Multiple sequence alignment - TraesCS2D01G581200

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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 TraesCS2D01G581200 chr2D 100.000 3647 0 0 1 3647 642964524 642968170 0.000000e+00 6735
1 TraesCS2D01G581200 chr2D 93.364 1748 107 6 954 2697 643071176 643069434 0.000000e+00 2577
2 TraesCS2D01G581200 chr2D 91.516 719 46 10 751 1456 642994707 642993991 0.000000e+00 976
3 TraesCS2D01G581200 chr2D 84.348 230 34 2 2851 3079 643068798 643068570 1.320000e-54 224
4 TraesCS2D01G581200 chrUn 91.102 1978 144 20 762 2714 31607379 31605409 0.000000e+00 2649
5 TraesCS2D01G581200 chrUn 95.084 1363 60 3 848 2207 31583066 31584424 0.000000e+00 2139
6 TraesCS2D01G581200 chrUn 88.343 712 29 14 2646 3336 31587850 31588528 0.000000e+00 806
7 TraesCS2D01G581200 chr2A 90.726 1984 149 15 751 2714 767952307 767950339 0.000000e+00 2612
8 TraesCS2D01G581200 chr2A 89.074 961 104 1 1553 2513 767728751 767729710 0.000000e+00 1192
9 TraesCS2D01G581200 chr2A 84.888 761 97 16 3 753 51014698 51013946 0.000000e+00 752
10 TraesCS2D01G581200 chr2A 86.111 252 30 5 2821 3071 767948360 767948113 2.160000e-67 267
11 TraesCS2D01G581200 chr2A 92.188 128 10 0 3518 3645 767817551 767817678 8.040000e-42 182
12 TraesCS2D01G581200 chr2A 89.899 99 10 0 751 849 767629757 767629855 1.060000e-25 128
13 TraesCS2D01G581200 chr5D 88.044 1723 179 16 947 2648 449688850 449687134 0.000000e+00 2015
14 TraesCS2D01G581200 chr5D 92.765 387 28 0 5 391 55832530 55832916 8.840000e-156 560
15 TraesCS2D01G581200 chr5D 90.833 360 30 3 395 754 440637483 440637839 2.550000e-131 479
16 TraesCS2D01G581200 chr5A 87.074 1702 180 30 960 2648 569068275 569066601 0.000000e+00 1888
17 TraesCS2D01G581200 chr5A 82.792 1633 253 19 1001 2616 663841608 663843229 0.000000e+00 1434
18 TraesCS2D01G581200 chr4D 83.139 1631 251 15 1001 2616 483951285 483952906 0.000000e+00 1467
19 TraesCS2D01G581200 chr4D 92.248 387 26 1 5 391 44196218 44195836 2.480000e-151 545
20 TraesCS2D01G581200 chr4D 91.460 363 29 1 392 754 44195808 44195448 7.030000e-137 497
21 TraesCS2D01G581200 chr4D 90.884 362 29 4 395 754 231204528 231204169 1.970000e-132 483
22 TraesCS2D01G581200 chr4B 82.936 1635 247 22 1001 2616 614719799 614721420 0.000000e+00 1445
23 TraesCS2D01G581200 chr3D 86.234 770 76 19 2 753 294348927 294348170 0.000000e+00 808
24 TraesCS2D01G581200 chr7D 84.556 777 93 19 2 756 412765505 412766276 0.000000e+00 745
25 TraesCS2D01G581200 chr7D 91.160 362 28 4 392 751 131313460 131313819 4.230000e-134 488
26 TraesCS2D01G581200 chr6D 93.282 387 26 0 5 391 16881248 16880862 4.090000e-159 571
27 TraesCS2D01G581200 chr6D 91.538 390 32 1 2 391 261018087 261017699 1.490000e-148 536
28 TraesCS2D01G581200 chr6D 91.233 365 28 4 392 754 16880829 16880467 9.100000e-136 494
29 TraesCS2D01G581200 chr1D 92.765 387 25 2 5 391 453079320 453079703 1.140000e-154 556
30 TraesCS2D01G581200 chr1D 93.575 358 20 3 395 751 453079737 453080092 6.930000e-147 531
31 TraesCS2D01G581200 chr1D 91.209 364 28 4 392 753 155720990 155721351 3.270000e-135 492
32 TraesCS2D01G581200 chr6A 91.990 387 31 0 5 391 588182032 588182418 8.910000e-151 544
33 TraesCS2D01G581200 chr6A 91.538 390 32 1 2 391 613083249 613083637 1.490000e-148 536
34 TraesCS2D01G581200 chr1B 79.888 179 34 2 1198 1375 52347318 52347495 2.960000e-26 130


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 TraesCS2D01G581200 chr2D 642964524 642968170 3646 False 6735.0 6735 100.0000 1 3647 1 chr2D.!!$F1 3646
1 TraesCS2D01G581200 chr2D 643068570 643071176 2606 True 1400.5 2577 88.8560 954 3079 2 chr2D.!!$R2 2125
2 TraesCS2D01G581200 chr2D 642993991 642994707 716 True 976.0 976 91.5160 751 1456 1 chr2D.!!$R1 705
3 TraesCS2D01G581200 chrUn 31605409 31607379 1970 True 2649.0 2649 91.1020 762 2714 1 chrUn.!!$R1 1952
4 TraesCS2D01G581200 chrUn 31583066 31588528 5462 False 1472.5 2139 91.7135 848 3336 2 chrUn.!!$F1 2488
5 TraesCS2D01G581200 chr2A 767948113 767952307 4194 True 1439.5 2612 88.4185 751 3071 2 chr2A.!!$R2 2320
6 TraesCS2D01G581200 chr2A 767728751 767729710 959 False 1192.0 1192 89.0740 1553 2513 1 chr2A.!!$F2 960
