Multiple sequence alignment - TraesCS1B01G201600

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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 TraesCS1B01G201600 chr1B 100.000 3128 0 0 1 3128 361017379 361014252 0.000000e+00 5777.0
1 TraesCS1B01G201600 chr1B 93.176 425 29 0 217 641 640427821 640428245 2.650000e-175 625.0
2 TraesCS1B01G201600 chr1B 97.500 160 3 1 2918 3076 181320516 181320357 3.980000e-69 272.0
3 TraesCS1B01G201600 chr1B 94.268 157 8 1 2919 3075 587500033 587500188 4.030000e-59 239.0
4 TraesCS1B01G201600 chr1B 90.164 122 12 0 520 641 191950936 191950815 3.230000e-35 159.0
5 TraesCS1B01G201600 chr1A 95.433 2146 93 3 776 2918 323192950 323190807 0.000000e+00 3415.0
6 TraesCS1B01G201600 chr1A 100.000 52 0 0 3077 3128 323190813 323190762 2.570000e-16 97.1
7 TraesCS1B01G201600 chr1D 94.468 2097 85 14 830 2918 252477389 252479462 0.000000e+00 3201.0
8 TraesCS1B01G201600 chr1D 100.000 52 0 0 3077 3128 252479456 252479507 2.570000e-16 97.1
9 TraesCS1B01G201600 chr5D 94.514 638 35 0 4 641 198961080 198960443 0.000000e+00 985.0
10 TraesCS1B01G201600 chr3B 93.916 641 39 0 1 641 720753851 720754491 0.000000e+00 968.0
11 TraesCS1B01G201600 chrUn 91.888 641 48 3 1 641 8753189 8753825 0.000000e+00 893.0
12 TraesCS1B01G201600 chr4D 80.938 640 118 4 4 641 6133916 6133279 1.290000e-138 503.0
13 TraesCS1B01G201600 chr4A 96.835 158 5 0 2919 3076 728427190 728427033 6.650000e-67 265.0
14 TraesCS1B01G201600 chr7B 94.410 161 7 2 2915 3075 23903204 23903362 2.410000e-61 246.0
15 TraesCS1B01G201600 chr7B 72.222 306 75 10 273 573 48270833 48271133 5.560000e-13 86.1
16 TraesCS1B01G201600 chr6B 95.139 144 5 2 2936 3077 71865323 71865180 3.140000e-55 226.0
17 TraesCS1B01G201600 chr7D 92.366 131 8 2 2947 3075 126467510 126467640 5.330000e-43 185.0
18 TraesCS1B01G201600 chr4B 71.287 303 83 3 273 573 660152530 660152830 1.200000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G201600 chr1B 361014252 361017379 3127 True 5777.00 5777 100.0000 1 3128 1 chr1B.!!$R3 3127
1 TraesCS1B01G201600 chr1A 323190762 323192950 2188 True 1756.05 3415 97.7165 776 3128 2 chr1A.!!$R1 2352
2 TraesCS1B01G201600 chr1D 252477389 252479507 2118 False 1649.05 3201 97.2340 830 3128 2 chr1D.!!$F1 2298
3 TraesCS1B01G201600 chr5D 198960443 198961080 637 True 985.00 985 94.5140 4 641 1 chr5D.!!$R1 637
4 TraesCS1B01G201600 chr3B 720753851 720754491 640 False 968.00 968 93.9160 1 641 1 chr3B.!!$F1 640
5 TraesCS1B01G201600 chrUn 8753189 8753825 636 False 893.00 893 91.8880 1 641 1 chrUn.!!$F1 640
6 TraesCS1B01G201600 chr4D 6133279 6133916 637 True 503.00 503 80.9380 4 641 1 chr4D.!!$R1 637

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
666 669 0.039888 GATAGAACTCGCCGGAGAGC 60.04 60.0 32.09 18.38 43.27 4.09 F
693 696 0.039978 CAGATCGGCAGCCTACTACG 60.04 60.0 10.54 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 1915 0.323360 TATGCCGCTTTCCCTTTGCT 60.323 50.000 0.00 0.0 0.00 3.91 R
2349 2359 1.388133 TGCCTAGCTCAGGGAGACA 59.612 57.895 10.17 0.0 45.66 3.41 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
140 141 1.955080 AGTCTCTTTCGGAGTTGTCGT 59.045 47.619 0.00 0.00 42.40 4.34
156 159 3.011513 CGTACTGTACGTGCCAGAC 57.988 57.895 27.27 13.34 46.41 3.51
157 160 0.239082 CGTACTGTACGTGCCAGACA 59.761 55.000 27.27 6.06 46.41 3.41
173 176 3.055385 CCAGACACCCGAATTCCTTAGAA 60.055 47.826 0.00 0.00 36.15 2.10
253 256 2.125147 CGAGCGCTGAATTCCCCA 60.125 61.111 18.48 0.00 0.00 4.96
268 271 4.396357 TTCCCCACCAAGTGTCATTAAT 57.604 40.909 0.00 0.00 0.00 1.40
556 559 2.545537 TGCATGGAGATCTCATCAGC 57.454 50.000 23.85 19.78 0.00 4.26
641 644 7.748847 ACGCGAATAAAGTTTCATTGTAATCT 58.251 30.769 15.93 0.00 0.00 2.40
642 645 7.903431 ACGCGAATAAAGTTTCATTGTAATCTC 59.097 33.333 15.93 0.00 0.00 2.75
643 646 7.902917 CGCGAATAAAGTTTCATTGTAATCTCA 59.097 33.333 0.00 0.00 0.00 3.27
644 647 9.554724 GCGAATAAAGTTTCATTGTAATCTCAA 57.445 29.630 0.00 0.00 0.00 3.02
656 659 9.809096 TCATTGTAATCTCAACAGATAGAACTC 57.191 33.333 0.00 0.00 38.55 3.01
657 660 8.750416 CATTGTAATCTCAACAGATAGAACTCG 58.250 37.037 0.00 0.00 38.55 4.18
