Multiple sequence alignment - TraesCS3D01G239800

Loading Multiple Alignment...

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 TraesCS3D01G239800 chr3D 100.000 2799 0 0 1 2799 332239348 332236550 0.000000e+00 5169.0
1 TraesCS3D01G239800 chr3D 93.294 2535 106 31 271 2799 332171430 332168954 0.000000e+00 3681.0
2 TraesCS3D01G239800 chr3D 84.061 527 60 20 273 783 234275743 234276261 1.170000e-133 486.0
3 TraesCS3D01G239800 chr3D 86.005 443 37 9 1979 2408 332326308 332325878 4.250000e-123 451.0
4 TraesCS3D01G239800 chr3D 90.496 242 20 3 2560 2799 332325623 332325383 1.620000e-82 316.0
5 TraesCS3D01G239800 chr3D 77.143 560 114 7 1103 1661 332327005 332326459 2.090000e-81 313.0
6 TraesCS3D01G239800 chr3D 93.793 145 9 0 2419 2563 332325895 332325751 4.690000e-53 219.0
7 TraesCS3D01G239800 chr3A 96.446 2026 58 10 783 2799 449515271 449513251 0.000000e+00 3330.0
8 TraesCS3D01G239800 chr3A 85.593 826 85 25 1979 2799 449656223 449655427 0.000000e+00 835.0
9 TraesCS3D01G239800 chr3A 76.630 552 113 10 1112 1661 449656910 449656373 9.810000e-75 291.0
10 TraesCS3D01G239800 chr3B 96.303 1785 51 5 1029 2799 431260851 431259068 0.000000e+00 2916.0
11 TraesCS3D01G239800 chr3B 94.043 789 31 9 261 1037 431264276 431263492 0.000000e+00 1182.0
12 TraesCS3D01G239800 chr3B 88.046 435 36 3 1979 2408 431516555 431516132 4.160000e-138 501.0
13 TraesCS3D01G239800 chr3B 89.256 242 22 4 2560 2799 431515929 431515690 1.630000e-77 300.0
14 TraesCS3D01G239800 chr3B 76.471 561 116 9 1103 1661 431517254 431516708 9.810000e-75 291.0
15 TraesCS3D01G239800 chr3B 78.824 340 50 15 273 599 59538689 59538359 2.830000e-50 209.0
16 TraesCS3D01G239800 chr3B 93.333 75 5 0 2419 2493 431516149 431516075 8.200000e-21 111.0
17 TraesCS3D01G239800 chr3B 77.901 181 23 10 282 452 344995318 344995491 2.290000e-16 97.1
18 TraesCS3D01G239800 chr2A 87.033 455 41 12 339 783 356699454 356699008 5.380000e-137 497.0
19 TraesCS3D01G239800 chr2A 74.172 604 140 14 1103 1698 764913464 764914059 1.300000e-58 237.0
20 TraesCS3D01G239800 chr7D 98.148 270 5 0 1 270 245804322 245804591 3.260000e-129 472.0
21 TraesCS3D01G239800 chr7D 98.148 270 5 0 1 270 245829471 245829740 3.260000e-129 472.0
22 TraesCS3D01G239800 chr7D 97.778 270 6 0 1 270 245821087 245821356 1.520000e-127 466.0
23 TraesCS3D01G239800 chr4D 98.502 267 4 0 4 270 311406807 311406541 3.260000e-129 472.0
24 TraesCS3D01G239800 chr4D 98.134 268 5 0 4 271 311397441 311397174 4.220000e-128 468.0
25 TraesCS3D01G239800 chr4D 97.778 270 6 0 1 270 122541621 122541890 1.520000e-127 466.0
26 TraesCS3D01G239800 chr6D 98.127 267 5 0 4 270 241603441 241603175 1.520000e-127 466.0
27 TraesCS3D01G239800 chr5D 98.127 267 5 0 4 270 67081974 67081708 1.520000e-127 466.0
28 TraesCS3D01G239800 chr5D 97.436 273 7 0 1 273 535433985 535434257 1.520000e-127 466.0
29 TraesCS3D01G239800 chrUn 84.649 456 52 13 339 783 343251892 343252340 3.310000e-119 438.0
30 TraesCS3D01G239800 chrUn 84.649 456 52 13 339 783 358257428 358256980 3.310000e-119 438.0
31 TraesCS3D01G239800 chrUn 84.649 456 52 13 339 783 358762534 358762086 3.310000e-119 438.0
32 TraesCS3D01G239800 chrUn 84.649 456 52 13 339 783 401478124 401477676 3.310000e-119 438.0
33 TraesCS3D01G239800 chr5B 83.624 458 55 17 339 783 232258395 232257945 2.010000e-111 412.0
34 TraesCS3D01G239800 chr1B 87.578 322 29 6 271 585 344775833 344775516 2.050000e-96 363.0
35 TraesCS3D01G239800 chr5A 75.331 604 131 16 1103 1697 4080772 4081366 9.880000e-70 274.0
36 TraesCS3D01G239800 chr4A 75.166 604 132 16 1103 1697 17887889 17888483 4.600000e-68 268.0
37 TraesCS3D01G239800 chr7B 77.676 327 48 15 271 585 279107003 279107316 2.870000e-40 176.0
38 TraesCS3D01G239800 chr7B 75.080 313 55 18 272 569 169346193 169346497 1.050000e-24 124.0
39 TraesCS3D01G239800 chr7B 97.059 34 0 1 273 305 726215471 726215438 3.890000e-04 56.5
40 TraesCS3D01G239800 chr6B 100.000 29 0 0 272 300 380667090 380667118 1.000000e-03 54.7


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 TraesCS3D01G239800 chr3D 332236550 332239348 2798 True 5169.00 5169 100.00000 1 2799 1 chr3D.!!$R2 2798
1 TraesCS3D01G239800 chr3D 332168954 332171430 2476 True 3681.00 3681 93.29400 271 2799 1 chr3D.!!$R1 2528
2 TraesCS3D01G239800 chr3D 234275743 234276261 518 False 486.00 486 84.06100 273 783 1 chr3D.!!$F1 510
3 TraesCS3D01G239800 chr3D 332325383 332327005 1622 True 324.75 451 86.85925 1103 2799 4 chr3D.!!$R3 1696
4 TraesCS3D01G239800 chr3A 449513251 449515271 2020 True 3330.00 3330 96.44600 783 2799 1 chr3A.!!$R1 2016
