Multiple sequence alignment - TraesCS1A01G426200

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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 TraesCS1A01G426200 chr1A 100.000 6996 0 0 1 6996 580965556 580958561 0.000000e+00 12920.0
1 TraesCS1A01G426200 chr1B 91.620 4308 238 56 698 4946 673978613 673974370 0.000000e+00 5842.0
2 TraesCS1A01G426200 chr1B 93.112 2105 87 25 4943 6996 673974227 673972130 0.000000e+00 3031.0
3 TraesCS1A01G426200 chr1B 97.222 36 0 1 469 503 145344620 145344585 7.580000e-05 60.2
4 TraesCS1A01G426200 chr1D 92.293 3581 176 40 1417 4946 483959862 483956331 0.000000e+00 4992.0
5 TraesCS1A01G426200 chr1D 92.406 2107 95 23 4943 6996 483956188 483954094 0.000000e+00 2944.0
6 TraesCS1A01G426200 chr1D 90.504 1211 56 31 185 1383 483961026 483959863 0.000000e+00 1544.0
7 TraesCS1A01G426200 chr7A 81.034 464 63 15 2107 2564 632034537 632034093 5.190000e-91 346.0
8 TraesCS1A01G426200 chr7A 92.143 140 9 1 6418 6555 552975389 552975528 5.540000e-46 196.0
9 TraesCS1A01G426200 chr7A 90.909 55 4 1 461 514 674313077 674313131 9.730000e-09 73.1
10 TraesCS1A01G426200 chr4D 78.044 501 63 25 2107 2563 381745562 381746059 8.940000e-69 272.0
11 TraesCS1A01G426200 chr4D 91.398 93 6 2 63 154 8783931 8784022 7.370000e-25 126.0
12 TraesCS1A01G426200 chr4D 96.970 33 0 1 34 65 341956321 341956353 4.000000e-03 54.7
13 TraesCS1A01G426200 chr6D 84.647 241 15 8 6337 6555 267533054 267532814 3.290000e-53 220.0
14 TraesCS1A01G426200 chr6A 83.817 241 17 8 6337 6555 381088947 381088707 7.110000e-50 209.0
15 TraesCS1A01G426200 chr6A 77.778 126 23 5 283 407 539703124 539703245 9.730000e-09 73.1
16 TraesCS1A01G426200 chr7D 93.571 140 7 1 6418 6555 236827520 236827381 2.560000e-49 207.0
17 TraesCS1A01G426200 chr7D 92.908 141 7 2 6418 6555 604292785 604292925 1.190000e-47 202.0
18 TraesCS1A01G426200 chr7B 92.857 140 8 1 6418 6555 213463580 213463441 1.190000e-47 202.0
19 TraesCS1A01G426200 chr7B 91.398 93 6 2 64 154 48190911 48190819 7.370000e-25 126.0
20 TraesCS1A01G426200 chr5D 83.065 248 17 11 6335 6558 360542101 360541855 1.190000e-47 202.0
21 TraesCS1A01G426200 chr5D 87.156 109 12 2 50 157 383747287 383747180 9.530000e-24 122.0
22 TraesCS1A01G426200 chr5D 85.345 116 11 4 40 153 238555783 238555672 1.590000e-21 115.0
23 TraesCS1A01G426200 chr5D 78.571 126 21 6 469 591 291875376 291875498 2.090000e-10 78.7
24 TraesCS1A01G426200 chr2A 86.131 137 16 2 6419 6552 716168277 716168413 2.030000e-30 145.0
25 TraesCS1A01G426200 chr4B 92.135 89 6 1 66 153 29662594 29662506 2.650000e-24 124.0
26 TraesCS1A01G426200 chr4B 93.023 86 5 1 69 153 484771734 484771819 2.650000e-24 124.0
27 TraesCS1A01G426200 chr3D 89.583 96 8 2 63 157 130722181 130722087 3.430000e-23 121.0
28 TraesCS1A01G426200 chr3D 90.323 93 7 2 60 150 284209404 284209496 3.430000e-23 121.0
29 TraesCS1A01G426200 chr3D 85.938 64 8 1 470 532 422726525 422726588 4.530000e-07 67.6
30 TraesCS1A01G426200 chr3D 100.000 31 0 0 473 503 141597865 141597835 2.730000e-04 58.4
31 TraesCS1A01G426200 chr2D 85.714 112 8 5 60 170 7646274 7646170 2.060000e-20 111.0
32 TraesCS1A01G426200 chr2D 89.286 56 5 1 464 518 577141842 577141897 1.260000e-07 69.4
33 TraesCS1A01G426200 chr2D 100.000 30 0 0 473 502 529352804 529352775 1.000000e-03 56.5
34 TraesCS1A01G426200 chr3A 89.831 59 5 1 8 65 9359855 9359913 2.710000e-09 75.0
35 TraesCS1A01G426200 chr5A 80.220 91 16 2 469 557 384186535 384186625 4.530000e-07 67.6
36 TraesCS1A01G426200 chr4A 96.970 33 0 1 34 65 124357475 124357443 4.000000e-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 TraesCS1A01G426200 chr1A 580958561 580965556 6995 True 12920.0 12920 100.000000 1 6996 1 chr1A.!!$R1 6995
1 TraesCS1A01G426200 chr1B 673972130 673978613 6483 True 4436.5 5842 92.366000 698 6996 2 chr1B.!!$R2 6298
2 TraesCS1A01G426200 chr1D 483954094 483961026 6932 True 3160.0 4992 91.734333 185 6996 3 chr1D.!!$R1 6811

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
669 677 0.251209 AGGTAGGAGTGACGTCTGCA 60.251 55.000 17.92 0.00 0.00 4.41 F
673 681 0.464036 AGGAGTGACGTCTGCAACAA 59.536 50.000 17.92 0.00 0.00 2.83 F
677 685 0.730265 GTGACGTCTGCAACAAACCA 59.270 50.000 17.92 0.00 0.00 3.67 F
807 816 0.774908 ACCCCCGTCTCATCCAAAAA 59.225 50.000 0.00 0.00 0.00 1.94 F
2189 2240 0.955919 GAAGCCAGTGGAAAGGTCGG 60.956 60.000 15.20 0.00 0.00 4.79 F
2207 2259 1.068954 CGGCTGTTCTCTTCCTTTTGC 60.069 52.381 0.00 0.00 0.00 3.68 F
3707 3787 0.385974 CGTAGCTGTTTGCAACCAGC 60.386 55.000 34.16 34.16 45.94 4.85 F
4106 4188 1.877443 GCCACGGTTGTGTATCTTTGT 59.123 47.619 0.00 0.00 44.92 2.83 F
4616 4700 1.938861 CAACACAGCCGCGTAGTTT 59.061 52.632 4.92 0.00 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 2229 0.034896 GAGAACAGCCGACCTTTCCA 59.965 55.000 0.00 0.0 0.00 3.53 R
2189 2240 3.067320 ACAAGCAAAAGGAAGAGAACAGC 59.933 43.478 0.00 0.0 0.00 4.40 R
2550 2605 4.201950 CCATGAACCAGAAGAATTAAGCCG 60.202 45.833 0.00 0.0 0.00 5.52 R
2739 2794 0.976641 AATCTCGCTCACAGGGTTCA 59.023 50.000 0.00 0.0 0.00 3.18 R
3016 3091 1.002773 TCTGGCCTTTCCCGTCTTTAC 59.997 52.381 3.32 0.0 0.00 2.01 R
4116 4198 1.072266 ACCATGGACAAACAGGGCTA 58.928 50.000 21.47 0.0 45.76 3.93 R
4738 4824 0.753479 TGGCGATGGTGTTGGTGTTT 60.753 50.000 0.00 0.0 0.00 2.83 R
