Multiple sequence alignment - TraesCS3D01G171500

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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 TraesCS3D01G171500 chr3D 100.000 4317 0 0 1 4317 152487438 152483122 0.000000e+00 7973.0
1 TraesCS3D01G171500 chr3D 90.541 74 5 2 3754 3825 567708623 567708550 3.550000e-16 97.1
2 TraesCS3D01G171500 chr3D 90.411 73 6 1 713 784 48797170 48797098 1.280000e-15 95.3
3 TraesCS3D01G171500 chr3D 91.304 69 5 1 3750 3817 84404729 84404661 4.600000e-15 93.5
4 TraesCS3D01G171500 chr3D 90.141 71 3 2 713 783 511330388 511330322 5.950000e-14 89.8
5 TraesCS3D01G171500 chr3B 92.908 2397 124 29 928 3306 222815951 222813583 0.000000e+00 3443.0
6 TraesCS3D01G171500 chr3B 90.870 690 33 12 1 682 222816707 222816040 0.000000e+00 898.0
7 TraesCS3D01G171500 chr3B 92.218 514 27 3 3817 4317 222805200 222804687 0.000000e+00 715.0
8 TraesCS3D01G171500 chr3B 82.090 201 21 6 3524 3719 222805445 222805255 1.610000e-34 158.0
9 TraesCS3D01G171500 chr3B 96.809 94 2 1 823 916 222816027 222815935 5.780000e-34 156.0
10 TraesCS3D01G171500 chr3A 93.500 1600 69 13 794 2376 178251604 178253185 0.000000e+00 2346.0
11 TraesCS3D01G171500 chr3A 94.617 1319 61 7 2418 3733 178253184 178254495 0.000000e+00 2034.0
12 TraesCS3D01G171500 chr3A 93.851 683 32 7 1 682 178250723 178251396 0.000000e+00 1020.0
13 TraesCS3D01G171500 chr3A 87.713 529 22 5 3814 4317 178254527 178255037 1.040000e-160 577.0
14 TraesCS3D01G171500 chr6A 97.183 71 2 0 713 783 501479360 501479290 2.110000e-23 121.0
15 TraesCS3D01G171500 chr6B 95.775 71 3 0 713 783 541936724 541936654 9.810000e-22 115.0
16 TraesCS3D01G171500 chr6B 87.500 88 8 3 3732 3819 594860801 594860717 9.880000e-17 99.0
17 TraesCS3D01G171500 chr2B 95.588 68 3 0 717 784 68243514 68243447 4.560000e-20 110.0
18 TraesCS3D01G171500 chr2B 87.342 79 5 3 710 784 792996766 792996843 7.690000e-13 86.1
19 TraesCS3D01G171500 chr2D 90.000 80 3 2 3742 3816 580704219 580704140 9.880000e-17 99.0
20 TraesCS3D01G171500 chr2D 91.549 71 4 1 3754 3822 233379750 233379680 3.550000e-16 97.1
21 TraesCS3D01G171500 chr7A 98.182 55 1 0 3761 3815 127675715 127675661 3.550000e-16 97.1
22 TraesCS3D01G171500 chr1B 88.608 79 9 0 709 787 93109391 93109313 3.550000e-16 97.1
23 TraesCS3D01G171500 chr1B 90.411 73 3 2 3747 3815 116260563 116260635 4.600000e-15 93.5
24 TraesCS3D01G171500 chr6D 93.750 64 3 1 3749 3812 446215207 446215269 1.280000e-15 95.3
25 TraesCS3D01G171500 chr5D 90.278 72 7 0 713 784 238553875 238553946 1.280000e-15 95.3
26 TraesCS3D01G171500 chr5A 89.189 74 5 3 3754 3825 41166054 41165982 5.950000e-14 89.8
27 TraesCS3D01G171500 chr2A 85.556 90 8 3 699 785 65400780 65400867 5.950000e-14 89.8


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 TraesCS3D01G171500 chr3D 152483122 152487438 4316 True 7973.00 7973 100.00000 1 4317 1 chr3D.!!$R3 4316
1 TraesCS3D01G171500 chr3B 222813583 222816707 3124 True 1499.00 3443 93.52900 1 3306 3 chr3B.!!$R2 3305
2 TraesCS3D01G171500 chr3B 222804687 222805445 758 True 436.50 715 87.15400 3524 4317 2 chr3B.!!$R1 793
3 TraesCS3D01G171500 chr3A 178250723 178255037 4314 False 1494.25 2346 92.42025 1 4317 4 chr3A.!!$F1 4316

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
928 1038 0.039618 AGCCCGGTCCAAAATGTGAT 59.960 50.000 0.0 0.0 0.00 3.06 F
1248 1386 0.034863 GATTGGTCTTTGCGGGGGTA 60.035 55.000 0.0 0.0 0.00 3.69 F
2231 2376 1.674962 GGCCATCTTGAGTGCTTCATC 59.325 52.381 0.0 0.0 35.27 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1868 2013 0.663153 ACCTGCAGAAAGTGAAACGC 59.337 50.000 17.39 0.00 45.86 4.84 R
2566 2740 1.070758 AGGTTCAATGCGACAGTGACT 59.929 47.619 8.99 3.11 38.18 3.41 R
3431 3614 0.041833 TTGGAGGGACAGGAGGAGAG 59.958 60.000 0.00 0.00 0.00 3.20 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
33 34 3.804325 AGCGGACATCGATAAAGATTGTG 59.196 43.478 0.00 0.00 42.43 3.33
84 85 2.427506 GCGGGAAGTTTGACAGAAGAT 58.572 47.619 0.00 0.00 0.00 2.40
89 90 5.501156 GGGAAGTTTGACAGAAGATATGGT 58.499 41.667 0.00 0.00 0.00 3.55
318 319 2.401766 GCAGGATGTTGCCGTGGAG 61.402 63.158 0.00 0.00 39.31 3.86
337 341 3.492829 GGAGGCAGAAAATACTACTCGGG 60.493 52.174 0.00 0.00 0.00 5.14
352 356 4.487714 ACTCGGGCTTCATAAATCAGAA 57.512 40.909 0.00 0.00 0.00 3.02
353 357 4.446371 ACTCGGGCTTCATAAATCAGAAG 58.554 43.478 0.00 0.00 43.12 2.85
