Multiple sequence alignment - TraesCS5D01G047800

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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 TraesCS5D01G047800 chr5D 100.000 4495 0 0 1 4495 45871024 45875518 0.000000e+00 8301.0
1 TraesCS5D01G047800 chr5D 85.932 789 89 17 3012 3787 46275098 46274319 0.000000e+00 822.0
2 TraesCS5D01G047800 chr5D 84.457 682 106 0 2137 2818 46128590 46127909 0.000000e+00 673.0
3 TraesCS5D01G047800 chr5D 84.380 621 92 3 2189 2808 46087957 46087341 4.970000e-169 604.0
4 TraesCS5D01G047800 chr5D 97.015 134 4 0 3997 4130 45874955 45875088 4.520000e-55 226.0
5 TraesCS5D01G047800 chr5D 97.015 134 4 0 3932 4065 45875020 45875153 4.520000e-55 226.0
6 TraesCS5D01G047800 chr5A 96.730 2599 64 6 1910 4495 36950805 36948215 0.000000e+00 4309.0
7 TraesCS5D01G047800 chr5A 86.726 791 82 18 3008 3784 37401599 37400818 0.000000e+00 857.0
8 TraesCS5D01G047800 chr5A 87.071 758 78 10 124 880 36954095 36953357 0.000000e+00 839.0
9 TraesCS5D01G047800 chr5A 84.906 689 101 1 2130 2818 37402282 37401597 0.000000e+00 693.0
10 TraesCS5D01G047800 chr5A 89.216 510 51 4 3007 3513 36826148 36825640 6.340000e-178 634.0
11 TraesCS5D01G047800 chr5A 83.483 666 109 1 2154 2818 36942966 36942301 1.780000e-173 619.0
12 TraesCS5D01G047800 chr5A 82.135 431 48 14 3593 3998 36825577 36825151 4.310000e-90 342.0
13 TraesCS5D01G047800 chr5A 82.514 366 35 5 1579 1918 36952434 36952072 1.220000e-75 294.0
14 TraesCS5D01G047800 chr5A 97.761 134 3 0 3997 4130 36948777 36948644 9.720000e-57 231.0
15 TraesCS5D01G047800 chr5A 97.015 134 4 0 3932 4065 36948712 36948579 4.520000e-55 226.0
16 TraesCS5D01G047800 chr5A 89.815 108 11 0 1107 1214 36953031 36952924 6.060000e-29 139.0
17 TraesCS5D01G047800 chr5A 98.551 69 1 0 4062 4130 36948777 36948709 6.110000e-24 122.0
18 TraesCS5D01G047800 chr5A 92.308 39 1 2 1770 1807 119071282 119071319 2.000000e-03 54.7
19 TraesCS5D01G047800 chr5B 85.989 885 98 16 3008 3872 46746602 46745724 0.000000e+00 924.0
20 TraesCS5D01G047800 chr5B 83.512 1025 122 32 3008 3995 46635320 46634306 0.000000e+00 913.0
21 TraesCS5D01G047800 chr5B 86.020 794 87 18 3008 3787 48147046 48147829 0.000000e+00 830.0
22 TraesCS5D01G047800 chr5B 83.531 759 116 6 2057 2814 46747354 46746604 0.000000e+00 701.0
23 TraesCS5D01G047800 chr5B 83.012 777 104 21 3008 3778 47127417 47126663 0.000000e+00 678.0
24 TraesCS5D01G047800 chr5B 82.654 761 116 6 2055 2808 47128176 47127425 0.000000e+00 660.0
25 TraesCS5D01G047800 chr5B 82.237 760 113 13 2048 2805 48146296 48147035 1.760000e-178 636.0
26 TraesCS5D01G047800 chr5B 82.058 758 115 12 2059 2814 46152953 46152215 1.060000e-175 627.0
27 TraesCS5D01G047800 chr5B 88.976 508 53 3 3008 3513 46767749 46767243 3.820000e-175 625.0
28 TraesCS5D01G047800 chr5B 88.655 238 18 6 4062 4298 46634368 46634139 9.520000e-72 281.0
29 TraesCS5D01G047800 chr5B 86.466 266 16 1 1 266 46877548 46877303 1.590000e-69 274.0
30 TraesCS5D01G047800 chr5B 82.298 322 33 13 4062 4361 46766348 46766029 1.600000e-64 257.0
31 TraesCS5D01G047800 chr5B 82.186 247 38 4 1274 1516 380649909 380649665 1.640000e-49 207.0
32 TraesCS5D01G047800 chr5B 92.157 102 8 0 291 392 46877240 46877139 1.300000e-30 145.0
33 TraesCS5D01G047800 chr5B 76.543 243 34 17 984 1209 638648759 638648523 1.320000e-20 111.0
34 TraesCS5D01G047800 chr5B 87.692 65 3 1 124 188 46877303 46877244 2.240000e-08 71.3
35 TraesCS5D01G047800 chr2B 85.112 759 95 15 3008 3760 731711269 731712015 0.000000e+00 760.0
36 TraesCS5D01G047800 chr2B 77.273 506 81 16 1265 1760 600510847 600510366 2.670000e-67 267.0
37 TraesCS5D01G047800 chr2B 74.500 600 119 24 1227 1800 766244367 766243776 3.500000e-56 230.0
38 TraesCS5D01G047800 chr2B 90.411 73 7 0 4363 4435 731713159 731713231 3.700000e-16 97.1
39 TraesCS5D01G047800 chr3D 81.550 542 79 20 1267 1799 101546610 101547139 1.160000e-115 427.0
40 TraesCS5D01G047800 chr3D 83.911 404 48 11 1265 1659 570048693 570048298 1.980000e-98 370.0
41 TraesCS5D01G047800 chr3D 86.364 110 12 3 984 1092 334638619 334638726 2.840000e-22 117.0
42 TraesCS5D01G047800 chr3A 82.470 502 63 17 1274 1760 458808638 458808147 2.500000e-112 416.0
43 TraesCS5D01G047800 chr3A 94.444 36 1 1 1770 1804 19567129 19567164 2.000000e-03 54.7
44 TraesCS5D01G047800 chr4A 80.268 522 60 22 1315 1799 84944969 84944454 1.990000e-93 353.0
45 TraesCS5D01G047800 chr4A 77.756 499 88 16 1317 1800 614421414 614420924 7.360000e-73 285.0
46 TraesCS5D01G047800 chr4A 81.275 251 32 11 1340 1579 732851334 732851088 5.940000e-44 189.0
47 TraesCS5D01G047800 chr4A 84.286 70 8 3 753 821 471471142 471471075 1.040000e-06 65.8
48 TraesCS5D01G047800 chr4A 85.714 63 6 3 763 823 666684297 666684358 3.750000e-06 63.9
49 TraesCS5D01G047800 chr7D 80.841 428 55 17 1397 1804 543242995 543243415 1.210000e-80 311.0
50 TraesCS5D01G047800 chr7D 86.087 115 12 3 981 1093 453132029 453132141 2.200000e-23 121.0
51 TraesCS5D01G047800 chr7D 100.000 31 0 0 1773 1803 626923800 626923770 1.750000e-04 58.4
52 TraesCS5D01G047800 chr2D 78.018 555 66 24 1264 1786 592290804 592290274 9.450000e-77 298.0
53 TraesCS5D01G047800 chr2D 78.215 381 46 22 1238 1606 14773640 14773995 4.560000e-50 209.0
54 TraesCS5D01G047800 chr2D 82.353 238 35 7 1580 1812 27551787 27552022 2.740000e-47 200.0
55 TraesCS5D01G047800 chr2D 85.315 143 18 3 4353 4495 601429587 601429726 1.300000e-30 145.0
