Multiple sequence alignment - TraesCS1D01G270100

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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 TraesCS1D01G270100 chr1D 100.000 2912 0 0 1 2912 365243969 365246880 0.000000e+00 5378.0
1 TraesCS1D01G270100 chr1D 86.349 945 63 35 916 1823 365297908 365298823 0.000000e+00 970.0
2 TraesCS1D01G270100 chr1A 86.851 2753 247 51 129 2853 464114743 464117408 0.000000e+00 2972.0
3 TraesCS1D01G270100 chr1A 86.023 880 69 24 960 1820 464121654 464122498 0.000000e+00 894.0
4 TraesCS1D01G270100 chr1B 83.929 1568 151 45 659 2174 488658499 488660017 0.000000e+00 1406.0
5 TraesCS1D01G270100 chr1B 90.254 708 48 12 916 1606 488749809 488750512 0.000000e+00 905.0
6 TraesCS1D01G270100 chr1B 85.952 541 33 11 2180 2719 488660066 488660564 3.300000e-149 538.0
7 TraesCS1D01G270100 chr1B 93.564 202 13 0 2711 2912 488661018 488661219 4.720000e-78 302.0
8 TraesCS1D01G270100 chr7D 85.659 258 30 5 403 655 194080974 194080719 6.190000e-67 265.0
9 TraesCS1D01G270100 chr7D 79.699 266 36 13 403 655 6778737 6778477 2.980000e-40 176.0
10 TraesCS1D01G270100 chr7D 80.808 99 18 1 33 130 619810327 619810229 3.110000e-10 76.8
11 TraesCS1D01G270100 chr3D 84.328 268 30 9 403 663 535778282 535778544 4.820000e-63 252.0
12 TraesCS1D01G270100 chr3D 100.000 28 0 0 2871 2898 100215950 100215977 5.000000e-03 52.8
13 TraesCS1D01G270100 chr2B 84.291 261 32 8 403 655 24242055 24241796 2.240000e-61 246.0
14 TraesCS1D01G270100 chr5A 85.124 242 32 3 415 653 670399001 670398761 8.060000e-61 244.0
15 TraesCS1D01G270100 chr5A 85.714 182 24 2 1953 2132 640401001 640401182 1.070000e-44 191.0
16 TraesCS1D01G270100 chr7B 85.185 243 28 6 415 652 13129794 13130033 2.900000e-60 243.0
17 TraesCS1D01G270100 chr7B 83.268 257 36 5 403 655 157803235 157802982 2.260000e-56 230.0
18 TraesCS1D01G270100 chr7B 85.714 182 24 2 1952 2131 36467426 36467607 1.070000e-44 191.0
19 TraesCS1D01G270100 chr7B 89.831 59 2 2 2858 2912 493522491 493522433 4.030000e-09 73.1
20 TraesCS1D01G270100 chr3A 83.969 262 32 8 403 657 19358466 19358724 2.900000e-60 243.0
21 TraesCS1D01G270100 chr3A 92.308 39 2 1 2871 2909 701176879 701176916 1.000000e-03 54.7
22 TraesCS1D01G270100 chr3A 96.774 31 1 0 2871 2901 226343296 226343266 5.000000e-03 52.8
23 TraesCS1D01G270100 chr6B 81.481 297 26 12 1840 2134 44058805 44059074 1.760000e-52 217.0
24 TraesCS1D01G270100 chr6B 86.782 174 21 2 1961 2132 66742437 66742264 2.960000e-45 193.0
25 TraesCS1D01G270100 chr6B 86.782 174 21 2 1961 2132 646139216 646139389 2.960000e-45 193.0
26 TraesCS1D01G270100 chrUn 86.782 174 22 1 1961 2133 314378032 314378205 2.960000e-45 193.0
27 TraesCS1D01G270100 chrUn 86.782 174 22 1 1961 2133 340878967 340879140 2.960000e-45 193.0
28 TraesCS1D01G270100 chrUn 85.156 128 18 1 1 127 2575632 2575759 2.360000e-26 130.0
29 TraesCS1D01G270100 chr3B 86.782 174 22 1 1961 2133 32615403 32615230 2.960000e-45 193.0
30 TraesCS1D01G270100 chr6A 85.156 128 16 3 1 127 529641887 529642012 8.470000e-26 128.0
31 TraesCS1D01G270100 chr5B 83.465 127 20 1 1 126 504173137 504173011 1.830000e-22 117.0
32 TraesCS1D01G270100 chr6D 95.238 42 2 0 2871 2912 402347304 402347263 1.870000e-07 67.6
33 TraesCS1D01G270100 chr4D 85.000 60 5 3 3 60 62726506 62726563 1.130000e-04 58.4
34 TraesCS1D01G270100 chr4D 90.476 42 4 0 2870 2911 48681035 48680994 4.050000e-04 56.5
35 TraesCS1D01G270100 chr5D 90.476 42 4 0 2871 2912 564975731 564975690 4.050000e-04 56.5
36 TraesCS1D01G270100 chr2D 94.286 35 1 1 2871 2905 7529358 7529325 5.000000e-03 52.8


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 TraesCS1D01G270100 chr1D 365243969 365246880 2911 False 5378.000000 5378 100.000 1 2912 1 chr1D.!!$F1 2911
1 TraesCS1D01G270100 chr1D 365297908 365298823 915 False 970.000000 970 86.349 916 1823 1 chr1D.!!$F2 907
2 TraesCS1D01G270100 chr1A 464114743 464117408 2665 False 2972.000000 2972 86.851 129 2853 1 chr1A.!!$F1 2724
3 TraesCS1D01G270100 chr1A 464121654 464122498 844 False 894.000000 894 86.023 960 1820 1 chr1A.!!$F2 860
4 TraesCS1D01G270100 chr1B 488749809 488750512 703 False 905.000000 905 90.254 916 1606 1 chr1B.!!$F1 690
5 TraesCS1D01G270100 chr1B 488658499 488661219 2720 False 748.666667 1406 87.815 659 2912 3 chr1B.!!$F2 2253

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
305 310 0.031994 AGGCGAACATTTTGTGCACC 59.968 50.0 15.69 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2297 2451 0.040692 CGAATGCTCCATGGCGAATG 60.041 55.0 6.96 0.0 35.89 2.67 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 2.489938 TAGCGAAACATGCCCTTTCT 57.510 45.000 0.00 0.00 0.00 2.52
20 21 1.168714 AGCGAAACATGCCCTTTCTC 58.831 50.000 0.00 0.00 0.00 2.87
21 22 1.168714 GCGAAACATGCCCTTTCTCT 58.831 50.000 0.00 0.00 0.00 3.10
22 23 1.541588 GCGAAACATGCCCTTTCTCTT 59.458 47.619 0.00 0.00 0.00 2.85
23 24 2.669391 GCGAAACATGCCCTTTCTCTTG 60.669 50.000 0.00 0.00 0.00 3.02
24 25 2.095059 CGAAACATGCCCTTTCTCTTGG 60.095 50.000 0.00 0.00 0.00 3.61