354 358 4.162320 ACTCGGGCTTCATAAATCAGAAGA 59.838 41.667 6.37 0.00 42.95 2.87
357 361 4.272018 CGGGCTTCATAAATCAGAAGAGTG 59.728 45.833 6.37 0.00 42.95 3.51
380 384 4.498682 GGATGCAAGATCAGCAATTGGTAC 60.499 45.833 10.31 5.31 46.27 3.34
382 386 3.825585 TGCAAGATCAGCAATTGGTACAA 59.174 39.130 10.31 0.00 41.24 2.41
384 388 5.221402 TGCAAGATCAGCAATTGGTACAAAA 60.221 36.000 10.31 0.00 41.24 2.44
385 389 6.684865 TGCAAGATCAGCAATTGGTACAAAAA 60.685 34.615 10.31 0.00 41.24 1.94
403 409 5.807011 ACAAAAATTCTCTGTGCTTGTTGTC 59.193 36.000 0.00 0.00 0.00 3.18
426 432 7.556275 TGTCCATATGGGTGAAGAATAAAGAAC 59.444 37.037 21.78 6.98 38.11 3.01
498 505 2.358015 ACTCGTAGCTAGGTGAGTGAC 58.642 52.381 19.25 0.00 40.03 3.67
549 557 9.994432 CAAATCAGGTGTAAAGATGTAAGATTC 57.006 33.333 0.00 0.00 0.00 2.52
568 576 6.650120 AGATTCCCAAACAATCTGTACGTAT 58.350 36.000 0.00 0.00 38.84 3.06
569 577 7.788026 AGATTCCCAAACAATCTGTACGTATA 58.212 34.615 0.00 0.00 38.84 1.47
632 641 3.859411 TTCCACGTAAATTTCATGGCC 57.141 42.857 0.00 0.00 0.00 5.36
660 669 9.685276 TGAGATAAATTTGGTGATGATACTGTT 57.315 29.630 0.00 0.00 0.00 3.16
687 696 9.868277 ATCTTTTACATGTTGTCAAAAGTCAAA 57.132 25.926 22.10 10.34 35.28 2.69
699 708 9.921637 TTGTCAAAAGTCAAACACTATTTTTCT 57.078 25.926 0.00 0.00 32.30 2.52
705 714 9.628500 AAAGTCAAACACTATTTTTCTACTCCT 57.372 29.630 0.00 0.00 32.30 3.69
707 716 9.930693 AGTCAAACACTATTTTTCTACTCCTAG 57.069 33.333 0.00 0.00 31.37 3.02
708 717 9.924650 GTCAAACACTATTTTTCTACTCCTAGA 57.075 33.333 0.00 0.00 0.00 2.43
719 728 8.912614 TTTTCTACTCCTAGAAAATACTCCCT 57.087 34.615 10.31 0.00 46.91 4.20
720 729 8.536340 TTTCTACTCCTAGAAAATACTCCCTC 57.464 38.462 0.00 0.00 43.24 4.30
721 730 6.612741 TCTACTCCTAGAAAATACTCCCTCC 58.387 44.000 0.00 0.00 0.00 4.30
722 731 4.216708 ACTCCTAGAAAATACTCCCTCCG 58.783 47.826 0.00 0.00 0.00 4.63
725 734 3.321396 CCTAGAAAATACTCCCTCCGTCC 59.679 52.174 0.00 0.00 0.00 4.79
726 735 2.117051 AGAAAATACTCCCTCCGTCCC 58.883 52.381 0.00 0.00 0.00 4.46
727 736 0.828677 AAAATACTCCCTCCGTCCCG 59.171 55.000 0.00 0.00 0.00 5.14
728 737 0.325016 AAATACTCCCTCCGTCCCGT 60.325 55.000 0.00 0.00 0.00 5.28
729 738 0.552848 AATACTCCCTCCGTCCCGTA 59.447 55.000 0.00 0.00 0.00 4.02
732 741 0.552848 ACTCCCTCCGTCCCGTAATA 59.447 55.000 0.00 0.00 0.00 0.98
733 742 1.146566 ACTCCCTCCGTCCCGTAATAT 59.853 52.381 0.00 0.00 0.00 1.28
734 743 2.376518 ACTCCCTCCGTCCCGTAATATA 59.623 50.000 0.00 0.00 0.00 0.86
735 744 3.181429 ACTCCCTCCGTCCCGTAATATAA 60.181 47.826 0.00 0.00 0.00 0.98
736 745 3.424703 TCCCTCCGTCCCGTAATATAAG 58.575 50.000 0.00 0.00 0.00 1.73
737 746 3.074390 TCCCTCCGTCCCGTAATATAAGA 59.926 47.826 0.00 0.00 0.00 2.10
738 747 3.442977 CCCTCCGTCCCGTAATATAAGAG 59.557 52.174 0.00 0.00 0.00 2.85
740 749 2.485426 TCCGTCCCGTAATATAAGAGCG 59.515 50.000 0.00 0.00 0.00 5.03
742 751 3.304928 CCGTCCCGTAATATAAGAGCGTT 60.305 47.826 0.00 0.00 0.00 4.84
743 752 4.293415 CGTCCCGTAATATAAGAGCGTTT 58.707 43.478 0.00 0.00 0.00 3.60
744 753 4.741676 CGTCCCGTAATATAAGAGCGTTTT 59.258 41.667 0.00 0.00 0.00 2.43
746 755 6.416514 GTCCCGTAATATAAGAGCGTTTTTG 58.583 40.000 0.00 0.00 0.00 2.44
747 756 6.256321 GTCCCGTAATATAAGAGCGTTTTTGA 59.744 38.462 0.00 0.00 0.00 2.69
748 757 6.256321 TCCCGTAATATAAGAGCGTTTTTGAC 59.744 38.462 0.00 0.00 0.00 3.18
749 758 6.036300 CCCGTAATATAAGAGCGTTTTTGACA 59.964 38.462 0.00 0.00 0.00 3.58
750 759 6.898189 CCGTAATATAAGAGCGTTTTTGACAC 59.102 38.462 0.00 0.00 0.00 3.67
751 760 7.201496 CCGTAATATAAGAGCGTTTTTGACACT 60.201 37.037 0.00 0.00 0.00 3.55
752 761 8.800972 CGTAATATAAGAGCGTTTTTGACACTA 58.199 33.333 0.00 0.00 0.00 2.74
755 764 3.854286 AGAGCGTTTTTGACACTAACG 57.146 42.857 13.96 13.96 45.31 3.18
759 768 3.854286 CGTTTTTGACACTAACGCTCT 57.146 42.857 7.95 0.00 38.27 4.09
761 770 5.319232 CGTTTTTGACACTAACGCTCTTA 57.681 39.130 7.95 0.00 38.27 2.10
762 771 5.912528 CGTTTTTGACACTAACGCTCTTAT 58.087 37.500 7.95 0.00 38.27 1.73
764 773 7.672738 CGTTTTTGACACTAACGCTCTTATAT 58.327 34.615 7.95 0.00 38.27 0.86
769 778 8.812147 TTGACACTAACGCTCTTATATTATGG 57.188 34.615 0.00 0.00 0.00 2.74
770 779 7.375834 TGACACTAACGCTCTTATATTATGGG 58.624 38.462 0.00 0.00 0.00 4.00
771 780 7.231925 TGACACTAACGCTCTTATATTATGGGA 59.768 37.037 0.00 0.00 0.00 4.37
772 781 7.376615 ACACTAACGCTCTTATATTATGGGAC 58.623 38.462 0.00 0.00 0.00 4.46
