Multiple sequence alignment - TraesCS2B01G627400

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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 TraesCS2B01G627400 chr2B 100.000 3911 0 0 1 3911 799287887 799291797 0.000000e+00 7223.0
1 TraesCS2B01G627400 chr2B 79.962 1043 170 28 1897 2915 799360076 799359049 0.000000e+00 732.0
2 TraesCS2B01G627400 chr2B 94.920 374 19 0 1331 1704 799969529 799969902 1.570000e-163 586.0
3 TraesCS2B01G627400 chr2B 74.639 1108 213 44 1844 2929 799255043 799256104 1.000000e-115 427.0
4 TraesCS2B01G627400 chr2B 76.471 850 125 37 871 1702 799258678 799259470 3.660000e-105 392.0
5 TraesCS2B01G627400 chr2B 79.469 565 88 17 1 558 799353157 799353700 3.690000e-100 375.0
6 TraesCS2B01G627400 chr2B 78.519 405 63 16 1323 1720 799254570 799254957 1.090000e-60 244.0
7 TraesCS2B01G627400 chrUn 98.253 1202 19 2 1711 2912 183018822 183017623 0.000000e+00 2102.0
8 TraesCS2B01G627400 chrUn 97.343 1016 23 2 2898 3911 183017456 183016443 0.000000e+00 1724.0
9 TraesCS2B01G627400 chrUn 96.572 671 21 1 3243 3911 327340392 327341062 0.000000e+00 1110.0
10 TraesCS2B01G627400 chr2D 92.571 875 44 11 925 1795 597826528 597825671 0.000000e+00 1236.0
11 TraesCS2B01G627400 chr2D 87.681 966 58 28 830 1795 641882092 641881188 0.000000e+00 1068.0
12 TraesCS2B01G627400 chr2D 93.978 548 25 2 1 548 642414919 642414380 0.000000e+00 822.0
13 TraesCS2B01G627400 chr2D 79.559 1042 177 25 1897 2915 642252538 642251510 0.000000e+00 712.0
14 TraesCS2B01G627400 chr2D 78.195 1064 176 32 1897 2915 598374502 598373450 2.560000e-176 628.0
15 TraesCS2B01G627400 chr2D 78.454 970 153 31 855 1795 642442289 642441347 2.030000e-162 582.0
16 TraesCS2B01G627400 chr2D 77.766 958 140 45 871 1795 642478962 642478045 4.480000e-144 521.0
17 TraesCS2B01G627400 chr2D 95.668 277 10 1 1901 2175 641881145 641880869 9.970000e-121 444.0
18 TraesCS2B01G627400 chr2D 96.578 263 9 0 1901 2163 597825628 597825366 1.670000e-118 436.0
19 TraesCS2B01G627400 chr2D 82.839 472 64 11 1 465 642241201 642241662 1.310000e-109 407.0
20 TraesCS2B01G627400 chr2D 85.263 380 46 6 1331 1707 597896224 597895852 2.200000e-102 383.0
21 TraesCS2B01G627400 chr2D 84.518 394 51 6 1331 1721 641950144 641949758 7.930000e-102 381.0
22 TraesCS2B01G627400 chr2D 75.429 350 69 14 144 483 642933452 642933110 1.880000e-33 154.0
23 TraesCS2B01G627400 chr2A 88.652 987 73 15 830 1795 766849104 766848136 0.000000e+00 1166.0
24 TraesCS2B01G627400 chr2A 88.229 977 49 27 2940 3911 767511691 767512606 0.000000e+00 1107.0
25 TraesCS2B01G627400 chr2A 91.074 661 27 9 1 639 767559589 767558939 0.000000e+00 865.0
26 TraesCS2B01G627400 chr2A 79.769 1038 175 25 1897 2912 767131492 767132516 0.000000e+00 721.0
27 TraesCS2B01G627400 chr2A 81.658 567 78 15 1 560 767137675 767137128 7.710000e-122 448.0
28 TraesCS2B01G627400 chr2A 94.946 277 12 2 1901 2175 766848093 766847817 2.160000e-117 433.0
29 TraesCS2B01G627400 chr2A 94.737 133 7 0 1096 1228 767463301 767463433 1.420000e-49 207.0
30 TraesCS2B01G627400 chr2A 78.201 289 58 4 1844 2131 762497522 762497806 3.100000e-41 180.0
31 TraesCS2B01G627400 chr2A 96.053 76 3 0 2881 2956 767489344 767489419 1.480000e-24 124.0
32 TraesCS2B01G627400 chr2A 97.143 35 1 0 1824 1858 766848128 766848094 4.220000e-05 60.2


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 TraesCS2B01G627400 chr2B 799287887 799291797 3910 False 7223.000000 7223 100.000000 1 3911 1 chr2B.!!$F1 3910
1 TraesCS2B01G627400 chr2B 799359049 799360076 1027 True 732.000000 732 79.962000 1897 2915 1 chr2B.!!$R1 1018
2 TraesCS2B01G627400 chr2B 799353157 799353700 543 False 375.000000 375 79.469000 1 558 1 chr2B.!!$F2 557
3 TraesCS2B01G627400 chr2B 799254570 799259470 4900 False 354.333333 427 76.543000 871 2929 3 chr2B.!!$F4 2058
4 TraesCS2B01G627400 chrUn 183016443 183018822 2379 True 1913.000000 2102 97.798000 1711 3911 2 chrUn.!!$R1 2200
5 TraesCS2B01G627400 chrUn 327340392 327341062 670 False 1110.000000 1110 96.572000 3243 3911 1 chrUn.!!$F1 668
6 TraesCS2B01G627400 chr2D 597825366 597826528 1162 True 836.000000 1236 94.574500 925 2163 2 chr2D.!!$R9 1238
7 TraesCS2B01G627400 chr2D 642414380 642414919 539 True 822.000000 822 93.978000 1 548 1 chr2D.!!$R5 547
8 TraesCS2B01G627400 chr2D 641880869 641882092 1223 True 756.000000 1068 91.674500 830 2175 2 chr2D.!!$R10 1345
9 TraesCS2B01G627400 chr2D 642251510 642252538 1028 True 712.000000 712 79.559000 1897 2915 1 chr2D.!!$R4 1018
10 TraesCS2B01G627400 chr2D 598373450 598374502 1052 True 628.000000 628 78.195000 1897 2915 1 chr2D.!!$R2 1018
11 TraesCS2B01G627400 chr2D 642441347 642442289 942 True 582.000000 582 78.454000 855 1795 1 chr2D.!!$R6 940
12 TraesCS2B01G627400 chr2D 642478045 642478962 917 True 521.000000 521 77.766000 871 1795 1 chr2D.!!$R7 924
13 TraesCS2B01G627400 chr2A 767511691 767512606 915 False 1107.000000 1107 88.229000 2940 3911 1 chr2A.!!$F5 971
14 TraesCS2B01G627400 chr2A 767558939 767559589 650 True 865.000000 865 91.074000 1 639 1 chr2A.!!$R2 638
