Multiple sequence alignment - TraesCS6B01G409600

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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 TraesCS6B01G409600 chr6B 100.000 3521 0 0 1 3521 683646192 683649712 0.000000e+00 6503.0
1 TraesCS6B01G409600 chr6B 89.070 1720 163 15 946 2658 683486829 683488530 0.000000e+00 2111.0
2 TraesCS6B01G409600 chr6B 85.047 321 31 8 180 495 633847179 633846871 9.490000e-81 311.0
3 TraesCS6B01G409600 chr6B 83.929 112 17 1 591 702 49733665 49733775 4.810000e-19 106.0
4 TraesCS6B01G409600 chr6B 83.333 72 5 5 533 600 482469296 482469364 3.800000e-05 60.2
5 TraesCS6B01G409600 chr6D 89.761 1719 154 16 946 2658 450344750 450343048 0.000000e+00 2180.0
6 TraesCS6B01G409600 chr6D 93.744 991 39 7 564 1543 450487949 450488927 0.000000e+00 1465.0
7 TraesCS6B01G409600 chr6D 89.666 329 33 1 2684 3012 3747373 3747046 5.440000e-113 418.0
8 TraesCS6B01G409600 chr6D 90.228 307 25 3 3009 3312 3747137 3746833 2.550000e-106 396.0
9 TraesCS6B01G409600 chr6D 88.991 218 23 1 2673 2889 54560065 54560282 5.790000e-68 268.0
10 TraesCS6B01G409600 chr6D 84.191 272 37 5 2392 2658 450488924 450489194 3.490000e-65 259.0
11 TraesCS6B01G409600 chr6D 89.109 202 22 0 3118 3319 54560279 54560480 5.830000e-63 252.0
12 TraesCS6B01G409600 chr6D 83.471 121 20 0 583 703 443751964 443751844 2.870000e-21 113.0
13 TraesCS6B01G409600 chr6D 83.333 114 19 0 578 691 86915170 86915057 4.810000e-19 106.0
14 TraesCS6B01G409600 chr6D 82.014 139 12 4 376 503 121625474 121625338 4.810000e-19 106.0
15 TraesCS6B01G409600 chr6A 89.750 1717 156 14 946 2658 595768919 595767219 0.000000e+00 2178.0
16 TraesCS6B01G409600 chr6A 90.939 1534 129 7 1133 2658 595892835 595894366 0.000000e+00 2054.0
17 TraesCS6B01G409600 chr6A 93.657 1072 47 5 850 1918 595827642 595828695 0.000000e+00 1583.0
18 TraesCS6B01G409600 chr6A 89.493 276 29 0 577 852 595827326 595827601 2.010000e-92 350.0
19 TraesCS6B01G409600 chr6A 94.737 209 9 2 937 1144 595891552 595891759 1.220000e-84 324.0
20 TraesCS6B01G409600 chr6A 84.466 206 31 1 3317 3521 595894377 595894582 5.960000e-48 202.0
21 TraesCS6B01G409600 chr6A 91.304 46 4 0 533 578 18854637 18854592 2.930000e-06 63.9
22 TraesCS6B01G409600 chr4B 97.168 565 14 2 1 565 502994369 502994931 0.000000e+00 953.0
23 TraesCS6B01G409600 chr4B 85.714 126 18 0 577 702 649597004 649597129 2.210000e-27 134.0
24 TraesCS6B01G409600 chr4B 89.583 96 10 0 2680 2775 624153789 624153694 4.770000e-24 122.0
25 TraesCS6B01G409600 chr5D 95.660 576 18 3 1 576 127882184 127882752 0.000000e+00 918.0
26 TraesCS6B01G409600 chr5D 96.491 57 1 1 119 174 535134813 535134869 3.740000e-15 93.5
27 TraesCS6B01G409600 chr1B 74.062 1253 245 47 989 2213 26857176 26855976 1.160000e-119 440.0
28 TraesCS6B01G409600 chr3D 75.801 905 164 34 1049 1942 426000125 425999265 1.180000e-109 407.0
29 TraesCS6B01G409600 chr3D 82.812 192 18 5 116 295 380383565 380383377 1.310000e-34 158.0
30 TraesCS6B01G409600 chr3D 80.672 119 18 5 2682 2797 9310580 9310696 1.740000e-13 87.9
31 TraesCS6B01G409600 chr7D 90.196 306 25 4 3014 3314 69054755 69055060 9.160000e-106 394.0
32 TraesCS6B01G409600 chr7D 89.109 303 29 2 3013 3312 612297834 612297533 1.190000e-99 374.0
33 TraesCS6B01G409600 chr7D 87.500 264 31 2 2749 3012 612298007 612297746 1.590000e-78 303.0
34 TraesCS6B01G409600 chr7D 87.550 249 27 4 2749 2995 69054582 69054828 5.750000e-73 285.0
35 TraesCS6B01G409600 chr7D 84.874 119 13 4 2877 2993 626254210 626254095 7.990000e-22 115.0
36 TraesCS6B01G409600 chr3B 84.031 382 35 9 140 507 770095901 770096270 9.360000e-91 344.0
37 TraesCS6B01G409600 chr3B 81.340 418 49 13 112 507 545009798 545009388 2.640000e-81 313.0
38 TraesCS6B01G409600 chr3B 78.338 397 40 21 120 503 598032757 598033120 7.660000e-52 215.0
39 TraesCS6B01G409600 chr3B 86.667 135 10 6 2681 2813 6301096 6301224 3.660000e-30 143.0
40 TraesCS6B01G409600 chr3B 74.320 331 71 13 2682 3005 543172398 543172721 1.030000e-25 128.0
41 TraesCS6B01G409600 chr3B 94.828 58 3 0 25 82 545009856 545009799 1.350000e-14 91.6
42 TraesCS6B01G409600 chr3B 76.821 151 35 0 3110 3260 144220189 144220039 6.260000e-13 86.1
43 TraesCS6B01G409600 chr4D 81.055 417 43 13 112 511 24696356 24695959 2.050000e-77 300.0
