Multiple sequence alignment - TraesCS1B01G349700

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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 TraesCS1B01G349700 chr1B 100.000 3137 0 0 1 3137 580210905 580214041 0.000000e+00 5794.0
1 TraesCS1B01G349700 chr1B 93.941 1601 69 12 503 2099 579943568 579945144 0.000000e+00 2394.0
2 TraesCS1B01G349700 chr1B 95.936 566 23 0 2572 3137 580227318 580227883 0.000000e+00 918.0
3 TraesCS1B01G349700 chr1B 88.387 155 13 5 1 153 127284999 127284848 6.910000e-42 182.0
4 TraesCS1B01G349700 chr1A 92.058 1662 85 16 503 2146 524700233 524701865 0.000000e+00 2294.0
5 TraesCS1B01G349700 chr1A 92.950 1461 81 8 702 2146 522972134 522973588 0.000000e+00 2108.0
6 TraesCS1B01G349700 chr1A 95.401 935 43 0 1212 2146 524286810 524287744 0.000000e+00 1489.0
7 TraesCS1B01G349700 chr1A 90.506 969 57 11 484 1435 524599103 524600053 0.000000e+00 1247.0
8 TraesCS1B01G349700 chr1A 90.302 959 58 11 504 1459 526621648 526622574 0.000000e+00 1223.0
9 TraesCS1B01G349700 chr1A 96.444 703 25 0 1458 2160 526622770 526623472 0.000000e+00 1160.0
10 TraesCS1B01G349700 chr1A 91.642 682 33 5 504 1181 524286148 524286809 0.000000e+00 922.0
11 TraesCS1B01G349700 chr1A 84.211 722 84 14 1433 2137 524600558 524601266 0.000000e+00 675.0
12 TraesCS1B01G349700 chr1A 89.059 457 44 5 2174 2626 524611667 524612121 2.110000e-156 562.0
13 TraesCS1B01G349700 chr1A 87.336 458 50 6 2174 2626 526623455 526623909 4.640000e-143 518.0
14 TraesCS1B01G349700 chr1A 94.785 326 16 1 1835 2160 524611360 524611684 1.000000e-139 507.0
15 TraesCS1B01G349700 chr1A 95.745 141 2 3 373 512 524598961 524599098 1.130000e-54 224.0
16 TraesCS1B01G349700 chr1A 87.402 127 13 3 153 277 524598649 524598774 3.260000e-30 143.0
17 TraesCS1B01G349700 chr1A 93.103 87 5 1 2898 2983 524612121 524612207 3.280000e-25 126.0
18 TraesCS1B01G349700 chr1A 93.023 86 6 0 2898 2983 526623909 526623994 3.280000e-25 126.0
19 TraesCS1B01G349700 chr1A 89.423 104 3 6 552 654 522972037 522972133 1.180000e-24 124.0
20 TraesCS1B01G349700 chr1A 77.326 172 27 8 2964 3134 524699776 524699936 1.200000e-14 91.6
21 TraesCS1B01G349700 chr1D 94.286 980 53 1 1170 2146 427634185 427635164 0.000000e+00 1496.0
22 TraesCS1B01G349700 chr1D 89.072 668 34 11 507 1171 427633249 427633880 0.000000e+00 793.0
23 TraesCS1B01G349700 chr1D 83.521 267 39 5 2633 2897 490055195 490054932 8.690000e-61 244.0
24 TraesCS1B01G349700 chr1D 82.772 267 41 4 2634 2895 411128785 411128519 1.880000e-57 233.0
25 TraesCS1B01G349700 chr5D 83.273 275 42 4 2629 2901 548292766 548292494 1.870000e-62 250.0
26 TraesCS1B01G349700 chr2A 83.459 266 40 3 2634 2898 40316547 40316809 8.690000e-61 244.0
27 TraesCS1B01G349700 chr5B 82.576 264 43 3 2636 2897 642320745 642321007 2.430000e-56 230.0
28 TraesCS1B01G349700 chr4A 83.613 238 35 3 2664 2898 628005297 628005533 1.460000e-53 220.0
29 TraesCS1B01G349700 chr6B 81.250 256 40 8 2645 2897 690419343 690419593 1.910000e-47 200.0
30 TraesCS1B01G349700 chr2B 90.196 153 12 3 1 152 542686091 542686241 2.470000e-46 196.0
31 TraesCS1B01G349700 chr7A 80.460 261 43 8 2643 2897 692979827 692980085 3.190000e-45 193.0
32 TraesCS1B01G349700 chr3D 88.961 154 14 3 1 153 595484744 595484593 1.490000e-43 187.0
33 TraesCS1B01G349700 chr3D 88.636 132 10 4 1 127 80587633 80587502 4.190000e-34 156.0
34 TraesCS1B01G349700 chrUn 85.526 152 10 2 1 151 243149502 243149362 7.010000e-32 148.0
35 TraesCS1B01G349700 chrUn 85.526 152 10 2 1 151 243162375 243162235 7.010000e-32 148.0
36 TraesCS1B01G349700 chrUn 85.526 152 10 2 1 151 270191146 270191286 7.010000e-32 148.0
37 TraesCS1B01G349700 chr3B 85.526 152 10 2 1 151 5867240 5867100 7.010000e-32 148.0
38 TraesCS1B01G349700 chr3B 83.824 68 11 0 2298 2365 828436313 828436246 7.260000e-07 65.8
39 TraesCS1B01G349700 chr7D 90.588 85 5 3 1 84 116985184 116985266 3.310000e-20 110.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G349700 chr1B 580210905 580214041 3136 False 5794.000000 5794 100.000000 1 3137 1 chr1B.!!$F2 3136
1 TraesCS1B01G349700 chr1B 579943568 579945144 1576 False 2394.000000 2394 93.941000 503 2099 1 chr1B.!!$F1 1596
