Multiple sequence alignment - TraesCS3D01G029400

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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 TraesCS3D01G029400 chr3D 100.000 3663 0 0 1 3663 10659561 10663223 0.000000e+00 6765.0
1 TraesCS3D01G029400 chr3D 79.754 1136 171 32 966 2077 10723548 10724648 0.000000e+00 769.0
2 TraesCS3D01G029400 chr3D 77.243 1081 189 34 1022 2077 10709680 10710728 6.820000e-162 580.0
3 TraesCS3D01G029400 chr3D 81.802 577 70 24 857 1411 10646681 10647244 5.580000e-123 451.0
4 TraesCS3D01G029400 chr3D 91.608 143 10 2 990 1131 10392614 10392473 2.890000e-46 196.0
5 TraesCS3D01G029400 chr3D 95.000 40 2 0 622 661 10377508 10377469 3.050000e-06 63.9
6 TraesCS3D01G029400 chr3A 92.667 2700 124 24 183 2862 17607606 17604961 0.000000e+00 3821.0
7 TraesCS3D01G029400 chr3A 85.516 794 68 22 2890 3663 17604963 17604197 0.000000e+00 785.0
8 TraesCS3D01G029400 chr3B 91.420 2063 111 25 1335 3364 26532128 26530099 0.000000e+00 2769.0
9 TraesCS3D01G029400 chr3B 90.111 1082 71 18 202 1275 26533177 26532124 0.000000e+00 1373.0
10 TraesCS3D01G029400 chr3B 84.066 1023 131 15 1070 2077 15054503 15055508 0.000000e+00 957.0
11 TraesCS3D01G029400 chr3B 82.404 1148 147 29 937 2069 14402624 14401517 0.000000e+00 950.0
12 TraesCS3D01G029400 chr3B 89.735 565 58 0 1596 2160 26578112 26577548 0.000000e+00 723.0
13 TraesCS3D01G029400 chr3B 82.201 736 95 22 878 1593 26583965 26583246 5.230000e-168 601.0
14 TraesCS3D01G029400 chr3B 98.361 61 1 0 2316 2376 26531189 26531129 1.390000e-19 108.0
15 TraesCS3D01G029400 chr6A 89.950 796 68 9 736 1527 318019283 318018496 0.000000e+00 1016.0
16 TraesCS3D01G029400 chr1B 80.455 1274 202 32 937 2177 61943797 61942538 0.000000e+00 929.0
17 TraesCS3D01G029400 chr1A 80.537 1228 185 39 937 2127 41759488 41758278 0.000000e+00 894.0
18 TraesCS3D01G029400 chr1D 86.041 788 101 7 1386 2165 41757551 41756765 0.000000e+00 837.0


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 TraesCS3D01G029400 chr3D 10659561 10663223 3662 False 6765.000000 6765 100.000000 1 3663 1 chr3D.!!$F2 3662
1 TraesCS3D01G029400 chr3D 10723548 10724648 1100 False 769.000000 769 79.754000 966 2077 1 chr3D.!!$F4 1111
2 TraesCS3D01G029400 chr3D 10709680 10710728 1048 False 580.000000 580 77.243000 1022 2077 1 chr3D.!!$F3 1055
3 TraesCS3D01G029400 chr3D 10646681 10647244 563 False 451.000000 451 81.802000 857 1411 1 chr3D.!!$F1 554
4 TraesCS3D01G029400 chr3A 17604197 17607606 3409 True 2303.000000 3821 89.091500 183 3663 2 chr3A.!!$R1 3480
5 TraesCS3D01G029400 chr3B 26530099 26533177 3078 True 1416.666667 2769 93.297333 202 3364 3 chr3B.!!$R4 3162
6 TraesCS3D01G029400 chr3B 15054503 15055508 1005 False 957.000000 957 84.066000 1070 2077 1 chr3B.!!$F1 1007
7 TraesCS3D01G029400 chr3B 14401517 14402624 1107 True 950.000000 950 82.404000 937 2069 1 chr3B.!!$R1 1132
8 TraesCS3D01G029400 chr3B 26577548 26578112 564 True 723.000000 723 89.735000 1596 2160 1 chr3B.!!$R2 564
9 TraesCS3D01G029400 chr3B 26583246 26583965 719 True 601.000000 601 82.201000 878 1593 1 chr3B.!!$R3 715
10 TraesCS3D01G029400 chr6A 318018496 318019283 787 True 1016.000000 1016 89.950000 736 1527 1 chr6A.!!$R1 791
11 TraesCS3D01G029400 chr1B 61942538 61943797 1259 True 929.000000 929 80.455000 937 2177 1 chr1B.!!$R1 1240
12 TraesCS3D01G029400 chr1A 41758278 41759488 1210 True 894.000000 894 80.537000 937 2127 1 chr1A.!!$R1 1190
13 TraesCS3D01G029400 chr1D 41756765 41757551 786 True 837.000000 837 86.041000 1386 2165 1 chr1D.!!$R1 779

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
23 24 0.031449 AAACGTTCGGTTTGCCATGG 59.969 50.000 7.63 7.63 46.81 3.66 F
226 227 0.321671 TTTTCCAGCCCACTCTCTCG 59.678 55.000 0.00 0.00 0.00 4.04 F
405 420 1.138661 GGAGGGAGCATCAGTCTTCTG 59.861 57.143 0.00 0.00 42.54 3.02 F
2243 2432 0.762461 GGTGGAGGAGGAGGATGAGG 60.762 65.000 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1288 1444 4.081406 TCATTGTTTGAGTTGCCATAGCT 58.919 39.130 0.0 0.0 40.80 3.32 R
2078 2252 4.453819 ACAAGATCTGCTGTGACTTAAAGC 59.546 41.667 0.0 0.0 37.46 3.51 R
2315 2516 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.0 0.0 0.00 3.71 R
