Multiple sequence alignment - TraesCS2A01G196000

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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 TraesCS2A01G196000 chr2A 100.000 5572 0 0 1 5572 165926005 165920434 0.000000e+00 10290.0
1 TraesCS2A01G196000 chr2A 93.194 191 12 1 3591 3780 70233383 70233573 4.250000e-71 279.0
2 TraesCS2A01G196000 chr2A 97.500 40 1 0 3161 3200 165922807 165922768 1.000000e-07 69.4
3 TraesCS2A01G196000 chr2A 97.500 40 1 0 3199 3238 165922845 165922806 1.000000e-07 69.4
4 TraesCS2A01G196000 chr2D 95.134 2528 93 17 2902 5416 155832181 155829671 0.000000e+00 3960.0
5 TraesCS2A01G196000 chr2D 97.632 1858 40 1 984 2837 155834037 155832180 0.000000e+00 3184.0
6 TraesCS2A01G196000 chr2D 88.977 1007 88 14 4 994 155835408 155834409 0.000000e+00 1223.0
7 TraesCS2A01G196000 chr2D 75.753 631 128 16 3 628 102286675 102287285 1.520000e-75 294.0
8 TraesCS2A01G196000 chr2D 100.000 38 0 0 3161 3198 155831885 155831848 2.780000e-08 71.3
9 TraesCS2A01G196000 chr2B 96.799 2218 63 3 988 3200 213807185 213804971 0.000000e+00 3696.0
10 TraesCS2A01G196000 chr2B 96.125 1187 33 9 3768 4948 213804641 213803462 0.000000e+00 1925.0
11 TraesCS2A01G196000 chr2B 95.573 384 14 2 3199 3579 213805010 213804627 3.690000e-171 612.0
12 TraesCS2A01G196000 chr2B 84.431 501 60 10 4933 5416 213803312 213802813 1.400000e-130 477.0
13 TraesCS2A01G196000 chr2B 82.014 417 65 10 3 414 213825963 213825552 4.130000e-91 346.0
14 TraesCS2A01G196000 chr2B 83.836 365 33 12 410 750 213808608 213808246 1.940000e-84 324.0
15 TraesCS2A01G196000 chr2B 82.581 155 11 4 5420 5572 213802493 213802353 7.580000e-24 122.0
16 TraesCS2A01G196000 chr4D 78.179 637 120 15 4 627 502041553 502040923 6.770000e-104 388.0
17 TraesCS2A01G196000 chr4D 77.760 625 125 11 2 616 374773910 374773290 6.820000e-99 372.0
18 TraesCS2A01G196000 chr3B 77.405 655 129 15 4 646 792264641 792265288 6.820000e-99 372.0
19 TraesCS2A01G196000 chr6B 78.029 619 115 16 6 614 623087021 623086414 2.450000e-98 370.0
20 TraesCS2A01G196000 chr5A 77.682 578 112 12 4 570 684694219 684693648 2.490000e-88 337.0
21 TraesCS2A01G196000 chrUn 96.648 179 5 1 3591 3769 15978136 15977959 4.220000e-76 296.0
22 TraesCS2A01G196000 chrUn 93.229 192 11 2 3591 3781 308182878 308182688 1.180000e-71 281.0
23 TraesCS2A01G196000 chr7B 96.133 181 7 0 3588 3768 536117766 536117586 4.220000e-76 296.0
24 TraesCS2A01G196000 chr7B 83.465 127 17 4 3 126 652139743 652139868 1.270000e-21 115.0
25 TraesCS2A01G196000 chr4B 94.086 186 9 2 3580 3765 638587713 638587896 1.180000e-71 281.0
26 TraesCS2A01G196000 chr3A 93.651 189 10 2 3591 3778 740537671 740537858 1.180000e-71 281.0
27 TraesCS2A01G196000 chr3A 93.651 189 10 2 3591 3778 740598931 740599118 1.180000e-71 281.0
28 TraesCS2A01G196000 chr7A 90.777 206 16 3 3591 3795 605165948 605165745 7.110000e-69 272.0
29 TraesCS2A01G196000 chr1D 80.156 257 51 0 100 356 74627435 74627691 5.700000e-45 193.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G196000 chr2A 165920434 165926005 5571 True 3476.266667 10290 98.333333 1 5572 3 chr2A.!!$R1 5571
1 TraesCS2A01G196000 chr2D 155829671 155835408 5737 True 2109.575000 3960 95.435750 4 5416 4 chr2D.!!$R1 5412
2 TraesCS2A01G196000 chr2D 102286675 102287285 610 False 294.000000 294 75.753000 3 628 1 chr2D.!!$F1 625
3 TraesCS2A01G196000 chr2B 213802353 213808608 6255 True 1192.666667 3696 89.890833 410 5572 6 chr2B.!!$R2 5162
4 TraesCS2A01G196000 chr4D 502040923 502041553 630 True 388.000000 388 78.179000 4 627 1 chr4D.!!$R2 623
5 TraesCS2A01G196000 chr4D 374773290 374773910 620 True 372.000000 372 77.760000 2 616 1 chr4D.!!$R1 614
6 TraesCS2A01G196000 chr3B 792264641 792265288 647 False 372.000000 372 77.405000 4 646 1 chr3B.!!$F1 642
7 TraesCS2A01G196000 chr6B 623086414 623087021 607 True 370.000000 370 78.029000 6 614 1 chr6B.!!$R1 608
8 TraesCS2A01G196000 chr5A 684693648 684694219 571 True 337.000000 337 77.682000 4 570 1 chr5A.!!$R1 566

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
526 575 0.538584 TGGTAGAGTCGGAGTCGCTA 59.461 55.000 7.17 0.69 36.13 4.26 F
