Multiple sequence alignment - TraesCS7B01G368000

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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 TraesCS7B01G368000 chr7B 100.000 3674 0 0 1 3674 632652579 632656252 0.000000e+00 6785.0
1 TraesCS7B01G368000 chr7D 94.489 2359 96 12 1339 3674 573822147 573824494 0.000000e+00 3605.0
2 TraesCS7B01G368000 chr7D 98.148 54 1 0 1 54 573822096 573822149 1.090000e-15 95.3
3 TraesCS7B01G368000 chr2B 74.508 2389 509 72 297 2650 10806422 10804099 0.000000e+00 946.0
4 TraesCS7B01G368000 chr2B 78.298 1046 216 7 538 1576 757057582 757056541 0.000000e+00 664.0
5 TraesCS7B01G368000 chr2B 77.680 681 118 22 297 969 10722572 10723226 5.760000e-103 385.0
6 TraesCS7B01G368000 chr2B 72.918 1237 276 33 2 1228 10770366 10771553 1.250000e-99 374.0
7 TraesCS7B01G368000 chr2B 85.714 91 10 2 3586 3673 329481041 329480951 3.910000e-15 93.5
8 TraesCS7B01G368000 chr2A 74.428 2405 497 76 318 2675 583784 581451 0.000000e+00 926.0
9 TraesCS7B01G368000 chr2A 75.238 1050 237 15 321 1366 565189 564159 9.230000e-131 477.0
10 TraesCS7B01G368000 chr2A 76.513 826 121 37 2382 3175 563203 562419 2.070000e-102 383.0
11 TraesCS7B01G368000 chr2A 75.463 648 125 22 297 939 514146 514764 6.000000e-73 285.0
12 TraesCS7B01G368000 chr2A 85.981 107 12 3 3437 3541 699061462 699061567 1.080000e-20 111.0
13 TraesCS7B01G368000 chr3B 77.039 1324 251 31 58 1374 733447033 733445756 0.000000e+00 712.0
14 TraesCS7B01G368000 chr3B 83.607 122 17 3 3419 3538 596444534 596444414 1.080000e-20 111.0
15 TraesCS7B01G368000 chr3B 85.714 91 10 2 3586 3673 215616055 215616145 3.910000e-15 93.5
16 TraesCS7B01G368000 chr3B 85.393 89 11 2 3586 3673 366143489 366143402 1.410000e-14 91.6
17 TraesCS7B01G368000 chrUn 74.436 1330 276 46 635 1932 300261660 300262957 7.040000e-142 514.0
18 TraesCS7B01G368000 chr2D 75.108 695 121 28 58 744 513876 514526 1.000000e-70 278.0
19 TraesCS7B01G368000 chr2D 85.981 107 12 3 3437 3541 502892602 502892497 1.080000e-20 111.0
20 TraesCS7B01G368000 chr2D 83.636 110 10 6 3571 3673 622877577 622877685 3.020000e-16 97.1
21 TraesCS7B01G368000 chr7A 85.981 107 12 3 3437 3541 655229313 655229208 1.080000e-20 111.0
22 TraesCS7B01G368000 chr5D 85.981 107 12 3 3437 3541 282659341 282659446 1.080000e-20 111.0
23 TraesCS7B01G368000 chr5D 86.111 108 10 4 3437 3541 455942186 455942081 1.080000e-20 111.0
24 TraesCS7B01G368000 chr5A 85.981 107 12 3 3437 3541 788899 788794 1.080000e-20 111.0
25 TraesCS7B01G368000 chr5B 83.065 124 18 3 3418 3539 31287935 31288057 3.880000e-20 110.0
26 TraesCS7B01G368000 chr6D 85.870 92 10 2 3585 3673 34021256 34021165 1.090000e-15 95.3
27 TraesCS7B01G368000 chr6B 91.304 69 4 2 3606 3673 408686295 408686228 3.910000e-15 93.5
28 TraesCS7B01G368000 chr4B 92.188 64 4 1 3611 3673 113965670 113965607 5.050000e-14 89.8
29 TraesCS7B01G368000 chr1B 92.188 64 4 1 3611 3673 229269229 229269166 5.050000e-14 89.8
30 TraesCS7B01G368000 chr4A 92.157 51 4 0 327 377 726717818 726717868 5.090000e-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 TraesCS7B01G368000 chr7B 632652579 632656252 3673 False 6785.00 6785 100.0000 1 3674 1 chr7B.!!$F1 3673
1 TraesCS7B01G368000 chr7D 573822096 573824494 2398 False 1850.15 3605 96.3185 1 3674 2 chr7D.!!$F1 3673
2 TraesCS7B01G368000 chr2B 10804099 10806422 2323 True 946.00 946 74.5080 297 2650 1 chr2B.!!$R1 2353
3 TraesCS7B01G368000 chr2B 757056541 757057582 1041 True 664.00 664 78.2980 538 1576 1 chr2B.!!$R3 1038
4 TraesCS7B01G368000 chr2B 10722572 10723226 654 False 385.00 385 77.6800 297 969 1 chr2B.!!$F1 672
5 TraesCS7B01G368000 chr2B 10770366 10771553 1187 False 374.00 374 72.9180 2 1228 1 chr2B.!!$F2 1226
6 TraesCS7B01G368000 chr2A 581451 583784 2333 True 926.00 926 74.4280 318 2675 1 chr2A.!!$R1 2357
7 TraesCS7B01G368000 chr2A 562419 565189 2770 True 430.00 477 75.8755 321 3175 2 chr2A.!!$R2 2854
8 TraesCS7B01G368000 chr2A 514146 514764 618 False 285.00 285 75.4630 297 939 1 chr2A.!!$F1 642
9 TraesCS7B01G368000 chr3B 733445756 733447033 1277 True 712.00 712 77.0390 58 1374 1 chr3B.!!$R3 1316
10 TraesCS7B01G368000 chrUn 300261660 300262957 1297 False 514.00 514 74.4360 635 1932 1 chrUn.!!$F1 1297
11 TraesCS7B01G368000 chr2D 513876 514526 650 False 278.00 278 75.1080 58 744 1 chr2D.!!$F1 686

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
289 290 0.034863 GTCACTAAATGCCCGGGGAA 60.035 55.0 22.46 6.78 0.00 3.97 F
292 293 0.185175 ACTAAATGCCCGGGGAATCC 59.815 55.0 22.46 2.71 0.00 3.01 F