5657 5902 1.451207 CCACAAATCGGGGCGATGA 60.451 57.895 0.00 0.0 46.30 2.92 R
6420 6677 0.257039 CCCCTGTTCATGGCTAGCTT 59.743 55.000 15.72 0.0 0.00 3.74 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
83 84 4.302559 AAAAATGTACTCCCTCTGTCCC 57.697 45.455 0.00 0.00 0.00 4.46
84 85 2.642171 AATGTACTCCCTCTGTCCCA 57.358 50.000 0.00 0.00 0.00 4.37
85 86 2.877154 ATGTACTCCCTCTGTCCCAT 57.123 50.000 0.00 0.00 0.00 4.00
86 87 3.993658 ATGTACTCCCTCTGTCCCATA 57.006 47.619 0.00 0.00 0.00 2.74
87 88 3.769189 TGTACTCCCTCTGTCCCATAA 57.231 47.619 0.00 0.00 0.00 1.90
88 89 4.280789 TGTACTCCCTCTGTCCCATAAT 57.719 45.455 0.00 0.00 0.00 1.28
89 90 5.412617 TGTACTCCCTCTGTCCCATAATA 57.587 43.478 0.00 0.00 0.00 0.98
90 91 5.977533 TGTACTCCCTCTGTCCCATAATAT 58.022 41.667 0.00 0.00 0.00 1.28
91 92 7.111136 TGTACTCCCTCTGTCCCATAATATA 57.889 40.000 0.00 0.00 0.00 0.86
92 93 7.541074 TGTACTCCCTCTGTCCCATAATATAA 58.459 38.462 0.00 0.00 0.00 0.98
93 94 7.674348 TGTACTCCCTCTGTCCCATAATATAAG 59.326 40.741 0.00 0.00 0.00 1.73
94 95 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
95 96 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
96 97 7.235812 ACTCCCTCTGTCCCATAATATAAGAAC 59.764 40.741 0.00 0.00 0.00 3.01
97 98 6.210784 TCCCTCTGTCCCATAATATAAGAACG 59.789 42.308 0.00 0.00 0.00 3.95
98 99 6.014499 CCCTCTGTCCCATAATATAAGAACGT 60.014 42.308 0.00 0.00 0.00 3.99
99 100 7.442656 CCTCTGTCCCATAATATAAGAACGTT 58.557 38.462 0.00 0.00 0.00 3.99
100 101 7.931948 CCTCTGTCCCATAATATAAGAACGTTT 59.068 37.037 0.46 0.00 0.00 3.60
101 102 9.326413 CTCTGTCCCATAATATAAGAACGTTTT 57.674 33.333 0.46 0.00 0.00 2.43
102 103 9.675464 TCTGTCCCATAATATAAGAACGTTTTT 57.325 29.630 9.22 9.22 0.00 1.94
103 104 9.716507 CTGTCCCATAATATAAGAACGTTTTTG 57.283 33.333 13.87 0.00 0.00 2.44
104 105 9.451002 TGTCCCATAATATAAGAACGTTTTTGA 57.549 29.630 13.87 2.81 0.00 2.69
105 106 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
106 107 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
107 108 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
116 117 6.656003 AGAACGTTTTTGACACTAATGTAGC 58.344 36.000 0.46 0.00 39.95 3.58
117 118 6.482308 AGAACGTTTTTGACACTAATGTAGCT 59.518 34.615 0.46 0.00 39.95 3.32
118 119 6.224420 ACGTTTTTGACACTAATGTAGCTC 57.776 37.500 0.00 0.00 39.95 4.09
119 120 5.756347 ACGTTTTTGACACTAATGTAGCTCA 59.244 36.000 0.00 0.00 39.95 4.26
120 121 6.073765 ACGTTTTTGACACTAATGTAGCTCAG 60.074 38.462 0.00 0.00 39.95 3.35
121 122 6.145534 CGTTTTTGACACTAATGTAGCTCAGA 59.854 38.462 0.00 0.00 39.95 3.27
122 123 7.307160 CGTTTTTGACACTAATGTAGCTCAGAA 60.307 37.037 0.00 0.00 39.95 3.02
123 124 8.342634 GTTTTTGACACTAATGTAGCTCAGAAA 58.657 33.333 0.00 0.00 39.95 2.52
124 125 7.421530 TTTGACACTAATGTAGCTCAGAAAC 57.578 36.000 0.00 0.00 39.95 2.78
125 126 5.161358 TGACACTAATGTAGCTCAGAAACG 58.839 41.667 0.00 0.00 39.95 3.60
126 127 3.927142 ACACTAATGTAGCTCAGAAACGC 59.073 43.478 0.00 0.00 37.26 4.84
127 128 4.177026 CACTAATGTAGCTCAGAAACGCT 58.823 43.478 0.00 0.00 40.15 5.07
128 129 4.266502 CACTAATGTAGCTCAGAAACGCTC 59.733 45.833 0.00 0.00 37.68 5.03
129 130 3.601443 AATGTAGCTCAGAAACGCTCT 57.399 42.857 0.00 0.00 37.68 4.09
130 131 3.601443 ATGTAGCTCAGAAACGCTCTT 57.399 42.857 0.00 0.00 37.68 2.85
131 132 4.720649 ATGTAGCTCAGAAACGCTCTTA 57.279 40.909 0.00 0.00 37.68 2.10
132 133 4.720649 TGTAGCTCAGAAACGCTCTTAT 57.279 40.909 0.00 0.00 37.68 1.73
133 134 5.830000 TGTAGCTCAGAAACGCTCTTATA 57.170 39.130 0.00 0.00 37.68 0.98
134 135 6.392625 TGTAGCTCAGAAACGCTCTTATAT 57.607 37.500 0.00 0.00 37.68 0.86
135 136 6.806751 TGTAGCTCAGAAACGCTCTTATATT 58.193 36.000 0.00 0.00 37.68 1.28
136 137 7.937649 TGTAGCTCAGAAACGCTCTTATATTA 58.062 34.615 0.00 0.00 37.68 0.98
137 138 8.577296 TGTAGCTCAGAAACGCTCTTATATTAT 58.423 33.333 0.00 0.00 37.68 1.28
138 139 7.881643 AGCTCAGAAACGCTCTTATATTATG 57.118 36.000 0.00 0.00 29.07 1.90
139 140 6.870965 AGCTCAGAAACGCTCTTATATTATGG 59.129 38.462 0.00 0.00 29.07 2.74
140 141 6.091441 GCTCAGAAACGCTCTTATATTATGGG 59.909 42.308 0.00 0.00 29.07 4.00
141 142 7.297936 TCAGAAACGCTCTTATATTATGGGA 57.702 36.000 0.00 0.00 29.07 4.37
142 143 7.907389 TCAGAAACGCTCTTATATTATGGGAT 58.093 34.615 0.00 0.00 29.07 3.85
143 144 8.375506 TCAGAAACGCTCTTATATTATGGGATT 58.624 33.333 0.00 0.00 29.07 3.01
144 145 8.446273 CAGAAACGCTCTTATATTATGGGATTG 58.554 37.037 0.00 0.00 29.07 2.67
145 146 8.375506 AGAAACGCTCTTATATTATGGGATTGA 58.624 33.333 0.00 0.00 0.00 2.57
146 147 8.553459 AAACGCTCTTATATTATGGGATTGAG 57.447 34.615 0.00 0.00 0.00 3.02
147 148 6.644347 ACGCTCTTATATTATGGGATTGAGG 58.356 40.000 0.00 0.00 0.00 3.86
148 149 6.051717 CGCTCTTATATTATGGGATTGAGGG 58.948 44.000 0.00 0.00 0.00 4.30
149 150 6.127054 CGCTCTTATATTATGGGATTGAGGGA 60.127 42.308 0.00 0.00 35.10 4.20
150 151 7.278875 GCTCTTATATTATGGGATTGAGGGAG 58.721 42.308 0.00 0.00 0.00 4.30
151 152 7.092668 GCTCTTATATTATGGGATTGAGGGAGT 60.093 40.741 0.00 0.00 0.00 3.85
152 153 9.494055 CTCTTATATTATGGGATTGAGGGAGTA 57.506 37.037 0.00 0.00 0.00 2.59
153 154 9.268282 TCTTATATTATGGGATTGAGGGAGTAC 57.732 37.037 0.00 0.00 0.00 2.73
154 155 8.982471 TTATATTATGGGATTGAGGGAGTACA 57.018 34.615 0.00 0.00 0.00 2.90
155 156 9.574577 TTATATTATGGGATTGAGGGAGTACAT 57.425 33.333 0.00 0.00 0.00 2.29
