Multiple sequence alignment - TraesCS6A01G311000

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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 TraesCS6A01G311000 chr6A 100.000 3458 0 0 1 3458 546989628 546993085 0.000000e+00 6386.0
1 TraesCS6A01G311000 chr6A 85.370 540 53 17 2434 2968 547028647 547029165 1.410000e-148 536.0
2 TraesCS6A01G311000 chr6A 74.965 719 154 16 1759 2460 547593362 547592653 1.210000e-79 307.0
3 TraesCS6A01G311000 chr6A 79.375 480 64 22 1098 1564 547279877 547279420 4.340000e-79 305.0
4 TraesCS6A01G311000 chr6A 87.209 172 21 1 2604 2774 547029172 547029343 9.790000e-46 195.0
5 TraesCS6A01G311000 chr6A 82.439 205 32 3 1362 1563 547594393 547594190 3.550000e-40 176.0
6 TraesCS6A01G311000 chr6B 87.330 3165 221 71 409 3458 599915326 599918425 0.000000e+00 3458.0
7 TraesCS6A01G311000 chr6B 74.935 774 162 22 1710 2460 600786267 600785503 3.330000e-85 326.0
8 TraesCS6A01G311000 chr6B 78.958 480 72 18 1098 1564 600596565 600597028 2.020000e-77 300.0
9 TraesCS6A01G311000 chr6B 80.882 204 35 3 1363 1563 600786931 600786729 1.280000e-34 158.0
10 TraesCS6A01G311000 chr6D 92.106 2331 83 44 391 2686 400793588 400795852 0.000000e+00 3192.0
11 TraesCS6A01G311000 chr6D 88.889 396 43 1 1 396 469209888 469210282 1.440000e-133 486.0
12 TraesCS6A01G311000 chr6D 89.003 391 40 3 1 391 355882232 355882619 6.710000e-132 481.0
13 TraesCS6A01G311000 chr6D 76.471 714 146 18 1759 2460 401150833 401150130 5.450000e-98 368.0
14 TraesCS6A01G311000 chr6D 73.997 573 97 32 987 1553 401151525 401150999 5.890000e-43 185.0
15 TraesCS6A01G311000 chr6D 90.625 64 4 2 425 487 400793294 400793356 2.210000e-12 84.2
16 TraesCS6A01G311000 chr3D 89.114 395 42 1 4 398 495236227 495235834 1.120000e-134 490.0
17 TraesCS6A01G311000 chr2D 89.460 389 38 3 4 391 25065757 25065371 4.010000e-134 488.0
18 TraesCS6A01G311000 chr2D 89.175 388 41 1 4 391 86069107 86069493 1.870000e-132 483.0
19 TraesCS6A01G311000 chr1D 89.086 394 40 3 4 395 362325109 362324717 1.440000e-133 486.0
20 TraesCS6A01G311000 chr5D 88.861 395 41 2 1 395 380847691 380847300 1.870000e-132 483.0
21 TraesCS6A01G311000 chr5D 88.804 393 40 3 4 396 238113109 238112721 2.410000e-131 479.0
22 TraesCS6A01G311000 chrUn 88.608 395 44 1 1 395 94194461 94194854 2.410000e-131 479.0
23 TraesCS6A01G311000 chrUn 90.741 54 5 0 1118 1171 12530018 12530071 4.790000e-09 73.1


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 TraesCS6A01G311000 chr6A 546989628 546993085 3457 False 6386.0 6386 100.0000 1 3458 1 chr6A.!!$F1 3457
1 TraesCS6A01G311000 chr6A 547028647 547029343 696 False 365.5 536 86.2895 2434 2968 2 chr6A.!!$F2 534
2 TraesCS6A01G311000 chr6A 547592653 547594393 1740 True 241.5 307 78.7020 1362 2460 2 chr6A.!!$R2 1098
3 TraesCS6A01G311000 chr6B 599915326 599918425 3099 False 3458.0 3458 87.3300 409 3458 1 chr6B.!!$F1 3049
4 TraesCS6A01G311000 chr6B 600785503 600786931 1428 True 242.0 326 77.9085 1363 2460 2 chr6B.!!$R1 1097
5 TraesCS6A01G311000 chr6D 400793294 400795852 2558 False 1638.1 3192 91.3655 391 2686 2 chr6D.!!$F3 2295
6 TraesCS6A01G311000 chr6D 401150130 401151525 1395 True 276.5 368 75.2340 987 2460 2 chr6D.!!$R1 1473

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
788 819 0.034896 ATAAATACGCAGGAGGGCCG 59.965 55.0 0.0 0.0 39.96 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2730 3633 0.099613 TCGAGCTCAGCGAGTTCATC 59.9 55.0 15.4 7.29 39.34 2.92 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
26 27 3.741476 GGAAACGCCCAGCTGCTG 61.741 66.667 22.44 22.44 0.00 4.41
27 28 2.980233 GAAACGCCCAGCTGCTGT 60.980 61.111 26.41 8.37 0.00 4.40
28 29 2.519302 AAACGCCCAGCTGCTGTT 60.519 55.556 26.41 12.55 32.28 3.16
29 30 2.737932 GAAACGCCCAGCTGCTGTTG 62.738 60.000 26.41 18.23 31.69 3.33
33 34 2.360852 CCCAGCTGCTGTTGGAGG 60.361 66.667 26.41 16.67 45.89 4.30
34 35 2.360852 CCAGCTGCTGTTGGAGGG 60.361 66.667 26.41 7.20 45.89 4.30
36 37 4.357279 AGCTGCTGTTGGAGGGGC 62.357 66.667 0.00 0.00 31.89 5.80
37 38 4.357279 GCTGCTGTTGGAGGGGCT 62.357 66.667 0.00 0.00 31.89 5.19
38 39 2.360852 CTGCTGTTGGAGGGGCTG 60.361 66.667 0.00 0.00 0.00 4.85
39 40 4.666253 TGCTGTTGGAGGGGCTGC 62.666 66.667 0.00 0.00 0.00 5.25
59 60 1.800681 GCGGCGAACCTTTGCTATT 59.199 52.632 12.98 0.00 37.71 1.73
60 61 0.170339 GCGGCGAACCTTTGCTATTT 59.830 50.000 12.98 0.00 37.71 1.40
61 62 1.402325 GCGGCGAACCTTTGCTATTTT 60.402 47.619 12.98 0.00 37.71 1.82
76 77 3.688086 TTTTTCGGCGGGGAATGG 58.312 55.556 7.21 0.00 0.00 3.16
79 80 2.199613 TTTTCGGCGGGGAATGGCTA 62.200 55.000 7.21 0.00 0.00 3.93
80 81 1.990160 TTTCGGCGGGGAATGGCTAT 61.990 55.000 7.21 0.00 0.00 2.97
81 82 2.358737 CGGCGGGGAATGGCTATC 60.359 66.667 0.00 0.00 0.00 2.08
82 83 2.883828 CGGCGGGGAATGGCTATCT 61.884 63.158 0.00 0.00 0.00 1.98
