Multiple sequence alignment - TraesCS2D01G534400

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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 TraesCS2D01G534400 chr2D 100.000 6501 0 0 1 6501 618144248 618137748 0.000000e+00 12006.0
1 TraesCS2D01G534400 chr2D 85.364 1346 155 21 1043 2355 586961710 586960374 0.000000e+00 1356.0
2 TraesCS2D01G534400 chr2D 85.486 1316 140 23 1076 2355 618333434 618334734 0.000000e+00 1325.0
3 TraesCS2D01G534400 chr2D 82.134 1265 171 40 1131 2354 586846897 586845647 0.000000e+00 1033.0
4 TraesCS2D01G534400 chr2D 79.540 1261 207 38 1131 2355 618876015 618877260 0.000000e+00 852.0
5 TraesCS2D01G534400 chr2A 91.074 3137 192 44 145 3247 748911441 748908359 0.000000e+00 4161.0
6 TraesCS2D01G534400 chr2A 94.059 2525 113 23 3995 6501 748907618 748905113 0.000000e+00 3797.0
7 TraesCS2D01G534400 chr2A 85.616 1314 142 21 1076 2355 749385158 749386458 0.000000e+00 1336.0
8 TraesCS2D01G534400 chr2A 84.892 1337 160 24 1052 2355 721729595 721728268 0.000000e+00 1312.0
9 TraesCS2D01G534400 chr2A 91.643 694 45 6 3253 3941 748908305 748907620 0.000000e+00 948.0
10 TraesCS2D01G534400 chr2A 84.886 880 107 13 2875 3741 748870864 748869998 0.000000e+00 865.0
11 TraesCS2D01G534400 chr2B 94.694 2563 104 18 3963 6501 754651811 754649257 0.000000e+00 3951.0
12 TraesCS2D01G534400 chr2B 88.984 3159 202 58 144 3270 754655519 754652475 0.000000e+00 3771.0
13 TraesCS2D01G534400 chr2B 86.489 1236 138 19 1132 2351 755150716 755149494 0.000000e+00 1330.0
14 TraesCS2D01G534400 chr2B 85.726 1268 144 22 1117 2355 708716245 708714986 0.000000e+00 1304.0
15 TraesCS2D01G534400 chr2B 89.511 696 41 7 3263 3957 754652447 754651783 0.000000e+00 852.0
16 TraesCS2D01G534400 chr2B 94.224 554 28 2 4795 5348 754622624 754622075 0.000000e+00 843.0
17 TraesCS2D01G534400 chr2B 85.128 585 73 6 1779 2355 755009815 755010393 2.610000e-163 586.0
18 TraesCS2D01G534400 chr2B 90.909 418 27 6 3527 3941 754628672 754628263 9.530000e-153 551.0
19 TraesCS2D01G534400 chr2B 89.728 331 23 5 4343 4663 754628099 754627770 4.690000e-111 412.0
20 TraesCS2D01G534400 chr2B 91.852 135 11 0 4659 4793 754623138 754623004 8.610000e-44 189.0
21 TraesCS2D01G534400 chr6A 82.955 264 37 6 4030 4290 224331575 224331317 1.410000e-56 231.0
22 TraesCS2D01G534400 chr5D 75.316 158 27 8 4094 4246 393979954 393979804 1.510000e-06 65.8
23 TraesCS2D01G534400 chrUn 89.130 46 4 1 404 449 244162749 244162705 1.000000e-03 56.5
24 TraesCS2D01G534400 chrUn 89.130 46 4 1 404 449 244175384 244175340 1.000000e-03 56.5
25 TraesCS2D01G534400 chrUn 89.130 46 4 1 404 449 316238998 316239042 1.000000e-03 56.5
26 TraesCS2D01G534400 chr5A 97.059 34 0 1 5632 5664 657242230 657242197 1.000000e-03 56.5


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 TraesCS2D01G534400 chr2D 618137748 618144248 6500 True 12006.000000 12006 100.000000 1 6501 1 chr2D.!!$R3 6500
1 TraesCS2D01G534400 chr2D 586960374 586961710 1336 True 1356.000000 1356 85.364000 1043 2355 1 chr2D.!!$R2 1312
2 TraesCS2D01G534400 chr2D 618333434 618334734 1300 False 1325.000000 1325 85.486000 1076 2355 1 chr2D.!!$F1 1279
3 TraesCS2D01G534400 chr2D 586845647 586846897 1250 True 1033.000000 1033 82.134000 1131 2354 1 chr2D.!!$R1 1223
4 TraesCS2D01G534400 chr2D 618876015 618877260 1245 False 852.000000 852 79.540000 1131 2355 1 chr2D.!!$F2 1224
5 TraesCS2D01G534400 chr2A 748905113 748911441 6328 True 2968.666667 4161 92.258667 145 6501 3 chr2A.!!$R3 6356
6 TraesCS2D01G534400 chr2A 749385158 749386458 1300 False 1336.000000 1336 85.616000 1076 2355 1 chr2A.!!$F1 1279
7 TraesCS2D01G534400 chr2A 721728268 721729595 1327 True 1312.000000 1312 84.892000 1052 2355 1 chr2A.!!$R1 1303
8 TraesCS2D01G534400 chr2A 748869998 748870864 866 True 865.000000 865 84.886000 2875 3741 1 chr2A.!!$R2 866
9 TraesCS2D01G534400 chr2B 754649257 754655519 6262 True 2858.000000 3951 91.063000 144 6501 3 chr2B.!!$R5 6357
10 TraesCS2D01G534400 chr2B 755149494 755150716 1222 True 1330.000000 1330 86.489000 1132 2351 1 chr2B.!!$R2 1219
11 TraesCS2D01G534400 chr2B 708714986 708716245 1259 True 1304.000000 1304 85.726000 1117 2355 1 chr2B.!!$R1 1238
12 TraesCS2D01G534400 chr2B 755009815 755010393 578 False 586.000000 586 85.128000 1779 2355 1 chr2B.!!$F1 576
13 TraesCS2D01G534400 chr2B 754622075 754623138 1063 True 516.000000 843 93.038000 4659 5348 2 chr2B.!!$R3 689
14 TraesCS2D01G534400 chr2B 754627770 754628672 902 True 481.500000 551 90.318500 3527 4663 2 chr2B.!!$R4 1136

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
82 83 0.036306 ACGCGGGAGAACCTTCAATT 59.964 50.000 12.47 0.00 36.97 2.32 F
210 211 0.248012 TGACACCGCGGTAACATGAT 59.752 50.000 33.70 10.36 0.00 2.45 F
714 733 1.347097 CTCCACACGCGTCACATCTG 61.347 60.000 9.86 0.00 0.00 2.90 F
1368 1455 2.343758 GTCCTGCTTGACGGCTCA 59.656 61.111 0.00 0.00 0.00 4.26 F
2647 2797 2.507407 ACCAGCCGGTCACATTTATT 57.493 45.000 1.90 0.00 44.71 1.40 F
3228 3383 1.823899 GGGCAGGGTGGATTTAGCG 60.824 63.158 0.00 0.00 0.00 4.26 F
3821 4075 1.333308 TGTGCAGGACAAAATCGTGTG 59.667 47.619 0.00 0.00 43.76 3.82 F
4281 4571 2.563702 ACGCGAAGTAAAAAGGACCAA 58.436 42.857 15.93 0.00 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1529 1619 1.676967 CAGAGGTTCTTGCCCAGCC 60.677 63.158 0.00 0.00 0.00 4.85 R
