Multiple sequence alignment - TraesCS5B01G203900

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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 TraesCS5B01G203900 chr5B 100.000 4345 0 0 1 4345 372084093 372079749 0.000000e+00 8024.0
1 TraesCS5B01G203900 chr5D 93.520 3148 118 35 774 3880 320875536 320872434 0.000000e+00 4604.0
2 TraesCS5B01G203900 chr5D 89.740 692 32 16 41 700 320876217 320875533 0.000000e+00 848.0
3 TraesCS5B01G203900 chr5D 88.114 387 41 4 3959 4345 320872424 320872043 5.120000e-124 455.0
4 TraesCS5B01G203900 chr5D 98.214 56 1 0 719 774 81731153 81731208 9.940000e-17 99.0
5 TraesCS5B01G203900 chr5A 93.284 2978 139 22 774 3692 413427753 413430728 0.000000e+00 4335.0
6 TraesCS5B01G203900 chr5A 90.149 670 43 8 41 692 413427080 413427744 0.000000e+00 850.0
7 TraesCS5B01G203900 chr5A 86.054 631 69 10 3718 4345 413430838 413431452 0.000000e+00 660.0
8 TraesCS5B01G203900 chr5A 96.610 59 2 0 719 777 502591944 502591886 9.940000e-17 99.0
9 TraesCS5B01G203900 chr7A 80.241 415 69 9 2406 2812 471551458 471551867 2.540000e-77 300.0
10 TraesCS5B01G203900 chr7A 80.952 105 20 0 2631 2735 107916701 107916597 2.780000e-12 84.2
11 TraesCS5B01G203900 chr7D 80.096 417 66 10 2406 2812 410522548 410522139 1.180000e-75 294.0
12 TraesCS5B01G203900 chr7D 96.667 60 1 1 719 778 605155284 605155226 9.940000e-17 99.0
13 TraesCS5B01G203900 chr7D 87.654 81 5 1 699 774 34961976 34961896 5.980000e-14 89.8
14 TraesCS5B01G203900 chr7B 85.098 255 35 3 1698 1950 425158274 425158527 1.550000e-64 257.0
15 TraesCS5B01G203900 chr7B 79.625 373 58 11 2406 2769 425158910 425159273 7.210000e-63 252.0
16 TraesCS5B01G203900 chr7B 81.905 105 19 0 2631 2735 61627835 61627731 5.980000e-14 89.8
17 TraesCS5B01G203900 chr3D 96.667 60 2 0 719 778 590284935 590284994 2.760000e-17 100.0
18 TraesCS5B01G203900 chr3D 98.214 56 1 0 719 774 68586421 68586476 9.940000e-17 99.0
19 TraesCS5B01G203900 chr6D 96.667 60 1 1 719 777 38859817 38859876 9.940000e-17 99.0
20 TraesCS5B01G203900 chr6A 98.214 56 1 0 719 774 121184526 121184581 9.940000e-17 99.0
21 TraesCS5B01G203900 chr2D 83.654 104 11 4 2629 2729 100432471 100432571 4.630000e-15 93.5
22 TraesCS5B01G203900 chr2D 92.424 66 4 1 719 784 151483435 151483499 4.630000e-15 93.5
23 TraesCS5B01G203900 chr2B 83.654 104 11 4 2629 2729 152504546 152504646 4.630000e-15 93.5
24 TraesCS5B01G203900 chr3B 100.000 39 0 0 2 40 490023441 490023403 6.030000e-09 73.1
25 TraesCS5B01G203900 chrUn 97.500 40 1 0 1 40 382168899 382168938 7.800000e-08 69.4


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 TraesCS5B01G203900 chr5B 372079749 372084093 4344 True 8024.000000 8024 100.0000 1 4345 1 chr5B.!!$R1 4344
1 TraesCS5B01G203900 chr5D 320872043 320876217 4174 True 1969.000000 4604 90.4580 41 4345 3 chr5D.!!$R1 4304
2 TraesCS5B01G203900 chr5A 413427080 413431452 4372 False 1948.333333 4335 89.8290 41 4345 3 chr5A.!!$F1 4304
3 TraesCS5B01G203900 chr7B 425158274 425159273 999 False 254.500000 257 82.3615 1698 2769 2 chr7B.!!$F1 1071

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
109 116 0.036858 TGTGGCACGTAAGCTATGCA 60.037 50.0 13.77 0.0 41.27 3.96 F
580 628 0.249120 TAATGGAGTGACCGCACCAG 59.751 55.0 5.98 0.0 46.32 4.00 F
2058 2145 0.657368 GCCACTTTCGTTCACTTGCG 60.657 55.0 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 2106 0.251165 GACAAGGGCCAGGCAAGTAA 60.251 55.0 15.19 0.00 0.00 2.24 R
2081 2170 1.348538 TTCCACACATTAGACGCGCG 61.349 55.0 30.96 30.96 0.00 6.86 R
3749 4151 0.038744 CCTCCAAGGTGAGGCAACAT 59.961 55.0 0.00 0.00 45.13 2.71 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
17 18 3.724494 GACCTCTAATGCCGCTGC 58.276 61.111 0.00 0.00 38.26 5.25
18 19 1.889573 GACCTCTAATGCCGCTGCC 60.890 63.158 0.00 0.00 36.33 4.85
19 20 2.317149 GACCTCTAATGCCGCTGCCT 62.317 60.000 0.00 0.00 36.33 4.75
20 21 1.048724 ACCTCTAATGCCGCTGCCTA 61.049 55.000 0.00 0.00 36.33 3.93
21 22 0.106708 CCTCTAATGCCGCTGCCTAA 59.893 55.000 0.00 0.00 36.33 2.69
22 23 1.271054 CCTCTAATGCCGCTGCCTAAT 60.271 52.381 0.00 0.00 36.33 1.73
23 24 2.072298 CTCTAATGCCGCTGCCTAATC 58.928 52.381 0.00 0.00 36.33 1.75
24 25 1.416030 TCTAATGCCGCTGCCTAATCA 59.584 47.619 0.00 0.00 36.33 2.57
25 26 1.802960 CTAATGCCGCTGCCTAATCAG 59.197 52.381 0.00 0.00 36.33 2.90
49 50 5.862860 GCCTTATAATTAGTACTCGAGTGCC 59.137 44.000 28.12 17.46 0.00 5.01