156 157 5.567037 TTATGGGATTGAGGGAGTACATG 57.433 43.478 0.00 0.00 0.00 3.21
157 158 2.126882 TGGGATTGAGGGAGTACATGG 58.873 52.381 0.00 0.00 0.00 3.66
158 159 2.293519 TGGGATTGAGGGAGTACATGGA 60.294 50.000 0.00 0.00 0.00 3.41
159 160 2.777692 GGGATTGAGGGAGTACATGGAA 59.222 50.000 0.00 0.00 0.00 3.53
160 161 3.395941 GGGATTGAGGGAGTACATGGAAT 59.604 47.826 0.00 0.00 0.00 3.01
161 162 4.141158 GGGATTGAGGGAGTACATGGAATT 60.141 45.833 0.00 0.00 0.00 2.17
162 163 5.449553 GGATTGAGGGAGTACATGGAATTT 58.550 41.667 0.00 0.00 0.00 1.82
163 164 5.893824 GGATTGAGGGAGTACATGGAATTTT 59.106 40.000 0.00 0.00 0.00 1.82
164 165 6.381133 GGATTGAGGGAGTACATGGAATTTTT 59.619 38.462 0.00 0.00 0.00 1.94
165 166 7.559897 GGATTGAGGGAGTACATGGAATTTTTA 59.440 37.037 0.00 0.00 0.00 1.52
166 167 8.893563 ATTGAGGGAGTACATGGAATTTTTAA 57.106 30.769 0.00 0.00 0.00 1.52
167 168 8.713708 TTGAGGGAGTACATGGAATTTTTAAA 57.286 30.769 0.00 0.00 0.00 1.52
168 169 8.713708 TGAGGGAGTACATGGAATTTTTAAAA 57.286 30.769 0.00 0.00 0.00 1.52
169 170 8.802267 TGAGGGAGTACATGGAATTTTTAAAAG 58.198 33.333 0.14 0.00 0.00 2.27
170 171 8.721133 AGGGAGTACATGGAATTTTTAAAAGT 57.279 30.769 0.14 0.00 0.00 2.66
171 172 8.585018 AGGGAGTACATGGAATTTTTAAAAGTG 58.415 33.333 0.14 0.00 0.00 3.16
172 173 7.330946 GGGAGTACATGGAATTTTTAAAAGTGC 59.669 37.037 2.62 2.62 0.00 4.40
173 174 7.870445 GGAGTACATGGAATTTTTAAAAGTGCA 59.130 33.333 13.62 13.62 0.00 4.57
174 175 9.423061 GAGTACATGGAATTTTTAAAAGTGCAT 57.577 29.630 16.60 16.60 0.00 3.96
175 176 9.777297 AGTACATGGAATTTTTAAAAGTGCATT 57.223 25.926 18.98 13.74 0.00 3.56
339 342 9.814899 TCATGTGTTTAAAGAAATTCAATGTGT 57.185 25.926 0.00 0.00 0.00 3.72
442 445 6.119536 ACCATGCTTCCGACTCATTTTATTA 58.880 36.000 0.00 0.00 0.00 0.98
446 449 7.715265 TGCTTCCGACTCATTTTATTATCTC 57.285 36.000 0.00 0.00 0.00 2.75
521 527 3.189080 TCTCAACACAAGAATCCAATGCG 59.811 43.478 0.00 0.00 0.00 4.73
533 539 3.799281 TCCAATGCGGAAAATGATTCC 57.201 42.857 0.00 0.00 42.52 3.01
534 540 3.364549 TCCAATGCGGAAAATGATTCCT 58.635 40.909 5.75 0.00 42.52 3.36
535 541 3.130869 TCCAATGCGGAAAATGATTCCTG 59.869 43.478 5.75 1.34 42.52 3.86
536 542 3.450578 CAATGCGGAAAATGATTCCTGG 58.549 45.455 5.75 0.00 36.45 4.45
539 545 2.896685 TGCGGAAAATGATTCCTGGTTT 59.103 40.909 5.75 0.00 36.45 3.27
551 557 0.673437 CCTGGTTTGAACGCATGGTT 59.327 50.000 0.00 0.00 42.96 3.67
553 559 2.294791 CCTGGTTTGAACGCATGGTTTA 59.705 45.455 0.00 0.00 39.50 2.01
568 574 8.974408 ACGCATGGTTTAAAAAGATAAAACTTC 58.026 29.630 0.00 0.00 34.31 3.01
622 628 4.751172 CGATAAATGACGCACTGTACATG 58.249 43.478 0.00 0.00 0.00 3.21
623 629 2.900122 AAATGACGCACTGTACATGC 57.100 45.000 15.90 15.90 39.81 4.06
624 630 1.807139 AATGACGCACTGTACATGCA 58.193 45.000 21.88 0.00 43.57 3.96
625 631 1.362768 ATGACGCACTGTACATGCAG 58.637 50.000 21.88 17.74 43.57 4.41
634 640 0.950836 TGTACATGCAGTGCACCAAC 59.049 50.000 22.44 17.94 43.04 3.77
665 673 1.000506 TGCAAAGGTAGGAGTGACGTC 59.999 52.381 9.11 9.11 0.00 4.34
666 674 1.272769 GCAAAGGTAGGAGTGACGTCT 59.727 52.381 17.92 0.00 0.00 4.18
667 675 2.927014 GCAAAGGTAGGAGTGACGTCTG 60.927 54.545 17.92 2.88 0.00 3.51
668 676 0.889306 AAGGTAGGAGTGACGTCTGC 59.111 55.000 17.92 9.73 0.00 4.26
669 677 0.251209 AGGTAGGAGTGACGTCTGCA 60.251 55.000 17.92 0.00 0.00 4.41
670 678 0.601558 GGTAGGAGTGACGTCTGCAA 59.398 55.000 17.92 0.00 0.00 4.08
671 679 1.669211 GGTAGGAGTGACGTCTGCAAC 60.669 57.143 17.92 6.37 0.00 4.17
672 680 1.000607 GTAGGAGTGACGTCTGCAACA 60.001 52.381 17.92 0.00 0.00 3.33
673 681 0.464036 AGGAGTGACGTCTGCAACAA 59.536 50.000 17.92 0.00 0.00 2.83
674 682 1.134521 AGGAGTGACGTCTGCAACAAA 60.135 47.619 17.92 0.00 0.00 2.83
675 683 1.003866 GGAGTGACGTCTGCAACAAAC 60.004 52.381 17.92 3.62 0.00 2.93
676 684 1.003866 GAGTGACGTCTGCAACAAACC 60.004 52.381 17.92 0.00 0.00 3.27
677 685 0.730265 GTGACGTCTGCAACAAACCA 59.270 50.000 17.92 0.00 0.00 3.67
678 686 1.131504 GTGACGTCTGCAACAAACCAA 59.868 47.619 17.92 0.00 0.00 3.67
679 687 1.813178 TGACGTCTGCAACAAACCAAA 59.187 42.857 17.92 0.00 0.00 3.28
680 688 2.229062 TGACGTCTGCAACAAACCAAAA 59.771 40.909 17.92 0.00 0.00 2.44
681 689 3.119316 TGACGTCTGCAACAAACCAAAAT 60.119 39.130 17.92 0.00 0.00 1.82
682 690 3.186119 ACGTCTGCAACAAACCAAAATG 58.814 40.909 0.00 0.00 0.00 2.32
683 691 3.186119 CGTCTGCAACAAACCAAAATGT 58.814 40.909 0.00 0.00 0.00 2.71
684 692 3.242712 CGTCTGCAACAAACCAAAATGTC 59.757 43.478 0.00 0.00 0.00 3.06
685 693 4.432712 GTCTGCAACAAACCAAAATGTCT 58.567 39.130 0.00 0.00 0.00 3.41
686 694 4.504097 GTCTGCAACAAACCAAAATGTCTC 59.496 41.667 0.00 0.00 0.00 3.36
687 695 3.791245 TGCAACAAACCAAAATGTCTCC 58.209 40.909 0.00 0.00 0.00 3.71
688 696 2.794350 GCAACAAACCAAAATGTCTCCG 59.206 45.455 0.00 0.00 0.00 4.63
689 697 3.380142 CAACAAACCAAAATGTCTCCGG 58.620 45.455 0.00 0.00 0.00 5.14
690 698 2.938838 ACAAACCAAAATGTCTCCGGA 58.061 42.857 2.93 2.93 0.00 5.14
807 816 0.774908 ACCCCCGTCTCATCCAAAAA 59.225 50.000 0.00 0.00 0.00 1.94
812 821 3.632145 CCCCGTCTCATCCAAAAATAAGG 59.368 47.826 0.00 0.00 0.00 2.69
814 823 4.576463 CCCGTCTCATCCAAAAATAAGGAG 59.424 45.833 0.00 0.00 37.34 3.69
923 939 1.065126 GGCAATGCAGTCTCTACCCTT 60.065 52.381 7.79 0.00 0.00 3.95
1005 1030 2.253758 CGATTCGCGGGCAATGGAT 61.254 57.895 6.13 0.00 36.03 3.41
