Multiple sequence alignment - TraesCS1A01G371500

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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 TraesCS1A01G371500 chr1A 100.000 4742 0 0 885 5626 548530842 548535583 0.000000e+00 8757.0
1 TraesCS1A01G371500 chr1A 100.000 541 0 0 1 541 548529958 548530498 0.000000e+00 1000.0
2 TraesCS1A01G371500 chr1A 93.316 374 21 2 5256 5626 24512751 24513123 2.960000e-152 549.0
3 TraesCS1A01G371500 chr1A 97.714 175 4 0 320 494 544743495 544743321 9.160000e-78 302.0
4 TraesCS1A01G371500 chr1A 98.810 168 2 0 5096 5263 548542620 548542453 3.290000e-77 300.0
5 TraesCS1A01G371500 chr1A 96.429 168 6 0 5096 5263 24512557 24512724 1.540000e-70 278.0
6 TraesCS1A01G371500 chr1B 96.118 4225 119 19 885 5096 624087012 624091204 0.000000e+00 6852.0
7 TraesCS1A01G371500 chr1B 81.359 1030 124 28 1287 2301 624502539 624503515 0.000000e+00 776.0
8 TraesCS1A01G371500 chr1B 80.357 952 127 31 3461 4383 624505180 624506100 0.000000e+00 667.0
9 TraesCS1A01G371500 chr1B 94.954 218 10 1 320 536 505074185 505073968 1.940000e-89 340.0
10 TraesCS1A01G371500 chr1B 85.965 285 16 12 1 267 624085907 624086185 3.320000e-72 283.0
11 TraesCS1A01G371500 chr1B 100.000 69 0 0 251 319 624086895 624086963 1.650000e-25 128.0
12 TraesCS1A01G371500 chr1B 92.754 69 4 1 1360 1427 624498959 624499027 1.290000e-16 99.0
13 TraesCS1A01G371500 chr1D 95.533 2306 61 18 2809 5096 453825046 453827327 0.000000e+00 3650.0
14 TraesCS1A01G371500 chr1D 94.326 1410 52 10 885 2286 453821643 453823032 0.000000e+00 2135.0
15 TraesCS1A01G371500 chr1D 98.394 498 8 0 2315 2812 453823366 453823863 0.000000e+00 876.0
16 TraesCS1A01G371500 chr1D 81.341 1029 126 29 1287 2301 453965506 453966482 0.000000e+00 776.0
17 TraesCS1A01G371500 chr1D 90.305 557 28 10 5096 5626 493857191 493857747 0.000000e+00 706.0
18 TraesCS1A01G371500 chr1D 80.967 951 122 32 3461 4383 453968133 453969052 0.000000e+00 699.0
19 TraesCS1A01G371500 chr1D 84.892 278 19 8 53 319 453821309 453821574 5.590000e-65 259.0
20 TraesCS1A01G371500 chr1D 81.206 282 34 8 964 1227 453961539 453961819 5.710000e-50 209.0
21 TraesCS1A01G371500 chr1D 93.846 65 4 0 1363 1427 453961916 453961980 1.290000e-16 99.0
22 TraesCS1A01G371500 chr7A 90.761 552 25 19 5096 5626 460976721 460977267 0.000000e+00 713.0
23 TraesCS1A01G371500 chr7A 95.442 373 10 4 5257 5626 70215560 70215928 6.280000e-164 588.0
24 TraesCS1A01G371500 chr7A 97.674 172 4 0 5095 5266 70233139 70232968 4.260000e-76 296.0
25 TraesCS1A01G371500 chr4A 95.652 368 12 2 5262 5626 24819991 24819625 6.280000e-164 588.0
26 TraesCS1A01G371500 chr4A 98.214 168 3 0 5096 5263 24812179 24812346 1.530000e-75 294.0
27 TraesCS1A01G371500 chr6A 94.906 373 15 2 5257 5626 99935599 99935970 1.050000e-161 580.0
28 TraesCS1A01G371500 chr6A 93.989 366 20 1 5263 5626 591275370 591275735 2.290000e-153 553.0
29 TraesCS1A01G371500 chr6A 97.899 238 4 1 5257 5494 98750138 98750374 1.460000e-110 411.0
30 TraesCS1A01G371500 chr6A 97.041 169 5 0 5095 5263 98749942 98750110 9.230000e-73 285.0
31 TraesCS1A01G371500 chr6A 97.024 168 5 0 5096 5263 98801159 98800992 3.320000e-72 283.0
32 TraesCS1A01G371500 chr6A 97.546 163 4 0 5101 5263 591275175 591275337 4.290000e-71 279.0
33 TraesCS1A01G371500 chr6A 76.250 320 71 4 1986 2301 556101195 556100877 1.250000e-36 165.0
34 TraesCS1A01G371500 chr6A 82.099 162 27 2 1072 1232 556094335 556094175 2.730000e-28 137.0
35 TraesCS1A01G371500 chr2A 93.029 373 22 2 5257 5626 735063210 735062839 4.960000e-150 542.0
36 TraesCS1A01G371500 chr4B 89.362 376 28 4 5257 5626 628627371 628627002 3.970000e-126 462.0
37 TraesCS1A01G371500 chr3A 97.209 215 6 0 320 534 66352965 66353179 1.150000e-96 364.0
38 TraesCS1A01G371500 chr3A 91.818 220 17 1 320 539 44223467 44223685 7.080000e-79 305.0
39 TraesCS1A01G371500 chr3A 91.743 218 17 1 321 538 43640591 43640807 9.160000e-78 302.0
40 TraesCS1A01G371500 chr3A 74.608 319 74 7 1986 2299 33585068 33584752 3.540000e-27 134.0
41 TraesCS1A01G371500 chr3A 82.609 92 14 2 1667 1757 33885845 33885755 4.670000e-11 80.5
42 TraesCS1A01G371500 chr7D 94.954 218 11 0 320 537 436876649 436876432 5.400000e-90 342.0
43 TraesCS1A01G371500 chr7D 93.119 218 15 0 320 537 150756315 150756532 2.530000e-83 320.0
44 TraesCS1A01G371500 chr6D 93.519 216 14 0 321 536 158110264 158110049 7.030000e-84 322.0
45 TraesCS1A01G371500 chr6D 95.906 171 7 0 5093 5263 318993790 318993960 1.540000e-70 278.0
46 TraesCS1A01G371500 chr6D 76.562 320 70 4 1986 2301 411497825 411497507 2.700000e-38 171.0
47 TraesCS1A01G371500 chr6D 81.595 163 26 4 1072 1232 411493013 411492853 1.270000e-26 132.0
