Multiple sequence alignment - TraesCS5A01G132700

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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 TraesCS5A01G132700 chr5A 100.000 3512 0 0 1 3512 299255597 299252086 0.000000e+00 6486.0
1 TraesCS5A01G132700 chr5A 83.625 629 96 6 2886 3512 406832073 406831450 5.050000e-163 584.0
2 TraesCS5A01G132700 chr5D 95.117 2089 77 13 545 2610 224762228 224760142 0.000000e+00 3269.0
3 TraesCS5A01G132700 chr5D 89.435 549 41 9 1 540 224787699 224787159 0.000000e+00 676.0
4 TraesCS5A01G132700 chr5B 95.181 1577 70 6 701 2275 246951135 246952707 0.000000e+00 2486.0
5 TraesCS5A01G132700 chr5B 90.769 650 45 9 41 685 246948286 246948925 0.000000e+00 854.0
6 TraesCS5A01G132700 chr5B 83.784 629 99 3 2887 3512 206502618 206503246 8.390000e-166 593.0
7 TraesCS5A01G132700 chr5B 97.353 340 9 0 2271 2610 246958161 246958500 2.350000e-161 579.0
8 TraesCS5A01G132700 chr5B 71.990 1246 259 71 1244 2447 20171423 20170226 5.740000e-73 285.0
9 TraesCS5A01G132700 chr5B 81.910 199 22 9 269 466 455986610 455986425 4.690000e-34 156.0
10 TraesCS5A01G132700 chr5B 92.929 99 6 1 2790 2888 246958491 246958588 3.650000e-30 143.0
11 TraesCS5A01G132700 chr5B 97.727 44 0 1 1 44 246897199 246897241 1.350000e-09 75.0
12 TraesCS5A01G132700 chr2D 83.168 1408 226 7 1047 2450 584897209 584898609 0.000000e+00 1277.0
13 TraesCS5A01G132700 chr2D 83.835 631 95 5 2885 3512 107463194 107463820 8.390000e-166 593.0
14 TraesCS5A01G132700 chr2B 82.536 1443 239 10 1047 2481 705530102 705531539 0.000000e+00 1256.0
15 TraesCS5A01G132700 chr2B 81.972 1420 237 14 1047 2458 705328130 705326722 0.000000e+00 1186.0
16 TraesCS5A01G132700 chr2B 83.596 317 39 12 275 583 711865610 711865921 5.740000e-73 285.0
17 TraesCS5A01G132700 chr2A 81.696 1415 240 12 1047 2450 719204617 719206023 0.000000e+00 1160.0
18 TraesCS5A01G132700 chr2A 90.116 172 12 4 2610 2780 755118128 755117961 5.900000e-53 219.0
19 TraesCS5A01G132700 chr3A 89.968 628 62 1 2886 3512 476348413 476347786 0.000000e+00 809.0
20 TraesCS5A01G132700 chr3A 85.075 134 18 2 2071 2203 90365157 90365289 6.110000e-28 135.0
21 TraesCS5A01G132700 chr3A 89.691 97 10 0 2071 2167 90294363 90294459 1.320000e-24 124.0
22 TraesCS5A01G132700 chr6D 90.772 596 55 0 2917 3512 107953831 107953236 0.000000e+00 797.0
23 TraesCS5A01G132700 chr3D 85.987 628 85 3 2888 3512 445829132 445829759 0.000000e+00 669.0
24 TraesCS5A01G132700 chr3D 89.041 73 8 0 312 384 571090326 571090254 1.340000e-14 91.6
25 TraesCS5A01G132700 chr1D 82.803 628 105 3 2888 3512 3735863 3735236 3.060000e-155 558.0
26 TraesCS5A01G132700 chr7B 82.803 628 101 7 2890 3512 517626944 517627569 3.960000e-154 555.0
27 TraesCS5A01G132700 chr1B 83.502 594 96 1 2888 3479 484365034 484364441 1.420000e-153 553.0
28 TraesCS5A01G132700 chr1B 80.000 295 53 6 269 562 65787674 65787385 2.750000e-51 213.0
29 TraesCS5A01G132700 chr1B 84.956 113 14 3 269 381 41648465 41648574 1.030000e-20 111.0
30 TraesCS5A01G132700 chr1A 90.710 183 15 2 2610 2790 502808934 502809116 3.500000e-60 243.0
31 TraesCS5A01G132700 chr6A 86.777 121 13 3 269 389 99035111 99034994 7.910000e-27 132.0


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 TraesCS5A01G132700 chr5A 299252086 299255597 3511 True 6486 6486 100.000 1 3512 1 chr5A.!!$R1 3511
1 TraesCS5A01G132700 chr5A 406831450 406832073 623 True 584 584 83.625 2886 3512 1 chr5A.!!$R2 626
2 TraesCS5A01G132700 chr5D 224760142 224762228 2086 True 3269 3269 95.117 545 2610 1 chr5D.!!$R1 2065
3 TraesCS5A01G132700 chr5D 224787159 224787699 540 True 676 676 89.435 1 540 1 chr5D.!!$R2 539
4 TraesCS5A01G132700 chr5B 246948286 246952707 4421 False 1670 2486 92.975 41 2275 2 chr5B.!!$F3 2234
5 TraesCS5A01G132700 chr5B 206502618 206503246 628 False 593 593 83.784 2887 3512 1 chr5B.!!$F1 625
6 TraesCS5A01G132700 chr5B 20170226 20171423 1197 True 285 285 71.990 1244 2447 1 chr5B.!!$R1 1203
7 TraesCS5A01G132700 chr2D 584897209 584898609 1400 False 1277 1277 83.168 1047 2450 1 chr2D.!!$F2 1403
8 TraesCS5A01G132700 chr2D 107463194 107463820 626 False 593 593 83.835 2885 3512 1 chr2D.!!$F1 627
9 TraesCS5A01G132700 chr2B 705530102 705531539 1437 False 1256 1256 82.536 1047 2481 1 chr2B.!!$F1 1434
10 TraesCS5A01G132700 chr2B 705326722 705328130 1408 True 1186 1186 81.972 1047 2458 1 chr2B.!!$R1 1411
11 TraesCS5A01G132700 chr2A 719204617 719206023 1406 False 1160 1160 81.696 1047 2450 1 chr2A.!!$F1 1403