56 TraesCS5D01G047800 chr2D 83.108 148 14 7 953 1091 592291258 592291113 1.700000e-24 124.0
57 TraesCS5D01G047800 chr2D 86.607 112 12 3 984 1093 43234001 43234111 2.200000e-23 121.0
58 TraesCS5D01G047800 chr2D 100.000 38 0 0 1107 1144 10215296 10215333 2.240000e-08 71.3
59 TraesCS5D01G047800 chr1A 76.951 551 64 28 1274 1799 571292812 571292300 5.770000e-64 255.0
60 TraesCS5D01G047800 chr1A 87.156 109 11 3 984 1091 3641605 3641711 2.200000e-23 121.0
61 TraesCS5D01G047800 chr1A 82.857 105 10 5 1111 1209 531022157 531022055 2.230000e-13 87.9
62 TraesCS5D01G047800 chr1A 86.667 60 5 3 764 821 144860662 144860720 3.750000e-06 63.9
63 TraesCS5D01G047800 chr6D 79.718 355 53 12 1267 1606 29760108 29759758 5.810000e-59 239.0
64 TraesCS5D01G047800 chr6D 80.702 114 9 9 1112 1214 472719029 472719140 4.820000e-10 76.8
65 TraesCS5D01G047800 chr6D 87.037 54 5 2 2821 2872 456115125 456115072 4.860000e-05 60.2
66 TraesCS5D01G047800 chr6D 85.000 60 6 3 764 821 307367343 307367285 1.750000e-04 58.4
67 TraesCS5D01G047800 chr6D 85.000 60 6 3 764 821 310642681 310642739 1.750000e-04 58.4
68 TraesCS5D01G047800 chr7A 84.100 239 28 8 1576 1807 412731906 412732141 5.850000e-54 222.0
69 TraesCS5D01G047800 chr7A 84.651 215 27 6 1598 1808 71072683 71072895 4.560000e-50 209.0
70 TraesCS5D01G047800 chr7A 82.812 128 11 5 1099 1216 139194968 139195094 2.210000e-18 104.0
71 TraesCS5D01G047800 chr7A 91.071 56 3 2 1107 1160 234853625 234853570 1.730000e-09 75.0
72 TraesCS5D01G047800 chr6A 81.356 236 33 9 1579 1807 180185419 180185188 9.930000e-42 182.0
73 TraesCS5D01G047800 chr6B 80.408 245 29 12 950 1177 67537467 67537709 7.730000e-38 169.0
74 TraesCS5D01G047800 chr6B 87.387 111 11 3 984 1093 130298556 130298448 1.700000e-24 124.0
75 TraesCS5D01G047800 chr2A 87.970 133 16 0 4363 4495 734802416 734802548 1.670000e-34 158.0
76 TraesCS5D01G047800 chr2A 80.220 91 16 2 1718 1806 2930262 2930352 2.900000e-07 67.6
77 TraesCS5D01G047800 chrUn 87.826 115 11 3 981 1093 341982603 341982716 1.010000e-26 132.0
78 TraesCS5D01G047800 chr1B 86.486 111 13 2 984 1093 610899844 610899735 2.200000e-23 121.0
79 TraesCS5D01G047800 chr1D 82.677 127 6 11 1099 1211 288793615 288793739 1.030000e-16 99.0
80 TraesCS5D01G047800 chr1D 85.000 60 6 3 764 821 137224299 137224357 1.750000e-04 58.4
81 TraesCS5D01G047800 chr1D 85.000 60 6 3 764 821 307006371 307006429 1.750000e-04 58.4
82 TraesCS5D01G047800 chr4D 95.556 45 1 1 768 811 487791269 487791225 2.240000e-08 71.3
83 TraesCS5D01G047800 chr4B 97.368 38 1 0 1108 1145 15599740 15599703 1.040000e-06 65.8
84 TraesCS5D01G047800 chr7B 100.000 31 0 0 953 983 746083955 746083925 1.750000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G047800 chr5D 45871024 45875518 4494 False 2917.666667 8301 98.010000 1 4495 3 chr5D.!!$F1 4494
1 TraesCS5D01G047800 chr5D 46274319 46275098 779 True 822.000000 822 85.932000 3012 3787 1 chr5D.!!$R3 775
2 TraesCS5D01G047800 chr5D 46127909 46128590 681 True 673.000000 673 84.457000 2137 2818 1 chr5D.!!$R2 681
3 TraesCS5D01G047800 chr5D 46087341 46087957 616 True 604.000000 604 84.380000 2189 2808 1 chr5D.!!$R1 619
4 TraesCS5D01G047800 chr5A 36948215 36954095 5880 True 880.000000 4309 92.779571 124 4495 7 chr5A.!!$R3 4371
5 TraesCS5D01G047800 chr5A 37400818 37402282 1464 True 775.000000 857 85.816000 2130 3784 2 chr5A.!!$R4 1654
6 TraesCS5D01G047800 chr5A 36942301 36942966 665 True 619.000000 619 83.483000 2154 2818 1 chr5A.!!$R1 664
7 TraesCS5D01G047800 chr5A 36825151 36826148 997 True 488.000000 634 85.675500 3007 3998 2 chr5A.!!$R2 991
8 TraesCS5D01G047800 chr5B 46745724 46747354 1630 True 812.500000 924 84.760000 2057 3872 2 chr5B.!!$R5 1815
9 TraesCS5D01G047800 chr5B 48146296 48147829 1533 False 733.000000 830 84.128500 2048 3787 2 chr5B.!!$F1 1739
10 TraesCS5D01G047800 chr5B 47126663 47128176 1513 True 669.000000 678 82.833000 2055 3778 2 chr5B.!!$R8 1723
11 TraesCS5D01G047800 chr5B 46152215 46152953 738 True 627.000000 627 82.058000 2059 2814 1 chr5B.!!$R1 755
12 TraesCS5D01G047800 chr5B 46634139 46635320 1181 True 597.000000 913 86.083500 3008 4298 2 chr5B.!!$R4 1290
13 TraesCS5D01G047800 chr5B 46766029 46767749 1720 True 441.000000 625 85.637000 3008 4361 2 chr5B.!!$R6 1353
14 TraesCS5D01G047800 chr2B 731711269 731713231 1962 False 428.550000 760 87.761500 3008 4435 2 chr2B.!!$F1 1427
15 TraesCS5D01G047800 chr2B 766243776 766244367 591 True 230.000000 230 74.500000 1227 1800 1 chr2B.!!$R2 573
16 TraesCS5D01G047800 chr3D 101546610 101547139 529 False 427.000000 427 81.550000 1267 1799 1 chr3D.!!$F1 532
17 TraesCS5D01G047800 chr4A 84944454 84944969 515 True 353.000000 353 80.268000 1315 1799 1 chr4A.!!$R1 484
18 TraesCS5D01G047800 chr2D 592290274 592291258 984 True 211.000000 298 80.563000 953 1786 2 chr2D.!!$R1 833
19 TraesCS5D01G047800 chr1A 571292300 571292812 512 True 255.000000 255 76.951000 1274 1799 1 chr1A.!!$R2 525

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
239 240 0.038455 AGTCTAGGTGTCTGGCTCGT 59.962 55.000 0.00 0.00 0.00 4.18 F
558 559 0.107643 GTGATTGGCTAGCCCTCCTC 59.892 60.000 30.81 20.20 34.56 3.71 F
559 560 0.326522 TGATTGGCTAGCCCTCCTCA 60.327 55.000 30.81 22.33 34.56 3.86 F
698 699 0.396060 GGAGATCCAGAGGTGGCATC 59.604 60.000 0.00 0.00 44.60 3.91 F
1105 1205 0.673333 CCCATGCGCTCTACACAACA 60.673 55.000 9.73 0.00 0.00 3.33 F
1899 2287 0.820871 AACTTTTGCAGCCGTTTGGA 59.179 45.000 0.00 0.00 37.49 3.53 F
