Multiple sequence alignment - TraesCS2A01G116500

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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 TraesCS2A01G116500 chr2A 100.000 4265 0 0 1 4265 66576231 66580495 0.000000e+00 7877.0
1 TraesCS2A01G116500 chr2B 94.891 3151 126 9 801 3951 102414628 102417743 0.000000e+00 4894.0
2 TraesCS2A01G116500 chr2B 85.021 474 42 13 1 462 102414027 102414483 5.030000e-124 455.0
3 TraesCS2A01G116500 chr2B 94.118 153 6 3 3948 4099 102417832 102417982 3.320000e-56 230.0
4 TraesCS2A01G116500 chr2B 100.000 29 0 0 770 798 102414572 102414600 2.000000e-03 54.7
5 TraesCS2A01G116500 chr2D 94.118 3145 125 28 817 3944 67976633 67973532 0.000000e+00 4728.0
6 TraesCS2A01G116500 chr2D 85.948 612 58 15 1 590 67977302 67976697 2.800000e-176 628.0
7 TraesCS2A01G116500 chr2D 96.000 150 3 3 3951 4099 67973440 67973293 1.530000e-59 241.0
8 TraesCS2A01G116500 chr7A 94.681 188 10 0 4078 4265 456614138 456614325 4.170000e-75 292.0
9 TraesCS2A01G116500 chr7A 92.821 195 13 1 4072 4265 393691844 393692038 9.030000e-72 281.0
10 TraesCS2A01G116500 chr3A 96.045 177 7 0 4089 4265 528986797 528986621 5.400000e-74 289.0
11 TraesCS2A01G116500 chr3A 96.045 177 7 0 4089 4265 715767664 715767488 5.400000e-74 289.0
12 TraesCS2A01G116500 chr3A 94.944 178 9 0 4088 4265 345981595 345981418 3.250000e-71 279.0
13 TraesCS2A01G116500 chr5A 95.506 178 8 0 4088 4265 160017605 160017782 6.980000e-73 285.0
14 TraesCS2A01G116500 chr6A 95.000 180 9 0 4086 4265 532779754 532779933 2.510000e-72 283.0
15 TraesCS2A01G116500 chr6A 94.944 178 8 1 4089 4265 64252081 64251904 1.170000e-70 278.0
16 TraesCS2A01G116500 chr6A 94.915 177 9 0 4089 4265 258132002 258132178 1.170000e-70 278.0


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 TraesCS2A01G116500 chr2A 66576231 66580495 4264 False 7877.000000 7877 100.0000 1 4265 1 chr2A.!!$F1 4264
1 TraesCS2A01G116500 chr2B 102414027 102417982 3955 False 1408.425000 4894 93.5075 1 4099 4 chr2B.!!$F1 4098
2 TraesCS2A01G116500 chr2D 67973293 67977302 4009 True 1865.666667 4728 92.0220 1 4099 3 chr2D.!!$R1 4098

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
368 375 0.467384 CACCATGCCTCTTCTCCGAT 59.533 55.0 0.00 0.0 0.0 4.18 F
1748 1812 0.250234 CTGTTCCTCCGGATGCTCAA 59.750 55.0 3.57 0.0 0.0 3.02 F
2752 2816 0.103208 GGCGATCTTCGACTCCATGT 59.897 55.0 0.32 0.0 46.2 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2268 2332 0.250209 CCGAGATCAGGGCATTCCAG 60.250 60.0 0.00 0.0 38.24 3.86 R
2884 2948 0.036010 GCTCCCAGCAAGCTCTGTAA 60.036 55.0 2.09 0.0 41.89 2.41 R
4091 4257 0.385473 GTTGCACGTGCGCATTTACT 60.385 50.0 33.22 0.0 45.83 2.24 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 1.296715 GCTCCACATCCCTTGTCGT 59.703 57.895 0.00 0.00 36.00 4.34
37 38 2.317040 TCCCTTGTCGTAGATCCATCC 58.683 52.381 0.00 0.00 40.67 3.51
47 48 3.244580 ATCCATCCCCAGCGCGAT 61.245 61.111 12.10 0.00 0.00 4.58
50 51 2.031616 CATCCCCAGCGCGATGAT 59.968 61.111 28.29 8.80 38.53 2.45
52 53 2.510551 ATCCCCAGCGCGATGATCA 61.511 57.895 28.29 8.85 0.00 2.92
82 83 2.039787 TGGACGCTCCACCCCATA 59.960 61.111 3.02 0.00 42.67 2.74
91 92 1.150986 CTCCACCCCATATCCTCCTCT 59.849 57.143 0.00 0.00 0.00 3.69
92 93 1.132721 TCCACCCCATATCCTCCTCTG 60.133 57.143 0.00 0.00 0.00 3.35
174 175 2.386661 CACGAGCTTATTGTGGGAGT 57.613 50.000 0.00 0.00 39.36 3.85
178 179 4.023193 CACGAGCTTATTGTGGGAGTTTTT 60.023 41.667 0.00 0.00 39.36 1.94
180 181 4.023193 CGAGCTTATTGTGGGAGTTTTTGT 60.023 41.667 0.00 0.00 0.00 2.83
234 237 0.884704 GTGACAAGCTTTGGAGGCGA 60.885 55.000 0.00 0.00 34.12 5.54
306 313 2.913617 AGACCCAAACTCCCTAAGGAAG 59.086 50.000 0.00 0.00 43.40 3.46
314 321 3.116174 ACTCCCTAAGGAAGCCCTAAAG 58.884 50.000 0.00 0.00 43.48 1.85
320 327 5.506708 CCTAAGGAAGCCCTAAAGCTAAAA 58.493 41.667 0.00 0.00 44.11 1.52
342 349 4.341487 ACTACTATGTACAGGAGTGCACA 58.659 43.478 21.04 0.00 43.19 4.57
368 375 0.467384 CACCATGCCTCTTCTCCGAT 59.533 55.000 0.00 0.00 0.00 4.18
397 404 3.000727 ACCGACAACAAAATCGAGGATC 58.999 45.455 0.00 0.00 40.86 3.36
442 457 5.700402 ATTTAGCTCTCAAAGGAGGCTTA 57.300 39.130 11.16 2.84 41.74 3.09
451 466 5.251700 TCTCAAAGGAGGCTTAAGAAGGATT 59.748 40.000 6.67 0.00 41.69 3.01
454 469 4.769345 AGGAGGCTTAAGAAGGATTGAG 57.231 45.455 6.67 0.00 0.00 3.02
463 478 7.102993 GCTTAAGAAGGATTGAGAGAGAAAGT 58.897 38.462 6.67 0.00 0.00 2.66
468 483 9.447157 AAGAAGGATTGAGAGAGAAAGTAATTG 57.553 33.333 0.00 0.00 0.00 2.32
584 614 6.670695 AAAGGCAAGAAGGACAACATATTT 57.329 33.333 0.00 0.00 0.00 1.40
585 615 5.649782 AGGCAAGAAGGACAACATATTTG 57.350 39.130 0.00 0.00 0.00 2.32
586 616 4.082026 AGGCAAGAAGGACAACATATTTGC 60.082 41.667 0.00 0.00 39.02 3.68
587 617 4.082026 GGCAAGAAGGACAACATATTTGCT 60.082 41.667 5.94 0.00 39.52 3.91
588 618 5.125417 GGCAAGAAGGACAACATATTTGCTA 59.875 40.000 5.94 0.00 39.52 3.49
589 619 6.183360 GGCAAGAAGGACAACATATTTGCTAT 60.183 38.462 5.94 0.00 39.52 2.97
590 620 6.694411 GCAAGAAGGACAACATATTTGCTATG 59.306 38.462 0.00 0.00 42.57 2.23
591 621 6.949352 AGAAGGACAACATATTTGCTATGG 57.051 37.500 0.00 0.00 41.41 2.74
592 622 6.662755 AGAAGGACAACATATTTGCTATGGA 58.337 36.000 0.00 0.00 41.41 3.41
593 623 7.293073 AGAAGGACAACATATTTGCTATGGAT 58.707 34.615 0.00 0.00 41.41 3.41