12 TraesCS5A01G132700 chr3A 476347786 476348413 627 True 809 809 89.968 2886 3512 1 chr3A.!!$R1 626
13 TraesCS5A01G132700 chr6D 107953236 107953831 595 True 797 797 90.772 2917 3512 1 chr6D.!!$R1 595
14 TraesCS5A01G132700 chr3D 445829132 445829759 627 False 669 669 85.987 2888 3512 1 chr3D.!!$F1 624
15 TraesCS5A01G132700 chr1D 3735236 3735863 627 True 558 558 82.803 2888 3512 1 chr1D.!!$R1 624
16 TraesCS5A01G132700 chr7B 517626944 517627569 625 False 555 555 82.803 2890 3512 1 chr7B.!!$F1 622
17 TraesCS5A01G132700 chr1B 484364441 484365034 593 True 553 553 83.502 2888 3479 1 chr1B.!!$R2 591

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
938 3156 0.458543 TTTCCAGCTCGACGATCAGC 60.459 55.000 0.00 0.0 35.73 4.26 F
940 3158 1.299014 CCAGCTCGACGATCAGCTC 60.299 63.158 7.08 0.0 44.47 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 4126 0.103208 GAGCCACTCCATGTACCTCG 59.897 60.0 0.0 0.0 0.0 4.63 R
2704 4982 0.253044 TTCCGCCCCTGATTCTTCTG 59.747 55.0 0.0 0.0 0.0 3.02 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
30 31 1.460504 CCCTACGAGACTAGCACACA 58.539 55.000 0.00 0.00 0.00 3.72
31 32 1.816835 CCCTACGAGACTAGCACACAA 59.183 52.381 0.00 0.00 0.00 3.33
33 34 2.415625 CCTACGAGACTAGCACACAACC 60.416 54.545 0.00 0.00 0.00 3.77
75 76 8.743714 GGAAGTAACTTGAGAATTGATTTCCAT 58.256 33.333 0.00 0.00 34.67 3.41
99 100 3.303351 AATGATCCCACCATTCTGTCC 57.697 47.619 0.00 0.00 28.89 4.02
115 116 1.061546 GTCCCCAGGTAGGTTGTTGA 58.938 55.000 0.00 0.00 34.66 3.18
117 118 2.136863 TCCCCAGGTAGGTTGTTGAAA 58.863 47.619 0.00 0.00 34.66 2.69
119 120 2.825532 CCCCAGGTAGGTTGTTGAAATG 59.174 50.000 0.00 0.00 34.66 2.32
135 136 5.659440 TGAAATGGTAAGCTTCCCAAATC 57.341 39.130 15.44 15.42 33.66 2.17
136 137 5.332743 TGAAATGGTAAGCTTCCCAAATCT 58.667 37.500 15.44 0.00 33.66 2.40
177 181 6.573664 TCTTATGTGTTGAGGAATTTGTGG 57.426 37.500 0.00 0.00 0.00 4.17
178 182 6.303054 TCTTATGTGTTGAGGAATTTGTGGA 58.697 36.000 0.00 0.00 0.00 4.02
179 183 6.430925 TCTTATGTGTTGAGGAATTTGTGGAG 59.569 38.462 0.00 0.00 0.00 3.86
196 200 3.939592 GTGGAGGTGTTTCATAAGTAGGC 59.060 47.826 0.00 0.00 0.00 3.93
230 234 6.742559 GGTAGAGATGTCCAATACCCTTAA 57.257 41.667 0.00 0.00 31.56 1.85
381 387 9.258826 TGTGAAACTGATTATTTCAAAATGTGG 57.741 29.630 1.94 0.00 45.19 4.17
453 460 6.097554 TCTCATTTAAAGGTTTTGGTGCAAGA 59.902 34.615 0.00 0.00 0.00 3.02
594 612 6.653740 GGTCTGCCATATTAGGGTTACATTAC 59.346 42.308 0.00 0.00 34.09 1.89
633 652 2.801077 AAGTTACATAGTGGTGGGCC 57.199 50.000 0.00 0.00 0.00 5.80
647 666 1.379576 GGGCCAGCTGCTGAAATCT 60.380 57.895 30.10 0.00 40.92 2.40
714 2928 7.591006 AAATAAGTATACGTTGTGAGGTGTG 57.409 36.000 0.00 0.00 0.00 3.82
718 2932 3.746045 ATACGTTGTGAGGTGTGACTT 57.254 42.857 0.00 0.00 0.00 3.01
765 2980 1.729149 CGCTCAATTTTCCACTTCGCC 60.729 52.381 0.00 0.00 0.00 5.54
839 3057 2.092158 TGACCTCACAATTGTTGACCCA 60.092 45.455 8.77 2.14 0.00 4.51
854 3072 1.002544 GACCCAGTCAAGGAACTCAGG 59.997 57.143 0.00 0.00 38.49 3.86
857 3075 1.699634 CCAGTCAAGGAACTCAGGGAA 59.300 52.381 0.00 0.00 38.49 3.97
884 3102 1.996191 GTGATTGGTGAGCTTCGTCTC 59.004 52.381 0.00 0.00 0.00 3.36
905 3123 3.702555 GCACGCTCACGGTCACAC 61.703 66.667 0.00 0.00 46.04 3.82
935 3153 1.133407 ACTCTTTCCAGCTCGACGATC 59.867 52.381 0.00 0.00 0.00 3.69
936 3154 1.133216 CTCTTTCCAGCTCGACGATCA 59.867 52.381 0.00 0.00 0.00 2.92
937 3155 1.133216 TCTTTCCAGCTCGACGATCAG 59.867 52.381 0.00 0.00 0.00 2.90
938 3156 0.458543 TTTCCAGCTCGACGATCAGC 60.459 55.000 0.00 0.00 35.73 4.26
940 3158 1.299014 CCAGCTCGACGATCAGCTC 60.299 63.158 7.08 0.00 44.47 4.09
1264 3509 1.503542 GGTGCCATCTCTTGCGTTG 59.496 57.895 0.00 0.00 0.00 4.10
1584 3829 4.459089 GTGACTCTGCCCGGGCTC 62.459 72.222 43.34 32.38 42.51 4.70
1706 3951 1.543944 TTCATGGACGAGCAGAGGCA 61.544 55.000 0.00 0.00 44.61 4.75
1777 4028 3.790437 CGGCCATGAGGGAGCACT 61.790 66.667 2.24 0.00 40.01 4.40
2504 4777 4.638865 GGATACAAACACCATAAGTCCACC 59.361 45.833 0.00 0.00 0.00 4.61
2533 4806 4.250464 ACGAAATCGATGCCAAACTTAGA 58.750 39.130 10.16 0.00 43.02 2.10
2610 4888 7.322664 AGGATTTGCATGTGTATGTTTTAAGG 58.677 34.615 0.00 0.00 36.65 2.69
2611 4889 6.534793 GGATTTGCATGTGTATGTTTTAAGGG 59.465 38.462 0.00 0.00 36.65 3.95
2612 4890 4.448537 TGCATGTGTATGTTTTAAGGGC 57.551 40.909 0.00 0.00 36.65 5.19
2613 4891 4.085733 TGCATGTGTATGTTTTAAGGGCT 58.914 39.130 0.00 0.00 36.65 5.19
2614 4892 4.526262 TGCATGTGTATGTTTTAAGGGCTT 59.474 37.500 0.00 0.00 36.65 4.35
2615 4893 5.011533 TGCATGTGTATGTTTTAAGGGCTTT 59.988 36.000 0.00 0.00 36.65 3.51