25 26 1.928868 AACATGCCCTTTCTCTTGGG 58.071 50.000 0.00 0.00 46.00 4.12
26 27 0.040204 ACATGCCCTTTCTCTTGGGG 59.960 55.000 0.00 0.00 43.53 4.96
27 28 0.685458 CATGCCCTTTCTCTTGGGGG 60.685 60.000 0.00 0.00 43.53 5.40
28 29 1.149133 ATGCCCTTTCTCTTGGGGGT 61.149 55.000 0.00 0.00 43.53 4.95
29 30 1.304464 GCCCTTTCTCTTGGGGGTG 60.304 63.158 0.00 0.00 43.53 4.61
30 31 1.384191 CCCTTTCTCTTGGGGGTGG 59.616 63.158 0.00 0.00 39.76 4.61
31 32 1.435346 CCCTTTCTCTTGGGGGTGGT 61.435 60.000 0.00 0.00 39.76 4.16
32 33 0.038310 CCTTTCTCTTGGGGGTGGTC 59.962 60.000 0.00 0.00 0.00 4.02
33 34 0.321653 CTTTCTCTTGGGGGTGGTCG 60.322 60.000 0.00 0.00 0.00 4.79
34 35 2.406002 TTTCTCTTGGGGGTGGTCGC 62.406 60.000 0.00 0.00 0.00 5.19
40 41 4.360405 GGGGGTGGTCGCCATGTT 62.360 66.667 2.81 0.00 46.73 2.71
41 42 2.282887 GGGGTGGTCGCCATGTTT 60.283 61.111 2.81 0.00 44.68 2.83
42 43 2.635443 GGGGTGGTCGCCATGTTTG 61.635 63.158 2.81 0.00 44.68 2.93
43 44 2.635443 GGGTGGTCGCCATGTTTGG 61.635 63.158 2.81 0.00 46.66 3.28
44 45 1.901464 GGTGGTCGCCATGTTTGGT 60.901 57.895 1.90 0.00 45.57 3.67
45 46 1.460273 GGTGGTCGCCATGTTTGGTT 61.460 55.000 1.90 0.00 45.57 3.67
46 47 1.240256 GTGGTCGCCATGTTTGGTTA 58.760 50.000 1.90 0.00 45.57 2.85
47 48 1.199097 GTGGTCGCCATGTTTGGTTAG 59.801 52.381 1.90 0.00 45.57 2.34
48 49 0.808755 GGTCGCCATGTTTGGTTAGG 59.191 55.000 0.00 0.00 45.57 2.69
49 50 1.530323 GTCGCCATGTTTGGTTAGGT 58.470 50.000 0.00 0.00 45.57 3.08
50 51 1.467342 GTCGCCATGTTTGGTTAGGTC 59.533 52.381 0.00 0.00 45.57 3.85
51 52 1.072489 TCGCCATGTTTGGTTAGGTCA 59.928 47.619 0.00 0.00 45.57 4.02
52 53 2.091541 CGCCATGTTTGGTTAGGTCAT 58.908 47.619 0.00 0.00 45.57 3.06
53 54 2.097466 CGCCATGTTTGGTTAGGTCATC 59.903 50.000 0.00 0.00 45.57 2.92
54 55 2.427095 GCCATGTTTGGTTAGGTCATCC 59.573 50.000 0.00 0.00 45.57 3.51
55 56 3.023832 CCATGTTTGGTTAGGTCATCCC 58.976 50.000 0.00 0.00 38.30 3.85
56 57 2.483014 TGTTTGGTTAGGTCATCCCG 57.517 50.000 0.00 0.00 38.74 5.14
57 58 1.003812 TGTTTGGTTAGGTCATCCCGG 59.996 52.381 0.00 0.00 38.74 5.73
58 59 1.279846 GTTTGGTTAGGTCATCCCGGA 59.720 52.381 0.73 0.00 38.74 5.14
59 60 1.200519 TTGGTTAGGTCATCCCGGAG 58.799 55.000 0.73 0.00 38.74 4.63
60 61 0.337082 TGGTTAGGTCATCCCGGAGA 59.663 55.000 0.73 0.00 38.74 3.71
61 62 1.062428 TGGTTAGGTCATCCCGGAGAT 60.062 52.381 0.73 0.29 38.74 2.75
62 63 1.619332 GGTTAGGTCATCCCGGAGATC 59.381 57.143 0.73 0.00 38.74 2.75
63 64 2.599677 GTTAGGTCATCCCGGAGATCT 58.400 52.381 0.73 6.26 38.74 2.75
64 65 2.966516 GTTAGGTCATCCCGGAGATCTT 59.033 50.000 0.73 0.00 38.74 2.40
65 66 2.182516 AGGTCATCCCGGAGATCTTT 57.817 50.000 0.73 0.00 38.74 2.52
66 67 2.043227 AGGTCATCCCGGAGATCTTTC 58.957 52.381 0.73 0.00 38.74 2.62
67 68 1.762957 GGTCATCCCGGAGATCTTTCA 59.237 52.381 0.73 0.00 30.59 2.69
68 69 2.370189 GGTCATCCCGGAGATCTTTCAT 59.630 50.000 0.73 0.00 30.59 2.57
69 70 3.181450 GGTCATCCCGGAGATCTTTCATT 60.181 47.826 0.73 0.00 30.59 2.57
70 71 4.061596 GTCATCCCGGAGATCTTTCATTC 58.938 47.826 0.73 0.00 30.59 2.67
71 72 3.711190 TCATCCCGGAGATCTTTCATTCA 59.289 43.478 0.73 0.00 30.59 2.57
72 73 4.349048 TCATCCCGGAGATCTTTCATTCAT 59.651 41.667 0.73 0.00 30.59 2.57
73 74 4.342862 TCCCGGAGATCTTTCATTCATC 57.657 45.455 0.73 0.00 0.00 2.92
74 75 3.071602 TCCCGGAGATCTTTCATTCATCC 59.928 47.826 0.73 0.00 0.00 3.51
75 76 3.406764 CCGGAGATCTTTCATTCATCCC 58.593 50.000 0.00 0.00 0.00 3.85
76 77 3.072184 CCGGAGATCTTTCATTCATCCCT 59.928 47.826 0.00 0.00 0.00 4.20
77 78 4.063689 CGGAGATCTTTCATTCATCCCTG 58.936 47.826 0.00 0.00 0.00 4.45
78 79 4.444022 CGGAGATCTTTCATTCATCCCTGT 60.444 45.833 0.00 0.00 0.00 4.00
79 80 5.221521 CGGAGATCTTTCATTCATCCCTGTA 60.222 44.000 0.00 0.00 0.00 2.74
80 81 6.595682 GGAGATCTTTCATTCATCCCTGTAA 58.404 40.000 0.00 0.00 0.00 2.41
81 82 7.056635 GGAGATCTTTCATTCATCCCTGTAAA 58.943 38.462 0.00 0.00 0.00 2.01
82 83 7.723172 GGAGATCTTTCATTCATCCCTGTAAAT 59.277 37.037 0.00 0.00 0.00 1.40
83 84 9.784531 GAGATCTTTCATTCATCCCTGTAAATA 57.215 33.333 0.00 0.00 0.00 1.40
91 92 9.435688 TCATTCATCCCTGTAAATATTATGACG 57.564 33.333 0.00 0.00 0.00 4.35
92 93 8.668353 CATTCATCCCTGTAAATATTATGACGG 58.332 37.037 0.00 0.00 0.00 4.79
93 94 6.707290 TCATCCCTGTAAATATTATGACGGG 58.293 40.000 12.82 12.82 37.97 5.28
94 95 6.271391 TCATCCCTGTAAATATTATGACGGGT 59.729 38.462 16.25 2.99 36.73 5.28
95 96 6.503560 TCCCTGTAAATATTATGACGGGTT 57.496 37.500 16.25 0.00 36.73 4.11
96 97 7.615039 TCCCTGTAAATATTATGACGGGTTA 57.385 36.000 16.25 6.64 36.73 2.85
97 98 8.032045 TCCCTGTAAATATTATGACGGGTTAA 57.968 34.615 16.25 4.98 36.73 2.01
98 99 8.662255 TCCCTGTAAATATTATGACGGGTTAAT 58.338 33.333 16.25 0.00 36.73 1.40
99 100 9.947433 CCCTGTAAATATTATGACGGGTTAATA 57.053 33.333 16.25 0.00 36.73 0.98
108 109 5.806366 ATGACGGGTTAATAAAGGTTTCG 57.194 39.130 0.00 0.00 0.00 3.46
109 110 3.436359 TGACGGGTTAATAAAGGTTTCGC 59.564 43.478 0.00 0.00 0.00 4.70
110 111 2.416202 ACGGGTTAATAAAGGTTTCGCG 59.584 45.455 0.00 0.00 36.26 5.87
111 112 2.672381 CGGGTTAATAAAGGTTTCGCGA 59.328 45.455 3.71 3.71 33.08 5.87