7 TraesCS2D01G581200 chr2A 51013946 51014698 752 True 752.0 752 84.8880 3 753 1 chr2A.!!$R1 750
8 TraesCS2D01G581200 chr5D 449687134 449688850 1716 True 2015.0 2015 88.0440 947 2648 1 chr5D.!!$R1 1701
9 TraesCS2D01G581200 chr5A 569066601 569068275 1674 True 1888.0 1888 87.0740 960 2648 1 chr5A.!!$R1 1688
10 TraesCS2D01G581200 chr5A 663841608 663843229 1621 False 1434.0 1434 82.7920 1001 2616 1 chr5A.!!$F1 1615
11 TraesCS2D01G581200 chr4D 483951285 483952906 1621 False 1467.0 1467 83.1390 1001 2616 1 chr4D.!!$F1 1615
12 TraesCS2D01G581200 chr4D 44195448 44196218 770 True 521.0 545 91.8540 5 754 2 chr4D.!!$R2 749
13 TraesCS2D01G581200 chr4B 614719799 614721420 1621 False 1445.0 1445 82.9360 1001 2616 1 chr4B.!!$F1 1615
14 TraesCS2D01G581200 chr3D 294348170 294348927 757 True 808.0 808 86.2340 2 753 1 chr3D.!!$R1 751
15 TraesCS2D01G581200 chr7D 412765505 412766276 771 False 745.0 745 84.5560 2 756 1 chr7D.!!$F2 754
16 TraesCS2D01G581200 chr6D 16880467 16881248 781 True 532.5 571 92.2575 5 754 2 chr6D.!!$R2 749
17 TraesCS2D01G581200 chr1D 453079320 453080092 772 False 543.5 556 93.1700 5 751 2 chr1D.!!$F2 746

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
48 49 0.107508 ATGAGCTACCGCAAGTGCAT 60.108 50.0 3.87 0.0 42.21 3.96 F
54 55 0.321996 TACCGCAAGTGCATGTACCA 59.678 50.0 10.59 0.0 42.21 3.25 F
678 718 0.744771 GGTCTGATCGGGCAGGTTTC 60.745 60.0 8.71 0.0 36.55 2.78 F
1501 1570 1.195115 TGAGTATGAGGCACTGGTCC 58.805 55.0 0.00 0.0 41.55 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 2025 0.682852 TCACCTTGAAACCGATCCGT 59.317 50.000 0.00 0.0 0.00 4.69 R
2052 2139 1.975407 CTGCCTGGCCTTGAGTTGG 60.975 63.158 17.53 0.0 0.00 3.77 R
2108 2201 0.458370 CATGGTGTCGTCATCGAGCA 60.458 55.000 0.00 0.0 46.96 4.26 R
3367 8761 0.034767 TGAGCTGGCCCATCTGAAAG 60.035 55.000 0.00 0.0 0.00 2.62 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
48 49 0.107508 ATGAGCTACCGCAAGTGCAT 60.108 50.000 3.87 0.00 42.21 3.96
54 55 0.321996 TACCGCAAGTGCATGTACCA 59.678 50.000 10.59 0.00 42.21 3.25
56 57 1.233950 CCGCAAGTGCATGTACCACA 61.234 55.000 10.59 0.00 42.21 4.17
59 60 2.418280 CGCAAGTGCATGTACCACATTA 59.582 45.455 10.59 0.00 36.53 1.90
85 86 2.489329 CGCATTTGAAGAACACCCATCT 59.511 45.455 0.00 0.00 0.00 2.90
87 88 3.507233 GCATTTGAAGAACACCCATCTGA 59.493 43.478 0.00 0.00 0.00 3.27
185 186 2.356313 CAGAGCCGTTGCGTGAGT 60.356 61.111 0.00 0.00 44.33 3.41
386 388 1.481871 GGTGAAGGTCCGTAGATCCA 58.518 55.000 0.00 0.00 0.00 3.41
498 536 2.542541 AGGTGGGGAGGGGAGGTA 60.543 66.667 0.00 0.00 0.00 3.08
605 645 2.194889 GCGTTTTTCCGGGTTGGGA 61.195 57.895 0.00 0.00 38.76 4.37
607 647 0.963225 CGTTTTTCCGGGTTGGGATT 59.037 50.000 0.00 0.00 38.76 3.01
642 682 1.342819 CCCCTCAAACAATTTTGCGGA 59.657 47.619 7.55 0.00 46.57 5.54
646 686 1.676529 TCAAACAATTTTGCGGACCGA 59.323 42.857 20.50 0.00 41.78 4.69
678 718 0.744771 GGTCTGATCGGGCAGGTTTC 60.745 60.000 8.71 0.00 36.55 2.78
756 796 2.102252 CTGCTAGAGTTGCTCTAAGGGG 59.898 54.545 7.22 0.00 41.74 4.79
774 814 1.445871 GGTCGGCTATGTTCGGTTTT 58.554 50.000 0.00 0.00 0.00 2.43
791 831 3.866883 TTTTGGCCCTCAAAATCGATC 57.133 42.857 0.00 0.00 46.73 3.69
798 843 4.398044 GGCCCTCAAAATCGATCTTTTACA 59.602 41.667 0.00 0.00 0.00 2.41
800 845 6.202226 GCCCTCAAAATCGATCTTTTACATC 58.798 40.000 0.00 0.00 0.00 3.06
804 849 8.333908 CCTCAAAATCGATCTTTTACATCTCTG 58.666 37.037 0.00 0.00 0.00 3.35
821 866 2.500098 CTCTGACCGGTTTTAGGGATCA 59.500 50.000 9.42 0.00 0.00 2.92
836 881 5.707066 AGGGATCAGTTAGAAATGCTCTT 57.293 39.130 0.00 0.00 35.41 2.85
838 883 6.825610 AGGGATCAGTTAGAAATGCTCTTAG 58.174 40.000 0.00 0.00 35.41 2.18
860 909 9.385902 CTTAGAACATGTACAAAGTTGAACATG 57.614 33.333 18.32 17.47 40.29 3.21
861 910 6.208644 AGAACATGTACAAAGTTGAACATGC 58.791 36.000 18.32 5.74 38.66 4.06
862 911 5.772825 ACATGTACAAAGTTGAACATGCT 57.227 34.783 18.38 8.71 38.66 3.79
863 912 5.762045 ACATGTACAAAGTTGAACATGCTC 58.238 37.500 18.38 0.00 38.66 4.26
864 913 4.829064 TGTACAAAGTTGAACATGCTCC 57.171 40.909 0.00 0.00 0.00 4.70
865 914 3.568007 TGTACAAAGTTGAACATGCTCCC 59.432 43.478 0.00 0.00 0.00 4.30
866 915 2.949447 ACAAAGTTGAACATGCTCCCT 58.051 42.857 0.00 0.00 0.00 4.20