594 624 6.889301 AGGACAACATATTTGCTATGGATG 57.111 37.500 0.00 0.00 41.41 3.51
595 625 6.367983 AGGACAACATATTTGCTATGGATGT 58.632 36.000 5.43 5.43 41.41 3.06
596 626 6.263842 AGGACAACATATTTGCTATGGATGTG 59.736 38.462 8.76 0.00 41.41 3.21
597 627 6.262944 GGACAACATATTTGCTATGGATGTGA 59.737 38.462 8.76 0.00 41.41 3.58
598 628 7.031226 ACAACATATTTGCTATGGATGTGAC 57.969 36.000 5.11 0.00 41.41 3.67
599 629 6.830324 ACAACATATTTGCTATGGATGTGACT 59.170 34.615 5.11 0.00 41.41 3.41
600 630 7.992608 ACAACATATTTGCTATGGATGTGACTA 59.007 33.333 5.11 0.00 41.41 2.59
601 631 7.969536 ACATATTTGCTATGGATGTGACTAC 57.030 36.000 0.00 0.00 41.41 2.73
602 632 7.508687 ACATATTTGCTATGGATGTGACTACA 58.491 34.615 0.00 0.00 41.41 2.74
603 633 8.159447 ACATATTTGCTATGGATGTGACTACAT 58.841 33.333 0.00 0.00 43.53 2.29
614 644 5.843673 ATGTGACTACATCTCAATCGACT 57.156 39.130 0.00 0.00 44.00 4.18
615 645 6.944234 ATGTGACTACATCTCAATCGACTA 57.056 37.500 0.00 0.00 44.00 2.59
616 646 6.753107 TGTGACTACATCTCAATCGACTAA 57.247 37.500 0.00 0.00 0.00 2.24
617 647 6.786207 TGTGACTACATCTCAATCGACTAAG 58.214 40.000 0.00 0.00 0.00 2.18
618 648 6.598064 TGTGACTACATCTCAATCGACTAAGA 59.402 38.462 0.00 0.00 0.00 2.10
619 649 6.908284 GTGACTACATCTCAATCGACTAAGAC 59.092 42.308 0.00 0.00 0.00 3.01
620 650 6.824196 TGACTACATCTCAATCGACTAAGACT 59.176 38.462 0.00 0.00 0.00 3.24
621 651 7.337184 TGACTACATCTCAATCGACTAAGACTT 59.663 37.037 0.00 0.00 0.00 3.01
622 652 8.734218 ACTACATCTCAATCGACTAAGACTTA 57.266 34.615 0.00 0.00 0.00 2.24
623 653 9.175312 ACTACATCTCAATCGACTAAGACTTAA 57.825 33.333 0.00 0.00 0.00 1.85
624 654 9.440784 CTACATCTCAATCGACTAAGACTTAAC 57.559 37.037 0.00 0.00 0.00 2.01
625 655 6.967767 ACATCTCAATCGACTAAGACTTAACG 59.032 38.462 12.37 12.37 0.00 3.18
626 656 6.732531 TCTCAATCGACTAAGACTTAACGA 57.267 37.500 19.22 19.22 0.00 3.85
627 657 6.773080 TCTCAATCGACTAAGACTTAACGAG 58.227 40.000 20.56 12.93 33.58 4.18
628 658 5.877031 TCAATCGACTAAGACTTAACGAGG 58.123 41.667 20.56 16.78 33.58 4.63
629 659 5.413833 TCAATCGACTAAGACTTAACGAGGT 59.586 40.000 20.56 12.98 33.58 3.85
630 660 4.935885 TCGACTAAGACTTAACGAGGTC 57.064 45.455 15.45 9.51 0.00 3.85
631 661 4.573900 TCGACTAAGACTTAACGAGGTCT 58.426 43.478 15.45 0.00 43.60 3.85
632 662 4.629200 TCGACTAAGACTTAACGAGGTCTC 59.371 45.833 15.45 0.00 41.28 3.36
643 673 1.897641 CGAGGTCTCGCTTAAGTGAC 58.102 55.000 14.70 13.86 46.50 3.67
644 674 1.199327 CGAGGTCTCGCTTAAGTGACA 59.801 52.381 14.70 2.01 46.50 3.58
645 675 2.597520 GAGGTCTCGCTTAAGTGACAC 58.402 52.381 14.70 14.35 36.63 3.67
646 676 1.961394 AGGTCTCGCTTAAGTGACACA 59.039 47.619 21.20 5.43 36.63 3.72
647 677 2.364324 AGGTCTCGCTTAAGTGACACAA 59.636 45.455 21.20 4.71 36.63 3.33
648 678 2.475487 GGTCTCGCTTAAGTGACACAAC 59.525 50.000 21.20 13.83 36.63 3.32
649 679 3.381949 GTCTCGCTTAAGTGACACAACT 58.618 45.455 14.70 0.00 35.44 3.16
650 680 3.802685 GTCTCGCTTAAGTGACACAACTT 59.197 43.478 14.70 0.00 42.89 2.66
651 681 4.980434 GTCTCGCTTAAGTGACACAACTTA 59.020 41.667 14.70 0.00 40.77 2.24
652 682 5.634020 GTCTCGCTTAAGTGACACAACTTAT 59.366 40.000 14.70 0.00 41.17 1.73
653 683 6.805271 GTCTCGCTTAAGTGACACAACTTATA 59.195 38.462 14.70 0.00 41.17 0.98
654 684 7.327761 GTCTCGCTTAAGTGACACAACTTATAA 59.672 37.037 14.70 0.00 41.17 0.98
655 685 7.868922 TCTCGCTTAAGTGACACAACTTATAAA 59.131 33.333 14.70 0.00 41.17 1.40
656 686 8.367943 TCGCTTAAGTGACACAACTTATAAAA 57.632 30.769 14.70 0.00 41.17 1.52
657 687 8.828644 TCGCTTAAGTGACACAACTTATAAAAA 58.171 29.630 14.70 0.00 41.17 1.94
658 688 9.607285 CGCTTAAGTGACACAACTTATAAAAAT 57.393 29.630 10.63 0.00 41.17 1.82
702 732 7.801547 AAAAATACACGAATCTTCATGCAAG 57.198 32.000 0.00 0.00 0.00 4.01
703 733 6.741992 AAATACACGAATCTTCATGCAAGA 57.258 33.333 9.18 9.18 45.60 3.02
712 742 4.765813 TCTTCATGCAAGATCTCATGGA 57.234 40.909 19.14 12.76 40.20 3.41
713 743 5.306114 TCTTCATGCAAGATCTCATGGAT 57.694 39.130 19.14 9.41 40.20 3.41
714 744 6.429521 TCTTCATGCAAGATCTCATGGATA 57.570 37.500 19.14 5.86 40.20 2.59
715 745 7.017319 TCTTCATGCAAGATCTCATGGATAT 57.983 36.000 19.14 0.00 40.20 1.63
716 746 7.459234 TCTTCATGCAAGATCTCATGGATATT 58.541 34.615 19.14 0.00 40.20 1.28
717 747 7.606839 TCTTCATGCAAGATCTCATGGATATTC 59.393 37.037 19.14 0.00 40.20 1.75
718 748 5.873164 TCATGCAAGATCTCATGGATATTCG 59.127 40.000 19.14 2.46 40.20 3.34
719 749 5.473066 TGCAAGATCTCATGGATATTCGA 57.527 39.130 0.00 0.00 34.10 3.71
720 750 6.046290 TGCAAGATCTCATGGATATTCGAT 57.954 37.500 0.00 0.00 34.10 3.59
721 751 6.104665 TGCAAGATCTCATGGATATTCGATC 58.895 40.000 0.00 0.00 34.10 3.69
722 752 5.231779 GCAAGATCTCATGGATATTCGATCG 59.768 44.000 9.36 9.36 34.10 3.69
723 753 6.558909 CAAGATCTCATGGATATTCGATCGA 58.441 40.000 15.15 15.15 34.10 3.59
724 754 6.130298 AGATCTCATGGATATTCGATCGAC 57.870 41.667 19.26 6.07 34.33 4.20
725 755 4.703645 TCTCATGGATATTCGATCGACC 57.296 45.455 19.26 16.13 0.00 4.79
726 756 3.127030 TCTCATGGATATTCGATCGACCG 59.873 47.826 19.26 0.00 0.00 4.79
727 757 3.078837 TCATGGATATTCGATCGACCGA 58.921 45.455 19.26 0.00 36.70 4.69
728 758 3.127030 TCATGGATATTCGATCGACCGAG 59.873 47.826 19.26 11.70 39.90 4.63
729 759 2.774687 TGGATATTCGATCGACCGAGA 58.225 47.619 19.26 2.54 39.90 4.04
730 760 2.742589 TGGATATTCGATCGACCGAGAG 59.257 50.000 19.26 0.00 39.90 3.20