65 66 4.248058 GAGTGCCCATTTTGGAATTTCTG 58.752 43.478 0.00 0.00 40.96 3.02
73 74 6.462207 CCCATTTTGGAATTTCTGTGTGTACA 60.462 38.462 0.00 0.00 40.96 2.90
80 81 8.402798 TGGAATTTCTGTGTGTACAATATTGT 57.597 30.769 23.80 23.80 44.86 2.71
95 96 5.182001 ACAATATTGTTGTCTCTTCTGTGGC 59.818 40.000 15.47 0.00 38.47 5.01
109 116 0.036858 TGTGGCACGTAAGCTATGCA 60.037 50.000 13.77 0.00 41.27 3.96
142 154 8.872845 GGGAACATTTTGCATAAATTGAGTAAG 58.127 33.333 0.00 0.00 33.54 2.34
192 204 2.438434 CGTCCATTGAGCCCACCC 60.438 66.667 0.00 0.00 0.00 4.61
207 219 1.078759 CACCCGTCAGTCAGCGATTC 61.079 60.000 0.00 0.00 0.00 2.52
298 343 7.014615 GGCATATGAATTTGGTAGGATCTTTGT 59.985 37.037 6.97 0.00 0.00 2.83
326 371 7.220741 TGATCTCTACCGATCTTGAAATAGG 57.779 40.000 0.00 0.00 40.32 2.57
364 409 7.148623 GGTTGGACGAATATTATTAGCAGCTAC 60.149 40.741 0.00 0.00 0.00 3.58
365 410 7.228314 TGGACGAATATTATTAGCAGCTACT 57.772 36.000 0.00 0.00 0.00 2.57
366 411 7.313646 TGGACGAATATTATTAGCAGCTACTC 58.686 38.462 0.00 0.00 0.00 2.59
367 412 7.176865 TGGACGAATATTATTAGCAGCTACTCT 59.823 37.037 0.00 0.00 0.00 3.24
368 413 8.675504 GGACGAATATTATTAGCAGCTACTCTA 58.324 37.037 0.00 0.00 0.00 2.43
436 481 5.841957 AATGGCTTCCAAATATGAGTGAC 57.158 39.130 0.00 0.00 36.95 3.67
514 562 1.053424 ACAAGTAAACCCTCTCGGCA 58.947 50.000 0.00 0.00 33.26 5.69
580 628 0.249120 TAATGGAGTGACCGCACCAG 59.751 55.000 5.98 0.00 46.32 4.00
582 630 1.480212 ATGGAGTGACCGCACCAGAA 61.480 55.000 5.98 0.00 46.32 3.02
709 757 4.563140 TTTTAGCAAATACTCCCTCCGT 57.437 40.909 0.00 0.00 0.00 4.69
710 758 4.563140 TTTAGCAAATACTCCCTCCGTT 57.437 40.909 0.00 0.00 0.00 4.44
711 759 4.563140 TTAGCAAATACTCCCTCCGTTT 57.437 40.909 0.00 0.00 0.00 3.60
712 760 2.987232 AGCAAATACTCCCTCCGTTTC 58.013 47.619 0.00 0.00 0.00 2.78
713 761 2.304761 AGCAAATACTCCCTCCGTTTCA 59.695 45.455 0.00 0.00 0.00 2.69
714 762 3.078837 GCAAATACTCCCTCCGTTTCAA 58.921 45.455 0.00 0.00 0.00 2.69
715 763 3.504520 GCAAATACTCCCTCCGTTTCAAA 59.495 43.478 0.00 0.00 0.00 2.69
716 764 4.022676 GCAAATACTCCCTCCGTTTCAAAA 60.023 41.667 0.00 0.00 0.00 2.44
717 765 5.699839 CAAATACTCCCTCCGTTTCAAAAG 58.300 41.667 0.00 0.00 0.00 2.27
718 766 4.635699 ATACTCCCTCCGTTTCAAAAGT 57.364 40.909 0.00 0.00 0.00 2.66
719 767 3.292492 ACTCCCTCCGTTTCAAAAGTT 57.708 42.857 0.00 0.00 0.00 2.66
720 768 2.949644 ACTCCCTCCGTTTCAAAAGTTG 59.050 45.455 0.00 0.00 0.00 3.16
721 769 3.211045 CTCCCTCCGTTTCAAAAGTTGA 58.789 45.455 0.00 0.00 38.04 3.18
722 770 3.821033 CTCCCTCCGTTTCAAAAGTTGAT 59.179 43.478 0.00 0.00 39.84 2.57
723 771 4.975631 TCCCTCCGTTTCAAAAGTTGATA 58.024 39.130 0.00 0.00 39.84 2.15
724 772 4.758165 TCCCTCCGTTTCAAAAGTTGATAC 59.242 41.667 2.58 2.58 39.84 2.24
725 773 4.517453 CCCTCCGTTTCAAAAGTTGATACA 59.483 41.667 10.70 0.00 40.29 2.29
726 774 5.183140 CCCTCCGTTTCAAAAGTTGATACAT 59.817 40.000 10.70 0.00 40.29 2.29
727 775 6.314784 CCTCCGTTTCAAAAGTTGATACATC 58.685 40.000 10.70 0.00 40.29 3.06
728 776 6.249035 TCCGTTTCAAAAGTTGATACATCC 57.751 37.500 10.70 0.00 40.29 3.51
729 777 5.086058 CCGTTTCAAAAGTTGATACATCCG 58.914 41.667 10.70 0.00 40.29 4.18
730 778 5.334569 CCGTTTCAAAAGTTGATACATCCGT 60.335 40.000 10.70 0.00 40.29 4.69
731 779 6.128499 CCGTTTCAAAAGTTGATACATCCGTA 60.128 38.462 10.70 0.00 40.29 4.02
732 780 7.413657 CCGTTTCAAAAGTTGATACATCCGTAT 60.414 37.037 10.70 0.00 40.29 3.06
733 781 7.960738 CGTTTCAAAAGTTGATACATCCGTATT 59.039 33.333 10.70 0.00 40.29 1.89
734 782 9.620660 GTTTCAAAAGTTGATACATCCGTATTT 57.379 29.630 6.68 0.00 40.11 1.40
737 785 9.878667 TCAAAAGTTGATACATCCGTATTTAGA 57.121 29.630 0.00 0.00 38.48 2.10
738 786 9.916397 CAAAAGTTGATACATCCGTATTTAGAC 57.084 33.333 0.00 0.00 38.48 2.59
739 787 9.661563 AAAAGTTGATACATCCGTATTTAGACA 57.338 29.630 0.00 0.00 38.48 3.41
740 788 9.661563 AAAGTTGATACATCCGTATTTAGACAA 57.338 29.630 0.00 0.00 38.48 3.18
741 789 9.661563 AAGTTGATACATCCGTATTTAGACAAA 57.338 29.630 0.00 0.00 38.48 2.83
742 790 9.832445 AGTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
744 792 8.827177 TGATACATCCGTATTTAGACAAATCC 57.173 34.615 0.00 0.00 38.48 3.01
745 793 8.425703 TGATACATCCGTATTTAGACAAATCCA 58.574 33.333 0.00 0.00 38.48 3.41
746 794 9.268268 GATACATCCGTATTTAGACAAATCCAA 57.732 33.333 0.00 0.00 38.48 3.53
747 795 7.553881 ACATCCGTATTTAGACAAATCCAAG 57.446 36.000 0.00 0.00 35.88 3.61
748 796 7.335627 ACATCCGTATTTAGACAAATCCAAGA 58.664 34.615 0.00 0.00 35.88 3.02