868 917 4.469657 ACAAAGTTGAACATGCTCCCTAA 58.530 39.130 0.00 0.00 0.00 2.69
897 953 2.418983 AATAAGCCTACTAGCGTCGC 57.581 50.000 9.80 9.80 38.01 5.19
945 1002 4.591321 TCTCCACAAATTAAGGCCTGAT 57.409 40.909 5.69 0.00 0.00 2.90
1085 1151 2.237751 CCAGTGCAGTATACGGCGC 61.238 63.158 27.39 27.39 45.53 6.53
1482 1551 1.968540 GCTCGGCCTGTTCAAGCTT 60.969 57.895 0.00 0.00 0.00 3.74
1494 1563 3.244526 TGTTCAAGCTTGAGTATGAGGCA 60.245 43.478 27.02 14.36 38.61 4.75
1501 1570 1.195115 TGAGTATGAGGCACTGGTCC 58.805 55.000 0.00 0.00 41.55 4.46
1578 1647 1.218316 GCTCAACTACACCTCGGGG 59.782 63.158 0.00 0.00 38.88 5.73
1653 1722 3.654143 ATGGGCCAGCTGCTGTCA 61.654 61.111 26.41 20.57 40.92 3.58
1905 1986 2.561956 CGTCCACGTCCTCACTGGT 61.562 63.158 0.00 0.00 37.07 4.00
1944 2025 2.338620 CTGCTGGACCGTGTCGAA 59.661 61.111 0.00 0.00 32.65 3.71
2651 5701 4.521146 GCCATGTCAAGGATATAGGATGG 58.479 47.826 0.00 0.00 33.61 3.51
2661 5711 3.704566 GGATATAGGATGGCCATGTACGA 59.295 47.826 26.56 9.93 36.29 3.43
2746 5833 5.121142 GTCCCGAGTTATTTGTCGATCAAAA 59.879 40.000 14.24 5.58 46.97 2.44
2761 5848 6.144724 GTCGATCAAAAGGATGTATCTAGCAC 59.855 42.308 0.00 0.00 36.00 4.40
2930 8305 9.693739 TGTTGTGTATTATGAGTTTATCCCAAT 57.306 29.630 0.00 0.00 0.00 3.16
2966 8342 7.148222 TGTGAAATTGACTAAGTTCGTGGAAAA 60.148 33.333 0.00 0.00 42.21 2.29
2967 8343 7.165318 GTGAAATTGACTAAGTTCGTGGAAAAC 59.835 37.037 0.00 0.00 42.21 2.43
2968 8344 6.687081 AATTGACTAAGTTCGTGGAAAACA 57.313 33.333 0.00 0.00 0.00 2.83
2969 8345 5.728351 TTGACTAAGTTCGTGGAAAACAG 57.272 39.130 0.00 0.00 0.00 3.16
2972 8348 5.750067 TGACTAAGTTCGTGGAAAACAGTAC 59.250 40.000 0.00 0.00 0.00 2.73
3071 8448 3.726557 TCTGGATGTTGCTCAAGGATT 57.273 42.857 0.00 0.00 0.00 3.01
3096 8473 4.773323 AGGTACAGTACGACTTAACACC 57.227 45.455 4.58 0.00 0.00 4.16
3127 8504 4.335400 TCAACTCAGAGCACACAACATA 57.665 40.909 0.00 0.00 0.00 2.29
3142 8519 5.711976 ACACAACATATTGAAAAGGGAGGAG 59.288 40.000 0.00 0.00 39.30 3.69
3143 8520 5.126061 CACAACATATTGAAAAGGGAGGAGG 59.874 44.000 0.00 0.00 39.30 4.30
3145 8522 2.710096 TATTGAAAAGGGAGGAGGCG 57.290 50.000 0.00 0.00 0.00 5.52
3286 8677 5.378292 TTTGTGACAAGTTGTTGCTGTTA 57.622 34.783 10.45 0.00 37.14 2.41
3321 8715 3.564027 CGAACCTCGATTGGCCGC 61.564 66.667 0.00 0.00 43.74 6.53
3336 8730 0.537371 GCCGCCCCATTAGCTACAAT 60.537 55.000 0.00 0.00 0.00 2.71
3337 8731 1.271163 GCCGCCCCATTAGCTACAATA 60.271 52.381 0.00 0.00 0.00 1.90
3338 8732 2.812613 GCCGCCCCATTAGCTACAATAA 60.813 50.000 0.00 0.00 0.00 1.40
3339 8733 3.074412 CCGCCCCATTAGCTACAATAAG 58.926 50.000 0.00 0.00 0.00 1.73
3340 8734 3.496160 CCGCCCCATTAGCTACAATAAGT 60.496 47.826 0.00 0.00 0.00 2.24
3341 8735 3.498397 CGCCCCATTAGCTACAATAAGTG 59.502 47.826 0.00 0.00 0.00 3.16
3342 8736 4.714632 GCCCCATTAGCTACAATAAGTGA 58.285 43.478 0.00 0.00 0.00 3.41
3343 8737 5.130350 GCCCCATTAGCTACAATAAGTGAA 58.870 41.667 0.00 0.00 0.00 3.18
3344 8738 5.592688 GCCCCATTAGCTACAATAAGTGAAA 59.407 40.000 0.00 0.00 0.00 2.69
3345 8739 6.238759 GCCCCATTAGCTACAATAAGTGAAAG 60.239 42.308 0.00 0.00 0.00 2.62
3346 8740 7.054124 CCCCATTAGCTACAATAAGTGAAAGA 58.946 38.462 0.00 0.00 0.00 2.52
3347 8741 7.227512 CCCCATTAGCTACAATAAGTGAAAGAG 59.772 40.741 0.00 0.00 0.00 2.85
3348 8742 7.987458 CCCATTAGCTACAATAAGTGAAAGAGA 59.013 37.037 0.00 0.00 0.00 3.10
3349 8743 9.039870 CCATTAGCTACAATAAGTGAAAGAGAG 57.960 37.037 0.00 0.00 0.00 3.20
3350 8744 9.809096 CATTAGCTACAATAAGTGAAAGAGAGA 57.191 33.333 0.00 0.00 0.00 3.10
3353 8747 7.496747 AGCTACAATAAGTGAAAGAGAGATCC 58.503 38.462 0.00 0.00 0.00 3.36
3354 8748 7.344352 AGCTACAATAAGTGAAAGAGAGATCCT 59.656 37.037 0.00 0.00 0.00 3.24
3355 8749 7.984617 GCTACAATAAGTGAAAGAGAGATCCTT 59.015 37.037 0.00 0.00 0.00 3.36
3356 8750 9.311916 CTACAATAAGTGAAAGAGAGATCCTTG 57.688 37.037 0.00 0.00 0.00 3.61
3357 8751 7.684529 ACAATAAGTGAAAGAGAGATCCTTGT 58.315 34.615 0.00 0.00 0.00 3.16
3358 8752 8.160106 ACAATAAGTGAAAGAGAGATCCTTGTT 58.840 33.333 0.00 0.00 0.00 2.83
3359 8753 9.007901 CAATAAGTGAAAGAGAGATCCTTGTTT 57.992 33.333 0.00 0.00 0.00 2.83
3360 8754 6.874288 AAGTGAAAGAGAGATCCTTGTTTG 57.126 37.500 0.00 0.00 0.00 2.93
3361 8755 5.312079 AGTGAAAGAGAGATCCTTGTTTGG 58.688 41.667 0.00 0.00 0.00 3.28