48 TraesCS1A01G371500 chr2B 92.760 221 16 0 320 540 603696273 603696493 2.530000e-83 320.0
49 TraesCS1A01G371500 chr2B 82.796 186 22 9 1049 1229 42177663 42177843 2.100000e-34 158.0
50 TraesCS1A01G371500 chr2B 83.133 166 24 4 1067 1230 42176381 42176544 1.260000e-31 148.0
51 TraesCS1A01G371500 chr2D 82.447 188 27 6 1045 1229 26931381 26931565 5.830000e-35 159.0
52 TraesCS1A01G371500 chr3D 75.312 320 74 5 1986 2301 24102832 24102514 1.260000e-31 148.0
53 TraesCS1A01G371500 chr3D 82.278 158 26 2 1072 1228 24095204 24095048 9.830000e-28 135.0
54 TraesCS1A01G371500 chr3D 82.609 92 14 2 1667 1757 24872827 24872737 4.670000e-11 80.5
55 TraesCS1A01G371500 chr3B 82.558 86 13 2 1673 1757 42475033 42474949 2.170000e-09 75.0


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 TraesCS1A01G371500 chr1A 548529958 548535583 5625 False 4878.50 8757 100.000000 1 5626 2 chr1A.!!$F2 5625
1 TraesCS1A01G371500 chr1A 24512557 24513123 566 False 413.50 549 94.872500 5096 5626 2 chr1A.!!$F1 530
2 TraesCS1A01G371500 chr1B 624085907 624091204 5297 False 2421.00 6852 94.027667 1 5096 3 chr1B.!!$F1 5095
3 TraesCS1A01G371500 chr1B 624498959 624506100 7141 False 514.00 776 84.823333 1287 4383 3 chr1B.!!$F2 3096
4 TraesCS1A01G371500 chr1D 453821309 453827327 6018 False 1730.00 3650 93.286250 53 5096 4 chr1D.!!$F2 5043
5 TraesCS1A01G371500 chr1D 493857191 493857747 556 False 706.00 706 90.305000 5096 5626 1 chr1D.!!$F1 530
6 TraesCS1A01G371500 chr1D 453961539 453969052 7513 False 445.75 776 84.340000 964 4383 4 chr1D.!!$F3 3419
7 TraesCS1A01G371500 chr7A 460976721 460977267 546 False 713.00 713 90.761000 5096 5626 1 chr7A.!!$F2 530
8 TraesCS1A01G371500 chr6A 591275175 591275735 560 False 416.00 553 95.767500 5101 5626 2 chr6A.!!$F3 525

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
326 1075 0.320421 TTTACGCTGGCTCTGTGGTC 60.320 55.000 0.00 0.00 0.00 4.02 F
335 1084 0.383949 GCTCTGTGGTCTCGGAGATC 59.616 60.000 11.46 11.43 41.76 2.75 F
1761 6204 0.814010 ATACATCCTGTTTCCCGCGC 60.814 55.000 0.00 0.00 0.00 6.86 F
1788 6237 1.539065 CGCCTTGCTCCGAACTATCAT 60.539 52.381 0.00 0.00 0.00 2.45 F
3114 9310 2.028020 CGAGACTGGCTTAGGGAACTTT 60.028 50.000 0.00 0.00 43.67 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2045 6494 0.608308 TGTCTGTCTCGTCGTCCCAT 60.608 55.000 0.00 0.00 0.00 4.00 R
2747 7602 8.190888 ACTTCTCATGAGTGAATTCGAATTAC 57.809 34.615 22.78 18.81 33.05 1.89 R
3524 9966 3.088532 TGACCTGCAATGGACCATAAAC 58.911 45.455 7.59 0.81 0.00 2.01 R
3936 10388 5.233476 CGTGTATATACCGTGAGCAAACATT 59.767 40.000 10.38 0.00 0.00 2.71 R
5072 11555 0.037326 CCCGTTCTAGCAGCACAGAA 60.037 55.000 5.56 5.56 0.00 3.02 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
80 81 6.259167 GCATTTTTATGCCATTGTGATGATGT 59.741 34.615 0.00 0.00 41.47 3.06
143 147 5.270853 CAGTTTTCCCTCTTTTTGTACACG 58.729 41.667 0.00 0.00 0.00 4.49
161 165 5.964958 ACACGAGATTTTGGTGATGATTT 57.035 34.783 0.00 0.00 35.68 2.17
163 167 6.151691 ACACGAGATTTTGGTGATGATTTTG 58.848 36.000 0.00 0.00 35.68 2.44
164 168 5.061311 CACGAGATTTTGGTGATGATTTTGC 59.939 40.000 0.00 0.00 33.58 3.68
165 169 4.563976 CGAGATTTTGGTGATGATTTTGCC 59.436 41.667 0.00 0.00 0.00 4.52
234 252 5.860941 TGTTTGCAGGAAAACAAATAGGA 57.139 34.783 3.08 0.00 44.79 2.94
319 1068 1.077716 ATGGGGTTTACGCTGGCTC 60.078 57.895 0.00 0.00 0.00 4.70
320 1069 1.562672 ATGGGGTTTACGCTGGCTCT 61.563 55.000 0.00 0.00 0.00 4.09
322 1071 1.003718 GGGTTTACGCTGGCTCTGT 60.004 57.895 0.00 0.00 0.00 3.41
323 1072 1.298859 GGGTTTACGCTGGCTCTGTG 61.299 60.000 0.00 0.00 0.00 3.66
325 1074 0.602905 GTTTACGCTGGCTCTGTGGT 60.603 55.000 0.00 0.00 0.00 4.16
326 1075 0.320421 TTTACGCTGGCTCTGTGGTC 60.320 55.000 0.00 0.00 0.00 4.02
327 1076 1.185618 TTACGCTGGCTCTGTGGTCT 61.186 55.000 0.00 0.00 0.00 3.85
328 1077 1.595993 TACGCTGGCTCTGTGGTCTC 61.596 60.000 0.00 0.00 0.00 3.36
329 1078 2.125753 GCTGGCTCTGTGGTCTCG 60.126 66.667 0.00 0.00 0.00 4.04
330 1079 2.575993 CTGGCTCTGTGGTCTCGG 59.424 66.667 0.00 0.00 0.00 4.63
331 1080 1.979155 CTGGCTCTGTGGTCTCGGA 60.979 63.158 0.00 0.00 0.00 4.55
334 1083 1.040339 GGCTCTGTGGTCTCGGAGAT 61.040 60.000 11.46 0.00 41.76 2.75
335 1084 0.383949 GCTCTGTGGTCTCGGAGATC 59.616 60.000 11.46 11.43 41.76 2.75
336 1085 1.756430 CTCTGTGGTCTCGGAGATCA 58.244 55.000 16.78 16.78 41.76 2.92
339 1088 2.493675 TCTGTGGTCTCGGAGATCAAAG 59.506 50.000 26.15 26.15 41.17 2.77
340 1089 2.493675 CTGTGGTCTCGGAGATCAAAGA 59.506 50.000 27.48 12.55 42.16 2.52
342 1091 3.118992 TGTGGTCTCGGAGATCAAAGATG 60.119 47.826 21.84 0.00 37.05 2.90