44 TraesCS6B01G409600 chr5A 83.737 289 21 11 73 339 589031088 589031372 2.100000e-62 250.0
45 TraesCS6B01G409600 chr5B 79.208 404 41 23 113 503 509469302 509469675 1.260000e-59 241.0
46 TraesCS6B01G409600 chr5B 80.000 200 16 10 112 291 675887416 675887611 3.690000e-25 126.0
47 TraesCS6B01G409600 chr5B 88.506 87 9 1 426 511 675888093 675888179 1.730000e-18 104.0
48 TraesCS6B01G409600 chr5B 89.583 48 2 2 536 580 32053913 32053960 1.370000e-04 58.4
49 TraesCS6B01G409600 chr5B 82.609 69 7 5 536 604 24673865 24673928 4.910000e-04 56.5
50 TraesCS6B01G409600 chr2A 81.373 204 15 10 142 341 734736637 734736821 1.020000e-30 145.0
51 TraesCS6B01G409600 chrUn 86.667 135 10 6 2681 2813 284911411 284911539 3.660000e-30 143.0
52 TraesCS6B01G409600 chrUn 89.583 48 2 2 536 580 301083541 301083494 1.370000e-04 58.4
53 TraesCS6B01G409600 chr4A 83.436 163 10 6 112 261 636650792 636650634 6.130000e-28 135.0
54 TraesCS6B01G409600 chr4A 83.803 142 23 0 2682 2823 713895340 713895481 6.130000e-28 135.0
55 TraesCS6B01G409600 chr3A 84.167 120 19 0 583 702 700207938 700207819 2.220000e-22 117.0
56 TraesCS6B01G409600 chr3A 84.348 115 18 0 577 691 700230076 700230190 2.870000e-21 113.0
57 TraesCS6B01G409600 chr2D 81.618 136 24 1 583 717 495102742 495102607 1.030000e-20 111.0
58 TraesCS6B01G409600 chr7A 80.159 126 21 4 2687 2810 66781787 66781664 1.350000e-14 91.6
59 TraesCS6B01G409600 chr2B 91.489 47 0 2 536 581 541163883 541163840 1.060000e-05 62.1
60 TraesCS6B01G409600 chr2B 97.143 35 1 0 1 35 1831678 1831712 3.800000e-05 60.2
61 TraesCS6B01G409600 chr1A 90.909 44 3 1 532 575 372636273 372636315 1.370000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G409600 chr6B 683646192 683649712 3520 False 6503.0 6503 100.000000 1 3521 1 chr6B.!!$F4 3520
1 TraesCS6B01G409600 chr6B 683486829 683488530 1701 False 2111.0 2111 89.070000 946 2658 1 chr6B.!!$F3 1712
2 TraesCS6B01G409600 chr6D 450343048 450344750 1702 True 2180.0 2180 89.761000 946 2658 1 chr6D.!!$R4 1712
3 TraesCS6B01G409600 chr6D 450487949 450489194 1245 False 862.0 1465 88.967500 564 2658 2 chr6D.!!$F2 2094
4 TraesCS6B01G409600 chr6D 3746833 3747373 540 True 407.0 418 89.947000 2684 3312 2 chr6D.!!$R5 628
5 TraesCS6B01G409600 chr6A 595767219 595768919 1700 True 2178.0 2178 89.750000 946 2658 1 chr6A.!!$R2 1712
6 TraesCS6B01G409600 chr6A 595827326 595828695 1369 False 966.5 1583 91.575000 577 1918 2 chr6A.!!$F1 1341
7 TraesCS6B01G409600 chr6A 595891552 595894582 3030 False 860.0 2054 90.047333 937 3521 3 chr6A.!!$F2 2584
8 TraesCS6B01G409600 chr4B 502994369 502994931 562 False 953.0 953 97.168000 1 565 1 chr4B.!!$F1 564
9 TraesCS6B01G409600 chr5D 127882184 127882752 568 False 918.0 918 95.660000 1 576 1 chr5D.!!$F1 575
10 TraesCS6B01G409600 chr1B 26855976 26857176 1200 True 440.0 440 74.062000 989 2213 1 chr1B.!!$R1 1224
11 TraesCS6B01G409600 chr3D 425999265 426000125 860 True 407.0 407 75.801000 1049 1942 1 chr3D.!!$R2 893

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
757 759 1.524621 GACATCCTGATGGCACCGG 60.525 63.158 8.12 0.0 46.06 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2584 3774 0.030235 GGGTGTCGCTTTCAAACCAC 59.97 55.0 0.0 0.0 32.28 4.16 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
261 262 3.576982 TCTGATGTTCCGTTGGTAGAACT 59.423 43.478 4.70 0.00 42.32 3.01
287 288 6.581166 CGCTTTTTGAGAAAATAGTACCCAAC 59.419 38.462 0.00 0.00 34.45 3.77
330 331 6.312426 CGCTTTTGGTGATTATTTTGCCATTA 59.688 34.615 0.00 0.00 0.00 1.90
481 483 6.380274 CAGGTCATTAGGTAGAGTTGGAGTTA 59.620 42.308 0.00 0.00 0.00 2.24
507 509 9.579932 AGTCATATGTTGTACATCTCTGATCTA 57.420 33.333 1.90 0.00 39.88 1.98
565 567 2.411547 GCACGTGCAAGCTTACTAGTTG 60.412 50.000 34.52 0.00 41.59 3.16
567 569 3.057734 ACGTGCAAGCTTACTAGTTGTC 58.942 45.455 0.00 0.00 0.00 3.18
605 607 6.524586 CACTCTCAAATTTCAAAATAGACCGC 59.475 38.462 0.00 0.00 0.00 5.68
608 610 6.093495 TCTCAAATTTCAAAATAGACCGCGAT 59.907 34.615 8.23 0.00 0.00 4.58
636 638 3.068590 AGTTTGGTGTGCTGATTTCAAGG 59.931 43.478 0.00 0.00 0.00 3.61
672 674 9.685276 TCAGGATTTGATTTAGCTTTCATCTAA 57.315 29.630 0.00 0.00 0.00 2.10
717 719 6.840527 ACATTTTCCCCTCAAATCAAAACAT 58.159 32.000 0.00 0.00 0.00 2.71
