36 9.36 0.00 3.69
1253 1610 1.134521 CAAATCCCCAACCTCGATCGA 60.135 52.381 18.32 18.32 0.00 3.59
1254 1611 1.424638 AATCCCCAACCTCGATCGAT 58.575 50.000 19.78 0.94 0.00 3.59
1255 1612 0.969894 ATCCCCAACCTCGATCGATC 59.030 55.000 19.78 15.68 0.00 3.69
1296 1653 1.080170 ACCGCCCAAATCCCCAATT 59.920 52.632 0.00 0.00 0.00 2.32
1300 1657 1.822615 CCCAAATCCCCAATTCCGC 59.177 57.895 0.00 0.00 0.00 5.54
1612 1969 1.134995 CAGCAGCACTTCATCTACCGA 60.135 52.381 0.00 0.00 0.00 4.69
1662 2019 0.175989 GACCTGATCCCGGACTTCAC 59.824 60.000 0.73 0.00 0.00 3.18
1665 2022 0.176680 CTGATCCCGGACTTCACTGG 59.823 60.000 0.73 0.00 36.18 4.00
1673 2030 2.629051 CGGACTTCACTGGTTATTCCC 58.371 52.381 0.00 0.00 34.77 3.97
1674 2031 2.629051 GGACTTCACTGGTTATTCCCG 58.371 52.381 0.00 0.00 34.77 5.14
1675 2032 2.629051 GACTTCACTGGTTATTCCCGG 58.371 52.381 0.00 0.00 36.89 5.73
1682 2042 1.526225 GGTTATTCCCGGGCAGAGC 60.526 63.158 18.49 3.72 0.00 4.09
1751 2111 2.829003 CGGCTCTGAGCTACGGGA 60.829 66.667 27.09 0.00 41.99 5.14
1891 2251 2.514824 GCCAAGGTGATCGCCCTC 60.515 66.667 21.82 4.93 0.00 4.30
1954 2314 0.596082 TGATCTGTGACGTGCTCGAA 59.404 50.000 16.04 0.00 40.62 3.71
2022 2382 1.531149 CAGCAACAAACCACTCTACGG 59.469 52.381 0.00 0.00 0.00 4.02
2033 2396 1.398390 CACTCTACGGCCAATCTTTGC 59.602 52.381 2.24 0.00 0.00 3.68
2035 2398 0.618458 TCTACGGCCAATCTTTGCCT 59.382 50.000 2.24 0.00 45.71 4.75
2107 2470 3.243724 ACTTGAGGAGCTGGTAGAACTT 58.756 45.455 0.00 0.00 0.00 2.66
2172 2535 1.902508 TGAGCTCCAAGACTCGGAATT 59.097 47.619 12.15 0.00 35.61 2.17
2185 2548 0.250467 CGGAATTGGCCATCGATCCT 60.250 55.000 6.09 0.00 0.00 3.24
2188 2551 0.250467 AATTGGCCATCGATCCTCCG 60.250 55.000 6.09 0.00 0.00 4.63
2212 2575 3.913163 AGGAGGATGGGGAAGAATATGTC 59.087 47.826 0.00 0.00 0.00 3.06
2214 2577 4.505742 GGAGGATGGGGAAGAATATGTCAC 60.506 50.000 0.00 0.00 0.00 3.67
2280 2643 2.597217 TTGGCGCAAGGGGAACAG 60.597 61.111 10.83 0.00 38.28 3.16
2691 3071 1.978782 GTACAGACGCAAAATGCTTGC 59.021 47.619 0.43 0.00 42.25 4.01
2748 3128 2.856032 CGGCAGCGACTTTCACAG 59.144 61.111 0.00 0.00 0.00 3.66
2820 3219 7.388460 AGGATTAGTGAAAGCTTCAGATTTG 57.612 36.000 0.00 0.00 41.01 2.32
2905 3304 5.496133 TGGTAGCGTGAGTTACTCTATTC 57.504 43.478 13.86 0.89 45.63 1.75
2912 3311 4.336993 CGTGAGTTACTCTATTCTGAGCCT 59.663 45.833 13.86 0.00 37.58 4.58
2913 3312 5.587289 GTGAGTTACTCTATTCTGAGCCTG 58.413 45.833 13.86 0.00 37.58 4.85
2914 3313 5.358442 GTGAGTTACTCTATTCTGAGCCTGA 59.642 44.000 13.86 0.00 37.58 3.86
2915 3314 5.358442 TGAGTTACTCTATTCTGAGCCTGAC 59.642 44.000 13.86 0.00 37.58 3.51
2916 3315 5.265191 AGTTACTCTATTCTGAGCCTGACA 58.735 41.667 0.00 0.00 37.58 3.58
2917 3316 5.896678 AGTTACTCTATTCTGAGCCTGACAT 59.103 40.000 0.00 0.00 37.58 3.06
2918 3317 6.382570 AGTTACTCTATTCTGAGCCTGACATT 59.617 38.462 0.00 0.00 37.58 2.71
2919 3318 5.690464 ACTCTATTCTGAGCCTGACATTT 57.310 39.130 0.00 0.00 37.58 2.32
2920 3319 5.669477 ACTCTATTCTGAGCCTGACATTTC 58.331 41.667 0.00 0.00 37.58 2.17
2921 3320 5.424895 ACTCTATTCTGAGCCTGACATTTCT 59.575 40.000 0.00 0.00 37.58 2.52
2985 3384 8.366401 TCATTTGTTGGCTTTTAGATTGATTGA 58.634 29.630 0.00 0.00 0.00 2.57
2986 3385 8.991026 CATTTGTTGGCTTTTAGATTGATTGAA 58.009 29.630 0.00 0.00 0.00 2.69