15 TraesCS2B01G627400 chr2A 767131492 767132516 1024 False 721.000000 721 79.769000 1897 2912 1 chr2A.!!$F2 1015
16 TraesCS2B01G627400 chr2A 766847817 766849104 1287 True 553.066667 1166 93.580333 830 2175 3 chr2A.!!$R3 1345
17 TraesCS2B01G627400 chr2A 767137128 767137675 547 True 448.000000 448 81.658000 1 560 1 chr2A.!!$R1 559

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
822 841 0.036010 AAATCCACGTCCTCCTGCTG 60.036 55.000 0.0 0.0 0.00 4.41 F
1029 1051 0.250234 ACACATCATCGGTCCCTGTG 59.750 55.000 0.0 0.0 42.19 3.66 F
2110 2203 1.200252 CTTCTCTTCGCTCGGTCAAGA 59.800 52.381 0.0 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 1974 0.184933 TGCAGCACCAAAGGTAAGGT 59.815 50.000 0.0 0.0 39.1 3.50 R
2759 2917 2.109425 AGGGAAGTAAACATGACCGC 57.891 50.000 0.0 0.0 0.0 5.68 R
3698 6316 2.602267 TGGTGGTGGGACGACGAT 60.602 61.111 0.0 0.0 0.0 3.73 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
82 83 8.352137 TGAGAATTAGATTTGCCTGAATTTGA 57.648 30.769 0.00 0.00 0.00 2.69
496 515 2.157668 CCATGTCTGTTTTCGAAGTCGG 59.842 50.000 0.00 1.17 40.29 4.79
503 522 4.735132 TTCGAAGTCGGCGCCCTG 62.735 66.667 23.46 8.15 40.29 4.45
534 553 0.969894 CGTCTCTTCTCCCCAACACT 59.030 55.000 0.00 0.00 0.00 3.55
581 600 4.873746 GCCTAGGGCTTTTTCTTTTTCT 57.126 40.909 11.72 0.00 46.69 2.52
582 601 5.215252 GCCTAGGGCTTTTTCTTTTTCTT 57.785 39.130 11.72 0.00 46.69 2.52
583 602 5.611374 GCCTAGGGCTTTTTCTTTTTCTTT 58.389 37.500 11.72 0.00 46.69 2.52
584 603 6.055588 GCCTAGGGCTTTTTCTTTTTCTTTT 58.944 36.000 11.72 0.00 46.69 2.27
585 604 6.542370 GCCTAGGGCTTTTTCTTTTTCTTTTT 59.458 34.615 11.72 0.00 46.69 1.94
586 605 7.713507 GCCTAGGGCTTTTTCTTTTTCTTTTTA 59.286 33.333 11.72 0.00 46.69 1.52
587 606 9.778741 CCTAGGGCTTTTTCTTTTTCTTTTTAT 57.221 29.630 0.00 0.00 0.00 1.40
590 609 9.778741 AGGGCTTTTTCTTTTTCTTTTTATAGG 57.221 29.630 0.00 0.00 0.00 2.57
591 610 9.772973 GGGCTTTTTCTTTTTCTTTTTATAGGA 57.227 29.630 0.00 0.00 0.00 2.94
602 621 9.475620 TTTTCTTTTTATAGGATCTCCCTTTCC 57.524 33.333 0.00 0.00 44.85 3.13
603 622 6.827727 TCTTTTTATAGGATCTCCCTTTCCG 58.172 40.000 0.00 0.00 44.85 4.30
604 623 4.618920 TTTATAGGATCTCCCTTTCCGC 57.381 45.455 0.00 0.00 44.85 5.54
605 624 1.353091 ATAGGATCTCCCTTTCCGCC 58.647 55.000 0.00 0.00 44.85 6.13
606 625 1.113517 TAGGATCTCCCTTTCCGCCG 61.114 60.000 0.00 0.00 44.85 6.46
607 626 2.589159 GATCTCCCTTTCCGCCGC 60.589 66.667 0.00 0.00 0.00 6.53
608 627 4.176752 ATCTCCCTTTCCGCCGCC 62.177 66.667 0.00 0.00 0.00 6.13
619 638 3.760035 CGCCGCCGCCTAGGATAT 61.760 66.667 14.75 0.00 45.00 1.63
620 639 2.125512 GCCGCCGCCTAGGATATG 60.126 66.667 14.75 0.00 45.00 1.78
621 640 2.646175 GCCGCCGCCTAGGATATGA 61.646 63.158 14.75 0.00 45.00 2.15
622 641 1.513158 CCGCCGCCTAGGATATGAG 59.487 63.158 14.75 0.00 45.00 2.90
623 642 1.153745 CGCCGCCTAGGATATGAGC 60.154 63.158 14.75 4.05 45.00 4.26
624 643 1.599606 CGCCGCCTAGGATATGAGCT 61.600 60.000 14.75 0.00 45.00 4.09
625 644 0.174617 GCCGCCTAGGATATGAGCTC 59.825 60.000 14.75 6.82 45.00 4.09
626 645 0.820871 CCGCCTAGGATATGAGCTCC 59.179 60.000 14.75 0.00 45.00 4.70
627 646 0.453793 CGCCTAGGATATGAGCTCCG 59.546 60.000 14.75 0.00 37.88 4.63
628 647 0.174617 GCCTAGGATATGAGCTCCGC 59.825 60.000 14.75 0.00 37.88 5.54
629 648 1.846007 CCTAGGATATGAGCTCCGCT 58.154 55.000 12.15 0.00 43.88 5.52
630 649 2.946341 GCCTAGGATATGAGCTCCGCTA 60.946 54.545 14.75 0.55 39.88 4.26
631 650 3.561143 CCTAGGATATGAGCTCCGCTAT 58.439 50.000 12.15 5.79 39.88 2.97
632 651 3.568007 CCTAGGATATGAGCTCCGCTATC 59.432 52.174 12.15 13.94 39.88 2.08
633 652 3.380471 AGGATATGAGCTCCGCTATCT 57.620 47.619 12.15 0.00 39.88 1.98
634 653 3.023119 AGGATATGAGCTCCGCTATCTG 58.977 50.000 12.15 0.00 39.88 2.90
635 654 3.020274 GGATATGAGCTCCGCTATCTGA 58.980 50.000 12.15 0.00 39.88 3.27
636 655 3.066621 GGATATGAGCTCCGCTATCTGAG 59.933 52.174 12.15 0.00 39.88 3.35
637 656 1.993956 ATGAGCTCCGCTATCTGAGT 58.006 50.000 12.15 0.00 39.88 3.41
638 657 1.313772 TGAGCTCCGCTATCTGAGTC 58.686 55.000 12.15 0.00 39.88 3.36
639 658 0.596082 GAGCTCCGCTATCTGAGTCC 59.404 60.000 0.87 0.00 39.88 3.85
640 659 1.169661 AGCTCCGCTATCTGAGTCCG 61.170 60.000 0.00 0.00 36.99 4.79
641 660 1.448922 GCTCCGCTATCTGAGTCCGT 61.449 60.000 0.00 0.00 0.00 4.69
642 661 0.589223 CTCCGCTATCTGAGTCCGTC 59.411 60.000 0.00 0.00 0.00 4.79
643 662 0.180642 TCCGCTATCTGAGTCCGTCT 59.819 55.000 0.00 0.00 0.00 4.18
644 663 0.589223 CCGCTATCTGAGTCCGTCTC 59.411 60.000 0.00 0.00 43.03 3.36
645 664 0.589223 CGCTATCTGAGTCCGTCTCC 59.411 60.000 3.10 0.00 42.12 3.71
646 665 1.681538 GCTATCTGAGTCCGTCTCCA 58.318 55.000 3.10 0.00 42.12 3.86
647 666 2.235016 GCTATCTGAGTCCGTCTCCAT 58.765 52.381 3.10 0.00 42.12 3.41
648 667 2.227865 GCTATCTGAGTCCGTCTCCATC 59.772 54.545 3.10 0.00 42.12 3.51
649 668 2.746279 ATCTGAGTCCGTCTCCATCT 57.254 50.000 3.10 0.00 42.12 2.90
650 669 3.866703 ATCTGAGTCCGTCTCCATCTA 57.133 47.619 3.10 0.00 42.12 1.98
651 670 3.866703 TCTGAGTCCGTCTCCATCTAT 57.133 47.619 3.10 0.00 42.12 1.98
652 671 3.481453 TCTGAGTCCGTCTCCATCTATG 58.519 50.000 3.10 0.00 42.12 2.23
