Multiple sequence alignment - TraesCS6B01G471200

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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 TraesCS6B01G471200 chr6B 100.000 6101 0 0 1 6101 719417854 719411754 0.000000e+00 11267.0
1 TraesCS6B01G471200 chr6B 97.707 1832 39 3 2806 4635 192914557 192916387 0.000000e+00 3147.0
2 TraesCS6B01G471200 chr6B 94.821 1506 46 11 1 1501 192901828 192903306 0.000000e+00 2320.0
3 TraesCS6B01G471200 chr6B 97.167 1165 26 4 4631 5794 192922206 192923364 0.000000e+00 1962.0
4 TraesCS6B01G471200 chr6B 98.234 453 6 2 1522 1974 192914118 192914568 0.000000e+00 791.0
5 TraesCS6B01G471200 chr6B 82.536 481 52 19 3919 4378 24725806 24726275 1.590000e-105 394.0
6 TraesCS6B01G471200 chr6B 96.250 240 9 0 5862 6101 502012786 502012547 1.590000e-105 394.0
7 TraesCS6B01G471200 chr6B 83.815 346 50 4 4685 5026 24726541 24726884 2.120000e-84 324.0
8 TraesCS6B01G471200 chr6B 90.789 152 11 3 4461 4612 24726275 24726423 3.730000e-47 200.0
9 TraesCS6B01G471200 chr6B 89.062 128 9 3 4392 4514 45011745 45011618 2.940000e-33 154.0
10 TraesCS6B01G471200 chr6B 97.368 38 1 0 3873 3910 24725777 24725814 1.420000e-06 65.8
11 TraesCS6B01G471200 chr6B 100.000 33 0 0 1498 1530 192913945 192913977 1.840000e-05 62.1
12 TraesCS6B01G471200 chr6D 97.727 2992 53 5 2806 5794 448385227 448382248 0.000000e+00 5134.0
13 TraesCS6B01G471200 chr6D 96.685 1991 46 6 1 1974 448387203 448385216 0.000000e+00 3293.0
14 TraesCS6B01G471200 chr6D 89.103 725 43 14 1972 2664 315793104 315792384 0.000000e+00 869.0
15 TraesCS6B01G471200 chr6D 94.444 72 4 0 5791 5862 471132206 471132277 1.800000e-20 111.0
16 TraesCS6B01G471200 chr3D 97.596 2995 62 7 2806 5794 250335380 250332390 0.000000e+00 5123.0
17 TraesCS6B01G471200 chr3D 96.836 1991 44 5 1 1974 250337357 250335369 0.000000e+00 3310.0
18 TraesCS6B01G471200 chr3A 96.663 2727 65 12 3070 5794 40336394 40333692 0.000000e+00 4508.0
19 TraesCS6B01G471200 chr3A 95.880 898 21 2 779 1660 40346328 40345431 0.000000e+00 1439.0
20 TraesCS6B01G471200 chr3A 96.927 423 11 2 362 782 40348216 40347794 0.000000e+00 708.0
21 TraesCS6B01G471200 chr3A 94.266 436 16 3 1 427 40348649 40348214 0.000000e+00 658.0
22 TraesCS6B01G471200 chr3A 98.227 282 4 1 1693 1974 40345429 40345149 5.490000e-135 492.0
23 TraesCS6B01G471200 chr3A 97.770 269 6 0 2806 3074 40345160 40344892 1.200000e-126 464.0
24 TraesCS6B01G471200 chr5A 96.796 2029 37 5 2806 4833 447313632 447311631 0.000000e+00 3362.0
25 TraesCS6B01G471200 chr5A 95.229 1991 49 17 1 1974 447315582 447313621 0.000000e+00 3109.0
26 TraesCS6B01G471200 chr5A 94.453 631 12 10 4893 5523 447311532 447310925 0.000000e+00 950.0
27 TraesCS6B01G471200 chr5A 82.780 482 50 20 3919 4378 362401224 362400754 3.430000e-107 399.0
28 TraesCS6B01G471200 chr5A 83.526 346 51 4 4685 5026 362400488 362400145 9.870000e-83 318.0
29 TraesCS6B01G471200 chr5A 91.447 152 10 3 4461 4612 362400754 362400606 8.020000e-49 206.0
30 TraesCS6B01G471200 chr5A 100.000 72 0 0 4781 4852 447311530 447311601 3.840000e-27 134.0
31 TraesCS6B01G471200 chr5A 80.808 99 12 5 2709 2807 386545148 386545239 3.050000e-08 71.3
32 TraesCS6B01G471200 chr5A 100.000 32 0 0 3875 3906 362401251 362401220 6.600000e-05 60.2
33 TraesCS6B01G471200 chr2A 95.605 1934 65 6 1 1915 611730253 611728321 0.000000e+00 3083.0
34 TraesCS6B01G471200 chr2A 83.368 481 48 20 3919 4378 32807458 32806989 3.400000e-112 416.0
35 TraesCS6B01G471200 chr2A 78.507 670 111 26 5148 5794 453245893 453245234 5.690000e-110 409.0
36 TraesCS6B01G471200 chr2A 86.111 288 39 1 272 558 667021700 667021413 5.940000e-80 309.0
37 TraesCS6B01G471200 chr2A 77.891 294 19 21 2252 2525 616202148 616201881 2.290000e-29 141.0
38 TraesCS6B01G471200 chr2A 89.423 104 9 2 1971 2072 616202435 616202332 4.960000e-26 130.0
39 TraesCS6B01G471200 chr2A 87.879 99 12 0 4665 4763 759819852 759819950 3.860000e-22 117.0
40 TraesCS6B01G471200 chr2A 86.538 104 6 6 2707 2808 7749081 7749178 2.330000e-19 108.0
41 TraesCS6B01G471200 chr2A 82.857 105 5 6 2707 2806 774922120 774922216 1.410000e-11 82.4
42 TraesCS6B01G471200 chr2A 100.000 34 0 0 3873 3906 32807487 32807454 5.110000e-06 63.9
43 TraesCS6B01G471200 chr7D 98.113 1431 23 2 4365 5794 616704690 616706117 0.000000e+00 2490.0
44 TraesCS6B01G471200 chr7D 82.158 482 52 20 3919 4378 565534306 565533837 3.450000e-102 383.0
45 TraesCS6B01G471200 chr7D 82.353 340 54 6 4691 5026 565533537 565533200 2.150000e-74 291.0
46 TraesCS6B01G471200 chr7D 80.874 366 26 19 2294 2642 47840247 47839909 1.310000e-61 248.0
47 TraesCS6B01G471200 chr7D 81.587 315 40 10 4816 5129 40484863 40484566 1.700000e-60 244.0
48 TraesCS6B01G471200 chr7D 92.105 152 9 3 4461 4612 565533837 565533689 1.720000e-50 211.0
49 TraesCS6B01G471200 chr7D 88.194 144 14 2 2663 2806 158770178 158770038 1.050000e-37 169.0
50 TraesCS6B01G471200 chr2B 92.742 868 28 6 1970 2806 87499742 87500605 0.000000e+00 1221.0
51 TraesCS6B01G471200 chr2B 96.250 240 9 0 5862 6101 76824800 76824561 1.590000e-105 394.0
52 TraesCS6B01G471200 chr2B 88.043 92 10 1 5704 5794 657726636 657726545 2.330000e-19 108.0
53 TraesCS6B01G471200 chr4B 92.650 449 31 2 5220 5667 240172976 240172529 0.000000e+00 645.0