2987 3386 8.592105 TTTGTTGGCTTTTAGATTGATTGAAG 57.408 30.769 0.00 0.00 0.00 3.02
2988 3387 6.690530 TGTTGGCTTTTAGATTGATTGAAGG 58.309 36.000 0.00 0.00 0.00 3.46
2989 3388 5.920193 TGGCTTTTAGATTGATTGAAGGG 57.080 39.130 0.00 0.00 0.00 3.95
3031 3430 4.042809 TCAAATTCTTAGGCAGGGAACAGA 59.957 41.667 0.00 0.00 0.00 3.41
3035 3434 0.320374 TTAGGCAGGGAACAGACACG 59.680 55.000 0.00 0.00 0.00 4.49
3104 3503 6.223138 TCTTTGTTACGTTTGAGCATAGTG 57.777 37.500 0.00 0.00 0.00 2.74
3135 3534 2.564504 AGCTTTCTTTGGGATGCCTTTC 59.435 45.455 4.35 0.00 0.00 2.62
3155 3554 6.595716 CCTTTCGGTCTTTGAACTCTGATATT 59.404 38.462 0.00 0.00 0.00 1.28
3170 3569 7.763356 ACTCTGATATTAATCCGTCTAATCCG 58.237 38.462 0.00 0.00 0.00 4.18
3192 3594 2.393764 GCATGCTGCACTTACGTTTTT 58.606 42.857 11.37 0.00 44.26 1.94
3364 3768 1.214424 AGCTGGGTGGTTTTGTACTGT 59.786 47.619 0.00 0.00 0.00 3.55
3374 3778 1.308047 TTTGTACTGTGCAGTGCTGG 58.692 50.000 17.60 8.67 43.22 4.85
3419 3823 6.966534 ACAATGGGGATTAATTCTGACATC 57.033 37.500 0.00 0.00 0.00 3.06
3448 3852 9.868277 TTCTGTGTCAACATTTTATTTTCAAGT 57.132 25.926 0.00 0.00 35.22 3.16
3450 3854 9.904647 CTGTGTCAACATTTTATTTTCAAGTTG 57.095 29.630 0.00 0.00 35.22 3.16
3451 3855 9.645059 TGTGTCAACATTTTATTTTCAAGTTGA 57.355 25.926 0.08 0.08 40.81 3.18
3454 3858 9.528018 GTCAACATTTTATTTTCAAGTTGAGGA 57.472 29.630 5.56 0.00 42.83 3.71
3514 3918 4.806571 CAATCATGCCACTGCTGC 57.193 55.556 0.00 0.00 38.71 5.25
3559 3963 5.099042 ACAGTCTTGGTTGAGTAGTTTGT 57.901 39.130 0.00 0.00 0.00 2.83
3610 4014 4.574674 TCTTGTAAACTGGGATCAGCAT 57.425 40.909 0.00 0.00 44.59 3.79
3695 4102 6.373779 CAGTCCAACTACAATTGTTGTGATC 58.626 40.000 23.24 14.69 45.03 2.92
3724 4131 7.766283 TCTTGTTGTTGTTGTGATAAACATCA 58.234 30.769 0.00 0.00 39.68 3.07
3779 4186 1.004394 ACAAAGCTTACCCCTGCCTAC 59.996 52.381 0.00 0.00 0.00 3.18
3780 4187 1.282157 CAAAGCTTACCCCTGCCTACT 59.718 52.381 0.00 0.00 0.00 2.57
3784 4191 3.187112 AGCTTACCCCTGCCTACTTAAA 58.813 45.455 0.00 0.00 0.00 1.52
3785 4192 3.786450 AGCTTACCCCTGCCTACTTAAAT 59.214 43.478 0.00 0.00 0.00 1.40
3786 4193 4.229812 AGCTTACCCCTGCCTACTTAAATT 59.770 41.667 0.00 0.00 0.00 1.82
3787 4194 5.430745 AGCTTACCCCTGCCTACTTAAATTA 59.569 40.000 0.00 0.00 0.00 1.40
3788 4195 6.102762 AGCTTACCCCTGCCTACTTAAATTAT 59.897 38.462 0.00 0.00 0.00 1.28
3789 4196 6.430308 GCTTACCCCTGCCTACTTAAATTATC 59.570 42.308 0.00 0.00 0.00 1.75
3790 4197 5.320488 ACCCCTGCCTACTTAAATTATCC 57.680 43.478 0.00 0.00 0.00 2.59
3791 4198 4.105858 ACCCCTGCCTACTTAAATTATCCC 59.894 45.833 0.00 0.00 0.00 3.85
3792 4199 4.324267 CCCTGCCTACTTAAATTATCCCG 58.676 47.826 0.00 0.00 0.00 5.14
3793 4200 3.751698 CCTGCCTACTTAAATTATCCCGC 59.248 47.826 0.00 0.00 0.00 6.13
3794 4201 3.395639 TGCCTACTTAAATTATCCCGCG 58.604 45.455 0.00 0.00 0.00 6.46
3795 4202 2.159037 GCCTACTTAAATTATCCCGCGC 59.841 50.000 0.00 0.00 0.00 6.86
3797 4204 1.223187 ACTTAAATTATCCCGCGCGG 58.777 50.000 41.00 41.00 0.00 6.46
3798 4205 0.110373 CTTAAATTATCCCGCGCGGC 60.110 55.000 42.39 0.00 0.00 6.53
3799 4206 1.508808 TTAAATTATCCCGCGCGGCC 61.509 55.000 42.39 0.00 0.00 6.13
3829 6918 2.908796 CCCGCTCCTAGGGTTTCC 59.091 66.667 9.46 0.00 43.89 3.13
3830 6919 2.743179 CCCGCTCCTAGGGTTTCCC 61.743 68.421 9.46 0.00 45.90 3.97