731 761 2.743126 GGATATTCGATCGACCGAGAGT 59.257 50.000 19.26 0.00 39.90 3.24
732 762 3.188873 GGATATTCGATCGACCGAGAGTT 59.811 47.826 19.26 0.00 39.90 3.01
733 763 4.320348 GGATATTCGATCGACCGAGAGTTT 60.320 45.833 19.26 0.00 39.90 2.66
734 764 2.257974 TTCGATCGACCGAGAGTTTG 57.742 50.000 19.26 0.00 39.90 2.93
735 765 1.162698 TCGATCGACCGAGAGTTTGT 58.837 50.000 15.15 0.00 34.19 2.83
736 766 1.538512 TCGATCGACCGAGAGTTTGTT 59.461 47.619 15.15 0.00 34.19 2.83
737 767 2.743664 TCGATCGACCGAGAGTTTGTTA 59.256 45.455 15.15 0.00 34.19 2.41
738 768 3.189080 TCGATCGACCGAGAGTTTGTTAA 59.811 43.478 15.15 0.00 34.19 2.01
739 769 3.542704 CGATCGACCGAGAGTTTGTTAAG 59.457 47.826 10.26 0.00 0.00 1.85
740 770 3.996150 TCGACCGAGAGTTTGTTAAGT 57.004 42.857 0.00 0.00 0.00 2.24
741 771 3.893720 TCGACCGAGAGTTTGTTAAGTC 58.106 45.455 0.00 0.00 34.51 3.01
742 772 3.567164 TCGACCGAGAGTTTGTTAAGTCT 59.433 43.478 0.00 0.00 44.79 3.24
748 778 4.236147 GAGAGTTTGTTAAGTCTCGGTCC 58.764 47.826 6.91 0.00 45.82 4.46
749 779 3.640029 AGAGTTTGTTAAGTCTCGGTCCA 59.360 43.478 0.00 0.00 39.34 4.02
750 780 4.100498 AGAGTTTGTTAAGTCTCGGTCCAA 59.900 41.667 0.00 0.00 39.34 3.53
751 781 4.969484 AGTTTGTTAAGTCTCGGTCCAAT 58.031 39.130 0.00 0.00 0.00 3.16
752 782 4.755123 AGTTTGTTAAGTCTCGGTCCAATG 59.245 41.667 0.00 0.00 0.00 2.82
753 783 4.610605 TTGTTAAGTCTCGGTCCAATGA 57.389 40.909 0.00 0.00 0.00 2.57
754 784 4.188247 TGTTAAGTCTCGGTCCAATGAG 57.812 45.455 0.00 0.00 0.00 2.90
755 785 3.830178 TGTTAAGTCTCGGTCCAATGAGA 59.170 43.478 0.00 0.00 38.85 3.27
756 786 4.466370 TGTTAAGTCTCGGTCCAATGAGAT 59.534 41.667 0.00 0.00 42.73 2.75
757 787 5.046591 TGTTAAGTCTCGGTCCAATGAGATT 60.047 40.000 0.00 0.00 42.73 2.40
758 788 4.559862 AAGTCTCGGTCCAATGAGATTT 57.440 40.909 0.00 0.00 42.73 2.17
759 789 5.677319 AAGTCTCGGTCCAATGAGATTTA 57.323 39.130 2.46 0.00 42.73 1.40
760 790 5.677319 AGTCTCGGTCCAATGAGATTTAA 57.323 39.130 0.00 0.00 42.73 1.52
761 791 5.420409 AGTCTCGGTCCAATGAGATTTAAC 58.580 41.667 0.00 0.00 42.73 2.01
762 792 5.046591 AGTCTCGGTCCAATGAGATTTAACA 60.047 40.000 0.00 0.00 42.73 2.41
763 793 5.642063 GTCTCGGTCCAATGAGATTTAACAA 59.358 40.000 0.00 0.00 42.73 2.83
764 794 6.316390 GTCTCGGTCCAATGAGATTTAACAAT 59.684 38.462 0.00 0.00 42.73 2.71
765 795 6.538742 TCTCGGTCCAATGAGATTTAACAATC 59.461 38.462 0.00 0.00 39.45 2.67
766 796 5.293324 TCGGTCCAATGAGATTTAACAATCG 59.707 40.000 0.00 0.00 43.38 3.34
767 797 5.293324 CGGTCCAATGAGATTTAACAATCGA 59.707 40.000 0.00 0.00 43.38 3.59
768 798 6.510157 CGGTCCAATGAGATTTAACAATCGAG 60.510 42.308 0.00 0.00 43.38 4.04
827 884 1.239968 GCTGCAGCAAACAGGCTAGT 61.240 55.000 33.36 0.00 43.68 2.57
845 902 3.542712 AGTAGCACGCACTGAAATTTG 57.457 42.857 0.00 0.00 0.00 2.32
846 903 3.138304 AGTAGCACGCACTGAAATTTGA 58.862 40.909 0.00 0.00 0.00 2.69
847 904 3.753272 AGTAGCACGCACTGAAATTTGAT 59.247 39.130 0.00 0.00 0.00 2.57
848 905 3.648339 AGCACGCACTGAAATTTGATT 57.352 38.095 0.00 0.00 0.00 2.57
849 906 3.981211 AGCACGCACTGAAATTTGATTT 58.019 36.364 0.00 0.00 34.64 2.17
852 909 3.490155 CACGCACTGAAATTTGATTTGCA 59.510 39.130 10.54 0.00 31.47 4.08
853 910 4.150980 CACGCACTGAAATTTGATTTGCAT 59.849 37.500 10.54 0.00 31.47 3.96
854 911 4.150980 ACGCACTGAAATTTGATTTGCATG 59.849 37.500 10.54 0.00 31.47 4.06
855 912 4.399978 GCACTGAAATTTGATTTGCATGC 58.600 39.130 11.82 11.82 31.47 4.06
856 913 4.083749 GCACTGAAATTTGATTTGCATGCA 60.084 37.500 18.46 18.46 31.47 3.96
876 933 1.865865 ATATCTGCGGTAAACAGGCG 58.134 50.000 0.00 0.00 35.78 5.52
877 934 0.808453 TATCTGCGGTAAACAGGCGC 60.808 55.000 0.00 0.00 35.78 6.53
882 939 3.799755 GGTAAACAGGCGCGGCAG 61.800 66.667 34.94 29.11 0.00 4.85
883 940 4.460873 GTAAACAGGCGCGGCAGC 62.461 66.667 34.94 10.08 40.74 5.25
939 1001 1.078285 GACGAGGAGAGGAGACGGT 60.078 63.158 0.00 0.00 0.00 4.83
1100 1164 2.513897 CGGAATCCCTCGCCCAAC 60.514 66.667 0.00 0.00 0.00 3.77
1123 1187 2.813042 GCAGCACGCCTCTCTGTC 60.813 66.667 0.00 0.00 32.94 3.51
1124 1188 2.969016 CAGCACGCCTCTCTGTCT 59.031 61.111 0.00 0.00 0.00 3.41
1125 1189 1.153862 CAGCACGCCTCTCTGTCTC 60.154 63.158 0.00 0.00 0.00 3.36
1174 1238 4.753662 CCCTCGTCTCGTCCCCCA 62.754 72.222 0.00 0.00 0.00 4.96
1748 1812 0.250234 CTGTTCCTCCGGATGCTCAA 59.750 55.000 3.57 0.00 0.00 3.02
1749 1813 0.690192 TGTTCCTCCGGATGCTCAAA 59.310 50.000 3.57 0.00 0.00 2.69
1839 1903 3.741476 GAGCTTGGCCGGCAAGTG 61.741 66.667 30.85 15.17 32.59 3.16
1945 2009 4.832608 CCTGCGGCCGGAAGTACC 62.833 72.222 29.38 8.68 0.00 3.34
2286 2350 0.250209 CCTGGAATGCCCTGATCTCG 60.250 60.000 0.00 0.00 36.07 4.04
2373 2437 2.337532 CCCGACGAGACCACGTTT 59.662 61.111 0.00 0.00 46.52 3.60
2727 2791 2.115266 AAAGGGGAGGTTGGCACG 59.885 61.111 0.00 0.00 0.00 5.34
2752 2816 0.103208 GGCGATCTTCGACTCCATGT 59.897 55.000 0.32 0.00 46.20 3.21
2756 2820 1.405821 GATCTTCGACTCCATGTCCGT 59.594 52.381 0.00 0.00 42.49 4.69
2766 2830 4.129737 ATGTCCGTCGAGCACCGG 62.130 66.667 0.00 0.00 45.55 5.28
3003 3067 0.391661 CCTACGTGCTGCTGTCCAAT 60.392 55.000 0.00 0.00 0.00 3.16
3063 3127 1.556911 GTGAGAAGGCAGATGAGGGAA 59.443 52.381 0.00 0.00 0.00 3.97
3229 3299 4.520492 GCTGGGAGATGAAACTTTTGAAGA 59.480 41.667 0.00 0.00 0.00 2.87
3273 3343 6.753897 GAAAGCGTTTCTTGATGTTTCAAT 57.246 33.333 0.00 0.00 40.95 2.57