1456 1486 6.639632 AATTATACATGCCACATGGTTCTC 57.360 37.500 11.91 0.00 37.57 2.87
1459 1489 2.165167 ACATGCCACATGGTTCTCTTG 58.835 47.619 11.91 0.00 37.57 3.02
1508 1538 2.170166 GATGTTTCAGGCCCACATTGA 58.830 47.619 0.00 0.00 31.10 2.57
1516 1546 1.106285 GGCCCACATTGACTCATTCC 58.894 55.000 0.00 0.00 0.00 3.01
1538 1568 4.876679 CCTACTGGTTTAGGAAGCTTAAGC 59.123 45.833 20.09 20.09 41.29 3.09
1539 1569 3.687125 ACTGGTTTAGGAAGCTTAAGCC 58.313 45.455 23.71 9.44 43.38 4.35
1540 1570 3.017442 CTGGTTTAGGAAGCTTAAGCCC 58.983 50.000 23.71 18.03 43.38 5.19
1569 1617 3.968837 ATGTGCAGGCCATGTGGGG 62.969 63.158 5.01 0.00 37.04 4.96
1584 1633 2.177451 TGTGGGGATCAATATGGCATGT 59.823 45.455 10.98 0.00 0.00 3.21
1600 1649 4.036262 TGGCATGTCAAAGTGTGTTTACTC 59.964 41.667 0.00 0.00 0.00 2.59
1624 1673 2.515429 ACCCTGCCTATGTTCATTCCAT 59.485 45.455 0.00 0.00 0.00 3.41
1694 1743 2.711542 ACCTGTTATCCCTTTCTTGCG 58.288 47.619 0.00 0.00 0.00 4.85
1696 1745 1.401905 CTGTTATCCCTTTCTTGCGGC 59.598 52.381 0.00 0.00 0.00 6.53
1697 1746 1.271652 TGTTATCCCTTTCTTGCGGCA 60.272 47.619 0.00 0.00 0.00 5.69
1822 1872 4.537135 TTGTCATAGGACTTCTGGTGTC 57.463 45.455 9.22 0.00 44.61 3.67
1825 1875 1.204704 CATAGGACTTCTGGTGTCGCA 59.795 52.381 0.00 0.00 35.45 5.10
1924 1974 3.428534 GGTTAATTGCTGGAAAACAAGCG 59.571 43.478 0.00 0.00 0.00 4.68
2095 2145 4.873259 GCTTTACAAGAAGATGAGACCCTC 59.127 45.833 0.00 0.00 0.00 4.30
2143 2193 2.315925 TTCACGATCATCTTCCAGCC 57.684 50.000 0.00 0.00 0.00 4.85
2146 2196 2.171237 TCACGATCATCTTCCAGCCATT 59.829 45.455 0.00 0.00 0.00 3.16
2178 2229 3.378427 GTGACAAACTTGAAGAAGCCAGT 59.622 43.478 0.00 0.00 31.68 4.00
2189 2240 0.955919 GAAGCCAGTGGAAAGGTCGG 60.956 60.000 15.20 0.00 0.00 4.79
2207 2259 1.068954 CGGCTGTTCTCTTCCTTTTGC 60.069 52.381 0.00 0.00 0.00 3.68
2219 2271 4.947388 TCTTCCTTTTGCTTGTGTGTTACT 59.053 37.500 0.00 0.00 0.00 2.24
2222 2274 5.646606 TCCTTTTGCTTGTGTGTTACTTTC 58.353 37.500 0.00 0.00 0.00 2.62
2231 2286 6.251376 GCTTGTGTGTTACTTTCTTTCAGTTG 59.749 38.462 0.00 0.00 0.00 3.16
2255 2310 8.220755 TGTCTAACTTTGTGCAACTATTTTCT 57.779 30.769 0.00 0.00 38.04 2.52
2402 2457 4.678256 ACTCCTGGATTCTACTGAGACAA 58.322 43.478 0.00 0.00 0.00 3.18
2471 2526 3.354089 AAATCAGTGCCAAAGTTGACG 57.646 42.857 0.00 0.00 0.00 4.35
2545 2600 9.938280 TTATTATCTCATACCATTTCCTAACGG 57.062 33.333 0.00 0.00 0.00 4.44
2550 2605 6.596497 TCTCATACCATTTCCTAACGGTTTTC 59.404 38.462 0.00 0.00 32.81 2.29
2585 2640 2.361757 TGGTTCATGGTGCTTCTTGTTG 59.638 45.455 0.00 0.00 0.00 3.33
2592 2647 1.815003 GGTGCTTCTTGTTGAGGATGG 59.185 52.381 0.00 0.00 0.00 3.51
2593 2648 2.553028 GGTGCTTCTTGTTGAGGATGGA 60.553 50.000 0.00 0.00 0.00 3.41
2783 2838 4.973055 TGGGTTCGAACGCGGGTG 62.973 66.667 31.94 0.00 43.97 4.61
2798 2853 2.159296 GCGGGTGTCACACTTTTCTTTT 60.159 45.455 8.12 0.00 34.40 2.27
2917 2992 5.290643 CGCTGGTGATTTTCTTTTTCACAAA 59.709 36.000 4.85 0.00 41.17 2.83
2979 3054 4.371786 TGAAGCAGAGTGTAAGTTGACAG 58.628 43.478 0.00 0.00 0.00 3.51
3012 3087 4.158764 CCGAGAGTCCAGATAAAACAGTCT 59.841 45.833 0.00 0.00 0.00 3.24
3016 3091 7.433719 CGAGAGTCCAGATAAAACAGTCTAATG 59.566 40.741 0.00 0.00 0.00 1.90
3052 3127 3.137533 GCCAGACTAGAGATTTCCATGC 58.862 50.000 0.00 0.00 0.00 4.06
3159 3234 6.662755 AGGATTGTAGCAGTTCCATTCAATA 58.337 36.000 0.00 0.00 0.00 1.90
3257 3332 1.188871 TCGGGCATGTAGTGACACCA 61.189 55.000 0.84 0.00 37.70 4.17
3315 3390 5.119931 TCATTTACGCAGTTGCATTCTTT 57.880 34.783 4.84 0.00 37.78 2.52
3389 3464 4.685169 TGCGCCTTCTGAAGAAATTTAG 57.315 40.909 18.68 1.45 33.07 1.85
3582 3657 1.959985 CAGGGCAATTGTGGTGTGTAA 59.040 47.619 7.40 0.00 0.00 2.41
3611 3686 7.665690 TCTTTTTGAAATGGCATGCTAACTTA 58.334 30.769 18.92 0.00 0.00 2.24
3612 3687 8.147058 TCTTTTTGAAATGGCATGCTAACTTAA 58.853 29.630 18.92 3.36 0.00 1.85
3620 3695 8.469309 AATGGCATGCTAACTTAAGTCATAAT 57.531 30.769 18.92 0.00 0.00 1.28
3686 3766 9.330063 CTTCAGTTATGCATATTCTTCACCTTA 57.670 33.333 7.36 0.00 0.00 2.69
3707 3787 0.385974 CGTAGCTGTTTGCAACCAGC 60.386 55.000 34.16 34.16 45.94 4.85
3805 3885 5.663106 ACAGCAGTAATCTTAATCCTCTCCA 59.337 40.000 0.00 0.00 0.00 3.86
3835 3915 7.605410 TCTCCATAAAACTATCCGACAAAAC 57.395 36.000 0.00 0.00 0.00 2.43
3852 3932 7.753580 CCGACAAAACTGAAAATAATACCTTCC 59.246 37.037 0.00 0.00 0.00 3.46
3893 3973 3.636153 ACCAACTTCTATCTCCCTTGC 57.364 47.619 0.00 0.00 0.00 4.01
3910 3990 4.298332 CCTTGCACAAATAGTGGTTTGTC 58.702 43.478 2.31 0.38 46.32 3.18
4009 4091 5.518812 GTGATCAGTCTCACACTATAGCAG 58.481 45.833 0.00 0.00 44.03 4.24
4069 4151 6.619744 CAACATCAATTGTGCATAGTGGTTA 58.380 36.000 5.13 0.00 38.99 2.85
4106 4188 1.877443 GCCACGGTTGTGTATCTTTGT 59.123 47.619 0.00 0.00 44.92 2.83
4116 4198 6.932960 GGTTGTGTATCTTTGTAGTGTAGGTT 59.067 38.462 0.00 0.00 0.00 3.50
4120 4202 6.755607 GTGTATCTTTGTAGTGTAGGTTAGCC 59.244 42.308 0.00 0.00 0.00 3.93
4153 4235 9.016438 GTCCATGGTTTCTACTGGTTTTTATAA 57.984 33.333 12.58 0.00 0.00 0.98
4154 4236 9.589461 TCCATGGTTTCTACTGGTTTTTATAAA 57.411 29.630 12.58 0.00 0.00 1.40
4211 4293 4.566907 GGCAGGTTCCACAGTATTTCCTTA 60.567 45.833 0.00 0.00 0.00 2.69
4250 4332 6.293626 GCTAACGAATTGCCATCAATAGTCAT 60.294 38.462 0.00 0.00 41.77 3.06
4259 4341 6.888105 TGCCATCAATAGTCATGAAGAAGTA 58.112 36.000 0.00 0.00 0.00 2.24
4535 4617 2.930826 AACACAACTCCCTTGTCGAT 57.069 45.000 0.00 0.00 41.50 3.59
