Multiple sequence alignment - TraesCS5B01G396400

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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 TraesCS5B01G396400 chr5B 100.000 3770 0 0 1 3770 573229081 573225312 0.000000e+00 6962.0
1 TraesCS5B01G396400 chr5D 94.714 3254 119 20 540 3770 466232832 466229609 0.000000e+00 5007.0
2 TraesCS5B01G396400 chr5A 90.786 3332 200 49 473 3766 586606839 586603577 0.000000e+00 4353.0
3 TraesCS5B01G396400 chr5A 88.104 538 42 11 2823 3354 538232495 538233016 1.490000e-173 619.0
4 TraesCS5B01G396400 chr5A 86.905 84 4 4 105 181 586607090 586607007 1.870000e-13 87.9
5 TraesCS5B01G396400 chr1B 93.701 508 25 4 806 1312 22642865 22643366 0.000000e+00 754.0
6 TraesCS5B01G396400 chr6A 87.146 529 46 11 2828 3350 218850534 218851046 7.020000e-162 580.0
7 TraesCS5B01G396400 chr3A 86.803 538 47 13 2823 3354 380636530 380636011 2.520000e-161 579.0


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 TraesCS5B01G396400 chr5B 573225312 573229081 3769 True 6962.00 6962 100.0000 1 3770 1 chr5B.!!$R1 3769
1 TraesCS5B01G396400 chr5D 466229609 466232832 3223 True 5007.00 5007 94.7140 540 3770 1 chr5D.!!$R1 3230
2 TraesCS5B01G396400 chr5A 586603577 586607090 3513 True 2220.45 4353 88.8455 105 3766 2 chr5A.!!$R1 3661
3 TraesCS5B01G396400 chr5A 538232495 538233016 521 False 619.00 619 88.1040 2823 3354 1 chr5A.!!$F1 531
4 TraesCS5B01G396400 chr1B 22642865 22643366 501 False 754.00 754 93.7010 806 1312 1 chr1B.!!$F1 506
5 TraesCS5B01G396400 chr6A 218850534 218851046 512 False 580.00 580 87.1460 2828 3350 1 chr6A.!!$F1 522
6 TraesCS5B01G396400 chr3A 380636011 380636530 519 True 579.00 579 86.8030 2823 3354 1 chr3A.!!$R1 531

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
101 102 0.035056 AAGACCACACAGCCCATAGC 60.035 55.0 0.00 0.00 44.25 2.97 F
235 270 0.035439 AGTGACATTTGGGCCCTACG 60.035 55.0 25.70 11.89 0.00 3.51 F
295 330 0.038892 CTCCTTGCGCAGTTGCATTT 60.039 50.0 11.31 0.00 45.78 2.32 F
296 331 0.039256 TCCTTGCGCAGTTGCATTTC 60.039 50.0 11.31 0.00 45.78 2.17 F
315 350 0.097674 CATTCAGCTAACACGCCTGC 59.902 55.0 0.00 0.00 0.00 4.85 F
675 711 0.108804 CGGCACCAACACGTAGAGAT 60.109 55.0 0.00 0.00 0.00 2.75 F
2392 2473 0.308993 GCACCATAATTCTGGCGCTC 59.691 55.0 13.93 0.00 40.45 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 2110 0.110056 GAGCAATAATCGCCATGCCG 60.110 55.000 0.00 0.00 39.59 5.69 R
2065 2146 1.584175 TCTCGACGAGATAGTCTGCC 58.416 55.000 23.27 0.00 38.90 4.85 R
2182 2263 1.805945 CAGAGCGGCCGTGTAGAAC 60.806 63.158 28.70 7.91 0.00 3.01 R
2303 2384 4.618378 AGCTTTTATCCCCATAACCCAA 57.382 40.909 0.00 0.00 0.00 4.12 R
2392 2473 1.134367 TCGGCGAGGTACATGAAGAAG 59.866 52.381 4.99 0.00 0.00 2.85 R
2410 2491 0.042013 GTCGCTCGGTGTAGATCTCG 60.042 60.000 0.00 0.00 0.00 4.04 R