3362 8756 4.457257 GTGAAAGAGAGATCCTTGTTTGGG 59.543 45.833 0.00 0.00 0.00 4.12
3363 8757 3.728385 AAGAGAGATCCTTGTTTGGGG 57.272 47.619 0.00 0.00 0.00 4.96
3364 8758 2.921221 AGAGAGATCCTTGTTTGGGGA 58.079 47.619 0.00 0.00 35.96 4.81
3365 8759 3.260205 AGAGAGATCCTTGTTTGGGGAA 58.740 45.455 0.00 0.00 35.08 3.97
3366 8760 3.009584 AGAGAGATCCTTGTTTGGGGAAC 59.990 47.826 0.00 0.00 38.78 3.62
3380 8774 2.887790 GGAACCTTTCAGATGGGCC 58.112 57.895 0.00 0.00 0.00 5.80
3381 8775 0.039618 GGAACCTTTCAGATGGGCCA 59.960 55.000 9.61 9.61 0.00 5.36
3382 8776 1.467920 GAACCTTTCAGATGGGCCAG 58.532 55.000 13.78 0.00 0.00 4.85
3383 8777 0.613012 AACCTTTCAGATGGGCCAGC 60.613 55.000 15.39 15.39 0.00 4.85
3384 8778 1.305623 CCTTTCAGATGGGCCAGCT 59.694 57.895 20.65 20.65 0.00 4.24
3385 8779 0.750911 CCTTTCAGATGGGCCAGCTC 60.751 60.000 23.80 10.60 0.00 4.09
3386 8780 0.034767 CTTTCAGATGGGCCAGCTCA 60.035 55.000 23.80 6.18 0.00 4.26
3387 8781 0.627451 TTTCAGATGGGCCAGCTCAT 59.373 50.000 23.80 4.26 40.32 2.90
3391 8785 4.672251 ATGGGCCAGCTCATCAAC 57.328 55.556 13.78 0.00 29.90 3.18
3392 8786 1.452651 ATGGGCCAGCTCATCAACG 60.453 57.895 13.78 0.00 29.90 4.10
3393 8787 2.825836 GGGCCAGCTCATCAACGG 60.826 66.667 4.39 0.00 0.00 4.44
3394 8788 2.825836 GGCCAGCTCATCAACGGG 60.826 66.667 0.00 0.00 0.00 5.28
3395 8789 2.045926 GCCAGCTCATCAACGGGT 60.046 61.111 0.00 0.00 0.00 5.28
3396 8790 1.675641 GCCAGCTCATCAACGGGTT 60.676 57.895 0.00 0.00 0.00 4.11
3397 8791 1.244019 GCCAGCTCATCAACGGGTTT 61.244 55.000 0.00 0.00 0.00 3.27
3398 8792 1.247567 CCAGCTCATCAACGGGTTTT 58.752 50.000 0.00 0.00 0.00 2.43
3399 8793 1.068333 CCAGCTCATCAACGGGTTTTG 60.068 52.381 0.00 0.00 0.00 2.44
3400 8794 1.068333 CAGCTCATCAACGGGTTTTGG 60.068 52.381 0.00 0.00 0.00 3.28
3401 8795 0.243636 GCTCATCAACGGGTTTTGGG 59.756 55.000 0.00 0.00 0.00 4.12
3402 8796 1.904287 CTCATCAACGGGTTTTGGGA 58.096 50.000 0.00 0.00 0.00 4.37
3403 8797 2.235016 CTCATCAACGGGTTTTGGGAA 58.765 47.619 0.00 0.00 0.00 3.97
3404 8798 1.957877 TCATCAACGGGTTTTGGGAAC 59.042 47.619 0.00 0.00 0.00 3.62
3420 8814 2.963548 GAACCTTCTAGAGGGTTCCG 57.036 55.000 38.50 12.96 45.88 4.30
3421 8815 1.481363 GAACCTTCTAGAGGGTTCCGG 59.519 57.143 38.50 16.15 45.88 5.14
3422 8816 1.203275 AACCTTCTAGAGGGTTCCGGT 60.203 52.381 28.64 10.92 45.88 5.28
3423 8817 1.112950 CCTTCTAGAGGGTTCCGGTC 58.887 60.000 12.74 0.00 42.26 4.79
3424 8818 1.342175 CCTTCTAGAGGGTTCCGGTCT 60.342 57.143 12.74 0.00 42.26 3.85
3425 8819 2.091994 CCTTCTAGAGGGTTCCGGTCTA 60.092 54.545 12.74 0.00 42.26 2.59
3426 8820 3.626729 CCTTCTAGAGGGTTCCGGTCTAA 60.627 52.174 12.74 0.00 42.26 2.10
3427 8821 3.967467 TCTAGAGGGTTCCGGTCTAAT 57.033 47.619 0.00 0.00 0.00 1.73
3428 8822 4.261411 TCTAGAGGGTTCCGGTCTAATT 57.739 45.455 0.00 0.00 0.00 1.40
3429 8823 4.617593 TCTAGAGGGTTCCGGTCTAATTT 58.382 43.478 0.00 0.00 0.00 1.82
3430 8824 5.028131 TCTAGAGGGTTCCGGTCTAATTTT 58.972 41.667 0.00 0.00 0.00 1.82
3431 8825 4.652679 AGAGGGTTCCGGTCTAATTTTT 57.347 40.909 0.00 0.00 0.00 1.94
3432 8826 4.586884 AGAGGGTTCCGGTCTAATTTTTC 58.413 43.478 0.00 0.00 0.00 2.29
3433 8827 4.042435 AGAGGGTTCCGGTCTAATTTTTCA 59.958 41.667 0.00 0.00 0.00 2.69
3434 8828 4.930696 AGGGTTCCGGTCTAATTTTTCAT 58.069 39.130 0.00 0.00 0.00 2.57
3435 8829 5.330233 AGGGTTCCGGTCTAATTTTTCATT 58.670 37.500 0.00 0.00 0.00 2.57
3436 8830 5.778241 AGGGTTCCGGTCTAATTTTTCATTT 59.222 36.000 0.00 0.00 0.00 2.32
3437 8831 6.269077 AGGGTTCCGGTCTAATTTTTCATTTT 59.731 34.615 0.00 0.00 0.00 1.82
3438 8832 6.588756 GGGTTCCGGTCTAATTTTTCATTTTC 59.411 38.462 0.00 0.00 0.00 2.29
3439 8833 6.588756 GGTTCCGGTCTAATTTTTCATTTTCC 59.411 38.462 0.00 0.00 0.00 3.13
3440 8834 7.375834 GTTCCGGTCTAATTTTTCATTTTCCT 58.624 34.615 0.00 0.00 0.00 3.36
3441 8835 6.919721 TCCGGTCTAATTTTTCATTTTCCTG 58.080 36.000 0.00 0.00 0.00 3.86
3442 8836 6.492087 TCCGGTCTAATTTTTCATTTTCCTGT 59.508 34.615 0.00 0.00 0.00 4.00
3443 8837 7.014808 TCCGGTCTAATTTTTCATTTTCCTGTT 59.985 33.333 0.00 0.00 0.00 3.16
3444 8838 7.655732 CCGGTCTAATTTTTCATTTTCCTGTTT 59.344 33.333 0.00 0.00 0.00 2.83
3445 8839 9.685828 CGGTCTAATTTTTCATTTTCCTGTTTA 57.314 29.630 0.00 0.00 0.00 2.01
3452 8846 9.783081 ATTTTTCATTTTCCTGTTTATTCAGCT 57.217 25.926 0.00 0.00 34.47 4.24
