Multiple sequence alignment - TraesCS3D01G228700

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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 TraesCS3D01G228700 chr3D 100.000 5453 0 0 1 5453 310924547 310919095 0.000000e+00 10070.0
1 TraesCS3D01G228700 chr3B 96.355 4060 82 30 149 4162 410039690 410043729 0.000000e+00 6617.0
2 TraesCS3D01G228700 chr3B 90.279 1327 57 12 4160 5453 410043887 410045174 0.000000e+00 1670.0
3 TraesCS3D01G228700 chr3B 85.684 475 48 8 149 603 672577841 672577367 2.950000e-132 483.0
4 TraesCS3D01G228700 chr3A 96.419 3491 79 21 773 4227 421118425 421121905 0.000000e+00 5712.0
5 TraesCS3D01G228700 chr3A 91.364 440 29 7 4491 4923 421122184 421122621 1.310000e-165 593.0
6 TraesCS3D01G228700 chr3A 97.131 244 7 0 4218 4461 421121946 421122189 3.930000e-111 412.0
7 TraesCS3D01G228700 chr5D 86.450 524 60 4 4930 5453 4340110 4340622 1.030000e-156 564.0
8 TraesCS3D01G228700 chr5D 85.443 474 48 10 149 603 217015068 217014597 1.780000e-129 473.0
9 TraesCS3D01G228700 chr5D 85.153 458 58 9 149 603 389366227 389365777 1.380000e-125 460.0
10 TraesCS3D01G228700 chr5D 83.745 486 49 12 4987 5451 468323090 468322614 3.020000e-117 433.0
11 TraesCS3D01G228700 chr5D 88.514 148 14 3 5 149 484037345 484037492 5.610000e-40 176.0
12 TraesCS3D01G228700 chr5D 88.356 146 14 3 8 150 285669012 285668867 7.260000e-39 172.0
13 TraesCS3D01G228700 chr1B 85.907 518 71 2 1150 1666 671202721 671202205 7.980000e-153 551.0
14 TraesCS3D01G228700 chr1B 81.973 527 75 11 4930 5446 511409255 511408739 3.900000e-116 429.0
15 TraesCS3D01G228700 chr1B 81.203 532 56 22 4933 5451 647243720 647243220 6.620000e-104 388.0
16 TraesCS3D01G228700 chr1B 80.781 333 54 8 3685 4008 671200688 671200357 9.070000e-63 252.0
17 TraesCS3D01G228700 chr1A 85.234 535 76 3 1147 1680 579296190 579296722 1.030000e-151 547.0
18 TraesCS3D01G228700 chr1A 80.896 335 50 11 3685 4008 579298168 579298499 9.070000e-63 252.0
19 TraesCS3D01G228700 chr1D 85.328 518 74 2 1150 1666 482839897 482839381 8.040000e-148 534.0
20 TraesCS3D01G228700 chr1D 86.287 474 46 12 149 603 55773910 55773437 1.050000e-136 497.0
21 TraesCS3D01G228700 chr1D 80.362 387 61 13 2968 3347 482838585 482838207 4.160000e-71 279.0
22 TraesCS3D01G228700 chr1D 81.416 339 41 14 3685 4008 482837893 482837562 1.950000e-64 257.0
23 TraesCS3D01G228700 chr1D 84.753 223 26 2 5230 5452 455542542 455542756 3.310000e-52 217.0
24 TraesCS3D01G228700 chr1D 88.816 152 14 3 2 150 122556130 122556281 3.350000e-42 183.0
25 TraesCS3D01G228700 chr1D 89.189 148 13 3 5 149 342846399 342846252 1.210000e-41 182.0
26 TraesCS3D01G228700 chr1D 92.647 68 5 0 2980 3047 243701831 243701764 1.250000e-16 99.0
27 TraesCS3D01G228700 chr4D 85.833 480 47 9 149 607 434176325 434176804 1.770000e-134 490.0
28 TraesCS3D01G228700 chr4D 87.179 117 6 3 5313 5429 95173559 95173666 2.060000e-24 124.0
29 TraesCS3D01G228700 chr2D 85.115 477 46 13 149 603 551459951 551460424 1.070000e-126 464.0
30 TraesCS3D01G228700 chr2D 82.537 544 54 18 4930 5453 325508712 325508190 1.800000e-119 440.0
31 TraesCS3D01G228700 chr2D 78.689 549 70 18 4930 5453 325468800 325468274 6.810000e-84 322.0
32 TraesCS3D01G228700 chr2D 87.919 149 15 3 5 150 622393180 622393032 7.260000e-39 172.0
33 TraesCS3D01G228700 chr7D 82.967 546 58 9 4930 5450 163667548 163667013 1.380000e-125 460.0
34 TraesCS3D01G228700 chr7D 84.534 472 53 10 149 603 45831928 45832396 3.000000e-122 449.0
35 TraesCS3D01G228700 chr7D 81.785 549 54 10 4930 5453 459753790 459754317 8.450000e-113 418.0
36 TraesCS3D01G228700 chr4A 87.728 383 46 1 149 531 387098055 387098436 3.880000e-121 446.0
37 TraesCS3D01G228700 chr4A 82.243 321 33 11 4937 5233 535041665 535041985 7.010000e-64 255.0
38 TraesCS3D01G228700 chr5B 81.644 523 59 15 4932 5446 480396883 480397376 3.060000e-107 399.0
39 TraesCS3D01G228700 chr5B 93.103 87 6 0 5367 5453 590802359 590802445 1.590000e-25 128.0
40 TraesCS3D01G228700 chr7B 88.591 149 14 3 5 150 727121619 727121767 1.560000e-40 178.0