2 TraesCS1B01G349700 chr1B 580227318 580227883 565 False 918.000000 918 95.936000 2572 3137 1 chr1B.!!$F3 565
3 TraesCS1B01G349700 chr1A 524286148 524287744 1596 False 1205.500000 1489 93.521500 504 2146 2 chr1A.!!$F2 1642
4 TraesCS1B01G349700 chr1A 524699776 524701865 2089 False 1192.800000 2294 84.692000 503 3134 2 chr1A.!!$F5 2631
5 TraesCS1B01G349700 chr1A 522972037 522973588 1551 False 1116.000000 2108 91.186500 552 2146 2 chr1A.!!$F1 1594
6 TraesCS1B01G349700 chr1A 526621648 526623994 2346 False 756.750000 1223 91.776250 504 2983 4 chr1A.!!$F6 2479
7 TraesCS1B01G349700 chr1A 524598649 524601266 2617 False 572.250000 1247 89.466000 153 2137 4 chr1A.!!$F3 1984
8 TraesCS1B01G349700 chr1A 524611360 524612207 847 False 398.333333 562 92.315667 1835 2983 3 chr1A.!!$F4 1148
9 TraesCS1B01G349700 chr1D 427633249 427635164 1915 False 1144.500000 1496 91.679000 507 2146 2 chr1D.!!$F1 1639

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
123 124 0.025898 TATGAGCGAACGAGACGACG 59.974 55.0 0.00 0.0 39.31 5.12 F
126 127 0.851198 GAGCGAACGAGACGACGTAC 60.851 60.0 0.00 0.0 45.83 3.67 F
584 735 0.911769 CTGGGTGGAGTCCATTGCTA 59.088 55.0 16.67 0.0 35.28 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1251 1730 0.459899 ACGAGAATGCGCTCATGGTA 59.540 50.000 9.73 0.0 34.56 3.25 R
2113 3328 2.836981 AGAGCTCACTATTGGCTTCTGT 59.163 45.455 17.77 0.0 36.37 3.41 R
2347 3562 0.032813 CTTGGCTGGGGGATCAATGT 60.033 55.000 0.00 0.0 0.00 2.71 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
22 23 3.704566 GGGGTTTATTTGGGGATTGTCTC 59.295 47.826 0.00 0.00 0.00 3.36
24 25 3.380320 GGTTTATTTGGGGATTGTCTCGG 59.620 47.826 0.00 0.00 0.00 4.63
25 26 4.014406 GTTTATTTGGGGATTGTCTCGGT 58.986 43.478 0.00 0.00 0.00 4.69
26 27 2.899303 ATTTGGGGATTGTCTCGGTT 57.101 45.000 0.00 0.00 0.00 4.44
27 28 5.438698 TTATTTGGGGATTGTCTCGGTTA 57.561 39.130 0.00 0.00 0.00 2.85
28 29 3.791953 TTTGGGGATTGTCTCGGTTAA 57.208 42.857 0.00 0.00 0.00 2.01
30 31 5.438698 TTTGGGGATTGTCTCGGTTAATA 57.561 39.130 0.00 0.00 0.00 0.98
31 32 5.438698 TTGGGGATTGTCTCGGTTAATAA 57.561 39.130 0.00 0.00 0.00 1.40
32 33 5.438698 TGGGGATTGTCTCGGTTAATAAA 57.561 39.130 0.00 0.00 0.00 1.40
33 34 5.433526 TGGGGATTGTCTCGGTTAATAAAG 58.566 41.667 0.00 0.00 0.00 1.85
34 35 5.190132 TGGGGATTGTCTCGGTTAATAAAGA 59.810 40.000 0.00 0.00 0.00 2.52
35 36 6.117488 GGGGATTGTCTCGGTTAATAAAGAA 58.883 40.000 0.00 0.00 0.00 2.52
36 37 6.600427 GGGGATTGTCTCGGTTAATAAAGAAA 59.400 38.462 0.00 0.00 0.00 2.52
37 38 7.121611 GGGGATTGTCTCGGTTAATAAAGAAAA 59.878 37.037 0.00 0.00 0.00 2.29
38 39 8.683615 GGGATTGTCTCGGTTAATAAAGAAAAT 58.316 33.333 0.00 0.00 30.18 1.82
65 66 1.616159 AAACGGTGAAAGTGGGATGG 58.384 50.000 0.00 0.00 0.00 3.51
66 67 0.251165 AACGGTGAAAGTGGGATGGG 60.251 55.000 0.00 0.00 0.00 4.00
67 68 1.378514 CGGTGAAAGTGGGATGGGG 60.379 63.158 0.00 0.00 0.00 4.96
68 69 1.774300 GGTGAAAGTGGGATGGGGT 59.226 57.895 0.00 0.00 0.00 4.95
69 70 0.323451 GGTGAAAGTGGGATGGGGTC 60.323 60.000 0.00 0.00 0.00 4.46
70 71 0.676782 GTGAAAGTGGGATGGGGTCG 60.677 60.000 0.00 0.00 0.00 4.79
72 73 0.107654 GAAAGTGGGATGGGGTCGAG 60.108 60.000 0.00 0.00 0.00 4.04
73 74 1.562672 AAAGTGGGATGGGGTCGAGG 61.563 60.000 0.00 0.00 0.00 4.63
74 75 3.480133 GTGGGATGGGGTCGAGGG 61.480 72.222 0.00 0.00 0.00 4.30
75 76 4.815973 TGGGATGGGGTCGAGGGG 62.816 72.222 0.00 0.00 0.00 4.79
76 77 4.817909 GGGATGGGGTCGAGGGGT 62.818 72.222 0.00 0.00 0.00 4.95
77 78 2.284493 GGATGGGGTCGAGGGGTA 59.716 66.667 0.00 0.00 0.00 3.69
78 79 1.837499 GGATGGGGTCGAGGGGTAG 60.837 68.421 0.00 0.00 0.00 3.18
80 81 4.791069 TGGGGTCGAGGGGTAGCC 62.791 72.222 1.07 1.07 0.00 3.93
81 82 4.477119 GGGGTCGAGGGGTAGCCT 62.477 72.222 11.48 0.00 33.67 4.58
83 84 2.279408 GGTCGAGGGGTAGCCTCT 59.721 66.667 11.48 6.29 36.82 3.69
89 90 2.827715 AGGGGTAGCCTCTCATTCG 58.172 57.895 11.48 0.00 17.07 3.34
90 91 0.261991 AGGGGTAGCCTCTCATTCGA 59.738 55.000 11.48 0.00 17.07 3.71
91 92 1.133009 AGGGGTAGCCTCTCATTCGAT 60.133 52.381 11.48 0.00 17.07 3.59
93 94 1.001406 GGGTAGCCTCTCATTCGATGG 59.999 57.143 2.95 0.00 0.00 3.51
94 95 1.001406 GGTAGCCTCTCATTCGATGGG 59.999 57.143 0.00 0.00 0.00 4.00
95 96 1.964223 GTAGCCTCTCATTCGATGGGA 59.036 52.381 0.00 0.00 37.45 4.37