2211 3894 1.368950 GAGGTGCACAGCAGAGACA 59.631 57.895 20.43 0.00 40.08 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1093 1157 0.600255 ACAGGCGTGTTGTGTAGAGC 60.600 55.000 6.15 0.0 30.3 4.09 R
1981 3657 1.071542 TGTGCGGAGGTGAGAAATTGA 59.928 47.619 0.00 0.0 0.0 2.57 R
2009 3685 1.913262 GAGGGTTTGGGCAAAGGGG 60.913 63.158 0.00 0.0 0.0 4.79 R
2016 3692 2.434359 CGAGACGAGGGTTTGGGC 60.434 66.667 0.00 0.0 0.0 5.36 R
2715 4405 2.024941 AGCAGAAAATACCTCCCCTTGG 60.025 50.000 0.00 0.0 0.0 3.61 R
3211 4902 2.048444 AATATGGCAGCCACAGTCTG 57.952 50.000 19.10 0.0 35.8 3.51 R
3506 5199 6.199937 AGAAAATGAGCGTGCTGAATTTAT 57.800 33.333 0.00 0.0 0.0 1.40 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
21 22 4.911514 GGGGCTTTTCTATAAAATCGCA 57.088 40.909 6.57 0.00 36.13 5.10
22 23 5.257082 GGGGCTTTTCTATAAAATCGCAA 57.743 39.130 6.57 0.00 36.13 4.85
23 24 5.281727 GGGGCTTTTCTATAAAATCGCAAG 58.718 41.667 6.57 0.00 36.13 4.01
24 25 5.281727 GGGCTTTTCTATAAAATCGCAAGG 58.718 41.667 1.13 0.00 35.15 3.61
25 26 5.281727 GGCTTTTCTATAAAATCGCAAGGG 58.718 41.667 0.00 0.00 34.18 3.95
26 27 5.067283 GGCTTTTCTATAAAATCGCAAGGGA 59.933 40.000 0.00 0.00 34.18 4.20
27 28 5.971792 GCTTTTCTATAAAATCGCAAGGGAC 59.028 40.000 0.00 0.00 34.18 4.46
28 29 5.728351 TTTCTATAAAATCGCAAGGGACG 57.272 39.130 0.00 0.00 38.47 4.79
29 30 3.724374 TCTATAAAATCGCAAGGGACGG 58.276 45.455 0.00 0.00 38.47 4.79
30 31 1.675552 ATAAAATCGCAAGGGACGGG 58.324 50.000 0.00 0.00 38.47 5.28
31 32 1.027792 TAAAATCGCAAGGGACGGGC 61.028 55.000 0.00 0.00 38.47 6.13
32 33 3.561120 AAATCGCAAGGGACGGGCA 62.561 57.895 0.00 0.00 38.47 5.36
33 34 3.976701 AATCGCAAGGGACGGGCAG 62.977 63.158 0.00 0.00 38.47 4.85
35 36 4.697756 CGCAAGGGACGGGCAGAA 62.698 66.667 0.00 0.00 32.80 3.02
36 37 2.282180 GCAAGGGACGGGCAGAAA 60.282 61.111 0.00 0.00 32.80 2.52
37 38 2.626780 GCAAGGGACGGGCAGAAAC 61.627 63.158 0.00 0.00 32.80 2.78
38 39 1.228124 CAAGGGACGGGCAGAAACA 60.228 57.895 0.00 0.00 0.00 2.83
39 40 1.228154 AAGGGACGGGCAGAAACAC 60.228 57.895 0.00 0.00 0.00 3.32
40 41 1.705997 AAGGGACGGGCAGAAACACT 61.706 55.000 0.00 0.00 0.00 3.55
41 42 1.228154 GGGACGGGCAGAAACACTT 60.228 57.895 0.00 0.00 0.00 3.16
42 43 1.235281 GGGACGGGCAGAAACACTTC 61.235 60.000 0.00 0.00 0.00 3.01
43 44 1.235281 GGACGGGCAGAAACACTTCC 61.235 60.000 0.00 0.00 31.28 3.46
44 45 1.228154 ACGGGCAGAAACACTTCCC 60.228 57.895 0.00 0.00 46.30 3.97
45 46 1.971695 CGGGCAGAAACACTTCCCC 60.972 63.158 0.00 0.00 46.92 4.81
46 47 1.606601 GGGCAGAAACACTTCCCCC 60.607 63.158 0.00 0.00 44.51 5.40
47 48 1.460699 GGCAGAAACACTTCCCCCT 59.539 57.895 0.00 0.00 31.28 4.79
48 49 0.178961 GGCAGAAACACTTCCCCCTT 60.179 55.000 0.00 0.00 31.28 3.95
49 50 1.704641 GCAGAAACACTTCCCCCTTT 58.295 50.000 0.00 0.00 31.28 3.11
50 51 2.490168 GGCAGAAACACTTCCCCCTTTA 60.490 50.000 0.00 0.00 31.28 1.85
51 52 3.431415 GCAGAAACACTTCCCCCTTTAT 58.569 45.455 0.00 0.00 31.28 1.40
52 53 3.832490 GCAGAAACACTTCCCCCTTTATT 59.168 43.478 0.00 0.00 31.28 1.40
53 54 5.014202 GCAGAAACACTTCCCCCTTTATTA 58.986 41.667 0.00 0.00 31.28 0.98
54 55 5.479027 GCAGAAACACTTCCCCCTTTATTAA 59.521 40.000 0.00 0.00 31.28 1.40
55 56 6.014925 GCAGAAACACTTCCCCCTTTATTAAA 60.015 38.462 0.00 0.00 31.28 1.52
56 57 7.310423 GCAGAAACACTTCCCCCTTTATTAAAT 60.310 37.037 0.00 0.00 31.28 1.40
57 58 9.250246 CAGAAACACTTCCCCCTTTATTAAATA 57.750 33.333 0.00 0.00 31.28 1.40
58 59 9.475620 AGAAACACTTCCCCCTTTATTAAATAG 57.524 33.333 0.00 0.00 31.28 1.73
59 60 8.603898 AAACACTTCCCCCTTTATTAAATAGG 57.396 34.615 0.00 0.00 0.00 2.57
60 61 7.293326 ACACTTCCCCCTTTATTAAATAGGT 57.707 36.000 0.00 0.00 0.00 3.08
61 62 8.410000 ACACTTCCCCCTTTATTAAATAGGTA 57.590 34.615 0.00 0.00 0.00 3.08
62 63 8.277197 ACACTTCCCCCTTTATTAAATAGGTAC 58.723 37.037 0.00 0.00 0.00 3.34
63 64 8.276477 CACTTCCCCCTTTATTAAATAGGTACA 58.724 37.037 0.00 0.00 0.00 2.90
64 65 8.277197 ACTTCCCCCTTTATTAAATAGGTACAC 58.723 37.037 0.00 0.00 0.00 2.90
65 66 7.768324 TCCCCCTTTATTAAATAGGTACACA 57.232 36.000 0.00 0.00 0.00 3.72
66 67 7.576403 TCCCCCTTTATTAAATAGGTACACAC 58.424 38.462 0.00 0.00 0.00 3.82
67 68 7.184204 TCCCCCTTTATTAAATAGGTACACACA 59.816 37.037 0.00 0.00 0.00 3.72
68 69 7.283807 CCCCCTTTATTAAATAGGTACACACAC 59.716 40.741 0.00 0.00 0.00 3.82
69 70 7.830201 CCCCTTTATTAAATAGGTACACACACA 59.170 37.037 0.00 0.00 0.00 3.72
70 71 8.671028 CCCTTTATTAAATAGGTACACACACAC 58.329 37.037 0.00 0.00 0.00 3.82
71 72 9.221933 CCTTTATTAAATAGGTACACACACACA 57.778 33.333 0.00 0.00 0.00 3.72
73 74 9.557061 TTTATTAAATAGGTACACACACACACA 57.443 29.630 0.00 0.00 0.00 3.72
74 75 6.847956 TTAAATAGGTACACACACACACAC 57.152 37.500 0.00 0.00 0.00 3.82
75 76 4.409718 AATAGGTACACACACACACACA 57.590 40.909 0.00 0.00 0.00 3.72
76 77 4.617253 ATAGGTACACACACACACACAT 57.383 40.909 0.00 0.00 0.00 3.21
77 78 5.731957 ATAGGTACACACACACACACATA 57.268 39.130 0.00 0.00 0.00 2.29
78 79 4.617253 AGGTACACACACACACACATAT 57.383 40.909 0.00 0.00 0.00 1.78
79 80 5.731957 AGGTACACACACACACACATATA 57.268 39.130 0.00 0.00 0.00 0.86
80 81 6.294361 AGGTACACACACACACACATATAT 57.706 37.500 0.00 0.00 0.00 0.86
81 82 7.412853 AGGTACACACACACACACATATATA 57.587 36.000 0.00 0.00 0.00 0.86
82 83 8.018537 AGGTACACACACACACACATATATAT 57.981 34.615 0.00 0.00 0.00 0.86
83 84 9.138596 AGGTACACACACACACACATATATATA 57.861 33.333 0.00 0.00 0.00 0.86
84 85 9.923143 GGTACACACACACACACATATATATAT 57.077 33.333 0.00 0.00 0.00 0.86