41 TraesCS3D01G228700 chr7A 87.417 151 16 3 2 149 627012918 627013068 2.610000e-38 171.0
42 TraesCS3D01G228700 chr7A 87.162 148 17 2 5 150 109075402 109075255 3.380000e-37 167.0
43 TraesCS3D01G228700 chr6D 86.667 150 18 2 2 149 315583246 315583395 1.220000e-36 165.0
44 TraesCS3D01G228700 chr6D 92.647 68 5 0 2980 3047 415303730 415303663 1.250000e-16 99.0
45 TraesCS3D01G228700 chr6D 88.235 68 8 0 2980 3047 441369959 441369892 1.260000e-11 82.4
46 TraesCS3D01G228700 chr2A 92.958 71 4 1 2980 3049 349734988 349735058 9.660000e-18 102.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G228700 chr3D 310919095 310924547 5452 True 10070.000000 10070 100.000000 1 5453 1 chr3D.!!$R1 5452
1 TraesCS3D01G228700 chr3B 410039690 410045174 5484 False 4143.500000 6617 93.317000 149 5453 2 chr3B.!!$F1 5304
2 TraesCS3D01G228700 chr3A 421118425 421122621 4196 False 2239.000000 5712 94.971333 773 4923 3 chr3A.!!$F1 4150
3 TraesCS3D01G228700 chr5D 4340110 4340622 512 False 564.000000 564 86.450000 4930 5453 1 chr5D.!!$F1 523
4 TraesCS3D01G228700 chr1B 511408739 511409255 516 True 429.000000 429 81.973000 4930 5446 1 chr1B.!!$R1 516
5 TraesCS3D01G228700 chr1B 671200357 671202721 2364 True 401.500000 551 83.344000 1150 4008 2 chr1B.!!$R3 2858
6 TraesCS3D01G228700 chr1B 647243220 647243720 500 True 388.000000 388 81.203000 4933 5451 1 chr1B.!!$R2 518
7 TraesCS3D01G228700 chr1A 579296190 579298499 2309 False 399.500000 547 83.065000 1147 4008 2 chr1A.!!$F1 2861
8 TraesCS3D01G228700 chr1D 482837562 482839897 2335 True 356.666667 534 82.368667 1150 4008 3 chr1D.!!$R4 2858
9 TraesCS3D01G228700 chr2D 325508190 325508712 522 True 440.000000 440 82.537000 4930 5453 1 chr2D.!!$R2 523
10 TraesCS3D01G228700 chr2D 325468274 325468800 526 True 322.000000 322 78.689000 4930 5453 1 chr2D.!!$R1 523
11 TraesCS3D01G228700 chr7D 163667013 163667548 535 True 460.000000 460 82.967000 4930 5450 1 chr7D.!!$R1 520
12 TraesCS3D01G228700 chr7D 459753790 459754317 527 False 418.000000 418 81.785000 4930 5453 1 chr7D.!!$F2 523

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
105 106 0.099968 TCCGCTCGTATCTTTGGTCG 59.900 55.000 0.00 0.0 0.00 4.79 F
108 109 0.175073 GCTCGTATCTTTGGTCGGGT 59.825 55.000 0.00 0.0 0.00 5.28 F
140 141 0.544595 GGGTGAGGTGGTGTCTAGGT 60.545 60.000 0.00 0.0 0.00 3.08 F
324 325 0.663568 CTTCTTGAAGGCGTCGTCGT 60.664 55.000 3.66 0.0 39.49 4.34 F
411 412 0.682852 CTGGTGTCGTAACCTTCCCA 59.317 55.000 10.01 0.0 41.16 4.37 F
556 575 0.947960 TTGTGCGTGTGTTATGGTGG 59.052 50.000 0.00 0.0 0.00 4.61 F
692 714 1.223187 AACACTCGCAAAACTACCCG 58.777 50.000 0.00 0.0 0.00 5.28 F
954 992 1.372128 CTGCTGCTTCAAAACCCGC 60.372 57.895 0.00 0.0 0.00 6.13 F
1686 1732 1.396301 CGCTTCATTTGACTCCTCAGC 59.604 52.381 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1335 1373 1.524002 CATGATCTGCACCTCCCGT 59.476 57.895 0.00 0.00 0.00 5.28 R
1686 1732 4.022935 CACAATTCAATCCATACATCCCGG 60.023 45.833 0.00 0.00 0.00 5.73 R
1970 2100 4.389890 TGCCATTTCATTATCACCTTGC 57.610 40.909 0.00 0.00 0.00 4.01 R
2202 2338 4.891992 AACAGCCAGCTCTACTTTCTAA 57.108 40.909 0.00 0.00 0.00 2.10 R
3383 3685 4.887071 TGGTATGGGAAAATGTAGCATGTC 59.113 41.667 0.00 0.00 0.00 3.06 R
3551 3853 7.169140 CCATCAAATGAGCACACAATGATATTG 59.831 37.037 7.48 0.28 32.89 1.90 R
3567 3869 4.455533 CGTCAAACTCTTCCCATCAAATGA 59.544 41.667 0.00 0.00 0.00 2.57 R
3613 3942 5.280654 ACTACGGAAACTTGGAAACAGTA 57.719 39.130 0.00 0.00 44.54 2.74 R
4485 5064 0.044092 TGGGGCCAGGAAGATGTCTA 59.956 55.000 4.39 0.00 0.00 2.59 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
18 19 3.861341 ACATGACGGGTCAATGGAG 57.139 52.632 5.50 0.00 43.58 3.86
19 20 0.253044 ACATGACGGGTCAATGGAGG 59.747 55.000 5.50 0.00 43.58 4.30
20 21 1.097547 CATGACGGGTCAATGGAGGC 61.098 60.000 5.50 0.00 43.58 4.70
21 22 2.124695 GACGGGTCAATGGAGGCC 60.125 66.667 0.00 0.00 0.00 5.19
22 23 2.933287 ACGGGTCAATGGAGGCCA 60.933 61.111 5.01 0.00 38.19 5.36
23 24 2.124570 CGGGTCAATGGAGGCCAG 60.125 66.667 5.01 0.00 36.75 4.85
24 25 2.971598 CGGGTCAATGGAGGCCAGT 61.972 63.158 5.01 0.00 36.75 4.00