1206 1677 0.687354 ACCTCCTCATCTGCGTTTGT 59.313 50.000 0.00 0.00 0.00 2.83 F
2052 2523 0.927537 CAAAGTTCACGACAGACGCA 59.072 50.000 0.00 0.00 46.94 5.24 F
2865 3403 1.630369 TGTCAGGCTCAGCTAAATGGT 59.370 47.619 0.00 0.00 0.00 3.55 F
3726 4275 1.306397 GACCCTTCCCCGGAACCTA 60.306 63.158 0.73 0.00 0.00 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1577 2048 0.329261 CAATTCCCTCCTCCTGCACA 59.671 55.000 0.00 0.00 0.00 4.57 R
2787 3262 0.036294 GGTGCACCCTCAGTAAGGTC 60.036 60.000 26.31 0.00 44.56 3.85 R
2898 3436 0.183492 AAGACCAAGAGCAGCAACCA 59.817 50.000 0.00 0.00 0.00 3.67 R
4171 4722 2.181205 GACTGCAGAAGATTCGTCTCG 58.819 52.381 23.35 0.00 0.00 4.04 R
5495 6558 1.160137 CCCTTTTCGAGAAGCACAGG 58.840 55.000 10.12 2.64 0.00 4.00 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
26 27 2.885616 TCGGGTGAAAGTCTAAGGTCT 58.114 47.619 0.00 0.00 0.00 3.85
98 101 1.114627 CCTTAAAGAGCATTGGCCCC 58.885 55.000 0.00 0.00 42.56 5.80
116 119 4.947147 TTTGCGCGCTCCTTGGGT 62.947 61.111 33.29 0.00 0.00 4.51
144 147 3.334691 CTCGTGTCATTGTGGTTGGTAT 58.665 45.455 0.00 0.00 0.00 2.73
173 177 1.744522 CCGATGATGTGGATGTTTGCA 59.255 47.619 0.00 0.00 0.00 4.08
206 210 1.006337 GCAACAATGGCGGCTTTGA 60.006 52.632 34.35 6.90 0.00 2.69
234 238 1.032014 GGGTTGCAGCTGAGTTTTGA 58.968 50.000 20.43 0.00 0.00 2.69
363 370 1.074872 GGTCGGTTTCGGTTCTAGCG 61.075 60.000 0.00 0.00 40.97 4.26
444 493 2.278142 GCATGCGGCGGATTGTTC 60.278 61.111 12.38 0.00 0.00 3.18
526 575 0.538584 TGGTAGAGTCGGAGTCGCTA 59.461 55.000 7.17 0.69 36.13 4.26
583 635 1.178276 ACCTCGACATCGCTCTTCTT 58.822 50.000 0.00 0.00 39.60 2.52
616 670 3.278574 GTGTGCATTCTTATGTGGGCTA 58.721 45.455 0.00 0.00 34.12 3.93
649 704 3.059352 AGATGCCTTGCTTTTACGAGT 57.941 42.857 0.00 0.00 0.00 4.18
651 706 3.933332 AGATGCCTTGCTTTTACGAGTAC 59.067 43.478 0.00 0.00 0.00 2.73
652 707 3.114668 TGCCTTGCTTTTACGAGTACA 57.885 42.857 0.00 0.00 0.00 2.90
653 708 3.468770 TGCCTTGCTTTTACGAGTACAA 58.531 40.909 0.00 0.00 0.00 2.41
660 734 7.646130 CCTTGCTTTTACGAGTACAATTTTTCA 59.354 33.333 0.00 0.00 0.00 2.69
705 779 7.555554 TCTCCTTTCTTGATGAATTTGAGATCC 59.444 37.037 0.00 0.00 32.76 3.36
706 780 7.408543 TCCTTTCTTGATGAATTTGAGATCCT 58.591 34.615 0.00 0.00 34.24 3.24
718 794 7.663905 TGAATTTGAGATCCTCCGACTTTAAAA 59.336 33.333 0.00 0.00 0.00 1.52
832 921 4.125703 GTTGGACTTGCTCTATCCATCTG 58.874 47.826 0.00 0.00 42.09 2.90
848 938 2.680312 TCTGTCATCAGCTTGCCTAC 57.320 50.000 0.00 0.00 41.10 3.18
852 942 2.168521 TGTCATCAGCTTGCCTACTACC 59.831 50.000 0.00 0.00 0.00 3.18
1083 1554 2.785389 ACAAAGCCCCCTTCCCCA 60.785 61.111 0.00 0.00 0.00 4.96
1092 1563 2.366972 CCTTCCCCATCCTCCCGT 60.367 66.667 0.00 0.00 0.00 5.28
1188 1659 3.834799 CTCTGGTCCCGCCGGTAC 61.835 72.222 1.90 0.00 44.16 3.34
1203 1674 0.824759 GGTACCTCCTCATCTGCGTT 59.175 55.000 4.06 0.00 0.00 4.84
1206 1677 0.687354 ACCTCCTCATCTGCGTTTGT 59.313 50.000 0.00 0.00 0.00 2.83
1209 1680 2.166459 CCTCCTCATCTGCGTTTGTCTA 59.834 50.000 0.00 0.00 0.00 2.59
1398 1869 1.302033 CCTCTTCAACCGCACTGCT 60.302 57.895 0.00 0.00 0.00 4.24
1501 1972 1.682684 AACCGCGAGATCCAGGAGT 60.683 57.895 8.23 0.00 0.00 3.85
1524 1995 1.374758 CCTCTCAACGCACCACTCC 60.375 63.158 0.00 0.00 0.00 3.85
1528 1999 4.308458 CAACGCACCACTCCGGGA 62.308 66.667 0.00 0.00 40.22 5.14
1529 2000 4.309950 AACGCACCACTCCGGGAC 62.310 66.667 0.00 0.00 40.22 4.46
1577 2048 1.903877 CTTGATCTGCCAGGTCCCGT 61.904 60.000 1.78 0.00 0.00 5.28
1594 2065 1.903877 CGTGTGCAGGAGGAGGGAAT 61.904 60.000 0.00 0.00 0.00 3.01
1713 2184 4.843220 CTTGGAGAAGCACATGTTCTTT 57.157 40.909 12.11 2.90 34.30 2.52
1962 2433 2.113414 AGTGGGGATTTCAATGGGGAAA 59.887 45.455 0.00 0.00 40.72 3.13
2052 2523 0.927537 CAAAGTTCACGACAGACGCA 59.072 50.000 0.00 0.00 46.94 5.24
2160 2631 3.319122 GCAAGACTTTGATCCAACCAAGT 59.681 43.478 0.00 0.00 36.36 3.16
2446 2921 7.068716 GGGTTGCTCATACATTATCCTCTTTTT 59.931 37.037 0.00 0.00 0.00 1.94
2713 3188 9.906660 ATCTTTCTTATGATAGAGTAAGCTTCG 57.093 33.333 0.00 0.00 34.63 3.79
2724 3199 4.276431 AGAGTAAGCTTCGTGTAGATAGCC 59.724 45.833 0.00 0.00 35.23 3.93
