Multiple sequence alignment - TraesCS5A01G422000

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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 TraesCS5A01G422000 chr5A 100.000 3709 0 0 1 3709 608362729 608359021 0.000000e+00 6850.0
1 TraesCS5A01G422000 chr5A 90.710 1098 92 6 880 1968 608447796 608446700 0.000000e+00 1454.0
2 TraesCS5A01G422000 chr5A 81.977 172 16 10 3541 3709 598256974 598257133 8.360000e-27 132.0
3 TraesCS5A01G422000 chr5A 77.866 253 22 16 1985 2234 608446716 608446495 3.890000e-25 126.0
4 TraesCS5A01G422000 chr5B 90.052 2905 210 41 1 2837 600136169 600133276 0.000000e+00 3690.0
5 TraesCS5A01G422000 chr5B 91.938 1104 74 8 878 1968 600338639 600337538 0.000000e+00 1531.0
6 TraesCS5A01G422000 chr5B 84.444 270 20 2 2152 2421 600337369 600337122 2.860000e-61 246.0
7 TraesCS5A01G422000 chr5B 90.411 73 4 2 1985 2054 600337554 600337482 3.940000e-15 93.5
8 TraesCS5A01G422000 chr5D 93.821 2282 107 15 567 2837 487600293 487598035 0.000000e+00 3402.0
9 TraesCS5A01G422000 chr5D 90.727 1100 93 4 878 1968 487836890 487835791 0.000000e+00 1458.0
10 TraesCS5A01G422000 chr5D 87.406 532 48 10 2 527 487600810 487600292 8.870000e-166 593.0
11 TraesCS5A01G422000 chr5D 91.693 313 26 0 1 313 394597665 394597977 5.690000e-118 435.0
12 TraesCS5A01G422000 chr5D 90.096 313 27 1 1 313 5552127 5551819 1.600000e-108 403.0
13 TraesCS5A01G422000 chr5D 94.776 134 7 0 2288 2421 487834352 487834219 3.750000e-50 209.0
14 TraesCS5A01G422000 chr5D 87.121 132 16 1 2979 3109 466560301 466560170 8.300000e-32 148.0
15 TraesCS5A01G422000 chr5D 78.423 241 27 15 1995 2234 487835794 487835578 2.320000e-27 134.0
16 TraesCS5A01G422000 chr3D 84.242 679 81 16 3040 3709 136255890 136255229 4.040000e-179 638.0
17 TraesCS5A01G422000 chr3D 90.566 53 5 0 2983 3035 517854714 517854662 1.850000e-08 71.3
18 TraesCS5A01G422000 chr4D 82.609 736 108 13 2982 3709 507877795 507878518 1.880000e-177 632.0
19 TraesCS5A01G422000 chr4D 83.333 618 78 16 3100 3709 83270307 83270907 7.000000e-152 547.0
20 TraesCS5A01G422000 chr4D 80.000 125 23 2 2290 2413 378449413 378449290 1.420000e-14 91.6
21 TraesCS5A01G422000 chr6D 84.006 669 80 16 3050 3709 7393634 7392984 5.260000e-173 617.0
22 TraesCS5A01G422000 chr6D 95.000 40 0 2 681 720 412458695 412458732 1.110000e-05 62.1
23 TraesCS5A01G422000 chr7D 83.915 659 91 7 3055 3709 194243047 194242400 1.890000e-172 616.0
24 TraesCS5A01G422000 chr6A 83.580 676 86 17 3039 3709 560633269 560633924 8.810000e-171 610.0
25 TraesCS5A01G422000 chr7B 83.161 677 97 10 3039 3709 718941382 718940717 1.470000e-168 603.0
26 TraesCS5A01G422000 chr3A 81.361 676 109 10 3039 3709 727236210 727235547 5.450000e-148 534.0
27 TraesCS5A01G422000 chr1A 81.651 654 94 21 3069 3709 440411115 440410475 1.530000e-143 520.0
28 TraesCS5A01G422000 chr4B 92.063 315 25 0 1 315 639086020 639086334 9.450000e-121 444.0
29 TraesCS5A01G422000 chr4B 80.328 122 22 2 2293 2413 464953857 464953737 1.420000e-14 91.6
30 TraesCS5A01G422000 chr1D 91.693 313 26 0 1 313 46490835 46491147 5.690000e-118 435.0
31 TraesCS5A01G422000 chr1D 89.809 314 32 0 1 314 465092083 465092396 1.600000e-108 403.0
32 TraesCS5A01G422000 chr2B 91.374 313 26 1 1 313 157269517 157269828 9.520000e-116 427.0
33 TraesCS5A01G422000 chr2B 90.385 312 29 1 1 312 639247469 639247779 3.450000e-110 409.0
34 TraesCS5A01G422000 chrUn 89.776 313 32 0 1 313 82327492 82327804 5.770000e-108 401.0
35 TraesCS5A01G422000 chrUn 89.776 313 32 0 1 313 82333716 82334028 5.770000e-108 401.0
36 TraesCS5A01G422000 chr4A 79.832 119 22 2 2287 2404 86991425 86991542 6.600000e-13 86.1
37 TraesCS5A01G422000 chr4A 100.000 30 0 0 2985 3014 96028960 96028989 5.170000e-04 56.5
38 TraesCS5A01G422000 chr4A 96.970 33 0 1 2980 3011 597058967 597058999 2.000000e-03 54.7


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 TraesCS5A01G422000 chr5A 608359021 608362729 3708 True 6850.000000 6850 100.000000 1 3709 1 chr5A.!!$R1 3708
1 TraesCS5A01G422000 chr5A 608446495 608447796 1301 True 790.000000 1454 84.288000 880 2234 2 chr5A.!!$R2 1354