25 26 1.384191 GGGTCAATGGAGGCCAGTT 59.616 57.895 5.01 0.00 36.75 3.16
26 27 0.251787 GGGTCAATGGAGGCCAGTTT 60.252 55.000 5.01 0.00 36.75 2.66
27 28 1.632589 GGTCAATGGAGGCCAGTTTT 58.367 50.000 5.01 0.00 36.75 2.43
28 29 1.273327 GGTCAATGGAGGCCAGTTTTG 59.727 52.381 5.01 3.71 36.75 2.44
38 39 3.569873 CCAGTTTTGGCCGACCTAT 57.430 52.632 0.00 0.00 37.73 2.57
39 40 1.834188 CCAGTTTTGGCCGACCTATT 58.166 50.000 0.00 0.00 37.73 1.73
40 41 1.472480 CCAGTTTTGGCCGACCTATTG 59.528 52.381 0.00 0.00 37.73 1.90
41 42 1.472480 CAGTTTTGGCCGACCTATTGG 59.528 52.381 0.00 0.00 36.63 3.16
42 43 0.815095 GTTTTGGCCGACCTATTGGG 59.185 55.000 0.00 0.00 41.89 4.12
51 52 2.900337 CCTATTGGGTTCCGGCGC 60.900 66.667 0.00 0.00 0.00 6.53
52 53 2.189521 CTATTGGGTTCCGGCGCT 59.810 61.111 7.64 0.00 0.00 5.92
53 54 2.124901 TATTGGGTTCCGGCGCTG 60.125 61.111 9.96 9.96 0.00 5.18
54 55 3.690685 TATTGGGTTCCGGCGCTGG 62.691 63.158 30.18 30.18 0.00 4.85
76 77 4.740822 CCCCAGGGGTGCGAAAGG 62.741 72.222 18.09 0.00 38.25 3.11
94 95 4.065281 CGGGTCCTTTCCGCTCGT 62.065 66.667 0.00 0.00 41.07 4.18
95 96 2.703798 CGGGTCCTTTCCGCTCGTA 61.704 63.158 0.00 0.00 41.07 3.43
96 97 1.821258 GGGTCCTTTCCGCTCGTAT 59.179 57.895 0.00 0.00 0.00 3.06
97 98 0.249363 GGGTCCTTTCCGCTCGTATC 60.249 60.000 0.00 0.00 0.00 2.24
98 99 0.745468 GGTCCTTTCCGCTCGTATCT 59.255 55.000 0.00 0.00 0.00 1.98
99 100 1.136500 GGTCCTTTCCGCTCGTATCTT 59.864 52.381 0.00 0.00 0.00 2.40
100 101 2.418334 GGTCCTTTCCGCTCGTATCTTT 60.418 50.000 0.00 0.00 0.00 2.52
101 102 2.603560 GTCCTTTCCGCTCGTATCTTTG 59.396 50.000 0.00 0.00 0.00 2.77
102 103 1.933853 CCTTTCCGCTCGTATCTTTGG 59.066 52.381 0.00 0.00 0.00 3.28
103 104 2.618053 CTTTCCGCTCGTATCTTTGGT 58.382 47.619 0.00 0.00 0.00 3.67
104 105 2.288961 TTCCGCTCGTATCTTTGGTC 57.711 50.000 0.00 0.00 0.00 4.02
105 106 0.099968 TCCGCTCGTATCTTTGGTCG 59.900 55.000 0.00 0.00 0.00 4.79
106 107 0.870307 CCGCTCGTATCTTTGGTCGG 60.870 60.000 0.00 0.00 0.00 4.79
107 108 0.870307 CGCTCGTATCTTTGGTCGGG 60.870 60.000 0.00 0.00 0.00 5.14
108 109 0.175073 GCTCGTATCTTTGGTCGGGT 59.825 55.000 0.00 0.00 0.00 5.28
109 110 1.406539 GCTCGTATCTTTGGTCGGGTA 59.593 52.381 0.00 0.00 0.00 3.69
110 111 2.543238 GCTCGTATCTTTGGTCGGGTAG 60.543 54.545 0.00 0.00 0.00 3.18
111 112 1.406539 TCGTATCTTTGGTCGGGTAGC 59.593 52.381 0.00 0.00 0.00 3.58
112 113 1.849097 GTATCTTTGGTCGGGTAGCG 58.151 55.000 0.00 0.00 0.00 4.26
113 114 0.748450 TATCTTTGGTCGGGTAGCGG 59.252 55.000 0.00 0.00 0.00 5.52
114 115 1.262640 ATCTTTGGTCGGGTAGCGGT 61.263 55.000 0.00 0.00 0.00 5.68
115 116 1.740296 CTTTGGTCGGGTAGCGGTG 60.740 63.158 0.00 0.00 0.00 4.94
116 117 2.162338 CTTTGGTCGGGTAGCGGTGA 62.162 60.000 0.00 0.00 0.00 4.02
117 118 1.546589 TTTGGTCGGGTAGCGGTGAT 61.547 55.000 0.00 0.00 0.00 3.06
118 119 1.952102 TTGGTCGGGTAGCGGTGATC 61.952 60.000 0.00 0.00 0.00 2.92
119 120 2.125961 GGTCGGGTAGCGGTGATCT 61.126 63.158 0.00 0.00 0.00 2.75
120 121 1.359475 GTCGGGTAGCGGTGATCTC 59.641 63.158 0.00 0.00 0.00 2.75
121 122 2.184830 TCGGGTAGCGGTGATCTCG 61.185 63.158 0.00 0.00 0.00 4.04
122 123 2.728817 GGGTAGCGGTGATCTCGG 59.271 66.667 0.00 4.87 0.00 4.63
123 124 2.728817 GGTAGCGGTGATCTCGGG 59.271 66.667 0.00 0.00 0.00 5.14
124 125 2.125961 GGTAGCGGTGATCTCGGGT 61.126 63.158 11.08 11.08 0.00 5.28
125 126 1.065928 GTAGCGGTGATCTCGGGTG 59.934 63.158 14.85 0.00 0.00 4.61
126 127 1.077285 TAGCGGTGATCTCGGGTGA 60.077 57.895 14.85 0.54 0.00 4.02
127 128 1.101635 TAGCGGTGATCTCGGGTGAG 61.102 60.000 14.85 0.00 43.99 3.51
128 129 2.808315 CGGTGATCTCGGGTGAGG 59.192 66.667 0.00 0.00 42.79 3.86
129 130 2.052690 CGGTGATCTCGGGTGAGGT 61.053 63.158 0.00 0.00 42.79 3.85
130 131 1.517832 GGTGATCTCGGGTGAGGTG 59.482 63.158 0.00 0.00 42.79 4.00
131 132 1.517832 GTGATCTCGGGTGAGGTGG 59.482 63.158 0.00 0.00 42.79 4.61
132 133 1.078528 TGATCTCGGGTGAGGTGGT 59.921 57.895 0.00 0.00 42.79 4.16
133 134 1.257750 TGATCTCGGGTGAGGTGGTG 61.258 60.000 0.00 0.00 42.79 4.17
134 135 1.229209 ATCTCGGGTGAGGTGGTGT 60.229 57.895 0.00 0.00 42.79 4.16
