Multiple sequence alignment - TraesCS1D01G175400

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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 TraesCS1D01G175400 chr1D 100.000 3136 0 0 1 3136 249559094 249562229 0.000000e+00 5792.0
1 TraesCS1D01G175400 chr1D 96.053 76 2 1 2503 2578 433912603 433912677 4.250000e-24 122.0
2 TraesCS1D01G175400 chr1A 92.601 2311 91 38 243 2501 319319293 319321575 0.000000e+00 3247.0
3 TraesCS1D01G175400 chr1A 89.835 364 13 12 2726 3085 319321690 319322033 2.220000e-121 446.0
4 TraesCS1D01G175400 chr1A 96.000 100 4 0 2580 2679 319321579 319321678 2.500000e-36 163.0
5 TraesCS1D01G175400 chr1B 90.279 2541 129 59 25 2505 364920617 364918135 0.000000e+00 3216.0
6 TraesCS1D01G175400 chr1B 88.787 437 15 13 2711 3136 364917674 364917261 3.610000e-139 505.0
7 TraesCS1D01G175400 chr1B 88.028 142 9 5 2580 2713 364918137 364917996 9.000000e-36 161.0
8 TraesCS1D01G175400 chr4B 79.682 566 78 25 1535 2077 670850350 670849799 1.060000e-99 374.0
9 TraesCS1D01G175400 chr4B 84.836 244 23 6 1122 1352 670850698 670850456 1.880000e-57 233.0
10 TraesCS1D01G175400 chr5A 78.723 564 83 26 1537 2077 708723262 708722713 2.990000e-90 342.0
11 TraesCS1D01G175400 chr5A 85.246 244 22 5 1122 1352 708723609 708723367 4.040000e-59 239.0
12 TraesCS1D01G175400 chr5A 84.615 117 13 5 1181 1293 645412954 645412839 9.190000e-21 111.0
13 TraesCS1D01G175400 chrUn 78.354 559 92 21 1535 2077 28674849 28675394 5.010000e-88 335.0
14 TraesCS1D01G175400 chrUn 84.836 244 23 8 1122 1352 28674504 28674746 1.880000e-57 233.0
15 TraesCS1D01G175400 chr6D 77.677 439 79 17 1448 1872 313187830 313187397 1.870000e-62 250.0
16 TraesCS1D01G175400 chr6D 80.365 219 40 3 1132 1347 313188161 313187943 2.500000e-36 163.0
17 TraesCS1D01G175400 chr6D 92.683 82 3 1 2497 2578 157373745 157373823 7.110000e-22 115.0
18 TraesCS1D01G175400 chr6D 90.698 86 4 2 2499 2584 296865629 296865710 9.190000e-21 111.0
19 TraesCS1D01G175400 chr6A 77.523 436 85 10 1448 1872 450107902 450107469 1.870000e-62 250.0
20 TraesCS1D01G175400 chr6A 80.822 219 39 3 1132 1347 450108236 450108018 5.380000e-38 169.0
21 TraesCS1D01G175400 chr6A 90.588 85 1 3 2503 2585 501479360 501479281 4.280000e-19 106.0
22 TraesCS1D01G175400 chr6B 77.251 422 79 12 1448 1856 513135974 513136391 6.760000e-57 231.0
23 TraesCS1D01G175400 chr6B 79.909 219 41 3 1132 1347 513135661 513135879 1.160000e-34 158.0
24 TraesCS1D01G175400 chr3D 93.827 81 2 2 2498 2578 110398466 110398389 5.490000e-23 119.0
25 TraesCS1D01G175400 chr5D 92.593 81 5 1 2499 2579 106658786 106658707 7.110000e-22 115.0
26 TraesCS1D01G175400 chr5D 89.362 94 6 2 2491 2580 389245510 389245417 7.110000e-22 115.0
27 TraesCS1D01G175400 chr7A 88.776 98 4 6 2503 2596 381248763 381248669 2.560000e-21 113.0
28 TraesCS1D01G175400 chr7A 90.196 51 4 1 1806 1856 103214920 103214871 7.260000e-07 65.8
29 TraesCS1D01G175400 chr2B 91.765 85 2 3 2500 2579 726552128 726552212 2.560000e-21 113.0
30 TraesCS1D01G175400 chr7D 90.196 51 4 1 1806 1856 101095138 101095089 7.260000e-07 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G175400 chr1D 249559094 249562229 3135 False 5792.000000 5792 100.000000 1 3136 1 chr1D.!!$F1 3135
1 TraesCS1D01G175400 chr1A 319319293 319322033 2740 False 1285.333333 3247 92.812000 243 3085 3 chr1A.!!$F1 2842
2 TraesCS1D01G175400 chr1B 364917261 364920617 3356 True 1294.000000 3216 89.031333 25 3136 3 chr1B.!!$R1 3111
3 TraesCS1D01G175400 chr4B 670849799 670850698 899 True 303.500000 374 82.259000 1122 2077 2 chr4B.!!$R1 955
4 TraesCS1D01G175400 chr5A 708722713 708723609 896 True 290.500000 342 81.984500 1122 2077 2 chr5A.!!$R2 955
5 TraesCS1D01G175400 chrUn 28674504 28675394 890 False 284.000000 335 81.595000 1122 2077 2 chrUn.!!$F1 955
6 TraesCS1D01G175400 chr6D 313187397 313188161 764 True 206.500000 250 79.021000 1132 1872 2 chr6D.!!$R1 740
7 TraesCS1D01G175400 chr6A 450107469 450108236 767 True 209.500000 250 79.172500 1132 1872 2 chr6A.!!$R2 740

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
631 665 0.099436 GCCCATGACTGATTTCGTGC 59.901 55.0 0.0 0.0 32.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 2400 0.997196 CTACTACCGCTTTGTTCGCC 59.003 55.0 0.0 0.0 0.0 5.54 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
20 21 1.616865 TGTCCTAGACAGACCCAAACG 59.383 52.381 0.00 0.00 37.67 3.60
21 22 1.891150 GTCCTAGACAGACCCAAACGA 59.109 52.381 0.00 0.00 32.09 3.85