83 84 1.541310 CGGCGGGGAATGGCTATCTA 61.541 60.000 0.00 0.00 0.00 1.98
96 97 2.857618 GCTATCTAGCGATGAAGGACG 58.142 52.381 0.00 0.00 39.82 4.79
98 99 0.315568 ATCTAGCGATGAAGGACGGC 59.684 55.000 0.00 0.00 0.00 5.68
99 100 1.658717 CTAGCGATGAAGGACGGCG 60.659 63.158 4.80 4.80 0.00 6.46
100 101 3.133767 TAGCGATGAAGGACGGCGG 62.134 63.158 13.24 0.00 0.00 6.13
121 122 2.202623 GCGCCGGGATATCGCTAG 60.203 66.667 16.79 9.64 44.79 3.42
122 123 2.991076 GCGCCGGGATATCGCTAGT 61.991 63.158 16.79 0.00 44.79 2.57
123 124 1.154016 CGCCGGGATATCGCTAGTG 60.154 63.158 16.79 10.94 0.00 2.74
124 125 1.215647 GCCGGGATATCGCTAGTGG 59.784 63.158 16.79 11.56 0.00 4.00
125 126 1.215647 CCGGGATATCGCTAGTGGC 59.784 63.158 16.79 0.00 37.64 5.01
163 164 3.839432 GGAGGCGAGTCGGGGAAG 61.839 72.222 15.52 0.00 0.00 3.46
167 168 1.004200 GGCGAGTCGGGGAAGAAAA 60.004 57.895 15.52 0.00 0.00 2.29
169 170 1.007580 GCGAGTCGGGGAAGAAAATC 58.992 55.000 15.52 0.00 0.00 2.17
170 171 1.405661 GCGAGTCGGGGAAGAAAATCT 60.406 52.381 15.52 0.00 0.00 2.40
171 172 2.935676 GCGAGTCGGGGAAGAAAATCTT 60.936 50.000 15.52 0.00 39.87 2.40
172 173 2.673368 CGAGTCGGGGAAGAAAATCTTG 59.327 50.000 4.10 0.00 36.73 3.02
173 174 3.616560 CGAGTCGGGGAAGAAAATCTTGA 60.617 47.826 4.10 0.00 36.73 3.02
174 175 3.676093 AGTCGGGGAAGAAAATCTTGAC 58.324 45.455 0.00 0.00 36.73 3.18
175 176 3.328050 AGTCGGGGAAGAAAATCTTGACT 59.672 43.478 0.00 1.86 36.73 3.41
176 177 4.072839 GTCGGGGAAGAAAATCTTGACTT 58.927 43.478 0.00 0.00 36.73 3.01
177 178 4.519350 GTCGGGGAAGAAAATCTTGACTTT 59.481 41.667 0.00 0.00 36.73 2.66
179 180 5.240844 TCGGGGAAGAAAATCTTGACTTTTC 59.759 40.000 0.00 0.00 36.73 2.29
180 181 5.009610 CGGGGAAGAAAATCTTGACTTTTCA 59.990 40.000 10.19 0.00 42.42 2.69
181 182 6.216569 GGGGAAGAAAATCTTGACTTTTCAC 58.783 40.000 10.19 4.95 42.42 3.18
182 183 6.216569 GGGAAGAAAATCTTGACTTTTCACC 58.783 40.000 10.19 11.31 42.42 4.02
184 185 7.417911 GGGAAGAAAATCTTGACTTTTCACCTT 60.418 37.037 16.35 0.00 42.42 3.50
186 187 9.452065 GAAGAAAATCTTGACTTTTCACCTTAC 57.548 33.333 10.19 0.00 42.42 2.34
187 188 7.639945 AGAAAATCTTGACTTTTCACCTTACG 58.360 34.615 10.19 0.00 42.42 3.18
188 189 6.937436 AAATCTTGACTTTTCACCTTACGT 57.063 33.333 0.00 0.00 0.00 3.57
189 190 6.937436 AATCTTGACTTTTCACCTTACGTT 57.063 33.333 0.00 0.00 0.00 3.99
190 191 5.728351 TCTTGACTTTTCACCTTACGTTG 57.272 39.130 0.00 0.00 0.00 4.10
192 193 5.522460 TCTTGACTTTTCACCTTACGTTGAG 59.478 40.000 0.00 0.00 0.00 3.02
193 194 4.124238 TGACTTTTCACCTTACGTTGAGG 58.876 43.478 14.20 14.20 40.24 3.86
194 195 3.473625 ACTTTTCACCTTACGTTGAGGG 58.526 45.455 18.48 4.03 38.65 4.30
199 200 1.810030 CCTTACGTTGAGGGCGAGC 60.810 63.158 9.24 0.00 0.00 5.03
200 201 1.810030 CTTACGTTGAGGGCGAGCC 60.810 63.158 5.37 5.37 0.00 4.70
201 202 3.636313 TTACGTTGAGGGCGAGCCG 62.636 63.158 8.14 0.00 36.85 5.52
213 214 3.056328 GAGCCGCGCTTTTCCCTT 61.056 61.111 5.56 0.00 39.88 3.95
214 215 3.328288 GAGCCGCGCTTTTCCCTTG 62.328 63.158 5.56 0.00 39.88 3.61
219 220 4.759096 CGCTTTTCCCTTGCGCCG 62.759 66.667 4.18 0.00 43.08 6.46
220 221 4.419939 GCTTTTCCCTTGCGCCGG 62.420 66.667 4.18 5.21 0.00 6.13
221 222 2.671619 CTTTTCCCTTGCGCCGGA 60.672 61.111 5.05 8.98 0.00 5.14
222 223 2.671619 TTTTCCCTTGCGCCGGAG 60.672 61.111 5.05 1.55 0.00 4.63
240 241 4.195334 CCCCCAATCGCCCCTCAG 62.195 72.222 0.00 0.00 0.00 3.35
242 243 2.124570 CCCAATCGCCCCTCAGTG 60.125 66.667 0.00 0.00 0.00 3.66
243 244 2.825836 CCAATCGCCCCTCAGTGC 60.826 66.667 0.00 0.00 0.00 4.40
263 264 4.052229 CGGGTTCGGTCTGCGAGT 62.052 66.667 0.00 0.00 0.00 4.18
264 265 2.432628 GGGTTCGGTCTGCGAGTG 60.433 66.667 0.00 0.00 0.00 3.51
266 267 1.733399 GGTTCGGTCTGCGAGTGTC 60.733 63.158 0.00 0.00 0.00 3.67
267 268 2.081212 GTTCGGTCTGCGAGTGTCG 61.081 63.158 0.00 0.00 43.89 4.35
268 269 3.263503 TTCGGTCTGCGAGTGTCGG 62.264 63.158 0.00 0.00 40.84 4.79
269 270 4.778415 CGGTCTGCGAGTGTCGGG 62.778 72.222 0.00 0.00 40.84 5.14
273 274 4.717629 CTGCGAGTGTCGGGCGAA 62.718 66.667 0.00 0.00 40.84 4.70
274 275 4.287781 TGCGAGTGTCGGGCGAAA 62.288 61.111 0.00 0.00 40.84 3.46
275 276 3.039588 GCGAGTGTCGGGCGAAAA 61.040 61.111 0.00 0.00 40.84 2.29
306 307 4.736896 GGCGCTTTCCGTCGTCCT 62.737 66.667 7.64 0.00 39.71 3.85
307 308 3.479269 GCGCTTTCCGTCGTCCTG 61.479 66.667 0.00 0.00 39.71 3.86
308 309 2.809601 CGCTTTCCGTCGTCCTGG 60.810 66.667 0.00 0.00 0.00 4.45
309 310 2.434359 GCTTTCCGTCGTCCTGGG 60.434 66.667 0.00 0.00 0.00 4.45
310 311 2.264794 CTTTCCGTCGTCCTGGGG 59.735 66.667 0.00 0.00 0.00 4.96
311 312 2.203669 TTTCCGTCGTCCTGGGGA 60.204 61.111 0.00 0.00 0.00 4.81
319 320 2.657237 GTCCTGGGGACGTGACTG 59.343 66.667 0.00 0.00 43.14 3.51
320 321 1.906824 GTCCTGGGGACGTGACTGA 60.907 63.158 0.00 0.00 43.14 3.41
321 322 1.606601 TCCTGGGGACGTGACTGAG 60.607 63.158 0.00 0.00 0.00 3.35
322 323 1.606601 CCTGGGGACGTGACTGAGA 60.607 63.158 0.00 0.00 0.00 3.27