135 136 1.258445 ATCTCGGGTGAGGTGGTGTC 61.258 60.000 0.00 0.00 42.79 3.67
136 137 1.908793 CTCGGGTGAGGTGGTGTCT 60.909 63.158 0.00 0.00 38.65 3.41
137 138 0.611062 CTCGGGTGAGGTGGTGTCTA 60.611 60.000 0.00 0.00 38.65 2.59
138 139 0.611062 TCGGGTGAGGTGGTGTCTAG 60.611 60.000 0.00 0.00 0.00 2.43
139 140 1.605058 CGGGTGAGGTGGTGTCTAGG 61.605 65.000 0.00 0.00 0.00 3.02
140 141 0.544595 GGGTGAGGTGGTGTCTAGGT 60.545 60.000 0.00 0.00 0.00 3.08
141 142 0.896226 GGTGAGGTGGTGTCTAGGTC 59.104 60.000 0.00 0.00 0.00 3.85
142 143 1.550409 GGTGAGGTGGTGTCTAGGTCT 60.550 57.143 0.00 0.00 0.00 3.85
143 144 2.249139 GTGAGGTGGTGTCTAGGTCTT 58.751 52.381 0.00 0.00 0.00 3.01
144 145 2.028930 GTGAGGTGGTGTCTAGGTCTTG 60.029 54.545 0.00 0.00 0.00 3.02
145 146 1.550976 GAGGTGGTGTCTAGGTCTTGG 59.449 57.143 0.00 0.00 0.00 3.61
146 147 1.149288 AGGTGGTGTCTAGGTCTTGGA 59.851 52.381 0.00 0.00 0.00 3.53
147 148 2.188817 GGTGGTGTCTAGGTCTTGGAT 58.811 52.381 0.00 0.00 0.00 3.41
148 149 2.093447 GGTGGTGTCTAGGTCTTGGATG 60.093 54.545 0.00 0.00 0.00 3.51
149 150 2.567615 GTGGTGTCTAGGTCTTGGATGT 59.432 50.000 0.00 0.00 0.00 3.06
150 151 2.567169 TGGTGTCTAGGTCTTGGATGTG 59.433 50.000 0.00 0.00 0.00 3.21
151 152 2.622436 GTGTCTAGGTCTTGGATGTGC 58.378 52.381 0.00 0.00 0.00 4.57
152 153 2.234908 GTGTCTAGGTCTTGGATGTGCT 59.765 50.000 0.00 0.00 0.00 4.40
153 154 2.497675 TGTCTAGGTCTTGGATGTGCTC 59.502 50.000 0.00 0.00 0.00 4.26
236 237 3.799755 GATGTGGCGTTCGGTGGC 61.800 66.667 0.00 0.00 0.00 5.01
237 238 4.634703 ATGTGGCGTTCGGTGGCA 62.635 61.111 0.00 0.00 39.86 4.92
253 254 2.425592 CAGTGAGTGTTGGCCGGA 59.574 61.111 5.05 0.00 0.00 5.14
262 263 2.909965 TTGGCCGGAGTGCAAACC 60.910 61.111 5.05 0.00 0.00 3.27
288 289 1.246056 ATCTTTGGACGGACCGACGA 61.246 55.000 23.38 9.27 42.61 4.20
324 325 0.663568 CTTCTTGAAGGCGTCGTCGT 60.664 55.000 3.66 0.00 39.49 4.34
326 327 2.355363 TTGAAGGCGTCGTCGTGG 60.355 61.111 3.66 0.00 39.49 4.94
367 368 3.196469 TCGCTCCAGATGAAACTCTGATT 59.804 43.478 2.73 0.00 44.48 2.57
410 411 0.971386 TCTGGTGTCGTAACCTTCCC 59.029 55.000 10.01 0.00 41.16 3.97
411 412 0.682852 CTGGTGTCGTAACCTTCCCA 59.317 55.000 10.01 0.00 41.16 4.37
436 437 2.281070 CGCCTTGGAGCACACAGT 60.281 61.111 0.00 0.00 0.00 3.55
461 462 5.631096 TCGTCATATGCGATTTCATCTCTTC 59.369 40.000 15.22 0.00 33.09 2.87
468 469 2.271800 GATTTCATCTCTTCGCGGTGT 58.728 47.619 6.13 0.00 0.00 4.16
477 478 1.282248 CTTCGCGGTGTCGTGTTCAT 61.282 55.000 6.13 0.00 45.94 2.57
515 516 4.464652 TGCTCTTATAGTACTAGGGGCA 57.535 45.455 18.03 18.03 0.00 5.36
531 532 2.250485 CAGTGTTGCTGCGCTCAC 59.750 61.111 9.73 10.16 38.52 3.51
532 533 3.341043 AGTGTTGCTGCGCTCACG 61.341 61.111 9.73 0.00 44.07 4.35
534 535 4.600576 TGTTGCTGCGCTCACGGA 62.601 61.111 9.73 0.00 40.57 4.69
556 575 0.947960 TTGTGCGTGTGTTATGGTGG 59.052 50.000 0.00 0.00 0.00 4.61
568 587 2.750712 GTTATGGTGGCGTGGTTTGTAT 59.249 45.455 0.00 0.00 0.00 2.29
580 599 4.134563 GTGGTTTGTATCTGAGTTGTGGT 58.865 43.478 0.00 0.00 0.00 4.16
603 622 9.175312 TGGTTGGTCGTTGCTTTATATATAAAA 57.825 29.630 16.69 3.10 32.39 1.52
604 623 9.659830 GGTTGGTCGTTGCTTTATATATAAAAG 57.340 33.333 16.69 12.32 37.08 2.27
608 627 9.227777 GGTCGTTGCTTTATATATAAAAGGGAT 57.772 33.333 16.69 0.00 35.04 3.85
630 652 8.414003 GGGATGAATTTTTCCCTGTAAAGATAC 58.586 37.037 15.93 0.00 46.91 2.24
642 664 6.043243 CCCTGTAAAGATACTATGGTGGTCAT 59.957 42.308 0.00 0.00 39.78 3.06
647 669 9.614792 GTAAAGATACTATGGTGGTCATCTTTT 57.385 33.333 17.60 7.28 40.95 2.27
692 714 1.223187 AACACTCGCAAAACTACCCG 58.777 50.000 0.00 0.00 0.00 5.28
724 746 8.812147 TTCGTCATCATATACACCTTAATGAC 57.188 34.615 0.00 0.00 38.61 3.06
787 813 5.296813 ACAAGAAAGAAACACACAGTGAC 57.703 39.130 7.81 0.00 36.96 3.67
954 992 1.372128 CTGCTGCTTCAAAACCCGC 60.372 57.895 0.00 0.00 0.00 6.13
1686 1732 1.396301 CGCTTCATTTGACTCCTCAGC 59.604 52.381 0.00 0.00 0.00 4.26
1970 2100 1.845809 GACAGTTCTGGCTTGGTGCG 61.846 60.000 4.82 0.00 44.05 5.34
2024 2154 5.389778 TGCATTATTTACACTTTGAGCACG 58.610 37.500 0.00 0.00 0.00 5.34
2108 2239 2.352651 CCTGCACGTGTATCAGAAATGG 59.647 50.000 18.38 3.60 0.00 3.16
