Multiple sequence alignment - TraesCS3B01G557400

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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 TraesCS3B01G557400 chr3B 100.000 2618 0 0 1 2618 791652197 791654814 0.000000e+00 4835.0
1 TraesCS3B01G557400 chr3B 82.231 484 76 6 1 477 384912743 384912263 2.430000e-110 409.0
2 TraesCS3B01G557400 chr5B 81.966 1841 285 15 805 2618 357155680 357153860 0.000000e+00 1517.0
3 TraesCS3B01G557400 chr5B 86.531 1329 136 12 1317 2618 352677613 352676301 0.000000e+00 1423.0
4 TraesCS3B01G557400 chr5B 88.051 544 61 3 788 1328 352893156 352892614 2.200000e-180 641.0
5 TraesCS3B01G557400 chr6D 85.443 632 84 5 1 625 83111887 83112517 0.000000e+00 651.0
6 TraesCS3B01G557400 chr6D 92.683 41 3 0 2194 2234 460014023 460014063 2.810000e-05 60.2
7 TraesCS3B01G557400 chr3D 84.953 638 82 8 2 625 87329491 87330128 3.680000e-178 634.0
8 TraesCS3B01G557400 chr4A 85.458 557 66 10 76 624 618116765 618117314 1.360000e-157 566.0
9 TraesCS3B01G557400 chr2D 82.622 633 99 6 1 625 545502959 545502330 1.370000e-152 549.0
10 TraesCS3B01G557400 chr2D 84.539 401 56 3 167 561 554348200 554348600 2.440000e-105 392.0
11 TraesCS3B01G557400 chr2A 82.306 633 100 7 1 625 687496595 687497223 2.960000e-149 538.0
12 TraesCS3B01G557400 chr3A 83.756 394 62 2 233 625 57468308 57468700 3.180000e-99 372.0
13 TraesCS3B01G557400 chr3A 87.402 127 12 3 649 773 484110789 484110913 2.720000e-30 143.0
14 TraesCS3B01G557400 chr1D 83.505 388 62 2 239 625 314005492 314005878 6.890000e-96 361.0
15 TraesCS3B01G557400 chr1D 73.296 719 177 13 977 1688 433176945 433176235 1.560000e-62 250.0
16 TraesCS3B01G557400 chr7D 100.000 28 0 0 1738 1765 547251275 547251248 5.000000e-03 52.8


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 TraesCS3B01G557400 chr3B 791652197 791654814 2617 False 4835 4835 100.000 1 2618 1 chr3B.!!$F1 2617
1 TraesCS3B01G557400 chr5B 357153860 357155680 1820 True 1517 1517 81.966 805 2618 1 chr5B.!!$R3 1813
2 TraesCS3B01G557400 chr5B 352676301 352677613 1312 True 1423 1423 86.531 1317 2618 1 chr5B.!!$R1 1301
3 TraesCS3B01G557400 chr5B 352892614 352893156 542 True 641 641 88.051 788 1328 1 chr5B.!!$R2 540
4 TraesCS3B01G557400 chr6D 83111887 83112517 630 False 651 651 85.443 1 625 1 chr6D.!!$F1 624
5 TraesCS3B01G557400 chr3D 87329491 87330128 637 False 634 634 84.953 2 625 1 chr3D.!!$F1 623
6 TraesCS3B01G557400 chr4A 618116765 618117314 549 False 566 566 85.458 76 624 1 chr4A.!!$F1 548
7 TraesCS3B01G557400 chr2D 545502330 545502959 629 True 549 549 82.622 1 625 1 chr2D.!!$R1 624
8 TraesCS3B01G557400 chr2A 687496595 687497223 628 False 538 538 82.306 1 625 1 chr2A.!!$F1 624
9 TraesCS3B01G557400 chr1D 433176235 433176945 710 True 250 250 73.296 977 1688 1 chr1D.!!$R1 711

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
670 686 0.036294 GCTGCTTCGGACCCTTAACT 60.036 55.0 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 1820 0.032416 TCCCCGTTGTTTCCCCAAAA 60.032 50.0 0.0 0.0 0.0 2.44 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
24 26 0.868406 CAAAGTGAGTCTGAACCCGC 59.132 55.000 0.00 0.00 0.00 6.13
28 30 2.144078 TGAGTCTGAACCCGCCCAA 61.144 57.895 0.00 0.00 0.00 4.12
37 39 0.178947 AACCCGCCCAATCCTTGAAA 60.179 50.000 0.00 0.00 0.00 2.69
40 42 1.241315 CCGCCCAATCCTTGAAACGT 61.241 55.000 0.00 0.00 0.00 3.99
45 47 3.632145 GCCCAATCCTTGAAACGTATCAT 59.368 43.478 0.00 0.00 0.00 2.45
60 62 5.715070 ACGTATCATAGAAGCTCTAATGCC 58.285 41.667 0.00 0.00 31.96 4.40
63 65 4.244425 TCATAGAAGCTCTAATGCCGTC 57.756 45.455 0.00 0.00 31.96 4.79
67 69 2.497675 AGAAGCTCTAATGCCGTCAGAA 59.502 45.455 0.00 0.00 0.00 3.02
105 107 1.568504 AGGATCTTGCCTGGTTACGA 58.431 50.000 0.00 0.00 36.76 3.43
121 123 1.218047 CGATTGGAGACCGCCTGAA 59.782 57.895 0.00 0.00 0.00 3.02
130 132 1.556911 AGACCGCCTGAATCAGAATGT 59.443 47.619 12.53 5.09 37.40 2.71
178 188 3.375922 GTCCCGTTGACTGAAAACAGAAA 59.624 43.478 0.00 0.00 41.03 2.52
185 195 4.206375 TGACTGAAAACAGAAATGGAGCA 58.794 39.130 0.00 0.00 0.00 4.26
207 217 1.623811 GTGGTCTAGCAAGAACTCCCA 59.376 52.381 0.00 0.00 40.39 4.37
219 229 1.871676 GAACTCCCACCGTCTTTGTTC 59.128 52.381 0.00 0.00 0.00 3.18
224 234 0.817634 CCACCGTCTTTGTTCCTGCA 60.818 55.000 0.00 0.00 0.00 4.41
236 252 3.896133 CCTGCATGGCCGCATCAC 61.896 66.667 5.73 0.00 42.06 3.06
244 260 0.680601 TGGCCGCATCACAATGTCAT 60.681 50.000 0.00 0.00 35.18 3.06
256 272 5.185454 TCACAATGTCATGGATCCACTTAC 58.815 41.667 18.99 15.58 0.00 2.34
286 302 0.972471 TTGGCTCTGCGAGATGGAGA 60.972 55.000 9.32 0.00 43.53 3.71
307 323 2.479566 ATCTTTGGCAAGCTTCGAGA 57.520 45.000 0.00 0.00 0.00 4.04