2616 4894 5.348451 GCATGTGTATGTTTTAAGGGCTTTG 59.652 40.000 0.00 0.00 36.65 2.77
2617 4895 4.877282 TGTGTATGTTTTAAGGGCTTTGC 58.123 39.130 0.00 0.00 0.00 3.68
2618 4896 4.586841 TGTGTATGTTTTAAGGGCTTTGCT 59.413 37.500 0.00 0.00 0.00 3.91
2619 4897 5.770663 TGTGTATGTTTTAAGGGCTTTGCTA 59.229 36.000 0.00 0.00 0.00 3.49
2620 4898 6.090783 GTGTATGTTTTAAGGGCTTTGCTAC 58.909 40.000 0.00 0.00 0.00 3.58
2621 4899 5.770663 TGTATGTTTTAAGGGCTTTGCTACA 59.229 36.000 0.00 0.00 0.00 2.74
2622 4900 4.577834 TGTTTTAAGGGCTTTGCTACAC 57.422 40.909 0.00 0.00 0.00 2.90
2623 4901 3.319689 TGTTTTAAGGGCTTTGCTACACC 59.680 43.478 0.00 0.00 0.00 4.16
2624 4902 3.518992 TTTAAGGGCTTTGCTACACCT 57.481 42.857 0.00 0.00 0.00 4.00
2625 4903 4.644163 TTTAAGGGCTTTGCTACACCTA 57.356 40.909 0.00 0.00 0.00 3.08
2626 4904 2.491675 AAGGGCTTTGCTACACCTAC 57.508 50.000 0.00 0.00 0.00 3.18
2627 4905 0.249398 AGGGCTTTGCTACACCTACG 59.751 55.000 0.00 0.00 0.00 3.51
2628 4906 0.036671 GGGCTTTGCTACACCTACGT 60.037 55.000 0.00 0.00 0.00 3.57
2629 4907 1.205417 GGGCTTTGCTACACCTACGTA 59.795 52.381 0.00 0.00 0.00 3.57
2630 4908 2.265683 GGCTTTGCTACACCTACGTAC 58.734 52.381 0.00 0.00 0.00 3.67
2631 4909 2.353011 GGCTTTGCTACACCTACGTACA 60.353 50.000 0.00 0.00 0.00 2.90
2632 4910 3.319755 GCTTTGCTACACCTACGTACAA 58.680 45.455 0.00 0.00 0.00 2.41
2633 4911 3.122445 GCTTTGCTACACCTACGTACAAC 59.878 47.826 0.00 0.00 0.00 3.32
2634 4912 4.300803 CTTTGCTACACCTACGTACAACA 58.699 43.478 0.00 0.00 0.00 3.33
2635 4913 3.287312 TGCTACACCTACGTACAACAC 57.713 47.619 0.00 0.00 0.00 3.32
2636 4914 2.030007 TGCTACACCTACGTACAACACC 60.030 50.000 0.00 0.00 0.00 4.16
2637 4915 2.672195 GCTACACCTACGTACAACACCC 60.672 54.545 0.00 0.00 0.00 4.61
2638 4916 0.681175 ACACCTACGTACAACACCCC 59.319 55.000 0.00 0.00 0.00 4.95
2639 4917 0.388907 CACCTACGTACAACACCCCG 60.389 60.000 0.00 0.00 0.00 5.73
2640 4918 0.827507 ACCTACGTACAACACCCCGT 60.828 55.000 0.00 0.00 37.33 5.28
2641 4919 1.173043 CCTACGTACAACACCCCGTA 58.827 55.000 0.00 0.00 34.95 4.02
2642 4920 1.543802 CCTACGTACAACACCCCGTAA 59.456 52.381 0.00 0.00 35.62 3.18
2643 4921 2.029470 CCTACGTACAACACCCCGTAAA 60.029 50.000 0.00 0.00 35.62 2.01
2644 4922 1.864565 ACGTACAACACCCCGTAAAC 58.135 50.000 0.00 0.00 0.00 2.01
2645 4923 1.147473 CGTACAACACCCCGTAAACC 58.853 55.000 0.00 0.00 0.00 3.27
2646 4924 1.270252 CGTACAACACCCCGTAAACCT 60.270 52.381 0.00 0.00 0.00 3.50
2647 4925 2.029470 CGTACAACACCCCGTAAACCTA 60.029 50.000 0.00 0.00 0.00 3.08
2648 4926 2.549064 ACAACACCCCGTAAACCTAC 57.451 50.000 0.00 0.00 0.00 3.18
2649 4927 1.072173 ACAACACCCCGTAAACCTACC 59.928 52.381 0.00 0.00 0.00 3.18
2650 4928 1.348696 CAACACCCCGTAAACCTACCT 59.651 52.381 0.00 0.00 0.00 3.08
2651 4929 0.978907 ACACCCCGTAAACCTACCTG 59.021 55.000 0.00 0.00 0.00 4.00
2652 4930 1.269012 CACCCCGTAAACCTACCTGA 58.731 55.000 0.00 0.00 0.00 3.86
2653 4931 1.624813 CACCCCGTAAACCTACCTGAA 59.375 52.381 0.00 0.00 0.00 3.02
2654 4932 1.904537 ACCCCGTAAACCTACCTGAAG 59.095 52.381 0.00 0.00 0.00 3.02
2655 4933 1.208776 CCCCGTAAACCTACCTGAAGG 59.791 57.143 0.00 0.00 42.82 3.46
2656 4934 1.406477 CCCGTAAACCTACCTGAAGGC 60.406 57.143 0.00 0.00 40.62 4.35
2657 4935 1.553704 CCGTAAACCTACCTGAAGGCT 59.446 52.381 0.00 0.00 40.62 4.58
2658 4936 2.618053 CGTAAACCTACCTGAAGGCTG 58.382 52.381 0.00 0.00 40.62 4.85
2659 4937 2.232941 CGTAAACCTACCTGAAGGCTGA 59.767 50.000 0.00 0.00 40.62 4.26
2660 4938 2.861147 AAACCTACCTGAAGGCTGAC 57.139 50.000 0.00 0.00 40.62 3.51
2661 4939 2.031495 AACCTACCTGAAGGCTGACT 57.969 50.000 0.00 0.00 40.62 3.41
2662 4940 2.031495 ACCTACCTGAAGGCTGACTT 57.969 50.000 0.00 0.00 43.65 3.01
2663 4941 1.625818 ACCTACCTGAAGGCTGACTTG 59.374 52.381 0.00 0.00 40.21 3.16
2664 4942 1.065854 CCTACCTGAAGGCTGACTTGG 60.066 57.143 0.00 0.00 40.21 3.61
2665 4943 0.324943 TACCTGAAGGCTGACTTGGC 59.675 55.000 0.00 0.00 40.21 4.52
2671 4949 2.116125 GGCTGACTTGGCCTGGTT 59.884 61.111 3.32 0.00 45.57 3.67
2672 4950 1.531602 GGCTGACTTGGCCTGGTTT 60.532 57.895 3.32 0.00 45.57 3.27
2673 4951 0.251165 GGCTGACTTGGCCTGGTTTA 60.251 55.000 3.32 0.00 45.57 2.01
2674 4952 1.616159 GCTGACTTGGCCTGGTTTAA 58.384 50.000 3.32 0.00 0.00 1.52
2675 4953 2.171003 GCTGACTTGGCCTGGTTTAAT 58.829 47.619 3.32 0.00 0.00 1.40
2676 4954 2.562738 GCTGACTTGGCCTGGTTTAATT 59.437 45.455 3.32 0.00 0.00 1.40
2677 4955 3.614870 GCTGACTTGGCCTGGTTTAATTG 60.615 47.826 3.32 0.00 0.00 2.32
2678 4956 2.896685 TGACTTGGCCTGGTTTAATTGG 59.103 45.455 3.32 0.00 0.00 3.16