3221 3436 0.109272 GCGACCTTGTGATCTCGTGA 60.109 55.000 0.0 0.0 0.00 4.35 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 3.560826 AAACGTTCGGTTTGCCATG 57.439 47.368 0.00 0.00 46.81 3.66
23 24 0.031449 AAACGTTCGGTTTGCCATGG 59.969 50.000 7.63 7.63 46.81 3.66
24 25 1.104577 AACGTTCGGTTTGCCATGGT 61.105 50.000 14.67 0.00 34.41 3.55
25 26 1.104577 ACGTTCGGTTTGCCATGGTT 61.105 50.000 14.67 0.00 34.09 3.67
26 27 0.875728 CGTTCGGTTTGCCATGGTTA 59.124 50.000 14.67 0.00 34.09 2.85
27 28 1.267261 CGTTCGGTTTGCCATGGTTAA 59.733 47.619 14.67 6.54 34.09 2.01
28 29 2.287668 CGTTCGGTTTGCCATGGTTAAA 60.288 45.455 14.67 12.44 34.09 1.52
29 30 3.718815 GTTCGGTTTGCCATGGTTAAAA 58.281 40.909 14.67 9.26 34.09 1.52
30 31 4.120589 GTTCGGTTTGCCATGGTTAAAAA 58.879 39.130 14.67 6.76 34.09 1.94
31 32 4.608948 TCGGTTTGCCATGGTTAAAAAT 57.391 36.364 14.67 0.00 34.09 1.82
32 33 5.723672 TCGGTTTGCCATGGTTAAAAATA 57.276 34.783 14.67 2.12 34.09 1.40
33 34 6.287589 TCGGTTTGCCATGGTTAAAAATAT 57.712 33.333 14.67 0.00 34.09 1.28
34 35 6.102663 TCGGTTTGCCATGGTTAAAAATATG 58.897 36.000 14.67 5.01 34.09 1.78
35 36 6.071334 TCGGTTTGCCATGGTTAAAAATATGA 60.071 34.615 14.67 6.92 34.09 2.15
36 37 6.035542 CGGTTTGCCATGGTTAAAAATATGAC 59.964 38.462 14.67 2.90 34.09 3.06
37 38 6.035542 GGTTTGCCATGGTTAAAAATATGACG 59.964 38.462 14.67 0.00 34.09 4.35
38 39 5.906113 TGCCATGGTTAAAAATATGACGT 57.094 34.783 14.67 0.00 0.00 4.34
39 40 5.885881 TGCCATGGTTAAAAATATGACGTC 58.114 37.500 14.67 9.11 0.00 4.34
40 41 5.416013 TGCCATGGTTAAAAATATGACGTCA 59.584 36.000 22.48 22.48 0.00 4.35
41 42 5.971202 GCCATGGTTAAAAATATGACGTCAG 59.029 40.000 24.41 5.22 0.00 3.51
42 43 6.183360 GCCATGGTTAAAAATATGACGTCAGA 60.183 38.462 24.41 20.51 0.00 3.27
43 44 7.468631 GCCATGGTTAAAAATATGACGTCAGAT 60.469 37.037 24.41 21.96 0.00 2.90
44 45 8.405531 CCATGGTTAAAAATATGACGTCAGATT 58.594 33.333 27.98 27.98 39.22 2.40
45 46 9.787532 CATGGTTAAAAATATGACGTCAGATTT 57.212 29.630 34.08 34.08 46.11 2.17
46 47 9.787532 ATGGTTAAAAATATGACGTCAGATTTG 57.212 29.630 37.67 0.00 44.19 2.32
47 48 8.788806 TGGTTAAAAATATGACGTCAGATTTGT 58.211 29.630 37.67 35.03 44.19 2.83
74 75 7.610580 TTTTTAGGGGAATGTCAGATTTTGT 57.389 32.000 0.00 0.00 0.00 2.83
75 76 8.713708 TTTTTAGGGGAATGTCAGATTTTGTA 57.286 30.769 0.00 0.00 0.00 2.41
76 77 7.938140 TTTAGGGGAATGTCAGATTTTGTAG 57.062 36.000 0.00 0.00 0.00 2.74
77 78 5.520748 AGGGGAATGTCAGATTTTGTAGT 57.479 39.130 0.00 0.00 0.00 2.73
78 79 5.892348 AGGGGAATGTCAGATTTTGTAGTT 58.108 37.500 0.00 0.00 0.00 2.24
79 80 6.314917 AGGGGAATGTCAGATTTTGTAGTTT 58.685 36.000 0.00 0.00 0.00 2.66
80 81 6.782494 AGGGGAATGTCAGATTTTGTAGTTTT 59.218 34.615 0.00 0.00 0.00 2.43
81 82 7.290014 AGGGGAATGTCAGATTTTGTAGTTTTT 59.710 33.333 0.00 0.00 0.00 1.94
105 106 8.519799 TTTTTGAGGAAAGTCAGATTTGTAGT 57.480 30.769 0.00 0.00 0.00 2.73
106 107 8.519799 TTTTGAGGAAAGTCAGATTTGTAGTT 57.480 30.769 0.00 0.00 0.00 2.24
107 108 8.519799 TTTGAGGAAAGTCAGATTTGTAGTTT 57.480 30.769 0.00 0.00 0.00 2.66
108 109 8.519799 TTGAGGAAAGTCAGATTTGTAGTTTT 57.480 30.769 0.00 0.00 0.00 2.43
109 110 8.519799 TGAGGAAAGTCAGATTTGTAGTTTTT 57.480 30.769 0.00 0.00 0.00 1.94
132 133 6.817765 TTTTAGGGCAAGTCAGATTTGTAG 57.182 37.500 7.44 0.00 0.00 2.74
133 134 5.499004 TTAGGGCAAGTCAGATTTGTAGT 57.501 39.130 7.44 0.00 0.00 2.73
134 135 4.373156 AGGGCAAGTCAGATTTGTAGTT 57.627 40.909 7.44 0.00 0.00 2.24
135 136 4.729868 AGGGCAAGTCAGATTTGTAGTTT 58.270 39.130 7.44 0.00 0.00 2.66
136 137 5.140454 AGGGCAAGTCAGATTTGTAGTTTT 58.860 37.500 7.44 0.00 0.00 2.43
137 138 5.010012 AGGGCAAGTCAGATTTGTAGTTTTG 59.990 40.000 7.44 0.00 0.00 2.44
138 139 5.221244 GGGCAAGTCAGATTTGTAGTTTTGT 60.221 40.000 7.44 0.00 0.00 2.83
139 140 6.273071 GGCAAGTCAGATTTGTAGTTTTGTT 58.727 36.000 7.44 0.00 0.00 2.83
140 141 6.756542 GGCAAGTCAGATTTGTAGTTTTGTTT 59.243 34.615 7.44 0.00 0.00 2.83
141 142 7.277760 GGCAAGTCAGATTTGTAGTTTTGTTTT 59.722 33.333 7.44 0.00 0.00 2.43
142 143 8.655970 GCAAGTCAGATTTGTAGTTTTGTTTTT 58.344 29.630 7.44 0.00 0.00 1.94
143 144 9.956797 CAAGTCAGATTTGTAGTTTTGTTTTTG 57.043 29.630 0.00 0.00 0.00 2.44
144 145 9.921637 AAGTCAGATTTGTAGTTTTGTTTTTGA 57.078 25.926 0.00 0.00 0.00 2.69
145 146 9.573133 AGTCAGATTTGTAGTTTTGTTTTTGAG 57.427 29.630 0.00 0.00 0.00 3.02