5 TraesCS3D01G239800 chr3A 449655427 449656910 1483 True 563.00 835 81.11150 1112 2799 2 chr3A.!!$R2 1687
6 TraesCS3D01G239800 chr3B 431259068 431264276 5208 True 2049.00 2916 95.17300 261 2799 2 chr3B.!!$R2 2538
7 TraesCS3D01G239800 chr3B 431515690 431517254 1564 True 300.75 501 86.77650 1103 2799 4 chr3B.!!$R3 1696
8 TraesCS3D01G239800 chr2A 764913464 764914059 595 False 237.00 237 74.17200 1103 1698 1 chr2A.!!$F1 595
9 TraesCS3D01G239800 chr5A 4080772 4081366 594 False 274.00 274 75.33100 1103 1697 1 chr5A.!!$F1 594
10 TraesCS3D01G239800 chr4A 17887889 17888483 594 False 268.00 268 75.16600 1103 1697 1 chr4A.!!$F1 594

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
211 212 0.030101 CGACAAAACCACAATGCGGT 59.970 50.0 0.00 0.0 38.85 5.68 F
264 265 0.037326 ATATAGCCGCATCGTGGGTG 60.037 55.0 8.47 0.0 44.01 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1572 4247 1.227147 CATCGTTATCCGCCGTGGT 60.227 57.895 0.0 0.0 39.52 4.16 R
1870 4553 1.738099 CTGTAGCAGACCGCCACAC 60.738 63.158 0.0 0.0 37.32 3.82 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
19 20 3.294750 TCCAGTTGGGACGATCGG 58.705 61.111 20.98 1.23 42.15 4.18
20 21 2.186903 CCAGTTGGGACGATCGGG 59.813 66.667 20.98 4.12 40.01 5.14
21 22 2.186903 CAGTTGGGACGATCGGGG 59.813 66.667 20.98 0.00 0.00 5.73
22 23 2.038329 AGTTGGGACGATCGGGGA 59.962 61.111 20.98 0.00 0.00 4.81
23 24 1.382695 AGTTGGGACGATCGGGGAT 60.383 57.895 20.98 0.00 0.00 3.85
24 25 1.069258 GTTGGGACGATCGGGGATC 59.931 63.158 20.98 7.51 35.88 3.36
25 26 1.075525 TTGGGACGATCGGGGATCT 60.076 57.895 20.98 0.00 36.96 2.75
26 27 0.186630 TTGGGACGATCGGGGATCTA 59.813 55.000 20.98 0.00 36.96 1.98
27 28 0.251209 TGGGACGATCGGGGATCTAG 60.251 60.000 20.98 0.00 36.96 2.43
28 29 1.596895 GGGACGATCGGGGATCTAGC 61.597 65.000 20.98 0.00 36.96 3.42
29 30 0.894184 GGACGATCGGGGATCTAGCA 60.894 60.000 20.98 0.00 36.96 3.49
30 31 0.523966 GACGATCGGGGATCTAGCAG 59.476 60.000 20.98 0.00 36.96 4.24
31 32 0.178987 ACGATCGGGGATCTAGCAGT 60.179 55.000 20.98 0.00 36.96 4.40
32 33 0.962489 CGATCGGGGATCTAGCAGTT 59.038 55.000 7.38 0.00 36.96 3.16
33 34 1.336332 CGATCGGGGATCTAGCAGTTG 60.336 57.143 7.38 0.00 36.96 3.16
34 35 1.001406 GATCGGGGATCTAGCAGTTGG 59.999 57.143 0.00 0.00 36.27 3.77
35 36 1.048724 TCGGGGATCTAGCAGTTGGG 61.049 60.000 0.00 0.00 0.00 4.12
36 37 1.338136 CGGGGATCTAGCAGTTGGGT 61.338 60.000 0.00 0.00 0.00 4.51
37 38 0.919710 GGGGATCTAGCAGTTGGGTT 59.080 55.000 0.00 0.00 0.00 4.11
38 39 1.408822 GGGGATCTAGCAGTTGGGTTG 60.409 57.143 0.00 0.00 0.00 3.77
39 40 1.282157 GGGATCTAGCAGTTGGGTTGT 59.718 52.381 0.00 0.00 0.00 3.32
40 41 2.633488 GGATCTAGCAGTTGGGTTGTC 58.367 52.381 0.00 0.00 0.00 3.18
41 42 2.237392 GGATCTAGCAGTTGGGTTGTCT 59.763 50.000 0.00 0.00 0.00 3.41
42 43 3.307762 GGATCTAGCAGTTGGGTTGTCTT 60.308 47.826 0.00 0.00 0.00 3.01
43 44 3.402628 TCTAGCAGTTGGGTTGTCTTC 57.597 47.619 0.00 0.00 0.00 2.87
44 45 2.972713 TCTAGCAGTTGGGTTGTCTTCT 59.027 45.455 0.00 0.00 0.00 2.85
45 46 2.736670 AGCAGTTGGGTTGTCTTCTT 57.263 45.000 0.00 0.00 0.00 2.52
46 47 3.018423 AGCAGTTGGGTTGTCTTCTTT 57.982 42.857 0.00 0.00 0.00 2.52
47 48 4.164843 AGCAGTTGGGTTGTCTTCTTTA 57.835 40.909 0.00 0.00 0.00 1.85
48 49 4.532834 AGCAGTTGGGTTGTCTTCTTTAA 58.467 39.130 0.00 0.00 0.00 1.52
49 50 5.140454 AGCAGTTGGGTTGTCTTCTTTAAT 58.860 37.500 0.00 0.00 0.00 1.40
50 51 5.598417 AGCAGTTGGGTTGTCTTCTTTAATT 59.402 36.000 0.00 0.00 0.00 1.40
51 52 6.098266 AGCAGTTGGGTTGTCTTCTTTAATTT 59.902 34.615 0.00 0.00 0.00 1.82
52 53 6.761242 GCAGTTGGGTTGTCTTCTTTAATTTT 59.239 34.615 0.00 0.00 0.00 1.82
53 54 7.254421 GCAGTTGGGTTGTCTTCTTTAATTTTG 60.254 37.037 0.00 0.00 0.00 2.44
54 55 7.224557 CAGTTGGGTTGTCTTCTTTAATTTTGG 59.775 37.037 0.00 0.00 0.00 3.28
55 56 6.800072 TGGGTTGTCTTCTTTAATTTTGGT 57.200 33.333 0.00 0.00 0.00 3.67
56 57 7.189079 TGGGTTGTCTTCTTTAATTTTGGTT 57.811 32.000 0.00 0.00 0.00 3.67
57 58 7.269316 TGGGTTGTCTTCTTTAATTTTGGTTC 58.731 34.615 0.00 0.00 0.00 3.62
58 59 6.704493 GGGTTGTCTTCTTTAATTTTGGTTCC 59.296 38.462 0.00 0.00 0.00 3.62
59 60 6.419710 GGTTGTCTTCTTTAATTTTGGTTCCG 59.580 38.462 0.00 0.00 0.00 4.30
60 61 6.702716 TGTCTTCTTTAATTTTGGTTCCGT 57.297 33.333 0.00 0.00 0.00 4.69
61 62 7.804843 TGTCTTCTTTAATTTTGGTTCCGTA 57.195 32.000 0.00 0.00 0.00 4.02
62 63 7.867752 TGTCTTCTTTAATTTTGGTTCCGTAG 58.132 34.615 0.00 0.00 0.00 3.51
63 64 7.499895 TGTCTTCTTTAATTTTGGTTCCGTAGT 59.500 33.333 0.00 0.00 0.00 2.73
64 65 8.013947 GTCTTCTTTAATTTTGGTTCCGTAGTC 58.986 37.037 0.00 0.00 0.00 2.59