1602 1692 3.450115 GTGCGGCGGTAGTCTCCT 61.450 66.667 9.78 0.00 0.00 3.69 R
2271 2421 2.866156 ACGTAGATCAACAATGGCATCG 59.134 45.455 0.00 0.00 0.00 3.84 R
3203 3358 2.060567 ATCCACCCTGCCCGATGATG 62.061 60.000 0.00 0.00 0.00 3.07 R
3677 3929 1.141881 CGAGGACCTAGCACGCAAT 59.858 57.895 0.00 0.00 0.00 3.56 R
4689 5038 1.729149 GCGATTTTTGGCTTCCACTCG 60.729 52.381 0.00 0.00 30.78 4.18 R
4822 5549 1.958579 TGTTAGGTATGTCGGATCCGG 59.041 52.381 32.79 15.22 40.25 5.14 R
6279 7014 2.283101 GCATGTCAGGGTGCCCAA 60.283 61.111 10.26 0.00 38.92 4.12 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
24 25 6.610741 ACACAAGTCACTCTGATCTTTTTC 57.389 37.500 0.00 0.00 0.00 2.29
25 26 6.115446 ACACAAGTCACTCTGATCTTTTTCA 58.885 36.000 0.00 0.00 0.00 2.69
26 27 6.599244 ACACAAGTCACTCTGATCTTTTTCAA 59.401 34.615 0.00 0.00 0.00 2.69
27 28 7.130917 CACAAGTCACTCTGATCTTTTTCAAG 58.869 38.462 0.00 0.00 0.00 3.02
28 29 6.261826 ACAAGTCACTCTGATCTTTTTCAAGG 59.738 38.462 0.00 0.00 0.00 3.61
29 30 5.934781 AGTCACTCTGATCTTTTTCAAGGT 58.065 37.500 0.00 0.00 0.00 3.50
30 31 7.067496 AGTCACTCTGATCTTTTTCAAGGTA 57.933 36.000 0.00 0.00 0.00 3.08
31 32 7.509546 AGTCACTCTGATCTTTTTCAAGGTAA 58.490 34.615 0.00 0.00 0.00 2.85
32 33 7.993183 AGTCACTCTGATCTTTTTCAAGGTAAA 59.007 33.333 0.00 0.00 0.00 2.01
33 34 8.621286 GTCACTCTGATCTTTTTCAAGGTAAAA 58.379 33.333 0.00 0.00 0.00 1.52
34 35 9.354673 TCACTCTGATCTTTTTCAAGGTAAAAT 57.645 29.630 0.00 0.00 0.00 1.82
35 36 9.617975 CACTCTGATCTTTTTCAAGGTAAAATC 57.382 33.333 0.00 0.00 0.00 2.17
36 37 8.507249 ACTCTGATCTTTTTCAAGGTAAAATCG 58.493 33.333 0.00 0.00 0.00 3.34
37 38 8.615878 TCTGATCTTTTTCAAGGTAAAATCGA 57.384 30.769 0.00 0.00 0.00 3.59
38 39 9.231297 TCTGATCTTTTTCAAGGTAAAATCGAT 57.769 29.630 0.00 0.00 0.00 3.59
39 40 9.282247 CTGATCTTTTTCAAGGTAAAATCGATG 57.718 33.333 0.00 0.00 0.00 3.84
40 41 9.008965 TGATCTTTTTCAAGGTAAAATCGATGA 57.991 29.630 0.00 0.00 0.00 2.92
41 42 9.278734 GATCTTTTTCAAGGTAAAATCGATGAC 57.721 33.333 0.00 0.00 0.00 3.06
42 43 7.295201 TCTTTTTCAAGGTAAAATCGATGACG 58.705 34.615 0.00 0.00 41.26 4.35
43 44 5.539582 TTTCAAGGTAAAATCGATGACGG 57.460 39.130 0.00 0.00 40.21 4.79
44 45 4.459390 TCAAGGTAAAATCGATGACGGA 57.541 40.909 0.00 0.00 40.21 4.69
45 46 5.018539 TCAAGGTAAAATCGATGACGGAT 57.981 39.130 0.00 0.00 40.21 4.18
46 47 6.151663 TCAAGGTAAAATCGATGACGGATA 57.848 37.500 0.00 0.00 40.21 2.59
47 48 6.755206 TCAAGGTAAAATCGATGACGGATAT 58.245 36.000 0.00 0.00 40.21 1.63
48 49 6.866770 TCAAGGTAAAATCGATGACGGATATC 59.133 38.462 0.00 0.00 40.21 1.63
49 50 6.340962 AGGTAAAATCGATGACGGATATCA 57.659 37.500 0.00 0.00 40.21 2.15
50 51 6.936279 AGGTAAAATCGATGACGGATATCAT 58.064 36.000 0.00 0.00 42.15 2.45
51 52 6.813649 AGGTAAAATCGATGACGGATATCATG 59.186 38.462 0.00 0.00 39.48 3.07
52 53 6.590292 GGTAAAATCGATGACGGATATCATGT 59.410 38.462 0.00 2.14 39.48 3.21
53 54 6.471976 AAAATCGATGACGGATATCATGTG 57.528 37.500 0.00 0.00 39.48 3.21
54 55 5.391312 AATCGATGACGGATATCATGTGA 57.609 39.130 0.00 0.00 39.48 3.58
55 56 4.160736 TCGATGACGGATATCATGTGAC 57.839 45.455 4.83 0.00 39.48 3.67
56 57 3.821033 TCGATGACGGATATCATGTGACT 59.179 43.478 4.83 0.00 39.48 3.41
57 58 4.278419 TCGATGACGGATATCATGTGACTT 59.722 41.667 4.83 0.00 39.48 3.01
58 59 4.618912 CGATGACGGATATCATGTGACTTC 59.381 45.833 4.83 0.15 39.48 3.01
59 60 5.563671 CGATGACGGATATCATGTGACTTCT 60.564 44.000 4.83 0.00 39.48 2.85
60 61 5.598416 TGACGGATATCATGTGACTTCTT 57.402 39.130 4.83 0.00 0.00 2.52
61 62 5.977635 TGACGGATATCATGTGACTTCTTT 58.022 37.500 4.83 0.00 0.00 2.52
62 63 5.812127 TGACGGATATCATGTGACTTCTTTG 59.188 40.000 4.83 0.00 0.00 2.77
63 64 5.977635 ACGGATATCATGTGACTTCTTTGA 58.022 37.500 4.83 0.00 0.00 2.69
64 65 5.812642 ACGGATATCATGTGACTTCTTTGAC 59.187 40.000 4.83 0.00 0.00 3.18
65 66 5.051441 CGGATATCATGTGACTTCTTTGACG 60.051 44.000 4.83 0.00 0.00 4.35
66 67 5.277058 GGATATCATGTGACTTCTTTGACGC 60.277 44.000 4.83 0.00 0.00 5.19
67 68 1.792367 TCATGTGACTTCTTTGACGCG 59.208 47.619 3.53 3.53 0.00 6.01
68 69 1.136252 CATGTGACTTCTTTGACGCGG 60.136 52.381 12.47 0.00 0.00 6.46
69 70 0.878523 TGTGACTTCTTTGACGCGGG 60.879 55.000 12.47 0.00 0.00 6.13
70 71 0.599204 GTGACTTCTTTGACGCGGGA 60.599 55.000 12.47 0.00 0.00 5.14
71 72 0.319555 TGACTTCTTTGACGCGGGAG 60.320 55.000 12.47 0.00 0.00 4.30
72 73 0.038526 GACTTCTTTGACGCGGGAGA 60.039 55.000 12.47 4.91 0.00 3.71
73 74 0.391597 ACTTCTTTGACGCGGGAGAA 59.608 50.000 12.47 12.63 0.00 2.87
74 75 0.790814 CTTCTTTGACGCGGGAGAAC 59.209 55.000 12.47 0.00 0.00 3.01
75 76 0.601841 TTCTTTGACGCGGGAGAACC 60.602 55.000 12.47 0.00 0.00 3.62
76 77 1.004918 CTTTGACGCGGGAGAACCT 60.005 57.895 12.47 0.00 36.97 3.50
77 78 0.602905 CTTTGACGCGGGAGAACCTT 60.603 55.000 12.47 0.00 36.97 3.50
78 79 0.601841 TTTGACGCGGGAGAACCTTC 60.602 55.000 12.47 0.00 36.97 3.46
79 80 1.750341 TTGACGCGGGAGAACCTTCA 61.750 55.000 12.47 0.00 36.97 3.02
80 81 1.005394 GACGCGGGAGAACCTTCAA 60.005 57.895 12.47 0.00 36.97 2.69
81 82 0.391263 GACGCGGGAGAACCTTCAAT 60.391 55.000 12.47 0.00 36.97 2.57
82 83 0.036306 ACGCGGGAGAACCTTCAATT 59.964 50.000 12.47 0.00 36.97 2.32
83 84 1.165270 CGCGGGAGAACCTTCAATTT 58.835 50.000 0.00 0.00 36.97 1.82
84 85 1.130561 CGCGGGAGAACCTTCAATTTC 59.869 52.381 0.00 0.00 36.97 2.17
85 86 1.472878 GCGGGAGAACCTTCAATTTCC 59.527 52.381 0.00 0.00 36.97 3.13