22 23 2.298163 GTCCTAGACAGACCCAAACGAA 59.702 50.000 0.00 0.00 32.09 3.85
23 24 2.967201 TCCTAGACAGACCCAAACGAAA 59.033 45.455 0.00 0.00 0.00 3.46
32 33 1.684450 ACCCAAACGAAAATGTCACCC 59.316 47.619 0.00 0.00 0.00 4.61
36 37 3.181480 CCAAACGAAAATGTCACCCAACT 60.181 43.478 0.00 0.00 0.00 3.16
38 39 5.278758 CCAAACGAAAATGTCACCCAACTAT 60.279 40.000 0.00 0.00 0.00 2.12
41 42 4.939439 ACGAAAATGTCACCCAACTATACC 59.061 41.667 0.00 0.00 0.00 2.73
42 43 4.938832 CGAAAATGTCACCCAACTATACCA 59.061 41.667 0.00 0.00 0.00 3.25
44 45 4.503714 AATGTCACCCAACTATACCAGG 57.496 45.455 0.00 0.00 0.00 4.45
46 47 3.253220 TGTCACCCAACTATACCAGGTT 58.747 45.455 0.00 0.00 0.00 3.50
47 48 3.008594 TGTCACCCAACTATACCAGGTTG 59.991 47.826 0.00 0.00 41.46 3.77
48 49 2.026636 TCACCCAACTATACCAGGTTGC 60.027 50.000 0.00 0.00 40.75 4.17
50 51 1.663695 CCAACTATACCAGGTTGCGG 58.336 55.000 0.00 0.00 40.75 5.69
54 55 3.706600 ACTATACCAGGTTGCGGAAAA 57.293 42.857 0.00 0.00 0.00 2.29
55 56 4.023726 ACTATACCAGGTTGCGGAAAAA 57.976 40.909 0.00 0.00 0.00 1.94
60 61 1.618343 CCAGGTTGCGGAAAAAGGATT 59.382 47.619 0.00 0.00 0.00 3.01
62 63 1.893137 AGGTTGCGGAAAAAGGATTCC 59.107 47.619 0.00 0.00 44.50 3.01
63 64 1.893137 GGTTGCGGAAAAAGGATTCCT 59.107 47.619 0.00 0.00 45.54 3.36
71 72 7.897864 TGCGGAAAAAGGATTCCTTAATTTTA 58.102 30.769 18.24 0.96 43.92 1.52
116 122 6.527722 CGTGAGGGACAAAATACATTTTCATG 59.472 38.462 0.00 0.00 37.86 3.07
117 123 7.378181 GTGAGGGACAAAATACATTTTCATGT 58.622 34.615 0.00 0.00 46.07 3.21
118 124 7.329226 GTGAGGGACAAAATACATTTTCATGTG 59.671 37.037 0.00 0.00 43.92 3.21
120 126 8.137745 AGGGACAAAATACATTTTCATGTGAT 57.862 30.769 0.00 0.00 43.92 3.06
121 127 9.253832 AGGGACAAAATACATTTTCATGTGATA 57.746 29.630 0.00 0.00 43.92 2.15
122 128 9.301153 GGGACAAAATACATTTTCATGTGATAC 57.699 33.333 0.00 0.00 43.92 2.24
123 129 9.853555 GGACAAAATACATTTTCATGTGATACA 57.146 29.630 0.00 0.00 43.92 2.29
165 171 3.430042 ACACCAAGTGAATGCTGATCT 57.570 42.857 0.96 0.00 36.96 2.75
167 173 4.147321 ACACCAAGTGAATGCTGATCTTT 58.853 39.130 0.96 0.00 36.96 2.52
168 174 5.316167 ACACCAAGTGAATGCTGATCTTTA 58.684 37.500 0.96 0.00 36.96 1.85
174 180 7.281774 CCAAGTGAATGCTGATCTTTACATAGT 59.718 37.037 0.00 0.00 0.00 2.12
176 182 8.879342 AGTGAATGCTGATCTTTACATAGTAC 57.121 34.615 0.00 0.00 0.00 2.73
185 191 7.433680 TGATCTTTACATAGTACGATGCACAT 58.566 34.615 15.04 0.00 0.00 3.21
187 193 9.406828 GATCTTTACATAGTACGATGCACATAA 57.593 33.333 15.04 4.67 0.00 1.90
193 199 2.927477 AGTACGATGCACATAACCAACG 59.073 45.455 0.00 0.00 34.11 4.10
195 201 0.586256 CGATGCACATAACCAACGCG 60.586 55.000 3.53 3.53 0.00 6.01
200 206 0.165079 CACATAACCAACGCGTCCAC 59.835 55.000 14.44 0.00 0.00 4.02
204 210 2.992607 TAACCAACGCGTCCACCACC 62.993 60.000 14.44 0.00 0.00 4.61
207 213 4.164087 AACGCGTCCACCACCACA 62.164 61.111 14.44 0.00 0.00 4.17
208 214 3.683966 AACGCGTCCACCACCACAA 62.684 57.895 14.44 0.00 0.00 3.33
212 218 1.725066 CGTCCACCACCACAACAAC 59.275 57.895 0.00 0.00 0.00 3.32
215 221 1.135228 GTCCACCACCACAACAACAAC 60.135 52.381 0.00 0.00 0.00 3.32
218 224 2.333014 CACCACCACAACAACAACAAC 58.667 47.619 0.00 0.00 0.00 3.32
220 226 2.365617 ACCACCACAACAACAACAACAA 59.634 40.909 0.00 0.00 0.00 2.83
221 227 3.181465 ACCACCACAACAACAACAACAAA 60.181 39.130 0.00 0.00 0.00 2.83
224 230 4.928615 CACCACAACAACAACAACAAATCT 59.071 37.500 0.00 0.00 0.00 2.40
231 237 8.217778 ACAACAACAACAACAAATCTTTTTACG 58.782 29.630 0.00 0.00 0.00 3.18
233 239 6.869388 ACAACAACAACAAATCTTTTTACGGT 59.131 30.769 0.00 0.00 0.00 4.83
236 242 6.528774 ACAACAACAAATCTTTTTACGGTGAC 59.471 34.615 0.00 0.00 0.00 3.67
237 243 6.445357 ACAACAAATCTTTTTACGGTGACT 57.555 33.333 0.00 0.00 0.00 3.41
238 244 6.859017 ACAACAAATCTTTTTACGGTGACTT 58.141 32.000 0.00 0.00 0.00 3.01
239 245 7.987649 ACAACAAATCTTTTTACGGTGACTTA 58.012 30.769 0.00 0.00 0.00 2.24
240 246 8.126700 ACAACAAATCTTTTTACGGTGACTTAG 58.873 33.333 0.00 0.00 0.00 2.18
241 247 7.198306 ACAAATCTTTTTACGGTGACTTAGG 57.802 36.000 0.00 0.00 0.00 2.69
250 259 1.450025 GGTGACTTAGGAAAAGCCCG 58.550 55.000 0.00 0.00 37.37 6.13
252 261 0.322187 TGACTTAGGAAAAGCCCGGC 60.322 55.000 0.00 0.00 37.37 6.13
305 317 3.120338 CGACAAATGTAAATGGCACGACT 60.120 43.478 0.00 0.00 0.00 4.18
349 361 4.055710 TCATCAGGTGTACCTTACTCCA 57.944 45.455 0.00 0.00 46.09 3.86
430 445 3.228017 GGTAGGGAGGCTCGGCTC 61.228 72.222 8.69 11.63 0.00 4.70
431 446 3.228017 GTAGGGAGGCTCGGCTCC 61.228 72.222 26.32 26.32 38.96 4.70