2 TraesCS5A01G422000 chr5B 600133276 600136169 2893 True 3690.000000 3690 90.052000 1 2837 1 chr5B.!!$R1 2836
3 TraesCS5A01G422000 chr5B 600337122 600338639 1517 True 623.500000 1531 88.931000 878 2421 3 chr5B.!!$R2 1543
4 TraesCS5A01G422000 chr5D 487598035 487600810 2775 True 1997.500000 3402 90.613500 2 2837 2 chr5D.!!$R3 2835
5 TraesCS5A01G422000 chr5D 487834219 487836890 2671 True 600.333333 1458 87.975333 878 2421 3 chr5D.!!$R4 1543
6 TraesCS5A01G422000 chr3D 136255229 136255890 661 True 638.000000 638 84.242000 3040 3709 1 chr3D.!!$R1 669
7 TraesCS5A01G422000 chr4D 507877795 507878518 723 False 632.000000 632 82.609000 2982 3709 1 chr4D.!!$F2 727
8 TraesCS5A01G422000 chr4D 83270307 83270907 600 False 547.000000 547 83.333000 3100 3709 1 chr4D.!!$F1 609
9 TraesCS5A01G422000 chr6D 7392984 7393634 650 True 617.000000 617 84.006000 3050 3709 1 chr6D.!!$R1 659
10 TraesCS5A01G422000 chr7D 194242400 194243047 647 True 616.000000 616 83.915000 3055 3709 1 chr7D.!!$R1 654
11 TraesCS5A01G422000 chr6A 560633269 560633924 655 False 610.000000 610 83.580000 3039 3709 1 chr6A.!!$F1 670
12 TraesCS5A01G422000 chr7B 718940717 718941382 665 True 603.000000 603 83.161000 3039 3709 1 chr7B.!!$R1 670
13 TraesCS5A01G422000 chr3A 727235547 727236210 663 True 534.000000 534 81.361000 3039 3709 1 chr3A.!!$R1 670
14 TraesCS5A01G422000 chr1A 440410475 440411115 640 True 520.000000 520 81.651000 3069 3709 1 chr1A.!!$R1 640

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
793 820 0.036388 TTGACAATCCTCCTCGCACC 60.036 55.0 0.0 0.0 0.0 5.01 F
1055 1101 0.459411 GAACGCCTCCTCTCAGCTTC 60.459 60.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2577 3872 0.322816 AGTGAACATGCGGCCTTCAT 60.323 50.0 7.55 4.76 0.00 2.57 R
2957 4275 0.099436 GTGGCGAGCATGAAATGGAC 59.901 55.0 0.00 0.00 46.86 4.02 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
19 20 1.813192 AACTTGCCGTTGGTTGTGG 59.187 52.632 0.00 0.00 33.72 4.17
40 41 3.782244 CGGACTGCGCTGAGTTGC 61.782 66.667 21.92 3.02 0.00 4.17
78 79 1.080995 AAGATGTTGAGCGCTCGAGC 61.081 55.000 30.75 27.64 37.78 5.03
102 103 1.936547 GCGAACCAGGTCAATGAGATC 59.063 52.381 0.00 0.00 0.00 2.75
140 141 6.018343 GCTCATGAAAGGAACATTAGTCTAGC 60.018 42.308 0.00 0.00 0.00 3.42
150 151 8.763601 AGGAACATTAGTCTAGCTAAAATCAGT 58.236 33.333 9.65 3.76 42.35 3.41
168 169 3.865164 TCAGTAGACATGCAAATGTAGCG 59.135 43.478 0.00 0.00 34.45 4.26
192 193 0.039618 ACACCCTTGCTTGTATGGGG 59.960 55.000 12.70 0.00 43.72 4.96
197 198 1.304052 TTGCTTGTATGGGGCGCTT 60.304 52.632 7.64 0.00 0.00 4.68
198 199 1.312371 TTGCTTGTATGGGGCGCTTC 61.312 55.000 7.64 0.00 0.00 3.86
215 216 1.723608 TTCCAACAGCGCACAACCTG 61.724 55.000 11.47 0.00 35.26 4.00
227 228 1.002468 CACAACCTGTTGGCTTCGAAG 60.002 52.381 21.02 21.02 44.45 3.79
238 239 3.840831 CTTCGAAGCTCCCATGTGA 57.159 52.632 13.09 0.00 0.00 3.58
240 241 2.005451 CTTCGAAGCTCCCATGTGAAG 58.995 52.381 13.09 0.00 0.00 3.02
252 253 4.349048 TCCCATGTGAAGATAGCTAGCATT 59.651 41.667 18.83 5.84 0.00 3.56
270 271 6.674694 AGCATTGTCATCTCTGAATGTAAC 57.325 37.500 0.00 0.00 31.85 2.50
284 285 4.080072 TGAATGTAACCACCATGGCTGATA 60.080 41.667 13.04 0.00 42.67 2.15
292 293 4.964262 ACCACCATGGCTGATAAATGAAAT 59.036 37.500 13.04 0.00 42.67 2.17
297 298 6.154877 ACCATGGCTGATAAATGAAATGTTCA 59.845 34.615 13.04 0.00 45.01 3.18
371 381 4.888326 AACCATTGGTTATGTGCACAAT 57.112 36.364 25.72 14.66 44.94 2.71
374 384 6.543430 ACCATTGGTTATGTGCACAATATT 57.457 33.333 25.72 10.02 32.71 1.28
381 391 8.116651 TGGTTATGTGCACAATATTACAAACT 57.883 30.769 25.72 4.92 0.00 2.66
423 433 2.171237 TCTTGATGAGGGTCAATGCGAT 59.829 45.455 0.00 0.00 37.47 4.58
428 439 3.836365 TGAGGGTCAATGCGATATGAA 57.164 42.857 0.00 0.00 0.00 2.57
437 448 2.078849 TGCGATATGAAGCCGGTATG 57.921 50.000 1.90 0.00 0.00 2.39
446 457 1.479323 GAAGCCGGTATGTAGTGTGGA 59.521 52.381 1.90 0.00 0.00 4.02
451 462 1.135199 CGGTATGTAGTGTGGAAGCGT 60.135 52.381 0.00 0.00 0.00 5.07
466 477 2.946752 GCGTTGGACCCGTTCGAAC 61.947 63.158 18.47 18.47 39.06 3.95
501 512 3.301835 CCATTCGAGCTATTTTCACGTCG 60.302 47.826 0.00 0.00 0.00 5.12
531 542 3.040147 TCGATCAAACAACTCACTCCC 57.960 47.619 0.00 0.00 0.00 4.30