3453 8847 9.612066 TTTTTCATTTTCCTGTTTATTCAGCTT 57.388 25.926 0.00 0.00 34.47 3.74
3454 8848 9.612066 TTTTCATTTTCCTGTTTATTCAGCTTT 57.388 25.926 0.00 0.00 34.47 3.51
3455 8849 9.612066 TTTCATTTTCCTGTTTATTCAGCTTTT 57.388 25.926 0.00 0.00 34.47 2.27
3456 8850 9.612066 TTCATTTTCCTGTTTATTCAGCTTTTT 57.388 25.926 0.00 0.00 34.47 1.94
3457 8851 9.260002 TCATTTTCCTGTTTATTCAGCTTTTTC 57.740 29.630 0.00 0.00 34.47 2.29
3458 8852 9.264719 CATTTTCCTGTTTATTCAGCTTTTTCT 57.735 29.630 0.00 0.00 34.47 2.52
3459 8853 8.647143 TTTTCCTGTTTATTCAGCTTTTTCTG 57.353 30.769 0.00 0.00 34.47 3.02
3460 8854 7.581213 TTCCTGTTTATTCAGCTTTTTCTGA 57.419 32.000 0.00 0.00 40.99 3.27
3461 8855 7.765695 TCCTGTTTATTCAGCTTTTTCTGAT 57.234 32.000 0.00 0.00 42.12 2.90
3462 8856 8.181904 TCCTGTTTATTCAGCTTTTTCTGATT 57.818 30.769 0.00 0.00 42.12 2.57
3463 8857 8.641541 TCCTGTTTATTCAGCTTTTTCTGATTT 58.358 29.630 0.00 0.00 42.12 2.17
3464 8858 9.264719 CCTGTTTATTCAGCTTTTTCTGATTTT 57.735 29.630 0.00 0.00 42.12 1.82
3546 8940 9.825972 TCAGAACTACAAATTCGAAATTTGATC 57.174 29.630 25.90 19.64 40.42 2.92
3547 8941 9.611284 CAGAACTACAAATTCGAAATTTGATCA 57.389 29.630 25.90 15.64 40.42 2.92
3590 8984 4.637276 GGAATTCCAAAAACAATTCCGGT 58.363 39.130 20.04 0.00 45.06 5.28
3591 8985 5.060506 GGAATTCCAAAAACAATTCCGGTT 58.939 37.500 20.04 0.00 45.06 4.44
3592 8986 5.178623 GGAATTCCAAAAACAATTCCGGTTC 59.821 40.000 20.04 0.00 45.06 3.62
3593 8987 5.545063 ATTCCAAAAACAATTCCGGTTCT 57.455 34.783 0.00 0.00 0.00 3.01
3594 8988 4.314740 TCCAAAAACAATTCCGGTTCTG 57.685 40.909 0.00 0.00 0.00 3.02
3595 8989 3.954904 TCCAAAAACAATTCCGGTTCTGA 59.045 39.130 0.00 0.00 0.00 3.27
3596 8990 4.402793 TCCAAAAACAATTCCGGTTCTGAA 59.597 37.500 0.00 0.00 0.00 3.02
3597 8991 5.105310 TCCAAAAACAATTCCGGTTCTGAAA 60.105 36.000 0.00 0.00 0.00 2.69
3598 8992 5.582665 CCAAAAACAATTCCGGTTCTGAAAA 59.417 36.000 0.00 0.00 0.00 2.29
3599 8993 6.092807 CCAAAAACAATTCCGGTTCTGAAAAA 59.907 34.615 0.00 0.00 0.00 1.94
3622 9016 9.872721 AAAAATGTTTGGATTTTCAAAGCAATT 57.127 22.222 0.00 0.00 37.31 2.32
3623 9017 8.859517 AAATGTTTGGATTTTCAAAGCAATTG 57.140 26.923 0.00 0.00 37.31 2.32
3624 9018 7.804843 ATGTTTGGATTTTCAAAGCAATTGA 57.195 28.000 10.34 1.23 46.22 2.57
3636 9030 6.849502 TCAAAGCAATTGAAATTTGCAAACA 58.150 28.000 15.41 5.37 44.94 2.83
3637 9031 6.967767 TCAAAGCAATTGAAATTTGCAAACAG 59.032 30.769 15.41 0.00 44.94 3.16
3638 9032 6.680874 AAGCAATTGAAATTTGCAAACAGA 57.319 29.167 15.41 0.00 0.00 3.41
3639 9033 6.680874 AGCAATTGAAATTTGCAAACAGAA 57.319 29.167 15.41 5.67 0.00 3.02
3640 9034 6.721321 AGCAATTGAAATTTGCAAACAGAAG 58.279 32.000 15.41 3.36 0.00 2.85
3641 9035 6.316890 AGCAATTGAAATTTGCAAACAGAAGT 59.683 30.769 15.41 1.81 0.00 3.01
3642 9036 7.495279 AGCAATTGAAATTTGCAAACAGAAGTA 59.505 29.630 15.41 0.00 0.00 2.24
3643 9037 8.284693 GCAATTGAAATTTGCAAACAGAAGTAT 58.715 29.630 15.41 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.017605 CGGTAGCTCATTTTGATAGCTCATTT 60.018 38.462 0.00 0.00 42.89 2.32
48 49 6.914259 TCAAATGCGAAAATAATGTGGTACA 58.086 32.000 0.00 0.00 0.00 2.90
54 55 7.116233 GGTGTTCTTCAAATGCGAAAATAATGT 59.884 33.333 0.00 0.00 0.00 2.71
56 57 6.589907 GGGTGTTCTTCAAATGCGAAAATAAT 59.410 34.615 0.00 0.00 0.00 1.28
59 60 4.202202 TGGGTGTTCTTCAAATGCGAAAAT 60.202 37.500 0.00 0.00 0.00 1.82
140 141 1.014044 CGTTGCCGCTCATACAGTGT 61.014 55.000 0.00 0.00 0.00 3.55
206 207 2.203070 GCGGGCATGGATTCGTCT 60.203 61.111 0.00 0.00 0.00 4.18
386 388 0.535102 CACGAGGCCTCCACTTTTGT 60.535 55.000 27.20 13.99 0.00 2.83
484 522 1.082206 CAACTACCTCCCCTCCCCA 59.918 63.158 0.00 0.00 0.00 4.96
498 536 2.115266 CGCTTTCCCCCACCAACT 59.885 61.111 0.00 0.00 0.00 3.16
594 634 1.218439 AATCCCAATCCCAACCCGGA 61.218 55.000 0.73 0.00 36.56 5.14
605 645 2.184066 GCGCGGCAAAATCCCAAT 59.816 55.556 8.83 0.00 0.00 3.16
631 671 1.154035 GCCTCGGTCCGCAAAATTG 60.154 57.895 6.34 0.00 0.00 2.32
633 673 3.124921 CGCCTCGGTCCGCAAAAT 61.125 61.111 6.34 0.00 0.00 1.82
756 796 1.129811 CCAAAACCGAACATAGCCGAC 59.870 52.381 0.00 0.00 0.00 4.79
774 814 2.806945 AAGATCGATTTTGAGGGCCA 57.193 45.000 6.18 0.00 0.00 5.36
788 828 5.012328 ACCGGTCAGAGATGTAAAAGATC 57.988 43.478 0.00 0.00 0.00 2.75