2176 2312 3.399330 TGGTCACCGAAGATTCTTGTTC 58.601 45.455 3.03 0.00 0.00 3.18
2181 2317 3.250762 CACCGAAGATTCTTGTTCTTGCA 59.749 43.478 3.03 0.00 33.65 4.08
2202 2338 5.939883 TGCAGTGCTGTTTATCACTAGAAAT 59.060 36.000 17.60 0.00 41.19 2.17
3473 3775 5.306114 AGTTTGGAAGCAACTACCTTACT 57.694 39.130 0.00 0.00 32.48 2.24
3474 3776 5.691896 AGTTTGGAAGCAACTACCTTACTT 58.308 37.500 0.00 0.00 32.48 2.24
3475 3777 6.127101 AGTTTGGAAGCAACTACCTTACTTT 58.873 36.000 0.00 0.00 32.48 2.66
3551 3853 4.740268 TGATGTATCAACGTAGACCACAC 58.260 43.478 0.00 0.00 33.08 3.82
3839 4195 8.238631 GCGGGTAATTGAACTTAAACTTGAATA 58.761 33.333 0.00 0.00 0.00 1.75
4035 4391 7.418840 TGTTACAAACATCAAAATCATTGCC 57.581 32.000 0.00 0.00 36.25 4.52
4076 4432 7.395190 TCAGGGATGAAAAGTTTGATATGTG 57.605 36.000 0.00 0.00 0.00 3.21
4077 4433 6.947733 TCAGGGATGAAAAGTTTGATATGTGT 59.052 34.615 0.00 0.00 0.00 3.72
4231 4761 9.398170 GAATGTGTGCAATGTATCATTATTACC 57.602 33.333 0.00 0.00 0.00 2.85
4311 4890 6.546034 AGCTACAACTTGAGTTAACAAATGGT 59.454 34.615 8.61 0.09 36.32 3.55
4481 5060 7.542025 TCTTCTACCGTAACTTCTTGAATACC 58.458 38.462 0.00 0.00 0.00 2.73
4482 5061 5.883661 TCTACCGTAACTTCTTGAATACCG 58.116 41.667 0.00 0.00 0.00 4.02
4483 5062 3.256558 ACCGTAACTTCTTGAATACCGC 58.743 45.455 0.00 0.00 0.00 5.68
4484 5063 3.056322 ACCGTAACTTCTTGAATACCGCT 60.056 43.478 0.00 0.00 0.00 5.52
4485 5064 3.930848 CCGTAACTTCTTGAATACCGCTT 59.069 43.478 0.00 0.00 0.00 4.68
4486 5065 5.104374 CCGTAACTTCTTGAATACCGCTTA 58.896 41.667 0.00 0.00 0.00 3.09
4487 5066 5.231568 CCGTAACTTCTTGAATACCGCTTAG 59.768 44.000 0.00 0.00 0.00 2.18
4488 5067 6.032094 CGTAACTTCTTGAATACCGCTTAGA 58.968 40.000 0.00 0.00 0.00 2.10
4489 5068 6.020837 CGTAACTTCTTGAATACCGCTTAGAC 60.021 42.308 0.00 0.00 0.00 2.59
4634 5213 6.384015 TGCTCCGAGGGTATTATGATCATATT 59.616 38.462 16.06 14.46 0.00 1.28
4635 5214 7.092891 TGCTCCGAGGGTATTATGATCATATTT 60.093 37.037 16.06 9.55 0.00 1.40
4800 5394 0.525668 CGCCACCTACAAGTAGCGAG 60.526 60.000 0.00 0.00 46.03 5.03
4862 5460 4.814234 TGCATATTTTAGACGTTAGCCCAG 59.186 41.667 0.00 0.00 0.00 4.45
4992 5601 2.539081 GGCCACCTTTCCCTCCAGT 61.539 63.158 0.00 0.00 0.00 4.00
5224 5884 2.243994 TCATCTAAAGACGGAGGGGAGA 59.756 50.000 0.00 0.00 0.00 3.71
5237 5897 0.329596 GGGGAGAAGAGTGCACCATT 59.670 55.000 14.63 8.69 0.00 3.16
5271 5931 1.148273 GCAGTTGTGGAGTGGTGGA 59.852 57.895 0.00 0.00 0.00 4.02
5286 5946 1.395635 GTGGAAACGGTTCAAGGGTT 58.604 50.000 16.38 0.00 35.25 4.11
5294 5967 2.193536 GTTCAAGGGTTGCGTGGCT 61.194 57.895 0.00 0.00 0.00 4.75
5301 5974 1.966451 GGTTGCGTGGCTTGTAGCT 60.966 57.895 0.00 0.00 41.99 3.32
5328 6001 3.909086 AAGCAGTGAAGCCGGAGCC 62.909 63.158 5.05 0.00 41.25 4.70
5343 6016 2.434185 GCCGCGTCTTCATGGTGA 60.434 61.111 4.92 0.00 0.00 4.02
5374 6047 3.628989 TCGGCACCAATCTCCGAT 58.371 55.556 0.00 0.00 46.12 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.253044 CCTCCATTGACCCGTCATGT 59.747 55.000 0.00 0.00 39.64 3.21
1 2 1.097547 GCCTCCATTGACCCGTCATG 61.098 60.000 0.00 0.30 39.64 3.07
2 3 1.224592 GCCTCCATTGACCCGTCAT 59.775 57.895 0.00 0.00 39.64 3.06
3 4 2.668632 GCCTCCATTGACCCGTCA 59.331 61.111 0.00 0.00 37.91 4.35
4 5 2.124695 GGCCTCCATTGACCCGTC 60.125 66.667 0.00 0.00 0.00 4.79
5 6 2.933287 TGGCCTCCATTGACCCGT 60.933 61.111 3.32 0.00 0.00 5.28
6 7 2.124570 CTGGCCTCCATTGACCCG 60.125 66.667 3.32 0.00 30.82 5.28
7 8 0.251787 AAACTGGCCTCCATTGACCC 60.252 55.000 3.32 0.00 30.82 4.46
8 9 1.273327 CAAAACTGGCCTCCATTGACC 59.727 52.381 3.32 0.00 30.82 4.02
9 10 1.273327 CCAAAACTGGCCTCCATTGAC 59.727 52.381 3.32 0.00 30.82 3.18
10 11 1.631405 CCAAAACTGGCCTCCATTGA 58.369 50.000 3.32 0.00 30.82 2.57
20 21 1.472480 CAATAGGTCGGCCAAAACTGG 59.528 52.381 9.71 0.00 37.19 4.00
21 22 1.472480 CCAATAGGTCGGCCAAAACTG 59.528 52.381 9.71 0.00 37.19 3.16
22 23 1.615919 CCCAATAGGTCGGCCAAAACT 60.616 52.381 9.71 0.00 37.19 2.66
23 24 0.815095 CCCAATAGGTCGGCCAAAAC 59.185 55.000 9.71 0.00 37.19 2.43
24 25 3.274601 CCCAATAGGTCGGCCAAAA 57.725 52.632 9.71 0.00 37.19 2.44