544 555 4.784177 ACTCACTCCCCGTAAAAGAAAAA 58.216 39.130 0.00 0.00 0.00 1.94
565 579 1.477553 AAGGGGCAATGCTACACATG 58.522 50.000 4.82 0.00 39.60 3.21
577 591 2.029728 GCTACACATGCAGAGCTTTACG 59.970 50.000 6.17 0.00 32.04 3.18
578 592 2.455674 ACACATGCAGAGCTTTACGA 57.544 45.000 0.00 0.00 0.00 3.43
593 607 7.070322 AGAGCTTTACGAGGGTATTATTGGTTA 59.930 37.037 0.00 0.00 0.00 2.85
605 619 8.532819 GGGTATTATTGGTTAACCATGAAACAA 58.467 33.333 27.57 11.64 46.97 2.83
626 640 1.431496 GCATGTGGCAATTTGTGGTC 58.569 50.000 0.00 0.00 43.97 4.02
628 642 1.000385 CATGTGGCAATTTGTGGTCGT 60.000 47.619 0.00 0.00 0.00 4.34
637 651 4.201724 GCAATTTGTGGTCGTCTATCAGTC 60.202 45.833 0.00 0.00 0.00 3.51
644 658 3.256383 TGGTCGTCTATCAGTCGGAAAAA 59.744 43.478 0.00 0.00 0.00 1.94
666 690 2.657459 TGACCCCCACCCTAAAATTCAT 59.343 45.455 0.00 0.00 0.00 2.57
689 713 6.142259 TGAGAGAAGTTTAGTACTCCCTCT 57.858 41.667 0.00 3.69 43.55 3.69
710 734 8.766151 CCCTCTAAAAAGAAATATAAGAGCGTC 58.234 37.037 0.00 0.00 0.00 5.19
731 755 6.345882 GCGTCTTTAGATCATTAAAGTAGGCG 60.346 42.308 11.97 12.40 40.12 5.52
789 816 2.093500 TCACCATTGACAATCCTCCTCG 60.093 50.000 0.00 0.00 0.00 4.63
793 820 0.036388 TTGACAATCCTCCTCGCACC 60.036 55.000 0.00 0.00 0.00 5.01
852 879 2.061773 GTCACGATCCTTGTCACACTG 58.938 52.381 0.00 0.00 0.00 3.66
855 882 2.926200 CACGATCCTTGTCACACTGATC 59.074 50.000 5.87 5.87 0.00 2.92
859 886 4.573900 GATCCTTGTCACACTGATCACTT 58.426 43.478 9.81 0.00 33.64 3.16
860 887 3.732212 TCCTTGTCACACTGATCACTTG 58.268 45.455 0.00 0.00 0.00 3.16
861 888 3.134623 TCCTTGTCACACTGATCACTTGT 59.865 43.478 0.00 0.00 0.00 3.16
862 889 4.343814 TCCTTGTCACACTGATCACTTGTA 59.656 41.667 5.13 0.00 0.00 2.41
863 890 4.449068 CCTTGTCACACTGATCACTTGTAC 59.551 45.833 5.13 5.60 0.00 2.90
1055 1101 0.459411 GAACGCCTCCTCTCAGCTTC 60.459 60.000 0.00 0.00 0.00 3.86
1744 1799 3.047718 CTACGACTTCCGCCTGCGA 62.048 63.158 13.94 0.00 43.32 5.10
2091 2187 5.516090 CACTAGAATTCTCTACCTTCGCTC 58.484 45.833 12.24 0.00 32.70 5.03
2114 2210 0.674895 AGCGAGGTCCATTCTTGCAC 60.675 55.000 6.16 0.00 42.53 4.57
2158 2254 1.801178 GCAAACTCTTCCTCCGACTTG 59.199 52.381 0.00 0.00 0.00 3.16
2166 2262 0.601841 TCCTCCGACTTGTTTTCCGC 60.602 55.000 0.00 0.00 0.00 5.54
2175 2271 1.104577 TTGTTTTCCGCCAGGTGGAC 61.105 55.000 22.46 11.72 42.31 4.02
2207 2303 1.939934 CATGGCGTTCGGACATAACAT 59.060 47.619 0.00 0.00 44.81 2.71
2340 3632 2.338984 GAGTCGGTGCTGTTCCGT 59.661 61.111 11.02 0.00 46.86 4.69
2343 3635 4.980805 TCGGTGCTGTTCCGTGGC 62.981 66.667 11.02 0.00 46.86 5.01
2537 3832 1.740025 GTTCACCAGCATCTTGTAGGC 59.260 52.381 0.00 0.00 34.24 3.93
2543 3838 1.134818 CAGCATCTTGTAGGCCGTGTA 60.135 52.381 0.00 0.00 34.71 2.90
2553 3848 2.507769 GCCGTGTACCGCTGTACC 60.508 66.667 14.85 6.44 45.59 3.34
2556 3851 1.582968 CGTGTACCGCTGTACCTGT 59.417 57.895 14.85 0.00 45.59 4.00
2557 3852 0.804364 CGTGTACCGCTGTACCTGTA 59.196 55.000 14.85 0.00 45.59 2.74
2558 3853 1.466360 CGTGTACCGCTGTACCTGTAC 60.466 57.143 14.85 6.32 45.59 2.90
2559 3854 0.804364 TGTACCGCTGTACCTGTACG 59.196 55.000 14.85 0.27 45.59 3.67
2560 3855 0.804989 GTACCGCTGTACCTGTACGT 59.195 55.000 7.15 0.00 41.27 3.57
2561 3856 0.804364 TACCGCTGTACCTGTACGTG 59.196 55.000 0.00 4.93 38.85 4.49
2577 3872 0.718904 CGTGCCGATCGAATGAAACA 59.281 50.000 18.66 0.00 0.00 2.83
2579 3874 2.708514 GTGCCGATCGAATGAAACATG 58.291 47.619 18.66 0.00 0.00 3.21
2580 3875 2.351418 GTGCCGATCGAATGAAACATGA 59.649 45.455 18.66 0.00 0.00 3.07
2581 3876 3.006247 TGCCGATCGAATGAAACATGAA 58.994 40.909 18.66 0.00 0.00 2.57
2602 3897 1.982073 GCCGCATGTTCACTGGTAGC 61.982 60.000 0.00 0.00 0.00 3.58
2607 3902 1.917955 CATGTTCACTGGTAGCGTACG 59.082 52.381 11.84 11.84 0.00 3.67
2608 3903 0.953727 TGTTCACTGGTAGCGTACGT 59.046 50.000 17.90 6.37 0.00 3.57
2609 3904 2.150390 TGTTCACTGGTAGCGTACGTA 58.850 47.619 17.90 5.34 0.00 3.57
2610 3905 2.095768 TGTTCACTGGTAGCGTACGTAC 60.096 50.000 17.90 15.90 0.00 3.67
2611 3906 2.099141 TCACTGGTAGCGTACGTACT 57.901 50.000 22.55 8.87 0.00 2.73
2613 3908 2.160219 TCACTGGTAGCGTACGTACTTG 59.840 50.000 22.55 9.91 0.00 3.16
