Multiple sequence alignment - TraesCS5B01G016000

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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 TraesCS5B01G016000 chr5B 100.000 2933 0 0 1 2933 15124537 15127469 0.000000e+00 5417
1 TraesCS5B01G016000 chr5B 94.377 1565 75 6 1206 2768 15054188 15055741 0.000000e+00 2390
2 TraesCS5B01G016000 chr5B 94.491 835 44 2 2099 2932 15079653 15080486 0.000000e+00 1286
3 TraesCS5B01G016000 chr5B 90.011 881 60 13 1212 2070 15187037 15186163 0.000000e+00 1114
4 TraesCS5B01G016000 chr5B 89.803 814 54 19 1095 1903 15005947 15005158 0.000000e+00 1016
5 TraesCS5B01G016000 chr5B 86.881 747 77 7 2102 2842 594963499 594964230 0.000000e+00 817
6 TraesCS5B01G016000 chr5B 91.562 557 47 0 1 557 367914994 367914438 0.000000e+00 769
7 TraesCS5B01G016000 chr5B 85.942 690 74 13 2099 2784 600061461 600060791 0.000000e+00 715
8 TraesCS5B01G016000 chr5B 94.488 381 20 1 1658 2037 15076598 15076978 1.170000e-163 586
9 TraesCS5B01G016000 chr5B 97.927 193 4 0 548 740 214934728 214934920 4.680000e-88 335
10 TraesCS5B01G016000 chr5B 88.318 214 10 4 888 1090 15006194 15005985 2.920000e-60 243
11 TraesCS5B01G016000 chr5B 93.571 140 8 1 748 887 367914452 367914314 1.070000e-49 207
12 TraesCS5B01G016000 chr7B 91.965 809 56 5 1095 1902 685479242 685478442 0.000000e+00 1125
13 TraesCS5B01G016000 chr7B 92.460 557 42 0 1 557 714484787 714484231 0.000000e+00 797
14 TraesCS5B01G016000 chr7B 94.064 219 11 2 541 758 68862231 68862014 6.060000e-87 331
15 TraesCS5B01G016000 chr7B 94.366 213 10 2 540 751 529951860 529951649 2.820000e-85 326
16 TraesCS5B01G016000 chr5A 90.024 822 64 9 1090 1902 14194302 14193490 0.000000e+00 1048
17 TraesCS5B01G016000 chr5A 90.657 792 65 6 1212 1999 14228136 14227350 0.000000e+00 1044
18 TraesCS5B01G016000 chr5A 86.297 686 72 11 2102 2784 608201626 608200960 0.000000e+00 726
19 TraesCS5B01G016000 chr5A 88.832 197 9 5 891 1078 14194539 14194347 2.270000e-56 230
20 TraesCS5B01G016000 chr1D 88.742 755 63 10 2099 2848 308562973 308562236 0.000000e+00 904
21 TraesCS5B01G016000 chr2D 86.526 757 79 9 2099 2848 608805842 608806582 0.000000e+00 811
22 TraesCS5B01G016000 chr2D 85.092 758 87 9 2099 2848 575607243 575606504 0.000000e+00 750
23 TraesCS5B01G016000 chr2D 89.946 557 56 0 1 557 448645165 448644609 0.000000e+00 719
24 TraesCS5B01G016000 chr3B 85.865 757 84 8 2099 2848 238303291 238304031 0.000000e+00 784
25 TraesCS5B01G016000 chr3B 85.714 749 76 20 2102 2841 460044483 460043757 0.000000e+00 761
26 TraesCS5B01G016000 chrUn 84.973 752 92 8 2102 2848 262698151 262697416 0.000000e+00 743
27 TraesCS5B01G016000 chr2A 89.568 556 58 0 2 557 70289067 70288512 0.000000e+00 706
28 TraesCS5B01G016000 chr2A 88.406 552 63 1 6 557 674157880 674157330 0.000000e+00 664
29 TraesCS5B01G016000 chr1A 84.554 751 72 11 2102 2848 573224955 573224245 0.000000e+00 704
30 TraesCS5B01G016000 chr1A 88.489 556 64 0 2 557 397064510 397065065 0.000000e+00 673
31 TraesCS5B01G016000 chr1B 98.438 192 3 0 554 745 110623002 110622811 3.620000e-89 339
32 TraesCS5B01G016000 chr1B 97.917 192 4 0 551 742 33923251 33923060 1.680000e-87 333
33 TraesCS5B01G016000 chr3A 98.429 191 3 0 554 744 642038750 642038940 1.300000e-88 337
34 TraesCS5B01G016000 chr4A 98.421 190 3 0 554 743 20234725 20234536 4.680000e-88 335
35 TraesCS5B01G016000 chr7A 97.917 192 4 0 557 748 105168808 105168999 1.680000e-87 333
36 TraesCS5B01G016000 chr7A 96.465 198 7 0 554 751 554383128 554383325 7.840000e-86 327
37 TraesCS5B01G016000 chr6B 89.011 91 10 0 2843 2933 700666361 700666451 2.390000e-21 113


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 TraesCS5B01G016000 chr5B 15124537 15127469 2932 False 5417.0 5417 100.0000 1 2933 1 chr5B.!!$F2 2932
1 TraesCS5B01G016000 chr5B 15054188 15055741 1553 False 2390.0 2390 94.3770 1206 2768 1 chr5B.!!$F1 1562
2 TraesCS5B01G016000 chr5B 15186163 15187037 874 True 1114.0 1114 90.0110 1212 2070 1 chr5B.!!$R1 858
3 TraesCS5B01G016000 chr5B 15076598 15080486 3888 False 936.0 1286 94.4895 1658 2932 2 chr5B.!!$F5 1274
4 TraesCS5B01G016000 chr5B 594963499 594964230 731 False 817.0 817 86.8810 2102 2842 1 chr5B.!!$F4 740