34 35 2.900337 GCGCCGGAACCCAATAGG 60.900 66.667 5.05 0.00 43.78 2.57
35 36 2.180204 CAGCGCCGGAACCCAATAG 61.180 63.158 5.05 0.00 0.00 1.73
36 37 2.124901 CAGCGCCGGAACCCAATA 60.125 61.111 5.05 0.00 0.00 1.90
78 79 0.249363 GATACGAGCGGAAAGGACCC 60.249 60.000 0.00 0.00 0.00 4.46
79 80 0.745468 AGATACGAGCGGAAAGGACC 59.255 55.000 0.00 0.00 0.00 4.46
80 81 2.580966 AAGATACGAGCGGAAAGGAC 57.419 50.000 0.00 0.00 0.00 3.85
81 82 2.418197 CCAAAGATACGAGCGGAAAGGA 60.418 50.000 0.00 0.00 0.00 3.36
82 83 1.933853 CCAAAGATACGAGCGGAAAGG 59.066 52.381 0.00 0.00 0.00 3.11
83 84 2.603560 GACCAAAGATACGAGCGGAAAG 59.396 50.000 0.00 0.00 0.00 2.62
84 85 2.613691 GACCAAAGATACGAGCGGAAA 58.386 47.619 0.00 0.00 0.00 3.13
85 86 1.468565 CGACCAAAGATACGAGCGGAA 60.469 52.381 0.00 0.00 0.00 4.30
86 87 0.099968 CGACCAAAGATACGAGCGGA 59.900 55.000 0.00 0.00 0.00 5.54
87 88 0.870307 CCGACCAAAGATACGAGCGG 60.870 60.000 0.00 0.00 0.00 5.52
88 89 0.870307 CCCGACCAAAGATACGAGCG 60.870 60.000 0.00 0.00 0.00 5.03
89 90 0.175073 ACCCGACCAAAGATACGAGC 59.825 55.000 0.00 0.00 0.00 5.03
90 91 2.543238 GCTACCCGACCAAAGATACGAG 60.543 54.545 0.00 0.00 0.00 4.18
91 92 1.406539 GCTACCCGACCAAAGATACGA 59.593 52.381 0.00 0.00 0.00 3.43
92 93 1.849097 GCTACCCGACCAAAGATACG 58.151 55.000 0.00 0.00 0.00 3.06
93 94 1.537562 CCGCTACCCGACCAAAGATAC 60.538 57.143 0.00 0.00 40.02 2.24
94 95 0.748450 CCGCTACCCGACCAAAGATA 59.252 55.000 0.00 0.00 40.02 1.98
95 96 1.262640 ACCGCTACCCGACCAAAGAT 61.263 55.000 0.00 0.00 40.02 2.40
96 97 1.909781 ACCGCTACCCGACCAAAGA 60.910 57.895 0.00 0.00 40.02 2.52
97 98 1.740296 CACCGCTACCCGACCAAAG 60.740 63.158 0.00 0.00 40.02 2.77
98 99 1.546589 ATCACCGCTACCCGACCAAA 61.547 55.000 0.00 0.00 40.02 3.28
99 100 1.952102 GATCACCGCTACCCGACCAA 61.952 60.000 0.00 0.00 40.02 3.67
100 101 2.363276 ATCACCGCTACCCGACCA 60.363 61.111 0.00 0.00 40.02 4.02
101 102 2.073037 GAGATCACCGCTACCCGACC 62.073 65.000 0.00 0.00 40.02 4.79
102 103 1.359475 GAGATCACCGCTACCCGAC 59.641 63.158 0.00 0.00 40.02 4.79
103 104 2.184830 CGAGATCACCGCTACCCGA 61.185 63.158 0.00 0.00 40.02 5.14
104 105 2.331805 CGAGATCACCGCTACCCG 59.668 66.667 0.00 0.00 0.00 5.28
105 106 2.728817 CCGAGATCACCGCTACCC 59.271 66.667 0.00 0.00 0.00 3.69
106 107 2.125961 ACCCGAGATCACCGCTACC 61.126 63.158 0.00 0.00 0.00 3.18
107 108 1.065928 CACCCGAGATCACCGCTAC 59.934 63.158 0.00 0.00 0.00 3.58
108 109 1.077285 TCACCCGAGATCACCGCTA 60.077 57.895 0.00 0.00 0.00 4.26
109 110 2.362503 TCACCCGAGATCACCGCT 60.363 61.111 0.00 0.00 0.00 5.52
110 111 2.105128 CTCACCCGAGATCACCGC 59.895 66.667 0.00 0.00 42.34 5.68
111 112 2.052690 ACCTCACCCGAGATCACCG 61.053 63.158 0.00 0.00 42.34 4.94
112 113 1.517832 CACCTCACCCGAGATCACC 59.482 63.158 0.00 0.00 42.34 4.02
113 114 1.258445 ACCACCTCACCCGAGATCAC 61.258 60.000 0.00 0.00 42.34 3.06
114 115 1.078528 ACCACCTCACCCGAGATCA 59.921 57.895 0.00 0.00 42.34 2.92
115 116 1.258445 ACACCACCTCACCCGAGATC 61.258 60.000 0.00 0.00 42.34 2.75
116 117 1.229209 ACACCACCTCACCCGAGAT 60.229 57.895 0.00 0.00 42.34 2.75
117 118 1.906824 GACACCACCTCACCCGAGA 60.907 63.158 0.00 0.00 42.34 4.04
118 119 0.611062 TAGACACCACCTCACCCGAG 60.611 60.000 0.00 0.00 39.16 4.63
119 120 0.611062 CTAGACACCACCTCACCCGA 60.611 60.000 0.00 0.00 0.00 5.14
120 121 1.605058 CCTAGACACCACCTCACCCG 61.605 65.000 0.00 0.00 0.00 5.28
121 122 0.544595 ACCTAGACACCACCTCACCC 60.545 60.000 0.00 0.00 0.00 4.61
122 123 0.896226 GACCTAGACACCACCTCACC 59.104 60.000 0.00 0.00 0.00 4.02
123 124 1.926108 AGACCTAGACACCACCTCAC 58.074 55.000 0.00 0.00 0.00 3.51
124 125 2.248248 CAAGACCTAGACACCACCTCA 58.752 52.381 0.00 0.00 0.00 3.86
125 126 1.550976 CCAAGACCTAGACACCACCTC 59.449 57.143 0.00 0.00 0.00 3.85
126 127 1.149288 TCCAAGACCTAGACACCACCT 59.851 52.381 0.00 0.00 0.00 4.00
127 128 1.640917 TCCAAGACCTAGACACCACC 58.359 55.000 0.00 0.00 0.00 4.61
128 129 2.567615 ACATCCAAGACCTAGACACCAC 59.432 50.000 0.00 0.00 0.00 4.16
129 130 2.567169 CACATCCAAGACCTAGACACCA 59.433 50.000 0.00 0.00 0.00 4.17
130 131 2.678190 GCACATCCAAGACCTAGACACC 60.678 54.545 0.00 0.00 0.00 4.16