749 797 7.280205 ACATCCGTATTTAGACAAATCCAAGAC 59.720 37.037 0.00 0.00 35.88 3.01
750 798 6.703319 TCCGTATTTAGACAAATCCAAGACA 58.297 36.000 0.00 0.00 35.88 3.41
751 799 7.162761 TCCGTATTTAGACAAATCCAAGACAA 58.837 34.615 0.00 0.00 35.88 3.18
752 800 7.333423 TCCGTATTTAGACAAATCCAAGACAAG 59.667 37.037 0.00 0.00 35.88 3.16
753 801 7.333423 CCGTATTTAGACAAATCCAAGACAAGA 59.667 37.037 0.00 0.00 35.88 3.02
754 802 8.717821 CGTATTTAGACAAATCCAAGACAAGAA 58.282 33.333 0.00 0.00 35.88 2.52
759 807 9.748708 TTAGACAAATCCAAGACAAGAATTTTG 57.251 29.630 0.00 0.00 0.00 2.44
760 808 7.212274 AGACAAATCCAAGACAAGAATTTTGG 58.788 34.615 0.00 0.00 41.09 3.28
761 809 6.290605 ACAAATCCAAGACAAGAATTTTGGG 58.709 36.000 4.84 0.00 40.33 4.12
762 810 6.099557 ACAAATCCAAGACAAGAATTTTGGGA 59.900 34.615 4.84 0.00 40.33 4.37
763 811 5.728637 ATCCAAGACAAGAATTTTGGGAC 57.271 39.130 4.84 0.00 40.33 4.46
764 812 3.568007 TCCAAGACAAGAATTTTGGGACG 59.432 43.478 4.84 0.00 40.33 4.79
765 813 3.305335 CCAAGACAAGAATTTTGGGACGG 60.305 47.826 0.00 0.00 37.11 4.79
766 814 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
767 815 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
768 816 3.072476 AGACAAGAATTTTGGGACGGAGA 59.928 43.478 0.00 0.00 0.00 3.71
769 817 3.412386 ACAAGAATTTTGGGACGGAGAG 58.588 45.455 0.00 0.00 0.00 3.20
770 818 3.072476 ACAAGAATTTTGGGACGGAGAGA 59.928 43.478 0.00 0.00 0.00 3.10
771 819 3.618690 AGAATTTTGGGACGGAGAGAG 57.381 47.619 0.00 0.00 0.00 3.20
772 820 2.907042 AGAATTTTGGGACGGAGAGAGT 59.093 45.455 0.00 0.00 0.00 3.24
773 821 4.094476 AGAATTTTGGGACGGAGAGAGTA 58.906 43.478 0.00 0.00 0.00 2.59
774 822 4.530946 AGAATTTTGGGACGGAGAGAGTAA 59.469 41.667 0.00 0.00 0.00 2.24
775 823 5.189934 AGAATTTTGGGACGGAGAGAGTAAT 59.810 40.000 0.00 0.00 0.00 1.89
776 824 6.383147 AGAATTTTGGGACGGAGAGAGTAATA 59.617 38.462 0.00 0.00 0.00 0.98
777 825 6.555463 ATTTTGGGACGGAGAGAGTAATAA 57.445 37.500 0.00 0.00 0.00 1.40
778 826 6.555463 TTTTGGGACGGAGAGAGTAATAAT 57.445 37.500 0.00 0.00 0.00 1.28
779 827 7.664552 TTTTGGGACGGAGAGAGTAATAATA 57.335 36.000 0.00 0.00 0.00 0.98
862 913 6.457355 TGAGAAGTTTATTACTACGTGCCAA 58.543 36.000 0.00 0.00 35.54 4.52
880 932 3.055819 GCCAATAATCTCCGGCTCTATCA 60.056 47.826 0.00 0.00 41.50 2.15
978 1039 6.824196 TCTCGCTATCTCAGTTTCTCTCTTTA 59.176 38.462 0.00 0.00 0.00 1.85
990 1055 9.535878 CAGTTTCTCTCTTTATTACATCCTACC 57.464 37.037 0.00 0.00 0.00 3.18
991 1056 9.495382 AGTTTCTCTCTTTATTACATCCTACCT 57.505 33.333 0.00 0.00 0.00 3.08
1009 1075 5.010719 CCTACCTATTCTCTAATGGCGTTCA 59.989 44.000 0.00 0.00 0.00 3.18
1026 1092 2.921435 ATGGCGGCCATGATCACT 59.079 55.556 32.54 8.59 43.39 3.41
1051 1117 3.374402 CCTCGGCTGTCTCGGTGT 61.374 66.667 0.00 0.00 0.00 4.16
1054 1120 2.029073 CGGCTGTCTCGGTGTTGT 59.971 61.111 0.00 0.00 0.00 3.32
1066 1132 3.286751 TGTTGTTGCTGAGGGCGC 61.287 61.111 0.00 0.00 45.43 6.53
1107 1173 0.687354 ACTTCCTGACGCCAATGAGT 59.313 50.000 0.00 0.00 0.00 3.41
1147 1213 2.122547 AGGGTGTTCACGGTCCCT 60.123 61.111 0.00 0.00 44.62 4.20
1276 1342 0.806102 CCATTACGTGCTCTGGTCGG 60.806 60.000 0.00 0.00 0.00 4.79
1304 1370 3.335579 ACGGTGAGAATTTAAGACAGCC 58.664 45.455 0.00 0.00 0.00 4.85
1385 1459 2.391389 CCGCGTTTCAGGGAAGCTC 61.391 63.158 4.92 0.00 0.00 4.09
1618 1694 1.361668 AAGCTCAAGGTACGCATGCG 61.362 55.000 36.79 36.79 46.03 4.73
1620 1696 2.047750 TCAAGGTACGCATGCGCA 60.048 55.556 38.15 25.56 44.19 6.09
1621 1697 2.098298 CAAGGTACGCATGCGCAC 59.902 61.111 38.15 34.28 44.19 5.34
1961 2044 2.413765 GAGTCACGATCGCCCTCC 59.586 66.667 16.60 0.00 0.00 4.30
2019 2106 1.152525 ACACCACTCACTCCCTCGT 60.153 57.895 0.00 0.00 0.00 4.18
2058 2145 0.657368 GCCACTTTCGTTCACTTGCG 60.657 55.000 0.00 0.00 0.00 4.85
2081 2170 2.733552 CCACATCTCGCATAGTGCATAC 59.266 50.000 2.63 0.00 45.36 2.39
2798 3074 1.078143 GCCGACCAGCTCTCCAAAT 60.078 57.895 0.00 0.00 0.00 2.32
2810 3086 3.670625 CTCTCCAAATTGACCGTGGTAA 58.329 45.455 0.00 0.00 33.88 2.85
2818 3099 0.516877 TGACCGTGGTAAGTCGTACG 59.483 55.000 9.53 9.53 35.71 3.67
2825 3108 0.039256 GGTAAGTCGTACGGTGCACA 60.039 55.000 20.43 0.00 33.01 4.57
2841 3124 3.129852 GCACATGCATACGTAAGCAAA 57.870 42.857 26.94 7.40 44.88 3.68
2860 3143 5.419788 AGCAAAGTCTTATGGCATTTGATCA 59.580 36.000 4.78 0.00 33.69 2.92
2863 3146 7.279313 GCAAAGTCTTATGGCATTTGATCATTT 59.721 33.333 4.78 5.20 33.69 2.32
2869 3152 2.832733 TGGCATTTGATCATTTGGCTCA 59.167 40.909 23.55 11.85 35.82 4.26