323 324 1.587054 CTGGGGACGTGACTGAGAC 59.413 63.158 0.00 0.00 0.00 3.36
324 325 2.201436 CTGGGGACGTGACTGAGACG 62.201 65.000 0.00 0.00 42.62 4.18
346 347 2.795175 TTTTTAACGCCAATGCCGAA 57.205 40.000 0.00 0.00 0.00 4.30
347 348 2.795175 TTTTAACGCCAATGCCGAAA 57.205 40.000 0.00 0.00 0.00 3.46
348 349 2.795175 TTTAACGCCAATGCCGAAAA 57.205 40.000 0.00 0.00 0.00 2.29
349 350 2.795175 TTAACGCCAATGCCGAAAAA 57.205 40.000 0.00 0.00 0.00 1.94
368 369 5.669798 AAAAATGGTATGAGGAGGCCTAT 57.330 39.130 4.42 0.00 31.76 2.57
369 370 5.669798 AAAATGGTATGAGGAGGCCTATT 57.330 39.130 4.42 0.00 31.76 1.73
370 371 4.647564 AATGGTATGAGGAGGCCTATTG 57.352 45.455 4.42 0.00 31.76 1.90
371 372 2.338809 TGGTATGAGGAGGCCTATTGG 58.661 52.381 4.42 0.00 31.76 3.16
372 373 2.090210 TGGTATGAGGAGGCCTATTGGA 60.090 50.000 4.42 0.00 31.76 3.53
373 374 2.569404 GGTATGAGGAGGCCTATTGGAG 59.431 54.545 4.42 0.00 31.76 3.86
374 375 2.803285 ATGAGGAGGCCTATTGGAGA 57.197 50.000 4.42 0.00 31.76 3.71
375 376 2.803285 TGAGGAGGCCTATTGGAGAT 57.197 50.000 4.42 0.00 31.76 2.75
376 377 2.333069 TGAGGAGGCCTATTGGAGATG 58.667 52.381 4.42 0.00 31.76 2.90
377 378 1.003003 GAGGAGGCCTATTGGAGATGC 59.997 57.143 4.42 0.00 31.76 3.91
378 379 0.321122 GGAGGCCTATTGGAGATGCG 60.321 60.000 4.42 0.00 34.57 4.73
379 380 0.321122 GAGGCCTATTGGAGATGCGG 60.321 60.000 4.42 0.00 34.57 5.69
380 381 1.968540 GGCCTATTGGAGATGCGGC 60.969 63.158 0.00 0.00 36.83 6.53
381 382 1.072159 GCCTATTGGAGATGCGGCT 59.928 57.895 0.00 0.00 34.80 5.52
382 383 1.233285 GCCTATTGGAGATGCGGCTG 61.233 60.000 0.00 0.00 34.80 4.85
383 384 0.604780 CCTATTGGAGATGCGGCTGG 60.605 60.000 0.00 0.00 34.57 4.85
384 385 0.394192 CTATTGGAGATGCGGCTGGA 59.606 55.000 0.00 0.00 0.00 3.86
385 386 0.394192 TATTGGAGATGCGGCTGGAG 59.606 55.000 0.00 0.00 0.00 3.86
386 387 1.340399 ATTGGAGATGCGGCTGGAGA 61.340 55.000 0.00 0.00 0.00 3.71
387 388 1.340399 TTGGAGATGCGGCTGGAGAT 61.340 55.000 0.00 0.00 0.00 2.75
388 389 1.301558 GGAGATGCGGCTGGAGATG 60.302 63.158 0.00 0.00 0.00 2.90
389 390 1.960250 GAGATGCGGCTGGAGATGC 60.960 63.158 0.00 0.00 0.00 3.91
390 391 2.110627 GATGCGGCTGGAGATGCT 59.889 61.111 0.00 0.00 0.00 3.79
391 392 1.117749 AGATGCGGCTGGAGATGCTA 61.118 55.000 0.00 0.00 0.00 3.49
392 393 0.036577 GATGCGGCTGGAGATGCTAT 60.037 55.000 0.00 0.00 0.00 2.97
393 394 1.205655 GATGCGGCTGGAGATGCTATA 59.794 52.381 0.00 0.00 0.00 1.31
394 395 1.047801 TGCGGCTGGAGATGCTATAA 58.952 50.000 0.00 0.00 0.00 0.98
406 407 4.774124 AGATGCTATAAGAACTGCAAGCA 58.226 39.130 7.81 7.81 43.43 3.91
416 417 1.372128 CTGCAAGCAGGCCGTTTTC 60.372 57.895 14.10 0.00 40.17 2.29
431 432 4.148174 GCCGTTTTCATAAGAACTGCAAAC 59.852 41.667 0.00 0.00 36.43 2.93
444 445 3.039134 CAAACCAGCCGTTGGGTC 58.961 61.111 6.20 0.00 46.95 4.46
502 503 4.214971 GTCATGGTCTTGCATATGGATCAC 59.785 45.833 4.56 1.37 0.00 3.06
551 552 4.020573 CAGGAAGTGGTAGTATTGGTCACA 60.021 45.833 0.00 0.00 0.00 3.58
552 553 4.223032 AGGAAGTGGTAGTATTGGTCACAG 59.777 45.833 0.00 0.00 0.00 3.66
553 554 3.611766 AGTGGTAGTATTGGTCACAGC 57.388 47.619 0.00 0.00 0.00 4.40
555 556 3.000727 GTGGTAGTATTGGTCACAGCAC 58.999 50.000 0.00 0.00 0.00 4.40
594 595 1.004745 ACCAACACATCCATCCACTCC 59.995 52.381 0.00 0.00 0.00 3.85
662 666 6.621596 GCTGTCATTTACTCATTCAACAGACC 60.622 42.308 0.00 0.00 35.95 3.85
718 722 2.629051 CCCCTAACCGTTTGACATCTC 58.371 52.381 0.00 0.00 0.00 2.75
719 723 2.268298 CCCTAACCGTTTGACATCTCG 58.732 52.381 0.00 0.00 0.00 4.04
720 724 2.353406 CCCTAACCGTTTGACATCTCGT 60.353 50.000 0.00 0.00 0.00 4.18
721 725 2.666508 CCTAACCGTTTGACATCTCGTG 59.333 50.000 0.00 0.00 0.00 4.35
758 789 0.522705 GCAATCAGCAGTGCATCGTG 60.523 55.000 19.20 10.88 43.36 4.35
788 819 0.034896 ATAAATACGCAGGAGGGCCG 59.965 55.000 0.00 0.00 39.96 6.13
816 847 1.402984 GCTTGGACTCACAGGTAGACG 60.403 57.143 0.00 0.00 0.00 4.18
897 928 1.889454 TTGCACCGCAATTCATCCC 59.111 52.632 0.00 0.00 43.99 3.85
936 975 4.899239 GTGGAGCAGCCCCGATCG 62.899 72.222 8.51 8.51 34.97 3.69
1014 1053 4.447342 GCCATGGTGGGGGTGAGG 62.447 72.222 14.67 0.00 38.19 3.86
1015 1054 2.613696 CCATGGTGGGGGTGAGGA 60.614 66.667 2.57 0.00 32.67 3.71
1016 1055 2.008723 CCATGGTGGGGGTGAGGAT 61.009 63.158 2.57 0.00 32.67 3.24
1029 1068 0.323633 TGAGGATGGTGTGCAATGGG 60.324 55.000 0.00 0.00 0.00 4.00
1063 1102 1.564622 CTGACTGCGGTGTTTGTCG 59.435 57.895 0.80 0.00 32.64 4.35
1257 1305 2.359975 GGGAGGTTCAGCAACGGG 60.360 66.667 0.00 0.00 32.68 5.28
1350 1414 9.415370 TCATTTGTCAGATGAAGCTAACGCAAG 62.415 40.741 3.62 0.00 39.10 4.01
1701 2581 6.015519 CCCCATTTGTTCATCTTTTCTGTGTA 60.016 38.462 0.00 0.00 0.00 2.90
1770 2657 0.106149 GGAACACCCTCACGTTGACT 59.894 55.000 0.00 0.00 0.00 3.41
1959 2858 1.726791 GACATGCTGACCAACTACACG 59.273 52.381 0.00 0.00 0.00 4.49
2372 3274 4.039092 CACCCAGGCCACCTCCAG 62.039 72.222 5.01 0.00 0.00 3.86
