Multiple sequence alignment - TraesCS5A01G520500

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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 TraesCS5A01G520500 chr5A 100.000 7388 0 0 1 7388 681201872 681209259 0.000000e+00 13644.0
1 TraesCS5A01G520500 chr5A 96.265 3963 127 7 3290 7233 681134793 681138753 0.000000e+00 6479.0
2 TraesCS5A01G520500 chr5A 98.932 2059 17 3 314 2372 681063574 681065627 0.000000e+00 3675.0
3 TraesCS5A01G520500 chr5A 92.692 2162 112 13 1441 3582 681154790 681156925 0.000000e+00 3075.0
4 TraesCS5A01G520500 chr5A 92.596 2161 115 13 1441 3582 681082472 681084606 0.000000e+00 3062.0
5 TraesCS5A01G520500 chr5A 99.204 1634 12 1 1 1634 681131058 681132690 0.000000e+00 2944.0
6 TraesCS5A01G520500 chr5A 96.073 1655 62 2 4274 5927 681162655 681164307 0.000000e+00 2693.0
7 TraesCS5A01G520500 chr5A 95.833 1656 65 3 4274 5927 681090338 681091991 0.000000e+00 2673.0
8 TraesCS5A01G520500 chr5A 95.813 1624 67 1 5610 7233 681065639 681067261 0.000000e+00 2621.0
9 TraesCS5A01G520500 chr5A 92.896 1478 94 9 5210 6682 681255570 681257041 0.000000e+00 2137.0
10 TraesCS5A01G520500 chr5A 91.486 1104 81 8 4116 5218 681254301 681255392 0.000000e+00 1506.0
11 TraesCS5A01G520500 chr5A 98.902 820 9 0 2478 3297 681133915 681134734 0.000000e+00 1465.0
12 TraesCS5A01G520500 chr5A 100.000 700 0 0 1673 2372 681132779 681133478 0.000000e+00 1293.0
13 TraesCS5A01G520500 chr5A 94.056 572 18 5 3688 4245 681084610 681085179 0.000000e+00 854.0
14 TraesCS5A01G520500 chr5A 94.056 572 18 5 3688 4245 681156929 681157498 0.000000e+00 854.0
15 TraesCS5A01G520500 chr5A 94.097 559 27 2 1441 1999 681153962 681154514 0.000000e+00 845.0
16 TraesCS5A01G520500 chr5A 88.632 475 39 8 1062 1525 681241885 681242355 1.390000e-156 564.0
17 TraesCS5A01G520500 chr5A 92.398 342 26 0 6360 6701 681164304 681164645 8.620000e-134 488.0
18 TraesCS5A01G520500 chr5A 91.813 342 26 2 6360 6701 681091988 681092327 6.710000e-130 475.0
19 TraesCS5A01G520500 chr5A 97.581 248 6 0 71 318 681121135 681121382 6.850000e-115 425.0
20 TraesCS5A01G520500 chr5A 97.177 248 7 0 71 318 94826796 94826549 3.190000e-113 420.0
21 TraesCS5A01G520500 chr5A 96.774 248 8 0 71 318 359756099 359755852 1.480000e-111 414.0
22 TraesCS5A01G520500 chr5A 96.774 248 8 0 71 318 681191978 681192225 1.480000e-111 414.0
23 TraesCS5A01G520500 chr5A 83.478 460 43 16 1930 2362 681247275 681247728 1.490000e-106 398.0
24 TraesCS5A01G520500 chr5A 86.813 273 12 6 3695 3951 681248255 681248519 4.360000e-72 283.0
25 TraesCS5A01G520500 chr5A 92.982 114 8 0 3578 3691 658993692 658993805 4.580000e-37 167.0
26 TraesCS5A01G520500 chr5A 98.889 90 1 0 7227 7316 196275876 196275787 2.130000e-35 161.0
27 TraesCS5A01G520500 chr5A 86.275 153 7 3 3978 4123 681249926 681250071 3.570000e-33 154.0
28 TraesCS5A01G520500 chr5A 79.675 123 15 8 643 757 681236462 681236582 6.140000e-11 80.5
29 TraesCS5A01G520500 chr4B 93.506 3588 176 28 3688 7233 643665588 643669160 0.000000e+00 5282.0
30 TraesCS5A01G520500 chr4B 90.857 2275 138 30 314 2543 643661948 643664197 0.000000e+00 2985.0
31 TraesCS5A01G520500 chr4B 89.001 1982 131 35 3695 5640 643764547 643766477 0.000000e+00 2372.0
32 TraesCS5A01G520500 chr4B 90.598 1053 67 12 2532 3583 643664564 643665585 0.000000e+00 1367.0
33 TraesCS5A01G520500 chr4B 86.611 478 41 12 1062 1519 643762680 643763154 2.380000e-139 507.0
34 TraesCS5A01G520500 chr4B 81.658 567 75 18 5693 6235 643766574 643767135 1.890000e-120 444.0
35 TraesCS5A01G520500 chr4B 83.660 459 37 18 1942 2368 643763573 643764025 1.490000e-106 398.0
36 TraesCS5A01G520500 chr4B 84.091 264 20 9 1585 1826 643763160 643763423 1.240000e-57 235.0
37 TraesCS5A01G520500 chr4B 85.143 175 17 4 3265 3439 643764016 643764181 3.540000e-38 171.0
38 TraesCS5A01G520500 chr4B 84.211 152 18 5 7231 7379 27992037 27992185 7.730000e-30 143.0
39 TraesCS5A01G520500 chr4B 93.056 72 4 1 3511 3581 643764179 643764250 3.650000e-18 104.0
40 TraesCS5A01G520500 chr4D 95.142 2985 115 15 3688 6649 500393272 500396249 0.000000e+00 4682.0
41 TraesCS5A01G520500 chr4D 92.438 1243 51 15 314 1541 500390355 500391569 0.000000e+00 1735.0
42 TraesCS5A01G520500 chr4D 91.545 615 30 6 2071 2665 500392248 500392860 0.000000e+00 828.0
43 TraesCS5A01G520500 chr4D 90.931 419 24 7 3170 3583 500392860 500393269 1.080000e-152 551.0
44 TraesCS5A01G520500 chr4D 93.175 337 18 4 1738 2071 500391809 500392143 2.400000e-134 490.0
45 TraesCS5A01G520500 chr4D 99.286 140 1 0 1539 1678 500391672 500391811 3.420000e-63 254.0
46 TraesCS5A01G520500 chr4D 80.000 235 41 6 2733 2963 266739338 266739106 1.270000e-37 169.0
47 TraesCS5A01G520500 chr4D 100.000 75 0 0 7314 7388 333667442 333667516 1.000000e-28 139.0