86 87 2.790433 CGGGAGAACCTTCAATTTCCA 58.210 47.619 0.00 0.00 36.97 3.53
87 88 3.153919 CGGGAGAACCTTCAATTTCCAA 58.846 45.455 0.00 0.00 36.97 3.53
88 89 3.191371 CGGGAGAACCTTCAATTTCCAAG 59.809 47.826 0.00 0.00 36.97 3.61
89 90 3.511540 GGGAGAACCTTCAATTTCCAAGG 59.488 47.826 6.17 6.17 44.36 3.61
90 91 3.056536 GGAGAACCTTCAATTTCCAAGGC 60.057 47.826 7.30 0.00 42.80 4.35
91 92 3.829026 GAGAACCTTCAATTTCCAAGGCT 59.171 43.478 7.30 0.00 42.80 4.58
92 93 4.998051 AGAACCTTCAATTTCCAAGGCTA 58.002 39.130 7.30 0.00 42.80 3.93
93 94 4.767409 AGAACCTTCAATTTCCAAGGCTAC 59.233 41.667 7.30 1.61 42.80 3.58
94 95 4.388577 ACCTTCAATTTCCAAGGCTACT 57.611 40.909 7.30 0.00 42.80 2.57
95 96 5.514500 ACCTTCAATTTCCAAGGCTACTA 57.486 39.130 7.30 0.00 42.80 1.82
96 97 5.887754 ACCTTCAATTTCCAAGGCTACTAA 58.112 37.500 7.30 0.00 42.80 2.24
97 98 5.946377 ACCTTCAATTTCCAAGGCTACTAAG 59.054 40.000 7.30 0.00 42.80 2.18
111 112 4.916983 CTACTAAGCAGAGCAGACATCT 57.083 45.455 0.00 0.00 0.00 2.90
112 113 3.523606 ACTAAGCAGAGCAGACATCTG 57.476 47.619 4.43 4.43 45.71 2.90
113 114 3.095332 ACTAAGCAGAGCAGACATCTGA 58.905 45.455 13.15 0.00 45.80 3.27
114 115 3.705579 ACTAAGCAGAGCAGACATCTGAT 59.294 43.478 13.15 6.18 45.80 2.90
123 124 4.757594 AGCAGACATCTGATCTCTTCAAC 58.242 43.478 13.15 0.00 46.59 3.18
124 125 3.870419 GCAGACATCTGATCTCTTCAACC 59.130 47.826 13.15 0.00 46.59 3.77
125 126 4.622457 GCAGACATCTGATCTCTTCAACCA 60.622 45.833 13.15 0.00 46.59 3.67
126 127 5.672503 CAGACATCTGATCTCTTCAACCAT 58.327 41.667 2.51 0.00 46.59 3.55
127 128 5.524281 CAGACATCTGATCTCTTCAACCATG 59.476 44.000 2.51 0.00 46.59 3.66
128 129 5.424573 AGACATCTGATCTCTTCAACCATGA 59.575 40.000 0.00 0.00 32.78 3.07
129 130 6.099990 AGACATCTGATCTCTTCAACCATGAT 59.900 38.462 0.00 0.00 34.96 2.45
130 131 6.660800 ACATCTGATCTCTTCAACCATGATT 58.339 36.000 0.00 0.00 34.96 2.57
131 132 7.117397 ACATCTGATCTCTTCAACCATGATTT 58.883 34.615 0.00 0.00 34.96 2.17
132 133 7.614583 ACATCTGATCTCTTCAACCATGATTTT 59.385 33.333 0.00 0.00 34.96 1.82
133 134 7.621428 TCTGATCTCTTCAACCATGATTTTC 57.379 36.000 0.00 0.00 34.96 2.29
134 135 6.314648 TCTGATCTCTTCAACCATGATTTTCG 59.685 38.462 0.00 0.00 34.96 3.46
135 136 5.939883 TGATCTCTTCAACCATGATTTTCGT 59.060 36.000 0.00 0.00 34.96 3.85
136 137 6.430925 TGATCTCTTCAACCATGATTTTCGTT 59.569 34.615 0.00 0.00 34.96 3.85
137 138 7.606073 TGATCTCTTCAACCATGATTTTCGTTA 59.394 33.333 0.00 0.00 34.96 3.18
138 139 7.737972 TCTCTTCAACCATGATTTTCGTTAA 57.262 32.000 0.00 0.00 34.96 2.01
139 140 7.581476 TCTCTTCAACCATGATTTTCGTTAAC 58.419 34.615 0.00 0.00 34.96 2.01
140 141 7.227711 TCTCTTCAACCATGATTTTCGTTAACA 59.772 33.333 6.39 0.00 34.96 2.41
141 142 7.881142 TCTTCAACCATGATTTTCGTTAACAT 58.119 30.769 6.39 0.00 34.96 2.71
142 143 7.807433 TCTTCAACCATGATTTTCGTTAACATG 59.193 33.333 6.39 0.00 38.28 3.21
143 144 6.976088 TCAACCATGATTTTCGTTAACATGT 58.024 32.000 6.39 0.00 37.29 3.21
144 145 7.429633 TCAACCATGATTTTCGTTAACATGTT 58.570 30.769 16.68 16.68 37.29 2.71
145 146 7.923344 TCAACCATGATTTTCGTTAACATGTTT 59.077 29.630 17.78 0.95 37.29 2.83
146 147 8.547069 CAACCATGATTTTCGTTAACATGTTTT 58.453 29.630 17.78 0.00 37.29 2.43
147 148 8.071122 ACCATGATTTTCGTTAACATGTTTTG 57.929 30.769 17.78 7.20 37.29 2.44
148 149 7.708752 ACCATGATTTTCGTTAACATGTTTTGT 59.291 29.630 17.78 0.00 41.53 2.83
149 150 8.003224 CCATGATTTTCGTTAACATGTTTTGTG 58.997 33.333 17.78 5.02 38.99 3.33
159 160 4.893424 ACATGTTTTGTGTGTGTAGACC 57.107 40.909 0.00 0.00 37.11 3.85
160 161 3.311322 ACATGTTTTGTGTGTGTAGACCG 59.689 43.478 0.00 0.00 37.11 4.79
169 170 1.338973 GTGTGTAGACCGACAAGGACA 59.661 52.381 0.00 0.00 45.00 4.02
183 184 5.278463 CGACAAGGACACTTCCAAAATGAAT 60.278 40.000 0.00 0.00 45.72 2.57
185 186 7.521423 CGACAAGGACACTTCCAAAATGAATTA 60.521 37.037 0.00 0.00 45.72 1.40
191 192 9.178758 GGACACTTCCAAAATGAATTAGTCTAT 57.821 33.333 0.00 0.00 42.30 1.98
203 204 2.330440 TAGTCTATGACACCGCGGTA 57.670 50.000 33.70 17.44 34.60 4.02
210 211 0.248012 TGACACCGCGGTAACATGAT 59.752 50.000 33.70 10.36 0.00 2.45
217 218 1.781429 CGCGGTAACATGATCTCTTCG 59.219 52.381 0.00 0.00 0.00 3.79
227 228 9.039870 GTAACATGATCTCTTCGAAGATTTGAT 57.960 33.333 27.19 24.07 36.13 2.57
228 229 7.712264 ACATGATCTCTTCGAAGATTTGATC 57.288 36.000 30.46 30.46 36.13 2.92
269 270 3.447586 TGAGTTACTCCCTCCATTCGAAG 59.552 47.826 10.10 0.00 0.00 3.79
285 286 7.602644 TCCATTCGAAGATATAAGGCACATTAC 59.397 37.037 3.35 0.00 35.04 1.89
358 359 8.807948 AAATAGCAACATCTACATTACCAACT 57.192 30.769 0.00 0.00 0.00 3.16
495 497 8.962679 TCAAAAGTTCAGTACACCTTGTATTTT 58.037 29.630 0.00 0.00 35.05 1.82
496 498 9.233232 CAAAAGTTCAGTACACCTTGTATTTTC 57.767 33.333 0.00 0.00 35.05 2.29
497 499 6.780706 AGTTCAGTACACCTTGTATTTTCG 57.219 37.500 0.00 0.00 35.05 3.46
500 502 7.170998 AGTTCAGTACACCTTGTATTTTCGAAG 59.829 37.037 0.00 0.00 35.05 3.79
714 733 1.347097 CTCCACACGCGTCACATCTG 61.347 60.000 9.86 0.00 0.00 2.90
938 976 9.216117 GTAACAACTTAATTACATGACCAGTCT 57.784 33.333 0.00 0.00 32.56 3.24
940 978 9.787435 AACAACTTAATTACATGACCAGTCTAA 57.213 29.630 0.00 0.00 0.00 2.10
941 979 9.959721 ACAACTTAATTACATGACCAGTCTAAT 57.040 29.630 0.00 0.00 0.00 1.73
990 1028 2.874457 GCCGTATACATCCCAATCCCAC 60.874 54.545 3.32 0.00 0.00 4.61
1368 1455 2.343758 GTCCTGCTTGACGGCTCA 59.656 61.111 0.00 0.00 0.00 4.26