2461 3363 2.079925 AGCTGGTTTCTTCTTGATCGC 58.920 47.619 0.00 0.00 0.00 4.58
2464 3366 0.727398 GGTTTCTTCTTGATCGCCGG 59.273 55.000 0.00 0.00 0.00 6.13
2481 3383 3.499737 GTCGAGGCATTGCACCGG 61.500 66.667 11.39 0.00 0.00 5.28
2518 3420 6.668323 TGTTGTCAGCTCTTAATTTAGTTGC 58.332 36.000 0.00 4.81 0.00 4.17
2529 3431 4.483476 AATTTAGTTGCGAGTGTTCACC 57.517 40.909 0.00 0.00 0.00 4.02
2530 3432 1.873698 TTAGTTGCGAGTGTTCACCC 58.126 50.000 0.00 0.00 0.00 4.61
2538 3440 3.071479 GCGAGTGTTCACCCTTTGATTA 58.929 45.455 0.00 0.00 32.84 1.75
2557 3459 2.928036 AAGGGAGGGGAAAAGAATGG 57.072 50.000 0.00 0.00 0.00 3.16
2620 3522 4.934602 GCAATAGAATCATAGAGAGGGTGC 59.065 45.833 0.00 0.00 0.00 5.01
2621 3523 5.512060 GCAATAGAATCATAGAGAGGGTGCA 60.512 44.000 0.00 0.00 0.00 4.57
2699 3602 9.657121 CACTCTTGAATAAAAGAAGTGAAAGTC 57.343 33.333 0.00 0.00 37.42 3.01
2703 3606 9.801873 CTTGAATAAAAGAAGTGAAAGTCCAAA 57.198 29.630 0.00 0.00 0.00 3.28
2704 3607 9.581099 TTGAATAAAAGAAGTGAAAGTCCAAAC 57.419 29.630 0.00 0.00 0.00 2.93
2705 3608 8.744652 TGAATAAAAGAAGTGAAAGTCCAAACA 58.255 29.630 0.00 0.00 0.00 2.83
2717 3620 9.589111 GTGAAAGTCCAAACAAATAAAAAGGTA 57.411 29.630 0.00 0.00 0.00 3.08
2730 3633 4.461992 AAAAAGGTACGTTGTGTGATCG 57.538 40.909 0.79 0.00 0.00 3.69
2731 3634 3.374220 AAAGGTACGTTGTGTGATCGA 57.626 42.857 0.79 0.00 0.00 3.59
2749 3652 0.099613 GATGAACTCGCTGAGCTCGA 59.900 55.000 9.64 2.19 32.04 4.04
2753 3656 4.878774 CTCGCTGAGCTCGAGTTT 57.121 55.556 15.13 2.46 45.86 2.66
2756 3659 2.023771 CGCTGAGCTCGAGTTTGCA 61.024 57.895 21.02 9.02 0.00 4.08
2757 3660 1.560004 CGCTGAGCTCGAGTTTGCAA 61.560 55.000 21.02 0.00 0.00 4.08
2758 3661 0.801251 GCTGAGCTCGAGTTTGCAAT 59.199 50.000 15.13 0.00 0.00 3.56
2761 3664 3.231965 CTGAGCTCGAGTTTGCAATTTG 58.768 45.455 15.13 0.00 0.00 2.32
2762 3665 2.877786 TGAGCTCGAGTTTGCAATTTGA 59.122 40.909 15.13 0.52 0.00 2.69
2763 3666 3.503363 TGAGCTCGAGTTTGCAATTTGAT 59.497 39.130 15.13 0.00 0.00 2.57
2764 3667 4.088823 AGCTCGAGTTTGCAATTTGATC 57.911 40.909 15.13 0.00 0.00 2.92
2765 3668 3.503363 AGCTCGAGTTTGCAATTTGATCA 59.497 39.130 15.13 0.00 0.00 2.92
2767 3670 4.614535 GCTCGAGTTTGCAATTTGATCAGT 60.615 41.667 15.13 0.00 0.00 3.41
2768 3671 4.786507 TCGAGTTTGCAATTTGATCAGTG 58.213 39.130 0.00 0.00 0.00 3.66
2770 3673 5.008514 TCGAGTTTGCAATTTGATCAGTGAA 59.991 36.000 0.00 0.00 0.00 3.18
2772 3675 6.152932 AGTTTGCAATTTGATCAGTGAACT 57.847 33.333 0.00 0.00 0.00 3.01
2785 3688 6.992123 TGATCAGTGAACTCAACACACTTATT 59.008 34.615 0.00 0.00 41.93 1.40
2790 3693 5.049405 GTGAACTCAACACACTTATTGGAGG 60.049 44.000 0.00 0.00 38.05 4.30
2793 3696 5.445964 ACTCAACACACTTATTGGAGGTTT 58.554 37.500 0.00 0.00 0.00 3.27
2812 3716 6.607019 AGGTTTGAAGTGAGTTGGGTAATAA 58.393 36.000 0.00 0.00 0.00 1.40
2834 3738 2.024319 GCGTCGGCATCATAGAGGC 61.024 63.158 0.00 0.00 38.72 4.70
2835 3739 1.363807 CGTCGGCATCATAGAGGCA 59.636 57.895 6.00 0.00 41.39 4.75
2836 3740 0.941463 CGTCGGCATCATAGAGGCAC 60.941 60.000 6.00 0.00 41.39 5.01
2837 3741 0.601311 GTCGGCATCATAGAGGCACC 60.601 60.000 6.00 0.00 41.39 5.01
2859 3763 6.211384 CACCCACTCCCTTCAAGAAATAAAAT 59.789 38.462 0.00 0.00 0.00 1.82
2881 3790 8.833231 AAATGAAAAAGAGAACGTCATAGAGA 57.167 30.769 0.00 0.00 0.00 3.10
2922 3844 5.392767 TTGTTGGCTTGTTCACTGTTTTA 57.607 34.783 0.00 0.00 0.00 1.52
2969 3894 3.309675 CGGCAAATAGACTCCGCG 58.690 61.111 0.00 0.00 35.20 6.46
3036 3961 2.846918 GCGTGTCTTGCGTCTGTC 59.153 61.111 0.00 0.00 0.00 3.51
3037 3962 1.949133 GCGTGTCTTGCGTCTGTCA 60.949 57.895 0.00 0.00 0.00 3.58
3038 3963 1.284982 GCGTGTCTTGCGTCTGTCAT 61.285 55.000 0.00 0.00 0.00 3.06
3039 3964 1.139989 CGTGTCTTGCGTCTGTCATT 58.860 50.000 0.00 0.00 0.00 2.57
3041 3966 2.135139 GTGTCTTGCGTCTGTCATTCA 58.865 47.619 0.00 0.00 0.00 2.57
3043 3968 2.135139 GTCTTGCGTCTGTCATTCACA 58.865 47.619 0.00 0.00 0.00 3.58
3044 3969 2.738846 GTCTTGCGTCTGTCATTCACAT 59.261 45.455 0.00 0.00 33.23 3.21
3045 3970 3.926527 GTCTTGCGTCTGTCATTCACATA 59.073 43.478 0.00 0.00 33.23 2.29
3059 3984 9.743057 TGTCATTCACATATTTTCTTTTCGTTT 57.257 25.926 0.00 0.00 0.00 3.60
3082 4007 1.748493 TCTGCTGTGGGTTTTGTGTTC 59.252 47.619 0.00 0.00 0.00 3.18
3083 4008 1.476085 CTGCTGTGGGTTTTGTGTTCA 59.524 47.619 0.00 0.00 0.00 3.18
3085 4010 1.748493 GCTGTGGGTTTTGTGTTCAGA 59.252 47.619 0.00 0.00 0.00 3.27
3167 4118 4.904253 TCTGGTTTGGTTTTTCTTACGG 57.096 40.909 0.00 0.00 0.00 4.02
3184 4135 7.499321 TCTTACGGATTCTTTTGCTGTTTTA 57.501 32.000 0.00 0.00 0.00 1.52
3187 4138 4.339814 ACGGATTCTTTTGCTGTTTTACCA 59.660 37.500 0.00 0.00 0.00 3.25
3254 4205 8.732413 ACAATGAACATATTTTATATGCGCTG 57.268 30.769 9.73 0.00 0.00 5.18
3256 4207 9.396938 CAATGAACATATTTTATATGCGCTGAA 57.603 29.630 9.73 0.00 0.00 3.02
3274 4225 9.018716 TGCGCTGAATATTGTTAATACAAATTG 57.981 29.630 9.73 0.00 46.62 2.32
