Multiple sequence alignment - TraesCS2A01G159100

Loading Multiple Alignment...

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 TraesCS2A01G159100 chr2A 100.000 2895 0 0 1 2895 105639935 105637041 0.000000e+00 5347.0
1 TraesCS2A01G159100 chr2A 80.263 304 45 8 76 366 13109132 13109433 6.280000e-52 215.0
2 TraesCS2A01G159100 chr2D 92.354 994 48 15 760 1748 110065589 110064619 0.000000e+00 1389.0
3 TraesCS2A01G159100 chr2D 87.882 1081 63 30 1859 2895 110064554 110063498 0.000000e+00 1208.0
4 TraesCS2A01G159100 chr2D 88.571 490 55 1 147 636 110066080 110065592 6.910000e-166 593.0
5 TraesCS2A01G159100 chr2D 84.014 294 44 2 361 651 593354315 593354608 2.200000e-71 279.0
6 TraesCS2A01G159100 chr2D 82.155 297 47 4 359 651 148247369 148247663 1.720000e-62 250.0
7 TraesCS2A01G159100 chr2D 78.378 296 54 4 81 366 88404479 88404184 1.770000e-42 183.0
8 TraesCS2A01G159100 chr2D 90.000 80 8 0 1 80 485997393 485997472 1.420000e-18 104.0
9 TraesCS2A01G159100 chr2D 87.654 81 9 1 1 80 569683456 569683376 3.070000e-15 93.5
10 TraesCS2A01G159100 chr2B 91.329 865 33 11 793 1651 159489900 159489072 0.000000e+00 1144.0
11 TraesCS2A01G159100 chr2B 90.731 766 46 13 2017 2769 159488742 159487989 0.000000e+00 998.0
12 TraesCS2A01G159100 chr2B 85.638 745 98 4 1 745 159506547 159505812 0.000000e+00 774.0
13 TraesCS2A01G159100 chr2B 93.701 127 8 0 2768 2894 159487895 159487769 1.060000e-44 191.0
14 TraesCS2A01G159100 chr2B 95.000 80 4 0 1 80 159585284 159585363 3.030000e-25 126.0
15 TraesCS2A01G159100 chr7B 83.618 293 42 4 361 649 741860337 741860627 1.320000e-68 270.0
16 TraesCS2A01G159100 chr7B 82.993 294 43 4 361 649 706246900 706247191 2.860000e-65 259.0
17 TraesCS2A01G159100 chr1D 83.390 295 42 5 361 651 38368832 38368541 1.710000e-67 267.0
18 TraesCS2A01G159100 chr3B 82.201 309 44 8 361 660 12591651 12591957 3.700000e-64 255.0
19 TraesCS2A01G159100 chr6D 82.069 290 47 3 361 646 433362198 433362486 2.880000e-60 243.0
20 TraesCS2A01G159100 chr4B 80.427 281 54 1 86 366 389136984 389137263 2.260000e-51 213.0
21 TraesCS2A01G159100 chr5A 79.787 282 47 6 95 366 4089321 4089602 2.280000e-46 196.0
22 TraesCS2A01G159100 chr7A 78.930 299 46 13 81 366 675456851 675457145 1.370000e-43 187.0
23 TraesCS2A01G159100 chr7A 88.750 80 9 0 1 80 35175824 35175745 6.600000e-17 99.0
24 TraesCS2A01G159100 chr1A 77.972 286 62 1 81 366 113544506 113544790 8.240000e-41 178.0
25 TraesCS2A01G159100 chr1A 87.500 80 10 0 1 80 111799421 111799342 3.070000e-15 93.5
26 TraesCS2A01G159100 chr5D 85.185 162 24 0 205 366 25041811 25041650 1.780000e-37 167.0
27 TraesCS2A01G159100 chr6A 88.750 80 9 0 1 80 359660173 359660252 6.600000e-17 99.0
28 TraesCS2A01G159100 chr3A 88.750 80 9 0 1 80 237555492 237555413 6.600000e-17 99.0
29 TraesCS2A01G159100 chr3A 92.424 66 5 0 15 80 139585116 139585051 8.540000e-16 95.3


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 TraesCS2A01G159100 chr2A 105637041 105639935 2894 True 5347.000000 5347 100.000000 1 2895 1 chr2A.!!$R1 2894
1 TraesCS2A01G159100 chr2D 110063498 110066080 2582 True 1063.333333 1389 89.602333 147 2895 3 chr2D.!!$R3 2748
2 TraesCS2A01G159100 chr2B 159487769 159489900 2131 True 777.666667 1144 91.920333 793 2894 3 chr2B.!!$R2 2101
3 TraesCS2A01G159100 chr2B 159505812 159506547 735 True 774.000000 774 85.638000 1 745 1 chr2B.!!$R1 744

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
731 732 0.030235 CGGCCGTGAGATGATTCGTA 59.970 55.0 19.5 0.0 0.0 3.43 F
820 821 0.032815 CGGCCCGGTTCATTTGTTTT 59.967 50.0 0.0 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 1917 0.038599 ACATGGCTGCAGATTGGTGA 59.961 50.0 20.43 0.0 0.0 4.02 R
2682 2747 0.106819 ATGTTCATGCAGCCTCCCTC 60.107 55.0 0.00 0.0 0.0 4.30 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
29 30 6.534475 TCAAAGCCAAATCAGCATATTCTT 57.466 33.333 0.00 0.00 0.00 2.52
61 62 6.751425 CGGCATGTGCTCATAATTTCTTTTAA 59.249 34.615 0.04 0.00 41.70 1.52
91 92 1.531748 CAACATAGACCCGGCCCAT 59.468 57.895 0.00 0.00 0.00 4.00
96 97 1.492133 ATAGACCCGGCCCATGATGG 61.492 60.000 3.98 3.98 37.25 3.51
109 110 3.488569 GATGGCCCATCCGACCCA 61.489 66.667 13.02 0.00 35.07 4.51
111 112 3.358932 ATGGCCCATCCGACCCAAC 62.359 63.158 0.00 0.00 37.80 3.77
126 127 4.618460 CGACCCAACATATATTCCTCCTCG 60.618 50.000 0.00 0.00 0.00 4.63
129 130 4.528596 CCCAACATATATTCCTCCTCGTCT 59.471 45.833 0.00 0.00 0.00 4.18
135 136 0.107945 ATTCCTCCTCGTCTGCTTGC 60.108 55.000 0.00 0.00 0.00 4.01
137 138 2.659016 CTCCTCGTCTGCTTGCCA 59.341 61.111 0.00 0.00 0.00 4.92
151 152 2.316108 CTTGCCAAACCAAACCCTAGT 58.684 47.619 0.00 0.00 0.00 2.57
159 160 5.316987 CAAACCAAACCCTAGTCTCTTCAT 58.683 41.667 0.00 0.00 0.00 2.57
186 187 1.280457 CCCTTCACTACCCAAGCTCT 58.720 55.000 0.00 0.00 0.00 4.09