658 661 6.266323 TGTAATCTCAACAGATAGAACTCGC 58.734 40.000 0.00 0.00 38.55 5.03
659 662 3.784701 TCTCAACAGATAGAACTCGCC 57.215 47.619 0.00 0.00 0.00 5.54
660 663 2.097629 TCTCAACAGATAGAACTCGCCG 59.902 50.000 0.00 0.00 0.00 6.46
661 664 1.134367 TCAACAGATAGAACTCGCCGG 59.866 52.381 0.00 0.00 0.00 6.13
662 665 1.134367 CAACAGATAGAACTCGCCGGA 59.866 52.381 5.05 0.00 0.00 5.14
663 666 1.025812 ACAGATAGAACTCGCCGGAG 58.974 55.000 5.05 0.00 46.13 4.63
664 667 1.309950 CAGATAGAACTCGCCGGAGA 58.690 55.000 5.05 6.70 43.27 3.71
665 668 1.265635 CAGATAGAACTCGCCGGAGAG 59.734 57.143 30.81 30.81 43.27 3.20
666 669 0.039888 GATAGAACTCGCCGGAGAGC 60.040 60.000 32.09 18.38 43.27 4.09
667 670 0.752009 ATAGAACTCGCCGGAGAGCA 60.752 55.000 32.09 16.73 43.27 4.26
668 671 1.654954 TAGAACTCGCCGGAGAGCAC 61.655 60.000 32.09 24.79 43.27 4.40
669 672 4.421479 AACTCGCCGGAGAGCACG 62.421 66.667 32.09 12.78 43.27 5.34
673 676 4.498520 CGCCGGAGAGCACGTGAT 62.499 66.667 22.23 14.87 0.00 3.06
674 677 2.583593 GCCGGAGAGCACGTGATC 60.584 66.667 25.68 25.68 0.00 2.92
675 678 2.885113 CCGGAGAGCACGTGATCA 59.115 61.111 32.88 0.00 31.88 2.92
676 679 1.226802 CCGGAGAGCACGTGATCAG 60.227 63.158 32.88 22.70 31.88 2.90
677 680 1.657751 CCGGAGAGCACGTGATCAGA 61.658 60.000 32.88 0.00 31.88 3.27
678 681 0.383590 CGGAGAGCACGTGATCAGAT 59.616 55.000 32.88 14.98 31.88 2.90
679 682 1.599171 CGGAGAGCACGTGATCAGATC 60.599 57.143 32.88 21.92 31.88 2.75
680 683 1.599171 GGAGAGCACGTGATCAGATCG 60.599 57.143 32.88 0.00 31.88 3.69
681 684 0.383590 AGAGCACGTGATCAGATCGG 59.616 55.000 32.88 3.13 31.88 4.18
682 685 1.211818 GAGCACGTGATCAGATCGGC 61.212 60.000 27.75 3.88 0.00 5.54
683 686 1.519234 GCACGTGATCAGATCGGCA 60.519 57.895 22.23 0.00 0.00 5.69
684 687 1.485838 GCACGTGATCAGATCGGCAG 61.486 60.000 22.23 0.15 0.00 4.85
685 688 1.227089 ACGTGATCAGATCGGCAGC 60.227 57.895 5.91 0.00 0.00 5.25
686 689 1.953138 CGTGATCAGATCGGCAGCC 60.953 63.158 0.00 0.00 0.00 4.85
687 690 1.445095 GTGATCAGATCGGCAGCCT 59.555 57.895 10.54 0.00 0.00 4.58
688 691 0.676184 GTGATCAGATCGGCAGCCTA 59.324 55.000 10.54 0.00 0.00 3.93
689 692 0.676184 TGATCAGATCGGCAGCCTAC 59.324 55.000 10.54 0.32 0.00 3.18
690 693 0.965439 GATCAGATCGGCAGCCTACT 59.035 55.000 10.54 2.90 0.00 2.57
691 694 2.163509 GATCAGATCGGCAGCCTACTA 58.836 52.381 10.54 0.00 0.00 1.82
692 695 1.319541 TCAGATCGGCAGCCTACTAC 58.680 55.000 10.54 0.00 0.00 2.73
693 696 0.039978 CAGATCGGCAGCCTACTACG 60.040 60.000 10.54 0.00 0.00 3.51
694 697 0.179026 AGATCGGCAGCCTACTACGA 60.179 55.000 10.54 0.09 38.38 3.43
695 698 0.882474 GATCGGCAGCCTACTACGAT 59.118 55.000 10.54 5.74 43.61 3.73
696 699 1.269998 GATCGGCAGCCTACTACGATT 59.730 52.381 10.54 0.00 42.05 3.34
697 700 1.108776 TCGGCAGCCTACTACGATTT 58.891 50.000 10.54 0.00 31.84 2.17
698 701 1.066605 TCGGCAGCCTACTACGATTTC 59.933 52.381 10.54 0.00 31.84 2.17
699 702 1.067212 CGGCAGCCTACTACGATTTCT 59.933 52.381 10.54 0.00 0.00 2.52
700 703 2.745102 GGCAGCCTACTACGATTTCTC 58.255 52.381 3.29 0.00 0.00 2.87
701 704 2.362717 GGCAGCCTACTACGATTTCTCT 59.637 50.000 3.29 0.00 0.00 3.10
702 705 3.568853 GGCAGCCTACTACGATTTCTCTA 59.431 47.826 3.29 0.00 0.00 2.43
703 706 4.218852 GGCAGCCTACTACGATTTCTCTAT 59.781 45.833 3.29 0.00 0.00 1.98
704 707 5.279056 GGCAGCCTACTACGATTTCTCTATT 60.279 44.000 3.29 0.00 0.00 1.73
705 708 6.217294 GCAGCCTACTACGATTTCTCTATTT 58.783 40.000 0.00 0.00 0.00 1.40
706 709 6.702282 GCAGCCTACTACGATTTCTCTATTTT 59.298 38.462 0.00 0.00 0.00 1.82
707 710 7.095982 GCAGCCTACTACGATTTCTCTATTTTC 60.096 40.741 0.00 0.00 0.00 2.29
708 711 8.138712 CAGCCTACTACGATTTCTCTATTTTCT 58.861 37.037 0.00 0.00 0.00 2.52
709 712 8.354426 AGCCTACTACGATTTCTCTATTTTCTC 58.646 37.037 0.00 0.00 0.00 2.87
710 713 7.595875 GCCTACTACGATTTCTCTATTTTCTCC 59.404 40.741 0.00 0.00 0.00 3.71
711 714 8.852135 CCTACTACGATTTCTCTATTTTCTCCT 58.148 37.037 0.00 0.00 0.00 3.69
712 715 9.887406 CTACTACGATTTCTCTATTTTCTCCTC 57.113 37.037 0.00 0.00 0.00 3.71
713 716 8.528044 ACTACGATTTCTCTATTTTCTCCTCT 57.472 34.615 0.00 0.00 0.00 3.69
714 717 8.626526 ACTACGATTTCTCTATTTTCTCCTCTC 58.373 37.037 0.00 0.00 0.00 3.20