719 721 8.435982 ACATTTTCCCCTCAAATCAAAACATAA 58.564 29.630 0.00 0.00 0.00 1.90
720 722 9.282569 CATTTTCCCCTCAAATCAAAACATAAA 57.717 29.630 0.00 0.00 0.00 1.40
757 759 1.524621 GACATCCTGATGGCACCGG 60.525 63.158 8.12 0.00 46.06 5.28
1104 1173 0.319125 GCCTCATAGTACGCAGGCTC 60.319 60.000 15.98 0.00 46.88 4.70
1137 1206 4.003788 CTGTCCACCGCCGTCCTT 62.004 66.667 0.00 0.00 0.00 3.36
1483 2640 2.364973 TAGGCGCATGGGGAGTGA 60.365 61.111 10.83 0.00 0.00 3.41
1497 2654 2.192263 GGAGTGAAGGATCTGGAGGTT 58.808 52.381 0.00 0.00 0.00 3.50
1557 2714 2.743183 GCCATACTGCTTTCCTCACGAT 60.743 50.000 0.00 0.00 0.00 3.73
1629 2801 4.976925 CTCCCGCCGCTGCATAGG 62.977 72.222 0.00 3.43 37.32 2.57
1767 2942 1.338105 TGCTGTGCACAGGACTATGTC 60.338 52.381 39.92 24.44 43.94 3.06
1860 3035 0.681175 GCCACCTTCCAATGCTTGTT 59.319 50.000 0.00 0.00 0.00 2.83
1944 3119 2.412870 CACACTAACCTCACATTCGCA 58.587 47.619 0.00 0.00 0.00 5.10
1976 3151 1.810151 GATAGTTCCAAAGCGGTGCAA 59.190 47.619 0.00 0.00 35.57 4.08
1982 3157 0.318120 CCAAAGCGGTGCAAGGATTT 59.682 50.000 0.00 0.00 0.00 2.17
1987 3162 0.881118 GCGGTGCAAGGATTTCTTCA 59.119 50.000 0.00 0.00 32.41 3.02
1988 3163 1.401539 GCGGTGCAAGGATTTCTTCAC 60.402 52.381 0.00 0.00 35.12 3.18
1991 3166 1.200020 GTGCAAGGATTTCTTCACCCG 59.800 52.381 0.00 0.00 32.41 5.28
1992 3167 0.811281 GCAAGGATTTCTTCACCCGG 59.189 55.000 0.00 0.00 32.41 5.73
2002 3180 1.076533 CTTCACCCGGTTCATCGACG 61.077 60.000 0.00 0.00 0.00 5.12
2007 3194 1.211969 CCGGTTCATCGACGTGTCT 59.788 57.895 0.00 0.00 0.00 3.41
2026 3213 3.632604 GTCTCCTACCATGACGAATCTCA 59.367 47.826 0.00 0.00 0.00 3.27
2037 3224 1.482593 ACGAATCTCATCCTCCGCTTT 59.517 47.619 0.00 0.00 0.00 3.51
2038 3225 2.093447 ACGAATCTCATCCTCCGCTTTT 60.093 45.455 0.00 0.00 0.00 2.27
2109 3296 3.381272 TCAACCTGAAAAAGCTCCTTGTG 59.619 43.478 0.00 0.00 0.00 3.33
2127 3314 2.590007 GCCGATCTGCCTGCGAAT 60.590 61.111 0.00 0.00 0.00 3.34
2131 3318 0.811219 CGATCTGCCTGCGAATTGGA 60.811 55.000 0.00 0.00 0.00 3.53
2190 3377 0.036952 CACTCGAGGTCCTGCACATT 60.037 55.000 18.41 0.00 0.00 2.71
2230 3417 1.597461 GAGCCAACTTACGGGAGCT 59.403 57.895 0.00 0.00 0.00 4.09
2283 3470 0.990374 ATCACTGCCTCAAGGAGCTT 59.010 50.000 0.00 0.00 37.39 3.74
2313 3500 0.524816 GATTCTTGCAGCGCCACATG 60.525 55.000 2.29 5.23 0.00 3.21
2370 3557 1.890876 TGCAACGTGTTATCCTGCTT 58.109 45.000 7.56 0.00 34.10 3.91
2373 3560 3.815962 TGCAACGTGTTATCCTGCTTAAA 59.184 39.130 7.56 0.00 34.10 1.52
2400 3587 4.214986 TGGTCATGTTCGATACAATGGT 57.785 40.909 4.87 0.00 40.89 3.55
2419 3606 2.242196 GGTCTTTGGGATTGGGAGATGA 59.758 50.000 0.00 0.00 0.00 2.92
2421 3608 4.540715 GTCTTTGGGATTGGGAGATGATT 58.459 43.478 0.00 0.00 0.00 2.57
2458 3647 4.583489 GTCCTTGGAGCAATGATGATGAAT 59.417 41.667 0.00 0.00 0.00 2.57
2506 3695 1.004560 TGCAGGCCTCTCGTTGAAG 60.005 57.895 0.00 0.00 0.00 3.02
2510 3699 0.318762 AGGCCTCTCGTTGAAGTCAC 59.681 55.000 0.00 0.00 0.00 3.67
2512 3701 0.670854 GCCTCTCGTTGAAGTCACCC 60.671 60.000 0.00 0.00 0.00 4.61
2525 3714 1.842562 AGTCACCCTGGGATGATCTTG 59.157 52.381 22.23 5.21 0.00 3.02
2529 3718 1.699054 CCCTGGGATGATCTTGGCGA 61.699 60.000 7.01 0.00 0.00 5.54
2552 3742 2.401195 GCATTGCCGACTTCGAGC 59.599 61.111 0.00 2.87 43.02 5.03
2567 3757 1.757118 TCGAGCGATTCAGAAGGGATT 59.243 47.619 0.00 0.00 0.00 3.01
2581 3771 1.305930 GGGATTTTCGGCTTCGCTGT 61.306 55.000 0.00 0.00 36.18 4.40
2584 3774 1.635663 ATTTTCGGCTTCGCTGTCCG 61.636 55.000 0.00 0.00 44.16 4.79
2595 3791 0.041312 CGCTGTCCGTGGTTTGAAAG 60.041 55.000 0.00 0.00 0.00 2.62
2600 3796 0.462225 TCCGTGGTTTGAAAGCGACA 60.462 50.000 2.47 0.00 0.00 4.35
2640 3836 3.054213 TGGGATCAAAGCATGTGATGAGA 60.054 43.478 2.25 0.00 44.89 3.27
2648 3844 5.728637 AAGCATGTGATGAGACGGATATA 57.271 39.130 0.00 0.00 0.00 0.86
2658 3854 9.745880 GTGATGAGACGGATATAGAACTTTTTA 57.254 33.333 0.00 0.00 0.00 1.52
2674 3870 8.864087 AGAACTTTTTATCTTTTTCATGCCTCT 58.136 29.630 0.00 0.00 0.00 3.69
2736 3932 2.106736 GGGCCGTATCCGCGTTTA 59.893 61.111 4.92 0.00 0.00 2.01
2740 3936 0.936297 GCCGTATCCGCGTTTATCGT 60.936 55.000 4.92 0.00 42.13 3.73
2744 3940 1.071041 GTATCCGCGTTTATCGTTGGC 60.071 52.381 4.92 0.00 42.13 4.52
2755 3951 1.595929 TCGTTGGCCCACGAGAAAC 60.596 57.895 26.71 8.81 44.18 2.78