2654 3963 2.913578 TGTTGCCTGCTGCCTTGG 60.914 61.111 0.00 0.00 40.16 3.61
2688 3997 6.183360 GGGTTTTGTAAATGAGGATGAGGATG 60.183 42.308 0.00 0.00 0.00 3.51
2698 4007 3.350833 AGGATGAGGATGAACAAAGTGC 58.649 45.455 0.00 0.00 0.00 4.40
2754 4065 3.842923 ATGTCGCTCTGCTCCCCG 61.843 66.667 0.00 0.00 0.00 5.73
2907 4225 8.861033 AAAATTGTAGTTAAAAACGAAGGACC 57.139 30.769 0.00 0.00 36.23 4.46
2908 4226 7.571080 AATTGTAGTTAAAAACGAAGGACCA 57.429 32.000 0.00 0.00 36.23 4.02
2909 4227 7.754851 ATTGTAGTTAAAAACGAAGGACCAT 57.245 32.000 0.00 0.00 36.23 3.55
2910 4228 8.851541 ATTGTAGTTAAAAACGAAGGACCATA 57.148 30.769 0.00 0.00 36.23 2.74
2911 4229 8.851541 TTGTAGTTAAAAACGAAGGACCATAT 57.148 30.769 0.00 0.00 36.23 1.78
2912 4230 9.941325 TTGTAGTTAAAAACGAAGGACCATATA 57.059 29.630 0.00 0.00 36.23 0.86
2921 4239 9.621629 AAAACGAAGGACCATATATATTCAACA 57.378 29.630 0.00 0.00 0.00 3.33
2922 4240 8.833231 AACGAAGGACCATATATATTCAACAG 57.167 34.615 0.00 0.00 0.00 3.16
2923 4241 7.963532 ACGAAGGACCATATATATTCAACAGT 58.036 34.615 0.00 0.00 0.00 3.55
2924 4242 8.088981 ACGAAGGACCATATATATTCAACAGTC 58.911 37.037 0.00 0.00 0.00 3.51
2925 4243 7.273598 CGAAGGACCATATATATTCAACAGTCG 59.726 40.741 0.00 0.00 0.00 4.18
2926 4244 7.540474 AGGACCATATATATTCAACAGTCGT 57.460 36.000 0.00 0.00 0.00 4.34
2927 4245 7.963532 AGGACCATATATATTCAACAGTCGTT 58.036 34.615 0.00 0.00 35.01 3.85
2928 4246 8.429641 AGGACCATATATATTCAACAGTCGTTT 58.570 33.333 0.00 0.00 31.13 3.60
2929 4247 8.495949 GGACCATATATATTCAACAGTCGTTTG 58.504 37.037 0.00 0.00 31.13 2.93
2930 4248 7.861630 ACCATATATATTCAACAGTCGTTTGC 58.138 34.615 0.00 0.00 31.13 3.68
2931 4249 7.497579 ACCATATATATTCAACAGTCGTTTGCA 59.502 33.333 0.00 0.00 31.13 4.08
2932 4250 8.011673 CCATATATATTCAACAGTCGTTTGCAG 58.988 37.037 0.00 0.00 31.13 4.41
2933 4251 4.685169 ATATTCAACAGTCGTTTGCAGG 57.315 40.909 0.00 0.00 31.13 4.85
2934 4252 1.021202 TTCAACAGTCGTTTGCAGGG 58.979 50.000 0.00 0.00 31.13 4.45
2935 4253 0.179234 TCAACAGTCGTTTGCAGGGA 59.821 50.000 0.00 0.00 31.13 4.20
2936 4254 1.021202 CAACAGTCGTTTGCAGGGAA 58.979 50.000 0.00 0.00 31.13 3.97
2937 4255 1.403679 CAACAGTCGTTTGCAGGGAAA 59.596 47.619 0.00 0.00 31.13 3.13
2938 4256 1.757682 ACAGTCGTTTGCAGGGAAAA 58.242 45.000 0.00 0.00 0.00 2.29
2939 4257 2.096248 ACAGTCGTTTGCAGGGAAAAA 58.904 42.857 0.00 0.00 0.00 1.94
2955 4273 2.951269 AAAAACCCGATTCGGTCCC 58.049 52.632 22.83 0.00 46.80 4.46
2956 4274 0.402887 AAAAACCCGATTCGGTCCCT 59.597 50.000 22.83 3.03 46.80 4.20
2957 4275 0.322187 AAAACCCGATTCGGTCCCTG 60.322 55.000 22.83 10.18 46.80 4.45
2958 4276 1.486145 AAACCCGATTCGGTCCCTGT 61.486 55.000 22.83 10.81 46.80 4.00
2959 4277 1.896122 AACCCGATTCGGTCCCTGTC 61.896 60.000 22.83 0.00 46.80 3.51
2960 4278 2.499685 CCGATTCGGTCCCTGTCC 59.500 66.667 17.08 0.00 42.73 4.02
2961 4279 2.355986 CCGATTCGGTCCCTGTCCA 61.356 63.158 17.08 0.00 42.73 4.02
2962 4280 1.686325 CCGATTCGGTCCCTGTCCAT 61.686 60.000 17.08 0.00 42.73 3.41
2963 4281 0.178068 CGATTCGGTCCCTGTCCATT 59.822 55.000 0.00 0.00 0.00 3.16
2964 4282 1.406887 CGATTCGGTCCCTGTCCATTT 60.407 52.381 0.00 0.00 0.00 2.32
2965 4283 2.289565 GATTCGGTCCCTGTCCATTTC 58.710 52.381 0.00 0.00 0.00 2.17
2966 4284 1.060729 TTCGGTCCCTGTCCATTTCA 58.939 50.000 0.00 0.00 0.00 2.69
2967 4285 1.285280 TCGGTCCCTGTCCATTTCAT 58.715 50.000 0.00 0.00 0.00 2.57
2968 4286 1.065491 TCGGTCCCTGTCCATTTCATG 60.065 52.381 0.00 0.00 0.00 3.07
2969 4287 1.106285 GGTCCCTGTCCATTTCATGC 58.894 55.000 0.00 0.00 0.00 4.06
2970 4288 1.341383 GGTCCCTGTCCATTTCATGCT 60.341 52.381 0.00 0.00 0.00 3.79
2971 4289 2.019984 GTCCCTGTCCATTTCATGCTC 58.980 52.381 0.00 0.00 0.00 4.26
2972 4290 1.019673 CCCTGTCCATTTCATGCTCG 58.980 55.000 0.00 0.00 0.00 5.03
2973 4291 0.379669 CCTGTCCATTTCATGCTCGC 59.620 55.000 0.00 0.00 0.00 5.03
2974 4292 0.379669 CTGTCCATTTCATGCTCGCC 59.620 55.000 0.00 0.00 0.00 5.54
2975 4293 0.322366 TGTCCATTTCATGCTCGCCA 60.322 50.000 0.00 0.00 0.00 5.69
2976 4294 0.099436 GTCCATTTCATGCTCGCCAC 59.901 55.000 0.00 0.00 0.00 5.01
2977 4295 1.031571 TCCATTTCATGCTCGCCACC 61.032 55.000 0.00 0.00 0.00 4.61
2978 4296 1.434696 CATTTCATGCTCGCCACCC 59.565 57.895 0.00 0.00 0.00 4.61