2871 3154 3.807622 GGCATTTGATCATTTGGCTCATG 59.192 43.478 18.91 0.00 0.00 3.07
2876 3159 1.266175 GATCATTTGGCTCATGGCGAG 59.734 52.381 0.00 0.00 45.37 5.03
2885 3168 2.545946 GGCTCATGGCGAGAATCTTAAC 59.454 50.000 0.00 0.00 45.45 2.01
2918 3201 4.783841 CGCGCGAACTTGCAGCTC 62.784 66.667 28.94 0.00 34.04 4.09
2993 3276 0.462047 GGATGGCGTTCGAGGACATT 60.462 55.000 8.14 0.00 0.00 2.71
3335 3618 4.593864 GTCCATCTCCGGCCGCTC 62.594 72.222 22.85 0.00 0.00 5.03
3628 3938 7.264221 TGTGCATCTTCTAAAACAACAAATGT 58.736 30.769 0.00 0.00 46.82 2.71
3660 3970 2.978010 GTGCAACGACCACCAGGG 60.978 66.667 0.00 0.00 44.81 4.45
3679 3989 1.602165 GGTGACCGTAGATACCATGCG 60.602 57.143 0.00 0.00 33.42 4.73
3692 4094 1.142262 ACCATGCGGATACCCTAAACC 59.858 52.381 0.00 0.00 35.59 3.27
3700 4102 2.422377 GGATACCCTAAACCGCCACAAT 60.422 50.000 0.00 0.00 0.00 2.71
3708 4110 0.894835 AACCGCCACAATTCAATCCC 59.105 50.000 0.00 0.00 0.00 3.85
3709 4111 1.312371 ACCGCCACAATTCAATCCCG 61.312 55.000 0.00 0.00 0.00 5.14
3710 4112 1.226660 CGCCACAATTCAATCCCGC 60.227 57.895 0.00 0.00 0.00 6.13
3711 4113 1.141665 GCCACAATTCAATCCCGCC 59.858 57.895 0.00 0.00 0.00 6.13
3712 4114 1.815866 CCACAATTCAATCCCGCCC 59.184 57.895 0.00 0.00 0.00 6.13
3713 4115 1.675720 CCACAATTCAATCCCGCCCC 61.676 60.000 0.00 0.00 0.00 5.80
3714 4116 0.684153 CACAATTCAATCCCGCCCCT 60.684 55.000 0.00 0.00 0.00 4.79
3715 4117 0.923358 ACAATTCAATCCCGCCCCTA 59.077 50.000 0.00 0.00 0.00 3.53
3716 4118 1.318576 CAATTCAATCCCGCCCCTAC 58.681 55.000 0.00 0.00 0.00 3.18
3730 4132 1.381327 CCTACCTCCGCTTCCTCCA 60.381 63.158 0.00 0.00 0.00 3.86
3732 4134 0.684805 CTACCTCCGCTTCCTCCACT 60.685 60.000 0.00 0.00 0.00 4.00
3733 4135 0.627451 TACCTCCGCTTCCTCCACTA 59.373 55.000 0.00 0.00 0.00 2.74
3820 4222 3.447025 ATCCCGGCTTCGCTAGTGC 62.447 63.158 0.00 0.00 0.00 4.40
3826 4228 1.444553 GCTTCGCTAGTGCTGTCGT 60.445 57.895 0.00 0.00 36.97 4.34
3828 4230 0.710567 CTTCGCTAGTGCTGTCGTTG 59.289 55.000 0.00 0.00 36.97 4.10
3830 4232 1.080772 CGCTAGTGCTGTCGTTGGA 60.081 57.895 0.00 0.00 36.97 3.53
3844 4246 1.766864 TTGGACGGTGGGTCTCCAA 60.767 57.895 0.00 0.00 46.04 3.53
3853 4255 1.185618 TGGGTCTCCAAGTCAGGTCG 61.186 60.000 0.00 0.00 40.73 4.79
3867 4269 4.753541 GTCGTCGACCTCGGTAAC 57.246 61.111 14.60 0.00 40.29 2.50
3883 4285 0.674581 TAACGACTCCTTCTCGGCGA 60.675 55.000 10.14 10.14 35.37 5.54
3900 4302 0.163788 CGACATCGTGTCTTGGCAAC 59.836 55.000 13.65 0.00 44.85 4.17
3903 4306 0.865111 CATCGTGTCTTGGCAACGAA 59.135 50.000 15.13 1.12 42.51 3.85
3913 4316 0.391130 TGGCAACGAATCCTTCTCGG 60.391 55.000 0.00 0.00 40.64 4.63
3914 4317 1.706287 GGCAACGAATCCTTCTCGGC 61.706 60.000 0.00 0.00 40.64 5.54
3929 4332 2.434185 GGCGGCATCGTGTCTTCA 60.434 61.111 3.07 0.00 38.89 3.02
3930 4333 2.740714 GGCGGCATCGTGTCTTCAC 61.741 63.158 3.07 0.00 40.79 3.18
3937 4340 1.129251 CATCGTGTCTTCACATGGTGC 59.871 52.381 0.00 0.00 42.46 5.01
3982 4385 1.480212 ATGGGTGAGACCGACTTGCA 61.480 55.000 0.00 0.00 39.83 4.08
3986 4389 1.338200 GGTGAGACCGACTTGCATCTT 60.338 52.381 0.00 0.00 0.00 2.40
3994 4397 1.363744 GACTTGCATCTTGTCGGGAG 58.636 55.000 0.00 0.00 0.00 4.30
4017 4420 1.272212 GTTCATGCCCGAATTGGTGTT 59.728 47.619 0.00 0.00 35.15 3.32
4050 4453 0.617535 GGGTAGGCTTTGGGGCAATT 60.618 55.000 0.00 0.00 43.56 2.32
4064 4467 1.255882 GCAATTGATGTGGGTGTGGA 58.744 50.000 10.34 0.00 0.00 4.02
4065 4468 1.067635 GCAATTGATGTGGGTGTGGAC 60.068 52.381 10.34 0.00 0.00 4.02
4081 4485 1.135344 TGGACGAAATCGATGTACGCA 60.135 47.619 10.16 7.02 43.02 5.24
4087 4491 2.209838 AATCGATGTACGCAGTCCAG 57.790 50.000 0.00 0.00 43.93 3.86
4111 4515 1.067084 TGGTGCAACATGCCAAACG 59.933 52.632 0.00 0.00 44.23 3.60
4130 4534 1.474855 CGTGGTGGACATGATGGCATA 60.475 52.381 0.00 0.00 38.41 3.14
4156 4560 2.910688 TTGTCGCTCTCCTTTGAAGT 57.089 45.000 0.00 0.00 0.00 3.01
4165 4569 0.034896 TCCTTTGAAGTGAGCGGGTC 59.965 55.000 0.00 0.00 0.00 4.46
4214 4618 1.731720 GTGATGCTCAGACCTTCACC 58.268 55.000 1.74 0.00 33.64 4.02
4215 4619 0.615331 TGATGCTCAGACCTTCACCC 59.385 55.000 0.00 0.00 0.00 4.61
4238 4645 4.260990 CGCAACAAGGTTAGATGACAACAA 60.261 41.667 0.00 0.00 0.00 2.83
4240 4647 6.348132 CGCAACAAGGTTAGATGACAACAATA 60.348 38.462 0.00 0.00 0.00 1.90
4241 4648 7.023575 GCAACAAGGTTAGATGACAACAATAG 58.976 38.462 0.00 0.00 0.00 1.73
4242 4649 6.743575 ACAAGGTTAGATGACAACAATAGC 57.256 37.500 0.00 0.00 0.00 2.97