2758 3954 0.818040 GTTGGCCCACGAGAAACACT 60.818 55.000 0.00 0.00 0.00 3.55
2827 4023 9.431887 TCAAACGCTCAAAGTCTATTAATTAGT 57.568 29.630 0.00 0.00 0.00 2.24
2829 4025 8.773404 AACGCTCAAAGTCTATTAATTAGTGT 57.227 30.769 0.00 0.00 0.00 3.55
2864 4060 2.972625 TCCAAGAATCTTAGTGTGGCG 58.027 47.619 0.00 0.00 0.00 5.69
2894 4090 5.183530 TGTGATCTGATTTCCTTGTCCAT 57.816 39.130 0.00 0.00 0.00 3.41
2908 4104 2.827755 TGTCCATAGGTAGCTGGTTCA 58.172 47.619 4.27 1.50 34.03 3.18
2913 4109 4.473196 TCCATAGGTAGCTGGTTCAAATCA 59.527 41.667 4.27 0.00 34.03 2.57
2915 4111 5.471456 CCATAGGTAGCTGGTTCAAATCATC 59.529 44.000 4.27 0.00 0.00 2.92
2916 4112 3.535561 AGGTAGCTGGTTCAAATCATCG 58.464 45.455 0.00 0.00 0.00 3.84
2921 4117 2.487762 GCTGGTTCAAATCATCGTTCCA 59.512 45.455 0.00 0.00 0.00 3.53
2924 4120 3.252215 TGGTTCAAATCATCGTTCCACAC 59.748 43.478 0.00 0.00 0.00 3.82
2997 4193 2.478894 GACCAAAAGAATCGAACTCGCA 59.521 45.455 0.00 0.00 39.60 5.10
3005 4201 1.714794 ATCGAACTCGCAACCTCAAG 58.285 50.000 0.00 0.00 39.60 3.02
3006 4202 0.944311 TCGAACTCGCAACCTCAAGC 60.944 55.000 0.00 0.00 39.60 4.01
3007 4203 1.221466 CGAACTCGCAACCTCAAGCA 61.221 55.000 0.00 0.00 0.00 3.91
3008 4204 0.235926 GAACTCGCAACCTCAAGCAC 59.764 55.000 0.00 0.00 0.00 4.40
3009 4205 1.166531 AACTCGCAACCTCAAGCACC 61.167 55.000 0.00 0.00 0.00 5.01
3010 4206 2.664851 TCGCAACCTCAAGCACCG 60.665 61.111 0.00 0.00 0.00 4.94
3011 4207 4.389576 CGCAACCTCAAGCACCGC 62.390 66.667 0.00 0.00 0.00 5.68
3012 4208 3.286751 GCAACCTCAAGCACCGCA 61.287 61.111 0.00 0.00 0.00 5.69
3013 4209 2.844451 GCAACCTCAAGCACCGCAA 61.844 57.895 0.00 0.00 0.00 4.85
3014 4210 1.008538 CAACCTCAAGCACCGCAAC 60.009 57.895 0.00 0.00 0.00 4.17
3015 4211 1.152963 AACCTCAAGCACCGCAACT 60.153 52.632 0.00 0.00 0.00 3.16
3016 4212 0.751643 AACCTCAAGCACCGCAACTT 60.752 50.000 0.00 0.00 0.00 2.66
3017 4213 0.751643 ACCTCAAGCACCGCAACTTT 60.752 50.000 0.00 0.00 0.00 2.66
3018 4214 0.385390 CCTCAAGCACCGCAACTTTT 59.615 50.000 0.00 0.00 0.00 2.27
3019 4215 1.202405 CCTCAAGCACCGCAACTTTTT 60.202 47.619 0.00 0.00 0.00 1.94
3044 4240 9.810545 TTTTGTTTATTTTTCAGACTGGGTAAG 57.189 29.630 1.81 0.00 0.00 2.34
3045 4241 8.528044 TTGTTTATTTTTCAGACTGGGTAAGT 57.472 30.769 1.81 0.00 43.85 2.24
3046 4242 9.629878 TTGTTTATTTTTCAGACTGGGTAAGTA 57.370 29.630 1.81 0.00 40.07 2.24
3047 4243 9.280174 TGTTTATTTTTCAGACTGGGTAAGTAG 57.720 33.333 1.81 0.00 40.07 2.57
3048 4244 9.498176 GTTTATTTTTCAGACTGGGTAAGTAGA 57.502 33.333 1.81 0.00 40.07 2.59
3051 4247 8.990163 ATTTTTCAGACTGGGTAAGTAGAAAA 57.010 30.769 1.81 11.30 43.78 2.29
3052 4248 7.797038 TTTTCAGACTGGGTAAGTAGAAAAC 57.203 36.000 1.81 0.00 42.32 2.43
3053 4249 5.130292 TCAGACTGGGTAAGTAGAAAACG 57.870 43.478 1.81 0.00 40.07 3.60
3054 4250 4.586001 TCAGACTGGGTAAGTAGAAAACGT 59.414 41.667 1.81 0.00 40.07 3.99
3055 4251 4.684703 CAGACTGGGTAAGTAGAAAACGTG 59.315 45.833 0.00 0.00 40.07 4.49
3056 4252 4.586001 AGACTGGGTAAGTAGAAAACGTGA 59.414 41.667 0.00 0.00 40.07 4.35
3057 4253 5.069516 AGACTGGGTAAGTAGAAAACGTGAA 59.930 40.000 0.00 0.00 40.07 3.18
3058 4254 5.673514 ACTGGGTAAGTAGAAAACGTGAAA 58.326 37.500 0.00 0.00 37.36 2.69
3059 4255 6.114767 ACTGGGTAAGTAGAAAACGTGAAAA 58.885 36.000 0.00 0.00 37.36 2.29
3060 4256 6.598850 ACTGGGTAAGTAGAAAACGTGAAAAA 59.401 34.615 0.00 0.00 37.36 1.94
3084 4280 9.764363 AAAATAAGGACCAAAAGAATCAAACTC 57.236 29.630 0.00 0.00 0.00 3.01
3085 4281 5.438761 AAGGACCAAAAGAATCAAACTCG 57.561 39.130 0.00 0.00 0.00 4.18
3086 4282 3.253432 AGGACCAAAAGAATCAAACTCGC 59.747 43.478 0.00 0.00 0.00 5.03
3087 4283 3.004315 GGACCAAAAGAATCAAACTCGCA 59.996 43.478 0.00 0.00 0.00 5.10
3088 4284 4.499019 GGACCAAAAGAATCAAACTCGCAA 60.499 41.667 0.00 0.00 0.00 4.85
3089 4285 4.359706 ACCAAAAGAATCAAACTCGCAAC 58.640 39.130 0.00 0.00 0.00 4.17
3090 4286 3.735746 CCAAAAGAATCAAACTCGCAACC 59.264 43.478 0.00 0.00 0.00 3.77
3091 4287 4.499696 CCAAAAGAATCAAACTCGCAACCT 60.500 41.667 0.00 0.00 0.00 3.50
3098 4294 2.933878 AAACTCGCAACCTCACCGCA 62.934 55.000 0.00 0.00 0.00 5.69
3126 4322 2.814280 ACGTAGTTGACCTTCCACTG 57.186 50.000 0.00 0.00 37.78 3.66
3136 4332 3.090037 GACCTTCCACTGAGCTACTACA 58.910 50.000 0.00 0.00 0.00 2.74