2679 4957 3.161866 GACTTGGCCTGGTTTAATTGGA 58.838 45.455 3.32 0.00 0.00 3.53
2680 4958 3.576550 GACTTGGCCTGGTTTAATTGGAA 59.423 43.478 3.32 0.00 0.00 3.53
2681 4959 3.323691 ACTTGGCCTGGTTTAATTGGAAC 59.676 43.478 3.32 0.00 0.00 3.62
2682 4960 2.964209 TGGCCTGGTTTAATTGGAACA 58.036 42.857 3.32 0.00 0.00 3.18
2683 4961 2.896685 TGGCCTGGTTTAATTGGAACAG 59.103 45.455 3.32 5.29 42.39 3.16
2684 4962 3.161866 GGCCTGGTTTAATTGGAACAGA 58.838 45.455 8.92 0.00 42.39 3.41
2685 4963 3.576550 GGCCTGGTTTAATTGGAACAGAA 59.423 43.478 8.92 0.00 42.39 3.02
2686 4964 4.039852 GGCCTGGTTTAATTGGAACAGAAA 59.960 41.667 8.92 0.00 42.39 2.52
2687 4965 5.454045 GGCCTGGTTTAATTGGAACAGAAAA 60.454 40.000 8.92 0.00 42.39 2.29
2688 4966 5.465390 GCCTGGTTTAATTGGAACAGAAAAC 59.535 40.000 8.92 0.00 42.39 2.43
2689 4967 5.689961 CCTGGTTTAATTGGAACAGAAAACG 59.310 40.000 8.92 0.00 42.39 3.60
2690 4968 5.593010 TGGTTTAATTGGAACAGAAAACGG 58.407 37.500 8.27 0.00 42.39 4.44
2691 4969 4.446385 GGTTTAATTGGAACAGAAAACGGC 59.554 41.667 8.27 0.00 42.39 5.68
2692 4970 2.812358 AATTGGAACAGAAAACGGCC 57.188 45.000 0.00 0.00 42.39 6.13
2693 4971 0.966179 ATTGGAACAGAAAACGGCCC 59.034 50.000 0.00 0.00 42.39 5.80
2694 4972 1.448922 TTGGAACAGAAAACGGCCCG 61.449 55.000 0.00 0.00 42.39 6.13
2695 4973 2.622962 GGAACAGAAAACGGCCCGG 61.623 63.158 8.57 0.00 0.00 5.73
2696 4974 2.596338 AACAGAAAACGGCCCGGG 60.596 61.111 19.09 19.09 0.00 5.73
2712 4990 3.100111 GGCCCCACCCAGAAGAAT 58.900 61.111 0.00 0.00 0.00 2.40
2713 4991 1.076705 GGCCCCACCCAGAAGAATC 60.077 63.158 0.00 0.00 0.00 2.52
2714 4992 1.691219 GCCCCACCCAGAAGAATCA 59.309 57.895 0.00 0.00 0.00 2.57
2715 4993 0.394899 GCCCCACCCAGAAGAATCAG 60.395 60.000 0.00 0.00 0.00 2.90
2716 4994 0.257039 CCCCACCCAGAAGAATCAGG 59.743 60.000 0.00 0.00 32.20 3.86
2719 4997 4.995594 CCCAGAAGAATCAGGGGC 57.004 61.111 0.00 0.00 46.18 5.80
2720 4998 1.153086 CCCAGAAGAATCAGGGGCG 60.153 63.158 0.00 0.00 46.18 6.13
2721 4999 1.153086 CCAGAAGAATCAGGGGCGG 60.153 63.158 0.00 0.00 0.00 6.13
2722 5000 1.626356 CCAGAAGAATCAGGGGCGGA 61.626 60.000 0.00 0.00 0.00 5.54
2723 5001 0.253044 CAGAAGAATCAGGGGCGGAA 59.747 55.000 0.00 0.00 0.00 4.30
2724 5002 0.543749 AGAAGAATCAGGGGCGGAAG 59.456 55.000 0.00 0.00 0.00 3.46
2725 5003 0.541863 GAAGAATCAGGGGCGGAAGA 59.458 55.000 0.00 0.00 0.00 2.87
2726 5004 0.543749 AAGAATCAGGGGCGGAAGAG 59.456 55.000 0.00 0.00 0.00 2.85
2727 5005 0.325671 AGAATCAGGGGCGGAAGAGA 60.326 55.000 0.00 0.00 0.00 3.10
2728 5006 0.541863 GAATCAGGGGCGGAAGAGAA 59.458 55.000 0.00 0.00 0.00 2.87
2729 5007 1.141858 GAATCAGGGGCGGAAGAGAAT 59.858 52.381 0.00 0.00 0.00 2.40
2730 5008 1.216990 ATCAGGGGCGGAAGAGAATT 58.783 50.000 0.00 0.00 0.00 2.17
2731 5009 1.874129 TCAGGGGCGGAAGAGAATTA 58.126 50.000 0.00 0.00 0.00 1.40
2732 5010 2.193127 TCAGGGGCGGAAGAGAATTAA 58.807 47.619 0.00 0.00 0.00 1.40
2733 5011 2.574369 TCAGGGGCGGAAGAGAATTAAA 59.426 45.455 0.00 0.00 0.00 1.52
2734 5012 3.202151 TCAGGGGCGGAAGAGAATTAAAT 59.798 43.478 0.00 0.00 0.00 1.40
2735 5013 3.954258 CAGGGGCGGAAGAGAATTAAATT 59.046 43.478 0.00 0.00 0.00 1.82
2736 5014 5.104277 TCAGGGGCGGAAGAGAATTAAATTA 60.104 40.000 0.00 0.00 0.00 1.40
2737 5015 5.770162 CAGGGGCGGAAGAGAATTAAATTAT 59.230 40.000 0.00 0.00 0.00 1.28
2738 5016 6.940298 CAGGGGCGGAAGAGAATTAAATTATA 59.060 38.462 0.00 0.00 0.00 0.98
2739 5017 7.119846 CAGGGGCGGAAGAGAATTAAATTATAG 59.880 40.741 0.00 0.00 0.00 1.31
2740 5018 7.017254 AGGGGCGGAAGAGAATTAAATTATAGA 59.983 37.037 0.00 0.00 0.00 1.98
2741 5019 7.664318 GGGGCGGAAGAGAATTAAATTATAGAA 59.336 37.037 0.00 0.00 0.00 2.10
2742 5020 9.063615 GGGCGGAAGAGAATTAAATTATAGAAA 57.936 33.333 0.00 0.00 0.00 2.52
2782 5060 8.226543 CGTAACAATTTTACGTAGGTGTAAGA 57.773 34.615 17.38 0.00 41.79 2.10
2783 5061 8.863049 CGTAACAATTTTACGTAGGTGTAAGAT 58.137 33.333 17.38 0.00 41.79 2.40
2795 5073 9.444600 ACGTAGGTGTAAGATTATTGATGTTTT 57.555 29.630 0.00 0.00 0.00 2.43
2805 5083 8.537728 AGATTATTGATGTTTTAAGATGCCCA 57.462 30.769 0.00 0.00 0.00 5.36
2806 5084 8.636213 AGATTATTGATGTTTTAAGATGCCCAG 58.364 33.333 0.00 0.00 0.00 4.45
2807 5085 4.454728 TTGATGTTTTAAGATGCCCAGC 57.545 40.909 0.00 0.00 0.00 4.85
2808 5086 2.423185 TGATGTTTTAAGATGCCCAGCG 59.577 45.455 0.00 0.00 0.00 5.18
2809 5087 0.525761 TGTTTTAAGATGCCCAGCGC 59.474 50.000 0.00 0.00 38.31 5.92
2828 5106 3.802722 GCAGAGCGAATGGATATTGTC 57.197 47.619 0.00 0.00 0.00 3.18
2846 5124 1.206878 TCCTGACAGGATGGACATGG 58.793 55.000 20.74 0.00 40.06 3.66
2847 5125 0.914644 CCTGACAGGATGGACATGGT 59.085 55.000 17.22 0.00 43.62 3.55