54 TraesCS6B01G471200 chr4B 97.881 236 5 0 5865 6100 119336738 119336503 5.690000e-110 409.0
55 TraesCS6B01G471200 chr4B 97.046 237 7 0 5865 6101 16081847 16082083 3.430000e-107 399.0
56 TraesCS6B01G471200 chr4B 92.381 105 6 2 5668 5771 240148089 240147986 1.370000e-31 148.0
57 TraesCS6B01G471200 chr4B 89.109 101 9 2 5707 5806 663777127 663777226 2.310000e-24 124.0
58 TraesCS6B01G471200 chr2D 82.292 672 90 22 5144 5794 343096851 343096188 6.910000e-154 555.0
59 TraesCS6B01G471200 chr2D 96.680 241 6 2 5862 6101 353318079 353317840 3.430000e-107 399.0
60 TraesCS6B01G471200 chr2D 86.513 304 20 13 1971 2257 61806652 61806353 1.280000e-81 315.0
61 TraesCS6B01G471200 chr2D 83.755 277 25 10 3873 4149 147127325 147127069 1.700000e-60 244.0
62 TraesCS6B01G471200 chr2D 81.699 153 13 3 2663 2806 61805837 61805691 5.000000e-21 113.0
63 TraesCS6B01G471200 chr3B 87.288 472 22 10 1970 2406 775492546 775492078 7.060000e-139 505.0
64 TraesCS6B01G471200 chr3B 97.500 240 6 0 5862 6101 85081619 85081380 1.580000e-110 411.0
65 TraesCS6B01G471200 chr3B 86.089 381 21 14 2457 2806 775492074 775491695 1.240000e-101 381.0
66 TraesCS6B01G471200 chr3B 84.762 105 6 7 2707 2808 782345734 782345637 5.030000e-16 97.1
67 TraesCS6B01G471200 chr3B 81.308 107 7 6 2704 2806 411883586 411883683 2.360000e-09 75.0
68 TraesCS6B01G471200 chr7B 96.667 240 7 1 5862 6101 217303949 217303711 1.230000e-106 398.0
69 TraesCS6B01G471200 chr7B 87.279 283 35 1 272 553 113917018 113917300 7.630000e-84 322.0
70 TraesCS6B01G471200 chr7B 92.308 104 5 3 1971 2072 712621886 712621784 1.770000e-30 145.0
71 TraesCS6B01G471200 chr5B 96.250 240 9 0 5862 6101 558705881 558705642 1.590000e-105 394.0
72 TraesCS6B01G471200 chr5B 96.266 241 8 1 5862 6101 671867607 671867847 1.590000e-105 394.0
73 TraesCS6B01G471200 chr5B 81.605 299 37 15 1974 2257 711543741 711543446 1.320000e-56 231.0
74 TraesCS6B01G471200 chr5B 88.889 72 5 3 1974 2042 711485699 711485628 1.090000e-12 86.1
75 TraesCS6B01G471200 chrUn 79.335 421 29 26 2252 2642 430909509 430909901 6.110000e-60 243.0
76 TraesCS6B01G471200 chrUn 79.335 421 29 26 2252 2642 469504577 469504185 6.110000e-60 243.0
77 TraesCS6B01G471200 chr4A 87.387 111 4 6 2252 2354 659118030 659117922 1.070000e-22 119.0
78 TraesCS6B01G471200 chr4A 82.222 135 16 4 2673 2806 659117721 659117594 6.470000e-20 110.0


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 TraesCS6B01G471200 chr6B 719411754 719417854 6100 True 11267.000000 11267 100.000000 1 6101 1 chr6B.!!$R3 6100
1 TraesCS6B01G471200 chr6B 192901828 192903306 1478 False 2320.000000 2320 94.821000 1 1501 1 chr6B.!!$F1 1500
2 TraesCS6B01G471200 chr6B 192922206 192923364 1158 False 1962.000000 1962 97.167000 4631 5794 1 chr6B.!!$F2 1163
3 TraesCS6B01G471200 chr6B 192913945 192916387 2442 False 1333.366667 3147 98.647000 1498 4635 3 chr6B.!!$F4 3137
4 TraesCS6B01G471200 chr6B 24725777 24726884 1107 False 245.950000 394 88.627000 3873 5026 4 chr6B.!!$F3 1153
5 TraesCS6B01G471200 chr6D 448382248 448387203 4955 True 4213.500000 5134 97.206000 1 5794 2 chr6D.!!$R2 5793
6 TraesCS6B01G471200 chr6D 315792384 315793104 720 True 869.000000 869 89.103000 1972 2664 1 chr6D.!!$R1 692
7 TraesCS6B01G471200 chr3D 250332390 250337357 4967 True 4216.500000 5123 97.216000 1 5794 2 chr3D.!!$R1 5793
8 TraesCS6B01G471200 chr3A 40333692 40336394 2702 True 4508.000000 4508 96.663000 3070 5794 1 chr3A.!!$R1 2724
9 TraesCS6B01G471200 chr3A 40344892 40348649 3757 True 752.200000 1439 96.614000 1 3074 5 chr3A.!!$R2 3073
10 TraesCS6B01G471200 chr5A 447310925 447315582 4657 True 2473.666667 3362 95.492667 1 5523 3 chr5A.!!$R2 5522
11 TraesCS6B01G471200 chr5A 362400145 362401251 1106 True 245.800000 399 89.438250 3875 5026 4 chr5A.!!$R1 1151
12 TraesCS6B01G471200 chr2A 611728321 611730253 1932 True 3083.000000 3083 95.605000 1 1915 1 chr2A.!!$R2 1914
13 TraesCS6B01G471200 chr2A 453245234 453245893 659 True 409.000000 409 78.507000 5148 5794 1 chr2A.!!$R1 646
14 TraesCS6B01G471200 chr7D 616704690 616706117 1427 False 2490.000000 2490 98.113000 4365 5794 1 chr7D.!!$F1 1429
15 TraesCS6B01G471200 chr7D 565533200 565534306 1106 True 295.000000 383 85.538667 3919 5026 3 chr7D.!!$R4 1107
16 TraesCS6B01G471200 chr2B 87499742 87500605 863 False 1221.000000 1221 92.742000 1970 2806 1 chr2B.!!$F1 836
17 TraesCS6B01G471200 chr2D 343096188 343096851 663 True 555.000000 555 82.292000 5144 5794 1 chr2D.!!$R2 650
18 TraesCS6B01G471200 chr2D 61805691 61806652 961 True 214.000000 315 84.106000 1971 2806 2 chr2D.!!$R4 835
19 TraesCS6B01G471200 chr3B 775491695 775492546 851 True 443.000000 505 86.688500 1970 2806 2 chr3B.!!$R3 836

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
217 226 0.527385 GTTTCGTTGCTTGCTTGCCA 60.527 50.000 0.00 0.00 0.00 4.92 F
953 2498 1.363744 CAGTCGCAGGTTCTCCATTC 58.636 55.000 0.00 0.00 35.89 2.67 F
2023 3806 4.443598 GGGGCCAACTTCACATAAAAACAA 60.444 41.667 4.39 0.00 0.00 2.83 F
2562 4565 0.538057 CTGCTCCAAGCCTCCAACAA 60.538 55.000 0.00 0.00 41.51 2.83 F
2563 4566 0.823356 TGCTCCAAGCCTCCAACAAC 60.823 55.000 0.00 0.00 41.51 3.32 F
2809 4882 1.078497 TATGCTCCGCCAGTGGTTG 60.078 57.895 11.74 3.68 0.00 3.77 F