2029 2081 0.109458 GTGTCGTGTGGAGCGATGTA 60.109 55.0 0.00 0.00 40.59 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1348 1370 0.108138 CGTTGGAGACATGGGACCTC 60.108 60.0 0.0 0.0 42.32 3.85 R
2136 2191 0.314302 AATACCTCGCCGATCCTTCG 59.686 55.0 0.0 0.0 45.08 3.79 R
3621 3749 0.690077 AGCTAGGGTTAGGTTCCCCG 60.690 60.0 0.0 0.0 46.17 5.73 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
49 50 0.817013 TGATTTTGGCATTCCTCGGC 59.183 50.000 0.00 0.00 0.00 5.54
56 57 1.450531 GGCATTCCTCGGCCTGAATG 61.451 60.000 24.24 24.24 46.74 2.67
68 69 3.809832 CGGCCTGAATGGTTTGATACTAG 59.190 47.826 0.00 0.00 38.35 2.57
81 82 8.867097 TGGTTTGATACTAGAGTATTATGGACC 58.133 37.037 0.00 8.59 40.99 4.46
90 91 4.589374 AGAGTATTATGGACCTTTCGAGGG 59.411 45.833 5.17 5.17 0.00 4.30
95 96 2.291043 GGACCTTTCGAGGGAGGCA 61.291 63.158 12.49 0.00 36.48 4.75
99 100 1.517832 CTTTCGAGGGAGGCATCGT 59.482 57.895 0.00 0.00 39.86 3.73
111 112 1.132640 GCATCGTCTCAACCAACGC 59.867 57.895 0.00 0.00 38.72 4.84
115 116 1.144969 TCGTCTCAACCAACGCATTC 58.855 50.000 0.00 0.00 38.72 2.67
116 117 1.148310 CGTCTCAACCAACGCATTCT 58.852 50.000 0.00 0.00 31.48 2.40
118 119 2.411547 CGTCTCAACCAACGCATTCTTC 60.412 50.000 0.00 0.00 31.48 2.87
120 121 3.003275 GTCTCAACCAACGCATTCTTCAA 59.997 43.478 0.00 0.00 0.00 2.69
131 132 4.156008 ACGCATTCTTCAAAAGGTGGATAC 59.844 41.667 0.00 0.00 0.00 2.24
132 133 4.662145 GCATTCTTCAAAAGGTGGATACG 58.338 43.478 0.00 0.00 42.51 3.06
136 137 4.963373 TCTTCAAAAGGTGGATACGTCAA 58.037 39.130 0.00 0.00 42.51 3.18
139 140 6.488683 TCTTCAAAAGGTGGATACGTCAAATT 59.511 34.615 0.00 0.00 42.51 1.82
143 144 7.436673 TCAAAAGGTGGATACGTCAAATTTTTG 59.563 33.333 0.00 3.03 42.51 2.44
148 149 6.362283 GGTGGATACGTCAAATTTTTGTCTTG 59.638 38.462 0.00 0.00 38.35 3.02
152 153 7.807907 GGATACGTCAAATTTTTGTCTTGATGT 59.192 33.333 12.13 12.13 46.13 3.06
167 168 9.692749 TTGTCTTGATGTTCAGTTAAGTAGTAG 57.307 33.333 0.00 0.00 0.00 2.57
169 170 9.344309 GTCTTGATGTTCAGTTAAGTAGTAGAC 57.656 37.037 0.00 0.00 0.00 2.59
170 171 9.074576 TCTTGATGTTCAGTTAAGTAGTAGACA 57.925 33.333 0.00 0.00 0.00 3.41
172 173 9.639601 TTGATGTTCAGTTAAGTAGTAGACATG 57.360 33.333 0.00 0.00 0.00 3.21
173 174 7.759886 TGATGTTCAGTTAAGTAGTAGACATGC 59.240 37.037 0.00 0.00 0.00 4.06
176 177 6.120378 TCAGTTAAGTAGTAGACATGCGAG 57.880 41.667 0.00 0.00 0.00 5.03
177 178 5.066117 TCAGTTAAGTAGTAGACATGCGAGG 59.934 44.000 0.00 0.00 0.00 4.63
178 179 5.066117 CAGTTAAGTAGTAGACATGCGAGGA 59.934 44.000 0.00 0.00 0.00 3.71
179 180 5.297278 AGTTAAGTAGTAGACATGCGAGGAG 59.703 44.000 0.00 0.00 0.00 3.69
180 181 2.577700 AGTAGTAGACATGCGAGGAGG 58.422 52.381 0.00 0.00 0.00 4.30
181 182 1.609555 GTAGTAGACATGCGAGGAGGG 59.390 57.143 0.00 0.00 0.00 4.30
182 183 0.259065 AGTAGACATGCGAGGAGGGA 59.741 55.000 0.00 0.00 0.00 4.20
183 184 1.112113 GTAGACATGCGAGGAGGGAA 58.888 55.000 0.00 0.00 0.00 3.97
184 185 1.480954 GTAGACATGCGAGGAGGGAAA 59.519 52.381 0.00 0.00 0.00 3.13
185 186 1.207791 AGACATGCGAGGAGGGAAAT 58.792 50.000 0.00 0.00 0.00 2.17
188 189 2.094675 ACATGCGAGGAGGGAAATTTG 58.905 47.619 0.00 0.00 0.00 2.32
196 197 1.066645 GGAGGGAAATTTGGCTGCAAG 60.067 52.381 0.50 0.00 0.00 4.01
223 224 1.667724 CTAGAGAAATTGCTGGGTGCG 59.332 52.381 0.00 0.00 46.63 5.34
227 228 2.824071 GAAATTGCTGGGTGCGCAGG 62.824 60.000 12.22 2.37 46.63 4.85
230 231 2.556840 ATTGCTGGGTGCGCAGGTAT 62.557 55.000 12.22 0.00 46.63 2.73
243 244 3.869623 AGGTATGCCTGCTGAAGTG 57.130 52.632 0.00 0.00 45.05 3.16
251 252 0.250640 CCTGCTGAAGTGGCTGAAGT 60.251 55.000 0.00 0.00 0.00 3.01
265 266 3.004734 GGCTGAAGTGTGTTGCTTGTATT 59.995 43.478 0.00 0.00 0.00 1.89
268 269 5.574891 TGAAGTGTGTTGCTTGTATTTGT 57.425 34.783 0.00 0.00 0.00 2.83
278 279 7.486551 GTGTTGCTTGTATTTGTTGTCACTAAA 59.513 33.333 0.00 0.00 0.00 1.85
279 280 8.194104 TGTTGCTTGTATTTGTTGTCACTAAAT 58.806 29.630 0.00 0.00 0.00 1.40
280 281 8.479280 GTTGCTTGTATTTGTTGTCACTAAATG 58.521 33.333 0.00 0.00 0.00 2.32
281 282 6.640499 TGCTTGTATTTGTTGTCACTAAATGC 59.360 34.615 0.00 0.00 0.00 3.56
282 283 6.089417 GCTTGTATTTGTTGTCACTAAATGCC 59.911 38.462 0.00 0.00 0.00 4.40
283 284 6.019779 TGTATTTGTTGTCACTAAATGCCC 57.980 37.500 0.00 0.00 0.00 5.36
284 285 3.634568 TTTGTTGTCACTAAATGCCCG 57.365 42.857 0.00 0.00 0.00 6.13
285 286 1.529226 TGTTGTCACTAAATGCCCGG 58.471 50.000 0.00 0.00 0.00 5.73
286 287 0.808755 GTTGTCACTAAATGCCCGGG 59.191 55.000 19.09 19.09 0.00 5.73
287 288 0.322997 TTGTCACTAAATGCCCGGGG 60.323 55.000 25.28 9.31 0.00 5.73
288 289 1.202099 TGTCACTAAATGCCCGGGGA 61.202 55.000 25.28 23.04 0.00 4.81
289 290 0.034863 GTCACTAAATGCCCGGGGAA 60.035 55.000 22.46 6.78 0.00 3.97