3140 4336 5.133941 CCTTCCACTGAGCTACTACATCTA 58.866 45.833 0.00 0.00 0.00 1.98
3148 4344 8.409371 CACTGAGCTACTACATCTATTCTGAAA 58.591 37.037 0.00 0.00 0.00 2.69
3149 4345 8.972127 ACTGAGCTACTACATCTATTCTGAAAA 58.028 33.333 0.00 0.00 0.00 2.29
3277 4473 1.379843 AAGAATTTCGCCCGCCCAT 60.380 52.632 0.00 0.00 0.00 4.00
3280 4476 2.063541 GAATTTCGCCCGCCCATGAG 62.064 60.000 0.00 0.00 0.00 2.90
3288 4484 1.740043 GCCCGCCCATGAGAAAATTTG 60.740 52.381 0.00 0.00 0.00 2.32
3302 4498 4.222588 AGAAAATTTGCCCATTCGGAATCA 59.777 37.500 0.00 0.00 0.00 2.57
3312 4508 4.021544 CCCATTCGGAATCAAAAACCTTGA 60.022 41.667 0.00 0.00 0.00 3.02
3313 4509 5.337491 CCCATTCGGAATCAAAAACCTTGAT 60.337 40.000 0.00 0.00 40.57 2.57
3315 4511 6.650390 CCATTCGGAATCAAAAACCTTGATTT 59.350 34.615 12.59 0.00 45.88 2.17
3327 4523 6.432403 AAACCTTGATTTCAATTGCCCTAA 57.568 33.333 0.00 0.00 35.02 2.69
3328 4524 5.405935 ACCTTGATTTCAATTGCCCTAAC 57.594 39.130 0.00 0.00 35.02 2.34
3331 4527 5.639082 CCTTGATTTCAATTGCCCTAACAAC 59.361 40.000 0.00 0.00 35.02 3.32
3334 4530 1.540267 TCAATTGCCCTAACAACGGG 58.460 50.000 0.00 0.00 44.89 5.28
3342 4538 0.392595 CCTAACAACGGGAGGAAGGC 60.393 60.000 0.00 0.00 31.45 4.35
3357 4553 1.880819 AAGGCGCTTTTCTGGCATGG 61.881 55.000 7.64 0.00 0.00 3.66
3359 4555 2.202518 CGCTTTTCTGGCATGGCG 60.203 61.111 15.27 9.60 36.89 5.69
3373 4569 0.822532 ATGGCGACTAGACGGGTAGG 60.823 60.000 16.03 0.00 0.00 3.18
3376 4572 1.225704 CGACTAGACGGGTAGGGGT 59.774 63.158 6.72 0.00 0.00 4.95
3381 4577 0.186873 TAGACGGGTAGGGGTCCATC 59.813 60.000 0.00 0.00 33.66 3.51
3394 4591 2.220586 TCCATCCAACACCTCGCCA 61.221 57.895 0.00 0.00 0.00 5.69
3395 4592 1.077501 CCATCCAACACCTCGCCAT 60.078 57.895 0.00 0.00 0.00 4.40
3411 4608 3.135348 TCGCCATGGATCTCTTCAAGATT 59.865 43.478 18.40 0.00 45.06 2.40
3441 4638 4.459337 AGGAAGCGAAGGAAGGTTTATTTG 59.541 41.667 0.00 0.00 0.00 2.32
3442 4639 4.457949 GGAAGCGAAGGAAGGTTTATTTGA 59.542 41.667 0.00 0.00 0.00 2.69
3447 4644 5.631992 CGAAGGAAGGTTTATTTGAAGCTC 58.368 41.667 0.00 0.00 36.42 4.09
3448 4645 5.392057 CGAAGGAAGGTTTATTTGAAGCTCC 60.392 44.000 0.00 0.00 36.42 4.70
3458 4655 4.821589 GAAGCTCCGCGGTGAGGG 62.822 72.222 30.07 14.49 32.81 4.30
3467 4664 4.263572 CGGTGAGGGTTGGGTGCA 62.264 66.667 0.00 0.00 0.00 4.57
3468 4665 2.440599 GGTGAGGGTTGGGTGCAT 59.559 61.111 0.00 0.00 0.00 3.96
3471 4668 3.443045 GAGGGTTGGGTGCATGCG 61.443 66.667 14.09 0.00 0.00 4.73
3474 4671 3.747976 GGTTGGGTGCATGCGGTC 61.748 66.667 14.09 6.01 0.00 4.79
3502 4699 4.742201 GCGCCCTCGAGCAACTCA 62.742 66.667 6.99 0.00 38.10 3.41
3515 4712 4.840772 CGAGCAACTCAAGTAATTTGTTCG 59.159 41.667 5.29 5.29 43.12 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
261 262 5.998981 TGGGTACTATTTTCTCAAAAAGCGA 59.001 36.000 0.00 0.00 37.76 4.93
287 288 0.443869 CGAGTGGAAAGCATGGAACG 59.556 55.000 0.00 0.00 0.00 3.95
330 331 8.934023 TCTCAACAGTTTCCCTTTATTTACAT 57.066 30.769 0.00 0.00 0.00 2.29
336 338 6.365520 AGTGTTCTCAACAGTTTCCCTTTAT 58.634 36.000 0.00 0.00 42.19 1.40
481 483 8.476064 AGATCAGAGATGTACAACATATGACT 57.524 34.615 10.38 0.69 39.27 3.41
547 549 3.318017 AGACAACTAGTAAGCTTGCACG 58.682 45.455 17.21 9.15 0.00 5.34
584 586 5.627172 TCGCGGTCTATTTTGAAATTTGAG 58.373 37.500 6.13 0.00 0.00 3.02
589 591 7.490962 TTATGATCGCGGTCTATTTTGAAAT 57.509 32.000 21.76 4.60 0.00 2.17
590 592 6.912203 TTATGATCGCGGTCTATTTTGAAA 57.088 33.333 21.76 0.00 0.00 2.69
592 594 6.046593 ACTTTATGATCGCGGTCTATTTTGA 58.953 36.000 21.76 0.00 0.00 2.69
605 607 4.154015 TCAGCACACCAAACTTTATGATCG 59.846 41.667 0.00 0.00 0.00 3.69
608 610 6.040278 TGAAATCAGCACACCAAACTTTATGA 59.960 34.615 0.00 0.00 0.00 2.15
636 638 9.080915 GCTAAATCAAATCCTGAGTTTTCAATC 57.919 33.333 0.00 0.00 39.25 2.67
672 674 9.920133 AAATGTTTAAAACAAACCTTGCATTTT 57.080 22.222 0.00 0.00 45.86 1.82
673 675 9.920133 AAAATGTTTAAAACAAACCTTGCATTT 57.080 22.222 0.00 0.00 45.86 2.32
675 677 8.187480 GGAAAATGTTTAAAACAAACCTTGCAT 58.813 29.630 0.00 0.00 45.86 3.96
695 697 9.859152 TTTTATGTTTTGATTTGAGGGGAAAAT 57.141 25.926 0.00 0.00 0.00 1.82
717 719 0.891904 GCGGGCACAACCTCCTTTTA 60.892 55.000 0.00 0.00 39.10 1.52
719 721 2.597510 GCGGGCACAACCTCCTTT 60.598 61.111 0.00 0.00 39.10 3.11
720 722 3.884774 TGCGGGCACAACCTCCTT 61.885 61.111 0.00 0.00 39.10 3.36