3333 4288 8.032952 TGCTGCACATTATCTATATACAAAGC 57.967 34.615 0.00 0.00 0.00 3.51
3441 4409 1.549203 AGGACAATGCCCATGTGTTC 58.451 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.555547 AACAGCAGCTGGGCGTTTC 61.556 57.895 26.38 0.00 39.27 2.78
11 12 2.519302 AACAGCAGCTGGGCGTTT 60.519 55.556 26.38 8.34 39.27 3.60
12 13 3.289834 CAACAGCAGCTGGGCGTT 61.290 61.111 26.38 8.73 39.27 4.84
16 17 2.360852 CCTCCAACAGCAGCTGGG 60.361 66.667 26.38 18.15 35.51 4.45
17 18 2.360852 CCCTCCAACAGCAGCTGG 60.361 66.667 26.38 10.14 35.51 4.85
18 19 2.360852 CCCCTCCAACAGCAGCTG 60.361 66.667 21.54 21.54 37.52 4.24
19 20 4.357279 GCCCCTCCAACAGCAGCT 62.357 66.667 0.00 0.00 0.00 4.24
21 22 2.360852 CAGCCCCTCCAACAGCAG 60.361 66.667 0.00 0.00 0.00 4.24
22 23 4.666253 GCAGCCCCTCCAACAGCA 62.666 66.667 0.00 0.00 0.00 4.41
40 41 1.977594 AATAGCAAAGGTTCGCCGCG 61.978 55.000 6.39 6.39 43.66 6.46
42 43 2.629639 AAAATAGCAAAGGTTCGCCG 57.370 45.000 0.00 0.00 43.66 6.46
59 60 2.641277 GCCATTCCCCGCCGAAAAA 61.641 57.895 0.00 0.00 0.00 1.94
60 61 2.199613 TAGCCATTCCCCGCCGAAAA 62.200 55.000 0.00 0.00 0.00 2.29
61 62 1.990160 ATAGCCATTCCCCGCCGAAA 61.990 55.000 0.00 0.00 0.00 3.46
63 64 2.847234 ATAGCCATTCCCCGCCGA 60.847 61.111 0.00 0.00 0.00 5.54
64 65 1.541310 TAGATAGCCATTCCCCGCCG 61.541 60.000 0.00 0.00 0.00 6.46
65 66 0.250513 CTAGATAGCCATTCCCCGCC 59.749 60.000 0.00 0.00 0.00 6.13
66 67 0.391793 GCTAGATAGCCATTCCCCGC 60.392 60.000 0.09 0.00 43.39 6.13
67 68 0.108615 CGCTAGATAGCCATTCCCCG 60.109 60.000 6.28 0.00 46.34 5.73
68 69 1.267121 TCGCTAGATAGCCATTCCCC 58.733 55.000 6.28 0.00 46.34 4.81
69 70 2.497675 TCATCGCTAGATAGCCATTCCC 59.502 50.000 6.28 0.00 46.34 3.97
70 71 3.876274 TCATCGCTAGATAGCCATTCC 57.124 47.619 6.28 0.00 46.34 3.01
71 72 4.081972 TCCTTCATCGCTAGATAGCCATTC 60.082 45.833 6.28 0.00 46.34 2.67
72 73 3.834813 TCCTTCATCGCTAGATAGCCATT 59.165 43.478 6.28 0.00 46.34 3.16
73 74 3.194542 GTCCTTCATCGCTAGATAGCCAT 59.805 47.826 6.28 0.00 46.34 4.40
74 75 2.558795 GTCCTTCATCGCTAGATAGCCA 59.441 50.000 6.28 0.00 46.34 4.75
75 76 2.414824 CGTCCTTCATCGCTAGATAGCC 60.415 54.545 6.28 0.00 46.34 3.93
76 77 2.414824 CCGTCCTTCATCGCTAGATAGC 60.415 54.545 1.59 1.59 45.62 2.97
79 80 0.315568 GCCGTCCTTCATCGCTAGAT 59.684 55.000 0.00 0.00 37.65 1.98
80 81 1.734137 GCCGTCCTTCATCGCTAGA 59.266 57.895 0.00 0.00 0.00 2.43
81 82 1.658717 CGCCGTCCTTCATCGCTAG 60.659 63.158 0.00 0.00 0.00 3.42
82 83 2.411701 CGCCGTCCTTCATCGCTA 59.588 61.111 0.00 0.00 0.00 4.26
83 84 4.514577 CCGCCGTCCTTCATCGCT 62.515 66.667 0.00 0.00 0.00 4.93
105 106 1.154016 CACTAGCGATATCCCGGCG 60.154 63.158 0.00 0.00 0.00 6.46
106 107 1.215647 CCACTAGCGATATCCCGGC 59.784 63.158 0.00 0.00 0.00 6.13
107 108 1.215647 GCCACTAGCGATATCCCGG 59.784 63.158 0.00 0.00 0.00 5.73
108 109 4.891566 GCCACTAGCGATATCCCG 57.108 61.111 0.00 0.00 0.00 5.14
148 149 1.477685 TTTTCTTCCCCGACTCGCCT 61.478 55.000 0.00 0.00 0.00 5.52
149 150 0.392595 ATTTTCTTCCCCGACTCGCC 60.393 55.000 0.00 0.00 0.00 5.54
150 151 1.007580 GATTTTCTTCCCCGACTCGC 58.992 55.000 0.00 0.00 0.00 5.03
152 153 3.685272 GTCAAGATTTTCTTCCCCGACTC 59.315 47.826 0.00 0.00 33.78 3.36
153 154 3.328050 AGTCAAGATTTTCTTCCCCGACT 59.672 43.478 0.00 0.00 33.78 4.18
154 155 3.676093 AGTCAAGATTTTCTTCCCCGAC 58.324 45.455 0.00 0.00 33.78 4.79
155 156 4.367039 AAGTCAAGATTTTCTTCCCCGA 57.633 40.909 0.00 0.00 33.78 5.14
156 157 5.009610 TGAAAAGTCAAGATTTTCTTCCCCG 59.990 40.000 11.23 0.00 43.74 5.73
157 158 6.216569 GTGAAAAGTCAAGATTTTCTTCCCC 58.783 40.000 11.23 0.00 43.74 4.81
158 159 6.040955 AGGTGAAAAGTCAAGATTTTCTTCCC 59.959 38.462 11.23 8.78 43.74 3.97
159 160 7.043961 AGGTGAAAAGTCAAGATTTTCTTCC 57.956 36.000 11.23 12.23 43.74 3.46
161 162 8.129211 CGTAAGGTGAAAAGTCAAGATTTTCTT 58.871 33.333 11.23 0.00 43.74 2.52
162 163 7.282450 ACGTAAGGTGAAAAGTCAAGATTTTCT 59.718 33.333 11.23 0.00 43.08 2.52
163 164 7.415229 ACGTAAGGTGAAAAGTCAAGATTTTC 58.585 34.615 4.61 4.61 43.03 2.29
180 181 1.590147 CTCGCCCTCAACGTAAGGT 59.410 57.895 14.07 0.00 46.39 3.50
181 182 1.810030 GCTCGCCCTCAACGTAAGG 60.810 63.158 9.45 9.45 46.39 2.69
184 185 4.124351 CGGCTCGCCCTCAACGTA 62.124 66.667 1.72 0.00 0.00 3.57
199 200 4.759096 CGCAAGGGAAAAGCGCGG 62.759 66.667 8.83 0.00 45.14 6.46
203 204 4.419939 CCGGCGCAAGGGAAAAGC 62.420 66.667 10.83 0.00 38.28 3.51
204 205 2.671619 TCCGGCGCAAGGGAAAAG 60.672 61.111 19.03 0.00 38.28 2.27
205 206 2.671619 CTCCGGCGCAAGGGAAAA 60.672 61.111 19.03 1.39 38.28 2.29
223 224 4.195334 CTGAGGGGCGATTGGGGG 62.195 72.222 0.00 0.00 0.00 5.40
225 226 2.124570 CACTGAGGGGCGATTGGG 60.125 66.667 0.00 0.00 0.00 4.12
226 227 2.825836 GCACTGAGGGGCGATTGG 60.826 66.667 0.00 0.00 0.00 3.16
246 247 4.052229 ACTCGCAGACCGAACCCG 62.052 66.667 0.00 0.00 46.81 5.28
247 248 2.432628 CACTCGCAGACCGAACCC 60.433 66.667 0.00 0.00 46.81 4.11