112 113 3.242188 CGGGTTAATAAAGGTTTCGCGAG 60.242 47.826 9.59 0.00 33.08 5.03
113 114 3.064408 GGGTTAATAAAGGTTTCGCGAGG 59.936 47.826 9.59 0.00 0.00 4.63
114 115 3.686241 GGTTAATAAAGGTTTCGCGAGGT 59.314 43.478 9.59 0.00 0.00 3.85
115 116 4.154737 GGTTAATAAAGGTTTCGCGAGGTT 59.845 41.667 9.59 3.08 0.00 3.50
116 117 3.824414 AATAAAGGTTTCGCGAGGTTG 57.176 42.857 9.59 0.00 0.00 3.77
117 118 2.243602 TAAAGGTTTCGCGAGGTTGT 57.756 45.000 9.59 0.00 0.00 3.32
118 119 0.942252 AAAGGTTTCGCGAGGTTGTC 59.058 50.000 9.59 0.00 0.00 3.18
119 120 0.883370 AAGGTTTCGCGAGGTTGTCC 60.883 55.000 9.59 7.02 0.00 4.02
120 121 1.595929 GGTTTCGCGAGGTTGTCCA 60.596 57.895 9.59 0.00 35.89 4.02
121 122 1.161563 GGTTTCGCGAGGTTGTCCAA 61.162 55.000 9.59 0.00 35.89 3.53
122 123 0.658897 GTTTCGCGAGGTTGTCCAAA 59.341 50.000 9.59 0.00 35.89 3.28
123 124 1.064357 GTTTCGCGAGGTTGTCCAAAA 59.936 47.619 9.59 0.00 35.89 2.44
124 125 1.380524 TTCGCGAGGTTGTCCAAAAA 58.619 45.000 9.59 0.00 35.89 1.94
152 153 0.807496 GTCTGTGAAGCAATCTGGGC 59.193 55.000 0.00 0.00 0.00 5.36
165 166 1.860641 TCTGGGCGTCTGAATTCCTA 58.139 50.000 2.27 0.00 0.00 2.94
188 189 8.273557 CCTATAAATCGATAACAAACGTGGAAG 58.726 37.037 0.00 0.00 0.00 3.46
198 199 3.775661 AAACGTGGAAGTGGTTTGAAG 57.224 42.857 0.00 0.00 33.01 3.02
201 202 2.294074 CGTGGAAGTGGTTTGAAGGAA 58.706 47.619 0.00 0.00 0.00 3.36
205 206 4.584743 GTGGAAGTGGTTTGAAGGAATTCT 59.415 41.667 5.23 0.00 0.00 2.40
215 216 6.431234 GGTTTGAAGGAATTCTGACACACTAT 59.569 38.462 5.23 0.00 0.00 2.12
216 217 7.301054 GTTTGAAGGAATTCTGACACACTATG 58.699 38.462 5.23 0.00 0.00 2.23
217 218 6.358974 TGAAGGAATTCTGACACACTATGA 57.641 37.500 5.23 0.00 0.00 2.15
218 219 6.950842 TGAAGGAATTCTGACACACTATGAT 58.049 36.000 5.23 0.00 0.00 2.45
219 220 6.820152 TGAAGGAATTCTGACACACTATGATG 59.180 38.462 5.23 0.00 0.00 3.07
229 231 3.457380 ACACACTATGATGAGCCTTGGAT 59.543 43.478 0.00 0.00 0.00 3.41
234 236 1.588239 TGATGAGCCTTGGATCCACT 58.412 50.000 15.91 8.72 0.00 4.00
258 260 2.717639 ATCCACATTTTCCTCCTCCG 57.282 50.000 0.00 0.00 0.00 4.63
263 268 3.003480 CACATTTTCCTCCTCCGTTCTC 58.997 50.000 0.00 0.00 0.00 2.87
283 288 5.267587 TCTCTCTCATCTCTTCATTGGACA 58.732 41.667 0.00 0.00 0.00 4.02
289 294 3.340814 TCTCTTCATTGGACAAGAGGC 57.659 47.619 11.56 0.00 44.03 4.70
305 310 0.031994 AGGCGAACATTTTGTGCACC 59.968 50.000 15.69 0.00 0.00 5.01
306 311 1.274798 GGCGAACATTTTGTGCACCG 61.275 55.000 15.69 8.94 0.00 4.94
325 330 1.076485 GATTGGATGGCAGCCCACT 60.076 57.895 20.74 10.18 45.77 4.00
330 335 0.538287 GGATGGCAGCCCACTTATCC 60.538 60.000 11.60 10.54 45.77 2.59
331 336 0.886490 GATGGCAGCCCACTTATCCG 60.886 60.000 9.64 0.00 45.77 4.18
335 340 2.182842 CAGCCCACTTATCCGCTGC 61.183 63.158 0.00 0.00 41.96 5.25
337 342 2.588877 CCCACTTATCCGCTGCCG 60.589 66.667 0.00 0.00 0.00 5.69
366 371 2.543777 TCCGGACTGTCCTTTTTGAG 57.456 50.000 23.49 6.93 33.30 3.02
375 380 1.534163 GTCCTTTTTGAGGTACACCGC 59.466 52.381 0.00 0.00 46.39 5.68
407 412 2.770164 AAGTCATGCAGGTGTACTCC 57.230 50.000 5.81 5.81 0.00 3.85
409 414 0.905357 GTCATGCAGGTGTACTCCCT 59.095 55.000 10.36 4.67 0.00 4.20
412 417 1.134580 CATGCAGGTGTACTCCCTCTG 60.135 57.143 10.36 4.09 0.00 3.35
413 418 1.219393 GCAGGTGTACTCCCTCTGC 59.781 63.158 10.36 10.12 42.89 4.26
426 431 8.161425 TGTACTCCCTCTGCTTTTATTTACTTT 58.839 33.333 0.00 0.00 0.00 2.66
449 454 8.519492 TTTGCATATTAGCTTTGTCTTTTGTC 57.481 30.769 0.00 0.00 34.99 3.18
516 521 7.969690 AACATCCACAATACCCAATCAATAA 57.030 32.000 0.00 0.00 0.00 1.40
657 664 4.698304 TGCAGTAAATAAAAACGGAGGAGG 59.302 41.667 0.00 0.00 0.00 4.30
666 673 5.391312 AAAAACGGAGGAGGATTTTCATG 57.609 39.130 0.00 0.00 0.00 3.07
685 694 1.552348 GAGAGCGTCAGTGTGTGCAC 61.552 60.000 10.75 10.75 45.57 4.57
724 733 4.083431 AGCTTACACACGTACAGTACAGAG 60.083 45.833 11.37 4.19 0.00 3.35
737 746 2.029828 AGTACAGAGCCTCACTGAAACG 60.030 50.000 0.00 0.00 38.55 3.60
739 748 0.318441 CAGAGCCTCACTGAAACGGA 59.682 55.000 0.00 0.00 37.54 4.69
765 782 7.147497 ACAAATGTATATGTCCAGTGATCAGGA 60.147 37.037 0.00 0.00 0.00 3.86
771 788 1.135257 GTCCAGTGATCAGGACGACAG 60.135 57.143 16.04 0.00 44.23 3.51
787 804 2.351253 CGACAGAGTGAGGACAGACTTG 60.351 54.545 0.00 0.00 0.00 3.16
809 826 1.068610 CCAAATTGATGGACGCAACGT 60.069 47.619 0.00 0.00 43.54 3.99
819 836 4.012895 CGCAACGTGTGGCACTCC 62.013 66.667 19.83 8.43 31.34 3.85
828 845 3.364441 TGGCACTCCGCATGCAAC 61.364 61.111 19.57 0.00 45.27 4.17
850 867 0.530744 GTGTGATACGTGGAGAGCCA 59.469 55.000 0.00 0.00 43.47 4.75
934 955 2.434884 CCACCACTGTGCGCCTAG 60.435 66.667 4.18 5.59 41.35 3.02
980 1022 1.137479 CCTATAAAACGTGGCCCTCGA 59.863 52.381 21.22 2.37 0.00 4.04
1151 1204 0.389166 CTGCTCCTTGTCGAGGTGAC 60.389 60.000 11.75 4.56 46.39 3.67
1170 1223 1.841277 ACCACCTAATCCATGGCGTTA 59.159 47.619 6.96 7.98 36.96 3.18
1178 1233 2.961526 TCCATGGCGTTAAGACTCTC 57.038 50.000 6.96 0.00 0.00 3.20
1184 1239 1.001633 GGCGTTAAGACTCTCCCACAA 59.998 52.381 0.00 0.00 0.00 3.33
1195 1250 3.054139 ACTCTCCCACAATACATGCATGT 60.054 43.478 33.20 33.20 44.48 3.21