65 66 6.470557 TCTTTAATTTTGGTTCCGTAGTCG 57.529 37.500 0.00 0.00 0.00 4.18
77 78 2.470196 CGTAGTCGGACCTATGTGTG 57.530 55.000 4.14 0.00 0.00 3.82
78 79 1.741706 CGTAGTCGGACCTATGTGTGT 59.258 52.381 4.14 0.00 0.00 3.72
79 80 2.938451 CGTAGTCGGACCTATGTGTGTA 59.062 50.000 4.14 0.00 0.00 2.90
80 81 3.242543 CGTAGTCGGACCTATGTGTGTAC 60.243 52.174 4.14 0.00 0.00 2.90
81 82 2.097825 AGTCGGACCTATGTGTGTACC 58.902 52.381 4.14 0.00 0.00 3.34
82 83 2.097825 GTCGGACCTATGTGTGTACCT 58.902 52.381 0.00 0.00 0.00 3.08
83 84 2.494870 GTCGGACCTATGTGTGTACCTT 59.505 50.000 0.00 0.00 0.00 3.50
84 85 2.494471 TCGGACCTATGTGTGTACCTTG 59.506 50.000 0.00 0.00 0.00 3.61
85 86 2.494471 CGGACCTATGTGTGTACCTTGA 59.506 50.000 0.00 0.00 0.00 3.02
86 87 3.056393 CGGACCTATGTGTGTACCTTGAA 60.056 47.826 0.00 0.00 0.00 2.69
87 88 4.382685 CGGACCTATGTGTGTACCTTGAAT 60.383 45.833 0.00 0.00 0.00 2.57
88 89 4.876107 GGACCTATGTGTGTACCTTGAATG 59.124 45.833 0.00 0.00 0.00 2.67
89 90 5.338056 GGACCTATGTGTGTACCTTGAATGA 60.338 44.000 0.00 0.00 0.00 2.57
90 91 6.313519 ACCTATGTGTGTACCTTGAATGAT 57.686 37.500 0.00 0.00 0.00 2.45
91 92 6.115446 ACCTATGTGTGTACCTTGAATGATG 58.885 40.000 0.00 0.00 0.00 3.07
92 93 6.115446 CCTATGTGTGTACCTTGAATGATGT 58.885 40.000 0.00 0.00 0.00 3.06
93 94 7.093068 ACCTATGTGTGTACCTTGAATGATGTA 60.093 37.037 0.00 0.00 0.00 2.29
94 95 7.933577 CCTATGTGTGTACCTTGAATGATGTAT 59.066 37.037 0.00 0.00 0.00 2.29
95 96 6.983474 TGTGTGTACCTTGAATGATGTATG 57.017 37.500 0.00 0.00 0.00 2.39
96 97 6.706295 TGTGTGTACCTTGAATGATGTATGA 58.294 36.000 0.00 0.00 0.00 2.15
97 98 7.164803 TGTGTGTACCTTGAATGATGTATGAA 58.835 34.615 0.00 0.00 0.00 2.57
98 99 7.828717 TGTGTGTACCTTGAATGATGTATGAAT 59.171 33.333 0.00 0.00 0.00 2.57
99 100 8.677300 GTGTGTACCTTGAATGATGTATGAATT 58.323 33.333 0.00 0.00 0.00 2.17
100 101 8.892723 TGTGTACCTTGAATGATGTATGAATTC 58.107 33.333 0.00 0.00 0.00 2.17
101 102 8.892723 GTGTACCTTGAATGATGTATGAATTCA 58.107 33.333 11.26 11.26 38.27 2.57
102 103 9.631257 TGTACCTTGAATGATGTATGAATTCAT 57.369 29.630 23.75 23.75 39.40 2.57
122 123 9.859427 AATTCATTTATGTATTGTGTGAAGTGG 57.141 29.630 0.00 0.00 0.00 4.00
123 124 6.851609 TCATTTATGTATTGTGTGAAGTGGC 58.148 36.000 0.00 0.00 0.00 5.01
124 125 4.937696 TTATGTATTGTGTGAAGTGGCG 57.062 40.909 0.00 0.00 0.00 5.69
125 126 2.535012 TGTATTGTGTGAAGTGGCGA 57.465 45.000 0.00 0.00 0.00 5.54
126 127 3.052455 TGTATTGTGTGAAGTGGCGAT 57.948 42.857 0.00 0.00 0.00 4.58
127 128 3.407698 TGTATTGTGTGAAGTGGCGATT 58.592 40.909 0.00 0.00 0.00 3.34
128 129 2.995466 ATTGTGTGAAGTGGCGATTG 57.005 45.000 0.00 0.00 0.00 2.67
129 130 1.674359 TTGTGTGAAGTGGCGATTGT 58.326 45.000 0.00 0.00 0.00 2.71
130 131 2.535012 TGTGTGAAGTGGCGATTGTA 57.465 45.000 0.00 0.00 0.00 2.41
131 132 2.839975 TGTGTGAAGTGGCGATTGTAA 58.160 42.857 0.00 0.00 0.00 2.41
132 133 2.805671 TGTGTGAAGTGGCGATTGTAAG 59.194 45.455 0.00 0.00 0.00 2.34
133 134 1.804151 TGTGAAGTGGCGATTGTAAGC 59.196 47.619 0.00 0.00 0.00 3.09
142 143 3.831715 GCGATTGTAAGCCAACTCTTT 57.168 42.857 0.00 0.00 35.44 2.52
143 144 4.939509 GCGATTGTAAGCCAACTCTTTA 57.060 40.909 0.00 0.00 35.44 1.85
144 145 5.485662 GCGATTGTAAGCCAACTCTTTAT 57.514 39.130 0.00 0.00 35.44 1.40
145 146 5.502606 GCGATTGTAAGCCAACTCTTTATC 58.497 41.667 0.00 0.00 35.44 1.75
146 147 5.504173 GCGATTGTAAGCCAACTCTTTATCC 60.504 44.000 0.00 0.00 35.44 2.59
147 148 5.007724 CGATTGTAAGCCAACTCTTTATCCC 59.992 44.000 0.00 0.00 35.44 3.85
148 149 4.919774 TGTAAGCCAACTCTTTATCCCA 57.080 40.909 0.00 0.00 0.00 4.37
149 150 5.450818 TGTAAGCCAACTCTTTATCCCAT 57.549 39.130 0.00 0.00 0.00 4.00
150 151 5.826643 TGTAAGCCAACTCTTTATCCCATT 58.173 37.500 0.00 0.00 0.00 3.16
151 152 5.885912 TGTAAGCCAACTCTTTATCCCATTC 59.114 40.000 0.00 0.00 0.00 2.67
152 153 4.870021 AGCCAACTCTTTATCCCATTCT 57.130 40.909 0.00 0.00 0.00 2.40
153 154 5.198602 AGCCAACTCTTTATCCCATTCTT 57.801 39.130 0.00 0.00 0.00 2.52
154 155 4.952335 AGCCAACTCTTTATCCCATTCTTG 59.048 41.667 0.00 0.00 0.00 3.02
155 156 4.706962 GCCAACTCTTTATCCCATTCTTGT 59.293 41.667 0.00 0.00 0.00 3.16
156 157 5.185828 GCCAACTCTTTATCCCATTCTTGTT 59.814 40.000 0.00 0.00 0.00 2.83
157 158 6.625960 GCCAACTCTTTATCCCATTCTTGTTC 60.626 42.308 0.00 0.00 0.00 3.18
158 159 6.434028 CCAACTCTTTATCCCATTCTTGTTCA 59.566 38.462 0.00 0.00 0.00 3.18
159 160 7.123247 CCAACTCTTTATCCCATTCTTGTTCAT 59.877 37.037 0.00 0.00 0.00 2.57
160 161 8.526147 CAACTCTTTATCCCATTCTTGTTCATT 58.474 33.333 0.00 0.00 0.00 2.57
161 162 9.753674 AACTCTTTATCCCATTCTTGTTCATTA 57.246 29.630 0.00 0.00 0.00 1.90