2979 4297 1.754234 ATTTCATGCTCGCCACCCC 60.754 57.895 0.00 0.00 0.00 4.95
2980 4298 2.215451 ATTTCATGCTCGCCACCCCT 62.215 55.000 0.00 0.00 0.00 4.79
3003 4322 2.748605 GAGCATCTACATCCGGACTTG 58.251 52.381 6.12 4.49 0.00 3.16
3004 4323 2.362397 GAGCATCTACATCCGGACTTGA 59.638 50.000 6.12 3.20 0.00 3.02
3019 4338 1.339151 ACTTGACAAATCCGGCCTCTC 60.339 52.381 0.00 0.00 0.00 3.20
3024 4343 1.202879 ACAAATCCGGCCTCTCAAACA 60.203 47.619 0.00 0.00 0.00 2.83
3025 4344 2.094675 CAAATCCGGCCTCTCAAACAT 58.905 47.619 0.00 0.00 0.00 2.71
3026 4345 2.493278 CAAATCCGGCCTCTCAAACATT 59.507 45.455 0.00 0.00 0.00 2.71
3030 4349 1.425428 GGCCTCTCAAACATTCGCG 59.575 57.895 0.00 0.00 0.00 5.87
3034 4353 0.366871 CTCTCAAACATTCGCGGACG 59.633 55.000 6.13 0.00 42.01 4.79
3035 4354 0.319211 TCTCAAACATTCGCGGACGT 60.319 50.000 6.13 0.00 41.18 4.34
3045 4364 4.961511 GCGGACGTGCCACTGACA 62.962 66.667 0.00 0.00 35.94 3.58
3047 4366 3.044305 GGACGTGCCACTGACAGC 61.044 66.667 1.25 0.00 36.34 4.40
3065 4384 0.098025 GCGCACGCCTTAAATTAGCA 59.902 50.000 0.30 0.00 34.56 3.49
3094 4413 5.104402 TGCATCCACCTCTCTCATATTTCAA 60.104 40.000 0.00 0.00 0.00 2.69
3114 4438 9.951866 ATTTCAACCCCTAAATCCATATAAAGT 57.048 29.630 0.00 0.00 0.00 2.66
3182 4507 6.809196 GCTAATTTTCGTCATCGGAGATATCT 59.191 38.462 4.47 4.47 45.12 1.98
3196 4521 4.215827 GGAGATATCTACGACGATGGTGTT 59.784 45.833 4.89 0.00 0.00 3.32
3278 4608 0.392863 CCATGGTGAACATCTCCGCA 60.393 55.000 2.57 0.00 37.84 5.69
3279 4609 1.452110 CATGGTGAACATCTCCGCAA 58.548 50.000 0.00 0.00 37.84 4.85
3311 4641 2.036992 CTCTTGCGCCTTCATCTCCTAT 59.963 50.000 4.18 0.00 0.00 2.57
3390 4720 1.919816 TGCTCCACCTGCAGATCCA 60.920 57.895 17.39 0.26 35.31 3.41
3394 4724 1.742880 CCACCTGCAGATCCACGTG 60.743 63.158 17.39 13.19 0.00 4.49
3403 4733 4.760047 ATCCACGTGGCCAGCGTC 62.760 66.667 30.25 5.76 40.90 5.19
3430 4760 2.937959 ATCCTCCTCCTCCGGCTCAC 62.938 65.000 0.00 0.00 0.00 3.51
3445 4776 0.327000 CTCACCCCCTCCTCCTCATT 60.327 60.000 0.00 0.00 0.00 2.57
3449 4783 1.690219 CCCCCTCCTCCTCATTGTCG 61.690 65.000 0.00 0.00 0.00 4.35
3471 4811 1.929088 TCGTCCTCCTCCTCCTCCA 60.929 63.158 0.00 0.00 0.00 3.86
3490 4830 0.193574 ACCTCCAACTCCTCCTCCAA 59.806 55.000 0.00 0.00 0.00 3.53
3492 4832 1.003696 CCTCCAACTCCTCCTCCAAAC 59.996 57.143 0.00 0.00 0.00 2.93
3502 4842 0.482446 TCCTCCAAACCCACTGCATT 59.518 50.000 0.00 0.00 0.00 3.56
3570 4911 3.764466 CAAGGAGCTCGAGCCGGT 61.764 66.667 32.94 16.02 43.38 5.28
3595 4936 1.600916 GCGGTGTCAGAAAGGGCTT 60.601 57.895 0.00 0.00 0.00 4.35
3615 4956 3.947132 CTCCTCACCCAGCAGCGTG 62.947 68.421 0.00 0.00 0.00 5.34
3641 4983 1.400530 GGGGCATGGCTACTAGTCGT 61.401 60.000 19.78 0.00 0.00 4.34
3659 5001 4.039973 AGTCGTATGGTTGGAGTGAAAAGA 59.960 41.667 0.00 0.00 0.00 2.52
3666 5008 2.391389 GGAGTGAAAAGAGGCGGCG 61.391 63.158 0.51 0.51 0.00 6.46
3667 5009 1.374252 GAGTGAAAAGAGGCGGCGA 60.374 57.895 12.98 0.00 0.00 5.54
3668 5010 1.627550 GAGTGAAAAGAGGCGGCGAC 61.628 60.000 12.98 8.50 0.00 5.19
3681 5029 4.415332 GCGACGGCGGACAGAAGA 62.415 66.667 15.06 0.00 38.16 2.87
3698 5046 4.159135 CAGAAGAAGGAAAATGTGGATGGG 59.841 45.833 0.00 0.00 0.00 4.00
3701 5049 1.560505 AGGAAAATGTGGATGGGTGC 58.439 50.000 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.202544 CTCAGCGCAGTCCGTCTC 60.203 66.667 11.47 0.00 39.71 3.36
40 41 6.318144 ACATCTTTAGATTGCACCATCTTCAG 59.682 38.462 6.23 3.88 31.21 3.02
78 79 2.868583 CTCATTGACCTGGTTCGCATAG 59.131 50.000 0.00 0.00 0.00 2.23
114 115 5.189180 AGACTAATGTTCCTTTCATGAGCC 58.811 41.667 0.00 0.00 29.33 4.70
140 141 9.926751 CTACATTTGCATGTCTACTGATTTTAG 57.073 33.333 0.00 0.00 43.06 1.85
150 151 4.112634 GACTCGCTACATTTGCATGTCTA 58.887 43.478 0.00 0.00 43.06 2.59
168 169 2.543777 TACAAGCAAGGGTGTGACTC 57.456 50.000 0.00 0.00 0.00 3.36
197 198 2.186160 CAGGTTGTGCGCTGTTGGA 61.186 57.895 9.73 0.00 0.00 3.53
198 199 2.003658 AACAGGTTGTGCGCTGTTGG 62.004 55.000 9.73 0.00 37.28 3.77
210 211 2.331265 GCTTCGAAGCCAACAGGTT 58.669 52.632 34.88 0.00 46.20 3.50
227 228 2.926778 AGCTATCTTCACATGGGAGC 57.073 50.000 0.00 0.00 0.00 4.70
233 234 5.922053 TGACAATGCTAGCTATCTTCACAT 58.078 37.500 17.23 0.00 0.00 3.21