2810 4883 1.836999 TATGCTCCGCCAGTGGTTGT 61.837 55.000 11.74 0.00 0.00 3.32 F
2812 4885 2.111043 CTCCGCCAGTGGTTGTGT 59.889 61.111 11.74 0.00 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1823 3605 4.797471 TCAAGCACTTCATTCCAAATTCG 58.203 39.130 0.00 0.00 0.00 3.34 R
2250 4070 0.551879 TGGGGAAACAACCGGAAGAA 59.448 50.000 9.46 0.00 0.00 2.52 R
3752 5826 0.235926 GAGCGAGTTTGCAAGGTCAC 59.764 55.000 9.88 1.33 37.31 3.67 R
3858 5932 2.358737 CTTGTGCCGGTCCTGGAC 60.359 66.667 18.65 18.65 0.00 4.02 R
4546 6642 4.660521 TGGTACCTCCAGCACCTT 57.339 55.556 14.36 0.00 41.93 3.50 R
5018 7268 8.275758 TGTGGGAATATACCTGCAGTTTTATAA 58.724 33.333 13.81 0.00 0.00 0.98 R
5065 7315 6.284891 CAGTATGTCCAAATCAACCCAATT 57.715 37.500 0.00 0.00 0.00 2.32 R
5141 7391 0.978667 GGAGAGGTGGAAGGGTCCTC 60.979 65.000 0.00 0.00 45.22 3.71 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 131 0.612174 AGGTAGAGTCGGAGCTGCAA 60.612 55.000 5.91 0.00 0.00 4.08
131 140 0.603707 CGGAGCTGCAACAGAAGGAA 60.604 55.000 5.91 0.00 32.44 3.36
171 180 3.561155 GCTTTAGCTTCGATGAGTTCG 57.439 47.619 1.89 0.00 42.82 3.95
217 226 0.527385 GTTTCGTTGCTTGCTTGCCA 60.527 50.000 0.00 0.00 0.00 4.92
306 316 5.022122 TGGCATCTGTTTGGATTTTGGATA 58.978 37.500 0.00 0.00 0.00 2.59
307 317 5.105392 TGGCATCTGTTTGGATTTTGGATAC 60.105 40.000 0.00 0.00 0.00 2.24
540 613 4.717877 TGATGGTGGCGAGATGAAATAAT 58.282 39.130 0.00 0.00 0.00 1.28
835 2379 5.118357 CACGTAGCATGATATGAAGCTTCTC 59.882 44.000 26.09 16.21 38.47 2.87
897 2441 3.256383 CCAAACTCCACATTCATTGAGCA 59.744 43.478 0.00 0.00 0.00 4.26
900 2444 6.183360 CCAAACTCCACATTCATTGAGCATAT 60.183 38.462 0.00 0.00 0.00 1.78
953 2498 1.363744 CAGTCGCAGGTTCTCCATTC 58.636 55.000 0.00 0.00 35.89 2.67
1390 3019 7.356089 TCGTTGGATAAGTACTGATATGGTT 57.644 36.000 0.00 0.00 0.00 3.67
2023 3806 4.443598 GGGGCCAACTTCACATAAAAACAA 60.444 41.667 4.39 0.00 0.00 2.83
2046 3837 7.170658 ACAAACAATATGAATGAAAAACCCACG 59.829 33.333 0.00 0.00 0.00 4.94
2121 3941 9.677567 AATATCTTGTTCACACAAATACAACAC 57.322 29.630 0.00 0.00 42.53 3.32
2177 3997 6.013379 TGGATAAGTAAATTTTGGTGCTCCA 58.987 36.000 2.64 2.64 42.66 3.86
2279 4099 2.214376 TGTTTCCCCATTGCTACCTG 57.786 50.000 0.00 0.00 0.00 4.00
2398 4227 5.127845 GTGACTAGAACATCAGATGAGGGAA 59.872 44.000 17.81 0.00 0.00 3.97
2495 4494 3.965539 GAGTGCATGACGGGCTGCT 62.966 63.158 0.00 0.00 39.16 4.24
2561 4564 1.073722 CTGCTCCAAGCCTCCAACA 59.926 57.895 0.00 0.00 41.51 3.33
2562 4565 0.538057 CTGCTCCAAGCCTCCAACAA 60.538 55.000 0.00 0.00 41.51 2.83
2563 4566 0.823356 TGCTCCAAGCCTCCAACAAC 60.823 55.000 0.00 0.00 41.51 3.32
2653 4683 2.438975 TCGAGGTACACGCCGGAT 60.439 61.111 5.05 0.00 43.29 4.18
2671 4735 3.650950 GGGGAGGCAGCTGAACCA 61.651 66.667 20.43 0.00 0.00 3.67
2806 4879 1.522355 CACTATGCTCCGCCAGTGG 60.522 63.158 4.20 4.20 37.13 4.00
2807 4880 1.990060 ACTATGCTCCGCCAGTGGT 60.990 57.895 11.74 0.00 0.00 4.16
2808 4881 1.221840 CTATGCTCCGCCAGTGGTT 59.778 57.895 11.74 0.00 0.00 3.67
2809 4882 1.078497 TATGCTCCGCCAGTGGTTG 60.078 57.895 11.74 3.68 0.00 3.77
2810 4883 1.836999 TATGCTCCGCCAGTGGTTGT 61.837 55.000 11.74 0.00 0.00 3.32
2811 4884 3.357079 GCTCCGCCAGTGGTTGTG 61.357 66.667 11.74 4.54 0.00 3.33
2812 4885 2.111043 CTCCGCCAGTGGTTGTGT 59.889 61.111 11.74 0.00 0.00 3.72
3011 5084 6.656632 TCAAACTCTAGACTGATGAAGTGT 57.343 37.500 0.00 0.00 40.07 3.55
3055 5128 8.642432 TCTTAGATATTGTGAATGGTCTACTGG 58.358 37.037 0.00 0.00 0.00 4.00
3062 5135 5.030147 TGTGAATGGTCTACTGGAGGTATT 58.970 41.667 0.00 0.00 0.00 1.89
3539 5613 5.597813 AAGTAGCTTCTGATTTGTTCACG 57.402 39.130 0.00 0.00 0.00 4.35
3614 5688 4.714632 TCTCAAATTAGGCTTTATCCCCG 58.285 43.478 0.00 0.00 0.00 5.73
3671 5745 6.931840 GCCCACATGTTTGATTTAGGTTTTTA 59.068 34.615 0.00 0.00 0.00 1.52
3752 5826 3.429141 CCTGCACTGCAAGCCTCG 61.429 66.667 4.99 0.00 38.41 4.63
3838 5912 2.951726 TCGTGCAGATTCACTCTTCTG 58.048 47.619 0.00 0.00 41.84 3.02
3858 5932 4.709840 CCTGAAGGCTCCTGTGTG 57.290 61.111 0.00 0.00 0.00 3.82
4090 6165 5.535333 ACACAAAGGAGCTGAAATTTCATG 58.465 37.500 20.76 15.81 36.46 3.07
4164 6241 8.657712 GGGTAGTGGTTCTAGGTTTATATTCAT 58.342 37.037 0.00 0.00 0.00 2.57
4349 6445 7.511371 TGATAATCCCTCTCTAAATTAACCCGA 59.489 37.037 0.00 0.00 0.00 5.14
5018 7268 8.776470 CATTTGTATTTGGCTGTTTCATTCTTT 58.224 29.630 0.00 0.00 0.00 2.52
5065 7315 7.416817 CCACATTGAACTCGATTATTGCAATA 58.583 34.615 15.21 15.21 0.00 1.90
5140 7390 3.273434 TCAAATGATGGAAGCCTCTTCG 58.727 45.455 1.07 0.00 0.00 3.79
5141 7391 2.338577 AATGATGGAAGCCTCTTCGG 57.661 50.000 1.07 0.00 0.00 4.30
5142 7392 1.500474 ATGATGGAAGCCTCTTCGGA 58.500 50.000 1.07 0.00 33.16 4.55
5464 7737 0.747283 CTGAGCCTGATGGACAAGGC 60.747 60.000 5.54 5.54 40.49 4.35
5578 7859 5.116882 GTTGATATTTCCCTACTTGCGTCT 58.883 41.667 0.00 0.00 0.00 4.18
5728 8016 0.343372 ATAGGAGAGTGGAAGGGGCA 59.657 55.000 0.00 0.00 0.00 5.36
5794 8083 2.033602 GCGCCCCAACCACTAGTT 59.966 61.111 0.00 0.00 40.16 2.24
5795 8084 1.602605 GCGCCCCAACCACTAGTTT 60.603 57.895 0.00 0.00 36.18 2.66
5796 8085 1.176619 GCGCCCCAACCACTAGTTTT 61.177 55.000 0.00 0.00 36.18 2.43
5797 8086 1.883209 GCGCCCCAACCACTAGTTTTA 60.883 52.381 0.00 0.00 36.18 1.52
