Multiple sequence alignment - TraesCS5D01G555700

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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 TraesCS5D01G555700 chr5D 100.000 6455 0 0 1 6455 559374342 559367888 0.000000e+00 11921.0
1 TraesCS5D01G555700 chr5D 88.850 1417 134 11 2340 3747 446911467 446910066 0.000000e+00 1720.0
2 TraesCS5D01G555700 chr5D 89.610 1232 93 20 1 1201 446913841 446912614 0.000000e+00 1533.0
3 TraesCS5D01G555700 chr5D 86.566 1191 123 20 3703 4869 446909990 446908813 0.000000e+00 1279.0
4 TraesCS5D01G555700 chr5D 88.696 920 71 16 1201 2097 446912647 446911738 0.000000e+00 1092.0
5 TraesCS5D01G555700 chr5D 87.778 360 39 4 1749 2104 565060966 565060608 3.600000e-112 416.0
6 TraesCS5D01G555700 chr5D 91.339 127 8 3 5126 5250 565060571 565060446 3.090000e-38 171.0
7 TraesCS5D01G555700 chr5D 92.593 108 2 1 5652 5759 412585932 412586033 4.030000e-32 150.0
8 TraesCS5D01G555700 chr4A 94.123 3335 148 17 2340 5653 612397550 612394243 0.000000e+00 5029.0
9 TraesCS5D01G555700 chr4A 93.857 1172 58 10 948 2108 612398943 612397775 0.000000e+00 1753.0
10 TraesCS5D01G555700 chr4A 93.651 945 33 15 1 918 612399890 612398946 0.000000e+00 1387.0
11 TraesCS5D01G555700 chr4A 94.810 867 45 0 898 1764 612607135 612608001 0.000000e+00 1352.0
12 TraesCS5D01G555700 chr4A 87.949 863 76 14 3145 4005 612610606 612611442 0.000000e+00 992.0
13 TraesCS5D01G555700 chr4A 84.992 613 63 19 5062 5655 613149449 613150051 4.310000e-166 595.0
14 TraesCS5D01G555700 chr4A 83.150 635 46 22 5651 6260 464545301 464545899 2.060000e-144 523.0
15 TraesCS5D01G555700 chr4A 88.599 421 42 2 2680 3097 612610189 612610606 2.080000e-139 507.0
16 TraesCS5D01G555700 chr4A 85.066 529 41 12 4621 5118 612657565 612658086 7.470000e-139 505.0
17 TraesCS5D01G555700 chr4A 89.474 304 24 5 4610 4907 613146496 613146797 1.700000e-100 377.0
18 TraesCS5D01G555700 chr4A 85.623 313 30 8 1795 2097 612607993 612608300 1.350000e-81 315.0
19 TraesCS5D01G555700 chr4A 94.388 196 11 0 6258 6453 674539801 674539606 1.050000e-77 302.0
20 TraesCS5D01G555700 chr4A 83.686 331 21 6 5114 5443 612661182 612661480 1.370000e-71 281.0
21 TraesCS5D01G555700 chr4A 91.620 179 11 3 5436 5613 612665455 612665630 1.800000e-60 244.0
22 TraesCS5D01G555700 chr4A 86.923 130 8 3 6131 6260 674539954 674539834 3.140000e-28 137.0
23 TraesCS5D01G555700 chr4A 95.238 42 2 0 4909 4950 613149411 613149452 4.180000e-07 67.6
24 TraesCS5D01G555700 chr5B 88.708 3321 245 52 2340 5614 693614554 693611318 0.000000e+00 3936.0
25 TraesCS5D01G555700 chr5B 91.178 2131 128 25 1 2104 693616878 693614781 0.000000e+00 2839.0
26 TraesCS5D01G555700 chr5B 87.975 1763 155 21 2428 4160 708226058 708227793 0.000000e+00 2028.0
27 TraesCS5D01G555700 chr5B 88.250 1234 106 15 1 1201 545797223 545798450 0.000000e+00 1439.0
28 TraesCS5D01G555700 chr5B 87.112 1063 111 13 3703 4747 545800932 545801986 0.000000e+00 1181.0
29 TraesCS5D01G555700 chr5B 88.553 926 74 16 1205 2105 545798421 545799339 0.000000e+00 1094.0
30 TraesCS5D01G555700 chr5B 88.748 791 71 7 2957 3744 545800138 545800913 0.000000e+00 952.0
31 TraesCS5D01G555700 chr5B 89.520 563 50 6 4382 4940 693690716 693691273 0.000000e+00 704.0
32 TraesCS5D01G555700 chr5B 90.359 529 45 4 2340 2862 545799605 545800133 0.000000e+00 689.0
33 TraesCS5D01G555700 chr5B 85.135 592 58 17 5087 5655 693691268 693691852 4.340000e-161 579.0
34 TraesCS5D01G555700 chr5B 89.858 424 40 2 2340 2760 708225637 708226060 5.690000e-150 542.0
35 TraesCS5D01G555700 chr5B 87.131 474 33 6 5806 6260 537595422 537594958 4.460000e-141 512.0
36 TraesCS5D01G555700 chr5B 84.644 547 49 17 4573 5088 708228332 708228874 4.460000e-141 512.0
37 TraesCS5D01G555700 chr5B 88.187 364 31 5 1748 2104 708225049 708225407 2.150000e-114 424.0
38 TraesCS5D01G555700 chr5B 95.408 196 9 0 6258 6453 537594925 537594730 4.860000e-81 313.0
39 TraesCS5D01G555700 chr5B 85.946 185 7 5 5652 5823 537600142 537599964 5.140000e-41 180.0
40 TraesCS5D01G555700 chr5B 90.076 131 7 2 5651 5781 682127379 682127503 1.440000e-36 165.0
41 TraesCS5D01G555700 chr5B 93.043 115 5 3 5138 5250 708228872 708228985 1.440000e-36 165.0
42 TraesCS5D01G555700 chr5B 88.710 124 8 1 5658 5781 85905091 85904974 5.220000e-31 147.0
43 TraesCS5D01G555700 chr5B 100.000 35 0 0 5648 5682 263939541 263939575 1.500000e-06 65.8
44 TraesCS5D01G555700 chr5B 95.000 40 0 1 5645 5684 523035998 523036035 1.940000e-05 62.1
45 TraesCS5D01G555700 chr7B 84.448 2810 285 68 2361 5114 740055106 740057819 0.000000e+00 2628.0
46 TraesCS5D01G555700 chr7B 88.384 1188 97 18 53 1201 740052859 740054044 0.000000e+00 1391.0
47 TraesCS5D01G555700 chr7B 85.118 934 77 26 1201 2105 740054011 740054911 0.000000e+00 898.0
48 TraesCS5D01G555700 chr7B 84.512 891 112 16 3938 4814 740379884 740380762 0.000000e+00 857.0
49 TraesCS5D01G555700 chr7B 83.559 888 118 16 3938 4814 740169604 740170474 0.000000e+00 806.0