5 TraesCS5B01G016000 chr5B 600060791 600061461 670 True 715.0 715 85.9420 2099 2784 1 chr5B.!!$R2 685
6 TraesCS5B01G016000 chr5B 15005158 15006194 1036 True 629.5 1016 89.0605 888 1903 2 chr5B.!!$R3 1015
7 TraesCS5B01G016000 chr5B 367914314 367914994 680 True 488.0 769 92.5665 1 887 2 chr5B.!!$R4 886
8 TraesCS5B01G016000 chr7B 685478442 685479242 800 True 1125.0 1125 91.9650 1095 1902 1 chr7B.!!$R3 807
9 TraesCS5B01G016000 chr7B 714484231 714484787 556 True 797.0 797 92.4600 1 557 1 chr7B.!!$R4 556
10 TraesCS5B01G016000 chr5A 14227350 14228136 786 True 1044.0 1044 90.6570 1212 1999 1 chr5A.!!$R1 787
11 TraesCS5B01G016000 chr5A 608200960 608201626 666 True 726.0 726 86.2970 2102 2784 1 chr5A.!!$R2 682
12 TraesCS5B01G016000 chr5A 14193490 14194539 1049 True 639.0 1048 89.4280 891 1902 2 chr5A.!!$R3 1011
13 TraesCS5B01G016000 chr1D 308562236 308562973 737 True 904.0 904 88.7420 2099 2848 1 chr1D.!!$R1 749
14 TraesCS5B01G016000 chr2D 608805842 608806582 740 False 811.0 811 86.5260 2099 2848 1 chr2D.!!$F1 749
15 TraesCS5B01G016000 chr2D 575606504 575607243 739 True 750.0 750 85.0920 2099 2848 1 chr2D.!!$R2 749
16 TraesCS5B01G016000 chr2D 448644609 448645165 556 True 719.0 719 89.9460 1 557 1 chr2D.!!$R1 556
17 TraesCS5B01G016000 chr3B 238303291 238304031 740 False 784.0 784 85.8650 2099 2848 1 chr3B.!!$F1 749
18 TraesCS5B01G016000 chr3B 460043757 460044483 726 True 761.0 761 85.7140 2102 2841 1 chr3B.!!$R1 739
19 TraesCS5B01G016000 chrUn 262697416 262698151 735 True 743.0 743 84.9730 2102 2848 1 chrUn.!!$R1 746
20 TraesCS5B01G016000 chr2A 70288512 70289067 555 True 706.0 706 89.5680 2 557 1 chr2A.!!$R1 555
21 TraesCS5B01G016000 chr2A 674157330 674157880 550 True 664.0 664 88.4060 6 557 1 chr2A.!!$R2 551
22 TraesCS5B01G016000 chr1A 573224245 573224955 710 True 704.0 704 84.5540 2102 2848 1 chr1A.!!$R1 746
23 TraesCS5B01G016000 chr1A 397064510 397065065 555 False 673.0 673 88.4890 2 557 1 chr1A.!!$F1 555

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
617 618 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2406 5130 0.17895 TCTCCACCAGTGCAGTCTCT 60.179 55.0 0.0 0.0 0.0 3.1 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
63 64 1.098050 ATTTGGAGTCGCTCATTGCC 58.902 50.000 8.71 0.00 38.78 4.52
70 71 0.313672 GTCGCTCATTGCCACCAAAA 59.686 50.000 0.00 0.00 38.78 2.44
118 119 2.076863 GCAAGGCGAGTTGTGTAATCT 58.923 47.619 0.00 0.00 0.00 2.40
167 168 0.398318 GAGCCAGAGTTGAAGTGGGT 59.602 55.000 0.00 0.00 44.74 4.51
218 219 2.596904 ACCGATGGTTCTTATGACGG 57.403 50.000 0.00 0.00 43.61 4.79
400 401 0.608130 TGTTGTGGAGATGGACTCGG 59.392 55.000 0.00 0.00 45.76 4.63
475 476 5.975939 GCTTCCATAGTCAATGAAATCAAGC 59.024 40.000 0.00 0.00 37.86 4.01
477 478 7.649533 TTCCATAGTCAATGAAATCAAGCAT 57.350 32.000 0.00 0.00 37.86 3.79
499 500 5.049398 TCTTAGAACTTTGAGAGAGACGC 57.951 43.478 0.00 0.00 0.00 5.19
513 514 4.395542 AGAGAGACGCGTATTACTCTTGTT 59.604 41.667 23.86 13.21 39.39 2.83
557 558 7.039784 AGCTAGTGATTGTTTAGCCAATTTTGA 60.040 33.333 0.00 0.00 40.44 2.69
558 559 7.598493 GCTAGTGATTGTTTAGCCAATTTTGAA 59.402 33.333 0.00 0.00 35.24 2.69
559 560 7.951530 AGTGATTGTTTAGCCAATTTTGAAG 57.048 32.000 0.00 0.00 35.24 3.02
560 561 6.930722 AGTGATTGTTTAGCCAATTTTGAAGG 59.069 34.615 0.00 0.00 35.24 3.46
561 562 6.147656 GTGATTGTTTAGCCAATTTTGAAGGG 59.852 38.462 0.00 0.00 35.24 3.95
562 563 4.615588 TGTTTAGCCAATTTTGAAGGGG 57.384 40.909 0.00 0.00 0.00 4.79
563 564 4.227197 TGTTTAGCCAATTTTGAAGGGGA 58.773 39.130 0.00 0.00 0.00 4.81
564 565 4.283212 TGTTTAGCCAATTTTGAAGGGGAG 59.717 41.667 0.00 0.00 0.00 4.30
565 566 1.269958 AGCCAATTTTGAAGGGGAGC 58.730 50.000 0.00 0.00 0.00 4.70
566 567 0.250234 GCCAATTTTGAAGGGGAGCC 59.750 55.000 0.00 0.00 0.00 4.70
567 568 1.942776 CCAATTTTGAAGGGGAGCCT 58.057 50.000 0.00 0.00 0.00 4.58
568 569 2.259917 CCAATTTTGAAGGGGAGCCTT 58.740 47.619 0.00 0.00 0.00 4.35
569 570 2.027837 CCAATTTTGAAGGGGAGCCTTG 60.028 50.000 0.00 0.00 0.00 3.61
570 571 1.942776 ATTTTGAAGGGGAGCCTTGG 58.057 50.000 0.00 0.00 0.00 3.61
571 572 0.831711 TTTTGAAGGGGAGCCTTGGC 60.832 55.000 2.97 2.97 0.00 4.52