853 902 2.352715 GGCATTGCAGTTTTCCAGGTAC 60.353 50.000 11.39 0.00 0.00 3.34
912 961 0.523966 GTAGGCTCGATCGGATCTGG 59.476 60.000 16.41 9.02 0.00 3.86
1483 2640 1.272147 GGCAACAACCTCCAGATCCTT 60.272 52.381 0.00 0.00 0.00 3.36
1497 2654 2.202395 GGAAGCTTGCCTGGCAACA 61.202 57.895 29.24 11.57 43.99 3.33
1543 2700 0.601057 TCGTGATCGTGAGGAAAGCA 59.399 50.000 0.00 0.00 38.33 3.91
1557 2714 1.666011 GTCCTTGAGGCAGTCGTGA 59.334 57.895 0.00 0.00 34.44 4.35
1650 2822 2.581354 GCCATGTCTCGCAGGACT 59.419 61.111 7.42 0.00 37.16 3.85
1813 2988 2.485426 CGATCACCATGAACTTGCACTT 59.515 45.455 0.00 0.00 0.00 3.16
1880 3055 5.084722 CGAATACGAGTCTTTTAGTGTCGT 58.915 41.667 1.01 1.01 45.32 4.34
1976 3151 1.702957 TGAACCGGGTGAAGAAATCCT 59.297 47.619 6.32 0.00 0.00 3.24
1982 3157 0.245539 GTCGATGAACCGGGTGAAGA 59.754 55.000 6.32 0.00 0.00 2.87
1987 3162 2.260434 CACGTCGATGAACCGGGT 59.740 61.111 12.58 0.00 0.00 5.28
1988 3163 1.804326 GACACGTCGATGAACCGGG 60.804 63.158 12.58 1.74 0.00 5.73
1991 3166 0.526662 AGGAGACACGTCGATGAACC 59.473 55.000 12.58 6.88 34.09 3.62
1992 3167 2.477525 GGTAGGAGACACGTCGATGAAC 60.478 54.545 12.58 2.21 34.09 3.18
2002 3180 3.381908 AGATTCGTCATGGTAGGAGACAC 59.618 47.826 0.00 0.00 32.68 3.67
2007 3194 3.574396 GGATGAGATTCGTCATGGTAGGA 59.426 47.826 0.00 0.00 37.29 2.94
2026 3213 2.590092 CCCGGAAAAGCGGAGGAT 59.410 61.111 0.73 0.00 0.00 3.24
2037 3224 0.617535 TCCATCTTCTCAGCCCGGAA 60.618 55.000 0.73 0.00 0.00 4.30
2038 3225 0.399091 ATCCATCTTCTCAGCCCGGA 60.399 55.000 0.73 0.00 0.00 5.14
2127 3314 1.255882 GTGGCCATGTGATGTTCCAA 58.744 50.000 9.72 0.00 34.34 3.53
2131 3318 2.689785 CGCGTGGCCATGTGATGTT 61.690 57.895 30.89 0.00 0.00 2.71
2169 3356 1.214062 GTGCAGGACCTCGAGTGAG 59.786 63.158 12.31 0.00 42.18 3.51
2190 3377 1.078918 CTCCGAGCAAGGCACATGA 60.079 57.895 0.00 0.00 0.00 3.07
2230 3417 2.165234 CCTCGAGTGAGCTCATTCTCAA 59.835 50.000 29.63 14.41 43.89 3.02
2283 3470 3.018856 CTGCAAGAATCCAGTAATGGCA 58.981 45.455 3.77 0.00 34.07 4.92
2313 3500 5.458779 GCTCACAACATACTTCAAAAACCAC 59.541 40.000 0.00 0.00 0.00 4.16
2370 3557 7.496747 TGTATCGAACATGACCATCATCTTTA 58.503 34.615 0.00 0.00 34.28 1.85
2373 3560 5.535753 TGTATCGAACATGACCATCATCT 57.464 39.130 0.00 0.00 34.28 2.90
2400 3587 4.539726 CAATCATCTCCCAATCCCAAAGA 58.460 43.478 0.00 0.00 0.00 2.52
2419 3606 1.610554 GGACATGCTTGCTGCCCAAT 61.611 55.000 0.00 0.00 42.00 3.16
2421 3608 2.677524 GGACATGCTTGCTGCCCA 60.678 61.111 0.00 0.00 42.00 5.36
2458 3647 5.512942 TTGATTATTCTCCTCACCACCAA 57.487 39.130 0.00 0.00 0.00 3.67
2506 3695 1.133976 CCAAGATCATCCCAGGGTGAC 60.134 57.143 5.01 4.42 0.00 3.67
2510 3699 1.228063 CGCCAAGATCATCCCAGGG 60.228 63.158 0.00 0.00 0.00 4.45
2512 3701 0.883814 GCTCGCCAAGATCATCCCAG 60.884 60.000 0.00 0.00 0.00 4.45
2542 3731 1.843149 CTTCTGAATCGCTCGAAGTCG 59.157 52.381 0.00 0.00 41.45 4.18
2548 3737 2.231215 AATCCCTTCTGAATCGCTCG 57.769 50.000 0.00 0.00 0.00 5.03
2552 3742 2.032178 GCCGAAAATCCCTTCTGAATCG 59.968 50.000 0.00 0.00 0.00 3.34
2581 3771 0.462225 TGTCGCTTTCAAACCACGGA 60.462 50.000 0.00 0.00 0.00 4.69
2584 3774 0.030235 GGGTGTCGCTTTCAAACCAC 59.970 55.000 0.00 0.00 32.28 4.16
2595 3791 4.603946 GGCCTATCGGGGTGTCGC 62.604 72.222 0.00 0.00 35.12 5.19
2600 3796 1.615424 ACACAAGGCCTATCGGGGT 60.615 57.895 5.16 0.00 35.12 4.95
2616 3812 2.583024 TCACATGCTTTGATCCCACA 57.417 45.000 0.00 0.00 0.00 4.17
2648 3844 8.864087 AGAGGCATGAAAAAGATAAAAAGTTCT 58.136 29.630 0.00 0.00 0.00 3.01
2658 3854 8.974238 TGATTGAAATAGAGGCATGAAAAAGAT 58.026 29.630 0.00 0.00 0.00 2.40
2659 3855 8.352137 TGATTGAAATAGAGGCATGAAAAAGA 57.648 30.769 0.00 0.00 0.00 2.52
2660 3856 9.031360 CATGATTGAAATAGAGGCATGAAAAAG 57.969 33.333 0.00 0.00 35.02 2.27
2661 3857 7.982919 CCATGATTGAAATAGAGGCATGAAAAA 59.017 33.333 0.00 0.00 35.02 1.94
2662 3858 7.124599 ACCATGATTGAAATAGAGGCATGAAAA 59.875 33.333 0.00 0.00 35.02 2.29
2663 3859 6.608405 ACCATGATTGAAATAGAGGCATGAAA 59.392 34.615 0.00 0.00 35.02 2.69
2665 3861 5.698104 ACCATGATTGAAATAGAGGCATGA 58.302 37.500 0.00 0.00 35.02 3.07
2666 3862 6.401047 AACCATGATTGAAATAGAGGCATG 57.599 37.500 0.00 0.00 33.38 4.06
2668 3864 6.351202 CCAAAACCATGATTGAAATAGAGGCA 60.351 38.462 0.00 0.00 0.00 4.75