200 201 1.917872 AGCTCTCGTCTGGTCTTCTT 58.082 50.000 0.00 0.00 0.00 2.52
227 228 3.717294 AGGCGGCGGATCCAAGTT 61.717 61.111 13.41 0.00 34.01 2.66
241 242 2.368875 TCCAAGTTCTTCACCTCCAGAC 59.631 50.000 0.00 0.00 0.00 3.51
244 245 0.037232 GTTCTTCACCTCCAGACCCG 60.037 60.000 0.00 0.00 0.00 5.28
265 266 0.833834 CGACCCCTAGCTCATCCCAT 60.834 60.000 0.00 0.00 0.00 4.00
288 289 1.575447 GCCCCAAGGAGGAGATGGTT 61.575 60.000 0.00 0.00 41.22 3.67
304 305 4.314440 TTGTCCGGCTTGCGCTCT 62.314 61.111 9.73 0.00 36.09 4.09
351 352 2.262915 CGGCGCTCAGACTCCTTT 59.737 61.111 7.64 0.00 0.00 3.11
353 354 0.108804 CGGCGCTCAGACTCCTTTTA 60.109 55.000 7.64 0.00 0.00 1.52
358 359 2.799917 CGCTCAGACTCCTTTTATCGGG 60.800 54.545 0.00 0.00 0.00 5.14
377 378 4.464244 TCGGGAATCCATCATCTATCTGAC 59.536 45.833 0.09 0.00 0.00 3.51
386 387 3.886123 TCATCTATCTGACGTCCACAGA 58.114 45.455 14.12 10.56 46.17 3.41
391 392 0.467474 TCTGACGTCCACAGACACCT 60.467 55.000 14.12 0.00 43.73 4.00
395 396 0.828022 ACGTCCACAGACACCTTTCA 59.172 50.000 0.00 0.00 43.73 2.69
396 397 1.208535 ACGTCCACAGACACCTTTCAA 59.791 47.619 0.00 0.00 43.73 2.69
487 488 2.520980 TCCCATGCCCTACTCTACCTTA 59.479 50.000 0.00 0.00 0.00 2.69
511 512 1.342174 GTGACCGGACCAACACTCTAA 59.658 52.381 9.46 0.00 0.00 2.10
658 659 4.574892 TCAAATATTTGAGACTGCCGACA 58.425 39.130 23.86 0.86 41.88 4.35
659 660 4.391830 TCAAATATTTGAGACTGCCGACAC 59.608 41.667 23.86 0.00 41.88 3.67
660 661 1.990799 TATTTGAGACTGCCGACACG 58.009 50.000 0.00 0.00 0.00 4.49
661 662 1.291877 ATTTGAGACTGCCGACACGC 61.292 55.000 0.00 0.00 0.00 5.34
662 663 4.700365 TGAGACTGCCGACACGCG 62.700 66.667 3.53 3.53 40.47 6.01
663 664 4.400109 GAGACTGCCGACACGCGA 62.400 66.667 15.93 0.00 44.57 5.87
664 665 4.702081 AGACTGCCGACACGCGAC 62.702 66.667 15.93 2.51 44.57 5.19
669 670 4.696172 GCCGACACGCGACGTTTG 62.696 66.667 15.93 1.61 44.57 2.93
670 671 3.025743 CCGACACGCGACGTTTGA 61.026 61.111 15.93 0.00 44.57 2.69
671 672 2.459904 CGACACGCGACGTTTGAG 59.540 61.111 15.93 0.00 44.57 3.02
672 673 2.007114 CGACACGCGACGTTTGAGA 61.007 57.895 15.93 0.00 44.57 3.27
673 674 1.767388 GACACGCGACGTTTGAGAG 59.233 57.895 15.93 0.00 38.32 3.20
674 675 0.659417 GACACGCGACGTTTGAGAGA 60.659 55.000 15.93 0.00 38.32 3.10
675 676 0.039437 ACACGCGACGTTTGAGAGAT 60.039 50.000 15.93 0.00 38.32 2.75
676 677 0.635731 CACGCGACGTTTGAGAGATC 59.364 55.000 15.93 0.00 38.32 2.75
677 678 0.793478 ACGCGACGTTTGAGAGATCG 60.793 55.000 15.93 0.00 36.35 3.69
678 679 1.464429 CGCGACGTTTGAGAGATCGG 61.464 60.000 0.00 0.00 33.45 4.18
679 680 0.179171 GCGACGTTTGAGAGATCGGA 60.179 55.000 0.00 0.00 33.45 4.55
680 681 1.534175 GCGACGTTTGAGAGATCGGAT 60.534 52.381 0.00 0.00 33.45 4.18
681 682 2.798680 CGACGTTTGAGAGATCGGATT 58.201 47.619 0.00 0.00 0.00 3.01
682 683 3.179830 CGACGTTTGAGAGATCGGATTT 58.820 45.455 0.00 0.00 0.00 2.17
683 684 4.348656 CGACGTTTGAGAGATCGGATTTA 58.651 43.478 0.00 0.00 0.00 1.40
684 685 4.796830 CGACGTTTGAGAGATCGGATTTAA 59.203 41.667 0.00 0.00 0.00 1.52
685 686 5.052304 CGACGTTTGAGAGATCGGATTTAAG 60.052 44.000 0.00 0.00 0.00 1.85
686 687 5.721232 ACGTTTGAGAGATCGGATTTAAGT 58.279 37.500 0.00 0.00 0.00 2.24
687 688 5.805994 ACGTTTGAGAGATCGGATTTAAGTC 59.194 40.000 0.00 0.00 0.00 3.01
688 689 6.037098 CGTTTGAGAGATCGGATTTAAGTCT 58.963 40.000 0.00 0.00 0.00 3.24
689 690 6.020281 CGTTTGAGAGATCGGATTTAAGTCTG 60.020 42.308 0.41 0.41 0.00 3.51
690 691 6.775594 TTGAGAGATCGGATTTAAGTCTGA 57.224 37.500 11.48 11.48 37.86 3.27
691 692 6.968263 TGAGAGATCGGATTTAAGTCTGAT 57.032 37.500 19.16 19.16 44.76 2.90
692 693 7.353414 TGAGAGATCGGATTTAAGTCTGATT 57.647 36.000 19.84 11.82 42.73 2.57
693 694 7.205992 TGAGAGATCGGATTTAAGTCTGATTG 58.794 38.462 19.84 0.00 42.73 2.67
694 695 7.118496 AGAGATCGGATTTAAGTCTGATTGT 57.882 36.000 19.84 12.42 42.73 2.71
695 696 8.239038 AGAGATCGGATTTAAGTCTGATTGTA 57.761 34.615 19.84 0.00 42.73 2.41
696 697 8.356657 AGAGATCGGATTTAAGTCTGATTGTAG 58.643 37.037 19.84 0.00 42.73 2.74
697 698 8.239038 AGATCGGATTTAAGTCTGATTGTAGA 57.761 34.615 19.84 0.00 42.73 2.59
698 699 8.865090 AGATCGGATTTAAGTCTGATTGTAGAT 58.135 33.333 19.84 1.06 42.73 1.98
699 700 8.824159 ATCGGATTTAAGTCTGATTGTAGATG 57.176 34.615 14.74 0.00 40.46 2.90
700 701 6.701841 TCGGATTTAAGTCTGATTGTAGATGC 59.298 38.462 5.44 0.00 0.00 3.91
701 702 6.703607 CGGATTTAAGTCTGATTGTAGATGCT 59.296 38.462 0.54 0.00 0.00 3.79
702 703 7.095857 CGGATTTAAGTCTGATTGTAGATGCTC 60.096 40.741 0.54 0.00 0.00 4.26
703 704 7.172361 GGATTTAAGTCTGATTGTAGATGCTCC 59.828 40.741 0.00 0.00 0.00 4.70
704 705 6.544928 TTAAGTCTGATTGTAGATGCTCCA 57.455 37.500 0.00 0.00 0.00 3.86
705 706 5.426689 AAGTCTGATTGTAGATGCTCCAA 57.573 39.130 0.00 0.00 0.00 3.53