715 718 7.411486 ACGATTTCTCTATTTTCTCCTCTCA 57.589 36.000 0.00 0.00 0.00 3.27
716 719 7.262048 ACGATTTCTCTATTTTCTCCTCTCAC 58.738 38.462 0.00 0.00 0.00 3.51
717 720 7.123547 ACGATTTCTCTATTTTCTCCTCTCACT 59.876 37.037 0.00 0.00 0.00 3.41
718 721 7.978975 CGATTTCTCTATTTTCTCCTCTCACTT 59.021 37.037 0.00 0.00 0.00 3.16
719 722 9.097257 GATTTCTCTATTTTCTCCTCTCACTTG 57.903 37.037 0.00 0.00 0.00 3.16
720 723 7.782897 TTCTCTATTTTCTCCTCTCACTTGA 57.217 36.000 0.00 0.00 0.00 3.02
721 724 7.403312 TCTCTATTTTCTCCTCTCACTTGAG 57.597 40.000 0.00 0.00 43.36 3.02
731 734 2.723273 TCTCACTTGAGATGCTACGGA 58.277 47.619 4.76 0.00 45.48 4.69
732 735 3.291584 TCTCACTTGAGATGCTACGGAT 58.708 45.455 4.76 0.00 45.48 4.18
733 736 3.701542 TCTCACTTGAGATGCTACGGATT 59.298 43.478 4.76 0.00 45.48 3.01
734 737 4.160439 TCTCACTTGAGATGCTACGGATTT 59.840 41.667 4.76 0.00 45.48 2.17
735 738 4.832248 TCACTTGAGATGCTACGGATTTT 58.168 39.130 0.00 0.00 0.00 1.82
736 739 5.245531 TCACTTGAGATGCTACGGATTTTT 58.754 37.500 0.00 0.00 0.00 1.94
760 763 4.963276 TTTTGAAATCCTGCTACGGATG 57.037 40.909 3.98 0.00 42.89 3.51
761 764 2.620251 TGAAATCCTGCTACGGATGG 57.380 50.000 3.98 0.00 42.89 3.51
762 765 1.837439 TGAAATCCTGCTACGGATGGT 59.163 47.619 3.98 0.00 42.89 3.55
763 766 2.158957 TGAAATCCTGCTACGGATGGTC 60.159 50.000 3.98 5.76 42.89 4.02
764 767 1.794714 AATCCTGCTACGGATGGTCT 58.205 50.000 3.98 0.00 42.89 3.85
765 768 1.333177 ATCCTGCTACGGATGGTCTC 58.667 55.000 2.59 0.00 42.13 3.36
766 769 0.755698 TCCTGCTACGGATGGTCTCC 60.756 60.000 0.00 0.00 41.07 3.71
767 770 0.757188 CCTGCTACGGATGGTCTCCT 60.757 60.000 0.00 0.00 42.47 3.69
768 771 1.478837 CCTGCTACGGATGGTCTCCTA 60.479 57.143 0.00 0.00 42.47 2.94
769 772 2.520069 CTGCTACGGATGGTCTCCTAT 58.480 52.381 0.00 0.00 42.47 2.57
770 773 2.230025 CTGCTACGGATGGTCTCCTATG 59.770 54.545 0.00 0.00 42.47 2.23
771 774 2.158519 TGCTACGGATGGTCTCCTATGA 60.159 50.000 0.00 0.00 42.47 2.15
772 775 2.490115 GCTACGGATGGTCTCCTATGAG 59.510 54.545 0.00 0.00 42.47 2.90
773 776 2.757894 ACGGATGGTCTCCTATGAGT 57.242 50.000 0.00 0.00 42.47 3.41
774 777 3.878237 ACGGATGGTCTCCTATGAGTA 57.122 47.619 0.00 0.00 42.47 2.59
804 807 4.291540 TGTATTGCGCAGATGGAAAATC 57.708 40.909 11.31 0.00 0.00 2.17
806 809 2.925578 TTGCGCAGATGGAAAATCTG 57.074 45.000 11.31 10.34 46.12 2.90
853 857 4.571580 GCACATTCATCTCCAGAAAGAGAG 59.428 45.833 0.00 0.00 45.77 3.20
854 858 5.626347 GCACATTCATCTCCAGAAAGAGAGA 60.626 44.000 0.00 0.00 45.77 3.10
871 875 1.954146 GATCTCGGCGCCGCATTTA 60.954 57.895 42.78 25.11 39.59 1.40
888 895 4.318475 GCATTTAGTTTTCGTTGGGTTTGC 60.318 41.667 0.00 0.00 0.00 3.68
1098 1105 2.417719 GACCACACATTCGAGAAGCTT 58.582 47.619 0.00 0.00 0.00 3.74
1515 1522 4.570663 CCCGCCGAGCCTAGAACG 62.571 72.222 0.00 0.00 0.00 3.95
1532 1539 2.434134 CGCACGTTCTACACCTCGC 61.434 63.158 0.00 0.00 0.00 5.03
1551 1558 4.524318 GCGGATCCGGCGAAGGAA 62.524 66.667 33.98 0.00 44.50 3.36
1583 1590 1.144057 CGGTGGATAAGAAGCGGCT 59.856 57.895 0.00 0.00 33.85 5.52
1692 1699 1.270625 CCATATGTTGGGCCGTACGAT 60.271 52.381 18.76 2.47 42.33 3.73
1713 1720 3.516586 TGTAGTGGATCAGAAGGTTGGA 58.483 45.455 0.00 0.00 0.00 3.53
1714 1721 3.907474 TGTAGTGGATCAGAAGGTTGGAA 59.093 43.478 0.00 0.00 0.00 3.53
1746 1753 1.880675 GTATCGAAGATGGCGAGGAGA 59.119 52.381 0.00 0.00 45.12 3.71
1839 1846 2.062519 GAGAAGTTCAGTCAGTTCCGC 58.937 52.381 5.50 0.00 0.00 5.54
1875 1882 0.319555 ACGTGAATGTCAGGGACGTG 60.320 55.000 0.00 0.00 41.44 4.49
1908 1915 6.150332 TCATCCTGGGATATTTTACCTCTCA 58.850 40.000 1.42 0.00 32.93 3.27
2112 2119 4.371855 AGAGAGCGATGACGATTTACAA 57.628 40.909 0.00 0.00 42.66 2.41
2135 2142 2.729194 ACTGGAGCTCTAGTAGTGTGG 58.271 52.381 29.23 4.08 35.84 4.17
2147 2154 5.880887 TCTAGTAGTGTGGTGTATCTGTGAG 59.119 44.000 0.00 0.00 0.00 3.51
2262 2271 4.438744 GGCAAATATGTTAGTGGTGCAGAC 60.439 45.833 0.00 0.00 32.18 3.51
2278 2288 3.244665 TGCAGACCCATATGATGATGACC 60.245 47.826 3.65 0.00 0.00 4.02
2349 2359 8.709308 AGCCAGTATACTCAAAACTCAGATTAT 58.291 33.333 1.26 0.00 0.00 1.28
2437 2447 7.254932 GGCAATGTATCTTTATCCTGACTGAAC 60.255 40.741 0.00 0.00 0.00 3.18