1529 1619 3.515286 CTTGCTGCCCGGCATGAG 61.515 66.667 13.86 7.45 42.09 2.90
2343 2493 5.381174 TGAGGCTGTCAAAATCAGAAATG 57.619 39.130 0.00 0.00 35.20 2.32
2355 2505 7.888021 TCAAAATCAGAAATGGGTATGTACAGT 59.112 33.333 0.33 0.00 0.00 3.55
2356 2506 9.173021 CAAAATCAGAAATGGGTATGTACAGTA 57.827 33.333 0.33 0.00 0.00 2.74
2357 2507 8.732746 AAATCAGAAATGGGTATGTACAGTAC 57.267 34.615 0.33 3.49 0.00 2.73
2358 2508 6.860790 TCAGAAATGGGTATGTACAGTACA 57.139 37.500 15.90 15.90 43.80 2.90
2359 2509 6.873997 TCAGAAATGGGTATGTACAGTACAG 58.126 40.000 18.30 1.38 42.77 2.74
2393 2543 3.056891 ACACTACATTTTCGCCCCAAATG 60.057 43.478 7.88 7.88 44.15 2.32
2485 2635 3.964688 TCTTATGGTCCGCTTTATGGAGA 59.035 43.478 0.00 0.00 35.82 3.71
2507 2657 8.184848 GGAGAGTAAATTATTCAGTGGAAAAGC 58.815 37.037 0.00 0.00 36.43 3.51
2526 2676 8.712363 GGAAAAGCTGAATTTGTTAAGGATTTC 58.288 33.333 0.00 0.00 0.00 2.17
2584 2734 9.880157 AGTATGAATTCAAGCAATTTAAAGCAT 57.120 25.926 13.09 0.00 34.60 3.79
2633 2783 7.770801 AGTTCTACAAAATTTTGAAACCAGC 57.229 32.000 32.20 16.89 40.55 4.85
2636 2786 3.202097 ACAAAATTTTGAAACCAGCCGG 58.798 40.909 32.20 0.00 40.55 6.13
2647 2797 2.507407 ACCAGCCGGTCACATTTATT 57.493 45.000 1.90 0.00 44.71 1.40
2648 2798 2.802719 ACCAGCCGGTCACATTTATTT 58.197 42.857 1.90 0.00 44.71 1.40
2653 2803 2.752903 GCCGGTCACATTTATTTGGAGT 59.247 45.455 1.90 0.00 0.00 3.85
2655 2805 4.732784 CCGGTCACATTTATTTGGAGTTG 58.267 43.478 0.00 0.00 0.00 3.16
2661 2811 7.273381 GGTCACATTTATTTGGAGTTGAAATCG 59.727 37.037 0.00 0.00 0.00 3.34
2732 2882 7.658179 TTGTTTTACAACATTTTGCAAGTGA 57.342 28.000 17.56 1.93 42.66 3.41
2734 2884 7.737395 TGTTTTACAACATTTTGCAAGTGAAG 58.263 30.769 17.56 12.18 38.03 3.02
2735 2885 7.600375 TGTTTTACAACATTTTGCAAGTGAAGA 59.400 29.630 17.56 0.00 38.03 2.87
2736 2886 7.518731 TTTACAACATTTTGCAAGTGAAGAC 57.481 32.000 17.56 0.00 36.00 3.01
2737 2887 5.070770 ACAACATTTTGCAAGTGAAGACA 57.929 34.783 17.56 0.00 36.00 3.41
2738 2888 5.663456 ACAACATTTTGCAAGTGAAGACAT 58.337 33.333 17.56 0.00 36.00 3.06
2739 2889 5.521010 ACAACATTTTGCAAGTGAAGACATG 59.479 36.000 17.56 0.00 36.00 3.21
2747 2898 3.738982 CAAGTGAAGACATGTGTGGGTA 58.261 45.455 1.15 0.00 0.00 3.69
2760 2911 3.139077 GTGTGGGTACAAGACTTCAAGG 58.861 50.000 0.00 0.00 38.82 3.61
2785 2936 5.052693 TCTGGATGGGGAACAATGATTAG 57.947 43.478 0.00 0.00 0.00 1.73
2829 2980 9.461312 AATACACTAAAGAAATGATACCTGCAA 57.539 29.630 0.00 0.00 0.00 4.08
2830 2981 7.759489 ACACTAAAGAAATGATACCTGCAAA 57.241 32.000 0.00 0.00 0.00 3.68
2831 2982 8.177119 ACACTAAAGAAATGATACCTGCAAAA 57.823 30.769 0.00 0.00 0.00 2.44
2832 2983 8.637986 ACACTAAAGAAATGATACCTGCAAAAA 58.362 29.630 0.00 0.00 0.00 1.94
2833 2984 9.643693 CACTAAAGAAATGATACCTGCAAAAAT 57.356 29.630 0.00 0.00 0.00 1.82
2999 3153 4.343814 TGATTTGGTGGAGAAGGAAAAACC 59.656 41.667 0.00 0.00 39.35 3.27
3014 3168 9.778993 GAAGGAAAAACCGAATAATAGGTAAAC 57.221 33.333 0.00 0.00 44.74 2.01
3023 3177 9.305555 ACCGAATAATAGGTAAACTATGCTCTA 57.694 33.333 0.00 0.00 41.54 2.43
3057 3211 9.491675 AATCTTGTTGTTATTTGCATGAATGAA 57.508 25.926 0.00 0.00 0.00 2.57
3185 3340 5.829924 AGCAATTATAAAGGATGTCACTGGG 59.170 40.000 0.00 0.00 0.00 4.45
3203 3358 8.504815 GTCACTGGGAATTTCTCTAAAAGTAAC 58.495 37.037 0.00 0.00 0.00 2.50
3228 3383 1.823899 GGGCAGGGTGGATTTAGCG 60.824 63.158 0.00 0.00 0.00 4.26
3287 3527 5.242838 TGTGTGTTATCCTTCATGGGAAAAC 59.757 40.000 0.00 0.00 39.02 2.43
3289 3529 6.015918 TGTGTTATCCTTCATGGGAAAACAT 58.984 36.000 0.00 0.00 39.02 2.71
3290 3530 6.152661 TGTGTTATCCTTCATGGGAAAACATC 59.847 38.462 0.00 0.00 39.02 3.06
3291 3531 6.378280 GTGTTATCCTTCATGGGAAAACATCT 59.622 38.462 0.00 0.00 39.02 2.90
3292 3532 6.603201 TGTTATCCTTCATGGGAAAACATCTC 59.397 38.462 0.00 0.00 39.02 2.75
3309 3549 5.969423 ACATCTCATTGTTTAAGGCATTGG 58.031 37.500 0.00 0.00 0.00 3.16
3351 3591 8.415553 CCATTGGCAAATCTAATTTCTGACATA 58.584 33.333 3.01 0.00 0.00 2.29
3506 3746 2.146342 CATGGCAGTCTTGTTCGTCTT 58.854 47.619 0.00 0.00 0.00 3.01
3570 3813 4.997395 ACGAATACATGCAGAACAAGAGTT 59.003 37.500 0.00 0.00 41.64 3.01
3600 3846 7.569111 ACATCTACATATTTGGTACTCCCTTCT 59.431 37.037 0.00 0.00 0.00 2.85
3603 3849 9.670442 TCTACATATTTGGTACTCCCTTCTTAT 57.330 33.333 0.00 0.00 0.00 1.73
3614 3864 7.283354 GGTACTCCCTTCTTATTGGAATTTCTG 59.717 40.741 0.00 0.00 0.00 3.02
3639 3889 7.431084 TGAAGTTCTTGCGAAAAGTTAAATGTC 59.569 33.333 4.17 0.00 0.00 3.06
3821 4075 1.333308 TGTGCAGGACAAAATCGTGTG 59.667 47.619 0.00 0.00 43.76 3.82
4041 4324 2.805194 ACGCTGTATATACTCCCTCCC 58.195 52.381 13.89 0.00 0.00 4.30
4045 4328 3.813240 GCTGTATATACTCCCTCCCGTCA 60.813 52.174 13.89 0.00 0.00 4.35
4061 4344 5.492895 TCCCGTCATTTTTAGTCTGCATAA 58.507 37.500 0.00 0.00 0.00 1.90
4071 4357 9.995003 ATTTTTAGTCTGCATAAATTTTGACCA 57.005 25.926 0.00 0.00 0.00 4.02
4100 4386 8.515414 GTTAAAGCATCTCTACTTTGACCAAAT 58.485 33.333 0.00 0.00 36.76 2.32
4102 4388 8.635765 AAAGCATCTCTACTTTGACCAAATTA 57.364 30.769 0.00 0.00 34.88 1.40
4239 4529 7.995463 TGTATTTGGTCAAACTTTGTAAAGC 57.005 32.000 4.35 0.00 39.63 3.51
4248 4538 6.329496 TCAAACTTTGTAAAGCTTGACTTGG 58.671 36.000 15.19 7.18 42.74 3.61
4254 4544 9.909177 ACTTTGTAAAGCTTGACTTGGCACAAG 62.909 40.741 15.19 10.94 41.24 3.16
4270 4560 4.100529 GCACAAGTCTAATACGCGAAGTA 58.899 43.478 15.93 0.00 40.03 2.24