162 163 9.178758 ACTCTTTATCCCATTCTTGTTCATTAC 57.821 33.333 0.00 0.00 0.00 1.89
163 164 9.177608 CTCTTTATCCCATTCTTGTTCATTACA 57.822 33.333 0.00 0.00 34.12 2.41
164 165 9.699410 TCTTTATCCCATTCTTGTTCATTACAT 57.301 29.630 0.00 0.00 36.44 2.29
165 166 9.740239 CTTTATCCCATTCTTGTTCATTACATG 57.260 33.333 0.00 0.00 36.44 3.21
166 167 6.720112 ATCCCATTCTTGTTCATTACATGG 57.280 37.500 0.00 0.00 36.44 3.66
167 168 5.266733 CCCATTCTTGTTCATTACATGGG 57.733 43.478 0.00 0.00 43.44 4.00
168 169 4.711355 CCCATTCTTGTTCATTACATGGGT 59.289 41.667 6.20 0.00 43.74 4.51
169 170 5.187576 CCCATTCTTGTTCATTACATGGGTT 59.812 40.000 6.20 0.00 43.74 4.11
170 171 6.295802 CCCATTCTTGTTCATTACATGGGTTT 60.296 38.462 6.20 0.00 43.74 3.27
171 172 6.591062 CCATTCTTGTTCATTACATGGGTTTG 59.409 38.462 0.00 0.00 36.44 2.93
172 173 6.723298 TTCTTGTTCATTACATGGGTTTGT 57.277 33.333 0.00 0.00 36.44 2.83
173 174 6.083098 TCTTGTTCATTACATGGGTTTGTG 57.917 37.500 0.00 0.00 36.44 3.33
174 175 5.596361 TCTTGTTCATTACATGGGTTTGTGT 59.404 36.000 0.00 0.00 36.44 3.72
175 176 5.193663 TGTTCATTACATGGGTTTGTGTG 57.806 39.130 0.00 0.00 0.00 3.82
176 177 4.889995 TGTTCATTACATGGGTTTGTGTGA 59.110 37.500 0.00 0.00 0.00 3.58
177 178 5.360999 TGTTCATTACATGGGTTTGTGTGAA 59.639 36.000 0.00 0.00 35.28 3.18
178 179 5.703978 TCATTACATGGGTTTGTGTGAAG 57.296 39.130 0.00 0.00 0.00 3.02
179 180 5.380900 TCATTACATGGGTTTGTGTGAAGA 58.619 37.500 0.00 0.00 0.00 2.87
180 181 6.009589 TCATTACATGGGTTTGTGTGAAGAT 58.990 36.000 0.00 0.00 0.00 2.40
181 182 5.703978 TTACATGGGTTTGTGTGAAGATG 57.296 39.130 0.00 0.00 0.00 2.90
182 183 3.831323 ACATGGGTTTGTGTGAAGATGA 58.169 40.909 0.00 0.00 0.00 2.92
183 184 3.569701 ACATGGGTTTGTGTGAAGATGAC 59.430 43.478 0.00 0.00 0.00 3.06
184 185 2.582052 TGGGTTTGTGTGAAGATGACC 58.418 47.619 0.00 0.00 0.00 4.02
185 186 1.886542 GGGTTTGTGTGAAGATGACCC 59.113 52.381 0.00 0.00 38.55 4.46
186 187 2.489073 GGGTTTGTGTGAAGATGACCCT 60.489 50.000 0.00 0.00 41.55 4.34
187 188 3.222603 GGTTTGTGTGAAGATGACCCTT 58.777 45.455 0.00 0.00 0.00 3.95
188 189 3.253432 GGTTTGTGTGAAGATGACCCTTC 59.747 47.826 0.00 0.00 42.09 3.46
189 190 4.137543 GTTTGTGTGAAGATGACCCTTCT 58.862 43.478 0.00 0.00 42.20 2.85
190 191 4.437682 TTGTGTGAAGATGACCCTTCTT 57.562 40.909 0.00 0.00 42.20 2.52
191 192 3.743521 TGTGTGAAGATGACCCTTCTTG 58.256 45.455 0.00 0.00 42.20 3.02
192 193 2.485814 GTGTGAAGATGACCCTTCTTGC 59.514 50.000 0.00 0.00 42.20 4.01
193 194 1.734465 GTGAAGATGACCCTTCTTGCG 59.266 52.381 0.00 0.00 42.20 4.85
194 195 1.623311 TGAAGATGACCCTTCTTGCGA 59.377 47.619 0.00 0.00 42.20 5.10
195 196 2.003301 GAAGATGACCCTTCTTGCGAC 58.997 52.381 0.00 0.00 39.44 5.19
196 197 0.976641 AGATGACCCTTCTTGCGACA 59.023 50.000 0.00 0.00 0.00 4.35
197 198 1.347707 AGATGACCCTTCTTGCGACAA 59.652 47.619 0.00 0.00 0.00 3.18
198 199 2.151202 GATGACCCTTCTTGCGACAAA 58.849 47.619 0.00 0.00 0.00 2.83
199 200 2.045561 TGACCCTTCTTGCGACAAAA 57.954 45.000 0.00 0.00 0.00 2.44
200 201 1.673920 TGACCCTTCTTGCGACAAAAC 59.326 47.619 0.00 0.00 0.00 2.43
201 202 1.001706 GACCCTTCTTGCGACAAAACC 60.002 52.381 0.00 0.00 0.00 3.27
202 203 1.028905 CCCTTCTTGCGACAAAACCA 58.971 50.000 0.00 0.00 0.00 3.67
203 204 1.269051 CCCTTCTTGCGACAAAACCAC 60.269 52.381 0.00 0.00 0.00 4.16
204 205 1.403679 CCTTCTTGCGACAAAACCACA 59.596 47.619 0.00 0.00 0.00 4.17
205 206 2.159310 CCTTCTTGCGACAAAACCACAA 60.159 45.455 0.00 0.00 0.00 3.33
206 207 3.490761 CCTTCTTGCGACAAAACCACAAT 60.491 43.478 0.00 0.00 0.00 2.71
207 208 3.077229 TCTTGCGACAAAACCACAATG 57.923 42.857 0.00 0.00 0.00 2.82
208 209 1.522258 CTTGCGACAAAACCACAATGC 59.478 47.619 0.00 0.00 0.00 3.56
209 210 0.593518 TGCGACAAAACCACAATGCG 60.594 50.000 0.00 0.00 0.00 4.73
210 211 1.274798 GCGACAAAACCACAATGCGG 61.275 55.000 0.00 0.00 0.00 5.69
211 212 0.030101 CGACAAAACCACAATGCGGT 59.970 50.000 0.00 0.00 38.85 5.68
213 214 2.287069 CGACAAAACCACAATGCGGTTA 60.287 45.455 6.07 0.00 46.12 2.85
214 215 3.610585 CGACAAAACCACAATGCGGTTAT 60.611 43.478 6.07 0.00 46.12 1.89
215 216 3.648009 ACAAAACCACAATGCGGTTATG 58.352 40.909 6.07 0.00 46.12 1.90
216 217 2.362169 AAACCACAATGCGGTTATGC 57.638 45.000 6.07 0.00 46.12 3.14
217 218 0.530288 AACCACAATGCGGTTATGCC 59.470 50.000 3.53 0.00 45.00 4.40
218 219 0.323360 ACCACAATGCGGTTATGCCT 60.323 50.000 0.00 0.00 30.53 4.75
219 220 0.381801 CCACAATGCGGTTATGCCTC 59.618 55.000 0.00 0.00 34.25 4.70
220 221 1.382522 CACAATGCGGTTATGCCTCT 58.617 50.000 0.00 0.00 34.25 3.69
221 222 2.560504 CACAATGCGGTTATGCCTCTA 58.439 47.619 0.00 0.00 34.25 2.43