3911 7271 2.124778 GCAGCCAGCTCCTTCCTC 60.125 66.667 0.00 0.00 41.15 3.71
3912 7272 2.588989 CAGCCAGCTCCTTCCTCC 59.411 66.667 0.00 0.00 0.00 4.30
3914 7274 1.688884 AGCCAGCTCCTTCCTCCTC 60.689 63.158 0.00 0.00 0.00 3.71
3915 7275 2.741055 GCCAGCTCCTTCCTCCTCC 61.741 68.421 0.00 0.00 0.00 4.30
3916 7276 2.069430 CCAGCTCCTTCCTCCTCCC 61.069 68.421 0.00 0.00 0.00 4.30
3917 7277 2.042435 AGCTCCTTCCTCCTCCCG 60.042 66.667 0.00 0.00 0.00 5.14
3918 7278 3.855853 GCTCCTTCCTCCTCCCGC 61.856 72.222 0.00 0.00 0.00 6.13
3919 7279 2.042435 CTCCTTCCTCCTCCCGCT 60.042 66.667 0.00 0.00 0.00 5.52
3920 7280 2.042843 TCCTTCCTCCTCCCGCTC 60.043 66.667 0.00 0.00 0.00 5.03
3926 7286 3.157949 CTCCTCCCGCTCCCCTTC 61.158 72.222 0.00 0.00 0.00 3.46
3927 7287 3.684628 TCCTCCCGCTCCCCTTCT 61.685 66.667 0.00 0.00 0.00 2.85
3928 7288 3.157949 CCTCCCGCTCCCCTTCTC 61.158 72.222 0.00 0.00 0.00 2.87
3929 7289 3.157949 CTCCCGCTCCCCTTCTCC 61.158 72.222 0.00 0.00 0.00 3.71
3930 7290 3.684628 TCCCGCTCCCCTTCTCCT 61.685 66.667 0.00 0.00 0.00 3.69
3931 7291 3.157949 CCCGCTCCCCTTCTCCTC 61.158 72.222 0.00 0.00 0.00 3.71
3932 7292 3.157949 CCGCTCCCCTTCTCCTCC 61.158 72.222 0.00 0.00 0.00 4.30
3934 7294 2.726351 CGCTCCCCTTCTCCTCCAC 61.726 68.421 0.00 0.00 0.00 4.02
3935 7295 2.726351 GCTCCCCTTCTCCTCCACG 61.726 68.421 0.00 0.00 0.00 4.94
3936 7296 2.683933 TCCCCTTCTCCTCCACGC 60.684 66.667 0.00 0.00 0.00 5.34
3938 7298 3.787001 CCCTTCTCCTCCACGCCC 61.787 72.222 0.00 0.00 0.00 6.13
3940 7300 3.787001 CTTCTCCTCCACGCCCCC 61.787 72.222 0.00 0.00 0.00 5.40
3996 7356 4.971125 GCCCTACCTCCGCGCATC 62.971 72.222 8.75 0.00 0.00 3.91
3998 7358 2.336809 CCTACCTCCGCGCATCTC 59.663 66.667 8.75 0.00 0.00 2.75
4000 7360 2.441348 TACCTCCGCGCATCTCCA 60.441 61.111 8.75 0.00 0.00 3.86
4001 7361 2.413437 CTACCTCCGCGCATCTCCAG 62.413 65.000 8.75 0.00 0.00 3.86
4008 7368 4.247380 CGCATCTCCAGCCCCTCC 62.247 72.222 0.00 0.00 0.00 4.30
4009 7369 3.883549 GCATCTCCAGCCCCTCCC 61.884 72.222 0.00 0.00 0.00 4.30
4010 7370 3.174265 CATCTCCAGCCCCTCCCC 61.174 72.222 0.00 0.00 0.00 4.81
4114 7474 4.643387 GTGGTGGTGCCGCCTCTT 62.643 66.667 20.11 0.00 46.12 2.85
4143 7503 4.699522 GGTCCGGTGGTGCTGGTC 62.700 72.222 0.00 0.00 44.16 4.02
4192 7552 4.730487 CCTTCTGGGTCCTTGCAG 57.270 61.111 0.00 0.00 0.00 4.41
4193 7553 1.001641 CCTTCTGGGTCCTTGCAGG 60.002 63.158 0.00 0.00 36.46 4.85
4194 7554 1.763770 CTTCTGGGTCCTTGCAGGT 59.236 57.895 0.00 0.00 36.53 4.00
4195 7555 0.111253 CTTCTGGGTCCTTGCAGGTT 59.889 55.000 0.00 0.00 36.53 3.50
4196 7556 0.178992 TTCTGGGTCCTTGCAGGTTG 60.179 55.000 0.00 0.00 36.53 3.77
4197 7557 1.604593 CTGGGTCCTTGCAGGTTGG 60.605 63.158 0.00 0.00 36.53 3.77
4198 7558 2.991540 GGGTCCTTGCAGGTTGGC 60.992 66.667 0.00 0.00 36.53 4.52
4199 7559 2.116125 GGTCCTTGCAGGTTGGCT 59.884 61.111 0.00 0.00 36.53 4.75
4200 7560 1.973812 GGTCCTTGCAGGTTGGCTC 60.974 63.158 0.00 0.00 36.53 4.70
4202 7562 3.058160 CCTTGCAGGTTGGCTCCG 61.058 66.667 0.00 0.00 34.04 4.63
4203 7563 3.058160 CTTGCAGGTTGGCTCCGG 61.058 66.667 0.00 0.00 34.04 5.14
4225 7585 2.745100 ACCGCGACGCTCTCTGTA 60.745 61.111 19.02 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.091545 GGCTCCTTCAACCATCATCAAA 58.908 45.455 0.00 0.00 0.00 2.69
170 171 2.625790 GGTAAACATTGTGTCCCTTGCA 59.374 45.455 0.00 0.00 0.00 4.08