572 573 3.567579 TTGAAGGGGAGCCTTGGCG 62.568 63.158 5.95 0.00 0.00 5.69
580 581 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
581 582 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
582 583 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
583 584 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
584 585 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
586 587 3.799755 GGCGCAGTGGTAAAGCCG 61.800 66.667 10.83 0.00 41.21 5.52
592 593 2.359975 GTGGTAAAGCCGCTGCCT 60.360 61.111 0.00 0.00 44.20 4.75
593 594 1.971695 GTGGTAAAGCCGCTGCCTT 60.972 57.895 0.00 0.00 44.20 4.35
594 595 1.971167 TGGTAAAGCCGCTGCCTTG 60.971 57.895 0.00 0.00 41.21 3.61
595 596 1.971695 GGTAAAGCCGCTGCCTTGT 60.972 57.895 0.00 0.00 38.69 3.16
596 597 1.210155 GTAAAGCCGCTGCCTTGTG 59.790 57.895 0.00 0.00 38.69 3.33
597 598 1.072332 TAAAGCCGCTGCCTTGTGA 59.928 52.632 0.00 0.00 38.69 3.58
598 599 1.234615 TAAAGCCGCTGCCTTGTGAC 61.235 55.000 0.00 0.00 38.69 3.67
601 602 2.360350 CCGCTGCCTTGTGACCAT 60.360 61.111 0.00 0.00 0.00 3.55
602 603 2.693762 CCGCTGCCTTGTGACCATG 61.694 63.158 0.00 0.00 0.00 3.66
603 604 1.672030 CGCTGCCTTGTGACCATGA 60.672 57.895 0.00 0.00 0.00 3.07
604 605 1.642037 CGCTGCCTTGTGACCATGAG 61.642 60.000 0.00 0.00 0.00 2.90
605 606 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
615 616 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
616 617 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18
617 618 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.000 0.00 0.00 0.00 2.69
618 619 1.442769 CATGAGGTCACGGGTTCAAG 58.557 55.000 0.00 0.00 0.00 3.02
619 620 1.056660 ATGAGGTCACGGGTTCAAGT 58.943 50.000 0.00 0.00 0.00 3.16
620 621 0.834612 TGAGGTCACGGGTTCAAGTT 59.165 50.000 0.00 0.00 0.00 2.66
621 622 1.202604 TGAGGTCACGGGTTCAAGTTC 60.203 52.381 0.00 0.00 0.00 3.01
622 623 1.070289 GAGGTCACGGGTTCAAGTTCT 59.930 52.381 0.00 0.00 0.00 3.01
623 624 1.202651 AGGTCACGGGTTCAAGTTCTG 60.203 52.381 0.00 0.00 0.00 3.02
624 625 1.226746 GTCACGGGTTCAAGTTCTGG 58.773 55.000 0.00 0.00 0.00 3.86
625 626 1.124780 TCACGGGTTCAAGTTCTGGA 58.875 50.000 0.00 0.00 0.00 3.86
626 627 1.487142 TCACGGGTTCAAGTTCTGGAA 59.513 47.619 0.00 0.00 0.00 3.53
627 628 2.092861 TCACGGGTTCAAGTTCTGGAAA 60.093 45.455 0.00 0.00 0.00 3.13
628 629 2.032924 CACGGGTTCAAGTTCTGGAAAC 59.967 50.000 0.00 0.00 0.00 2.78
629 630 2.294074 CGGGTTCAAGTTCTGGAAACA 58.706 47.619 7.21 0.00 32.36 2.83
640 641 3.025924 TGGAAACAGCCTCTTGCAG 57.974 52.632 0.00 0.00 44.83 4.41
641 642 0.473755 TGGAAACAGCCTCTTGCAGA 59.526 50.000 0.00 0.00 44.83 4.26
642 643 1.133823 TGGAAACAGCCTCTTGCAGAA 60.134 47.619 0.00 0.00 44.83 3.02
643 644 1.956477 GGAAACAGCCTCTTGCAGAAA 59.044 47.619 0.00 0.00 44.83 2.52
644 645 2.560105 GGAAACAGCCTCTTGCAGAAAT 59.440 45.455 0.00 0.00 44.83 2.17
645 646 3.572584 GAAACAGCCTCTTGCAGAAATG 58.427 45.455 0.00 0.00 44.83 2.32
646 647 2.283145 ACAGCCTCTTGCAGAAATGT 57.717 45.000 0.00 0.00 44.83 2.71
647 648 3.423539 ACAGCCTCTTGCAGAAATGTA 57.576 42.857 0.00 0.00 44.83 2.29
648 649 3.341823 ACAGCCTCTTGCAGAAATGTAG 58.658 45.455 0.00 0.00 44.83 2.74
649 650 2.681848 CAGCCTCTTGCAGAAATGTAGG 59.318 50.000 0.00 0.00 44.83 3.18
650 651 2.019984 GCCTCTTGCAGAAATGTAGGG 58.980 52.381 0.00 0.00 40.77 3.53
651 652 2.356125 GCCTCTTGCAGAAATGTAGGGA 60.356 50.000 0.00 0.00 40.77 4.20
652 653 3.873801 GCCTCTTGCAGAAATGTAGGGAA 60.874 47.826 0.00 0.00 40.77 3.97
653 654 4.335416 CCTCTTGCAGAAATGTAGGGAAA 58.665 43.478 0.00 0.00 0.00 3.13
654 655 4.397417 CCTCTTGCAGAAATGTAGGGAAAG 59.603 45.833 0.00 0.00 0.00 2.62
655 656 4.335416 TCTTGCAGAAATGTAGGGAAAGG 58.665 43.478 0.00 0.00 0.00 3.11
656 657 2.446435 TGCAGAAATGTAGGGAAAGGC 58.554 47.619 0.00 0.00 0.00 4.35
657 658 2.041620 TGCAGAAATGTAGGGAAAGGCT 59.958 45.455 0.00 0.00 0.00 4.58
658 659 2.424956 GCAGAAATGTAGGGAAAGGCTG 59.575 50.000 0.00 0.00 0.00 4.85
659 660 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
660 661 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
661 662 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
662 663 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