2725 3200 3.952323 AGTAAGCTTCGTGTAGATAGCCA 59.048 43.478 0.00 0.00 35.23 4.75
2749 3224 7.547370 CCAATAGTTTCTCTTCTACTGGTCAAG 59.453 40.741 0.00 0.00 31.49 3.02
2836 3374 3.272766 GCGCTCTGCCTTTTGTTTT 57.727 47.368 0.00 0.00 37.76 2.43
2837 3375 2.415697 GCGCTCTGCCTTTTGTTTTA 57.584 45.000 0.00 0.00 37.76 1.52
2838 3376 2.738135 GCGCTCTGCCTTTTGTTTTAA 58.262 42.857 0.00 0.00 37.76 1.52
2839 3377 3.317150 GCGCTCTGCCTTTTGTTTTAAT 58.683 40.909 0.00 0.00 37.76 1.40
2840 3378 3.740832 GCGCTCTGCCTTTTGTTTTAATT 59.259 39.130 0.00 0.00 37.76 1.40
2841 3379 4.920927 GCGCTCTGCCTTTTGTTTTAATTA 59.079 37.500 0.00 0.00 37.76 1.40
2842 3380 5.404066 GCGCTCTGCCTTTTGTTTTAATTAA 59.596 36.000 0.00 0.00 37.76 1.40
2843 3381 6.615628 GCGCTCTGCCTTTTGTTTTAATTAAC 60.616 38.462 0.00 0.00 37.76 2.01
2844 3382 6.640907 CGCTCTGCCTTTTGTTTTAATTAACT 59.359 34.615 0.00 0.00 0.00 2.24
2845 3383 7.169140 CGCTCTGCCTTTTGTTTTAATTAACTT 59.831 33.333 0.00 0.00 0.00 2.66
2846 3384 8.275632 GCTCTGCCTTTTGTTTTAATTAACTTG 58.724 33.333 0.00 0.00 0.00 3.16
2847 3385 9.313118 CTCTGCCTTTTGTTTTAATTAACTTGT 57.687 29.630 0.00 0.00 0.00 3.16
2848 3386 9.308318 TCTGCCTTTTGTTTTAATTAACTTGTC 57.692 29.630 0.00 0.00 0.00 3.18
2849 3387 9.092876 CTGCCTTTTGTTTTAATTAACTTGTCA 57.907 29.630 0.00 0.00 0.00 3.58
2850 3388 9.092876 TGCCTTTTGTTTTAATTAACTTGTCAG 57.907 29.630 0.00 0.00 0.00 3.51
2851 3389 8.547894 GCCTTTTGTTTTAATTAACTTGTCAGG 58.452 33.333 0.00 1.99 0.00 3.86
2852 3390 8.547894 CCTTTTGTTTTAATTAACTTGTCAGGC 58.452 33.333 0.00 0.00 0.00 4.85
2853 3391 9.313118 CTTTTGTTTTAATTAACTTGTCAGGCT 57.687 29.630 0.00 0.00 0.00 4.58
2854 3392 8.865590 TTTGTTTTAATTAACTTGTCAGGCTC 57.134 30.769 0.00 0.00 0.00 4.70
2855 3393 7.575414 TGTTTTAATTAACTTGTCAGGCTCA 57.425 32.000 0.00 0.00 0.00 4.26
2856 3394 7.648142 TGTTTTAATTAACTTGTCAGGCTCAG 58.352 34.615 0.00 0.00 0.00 3.35
2857 3395 5.880054 TTAATTAACTTGTCAGGCTCAGC 57.120 39.130 0.00 0.00 0.00 4.26
2858 3396 3.710209 ATTAACTTGTCAGGCTCAGCT 57.290 42.857 0.00 0.00 0.00 4.24
2859 3397 4.826274 ATTAACTTGTCAGGCTCAGCTA 57.174 40.909 0.00 0.00 0.00 3.32
2860 3398 4.617253 TTAACTTGTCAGGCTCAGCTAA 57.383 40.909 0.00 0.00 0.00 3.09
2861 3399 3.492102 AACTTGTCAGGCTCAGCTAAA 57.508 42.857 0.00 0.00 0.00 1.85
2862 3400 3.710209 ACTTGTCAGGCTCAGCTAAAT 57.290 42.857 0.00 0.00 0.00 1.40
2863 3401 3.341823 ACTTGTCAGGCTCAGCTAAATG 58.658 45.455 0.00 0.00 0.00 2.32
2864 3402 2.408271 TGTCAGGCTCAGCTAAATGG 57.592 50.000 0.00 0.00 0.00 3.16
2865 3403 1.630369 TGTCAGGCTCAGCTAAATGGT 59.370 47.619 0.00 0.00 0.00 3.55
2866 3404 2.040278 TGTCAGGCTCAGCTAAATGGTT 59.960 45.455 0.00 0.00 0.00 3.67
2867 3405 3.084786 GTCAGGCTCAGCTAAATGGTTT 58.915 45.455 0.00 0.00 0.00 3.27
2868 3406 4.261801 GTCAGGCTCAGCTAAATGGTTTA 58.738 43.478 0.00 0.00 0.00 2.01
2869 3407 4.700213 GTCAGGCTCAGCTAAATGGTTTAA 59.300 41.667 0.00 0.00 0.00 1.52
2870 3408 4.700213 TCAGGCTCAGCTAAATGGTTTAAC 59.300 41.667 0.00 0.00 0.00 2.01
2871 3409 4.702131 CAGGCTCAGCTAAATGGTTTAACT 59.298 41.667 0.00 0.00 0.00 2.24
2872 3410 5.183904 CAGGCTCAGCTAAATGGTTTAACTT 59.816 40.000 0.00 0.00 0.00 2.66
2873 3411 5.183904 AGGCTCAGCTAAATGGTTTAACTTG 59.816 40.000 0.00 0.00 0.00 3.16
2874 3412 4.859245 GCTCAGCTAAATGGTTTAACTTGC 59.141 41.667 0.00 0.00 0.00 4.01
2875 3413 5.335976 GCTCAGCTAAATGGTTTAACTTGCT 60.336 40.000 0.00 0.00 0.00 3.91
2876 3414 6.128007 GCTCAGCTAAATGGTTTAACTTGCTA 60.128 38.462 0.00 0.00 0.00 3.49
2877 3415 7.574967 GCTCAGCTAAATGGTTTAACTTGCTAA 60.575 37.037 0.00 0.00 0.00 3.09
2878 3416 7.590279 TCAGCTAAATGGTTTAACTTGCTAAC 58.410 34.615 0.00 0.00 0.00 2.34
2879 3417 7.447238 TCAGCTAAATGGTTTAACTTGCTAACT 59.553 33.333 0.00 0.00 0.00 2.24
2880 3418 8.082242 CAGCTAAATGGTTTAACTTGCTAACTT 58.918 33.333 0.00 0.00 0.00 2.66
2881 3419 8.297426 AGCTAAATGGTTTAACTTGCTAACTTC 58.703 33.333 0.00 0.00 0.00 3.01
2882 3420 8.079809 GCTAAATGGTTTAACTTGCTAACTTCA 58.920 33.333 0.00 0.00 0.00 3.02
2884 3422 8.816640 AAATGGTTTAACTTGCTAACTTCATG 57.183 30.769 0.00 0.00 0.00 3.07
2885 3423 7.759489 ATGGTTTAACTTGCTAACTTCATGA 57.241 32.000 0.00 0.00 0.00 3.07