313 329 2.783135 TGGCAAGCTTCGAGATTTTCT 58.217 42.857 0.00 0.00 0.00 2.52
315 331 2.485814 GGCAAGCTTCGAGATTTTCTGT 59.514 45.455 0.00 0.00 0.00 3.41
323 339 3.914312 TCGAGATTTTCTGTGAGTGGTC 58.086 45.455 0.00 0.00 0.00 4.02
332 348 2.693591 TCTGTGAGTGGTCTTCGAAGTT 59.306 45.455 23.85 6.80 0.00 2.66
374 390 1.656095 CTCTGGAACTCGCGACAATTC 59.344 52.381 3.71 9.58 0.00 2.17
391 407 3.992260 ATTCTCGCGCTCTGTAATAGT 57.008 42.857 5.56 0.00 0.00 2.12
431 447 2.290323 TGAAGGGCTAGCCTCAACTTTC 60.290 50.000 32.18 22.70 36.10 2.62
434 450 1.838077 GGGCTAGCCTCAACTTTCCTA 59.162 52.381 32.18 0.00 36.10 2.94
473 489 4.829064 TGTAATGAGACAAGCCAACAAC 57.171 40.909 0.00 0.00 0.00 3.32
477 493 2.997980 TGAGACAAGCCAACAACTCAA 58.002 42.857 0.00 0.00 32.66 3.02
482 498 3.290710 ACAAGCCAACAACTCAACTCAT 58.709 40.909 0.00 0.00 0.00 2.90
483 499 3.067180 ACAAGCCAACAACTCAACTCATG 59.933 43.478 0.00 0.00 0.00 3.07
541 557 0.547471 TGCTGGATGAACTCCCCTCA 60.547 55.000 0.00 0.00 44.23 3.86
545 561 0.976073 GGATGAACTCCCCTCACGGA 60.976 60.000 0.00 0.00 38.19 4.69
548 564 1.358152 TGAACTCCCCTCACGGATTT 58.642 50.000 0.00 0.00 0.00 2.17
551 567 1.657804 ACTCCCCTCACGGATTTCTT 58.342 50.000 0.00 0.00 0.00 2.52
591 607 0.248012 TCGCGCTGGAGTTGGAAATA 59.752 50.000 5.56 0.00 0.00 1.40
602 618 9.651913 GCTGGAGTTGGAAATAATTGAATAAAA 57.348 29.630 0.00 0.00 0.00 1.52
640 656 3.855689 AAAAAGATTGCGACCTCCATG 57.144 42.857 0.00 0.00 0.00 3.66
641 657 2.496899 AAAGATTGCGACCTCCATGT 57.503 45.000 0.00 0.00 0.00 3.21
642 658 3.627395 AAAGATTGCGACCTCCATGTA 57.373 42.857 0.00 0.00 0.00 2.29
643 659 2.898729 AGATTGCGACCTCCATGTAG 57.101 50.000 0.00 0.00 0.00 2.74
644 660 1.202580 AGATTGCGACCTCCATGTAGC 60.203 52.381 0.00 0.00 37.38 3.58
645 661 0.833287 ATTGCGACCTCCATGTAGCT 59.167 50.000 0.00 0.00 37.69 3.32
646 662 0.175760 TTGCGACCTCCATGTAGCTC 59.824 55.000 0.00 0.00 37.69 4.09
647 663 0.970427 TGCGACCTCCATGTAGCTCA 60.970 55.000 0.00 0.00 37.69 4.26
648 664 0.249238 GCGACCTCCATGTAGCTCAG 60.249 60.000 0.00 0.00 34.50 3.35
649 665 1.393603 CGACCTCCATGTAGCTCAGA 58.606 55.000 0.00 0.00 0.00 3.27
650 666 1.066303 CGACCTCCATGTAGCTCAGAC 59.934 57.143 0.00 0.00 0.00 3.51
651 667 1.066303 GACCTCCATGTAGCTCAGACG 59.934 57.143 0.00 0.00 0.00 4.18
652 668 0.249238 CCTCCATGTAGCTCAGACGC 60.249 60.000 0.00 0.00 0.00 5.19
653 669 0.743688 CTCCATGTAGCTCAGACGCT 59.256 55.000 0.00 0.00 43.83 5.07
654 670 0.457443 TCCATGTAGCTCAGACGCTG 59.543 55.000 0.00 1.02 41.12 5.18
655 671 1.150567 CCATGTAGCTCAGACGCTGC 61.151 60.000 0.00 4.45 41.12 5.25
656 672 0.179116 CATGTAGCTCAGACGCTGCT 60.179 55.000 0.00 0.00 42.21 4.24
657 673 0.534412 ATGTAGCTCAGACGCTGCTT 59.466 50.000 0.00 0.00 42.21 3.91
658 674 0.109086 TGTAGCTCAGACGCTGCTTC 60.109 55.000 0.00 0.00 42.21 3.86
659 675 1.136872 GTAGCTCAGACGCTGCTTCG 61.137 60.000 0.00 0.00 41.12 3.79
660 676 2.271607 TAGCTCAGACGCTGCTTCGG 62.272 60.000 0.00 0.07 41.12 4.30
661 677 2.568612 CTCAGACGCTGCTTCGGA 59.431 61.111 8.50 8.50 0.00 4.55
662 678 1.803519 CTCAGACGCTGCTTCGGAC 60.804 63.158 4.96 0.00 0.00 4.79
663 679 2.811317 CAGACGCTGCTTCGGACC 60.811 66.667 0.08 0.00 0.00 4.46
664 680 4.070552 AGACGCTGCTTCGGACCC 62.071 66.667 0.16 0.00 0.00 4.46
665 681 4.070552 GACGCTGCTTCGGACCCT 62.071 66.667 0.00 0.00 0.00 4.34
666 682 3.591254 GACGCTGCTTCGGACCCTT 62.591 63.158 0.00 0.00 0.00 3.95
667 683 2.221906 GACGCTGCTTCGGACCCTTA 62.222 60.000 0.00 0.00 0.00 2.69
668 684 1.079405 CGCTGCTTCGGACCCTTAA 60.079 57.895 0.00 0.00 0.00 1.85
669 685 1.359459 CGCTGCTTCGGACCCTTAAC 61.359 60.000 0.00 0.00 0.00 2.01
670 686 0.036294 GCTGCTTCGGACCCTTAACT 60.036 55.000 0.00 0.00 0.00 2.24
671 687 1.206371 GCTGCTTCGGACCCTTAACTA 59.794 52.381 0.00 0.00 0.00 2.24
672 688 2.889852 CTGCTTCGGACCCTTAACTAC 58.110 52.381 0.00 0.00 0.00 2.73
673 689 2.232941 CTGCTTCGGACCCTTAACTACA 59.767 50.000 0.00 0.00 0.00 2.74
674 690 2.028748 TGCTTCGGACCCTTAACTACAC 60.029 50.000 0.00 0.00 0.00 2.90
675 691 2.028748 GCTTCGGACCCTTAACTACACA 60.029 50.000 0.00 0.00 0.00 3.72
676 692 3.369157 GCTTCGGACCCTTAACTACACAT 60.369 47.826 0.00 0.00 0.00 3.21
677 693 3.880047 TCGGACCCTTAACTACACATG 57.120 47.619 0.00 0.00 0.00 3.21
678 694 2.093869 TCGGACCCTTAACTACACATGC 60.094 50.000 0.00 0.00 0.00 4.06
679 695 2.640184 GGACCCTTAACTACACATGCC 58.360 52.381 0.00 0.00 0.00 4.40
680 696 2.238898 GGACCCTTAACTACACATGCCT 59.761 50.000 0.00 0.00 0.00 4.75
681 697 3.308188 GGACCCTTAACTACACATGCCTT 60.308 47.826 0.00 0.00 0.00 4.35
682 698 4.332828 GACCCTTAACTACACATGCCTTT 58.667 43.478 0.00 0.00 0.00 3.11
683 699 4.079253 ACCCTTAACTACACATGCCTTTG 58.921 43.478 0.00 0.00 0.00 2.77
684 700 4.079253 CCCTTAACTACACATGCCTTTGT 58.921 43.478 0.00 0.00 0.00 2.83