2452 2462 6.024552 TGACTGAACAAGTTTTGAAAGCTT 57.975 33.333 0.96 0.96 40.07 3.74
2501 2511 2.985809 CAAGACTCAAGACTGAAGCTCG 59.014 50.000 0.00 0.00 0.00 5.03
2620 2630 1.680338 AAGGACCTCAGTTGTGCAAC 58.320 50.000 6.94 6.94 41.45 4.17
2667 2677 9.891828 CTACAGTTAATTTTCAGTTTATGCACA 57.108 29.630 0.00 0.00 0.00 4.57
2755 2765 4.470334 TGATGCTTATTTGGGCTTTTCC 57.530 40.909 0.00 0.00 0.00 3.13
2756 2766 4.095946 TGATGCTTATTTGGGCTTTTCCT 58.904 39.130 0.00 0.00 34.39 3.36
2807 2817 4.398319 TCCTGAAATTTGGAAGTCCTGAC 58.602 43.478 0.00 0.00 36.82 3.51
2847 2857 7.775561 ACCTGTAAATATTTGAGATGGAACCTC 59.224 37.037 11.05 0.00 0.00 3.85
2918 2928 4.281182 AGTTGGACGTCTTCTGTATTCTGT 59.719 41.667 16.46 0.00 0.00 3.41
2919 2929 5.475909 AGTTGGACGTCTTCTGTATTCTGTA 59.524 40.000 16.46 0.00 0.00 2.74
2920 2930 5.562506 TGGACGTCTTCTGTATTCTGTAG 57.437 43.478 16.46 0.00 0.00 2.74
2921 2931 4.398358 TGGACGTCTTCTGTATTCTGTAGG 59.602 45.833 16.46 0.00 0.00 3.18
2922 2932 4.202030 GGACGTCTTCTGTATTCTGTAGGG 60.202 50.000 16.46 0.00 0.00 3.53
2923 2933 3.700038 ACGTCTTCTGTATTCTGTAGGGG 59.300 47.826 0.00 0.00 0.00 4.79
2924 2934 3.700038 CGTCTTCTGTATTCTGTAGGGGT 59.300 47.826 0.00 0.00 0.00 4.95
2925 2935 4.440250 CGTCTTCTGTATTCTGTAGGGGTG 60.440 50.000 0.00 0.00 0.00 4.61
2926 2936 3.451178 TCTTCTGTATTCTGTAGGGGTGC 59.549 47.826 0.00 0.00 0.00 5.01
2927 2937 2.827755 TCTGTATTCTGTAGGGGTGCA 58.172 47.619 0.00 0.00 0.00 4.57
2928 2938 2.766263 TCTGTATTCTGTAGGGGTGCAG 59.234 50.000 0.00 0.00 0.00 4.41
2929 2939 1.837439 TGTATTCTGTAGGGGTGCAGG 59.163 52.381 0.00 0.00 33.81 4.85
2930 2940 2.116238 GTATTCTGTAGGGGTGCAGGA 58.884 52.381 0.00 0.00 33.81 3.86
2931 2941 1.898863 ATTCTGTAGGGGTGCAGGAT 58.101 50.000 0.00 0.00 33.81 3.24
2932 2942 0.911769 TTCTGTAGGGGTGCAGGATG 59.088 55.000 0.00 0.00 40.87 3.51
2933 2943 0.982852 TCTGTAGGGGTGCAGGATGG 60.983 60.000 0.00 0.00 35.86 3.51
2934 2944 2.193248 GTAGGGGTGCAGGATGGC 59.807 66.667 0.00 0.00 35.86 4.40
2935 2945 3.479203 TAGGGGTGCAGGATGGCG 61.479 66.667 0.00 0.00 35.86 5.69
2951 2961 4.174129 CGTCCCGCAAAATCCCGC 62.174 66.667 0.00 0.00 0.00 6.13
2952 2962 3.059386 GTCCCGCAAAATCCCGCA 61.059 61.111 0.00 0.00 0.00 5.69
2953 2963 2.282532 TCCCGCAAAATCCCGCAA 60.283 55.556 0.00 0.00 0.00 4.85
2954 2964 1.903890 TCCCGCAAAATCCCGCAAA 60.904 52.632 0.00 0.00 0.00 3.68
2955 2965 1.005630 CCCGCAAAATCCCGCAAAA 60.006 52.632 0.00 0.00 0.00 2.44
2956 2966 0.601311 CCCGCAAAATCCCGCAAAAA 60.601 50.000 0.00 0.00 0.00 1.94
2957 2967 0.510790 CCGCAAAATCCCGCAAAAAC 59.489 50.000 0.00 0.00 0.00 2.43
2958 2968 1.212616 CGCAAAATCCCGCAAAAACA 58.787 45.000 0.00 0.00 0.00 2.83
2959 2969 1.192090 CGCAAAATCCCGCAAAAACAG 59.808 47.619 0.00 0.00 0.00 3.16
2960 2970 1.069973 GCAAAATCCCGCAAAAACAGC 60.070 47.619 0.00 0.00 0.00 4.40
2961 2971 1.530720 CAAAATCCCGCAAAAACAGCC 59.469 47.619 0.00 0.00 0.00 4.85
2962 2972 0.755686 AAATCCCGCAAAAACAGCCA 59.244 45.000 0.00 0.00 0.00 4.75
2963 2973 0.318120 AATCCCGCAAAAACAGCCAG 59.682 50.000 0.00 0.00 0.00 4.85
2964 2974 2.158561 ATCCCGCAAAAACAGCCAGC 62.159 55.000 0.00 0.00 0.00 4.85
2965 2975 2.730094 CCGCAAAAACAGCCAGCT 59.270 55.556 0.00 0.00 0.00 4.24
2966 2976 1.523154 CCCGCAAAAACAGCCAGCTA 61.523 55.000 0.00 0.00 0.00 3.32
2967 2977 0.109597 CCGCAAAAACAGCCAGCTAG 60.110 55.000 0.00 0.00 0.00 3.42
2968 2978 0.730494 CGCAAAAACAGCCAGCTAGC 60.730 55.000 6.62 6.62 0.00 3.42
2969 2979 0.314935 GCAAAAACAGCCAGCTAGCA 59.685 50.000 18.83 0.00 34.23 3.49
2970 2980 1.932156 GCAAAAACAGCCAGCTAGCAC 60.932 52.381 18.83 5.87 34.23 4.40
2971 2981 1.337703 CAAAAACAGCCAGCTAGCACA 59.662 47.619 18.83 0.00 34.23 4.57
2972 2982 0.954452 AAAACAGCCAGCTAGCACAC 59.046 50.000 18.83 5.07 34.23 3.82
2973 2983 0.179020 AAACAGCCAGCTAGCACACA 60.179 50.000 18.83 0.00 34.23 3.72
2974 2984 0.604780 AACAGCCAGCTAGCACACAG 60.605 55.000 18.83 6.23 34.23 3.66
2975 2985 2.046507 AGCCAGCTAGCACACAGC 60.047 61.111 18.83 11.55 46.19 4.40
2989 2999 5.551760 GCACACAGCTAGTACAAATTGAT 57.448 39.130 0.00 0.00 41.15 2.57
2990 3000 5.327091 GCACACAGCTAGTACAAATTGATG 58.673 41.667 0.00 0.00 41.15 3.07