2886 3424 6.966021 TGGTTTAACTTGCTAACTTCATGAC 58.034 36.000 0.00 0.00 0.00 3.06
2887 3425 6.016610 TGGTTTAACTTGCTAACTTCATGACC 60.017 38.462 0.00 0.00 0.00 4.02
2888 3426 6.016610 GGTTTAACTTGCTAACTTCATGACCA 60.017 38.462 0.00 0.00 0.00 4.02
2889 3427 7.422399 GTTTAACTTGCTAACTTCATGACCAA 58.578 34.615 0.00 0.00 0.00 3.67
2890 3428 5.438761 AACTTGCTAACTTCATGACCAAC 57.561 39.130 0.00 0.00 0.00 3.77
2891 3429 4.718961 ACTTGCTAACTTCATGACCAACT 58.281 39.130 0.00 0.00 0.00 3.16
2892 3430 5.133221 ACTTGCTAACTTCATGACCAACTT 58.867 37.500 0.00 0.00 0.00 2.66
2893 3431 5.594317 ACTTGCTAACTTCATGACCAACTTT 59.406 36.000 0.00 0.00 0.00 2.66
2894 3432 5.437289 TGCTAACTTCATGACCAACTTTG 57.563 39.130 0.00 0.00 0.00 2.77
2895 3433 5.129634 TGCTAACTTCATGACCAACTTTGA 58.870 37.500 0.00 0.00 0.00 2.69
2896 3434 5.239306 TGCTAACTTCATGACCAACTTTGAG 59.761 40.000 0.00 0.00 0.00 3.02
2897 3435 4.574599 AACTTCATGACCAACTTTGAGC 57.425 40.909 0.00 0.00 0.00 4.26
2898 3436 3.825328 ACTTCATGACCAACTTTGAGCT 58.175 40.909 0.00 0.00 0.00 4.09
2899 3437 3.567164 ACTTCATGACCAACTTTGAGCTG 59.433 43.478 0.00 0.00 0.00 4.24
2900 3438 2.507484 TCATGACCAACTTTGAGCTGG 58.493 47.619 0.00 0.00 36.24 4.85
2901 3439 2.158623 TCATGACCAACTTTGAGCTGGT 60.159 45.455 2.84 2.84 46.22 4.00
3142 3682 4.523083 AGTACAGCTGTGTCCAAAGAAAA 58.477 39.130 29.57 1.01 38.19 2.29
3231 3771 1.967319 TCCTTGTCAACAGTTCCTGC 58.033 50.000 0.00 0.00 34.37 4.85
3283 3823 1.623311 TGACCATGTGAGTTCCGTGAT 59.377 47.619 0.00 0.00 0.00 3.06
3302 3842 5.462068 CGTGATCTCACTTGTTAACTGAACA 59.538 40.000 7.22 1.50 43.84 3.18
3338 3881 4.790878 CTCATTGTTTCACCATGTCACAG 58.209 43.478 0.00 0.00 0.00 3.66
3434 3983 4.020928 TGCCAAAGAAGCATGATGTTTGAT 60.021 37.500 16.68 0.00 34.08 2.57
3435 3984 4.933400 GCCAAAGAAGCATGATGTTTGATT 59.067 37.500 16.68 0.00 34.08 2.57
3436 3985 5.163893 GCCAAAGAAGCATGATGTTTGATTG 60.164 40.000 16.68 4.64 34.08 2.67
3437 3986 5.929992 CCAAAGAAGCATGATGTTTGATTGT 59.070 36.000 16.68 0.00 34.08 2.71
3438 3987 6.128661 CCAAAGAAGCATGATGTTTGATTGTG 60.129 38.462 16.68 1.23 34.08 3.33
3439 3988 5.970317 AGAAGCATGATGTTTGATTGTGA 57.030 34.783 0.00 0.00 0.00 3.58
3450 3999 5.353111 TGTTTGATTGTGACGAGACAGTTA 58.647 37.500 0.00 0.00 0.00 2.24
3622 4171 1.541588 GGTAAAGCTGCTTCCTTGTGG 59.458 52.381 16.28 0.00 0.00 4.17
3623 4172 2.230660 GTAAAGCTGCTTCCTTGTGGT 58.769 47.619 16.28 0.00 34.23 4.16
3634 4183 2.269023 TCCTTGTGGTCATGAGGTCAT 58.731 47.619 0.00 0.00 33.94 3.06
3722 4271 4.319949 TCGGACCCTTCCCCGGAA 62.320 66.667 0.73 0.00 45.36 4.30
3726 4275 1.306397 GACCCTTCCCCGGAACCTA 60.306 63.158 0.73 0.00 0.00 3.08
3825 4375 3.072330 TGGTTAGAGCTTGGATTGACACA 59.928 43.478 0.00 0.00 0.00 3.72
3833 4383 6.150140 AGAGCTTGGATTGACACAAAATCTAC 59.850 38.462 0.00 0.00 34.95 2.59
4171 4722 1.818785 GACTGATGCTGCTGGGAGC 60.819 63.158 7.14 7.14 42.82 4.70
4334 4885 6.345096 TCAATTCCCATCCACTTTCTTTTC 57.655 37.500 0.00 0.00 0.00 2.29
4502 5053 4.475444 CTACGGAGGGGCTGGGGA 62.475 72.222 0.00 0.00 0.00 4.81
4517 5068 1.063190 TGGGGATCGATGTCCTACTGT 60.063 52.381 0.54 0.00 38.38 3.55
4772 5323 2.242452 AGAGAATACAAAGGGGGCCTTC 59.758 50.000 0.84 0.00 43.92 3.46
4834 5385 4.679373 ATGCCCATTCTCTGTACTACTG 57.321 45.455 0.00 0.00 0.00 2.74
4840 5391 4.160439 CCATTCTCTGTACTACTGCTTGGA 59.840 45.833 0.00 0.00 0.00 3.53
4841 5392 5.337571 CCATTCTCTGTACTACTGCTTGGAA 60.338 44.000 0.00 0.00 0.00 3.53
4842 5393 6.344500 CATTCTCTGTACTACTGCTTGGAAT 58.656 40.000 0.00 0.00 0.00 3.01
4843 5394 6.360370 TTCTCTGTACTACTGCTTGGAATT 57.640 37.500 0.00 0.00 0.00 2.17
4844 5395 5.724328 TCTCTGTACTACTGCTTGGAATTG 58.276 41.667 0.00 0.00 0.00 2.32
4845 5396 5.480422 TCTCTGTACTACTGCTTGGAATTGA 59.520 40.000 0.00 0.00 0.00 2.57
4846 5397 6.014584 TCTCTGTACTACTGCTTGGAATTGAA 60.015 38.462 0.00 0.00 0.00 2.69
4855 5410 9.696917 CTACTGCTTGGAATTGAATTTAGTTTT 57.303 29.630 0.00 0.00 0.00 2.43
4857 5412 8.424133 ACTGCTTGGAATTGAATTTAGTTTTCT 58.576 29.630 0.00 0.00 0.00 2.52
4917 5472 1.066215 AGCGTGCAATATGAGGTGACA 60.066 47.619 0.00 0.00 0.00 3.58
4923 5478 5.562696 CGTGCAATATGAGGTGACAAAGTTT 60.563 40.000 0.00 0.00 0.00 2.66