691 707 0.599558 CACATGCCTTTGTGTCAGGG 59.400 55.000 0.00 0.00 41.65 4.45
692 708 0.478072 ACATGCCTTTGTGTCAGGGA 59.522 50.000 0.00 0.00 35.99 4.20
693 709 0.883833 CATGCCTTTGTGTCAGGGAC 59.116 55.000 0.00 0.00 34.03 4.46
694 710 0.478072 ATGCCTTTGTGTCAGGGACA 59.522 50.000 0.00 0.00 40.50 4.02
695 711 0.478072 TGCCTTTGTGTCAGGGACAT 59.522 50.000 2.02 0.00 44.63 3.06
696 712 0.883833 GCCTTTGTGTCAGGGACATG 59.116 55.000 2.02 0.00 44.63 3.21
697 713 1.819305 GCCTTTGTGTCAGGGACATGT 60.819 52.381 0.00 0.00 44.63 3.21
698 714 1.881973 CCTTTGTGTCAGGGACATGTG 59.118 52.381 1.15 0.00 44.63 3.21
699 715 1.881973 CTTTGTGTCAGGGACATGTGG 59.118 52.381 1.15 0.00 44.63 4.17
700 716 0.110295 TTGTGTCAGGGACATGTGGG 59.890 55.000 1.15 0.00 44.63 4.61
701 717 1.675641 GTGTCAGGGACATGTGGGC 60.676 63.158 1.15 0.00 44.63 5.36
702 718 2.044946 GTCAGGGACATGTGGGCC 60.045 66.667 1.15 0.00 32.09 5.80
703 719 2.531428 TCAGGGACATGTGGGCCA 60.531 61.111 1.15 0.00 0.00 5.36
704 720 2.044650 CAGGGACATGTGGGCCAG 60.045 66.667 6.40 0.00 0.00 4.85
705 721 4.052518 AGGGACATGTGGGCCAGC 62.053 66.667 6.40 2.28 0.00 4.85
706 722 4.052518 GGGACATGTGGGCCAGCT 62.053 66.667 6.40 0.00 0.00 4.24
707 723 2.753043 GGACATGTGGGCCAGCTG 60.753 66.667 6.40 10.38 0.00 4.24
708 724 2.352422 GACATGTGGGCCAGCTGA 59.648 61.111 17.39 0.00 0.00 4.26
709 725 2.034687 ACATGTGGGCCAGCTGAC 59.965 61.111 17.39 2.25 0.00 3.51
710 726 2.353958 CATGTGGGCCAGCTGACT 59.646 61.111 17.39 0.00 0.00 3.41
711 727 2.044555 CATGTGGGCCAGCTGACTG 61.045 63.158 17.39 0.00 44.05 3.51
712 728 2.532532 ATGTGGGCCAGCTGACTGT 61.533 57.895 17.39 0.00 42.81 3.55
713 729 2.072874 ATGTGGGCCAGCTGACTGTT 62.073 55.000 17.39 0.00 42.81 3.16
714 730 2.113774 TGGGCCAGCTGACTGTTG 59.886 61.111 17.39 0.00 42.81 3.33
719 735 4.386413 CAGCTGACTGTTGGACCC 57.614 61.111 8.42 0.00 39.22 4.46
720 736 1.451504 CAGCTGACTGTTGGACCCA 59.548 57.895 8.42 0.00 39.22 4.51
721 737 0.886490 CAGCTGACTGTTGGACCCAC 60.886 60.000 8.42 0.00 39.22 4.61
722 738 1.056700 AGCTGACTGTTGGACCCACT 61.057 55.000 0.00 0.00 0.00 4.00
723 739 0.179018 GCTGACTGTTGGACCCACTT 60.179 55.000 0.00 0.00 0.00 3.16
724 740 1.071699 GCTGACTGTTGGACCCACTTA 59.928 52.381 0.00 0.00 0.00 2.24
725 741 2.290323 GCTGACTGTTGGACCCACTTAT 60.290 50.000 0.00 0.00 0.00 1.73
726 742 3.600388 CTGACTGTTGGACCCACTTATC 58.400 50.000 0.00 0.00 0.00 1.75
727 743 2.976185 TGACTGTTGGACCCACTTATCA 59.024 45.455 0.00 0.00 0.00 2.15
728 744 3.007940 TGACTGTTGGACCCACTTATCAG 59.992 47.826 0.00 0.00 0.00 2.90
729 745 2.979678 ACTGTTGGACCCACTTATCAGT 59.020 45.455 0.00 0.00 0.00 3.41
739 755 2.094675 CACTTATCAGTGGCCCAAAGG 58.905 52.381 0.00 0.00 46.10 3.11
749 765 2.203538 CCCAAAGGCACCTGCAGT 60.204 61.111 13.81 0.00 44.36 4.40
750 766 1.833934 CCCAAAGGCACCTGCAGTT 60.834 57.895 13.81 0.00 44.36 3.16
751 767 0.539438 CCCAAAGGCACCTGCAGTTA 60.539 55.000 13.81 0.00 44.36 2.24
752 768 1.327303 CCAAAGGCACCTGCAGTTAA 58.673 50.000 13.81 0.00 44.36 2.01
753 769 1.270550 CCAAAGGCACCTGCAGTTAAG 59.729 52.381 13.81 0.00 44.36 1.85
754 770 1.270550 CAAAGGCACCTGCAGTTAAGG 59.729 52.381 13.81 0.00 44.36 2.69
755 771 0.895559 AAGGCACCTGCAGTTAAGGC 60.896 55.000 13.81 11.21 44.36 4.35
756 772 1.603455 GGCACCTGCAGTTAAGGCA 60.603 57.895 13.81 2.13 44.36 4.75
757 773 1.581447 GCACCTGCAGTTAAGGCAC 59.419 57.895 13.81 0.00 41.59 5.01
758 774 1.868997 CACCTGCAGTTAAGGCACG 59.131 57.895 13.81 0.00 38.48 5.34
759 775 1.302511 ACCTGCAGTTAAGGCACGG 60.303 57.895 13.81 12.17 38.48 4.94
760 776 1.003839 CCTGCAGTTAAGGCACGGA 60.004 57.895 13.81 0.00 36.11 4.69
761 777 0.605319 CCTGCAGTTAAGGCACGGAA 60.605 55.000 13.81 0.00 36.11 4.30
762 778 0.798776 CTGCAGTTAAGGCACGGAAG 59.201 55.000 5.25 0.00 36.11 3.46
763 779 1.234615 TGCAGTTAAGGCACGGAAGC 61.235 55.000 0.00 0.00 36.11 3.86
764 780 0.955919 GCAGTTAAGGCACGGAAGCT 60.956 55.000 0.00 0.00 34.17 3.74
765 781 1.079503 CAGTTAAGGCACGGAAGCTC 58.920 55.000 0.00 0.00 34.17 4.09
766 782 0.685097 AGTTAAGGCACGGAAGCTCA 59.315 50.000 0.00 0.00 34.17 4.26
767 783 1.079503 GTTAAGGCACGGAAGCTCAG 58.920 55.000 0.00 0.00 34.17 3.35
768 784 0.685097 TTAAGGCACGGAAGCTCAGT 59.315 50.000 0.00 0.00 34.17 3.41
769 785 0.246635 TAAGGCACGGAAGCTCAGTC 59.753 55.000 0.00 0.00 34.17 3.51
770 786 2.435059 GGCACGGAAGCTCAGTCC 60.435 66.667 0.00 0.00 34.17 3.85
771 787 2.343758 GCACGGAAGCTCAGTCCA 59.656 61.111 3.87 0.00 34.56 4.02
772 788 1.078848 GCACGGAAGCTCAGTCCAT 60.079 57.895 3.87 0.00 34.56 3.41
773 789 1.364626 GCACGGAAGCTCAGTCCATG 61.365 60.000 3.87 0.00 34.56 3.66
774 790 0.036952 CACGGAAGCTCAGTCCATGT 60.037 55.000 3.87 0.00 34.56 3.21
775 791 1.204704 CACGGAAGCTCAGTCCATGTA 59.795 52.381 3.87 0.00 34.56 2.29