222 223 2.942376 CACAATGCGGTTATGCCTCTAA 59.058 45.455 0.00 0.00 34.25 2.10
223 224 3.002656 CACAATGCGGTTATGCCTCTAAG 59.997 47.826 0.00 0.00 34.25 2.18
224 225 3.206150 CAATGCGGTTATGCCTCTAAGT 58.794 45.455 0.00 0.00 34.25 2.24
225 226 2.596904 TGCGGTTATGCCTCTAAGTC 57.403 50.000 0.00 0.00 34.25 3.01
226 227 1.202371 TGCGGTTATGCCTCTAAGTCG 60.202 52.381 0.00 0.00 34.25 4.18
227 228 1.202382 GCGGTTATGCCTCTAAGTCGT 60.202 52.381 0.00 0.00 34.25 4.34
228 229 2.460918 CGGTTATGCCTCTAAGTCGTG 58.539 52.381 0.00 0.00 34.25 4.35
229 230 2.202566 GGTTATGCCTCTAAGTCGTGC 58.797 52.381 0.00 0.00 0.00 5.34
230 231 2.202566 GTTATGCCTCTAAGTCGTGCC 58.797 52.381 0.00 0.00 0.00 5.01
231 232 0.750850 TATGCCTCTAAGTCGTGCCC 59.249 55.000 0.00 0.00 0.00 5.36
232 233 1.972660 ATGCCTCTAAGTCGTGCCCC 61.973 60.000 0.00 0.00 0.00 5.80
233 234 2.494918 CCTCTAAGTCGTGCCCCG 59.505 66.667 0.00 0.00 38.13 5.73
234 235 2.050350 CCTCTAAGTCGTGCCCCGA 61.050 63.158 0.00 0.00 45.00 5.14
250 251 2.991434 CCGACACGTGGGAGATATAG 57.009 55.000 21.57 0.00 0.00 1.31
251 252 1.068472 CCGACACGTGGGAGATATAGC 60.068 57.143 21.57 0.00 0.00 2.97
252 253 1.068472 CGACACGTGGGAGATATAGCC 60.068 57.143 21.57 0.00 0.00 3.93
253 254 0.959553 ACACGTGGGAGATATAGCCG 59.040 55.000 21.57 0.00 0.00 5.52
254 255 0.388649 CACGTGGGAGATATAGCCGC 60.389 60.000 7.95 0.00 0.00 6.53
255 256 0.826256 ACGTGGGAGATATAGCCGCA 60.826 55.000 0.00 0.00 0.00 5.69
256 257 0.532573 CGTGGGAGATATAGCCGCAT 59.467 55.000 0.00 0.00 0.00 4.73
257 258 1.469940 CGTGGGAGATATAGCCGCATC 60.470 57.143 0.00 0.00 0.00 3.91
258 259 0.817654 TGGGAGATATAGCCGCATCG 59.182 55.000 0.00 0.00 0.00 3.84
259 260 0.818296 GGGAGATATAGCCGCATCGT 59.182 55.000 0.00 0.00 0.00 3.73
260 261 1.469940 GGGAGATATAGCCGCATCGTG 60.470 57.143 0.00 0.00 0.00 4.35
261 262 1.469940 GGAGATATAGCCGCATCGTGG 60.470 57.143 0.00 0.00 36.10 4.94
262 263 0.532573 AGATATAGCCGCATCGTGGG 59.467 55.000 0.00 0.00 33.18 4.61
263 264 0.246635 GATATAGCCGCATCGTGGGT 59.753 55.000 3.52 3.52 46.10 4.51
264 265 0.037326 ATATAGCCGCATCGTGGGTG 60.037 55.000 8.47 0.00 44.01 4.61
265 266 1.396607 TATAGCCGCATCGTGGGTGT 61.397 55.000 8.47 4.53 44.01 4.16
266 267 2.923426 ATAGCCGCATCGTGGGTGTG 62.923 60.000 8.47 0.00 44.01 3.82
268 269 3.118454 CCGCATCGTGGGTGTGAC 61.118 66.667 0.00 0.00 0.00 3.67
269 270 2.356913 CGCATCGTGGGTGTGACA 60.357 61.111 0.00 0.00 0.00 3.58
466 479 7.717875 CCTAGCCTATATGTACTCCTCATCTAC 59.282 44.444 0.00 0.00 0.00 2.59
691 705 7.404671 AGTGGATGTGTTATTTGGGTTTATC 57.595 36.000 0.00 0.00 0.00 1.75
724 738 3.947834 CCTCCTTGTGTTCTTGAGTGTTT 59.052 43.478 0.00 0.00 0.00 2.83
725 739 4.035675 CCTCCTTGTGTTCTTGAGTGTTTC 59.964 45.833 0.00 0.00 0.00 2.78
795 809 2.165641 CGTACAACAGGTGCTCATAGGA 59.834 50.000 0.00 0.00 0.00 2.94
817 831 1.533625 AGGTATGTGTGCATGCGTTT 58.466 45.000 14.09 0.00 38.38 3.60
826 840 4.695928 TGTGTGCATGCGTTTATAAGGTTA 59.304 37.500 14.09 0.00 0.00 2.85
827 841 5.163804 TGTGTGCATGCGTTTATAAGGTTAG 60.164 40.000 14.09 0.00 0.00 2.34
828 842 4.201871 TGTGCATGCGTTTATAAGGTTAGC 60.202 41.667 14.09 0.00 0.00 3.09
1544 4219 3.435186 GCTGAAAGACCTGGCGCC 61.435 66.667 22.73 22.73 34.07 6.53
1572 4247 0.780637 TGGGGGTTACCATGCAGAAA 59.219 50.000 2.98 0.00 42.91 2.52
1584 4259 1.448893 GCAGAAACCACGGCGGATA 60.449 57.895 13.24 0.00 38.63 2.59
1810 4493 8.499162 CATTTTGTTCTTACTCTCCTAGTGTTG 58.501 37.037 0.00 0.00 39.39 3.33
1870 4553 3.554752 GGGGAATGGTTGTCAACATGTTG 60.555 47.826 29.01 29.01 41.71 3.33
1949 4641 4.320861 CGGATGTTCCAAAATTGTAGTGCA 60.321 41.667 0.00 0.00 35.91 4.57
2002 4696 7.134362 TGATTCTCTGCTGGAAGAATTAGAT 57.866 36.000 8.36 0.00 34.07 1.98
2033 4727 4.092091 GTGTTGAGGATTAACTTCAGAGCG 59.908 45.833 0.00 0.00 36.06 5.03
2260 4962 7.147976 GCCATTATAATTTTTCGATCTGCCTT 58.852 34.615 0.00 0.00 0.00 4.35
2405 5112 7.768807 TGGTGTGCCAACTATTTTTAGTTAT 57.231 32.000 0.00 0.00 42.83 1.89
2406 5113 7.598278 TGGTGTGCCAACTATTTTTAGTTATG 58.402 34.615 0.00 0.00 42.83 1.90
2407 5114 7.231722 TGGTGTGCCAACTATTTTTAGTTATGT 59.768 33.333 0.00 0.00 42.83 2.29
2408 5115 8.085909 GGTGTGCCAACTATTTTTAGTTATGTT 58.914 33.333 0.00 0.00 38.14 2.71
2409 5116 8.911662 GTGTGCCAACTATTTTTAGTTATGTTG 58.088 33.333 0.00 0.00 38.14 3.33
2410 5117 8.634444 TGTGCCAACTATTTTTAGTTATGTTGT 58.366 29.630 0.00 0.00 38.14 3.32
2411 5118 9.471084 GTGCCAACTATTTTTAGTTATGTTGTT 57.529 29.630 0.00 0.00 38.14 2.83
2538 5304 7.093771 TGACAGCTATCAGTTCATAGAGTTTCA 60.094 37.037 0.00 0.00 0.00 2.69