248 249 1.733399 GACACTCGCAGACCGAACC 60.733 63.158 0.00 0.00 46.81 3.62
249 250 2.081212 CGACACTCGCAGACCGAAC 61.081 63.158 0.00 0.00 46.81 3.95
250 251 2.254350 CGACACTCGCAGACCGAA 59.746 61.111 0.00 0.00 46.81 4.30
251 252 3.733960 CCGACACTCGCAGACCGA 61.734 66.667 0.00 0.00 45.15 4.69
252 253 4.778415 CCCGACACTCGCAGACCG 62.778 72.222 0.00 0.00 38.82 4.79
257 258 3.793775 TTTTCGCCCGACACTCGCA 62.794 57.895 0.00 0.00 38.82 5.10
258 259 2.600475 TTTTTCGCCCGACACTCGC 61.600 57.895 0.00 0.00 38.82 5.03
259 260 3.632700 TTTTTCGCCCGACACTCG 58.367 55.556 0.00 0.00 40.07 4.18
289 290 4.736896 AGGACGACGGAAAGCGCC 62.737 66.667 2.29 0.00 0.00 6.53
291 292 2.809601 CCAGGACGACGGAAAGCG 60.810 66.667 0.00 0.00 0.00 4.68
292 293 2.434359 CCCAGGACGACGGAAAGC 60.434 66.667 0.00 0.00 0.00 3.51
293 294 2.264794 CCCCAGGACGACGGAAAG 59.735 66.667 0.00 0.00 0.00 2.62
295 296 2.993264 GTCCCCAGGACGACGGAA 60.993 66.667 0.00 0.00 43.14 4.30
303 304 1.606601 CTCAGTCACGTCCCCAGGA 60.607 63.158 0.00 0.00 0.00 3.86
304 305 1.606601 TCTCAGTCACGTCCCCAGG 60.607 63.158 0.00 0.00 0.00 4.45
305 306 1.587054 GTCTCAGTCACGTCCCCAG 59.413 63.158 0.00 0.00 0.00 4.45
306 307 2.265904 CGTCTCAGTCACGTCCCCA 61.266 63.158 0.00 0.00 32.41 4.96
307 308 2.567049 CGTCTCAGTCACGTCCCC 59.433 66.667 0.00 0.00 32.41 4.81
346 347 5.669798 ATAGGCCTCCTCATACCATTTTT 57.330 39.130 9.68 0.00 34.61 1.94
347 348 5.388654 CAATAGGCCTCCTCATACCATTTT 58.611 41.667 9.68 0.00 34.61 1.82
348 349 4.202609 CCAATAGGCCTCCTCATACCATTT 60.203 45.833 9.68 0.00 34.61 2.32
349 350 3.331889 CCAATAGGCCTCCTCATACCATT 59.668 47.826 9.68 0.00 34.61 3.16
350 351 2.915604 CCAATAGGCCTCCTCATACCAT 59.084 50.000 9.68 0.00 34.61 3.55
351 352 2.090210 TCCAATAGGCCTCCTCATACCA 60.090 50.000 9.68 0.00 34.61 3.25
352 353 2.569404 CTCCAATAGGCCTCCTCATACC 59.431 54.545 9.68 0.00 34.61 2.73
353 354 3.511477 TCTCCAATAGGCCTCCTCATAC 58.489 50.000 9.68 0.00 34.61 2.39
354 355 3.923273 TCTCCAATAGGCCTCCTCATA 57.077 47.619 9.68 0.00 34.61 2.15
355 356 2.803285 TCTCCAATAGGCCTCCTCAT 57.197 50.000 9.68 0.00 34.61 2.90
356 357 2.333069 CATCTCCAATAGGCCTCCTCA 58.667 52.381 9.68 0.00 34.61 3.86
357 358 1.003003 GCATCTCCAATAGGCCTCCTC 59.997 57.143 9.68 0.00 34.61 3.71
358 359 1.063183 GCATCTCCAATAGGCCTCCT 58.937 55.000 9.68 0.00 37.71 3.69
359 360 0.321122 CGCATCTCCAATAGGCCTCC 60.321 60.000 9.68 0.00 33.74 4.30
360 361 0.321122 CCGCATCTCCAATAGGCCTC 60.321 60.000 9.68 0.00 33.74 4.70
361 362 1.757306 CCGCATCTCCAATAGGCCT 59.243 57.895 11.78 11.78 33.74 5.19
362 363 1.968540 GCCGCATCTCCAATAGGCC 60.969 63.158 0.00 0.00 38.72 5.19
363 364 1.072159 AGCCGCATCTCCAATAGGC 59.928 57.895 0.00 0.00 44.45 3.93
364 365 0.604780 CCAGCCGCATCTCCAATAGG 60.605 60.000 0.00 0.00 0.00 2.57
365 366 0.394192 TCCAGCCGCATCTCCAATAG 59.606 55.000 0.00 0.00 0.00 1.73
366 367 0.394192 CTCCAGCCGCATCTCCAATA 59.606 55.000 0.00 0.00 0.00 1.90
367 368 1.147824 CTCCAGCCGCATCTCCAAT 59.852 57.895 0.00 0.00 0.00 3.16
368 369 1.340399 ATCTCCAGCCGCATCTCCAA 61.340 55.000 0.00 0.00 0.00 3.53
369 370 1.763655 ATCTCCAGCCGCATCTCCA 60.764 57.895 0.00 0.00 0.00 3.86
370 371 1.301558 CATCTCCAGCCGCATCTCC 60.302 63.158 0.00 0.00 0.00 3.71
371 372 1.960250 GCATCTCCAGCCGCATCTC 60.960 63.158 0.00 0.00 0.00 2.75
372 373 1.117749 TAGCATCTCCAGCCGCATCT 61.118 55.000 0.00 0.00 0.00 2.90
373 374 0.036577 ATAGCATCTCCAGCCGCATC 60.037 55.000 0.00 0.00 0.00 3.91
374 375 1.269958 TATAGCATCTCCAGCCGCAT 58.730 50.000 0.00 0.00 0.00 4.73
375 376 1.001293 CTTATAGCATCTCCAGCCGCA 59.999 52.381 0.00 0.00 0.00 5.69
376 377 1.273606 TCTTATAGCATCTCCAGCCGC 59.726 52.381 0.00 0.00 0.00 6.53
377 378 3.006323 AGTTCTTATAGCATCTCCAGCCG 59.994 47.826 0.00 0.00 0.00 5.52
378 379 4.314121 CAGTTCTTATAGCATCTCCAGCC 58.686 47.826 0.00 0.00 0.00 4.85
379 380 3.745458 GCAGTTCTTATAGCATCTCCAGC 59.255 47.826 0.00 0.00 0.00 4.85
380 381 4.953667 TGCAGTTCTTATAGCATCTCCAG 58.046 43.478 0.00 0.00 31.05 3.86
381 382 5.357742 TTGCAGTTCTTATAGCATCTCCA 57.642 39.130 0.00 0.00 36.80 3.86
382 383 4.213059 GCTTGCAGTTCTTATAGCATCTCC 59.787 45.833 0.00 0.00 36.80 3.71
383 384 4.813161 TGCTTGCAGTTCTTATAGCATCTC 59.187 41.667 1.41 0.00 36.80 2.75
384 385 4.774124 TGCTTGCAGTTCTTATAGCATCT 58.226 39.130 1.41 0.00 36.80 2.90
385 386 4.024218 CCTGCTTGCAGTTCTTATAGCATC 60.024 45.833 19.49 0.00 37.91 3.91
386 387 3.881688 CCTGCTTGCAGTTCTTATAGCAT 59.118 43.478 19.49 0.00 37.91 3.79
387 388 3.273434 CCTGCTTGCAGTTCTTATAGCA 58.727 45.455 19.49 5.42 37.14 3.49
388 389 2.032675 GCCTGCTTGCAGTTCTTATAGC 59.967 50.000 19.49 10.29 0.00 2.97
389 390 2.615912 GGCCTGCTTGCAGTTCTTATAG 59.384 50.000 19.49 4.73 0.00 1.31
390 391 2.643551 GGCCTGCTTGCAGTTCTTATA 58.356 47.619 19.49 0.00 0.00 0.98
391 392 1.467920 GGCCTGCTTGCAGTTCTTAT 58.532 50.000 19.49 0.00 0.00 1.73
392 393 0.955428 CGGCCTGCTTGCAGTTCTTA 60.955 55.000 19.49 0.00 0.00 2.10