48 TraesCS5A01G520500 chr4D 97.403 77 1 1 1 77 72072305 72072230 6.020000e-26 130.0
49 TraesCS5A01G520500 chr4D 77.907 172 24 8 6331 6501 16648160 16648002 2.190000e-15 95.3
50 TraesCS5A01G520500 chrUn 96.711 2341 53 8 3290 5607 321511736 321514075 0.000000e+00 3875.0
51 TraesCS5A01G520500 chrUn 99.863 1459 1 1 1673 3131 398013865 398015322 0.000000e+00 2682.0
52 TraesCS5A01G520500 chrUn 98.902 820 9 0 2478 3297 321510882 321511701 0.000000e+00 1465.0
53 TraesCS5A01G520500 chrUn 100.000 75 0 0 7314 7388 6680149 6680075 1.000000e-28 139.0
54 TraesCS5A01G520500 chrUn 100.000 75 0 0 7314 7388 58812457 58812383 1.000000e-28 139.0
55 TraesCS5A01G520500 chrUn 100.000 75 0 0 7314 7388 175169099 175169025 1.000000e-28 139.0
56 TraesCS5A01G520500 chrUn 100.000 75 0 0 7314 7388 317190856 317190782 1.000000e-28 139.0
57 TraesCS5A01G520500 chr2B 86.562 826 96 7 2442 3263 453063073 453063887 0.000000e+00 896.0
58 TraesCS5A01G520500 chr1D 86.890 717 81 10 6525 7233 250735006 250734295 0.000000e+00 791.0
59 TraesCS5A01G520500 chr1D 93.694 111 7 0 3582 3692 465596911 465596801 4.580000e-37 167.0
60 TraesCS5A01G520500 chr1D 91.304 115 8 2 3582 3694 495410382 495410268 9.920000e-34 156.0
61 TraesCS5A01G520500 chr1D 97.403 77 1 1 1 77 465870156 465870231 6.020000e-26 130.0
62 TraesCS5A01G520500 chr1D 92.683 41 2 1 3464 3504 462461962 462461923 2.880000e-04 58.4
63 TraesCS5A01G520500 chr4A 86.357 733 89 9 6508 7233 567645973 567646701 0.000000e+00 789.0
64 TraesCS5A01G520500 chr4A 97.403 77 1 1 1 77 91015219 91015144 6.020000e-26 130.0
65 TraesCS5A01G520500 chr5D 86.008 729 89 9 6505 7224 318448007 318448731 0.000000e+00 769.0
66 TraesCS5A01G520500 chr5D 84.324 370 47 6 2434 2798 432936627 432936990 1.180000e-92 351.0
67 TraesCS5A01G520500 chr7D 85.714 728 93 8 6506 7228 190087648 190088369 0.000000e+00 758.0
68 TraesCS5A01G520500 chr7D 93.750 112 5 2 3582 3692 60693479 60693369 4.580000e-37 167.0
69 TraesCS5A01G520500 chr7D 90.164 122 11 1 3568 3689 271752962 271752842 2.760000e-34 158.0
70 TraesCS5A01G520500 chr7D 97.403 77 1 1 1 77 46009885 46009960 6.020000e-26 130.0
71 TraesCS5A01G520500 chr3D 85.170 735 96 12 6506 7233 295288405 295287677 0.000000e+00 741.0
72 TraesCS5A01G520500 chr3D 92.174 115 9 0 3582 3696 388791486 388791372 5.930000e-36 163.0
73 TraesCS5A01G520500 chr3B 85.095 738 93 14 6505 7233 241670651 241669922 0.000000e+00 737.0
74 TraesCS5A01G520500 chr3B 90.446 157 12 2 7234 7388 262132155 262132000 3.490000e-48 204.0
75 TraesCS5A01G520500 chr3B 87.500 104 8 1 2435 2538 823162675 823162577 1.680000e-21 115.0
76 TraesCS5A01G520500 chr3B 87.179 78 4 6 3435 3512 440404857 440404786 4.750000e-12 84.2
77 TraesCS5A01G520500 chr2A 96.850 254 8 0 71 324 683444782 683445035 6.850000e-115 425.0
78 TraesCS5A01G520500 chr2A 96.774 248 8 0 71 318 421330890 421331137 1.480000e-111 414.0
79 TraesCS5A01G520500 chr2A 95.413 109 5 0 3581 3689 449280030 449280138 2.740000e-39 174.0
80 TraesCS5A01G520500 chr2A 97.778 90 1 1 7227 7316 300297044 300296956 3.570000e-33 154.0
81 TraesCS5A01G520500 chr2A 91.837 49 3 1 3464 3512 613878680 613878727 4.780000e-07 67.6
82 TraesCS5A01G520500 chr2A 96.970 33 1 0 3431 3463 17843755 17843787 1.000000e-03 56.5
83 TraesCS5A01G520500 chr6A 79.248 665 90 28 6657 7316 70226031 70226652 3.190000e-113 420.0
84 TraesCS5A01G520500 chr6A 96.787 249 8 0 71 319 551120869 551121117 4.120000e-112 416.0
85 TraesCS5A01G520500 chr6A 98.701 77 0 1 1 77 232268220 232268145 1.290000e-27 135.0
86 TraesCS5A01G520500 chr1A 97.177 248 7 0 71 318 506342681 506342928 3.190000e-113 420.0
87 TraesCS5A01G520500 chr1A 92.105 114 9 0 3582 3695 498166988 498166875 2.130000e-35 161.0
88 TraesCS5A01G520500 chr1A 89.565 115 12 0 3582 3696 490884098 490883984 5.970000e-31 147.0
89 TraesCS5A01G520500 chr1A 87.931 116 13 1 3582 3697 533667875 533667761 1.290000e-27 135.0
90 TraesCS5A01G520500 chr1A 97.403 77 1 1 1 77 506985573 506985648 6.020000e-26 130.0
91 TraesCS5A01G520500 chr5B 92.899 169 6 5 7222 7388 114172753 114172917 2.660000e-59 241.0
92 TraesCS5A01G520500 chr5B 94.872 39 2 0 3437 3475 594200657 594200619 2.230000e-05 62.1
93 TraesCS5A01G520500 chr6B 94.737 114 6 0 3582 3695 506128090 506127977 2.120000e-40 178.0
94 TraesCS5A01G520500 chr3A 92.920 113 8 0 3578 3690 362337434 362337546 1.650000e-36 165.0
95 TraesCS5A01G520500 chr3A 92.920 113 7 1 3582 3694 688902018 688901907 5.930000e-36 163.0
96 TraesCS5A01G520500 chr3A 95.960 99 3 1 7219 7316 502476343 502476245 7.670000e-35 159.0
97 TraesCS5A01G520500 chr3A 92.453 106 7 1 7211 7316 310088158 310088262 4.620000e-32 150.0