4281 4571 2.563702 ACGCGAAGTAAAAAGGACCAA 58.436 42.857 15.93 0.00 0.00 3.67
4396 4737 8.394121 CCTCTTAGAGCATATTTTGTTTGAGAC 58.606 37.037 3.26 0.00 0.00 3.36
4421 4762 9.014297 ACTTGATAGTGTTTATAAGCAGCTTTT 57.986 29.630 14.29 8.27 31.99 2.27
4481 4822 7.593273 TGAAGTAACATAGGCATTTTGTTTTCG 59.407 33.333 4.97 0.00 35.37 3.46
4483 4824 7.653647 AGTAACATAGGCATTTTGTTTTCGAA 58.346 30.769 0.00 0.00 35.37 3.71
4689 5038 3.375299 CCGGGAACATTCTTCTTGATGAC 59.625 47.826 0.00 0.00 0.00 3.06
4822 5549 9.638239 ATGTATATTCACCACACAAAAATGTTC 57.362 29.630 0.00 0.00 0.00 3.18
5232 5960 2.093537 GAGCCTGAGATACTGCCCGG 62.094 65.000 0.00 0.00 0.00 5.73
5327 6055 1.295357 TGTGGCCATGTTTACGAGCG 61.295 55.000 9.72 0.00 0.00 5.03
5441 6169 4.104102 ACTTGAACCCCACTACAATTGAGA 59.896 41.667 13.59 0.00 0.00 3.27
5455 6183 4.062991 CAATTGAGATGAGATCGCCATCA 58.937 43.478 23.62 10.93 42.03 3.07
5527 6255 7.997107 TCGTACATAGGAATCATTTACACAC 57.003 36.000 0.00 0.00 0.00 3.82
5680 6410 5.776173 AGGTAAACATCTATCCTCGTCTG 57.224 43.478 0.00 0.00 0.00 3.51
5973 6703 0.854218 TCCTTTTTGTAGGCCCACCA 59.146 50.000 0.00 0.00 39.06 4.17
5974 6704 1.431243 TCCTTTTTGTAGGCCCACCAT 59.569 47.619 0.00 0.00 39.06 3.55
5985 6715 0.684479 GCCCACCATTCCCCTTTCTC 60.684 60.000 0.00 0.00 0.00 2.87
5997 6727 6.668133 TTCCCCTTTCTCTGGGTATTTATT 57.332 37.500 0.00 0.00 43.09 1.40
6007 6737 7.570132 TCTCTGGGTATTTATTCGGAATCAAA 58.430 34.615 6.49 7.07 0.00 2.69
6244 6979 0.597637 GTGGACGGCGGATGTGATAG 60.598 60.000 13.24 0.00 0.00 2.08
6246 6981 1.067416 GACGGCGGATGTGATAGCA 59.933 57.895 13.24 0.00 0.00 3.49
6279 7014 5.982890 ATTTCACCATTCGGAAGTCATTT 57.017 34.783 0.00 0.00 35.59 2.32
6312 7047 3.316283 ACATGCAAAACAATGCTTACGG 58.684 40.909 0.00 0.00 46.54 4.02
6364 7099 1.952621 TAGTTAGCAAGCTGAGGGGT 58.047 50.000 4.53 0.00 0.00 4.95
6428 7163 2.734276 ACGGAAAGAGAGTTGAGCTC 57.266 50.000 6.82 6.82 44.45 4.09
6445 7180 9.732130 AGTTGAGCTCTTTTGTTCTATTAAGAT 57.268 29.630 16.19 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.599244 TGAAAAAGATCAGAGTGACTTGTGTT 59.401 34.615 0.00 0.00 0.00 3.32
1 2 6.115446 TGAAAAAGATCAGAGTGACTTGTGT 58.885 36.000 0.00 0.00 0.00 3.72
2 3 6.609237 TGAAAAAGATCAGAGTGACTTGTG 57.391 37.500 0.00 0.00 0.00 3.33
3 4 6.261826 CCTTGAAAAAGATCAGAGTGACTTGT 59.738 38.462 0.00 0.00 0.00 3.16
4 5 6.261826 ACCTTGAAAAAGATCAGAGTGACTTG 59.738 38.462 0.00 0.00 0.00 3.16
5 6 6.360618 ACCTTGAAAAAGATCAGAGTGACTT 58.639 36.000 0.00 0.00 0.00 3.01
6 7 5.934781 ACCTTGAAAAAGATCAGAGTGACT 58.065 37.500 0.00 0.00 0.00 3.41
7 8 7.730364 TTACCTTGAAAAAGATCAGAGTGAC 57.270 36.000 0.00 0.00 0.00 3.67
8 9 8.746052 TTTTACCTTGAAAAAGATCAGAGTGA 57.254 30.769 0.00 0.00 0.00 3.41
9 10 9.617975 GATTTTACCTTGAAAAAGATCAGAGTG 57.382 33.333 0.00 0.00 32.29 3.51
10 11 8.507249 CGATTTTACCTTGAAAAAGATCAGAGT 58.493 33.333 0.00 0.00 32.29 3.24
11 12 8.721478 TCGATTTTACCTTGAAAAAGATCAGAG 58.279 33.333 0.00 0.00 32.29 3.35
12 13 8.615878 TCGATTTTACCTTGAAAAAGATCAGA 57.384 30.769 0.00 0.00 32.29 3.27
13 14 9.282247 CATCGATTTTACCTTGAAAAAGATCAG 57.718 33.333 0.00 0.00 32.34 2.90
14 15 9.008965 TCATCGATTTTACCTTGAAAAAGATCA 57.991 29.630 0.00 0.00 32.34 2.92
15 16 9.278734 GTCATCGATTTTACCTTGAAAAAGATC 57.721 33.333 0.00 0.00 32.34 2.75
16 17 7.962918 CGTCATCGATTTTACCTTGAAAAAGAT 59.037 33.333 0.00 0.00 39.71 2.40
17 18 7.295201 CGTCATCGATTTTACCTTGAAAAAGA 58.705 34.615 0.00 0.00 39.71 2.52
18 19 6.523201 CCGTCATCGATTTTACCTTGAAAAAG 59.477 38.462 0.00 0.00 39.71 2.27
19 20 6.205076 TCCGTCATCGATTTTACCTTGAAAAA 59.795 34.615 0.00 0.00 39.71 1.94
20 21 5.701750 TCCGTCATCGATTTTACCTTGAAAA 59.298 36.000 0.00 0.00 39.71 2.29
21 22 5.239351 TCCGTCATCGATTTTACCTTGAAA 58.761 37.500 0.00 0.00 39.71 2.69
22 23 4.823157 TCCGTCATCGATTTTACCTTGAA 58.177 39.130 0.00 0.00 39.71 2.69
23 24 4.459390 TCCGTCATCGATTTTACCTTGA 57.541 40.909 0.00 0.00 39.71 3.02
24 25 6.645003 TGATATCCGTCATCGATTTTACCTTG 59.355 38.462 0.00 0.00 39.71 3.61
25 26 6.755206 TGATATCCGTCATCGATTTTACCTT 58.245 36.000 0.00 0.00 39.71 3.50
26 27 6.340962 TGATATCCGTCATCGATTTTACCT 57.659 37.500 0.00 0.00 39.71 3.08
27 28 6.590292 ACATGATATCCGTCATCGATTTTACC 59.410 38.462 0.00 0.00 36.72 2.85
28 29 7.328493 TCACATGATATCCGTCATCGATTTTAC 59.672 37.037 0.00 0.00 36.72 2.01
29 30 7.328493 GTCACATGATATCCGTCATCGATTTTA 59.672 37.037 0.00 0.00 36.72 1.52
30 31 6.146184 GTCACATGATATCCGTCATCGATTTT 59.854 38.462 0.00 0.00 36.72 1.82
31 32 5.635280 GTCACATGATATCCGTCATCGATTT 59.365 40.000 0.00 0.00 36.72 2.17
32 33 5.047731 AGTCACATGATATCCGTCATCGATT 60.048 40.000 0.00 0.00 36.72 3.34
33 34 4.460731 AGTCACATGATATCCGTCATCGAT 59.539 41.667 0.00 0.00 36.72 3.59
34 35 3.821033 AGTCACATGATATCCGTCATCGA 59.179 43.478 0.00 0.00 36.72 3.59
35 36 4.166187 AGTCACATGATATCCGTCATCG 57.834 45.455 0.00 0.00 36.72 3.84
36 37 5.777802 AGAAGTCACATGATATCCGTCATC 58.222 41.667 0.00 0.00 36.72 2.92
37 38 5.798125 AGAAGTCACATGATATCCGTCAT 57.202 39.130 0.00 0.00 39.34 3.06
38 39 5.598416 AAGAAGTCACATGATATCCGTCA 57.402 39.130 0.00 0.00 0.00 4.35
39 40 6.019479 GTCAAAGAAGTCACATGATATCCGTC 60.019 42.308 0.00 0.00 0.00 4.79
40 41 5.812642 GTCAAAGAAGTCACATGATATCCGT 59.187 40.000 0.00 0.00 0.00 4.69
41 42 5.051441 CGTCAAAGAAGTCACATGATATCCG 60.051 44.000 0.00 0.00 0.00 4.18
42 43 5.277058 GCGTCAAAGAAGTCACATGATATCC 60.277 44.000 0.00 0.00 0.00 2.59