50 TraesCS5D01G555700 chr7B 100.000 31 0 0 5652 5682 750553678 750553648 2.510000e-04 58.4
51 TraesCS5D01G555700 chr7A 86.261 2431 253 40 2340 4743 730461678 730464054 0.000000e+00 2564.0
52 TraesCS5D01G555700 chr7A 87.983 1190 98 21 53 1201 730459369 730460554 0.000000e+00 1363.0
53 TraesCS5D01G555700 chr7A 89.355 930 71 13 1201 2105 730460521 730461447 0.000000e+00 1144.0
54 TraesCS5D01G555700 chr7A 86.978 407 23 9 5651 6041 239891873 239892265 1.290000e-116 431.0
55 TraesCS5D01G555700 chr7A 93.909 197 12 0 6258 6454 239944102 239944298 1.360000e-76 298.0
56 TraesCS5D01G555700 chr7A 97.110 173 4 1 2096 2268 431989284 431989113 2.280000e-74 291.0
57 TraesCS5D01G555700 chr7A 88.034 117 5 3 5646 5759 727011363 727011253 5.250000e-26 130.0
58 TraesCS5D01G555700 chr7D 86.688 2201 224 34 2340 4517 635561702 635559548 0.000000e+00 2377.0
59 TraesCS5D01G555700 chr7D 88.487 1190 93 19 53 1201 635563996 635562810 0.000000e+00 1399.0
60 TraesCS5D01G555700 chr7D 88.000 925 73 20 1201 2105 635562843 635561937 0.000000e+00 1059.0
61 TraesCS5D01G555700 chr7D 80.303 396 36 17 5652 6043 111077584 111077227 1.790000e-65 261.0
62 TraesCS5D01G555700 chr7D 79.494 395 40 21 5652 6043 37442822 37443178 6.470000e-60 243.0
63 TraesCS5D01G555700 chr3A 93.291 1580 65 15 1 1553 743538073 743539638 0.000000e+00 2292.0
64 TraesCS5D01G555700 chr3A 85.714 1288 120 32 3757 4989 743545356 743546634 0.000000e+00 1301.0
65 TraesCS5D01G555700 chr3A 83.726 977 75 32 4705 5626 743633799 743634746 0.000000e+00 846.0
66 TraesCS5D01G555700 chr3A 91.373 568 37 9 3147 3711 743544800 743545358 0.000000e+00 767.0
67 TraesCS5D01G555700 chr3A 87.796 549 37 9 5120 5641 743548264 743548809 3.310000e-172 616.0
68 TraesCS5D01G555700 chr3A 91.866 209 7 8 2099 2306 70479041 70479240 3.810000e-72 283.0
69 TraesCS5D01G555700 chr3A 88.312 154 16 2 4994 5147 240991766 240991917 3.980000e-42 183.0
70 TraesCS5D01G555700 chr3A 95.918 49 2 0 5049 5097 743548215 743548263 5.370000e-11 80.5
71 TraesCS5D01G555700 chr5A 88.677 1413 130 11 2340 3743 565548130 565549521 0.000000e+00 1696.0
72 TraesCS5D01G555700 chr5A 88.659 917 77 11 1201 2097 565546946 565547855 0.000000e+00 1092.0
73 TraesCS5D01G555700 chr5A 86.348 857 75 18 1 827 565545734 565546578 0.000000e+00 896.0
74 TraesCS5D01G555700 chr5A 93.703 397 25 0 802 1198 565546580 565546976 4.310000e-166 595.0
75 TraesCS5D01G555700 chr5A 97.674 172 4 0 2103 2274 290391862 290391691 4.890000e-76 296.0
76 TraesCS5D01G555700 chr5A 80.407 393 37 16 5653 6043 170094019 170094373 4.960000e-66 263.0
77 TraesCS5D01G555700 chr5A 89.855 69 7 0 4774 4842 228896328 228896396 8.910000e-14 89.8
78 TraesCS5D01G555700 chr6B 88.298 282 9 5 5652 5915 24968313 24968588 3.760000e-82 316.0
79 TraesCS5D01G555700 chr6B 94.924 197 10 0 6258 6454 24970622 24970818 6.290000e-80 309.0
80 TraesCS5D01G555700 chr6B 84.211 304 22 6 5895 6175 24969537 24969837 8.250000e-69 272.0
81 TraesCS5D01G555700 chr3D 79.665 477 46 22 5652 6118 500539314 500538879 4.890000e-76 296.0
82 TraesCS5D01G555700 chr3D 97.647 170 4 0 2101 2270 7607391 7607560 6.330000e-75 292.0
83 TraesCS5D01G555700 chr3D 79.241 395 41 21 5652 6043 25357684 25357328 3.010000e-58 237.0
84 TraesCS5D01G555700 chr2D 97.143 175 5 0 2095 2269 560959476 560959650 4.890000e-76 296.0
85 TraesCS5D01G555700 chr2D 97.110 173 4 1 2099 2271 426427797 426427968 2.280000e-74 291.0
86 TraesCS5D01G555700 chr2D 85.484 124 10 3 5636 5759 140632162 140632047 8.790000e-24 122.0
87 TraesCS5D01G555700 chr3B 97.674 172 3 1 2098 2269 120617082 120616912 1.760000e-75 294.0
88 TraesCS5D01G555700 chr3B 97.059 34 1 0 5651 5684 488352547 488352514 2.510000e-04 58.4
89 TraesCS5D01G555700 chr2B 96.552 174 5 1 2096 2269 342280950 342280778 2.950000e-73 287.0
90 TraesCS5D01G555700 chr2B 92.424 198 11 4 2072 2268 736244853 736245047 4.930000e-71 279.0
91 TraesCS5D01G555700 chr1D 92.593 108 2 1 5652 5759 21882343 21882242 4.030000e-32 150.0
92 TraesCS5D01G555700 chr1D 87.273 55 7 0 5106 5160 463487579 463487633 5.400000e-06 63.9


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 TraesCS5D01G555700 chr5D 559367888 559374342 6454 True 11921.000000 11921 100.000000 1 6455 1 chr5D.!!$R1 6454
1 TraesCS5D01G555700 chr5D 446908813 446913841 5028 True 1406.000000 1720 88.430500 1 4869 4 chr5D.!!$R2 4868
2 TraesCS5D01G555700 chr5D 565060446 565060966 520 True 293.500000 416 89.558500 1749 5250 2 chr5D.!!$R3 3501
3 TraesCS5D01G555700 chr4A 612394243 612399890 5647 True 2723.000000 5029 93.877000 1 5653 3 chr4A.!!$R1 5652
4 TraesCS5D01G555700 chr4A 612607135 612611442 4307 False 791.500000 1352 89.245250 898 4005 4 chr4A.!!$F2 3107
5 TraesCS5D01G555700 chr4A 464545301 464545899 598 False 523.000000 523 83.150000 5651 6260 1 chr4A.!!$F1 609
6 TraesCS5D01G555700 chr4A 613146496 613150051 3555 False 346.533333 595 89.901333 4610 5655 3 chr4A.!!$F4 1045