774 783 7.542477 CACTAACGCTCTTATATTATGGGACTG 59.458 40.741 0.00 0.00 0.00 3.51
775 784 6.665992 AACGCTCTTATATTATGGGACTGA 57.334 37.500 0.00 0.00 0.00 3.41
776 785 6.274157 ACGCTCTTATATTATGGGACTGAG 57.726 41.667 0.00 0.00 0.00 3.35
778 787 5.394663 CGCTCTTATATTATGGGACTGAGGG 60.395 48.000 0.00 0.00 0.00 4.30
779 788 5.721960 GCTCTTATATTATGGGACTGAGGGA 59.278 44.000 0.00 0.00 0.00 4.20
780 789 6.127196 GCTCTTATATTATGGGACTGAGGGAG 60.127 46.154 0.00 0.00 0.00 4.30
783 792 8.116669 TCTTATATTATGGGACTGAGGGAGTAG 58.883 40.741 0.00 0.00 33.83 2.57
784 793 4.834406 ATTATGGGACTGAGGGAGTAGA 57.166 45.455 0.00 0.00 33.83 2.59
785 794 4.620086 TTATGGGACTGAGGGAGTAGAA 57.380 45.455 0.00 0.00 33.83 2.10
786 795 3.491766 ATGGGACTGAGGGAGTAGAAA 57.508 47.619 0.00 0.00 33.83 2.52
787 796 3.269592 TGGGACTGAGGGAGTAGAAAA 57.730 47.619 0.00 0.00 33.83 2.29
788 797 3.803340 TGGGACTGAGGGAGTAGAAAAT 58.197 45.455 0.00 0.00 33.83 1.82
789 798 4.955335 TGGGACTGAGGGAGTAGAAAATA 58.045 43.478 0.00 0.00 33.83 1.40
790 799 4.962995 TGGGACTGAGGGAGTAGAAAATAG 59.037 45.833 0.00 0.00 33.83 1.73
792 801 5.163395 GGGACTGAGGGAGTAGAAAATAGTG 60.163 48.000 0.00 0.00 33.83 2.74
795 804 7.317722 ACTGAGGGAGTAGAAAATAGTGTTT 57.682 36.000 0.00 0.00 30.86 2.83
797 806 7.661847 ACTGAGGGAGTAGAAAATAGTGTTTTG 59.338 37.037 1.94 0.00 30.86 2.44
798 807 7.741785 TGAGGGAGTAGAAAATAGTGTTTTGA 58.258 34.615 1.94 0.00 0.00 2.69
799 808 7.660208 TGAGGGAGTAGAAAATAGTGTTTTGAC 59.340 37.037 1.94 1.26 0.00 3.18
802 911 8.074370 GGGAGTAGAAAATAGTGTTTTGACAAC 58.926 37.037 1.94 0.00 0.00 3.32
821 930 8.864069 TGACAACAAGTAAACAATACAATTGG 57.136 30.769 10.83 0.00 0.00 3.16
903 1013 5.796424 AAAATGTCAAGAGTGCAAATCCT 57.204 34.783 0.00 0.00 0.00 3.24
904 1014 4.778534 AATGTCAAGAGTGCAAATCCTG 57.221 40.909 0.00 0.00 0.00 3.86
905 1015 2.507484 TGTCAAGAGTGCAAATCCTGG 58.493 47.619 0.00 0.00 0.00 4.45
906 1016 1.200948 GTCAAGAGTGCAAATCCTGGC 59.799 52.381 0.00 0.00 0.00 4.85
907 1017 1.202915 TCAAGAGTGCAAATCCTGGCA 60.203 47.619 0.00 0.00 37.77 4.92
908 1018 1.614903 CAAGAGTGCAAATCCTGGCAA 59.385 47.619 0.00 0.00 42.45 4.52
909 1019 1.999648 AGAGTGCAAATCCTGGCAAA 58.000 45.000 0.00 0.00 42.45 3.68
910 1020 1.891150 AGAGTGCAAATCCTGGCAAAG 59.109 47.619 0.00 0.00 42.45 2.77
911 1021 0.319405 AGTGCAAATCCTGGCAAAGC 59.681 50.000 0.00 0.00 42.45 3.51
921 1031 2.915137 GGCAAAGCCCGGTCCAAA 60.915 61.111 0.00 0.00 44.06 3.28
922 1032 2.503382 GGCAAAGCCCGGTCCAAAA 61.503 57.895 0.00 0.00 44.06 2.44
923 1033 1.671166 GCAAAGCCCGGTCCAAAAT 59.329 52.632 0.00 0.00 0.00 1.82
924 1034 0.670239 GCAAAGCCCGGTCCAAAATG 60.670 55.000 0.00 0.00 0.00 2.32
925 1035 0.678950 CAAAGCCCGGTCCAAAATGT 59.321 50.000 0.00 0.00 0.00 2.71
926 1036 0.678950 AAAGCCCGGTCCAAAATGTG 59.321 50.000 0.00 0.00 0.00 3.21
927 1037 0.178975 AAGCCCGGTCCAAAATGTGA 60.179 50.000 0.00 0.00 0.00 3.58
928 1038 0.039618 AGCCCGGTCCAAAATGTGAT 59.960 50.000 0.00 0.00 0.00 3.06
929 1039 0.455815 GCCCGGTCCAAAATGTGATC 59.544 55.000 0.00 0.00 0.00 2.92
1116 1254 1.616628 GGAGGCCAGAAGGAAGGGA 60.617 63.158 5.01 0.00 36.89 4.20
1220 1358 1.959042 CACGGAATCATTGGGAGAGG 58.041 55.000 0.00 0.00 0.00 3.69
1248 1386 0.034863 GATTGGTCTTTGCGGGGGTA 60.035 55.000 0.00 0.00 0.00 3.69
1507 1647 9.687210 AATCGTTAGCGTATCAATAAATAGTGA 57.313 29.630 0.00 0.00 39.49 3.41
1509 1649 9.124807 TCGTTAGCGTATCAATAAATAGTGATG 57.875 33.333 12.29 0.26 38.16 3.07
1510 1650 8.912658 CGTTAGCGTATCAATAAATAGTGATGT 58.087 33.333 12.29 0.11 40.69 3.06
1512 1652 9.758651 TTAGCGTATCAATAAATAGTGATGTGT 57.241 29.630 12.29 0.11 40.69 3.72
1605 1750 5.531634 ACTTTTGTGCAATTCATGTACCAG 58.468 37.500 0.00 0.00 43.29 4.00
1681 1826 9.698309 CTGAAATGTCCAGTAAATATATCTCGT 57.302 33.333 0.00 0.00 0.00 4.18
1852 1997 3.709987 GCATTCAGCATGTTGATTACCC 58.290 45.455 13.38 0.00 44.79 3.69
1868 2013 7.475137 TGATTACCCCCTGAACTTTATTTTG 57.525 36.000 0.00 0.00 0.00 2.44
1882 2027 7.449934 ACTTTATTTTGCGTTTCACTTTCTG 57.550 32.000 0.00 0.00 0.00 3.02
1951 2096 5.336055 GCAACTTGCTCTCTCTACTTCTGTA 60.336 44.000 6.50 0.00 40.96 2.74
2124 2269 3.400255 ACCTTTCTACGCTTCTTTGGTC 58.600 45.455 0.00 0.00 0.00 4.02
2231 2376 1.674962 GGCCATCTTGAGTGCTTCATC 59.325 52.381 0.00 0.00 35.27 2.92
2306 2451 5.540719 TCACATGGTAACCGATGTATGGATA 59.459 40.000 0.00 0.00 31.46 2.59
2465 2610 3.743521 TGATACCTTGCCATGAGTATGC 58.256 45.455 0.00 0.00 32.79 3.14