109 110 5.692115 ATATATATGAATCACCACCGCCA 57.308 39.130 0.00 0.00 0.00 5.69
110 111 1.967319 ATATGAATCACCACCGCCAC 58.033 50.000 0.00 0.00 0.00 5.01
111 112 0.107410 TATGAATCACCACCGCCACC 60.107 55.000 0.00 0.00 0.00 4.61
112 113 3.124921 GAATCACCACCGCCACCG 61.125 66.667 0.00 0.00 0.00 4.94
122 123 2.202570 CGCCACCGGTTACTCTCG 60.203 66.667 2.97 0.00 0.00 4.04
123 124 2.508663 GCCACCGGTTACTCTCGC 60.509 66.667 2.97 0.00 0.00 5.03
124 125 3.003113 GCCACCGGTTACTCTCGCT 62.003 63.158 2.97 0.00 0.00 4.93
125 126 1.590147 CCACCGGTTACTCTCGCTT 59.410 57.895 2.97 0.00 0.00 4.68
126 127 0.458025 CCACCGGTTACTCTCGCTTC 60.458 60.000 2.97 0.00 0.00 3.86
167 168 2.530958 GATGCGGAGGAAAACCCCGA 62.531 60.000 16.05 5.93 45.58 5.14
170 171 2.590114 CGGAGGAAAACCCCGACCT 61.590 63.158 0.00 0.00 45.58 3.85
183 184 4.495565 ACCCCGACCTAATATGATTGGTA 58.504 43.478 0.00 0.00 32.30 3.25
190 191 7.386851 CGACCTAATATGATTGGTATTGGAGT 58.613 38.462 0.00 0.00 32.30 3.85
197 198 4.016444 TGATTGGTATTGGAGTTTGAGCC 58.984 43.478 0.00 0.00 0.00 4.70
205 206 0.460459 GGAGTTTGAGCCGTCCTAGC 60.460 60.000 0.00 0.00 0.00 3.42
207 208 0.905357 AGTTTGAGCCGTCCTAGCAT 59.095 50.000 0.00 0.00 0.00 3.79
213 214 1.869767 GAGCCGTCCTAGCATTGAATG 59.130 52.381 0.00 0.00 0.00 2.67
216 217 1.134098 CCGTCCTAGCATTGAATGGGT 60.134 52.381 7.35 0.00 0.00 4.51
237 238 4.496360 GTTTTAGTCTAGGTGTCTGGCTC 58.504 47.826 0.00 0.00 0.00 4.70
239 240 0.038455 AGTCTAGGTGTCTGGCTCGT 59.962 55.000 0.00 0.00 0.00 4.18
242 243 1.228769 TAGGTGTCTGGCTCGTGGT 60.229 57.895 0.00 0.00 0.00 4.16
253 254 3.362399 CTCGTGGTGCAGAGGCGAT 62.362 63.158 0.00 0.00 45.35 4.58
320 321 3.274095 TCGGTGATGTTGATTGGCATA 57.726 42.857 0.00 0.00 0.00 3.14
323 324 3.817084 CGGTGATGTTGATTGGCATAGAT 59.183 43.478 0.00 0.00 0.00 1.98
331 332 3.732212 TGATTGGCATAGATGGAGAACG 58.268 45.455 0.00 0.00 0.00 3.95
339 340 1.924731 AGATGGAGAACGTGTGGAGA 58.075 50.000 0.00 0.00 0.00 3.71
344 345 2.076863 GGAGAACGTGTGGAGATTTGG 58.923 52.381 0.00 0.00 0.00 3.28
350 351 1.826385 GTGTGGAGATTTGGTCAGGG 58.174 55.000 0.00 0.00 0.00 4.45
357 358 1.177401 GATTTGGTCAGGGCCAGAAC 58.823 55.000 7.09 7.09 40.01 3.01
360 361 2.067932 TTGGTCAGGGCCAGAACAGG 62.068 60.000 16.65 0.00 40.01 4.00
381 382 1.600413 GCCCTGCTTTTGTCTGTTTCG 60.600 52.381 0.00 0.00 0.00 3.46
434 435 6.075984 GGGGAGTGGATAGTGACTATTTCTA 58.924 44.000 6.56 0.00 0.00 2.10
459 460 5.489792 TTAGTCATCTGGCTTCTCTGTTT 57.510 39.130 0.00 0.00 0.00 2.83
491 492 1.164041 CCAACTTTGCCTTCGTCGGT 61.164 55.000 0.00 0.00 0.00 4.69
539 540 3.633986 GCTTTGTCTGGAAATATCAGGGG 59.366 47.826 0.00 0.00 33.36 4.79
542 543 3.459828 TGTCTGGAAATATCAGGGGTGA 58.540 45.455 0.00 0.00 33.36 4.02
543 544 4.047166 TGTCTGGAAATATCAGGGGTGAT 58.953 43.478 0.00 0.00 33.36 3.06
544 545 4.478317 TGTCTGGAAATATCAGGGGTGATT 59.522 41.667 0.00 0.00 33.36 2.57
545 546 4.823989 GTCTGGAAATATCAGGGGTGATTG 59.176 45.833 0.00 0.00 33.36 2.67
546 547 4.141181 TCTGGAAATATCAGGGGTGATTGG 60.141 45.833 0.00 0.00 33.36 3.16
547 548 2.893489 GGAAATATCAGGGGTGATTGGC 59.107 50.000 0.00 0.00 0.00 4.52
548 549 3.437052 GGAAATATCAGGGGTGATTGGCT 60.437 47.826 0.00 0.00 0.00 4.75
549 550 4.202567 GGAAATATCAGGGGTGATTGGCTA 60.203 45.833 0.00 0.00 0.00 3.93
550 551 4.647564 AATATCAGGGGTGATTGGCTAG 57.352 45.455 0.00 0.00 0.00 3.42
551 552 0.475906 ATCAGGGGTGATTGGCTAGC 59.524 55.000 6.04 6.04 0.00 3.42
552 553 1.152881 CAGGGGTGATTGGCTAGCC 60.153 63.158 27.71 27.71 0.00 3.93
553 554 2.195956 GGGGTGATTGGCTAGCCC 59.804 66.667 30.81 16.10 46.26 5.19
554 555 3.335711 GGGTGATTGGCTAGCCCT 58.664 61.111 30.81 18.25 36.49 5.19
555 556 1.149401 GGGTGATTGGCTAGCCCTC 59.851 63.158 30.81 25.23 36.49 4.30
556 557 1.149401 GGTGATTGGCTAGCCCTCC 59.851 63.158 30.81 20.28 34.56 4.30
557 558 1.348775 GGTGATTGGCTAGCCCTCCT 61.349 60.000 30.81 12.50 34.56 3.69
558 559 0.107643 GTGATTGGCTAGCCCTCCTC 59.892 60.000 30.81 20.20 34.56 3.71
559 560 0.326522 TGATTGGCTAGCCCTCCTCA 60.327 55.000 30.81 22.33 34.56 3.86
562 563 0.548031 TTGGCTAGCCCTCCTCAATG 59.452 55.000 30.81 0.00 34.56 2.82
572 573 3.615155 CCCTCCTCAATGGTTTCTTCTC 58.385 50.000 0.00 0.00 37.07 2.87
573 574 3.265479 CCCTCCTCAATGGTTTCTTCTCT 59.735 47.826 0.00 0.00 37.07 3.10
577 578 3.009473 CCTCAATGGTTTCTTCTCTGGGA 59.991 47.826 0.00 0.00 0.00 4.37
582 583 2.507886 TGGTTTCTTCTCTGGGACAACA 59.492 45.455 0.00 0.00 38.70 3.33
586 587 3.703001 TCTTCTCTGGGACAACAATCC 57.297 47.619 0.00 0.00 38.70 3.01
595 596 4.513442 TGGGACAACAATCCGATCTTTAG 58.487 43.478 0.00 0.00 39.97 1.85
598 599 5.064834 GGGACAACAATCCGATCTTTAGTTC 59.935 44.000 0.00 0.00 39.97 3.01
610 611 1.990563 CTTTAGTTCGTTGTCGCCGAT 59.009 47.619 0.00 0.00 36.96 4.18
626 627 1.438651 CGATTTCTGGCTTTGACCGA 58.561 50.000 0.00 0.00 0.00 4.69
636 637 2.612972 GGCTTTGACCGATGACTTCTCA 60.613 50.000 0.00 0.00 0.00 3.27
643 644 4.021104 TGACCGATGACTTCTCATCTGTTT 60.021 41.667 8.57 0.00 46.00 2.83
646 647 6.080173 ACCGATGACTTCTCATCTGTTTCAC 61.080 44.000 8.64 0.00 44.57 3.18
653 654 6.302269 ACTTCTCATCTGTTTCACCAAGAAT 58.698 36.000 0.00 0.00 35.83 2.40
656 657 6.768483 TCTCATCTGTTTCACCAAGAATGTA 58.232 36.000 0.00 0.00 35.83 2.29
668 669 4.103785 ACCAAGAATGTATCCCTGGATCTG 59.896 45.833 0.99 0.00 35.83 2.90
669 670 4.349048 CCAAGAATGTATCCCTGGATCTGA 59.651 45.833 0.99 0.00 34.74 3.27
670 671 5.512749 CCAAGAATGTATCCCTGGATCTGAG 60.513 48.000 0.99 0.00 34.74 3.35
671 672 4.166539 AGAATGTATCCCTGGATCTGAGG 58.833 47.826 0.99 4.74 36.17 3.86