1223 1283 2.010497 GGTTGCCTAGCTAAACTCTGC 58.990 52.381 6.72 0.00 0.00 4.26
1226 1286 0.833949 GCCTAGCTAAACTCTGCCCT 59.166 55.000 0.00 0.00 0.00 5.19
1590 1675 2.257371 CAACCGCCTTCTCGACGA 59.743 61.111 0.00 0.00 0.00 4.20
1610 1695 1.073964 CCGATCGAGGCTAATGCATG 58.926 55.000 18.66 0.00 41.91 4.06
1678 1769 5.259632 ACCAACGATAACTAGACTACCAGT 58.740 41.667 0.00 0.00 0.00 4.00
1753 1861 2.989909 TGTGCTCATCCATTCGTGATT 58.010 42.857 0.00 0.00 0.00 2.57
1831 1942 9.891828 CTGTCAATTGCACTAAAACAATTAGTA 57.108 29.630 0.00 0.00 42.93 1.82
1833 1944 9.893305 GTCAATTGCACTAAAACAATTAGTACT 57.107 29.630 0.00 0.00 42.93 2.73
1867 1978 7.791029 TGTATTCATACTTCAGCCAACTCATA 58.209 34.615 0.00 0.00 34.41 2.15
1888 1999 9.605275 CTCATATAAAAGTCTGAACTGATGGAA 57.395 33.333 0.00 0.00 35.36 3.53
1908 2019 7.727578 TGGAAAGAGGCGGACAATATATATA 57.272 36.000 0.00 0.00 0.00 0.86
1910 2021 9.429109 TGGAAAGAGGCGGACAATATATATATA 57.571 33.333 5.66 4.92 0.00 0.86
1941 2052 2.041350 ACCTTTCTCCCTCACGTCTAGA 59.959 50.000 0.00 0.00 0.00 2.43
1952 2063 6.888632 TCCCTCACGTCTAGACTTATTTACTT 59.111 38.462 20.34 0.00 0.00 2.24
1953 2064 8.049117 TCCCTCACGTCTAGACTTATTTACTTA 58.951 37.037 20.34 0.00 0.00 2.24
1954 2065 8.344098 CCCTCACGTCTAGACTTATTTACTTAG 58.656 40.741 20.34 3.20 0.00 2.18
1955 2066 9.107177 CCTCACGTCTAGACTTATTTACTTAGA 57.893 37.037 20.34 1.41 0.00 2.10
1956 2067 9.919348 CTCACGTCTAGACTTATTTACTTAGAC 57.081 37.037 20.34 0.00 0.00 2.59
1957 2068 9.664332 TCACGTCTAGACTTATTTACTTAGACT 57.336 33.333 20.34 0.00 32.81 3.24
1999 2110 7.971168 CGTAGGATTTATCTAGATCGCAGAATT 59.029 37.037 8.95 0.00 43.58 2.17
2055 2166 0.485099 AGACCTCCCGGCTCTGATAT 59.515 55.000 0.00 0.00 0.00 1.63
2083 2194 5.618056 TGAATTCATGCTTCAGTCAACTC 57.382 39.130 3.38 0.00 0.00 3.01
2105 2216 5.005740 TCATCCAAAAGTCTGAACTGATGG 58.994 41.667 0.00 4.37 40.74 3.51
2135 2246 9.733556 AAGGCGGATAATATATTTCAACACATA 57.266 29.630 2.68 0.00 0.00 2.29
2164 2275 3.997561 ACGTGAGTATGCGCATCG 58.002 55.556 29.11 24.95 46.88 3.84
2166 2277 1.139816 ACGTGAGTATGCGCATCGTG 61.140 55.000 29.11 14.08 46.88 4.35
2291 2445 1.813862 GCTTGTGGCAGTAGTTGGTGA 60.814 52.381 0.00 0.00 41.35 4.02
2292 2446 2.783135 CTTGTGGCAGTAGTTGGTGAT 58.217 47.619 0.00 0.00 0.00 3.06
2293 2447 2.183478 TGTGGCAGTAGTTGGTGATG 57.817 50.000 0.00 0.00 0.00 3.07
2294 2448 1.271325 TGTGGCAGTAGTTGGTGATGG 60.271 52.381 0.00 0.00 0.00 3.51
2295 2449 1.003118 GTGGCAGTAGTTGGTGATGGA 59.997 52.381 0.00 0.00 0.00 3.41
2296 2450 1.278985 TGGCAGTAGTTGGTGATGGAG 59.721 52.381 0.00 0.00 0.00 3.86
2297 2451 1.373570 GCAGTAGTTGGTGATGGAGC 58.626 55.000 0.00 0.00 0.00 4.70
2298 2452 1.339055 GCAGTAGTTGGTGATGGAGCA 60.339 52.381 0.00 0.00 0.00 4.26
2299 2453 2.681976 GCAGTAGTTGGTGATGGAGCAT 60.682 50.000 0.00 0.00 0.00 3.79
2300 2454 3.614092 CAGTAGTTGGTGATGGAGCATT 58.386 45.455 0.00 0.00 0.00 3.56
2301 2455 3.624861 CAGTAGTTGGTGATGGAGCATTC 59.375 47.826 0.00 0.00 0.00 2.67
2302 2456 1.742761 AGTTGGTGATGGAGCATTCG 58.257 50.000 0.00 0.00 0.00 3.34
2303 2457 0.099436 GTTGGTGATGGAGCATTCGC 59.901 55.000 0.00 0.00 38.99 4.70
2304 2458 1.031571 TTGGTGATGGAGCATTCGCC 61.032 55.000 0.00 0.00 39.83 5.54
2313 2467 1.152819 AGCATTCGCCATGGAGCAT 60.153 52.632 18.40 5.08 39.83 3.79
2345 2499 1.541588 GAGGTTGCGGAATTCTTTGCT 59.458 47.619 5.23 0.00 0.00 3.91
2387 2541 2.050934 GGTAGTCGCGGAAGAGGGT 61.051 63.158 6.13 0.00 0.00 4.34
2398 2552 1.487976 GGAAGAGGGTGATGATGCTCA 59.512 52.381 0.00 0.00 0.00 4.26
2433 2587 2.690881 TCCCCTTCCATCACCGGG 60.691 66.667 6.32 0.00 36.42 5.73
2434 2588 3.015145 CCCCTTCCATCACCGGGT 61.015 66.667 6.32 0.00 34.81 5.28
2435 2589 2.590092 CCCTTCCATCACCGGGTC 59.410 66.667 6.32 0.00 31.89 4.46
2436 2590 2.186903 CCTTCCATCACCGGGTCG 59.813 66.667 6.32 0.00 0.00 4.79
2437 2591 2.355986 CCTTCCATCACCGGGTCGA 61.356 63.158 6.32 0.00 0.00 4.20
2438 2592 1.141881 CTTCCATCACCGGGTCGAG 59.858 63.158 6.32 0.00 0.00 4.04
2439 2593 2.298158 CTTCCATCACCGGGTCGAGG 62.298 65.000 6.32 0.28 0.00 4.63
2440 2594 2.758327 CCATCACCGGGTCGAGGA 60.758 66.667 6.32 0.00 0.00 3.71
2441 2595 2.134287 CCATCACCGGGTCGAGGAT 61.134 63.158 6.32 0.00 0.00 3.24
2442 2596 1.068083 CATCACCGGGTCGAGGATG 59.932 63.158 6.32 9.89 33.69 3.51
2443 2597 1.381327 ATCACCGGGTCGAGGATGT 60.381 57.895 6.32 0.00 0.00 3.06
2444 2598 1.392710 ATCACCGGGTCGAGGATGTC 61.393 60.000 6.32 0.00 0.00 3.06
2455 2609 2.810439 GAGGATGTCGAAGGAGATGG 57.190 55.000 0.00 0.00 0.00 3.51
2456 2610 2.311463 GAGGATGTCGAAGGAGATGGA 58.689 52.381 0.00 0.00 0.00 3.41
2457 2611 2.295909 GAGGATGTCGAAGGAGATGGAG 59.704 54.545 0.00 0.00 0.00 3.86
2458 2612 1.270041 GGATGTCGAAGGAGATGGAGC 60.270 57.143 0.00 0.00 0.00 4.70
2459 2613 0.755686 ATGTCGAAGGAGATGGAGCC 59.244 55.000 0.00 0.00 0.00 4.70
2460 2614 0.324738 TGTCGAAGGAGATGGAGCCT 60.325 55.000 0.00 0.00 35.61 4.58
2713 2867 2.678934 AGTGAGGCGAGCGGGTTA 60.679 61.111 0.00 0.00 0.00 2.85
2846 3462 4.226384 GGAAGCAATTATGGGAAGGGATT 58.774 43.478 0.00 0.00 0.00 3.01