2669 3865 6.044682 CCAAAACCATGATTGAAATAGAGGC 58.955 40.000 0.00 0.00 0.00 4.70
2670 3866 6.155049 ACCCAAAACCATGATTGAAATAGAGG 59.845 38.462 0.00 0.00 0.00 3.69
2671 3867 7.174107 ACCCAAAACCATGATTGAAATAGAG 57.826 36.000 0.00 0.00 0.00 2.43
2672 3868 7.123547 GGTACCCAAAACCATGATTGAAATAGA 59.876 37.037 0.00 0.00 36.96 1.98
2673 3869 7.264947 GGTACCCAAAACCATGATTGAAATAG 58.735 38.462 0.00 0.00 36.96 1.73
2674 3870 6.127591 CGGTACCCAAAACCATGATTGAAATA 60.128 38.462 6.25 0.00 36.78 1.40
2675 3871 5.337169 CGGTACCCAAAACCATGATTGAAAT 60.337 40.000 6.25 0.00 36.78 2.17
2676 3872 4.021894 CGGTACCCAAAACCATGATTGAAA 60.022 41.667 6.25 0.00 36.78 2.69
2677 3873 3.508012 CGGTACCCAAAACCATGATTGAA 59.492 43.478 6.25 0.00 36.78 2.69
2678 3874 3.085533 CGGTACCCAAAACCATGATTGA 58.914 45.455 6.25 0.00 36.78 2.57
2679 3875 2.416701 GCGGTACCCAAAACCATGATTG 60.417 50.000 6.25 0.00 36.78 2.67
2680 3876 1.822371 GCGGTACCCAAAACCATGATT 59.178 47.619 6.25 0.00 36.78 2.57
2681 3877 1.470051 GCGGTACCCAAAACCATGAT 58.530 50.000 6.25 0.00 36.78 2.45
2682 3878 0.609681 GGCGGTACCCAAAACCATGA 60.610 55.000 6.25 0.00 36.78 3.07
2740 3936 0.817634 CAGTGTTTCTCGTGGGCCAA 60.818 55.000 8.40 0.00 0.00 4.52
2744 3940 2.611518 GAGATCAGTGTTTCTCGTGGG 58.388 52.381 9.16 0.00 29.96 4.61
2837 4033 7.283127 GCCACACTAAGATTCTTGGATCAAATA 59.717 37.037 15.78 0.00 0.00 1.40
2843 4039 3.055094 ACGCCACACTAAGATTCTTGGAT 60.055 43.478 15.78 1.85 0.00 3.41
2844 4040 2.301870 ACGCCACACTAAGATTCTTGGA 59.698 45.455 15.78 0.00 0.00 3.53
2851 4047 0.815734 ACGCTACGCCACACTAAGAT 59.184 50.000 0.00 0.00 0.00 2.40
2852 4048 0.599558 AACGCTACGCCACACTAAGA 59.400 50.000 0.00 0.00 0.00 2.10
2860 4056 0.037697 AGATCACAAACGCTACGCCA 60.038 50.000 0.00 0.00 0.00 5.69
2864 4060 4.631813 AGGAAATCAGATCACAAACGCTAC 59.368 41.667 0.00 0.00 0.00 3.58
2869 4065 5.241506 TGGACAAGGAAATCAGATCACAAAC 59.758 40.000 0.00 0.00 0.00 2.93
2870 4066 5.384336 TGGACAAGGAAATCAGATCACAAA 58.616 37.500 0.00 0.00 0.00 2.83
2872 4068 4.639078 TGGACAAGGAAATCAGATCACA 57.361 40.909 0.00 0.00 0.00 3.58
2881 4077 4.141390 CCAGCTACCTATGGACAAGGAAAT 60.141 45.833 0.00 0.00 39.02 2.17
2894 4090 4.161565 ACGATGATTTGAACCAGCTACCTA 59.838 41.667 0.00 0.00 0.00 3.08
2940 4136 6.425721 CACGTTTTCTACTTACCCATTCTGAA 59.574 38.462 0.00 0.00 0.00 3.02
2984 4180 1.710013 TGAGGTTGCGAGTTCGATTC 58.290 50.000 5.60 0.00 43.02 2.52
2997 4193 0.751643 AAGTTGCGGTGCTTGAGGTT 60.752 50.000 0.00 0.00 0.00 3.50
3018 4214 9.810545 CTTACCCAGTCTGAAAAATAAACAAAA 57.189 29.630 0.00 0.00 0.00 2.44
3019 4215 8.973182 ACTTACCCAGTCTGAAAAATAAACAAA 58.027 29.630 0.00 0.00 0.00 2.83
3020 4216 8.528044 ACTTACCCAGTCTGAAAAATAAACAA 57.472 30.769 0.00 0.00 0.00 2.83
3021 4217 9.280174 CTACTTACCCAGTCTGAAAAATAAACA 57.720 33.333 0.00 0.00 36.88 2.83
3022 4218 9.498176 TCTACTTACCCAGTCTGAAAAATAAAC 57.502 33.333 0.00 0.00 36.88 2.01
3026 4222 8.847196 GTTTTCTACTTACCCAGTCTGAAAAAT 58.153 33.333 0.00 0.00 42.88 1.82
3027 4223 7.011669 CGTTTTCTACTTACCCAGTCTGAAAAA 59.988 37.037 0.00 0.00 42.88 1.94
3028 4224 6.480981 CGTTTTCTACTTACCCAGTCTGAAAA 59.519 38.462 0.00 9.71 41.18 2.29
3029 4225 5.987347 CGTTTTCTACTTACCCAGTCTGAAA 59.013 40.000 0.00 0.00 36.81 2.69
3030 4226 5.069516 ACGTTTTCTACTTACCCAGTCTGAA 59.930 40.000 0.00 0.00 36.88 3.02
3031 4227 4.586001 ACGTTTTCTACTTACCCAGTCTGA 59.414 41.667 0.00 0.00 36.88 3.27
3032 4228 4.684703 CACGTTTTCTACTTACCCAGTCTG 59.315 45.833 0.00 0.00 36.88 3.51
3033 4229 4.586001 TCACGTTTTCTACTTACCCAGTCT 59.414 41.667 0.00 0.00 36.88 3.24
3034 4230 4.874970 TCACGTTTTCTACTTACCCAGTC 58.125 43.478 0.00 0.00 36.88 3.51
3035 4231 4.942761 TCACGTTTTCTACTTACCCAGT 57.057 40.909 0.00 0.00 39.87 4.00
3036 4232 6.607735 TTTTCACGTTTTCTACTTACCCAG 57.392 37.500 0.00 0.00 0.00 4.45
3037 4233 6.998968 TTTTTCACGTTTTCTACTTACCCA 57.001 33.333 0.00 0.00 0.00 4.51
3058 4254 9.764363 GAGTTTGATTCTTTTGGTCCTTATTTT 57.236 29.630 0.00 0.00 0.00 1.82
3059 4255 8.082242 CGAGTTTGATTCTTTTGGTCCTTATTT 58.918 33.333 0.00 0.00 0.00 1.40
3060 4256 7.593825 CGAGTTTGATTCTTTTGGTCCTTATT 58.406 34.615 0.00 0.00 0.00 1.40
3061 4257 6.349363 GCGAGTTTGATTCTTTTGGTCCTTAT 60.349 38.462 0.00 0.00 0.00 1.73