393 394 2.263741 CGGCCTGCTTGCAGTTCTT 61.264 57.895 19.49 0.00 0.00 2.52
394 395 2.670934 CGGCCTGCTTGCAGTTCT 60.671 61.111 19.49 0.00 0.00 3.01
406 407 2.488153 GCAGTTCTTATGAAAACGGCCT 59.512 45.455 0.00 0.00 39.61 5.19
416 417 2.414559 CGGCTGGTTTGCAGTTCTTATG 60.415 50.000 0.00 0.00 34.04 1.90
431 432 3.353836 CAACGACCCAACGGCTGG 61.354 66.667 0.00 0.00 45.97 4.85
444 445 6.017440 TCTCCTTTTCAACAGTTTATCCAACG 60.017 38.462 0.00 0.00 40.75 4.10
540 541 0.953471 TGGCGTGCTGTGACCAATAC 60.953 55.000 0.00 0.00 0.00 1.89
541 542 0.953471 GTGGCGTGCTGTGACCAATA 60.953 55.000 0.00 0.00 33.03 1.90
542 543 2.112928 TGGCGTGCTGTGACCAAT 59.887 55.556 0.00 0.00 0.00 3.16
551 552 2.069465 TTGCAATTTCGTGGCGTGCT 62.069 50.000 0.00 0.00 36.18 4.40
552 553 1.608093 CTTGCAATTTCGTGGCGTGC 61.608 55.000 0.00 0.00 35.75 5.34
553 554 0.317770 ACTTGCAATTTCGTGGCGTG 60.318 50.000 0.00 0.00 0.00 5.34
555 556 0.040514 TCACTTGCAATTTCGTGGCG 60.041 50.000 14.44 0.00 0.00 5.69
662 666 0.456142 TCTTGACCGTGAAGCGATCG 60.456 55.000 11.69 11.69 44.77 3.69
788 819 2.361737 GAGTCCAAGCAAGGCCCC 60.362 66.667 0.00 0.00 0.00 5.80
816 847 2.440247 AATGGTAGCGGGGCAAGC 60.440 61.111 0.00 0.00 0.00 4.01
897 928 2.926778 TTTTGGGTTTGCTGAATGGG 57.073 45.000 0.00 0.00 0.00 4.00
936 975 6.005583 TCCGTATCTGTATAACACGATTCC 57.994 41.667 0.00 0.00 34.66 3.01
942 981 5.634896 CCCGTATCCGTATCTGTATAACAC 58.365 45.833 0.00 0.00 0.00 3.32
948 987 1.159285 CGCCCGTATCCGTATCTGTA 58.841 55.000 0.00 0.00 0.00 2.74
950 989 1.129998 CTACGCCCGTATCCGTATCTG 59.870 57.143 0.58 0.00 38.97 2.90
952 991 0.179179 GCTACGCCCGTATCCGTATC 60.179 60.000 0.58 0.00 38.97 2.24
1003 1042 2.231380 ACACCATCCTCACCCCCAC 61.231 63.158 0.00 0.00 0.00 4.61
1014 1053 0.819582 CCTTCCCATTGCACACCATC 59.180 55.000 0.00 0.00 0.00 3.51
1015 1054 1.259840 GCCTTCCCATTGCACACCAT 61.260 55.000 0.00 0.00 0.00 3.55
1016 1055 1.907807 GCCTTCCCATTGCACACCA 60.908 57.895 0.00 0.00 0.00 4.17
1048 1087 1.143183 AGACGACAAACACCGCAGT 59.857 52.632 0.00 0.00 0.00 4.40
1131 1179 1.513586 GGAGTCGCCGAACACGTAG 60.514 63.158 0.00 0.00 0.00 3.51
1306 1366 4.686191 ATGAAATGGAAACCAAGTGCAA 57.314 36.364 0.00 0.00 36.95 4.08
1355 1419 2.481185 GCATTTCCAGTTTGCACCATTG 59.519 45.455 0.00 0.00 36.40 2.82
1356 1420 2.104451 TGCATTTCCAGTTTGCACCATT 59.896 40.909 0.00 0.00 41.18 3.16
1357 1421 1.693062 TGCATTTCCAGTTTGCACCAT 59.307 42.857 0.00 0.00 41.18 3.55
1358 1422 1.068895 CTGCATTTCCAGTTTGCACCA 59.931 47.619 0.00 0.00 41.18 4.17
1368 1432 2.352422 AGCCTCGCTGCATTTCCA 59.648 55.556 0.00 0.00 37.57 3.53
1443 1507 0.671251 GGTAGCCTCTGACGATCTGG 59.329 60.000 0.00 0.00 0.00 3.86
1575 1644 8.873215 AAACTCATATGATAGTAACTCCAACG 57.127 34.615 5.72 0.00 0.00 4.10
1625 2320 4.707448 TGAATATGTTGTTTTATGCCGGGT 59.293 37.500 2.18 0.00 0.00 5.28
1676 2371 5.221501 ACACAGAAAAGATGAACAAATGGGG 60.222 40.000 0.00 0.00 0.00 4.96
1678 2373 9.480053 AATTACACAGAAAAGATGAACAAATGG 57.520 29.630 0.00 0.00 0.00 3.16
1706 2586 7.903431 GCCGACATGAAACAAAATTAGTACTAG 59.097 37.037 0.00 0.00 0.00 2.57
1707 2587 7.388224 TGCCGACATGAAACAAAATTAGTACTA 59.612 33.333 0.00 0.00 0.00 1.82
1708 2588 6.205853 TGCCGACATGAAACAAAATTAGTACT 59.794 34.615 0.00 0.00 0.00 2.73
1770 2657 1.203994 GCGAAGTACTCCACCTGCTTA 59.796 52.381 0.00 0.00 0.00 3.09
2317 3219 1.389106 GTAGACATTGTCGTTGCGGTC 59.611 52.381 11.01 0.00 37.67 4.79
2329 3231 1.825474 CACCTCGTCCCAGTAGACATT 59.175 52.381 0.00 0.00 36.52 2.71
2461 3363 3.499737 GTGCAATGCCTCGACCGG 61.500 66.667 1.53 0.00 0.00 5.28
2464 3366 3.499737 CCGGTGCAATGCCTCGAC 61.500 66.667 16.36 2.22 0.00 4.20
2481 3383 1.335597 TGACAACAGATCGTGTCCGTC 60.336 52.381 18.59 16.21 39.03 4.79
2497 3399 5.234752 TCGCAACTAAATTAAGAGCTGACA 58.765 37.500 0.00 0.00 0.00 3.58
2518 3420 5.283060 CTTAATCAAAGGGTGAACACTCG 57.717 43.478 4.96 0.00 40.50 4.18
2530 3432 5.580022 TCTTTTCCCCTCCCTTAATCAAAG 58.420 41.667 0.00 0.00 34.73 2.77
2538 3440 1.362584 CCCATTCTTTTCCCCTCCCTT 59.637 52.381 0.00 0.00 0.00 3.95
2547 3449 5.453567 AAAGTGTGCTACCCATTCTTTTC 57.546 39.130 0.00 0.00 30.70 2.29
2557 3459 6.756542 ACAAAAGAATCAAAAAGTGTGCTACC 59.243 34.615 0.00 0.00 0.00 3.18
2620 3522 4.603985 ACATAAAATCGCATGCATCACTG 58.396 39.130 19.57 8.15 0.00 3.66
2621 3523 4.906065 ACATAAAATCGCATGCATCACT 57.094 36.364 19.57 0.96 0.00 3.41
2696 3599 7.337480 ACGTACCTTTTTATTTGTTTGGACT 57.663 32.000 0.00 0.00 0.00 3.85
2697 3600 7.488792 ACAACGTACCTTTTTATTTGTTTGGAC 59.511 33.333 0.00 0.00 0.00 4.02
2699 3602 7.275999 ACACAACGTACCTTTTTATTTGTTTGG 59.724 33.333 0.00 0.00 0.00 3.28
2703 3606 7.086230 TCACACAACGTACCTTTTTATTTGT 57.914 32.000 0.00 0.00 0.00 2.83
2704 3607 7.059033 CGATCACACAACGTACCTTTTTATTTG 59.941 37.037 0.00 0.00 0.00 2.32
2705 3608 7.041916 TCGATCACACAACGTACCTTTTTATTT 60.042 33.333 0.00 0.00 0.00 1.40