100 101 0.264657 TCTCATTCGATGGGAGGGGA 59.735 55.000 8.17 0.00 34.11 4.81
101 102 0.683973 CTCATTCGATGGGAGGGGAG 59.316 60.000 0.00 0.00 30.24 4.30
102 103 0.764369 TCATTCGATGGGAGGGGAGG 60.764 60.000 0.00 0.00 0.00 4.30
103 104 1.462238 ATTCGATGGGAGGGGAGGG 60.462 63.158 0.00 0.00 0.00 4.30
104 105 2.271493 ATTCGATGGGAGGGGAGGGT 62.271 60.000 0.00 0.00 0.00 4.34
106 107 1.158705 CGATGGGAGGGGAGGGTAT 59.841 63.158 0.00 0.00 0.00 2.73
107 108 1.194781 CGATGGGAGGGGAGGGTATG 61.195 65.000 0.00 0.00 0.00 2.39
108 109 0.193574 GATGGGAGGGGAGGGTATGA 59.806 60.000 0.00 0.00 0.00 2.15
109 110 0.194587 ATGGGAGGGGAGGGTATGAG 59.805 60.000 0.00 0.00 0.00 2.90
111 112 2.210711 GGAGGGGAGGGTATGAGCG 61.211 68.421 0.00 0.00 0.00 5.03
112 113 1.152525 GAGGGGAGGGTATGAGCGA 60.153 63.158 0.00 0.00 0.00 4.93
113 114 0.759436 GAGGGGAGGGTATGAGCGAA 60.759 60.000 0.00 0.00 0.00 4.70
114 115 1.049289 AGGGGAGGGTATGAGCGAAC 61.049 60.000 0.00 0.00 0.00 3.95
115 116 1.067582 GGGAGGGTATGAGCGAACG 59.932 63.158 0.00 0.00 0.00 3.95
116 117 1.389609 GGGAGGGTATGAGCGAACGA 61.390 60.000 0.00 0.00 0.00 3.85
117 118 0.030908 GGAGGGTATGAGCGAACGAG 59.969 60.000 0.00 0.00 0.00 4.18
118 119 1.022735 GAGGGTATGAGCGAACGAGA 58.977 55.000 0.00 0.00 0.00 4.04
119 120 0.739561 AGGGTATGAGCGAACGAGAC 59.260 55.000 0.00 0.00 0.00 3.36
120 121 0.591741 GGGTATGAGCGAACGAGACG 60.592 60.000 0.00 0.00 0.00 4.18
121 122 0.376152 GGTATGAGCGAACGAGACGA 59.624 55.000 0.00 0.00 0.00 4.20
122 123 1.454722 GTATGAGCGAACGAGACGAC 58.545 55.000 0.00 0.00 0.00 4.34
123 124 0.025898 TATGAGCGAACGAGACGACG 59.974 55.000 0.00 0.00 39.31 5.12
125 126 1.284297 TGAGCGAACGAGACGACGTA 61.284 55.000 0.00 0.00 45.83 3.57
126 127 0.851198 GAGCGAACGAGACGACGTAC 60.851 60.000 0.00 0.00 45.83 3.67
129 130 1.267038 GCGAACGAGACGACGTACATA 60.267 52.381 0.00 0.00 45.83 2.29
130 131 2.348833 CGAACGAGACGACGTACATAC 58.651 52.381 0.00 0.00 45.83 2.39
132 133 3.340552 GAACGAGACGACGTACATACTG 58.659 50.000 0.00 0.00 45.83 2.74
133 134 2.610433 ACGAGACGACGTACATACTGA 58.390 47.619 0.00 0.00 44.72 3.41
134 135 2.602211 ACGAGACGACGTACATACTGAG 59.398 50.000 0.00 0.00 44.72 3.35
135 136 2.856557 CGAGACGACGTACATACTGAGA 59.143 50.000 0.00 0.00 0.00 3.27
136 137 3.301707 CGAGACGACGTACATACTGAGAC 60.302 52.174 0.00 0.00 0.00 3.36
137 138 3.593096 AGACGACGTACATACTGAGACA 58.407 45.455 0.00 0.00 0.00 3.41
138 139 4.190001 AGACGACGTACATACTGAGACAT 58.810 43.478 0.00 0.00 0.00 3.06
139 140 4.634883 AGACGACGTACATACTGAGACATT 59.365 41.667 0.00 0.00 0.00 2.71
141 142 6.018913 AGACGACGTACATACTGAGACATTAG 60.019 42.308 0.00 0.00 0.00 1.73
142 143 5.007430 ACGACGTACATACTGAGACATTAGG 59.993 44.000 0.00 0.00 0.00 2.69
143 144 5.235831 CGACGTACATACTGAGACATTAGGA 59.764 44.000 0.00 0.00 0.00 2.94
145 146 7.520131 CGACGTACATACTGAGACATTAGGAAT 60.520 40.741 0.00 0.00 0.00 3.01
148 149 9.000486 CGTACATACTGAGACATTAGGAATAGA 58.000 37.037 0.00 0.00 0.00 1.98
155 156 9.875708 ACTGAGACATTAGGAATAGAGATAGTT 57.124 33.333 0.00 0.00 0.00 2.24
202 204 9.973661 TTTACACTAGGTAGTACTATAACACCA 57.026 33.333 13.09 0.81 34.13 4.17
210 212 8.989131 AGGTAGTACTATAACACCATGACATTT 58.011 33.333 13.09 0.00 0.00 2.32
243 245 5.128827 TGTTCTATGTTAGAGGATCCGCTTT 59.871 40.000 23.89 8.91 35.96 3.51
245 247 5.601662 TCTATGTTAGAGGATCCGCTTTTG 58.398 41.667 23.89 8.44 33.66 2.44
282 284 3.977134 AGTGACTACTGGTAGACGAGA 57.023 47.619 13.83 0.00 35.34 4.04
283 285 4.283363 AGTGACTACTGGTAGACGAGAA 57.717 45.455 13.83 0.00 35.34 2.87
284 286 4.002316 AGTGACTACTGGTAGACGAGAAC 58.998 47.826 13.83 3.45 35.34 3.01
285 287 3.750130 GTGACTACTGGTAGACGAGAACA 59.250 47.826 13.83 1.65 36.97 3.18
286 288 4.214971 GTGACTACTGGTAGACGAGAACAA 59.785 45.833 13.83 0.00 36.97 2.83
287 289 4.214971 TGACTACTGGTAGACGAGAACAAC 59.785 45.833 13.83 0.00 36.97 3.32
288 290 4.139786 ACTACTGGTAGACGAGAACAACA 58.860 43.478 13.83 0.00 36.97 3.33
294 296 1.420430 AGACGAGAACAACAAGGGGA 58.580 50.000 0.00 0.00 0.00 4.81
295 297 1.978580 AGACGAGAACAACAAGGGGAT 59.021 47.619 0.00 0.00 0.00 3.85
296 298 2.372172 AGACGAGAACAACAAGGGGATT 59.628 45.455 0.00 0.00 0.00 3.01
311 429 0.954452 GGATTGGGATGAATCGGCAC 59.046 55.000 0.00 0.00 33.75 5.01
312 430 1.679139 GATTGGGATGAATCGGCACA 58.321 50.000 0.00 0.00 0.00 4.57