5798 8087 1.808343 CGCCCCAACCACTAGTTTTAC 59.192 52.381 0.00 0.00 36.18 2.01
5799 8088 2.811136 CGCCCCAACCACTAGTTTTACA 60.811 50.000 0.00 0.00 36.18 2.41
5800 8089 3.224269 GCCCCAACCACTAGTTTTACAA 58.776 45.455 0.00 0.00 36.18 2.41
5801 8090 3.254903 GCCCCAACCACTAGTTTTACAAG 59.745 47.826 0.00 0.00 36.18 3.16
5802 8091 3.254903 CCCCAACCACTAGTTTTACAAGC 59.745 47.826 0.00 0.00 36.18 4.01
5803 8092 3.886505 CCCAACCACTAGTTTTACAAGCA 59.113 43.478 0.00 0.00 36.18 3.91
5804 8093 4.339814 CCCAACCACTAGTTTTACAAGCAA 59.660 41.667 0.00 0.00 36.18 3.91
5805 8094 5.507315 CCCAACCACTAGTTTTACAAGCAAG 60.507 44.000 0.00 0.00 36.18 4.01
5806 8095 4.830826 ACCACTAGTTTTACAAGCAAGC 57.169 40.909 0.00 0.00 0.00 4.01
5807 8096 4.461198 ACCACTAGTTTTACAAGCAAGCT 58.539 39.130 0.00 0.00 0.00 3.74
5808 8097 5.617252 ACCACTAGTTTTACAAGCAAGCTA 58.383 37.500 0.00 0.00 0.00 3.32
5809 8098 5.701290 ACCACTAGTTTTACAAGCAAGCTAG 59.299 40.000 0.00 3.92 0.00 3.42
5810 8099 5.701290 CCACTAGTTTTACAAGCAAGCTAGT 59.299 40.000 0.00 4.95 38.39 2.57
5811 8100 6.872020 CCACTAGTTTTACAAGCAAGCTAGTA 59.128 38.462 9.06 0.00 36.52 1.82
5812 8101 7.386848 CCACTAGTTTTACAAGCAAGCTAGTAA 59.613 37.037 9.06 0.00 36.52 2.24
5813 8102 8.221766 CACTAGTTTTACAAGCAAGCTAGTAAC 58.778 37.037 9.06 0.00 36.52 2.50
5814 8103 7.929785 ACTAGTTTTACAAGCAAGCTAGTAACA 59.070 33.333 8.03 0.00 36.79 2.41
5815 8104 7.745620 AGTTTTACAAGCAAGCTAGTAACAT 57.254 32.000 0.00 0.00 0.00 2.71
5816 8105 8.842358 AGTTTTACAAGCAAGCTAGTAACATA 57.158 30.769 0.00 0.00 0.00 2.29
5817 8106 9.280174 AGTTTTACAAGCAAGCTAGTAACATAA 57.720 29.630 0.00 0.00 0.00 1.90
5818 8107 9.326339 GTTTTACAAGCAAGCTAGTAACATAAC 57.674 33.333 0.00 0.00 0.00 1.89
5819 8108 8.610248 TTTACAAGCAAGCTAGTAACATAACA 57.390 30.769 0.00 0.00 0.00 2.41
5820 8109 8.786826 TTACAAGCAAGCTAGTAACATAACAT 57.213 30.769 0.00 0.00 0.00 2.71
5821 8110 7.687941 ACAAGCAAGCTAGTAACATAACATT 57.312 32.000 0.00 0.00 0.00 2.71
5822 8111 7.530010 ACAAGCAAGCTAGTAACATAACATTG 58.470 34.615 0.00 0.00 0.00 2.82
5823 8112 6.683974 AGCAAGCTAGTAACATAACATTGG 57.316 37.500 0.00 0.00 0.00 3.16
5824 8113 6.180472 AGCAAGCTAGTAACATAACATTGGT 58.820 36.000 0.00 0.00 0.00 3.67
5825 8114 6.094048 AGCAAGCTAGTAACATAACATTGGTG 59.906 38.462 0.00 0.00 0.00 4.17
5826 8115 6.093495 GCAAGCTAGTAACATAACATTGGTGA 59.907 38.462 0.00 0.00 0.00 4.02
5827 8116 7.361713 GCAAGCTAGTAACATAACATTGGTGAA 60.362 37.037 0.00 0.00 0.00 3.18
5828 8117 7.849804 AGCTAGTAACATAACATTGGTGAAG 57.150 36.000 0.00 0.00 0.00 3.02
5829 8118 6.823689 AGCTAGTAACATAACATTGGTGAAGG 59.176 38.462 0.00 0.00 0.00 3.46
5830 8119 6.598064 GCTAGTAACATAACATTGGTGAAGGT 59.402 38.462 0.00 0.00 0.00 3.50
5831 8120 7.120726 GCTAGTAACATAACATTGGTGAAGGTT 59.879 37.037 0.00 0.00 39.36 3.50
5832 8121 7.833285 AGTAACATAACATTGGTGAAGGTTT 57.167 32.000 0.00 0.00 37.30 3.27
5833 8122 8.927675 AGTAACATAACATTGGTGAAGGTTTA 57.072 30.769 0.00 0.00 37.30 2.01
5834 8123 8.789762 AGTAACATAACATTGGTGAAGGTTTAC 58.210 33.333 0.00 0.00 37.30 2.01
5835 8124 7.589958 AACATAACATTGGTGAAGGTTTACA 57.410 32.000 0.00 0.00 37.30 2.41
5836 8125 7.589958 ACATAACATTGGTGAAGGTTTACAA 57.410 32.000 0.00 0.00 37.30 2.41
5837 8126 7.430441 ACATAACATTGGTGAAGGTTTACAAC 58.570 34.615 0.00 0.00 37.30 3.32
5838 8127 4.561735 ACATTGGTGAAGGTTTACAACG 57.438 40.909 0.00 0.00 0.00 4.10
5839 8128 3.243267 ACATTGGTGAAGGTTTACAACGC 60.243 43.478 0.00 0.00 0.00 4.84
5840 8129 2.039818 TGGTGAAGGTTTACAACGCA 57.960 45.000 0.00 0.00 0.00 5.24
5841 8130 2.577700 TGGTGAAGGTTTACAACGCAT 58.422 42.857 0.00 0.00 0.00 4.73
5842 8131 2.550606 TGGTGAAGGTTTACAACGCATC 59.449 45.455 0.00 0.00 0.00 3.91
5843 8132 2.095415 GGTGAAGGTTTACAACGCATCC 60.095 50.000 0.00 0.00 0.00 3.51
5844 8133 1.801771 TGAAGGTTTACAACGCATCCG 59.198 47.619 0.00 0.00 41.14 4.18
5845 8134 0.519961 AAGGTTTACAACGCATCCGC 59.480 50.000 0.00 0.00 38.22 5.54
5846 8135 0.604243 AGGTTTACAACGCATCCGCA 60.604 50.000 0.00 0.00 38.40 5.69
5847 8136 0.450184 GGTTTACAACGCATCCGCAT 59.550 50.000 0.00 0.00 38.40 4.73
5848 8137 1.534028 GTTTACAACGCATCCGCATG 58.466 50.000 0.00 0.00 38.40 4.06
5849 8138 1.129624 GTTTACAACGCATCCGCATGA 59.870 47.619 0.00 0.00 38.40 3.07
5850 8139 1.006086 TTACAACGCATCCGCATGAG 58.994 50.000 0.00 0.00 38.40 2.90
5851 8140 1.428370 TACAACGCATCCGCATGAGC 61.428 55.000 0.00 0.00 38.40 4.26
5852 8141 2.436469 AACGCATCCGCATGAGCA 60.436 55.556 0.00 0.00 42.27 4.26
5853 8142 2.039974 AACGCATCCGCATGAGCAA 61.040 52.632 0.00 0.00 42.27 3.91
5854 8143 1.585267 AACGCATCCGCATGAGCAAA 61.585 50.000 0.00 0.00 42.27 3.68
5855 8144 1.584483 CGCATCCGCATGAGCAAAC 60.584 57.895 0.00 0.00 42.27 2.93
5856 8145 1.507630 GCATCCGCATGAGCAAACA 59.492 52.632 0.00 0.00 42.27 2.83
5857 8146 0.109179 GCATCCGCATGAGCAAACAA 60.109 50.000 0.00 0.00 42.27 2.83
5858 8147 1.904144 CATCCGCATGAGCAAACAAG 58.096 50.000 0.00 0.00 42.27 3.16
5859 8148 1.469703 CATCCGCATGAGCAAACAAGA 59.530 47.619 0.00 0.00 42.27 3.02
5860 8149 1.159285 TCCGCATGAGCAAACAAGAG 58.841 50.000 0.00 0.00 42.27 2.85
5861 8150 1.159285 CCGCATGAGCAAACAAGAGA 58.841 50.000 0.00 0.00 42.27 3.10
5862 8151 1.129998 CCGCATGAGCAAACAAGAGAG 59.870 52.381 0.00 0.00 42.27 3.20
5863 8152 1.129998 CGCATGAGCAAACAAGAGAGG 59.870 52.381 0.00 0.00 42.27 3.69