4924 5479 6.348132 CGTGCAATATGAGGTGACAAAGTTTA 60.348 38.462 0.00 0.00 0.00 2.01
4996 5730 4.719369 GAACCGCGCGTCAGGTCT 62.719 66.667 29.95 9.78 40.37 3.85
5013 5748 5.047943 TCAGGTCTTTCTAAGAAGAAGGTCG 60.048 44.000 0.00 0.00 42.60 4.79
5030 5765 2.758979 GGTCGGACAATCTTACAGGAGA 59.241 50.000 10.76 0.00 0.00 3.71
5063 5798 5.070313 GGCCCAATAAATTCCAATAAGCTGA 59.930 40.000 0.00 0.00 0.00 4.26
5066 5801 8.534496 GCCCAATAAATTCCAATAAGCTGATAT 58.466 33.333 0.00 0.00 0.00 1.63
5195 5931 5.826601 TTTTCATTTTCAGGTTTTTGCCC 57.173 34.783 0.00 0.00 0.00 5.36
5199 5935 6.240549 TCATTTTCAGGTTTTTGCCCTTTA 57.759 33.333 0.00 0.00 0.00 1.85
5200 5936 6.653989 TCATTTTCAGGTTTTTGCCCTTTAA 58.346 32.000 0.00 0.00 0.00 1.52
5339 6085 9.593134 AACTAAAATATTTGATAAAATGGCGCA 57.407 25.926 10.83 0.00 0.00 6.09
5343 6090 9.934190 AAAATATTTGATAAAATGGCGCATTTC 57.066 25.926 10.83 3.13 42.32 2.17
5352 6099 9.934190 GATAAAATGGCGCATTTCAAAATATTT 57.066 25.926 10.83 0.00 42.32 1.40
5417 6164 9.952188 TCACAAAACATTTTCGTAATATTCACA 57.048 25.926 0.00 0.00 0.00 3.58
5453 6516 0.387565 TCGGCTTTTGCTTGGTTTCC 59.612 50.000 0.00 0.00 46.54 3.13
5463 6526 3.904717 TGCTTGGTTTCCTAGGTTTTGA 58.095 40.909 9.08 0.00 0.00 2.69
5464 6527 4.282496 TGCTTGGTTTCCTAGGTTTTGAA 58.718 39.130 9.08 0.00 0.00 2.69
5466 6529 4.583073 GCTTGGTTTCCTAGGTTTTGAAGA 59.417 41.667 9.08 0.00 0.00 2.87
5493 6556 1.881973 GTGCTTCCATGAGAAAGCACA 59.118 47.619 32.66 14.68 46.98 4.57
5494 6557 2.294233 GTGCTTCCATGAGAAAGCACAA 59.706 45.455 32.66 14.19 46.98 3.33
5495 6558 2.294233 TGCTTCCATGAGAAAGCACAAC 59.706 45.455 19.64 0.59 35.25 3.32
5496 6559 2.352127 GCTTCCATGAGAAAGCACAACC 60.352 50.000 17.31 0.00 32.88 3.77
5497 6560 2.957402 TCCATGAGAAAGCACAACCT 57.043 45.000 0.00 0.00 0.00 3.50
5498 6561 2.507484 TCCATGAGAAAGCACAACCTG 58.493 47.619 0.00 0.00 0.00 4.00
5499 6562 2.158623 TCCATGAGAAAGCACAACCTGT 60.159 45.455 0.00 0.00 0.00 4.00
5508 6571 3.289128 CACAACCTGTGCTTCTCGA 57.711 52.632 0.00 0.00 41.89 4.04
5509 6572 1.581934 CACAACCTGTGCTTCTCGAA 58.418 50.000 0.00 0.00 41.89 3.71
5510 6573 1.939934 CACAACCTGTGCTTCTCGAAA 59.060 47.619 0.00 0.00 41.89 3.46
5511 6574 2.354510 CACAACCTGTGCTTCTCGAAAA 59.645 45.455 0.00 0.00 41.89 2.29
5512 6575 2.614057 ACAACCTGTGCTTCTCGAAAAG 59.386 45.455 0.00 0.00 0.00 2.27
5513 6576 1.884235 ACCTGTGCTTCTCGAAAAGG 58.116 50.000 0.00 0.00 0.00 3.11
5514 6577 1.160137 CCTGTGCTTCTCGAAAAGGG 58.840 55.000 0.00 0.00 0.00 3.95
5543 6606 4.934001 CACAGAGTGTGCTTACATGAGAAT 59.066 41.667 0.00 0.00 41.89 2.40
5545 6608 4.331992 CAGAGTGTGCTTACATGAGAATGG 59.668 45.833 0.00 0.00 0.00 3.16
5552 6615 4.646040 TGCTTACATGAGAATGGAAATGGG 59.354 41.667 0.00 0.00 0.00 4.00
5557 6620 5.582953 ACATGAGAATGGAAATGGGAAAGA 58.417 37.500 0.00 0.00 0.00 2.52
5559 6622 5.982890 TGAGAATGGAAATGGGAAAGAAC 57.017 39.130 0.00 0.00 0.00 3.01
5561 6624 5.243730 TGAGAATGGAAATGGGAAAGAACAC 59.756 40.000 0.00 0.00 0.00 3.32
5562 6625 5.147032 AGAATGGAAATGGGAAAGAACACA 58.853 37.500 0.00 0.00 0.00 3.72
5563 6626 5.244626 AGAATGGAAATGGGAAAGAACACAG 59.755 40.000 0.00 0.00 0.00 3.66
5565 6628 4.285863 TGGAAATGGGAAAGAACACAGTT 58.714 39.130 0.00 0.00 34.21 3.16
5566 6629 4.099266 TGGAAATGGGAAAGAACACAGTTG 59.901 41.667 0.00 0.00 31.70 3.16
5567 6630 4.099419 GGAAATGGGAAAGAACACAGTTGT 59.901 41.667 0.00 0.00 31.70 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.821991 AGACTTTCACCCGAAGAGTG 57.178 50.000 0.00 0.00 37.70 3.51
26 27 1.888436 GCCGTCACCTGACCTGATCA 61.888 60.000 0.00 0.00 41.86 2.92
39 40 4.673298 ACAATGCCGACGCCGTCA 62.673 61.111 18.40 0.00 32.09 4.35
76 77 0.101219 GCCAATGCTCTTTAAGGCGG 59.899 55.000 0.00 0.00 31.88 6.13
98 101 4.107051 CCCAAGGAGCGCGCAAAG 62.107 66.667 35.10 17.27 0.00 2.77
111 114 0.605319 GACACGAGCATCCAACCCAA 60.605 55.000 0.00 0.00 0.00 4.12
116 119 1.805943 CACAATGACACGAGCATCCAA 59.194 47.619 0.00 0.00 0.00 3.53
144 147 0.108851 CACATCATCGGACGGACACA 60.109 55.000 0.00 0.00 0.00 3.72
173 177 2.326222 TTGCCACGCAAGAAATCGT 58.674 47.368 0.00 0.00 43.99 3.73
206 210 2.555547 GCTGCAACCCAACTTCGCT 61.556 57.895 0.00 0.00 0.00 4.93