4581 4663 2.869192 GCTCTCTGCACCTGCTTTATAC 59.131 50.000 0.00 0.00 42.66 1.47
4605 4689 7.755591 ACAATAACTATCTTCATGCAACACAG 58.244 34.615 0.00 0.00 0.00 3.66
4616 4700 1.938861 CAACACAGCCGCGTAGTTT 59.061 52.632 4.92 0.00 0.00 2.66
4703 4789 4.518970 ACTTGTGTACATGTTTCCATCCAC 59.481 41.667 2.30 0.00 31.23 4.02
4704 4790 4.092116 TGTGTACATGTTTCCATCCACA 57.908 40.909 2.30 0.00 32.80 4.17
4738 4824 2.413963 GCACACCAGCACCAACACA 61.414 57.895 0.00 0.00 0.00 3.72
4834 4920 6.524734 CCTTACTATGTATGAGCCACAATGA 58.475 40.000 0.00 0.00 0.00 2.57
4891 4979 3.813166 GGTTGTATAGTGTGCAAGTGTGT 59.187 43.478 0.00 0.00 32.88 3.72
4897 4985 2.945278 AGTGTGCAAGTGTGTTTTGTG 58.055 42.857 0.00 0.00 0.00 3.33
5100 5338 6.207691 AGCTTCAATGGCATTAATACGTTT 57.792 33.333 13.23 0.00 0.00 3.60
5151 5393 9.941664 ATAAGATAAAGACATGAAATTCTTGCG 57.058 29.630 0.00 0.00 32.26 4.85
5377 5622 8.268850 CACAAGTTGCTAGTGTAATAAGGAAT 57.731 34.615 1.81 0.00 0.00 3.01
5505 5750 4.379918 GCAATCCAAAAGAGCTTGGTAGAC 60.380 45.833 2.14 0.00 45.29 2.59
5657 5902 4.182339 GTGATGCGCTAGATGATCATGAT 58.818 43.478 14.30 8.25 0.00 2.45
5772 6017 8.924691 TGTTTGAAGAAGATTGTTGTGAAAAAG 58.075 29.630 0.00 0.00 0.00 2.27
5819 6064 4.396166 CCGAATAACCATGAAGCTTCTGTT 59.604 41.667 26.09 24.43 0.00 3.16
5854 6099 3.134574 TGAACAAGGTACGGCAATCTT 57.865 42.857 0.00 0.00 0.00 2.40
5930 6175 2.094078 GGAATTGCCATGCTGCTGTAAA 60.094 45.455 0.00 0.00 36.34 2.01
5960 6205 3.005791 GGTATTTGTGCTGCCTGAAACTT 59.994 43.478 0.00 0.00 0.00 2.66
5997 6242 4.365514 TGACTTTTGAGCACCCATAGAA 57.634 40.909 0.00 0.00 0.00 2.10
6017 6262 6.855763 AGAACCAAATGGCTTCATAATTCA 57.144 33.333 0.00 0.00 39.32 2.57
6020 6265 5.733676 ACCAAATGGCTTCATAATTCAACC 58.266 37.500 0.00 0.00 39.32 3.77
6028 6282 5.464389 GGCTTCATAATTCAACCATGCAATC 59.536 40.000 0.00 0.00 0.00 2.67
6048 6302 9.276590 TGCAATCAGGTAGTATGATCTATTTTG 57.723 33.333 0.00 0.00 36.38 2.44
6076 6330 1.002134 ACATTCTGTTGAGGGGGCG 60.002 57.895 0.00 0.00 0.00 6.13
6105 6359 6.317391 GGCAGATGATAGCTAAAAACAAGTCT 59.683 38.462 0.00 0.00 0.00 3.24
6169 6423 3.748048 TGTTCAACATACTGCTCTGCTTC 59.252 43.478 0.00 0.00 0.00 3.86
6241 6495 1.131693 CGTTCCTTTATTGGTTCCGGC 59.868 52.381 0.00 0.00 0.00 6.13
6262 6517 0.311790 ATGCGTGGTTTGACTTGCAG 59.688 50.000 0.00 0.00 35.60 4.41
6350 6607 0.036765 ATGAACGGTCGGCTAAAGCA 60.037 50.000 4.07 0.00 44.36 3.91
6361 6618 4.690748 GTCGGCTAAAGCATGCTGATAATA 59.309 41.667 23.48 8.86 44.90 0.98
6374 6631 6.983906 TGCTGATAATATCAAGAGAGGTCA 57.016 37.500 4.37 0.00 39.11 4.02
6396 6653 2.304761 GGGTAGACCAAACTGGACATGA 59.695 50.000 0.00 0.00 40.96 3.07
6416 6673 2.946990 GAGAGGAGTCCGTAAAGAGAGG 59.053 54.545 2.76 0.00 0.00 3.69
6417 6674 1.406180 GAGGAGTCCGTAAAGAGAGGC 59.594 57.143 2.76 0.00 0.00 4.70
6419 6676 1.183549 GAGTCCGTAAAGAGAGGCCA 58.816 55.000 5.01 0.00 0.00 5.36
6420 6677 1.549170 GAGTCCGTAAAGAGAGGCCAA 59.451 52.381 5.01 0.00 0.00 4.52
6422 6679 2.028020 AGTCCGTAAAGAGAGGCCAAAG 60.028 50.000 5.01 0.00 0.00 2.77
6521 6800 1.062121 TCAGCTCTAGCCTACCCCAAT 60.062 52.381 0.00 0.00 43.38 3.16
6600 6885 9.659830 ATTGTGAATTTACGTGACTTCTTTTAC 57.340 29.630 10.93 2.91 0.00 2.01
6773 7070 3.784511 ATACGTAGCAGAGTAGGGCTA 57.215 47.619 0.08 0.00 41.41 3.93
6819 7116 7.229506 ACAAAGAAAAAGAGTACTGCTATGCTT 59.770 33.333 0.00 0.00 0.00 3.91
6821 7118 8.485976 AAGAAAAAGAGTACTGCTATGCTTAG 57.514 34.615 0.00 2.28 0.00 2.18
6948 7245 7.068716 AGGATTCTTCACATATTAAAGGTTGGC 59.931 37.037 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 3.655777 TGGGACAGAGGGAGTACATTTTT 59.344 43.478 0.00 0.00 0.00 1.94
63 64 3.256704 TGGGACAGAGGGAGTACATTTT 58.743 45.455 0.00 0.00 0.00 1.82
64 65 2.915869 TGGGACAGAGGGAGTACATTT 58.084 47.619 0.00 0.00 0.00 2.32
65 66 2.642171 TGGGACAGAGGGAGTACATT 57.358 50.000 0.00 0.00 0.00 2.71
79 80 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
80 81 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
81 82 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
90 91 8.277713 GCTACATTAGTGTCAAAAACGTTCTTA 58.722 33.333 0.00 0.00 39.77 2.10
91 92 7.012044 AGCTACATTAGTGTCAAAAACGTTCTT 59.988 33.333 0.00 0.00 39.77 2.52
92 93 6.482308 AGCTACATTAGTGTCAAAAACGTTCT 59.518 34.615 0.00 0.00 39.77 3.01
93 94 6.656003 AGCTACATTAGTGTCAAAAACGTTC 58.344 36.000 0.00 0.00 39.77 3.95
94 95 6.259167 TGAGCTACATTAGTGTCAAAAACGTT 59.741 34.615 0.00 0.00 39.77 3.99
95 96 5.756347 TGAGCTACATTAGTGTCAAAAACGT 59.244 36.000 0.00 0.00 39.77 3.99
96 97 6.145534 TCTGAGCTACATTAGTGTCAAAAACG 59.854 38.462 0.00 0.00 39.77 3.60
97 98 7.421530 TCTGAGCTACATTAGTGTCAAAAAC 57.578 36.000 0.00 0.00 39.77 2.43
98 99 8.342634 GTTTCTGAGCTACATTAGTGTCAAAAA 58.657 33.333 0.00 0.00 39.77 1.94
99 100 7.307160 CGTTTCTGAGCTACATTAGTGTCAAAA 60.307 37.037 0.00 0.00 39.77 2.44
100 101 6.145534 CGTTTCTGAGCTACATTAGTGTCAAA 59.854 38.462 0.00 0.00 39.77 2.69
101 102 5.633601 CGTTTCTGAGCTACATTAGTGTCAA 59.366 40.000 0.00 0.00 39.77 3.18
102 103 5.161358 CGTTTCTGAGCTACATTAGTGTCA 58.839 41.667 0.00 0.00 39.77 3.58
103 104 4.031878 GCGTTTCTGAGCTACATTAGTGTC 59.968 45.833 0.00 0.00 39.77 3.67
104 105 3.927142 GCGTTTCTGAGCTACATTAGTGT 59.073 43.478 0.00 0.00 42.39 3.55
105 106 4.177026 AGCGTTTCTGAGCTACATTAGTG 58.823 43.478 0.00 0.00 42.60 2.74