43 44 5.555256 CGCGTCAAAGAAGTCACATGATATC 60.555 44.000 0.00 0.00 0.00 1.63
44 45 4.268644 CGCGTCAAAGAAGTCACATGATAT 59.731 41.667 0.00 0.00 0.00 1.63
45 46 3.612423 CGCGTCAAAGAAGTCACATGATA 59.388 43.478 0.00 0.00 0.00 2.15
46 47 2.413112 CGCGTCAAAGAAGTCACATGAT 59.587 45.455 0.00 0.00 0.00 2.45
47 48 1.792367 CGCGTCAAAGAAGTCACATGA 59.208 47.619 0.00 0.00 0.00 3.07
48 49 1.136252 CCGCGTCAAAGAAGTCACATG 60.136 52.381 4.92 0.00 0.00 3.21
49 50 1.148310 CCGCGTCAAAGAAGTCACAT 58.852 50.000 4.92 0.00 0.00 3.21
50 51 0.878523 CCCGCGTCAAAGAAGTCACA 60.879 55.000 4.92 0.00 0.00 3.58
51 52 0.599204 TCCCGCGTCAAAGAAGTCAC 60.599 55.000 4.92 0.00 0.00 3.67
52 53 0.319555 CTCCCGCGTCAAAGAAGTCA 60.320 55.000 4.92 0.00 0.00 3.41
53 54 0.038526 TCTCCCGCGTCAAAGAAGTC 60.039 55.000 4.92 0.00 0.00 3.01
54 55 0.391597 TTCTCCCGCGTCAAAGAAGT 59.608 50.000 4.92 0.00 0.00 3.01
55 56 0.790814 GTTCTCCCGCGTCAAAGAAG 59.209 55.000 4.92 0.00 0.00 2.85
56 57 0.601841 GGTTCTCCCGCGTCAAAGAA 60.602 55.000 4.92 5.51 0.00 2.52
57 58 1.005394 GGTTCTCCCGCGTCAAAGA 60.005 57.895 4.92 0.00 0.00 2.52
58 59 0.602905 AAGGTTCTCCCGCGTCAAAG 60.603 55.000 4.92 0.00 38.74 2.77
59 60 0.601841 GAAGGTTCTCCCGCGTCAAA 60.602 55.000 4.92 0.00 38.74 2.69
60 61 1.005394 GAAGGTTCTCCCGCGTCAA 60.005 57.895 4.92 0.00 38.74 3.18
61 62 1.750341 TTGAAGGTTCTCCCGCGTCA 61.750 55.000 4.92 0.00 38.74 4.35
62 63 0.391263 ATTGAAGGTTCTCCCGCGTC 60.391 55.000 4.92 0.00 38.74 5.19
63 64 0.036306 AATTGAAGGTTCTCCCGCGT 59.964 50.000 4.92 0.00 38.74 6.01
64 65 1.130561 GAAATTGAAGGTTCTCCCGCG 59.869 52.381 0.00 0.00 38.74 6.46
65 66 1.472878 GGAAATTGAAGGTTCTCCCGC 59.527 52.381 0.00 0.00 38.74 6.13
66 67 2.790433 TGGAAATTGAAGGTTCTCCCG 58.210 47.619 0.00 0.00 38.74 5.14
67 68 3.511540 CCTTGGAAATTGAAGGTTCTCCC 59.488 47.826 0.00 0.00 35.01 4.30
68 69 3.056536 GCCTTGGAAATTGAAGGTTCTCC 60.057 47.826 11.08 0.00 40.89 3.71
69 70 3.829026 AGCCTTGGAAATTGAAGGTTCTC 59.171 43.478 11.08 0.00 40.89 2.87
70 71 3.849527 AGCCTTGGAAATTGAAGGTTCT 58.150 40.909 11.08 1.44 40.89 3.01
71 72 4.767409 AGTAGCCTTGGAAATTGAAGGTTC 59.233 41.667 11.08 4.73 40.89 3.62
72 73 4.740902 AGTAGCCTTGGAAATTGAAGGTT 58.259 39.130 11.08 8.56 40.89 3.50
73 74 4.388577 AGTAGCCTTGGAAATTGAAGGT 57.611 40.909 11.08 3.76 40.89 3.50
74 75 5.163612 GCTTAGTAGCCTTGGAAATTGAAGG 60.164 44.000 6.75 6.75 41.74 3.46
75 76 5.884771 GCTTAGTAGCCTTGGAAATTGAAG 58.115 41.667 0.00 0.00 41.74 3.02
76 77 5.897377 GCTTAGTAGCCTTGGAAATTGAA 57.103 39.130 0.00 0.00 41.74 2.69
88 89 7.954705 CAGATGTCTGCTCTGCTTAGTAGCC 62.955 52.000 0.00 0.00 40.85 3.93
89 90 5.028291 CAGATGTCTGCTCTGCTTAGTAGC 61.028 50.000 0.00 0.00 41.42 3.58
90 91 4.337836 TCAGATGTCTGCTCTGCTTAGTAG 59.662 45.833 5.14 0.00 43.46 2.57
91 92 4.273318 TCAGATGTCTGCTCTGCTTAGTA 58.727 43.478 5.14 0.00 43.46 1.82
92 93 3.095332 TCAGATGTCTGCTCTGCTTAGT 58.905 45.455 5.14 0.00 43.46 2.24
93 94 3.797451 TCAGATGTCTGCTCTGCTTAG 57.203 47.619 5.14 0.00 43.46 2.18
94 95 3.959449 AGATCAGATGTCTGCTCTGCTTA 59.041 43.478 13.81 0.00 44.81 3.09
95 96 2.767394 AGATCAGATGTCTGCTCTGCTT 59.233 45.455 13.81 0.00 44.81 3.91
96 97 2.363038 GAGATCAGATGTCTGCTCTGCT 59.637 50.000 18.12 5.68 46.01 4.24
97 98 2.363038 AGAGATCAGATGTCTGCTCTGC 59.637 50.000 18.12 11.10 46.01 4.26
98 99 4.098196 TGAAGAGATCAGATGTCTGCTCTG 59.902 45.833 18.12 1.08 46.01 3.35
100 101 4.652421 TGAAGAGATCAGATGTCTGCTC 57.348 45.455 15.24 9.07 43.46 4.26
101 102 4.382901 GGTTGAAGAGATCAGATGTCTGCT 60.383 45.833 15.24 0.00 43.46 4.24
102 103 3.870419 GGTTGAAGAGATCAGATGTCTGC 59.130 47.826 10.79 9.57 43.46 4.26
103 104 5.082251 TGGTTGAAGAGATCAGATGTCTG 57.918 43.478 10.79 3.61 45.08 3.51
104 105 5.424573 TCATGGTTGAAGAGATCAGATGTCT 59.575 40.000 4.16 4.16 39.77 3.41
105 106 5.668471 TCATGGTTGAAGAGATCAGATGTC 58.332 41.667 0.00 0.00 39.77 3.06
106 107 5.688814 TCATGGTTGAAGAGATCAGATGT 57.311 39.130 0.00 0.00 39.77 3.06
107 108 7.569639 AAATCATGGTTGAAGAGATCAGATG 57.430 36.000 0.00 0.00 39.77 2.90
108 109 7.012138 CGAAAATCATGGTTGAAGAGATCAGAT 59.988 37.037 0.00 0.00 39.77 2.90
109 110 6.314648 CGAAAATCATGGTTGAAGAGATCAGA 59.685 38.462 0.00 0.00 39.77 3.27
110 111 6.093219 ACGAAAATCATGGTTGAAGAGATCAG 59.907 38.462 0.00 0.00 39.77 2.90
111 112 5.939883 ACGAAAATCATGGTTGAAGAGATCA 59.060 36.000 0.00 0.00 34.96 2.92
112 113 6.428385 ACGAAAATCATGGTTGAAGAGATC 57.572 37.500 0.00 0.00 34.96 2.75
113 114 6.824305 AACGAAAATCATGGTTGAAGAGAT 57.176 33.333 0.00 0.00 34.96 2.75
114 115 7.227711 TGTTAACGAAAATCATGGTTGAAGAGA 59.772 33.333 0.26 0.00 34.96 3.10
115 116 7.359595 TGTTAACGAAAATCATGGTTGAAGAG 58.640 34.615 0.26 0.00 34.96 2.85
116 117 7.265647 TGTTAACGAAAATCATGGTTGAAGA 57.734 32.000 0.26 0.00 34.96 2.87
117 118 7.594758 ACATGTTAACGAAAATCATGGTTGAAG 59.405 33.333 0.26 0.00 39.76 3.02
118 119 7.429633 ACATGTTAACGAAAATCATGGTTGAA 58.570 30.769 0.26 0.00 39.76 2.69
119 120 6.976088 ACATGTTAACGAAAATCATGGTTGA 58.024 32.000 0.26 0.00 39.76 3.18
120 121 7.636259 AACATGTTAACGAAAATCATGGTTG 57.364 32.000 9.97 0.00 39.76 3.77
121 122 8.547069 CAAAACATGTTAACGAAAATCATGGTT 58.453 29.630 12.39 0.00 44.66 3.67
122 123 7.708752 ACAAAACATGTTAACGAAAATCATGGT 59.291 29.630 12.39 0.00 40.06 3.55
123 124 8.003224 CACAAAACATGTTAACGAAAATCATGG 58.997 33.333 12.39 0.00 41.46 3.66