290 291 0.923358 TCACTAAATGCCCGGGGAAT 59.077 50.000 22.46 8.21 0.00 3.01
291 292 1.133915 TCACTAAATGCCCGGGGAATC 60.134 52.381 22.46 3.19 0.00 2.52
292 293 0.185175 ACTAAATGCCCGGGGAATCC 59.815 55.000 22.46 2.71 0.00 3.01
293 294 0.478507 CTAAATGCCCGGGGAATCCT 59.521 55.000 22.46 6.23 0.00 3.24
294 295 0.476771 TAAATGCCCGGGGAATCCTC 59.523 55.000 22.46 0.88 0.00 3.71
295 296 1.289244 AAATGCCCGGGGAATCCTCT 61.289 55.000 22.46 0.00 0.00 3.69
305 306 3.755483 CGGGGAATCCTCTATTCTCAGGA 60.755 52.174 0.00 0.00 45.62 3.86
306 307 3.580895 GGGGAATCCTCTATTCTCAGGAC 59.419 52.174 0.00 0.00 45.62 3.85
307 308 4.227197 GGGAATCCTCTATTCTCAGGACA 58.773 47.826 0.00 0.00 43.59 4.02
311 312 3.027412 TCCTCTATTCTCAGGACAGCAC 58.973 50.000 0.00 0.00 33.57 4.40
315 316 2.414994 ATTCTCAGGACAGCACCATG 57.585 50.000 0.00 0.00 0.00 3.66
316 317 1.059098 TTCTCAGGACAGCACCATGT 58.941 50.000 0.00 0.00 35.68 3.21
385 386 4.890988 TGGGATTATACAAGGAGGTCAGA 58.109 43.478 0.00 0.00 0.00 3.27
390 391 6.239176 GGATTATACAAGGAGGTCAGACTGAG 60.239 46.154 5.10 0.00 0.00 3.35
412 413 0.841961 AGCATGGGAGATTGCTGCTA 59.158 50.000 0.00 0.00 46.96 3.49
427 428 1.664659 CTGCTACTCTGCATCAACAGC 59.335 52.381 0.00 0.00 42.48 4.40
458 459 6.591750 AGAGGATTATACATCTGGTAACCG 57.408 41.667 0.00 0.00 35.14 4.44
460 461 5.152934 AGGATTATACATCTGGTAACCGGT 58.847 41.667 0.00 0.00 35.14 5.28
461 462 5.605488 AGGATTATACATCTGGTAACCGGTT 59.395 40.000 25.64 25.64 35.14 4.44
464 465 7.039504 GGATTATACATCTGGTAACCGGTTCTA 60.040 40.741 26.16 12.46 35.14 2.10
467 468 7.844493 ATACATCTGGTAACCGGTTCTATTA 57.156 36.000 26.16 8.63 35.14 0.98
471 472 4.062991 CTGGTAACCGGTTCTATTATGGC 58.937 47.826 26.16 3.92 0.00 4.40
473 474 2.651382 AACCGGTTCTATTATGGCCC 57.349 50.000 15.86 0.00 0.00 5.80
477 478 2.305927 CCGGTTCTATTATGGCCCTGAT 59.694 50.000 0.00 0.00 0.00 2.90
478 479 3.517901 CCGGTTCTATTATGGCCCTGATA 59.482 47.826 0.00 0.00 0.00 2.15
480 481 5.118990 CGGTTCTATTATGGCCCTGATATG 58.881 45.833 0.00 0.00 0.00 1.78
481 482 5.104941 CGGTTCTATTATGGCCCTGATATGA 60.105 44.000 0.00 0.00 0.00 2.15
482 483 6.576244 CGGTTCTATTATGGCCCTGATATGAA 60.576 42.308 0.00 1.11 0.00 2.57
483 484 7.349598 GGTTCTATTATGGCCCTGATATGAAT 58.650 38.462 0.00 0.00 0.00 2.57
484 485 7.836183 GGTTCTATTATGGCCCTGATATGAATT 59.164 37.037 0.00 0.00 0.00 2.17
485 486 8.897752 GTTCTATTATGGCCCTGATATGAATTC 58.102 37.037 0.00 0.00 0.00 2.17
486 487 8.161640 TCTATTATGGCCCTGATATGAATTCA 57.838 34.615 11.26 11.26 0.00 2.57
487 488 8.613923 TCTATTATGGCCCTGATATGAATTCAA 58.386 33.333 13.09 2.57 0.00 2.69
488 489 9.417561 CTATTATGGCCCTGATATGAATTCAAT 57.582 33.333 13.09 7.46 0.00 2.57
489 490 5.995565 ATGGCCCTGATATGAATTCAATG 57.004 39.130 13.09 1.38 0.00 2.82
490 491 3.575256 TGGCCCTGATATGAATTCAATGC 59.425 43.478 13.09 5.13 0.00 3.56
491 492 3.056322 GGCCCTGATATGAATTCAATGCC 60.056 47.826 13.09 12.17 34.59 4.40
497 498 4.886489 TGATATGAATTCAATGCCGGTGAA 59.114 37.500 13.09 8.28 39.24 3.18
504 505 1.212688 TCAATGCCGGTGAATCCTCAT 59.787 47.619 1.90 0.00 33.05 2.90
508 509 3.358111 TGCCGGTGAATCCTCATAAAA 57.642 42.857 1.90 0.00 33.05 1.52
519 520 9.136323 GTGAATCCTCATAAAAGGTGGATATTT 57.864 33.333 0.00 0.00 36.61 1.40
522 523 8.848474 ATCCTCATAAAAGGTGGATATTTACG 57.152 34.615 0.00 0.00 35.95 3.18
525 526 7.931948 CCTCATAAAAGGTGGATATTTACGAGT 59.068 37.037 0.00 0.00 30.79 4.18
589 590 6.071672 CCTTGAGACAGTCACAAGAAGATCTA 60.072 42.308 31.32 3.37 44.33 1.98
601 602 9.770097 TCACAAGAAGATCTAATCCATCATTAC 57.230 33.333 0.00 0.00 0.00 1.89
645 646 6.808008 TTTCATCAATCAGAGAACCTTCAC 57.192 37.500 0.00 0.00 0.00 3.18
648 649 5.185056 TCATCAATCAGAGAACCTTCACGTA 59.815 40.000 0.00 0.00 0.00 3.57
663 664 5.220662 CCTTCACGTACTCAAATTATGCCAG 60.221 44.000 0.00 0.00 0.00 4.85
705 706 1.153127 TCCTTTCCGTTGTTGCCGT 60.153 52.632 0.00 0.00 0.00 5.68
747 748 3.362706 AGATGGCTGCAAAGATCAACAT 58.637 40.909 0.50 0.00 0.00 2.71
748 749 4.529897 AGATGGCTGCAAAGATCAACATA 58.470 39.130 0.50 0.00 0.00 2.29
749 750 4.951715 AGATGGCTGCAAAGATCAACATAA 59.048 37.500 0.50 0.00 0.00 1.90
752 753 4.766373 TGGCTGCAAAGATCAACATAAAGA 59.234 37.500 0.50 0.00 0.00 2.52
757 758 7.061557 GCTGCAAAGATCAACATAAAGAAGAAC 59.938 37.037 0.00 0.00 0.00 3.01
759 760 8.579006 TGCAAAGATCAACATAAAGAAGAACAT 58.421 29.630 0.00 0.00 0.00 2.71
760 761 9.070149 GCAAAGATCAACATAAAGAAGAACATC 57.930 33.333 0.00 0.00 0.00 3.06
811 824 0.918983 TTTCCAGAGCCTATGGGTGG 59.081 55.000 5.37 0.00 38.44 4.61
816 829 2.614259 CAGAGCCTATGGGTGGTAGAT 58.386 52.381 0.00 0.00 31.55 1.98
828 841 3.368116 GGGTGGTAGATATATGCGACACC 60.368 52.174 13.77 13.77 44.73 4.16