2991 3001 5.106555 GCACACAGCTAGTACAAATTGATGT 60.107 40.000 0.00 0.00 41.15 3.06
2992 3002 6.309436 CACACAGCTAGTACAAATTGATGTG 58.691 40.000 15.11 15.11 40.90 3.21
2993 3003 6.147656 CACACAGCTAGTACAAATTGATGTGA 59.852 38.462 20.10 0.00 38.99 3.58
2994 3004 6.147821 ACACAGCTAGTACAAATTGATGTGAC 59.852 38.462 20.10 0.56 38.99 3.67
2995 3005 5.348724 ACAGCTAGTACAAATTGATGTGACG 59.651 40.000 0.00 0.00 34.75 4.35
2996 3006 5.348724 CAGCTAGTACAAATTGATGTGACGT 59.651 40.000 0.00 0.00 34.75 4.34
2997 3007 6.530181 CAGCTAGTACAAATTGATGTGACGTA 59.470 38.462 0.00 0.00 34.75 3.57
2998 3008 6.752351 AGCTAGTACAAATTGATGTGACGTAG 59.248 38.462 0.00 0.00 34.75 3.51
2999 3009 6.530534 GCTAGTACAAATTGATGTGACGTAGT 59.469 38.462 0.00 0.00 38.01 2.73
3000 3010 7.063074 GCTAGTACAAATTGATGTGACGTAGTT 59.937 37.037 0.00 0.00 36.13 2.24
3001 3011 7.724305 AGTACAAATTGATGTGACGTAGTTT 57.276 32.000 0.00 0.00 36.13 2.66
3002 3012 8.821147 AGTACAAATTGATGTGACGTAGTTTA 57.179 30.769 0.00 0.00 36.13 2.01
3003 3013 9.263538 AGTACAAATTGATGTGACGTAGTTTAA 57.736 29.630 0.00 0.00 36.13 1.52
3046 3056 0.382158 GCTTTGAATAGGAAGCGGGC 59.618 55.000 0.00 0.00 38.89 6.13
3047 3057 1.025041 CTTTGAATAGGAAGCGGGCC 58.975 55.000 0.00 0.00 0.00 5.80
3048 3058 0.746563 TTTGAATAGGAAGCGGGCCG 60.747 55.000 24.35 24.35 0.00 6.13
3049 3059 2.280865 GAATAGGAAGCGGGCCGG 60.281 66.667 29.48 9.71 0.00 6.13
3050 3060 2.766651 AATAGGAAGCGGGCCGGA 60.767 61.111 29.48 0.00 0.00 5.14
3051 3061 2.113243 GAATAGGAAGCGGGCCGGAT 62.113 60.000 29.48 4.39 0.00 4.18
3052 3062 1.705997 AATAGGAAGCGGGCCGGATT 61.706 55.000 29.48 14.23 0.00 3.01
3053 3063 2.113243 ATAGGAAGCGGGCCGGATTC 62.113 60.000 27.76 27.76 0.00 2.52
3077 3087 2.762459 CGCCCTGCACCCCTACTA 60.762 66.667 0.00 0.00 0.00 1.82
3078 3088 2.140792 CGCCCTGCACCCCTACTAT 61.141 63.158 0.00 0.00 0.00 2.12
3079 3089 1.696097 CGCCCTGCACCCCTACTATT 61.696 60.000 0.00 0.00 0.00 1.73
3080 3090 0.108774 GCCCTGCACCCCTACTATTC 59.891 60.000 0.00 0.00 0.00 1.75
3081 3091 1.807814 CCCTGCACCCCTACTATTCT 58.192 55.000 0.00 0.00 0.00 2.40
3082 3092 1.417890 CCCTGCACCCCTACTATTCTG 59.582 57.143 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
156 159 2.640184 GGGTTCTAAGGAATTCGGGTG 58.360 52.381 0.00 0.00 33.71 4.61
157 160 1.562942 GGGGTTCTAAGGAATTCGGGT 59.437 52.381 0.00 0.00 33.71 5.28
173 176 2.162906 AACACTGGAGCCATGGGGT 61.163 57.895 15.13 0.00 36.17 4.95
213 216 1.250840 GGGCTCCAAGGAATTGCGTT 61.251 55.000 0.00 0.00 0.00 4.84
253 256 3.440173 CCGCTTGATTAATGACACTTGGT 59.560 43.478 0.00 0.00 0.00 3.67
268 271 0.240145 CACTGACTACGACCGCTTGA 59.760 55.000 0.00 0.00 0.00 3.02
382 385 1.202818 ACTTGCCTTTGGTGGAGTCTC 60.203 52.381 0.00 0.00 0.00 3.36
393 396 3.515602 AAGGATCAGACACTTGCCTTT 57.484 42.857 0.00 0.00 32.11 3.11
556 559 0.528684 GAGAGCATTTCGGGAGGTCG 60.529 60.000 0.00 0.00 35.12 4.79
641 644 1.134367 CCGGCGAGTTCTATCTGTTGA 59.866 52.381 9.30 0.00 0.00 3.18
642 645 1.134367 TCCGGCGAGTTCTATCTGTTG 59.866 52.381 9.30 0.00 0.00 3.33
643 646 1.405821 CTCCGGCGAGTTCTATCTGTT 59.594 52.381 9.30 0.00 0.00 3.16
644 647 1.025812 CTCCGGCGAGTTCTATCTGT 58.974 55.000 9.30 0.00 0.00 3.41
645 648 1.265635 CTCTCCGGCGAGTTCTATCTG 59.734 57.143 13.50 0.00 37.40 2.90
646 649 1.600023 CTCTCCGGCGAGTTCTATCT 58.400 55.000 13.50 0.00 37.40 1.98
647 650 0.039888 GCTCTCCGGCGAGTTCTATC 60.040 60.000 21.96 1.16 37.40 2.08
648 651 0.752009 TGCTCTCCGGCGAGTTCTAT 60.752 55.000 21.96 0.00 37.40 1.98
649 652 1.378119 TGCTCTCCGGCGAGTTCTA 60.378 57.895 21.96 4.76 37.40 2.10
650 653 2.676822 TGCTCTCCGGCGAGTTCT 60.677 61.111 21.96 0.00 37.40 3.01
651 654 2.507324 GTGCTCTCCGGCGAGTTC 60.507 66.667 21.96 11.83 37.40 3.01
652 655 4.421479 CGTGCTCTCCGGCGAGTT 62.421 66.667 21.96 0.00 37.40 3.01
656 659 4.498520 ATCACGTGCTCTCCGGCG 62.499 66.667 11.67 0.00 34.52 6.46
657 660 2.583593 GATCACGTGCTCTCCGGC 60.584 66.667 11.67 0.00 0.00 6.13
658 661 1.226802 CTGATCACGTGCTCTCCGG 60.227 63.158 19.20 0.00 0.00 5.14
659 662 0.383590 ATCTGATCACGTGCTCTCCG 59.616 55.000 19.20 8.75 0.00 4.63
660 663 1.599171 CGATCTGATCACGTGCTCTCC 60.599 57.143 19.20 6.04 0.00 3.71