3512 3622 1.798223 TCCATTTCGTTTCTGTCGCAG 59.202 47.619 1.02 1.02 0.00 5.18 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
18 19 2.533318 CGAAGTGCTCCTGTTGACC 58.467 57.895 0.00 0.00 0.00 4.02
19 20 0.249868 CGAAGTGCTCCTGTTGACCA 60.250 55.000 0.00 0.00 0.00 4.02
20 21 1.609061 CGAAGTGCTCCTGTTGACCAT 60.609 52.381 0.00 0.00 0.00 3.55
21 22 2.353704 CGAAGTGCTCCTGTTGACCATA 60.354 50.000 0.00 0.00 0.00 2.74
22 23 3.679917 CGAAGTGCTCCTGTTGACCATAT 60.680 47.826 0.00 0.00 0.00 1.78
23 24 3.550437 AGTGCTCCTGTTGACCATATC 57.450 47.619 0.00 0.00 0.00 1.63
24 25 3.110705 AGTGCTCCTGTTGACCATATCT 58.889 45.455 0.00 0.00 0.00 1.98
25 26 3.521126 AGTGCTCCTGTTGACCATATCTT 59.479 43.478 0.00 0.00 0.00 2.40
26 27 3.624861 GTGCTCCTGTTGACCATATCTTG 59.375 47.826 0.00 0.00 0.00 3.02
38 39 4.739046 CCATATCTTGGCGTTGAAGATC 57.261 45.455 8.41 0.00 40.09 2.75
39 40 3.499918 CCATATCTTGGCGTTGAAGATCC 59.500 47.826 8.41 0.00 40.09 3.36
40 41 4.384056 CATATCTTGGCGTTGAAGATCCT 58.616 43.478 8.41 0.00 40.09 3.24
41 42 2.099141 TCTTGGCGTTGAAGATCCTG 57.901 50.000 0.00 0.00 0.00 3.86
42 43 1.347707 TCTTGGCGTTGAAGATCCTGT 59.652 47.619 0.00 0.00 0.00 4.00
43 44 1.734465 CTTGGCGTTGAAGATCCTGTC 59.266 52.381 0.00 0.00 0.00 3.51
44 45 0.684535 TGGCGTTGAAGATCCTGTCA 59.315 50.000 0.00 0.00 0.00 3.58
45 46 1.278985 TGGCGTTGAAGATCCTGTCAT 59.721 47.619 0.00 0.00 0.00 3.06
46 47 2.290260 TGGCGTTGAAGATCCTGTCATT 60.290 45.455 0.00 0.00 0.00 2.57
47 48 2.352960 GGCGTTGAAGATCCTGTCATTC 59.647 50.000 0.00 0.00 0.00 2.67
48 49 2.352960 GCGTTGAAGATCCTGTCATTCC 59.647 50.000 0.00 0.00 0.00 3.01
49 50 2.604914 CGTTGAAGATCCTGTCATTCCG 59.395 50.000 0.00 0.00 0.00 4.30
50 51 3.676049 CGTTGAAGATCCTGTCATTCCGA 60.676 47.826 0.00 0.00 0.00 4.55
51 52 3.808466 TGAAGATCCTGTCATTCCGAG 57.192 47.619 0.00 0.00 0.00 4.63
52 53 2.159043 TGAAGATCCTGTCATTCCGAGC 60.159 50.000 0.00 0.00 0.00 5.03
53 54 1.786937 AGATCCTGTCATTCCGAGCT 58.213 50.000 0.00 0.00 0.00 4.09
54 55 2.114616 AGATCCTGTCATTCCGAGCTT 58.885 47.619 0.00 0.00 0.00 3.74
55 56 2.503356 AGATCCTGTCATTCCGAGCTTT 59.497 45.455 0.00 0.00 0.00 3.51
56 57 2.099141 TCCTGTCATTCCGAGCTTTG 57.901 50.000 0.00 0.00 0.00 2.77
57 58 0.449388 CCTGTCATTCCGAGCTTTGC 59.551 55.000 0.00 0.00 0.00 3.68
58 59 0.449388 CTGTCATTCCGAGCTTTGCC 59.551 55.000 0.00 0.00 0.00 4.52
59 60 0.250684 TGTCATTCCGAGCTTTGCCA 60.251 50.000 0.00 0.00 0.00 4.92
60 61 0.881118 GTCATTCCGAGCTTTGCCAA 59.119 50.000 0.00 0.00 0.00 4.52
61 62 1.269448 GTCATTCCGAGCTTTGCCAAA 59.731 47.619 0.00 0.00 0.00 3.28
62 63 1.541147 TCATTCCGAGCTTTGCCAAAG 59.459 47.619 12.87 12.87 41.46 2.77
63 64 0.890683 ATTCCGAGCTTTGCCAAAGG 59.109 50.000 18.29 3.21 38.93 3.11
64 65 1.178534 TTCCGAGCTTTGCCAAAGGG 61.179 55.000 18.29 11.23 38.93 3.95