2877 3493 6.876257 GCTGATACTACTCCATCCTTTATTGG 59.124 42.308 0.00 0.00 0.00 3.16
2880 3496 5.632034 ACTACTCCATCCTTTATTGGTCC 57.368 43.478 0.00 0.00 34.48 4.46
2898 3514 2.418976 GTCCTCTTCGTATTTTGTGCCC 59.581 50.000 0.00 0.00 0.00 5.36
2905 3521 5.923684 TCTTCGTATTTTGTGCCCAAATTTC 59.076 36.000 0.00 0.00 40.14 2.17
2907 3523 4.985409 TCGTATTTTGTGCCCAAATTTCAC 59.015 37.500 0.00 2.38 40.14 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.027192 AGAGAAAGGGCATGTTTCGCTA 60.027 45.455 10.46 0.00 40.80 4.26
2 3 1.168714 AGAGAAAGGGCATGTTTCGC 58.831 50.000 0.00 0.00 38.67 4.70
3 4 2.095059 CCAAGAGAAAGGGCATGTTTCG 60.095 50.000 0.00 0.00 38.67 3.46
5 6 2.250924 CCCAAGAGAAAGGGCATGTTT 58.749 47.619 0.00 0.00 38.44 2.83
6 7 1.550869 CCCCAAGAGAAAGGGCATGTT 60.551 52.381 0.00 0.00 44.06 2.71
7 8 0.040204 CCCCAAGAGAAAGGGCATGT 59.960 55.000 0.00 0.00 44.06 3.21
8 9 0.685458 CCCCCAAGAGAAAGGGCATG 60.685 60.000 0.00 0.00 44.06 4.06
12 13 1.384191 CCACCCCCAAGAGAAAGGG 59.616 63.158 0.00 0.00 45.75 3.95
13 14 0.038310 GACCACCCCCAAGAGAAAGG 59.962 60.000 0.00 0.00 0.00 3.11
14 15 0.321653 CGACCACCCCCAAGAGAAAG 60.322 60.000 0.00 0.00 0.00 2.62
15 16 1.758592 CGACCACCCCCAAGAGAAA 59.241 57.895 0.00 0.00 0.00 2.52
16 17 2.890766 GCGACCACCCCCAAGAGAA 61.891 63.158 0.00 0.00 0.00 2.87
17 18 3.319198 GCGACCACCCCCAAGAGA 61.319 66.667 0.00 0.00 0.00 3.10
18 19 4.410400 GGCGACCACCCCCAAGAG 62.410 72.222 0.00 0.00 0.00 2.85
20 21 4.047125 ATGGCGACCACCCCCAAG 62.047 66.667 0.50 0.00 35.80 3.61
21 22 4.358841 CATGGCGACCACCCCCAA 62.359 66.667 0.50 0.00 35.80 4.12
23 24 3.879180 AAACATGGCGACCACCCCC 62.879 63.158 0.00 0.00 35.80 5.40
24 25 2.282887 AAACATGGCGACCACCCC 60.283 61.111 0.00 0.00 35.80 4.95
25 26 2.635443 CCAAACATGGCGACCACCC 61.635 63.158 0.00 0.00 35.80 4.61
26 27 1.460273 AACCAAACATGGCGACCACC 61.460 55.000 0.00 0.00 35.80 4.61
27 28 1.199097 CTAACCAAACATGGCGACCAC 59.801 52.381 0.00 0.00 35.80 4.16
28 29 1.529226 CTAACCAAACATGGCGACCA 58.471 50.000 0.00 1.01 38.19 4.02
29 30 0.808755 CCTAACCAAACATGGCGACC 59.191 55.000 0.00 0.00 0.00 4.79
30 31 1.467342 GACCTAACCAAACATGGCGAC 59.533 52.381 0.00 0.00 0.00 5.19
31 32 1.072489 TGACCTAACCAAACATGGCGA 59.928 47.619 0.00 0.00 0.00 5.54
32 33 1.529226 TGACCTAACCAAACATGGCG 58.471 50.000 0.00 0.00 0.00 5.69
33 34 2.427095 GGATGACCTAACCAAACATGGC 59.573 50.000 0.00 0.00 0.00 4.40
34 35 3.023832 GGGATGACCTAACCAAACATGG 58.976 50.000 0.00 0.00 35.85 3.66
35 36 2.682856 CGGGATGACCTAACCAAACATG 59.317 50.000 0.00 0.00 36.97 3.21
36 37 2.356741 CCGGGATGACCTAACCAAACAT 60.357 50.000 0.00 0.00 36.97 2.71
37 38 1.003812 CCGGGATGACCTAACCAAACA 59.996 52.381 0.00 0.00 36.97 2.83
38 39 1.279846 TCCGGGATGACCTAACCAAAC 59.720 52.381 0.00 0.00 36.97 2.93
39 40 1.557832 CTCCGGGATGACCTAACCAAA 59.442 52.381 0.00 0.00 36.97 3.28
40 41 1.200519 CTCCGGGATGACCTAACCAA 58.799 55.000 0.00 0.00 36.97 3.67
41 42 0.337082 TCTCCGGGATGACCTAACCA 59.663 55.000 0.00 0.00 36.97 3.67
42 43 1.619332 GATCTCCGGGATGACCTAACC 59.381 57.143 0.00 0.00 36.97 2.85
43 44 2.599677 AGATCTCCGGGATGACCTAAC 58.400 52.381 0.00 0.00 36.97 2.34
44 45 3.330126 AAGATCTCCGGGATGACCTAA 57.670 47.619 0.00 0.00 36.97 2.69
45 46 3.231818 GAAAGATCTCCGGGATGACCTA 58.768 50.000 0.00 0.00 36.97 3.08
46 47 2.043227 GAAAGATCTCCGGGATGACCT 58.957 52.381 0.00 0.00 36.97 3.85
47 48 1.762957 TGAAAGATCTCCGGGATGACC 59.237 52.381 0.00 0.00 34.33 4.02
48 49 3.760580 ATGAAAGATCTCCGGGATGAC 57.239 47.619 0.00 0.00 34.33 3.06
49 50 3.711190 TGAATGAAAGATCTCCGGGATGA 59.289 43.478 0.00 0.00 34.33 2.92
50 51 4.077300 TGAATGAAAGATCTCCGGGATG 57.923 45.455 0.00 0.00 34.33 3.51
51 52 4.263243 GGATGAATGAAAGATCTCCGGGAT 60.263 45.833 0.00 2.89 37.37 3.85
52 53 3.071602 GGATGAATGAAAGATCTCCGGGA 59.928 47.826 0.00 0.00 0.00 5.14
53 54 3.406764 GGATGAATGAAAGATCTCCGGG 58.593 50.000 0.00 0.00 0.00 5.73
54 55 3.072184 AGGGATGAATGAAAGATCTCCGG 59.928 47.826 0.00 0.00 0.00 5.14
55 56 4.063689 CAGGGATGAATGAAAGATCTCCG 58.936 47.826 0.00 0.00 0.00 4.63
56 57 5.046288 ACAGGGATGAATGAAAGATCTCC 57.954 43.478 0.00 0.00 0.00 3.71
57 58 8.688747 ATTTACAGGGATGAATGAAAGATCTC 57.311 34.615 0.00 0.00 0.00 2.75
65 66 9.435688 CGTCATAATATTTACAGGGATGAATGA 57.564 33.333 0.00 0.00 0.00 2.57
66 67 8.668353 CCGTCATAATATTTACAGGGATGAATG 58.332 37.037 0.00 0.00 0.00 2.67
67 68 7.829211 CCCGTCATAATATTTACAGGGATGAAT 59.171 37.037 8.97 0.00 38.62 2.57
68 69 7.165485 CCCGTCATAATATTTACAGGGATGAA 58.835 38.462 8.97 0.00 38.62 2.57
69 70 6.271391 ACCCGTCATAATATTTACAGGGATGA 59.729 38.462 17.17 6.69 39.55 2.92
70 71 6.472887 ACCCGTCATAATATTTACAGGGATG 58.527 40.000 17.17 4.81 39.55 3.51
71 72 6.697641 ACCCGTCATAATATTTACAGGGAT 57.302 37.500 17.17 4.83 39.55 3.85
72 73 6.503560 AACCCGTCATAATATTTACAGGGA 57.496 37.500 17.17 0.00 39.55 4.20
73 74 8.857694 ATTAACCCGTCATAATATTTACAGGG 57.142 34.615 11.67 11.67 41.87 4.45
82 83 9.044150 CGAAACCTTTATTAACCCGTCATAATA 57.956 33.333 0.00 0.00 0.00 0.98
83 84 7.467675 GCGAAACCTTTATTAACCCGTCATAAT 60.468 37.037 0.00 0.00 0.00 1.28