3062 4258 5.048991 GCGAGTTTGATTCTTTTGGTCCTTA 60.049 40.000 0.00 0.00 0.00 2.69
3063 4259 4.261614 GCGAGTTTGATTCTTTTGGTCCTT 60.262 41.667 0.00 0.00 0.00 3.36
3064 4260 3.253432 GCGAGTTTGATTCTTTTGGTCCT 59.747 43.478 0.00 0.00 0.00 3.85
3065 4261 3.004315 TGCGAGTTTGATTCTTTTGGTCC 59.996 43.478 0.00 0.00 0.00 4.46
3066 4262 4.223320 TGCGAGTTTGATTCTTTTGGTC 57.777 40.909 0.00 0.00 0.00 4.02
3067 4263 4.359706 GTTGCGAGTTTGATTCTTTTGGT 58.640 39.130 0.00 0.00 0.00 3.67
3068 4264 3.735746 GGTTGCGAGTTTGATTCTTTTGG 59.264 43.478 0.00 0.00 0.00 3.28
3069 4265 4.610945 AGGTTGCGAGTTTGATTCTTTTG 58.389 39.130 0.00 0.00 0.00 2.44
3070 4266 4.338118 TGAGGTTGCGAGTTTGATTCTTTT 59.662 37.500 0.00 0.00 0.00 2.27
3071 4267 3.882888 TGAGGTTGCGAGTTTGATTCTTT 59.117 39.130 0.00 0.00 0.00 2.52
3072 4268 3.251004 GTGAGGTTGCGAGTTTGATTCTT 59.749 43.478 0.00 0.00 0.00 2.52
3073 4269 2.808543 GTGAGGTTGCGAGTTTGATTCT 59.191 45.455 0.00 0.00 0.00 2.40
3074 4270 2.095718 GGTGAGGTTGCGAGTTTGATTC 60.096 50.000 0.00 0.00 0.00 2.52
3075 4271 1.880027 GGTGAGGTTGCGAGTTTGATT 59.120 47.619 0.00 0.00 0.00 2.57
3076 4272 1.523758 GGTGAGGTTGCGAGTTTGAT 58.476 50.000 0.00 0.00 0.00 2.57
3077 4273 0.878523 CGGTGAGGTTGCGAGTTTGA 60.879 55.000 0.00 0.00 0.00 2.69
3078 4274 1.569493 CGGTGAGGTTGCGAGTTTG 59.431 57.895 0.00 0.00 0.00 2.93
3079 4275 2.251642 GCGGTGAGGTTGCGAGTTT 61.252 57.895 0.00 0.00 0.00 2.66
3080 4276 2.665185 GCGGTGAGGTTGCGAGTT 60.665 61.111 0.00 0.00 0.00 3.01
3081 4277 1.884075 TATGCGGTGAGGTTGCGAGT 61.884 55.000 0.00 0.00 0.00 4.18
3082 4278 1.148157 CTATGCGGTGAGGTTGCGAG 61.148 60.000 0.00 0.00 0.00 5.03
3083 4279 1.153647 CTATGCGGTGAGGTTGCGA 60.154 57.895 0.00 0.00 0.00 5.10
3084 4280 2.813179 GCTATGCGGTGAGGTTGCG 61.813 63.158 0.00 0.00 0.00 4.85
3085 4281 3.102097 GCTATGCGGTGAGGTTGC 58.898 61.111 0.00 0.00 0.00 4.17
3098 4294 1.997606 GGTCAACTACGTTTGCGCTAT 59.002 47.619 9.73 0.00 42.83 2.97
3106 4302 2.696707 TCAGTGGAAGGTCAACTACGTT 59.303 45.455 0.00 0.00 38.85 3.99
3109 4305 2.300437 AGCTCAGTGGAAGGTCAACTAC 59.700 50.000 0.00 0.00 0.00 2.73
3259 4455 1.379843 ATGGGCGGGCGAAATTCTT 60.380 52.632 0.00 0.00 0.00 2.52
3277 4473 3.161067 TCCGAATGGGCAAATTTTCTCA 58.839 40.909 0.00 0.00 35.24 3.27
3280 4476 4.502962 TGATTCCGAATGGGCAAATTTTC 58.497 39.130 0.00 0.00 35.24 2.29
3288 4484 2.233676 AGGTTTTTGATTCCGAATGGGC 59.766 45.455 0.00 0.00 35.24 5.36
3302 4498 5.693961 AGGGCAATTGAAATCAAGGTTTTT 58.306 33.333 10.34 0.00 39.47 1.94
3312 4508 3.056179 CCCGTTGTTAGGGCAATTGAAAT 60.056 43.478 10.34 0.00 42.77 2.17
3313 4509 2.297597 CCCGTTGTTAGGGCAATTGAAA 59.702 45.455 10.34 0.00 42.77 2.69
3314 4510 1.889829 CCCGTTGTTAGGGCAATTGAA 59.110 47.619 10.34 0.00 42.77 2.69
3315 4511 1.540267 CCCGTTGTTAGGGCAATTGA 58.460 50.000 10.34 0.00 42.77 2.57
3327 4523 4.699522 GCGCCTTCCTCCCGTTGT 62.700 66.667 0.00 0.00 0.00 3.32
3328 4524 3.901797 AAGCGCCTTCCTCCCGTTG 62.902 63.158 2.29 0.00 0.00 4.10
3331 4527 2.359975 AAAAGCGCCTTCCTCCCG 60.360 61.111 2.29 0.00 0.00 5.14
3334 4530 1.927608 GCCAGAAAAGCGCCTTCCTC 61.928 60.000 14.43 0.00 0.00 3.71
3342 4538 2.202518 CGCCATGCCAGAAAAGCG 60.203 61.111 0.00 0.00 37.39 4.68
3357 4553 2.192187 CCCCTACCCGTCTAGTCGC 61.192 68.421 3.70 0.00 0.00 5.19
3359 4555 0.467106 GGACCCCTACCCGTCTAGTC 60.467 65.000 0.00 0.00 0.00 2.59
3373 4569 1.078426 CGAGGTGTTGGATGGACCC 60.078 63.158 0.00 0.00 38.00 4.46
3376 4572 1.561769 ATGGCGAGGTGTTGGATGGA 61.562 55.000 0.00 0.00 0.00 3.41
3381 4577 1.077501 ATCCATGGCGAGGTGTTGG 60.078 57.895 6.96 0.00 0.00 3.77
3394 4591 4.205587 GTGGCAATCTTGAAGAGATCCAT 58.794 43.478 12.84 0.00 44.41 3.41
3395 4592 3.614092 GTGGCAATCTTGAAGAGATCCA 58.386 45.455 0.00 4.67 44.41 3.41
3410 4607 1.600636 CTTCGCTTCCTGGTGGCAA 60.601 57.895 12.28 6.48 0.00 4.52
3411 4608 2.032528 CTTCGCTTCCTGGTGGCA 59.967 61.111 12.28 0.00 0.00 4.92
3458 4655 4.101790 CGACCGCATGCACCCAAC 62.102 66.667 19.57 1.62 0.00 3.77
3481 4678 2.125673 TTGCTCGAGGGCGCTAAC 60.126 61.111 15.58 0.00 37.46 2.34
3487 4684 0.246635 TACTTGAGTTGCTCGAGGGC 59.753 55.000 15.58 1.44 44.09 5.19
3490 4687 5.597813 ACAAATTACTTGAGTTGCTCGAG 57.402 39.130 8.45 8.45 45.02 4.04


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

AutoCloner maintained by Alex Coulton.