4243 4650 6.237901 ACAAGGTTAGATGACAACAATAGCA 58.762 36.000 0.00 0.00 0.00 3.49
4251 4658 4.661993 TGACAACAATAGCATCGACAAC 57.338 40.909 0.00 0.00 0.00 3.32
4276 4683 1.681264 GTGTGTTCTTTGGGGGTGAAG 59.319 52.381 0.00 0.00 0.00 3.02
4289 4696 3.944476 GTGAAGACACCATGCCTCT 57.056 52.632 0.00 0.00 40.74 3.69
4297 4704 3.327757 AGACACCATGCCTCTACTTTTCA 59.672 43.478 0.00 0.00 0.00 2.69
4301 4708 6.245408 ACACCATGCCTCTACTTTTCAATTA 58.755 36.000 0.00 0.00 0.00 1.40
4308 4715 9.959721 ATGCCTCTACTTTTCAATTAGAGTAAA 57.040 29.630 9.02 0.00 38.01 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.889573 GGCAGCGGCATTAGAGGTC 60.890 63.158 11.88 0.00 43.71 3.85
2 3 0.106708 TTAGGCAGCGGCATTAGAGG 59.893 55.000 11.88 0.00 43.71 3.69
3 4 2.072298 GATTAGGCAGCGGCATTAGAG 58.928 52.381 11.88 0.00 43.71 2.43
4 5 1.416030 TGATTAGGCAGCGGCATTAGA 59.584 47.619 11.88 0.00 43.71 2.10
5 6 1.802960 CTGATTAGGCAGCGGCATTAG 59.197 52.381 11.88 0.00 43.71 1.73
6 7 1.882912 CTGATTAGGCAGCGGCATTA 58.117 50.000 11.88 0.00 43.71 1.90
8 9 4.469883 CTGATTAGGCAGCGGCAT 57.530 55.556 11.88 6.11 43.71 4.40
17 18 9.790389 CGAGTACTAATTATAAGGCTGATTAGG 57.210 37.037 17.20 6.62 36.74 2.69
20 21 9.080097 ACTCGAGTACTAATTATAAGGCTGATT 57.920 33.333 18.46 0.00 0.00 2.57
21 22 8.516234 CACTCGAGTACTAATTATAAGGCTGAT 58.484 37.037 19.57 0.00 0.00 2.90
22 23 7.521748 GCACTCGAGTACTAATTATAAGGCTGA 60.522 40.741 19.57 0.00 0.00 4.26
23 24 6.583050 GCACTCGAGTACTAATTATAAGGCTG 59.417 42.308 19.57 0.34 0.00 4.85
24 25 6.294620 GGCACTCGAGTACTAATTATAAGGCT 60.295 42.308 19.57 0.00 0.00 4.58
25 26 5.862860 GGCACTCGAGTACTAATTATAAGGC 59.137 44.000 19.57 12.16 0.00 4.35
26 27 6.015688 TGGGCACTCGAGTACTAATTATAAGG 60.016 42.308 19.57 1.84 0.00 2.69
27 28 6.978338 TGGGCACTCGAGTACTAATTATAAG 58.022 40.000 19.57 2.06 0.00 1.73
28 29 6.964807 TGGGCACTCGAGTACTAATTATAA 57.035 37.500 19.57 0.00 0.00 0.98
29 30 7.534723 AATGGGCACTCGAGTACTAATTATA 57.465 36.000 19.57 0.00 0.00 0.98
30 31 6.420913 AATGGGCACTCGAGTACTAATTAT 57.579 37.500 19.57 4.07 0.00 1.28
31 32 5.864418 AATGGGCACTCGAGTACTAATTA 57.136 39.130 19.57 1.71 0.00 1.40
32 33 4.755266 AATGGGCACTCGAGTACTAATT 57.245 40.909 19.57 13.15 0.00 1.40
33 34 4.755266 AAATGGGCACTCGAGTACTAAT 57.245 40.909 19.57 7.77 0.00 1.73
34 35 4.250464 CAAAATGGGCACTCGAGTACTAA 58.750 43.478 19.57 5.59 0.00 2.24
35 36 3.369052 CCAAAATGGGCACTCGAGTACTA 60.369 47.826 19.57 12.65 32.67 1.82
36 37 2.615493 CCAAAATGGGCACTCGAGTACT 60.615 50.000 19.57 0.00 32.67 2.73
37 38 1.737793 CCAAAATGGGCACTCGAGTAC 59.262 52.381 19.57 13.19 32.67 2.73
38 39 1.626321 TCCAAAATGGGCACTCGAGTA 59.374 47.619 19.57 2.37 38.32 2.59
39 40 0.400213 TCCAAAATGGGCACTCGAGT 59.600 50.000 13.58 13.58 38.32 4.18
49 50 6.511416 TGTACACACAGAAATTCCAAAATGG 58.489 36.000 0.00 0.00 39.43 3.16
65 66 8.223769 CAGAAGAGACAACAATATTGTACACAC 58.776 37.037 21.07 12.60 41.31 3.82
73 74 5.182001 GTGCCACAGAAGAGACAACAATATT 59.818 40.000 0.00 0.00 0.00 1.28
80 81 0.464036 ACGTGCCACAGAAGAGACAA 59.536 50.000 0.00 0.00 0.00 3.18
109 116 6.767524 TTATGCAAAATGTTCCCTTCGTAT 57.232 33.333 0.00 0.00 0.00 3.06
142 154 7.303998 ACTAGACGACCGCTATACAATAATTC 58.696 38.462 0.00 0.00 0.00 2.17
192 204 0.171231 TCTGGAATCGCTGACTGACG 59.829 55.000 0.00 0.00 0.00 4.35
229 265 6.606395 ACCGGAGTCCTAATATCCACATATAC 59.394 42.308 9.46 0.00 32.31 1.47
238 281 8.298140 GCATATACATACCGGAGTCCTAATATC 58.702 40.741 9.46 0.00 0.00 1.63
244 287 3.774734 TGCATATACATACCGGAGTCCT 58.225 45.455 9.46 0.00 0.00 3.85
326 371 4.567318 CCAACCTATGGCCAGAGC 57.433 61.111 22.40 0.00 43.80 4.09
367 412 9.886132 GGATATAAAGGAGGCGATTCTTAATTA 57.114 33.333 0.00 0.00 0.00 1.40
368 413 7.829706 GGGATATAAAGGAGGCGATTCTTAATT 59.170 37.037 0.00 0.00 0.00 1.40
410 455 8.416329 GTCACTCATATTTGGAAGCCATTTATT 58.584 33.333 0.00 0.00 31.53 1.40
436 481 4.929808 CCCACTAGCAAAAGTAGTAGTGTG 59.070 45.833 7.40 0.00 40.46 3.82
514 562 3.646162 TCTACGGGATTGGATTGCTATGT 59.354 43.478 0.00 0.00 0.00 2.29
692 740 2.304761 TGAAACGGAGGGAGTATTTGCT 59.695 45.455 0.00 0.00 0.00 3.91
693 741 2.706890 TGAAACGGAGGGAGTATTTGC 58.293 47.619 0.00 0.00 0.00 3.68
694 742 5.240844 ACTTTTGAAACGGAGGGAGTATTTG 59.759 40.000 0.00 0.00 0.00 2.32
695 743 5.382616 ACTTTTGAAACGGAGGGAGTATTT 58.617 37.500 0.00 0.00 0.00 1.40
697 745 4.635699 ACTTTTGAAACGGAGGGAGTAT 57.364 40.909 0.00 0.00 0.00 2.12