313 431 2.023673 GATTGGGATGAATCGGCACAA 58.976 47.619 0.00 0.00 0.00 3.33
314 432 1.916506 TTGGGATGAATCGGCACAAA 58.083 45.000 0.00 0.00 0.00 2.83
315 433 1.916506 TGGGATGAATCGGCACAAAA 58.083 45.000 0.00 0.00 0.00 2.44
318 436 1.818674 GGATGAATCGGCACAAAAGGT 59.181 47.619 0.00 0.00 0.00 3.50
418 536 4.236724 GCTCGAGAGCGCCTAATC 57.763 61.111 18.75 0.00 45.29 1.75
419 537 1.727723 GCTCGAGAGCGCCTAATCG 60.728 63.158 18.75 9.40 45.29 3.34
517 668 5.242838 AGTCCATTGCTAAAACAAATCGGAA 59.757 36.000 0.00 0.00 31.92 4.30
571 722 2.681064 CACCATTGGCCCTGGGTG 60.681 66.667 21.92 20.34 44.17 4.61
572 723 3.996621 ACCATTGGCCCTGGGTGG 61.997 66.667 21.92 16.07 38.14 4.61
574 725 2.043652 CATTGGCCCTGGGTGGAG 60.044 66.667 15.56 0.00 38.35 3.86
575 726 2.535317 ATTGGCCCTGGGTGGAGT 60.535 61.111 15.56 0.00 38.35 3.85
576 727 2.616458 ATTGGCCCTGGGTGGAGTC 61.616 63.158 15.56 0.00 38.35 3.36
579 730 3.017581 GCCCTGGGTGGAGTCCAT 61.018 66.667 16.67 0.00 35.28 3.41
580 731 2.616458 GCCCTGGGTGGAGTCCATT 61.616 63.158 16.67 0.00 35.28 3.16
581 732 1.304282 CCCTGGGTGGAGTCCATTG 59.696 63.158 16.67 5.96 35.28 2.82
582 733 1.379044 CCTGGGTGGAGTCCATTGC 60.379 63.158 16.67 1.96 35.28 3.56
583 734 1.687612 CTGGGTGGAGTCCATTGCT 59.312 57.895 16.67 0.00 35.28 3.91
584 735 0.911769 CTGGGTGGAGTCCATTGCTA 59.088 55.000 16.67 0.00 35.28 3.49
585 736 1.492176 CTGGGTGGAGTCCATTGCTAT 59.508 52.381 16.67 0.00 35.28 2.97
586 737 2.705658 CTGGGTGGAGTCCATTGCTATA 59.294 50.000 16.67 0.00 35.28 1.31
587 738 3.326521 TGGGTGGAGTCCATTGCTATAT 58.673 45.455 16.67 0.00 35.28 0.86
902 1060 1.798368 CGCTTCGTTGACGGCTATCG 61.798 60.000 3.48 0.00 45.88 2.92
960 1118 2.291605 GGGCAAGATCCAAGGTAACCTT 60.292 50.000 0.00 0.00 45.88 3.50
1164 1325 1.139256 TCGCCACACTTTGAGGTGTTA 59.861 47.619 0.00 0.00 46.71 2.41
1251 1730 4.853142 TGGCCTCCGTCGCCCTAT 62.853 66.667 3.32 0.00 46.48 2.57
2154 3369 5.232414 GCTCTAGAATGTATTGACGTTGGAC 59.768 44.000 0.00 0.00 34.83 4.02
2160 3375 4.345859 TGTATTGACGTTGGACTCCTTT 57.654 40.909 0.00 0.00 0.00 3.11
2161 3376 4.710324 TGTATTGACGTTGGACTCCTTTT 58.290 39.130 0.00 0.00 0.00 2.27
2162 3377 5.856156 TGTATTGACGTTGGACTCCTTTTA 58.144 37.500 0.00 0.00 0.00 1.52
2163 3378 6.469410 TGTATTGACGTTGGACTCCTTTTAT 58.531 36.000 0.00 0.00 0.00 1.40
2164 3379 6.938030 TGTATTGACGTTGGACTCCTTTTATT 59.062 34.615 0.00 0.00 0.00 1.40
2165 3380 6.894339 ATTGACGTTGGACTCCTTTTATTT 57.106 33.333 0.00 0.00 0.00 1.40
2166 3381 7.989416 ATTGACGTTGGACTCCTTTTATTTA 57.011 32.000 0.00 0.00 0.00 1.40
2167 3382 7.804843 TTGACGTTGGACTCCTTTTATTTAA 57.195 32.000 0.00 0.00 0.00 1.52
2168 3383 7.429636 TGACGTTGGACTCCTTTTATTTAAG 57.570 36.000 0.00 0.00 0.00 1.85
2169 3384 6.072893 TGACGTTGGACTCCTTTTATTTAAGC 60.073 38.462 0.00 0.00 0.00 3.09
2170 3385 6.002082 ACGTTGGACTCCTTTTATTTAAGCT 58.998 36.000 0.00 0.00 0.00 3.74
2171 3386 6.148976 ACGTTGGACTCCTTTTATTTAAGCTC 59.851 38.462 0.00 0.00 0.00 4.09
2172 3387 6.148811 CGTTGGACTCCTTTTATTTAAGCTCA 59.851 38.462 0.00 0.00 0.00 4.26
2173 3388 7.308348 CGTTGGACTCCTTTTATTTAAGCTCAA 60.308 37.037 0.00 0.00 0.00 3.02
2174 3389 8.523658 GTTGGACTCCTTTTATTTAAGCTCAAT 58.476 33.333 0.00 0.00 0.00 2.57
2175 3390 8.650143 TGGACTCCTTTTATTTAAGCTCAATT 57.350 30.769 0.00 0.00 0.00 2.32
2176 3391 9.088987 TGGACTCCTTTTATTTAAGCTCAATTT 57.911 29.630 0.00 0.00 0.00 1.82
2186 3401 9.528489 TTATTTAAGCTCAATTTAGGTTGGACT 57.472 29.630 13.09 1.39 37.72 3.85
2187 3402 7.448748 TTTAAGCTCAATTTAGGTTGGACTC 57.551 36.000 13.09 0.00 37.72 3.36
2188 3403 3.956744 AGCTCAATTTAGGTTGGACTCC 58.043 45.455 0.00 0.00 0.00 3.85
2189 3404 3.589288 AGCTCAATTTAGGTTGGACTCCT 59.411 43.478 0.00 0.00 38.91 3.69
2190 3405 4.043435 AGCTCAATTTAGGTTGGACTCCTT 59.957 41.667 0.00 0.00 36.60 3.36
2196 3411 5.382664 TTTAGGTTGGACTCCTTGACTTT 57.617 39.130 0.00 0.00 36.60 2.66
2213 3428 7.924412 CCTTGACTTTCATATGCAAGCATATTT 59.076 33.333 21.47 3.89 44.49 1.40
2282 3497 2.268076 GCGTGGCACAATTGGAGGT 61.268 57.895 19.09 0.00 44.16 3.85
2290 3505 0.324645 ACAATTGGAGGTGGCCCATC 60.325 55.000 10.83 0.00 33.04 3.51
2316 3531 0.034670 ATTGGGTCTCTGCAGAAGCC 60.035 55.000 26.68 26.68 41.13 4.35
2318 3533 2.650116 GGGTCTCTGCAGAAGCCGA 61.650 63.158 18.85 8.63 41.13 5.54