653 672 3.117851 TCTGAGTCCGTCTCCATCTATGT 60.118 47.826 3.10 0.00 42.12 2.29
654 673 3.215151 TGAGTCCGTCTCCATCTATGTC 58.785 50.000 3.10 0.00 42.12 3.06
655 674 3.117851 TGAGTCCGTCTCCATCTATGTCT 60.118 47.826 3.10 0.00 42.12 3.41
656 675 3.482436 AGTCCGTCTCCATCTATGTCTC 58.518 50.000 0.00 0.00 0.00 3.36
657 676 2.554893 GTCCGTCTCCATCTATGTCTCC 59.445 54.545 0.00 0.00 0.00 3.71
658 677 1.537638 CCGTCTCCATCTATGTCTCCG 59.462 57.143 0.00 0.00 0.00 4.63
659 678 1.068885 CGTCTCCATCTATGTCTCCGC 60.069 57.143 0.00 0.00 0.00 5.54
660 679 1.271102 GTCTCCATCTATGTCTCCGCC 59.729 57.143 0.00 0.00 0.00 6.13
661 680 0.242286 CTCCATCTATGTCTCCGCCG 59.758 60.000 0.00 0.00 0.00 6.46
662 681 1.373497 CCATCTATGTCTCCGCCGC 60.373 63.158 0.00 0.00 0.00 6.53
663 682 1.373497 CATCTATGTCTCCGCCGCC 60.373 63.158 0.00 0.00 0.00 6.13
664 683 2.920645 ATCTATGTCTCCGCCGCCG 61.921 63.158 0.00 0.00 0.00 6.46
678 697 3.056328 GCCGCCGCCTTCTTCTTT 61.056 61.111 0.00 0.00 0.00 2.52
679 698 2.870372 CCGCCGCCTTCTTCTTTG 59.130 61.111 0.00 0.00 0.00 2.77
680 699 1.671054 CCGCCGCCTTCTTCTTTGA 60.671 57.895 0.00 0.00 0.00 2.69
681 700 1.497722 CGCCGCCTTCTTCTTTGAC 59.502 57.895 0.00 0.00 0.00 3.18
682 701 1.876664 GCCGCCTTCTTCTTTGACC 59.123 57.895 0.00 0.00 0.00 4.02
683 702 1.912371 GCCGCCTTCTTCTTTGACCG 61.912 60.000 0.00 0.00 0.00 4.79
684 703 0.320421 CCGCCTTCTTCTTTGACCGA 60.320 55.000 0.00 0.00 0.00 4.69
685 704 1.508632 CGCCTTCTTCTTTGACCGAA 58.491 50.000 0.00 0.00 0.00 4.30
686 705 1.871039 CGCCTTCTTCTTTGACCGAAA 59.129 47.619 0.00 0.00 0.00 3.46
687 706 2.349532 CGCCTTCTTCTTTGACCGAAAC 60.350 50.000 0.00 0.00 0.00 2.78
688 707 2.031069 GCCTTCTTCTTTGACCGAAACC 60.031 50.000 0.00 0.00 0.00 3.27
689 708 3.211045 CCTTCTTCTTTGACCGAAACCA 58.789 45.455 0.00 0.00 0.00 3.67
690 709 3.251004 CCTTCTTCTTTGACCGAAACCAG 59.749 47.826 0.00 0.00 0.00 4.00
691 710 2.218603 TCTTCTTTGACCGAAACCAGC 58.781 47.619 0.00 0.00 0.00 4.85
692 711 1.946768 CTTCTTTGACCGAAACCAGCA 59.053 47.619 0.00 0.00 0.00 4.41
693 712 1.593196 TCTTTGACCGAAACCAGCAG 58.407 50.000 0.00 0.00 0.00 4.24
694 713 1.134220 TCTTTGACCGAAACCAGCAGT 60.134 47.619 0.00 0.00 0.00 4.40
695 714 1.676006 CTTTGACCGAAACCAGCAGTT 59.324 47.619 0.00 0.00 41.81 3.16
714 733 7.608974 GCAGTTTGCGTAATATAATGGAAAG 57.391 36.000 0.00 0.00 31.71 2.62
715 734 6.636850 GCAGTTTGCGTAATATAATGGAAAGG 59.363 38.462 0.00 0.00 31.71 3.11
716 735 7.138736 CAGTTTGCGTAATATAATGGAAAGGG 58.861 38.462 0.00 0.00 0.00 3.95
717 736 5.699097 TTGCGTAATATAATGGAAAGGGC 57.301 39.130 0.00 0.00 0.00 5.19
718 737 4.720046 TGCGTAATATAATGGAAAGGGCA 58.280 39.130 0.00 0.00 0.00 5.36
719 738 4.517453 TGCGTAATATAATGGAAAGGGCAC 59.483 41.667 0.00 0.00 0.00 5.01
720 739 4.378046 GCGTAATATAATGGAAAGGGCACG 60.378 45.833 0.00 0.00 0.00 5.34
721 740 4.153475 CGTAATATAATGGAAAGGGCACGG 59.847 45.833 0.00 0.00 0.00 4.94
722 741 1.975660 TATAATGGAAAGGGCACGGC 58.024 50.000 0.00 0.00 0.00 5.68
723 742 1.101049 ATAATGGAAAGGGCACGGCG 61.101 55.000 4.80 4.80 0.00 6.46
724 743 2.472414 TAATGGAAAGGGCACGGCGT 62.472 55.000 6.77 6.77 0.00 5.68
733 752 4.148825 GCACGGCGTGGAGAGGAT 62.149 66.667 37.33 0.00 33.64 3.24
734 753 2.105128 CACGGCGTGGAGAGGATC 59.895 66.667 31.19 0.00 0.00 3.36
735 754 3.518998 ACGGCGTGGAGAGGATCG 61.519 66.667 13.76 0.00 42.67 3.69
736 755 4.933064 CGGCGTGGAGAGGATCGC 62.933 72.222 0.00 0.00 46.42 4.58
737 756 3.532155 GGCGTGGAGAGGATCGCT 61.532 66.667 8.18 0.00 46.37 4.93
738 757 2.496817 GCGTGGAGAGGATCGCTT 59.503 61.111 0.00 0.00 44.28 4.68
739 758 1.734137 GCGTGGAGAGGATCGCTTA 59.266 57.895 0.00 0.00 44.28 3.09
740 759 0.315568 GCGTGGAGAGGATCGCTTAT 59.684 55.000 0.00 0.00 44.28 1.73
741 760 1.269831 GCGTGGAGAGGATCGCTTATT 60.270 52.381 0.00 0.00 44.28 1.40
742 761 2.030185 GCGTGGAGAGGATCGCTTATTA 60.030 50.000 0.00 0.00 44.28 0.98
743 762 3.827625 CGTGGAGAGGATCGCTTATTAG 58.172 50.000 0.00 0.00 42.67 1.73
744 763 3.253677 CGTGGAGAGGATCGCTTATTAGT 59.746 47.826 0.00 0.00 42.67 2.24
745 764 4.551388 GTGGAGAGGATCGCTTATTAGTG 58.449 47.826 0.00 0.00 42.67 2.74
746 765 3.005897 TGGAGAGGATCGCTTATTAGTGC 59.994 47.826 0.00 0.00 42.67 4.40
747 766 3.257127 GGAGAGGATCGCTTATTAGTGCT 59.743 47.826 0.00 0.00 42.67 4.40
748 767 4.481463 GAGAGGATCGCTTATTAGTGCTC 58.519 47.826 0.00 0.00 42.67 4.26
749 768 3.057876 AGAGGATCGCTTATTAGTGCTCG 60.058 47.826 0.00 0.00 42.67 5.03
750 769 1.721926 GGATCGCTTATTAGTGCTCGC 59.278 52.381 0.00 0.00 29.81 5.03
751 770 1.383744 GATCGCTTATTAGTGCTCGCG 59.616 52.381 0.00 0.00 41.69 5.87
752 771 0.379316 TCGCTTATTAGTGCTCGCGA 59.621 50.000 9.26 9.26 45.96 5.87
753 772 0.498927 CGCTTATTAGTGCTCGCGAC 59.501 55.000 3.71 2.83 42.82 5.19
754 773 0.498927 GCTTATTAGTGCTCGCGACG 59.501 55.000 3.71 2.50 0.00 5.12
755 774 1.121240 CTTATTAGTGCTCGCGACGG 58.879 55.000 3.71 0.00 0.00 4.79
756 775 0.734309 TTATTAGTGCTCGCGACGGA 59.266 50.000 3.71 0.00 0.00 4.69
757 776 0.734309 TATTAGTGCTCGCGACGGAA 59.266 50.000 3.71 0.00 0.00 4.30
758 777 0.108992 ATTAGTGCTCGCGACGGAAA 60.109 50.000 3.71 0.00 0.00 3.13