679 680 1.406069 CCTGGATCTGAGGGTGTTTCG 60.406 57.143 3.95 0.00 0.00 3.46
688 689 0.905357 AGGGTGTTTCGGAGATCCAG 59.095 55.000 0.00 0.00 35.04 3.86
692 693 1.550976 GTGTTTCGGAGATCCAGAGGT 59.449 52.381 0.00 0.00 35.04 3.85
693 694 1.550524 TGTTTCGGAGATCCAGAGGTG 59.449 52.381 0.00 0.00 35.04 4.00
698 699 0.396060 GGAGATCCAGAGGTGGCATC 59.604 60.000 0.00 0.00 44.60 3.91
704 705 1.227205 CAGAGGTGGCATCGAGCTC 60.227 63.158 2.73 2.73 44.79 4.09
713 714 1.478622 GCATCGAGCTCTTCTCACGC 61.479 60.000 12.85 0.97 41.98 5.34
718 719 4.778415 GCTCTTCTCACGCGCCGA 62.778 66.667 5.73 1.41 0.00 5.54
731 732 2.097038 CGCCGAGTGCAGAAGGAAG 61.097 63.158 5.54 0.00 41.33 3.46
738 739 2.999355 GAGTGCAGAAGGAAGACATCAC 59.001 50.000 0.00 0.00 0.00 3.06
758 759 9.381038 ACATCACTGATATACCCAATAACTAGT 57.619 33.333 0.00 0.00 0.00 2.57
836 837 4.830600 GGAACTACCAAAACATCAAAGGGA 59.169 41.667 0.00 0.00 38.79 4.20
840 841 6.790319 ACTACCAAAACATCAAAGGGAGTAT 58.210 36.000 0.00 0.00 41.67 2.12
858 859 9.275572 AGGGAGTATTTTGTAAGTATGGTCTTA 57.724 33.333 0.00 0.00 0.00 2.10
903 957 3.350833 ACTATCTTGGCCTTTGAAGCAG 58.649 45.455 3.32 2.70 0.00 4.24
913 967 3.480470 CCTTTGAAGCAGGAGAAACTCA 58.520 45.455 0.00 0.00 32.41 3.41
941 995 9.353999 GTTGATTAAGTCTTGTCAACAAAACTT 57.646 29.630 25.41 16.36 45.75 2.66
942 996 9.921637 TTGATTAAGTCTTGTCAACAAAACTTT 57.078 25.926 17.11 3.60 42.56 2.66
1003 1067 1.750193 ACGTCATCGAAATTGCCCAT 58.250 45.000 0.00 0.00 40.62 4.00
1039 1103 1.332144 TACCCACCGATGCCACCTAC 61.332 60.000 0.00 0.00 0.00 3.18
1103 1203 1.745115 GCCCATGCGCTCTACACAA 60.745 57.895 9.73 0.00 0.00 3.33
1105 1205 0.673333 CCCATGCGCTCTACACAACA 60.673 55.000 9.73 0.00 0.00 3.33
1267 1463 7.272978 TGGAAACAAATGTTCGGGAAATAAAA 58.727 30.769 0.00 0.00 37.25 1.52
1408 1660 9.726034 GTTTATTGATTCGTAAAATGTTTGCTG 57.274 29.630 0.00 0.00 0.00 4.41
1424 1676 7.410800 TGTTTGCTGATTCAAAAATGATCAC 57.589 32.000 0.00 0.00 37.65 3.06
1494 1750 9.495572 TTTAACATTATTCCACCAATTTCCAAC 57.504 29.630 0.00 0.00 0.00 3.77
1516 1772 6.633668 ACAAATGTTCGTCGATTCTAGAAG 57.366 37.500 11.53 0.00 0.00 2.85
1523 1779 3.099362 CGTCGATTCTAGAAGTGTTCGG 58.901 50.000 20.38 7.05 34.02 4.30
1813 2200 9.973246 CATTTTGCTAGTACTAATAACACACTG 57.027 33.333 3.76 0.00 0.00 3.66
1818 2205 9.630098 TGCTAGTACTAATAACACACTGTTTAC 57.370 33.333 3.76 0.00 41.45 2.01
1834 2221 9.005777 ACACTGTTTACTTTTGTACTTCTTTGA 57.994 29.630 0.00 0.00 34.15 2.69
1893 2281 5.118510 CCAAATAGTAAAACTTTTGCAGCCG 59.881 40.000 5.30 0.00 31.29 5.52
1899 2287 0.820871 AACTTTTGCAGCCGTTTGGA 59.179 45.000 0.00 0.00 37.49 3.53
1920 3583 4.991056 GGAATGCAGGAAAAGGAGAAAAAC 59.009 41.667 0.00 0.00 0.00 2.43
1940 3603 9.741647 GAAAAACATGAGAACTTCTTGAGAAAT 57.258 29.630 0.00 0.00 35.51 2.17
1996 3672 5.983540 AGTACATCTCAATTTCTCACCTCC 58.016 41.667 0.00 0.00 0.00 4.30
2009 3685 1.673920 TCACCTCCGCACAAAACTTTC 59.326 47.619 0.00 0.00 0.00 2.62
2016 3692 2.200899 CGCACAAAACTTTCCCCTTTG 58.799 47.619 0.00 0.00 36.37 2.77
2125 3801 3.158648 CGACCCGCCCCATCCTTA 61.159 66.667 0.00 0.00 0.00 2.69
2128 3804 3.886001 CCCGCCCCATCCTTACCC 61.886 72.222 0.00 0.00 0.00 3.69
2211 3894 1.368950 GAGGTGCACAGCAGAGACA 59.631 57.895 20.43 0.00 40.08 3.41
2508 4198 2.935955 CCACAAGTGTTCGACCGC 59.064 61.111 0.00 0.00 0.00 5.68
2564 4254 4.035612 AGACCACTGCTGAAGTAGAGTA 57.964 45.455 2.19 0.00 36.83 2.59
2619 4309 4.632153 AGTGTGAGGTCACTGTTATCAAC 58.368 43.478 11.31 0.00 45.40 3.18
2631 4321 7.111593 GTCACTGTTATCAACGAAACATTTGAC 59.888 37.037 11.28 11.28 39.15 3.18
2670 4360 3.541632 TGACCTTTCGGATAATCTTGCC 58.458 45.455 0.00 0.00 0.00 4.52
2715 4405 1.461127 GCAGACGTGACATTCAAGGTC 59.539 52.381 0.00 0.00 34.32 3.85
2884 4575 3.854784 GCATTTCCAACAAGTGACAGCTC 60.855 47.826 0.00 0.00 0.00 4.09
2976 4667 3.509575 TGGTTTGCTTACCTATTGGCAAG 59.490 43.478 5.96 2.07 43.84 4.01
3005 4696 2.341176 CAGCAAACCAAGCAGCCC 59.659 61.111 0.00 0.00 0.00 5.19
3082 4773 5.363101 TCATCTACACAGATTCAATGCCTC 58.637 41.667 0.00 0.00 39.62 4.70
3102 4793 3.574749 TCCCATGAGAGATCTTGAGGAG 58.425 50.000 0.00 0.00 0.00 3.69
3211 4902 4.633126 TGCTATGCAAGAGTCTTGATGTTC 59.367 41.667 32.39 16.65 34.76 3.18
3506 5199 5.147330 TCGAGAAGGCAATTAAGTCTTGA 57.853 39.130 0.00 0.00 32.72 3.02
3619 5885 4.410883 TCTTTTGGAGGAACTGAGTTGGTA 59.589 41.667 0.90 0.00 41.55 3.25
3707 5977 3.149981 AGCTCACCTAGTTGCCTTTTTC 58.850 45.455 0.00 0.00 0.00 2.29
3779 6121 6.486657 TGAGTTCTTGGACATAACTTTTGAGG 59.513 38.462 0.00 0.00 33.72 3.86
3888 6941 0.764890 AACCTTGGTAGCACAGCAGA 59.235 50.000 0.00 0.00 35.70 4.26
3953 7019 7.117523 CCAAACTACTTTGAGATCAGAGAACAG 59.882 40.741 7.33 4.36 39.43 3.16
3955 7021 5.777732 ACTACTTTGAGATCAGAGAACAGGT 59.222 40.000 7.33 0.00 32.92 4.00
4249 7325 8.344939 ACATAATTTAGGGAGGGATTAAGTGA 57.655 34.615 0.00 0.00 0.00 3.41
4349 7436 1.915141 GGATCGAATCCCCTACGGTA 58.085 55.000 0.00 0.00 43.88 4.02
4484 7642 9.871238 GGTAATATGTTCGTGATACCTTCATAT 57.129 33.333 0.00 0.00 36.54 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.911514 TGCGATTTTATAGAAAAGCCCC 57.088 40.909 5.33 0.00 37.61 5.80
1 2 5.281727 CCTTGCGATTTTATAGAAAAGCCC 58.718 41.667 5.33 0.00 37.61 5.19
5 6 5.065474 CCGTCCCTTGCGATTTTATAGAAAA 59.935 40.000 0.00 0.00 38.87 2.29
6 7 4.573201 CCGTCCCTTGCGATTTTATAGAAA 59.427 41.667 0.00 0.00 0.00 2.52
7 8 4.124238 CCGTCCCTTGCGATTTTATAGAA 58.876 43.478 0.00 0.00 0.00 2.10
8 9 3.493699 CCCGTCCCTTGCGATTTTATAGA 60.494 47.826 0.00 0.00 0.00 1.98