146 147 9.567848 GTCAGATTTGTAGTTTTGTTTTTGAGA 57.432 29.630 0.00 0.00 0.00 3.27
176 177 9.141400 AGTCAGATTTGTAGTTAAGTCGAATTC 57.859 33.333 0.00 0.00 0.00 2.17
177 178 9.141400 GTCAGATTTGTAGTTAAGTCGAATTCT 57.859 33.333 0.00 0.00 0.00 2.40
178 179 9.706691 TCAGATTTGTAGTTAAGTCGAATTCTT 57.293 29.630 0.00 0.00 0.00 2.52
184 185 8.538409 TGTAGTTAAGTCGAATTCTTTTACCC 57.462 34.615 0.00 0.00 0.00 3.69
185 186 8.149647 TGTAGTTAAGTCGAATTCTTTTACCCA 58.850 33.333 0.00 0.00 0.00 4.51
186 187 8.992073 GTAGTTAAGTCGAATTCTTTTACCCAA 58.008 33.333 0.00 0.00 0.00 4.12
193 194 4.381566 CGAATTCTTTTACCCAAAACGCAG 59.618 41.667 3.52 0.00 30.52 5.18
197 198 1.950828 TTTACCCAAAACGCAGACGA 58.049 45.000 0.00 0.00 43.93 4.20
209 210 1.002134 CAGACGACCAGGCCCATTT 60.002 57.895 0.00 0.00 0.00 2.32
226 227 0.321671 TTTTCCAGCCCACTCTCTCG 59.678 55.000 0.00 0.00 0.00 4.04
405 420 1.138661 GGAGGGAGCATCAGTCTTCTG 59.861 57.143 0.00 0.00 42.54 3.02
484 499 1.375396 CATCAGGAAACGGCGACCA 60.375 57.895 16.62 0.00 0.00 4.02
550 566 2.751806 CGGAGAAAACCTAGGTACGTCT 59.248 50.000 16.67 17.24 0.00 4.18
582 598 1.931841 GATTCGAAAACCTAGGTCCGC 59.068 52.381 16.64 6.34 0.00 5.54
605 622 2.523015 GCAGTGCCAAAATCTGAATCG 58.477 47.619 2.85 0.00 0.00 3.34
607 625 2.094675 AGTGCCAAAATCTGAATCGGG 58.905 47.619 0.00 0.00 0.00 5.14
674 692 2.800881 TGCATCGTCGCTCTGATTAT 57.199 45.000 0.00 0.00 0.00 1.28
675 693 3.097877 TGCATCGTCGCTCTGATTATT 57.902 42.857 0.00 0.00 0.00 1.40
676 694 4.237349 TGCATCGTCGCTCTGATTATTA 57.763 40.909 0.00 0.00 0.00 0.98
686 704 5.924254 TCGCTCTGATTATTACCCAATAACG 59.076 40.000 0.00 0.00 38.98 3.18
698 716 2.729882 CCCAATAACGTACTGCTATCGC 59.270 50.000 0.00 0.00 0.00 4.58
717 735 2.206750 GCATCGGCGAACACCTAATAA 58.793 47.619 15.93 0.00 0.00 1.40
741 759 3.554324 GCAAATCGGCTCGAATACACTTA 59.446 43.478 1.44 0.00 39.99 2.24
745 763 4.485024 TCGGCTCGAATACACTTATCTC 57.515 45.455 0.00 0.00 31.06 2.75
824 845 4.695217 TCAATTATTCAGTCCCGTTTGC 57.305 40.909 0.00 0.00 0.00 3.68
826 847 4.155826 TCAATTATTCAGTCCCGTTTGCAG 59.844 41.667 0.00 0.00 0.00 4.41
831 852 1.202758 TCAGTCCCGTTTGCAGATGTT 60.203 47.619 0.00 0.00 0.00 2.71
836 857 2.039216 TCCCGTTTGCAGATGTTCCTTA 59.961 45.455 0.00 0.00 0.00 2.69
840 861 3.429085 GTTTGCAGATGTTCCTTATGCG 58.571 45.455 0.00 0.00 39.74 4.73
982 1016 3.498834 CAAGCCAGTGCGCGCATA 61.499 61.111 38.62 13.19 44.33 3.14
1172 1242 2.034842 CACGACGTGTTGTCTTGTCTTC 60.035 50.000 19.77 0.00 45.87 2.87
1210 1290 5.474578 TCTCAGTGATAAAGCTCAAGTGT 57.525 39.130 0.00 0.00 0.00 3.55
1280 1436 3.005050 AGGACATGTTTCTCGTGAACGTA 59.995 43.478 0.00 0.00 40.80 3.57
1281 1437 3.737266 GGACATGTTTCTCGTGAACGTAA 59.263 43.478 0.00 0.00 40.80 3.18
1288 1444 8.588789 CATGTTTCTCGTGAACGTAACATAATA 58.411 33.333 21.16 5.98 40.69 0.98
1292 1448 7.250445 TCTCGTGAACGTAACATAATAGCTA 57.750 36.000 0.00 0.00 40.80 3.32
1293 1449 7.868775 TCTCGTGAACGTAACATAATAGCTAT 58.131 34.615 0.00 0.00 40.80 2.97
1294 1450 7.801783 TCTCGTGAACGTAACATAATAGCTATG 59.198 37.037 7.09 0.00 40.74 2.23
1295 1451 6.859508 TCGTGAACGTAACATAATAGCTATGG 59.140 38.462 7.09 2.97 40.04 2.74
1296 1452 6.399669 CGTGAACGTAACATAATAGCTATGGC 60.400 42.308 7.09 0.00 37.17 4.40
1307 1463 7.339212 ACATAATAGCTATGGCAACTCAAACAA 59.661 33.333 7.09 0.00 41.66 2.83
1315 1471 5.437289 TGGCAACTCAAACAATGAACTAG 57.563 39.130 0.00 0.00 37.67 2.57
1316 1472 4.887071 TGGCAACTCAAACAATGAACTAGT 59.113 37.500 0.00 0.00 37.67 2.57
1318 1474 6.714810 TGGCAACTCAAACAATGAACTAGTAT 59.285 34.615 0.00 0.00 37.67 2.12
1319 1475 7.880713 TGGCAACTCAAACAATGAACTAGTATA 59.119 33.333 0.00 0.00 37.67 1.47
1320 1476 8.726988 GGCAACTCAAACAATGAACTAGTATAA 58.273 33.333 0.00 0.00 37.67 0.98
2078 2252 3.285484 AGAGCCACCATTAATCAGCAAG 58.715 45.455 0.00 0.00 0.00 4.01
2164 2338 4.554292 CCGATACTTGTGATGATGAGGAG 58.446 47.826 0.00 0.00 0.00 3.69
2243 2432 0.762461 GGTGGAGGAGGAGGATGAGG 60.762 65.000 0.00 0.00 0.00 3.86
2272 2473 2.038659 GACAATGAGGAGGAGGAGGAG 58.961 57.143 0.00 0.00 0.00 3.69
2273 2474 1.343884 ACAATGAGGAGGAGGAGGAGG 60.344 57.143 0.00 0.00 0.00 4.30
2274 2475 1.062581 CAATGAGGAGGAGGAGGAGGA 60.063 57.143 0.00 0.00 0.00 3.71