3275 3345 5.437289 AGCGTTTCTTGATGTTTCAATCA 57.563 34.783 0.00 0.00 40.95 2.57
3276 3346 5.830912 AGCGTTTCTTGATGTTTCAATCAA 58.169 33.333 0.18 0.18 42.78 2.57
3277 3347 6.272318 AGCGTTTCTTGATGTTTCAATCAAA 58.728 32.000 1.69 0.00 43.97 2.69
3278 3348 6.198966 AGCGTTTCTTGATGTTTCAATCAAAC 59.801 34.615 1.69 10.49 43.97 2.93
3280 3350 7.565789 GCGTTTCTTGATGTTTCAATCAAACTC 60.566 37.037 14.79 8.40 43.97 3.01
3281 3351 7.096477 CGTTTCTTGATGTTTCAATCAAACTCC 60.096 37.037 14.79 0.00 43.97 3.85
3305 3375 6.582295 CCTAACTTCGAAATTGTTTGACCATG 59.418 38.462 1.38 0.00 0.00 3.66
3321 3391 6.633500 TGACCATGAAAAAGGAAACTACAG 57.367 37.500 0.00 0.00 42.68 2.74
3330 3400 7.495934 TGAAAAAGGAAACTACAGAGTGAGAAG 59.504 37.037 0.00 0.00 42.68 2.85
3389 3459 6.872020 GTGGTGCTACAAAGTACAGAATAGAA 59.128 38.462 0.00 0.00 39.87 2.10
3439 3509 8.480643 ACGTTCTTGGTCAAGATTAATTCTAG 57.519 34.615 13.36 0.00 45.78 2.43
3484 3554 4.942761 ATGTGAAACTGGCAAGATTTGT 57.057 36.364 0.00 0.00 38.04 2.83
3730 3800 4.035675 CCACAGAACTGGACTCTCAAAAAC 59.964 45.833 6.76 0.00 32.30 2.43
3775 3845 8.677300 TCTTATTTTTCAGCTTACTAATGCCAG 58.323 33.333 0.00 0.00 0.00 4.85
3938 4012 0.830648 AGGCGGTGTATGCAGTATGT 59.169 50.000 0.00 0.00 39.31 2.29
4061 4227 7.232534 AGTCACTTAAAATTGTTTCATAGGCCA 59.767 33.333 5.01 0.00 0.00 5.36
4090 4256 5.041191 GACATGGGATCCTTATGTCAACT 57.959 43.478 33.71 17.06 46.12 3.16
4091 4257 6.174720 GACATGGGATCCTTATGTCAACTA 57.825 41.667 33.71 3.25 46.12 2.24
4092 4258 6.179906 ACATGGGATCCTTATGTCAACTAG 57.820 41.667 21.81 0.00 29.55 2.57
4093 4259 5.667626 ACATGGGATCCTTATGTCAACTAGT 59.332 40.000 21.81 0.00 29.55 2.57
4094 4260 6.844388 ACATGGGATCCTTATGTCAACTAGTA 59.156 38.462 21.81 0.00 29.55 1.82
4096 4262 7.743116 TGGGATCCTTATGTCAACTAGTAAA 57.257 36.000 12.58 0.00 0.00 2.01
4097 4263 8.331931 TGGGATCCTTATGTCAACTAGTAAAT 57.668 34.615 12.58 0.00 0.00 1.40
4098 4264 8.210946 TGGGATCCTTATGTCAACTAGTAAATG 58.789 37.037 12.58 0.00 0.00 2.32
4099 4265 7.173390 GGGATCCTTATGTCAACTAGTAAATGC 59.827 40.741 12.58 0.00 0.00 3.56
4100 4266 7.095607 GGATCCTTATGTCAACTAGTAAATGCG 60.096 40.741 3.84 0.00 0.00 4.73
4101 4267 5.522460 TCCTTATGTCAACTAGTAAATGCGC 59.478 40.000 0.00 0.00 0.00 6.09
4102 4268 5.293324 CCTTATGTCAACTAGTAAATGCGCA 59.707 40.000 14.96 14.96 0.00 6.09
4103 4269 4.600012 ATGTCAACTAGTAAATGCGCAC 57.400 40.909 14.90 0.00 0.00 5.34
4104 4270 2.410392 TGTCAACTAGTAAATGCGCACG 59.590 45.455 14.90 0.00 0.00 5.34
4105 4271 2.410730 GTCAACTAGTAAATGCGCACGT 59.589 45.455 14.90 5.96 0.00 4.49
4106 4272 2.410392 TCAACTAGTAAATGCGCACGTG 59.590 45.455 14.90 12.28 0.00 4.49
4107 4273 0.719465 ACTAGTAAATGCGCACGTGC 59.281 50.000 30.42 30.42 37.78 5.34
4127 4293 4.899516 TGCAACGCACGTTAATATTTAGG 58.100 39.130 8.26 0.00 36.46 2.69
4128 4294 3.722289 GCAACGCACGTTAATATTTAGGC 59.278 43.478 8.26 0.98 36.46 3.93
4129 4295 4.728307 GCAACGCACGTTAATATTTAGGCA 60.728 41.667 8.26 0.00 36.46 4.75
4130 4296 5.325494 CAACGCACGTTAATATTTAGGCAA 58.675 37.500 8.26 0.00 36.46 4.52
4131 4297 5.744666 ACGCACGTTAATATTTAGGCAAT 57.255 34.783 0.00 0.00 0.00 3.56
4132 4298 6.847956 ACGCACGTTAATATTTAGGCAATA 57.152 33.333 0.00 0.00 0.00 1.90
4133 4299 7.429636 ACGCACGTTAATATTTAGGCAATAT 57.570 32.000 0.00 0.00 39.43 1.28
4134 4300 8.537049 ACGCACGTTAATATTTAGGCAATATA 57.463 30.769 0.00 0.00 37.11 0.86
4135 4301 9.158233 ACGCACGTTAATATTTAGGCAATATAT 57.842 29.630 0.00 0.00 37.11 0.86
4136 4302 9.982291 CGCACGTTAATATTTAGGCAATATATT 57.018 29.630 0.00 0.00 37.11 1.28
4156 4322 5.545658 ATTAATTGCACGCGGATATTAGG 57.454 39.130 12.47 0.00 0.00 2.69
4157 4323 2.543777 ATTGCACGCGGATATTAGGT 57.456 45.000 12.47 0.00 0.00 3.08
4158 4324 3.671008 ATTGCACGCGGATATTAGGTA 57.329 42.857 12.47 0.00 0.00 3.08
4159 4325 3.671008 TTGCACGCGGATATTAGGTAT 57.329 42.857 12.47 0.00 0.00 2.73
4160 4326 2.954316 TGCACGCGGATATTAGGTATG 58.046 47.619 12.47 0.00 0.00 2.39
4161 4327 1.659098 GCACGCGGATATTAGGTATGC 59.341 52.381 12.47 2.06 0.00 3.14
4162 4328 2.674177 GCACGCGGATATTAGGTATGCT 60.674 50.000 12.47 0.00 0.00 3.79
4163 4329 3.428452 GCACGCGGATATTAGGTATGCTA 60.428 47.826 12.47 0.00 0.00 3.49
4164 4330 4.736759 GCACGCGGATATTAGGTATGCTAT 60.737 45.833 12.47 0.00 0.00 2.97
4165 4331 5.348986 CACGCGGATATTAGGTATGCTATT 58.651 41.667 12.47 0.00 0.00 1.73
4166 4332 6.500910 CACGCGGATATTAGGTATGCTATTA 58.499 40.000 12.47 0.00 0.00 0.98
4167 4333 7.145985 CACGCGGATATTAGGTATGCTATTAT 58.854 38.462 12.47 0.00 0.00 1.28
4168 4334 7.652105 CACGCGGATATTAGGTATGCTATTATT 59.348 37.037 12.47 0.00 0.00 1.40
4169 4335 8.202137 ACGCGGATATTAGGTATGCTATTATTT 58.798 33.333 12.47 0.00 0.00 1.40
4170 4336 8.487970 CGCGGATATTAGGTATGCTATTATTTG 58.512 37.037 0.00 0.00 0.00 2.32
4171 4337 9.326413 GCGGATATTAGGTATGCTATTATTTGT 57.674 33.333 0.00 0.00 0.00 2.83
4185 4351 9.786105 TGCTATTATTTGTGTGTTAATCATGTG 57.214 29.630 0.00 0.00 0.00 3.21
4220 4386 8.692110 ATATTTGGCATGATATTAATTGCACG 57.308 30.769 11.02 0.00 36.82 5.34
4221 4387 5.512753 TTGGCATGATATTAATTGCACGT 57.487 34.783 11.02 0.00 36.82 4.49
4222 4388 5.512753 TGGCATGATATTAATTGCACGTT 57.487 34.783 11.02 0.00 36.82 3.99
4223 4389 6.625873 TGGCATGATATTAATTGCACGTTA 57.374 33.333 11.02 0.00 36.82 3.18
4224 4390 7.032377 TGGCATGATATTAATTGCACGTTAA 57.968 32.000 11.02 6.07 36.82 2.01