853 866 1.064463 GGGATCTGGCTTCATCACCAA 60.064 52.381 0.00 0.00 34.96 3.67
856 869 2.205022 TCTGGCTTCATCACCAAAGG 57.795 50.000 0.00 0.00 34.96 3.11
908 921 8.855804 AGAGAGGTACATATAAAGAAGGGAAA 57.144 34.615 0.00 0.00 0.00 3.13
944 957 2.350899 TTTGCATGGAGACAATTGCG 57.649 45.000 5.05 0.00 46.83 4.85
961 974 1.966451 CGGAACCTTCGCAGGCTTT 60.966 57.895 0.00 0.00 45.56 3.51
975 988 2.832672 GGCTTTGAGTAATTGAGCCG 57.167 50.000 0.00 0.00 42.91 5.52
977 990 2.352960 GGCTTTGAGTAATTGAGCCGAG 59.647 50.000 0.00 0.00 42.91 4.63
990 1003 2.998097 CCGAGATGCCCTTGGGAA 59.002 61.111 10.36 0.00 41.91 3.97
1041 1054 2.028020 GGTGAAGTTGGAGTTCCTCGAT 60.028 50.000 0.00 0.00 36.82 3.59
1055 1068 4.171878 TCCTCGATCTGTCTAGGAATGT 57.828 45.455 0.00 0.00 41.79 2.71
1078 1091 7.606349 TGTTACAATACAATATTTGCCAAGCA 58.394 30.769 0.00 0.00 36.47 3.91
1129 1142 2.488153 GTTCTAGATGGTTGTGTTGGGC 59.512 50.000 0.00 0.00 0.00 5.36
1131 1144 2.027192 TCTAGATGGTTGTGTTGGGCTC 60.027 50.000 0.00 0.00 0.00 4.70
1132 1145 0.478072 AGATGGTTGTGTTGGGCTCA 59.522 50.000 0.00 0.00 0.00 4.26
1136 1149 1.008538 GTTGTGTTGGGCTCAAGCG 60.009 57.895 0.00 0.00 43.26 4.68
1146 1165 1.576421 GCTCAAGCGTGTTGAAGGG 59.424 57.895 0.00 0.00 0.00 3.95
1152 1171 2.359975 CGTGTTGAAGGGCTCCCC 60.360 66.667 0.32 0.00 45.90 4.81
1185 1207 3.204306 TCATTCAGCTTAGATGCAGGG 57.796 47.619 0.00 0.00 34.99 4.45
1186 1208 2.507058 TCATTCAGCTTAGATGCAGGGT 59.493 45.455 0.00 0.00 34.99 4.34
1188 1210 0.833287 TCAGCTTAGATGCAGGGTCC 59.167 55.000 0.00 0.00 34.99 4.46
1209 1231 4.156556 TCCGGAAAAGATGATTGCAAGAAG 59.843 41.667 0.00 0.00 0.00 2.85
1223 1245 2.301583 GCAAGAAGGCCAAAATAACCCA 59.698 45.455 5.01 0.00 0.00 4.51
1228 1250 3.182887 AGGCCAAAATAACCCACATCA 57.817 42.857 5.01 0.00 0.00 3.07
1247 1269 2.349672 CCATGGCCGGATGTGCAAA 61.350 57.895 5.05 0.00 0.00 3.68
1260 1282 6.324819 CGGATGTGCAAAATTATCTGACTTT 58.675 36.000 0.00 0.00 0.00 2.66
1261 1283 6.252015 CGGATGTGCAAAATTATCTGACTTTG 59.748 38.462 0.00 0.00 32.99 2.77
1262 1284 7.092716 GGATGTGCAAAATTATCTGACTTTGT 58.907 34.615 0.00 0.00 32.54 2.83
1306 1328 2.496899 TGAGGAGCTGAATTTGTCCC 57.503 50.000 0.00 0.00 0.00 4.46
1314 1336 2.094545 GCTGAATTTGTCCCACACATCC 60.095 50.000 0.00 0.00 33.90 3.51
1454 1476 6.426937 GGACTAACTTTGCTAGTCATTGACAA 59.573 38.462 18.57 1.73 44.75 3.18
1457 1479 3.498397 ACTTTGCTAGTCATTGACAACCG 59.502 43.478 18.57 5.20 34.60 4.44
1458 1480 3.394674 TTGCTAGTCATTGACAACCGA 57.605 42.857 18.57 3.53 34.60 4.69
1459 1481 2.959516 TGCTAGTCATTGACAACCGAG 58.040 47.619 18.57 8.45 34.60 4.63
1567 1592 6.840780 TGAGATTCATTCAGTCACTAGTGA 57.159 37.500 21.74 21.74 37.24 3.41
1576 1601 8.462811 TCATTCAGTCACTAGTGATAAGAAGTC 58.537 37.037 27.54 12.58 42.18 3.01
1580 1605 5.124138 AGTCACTAGTGATAAGAAGTCACCG 59.876 44.000 27.54 0.00 45.47 4.94
1760 1812 8.927721 CAATGATTTTGCTGTTGATGACATAAA 58.072 29.630 0.00 0.00 37.69 1.40
1766 1818 8.929827 TTTGCTGTTGATGACATAAATATTGG 57.070 30.769 0.00 0.00 37.69 3.16
1799 1851 2.901292 GCGCAGTGCAGTTTCAGCT 61.901 57.895 16.83 0.00 45.45 4.24
1898 1950 2.237143 TCTTAGTGATGGACAAGGCTGG 59.763 50.000 0.00 0.00 0.00 4.85
1934 1986 7.443272 TGTGCATGATAATTCTTCCATCACTAG 59.557 37.037 0.00 0.00 31.83 2.57
1996 2048 1.402787 AGTGCTGAAACTTGGTTGGG 58.597 50.000 0.00 0.00 0.00 4.12
2029 2081 0.109458 GTGTCGTGTGGAGCGATGTA 60.109 55.000 0.00 0.00 40.59 2.29
2072 2124 4.588278 GATGCTAACCACGTTTATTGCTC 58.412 43.478 0.00 0.00 0.00 4.26
2077 2132 6.205076 TGCTAACCACGTTTATTGCTCTTTTA 59.795 34.615 0.00 0.00 0.00 1.52
2161 2216 1.549170 GATCGGCGAGGTATTACCCAT 59.451 52.381 17.22 0.00 39.75 4.00
2166 2221 1.604693 GCGAGGTATTACCCATCACGG 60.605 57.143 9.31 0.00 39.75 4.94
2180 2235 0.671796 TCACGGCGTCATAGGTATGG 59.328 55.000 10.85 0.00 34.50 2.74
2245 2300 1.131638 TATCCTCCCACTGTCATGGC 58.868 55.000 0.00 0.00 38.55 4.40
2313 2377 2.076863 GATCTGAAAGTGGTGTTCCCG 58.923 52.381 0.00 0.00 35.15 5.14
2351 2415 4.436050 CGACCTGAGCATTTCAACATACAC 60.436 45.833 0.00 0.00 34.81 2.90
2357 2421 5.643348 TGAGCATTTCAACATACACACCTAG 59.357 40.000 0.00 0.00 31.34 3.02
2369 2433 2.504175 ACACACCTAGGGCGTTCATAAT 59.496 45.455 14.81 0.00 0.00 1.28
2451 2515 5.645067 GCAGCATATATGTGAAGCCAAGATA 59.355 40.000 14.14 0.00 0.00 1.98
2605 2669 2.122413 AGGCCGGCCATCATCCTA 60.122 61.111 45.13 0.00 38.92 2.94
2606 2670 1.768684 GAGGCCGGCCATCATCCTAA 61.769 60.000 45.13 0.00 38.92 2.69
2626 2690 0.951040 CCTCTTCAAGACGCACCACC 60.951 60.000 0.00 0.00 0.00 4.61
2688 2752 2.112029 GTGAAACCGTTGCAACCCT 58.888 52.632 23.42 5.91 0.00 4.34