131 132 2.234908 AGCACATCCAAGACCTAGACAC 59.765 50.000 0.00 0.00 0.00 3.67
132 133 2.497675 GAGCACATCCAAGACCTAGACA 59.502 50.000 0.00 0.00 0.00 3.41
133 134 2.497675 TGAGCACATCCAAGACCTAGAC 59.502 50.000 0.00 0.00 0.00 2.59
134 135 2.820178 TGAGCACATCCAAGACCTAGA 58.180 47.619 0.00 0.00 0.00 2.43
135 136 3.464907 CATGAGCACATCCAAGACCTAG 58.535 50.000 0.00 0.00 34.15 3.02
136 137 2.171237 CCATGAGCACATCCAAGACCTA 59.829 50.000 0.00 0.00 34.15 3.08
137 138 1.064906 CCATGAGCACATCCAAGACCT 60.065 52.381 0.00 0.00 34.15 3.85
138 139 1.386533 CCATGAGCACATCCAAGACC 58.613 55.000 0.00 0.00 34.15 3.85
139 140 1.386533 CCCATGAGCACATCCAAGAC 58.613 55.000 0.00 0.00 34.15 3.01
140 141 0.394762 GCCCATGAGCACATCCAAGA 60.395 55.000 0.00 0.00 34.15 3.02
141 142 0.681887 TGCCCATGAGCACATCCAAG 60.682 55.000 0.00 0.00 38.00 3.61
142 143 0.681887 CTGCCCATGAGCACATCCAA 60.682 55.000 0.00 0.00 38.00 3.53
143 144 1.077285 CTGCCCATGAGCACATCCA 60.077 57.895 0.00 0.00 38.00 3.41
144 145 0.818445 CTCTGCCCATGAGCACATCC 60.818 60.000 0.00 0.00 38.00 3.51
145 146 2.704108 CTCTGCCCATGAGCACATC 58.296 57.895 0.00 0.00 38.00 3.06
146 147 4.979657 CTCTGCCCATGAGCACAT 57.020 55.556 0.00 0.00 38.00 3.21
236 237 1.669115 CTCCGGCCAACACTCACTG 60.669 63.158 2.24 0.00 0.00 3.66
237 238 2.140792 ACTCCGGCCAACACTCACT 61.141 57.895 2.24 0.00 0.00 3.41
253 254 4.946157 CCAAAGATAGATCAGGTTTGCACT 59.054 41.667 0.00 0.00 0.00 4.40
262 263 3.551046 CGGTCCGTCCAAAGATAGATCAG 60.551 52.174 2.08 0.00 35.57 2.90
288 289 2.125106 GGGAATGAGCTTCGCCGT 60.125 61.111 0.00 0.00 40.10 5.68
326 327 2.125512 ACGACGGGCAATGAGAGC 60.126 61.111 0.00 0.00 0.00 4.09
337 338 3.052620 ATCTGGAGCGACACGACGG 62.053 63.158 0.00 0.00 0.00 4.79
386 387 0.731855 GGTTACGACACCAGAGCGTC 60.732 60.000 0.00 0.00 39.24 5.19
388 389 0.038526 AAGGTTACGACACCAGAGCG 60.039 55.000 9.91 0.00 39.62 5.03
395 396 2.148768 CCTTTGGGAAGGTTACGACAC 58.851 52.381 0.00 0.00 46.16 3.67
422 423 0.861837 GACGAACTGTGTGCTCCAAG 59.138 55.000 0.00 0.00 0.00 3.61
461 462 2.469847 CATGAACACGACACCGCG 59.530 61.111 0.00 0.00 39.95 6.46
463 464 0.234625 CAACCATGAACACGACACCG 59.765 55.000 0.00 0.00 42.50 4.94
468 469 1.691976 AGTCCTCAACCATGAACACGA 59.308 47.619 0.00 0.00 34.49 4.35
477 478 1.752198 CAACCGGAGTCCTCAACCA 59.248 57.895 9.46 0.00 0.00 3.67
536 537 1.334599 CCACCATAACACACGCACAAC 60.335 52.381 0.00 0.00 0.00 3.32
537 538 0.947960 CCACCATAACACACGCACAA 59.052 50.000 0.00 0.00 0.00 3.33
550 569 1.004277 AGATACAAACCACGCCACCAT 59.996 47.619 0.00 0.00 0.00 3.55
556 575 2.806244 ACAACTCAGATACAAACCACGC 59.194 45.455 0.00 0.00 0.00 5.34
568 587 0.828022 ACGACCAACCACAACTCAGA 59.172 50.000 0.00 0.00 0.00 3.27
580 599 8.842280 CCCTTTTATATATAAAGCAACGACCAA 58.158 33.333 15.65 0.09 34.13 3.67
610 629 9.990868 ACCATAGTATCTTTACAGGGAAAAATT 57.009 29.630 0.00 0.00 0.00 1.82
612 631 7.832187 CCACCATAGTATCTTTACAGGGAAAAA 59.168 37.037 0.00 0.00 0.00 1.94
613 632 7.037153 ACCACCATAGTATCTTTACAGGGAAAA 60.037 37.037 0.00 0.00 0.00 2.29
614 633 6.445786 ACCACCATAGTATCTTTACAGGGAAA 59.554 38.462 0.00 0.00 0.00 3.13
617 636 5.365605 TGACCACCATAGTATCTTTACAGGG 59.634 44.000 0.00 0.00 0.00 4.45
618 637 6.479972 TGACCACCATAGTATCTTTACAGG 57.520 41.667 0.00 0.00 0.00 4.00
619 638 7.957002 AGATGACCACCATAGTATCTTTACAG 58.043 38.462 0.00 0.00 35.17 2.74
621 640 9.614792 AAAAGATGACCACCATAGTATCTTTAC 57.385 33.333 0.00 0.00 41.42 2.01
675 697 1.504359 TTCGGGTAGTTTTGCGAGTG 58.496 50.000 0.00 0.00 0.00 3.51
724 746 0.108207 GCATGATCTGACCCTCCCAG 59.892 60.000 0.00 0.00 0.00 4.45
787 813 1.291877 CCGTGAGCCCGTGAAAGAAG 61.292 60.000 0.00 0.00 0.00 2.85
1335 1373 1.524002 CATGATCTGCACCTCCCGT 59.476 57.895 0.00 0.00 0.00 5.28
1686 1732 4.022935 CACAATTCAATCCATACATCCCGG 60.023 45.833 0.00 0.00 0.00 5.73
1970 2100 4.389890 TGCCATTTCATTATCACCTTGC 57.610 40.909 0.00 0.00 0.00 4.01
2024 2154 8.946085 TCAACTATCAATCATAGAAACAACACC 58.054 33.333 0.00 0.00 37.27 4.16
2108 2239 5.260900 GTTTCGTCGGATAATTTTAGGTGC 58.739 41.667 0.00 0.00 0.00 5.01