106 107 4.158764 AGAGCGTTTCTGAGCTACATTAGT 59.841 41.667 0.00 0.00 44.69 2.24
107 108 4.677584 AGAGCGTTTCTGAGCTACATTAG 58.322 43.478 0.00 0.00 44.69 1.73
108 109 4.720649 AGAGCGTTTCTGAGCTACATTA 57.279 40.909 0.00 0.00 44.69 1.90
109 110 3.601443 AGAGCGTTTCTGAGCTACATT 57.399 42.857 0.00 0.00 44.69 2.71
110 111 3.601443 AAGAGCGTTTCTGAGCTACAT 57.399 42.857 0.00 0.00 44.69 2.29
111 112 4.720649 ATAAGAGCGTTTCTGAGCTACA 57.279 40.909 0.00 0.00 44.69 2.74
112 113 8.855279 CATAATATAAGAGCGTTTCTGAGCTAC 58.145 37.037 0.00 0.00 44.69 3.58
113 114 8.029522 CCATAATATAAGAGCGTTTCTGAGCTA 58.970 37.037 0.00 0.00 44.69 3.32
115 116 6.091441 CCCATAATATAAGAGCGTTTCTGAGC 59.909 42.308 0.00 0.00 35.91 4.26
116 117 7.378966 TCCCATAATATAAGAGCGTTTCTGAG 58.621 38.462 0.00 0.00 35.91 3.35
117 118 7.297936 TCCCATAATATAAGAGCGTTTCTGA 57.702 36.000 0.00 0.00 35.91 3.27
118 119 8.446273 CAATCCCATAATATAAGAGCGTTTCTG 58.554 37.037 0.00 0.00 35.91 3.02
119 120 8.375506 TCAATCCCATAATATAAGAGCGTTTCT 58.624 33.333 0.00 0.00 37.93 2.52
120 121 8.547967 TCAATCCCATAATATAAGAGCGTTTC 57.452 34.615 0.00 0.00 0.00 2.78
121 122 7.607991 CCTCAATCCCATAATATAAGAGCGTTT 59.392 37.037 0.00 0.00 0.00 3.60
122 123 7.106239 CCTCAATCCCATAATATAAGAGCGTT 58.894 38.462 0.00 0.00 0.00 4.84
123 124 6.352222 CCCTCAATCCCATAATATAAGAGCGT 60.352 42.308 0.00 0.00 0.00 5.07
124 125 6.051717 CCCTCAATCCCATAATATAAGAGCG 58.948 44.000 0.00 0.00 0.00 5.03
125 126 7.092668 ACTCCCTCAATCCCATAATATAAGAGC 60.093 40.741 0.00 0.00 0.00 4.09
126 127 8.386012 ACTCCCTCAATCCCATAATATAAGAG 57.614 38.462 0.00 0.00 0.00 2.85
127 128 9.268282 GTACTCCCTCAATCCCATAATATAAGA 57.732 37.037 0.00 0.00 0.00 2.10
128 129 9.046846 TGTACTCCCTCAATCCCATAATATAAG 57.953 37.037 0.00 0.00 0.00 1.73
129 130 8.982471 TGTACTCCCTCAATCCCATAATATAA 57.018 34.615 0.00 0.00 0.00 0.98
130 131 8.992349 CATGTACTCCCTCAATCCCATAATATA 58.008 37.037 0.00 0.00 0.00 0.86
131 132 7.092264 CCATGTACTCCCTCAATCCCATAATAT 60.092 40.741 0.00 0.00 0.00 1.28
132 133 6.215431 CCATGTACTCCCTCAATCCCATAATA 59.785 42.308 0.00 0.00 0.00 0.98
133 134 5.014544 CCATGTACTCCCTCAATCCCATAAT 59.985 44.000 0.00 0.00 0.00 1.28
134 135 4.350816 CCATGTACTCCCTCAATCCCATAA 59.649 45.833 0.00 0.00 0.00 1.90
135 136 3.909995 CCATGTACTCCCTCAATCCCATA 59.090 47.826 0.00 0.00 0.00 2.74
136 137 2.713167 CCATGTACTCCCTCAATCCCAT 59.287 50.000 0.00 0.00 0.00 4.00
137 138 2.126882 CCATGTACTCCCTCAATCCCA 58.873 52.381 0.00 0.00 0.00 4.37
138 139 2.408565 TCCATGTACTCCCTCAATCCC 58.591 52.381 0.00 0.00 0.00 3.85
139 140 4.713792 ATTCCATGTACTCCCTCAATCC 57.286 45.455 0.00 0.00 0.00 3.01
140 141 7.410120 AAAAATTCCATGTACTCCCTCAATC 57.590 36.000 0.00 0.00 0.00 2.67
141 142 8.893563 TTAAAAATTCCATGTACTCCCTCAAT 57.106 30.769 0.00 0.00 0.00 2.57
142 143 8.713708 TTTAAAAATTCCATGTACTCCCTCAA 57.286 30.769 0.00 0.00 0.00 3.02
143 144 8.713708 TTTTAAAAATTCCATGTACTCCCTCA 57.286 30.769 0.00 0.00 0.00 3.86
144 145 8.803235 ACTTTTAAAAATTCCATGTACTCCCTC 58.197 33.333 1.66 0.00 0.00 4.30
145 146 8.585018 CACTTTTAAAAATTCCATGTACTCCCT 58.415 33.333 1.66 0.00 0.00 4.20
146 147 7.330946 GCACTTTTAAAAATTCCATGTACTCCC 59.669 37.037 1.66 0.00 0.00 4.30
147 148 7.870445 TGCACTTTTAAAAATTCCATGTACTCC 59.130 33.333 1.66 0.00 0.00 3.85
148 149 8.810652 TGCACTTTTAAAAATTCCATGTACTC 57.189 30.769 1.66 0.00 0.00 2.59
149 150 9.777297 AATGCACTTTTAAAAATTCCATGTACT 57.223 25.926 1.66 0.00 0.00 2.73
410 413 5.106317 TGAGTCGGAAGCATGGTTTTATTTC 60.106 40.000 12.13 8.21 0.00 2.17
494 500 6.808008 TTGGATTCTTGTGTTGAGATCTTC 57.192 37.500 0.00 0.00 0.00 2.87
503 509 2.513753 TCCGCATTGGATTCTTGTGTT 58.486 42.857 0.00 0.00 43.74 3.32
521 527 4.923281 CGTTCAAACCAGGAATCATTTTCC 59.077 41.667 0.00 0.00 38.86 3.13
527 533 1.974265 TGCGTTCAAACCAGGAATCA 58.026 45.000 0.00 0.00 0.00 2.57
529 535 1.545582 CCATGCGTTCAAACCAGGAAT 59.454 47.619 0.00 0.00 0.00 3.01
533 539 2.507339 AAACCATGCGTTCAAACCAG 57.493 45.000 0.83 0.00 31.78 4.00
534 540 4.386867 TTTAAACCATGCGTTCAAACCA 57.613 36.364 0.83 0.00 31.78 3.67
535 541 5.520649 TCTTTTTAAACCATGCGTTCAAACC 59.479 36.000 0.83 0.00 31.78 3.27
536 542 6.576551 TCTTTTTAAACCATGCGTTCAAAC 57.423 33.333 0.83 0.00 31.78 2.93
539 545 8.756864 GTTTTATCTTTTTAAACCATGCGTTCA 58.243 29.630 0.83 0.00 31.78 3.18
586 592 6.022251 CGTCATTTATCGCAACATGAGTTTTC 60.022 38.462 0.00 0.00 35.28 2.29
617 623 1.237533 CAGTTGGTGCACTGCATGTA 58.762 50.000 17.98 0.00 41.91 2.29
618 624 2.035421 CAGTTGGTGCACTGCATGT 58.965 52.632 17.98 0.00 41.91 3.21
619 625 4.957266 CAGTTGGTGCACTGCATG 57.043 55.556 17.98 7.48 41.91 4.06
624 630 1.451207 TTGCGACAGTTGGTGCACT 60.451 52.632 17.98 0.00 34.69 4.40
625 631 1.298339 GTTGCGACAGTTGGTGCAC 60.298 57.895 8.80 8.80 34.69 4.57
626 632 2.477176 GGTTGCGACAGTTGGTGCA 61.477 57.895 6.39 0.00 33.65 4.57
627 633 2.186826 AGGTTGCGACAGTTGGTGC 61.187 57.895 6.39 0.00 0.00 5.01
659 667 1.454201 TTGGTTTGTTGCAGACGTCA 58.546 45.000 19.50 0.00 0.00 4.35
665 673 3.803778 GGAGACATTTTGGTTTGTTGCAG 59.196 43.478 0.00 0.00 0.00 4.41
666 674 3.736433 CGGAGACATTTTGGTTTGTTGCA 60.736 43.478 0.00 0.00 0.00 4.08
667 675 2.794350 CGGAGACATTTTGGTTTGTTGC 59.206 45.455 0.00 0.00 0.00 4.17
668 676 3.067461 TCCGGAGACATTTTGGTTTGTTG 59.933 43.478 0.00 0.00 0.00 3.33