263 265 6.157904 CGATCTCGTGGTAGATCTACTCTTA 58.842 44.000 27.68 13.35 46.50 2.10
366 368 6.326970 AGCCCTCTCTGGTGTCTATATAAAT 58.673 40.000 0.00 0.00 0.00 1.40
429 431 0.468226 AAGCTTGGCGATCCGGATAA 59.532 50.000 19.15 7.09 34.14 1.75
483 485 4.657436 ACAAGACTCAAGACTTCGACTT 57.343 40.909 0.00 0.00 0.00 3.01
586 588 1.212751 GCCAGGGTGAAACATTCGC 59.787 57.895 0.00 0.00 39.98 4.70
588 590 0.541764 TGGGCCAGGGTGAAACATTC 60.542 55.000 0.00 0.00 39.98 2.67
589 591 0.116940 ATGGGCCAGGGTGAAACATT 59.883 50.000 13.78 0.00 39.98 2.71
590 592 0.615544 CATGGGCCAGGGTGAAACAT 60.616 55.000 13.78 0.00 39.98 2.71
591 593 1.228831 CATGGGCCAGGGTGAAACA 60.229 57.895 13.78 0.00 39.98 2.83
592 594 0.831711 AACATGGGCCAGGGTGAAAC 60.832 55.000 23.64 0.00 0.00 2.78
593 595 0.541764 GAACATGGGCCAGGGTGAAA 60.542 55.000 23.64 0.00 0.00 2.69
595 597 2.763215 GAACATGGGCCAGGGTGA 59.237 61.111 23.64 0.00 0.00 4.02
596 598 2.751436 CGAACATGGGCCAGGGTG 60.751 66.667 23.64 13.70 0.00 4.61
598 600 2.556840 ATCACGAACATGGGCCAGGG 62.557 60.000 23.64 14.65 0.00 4.45
600 602 0.677731 ACATCACGAACATGGGCCAG 60.678 55.000 13.78 6.92 0.00 4.85
601 603 0.676466 GACATCACGAACATGGGCCA 60.676 55.000 9.61 9.61 0.00 5.36
602 604 0.392998 AGACATCACGAACATGGGCC 60.393 55.000 0.00 0.00 0.00 5.80
604 606 3.861840 ACTTAGACATCACGAACATGGG 58.138 45.455 0.00 0.00 0.00 4.00
605 607 5.891451 TCTACTTAGACATCACGAACATGG 58.109 41.667 0.00 0.00 0.00 3.66
606 608 8.959058 GTTATCTACTTAGACATCACGAACATG 58.041 37.037 0.00 0.00 34.72 3.21
607 609 8.683615 TGTTATCTACTTAGACATCACGAACAT 58.316 33.333 0.00 0.00 34.72 2.71
608 610 7.966753 GTGTTATCTACTTAGACATCACGAACA 59.033 37.037 0.00 0.00 34.72 3.18
609 611 7.431668 GGTGTTATCTACTTAGACATCACGAAC 59.568 40.741 0.00 0.00 34.72 3.95
610 612 7.338703 AGGTGTTATCTACTTAGACATCACGAA 59.661 37.037 0.00 0.00 34.72 3.85
611 613 6.827251 AGGTGTTATCTACTTAGACATCACGA 59.173 38.462 0.00 0.00 34.72 4.35
612 614 7.028926 AGGTGTTATCTACTTAGACATCACG 57.971 40.000 0.00 0.00 34.72 4.35
614 616 9.470399 TGTAAGGTGTTATCTACTTAGACATCA 57.530 33.333 0.00 0.00 34.72 3.07
617 619 8.910944 GGATGTAAGGTGTTATCTACTTAGACA 58.089 37.037 0.00 0.00 34.72 3.41
622 624 9.490083 AAGTAGGATGTAAGGTGTTATCTACTT 57.510 33.333 0.00 0.00 0.00 2.24
623 625 8.915036 CAAGTAGGATGTAAGGTGTTATCTACT 58.085 37.037 0.00 0.00 0.00 2.57
626 628 7.180408 ACACAAGTAGGATGTAAGGTGTTATCT 59.820 37.037 0.00 0.00 34.89 1.98
627 629 7.328737 ACACAAGTAGGATGTAAGGTGTTATC 58.671 38.462 0.00 0.00 34.89 1.75
628 630 7.253905 ACACAAGTAGGATGTAAGGTGTTAT 57.746 36.000 0.00 0.00 34.89 1.89
629 631 6.675413 ACACAAGTAGGATGTAAGGTGTTA 57.325 37.500 0.00 0.00 34.89 2.41
630 632 5.562298 ACACAAGTAGGATGTAAGGTGTT 57.438 39.130 0.00 0.00 34.89 3.32
631 633 5.562298 AACACAAGTAGGATGTAAGGTGT 57.438 39.130 0.00 0.00 39.67 4.16
632 634 8.561738 AATTAACACAAGTAGGATGTAAGGTG 57.438 34.615 0.00 0.00 0.00 4.00
633 635 9.662947 GTAATTAACACAAGTAGGATGTAAGGT 57.337 33.333 0.00 0.00 0.00 3.50
634 636 9.886132 AGTAATTAACACAAGTAGGATGTAAGG 57.114 33.333 0.00 0.00 0.00 2.69
638 640 9.010029 CCAAAGTAATTAACACAAGTAGGATGT 57.990 33.333 0.00 0.00 0.00 3.06
639 641 9.226606 TCCAAAGTAATTAACACAAGTAGGATG 57.773 33.333 0.00 0.00 0.00 3.51