4225 4391 7.484140 TGGCATGATATTAATTGCACGTTAAA 58.516 30.769 11.02 0.00 36.82 1.52
4226 4392 7.433719 TGGCATGATATTAATTGCACGTTAAAC 59.566 33.333 11.02 4.41 36.82 2.01
4227 4393 7.433719 GGCATGATATTAATTGCACGTTAAACA 59.566 33.333 11.02 8.38 36.82 2.83
4228 4394 8.259194 GCATGATATTAATTGCACGTTAAACAC 58.741 33.333 0.00 3.91 35.22 3.32
4241 4407 3.293605 CGTTAAACACGTTTAATGCTCGC 59.706 43.478 17.25 5.49 44.01 5.03
4242 4408 2.325509 AAACACGTTTAATGCTCGCC 57.674 45.000 0.00 0.00 0.00 5.54
4243 4409 1.231221 AACACGTTTAATGCTCGCCA 58.769 45.000 0.00 0.00 0.00 5.69
4244 4410 1.448985 ACACGTTTAATGCTCGCCAT 58.551 45.000 0.00 0.00 35.06 4.40
4245 4411 1.810151 ACACGTTTAATGCTCGCCATT 59.190 42.857 6.42 6.42 45.75 3.16
4246 4412 2.176369 CACGTTTAATGCTCGCCATTG 58.824 47.619 10.25 0.00 43.77 2.82
4247 4413 1.132262 ACGTTTAATGCTCGCCATTGG 59.868 47.619 0.00 0.00 43.77 3.16
4248 4414 1.400142 CGTTTAATGCTCGCCATTGGA 59.600 47.619 6.95 0.00 43.77 3.53
4249 4415 2.539547 CGTTTAATGCTCGCCATTGGAG 60.540 50.000 6.95 2.84 43.77 3.86
4257 4423 3.344904 CTCGCCATTGGAGCAATTTAG 57.655 47.619 6.95 0.00 31.05 1.85
4258 4424 2.023673 TCGCCATTGGAGCAATTTAGG 58.976 47.619 6.95 0.00 31.05 2.69
4259 4425 1.750778 CGCCATTGGAGCAATTTAGGT 59.249 47.619 6.95 0.00 31.05 3.08
4260 4426 2.223572 CGCCATTGGAGCAATTTAGGTC 60.224 50.000 6.95 0.00 31.05 3.85
4261 4427 2.223572 GCCATTGGAGCAATTTAGGTCG 60.224 50.000 6.95 0.00 36.90 4.79
4262 4428 3.016736 CCATTGGAGCAATTTAGGTCGT 58.983 45.455 0.00 0.00 36.90 4.34
4263 4429 3.443681 CCATTGGAGCAATTTAGGTCGTT 59.556 43.478 0.00 0.00 36.90 3.85
4264 4430 4.414852 CATTGGAGCAATTTAGGTCGTTG 58.585 43.478 0.00 0.00 36.90 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.574018 CGCGCTGGGGATGGATCTA 61.574 63.158 5.56 0.00 0.00 1.98
37 38 1.091771 AGTTTGATCATCGCGCTGGG 61.092 55.000 10.42 0.00 0.00 4.45
47 48 4.988540 CGTCCAACTTCTACAGTTTGATCA 59.011 41.667 0.00 0.00 43.89 2.92
50 51 3.128349 GCGTCCAACTTCTACAGTTTGA 58.872 45.455 0.00 0.00 43.89 2.69
52 53 3.391049 GAGCGTCCAACTTCTACAGTTT 58.609 45.455 0.00 0.00 43.89 2.66
82 83 2.761208 CGTTGAGGTAACAGAGGAGGAT 59.239 50.000 0.00 0.00 39.30 3.24
91 92 2.841215 CCCTTTGTCGTTGAGGTAACA 58.159 47.619 0.00 0.00 39.30 2.41
92 93 1.534163 GCCCTTTGTCGTTGAGGTAAC 59.466 52.381 0.00 0.00 35.90 2.50
167 168 2.095919 CGGATTCGACAAAAACTCCCAC 60.096 50.000 0.00 0.00 39.00 4.61
174 175 1.208103 GCGGCGGATTCGACAAAAA 59.792 52.632 9.78 0.00 46.65 1.94
178 179 4.812476 CAGGCGGCGGATTCGACA 62.812 66.667 9.78 0.00 46.65 4.35
180 181 3.133767 CTACAGGCGGCGGATTCGA 62.134 63.158 17.37 0.00 39.00 3.71
234 237 1.104577 AACGTTTGGTGGACGCCAAT 61.105 50.000 17.14 1.10 46.60 3.16
306 313 7.983484 TGTACATAGTAGTTTTAGCTTTAGGGC 59.017 37.037 0.00 0.00 0.00 5.19
314 321 6.476053 GCACTCCTGTACATAGTAGTTTTAGC 59.524 42.308 9.90 5.32 0.00 3.09
320 327 4.341487 TGTGCACTCCTGTACATAGTAGT 58.659 43.478 19.41 3.05 38.01 2.73
353 360 0.392336 GCTGATCGGAGAAGAGGCAT 59.608 55.000 5.48 0.00 43.58 4.40
354 361 0.972471 TGCTGATCGGAGAAGAGGCA 60.972 55.000 5.48 0.00 43.58 4.75
357 364 2.266554 GTGTTGCTGATCGGAGAAGAG 58.733 52.381 5.48 0.00 43.58 2.85
368 375 1.454201 TTTGTTGTCGGTGTTGCTGA 58.546 45.000 0.00 0.00 0.00 4.26
397 404 4.821589 GAGCTTGGGCCCGTCTCG 62.822 72.222 19.37 4.15 39.73 4.04
399 406 3.011517 ATGAGCTTGGGCCCGTCT 61.012 61.111 19.37 13.91 39.73 4.18
401 408 4.473520 CGATGAGCTTGGGCCCGT 62.474 66.667 19.37 0.30 39.73 5.28
442 457 9.447157 CAATTACTTTCTCTCTCAATCCTTCTT 57.553 33.333 0.00 0.00 0.00 2.52
542 569 8.133024 TGCCTTTTTGTTGGAATATATTGTCT 57.867 30.769 1.78 0.00 0.00 3.41
553 580 3.132111 GTCCTTCTTGCCTTTTTGTTGGA 59.868 43.478 0.00 0.00 0.00 3.53
554 581 3.118811 TGTCCTTCTTGCCTTTTTGTTGG 60.119 43.478 0.00 0.00 0.00 3.77
555 582 4.122143 TGTCCTTCTTGCCTTTTTGTTG 57.878 40.909 0.00 0.00 0.00 3.33
556 583 4.020662 TGTTGTCCTTCTTGCCTTTTTGTT 60.021 37.500 0.00 0.00 0.00 2.83
557 584 3.513515 TGTTGTCCTTCTTGCCTTTTTGT 59.486 39.130 0.00 0.00 0.00 2.83
558 585 4.122143 TGTTGTCCTTCTTGCCTTTTTG 57.878 40.909 0.00 0.00 0.00 2.44
563 593 4.082026 GCAAATATGTTGTCCTTCTTGCCT 60.082 41.667 0.00 0.00 33.50 4.75
593 623 6.598064 TCTTAGTCGATTGAGATGTAGTCACA 59.402 38.462 0.00 0.00 39.52 3.58
594 624 6.908284 GTCTTAGTCGATTGAGATGTAGTCAC 59.092 42.308 5.71 0.00 0.00 3.67
595 625 6.824196 AGTCTTAGTCGATTGAGATGTAGTCA 59.176 38.462 5.71 0.00 0.00 3.41
596 626 7.254227 AGTCTTAGTCGATTGAGATGTAGTC 57.746 40.000 5.71 0.00 0.00 2.59
597 627 7.633193 AAGTCTTAGTCGATTGAGATGTAGT 57.367 36.000 5.71 0.00 0.00 2.73
598 628 9.440784 GTTAAGTCTTAGTCGATTGAGATGTAG 57.559 37.037 5.71 0.00 0.00 2.74
599 629 8.121086 CGTTAAGTCTTAGTCGATTGAGATGTA 58.879 37.037 5.71 0.00 0.00 2.29
600 630 6.967767 CGTTAAGTCTTAGTCGATTGAGATGT 59.032 38.462 5.71 0.58 0.00 3.06
601 631 7.187480 TCGTTAAGTCTTAGTCGATTGAGATG 58.813 38.462 5.71 0.00 0.00 2.90
602 632 7.317842 TCGTTAAGTCTTAGTCGATTGAGAT 57.682 36.000 5.71 0.00 0.00 2.75
603 633 6.183360 CCTCGTTAAGTCTTAGTCGATTGAGA 60.183 42.308 16.54 0.00 0.00 3.27
604 634 5.966503 CCTCGTTAAGTCTTAGTCGATTGAG 59.033 44.000 16.54 0.00 0.00 3.02
605 635 5.413833 ACCTCGTTAAGTCTTAGTCGATTGA 59.586 40.000 16.54 0.00 0.00 2.57
606 636 5.638783 ACCTCGTTAAGTCTTAGTCGATTG 58.361 41.667 16.54 14.09 0.00 2.67