2176 2312 4.931601 TCTAGTGATAAACAGCACTGCAAG 59.068 41.667 3.30 0.00 44.47 4.01
2181 2317 9.944376 TTCTAATTTCTAGTGATAAACAGCACT 57.056 29.630 0.00 0.00 46.31 4.40
2202 2338 4.891992 AACAGCCAGCTCTACTTTCTAA 57.108 40.909 0.00 0.00 0.00 2.10
3383 3685 4.887071 TGGTATGGGAAAATGTAGCATGTC 59.113 41.667 0.00 0.00 0.00 3.06
3551 3853 7.169140 CCATCAAATGAGCACACAATGATATTG 59.831 37.037 7.48 0.28 32.89 1.90
3567 3869 4.455533 CGTCAAACTCTTCCCATCAAATGA 59.544 41.667 0.00 0.00 0.00 2.57
3613 3942 5.280654 ACTACGGAAACTTGGAAACAGTA 57.719 39.130 0.00 0.00 44.54 2.74
3839 4195 8.658609 CAAACAGTCACAACTCAAAATTTTGAT 58.341 29.630 28.86 15.87 45.26 2.57
4035 4391 5.016173 TCCCTGAACAAGTGGATTTTATGG 58.984 41.667 0.00 0.00 0.00 2.74
4121 4479 8.093927 AGATAGATGAGTAAATCCTAGCAAAGC 58.906 37.037 0.00 0.00 0.00 3.51
4218 4748 7.217200 TGGTGAAGCAGAGGTAATAATGATAC 58.783 38.462 0.00 0.00 0.00 2.24
4223 4753 5.132648 TCCATGGTGAAGCAGAGGTAATAAT 59.867 40.000 12.58 0.00 0.00 1.28
4225 4755 4.037222 TCCATGGTGAAGCAGAGGTAATA 58.963 43.478 12.58 0.00 0.00 0.98
4227 4757 2.237143 CTCCATGGTGAAGCAGAGGTAA 59.763 50.000 12.58 0.00 0.00 2.85
4228 4758 1.833630 CTCCATGGTGAAGCAGAGGTA 59.166 52.381 12.58 0.00 0.00 3.08
4230 4760 0.907486 TCTCCATGGTGAAGCAGAGG 59.093 55.000 14.08 0.00 0.00 3.69
4231 4761 2.775911 TTCTCCATGGTGAAGCAGAG 57.224 50.000 22.34 5.87 0.00 3.35
4311 4890 0.401356 TGATGAACTGAGCCAGGCAA 59.599 50.000 15.80 0.00 35.51 4.52
4470 5049 6.222038 AGATGTCTAAGCGGTATTCAAGAA 57.778 37.500 0.00 0.00 0.00 2.52
4471 5050 5.854010 AGATGTCTAAGCGGTATTCAAGA 57.146 39.130 0.00 0.00 0.00 3.02
4472 5051 5.463724 GGAAGATGTCTAAGCGGTATTCAAG 59.536 44.000 0.00 0.00 0.00 3.02
4473 5052 5.128827 AGGAAGATGTCTAAGCGGTATTCAA 59.871 40.000 0.00 0.00 0.00 2.69
4474 5053 4.649674 AGGAAGATGTCTAAGCGGTATTCA 59.350 41.667 0.00 0.00 0.00 2.57
4475 5054 4.985409 CAGGAAGATGTCTAAGCGGTATTC 59.015 45.833 0.00 0.00 0.00 1.75
4476 5055 4.202264 CCAGGAAGATGTCTAAGCGGTATT 60.202 45.833 0.00 0.00 0.00 1.89
4477 5056 3.322254 CCAGGAAGATGTCTAAGCGGTAT 59.678 47.826 0.00 0.00 0.00 2.73
4478 5057 2.693591 CCAGGAAGATGTCTAAGCGGTA 59.306 50.000 0.00 0.00 0.00 4.02
4479 5058 1.482593 CCAGGAAGATGTCTAAGCGGT 59.517 52.381 0.00 0.00 0.00 5.68
4480 5059 1.808133 GCCAGGAAGATGTCTAAGCGG 60.808 57.143 0.00 0.00 0.00 5.52
4481 5060 1.576356 GCCAGGAAGATGTCTAAGCG 58.424 55.000 0.00 0.00 0.00 4.68
4482 5061 1.475930 GGGCCAGGAAGATGTCTAAGC 60.476 57.143 4.39 0.00 0.00 3.09
4483 5062 1.141858 GGGGCCAGGAAGATGTCTAAG 59.858 57.143 4.39 0.00 0.00 2.18
4484 5063 1.213296 GGGGCCAGGAAGATGTCTAA 58.787 55.000 4.39 0.00 0.00 2.10
4485 5064 0.044092 TGGGGCCAGGAAGATGTCTA 59.956 55.000 4.39 0.00 0.00 2.59
4486 5065 0.625683 ATGGGGCCAGGAAGATGTCT 60.626 55.000 4.39 0.00 0.00 3.41
4487 5066 0.259938 AATGGGGCCAGGAAGATGTC 59.740 55.000 4.39 0.00 0.00 3.06
4488 5067 1.607225 TAATGGGGCCAGGAAGATGT 58.393 50.000 4.39 0.00 0.00 3.06
4489 5068 2.800250 GATAATGGGGCCAGGAAGATG 58.200 52.381 4.39 0.00 0.00 2.90
4634 5213 8.597167 CCATATAAATGATCAGGAGGAGTACAA 58.403 37.037 0.09 0.00 34.84 2.41
4635 5214 7.955750 TCCATATAAATGATCAGGAGGAGTACA 59.044 37.037 0.09 0.00 34.84 2.90
4978 5587 1.763770 CAGCACTGGAGGGAAAGGT 59.236 57.895 0.00 0.00 0.00 3.50
5017 5626 2.715763 TGGTAGAGAAGGTGAGGGTT 57.284 50.000 0.00 0.00 0.00 4.11
5143 5769 1.689233 ACGCTGATGAAGGGGGCTA 60.689 57.895 0.00 0.00 43.07 3.93
5192 5827 3.096852 TCTTTAGATGAGAAGGACGCCA 58.903 45.455 0.00 0.00 0.00 5.69
5197 5856 3.954904 CCTCCGTCTTTAGATGAGAAGGA 59.045 47.826 8.19 8.19 45.44 3.36
5255 5915 1.745827 CGTTTCCACCACTCCACAACT 60.746 52.381 0.00 0.00 0.00 3.16
5271 5931 1.033202 ACGCAACCCTTGAACCGTTT 61.033 50.000 0.00 0.00 0.00 3.60
5286 5946 1.960763 CACAGCTACAAGCCACGCA 60.961 57.895 0.00 0.00 43.77 5.24
5301 5974 1.311859 CTTCACTGCTTCAAGCCACA 58.688 50.000 7.01 0.00 41.51 4.17
5307 5980 0.603707 CTCCGGCTTCACTGCTTCAA 60.604 55.000 0.00 0.00 0.00 2.69
5328 6001 1.354337 CCACTCACCATGAAGACGCG 61.354 60.000 3.53 3.53 0.00 6.01


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

AutoCloner maintained by Alex Coulton.