2315 2516 1.280133 TCAGAAGATCCCACCTTGCTG 59.720 52.381 0.00 0.00 0.00 4.41
2316 2517 1.280133 CAGAAGATCCCACCTTGCTGA 59.720 52.381 0.00 0.00 0.00 4.26
2317 2518 1.558756 AGAAGATCCCACCTTGCTGAG 59.441 52.381 0.00 0.00 0.00 3.35
2393 2594 2.094545 GCTGTTCAACTAAGGCCCAATG 60.095 50.000 0.00 0.00 0.00 2.82
2415 2616 3.353557 CTTATCATGATGATGGGCAGGG 58.646 50.000 18.72 0.00 37.70 4.45
2522 2732 5.595257 ATCTGATACCGATGATGAGGATG 57.405 43.478 0.00 0.00 0.00 3.51
2562 2772 3.528370 CGCCCGTCTCCGAGGAAT 61.528 66.667 0.00 0.00 35.63 3.01
2565 2775 2.278857 CCGTCTCCGAGGAATGCG 60.279 66.667 0.00 0.00 35.63 4.73
2690 2900 2.076863 CAGTTCAAAGAAGGGGCGTAG 58.923 52.381 0.00 0.00 0.00 3.51
2878 3093 0.964358 GGCTGCAGCTCCTTGAACAT 60.964 55.000 35.82 0.00 41.70 2.71
2889 3104 3.804036 TCCTTGAACATATTACTGGGCG 58.196 45.455 0.00 0.00 0.00 6.13
2912 3127 3.179830 CGTGTGGCTGTATAGTCTGAAC 58.820 50.000 0.00 0.00 0.00 3.18
2974 3189 0.700564 AGGAAATCAAGCTCCTGGCA 59.299 50.000 0.00 0.00 40.70 4.92
2983 3198 1.902938 AGCTCCTGGCAAAGTTTCTC 58.097 50.000 0.00 0.00 44.79 2.87
2986 3201 0.250727 TCCTGGCAAAGTTTCTCCCG 60.251 55.000 0.00 0.00 0.00 5.14
2987 3202 0.537371 CCTGGCAAAGTTTCTCCCGT 60.537 55.000 0.00 0.00 0.00 5.28
3067 3282 3.246699 TGAGTTTTTACAAGAAGACCGCG 59.753 43.478 0.00 0.00 0.00 6.46
3109 3324 8.033626 GTGGCTACTAGAAAACAGTACTGTATT 58.966 37.037 28.13 19.85 44.13 1.89
3143 3358 7.875041 GGTACATATCTCTGCATTTACATGACT 59.125 37.037 0.00 0.00 31.07 3.41
3173 3388 4.695455 CGAGTATGAACCATGACCTTTTGT 59.305 41.667 0.00 0.00 0.00 2.83
3174 3389 5.390885 CGAGTATGAACCATGACCTTTTGTG 60.391 44.000 0.00 0.00 0.00 3.33
3191 3406 8.303876 ACCTTTTGTGGTTATGATGTTTGTATC 58.696 33.333 0.00 0.00 36.89 2.24
3221 3436 3.903090 TCCTTTTCATTTCTGCATGGGTT 59.097 39.130 0.00 0.00 0.00 4.11
3274 3492 4.100189 ACAGTATCTGCAGGGTGATAAGAC 59.900 45.833 15.13 0.00 34.37 3.01
3282 3500 2.034179 CAGGGTGATAAGACGCGATGTA 59.966 50.000 15.93 0.80 34.11 2.29
3285 3503 4.056050 GGGTGATAAGACGCGATGTATTT 58.944 43.478 15.93 0.00 33.26 1.40
3309 3530 3.990469 TCTTCTGAATCGTGCTTTGACTC 59.010 43.478 0.00 0.00 0.00 3.36
3339 3560 9.775854 AGATGTTTGGTTATCTGAAGATATGAG 57.224 33.333 0.96 0.00 36.94 2.90
3364 3601 6.036083 GCGAAATTCTCTGTCATTTGTAGCTA 59.964 38.462 0.00 0.00 0.00 3.32
3365 3602 7.616673 CGAAATTCTCTGTCATTTGTAGCTAG 58.383 38.462 0.00 0.00 0.00 3.42
3396 3633 7.917597 TCTTTGTCAGCGAGTTATACTACTAG 58.082 38.462 0.00 0.00 0.00 2.57
3407 3644 8.121708 CGAGTTATACTACTAGAGTTGTTGGAC 58.878 40.741 0.00 0.54 39.81 4.02
3410 3647 8.738106 GTTATACTACTAGAGTTGTTGGACACT 58.262 37.037 0.00 0.00 39.81 3.55
3460 3697 7.604545 TCATGAATTTTGACGGTGAGTTATACA 59.395 33.333 0.00 0.00 0.00 2.29
3464 3701 8.836268 AATTTTGACGGTGAGTTATACAACTA 57.164 30.769 0.00 0.00 45.18 2.24
3465 3702 7.878477 TTTTGACGGTGAGTTATACAACTAG 57.122 36.000 0.00 0.00 45.18 2.57
3466 3703 6.579666 TTGACGGTGAGTTATACAACTAGT 57.420 37.500 0.00 0.00 45.18 2.57
3477 3714 2.211250 ACAACTAGTCGTAGCCCTCA 57.789 50.000 0.00 0.00 0.00 3.86
3513 3750 1.440145 GCCTTCCAGCGGCATTAGTC 61.440 60.000 1.45 0.00 46.77 2.59
3516 3753 0.459585 TTCCAGCGGCATTAGTCGTC 60.460 55.000 1.45 0.00 46.51 4.20
3519 3756 0.458543 CAGCGGCATTAGTCGTCTGT 60.459 55.000 1.45 0.00 46.51 3.41
3520 3757 1.100510 AGCGGCATTAGTCGTCTGTA 58.899 50.000 1.45 0.00 46.51 2.74
3521 3758 1.065701 AGCGGCATTAGTCGTCTGTAG 59.934 52.381 1.45 0.00 46.51 2.74
3522 3759 1.478137 CGGCATTAGTCGTCTGTAGC 58.522 55.000 0.00 0.00 38.25 3.58
3523 3760 1.065701 CGGCATTAGTCGTCTGTAGCT 59.934 52.381 0.00 0.00 38.25 3.32
3524 3761 2.479730 CGGCATTAGTCGTCTGTAGCTT 60.480 50.000 0.00 0.00 38.25 3.74
3525 3762 3.117046 GGCATTAGTCGTCTGTAGCTTC 58.883 50.000 0.00 0.00 0.00 3.86
3526 3763 3.117046 GCATTAGTCGTCTGTAGCTTCC 58.883 50.000 0.00 0.00 0.00 3.46
3527 3764 3.181485 GCATTAGTCGTCTGTAGCTTCCT 60.181 47.826 0.00 0.00 0.00 3.36
3528 3765 4.678309 GCATTAGTCGTCTGTAGCTTCCTT 60.678 45.833 0.00 0.00 0.00 3.36
3529 3766 5.411781 CATTAGTCGTCTGTAGCTTCCTTT 58.588 41.667 0.00 0.00 0.00 3.11
3530 3767 5.464030 TTAGTCGTCTGTAGCTTCCTTTT 57.536 39.130 0.00 0.00 0.00 2.27
3531 3768 6.579666 TTAGTCGTCTGTAGCTTCCTTTTA 57.420 37.500 0.00 0.00 0.00 1.52