791 831 5.941948 AAAACCGGTCAGAGATGTAAAAG 57.058 39.130 8.04 0.00 0.00 2.27
798 843 2.829023 TCCCTAAAACCGGTCAGAGAT 58.171 47.619 8.04 0.00 0.00 2.75
800 845 2.500098 TGATCCCTAAAACCGGTCAGAG 59.500 50.000 8.04 4.96 0.00 3.35
804 849 3.345508 AACTGATCCCTAAAACCGGTC 57.654 47.619 8.04 0.00 0.00 4.79
821 866 9.372369 GTACATGTTCTAAGAGCATTTCTAACT 57.628 33.333 2.30 0.00 31.41 2.24
860 909 8.268605 AGGCTTATTTATAGCTTATTAGGGAGC 58.731 37.037 0.00 0.00 38.67 4.70
868 917 8.968969 ACGCTAGTAGGCTTATTTATAGCTTAT 58.031 33.333 0.00 0.00 38.67 1.73
882 938 3.111939 CTGCGACGCTAGTAGGCT 58.888 61.111 22.08 0.00 32.90 4.58
897 953 0.967887 TCCCGAGAGTTGAGAGGCTG 60.968 60.000 0.00 0.00 0.00 4.85
1026 1092 1.609841 GGGCTAAGTGGCACGTAGTTT 60.610 52.381 31.44 16.05 41.61 2.66
1473 1542 3.126000 GTGCCTCATACTCAAGCTTGAAC 59.874 47.826 28.16 16.67 36.64 3.18
1482 1551 1.195115 GGACCAGTGCCTCATACTCA 58.805 55.000 0.00 0.00 0.00 3.41
1494 1563 1.371558 GTCTCCTTTGCGGACCAGT 59.628 57.895 0.00 0.00 36.69 4.00
1501 1570 3.121030 CGCTGGGTCTCCTTTGCG 61.121 66.667 0.00 0.00 39.66 4.85
1758 1827 2.813474 CGGTTCTCGCGGATGCAA 60.813 61.111 6.13 0.00 42.97 4.08
1944 2025 0.682852 TCACCTTGAAACCGATCCGT 59.317 50.000 0.00 0.00 0.00 4.69
2020 2107 3.322466 CGGCAGGAGGTCCCACTT 61.322 66.667 0.00 0.00 37.41 3.16
2052 2139 1.975407 CTGCCTGGCCTTGAGTTGG 60.975 63.158 17.53 0.00 0.00 3.77
2055 2142 3.655211 CCCTGCCTGGCCTTGAGT 61.655 66.667 17.53 0.00 0.00 3.41
2108 2201 0.458370 CATGGTGTCGTCATCGAGCA 60.458 55.000 0.00 0.00 46.96 4.26
2109 2202 0.458543 ACATGGTGTCGTCATCGAGC 60.459 55.000 0.00 0.00 46.96 5.03
2110 2203 1.550065 GACATGGTGTCGTCATCGAG 58.450 55.000 0.00 0.00 46.96 4.04
2319 5366 1.141019 GTTCTCACCGCCGCTGATA 59.859 57.895 0.00 0.00 0.00 2.15
2651 5701 0.464036 TGATGGGACTCGTACATGGC 59.536 55.000 0.00 0.00 0.00 4.40
2661 5711 4.508047 GCCCTTTATCATCATGATGGGACT 60.508 45.833 30.54 17.32 38.98 3.85
2746 5833 4.328536 CTCCGTAGTGCTAGATACATCCT 58.671 47.826 0.00 0.00 0.00 3.24
2761 5848 7.134362 TCCATATATACTACTCCCTCCGTAG 57.866 44.000 0.00 0.00 40.07 3.51
2883 8258 9.598517 ACAACATTGTCAAAAATGACTTAACAT 57.401 25.926 10.03 0.00 39.46 2.71
2966 8342 5.794726 TGTTGTACATACACTGGTACTGT 57.205 39.130 0.00 0.00 42.57 3.55
2967 8343 6.394809 TGATGTTGTACATACACTGGTACTG 58.605 40.000 11.42 0.00 39.27 2.74
2968 8344 6.599356 TGATGTTGTACATACACTGGTACT 57.401 37.500 11.42 0.00 39.27 2.73
2969 8345 7.661127 TTTGATGTTGTACATACACTGGTAC 57.339 36.000 11.42 0.00 39.27 3.34
2972 8348 7.910162 GCTAATTTGATGTTGTACATACACTGG 59.090 37.037 11.42 1.95 39.27 4.00
3071 8448 6.094048 GGTGTTAAGTCGTACTGTACCTATCA 59.906 42.308 12.08 2.79 0.00 2.15
3081 8458 5.470098 TCTTAAGACGGTGTTAAGTCGTACT 59.530 40.000 27.03 0.00 41.86 2.73
3082 8459 5.689819 TCTTAAGACGGTGTTAAGTCGTAC 58.310 41.667 27.03 0.00 41.86 3.67
3083 8460 5.940192 TCTTAAGACGGTGTTAAGTCGTA 57.060 39.130 27.03 12.74 41.86 3.43
3084 8461 4.836125 TCTTAAGACGGTGTTAAGTCGT 57.164 40.909 27.03 0.00 41.86 4.34
3085 8462 5.396484 TGATCTTAAGACGGTGTTAAGTCG 58.604 41.667 27.03 11.51 41.86 4.18
3096 8473 4.560819 GTGCTCTGAGTTGATCTTAAGACG 59.439 45.833 7.48 0.00 0.00 4.18
3127 8504 0.991920 TCGCCTCCTCCCTTTTCAAT 59.008 50.000 0.00 0.00 0.00 2.57
3262 8653 5.574891 ACAGCAACAACTTGTCACAAATA 57.425 34.783 0.00 0.00 0.00 1.40
3279 8670 7.327275 CGGTTACTTAATTTTTGCATAACAGCA 59.673 33.333 0.00 0.00 43.99 4.41
3286 8677 6.988522 AGGTTCGGTTACTTAATTTTTGCAT 58.011 32.000 0.00 0.00 0.00 3.96
3295 8686 4.497300 CCAATCGAGGTTCGGTTACTTAA 58.503 43.478 0.00 0.00 41.88 1.85
3296 8687 3.676873 GCCAATCGAGGTTCGGTTACTTA 60.677 47.826 0.00 0.00 41.88 2.24
3300 8694 0.108041 GGCCAATCGAGGTTCGGTTA 60.108 55.000 0.00 0.00 41.88 2.85
3321 8715 7.054124 TCTTTCACTTATTGTAGCTAATGGGG 58.946 38.462 0.00 0.00 0.00 4.96
3336 8730 6.936900 CCAAACAAGGATCTCTCTTTCACTTA 59.063 38.462 0.00 0.00 0.00 2.24
3337 8731 5.767168 CCAAACAAGGATCTCTCTTTCACTT 59.233 40.000 0.00 0.00 0.00 3.16
3338 8732 5.312079 CCAAACAAGGATCTCTCTTTCACT 58.688 41.667 0.00 0.00 0.00 3.41
3339 8733 4.457257 CCCAAACAAGGATCTCTCTTTCAC 59.543 45.833 0.00 0.00 0.00 3.18
3340 8734 4.507335 CCCCAAACAAGGATCTCTCTTTCA 60.507 45.833 0.00 0.00 0.00 2.69