663 664 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
664 665 0.248289 GTAGGGAAAGGCTGCGTACA 59.752 55.000 0.00 0.00 36.89 2.90
665 666 0.978151 TAGGGAAAGGCTGCGTACAA 59.022 50.000 0.00 0.00 0.00 2.41
666 667 0.328258 AGGGAAAGGCTGCGTACAAT 59.672 50.000 0.00 0.00 0.00 2.71
667 668 1.557832 AGGGAAAGGCTGCGTACAATA 59.442 47.619 0.00 0.00 0.00 1.90
668 669 1.940613 GGGAAAGGCTGCGTACAATAG 59.059 52.381 0.00 0.00 0.00 1.73
669 670 2.419574 GGGAAAGGCTGCGTACAATAGA 60.420 50.000 0.00 0.00 0.00 1.98
670 671 2.608090 GGAAAGGCTGCGTACAATAGAC 59.392 50.000 0.00 0.00 0.00 2.59
671 672 2.311124 AAGGCTGCGTACAATAGACC 57.689 50.000 0.00 0.00 0.00 3.85
672 673 0.464452 AGGCTGCGTACAATAGACCC 59.536 55.000 0.00 0.00 0.00 4.46
673 674 0.177141 GGCTGCGTACAATAGACCCA 59.823 55.000 0.00 0.00 0.00 4.51
674 675 1.406341 GGCTGCGTACAATAGACCCAA 60.406 52.381 0.00 0.00 0.00 4.12
675 676 2.352388 GCTGCGTACAATAGACCCAAA 58.648 47.619 0.00 0.00 0.00 3.28
676 677 2.351726 GCTGCGTACAATAGACCCAAAG 59.648 50.000 0.00 0.00 0.00 2.77
677 678 3.596214 CTGCGTACAATAGACCCAAAGT 58.404 45.455 0.00 0.00 0.00 2.66
678 679 4.000988 CTGCGTACAATAGACCCAAAGTT 58.999 43.478 0.00 0.00 0.00 2.66
679 680 3.749088 TGCGTACAATAGACCCAAAGTTG 59.251 43.478 0.00 0.00 0.00 3.16
680 681 3.749609 GCGTACAATAGACCCAAAGTTGT 59.250 43.478 0.00 0.00 36.94 3.32
681 682 4.142966 GCGTACAATAGACCCAAAGTTGTC 60.143 45.833 0.00 0.00 35.01 3.18
682 683 4.090930 CGTACAATAGACCCAAAGTTGTCG 59.909 45.833 0.00 0.00 36.61 4.35
683 684 3.408634 ACAATAGACCCAAAGTTGTCGG 58.591 45.455 0.00 0.00 36.61 4.79
684 685 3.071892 ACAATAGACCCAAAGTTGTCGGA 59.928 43.478 0.00 0.00 36.61 4.55
685 686 2.825861 TAGACCCAAAGTTGTCGGAC 57.174 50.000 0.00 0.00 36.61 4.79
686 687 0.108019 AGACCCAAAGTTGTCGGACC 59.892 55.000 5.55 0.00 36.61 4.46
687 688 0.887836 GACCCAAAGTTGTCGGACCC 60.888 60.000 5.55 0.00 0.00 4.46
688 689 1.350310 ACCCAAAGTTGTCGGACCCT 61.350 55.000 5.55 0.00 0.00 4.34
689 690 0.179001 CCCAAAGTTGTCGGACCCTT 60.179 55.000 5.55 5.11 0.00 3.95
690 691 1.235724 CCAAAGTTGTCGGACCCTTC 58.764 55.000 5.55 0.00 0.00 3.46
691 692 1.235724 CAAAGTTGTCGGACCCTTCC 58.764 55.000 5.55 0.00 38.77 3.46
692 693 0.109913 AAAGTTGTCGGACCCTTCCC 59.890 55.000 5.55 0.00 38.99 3.97
693 694 1.775934 AAGTTGTCGGACCCTTCCCC 61.776 60.000 5.55 0.00 38.99 4.81
694 695 2.122324 TTGTCGGACCCTTCCCCA 60.122 61.111 5.55 0.00 38.99 4.96
695 696 2.221299 TTGTCGGACCCTTCCCCAG 61.221 63.158 5.55 0.00 38.99 4.45
696 697 2.284405 GTCGGACCCTTCCCCAGA 60.284 66.667 0.00 0.00 38.99 3.86
697 698 2.284405 TCGGACCCTTCCCCAGAC 60.284 66.667 0.00 0.00 38.99 3.51
698 699 3.400054 CGGACCCTTCCCCAGACC 61.400 72.222 0.00 0.00 38.99 3.85
699 700 3.015753 GGACCCTTCCCCAGACCC 61.016 72.222 0.00 0.00 35.57 4.46
700 701 2.125225 GACCCTTCCCCAGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
701 702 2.204151 ACCCTTCCCCAGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
702 703 3.732849 CCCTTCCCCAGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
703 704 4.101448 CCTTCCCCAGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
704 705 4.785453 CTTCCCCAGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
725 726 4.115279 CGGGAGCTACATGCACTG 57.885 61.111 0.00 0.00 45.94 3.66
726 727 1.522355 CGGGAGCTACATGCACTGG 60.522 63.158 0.00 0.00 45.94 4.00
727 728 1.153086 GGGAGCTACATGCACTGGG 60.153 63.158 0.00 0.00 45.94 4.45
728 729 1.153086 GGAGCTACATGCACTGGGG 60.153 63.158 0.00 0.00 45.94 4.96
729 730 1.821332 GAGCTACATGCACTGGGGC 60.821 63.158 0.00 0.00 45.94 5.80
730 731 2.262774 GAGCTACATGCACTGGGGCT 62.263 60.000 13.29 13.29 45.94 5.19
731 732 2.117156 GCTACATGCACTGGGGCTG 61.117 63.158 0.00 0.00 42.31 4.85
732 733 2.045045 TACATGCACTGGGGCTGC 60.045 61.111 0.00 0.00 35.03 5.25
733 734 3.643595 TACATGCACTGGGGCTGCC 62.644 63.158 11.05 11.05 33.36 4.85
738 739 2.203684 CACTGGGGCTGCCCTTTT 60.204 61.111 34.99 17.53 44.66 2.27
739 740 1.838396 CACTGGGGCTGCCCTTTTT 60.838 57.895 34.99 15.74 44.66 1.94
808 809 3.043419 CTACGATCAGGCCCTCCG 58.957 66.667 0.00 0.21 37.47 4.63
837 838 3.763360 CTGGGTTTGGTGCAAGATGATTA 59.237 43.478 0.00 0.00 0.00 1.75
847 848 6.064717 GGTGCAAGATGATTATAAGGACCTT 58.935 40.000 12.41 12.41 33.85 3.50