124 125 8.538856 ACACAAAACATGTTAACGAAAATCATG 58.461 29.630 12.39 0.00 41.46 3.07
125 126 8.538856 CACACAAAACATGTTAACGAAAATCAT 58.461 29.630 12.39 0.00 41.46 2.45
126 127 7.542477 ACACACAAAACATGTTAACGAAAATCA 59.458 29.630 12.39 0.00 41.46 2.57
127 128 7.838879 CACACACAAAACATGTTAACGAAAATC 59.161 33.333 12.39 0.00 41.46 2.17
128 129 7.329717 ACACACACAAAACATGTTAACGAAAAT 59.670 29.630 12.39 0.00 41.46 1.82
129 130 6.641314 ACACACACAAAACATGTTAACGAAAA 59.359 30.769 12.39 0.00 41.46 2.29
130 131 6.150318 ACACACACAAAACATGTTAACGAAA 58.850 32.000 12.39 0.00 41.46 3.46
131 132 5.700846 ACACACACAAAACATGTTAACGAA 58.299 33.333 12.39 0.00 41.46 3.85
132 133 5.298197 ACACACACAAAACATGTTAACGA 57.702 34.783 12.39 0.00 41.46 3.85
133 134 6.409761 GTCTACACACACAAAACATGTTAACG 59.590 38.462 12.39 5.92 41.46 3.18
134 135 6.689669 GGTCTACACACACAAAACATGTTAAC 59.310 38.462 12.39 0.00 41.46 2.01
135 136 6.457122 CGGTCTACACACACAAAACATGTTAA 60.457 38.462 12.39 0.00 41.46 2.01
136 137 5.006844 CGGTCTACACACACAAAACATGTTA 59.993 40.000 12.39 0.00 41.46 2.41
137 138 4.201871 CGGTCTACACACACAAAACATGTT 60.202 41.667 4.92 4.92 41.46 2.71
138 139 3.311322 CGGTCTACACACACAAAACATGT 59.689 43.478 0.00 0.00 45.34 3.21
139 140 3.558006 TCGGTCTACACACACAAAACATG 59.442 43.478 0.00 0.00 0.00 3.21
140 141 3.558418 GTCGGTCTACACACACAAAACAT 59.442 43.478 0.00 0.00 0.00 2.71
141 142 2.931325 GTCGGTCTACACACACAAAACA 59.069 45.455 0.00 0.00 0.00 2.83
142 143 2.931325 TGTCGGTCTACACACACAAAAC 59.069 45.455 0.00 0.00 0.00 2.43
143 144 3.248495 TGTCGGTCTACACACACAAAA 57.752 42.857 0.00 0.00 0.00 2.44
144 145 2.963548 TGTCGGTCTACACACACAAA 57.036 45.000 0.00 0.00 0.00 2.83
145 146 2.482316 CCTTGTCGGTCTACACACACAA 60.482 50.000 0.00 0.00 0.00 3.33
146 147 1.067974 CCTTGTCGGTCTACACACACA 59.932 52.381 0.00 0.00 0.00 3.72
147 148 1.338973 TCCTTGTCGGTCTACACACAC 59.661 52.381 0.00 0.00 0.00 3.82
148 149 1.338973 GTCCTTGTCGGTCTACACACA 59.661 52.381 0.00 0.00 0.00 3.72
149 150 1.338973 TGTCCTTGTCGGTCTACACAC 59.661 52.381 0.00 0.00 0.00 3.82
159 160 3.563808 TCATTTTGGAAGTGTCCTTGTCG 59.436 43.478 0.00 0.00 45.22 4.35
160 161 5.514274 TTCATTTTGGAAGTGTCCTTGTC 57.486 39.130 0.00 0.00 45.22 3.18
169 170 9.739276 TGTCATAGACTAATTCATTTTGGAAGT 57.261 29.630 0.00 0.00 33.15 3.01
183 184 1.466856 ACCGCGGTGTCATAGACTAA 58.533 50.000 33.75 0.00 33.15 2.24
185 186 1.133790 GTTACCGCGGTGTCATAGACT 59.866 52.381 40.02 12.21 33.15 3.24
191 192 0.248012 ATCATGTTACCGCGGTGTCA 59.752 50.000 40.02 33.65 0.00 3.58
203 204 7.042858 CGATCAAATCTTCGAAGAGATCATGTT 60.043 37.037 32.99 21.39 38.66 2.71
210 211 4.202060 CCCTCGATCAAATCTTCGAAGAGA 60.202 45.833 29.89 22.35 43.14 3.10
217 218 3.166489 ACGACCCTCGATCAAATCTTC 57.834 47.619 0.00 0.00 43.74 2.87
227 228 3.318839 TCAAAGTCTTAAACGACCCTCGA 59.681 43.478 0.00 0.00 43.74 4.04
228 229 3.645884 TCAAAGTCTTAAACGACCCTCG 58.354 45.455 0.00 0.00 46.93 4.63
495 497 3.744719 CGTGCTCCGTCCCTTCGA 61.745 66.667 0.00 0.00 0.00 3.71
564 571 2.009042 GCCGCCATCTGATATGCCTAC 61.009 57.143 5.94 0.00 0.00 3.18
626 633 6.238953 CGGAATAGTACAAGCTATAGTGTGGT 60.239 42.308 0.84 0.00 31.94 4.16
730 749 8.661145 TCAAGGAAGTTGCAATCATCAGTTGAT 61.661 37.037 0.59 0.00 40.31 2.57
883 910 8.568676 TCTTGGACCGATATCAAAACATTTAA 57.431 30.769 3.12 0.00 0.00 1.52
886 913 6.414732 TCTCTTGGACCGATATCAAAACATT 58.585 36.000 3.12 0.00 0.00 2.71
888 915 5.414789 TCTCTTGGACCGATATCAAAACA 57.585 39.130 3.12 0.00 0.00 2.83
894 930 4.583489 TGTTACCTCTCTTGGACCGATATC 59.417 45.833 0.00 0.00 0.00 1.63
895 931 4.543689 TGTTACCTCTCTTGGACCGATAT 58.456 43.478 0.00 0.00 0.00 1.63
896 932 3.972133 TGTTACCTCTCTTGGACCGATA 58.028 45.455 0.00 0.00 0.00 2.92
938 976 5.242434 TGCGACCTTTTCAAAGCTAGATTA 58.758 37.500 0.00 0.00 34.69 1.75
939 977 4.072131 TGCGACCTTTTCAAAGCTAGATT 58.928 39.130 0.00 0.00 34.69 2.40
940 978 3.674997 TGCGACCTTTTCAAAGCTAGAT 58.325 40.909 0.00 0.00 34.69 1.98
941 979 3.067106 CTGCGACCTTTTCAAAGCTAGA 58.933 45.455 0.00 0.00 34.69 2.43
942 980 3.067106 TCTGCGACCTTTTCAAAGCTAG 58.933 45.455 0.00 0.00 34.69 3.42
990 1028 1.450848 ACAGCTCATGCATGGACCG 60.451 57.895 25.97 14.70 42.74 4.79
1294 1381 2.032681 GTCAAGGAGCGGCTGGTT 59.967 61.111 7.50 0.00 0.00 3.67
1327 1414 3.470567 GCCGACGTCGTTGAGCAG 61.471 66.667 33.49 18.76 37.74 4.24
1529 1619 1.676967 CAGAGGTTCTTGCCCAGCC 60.677 63.158 0.00 0.00 0.00 4.85
1602 1692 3.450115 GTGCGGCGGTAGTCTCCT 61.450 66.667 9.78 0.00 0.00 3.69
1752 1842 4.436998 GGGCTCGTCGTCACCAGG 62.437 72.222 0.00 0.00 0.00 4.45
2271 2421 2.866156 ACGTAGATCAACAATGGCATCG 59.134 45.455 0.00 0.00 0.00 3.84
2343 2493 6.269307 ACCCATAATCTGTACTGTACATACCC 59.731 42.308 19.99 0.00 38.15 3.69
2355 2505 5.274015 TGTAGTGTCCACCCATAATCTGTA 58.726 41.667 0.00 0.00 0.00 2.74
2356 2506 4.101114 TGTAGTGTCCACCCATAATCTGT 58.899 43.478 0.00 0.00 0.00 3.41
2357 2507 4.753516 TGTAGTGTCCACCCATAATCTG 57.246 45.455 0.00 0.00 0.00 2.90
2358 2508 5.975988 AATGTAGTGTCCACCCATAATCT 57.024 39.130 0.00 0.00 0.00 2.40
2359 2509 6.238374 CGAAAATGTAGTGTCCACCCATAATC 60.238 42.308 0.00 0.22 0.00 1.75
2393 2543 7.981102 ACAAGGATTAGGACTGAAGTTAAAC 57.019 36.000 0.00 0.00 0.00 2.01
2397 2547 7.690256 ACAATACAAGGATTAGGACTGAAGTT 58.310 34.615 0.00 0.00 0.00 2.66
2464 2614 4.202264 ACTCTCCATAAAGCGGACCATAAG 60.202 45.833 0.00 0.00 0.00 1.73