9 10 2.806244 CCCGTCCCTTGCGATTTTATAG 59.194 50.000 0.00 0.00 0.00 1.31
10 11 2.841215 CCCGTCCCTTGCGATTTTATA 58.159 47.619 0.00 0.00 0.00 0.98
11 12 1.675552 CCCGTCCCTTGCGATTTTAT 58.324 50.000 0.00 0.00 0.00 1.40
12 13 1.027792 GCCCGTCCCTTGCGATTTTA 61.028 55.000 0.00 0.00 0.00 1.52
13 14 2.340328 GCCCGTCCCTTGCGATTTT 61.340 57.895 0.00 0.00 0.00 1.82
14 15 2.750237 GCCCGTCCCTTGCGATTT 60.750 61.111 0.00 0.00 0.00 2.17
15 16 3.976701 CTGCCCGTCCCTTGCGATT 62.977 63.158 0.00 0.00 0.00 3.34
16 17 4.473520 CTGCCCGTCCCTTGCGAT 62.474 66.667 0.00 0.00 0.00 4.58
18 19 4.697756 TTCTGCCCGTCCCTTGCG 62.698 66.667 0.00 0.00 0.00 4.85
19 20 2.282180 TTTCTGCCCGTCCCTTGC 60.282 61.111 0.00 0.00 0.00 4.01
20 21 1.228124 TGTTTCTGCCCGTCCCTTG 60.228 57.895 0.00 0.00 0.00 3.61
21 22 1.228154 GTGTTTCTGCCCGTCCCTT 60.228 57.895 0.00 0.00 0.00 3.95
22 23 1.705997 AAGTGTTTCTGCCCGTCCCT 61.706 55.000 0.00 0.00 0.00 4.20
23 24 1.228154 AAGTGTTTCTGCCCGTCCC 60.228 57.895 0.00 0.00 0.00 4.46
24 25 1.235281 GGAAGTGTTTCTGCCCGTCC 61.235 60.000 0.00 0.00 35.81 4.79
25 26 2.244946 GGAAGTGTTTCTGCCCGTC 58.755 57.895 0.00 0.00 35.81 4.79
26 27 4.475527 GGAAGTGTTTCTGCCCGT 57.524 55.556 0.00 0.00 35.81 5.28
29 30 0.178961 AAGGGGGAAGTGTTTCTGCC 60.179 55.000 0.00 0.00 41.21 4.85
30 31 1.704641 AAAGGGGGAAGTGTTTCTGC 58.295 50.000 0.00 0.00 33.68 4.26
31 32 7.533289 TTTAATAAAGGGGGAAGTGTTTCTG 57.467 36.000 0.00 0.00 33.68 3.02
32 33 9.475620 CTATTTAATAAAGGGGGAAGTGTTTCT 57.524 33.333 0.00 0.00 33.68 2.52
33 34 8.692710 CCTATTTAATAAAGGGGGAAGTGTTTC 58.307 37.037 0.00 0.00 0.00 2.78
34 35 8.181524 ACCTATTTAATAAAGGGGGAAGTGTTT 58.818 33.333 10.63 0.00 34.52 2.83
35 36 7.715482 ACCTATTTAATAAAGGGGGAAGTGTT 58.285 34.615 10.63 0.00 34.52 3.32
36 37 7.293326 ACCTATTTAATAAAGGGGGAAGTGT 57.707 36.000 10.63 0.00 34.52 3.55
37 38 8.276477 TGTACCTATTTAATAAAGGGGGAAGTG 58.724 37.037 10.63 0.00 34.52 3.16
38 39 8.277197 GTGTACCTATTTAATAAAGGGGGAAGT 58.723 37.037 10.63 0.00 34.52 3.01
39 40 8.276477 TGTGTACCTATTTAATAAAGGGGGAAG 58.724 37.037 10.63 0.00 34.52 3.46
40 41 8.054572 GTGTGTACCTATTTAATAAAGGGGGAA 58.945 37.037 10.63 0.00 34.52 3.97
41 42 7.184204 TGTGTGTACCTATTTAATAAAGGGGGA 59.816 37.037 10.63 1.57 34.52 4.81
42 43 7.283807 GTGTGTGTACCTATTTAATAAAGGGGG 59.716 40.741 10.63 6.31 34.52 5.40
43 44 7.830201 TGTGTGTGTACCTATTTAATAAAGGGG 59.170 37.037 10.63 8.20 34.52 4.79
44 45 8.671028 GTGTGTGTGTACCTATTTAATAAAGGG 58.329 37.037 6.16 6.16 34.52 3.95
45 46 9.221933 TGTGTGTGTGTACCTATTTAATAAAGG 57.778 33.333 0.00 0.00 36.42 3.11
47 48 9.557061 TGTGTGTGTGTGTACCTATTTAATAAA 57.443 29.630 0.00 0.00 0.00 1.40
48 49 8.991026 GTGTGTGTGTGTGTACCTATTTAATAA 58.009 33.333 0.00 0.00 0.00 1.40
49 50 8.148999 TGTGTGTGTGTGTGTACCTATTTAATA 58.851 33.333 0.00 0.00 0.00 0.98
50 51 6.993308 TGTGTGTGTGTGTGTACCTATTTAAT 59.007 34.615 0.00 0.00 0.00 1.40
51 52 6.346896 TGTGTGTGTGTGTGTACCTATTTAA 58.653 36.000 0.00 0.00 0.00 1.52
52 53 5.915175 TGTGTGTGTGTGTGTACCTATTTA 58.085 37.500 0.00 0.00 0.00 1.40
53 54 4.771903 TGTGTGTGTGTGTGTACCTATTT 58.228 39.130 0.00 0.00 0.00 1.40
54 55 4.409718 TGTGTGTGTGTGTGTACCTATT 57.590 40.909 0.00 0.00 0.00 1.73
55 56 4.617253 ATGTGTGTGTGTGTGTACCTAT 57.383 40.909 0.00 0.00 0.00 2.57
56 57 5.731957 ATATGTGTGTGTGTGTGTACCTA 57.268 39.130 0.00 0.00 0.00 3.08
57 58 4.617253 ATATGTGTGTGTGTGTGTACCT 57.383 40.909 0.00 0.00 0.00 3.08
58 59 9.923143 ATATATATATGTGTGTGTGTGTGTACC 57.077 33.333 4.37 0.00 0.00 3.34
83 84 9.100197 TGGCGGTGGTGATTCATATATATATAT 57.900 33.333 9.12 9.12 0.00 0.86
84 85 8.364894 GTGGCGGTGGTGATTCATATATATATA 58.635 37.037 4.90 4.92 0.00 0.86
85 86 7.217200 GTGGCGGTGGTGATTCATATATATAT 58.783 38.462 0.00 0.00 0.00 0.86
86 87 6.407639 GGTGGCGGTGGTGATTCATATATATA 60.408 42.308 0.00 0.00 0.00 0.86
87 88 5.428253 GTGGCGGTGGTGATTCATATATAT 58.572 41.667 0.00 0.00 0.00 0.86
88 89 4.323180 GGTGGCGGTGGTGATTCATATATA 60.323 45.833 0.00 0.00 0.00 0.86
89 90 3.559171 GGTGGCGGTGGTGATTCATATAT 60.559 47.826 0.00 0.00 0.00 0.86
90 91 2.224426 GGTGGCGGTGGTGATTCATATA 60.224 50.000 0.00 0.00 0.00 0.86
91 92 1.476833 GGTGGCGGTGGTGATTCATAT 60.477 52.381 0.00 0.00 0.00 1.78
92 93 0.107410 GGTGGCGGTGGTGATTCATA 60.107 55.000 0.00 0.00 0.00 2.15
93 94 1.378514 GGTGGCGGTGGTGATTCAT 60.379 57.895 0.00 0.00 0.00 2.57
94 95 2.033448 GGTGGCGGTGGTGATTCA 59.967 61.111 0.00 0.00 0.00 2.57
95 96 3.124921 CGGTGGCGGTGGTGATTC 61.125 66.667 0.00 0.00 0.00 2.52
96 97 4.715523 CCGGTGGCGGTGGTGATT 62.716 66.667 0.00 0.00 0.00 2.57
99 100 4.317444 TAACCGGTGGCGGTGGTG 62.317 66.667 8.52 0.00 42.06 4.17
100 101 4.318949 GTAACCGGTGGCGGTGGT 62.319 66.667 8.52 0.00 42.06 4.16
101 102 3.945304 GAGTAACCGGTGGCGGTGG 62.945 68.421 8.52 0.00 42.06 4.61
102 103 2.433664 GAGTAACCGGTGGCGGTG 60.434 66.667 8.52 0.00 42.06 4.94
103 104 2.602568 AGAGTAACCGGTGGCGGT 60.603 61.111 8.52 0.00 45.25 5.68
104 105 2.183555 GAGAGTAACCGGTGGCGG 59.816 66.667 8.52 0.00 0.00 6.13
105 106 2.202570 CGAGAGTAACCGGTGGCG 60.203 66.667 8.52 1.93 0.00 5.69
106 107 2.502692 AAGCGAGAGTAACCGGTGGC 62.503 60.000 8.52 3.77 36.58 5.01
107 108 0.458025 GAAGCGAGAGTAACCGGTGG 60.458 60.000 8.52 0.00 36.58 4.61
108 109 0.458025 GGAAGCGAGAGTAACCGGTG 60.458 60.000 8.52 0.00 36.58 4.94
109 110 1.888736 GGAAGCGAGAGTAACCGGT 59.111 57.895 0.00 0.00 38.19 5.28
110 111 1.226603 CGGAAGCGAGAGTAACCGG 60.227 63.158 0.00 0.00 37.88 5.28