2347 3562 0.321671 CTCTGGAGAGGCACCGAAAA 59.678 55.000 0.00 0.00 38.48 2.29
2351 3566 1.202879 TGGAGAGGCACCGAAAACATT 60.203 47.619 0.00 0.00 0.00 2.71
2358 3573 1.135112 GCACCGAAAACATTGATCCCC 60.135 52.381 0.00 0.00 0.00 4.81
2376 3591 1.147824 CCAGCCAAGCATCGATCCT 59.852 57.895 0.00 0.00 0.00 3.24
2387 3602 4.521146 AGCATCGATCCTTGATGTTTCTT 58.479 39.130 0.00 0.00 44.02 2.52
2417 3632 4.627467 ACTATTCTCATTGCTCGTTGACAC 59.373 41.667 0.00 0.00 0.00 3.67
2427 3642 2.167900 GCTCGTTGACACCCCTACTATT 59.832 50.000 0.00 0.00 0.00 1.73
2455 3670 7.276878 TGTTAACAGTATACATCACGACCAATG 59.723 37.037 3.59 0.00 0.00 2.82
2461 3676 7.438160 CAGTATACATCACGACCAATGTTGTAT 59.562 37.037 5.50 11.43 41.99 2.29
2469 3684 3.938963 CGACCAATGTTGTATGGCTACTT 59.061 43.478 0.00 0.00 40.51 2.24
2472 3687 3.381272 CCAATGTTGTATGGCTACTTGGG 59.619 47.826 0.00 0.00 32.97 4.12
2480 3695 2.757894 TGGCTACTTGGGTTTGGAAA 57.242 45.000 0.00 0.00 0.00 3.13
2481 3696 3.252554 TGGCTACTTGGGTTTGGAAAT 57.747 42.857 0.00 0.00 0.00 2.17
2482 3697 4.390129 TGGCTACTTGGGTTTGGAAATA 57.610 40.909 0.00 0.00 0.00 1.40
2483 3698 4.083565 TGGCTACTTGGGTTTGGAAATAC 58.916 43.478 0.00 0.00 0.00 1.89
2494 3710 5.047188 GGTTTGGAAATACAGTGTTTGGTG 58.953 41.667 0.00 0.00 0.00 4.17
2495 3711 5.394773 GGTTTGGAAATACAGTGTTTGGTGT 60.395 40.000 0.00 0.00 0.00 4.16
2501 3717 1.261480 ACAGTGTTTGGTGTTGGCAA 58.739 45.000 0.00 0.00 0.00 4.52
2503 3719 2.235898 ACAGTGTTTGGTGTTGGCAATT 59.764 40.909 1.92 0.00 0.00 2.32
2505 3721 3.688673 CAGTGTTTGGTGTTGGCAATTTT 59.311 39.130 1.92 0.00 0.00 1.82
2550 3768 4.824537 TCTATTGTAGTTGGCTTGTTGCAA 59.175 37.500 0.00 0.00 45.15 4.08
2565 3783 5.415415 TGTTGCAATAAACAAAATGGCAC 57.585 34.783 0.59 0.00 37.12 5.01
2569 3787 7.117523 TGTTGCAATAAACAAAATGGCACTATC 59.882 33.333 0.59 0.00 37.12 2.08
2594 3812 7.014134 TCTGGAAGCAAAGTTTCATATTGTTGA 59.986 33.333 0.00 0.00 0.00 3.18
2628 3846 0.526524 TTTTGTTGGAGCCAAACGCG 60.527 50.000 3.53 3.53 44.76 6.01
2841 4059 9.434420 TTCTGAAATATGCGAAATTTTGGAAAT 57.566 25.926 3.50 0.00 0.00 2.17
2877 4095 5.514659 GGATGGGGTCCAAAATCATTTTGTT 60.515 40.000 19.35 0.00 46.53 2.83
2906 4124 7.411804 CGAAATTAAAAACCTTGCATGTGATCC 60.412 37.037 0.00 0.00 0.00 3.36
2952 4170 8.908903 TGGAAACAAACAATAGTACATTGAAGT 58.091 29.630 18.72 12.70 37.44 3.01
3025 4244 7.581011 AGGTTAAAGCAAATTTTAATCAGCG 57.419 32.000 4.82 0.00 36.52 5.18
3038 4257 5.888691 TTAATCAGCGTGGAAGCAAAATA 57.111 34.783 0.00 0.00 40.15 1.40
3045 4264 2.817258 CGTGGAAGCAAAATAACCCAGA 59.183 45.455 0.00 0.00 0.00 3.86
3081 4300 4.857871 TGATCTGCGTAGTAATGCAAAC 57.142 40.909 0.00 0.00 46.75 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.704566 GAGACAATCCCCAAATAAACCCC 59.295 47.826 0.00 0.00 0.00 4.95
2 3 3.380320 CCGAGACAATCCCCAAATAAACC 59.620 47.826 0.00 0.00 0.00 3.27
3 4 4.014406 ACCGAGACAATCCCCAAATAAAC 58.986 43.478 0.00 0.00 0.00 2.01
46 47 1.616159 CCATCCCACTTTCACCGTTT 58.384 50.000 0.00 0.00 0.00 3.60
47 48 0.251165 CCCATCCCACTTTCACCGTT 60.251 55.000 0.00 0.00 0.00 4.44
49 50 1.378514 CCCCATCCCACTTTCACCG 60.379 63.158 0.00 0.00 0.00 4.94
50 51 0.323451 GACCCCATCCCACTTTCACC 60.323 60.000 0.00 0.00 0.00 4.02
51 52 0.676782 CGACCCCATCCCACTTTCAC 60.677 60.000 0.00 0.00 0.00 3.18
53 54 0.107654 CTCGACCCCATCCCACTTTC 60.108 60.000 0.00 0.00 0.00 2.62
54 55 1.562672 CCTCGACCCCATCCCACTTT 61.563 60.000 0.00 0.00 0.00 2.66
57 58 3.480133 CCCTCGACCCCATCCCAC 61.480 72.222 0.00 0.00 0.00 4.61
58 59 4.815973 CCCCTCGACCCCATCCCA 62.816 72.222 0.00 0.00 0.00 4.37
59 60 3.399911 TACCCCTCGACCCCATCCC 62.400 68.421 0.00 0.00 0.00 3.85
60 61 1.837499 CTACCCCTCGACCCCATCC 60.837 68.421 0.00 0.00 0.00 3.51
61 62 2.508751 GCTACCCCTCGACCCCATC 61.509 68.421 0.00 0.00 0.00 3.51
72 73 1.001406 CATCGAATGAGAGGCTACCCC 59.999 57.143 0.00 0.00 0.00 4.95
73 74 1.001406 CCATCGAATGAGAGGCTACCC 59.999 57.143 0.00 0.00 0.00 3.69
74 75 1.001406 CCCATCGAATGAGAGGCTACC 59.999 57.143 0.00 0.00 0.00 3.18
75 76 1.964223 TCCCATCGAATGAGAGGCTAC 59.036 52.381 0.00 0.00 0.00 3.58
76 77 2.242926 CTCCCATCGAATGAGAGGCTA 58.757 52.381 0.00 0.00 32.15 3.93
77 78 1.047002 CTCCCATCGAATGAGAGGCT 58.953 55.000 0.00 0.00 32.15 4.58