759 778 1.005294 TTAGTGCTCGCGACGGAAAC 61.005 55.000 3.71 0.00 0.00 2.78
760 779 1.859427 TAGTGCTCGCGACGGAAACT 61.859 55.000 3.71 7.16 0.00 2.66
761 780 2.733218 TGCTCGCGACGGAAACTG 60.733 61.111 3.71 0.00 0.00 3.16
762 781 2.733593 GCTCGCGACGGAAACTGT 60.734 61.111 3.71 0.00 0.00 3.55
763 782 2.717809 GCTCGCGACGGAAACTGTC 61.718 63.158 3.71 0.00 0.00 3.51
764 783 1.081376 CTCGCGACGGAAACTGTCT 60.081 57.895 3.71 0.00 33.60 3.41
765 784 0.167470 CTCGCGACGGAAACTGTCTA 59.833 55.000 3.71 0.00 33.60 2.59
766 785 0.592637 TCGCGACGGAAACTGTCTAA 59.407 50.000 3.71 0.00 33.60 2.10
767 786 1.001487 TCGCGACGGAAACTGTCTAAA 60.001 47.619 3.71 0.00 33.60 1.85
768 787 1.123756 CGCGACGGAAACTGTCTAAAC 59.876 52.381 0.00 0.00 33.60 2.01
769 788 2.401351 GCGACGGAAACTGTCTAAACT 58.599 47.619 8.69 0.00 33.60 2.66
770 789 2.155155 GCGACGGAAACTGTCTAAACTG 59.845 50.000 8.69 0.00 33.60 3.16
771 790 3.635331 CGACGGAAACTGTCTAAACTGA 58.365 45.455 8.69 0.00 33.60 3.41
772 791 4.046462 CGACGGAAACTGTCTAAACTGAA 58.954 43.478 8.69 0.00 33.60 3.02
773 792 4.505191 CGACGGAAACTGTCTAAACTGAAA 59.495 41.667 8.69 0.00 33.60 2.69
774 793 5.555818 CGACGGAAACTGTCTAAACTGAAAC 60.556 44.000 8.69 0.00 33.60 2.78
775 794 5.180271 ACGGAAACTGTCTAAACTGAAACA 58.820 37.500 0.00 0.00 0.00 2.83
776 795 5.064325 ACGGAAACTGTCTAAACTGAAACAC 59.936 40.000 0.00 0.00 0.00 3.32
777 796 5.064198 CGGAAACTGTCTAAACTGAAACACA 59.936 40.000 0.00 0.00 0.00 3.72
788 807 2.654749 TGAAACACAGATCGCTCGAT 57.345 45.000 4.26 4.26 37.59 3.59
796 815 2.789813 GATCGCTCGATCGTCCAAG 58.210 57.895 15.94 6.07 41.09 3.61
797 816 1.272114 GATCGCTCGATCGTCCAAGC 61.272 60.000 15.94 15.18 41.09 4.01
798 817 1.729470 ATCGCTCGATCGTCCAAGCT 61.729 55.000 20.15 4.24 32.55 3.74
799 818 1.941734 CGCTCGATCGTCCAAGCTC 60.942 63.158 20.15 0.00 32.55 4.09
800 819 1.435515 GCTCGATCGTCCAAGCTCT 59.564 57.895 15.94 0.00 0.00 4.09
801 820 0.663688 GCTCGATCGTCCAAGCTCTA 59.336 55.000 15.94 0.00 0.00 2.43
802 821 1.065701 GCTCGATCGTCCAAGCTCTAA 59.934 52.381 15.94 0.00 0.00 2.10
803 822 2.479730 GCTCGATCGTCCAAGCTCTAAA 60.480 50.000 15.94 0.00 0.00 1.85
804 823 3.770666 CTCGATCGTCCAAGCTCTAAAA 58.229 45.455 15.94 0.00 0.00 1.52
805 824 4.174009 CTCGATCGTCCAAGCTCTAAAAA 58.826 43.478 15.94 0.00 0.00 1.94
806 825 4.755411 TCGATCGTCCAAGCTCTAAAAAT 58.245 39.130 15.94 0.00 0.00 1.82
807 826 4.804139 TCGATCGTCCAAGCTCTAAAAATC 59.196 41.667 15.94 0.00 0.00 2.17
808 827 4.025647 CGATCGTCCAAGCTCTAAAAATCC 60.026 45.833 7.03 0.00 0.00 3.01
809 828 4.280436 TCGTCCAAGCTCTAAAAATCCA 57.720 40.909 0.00 0.00 0.00 3.41
810 829 4.000988 TCGTCCAAGCTCTAAAAATCCAC 58.999 43.478 0.00 0.00 0.00 4.02
811 830 3.181520 CGTCCAAGCTCTAAAAATCCACG 60.182 47.826 0.00 0.00 0.00 4.94
812 831 3.751698 GTCCAAGCTCTAAAAATCCACGT 59.248 43.478 0.00 0.00 0.00 4.49
813 832 4.000988 TCCAAGCTCTAAAAATCCACGTC 58.999 43.478 0.00 0.00 0.00 4.34
814 833 3.127030 CCAAGCTCTAAAAATCCACGTCC 59.873 47.826 0.00 0.00 0.00 4.79
815 834 3.983044 AGCTCTAAAAATCCACGTCCT 57.017 42.857 0.00 0.00 0.00 3.85
816 835 3.863041 AGCTCTAAAAATCCACGTCCTC 58.137 45.455 0.00 0.00 0.00 3.71
817 836 2.937149 GCTCTAAAAATCCACGTCCTCC 59.063 50.000 0.00 0.00 0.00 4.30
818 837 3.369576 GCTCTAAAAATCCACGTCCTCCT 60.370 47.826 0.00 0.00 0.00 3.69
819 838 4.184629 CTCTAAAAATCCACGTCCTCCTG 58.815 47.826 0.00 0.00 0.00 3.86
820 839 1.534729 AAAAATCCACGTCCTCCTGC 58.465 50.000 0.00 0.00 0.00 4.85
821 840 0.693049 AAAATCCACGTCCTCCTGCT 59.307 50.000 0.00 0.00 0.00 4.24
822 841 0.036010 AAATCCACGTCCTCCTGCTG 60.036 55.000 0.00 0.00 0.00 4.41
823 842 1.903877 AATCCACGTCCTCCTGCTGG 61.904 60.000 2.58 2.58 0.00 4.85
824 843 4.087892 CCACGTCCTCCTGCTGGG 62.088 72.222 10.07 0.00 0.00 4.45
825 844 3.314331 CACGTCCTCCTGCTGGGT 61.314 66.667 10.07 0.00 36.25 4.51
826 845 1.982395 CACGTCCTCCTGCTGGGTA 60.982 63.158 10.07 0.00 36.25 3.69
827 846 1.682684 ACGTCCTCCTGCTGGGTAG 60.683 63.158 10.07 0.47 36.25 3.18
828 847 2.427245 CGTCCTCCTGCTGGGTAGG 61.427 68.421 10.07 10.19 36.75 3.18
852 871 2.967599 TGGAATCCGTGACAGATCAG 57.032 50.000 0.00 0.00 34.75 2.90
889 908 4.551797 CGACGCTGATAGAGGATATCATCG 60.552 50.000 11.47 15.57 44.32 3.84
895 914 0.901124 AGAGGATATCATCGCCCTGC 59.099 55.000 11.47 0.00 0.00 4.85
981 1003 1.737201 TGGAACAGCAACGTCGAGA 59.263 52.632 0.00 0.00 0.00 4.04
988 1010 2.429351 GCAACGTCGAGAGTCGCTG 61.429 63.158 0.00 0.00 46.25 5.18
989 1011 1.206831 CAACGTCGAGAGTCGCTGA 59.793 57.895 0.00 0.00 46.25 4.26
999 1021 3.428999 CGAGAGTCGCTGAAAAGGGAATA 60.429 47.826 0.00 0.00 31.14 1.75
1017 1039 2.481289 TAATGGCCGACAACACATCA 57.519 45.000 0.00 0.00 0.00 3.07
1020 1042 1.018752 TGGCCGACAACACATCATCG 61.019 55.000 0.00 0.00 0.00 3.84
1029 1051 0.250234 ACACATCATCGGTCCCTGTG 59.750 55.000 0.00 0.00 42.19 3.66
1065 1090 2.292016 CTCACCGCAGATTAGAGACGAT 59.708 50.000 0.00 0.00 0.00 3.73
1077 1102 8.616942 CAGATTAGAGACGATGAGAAAGAACTA 58.383 37.037 0.00 0.00 0.00 2.24
1080 1123 9.616156 ATTAGAGACGATGAGAAAGAACTAGTA 57.384 33.333 0.00 0.00 0.00 1.82