698 746 4.131596 CAACTTTTGAAACGGAGGGAGTA 58.868 43.478 0.00 0.00 0.00 2.59
700 748 3.211045 TCAACTTTTGAAACGGAGGGAG 58.789 45.455 0.00 0.00 36.59 4.30
701 749 3.284793 TCAACTTTTGAAACGGAGGGA 57.715 42.857 0.00 0.00 36.59 4.20
702 750 4.517453 TGTATCAACTTTTGAAACGGAGGG 59.483 41.667 0.00 0.00 43.95 4.30
703 751 5.682943 TGTATCAACTTTTGAAACGGAGG 57.317 39.130 0.00 0.00 43.95 4.30
704 752 6.314784 GGATGTATCAACTTTTGAAACGGAG 58.685 40.000 0.00 0.00 43.95 4.63
706 754 5.086058 CGGATGTATCAACTTTTGAAACGG 58.914 41.667 0.00 0.00 43.95 4.44
707 755 5.685841 ACGGATGTATCAACTTTTGAAACG 58.314 37.500 0.00 0.00 43.95 3.60
708 756 9.620660 AAATACGGATGTATCAACTTTTGAAAC 57.379 29.630 0.00 0.00 43.95 2.78
711 759 9.878667 TCTAAATACGGATGTATCAACTTTTGA 57.121 29.630 0.00 0.00 40.42 2.69
712 760 9.916397 GTCTAAATACGGATGTATCAACTTTTG 57.084 33.333 0.00 0.00 40.42 2.44
713 761 9.661563 TGTCTAAATACGGATGTATCAACTTTT 57.338 29.630 0.00 0.00 40.42 2.27
714 762 9.661563 TTGTCTAAATACGGATGTATCAACTTT 57.338 29.630 0.00 0.00 40.42 2.66
715 763 9.661563 TTTGTCTAAATACGGATGTATCAACTT 57.338 29.630 0.00 0.00 40.42 2.66
716 764 9.832445 ATTTGTCTAAATACGGATGTATCAACT 57.168 29.630 0.00 0.00 40.42 3.16
718 766 9.268268 GGATTTGTCTAAATACGGATGTATCAA 57.732 33.333 0.00 0.00 40.42 2.57
719 767 8.425703 TGGATTTGTCTAAATACGGATGTATCA 58.574 33.333 0.00 0.00 40.42 2.15
720 768 8.827177 TGGATTTGTCTAAATACGGATGTATC 57.173 34.615 0.00 0.00 40.42 2.24
721 769 9.273016 CTTGGATTTGTCTAAATACGGATGTAT 57.727 33.333 0.00 0.00 43.14 2.29
722 770 8.479689 TCTTGGATTTGTCTAAATACGGATGTA 58.520 33.333 0.00 0.00 39.54 2.29
723 771 7.280205 GTCTTGGATTTGTCTAAATACGGATGT 59.720 37.037 0.00 0.00 39.54 3.06
724 772 7.279981 TGTCTTGGATTTGTCTAAATACGGATG 59.720 37.037 0.00 0.00 39.54 3.51
725 773 7.335627 TGTCTTGGATTTGTCTAAATACGGAT 58.664 34.615 0.00 0.00 39.54 4.18
726 774 6.703319 TGTCTTGGATTTGTCTAAATACGGA 58.297 36.000 0.00 0.00 39.54 4.69
727 775 6.978343 TGTCTTGGATTTGTCTAAATACGG 57.022 37.500 0.00 0.00 39.54 4.02
728 776 8.251750 TCTTGTCTTGGATTTGTCTAAATACG 57.748 34.615 0.00 0.00 39.54 3.06
733 781 9.748708 CAAAATTCTTGTCTTGGATTTGTCTAA 57.251 29.630 0.00 0.00 0.00 2.10
734 782 8.359642 CCAAAATTCTTGTCTTGGATTTGTCTA 58.640 33.333 0.00 0.00 40.72 2.59
735 783 7.212274 CCAAAATTCTTGTCTTGGATTTGTCT 58.788 34.615 0.00 0.00 40.72 3.41
736 784 6.424812 CCCAAAATTCTTGTCTTGGATTTGTC 59.575 38.462 5.99 0.00 40.72 3.18
737 785 6.099557 TCCCAAAATTCTTGTCTTGGATTTGT 59.900 34.615 5.99 0.00 40.72 2.83
738 786 6.424812 GTCCCAAAATTCTTGTCTTGGATTTG 59.575 38.462 5.99 0.00 40.72 2.32
739 787 6.524734 GTCCCAAAATTCTTGTCTTGGATTT 58.475 36.000 5.99 0.00 40.72 2.17
740 788 5.278957 CGTCCCAAAATTCTTGTCTTGGATT 60.279 40.000 5.99 0.00 40.72 3.01
741 789 4.218417 CGTCCCAAAATTCTTGTCTTGGAT 59.782 41.667 5.99 0.00 40.72 3.41
742 790 3.568007 CGTCCCAAAATTCTTGTCTTGGA 59.432 43.478 5.99 0.95 40.72 3.53
743 791 3.305335 CCGTCCCAAAATTCTTGTCTTGG 60.305 47.826 0.00 0.00 38.45 3.61
744 792 3.568007 TCCGTCCCAAAATTCTTGTCTTG 59.432 43.478 0.00 0.00 0.00 3.02
745 793 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
746 794 3.072476 TCTCCGTCCCAAAATTCTTGTCT 59.928 43.478 0.00 0.00 0.00 3.41
747 795 3.408634 TCTCCGTCCCAAAATTCTTGTC 58.591 45.455 0.00 0.00 0.00 3.18
748 796 3.072476 TCTCTCCGTCCCAAAATTCTTGT 59.928 43.478 0.00 0.00 0.00 3.16
749 797 3.674997 TCTCTCCGTCCCAAAATTCTTG 58.325 45.455 0.00 0.00 0.00 3.02
750 798 3.328050 ACTCTCTCCGTCCCAAAATTCTT 59.672 43.478 0.00 0.00 0.00 2.52
751 799 2.907042 ACTCTCTCCGTCCCAAAATTCT 59.093 45.455 0.00 0.00 0.00 2.40
752 800 3.336138 ACTCTCTCCGTCCCAAAATTC 57.664 47.619 0.00 0.00 0.00 2.17
753 801 4.903045 TTACTCTCTCCGTCCCAAAATT 57.097 40.909 0.00 0.00 0.00 1.82
754 802 6.555463 TTATTACTCTCTCCGTCCCAAAAT 57.445 37.500 0.00 0.00 0.00 1.82
755 803 6.555463 ATTATTACTCTCTCCGTCCCAAAA 57.445 37.500 0.00 0.00 0.00 2.44
756 804 7.664552 TTATTATTACTCTCTCCGTCCCAAA 57.335 36.000 0.00 0.00 0.00 3.28
757 805 7.664552 TTTATTATTACTCTCTCCGTCCCAA 57.335 36.000 0.00 0.00 0.00 4.12
758 806 7.664552 TTTTATTATTACTCTCTCCGTCCCA 57.335 36.000 0.00 0.00 0.00 4.37
759 807 8.202811 ACTTTTTATTATTACTCTCTCCGTCCC 58.797 37.037 0.00 0.00 0.00 4.46
773 821 9.984190 TCGGTTGCCTTTTTACTTTTTATTATT 57.016 25.926 0.00 0.00 0.00 1.40
775 823 9.628746 GATCGGTTGCCTTTTTACTTTTTATTA 57.371 29.630 0.00 0.00 0.00 0.98
776 824 8.364894 AGATCGGTTGCCTTTTTACTTTTTATT 58.635 29.630 0.00 0.00 0.00 1.40