343 1092 2.432146 TGGTCTCGGAGATCAAAGATGG 59.568 50.000 18.29 0.00 31.27 3.51
344 1093 2.478831 GTCTCGGAGATCAAAGATGGC 58.521 52.381 11.46 0.00 33.89 4.40
345 1094 2.110578 TCTCGGAGATCAAAGATGGCA 58.889 47.619 2.97 0.00 33.89 4.92
347 1096 2.806818 CTCGGAGATCAAAGATGGCATG 59.193 50.000 3.81 0.00 33.89 4.06
348 1097 2.171237 TCGGAGATCAAAGATGGCATGT 59.829 45.455 3.81 0.00 0.00 3.21
350 1099 2.547211 GGAGATCAAAGATGGCATGTCG 59.453 50.000 3.81 0.00 0.00 4.35
352 1101 3.873361 GAGATCAAAGATGGCATGTCGAA 59.127 43.478 3.81 0.00 0.00 3.71
353 1102 4.458397 AGATCAAAGATGGCATGTCGAAT 58.542 39.130 3.81 0.00 0.00 3.34
354 1103 5.614308 AGATCAAAGATGGCATGTCGAATA 58.386 37.500 3.81 0.00 0.00 1.75
355 1104 6.236409 AGATCAAAGATGGCATGTCGAATAT 58.764 36.000 3.81 0.00 0.00 1.28
356 1105 6.713903 AGATCAAAGATGGCATGTCGAATATT 59.286 34.615 3.81 0.00 0.00 1.28
357 1106 6.698008 TCAAAGATGGCATGTCGAATATTT 57.302 33.333 3.81 0.00 0.00 1.40
359 1108 7.546358 TCAAAGATGGCATGTCGAATATTTTT 58.454 30.769 3.81 0.00 0.00 1.94
382 1131 5.600908 TTTTCTCGGGTCAAGTTTATTCG 57.399 39.130 0.00 0.00 0.00 3.34
383 1132 3.947910 TCTCGGGTCAAGTTTATTCGT 57.052 42.857 0.00 0.00 0.00 3.85
384 1133 3.841643 TCTCGGGTCAAGTTTATTCGTC 58.158 45.455 0.00 0.00 0.00 4.20
385 1134 2.597305 CTCGGGTCAAGTTTATTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
386 1135 1.657094 CGGGTCAAGTTTATTCGTCGG 59.343 52.381 0.00 0.00 0.00 4.79
387 1136 1.395954 GGGTCAAGTTTATTCGTCGGC 59.604 52.381 0.00 0.00 0.00 5.54
388 1137 2.070783 GGTCAAGTTTATTCGTCGGCA 58.929 47.619 0.00 0.00 0.00 5.69
389 1138 2.093783 GGTCAAGTTTATTCGTCGGCAG 59.906 50.000 0.00 0.00 0.00 4.85
390 1139 2.735134 GTCAAGTTTATTCGTCGGCAGT 59.265 45.455 0.00 0.00 0.00 4.40
391 1140 2.991190 TCAAGTTTATTCGTCGGCAGTC 59.009 45.455 0.00 0.00 0.00 3.51
392 1141 2.993899 CAAGTTTATTCGTCGGCAGTCT 59.006 45.455 0.00 0.00 0.00 3.24
393 1142 4.082625 TCAAGTTTATTCGTCGGCAGTCTA 60.083 41.667 0.00 0.00 0.00 2.59
394 1143 4.445452 AGTTTATTCGTCGGCAGTCTAA 57.555 40.909 0.00 0.00 0.00 2.10
395 1144 5.007385 AGTTTATTCGTCGGCAGTCTAAT 57.993 39.130 0.00 0.00 0.00 1.73
396 1145 4.804139 AGTTTATTCGTCGGCAGTCTAATG 59.196 41.667 0.00 0.00 0.00 1.90
397 1146 2.961526 ATTCGTCGGCAGTCTAATGT 57.038 45.000 0.00 0.00 0.00 2.71
398 1147 2.736144 TTCGTCGGCAGTCTAATGTT 57.264 45.000 0.00 0.00 0.00 2.71
399 1148 2.736144 TCGTCGGCAGTCTAATGTTT 57.264 45.000 0.00 0.00 0.00 2.83
400 1149 3.034721 TCGTCGGCAGTCTAATGTTTT 57.965 42.857 0.00 0.00 0.00 2.43
401 1150 4.177165 TCGTCGGCAGTCTAATGTTTTA 57.823 40.909 0.00 0.00 0.00 1.52
402 1151 4.171005 TCGTCGGCAGTCTAATGTTTTAG 58.829 43.478 0.00 0.00 36.87 1.85
403 1152 3.241995 CGTCGGCAGTCTAATGTTTTAGC 60.242 47.826 0.00 0.00 35.72 3.09
404 1153 3.933332 GTCGGCAGTCTAATGTTTTAGCT 59.067 43.478 0.00 0.00 35.72 3.32
405 1154 4.033014 GTCGGCAGTCTAATGTTTTAGCTC 59.967 45.833 0.00 0.00 35.72 4.09
406 1155 3.932710 CGGCAGTCTAATGTTTTAGCTCA 59.067 43.478 0.00 0.00 35.72 4.26
407 1156 4.572389 CGGCAGTCTAATGTTTTAGCTCAT 59.428 41.667 0.00 0.00 35.72 2.90
408 1157 5.753438 CGGCAGTCTAATGTTTTAGCTCATA 59.247 40.000 0.00 0.00 35.72 2.15
409 1158 6.257849 CGGCAGTCTAATGTTTTAGCTCATAA 59.742 38.462 0.00 0.00 35.72 1.90
410 1159 7.041780 CGGCAGTCTAATGTTTTAGCTCATAAT 60.042 37.037 0.00 0.00 35.72 1.28
411 1160 8.624776 GGCAGTCTAATGTTTTAGCTCATAATT 58.375 33.333 0.00 0.00 35.72 1.40
428 1177 8.947940 GCTCATAATTTAGCTAAATCGTGTTTG 58.052 33.333 27.56 17.86 35.00 2.93
431 1180 8.947940 CATAATTTAGCTAAATCGTGTTTGAGC 58.052 33.333 27.56 0.00 35.00 4.26
432 1181 6.743575 ATTTAGCTAAATCGTGTTTGAGCT 57.256 33.333 23.22 7.50 42.64 4.09
433 1182 5.530519 TTAGCTAAATCGTGTTTGAGCTG 57.469 39.130 2.97 0.00 40.37 4.24
434 1183 3.403038 AGCTAAATCGTGTTTGAGCTGT 58.597 40.909 0.00 0.00 38.78 4.40
435 1184 4.566004 AGCTAAATCGTGTTTGAGCTGTA 58.434 39.130 0.00 0.00 38.78 2.74
436 1185 4.994852 AGCTAAATCGTGTTTGAGCTGTAA 59.005 37.500 0.00 0.00 38.78 2.41
437 1186 5.643777 AGCTAAATCGTGTTTGAGCTGTAAT 59.356 36.000 0.00 0.00 38.78 1.89
438 1187 5.734498 GCTAAATCGTGTTTGAGCTGTAATG 59.266 40.000 0.00 0.00 0.00 1.90
439 1188 4.685169 AATCGTGTTTGAGCTGTAATGG 57.315 40.909 0.00 0.00 0.00 3.16
440 1189 3.120321 TCGTGTTTGAGCTGTAATGGT 57.880 42.857 0.00 0.00 0.00 3.55
441 1190 3.472652 TCGTGTTTGAGCTGTAATGGTT 58.527 40.909 0.00 0.00 0.00 3.67
442 1191 3.880490 TCGTGTTTGAGCTGTAATGGTTT 59.120 39.130 0.00 0.00 0.00 3.27
443 1192 4.336993 TCGTGTTTGAGCTGTAATGGTTTT 59.663 37.500 0.00 0.00 0.00 2.43
444 1193 5.040635 CGTGTTTGAGCTGTAATGGTTTTT 58.959 37.500 0.00 0.00 0.00 1.94
445 1194 5.051774 CGTGTTTGAGCTGTAATGGTTTTTG 60.052 40.000 0.00 0.00 0.00 2.44