2731 2795 2.952310 GCTTTCTCCAGTGGTTTCTTGT 59.048 45.455 9.54 0.00 0.00 3.16
2812 2876 6.037610 CCCTTCAAAGAATACTCTGCATGTAC 59.962 42.308 0.00 0.00 30.03 2.90
2843 2907 7.228507 AGTGCAGATGTACATCAACAAGTTAAA 59.771 33.333 32.01 7.94 40.22 1.52
2854 2918 7.701924 ACATCAACAAGTTAAATAATCATGCCG 59.298 33.333 0.00 0.00 0.00 5.69
2865 2929 6.463995 AATAATCATGCCGGTATTGTGTTT 57.536 33.333 0.66 0.00 0.00 2.83
2866 2930 3.781079 ATCATGCCGGTATTGTGTTTG 57.219 42.857 0.66 0.00 0.00 2.93
2875 2942 5.761234 GCCGGTATTGTGTTTGATTCCTATA 59.239 40.000 1.90 0.00 0.00 1.31
2880 2947 9.574516 GGTATTGTGTTTGATTCCTATAATCCT 57.425 33.333 0.00 0.00 0.00 3.24
2918 2985 5.357742 TTCTGCTCTCAACTATAATGCCA 57.642 39.130 0.00 0.00 0.00 4.92
2920 2987 5.303165 TCTGCTCTCAACTATAATGCCATG 58.697 41.667 0.00 0.00 0.00 3.66
3085 3185 5.163141 TGTGTTTTCCCAAGATCAGGAGTAA 60.163 40.000 5.83 0.51 32.57 2.24
3094 3194 7.623677 TCCCAAGATCAGGAGTAAATCTTCTTA 59.376 37.037 5.83 0.00 37.59 2.10
3158 3264 2.997303 GTGTGTGGTTTGGTTTGGTTTC 59.003 45.455 0.00 0.00 0.00 2.78
3194 3303 9.913451 CATGTTTGTGTTTGTAATAAGGTTTTG 57.087 29.630 0.00 0.00 0.00 2.44
3200 3309 7.436673 TGTGTTTGTAATAAGGTTTTGATGTGC 59.563 33.333 0.00 0.00 0.00 4.57
3201 3310 7.651704 GTGTTTGTAATAAGGTTTTGATGTGCT 59.348 33.333 0.00 0.00 0.00 4.40
3213 3322 1.134128 TGATGTGCTTGTGGTGTGTCT 60.134 47.619 0.00 0.00 0.00 3.41
3242 3351 3.893521 ACCGTCATAAAACCCCTATTGG 58.106 45.455 0.00 0.00 0.00 3.16
3253 3362 2.640826 ACCCCTATTGGTTTGACGAGAA 59.359 45.455 0.00 0.00 33.91 2.87
3302 3411 1.820519 CAATGCTAAGTGTGTGCCCAT 59.179 47.619 0.00 0.00 0.00 4.00
3316 3425 0.393808 GCCCATGTATCGGTGTGGTT 60.394 55.000 0.00 0.00 0.00 3.67
3387 3513 5.163652 CCTCCGTTCCATAATTTTTGTCCTC 60.164 44.000 0.00 0.00 0.00 3.71
3397 3524 4.625972 ATTTTTGTCCTCGTTTTGTCGT 57.374 36.364 0.00 0.00 0.00 4.34
3471 3599 8.631480 TTCTAGATGCGGATGTATCTAACTTA 57.369 34.615 0.00 0.00 45.39 2.24
3542 3670 9.753674 AAATTTTAGGACAGATGGAGTATTTGA 57.246 29.630 0.00 0.00 0.00 2.69
3568 3696 5.001237 GGTTATTCACCGTTAATTTGGGG 57.999 43.478 0.00 0.00 35.12 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 9.091220 AGGTCCATAATACTCTAGTATCAAACC 57.909 37.037 3.19 7.29 40.10 3.27
68 69 4.587684 TCCCTCGAAAGGTCCATAATACTC 59.412 45.833 1.32 0.00 41.59 2.59
75 76 1.627297 GCCTCCCTCGAAAGGTCCAT 61.627 60.000 9.26 0.00 41.59 3.41
81 82 0.528684 GACGATGCCTCCCTCGAAAG 60.529 60.000 0.00 0.00 38.24 2.62
90 91 1.079503 GTTGGTTGAGACGATGCCTC 58.920 55.000 0.00 0.00 0.00 4.70
95 96 1.732259 GAATGCGTTGGTTGAGACGAT 59.268 47.619 0.00 0.00 41.53 3.73
99 100 2.844946 TGAAGAATGCGTTGGTTGAGA 58.155 42.857 0.00 0.00 0.00 3.27
111 112 5.411361 TGACGTATCCACCTTTTGAAGAATG 59.589 40.000 0.00 0.00 0.00 2.67
115 116 5.682943 TTTGACGTATCCACCTTTTGAAG 57.317 39.130 0.00 0.00 0.00 3.02
116 117 6.642707 AATTTGACGTATCCACCTTTTGAA 57.357 33.333 0.00 0.00 0.00 2.69
118 119 7.223777 ACAAAAATTTGACGTATCCACCTTTTG 59.776 33.333 12.54 12.41 40.55 2.44
120 121 6.811954 ACAAAAATTTGACGTATCCACCTTT 58.188 32.000 12.54 0.00 40.55 3.11
131 132 7.220683 ACTGAACATCAAGACAAAAATTTGACG 59.779 33.333 12.54 0.00 40.55 4.35
132 133 8.411318 ACTGAACATCAAGACAAAAATTTGAC 57.589 30.769 12.54 6.57 40.55 3.18
139 140 9.391006 ACTACTTAACTGAACATCAAGACAAAA 57.609 29.630 0.00 0.00 0.00 2.44
143 144 9.344309 GTCTACTACTTAACTGAACATCAAGAC 57.656 37.037 0.00 0.00 0.00 3.01
148 149 7.043986 CGCATGTCTACTACTTAACTGAACATC 60.044 40.741 0.00 0.00 0.00 3.06
152 153 6.404403 CCTCGCATGTCTACTACTTAACTGAA 60.404 42.308 0.00 0.00 0.00 3.02
159 160 2.952978 CCTCCTCGCATGTCTACTACTT 59.047 50.000 0.00 0.00 0.00 2.24
161 162 1.609555 CCCTCCTCGCATGTCTACTAC 59.390 57.143 0.00 0.00 0.00 2.73
163 164 0.259065 TCCCTCCTCGCATGTCTACT 59.741 55.000 0.00 0.00 0.00 2.57
166 167 1.207791 ATTTCCCTCCTCGCATGTCT 58.792 50.000 0.00 0.00 0.00 3.41
167 168 2.044123 AATTTCCCTCCTCGCATGTC 57.956 50.000 0.00 0.00 0.00 3.06
169 170 1.406539 CCAAATTTCCCTCCTCGCATG 59.593 52.381 0.00 0.00 0.00 4.06
170 171 1.767759 CCAAATTTCCCTCCTCGCAT 58.232 50.000 0.00 0.00 0.00 4.73
172 173 0.681243 AGCCAAATTTCCCTCCTCGC 60.681 55.000 0.00 0.00 0.00 5.03
173 174 1.098050 CAGCCAAATTTCCCTCCTCG 58.902 55.000 0.00 0.00 0.00 4.63
176 177 0.975887 TTGCAGCCAAATTTCCCTCC 59.024 50.000 0.00 0.00 0.00 4.30
177 178 1.895131 TCTTGCAGCCAAATTTCCCTC 59.105 47.619 0.00 0.00 0.00 4.30
178 179 2.014010 TCTTGCAGCCAAATTTCCCT 57.986 45.000 0.00 0.00 0.00 4.20
179 180 2.299867 TCTTCTTGCAGCCAAATTTCCC 59.700 45.455 0.00 0.00 0.00 3.97
180 181 3.582780 CTCTTCTTGCAGCCAAATTTCC 58.417 45.455 0.00 0.00 0.00 3.13