98 TraesCS5A01G520500 chr3A 100.000 76 0 0 7313 7388 133932370 133932295 2.780000e-29 141.0
99 TraesCS5A01G520500 chr7A 96.000 100 3 1 7228 7326 704951417 704951318 2.130000e-35 161.0
100 TraesCS5A01G520500 chr6D 97.403 77 1 1 1 77 376727083 376727008 6.020000e-26 130.0
101 TraesCS5A01G520500 chr2D 97.403 77 1 1 1 77 363201261 363201186 6.020000e-26 130.0


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 TraesCS5A01G520500 chr5A 681201872 681209259 7387 False 13644.000000 13644 100.000000 1 7388 1 chr5A.!!$F4 7387
1 TraesCS5A01G520500 chr5A 681063574 681067261 3687 False 3148.000000 3675 97.372500 314 7233 2 chr5A.!!$F7 6919
2 TraesCS5A01G520500 chr5A 681131058 681138753 7695 False 3045.250000 6479 98.592750 1 7233 4 chr5A.!!$F10 7232
3 TraesCS5A01G520500 chr5A 681082472 681085179 2707 False 1958.000000 3062 93.326000 1441 4245 2 chr5A.!!$F8 2804
4 TraesCS5A01G520500 chr5A 681254301 681257041 2740 False 1821.500000 2137 92.191000 4116 6682 2 chr5A.!!$F14 2566
5 TraesCS5A01G520500 chr5A 681153962 681157498 3536 False 1591.333333 3075 93.615000 1441 4245 3 chr5A.!!$F11 2804
6 TraesCS5A01G520500 chr5A 681162655 681164645 1990 False 1590.500000 2693 94.235500 4274 6701 2 chr5A.!!$F12 2427
7 TraesCS5A01G520500 chr5A 681090338 681092327 1989 False 1574.000000 2673 93.823000 4274 6701 2 chr5A.!!$F9 2427
8 TraesCS5A01G520500 chr5A 681247275 681250071 2796 False 278.333333 398 85.522000 1930 4123 3 chr5A.!!$F13 2193
9 TraesCS5A01G520500 chr4B 643661948 643669160 7212 False 3211.333333 5282 91.653667 314 7233 3 chr4B.!!$F2 6919
10 TraesCS5A01G520500 chr4B 643762680 643767135 4455 False 604.428571 2372 86.174286 1062 6235 7 chr4B.!!$F3 5173
11 TraesCS5A01G520500 chr4D 500390355 500396249 5894 False 1423.333333 4682 93.752833 314 6649 6 chr4D.!!$F2 6335
12 TraesCS5A01G520500 chrUn 398013865 398015322 1457 False 2682.000000 2682 99.863000 1673 3131 1 chrUn.!!$F1 1458
13 TraesCS5A01G520500 chrUn 321510882 321514075 3193 False 2670.000000 3875 97.806500 2478 5607 2 chrUn.!!$F2 3129
14 TraesCS5A01G520500 chr2B 453063073 453063887 814 False 896.000000 896 86.562000 2442 3263 1 chr2B.!!$F1 821
15 TraesCS5A01G520500 chr1D 250734295 250735006 711 True 791.000000 791 86.890000 6525 7233 1 chr1D.!!$R1 708
16 TraesCS5A01G520500 chr4A 567645973 567646701 728 False 789.000000 789 86.357000 6508 7233 1 chr4A.!!$F1 725
17 TraesCS5A01G520500 chr5D 318448007 318448731 724 False 769.000000 769 86.008000 6505 7224 1 chr5D.!!$F1 719
18 TraesCS5A01G520500 chr7D 190087648 190088369 721 False 758.000000 758 85.714000 6506 7228 1 chr7D.!!$F2 722
19 TraesCS5A01G520500 chr3D 295287677 295288405 728 True 741.000000 741 85.170000 6506 7233 1 chr3D.!!$R1 727
20 TraesCS5A01G520500 chr3B 241669922 241670651 729 True 737.000000 737 85.095000 6505 7233 1 chr3B.!!$R1 728
21 TraesCS5A01G520500 chr6A 70226031 70226652 621 False 420.000000 420 79.248000 6657 7316 1 chr6A.!!$F1 659

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
113 114 1.004918 CAGAGTCCCAACACCGGTC 60.005 63.158 2.59 0.00 0.00 4.79 F
240 241 2.641815 GCCCTCATCTATCTTCATGGGT 59.358 50.000 0.00 0.00 36.00 4.51 F
346 347 2.915604 TGGGAAAGAAGAGAAGAGGCAT 59.084 45.455 0.00 0.00 0.00 4.40 F
3270 5228 3.494254 TGCAAGTCCAACCCGGGT 61.494 61.111 24.16 24.16 34.36 5.28 F
4183 7895 0.333312 ACAAAGGTGGTGGTGGACAA 59.667 50.000 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3270 5228 4.890158 TGTCATGAAAGGCTAGTGAGAA 57.110 40.909 0.0 0.0 0.00 2.87 R
3373 5397 3.507233 TGGTGAAATACTACTCGTTCGGT 59.493 43.478 0.0 0.0 0.00 4.69 R
3431 5455 7.510675 AATTTGGATCAAAGGGAGTAGTCTA 57.489 36.000 0.0 0.0 36.76 2.59 R
6248 10243 0.178861 AGGAGGAAAAGGCAGGAGGA 60.179 55.000 0.0 0.0 0.00 3.71 R
7272 11287 0.666274 CGCCTTAGACGCACAGTTCA 60.666 55.000 0.0 0.0 0.00 3.18 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
42 43 1.946768 CAACTGTCGTGGGTTTGTCAT 59.053 47.619 0.00 0.00 0.00 3.06
113 114 1.004918 CAGAGTCCCAACACCGGTC 60.005 63.158 2.59 0.00 0.00 4.79
133 134 2.835156 TCCATAGATGTGTCCGGTTTGA 59.165 45.455 0.00 0.00 0.00 2.69
179 180 6.596106 ACAATACAAGTTACATATTGACGCCA 59.404 34.615 15.82 0.00 38.17 5.69
240 241 2.641815 GCCCTCATCTATCTTCATGGGT 59.358 50.000 0.00 0.00 36.00 4.51
346 347 2.915604 TGGGAAAGAAGAGAAGAGGCAT 59.084 45.455 0.00 0.00 0.00 4.40
3270 5228 3.494254 TGCAAGTCCAACCCGGGT 61.494 61.111 24.16 24.16 34.36 5.28
3428 5452 7.769044 GCTTACAAGGAAATTCCACTAGTATCA 59.231 37.037 15.21 0.00 39.61 2.15
3506 5534 7.773489 TGTGTCAATTAATTTGGATTGGAGA 57.227 32.000 0.00 0.00 35.92 3.71
3576 5605 5.622770 ACAACAAAAGGCTAGGAATTACG 57.377 39.130 0.00 0.00 0.00 3.18
3583 5863 8.886719 ACAAAAGGCTAGGAATTACGTTATTAC 58.113 33.333 1.13 1.13 0.00 1.89