84 85 6.183360 GCGAAACCTTTATTAACCCGTCATAA 60.183 38.462 0.00 0.00 0.00 1.90
85 86 5.294060 GCGAAACCTTTATTAACCCGTCATA 59.706 40.000 0.00 0.00 0.00 2.15
86 87 4.095334 GCGAAACCTTTATTAACCCGTCAT 59.905 41.667 0.00 0.00 0.00 3.06
87 88 3.436359 GCGAAACCTTTATTAACCCGTCA 59.564 43.478 0.00 0.00 0.00 4.35
88 89 3.484065 CGCGAAACCTTTATTAACCCGTC 60.484 47.826 0.00 0.00 0.00 4.79
89 90 2.416202 CGCGAAACCTTTATTAACCCGT 59.584 45.455 0.00 0.00 0.00 5.28
90 91 2.672381 TCGCGAAACCTTTATTAACCCG 59.328 45.455 6.20 0.00 0.00 5.28
91 92 3.064408 CCTCGCGAAACCTTTATTAACCC 59.936 47.826 11.33 0.00 0.00 4.11
92 93 3.686241 ACCTCGCGAAACCTTTATTAACC 59.314 43.478 11.33 0.00 0.00 2.85
93 94 4.934075 ACCTCGCGAAACCTTTATTAAC 57.066 40.909 11.33 0.00 0.00 2.01
94 95 4.756135 ACAACCTCGCGAAACCTTTATTAA 59.244 37.500 11.33 0.00 0.00 1.40
95 96 4.317488 ACAACCTCGCGAAACCTTTATTA 58.683 39.130 11.33 0.00 0.00 0.98
96 97 3.143728 ACAACCTCGCGAAACCTTTATT 58.856 40.909 11.33 0.00 0.00 1.40
97 98 2.740447 GACAACCTCGCGAAACCTTTAT 59.260 45.455 11.33 0.00 0.00 1.40
98 99 2.137523 GACAACCTCGCGAAACCTTTA 58.862 47.619 11.33 0.00 0.00 1.85
99 100 0.942252 GACAACCTCGCGAAACCTTT 59.058 50.000 11.33 0.00 0.00 3.11
100 101 0.883370 GGACAACCTCGCGAAACCTT 60.883 55.000 11.33 0.00 0.00 3.50
101 102 1.301479 GGACAACCTCGCGAAACCT 60.301 57.895 11.33 0.00 0.00 3.50
102 103 1.161563 TTGGACAACCTCGCGAAACC 61.162 55.000 11.33 7.98 37.04 3.27
103 104 0.658897 TTTGGACAACCTCGCGAAAC 59.341 50.000 11.33 0.00 37.04 2.78
104 105 1.380524 TTTTGGACAACCTCGCGAAA 58.619 45.000 11.33 0.00 37.04 3.46
105 106 1.380524 TTTTTGGACAACCTCGCGAA 58.619 45.000 11.33 0.00 37.04 4.70
106 107 3.082165 TTTTTGGACAACCTCGCGA 57.918 47.368 9.26 9.26 37.04 5.87
122 123 5.083533 TGCTTCACAGACATTTGGTTTTT 57.916 34.783 0.00 0.00 0.00 1.94
123 124 4.734398 TGCTTCACAGACATTTGGTTTT 57.266 36.364 0.00 0.00 0.00 2.43
124 125 4.734398 TTGCTTCACAGACATTTGGTTT 57.266 36.364 0.00 0.00 0.00 3.27
125 126 4.586001 AGATTGCTTCACAGACATTTGGTT 59.414 37.500 0.00 0.00 0.00 3.67
126 127 4.022589 CAGATTGCTTCACAGACATTTGGT 60.023 41.667 0.00 0.00 0.00 3.67
127 128 4.482386 CAGATTGCTTCACAGACATTTGG 58.518 43.478 0.00 0.00 0.00 3.28
128 129 4.482386 CCAGATTGCTTCACAGACATTTG 58.518 43.478 0.00 0.00 0.00 2.32
129 130 3.508793 CCCAGATTGCTTCACAGACATTT 59.491 43.478 0.00 0.00 0.00 2.32
130 131 3.087031 CCCAGATTGCTTCACAGACATT 58.913 45.455 0.00 0.00 0.00 2.71
131 132 2.719739 CCCAGATTGCTTCACAGACAT 58.280 47.619 0.00 0.00 0.00 3.06
132 133 1.883638 GCCCAGATTGCTTCACAGACA 60.884 52.381 0.00 0.00 0.00 3.41
133 134 0.807496 GCCCAGATTGCTTCACAGAC 59.193 55.000 0.00 0.00 0.00 3.51
134 135 0.674581 CGCCCAGATTGCTTCACAGA 60.675 55.000 0.00 0.00 0.00 3.41
135 136 0.957395 ACGCCCAGATTGCTTCACAG 60.957 55.000 0.00 0.00 0.00 3.66
136 137 0.955428 GACGCCCAGATTGCTTCACA 60.955 55.000 0.00 0.00 0.00 3.58
137 138 0.674895 AGACGCCCAGATTGCTTCAC 60.675 55.000 0.00 0.00 30.07 3.18
138 139 0.674581 CAGACGCCCAGATTGCTTCA 60.675 55.000 0.00 0.00 30.07 3.02
139 140 0.391661 TCAGACGCCCAGATTGCTTC 60.392 55.000 0.00 0.00 0.00 3.86
140 141 0.036732 TTCAGACGCCCAGATTGCTT 59.963 50.000 0.00 0.00 0.00 3.91
152 153 9.406828 TGTTATCGATTTATAGGAATTCAGACG 57.593 33.333 1.71 1.98 0.00 4.18
165 166 7.413657 CCACTTCCACGTTTGTTATCGATTTAT 60.414 37.037 1.71 0.00 0.00 1.40
181 182 1.961793 TCCTTCAAACCACTTCCACG 58.038 50.000 0.00 0.00 0.00 4.94
184 185 4.827284 TCAGAATTCCTTCAAACCACTTCC 59.173 41.667 0.65 0.00 33.56 3.46
188 189 4.338118 TGTGTCAGAATTCCTTCAAACCAC 59.662 41.667 0.65 0.00 33.56 4.16
198 199 5.236047 GCTCATCATAGTGTGTCAGAATTCC 59.764 44.000 0.65 0.00 0.00 3.01
201 202 4.408270 AGGCTCATCATAGTGTGTCAGAAT 59.592 41.667 0.00 0.00 0.00 2.40
205 206 3.369787 CCAAGGCTCATCATAGTGTGTCA 60.370 47.826 0.00 0.00 0.00 3.58
215 216 1.588239 AGTGGATCCAAGGCTCATCA 58.412 50.000 18.20 0.00 0.00 3.07
216 217 5.489792 TTATAGTGGATCCAAGGCTCATC 57.510 43.478 18.20 0.67 0.00 2.92
217 218 5.912149 TTTATAGTGGATCCAAGGCTCAT 57.088 39.130 18.20 6.16 0.00 2.90
218 219 5.221925 GGATTTATAGTGGATCCAAGGCTCA 60.222 44.000 18.20 0.00 39.30 4.26
219 220 5.221925 TGGATTTATAGTGGATCCAAGGCTC 60.222 44.000 18.20 3.21 44.63 4.70
229 231 7.060421 GGAGGAAAATGTGGATTTATAGTGGA 58.940 38.462 0.00 0.00 31.18 4.02
234 236 6.126594 ACGGAGGAGGAAAATGTGGATTTATA 60.127 38.462 0.00 0.00 31.18 0.98
258 260 6.042143 GTCCAATGAAGAGATGAGAGAGAAC 58.958 44.000 0.00 0.00 0.00 3.01
263 268 5.975282 TCTTGTCCAATGAAGAGATGAGAG 58.025 41.667 0.00 0.00 0.00 3.20
283 288 1.680735 TGCACAAAATGTTCGCCTCTT 59.319 42.857 0.00 0.00 0.00 2.85
289 294 0.309302 TCCGGTGCACAAAATGTTCG 59.691 50.000 20.43 9.96 0.00 3.95
305 310 2.908940 GGGCTGCCATCCAATCCG 60.909 66.667 22.05 0.00 0.00 4.18
306 311 2.129785 GTGGGCTGCCATCCAATCC 61.130 63.158 22.05 0.25 34.47 3.01
331 336 2.967615 GAAGTATCCGCCGGCAGC 60.968 66.667 28.98 10.85 38.52 5.25
343 348 3.388676 TCAAAAAGGACAGTCCGGAAGTA 59.611 43.478 14.32 0.00 42.75 2.24
346 351 2.846193 CTCAAAAAGGACAGTCCGGAA 58.154 47.619 14.32 0.00 42.75 4.30