640 642 9.975218 ATCCAAAGTAATTAACACAAGTAGGAT 57.025 29.630 0.00 0.00 0.00 3.24
641 643 9.802039 AATCCAAAGTAATTAACACAAGTAGGA 57.198 29.630 0.00 0.00 0.00 2.94
646 648 8.576442 ACTCCAATCCAAAGTAATTAACACAAG 58.424 33.333 0.00 0.00 0.00 3.16
647 649 8.472007 ACTCCAATCCAAAGTAATTAACACAA 57.528 30.769 0.00 0.00 0.00 3.33
656 658 8.776470 CGTACTTTTTACTCCAATCCAAAGTAA 58.224 33.333 4.35 0.00 38.05 2.24
657 659 7.388500 CCGTACTTTTTACTCCAATCCAAAGTA 59.612 37.037 0.00 0.00 36.24 2.24
658 660 6.206048 CCGTACTTTTTACTCCAATCCAAAGT 59.794 38.462 0.00 0.00 37.95 2.66
659 661 6.428771 TCCGTACTTTTTACTCCAATCCAAAG 59.571 38.462 0.00 0.00 0.00 2.77
660 662 6.297582 TCCGTACTTTTTACTCCAATCCAAA 58.702 36.000 0.00 0.00 0.00 3.28
661 663 5.867330 TCCGTACTTTTTACTCCAATCCAA 58.133 37.500 0.00 0.00 0.00 3.53
694 696 7.864686 TCATAGAAAACACACAACAATCTCAG 58.135 34.615 0.00 0.00 0.00 3.35
707 709 2.092323 GGTGGGGCTCATAGAAAACAC 58.908 52.381 0.00 0.00 0.00 3.32
712 714 1.306654 ACGGGTGGGGCTCATAGAA 60.307 57.895 0.00 0.00 0.00 2.10
731 733 6.354794 TCCCCCACGTATCTATCTAAATTG 57.645 41.667 0.00 0.00 0.00 2.32
732 734 5.484290 CCTCCCCCACGTATCTATCTAAATT 59.516 44.000 0.00 0.00 0.00 1.82
733 735 5.024118 CCTCCCCCACGTATCTATCTAAAT 58.976 45.833 0.00 0.00 0.00 1.40
735 737 3.245514 CCCTCCCCCACGTATCTATCTAA 60.246 52.174 0.00 0.00 0.00 2.10
736 738 2.310945 CCCTCCCCCACGTATCTATCTA 59.689 54.545 0.00 0.00 0.00 1.98
738 740 1.558233 CCCTCCCCCACGTATCTATC 58.442 60.000 0.00 0.00 0.00 2.08
740 742 1.545211 CCCCTCCCCCACGTATCTA 59.455 63.158 0.00 0.00 0.00 1.98
741 743 2.285868 CCCCTCCCCCACGTATCT 59.714 66.667 0.00 0.00 0.00 1.98
742 744 2.847715 CCCCCTCCCCCACGTATC 60.848 72.222 0.00 0.00 0.00 2.24
757 759 0.989602 AACACAAGTAGCCCTACCCC 59.010 55.000 1.98 0.00 36.75 4.95
758 760 2.873094 AAACACAAGTAGCCCTACCC 57.127 50.000 1.98 0.00 36.75 3.69
779 781 1.807142 TGCACGAAGACACACACAAAA 59.193 42.857 0.00 0.00 0.00 2.44
780 782 1.129624 GTGCACGAAGACACACACAAA 59.870 47.619 0.00 0.00 37.85 2.83
781 783 0.724549 GTGCACGAAGACACACACAA 59.275 50.000 0.00 0.00 37.85 3.33
782 784 0.108377 AGTGCACGAAGACACACACA 60.108 50.000 12.01 0.00 39.71 3.72
783 785 1.787155 CTAGTGCACGAAGACACACAC 59.213 52.381 12.01 0.00 39.71 3.82
784 786 1.679153 TCTAGTGCACGAAGACACACA 59.321 47.619 17.72 0.00 39.71 3.72
785 787 2.031069 TCTCTAGTGCACGAAGACACAC 60.031 50.000 17.72 0.00 39.71 3.82
786 788 2.227194 TCTCTAGTGCACGAAGACACA 58.773 47.619 17.72 5.62 39.71 3.72
788 790 2.621526 TGTTCTCTAGTGCACGAAGACA 59.378 45.455 17.72 13.33 0.00 3.41
789 791 3.284323 TGTTCTCTAGTGCACGAAGAC 57.716 47.619 17.72 11.39 0.00 3.01
792 794 4.451096 GGAAAATGTTCTCTAGTGCACGAA 59.549 41.667 12.01 5.98 33.92 3.85
793 795 3.994392 GGAAAATGTTCTCTAGTGCACGA 59.006 43.478 12.01 5.11 33.92 4.35
795 797 4.327680 AGGGAAAATGTTCTCTAGTGCAC 58.672 43.478 9.40 9.40 43.16 4.57
796 798 4.640771 AGGGAAAATGTTCTCTAGTGCA 57.359 40.909 0.00 0.00 43.16 4.57
797 799 5.003804 TGAAGGGAAAATGTTCTCTAGTGC 58.996 41.667 0.00 0.00 44.28 4.40
831 1157 3.059188 AGGCAACGTAAAAATCACTCACG 60.059 43.478 0.00 0.00 46.39 4.35
863 1189 8.706492 ATACCATAAATGCTGTGACATTTTTG 57.294 30.769 7.70 9.72 45.63 2.44
866 1192 7.981225 GGAAATACCATAAATGCTGTGACATTT 59.019 33.333 7.55 7.55 43.71 2.32
867 1193 7.123997 TGGAAATACCATAAATGCTGTGACATT 59.876 33.333 0.00 0.00 44.64 2.71