3585 5865 8.883954 AAAGGCTAGGAATTACGTTATTACTC 57.116 34.615 15.00 2.86 31.21 2.59
3586 5866 6.990798 AGGCTAGGAATTACGTTATTACTCC 58.009 40.000 15.00 11.34 31.21 3.85
3587 5867 6.014755 AGGCTAGGAATTACGTTATTACTCCC 60.015 42.308 15.00 15.53 31.21 4.30
3589 5869 7.089538 GCTAGGAATTACGTTATTACTCCCTC 58.910 42.308 15.00 1.00 31.21 4.30
3590 5870 6.416631 AGGAATTACGTTATTACTCCCTCC 57.583 41.667 6.20 0.00 0.00 4.30
3591 5871 5.010415 AGGAATTACGTTATTACTCCCTCCG 59.990 44.000 6.20 0.00 0.00 4.63
3592 5872 5.221322 GGAATTACGTTATTACTCCCTCCGT 60.221 44.000 2.23 0.00 0.00 4.69
3593 5873 5.859205 ATTACGTTATTACTCCCTCCGTT 57.141 39.130 0.00 0.00 0.00 4.44
3594 5874 3.790152 ACGTTATTACTCCCTCCGTTC 57.210 47.619 0.00 0.00 0.00 3.95
3595 5875 3.091545 ACGTTATTACTCCCTCCGTTCA 58.908 45.455 0.00 0.00 0.00 3.18
3596 5876 3.119352 ACGTTATTACTCCCTCCGTTCAC 60.119 47.826 0.00 0.00 0.00 3.18
3597 5877 3.129988 CGTTATTACTCCCTCCGTTCACT 59.870 47.826 0.00 0.00 0.00 3.41
3598 5878 4.381292 CGTTATTACTCCCTCCGTTCACTT 60.381 45.833 0.00 0.00 0.00 3.16
3599 5879 5.485620 GTTATTACTCCCTCCGTTCACTTT 58.514 41.667 0.00 0.00 0.00 2.66
3600 5880 4.635699 ATTACTCCCTCCGTTCACTTTT 57.364 40.909 0.00 0.00 0.00 2.27
3601 5881 5.750352 ATTACTCCCTCCGTTCACTTTTA 57.250 39.130 0.00 0.00 0.00 1.52
3602 5882 5.750352 TTACTCCCTCCGTTCACTTTTAT 57.250 39.130 0.00 0.00 0.00 1.40
3603 5883 6.855763 TTACTCCCTCCGTTCACTTTTATA 57.144 37.500 0.00 0.00 0.00 0.98
3604 5884 5.750352 ACTCCCTCCGTTCACTTTTATAA 57.250 39.130 0.00 0.00 0.00 0.98
3605 5885 5.731591 ACTCCCTCCGTTCACTTTTATAAG 58.268 41.667 0.00 0.00 37.40 1.73
3606 5886 5.247792 ACTCCCTCCGTTCACTTTTATAAGT 59.752 40.000 0.00 0.00 45.40 2.24
3607 5887 5.727434 TCCCTCCGTTCACTTTTATAAGTC 58.273 41.667 0.00 0.00 42.67 3.01
3608 5888 4.565564 CCCTCCGTTCACTTTTATAAGTCG 59.434 45.833 0.00 0.00 42.67 4.18
3609 5889 5.166398 CCTCCGTTCACTTTTATAAGTCGT 58.834 41.667 0.00 0.00 42.67 4.34
3610 5890 5.636543 CCTCCGTTCACTTTTATAAGTCGTT 59.363 40.000 0.00 0.00 42.67 3.85
3611 5891 6.146673 CCTCCGTTCACTTTTATAAGTCGTTT 59.853 38.462 0.00 0.00 42.67 3.60
3612 5892 7.307573 CCTCCGTTCACTTTTATAAGTCGTTTT 60.308 37.037 0.00 0.00 42.67 2.43
3613 5893 8.586570 TCCGTTCACTTTTATAAGTCGTTTTA 57.413 30.769 0.00 0.00 42.67 1.52
3614 5894 8.702438 TCCGTTCACTTTTATAAGTCGTTTTAG 58.298 33.333 0.00 0.00 42.67 1.85
3615 5895 8.702438 CCGTTCACTTTTATAAGTCGTTTTAGA 58.298 33.333 0.00 0.00 42.67 2.10
3616 5896 9.508495 CGTTCACTTTTATAAGTCGTTTTAGAC 57.492 33.333 0.00 0.00 42.67 2.59
3627 5907 9.878599 ATAAGTCGTTTTAGACAACTGAAAATG 57.121 29.630 0.00 0.00 43.24 2.32
3628 5908 7.548196 AGTCGTTTTAGACAACTGAAAATGA 57.452 32.000 0.00 0.00 43.24 2.57
3629 5909 7.630924 AGTCGTTTTAGACAACTGAAAATGAG 58.369 34.615 0.00 0.00 43.24 2.90
3630 5910 6.357240 GTCGTTTTAGACAACTGAAAATGAGC 59.643 38.462 0.00 0.00 38.24 4.26
3631 5911 6.260050 TCGTTTTAGACAACTGAAAATGAGCT 59.740 34.615 0.00 0.00 34.66 4.09
3632 5912 7.439955 TCGTTTTAGACAACTGAAAATGAGCTA 59.560 33.333 0.00 0.00 34.66 3.32
3633 5913 8.067784 CGTTTTAGACAACTGAAAATGAGCTAA 58.932 33.333 0.00 0.00 34.35 3.09
3634 5914 9.899226 GTTTTAGACAACTGAAAATGAGCTAAT 57.101 29.630 0.00 0.00 34.35 1.73
3637 5917 9.897744 TTAGACAACTGAAAATGAGCTAATTTG 57.102 29.630 9.94 0.63 30.21 2.32
3638 5918 6.865205 AGACAACTGAAAATGAGCTAATTTGC 59.135 34.615 9.94 8.69 30.21 3.68
3639 5919 6.514947 ACAACTGAAAATGAGCTAATTTGCA 58.485 32.000 15.51 15.51 33.49 4.08
3640 5920 6.421801 ACAACTGAAAATGAGCTAATTTGCAC 59.578 34.615 12.74 8.40 31.37 4.57
3641 5921 5.473039 ACTGAAAATGAGCTAATTTGCACC 58.527 37.500 12.74 6.08 31.37 5.01
3642 5922 5.244626 ACTGAAAATGAGCTAATTTGCACCT 59.755 36.000 12.74 0.00 31.37 4.00
3643 5923 6.100404 TGAAAATGAGCTAATTTGCACCTT 57.900 33.333 12.74 4.57 31.37 3.50
3644 5924 5.927689 TGAAAATGAGCTAATTTGCACCTTG 59.072 36.000 12.74 0.00 31.37 3.61
3645 5925 5.473066 AAATGAGCTAATTTGCACCTTGT 57.527 34.783 8.34 0.00 34.99 3.16
3646 5926 4.708726 ATGAGCTAATTTGCACCTTGTC 57.291 40.909 14.27 2.59 34.99 3.18
3650 5930 4.144297 AGCTAATTTGCACCTTGTCTGAA 58.856 39.130 14.27 0.00 34.99 3.02
3653 5933 5.346822 GCTAATTTGCACCTTGTCTGAAATG 59.653 40.000 7.02 0.00 0.00 2.32
3654 5934 4.942761 ATTTGCACCTTGTCTGAAATGT 57.057 36.364 0.00 0.00 0.00 2.71
3655 5935 3.988379 TTGCACCTTGTCTGAAATGTC 57.012 42.857 0.00 0.00 0.00 3.06
3657 5937 3.554934 TGCACCTTGTCTGAAATGTCTT 58.445 40.909 0.00 0.00 0.00 3.01
3663 5943 5.218139 CCTTGTCTGAAATGTCTTCAAAGC 58.782 41.667 0.00 0.00 0.00 3.51
3665 5945 4.464008 TGTCTGAAATGTCTTCAAAGCCT 58.536 39.130 0.00 0.00 0.00 4.58
3666 5946 4.889409 TGTCTGAAATGTCTTCAAAGCCTT 59.111 37.500 0.00 0.00 0.00 4.35
3673 5953 8.084073 TGAAATGTCTTCAAAGCCTTATCAAAG 58.916 33.333 0.00 0.00 0.00 2.77