867 868 9.574516 GGACCTTTTGAATGAGTAATATATGGT 57.425 33.333 0.00 0.00 0.00 3.55
908 909 5.629079 AAAGTCTTCATTTTGATCGTCCC 57.371 39.130 0.00 0.00 0.00 4.46
917 918 6.649155 TCATTTTGATCGTCCCTTCATTAGA 58.351 36.000 0.00 0.00 0.00 2.10
988 989 0.592637 GTGCATTGTACACTGCTGCA 59.407 50.000 30.72 22.36 40.29 4.41
989 990 1.001487 GTGCATTGTACACTGCTGCAA 60.001 47.619 30.72 14.02 43.73 4.08
990 991 1.267533 TGCATTGTACACTGCTGCAAG 59.732 47.619 30.72 1.71 39.68 4.01
991 992 1.267806 GCATTGTACACTGCTGCAAGT 59.732 47.619 25.96 8.18 34.61 3.16
1025 1026 4.019174 AGGTGGCACAATTTGGATTCTAG 58.981 43.478 20.82 0.00 44.16 2.43
1026 1027 4.016444 GGTGGCACAATTTGGATTCTAGA 58.984 43.478 20.82 0.00 44.16 2.43
1028 1029 5.402398 GTGGCACAATTTGGATTCTAGAAC 58.598 41.667 13.86 2.04 44.16 3.01
1029 1030 4.462483 TGGCACAATTTGGATTCTAGAACC 59.538 41.667 7.48 11.60 31.92 3.62
1079 1089 0.249911 AGAAAACGTCGAGCCAGCTT 60.250 50.000 0.00 0.00 0.00 3.74
1093 1139 2.615912 GCCAGCTTGCTTTGGACTATAG 59.384 50.000 1.78 0.00 36.55 1.31
1125 1171 3.058293 GCAGCATTGCGGCTATAAATACA 60.058 43.478 23.79 0.00 45.50 2.29
1189 1239 1.870402 CACGCACACTACCATCACAAA 59.130 47.619 0.00 0.00 0.00 2.83
1197 1251 2.631062 ACTACCATCACAAACTCGTCCA 59.369 45.455 0.00 0.00 0.00 4.02
1252 1307 2.710902 CGCGTCCTCCACCTCATCA 61.711 63.158 0.00 0.00 0.00 3.07
1253 1308 1.826024 GCGTCCTCCACCTCATCAT 59.174 57.895 0.00 0.00 0.00 2.45
1254 1309 0.249657 GCGTCCTCCACCTCATCATC 60.250 60.000 0.00 0.00 0.00 2.92
1302 1357 3.576356 GATGCGGCCACCATCACG 61.576 66.667 22.15 0.00 39.07 4.35
1693 1748 1.077930 GAATGCCTGCCAGAGCTGA 60.078 57.895 0.00 0.00 40.18 4.26
1755 1810 2.049433 GACACGTACTGCTGCCGT 60.049 61.111 1.58 1.58 34.71 5.68
1938 1993 9.988815 GATTTACACATGGATCAGTAAGTAGAT 57.011 33.333 0.00 0.00 0.00 1.98
1946 2005 6.931838 TGGATCAGTAAGTAGATGACGTTTT 58.068 36.000 0.00 0.00 0.00 2.43
1947 2006 7.383687 TGGATCAGTAAGTAGATGACGTTTTT 58.616 34.615 0.00 0.00 0.00 1.94
2074 2153 7.495901 TGAAATGGAAGTGTAATTTCTTTGCA 58.504 30.769 8.36 0.00 39.79 4.08
2256 4980 6.887545 ACAATAAAGAACGGGGATATGTGAAA 59.112 34.615 0.00 0.00 0.00 2.69
2270 4994 7.770897 GGGATATGTGAAAGAGAACATGTAGTT 59.229 37.037 0.00 0.00 44.93 2.24
2286 5010 4.416516 TGTAGTTTGAGATGACCTCCTGA 58.583 43.478 0.00 0.00 41.25 3.86
2333 5057 7.335924 GTGGCAGTACATGTAAAAAGGATTAGA 59.664 37.037 7.25 0.00 0.00 2.10
2374 5098 2.243810 GGAGTAGGGGATCTGTAGCTG 58.756 57.143 0.00 0.00 0.00 4.24
2419 5143 0.531657 CTCTGGAGAGACTGCACTGG 59.468 60.000 0.00 0.00 44.74 4.00
2450 5178 9.622004 GAAAATATTTGCATAGATGACCTCATG 57.378 33.333 0.39 0.00 36.57 3.07
2476 5204 1.818060 CCAAATCAATTCTGTCGGCCA 59.182 47.619 2.24 0.00 0.00 5.36
2535 5263 2.080693 GCCGTGTATCCATGTTGACAA 58.919 47.619 0.00 0.00 0.00 3.18
2725 5455 1.741732 CGTGCATTCTTCTCCCCTGAG 60.742 57.143 0.00 0.00 40.17 3.35
2735 5465 2.752030 TCTCCCCTGAGTGTGGATTAG 58.248 52.381 0.00 0.00 39.75 1.73
2772 5505 2.075566 TGCCGGCATATCCTTGGGA 61.076 57.895 29.03 0.00 35.55 4.37
2828 5561 0.951040 GTGGCTCAGGGTCACTTTCG 60.951 60.000 0.00 0.00 46.12 3.46
2852 5585 0.930310 CATATTGACACCGTCGGCAG 59.070 55.000 12.28 7.01 34.95 4.85
2873 5606 1.135859 CAGCGAGTTGTCATGCCTTTC 60.136 52.381 0.00 0.00 0.00 2.62
2884 5617 1.737793 CATGCCTTTCGTGTTACCCTC 59.262 52.381 0.00 0.00 0.00 4.30
2908 5641 4.927267 ACCTACATGATTTTGAGTGGGA 57.073 40.909 0.00 0.00 36.29 4.37
2932 5665 0.453282 TAACGAAGACGACGAAGGCG 60.453 55.000 0.00 2.58 42.66 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 3.010138 CGGGGGTCCATATCACCATTTAT 59.990 47.826 3.28 0.00 35.35 1.40
118 119 1.422402 AGTTCGAGGGGGTTTAGCAAA 59.578 47.619 0.00 0.00 0.00 3.68
167 168 3.338250 ATCCTTGCTGGGGCGGAA 61.338 61.111 0.00 0.00 42.25 4.30
218 219 4.660938 AACCTGCAGAACCCCCGC 62.661 66.667 17.39 0.00 0.00 6.13
318 319 1.016627 TGCATGCATTAAGCTCCGAC 58.983 50.000 18.46 0.00 45.94 4.79
475 476 5.514914 GCGTCTCTCTCAAAGTTCTAAGATG 59.485 44.000 0.00 0.00 0.00 2.90
477 478 4.378563 CGCGTCTCTCTCAAAGTTCTAAGA 60.379 45.833 0.00 0.00 0.00 2.10
499 500 4.501921 GCTACGGGAAACAAGAGTAATACG 59.498 45.833 0.00 0.00 0.00 3.06