2474 2619 4.535781 TGCCATGAGTATGCCAGTTTATT 58.464 39.130 0.00 0.00 32.79 1.40
2490 2635 9.180678 GCCAGTTTATTGATTATATGGTTTTCG 57.819 33.333 0.00 0.00 0.00 3.46
2522 2667 6.604795 ACAATATTGAGGCTGCTATTTCTGTT 59.395 34.615 22.16 0.00 0.00 3.16
2566 2740 4.228210 ACATTTGAAGGATCCCTGCTAGAA 59.772 41.667 8.55 0.00 32.13 2.10
2571 2745 2.393646 AGGATCCCTGCTAGAAGTCAC 58.606 52.381 8.55 0.00 29.57 3.67
2593 2767 3.270027 TGTCGCATTGAACCTATTCCTG 58.730 45.455 0.00 0.00 33.49 3.86
2821 2995 2.757868 CAGTCAAGGTGAGGTCTCCTAG 59.242 54.545 1.05 0.00 38.77 3.02
2879 3053 7.170277 TGCTGGTTATAATGTCATGCTCATAT 58.830 34.615 4.20 0.00 0.00 1.78
3043 3217 6.017605 GGTGAACATCTGAGTTATATGGCTTG 60.018 42.308 0.00 0.00 0.00 4.01
3046 3220 6.491714 ACATCTGAGTTATATGGCTTGAGT 57.508 37.500 0.00 0.00 0.00 3.41
3293 3476 0.798776 GTCATCTCCAGTTTGTGCCG 59.201 55.000 0.00 0.00 0.00 5.69
3308 3491 2.161410 TGTGCCGACATAGAATTTGTGC 59.839 45.455 0.00 0.00 0.00 4.57
3309 3492 1.396648 TGCCGACATAGAATTTGTGCG 59.603 47.619 0.00 0.00 0.00 5.34
3310 3493 1.856014 GCCGACATAGAATTTGTGCGC 60.856 52.381 0.00 0.00 0.00 6.09
3315 3498 4.209080 CGACATAGAATTTGTGCGCTCATA 59.791 41.667 13.60 9.10 0.00 2.15
3319 3502 6.094048 ACATAGAATTTGTGCGCTCATAAGTT 59.906 34.615 13.60 2.33 0.00 2.66
3322 3505 6.215845 AGAATTTGTGCGCTCATAAGTTTTT 58.784 32.000 13.60 0.00 0.00 1.94
3353 3536 7.416777 GGTCACATTTGGGGAGAAATCTTTATC 60.417 40.741 0.00 0.00 0.00 1.75
3358 3541 8.534496 CATTTGGGGAGAAATCTTTATCAGTTT 58.466 33.333 0.35 0.00 30.33 2.66
3369 3552 0.623723 TATCAGTTTCACCAGGGCCC 59.376 55.000 16.46 16.46 0.00 5.80
3377 3560 2.683933 ACCAGGGCCCGTACTCAG 60.684 66.667 18.44 3.56 0.00 3.35
3388 3571 3.887716 GCCCGTACTCAGGAGTTTAGATA 59.112 47.826 7.33 0.00 42.54 1.98
3420 3603 8.437360 TTGATTTCATCGAGTAGCAATACATT 57.563 30.769 0.00 0.00 0.00 2.71
3428 3611 6.288294 TCGAGTAGCAATACATTAAGGCAAT 58.712 36.000 0.00 0.00 0.00 3.56
3449 3632 1.700368 CTCTCCTCCTGTCCCTCCA 59.300 63.158 0.00 0.00 0.00 3.86
3460 3643 2.167487 CTGTCCCTCCAAAGCTACTCTC 59.833 54.545 0.00 0.00 0.00 3.20
3461 3644 2.225394 TGTCCCTCCAAAGCTACTCTCT 60.225 50.000 0.00 0.00 0.00 3.10
3463 3646 1.760029 CCCTCCAAAGCTACTCTCTCC 59.240 57.143 0.00 0.00 0.00 3.71
3479 3662 4.628074 TCTCTCCGTTCCTGTGTTTTTAG 58.372 43.478 0.00 0.00 0.00 1.85
3486 3669 5.243207 CGTTCCTGTGTTTTTAGTCCCTAT 58.757 41.667 0.00 0.00 0.00 2.57
3487 3670 6.400568 CGTTCCTGTGTTTTTAGTCCCTATA 58.599 40.000 0.00 0.00 0.00 1.31
3488 3671 6.534079 CGTTCCTGTGTTTTTAGTCCCTATAG 59.466 42.308 0.00 0.00 0.00 1.31
3507 3690 7.364762 CCCTATAGTATTTGTGACTTGTGAGGT 60.365 40.741 0.00 0.00 0.00 3.85
3607 3790 3.891366 ACCAGCTGCTTAAATCAACAAGT 59.109 39.130 8.66 0.00 0.00 3.16
3635 3820 5.180117 GCTTGAAAGTCTCTAAACTGCATGA 59.820 40.000 0.00 0.00 0.00 3.07
3759 3969 9.451002 AAAAAGAGTAAAGCTAGTATTCCCTTC 57.549 33.333 0.00 0.00 0.00 3.46
3760 3970 6.394025 AGAGTAAAGCTAGTATTCCCTTCG 57.606 41.667 0.00 0.00 0.00 3.79
3762 3972 6.039605 AGAGTAAAGCTAGTATTCCCTTCGTC 59.960 42.308 0.00 0.00 0.00 4.20
3763 3973 4.403585 AAAGCTAGTATTCCCTTCGTCC 57.596 45.455 0.00 0.00 0.00 4.79
3764 3974 2.317973 AGCTAGTATTCCCTTCGTCCC 58.682 52.381 0.00 0.00 0.00 4.46
3765 3975 2.037144 GCTAGTATTCCCTTCGTCCCA 58.963 52.381 0.00 0.00 0.00 4.37
3766 3976 2.633481 GCTAGTATTCCCTTCGTCCCAT 59.367 50.000 0.00 0.00 0.00 4.00
3767 3977 3.830755 GCTAGTATTCCCTTCGTCCCATA 59.169 47.826 0.00 0.00 0.00 2.74
3768 3978 4.282703 GCTAGTATTCCCTTCGTCCCATAA 59.717 45.833 0.00 0.00 0.00 1.90
3769 3979 5.046520 GCTAGTATTCCCTTCGTCCCATAAT 60.047 44.000 0.00 0.00 0.00 1.28
3770 3980 6.154021 GCTAGTATTCCCTTCGTCCCATAATA 59.846 42.308 0.00 0.00 0.00 0.98
3771 3981 7.147707 GCTAGTATTCCCTTCGTCCCATAATAT 60.148 40.741 0.00 0.00 0.00 1.28
3772 3982 9.417561 CTAGTATTCCCTTCGTCCCATAATATA 57.582 37.037 0.00 0.00 0.00 0.86
3773 3983 8.674925 AGTATTCCCTTCGTCCCATAATATAA 57.325 34.615 0.00 0.00 0.00 0.98
3774 3984 8.759782 AGTATTCCCTTCGTCCCATAATATAAG 58.240 37.037 0.00 0.00 0.00 1.73
3775 3985 7.808279 ATTCCCTTCGTCCCATAATATAAGA 57.192 36.000 0.00 0.00 0.00 2.10
3776 3986 7.621006 TTCCCTTCGTCCCATAATATAAGAA 57.379 36.000 0.00 0.00 0.00 2.52
3777 3987 7.001099 TCCCTTCGTCCCATAATATAAGAAC 57.999 40.000 0.00 0.00 0.00 3.01
3778 3988 5.867716 CCCTTCGTCCCATAATATAAGAACG 59.132 44.000 0.00 0.00 0.00 3.95