432 447 3.430497 TAGGGAGGCTCGGCTCCT 61.430 66.667 30.72 21.37 39.58 3.69
543 558 7.415541 CGTCCATGTGTTGATCCAATTATTTCT 60.416 37.037 0.00 0.00 0.00 2.52
548 563 5.656416 GTGTTGATCCAATTATTTCTCCCCA 59.344 40.000 0.00 0.00 0.00 4.96
549 564 5.893255 TGTTGATCCAATTATTTCTCCCCAG 59.107 40.000 0.00 0.00 0.00 4.45
572 588 0.466963 GGACCATTATTCCCGTCCGT 59.533 55.000 0.00 0.00 35.78 4.69
588 614 4.202080 CCGTCCGTTGTAATCTATTGGAGA 60.202 45.833 0.00 0.00 39.01 3.71
589 615 4.976731 CGTCCGTTGTAATCTATTGGAGAG 59.023 45.833 0.00 0.00 37.70 3.20
631 665 0.099436 GCCCATGACTGATTTCGTGC 59.901 55.000 0.00 0.00 32.00 5.34
640 674 6.588348 TGACTGATTTCGTGCATGTATTAG 57.412 37.500 5.68 9.32 0.00 1.73
643 677 7.926018 TGACTGATTTCGTGCATGTATTAGTAT 59.074 33.333 15.63 0.00 0.00 2.12
742 778 1.375908 GCCACAGCGAGATGGTTCA 60.376 57.895 0.00 0.00 38.34 3.18
789 829 3.558533 CCTGCCTGCATAATGATCTGCTA 60.559 47.826 6.27 0.00 39.16 3.49
901 941 1.202533 CCGCCGTTCTCTCCACAATAT 60.203 52.381 0.00 0.00 0.00 1.28
908 948 4.979197 CGTTCTCTCCACAATATACAGAGC 59.021 45.833 0.00 0.00 32.19 4.09
910 950 5.521906 TCTCTCCACAATATACAGAGCAC 57.478 43.478 0.00 0.00 32.19 4.40
911 951 4.956075 TCTCTCCACAATATACAGAGCACA 59.044 41.667 0.00 0.00 32.19 4.57
912 952 5.068329 TCTCTCCACAATATACAGAGCACAG 59.932 44.000 0.00 0.00 32.19 3.66
966 1031 2.075489 CGTCTCGTCTCGTGTGTGC 61.075 63.158 0.00 0.00 0.00 4.57
971 1036 2.237066 CGTCTCGTGTGTGCTTGCA 61.237 57.895 0.00 0.00 0.00 4.08
976 1041 1.063912 CTCGTGTGTGCTTGCAAGAAA 59.936 47.619 30.39 14.20 0.00 2.52
1068 1133 1.292223 CGACGGTGACATGGAGGTT 59.708 57.895 0.00 0.00 0.00 3.50
1113 1178 3.330720 AAAGGGGGCGAGGAGGTG 61.331 66.667 0.00 0.00 0.00 4.00
1396 1500 4.724602 TCTGCTCTGTGCCGCGTC 62.725 66.667 4.92 0.00 42.00 5.19
1441 1545 6.347696 TGAAGCTGAATTGTTTGTGGATTTT 58.652 32.000 0.00 0.00 0.00 1.82
1460 1564 2.660064 GGTCGGTGCAGATGAGGGT 61.660 63.158 0.00 0.00 0.00 4.34
2137 2289 1.452833 GCCAGGGGAAGCTGTGATC 60.453 63.158 0.00 0.00 0.00 2.92
2190 2350 2.625737 CCAGCTGTAACCTGTGATGAG 58.374 52.381 13.81 0.00 0.00 2.90
2204 2364 0.321034 GATGAGTGGTGTGAGCTGCA 60.321 55.000 1.02 0.00 0.00 4.41
2213 2373 1.890979 GTGAGCTGCACTGCACACT 60.891 57.895 17.34 8.32 46.05 3.55
2225 2385 2.046892 CACACTTGGAGCCTCGGG 60.047 66.667 0.00 0.00 0.00 5.14
2286 2447 4.660352 GAGCATATCGAAAAGCCATCTC 57.340 45.455 0.00 0.00 0.00 2.75
2287 2448 3.062763 AGCATATCGAAAAGCCATCTCG 58.937 45.455 0.00 0.00 0.00 4.04
2319 2481 3.175438 AGGATGGGGAAAAAGAGTTGG 57.825 47.619 0.00 0.00 0.00 3.77
2337 2499 5.023452 AGTTGGTTTGGAAGAGAAAAAGGT 58.977 37.500 0.00 0.00 0.00 3.50
2338 2500 6.192044 AGTTGGTTTGGAAGAGAAAAAGGTA 58.808 36.000 0.00 0.00 0.00 3.08
2339 2501 6.666113 AGTTGGTTTGGAAGAGAAAAAGGTAA 59.334 34.615 0.00 0.00 0.00 2.85
2340 2502 6.459670 TGGTTTGGAAGAGAAAAAGGTAAC 57.540 37.500 0.00 0.00 0.00 2.50
2501 2664 6.036626 GGTGATTGTTTGGTTGGTTTGTAAAG 59.963 38.462 0.00 0.00 0.00 1.85
2502 2665 6.592220 GTGATTGTTTGGTTGGTTTGTAAAGT 59.408 34.615 0.00 0.00 0.00 2.66
2503 2666 7.760340 GTGATTGTTTGGTTGGTTTGTAAAGTA 59.240 33.333 0.00 0.00 0.00 2.24
2504 2667 7.760340 TGATTGTTTGGTTGGTTTGTAAAGTAC 59.240 33.333 0.00 0.00 0.00 2.73
2505 2668 6.837471 TGTTTGGTTGGTTTGTAAAGTACT 57.163 33.333 0.00 0.00 0.00 2.73
2506 2669 6.854778 TGTTTGGTTGGTTTGTAAAGTACTC 58.145 36.000 0.00 0.00 0.00 2.59
2507 2670 6.127675 TGTTTGGTTGGTTTGTAAAGTACTCC 60.128 38.462 0.00 0.00 0.00 3.85
2508 2671 4.463070 TGGTTGGTTTGTAAAGTACTCCC 58.537 43.478 0.00 0.00 0.00 4.30
2509 2672 4.166531 TGGTTGGTTTGTAAAGTACTCCCT 59.833 41.667 0.00 0.00 0.00 4.20
2510 2673 4.758674 GGTTGGTTTGTAAAGTACTCCCTC 59.241 45.833 0.00 0.00 0.00 4.30
2511 2674 4.628963 TGGTTTGTAAAGTACTCCCTCC 57.371 45.455 0.00 0.00 0.00 4.30
2512 2675 3.007182 TGGTTTGTAAAGTACTCCCTCCG 59.993 47.826 0.00 0.00 0.00 4.63
2513 2676 3.007290 GGTTTGTAAAGTACTCCCTCCGT 59.993 47.826 0.00 0.00 0.00 4.69
2514 2677 4.240888 GTTTGTAAAGTACTCCCTCCGTC 58.759 47.826 0.00 0.00 0.00 4.79
2515 2678 2.450476 TGTAAAGTACTCCCTCCGTCC 58.550 52.381 0.00 0.00 0.00 4.79
2516 2679 1.753649 GTAAAGTACTCCCTCCGTCCC 59.246 57.143 0.00 0.00 0.00 4.46
2517 2680 0.115745 AAAGTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
2518 2681 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
2519 2682 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2520 2683 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2521 2684 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2522 2685 3.400322 AGTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