374 381 3.496155 CGAGGATTGCTGAAGAAAAAGC 58.504 45.455 0.00 0.00 39.96 3.51
526 575 0.323816 TCATCACTCCTCCACGAGCT 60.324 55.000 0.00 0.00 32.79 4.09
583 635 4.994201 GCACACACGCCGTCGAGA 62.994 66.667 0.00 0.00 39.41 4.04
616 670 4.687219 GCAAGGCATCTTAGGTGACCTAAT 60.687 45.833 23.25 8.06 44.01 1.73
651 706 9.643693 AGTTGCCTGATAATTAGTGAAAAATTG 57.356 29.630 0.00 0.00 0.00 2.32
652 707 9.860898 GAGTTGCCTGATAATTAGTGAAAAATT 57.139 29.630 0.00 0.00 0.00 1.82
653 708 9.247861 AGAGTTGCCTGATAATTAGTGAAAAAT 57.752 29.630 0.00 0.00 0.00 1.82
660 734 5.902431 AGGAGAGAGTTGCCTGATAATTAGT 59.098 40.000 0.00 0.00 0.00 2.24
682 756 7.201803 GGAGGATCTCAAATTCATCAAGAAAGG 60.202 40.741 0.00 0.00 35.80 3.11
718 794 8.324191 TGACATCTAAGGTCATATCCTTCTTT 57.676 34.615 1.07 0.00 45.35 2.52
721 797 8.964476 TTTTGACATCTAAGGTCATATCCTTC 57.036 34.615 1.07 0.00 45.35 3.46
781 864 6.229733 TCTTCTTAACCCAAAAATGCCAATG 58.770 36.000 0.00 0.00 0.00 2.82
784 867 4.898861 ACTCTTCTTAACCCAAAAATGCCA 59.101 37.500 0.00 0.00 0.00 4.92
785 868 5.468540 ACTCTTCTTAACCCAAAAATGCC 57.531 39.130 0.00 0.00 0.00 4.40
786 869 5.154222 CGACTCTTCTTAACCCAAAAATGC 58.846 41.667 0.00 0.00 0.00 3.56
787 870 5.240844 ACCGACTCTTCTTAACCCAAAAATG 59.759 40.000 0.00 0.00 0.00 2.32
788 871 5.382616 ACCGACTCTTCTTAACCCAAAAAT 58.617 37.500 0.00 0.00 0.00 1.82
832 921 2.483889 GGGTAGTAGGCAAGCTGATGAC 60.484 54.545 0.00 0.00 0.00 3.06
852 942 1.300971 TGACCGTCGTCTACCTTCGG 61.301 60.000 0.00 0.00 45.53 4.30
867 957 2.125269 CGAACGGTGGGGATGACC 60.125 66.667 0.00 0.00 39.11 4.02
969 1059 0.902531 ATAGGGGAAGTGTCGGTGTG 59.097 55.000 0.00 0.00 0.00 3.82
1092 1563 3.792736 CCGAATGAGGCCCGGGAA 61.793 66.667 29.31 6.33 39.59 3.97
1104 1575 0.319728 CGGAGATGGAGATGCCGAAT 59.680 55.000 0.00 0.00 44.43 3.34
1185 1656 2.271800 CAAACGCAGATGAGGAGGTAC 58.728 52.381 0.00 0.00 0.00 3.34
1188 1659 1.066573 AGACAAACGCAGATGAGGAGG 60.067 52.381 0.00 0.00 0.00 4.30
1203 1674 2.297698 TGAAGAGGACGGGTAGACAA 57.702 50.000 0.00 0.00 0.00 3.18
1206 1677 2.820728 TGATGAAGAGGACGGGTAGA 57.179 50.000 0.00 0.00 0.00 2.59
1209 1680 1.123928 GGATGATGAAGAGGACGGGT 58.876 55.000 0.00 0.00 0.00 5.28
1501 1972 2.258591 GTGCGTTGAGAGGAGCGA 59.741 61.111 0.00 0.00 0.00 4.93
1524 1995 2.895372 GTAGCATTGCCGGTCCCG 60.895 66.667 1.90 0.00 39.44 5.14
1528 1999 2.186903 CTCCGTAGCATTGCCGGT 59.813 61.111 20.82 0.77 42.30 5.28
1529 2000 2.383245 ATCCTCCGTAGCATTGCCGG 62.383 60.000 17.16 17.16 43.03 6.13
1577 2048 0.329261 CAATTCCCTCCTCCTGCACA 59.671 55.000 0.00 0.00 0.00 4.57
2052 2523 2.345244 CCGACTGCAAGCACCTCT 59.655 61.111 0.00 0.00 37.60 3.69
2287 2758 6.563422 TGTTGCTAAATATTGAGGTGATTGC 58.437 36.000 1.84 0.00 0.00 3.56
2446 2921 3.799574 GCAACATCAACCAAGCAATGACA 60.800 43.478 0.00 0.00 0.00 3.58
2592 3067 3.675698 GCTGTGTAGTAGTCAGACTTTGC 59.324 47.826 8.80 2.34 0.00 3.68
2692 3167 7.569639 ACACGAAGCTTACTCTATCATAAGA 57.430 36.000 0.00 0.00 31.20 2.10
2713 3188 8.417884 AGAAGAGAAACTATTGGCTATCTACAC 58.582 37.037 0.00 0.00 0.00 2.90
2724 3199 7.547370 CCTTGACCAGTAGAAGAGAAACTATTG 59.453 40.741 0.00 0.00 0.00 1.90
2725 3200 7.235812 ACCTTGACCAGTAGAAGAGAAACTATT 59.764 37.037 0.00 0.00 0.00 1.73
2787 3262 0.036294 GGTGCACCCTCAGTAAGGTC 60.036 60.000 26.31 0.00 44.56 3.85
2836 3374 5.165961 AGCTGAGCCTGACAAGTTAATTA 57.834 39.130 0.00 0.00 0.00 1.40
2837 3375 4.026356 AGCTGAGCCTGACAAGTTAATT 57.974 40.909 0.00 0.00 0.00 1.40
2838 3376 3.710209 AGCTGAGCCTGACAAGTTAAT 57.290 42.857 0.00 0.00 0.00 1.40
2839 3377 4.617253 TTAGCTGAGCCTGACAAGTTAA 57.383 40.909 0.00 0.00 0.00 2.01
2840 3378 4.617253 TTTAGCTGAGCCTGACAAGTTA 57.383 40.909 0.00 0.00 0.00 2.24
2841 3379 3.492102 TTTAGCTGAGCCTGACAAGTT 57.508 42.857 0.00 0.00 0.00 2.66
2842 3380 3.341823 CATTTAGCTGAGCCTGACAAGT 58.658 45.455 0.00 0.00 0.00 3.16
2843 3381 2.681848 CCATTTAGCTGAGCCTGACAAG 59.318 50.000 0.00 0.00 0.00 3.16
2844 3382 2.040278 ACCATTTAGCTGAGCCTGACAA 59.960 45.455 0.00 0.00 0.00 3.18
2845 3383 1.630369 ACCATTTAGCTGAGCCTGACA 59.370 47.619 0.00 0.00 0.00 3.58