868 1194 6.606796 TGGAAATACCATAAATGCTGTGACAT 59.393 34.615 0.00 0.00 44.64 3.06
869 1195 5.948758 TGGAAATACCATAAATGCTGTGACA 59.051 36.000 0.00 0.00 44.64 3.58
870 1196 6.449635 TGGAAATACCATAAATGCTGTGAC 57.550 37.500 0.00 0.00 44.64 3.67
979 1305 7.765695 AGGTGCCTACATGATAAAAATATGG 57.234 36.000 0.00 0.00 0.00 2.74
989 1315 7.906327 ACAAAATAAAAAGGTGCCTACATGAT 58.094 30.769 0.00 0.00 0.00 2.45
1110 1467 6.867662 TGAAAAGCAAAAACACCTCAAAAA 57.132 29.167 0.00 0.00 0.00 1.94
1112 1469 7.173907 TCAAATGAAAAGCAAAAACACCTCAAA 59.826 29.630 0.00 0.00 0.00 2.69
1113 1470 6.652481 TCAAATGAAAAGCAAAAACACCTCAA 59.348 30.769 0.00 0.00 0.00 3.02
1114 1471 6.169094 TCAAATGAAAAGCAAAAACACCTCA 58.831 32.000 0.00 0.00 0.00 3.86
1115 1472 6.238184 CCTCAAATGAAAAGCAAAAACACCTC 60.238 38.462 0.00 0.00 0.00 3.85
1116 1473 5.585844 CCTCAAATGAAAAGCAAAAACACCT 59.414 36.000 0.00 0.00 0.00 4.00
1117 1474 5.220835 CCCTCAAATGAAAAGCAAAAACACC 60.221 40.000 0.00 0.00 0.00 4.16
1118 1475 5.220835 CCCCTCAAATGAAAAGCAAAAACAC 60.221 40.000 0.00 0.00 0.00 3.32
1119 1476 4.880696 CCCCTCAAATGAAAAGCAAAAACA 59.119 37.500 0.00 0.00 0.00 2.83
1120 1477 4.881273 ACCCCTCAAATGAAAAGCAAAAAC 59.119 37.500 0.00 0.00 0.00 2.43
1123 1480 3.708631 TGACCCCTCAAATGAAAAGCAAA 59.291 39.130 0.00 0.00 0.00 3.68
1126 1483 2.029020 GGTGACCCCTCAAATGAAAAGC 60.029 50.000 0.00 0.00 0.00 3.51
1127 1484 3.230134 TGGTGACCCCTCAAATGAAAAG 58.770 45.455 0.00 0.00 0.00 2.27
1130 1487 3.230134 CTTTGGTGACCCCTCAAATGAA 58.770 45.455 0.00 0.00 31.21 2.57
1131 1488 2.176798 ACTTTGGTGACCCCTCAAATGA 59.823 45.455 0.00 0.00 31.21 2.57
1133 1490 2.091333 ACACTTTGGTGACCCCTCAAAT 60.091 45.455 0.00 0.00 45.61 2.32
1134 1491 1.286553 ACACTTTGGTGACCCCTCAAA 59.713 47.619 0.00 0.00 45.61 2.69
1252 1609 1.521450 TAGGGTTCGGCCGATCGATC 61.521 60.000 31.56 15.09 39.03 3.69
1253 1610 1.111116 TTAGGGTTCGGCCGATCGAT 61.111 55.000 31.56 20.82 39.03 3.59
1254 1611 1.753848 TTAGGGTTCGGCCGATCGA 60.754 57.895 31.56 12.17 38.44 3.59
1255 1612 1.590792 GTTAGGGTTCGGCCGATCG 60.591 63.158 31.56 8.51 38.44 3.69
1555 1912 2.428925 GGTGAAGTCGGCCCGGATA 61.429 63.158 0.73 0.00 0.00 2.59
1566 1923 3.222354 GAGTCGCCGGTGGTGAAGT 62.222 63.158 16.49 0.00 44.24 3.01
1586 1943 1.018226 ATGAAGTGCTGCTGCGACTC 61.018 55.000 16.58 10.78 43.34 3.36
1587 1944 1.004080 ATGAAGTGCTGCTGCGACT 60.004 52.632 11.21 11.97 43.34 4.18
1589 1946 0.532115 TAGATGAAGTGCTGCTGCGA 59.468 50.000 11.21 0.00 43.34 5.10
1590 1947 0.649475 GTAGATGAAGTGCTGCTGCG 59.351 55.000 11.21 0.00 43.34 5.18
1662 2019 0.179045 CTCTGCCCGGGAATAACCAG 60.179 60.000 29.31 20.83 41.20 4.00
1665 2022 0.107165 AAGCTCTGCCCGGGAATAAC 60.107 55.000 29.31 10.24 0.00 1.89
1682 2042 1.523258 CGAGGGGCAGATGCAGAAG 60.523 63.158 7.19 0.00 44.36 2.85
1689 2049 2.240162 GACGAAACCGAGGGGCAGAT 62.240 60.000 0.00 0.00 36.48 2.90
1755 2115 2.172930 TGGAGATAGTACTGCGAGTCCT 59.827 50.000 5.39 0.00 0.00 3.85
1761 2121 1.067212 GGGTGTGGAGATAGTACTGCG 59.933 57.143 5.39 0.00 0.00 5.18
1803 2163 0.250640 CAGCAGCTTCTTGGTCCACT 60.251 55.000 0.00 0.00 0.00 4.00
1808 2168 1.602888 CCTGCAGCAGCTTCTTGGT 60.603 57.895 17.81 0.00 42.74 3.67
1875 2235 2.202932 CGAGGGCGATCACCTTGG 60.203 66.667 11.33 0.00 38.79 3.61