706 707 5.627182 AGTCTGATTGTAGATGCTCCAAT 57.373 39.130 0.00 0.00 0.00 3.16
707 708 5.366460 AGTCTGATTGTAGATGCTCCAATG 58.634 41.667 0.00 0.00 0.00 2.82
708 709 4.514441 GTCTGATTGTAGATGCTCCAATGG 59.486 45.833 0.00 0.00 0.00 3.16
709 710 4.164796 TCTGATTGTAGATGCTCCAATGGT 59.835 41.667 0.00 0.00 0.00 3.55
710 711 5.366477 TCTGATTGTAGATGCTCCAATGGTA 59.634 40.000 0.00 0.00 0.00 3.25
711 712 6.043590 TCTGATTGTAGATGCTCCAATGGTAT 59.956 38.462 0.00 0.00 0.00 2.73
712 713 6.233434 TGATTGTAGATGCTCCAATGGTATC 58.767 40.000 0.00 2.74 0.00 2.24
713 714 4.257267 TGTAGATGCTCCAATGGTATCG 57.743 45.455 0.00 0.00 0.00 2.92
714 715 2.847327 AGATGCTCCAATGGTATCGG 57.153 50.000 0.00 0.00 0.00 4.18
715 716 1.160137 GATGCTCCAATGGTATCGGC 58.840 55.000 0.00 0.00 0.00 5.54
716 717 0.250901 ATGCTCCAATGGTATCGGCC 60.251 55.000 0.00 0.00 0.00 6.13
717 718 1.961277 GCTCCAATGGTATCGGCCG 60.961 63.158 22.12 22.12 0.00 6.13
718 719 1.445942 CTCCAATGGTATCGGCCGT 59.554 57.895 27.15 15.22 0.00 5.68
719 720 0.880278 CTCCAATGGTATCGGCCGTG 60.880 60.000 27.15 14.07 0.00 4.94
720 721 1.145156 CCAATGGTATCGGCCGTGA 59.855 57.895 27.15 11.71 0.00 4.35
721 722 0.880278 CCAATGGTATCGGCCGTGAG 60.880 60.000 27.15 7.50 0.00 3.51
722 723 0.104120 CAATGGTATCGGCCGTGAGA 59.896 55.000 27.15 5.72 0.00 3.27
723 724 1.048601 AATGGTATCGGCCGTGAGAT 58.951 50.000 27.15 13.98 0.00 2.75
724 725 0.318441 ATGGTATCGGCCGTGAGATG 59.682 55.000 27.15 0.00 0.00 2.90
725 726 0.753848 TGGTATCGGCCGTGAGATGA 60.754 55.000 27.15 3.40 0.00 2.92
726 727 0.603569 GGTATCGGCCGTGAGATGAT 59.396 55.000 27.15 11.95 0.00 2.45
727 728 1.000955 GGTATCGGCCGTGAGATGATT 59.999 52.381 27.15 2.58 0.00 2.57
728 729 2.329379 GTATCGGCCGTGAGATGATTC 58.671 52.381 27.15 3.16 0.00 2.52
729 730 0.319040 ATCGGCCGTGAGATGATTCG 60.319 55.000 27.15 0.00 0.00 3.34
730 731 1.226974 CGGCCGTGAGATGATTCGT 60.227 57.895 19.50 0.00 0.00 3.85
731 732 0.030235 CGGCCGTGAGATGATTCGTA 59.970 55.000 19.50 0.00 0.00 3.43
732 733 1.335964 CGGCCGTGAGATGATTCGTAT 60.336 52.381 19.50 0.00 0.00 3.06
733 734 2.329379 GGCCGTGAGATGATTCGTATC 58.671 52.381 0.00 0.00 0.00 2.24
734 735 2.288213 GGCCGTGAGATGATTCGTATCA 60.288 50.000 7.21 7.21 44.52 2.15
735 736 2.983136 GCCGTGAGATGATTCGTATCAG 59.017 50.000 10.58 0.00 43.70 2.90
736 737 3.569548 CCGTGAGATGATTCGTATCAGG 58.430 50.000 10.58 13.61 43.70 3.86
737 738 3.253432 CCGTGAGATGATTCGTATCAGGA 59.747 47.826 19.52 0.00 43.70 3.86
738 739 4.471373 CGTGAGATGATTCGTATCAGGAG 58.529 47.826 14.88 2.91 43.70 3.69
739 740 4.614764 CGTGAGATGATTCGTATCAGGAGG 60.615 50.000 14.88 0.00 43.70 4.30
740 741 3.256879 TGAGATGATTCGTATCAGGAGGC 59.743 47.826 10.58 0.00 43.70 4.70
741 742 3.505386 AGATGATTCGTATCAGGAGGCT 58.495 45.455 10.58 0.00 43.70 4.58
742 743 4.667573 AGATGATTCGTATCAGGAGGCTA 58.332 43.478 10.58 0.00 43.70 3.93
743 744 4.704540 AGATGATTCGTATCAGGAGGCTAG 59.295 45.833 10.58 0.00 43.70 3.42
744 745 4.100279 TGATTCGTATCAGGAGGCTAGA 57.900 45.455 0.00 0.00 35.87 2.43
745 746 3.821600 TGATTCGTATCAGGAGGCTAGAC 59.178 47.826 0.00 0.00 35.87 2.59
746 747 2.273538 TCGTATCAGGAGGCTAGACC 57.726 55.000 0.00 0.00 39.61 3.85
747 748 0.875728 CGTATCAGGAGGCTAGACCG 59.124 60.000 0.00 0.00 46.52 4.79
748 749 1.249407 GTATCAGGAGGCTAGACCGG 58.751 60.000 0.00 0.00 46.52 5.28
749 750 0.539901 TATCAGGAGGCTAGACCGGC 60.540 60.000 0.00 0.00 46.52 6.13
750 751 3.905678 CAGGAGGCTAGACCGGCG 61.906 72.222 0.00 0.00 46.52 6.46
757 758 4.077184 CTAGACCGGCGGGCACAA 62.077 66.667 36.46 18.15 36.48 3.33
758 759 3.385749 CTAGACCGGCGGGCACAAT 62.386 63.158 36.46 16.55 36.48 2.71
768 769 1.789078 CGGGCACAATAGGCTGATGC 61.789 60.000 0.00 1.15 42.62 3.91
775 776 3.313526 CACAATAGGCTGATGCACTAACC 59.686 47.826 0.00 0.00 41.91 2.85
791 792 5.560953 GCACTAACCTTTTGACATCTGACAC 60.561 44.000 0.00 0.00 0.00 3.67
820 821 0.032815 CGGCCCGGTTCATTTGTTTT 59.967 50.000 0.00 0.00 0.00 2.43
821 822 1.269998 CGGCCCGGTTCATTTGTTTTA 59.730 47.619 0.00 0.00 0.00 1.52
822 823 2.679450 GGCCCGGTTCATTTGTTTTAC 58.321 47.619 0.00 0.00 0.00 2.01
823 824 2.297880 GGCCCGGTTCATTTGTTTTACT 59.702 45.455 0.00 0.00 0.00 2.24
824 825 3.243941 GGCCCGGTTCATTTGTTTTACTT 60.244 43.478 0.00 0.00 0.00 2.24
825 826 4.373527 GCCCGGTTCATTTGTTTTACTTT 58.626 39.130 0.00 0.00 0.00 2.66
1188 1194 1.424635 CTCGGTCGTCGTCTTCCTC 59.575 63.158 0.00 0.00 40.32 3.71
1347 1356 2.135933 GAGCCAAGGTACATATCGTGC 58.864 52.381 0.00 0.00 0.00 5.34
1354 1363 4.839668 AGGTACATATCGTGCTCTCTTC 57.160 45.455 0.00 0.00 0.00 2.87
1355 1364 4.465886 AGGTACATATCGTGCTCTCTTCT 58.534 43.478 0.00 0.00 0.00 2.85
1482 1491 1.745115 CGATGAAGAAGGCGGCCAA 60.745 57.895 23.09 0.00 0.00 4.52
1519 1528 3.710722 AAGGAGGCCGTGGAGCAG 61.711 66.667 0.00 0.00 0.00 4.24
1677 1689 0.858583 ACGCAAGCGCCAAAATTTTC 59.141 45.000 15.09 0.00 44.19 2.29