776 792 1.478510 ACGGAAGCTCAGTCCATGTAG 59.521 52.381 3.87 0.00 34.56 2.74
777 793 1.804372 CGGAAGCTCAGTCCATGTAGC 60.804 57.143 3.87 0.00 34.56 3.58
778 794 1.484240 GGAAGCTCAGTCCATGTAGCT 59.516 52.381 0.00 0.00 41.32 3.32
779 795 2.482839 GGAAGCTCAGTCCATGTAGCTC 60.483 54.545 0.00 0.00 39.77 4.09
780 796 0.743688 AGCTCAGTCCATGTAGCTCG 59.256 55.000 0.00 0.00 37.67 5.03
781 797 0.249238 GCTCAGTCCATGTAGCTCGG 60.249 60.000 0.00 0.00 32.54 4.63
782 798 0.249238 CTCAGTCCATGTAGCTCGGC 60.249 60.000 0.00 0.00 0.00 5.54
783 799 1.227380 CAGTCCATGTAGCTCGGCC 60.227 63.158 0.00 0.00 0.00 6.13
784 800 1.685765 AGTCCATGTAGCTCGGCCA 60.686 57.895 2.24 0.00 0.00 5.36
785 801 1.521681 GTCCATGTAGCTCGGCCAC 60.522 63.158 2.24 0.00 0.00 5.01
786 802 1.987306 TCCATGTAGCTCGGCCACA 60.987 57.895 2.24 0.00 0.00 4.17
791 807 4.129737 TAGCTCGGCCACACTCGC 62.130 66.667 2.24 0.00 0.00 5.03
801 817 1.134491 GCCACACTCGCTTAGGGTTAT 60.134 52.381 0.00 0.00 39.51 1.89
803 819 2.167693 CCACACTCGCTTAGGGTTATCA 59.832 50.000 0.00 0.00 39.51 2.15
827 843 2.255252 CCGCTGGCGACTTTTTGG 59.745 61.111 16.79 0.00 42.83 3.28
847 863 4.778143 GCCGGTGGGATCGCTGTT 62.778 66.667 11.46 0.00 34.06 3.16
867 883 5.309638 TGTTTTCTGATCATTACCGAACCA 58.690 37.500 0.00 0.00 0.00 3.67
870 886 2.756207 TCTGATCATTACCGAACCACGA 59.244 45.455 0.00 0.00 45.77 4.35
874 890 2.165167 TCATTACCGAACCACGACTCT 58.835 47.619 0.00 0.00 45.77 3.24
906 922 1.911766 GGGGGAGTCACAGGAACGA 60.912 63.158 0.00 0.00 0.00 3.85
910 926 1.733399 GAGTCACAGGAACGACCGC 60.733 63.158 0.00 0.00 44.74 5.68
955 971 2.861147 AAAGGGTTCTTCCTCGAAGG 57.139 50.000 1.76 0.00 39.82 3.46
963 979 2.124507 CTTCCTCGAAGGTGGGGCAA 62.125 60.000 0.00 0.00 36.16 4.52
964 980 1.710996 TTCCTCGAAGGTGGGGCAAA 61.711 55.000 0.00 0.00 36.53 3.68
975 991 1.963515 GTGGGGCAAACAACTGAGATT 59.036 47.619 0.00 0.00 0.00 2.40
1039 1055 3.953612 GGAATTGGATGCAGTGGTGATTA 59.046 43.478 0.00 0.00 0.00 1.75
1058 1074 0.673022 AGCAAGGCTGAAGCGAAGAG 60.673 55.000 0.00 0.00 43.26 2.85
1070 1086 1.432270 GCGAAGAGATTTGAGGCGGG 61.432 60.000 0.00 0.00 0.00 6.13
1086 1102 3.824425 GGGGCAGGATGGATGGCA 61.824 66.667 0.00 0.00 44.55 4.92
1173 1189 2.600470 GGTCTGGCCCAAACACCC 60.600 66.667 0.00 0.00 0.00 4.61
1275 1291 2.683916 CTGGCTGTTCAGGGGTCTA 58.316 57.895 1.97 0.00 0.00 2.59
1287 1303 1.132689 AGGGGTCTAGGGGTGATCATC 60.133 57.143 0.00 0.00 0.00 2.92
1356 1372 3.758554 GTCTGTATGTGTGGGCTCAAATT 59.241 43.478 0.00 0.00 0.00 1.82
1365 1381 4.016444 TGTGGGCTCAAATTCATAAGGTC 58.984 43.478 0.00 0.00 0.00 3.85
1391 1407 1.869767 CATTTATCGACAGGAGCCAGC 59.130 52.381 0.00 0.00 0.00 4.85
1410 1426 2.232452 AGCAGTAGATCAACTTGCTCGT 59.768 45.455 7.83 0.00 32.19 4.18
1416 1432 7.418408 CAGTAGATCAACTTGCTCGTAGAATA 58.582 38.462 0.00 0.00 34.09 1.75
1501 1517 0.597377 GGCAAAGGTTTTGACTGCGG 60.597 55.000 5.77 0.00 33.76 5.69
1688 1704 1.683943 CCGATGGATGATTGCCAAGT 58.316 50.000 0.00 0.00 39.21 3.16
1692 1708 2.583024 TGGATGATTGCCAAGTGTCA 57.417 45.000 0.00 0.00 31.13 3.58
1728 1744 1.121407 CAGCCCATGGGAGGACGATA 61.121 60.000 36.00 0.00 37.50 2.92
1756 1772 3.471806 GGAGGAAGGGGACGAGGC 61.472 72.222 0.00 0.00 0.00 4.70
1798 1814 1.202722 GGTTCCGACCAAACTCAAGGA 60.203 52.381 0.00 0.00 45.77 3.36
1804 1820 1.070289 GACCAAACTCAAGGACGAGGT 59.930 52.381 0.00 0.00 37.34 3.85
1812 1828 0.109723 CAAGGACGAGGTTTTGGGGA 59.890 55.000 0.00 0.00 0.00 4.81
1830 1846 2.622190 GGGAAACAACGGGGAATATGGT 60.622 50.000 0.00 0.00 0.00 3.55
1858 1874 5.300792 GGACAGGAACACAAAGGATGTAAAA 59.699 40.000 0.00 0.00 41.46 1.52
1893 1909 5.595885 AGAGTCAGATGTTAATGGTGATCG 58.404 41.667 0.00 0.00 0.00 3.69
1897 1913 3.809832 CAGATGTTAATGGTGATCGGGAC 59.190 47.826 0.00 0.00 0.00 4.46
1918 1935 1.376543 CAGTGAAAGCGCAGGATGAT 58.623 50.000 11.47 0.00 39.69 2.45
1947 1964 1.182385 GGGGTAGCCGAGGAGATCAG 61.182 65.000 4.56 0.00 0.00 2.90
1953 1970 1.112113 GCCGAGGAGATCAGTACCAA 58.888 55.000 0.00 0.00 0.00 3.67
1987 2004 3.623848 TGCAGATAACACGCAGGTT 57.376 47.368 0.00 0.00 34.81 3.50
2029 2046 5.107837 CGTACACACAAACTCAGATCAGAAC 60.108 44.000 0.00 0.00 0.00 3.01
2041 2058 4.594920 TCAGATCAGAACTTTCAGAAGGGT 59.405 41.667 0.00 0.00 37.19 4.34
2042 2059 4.694509 CAGATCAGAACTTTCAGAAGGGTG 59.305 45.833 0.00 0.00 37.19 4.61
2044 2061 4.503714 TCAGAACTTTCAGAAGGGTGTT 57.496 40.909 0.00 0.00 37.19 3.32
2048 2065 5.182001 CAGAACTTTCAGAAGGGTGTTATGG 59.818 44.000 0.00 0.00 37.19 2.74
2075 2092 0.253347 AGGGAATCAGCCAGAAGGGA 60.253 55.000 0.00 0.00 40.01 4.20
2083 2100 2.683465 GCCAGAAGGGATGCCTCCA 61.683 63.158 6.10 0.00 44.08 3.86
2104 2121 1.947597 TACCGCCGGTGTATGTGTCC 61.948 60.000 21.20 0.00 36.19 4.02