3676 5956 6.061441 TGTCTTCAAAGCCTTATCAAAGTGA 58.939 36.000 0.00 0.00 0.00 3.41
3677 5957 6.545666 TGTCTTCAAAGCCTTATCAAAGTGAA 59.454 34.615 0.00 0.00 0.00 3.18
3678 5958 6.858478 GTCTTCAAAGCCTTATCAAAGTGAAC 59.142 38.462 0.00 0.00 0.00 3.18
3679 5959 6.545666 TCTTCAAAGCCTTATCAAAGTGAACA 59.454 34.615 0.00 0.00 0.00 3.18
3680 5960 6.317789 TCAAAGCCTTATCAAAGTGAACAG 57.682 37.500 0.00 0.00 0.00 3.16
3682 5962 6.205464 TCAAAGCCTTATCAAAGTGAACAGAG 59.795 38.462 0.00 0.00 0.00 3.35
3683 5963 4.583871 AGCCTTATCAAAGTGAACAGAGG 58.416 43.478 0.00 0.00 0.00 3.69
3685 5965 4.565652 GCCTTATCAAAGTGAACAGAGGGA 60.566 45.833 0.00 0.00 0.00 4.20
3686 5966 5.181748 CCTTATCAAAGTGAACAGAGGGAG 58.818 45.833 0.00 0.00 0.00 4.30
3687 5967 5.280215 CCTTATCAAAGTGAACAGAGGGAGT 60.280 44.000 0.00 0.00 0.00 3.85
3688 5968 6.070767 CCTTATCAAAGTGAACAGAGGGAGTA 60.071 42.308 0.00 0.00 0.00 2.59
3690 5970 5.825593 TCAAAGTGAACAGAGGGAGTAAT 57.174 39.130 0.00 0.00 0.00 1.89
3691 5971 6.187727 TCAAAGTGAACAGAGGGAGTAATT 57.812 37.500 0.00 0.00 0.00 1.40
3692 5972 7.311092 TCAAAGTGAACAGAGGGAGTAATTA 57.689 36.000 0.00 0.00 0.00 1.40
3693 5973 7.741785 TCAAAGTGAACAGAGGGAGTAATTAA 58.258 34.615 0.00 0.00 0.00 1.40
3705 6005 6.143915 AGGGAGTAATTAAGAGGCATGTAGA 58.856 40.000 0.00 0.00 0.00 2.59
3778 6078 7.040478 AGCTAATTAGATGCAAACACAAGTTCA 60.040 33.333 16.85 0.00 36.84 3.18
3880 6201 7.615757 ACATAAAGAGAAAAATTAGAGGGTGGG 59.384 37.037 0.00 0.00 0.00 4.61
4045 7746 4.202346 GCTCAAAGGCTATCTCCATTCTCT 60.202 45.833 0.00 0.00 0.00 3.10
4183 7895 0.333312 ACAAAGGTGGTGGTGGACAA 59.667 50.000 0.00 0.00 0.00 3.18
4640 8354 1.227234 CACATCGCCAGGATACGCA 60.227 57.895 0.00 0.00 46.39 5.24
4788 8517 6.725246 CAACAACCGACTGTTATTTTTCTCT 58.275 36.000 2.32 0.00 37.43 3.10
5404 9323 5.904941 TCGGTAAAACTATTCGGCTATTCA 58.095 37.500 0.00 0.00 0.00 2.57
5508 9430 4.691685 GCTGCCAAATTTGTGATGATTTCA 59.308 37.500 16.73 0.72 0.00 2.69
5519 9441 3.879295 GTGATGATTTCATGGGTCGTCAT 59.121 43.478 15.75 9.18 39.34 3.06
5777 9750 5.666969 TCCTTGCAATTAATAACCGATCG 57.333 39.130 8.51 8.51 0.00 3.69
5841 9814 3.629855 GCTGGGCTCTATCTTTTCCTTTC 59.370 47.826 0.00 0.00 0.00 2.62
5997 9970 9.614792 GGGACTATTCAGAAGTTTGTGTATTAT 57.385 33.333 0.00 0.00 0.00 1.28
6065 10053 7.612065 ACCATTCATCCAATTTGATCATCAT 57.388 32.000 0.00 0.00 0.00 2.45
6067 10055 7.289084 ACCATTCATCCAATTTGATCATCATGA 59.711 33.333 0.00 0.00 0.00 3.07
6217 10212 8.793592 GTTTGGTTTTATATGAAGTCCTCAAGT 58.206 33.333 0.00 0.00 37.67 3.16
6248 10243 6.294473 CCTGCATTATTGTATCTCTCCACTT 58.706 40.000 0.00 0.00 0.00 3.16
6253 10248 6.732896 TTATTGTATCTCTCCACTTCCTCC 57.267 41.667 0.00 0.00 0.00 4.30
6440 10436 8.265055 AGATTTATTTCGATGTTCACTCCCTTA 58.735 33.333 0.00 0.00 0.00 2.69
6444 10440 3.964411 TCGATGTTCACTCCCTTAGAGA 58.036 45.455 0.00 0.00 46.50 3.10
6471 10467 0.389948 GTCGCATCGTTGGAGAGGTT 60.390 55.000 0.00 0.00 0.00 3.50
6673 10672 6.120507 TGCATAAATTTTAAAAGGCCCACT 57.879 33.333 6.79 0.00 0.00 4.00
7137 11151 2.708051 CATCTTGGCTTGCTTCTCTCA 58.292 47.619 0.00 0.00 0.00 3.27
7193 11208 9.396022 GAAGGTGTTCATTTGATCTTCCTTATA 57.604 33.333 13.30 0.00 33.60 0.98
7237 11252 2.158449 GTGTCCTTCTTGCTCATTGTCG 59.842 50.000 0.00 0.00 0.00 4.35
7272 11287 2.019272 ATCTCGGGTAGGGGGTCCT 61.019 63.158 0.00 0.00 46.96 3.85
7287 11302 1.000506 GGTCCTGAACTGTGCGTCTAA 59.999 52.381 0.00 0.00 0.00 2.10
7289 11304 1.272490 TCCTGAACTGTGCGTCTAAGG 59.728 52.381 0.00 0.00 0.00 2.69
7299 11314 0.103572 GCGTCTAAGGCGGATGGTAA 59.896 55.000 0.00 0.00 0.00 2.85
7312 11327 1.923395 TGGTAACAGGAGGCAGGGG 60.923 63.158 0.00 0.00 46.17 4.79
7316 11331 0.909610 TAACAGGAGGCAGGGGACAG 60.910 60.000 0.00 0.00 0.00 3.51
7317 11332 2.608988 CAGGAGGCAGGGGACAGT 60.609 66.667 0.00 0.00 0.00 3.55
7318 11333 2.208349 AGGAGGCAGGGGACAGTT 59.792 61.111 0.00 0.00 0.00 3.16
7319 11334 1.920835 AGGAGGCAGGGGACAGTTC 60.921 63.158 0.00 0.00 0.00 3.01
7320 11335 2.266055 GAGGCAGGGGACAGTTCG 59.734 66.667 0.00 0.00 0.00 3.95
7321 11336 3.316573 GAGGCAGGGGACAGTTCGG 62.317 68.421 0.00 0.00 0.00 4.30
7322 11337 4.410400 GGCAGGGGACAGTTCGGG 62.410 72.222 0.00 0.00 0.00 5.14
7323 11338 3.319198 GCAGGGGACAGTTCGGGA 61.319 66.667 0.00 0.00 0.00 5.14
7324 11339 2.663196 CAGGGGACAGTTCGGGAC 59.337 66.667 0.00 0.00 0.00 4.46
7325 11340 2.606826 AGGGGACAGTTCGGGACC 60.607 66.667 0.00 0.00 0.00 4.46
7326 11341 3.714001 GGGGACAGTTCGGGACCC 61.714 72.222 0.00 0.00 39.79 4.46
7327 11342 3.714001 GGGACAGTTCGGGACCCC 61.714 72.222 4.46 0.00 35.00 4.95
7328 11343 3.714001 GGACAGTTCGGGACCCCC 61.714 72.222 4.46 0.00 41.09 5.40
7329 11344 2.606826 GACAGTTCGGGACCCCCT 60.607 66.667 4.46 0.00 42.67 4.79
7330 11345 1.305549 GACAGTTCGGGACCCCCTA 60.306 63.158 4.46 0.00 42.67 3.53