1697 1709 1.115467 CGAGCTGTATCCCTCCACTT 58.885 55.000 0.00 0.00 0.00 3.16
1703 1719 4.475016 AGCTGTATCCCTCCACTTTATGTT 59.525 41.667 0.00 0.00 0.00 2.71
1704 1720 5.665812 AGCTGTATCCCTCCACTTTATGTTA 59.334 40.000 0.00 0.00 0.00 2.41
1705 1721 5.758784 GCTGTATCCCTCCACTTTATGTTAC 59.241 44.000 0.00 0.00 0.00 2.50
1706 1722 6.243216 TGTATCCCTCCACTTTATGTTACC 57.757 41.667 0.00 0.00 0.00 2.85
1707 1723 5.968167 TGTATCCCTCCACTTTATGTTACCT 59.032 40.000 0.00 0.00 0.00 3.08
1708 1724 4.837093 TCCCTCCACTTTATGTTACCTG 57.163 45.455 0.00 0.00 0.00 4.00
1709 1725 4.172807 TCCCTCCACTTTATGTTACCTGT 58.827 43.478 0.00 0.00 0.00 4.00
1710 1726 5.343715 TCCCTCCACTTTATGTTACCTGTA 58.656 41.667 0.00 0.00 0.00 2.74
1711 1727 5.786457 TCCCTCCACTTTATGTTACCTGTAA 59.214 40.000 0.00 0.00 0.00 2.41
1712 1728 6.070424 TCCCTCCACTTTATGTTACCTGTAAG 60.070 42.308 0.00 0.00 0.00 2.34
1748 1764 2.079925 AGTGCGAGAAGAAAAGATGGC 58.920 47.619 0.00 0.00 0.00 4.40
1749 1765 1.131315 GTGCGAGAAGAAAAGATGGCC 59.869 52.381 0.00 0.00 0.00 5.36
1750 1766 0.735471 GCGAGAAGAAAAGATGGCCC 59.265 55.000 0.00 0.00 0.00 5.80
1751 1767 1.383523 CGAGAAGAAAAGATGGCCCC 58.616 55.000 0.00 0.00 0.00 5.80
1756 1772 1.453928 GAAAAGATGGCCCCCTCGG 60.454 63.158 0.00 0.00 0.00 4.63
1768 1792 0.460284 CCCCTCGGCGATATGTATGC 60.460 60.000 11.27 0.00 0.00 3.14
1774 1798 2.420722 TCGGCGATATGTATGCGTATGA 59.579 45.455 4.99 0.00 0.00 2.15
1775 1799 3.119779 TCGGCGATATGTATGCGTATGAA 60.120 43.478 4.99 0.00 0.00 2.57
1792 1816 5.635280 CGTATGAATATCCTGCGATTCTGTT 59.365 40.000 0.00 0.00 33.92 3.16
1796 1820 6.785191 TGAATATCCTGCGATTCTGTTTTTC 58.215 36.000 0.00 0.00 33.92 2.29
1802 1826 4.690748 CCTGCGATTCTGTTTTTCTCTGTA 59.309 41.667 0.00 0.00 0.00 2.74
1805 1829 4.142881 GCGATTCTGTTTTTCTCTGTACCC 60.143 45.833 0.00 0.00 0.00 3.69
1825 1849 2.868583 CCTGCTTGTGAATATGAGACGG 59.131 50.000 0.00 0.00 0.00 4.79
1826 1850 3.525537 CTGCTTGTGAATATGAGACGGT 58.474 45.455 0.00 0.00 0.00 4.83
1827 1851 3.521560 TGCTTGTGAATATGAGACGGTC 58.478 45.455 0.00 0.00 0.00 4.79
1828 1852 3.195610 TGCTTGTGAATATGAGACGGTCT 59.804 43.478 11.09 11.09 0.00 3.85
1829 1853 4.401202 TGCTTGTGAATATGAGACGGTCTA 59.599 41.667 11.27 0.00 0.00 2.59
1830 1854 4.979197 GCTTGTGAATATGAGACGGTCTAG 59.021 45.833 11.27 1.89 0.00 2.43
1831 1855 5.221067 GCTTGTGAATATGAGACGGTCTAGA 60.221 44.000 11.27 0.99 0.00 2.43
1832 1856 6.515862 GCTTGTGAATATGAGACGGTCTAGAT 60.516 42.308 11.27 8.79 0.00 1.98
1833 1857 6.561737 TGTGAATATGAGACGGTCTAGATC 57.438 41.667 11.27 6.34 0.00 2.75
1834 1858 5.179555 TGTGAATATGAGACGGTCTAGATCG 59.820 44.000 23.57 23.57 41.46 3.69
1835 1859 4.695928 TGAATATGAGACGGTCTAGATCGG 59.304 45.833 27.97 11.27 39.68 4.18
1836 1860 2.932855 ATGAGACGGTCTAGATCGGA 57.067 50.000 27.97 10.29 39.68 4.55
1837 1861 2.704464 TGAGACGGTCTAGATCGGAA 57.296 50.000 27.97 8.70 39.68 4.30
1838 1862 2.562635 TGAGACGGTCTAGATCGGAAG 58.437 52.381 27.97 2.18 39.68 3.46
1839 1863 2.093075 TGAGACGGTCTAGATCGGAAGT 60.093 50.000 27.97 8.17 39.68 3.01
1840 1864 2.944349 GAGACGGTCTAGATCGGAAGTT 59.056 50.000 27.97 7.77 39.68 2.66
1841 1865 3.354467 AGACGGTCTAGATCGGAAGTTT 58.646 45.455 27.97 7.01 39.68 2.66
1842 1866 3.762823 AGACGGTCTAGATCGGAAGTTTT 59.237 43.478 27.97 6.24 39.68 2.43
1843 1867 4.104066 GACGGTCTAGATCGGAAGTTTTC 58.896 47.826 27.97 11.69 39.68 2.29
1844 1868 3.762823 ACGGTCTAGATCGGAAGTTTTCT 59.237 43.478 27.97 1.91 39.68 2.52
1845 1869 4.142425 ACGGTCTAGATCGGAAGTTTTCTC 60.142 45.833 27.97 0.00 39.68 2.87
1846 1870 4.352887 GGTCTAGATCGGAAGTTTTCTCG 58.647 47.826 0.00 0.00 0.00 4.04
1847 1871 4.352887 GTCTAGATCGGAAGTTTTCTCGG 58.647 47.826 0.00 0.00 0.00 4.63
1848 1872 2.011540 AGATCGGAAGTTTTCTCGGC 57.988 50.000 0.00 0.00 0.00 5.54
1849 1873 1.275291 AGATCGGAAGTTTTCTCGGCA 59.725 47.619 0.00 0.00 0.00 5.69
1850 1874 2.073816 GATCGGAAGTTTTCTCGGCAA 58.926 47.619 0.00 0.00 0.00 4.52
1851 1875 1.956297 TCGGAAGTTTTCTCGGCAAA 58.044 45.000 0.00 0.00 0.00 3.68
1852 1876 2.290464 TCGGAAGTTTTCTCGGCAAAA 58.710 42.857 0.00 0.00 0.00 2.44
1853 1877 2.683867 TCGGAAGTTTTCTCGGCAAAAA 59.316 40.909 0.00 0.00 0.00 1.94
1879 1903 0.722848 GGAAATGCATTTTGGCTGCG 59.277 50.000 24.81 0.00 42.62 5.18
1893 1917 1.490621 GCTGCGAAAAGTTGCATTGT 58.509 45.000 0.00 0.00 40.89 2.71
1896 1920 2.458951 TGCGAAAAGTTGCATTGTCAC 58.541 42.857 0.00 0.00 35.90 3.67
1899 1923 3.443037 CGAAAAGTTGCATTGTCACCAA 58.557 40.909 0.00 0.00 34.45 3.67
1911 1935 0.454600 GTCACCAATCTGCAGCCATG 59.545 55.000 9.47 7.52 0.00 3.66
1912 1936 0.038599 TCACCAATCTGCAGCCATGT 59.961 50.000 9.47 0.60 0.00 3.21
1913 1937 0.454600 CACCAATCTGCAGCCATGTC 59.545 55.000 9.47 0.00 0.00 3.06
1914 1938 1.028330 ACCAATCTGCAGCCATGTCG 61.028 55.000 9.47 0.00 0.00 4.35