446 1195 5.810074 GTGTTTGAGCTGTAATGGTTTTTGT 59.190 36.000 0.00 0.00 0.00 2.83
447 1196 5.809562 TGTTTGAGCTGTAATGGTTTTTGTG 59.190 36.000 0.00 0.00 0.00 3.33
448 1197 5.590530 TTGAGCTGTAATGGTTTTTGTGT 57.409 34.783 0.00 0.00 0.00 3.72
449 1198 5.590530 TGAGCTGTAATGGTTTTTGTGTT 57.409 34.783 0.00 0.00 0.00 3.32
450 1199 5.971763 TGAGCTGTAATGGTTTTTGTGTTT 58.028 33.333 0.00 0.00 0.00 2.83
451 1200 6.402222 TGAGCTGTAATGGTTTTTGTGTTTT 58.598 32.000 0.00 0.00 0.00 2.43
452 1201 6.533367 TGAGCTGTAATGGTTTTTGTGTTTTC 59.467 34.615 0.00 0.00 0.00 2.29
453 1202 6.402222 AGCTGTAATGGTTTTTGTGTTTTCA 58.598 32.000 0.00 0.00 0.00 2.69
466 1215 3.986277 GTGTTTTCACTTCTACTCCGGA 58.014 45.455 2.93 2.93 46.30 5.14
467 1216 4.374399 GTGTTTTCACTTCTACTCCGGAA 58.626 43.478 5.23 0.00 46.30 4.30
468 1217 4.995487 GTGTTTTCACTTCTACTCCGGAAT 59.005 41.667 5.23 0.00 46.30 3.01
469 1218 6.161381 GTGTTTTCACTTCTACTCCGGAATA 58.839 40.000 5.23 0.00 46.30 1.75
470 1219 6.817140 GTGTTTTCACTTCTACTCCGGAATAT 59.183 38.462 5.23 0.00 46.30 1.28
471 1220 7.977853 GTGTTTTCACTTCTACTCCGGAATATA 59.022 37.037 5.23 0.00 46.30 0.86
472 1221 8.701895 TGTTTTCACTTCTACTCCGGAATATAT 58.298 33.333 5.23 0.00 0.00 0.86
473 1222 9.194271 GTTTTCACTTCTACTCCGGAATATATC 57.806 37.037 5.23 0.00 0.00 1.63
474 1223 7.463961 TTCACTTCTACTCCGGAATATATCC 57.536 40.000 5.23 0.00 45.57 2.59
488 1237 7.222000 GGAATATATCCGAGAGACTCTTTGT 57.778 40.000 6.40 0.00 38.79 2.83
489 1238 8.338072 GGAATATATCCGAGAGACTCTTTGTA 57.662 38.462 6.40 0.00 38.79 2.41
490 1239 8.794553 GGAATATATCCGAGAGACTCTTTGTAA 58.205 37.037 6.40 0.00 38.79 2.41
496 1245 7.406031 TCCGAGAGACTCTTTGTAATTATGT 57.594 36.000 6.40 0.00 0.00 2.29
497 1246 7.837863 TCCGAGAGACTCTTTGTAATTATGTT 58.162 34.615 6.40 0.00 0.00 2.71
498 1247 8.963725 TCCGAGAGACTCTTTGTAATTATGTTA 58.036 33.333 6.40 0.00 0.00 2.41
499 1248 9.021863 CCGAGAGACTCTTTGTAATTATGTTAC 57.978 37.037 6.40 0.00 0.00 2.50
500 1249 9.790389 CGAGAGACTCTTTGTAATTATGTTACT 57.210 33.333 6.40 0.00 0.00 2.24
518 1267 7.908827 TGTTACTTGATTAATAAAGTGCCGA 57.091 32.000 23.49 5.35 37.23 5.54
519 1268 7.745015 TGTTACTTGATTAATAAAGTGCCGAC 58.255 34.615 23.49 16.91 37.23 4.79
520 1269 5.464965 ACTTGATTAATAAAGTGCCGACG 57.535 39.130 16.21 0.00 35.34 5.12
521 1270 4.933400 ACTTGATTAATAAAGTGCCGACGT 59.067 37.500 16.21 0.00 35.34 4.34
522 1271 5.410439 ACTTGATTAATAAAGTGCCGACGTT 59.590 36.000 16.21 0.00 35.34 3.99
523 1272 5.866335 TGATTAATAAAGTGCCGACGTTT 57.134 34.783 0.00 0.00 0.00 3.60
524 1273 6.243811 TGATTAATAAAGTGCCGACGTTTT 57.756 33.333 0.00 0.00 0.00 2.43
525 1274 6.308675 TGATTAATAAAGTGCCGACGTTTTC 58.691 36.000 0.00 0.00 0.00 2.29
526 1275 5.927954 TTAATAAAGTGCCGACGTTTTCT 57.072 34.783 0.00 0.00 0.00 2.52
527 1276 7.331440 TGATTAATAAAGTGCCGACGTTTTCTA 59.669 33.333 0.00 0.00 0.00 2.10
528 1277 5.927954 AATAAAGTGCCGACGTTTTCTAA 57.072 34.783 0.00 0.00 0.00 2.10
529 1278 5.927954 ATAAAGTGCCGACGTTTTCTAAA 57.072 34.783 0.00 0.00 0.00 1.85
530 1279 4.619437 AAAGTGCCGACGTTTTCTAAAA 57.381 36.364 0.00 0.00 0.00 1.52
531 1280 4.619437 AAGTGCCGACGTTTTCTAAAAA 57.381 36.364 0.00 0.00 0.00 1.94
939 1688 4.530857 CCCGAGTCCATCACGCCC 62.531 72.222 0.00 0.00 0.00 6.13
955 1704 3.554342 CCCCCTCTCCATCGCCTG 61.554 72.222 0.00 0.00 0.00 4.85
956 1705 2.765807 CCCCTCTCCATCGCCTGT 60.766 66.667 0.00 0.00 0.00 4.00
974 1723 3.165071 CTGTTGCAAAACCTAATCCCCT 58.835 45.455 0.00 0.00 0.00 4.79
1129 1895 2.517402 TCCACAACGCAACCACCC 60.517 61.111 0.00 0.00 0.00 4.61
1145 1911 2.567049 CCTCGTGTCCAGGACGAC 59.433 66.667 15.24 12.52 40.79 4.34
1239 2005 1.614317 CCCGGCCTCAAAGTTTCAGAT 60.614 52.381 0.00 0.00 0.00 2.90
1269 2035 4.867599 GCCCACGACGATCCCGAC 62.868 72.222 0.00 0.00 39.50 4.79
1344 5771 2.671963 GTGACCTTCAACGCCCCC 60.672 66.667 0.00 0.00 0.00 5.40
1378 5805 1.375326 GAGTCCACCCACCACTTCC 59.625 63.158 0.00 0.00 0.00 3.46
1423 5850 4.007644 CACTGCACCTGCTCCCGA 62.008 66.667 0.00 0.00 42.66 5.14
1445 5876 4.330944 ACCGATATTCCAGCATACGAAA 57.669 40.909 0.00 0.00 0.00 3.46
1634 6077 7.664082 AAGAGATATTTTAGTCGGCATGATG 57.336 36.000 0.00 0.00 0.00 3.07
1635 6078 5.641209 AGAGATATTTTAGTCGGCATGATGC 59.359 40.000 9.33 9.33 44.08 3.91
1734 6177 2.159226 AGACCGTTCGATGAACATCCTC 60.159 50.000 10.01 0.00 42.05 3.71
1750 6193 5.083122 ACATCCTCTGATCGAATACATCCT 58.917 41.667 0.00 0.00 0.00 3.24
1757 6200 4.703897 TGATCGAATACATCCTGTTTCCC 58.296 43.478 0.00 0.00 0.00 3.97
1759 6202 1.597663 CGAATACATCCTGTTTCCCGC 59.402 52.381 0.00 0.00 0.00 6.13
1761 6204 0.814010 ATACATCCTGTTTCCCGCGC 60.814 55.000 0.00 0.00 0.00 6.86