2669 5567 7.147159 ACCCTATAACTAACTAGCTACTGGTCT 60.147 40.741 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.355986 CCCGATCGTCCCAACTGGA 61.356 63.158 15.09 0.00 42.41 3.86
3 4 2.186903 CCCGATCGTCCCAACTGG 59.813 66.667 15.09 1.09 0.00 4.00
4 5 1.686325 ATCCCCGATCGTCCCAACTG 61.686 60.000 15.09 0.00 0.00 3.16
5 6 1.382695 ATCCCCGATCGTCCCAACT 60.383 57.895 15.09 0.00 0.00 3.16
7 8 0.186630 TAGATCCCCGATCGTCCCAA 59.813 55.000 15.09 0.00 43.17 4.12
9 10 1.596895 GCTAGATCCCCGATCGTCCC 61.597 65.000 15.09 0.00 43.17 4.46
10 11 0.894184 TGCTAGATCCCCGATCGTCC 60.894 60.000 15.09 0.00 43.17 4.79
11 12 0.523966 CTGCTAGATCCCCGATCGTC 59.476 60.000 15.09 4.78 43.17 4.20
12 13 0.178987 ACTGCTAGATCCCCGATCGT 60.179 55.000 15.09 0.00 43.17 3.73
13 14 0.962489 AACTGCTAGATCCCCGATCG 59.038 55.000 8.51 8.51 43.17 3.69
14 15 1.001406 CCAACTGCTAGATCCCCGATC 59.999 57.143 0.00 0.00 39.17 3.69
15 16 1.051812 CCAACTGCTAGATCCCCGAT 58.948 55.000 0.00 0.00 0.00 4.18
16 17 1.048724 CCCAACTGCTAGATCCCCGA 61.049 60.000 0.00 0.00 0.00 5.14
17 18 1.338136 ACCCAACTGCTAGATCCCCG 61.338 60.000 0.00 0.00 0.00 5.73
18 19 0.919710 AACCCAACTGCTAGATCCCC 59.080 55.000 0.00 0.00 0.00 4.81
19 20 1.282157 ACAACCCAACTGCTAGATCCC 59.718 52.381 0.00 0.00 0.00 3.85
20 21 2.237392 AGACAACCCAACTGCTAGATCC 59.763 50.000 0.00 0.00 0.00 3.36
21 22 3.618690 AGACAACCCAACTGCTAGATC 57.381 47.619 0.00 0.00 0.00 2.75
22 23 3.584848 AGAAGACAACCCAACTGCTAGAT 59.415 43.478 0.00 0.00 0.00 1.98
23 24 2.972713 AGAAGACAACCCAACTGCTAGA 59.027 45.455 0.00 0.00 0.00 2.43
24 25 3.409026 AGAAGACAACCCAACTGCTAG 57.591 47.619 0.00 0.00 0.00 3.42
25 26 3.857157 AAGAAGACAACCCAACTGCTA 57.143 42.857 0.00 0.00 0.00 3.49
26 27 2.736670 AAGAAGACAACCCAACTGCT 57.263 45.000 0.00 0.00 0.00 4.24
27 28 4.911514 TTAAAGAAGACAACCCAACTGC 57.088 40.909 0.00 0.00 0.00 4.40
28 29 7.224557 CCAAAATTAAAGAAGACAACCCAACTG 59.775 37.037 0.00 0.00 0.00 3.16
29 30 7.093068 ACCAAAATTAAAGAAGACAACCCAACT 60.093 33.333 0.00 0.00 0.00 3.16
30 31 7.045416 ACCAAAATTAAAGAAGACAACCCAAC 58.955 34.615 0.00 0.00 0.00 3.77
31 32 7.189079 ACCAAAATTAAAGAAGACAACCCAA 57.811 32.000 0.00 0.00 0.00 4.12
32 33 6.800072 ACCAAAATTAAAGAAGACAACCCA 57.200 33.333 0.00 0.00 0.00 4.51
33 34 6.704493 GGAACCAAAATTAAAGAAGACAACCC 59.296 38.462 0.00 0.00 0.00 4.11
34 35 6.419710 CGGAACCAAAATTAAAGAAGACAACC 59.580 38.462 0.00 0.00 0.00 3.77
35 36 6.976349 ACGGAACCAAAATTAAAGAAGACAAC 59.024 34.615 0.00 0.00 0.00 3.32
36 37 7.102847 ACGGAACCAAAATTAAAGAAGACAA 57.897 32.000 0.00 0.00 0.00 3.18
37 38 6.702716 ACGGAACCAAAATTAAAGAAGACA 57.297 33.333 0.00 0.00 0.00 3.41
38 39 7.868775 ACTACGGAACCAAAATTAAAGAAGAC 58.131 34.615 0.00 0.00 0.00 3.01
39 40 7.095523 CGACTACGGAACCAAAATTAAAGAAGA 60.096 37.037 0.00 0.00 35.72 2.87
40 41 7.013529 CGACTACGGAACCAAAATTAAAGAAG 58.986 38.462 0.00 0.00 35.72 2.85
41 42 6.890558 CGACTACGGAACCAAAATTAAAGAA 58.109 36.000 0.00 0.00 35.72 2.52
42 43 6.470557 CGACTACGGAACCAAAATTAAAGA 57.529 37.500 0.00 0.00 35.72 2.52
58 59 1.741706 ACACACATAGGTCCGACTACG 59.258 52.381 0.00 0.00 39.43 3.51
59 60 3.065925 GGTACACACATAGGTCCGACTAC 59.934 52.174 0.00 0.00 0.00 2.73
60 61 3.054139 AGGTACACACATAGGTCCGACTA 60.054 47.826 0.00 0.00 0.00 2.59
61 62 2.097825 GGTACACACATAGGTCCGACT 58.902 52.381 0.00 0.00 0.00 4.18
62 63 2.097825 AGGTACACACATAGGTCCGAC 58.902 52.381 0.00 0.00 0.00 4.79
63 64 2.494471 CAAGGTACACACATAGGTCCGA 59.506 50.000 0.00 0.00 0.00 4.55
64 65 2.494471 TCAAGGTACACACATAGGTCCG 59.506 50.000 0.00 0.00 0.00 4.79
65 66 4.546829 TTCAAGGTACACACATAGGTCC 57.453 45.455 0.00 0.00 0.00 4.46
66 67 5.730550 TCATTCAAGGTACACACATAGGTC 58.269 41.667 0.00 0.00 0.00 3.85
67 68 5.755409 TCATTCAAGGTACACACATAGGT 57.245 39.130 0.00 0.00 0.00 3.08
68 69 6.115446 ACATCATTCAAGGTACACACATAGG 58.885 40.000 0.00 0.00 0.00 2.57
69 70 8.768019 CATACATCATTCAAGGTACACACATAG 58.232 37.037 0.00 0.00 0.00 2.23
70 71 8.482128 TCATACATCATTCAAGGTACACACATA 58.518 33.333 0.00 0.00 0.00 2.29
71 72 7.337938 TCATACATCATTCAAGGTACACACAT 58.662 34.615 0.00 0.00 0.00 3.21
72 73 6.706295 TCATACATCATTCAAGGTACACACA 58.294 36.000 0.00 0.00 0.00 3.72
73 74 7.609760 TTCATACATCATTCAAGGTACACAC 57.390 36.000 0.00 0.00 0.00 3.82
74 75 8.806429 AATTCATACATCATTCAAGGTACACA 57.194 30.769 0.00 0.00 0.00 3.72
75 76 8.892723 TGAATTCATACATCATTCAAGGTACAC 58.107 33.333 3.38 0.00 34.66 2.90
76 77 9.631257 ATGAATTCATACATCATTCAAGGTACA 57.369 29.630 19.42 0.00 39.69 2.90
96 97 9.859427 CCACTTCACACAATACATAAATGAATT 57.141 29.630 0.00 0.00 0.00 2.17