366 371 1.521681 GCATCTCCAGCGGTGTACC 60.522 63.158 14.40 0.00 0.00 3.34
375 380 2.809665 GCATGACTTAGGGCATCTCCAG 60.810 54.545 0.00 0.00 36.21 3.86
407 412 9.807649 AATATGCAAAGTAAATAAAAGCAGAGG 57.192 29.630 0.00 0.00 33.69 3.69
426 431 7.213216 TGACAAAAGACAAAGCTAATATGCA 57.787 32.000 0.00 0.00 34.99 3.96
446 451 9.849166 CTTGGTTAAAGTTTAGAAAGTTTGACA 57.151 29.630 21.84 13.64 43.72 3.58
482 487 9.315363 TGGGTATTGTGGATGTTAAATTACTTT 57.685 29.630 0.00 0.00 0.00 2.66
483 488 8.887264 TGGGTATTGTGGATGTTAAATTACTT 57.113 30.769 0.00 0.00 0.00 2.24
486 491 9.480861 TGATTGGGTATTGTGGATGTTAAATTA 57.519 29.630 0.00 0.00 0.00 1.40
497 502 9.130661 TCTAATGTTATTGATTGGGTATTGTGG 57.869 33.333 0.00 0.00 0.00 4.17
600 607 9.699703 GGTTTGACCTAAGTGCAATTTTATAAA 57.300 29.630 4.05 0.00 34.73 1.40
636 643 7.625828 AATCCTCCTCCGTTTTTATTTACTG 57.374 36.000 0.00 0.00 0.00 2.74
657 664 3.681897 ACACTGACGCTCTCATGAAAATC 59.318 43.478 0.00 0.00 0.00 2.17
666 673 1.300156 TGCACACACTGACGCTCTC 60.300 57.895 0.00 0.00 0.00 3.20
685 694 2.440539 AGCTTGTTACACTCCGTGAG 57.559 50.000 0.38 0.03 36.96 3.51
703 712 4.156915 GCTCTGTACTGTACGTGTGTAAG 58.843 47.826 12.87 3.64 30.94 2.34
724 733 1.305201 TTTGTCCGTTTCAGTGAGGC 58.695 50.000 0.00 0.00 0.00 4.70
739 748 6.994496 CCTGATCACTGGACATATACATTTGT 59.006 38.462 0.00 0.00 37.31 2.83
765 782 1.202830 AGTCTGTCCTCACTCTGTCGT 60.203 52.381 0.00 0.00 0.00 4.34
771 788 0.036858 GGCCAAGTCTGTCCTCACTC 60.037 60.000 0.00 0.00 0.00 3.51
787 804 0.246086 TTGCGTCCATCAATTTGGCC 59.754 50.000 0.00 0.00 36.66 5.36
809 826 4.639906 TGCATGCGGAGTGCCACA 62.640 61.111 14.09 0.00 45.60 4.17
819 836 2.508867 GTATCACACAAGTTGCATGCG 58.491 47.619 14.09 0.00 0.00 4.73
823 840 1.870402 CCACGTATCACACAAGTTGCA 59.130 47.619 1.81 0.00 0.00 4.08
828 845 2.263077 GCTCTCCACGTATCACACAAG 58.737 52.381 0.00 0.00 0.00 3.16
850 867 2.430367 GTTCCGTGTTGGGCTCCT 59.570 61.111 0.00 0.00 38.76 3.69
851 868 2.671963 GGTTCCGTGTTGGGCTCC 60.672 66.667 0.00 0.00 38.76 4.70
932 953 0.249676 AGGACTCGAGACTCGCACTA 59.750 55.000 21.68 1.79 40.21 2.74
934 955 1.299562 TGAGGACTCGAGACTCGCAC 61.300 60.000 21.68 12.47 40.21 5.34
980 1022 2.670148 CCTTTGCTAGCGGAGGGGT 61.670 63.158 22.30 0.00 0.00 4.95
1151 1204 2.631160 TAACGCCATGGATTAGGTGG 57.369 50.000 18.40 0.00 39.69 4.61
1157 1210 3.432326 GGAGAGTCTTAACGCCATGGATT 60.432 47.826 18.40 11.52 0.00 3.01
1170 1223 3.264193 TGCATGTATTGTGGGAGAGTCTT 59.736 43.478 0.00 0.00 0.00 3.01
1178 1233 5.518848 ACATAACATGCATGTATTGTGGG 57.481 39.130 31.23 20.50 40.80 4.61
1184 1239 5.811613 GCAACCAAACATAACATGCATGTAT 59.188 36.000 31.55 22.23 40.80 2.29
1195 1250 6.007703 AGTTTAGCTAGGCAACCAAACATAA 58.992 36.000 7.11 0.00 37.17 1.90
1223 1283 4.160736 GGAAGACGAAAATGAACAAGGG 57.839 45.455 0.00 0.00 0.00 3.95
1226 1286 7.474772 GTCTGCGGAAGACGAAAATGAACAA 62.475 44.000 0.00 0.00 45.76 2.83
1590 1675 0.681733 ATGCATTAGCCTCGATCGGT 59.318 50.000 16.41 0.30 41.13 4.69
1610 1695 0.938637 CTGAGACGCCATGATCGAGC 60.939 60.000 12.99 0.00 0.00 5.03
1678 1769 4.981806 TGATATCATATCGATCGTGCCA 57.018 40.909 15.94 0.00 35.39 4.92
1727 1830 2.868583 CGAATGGATGAGCACAAGGTAG 59.131 50.000 0.00 0.00 0.00 3.18
1753 1861 3.541996 ACATGCTTACACGATGGATCA 57.458 42.857 0.00 0.00 0.00 2.92
1806 1917 9.672086 GTACTAATTGTTTTAGTGCAATTGACA 57.328 29.630 10.34 3.95 42.88 3.58
1831 1942 9.770097 CTGAAGTATGAATACAATACCATGAGT 57.230 33.333 0.00 0.00 35.74 3.41
1833 1944 7.661437 GGCTGAAGTATGAATACAATACCATGA 59.339 37.037 0.00 0.00 35.74 3.07
1834 1945 7.445096 TGGCTGAAGTATGAATACAATACCATG 59.555 37.037 3.43 0.00 35.74 3.66
1867 1978 7.609532 CCTCTTTCCATCAGTTCAGACTTTTAT 59.390 37.037 0.00 0.00 32.54 1.40
1908 2019 4.783227 AGGGAGAAAGGTGTGTGTGTATAT 59.217 41.667 0.00 0.00 0.00 0.86
1910 2021 2.979678 AGGGAGAAAGGTGTGTGTGTAT 59.020 45.455 0.00 0.00 0.00 2.29
1911 2022 2.367567 GAGGGAGAAAGGTGTGTGTGTA 59.632 50.000 0.00 0.00 0.00 2.90
1912 2023 1.141053 GAGGGAGAAAGGTGTGTGTGT 59.859 52.381 0.00 0.00 0.00 3.72
1913 2024 1.140852 TGAGGGAGAAAGGTGTGTGTG 59.859 52.381 0.00 0.00 0.00 3.82
1914 2025 1.141053 GTGAGGGAGAAAGGTGTGTGT 59.859 52.381 0.00 0.00 0.00 3.72
1915 2026 1.873903 CGTGAGGGAGAAAGGTGTGTG 60.874 57.143 0.00 0.00 0.00 3.82
1916 2027 0.393077 CGTGAGGGAGAAAGGTGTGT 59.607 55.000 0.00 0.00 0.00 3.72
1917 2028 0.393077 ACGTGAGGGAGAAAGGTGTG 59.607 55.000 0.00 0.00 0.00 3.82
1923 2034 3.436577 AGTCTAGACGTGAGGGAGAAA 57.563 47.619 17.07 0.00 36.20 2.52
1952 2063 7.446625 CCTACGGCTAAGGAGTAAATAAGTCTA 59.553 40.741 0.00 0.00 36.08 2.59
1953 2064 6.264970 CCTACGGCTAAGGAGTAAATAAGTCT 59.735 42.308 0.00 0.00 36.08 3.24
1954 2065 6.264067 TCCTACGGCTAAGGAGTAAATAAGTC 59.736 42.308 0.91 0.00 38.24 3.01
1955 2066 6.131961 TCCTACGGCTAAGGAGTAAATAAGT 58.868 40.000 0.91 0.00 38.24 2.24
1956 2067 6.645790 TCCTACGGCTAAGGAGTAAATAAG 57.354 41.667 0.91 0.00 38.24 1.73
1957 2068 7.607615 AATCCTACGGCTAAGGAGTAAATAA 57.392 36.000 10.05 0.00 46.14 1.40
1958 2069 7.607615 AAATCCTACGGCTAAGGAGTAAATA 57.392 36.000 10.05 0.00 46.14 1.40