669 677 3.292460 TCCGGAGACATTTTGGTTTGTT 58.708 40.909 0.00 0.00 0.00 2.83
670 678 2.938838 TCCGGAGACATTTTGGTTTGT 58.061 42.857 0.00 0.00 0.00 2.83
671 679 3.836949 CATCCGGAGACATTTTGGTTTG 58.163 45.455 11.34 0.00 0.00 2.93
672 680 2.231235 GCATCCGGAGACATTTTGGTTT 59.769 45.455 11.34 0.00 0.00 3.27
673 681 1.818674 GCATCCGGAGACATTTTGGTT 59.181 47.619 11.34 0.00 0.00 3.67
674 682 1.271871 TGCATCCGGAGACATTTTGGT 60.272 47.619 11.34 0.00 0.00 3.67
675 683 1.462616 TGCATCCGGAGACATTTTGG 58.537 50.000 11.34 0.00 0.00 3.28
676 684 2.228582 TGTTGCATCCGGAGACATTTTG 59.771 45.455 11.34 1.85 0.00 2.44
677 685 2.513753 TGTTGCATCCGGAGACATTTT 58.486 42.857 11.34 0.00 0.00 1.82
678 686 2.198827 TGTTGCATCCGGAGACATTT 57.801 45.000 11.34 0.00 0.00 2.32
679 687 2.198827 TTGTTGCATCCGGAGACATT 57.801 45.000 11.34 0.00 0.00 2.71
680 688 1.812571 GTTTGTTGCATCCGGAGACAT 59.187 47.619 11.34 0.00 0.00 3.06
681 689 1.234821 GTTTGTTGCATCCGGAGACA 58.765 50.000 11.34 7.82 0.00 3.41
682 690 0.521735 GGTTTGTTGCATCCGGAGAC 59.478 55.000 11.34 4.71 0.00 3.36
683 691 0.109532 TGGTTTGTTGCATCCGGAGA 59.890 50.000 11.34 0.00 0.00 3.71
684 692 0.958091 TTGGTTTGTTGCATCCGGAG 59.042 50.000 11.34 3.17 0.00 4.63
685 693 0.671251 GTTGGTTTGTTGCATCCGGA 59.329 50.000 6.61 6.61 0.00 5.14
686 694 0.387202 TGTTGGTTTGTTGCATCCGG 59.613 50.000 0.00 0.00 0.00 5.14
687 695 2.215907 TTGTTGGTTTGTTGCATCCG 57.784 45.000 0.00 0.00 0.00 4.18
688 696 3.465871 ACATTGTTGGTTTGTTGCATCC 58.534 40.909 0.00 0.00 0.00 3.51
689 697 4.370917 AGACATTGTTGGTTTGTTGCATC 58.629 39.130 0.00 0.00 0.00 3.91
690 698 4.405116 AGACATTGTTGGTTTGTTGCAT 57.595 36.364 0.00 0.00 0.00 3.96
770 779 2.267426 GGTGTTGTGTTTGGTTGCTTC 58.733 47.619 0.00 0.00 0.00 3.86
881 891 1.982938 CGGGAGAAGGAACCGGAGT 60.983 63.158 9.46 0.00 43.69 3.85
891 901 2.117156 CATTGCCTGGCGGGAGAAG 61.117 63.158 18.84 0.00 37.23 2.85
892 902 2.045045 CATTGCCTGGCGGGAGAA 60.045 61.111 18.84 8.21 37.23 2.87
951 967 3.818787 GCCCTTAGTCGTCGGCGA 61.819 66.667 8.66 8.66 45.79 5.54
1161 1186 3.453070 GAGGCTGATGACGGGGAGC 62.453 68.421 0.00 0.00 0.00 4.70
1315 1343 0.106708 TTGTCGCTGAGCTTGGAACT 59.893 50.000 1.78 0.00 0.00 3.01
1456 1486 9.884465 CAACTTCTCCTTTGAGTAAATTACAAG 57.116 33.333 5.89 0.95 39.75 3.16
1516 1546 4.876679 GGCTTAAGCTTCCTAAACCAGTAG 59.123 45.833 25.88 0.00 41.70 2.57
1569 1617 5.975344 CACACTTTGACATGCCATATTGATC 59.025 40.000 0.00 0.00 0.00 2.92
1600 1649 2.425143 ATGAACATAGGCAGGGTGTG 57.575 50.000 0.00 0.00 0.00 3.82
1649 1698 5.072193 AGCAATTCCCTTCCAAAAGTTGATT 59.928 36.000 0.00 0.00 0.00 2.57
1650 1699 4.594491 AGCAATTCCCTTCCAAAAGTTGAT 59.406 37.500 0.00 0.00 0.00 2.57
1651 1700 3.966665 AGCAATTCCCTTCCAAAAGTTGA 59.033 39.130 0.00 0.00 0.00 3.18
1671 1720 3.628032 GCAAGAAAGGGATAACAGGTAGC 59.372 47.826 0.00 0.00 0.00 3.58
1696 1745 1.272490 AGGTACACGATATGGCCGATG 59.728 52.381 0.00 0.00 33.96 3.84
1697 1746 1.629043 AGGTACACGATATGGCCGAT 58.371 50.000 0.00 0.00 33.96 4.18
1816 1866 0.531974 GAGTCCTTTGTGCGACACCA 60.532 55.000 7.38 0.00 32.73 4.17
1822 1872 0.318699 TCGACAGAGTCCTTTGTGCG 60.319 55.000 0.00 0.67 0.00 5.34
1825 1875 3.651803 CTCTTCGACAGAGTCCTTTGT 57.348 47.619 13.34 0.00 43.96 2.83
1873 1923 2.802816 CTGAAGGGTCTTGACAACGAAG 59.197 50.000 3.08 0.00 0.00 3.79
1876 1926 2.135933 GACTGAAGGGTCTTGACAACG 58.864 52.381 3.08 0.00 33.81 4.10
1924 1974 5.049405 CCCAATGCCATTAGACTTTACGATC 60.049 44.000 0.00 0.00 0.00 3.69
2143 2193 7.537715 TCAAGTTTGTCACATATGGCTTAATG 58.462 34.615 7.80 0.00 0.00 1.90
2146 2196 6.939730 TCTTCAAGTTTGTCACATATGGCTTA 59.060 34.615 7.80 0.00 0.00 3.09
2178 2229 0.034896 GAGAACAGCCGACCTTTCCA 59.965 55.000 0.00 0.00 0.00 3.53
2189 2240 3.067320 ACAAGCAAAAGGAAGAGAACAGC 59.933 43.478 0.00 0.00 0.00 4.40
2207 2259 7.305474 ACAACTGAAAGAAAGTAACACACAAG 58.695 34.615 0.00 0.00 37.43 3.16
2219 2271 7.027161 GCACAAAGTTAGACAACTGAAAGAAA 58.973 34.615 0.00 0.00 44.41 2.52
2222 2274 5.879237 TGCACAAAGTTAGACAACTGAAAG 58.121 37.500 0.00 0.00 44.41 2.62
2545 2600 5.372547 ACCAGAAGAATTAAGCCGAAAAC 57.627 39.130 0.00 0.00 0.00 2.43
2550 2605 4.201950 CCATGAACCAGAAGAATTAAGCCG 60.202 45.833 0.00 0.00 0.00 5.52
2585 2640 7.605449 TGTCAATTTCTTGAATTTCCATCCTC 58.395 34.615 0.00 0.00 42.85 3.71
2720 2775 2.085343 AAACCTGTGCCAGCTGGGAT 62.085 55.000 33.46 13.87 40.01 3.85
2739 2794 0.976641 AATCTCGCTCACAGGGTTCA 59.023 50.000 0.00 0.00 0.00 3.18
2778 2833 3.119637 ACAAAAGAAAAGTGTGACACCCG 60.120 43.478 12.81 0.00 34.49 5.28
2798 2853 5.127031 GGAGCCCTGCAGATTTTTAATTACA 59.873 40.000 17.39 0.00 0.00 2.41
2917 2992 3.457380 ACAGAACTGTGGCCATATCATCT 59.543 43.478 9.72 7.37 43.11 2.90
2979 3054 0.812549 GGACTCTCGGGTCTCAGTTC 59.187 60.000 0.00 0.00 36.55 3.01
3012 3087 3.009253 TGGCCTTTCCCGTCTTTACATTA 59.991 43.478 3.32 0.00 0.00 1.90
3016 3091 1.002773 TCTGGCCTTTCCCGTCTTTAC 59.997 52.381 3.32 0.00 0.00 2.01
3066 3141 7.867403 ACTTCAATGCGAGTAATTTGTCAATTT 59.133 29.630 0.00 0.00 34.29 1.82
3115 3190 3.431626 CCTTGAGATAACGTGTGGGCATA 60.432 47.826 0.00 0.00 0.00 3.14
3159 3234 3.372025 GCAGTCCCCAAATAGGTCAGATT 60.372 47.826 0.00 0.00 34.66 2.40
3257 3332 3.441572 GGTGCACTGCAGACTGAATTAAT 59.558 43.478 23.35 0.00 40.08 1.40
3315 3390 1.308047 CACAGCTTGTAGGTTGCACA 58.692 50.000 0.00 0.00 0.00 4.57