3532 3769 5.662674 AGTCGTCTGTAGCTTCCTTTTAT 57.337 39.130 0.00 0.00 0.00 1.40
3533 3770 5.652518 AGTCGTCTGTAGCTTCCTTTTATC 58.347 41.667 0.00 0.00 0.00 1.75
3534 3771 5.419471 AGTCGTCTGTAGCTTCCTTTTATCT 59.581 40.000 0.00 0.00 0.00 1.98
3535 3772 5.744819 GTCGTCTGTAGCTTCCTTTTATCTC 59.255 44.000 0.00 0.00 0.00 2.75
3544 3781 6.112058 AGCTTCCTTTTATCTCTAGCAACTG 58.888 40.000 0.00 0.00 0.00 3.16
3549 3786 7.680730 TCCTTTTATCTCTAGCAACTGAAACT 58.319 34.615 0.00 0.00 0.00 2.66
3556 3793 6.119536 TCTCTAGCAACTGAAACTTTTTCCA 58.880 36.000 0.00 0.00 0.00 3.53
3570 3807 6.767524 ACTTTTTCCACTGTTGTGTGAATA 57.232 33.333 0.00 0.00 42.34 1.75
3576 3813 5.432645 TCCACTGTTGTGTGAATAGTCAAA 58.567 37.500 0.00 0.00 42.34 2.69
3579 3816 6.373779 CACTGTTGTGTGAATAGTCAAATCC 58.626 40.000 0.00 0.00 40.12 3.01
3581 3818 6.205464 ACTGTTGTGTGAATAGTCAAATCCAG 59.795 38.462 0.00 0.36 34.87 3.86
3585 3822 6.710278 TGTGTGAATAGTCAAATCCAGATGA 58.290 36.000 0.00 0.00 34.87 2.92
3598 3835 4.492182 TCCAGATGAGGATCCCATCTAA 57.508 45.455 29.94 22.55 46.35 2.10
3599 3836 4.163427 TCCAGATGAGGATCCCATCTAAC 58.837 47.826 29.94 14.32 46.35 2.34
3601 3838 3.262915 CAGATGAGGATCCCATCTAACCC 59.737 52.174 29.94 13.55 46.35 4.11
3607 3844 3.395941 AGGATCCCATCTAACCCAACATC 59.604 47.826 8.55 0.00 0.00 3.06
3617 3854 2.691409 ACCCAACATCGGTCTACATG 57.309 50.000 0.00 0.00 0.00 3.21
3624 3861 4.415881 ACATCGGTCTACATGGCAAATA 57.584 40.909 0.00 0.00 0.00 1.40
3626 3863 4.100963 ACATCGGTCTACATGGCAAATAGA 59.899 41.667 6.92 6.92 0.00 1.98
3633 3870 6.183360 GGTCTACATGGCAAATAGACAAAGTC 60.183 42.308 28.45 15.65 44.40 3.01
3641 3878 7.422399 TGGCAAATAGACAAAGTCAACTTAAC 58.578 34.615 0.00 0.00 34.61 2.01
3652 3889 8.188139 ACAAAGTCAACTTAACAAATGTACAGG 58.812 33.333 0.33 0.00 34.61 4.00
3653 3890 7.875327 AAGTCAACTTAACAAATGTACAGGT 57.125 32.000 0.33 0.00 33.79 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.197577 CATGGCAAACCGAACGTTTTT 58.802 42.857 0.46 0.00 42.15 1.94
4 5 0.031449 CCATGGCAAACCGAACGTTT 59.969 50.000 0.46 0.00 45.83 3.60
5 6 1.104577 ACCATGGCAAACCGAACGTT 61.105 50.000 13.04 0.00 39.70 3.99
6 7 1.104577 AACCATGGCAAACCGAACGT 61.105 50.000 13.04 0.00 39.70 3.99
7 8 0.875728 TAACCATGGCAAACCGAACG 59.124 50.000 13.04 0.00 39.70 3.95
8 9 3.372660 TTTAACCATGGCAAACCGAAC 57.627 42.857 13.04 0.00 39.70 3.95
9 10 4.402056 TTTTTAACCATGGCAAACCGAA 57.598 36.364 13.04 1.62 39.70 4.30
10 11 4.608948 ATTTTTAACCATGGCAAACCGA 57.391 36.364 13.04 2.25 39.70 4.69
11 12 6.035542 GTCATATTTTTAACCATGGCAAACCG 59.964 38.462 13.04 0.11 39.70 4.44
12 13 6.035542 CGTCATATTTTTAACCATGGCAAACC 59.964 38.462 13.04 0.00 0.00 3.27
13 14 6.588373 ACGTCATATTTTTAACCATGGCAAAC 59.412 34.615 13.04 0.00 0.00 2.93
14 15 6.692486 ACGTCATATTTTTAACCATGGCAAA 58.308 32.000 13.04 9.90 0.00 3.68
15 16 6.071896 TGACGTCATATTTTTAACCATGGCAA 60.072 34.615 15.76 3.06 0.00 4.52
16 17 5.416013 TGACGTCATATTTTTAACCATGGCA 59.584 36.000 15.76 0.00 0.00 4.92
17 18 5.885881 TGACGTCATATTTTTAACCATGGC 58.114 37.500 15.76 0.00 0.00 4.40
18 19 7.315247 TCTGACGTCATATTTTTAACCATGG 57.685 36.000 20.40 11.19 0.00 3.66
19 20 9.787532 AAATCTGACGTCATATTTTTAACCATG 57.212 29.630 27.04 9.90 31.34 3.66
20 21 9.787532 CAAATCTGACGTCATATTTTTAACCAT 57.212 29.630 29.03 11.56 32.55 3.55
21 22 8.788806 ACAAATCTGACGTCATATTTTTAACCA 58.211 29.630 29.03 2.42 32.55 3.67
50 51 7.610580 ACAAAATCTGACATTCCCCTAAAAA 57.389 32.000 0.00 0.00 0.00 1.94
51 52 7.947890 ACTACAAAATCTGACATTCCCCTAAAA 59.052 33.333 0.00 0.00 0.00 1.52
52 53 7.466804 ACTACAAAATCTGACATTCCCCTAAA 58.533 34.615 0.00 0.00 0.00 1.85
53 54 7.027874 ACTACAAAATCTGACATTCCCCTAA 57.972 36.000 0.00 0.00 0.00 2.69
54 55 6.636454 ACTACAAAATCTGACATTCCCCTA 57.364 37.500 0.00 0.00 0.00 3.53
55 56 5.520748 ACTACAAAATCTGACATTCCCCT 57.479 39.130 0.00 0.00 0.00 4.79
56 57 6.590234 AAACTACAAAATCTGACATTCCCC 57.410 37.500 0.00 0.00 0.00 4.81
80 81 8.519799 ACTACAAATCTGACTTTCCTCAAAAA 57.480 30.769 0.00 0.00 0.00 1.94
81 82 8.519799 AACTACAAATCTGACTTTCCTCAAAA 57.480 30.769 0.00 0.00 0.00 2.44
82 83 8.519799 AAACTACAAATCTGACTTTCCTCAAA 57.480 30.769 0.00 0.00 0.00 2.69
83 84 8.519799 AAAACTACAAATCTGACTTTCCTCAA 57.480 30.769 0.00 0.00 0.00 3.02