5864 8153 1.135460 GCATGAGCAAACAAGAGAGGC 60.135 52.381 0.00 0.00 41.58 4.70
5865 8154 2.434428 CATGAGCAAACAAGAGAGGCT 58.566 47.619 0.00 0.00 37.56 4.58
5866 8155 3.603532 CATGAGCAAACAAGAGAGGCTA 58.396 45.455 0.00 0.00 34.44 3.93
5867 8156 3.325293 TGAGCAAACAAGAGAGGCTAG 57.675 47.619 0.00 0.00 34.44 3.42
5868 8157 2.006169 GAGCAAACAAGAGAGGCTAGC 58.994 52.381 6.04 6.04 34.44 3.42
5869 8158 1.090728 GCAAACAAGAGAGGCTAGCC 58.909 55.000 27.19 27.19 0.00 3.93
5870 8159 1.363744 CAAACAAGAGAGGCTAGCCG 58.636 55.000 27.83 14.91 41.95 5.52
5871 8160 0.391793 AAACAAGAGAGGCTAGCCGC 60.392 55.000 28.28 28.28 41.95 6.53
5887 8176 3.855853 GCCGCCTCCTCCTTCCTC 61.856 72.222 0.00 0.00 0.00 3.71
5888 8177 3.157949 CCGCCTCCTCCTTCCTCC 61.158 72.222 0.00 0.00 0.00 4.30
5889 8178 2.364317 CGCCTCCTCCTTCCTCCA 60.364 66.667 0.00 0.00 0.00 3.86
5890 8179 2.726351 CGCCTCCTCCTTCCTCCAC 61.726 68.421 0.00 0.00 0.00 4.02
5891 8180 1.613630 GCCTCCTCCTTCCTCCACA 60.614 63.158 0.00 0.00 0.00 4.17
5892 8181 1.201429 GCCTCCTCCTTCCTCCACAA 61.201 60.000 0.00 0.00 0.00 3.33
5893 8182 1.362224 CCTCCTCCTTCCTCCACAAA 58.638 55.000 0.00 0.00 0.00 2.83
5894 8183 1.705186 CCTCCTCCTTCCTCCACAAAA 59.295 52.381 0.00 0.00 0.00 2.44
5895 8184 2.108250 CCTCCTCCTTCCTCCACAAAAA 59.892 50.000 0.00 0.00 0.00 1.94
5945 8234 3.844090 GCAGGTCCGCCTCCTCTC 61.844 72.222 0.00 0.00 44.97 3.20
5946 8235 3.151022 CAGGTCCGCCTCCTCTCC 61.151 72.222 0.00 0.00 44.97 3.71
5947 8236 4.824515 AGGTCCGCCTCCTCTCCG 62.825 72.222 0.00 0.00 42.67 4.63
5955 8244 4.787280 CTCCTCTCCGGTGGCCCT 62.787 72.222 0.00 0.00 0.00 5.19
5956 8245 3.352748 TCCTCTCCGGTGGCCCTA 61.353 66.667 0.00 0.00 0.00 3.53
5957 8246 2.840102 CCTCTCCGGTGGCCCTAG 60.840 72.222 0.00 0.00 0.00 3.02
5958 8247 2.840102 CTCTCCGGTGGCCCTAGG 60.840 72.222 0.06 0.06 0.00 3.02
5959 8248 4.475444 TCTCCGGTGGCCCTAGGG 62.475 72.222 24.89 24.89 38.57 3.53
5986 8275 4.812476 CGCGGTGGATCTCGGCAA 62.812 66.667 0.00 0.00 0.00 4.52
5987 8276 2.892425 GCGGTGGATCTCGGCAAG 60.892 66.667 12.88 0.00 0.00 4.01
5988 8277 2.202932 CGGTGGATCTCGGCAAGG 60.203 66.667 0.00 0.00 0.00 3.61
5989 8278 2.721167 CGGTGGATCTCGGCAAGGA 61.721 63.158 0.00 0.00 0.00 3.36
5990 8279 1.153349 GGTGGATCTCGGCAAGGAC 60.153 63.158 0.00 0.00 0.00 3.85
5991 8280 1.153349 GTGGATCTCGGCAAGGACC 60.153 63.158 0.00 0.00 0.00 4.46
6017 8306 2.987232 GAGGGCTCCATTTTTAGTCGT 58.013 47.619 0.00 0.00 0.00 4.34
6018 8307 3.344515 GAGGGCTCCATTTTTAGTCGTT 58.655 45.455 0.00 0.00 0.00 3.85
6019 8308 3.756963 GAGGGCTCCATTTTTAGTCGTTT 59.243 43.478 0.00 0.00 0.00 3.60
6020 8309 3.756963 AGGGCTCCATTTTTAGTCGTTTC 59.243 43.478 0.00 0.00 0.00 2.78
6021 8310 3.756963 GGGCTCCATTTTTAGTCGTTTCT 59.243 43.478 0.00 0.00 0.00 2.52
6022 8311 4.217767 GGGCTCCATTTTTAGTCGTTTCTT 59.782 41.667 0.00 0.00 0.00 2.52
6023 8312 5.278808 GGGCTCCATTTTTAGTCGTTTCTTT 60.279 40.000 0.00 0.00 0.00 2.52
6024 8313 5.856986 GGCTCCATTTTTAGTCGTTTCTTTC 59.143 40.000 0.00 0.00 0.00 2.62
6025 8314 6.435428 GCTCCATTTTTAGTCGTTTCTTTCA 58.565 36.000 0.00 0.00 0.00 2.69
6026 8315 6.578919 GCTCCATTTTTAGTCGTTTCTTTCAG 59.421 38.462 0.00 0.00 0.00 3.02
6027 8316 7.562454 TCCATTTTTAGTCGTTTCTTTCAGT 57.438 32.000 0.00 0.00 0.00 3.41
6028 8317 7.992008 TCCATTTTTAGTCGTTTCTTTCAGTT 58.008 30.769 0.00 0.00 0.00 3.16
6029 8318 8.463607 TCCATTTTTAGTCGTTTCTTTCAGTTT 58.536 29.630 0.00 0.00 0.00 2.66
6030 8319 9.083080 CCATTTTTAGTCGTTTCTTTCAGTTTT 57.917 29.630 0.00 0.00 0.00 2.43
6031 8320 9.885743 CATTTTTAGTCGTTTCTTTCAGTTTTG 57.114 29.630 0.00 0.00 0.00 2.44
6032 8321 7.500807 TTTTAGTCGTTTCTTTCAGTTTTGC 57.499 32.000 0.00 0.00 0.00 3.68
6033 8322 4.965119 AGTCGTTTCTTTCAGTTTTGCT 57.035 36.364 0.00 0.00 0.00 3.91
6034 8323 7.542534 TTAGTCGTTTCTTTCAGTTTTGCTA 57.457 32.000 0.00 0.00 0.00 3.49
6035 8324 6.049263 AGTCGTTTCTTTCAGTTTTGCTAG 57.951 37.500 0.00 0.00 0.00 3.42
6036 8325 5.007724 AGTCGTTTCTTTCAGTTTTGCTAGG 59.992 40.000 0.00 0.00 0.00 3.02
6037 8326 4.274950 TCGTTTCTTTCAGTTTTGCTAGGG 59.725 41.667 0.00 0.00 0.00 3.53
6038 8327 4.036380 CGTTTCTTTCAGTTTTGCTAGGGT 59.964 41.667 0.00 0.00 0.00 4.34
6039 8328 5.449999 CGTTTCTTTCAGTTTTGCTAGGGTT 60.450 40.000 0.00 0.00 0.00 4.11
6040 8329 6.338146 GTTTCTTTCAGTTTTGCTAGGGTTT 58.662 36.000 0.00 0.00 0.00 3.27
6041 8330 5.514274 TCTTTCAGTTTTGCTAGGGTTTG 57.486 39.130 0.00 0.00 0.00 2.93
6042 8331 4.953579 TCTTTCAGTTTTGCTAGGGTTTGT 59.046 37.500 0.00 0.00 0.00 2.83
6043 8332 4.647424 TTCAGTTTTGCTAGGGTTTGTG 57.353 40.909 0.00 0.00 0.00 3.33
6044 8333 3.626930 TCAGTTTTGCTAGGGTTTGTGT 58.373 40.909 0.00 0.00 0.00 3.72
6045 8334 3.630312 TCAGTTTTGCTAGGGTTTGTGTC 59.370 43.478 0.00 0.00 0.00 3.67
6046 8335 2.956333 AGTTTTGCTAGGGTTTGTGTCC 59.044 45.455 0.00 0.00 0.00 4.02
6047 8336 2.956333 GTTTTGCTAGGGTTTGTGTCCT 59.044 45.455 0.00 0.00 37.18 3.85
6048 8337 2.270352 TTGCTAGGGTTTGTGTCCTG 57.730 50.000 0.00 0.00 34.75 3.86
6049 8338 0.250727 TGCTAGGGTTTGTGTCCTGC 60.251 55.000 0.00 0.00 34.75 4.85
6050 8339 0.036875 GCTAGGGTTTGTGTCCTGCT 59.963 55.000 0.00 0.00 34.75 4.24
6051 8340 1.946283 GCTAGGGTTTGTGTCCTGCTC 60.946 57.143 0.00 0.00 34.75 4.26
6052 8341 1.347707 CTAGGGTTTGTGTCCTGCTCA 59.652 52.381 0.00 0.00 34.75 4.26