78 79 0.034616 CCTCCCATCGAATGAGAGGC 59.965 60.000 10.75 0.00 46.27 4.70
80 81 0.683973 CCCCTCCCATCGAATGAGAG 59.316 60.000 9.91 5.45 35.18 3.20
81 82 0.264657 TCCCCTCCCATCGAATGAGA 59.735 55.000 9.91 0.00 0.00 3.27
83 84 0.764369 CCTCCCCTCCCATCGAATGA 60.764 60.000 0.00 0.00 0.00 2.57
84 85 1.757306 CCTCCCCTCCCATCGAATG 59.243 63.158 0.00 0.00 0.00 2.67
87 88 1.377053 ATACCCTCCCCTCCCATCGA 61.377 60.000 0.00 0.00 0.00 3.59
89 90 0.193574 TCATACCCTCCCCTCCCATC 59.806 60.000 0.00 0.00 0.00 3.51
90 91 0.194587 CTCATACCCTCCCCTCCCAT 59.805 60.000 0.00 0.00 0.00 4.00
91 92 1.632164 CTCATACCCTCCCCTCCCA 59.368 63.158 0.00 0.00 0.00 4.37
93 94 2.210711 CGCTCATACCCTCCCCTCC 61.211 68.421 0.00 0.00 0.00 4.30
94 95 0.759436 TTCGCTCATACCCTCCCCTC 60.759 60.000 0.00 0.00 0.00 4.30
95 96 1.049289 GTTCGCTCATACCCTCCCCT 61.049 60.000 0.00 0.00 0.00 4.79
97 98 1.067582 CGTTCGCTCATACCCTCCC 59.932 63.158 0.00 0.00 0.00 4.30
98 99 0.030908 CTCGTTCGCTCATACCCTCC 59.969 60.000 0.00 0.00 0.00 4.30
100 101 0.739561 GTCTCGTTCGCTCATACCCT 59.260 55.000 0.00 0.00 0.00 4.34
101 102 0.591741 CGTCTCGTTCGCTCATACCC 60.592 60.000 0.00 0.00 0.00 3.69
102 103 0.376152 TCGTCTCGTTCGCTCATACC 59.624 55.000 0.00 0.00 0.00 2.73
103 104 1.454722 GTCGTCTCGTTCGCTCATAC 58.545 55.000 0.00 0.00 0.00 2.39
104 105 0.025898 CGTCGTCTCGTTCGCTCATA 59.974 55.000 0.00 0.00 0.00 2.15
106 107 1.284297 TACGTCGTCTCGTTCGCTCA 61.284 55.000 0.00 0.00 43.80 4.26
107 108 0.851198 GTACGTCGTCTCGTTCGCTC 60.851 60.000 0.00 0.00 43.80 5.03
108 109 1.131420 GTACGTCGTCTCGTTCGCT 59.869 57.895 0.00 0.00 43.80 4.93
109 110 0.519999 ATGTACGTCGTCTCGTTCGC 60.520 55.000 0.00 2.33 43.80 4.70
111 112 3.061295 TCAGTATGTACGTCGTCTCGTTC 59.939 47.826 0.00 0.00 39.00 3.95
112 113 2.995939 TCAGTATGTACGTCGTCTCGTT 59.004 45.455 0.00 0.00 39.00 3.85
113 114 2.602211 CTCAGTATGTACGTCGTCTCGT 59.398 50.000 0.00 0.71 40.52 4.18
114 115 2.856557 TCTCAGTATGTACGTCGTCTCG 59.143 50.000 0.00 0.00 37.40 4.04
115 116 3.615937 TGTCTCAGTATGTACGTCGTCTC 59.384 47.826 0.00 0.00 37.40 3.36
116 117 3.593096 TGTCTCAGTATGTACGTCGTCT 58.407 45.455 0.00 0.00 37.40 4.18
117 118 4.533225 ATGTCTCAGTATGTACGTCGTC 57.467 45.455 0.00 0.00 37.40 4.20
118 119 4.959596 AATGTCTCAGTATGTACGTCGT 57.040 40.909 2.21 2.21 37.40 4.34
119 120 5.235831 TCCTAATGTCTCAGTATGTACGTCG 59.764 44.000 0.00 0.00 37.40 5.12
120 121 6.615264 TCCTAATGTCTCAGTATGTACGTC 57.385 41.667 0.00 0.00 37.40 4.34
121 122 7.584122 ATTCCTAATGTCTCAGTATGTACGT 57.416 36.000 0.00 0.00 37.40 3.57
122 123 9.000486 TCTATTCCTAATGTCTCAGTATGTACG 58.000 37.037 0.00 0.00 37.40 3.67
125 126 9.821240 ATCTCTATTCCTAATGTCTCAGTATGT 57.179 33.333 0.00 0.00 37.40 2.29
129 130 9.875708 AACTATCTCTATTCCTAATGTCTCAGT 57.124 33.333 0.00 0.00 0.00 3.41
192 194 8.954950 AGAGAAGAAATGTCATGGTGTTATAG 57.045 34.615 0.00 0.00 0.00 1.31
243 245 2.031465 GCGTTCCTCGTTCCCCAA 59.969 61.111 0.00 0.00 42.13 4.12
245 247 2.031465 TTGCGTTCCTCGTTCCCC 59.969 61.111 0.00 0.00 42.13 4.81
251 253 1.068472 AGTAGTCACTTGCGTTCCTCG 60.068 52.381 0.00 0.00 43.12 4.63
269 271 3.243771 CCTTGTTGTTCTCGTCTACCAGT 60.244 47.826 0.00 0.00 0.00 4.00
274 276 2.600790 TCCCCTTGTTGTTCTCGTCTA 58.399 47.619 0.00 0.00 0.00 2.59
275 277 1.420430 TCCCCTTGTTGTTCTCGTCT 58.580 50.000 0.00 0.00 0.00 4.18
276 278 2.474410 ATCCCCTTGTTGTTCTCGTC 57.526 50.000 0.00 0.00 0.00 4.20
277 279 2.504367 CAATCCCCTTGTTGTTCTCGT 58.496 47.619 0.00 0.00 0.00 4.18
282 284 2.111613 TCATCCCAATCCCCTTGTTGTT 59.888 45.455 0.00 0.00 32.61 2.83
283 285 1.715931 TCATCCCAATCCCCTTGTTGT 59.284 47.619 0.00 0.00 32.61 3.32
284 286 2.530460 TCATCCCAATCCCCTTGTTG 57.470 50.000 0.00 0.00 32.61 3.33
285 287 3.646534 GATTCATCCCAATCCCCTTGTT 58.353 45.455 0.00 0.00 32.61 2.83
286 288 2.423373 CGATTCATCCCAATCCCCTTGT 60.423 50.000 0.00 0.00 32.61 3.16
287 289 2.233271 CGATTCATCCCAATCCCCTTG 58.767 52.381 0.00 0.00 30.03 3.61
288 290 1.145738 CCGATTCATCCCAATCCCCTT 59.854 52.381 0.00 0.00 30.03 3.95
294 296 2.142356 TTGTGCCGATTCATCCCAAT 57.858 45.000 0.00 0.00 0.00 3.16
295 297 1.916506 TTTGTGCCGATTCATCCCAA 58.083 45.000 0.00 0.00 0.00 4.12
296 298 1.818060 CTTTTGTGCCGATTCATCCCA 59.182 47.619 0.00 0.00 0.00 4.37