1915 1939 0.745486 CCAATCTGCAGCCATGTCGA 60.745 55.000 9.47 0.00 0.00 4.20
1916 1940 1.306148 CAATCTGCAGCCATGTCGAT 58.694 50.000 9.47 0.00 0.00 3.59
1917 1941 1.002792 CAATCTGCAGCCATGTCGATG 60.003 52.381 9.47 0.00 0.00 3.84
1918 1942 0.466963 ATCTGCAGCCATGTCGATGA 59.533 50.000 9.47 0.00 0.00 2.92
1919 1943 0.179092 TCTGCAGCCATGTCGATGAG 60.179 55.000 9.47 0.00 0.00 2.90
1920 1944 0.179092 CTGCAGCCATGTCGATGAGA 60.179 55.000 0.00 0.00 0.00 3.27
1921 1945 0.179092 TGCAGCCATGTCGATGAGAG 60.179 55.000 0.00 0.00 0.00 3.20
1944 1968 0.400594 AGAGCCCAGGTGTTGGTAAC 59.599 55.000 0.00 0.00 46.25 2.50
2031 2084 2.286772 ACTCTTTAACAAACGGCAAGCG 60.287 45.455 0.00 0.00 0.00 4.68
2040 2093 3.508840 CGGCAAGCGAATGGGTCC 61.509 66.667 0.00 0.00 0.00 4.46
2078 2132 5.050499 GTCGACCATAGCATGATTTTCTCAG 60.050 44.000 3.51 0.00 37.28 3.35
2079 2133 5.052481 CGACCATAGCATGATTTTCTCAGA 58.948 41.667 0.00 0.00 37.28 3.27
2080 2134 5.177142 CGACCATAGCATGATTTTCTCAGAG 59.823 44.000 0.00 0.00 37.28 3.35
2081 2135 6.244552 ACCATAGCATGATTTTCTCAGAGA 57.755 37.500 0.00 0.00 37.28 3.10
2117 2171 7.536312 GAGAGATTCTCCACTGGGAAACTAGT 61.536 46.154 10.09 0.00 42.59 2.57
2161 2215 7.651304 CAGGAGTAACATAACATCTGATCTCAC 59.349 40.741 0.00 0.00 0.00 3.51
2163 2217 7.651304 GGAGTAACATAACATCTGATCTCACAG 59.349 40.741 0.00 0.00 39.02 3.66
2233 2287 3.635331 CAATCCATTTCATCCATGTCGC 58.365 45.455 0.00 0.00 0.00 5.19
2337 2391 2.336809 GCCTCGGCTATCAGGTCG 59.663 66.667 0.00 0.00 38.26 4.79
2349 2403 0.677098 TCAGGTCGTCTTCCTCCTCG 60.677 60.000 0.00 0.00 32.37 4.63
2445 2499 1.559682 GGCCTGTTTCCTAGGATGACA 59.440 52.381 21.03 21.03 37.52 3.58
2478 2532 4.022329 GGTGATCGGAAGTTGGAAAATGTT 60.022 41.667 0.00 0.00 0.00 2.71
2493 2547 2.270352 ATGTTTGCTTGAGTTCGGGA 57.730 45.000 0.00 0.00 0.00 5.14
2539 2593 2.492881 CCAGCCTATGCAACATGAAACA 59.507 45.455 0.00 0.00 41.13 2.83
2545 2599 5.396484 CCTATGCAACATGAAACAAGACAG 58.604 41.667 0.00 0.00 0.00 3.51
2682 2747 7.447374 TCATCTTATGGTTGTGTTGGTTTAG 57.553 36.000 0.00 0.00 0.00 1.85
2844 3026 5.852738 ATTGTCTCTGCGTATATGAATGC 57.147 39.130 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 5.826601 TTATGAGCACATGCCGATAAAAA 57.173 34.783 6.91 0.00 43.38 1.94
36 37 3.976793 AGAAATTATGAGCACATGCCG 57.023 42.857 6.91 0.00 43.38 5.69
61 62 5.631119 GGGTCTATGTTGGTTGGCTATAAT 58.369 41.667 0.00 0.00 0.00 1.28
91 92 3.488569 GGGTCGGATGGGCCATCA 61.489 66.667 39.34 23.04 42.13 3.07
96 97 0.110486 ATATGTTGGGTCGGATGGGC 59.890 55.000 0.00 0.00 0.00 5.36
101 102 3.581332 GGAGGAATATATGTTGGGTCGGA 59.419 47.826 0.00 0.00 0.00 4.55
109 110 4.835615 AGCAGACGAGGAGGAATATATGTT 59.164 41.667 0.00 0.00 0.00 2.71
111 112 5.167121 CAAGCAGACGAGGAGGAATATATG 58.833 45.833 0.00 0.00 0.00 1.78
126 127 1.570813 GTTTGGTTTGGCAAGCAGAC 58.429 50.000 16.03 10.58 41.38 3.51
129 130 0.980231 AGGGTTTGGTTTGGCAAGCA 60.980 50.000 16.03 6.90 38.66 3.91
135 136 3.790089 AGAGACTAGGGTTTGGTTTGG 57.210 47.619 0.00 0.00 0.00 3.28
137 138 5.584551 ATGAAGAGACTAGGGTTTGGTTT 57.415 39.130 0.00 0.00 0.00 3.27
151 152 2.649742 AGGGGAGTGGAATGAAGAGA 57.350 50.000 0.00 0.00 0.00 3.10
159 160 1.652947 GGTAGTGAAGGGGAGTGGAA 58.347 55.000 0.00 0.00 0.00 3.53
186 187 1.176619 TGCCGAAGAAGACCAGACGA 61.177 55.000 0.00 0.00 0.00 4.20
214 215 1.087501 GTGAAGAACTTGGATCCGCC 58.912 55.000 7.39 0.00 37.10 6.13
223 224 1.700186 GGGTCTGGAGGTGAAGAACTT 59.300 52.381 0.00 0.00 30.51 2.66
227 228 0.898789 GACGGGTCTGGAGGTGAAGA 60.899 60.000 0.00 0.00 0.00 2.87
241 242 3.217743 GAGCTAGGGGTCGACGGG 61.218 72.222 9.92 0.00 0.00 5.28
244 245 1.465200 GGGATGAGCTAGGGGTCGAC 61.465 65.000 7.13 7.13 42.30 4.20
253 254 2.427320 GCCGCATGGGATGAGCTA 59.573 61.111 12.02 0.00 38.47 3.32
335 336 2.205911 GATAAAAGGAGTCTGAGCGCC 58.794 52.381 2.29 0.00 0.00 6.53
342 343 4.037927 TGGATTCCCGATAAAAGGAGTCT 58.962 43.478 0.00 0.00 38.57 3.24
351 352 6.897413 TCAGATAGATGATGGATTCCCGATAA 59.103 38.462 0.00 0.00 34.29 1.75
353 354 5.128499 GTCAGATAGATGATGGATTCCCGAT 59.872 44.000 0.00 0.00 34.29 4.18
358 359 5.047731 TGGACGTCAGATAGATGATGGATTC 60.048 44.000 18.91 0.00 39.97 2.52
377 378 1.948104 TTGAAAGGTGTCTGTGGACG 58.052 50.000 0.00 0.00 44.83 4.79
386 387 2.296190 GAGCCCGAAAATTGAAAGGTGT 59.704 45.455 0.00 0.00 0.00 4.16
415 416 2.761208 CGTCTCCCATGTCCTACTCTTT 59.239 50.000 0.00 0.00 0.00 2.52
492 493 1.616865 CTTAGAGTGTTGGTCCGGTCA 59.383 52.381 0.00 0.00 0.00 4.02
525 526 2.186644 CATGTCCATGTCCGGCGA 59.813 61.111 9.30 0.00 34.23 5.54
565 566 6.481954 ACATGAAACGTGAAACCTAATCTC 57.518 37.500 0.00 0.00 0.00 2.75
653 654 2.983977 CTCAAACGTCGCGTGTCGG 61.984 63.158 18.98 2.68 39.99 4.79
654 655 1.920285 CTCTCAAACGTCGCGTGTCG 61.920 60.000 13.83 13.83 39.99 4.35