238 239 6.267242 TCAGAGATGACAATGCTAGCTATCTT 59.733 38.462 17.23 6.28 0.00 2.40
240 241 6.023357 TCAGAGATGACAATGCTAGCTATC 57.977 41.667 17.23 8.52 0.00 2.08
252 253 4.285775 TGGTGGTTACATTCAGAGATGACA 59.714 41.667 0.00 0.00 0.00 3.58
270 271 5.163385 ACATTTCATTTATCAGCCATGGTGG 60.163 40.000 14.67 6.00 41.55 4.61
416 426 2.831685 TACCGGCTTCATATCGCATT 57.168 45.000 0.00 0.00 0.00 3.56
423 433 3.069016 CCACACTACATACCGGCTTCATA 59.931 47.826 0.00 0.00 0.00 2.15
428 439 1.480954 CTTCCACACTACATACCGGCT 59.519 52.381 0.00 0.00 0.00 5.52
437 448 1.145803 GTCCAACGCTTCCACACTAC 58.854 55.000 0.00 0.00 0.00 2.73
446 457 2.647680 TTCGAACGGGTCCAACGCTT 62.648 55.000 0.00 0.00 34.00 4.68
451 462 2.426887 GGGTTCGAACGGGTCCAA 59.573 61.111 21.34 0.00 0.00 3.53
490 501 1.876799 TGTCCAATGCGACGTGAAAAT 59.123 42.857 0.00 0.00 35.40 1.82
494 505 1.075979 CGATGTCCAATGCGACGTGA 61.076 55.000 0.00 0.00 35.40 4.35
501 512 3.763097 TGTTTGATCGATGTCCAATGC 57.237 42.857 0.54 0.00 0.00 3.56
544 555 2.008242 TGTGTAGCATTGCCCCTTTT 57.992 45.000 4.70 0.00 0.00 2.27
546 557 1.477553 CATGTGTAGCATTGCCCCTT 58.522 50.000 4.70 0.00 35.19 3.95
547 558 1.039233 GCATGTGTAGCATTGCCCCT 61.039 55.000 4.70 0.00 35.19 4.79
548 559 1.321805 TGCATGTGTAGCATTGCCCC 61.322 55.000 4.70 0.00 37.02 5.80
549 560 0.101759 CTGCATGTGTAGCATTGCCC 59.898 55.000 4.70 0.00 41.82 5.36
550 561 1.065102 CTCTGCATGTGTAGCATTGCC 59.935 52.381 4.70 0.00 41.82 4.52
551 562 1.533338 GCTCTGCATGTGTAGCATTGC 60.533 52.381 0.00 0.00 41.82 3.56
552 563 2.014857 AGCTCTGCATGTGTAGCATTG 58.985 47.619 14.80 0.00 41.82 2.82
556 567 2.029728 CGTAAAGCTCTGCATGTGTAGC 59.970 50.000 7.08 7.08 35.16 3.58
557 568 3.511699 TCGTAAAGCTCTGCATGTGTAG 58.488 45.455 0.00 0.00 0.00 2.74
565 579 2.892784 ATACCCTCGTAAAGCTCTGC 57.107 50.000 0.00 0.00 0.00 4.26
593 607 3.666274 CCACATGCATTGTTTCATGGTT 58.334 40.909 0.00 0.00 43.11 3.67
626 640 4.267928 GGTCATTTTTCCGACTGATAGACG 59.732 45.833 0.00 0.00 33.43 4.18
628 642 4.383770 GGGGTCATTTTTCCGACTGATAGA 60.384 45.833 0.00 0.00 32.57 1.98
637 651 1.254975 GGGTGGGGGTCATTTTTCCG 61.255 60.000 0.00 0.00 0.00 4.30
644 658 2.657459 TGAATTTTAGGGTGGGGGTCAT 59.343 45.455 0.00 0.00 0.00 3.06
666 690 6.142259 AGAGGGAGTACTAAACTTCTCTCA 57.858 41.667 9.40 0.00 41.37 3.27
710 734 8.142551 ACTACCGCCTACTTTAATGATCTAAAG 58.857 37.037 11.16 11.16 42.29 1.85
763 787 5.781818 AGGAGGATTGTCAATGGTGAATTTT 59.218 36.000 1.88 0.00 34.87 1.82
767 791 3.619733 CGAGGAGGATTGTCAATGGTGAA 60.620 47.826 1.88 0.00 34.87 3.18
776 803 0.250513 AAGGTGCGAGGAGGATTGTC 59.749 55.000 0.00 0.00 0.00 3.18
808 835 5.684704 TGTCAGAAGAAGTGTGAGGATTTT 58.315 37.500 0.00 0.00 28.26 1.82
823 850 3.249091 CAAGGATCGTGACTGTCAGAAG 58.751 50.000 11.41 6.16 0.00 2.85
1081 1127 1.435408 GAGCCGCTTCCATTCTCTGC 61.435 60.000 0.00 0.00 0.00 4.26
1276 1331 1.743394 TCGATCGACAGTATGCACACT 59.257 47.619 15.15 0.00 42.53 3.55
1999 2057 1.012453 GACGATCTCGGACGTCGAC 60.012 63.158 9.92 5.18 46.39 4.20
2091 2187 1.021390 AAGAATGGACCTCGCTTGCG 61.021 55.000 8.87 8.87 0.00 4.85
2114 2210 1.016130 AGCACGGAGAACAAGATGCG 61.016 55.000 0.00 0.00 38.12 4.73
2140 2236 3.840124 AACAAGTCGGAGGAAGAGTTT 57.160 42.857 0.00 0.00 0.00 2.66
2158 2254 2.265904 GGTCCACCTGGCGGAAAAC 61.266 63.158 4.72 0.00 33.29 2.43
2166 2262 3.953775 ACCGCTTGGTCCACCTGG 61.954 66.667 0.00 0.00 45.05 4.45
2207 2303 0.882927 GCGGGTGTAGTTGCTTGTCA 60.883 55.000 0.00 0.00 0.00 3.58
2340 3632 3.907260 CTCCGCCAGCTTCTTGCCA 62.907 63.158 0.00 0.00 44.23 4.92
2543 3838 1.582968 CACGTACAGGTACAGCGGT 59.417 57.895 9.97 0.00 35.87 5.68
2559 3854 2.351418 TCATGTTTCATTCGATCGGCAC 59.649 45.455 16.41 4.05 0.00 5.01
2560 3855 2.626840 TCATGTTTCATTCGATCGGCA 58.373 42.857 16.41 2.48 0.00 5.69
2561 3856 3.546815 CCTTCATGTTTCATTCGATCGGC 60.547 47.826 16.41 0.00 0.00 5.54
2577 3872 0.322816 AGTGAACATGCGGCCTTCAT 60.323 50.000 7.55 4.76 0.00 2.57
2579 3874 1.503542 CAGTGAACATGCGGCCTTC 59.496 57.895 0.00 0.00 0.00 3.46
2580 3875 1.973281 CCAGTGAACATGCGGCCTT 60.973 57.895 0.00 0.00 0.00 4.35
2581 3876 1.836999 TACCAGTGAACATGCGGCCT 61.837 55.000 0.00 0.00 0.00 5.19