2708 3611 5.288015 TCGATCACACAACGTACCTTTTTA 58.712 37.500 0.00 0.00 0.00 1.52
2714 3617 2.871133 TCATCGATCACACAACGTACC 58.129 47.619 0.00 0.00 0.00 3.34
2717 3620 2.987149 GAGTTCATCGATCACACAACGT 59.013 45.455 0.00 0.00 0.00 3.99
2730 3633 0.099613 TCGAGCTCAGCGAGTTCATC 59.900 55.000 15.40 7.29 39.34 2.92
2731 3634 2.184323 TCGAGCTCAGCGAGTTCAT 58.816 52.632 15.40 1.11 39.34 2.57
2740 3643 3.058708 TCAAATTGCAAACTCGAGCTCAG 60.059 43.478 13.61 12.50 0.00 3.35
2744 3647 3.825308 TGATCAAATTGCAAACTCGAGC 58.175 40.909 13.61 0.00 0.00 5.03
2749 3652 6.152932 AGTTCACTGATCAAATTGCAAACT 57.847 33.333 1.71 0.00 0.00 2.66
2750 3653 5.978919 TGAGTTCACTGATCAAATTGCAAAC 59.021 36.000 1.71 0.00 0.00 2.93
2751 3654 6.146601 TGAGTTCACTGATCAAATTGCAAA 57.853 33.333 1.71 0.00 0.00 3.68
2752 3655 5.771153 TGAGTTCACTGATCAAATTGCAA 57.229 34.783 0.00 0.00 0.00 4.08
2753 3656 5.067544 TGTTGAGTTCACTGATCAAATTGCA 59.932 36.000 0.00 0.00 34.91 4.08
2756 3659 6.319658 AGTGTGTTGAGTTCACTGATCAAATT 59.680 34.615 0.00 0.00 40.29 1.82
2757 3660 5.824624 AGTGTGTTGAGTTCACTGATCAAAT 59.175 36.000 0.00 0.00 40.29 2.32
2758 3661 5.185454 AGTGTGTTGAGTTCACTGATCAAA 58.815 37.500 0.00 0.00 40.29 2.69
2761 3664 7.293745 CAATAAGTGTGTTGAGTTCACTGATC 58.706 38.462 0.00 0.00 41.37 2.92
2762 3665 6.205464 CCAATAAGTGTGTTGAGTTCACTGAT 59.795 38.462 0.00 0.00 41.37 2.90
2763 3666 5.527214 CCAATAAGTGTGTTGAGTTCACTGA 59.473 40.000 0.00 0.00 41.37 3.41
2764 3667 5.527214 TCCAATAAGTGTGTTGAGTTCACTG 59.473 40.000 0.00 0.00 41.37 3.66
2765 3668 5.680619 TCCAATAAGTGTGTTGAGTTCACT 58.319 37.500 0.00 0.00 43.04 3.41
2767 3670 5.063204 CCTCCAATAAGTGTGTTGAGTTCA 58.937 41.667 0.00 0.00 0.00 3.18
2768 3671 5.063880 ACCTCCAATAAGTGTGTTGAGTTC 58.936 41.667 0.00 0.00 0.00 3.01
2770 3673 4.706842 ACCTCCAATAAGTGTGTTGAGT 57.293 40.909 0.00 0.00 0.00 3.41
2772 3675 5.441500 TCAAACCTCCAATAAGTGTGTTGA 58.558 37.500 0.00 0.00 0.00 3.18
2785 3688 2.422803 CCCAACTCACTTCAAACCTCCA 60.423 50.000 0.00 0.00 0.00 3.86
2790 3693 7.143340 GGTTTATTACCCAACTCACTTCAAAC 58.857 38.462 0.00 0.00 41.43 2.93
2793 3696 4.998672 CGGTTTATTACCCAACTCACTTCA 59.001 41.667 0.00 0.00 44.70 3.02
2815 3719 1.730902 CCTCTATGATGCCGACGCG 60.731 63.158 3.53 3.53 38.08 6.01
2816 3720 2.024319 GCCTCTATGATGCCGACGC 61.024 63.158 0.00 0.00 0.00 5.19
2820 3724 1.302033 GGGTGCCTCTATGATGCCG 60.302 63.158 0.00 0.00 0.00 5.69
2821 3725 0.536006 GTGGGTGCCTCTATGATGCC 60.536 60.000 0.00 0.00 0.00 4.40
2829 3733 1.920835 GAAGGGAGTGGGTGCCTCT 60.921 63.158 0.00 0.00 46.16 3.69
2834 3738 2.656947 TTTCTTGAAGGGAGTGGGTG 57.343 50.000 0.00 0.00 0.00 4.61
2835 3739 5.333566 TTTATTTCTTGAAGGGAGTGGGT 57.666 39.130 0.00 0.00 0.00 4.51
2836 3740 6.437162 TCATTTTATTTCTTGAAGGGAGTGGG 59.563 38.462 0.00 0.00 0.00 4.61
2837 3741 7.466746 TCATTTTATTTCTTGAAGGGAGTGG 57.533 36.000 0.00 0.00 0.00 4.00
2859 3763 6.311445 GCATCTCTATGACGTTCTCTTTTTCA 59.689 38.462 0.00 0.00 34.84 2.69
2868 3772 4.795795 CCGATATGCATCTCTATGACGTTC 59.204 45.833 0.19 0.00 34.84 3.95
2871 3775 4.622701 TCCGATATGCATCTCTATGACG 57.377 45.455 0.19 0.00 34.84 4.35
2922 3844 0.608640 GCGAATAGGATCCACCGGAT 59.391 55.000 15.82 0.00 46.28 4.18
2987 3912 3.682292 GAACTGGGCCGGCCTACTG 62.682 68.421 42.70 30.95 36.10 2.74
3022 3947 2.135139 GTGAATGACAGACGCAAGACA 58.865 47.619 0.00 0.00 43.62 3.41
3044 3969 9.393249 CACAGCAGATAAAACGAAAAGAAAATA 57.607 29.630 0.00 0.00 0.00 1.40
3045 3970 7.382218 CCACAGCAGATAAAACGAAAAGAAAAT 59.618 33.333 0.00 0.00 0.00 1.82
3059 3984 3.561143 ACACAAAACCCACAGCAGATAA 58.439 40.909 0.00 0.00 0.00 1.75
3063 3988 1.476085 TGAACACAAAACCCACAGCAG 59.524 47.619 0.00 0.00 0.00 4.24
3066 3991 4.654091 AATCTGAACACAAAACCCACAG 57.346 40.909 0.00 0.00 0.00 3.66
3092 4017 6.316140 ACAAAATGCAGAAGGAAAAGAAAACC 59.684 34.615 0.00 0.00 0.00 3.27
3096 4021 7.920160 AAAACAAAATGCAGAAGGAAAAGAA 57.080 28.000 0.00 0.00 0.00 2.52
3230 4181 8.953507 TCAGCGCATATAAAATATGTTCATTG 57.046 30.769 11.47 0.00 0.00 2.82
3247 4198 9.748708 AATTTGTATTAACAATATTCAGCGCAT 57.251 25.926 11.47 0.00 44.85 4.73
3248 4199 9.018716 CAATTTGTATTAACAATATTCAGCGCA 57.981 29.630 11.47 0.00 44.85 6.09
3249 4200 9.232082 TCAATTTGTATTAACAATATTCAGCGC 57.768 29.630 0.00 0.00 44.85 5.92
3327 4282 5.527951 TGCACATTAAAGAAATCGCTTTGT 58.472 33.333 0.00 0.00 38.47 2.83
3330 4285 8.931385 ATAATTGCACATTAAAGAAATCGCTT 57.069 26.923 0.00 0.00 0.00 4.68
3333 4288 9.941664 AGAGATAATTGCACATTAAAGAAATCG 57.058 29.630 0.00 0.00 0.00 3.34
3387 4342 9.736023 AAAAAGTTTGTTGTGCATTTTTAAACA 57.264 22.222 14.53 6.62 29.89 2.83
3421 4389 1.895131 GAACACATGGGCATTGTCCTT 59.105 47.619 9.08 0.00 0.00 3.36
3431 4399 3.743714 TCCAGTTGGAACACATGGG 57.256 52.632 0.00 0.00 42.57 4.00


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

AutoCloner maintained by Alex Coulton.