661 664 1.599171 CCGATCTGATCACGTGCTCTC 60.599 57.143 19.20 12.13 0.00 3.20
662 665 0.383590 CCGATCTGATCACGTGCTCT 59.616 55.000 19.20 3.01 0.00 4.09
663 666 1.211818 GCCGATCTGATCACGTGCTC 61.212 60.000 11.67 12.07 0.00 4.26
664 667 1.227089 GCCGATCTGATCACGTGCT 60.227 57.895 11.67 0.00 0.00 4.40
665 668 1.485838 CTGCCGATCTGATCACGTGC 61.486 60.000 11.67 13.08 0.00 5.34
666 669 1.485838 GCTGCCGATCTGATCACGTG 61.486 60.000 17.19 9.94 0.00 4.49
667 670 1.227089 GCTGCCGATCTGATCACGT 60.227 57.895 17.19 0.00 0.00 4.49
668 671 1.953138 GGCTGCCGATCTGATCACG 60.953 63.158 17.19 7.74 0.00 4.35
669 672 0.676184 TAGGCTGCCGATCTGATCAC 59.324 55.000 13.96 9.17 0.00 3.06
670 673 0.676184 GTAGGCTGCCGATCTGATCA 59.324 55.000 13.96 0.00 0.00 2.92
671 674 0.965439 AGTAGGCTGCCGATCTGATC 59.035 55.000 13.96 7.60 0.00 2.92
672 675 1.889829 GTAGTAGGCTGCCGATCTGAT 59.110 52.381 13.96 0.00 0.00 2.90
673 676 1.319541 GTAGTAGGCTGCCGATCTGA 58.680 55.000 13.96 0.00 0.00 3.27
674 677 0.039978 CGTAGTAGGCTGCCGATCTG 60.040 60.000 13.96 0.00 0.00 2.90
675 678 0.179026 TCGTAGTAGGCTGCCGATCT 60.179 55.000 13.96 14.58 0.00 2.75
676 679 0.882474 ATCGTAGTAGGCTGCCGATC 59.118 55.000 13.96 7.81 36.24 3.69
677 680 1.329256 AATCGTAGTAGGCTGCCGAT 58.671 50.000 13.96 10.04 39.84 4.18
678 681 1.066605 GAAATCGTAGTAGGCTGCCGA 59.933 52.381 13.96 4.89 35.18 5.54
679 682 1.067212 AGAAATCGTAGTAGGCTGCCG 59.933 52.381 13.96 0.00 0.00 5.69
680 683 2.362717 AGAGAAATCGTAGTAGGCTGCC 59.637 50.000 11.65 11.65 0.00 4.85
681 684 3.719173 AGAGAAATCGTAGTAGGCTGC 57.281 47.619 0.00 0.00 0.00 5.25
682 685 8.138712 AGAAAATAGAGAAATCGTAGTAGGCTG 58.861 37.037 0.00 0.00 0.00 4.85
683 686 8.240267 AGAAAATAGAGAAATCGTAGTAGGCT 57.760 34.615 0.00 0.00 0.00 4.58
684 687 7.595875 GGAGAAAATAGAGAAATCGTAGTAGGC 59.404 40.741 0.00 0.00 0.00 3.93
685 688 8.852135 AGGAGAAAATAGAGAAATCGTAGTAGG 58.148 37.037 0.00 0.00 0.00 3.18
686 689 9.887406 GAGGAGAAAATAGAGAAATCGTAGTAG 57.113 37.037 0.00 0.00 0.00 2.57
687 690 9.629878 AGAGGAGAAAATAGAGAAATCGTAGTA 57.370 33.333 0.00 0.00 0.00 1.82
688 691 8.528044 AGAGGAGAAAATAGAGAAATCGTAGT 57.472 34.615 0.00 0.00 0.00 2.73
689 692 8.625651 TGAGAGGAGAAAATAGAGAAATCGTAG 58.374 37.037 0.00 0.00 0.00 3.51
690 693 8.407064 GTGAGAGGAGAAAATAGAGAAATCGTA 58.593 37.037 0.00 0.00 0.00 3.43
691 694 7.123547 AGTGAGAGGAGAAAATAGAGAAATCGT 59.876 37.037 0.00 0.00 0.00 3.73
692 695 7.488322 AGTGAGAGGAGAAAATAGAGAAATCG 58.512 38.462 0.00 0.00 0.00 3.34
693 696 9.097257 CAAGTGAGAGGAGAAAATAGAGAAATC 57.903 37.037 0.00 0.00 0.00 2.17
694 697 8.820831 TCAAGTGAGAGGAGAAAATAGAGAAAT 58.179 33.333 0.00 0.00 0.00 2.17
695 698 8.195165 TCAAGTGAGAGGAGAAAATAGAGAAA 57.805 34.615 0.00 0.00 0.00 2.52
696 699 7.671819 TCTCAAGTGAGAGGAGAAAATAGAGAA 59.328 37.037 6.92 0.00 45.48 2.87
697 700 7.178573 TCTCAAGTGAGAGGAGAAAATAGAGA 58.821 38.462 6.92 0.00 45.48 3.10
698 701 7.403312 TCTCAAGTGAGAGGAGAAAATAGAG 57.597 40.000 6.92 0.00 45.48 2.43
712 715 3.724508 ATCCGTAGCATCTCAAGTGAG 57.275 47.619 1.65 1.65 43.36 3.51
713 716 4.471904 AAATCCGTAGCATCTCAAGTGA 57.528 40.909 0.00 0.00 0.00 3.41
714 717 5.551760 AAAAATCCGTAGCATCTCAAGTG 57.448 39.130 0.00 0.00 0.00 3.16
738 741 4.157656 CCATCCGTAGCAGGATTTCAAAAA 59.842 41.667 5.76 0.00 45.23 1.94
739 742 3.694072 CCATCCGTAGCAGGATTTCAAAA 59.306 43.478 5.76 0.00 45.23 2.44
740 743 3.278574 CCATCCGTAGCAGGATTTCAAA 58.721 45.455 5.76 0.00 45.23 2.69
741 744 2.238646 ACCATCCGTAGCAGGATTTCAA 59.761 45.455 5.76 0.00 45.23 2.69
742 745 1.837439 ACCATCCGTAGCAGGATTTCA 59.163 47.619 5.76 0.00 45.23 2.69
743 746 2.103263 AGACCATCCGTAGCAGGATTTC 59.897 50.000 5.76 6.08 45.23 2.17
744 747 2.103263 GAGACCATCCGTAGCAGGATTT 59.897 50.000 5.76 0.00 45.23 2.17
745 748 1.689273 GAGACCATCCGTAGCAGGATT 59.311 52.381 5.76 0.00 45.23 3.01
746 749 1.333177 GAGACCATCCGTAGCAGGAT 58.667 55.000 2.98 2.98 45.23 3.24
747 750 0.755698 GGAGACCATCCGTAGCAGGA 60.756 60.000 0.00 0.00 45.54 3.86
748 751 1.742768 GGAGACCATCCGTAGCAGG 59.257 63.158 0.00 0.00 38.67 4.85
757 760 5.221521 TGCAACATACTCATAGGAGACCATC 60.222 44.000 12.12 0.00 44.26 3.51
758 761 4.655649 TGCAACATACTCATAGGAGACCAT 59.344 41.667 12.12 0.00 44.26 3.55