111 112 1.226603 CCGGAAGCGAGAGTAACCG 60.227 63.158 0.00 0.00 39.81 4.44
112 113 1.141234 CCCGGAAGCGAGAGTAACC 59.859 63.158 0.73 0.00 0.00 2.85
113 114 0.458025 CACCCGGAAGCGAGAGTAAC 60.458 60.000 0.73 0.00 0.00 2.50
114 115 1.888018 CACCCGGAAGCGAGAGTAA 59.112 57.895 0.73 0.00 0.00 2.24
115 116 2.707849 GCACCCGGAAGCGAGAGTA 61.708 63.158 0.73 0.00 0.00 2.59
116 117 4.070552 GCACCCGGAAGCGAGAGT 62.071 66.667 0.73 0.00 0.00 3.24
117 118 4.821589 GGCACCCGGAAGCGAGAG 62.822 72.222 0.73 0.00 0.00 3.20
119 120 4.394712 AAGGCACCCGGAAGCGAG 62.395 66.667 0.73 0.00 0.00 5.03
120 121 4.697756 CAAGGCACCCGGAAGCGA 62.698 66.667 0.73 0.00 0.00 4.93
122 123 4.660938 ACCAAGGCACCCGGAAGC 62.661 66.667 0.73 6.22 0.00 3.86
123 124 2.672996 CACCAAGGCACCCGGAAG 60.673 66.667 0.73 0.00 0.00 3.46
124 125 4.966787 GCACCAAGGCACCCGGAA 62.967 66.667 0.73 0.00 0.00 4.30
150 151 3.243053 TCGGGGTTTTCCTCCGCA 61.243 61.111 0.00 0.00 46.19 5.69
167 168 9.354673 CAAACTCCAATACCAATCATATTAGGT 57.645 33.333 0.00 0.00 38.14 3.08
170 171 9.066892 GCTCAAACTCCAATACCAATCATATTA 57.933 33.333 0.00 0.00 0.00 0.98
183 184 0.693049 AGGACGGCTCAAACTCCAAT 59.307 50.000 0.00 0.00 0.00 3.16
190 191 1.277842 TCAATGCTAGGACGGCTCAAA 59.722 47.619 0.00 0.00 0.00 2.69
197 198 2.332063 ACCCATTCAATGCTAGGACG 57.668 50.000 0.00 0.00 0.00 4.79
205 206 6.659242 ACACCTAGACTAAAACCCATTCAATG 59.341 38.462 0.00 0.00 0.00 2.82
207 208 6.043938 AGACACCTAGACTAAAACCCATTCAA 59.956 38.462 0.00 0.00 0.00 2.69
213 214 3.619242 GCCAGACACCTAGACTAAAACCC 60.619 52.174 0.00 0.00 0.00 4.11
216 217 3.192844 CGAGCCAGACACCTAGACTAAAA 59.807 47.826 0.00 0.00 0.00 1.52
237 238 3.190849 CATCGCCTCTGCACCACG 61.191 66.667 0.00 0.00 37.32 4.94
239 240 4.783621 GCCATCGCCTCTGCACCA 62.784 66.667 0.00 0.00 37.32 4.17
242 243 4.819761 GACGCCATCGCCTCTGCA 62.820 66.667 0.00 0.00 39.84 4.41
253 254 0.880441 CCATGTTGTTGATGACGCCA 59.120 50.000 0.00 0.00 0.00 5.69
320 321 1.924731 TCTCCACACGTTCTCCATCT 58.075 50.000 0.00 0.00 0.00 2.90
323 324 2.549992 CCAAATCTCCACACGTTCTCCA 60.550 50.000 0.00 0.00 0.00 3.86
331 332 1.826385 CCCTGACCAAATCTCCACAC 58.174 55.000 0.00 0.00 0.00 3.82
339 340 0.482446 TGTTCTGGCCCTGACCAAAT 59.518 50.000 0.00 0.00 39.86 2.32
344 345 2.352805 CCCTGTTCTGGCCCTGAC 59.647 66.667 0.00 0.00 0.00 3.51
357 358 1.228675 AGACAAAAGCAGGGCCCTG 60.229 57.895 42.66 42.66 46.15 4.45
360 361 0.752658 AAACAGACAAAAGCAGGGCC 59.247 50.000 0.00 0.00 0.00 5.80
363 364 3.420839 AACGAAACAGACAAAAGCAGG 57.579 42.857 0.00 0.00 0.00 4.85
410 411 4.902448 AGAAATAGTCACTATCCACTCCCC 59.098 45.833 0.00 0.00 0.00 4.81
411 412 7.784470 ATAGAAATAGTCACTATCCACTCCC 57.216 40.000 0.00 0.00 0.00 4.30
434 435 6.059787 ACAGAGAAGCCAGATGACTAAAAT 57.940 37.500 0.00 0.00 0.00 1.82
439 440 3.558746 CCAAACAGAGAAGCCAGATGACT 60.559 47.826 0.00 0.00 0.00 3.41
459 460 1.904287 AAGTTGGTTATGCTTCGCCA 58.096 45.000 0.00 0.00 0.00 5.69
471 472 1.164041 CCGACGAAGGCAAAGTTGGT 61.164 55.000 0.00 0.00 35.29 3.67
481 482 1.741706 TCACTAGCTTACCGACGAAGG 59.258 52.381 0.00 0.00 37.30 3.46
533 534 1.635817 GGCTAGCCAATCACCCCTGA 61.636 60.000 29.33 0.00 35.81 3.86
536 537 2.195956 GGGCTAGCCAATCACCCC 59.804 66.667 34.09 11.30 37.98 4.95
539 540 0.107643 GAGGAGGGCTAGCCAATCAC 59.892 60.000 34.09 22.00 37.98 3.06
542 543 1.144503 CATTGAGGAGGGCTAGCCAAT 59.855 52.381 34.09 22.46 37.98 3.16
543 544 0.548031 CATTGAGGAGGGCTAGCCAA 59.452 55.000 34.09 19.26 37.98 4.52
544 545 1.348008 CCATTGAGGAGGGCTAGCCA 61.348 60.000 34.09 13.23 41.22 4.75
545 546 1.348775 ACCATTGAGGAGGGCTAGCC 61.349 60.000 26.55 26.55 41.22 3.93
546 547 0.548510 AACCATTGAGGAGGGCTAGC 59.451 55.000 6.04 6.04 41.22 3.42
547 548 2.507471 AGAAACCATTGAGGAGGGCTAG 59.493 50.000 0.00 0.00 41.22 3.42
548 549 2.562296 AGAAACCATTGAGGAGGGCTA 58.438 47.619 0.00 0.00 41.22 3.93
549 550 1.376649 AGAAACCATTGAGGAGGGCT 58.623 50.000 0.00 0.00 41.22 5.19
550 551 2.095461 GAAGAAACCATTGAGGAGGGC 58.905 52.381 0.00 0.00 41.22 5.19
551 552 3.265479 AGAGAAGAAACCATTGAGGAGGG 59.735 47.826 0.00 0.00 41.22 4.30
552 553 4.260170 CAGAGAAGAAACCATTGAGGAGG 58.740 47.826 0.00 0.00 41.22 4.30
553 554 4.260170 CCAGAGAAGAAACCATTGAGGAG 58.740 47.826 0.00 0.00 41.22 3.69
554 555 3.009473 CCCAGAGAAGAAACCATTGAGGA 59.991 47.826 0.00 0.00 41.22 3.71
555 556 3.009473 TCCCAGAGAAGAAACCATTGAGG 59.991 47.826 0.00 0.00 45.67 3.86
556 557 4.006319 GTCCCAGAGAAGAAACCATTGAG 58.994 47.826 0.00 0.00 0.00 3.02
557 558 3.394274 TGTCCCAGAGAAGAAACCATTGA 59.606 43.478 0.00 0.00 0.00 2.57
558 559 3.754965 TGTCCCAGAGAAGAAACCATTG 58.245 45.455 0.00 0.00 0.00 2.82
559 560 4.145052 GTTGTCCCAGAGAAGAAACCATT 58.855 43.478 0.00 0.00 0.00 3.16
562 563 3.208747 TGTTGTCCCAGAGAAGAAACC 57.791 47.619 0.00 0.00 0.00 3.27
572 573 2.698855 AGATCGGATTGTTGTCCCAG 57.301 50.000 0.00 0.00 34.67 4.45
573 574 3.433306 AAAGATCGGATTGTTGTCCCA 57.567 42.857 0.00 0.00 34.67 4.37
577 578 5.235516 ACGAACTAAAGATCGGATTGTTGT 58.764 37.500 13.21 0.00 43.30 3.32
582 583 4.561606 CGACAACGAACTAAAGATCGGATT 59.438 41.667 13.21 0.00 43.30 3.01
586 587 2.027688 GGCGACAACGAACTAAAGATCG 59.972 50.000 7.95 7.95 44.34 3.69
595 596 0.788391 AGAAATCGGCGACAACGAAC 59.212 50.000 13.76 0.00 44.20 3.95
598 599 1.419922 CCAGAAATCGGCGACAACG 59.580 57.895 13.76 0.00 42.93 4.10
610 611 2.151202 GTCATCGGTCAAAGCCAGAAA 58.849 47.619 0.00 0.00 0.00 2.52
626 627 5.233083 TGGTGAAACAGATGAGAAGTCAT 57.767 39.130 0.00 0.00 42.62 3.06