84 85 8.519799 AAAAACTACAAATCTGACTTTCCTCA 57.480 30.769 0.00 0.00 0.00 3.86
108 109 6.775629 ACTACAAATCTGACTTGCCCTAAAAA 59.224 34.615 0.00 0.00 0.00 1.94
109 110 6.303839 ACTACAAATCTGACTTGCCCTAAAA 58.696 36.000 0.00 0.00 0.00 1.52
110 111 5.876357 ACTACAAATCTGACTTGCCCTAAA 58.124 37.500 0.00 0.00 0.00 1.85
111 112 5.499004 ACTACAAATCTGACTTGCCCTAA 57.501 39.130 0.00 0.00 0.00 2.69
112 113 5.499004 AACTACAAATCTGACTTGCCCTA 57.501 39.130 0.00 0.00 0.00 3.53
113 114 4.373156 AACTACAAATCTGACTTGCCCT 57.627 40.909 0.00 0.00 0.00 5.19
114 115 5.221244 ACAAAACTACAAATCTGACTTGCCC 60.221 40.000 0.00 0.00 0.00 5.36
115 116 5.831997 ACAAAACTACAAATCTGACTTGCC 58.168 37.500 0.00 0.00 0.00 4.52
116 117 7.755582 AAACAAAACTACAAATCTGACTTGC 57.244 32.000 0.00 0.00 0.00 4.01
117 118 9.956797 CAAAAACAAAACTACAAATCTGACTTG 57.043 29.630 0.00 0.00 0.00 3.16
118 119 9.921637 TCAAAAACAAAACTACAAATCTGACTT 57.078 25.926 0.00 0.00 0.00 3.01
119 120 9.573133 CTCAAAAACAAAACTACAAATCTGACT 57.427 29.630 0.00 0.00 0.00 3.41
120 121 9.567848 TCTCAAAAACAAAACTACAAATCTGAC 57.432 29.630 0.00 0.00 0.00 3.51
150 151 9.141400 GAATTCGACTTAACTACAAATCTGACT 57.859 33.333 0.00 0.00 0.00 3.41
151 152 9.141400 AGAATTCGACTTAACTACAAATCTGAC 57.859 33.333 0.00 0.00 0.00 3.51
152 153 9.706691 AAGAATTCGACTTAACTACAAATCTGA 57.293 29.630 0.00 0.00 0.00 3.27
158 159 8.992073 GGGTAAAAGAATTCGACTTAACTACAA 58.008 33.333 0.00 0.00 0.00 2.41
159 160 8.149647 TGGGTAAAAGAATTCGACTTAACTACA 58.850 33.333 0.00 0.00 0.00 2.74
160 161 8.538409 TGGGTAAAAGAATTCGACTTAACTAC 57.462 34.615 0.00 0.00 0.00 2.73
161 162 9.558396 TTTGGGTAAAAGAATTCGACTTAACTA 57.442 29.630 0.00 0.00 0.00 2.24
162 163 8.454570 TTTGGGTAAAAGAATTCGACTTAACT 57.545 30.769 0.00 0.00 0.00 2.24
163 164 8.961092 GTTTTGGGTAAAAGAATTCGACTTAAC 58.039 33.333 0.00 2.28 36.51 2.01
164 165 7.856894 CGTTTTGGGTAAAAGAATTCGACTTAA 59.143 33.333 0.00 0.00 36.51 1.85
165 166 7.354257 CGTTTTGGGTAAAAGAATTCGACTTA 58.646 34.615 0.00 0.00 36.51 2.24
166 167 6.203647 CGTTTTGGGTAAAAGAATTCGACTT 58.796 36.000 0.00 0.00 36.51 3.01
167 168 5.754778 CGTTTTGGGTAAAAGAATTCGACT 58.245 37.500 0.00 0.00 36.51 4.18
168 169 4.380678 GCGTTTTGGGTAAAAGAATTCGAC 59.619 41.667 0.00 0.00 36.51 4.20
169 170 4.036498 TGCGTTTTGGGTAAAAGAATTCGA 59.964 37.500 0.00 0.00 36.51 3.71
170 171 4.291783 TGCGTTTTGGGTAAAAGAATTCG 58.708 39.130 0.00 0.00 36.51 3.34
171 172 5.401376 GTCTGCGTTTTGGGTAAAAGAATTC 59.599 40.000 0.00 0.00 36.51 2.17
172 173 5.286438 GTCTGCGTTTTGGGTAAAAGAATT 58.714 37.500 0.00 0.00 36.51 2.17
173 174 4.555906 CGTCTGCGTTTTGGGTAAAAGAAT 60.556 41.667 0.00 0.00 36.51 2.40
174 175 3.242804 CGTCTGCGTTTTGGGTAAAAGAA 60.243 43.478 0.00 0.00 36.51 2.52
175 176 2.288458 CGTCTGCGTTTTGGGTAAAAGA 59.712 45.455 0.00 0.00 36.51 2.52
176 177 2.288458 TCGTCTGCGTTTTGGGTAAAAG 59.712 45.455 0.00 0.00 36.51 2.27
177 178 2.031930 GTCGTCTGCGTTTTGGGTAAAA 59.968 45.455 0.00 0.00 39.49 1.52
178 179 1.598601 GTCGTCTGCGTTTTGGGTAAA 59.401 47.619 0.00 0.00 39.49 2.01
179 180 1.219646 GTCGTCTGCGTTTTGGGTAA 58.780 50.000 0.00 0.00 39.49 2.85
180 181 0.600782 GGTCGTCTGCGTTTTGGGTA 60.601 55.000 0.00 0.00 39.49 3.69
181 182 1.890510 GGTCGTCTGCGTTTTGGGT 60.891 57.895 0.00 0.00 39.49 4.51
182 183 1.841663 CTGGTCGTCTGCGTTTTGGG 61.842 60.000 0.00 0.00 39.49 4.12
183 184 1.569493 CTGGTCGTCTGCGTTTTGG 59.431 57.895 0.00 0.00 39.49 3.28
184 185 1.569493 CCTGGTCGTCTGCGTTTTG 59.431 57.895 0.00 0.00 39.49 2.44
185 186 2.251642 GCCTGGTCGTCTGCGTTTT 61.252 57.895 0.00 0.00 39.49 2.43
186 187 2.665185 GCCTGGTCGTCTGCGTTT 60.665 61.111 0.00 0.00 39.49 3.60
193 194 1.313091 GGAAAATGGGCCTGGTCGTC 61.313 60.000 4.53 0.00 0.00 4.20
197 198 1.610379 GCTGGAAAATGGGCCTGGT 60.610 57.895 4.53 0.00 0.00 4.00
209 210 1.984570 CCGAGAGAGTGGGCTGGAA 60.985 63.158 0.00 0.00 0.00 3.53
226 227 0.325765 AGCTTGGGGTAGGAGAGACC 60.326 60.000 0.00 0.00 39.35 3.85
310 313 0.614979 CGGAGTTGGGGAAGAGGAGA 60.615 60.000 0.00 0.00 0.00 3.71
385 400 1.138661 CAGAAGACTGATGCTCCCTCC 59.861 57.143 0.00 0.00 46.03 4.30
392 407 0.035630 AGTGGGCAGAAGACTGATGC 60.036 55.000 0.00 4.00 46.03 3.91
405 420 1.219393 CTCTCCGAGGAAAGTGGGC 59.781 63.158 0.00 0.00 0.00 5.36