759 762 4.030216 TGCAACATACTCATAGGAGACCA 58.970 43.478 12.12 0.00 44.26 4.02
760 763 4.672587 TGCAACATACTCATAGGAGACC 57.327 45.455 12.12 0.00 44.26 3.85
761 764 6.051717 ACATTGCAACATACTCATAGGAGAC 58.948 40.000 12.12 0.00 44.26 3.36
762 765 6.239217 ACATTGCAACATACTCATAGGAGA 57.761 37.500 12.12 0.00 44.26 3.71
763 766 8.501580 CAATACATTGCAACATACTCATAGGAG 58.498 37.037 0.00 2.12 46.96 3.69
764 767 8.382030 CAATACATTGCAACATACTCATAGGA 57.618 34.615 0.00 0.00 0.00 2.94
799 802 6.497954 TCAAACCATTCCTGGAATCAGATTTT 59.502 34.615 18.87 10.56 46.37 1.82
804 807 5.927281 ATTCAAACCATTCCTGGAATCAG 57.073 39.130 18.87 15.12 46.37 2.90
806 809 6.128200 GCAAAATTCAAACCATTCCTGGAATC 60.128 38.462 18.87 0.00 46.37 2.52
871 875 0.101579 CGGCAAACCCAACGAAAACT 59.898 50.000 0.00 0.00 0.00 2.66
888 895 2.032071 AACCAAGGGCTTCGTCGG 59.968 61.111 0.00 0.00 0.00 4.79
1221 1228 3.068691 CGGAGGAAGTGGAGCGGA 61.069 66.667 0.00 0.00 0.00 5.54
1515 1522 2.092882 GGCGAGGTGTAGAACGTGC 61.093 63.158 0.00 0.00 0.00 5.34
1551 1558 2.600769 ACCGCCGGAGTGAACTCT 60.601 61.111 11.71 0.00 42.48 3.24
1583 1590 1.337823 GCTGGAAAGCGTACTTCTCCA 60.338 52.381 0.00 0.00 34.05 3.86
1692 1699 3.516586 TCCAACCTTCTGATCCACTACA 58.483 45.455 0.00 0.00 0.00 2.74
1713 1720 3.690139 TCTTCGATACTCTCTTGCTCGTT 59.310 43.478 0.00 0.00 0.00 3.85
1714 1721 3.271729 TCTTCGATACTCTCTTGCTCGT 58.728 45.455 0.00 0.00 0.00 4.18
1746 1753 2.238395 GACTGCCCTCTTCTCCATCTTT 59.762 50.000 0.00 0.00 0.00 2.52
1839 1846 0.796312 CGTCGATCCCAAACCACTTG 59.204 55.000 0.00 0.00 34.52 3.16
1875 1882 3.872459 ATCCCAGGATGATCCAAGAAC 57.128 47.619 14.90 0.00 39.61 3.01
1908 1915 0.323360 TATGCCGCTTTCCCTTTGCT 60.323 50.000 0.00 0.00 0.00 3.91
1947 1954 2.710377 ACAAGCTTGCCACGATCATAA 58.290 42.857 26.27 0.00 0.00 1.90
2112 2119 4.013728 CACACTACTAGAGCTCCAGTTCT 58.986 47.826 20.05 3.06 39.05 3.01
2135 2142 1.649664 CTGCAGCCTCACAGATACAC 58.350 55.000 0.00 0.00 35.90 2.90
2147 2154 1.968540 GTTGTCCTGTCCTGCAGCC 60.969 63.158 8.66 0.90 43.71 4.85
2262 2271 4.579647 TCCATGGTCATCATCATATGGG 57.420 45.455 12.58 0.00 36.57 4.00
2278 2288 3.635373 CCATCCCTGAAGAAACATCCATG 59.365 47.826 0.00 0.00 0.00 3.66
2349 2359 1.388133 TGCCTAGCTCAGGGAGACA 59.612 57.895 10.17 0.00 45.66 3.41
2413 2423 8.722480 TGTTCAGTCAGGATAAAGATACATTG 57.278 34.615 0.00 0.00 0.00 2.82
2437 2447 7.275341 TGACACAACATAAGCTTTCAAAACTTG 59.725 33.333 3.20 0.14 0.00 3.16
2501 2511 2.514803 ACCAATCAACCAAGTGCTACC 58.485 47.619 0.00 0.00 0.00 3.18
2538 2548 4.142469 ACCAAGGAACTGAAACAAAACTCG 60.142 41.667 0.00 0.00 40.86 4.18
2600 2610 2.024414 GTTGCACAACTGAGGTCCTTT 58.976 47.619 6.27 0.00 38.25 3.11
2620 2630 2.198827 TGTTGGTCTGGGTTAGCATG 57.801 50.000 0.00 0.00 0.00 4.06
2630 2640 8.402472 TGAAAATTAACTGTAGTTGTTGGTCTG 58.598 33.333 7.50 0.00 38.90 3.51
2663 2673 5.124457 TCCTGCAGAAAGAATAATCTTGTGC 59.876 40.000 17.39 16.24 45.19 4.57
2797 2807 5.105310 TGCCTATCAACTTAGTCAGGACTTC 60.105 44.000 7.33 0.00 42.54 3.01
2807 2817 9.561069 AATATTTACAGGTGCCTATCAACTTAG 57.439 33.333 0.00 0.00 40.58 2.18
2847 2857 7.372714 AGCACATACACCATATAATGCAAATG 58.627 34.615 0.00 0.00 34.27 2.32
2918 2928 3.479203 CGCCATCCTGCACCCCTA 61.479 66.667 0.00 0.00 0.00 3.53
2935 2945 2.148558 TTTGCGGGATTTTGCGGGAC 62.149 55.000 0.00 0.00 0.00 4.46
2936 2946 1.464376 TTTTGCGGGATTTTGCGGGA 61.464 50.000 0.00 0.00 0.00 5.14
2937 2947 0.601311 TTTTTGCGGGATTTTGCGGG 60.601 50.000 0.00 0.00 0.00 6.13
2938 2948 0.510790 GTTTTTGCGGGATTTTGCGG 59.489 50.000 0.00 0.00 0.00 5.69
2939 2949 1.192090 CTGTTTTTGCGGGATTTTGCG 59.808 47.619 0.00 0.00 0.00 4.85
2940 2950 1.069973 GCTGTTTTTGCGGGATTTTGC 60.070 47.619 0.00 0.00 0.00 3.68
2941 2951 1.530720 GGCTGTTTTTGCGGGATTTTG 59.469 47.619 0.00 0.00 0.00 2.44
2942 2952 1.139853 TGGCTGTTTTTGCGGGATTTT 59.860 42.857 0.00 0.00 0.00 1.82
2943 2953 0.755686 TGGCTGTTTTTGCGGGATTT 59.244 45.000 0.00 0.00 0.00 2.17
2944 2954 0.318120 CTGGCTGTTTTTGCGGGATT 59.682 50.000 0.00 0.00 0.00 3.01
2945 2955 1.966762 CTGGCTGTTTTTGCGGGAT 59.033 52.632 0.00 0.00 0.00 3.85