2523 2686 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2524 2687 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2525 2688 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2526 2689 5.408824 ACTCCCTCCGTCCCATAATATAAA 58.591 41.667 0.00 0.00 0.00 1.40
2527 2690 5.847817 ACTCCCTCCGTCCCATAATATAAAA 59.152 40.000 0.00 0.00 0.00 1.52
2528 2691 6.013639 ACTCCCTCCGTCCCATAATATAAAAG 60.014 42.308 0.00 0.00 0.00 2.27
2529 2692 4.941873 CCCTCCGTCCCATAATATAAAAGC 59.058 45.833 0.00 0.00 0.00 3.51
2530 2693 4.630069 CCTCCGTCCCATAATATAAAAGCG 59.370 45.833 0.00 0.00 0.00 4.68
2531 2694 5.217978 TCCGTCCCATAATATAAAAGCGT 57.782 39.130 0.00 0.00 0.00 5.07
2532 2695 5.613329 TCCGTCCCATAATATAAAAGCGTT 58.387 37.500 0.00 0.00 0.00 4.84
2533 2696 6.056884 TCCGTCCCATAATATAAAAGCGTTT 58.943 36.000 2.53 2.53 0.00 3.60
2534 2697 6.543100 TCCGTCCCATAATATAAAAGCGTTTT 59.457 34.615 2.19 1.29 36.67 2.43
2535 2698 7.067251 TCCGTCCCATAATATAAAAGCGTTTTT 59.933 33.333 14.50 14.50 39.69 1.94
2536 2699 7.166804 CCGTCCCATAATATAAAAGCGTTTTTG 59.833 37.037 18.77 2.23 37.12 2.44
2537 2700 7.911205 CGTCCCATAATATAAAAGCGTTTTTGA 59.089 33.333 18.77 8.06 37.12 2.69
2538 2701 9.016623 GTCCCATAATATAAAAGCGTTTTTGAC 57.983 33.333 18.77 10.56 37.12 3.18
2539 2702 8.740906 TCCCATAATATAAAAGCGTTTTTGACA 58.259 29.630 18.77 5.33 37.12 3.58
2540 2703 8.803799 CCCATAATATAAAAGCGTTTTTGACAC 58.196 33.333 18.77 0.00 37.12 3.67
2541 2704 9.567848 CCATAATATAAAAGCGTTTTTGACACT 57.432 29.630 18.77 3.85 37.12 3.55
2548 2711 7.820044 AAAAGCGTTTTTGACACTAATCAAA 57.180 28.000 9.31 0.00 44.80 2.69
2549 2712 6.806120 AAGCGTTTTTGACACTAATCAAAC 57.194 33.333 0.55 0.00 45.84 2.93
2550 2713 4.967575 AGCGTTTTTGACACTAATCAAACG 59.032 37.500 9.92 9.92 45.84 3.60
2551 2714 5.219113 CGTTTTTGACACTAATCAAACGC 57.781 39.130 0.55 0.00 45.84 4.84
2552 2715 4.967575 CGTTTTTGACACTAATCAAACGCT 59.032 37.500 0.55 0.00 45.84 5.07
2553 2716 5.113529 CGTTTTTGACACTAATCAAACGCTC 59.886 40.000 0.55 0.00 45.84 5.03
2554 2717 6.199393 GTTTTTGACACTAATCAAACGCTCT 58.801 36.000 0.55 0.00 45.84 4.09
2555 2718 6.371809 TTTTGACACTAATCAAACGCTCTT 57.628 33.333 0.55 0.00 45.84 2.85
2556 2719 7.485418 TTTTGACACTAATCAAACGCTCTTA 57.515 32.000 0.55 0.00 45.84 2.10
2557 2720 7.667043 TTTGACACTAATCAAACGCTCTTAT 57.333 32.000 0.00 0.00 42.32 1.73
2558 2721 8.766000 TTTGACACTAATCAAACGCTCTTATA 57.234 30.769 0.00 0.00 42.32 0.98
2559 2722 8.942338 TTGACACTAATCAAACGCTCTTATAT 57.058 30.769 0.00 0.00 35.65 0.86
2560 2723 8.942338 TGACACTAATCAAACGCTCTTATATT 57.058 30.769 0.00 0.00 0.00 1.28
2565 2728 9.436957 ACTAATCAAACGCTCTTATATTATGGG 57.563 33.333 0.00 0.00 0.00 4.00
2566 2729 9.653287 CTAATCAAACGCTCTTATATTATGGGA 57.347 33.333 0.00 0.00 0.00 4.37
2567 2730 7.907214 ATCAAACGCTCTTATATTATGGGAC 57.093 36.000 0.00 0.00 0.00 4.46
2568 2731 5.924254 TCAAACGCTCTTATATTATGGGACG 59.076 40.000 0.00 0.00 0.00 4.79
2569 2732 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
2570 2733 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
2571 2734 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
2572 2735 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
2573 2736 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
2574 2737 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
2575 2738 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2576 2739 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2577 2740 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2578 2741 3.562108 ATTATGGGACGGAGGGAGTAT 57.438 47.619 0.00 0.00 0.00 2.12
2611 2778 4.176271 GTTCTTGCTGCTGTTCAAAGTTT 58.824 39.130 0.00 0.00 0.00 2.66
2612 2779 3.772932 TCTTGCTGCTGTTCAAAGTTTG 58.227 40.909 9.44 9.44 0.00 2.93
2613 2780 3.193267 TCTTGCTGCTGTTCAAAGTTTGT 59.807 39.130 15.08 0.00 0.00 2.83
2614 2781 3.591196 TGCTGCTGTTCAAAGTTTGTT 57.409 38.095 15.08 0.00 0.00 2.83
2646 2825 3.181469 TGTTTGTGGTTCGAGCTTCTACT 60.181 43.478 0.00 0.00 0.00 2.57
2737 3240 5.449588 CCGCTATAGTAATATGGTACGGTGG 60.450 48.000 0.84 0.00 32.53 4.61
2749 3252 1.940883 TACGGTGGCGTCAGATGGAC 61.941 60.000 0.00 0.00 43.36 4.02
2791 3294 6.329496 CAGGTTCAAAAGCAGAAAGTAAACA 58.671 36.000 0.00 0.00 0.00 2.83
2860 3370 0.967380 GGGTTTGGATCCTGGCACTG 60.967 60.000 14.23 0.00 0.00 3.66
2892 3402 2.586245 CCAGAGCGCCAGATTCCA 59.414 61.111 2.29 0.00 0.00 3.53