2106 2123 2.987125 GCCGGTGTATGTGTCCCT 59.013 61.111 1.90 0.00 0.00 4.20
2108 2125 1.980052 CCGGTGTATGTGTCCCTGT 59.020 57.895 0.00 0.00 0.00 4.00
2123 2140 5.476945 GTGTCCCTGTGGAAGATAAACAAAT 59.523 40.000 0.00 0.00 44.07 2.32
2125 2142 4.462483 TCCCTGTGGAAGATAAACAAATGC 59.538 41.667 0.00 0.00 37.86 3.56
2128 2145 5.652014 CCTGTGGAAGATAAACAAATGCCTA 59.348 40.000 0.00 0.00 0.00 3.93
2155 2173 1.077169 GGAGTTGACCAGGGGGAAATT 59.923 52.381 0.00 0.00 38.05 1.82
2159 2177 2.042569 GTTGACCAGGGGGAAATTAGGT 59.957 50.000 0.00 0.00 38.05 3.08
2163 2181 3.391626 GACCAGGGGGAAATTAGGTAGAG 59.608 52.174 0.00 0.00 38.05 2.43
2174 2192 1.956629 TAGGTAGAGGCTGCGGCAAC 61.957 60.000 21.31 12.38 40.87 4.17
2288 2330 2.279136 CGAGCTCGTGAAGGAATTTACG 59.721 50.000 27.79 0.00 37.85 3.18
2350 2392 3.591977 AGTAGGGTGGAAGGTTTAGCAAT 59.408 43.478 0.00 0.00 0.00 3.56
2458 2501 9.520515 AAGATTGATATTGTTGGTTACTCTGTT 57.479 29.630 0.00 0.00 0.00 3.16
2491 2534 0.906282 GTGAAGTAAGGGACCCGGGA 60.906 60.000 32.02 0.00 0.00 5.14
2567 2610 3.282021 CATCAAACCTGGGACACTATGG 58.718 50.000 0.00 0.00 0.00 2.74
2575 2618 7.460214 AACCTGGGACACTATGGAAAATATA 57.540 36.000 0.00 0.00 0.00 0.86
2609 2652 4.247258 CAACTTACCGTGGCTGTGTATTA 58.753 43.478 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.488705 ATTGGGCGGGTTCAGACTCA 61.489 55.000 0.00 0.00 0.00 3.41
28 30 6.821388 AGCTTCTATGATACGTTTCAAGGAT 58.179 36.000 12.74 0.00 0.00 3.24
37 39 5.620205 CGGCATTAGAGCTTCTATGATACGT 60.620 44.000 0.00 0.00 34.17 3.57
40 42 5.476945 TGACGGCATTAGAGCTTCTATGATA 59.523 40.000 0.00 0.00 34.17 2.15
45 47 3.288092 TCTGACGGCATTAGAGCTTCTA 58.712 45.455 0.00 0.00 34.17 2.10
60 62 0.679505 TTCCACTGGGAGTTCTGACG 59.320 55.000 0.00 0.00 46.01 4.35
63 65 2.867109 ATGTTCCACTGGGAGTTCTG 57.133 50.000 0.00 0.00 46.01 3.02
67 69 1.909302 CTGGTATGTTCCACTGGGAGT 59.091 52.381 0.00 0.00 46.01 3.85
103 105 0.179073 ATTCAGGCGGTCTCCAATCG 60.179 55.000 0.00 0.00 0.00 3.34
105 107 0.911769 TGATTCAGGCGGTCTCCAAT 59.088 50.000 0.00 0.00 0.00 3.16
138 140 1.806542 GACACTTGCATCCGTGTTGAT 59.193 47.619 15.28 0.00 43.80 2.57
159 169 4.036262 TCCATTTCTGTTTTCAGTCAACGG 59.964 41.667 0.00 0.00 46.98 4.44
178 188 0.618680 TGCTAGACCACCTGCTCCAT 60.619 55.000 0.00 0.00 0.00 3.41
185 195 1.903183 GGAGTTCTTGCTAGACCACCT 59.097 52.381 0.00 0.00 0.00 4.00
207 217 1.238439 CATGCAGGAACAAAGACGGT 58.762 50.000 0.00 0.00 0.00 4.83
224 234 0.680601 TGACATTGTGATGCGGCCAT 60.681 50.000 2.24 0.00 36.72 4.40
236 252 4.036027 GCAGTAAGTGGATCCATGACATTG 59.964 45.833 19.62 13.21 0.00 2.82
244 260 2.355108 GCTTCTGCAGTAAGTGGATCCA 60.355 50.000 11.44 11.44 39.41 3.41
275 291 2.032675 GCCAAAGATTTCTCCATCTCGC 59.967 50.000 0.00 0.00 31.87 5.03
286 302 3.149196 TCTCGAAGCTTGCCAAAGATTT 58.851 40.909 2.10 0.00 41.97 2.17
307 323 4.336889 TCGAAGACCACTCACAGAAAAT 57.663 40.909 0.00 0.00 0.00 1.82
313 329 2.429250 TCAACTTCGAAGACCACTCACA 59.571 45.455 31.08 2.02 34.32 3.58
315 331 2.693591 AGTCAACTTCGAAGACCACTCA 59.306 45.455 31.08 5.06 34.32 3.41
323 339 2.478134 CTCCAAGCAGTCAACTTCGAAG 59.522 50.000 23.43 23.43 0.00 3.79
332 348 1.765904 TGTACCAACTCCAAGCAGTCA 59.234 47.619 0.00 0.00 0.00 3.41
374 390 1.124462 GCACTATTACAGAGCGCGAG 58.876 55.000 12.10 0.00 30.94 5.03
391 407 5.586243 CCTTCAATTTCGAGAAGAATAGGCA 59.414 40.000 12.36 0.00 42.95 4.75
434 450 9.630098 CTCATTACATGCTGAACATTAAAACTT 57.370 29.630 0.00 0.00 36.64 2.66
441 457 6.624423 GCTTGTCTCATTACATGCTGAACATT 60.624 38.462 7.40 0.00 43.50 2.71
449 465 3.191162 TGTTGGCTTGTCTCATTACATGC 59.809 43.478 0.00 6.37 45.14 4.06
473 489 1.501169 TCGCACACACATGAGTTGAG 58.499 50.000 0.00 1.65 0.00 3.02
477 493 0.532640 TGCTTCGCACACACATGAGT 60.533 50.000 0.00 0.00 31.71 3.41
482 498 1.722636 TTGCATGCTTCGCACACACA 61.723 50.000 20.33 0.00 43.04 3.72
483 499 1.000233 CTTGCATGCTTCGCACACAC 61.000 55.000 20.33 0.00 43.04 3.82
541 557 2.571212 TGCTTGTCACAAGAAATCCGT 58.429 42.857 22.30 0.00 0.00 4.69
545 561 4.624015 CCAACATGCTTGTCACAAGAAAT 58.376 39.130 22.30 10.74 34.06 2.17
548 564 1.337703 GCCAACATGCTTGTCACAAGA 59.662 47.619 22.30 6.92 34.06 3.02
551 567 0.669619 CAGCCAACATGCTTGTCACA 59.330 50.000 5.61 0.00 40.32 3.58
625 641 1.202580 AGCTACATGGAGGTCGCAATC 60.203 52.381 3.04 0.00 32.39 2.67
626 642 0.833287 AGCTACATGGAGGTCGCAAT 59.167 50.000 3.04 0.00 32.39 3.56
627 643 0.175760 GAGCTACATGGAGGTCGCAA 59.824 55.000 20.89 0.00 34.50 4.85
628 644 0.970427 TGAGCTACATGGAGGTCGCA 60.970 55.000 27.62 12.78 45.12 5.10
629 645 0.249238 CTGAGCTACATGGAGGTCGC 60.249 60.000 27.62 10.35 45.12 5.19
630 646 1.066303 GTCTGAGCTACATGGAGGTCG 59.934 57.143 27.62 22.13 45.12 4.79
631 647 1.066303 CGTCTGAGCTACATGGAGGTC 59.934 57.143 27.09 27.09 42.99 3.85