607 637 5.647225 AGACCTCGTTAAGTCTTAGTCGATT 59.353 40.000 16.54 10.37 40.43 3.34
608 638 5.184711 AGACCTCGTTAAGTCTTAGTCGAT 58.815 41.667 16.54 7.99 40.43 3.59
609 639 4.573900 AGACCTCGTTAAGTCTTAGTCGA 58.426 43.478 15.81 15.81 40.43 4.20
610 640 4.492247 CGAGACCTCGTTAAGTCTTAGTCG 60.492 50.000 10.96 10.84 46.99 4.18
611 641 4.896080 CGAGACCTCGTTAAGTCTTAGTC 58.104 47.826 10.96 0.00 46.99 2.59
612 642 4.943142 CGAGACCTCGTTAAGTCTTAGT 57.057 45.455 10.96 0.00 46.99 2.24
625 655 2.030185 TGTGTCACTTAAGCGAGACCTC 60.030 50.000 15.77 11.11 0.00 3.85
626 656 1.961394 TGTGTCACTTAAGCGAGACCT 59.039 47.619 15.77 0.00 0.00 3.85
627 657 2.433868 TGTGTCACTTAAGCGAGACC 57.566 50.000 15.77 9.94 0.00 3.85
628 658 3.381949 AGTTGTGTCACTTAAGCGAGAC 58.618 45.455 12.55 12.55 0.00 3.36
629 659 3.728076 AGTTGTGTCACTTAAGCGAGA 57.272 42.857 1.29 0.00 0.00 4.04
630 660 7.576750 TTATAAGTTGTGTCACTTAAGCGAG 57.423 36.000 1.29 0.00 41.52 5.03
631 661 7.949903 TTTATAAGTTGTGTCACTTAAGCGA 57.050 32.000 1.29 0.00 41.52 4.93
632 662 8.996988 TTTTTATAAGTTGTGTCACTTAAGCG 57.003 30.769 1.29 0.00 41.52 4.68
678 708 7.592938 TCTTGCATGAAGATTCGTGTATTTTT 58.407 30.769 14.52 0.00 44.17 1.94
679 709 7.144722 TCTTGCATGAAGATTCGTGTATTTT 57.855 32.000 14.52 0.00 44.17 1.82
680 710 6.741992 TCTTGCATGAAGATTCGTGTATTT 57.258 33.333 14.52 0.00 44.17 1.40
691 721 4.765813 TCCATGAGATCTTGCATGAAGA 57.234 40.909 20.59 10.83 45.03 2.87
692 722 7.413109 CGAATATCCATGAGATCTTGCATGAAG 60.413 40.741 20.59 9.13 43.43 3.02
693 723 6.370718 CGAATATCCATGAGATCTTGCATGAA 59.629 38.462 20.59 5.99 43.43 2.57
694 724 5.873164 CGAATATCCATGAGATCTTGCATGA 59.127 40.000 20.59 4.57 43.43 3.07
695 725 5.873164 TCGAATATCCATGAGATCTTGCATG 59.127 40.000 14.61 14.61 41.11 4.06
696 726 6.046290 TCGAATATCCATGAGATCTTGCAT 57.954 37.500 0.00 0.00 36.33 3.96
697 727 5.473066 TCGAATATCCATGAGATCTTGCA 57.527 39.130 0.00 0.00 36.33 4.08
698 728 5.231779 CGATCGAATATCCATGAGATCTTGC 59.768 44.000 10.26 0.00 36.33 4.01
699 729 6.471841 GTCGATCGAATATCCATGAGATCTTG 59.528 42.308 21.31 0.00 36.33 3.02
700 730 6.405286 GGTCGATCGAATATCCATGAGATCTT 60.405 42.308 21.31 0.00 36.33 2.40
701 731 5.067153 GGTCGATCGAATATCCATGAGATCT 59.933 44.000 21.31 0.00 36.33 2.75
702 732 5.277825 GGTCGATCGAATATCCATGAGATC 58.722 45.833 21.31 1.53 36.33 2.75
703 733 4.201960 CGGTCGATCGAATATCCATGAGAT 60.202 45.833 21.31 0.00 39.15 2.75
704 734 3.127030 CGGTCGATCGAATATCCATGAGA 59.873 47.826 21.31 0.00 0.00 3.27
705 735 3.127030 TCGGTCGATCGAATATCCATGAG 59.873 47.826 20.25 4.26 36.12 2.90
706 736 3.078837 TCGGTCGATCGAATATCCATGA 58.921 45.455 20.25 7.59 36.12 3.07
707 737 3.127030 TCTCGGTCGATCGAATATCCATG 59.873 47.826 22.75 7.79 38.77 3.66
708 738 3.344515 TCTCGGTCGATCGAATATCCAT 58.655 45.455 22.75 0.00 38.77 3.41
709 739 2.742589 CTCTCGGTCGATCGAATATCCA 59.257 50.000 22.75 6.87 38.77 3.41
710 740 2.743126 ACTCTCGGTCGATCGAATATCC 59.257 50.000 22.75 15.59 38.77 2.59
711 741 4.407496 AACTCTCGGTCGATCGAATATC 57.593 45.455 22.75 7.18 38.77 1.63
712 742 4.036498 ACAAACTCTCGGTCGATCGAATAT 59.964 41.667 22.75 7.02 38.77 1.28
713 743 3.376234 ACAAACTCTCGGTCGATCGAATA 59.624 43.478 22.75 12.11 38.77 1.75
714 744 2.163815 ACAAACTCTCGGTCGATCGAAT 59.836 45.455 22.75 7.79 38.77 3.34
715 745 1.538512 ACAAACTCTCGGTCGATCGAA 59.461 47.619 22.75 11.90 38.77 3.71
716 746 1.162698 ACAAACTCTCGGTCGATCGA 58.837 50.000 21.21 21.21 37.60 3.59
717 747 1.978542 AACAAACTCTCGGTCGATCG 58.021 50.000 12.98 12.98 0.00 3.69
718 748 4.483311 ACTTAACAAACTCTCGGTCGATC 58.517 43.478 0.00 0.00 0.00 3.69
719 749 4.217983 AGACTTAACAAACTCTCGGTCGAT 59.782 41.667 0.00 0.00 0.00 3.59
720 750 3.567164 AGACTTAACAAACTCTCGGTCGA 59.433 43.478 0.00 0.00 0.00 4.20
721 751 3.898529 AGACTTAACAAACTCTCGGTCG 58.101 45.455 0.00 0.00 0.00 4.79
722 752 3.913163 CGAGACTTAACAAACTCTCGGTC 59.087 47.826 7.82 0.00 45.42 4.79
723 753 3.898529 CGAGACTTAACAAACTCTCGGT 58.101 45.455 7.82 0.00 45.42 4.69
726 756 4.236147 GGACCGAGACTTAACAAACTCTC 58.764 47.826 0.00 0.00 0.00 3.20
727 757 3.640029 TGGACCGAGACTTAACAAACTCT 59.360 43.478 0.00 0.00 0.00 3.24
728 758 3.986277 TGGACCGAGACTTAACAAACTC 58.014 45.455 0.00 0.00 0.00 3.01
729 759 4.411256 TTGGACCGAGACTTAACAAACT 57.589 40.909 0.00 0.00 0.00 2.66
730 760 4.753107 TCATTGGACCGAGACTTAACAAAC 59.247 41.667 0.00 0.00 0.00 2.93
731 761 4.963373 TCATTGGACCGAGACTTAACAAA 58.037 39.130 0.00 0.00 0.00 2.83
732 762 4.282449 TCTCATTGGACCGAGACTTAACAA 59.718 41.667 0.00 0.00 33.37 2.83
733 763 3.830178 TCTCATTGGACCGAGACTTAACA 59.170 43.478 0.00 0.00 33.37 2.41
734 764 4.451629 TCTCATTGGACCGAGACTTAAC 57.548 45.455 0.00 0.00 33.37 2.01
735 765 5.677319 AATCTCATTGGACCGAGACTTAA 57.323 39.130 0.19 0.00 40.92 1.85
736 766 5.677319 AAATCTCATTGGACCGAGACTTA 57.323 39.130 0.19 0.00 40.92 2.24
737 767 4.559862 AAATCTCATTGGACCGAGACTT 57.440 40.909 0.19 0.00 40.92 3.01
738 768 5.046591 TGTTAAATCTCATTGGACCGAGACT 60.047 40.000 0.19 0.00 40.92 3.24
739 769 5.175859 TGTTAAATCTCATTGGACCGAGAC 58.824 41.667 0.19 0.00 40.92 3.36
740 770 5.414789 TGTTAAATCTCATTGGACCGAGA 57.585 39.130 0.66 0.66 42.25 4.04
741 771 6.510157 CGATTGTTAAATCTCATTGGACCGAG 60.510 42.308 0.00 0.00 40.15 4.63
742 772 5.293324 CGATTGTTAAATCTCATTGGACCGA 59.707 40.000 0.00 0.00 40.15 4.69