513 514 3.692690 AGCTTTATTTTGGCTACGGGAA 58.307 40.909 0.00 0.00 34.31 3.97
562 563 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
563 564 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
564 565 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
565 566 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
566 567 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
567 568 2.265182 GGCTTTACCACTGCGCCAA 61.265 57.895 4.18 0.00 40.41 4.52
568 569 2.671619 GGCTTTACCACTGCGCCA 60.672 61.111 4.18 0.00 40.41 5.69
569 570 3.799755 CGGCTTTACCACTGCGCC 61.800 66.667 4.18 0.00 39.03 6.53
570 571 4.460873 GCGGCTTTACCACTGCGC 62.461 66.667 0.00 0.00 39.03 6.09
571 572 2.742372 AGCGGCTTTACCACTGCG 60.742 61.111 0.00 0.00 43.12 5.18
572 573 2.870372 CAGCGGCTTTACCACTGC 59.130 61.111 0.00 0.00 41.57 4.40
574 575 2.359975 GGCAGCGGCTTTACCACT 60.360 61.111 9.17 0.00 40.87 4.00
575 576 1.971695 AAGGCAGCGGCTTTACCAC 60.972 57.895 9.17 0.00 46.16 4.16
576 577 1.971167 CAAGGCAGCGGCTTTACCA 60.971 57.895 9.17 0.00 46.16 3.25
577 578 1.971695 ACAAGGCAGCGGCTTTACC 60.972 57.895 9.17 2.14 46.16 2.85
578 579 1.210155 CACAAGGCAGCGGCTTTAC 59.790 57.895 9.17 0.00 46.16 2.01
579 580 1.072332 TCACAAGGCAGCGGCTTTA 59.928 52.632 9.17 0.00 46.16 1.85
580 581 2.203337 TCACAAGGCAGCGGCTTT 60.203 55.556 9.17 4.21 46.16 3.51
584 585 2.360350 ATGGTCACAAGGCAGCGG 60.360 61.111 0.00 0.00 0.00 5.52
585 586 1.642037 CTCATGGTCACAAGGCAGCG 61.642 60.000 0.00 0.00 0.00 5.18
586 587 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
587 588 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
588 589 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
599 600 1.270839 ACTTGAACCCGTGACCTCATG 60.271 52.381 0.00 0.00 0.00 3.07
600 601 1.056660 ACTTGAACCCGTGACCTCAT 58.943 50.000 0.00 0.00 0.00 2.90
601 602 0.834612 AACTTGAACCCGTGACCTCA 59.165 50.000 0.00 0.00 0.00 3.86
602 603 1.070289 AGAACTTGAACCCGTGACCTC 59.930 52.381 0.00 0.00 0.00 3.85
603 604 1.129058 AGAACTTGAACCCGTGACCT 58.871 50.000 0.00 0.00 0.00 3.85
604 605 1.226746 CAGAACTTGAACCCGTGACC 58.773 55.000 0.00 0.00 0.00 4.02
605 606 1.202604 TCCAGAACTTGAACCCGTGAC 60.203 52.381 0.00 0.00 0.00 3.67
606 607 1.124780 TCCAGAACTTGAACCCGTGA 58.875 50.000 0.00 0.00 0.00 4.35
607 608 1.961793 TTCCAGAACTTGAACCCGTG 58.038 50.000 0.00 0.00 0.00 4.94
608 609 2.294979 GTTTCCAGAACTTGAACCCGT 58.705 47.619 0.00 0.00 0.00 5.28
609 610 2.290641 CTGTTTCCAGAACTTGAACCCG 59.709 50.000 0.00 0.00 41.50 5.28
610 611 2.034685 GCTGTTTCCAGAACTTGAACCC 59.965 50.000 0.00 0.00 41.50 4.11
611 612 2.034685 GGCTGTTTCCAGAACTTGAACC 59.965 50.000 0.00 0.00 41.50 3.62
612 613 2.952310 AGGCTGTTTCCAGAACTTGAAC 59.048 45.455 0.00 0.00 41.50 3.18
613 614 3.117888 AGAGGCTGTTTCCAGAACTTGAA 60.118 43.478 0.00 0.00 41.50 2.69
614 615 2.439507 AGAGGCTGTTTCCAGAACTTGA 59.560 45.455 0.00 0.00 41.50 3.02
615 616 2.856222 AGAGGCTGTTTCCAGAACTTG 58.144 47.619 0.00 0.00 41.50 3.16
616 617 3.217626 CAAGAGGCTGTTTCCAGAACTT 58.782 45.455 0.00 0.00 41.50 2.66
617 618 2.856222 CAAGAGGCTGTTTCCAGAACT 58.144 47.619 0.00 0.00 41.50 3.01
618 619 1.268079 GCAAGAGGCTGTTTCCAGAAC 59.732 52.381 0.00 0.00 41.50 3.01
619 620 1.133823 TGCAAGAGGCTGTTTCCAGAA 60.134 47.619 0.00 0.00 45.15 3.02
620 621 0.473755 TGCAAGAGGCTGTTTCCAGA 59.526 50.000 0.00 0.00 45.15 3.86
621 622 0.879765 CTGCAAGAGGCTGTTTCCAG 59.120 55.000 0.00 0.00 45.15 3.86
622 623 0.473755 TCTGCAAGAGGCTGTTTCCA 59.526 50.000 0.00 0.00 38.67 3.53
623 624 3.329300 TCTGCAAGAGGCTGTTTCC 57.671 52.632 0.00 0.00 38.67 3.13
633 634 4.335416 CCTTTCCCTACATTTCTGCAAGA 58.665 43.478 0.00 0.00 44.68 3.02
634 635 3.119352 GCCTTTCCCTACATTTCTGCAAG 60.119 47.826 0.00 0.00 0.00 4.01
635 636 2.825532 GCCTTTCCCTACATTTCTGCAA 59.174 45.455 0.00 0.00 0.00 4.08
636 637 2.041620 AGCCTTTCCCTACATTTCTGCA 59.958 45.455 0.00 0.00 0.00 4.41
637 638 2.424956 CAGCCTTTCCCTACATTTCTGC 59.575 50.000 0.00 0.00 0.00 4.26
638 639 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
639 640 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
640 641 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
641 642 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