97 98 7.975616 GCCACTTCACACAATACATAAATGAAT 59.024 33.333 0.00 0.00 0.00 2.57
98 99 7.312154 GCCACTTCACACAATACATAAATGAA 58.688 34.615 0.00 0.00 0.00 2.57
99 100 6.403092 CGCCACTTCACACAATACATAAATGA 60.403 38.462 0.00 0.00 0.00 2.57
100 101 5.738693 CGCCACTTCACACAATACATAAATG 59.261 40.000 0.00 0.00 0.00 2.32
101 102 5.645929 TCGCCACTTCACACAATACATAAAT 59.354 36.000 0.00 0.00 0.00 1.40
102 103 4.998033 TCGCCACTTCACACAATACATAAA 59.002 37.500 0.00 0.00 0.00 1.40
103 104 4.570930 TCGCCACTTCACACAATACATAA 58.429 39.130 0.00 0.00 0.00 1.90
104 105 4.195225 TCGCCACTTCACACAATACATA 57.805 40.909 0.00 0.00 0.00 2.29
105 106 3.052455 TCGCCACTTCACACAATACAT 57.948 42.857 0.00 0.00 0.00 2.29
106 107 2.535012 TCGCCACTTCACACAATACA 57.465 45.000 0.00 0.00 0.00 2.29
107 108 3.188460 ACAATCGCCACTTCACACAATAC 59.812 43.478 0.00 0.00 0.00 1.89
108 109 3.407698 ACAATCGCCACTTCACACAATA 58.592 40.909 0.00 0.00 0.00 1.90
109 110 2.229792 ACAATCGCCACTTCACACAAT 58.770 42.857 0.00 0.00 0.00 2.71
110 111 1.674359 ACAATCGCCACTTCACACAA 58.326 45.000 0.00 0.00 0.00 3.33
111 112 2.535012 TACAATCGCCACTTCACACA 57.465 45.000 0.00 0.00 0.00 3.72
112 113 2.412847 GCTTACAATCGCCACTTCACAC 60.413 50.000 0.00 0.00 0.00 3.82
113 114 1.804151 GCTTACAATCGCCACTTCACA 59.196 47.619 0.00 0.00 0.00 3.58
114 115 1.130561 GGCTTACAATCGCCACTTCAC 59.869 52.381 0.00 0.00 45.59 3.18
115 116 1.448985 GGCTTACAATCGCCACTTCA 58.551 50.000 0.00 0.00 45.59 3.02
121 122 1.739067 AGAGTTGGCTTACAATCGCC 58.261 50.000 0.00 0.00 46.46 5.54
122 123 3.831715 AAAGAGTTGGCTTACAATCGC 57.168 42.857 0.00 0.00 41.95 4.58
123 124 5.007724 GGGATAAAGAGTTGGCTTACAATCG 59.992 44.000 0.00 0.00 41.95 3.34
124 125 5.885912 TGGGATAAAGAGTTGGCTTACAATC 59.114 40.000 0.00 0.00 41.95 2.67
125 126 5.826643 TGGGATAAAGAGTTGGCTTACAAT 58.173 37.500 0.00 0.00 41.95 2.71
126 127 5.249780 TGGGATAAAGAGTTGGCTTACAA 57.750 39.130 0.00 0.00 36.54 2.41
127 128 4.919774 TGGGATAAAGAGTTGGCTTACA 57.080 40.909 0.00 0.00 0.00 2.41
128 129 6.122964 AGAATGGGATAAAGAGTTGGCTTAC 58.877 40.000 0.00 0.00 0.00 2.34
129 130 6.327386 AGAATGGGATAAAGAGTTGGCTTA 57.673 37.500 0.00 0.00 0.00 3.09
130 131 5.198602 AGAATGGGATAAAGAGTTGGCTT 57.801 39.130 0.00 0.00 0.00 4.35
131 132 4.870021 AGAATGGGATAAAGAGTTGGCT 57.130 40.909 0.00 0.00 0.00 4.75
132 133 4.706962 ACAAGAATGGGATAAAGAGTTGGC 59.293 41.667 0.00 0.00 0.00 4.52
133 134 6.434028 TGAACAAGAATGGGATAAAGAGTTGG 59.566 38.462 0.00 0.00 0.00 3.77
134 135 7.452880 TGAACAAGAATGGGATAAAGAGTTG 57.547 36.000 0.00 0.00 0.00 3.16
135 136 8.655935 AATGAACAAGAATGGGATAAAGAGTT 57.344 30.769 0.00 0.00 0.00 3.01
136 137 9.178758 GTAATGAACAAGAATGGGATAAAGAGT 57.821 33.333 0.00 0.00 0.00 3.24
137 138 9.177608 TGTAATGAACAAGAATGGGATAAAGAG 57.822 33.333 0.00 0.00 34.29 2.85
138 139 9.699410 ATGTAATGAACAAGAATGGGATAAAGA 57.301 29.630 0.00 0.00 42.70 2.52
157 158 5.703978 TCTTCACACAAACCCATGTAATG 57.296 39.130 0.00 0.00 46.21 1.90
158 159 6.009589 TCATCTTCACACAAACCCATGTAAT 58.990 36.000 0.00 0.00 30.84 1.89
159 160 5.240623 GTCATCTTCACACAAACCCATGTAA 59.759 40.000 0.00 0.00 30.84 2.41
160 161 4.759693 GTCATCTTCACACAAACCCATGTA 59.240 41.667 0.00 0.00 30.84 2.29
161 162 3.569701 GTCATCTTCACACAAACCCATGT 59.430 43.478 0.00 0.00 0.00 3.21
162 163 3.057315 GGTCATCTTCACACAAACCCATG 60.057 47.826 0.00 0.00 0.00 3.66
163 164 3.157087 GGTCATCTTCACACAAACCCAT 58.843 45.455 0.00 0.00 0.00 4.00
164 165 2.582052 GGTCATCTTCACACAAACCCA 58.418 47.619 0.00 0.00 0.00 4.51
165 166 1.886542 GGGTCATCTTCACACAAACCC 59.113 52.381 0.00 0.00 38.23 4.11
166 167 2.863809 AGGGTCATCTTCACACAAACC 58.136 47.619 0.00 0.00 0.00 3.27
167 168 4.137543 AGAAGGGTCATCTTCACACAAAC 58.862 43.478 7.26 0.00 44.01 2.93
168 169 4.437682 AGAAGGGTCATCTTCACACAAA 57.562 40.909 7.26 0.00 44.01 2.83
169 170 4.136796 CAAGAAGGGTCATCTTCACACAA 58.863 43.478 7.26 0.00 44.01 3.33
170 171 3.743521 CAAGAAGGGTCATCTTCACACA 58.256 45.455 7.26 0.00 44.01 3.72
171 172 2.485814 GCAAGAAGGGTCATCTTCACAC 59.514 50.000 7.26 0.00 44.01 3.82
172 173 2.783135 GCAAGAAGGGTCATCTTCACA 58.217 47.619 7.26 0.00 44.01 3.58
173 174 1.734465 CGCAAGAAGGGTCATCTTCAC 59.266 52.381 7.26 0.00 44.01 3.18
174 175 2.099141 CGCAAGAAGGGTCATCTTCA 57.901 50.000 7.26 0.00 44.01 3.02
188 189 1.522258 GCATTGTGGTTTTGTCGCAAG 59.478 47.619 0.00 0.00 37.91 4.01
189 190 1.565305 GCATTGTGGTTTTGTCGCAA 58.435 45.000 0.00 0.00 38.69 4.85
190 191 0.593518 CGCATTGTGGTTTTGTCGCA 60.594 50.000 0.00 0.00 0.00 5.10
191 192 1.274798 CCGCATTGTGGTTTTGTCGC 61.275 55.000 8.14 0.00 0.00 5.19