2654 3963 0.673437 TTACAAAACCCAGCTGCAGC 59.327 50.000 31.53 31.53 42.49 5.25
2688 3997 4.755123 ACCATGTAGTAGTGCACTTTGTTC 59.245 41.667 27.06 12.46 38.80 3.18
2698 4007 0.999406 GCACGCACCATGTAGTAGTG 59.001 55.000 0.00 0.00 33.37 2.74
2754 4065 4.829492 AGCATCCTAATAAAATCTGGTGGC 59.171 41.667 0.00 0.00 0.00 5.01
2881 4199 9.949174 GGTCCTTCGTTTTTAACTACAATTTTA 57.051 29.630 0.00 0.00 0.00 1.52
2882 4200 8.468399 TGGTCCTTCGTTTTTAACTACAATTTT 58.532 29.630 0.00 0.00 0.00 1.82
2883 4201 7.998580 TGGTCCTTCGTTTTTAACTACAATTT 58.001 30.769 0.00 0.00 0.00 1.82
2884 4202 7.571080 TGGTCCTTCGTTTTTAACTACAATT 57.429 32.000 0.00 0.00 0.00 2.32
2885 4203 7.754851 ATGGTCCTTCGTTTTTAACTACAAT 57.245 32.000 0.00 0.00 0.00 2.71
2886 4204 8.851541 ATATGGTCCTTCGTTTTTAACTACAA 57.148 30.769 0.00 0.00 0.00 2.41
2895 4213 9.621629 TGTTGAATATATATGGTCCTTCGTTTT 57.378 29.630 0.00 0.00 0.00 2.43
2896 4214 9.273016 CTGTTGAATATATATGGTCCTTCGTTT 57.727 33.333 0.00 0.00 0.00 3.60
2897 4215 8.429641 ACTGTTGAATATATATGGTCCTTCGTT 58.570 33.333 0.00 0.00 0.00 3.85
2898 4216 7.963532 ACTGTTGAATATATATGGTCCTTCGT 58.036 34.615 0.00 0.00 0.00 3.85
2899 4217 7.273598 CGACTGTTGAATATATATGGTCCTTCG 59.726 40.741 0.00 0.00 0.00 3.79
2900 4218 8.088981 ACGACTGTTGAATATATATGGTCCTTC 58.911 37.037 1.15 0.00 0.00 3.46
2901 4219 7.963532 ACGACTGTTGAATATATATGGTCCTT 58.036 34.615 1.15 0.00 0.00 3.36
2902 4220 7.540474 ACGACTGTTGAATATATATGGTCCT 57.460 36.000 1.15 0.00 0.00 3.85
2903 4221 8.495949 CAAACGACTGTTGAATATATATGGTCC 58.504 37.037 1.15 0.00 38.62 4.46
2904 4222 8.009974 GCAAACGACTGTTGAATATATATGGTC 58.990 37.037 1.15 0.00 38.62 4.02
2905 4223 7.497579 TGCAAACGACTGTTGAATATATATGGT 59.502 33.333 1.15 0.00 38.62 3.55
2906 4224 7.860613 TGCAAACGACTGTTGAATATATATGG 58.139 34.615 1.15 0.00 38.62 2.74
2907 4225 8.011673 CCTGCAAACGACTGTTGAATATATATG 58.988 37.037 1.15 0.00 38.62 1.78
2908 4226 7.173218 CCCTGCAAACGACTGTTGAATATATAT 59.827 37.037 1.15 0.00 38.62 0.86
2909 4227 6.481976 CCCTGCAAACGACTGTTGAATATATA 59.518 38.462 1.15 0.00 38.62 0.86
2910 4228 5.296780 CCCTGCAAACGACTGTTGAATATAT 59.703 40.000 1.15 0.00 38.62 0.86
2911 4229 4.634004 CCCTGCAAACGACTGTTGAATATA 59.366 41.667 1.15 0.00 38.62 0.86
2912 4230 3.440173 CCCTGCAAACGACTGTTGAATAT 59.560 43.478 1.15 0.00 38.62 1.28
2913 4231 2.811431 CCCTGCAAACGACTGTTGAATA 59.189 45.455 1.15 0.00 38.62 1.75
2914 4232 1.608590 CCCTGCAAACGACTGTTGAAT 59.391 47.619 1.15 0.00 38.62 2.57
2915 4233 1.021202 CCCTGCAAACGACTGTTGAA 58.979 50.000 1.15 0.00 38.62 2.69
2916 4234 0.179234 TCCCTGCAAACGACTGTTGA 59.821 50.000 1.15 0.00 38.62 3.18
2917 4235 1.021202 TTCCCTGCAAACGACTGTTG 58.979 50.000 0.00 0.00 38.62 3.33
2918 4236 1.757682 TTTCCCTGCAAACGACTGTT 58.242 45.000 0.00 0.00 40.98 3.16
2919 4237 1.757682 TTTTCCCTGCAAACGACTGT 58.242 45.000 0.00 0.00 0.00 3.55
2920 4238 2.861462 TTTTTCCCTGCAAACGACTG 57.139 45.000 0.00 0.00 0.00 3.51
2944 4262 0.178068 AATGGACAGGGACCGAATCG 59.822 55.000 0.00 0.00 0.00 3.34
2945 4263 2.289565 GAAATGGACAGGGACCGAATC 58.710 52.381 0.00 0.00 0.00 2.52
2946 4264 1.633432 TGAAATGGACAGGGACCGAAT 59.367 47.619 0.00 0.00 0.00 3.34
2947 4265 1.060729 TGAAATGGACAGGGACCGAA 58.939 50.000 0.00 0.00 0.00 4.30
2948 4266 1.065491 CATGAAATGGACAGGGACCGA 60.065 52.381 0.00 0.00 41.79 4.69
2949 4267 1.382522 CATGAAATGGACAGGGACCG 58.617 55.000 0.00 0.00 41.79 4.79
2950 4268 1.106285 GCATGAAATGGACAGGGACC 58.894 55.000 0.00 0.00 46.86 4.46
2951 4269 2.019984 GAGCATGAAATGGACAGGGAC 58.980 52.381 0.00 0.00 46.86 4.46
2952 4270 1.407299 CGAGCATGAAATGGACAGGGA 60.407 52.381 0.00 0.00 46.86 4.20
2953 4271 1.019673 CGAGCATGAAATGGACAGGG 58.980 55.000 0.00 0.00 46.86 4.45
2954 4272 0.379669 GCGAGCATGAAATGGACAGG 59.620 55.000 0.00 0.00 46.86 4.00
2955 4273 0.379669 GGCGAGCATGAAATGGACAG 59.620 55.000 0.00 0.00 46.86 3.51
2956 4274 0.322366 TGGCGAGCATGAAATGGACA 60.322 50.000 0.00 0.00 46.86 4.02
2957 4275 0.099436 GTGGCGAGCATGAAATGGAC 59.901 55.000 0.00 0.00 46.86 4.02
2958 4276 1.031571 GGTGGCGAGCATGAAATGGA 61.032 55.000 0.00 0.00 46.86 3.41
2959 4277 1.434696 GGTGGCGAGCATGAAATGG 59.565 57.895 0.00 0.00 46.86 3.16