657 658 0.635731 GATCTCTCAAACGTCGCGTG 59.364 55.000 5.77 2.22 39.99 5.34
658 659 0.793478 CGATCTCTCAAACGTCGCGT 60.793 55.000 5.77 0.00 43.97 6.01
659 660 1.464429 CCGATCTCTCAAACGTCGCG 61.464 60.000 0.00 0.00 0.00 5.87
660 661 0.179171 TCCGATCTCTCAAACGTCGC 60.179 55.000 0.00 0.00 0.00 5.19
661 662 2.476873 ATCCGATCTCTCAAACGTCG 57.523 50.000 0.00 0.00 0.00 5.12
662 663 5.805994 ACTTAAATCCGATCTCTCAAACGTC 59.194 40.000 0.00 0.00 0.00 4.34
663 664 5.721232 ACTTAAATCCGATCTCTCAAACGT 58.279 37.500 0.00 0.00 0.00 3.99
664 665 6.020281 CAGACTTAAATCCGATCTCTCAAACG 60.020 42.308 0.00 0.00 0.00 3.60
665 666 7.036220 TCAGACTTAAATCCGATCTCTCAAAC 58.964 38.462 0.00 0.00 0.00 2.93
666 667 7.170393 TCAGACTTAAATCCGATCTCTCAAA 57.830 36.000 0.00 0.00 0.00 2.69
667 668 6.775594 TCAGACTTAAATCCGATCTCTCAA 57.224 37.500 0.00 0.00 0.00 3.02
668 669 6.968263 ATCAGACTTAAATCCGATCTCTCA 57.032 37.500 0.00 0.00 0.00 3.27
669 670 7.206687 ACAATCAGACTTAAATCCGATCTCTC 58.793 38.462 0.00 0.00 0.00 3.20
670 671 7.118496 ACAATCAGACTTAAATCCGATCTCT 57.882 36.000 0.00 0.00 0.00 3.10
671 672 8.353684 TCTACAATCAGACTTAAATCCGATCTC 58.646 37.037 0.00 0.00 0.00 2.75
672 673 8.239038 TCTACAATCAGACTTAAATCCGATCT 57.761 34.615 0.00 0.00 0.00 2.75
673 674 8.920665 CATCTACAATCAGACTTAAATCCGATC 58.079 37.037 0.00 0.00 0.00 3.69
674 675 7.386299 GCATCTACAATCAGACTTAAATCCGAT 59.614 37.037 0.00 0.00 0.00 4.18
675 676 6.701841 GCATCTACAATCAGACTTAAATCCGA 59.298 38.462 0.00 0.00 0.00 4.55
676 677 6.703607 AGCATCTACAATCAGACTTAAATCCG 59.296 38.462 0.00 0.00 0.00 4.18
677 678 7.172361 GGAGCATCTACAATCAGACTTAAATCC 59.828 40.741 0.00 0.00 33.73 3.01
678 679 7.712639 TGGAGCATCTACAATCAGACTTAAATC 59.287 37.037 0.00 0.00 33.73 2.17
679 680 7.568349 TGGAGCATCTACAATCAGACTTAAAT 58.432 34.615 0.00 0.00 33.73 1.40
680 681 6.946340 TGGAGCATCTACAATCAGACTTAAA 58.054 36.000 0.00 0.00 33.73 1.52
681 682 6.544928 TGGAGCATCTACAATCAGACTTAA 57.455 37.500 0.00 0.00 33.73 1.85
682 683 6.544928 TTGGAGCATCTACAATCAGACTTA 57.455 37.500 0.00 0.00 28.11 2.24
683 684 5.426689 TTGGAGCATCTACAATCAGACTT 57.573 39.130 0.00 0.00 28.11 3.01
684 685 5.366460 CATTGGAGCATCTACAATCAGACT 58.634 41.667 1.48 0.00 40.65 3.24
685 686 4.514441 CCATTGGAGCATCTACAATCAGAC 59.486 45.833 0.00 0.00 40.65 3.51
686 687 4.164796 ACCATTGGAGCATCTACAATCAGA 59.835 41.667 10.37 0.00 40.65 3.27
687 688 4.458397 ACCATTGGAGCATCTACAATCAG 58.542 43.478 10.37 0.37 40.65 2.90
688 689 4.508551 ACCATTGGAGCATCTACAATCA 57.491 40.909 10.37 0.00 40.65 2.57
689 690 5.349817 CGATACCATTGGAGCATCTACAATC 59.650 44.000 10.37 0.00 40.65 2.67
690 691 5.240891 CGATACCATTGGAGCATCTACAAT 58.759 41.667 10.37 0.00 44.93 2.71
691 692 4.503123 CCGATACCATTGGAGCATCTACAA 60.503 45.833 10.37 0.00 38.79 2.41
692 693 3.006859 CCGATACCATTGGAGCATCTACA 59.993 47.826 10.37 0.00 35.72 2.74
693 694 3.589988 CCGATACCATTGGAGCATCTAC 58.410 50.000 10.37 0.00 35.72 2.59
694 695 2.028112 GCCGATACCATTGGAGCATCTA 60.028 50.000 10.37 0.00 35.72 1.98
695 696 1.271054 GCCGATACCATTGGAGCATCT 60.271 52.381 10.37 0.00 35.72 2.90
696 697 1.160137 GCCGATACCATTGGAGCATC 58.840 55.000 10.37 7.96 35.72 3.91
697 698 0.250901 GGCCGATACCATTGGAGCAT 60.251 55.000 10.37 0.00 35.72 3.79
698 699 1.148273 GGCCGATACCATTGGAGCA 59.852 57.895 10.37 0.00 35.72 4.26
699 700 1.961277 CGGCCGATACCATTGGAGC 60.961 63.158 24.07 4.01 35.72 4.70
700 701 0.880278 CACGGCCGATACCATTGGAG 60.880 60.000 35.90 0.00 35.72 3.86
701 702 1.145156 CACGGCCGATACCATTGGA 59.855 57.895 35.90 0.00 35.72 3.53
702 703 0.880278 CTCACGGCCGATACCATTGG 60.880 60.000 35.90 7.89 36.85 3.16
703 704 0.104120 TCTCACGGCCGATACCATTG 59.896 55.000 35.90 18.30 0.00 2.82
704 705 1.048601 ATCTCACGGCCGATACCATT 58.951 50.000 35.90 3.57 0.00 3.16
705 706 0.318441 CATCTCACGGCCGATACCAT 59.682 55.000 35.90 13.72 0.00 3.55
706 707 0.753848 TCATCTCACGGCCGATACCA 60.754 55.000 35.90 11.79 0.00 3.25
707 708 0.603569 ATCATCTCACGGCCGATACC 59.396 55.000 35.90 0.00 0.00 2.73
708 709 2.329379 GAATCATCTCACGGCCGATAC 58.671 52.381 35.90 6.75 0.00 2.24
709 710 1.068541 CGAATCATCTCACGGCCGATA 60.069 52.381 35.90 18.28 0.00 2.92
710 711 0.319040 CGAATCATCTCACGGCCGAT 60.319 55.000 35.90 12.52 0.00 4.18
711 712 1.065764 CGAATCATCTCACGGCCGA 59.934 57.895 35.90 10.13 0.00 5.54
712 713 0.030235 TACGAATCATCTCACGGCCG 59.970 55.000 26.86 26.86 0.00 6.13
713 714 2.288213 TGATACGAATCATCTCACGGCC 60.288 50.000 0.00 0.00 37.20 6.13
714 715 2.983136 CTGATACGAATCATCTCACGGC 59.017 50.000 0.00 0.00 41.29 5.68
715 716 3.253432 TCCTGATACGAATCATCTCACGG 59.747 47.826 0.00 0.00 41.29 4.94
716 717 4.471373 CTCCTGATACGAATCATCTCACG 58.529 47.826 0.00 0.00 41.29 4.35
717 718 4.804108 CCTCCTGATACGAATCATCTCAC 58.196 47.826 0.00 0.00 41.29 3.51