2848 5126 1.283029 CCTGACAGGATGGACATGGTT 59.717 52.381 17.22 0.00 43.62 3.67
2849 5127 2.291153 CCTGACAGGATGGACATGGTTT 60.291 50.000 17.22 0.00 43.62 3.27
2850 5128 2.751259 CTGACAGGATGGACATGGTTTG 59.249 50.000 0.00 0.00 43.62 2.93
2851 5129 2.108075 TGACAGGATGGACATGGTTTGT 59.892 45.455 0.00 0.00 43.62 2.83
2862 5140 3.551846 ACATGGTTTGTCCTTTTCTCGT 58.448 40.909 0.00 0.00 30.89 4.18
2863 5141 3.951680 ACATGGTTTGTCCTTTTCTCGTT 59.048 39.130 0.00 0.00 30.89 3.85
2864 5142 4.202010 ACATGGTTTGTCCTTTTCTCGTTG 60.202 41.667 0.00 0.00 30.89 4.10
2865 5143 3.611970 TGGTTTGTCCTTTTCTCGTTGA 58.388 40.909 0.00 0.00 37.07 3.18
2866 5144 4.204012 TGGTTTGTCCTTTTCTCGTTGAT 58.796 39.130 0.00 0.00 37.07 2.57
2867 5145 5.369833 TGGTTTGTCCTTTTCTCGTTGATA 58.630 37.500 0.00 0.00 37.07 2.15
2868 5146 5.237779 TGGTTTGTCCTTTTCTCGTTGATAC 59.762 40.000 0.00 0.00 37.07 2.24
2869 5147 5.469084 GGTTTGTCCTTTTCTCGTTGATACT 59.531 40.000 0.00 0.00 0.00 2.12
2870 5148 6.347483 GGTTTGTCCTTTTCTCGTTGATACTC 60.347 42.308 0.00 0.00 0.00 2.59
2871 5149 4.817517 TGTCCTTTTCTCGTTGATACTCC 58.182 43.478 0.00 0.00 0.00 3.85
2872 5150 4.182339 GTCCTTTTCTCGTTGATACTCCC 58.818 47.826 0.00 0.00 0.00 4.30
2873 5151 4.081586 GTCCTTTTCTCGTTGATACTCCCT 60.082 45.833 0.00 0.00 0.00 4.20
2874 5152 4.159879 TCCTTTTCTCGTTGATACTCCCTC 59.840 45.833 0.00 0.00 0.00 4.30
2875 5153 4.160626 CCTTTTCTCGTTGATACTCCCTCT 59.839 45.833 0.00 0.00 0.00 3.69
2876 5154 4.720649 TTTCTCGTTGATACTCCCTCTG 57.279 45.455 0.00 0.00 0.00 3.35
2877 5155 2.025155 TCTCGTTGATACTCCCTCTGC 58.975 52.381 0.00 0.00 0.00 4.26
2878 5156 1.067821 CTCGTTGATACTCCCTCTGCC 59.932 57.143 0.00 0.00 0.00 4.85
2879 5157 1.115467 CGTTGATACTCCCTCTGCCT 58.885 55.000 0.00 0.00 0.00 4.75
2880 5158 1.067821 CGTTGATACTCCCTCTGCCTC 59.932 57.143 0.00 0.00 0.00 4.70
2881 5159 1.067821 GTTGATACTCCCTCTGCCTCG 59.932 57.143 0.00 0.00 0.00 4.63
2882 5160 0.551396 TGATACTCCCTCTGCCTCGA 59.449 55.000 0.00 0.00 0.00 4.04
2883 5161 1.063942 TGATACTCCCTCTGCCTCGAA 60.064 52.381 0.00 0.00 0.00 3.71
2925 5203 5.494863 GCAAATTGCGTACCTTAACTTTG 57.505 39.130 0.90 0.00 31.71 2.77
3036 5317 7.828223 GCTAGGCTACTACTCTATACCATGTTA 59.172 40.741 0.00 0.00 0.00 2.41
3053 5334 4.890499 TGTTAATCTCCTCTCCCTCTCT 57.110 45.455 0.00 0.00 0.00 3.10
3098 5379 4.511527 CTGATGGATTATATCAGCCGCTT 58.488 43.478 0.00 0.00 43.38 4.68
3197 5478 2.114616 AGATTGTGCCGAATCCTCTCT 58.885 47.619 2.05 0.00 33.46 3.10
3210 5491 5.068460 CGAATCCTCTCTGGTATCTCTTGTT 59.932 44.000 0.00 0.00 37.07 2.83
3212 5493 7.521423 CGAATCCTCTCTGGTATCTCTTGTTAG 60.521 44.444 0.00 0.00 37.07 2.34
3243 5524 2.200081 AGCAGATACCCACCAATCACT 58.800 47.619 0.00 0.00 0.00 3.41
3326 5609 2.688507 ACCACACTTGTCTCGCATAAG 58.311 47.619 0.00 0.00 0.00 1.73
3348 5631 5.039480 GCGCATTGCAAGAGTATATGATT 57.961 39.130 9.69 0.00 45.45 2.57
3369 5652 0.104409 ACCTTGTCCTCCTCCTGGTT 60.104 55.000 0.00 0.00 34.23 3.67
3419 5702 1.406069 GCAATCCATGTCTCTGTCGGT 60.406 52.381 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.158385 TCCCACCTACAAGCAATTGGTT 60.158 45.455 16.92 16.92 35.98 3.67
31 32 1.427368 TCCCACCTACAAGCAATTGGT 59.573 47.619 3.82 3.82 0.00 3.67
33 34 3.157087 ACTTCCCACCTACAAGCAATTG 58.843 45.455 0.00 0.00 0.00 2.32
75 76 4.676109 ACAGAATGGTGGGATCATTTTGA 58.324 39.130 12.22 0.00 43.62 2.69
99 100 2.825532 CCATTTCAACAACCTACCTGGG 59.174 50.000 0.00 0.00 41.11 4.45
115 116 5.543790 ACAAGATTTGGGAAGCTTACCATTT 59.456 36.000 31.18 20.68 41.86 2.32
117 118 4.463891 CACAAGATTTGGGAAGCTTACCAT 59.536 41.667 31.18 17.77 41.86 3.55
119 120 3.826729 ACACAAGATTTGGGAAGCTTACC 59.173 43.478 21.92 21.92 39.34 2.85
135 136 7.993183 ACATAAGATATTCCTTGGGTACACAAG 59.007 37.037 27.79 27.79 45.71 3.16
136 137 7.773224 CACATAAGATATTCCTTGGGTACACAA 59.227 37.037 10.76 10.76 0.00 3.33
177 181 4.489306 AGGCCTACTTATGAAACACCTC 57.511 45.455 1.29 0.00 0.00 3.85
178 182 4.567747 CCAAGGCCTACTTATGAAACACCT 60.568 45.833 5.16 0.00 37.29 4.00
179 183 3.694566 CCAAGGCCTACTTATGAAACACC 59.305 47.826 5.16 0.00 37.29 4.16
196 200 4.202367 GGACATCTCTACCCATAACCAAGG 60.202 50.000 0.00 0.00 0.00 3.61
230 234 0.476771 AAACCCGAGTCATGGTGGTT 59.523 50.000 2.25 0.00 40.91 3.67
547 561 4.098349 CCCATTCTCTCTTCTCTCAGACAG 59.902 50.000 0.00 0.00 0.00 3.51
551 565 4.098349 CAGACCCATTCTCTCTTCTCTCAG 59.902 50.000 0.00 0.00 28.96 3.35
629 648 0.969409 AAGATTTCAGCAGCTGGCCC 60.969 55.000 22.62 9.35 46.50 5.80
714 2928 2.328099 CCGAGCCAACCAGCAAGTC 61.328 63.158 0.00 0.00 34.23 3.01