7 TraesCS5D01G555700 chr4A 612657565 612665630 8065 False 343.333333 505 86.790667 4621 5613 3 chr4A.!!$F3 992
8 TraesCS5D01G555700 chr5B 693611318 693616878 5560 True 3387.500000 3936 89.943000 1 5614 2 chr5B.!!$R4 5613
9 TraesCS5D01G555700 chr5B 545797223 545801986 4763 False 1071.000000 1439 88.604400 1 4747 5 chr5B.!!$F4 4746
10 TraesCS5D01G555700 chr5B 708225049 708228985 3936 False 734.200000 2028 88.741400 1748 5250 5 chr5B.!!$F6 3502
11 TraesCS5D01G555700 chr5B 693690716 693691852 1136 False 641.500000 704 87.327500 4382 5655 2 chr5B.!!$F5 1273
12 TraesCS5D01G555700 chr5B 537594730 537595422 692 True 412.500000 512 91.269500 5806 6453 2 chr5B.!!$R3 647
13 TraesCS5D01G555700 chr7B 740052859 740057819 4960 False 1639.000000 2628 85.983333 53 5114 3 chr7B.!!$F3 5061
14 TraesCS5D01G555700 chr7B 740379884 740380762 878 False 857.000000 857 84.512000 3938 4814 1 chr7B.!!$F2 876
15 TraesCS5D01G555700 chr7B 740169604 740170474 870 False 806.000000 806 83.559000 3938 4814 1 chr7B.!!$F1 876
16 TraesCS5D01G555700 chr7A 730459369 730464054 4685 False 1690.333333 2564 87.866333 53 4743 3 chr7A.!!$F3 4690
17 TraesCS5D01G555700 chr7D 635559548 635563996 4448 True 1611.666667 2377 87.725000 53 4517 3 chr7D.!!$R2 4464
18 TraesCS5D01G555700 chr3A 743538073 743539638 1565 False 2292.000000 2292 93.291000 1 1553 1 chr3A.!!$F3 1552
19 TraesCS5D01G555700 chr3A 743633799 743634746 947 False 846.000000 846 83.726000 4705 5626 1 chr3A.!!$F4 921
20 TraesCS5D01G555700 chr3A 743544800 743548809 4009 False 691.125000 1301 90.200250 3147 5641 4 chr3A.!!$F5 2494
21 TraesCS5D01G555700 chr5A 565545734 565549521 3787 False 1069.750000 1696 89.346750 1 3743 4 chr5A.!!$F3 3742
22 TraesCS5D01G555700 chr6B 24968313 24970818 2505 False 299.000000 316 89.144333 5652 6454 3 chr6B.!!$F1 802

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
207 215 1.461127 GTGCCTTAACTGAAGAGTGCG 59.539 52.381 0.00 0.00 37.33 5.34 F
392 419 2.228822 GCAGGGGAGTGTTAAATGTGTG 59.771 50.000 0.00 0.00 0.00 3.82 F
410 437 3.309954 GTGTGTGTGAGGAACTTCTTGAC 59.690 47.826 0.00 0.00 41.55 3.18 F
2053 2263 1.035932 ACTTGCTCATCATGGGCTGC 61.036 55.000 11.79 0.00 46.08 5.25 F
2476 4177 0.671781 ATGTTGAGCGACAGAGTGGC 60.672 55.000 0.00 0.00 37.53 5.01 F
4084 6359 0.033601 TTGCACCCAAGTTCACACCT 60.034 50.000 0.00 0.00 0.00 4.00 F
4143 6574 0.962356 AATTCGGCAGGTTCCAGCAG 60.962 55.000 8.38 4.51 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1706 1.135859 GCAGAACCATTTCTCGCTGTG 60.136 52.381 0.00 0.00 40.34 3.66 R
1546 1707 1.160137 GCAGAACCATTTCTCGCTGT 58.840 50.000 0.00 0.00 40.34 4.40 R
2252 2467 1.272816 TGACATACTCCCTCCGTTCCA 60.273 52.381 0.00 0.00 0.00 3.53 R
2902 4942 1.198637 GCAGATGGCAAACACTGAGAC 59.801 52.381 14.88 0.00 43.97 3.36 R
4143 6574 0.598065 GGGTGTGAACTTGATGGCAC 59.402 55.000 0.00 0.00 0.00 5.01 R
5384 15216 0.108472 CTCTTCAGTGATGAGCGCCA 60.108 55.000 19.68 1.52 29.56 5.69 R
5998 20828 1.668151 GTGTGGGCACGAAGAGGTC 60.668 63.158 0.00 0.00 35.75 3.85 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
81 83 5.367945 TCCTTTGGTCAGAAGTACAAACT 57.632 39.130 0.00 0.00 37.65 2.66
193 201 7.613585 TGATCAACAATCATAAATTGTGCCTT 58.386 30.769 4.31 0.00 40.94 4.35
207 215 1.461127 GTGCCTTAACTGAAGAGTGCG 59.539 52.381 0.00 0.00 37.33 5.34
297 320 5.532406 TCAGTGAGGTTGAAATTTCTGAAGG 59.468 40.000 18.64 1.25 0.00 3.46
392 419 2.228822 GCAGGGGAGTGTTAAATGTGTG 59.771 50.000 0.00 0.00 0.00 3.82
410 437 3.309954 GTGTGTGTGAGGAACTTCTTGAC 59.690 47.826 0.00 0.00 41.55 3.18
541 594 4.862350 TGTTGCTGTTCTTCATGAATGTG 58.138 39.130 8.96 0.00 36.99 3.21
543 596 5.530543 TGTTGCTGTTCTTCATGAATGTGTA 59.469 36.000 8.96 0.00 36.99 2.90
743 802 5.276270 CGGAACAGGCAAGAATAATCAATG 58.724 41.667 0.00 0.00 0.00 2.82
1032 1127 7.358770 CTCCTTGAGAGAGAAGAATATCCAA 57.641 40.000 0.00 0.00 46.50 3.53
1533 1694 5.660864 TGGTAGTGTGATTCCATCTGATGTA 59.339 40.000 15.95 4.75 0.00 2.29
1642 1806 7.117285 ACAGAGAACATGATCAGCAATAGTA 57.883 36.000 0.00 0.00 0.00 1.82
1689 1853 2.089980 GCATCTCTGGCTGTTCAACAT 58.910 47.619 0.00 0.00 0.00 2.71
1693 1857 3.141398 TCTCTGGCTGTTCAACATCAAC 58.859 45.455 0.00 0.00 0.00 3.18
1752 1916 3.084786 GGTAGGGCATGGATTAATCAGC 58.915 50.000 17.07 15.72 0.00 4.26
1820 2002 3.012518 AGCTTATCCATGTCACAACTGC 58.987 45.455 0.00 0.00 0.00 4.40
1916 2116 7.704472 TGGTTCAAGTTTCATGTCATGTTTTAC 59.296 33.333 12.54 6.91 0.00 2.01
1971 2173 9.573133 CTTTGTGATATAGCAAAAAGTAAAGGG 57.427 33.333 20.81 0.25 37.99 3.95
1978 2180 5.468540 AGCAAAAAGTAAAGGGGATGTTC 57.531 39.130 0.00 0.00 0.00 3.18
1980 2182 5.365314 AGCAAAAAGTAAAGGGGATGTTCAA 59.635 36.000 0.00 0.00 0.00 2.69
1981 2183 5.696270 GCAAAAAGTAAAGGGGATGTTCAAG 59.304 40.000 0.00 0.00 0.00 3.02
1982 2184 6.685368 GCAAAAAGTAAAGGGGATGTTCAAGT 60.685 38.462 0.00 0.00 0.00 3.16
1983 2185 7.272244 CAAAAAGTAAAGGGGATGTTCAAGTT 58.728 34.615 0.00 0.00 0.00 2.66
2053 2263 1.035932 ACTTGCTCATCATGGGCTGC 61.036 55.000 11.79 0.00 46.08 5.25