1081 1124 7.925043 AGAGACGATGAGAAAGAACTAGTAA 57.075 36.000 0.00 0.00 0.00 2.24
1083 1126 8.238631 AGAGACGATGAGAAAGAACTAGTAAAC 58.761 37.037 0.00 0.00 0.00 2.01
1098 1141 6.206042 ACTAGTAAACTCCATCCTCCAAGAT 58.794 40.000 0.00 0.00 0.00 2.40
1223 1266 9.484806 AACATCCAGATTAAAGAAAATCTCCAT 57.515 29.630 0.00 0.00 42.90 3.41
1299 1360 3.077391 AGGAGAGGGATAGGATGAGGAAG 59.923 52.174 0.00 0.00 0.00 3.46
1300 1361 3.076785 GGAGAGGGATAGGATGAGGAAGA 59.923 52.174 0.00 0.00 0.00 2.87
1301 1362 4.449968 GGAGAGGGATAGGATGAGGAAGAA 60.450 50.000 0.00 0.00 0.00 2.52
1302 1363 4.750941 AGAGGGATAGGATGAGGAAGAAG 58.249 47.826 0.00 0.00 0.00 2.85
1325 1386 1.344114 GGATGCAGAGAGGGATCAGAC 59.656 57.143 0.00 0.00 37.36 3.51
1572 1651 2.288825 TGACGAGCAGGAAACGAAATCT 60.289 45.455 0.00 0.00 0.00 2.40
1773 1862 7.246311 CGTTTGCTCTATTCATGTCTCAAAAT 58.754 34.615 0.00 0.00 0.00 1.82
1884 1974 8.122472 TCATACTAGATTTCTGACACTTCACA 57.878 34.615 0.00 0.00 0.00 3.58
2110 2203 1.200252 CTTCTCTTCGCTCGGTCAAGA 59.800 52.381 0.00 0.00 0.00 3.02
2232 2344 4.828939 TCTTCAGCAAAACACTCCATTCAT 59.171 37.500 0.00 0.00 0.00 2.57
2235 2347 4.022935 TCAGCAAAACACTCCATTCATGTC 60.023 41.667 0.00 0.00 0.00 3.06
2759 2917 1.563879 TGGGGGATCTGGTTGTACATG 59.436 52.381 0.00 0.00 0.00 3.21
3257 3722 6.560253 AAAATGATTACTGAGCTTTCGTGT 57.440 33.333 0.00 0.00 0.00 4.49
3300 3765 7.566760 TCTAAGCTGAACATTGTTCTTTCAA 57.433 32.000 25.49 8.34 0.00 2.69
3301 3766 7.995289 TCTAAGCTGAACATTGTTCTTTCAAA 58.005 30.769 25.49 7.71 0.00 2.69
3681 6299 0.178068 CACCTCCCACACCTTATCCG 59.822 60.000 0.00 0.00 0.00 4.18
3698 6316 1.497716 TCCGCTCATCCTACCTCCTTA 59.502 52.381 0.00 0.00 0.00 2.69
3782 6509 3.296709 CTCCCAGTTACGCGGCTGT 62.297 63.158 12.47 0.32 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.046023 CGTGCCAGCTGGGAATCA 60.046 61.111 33.46 19.96 40.01 2.57
18 19 2.740714 CTTACAAGGAGCGCCGTGC 61.741 63.158 21.37 0.00 46.13 5.34
29 30 2.487762 TCCTGCAATTTCGGCTTACAAG 59.512 45.455 0.00 0.00 0.00 3.16
54 55 5.441718 TCAGGCAAATCTAATTCTCAGGT 57.558 39.130 0.00 0.00 0.00 4.00
82 83 2.058595 ATAGCGAGGCAAGGGTCGT 61.059 57.895 0.00 0.00 38.48 4.34
170 171 2.003658 CTCTGAGGGAGCTCGCTGTC 62.004 65.000 35.19 22.62 39.39 3.51
348 367 2.037251 ACCTAAATCGTCATCATCCCGG 59.963 50.000 0.00 0.00 0.00 5.73
496 515 1.153086 AAGATGGACATCAGGGCGC 60.153 57.895 14.16 0.00 40.22 6.53
503 522 4.499019 GGAGAAGAGACGAAGATGGACATC 60.499 50.000 4.15 4.15 38.09 3.06
534 553 1.808411 GGCGGAAACAGAGATCAACA 58.192 50.000 0.00 0.00 0.00 3.33
561 580 9.778741 ATAAAAAGAAAAAGAAAAAGCCCTAGG 57.221 29.630 0.06 0.06 0.00 3.02
589 608 2.109181 CGGCGGAAAGGGAGATCC 59.891 66.667 0.00 0.00 0.00 3.36
590 609 2.589159 GCGGCGGAAAGGGAGATC 60.589 66.667 9.78 0.00 0.00 2.75
591 610 4.176752 GGCGGCGGAAAGGGAGAT 62.177 66.667 9.78 0.00 0.00 2.75
602 621 3.760035 ATATCCTAGGCGGCGGCG 61.760 66.667 28.70 28.70 41.24 6.46
603 622 2.125512 CATATCCTAGGCGGCGGC 60.126 66.667 27.24 27.24 38.90 6.53
604 623 1.513158 CTCATATCCTAGGCGGCGG 59.487 63.158 9.78 0.00 0.00 6.13
605 624 1.153745 GCTCATATCCTAGGCGGCG 60.154 63.158 2.96 0.51 0.00 6.46
606 625 0.174617 GAGCTCATATCCTAGGCGGC 59.825 60.000 9.40 0.00 0.00 6.53
607 626 0.820871 GGAGCTCATATCCTAGGCGG 59.179 60.000 17.19 0.00 33.77 6.13
608 627 0.453793 CGGAGCTCATATCCTAGGCG 59.546 60.000 17.19 1.45 34.45 5.52
623 642 0.589223 GACGGACTCAGATAGCGGAG 59.411 60.000 6.59 6.59 41.39 4.63
624 643 0.180642 AGACGGACTCAGATAGCGGA 59.819 55.000 0.00 0.00 0.00 5.54
625 644 0.589223 GAGACGGACTCAGATAGCGG 59.411 60.000 2.60 0.00 44.36 5.52
626 645 0.589223 GGAGACGGACTCAGATAGCG 59.411 60.000 9.54 0.00 46.54 4.26
627 646 1.681538 TGGAGACGGACTCAGATAGC 58.318 55.000 9.54 0.00 46.54 2.97
628 647 3.750371 AGATGGAGACGGACTCAGATAG 58.250 50.000 9.54 0.00 46.54 2.08
629 648 3.866703 AGATGGAGACGGACTCAGATA 57.133 47.619 9.54 0.00 46.54 1.98
630 649 2.746279 AGATGGAGACGGACTCAGAT 57.254 50.000 9.54 1.16 46.54 2.90
631 650 3.117851 ACATAGATGGAGACGGACTCAGA 60.118 47.826 9.54 0.00 46.54 3.27
632 651 3.218453 ACATAGATGGAGACGGACTCAG 58.782 50.000 9.54 0.00 46.54 3.35
633 652 3.117851 AGACATAGATGGAGACGGACTCA 60.118 47.826 9.54 0.00 46.54 3.41
634 653 3.482436 AGACATAGATGGAGACGGACTC 58.518 50.000 0.00 0.00 44.24 3.36
635 654 3.482436 GAGACATAGATGGAGACGGACT 58.518 50.000 0.00 0.00 0.00 3.85
636 655 2.554893 GGAGACATAGATGGAGACGGAC 59.445 54.545 0.00 0.00 0.00 4.79
637 656 2.810767 CGGAGACATAGATGGAGACGGA 60.811 54.545 0.00 0.00 0.00 4.69
638 657 1.537638 CGGAGACATAGATGGAGACGG 59.462 57.143 0.00 0.00 0.00 4.79
639 658 1.068885 GCGGAGACATAGATGGAGACG 60.069 57.143 0.00 0.00 0.00 4.18
640 659 1.271102 GGCGGAGACATAGATGGAGAC 59.729 57.143 0.00 0.00 31.66 3.36
641 660 1.621992 GGCGGAGACATAGATGGAGA 58.378 55.000 0.00 0.00 31.66 3.71
642 661 0.242286 CGGCGGAGACATAGATGGAG 59.758 60.000 0.00 0.00 27.25 3.86
643 662 1.806461 GCGGCGGAGACATAGATGGA 61.806 60.000 9.78 0.00 27.25 3.41
644 663 1.373497 GCGGCGGAGACATAGATGG 60.373 63.158 9.78 0.00 27.25 3.51
645 664 1.373497 GGCGGCGGAGACATAGATG 60.373 63.158 9.78 0.00 27.25 2.90