2893 3403 1.078214 CCAGAGCGCCAGATTCCAA 60.078 57.895 2.29 0.00 0.00 3.53
2942 3455 2.844654 TTCTCCTCCTCTCTCTGCAT 57.155 50.000 0.00 0.00 0.00 3.96
2948 3461 5.664908 TCTCCTCCTCTCTCTGCATAAAAAT 59.335 40.000 0.00 0.00 0.00 1.82
2976 3489 3.118847 CCATGGCGCTCTCTGACATATAT 60.119 47.826 7.64 0.00 0.00 0.86
2977 3490 3.582714 TGGCGCTCTCTGACATATATG 57.417 47.619 7.64 11.29 0.00 1.78
2979 3492 2.232452 GGCGCTCTCTGACATATATGGT 59.768 50.000 16.96 2.89 0.00 3.55
2980 3493 3.444034 GGCGCTCTCTGACATATATGGTA 59.556 47.826 16.96 4.58 0.00 3.25
2981 3494 4.098654 GGCGCTCTCTGACATATATGGTAT 59.901 45.833 16.96 0.00 0.00 2.73
2985 3498 7.923344 GCGCTCTCTGACATATATGGTATTAAT 59.077 37.037 16.96 0.00 0.00 1.40
3029 3542 6.040878 GTCAAACAAGCGTATACTACTCCAT 58.959 40.000 0.56 0.00 0.00 3.41
3036 3549 4.694509 AGCGTATACTACTCCATTCCGTAG 59.305 45.833 0.56 0.00 39.14 3.51
3037 3550 4.453819 GCGTATACTACTCCATTCCGTAGT 59.546 45.833 0.56 7.19 45.82 2.73
3038 3551 5.639506 GCGTATACTACTCCATTCCGTAGTA 59.360 44.000 10.58 10.58 46.91 1.82
3039 3552 6.401581 GCGTATACTACTCCATTCCGTAGTAC 60.402 46.154 10.43 3.07 46.19 2.73
3101 3618 3.119779 TCCAAAGAACCAAAACGTGTCAC 60.120 43.478 0.00 0.00 0.00 3.67
3102 3619 3.119637 CCAAAGAACCAAAACGTGTCACT 60.120 43.478 0.65 0.00 0.00 3.41
3105 3622 2.936498 AGAACCAAAACGTGTCACTGAG 59.064 45.455 0.65 0.00 0.00 3.35
3126 3643 1.589803 ACCCGAAACTCTTCCAAACG 58.410 50.000 0.00 0.00 0.00 3.60
3131 3648 2.349532 CGAAACTCTTCCAAACGCTTCC 60.350 50.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.616865 CGTTTGGGTCTGTCTAGGACA 59.383 52.381 0.43 0.43 40.50 4.02
1 2 1.891150 TCGTTTGGGTCTGTCTAGGAC 59.109 52.381 0.00 0.00 0.00 3.85
2 3 2.297698 TCGTTTGGGTCTGTCTAGGA 57.702 50.000 0.00 0.00 0.00 2.94
3 4 3.396260 TTTCGTTTGGGTCTGTCTAGG 57.604 47.619 0.00 0.00 0.00 3.02
4 5 4.755123 ACATTTTCGTTTGGGTCTGTCTAG 59.245 41.667 0.00 0.00 0.00 2.43
5 6 4.710324 ACATTTTCGTTTGGGTCTGTCTA 58.290 39.130 0.00 0.00 0.00 2.59
6 7 3.551846 ACATTTTCGTTTGGGTCTGTCT 58.448 40.909 0.00 0.00 0.00 3.41
7 8 3.314080 TGACATTTTCGTTTGGGTCTGTC 59.686 43.478 0.00 0.00 33.97 3.51
8 9 3.066203 GTGACATTTTCGTTTGGGTCTGT 59.934 43.478 0.00 0.00 0.00 3.41
9 10 3.550030 GGTGACATTTTCGTTTGGGTCTG 60.550 47.826 0.00 0.00 0.00 3.51
10 11 2.621526 GGTGACATTTTCGTTTGGGTCT 59.378 45.455 0.00 0.00 0.00 3.85
11 12 2.287970 GGGTGACATTTTCGTTTGGGTC 60.288 50.000 0.00 0.00 0.00 4.46
12 13 1.684450 GGGTGACATTTTCGTTTGGGT 59.316 47.619 0.00 0.00 0.00 4.51
13 14 1.683917 TGGGTGACATTTTCGTTTGGG 59.316 47.619 0.00 0.00 0.00 4.12
14 15 3.120041 GTTGGGTGACATTTTCGTTTGG 58.880 45.455 0.00 0.00 0.00 3.28
15 16 4.040445 AGTTGGGTGACATTTTCGTTTG 57.960 40.909 0.00 0.00 0.00 2.93
16 17 6.072342 GGTATAGTTGGGTGACATTTTCGTTT 60.072 38.462 0.00 0.00 0.00 3.60
17 18 5.413523 GGTATAGTTGGGTGACATTTTCGTT 59.586 40.000 0.00 0.00 0.00 3.85
18 19 4.939439 GGTATAGTTGGGTGACATTTTCGT 59.061 41.667 0.00 0.00 0.00 3.85
19 20 4.938832 TGGTATAGTTGGGTGACATTTTCG 59.061 41.667 0.00 0.00 0.00 3.46
20 21 5.357032 CCTGGTATAGTTGGGTGACATTTTC 59.643 44.000 0.00 0.00 0.00 2.29
21 22 5.222254 ACCTGGTATAGTTGGGTGACATTTT 60.222 40.000 0.00 0.00 0.00 1.82
22 23 4.291249 ACCTGGTATAGTTGGGTGACATTT 59.709 41.667 0.00 0.00 0.00 2.32
23 24 3.850173 ACCTGGTATAGTTGGGTGACATT 59.150 43.478 0.00 0.00 0.00 2.71
32 33 2.684001 TCCGCAACCTGGTATAGTTG 57.316 50.000 0.00 0.00 44.93 3.16
36 37 3.009253 TCCTTTTTCCGCAACCTGGTATA 59.991 43.478 0.00 0.00 0.00 1.47
38 39 1.143277 TCCTTTTTCCGCAACCTGGTA 59.857 47.619 0.00 0.00 0.00 3.25
41 42 2.352715 GGAATCCTTTTTCCGCAACCTG 60.353 50.000 0.00 0.00 36.12 4.00
42 43 1.893137 GGAATCCTTTTTCCGCAACCT 59.107 47.619 0.00 0.00 36.12 3.50
84 85 5.536916 TGTATTTTGTCCCTCACGGATTTTT 59.463 36.000 0.00 0.00 44.66 1.94
85 86 5.074115 TGTATTTTGTCCCTCACGGATTTT 58.926 37.500 0.00 0.00 44.66 1.82
87 88 4.295141 TGTATTTTGTCCCTCACGGATT 57.705 40.909 0.00 0.00 44.66 3.01
88 89 3.992943 TGTATTTTGTCCCTCACGGAT 57.007 42.857 0.00 0.00 44.66 4.18
89 90 3.992943 ATGTATTTTGTCCCTCACGGA 57.007 42.857 0.00 0.00 38.83 4.69
90 91 5.048364 TGAAAATGTATTTTGTCCCTCACGG 60.048 40.000 7.27 0.00 39.86 4.94
92 93 7.329226 CACATGAAAATGTATTTTGTCCCTCAC 59.671 37.037 7.27 0.00 39.86 3.51
93 94 7.232330 TCACATGAAAATGTATTTTGTCCCTCA 59.768 33.333 7.27 0.00 39.86 3.86
94 95 7.601856 TCACATGAAAATGTATTTTGTCCCTC 58.398 34.615 7.27 0.00 39.86 4.30
96 97 9.301153 GTATCACATGAAAATGTATTTTGTCCC 57.699 33.333 7.27 0.00 39.86 4.46