2097 2312 7.611213 AAACTGTATGTAGTATGTTGCCTTC 57.389 36.000 0.00 0.00 0.00 3.46
2099 2314 5.425539 ACTGTATGTAGTATGTTGCCTTCCT 59.574 40.000 0.00 0.00 0.00 3.36
2104 2319 7.670605 ATGTAGTATGTTGCCTTCCTTACTA 57.329 36.000 0.00 0.00 0.00 1.82
2105 2320 6.870769 TGTAGTATGTTGCCTTCCTTACTAC 58.129 40.000 9.87 9.87 41.03 2.73
2107 2322 6.223351 AGTATGTTGCCTTCCTTACTACTC 57.777 41.667 0.00 0.00 0.00 2.59
2108 2323 3.975168 TGTTGCCTTCCTTACTACTCC 57.025 47.619 0.00 0.00 0.00 3.85
2109 2324 2.570302 TGTTGCCTTCCTTACTACTCCC 59.430 50.000 0.00 0.00 0.00 4.30
2110 2325 2.838813 GTTGCCTTCCTTACTACTCCCT 59.161 50.000 0.00 0.00 0.00 4.20
2111 2326 2.748388 TGCCTTCCTTACTACTCCCTC 58.252 52.381 0.00 0.00 0.00 4.30
2112 2327 2.040939 GCCTTCCTTACTACTCCCTCC 58.959 57.143 0.00 0.00 0.00 4.30
2113 2328 2.308690 CCTTCCTTACTACTCCCTCCG 58.691 57.143 0.00 0.00 0.00 4.63
2114 2329 2.357986 CCTTCCTTACTACTCCCTCCGT 60.358 54.545 0.00 0.00 0.00 4.69
2115 2330 3.363627 CTTCCTTACTACTCCCTCCGTT 58.636 50.000 0.00 0.00 0.00 4.44
2116 2331 3.010200 TCCTTACTACTCCCTCCGTTC 57.990 52.381 0.00 0.00 0.00 3.95
2117 2332 2.030371 CCTTACTACTCCCTCCGTTCC 58.970 57.143 0.00 0.00 0.00 3.62
2118 2333 2.357986 CCTTACTACTCCCTCCGTTCCT 60.358 54.545 0.00 0.00 0.00 3.36
2119 2334 3.117738 CCTTACTACTCCCTCCGTTCCTA 60.118 52.174 0.00 0.00 0.00 2.94
2121 2336 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2122 2337 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2124 2339 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2125 2340 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
2126 2341 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2127 2342 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2128 2343 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2129 2344 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2130 2345 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2131 2346 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2132 2347 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2134 2349 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
2150 2365 9.573166 TTTGTCTTTTTAGAGATCTCAAATGGA 57.427 29.630 24.39 16.86 0.00 3.41
2151 2366 8.553459 TGTCTTTTTAGAGATCTCAAATGGAC 57.447 34.615 24.39 23.82 0.00 4.02
2153 2368 9.877178 GTCTTTTTAGAGATCTCAAATGGACTA 57.123 33.333 24.39 2.88 0.00 2.59
2155 2370 9.103861 CTTTTTAGAGATCTCAAATGGACTACC 57.896 37.037 24.39 0.00 0.00 3.18
2168 2383 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
2172 2387 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
2173 2388 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
2174 2389 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
2175 2390 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
2177 2392 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
2179 2394 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
2198 2413 9.860650 AGACATATTCTAGAGTGTAGATTCACT 57.139 33.333 0.00 0.00 41.09 3.41
2208 2423 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2209 2424 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2210 2425 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2212 2427 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2213 2428 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2214 2429 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2215 2430 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2216 2431 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2217 2432 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2220 2435 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2221 2436 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2222 2437 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
2223 2438 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2224 2439 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2225 2440 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
2226 2441 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2227 2442 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
2229 2444 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
2230 2445 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2232 2447 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
2233 2448 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
2235 2450 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
2236 2451 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
2237 2452 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
2239 2454 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
2240 2455 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
2241 2456 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
2242 2457 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
2243 2458 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
2245 2460 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
2246 2461 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