605 622 9.151471 GCAGTAAAAGGAAGAAATTTTTATCCC 57.849 33.333 11.89 2.00 31.41 3.85
674 692 5.522456 CGATAGCAGTACGTTATTGGGTAA 58.478 41.667 0.00 0.00 0.00 2.85
675 693 5.112220 CGATAGCAGTACGTTATTGGGTA 57.888 43.478 0.00 0.00 0.00 3.69
676 694 3.973657 CGATAGCAGTACGTTATTGGGT 58.026 45.455 0.00 0.00 0.00 4.51
698 716 2.217847 CGTTATTAGGTGTTCGCCGATG 59.782 50.000 0.00 0.00 0.00 3.84
706 724 3.181504 GCCGATTTGCGTTATTAGGTGTT 60.182 43.478 0.00 0.00 38.67 3.32
709 727 2.870411 GAGCCGATTTGCGTTATTAGGT 59.130 45.455 0.00 0.00 38.67 3.08
717 735 0.928229 GTATTCGAGCCGATTTGCGT 59.072 50.000 0.00 0.00 38.67 5.24
741 759 4.568592 GGTGGTTTTCTTGATCTGGGAGAT 60.569 45.833 0.00 0.00 37.73 2.75
745 763 2.875296 TGGTGGTTTTCTTGATCTGGG 58.125 47.619 0.00 0.00 0.00 4.45
780 801 2.624838 CAAACAGGTTGAGGACTGCAAT 59.375 45.455 0.00 0.00 39.87 3.56
824 845 1.331756 GGTGCGCATAAGGAACATCTG 59.668 52.381 15.91 0.00 0.00 2.90
826 847 1.064060 GTGGTGCGCATAAGGAACATC 59.936 52.381 15.91 0.00 30.35 3.06
831 852 0.250510 TTGTGTGGTGCGCATAAGGA 60.251 50.000 15.91 0.00 37.45 3.36
836 857 3.033184 CACTTGTGTGGTGCGCAT 58.967 55.556 15.91 0.00 40.33 4.73
865 886 8.862325 TGTTCCACAAGATACACAGATAAAAT 57.138 30.769 0.00 0.00 0.00 1.82
898 921 1.153628 ACAATCTCACCGCCGCTAC 60.154 57.895 0.00 0.00 0.00 3.58
981 1015 4.464244 TCCATCGCCAACAAAATTCCAATA 59.536 37.500 0.00 0.00 0.00 1.90
982 1016 3.260380 TCCATCGCCAACAAAATTCCAAT 59.740 39.130 0.00 0.00 0.00 3.16
1172 1242 5.702670 TCACTGAGATAAAAGCTTGAGTTGG 59.297 40.000 0.00 0.00 0.00 3.77
1280 1436 7.339212 TGTTTGAGTTGCCATAGCTATTATGTT 59.661 33.333 2.64 0.00 37.96 2.71
1281 1437 6.828273 TGTTTGAGTTGCCATAGCTATTATGT 59.172 34.615 2.64 0.00 37.96 2.29
1288 1444 4.081406 TCATTGTTTGAGTTGCCATAGCT 58.919 39.130 0.00 0.00 40.80 3.32
1292 1448 4.942761 AGTTCATTGTTTGAGTTGCCAT 57.057 36.364 0.00 0.00 35.27 4.40
1293 1449 4.887071 ACTAGTTCATTGTTTGAGTTGCCA 59.113 37.500 0.00 0.00 35.27 4.92
1294 1450 5.438761 ACTAGTTCATTGTTTGAGTTGCC 57.561 39.130 0.00 0.00 35.27 4.52
1319 1475 9.515226 ACAACAACATGACAGGTAAGTAATATT 57.485 29.630 0.00 0.00 0.00 1.28
1320 1476 9.515226 AACAACAACATGACAGGTAAGTAATAT 57.485 29.630 0.00 0.00 0.00 1.28
1321 1477 8.911918 AACAACAACATGACAGGTAAGTAATA 57.088 30.769 0.00 0.00 0.00 0.98
1333 1489 9.081997 TCAAGAAACATAAAACAACAACATGAC 57.918 29.630 0.00 0.00 0.00 3.06
1334 1490 9.645059 TTCAAGAAACATAAAACAACAACATGA 57.355 25.926 0.00 0.00 0.00 3.07
2078 2252 4.453819 ACAAGATCTGCTGTGACTTAAAGC 59.546 41.667 0.00 0.00 37.46 3.51
2243 2432 3.645212 TCCTCCTCATTGTCCTCATCATC 59.355 47.826 0.00 0.00 0.00 2.92
2272 2473 6.710744 TGACACTTAAAGGTCTTTCATCTTCC 59.289 38.462 0.00 0.00 35.11 3.46
2273 2474 7.657761 TCTGACACTTAAAGGTCTTTCATCTTC 59.342 37.037 0.00 0.00 35.11 2.87
2274 2475 7.509546 TCTGACACTTAAAGGTCTTTCATCTT 58.490 34.615 0.00 0.00 35.11 2.40
2315 2516 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
2316 2517 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
2317 2518 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
2393 2594 2.753452 CCTGCCCATCATCATGATAAGC 59.247 50.000 8.15 12.28 34.28 3.09
2415 2616 2.014033 ATCCTCCTCGTCCTCCTCCC 62.014 65.000 0.00 0.00 0.00 4.30
2556 2766 1.522580 GGAGCTGGACGCATTCCTC 60.523 63.158 0.00 0.00 46.10 3.71
2562 2772 4.383861 CTGCAGGAGCTGGACGCA 62.384 66.667 5.57 0.00 42.61 5.24
2565 2775 0.250467 TTGAACTGCAGGAGCTGGAC 60.250 55.000 19.93 0.70 43.24 4.02
2690 2900 4.586421 TCATCCTCACCATCAGTATCAGAC 59.414 45.833 0.00 0.00 0.00 3.51
2878 3093 1.153529 CACACGCCGCCCAGTAATA 60.154 57.895 0.00 0.00 0.00 0.98
2889 3104 0.460311 AGACTATACAGCCACACGCC 59.540 55.000 0.00 0.00 38.78 5.68
2901 3116 3.521560 CCAAAGCTGCGTTCAGACTATA 58.478 45.455 0.00 0.00 42.95 1.31
2903 3118 1.608025 CCCAAAGCTGCGTTCAGACTA 60.608 52.381 0.00 0.00 42.95 2.59
2912 3127 0.597568 TCATCAAACCCAAAGCTGCG 59.402 50.000 0.00 0.00 0.00 5.18
2974 3189 0.106419 TTGCCCACGGGAGAAACTTT 60.106 50.000 6.21 0.00 37.50 2.66
2999 3214 7.713764 TTATTCATGACTGTTACATCATCCG 57.286 36.000 0.00 0.82 33.18 4.18
3067 3282 2.035066 AGCCACATTGTTGAAGCAACTC 59.965 45.455 11.11 0.00 43.85 3.01
3143 3358 1.262417 TGGTTCATACTCGGCAGTCA 58.738 50.000 0.00 0.00 33.62 3.41