2961 4279 1.754234 GGGGTGGCGAGCATGAAAT 60.754 57.895 0.00 0.00 0.00 2.17
2962 4280 2.361104 GGGGTGGCGAGCATGAAA 60.361 61.111 0.00 0.00 0.00 2.69
2963 4281 1.558167 TAAGGGGTGGCGAGCATGAA 61.558 55.000 0.00 0.00 0.00 2.57
2964 4282 1.971505 CTAAGGGGTGGCGAGCATGA 61.972 60.000 0.00 0.00 0.00 3.07
2965 4283 1.524621 CTAAGGGGTGGCGAGCATG 60.525 63.158 0.00 0.00 0.00 4.06
2966 4284 1.689233 TCTAAGGGGTGGCGAGCAT 60.689 57.895 0.00 0.00 0.00 3.79
2967 4285 2.284331 TCTAAGGGGTGGCGAGCA 60.284 61.111 0.00 0.00 0.00 4.26
2968 4286 2.501610 CTCTAAGGGGTGGCGAGC 59.498 66.667 0.00 0.00 0.00 5.03
2969 4287 1.690219 ATGCTCTAAGGGGTGGCGAG 61.690 60.000 0.00 0.00 0.00 5.03
2970 4288 1.686325 GATGCTCTAAGGGGTGGCGA 61.686 60.000 0.00 0.00 0.00 5.54
2971 4289 1.227674 GATGCTCTAAGGGGTGGCG 60.228 63.158 0.00 0.00 0.00 5.69
2972 4290 1.070914 GTAGATGCTCTAAGGGGTGGC 59.929 57.143 0.00 0.00 29.58 5.01
2973 4291 2.398588 TGTAGATGCTCTAAGGGGTGG 58.601 52.381 0.00 0.00 29.58 4.61
2974 4292 3.007398 GGATGTAGATGCTCTAAGGGGTG 59.993 52.174 0.00 0.00 29.58 4.61
2975 4293 3.243724 GGATGTAGATGCTCTAAGGGGT 58.756 50.000 0.00 0.00 29.58 4.95
2976 4294 2.232452 CGGATGTAGATGCTCTAAGGGG 59.768 54.545 0.00 0.00 29.58 4.79
2977 4295 2.232452 CCGGATGTAGATGCTCTAAGGG 59.768 54.545 0.00 0.00 29.58 3.95
2978 4296 3.057174 GTCCGGATGTAGATGCTCTAAGG 60.057 52.174 7.81 0.00 29.58 2.69
2979 4297 3.823873 AGTCCGGATGTAGATGCTCTAAG 59.176 47.826 7.81 0.00 29.58 2.18
2980 4298 3.833732 AGTCCGGATGTAGATGCTCTAA 58.166 45.455 7.81 0.00 29.58 2.10
3002 4321 0.690192 TTGAGAGGCCGGATTTGTCA 59.310 50.000 5.05 0.08 0.00 3.58
3003 4322 1.468914 GTTTGAGAGGCCGGATTTGTC 59.531 52.381 5.05 0.00 0.00 3.18
3004 4323 1.202879 TGTTTGAGAGGCCGGATTTGT 60.203 47.619 5.05 0.00 0.00 2.83
3019 4338 1.792057 GCACGTCCGCGAATGTTTG 60.792 57.895 8.23 0.00 42.00 2.93
3030 4349 3.044305 GCTGTCAGTGGCACGTCC 61.044 66.667 12.71 4.28 0.00 4.79
3045 4364 0.377203 GCTAATTTAAGGCGTGCGCT 59.623 50.000 16.21 0.00 41.60 5.92
3047 4366 2.159572 AGTTGCTAATTTAAGGCGTGCG 60.160 45.455 0.00 0.00 0.00 5.34
3065 4384 2.373169 TGAGAGAGGTGGATGCAAAGTT 59.627 45.455 0.00 0.00 0.00 2.66
3094 4413 7.995663 TGCATACTTTATATGGATTTAGGGGT 58.004 34.615 0.00 0.00 0.00 4.95
3114 4438 4.941263 AGTACGCAGGATTTCTTTTGCATA 59.059 37.500 0.00 0.00 36.37 3.14
3131 4456 0.449388 AGCACGTAGGTGTAGTACGC 59.551 55.000 16.36 5.22 45.76 4.42
3161 4486 6.148976 TCGTAGATATCTCCGATGACGAAAAT 59.851 38.462 15.56 0.00 42.66 1.82
3163 4488 4.992951 TCGTAGATATCTCCGATGACGAAA 59.007 41.667 15.56 0.00 42.66 3.46
3170 4495 3.872182 CCATCGTCGTAGATATCTCCGAT 59.128 47.826 21.29 18.82 40.67 4.18
3182 4507 1.079681 GCCCAACACCATCGTCGTA 60.080 57.895 0.00 0.00 0.00 3.43
3278 4608 4.394712 CAAGAGGCCGCGGAGGTT 62.395 66.667 33.48 13.23 43.70 3.50
3334 4664 4.100084 TCCGGTCGGAGTCGGCTA 62.100 66.667 8.14 0.00 42.59 3.93
3430 4760 1.690219 CGACAATGAGGAGGAGGGGG 61.690 65.000 0.00 0.00 0.00 5.40
3445 4776 2.031516 GAGGAGGACGACGACGACA 61.032 63.158 15.32 0.00 42.66 4.35
3449 4783 2.114051 GGAGGAGGAGGACGACGAC 61.114 68.421 0.00 0.00 0.00 4.34
3471 4811 0.193574 TTGGAGGAGGAGTTGGAGGT 59.806 55.000 0.00 0.00 0.00 3.85
3490 4830 1.002134 CCTCCGAATGCAGTGGGTT 60.002 57.895 15.02 0.00 0.00 4.11
3492 4832 0.179073 CTACCTCCGAATGCAGTGGG 60.179 60.000 9.12 9.12 0.00 4.61
3533 4873 2.801631 GCAGATCCAGGCTAGGCGT 61.802 63.158 11.10 0.00 0.00 5.68
3580 4921 0.877743 GAGCAAGCCCTTTCTGACAC 59.122 55.000 0.00 0.00 0.00 3.67
3581 4922 0.250901 GGAGCAAGCCCTTTCTGACA 60.251 55.000 0.00 0.00 0.00 3.58
3582 4923 0.037447 AGGAGCAAGCCCTTTCTGAC 59.963 55.000 0.00 0.00 0.00 3.51
3641 4983 3.686016 GCCTCTTTTCACTCCAACCATA 58.314 45.455 0.00 0.00 0.00 2.74
3666 5008 1.446272 CCTTCTTCTGTCCGCCGTC 60.446 63.158 0.00 0.00 0.00 4.79
3667 5009 1.469335 TTCCTTCTTCTGTCCGCCGT 61.469 55.000 0.00 0.00 0.00 5.68
3668 5010 0.320421 TTTCCTTCTTCTGTCCGCCG 60.320 55.000 0.00 0.00 0.00 6.46
3678 5026 3.834231 CACCCATCCACATTTTCCTTCTT 59.166 43.478 0.00 0.00 0.00 2.52
3681 5029 1.901833 GCACCCATCCACATTTTCCTT 59.098 47.619 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.