646 665 2.920645 CGGCGGCGGAGACATAGAT 61.921 63.158 25.36 0.00 27.25 1.98
647 666 3.592814 CGGCGGCGGAGACATAGA 61.593 66.667 25.36 0.00 27.25 1.98
661 680 3.056328 AAAGAAGAAGGCGGCGGC 61.056 61.111 27.24 27.24 38.90 6.53
662 681 1.671054 TCAAAGAAGAAGGCGGCGG 60.671 57.895 9.78 0.00 0.00 6.13
663 682 1.497722 GTCAAAGAAGAAGGCGGCG 59.502 57.895 0.51 0.51 0.00 6.46
664 683 1.876664 GGTCAAAGAAGAAGGCGGC 59.123 57.895 0.00 0.00 0.00 6.53
665 684 0.320421 TCGGTCAAAGAAGAAGGCGG 60.320 55.000 0.00 0.00 0.00 6.13
666 685 1.508632 TTCGGTCAAAGAAGAAGGCG 58.491 50.000 0.00 0.00 0.00 5.52
667 686 2.031069 GGTTTCGGTCAAAGAAGAAGGC 60.031 50.000 0.00 0.00 0.00 4.35
668 687 3.211045 TGGTTTCGGTCAAAGAAGAAGG 58.789 45.455 0.00 0.00 0.00 3.46
669 688 3.304057 GCTGGTTTCGGTCAAAGAAGAAG 60.304 47.826 0.00 0.00 0.00 2.85
670 689 2.616842 GCTGGTTTCGGTCAAAGAAGAA 59.383 45.455 0.00 0.00 0.00 2.52
671 690 2.218603 GCTGGTTTCGGTCAAAGAAGA 58.781 47.619 0.00 0.00 0.00 2.87
672 691 1.946768 TGCTGGTTTCGGTCAAAGAAG 59.053 47.619 0.00 0.00 0.00 2.85
673 692 1.946768 CTGCTGGTTTCGGTCAAAGAA 59.053 47.619 0.00 0.00 0.00 2.52
674 693 1.134220 ACTGCTGGTTTCGGTCAAAGA 60.134 47.619 0.00 0.00 0.00 2.52
675 694 1.308998 ACTGCTGGTTTCGGTCAAAG 58.691 50.000 0.00 0.00 0.00 2.77
676 695 1.757682 AACTGCTGGTTTCGGTCAAA 58.242 45.000 0.00 0.00 33.90 2.69
677 696 1.403679 CAAACTGCTGGTTTCGGTCAA 59.596 47.619 5.62 0.00 45.26 3.18
678 697 1.021202 CAAACTGCTGGTTTCGGTCA 58.979 50.000 5.62 0.00 45.26 4.02
679 698 0.317854 GCAAACTGCTGGTTTCGGTC 60.318 55.000 5.62 0.00 45.26 4.79
680 699 1.733526 GCAAACTGCTGGTTTCGGT 59.266 52.632 5.62 0.00 45.26 4.69
681 700 1.370414 CGCAAACTGCTGGTTTCGG 60.370 57.895 5.56 0.00 45.26 4.30
682 701 0.584396 TACGCAAACTGCTGGTTTCG 59.416 50.000 11.46 11.46 45.26 3.46
683 702 2.766970 TTACGCAAACTGCTGGTTTC 57.233 45.000 5.62 0.00 45.26 2.78
685 704 6.459573 CCATTATATTACGCAAACTGCTGGTT 60.460 38.462 0.00 0.00 42.25 3.67
686 705 5.008613 CCATTATATTACGCAAACTGCTGGT 59.991 40.000 0.00 0.00 42.25 4.00
687 706 5.238432 TCCATTATATTACGCAAACTGCTGG 59.762 40.000 0.00 0.00 42.25 4.85
688 707 6.299023 TCCATTATATTACGCAAACTGCTG 57.701 37.500 0.00 0.00 42.25 4.41
689 708 6.935741 TTCCATTATATTACGCAAACTGCT 57.064 33.333 0.00 0.00 42.25 4.24
690 709 6.636850 CCTTTCCATTATATTACGCAAACTGC 59.363 38.462 0.00 0.00 40.69 4.40
691 710 7.138736 CCCTTTCCATTATATTACGCAAACTG 58.861 38.462 0.00 0.00 0.00 3.16
692 711 6.238925 GCCCTTTCCATTATATTACGCAAACT 60.239 38.462 0.00 0.00 0.00 2.66
693 712 5.918576 GCCCTTTCCATTATATTACGCAAAC 59.081 40.000 0.00 0.00 0.00 2.93
694 713 5.594725 TGCCCTTTCCATTATATTACGCAAA 59.405 36.000 0.00 0.00 0.00 3.68
695 714 5.009210 GTGCCCTTTCCATTATATTACGCAA 59.991 40.000 0.00 0.00 0.00 4.85
696 715 4.517453 GTGCCCTTTCCATTATATTACGCA 59.483 41.667 0.00 0.00 0.00 5.24
697 716 4.378046 CGTGCCCTTTCCATTATATTACGC 60.378 45.833 0.00 0.00 0.00 4.42
698 717 4.153475 CCGTGCCCTTTCCATTATATTACG 59.847 45.833 0.00 0.00 0.00 3.18
699 718 4.082949 GCCGTGCCCTTTCCATTATATTAC 60.083 45.833 0.00 0.00 0.00 1.89
700 719 4.076394 GCCGTGCCCTTTCCATTATATTA 58.924 43.478 0.00 0.00 0.00 0.98
701 720 2.890945 GCCGTGCCCTTTCCATTATATT 59.109 45.455 0.00 0.00 0.00 1.28
702 721 2.514803 GCCGTGCCCTTTCCATTATAT 58.485 47.619 0.00 0.00 0.00 0.86
703 722 1.812324 CGCCGTGCCCTTTCCATTATA 60.812 52.381 0.00 0.00 0.00 0.98
704 723 1.101049 CGCCGTGCCCTTTCCATTAT 61.101 55.000 0.00 0.00 0.00 1.28
705 724 1.747367 CGCCGTGCCCTTTCCATTA 60.747 57.895 0.00 0.00 0.00 1.90
706 725 3.061848 CGCCGTGCCCTTTCCATT 61.062 61.111 0.00 0.00 0.00 3.16
707 726 4.344865 ACGCCGTGCCCTTTCCAT 62.345 61.111 0.00 0.00 0.00 3.41
716 735 4.148825 ATCCTCTCCACGCCGTGC 62.149 66.667 12.68 0.00 31.34 5.34
717 736 2.105128 GATCCTCTCCACGCCGTG 59.895 66.667 10.95 10.95 0.00 4.94
718 737 3.518998 CGATCCTCTCCACGCCGT 61.519 66.667 0.00 0.00 0.00 5.68
719 738 4.933064 GCGATCCTCTCCACGCCG 62.933 72.222 0.00 0.00 44.27 6.46
722 741 2.802787 AATAAGCGATCCTCTCCACG 57.197 50.000 0.00 0.00 0.00 4.94
723 742 4.551388 CACTAATAAGCGATCCTCTCCAC 58.449 47.826 0.00 0.00 0.00 4.02
724 743 3.005897 GCACTAATAAGCGATCCTCTCCA 59.994 47.826 0.00 0.00 0.00 3.86
725 744 3.257127 AGCACTAATAAGCGATCCTCTCC 59.743 47.826 0.00 0.00 35.48 3.71
726 745 4.481463 GAGCACTAATAAGCGATCCTCTC 58.519 47.826 0.00 0.00 35.48 3.20
727 746 3.057876 CGAGCACTAATAAGCGATCCTCT 60.058 47.826 0.00 0.00 35.48 3.69
728 747 3.238441 CGAGCACTAATAAGCGATCCTC 58.762 50.000 0.00 0.00 35.48 3.71
729 748 2.608261 GCGAGCACTAATAAGCGATCCT 60.608 50.000 0.00 0.00 35.48 3.24
730 749 1.721926 GCGAGCACTAATAAGCGATCC 59.278 52.381 0.00 0.00 35.48 3.36
735 754 0.498927 CGTCGCGAGCACTAATAAGC 59.501 55.000 10.24 0.00 0.00 3.09
736 755 1.121240 CCGTCGCGAGCACTAATAAG 58.879 55.000 10.24 0.00 0.00 1.73
737 756 0.734309 TCCGTCGCGAGCACTAATAA 59.266 50.000 10.24 0.00 0.00 1.40
738 757 0.734309 TTCCGTCGCGAGCACTAATA 59.266 50.000 10.24 0.00 0.00 0.98
739 758 0.108992 TTTCCGTCGCGAGCACTAAT 60.109 50.000 10.24 0.00 0.00 1.73