636 637 5.888161 GGGATACATTCTTGGTGAAACAGAT 59.112 40.000 0.00 0.00 38.29 2.90
640 641 4.399303 CCAGGGATACATTCTTGGTGAAAC 59.601 45.833 0.00 0.00 38.29 2.78
643 644 3.459828 TCCAGGGATACATTCTTGGTGA 58.540 45.455 0.00 0.00 39.74 4.02
646 647 4.349048 TCAGATCCAGGGATACATTCTTGG 59.651 45.833 0.00 0.00 34.60 3.61
668 669 0.902531 TGGATCTCCGAAACACCCTC 59.097 55.000 0.00 0.00 39.43 4.30
669 670 0.905357 CTGGATCTCCGAAACACCCT 59.095 55.000 0.00 0.00 39.43 4.34
670 671 0.902531 TCTGGATCTCCGAAACACCC 59.097 55.000 0.00 0.00 39.43 4.61
671 672 1.134670 CCTCTGGATCTCCGAAACACC 60.135 57.143 0.00 0.00 39.43 4.16
672 673 1.550976 ACCTCTGGATCTCCGAAACAC 59.449 52.381 0.00 0.00 39.43 3.32
679 680 0.396060 GATGCCACCTCTGGATCTCC 59.604 60.000 0.00 0.00 40.55 3.71
688 689 0.529555 GAAGAGCTCGATGCCACCTC 60.530 60.000 8.37 0.00 44.23 3.85
704 705 3.175240 CACTCGGCGCGTGAGAAG 61.175 66.667 28.86 19.22 36.93 2.85
718 719 2.636893 AGTGATGTCTTCCTTCTGCACT 59.363 45.455 0.00 0.00 0.00 4.40
731 732 9.862371 CTAGTTATTGGGTATATCAGTGATGTC 57.138 37.037 16.15 5.80 0.00 3.06
758 759 6.681729 ACAGAGGGAGTAGAAAATAACACA 57.318 37.500 0.00 0.00 0.00 3.72
808 809 7.171337 CCTTTGATGTTTTGGTAGTTCCATTTG 59.829 37.037 0.00 0.00 46.60 2.32
813 814 4.830600 TCCCTTTGATGTTTTGGTAGTTCC 59.169 41.667 0.00 0.00 0.00 3.62
814 815 5.535030 ACTCCCTTTGATGTTTTGGTAGTTC 59.465 40.000 0.00 0.00 0.00 3.01
827 828 9.408648 CCATACTTACAAAATACTCCCTTTGAT 57.591 33.333 1.80 0.00 36.30 2.57
883 937 2.686915 CCTGCTTCAAAGGCCAAGATAG 59.313 50.000 5.01 2.18 0.00 2.08
903 957 7.971183 AGACTTAATCAACTTGAGTTTCTCC 57.029 36.000 0.00 0.00 34.09 3.71
976 1031 4.898488 GCAATTTCGATGACGTAGCAATAC 59.102 41.667 0.00 0.00 40.69 1.89
977 1032 4.025229 GGCAATTTCGATGACGTAGCAATA 60.025 41.667 0.00 0.00 40.69 1.90
1003 1067 7.039923 TCGGTGGGTAATATTTTGCAACTTTTA 60.040 33.333 0.00 0.00 0.00 1.52
1093 1157 0.600255 ACAGGCGTGTTGTGTAGAGC 60.600 55.000 6.15 0.00 30.30 4.09
1094 1158 1.865865 AACAGGCGTGTTGTGTAGAG 58.134 50.000 23.02 0.00 45.58 2.43
1096 1160 1.002900 CCAAACAGGCGTGTTGTGTAG 60.003 52.381 24.19 12.17 46.68 2.74
1097 1161 1.018148 CCAAACAGGCGTGTTGTGTA 58.982 50.000 24.19 0.00 46.68 2.90
1098 1162 1.662438 CCCAAACAGGCGTGTTGTGT 61.662 55.000 24.19 7.31 46.68 3.72
1099 1163 1.065600 CCCAAACAGGCGTGTTGTG 59.934 57.895 24.19 20.97 46.68 3.33
1236 1432 6.817184 TCCCGAACATTTGTTTCCAAAATTA 58.183 32.000 0.00 0.00 43.43 1.40
1296 1523 8.517062 TTTTGAATTGGTGGAATTTTGTTCAT 57.483 26.923 0.00 0.00 34.18 2.57
1326 1554 4.213564 AGGACATTTCTCAGGTCATGAC 57.786 45.455 17.91 17.91 33.22 3.06
1333 1561 9.762933 TTTTGAATTTTTAGGACATTTCTCAGG 57.237 29.630 0.00 0.00 0.00 3.86
1401 1652 6.519315 CGTGATCATTTTTGAATCAGCAAAC 58.481 36.000 0.00 0.00 37.48 2.93
1403 1654 4.622313 GCGTGATCATTTTTGAATCAGCAA 59.378 37.500 0.00 0.00 0.00 3.91
1404 1655 4.168014 GCGTGATCATTTTTGAATCAGCA 58.832 39.130 0.00 0.00 0.00 4.41
1408 1660 7.280730 TGAAATGCGTGATCATTTTTGAATC 57.719 32.000 0.00 0.00 44.15 2.52
1473 1727 7.976135 TTTGTTGGAAATTGGTGGAATAATG 57.024 32.000 0.00 0.00 0.00 1.90
1491 1747 6.389622 TCTAGAATCGACGAACATTTGTTG 57.610 37.500 0.00 0.00 38.56 3.33
1494 1750 6.089551 ACACTTCTAGAATCGACGAACATTTG 59.910 38.462 5.44 0.00 0.00 2.32
1516 1772 5.758924 ACTTTTTCTTGAATAGCCGAACAC 58.241 37.500 0.00 0.00 0.00 3.32
1620 1957 5.291858 TGAGCATATCTGAAATCGTGAACAC 59.708 40.000 0.00 0.00 0.00 3.32
1670 2026 6.747739 TCGTGAAATCGTGAACAATTTTTGAA 59.252 30.769 0.00 0.00 0.00 2.69
1860 2248 9.945904 AAAAGTTTTACTATTTGGTTTCCAACA 57.054 25.926 0.00 0.00 43.82 3.33
1893 2281 3.573967 TCTCCTTTTCCTGCATTCCAAAC 59.426 43.478 0.00 0.00 0.00 2.93
1899 2287 5.612725 TGTTTTTCTCCTTTTCCTGCATT 57.387 34.783 0.00 0.00 0.00 3.56
1920 3583 9.525409 AAAAACATTTCTCAAGAAGTTCTCATG 57.475 29.630 5.70 1.86 35.21 3.07
1950 3613 5.552870 ACCAGTACTTCTCAAGTTCATGT 57.447 39.130 0.00 0.00 42.81 3.21
1951 3614 6.692486 ACTACCAGTACTTCTCAAGTTCATG 58.308 40.000 0.00 0.00 42.81 3.07
1981 3657 1.071542 TGTGCGGAGGTGAGAAATTGA 59.928 47.619 0.00 0.00 0.00 2.57
1996 3672 2.200899 CAAAGGGGAAAGTTTTGTGCG 58.799 47.619 0.00 0.00 0.00 5.34
2009 3685 1.913262 GAGGGTTTGGGCAAAGGGG 60.913 63.158 0.00 0.00 0.00 4.79
2016 3692 2.434359 CGAGACGAGGGTTTGGGC 60.434 66.667 0.00 0.00 0.00 5.36
2619 4309 3.225548 CACATGGACGTCAAATGTTTCG 58.774 45.455 25.20 15.12 32.27 3.46
2670 4360 3.634397 TTCTTCCCCTCTAGCAATGTG 57.366 47.619 0.00 0.00 0.00 3.21
2715 4405 2.024941 AGCAGAAAATACCTCCCCTTGG 60.025 50.000 0.00 0.00 0.00 3.61
2770 4460 2.815478 CCCATAGAACTCTGCTTCGAC 58.185 52.381 0.00 0.00 0.00 4.20
2884 4575 8.141835 ACTAGCAAAATTTTGGCAAGTTTTAG 57.858 30.769 27.60 17.71 38.57 1.85
3005 4696 6.557110 TGCATGTCATCAATTGTTATGTCAG 58.443 36.000 5.13 3.46 0.00 3.51
3082 4773 2.633967 CCTCCTCAAGATCTCTCATGGG 59.366 54.545 0.00 0.00 0.00 4.00
3102 4793 8.250332 TGCTTAACCATTTCTATTTTGTCATCC 58.750 33.333 0.00 0.00 0.00 3.51
3211 4902 2.048444 AATATGGCAGCCACAGTCTG 57.952 50.000 19.10 0.00 35.80 3.51
3506 5199 6.199937 AGAAAATGAGCGTGCTGAATTTAT 57.800 33.333 0.00 0.00 0.00 1.40
3707 5977 8.273780 AGGACAGAAATTAAAGTAAGCAGATG 57.726 34.615 0.00 0.00 0.00 2.90
3888 6941 8.307483 TCTAACTGATTTTCTGAATCGAAGACT 58.693 33.333 0.00 0.00 42.51 3.24
4249 7325 2.234300 TCGCTCTCTCGGTTTTTGTT 57.766 45.000 0.00 0.00 0.00 2.83
4349 7436 0.106149 CTTCGGGCGTAGGGCTAAAT 59.894 55.000 8.99 0.00 42.94 1.40


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

AutoCloner maintained by Alex Coulton.