1963 2323 4.235762 ACCAAGCGTGACACGGCT 62.236 61.111 27.86 21.33 42.82 5.52
1968 2328 2.579657 ATCGGGACCAAGCGTGACA 61.580 57.895 0.00 0.00 0.00 3.58
1971 2331 3.499737 GCATCGGGACCAAGCGTG 61.500 66.667 0.00 0.00 0.00 5.34
1972 2332 4.778143 GGCATCGGGACCAAGCGT 62.778 66.667 0.00 0.00 0.00 5.07
2013 2373 1.398390 GCAAAGATTGGCCGTAGAGTG 59.602 52.381 0.00 0.00 0.00 3.51
2074 2437 1.135373 TCCTCAAGTTCGACGCATCTC 60.135 52.381 0.00 0.00 0.00 2.75
2107 2470 0.243907 GCGGCACAGTTCTGACTCTA 59.756 55.000 6.83 0.00 32.54 2.43
2172 2535 3.928779 GCGGAGGATCGATGGCCA 61.929 66.667 8.56 8.56 34.37 5.36
2185 2548 3.634157 TTCCCCATCCTCCTGCGGA 62.634 63.158 0.00 0.00 37.50 5.54
2188 2551 0.849417 ATTCTTCCCCATCCTCCTGC 59.151 55.000 0.00 0.00 0.00 4.85
2212 2575 1.966451 GAGCCTCCAACCAACGGTG 60.966 63.158 0.00 0.00 35.34 4.94
2214 2577 1.002134 ATGAGCCTCCAACCAACGG 60.002 57.895 0.00 0.00 0.00 4.44
2280 2643 1.587547 GAGCTCATCGGAATGAACCC 58.412 55.000 9.40 0.00 41.33 4.11
2304 2667 0.033011 TCCTAGCTGAGGGGAGACAC 60.033 60.000 0.00 0.00 46.70 3.67
2426 2798 3.210012 ATGCAGTTGGGTCCCGCTT 62.210 57.895 2.65 0.00 0.00 4.68
2691 3071 0.250727 AGTTTCGTGGGGTGTGATGG 60.251 55.000 0.00 0.00 0.00 3.51
2748 3128 7.172190 TCAACATTTCAGACTTCAGATTCTGTC 59.828 37.037 13.23 4.35 40.25 3.51
2867 3266 5.346822 ACGCTACCAAACTTACTCGTAAATG 59.653 40.000 0.00 0.00 0.00 2.32
2871 3270 3.501828 TCACGCTACCAAACTTACTCGTA 59.498 43.478 0.00 0.00 0.00 3.43
2873 3272 2.915463 CTCACGCTACCAAACTTACTCG 59.085 50.000 0.00 0.00 0.00 4.18
2905 3304 4.744137 CGATTCTAGAAATGTCAGGCTCAG 59.256 45.833 9.71 0.00 0.00 3.35
2940 3339 8.567948 ACAAATGACGAAACTTCATGACTAATT 58.432 29.630 0.00 0.00 33.84 1.40
2941 3340 8.099364 ACAAATGACGAAACTTCATGACTAAT 57.901 30.769 0.00 0.00 33.84 1.73
2942 3341 7.490962 ACAAATGACGAAACTTCATGACTAA 57.509 32.000 0.00 0.00 33.84 2.24
2943 3342 7.351981 CAACAAATGACGAAACTTCATGACTA 58.648 34.615 0.00 0.00 33.84 2.59
2944 3343 6.201517 CAACAAATGACGAAACTTCATGACT 58.798 36.000 0.00 0.00 33.84 3.41
2958 3357 8.437742 CAATCAATCTAAAAGCCAACAAATGAC 58.562 33.333 0.00 0.00 0.00 3.06
2985 3384 8.017418 TGACAATGAAATTAACAGTTTCCCTT 57.983 30.769 0.00 0.00 32.46 3.95
2986 3385 7.595819 TGACAATGAAATTAACAGTTTCCCT 57.404 32.000 0.00 0.00 32.46 4.20
2987 3386 8.655651 TTTGACAATGAAATTAACAGTTTCCC 57.344 30.769 0.00 0.00 32.46 3.97
3057 3456 8.190784 AGAAATATAAAGGAAAGCCAATGAACG 58.809 33.333 0.00 0.00 36.29 3.95
3104 3503 6.584185 TCCCAAAGAAAGCTTAACCATTAC 57.416 37.500 0.00 0.00 32.98 1.89
3135 3534 7.096023 CGGATTAATATCAGAGTTCAAAGACCG 60.096 40.741 0.00 0.00 32.09 4.79
3155 3554 3.649073 CATGCACGGATTAGACGGATTA 58.351 45.455 0.00 0.00 35.23 1.75
3242 3646 6.267928 GGAGAACTCTTAGCCCACATTAGATA 59.732 42.308 1.86 0.00 0.00 1.98
3246 3650 4.162320 CAGGAGAACTCTTAGCCCACATTA 59.838 45.833 1.86 0.00 0.00 1.90
3253 3657 1.276421 TGTGCAGGAGAACTCTTAGCC 59.724 52.381 0.00 0.00 0.00 3.93
3309 3713 1.680555 GGTCATGCAACCCCATCGTTA 60.681 52.381 0.00 0.00 32.82 3.18
3312 3716 1.077501 AGGTCATGCAACCCCATCG 60.078 57.895 3.86 0.00 40.42 3.84
3364 3768 1.448365 CTACGATGCCAGCACTGCA 60.448 57.895 3.30 0.00 43.97 4.41
3447 3851 4.054671 CGAGCATATTCTTCCTCCTCAAC 58.945 47.826 0.00 0.00 0.00 3.18