718 719 3.256879 GCCTCCTGATACGAATCATCTCA 59.743 47.826 0.00 0.00 41.29 3.27
719 720 3.509575 AGCCTCCTGATACGAATCATCTC 59.490 47.826 0.00 0.00 41.29 2.75
720 721 3.505386 AGCCTCCTGATACGAATCATCT 58.495 45.455 0.00 0.00 41.29 2.90
721 722 3.951775 AGCCTCCTGATACGAATCATC 57.048 47.619 0.00 0.00 41.29 2.92
722 723 4.461081 GTCTAGCCTCCTGATACGAATCAT 59.539 45.833 0.00 0.00 41.29 2.45
723 724 3.821600 GTCTAGCCTCCTGATACGAATCA 59.178 47.826 0.00 0.00 39.87 2.57
724 725 3.191791 GGTCTAGCCTCCTGATACGAATC 59.808 52.174 0.00 0.00 0.00 2.52
725 726 3.158676 GGTCTAGCCTCCTGATACGAAT 58.841 50.000 0.00 0.00 0.00 3.34
726 727 2.584236 GGTCTAGCCTCCTGATACGAA 58.416 52.381 0.00 0.00 0.00 3.85
727 728 1.542767 CGGTCTAGCCTCCTGATACGA 60.543 57.143 0.00 0.00 34.25 3.43
728 729 0.875728 CGGTCTAGCCTCCTGATACG 59.124 60.000 2.39 0.00 34.25 3.06
729 730 1.249407 CCGGTCTAGCCTCCTGATAC 58.751 60.000 0.00 0.00 34.25 2.24
730 731 0.539901 GCCGGTCTAGCCTCCTGATA 60.540 60.000 1.90 0.00 34.25 2.15
731 732 1.834822 GCCGGTCTAGCCTCCTGAT 60.835 63.158 1.90 0.00 34.25 2.90
732 733 2.442272 GCCGGTCTAGCCTCCTGA 60.442 66.667 1.90 0.00 34.25 3.86
733 734 3.905678 CGCCGGTCTAGCCTCCTG 61.906 72.222 1.90 0.00 34.25 3.86
740 741 2.023414 TATTGTGCCCGCCGGTCTAG 62.023 60.000 1.90 0.00 0.00 2.43
741 742 2.023414 CTATTGTGCCCGCCGGTCTA 62.023 60.000 1.90 0.00 0.00 2.59
742 743 3.385749 CTATTGTGCCCGCCGGTCT 62.386 63.158 1.90 0.00 0.00 3.85
743 744 2.895372 CTATTGTGCCCGCCGGTC 60.895 66.667 1.90 0.00 0.00 4.79
744 745 4.483243 CCTATTGTGCCCGCCGGT 62.483 66.667 1.90 0.00 0.00 5.28
746 747 4.856801 AGCCTATTGTGCCCGCCG 62.857 66.667 0.00 0.00 0.00 6.46
747 748 2.965716 ATCAGCCTATTGTGCCCGCC 62.966 60.000 0.00 0.00 0.00 6.13
748 749 1.526917 ATCAGCCTATTGTGCCCGC 60.527 57.895 0.00 0.00 0.00 6.13
749 750 1.789078 GCATCAGCCTATTGTGCCCG 61.789 60.000 0.00 0.00 33.58 6.13
750 751 0.752743 TGCATCAGCCTATTGTGCCC 60.753 55.000 0.00 0.00 41.13 5.36
751 752 0.383231 GTGCATCAGCCTATTGTGCC 59.617 55.000 0.00 0.00 41.13 5.01
752 753 1.386533 AGTGCATCAGCCTATTGTGC 58.613 50.000 0.00 0.00 41.13 4.57
753 754 3.313526 GGTTAGTGCATCAGCCTATTGTG 59.686 47.826 0.00 0.00 41.13 3.33
754 755 3.200825 AGGTTAGTGCATCAGCCTATTGT 59.799 43.478 4.39 0.00 41.13 2.71
755 756 3.813443 AGGTTAGTGCATCAGCCTATTG 58.187 45.455 4.39 0.00 41.13 1.90
756 757 4.510167 AAGGTTAGTGCATCAGCCTATT 57.490 40.909 6.37 0.00 41.13 1.73
757 758 4.510167 AAAGGTTAGTGCATCAGCCTAT 57.490 40.909 6.37 0.00 41.13 2.57
758 759 4.009675 CAAAAGGTTAGTGCATCAGCCTA 58.990 43.478 6.37 0.00 41.13 3.93
768 769 5.333339 CGTGTCAGATGTCAAAAGGTTAGTG 60.333 44.000 0.00 0.00 0.00 2.74
775 776 4.212004 ACATGTCGTGTCAGATGTCAAAAG 59.788 41.667 0.00 0.00 35.77 2.27
798 799 1.969064 CAAATGAACCGGGCCGTGA 60.969 57.895 26.32 0.60 0.00 4.35
799 800 1.801309 AACAAATGAACCGGGCCGTG 61.801 55.000 26.32 18.46 0.00 4.94
820 821 2.225491 CGCAGCTGCTTTGGTAAAAGTA 59.775 45.455 34.22 0.00 44.02 2.24
821 822 1.001378 CGCAGCTGCTTTGGTAAAAGT 60.001 47.619 34.22 0.00 44.02 2.66
822 823 1.001378 ACGCAGCTGCTTTGGTAAAAG 60.001 47.619 34.22 17.84 44.81 2.27
823 824 1.028905 ACGCAGCTGCTTTGGTAAAA 58.971 45.000 34.22 0.00 39.32 1.52
824 825 0.310543 CACGCAGCTGCTTTGGTAAA 59.689 50.000 34.22 0.00 39.32 2.01
825 826 0.817634 ACACGCAGCTGCTTTGGTAA 60.818 50.000 34.22 0.00 39.32 2.85
1028 1029 1.870167 GCGGAGAGAAATGATCGGGAC 60.870 57.143 0.00 0.00 0.00 4.46
1178 1181 2.559840 GCGACACGAGGAAGACGA 59.440 61.111 0.00 0.00 34.70 4.20
1347 1356 3.677596 GCACGGAGAAAGAAAGAAGAGAG 59.322 47.826 0.00 0.00 0.00 3.20
1389 1398 0.107508 AACACGCCATGAGATGAGGG 60.108 55.000 0.00 0.00 0.00 4.30
1482 1491 4.172512 CCATCGCCAGGCTCTGCT 62.173 66.667 10.54 0.00 0.00 4.24
1623 1635 2.362503 ACAGGTCTCCATCGGCGA 60.363 61.111 13.87 13.87 0.00 5.54
1677 1689 0.757188 AGTGGAGGGATACAGCTCGG 60.757 60.000 0.00 0.00 39.74 4.63
1748 1764 0.175760 CATACATATCGCCGAGGGGG 59.824 60.000 6.35 0.00 36.96 5.40
1749 1765 0.460284 GCATACATATCGCCGAGGGG 60.460 60.000 0.00 0.00 0.00 4.79
1750 1766 0.802222 CGCATACATATCGCCGAGGG 60.802 60.000 0.00 0.00 0.00 4.30
1751 1767 0.109272 ACGCATACATATCGCCGAGG 60.109 55.000 0.00 0.00 0.00 4.63
1756 1772 6.863645 AGGATATTCATACGCATACATATCGC 59.136 38.462 0.00 0.00 0.00 4.58
1757 1773 7.148902 GCAGGATATTCATACGCATACATATCG 60.149 40.741 0.00 0.00 0.00 2.92
1759 1775 6.642540 CGCAGGATATTCATACGCATACATAT 59.357 38.462 0.00 0.00 0.00 1.78
1760 1776 5.977129 CGCAGGATATTCATACGCATACATA 59.023 40.000 0.00 0.00 0.00 2.29
1762 1778 4.082463 TCGCAGGATATTCATACGCATACA 60.082 41.667 0.00 0.00 0.00 2.29
1768 1792 5.164233 ACAGAATCGCAGGATATTCATACG 58.836 41.667 0.00 0.00 35.07 3.06
1774 1798 6.825721 AGAGAAAAACAGAATCGCAGGATATT 59.174 34.615 0.00 0.00 31.01 1.28
1775 1799 6.259608 CAGAGAAAAACAGAATCGCAGGATAT 59.740 38.462 0.00 0.00 31.01 1.63