97 98 9.853555 TGTATCACATGAAAATGTATTTTGTCC 57.146 29.630 7.27 0.00 39.86 4.02
141 147 1.001048 CAGCATTCACTTGGTGTGGTG 60.001 52.381 6.24 6.24 46.20 4.17
142 148 1.133823 TCAGCATTCACTTGGTGTGGT 60.134 47.619 3.87 0.00 46.20 4.16
145 151 3.430042 AGATCAGCATTCACTTGGTGT 57.570 42.857 0.00 0.00 43.74 4.16
150 156 9.319143 GTACTATGTAAAGATCAGCATTCACTT 57.681 33.333 0.00 0.00 0.00 3.16
153 159 7.712797 TCGTACTATGTAAAGATCAGCATTCA 58.287 34.615 0.00 0.00 0.00 2.57
154 160 8.642885 CATCGTACTATGTAAAGATCAGCATTC 58.357 37.037 0.00 0.00 0.00 2.67
160 166 6.801575 TGTGCATCGTACTATGTAAAGATCA 58.198 36.000 8.95 0.00 0.00 2.92
162 168 9.193133 GTTATGTGCATCGTACTATGTAAAGAT 57.807 33.333 8.95 3.14 0.00 2.40
163 169 7.650504 GGTTATGTGCATCGTACTATGTAAAGA 59.349 37.037 8.95 0.00 0.00 2.52
164 170 7.436970 TGGTTATGTGCATCGTACTATGTAAAG 59.563 37.037 8.95 0.00 0.00 1.85
165 171 7.266400 TGGTTATGTGCATCGTACTATGTAAA 58.734 34.615 8.95 0.36 0.00 2.01
167 173 6.394025 TGGTTATGTGCATCGTACTATGTA 57.606 37.500 8.95 1.85 0.00 2.29
168 174 5.270893 TGGTTATGTGCATCGTACTATGT 57.729 39.130 8.95 0.00 0.00 2.29
174 180 1.661617 GCGTTGGTTATGTGCATCGTA 59.338 47.619 0.00 0.00 0.00 3.43
176 182 0.586256 CGCGTTGGTTATGTGCATCG 60.586 55.000 0.00 0.00 0.00 3.84
185 191 1.594836 GTGGTGGACGCGTTGGTTA 60.595 57.895 15.53 0.00 0.00 2.85
187 193 4.922026 GGTGGTGGACGCGTTGGT 62.922 66.667 15.53 0.00 0.00 3.67
193 199 2.115911 TTGTTGTGGTGGTGGACGC 61.116 57.895 0.00 0.00 0.00 5.19
195 201 1.135228 GTTGTTGTTGTGGTGGTGGAC 60.135 52.381 0.00 0.00 0.00 4.02
200 206 2.732412 TGTTGTTGTTGTTGTGGTGG 57.268 45.000 0.00 0.00 0.00 4.61
204 210 9.312146 GTAAAAAGATTTGTTGTTGTTGTTGTG 57.688 29.630 0.00 0.00 0.00 3.33
207 213 7.385478 ACCGTAAAAAGATTTGTTGTTGTTGTT 59.615 29.630 0.00 0.00 0.00 2.83
208 214 6.869388 ACCGTAAAAAGATTTGTTGTTGTTGT 59.131 30.769 0.00 0.00 0.00 3.32
212 218 6.750039 AGTCACCGTAAAAAGATTTGTTGTTG 59.250 34.615 0.00 0.00 0.00 3.33
215 221 7.589954 CCTAAGTCACCGTAAAAAGATTTGTTG 59.410 37.037 0.00 0.00 0.00 3.33
218 224 7.429636 TCCTAAGTCACCGTAAAAAGATTTG 57.570 36.000 0.00 0.00 0.00 2.32
220 226 8.454570 TTTTCCTAAGTCACCGTAAAAAGATT 57.545 30.769 0.00 0.00 0.00 2.40
221 227 7.308408 GCTTTTCCTAAGTCACCGTAAAAAGAT 60.308 37.037 8.08 0.00 35.52 2.40
224 230 5.008911 GGCTTTTCCTAAGTCACCGTAAAAA 59.991 40.000 0.00 0.00 0.00 1.94
231 237 1.450025 CGGGCTTTTCCTAAGTCACC 58.550 55.000 0.00 0.00 34.39 4.02
233 239 0.322187 GCCGGGCTTTTCCTAAGTCA 60.322 55.000 12.87 0.00 34.39 3.41
236 242 0.748367 GAGGCCGGGCTTTTCCTAAG 60.748 60.000 33.28 0.00 34.39 2.18
237 243 1.205460 AGAGGCCGGGCTTTTCCTAA 61.205 55.000 33.28 0.00 34.39 2.69
238 244 1.615424 AGAGGCCGGGCTTTTCCTA 60.615 57.895 33.28 0.00 34.39 2.94
239 245 2.936032 AGAGGCCGGGCTTTTCCT 60.936 61.111 33.28 21.28 34.39 3.36
240 246 2.438614 GAGAGGCCGGGCTTTTCC 60.439 66.667 33.28 19.17 0.00 3.13
241 247 1.623542 TAGGAGAGGCCGGGCTTTTC 61.624 60.000 33.28 28.78 43.43 2.29
250 259 4.504689 CCTGATCAAGAAATAGGAGAGGCC 60.505 50.000 0.00 0.00 0.00 5.19
252 261 4.504689 GCCCTGATCAAGAAATAGGAGAGG 60.505 50.000 0.00 0.00 0.00 3.69
284 296 4.419522 AGTCGTGCCATTTACATTTGTC 57.580 40.909 0.00 0.00 0.00 3.18
305 317 3.762288 TGCTCGTCTCTAGAAAAGGCTTA 59.238 43.478 0.00 0.00 0.00 3.09
349 361 7.042335 GCAACTACTACCACTGATATGACTTT 58.958 38.462 0.00 0.00 0.00 2.66
430 445 2.249309 CGCCAATTATGCGCGAGG 59.751 61.111 12.10 0.00 46.01 4.63
543 558 3.204382 GGAATAATGGTCCTTTCTGGGGA 59.796 47.826 0.00 0.00 36.20 4.81
548 563 3.118000 GGACGGGAATAATGGTCCTTTCT 60.118 47.826 1.96 0.00 44.35 2.52
549 564 3.211865 GGACGGGAATAATGGTCCTTTC 58.788 50.000 1.96 0.00 44.35 2.62
588 614 1.077068 CTCCCTCGTCTCTGGAGCT 60.077 63.158 0.00 0.00 39.29 4.09
589 615 2.124693 CCTCCCTCGTCTCTGGAGC 61.125 68.421 0.00 0.00 43.56 4.70
596 622 2.363147 GCTCACCCTCCCTCGTCT 60.363 66.667 0.00 0.00 0.00 4.18
662 696 6.975471 TCCATCATAACCTTCCATCCATAT 57.025 37.500 0.00 0.00 0.00 1.78
664 698 5.517833 CCATCCATCATAACCTTCCATCCAT 60.518 44.000 0.00 0.00 0.00 3.41
665 699 4.202599 CCATCCATCATAACCTTCCATCCA 60.203 45.833 0.00 0.00 0.00 3.41
742 778 2.644798 AGGAATGGCAAGTGTAGAACCT 59.355 45.455 0.00 0.00 0.00 3.50
789 829 3.446873 TGAACTGTGAAGTGCCAACATTT 59.553 39.130 0.00 0.00 0.00 2.32
901 941 1.273606 GTTCTGGCTCTGTGCTCTGTA 59.726 52.381 1.44 0.00 42.39 2.74
908 948 0.178992 TTTGGGGTTCTGGCTCTGTG 60.179 55.000 0.00 0.00 0.00 3.66
910 950 1.246737 GCTTTGGGGTTCTGGCTCTG 61.247 60.000 0.00 0.00 0.00 3.35