777 825 7.892609 AGATCGGTTGCCTTTTTACTTTTTAT 58.107 30.769 0.00 0.00 0.00 1.40
778 826 7.279750 AGATCGGTTGCCTTTTTACTTTTTA 57.720 32.000 0.00 0.00 0.00 1.52
779 827 6.156748 AGATCGGTTGCCTTTTTACTTTTT 57.843 33.333 0.00 0.00 0.00 1.94
840 891 9.609346 ATTATTGGCACGTAGTAATAAACTTCT 57.391 29.630 11.71 0.00 41.61 2.85
844 895 8.493547 GGAGATTATTGGCACGTAGTAATAAAC 58.506 37.037 11.71 10.03 41.61 2.01
880 932 6.207810 GCGCTTCTCTGGGCTATATATATACT 59.792 42.308 0.00 0.00 41.74 2.12
978 1039 8.763601 GCCATTAGAGAATAGGTAGGATGTAAT 58.236 37.037 0.00 0.00 0.00 1.89
989 1054 4.692625 CCATGAACGCCATTAGAGAATAGG 59.307 45.833 0.00 0.00 31.94 2.57
990 1055 4.153117 GCCATGAACGCCATTAGAGAATAG 59.847 45.833 0.00 0.00 31.94 1.73
991 1056 4.065088 GCCATGAACGCCATTAGAGAATA 58.935 43.478 0.00 0.00 31.94 1.75
1009 1075 1.527611 CAGTGATCATGGCCGCCAT 60.528 57.895 19.79 19.79 46.37 4.40
1051 1117 1.026182 CATAGCGCCCTCAGCAACAA 61.026 55.000 2.29 0.00 44.04 2.83
1054 1120 2.190313 CCATAGCGCCCTCAGCAA 59.810 61.111 2.29 0.00 44.04 3.91
1107 1173 0.677288 CCGCCATGGTTCTACGGATA 59.323 55.000 19.59 0.00 46.71 2.59
1134 1200 3.998672 GGCGAGGGACCGTGAACA 61.999 66.667 0.00 0.00 0.00 3.18
1214 1280 2.187946 GGCTCAGGGACGTCATGG 59.812 66.667 18.91 10.22 0.00 3.66
1276 1342 7.033791 TGTCTTAAATTCTCACCGTATGTCTC 58.966 38.462 0.00 0.00 0.00 3.36
1385 1459 1.131883 CTCCCGTACCAGTACACGAAG 59.868 57.143 8.57 0.00 40.56 3.79
1505 1579 1.468565 CGGCCGATGAAGTTCTTCGTA 60.469 52.381 28.75 1.88 40.89 3.43
1618 1694 1.959226 ACCATGTGTTCGACGGTGC 60.959 57.895 0.00 0.00 0.00 5.01
1620 1696 1.301401 CCACCATGTGTTCGACGGT 60.301 57.895 0.00 0.00 0.00 4.83
1621 1697 2.677003 GCCACCATGTGTTCGACGG 61.677 63.158 0.00 0.00 0.00 4.79
1650 1726 1.808343 GGCAAACGAACCGGTAGAAAT 59.192 47.619 8.00 0.00 0.00 2.17
2019 2106 0.251165 GACAAGGGCCAGGCAAGTAA 60.251 55.000 15.19 0.00 0.00 2.24
2058 2145 1.502163 GCACTATGCGAGATGTGGCC 61.502 60.000 0.00 0.00 31.71 5.36
2081 2170 1.348538 TTCCACACATTAGACGCGCG 61.349 55.000 30.96 30.96 0.00 6.86
2560 2836 2.965147 CTCCCTCTTCTTCTCCATCTCC 59.035 54.545 0.00 0.00 0.00 3.71
2798 3074 1.069296 CGTACGACTTACCACGGTCAA 60.069 52.381 10.44 0.00 33.19 3.18
2810 3086 1.736645 GCATGTGCACCGTACGACT 60.737 57.895 18.76 0.00 41.59 4.18
2825 3108 6.017934 CCATAAGACTTTGCTTACGTATGCAT 60.018 38.462 29.70 18.91 39.07 3.96
2841 3124 6.684613 GCCAAATGATCAAATGCCATAAGACT 60.685 38.462 0.00 0.00 0.00 3.24
2860 3143 1.952296 GATTCTCGCCATGAGCCAAAT 59.048 47.619 0.00 0.00 44.86 2.32
2863 3146 0.543277 AAGATTCTCGCCATGAGCCA 59.457 50.000 0.00 0.00 44.86 4.75
2869 3152 5.622770 AAAAACGTTAAGATTCTCGCCAT 57.377 34.783 0.00 0.00 0.00 4.40
2894 3177 3.406361 AAGTTCGCGCGCACAGAG 61.406 61.111 32.32 14.68 0.00 3.35
2918 3201 2.606551 CGTCTCGTGGATGATCATCTGG 60.607 54.545 29.85 20.24 37.92 3.86
3032 3315 1.920734 TTGCCAGCACGGGTATCCAT 61.921 55.000 0.00 0.00 34.06 3.41
3398 3681 8.330302 CAACCAATCAGAAAACACAAAATCTTC 58.670 33.333 0.00 0.00 0.00 2.87
3585 3892 8.457261 AGATGCACATGTAAATTCTTCTTCTTC 58.543 33.333 0.00 0.00 0.00 2.87
3586 3893 8.345724 AGATGCACATGTAAATTCTTCTTCTT 57.654 30.769 0.00 0.00 0.00 2.52
3587 3894 7.934855 AGATGCACATGTAAATTCTTCTTCT 57.065 32.000 0.00 0.00 0.00 2.85
3588 3895 8.457261 AGAAGATGCACATGTAAATTCTTCTTC 58.543 33.333 23.38 20.93 43.10 2.87
3597 3907 8.409371 TGTTGTTTTAGAAGATGCACATGTAAA 58.591 29.630 0.00 0.00 0.00 2.01
3598 3908 7.935520 TGTTGTTTTAGAAGATGCACATGTAA 58.064 30.769 0.00 0.00 0.00 2.41
3660 3970 1.602165 CCGCATGGTATCTACGGTCAC 60.602 57.143 0.00 0.00 39.05 3.67
3661 3971 0.671796 CCGCATGGTATCTACGGTCA 59.328 55.000 0.00 0.00 39.05 4.02
3671 3981 2.369532 GGTTTAGGGTATCCGCATGGTA 59.630 50.000 0.00 0.00 38.33 3.25
3679 3989 0.542805 TGTGGCGGTTTAGGGTATCC 59.457 55.000 0.00 0.00 0.00 2.59
3692 4094 1.226660 GCGGGATTGAATTGTGGCG 60.227 57.895 0.00 0.00 0.00 5.69
3700 4102 1.307517 AGGTAGGGGCGGGATTGAA 60.308 57.895 0.00 0.00 0.00 2.69
3708 4110 4.222847 GAAGCGGAGGTAGGGGCG 62.223 72.222 0.00 0.00 37.06 6.13
3709 4111 3.862991 GGAAGCGGAGGTAGGGGC 61.863 72.222 0.00 0.00 37.06 5.80
3710 4112 2.041819 AGGAAGCGGAGGTAGGGG 60.042 66.667 0.00 0.00 37.06 4.79
3711 4113 2.134933 GGAGGAAGCGGAGGTAGGG 61.135 68.421 0.00 0.00 37.06 3.53
3712 4114 1.381327 TGGAGGAAGCGGAGGTAGG 60.381 63.158 0.00 0.00 37.06 3.18
3713 4115 0.684805 AGTGGAGGAAGCGGAGGTAG 60.685 60.000 0.00 0.00 37.06 3.18