3779 3989 6.453092 CCTTCGTCCCATAATATAAGAACGT 58.547 40.000 0.00 0.00 0.00 3.99
3780 3990 6.927381 CCTTCGTCCCATAATATAAGAACGTT 59.073 38.462 0.00 0.00 0.00 3.99
3781 3991 7.440255 CCTTCGTCCCATAATATAAGAACGTTT 59.560 37.037 0.46 0.00 0.00 3.60
3782 3992 8.721019 TTCGTCCCATAATATAAGAACGTTTT 57.279 30.769 0.46 0.00 0.00 2.43
3783 3993 8.721019 TCGTCCCATAATATAAGAACGTTTTT 57.279 30.769 9.22 9.22 0.00 1.94
3784 3994 8.605746 TCGTCCCATAATATAAGAACGTTTTTG 58.394 33.333 13.87 0.00 0.00 2.44
3785 3995 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
3786 3996 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
3787 3997 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
3788 3998 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
3806 4016 9.496873 TTTTGACACTATTATATTATGGGACGG 57.503 33.333 0.00 0.00 0.00 4.79
3807 4017 8.425237 TTGACACTATTATATTATGGGACGGA 57.575 34.615 0.00 0.00 0.00 4.69
3808 4018 8.063200 TGACACTATTATATTATGGGACGGAG 57.937 38.462 0.00 0.00 0.00 4.63
3809 4019 7.123697 TGACACTATTATATTATGGGACGGAGG 59.876 40.741 0.00 0.00 0.00 4.30
3810 4020 6.383147 ACACTATTATATTATGGGACGGAGGG 59.617 42.308 0.00 0.00 0.00 4.30
3811 4021 6.610020 CACTATTATATTATGGGACGGAGGGA 59.390 42.308 0.00 0.00 0.00 4.20
3812 4022 6.839657 ACTATTATATTATGGGACGGAGGGAG 59.160 42.308 0.00 0.00 0.00 4.30
3834 4044 7.654520 GGGAGTACTTTTTATTCCAAAACCAAC 59.345 37.037 0.00 0.00 0.00 3.77
3846 4059 3.133901 CCAAAACCAACACTTAGGGCTTT 59.866 43.478 0.00 0.00 0.00 3.51
3879 4092 9.655769 CTTAGGACATGAATTTCATATGAAACG 57.344 33.333 28.59 17.85 45.55 3.60
4202 4446 2.262915 GGAGCTGACACGTGAGGG 59.737 66.667 25.01 11.90 43.28 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.084579 CTTGCATCGTCGCTGACC 58.915 61.111 0.00 0.00 0.00 4.02
84 85 2.335681 TCTCCACCACCTTCACCATA 57.664 50.000 0.00 0.00 0.00 2.74
89 90 1.070134 CGTTCTTCTCCACCACCTTCA 59.930 52.381 0.00 0.00 0.00 3.02
210 211 1.001633 ACCACCAACTCACGTCCATAC 59.998 52.381 0.00 0.00 0.00 2.39
223 224 0.541764 GGCCCTTCATTCACCACCAA 60.542 55.000 0.00 0.00 0.00 3.67
279 280 1.541147 ACATTGCCATCTTCCGTTGTG 59.459 47.619 0.00 0.00 0.00 3.33
318 319 2.158943 AGCCCGAGTAGTATTTTCTGCC 60.159 50.000 0.00 0.00 0.00 4.85
337 341 6.513066 GCATCCACTCTTCTGATTTATGAAGC 60.513 42.308 0.00 0.00 39.41 3.86
352 356 1.558294 TGCTGATCTTGCATCCACTCT 59.442 47.619 9.33 0.00 35.31 3.24
353 357 2.034104 TGCTGATCTTGCATCCACTC 57.966 50.000 9.33 0.00 35.31 3.51
354 358 2.502142 TTGCTGATCTTGCATCCACT 57.498 45.000 13.14 0.00 40.34 4.00
357 361 2.429610 ACCAATTGCTGATCTTGCATCC 59.570 45.455 13.14 0.00 40.34 3.51
380 384 5.232838 GGACAACAAGCACAGAGAATTTTTG 59.767 40.000 0.00 0.00 0.00 2.44
382 386 4.402155 TGGACAACAAGCACAGAGAATTTT 59.598 37.500 0.00 0.00 0.00 1.82
384 388 3.554934 TGGACAACAAGCACAGAGAATT 58.445 40.909 0.00 0.00 0.00 2.17
385 389 3.213206 TGGACAACAAGCACAGAGAAT 57.787 42.857 0.00 0.00 0.00 2.40
403 409 8.525290 AAGTTCTTTATTCTTCACCCATATGG 57.475 34.615 15.41 15.41 41.37 2.74
426 432 5.869888 GTCACATTCTACAACCACCTCTAAG 59.130 44.000 0.00 0.00 0.00 2.18
498 505 5.887598 TCCAGAAATCCATCTTACAACATGG 59.112 40.000 0.00 0.00 41.04 3.66
594 602 6.377146 ACGTGGAAAATAGCACTAATTCCATT 59.623 34.615 21.53 13.90 42.14 3.16
632 641 8.278408 CAGTATCATCACCAAATTTATCTCACG 58.722 37.037 0.00 0.00 0.00 4.35
682 691 9.924650 TCTAGGAGTAGAAAAATAGTGTTTGAC 57.075 33.333 0.00 0.00 31.94 3.18
699 708 5.103771 ACGGAGGGAGTATTTTCTAGGAGTA 60.104 44.000 0.00 0.00 0.00 2.59
701 710 4.216708 ACGGAGGGAGTATTTTCTAGGAG 58.783 47.826 0.00 0.00 0.00 3.69
702 711 4.213513 GACGGAGGGAGTATTTTCTAGGA 58.786 47.826 0.00 0.00 0.00 2.94
704 713 3.321396 GGGACGGAGGGAGTATTTTCTAG 59.679 52.174 0.00 0.00 0.00 2.43
705 714 3.303049 GGGACGGAGGGAGTATTTTCTA 58.697 50.000 0.00 0.00 0.00 2.10
706 715 2.117051 GGGACGGAGGGAGTATTTTCT 58.883 52.381 0.00 0.00 0.00 2.52
707 716 2.616634 GGGACGGAGGGAGTATTTTC 57.383 55.000 0.00 0.00 0.00 2.29
722 731 6.256321 TCAAAAACGCTCTTATATTACGGGAC 59.744 38.462 0.00 0.00 0.00 4.46
725 734 6.898189 GTGTCAAAAACGCTCTTATATTACGG 59.102 38.462 0.00 0.00 35.42 4.02
726 735 7.672738 AGTGTCAAAAACGCTCTTATATTACG 58.327 34.615 0.00 0.00 45.69 3.18
729 738 8.166706 CGTTAGTGTCAAAAACGCTCTTATATT 58.833 33.333 7.72 0.00 45.69 1.28
732 741 5.912528 CGTTAGTGTCAAAAACGCTCTTAT 58.087 37.500 7.72 0.00 45.69 1.73