3341 8735 4.013050 CCCCAAACAAGGATCTCTCTTTC 58.987 47.826 0.00 0.00 0.00 2.62
3342 8736 3.657727 TCCCCAAACAAGGATCTCTCTTT 59.342 43.478 0.00 0.00 0.00 2.52
3343 8737 3.260205 TCCCCAAACAAGGATCTCTCTT 58.740 45.455 0.00 0.00 0.00 2.85
3344 8738 2.921221 TCCCCAAACAAGGATCTCTCT 58.079 47.619 0.00 0.00 0.00 3.10
3345 8739 3.348119 GTTCCCCAAACAAGGATCTCTC 58.652 50.000 0.00 0.00 37.82 3.20
3346 8740 2.041755 GGTTCCCCAAACAAGGATCTCT 59.958 50.000 0.00 0.00 39.81 3.10
3347 8741 2.041755 AGGTTCCCCAAACAAGGATCTC 59.958 50.000 0.00 0.00 39.81 2.75
3348 8742 2.073776 AGGTTCCCCAAACAAGGATCT 58.926 47.619 0.00 0.00 39.81 2.75
3349 8743 2.604912 AGGTTCCCCAAACAAGGATC 57.395 50.000 0.00 0.00 39.81 3.36
3350 8744 3.239449 GAAAGGTTCCCCAAACAAGGAT 58.761 45.455 0.00 0.00 39.81 3.24
3351 8745 2.023888 TGAAAGGTTCCCCAAACAAGGA 60.024 45.455 0.00 0.00 39.81 3.36
3352 8746 2.365293 CTGAAAGGTTCCCCAAACAAGG 59.635 50.000 0.00 0.00 39.81 3.61
3353 8747 3.295973 TCTGAAAGGTTCCCCAAACAAG 58.704 45.455 0.00 0.00 39.81 3.16
3354 8748 3.390175 TCTGAAAGGTTCCCCAAACAA 57.610 42.857 0.00 0.00 39.81 2.83
3355 8749 3.230134 CATCTGAAAGGTTCCCCAAACA 58.770 45.455 0.00 0.00 39.81 2.83
3356 8750 2.562738 CCATCTGAAAGGTTCCCCAAAC 59.437 50.000 0.00 0.00 37.12 2.93
3357 8751 2.492567 CCCATCTGAAAGGTTCCCCAAA 60.493 50.000 0.00 0.00 0.00 3.28
3358 8752 1.077005 CCCATCTGAAAGGTTCCCCAA 59.923 52.381 0.00 0.00 0.00 4.12
3359 8753 0.704076 CCCATCTGAAAGGTTCCCCA 59.296 55.000 0.00 0.00 0.00 4.96
3360 8754 0.684479 GCCCATCTGAAAGGTTCCCC 60.684 60.000 0.00 0.00 0.00 4.81
3361 8755 0.684479 GGCCCATCTGAAAGGTTCCC 60.684 60.000 0.00 0.00 0.00 3.97
3362 8756 0.039618 TGGCCCATCTGAAAGGTTCC 59.960 55.000 0.00 1.35 0.00 3.62
3363 8757 1.467920 CTGGCCCATCTGAAAGGTTC 58.532 55.000 0.00 0.00 0.00 3.62
3364 8758 0.613012 GCTGGCCCATCTGAAAGGTT 60.613 55.000 0.00 0.00 0.00 3.50
3365 8759 1.000396 GCTGGCCCATCTGAAAGGT 60.000 57.895 0.00 0.00 0.00 3.50
3366 8760 0.750911 GAGCTGGCCCATCTGAAAGG 60.751 60.000 0.00 0.00 0.00 3.11
3367 8761 0.034767 TGAGCTGGCCCATCTGAAAG 60.035 55.000 0.00 0.00 0.00 2.62
3368 8762 0.627451 ATGAGCTGGCCCATCTGAAA 59.373 50.000 0.00 0.00 0.00 2.69
3369 8763 0.182061 GATGAGCTGGCCCATCTGAA 59.818 55.000 11.30 0.00 36.97 3.02
3370 8764 0.984432 TGATGAGCTGGCCCATCTGA 60.984 55.000 17.35 0.27 39.75 3.27
3371 8765 0.106868 TTGATGAGCTGGCCCATCTG 60.107 55.000 17.35 0.00 39.75 2.90
3372 8766 0.106819 GTTGATGAGCTGGCCCATCT 60.107 55.000 17.35 4.96 39.75 2.90
3373 8767 1.442526 CGTTGATGAGCTGGCCCATC 61.443 60.000 11.58 11.58 39.55 3.51
3374 8768 1.452651 CGTTGATGAGCTGGCCCAT 60.453 57.895 0.00 0.00 0.00 4.00
3375 8769 2.046023 CGTTGATGAGCTGGCCCA 60.046 61.111 0.00 0.00 0.00 5.36
3376 8770 2.825836 CCGTTGATGAGCTGGCCC 60.826 66.667 0.00 0.00 0.00 5.80
3377 8771 2.825836 CCCGTTGATGAGCTGGCC 60.826 66.667 0.00 0.00 0.00 5.36
3378 8772 1.244019 AAACCCGTTGATGAGCTGGC 61.244 55.000 0.00 0.00 0.00 4.85
3379 8773 1.068333 CAAAACCCGTTGATGAGCTGG 60.068 52.381 0.00 0.00 0.00 4.85
3380 8774 1.068333 CCAAAACCCGTTGATGAGCTG 60.068 52.381 0.00 0.00 0.00 4.24
3381 8775 1.247567 CCAAAACCCGTTGATGAGCT 58.752 50.000 0.00 0.00 0.00 4.09
3382 8776 0.243636 CCCAAAACCCGTTGATGAGC 59.756 55.000 0.00 0.00 0.00 4.26
3383 8777 1.904287 TCCCAAAACCCGTTGATGAG 58.096 50.000 0.00 0.00 0.00 2.90
3384 8778 1.957877 GTTCCCAAAACCCGTTGATGA 59.042 47.619 0.00 0.00 0.00 2.92
3385 8779 1.000394 GGTTCCCAAAACCCGTTGATG 60.000 52.381 0.00 0.00 34.26 3.07
3386 8780 1.133294 AGGTTCCCAAAACCCGTTGAT 60.133 47.619 3.39 0.00 41.18 2.57
3387 8781 0.259356 AGGTTCCCAAAACCCGTTGA 59.741 50.000 3.39 0.00 41.18 3.18
3388 8782 1.067974 GAAGGTTCCCAAAACCCGTTG 59.932 52.381 3.39 0.00 41.18 4.10
3389 8783 1.063492 AGAAGGTTCCCAAAACCCGTT 60.063 47.619 3.39 0.00 41.18 4.44
3390 8784 0.554305 AGAAGGTTCCCAAAACCCGT 59.446 50.000 3.39 0.00 41.18 5.28
3391 8785 2.039348 TCTAGAAGGTTCCCAAAACCCG 59.961 50.000 3.39 0.00 41.18 5.28
3392 8786 3.561528 CCTCTAGAAGGTTCCCAAAACCC 60.562 52.174 3.39 0.00 41.18 4.11
3393 8787 3.561528 CCCTCTAGAAGGTTCCCAAAACC 60.562 52.174 0.00 0.00 44.56 3.27
3394 8788 3.074094 ACCCTCTAGAAGGTTCCCAAAAC 59.926 47.826 7.25 0.00 44.56 2.43