318 436 0.730265 GAAAACGACACACAGGCACA 59.270 50.000 0.00 0.00 0.00 4.57
319 437 1.014352 AGAAAACGACACACAGGCAC 58.986 50.000 0.00 0.00 0.00 5.01
321 439 1.295792 TCAGAAAACGACACACAGGC 58.704 50.000 0.00 0.00 0.00 4.85
351 469 6.606234 TCGATAGAGAGGCGCTATAATTAG 57.394 41.667 7.64 0.00 42.67 1.73
427 545 1.077787 CCCCCAAACGCTGCATAGA 60.078 57.895 0.00 0.00 0.00 1.98
517 668 4.138487 AGAGTTCGTTCCAGTTTCAAGT 57.862 40.909 0.00 0.00 0.00 3.16
571 722 7.051000 GGGAAGATAATATAGCAATGGACTCC 58.949 42.308 0.00 0.00 0.00 3.85
572 723 7.856415 AGGGAAGATAATATAGCAATGGACTC 58.144 38.462 0.00 0.00 0.00 3.36
574 725 7.885399 ACAAGGGAAGATAATATAGCAATGGAC 59.115 37.037 0.00 0.00 0.00 4.02
575 726 7.988937 ACAAGGGAAGATAATATAGCAATGGA 58.011 34.615 0.00 0.00 0.00 3.41
576 727 8.517878 CAACAAGGGAAGATAATATAGCAATGG 58.482 37.037 0.00 0.00 0.00 3.16
577 728 8.517878 CCAACAAGGGAAGATAATATAGCAATG 58.482 37.037 0.00 0.00 0.00 2.82
578 729 8.227507 ACCAACAAGGGAAGATAATATAGCAAT 58.772 33.333 0.00 0.00 43.89 3.56
579 730 7.582719 ACCAACAAGGGAAGATAATATAGCAA 58.417 34.615 0.00 0.00 43.89 3.91
580 731 7.149202 ACCAACAAGGGAAGATAATATAGCA 57.851 36.000 0.00 0.00 43.89 3.49
581 732 7.334671 GCTACCAACAAGGGAAGATAATATAGC 59.665 40.741 0.00 0.00 43.89 2.97
582 733 7.824779 GGCTACCAACAAGGGAAGATAATATAG 59.175 40.741 0.00 0.00 43.89 1.31
583 734 7.526526 CGGCTACCAACAAGGGAAGATAATATA 60.527 40.741 0.00 0.00 43.89 0.86
584 735 6.543735 GGCTACCAACAAGGGAAGATAATAT 58.456 40.000 0.00 0.00 43.89 1.28
585 736 5.454187 CGGCTACCAACAAGGGAAGATAATA 60.454 44.000 0.00 0.00 43.89 0.98
586 737 4.686122 CGGCTACCAACAAGGGAAGATAAT 60.686 45.833 0.00 0.00 43.89 1.28
587 738 3.370103 CGGCTACCAACAAGGGAAGATAA 60.370 47.826 0.00 0.00 43.89 1.75
853 1011 3.564218 GATGCCGGCCAGGGAGAT 61.564 66.667 26.77 8.72 46.12 2.75
960 1118 2.359107 ACGTCGTCGAGGTAGCCA 60.359 61.111 18.32 0.00 40.62 4.75
1164 1325 0.523072 GGCGAACACACTGCATGAAT 59.477 50.000 0.00 0.00 0.00 2.57
1251 1730 0.459899 ACGAGAATGCGCTCATGGTA 59.540 50.000 9.73 0.00 34.56 3.25
1913 3125 5.296780 TGAAATCCAAGTATCCTCGAAATGC 59.703 40.000 0.00 0.00 0.00 3.56
2112 3327 2.935201 GAGCTCACTATTGGCTTCTGTG 59.065 50.000 9.40 0.00 36.37 3.66
2113 3328 2.836981 AGAGCTCACTATTGGCTTCTGT 59.163 45.455 17.77 0.00 36.37 3.41
2114 3329 3.540314 AGAGCTCACTATTGGCTTCTG 57.460 47.619 17.77 0.00 36.37 3.02
2160 3375 9.528489 AGTCCAACCTAAATTGAGCTTAAATAA 57.472 29.630 0.00 0.00 0.00 1.40
2161 3376 9.174166 GAGTCCAACCTAAATTGAGCTTAAATA 57.826 33.333 0.00 0.00 0.00 1.40
2162 3377 7.122799 GGAGTCCAACCTAAATTGAGCTTAAAT 59.877 37.037 3.60 0.00 0.00 1.40
2163 3378 6.433093 GGAGTCCAACCTAAATTGAGCTTAAA 59.567 38.462 3.60 0.00 0.00 1.52
2164 3379 5.944007 GGAGTCCAACCTAAATTGAGCTTAA 59.056 40.000 3.60 0.00 0.00 1.85
2165 3380 5.250774 AGGAGTCCAACCTAAATTGAGCTTA 59.749 40.000 12.86 0.00 35.84 3.09
2166 3381 4.043435 AGGAGTCCAACCTAAATTGAGCTT 59.957 41.667 12.86 0.00 35.84 3.74
2167 3382 3.589288 AGGAGTCCAACCTAAATTGAGCT 59.411 43.478 12.86 0.00 35.84 4.09
2168 3383 3.956744 AGGAGTCCAACCTAAATTGAGC 58.043 45.455 12.86 0.00 35.84 4.26
2169 3384 5.412904 GTCAAGGAGTCCAACCTAAATTGAG 59.587 44.000 12.86 0.00 36.67 3.02
2170 3385 5.073144 AGTCAAGGAGTCCAACCTAAATTGA 59.927 40.000 12.86 7.02 36.67 2.57
2171 3386 5.316987 AGTCAAGGAGTCCAACCTAAATTG 58.683 41.667 12.86 4.58 36.67 2.32
2172 3387 5.584551 AGTCAAGGAGTCCAACCTAAATT 57.415 39.130 12.86 0.00 36.67 1.82
2173 3388 5.584551 AAGTCAAGGAGTCCAACCTAAAT 57.415 39.130 12.86 0.00 36.67 1.40
2174 3389 5.104277 TGAAAGTCAAGGAGTCCAACCTAAA 60.104 40.000 12.86 0.00 36.67 1.85
2175 3390 4.410883 TGAAAGTCAAGGAGTCCAACCTAA 59.589 41.667 12.86 0.00 36.67 2.69
2176 3391 3.971305 TGAAAGTCAAGGAGTCCAACCTA 59.029 43.478 12.86 0.00 36.67 3.08
2177 3392 2.777692 TGAAAGTCAAGGAGTCCAACCT 59.222 45.455 12.86 0.00 39.69 3.50
2178 3393 3.208747 TGAAAGTCAAGGAGTCCAACC 57.791 47.619 12.86 0.00 0.00 3.77
2179 3394 5.163713 GCATATGAAAGTCAAGGAGTCCAAC 60.164 44.000 12.86 6.60 0.00 3.77
2180 3395 4.943705 GCATATGAAAGTCAAGGAGTCCAA 59.056 41.667 12.86 0.00 0.00 3.53
2181 3396 4.019411 TGCATATGAAAGTCAAGGAGTCCA 60.019 41.667 12.86 0.00 0.00 4.02
2182 3397 4.517285 TGCATATGAAAGTCAAGGAGTCC 58.483 43.478 6.97 0.00 0.00 3.85