6053 8342 0.109342 AGGGTTTGTGTCCTGCTCAG 59.891 55.000 0.00 0.00 31.11 3.35
6064 8353 3.712020 CTGCTCAGGAAGACGAGAC 57.288 57.895 0.00 0.00 0.00 3.36
6065 8354 0.179176 CTGCTCAGGAAGACGAGACG 60.179 60.000 0.00 0.00 0.00 4.18
6066 8355 1.137825 GCTCAGGAAGACGAGACGG 59.862 63.158 0.00 0.00 0.00 4.79
6067 8356 1.137825 CTCAGGAAGACGAGACGGC 59.862 63.158 0.00 0.00 33.59 5.68
6068 8357 2.202492 CAGGAAGACGAGACGGCG 60.202 66.667 4.80 4.80 41.28 6.46
6069 8358 3.441290 AGGAAGACGAGACGGCGG 61.441 66.667 13.24 0.00 41.28 6.13
6084 8373 3.854669 CGGCGGCTCCCTGAAGAT 61.855 66.667 7.61 0.00 0.00 2.40
6085 8374 2.203126 GGCGGCTCCCTGAAGATG 60.203 66.667 0.00 0.00 0.00 2.90
6086 8375 2.203126 GCGGCTCCCTGAAGATGG 60.203 66.667 0.00 0.00 0.00 3.51
6087 8376 2.735772 GCGGCTCCCTGAAGATGGA 61.736 63.158 0.00 0.00 0.00 3.41
6088 8377 1.907739 CGGCTCCCTGAAGATGGAA 59.092 57.895 0.00 0.00 0.00 3.53
6089 8378 0.471617 CGGCTCCCTGAAGATGGAAT 59.528 55.000 0.00 0.00 0.00 3.01
6090 8379 1.694150 CGGCTCCCTGAAGATGGAATA 59.306 52.381 0.00 0.00 0.00 1.75
6091 8380 2.104792 CGGCTCCCTGAAGATGGAATAA 59.895 50.000 0.00 0.00 0.00 1.40
6092 8381 3.433598 CGGCTCCCTGAAGATGGAATAAA 60.434 47.826 0.00 0.00 0.00 1.40
6093 8382 4.140536 GGCTCCCTGAAGATGGAATAAAG 58.859 47.826 0.00 0.00 0.00 1.85
6094 8383 4.140536 GCTCCCTGAAGATGGAATAAAGG 58.859 47.826 0.00 0.00 0.00 3.11
6095 8384 4.385754 GCTCCCTGAAGATGGAATAAAGGT 60.386 45.833 0.00 0.00 0.00 3.50
6096 8385 5.372373 CTCCCTGAAGATGGAATAAAGGTC 58.628 45.833 0.00 0.00 0.00 3.85
6097 8386 5.039645 TCCCTGAAGATGGAATAAAGGTCT 58.960 41.667 0.00 0.00 0.00 3.85
6098 8387 5.131142 TCCCTGAAGATGGAATAAAGGTCTC 59.869 44.000 0.00 0.00 0.00 3.36
6099 8388 5.372373 CCTGAAGATGGAATAAAGGTCTCC 58.628 45.833 0.00 0.00 0.00 3.71
6100 8389 5.372373 CTGAAGATGGAATAAAGGTCTCCC 58.628 45.833 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 105 1.077930 CCGACTCTACCTCCACGGA 60.078 63.158 0.00 0.00 42.40 4.69
107 116 1.181741 TCTGTTGCAGCTCCGACTCT 61.182 55.000 1.17 0.00 0.00 3.24
122 131 1.371558 GCCGTCCACTTCCTTCTGT 59.628 57.895 0.00 0.00 0.00 3.41
171 180 4.563168 CCTGAGATAGCAATGGAGGTGATC 60.563 50.000 0.00 0.00 0.00 2.92
306 316 3.782656 ACAACCTCCTAAATGTTCCGT 57.217 42.857 0.00 0.00 0.00 4.69
307 317 4.680171 GAACAACCTCCTAAATGTTCCG 57.320 45.455 6.28 0.00 43.56 4.30
457 530 2.841442 AACCTGCAGGACAGTAAGAC 57.159 50.000 39.19 0.00 45.68 3.01
540 613 5.186256 TGTCCCAGCATCAGGTTTAATTA 57.814 39.130 0.00 0.00 0.00 1.40
835 2379 5.106555 ACGAGAACTCTGCAACCAATTATTG 60.107 40.000 0.00 0.00 0.00 1.90
953 2498 5.592688 ACCCCGTCAACTATTAAAATCATGG 59.407 40.000 0.00 0.00 0.00 3.66
1617 3396 7.712204 TCTCATTTATACCAAAGGGAAAACC 57.288 36.000 0.00 0.00 38.05 3.27
1690 3472 9.915629 ACAGAATACACTAAGAAGTTACAGAAG 57.084 33.333 0.00 0.00 31.97 2.85
1823 3605 4.797471 TCAAGCACTTCATTCCAAATTCG 58.203 39.130 0.00 0.00 0.00 3.34
2023 3806 5.637387 GCGTGGGTTTTTCATTCATATTGTT 59.363 36.000 0.00 0.00 0.00 2.83
2121 3941 7.381408 CGTAGGTATGTGTGAACCTGTTATATG 59.619 40.741 4.29 0.00 45.75 1.78
2250 4070 0.551879 TGGGGAAACAACCGGAAGAA 59.448 50.000 9.46 0.00 0.00 2.52
2398 4227 8.677148 ACAGTAATTTAGATGTTGTTCTGTGT 57.323 30.769 0.00 0.00 32.45 3.72
2495 4494 3.215568 CACACCACGCCAAAGCCA 61.216 61.111 0.00 0.00 34.57 4.75
2561 4564 2.909006 TGATTCCTCAGCTTCTCTGGTT 59.091 45.455 0.00 0.00 43.06 3.67
2562 4565 2.500910 CTGATTCCTCAGCTTCTCTGGT 59.499 50.000 0.00 0.00 42.36 4.00
2563 4566 3.182341 CTGATTCCTCAGCTTCTCTGG 57.818 52.381 0.00 0.00 42.36 3.86
2653 4683 3.650950 GGTTCAGCTGCCTCCCCA 61.651 66.667 9.47 0.00 0.00 4.96
2671 4735 0.598562 ATCTGTGAGTCAACGCGTCT 59.401 50.000 14.44 5.14 0.00 4.18
2806 4879 7.806014 TCTTTCAACAAAGTCAACTAACACAAC 59.194 33.333 0.00 0.00 40.16 3.32
2807 4880 7.877003 TCTTTCAACAAAGTCAACTAACACAA 58.123 30.769 0.00 0.00 40.16 3.33
2808 4881 7.441890 TCTTTCAACAAAGTCAACTAACACA 57.558 32.000 0.00 0.00 40.16 3.72
2809 4882 8.736751 TTTCTTTCAACAAAGTCAACTAACAC 57.263 30.769 0.00 0.00 40.16 3.32
2810 4883 9.352784 CATTTCTTTCAACAAAGTCAACTAACA 57.647 29.630 0.00 0.00 40.16 2.41
2811 4884 9.567848 TCATTTCTTTCAACAAAGTCAACTAAC 57.432 29.630 0.00 0.00 40.16 2.34
3080 5153 8.954950 AGGAAAGTATGAATCTTGACTATGTG 57.045 34.615 0.00 0.00 0.00 3.21
3539 5613 6.018262 TGTGCAGATTGTGTAGTTCTACAAAC 60.018 38.462 13.24 4.45 39.89 2.93
3614 5688 8.614469 ATTTAAGTAGCTCAGAATGCTAATCC 57.386 34.615 0.00 0.00 43.50 3.01
3671 5745 7.927629 ACTTGCAAACATTTGTCATGTCTAAAT 59.072 29.630 0.00 0.00 40.24 1.40
3740 5814 2.031163 GGTCACGAGGCTTGCAGT 59.969 61.111 0.37 0.00 0.00 4.40
3752 5826 0.235926 GAGCGAGTTTGCAAGGTCAC 59.764 55.000 9.88 1.33 37.31 3.67
3858 5932 2.358737 CTTGTGCCGGTCCTGGAC 60.359 66.667 18.65 18.65 0.00 4.02
3939 6013 6.639632 ATGTTCAGTTTATACCCATGCATC 57.360 37.500 0.00 0.00 0.00 3.91
3993 6068 8.199449 GGGATTTCTCATCTATTTGCATTTTCA 58.801 33.333 0.00 0.00 0.00 2.69
4349 6445 5.423610 AGAGTTGTCTACATAGCAATCTGGT 59.576 40.000 0.00 0.00 0.00 4.00
4546 6642 4.660521 TGGTACCTCCAGCACCTT 57.339 55.556 14.36 0.00 41.93 3.50
5018 7268 8.275758 TGTGGGAATATACCTGCAGTTTTATAA 58.724 33.333 13.81 0.00 0.00 0.98
5065 7315 6.284891 CAGTATGTCCAAATCAACCCAATT 57.715 37.500 0.00 0.00 0.00 2.32
5141 7391 0.978667 GGAGAGGTGGAAGGGTCCTC 60.979 65.000 0.00 0.00 45.22 3.71