3173 3388 9.739276 AAAAGAGAGATACAAACATCATAACCA 57.261 29.630 0.00 0.00 0.00 3.67
3191 3406 6.742109 TGCAGAAATGAAAAGGAAAAGAGAG 58.258 36.000 0.00 0.00 0.00 3.20
3221 3436 0.109272 GCGACCTTGTGATCTCGTGA 60.109 55.000 0.00 0.00 0.00 4.35
3274 3492 5.613186 CGATTCAGAAGAAAAATACATCGCG 59.387 40.000 0.00 0.00 37.29 5.87
3282 3500 6.638468 GTCAAAGCACGATTCAGAAGAAAAAT 59.362 34.615 0.00 0.00 37.29 1.82
3285 3503 4.816385 AGTCAAAGCACGATTCAGAAGAAA 59.184 37.500 0.00 0.00 37.29 2.52
3309 3530 7.439157 TCTTCAGATAACCAAACATCTGTTG 57.561 36.000 10.45 6.08 45.50 3.33
3339 3560 5.024555 GCTACAAATGACAGAGAATTTCGC 58.975 41.667 0.00 0.00 0.00 4.70
3376 3613 7.011295 ACAACTCTAGTAGTATAACTCGCTGAC 59.989 40.741 0.00 0.00 37.50 3.51
3379 3616 7.201714 CCAACAACTCTAGTAGTATAACTCGCT 60.202 40.741 0.00 0.00 37.50 4.93
3396 3633 3.531538 TGTTCTGAGTGTCCAACAACTC 58.468 45.455 0.00 0.00 31.49 3.01
3407 3644 6.332630 ACTTCCACAAAAATTGTTCTGAGTG 58.667 36.000 0.00 0.00 43.23 3.51
3410 3647 8.690884 TGATTACTTCCACAAAAATTGTTCTGA 58.309 29.630 0.00 0.00 43.23 3.27
3446 3683 4.697352 ACGACTAGTTGTATAACTCACCGT 59.303 41.667 14.42 12.54 43.53 4.83
3460 3697 2.093106 CTGTGAGGGCTACGACTAGTT 58.907 52.381 0.00 0.00 0.00 2.24
3464 3701 0.681564 CTCCTGTGAGGGCTACGACT 60.682 60.000 0.00 0.00 35.59 4.18
3465 3702 1.810532 CTCCTGTGAGGGCTACGAC 59.189 63.158 0.00 0.00 35.59 4.34
3466 3703 2.052690 GCTCCTGTGAGGGCTACGA 61.053 63.158 0.00 0.00 39.14 3.43
3477 3714 3.067091 CTCCACAGCTGCTCCTGT 58.933 61.111 15.27 4.32 46.47 4.00
3503 3740 1.065701 AGCTACAGACGACTAATGCCG 59.934 52.381 0.00 0.00 0.00 5.69
3510 3747 5.419471 AGATAAAAGGAAGCTACAGACGACT 59.581 40.000 0.00 0.00 0.00 4.18
3513 3750 5.897050 AGAGATAAAAGGAAGCTACAGACG 58.103 41.667 0.00 0.00 0.00 4.18
3516 3753 6.810911 TGCTAGAGATAAAAGGAAGCTACAG 58.189 40.000 0.00 0.00 0.00 2.74
3519 3756 7.124298 TCAGTTGCTAGAGATAAAAGGAAGCTA 59.876 37.037 0.00 0.00 0.00 3.32
3520 3757 6.070538 TCAGTTGCTAGAGATAAAAGGAAGCT 60.071 38.462 0.00 0.00 0.00 3.74
3521 3758 6.109359 TCAGTTGCTAGAGATAAAAGGAAGC 58.891 40.000 0.00 0.00 0.00 3.86
3522 3759 8.447053 GTTTCAGTTGCTAGAGATAAAAGGAAG 58.553 37.037 0.00 0.00 0.00 3.46
3523 3760 8.157476 AGTTTCAGTTGCTAGAGATAAAAGGAA 58.843 33.333 0.00 0.00 0.00 3.36
3524 3761 7.680730 AGTTTCAGTTGCTAGAGATAAAAGGA 58.319 34.615 0.00 0.00 0.00 3.36
3525 3762 7.913674 AGTTTCAGTTGCTAGAGATAAAAGG 57.086 36.000 0.00 0.00 0.00 3.11
3529 3766 8.784043 GGAAAAAGTTTCAGTTGCTAGAGATAA 58.216 33.333 0.00 0.00 0.00 1.75
3530 3767 7.936847 TGGAAAAAGTTTCAGTTGCTAGAGATA 59.063 33.333 0.00 0.00 0.00 1.98
3531 3768 6.772716 TGGAAAAAGTTTCAGTTGCTAGAGAT 59.227 34.615 0.00 0.00 0.00 2.75
3532 3769 6.038271 GTGGAAAAAGTTTCAGTTGCTAGAGA 59.962 38.462 0.00 0.00 0.00 3.10
3533 3770 6.038714 AGTGGAAAAAGTTTCAGTTGCTAGAG 59.961 38.462 0.00 0.00 0.00 2.43
3534 3771 5.885912 AGTGGAAAAAGTTTCAGTTGCTAGA 59.114 36.000 0.00 0.00 0.00 2.43
3535 3772 5.973565 CAGTGGAAAAAGTTTCAGTTGCTAG 59.026 40.000 3.35 0.00 0.00 3.42
3544 3781 5.465935 TCACACAACAGTGGAAAAAGTTTC 58.534 37.500 0.00 0.00 39.93 2.78
3549 3786 6.375736 TGACTATTCACACAACAGTGGAAAAA 59.624 34.615 0.00 0.00 39.93 1.94
3556 3793 6.061441 TGGATTTGACTATTCACACAACAGT 58.939 36.000 0.00 0.00 0.00 3.55
3570 3807 3.393941 GGGATCCTCATCTGGATTTGACT 59.606 47.826 12.58 0.00 46.00 3.41
3576 3813 3.581518 AGATGGGATCCTCATCTGGAT 57.418 47.619 29.92 15.81 46.56 3.41
3581 3818 3.251484 TGGGTTAGATGGGATCCTCATC 58.749 50.000 24.73 24.73 40.79 2.92
3585 3822 2.858644 TGTTGGGTTAGATGGGATCCT 58.141 47.619 12.58 0.00 0.00 3.24
3598 3835 1.209504 CCATGTAGACCGATGTTGGGT 59.790 52.381 0.00 0.00 41.48 4.51
3599 3836 1.953559 CCATGTAGACCGATGTTGGG 58.046 55.000 0.00 0.00 0.00 4.12
3601 3838 2.022764 TGCCATGTAGACCGATGTTG 57.977 50.000 0.00 0.00 0.00 3.33
3607 3844 3.792401 TGTCTATTTGCCATGTAGACCG 58.208 45.455 14.50 0.00 42.17 4.79
3617 3854 7.422399 TGTTAAGTTGACTTTGTCTATTTGCC 58.578 34.615 1.20 0.00 37.40 4.52
3624 3861 8.952278 TGTACATTTGTTAAGTTGACTTTGTCT 58.048 29.630 1.20 0.00 37.40 3.41
3626 3863 8.188139 CCTGTACATTTGTTAAGTTGACTTTGT 58.812 33.333 0.00 2.38 37.40 2.83
3633 3870 8.007716 CGAGTTACCTGTACATTTGTTAAGTTG 58.992 37.037 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.