1766 6215 2.978010 CTGTTTCCCGCGCCAAGT 60.978 61.111 0.00 0.00 0.00 3.16
1788 6237 1.539065 CGCCTTGCTCCGAACTATCAT 60.539 52.381 0.00 0.00 0.00 2.45
2042 6491 4.081087 AGCTATTCTTCTTTACTGCCGGAA 60.081 41.667 5.05 0.00 0.00 4.30
2045 6494 4.877378 TTCTTCTTTACTGCCGGAACTA 57.123 40.909 5.05 0.00 0.00 2.24
2497 7261 3.321111 TGGACTCATCTATAAAGGCCGAC 59.679 47.826 0.00 0.00 41.47 4.79
3114 9310 2.028020 CGAGACTGGCTTAGGGAACTTT 60.028 50.000 0.00 0.00 43.67 2.66
3211 9412 6.225318 GCATATGCATCCAACATTTACCAAT 58.775 36.000 22.84 0.00 41.59 3.16
3291 9492 6.650807 TCTGCTCAGTTTACTCTGTTTTATGG 59.349 38.462 0.00 0.00 36.85 2.74
3628 10073 7.033791 GTCATCTCTACGTTTGATTACTCCAA 58.966 38.462 0.00 0.00 0.00 3.53
3791 10236 5.009911 ACAATGCACACAACTGTTGATACAT 59.990 36.000 26.00 18.36 32.86 2.29
3936 10388 2.031012 CTGCCACCGAAGCTGTGA 59.969 61.111 4.32 0.00 35.74 3.58
4302 10774 2.257353 GCAACGACCCTTGCAGATT 58.743 52.632 3.80 0.00 45.07 2.40
4324 10796 0.250295 TGCCACCAAAAGAGACGGAG 60.250 55.000 0.00 0.00 0.00 4.63
4359 10831 2.592308 GTGAGGGACCAGGCCATC 59.408 66.667 5.01 0.00 39.13 3.51
4413 10885 3.181462 TGCCAATCTATTCTGTGATCGCT 60.181 43.478 7.94 0.00 0.00 4.93
4505 10977 2.287668 ACTCGACGAGTTTCAAGTGGAG 60.288 50.000 24.44 5.53 40.28 3.86
4531 11003 1.679139 CAACTGCAACAGAACCTCCA 58.321 50.000 0.78 0.00 35.18 3.86
4582 11054 1.620323 AGAGGTTTGGCTCATTTTGGC 59.380 47.619 0.00 0.00 0.00 4.52
4646 11118 8.058667 TGTAAAGTAGTATCTTCATTCGGACA 57.941 34.615 0.00 0.00 0.00 4.02
4678 11150 2.076863 GAACGGTCTGCTATGCAAAGT 58.923 47.619 0.00 0.00 38.41 2.66
4730 11202 4.037446 TCTGTTGCCTGTAAATGTTTGGTC 59.963 41.667 0.00 0.00 0.00 4.02
4800 11279 5.841957 AGTTGAAGCAAAGTTCTGTTGAT 57.158 34.783 0.00 0.00 0.00 2.57
4828 11307 4.702612 TCTTTGTTTGTGTTAAGCTGGTGA 59.297 37.500 0.00 0.00 0.00 4.02
4908 11391 6.662755 ACTGAAGCCAATATTGAGATGGTTA 58.337 36.000 17.23 1.81 36.57 2.85
4960 11443 9.866655 AGGAAGCATGGATATTTTATTTCACTA 57.133 29.630 0.00 0.00 0.00 2.74
4979 11462 1.949465 ACCTTGTCTTGGTGAACGAC 58.051 50.000 0.00 0.00 36.30 4.34
4990 11473 2.747989 TGGTGAACGACTACTAGCTGAG 59.252 50.000 0.00 0.00 0.00 3.35
5002 11485 2.666190 GCTGAGTGCTGCGTTGGA 60.666 61.111 0.00 0.00 38.95 3.53
5003 11486 2.037136 GCTGAGTGCTGCGTTGGAT 61.037 57.895 0.00 0.00 38.95 3.41
5004 11487 1.975363 GCTGAGTGCTGCGTTGGATC 61.975 60.000 0.00 0.00 38.95 3.36
5005 11488 0.390866 CTGAGTGCTGCGTTGGATCT 60.391 55.000 0.00 0.00 0.00 2.75
5006 11489 0.035317 TGAGTGCTGCGTTGGATCTT 59.965 50.000 0.00 0.00 0.00 2.40
5007 11490 1.160137 GAGTGCTGCGTTGGATCTTT 58.840 50.000 0.00 0.00 0.00 2.52
5012 11495 1.470098 GCTGCGTTGGATCTTTGATGT 59.530 47.619 0.00 0.00 0.00 3.06
5018 11501 3.189080 CGTTGGATCTTTGATGTCAAGCA 59.811 43.478 0.00 0.00 37.15 3.91
5032 11515 3.059868 TGTCAAGCAAGAAATTCGTCGTC 60.060 43.478 0.00 0.00 0.00 4.20
5037 11520 2.092838 GCAAGAAATTCGTCGTCAGGAG 59.907 50.000 0.00 0.00 0.00 3.69
5038 11521 1.997669 AGAAATTCGTCGTCAGGAGC 58.002 50.000 0.00 0.00 0.00 4.70
5039 11522 1.546476 AGAAATTCGTCGTCAGGAGCT 59.454 47.619 0.00 0.00 0.00 4.09
5040 11523 2.028930 AGAAATTCGTCGTCAGGAGCTT 60.029 45.455 0.00 0.00 0.00 3.74
5041 11524 1.714794 AATTCGTCGTCAGGAGCTTG 58.285 50.000 0.00 0.00 0.00 4.01
5042 11525 0.108615 ATTCGTCGTCAGGAGCTTGG 60.109 55.000 0.00 0.00 0.00 3.61
5043 11526 1.461091 TTCGTCGTCAGGAGCTTGGT 61.461 55.000 0.00 0.00 0.00 3.67
5044 11527 1.734477 CGTCGTCAGGAGCTTGGTG 60.734 63.158 0.00 0.00 0.00 4.17
5045 11528 1.666011 GTCGTCAGGAGCTTGGTGA 59.334 57.895 0.00 0.00 0.00 4.02
5046 11529 0.247736 GTCGTCAGGAGCTTGGTGAT 59.752 55.000 0.00 0.00 0.00 3.06
5047 11530 1.476891 GTCGTCAGGAGCTTGGTGATA 59.523 52.381 0.00 0.00 0.00 2.15
5048 11531 1.751351 TCGTCAGGAGCTTGGTGATAG 59.249 52.381 0.00 0.00 0.00 2.08
5049 11532 1.202463 CGTCAGGAGCTTGGTGATAGG 60.202 57.143 0.00 0.00 0.00 2.57
5050 11533 2.111384 GTCAGGAGCTTGGTGATAGGA 58.889 52.381 0.00 0.00 0.00 2.94
5058 11541 2.836360 GGTGATAGGACGGGCGGA 60.836 66.667 0.00 0.00 0.00 5.54
5082 11565 1.012841 GTCCATAGCTTCTGTGCTGC 58.987 55.000 0.00 0.00 43.87 5.25
5308 11824 3.020627 CGCCCGTCTACTAGGTCG 58.979 66.667 0.00 0.00 0.00 4.79
5319 11838 2.757099 TAGGTCGAGCCGTTCCCC 60.757 66.667 11.73 0.00 43.70 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 135 6.491394 TCACCAAAATCTCGTGTACAAAAAG 58.509 36.000 0.00 0.00 0.00 2.27
143 147 5.481105 TGGCAAAATCATCACCAAAATCTC 58.519 37.500 0.00 0.00 0.00 2.75
211 229 6.418057 TCCTATTTGTTTTCCTGCAAACAT 57.582 33.333 2.68 0.00 44.27 2.71
319 1068 2.493675 TCTTTGATCTCCGAGACCACAG 59.506 50.000 0.00 0.00 0.00 3.66
320 1069 2.525368 TCTTTGATCTCCGAGACCACA 58.475 47.619 0.00 0.00 0.00 4.17