181 182 3.582780 CCTCTTCTTGCAGCCAAATTTC 58.417 45.455 0.00 0.00 0.00 2.17
182 183 2.289257 GCCTCTTCTTGCAGCCAAATTT 60.289 45.455 0.00 0.00 0.00 1.82
183 184 1.274447 GCCTCTTCTTGCAGCCAAATT 59.726 47.619 0.00 0.00 0.00 1.82
184 185 0.893447 GCCTCTTCTTGCAGCCAAAT 59.107 50.000 0.00 0.00 0.00 2.32
185 186 0.178981 AGCCTCTTCTTGCAGCCAAA 60.179 50.000 0.00 0.00 0.00 3.28
188 189 0.539051 TCTAGCCTCTTCTTGCAGCC 59.461 55.000 0.00 0.00 0.00 4.85
196 197 3.876320 CCAGCAATTTCTCTAGCCTCTTC 59.124 47.826 0.00 0.00 0.00 2.87
233 234 0.873054 CACTTCAGCCACTTCAGCAG 59.127 55.000 0.00 0.00 0.00 4.24
243 244 0.740737 ACAAGCAACACACTTCAGCC 59.259 50.000 0.00 0.00 0.00 4.85
251 252 5.098893 GTGACAACAAATACAAGCAACACA 58.901 37.500 0.00 0.00 0.00 3.72
265 266 1.883275 CCGGGCATTTAGTGACAACAA 59.117 47.619 0.00 0.00 37.70 2.83
268 269 0.322997 CCCCGGGCATTTAGTGACAA 60.323 55.000 17.73 0.00 37.70 3.18
278 279 0.178861 ATAGAGGATTCCCCGGGCAT 60.179 55.000 17.73 9.42 40.87 4.40
279 280 0.401395 AATAGAGGATTCCCCGGGCA 60.401 55.000 17.73 0.00 40.87 5.36
280 281 0.325272 GAATAGAGGATTCCCCGGGC 59.675 60.000 17.73 0.00 38.45 6.13
281 282 1.903183 GAGAATAGAGGATTCCCCGGG 59.097 57.143 15.80 15.80 44.54 5.73
282 283 2.564947 CTGAGAATAGAGGATTCCCCGG 59.435 54.545 0.00 0.00 44.54 5.73
283 284 2.564947 CCTGAGAATAGAGGATTCCCCG 59.435 54.545 0.00 0.00 44.54 5.73
284 285 3.580895 GTCCTGAGAATAGAGGATTCCCC 59.419 52.174 0.00 0.00 44.54 4.81
285 286 4.227197 TGTCCTGAGAATAGAGGATTCCC 58.773 47.826 0.00 0.00 44.54 3.97
286 287 4.262420 GCTGTCCTGAGAATAGAGGATTCC 60.262 50.000 0.00 0.00 44.54 3.01
287 288 4.343526 TGCTGTCCTGAGAATAGAGGATTC 59.656 45.833 0.00 0.00 43.89 2.52
288 289 4.100808 GTGCTGTCCTGAGAATAGAGGATT 59.899 45.833 0.00 0.00 40.55 3.01
289 290 3.640967 GTGCTGTCCTGAGAATAGAGGAT 59.359 47.826 0.00 0.00 40.55 3.24
290 291 3.027412 GTGCTGTCCTGAGAATAGAGGA 58.973 50.000 0.00 0.00 35.93 3.71
291 292 2.102252 GGTGCTGTCCTGAGAATAGAGG 59.898 54.545 0.00 0.00 0.00 3.69
292 293 2.762887 TGGTGCTGTCCTGAGAATAGAG 59.237 50.000 0.00 0.00 0.00 2.43
293 294 2.820178 TGGTGCTGTCCTGAGAATAGA 58.180 47.619 0.00 0.00 0.00 1.98
294 295 3.118482 ACATGGTGCTGTCCTGAGAATAG 60.118 47.826 0.00 0.00 0.00 1.73
295 296 2.840038 ACATGGTGCTGTCCTGAGAATA 59.160 45.455 0.00 0.00 0.00 1.75
305 306 1.419762 TGTAGTCCAACATGGTGCTGT 59.580 47.619 4.81 0.00 39.03 4.40
306 307 2.183478 TGTAGTCCAACATGGTGCTG 57.817 50.000 4.81 0.00 39.03 4.41
307 308 2.949177 TTGTAGTCCAACATGGTGCT 57.051 45.000 4.81 0.04 39.03 4.40
316 317 0.109723 GTGGCCCAGTTGTAGTCCAA 59.890 55.000 0.00 0.00 0.00 3.53
385 386 1.890552 ATCTCCCATGCTTCCTCAGT 58.109 50.000 0.00 0.00 0.00 3.41
412 413 3.623906 ACATAGCTGTTGATGCAGAGT 57.376 42.857 0.00 0.00 38.70 3.24
445 446 6.463897 CCATAATAGAACCGGTTACCAGATGT 60.464 42.308 22.33 0.00 0.00 3.06
451 452 3.405831 GGCCATAATAGAACCGGTTACC 58.594 50.000 22.33 9.10 0.00 2.85
452 453 3.072038 AGGGCCATAATAGAACCGGTTAC 59.928 47.826 22.33 13.92 0.00 2.50
454 455 2.132686 AGGGCCATAATAGAACCGGTT 58.867 47.619 22.50 22.50 0.00 4.44
456 457 1.697432 TCAGGGCCATAATAGAACCGG 59.303 52.381 6.18 0.00 0.00 5.28
458 459 6.313519 TCATATCAGGGCCATAATAGAACC 57.686 41.667 6.18 0.00 0.00 3.62
460 461 8.613923 TGAATTCATATCAGGGCCATAATAGAA 58.386 33.333 6.18 3.48 0.00 2.10
461 462 8.161640 TGAATTCATATCAGGGCCATAATAGA 57.838 34.615 6.18 0.00 0.00 1.98
464 465 7.364408 GCATTGAATTCATATCAGGGCCATAAT 60.364 37.037 9.40 0.00 0.00 1.28
467 468 4.222145 GCATTGAATTCATATCAGGGCCAT 59.778 41.667 9.40 0.00 0.00 4.40
471 472 3.192001 CCGGCATTGAATTCATATCAGGG 59.808 47.826 9.40 3.52 0.00 4.45
473 474 4.516321 TCACCGGCATTGAATTCATATCAG 59.484 41.667 9.40 1.70 0.00 2.90
477 478 4.278170 GGATTCACCGGCATTGAATTCATA 59.722 41.667 17.17 0.91 42.53 2.15
478 479 3.068590 GGATTCACCGGCATTGAATTCAT 59.931 43.478 17.17 0.00 42.53 2.57
480 481 2.689983 AGGATTCACCGGCATTGAATTC 59.310 45.455 17.17 15.62 42.53 2.17
481 482 2.689983 GAGGATTCACCGGCATTGAATT 59.310 45.455 17.17 5.47 42.53 2.17
482 483 2.301346 GAGGATTCACCGGCATTGAAT 58.699 47.619 16.34 16.34 44.64 2.57
483 484 1.004161 TGAGGATTCACCGGCATTGAA 59.996 47.619 0.00 4.61 44.74 2.69
484 485 0.617935 TGAGGATTCACCGGCATTGA 59.382 50.000 0.00 0.00 44.74 2.57
485 486 1.683943 ATGAGGATTCACCGGCATTG 58.316 50.000 0.00 0.00 44.74 2.82
486 487 3.576078 TTATGAGGATTCACCGGCATT 57.424 42.857 0.00 0.00 44.74 3.56
487 488 3.576078 TTTATGAGGATTCACCGGCAT 57.424 42.857 0.00 0.00 44.74 4.40
488 489 3.278574 CTTTTATGAGGATTCACCGGCA 58.721 45.455 0.00 0.00 44.74 5.69
489 490 2.618709 CCTTTTATGAGGATTCACCGGC 59.381 50.000 0.00 0.00 44.74 6.13