7331 11346 1.611474 GACAGTTCGGGACCCCCTAC 61.611 65.000 4.46 0.29 42.67 3.18
7332 11347 2.040114 AGTTCGGGACCCCCTACC 59.960 66.667 4.46 0.00 42.67 3.18
7333 11348 3.085947 GTTCGGGACCCCCTACCC 61.086 72.222 4.46 0.00 42.67 3.69
7337 11352 3.759101 GGGACCCCCTACCCGAGA 61.759 72.222 0.00 0.00 41.34 4.04
7338 11353 2.613421 GGACCCCCTACCCGAGAT 59.387 66.667 0.00 0.00 0.00 2.75
7339 11354 1.533513 GGACCCCCTACCCGAGATC 60.534 68.421 0.00 0.00 0.00 2.75
7340 11355 1.533513 GACCCCCTACCCGAGATCC 60.534 68.421 0.00 0.00 0.00 3.36
7341 11356 2.600769 CCCCCTACCCGAGATCCG 60.601 72.222 0.00 0.00 38.18 4.18
7342 11357 3.303928 CCCCTACCCGAGATCCGC 61.304 72.222 0.00 0.00 36.84 5.54
7343 11358 3.303928 CCCTACCCGAGATCCGCC 61.304 72.222 0.00 0.00 36.84 6.13
7344 11359 3.671411 CCTACCCGAGATCCGCCG 61.671 72.222 0.00 0.00 36.84 6.46
7345 11360 3.671411 CTACCCGAGATCCGCCGG 61.671 72.222 0.00 0.00 44.94 6.13
7346 11361 4.511246 TACCCGAGATCCGCCGGT 62.511 66.667 1.63 11.60 43.93 5.28
7348 11363 4.157120 CCCGAGATCCGCCGGTTT 62.157 66.667 1.63 0.00 43.93 3.27
7349 11364 2.125269 CCGAGATCCGCCGGTTTT 60.125 61.111 1.63 0.00 40.78 2.43
7350 11365 2.461110 CCGAGATCCGCCGGTTTTG 61.461 63.158 1.63 0.00 40.78 2.44
7351 11366 1.447140 CGAGATCCGCCGGTTTTGA 60.447 57.895 1.63 0.00 0.00 2.69
7352 11367 1.693083 CGAGATCCGCCGGTTTTGAC 61.693 60.000 1.63 0.00 0.00 3.18
7353 11368 0.672401 GAGATCCGCCGGTTTTGACA 60.672 55.000 1.63 0.00 0.00 3.58
7354 11369 0.953960 AGATCCGCCGGTTTTGACAC 60.954 55.000 1.63 0.00 0.00 3.67
7355 11370 1.918868 GATCCGCCGGTTTTGACACC 61.919 60.000 1.63 0.00 0.00 4.16
7363 11378 2.415697 GGTTTTGACACCGACATTGG 57.584 50.000 0.00 0.00 0.00 3.16
7364 11379 1.679153 GGTTTTGACACCGACATTGGT 59.321 47.619 0.00 0.00 45.21 3.67
7371 11386 2.244000 ACCGACATTGGTGCTTTCG 58.756 52.632 0.00 0.00 41.85 3.46
7372 11387 0.534203 ACCGACATTGGTGCTTTCGT 60.534 50.000 0.00 0.00 41.85 3.85
7373 11388 0.591170 CCGACATTGGTGCTTTCGTT 59.409 50.000 0.00 0.00 0.00 3.85
7374 11389 1.662876 CCGACATTGGTGCTTTCGTTG 60.663 52.381 0.00 0.00 0.00 4.10
7375 11390 1.262950 CGACATTGGTGCTTTCGTTGA 59.737 47.619 0.00 0.00 0.00 3.18
7376 11391 2.662791 CGACATTGGTGCTTTCGTTGAG 60.663 50.000 0.00 0.00 0.00 3.02
7377 11392 2.548057 GACATTGGTGCTTTCGTTGAGA 59.452 45.455 0.00 0.00 0.00 3.27
7378 11393 2.549754 ACATTGGTGCTTTCGTTGAGAG 59.450 45.455 0.00 0.00 0.00 3.20
7379 11394 2.325583 TTGGTGCTTTCGTTGAGAGT 57.674 45.000 0.00 0.00 0.00 3.24
7380 11395 2.325583 TGGTGCTTTCGTTGAGAGTT 57.674 45.000 0.00 0.00 0.00 3.01
7381 11396 2.210116 TGGTGCTTTCGTTGAGAGTTC 58.790 47.619 0.00 0.00 0.00 3.01
7382 11397 1.531578 GGTGCTTTCGTTGAGAGTTCC 59.468 52.381 0.00 0.00 0.00 3.62
7383 11398 2.484889 GTGCTTTCGTTGAGAGTTCCT 58.515 47.619 0.00 0.00 0.00 3.36
7384 11399 2.476997 GTGCTTTCGTTGAGAGTTCCTC 59.523 50.000 0.00 0.00 42.30 3.71
7385 11400 2.365617 TGCTTTCGTTGAGAGTTCCTCT 59.634 45.455 0.00 0.00 44.28 3.69
7386 11401 2.734079 GCTTTCGTTGAGAGTTCCTCTG 59.266 50.000 0.00 0.00 41.35 3.35
7387 11402 3.800604 GCTTTCGTTGAGAGTTCCTCTGT 60.801 47.826 0.00 0.00 41.35 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.474077 GGACATCTGCCATGACAAACC 59.526 52.381 0.00 0.00 0.00 3.27
42 43 2.768527 CCTTTCTCTAGGACATCTGCCA 59.231 50.000 0.00 0.00 37.50 4.92
113 114 3.260475 TCAAACCGGACACATCTATGG 57.740 47.619 9.46 0.00 0.00 2.74
179 180 1.477295 GAGAGCCTGTAGCCGTAAACT 59.523 52.381 0.00 0.00 45.47 2.66
240 241 6.465948 TCATCGGTAGTTAAGCAGGTTAAAA 58.534 36.000 6.37 0.00 32.22 1.52
346 347 0.178938 ACATGGGGTTTGCATGGTCA 60.179 50.000 0.00 0.00 0.00 4.02
3270 5228 4.890158 TGTCATGAAAGGCTAGTGAGAA 57.110 40.909 0.00 0.00 0.00 2.87
3373 5397 3.507233 TGGTGAAATACTACTCGTTCGGT 59.493 43.478 0.00 0.00 0.00 4.69
3428 5452 8.798975 TTTGGATCAAAGGGAGTAGTCTATAT 57.201 34.615 0.00 0.00 0.00 0.86
3431 5455 7.510675 AATTTGGATCAAAGGGAGTAGTCTA 57.489 36.000 0.00 0.00 36.76 2.59
3506 5534 5.454062 AGCTCAACCTCTATCATGTACTCT 58.546 41.667 0.00 0.00 0.00 3.24
3576 5605 4.732672 AGTGAACGGAGGGAGTAATAAC 57.267 45.455 0.00 0.00 0.00 1.89
3583 5863 5.731591 ACTTATAAAAGTGAACGGAGGGAG 58.268 41.667 0.00 0.00 44.40 4.30
3585 5865 4.565564 CGACTTATAAAAGTGAACGGAGGG 59.434 45.833 0.00 0.00 46.09 4.30
3586 5866 5.166398 ACGACTTATAAAAGTGAACGGAGG 58.834 41.667 0.00 0.00 46.09 4.30
3587 5867 6.701432 AACGACTTATAAAAGTGAACGGAG 57.299 37.500 0.00 0.00 46.09 4.63
3589 5869 8.702438 TCTAAAACGACTTATAAAAGTGAACGG 58.298 33.333 0.00 0.00 46.09 4.44
3590 5870 9.508495 GTCTAAAACGACTTATAAAAGTGAACG 57.492 33.333 0.00 0.00 46.09 3.95
3605 5885 6.357240 GCTCATTTTCAGTTGTCTAAAACGAC 59.643 38.462 0.00 0.00 41.93 4.34
3606 5886 6.260050 AGCTCATTTTCAGTTGTCTAAAACGA 59.740 34.615 0.00 0.00 35.13 3.85