192 193 0.030101 ACCGCATTGTGGTTTTGTCG 59.970 50.000 16.17 0.00 44.78 4.35
193 194 3.957383 ACCGCATTGTGGTTTTGTC 57.043 47.368 16.17 0.00 44.78 3.18
200 201 0.381801 GAGGCATAACCGCATTGTGG 59.618 55.000 14.72 14.72 46.52 4.17
201 202 1.382522 AGAGGCATAACCGCATTGTG 58.617 50.000 0.00 0.00 46.52 3.33
202 203 3.206150 CTTAGAGGCATAACCGCATTGT 58.794 45.455 0.00 0.00 46.52 2.71
203 204 3.206150 ACTTAGAGGCATAACCGCATTG 58.794 45.455 0.00 0.00 46.52 2.82
204 205 3.467803 GACTTAGAGGCATAACCGCATT 58.532 45.455 0.00 0.00 46.52 3.56
205 206 2.545952 CGACTTAGAGGCATAACCGCAT 60.546 50.000 0.00 0.00 46.52 4.73
206 207 1.202371 CGACTTAGAGGCATAACCGCA 60.202 52.381 0.00 0.00 46.52 5.69
207 208 1.202382 ACGACTTAGAGGCATAACCGC 60.202 52.381 0.00 0.00 46.52 5.68
208 209 2.460918 CACGACTTAGAGGCATAACCG 58.539 52.381 0.00 0.00 46.52 4.44
209 210 2.202566 GCACGACTTAGAGGCATAACC 58.797 52.381 0.00 0.00 39.61 2.85
210 211 2.202566 GGCACGACTTAGAGGCATAAC 58.797 52.381 0.00 0.00 0.00 1.89
211 212 1.138266 GGGCACGACTTAGAGGCATAA 59.862 52.381 0.00 0.00 0.00 1.90
212 213 0.750850 GGGCACGACTTAGAGGCATA 59.249 55.000 0.00 0.00 0.00 3.14
213 214 1.522569 GGGCACGACTTAGAGGCAT 59.477 57.895 0.00 0.00 0.00 4.40
214 215 2.656069 GGGGCACGACTTAGAGGCA 61.656 63.158 0.00 0.00 0.00 4.75
215 216 2.187163 GGGGCACGACTTAGAGGC 59.813 66.667 0.00 0.00 0.00 4.70
230 231 1.540267 CTATATCTCCCACGTGTCGGG 59.460 57.143 15.65 9.12 46.03 5.14
231 232 1.068472 GCTATATCTCCCACGTGTCGG 60.068 57.143 15.65 9.74 0.00 4.79
232 233 1.068472 GGCTATATCTCCCACGTGTCG 60.068 57.143 15.65 4.04 0.00 4.35
233 234 1.068472 CGGCTATATCTCCCACGTGTC 60.068 57.143 15.65 0.00 0.00 3.67
234 235 0.959553 CGGCTATATCTCCCACGTGT 59.040 55.000 15.65 0.00 0.00 4.49
235 236 0.388649 GCGGCTATATCTCCCACGTG 60.389 60.000 9.08 9.08 0.00 4.49
236 237 0.826256 TGCGGCTATATCTCCCACGT 60.826 55.000 0.00 0.00 0.00 4.49
237 238 0.532573 ATGCGGCTATATCTCCCACG 59.467 55.000 0.00 0.00 0.00 4.94
238 239 1.469940 CGATGCGGCTATATCTCCCAC 60.470 57.143 0.00 0.00 0.00 4.61
239 240 0.817654 CGATGCGGCTATATCTCCCA 59.182 55.000 0.00 0.00 0.00 4.37
240 241 0.818296 ACGATGCGGCTATATCTCCC 59.182 55.000 0.00 0.00 0.00 4.30
241 242 1.469940 CCACGATGCGGCTATATCTCC 60.470 57.143 0.00 0.00 0.00 3.71
242 243 1.469940 CCCACGATGCGGCTATATCTC 60.470 57.143 0.00 0.00 0.00 2.75
243 244 0.532573 CCCACGATGCGGCTATATCT 59.467 55.000 0.00 0.00 0.00 1.98
244 245 0.246635 ACCCACGATGCGGCTATATC 59.753 55.000 0.00 0.00 0.00 1.63
245 246 0.037326 CACCCACGATGCGGCTATAT 60.037 55.000 0.00 0.00 0.00 0.86
246 247 1.365999 CACCCACGATGCGGCTATA 59.634 57.895 0.00 0.00 0.00 1.31
247 248 2.108976 CACCCACGATGCGGCTAT 59.891 61.111 0.00 0.00 0.00 2.97
248 249 3.387091 ACACCCACGATGCGGCTA 61.387 61.111 0.00 0.00 0.00 3.93
251 252 3.118454 GTCACACCCACGATGCGG 61.118 66.667 0.00 0.00 0.00 5.69
252 253 2.356913 TGTCACACCCACGATGCG 60.357 61.111 0.00 0.00 0.00 4.73
253 254 3.253955 GTGTCACACCCACGATGC 58.746 61.111 0.00 0.00 0.00 3.91
262 263 2.430367 GGTCAGGGGGTGTCACAC 59.570 66.667 0.00 0.00 0.00 3.82
263 264 3.238497 CGGTCAGGGGGTGTCACA 61.238 66.667 5.12 0.00 0.00 3.58
264 265 4.016706 CCGGTCAGGGGGTGTCAC 62.017 72.222 0.00 0.00 35.97 3.67
265 266 4.567597 ACCGGTCAGGGGGTGTCA 62.568 66.667 0.00 0.00 46.96 3.58
266 267 3.703127 GACCGGTCAGGGGGTGTC 61.703 72.222 29.75 0.00 46.96 3.67
640 654 4.767578 AGCATACATGAGATCCACAAGT 57.232 40.909 0.00 0.00 0.00 3.16
691 705 4.013267 ACACAAGGAGGAAATCACTCAG 57.987 45.455 0.00 0.00 36.70 3.35
724 738 0.475632 TGGAGGGGGCAAAGAGAAGA 60.476 55.000 0.00 0.00 0.00 2.87
725 739 0.405585 TTGGAGGGGGCAAAGAGAAG 59.594 55.000 0.00 0.00 0.00 2.85
775 789 3.195825 ACTCCTATGAGCACCTGTTGTAC 59.804 47.826 0.00 0.00 42.74 2.90
795 809 1.207089 ACGCATGCACACATACCTACT 59.793 47.619 19.57 0.00 33.67 2.57
828 842 3.920412 ACACTCATACGCACGCATATATG 59.080 43.478 8.45 8.45 0.00 1.78
1572 4247 1.227147 CATCGTTATCCGCCGTGGT 60.227 57.895 0.00 0.00 39.52 4.16
1810 4493 4.386049 AGCTAATACGCGACATAAGCAATC 59.614 41.667 15.93 0.00 34.40 2.67
1870 4553 1.738099 CTGTAGCAGACCGCCACAC 60.738 63.158 0.00 0.00 37.32 3.82
2002 4696 6.134535 AGTTAATCCTCAACACCACCAATA 57.865 37.500 0.00 0.00 0.00 1.90
2033 4727 2.247358 TGAAGCCACAATCTTTTCCCC 58.753 47.619 0.00 0.00 0.00 4.81
2169 4871 2.677836 GGTGATAACTGAAAGCATCGCA 59.322 45.455 0.00 0.00 39.58 5.10
2384 5091 8.634444 ACAACATAACTAAAAATAGTTGGCACA 58.366 29.630 10.64 0.00 40.22 4.57
2548 5314 6.079424 TGCCAAATACTAAACAGACCAAAC 57.921 37.500 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.