1959 2070 6.496144 AAATCCTACGGCTAAGGAGTAAAT 57.504 37.500 10.05 0.00 46.14 1.40
1960 2071 5.945144 AAATCCTACGGCTAAGGAGTAAA 57.055 39.130 10.05 0.00 46.14 2.01
1961 2072 7.008941 AGATAAATCCTACGGCTAAGGAGTAA 58.991 38.462 10.05 0.03 46.14 2.24
1962 2073 6.550163 AGATAAATCCTACGGCTAAGGAGTA 58.450 40.000 10.05 5.97 46.14 2.59
1963 2074 5.395611 AGATAAATCCTACGGCTAAGGAGT 58.604 41.667 10.05 5.22 46.14 3.85
1964 2075 5.986501 AGATAAATCCTACGGCTAAGGAG 57.013 43.478 10.05 0.00 46.14 3.69
1965 2076 6.787170 TCTAGATAAATCCTACGGCTAAGGA 58.213 40.000 7.10 7.10 46.96 3.36
1972 2083 5.354513 TCTGCGATCTAGATAAATCCTACGG 59.645 44.000 4.89 0.00 0.00 4.02
2021 2132 1.884235 GGTCTTGTGTTCAGACCCTG 58.116 55.000 7.76 0.00 44.56 4.45
2055 2166 7.868906 TGACTGAAGCATGAATTCAATATGA 57.131 32.000 13.09 0.00 36.30 2.15
2083 2194 5.005740 TCCATCAGTTCAGACTTTTGGATG 58.994 41.667 0.00 0.00 38.50 3.51
2105 2216 8.999431 TGTTGAAATATATTATCCGCCTTTCTC 58.001 33.333 0.00 0.00 0.00 2.87
2135 2246 4.212004 GCATACTCACGTGCACATATGAAT 59.788 41.667 18.64 9.58 40.94 2.57
2152 2263 0.457853 ACGAACACGATGCGCATACT 60.458 50.000 25.40 8.30 0.00 2.12
2164 2275 0.228742 CTACACACGTGCACGAACAC 59.771 55.000 42.94 2.36 43.02 3.32
2166 2277 1.200839 GCTACACACGTGCACGAAC 59.799 57.895 42.94 19.81 43.02 3.95
2257 2411 2.233271 CACAAGCAGAAGATGGTGGTT 58.767 47.619 0.00 0.00 40.83 3.67
2286 2440 1.451927 GGCGAATGCTCCATCACCA 60.452 57.895 0.00 0.00 42.25 4.17
2291 2445 0.536687 CTCCATGGCGAATGCTCCAT 60.537 55.000 6.96 0.00 43.45 3.41
2292 2446 1.153107 CTCCATGGCGAATGCTCCA 60.153 57.895 6.96 0.00 42.25 3.86
2293 2447 2.550101 GCTCCATGGCGAATGCTCC 61.550 63.158 6.96 0.00 42.25 4.70
2294 2448 1.170919 ATGCTCCATGGCGAATGCTC 61.171 55.000 6.96 0.00 42.25 4.26
2295 2449 0.754217 AATGCTCCATGGCGAATGCT 60.754 50.000 6.96 0.00 42.25 3.79
2296 2450 0.318445 GAATGCTCCATGGCGAATGC 60.318 55.000 6.96 0.00 41.71 3.56
2297 2451 0.040692 CGAATGCTCCATGGCGAATG 60.041 55.000 6.96 0.00 35.89 2.67
2298 2452 1.789078 GCGAATGCTCCATGGCGAAT 61.789 55.000 6.96 0.00 38.39 3.34
2299 2453 2.472059 GCGAATGCTCCATGGCGAA 61.472 57.895 6.96 0.00 38.39 4.70
2300 2454 2.896854 GCGAATGCTCCATGGCGA 60.897 61.111 6.96 0.00 38.39 5.54
2301 2455 3.957535 GGCGAATGCTCCATGGCG 61.958 66.667 6.96 0.71 42.25 5.69
2302 2456 2.198287 ATGGCGAATGCTCCATGGC 61.198 57.895 6.96 0.00 41.26 4.40
2303 2457 4.169271 ATGGCGAATGCTCCATGG 57.831 55.556 4.97 4.97 41.26 3.66
2345 2499 2.125713 CACGCGCCATGTACCTCA 60.126 61.111 5.73 0.00 0.00 3.86
2398 2552 2.555670 GGGAGACTATAGCGGTCTGGAT 60.556 54.545 0.00 0.00 43.13 3.41
2435 2589 1.000827 CCATCTCCTTCGACATCCTCG 60.001 57.143 0.00 0.00 44.44 4.63
2436 2590 2.295909 CTCCATCTCCTTCGACATCCTC 59.704 54.545 0.00 0.00 0.00 3.71
2437 2591 2.315176 CTCCATCTCCTTCGACATCCT 58.685 52.381 0.00 0.00 0.00 3.24
2438 2592 1.270041 GCTCCATCTCCTTCGACATCC 60.270 57.143 0.00 0.00 0.00 3.51
2439 2593 1.270041 GGCTCCATCTCCTTCGACATC 60.270 57.143 0.00 0.00 0.00 3.06
2440 2594 0.755686 GGCTCCATCTCCTTCGACAT 59.244 55.000 0.00 0.00 0.00 3.06
2441 2595 0.324738 AGGCTCCATCTCCTTCGACA 60.325 55.000 0.00 0.00 0.00 4.35
2442 2596 0.103937 CAGGCTCCATCTCCTTCGAC 59.896 60.000 0.00 0.00 0.00 4.20
2443 2597 0.324738 ACAGGCTCCATCTCCTTCGA 60.325 55.000 0.00 0.00 0.00 3.71
2444 2598 0.103937 GACAGGCTCCATCTCCTTCG 59.896 60.000 0.00 0.00 0.00 3.79
2445 2599 0.103937 CGACAGGCTCCATCTCCTTC 59.896 60.000 0.00 0.00 0.00 3.46
2446 2600 0.324738 TCGACAGGCTCCATCTCCTT 60.325 55.000 0.00 0.00 0.00 3.36
2447 2601 0.754957 CTCGACAGGCTCCATCTCCT 60.755 60.000 0.00 0.00 0.00 3.69
2448 2602 1.739049 CTCGACAGGCTCCATCTCC 59.261 63.158 0.00 0.00 0.00 3.71
2449 2603 0.753479 TCCTCGACAGGCTCCATCTC 60.753 60.000 0.00 0.00 40.12 2.75
2450 2604 0.105760 ATCCTCGACAGGCTCCATCT 60.106 55.000 0.00 0.00 40.12 2.90
2451 2605 0.033228 CATCCTCGACAGGCTCCATC 59.967 60.000 0.00 0.00 40.12 3.51
2452 2606 0.689080 ACATCCTCGACAGGCTCCAT 60.689 55.000 0.00 0.00 40.12 3.41
2453 2607 1.305297 ACATCCTCGACAGGCTCCA 60.305 57.895 0.00 0.00 40.12 3.86
2454 2608 1.439644 GACATCCTCGACAGGCTCC 59.560 63.158 0.00 0.00 40.12 4.70
2455 2609 1.064946 CGACATCCTCGACAGGCTC 59.935 63.158 0.00 0.00 46.14 4.70
2456 2610 1.378646 TCGACATCCTCGACAGGCT 60.379 57.895 0.00 0.00 46.75 4.58
2457 2611 3.197614 TCGACATCCTCGACAGGC 58.802 61.111 0.00 0.00 46.75 4.85
2581 2735 0.037447 TCCGCATTGTCATCACCCAA 59.963 50.000 0.00 0.00 0.00 4.12
2713 2867 3.532155 GCCGAGGTCGATGCTCCT 61.532 66.667 0.00 0.00 43.02 3.69
2820 3436 1.967319 TCCCATAATTGCTTCCGCTC 58.033 50.000 0.00 0.00 36.97 5.03
2866 3482 6.749036 ATACGAAGAGGACCAATAAAGGAT 57.251 37.500 0.00 0.00 0.00 3.24
2868 3484 7.120726 ACAAAATACGAAGAGGACCAATAAAGG 59.879 37.037 0.00 0.00 0.00 3.11
2877 3493 2.418976 GGGCACAAAATACGAAGAGGAC 59.581 50.000 0.00 0.00 0.00 3.85
2880 3496 4.497473 TTTGGGCACAAAATACGAAGAG 57.503 40.909 12.78 0.00 43.21 2.85


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

AutoCloner maintained by Alex Coulton.