2846 3384 2.409948 ACCATTTAGCTGAGCCTGAC 57.590 50.000 0.00 0.00 0.00 3.51
2847 3385 3.439857 AAACCATTTAGCTGAGCCTGA 57.560 42.857 0.00 0.00 0.00 3.86
2848 3386 4.702131 AGTTAAACCATTTAGCTGAGCCTG 59.298 41.667 0.00 0.00 35.69 4.85
2849 3387 4.923415 AGTTAAACCATTTAGCTGAGCCT 58.077 39.130 0.00 0.00 35.69 4.58
2850 3388 5.402398 CAAGTTAAACCATTTAGCTGAGCC 58.598 41.667 0.00 0.00 36.88 4.70
2851 3389 4.859245 GCAAGTTAAACCATTTAGCTGAGC 59.141 41.667 0.00 0.00 36.88 4.26
2852 3390 6.259550 AGCAAGTTAAACCATTTAGCTGAG 57.740 37.500 0.00 0.00 36.88 3.35
2853 3391 7.447238 AGTTAGCAAGTTAAACCATTTAGCTGA 59.553 33.333 0.00 0.00 36.88 4.26
2854 3392 7.593825 AGTTAGCAAGTTAAACCATTTAGCTG 58.406 34.615 0.00 0.00 36.88 4.24
2855 3393 7.761038 AGTTAGCAAGTTAAACCATTTAGCT 57.239 32.000 0.00 0.00 38.15 3.32
2856 3394 8.079809 TGAAGTTAGCAAGTTAAACCATTTAGC 58.920 33.333 0.00 0.00 0.00 3.09
2858 3396 9.906660 CATGAAGTTAGCAAGTTAAACCATTTA 57.093 29.630 0.00 0.00 0.00 1.40
2859 3397 8.637986 TCATGAAGTTAGCAAGTTAAACCATTT 58.362 29.630 0.00 0.00 0.00 2.32
2860 3398 8.082242 GTCATGAAGTTAGCAAGTTAAACCATT 58.918 33.333 0.00 0.00 0.00 3.16
2861 3399 7.309194 GGTCATGAAGTTAGCAAGTTAAACCAT 60.309 37.037 0.00 0.00 0.00 3.55
2862 3400 6.016610 GGTCATGAAGTTAGCAAGTTAAACCA 60.017 38.462 0.00 0.00 0.00 3.67
2863 3401 6.016610 TGGTCATGAAGTTAGCAAGTTAAACC 60.017 38.462 0.00 0.00 0.00 3.27
2864 3402 6.966021 TGGTCATGAAGTTAGCAAGTTAAAC 58.034 36.000 0.00 0.00 0.00 2.01
2865 3403 7.284489 AGTTGGTCATGAAGTTAGCAAGTTAAA 59.716 33.333 0.00 0.00 32.00 1.52
2866 3404 6.770785 AGTTGGTCATGAAGTTAGCAAGTTAA 59.229 34.615 0.00 0.00 32.00 2.01
2867 3405 6.296026 AGTTGGTCATGAAGTTAGCAAGTTA 58.704 36.000 0.00 0.00 32.00 2.24
2868 3406 5.133221 AGTTGGTCATGAAGTTAGCAAGTT 58.867 37.500 0.00 0.00 32.00 2.66
2869 3407 4.718961 AGTTGGTCATGAAGTTAGCAAGT 58.281 39.130 0.00 0.00 31.85 3.16
2870 3408 5.695851 AAGTTGGTCATGAAGTTAGCAAG 57.304 39.130 0.00 0.00 31.85 4.01
2871 3409 5.592282 TCAAAGTTGGTCATGAAGTTAGCAA 59.408 36.000 0.00 0.00 0.00 3.91
2872 3410 5.129634 TCAAAGTTGGTCATGAAGTTAGCA 58.870 37.500 0.00 0.00 0.00 3.49
2873 3411 5.689383 TCAAAGTTGGTCATGAAGTTAGC 57.311 39.130 0.00 0.00 0.00 3.09
2874 3412 5.471456 AGCTCAAAGTTGGTCATGAAGTTAG 59.529 40.000 0.00 0.00 0.00 2.34
2875 3413 5.239306 CAGCTCAAAGTTGGTCATGAAGTTA 59.761 40.000 0.00 0.00 0.00 2.24
2876 3414 4.037208 CAGCTCAAAGTTGGTCATGAAGTT 59.963 41.667 0.00 0.00 0.00 2.66
2877 3415 3.567164 CAGCTCAAAGTTGGTCATGAAGT 59.433 43.478 0.00 0.00 0.00 3.01
2878 3416 3.057736 CCAGCTCAAAGTTGGTCATGAAG 60.058 47.826 0.00 0.00 41.12 3.02
2879 3417 2.886523 CCAGCTCAAAGTTGGTCATGAA 59.113 45.455 0.00 0.00 41.12 2.57
2880 3418 2.507484 CCAGCTCAAAGTTGGTCATGA 58.493 47.619 0.00 0.00 41.12 3.07
2896 3434 1.860484 GACCAAGAGCAGCAACCAGC 61.860 60.000 0.00 0.00 46.19 4.85
2897 3435 0.250640 AGACCAAGAGCAGCAACCAG 60.251 55.000 0.00 0.00 0.00 4.00
2898 3436 0.183492 AAGACCAAGAGCAGCAACCA 59.817 50.000 0.00 0.00 0.00 3.67
2899 3437 0.595095 CAAGACCAAGAGCAGCAACC 59.405 55.000 0.00 0.00 0.00 3.77
2900 3438 0.595095 CCAAGACCAAGAGCAGCAAC 59.405 55.000 0.00 0.00 0.00 4.17
2901 3439 0.183492 ACCAAGACCAAGAGCAGCAA 59.817 50.000 0.00 0.00 0.00 3.91
3142 3682 3.390311 TGCATTGCTCATCTCTGTAGGAT 59.610 43.478 10.49 0.00 0.00 3.24
3302 3842 3.686016 ACAATGAGCCAAAGATAACGGT 58.314 40.909 0.00 0.00 0.00 4.83
3338 3881 8.677300 TCACCTAAATATGTTTCTCTGAAATGC 58.323 33.333 0.00 0.00 0.00 3.56
3434 3983 5.805486 GCAGATAATAACTGTCTCGTCACAA 59.195 40.000 0.00 0.00 37.64 3.33
3435 3984 5.125578 AGCAGATAATAACTGTCTCGTCACA 59.874 40.000 0.00 0.00 37.64 3.58
3436 3985 5.583495 AGCAGATAATAACTGTCTCGTCAC 58.417 41.667 0.00 0.00 37.64 3.67
3437 3986 5.836821 AGCAGATAATAACTGTCTCGTCA 57.163 39.130 0.00 0.00 37.64 4.35
3438 3987 6.752351 TGAAAGCAGATAATAACTGTCTCGTC 59.248 38.462 0.00 1.32 37.64 4.20
3439 3988 6.631016 TGAAAGCAGATAATAACTGTCTCGT 58.369 36.000 0.00 0.00 37.64 4.18
3450 3999 7.337689 TGTTAGCATGAACTGAAAGCAGATAAT 59.662 33.333 0.00 0.00 45.17 1.28
3614 4163 1.728323 TGACCTCATGACCACAAGGA 58.272 50.000 3.59 0.00 38.69 3.36
3634 4183 1.566703 TGTTTCCAGGACTTGAACCCA 59.433 47.619 0.00 0.00 0.00 4.51