3607 5887 6.430451 AGCTCATTTTCAGTTGTCTAAAACG 58.570 36.000 0.00 0.00 35.13 3.60
3608 5888 9.899226 ATTAGCTCATTTTCAGTTGTCTAAAAC 57.101 29.630 0.00 0.00 0.00 2.43
3611 5891 9.897744 CAAATTAGCTCATTTTCAGTTGTCTAA 57.102 29.630 3.06 0.00 0.00 2.10
3612 5892 8.023128 GCAAATTAGCTCATTTTCAGTTGTCTA 58.977 33.333 3.06 0.00 0.00 2.59
3613 5893 6.865205 GCAAATTAGCTCATTTTCAGTTGTCT 59.135 34.615 3.06 0.00 0.00 3.41
3614 5894 6.642131 TGCAAATTAGCTCATTTTCAGTTGTC 59.358 34.615 3.06 0.00 34.99 3.18
3615 5895 6.421801 GTGCAAATTAGCTCATTTTCAGTTGT 59.578 34.615 6.03 0.00 34.99 3.32
3616 5896 6.128742 GGTGCAAATTAGCTCATTTTCAGTTG 60.129 38.462 6.03 0.00 34.99 3.16
3617 5897 5.928264 GGTGCAAATTAGCTCATTTTCAGTT 59.072 36.000 6.03 0.00 34.99 3.16
3618 5898 5.244626 AGGTGCAAATTAGCTCATTTTCAGT 59.755 36.000 6.03 0.00 34.99 3.41
3619 5899 5.717119 AGGTGCAAATTAGCTCATTTTCAG 58.283 37.500 6.03 0.00 34.99 3.02
3620 5900 5.726980 AGGTGCAAATTAGCTCATTTTCA 57.273 34.783 3.06 2.57 34.99 2.69
3621 5901 5.928264 ACAAGGTGCAAATTAGCTCATTTTC 59.072 36.000 3.06 0.00 30.83 2.29
3622 5902 5.857268 ACAAGGTGCAAATTAGCTCATTTT 58.143 33.333 3.06 0.00 30.83 1.82
3623 5903 5.244626 AGACAAGGTGCAAATTAGCTCATTT 59.755 36.000 0.00 0.00 30.83 2.32
3624 5904 4.768968 AGACAAGGTGCAAATTAGCTCATT 59.231 37.500 0.00 0.00 33.06 2.57
3625 5905 4.157289 CAGACAAGGTGCAAATTAGCTCAT 59.843 41.667 0.00 0.00 34.99 2.90
3626 5906 3.503363 CAGACAAGGTGCAAATTAGCTCA 59.497 43.478 0.00 0.00 34.99 4.26
3627 5907 3.753272 TCAGACAAGGTGCAAATTAGCTC 59.247 43.478 0.00 0.00 34.99 4.09
3628 5908 3.754965 TCAGACAAGGTGCAAATTAGCT 58.245 40.909 0.00 0.00 34.99 3.32
3629 5909 4.503741 TTCAGACAAGGTGCAAATTAGC 57.496 40.909 0.00 0.00 0.00 3.09
3630 5910 6.449698 ACATTTCAGACAAGGTGCAAATTAG 58.550 36.000 0.00 0.00 0.00 1.73
3631 5911 6.265196 AGACATTTCAGACAAGGTGCAAATTA 59.735 34.615 0.00 0.00 0.00 1.40
3632 5912 5.069516 AGACATTTCAGACAAGGTGCAAATT 59.930 36.000 0.00 0.00 0.00 1.82
3633 5913 4.586001 AGACATTTCAGACAAGGTGCAAAT 59.414 37.500 0.00 0.00 0.00 2.32
3634 5914 3.953612 AGACATTTCAGACAAGGTGCAAA 59.046 39.130 0.00 0.00 0.00 3.68
3635 5915 3.554934 AGACATTTCAGACAAGGTGCAA 58.445 40.909 0.00 0.00 0.00 4.08
3636 5916 3.213206 AGACATTTCAGACAAGGTGCA 57.787 42.857 0.00 0.00 0.00 4.57
3637 5917 3.565482 TGAAGACATTTCAGACAAGGTGC 59.435 43.478 0.00 0.00 0.00 5.01
3638 5918 5.756195 TTGAAGACATTTCAGACAAGGTG 57.244 39.130 0.00 0.00 0.00 4.00
3639 5919 5.221126 GCTTTGAAGACATTTCAGACAAGGT 60.221 40.000 0.00 0.00 0.00 3.50
3640 5920 5.218139 GCTTTGAAGACATTTCAGACAAGG 58.782 41.667 0.00 0.00 0.00 3.61
3641 5921 5.009410 AGGCTTTGAAGACATTTCAGACAAG 59.991 40.000 0.00 0.00 36.14 3.16
3642 5922 4.889409 AGGCTTTGAAGACATTTCAGACAA 59.111 37.500 0.00 0.00 36.14 3.18
3643 5923 4.464008 AGGCTTTGAAGACATTTCAGACA 58.536 39.130 0.00 0.00 36.14 3.41
3644 5924 5.444663 AAGGCTTTGAAGACATTTCAGAC 57.555 39.130 0.00 0.00 36.14 3.51
3645 5925 6.942005 TGATAAGGCTTTGAAGACATTTCAGA 59.058 34.615 4.45 0.00 36.14 3.27
3646 5926 7.149569 TGATAAGGCTTTGAAGACATTTCAG 57.850 36.000 4.45 0.00 36.14 3.02
3650 5930 7.231317 TCACTTTGATAAGGCTTTGAAGACATT 59.769 33.333 4.45 0.00 36.14 2.71
3653 5933 6.560253 TCACTTTGATAAGGCTTTGAAGAC 57.440 37.500 4.45 0.00 35.61 3.01
3654 5934 6.545666 TGTTCACTTTGATAAGGCTTTGAAGA 59.454 34.615 4.45 3.15 35.61 2.87
3655 5935 6.738114 TGTTCACTTTGATAAGGCTTTGAAG 58.262 36.000 4.45 7.46 35.61 3.02
3657 5937 6.061441 TCTGTTCACTTTGATAAGGCTTTGA 58.939 36.000 4.45 0.00 35.61 2.69
3663 5943 5.165961 TCCCTCTGTTCACTTTGATAAGG 57.834 43.478 0.00 0.00 35.61 2.69
3665 5945 5.825593 ACTCCCTCTGTTCACTTTGATAA 57.174 39.130 0.00 0.00 0.00 1.75
3666 5946 6.928348 TTACTCCCTCTGTTCACTTTGATA 57.072 37.500 0.00 0.00 0.00 2.15
3673 5953 6.342111 CCTCTTAATTACTCCCTCTGTTCAC 58.658 44.000 0.00 0.00 0.00 3.18
3676 5956 4.783227 TGCCTCTTAATTACTCCCTCTGTT 59.217 41.667 0.00 0.00 0.00 3.16
3677 5957 4.362677 TGCCTCTTAATTACTCCCTCTGT 58.637 43.478 0.00 0.00 0.00 3.41
3678 5958 5.163258 ACATGCCTCTTAATTACTCCCTCTG 60.163 44.000 0.00 0.00 0.00 3.35
3679 5959 4.971924 ACATGCCTCTTAATTACTCCCTCT 59.028 41.667 0.00 0.00 0.00 3.69
3680 5960 5.297569 ACATGCCTCTTAATTACTCCCTC 57.702 43.478 0.00 0.00 0.00 4.30
3682 5962 6.420913 TCTACATGCCTCTTAATTACTCCC 57.579 41.667 0.00 0.00 0.00 4.30
3683 5963 9.425577 GTTATCTACATGCCTCTTAATTACTCC 57.574 37.037 0.00 0.00 0.00 3.85
3685 5965 9.988815 CTGTTATCTACATGCCTCTTAATTACT 57.011 33.333 0.00 0.00 35.85 2.24
3686 5966 9.982651 TCTGTTATCTACATGCCTCTTAATTAC 57.017 33.333 0.00 0.00 35.85 1.89
3688 5968 7.659390 GCTCTGTTATCTACATGCCTCTTAATT 59.341 37.037 0.00 0.00 35.85 1.40
3690 5970 6.098266 TGCTCTGTTATCTACATGCCTCTTAA 59.902 38.462 0.00 0.00 36.14 1.85