2183 3398 5.448360 GCTTGCATATGAAAGTCAAGGAGTC 60.448 44.000 22.12 1.49 35.83 3.36
2184 3399 4.397417 GCTTGCATATGAAAGTCAAGGAGT 59.603 41.667 22.12 0.00 35.83 3.85
2185 3400 4.397103 TGCTTGCATATGAAAGTCAAGGAG 59.603 41.667 22.12 0.00 35.83 3.69
2186 3401 4.334552 TGCTTGCATATGAAAGTCAAGGA 58.665 39.130 22.12 15.24 35.83 3.36
2187 3402 4.707030 TGCTTGCATATGAAAGTCAAGG 57.293 40.909 22.12 0.04 35.83 3.61
2188 3403 8.867112 AAATATGCTTGCATATGAAAGTCAAG 57.133 30.769 23.52 17.11 37.70 3.02
2225 3440 4.647853 TGTAAAGCTCCGCTCTAGGAATAA 59.352 41.667 0.00 0.00 38.25 1.40
2233 3448 1.219393 GCCTGTAAAGCTCCGCTCT 59.781 57.895 0.00 0.00 38.25 4.09
2267 3482 1.907807 GCCACCTCCAATTGTGCCA 60.908 57.895 4.43 0.00 0.00 4.92
2282 3497 3.419580 AATCCGCTGGATGGGCCA 61.420 61.111 9.61 9.61 42.27 5.36
2290 3505 1.153289 CAGAGACCCAATCCGCTGG 60.153 63.158 0.00 0.00 36.10 4.85
2316 3531 0.660488 CTCCAGAGGTCATCGAGTCG 59.340 60.000 6.09 6.09 0.00 4.18
2318 3533 2.051334 CTCTCCAGAGGTCATCGAGT 57.949 55.000 0.00 0.00 38.48 4.18
2347 3562 0.032813 CTTGGCTGGGGGATCAATGT 60.033 55.000 0.00 0.00 0.00 2.71
2351 3566 2.288642 GATGCTTGGCTGGGGGATCA 62.289 60.000 0.00 0.00 0.00 2.92
2358 3573 0.465097 AAGGATCGATGCTTGGCTGG 60.465 55.000 28.60 0.00 37.07 4.85
2387 3602 6.573434 ACGAGCAATGAGAATAGTGATGTTA 58.427 36.000 0.00 0.00 0.00 2.41
2396 3611 3.932710 GGTGTCAACGAGCAATGAGAATA 59.067 43.478 0.00 0.00 0.00 1.75
2427 3642 7.153315 TGGTCGTGATGTATACTGTTAACAAA 58.847 34.615 10.03 1.18 0.00 2.83
2441 3656 3.689161 CCATACAACATTGGTCGTGATGT 59.311 43.478 0.00 0.00 38.08 3.06
2446 3661 2.489938 AGCCATACAACATTGGTCGT 57.510 45.000 0.00 0.00 35.34 4.34
2447 3662 3.531538 AGTAGCCATACAACATTGGTCG 58.468 45.455 0.00 0.00 35.34 4.79
2455 3670 3.192633 CCAAACCCAAGTAGCCATACAAC 59.807 47.826 0.00 0.00 34.07 3.32
2461 3676 2.757894 TTTCCAAACCCAAGTAGCCA 57.242 45.000 0.00 0.00 0.00 4.75
2469 3684 4.100189 CCAAACACTGTATTTCCAAACCCA 59.900 41.667 0.00 0.00 0.00 4.51
2472 3687 5.656480 ACACCAAACACTGTATTTCCAAAC 58.344 37.500 0.00 0.00 0.00 2.93
2480 3695 2.660572 TGCCAACACCAAACACTGTAT 58.339 42.857 0.00 0.00 0.00 2.29
2481 3696 2.130272 TGCCAACACCAAACACTGTA 57.870 45.000 0.00 0.00 0.00 2.74
2482 3697 1.261480 TTGCCAACACCAAACACTGT 58.739 45.000 0.00 0.00 0.00 3.55
2483 3698 2.600470 ATTGCCAACACCAAACACTG 57.400 45.000 0.00 0.00 0.00 3.66
2501 3717 9.715121 AATCATTGTAGAATTCAACAGCAAAAT 57.285 25.926 8.44 2.05 0.00 1.82
2503 3719 8.579006 AGAATCATTGTAGAATTCAACAGCAAA 58.421 29.630 8.44 0.00 0.00 3.68
2505 3721 7.692460 AGAATCATTGTAGAATTCAACAGCA 57.308 32.000 8.44 0.00 0.00 4.41
2520 3736 7.765307 ACAAGCCAACTACAATAGAATCATTG 58.235 34.615 4.62 4.62 40.93 2.82
2521 3737 7.944729 ACAAGCCAACTACAATAGAATCATT 57.055 32.000 0.00 0.00 0.00 2.57
2523 3739 6.349280 GCAACAAGCCAACTACAATAGAATCA 60.349 38.462 0.00 0.00 37.23 2.57
2524 3740 6.030228 GCAACAAGCCAACTACAATAGAATC 58.970 40.000 0.00 0.00 37.23 2.52
2550 3768 7.631377 GCTTCCAGATAGTGCCATTTTGTTTAT 60.631 37.037 0.00 0.00 0.00 1.40
2565 3783 8.680903 ACAATATGAAACTTTGCTTCCAGATAG 58.319 33.333 0.00 0.00 0.00 2.08
2569 3787 7.147312 TCAACAATATGAAACTTTGCTTCCAG 58.853 34.615 0.00 0.00 0.00 3.86
2675 3893 4.155709 TGGACCCACTGAAATATGCAAAA 58.844 39.130 0.00 0.00 0.00 2.44
2835 4053 5.453057 CCCATCCAAATATGCGAAATTTCCA 60.453 40.000 12.54 11.39 0.00 3.53
2836 4054 4.990426 CCCATCCAAATATGCGAAATTTCC 59.010 41.667 12.54 6.21 0.00 3.13
2837 4055 4.990426 CCCCATCCAAATATGCGAAATTTC 59.010 41.667 8.20 8.20 0.00 2.17
2841 4059 2.955660 GACCCCATCCAAATATGCGAAA 59.044 45.455 0.00 0.00 0.00 3.46
2869 4087 9.995957 AAGGTTTTTAATTTCGGAAACAAAATG 57.004 25.926 18.13 0.00 34.54 2.32
2877 4095 6.201806 CACATGCAAGGTTTTTAATTTCGGAA 59.798 34.615 0.00 0.00 0.00 4.30
2906 4124 9.626045 GTTTCCATAAAACAAATTCACTCTAGG 57.374 33.333 0.00 0.00 45.49 3.02
2943 4161 8.510243 TGAGCATCACAATATTACTTCAATGT 57.490 30.769 0.00 0.00 42.56 2.71
3025 4244 3.365969 CGTCTGGGTTATTTTGCTTCCAC 60.366 47.826 0.00 0.00 0.00 4.02
3038 4257 2.879103 ATGTTTCCATCGTCTGGGTT 57.121 45.000 6.89 0.00 45.98 4.11
3045 4264 4.212004 CGCAGATCAATATGTTTCCATCGT 59.788 41.667 0.00 0.00 32.29 3.73


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

AutoCloner maintained by Alex Coulton.