3448 3852 3.706594 ACGAGCATATTCTTCCTCCTCAA 59.293 43.478 0.00 0.00 0.00 3.02
3450 3854 4.038642 AGAACGAGCATATTCTTCCTCCTC 59.961 45.833 0.00 0.00 30.88 3.71
3451 3855 3.964031 AGAACGAGCATATTCTTCCTCCT 59.036 43.478 0.00 0.00 30.88 3.69
3452 3856 4.329462 AGAACGAGCATATTCTTCCTCC 57.671 45.455 0.00 0.00 30.88 4.30
3454 3858 5.586643 GGAAAAGAACGAGCATATTCTTCCT 59.413 40.000 8.89 1.95 42.89 3.36
3514 3918 1.813513 AGAATCAGCGTCACCAAAGG 58.186 50.000 0.00 0.00 0.00 3.11
3559 3963 0.313672 GCAGGTCCATGTCGCAAAAA 59.686 50.000 0.00 0.00 0.00 1.94
3610 4014 7.976175 TGCACACAACAAAATTTACATGAGTAA 59.024 29.630 0.00 0.00 38.40 2.24
3665 4072 7.315142 CAACAATTGTAGTTGGACTGCATAAT 58.685 34.615 12.39 0.00 40.42 1.28
3668 4075 5.125100 CAACAATTGTAGTTGGACTGCAT 57.875 39.130 12.39 0.00 40.42 3.96
3779 4186 0.110373 GCCGCGCGGGATAATTTAAG 60.110 55.000 45.81 19.65 38.47 1.85
3780 4187 1.508808 GGCCGCGCGGGATAATTTAA 61.509 55.000 45.81 0.00 38.47 1.52
3808 4215 3.698263 AACCCTAGGAGCGGGGGAG 62.698 68.421 11.48 0.00 46.40 4.30
3810 4217 2.691252 AAACCCTAGGAGCGGGGG 60.691 66.667 11.48 0.00 46.40 5.40
3811 4218 2.743179 GGAAACCCTAGGAGCGGGG 61.743 68.421 11.48 0.00 46.40 5.73
3902 7262 2.042435 AGCGGGAGGAGGAAGGAG 60.042 66.667 0.00 0.00 0.00 3.69
3903 7263 2.042843 GAGCGGGAGGAGGAAGGA 60.043 66.667 0.00 0.00 0.00 3.36
3904 7264 3.157949 GGAGCGGGAGGAGGAAGG 61.158 72.222 0.00 0.00 0.00 3.46
3905 7265 3.157949 GGGAGCGGGAGGAGGAAG 61.158 72.222 0.00 0.00 0.00 3.46
3908 7268 4.806339 AAGGGGAGCGGGAGGAGG 62.806 72.222 0.00 0.00 0.00 4.30
3909 7269 3.157949 GAAGGGGAGCGGGAGGAG 61.158 72.222 0.00 0.00 0.00 3.69
3910 7270 3.680920 GAGAAGGGGAGCGGGAGGA 62.681 68.421 0.00 0.00 0.00 3.71
3911 7271 3.157949 GAGAAGGGGAGCGGGAGG 61.158 72.222 0.00 0.00 0.00 4.30
3912 7272 3.157949 GGAGAAGGGGAGCGGGAG 61.158 72.222 0.00 0.00 0.00 4.30
3914 7274 3.157949 GAGGAGAAGGGGAGCGGG 61.158 72.222 0.00 0.00 0.00 6.13
3915 7275 3.157949 GGAGGAGAAGGGGAGCGG 61.158 72.222 0.00 0.00 0.00 5.52
3916 7276 2.364317 TGGAGGAGAAGGGGAGCG 60.364 66.667 0.00 0.00 0.00 5.03
3917 7277 2.726351 CGTGGAGGAGAAGGGGAGC 61.726 68.421 0.00 0.00 0.00 4.70
3918 7278 2.726351 GCGTGGAGGAGAAGGGGAG 61.726 68.421 0.00 0.00 0.00 4.30
3919 7279 2.683933 GCGTGGAGGAGAAGGGGA 60.684 66.667 0.00 0.00 0.00 4.81
3920 7280 3.787001 GGCGTGGAGGAGAAGGGG 61.787 72.222 0.00 0.00 0.00 4.79
3981 7341 2.336809 GAGATGCGCGGAGGTAGG 59.663 66.667 8.83 0.00 0.00 3.18
3982 7342 2.336809 GGAGATGCGCGGAGGTAG 59.663 66.667 8.83 0.00 0.00 3.18
3983 7343 2.441348 TGGAGATGCGCGGAGGTA 60.441 61.111 8.83 0.00 0.00 3.08
3984 7344 3.842923 CTGGAGATGCGCGGAGGT 61.843 66.667 8.83 0.00 0.00 3.85
3990 7350 4.925861 GAGGGGCTGGAGATGCGC 62.926 72.222 0.00 0.00 41.70 6.09
3991 7351 4.247380 GGAGGGGCTGGAGATGCG 62.247 72.222 0.00 0.00 0.00 4.73
3992 7352 3.883549 GGGAGGGGCTGGAGATGC 61.884 72.222 0.00 0.00 0.00 3.91
3993 7353 3.174265 GGGGAGGGGCTGGAGATG 61.174 72.222 0.00 0.00 0.00 2.90
4126 7486 4.699522 GACCAGCACCACCGGACC 62.700 72.222 9.46 0.00 0.00 4.46
4165 7525 3.630289 CCAGAAGGGACCCTACGG 58.370 66.667 15.29 10.97 40.01 4.02
4175 7535 4.730487 CTGCAAGGACCCAGAAGG 57.270 61.111 0.00 0.00 43.78 3.46
4186 7546 3.058160 CCGGAGCCAACCTGCAAG 61.058 66.667 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.