718 2932 2.662596 CTACCGAGCCAACCAGCA 59.337 61.111 0.00 0.00 34.23 4.41
765 2980 2.287547 GCACTCGATCTAGCAGGAGAAG 60.288 54.545 9.73 4.65 0.00 2.85
839 3057 2.370189 CAGTTCCCTGAGTTCCTTGACT 59.630 50.000 0.00 0.00 41.50 3.41
849 3067 0.987294 ATCACCACCAGTTCCCTGAG 59.013 55.000 0.00 0.00 41.50 3.35
854 3072 1.202879 TCACCAATCACCACCAGTTCC 60.203 52.381 0.00 0.00 0.00 3.62
857 3075 0.250901 GCTCACCAATCACCACCAGT 60.251 55.000 0.00 0.00 0.00 4.00
884 3102 3.414700 GACCGTGAGCGTGCTTGG 61.415 66.667 0.00 1.57 36.15 3.61
905 3123 2.353605 GCTGGAAAGAGTCAGAGTGAGG 60.354 54.545 0.00 0.00 33.11 3.86
935 3153 1.128692 GTTGGGAAAATCGTCGAGCTG 59.871 52.381 0.00 0.00 0.00 4.24
936 3154 1.439679 GTTGGGAAAATCGTCGAGCT 58.560 50.000 0.00 0.00 0.00 4.09
937 3155 0.446616 GGTTGGGAAAATCGTCGAGC 59.553 55.000 0.00 0.00 0.00 5.03
938 3156 2.094762 AGGTTGGGAAAATCGTCGAG 57.905 50.000 0.00 0.00 0.00 4.04
939 3157 2.554370 AAGGTTGGGAAAATCGTCGA 57.446 45.000 0.00 0.00 0.00 4.20
940 3158 3.636282 AAAAGGTTGGGAAAATCGTCG 57.364 42.857 0.00 0.00 0.00 5.12
941 3159 6.321848 TCTTAAAAGGTTGGGAAAATCGTC 57.678 37.500 0.00 0.00 0.00 4.20
942 3160 5.278808 GCTCTTAAAAGGTTGGGAAAATCGT 60.279 40.000 0.00 0.00 0.00 3.73
943 3161 5.161358 GCTCTTAAAAGGTTGGGAAAATCG 58.839 41.667 0.00 0.00 0.00 3.34
944 3162 5.011635 TGGCTCTTAAAAGGTTGGGAAAATC 59.988 40.000 0.00 0.00 0.00 2.17
945 3163 4.904853 TGGCTCTTAAAAGGTTGGGAAAAT 59.095 37.500 0.00 0.00 0.00 1.82
946 3164 4.100344 GTGGCTCTTAAAAGGTTGGGAAAA 59.900 41.667 0.00 0.00 0.00 2.29
1120 3362 4.190350 TGCATCGTGTAGCTGCAG 57.810 55.556 10.11 10.11 45.76 4.41
1584 3829 3.160047 ATCCTGAGAGGCCGGCTG 61.160 66.667 28.56 9.52 34.61 4.85
1706 3951 2.248248 TCACGAGGACCTTGACATTCT 58.752 47.619 16.24 0.00 0.00 2.40
1777 4028 2.024868 CGACGGCGAACACATCCAA 61.025 57.895 16.62 0.00 40.82 3.53
1862 4126 0.103208 GAGCCACTCCATGTACCTCG 59.897 60.000 0.00 0.00 0.00 4.63
2175 4448 3.161450 ACGACAGCCACACCCAGT 61.161 61.111 0.00 0.00 0.00 4.00
2504 4777 1.003545 GGCATCGATTTCGTCATGGTG 60.004 52.381 0.00 0.00 40.80 4.17
2533 4806 6.398234 AGAATGACTGTGCGAATCTATAGT 57.602 37.500 0.00 0.00 0.00 2.12
2595 4873 4.586841 AGCAAAGCCCTTAAAACATACACA 59.413 37.500 0.00 0.00 0.00 3.72
2610 4888 2.265683 GTACGTAGGTGTAGCAAAGCC 58.734 52.381 0.00 0.00 0.00 4.35
2611 4889 2.950433 TGTACGTAGGTGTAGCAAAGC 58.050 47.619 0.00 0.00 0.00 3.51
2612 4890 4.149396 GTGTTGTACGTAGGTGTAGCAAAG 59.851 45.833 0.00 0.00 0.00 2.77
2613 4891 4.050553 GTGTTGTACGTAGGTGTAGCAAA 58.949 43.478 0.00 0.00 0.00 3.68
2614 4892 3.552684 GGTGTTGTACGTAGGTGTAGCAA 60.553 47.826 0.00 0.00 0.00 3.91
2615 4893 2.030007 GGTGTTGTACGTAGGTGTAGCA 60.030 50.000 0.00 0.00 0.00 3.49
2616 4894 2.599659 GGTGTTGTACGTAGGTGTAGC 58.400 52.381 0.00 0.00 0.00 3.58
2617 4895 2.094545 GGGGTGTTGTACGTAGGTGTAG 60.095 54.545 0.00 0.00 0.00 2.74
2618 4896 1.892474 GGGGTGTTGTACGTAGGTGTA 59.108 52.381 0.00 0.00 0.00 2.90
2619 4897 0.681175 GGGGTGTTGTACGTAGGTGT 59.319 55.000 0.00 0.00 0.00 4.16
2620 4898 0.388907 CGGGGTGTTGTACGTAGGTG 60.389 60.000 0.00 0.00 0.00 4.00
2621 4899 0.827507 ACGGGGTGTTGTACGTAGGT 60.828 55.000 0.00 0.00 37.85 3.08
2622 4900 1.173043 TACGGGGTGTTGTACGTAGG 58.827 55.000 0.00 0.00 40.38 3.18
2623 4901 2.986479 GTTTACGGGGTGTTGTACGTAG 59.014 50.000 0.00 0.00 41.93 3.51
2624 4902 2.288518 GGTTTACGGGGTGTTGTACGTA 60.289 50.000 0.00 0.00 40.38 3.57
2625 4903 1.540146 GGTTTACGGGGTGTTGTACGT 60.540 52.381 0.00 0.00 42.71 3.57
2626 4904 1.147473 GGTTTACGGGGTGTTGTACG 58.853 55.000 0.00 0.00 0.00 3.67
2627 4905 2.549064 AGGTTTACGGGGTGTTGTAC 57.451 50.000 0.00 0.00 0.00 2.90
2628 4906 2.301583 GGTAGGTTTACGGGGTGTTGTA 59.698 50.000 0.00 0.00 0.00 2.41
2629 4907 1.072173 GGTAGGTTTACGGGGTGTTGT 59.928 52.381 0.00 0.00 0.00 3.32
2630 4908 1.348696 AGGTAGGTTTACGGGGTGTTG 59.651 52.381 0.00 0.00 0.00 3.33
2631 4909 1.348696 CAGGTAGGTTTACGGGGTGTT 59.651 52.381 0.00 0.00 0.00 3.32
2632 4910 0.978907 CAGGTAGGTTTACGGGGTGT 59.021 55.000 0.00 0.00 0.00 4.16
2633 4911 1.269012 TCAGGTAGGTTTACGGGGTG 58.731 55.000 0.00 0.00 0.00 4.61
2634 4912 1.904537 CTTCAGGTAGGTTTACGGGGT 59.095 52.381 0.00 0.00 0.00 4.95
2635 4913 1.208776 CCTTCAGGTAGGTTTACGGGG 59.791 57.143 0.00 0.00 0.00 5.73
2636 4914 1.406477 GCCTTCAGGTAGGTTTACGGG 60.406 57.143 0.00 0.00 37.63 5.28
2637 4915 1.553704 AGCCTTCAGGTAGGTTTACGG 59.446 52.381 0.00 0.00 37.63 4.02
2638 4916 2.232941 TCAGCCTTCAGGTAGGTTTACG 59.767 50.000 0.00 0.00 37.63 3.18
2639 4917 3.261137 AGTCAGCCTTCAGGTAGGTTTAC 59.739 47.826 0.00 0.00 37.63 2.01