733 742 5.319232 CGTTAGTGTCAAAAACGCTCTTA 57.681 39.130 7.72 0.00 45.69 2.10
734 743 4.191662 CGTTAGTGTCAAAAACGCTCTT 57.808 40.909 7.72 0.00 45.69 2.85
735 744 3.854286 CGTTAGTGTCAAAAACGCTCT 57.146 42.857 7.72 0.00 45.69 4.09
743 752 9.256477 CCATAATATAAGAGCGTTAGTGTCAAA 57.744 33.333 0.00 0.00 0.00 2.69
744 753 7.870954 CCCATAATATAAGAGCGTTAGTGTCAA 59.129 37.037 0.00 0.00 0.00 3.18
746 755 7.541437 GTCCCATAATATAAGAGCGTTAGTGTC 59.459 40.741 0.00 0.00 0.00 3.67
747 756 7.232941 AGTCCCATAATATAAGAGCGTTAGTGT 59.767 37.037 0.00 0.00 0.00 3.55
748 757 7.542477 CAGTCCCATAATATAAGAGCGTTAGTG 59.458 40.741 0.00 0.00 0.00 2.74
749 758 7.450634 TCAGTCCCATAATATAAGAGCGTTAGT 59.549 37.037 0.00 0.00 0.00 2.24
750 759 7.827701 TCAGTCCCATAATATAAGAGCGTTAG 58.172 38.462 0.00 0.00 0.00 2.34
751 760 7.093902 CCTCAGTCCCATAATATAAGAGCGTTA 60.094 40.741 0.00 0.00 0.00 3.18
752 761 6.295349 CCTCAGTCCCATAATATAAGAGCGTT 60.295 42.308 0.00 0.00 0.00 4.84
753 762 5.186021 CCTCAGTCCCATAATATAAGAGCGT 59.814 44.000 0.00 0.00 0.00 5.07
754 763 5.394663 CCCTCAGTCCCATAATATAAGAGCG 60.395 48.000 0.00 0.00 0.00 5.03
755 764 5.721960 TCCCTCAGTCCCATAATATAAGAGC 59.278 44.000 0.00 0.00 0.00 4.09
756 765 6.957020 ACTCCCTCAGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
757 766 6.875469 ACTCCCTCAGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
758 767 8.116669 TCTACTCCCTCAGTCCCATAATATAAG 58.883 40.741 0.00 0.00 36.43 1.73
759 768 8.008104 TCTACTCCCTCAGTCCCATAATATAA 57.992 38.462 0.00 0.00 36.43 0.98
761 770 6.485388 TCTACTCCCTCAGTCCCATAATAT 57.515 41.667 0.00 0.00 36.43 1.28
762 771 5.942977 TCTACTCCCTCAGTCCCATAATA 57.057 43.478 0.00 0.00 36.43 0.98
764 773 4.620086 TTCTACTCCCTCAGTCCCATAA 57.380 45.455 0.00 0.00 36.43 1.90
766 775 3.491766 TTTCTACTCCCTCAGTCCCAT 57.508 47.619 0.00 0.00 36.43 4.00
768 777 4.963628 ACTATTTTCTACTCCCTCAGTCCC 59.036 45.833 0.00 0.00 36.43 4.46
769 778 5.422650 ACACTATTTTCTACTCCCTCAGTCC 59.577 44.000 0.00 0.00 36.43 3.85
770 779 6.532988 ACACTATTTTCTACTCCCTCAGTC 57.467 41.667 0.00 0.00 36.43 3.51
771 780 6.936968 AACACTATTTTCTACTCCCTCAGT 57.063 37.500 0.00 0.00 39.41 3.41
772 781 7.878127 TCAAAACACTATTTTCTACTCCCTCAG 59.122 37.037 0.00 0.00 0.00 3.35
774 783 7.660208 TGTCAAAACACTATTTTCTACTCCCTC 59.340 37.037 0.00 0.00 0.00 4.30
775 784 7.514721 TGTCAAAACACTATTTTCTACTCCCT 58.485 34.615 0.00 0.00 0.00 4.20
776 785 7.739498 TGTCAAAACACTATTTTCTACTCCC 57.261 36.000 0.00 0.00 0.00 4.30
778 787 9.997482 TTGTTGTCAAAACACTATTTTCTACTC 57.003 29.630 0.00 0.00 34.35 2.59
780 789 9.783256 ACTTGTTGTCAAAACACTATTTTCTAC 57.217 29.630 0.00 0.00 34.35 2.59
785 794 9.915629 TGTTTACTTGTTGTCAAAACACTATTT 57.084 25.926 0.00 0.00 34.35 1.40
786 795 9.915629 TTGTTTACTTGTTGTCAAAACACTATT 57.084 25.926 0.00 0.00 34.02 1.73
789 798 9.349145 GTATTGTTTACTTGTTGTCAAAACACT 57.651 29.630 0.00 0.00 34.02 3.55
790 799 9.130312 TGTATTGTTTACTTGTTGTCAAAACAC 57.870 29.630 0.00 0.00 34.02 3.32
795 804 9.307121 CCAATTGTATTGTTTACTTGTTGTCAA 57.693 29.630 4.43 0.00 0.00 3.18
797 806 9.691362 ATCCAATTGTATTGTTTACTTGTTGTC 57.309 29.630 4.43 0.00 0.00 3.18
820 929 9.601217 TTGTTAGAGCTTGACTTAGAAATATCC 57.399 33.333 0.00 0.00 0.00 2.59
828 938 4.390297 GCCACTTGTTAGAGCTTGACTTAG 59.610 45.833 0.00 0.00 0.00 2.18
859 969 2.949177 TTTCCTGTTAGAGCTTGGCA 57.051 45.000 0.00 0.00 0.00 4.92
905 1015 0.670239 CATTTTGGACCGGGCTTTGC 60.670 55.000 7.57 0.00 0.00 3.68
906 1016 0.678950 ACATTTTGGACCGGGCTTTG 59.321 50.000 7.57 0.09 0.00 2.77
907 1017 0.678950 CACATTTTGGACCGGGCTTT 59.321 50.000 7.57 0.00 0.00 3.51
908 1018 0.178975 TCACATTTTGGACCGGGCTT 60.179 50.000 7.57 0.00 0.00 4.35
909 1019 0.039618 ATCACATTTTGGACCGGGCT 59.960 50.000 7.57 0.00 0.00 5.19
910 1020 0.455815 GATCACATTTTGGACCGGGC 59.544 55.000 6.32 0.21 0.00 6.13
911 1021 1.102978 GGATCACATTTTGGACCGGG 58.897 55.000 6.32 0.00 0.00 5.73
912 1022 1.745087 CAGGATCACATTTTGGACCGG 59.255 52.381 0.00 0.00 0.00 5.28
913 1023 1.745087 CCAGGATCACATTTTGGACCG 59.255 52.381 0.00 0.00 0.00 4.79
914 1024 1.478105 GCCAGGATCACATTTTGGACC 59.522 52.381 0.00 0.00 0.00 4.46
915 1025 2.170166 TGCCAGGATCACATTTTGGAC 58.830 47.619 0.00 0.00 0.00 4.02
916 1026 2.601240 TGCCAGGATCACATTTTGGA 57.399 45.000 0.00 0.00 0.00 3.53
917 1027 3.592059 CTTTGCCAGGATCACATTTTGG 58.408 45.455 0.00 0.00 0.00 3.28
918 1028 2.997986 GCTTTGCCAGGATCACATTTTG 59.002 45.455 0.00 0.00 0.00 2.44