642 643 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
643 644 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
644 645 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
645 646 0.248289 TGTACGCAGCCTTTCCCTAC 59.752 55.000 0.00 0.00 0.00 3.18
646 647 0.978151 TTGTACGCAGCCTTTCCCTA 59.022 50.000 0.00 0.00 0.00 3.53
647 648 0.328258 ATTGTACGCAGCCTTTCCCT 59.672 50.000 0.00 0.00 0.00 4.20
648 649 1.940613 CTATTGTACGCAGCCTTTCCC 59.059 52.381 0.00 0.00 0.00 3.97
649 650 2.608090 GTCTATTGTACGCAGCCTTTCC 59.392 50.000 0.00 0.00 0.00 3.13
650 651 2.608090 GGTCTATTGTACGCAGCCTTTC 59.392 50.000 0.00 0.00 0.00 2.62
651 652 2.629051 GGTCTATTGTACGCAGCCTTT 58.371 47.619 0.00 0.00 0.00 3.11
652 653 1.134491 GGGTCTATTGTACGCAGCCTT 60.134 52.381 0.00 0.00 0.00 4.35
653 654 0.464452 GGGTCTATTGTACGCAGCCT 59.536 55.000 0.00 0.00 0.00 4.58
654 655 0.177141 TGGGTCTATTGTACGCAGCC 59.823 55.000 0.00 0.00 35.18 4.85
655 656 2.018542 TTGGGTCTATTGTACGCAGC 57.981 50.000 0.00 0.00 40.36 5.25
656 657 3.596214 ACTTTGGGTCTATTGTACGCAG 58.404 45.455 0.00 0.00 40.36 5.18
657 658 3.688694 ACTTTGGGTCTATTGTACGCA 57.311 42.857 0.00 0.00 37.94 5.24
658 659 3.749609 ACAACTTTGGGTCTATTGTACGC 59.250 43.478 0.00 0.00 31.88 4.42
659 660 4.090930 CGACAACTTTGGGTCTATTGTACG 59.909 45.833 0.00 0.00 33.76 3.67
660 661 4.390909 CCGACAACTTTGGGTCTATTGTAC 59.609 45.833 0.00 0.00 33.76 2.90
661 662 4.283978 TCCGACAACTTTGGGTCTATTGTA 59.716 41.667 0.00 0.00 33.76 2.41
662 663 3.071892 TCCGACAACTTTGGGTCTATTGT 59.928 43.478 0.00 0.00 36.24 2.71
663 664 3.435671 GTCCGACAACTTTGGGTCTATTG 59.564 47.826 0.00 0.00 31.88 1.90
664 665 3.558533 GGTCCGACAACTTTGGGTCTATT 60.559 47.826 0.00 0.00 31.88 1.73
665 666 2.027469 GGTCCGACAACTTTGGGTCTAT 60.027 50.000 0.00 0.00 31.88 1.98
666 667 1.345415 GGTCCGACAACTTTGGGTCTA 59.655 52.381 0.00 0.00 31.88 2.59
667 668 0.108019 GGTCCGACAACTTTGGGTCT 59.892 55.000 0.00 0.00 31.88 3.85
668 669 0.887836 GGGTCCGACAACTTTGGGTC 60.888 60.000 0.00 0.00 0.00 4.46
669 670 1.149854 GGGTCCGACAACTTTGGGT 59.850 57.895 0.00 0.00 0.00 4.51
670 671 0.179001 AAGGGTCCGACAACTTTGGG 60.179 55.000 0.00 0.00 0.00 4.12
671 672 1.235724 GAAGGGTCCGACAACTTTGG 58.764 55.000 0.00 0.00 0.00 3.28
672 673 1.235724 GGAAGGGTCCGACAACTTTG 58.764 55.000 0.00 0.00 33.05 2.77
673 674 0.109913 GGGAAGGGTCCGACAACTTT 59.890 55.000 0.00 0.00 46.04 2.66
674 675 1.759236 GGGAAGGGTCCGACAACTT 59.241 57.895 7.26 7.26 46.04 2.66
675 676 2.222013 GGGGAAGGGTCCGACAACT 61.222 63.158 0.00 0.00 46.04 3.16
676 677 2.350134 GGGGAAGGGTCCGACAAC 59.650 66.667 0.00 0.00 46.04 3.32
677 678 2.122324 TGGGGAAGGGTCCGACAA 60.122 61.111 0.00 0.00 46.04 3.18
678 679 2.606519 CTGGGGAAGGGTCCGACA 60.607 66.667 0.00 0.00 46.04 4.35
679 680 2.284405 TCTGGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
680 681 2.284405 GTCTGGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
681 682 3.400054 GGTCTGGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
682 683 3.015753 GGGTCTGGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
683 684 2.125225 AGGGTCTGGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
684 685 2.204151 CAGGGTCTGGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
685 686 3.732849 GCAGGGTCTGGGGAAGGG 61.733 72.222 0.00 0.00 31.21 3.95
686 687 4.101448 CGCAGGGTCTGGGGAAGG 62.101 72.222 4.35 0.00 40.11 3.46
687 688 4.785453 GCGCAGGGTCTGGGGAAG 62.785 72.222 0.30 0.00 43.28 3.46
699 700 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
702 703 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
703 704 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
704 705 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
705 706 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
707 708 2.176273 CAGTGCATGTAGCTCCCGC 61.176 63.158 0.00 0.00 45.94 6.13
708 709 1.522355 CCAGTGCATGTAGCTCCCG 60.522 63.158 0.00 0.00 45.94 5.14
709 710 1.153086 CCCAGTGCATGTAGCTCCC 60.153 63.158 0.00 0.00 45.94 4.30
710 711 1.153086 CCCCAGTGCATGTAGCTCC 60.153 63.158 0.00 0.00 45.94 4.70
711 712 1.821332 GCCCCAGTGCATGTAGCTC 60.821 63.158 0.00 0.00 45.94 4.09
712 713 2.273449 GCCCCAGTGCATGTAGCT 59.727 61.111 0.00 0.00 45.94 3.32