2640 4918 3.517612 AGTCAGCCTTCAGGTAGGTTTA 58.482 45.455 0.00 0.00 37.63 2.01
2641 4919 2.339769 AGTCAGCCTTCAGGTAGGTTT 58.660 47.619 0.00 0.00 37.63 3.27
2642 4920 2.031495 AGTCAGCCTTCAGGTAGGTT 57.969 50.000 0.00 0.00 37.63 3.50
2643 4921 1.625818 CAAGTCAGCCTTCAGGTAGGT 59.374 52.381 0.00 0.00 37.63 3.08
2644 4922 1.065854 CCAAGTCAGCCTTCAGGTAGG 60.066 57.143 0.00 0.00 38.40 3.18
2645 4923 1.677217 GCCAAGTCAGCCTTCAGGTAG 60.677 57.143 0.00 0.00 37.57 3.18
2646 4924 0.324943 GCCAAGTCAGCCTTCAGGTA 59.675 55.000 0.00 0.00 37.57 3.08
2647 4925 1.073897 GCCAAGTCAGCCTTCAGGT 59.926 57.895 0.00 0.00 37.57 4.00
2648 4926 3.993535 GCCAAGTCAGCCTTCAGG 58.006 61.111 0.00 0.00 38.53 3.86
2655 4933 1.616159 TTAAACCAGGCCAAGTCAGC 58.384 50.000 5.01 0.00 0.00 4.26
2656 4934 3.056607 CCAATTAAACCAGGCCAAGTCAG 60.057 47.826 5.01 0.00 0.00 3.51
2657 4935 2.896685 CCAATTAAACCAGGCCAAGTCA 59.103 45.455 5.01 0.00 0.00 3.41
2658 4936 3.161866 TCCAATTAAACCAGGCCAAGTC 58.838 45.455 5.01 0.00 0.00 3.01
2659 4937 3.252554 TCCAATTAAACCAGGCCAAGT 57.747 42.857 5.01 0.00 0.00 3.16
2660 4938 3.323403 TGTTCCAATTAAACCAGGCCAAG 59.677 43.478 5.01 0.00 0.00 3.61
2661 4939 3.309296 TGTTCCAATTAAACCAGGCCAA 58.691 40.909 5.01 0.00 0.00 4.52
2662 4940 2.896685 CTGTTCCAATTAAACCAGGCCA 59.103 45.455 5.01 0.00 0.00 5.36
2663 4941 3.161866 TCTGTTCCAATTAAACCAGGCC 58.838 45.455 0.00 0.00 0.00 5.19
2664 4942 4.864704 TTCTGTTCCAATTAAACCAGGC 57.135 40.909 0.00 0.00 0.00 4.85
2665 4943 5.689961 CGTTTTCTGTTCCAATTAAACCAGG 59.310 40.000 0.00 0.00 0.00 4.45
2666 4944 5.689961 CCGTTTTCTGTTCCAATTAAACCAG 59.310 40.000 0.00 0.00 0.00 4.00
2667 4945 5.593010 CCGTTTTCTGTTCCAATTAAACCA 58.407 37.500 0.00 0.00 0.00 3.67
2668 4946 4.446385 GCCGTTTTCTGTTCCAATTAAACC 59.554 41.667 0.00 0.00 0.00 3.27
2669 4947 4.446385 GGCCGTTTTCTGTTCCAATTAAAC 59.554 41.667 0.00 0.00 0.00 2.01
2670 4948 4.501743 GGGCCGTTTTCTGTTCCAATTAAA 60.502 41.667 0.00 0.00 0.00 1.52
2671 4949 3.006003 GGGCCGTTTTCTGTTCCAATTAA 59.994 43.478 0.00 0.00 0.00 1.40
2672 4950 2.559231 GGGCCGTTTTCTGTTCCAATTA 59.441 45.455 0.00 0.00 0.00 1.40
2673 4951 1.343142 GGGCCGTTTTCTGTTCCAATT 59.657 47.619 0.00 0.00 0.00 2.32
2674 4952 0.966179 GGGCCGTTTTCTGTTCCAAT 59.034 50.000 0.00 0.00 0.00 3.16
2675 4953 1.448922 CGGGCCGTTTTCTGTTCCAA 61.449 55.000 19.97 0.00 0.00 3.53
2676 4954 1.894756 CGGGCCGTTTTCTGTTCCA 60.895 57.895 19.97 0.00 0.00 3.53
2677 4955 2.622962 CCGGGCCGTTTTCTGTTCC 61.623 63.158 26.32 0.00 0.00 3.62
2678 4956 2.622962 CCCGGGCCGTTTTCTGTTC 61.623 63.158 26.32 0.00 0.00 3.18
2679 4957 2.596338 CCCGGGCCGTTTTCTGTT 60.596 61.111 26.32 0.00 0.00 3.16
2695 4973 1.076705 GATTCTTCTGGGTGGGGCC 60.077 63.158 0.00 0.00 0.00 5.80
2696 4974 0.394899 CTGATTCTTCTGGGTGGGGC 60.395 60.000 0.00 0.00 0.00 5.80
2697 4975 0.257039 CCTGATTCTTCTGGGTGGGG 59.743 60.000 0.00 0.00 37.33 4.96
2698 4976 3.890527 CCTGATTCTTCTGGGTGGG 57.109 57.895 0.00 0.00 37.33 4.61
2703 4981 1.153086 CCGCCCCTGATTCTTCTGG 60.153 63.158 0.00 0.00 39.91 3.86
2704 4982 0.253044 TTCCGCCCCTGATTCTTCTG 59.747 55.000 0.00 0.00 0.00 3.02
2705 4983 0.543749 CTTCCGCCCCTGATTCTTCT 59.456 55.000 0.00 0.00 0.00 2.85
2706 4984 0.541863 TCTTCCGCCCCTGATTCTTC 59.458 55.000 0.00 0.00 0.00 2.87
2707 4985 0.543749 CTCTTCCGCCCCTGATTCTT 59.456 55.000 0.00 0.00 0.00 2.52
2708 4986 0.325671 TCTCTTCCGCCCCTGATTCT 60.326 55.000 0.00 0.00 0.00 2.40
2709 4987 0.541863 TTCTCTTCCGCCCCTGATTC 59.458 55.000 0.00 0.00 0.00 2.52
2710 4988 1.216990 ATTCTCTTCCGCCCCTGATT 58.783 50.000 0.00 0.00 0.00 2.57
2711 4989 1.216990 AATTCTCTTCCGCCCCTGAT 58.783 50.000 0.00 0.00 0.00 2.90
2712 4990 1.874129 TAATTCTCTTCCGCCCCTGA 58.126 50.000 0.00 0.00 0.00 3.86
2713 4991 2.710096 TTAATTCTCTTCCGCCCCTG 57.290 50.000 0.00 0.00 0.00 4.45
2714 4992 3.953542 ATTTAATTCTCTTCCGCCCCT 57.046 42.857 0.00 0.00 0.00 4.79
2715 4993 7.166167 TCTATAATTTAATTCTCTTCCGCCCC 58.834 38.462 0.00 0.00 0.00 5.80
2716 4994 8.617290 TTCTATAATTTAATTCTCTTCCGCCC 57.383 34.615 0.00 0.00 0.00 6.13
2769 5047 9.444600 AAAACATCAATAATCTTACACCTACGT 57.555 29.630 0.00 0.00 0.00 3.57
2779 5057 8.980596 TGGGCATCTTAAAACATCAATAATCTT 58.019 29.630 0.00 0.00 0.00 2.40
2780 5058 8.537728 TGGGCATCTTAAAACATCAATAATCT 57.462 30.769 0.00 0.00 0.00 2.40
2781 5059 7.383300 GCTGGGCATCTTAAAACATCAATAATC 59.617 37.037 0.00 0.00 0.00 1.75
2782 5060 7.212274 GCTGGGCATCTTAAAACATCAATAAT 58.788 34.615 0.00 0.00 0.00 1.28
2783 5061 6.572519 GCTGGGCATCTTAAAACATCAATAA 58.427 36.000 0.00 0.00 0.00 1.40