3714 4116 0.627451 TAGTGGAGGAAGCGGAGGTA 59.373 55.000 0.00 0.00 37.06 3.08
3715 4117 0.252103 TTAGTGGAGGAAGCGGAGGT 60.252 55.000 0.00 0.00 44.60 3.85
3716 4118 1.123928 ATTAGTGGAGGAAGCGGAGG 58.876 55.000 0.00 0.00 0.00 4.30
3730 4132 7.175641 GGCAACATATAAATCAGCTCCATTAGT 59.824 37.037 0.00 0.00 0.00 2.24
3732 4134 7.233632 AGGCAACATATAAATCAGCTCCATTA 58.766 34.615 0.00 0.00 41.41 1.90
3733 4135 6.073314 AGGCAACATATAAATCAGCTCCATT 58.927 36.000 0.00 0.00 41.41 3.16
3737 4139 5.049129 GGTGAGGCAACATATAAATCAGCTC 60.049 44.000 0.00 0.00 41.41 4.09
3749 4151 0.038744 CCTCCAAGGTGAGGCAACAT 59.961 55.000 0.00 0.00 45.13 2.71
3779 4181 7.283354 GGATCGTGTGAGGAGTGATATATGATA 59.717 40.741 0.00 0.00 0.00 2.15
3780 4182 6.096141 GGATCGTGTGAGGAGTGATATATGAT 59.904 42.308 0.00 0.00 0.00 2.45
3781 4183 5.416013 GGATCGTGTGAGGAGTGATATATGA 59.584 44.000 0.00 0.00 0.00 2.15
3782 4184 5.393569 GGGATCGTGTGAGGAGTGATATATG 60.394 48.000 0.00 0.00 0.00 1.78
3783 4185 4.707448 GGGATCGTGTGAGGAGTGATATAT 59.293 45.833 0.00 0.00 0.00 0.86
3784 4186 4.079970 GGGATCGTGTGAGGAGTGATATA 58.920 47.826 0.00 0.00 0.00 0.86
3785 4187 2.894126 GGGATCGTGTGAGGAGTGATAT 59.106 50.000 0.00 0.00 0.00 1.63
3786 4188 2.307768 GGGATCGTGTGAGGAGTGATA 58.692 52.381 0.00 0.00 0.00 2.15
3820 4222 2.357034 CCCACCGTCCAACGACAG 60.357 66.667 0.24 0.00 46.05 3.51
3826 4228 1.764571 CTTGGAGACCCACCGTCCAA 61.765 60.000 3.17 3.17 46.01 3.53
3828 4230 2.168666 GACTTGGAGACCCACCGTCC 62.169 65.000 0.00 0.00 43.41 4.79
3830 4232 1.458777 TGACTTGGAGACCCACCGT 60.459 57.895 0.00 0.00 43.41 4.83
3853 4255 0.096108 GAGTCGTTACCGAGGTCGAC 59.904 60.000 21.46 21.46 45.26 4.20
3867 4269 1.994507 ATGTCGCCGAGAAGGAGTCG 61.995 60.000 0.00 0.00 45.00 4.18
3883 4285 0.249699 TCGTTGCCAAGACACGATGT 60.250 50.000 0.00 0.00 0.00 3.06
3903 4306 2.423446 GATGCCGCCGAGAAGGAT 59.577 61.111 0.00 0.00 45.00 3.24
3913 4316 2.778679 GTGAAGACACGATGCCGC 59.221 61.111 0.00 0.00 39.95 6.53
3929 4332 2.591753 CATCCCTCCGCACCATGT 59.408 61.111 0.00 0.00 0.00 3.21
3930 4333 2.903855 GCATCCCTCCGCACCATG 60.904 66.667 0.00 0.00 0.00 3.66
3937 4340 1.300465 CATCACTCGCATCCCTCCG 60.300 63.158 0.00 0.00 0.00 4.63
3982 4385 1.938585 TGAACTCCTCCCGACAAGAT 58.061 50.000 0.00 0.00 0.00 2.40
3986 4389 1.596934 GCATGAACTCCTCCCGACA 59.403 57.895 0.00 0.00 0.00 4.35
3994 4397 0.740737 CCAATTCGGGCATGAACTCC 59.259 55.000 0.00 0.00 0.00 3.85
4017 4420 3.665515 TACCCGAGATCCACCGCCA 62.666 63.158 0.00 0.00 0.00 5.69
4050 4453 0.470341 TTTCGTCCACACCCACATCA 59.530 50.000 0.00 0.00 0.00 3.07
4064 4467 2.182825 GACTGCGTACATCGATTTCGT 58.817 47.619 0.00 0.00 42.86 3.85
4065 4468 1.517276 GGACTGCGTACATCGATTTCG 59.483 52.381 0.00 2.12 42.86 3.46
4081 4485 0.478072 TTGCACCACCATTCTGGACT 59.522 50.000 0.00 0.00 40.96 3.85
4087 4491 3.126729 GCATGTTGCACCACCATTC 57.873 52.632 0.00 0.00 44.26 2.67
4111 4515 2.346766 TATGCCATCATGTCCACCAC 57.653 50.000 0.00 0.00 34.22 4.16
4130 4534 2.191128 AGGAGAGCGACAAAAGCATT 57.809 45.000 0.00 0.00 37.01 3.56
4165 4569 5.623264 CGTCTCGATGTAGAAAGAGCTATTG 59.377 44.000 0.00 0.00 0.00 1.90
4174 4578 1.404391 GAGCCCGTCTCGATGTAGAAA 59.596 52.381 0.00 0.00 31.20 2.52
4214 4618 2.422597 TGTCATCTAACCTTGTTGCGG 58.577 47.619 0.00 0.00 0.00 5.69
4215 4619 3.249799 TGTTGTCATCTAACCTTGTTGCG 59.750 43.478 0.00 0.00 0.00 4.85
4238 4645 2.094700 ACACACTCGTTGTCGATGCTAT 60.095 45.455 0.00 0.00 45.21 2.97
4240 4647 0.032130 ACACACTCGTTGTCGATGCT 59.968 50.000 0.00 0.00 45.21 3.79
4241 4648 0.161658 CACACACTCGTTGTCGATGC 59.838 55.000 0.00 0.00 45.21 3.91
4242 4649 1.487482 ACACACACTCGTTGTCGATG 58.513 50.000 0.00 0.00 45.21 3.84
4243 4650 2.124903 GAACACACACTCGTTGTCGAT 58.875 47.619 0.00 0.00 45.21 3.59
4251 4658 0.944386 CCCCAAAGAACACACACTCG 59.056 55.000 0.00 0.00 0.00 4.18
4276 4683 3.674997 TGAAAAGTAGAGGCATGGTGTC 58.325 45.455 0.00 0.00 0.00 3.67
4297 4704 7.933033 TGTACGTCCAACCTTTTTACTCTAATT 59.067 33.333 0.00 0.00 0.00 1.40
4301 4708 5.280654 TGTACGTCCAACCTTTTTACTCT 57.719 39.130 0.00 0.00 0.00 3.24
4308 4715 5.155278 TCATGTATGTACGTCCAACCTTT 57.845 39.130 0.00 0.00 0.00 3.11
4313 4720 6.954487 AGAGTATCATGTATGTACGTCCAA 57.046 37.500 0.00 0.00 37.82 3.53
4315 4722 6.736123 ACAAGAGTATCATGTATGTACGTCC 58.264 40.000 0.00 0.00 46.32 4.79


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

AutoCloner maintained by Alex Coulton.