322 1071 2.432146 CCATCTTTGATCTCCGAGACCA 59.568 50.000 0.00 0.00 0.00 4.02
323 1072 2.804933 GCCATCTTTGATCTCCGAGACC 60.805 54.545 0.00 0.00 0.00 3.85
325 1074 2.110578 TGCCATCTTTGATCTCCGAGA 58.889 47.619 0.00 0.00 0.00 4.04
326 1075 2.609427 TGCCATCTTTGATCTCCGAG 57.391 50.000 0.00 0.00 0.00 4.63
327 1076 2.171237 ACATGCCATCTTTGATCTCCGA 59.829 45.455 0.00 0.00 0.00 4.55
328 1077 2.547211 GACATGCCATCTTTGATCTCCG 59.453 50.000 0.00 0.00 0.00 4.63
329 1078 2.547211 CGACATGCCATCTTTGATCTCC 59.453 50.000 0.00 0.00 0.00 3.71
330 1079 3.461061 TCGACATGCCATCTTTGATCTC 58.539 45.455 0.00 0.00 0.00 2.75
331 1080 3.548745 TCGACATGCCATCTTTGATCT 57.451 42.857 0.00 0.00 0.00 2.75
334 1083 6.698008 AAATATTCGACATGCCATCTTTGA 57.302 33.333 0.00 0.00 0.00 2.69
335 1084 7.760131 AAAAATATTCGACATGCCATCTTTG 57.240 32.000 0.00 0.00 0.00 2.77
359 1108 5.528320 ACGAATAAACTTGACCCGAGAAAAA 59.472 36.000 0.00 0.00 0.00 1.94
361 1110 4.634199 ACGAATAAACTTGACCCGAGAAA 58.366 39.130 0.00 0.00 0.00 2.52
362 1111 4.240096 GACGAATAAACTTGACCCGAGAA 58.760 43.478 0.00 0.00 0.00 2.87
363 1112 3.671433 CGACGAATAAACTTGACCCGAGA 60.671 47.826 0.00 0.00 0.00 4.04
364 1113 2.597305 CGACGAATAAACTTGACCCGAG 59.403 50.000 0.00 0.00 0.00 4.63
365 1114 2.598589 CGACGAATAAACTTGACCCGA 58.401 47.619 0.00 0.00 0.00 5.14
366 1115 1.657094 CCGACGAATAAACTTGACCCG 59.343 52.381 0.00 0.00 0.00 5.28
367 1116 1.395954 GCCGACGAATAAACTTGACCC 59.604 52.381 0.00 0.00 0.00 4.46
368 1117 2.070783 TGCCGACGAATAAACTTGACC 58.929 47.619 0.00 0.00 0.00 4.02
369 1118 2.735134 ACTGCCGACGAATAAACTTGAC 59.265 45.455 0.00 0.00 0.00 3.18
371 1120 2.993899 AGACTGCCGACGAATAAACTTG 59.006 45.455 0.00 0.00 0.00 3.16
372 1121 3.314541 AGACTGCCGACGAATAAACTT 57.685 42.857 0.00 0.00 0.00 2.66
373 1122 4.445452 TTAGACTGCCGACGAATAAACT 57.555 40.909 0.00 0.00 0.00 2.66
374 1123 4.565564 ACATTAGACTGCCGACGAATAAAC 59.434 41.667 0.00 0.00 0.00 2.01
375 1124 4.751060 ACATTAGACTGCCGACGAATAAA 58.249 39.130 0.00 0.00 0.00 1.40
377 1126 4.380841 AACATTAGACTGCCGACGAATA 57.619 40.909 0.00 0.00 0.00 1.75
378 1127 2.961526 ACATTAGACTGCCGACGAAT 57.038 45.000 0.00 0.00 0.00 3.34
379 1128 2.736144 AACATTAGACTGCCGACGAA 57.264 45.000 0.00 0.00 0.00 3.85
380 1129 2.736144 AAACATTAGACTGCCGACGA 57.264 45.000 0.00 0.00 0.00 4.20
381 1130 3.241995 GCTAAAACATTAGACTGCCGACG 60.242 47.826 0.00 0.00 0.00 5.12
382 1131 3.933332 AGCTAAAACATTAGACTGCCGAC 59.067 43.478 0.00 0.00 0.00 4.79
383 1132 4.181578 GAGCTAAAACATTAGACTGCCGA 58.818 43.478 0.00 0.00 0.00 5.54
384 1133 3.932710 TGAGCTAAAACATTAGACTGCCG 59.067 43.478 0.00 0.00 0.00 5.69
385 1134 7.553881 TTATGAGCTAAAACATTAGACTGCC 57.446 36.000 0.00 0.00 0.00 4.85
402 1151 8.947940 CAAACACGATTTAGCTAAATTATGAGC 58.052 33.333 30.88 19.41 36.13 4.26
405 1154 8.947940 GCTCAAACACGATTTAGCTAAATTATG 58.052 33.333 27.96 27.12 36.13 1.90
406 1155 8.893727 AGCTCAAACACGATTTAGCTAAATTAT 58.106 29.630 27.96 18.15 38.48 1.28
407 1156 8.175069 CAGCTCAAACACGATTTAGCTAAATTA 58.825 33.333 27.96 6.00 38.20 1.40
408 1157 7.023575 CAGCTCAAACACGATTTAGCTAAATT 58.976 34.615 27.96 13.99 38.20 1.82
409 1158 6.149474 ACAGCTCAAACACGATTTAGCTAAAT 59.851 34.615 27.73 27.73 38.20 1.40
410 1159 5.468746 ACAGCTCAAACACGATTTAGCTAAA 59.531 36.000 20.71 20.71 38.20 1.85
411 1160 4.994852 ACAGCTCAAACACGATTTAGCTAA 59.005 37.500 0.86 0.86 38.20 3.09
412 1161 4.566004 ACAGCTCAAACACGATTTAGCTA 58.434 39.130 14.06 0.00 38.20 3.32
413 1162 3.403038 ACAGCTCAAACACGATTTAGCT 58.597 40.909 0.00 0.00 40.79 3.32
414 1163 3.813529 ACAGCTCAAACACGATTTAGC 57.186 42.857 0.00 0.00 0.00 3.09
415 1164 6.128282 ACCATTACAGCTCAAACACGATTTAG 60.128 38.462 0.00 0.00 0.00 1.85
416 1165 5.703592 ACCATTACAGCTCAAACACGATTTA 59.296 36.000 0.00 0.00 0.00 1.40
417 1166 4.518970 ACCATTACAGCTCAAACACGATTT 59.481 37.500 0.00 0.00 0.00 2.17
418 1167 4.072131 ACCATTACAGCTCAAACACGATT 58.928 39.130 0.00 0.00 0.00 3.34
419 1168 3.674997 ACCATTACAGCTCAAACACGAT 58.325 40.909 0.00 0.00 0.00 3.73
420 1169 3.120321 ACCATTACAGCTCAAACACGA 57.880 42.857 0.00 0.00 0.00 4.35
421 1170 3.896648 AACCATTACAGCTCAAACACG 57.103 42.857 0.00 0.00 0.00 4.49
422 1171 5.810074 ACAAAAACCATTACAGCTCAAACAC 59.190 36.000 0.00 0.00 0.00 3.32
423 1172 5.809562 CACAAAAACCATTACAGCTCAAACA 59.190 36.000 0.00 0.00 0.00 2.83
424 1173 5.810074 ACACAAAAACCATTACAGCTCAAAC 59.190 36.000 0.00 0.00 0.00 2.93
425 1174 5.971763 ACACAAAAACCATTACAGCTCAAA 58.028 33.333 0.00 0.00 0.00 2.69
426 1175 5.590530 ACACAAAAACCATTACAGCTCAA 57.409 34.783 0.00 0.00 0.00 3.02
427 1176 5.590530 AACACAAAAACCATTACAGCTCA 57.409 34.783 0.00 0.00 0.00 4.26