2784 5062 5.221028 CGCTGGGCATCTTAAAACATCAATA 60.221 40.000 0.00 0.00 0.00 1.90
2785 5063 4.440525 CGCTGGGCATCTTAAAACATCAAT 60.441 41.667 0.00 0.00 0.00 2.57
2786 5064 3.119531 CGCTGGGCATCTTAAAACATCAA 60.120 43.478 0.00 0.00 0.00 2.57
2787 5065 2.423185 CGCTGGGCATCTTAAAACATCA 59.577 45.455 0.00 0.00 0.00 3.07
2788 5066 2.796032 GCGCTGGGCATCTTAAAACATC 60.796 50.000 12.19 0.00 42.87 3.06
2789 5067 1.134946 GCGCTGGGCATCTTAAAACAT 59.865 47.619 12.19 0.00 42.87 2.71
2790 5068 0.525761 GCGCTGGGCATCTTAAAACA 59.474 50.000 12.19 0.00 42.87 2.83
2791 5069 3.329114 GCGCTGGGCATCTTAAAAC 57.671 52.632 12.19 0.00 42.87 2.43
2808 5086 3.802722 GACAATATCCATTCGCTCTGC 57.197 47.619 0.00 0.00 0.00 4.26
2828 5106 0.914644 ACCATGTCCATCCTGTCAGG 59.085 55.000 13.21 13.21 36.46 3.86
2829 5107 2.751259 CAAACCATGTCCATCCTGTCAG 59.249 50.000 0.00 0.00 0.00 3.51
2830 5108 2.108075 ACAAACCATGTCCATCCTGTCA 59.892 45.455 0.00 0.00 37.96 3.58
2831 5109 2.795329 ACAAACCATGTCCATCCTGTC 58.205 47.619 0.00 0.00 37.96 3.51
2832 5110 2.978156 ACAAACCATGTCCATCCTGT 57.022 45.000 0.00 0.00 37.96 4.00
2842 5120 4.036262 TCAACGAGAAAAGGACAAACCATG 59.964 41.667 0.00 0.00 42.04 3.66
2843 5121 4.204012 TCAACGAGAAAAGGACAAACCAT 58.796 39.130 0.00 0.00 42.04 3.55
2844 5122 3.611970 TCAACGAGAAAAGGACAAACCA 58.388 40.909 0.00 0.00 42.04 3.67
2845 5123 4.830826 ATCAACGAGAAAAGGACAAACC 57.169 40.909 0.00 0.00 39.35 3.27
2846 5124 6.347483 GGAGTATCAACGAGAAAAGGACAAAC 60.347 42.308 0.00 0.00 36.25 2.93
2847 5125 5.699458 GGAGTATCAACGAGAAAAGGACAAA 59.301 40.000 0.00 0.00 36.25 2.83
2848 5126 5.235516 GGAGTATCAACGAGAAAAGGACAA 58.764 41.667 0.00 0.00 36.25 3.18
2849 5127 4.322499 GGGAGTATCAACGAGAAAAGGACA 60.322 45.833 0.00 0.00 36.25 4.02
2850 5128 4.081586 AGGGAGTATCAACGAGAAAAGGAC 60.082 45.833 0.00 0.00 36.25 3.85
2851 5129 4.094476 AGGGAGTATCAACGAGAAAAGGA 58.906 43.478 0.00 0.00 36.25 3.36
2852 5130 4.160626 AGAGGGAGTATCAACGAGAAAAGG 59.839 45.833 0.00 0.00 36.25 3.11
2853 5131 5.105752 CAGAGGGAGTATCAACGAGAAAAG 58.894 45.833 0.00 0.00 36.25 2.27
2854 5132 4.620803 GCAGAGGGAGTATCAACGAGAAAA 60.621 45.833 0.00 0.00 36.25 2.29
2855 5133 3.119101 GCAGAGGGAGTATCAACGAGAAA 60.119 47.826 0.00 0.00 36.25 2.52
2856 5134 2.427453 GCAGAGGGAGTATCAACGAGAA 59.573 50.000 0.00 0.00 36.25 2.87
2857 5135 2.025155 GCAGAGGGAGTATCAACGAGA 58.975 52.381 0.00 0.00 36.25 4.04
2858 5136 1.067821 GGCAGAGGGAGTATCAACGAG 59.932 57.143 0.00 0.00 36.25 4.18
2859 5137 1.112113 GGCAGAGGGAGTATCAACGA 58.888 55.000 0.00 0.00 36.25 3.85
2860 5138 1.067821 GAGGCAGAGGGAGTATCAACG 59.932 57.143 0.00 0.00 36.25 4.10
2861 5139 1.067821 CGAGGCAGAGGGAGTATCAAC 59.932 57.143 0.00 0.00 36.25 3.18
2862 5140 1.063942 TCGAGGCAGAGGGAGTATCAA 60.064 52.381 0.00 0.00 36.25 2.57
2863 5141 0.551396 TCGAGGCAGAGGGAGTATCA 59.449 55.000 0.00 0.00 36.25 2.15
2864 5142 1.611491 CTTCGAGGCAGAGGGAGTATC 59.389 57.143 0.00 0.00 0.00 2.24
2865 5143 1.063567 ACTTCGAGGCAGAGGGAGTAT 60.064 52.381 0.00 0.00 0.00 2.12
2866 5144 0.331954 ACTTCGAGGCAGAGGGAGTA 59.668 55.000 0.00 0.00 0.00 2.59
2867 5145 0.543174 AACTTCGAGGCAGAGGGAGT 60.543 55.000 0.00 0.00 0.00 3.85
2868 5146 0.610687 AAACTTCGAGGCAGAGGGAG 59.389 55.000 0.00 0.00 0.00 4.30
2869 5147 1.056660 AAAACTTCGAGGCAGAGGGA 58.943 50.000 0.00 0.00 0.00 4.20
2870 5148 1.897560 AAAAACTTCGAGGCAGAGGG 58.102 50.000 0.00 0.00 0.00 4.30
2947 5225 5.424757 AGTGCATACCGCTTGTATTTCTTA 58.575 37.500 0.00 0.00 43.06 2.10
2959 5240 2.106683 GTGTGGGAGTGCATACCGC 61.107 63.158 9.95 9.95 42.89 5.68
3036 5317 1.144913 CGGAGAGAGGGAGAGGAGATT 59.855 57.143 0.00 0.00 0.00 2.40
3185 5466 3.761897 AGAGATACCAGAGAGGATTCGG 58.238 50.000 0.00 0.00 41.22 4.30
3197 5478 4.530710 AACGCACTAACAAGAGATACCA 57.469 40.909 0.00 0.00 0.00 3.25
3210 5491 3.067742 GGTATCTGCTAGGAAACGCACTA 59.932 47.826 0.00 0.00 31.95 2.74
3212 5493 2.202566 GGTATCTGCTAGGAAACGCAC 58.797 52.381 0.00 0.00 31.95 5.34
3243 5524 2.679450 CGACCACGGAAGACACATTAA 58.321 47.619 0.00 0.00 35.72 1.40
3277 5558 4.000988 GCTTCAGGAAGTTTGGTATCGAA 58.999 43.478 10.47 0.00 40.45 3.71
3326 5609 4.675190 ATCATATACTCTTGCAATGCGC 57.325 40.909 0.00 0.00 42.89 6.09
3348 5631 0.545309 CCAGGAGGAGGACAAGGTGA 60.545 60.000 0.00 0.00 36.89 4.02
3369 5652 0.667993 CTCGGCTTGTTTCCTTTGCA 59.332 50.000 0.00 0.00 0.00 4.08
3391 5674 4.638865 CAGAGACATGGATTGCAAGATCAA 59.361 41.667 4.94 0.00 0.00 2.57
3419 5702 2.567169 ACAGAGTTTGGACATCGGATCA 59.433 45.455 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.