743 773 5.293324 TCGATTGTTAAATCTCATTGGACCG 59.707 40.000 0.00 0.00 40.15 4.79
744 774 6.316390 ACTCGATTGTTAAATCTCATTGGACC 59.684 38.462 0.00 0.00 40.15 4.46
745 775 7.308782 ACTCGATTGTTAAATCTCATTGGAC 57.691 36.000 0.00 0.00 40.15 4.02
746 776 7.626240 GCAACTCGATTGTTAAATCTCATTGGA 60.626 37.037 8.64 0.00 40.15 3.53
747 777 6.470235 GCAACTCGATTGTTAAATCTCATTGG 59.530 38.462 8.64 0.00 40.15 3.16
748 778 7.246311 AGCAACTCGATTGTTAAATCTCATTG 58.754 34.615 8.64 0.00 40.15 2.82
749 779 7.383102 AGCAACTCGATTGTTAAATCTCATT 57.617 32.000 8.64 0.00 40.15 2.57
750 780 6.992063 AGCAACTCGATTGTTAAATCTCAT 57.008 33.333 8.64 0.00 40.15 2.90
751 781 8.390354 CAATAGCAACTCGATTGTTAAATCTCA 58.610 33.333 7.72 0.00 40.15 3.27
752 782 7.374491 GCAATAGCAACTCGATTGTTAAATCTC 59.626 37.037 7.72 0.00 37.51 2.75
753 783 7.066284 AGCAATAGCAACTCGATTGTTAAATCT 59.934 33.333 7.72 4.20 45.49 2.40
754 784 7.189512 AGCAATAGCAACTCGATTGTTAAATC 58.810 34.615 7.72 0.00 45.49 2.17
755 785 7.088589 AGCAATAGCAACTCGATTGTTAAAT 57.911 32.000 7.72 0.00 45.49 1.40
756 786 6.494893 AGCAATAGCAACTCGATTGTTAAA 57.505 33.333 7.72 0.00 45.49 1.52
757 787 7.786178 ATAGCAATAGCAACTCGATTGTTAA 57.214 32.000 7.72 0.00 45.49 2.01
758 788 7.630026 CAATAGCAATAGCAACTCGATTGTTA 58.370 34.615 8.64 7.60 45.49 2.41
759 789 6.489675 CAATAGCAATAGCAACTCGATTGTT 58.510 36.000 8.64 6.03 45.49 2.83
760 790 5.504665 GCAATAGCAATAGCAACTCGATTGT 60.505 40.000 8.64 0.00 45.49 2.71
761 791 4.908156 GCAATAGCAATAGCAACTCGATTG 59.092 41.667 0.00 0.00 45.49 2.67
762 792 4.319046 CGCAATAGCAATAGCAACTCGATT 60.319 41.667 0.00 0.00 45.49 3.34
763 793 3.185188 CGCAATAGCAATAGCAACTCGAT 59.815 43.478 0.00 0.00 45.49 3.59
764 794 2.539688 CGCAATAGCAATAGCAACTCGA 59.460 45.455 0.00 0.00 45.49 4.04
765 795 2.896289 CGCAATAGCAATAGCAACTCG 58.104 47.619 0.00 0.00 45.49 4.18
766 796 2.032054 TGCGCAATAGCAATAGCAACTC 59.968 45.455 8.16 0.00 45.06 3.01
767 797 2.016318 TGCGCAATAGCAATAGCAACT 58.984 42.857 8.16 0.00 45.06 3.16
768 798 2.473530 TGCGCAATAGCAATAGCAAC 57.526 45.000 8.16 0.00 45.06 4.17
827 884 4.764679 AATCAAATTTCAGTGCGTGCTA 57.235 36.364 0.00 0.00 0.00 3.49
855 912 2.032894 CGCCTGTTTACCGCAGATATTG 60.033 50.000 0.00 0.00 36.12 1.90
856 913 2.210116 CGCCTGTTTACCGCAGATATT 58.790 47.619 0.00 0.00 36.12 1.28
865 922 3.799755 CTGCCGCGCCTGTTTACC 61.800 66.667 0.00 0.00 0.00 2.85
867 924 4.697756 AGCTGCCGCGCCTGTTTA 62.698 61.111 0.00 0.00 42.32 2.01
876 933 1.997928 GATTCTTGGGAAGCTGCCGC 61.998 60.000 4.08 0.00 35.27 6.53
877 934 0.677731 TGATTCTTGGGAAGCTGCCG 60.678 55.000 4.08 0.00 38.52 5.69
879 936 3.194116 TGAATTGATTCTTGGGAAGCTGC 59.806 43.478 5.42 0.00 38.52 5.25
880 937 5.395682 TTGAATTGATTCTTGGGAAGCTG 57.604 39.130 5.42 0.00 38.52 4.24
881 938 5.279657 GGTTTGAATTGATTCTTGGGAAGCT 60.280 40.000 5.42 0.00 38.52 3.74
882 939 4.931601 GGTTTGAATTGATTCTTGGGAAGC 59.068 41.667 5.42 0.00 38.23 3.86
883 940 6.015180 TCTGGTTTGAATTGATTCTTGGGAAG 60.015 38.462 5.42 0.00 37.67 3.46
885 942 5.243730 GTCTGGTTTGAATTGATTCTTGGGA 59.756 40.000 5.42 0.00 37.67 4.37
886 943 5.473039 GTCTGGTTTGAATTGATTCTTGGG 58.527 41.667 5.42 0.00 37.67 4.12
887 944 5.156355 CGTCTGGTTTGAATTGATTCTTGG 58.844 41.667 5.42 0.00 37.67 3.61
1110 1174 0.679640 AGGAGAGACAGAGAGGCGTG 60.680 60.000 0.00 0.00 0.00 5.34
1512 1576 3.718210 GAGCTGCCGAACTACCCCG 62.718 68.421 0.00 0.00 0.00 5.73
1516 1580 1.805945 CGTGGAGCTGCCGAACTAC 60.806 63.158 1.53 0.00 40.66 2.73
1872 1936 3.047280 TTGCCGATGGTGACGTGC 61.047 61.111 0.00 0.00 0.00 5.34
1942 2006 2.998097 GCCCATGGACTGCAGGTA 59.002 61.111 19.93 3.81 0.00 3.08
1943 2007 4.415150 CGCCCATGGACTGCAGGT 62.415 66.667 19.93 3.31 0.00 4.00
1945 2009 2.513204 CTCGCCCATGGACTGCAG 60.513 66.667 15.22 13.48 0.00 4.41
2017 2081 0.523072 ATGCCATTGAACAGTGCGAC 59.477 50.000 0.00 0.00 0.00 5.19
2022 2086 1.885157 CCGCATGCCATTGAACAGT 59.115 52.632 13.15 0.00 0.00 3.55
2268 2332 0.250209 CCGAGATCAGGGCATTCCAG 60.250 60.000 0.00 0.00 38.24 3.86
2607 2671 2.758327 ACGGCGTCATAGCTCCCA 60.758 61.111 6.77 0.00 37.29 4.37
2634 2698 2.769617 CGCACCATGTCGTCGAAC 59.230 61.111 0.00 0.00 0.00 3.95
2727 2791 2.174319 GTCGAAGATCGCCTTGCCC 61.174 63.158 0.00 0.00 40.67 5.36
2748 2812 2.880879 CGGTGCTCGACGGACATG 60.881 66.667 0.00 0.00 42.43 3.21
2796 2860 1.138883 GCCTAGCATGTCGACGACA 59.861 57.895 30.90 30.90 46.90 4.35
2884 2948 0.036010 GCTCCCAGCAAGCTCTGTAA 60.036 55.000 2.09 0.00 41.89 2.41
2886 2950 2.350514 GCTCCCAGCAAGCTCTGT 59.649 61.111 2.09 0.00 41.89 3.41
3003 3067 0.538977 CCCCCTTCTCGGCGTAGATA 60.539 60.000 6.85 0.04 0.00 1.98
3063 3127 2.203938 TCCTTCCTCACGCCCCTT 60.204 61.111 0.00 0.00 0.00 3.95
3204 3274 2.222227 AAAGTTTCATCTCCCAGCCC 57.778 50.000 0.00 0.00 0.00 5.19
3229 3299 1.069823 TGTTTCCATGCGCAAATGGTT 59.930 42.857 25.27 1.20 46.24 3.67
3273 3343 7.562454 AACAATTTCGAAGTTAGGAGTTTGA 57.438 32.000 5.52 0.00 0.00 2.69
3275 3345 7.913821 GTCAAACAATTTCGAAGTTAGGAGTTT 59.086 33.333 5.52 9.12 0.00 2.66
3276 3346 7.415229 GTCAAACAATTTCGAAGTTAGGAGTT 58.585 34.615 5.52 3.66 0.00 3.01
3277 3347 6.017357 GGTCAAACAATTTCGAAGTTAGGAGT 60.017 38.462 5.52 0.00 0.00 3.85
3278 3348 6.017440 TGGTCAAACAATTTCGAAGTTAGGAG 60.017 38.462 5.52 0.00 0.00 3.69