632 648 1.107114 CGTCTGAGCTACATGGAGGT 58.893 55.000 10.05 10.05 0.00 3.85
633 649 0.249238 GCGTCTGAGCTACATGGAGG 60.249 60.000 7.16 0.00 0.00 4.30
634 650 3.264666 GCGTCTGAGCTACATGGAG 57.735 57.895 0.00 0.00 0.00 3.86
643 659 3.184683 CCGAAGCAGCGTCTGAGC 61.185 66.667 6.77 0.00 32.44 4.26
644 660 1.803519 GTCCGAAGCAGCGTCTGAG 60.804 63.158 6.77 0.00 32.44 3.35
645 661 2.258591 GTCCGAAGCAGCGTCTGA 59.741 61.111 6.77 2.52 32.44 3.27
646 662 2.811317 GGTCCGAAGCAGCGTCTG 60.811 66.667 6.77 0.00 34.12 3.51
647 663 4.070552 GGGTCCGAAGCAGCGTCT 62.071 66.667 6.77 0.00 0.00 4.18
648 664 2.221906 TAAGGGTCCGAAGCAGCGTC 62.222 60.000 0.00 0.00 0.00 5.19
649 665 1.823169 TTAAGGGTCCGAAGCAGCGT 61.823 55.000 0.00 0.00 0.00 5.07
650 666 1.079405 TTAAGGGTCCGAAGCAGCG 60.079 57.895 0.00 0.00 0.00 5.18
651 667 0.036294 AGTTAAGGGTCCGAAGCAGC 60.036 55.000 0.00 0.00 0.00 5.25
652 668 2.232941 TGTAGTTAAGGGTCCGAAGCAG 59.767 50.000 0.00 0.00 0.00 4.24
653 669 2.028748 GTGTAGTTAAGGGTCCGAAGCA 60.029 50.000 0.00 0.00 0.00 3.91
654 670 2.028748 TGTGTAGTTAAGGGTCCGAAGC 60.029 50.000 0.00 0.00 0.00 3.86
655 671 3.947910 TGTGTAGTTAAGGGTCCGAAG 57.052 47.619 0.00 0.00 0.00 3.79
656 672 3.618019 GCATGTGTAGTTAAGGGTCCGAA 60.618 47.826 0.00 0.00 0.00 4.30
657 673 2.093869 GCATGTGTAGTTAAGGGTCCGA 60.094 50.000 0.00 0.00 0.00 4.55
658 674 2.277084 GCATGTGTAGTTAAGGGTCCG 58.723 52.381 0.00 0.00 0.00 4.79
659 675 2.238898 AGGCATGTGTAGTTAAGGGTCC 59.761 50.000 0.00 0.00 0.00 4.46
660 676 3.629142 AGGCATGTGTAGTTAAGGGTC 57.371 47.619 0.00 0.00 0.00 4.46
661 677 4.079253 CAAAGGCATGTGTAGTTAAGGGT 58.921 43.478 0.00 0.00 0.00 4.34
662 678 4.079253 ACAAAGGCATGTGTAGTTAAGGG 58.921 43.478 0.00 0.00 30.82 3.95
663 679 5.046910 CACAAAGGCATGTGTAGTTAAGG 57.953 43.478 13.41 0.00 44.46 2.69
673 689 0.478072 TCCCTGACACAAAGGCATGT 59.522 50.000 0.00 0.00 32.22 3.21
674 690 0.883833 GTCCCTGACACAAAGGCATG 59.116 55.000 0.00 0.00 32.22 4.06
675 691 0.478072 TGTCCCTGACACAAAGGCAT 59.522 50.000 0.00 0.00 37.67 4.40
676 692 0.478072 ATGTCCCTGACACAAAGGCA 59.522 50.000 0.00 0.00 45.65 4.75
677 693 0.883833 CATGTCCCTGACACAAAGGC 59.116 55.000 0.00 0.00 45.65 4.35
678 694 1.881973 CACATGTCCCTGACACAAAGG 59.118 52.381 0.00 0.00 45.65 3.11
679 695 1.881973 CCACATGTCCCTGACACAAAG 59.118 52.381 0.00 0.00 45.65 2.77
680 696 1.478471 CCCACATGTCCCTGACACAAA 60.478 52.381 0.00 0.00 45.65 2.83
681 697 0.110295 CCCACATGTCCCTGACACAA 59.890 55.000 0.00 0.00 45.65 3.33
682 698 1.760527 CCCACATGTCCCTGACACA 59.239 57.895 0.00 0.00 45.65 3.72
683 699 1.675641 GCCCACATGTCCCTGACAC 60.676 63.158 0.00 0.00 45.65 3.67
684 700 2.756400 GCCCACATGTCCCTGACA 59.244 61.111 0.00 0.00 46.90 3.58
685 701 2.044946 GGCCCACATGTCCCTGAC 60.045 66.667 0.00 0.00 0.00 3.51
686 702 2.531428 TGGCCCACATGTCCCTGA 60.531 61.111 0.00 0.00 0.00 3.86
687 703 2.044650 CTGGCCCACATGTCCCTG 60.045 66.667 0.00 0.00 0.00 4.45
688 704 4.052518 GCTGGCCCACATGTCCCT 62.053 66.667 0.00 0.00 0.00 4.20
689 705 4.052518 AGCTGGCCCACATGTCCC 62.053 66.667 0.00 0.00 0.00 4.46
690 706 2.753043 CAGCTGGCCCACATGTCC 60.753 66.667 5.57 0.00 0.00 4.02
691 707 2.042831 GTCAGCTGGCCCACATGTC 61.043 63.158 15.13 0.00 0.00 3.06
692 708 2.034687 GTCAGCTGGCCCACATGT 59.965 61.111 15.13 0.00 0.00 3.21
693 709 2.044555 CAGTCAGCTGGCCCACATG 61.045 63.158 16.31 1.82 39.01 3.21
694 710 2.072874 AACAGTCAGCTGGCCCACAT 62.073 55.000 16.31 0.00 46.62 3.21
695 711 2.756042 AACAGTCAGCTGGCCCACA 61.756 57.895 16.31 0.00 46.62 4.17
696 712 2.113986 AACAGTCAGCTGGCCCAC 59.886 61.111 16.31 4.76 46.62 4.61
697 713 2.113774 CAACAGTCAGCTGGCCCA 59.886 61.111 16.31 0.00 46.62 5.36
698 714 2.674380 CCAACAGTCAGCTGGCCC 60.674 66.667 16.31 2.58 46.62 5.80
699 715 1.968540 GTCCAACAGTCAGCTGGCC 60.969 63.158 16.31 5.38 46.62 5.36
700 716 1.968540 GGTCCAACAGTCAGCTGGC 60.969 63.158 11.28 11.28 46.62 4.85
701 717 1.302832 GGGTCCAACAGTCAGCTGG 60.303 63.158 15.13 0.00 46.62 4.85
703 719 1.056700 AGTGGGTCCAACAGTCAGCT 61.057 55.000 0.00 0.00 0.00 4.24
704 720 0.179018 AAGTGGGTCCAACAGTCAGC 60.179 55.000 0.00 0.00 0.00 4.26
705 721 3.007940 TGATAAGTGGGTCCAACAGTCAG 59.992 47.826 0.00 0.00 0.00 3.51
706 722 2.976185 TGATAAGTGGGTCCAACAGTCA 59.024 45.455 0.00 0.00 0.00 3.41
707 723 3.008049 ACTGATAAGTGGGTCCAACAGTC 59.992 47.826 0.00 0.00 33.06 3.51
708 724 2.979678 ACTGATAAGTGGGTCCAACAGT 59.020 45.455 0.00 0.00 33.47 3.55
709 725 3.338249 CACTGATAAGTGGGTCCAACAG 58.662 50.000 1.71 0.00 36.24 3.16
710 726 3.417069 CACTGATAAGTGGGTCCAACA 57.583 47.619 1.71 0.00 36.24 3.33
719 735 2.094675 CCTTTGGGCCACTGATAAGTG 58.905 52.381 5.23 2.81 39.37 3.16