919 1029 3.323751 GCTTTGCCAGGATCACATTTT 57.676 42.857 0.00 0.00 0.00 1.82
1116 1254 3.925630 CTGCACCACGGCCCTCATT 62.926 63.158 0.00 0.00 0.00 2.57
1163 1301 1.355066 GCGAACTGAAGAGGAAGCGG 61.355 60.000 0.00 0.00 0.00 5.52
1220 1358 1.244019 AAAGACCAATCAGCGCCCAC 61.244 55.000 2.29 0.00 0.00 4.61
1248 1386 2.437897 CTTGCCCTTCCACCTGCT 59.562 61.111 0.00 0.00 0.00 4.24
1507 1647 4.937620 CAGAATACAGCACCAAGTACACAT 59.062 41.667 0.00 0.00 0.00 3.21
1509 1649 3.684788 CCAGAATACAGCACCAAGTACAC 59.315 47.826 0.00 0.00 0.00 2.90
1510 1650 3.326588 ACCAGAATACAGCACCAAGTACA 59.673 43.478 0.00 0.00 0.00 2.90
1511 1651 3.684788 CACCAGAATACAGCACCAAGTAC 59.315 47.826 0.00 0.00 0.00 2.73
1512 1652 3.868369 GCACCAGAATACAGCACCAAGTA 60.868 47.826 0.00 0.00 0.00 2.24
1586 1731 4.023279 GTCACTGGTACATGAATTGCACAA 60.023 41.667 0.00 0.00 38.20 3.33
1681 1826 3.004629 GCATGAAACAGACACCATCACAA 59.995 43.478 0.00 0.00 0.00 3.33
1852 1997 5.174943 GTGAAACGCAAAATAAAGTTCAGGG 59.825 40.000 0.00 0.00 0.00 4.45
1868 2013 0.663153 ACCTGCAGAAAGTGAAACGC 59.337 50.000 17.39 0.00 45.86 4.84
2008 2153 5.692115 TGGCTCACTGAATAGGATAACAA 57.308 39.130 0.00 0.00 0.00 2.83
2124 2269 5.630896 TGTACGACTTTTGAAACTTCTCG 57.369 39.130 0.00 0.00 0.00 4.04
2199 2344 5.183904 ACTCAAGATGGCCAACTTCATAAAC 59.816 40.000 24.23 0.00 0.00 2.01
2306 2451 8.954350 CAGGAACATTGAGAAATATGAGAAAGT 58.046 33.333 0.00 0.00 0.00 2.66
2421 2566 4.597507 AGGGGAGTACAAATCTGAACAAGA 59.402 41.667 0.00 0.00 39.94 3.02
2465 2610 9.180678 GCGAAAACCATATAATCAATAAACTGG 57.819 33.333 0.00 0.00 0.00 4.00
2484 2629 8.076178 AGCCTCAATATTGTATTATGCGAAAAC 58.924 33.333 14.97 0.00 0.00 2.43
2490 2635 6.506500 AGCAGCCTCAATATTGTATTATGC 57.493 37.500 14.97 17.28 0.00 3.14
2500 2645 7.651027 AAAACAGAAATAGCAGCCTCAATAT 57.349 32.000 0.00 0.00 0.00 1.28
2566 2740 1.070758 AGGTTCAATGCGACAGTGACT 59.929 47.619 8.99 3.11 38.18 3.41
2571 2745 3.310774 CAGGAATAGGTTCAATGCGACAG 59.689 47.826 0.00 0.00 36.01 3.51
2593 2767 5.983540 AGAGATGAAGTAGGGACAATTGTC 58.016 41.667 27.16 27.16 44.04 3.18
2821 2995 6.735130 ACAAAACATCACAGTAGGTTTAAGC 58.265 36.000 0.00 0.00 33.46 3.09
3046 3220 8.966868 ACCTCAAAAGAAACTGAAAATTCTACA 58.033 29.630 0.00 0.00 34.90 2.74
3269 3452 2.733552 CACAAACTGGAGATGACTCACG 59.266 50.000 0.00 0.00 44.22 4.35
3293 3476 4.542662 ATGAGCGCACAAATTCTATGTC 57.457 40.909 12.53 0.00 0.00 3.06
3319 3502 2.625790 CCCCAAATGTGACCGAGAAAAA 59.374 45.455 0.00 0.00 0.00 1.94
3322 3505 1.003118 CTCCCCAAATGTGACCGAGAA 59.997 52.381 0.00 0.00 0.00 2.87
3323 3506 0.613260 CTCCCCAAATGTGACCGAGA 59.387 55.000 0.00 0.00 0.00 4.04
3334 3517 7.728083 TGAAACTGATAAAGATTTCTCCCCAAA 59.272 33.333 0.00 0.00 32.07 3.28
3337 3520 6.095580 GGTGAAACTGATAAAGATTTCTCCCC 59.904 42.308 0.00 0.00 35.82 4.81
3339 3522 7.148171 CCTGGTGAAACTGATAAAGATTTCTCC 60.148 40.741 8.87 8.87 38.44 3.71
3353 3536 2.119484 TACGGGCCCTGGTGAAACTG 62.119 60.000 22.43 1.74 36.74 3.16
3358 3541 2.682494 GAGTACGGGCCCTGGTGA 60.682 66.667 22.43 0.00 0.00 4.02
3395 3578 8.437360 AATGTATTGCTACTCGATGAAATCAA 57.563 30.769 0.00 0.00 45.97 2.57
3428 3611 2.039624 GGGACAGGAGGAGAGGCA 59.960 66.667 0.00 0.00 0.00 4.75
3431 3614 0.041833 TTGGAGGGACAGGAGGAGAG 59.958 60.000 0.00 0.00 0.00 3.20
3438 3621 1.208293 GAGTAGCTTTGGAGGGACAGG 59.792 57.143 0.00 0.00 0.00 4.00
3449 3632 2.494073 CAGGAACGGAGAGAGTAGCTTT 59.506 50.000 0.00 0.00 0.00 3.51
3460 3643 3.497262 GGACTAAAAACACAGGAACGGAG 59.503 47.826 0.00 0.00 0.00 4.63
3461 3644 3.469739 GGACTAAAAACACAGGAACGGA 58.530 45.455 0.00 0.00 0.00 4.69
3463 3646 3.473625 AGGGACTAAAAACACAGGAACG 58.526 45.455 0.00 0.00 36.02 3.95
3479 3662 7.553334 TCACAAGTCACAAATACTATAGGGAC 58.447 38.462 4.43 0.00 0.00 4.46
3486 3669 6.169557 ACACCTCACAAGTCACAAATACTA 57.830 37.500 0.00 0.00 0.00 1.82
3487 3670 5.036117 ACACCTCACAAGTCACAAATACT 57.964 39.130 0.00 0.00 0.00 2.12
3488 3671 5.989777 AGTACACCTCACAAGTCACAAATAC 59.010 40.000 0.00 0.00 0.00 1.89
3507 3690 3.832490 AGCACATGAACTGGAGTAGTACA 59.168 43.478 0.00 0.00 39.18 2.90
3607 3790 7.611770 TGCAGTTTAGAGACTTTCAAGCTATA 58.388 34.615 0.00 0.00 0.00 1.31
3619 3802 7.495279 AGAAGATGATTCATGCAGTTTAGAGAC 59.505 37.037 3.32 0.00 0.00 3.36
3628 3813 3.215151 AGCCAGAAGATGATTCATGCAG 58.785 45.455 3.32 0.00 0.00 4.41