911 951 1.075659 GCTTTGGGGTTCTGGCTCT 59.924 57.895 0.00 0.00 0.00 4.09
912 952 1.979155 GGCTTTGGGGTTCTGGCTC 60.979 63.158 0.00 0.00 0.00 4.70
966 1031 5.335127 CGGTTTCTATGGATTTCTTGCAAG 58.665 41.667 20.81 20.81 0.00 4.01
971 1036 2.943033 CGCCGGTTTCTATGGATTTCTT 59.057 45.455 1.90 0.00 0.00 2.52
976 1041 0.393077 CCTCGCCGGTTTCTATGGAT 59.607 55.000 1.90 0.00 0.00 3.41
1056 1121 0.038618 CGTCGTCAACCTCCATGTCA 60.039 55.000 0.00 0.00 0.00 3.58
1441 1545 2.659063 CCCTCATCTGCACCGACCA 61.659 63.158 0.00 0.00 0.00 4.02
1460 1564 1.227943 GAACTCCAGCACCAGCACA 60.228 57.895 0.00 0.00 45.49 4.57
2102 2254 2.196229 CCGTCCGATCCTCTCCCT 59.804 66.667 0.00 0.00 0.00 4.20
2204 2364 1.072159 GAGGCTCCAAGTGTGCAGT 59.928 57.895 2.15 0.00 35.15 4.40
2213 2373 3.003173 CCTGTCCCGAGGCTCCAA 61.003 66.667 9.32 0.00 0.00 3.53
2240 2400 0.997196 CTACTACCGCTTTGTTCGCC 59.003 55.000 0.00 0.00 0.00 5.54
2241 2401 1.389106 CACTACTACCGCTTTGTTCGC 59.611 52.381 0.00 0.00 0.00 4.70
2242 2402 1.990563 CCACTACTACCGCTTTGTTCG 59.009 52.381 0.00 0.00 0.00 3.95
2243 2403 2.344025 CCCACTACTACCGCTTTGTTC 58.656 52.381 0.00 0.00 0.00 3.18
2302 2463 3.390967 CCAAACCAACTCTTTTTCCCCAT 59.609 43.478 0.00 0.00 0.00 4.00
2317 2479 6.096282 CAGTTACCTTTTTCTCTTCCAAACCA 59.904 38.462 0.00 0.00 0.00 3.67
2319 2481 7.096884 ACAGTTACCTTTTTCTCTTCCAAAC 57.903 36.000 0.00 0.00 0.00 2.93
2337 2499 1.515081 GCGCACAAACCCTACAGTTA 58.485 50.000 0.30 0.00 0.00 2.24
2338 2500 1.503818 CGCGCACAAACCCTACAGTT 61.504 55.000 8.75 0.00 0.00 3.16
2339 2501 1.959226 CGCGCACAAACCCTACAGT 60.959 57.895 8.75 0.00 0.00 3.55
2340 2502 2.860293 CGCGCACAAACCCTACAG 59.140 61.111 8.75 0.00 0.00 2.74
2341 2503 3.350612 GCGCGCACAAACCCTACA 61.351 61.111 29.10 0.00 0.00 2.74
2501 2664 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
2502 2665 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2503 2666 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2504 2667 6.368779 TTTTATATTATGGGACGGAGGGAG 57.631 41.667 0.00 0.00 0.00 4.30
2505 2668 5.280317 GCTTTTATATTATGGGACGGAGGGA 60.280 44.000 0.00 0.00 0.00 4.20
2506 2669 4.941873 GCTTTTATATTATGGGACGGAGGG 59.058 45.833 0.00 0.00 0.00 4.30
2507 2670 4.630069 CGCTTTTATATTATGGGACGGAGG 59.370 45.833 0.00 0.00 0.00 4.30
2508 2671 5.235516 ACGCTTTTATATTATGGGACGGAG 58.764 41.667 0.00 0.00 0.00 4.63
2509 2672 5.217978 ACGCTTTTATATTATGGGACGGA 57.782 39.130 0.00 0.00 0.00 4.69
2510 2673 5.934935 AACGCTTTTATATTATGGGACGG 57.065 39.130 0.00 0.00 0.00 4.79
2511 2674 7.911205 TCAAAAACGCTTTTATATTATGGGACG 59.089 33.333 0.00 0.00 32.85 4.79
2512 2675 9.016623 GTCAAAAACGCTTTTATATTATGGGAC 57.983 33.333 0.00 0.00 32.85 4.46
2513 2676 8.740906 TGTCAAAAACGCTTTTATATTATGGGA 58.259 29.630 0.00 0.00 32.85 4.37
2514 2677 8.803799 GTGTCAAAAACGCTTTTATATTATGGG 58.196 33.333 0.00 0.00 32.85 4.00
2515 2678 9.567848 AGTGTCAAAAACGCTTTTATATTATGG 57.432 29.630 0.00 0.00 46.62 2.74
2522 2685 9.522804 TTTGATTAGTGTCAAAAACGCTTTTAT 57.477 25.926 0.00 0.00 46.62 1.40
2523 2686 8.800031 GTTTGATTAGTGTCAAAAACGCTTTTA 58.200 29.630 3.88 0.00 46.62 1.52
2524 2687 7.462200 CGTTTGATTAGTGTCAAAAACGCTTTT 60.462 33.333 5.67 0.00 46.62 2.27
2525 2688 6.020995 CGTTTGATTAGTGTCAAAAACGCTTT 60.021 34.615 5.67 0.00 46.62 3.51
2526 2689 5.454232 CGTTTGATTAGTGTCAAAAACGCTT 59.546 36.000 5.67 0.00 46.62 4.68
2527 2690 4.967575 CGTTTGATTAGTGTCAAAAACGCT 59.032 37.500 5.67 0.00 46.31 5.07
2528 2691 5.219113 CGTTTGATTAGTGTCAAAAACGC 57.781 39.130 5.67 0.00 46.31 4.84
2529 2692 4.967575 AGCGTTTGATTAGTGTCAAAAACG 59.032 37.500 12.61 12.61 46.31 3.60
2530 2693 6.199393 AGAGCGTTTGATTAGTGTCAAAAAC 58.801 36.000 3.88 0.65 46.31 2.43
2531 2694 6.371809 AGAGCGTTTGATTAGTGTCAAAAA 57.628 33.333 3.88 0.00 46.31 1.94
2532 2695 6.371809 AAGAGCGTTTGATTAGTGTCAAAA 57.628 33.333 3.88 0.00 46.31 2.44
2533 2696 7.667043 ATAAGAGCGTTTGATTAGTGTCAAA 57.333 32.000 0.00 0.00 43.66 2.69
2534 2697 8.942338 ATATAAGAGCGTTTGATTAGTGTCAA 57.058 30.769 0.00 0.00 36.38 3.18
2535 2698 8.942338 AATATAAGAGCGTTTGATTAGTGTCA 57.058 30.769 0.00 0.00 0.00 3.58
2539 2702 9.436957 CCCATAATATAAGAGCGTTTGATTAGT 57.563 33.333 0.00 0.00 0.00 2.24
2540 2703 9.653287 TCCCATAATATAAGAGCGTTTGATTAG 57.347 33.333 0.00 0.00 0.00 1.73
2541 2704 9.431887 GTCCCATAATATAAGAGCGTTTGATTA 57.568 33.333 0.00 0.00 0.00 1.75
2542 2705 7.117812 CGTCCCATAATATAAGAGCGTTTGATT 59.882 37.037 0.00 0.00 0.00 2.57
2543 2706 6.590292 CGTCCCATAATATAAGAGCGTTTGAT 59.410 38.462 0.00 0.00 0.00 2.57