720 736 2.514458 CCTTTGGGCCACTGATAAGT 57.486 50.000 5.23 0.00 0.00 2.24
732 748 0.539438 TAACTGCAGGTGCCTTTGGG 60.539 55.000 16.44 0.00 41.18 4.12
733 749 1.270550 CTTAACTGCAGGTGCCTTTGG 59.729 52.381 16.44 0.00 41.18 3.28
734 750 1.270550 CCTTAACTGCAGGTGCCTTTG 59.729 52.381 16.44 0.00 41.18 2.77
735 751 1.620822 CCTTAACTGCAGGTGCCTTT 58.379 50.000 16.44 1.95 41.18 3.11
736 752 0.895559 GCCTTAACTGCAGGTGCCTT 60.896 55.000 16.44 2.77 41.18 4.35
737 753 1.303643 GCCTTAACTGCAGGTGCCT 60.304 57.895 16.44 0.00 41.18 4.75
738 754 1.603455 TGCCTTAACTGCAGGTGCC 60.603 57.895 16.44 0.00 41.18 5.01
739 755 1.581447 GTGCCTTAACTGCAGGTGC 59.419 57.895 16.44 10.39 39.87 5.01
740 756 1.577328 CCGTGCCTTAACTGCAGGTG 61.577 60.000 16.44 0.00 41.66 4.00
741 757 1.302511 CCGTGCCTTAACTGCAGGT 60.303 57.895 19.93 15.51 41.66 4.00
742 758 0.605319 TTCCGTGCCTTAACTGCAGG 60.605 55.000 19.93 0.79 42.58 4.85
743 759 0.798776 CTTCCGTGCCTTAACTGCAG 59.201 55.000 13.48 13.48 39.87 4.41
744 760 1.234615 GCTTCCGTGCCTTAACTGCA 61.235 55.000 0.00 0.00 36.12 4.41
745 761 0.955919 AGCTTCCGTGCCTTAACTGC 60.956 55.000 0.00 0.00 0.00 4.40
746 762 1.079503 GAGCTTCCGTGCCTTAACTG 58.920 55.000 0.00 0.00 0.00 3.16
747 763 0.685097 TGAGCTTCCGTGCCTTAACT 59.315 50.000 0.00 0.00 0.00 2.24
748 764 1.079503 CTGAGCTTCCGTGCCTTAAC 58.920 55.000 0.00 0.00 0.00 2.01
749 765 0.685097 ACTGAGCTTCCGTGCCTTAA 59.315 50.000 0.00 0.00 0.00 1.85
750 766 0.246635 GACTGAGCTTCCGTGCCTTA 59.753 55.000 0.00 0.00 0.00 2.69
751 767 1.004440 GACTGAGCTTCCGTGCCTT 60.004 57.895 0.00 0.00 0.00 4.35
752 768 2.659610 GACTGAGCTTCCGTGCCT 59.340 61.111 0.00 0.00 0.00 4.75
753 769 2.435059 GGACTGAGCTTCCGTGCC 60.435 66.667 0.00 0.00 0.00 5.01
754 770 1.078848 ATGGACTGAGCTTCCGTGC 60.079 57.895 0.00 0.00 35.70 5.34
755 771 2.759783 CATGGACTGAGCTTCCGTG 58.240 57.895 10.11 10.11 42.42 4.94
756 772 1.478510 CTACATGGACTGAGCTTCCGT 59.521 52.381 0.00 0.00 35.70 4.69
757 773 1.804372 GCTACATGGACTGAGCTTCCG 60.804 57.143 0.00 0.00 35.70 4.30
758 774 1.484240 AGCTACATGGACTGAGCTTCC 59.516 52.381 0.00 0.00 42.59 3.46
759 775 2.797792 CGAGCTACATGGACTGAGCTTC 60.798 54.545 0.00 0.00 45.15 3.86
760 776 1.135915 CGAGCTACATGGACTGAGCTT 59.864 52.381 0.00 0.00 45.15 3.74
762 778 0.249238 CCGAGCTACATGGACTGAGC 60.249 60.000 0.00 0.00 35.07 4.26
763 779 0.249238 GCCGAGCTACATGGACTGAG 60.249 60.000 0.00 0.00 0.00 3.35
764 780 1.676678 GGCCGAGCTACATGGACTGA 61.677 60.000 0.00 0.00 0.00 3.41
765 781 1.227380 GGCCGAGCTACATGGACTG 60.227 63.158 0.00 0.00 0.00 3.51
766 782 1.685765 TGGCCGAGCTACATGGACT 60.686 57.895 0.00 0.00 0.00 3.85
767 783 1.521681 GTGGCCGAGCTACATGGAC 60.522 63.158 0.00 0.00 39.80 4.02
768 784 1.987306 TGTGGCCGAGCTACATGGA 60.987 57.895 10.21 0.00 44.56 3.41
769 785 2.584064 TGTGGCCGAGCTACATGG 59.416 61.111 10.21 0.00 44.56 3.66
773 789 2.202623 CGAGTGTGGCCGAGCTAC 60.203 66.667 0.00 5.62 40.44 3.58
774 790 4.129737 GCGAGTGTGGCCGAGCTA 62.130 66.667 0.00 0.00 0.00 3.32
776 792 3.642778 TAAGCGAGTGTGGCCGAGC 62.643 63.158 0.00 0.00 0.00 5.03
777 793 1.517257 CTAAGCGAGTGTGGCCGAG 60.517 63.158 0.00 0.00 0.00 4.63
778 794 2.571757 CTAAGCGAGTGTGGCCGA 59.428 61.111 0.00 0.00 0.00 5.54
779 795 2.509336 CCTAAGCGAGTGTGGCCG 60.509 66.667 0.00 0.00 0.00 6.13
780 796 2.125106 CCCTAAGCGAGTGTGGCC 60.125 66.667 0.00 0.00 0.00 5.36
781 797 0.248289 TAACCCTAAGCGAGTGTGGC 59.752 55.000 0.00 0.00 0.00 5.01
782 798 2.167693 TGATAACCCTAAGCGAGTGTGG 59.832 50.000 0.00 0.00 0.00 4.17
783 799 3.448686 CTGATAACCCTAAGCGAGTGTG 58.551 50.000 0.00 0.00 0.00 3.82
784 800 2.159085 GCTGATAACCCTAAGCGAGTGT 60.159 50.000 0.00 0.00 0.00 3.55
785 801 2.474816 GCTGATAACCCTAAGCGAGTG 58.525 52.381 0.00 0.00 0.00 3.51
786 802 2.892784 GCTGATAACCCTAAGCGAGT 57.107 50.000 0.00 0.00 0.00 4.18
791 807 1.583054 GCACCGCTGATAACCCTAAG 58.417 55.000 0.00 0.00 0.00 2.18
820 836 4.356442 CCACCGGCGGCCAAAAAG 62.356 66.667 28.71 7.06 0.00 2.27
847 863 3.930229 CGTGGTTCGGTAATGATCAGAAA 59.070 43.478 0.09 0.00 35.71 2.52
867 883 0.034283 GTGACCCCCTAGAGAGTCGT 60.034 60.000 0.00 0.00 31.75 4.34
870 886 1.306970 CCGTGACCCCCTAGAGAGT 59.693 63.158 0.00 0.00 0.00 3.24
874 890 4.084147 CCCCCGTGACCCCCTAGA 62.084 72.222 0.00 0.00 0.00 2.43
910 926 2.032860 ATGGTTGGATCCTCGCCTCG 62.033 60.000 14.23 0.00 0.00 4.63
936 952 2.055579 ACCTTCGAGGAAGAACCCTTT 58.944 47.619 6.93 0.00 41.71 3.11
955 971 1.620822 ATCTCAGTTGTTTGCCCCAC 58.379 50.000 0.00 0.00 0.00 4.61
963 979 4.533707 TCCTCCAGATCAATCTCAGTTGTT 59.466 41.667 0.00 0.00 34.22 2.83
964 980 4.099633 TCCTCCAGATCAATCTCAGTTGT 58.900 43.478 0.00 0.00 34.22 3.32
975 991 4.102210 CCTTTTAGCATCTCCTCCAGATCA 59.898 45.833 0.00 0.00 40.20 2.92