5142 7392 1.081277 GGAGAGGTGGAAGGGTCCT 59.919 63.158 0.00 0.00 45.22 3.85
5223 7473 2.027377 CCTCTGGATTCTTGTGTGAGCT 60.027 50.000 0.00 0.00 0.00 4.09
5322 7594 2.083774 CAGAACATGGCATGTACGGTT 58.916 47.619 31.58 17.00 44.07 4.44
5415 7688 2.750237 GATCAACACGGGGGTGGC 60.750 66.667 0.00 0.00 0.00 5.01
5464 7737 3.213506 TCAAAATCAGATGCCCGTATGG 58.786 45.455 0.00 0.00 37.09 2.74
5523 7796 9.386010 ACAATCGGTAGCATAGTTTTATAACAA 57.614 29.630 0.00 0.00 36.70 2.83
5578 7859 9.434275 TCTAACTACCTCAGATCCATTAATCAA 57.566 33.333 0.00 0.00 0.00 2.57
5728 8016 3.031417 GCGGTGCCAGGTAGGACAT 62.031 63.158 0.00 0.00 41.22 3.06
5794 8083 8.610248 TGTTATGTTACTAGCTTGCTTGTAAA 57.390 30.769 23.30 16.46 0.00 2.01
5795 8084 8.786826 ATGTTATGTTACTAGCTTGCTTGTAA 57.213 30.769 19.79 19.79 0.00 2.41
5796 8085 8.664798 CAATGTTATGTTACTAGCTTGCTTGTA 58.335 33.333 11.61 11.61 0.00 2.41
5797 8086 7.362056 CCAATGTTATGTTACTAGCTTGCTTGT 60.362 37.037 13.40 13.40 0.00 3.16
5798 8087 6.968904 CCAATGTTATGTTACTAGCTTGCTTG 59.031 38.462 0.00 1.08 0.00 4.01
5799 8088 6.659242 ACCAATGTTATGTTACTAGCTTGCTT 59.341 34.615 0.00 0.00 0.00 3.91
5800 8089 6.094048 CACCAATGTTATGTTACTAGCTTGCT 59.906 38.462 0.00 0.00 0.00 3.91
5801 8090 6.093495 TCACCAATGTTATGTTACTAGCTTGC 59.907 38.462 0.00 0.00 0.00 4.01
5802 8091 7.609760 TCACCAATGTTATGTTACTAGCTTG 57.390 36.000 0.00 0.00 0.00 4.01
5803 8092 7.336931 CCTTCACCAATGTTATGTTACTAGCTT 59.663 37.037 0.00 0.00 0.00 3.74
5804 8093 6.823689 CCTTCACCAATGTTATGTTACTAGCT 59.176 38.462 0.00 0.00 0.00 3.32
5805 8094 6.598064 ACCTTCACCAATGTTATGTTACTAGC 59.402 38.462 0.00 0.00 0.00 3.42
5806 8095 8.561738 AACCTTCACCAATGTTATGTTACTAG 57.438 34.615 0.00 0.00 0.00 2.57
5807 8096 8.927675 AAACCTTCACCAATGTTATGTTACTA 57.072 30.769 0.00 0.00 0.00 1.82
5808 8097 7.833285 AAACCTTCACCAATGTTATGTTACT 57.167 32.000 0.00 0.00 0.00 2.24
5809 8098 8.569641 TGTAAACCTTCACCAATGTTATGTTAC 58.430 33.333 0.00 0.00 0.00 2.50
5810 8099 8.693120 TGTAAACCTTCACCAATGTTATGTTA 57.307 30.769 0.00 0.00 0.00 2.41
5811 8100 7.589958 TGTAAACCTTCACCAATGTTATGTT 57.410 32.000 0.00 0.00 0.00 2.71
5812 8101 7.430441 GTTGTAAACCTTCACCAATGTTATGT 58.570 34.615 0.00 0.00 42.21 2.29
5813 8102 6.580791 CGTTGTAAACCTTCACCAATGTTATG 59.419 38.462 0.00 0.00 46.28 1.90
5814 8103 6.674066 CGTTGTAAACCTTCACCAATGTTAT 58.326 36.000 0.00 0.00 46.28 1.89
5815 8104 5.505985 GCGTTGTAAACCTTCACCAATGTTA 60.506 40.000 0.00 0.00 46.28 2.41
5816 8105 4.735283 GCGTTGTAAACCTTCACCAATGTT 60.735 41.667 0.00 0.00 46.28 2.71
5817 8106 3.243267 GCGTTGTAAACCTTCACCAATGT 60.243 43.478 0.00 0.00 46.28 2.71
5818 8107 3.243234 TGCGTTGTAAACCTTCACCAATG 60.243 43.478 0.00 0.00 46.28 2.82
5819 8108 2.952978 TGCGTTGTAAACCTTCACCAAT 59.047 40.909 0.00 0.00 46.28 3.16
5820 8109 2.366533 TGCGTTGTAAACCTTCACCAA 58.633 42.857 0.00 0.00 46.28 3.67
5821 8110 2.039818 TGCGTTGTAAACCTTCACCA 57.960 45.000 0.00 0.00 46.28 4.17
5822 8111 2.095415 GGATGCGTTGTAAACCTTCACC 60.095 50.000 0.00 0.00 46.28 4.02
5823 8112 2.412325 CGGATGCGTTGTAAACCTTCAC 60.412 50.000 0.00 0.00 46.28 3.18
5824 8113 1.801771 CGGATGCGTTGTAAACCTTCA 59.198 47.619 0.00 0.00 46.28 3.02
5825 8114 1.465187 GCGGATGCGTTGTAAACCTTC 60.465 52.381 8.84 0.00 46.28 3.46
5826 8115 0.519961 GCGGATGCGTTGTAAACCTT 59.480 50.000 8.84 0.00 46.28 3.50
5827 8116 0.604243 TGCGGATGCGTTGTAAACCT 60.604 50.000 8.84 0.00 46.28 3.50
5828 8117 0.450184 ATGCGGATGCGTTGTAAACC 59.550 50.000 8.84 0.00 46.28 3.27
5838 8127 0.109179 TTGTTTGCTCATGCGGATGC 60.109 50.000 12.67 1.76 43.34 3.91
5839 8128 1.469703 TCTTGTTTGCTCATGCGGATG 59.530 47.619 11.15 11.15 43.34 3.51
5840 8129 1.741706 CTCTTGTTTGCTCATGCGGAT 59.258 47.619 0.00 0.00 43.34 4.18
5841 8130 1.159285 CTCTTGTTTGCTCATGCGGA 58.841 50.000 0.00 0.00 43.34 5.54
5842 8131 1.129998 CTCTCTTGTTTGCTCATGCGG 59.870 52.381 0.00 0.00 43.34 5.69
5843 8132 1.129998 CCTCTCTTGTTTGCTCATGCG 59.870 52.381 0.00 0.00 43.34 4.73
5844 8133 1.135460 GCCTCTCTTGTTTGCTCATGC 60.135 52.381 0.00 0.00 40.20 4.06
5845 8134 2.434428 AGCCTCTCTTGTTTGCTCATG 58.566 47.619 0.00 0.00 0.00 3.07
5846 8135 2.875094 AGCCTCTCTTGTTTGCTCAT 57.125 45.000 0.00 0.00 0.00 2.90
5847 8136 2.613977 GCTAGCCTCTCTTGTTTGCTCA 60.614 50.000 2.29 0.00 33.63 4.26
5848 8137 2.006169 GCTAGCCTCTCTTGTTTGCTC 58.994 52.381 2.29 0.00 33.63 4.26
5849 8138 1.339535 GGCTAGCCTCTCTTGTTTGCT 60.340 52.381 27.17 0.00 36.11 3.91
5850 8139 1.090728 GGCTAGCCTCTCTTGTTTGC 58.909 55.000 27.17 0.00 0.00 3.68
5851 8140 1.363744 CGGCTAGCCTCTCTTGTTTG 58.636 55.000 30.55 7.86 0.00 2.93
5852 8141 0.391793 GCGGCTAGCCTCTCTTGTTT 60.392 55.000 30.55 0.00 40.81 2.83
5853 8142 1.219393 GCGGCTAGCCTCTCTTGTT 59.781 57.895 30.55 0.00 40.81 2.83
5854 8143 2.896443 GCGGCTAGCCTCTCTTGT 59.104 61.111 30.55 0.00 40.81 3.16
5870 8159 3.855853 GAGGAAGGAGGAGGCGGC 61.856 72.222 0.00 0.00 0.00 6.53
5871 8160 3.157949 GGAGGAAGGAGGAGGCGG 61.158 72.222 0.00 0.00 0.00 6.13
5872 8161 2.364317 TGGAGGAAGGAGGAGGCG 60.364 66.667 0.00 0.00 0.00 5.52
5873 8162 1.201429 TTGTGGAGGAAGGAGGAGGC 61.201 60.000 0.00 0.00 0.00 4.70
5874 8163 1.362224 TTTGTGGAGGAAGGAGGAGG 58.638 55.000 0.00 0.00 0.00 4.30
5875 8164 3.508845 TTTTTGTGGAGGAAGGAGGAG 57.491 47.619 0.00 0.00 0.00 3.69