2260 2475 7.519032 AGAAAGACAAATATTTTGGAACGGA 57.481 32.000 0.00 0.00 0.00 4.69
2262 2477 5.897377 AGACAAATATTTTGGAACGGAGG 57.103 39.130 0.00 0.00 0.00 4.30
2264 2479 4.668636 ACAAATATTTTGGAACGGAGGGA 58.331 39.130 0.00 0.00 0.00 4.20
2265 2480 4.705023 ACAAATATTTTGGAACGGAGGGAG 59.295 41.667 0.00 0.00 0.00 4.30
2281 2497 5.625886 CGGAGGGAGTATGTCATGTTTTACA 60.626 44.000 0.00 0.00 0.00 2.41
2360 4053 9.899661 TGTTTATTATGGTTGCACTAGTATTCT 57.100 29.630 0.00 0.00 0.00 2.40
2365 4058 6.743575 ATGGTTGCACTAGTATTCTTTGAC 57.256 37.500 0.00 0.00 0.00 3.18
2366 4059 5.001232 TGGTTGCACTAGTATTCTTTGACC 58.999 41.667 0.00 0.00 0.00 4.02
2437 4138 7.456725 ACATATATCAGGAATCTTCAAGTGGG 58.543 38.462 0.00 0.00 0.00 4.61
2440 4141 2.986019 TCAGGAATCTTCAAGTGGGGAA 59.014 45.455 0.00 0.00 0.00 3.97
2476 4177 0.671781 ATGTTGAGCGACAGAGTGGC 60.672 55.000 0.00 0.00 37.53 5.01
2490 4191 2.755876 TGGCGTGGGTTTGCAACA 60.756 55.556 0.00 0.00 0.00 3.33
2540 4241 4.015084 AGGAGATGCTGAAATGGAAGTTG 58.985 43.478 0.00 0.00 0.00 3.16
2631 4665 1.067250 GCCACGCTTCCTTGCAAAA 59.933 52.632 0.00 0.00 0.00 2.44
2633 4667 0.940991 CCACGCTTCCTTGCAAAAGC 60.941 55.000 20.99 20.99 43.49 3.51
2644 4678 3.057245 CCTTGCAAAAGCCTAAGGAAGTC 60.057 47.826 0.00 0.00 41.71 3.01
2652 4686 1.066787 GCCTAAGGAAGTCGAAGCTGT 60.067 52.381 0.00 0.00 0.00 4.40
2684 4718 1.181098 AATGCAGTCAGCCCAACCAC 61.181 55.000 0.00 0.00 44.83 4.16
2703 4737 1.617755 CTTGTAGCACCAGCACGACG 61.618 60.000 0.00 0.00 45.49 5.12
2727 4761 1.068679 GCAAAGAGAGGCAGAACAAGC 60.069 52.381 0.00 0.00 0.00 4.01
2731 4765 1.907936 AGAGAGGCAGAACAAGCAGAT 59.092 47.619 0.00 0.00 0.00 2.90
2813 4847 5.304101 AGGGAAGCTTATACTCAGACAGATG 59.696 44.000 0.00 0.00 0.00 2.90
2899 4939 1.961277 AAGCCTTTCTCGTGCACCG 60.961 57.895 12.15 6.81 38.13 4.94
2901 4941 2.251642 GCCTTTCTCGTGCACCGTT 61.252 57.895 12.15 0.00 37.94 4.44
2902 4942 1.569493 CCTTTCTCGTGCACCGTTG 59.431 57.895 12.15 0.00 37.94 4.10
2937 4992 1.007734 CTGCAATGCATCCATCGGC 60.008 57.895 8.91 0.00 38.13 5.54
3052 5110 2.142356 TTCCGGTGGCATCAATGATT 57.858 45.000 0.00 0.00 0.00 2.57
3053 5111 1.679139 TCCGGTGGCATCAATGATTC 58.321 50.000 0.00 0.00 0.00 2.52
3058 5116 4.498009 CCGGTGGCATCAATGATTCTTAAC 60.498 45.833 0.00 0.00 0.00 2.01
3068 5126 5.652014 TCAATGATTCTTAACCATCCACCAC 59.348 40.000 0.00 0.00 0.00 4.16
3087 5145 2.418976 CACTTGGTGATGATGCACTGAG 59.581 50.000 0.00 0.00 38.78 3.35
3109 5167 5.237815 AGAAATGAGTTGCACAGATTACGA 58.762 37.500 0.00 0.00 0.00 3.43
3161 5219 6.015434 CCACCAACTAAAGGTTTGCTATTTCT 60.015 38.462 0.00 0.00 37.23 2.52
3162 5220 7.433680 CACCAACTAAAGGTTTGCTATTTCTT 58.566 34.615 0.00 0.00 37.23 2.52
3163 5221 7.595130 CACCAACTAAAGGTTTGCTATTTCTTC 59.405 37.037 0.00 0.00 37.23 2.87
3210 5268 8.836413 TCTTGTTTGTGAATTTCTTACACTAGG 58.164 33.333 0.00 0.00 35.83 3.02
3422 5495 0.312416 CTAGCTGACGATCTTCGGGG 59.688 60.000 9.85 0.00 45.59 5.73
3424 5497 1.227002 GCTGACGATCTTCGGGGTC 60.227 63.158 9.85 0.22 45.59 4.46
3437 5513 6.740944 TCTTCGGGGTCAATTCATATCTTA 57.259 37.500 0.00 0.00 0.00 2.10
3544 5638 4.693283 TCCGTACCAAATCTCTATTGCTG 58.307 43.478 0.00 0.00 0.00 4.41
3561 5659 8.830580 TCTATTGCTGATGCTAATTACTTTGAC 58.169 33.333 0.00 0.00 40.48 3.18
3570 5674 5.048782 TGCTAATTACTTTGACCTGCAGTTG 60.049 40.000 13.81 0.00 0.00 3.16
3629 5739 0.034059 CTCAGCAAGTTCCCACGAGT 59.966 55.000 0.00 0.00 0.00 4.18
3716 5835 0.179192 CGCATCATGTCCAACCGTTG 60.179 55.000 4.12 4.12 0.00 4.10
3998 6272 0.831307 GGACATGGTCTACCCCTGTC 59.169 60.000 17.42 17.42 42.36 3.51
4084 6359 0.033601 TTGCACCCAAGTTCACACCT 60.034 50.000 0.00 0.00 0.00 4.00
4143 6574 0.962356 AATTCGGCAGGTTCCAGCAG 60.962 55.000 8.38 4.51 0.00 4.24
4240 6677 1.928653 CGCGAGGTTTGACAACGAA 59.071 52.632 0.00 0.00 33.13 3.85
4650 7138 9.841295 AACTAATAGTTCACAGTAACAAAGGAA 57.159 29.630 0.00 0.00 31.77 3.36
4882 7412 2.006888 ACACTTATGGCGTTGAATCCG 58.993 47.619 0.00 0.00 0.00 4.18
4952 10120 5.582689 TTCTCAAGAGAATACATCTGCGA 57.417 39.130 8.37 0.00 42.06 5.10
5250 15067 8.834465 ACAGCTAAATCTGCTATACTTTTGATG 58.166 33.333 0.00 0.00 38.92 3.07
5354 15185 7.218228 TGTGTAACTGATTGAATCATTTGCT 57.782 32.000 20.51 2.25 38.85 3.91
5355 15186 8.334263 TGTGTAACTGATTGAATCATTTGCTA 57.666 30.769 20.51 11.28 38.85 3.49
5618 19456 4.520179 TGACATGGATGGATTGACTGAAG 58.480 43.478 0.00 0.00 0.00 3.02
5695 19533 3.381335 TCCCCACTACAAGGTATTCTCC 58.619 50.000 0.00 0.00 0.00 3.71
5696 19534 3.013648 TCCCCACTACAAGGTATTCTCCT 59.986 47.826 0.00 0.00 39.84 3.69
5698 19536 4.141688 CCCCACTACAAGGTATTCTCCTTC 60.142 50.000 0.00 0.00 44.87 3.46
5699 19537 4.717280 CCCACTACAAGGTATTCTCCTTCT 59.283 45.833 0.00 0.00 44.87 2.85
5700 19538 5.189934 CCCACTACAAGGTATTCTCCTTCTT 59.810 44.000 0.00 0.00 44.87 2.52
5741 19579 2.230660 CTCAGCATGCCATGTCATCAT 58.769 47.619 15.66 0.00 34.76 2.45
5759 19597 6.432162 GTCATCATATACCAGCCAATCACAAT 59.568 38.462 0.00 0.00 0.00 2.71
5767 19605 3.991773 CCAGCCAATCACAATTTCACAAG 59.008 43.478 0.00 0.00 0.00 3.16