740 759 1.005294 GTTTCCGTCGCGAGCACTAA 61.005 55.000 10.24 0.00 0.00 2.24
741 760 1.443194 GTTTCCGTCGCGAGCACTA 60.443 57.895 10.24 0.00 0.00 2.74
742 761 2.733593 GTTTCCGTCGCGAGCACT 60.734 61.111 10.24 0.00 0.00 4.40
743 762 2.733593 AGTTTCCGTCGCGAGCAC 60.734 61.111 10.24 1.63 0.00 4.40
744 763 2.733218 CAGTTTCCGTCGCGAGCA 60.733 61.111 10.24 0.00 0.00 4.26
745 764 2.717809 GACAGTTTCCGTCGCGAGC 61.718 63.158 10.24 3.52 0.00 5.03
746 765 0.167470 TAGACAGTTTCCGTCGCGAG 59.833 55.000 10.24 3.49 38.46 5.03
747 766 0.592637 TTAGACAGTTTCCGTCGCGA 59.407 50.000 3.71 3.71 38.46 5.87
748 767 1.123756 GTTTAGACAGTTTCCGTCGCG 59.876 52.381 0.00 0.00 38.46 5.87
749 768 2.155155 CAGTTTAGACAGTTTCCGTCGC 59.845 50.000 0.00 0.00 38.46 5.19
750 769 3.635331 TCAGTTTAGACAGTTTCCGTCG 58.365 45.455 0.00 0.00 38.46 5.12
751 770 5.292589 TGTTTCAGTTTAGACAGTTTCCGTC 59.707 40.000 0.00 0.00 0.00 4.79
752 771 5.064325 GTGTTTCAGTTTAGACAGTTTCCGT 59.936 40.000 0.00 0.00 0.00 4.69
753 772 5.064198 TGTGTTTCAGTTTAGACAGTTTCCG 59.936 40.000 0.00 0.00 0.00 4.30
754 773 6.315393 TCTGTGTTTCAGTTTAGACAGTTTCC 59.685 38.462 0.00 0.00 43.97 3.13
755 774 7.303634 TCTGTGTTTCAGTTTAGACAGTTTC 57.696 36.000 0.00 0.00 43.97 2.78
756 775 7.254455 CGATCTGTGTTTCAGTTTAGACAGTTT 60.254 37.037 0.00 0.00 43.97 2.66
757 776 6.201044 CGATCTGTGTTTCAGTTTAGACAGTT 59.799 38.462 0.00 0.00 43.97 3.16
758 777 5.692204 CGATCTGTGTTTCAGTTTAGACAGT 59.308 40.000 0.00 0.00 43.97 3.55
759 778 5.388890 GCGATCTGTGTTTCAGTTTAGACAG 60.389 44.000 0.00 0.00 43.97 3.51
760 779 4.447724 GCGATCTGTGTTTCAGTTTAGACA 59.552 41.667 0.00 0.00 43.97 3.41
761 780 4.686554 AGCGATCTGTGTTTCAGTTTAGAC 59.313 41.667 0.00 0.00 43.97 2.59
762 781 4.883083 AGCGATCTGTGTTTCAGTTTAGA 58.117 39.130 0.00 0.00 43.97 2.10
763 782 4.201532 CGAGCGATCTGTGTTTCAGTTTAG 60.202 45.833 0.00 0.00 43.97 1.85
764 783 3.673338 CGAGCGATCTGTGTTTCAGTTTA 59.327 43.478 0.00 0.00 43.97 2.01
765 784 2.476619 CGAGCGATCTGTGTTTCAGTTT 59.523 45.455 0.00 0.00 43.97 2.66
766 785 2.061773 CGAGCGATCTGTGTTTCAGTT 58.938 47.619 0.00 0.00 43.97 3.16
767 786 1.269723 TCGAGCGATCTGTGTTTCAGT 59.730 47.619 0.00 0.00 43.97 3.41
768 787 1.982612 TCGAGCGATCTGTGTTTCAG 58.017 50.000 0.00 0.00 44.85 3.02
769 788 2.530177 GATCGAGCGATCTGTGTTTCA 58.470 47.619 21.79 0.00 45.42 2.69
770 789 1.514811 CGATCGAGCGATCTGTGTTTC 59.485 52.381 20.02 4.06 46.36 2.78
771 790 1.135373 ACGATCGAGCGATCTGTGTTT 60.135 47.619 31.66 0.00 46.36 2.83
772 791 0.452184 ACGATCGAGCGATCTGTGTT 59.548 50.000 31.66 0.46 46.36 3.32
773 792 0.028242 GACGATCGAGCGATCTGTGT 59.972 55.000 31.66 17.53 46.36 3.72
774 793 0.658829 GGACGATCGAGCGATCTGTG 60.659 60.000 31.66 15.01 46.36 3.66
775 794 1.095807 TGGACGATCGAGCGATCTGT 61.096 55.000 31.66 22.80 46.36 3.41
776 795 0.029433 TTGGACGATCGAGCGATCTG 59.971 55.000 31.66 20.51 46.36 2.90
777 796 0.309302 CTTGGACGATCGAGCGATCT 59.691 55.000 31.66 7.35 46.36 2.75
778 797 1.272114 GCTTGGACGATCGAGCGATC 61.272 60.000 31.66 21.47 45.42 3.69
779 798 1.299468 GCTTGGACGATCGAGCGAT 60.299 57.895 31.66 14.14 34.83 4.58
780 799 2.102357 GCTTGGACGATCGAGCGA 59.898 61.111 31.66 4.04 34.83 4.93
781 800 1.941734 GAGCTTGGACGATCGAGCG 60.942 63.158 23.12 23.12 46.12 5.03
782 801 0.663688 TAGAGCTTGGACGATCGAGC 59.336 55.000 24.34 19.70 42.88 5.03
783 802 3.422417 TTTAGAGCTTGGACGATCGAG 57.578 47.619 24.34 9.80 0.00 4.04
784 803 3.861276 TTTTAGAGCTTGGACGATCGA 57.139 42.857 24.34 0.00 0.00 3.59
785 804 4.025647 GGATTTTTAGAGCTTGGACGATCG 60.026 45.833 14.88 14.88 0.00 3.69
786 805 4.876107 TGGATTTTTAGAGCTTGGACGATC 59.124 41.667 0.00 0.00 0.00 3.69
787 806 4.636206 GTGGATTTTTAGAGCTTGGACGAT 59.364 41.667 0.00 0.00 0.00 3.73
788 807 4.000988 GTGGATTTTTAGAGCTTGGACGA 58.999 43.478 0.00 0.00 0.00 4.20
789 808 3.181520 CGTGGATTTTTAGAGCTTGGACG 60.182 47.826 0.00 0.00 0.00 4.79
790 809 3.751698 ACGTGGATTTTTAGAGCTTGGAC 59.248 43.478 0.00 0.00 0.00 4.02
791 810 4.000988 GACGTGGATTTTTAGAGCTTGGA 58.999 43.478 0.00 0.00 0.00 3.53
792 811 3.127030 GGACGTGGATTTTTAGAGCTTGG 59.873 47.826 0.00 0.00 0.00 3.61
793 812 4.003648 AGGACGTGGATTTTTAGAGCTTG 58.996 43.478 0.00 0.00 0.00 4.01
794 813 4.254492 GAGGACGTGGATTTTTAGAGCTT 58.746 43.478 0.00 0.00 0.00 3.74
795 814 3.369576 GGAGGACGTGGATTTTTAGAGCT 60.370 47.826 0.00 0.00 0.00 4.09
796 815 2.937149 GGAGGACGTGGATTTTTAGAGC 59.063 50.000 0.00 0.00 0.00 4.09
797 816 4.184629 CAGGAGGACGTGGATTTTTAGAG 58.815 47.826 0.00 0.00 0.00 2.43
798 817 3.618997 GCAGGAGGACGTGGATTTTTAGA 60.619 47.826 0.00 0.00 33.23 2.10
799 818 2.678336 GCAGGAGGACGTGGATTTTTAG 59.322 50.000 0.00 0.00 33.23 1.85
800 819 2.304761 AGCAGGAGGACGTGGATTTTTA 59.695 45.455 0.00 0.00 33.23 1.52
801 820 1.073923 AGCAGGAGGACGTGGATTTTT 59.926 47.619 0.00 0.00 33.23 1.94
802 821 0.693049 AGCAGGAGGACGTGGATTTT 59.307 50.000 0.00 0.00 33.23 1.82
803 822 0.036010 CAGCAGGAGGACGTGGATTT 60.036 55.000 0.00 0.00 33.23 2.17
804 823 1.599047 CAGCAGGAGGACGTGGATT 59.401 57.895 0.00 0.00 33.23 3.01
805 824 2.362369 CCAGCAGGAGGACGTGGAT 61.362 63.158 0.00 0.00 36.89 3.41