5938 8227 3.375443 TAGGGCCACCGGAGAGGAG 62.375 68.421 9.46 0.00 45.00 3.69
5939 8228 3.352748 TAGGGCCACCGGAGAGGA 61.353 66.667 9.46 0.00 45.00 3.71
5941 8230 2.840102 CCTAGGGCCACCGGAGAG 60.840 72.222 9.46 0.00 43.47 3.20
5942 8231 4.475444 CCCTAGGGCCACCGGAGA 62.475 72.222 16.90 0.00 43.47 3.71
5969 8258 4.812476 TTGCCGAGATCCACCGCG 62.812 66.667 0.00 0.00 0.00 6.46
5970 8259 2.892425 CTTGCCGAGATCCACCGC 60.892 66.667 0.00 0.00 0.00 5.68
5971 8260 2.202932 CCTTGCCGAGATCCACCG 60.203 66.667 0.00 0.00 0.00 4.94
5972 8261 1.153349 GTCCTTGCCGAGATCCACC 60.153 63.158 0.00 0.00 0.00 4.61
5973 8262 1.153349 GGTCCTTGCCGAGATCCAC 60.153 63.158 0.00 0.00 0.00 4.02
5974 8263 3.309582 GGTCCTTGCCGAGATCCA 58.690 61.111 0.00 0.00 0.00 3.41
5997 8286 2.987232 ACGACTAAAAATGGAGCCCTC 58.013 47.619 0.00 0.00 0.00 4.30
5998 8287 3.434940 AACGACTAAAAATGGAGCCCT 57.565 42.857 0.00 0.00 0.00 5.19
5999 8288 3.756963 AGAAACGACTAAAAATGGAGCCC 59.243 43.478 0.00 0.00 0.00 5.19
6000 8289 5.372547 AAGAAACGACTAAAAATGGAGCC 57.627 39.130 0.00 0.00 0.00 4.70
6001 8290 6.435428 TGAAAGAAACGACTAAAAATGGAGC 58.565 36.000 0.00 0.00 0.00 4.70
6002 8291 7.639945 ACTGAAAGAAACGACTAAAAATGGAG 58.360 34.615 0.00 0.00 37.43 3.86
6003 8292 7.562454 ACTGAAAGAAACGACTAAAAATGGA 57.438 32.000 0.00 0.00 37.43 3.41
6004 8293 8.628882 AAACTGAAAGAAACGACTAAAAATGG 57.371 30.769 0.00 0.00 37.43 3.16
6005 8294 9.885743 CAAAACTGAAAGAAACGACTAAAAATG 57.114 29.630 0.00 0.00 37.43 2.32
6006 8295 8.592155 GCAAAACTGAAAGAAACGACTAAAAAT 58.408 29.630 0.00 0.00 37.43 1.82
6007 8296 7.810759 AGCAAAACTGAAAGAAACGACTAAAAA 59.189 29.630 0.00 0.00 37.43 1.94
6008 8297 7.309920 AGCAAAACTGAAAGAAACGACTAAAA 58.690 30.769 0.00 0.00 37.43 1.52
6009 8298 6.848451 AGCAAAACTGAAAGAAACGACTAAA 58.152 32.000 0.00 0.00 37.43 1.85
6010 8299 6.431198 AGCAAAACTGAAAGAAACGACTAA 57.569 33.333 0.00 0.00 37.43 2.24
6011 8300 6.202188 CCTAGCAAAACTGAAAGAAACGACTA 59.798 38.462 0.00 0.00 37.43 2.59
6012 8301 4.965119 AGCAAAACTGAAAGAAACGACT 57.035 36.364 0.00 0.00 37.43 4.18
6013 8302 5.205565 CCTAGCAAAACTGAAAGAAACGAC 58.794 41.667 0.00 0.00 37.43 4.34
6014 8303 4.274950 CCCTAGCAAAACTGAAAGAAACGA 59.725 41.667 0.00 0.00 37.43 3.85
6015 8304 4.036380 ACCCTAGCAAAACTGAAAGAAACG 59.964 41.667 0.00 0.00 37.43 3.60
6016 8305 5.515797 ACCCTAGCAAAACTGAAAGAAAC 57.484 39.130 0.00 0.00 37.43 2.78
6017 8306 6.071051 ACAAACCCTAGCAAAACTGAAAGAAA 60.071 34.615 0.00 0.00 37.43 2.52
6018 8307 5.420739 ACAAACCCTAGCAAAACTGAAAGAA 59.579 36.000 0.00 0.00 37.43 2.52
6019 8308 4.953579 ACAAACCCTAGCAAAACTGAAAGA 59.046 37.500 0.00 0.00 37.43 2.52
6020 8309 5.043248 CACAAACCCTAGCAAAACTGAAAG 58.957 41.667 0.00 0.00 42.29 2.62
6021 8310 4.464597 ACACAAACCCTAGCAAAACTGAAA 59.535 37.500 0.00 0.00 0.00 2.69
6022 8311 4.020543 ACACAAACCCTAGCAAAACTGAA 58.979 39.130 0.00 0.00 0.00 3.02
6023 8312 3.626930 ACACAAACCCTAGCAAAACTGA 58.373 40.909 0.00 0.00 0.00 3.41
6024 8313 3.243401 GGACACAAACCCTAGCAAAACTG 60.243 47.826 0.00 0.00 0.00 3.16
6025 8314 2.956333 GGACACAAACCCTAGCAAAACT 59.044 45.455 0.00 0.00 0.00 2.66
6026 8315 2.956333 AGGACACAAACCCTAGCAAAAC 59.044 45.455 0.00 0.00 0.00 2.43
6027 8316 2.955660 CAGGACACAAACCCTAGCAAAA 59.044 45.455 0.00 0.00 0.00 2.44
6028 8317 2.582052 CAGGACACAAACCCTAGCAAA 58.418 47.619 0.00 0.00 0.00 3.68
6029 8318 1.817740 GCAGGACACAAACCCTAGCAA 60.818 52.381 0.00 0.00 31.50 3.91
6030 8319 0.250727 GCAGGACACAAACCCTAGCA 60.251 55.000 0.00 0.00 31.50 3.49
6031 8320 0.036875 AGCAGGACACAAACCCTAGC 59.963 55.000 0.00 0.00 0.00 3.42
6032 8321 1.347707 TGAGCAGGACACAAACCCTAG 59.652 52.381 0.00 0.00 0.00 3.02
6033 8322 1.347707 CTGAGCAGGACACAAACCCTA 59.652 52.381 0.00 0.00 0.00 3.53
6034 8323 0.109342 CTGAGCAGGACACAAACCCT 59.891 55.000 0.00 0.00 0.00 4.34
6035 8324 2.633860 CTGAGCAGGACACAAACCC 58.366 57.895 0.00 0.00 0.00 4.11
6046 8335 0.179176 CGTCTCGTCTTCCTGAGCAG 60.179 60.000 0.00 0.00 32.20 4.24
6047 8336 1.587043 CCGTCTCGTCTTCCTGAGCA 61.587 60.000 0.00 0.00 32.20 4.26
6048 8337 1.137825 CCGTCTCGTCTTCCTGAGC 59.862 63.158 0.00 0.00 32.20 4.26
6049 8338 1.137825 GCCGTCTCGTCTTCCTGAG 59.862 63.158 0.00 0.00 0.00 3.35
6050 8339 2.687805 CGCCGTCTCGTCTTCCTGA 61.688 63.158 0.00 0.00 0.00 3.86
6051 8340 2.202492 CGCCGTCTCGTCTTCCTG 60.202 66.667 0.00 0.00 0.00 3.86
6052 8341 3.441290 CCGCCGTCTCGTCTTCCT 61.441 66.667 0.00 0.00 0.00 3.36
6067 8356 3.854669 ATCTTCAGGGAGCCGCCG 61.855 66.667 0.00 0.00 37.63 6.46
6068 8357 2.203126 CATCTTCAGGGAGCCGCC 60.203 66.667 0.00 0.00 0.00 6.13
6069 8358 2.203126 CCATCTTCAGGGAGCCGC 60.203 66.667 0.00 0.00 0.00 6.53
6070 8359 0.471617 ATTCCATCTTCAGGGAGCCG 59.528 55.000 0.00 0.00 34.02 5.52
6071 8360 3.864789 TTATTCCATCTTCAGGGAGCC 57.135 47.619 0.00 0.00 34.02 4.70
6072 8361 4.140536 CCTTTATTCCATCTTCAGGGAGC 58.859 47.826 0.00 0.00 34.02 4.70
6073 8362 5.131809 AGACCTTTATTCCATCTTCAGGGAG 59.868 44.000 0.00 0.00 34.02 4.30
6074 8363 5.039645 AGACCTTTATTCCATCTTCAGGGA 58.960 41.667 0.00 0.00 0.00 4.20
6075 8364 5.372373 GAGACCTTTATTCCATCTTCAGGG 58.628 45.833 0.00 0.00 0.00 4.45
6076 8365 5.372373 GGAGACCTTTATTCCATCTTCAGG 58.628 45.833 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.