428 1177 6.533367 TGAAAACACAAAAACCATTACAGCTC 59.467 34.615 0.00 0.00 0.00 4.09
429 1178 6.312672 GTGAAAACACAAAAACCATTACAGCT 59.687 34.615 0.00 0.00 0.00 4.24
430 1179 6.312672 AGTGAAAACACAAAAACCATTACAGC 59.687 34.615 0.00 0.00 0.00 4.40
431 1180 7.826260 AGTGAAAACACAAAAACCATTACAG 57.174 32.000 0.00 0.00 0.00 2.74
432 1181 8.091449 AGAAGTGAAAACACAAAAACCATTACA 58.909 29.630 0.00 0.00 0.00 2.41
433 1182 8.474006 AGAAGTGAAAACACAAAAACCATTAC 57.526 30.769 0.00 0.00 0.00 1.89
434 1183 9.575783 GTAGAAGTGAAAACACAAAAACCATTA 57.424 29.630 0.00 0.00 0.00 1.90
435 1184 8.311109 AGTAGAAGTGAAAACACAAAAACCATT 58.689 29.630 0.00 0.00 0.00 3.16
436 1185 7.836842 AGTAGAAGTGAAAACACAAAAACCAT 58.163 30.769 0.00 0.00 0.00 3.55
437 1186 7.222000 AGTAGAAGTGAAAACACAAAAACCA 57.778 32.000 0.00 0.00 0.00 3.67
438 1187 6.750501 GGAGTAGAAGTGAAAACACAAAAACC 59.249 38.462 0.00 0.00 0.00 3.27
439 1188 6.468000 CGGAGTAGAAGTGAAAACACAAAAAC 59.532 38.462 0.00 0.00 0.00 2.43
440 1189 6.403855 CCGGAGTAGAAGTGAAAACACAAAAA 60.404 38.462 0.00 0.00 0.00 1.94
441 1190 5.065474 CCGGAGTAGAAGTGAAAACACAAAA 59.935 40.000 0.00 0.00 0.00 2.44
442 1191 4.573201 CCGGAGTAGAAGTGAAAACACAAA 59.427 41.667 0.00 0.00 0.00 2.83
443 1192 4.124238 CCGGAGTAGAAGTGAAAACACAA 58.876 43.478 0.00 0.00 0.00 3.33
444 1193 3.385433 TCCGGAGTAGAAGTGAAAACACA 59.615 43.478 0.00 0.00 0.00 3.72
445 1194 3.986277 TCCGGAGTAGAAGTGAAAACAC 58.014 45.455 0.00 0.00 0.00 3.32
446 1195 4.675976 TTCCGGAGTAGAAGTGAAAACA 57.324 40.909 3.34 0.00 0.00 2.83
447 1196 9.194271 GATATATTCCGGAGTAGAAGTGAAAAC 57.806 37.037 12.62 0.00 0.00 2.43
448 1197 8.365647 GGATATATTCCGGAGTAGAAGTGAAAA 58.634 37.037 12.62 0.00 33.93 2.29
449 1198 7.893658 GGATATATTCCGGAGTAGAAGTGAAA 58.106 38.462 12.62 0.00 33.93 2.69
450 1199 7.463961 GGATATATTCCGGAGTAGAAGTGAA 57.536 40.000 12.62 0.00 33.93 3.18
464 1213 7.222000 ACAAAGAGTCTCTCGGATATATTCC 57.778 40.000 1.96 0.00 41.59 3.01
470 1219 9.132923 ACATAATTACAAAGAGTCTCTCGGATA 57.867 33.333 1.96 0.00 35.36 2.59
471 1220 8.012957 ACATAATTACAAAGAGTCTCTCGGAT 57.987 34.615 1.96 0.00 35.36 4.18
472 1221 7.406031 ACATAATTACAAAGAGTCTCTCGGA 57.594 36.000 1.96 0.00 35.36 4.55
473 1222 9.021863 GTAACATAATTACAAAGAGTCTCTCGG 57.978 37.037 1.96 1.04 35.36 4.63
474 1223 9.790389 AGTAACATAATTACAAAGAGTCTCTCG 57.210 33.333 1.96 0.20 35.36 4.04
492 1241 9.602568 TCGGCACTTTATTAATCAAGTAACATA 57.397 29.630 13.35 1.48 31.78 2.29
493 1242 8.395633 GTCGGCACTTTATTAATCAAGTAACAT 58.604 33.333 13.35 0.00 31.78 2.71
494 1243 7.412129 CGTCGGCACTTTATTAATCAAGTAACA 60.412 37.037 13.35 0.00 31.78 2.41
495 1244 6.898189 CGTCGGCACTTTATTAATCAAGTAAC 59.102 38.462 13.35 9.43 31.78 2.50
496 1245 6.591062 ACGTCGGCACTTTATTAATCAAGTAA 59.409 34.615 13.35 0.25 31.78 2.24
497 1246 6.101332 ACGTCGGCACTTTATTAATCAAGTA 58.899 36.000 13.35 0.00 31.78 2.24
498 1247 4.933400 ACGTCGGCACTTTATTAATCAAGT 59.067 37.500 8.87 8.87 33.29 3.16
499 1248 5.464965 ACGTCGGCACTTTATTAATCAAG 57.535 39.130 7.67 7.67 0.00 3.02
500 1249 5.866335 AACGTCGGCACTTTATTAATCAA 57.134 34.783 0.00 0.00 0.00 2.57
501 1250 5.866335 AAACGTCGGCACTTTATTAATCA 57.134 34.783 0.00 0.00 0.00 2.57
502 1251 6.540205 AGAAAACGTCGGCACTTTATTAATC 58.460 36.000 0.00 0.00 0.00 1.75
503 1252 6.490566 AGAAAACGTCGGCACTTTATTAAT 57.509 33.333 0.00 0.00 0.00 1.40
504 1253 5.927954 AGAAAACGTCGGCACTTTATTAA 57.072 34.783 0.00 0.00 0.00 1.40
505 1254 7.418840 TTTAGAAAACGTCGGCACTTTATTA 57.581 32.000 0.00 0.00 0.00 0.98
506 1255 5.927954 TTAGAAAACGTCGGCACTTTATT 57.072 34.783 0.00 0.00 0.00 1.40
507 1256 5.927954 TTTAGAAAACGTCGGCACTTTAT 57.072 34.783 0.00 0.00 0.00 1.40
508 1257 5.731599 TTTTAGAAAACGTCGGCACTTTA 57.268 34.783 0.00 0.00 0.00 1.85
509 1258 4.619437 TTTTAGAAAACGTCGGCACTTT 57.381 36.364 0.00 0.00 0.00 2.66
510 1259 4.619437 TTTTTAGAAAACGTCGGCACTT 57.381 36.364 0.00 0.00 0.00 3.16
939 1688 2.370445 AACAGGCGATGGAGAGGGG 61.370 63.158 0.00 0.00 0.00 4.79
954 1703 3.252554 AGGGGATTAGGTTTTGCAACA 57.747 42.857 0.00 0.00 34.15 3.33
955 1704 4.081862 GGTTAGGGGATTAGGTTTTGCAAC 60.082 45.833 0.00 0.00 0.00 4.17
956 1705 4.090819 GGTTAGGGGATTAGGTTTTGCAA 58.909 43.478 0.00 0.00 0.00 4.08
974 1723 0.906775 GGATGTTGAGGTCGGGGTTA 59.093 55.000 0.00 0.00 0.00 2.85
1129 1895 2.176055 CGTCGTCCTGGACACGAG 59.824 66.667 30.48 16.15 46.52 4.18
1378 5805 3.541713 GGGGCCGGCTCTGTAGAG 61.542 72.222 28.78 4.53 44.75 2.43
1423 5850 4.330944 TTCGTATGCTGGAATATCGGTT 57.669 40.909 0.00 0.00 0.00 4.44
1750 6193 2.975799 GACTTGGCGCGGGAAACA 60.976 61.111 8.83 0.00 0.00 2.83
1766 6215 1.327690 ATAGTTCGGAGCAAGGCGGA 61.328 55.000 0.00 0.00 0.00 5.54