490 491 3.627577 CACCTTTTATGAGGATTCACCGG 59.372 47.826 0.00 0.00 44.74 5.28
491 492 3.627577 CCACCTTTTATGAGGATTCACCG 59.372 47.826 0.00 0.00 44.74 4.94
497 498 8.656806 TCGTAAATATCCACCTTTTATGAGGAT 58.343 33.333 0.00 0.00 41.65 3.24
504 505 7.613585 TGTCACTCGTAAATATCCACCTTTTA 58.386 34.615 0.00 0.00 0.00 1.52
508 509 5.187186 AGTTGTCACTCGTAAATATCCACCT 59.813 40.000 0.00 0.00 0.00 4.00
525 526 4.129380 CTGGATGAACAACAGAGTTGTCA 58.871 43.478 15.03 14.07 36.23 3.58
540 541 3.961480 AATGACGTTGACTCTGGATGA 57.039 42.857 0.00 0.00 0.00 2.92
610 611 5.072055 TGATTGATGAAATGTGTCACTGGT 58.928 37.500 4.27 0.00 0.00 4.00
612 613 6.370718 TCTCTGATTGATGAAATGTGTCACTG 59.629 38.462 4.27 0.00 0.00 3.66
614 615 6.732531 TCTCTGATTGATGAAATGTGTCAC 57.267 37.500 0.00 0.00 0.00 3.67
620 621 7.249147 GTGAAGGTTCTCTGATTGATGAAATG 58.751 38.462 0.00 0.00 0.00 2.32
621 622 6.093219 CGTGAAGGTTCTCTGATTGATGAAAT 59.907 38.462 0.00 0.00 0.00 2.17
645 646 3.940303 GCACTGGCATAATTTGAGTACG 58.060 45.455 0.00 0.00 40.72 3.67
663 664 5.041287 GGTGAAGAAAAACTAAAGGTGCAC 58.959 41.667 8.80 8.80 0.00 4.57
672 673 5.061179 CGGAAAGGAGGTGAAGAAAAACTA 58.939 41.667 0.00 0.00 0.00 2.24
705 706 7.147373 CCATCTAATCCAAGGAACCTTAACCTA 60.147 40.741 5.75 0.00 35.25 3.08
795 808 1.051812 CTACCACCCATAGGCTCTGG 58.948 60.000 11.80 11.80 36.11 3.86
811 824 5.351465 CCCAATTGGTGTCGCATATATCTAC 59.649 44.000 22.91 0.00 0.00 2.59
816 829 3.847671 TCCCAATTGGTGTCGCATATA 57.152 42.857 22.91 0.00 34.77 0.86
828 841 3.067742 GTGATGAAGCCAGATCCCAATTG 59.932 47.826 0.00 0.00 0.00 2.32
853 866 4.349048 TGCAGCCATCTGATCTATTACCTT 59.651 41.667 0.00 0.00 42.95 3.50
856 869 5.528690 TGTTTGCAGCCATCTGATCTATTAC 59.471 40.000 0.00 0.00 42.95 1.89
908 921 2.415776 CAAAATTGCGGCACCAAATCT 58.584 42.857 0.05 0.00 0.00 2.40
944 957 0.889186 TCAAAGCCTGCGAAGGTTCC 60.889 55.000 12.24 0.00 0.00 3.62
961 974 2.483714 GGCATCTCGGCTCAATTACTCA 60.484 50.000 0.00 0.00 37.17 3.41
975 988 1.467920 CTGTTTCCCAAGGGCATCTC 58.532 55.000 0.00 0.00 34.68 2.75
977 990 1.607801 GCCTGTTTCCCAAGGGCATC 61.608 60.000 0.00 0.00 42.08 3.91
990 1003 5.240121 GTGAATTCATCCATTTTGCCTGTT 58.760 37.500 12.12 0.00 0.00 3.16
1054 1067 8.542132 CATGCTTGGCAAATATTGTATTGTAAC 58.458 33.333 0.00 0.00 43.62 2.50
1055 1068 8.256605 ACATGCTTGGCAAATATTGTATTGTAA 58.743 29.630 0.00 0.00 43.62 2.41
1066 1079 2.101783 CCCTGACATGCTTGGCAAATA 58.898 47.619 9.72 0.00 41.45 1.40
1067 1080 0.899720 CCCTGACATGCTTGGCAAAT 59.100 50.000 9.72 0.00 41.45 2.32
1078 1091 4.102113 GCTTGTTGCCCCTGACAT 57.898 55.556 0.00 0.00 35.15 3.06
1103 1116 6.122277 CCAACACAACCATCTAGAACCATAT 58.878 40.000 0.00 0.00 0.00 1.78
1129 1142 0.886490 AGCCCTTCAACACGCTTGAG 60.886 55.000 0.00 0.00 0.00 3.02
1131 1144 1.576421 GAGCCCTTCAACACGCTTG 59.424 57.895 0.00 0.00 0.00 4.01
1132 1145 1.600916 GGAGCCCTTCAACACGCTT 60.601 57.895 0.00 0.00 0.00 4.68
1136 1149 2.359975 CGGGGAGCCCTTCAACAC 60.360 66.667 5.38 0.00 42.67 3.32
1146 1165 0.321653 ATTCAAGTGACACGGGGAGC 60.322 55.000 0.00 0.00 0.00 4.70
1152 1171 3.434641 AGCTGAATGATTCAAGTGACACG 59.565 43.478 9.39 0.00 39.58 4.49
1153 1172 5.368256 AAGCTGAATGATTCAAGTGACAC 57.632 39.130 9.39 0.00 39.58 3.67
1154 1173 6.466812 TCTAAGCTGAATGATTCAAGTGACA 58.533 36.000 9.39 0.00 39.58 3.58
1185 1207 3.440173 TCTTGCAATCATCTTTTCCGGAC 59.560 43.478 1.83 0.00 0.00 4.79
1186 1208 3.684908 TCTTGCAATCATCTTTTCCGGA 58.315 40.909 0.00 0.00 0.00 5.14
1188 1210 4.418392 CCTTCTTGCAATCATCTTTTCCG 58.582 43.478 0.00 0.00 0.00 4.30
1209 1231 2.093711 GGTGATGTGGGTTATTTTGGCC 60.094 50.000 0.00 0.00 0.00 5.36
1223 1245 1.152902 CATCCGGCCATGGTGATGT 60.153 57.895 22.59 4.64 32.00 3.06
1228 1250 3.582242 TTGCACATCCGGCCATGGT 62.582 57.895 14.67 0.00 0.00 3.55
1247 1269 5.451908 CACGCAACACAAAGTCAGATAATT 58.548 37.500 0.00 0.00 0.00 1.40
1260 1282 1.225855 GAAGTGATCCACGCAACACA 58.774 50.000 0.00 0.00 39.64 3.72
1302 1324 1.265905 GTTTTGACGGATGTGTGGGAC 59.734 52.381 0.00 0.00 0.00 4.46
1305 1327 1.946768 AGTGTTTTGACGGATGTGTGG 59.053 47.619 0.00 0.00 0.00 4.17
1306 1328 3.064682 TCAAGTGTTTTGACGGATGTGTG 59.935 43.478 0.00 0.00 0.00 3.82
1348 1370 0.108138 CGTTGGAGACATGGGACCTC 60.108 60.000 0.00 0.00 42.32 3.85
1454 1476 1.268066 GACCTTTTCTCCTCCTCGGT 58.732 55.000 0.00 0.00 0.00 4.69
1457 1479 3.258622 TCTTTCGACCTTTTCTCCTCCTC 59.741 47.826 0.00 0.00 0.00 3.71
1458 1480 3.240302 TCTTTCGACCTTTTCTCCTCCT 58.760 45.455 0.00 0.00 0.00 3.69
1459 1481 3.679824 TCTTTCGACCTTTTCTCCTCC 57.320 47.619 0.00 0.00 0.00 4.30