3740 3950 5.288015 GGACGAAGGGAATACTAGCTTTAC 58.712 45.833 0.00 0.00 0.00 2.01
3741 3951 4.343239 GGGACGAAGGGAATACTAGCTTTA 59.657 45.833 0.00 0.00 0.00 1.85
3744 3954 2.317973 GGGACGAAGGGAATACTAGCT 58.682 52.381 0.00 0.00 0.00 3.32
3745 3955 2.037144 TGGGACGAAGGGAATACTAGC 58.963 52.381 0.00 0.00 0.00 3.42
3746 3956 6.607004 ATTATGGGACGAAGGGAATACTAG 57.393 41.667 0.00 0.00 0.00 2.57
3747 3957 9.772605 TTATATTATGGGACGAAGGGAATACTA 57.227 33.333 0.00 0.00 0.00 1.82
3749 3959 8.755977 TCTTATATTATGGGACGAAGGGAATAC 58.244 37.037 0.00 0.00 0.00 1.89
3750 3960 8.904648 TCTTATATTATGGGACGAAGGGAATA 57.095 34.615 0.00 0.00 0.00 1.75
3751 3961 7.808279 TCTTATATTATGGGACGAAGGGAAT 57.192 36.000 0.00 0.00 0.00 3.01
3752 3962 7.447594 GTTCTTATATTATGGGACGAAGGGAA 58.552 38.462 0.00 0.00 0.00 3.97
3753 3963 6.294899 CGTTCTTATATTATGGGACGAAGGGA 60.295 42.308 0.00 0.00 0.00 4.20
3754 3964 5.867716 CGTTCTTATATTATGGGACGAAGGG 59.132 44.000 0.00 0.00 0.00 3.95
3755 3965 6.453092 ACGTTCTTATATTATGGGACGAAGG 58.547 40.000 14.76 0.00 0.00 3.46
3757 3967 8.721019 AAAACGTTCTTATATTATGGGACGAA 57.279 30.769 0.00 0.00 0.00 3.85
3759 3969 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
3760 3970 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
3762 3972 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
3780 3990 9.496873 CCGTCCCATAATATAATAGTGTCAAAA 57.503 33.333 0.00 0.00 0.00 2.44
3781 3991 8.872134 TCCGTCCCATAATATAATAGTGTCAAA 58.128 33.333 0.00 0.00 0.00 2.69
3782 3992 8.425237 TCCGTCCCATAATATAATAGTGTCAA 57.575 34.615 0.00 0.00 0.00 3.18
3783 3993 7.123697 CCTCCGTCCCATAATATAATAGTGTCA 59.876 40.741 0.00 0.00 0.00 3.58
3784 3994 7.417570 CCCTCCGTCCCATAATATAATAGTGTC 60.418 44.444 0.00 0.00 0.00 3.67
3785 3995 6.383147 CCCTCCGTCCCATAATATAATAGTGT 59.617 42.308 0.00 0.00 0.00 3.55
3786 3996 6.610020 TCCCTCCGTCCCATAATATAATAGTG 59.390 42.308 0.00 0.00 0.00 2.74
3787 3997 6.748969 TCCCTCCGTCCCATAATATAATAGT 58.251 40.000 0.00 0.00 0.00 2.12
3788 3998 6.839657 ACTCCCTCCGTCCCATAATATAATAG 59.160 42.308 0.00 0.00 0.00 1.73
3789 3999 6.748969 ACTCCCTCCGTCCCATAATATAATA 58.251 40.000 0.00 0.00 0.00 0.98
3790 4000 5.600749 ACTCCCTCCGTCCCATAATATAAT 58.399 41.667 0.00 0.00 0.00 1.28
3791 4001 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3792 4002 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3793 4003 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3794 4004 3.400322 AGTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
3795 4005 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3796 4006 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3797 4007 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3798 4008 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
3799 4009 0.115745 AAAGTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
3800 4010 1.273759 AAAAGTACTCCCTCCGTCCC 58.726 55.000 0.00 0.00 0.00 4.46
3801 4011 4.750021 ATAAAAAGTACTCCCTCCGTCC 57.250 45.455 0.00 0.00 0.00 4.79
3802 4012 5.114780 GGAATAAAAAGTACTCCCTCCGTC 58.885 45.833 0.00 0.00 0.00 4.79
3803 4013 4.533311 TGGAATAAAAAGTACTCCCTCCGT 59.467 41.667 0.00 0.00 0.00 4.69
3804 4014 5.093849 TGGAATAAAAAGTACTCCCTCCG 57.906 43.478 0.00 0.00 0.00 4.63
3805 4015 7.309621 GGTTTTGGAATAAAAAGTACTCCCTCC 60.310 40.741 0.00 0.00 29.93 4.30
3806 4016 7.231925 TGGTTTTGGAATAAAAAGTACTCCCTC 59.768 37.037 0.00 0.00 29.93 4.30
3807 4017 7.070629 TGGTTTTGGAATAAAAAGTACTCCCT 58.929 34.615 0.00 0.00 29.93 4.20
3808 4018 7.292713 TGGTTTTGGAATAAAAAGTACTCCC 57.707 36.000 0.00 0.00 29.93 4.30
3809 4019 8.198778 TGTTGGTTTTGGAATAAAAAGTACTCC 58.801 33.333 0.00 0.00 29.93 3.85
3810 4020 9.027129 GTGTTGGTTTTGGAATAAAAAGTACTC 57.973 33.333 0.00 0.00 29.93 2.59
3811 4021 8.755028 AGTGTTGGTTTTGGAATAAAAAGTACT 58.245 29.630 0.00 0.00 29.93 2.73
3812 4022 8.936070 AGTGTTGGTTTTGGAATAAAAAGTAC 57.064 30.769 0.00 0.00 29.93 2.73
3834 4044 5.880887 CCTAAGTAGGAAAAAGCCCTAAGTG 59.119 44.000 0.00 0.00 46.63 3.16
3873 4086 2.955660 AGGCAGAAATTCAACCGTTTCA 59.044 40.909 0.00 0.00 36.92 2.69
3879 4092 5.184671 AGAAGATGAAGGCAGAAATTCAACC 59.815 40.000 0.00 0.00 38.80 3.77
3959 4193 2.484264 GGCTTCTTCTATGCGTTGTGTT 59.516 45.455 0.00 0.00 0.00 3.32
4164 4408 4.796231 GCCGCAGACGACGATGGT 62.796 66.667 0.00 0.00 43.93 3.55


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

AutoCloner maintained by Alex Coulton.