1039 1055 0.673022 CTCTTCGCTTCAGCCTTGCT 60.673 55.000 0.00 0.00 40.77 3.91
1058 1074 2.830370 CTGCCCCCGCCTCAAATC 60.830 66.667 0.00 0.00 0.00 2.17
1070 1086 0.761702 AATTGCCATCCATCCTGCCC 60.762 55.000 0.00 0.00 0.00 5.36
1086 1102 3.244630 TGTCCGTGTTAACCCTAGCAATT 60.245 43.478 2.48 0.00 0.00 2.32
1141 1157 2.558359 CCAGACCCCAAATGAACTTCAC 59.442 50.000 0.00 0.00 0.00 3.18
1173 1189 1.202806 TCACCAGCTTCCCTGAACTTG 60.203 52.381 0.00 0.00 44.64 3.16
1185 1201 5.234466 AGATAAACAAGTTCTCACCAGCT 57.766 39.130 0.00 0.00 0.00 4.24
1266 1282 0.031111 TGATCACCCCTAGACCCCTG 60.031 60.000 0.00 0.00 0.00 4.45
1272 1288 3.595190 TCTTCGATGATCACCCCTAGA 57.405 47.619 0.00 0.00 0.00 2.43
1275 1291 4.840680 TCATAATCTTCGATGATCACCCCT 59.159 41.667 13.61 1.00 0.00 4.79
1287 1303 3.185188 CGGTCTTGCCATCATAATCTTCG 59.815 47.826 0.00 0.00 36.97 3.79
1356 1372 5.600898 TCGATAAATGTCAGGGACCTTATGA 59.399 40.000 0.00 0.00 0.00 2.15
1365 1381 3.722147 CTCCTGTCGATAAATGTCAGGG 58.278 50.000 14.05 3.97 43.83 4.45
1386 1402 1.399791 GCAAGTTGATCTACTGCTGGC 59.600 52.381 10.65 8.69 0.00 4.85
1391 1407 5.236655 TCTACGAGCAAGTTGATCTACTG 57.763 43.478 18.30 5.95 29.10 2.74
1410 1426 5.273208 ACCTCTCTGACTTTGCCTATTCTA 58.727 41.667 0.00 0.00 0.00 2.10
1416 1432 2.038295 CTGAACCTCTCTGACTTTGCCT 59.962 50.000 0.00 0.00 0.00 4.75
1501 1517 4.422840 GGAGTAAAGCGAGTAAGAGGTTC 58.577 47.826 0.00 0.00 0.00 3.62
1590 1606 3.527253 TCCCATGTACCCACAAATCTGAT 59.473 43.478 0.00 0.00 38.42 2.90
1629 1645 3.718956 CTCCTTCCATACTCCCTTTCCAT 59.281 47.826 0.00 0.00 0.00 3.41
1688 1704 2.417239 GCGAATATTCCACCGTTTGACA 59.583 45.455 9.87 0.00 0.00 3.58
1692 1708 1.400494 GCTGCGAATATTCCACCGTTT 59.600 47.619 9.87 0.00 0.00 3.60
1728 1744 1.694048 CCCTTCCTCCTCTAGCACCAT 60.694 57.143 0.00 0.00 0.00 3.55
1768 1784 3.781307 TCGGAACCATGGCCTCGG 61.781 66.667 13.04 13.11 0.00 4.63
1788 1804 2.949644 CCAAAACCTCGTCCTTGAGTTT 59.050 45.455 0.00 0.00 34.04 2.66
1790 1806 1.202770 CCCAAAACCTCGTCCTTGAGT 60.203 52.381 0.00 0.00 34.04 3.41
1798 1814 1.752498 GTTGTTTCCCCAAAACCTCGT 59.248 47.619 0.00 0.00 45.58 4.18
1804 1820 0.032416 TCCCCGTTGTTTCCCCAAAA 60.032 50.000 0.00 0.00 0.00 2.44
1812 1828 2.232696 GCAACCATATTCCCCGTTGTTT 59.767 45.455 0.00 0.00 38.26 2.83
1819 1835 0.106918 TGTCCGCAACCATATTCCCC 60.107 55.000 0.00 0.00 0.00 4.81
1830 1846 1.021202 CTTTGTGTTCCTGTCCGCAA 58.979 50.000 0.00 0.00 0.00 4.85
1858 1874 2.050144 TCTGACTCTTGTCCTTTGCCT 58.950 47.619 0.00 0.00 42.28 4.75
1902 1918 1.942657 GCTTATCATCCTGCGCTTTCA 59.057 47.619 9.73 0.00 0.00 2.69
1918 1935 1.607612 GGCTACCCCTTGCTGCTTA 59.392 57.895 0.00 0.00 0.00 3.09
1947 1964 6.981559 TGCAGAAAACCTTTTGTTATTGGTAC 59.018 34.615 0.00 0.00 35.67 3.34
1953 1970 8.637986 TGTTATCTGCAGAAAACCTTTTGTTAT 58.362 29.630 22.50 0.81 35.67 1.89
1987 2004 1.657751 CGACAGTCGCTCCCAGATCA 61.658 60.000 10.66 0.00 31.14 2.92
2029 2046 4.455877 GTGACCATAACACCCTTCTGAAAG 59.544 45.833 0.00 0.00 32.84 2.62
2041 2058 1.634960 TCCCTGTCGTGACCATAACA 58.365 50.000 0.00 0.00 0.00 2.41
2042 2059 2.754946 TTCCCTGTCGTGACCATAAC 57.245 50.000 0.00 0.00 0.00 1.89
2044 2061 2.430694 CTGATTCCCTGTCGTGACCATA 59.569 50.000 0.00 0.00 0.00 2.74
2048 2065 0.741221 GGCTGATTCCCTGTCGTGAC 60.741 60.000 0.00 0.00 0.00 3.67
2075 2092 3.849951 CGGCGGTAGTGGAGGCAT 61.850 66.667 0.00 0.00 0.00 4.40
2083 2100 1.252904 ACACATACACCGGCGGTAGT 61.253 55.000 33.65 30.10 32.11 2.73
2104 2121 4.463891 AGGCATTTGTTTATCTTCCACAGG 59.536 41.667 0.00 0.00 0.00 4.00
2106 2123 7.450014 TCTTTAGGCATTTGTTTATCTTCCACA 59.550 33.333 0.00 0.00 0.00 4.17
2108 2125 8.415950 TTCTTTAGGCATTTGTTTATCTTCCA 57.584 30.769 0.00 0.00 0.00 3.53
2123 2140 2.039879 GGTCAACTCCCTTCTTTAGGCA 59.960 50.000 0.00 0.00 43.27 4.75
2125 2142 3.307762 CCTGGTCAACTCCCTTCTTTAGG 60.308 52.174 0.00 0.00 44.33 2.69
2128 2145 1.425448 CCCTGGTCAACTCCCTTCTTT 59.575 52.381 0.00 0.00 0.00 2.52
2139 2156 2.364190 ACCTAATTTCCCCCTGGTCAA 58.636 47.619 0.00 0.00 0.00 3.18
2155 2173 1.684391 TTGCCGCAGCCTCTACCTA 60.684 57.895 0.00 0.00 38.69 3.08
2159 2177 4.451150 CCGTTGCCGCAGCCTCTA 62.451 66.667 1.19 0.00 38.69 2.43
2187 2205 1.961277 GGAGCCCGCCGATAATGTG 60.961 63.158 0.00 0.00 0.00 3.21
2188 2206 2.426023 GGAGCCCGCCGATAATGT 59.574 61.111 0.00 0.00 0.00 2.71
2288 2330 2.914059 ACGATACAAAGTATGGTGGGC 58.086 47.619 4.38 0.00 0.00 5.36
2458 2501 6.828273 CCCTTACTTCACAATCCACATGATAA 59.172 38.462 0.00 0.00 31.83 1.75
2500 2543 1.434188 ACACCACTGTCATCCTCCAA 58.566 50.000 0.00 0.00 0.00 3.53
2575 2618 5.220970 CCACGGTAAGTTGTTCAAACTTGAT 60.221 40.000 12.52 0.00 40.38 2.57


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

AutoCloner maintained by Alex Coulton.