1792 1816 3.135712 TCACAAGCAGGGTACAGAGAAAA 59.864 43.478 0.00 0.00 0.00 2.29
1796 1820 2.839486 TTCACAAGCAGGGTACAGAG 57.161 50.000 0.00 0.00 0.00 3.35
1802 1826 3.679917 CGTCTCATATTCACAAGCAGGGT 60.680 47.826 0.00 0.00 0.00 4.34
1805 1829 3.525537 ACCGTCTCATATTCACAAGCAG 58.474 45.455 0.00 0.00 0.00 4.24
1825 1849 4.352887 CCGAGAAAACTTCCGATCTAGAC 58.647 47.826 0.00 0.00 0.00 2.59
1826 1850 3.181489 GCCGAGAAAACTTCCGATCTAGA 60.181 47.826 0.00 0.00 0.00 2.43
1827 1851 3.117046 GCCGAGAAAACTTCCGATCTAG 58.883 50.000 0.00 0.00 0.00 2.43
1828 1852 2.494471 TGCCGAGAAAACTTCCGATCTA 59.506 45.455 0.00 0.00 0.00 1.98
1829 1853 1.275291 TGCCGAGAAAACTTCCGATCT 59.725 47.619 0.00 0.00 0.00 2.75
1830 1854 1.722011 TGCCGAGAAAACTTCCGATC 58.278 50.000 0.00 0.00 0.00 3.69
1831 1855 2.178912 TTGCCGAGAAAACTTCCGAT 57.821 45.000 0.00 0.00 0.00 4.18
1832 1856 1.956297 TTTGCCGAGAAAACTTCCGA 58.044 45.000 0.00 0.00 0.00 4.55
1833 1857 2.766970 TTTTGCCGAGAAAACTTCCG 57.233 45.000 0.00 0.00 0.00 4.30
1855 1879 4.261698 GCAGCCAAAATGCATTTCCTTTTT 60.262 37.500 24.28 6.39 43.31 1.94
1856 1880 3.253921 GCAGCCAAAATGCATTTCCTTTT 59.746 39.130 24.28 7.13 43.31 2.27
1857 1881 2.815503 GCAGCCAAAATGCATTTCCTTT 59.184 40.909 24.28 6.70 43.31 3.11
1875 1899 2.468777 GTGACAATGCAACTTTTCGCAG 59.531 45.455 0.00 0.00 42.37 5.18
1893 1917 0.038599 ACATGGCTGCAGATTGGTGA 59.961 50.000 20.43 0.00 0.00 4.02
1896 1920 0.745486 TCGACATGGCTGCAGATTGG 60.745 55.000 20.43 6.10 0.00 3.16
1899 1923 0.466963 TCATCGACATGGCTGCAGAT 59.533 50.000 20.43 0.00 0.00 2.90
1911 1935 0.383949 GGCTCTGACCTCTCATCGAC 59.616 60.000 0.00 0.00 0.00 4.20
1912 1936 0.753479 GGGCTCTGACCTCTCATCGA 60.753 60.000 0.00 0.00 0.00 3.59
1913 1937 1.039785 TGGGCTCTGACCTCTCATCG 61.040 60.000 0.00 0.00 0.00 3.84
1914 1938 0.752054 CTGGGCTCTGACCTCTCATC 59.248 60.000 0.00 0.00 0.00 2.92
1915 1939 0.690411 CCTGGGCTCTGACCTCTCAT 60.690 60.000 0.00 0.00 0.00 2.90
1916 1940 1.305633 CCTGGGCTCTGACCTCTCA 60.306 63.158 0.00 0.00 0.00 3.27
1917 1941 1.305718 ACCTGGGCTCTGACCTCTC 60.306 63.158 0.00 0.00 0.00 3.20
1918 1942 1.611851 CACCTGGGCTCTGACCTCT 60.612 63.158 0.00 0.00 0.00 3.69
1919 1943 1.484444 AACACCTGGGCTCTGACCTC 61.484 60.000 0.00 0.00 0.00 3.85
1920 1944 1.462238 AACACCTGGGCTCTGACCT 60.462 57.895 0.00 0.00 0.00 3.85
1921 1945 1.302832 CAACACCTGGGCTCTGACC 60.303 63.158 0.00 0.00 0.00 4.02
1940 1964 6.721571 TGCAACTGCTACTAATTCTGTTAC 57.278 37.500 2.95 0.00 42.66 2.50
1944 1968 6.426980 TTGATGCAACTGCTACTAATTCTG 57.573 37.500 2.95 0.00 42.66 3.02
1945 1969 6.039047 CCATTGATGCAACTGCTACTAATTCT 59.961 38.462 2.95 0.00 42.66 2.40
1946 1970 6.038603 TCCATTGATGCAACTGCTACTAATTC 59.961 38.462 2.95 0.00 42.66 2.17
1947 1971 5.887598 TCCATTGATGCAACTGCTACTAATT 59.112 36.000 2.95 0.00 42.66 1.40
1950 1974 4.445453 CTCCATTGATGCAACTGCTACTA 58.555 43.478 2.95 0.00 42.66 1.82
1952 1976 2.223433 GCTCCATTGATGCAACTGCTAC 60.223 50.000 2.95 0.00 42.66 3.58
1961 1990 0.528924 TTGTGCTGCTCCATTGATGC 59.471 50.000 0.00 0.00 0.00 3.91
1996 2040 7.202016 TGTTAAAGAGTATTGCAAGGAGTTG 57.798 36.000 4.94 0.00 36.67 3.16
1997 2041 7.817418 TTGTTAAAGAGTATTGCAAGGAGTT 57.183 32.000 4.94 0.00 0.00 3.01
1998 2042 7.519970 CGTTTGTTAAAGAGTATTGCAAGGAGT 60.520 37.037 4.94 0.00 0.00 3.85
2009 2053 3.059461 CGCTTGCCGTTTGTTAAAGAGTA 60.059 43.478 0.00 0.00 0.00 2.59
2011 2055 2.032377 TCGCTTGCCGTTTGTTAAAGAG 60.032 45.455 0.00 0.00 38.35 2.85
2013 2057 2.392933 TCGCTTGCCGTTTGTTAAAG 57.607 45.000 0.00 0.00 38.35 1.85
2078 2132 5.930135 AGAATCTCTCTCCACTCTAGTCTC 58.070 45.833 0.00 0.00 0.00 3.36
2079 2133 5.930135 GAGAATCTCTCTCCACTCTAGTCT 58.070 45.833 2.45 0.00 44.39 3.24
2107 2161 6.649973 GGAAGAAGACTGTTTACTAGTTTCCC 59.350 42.308 0.00 0.00 0.00 3.97
2108 2162 7.443477 AGGAAGAAGACTGTTTACTAGTTTCC 58.557 38.462 0.00 3.54 0.00 3.13
2117 2171 5.602978 ACTCCTGAAGGAAGAAGACTGTTTA 59.397 40.000 0.00 0.00 44.91 2.01
2161 2215 1.768275 TGTGTCCATACCATAGGCCTG 59.232 52.381 17.99 0.00 0.00 4.85
2163 2217 1.072331 CCTGTGTCCATACCATAGGCC 59.928 57.143 0.00 0.00 34.93 5.19
2337 2391 1.079057 GCCAACCGAGGAGGAAGAC 60.079 63.158 8.99 0.00 45.00 3.01
2349 2403 4.353437 GCAGCAGCACAGCCAACC 62.353 66.667 0.00 0.00 41.58 3.77
2478 2532 1.679153 GGTTTTCCCGAACTCAAGCAA 59.321 47.619 0.00 0.00 0.00 3.91
2539 2593 4.960938 TGCAGTAACATCTGTTCTGTCTT 58.039 39.130 16.57 0.00 39.31 3.01
2658 2723 7.227873 TCTAAACCAACACAACCATAAGATGA 58.772 34.615 0.00 0.00 0.00 2.92
2682 2747 0.106819 ATGTTCATGCAGCCTCCCTC 60.107 55.000 0.00 0.00 0.00 4.30
2844 3026 3.444034 TCTCCAGTGTCAGGATCTAAACG 59.556 47.826 0.00 0.00 33.99 3.60


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

AutoCloner maintained by Alex Coulton.