1524 1549 6.413892 TCTCATGTCCATTGTAGCAACATAA 58.586 36.000 0.00 0.00 34.97 1.90
1567 1592 7.333672 GGACAAAAAGATACGGTGACTTCTTAT 59.666 37.037 0.00 0.00 0.00 1.73
1576 1601 2.785562 TGGGGACAAAAAGATACGGTG 58.214 47.619 0.00 0.00 37.44 4.94
1641 1684 1.595109 CTCGTTGCTGCACCACTGA 60.595 57.895 0.00 0.80 0.00 3.41
1700 1752 8.106462 TGTAAGAGTGATTGGGAAATAATGACA 58.894 33.333 0.00 0.00 0.00 3.58
1760 1812 4.384056 GCTGCTGTAGTCATGACCAATAT 58.616 43.478 22.21 6.01 0.00 1.28
1766 1818 0.737367 TGCGCTGCTGTAGTCATGAC 60.737 55.000 18.47 18.47 0.00 3.06
1799 1851 0.620410 CTCCACATGGTAGTCCCCCA 60.620 60.000 0.00 0.00 36.34 4.96
1859 1911 6.873076 CACTAAGATGATAGCTTCCATTCCTC 59.127 42.308 0.00 0.00 0.00 3.71
1934 1986 0.603065 GATGTTTCCAGGGTTGGCAC 59.397 55.000 0.00 0.00 44.63 5.01
1996 2048 3.498397 ACACGACACCATTTGAGACAATC 59.502 43.478 0.00 0.00 0.00 2.67
2029 2081 3.257375 TCGAATACTGTGTGTAGCTTGGT 59.743 43.478 0.00 0.00 34.24 3.67
2072 2124 8.239998 CCCAAATGCTCTCTAGTTCTTTAAAAG 58.760 37.037 0.00 0.00 0.00 2.27
2077 2132 4.013050 GCCCAAATGCTCTCTAGTTCTTT 58.987 43.478 0.00 0.00 0.00 2.52
2134 2189 3.905678 CCTCGCCGATCCTTCGCT 61.906 66.667 0.00 0.00 44.12 4.93
2135 2190 2.143594 ATACCTCGCCGATCCTTCGC 62.144 60.000 0.00 0.00 44.12 4.70
2136 2191 0.314302 AATACCTCGCCGATCCTTCG 59.686 55.000 0.00 0.00 45.08 3.79
2161 2216 0.671796 CCATACCTATGACGCCGTGA 59.328 55.000 0.00 0.00 35.75 4.35
2166 2221 3.131396 CAGTTTCCCATACCTATGACGC 58.869 50.000 0.00 0.00 35.75 5.19
2180 2235 1.740025 GGTGTATGCTCTGCAGTTTCC 59.260 52.381 14.67 1.33 43.65 3.13
2245 2300 2.880890 CCAAGTTTCTCAAGGTGTCCAG 59.119 50.000 0.00 0.00 0.00 3.86
2351 2415 2.878406 CCAATTATGAACGCCCTAGGTG 59.122 50.000 8.29 2.06 39.41 4.00
2357 2421 3.064820 CAGTGTACCAATTATGAACGCCC 59.935 47.826 0.00 0.00 0.00 6.13
2369 2433 1.061546 GGGGAACTCCAGTGTACCAA 58.938 55.000 0.00 0.00 37.91 3.67
2605 2669 0.468226 TGGTGCGTCTTGAAGAGGTT 59.532 50.000 15.31 0.00 33.01 3.50
2606 2670 0.249911 GTGGTGCGTCTTGAAGAGGT 60.250 55.000 15.31 0.00 33.01 3.85
2626 2690 3.139077 GGGGCATCTTGTAATAAGACGG 58.861 50.000 0.00 0.00 0.00 4.79
2680 2744 3.899726 TGTGTACCTAAAAAGGGTTGCA 58.100 40.909 0.00 0.00 38.19 4.08
2688 2752 5.226396 GCATTGTGCATGTGTACCTAAAAA 58.774 37.500 0.00 0.00 44.26 1.94
2788 2852 6.595326 TGTACATGCAGAGTATTCTTTGAAGG 59.405 38.462 5.25 0.00 0.00 3.46
2812 2876 5.122711 TGTTGATGTACATCTGCACTTGATG 59.877 40.000 30.67 11.71 44.79 3.07
2843 2907 5.592282 TCAAACACAATACCGGCATGATTAT 59.408 36.000 0.00 0.00 0.00 1.28
2854 2918 9.574516 AGGATTATAGGAATCAAACACAATACC 57.425 33.333 0.17 0.00 0.00 2.73
2865 2929 5.127845 GCCGAGATCAGGATTATAGGAATCA 59.872 44.000 10.95 0.00 0.00 2.57
2866 2930 5.362430 AGCCGAGATCAGGATTATAGGAATC 59.638 44.000 10.95 0.00 0.00 2.52
2875 2942 1.973515 TGCATAGCCGAGATCAGGATT 59.026 47.619 10.95 1.76 0.00 3.01
2880 2947 3.036075 CAGAATGCATAGCCGAGATCA 57.964 47.619 0.00 0.00 0.00 2.92
2918 2985 5.945784 ACCAAATCTACACAACATAGCACAT 59.054 36.000 0.00 0.00 0.00 3.21
2920 2987 5.391950 CCACCAAATCTACACAACATAGCAC 60.392 44.000 0.00 0.00 0.00 4.40
3131 3237 3.311486 AACCAAACCACACACAAACAG 57.689 42.857 0.00 0.00 0.00 3.16
3158 3264 1.065401 ACACAAACATGACCACAAGCG 59.935 47.619 0.00 0.00 0.00 4.68
3194 3303 1.597742 AGACACACCACAAGCACATC 58.402 50.000 0.00 0.00 0.00 3.06
3213 3322 4.383989 GGGGTTTTATGACGGTACATGGTA 60.384 45.833 0.00 0.00 0.00 3.25
3242 3351 2.721090 GCAAACAGCATTCTCGTCAAAC 59.279 45.455 0.00 0.00 44.79 2.93
3287 3396 2.866156 CGATACATGGGCACACACTTAG 59.134 50.000 0.00 0.00 0.00 2.18
3302 3411 4.643463 ACATGTAAAACCACACCGATACA 58.357 39.130 0.00 0.00 0.00 2.29
3316 3425 3.023119 CCCAGGCAAGCATACATGTAAA 58.977 45.455 10.14 0.00 0.00 2.01
3363 3489 4.705023 AGGACAAAAATTATGGAACGGAGG 59.295 41.667 0.00 0.00 0.00 4.30
3387 3513 4.509915 ACTTTGTACTCACGACAAAACG 57.490 40.909 0.00 0.00 44.05 3.60
3397 3524 6.869913 CGGAGGTAATGTAAACTTTGTACTCA 59.130 38.462 0.00 0.00 0.00 3.41
3434 3561 9.956720 CATCCGCATCTAGAAAAATTTAAGAAT 57.043 29.630 0.00 0.00 0.00 2.40
3471 3599 9.262358 GATAAGGATTTATCTAGTCACGCTTTT 57.738 33.333 0.00 0.00 41.21 2.27
3519 3647 9.753674 AAATCAAATACTCCATCTGTCCTAAAA 57.246 29.630 0.00 0.00 0.00 1.52
3528 3656 9.699410 TGAATAACCAAATCAAATACTCCATCT 57.301 29.630 0.00 0.00 0.00 2.90
3567 3695 4.547367 CATCCTTCCCGGCCGACC 62.547 72.222 30.73 0.00 0.00 4.79
3568 3696 4.547367 CCATCCTTCCCGGCCGAC 62.547 72.222 30.73 0.00 0.00 4.79
3621 3749 0.690077 AGCTAGGGTTAGGTTCCCCG 60.690 60.000 0.00 0.00 46.17 5.73


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

AutoCloner maintained by Alex Coulton.