3389 3464 5.705609 TTTTGGCTTAAACTCATCTGGAC 57.294 39.130 0.00 0.00 0.00 4.02
3582 3657 5.310451 AGCATGCCATTTCAAAAAGAACAT 58.690 33.333 15.66 0.00 35.56 2.71
3611 3686 5.220710 AGGCGCTCTTGATATTATGACTT 57.779 39.130 7.64 0.00 0.00 3.01
3612 3687 4.881019 AGGCGCTCTTGATATTATGACT 57.119 40.909 7.64 0.00 0.00 3.41
3620 3695 2.988010 ACATGAAGGCGCTCTTGATA 57.012 45.000 14.63 3.46 35.50 2.15
3827 3907 7.480542 CGGAAGGTATTATTTTCAGTTTTGTCG 59.519 37.037 0.00 0.00 0.00 4.35
3910 3990 1.078848 GTGGTGGCAGCTAGGACTG 60.079 63.158 18.53 0.00 40.80 3.51
4004 4086 2.179267 CAGTCGTCGCTGCTGCTA 59.821 61.111 14.03 0.00 36.97 3.49
4005 4087 4.731612 CCAGTCGTCGCTGCTGCT 62.732 66.667 14.03 0.00 36.97 4.24
4009 4091 4.664677 ACACCCAGTCGTCGCTGC 62.665 66.667 10.11 0.00 35.28 5.25
4094 4176 7.318141 GCTAACCTACACTACAAAGATACACA 58.682 38.462 0.00 0.00 0.00 3.72
4116 4198 1.072266 ACCATGGACAAACAGGGCTA 58.928 50.000 21.47 0.00 45.76 3.93
4120 4202 4.216257 CAGTAGAAACCATGGACAAACAGG 59.784 45.833 21.47 0.00 0.00 4.00
4250 4332 3.056107 CGATGGGGTTGACTACTTCTTCA 60.056 47.826 0.00 0.00 0.00 3.02
4259 4341 1.348064 TGAGTTCGATGGGGTTGACT 58.652 50.000 0.00 0.00 0.00 3.41
4356 4438 0.966920 ACTCCAGGTACCAGTTCACG 59.033 55.000 15.94 0.00 0.00 4.35
4477 4559 3.958860 GGAGCCCTGGTGTGCTGT 61.959 66.667 0.42 0.00 38.11 4.40
4581 4663 6.690098 GCTGTGTTGCATGAAGATAGTTATTG 59.310 38.462 0.00 0.00 0.00 1.90
4596 4680 3.041351 CTACGCGGCTGTGTTGCA 61.041 61.111 18.43 0.00 40.00 4.08
4605 4689 5.005586 TGTGTATATGTAAAAACTACGCGGC 59.994 40.000 12.47 0.00 0.00 6.53
4616 4700 7.680442 ACAACTGCACATGTGTATATGTAAA 57.320 32.000 26.01 1.85 39.17 2.01
4703 4789 2.227149 TGTGCTGTATGCTGAGCTTTTG 59.773 45.455 5.83 0.00 43.37 2.44
4704 4790 2.227388 GTGTGCTGTATGCTGAGCTTTT 59.773 45.455 5.83 0.00 43.37 2.27
4738 4824 0.753479 TGGCGATGGTGTTGGTGTTT 60.753 50.000 0.00 0.00 0.00 2.83
4834 4920 2.359107 CGATGGCCACAGCAGTGT 60.359 61.111 8.16 0.00 44.39 3.55
4897 4985 5.602628 AGTCTTTACCTCTGTGTTTCAGAC 58.397 41.667 0.00 0.00 46.77 3.51
4939 5030 6.092807 GCCAGAAACGATTCAGACTAGAAAAT 59.907 38.462 8.22 0.00 38.06 1.82
4946 5037 2.300152 TCTGCCAGAAACGATTCAGACT 59.700 45.455 8.22 0.00 38.06 3.24
4947 5038 2.688507 TCTGCCAGAAACGATTCAGAC 58.311 47.619 8.22 0.00 38.06 3.51
4948 5039 3.401033 TTCTGCCAGAAACGATTCAGA 57.599 42.857 4.27 0.00 38.06 3.27
5151 5393 6.690194 AGAGTCAAGAATGGTAATGCAATC 57.310 37.500 0.00 0.00 0.00 2.67
5191 5433 4.789012 TCATGCCAGAGAATTTTGTTCC 57.211 40.909 0.00 0.00 0.00 3.62
5238 5480 9.461312 AAAAGGATGCATAGTACAGAAAACATA 57.539 29.630 0.00 0.00 0.00 2.29
5239 5481 7.944729 AAAGGATGCATAGTACAGAAAACAT 57.055 32.000 0.00 0.00 0.00 2.71
5657 5902 1.451207 CCACAAATCGGGGCGATGA 60.451 57.895 0.00 0.00 46.30 2.92
5772 6017 4.673441 AGATGATGTACAAGTACGACTGC 58.327 43.478 0.00 0.00 38.85 4.40
5819 6064 4.640201 CCTTGTTCAACTTGAGAAACTCCA 59.360 41.667 0.00 0.00 0.00 3.86
5887 6132 3.341823 CAAAGAGGTATTGAGCACAGCT 58.658 45.455 0.00 0.00 43.88 4.24
5930 6175 2.288395 GCAGCACAAATACCACAAGCTT 60.288 45.455 0.00 0.00 0.00 3.74
5960 6205 6.097554 TCAAAAGTCAAGGCCAAATTAAGTCA 59.902 34.615 5.01 0.00 0.00 3.41
5997 6242 5.248020 TGGTTGAATTATGAAGCCATTTGGT 59.752 36.000 0.00 0.00 37.57 3.67
6017 6262 5.372343 TCATACTACCTGATTGCATGGTT 57.628 39.130 6.53 0.00 35.48 3.67
6020 6265 9.445878 AAATAGATCATACTACCTGATTGCATG 57.554 33.333 0.00 0.00 33.56 4.06
6028 6282 9.057089 GGGTTTCAAAATAGATCATACTACCTG 57.943 37.037 0.00 0.00 0.00 4.00
6076 6330 2.154854 TTAGCTATCATCTGCCGTGC 57.845 50.000 0.00 0.00 0.00 5.34
6112 6366 7.229306 TGGAAGAAATATTACATCTGACATGCC 59.771 37.037 0.00 0.00 0.00 4.40
6164 6418 8.539770 TCAAAACAAGTAAACAAAATGAAGCA 57.460 26.923 0.00 0.00 0.00 3.91
6221 6475 1.131693 GCCGGAACCAATAAAGGAACG 59.868 52.381 5.05 0.00 0.00 3.95
6241 6495 1.130955 GCAAGTCAAACCACGCATTG 58.869 50.000 0.00 0.00 0.00 2.82
6262 6517 8.758633 TGCTAAAGTTACAGTTTCATAGACTC 57.241 34.615 0.00 0.00 0.00 3.36
6308 6565 9.615295 TCATACGATCATTGCATCAAATTATTG 57.385 29.630 0.00 0.00 37.92 1.90
6343 6600 9.433153 TCTCTTGATATTATCAGCATGCTTTAG 57.567 33.333 19.98 7.41 40.94 1.85
6350 6607 7.310547 CCTGACCTCTCTTGATATTATCAGCAT 60.311 40.741 6.48 0.00 40.94 3.79
6361 6618 3.637769 GTCTACCCTGACCTCTCTTGAT 58.362 50.000 0.00 0.00 0.00 2.57
6374 6631 2.112279 TGTCCAGTTTGGTCTACCCT 57.888 50.000 0.00 0.00 39.03 4.34
6396 6653 2.946791 GCCTCTCTTTACGGACTCCTCT 60.947 54.545 0.00 0.00 0.00 3.69
6416 6673 1.133790 CTGTTCATGGCTAGCTTTGGC 59.866 52.381 15.72 9.52 39.06 4.52
6417 6674 1.747355 CCTGTTCATGGCTAGCTTTGG 59.253 52.381 15.72 2.33 0.00 3.28
6419 6676 1.341383 CCCCTGTTCATGGCTAGCTTT 60.341 52.381 15.72 0.00 0.00 3.51
6420 6677 0.257039 CCCCTGTTCATGGCTAGCTT 59.743 55.000 15.72 0.00 0.00 3.74
6422 6679 0.749454 CACCCCTGTTCATGGCTAGC 60.749 60.000 6.04 6.04 0.00 3.42
6432 6711 2.906897 CTTGCACGCACCCCTGTT 60.907 61.111 0.00 0.00 0.00 3.16
6521 6800 5.451354 ACTAAGCCTTTAGTCCCAAACAAA 58.549 37.500 0.00 0.00 44.83 2.83
6645 6930 9.162764 GTCTCTGCAACTAAACCTATATTTTCA 57.837 33.333 0.00 0.00 0.00 2.69
6773 7070 8.100791 TCTTTGTAAGCAAATACAGTACTGGAT 58.899 33.333 26.12 21.10 42.88 3.41
6940 7237 2.821969 CAAATACTCAGCAGCCAACCTT 59.178 45.455 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.