806 825 2.997315 CCAGCAGGAGGACGTGGA 60.997 66.667 0.00 0.00 36.89 4.02
807 826 4.087892 CCCAGCAGGAGGACGTGG 62.088 72.222 0.00 0.00 38.24 4.94
808 827 1.949847 CTACCCAGCAGGAGGACGTG 61.950 65.000 0.00 0.00 39.89 4.49
809 828 1.682684 CTACCCAGCAGGAGGACGT 60.683 63.158 0.00 0.00 39.89 4.34
810 829 2.427245 CCTACCCAGCAGGAGGACG 61.427 68.421 0.00 0.00 39.89 4.79
811 830 2.066999 CCCTACCCAGCAGGAGGAC 61.067 68.421 4.58 0.00 39.89 3.85
812 831 2.243774 CTCCCTACCCAGCAGGAGGA 62.244 65.000 4.58 4.66 41.90 3.71
813 832 1.764054 CTCCCTACCCAGCAGGAGG 60.764 68.421 0.00 0.00 41.90 4.30
814 833 0.105246 ATCTCCCTACCCAGCAGGAG 60.105 60.000 0.00 0.00 46.11 3.69
815 834 0.399091 CATCTCCCTACCCAGCAGGA 60.399 60.000 0.00 0.00 39.89 3.86
816 835 1.414061 CCATCTCCCTACCCAGCAGG 61.414 65.000 0.00 0.00 43.78 4.85
817 836 0.399091 TCCATCTCCCTACCCAGCAG 60.399 60.000 0.00 0.00 0.00 4.24
818 837 0.044092 TTCCATCTCCCTACCCAGCA 59.956 55.000 0.00 0.00 0.00 4.41
819 838 1.349357 GATTCCATCTCCCTACCCAGC 59.651 57.143 0.00 0.00 0.00 4.85
820 839 1.981495 GGATTCCATCTCCCTACCCAG 59.019 57.143 0.00 0.00 0.00 4.45
821 840 1.761371 CGGATTCCATCTCCCTACCCA 60.761 57.143 3.09 0.00 0.00 4.51
822 841 0.977395 CGGATTCCATCTCCCTACCC 59.023 60.000 3.09 0.00 0.00 3.69
823 842 1.344763 CACGGATTCCATCTCCCTACC 59.655 57.143 3.09 0.00 0.00 3.18
824 843 2.036089 GTCACGGATTCCATCTCCCTAC 59.964 54.545 3.09 0.00 0.00 3.18
825 844 2.317040 GTCACGGATTCCATCTCCCTA 58.683 52.381 3.09 0.00 0.00 3.53
826 845 1.123928 GTCACGGATTCCATCTCCCT 58.876 55.000 3.09 0.00 0.00 4.20
827 846 0.830648 TGTCACGGATTCCATCTCCC 59.169 55.000 3.09 0.00 0.00 4.30
828 847 1.757118 TCTGTCACGGATTCCATCTCC 59.243 52.381 3.09 0.00 0.00 3.71
852 871 0.985549 GCGTCGACAACTCATCAGAC 59.014 55.000 17.16 0.00 0.00 3.51
895 914 0.321122 AAGTCTTTGCGCTCCCTCTG 60.321 55.000 9.73 0.00 0.00 3.35
933 952 1.573108 TCTCCCAGCGAGAAATCCTT 58.427 50.000 0.00 0.00 44.94 3.36
952 971 4.813161 CGTTGCTGTTCCAGAGATGATATT 59.187 41.667 0.00 0.00 32.44 1.28
981 1003 3.947834 CCATTATTCCCTTTTCAGCGACT 59.052 43.478 0.00 0.00 0.00 4.18
988 1010 3.020984 TGTCGGCCATTATTCCCTTTTC 58.979 45.455 2.24 0.00 0.00 2.29
989 1011 3.094484 TGTCGGCCATTATTCCCTTTT 57.906 42.857 2.24 0.00 0.00 2.27
999 1021 1.745087 GATGATGTGTTGTCGGCCATT 59.255 47.619 2.24 0.00 0.00 3.16
1017 1039 0.904865 TCTTCTGCACAGGGACCGAT 60.905 55.000 0.00 0.00 0.00 4.18
1020 1042 0.108585 TGTTCTTCTGCACAGGGACC 59.891 55.000 0.00 0.00 0.00 4.46
1029 1051 1.140816 GTGAGTCCGTGTTCTTCTGC 58.859 55.000 0.00 0.00 0.00 4.26
1054 1079 8.514330 ACTAGTTCTTTCTCATCGTCTCTAAT 57.486 34.615 0.00 0.00 0.00 1.73
1065 1090 7.455008 AGGATGGAGTTTACTAGTTCTTTCTCA 59.545 37.037 0.00 0.00 0.00 3.27
1077 1102 5.069251 CGTATCTTGGAGGATGGAGTTTACT 59.931 44.000 0.00 0.00 0.00 2.24
1080 1123 3.134804 CCGTATCTTGGAGGATGGAGTTT 59.865 47.826 0.00 0.00 0.00 2.66
1081 1124 2.700897 CCGTATCTTGGAGGATGGAGTT 59.299 50.000 0.00 0.00 0.00 3.01
1083 1126 2.598565 TCCGTATCTTGGAGGATGGAG 58.401 52.381 0.00 0.00 0.00 3.86
1098 1141 2.120940 TGGCCCAAGTCCTCCGTA 59.879 61.111 0.00 0.00 0.00 4.02
1125 1168 4.832248 TCCAAAGATACTGTGACATGGAC 58.168 43.478 0.00 0.00 31.12 4.02
1223 1266 1.678728 CGGCAGCCTTGTAGAAATCCA 60.679 52.381 10.54 0.00 0.00 3.41
1253 1311 2.383683 TCTTCCTTCCTCTTCTCCTCCA 59.616 50.000 0.00 0.00 0.00 3.86
1254 1312 3.031013 CTCTTCCTTCCTCTTCTCCTCC 58.969 54.545 0.00 0.00 0.00 4.30
1299 1360 2.114616 TCCCTCTCTGCATCCTTCTTC 58.885 52.381 0.00 0.00 0.00 2.87
1300 1361 2.260639 TCCCTCTCTGCATCCTTCTT 57.739 50.000 0.00 0.00 0.00 2.52
1301 1362 2.328319 GATCCCTCTCTGCATCCTTCT 58.672 52.381 0.00 0.00 0.00 2.85
1302 1363 2.037511 CTGATCCCTCTCTGCATCCTTC 59.962 54.545 0.00 0.00 0.00 3.46
1325 1386 0.652592 GAATTCGTGGGTCAGCATCG 59.347 55.000 0.00 0.00 0.00 3.84
1487 1551 1.362406 CTTCTTTCTTCTCCGCCGCC 61.362 60.000 0.00 0.00 0.00 6.13
1572 1651 2.872245 CTCTTTGAGTTGCTCCGTTTGA 59.128 45.455 0.00 0.00 0.00 2.69
1819 1909 6.187125 AGACAATCAATTCACTTCCATTCG 57.813 37.500 0.00 0.00 0.00 3.34
1884 1974 0.184933 TGCAGCACCAAAGGTAAGGT 59.815 50.000 0.00 0.00 39.10 3.50
2110 2203 4.286032 TCAGTGAGTACTTGGCACCTAATT 59.714 41.667 9.03 0.00 34.07 1.40
2232 2344 7.499895 TGCAAAGCATTAGATCATCATTAGACA 59.500 33.333 0.00 0.00 31.71 3.41
2235 2347 7.174426 TCCTGCAAAGCATTAGATCATCATTAG 59.826 37.037 0.00 0.00 38.13 1.73
2646 2795 5.028549 AGCCATCTAGATGTCGTTCATTT 57.971 39.130 27.03 0.00 36.83 2.32
2759 2917 2.109425 AGGGAAGTAAACATGACCGC 57.891 50.000 0.00 0.00 0.00 5.68
3257 3722 7.232330 AGCTTAGATAATGTGAGACTAGATGCA 59.768 37.037 0.00 0.00 0.00 3.96
3300 3765 5.147767 AGAAAGGCAGGAACCAACTAATTT 58.852 37.500 0.00 0.00 0.00 1.82
3301 3766 4.740902 AGAAAGGCAGGAACCAACTAATT 58.259 39.130 0.00 0.00 0.00 1.40
3681 6299 3.158676 ACGATAAGGAGGTAGGATGAGC 58.841 50.000 0.00 0.00 0.00 4.26
3698 6316 2.602267 TGGTGGTGGGACGACGAT 60.602 61.111 0.00 0.00 0.00 3.73
3782 6509 3.390521 AGCGCAAGATCGGGGTGA 61.391 61.111 11.47 0.00 43.02 4.02


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

AutoCloner maintained by Alex Coulton.