5908 20734 4.702612 ACTGACGAGAGAAATAAGAGAGCA 59.297 41.667 0.00 0.00 0.00 4.26
5975 20805 1.557269 ATCGCTTCTTCACTGGGCCT 61.557 55.000 4.53 0.00 0.00 5.19
5991 20821 2.431942 CTTTCGTGCCGCCGTACT 60.432 61.111 0.00 0.00 0.00 2.73
5992 20822 1.153978 CTTTCGTGCCGCCGTACTA 60.154 57.895 0.00 0.00 0.00 1.82
6072 20924 3.117657 TCGGAATCGATGCTCCTCT 57.882 52.632 13.07 0.00 40.88 3.69
6081 20933 0.465824 GATGCTCCTCTGCCATTGCT 60.466 55.000 0.00 0.00 38.71 3.91
6230 21763 4.662179 TCCAGAAGCATCTCCTTCCATTAT 59.338 41.667 0.00 0.00 41.65 1.28
6231 21764 5.133322 TCCAGAAGCATCTCCTTCCATTATT 59.867 40.000 0.00 0.00 41.65 1.40
6232 21765 5.241064 CCAGAAGCATCTCCTTCCATTATTG 59.759 44.000 0.00 0.00 41.65 1.90
6233 21766 5.826737 CAGAAGCATCTCCTTCCATTATTGT 59.173 40.000 0.00 0.00 41.65 2.71
6278 21846 4.184629 GTGCCACCTGTTACTTCATCTAG 58.815 47.826 0.00 0.00 0.00 2.43
6300 21868 2.159085 CCCACGGAGGTAAGAACTGATC 60.159 54.545 0.00 0.00 34.66 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 83 6.620678 GCAGAACTTTCAATACTGCCAATAA 58.379 36.000 0.00 0.00 45.19 1.40
193 201 2.472695 ATTGCCGCACTCTTCAGTTA 57.527 45.000 0.00 0.00 0.00 2.24
207 215 4.439305 TGTATTGCTGTTCAGAATTGCC 57.561 40.909 3.84 0.00 0.00 4.52
255 278 7.832187 CCTCACTGAAATGGTAGGGTAAATTAA 59.168 37.037 0.00 0.00 0.00 1.40
342 366 6.882140 ACATGTTACCGTTCCATCAAAGAATA 59.118 34.615 0.00 0.00 0.00 1.75
392 419 4.390297 GCATAGTCAAGAAGTTCCTCACAC 59.610 45.833 0.00 0.00 0.00 3.82
410 437 6.149973 TGACTTGGTGATTCTTCAAAGCATAG 59.850 38.462 0.00 0.00 32.48 2.23
541 594 5.048713 ACTGAAGTAAAGCATGCAAAGGTAC 60.049 40.000 21.98 13.22 0.00 3.34
543 596 3.891366 ACTGAAGTAAAGCATGCAAAGGT 59.109 39.130 21.98 0.00 0.00 3.50
672 728 8.147244 TCTGGTTCCTTAGCTTCTTATAAACT 57.853 34.615 0.00 0.00 0.00 2.66
946 1041 9.495572 GATCCTATTAAGAAGTACATCCTTTGG 57.504 37.037 0.00 0.00 0.00 3.28
987 1082 8.250143 AGGAGAAAACCATGTCAACTAAATTT 57.750 30.769 0.00 0.00 0.00 1.82
1032 1127 4.142600 GCGACCTCATTTGCTTGTTTATCT 60.143 41.667 0.00 0.00 0.00 1.98
1533 1694 1.736126 CTCGCTGTGTCTGCATTGATT 59.264 47.619 0.00 0.00 0.00 2.57
1545 1706 1.135859 GCAGAACCATTTCTCGCTGTG 60.136 52.381 0.00 0.00 40.34 3.66
1546 1707 1.160137 GCAGAACCATTTCTCGCTGT 58.840 50.000 0.00 0.00 40.34 4.40
1642 1806 1.655484 TGCGAGTCGATGCAATCAAT 58.345 45.000 18.61 0.00 45.97 2.57
1689 1853 7.882791 TCAATTGCAGGACTAGAATTTAGTTGA 59.117 33.333 0.00 0.00 0.00 3.18
1875 2073 5.359576 ACTTGAACCAAAGCTTCAATGTGTA 59.640 36.000 0.00 0.00 37.09 2.90
1916 2116 9.840427 AAACTTGTATGAAAAATCTACAATCCG 57.160 29.630 0.00 0.00 35.47 4.18
1955 2157 6.071984 TGAACATCCCCTTTACTTTTTGCTA 58.928 36.000 0.00 0.00 0.00 3.49
1956 2158 4.898861 TGAACATCCCCTTTACTTTTTGCT 59.101 37.500 0.00 0.00 0.00 3.91
1965 2167 6.273730 TCCTAGAAACTTGAACATCCCCTTTA 59.726 38.462 0.00 0.00 0.00 1.85
1971 2173 5.940470 ACACATCCTAGAAACTTGAACATCC 59.060 40.000 0.00 0.00 0.00 3.51
1978 2180 5.924475 AAACGACACATCCTAGAAACTTG 57.076 39.130 0.00 0.00 0.00 3.16
1980 2182 5.277828 GCAAAAACGACACATCCTAGAAACT 60.278 40.000 0.00 0.00 0.00 2.66
1981 2183 4.909880 GCAAAAACGACACATCCTAGAAAC 59.090 41.667 0.00 0.00 0.00 2.78
1982 2184 4.819630 AGCAAAAACGACACATCCTAGAAA 59.180 37.500 0.00 0.00 0.00 2.52
1983 2185 4.385825 AGCAAAAACGACACATCCTAGAA 58.614 39.130 0.00 0.00 0.00 2.10
2053 2263 6.311445 CAGTTTTCTATGCCTAGTGTACTGTG 59.689 42.308 13.43 0.00 31.09 3.66
2097 2312 2.030371 GGAACGGAGGGAGTAGTAAGG 58.970 57.143 0.00 0.00 0.00 2.69
2099 2314 4.591321 TTAGGAACGGAGGGAGTAGTAA 57.409 45.455 0.00 0.00 0.00 2.24
2104 2319 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2105 2320 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2107 2322 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2108 2323 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2124 2339 9.573166 TCCATTTGAGATCTCTAAAAAGACAAA 57.427 29.630 22.95 12.48 30.56 2.83
2125 2340 9.003658 GTCCATTTGAGATCTCTAAAAAGACAA 57.996 33.333 24.97 10.90 35.65 3.18
2126 2341 8.378565 AGTCCATTTGAGATCTCTAAAAAGACA 58.621 33.333 27.96 10.52 36.78 3.41
2127 2342 8.785329 AGTCCATTTGAGATCTCTAAAAAGAC 57.215 34.615 22.95 23.49 35.73 3.01
2128 2343 9.877178 GTAGTCCATTTGAGATCTCTAAAAAGA 57.123 33.333 22.95 15.64 30.56 2.52
2129 2344 9.103861 GGTAGTCCATTTGAGATCTCTAAAAAG 57.896 37.037 22.95 12.63 30.56 2.27
2130 2345 8.602424 TGGTAGTCCATTTGAGATCTCTAAAAA 58.398 33.333 22.95 15.24 39.03 1.94
2131 2346 8.041323 GTGGTAGTCCATTTGAGATCTCTAAAA 58.959 37.037 22.95 15.91 46.20 1.52
2132 2347 7.180229 TGTGGTAGTCCATTTGAGATCTCTAAA 59.820 37.037 22.95 19.53 46.20 1.85
2134 2349 6.194967 TGTGGTAGTCCATTTGAGATCTCTA 58.805 40.000 22.95 13.48 46.20 2.43
2135 2350 5.026121 TGTGGTAGTCCATTTGAGATCTCT 58.974 41.667 22.95 0.38 46.20 3.10
2137 2352 5.965033 ATGTGGTAGTCCATTTGAGATCT 57.035 39.130 0.00 0.00 46.20 2.75
2138 2353 5.692204 CGTATGTGGTAGTCCATTTGAGATC 59.308 44.000 0.00 0.00 46.20 2.75