3722 4271 4.452733 GCTCCCGCTTGCGTAGGT 62.453 66.667 13.97 0.00 0.00 3.08
3726 4275 3.019003 ATGTAGCTCCCGCTTGCGT 62.019 57.895 13.97 0.00 46.47 5.24
4036 4586 7.264221 TCACATTACTGCACAAAGACAAAAAT 58.736 30.769 0.00 0.00 0.00 1.82
4171 4722 2.181205 GACTGCAGAAGATTCGTCTCG 58.819 52.381 23.35 0.00 0.00 4.04
4359 4910 2.870411 GACACGGTTTGCTAACTGAACT 59.130 45.455 23.84 7.44 42.20 3.01
4502 5053 2.614520 CTCGTCACAGTAGGACATCGAT 59.385 50.000 0.00 0.00 34.97 3.59
4573 5124 7.502895 TGAATCTCTCTACCATGGTACTACTTC 59.497 40.741 21.05 16.80 0.00 3.01
4772 5323 3.363341 AATAAAACACTGCACAACCCG 57.637 42.857 0.00 0.00 0.00 5.28
4840 5391 9.822185 AGTGCAGAAAGAAAACTAAATTCAATT 57.178 25.926 0.00 0.00 0.00 2.32
4841 5392 9.468532 GAGTGCAGAAAGAAAACTAAATTCAAT 57.531 29.630 0.00 0.00 0.00 2.57
4842 5393 8.686334 AGAGTGCAGAAAGAAAACTAAATTCAA 58.314 29.630 0.00 0.00 0.00 2.69
4843 5394 8.131100 CAGAGTGCAGAAAGAAAACTAAATTCA 58.869 33.333 0.00 0.00 0.00 2.57
4844 5395 8.131731 ACAGAGTGCAGAAAGAAAACTAAATTC 58.868 33.333 0.00 0.00 0.00 2.17
4845 5396 8.000780 ACAGAGTGCAGAAAGAAAACTAAATT 57.999 30.769 0.00 0.00 0.00 1.82
4846 5397 7.573968 ACAGAGTGCAGAAAGAAAACTAAAT 57.426 32.000 0.00 0.00 0.00 1.40
4855 5410 3.558931 TGGAAACAGAGTGCAGAAAGA 57.441 42.857 0.00 0.00 35.01 2.52
4917 5472 2.556622 CGAGGCAACCCATGTAAACTTT 59.443 45.455 0.00 0.00 37.17 2.66
4923 5478 1.220749 GCTCGAGGCAACCCATGTA 59.779 57.895 15.58 0.00 41.35 2.29
4924 5479 1.264749 TAGCTCGAGGCAACCCATGT 61.265 55.000 15.58 0.00 44.79 3.21
4967 5689 4.038080 CGGTTCCTGCGGTTTGCC 62.038 66.667 0.00 0.00 45.60 4.52
4996 5730 5.540400 TTGTCCGACCTTCTTCTTAGAAA 57.460 39.130 0.00 0.00 39.80 2.52
5013 5748 4.884164 CCCATTTCTCCTGTAAGATTGTCC 59.116 45.833 0.00 0.00 34.07 4.02
5063 5798 8.981659 CCTAAAACCAGAAAAAGGATCCAATAT 58.018 33.333 15.82 0.00 0.00 1.28
5066 5801 6.377912 TCCTAAAACCAGAAAAAGGATCCAA 58.622 36.000 15.82 0.00 0.00 3.53
5074 5809 5.773091 AGAGGGTTCCTAAAACCAGAAAAA 58.227 37.500 9.04 0.00 45.51 1.94
5313 6059 9.593134 TGCGCCATTTTATCAAATATTTTAGTT 57.407 25.926 4.18 0.00 30.90 2.24
5314 6060 9.762933 ATGCGCCATTTTATCAAATATTTTAGT 57.237 25.926 4.18 0.00 30.90 2.24
5369 6116 7.646130 TGTGAATATTCTTTTTGAACCGTGAAC 59.354 33.333 16.24 1.52 37.52 3.18
5437 6500 2.628178 ACCTAGGAAACCAAGCAAAAGC 59.372 45.455 17.98 0.00 0.00 3.51
5443 6506 4.583073 TCTTCAAAACCTAGGAAACCAAGC 59.417 41.667 17.98 0.00 0.00 4.01
5493 6556 2.222027 CCTTTTCGAGAAGCACAGGTT 58.778 47.619 10.12 0.00 0.00 3.50
5494 6557 1.543429 CCCTTTTCGAGAAGCACAGGT 60.543 52.381 10.12 0.00 0.00 4.00
5495 6558 1.160137 CCCTTTTCGAGAAGCACAGG 58.840 55.000 10.12 2.64 0.00 4.00
5496 6559 2.169832 TCCCTTTTCGAGAAGCACAG 57.830 50.000 10.12 0.00 0.00 3.66
5497 6560 2.631160 TTCCCTTTTCGAGAAGCACA 57.369 45.000 10.12 0.00 0.00 4.57
5498 6561 3.853676 GCTTTTCCCTTTTCGAGAAGCAC 60.854 47.826 10.12 0.00 43.43 4.40
5499 6562 2.293399 GCTTTTCCCTTTTCGAGAAGCA 59.707 45.455 10.12 0.00 43.43 3.91
5501 6564 3.315191 TGTGCTTTTCCCTTTTCGAGAAG 59.685 43.478 8.69 8.69 0.00 2.85
5502 6565 3.283751 TGTGCTTTTCCCTTTTCGAGAA 58.716 40.909 0.00 0.00 0.00 2.87
5503 6566 2.878406 CTGTGCTTTTCCCTTTTCGAGA 59.122 45.455 0.00 0.00 0.00 4.04
5504 6567 2.878406 TCTGTGCTTTTCCCTTTTCGAG 59.122 45.455 0.00 0.00 0.00 4.04
5505 6568 2.878406 CTCTGTGCTTTTCCCTTTTCGA 59.122 45.455 0.00 0.00 0.00 3.71
5506 6569 2.618709 ACTCTGTGCTTTTCCCTTTTCG 59.381 45.455 0.00 0.00 0.00 3.46
5507 6570 3.381590 ACACTCTGTGCTTTTCCCTTTTC 59.618 43.478 0.00 0.00 36.98 2.29
5508 6571 3.131046 CACACTCTGTGCTTTTCCCTTTT 59.869 43.478 0.00 0.00 41.89 2.27
5509 6572 2.689983 CACACTCTGTGCTTTTCCCTTT 59.310 45.455 0.00 0.00 41.89 3.11
5510 6573 2.301346 CACACTCTGTGCTTTTCCCTT 58.699 47.619 0.00 0.00 41.89 3.95
5511 6574 1.972872 CACACTCTGTGCTTTTCCCT 58.027 50.000 0.00 0.00 41.89 4.20
5543 6606 3.909732 ACTGTGTTCTTTCCCATTTCCA 58.090 40.909 0.00 0.00 0.00 3.53
5545 6608 5.043248 CACAACTGTGTTCTTTCCCATTTC 58.957 41.667 1.51 0.00 40.96 2.17


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

AutoCloner maintained by Alex Coulton.