2544 2707 5.924254 CGTCCCATAATATAAGAGCGTTTGA 59.076 40.000 0.00 0.00 0.00 2.69
2545 2708 5.120208 CCGTCCCATAATATAAGAGCGTTTG 59.880 44.000 0.00 0.00 0.00 2.93
2546 2709 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
2547 2710 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2548 2711 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
2549 2712 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2550 2713 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2551 2714 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2552 2715 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2553 2716 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2554 2717 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2555 2718 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2556 2719 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2557 2720 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
2558 2721 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
2559 2722 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
2560 2723 3.140707 TGTAATACTCCCTCCGTCCCATA 59.859 47.826 0.00 0.00 0.00 2.74
2561 2724 2.090943 TGTAATACTCCCTCCGTCCCAT 60.091 50.000 0.00 0.00 0.00 4.00
2562 2725 1.288633 TGTAATACTCCCTCCGTCCCA 59.711 52.381 0.00 0.00 0.00 4.37
2563 2726 2.077687 TGTAATACTCCCTCCGTCCC 57.922 55.000 0.00 0.00 0.00 4.46
2564 2727 3.640029 TCAATGTAATACTCCCTCCGTCC 59.360 47.826 0.00 0.00 0.00 4.79
2565 2728 4.341520 ACTCAATGTAATACTCCCTCCGTC 59.658 45.833 0.00 0.00 0.00 4.79
2566 2729 4.099573 CACTCAATGTAATACTCCCTCCGT 59.900 45.833 0.00 0.00 0.00 4.69
2567 2730 4.099573 ACACTCAATGTAATACTCCCTCCG 59.900 45.833 0.00 0.00 40.88 4.63
2568 2731 5.615925 ACACTCAATGTAATACTCCCTCC 57.384 43.478 0.00 0.00 40.88 4.30
2569 2732 6.879400 AGAACACTCAATGTAATACTCCCTC 58.121 40.000 0.00 0.00 42.31 4.30
2570 2733 6.875972 AGAACACTCAATGTAATACTCCCT 57.124 37.500 0.00 0.00 42.31 4.20
2571 2734 6.183360 GCAAGAACACTCAATGTAATACTCCC 60.183 42.308 0.00 0.00 42.31 4.30
2572 2735 6.595716 AGCAAGAACACTCAATGTAATACTCC 59.404 38.462 0.00 0.00 42.31 3.85
2573 2736 7.459486 CAGCAAGAACACTCAATGTAATACTC 58.541 38.462 0.00 0.00 42.31 2.59
2574 2737 6.128172 GCAGCAAGAACACTCAATGTAATACT 60.128 38.462 0.00 0.00 42.31 2.12
2575 2738 6.024049 GCAGCAAGAACACTCAATGTAATAC 58.976 40.000 0.00 0.00 42.31 1.89
2576 2739 5.939883 AGCAGCAAGAACACTCAATGTAATA 59.060 36.000 0.00 0.00 42.31 0.98
2577 2740 4.763793 AGCAGCAAGAACACTCAATGTAAT 59.236 37.500 0.00 0.00 42.31 1.89
2578 2741 4.023792 CAGCAGCAAGAACACTCAATGTAA 60.024 41.667 0.00 0.00 42.31 2.41
2611 2778 3.235195 CCACAAACAAAACGAACGAACA 58.765 40.909 0.14 0.00 0.00 3.18
2612 2779 3.236005 ACCACAAACAAAACGAACGAAC 58.764 40.909 0.14 0.00 0.00 3.95
2613 2780 3.555917 ACCACAAACAAAACGAACGAA 57.444 38.095 0.14 0.00 0.00 3.85
2614 2781 3.490399 GAACCACAAACAAAACGAACGA 58.510 40.909 0.14 0.00 0.00 3.85
2646 2825 1.098712 GGCTGTCAAACCCGTCACAA 61.099 55.000 0.00 0.00 0.00 3.33
2749 3252 2.932614 CCTGGACTGCTAGATTTGTTCG 59.067 50.000 0.00 0.00 0.00 3.95
2791 3294 2.752144 CGTCGTATTAAGAGGACGCT 57.248 50.000 26.07 0.00 46.64 5.07
2862 3372 3.557903 CTCTGGGTGGGTGCCAGTG 62.558 68.421 0.00 0.00 32.34 3.66
2863 3373 3.252284 CTCTGGGTGGGTGCCAGT 61.252 66.667 0.00 0.00 32.34 4.00
2864 3374 4.729918 GCTCTGGGTGGGTGCCAG 62.730 72.222 0.00 0.00 32.34 4.85
2942 3455 3.088532 AGCGCCATGGACTGAATTTTTA 58.911 40.909 18.40 0.00 0.00 1.52
2948 3461 1.219124 GAGAGCGCCATGGACTGAA 59.781 57.895 18.40 0.00 0.00 3.02
2986 3499 9.639563 TGTTTGACCAACATGGATTGTATATAT 57.360 29.630 2.85 0.00 40.71 0.86
2987 3500 9.467796 TTGTTTGACCAACATGGATTGTATATA 57.532 29.630 2.85 0.00 45.17 0.86
3029 3542 5.942236 AGAGAACATGTACTGTACTACGGAA 59.058 40.000 17.98 0.00 36.98 4.30
3036 3549 8.721019 AGAGTAGTAGAGAACATGTACTGTAC 57.279 38.462 10.98 10.98 38.40 2.90
3037 3550 9.736414 AAAGAGTAGTAGAGAACATGTACTGTA 57.264 33.333 0.00 0.00 38.40 2.74
3038 3551 8.638629 AAAGAGTAGTAGAGAACATGTACTGT 57.361 34.615 0.00 0.00 38.40 3.55
3039 3552 9.562583 GAAAAGAGTAGTAGAGAACATGTACTG 57.437 37.037 0.00 0.00 38.40 2.74
3101 3618 2.037251 TGGAAGAGTTTCGGGTTCTCAG 59.963 50.000 0.00 0.00 33.98 3.35
3102 3619 2.043992 TGGAAGAGTTTCGGGTTCTCA 58.956 47.619 0.00 0.00 33.98 3.27
3105 3622 2.032290 CGTTTGGAAGAGTTTCGGGTTC 60.032 50.000 0.00 0.00 33.98 3.62


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

AutoCloner maintained by Alex Coulton.