3280 3350 6.067263 TGGTCAAACAATTTCGAAGTTAGG 57.933 37.500 5.52 0.00 0.00 2.69
3281 3351 7.359595 TCATGGTCAAACAATTTCGAAGTTAG 58.640 34.615 5.52 3.89 0.00 2.34
3305 3375 7.711339 TCTTCTCACTCTGTAGTTTCCTTTTTC 59.289 37.037 0.00 0.00 31.97 2.29
3321 3391 1.001860 AGTTGCTGCCTCTTCTCACTC 59.998 52.381 0.00 0.00 0.00 3.51
3330 3400 2.806856 CGATGCGAGTTGCTGCCTC 61.807 63.158 3.50 0.00 46.63 4.70
3439 3509 9.722056 CATTTGGTTGCTTATGTTAAGATAGTC 57.278 33.333 0.00 0.00 0.00 2.59
3484 3554 6.486657 CCAAGTTTTAGTCATCCTTGTTCTCA 59.513 38.462 0.00 0.00 32.56 3.27
3730 3800 4.021102 AGAAGGTACCTGTTCCATGTTG 57.979 45.455 17.14 0.00 0.00 3.33
4043 4209 5.012975 ACCATGTGGCCTATGAAACAATTTT 59.987 36.000 18.48 0.00 39.32 1.82
4061 4227 1.600058 AGGATCCCATGTCACCATGT 58.400 50.000 8.55 0.00 45.83 3.21
4089 4255 0.718904 TGCACGTGCGCATTTACTAG 59.281 50.000 33.22 0.66 45.83 2.57
4090 4256 1.136197 GTTGCACGTGCGCATTTACTA 60.136 47.619 33.22 11.66 45.83 1.82
4091 4257 0.385473 GTTGCACGTGCGCATTTACT 60.385 50.000 33.22 0.00 45.83 2.24
4092 4258 1.652148 CGTTGCACGTGCGCATTTAC 61.652 55.000 33.22 21.25 45.83 2.01
4093 4259 1.439529 CGTTGCACGTGCGCATTTA 60.440 52.632 33.22 14.00 45.83 1.40
4094 4260 2.725450 CGTTGCACGTGCGCATTT 60.725 55.556 33.22 0.00 45.83 2.32
4105 4271 4.728307 GCCTAAATATTAACGTGCGTTGCA 60.728 41.667 18.63 6.89 38.92 4.08
4106 4272 3.722289 GCCTAAATATTAACGTGCGTTGC 59.278 43.478 18.63 7.40 38.92 4.17
4107 4273 4.899516 TGCCTAAATATTAACGTGCGTTG 58.100 39.130 18.63 1.52 38.92 4.10
4108 4274 5.548706 TTGCCTAAATATTAACGTGCGTT 57.451 34.783 14.41 14.41 41.65 4.84
4109 4275 5.744666 ATTGCCTAAATATTAACGTGCGT 57.255 34.783 0.00 0.00 0.00 5.24
4110 4276 9.982291 AATATATTGCCTAAATATTAACGTGCG 57.018 29.630 0.00 0.00 41.01 5.34
4130 4296 8.988934 CCTAATATCCGCGTGCAATTAATATAT 58.011 33.333 4.92 0.00 0.00 0.86
4131 4297 7.982919 ACCTAATATCCGCGTGCAATTAATATA 59.017 33.333 4.92 0.00 0.00 0.86
4132 4298 6.821665 ACCTAATATCCGCGTGCAATTAATAT 59.178 34.615 4.92 0.00 0.00 1.28
4133 4299 6.167685 ACCTAATATCCGCGTGCAATTAATA 58.832 36.000 4.92 0.00 0.00 0.98
4134 4300 5.001232 ACCTAATATCCGCGTGCAATTAAT 58.999 37.500 4.92 0.00 0.00 1.40
4135 4301 4.382291 ACCTAATATCCGCGTGCAATTAA 58.618 39.130 4.92 0.00 0.00 1.40
4136 4302 3.997762 ACCTAATATCCGCGTGCAATTA 58.002 40.909 4.92 3.03 0.00 1.40
4137 4303 2.846193 ACCTAATATCCGCGTGCAATT 58.154 42.857 4.92 1.90 0.00 2.32
4138 4304 2.543777 ACCTAATATCCGCGTGCAAT 57.456 45.000 4.92 0.00 0.00 3.56
4139 4305 3.322369 CATACCTAATATCCGCGTGCAA 58.678 45.455 4.92 0.00 0.00 4.08
4140 4306 2.929161 GCATACCTAATATCCGCGTGCA 60.929 50.000 4.92 0.00 0.00 4.57
4141 4307 1.659098 GCATACCTAATATCCGCGTGC 59.341 52.381 4.92 0.00 0.00 5.34
4142 4308 3.232213 AGCATACCTAATATCCGCGTG 57.768 47.619 4.92 0.00 0.00 5.34
4143 4309 5.593679 AATAGCATACCTAATATCCGCGT 57.406 39.130 4.92 0.00 0.00 6.01
4144 4310 8.487970 CAAATAATAGCATACCTAATATCCGCG 58.512 37.037 0.00 0.00 0.00 6.46
4145 4311 9.326413 ACAAATAATAGCATACCTAATATCCGC 57.674 33.333 0.00 0.00 0.00 5.54
4159 4325 9.786105 CACATGATTAACACACAAATAATAGCA 57.214 29.630 0.00 0.00 0.00 3.49
4194 4360 9.142515 CGTGCAATTAATATCATGCCAAATATT 57.857 29.630 7.25 3.64 38.00 1.28
4195 4361 8.306038 ACGTGCAATTAATATCATGCCAAATAT 58.694 29.630 7.25 0.00 38.00 1.28
4196 4362 7.656412 ACGTGCAATTAATATCATGCCAAATA 58.344 30.769 7.25 0.00 38.00 1.40
4197 4363 6.514947 ACGTGCAATTAATATCATGCCAAAT 58.485 32.000 7.25 0.00 38.00 2.32
4198 4364 5.900425 ACGTGCAATTAATATCATGCCAAA 58.100 33.333 7.25 0.00 38.00 3.28
4199 4365 5.512753 ACGTGCAATTAATATCATGCCAA 57.487 34.783 7.25 0.00 38.00 4.52
4200 4366 5.512753 AACGTGCAATTAATATCATGCCA 57.487 34.783 7.25 0.00 38.00 4.92
4201 4367 7.433719 TGTTTAACGTGCAATTAATATCATGCC 59.566 33.333 7.25 0.00 38.00 4.40
4202 4368 8.259194 GTGTTTAACGTGCAATTAATATCATGC 58.741 33.333 5.50 3.37 39.22 4.06
4220 4386 3.600786 GGCGAGCATTAAACGTGTTTAAC 59.399 43.478 17.45 8.36 44.68 2.01
4221 4387 3.250280 TGGCGAGCATTAAACGTGTTTAA 59.750 39.130 17.42 17.42 45.56 1.52
4222 4388 2.806818 TGGCGAGCATTAAACGTGTTTA 59.193 40.909 1.18 1.18 34.23 2.01
4223 4389 1.604755 TGGCGAGCATTAAACGTGTTT 59.395 42.857 3.21 3.21 36.63 2.83
4224 4390 1.231221 TGGCGAGCATTAAACGTGTT 58.769 45.000 0.00 0.00 0.00 3.32
4225 4391 1.448985 ATGGCGAGCATTAAACGTGT 58.551 45.000 0.00 0.00 0.00 4.49
4226 4392 2.176369 CAATGGCGAGCATTAAACGTG 58.824 47.619 0.00 0.00 0.00 4.49
4227 4393 1.132262 CCAATGGCGAGCATTAAACGT 59.868 47.619 0.00 0.00 0.00 3.99
4228 4394 1.400142 TCCAATGGCGAGCATTAAACG 59.600 47.619 0.00 0.00 0.00 3.60
4229 4395 3.070429 CTCCAATGGCGAGCATTAAAC 57.930 47.619 0.00 0.00 0.00 2.01
4237 4403 2.033801 CCTAAATTGCTCCAATGGCGAG 59.966 50.000 0.00 0.00 34.04 5.03
4238 4404 2.023673 CCTAAATTGCTCCAATGGCGA 58.976 47.619 0.00 0.00 34.04 5.54
4239 4405 1.750778 ACCTAAATTGCTCCAATGGCG 59.249 47.619 0.00 0.00 34.04 5.69
4240 4406 2.223572 CGACCTAAATTGCTCCAATGGC 60.224 50.000 0.00 0.00 34.04 4.40
4241 4407 3.016736 ACGACCTAAATTGCTCCAATGG 58.983 45.455 0.00 0.00 34.04 3.16
4242 4408 4.414852 CAACGACCTAAATTGCTCCAATG 58.585 43.478 0.00 0.00 34.04 2.82
4243 4409 4.701956 CAACGACCTAAATTGCTCCAAT 57.298 40.909 0.00 0.00 35.39 3.16


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

AutoCloner maintained by Alex Coulton.