2485 2635 8.635765 TCAGCTTTTCCACTGAATAATTTACT 57.364 30.769 0.00 0.00 39.89 2.24
2633 2783 4.457603 TCAACTCCAAATAAATGTGACCGG 59.542 41.667 0.00 0.00 0.00 5.28
2636 2786 8.020819 TCGATTTCAACTCCAAATAAATGTGAC 58.979 33.333 0.00 0.00 0.00 3.67
2644 2794 7.770433 ACATCTCATCGATTTCAACTCCAAATA 59.230 33.333 0.00 0.00 0.00 1.40
2645 2795 6.600822 ACATCTCATCGATTTCAACTCCAAAT 59.399 34.615 0.00 0.00 0.00 2.32
2646 2796 5.939883 ACATCTCATCGATTTCAACTCCAAA 59.060 36.000 0.00 0.00 0.00 3.28
2647 2797 5.352293 CACATCTCATCGATTTCAACTCCAA 59.648 40.000 0.00 0.00 0.00 3.53
2648 2798 4.872124 CACATCTCATCGATTTCAACTCCA 59.128 41.667 0.00 0.00 0.00 3.86
2709 2859 7.600375 TCTTCACTTGCAAAATGTTGTAAAACA 59.400 29.630 0.00 0.00 38.63 2.83
2731 2881 3.746492 GTCTTGTACCCACACATGTCTTC 59.254 47.826 0.00 0.00 33.30 2.87
2732 2882 3.391296 AGTCTTGTACCCACACATGTCTT 59.609 43.478 0.00 0.00 33.30 3.01
2734 2884 3.402628 AGTCTTGTACCCACACATGTC 57.597 47.619 0.00 0.00 33.30 3.06
2735 2885 3.135712 TGAAGTCTTGTACCCACACATGT 59.864 43.478 0.00 0.00 33.30 3.21
2736 2886 3.738982 TGAAGTCTTGTACCCACACATG 58.261 45.455 0.00 0.00 33.30 3.21
2737 2887 4.389374 CTTGAAGTCTTGTACCCACACAT 58.611 43.478 0.00 0.00 33.30 3.21
2738 2888 3.433031 CCTTGAAGTCTTGTACCCACACA 60.433 47.826 0.00 0.00 33.30 3.72
2739 2889 3.139077 CCTTGAAGTCTTGTACCCACAC 58.861 50.000 0.00 0.00 33.30 3.82
2747 2898 4.503714 TCCAGAAACCTTGAAGTCTTGT 57.496 40.909 0.00 0.00 0.00 3.16
2760 2911 3.430453 TCATTGTTCCCCATCCAGAAAC 58.570 45.455 0.00 0.00 0.00 2.78
2807 2958 9.643693 ATTTTTGCAGGTATCATTTCTTTAGTG 57.356 29.630 0.00 0.00 0.00 2.74
3023 3177 8.306038 TGCAAATAACAACAAGATTGAGCTATT 58.694 29.630 0.00 0.00 0.00 1.73
3185 3340 9.922305 CCGATGATGTTACTTTTAGAGAAATTC 57.078 33.333 0.00 0.00 0.00 2.17
3203 3358 2.060567 ATCCACCCTGCCCGATGATG 62.061 60.000 0.00 0.00 0.00 3.07
3228 3383 5.454232 CACATTGACGAACCTTGTAAACAAC 59.546 40.000 0.00 0.00 0.00 3.32
3287 3527 4.807304 GCCAATGCCTTAAACAATGAGATG 59.193 41.667 0.00 0.00 0.00 2.90
3289 3529 3.831333 TGCCAATGCCTTAAACAATGAGA 59.169 39.130 0.00 0.00 36.33 3.27
3290 3530 4.191033 TGCCAATGCCTTAAACAATGAG 57.809 40.909 0.00 0.00 36.33 2.90
3291 3531 4.822685 ATGCCAATGCCTTAAACAATGA 57.177 36.364 0.00 0.00 36.33 2.57
3292 3532 7.660112 TCTATATGCCAATGCCTTAAACAATG 58.340 34.615 0.00 0.00 36.33 2.82
3296 3536 7.169813 GCTTTTCTATATGCCAATGCCTTAAAC 59.830 37.037 0.00 0.00 36.33 2.01
3309 3549 4.553323 CCAATGGCTGCTTTTCTATATGC 58.447 43.478 0.00 0.00 0.00 3.14
3351 3591 5.129320 GCCCCTGGTGATTTTAGAATTTGAT 59.871 40.000 0.00 0.00 0.00 2.57
3506 3746 2.417379 GCCTTCATCACAGTAAGCGAGA 60.417 50.000 0.00 0.00 0.00 4.04
3570 3813 7.990886 GGGAGTACCAAATATGTAGATGTTCAA 59.009 37.037 0.00 0.00 39.85 2.69
3600 3846 7.083858 CGCAAGAACTTCAGAAATTCCAATAA 58.916 34.615 0.62 0.00 43.02 1.40
3603 3849 4.858935 CGCAAGAACTTCAGAAATTCCAA 58.141 39.130 0.62 0.00 43.02 3.53
3622 3872 5.180492 AGGATTCGACATTTAACTTTTCGCA 59.820 36.000 0.00 0.00 0.00 5.10
3623 3873 5.628134 AGGATTCGACATTTAACTTTTCGC 58.372 37.500 0.00 0.00 0.00 4.70
3639 3889 3.980646 TGTTTGGAACACAAGGATTCG 57.019 42.857 0.00 0.00 40.82 3.34
3677 3929 1.141881 CGAGGACCTAGCACGCAAT 59.858 57.895 0.00 0.00 0.00 3.56
3678 3930 2.273179 ACGAGGACCTAGCACGCAA 61.273 57.895 0.82 0.00 0.00 4.85
4041 4324 9.941991 CAAAATTTATGCAGACTAAAAATGACG 57.058 29.630 0.00 0.00 0.00 4.35
4045 4328 9.995003 TGGTCAAAATTTATGCAGACTAAAAAT 57.005 25.926 0.00 0.00 0.00 1.82
4061 4344 8.424133 AGAGATGCTTTAACTTTGGTCAAAATT 58.576 29.630 0.00 0.00 0.00 1.82
4068 4353 7.719633 TCAAAGTAGAGATGCTTTAACTTTGGT 59.280 33.333 19.74 0.00 41.50 3.67
4071 4357 7.719633 TGGTCAAAGTAGAGATGCTTTAACTTT 59.280 33.333 0.00 0.00 34.04 2.66
4239 4529 5.163953 CGTATTAGACTTGTGCCAAGTCAAG 60.164 44.000 31.80 18.84 46.78 3.02
4248 4538 2.921754 ACTTCGCGTATTAGACTTGTGC 59.078 45.455 5.77 0.00 0.00 4.57
4254 4544 6.237675 GGTCCTTTTTACTTCGCGTATTAGAC 60.238 42.308 5.77 0.00 0.00 2.59
4270 4560 3.052414 AGGTACACCCTTTGGTCCTTTTT 60.052 43.478 0.00 0.00 45.57 1.94
4281 4571 4.783227 AGATTGTATGTGAGGTACACCCTT 59.217 41.667 0.00 0.00 46.51 3.95
4286 4576 4.817318 TGCAGATTGTATGTGAGGTACA 57.183 40.909 0.00 0.00 44.87 2.90
4302 4599 5.850557 TGAAAGAAGGAAAAACATGCAGA 57.149 34.783 0.00 0.00 0.00 4.26
4339 4636 8.455903 AGAATGAAAACTTCACTCTTGATTCA 57.544 30.769 0.00 0.00 43.03 2.57
4421 4762 6.971726 TCCAAATTATTAGCGGACTCTCTA 57.028 37.500 0.00 0.00 0.00 2.43
4689 5038 1.729149 GCGATTTTTGGCTTCCACTCG 60.729 52.381 0.00 0.00 30.78 4.18
4822 5549 1.958579 TGTTAGGTATGTCGGATCCGG 59.041 52.381 32.79 15.22 40.25 5.14
5043 5770 5.243507 TGCAACACCAATGTCAATATGAACT 59.756 36.000 0.00 0.00 38.45 3.01
5327 6055 3.619929 GGCCAATCAATTTGAGATGTTGC 59.380 43.478 0.00 6.49 37.53 4.17
5455 6183 4.081420 AGACAACAATAGCTGGATCGACTT 60.081 41.667 0.00 0.00 0.00 3.01
5527 6255 3.125316 CAACATCACAACCAAAAGGCTG 58.875 45.455 0.00 0.00 0.00 4.85
6244 6979 8.177663 CCGAATGGTGAAATAAGATATGTATGC 58.822 37.037 0.00 0.00 0.00 3.14
6279 7014 2.283101 GCATGTCAGGGTGCCCAA 60.283 61.111 10.26 0.00 38.92 4.12
6312 7047 7.390718 ACAACCCTTATTTCAGTCTACAACATC 59.609 37.037 0.00 0.00 0.00 3.06
6364 7099 6.767902 CCTATGTAAATAGCTTTGCAGGAAGA 59.232 38.462 2.23 0.00 39.78 2.87
6445 7180 6.042781 TCTCACTCTTCTGCTTACCCTAAAAA 59.957 38.462 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.