1788 6237 1.142185 CCTAGCTCGTCGTCGTCGTA 61.142 60.000 11.41 0.00 38.33 3.43
1964 6413 3.470888 CCCCGTCGCCAATCTCCT 61.471 66.667 0.00 0.00 0.00 3.69
2042 6491 1.065636 TCTGTCTCGTCGTCCCATAGT 60.066 52.381 0.00 0.00 0.00 2.12
2045 6494 0.608308 TGTCTGTCTCGTCGTCCCAT 60.608 55.000 0.00 0.00 0.00 4.00
2747 7602 8.190888 ACTTCTCATGAGTGAATTCGAATTAC 57.809 34.615 22.78 18.81 33.05 1.89
2906 9101 3.660501 TGGTTATATCTACGCCTGCAG 57.339 47.619 6.78 6.78 0.00 4.41
3211 9412 5.682943 ACTTAAAGACGCTAAACATGCAA 57.317 34.783 0.00 0.00 0.00 4.08
3291 9492 6.701400 ACTTGACTTGAACAATTGTTTATGGC 59.299 34.615 24.02 22.46 38.56 4.40
3524 9966 3.088532 TGACCTGCAATGGACCATAAAC 58.911 45.455 7.59 0.81 0.00 2.01
3628 10073 7.889073 TCTGGACACTAGAACAGAACTTACTAT 59.111 37.037 0.00 0.00 37.06 2.12
3936 10388 5.233476 CGTGTATATACCGTGAGCAAACATT 59.767 40.000 10.38 0.00 0.00 2.71
4302 10774 0.250295 CGTCTCTTTTGGTGGCAGGA 60.250 55.000 0.00 0.00 0.00 3.86
4324 10796 3.311106 TCACGACGTTCAAATACTGGTC 58.689 45.455 0.00 0.00 0.00 4.02
4359 10831 4.274459 GCCAGGCTCTATGTACTCAATTTG 59.726 45.833 3.29 0.00 0.00 2.32
4413 10885 1.001764 CATGGCCTGCCTTCTCACA 60.002 57.895 9.97 0.00 36.94 3.58
4505 10977 3.259425 CTGTTGCAGTTGCCGGAGC 62.259 63.158 5.05 0.22 41.18 4.70
4531 11003 1.692042 CAGGGACCCAGAGAGCCAT 60.692 63.158 14.60 0.00 0.00 4.40
4582 11054 6.467047 CAGAAATAGTGCACTAAAAGCAATCG 59.533 38.462 29.26 9.10 44.64 3.34
4646 11118 3.368116 GCAGACCGTTCACCTACACTTAT 60.368 47.826 0.00 0.00 0.00 1.73
4648 11120 1.270147 GCAGACCGTTCACCTACACTT 60.270 52.381 0.00 0.00 0.00 3.16
4678 11150 8.079211 ACAAGTAGCACCTAGAATATCTTTGA 57.921 34.615 0.00 0.00 0.00 2.69
4730 11202 2.805845 CTCATACGTCGTTAACCCCAG 58.194 52.381 1.78 0.00 0.00 4.45
4800 11279 6.252281 CAGCTTAACACAAACAAAGAACGTA 58.748 36.000 0.00 0.00 0.00 3.57
4828 11307 7.653713 GGTCGTCATGAGAAATTCAGTATGTAT 59.346 37.037 0.00 0.00 39.68 2.29
4873 11356 1.251251 GGCTTCAGTTGATTGCCAGT 58.749 50.000 16.59 0.00 40.96 4.00
4914 11397 7.709613 GCTTCCTTTTCTGCAATTGATGATTAT 59.290 33.333 10.34 0.00 0.00 1.28
4915 11398 7.037438 GCTTCCTTTTCTGCAATTGATGATTA 58.963 34.615 10.34 0.00 0.00 1.75
4924 11407 3.167485 TCCATGCTTCCTTTTCTGCAAT 58.833 40.909 0.00 0.00 38.96 3.56
4957 11440 2.696707 TCGTTCACCAAGACAAGGTAGT 59.303 45.455 0.00 0.00 37.23 2.73
4960 11443 1.485066 AGTCGTTCACCAAGACAAGGT 59.515 47.619 0.00 0.00 40.85 3.50
4990 11473 0.874390 TCAAAGATCCAACGCAGCAC 59.126 50.000 0.00 0.00 0.00 4.40
4996 11479 3.189080 TGCTTGACATCAAAGATCCAACG 59.811 43.478 0.00 0.00 35.15 4.10
5001 11484 7.008086 CGAATTTCTTGCTTGACATCAAAGATC 59.992 37.037 0.00 0.00 35.15 2.75
5002 11485 6.805271 CGAATTTCTTGCTTGACATCAAAGAT 59.195 34.615 0.00 0.00 35.15 2.40
5003 11486 6.144854 CGAATTTCTTGCTTGACATCAAAGA 58.855 36.000 0.00 0.00 35.15 2.52
5004 11487 5.916883 ACGAATTTCTTGCTTGACATCAAAG 59.083 36.000 0.00 0.00 35.15 2.77
5005 11488 5.830912 ACGAATTTCTTGCTTGACATCAAA 58.169 33.333 0.00 0.00 35.15 2.69
5006 11489 5.437289 ACGAATTTCTTGCTTGACATCAA 57.563 34.783 0.00 0.00 0.00 2.57
5007 11490 4.377328 CGACGAATTTCTTGCTTGACATCA 60.377 41.667 0.00 0.00 0.00 3.07
5012 11495 3.127589 TGACGACGAATTTCTTGCTTGA 58.872 40.909 0.00 0.00 0.00 3.02
5018 11501 2.028930 AGCTCCTGACGACGAATTTCTT 60.029 45.455 0.00 0.00 0.00 2.52
5032 11515 1.202463 CGTCCTATCACCAAGCTCCTG 60.202 57.143 0.00 0.00 0.00 3.86
5037 11520 1.523938 GCCCGTCCTATCACCAAGC 60.524 63.158 0.00 0.00 0.00 4.01
5038 11521 1.227263 CGCCCGTCCTATCACCAAG 60.227 63.158 0.00 0.00 0.00 3.61
5039 11522 2.727392 CCGCCCGTCCTATCACCAA 61.727 63.158 0.00 0.00 0.00 3.67
5040 11523 3.151710 CCGCCCGTCCTATCACCA 61.152 66.667 0.00 0.00 0.00 4.17
5041 11524 2.836360 TCCGCCCGTCCTATCACC 60.836 66.667 0.00 0.00 0.00 4.02
5042 11525 2.416260 GTCCGCCCGTCCTATCAC 59.584 66.667 0.00 0.00 0.00 3.06
5043 11526 3.214123 CGTCCGCCCGTCCTATCA 61.214 66.667 0.00 0.00 0.00 2.15
5044 11527 3.214845 ACGTCCGCCCGTCCTATC 61.215 66.667 0.00 0.00 35.95 2.08
5045 11528 3.524606 CACGTCCGCCCGTCCTAT 61.525 66.667 0.00 0.00 39.45 2.57
5058 11541 1.066858 CACAGAAGCTATGGACCACGT 60.067 52.381 0.00 0.00 0.00 4.49
5065 11548 2.102084 TCTAGCAGCACAGAAGCTATGG 59.898 50.000 0.00 0.00 44.54 2.74
5072 11555 0.037326 CCCGTTCTAGCAGCACAGAA 60.037 55.000 5.56 5.56 0.00 3.02
5082 11565 7.274603 AGTAAATTACTCTAGCCCGTTCTAG 57.725 40.000 0.00 2.73 37.87 2.43
5308 11824 1.227292 GAATCGAGGGGAACGGCTC 60.227 63.158 0.00 0.00 0.00 4.70
5319 11838 0.461961 GAGGGGTGGACTGAATCGAG 59.538 60.000 0.00 0.00 0.00 4.04
5404 11942 4.287781 TCGTTGCCGCTTCCGTCA 62.288 61.111 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.