3395 8789 3.332968 ACCCTCTAGAAGGTTCCCAAAA 58.667 45.455 7.25 0.00 44.56 2.44
3396 8790 2.999928 ACCCTCTAGAAGGTTCCCAAA 58.000 47.619 7.25 0.00 44.56 3.28
3397 8791 2.735259 ACCCTCTAGAAGGTTCCCAA 57.265 50.000 7.25 0.00 44.56 4.12
3398 8792 2.735259 AACCCTCTAGAAGGTTCCCA 57.265 50.000 18.47 0.00 42.85 4.37
3403 8797 0.412640 ACCGGAACCCTCTAGAAGGT 59.587 55.000 9.46 7.25 44.56 3.50
3404 8798 1.112950 GACCGGAACCCTCTAGAAGG 58.887 60.000 9.46 5.79 45.77 3.46
3405 8799 2.146920 AGACCGGAACCCTCTAGAAG 57.853 55.000 9.46 0.00 0.00 2.85
3406 8800 3.744940 TTAGACCGGAACCCTCTAGAA 57.255 47.619 9.46 0.00 0.00 2.10
3407 8801 3.967467 ATTAGACCGGAACCCTCTAGA 57.033 47.619 9.46 0.00 0.00 2.43
3408 8802 5.354842 AAAATTAGACCGGAACCCTCTAG 57.645 43.478 9.46 0.00 0.00 2.43
3409 8803 5.248934 TGAAAAATTAGACCGGAACCCTCTA 59.751 40.000 9.46 0.51 0.00 2.43
3410 8804 4.042435 TGAAAAATTAGACCGGAACCCTCT 59.958 41.667 9.46 1.74 0.00 3.69
3411 8805 4.329392 TGAAAAATTAGACCGGAACCCTC 58.671 43.478 9.46 0.00 0.00 4.30
3412 8806 4.376225 TGAAAAATTAGACCGGAACCCT 57.624 40.909 9.46 1.71 0.00 4.34
3413 8807 5.654603 AATGAAAAATTAGACCGGAACCC 57.345 39.130 9.46 0.00 0.00 4.11
3414 8808 6.588756 GGAAAATGAAAAATTAGACCGGAACC 59.411 38.462 9.46 0.00 0.00 3.62
3415 8809 7.328493 CAGGAAAATGAAAAATTAGACCGGAAC 59.672 37.037 9.46 0.99 0.00 3.62
3416 8810 7.014808 ACAGGAAAATGAAAAATTAGACCGGAA 59.985 33.333 9.46 0.00 0.00 4.30
3417 8811 6.492087 ACAGGAAAATGAAAAATTAGACCGGA 59.508 34.615 9.46 0.00 0.00 5.14
3418 8812 6.687604 ACAGGAAAATGAAAAATTAGACCGG 58.312 36.000 0.00 0.00 0.00 5.28
3419 8813 8.587952 AAACAGGAAAATGAAAAATTAGACCG 57.412 30.769 0.00 0.00 0.00 4.79
3426 8820 9.783081 AGCTGAATAAACAGGAAAATGAAAAAT 57.217 25.926 0.00 0.00 38.22 1.82
3427 8821 9.612066 AAGCTGAATAAACAGGAAAATGAAAAA 57.388 25.926 0.00 0.00 38.22 1.94
3428 8822 9.612066 AAAGCTGAATAAACAGGAAAATGAAAA 57.388 25.926 0.00 0.00 38.22 2.29
3429 8823 9.612066 AAAAGCTGAATAAACAGGAAAATGAAA 57.388 25.926 0.00 0.00 38.22 2.69
3430 8824 9.612066 AAAAAGCTGAATAAACAGGAAAATGAA 57.388 25.926 0.00 0.00 38.22 2.57
3431 8825 9.260002 GAAAAAGCTGAATAAACAGGAAAATGA 57.740 29.630 0.00 0.00 38.22 2.57
3432 8826 9.264719 AGAAAAAGCTGAATAAACAGGAAAATG 57.735 29.630 0.00 0.00 38.22 2.32
3433 8827 9.264719 CAGAAAAAGCTGAATAAACAGGAAAAT 57.735 29.630 0.00 0.00 38.14 1.82
3434 8828 8.474025 TCAGAAAAAGCTGAATAAACAGGAAAA 58.526 29.630 0.00 0.00 41.65 2.29
3435 8829 8.006298 TCAGAAAAAGCTGAATAAACAGGAAA 57.994 30.769 0.00 0.00 41.65 3.13
3436 8830 7.581213 TCAGAAAAAGCTGAATAAACAGGAA 57.419 32.000 0.00 0.00 41.65 3.36
3437 8831 7.765695 ATCAGAAAAAGCTGAATAAACAGGA 57.234 32.000 0.00 0.00 46.94 3.86
3438 8832 8.822652 AAATCAGAAAAAGCTGAATAAACAGG 57.177 30.769 0.00 0.00 46.94 4.00
3520 8914 9.825972 GATCAAATTTCGAATTTGTAGTTCTGA 57.174 29.630 21.58 13.85 39.36 3.27
3521 8915 9.611284 TGATCAAATTTCGAATTTGTAGTTCTG 57.389 29.630 21.58 10.40 39.36 3.02
3569 8963 5.989168 AGAACCGGAATTGTTTTTGGAATTC 59.011 36.000 9.46 0.00 37.69 2.17
3570 8964 5.757808 CAGAACCGGAATTGTTTTTGGAATT 59.242 36.000 9.46 0.00 0.00 2.17
3571 8965 5.069781 TCAGAACCGGAATTGTTTTTGGAAT 59.930 36.000 9.46 0.00 0.00 3.01
3572 8966 4.402793 TCAGAACCGGAATTGTTTTTGGAA 59.597 37.500 9.46 0.00 0.00 3.53
3573 8967 3.954904 TCAGAACCGGAATTGTTTTTGGA 59.045 39.130 9.46 0.00 0.00 3.53
3574 8968 4.314740 TCAGAACCGGAATTGTTTTTGG 57.685 40.909 9.46 0.00 0.00 3.28
3575 8969 6.654793 TTTTCAGAACCGGAATTGTTTTTG 57.345 33.333 9.46 0.00 0.00 2.44
3596 8990 9.872721 AATTGCTTTGAAAATCCAAACATTTTT 57.127 22.222 0.00 0.00 36.33 1.94
3597 8991 9.303537 CAATTGCTTTGAAAATCCAAACATTTT 57.696 25.926 0.00 0.00 38.43 1.82
3598 8992 8.684520 TCAATTGCTTTGAAAATCCAAACATTT 58.315 25.926 0.00 0.00 41.38 2.32
3599 8993 8.223177 TCAATTGCTTTGAAAATCCAAACATT 57.777 26.923 0.00 0.00 41.38 2.71
3600 8994 7.804843 TCAATTGCTTTGAAAATCCAAACAT 57.195 28.000 0.00 0.00 41.38 2.71
3620 9014 8.702438 CGAATACTTCTGTTTGCAAATTTCAAT 58.298 29.630 16.21 3.36 0.00 2.57
3621 9015 8.060020 CGAATACTTCTGTTTGCAAATTTCAA 57.940 30.769 16.21 5.52 0.00 2.69
3622 9016 7.621832 CGAATACTTCTGTTTGCAAATTTCA 57.378 32.000 16.21 7.95 0.00 2.69


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

AutoCloner maintained by Alex Coulton.