2139 2354 5.453339 CCGTATGTGGTAGTCCATTTGAGAT 60.453 44.000 0.00 0.00 46.20 2.75
2140 2355 4.142026 CCGTATGTGGTAGTCCATTTGAGA 60.142 45.833 0.00 0.00 46.20 3.27
2141 2356 4.119862 CCGTATGTGGTAGTCCATTTGAG 58.880 47.826 0.00 0.00 46.20 3.02
2142 2357 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
2143 2358 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
2146 2361 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
2147 2362 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
2148 2363 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
2150 2365 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
2151 2366 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
2153 2368 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
2172 2387 9.860650 AGTGAATCTACACTCTAGAATATGTCT 57.139 33.333 7.12 0.00 46.36 3.41
2186 2401 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2187 2402 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2188 2403 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2189 2404 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2190 2405 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2191 2406 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2192 2407 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2193 2408 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2194 2409 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2197 2412 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
2198 2413 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2199 2414 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2202 2417 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2204 2419 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2205 2420 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2206 2421 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2208 2423 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
2209 2424 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2210 2425 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2212 2427 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
2213 2428 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
2214 2429 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
2215 2430 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
2216 2431 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
2217 2432 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2220 2435 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2232 2447 9.760660 CGTTCCAAAATATTTGTCTTTCTAGAG 57.239 33.333 0.39 0.00 0.00 2.43
2233 2448 8.726988 CCGTTCCAAAATATTTGTCTTTCTAGA 58.273 33.333 0.39 0.00 0.00 2.43
2235 2450 8.624367 TCCGTTCCAAAATATTTGTCTTTCTA 57.376 30.769 0.39 0.00 0.00 2.10
2236 2451 7.309194 CCTCCGTTCCAAAATATTTGTCTTTCT 60.309 37.037 0.39 0.00 0.00 2.52
2237 2452 6.806739 CCTCCGTTCCAAAATATTTGTCTTTC 59.193 38.462 0.39 0.00 0.00 2.62
2239 2454 5.185056 CCCTCCGTTCCAAAATATTTGTCTT 59.815 40.000 0.39 0.00 0.00 3.01
2240 2455 4.705023 CCCTCCGTTCCAAAATATTTGTCT 59.295 41.667 0.39 0.00 0.00 3.41
2241 2456 4.703093 TCCCTCCGTTCCAAAATATTTGTC 59.297 41.667 0.39 0.00 0.00 3.18
2242 2457 4.668636 TCCCTCCGTTCCAAAATATTTGT 58.331 39.130 0.39 0.00 0.00 2.83
2243 2458 4.705023 ACTCCCTCCGTTCCAAAATATTTG 59.295 41.667 0.39 0.00 0.00 2.32
2245 2460 4.586306 ACTCCCTCCGTTCCAAAATATT 57.414 40.909 0.00 0.00 0.00 1.28
2246 2461 5.132144 ACATACTCCCTCCGTTCCAAAATAT 59.868 40.000 0.00 0.00 0.00 1.28
2247 2462 4.472108 ACATACTCCCTCCGTTCCAAAATA 59.528 41.667 0.00 0.00 0.00 1.40
2249 2464 2.640826 ACATACTCCCTCCGTTCCAAAA 59.359 45.455 0.00 0.00 0.00 2.44
2250 2465 2.235402 GACATACTCCCTCCGTTCCAAA 59.765 50.000 0.00 0.00 0.00 3.28
2252 2467 1.272816 TGACATACTCCCTCCGTTCCA 60.273 52.381 0.00 0.00 0.00 3.53
2253 2468 1.481871 TGACATACTCCCTCCGTTCC 58.518 55.000 0.00 0.00 0.00 3.62
2254 2469 2.431057 ACATGACATACTCCCTCCGTTC 59.569 50.000 0.00 0.00 0.00 3.95
2255 2470 2.467880 ACATGACATACTCCCTCCGTT 58.532 47.619 0.00 0.00 0.00 4.44
2257 2472 3.543680 AAACATGACATACTCCCTCCG 57.456 47.619 0.00 0.00 0.00 4.63
2260 2475 6.374417 ACTGTAAAACATGACATACTCCCT 57.626 37.500 0.00 0.00 0.00 4.20
2262 2477 7.871853 ACAAACTGTAAAACATGACATACTCC 58.128 34.615 0.00 0.00 0.00 3.85
2264 2479 9.772973 TCTACAAACTGTAAAACATGACATACT 57.227 29.630 0.00 0.00 31.67 2.12
2437 4138 5.491982 ACATGTTCAGTCCTTCTATGTTCC 58.508 41.667 0.00 0.00 0.00 3.62
2440 4141 6.114187 TCAACATGTTCAGTCCTTCTATGT 57.886 37.500 8.48 0.00 0.00 2.29
2490 4191 2.108970 GGTCAGTCTCTCCCGGTAATT 58.891 52.381 0.00 0.00 0.00 1.40
2540 4241 2.750237 GTCCCCATTGCCGGTGTC 60.750 66.667 1.90 0.00 0.00 3.67
2617 4651 5.756916 CCTTAGGCTTTTGCAAGGAAGCG 62.757 52.174 23.00 12.95 45.94 4.68
2631 4665 1.205893 CAGCTTCGACTTCCTTAGGCT 59.794 52.381 0.00 0.00 0.00 4.58
2633 4667 2.611518 CACAGCTTCGACTTCCTTAGG 58.388 52.381 0.00 0.00 0.00 2.69
2644 4678 0.169672 CAAGATTGGCCACAGCTTCG 59.830 55.000 3.88 3.42 39.73 3.79