3691 5971 5.598417 TGCTCTGTTATCTACATGCCTCTTA 59.402 40.000 0.00 0.00 36.14 2.10
3692 5972 4.406972 TGCTCTGTTATCTACATGCCTCTT 59.593 41.667 0.00 0.00 36.14 2.85
3693 5973 3.963374 TGCTCTGTTATCTACATGCCTCT 59.037 43.478 0.00 0.00 36.14 3.69
3705 6005 3.718956 AGATTTAGGGCCTGCTCTGTTAT 59.281 43.478 18.53 0.00 0.00 1.89
3778 6078 3.762247 GTGGGCGGTGCATGCAAT 61.762 61.111 24.58 0.00 0.00 3.56
3880 6201 3.715628 ACTTGTGTTTGCAAGATGTCC 57.284 42.857 12.05 0.00 46.34 4.02
4045 7746 2.164219 GGACGTACGTGGTGGAGAATTA 59.836 50.000 28.16 0.00 0.00 1.40
4183 7895 0.251341 GGTCCAAGCAAGTGACCCAT 60.251 55.000 0.00 0.00 42.21 4.00
4788 8517 1.833630 CATGTCTAGTGGCTCCTTCCA 59.166 52.381 0.00 0.00 0.00 3.53
5119 8848 5.047519 AGGAGGAGTTGAATTTTGCATGAAG 60.048 40.000 0.00 0.00 0.00 3.02
5404 9323 5.266733 AGTGAACTGATGCACAACAAAAT 57.733 34.783 0.00 0.00 37.48 1.82
5508 9430 1.099295 CATGCTGCATGACGACCCAT 61.099 55.000 33.22 0.00 43.81 4.00
5519 9441 2.227494 ATAGGTTGGCCCATGCTGCA 62.227 55.000 4.13 4.13 37.74 4.41
5608 9530 0.180406 GCATACCTCCCAACGGACAT 59.820 55.000 0.00 0.00 33.32 3.06
5777 9750 3.057315 AGAACACTGCATGCATGTAAACC 60.057 43.478 26.79 11.08 0.00 3.27
5841 9814 3.335579 ACCGATTCTTTTCTCTTTCCCG 58.664 45.455 0.00 0.00 0.00 5.14
6004 9977 9.308000 ACAAACAATATTGACCATTTTCCTCTA 57.692 29.630 22.16 0.00 34.38 2.43
6014 9987 6.009589 AGGACATCACAAACAATATTGACCA 58.990 36.000 22.16 0.32 34.38 4.02
6217 10212 7.977818 AGAGATACAATAATGCAGGGTCAATA 58.022 34.615 0.00 0.00 0.00 1.90
6248 10243 0.178861 AGGAGGAAAAGGCAGGAGGA 60.179 55.000 0.00 0.00 0.00 3.71
6253 10248 1.349026 TCAGACAGGAGGAAAAGGCAG 59.651 52.381 0.00 0.00 0.00 4.85
6440 10436 2.224426 ACGATGCGACTATCTCCTCTCT 60.224 50.000 0.00 0.00 0.00 3.10
6444 10440 1.338337 CCAACGATGCGACTATCTCCT 59.662 52.381 0.00 0.00 0.00 3.69
6471 10467 3.611025 AGGTTTCCTTTGTGGATTCCA 57.389 42.857 0.00 0.00 45.68 3.53
7037 11046 4.170468 AGAGAAAGGCAAAAGAAGTGGA 57.830 40.909 0.00 0.00 0.00 4.02
7193 11208 4.101448 AGGAGAAGCGCCGGCAAT 62.101 61.111 28.98 11.52 43.41 3.56
7237 11252 1.918868 GATCCGCCGGTTTTGACACC 61.919 60.000 1.63 0.00 0.00 4.16
7272 11287 0.666274 CGCCTTAGACGCACAGTTCA 60.666 55.000 0.00 0.00 0.00 3.18
7287 11302 1.338136 CCTCCTGTTACCATCCGCCT 61.338 60.000 0.00 0.00 0.00 5.52
7289 11304 1.523938 GCCTCCTGTTACCATCCGC 60.524 63.158 0.00 0.00 0.00 5.54
7299 11314 2.608988 CTGTCCCCTGCCTCCTGT 60.609 66.667 0.00 0.00 0.00 4.00
7309 11324 3.714001 GGGTCCCGAACTGTCCCC 61.714 72.222 0.00 0.00 32.66 4.81
7320 11335 3.097429 ATCTCGGGTAGGGGGTCCC 62.097 68.421 0.00 0.00 45.90 4.46
7321 11336 1.533513 GATCTCGGGTAGGGGGTCC 60.534 68.421 0.00 0.00 0.00 4.46
7322 11337 1.533513 GGATCTCGGGTAGGGGGTC 60.534 68.421 0.00 0.00 0.00 4.46
7323 11338 2.613421 GGATCTCGGGTAGGGGGT 59.387 66.667 0.00 0.00 0.00 4.95
7324 11339 2.600769 CGGATCTCGGGTAGGGGG 60.601 72.222 0.00 0.00 34.75 5.40
7325 11340 3.303928 GCGGATCTCGGGTAGGGG 61.304 72.222 5.87 0.00 39.69 4.79
7326 11341 3.303928 GGCGGATCTCGGGTAGGG 61.304 72.222 5.87 0.00 39.69 3.53
7327 11342 3.671411 CGGCGGATCTCGGGTAGG 61.671 72.222 0.00 0.00 39.69 3.18
7328 11343 3.671411 CCGGCGGATCTCGGGTAG 61.671 72.222 24.41 0.00 42.32 3.18
7333 11348 1.447140 TCAAAACCGGCGGATCTCG 60.447 57.895 35.78 16.34 42.76 4.04
7334 11349 0.672401 TGTCAAAACCGGCGGATCTC 60.672 55.000 35.78 16.90 0.00 2.75
7335 11350 0.953960 GTGTCAAAACCGGCGGATCT 60.954 55.000 35.78 13.84 0.00 2.75
7336 11351 1.500396 GTGTCAAAACCGGCGGATC 59.500 57.895 35.78 9.52 0.00 3.36
7337 11352 1.969589 GGTGTCAAAACCGGCGGAT 60.970 57.895 35.78 20.37 0.00 4.18
7338 11353 2.592287 GGTGTCAAAACCGGCGGA 60.592 61.111 35.78 6.54 0.00 5.54
7344 11359 1.679153 ACCAATGTCGGTGTCAAAACC 59.321 47.619 0.00 0.00 38.07 3.27
7353 11368 0.534203 ACGAAAGCACCAATGTCGGT 60.534 50.000 0.00 0.00 41.07 4.69
7354 11369 0.591170 AACGAAAGCACCAATGTCGG 59.409 50.000 0.00 0.00 36.06 4.79
7355 11370 1.262950 TCAACGAAAGCACCAATGTCG 59.737 47.619 0.00 0.00 37.71 4.35
7356 11371 2.548057 TCTCAACGAAAGCACCAATGTC 59.452 45.455 0.00 0.00 0.00 3.06
7357 11372 2.549754 CTCTCAACGAAAGCACCAATGT 59.450 45.455 0.00 0.00 0.00 2.71
7358 11373 2.549754 ACTCTCAACGAAAGCACCAATG 59.450 45.455 0.00 0.00 0.00 2.82
7359 11374 2.851195 ACTCTCAACGAAAGCACCAAT 58.149 42.857 0.00 0.00 0.00 3.16
7360 11375 2.325583 ACTCTCAACGAAAGCACCAA 57.674 45.000 0.00 0.00 0.00 3.67
7361 11376 2.210116 GAACTCTCAACGAAAGCACCA 58.790 47.619 0.00 0.00 0.00 4.17
7362 11377 1.531578 GGAACTCTCAACGAAAGCACC 59.468 52.381 0.00 0.00 0.00 5.01
7363 11378 2.484889 AGGAACTCTCAACGAAAGCAC 58.515 47.619 0.00 0.00 0.00 4.40
7364 11379 2.910688 AGGAACTCTCAACGAAAGCA 57.089 45.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.