713 714 2.117156 CAGCCCCAGTGCATGTAGC 61.117 63.158 0.00 0.00 45.96 3.58
714 715 2.117156 GCAGCCCCAGTGCATGTAG 61.117 63.158 0.00 0.00 40.86 2.74
715 716 2.045045 GCAGCCCCAGTGCATGTA 60.045 61.111 0.00 0.00 40.86 2.29
740 741 9.988815 TCTAGCAAAATTGGCTAAACAATAAAA 57.011 25.926 3.43 0.00 42.80 1.52
741 742 9.638239 CTCTAGCAAAATTGGCTAAACAATAAA 57.362 29.630 3.43 0.00 42.80 1.40
742 743 8.802267 ACTCTAGCAAAATTGGCTAAACAATAA 58.198 29.630 3.43 0.00 42.80 1.40
743 744 8.348285 ACTCTAGCAAAATTGGCTAAACAATA 57.652 30.769 3.43 0.00 42.80 1.90
744 745 7.232118 ACTCTAGCAAAATTGGCTAAACAAT 57.768 32.000 3.43 0.00 42.80 2.71
745 746 6.648879 ACTCTAGCAAAATTGGCTAAACAA 57.351 33.333 3.43 0.00 42.80 2.83
746 747 6.648879 AACTCTAGCAAAATTGGCTAAACA 57.351 33.333 3.43 0.00 42.80 2.83
799 800 3.999285 AGGACACTCGGAGGGCCT 61.999 66.667 5.25 5.25 0.00 5.19
802 803 3.077556 CCCAGGACACTCGGAGGG 61.078 72.222 5.53 5.53 0.00 4.30
808 809 1.172812 GCACCAAACCCAGGACACTC 61.173 60.000 0.00 0.00 0.00 3.51
944 945 4.644234 ACATGTGAGTCCAATGTTTGAACA 59.356 37.500 0.00 0.00 44.06 3.18
988 989 3.054434 TGCCACCTCATGTATGCTTACTT 60.054 43.478 10.74 2.28 0.00 2.24
989 990 2.505407 TGCCACCTCATGTATGCTTACT 59.495 45.455 10.74 0.00 0.00 2.24
990 991 2.614057 GTGCCACCTCATGTATGCTTAC 59.386 50.000 2.86 2.86 0.00 2.34
991 992 2.238395 TGTGCCACCTCATGTATGCTTA 59.762 45.455 0.00 0.00 0.00 3.09
1055 1065 1.130009 GCTCGACGTTTTCTTCGGC 59.870 57.895 0.00 0.00 41.01 5.54
1059 1069 0.249911 AGCTGGCTCGACGTTTTCTT 60.250 50.000 0.00 0.00 0.00 2.52
1060 1070 0.249911 AAGCTGGCTCGACGTTTTCT 60.250 50.000 0.00 0.00 0.00 2.52
1079 1089 5.414789 TGTTGCTACTATAGTCCAAAGCA 57.585 39.130 19.53 19.53 35.02 3.91
1093 1139 0.457337 GCAATGCTGCCTGTTGCTAC 60.457 55.000 20.14 0.00 43.56 3.58
1189 1239 3.368531 GCTCTTGGTATTCTTGGACGAGT 60.369 47.826 0.00 0.00 0.00 4.18
1197 1251 2.092968 TGATGCCGCTCTTGGTATTCTT 60.093 45.455 0.00 0.00 34.18 2.52
1252 1307 4.162690 GGCAAGGACGAGGGCGAT 62.163 66.667 0.00 0.00 41.64 4.58
1282 1337 2.124570 GATGGTGGCCGCATCTGT 60.125 61.111 19.98 0.00 0.00 3.41
1302 1357 2.668550 GAGCACCGGTTCACCACC 60.669 66.667 2.97 0.00 43.16 4.61
1437 1492 2.434884 CTGCCGTCGAAGGTGCAT 60.435 61.111 18.88 0.00 32.53 3.96
1565 1620 0.246910 GGACAGGTCGAAGAAGTCCC 59.753 60.000 13.63 0.00 44.30 4.46
1755 1810 1.891919 GTTGTGCTCGAACTGGCCA 60.892 57.895 4.71 4.71 0.00 5.36
2074 2153 7.212274 GCTTCCATTTCATTTATTGCCATACT 58.788 34.615 0.00 0.00 0.00 2.12
2256 4980 6.212388 AGGTCATCTCAAACTACATGTTCTCT 59.788 38.462 2.30 0.00 38.03 3.10
2270 4994 4.020751 CAGAAGTTCAGGAGGTCATCTCAA 60.021 45.833 5.50 0.00 44.19 3.02
2286 5010 3.023832 CAACCTGGAAACCACAGAAGTT 58.976 45.455 0.00 0.00 38.20 2.66
2333 5057 3.541632 CCGCATGGTAAAGTGTCCTTAT 58.458 45.455 0.00 0.00 0.00 1.73
2374 5098 3.309296 TGAGGATCTGGGTACTTCATCC 58.691 50.000 0.00 0.00 34.92 3.51
2390 5114 4.952957 CAGTCTCTCCAGAGTTAATGAGGA 59.047 45.833 3.50 0.00 42.60 3.71
2406 5130 0.178950 TCTCCACCAGTGCAGTCTCT 60.179 55.000 0.00 0.00 0.00 3.10
2419 5143 8.078596 GGTCATCTATGCAAATATTTTCTCCAC 58.921 37.037 0.00 0.00 0.00 4.02
2450 5178 4.168760 CGACAGAATTGATTTGGCCTTTC 58.831 43.478 3.32 0.00 0.00 2.62
2476 5204 6.070710 GGTTATAGTTTTGTCCCAGAGTCTCT 60.071 42.308 0.00 0.00 0.00 3.10
2535 5263 7.500141 GCCCATGTGGTAGATAAATCAAAAAT 58.500 34.615 0.00 0.00 36.04 1.82
2725 5455 2.280628 GTAGTGCCAGCTAATCCACAC 58.719 52.381 0.00 0.00 0.00 3.82
2772 5505 7.833183 GGCCAATGAATGATATAGAGGAGATTT 59.167 37.037 0.00 0.00 0.00 2.17
2828 5561 3.183775 GCCGACGGTGTCAATATGTTATC 59.816 47.826 16.73 0.00 32.09 1.75
2852 5585 1.580845 AAGGCATGACAACTCGCTGC 61.581 55.000 0.00 0.00 0.00 5.25
2873 5606 1.541147 TGTAGGTTCGAGGGTAACACG 59.459 52.381 0.00 0.00 38.80 4.49
2884 5617 4.094887 CCCACTCAAAATCATGTAGGTTCG 59.905 45.833 0.00 0.00 0.00 3.95
2908 5641 1.229428 TCGTCGTCTTCGTTAGGTGT 58.771 50.000 0.00 0.00 38.33 4.16
2914 5647 1.728426 CGCCTTCGTCGTCTTCGTT 60.728 57.895 0.00 0.00 38.33 3.85
2915 5648 2.126965 CGCCTTCGTCGTCTTCGT 60.127 61.111 0.00 0.00 38.33 3.85


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

AutoCloner maintained by Alex Coulton.