2652 4686 2.754552 GACTGCATTACAAGATTGGCCA 59.245 45.455 0.00 0.00 0.00 5.36
2684 4718 1.617755 CGTCGTGCTGGTGCTACAAG 61.618 60.000 0.00 0.00 40.48 3.16
2731 4765 4.021807 TGAGCTTGTGTTATACCAGAACGA 60.022 41.667 0.00 0.00 0.00 3.85
2748 4782 1.952296 CAGGTTGCAAAGTCTGAGCTT 59.048 47.619 16.20 0.00 32.17 3.74
2813 4847 4.455533 TGGTTGTGCAGACTGAATTATCAC 59.544 41.667 6.65 4.23 0.00 3.06
2899 4939 2.880890 AGATGGCAAACACTGAGACAAC 59.119 45.455 0.00 0.00 0.00 3.32
2901 4941 2.497138 CAGATGGCAAACACTGAGACA 58.503 47.619 0.00 0.00 33.08 3.41
2902 4942 1.198637 GCAGATGGCAAACACTGAGAC 59.801 52.381 14.88 0.00 43.97 3.36
2937 4992 1.471676 GCGGAATACTGGACAGTGGAG 60.472 57.143 14.86 3.69 42.52 3.86
3068 5126 2.981898 TCTCAGTGCATCATCACCAAG 58.018 47.619 0.00 0.00 37.68 3.61
3080 5138 2.291465 TGTGCAACTCATTTCTCAGTGC 59.709 45.455 0.00 0.00 38.04 4.40
3087 5145 5.530519 TCGTAATCTGTGCAACTCATTTC 57.469 39.130 0.00 0.00 38.04 2.17
3109 5167 9.769093 GTTTTATTAAGCGAGTCAATGTGTAAT 57.231 29.630 0.00 0.00 0.00 1.89
3189 5247 9.841295 AACTACCTAGTGTAAGAAATTCACAAA 57.159 29.630 0.00 0.00 36.50 2.83
3207 5265 4.194678 AGATGAATCCCGGAACTACCTA 57.805 45.455 0.73 0.00 36.31 3.08
3208 5266 3.047695 AGATGAATCCCGGAACTACCT 57.952 47.619 0.73 0.00 36.31 3.08
3209 5267 3.118371 ACAAGATGAATCCCGGAACTACC 60.118 47.826 0.73 0.00 0.00 3.18
3210 5268 4.138487 ACAAGATGAATCCCGGAACTAC 57.862 45.455 0.73 0.00 0.00 2.73
3424 5497 9.347240 ACCTTGTTCTCCATAAGATATGAATTG 57.653 33.333 0.00 0.00 32.82 2.32
3437 5513 7.770897 GTCAATACTCAATACCTTGTTCTCCAT 59.229 37.037 0.00 0.00 33.87 3.41
3544 5638 5.355350 ACTGCAGGTCAAAGTAATTAGCATC 59.645 40.000 19.93 0.00 0.00 3.91
3561 5659 2.674380 GTGGGCTCCAACTGCAGG 60.674 66.667 19.93 0.43 34.18 4.85
3629 5739 2.268920 GATGCCACCGCTGAAGGA 59.731 61.111 0.00 0.00 35.36 3.36
3691 5810 3.630148 GGACATGATGCGTCGGCG 61.630 66.667 4.29 4.29 44.10 6.46
3842 6108 1.627834 CTCTGGACTCCAAAGCTTCCT 59.372 52.381 0.00 0.00 30.80 3.36
4084 6359 0.828022 CAAGGGTGCCGGTATAGTGA 59.172 55.000 1.90 0.00 0.00 3.41
4143 6574 0.598065 GGGTGTGAACTTGATGGCAC 59.402 55.000 0.00 0.00 0.00 5.01
4240 6677 2.611292 GCAGCTGATGAAACGCTAGATT 59.389 45.455 20.43 0.00 31.80 2.40
4663 7151 9.831737 CTCCAGTTGACAATTTAATCTTAACAG 57.168 33.333 0.00 0.00 0.00 3.16
4846 7360 4.955811 AAGTGTGTGTCATCCTAAGTGA 57.044 40.909 0.00 0.00 0.00 3.41
4857 7371 2.139917 TCAACGCCATAAGTGTGTGTC 58.860 47.619 0.00 0.00 39.79 3.67
4981 10165 5.804979 GCAAAAACAAAGACAGCTCACTTAA 59.195 36.000 2.89 0.00 0.00 1.85
4989 10173 5.723492 AATGAAGCAAAAACAAAGACAGC 57.277 34.783 0.00 0.00 0.00 4.40
5250 15067 8.926710 AGCAAGCAAGTATTCGTGAATATATAC 58.073 33.333 5.66 0.00 35.90 1.47
5354 15185 9.688091 TTTGCTTGTTTTGGTCACCTATATATA 57.312 29.630 0.00 0.00 0.00 0.86
5355 15186 8.588290 TTTGCTTGTTTTGGTCACCTATATAT 57.412 30.769 0.00 0.00 0.00 0.86
5384 15216 0.108472 CTCTTCAGTGATGAGCGCCA 60.108 55.000 19.68 1.52 29.56 5.69
5523 19354 3.802685 GCTAATCCCAGTTACATGTCGTC 59.197 47.826 0.00 0.00 0.00 4.20
5618 19456 5.203060 AGGCTACTCGAGATTTATTGTCC 57.797 43.478 21.68 6.54 0.00 4.02
5695 19533 6.222389 TGGACCATTTGCATGTTAAAAGAAG 58.778 36.000 0.00 0.00 0.00 2.85
5696 19534 6.166984 TGGACCATTTGCATGTTAAAAGAA 57.833 33.333 0.00 0.00 0.00 2.52
5697 19535 5.798125 TGGACCATTTGCATGTTAAAAGA 57.202 34.783 0.00 0.00 0.00 2.52
5698 19536 5.990996 AGTTGGACCATTTGCATGTTAAAAG 59.009 36.000 0.00 0.00 0.00 2.27
5699 19537 5.923204 AGTTGGACCATTTGCATGTTAAAA 58.077 33.333 0.00 0.00 0.00 1.52
5700 19538 5.069648 TGAGTTGGACCATTTGCATGTTAAA 59.930 36.000 0.00 0.00 0.00 1.52
5741 19579 5.948758 TGTGAAATTGTGATTGGCTGGTATA 59.051 36.000 0.00 0.00 0.00 1.47
5759 19597 5.187967 GGAAGGGAGAGAGATACTTGTGAAA 59.812 44.000 0.00 0.00 0.00 2.69
5767 19605 2.321719 GTGGGGAAGGGAGAGAGATAC 58.678 57.143 0.00 0.00 0.00 2.24
5908 20734 1.837439 TGGGAGATAAGACCATGCGTT 59.163 47.619 0.00 0.00 0.00 4.84
5989 20819 2.181584 CGAAGAGGTCGTGGCTAGT 58.818 57.895 0.00 0.00 45.09 2.57
5998 20828 1.668151 GTGTGGGCACGAAGAGGTC 60.668 63.158 0.00 0.00 35.75 3.85
6072 20924 2.628696 CGAGGTTGCAGCAATGGCA 61.629 57.895 11.96 0.00 44.61 4.92
6184 21717 9.319060 TGGATGCTGAATAGATAGATTAGAAGT 57.681 33.333 0.00 0.00 0.00 3.01
6185 21718 9.806203 CTGGATGCTGAATAGATAGATTAGAAG 57.194 37.037 0.00 0.00 0.00 2.85
6230 21763 4.154918 GGCCATTCAAAACAACAACAACAA 59.845 37.500 0.00 0.00 0.00 2.83
6231 21764 3.686726 GGCCATTCAAAACAACAACAACA 59.313 39.130 0.00 0.00 0.00 3.33
6232 21765 3.064682 GGGCCATTCAAAACAACAACAAC 59.935 43.478 4.39 0.00 0.00 3.32
6233 21766 3.054802 AGGGCCATTCAAAACAACAACAA 60.055 39.130 6.18 0.00 0.00 2.83
6278 21846 0.391263 CAGTTCTTACCTCCGTGGGC 60.391 60.000 0.00 0.00 41.11 5.36
6300 21868 2.602211 CAGCTCAAACGCTAGATGACAG 59.398 50.000 0.00 0.00 38.41 3.51
6419 21987 9.481340 TCATACAGTCATATTTGTAATCTCAGC 57.519 33.333 0.00 0.00 33.85 4.26


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

AutoCloner maintained by Alex Coulton.