2946 2956 2.855514 GCTGGCTGTTTTTGCGGGA 61.856 57.895 0.00 0.00 0.00 5.14
2947 2957 1.523154 TAGCTGGCTGTTTTTGCGGG 61.523 55.000 5.25 0.00 0.00 6.13
2948 2958 0.109597 CTAGCTGGCTGTTTTTGCGG 60.110 55.000 5.25 0.00 0.00 5.69
2949 2959 0.730494 GCTAGCTGGCTGTTTTTGCG 60.730 55.000 15.78 0.00 0.00 4.85
2950 2960 0.314935 TGCTAGCTGGCTGTTTTTGC 59.685 50.000 23.43 0.00 0.00 3.68
2951 2961 1.337703 TGTGCTAGCTGGCTGTTTTTG 59.662 47.619 23.43 0.00 0.00 2.44
2952 2962 1.338020 GTGTGCTAGCTGGCTGTTTTT 59.662 47.619 23.43 0.00 0.00 1.94
2953 2963 0.954452 GTGTGCTAGCTGGCTGTTTT 59.046 50.000 23.43 0.00 0.00 2.43
2954 2964 0.179020 TGTGTGCTAGCTGGCTGTTT 60.179 50.000 23.43 0.00 0.00 2.83
2955 2965 0.604780 CTGTGTGCTAGCTGGCTGTT 60.605 55.000 23.43 0.00 0.00 3.16
2956 2966 1.004080 CTGTGTGCTAGCTGGCTGT 60.004 57.895 23.43 0.00 0.00 4.40
2957 2967 2.396955 GCTGTGTGCTAGCTGGCTG 61.397 63.158 23.43 10.22 38.14 4.85
2958 2968 2.046507 GCTGTGTGCTAGCTGGCT 60.047 61.111 23.43 0.00 38.14 4.75
2967 2977 5.106555 ACATCAATTTGTACTAGCTGTGTGC 60.107 40.000 0.00 0.00 43.29 4.57
2968 2978 6.147656 TCACATCAATTTGTACTAGCTGTGTG 59.852 38.462 0.00 0.00 34.56 3.82
2969 2979 6.147821 GTCACATCAATTTGTACTAGCTGTGT 59.852 38.462 0.00 0.00 34.56 3.72
2970 2980 6.537566 GTCACATCAATTTGTACTAGCTGTG 58.462 40.000 0.00 0.00 34.31 3.66
2971 2981 5.348724 CGTCACATCAATTTGTACTAGCTGT 59.651 40.000 0.00 0.00 0.00 4.40
2972 2982 5.348724 ACGTCACATCAATTTGTACTAGCTG 59.651 40.000 0.00 0.00 0.00 4.24
2973 2983 5.479306 ACGTCACATCAATTTGTACTAGCT 58.521 37.500 0.00 0.00 0.00 3.32
2974 2984 5.779806 ACGTCACATCAATTTGTACTAGC 57.220 39.130 0.00 0.00 0.00 3.42
2975 2985 8.462143 AACTACGTCACATCAATTTGTACTAG 57.538 34.615 0.00 0.00 0.00 2.57
2976 2986 8.821147 AAACTACGTCACATCAATTTGTACTA 57.179 30.769 0.00 0.00 0.00 1.82
2977 2987 7.724305 AAACTACGTCACATCAATTTGTACT 57.276 32.000 0.00 0.00 0.00 2.73
2980 2990 9.959749 AAATTAAACTACGTCACATCAATTTGT 57.040 25.926 0.00 0.00 0.00 2.83
3021 3031 5.105917 CCCGCTTCCTATTCAAAGCTAAAAA 60.106 40.000 5.65 0.00 44.49 1.94
3022 3032 4.398044 CCCGCTTCCTATTCAAAGCTAAAA 59.602 41.667 5.65 0.00 44.49 1.52
3023 3033 3.945285 CCCGCTTCCTATTCAAAGCTAAA 59.055 43.478 5.65 0.00 44.49 1.85
3024 3034 3.541632 CCCGCTTCCTATTCAAAGCTAA 58.458 45.455 5.65 0.00 44.49 3.09
3025 3035 2.745152 GCCCGCTTCCTATTCAAAGCTA 60.745 50.000 5.65 0.00 44.49 3.32
3026 3036 2.019156 GCCCGCTTCCTATTCAAAGCT 61.019 52.381 5.65 0.00 44.49 3.74
3027 3037 0.382158 GCCCGCTTCCTATTCAAAGC 59.618 55.000 0.00 0.00 43.49 3.51
3028 3038 1.025041 GGCCCGCTTCCTATTCAAAG 58.975 55.000 0.00 0.00 0.00 2.77
3029 3039 0.746563 CGGCCCGCTTCCTATTCAAA 60.747 55.000 0.00 0.00 0.00 2.69
3030 3040 1.153249 CGGCCCGCTTCCTATTCAA 60.153 57.895 0.00 0.00 0.00 2.69
3031 3041 2.504032 CGGCCCGCTTCCTATTCA 59.496 61.111 0.00 0.00 0.00 2.57
3032 3042 2.113243 ATCCGGCCCGCTTCCTATTC 62.113 60.000 0.00 0.00 0.00 1.75
3033 3043 1.705997 AATCCGGCCCGCTTCCTATT 61.706 55.000 0.00 0.00 0.00 1.73
3034 3044 2.113243 GAATCCGGCCCGCTTCCTAT 62.113 60.000 0.00 0.00 0.00 2.57
3035 3045 2.766651 AATCCGGCCCGCTTCCTA 60.767 61.111 0.00 0.00 0.00 2.94
3036 3046 4.176752 GAATCCGGCCCGCTTCCT 62.177 66.667 0.00 0.00 0.00 3.36
3060 3070 1.696097 AATAGTAGGGGTGCAGGGCG 61.696 60.000 0.00 0.00 0.00 6.13
3061 3071 0.108774 GAATAGTAGGGGTGCAGGGC 59.891 60.000 0.00 0.00 0.00 5.19
3062 3072 1.417890 CAGAATAGTAGGGGTGCAGGG 59.582 57.143 0.00 0.00 0.00 4.45
3063 3073 1.417890 CCAGAATAGTAGGGGTGCAGG 59.582 57.143 0.00 0.00 0.00 4.85
3064 3074 1.202698 GCCAGAATAGTAGGGGTGCAG 60.203 57.143 0.00 0.00 0.00 4.41
3065 3075 0.837272 GCCAGAATAGTAGGGGTGCA 59.163 55.000 0.00 0.00 0.00 4.57
3066 3076 1.132500 AGCCAGAATAGTAGGGGTGC 58.868 55.000 0.00 0.00 0.00 5.01
3067 3077 4.020128 GGATAAGCCAGAATAGTAGGGGTG 60.020 50.000 0.00 0.00 36.34 4.61
3068 3078 4.168883 GGATAAGCCAGAATAGTAGGGGT 58.831 47.826 0.00 0.00 36.34 4.95
3069 3079 4.168101 TGGATAAGCCAGAATAGTAGGGG 58.832 47.826 0.00 0.00 43.33 4.79
3082 3092 2.949447 ACAATGGTCCATGGATAAGCC 58.051 47.619 19.62 14.89 37.10 4.35


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

AutoCloner maintained by Alex Coulton.