74 75 2.280524 CCAAAGGGCGACGACACA 60.281 61.111 1.63 0.00 0.00 3.72
75 76 1.671054 CCAAAGGGCGACGACACAT 60.671 57.895 1.63 0.00 0.00 3.21
76 77 1.497278 CAAAGGGCGACGACACATG 59.503 57.895 1.63 0.00 0.00 3.21
77 78 2.325082 AAAGGGCGACGACACATGC 61.325 57.895 1.63 0.00 0.00 4.06
83 84 3.109547 GACGACACATGCGGCGAA 61.110 61.111 17.35 0.00 0.00 4.70
84 85 3.071459 GACGACACATGCGGCGAAG 62.071 63.158 17.35 0.73 0.00 3.79
85 86 2.809174 CGACACATGCGGCGAAGA 60.809 61.111 12.98 0.00 0.00 2.87
86 87 2.778679 GACACATGCGGCGAAGAC 59.221 61.111 12.98 0.00 0.00 3.01
87 88 2.740714 GACACATGCGGCGAAGACC 61.741 63.158 12.98 0.00 0.00 3.85
88 89 2.741985 CACATGCGGCGAAGACCA 60.742 61.111 12.98 0.00 0.00 4.02
89 90 2.742372 ACATGCGGCGAAGACCAC 60.742 61.111 12.98 0.00 0.00 4.16
90 91 2.741985 CATGCGGCGAAGACCACA 60.742 61.111 12.98 0.00 0.00 4.17
91 92 2.742372 ATGCGGCGAAGACCACAC 60.742 61.111 12.98 0.00 0.00 3.82
92 93 3.529341 ATGCGGCGAAGACCACACA 62.529 57.895 12.98 0.00 0.00 3.72
93 94 3.414700 GCGGCGAAGACCACACAG 61.415 66.667 12.98 0.00 0.00 3.66
94 95 3.414700 CGGCGAAGACCACACAGC 61.415 66.667 0.00 0.00 0.00 4.40
95 96 3.050275 GGCGAAGACCACACAGCC 61.050 66.667 0.00 0.00 37.61 4.85
96 97 3.050275 GCGAAGACCACACAGCCC 61.050 66.667 0.00 0.00 0.00 5.19
97 98 2.425592 CGAAGACCACACAGCCCA 59.574 61.111 0.00 0.00 0.00 5.36
98 99 1.003355 CGAAGACCACACAGCCCAT 60.003 57.895 0.00 0.00 0.00 4.00
99 100 0.249120 CGAAGACCACACAGCCCATA 59.751 55.000 0.00 0.00 0.00 2.74
100 101 1.740380 CGAAGACCACACAGCCCATAG 60.740 57.143 0.00 0.00 0.00 2.23
101 102 0.035056 AAGACCACACAGCCCATAGC 60.035 55.000 0.00 0.00 44.25 2.97
111 112 3.832704 GCCCATAGCAAAACCCAAC 57.167 52.632 0.00 0.00 42.97 3.77
146 147 2.603075 AATGCTTACCCACACCACAT 57.397 45.000 0.00 0.00 0.00 3.21
147 148 2.128771 ATGCTTACCCACACCACATC 57.871 50.000 0.00 0.00 0.00 3.06
200 235 0.402121 GGAGGTTGGAGCTTTCAGGT 59.598 55.000 0.00 0.00 0.00 4.00
202 237 2.039879 GGAGGTTGGAGCTTTCAGGTAA 59.960 50.000 0.00 0.00 0.00 2.85
224 259 1.203523 GCACGAGGAGAGAGTGACATT 59.796 52.381 0.00 0.00 38.06 2.71
232 267 0.329596 GAGAGTGACATTTGGGCCCT 59.670 55.000 25.70 0.15 0.00 5.19
235 270 0.035439 AGTGACATTTGGGCCCTACG 60.035 55.000 25.70 11.89 0.00 3.51
260 295 1.536284 CCCGATTCTCTAGTTCGTGCC 60.536 57.143 0.00 0.00 0.00 5.01
292 327 2.979676 CCTCCTTGCGCAGTTGCA 60.980 61.111 11.31 0.00 44.61 4.08
293 328 2.338015 CCTCCTTGCGCAGTTGCAT 61.338 57.895 11.31 0.00 45.78 3.96
294 329 1.582968 CTCCTTGCGCAGTTGCATT 59.417 52.632 11.31 0.00 45.78 3.56
295 330 0.038892 CTCCTTGCGCAGTTGCATTT 60.039 50.000 11.31 0.00 45.78 2.32
296 331 0.039256 TCCTTGCGCAGTTGCATTTC 60.039 50.000 11.31 0.00 45.78 2.17
297 332 0.318869 CCTTGCGCAGTTGCATTTCA 60.319 50.000 11.31 0.00 45.78 2.69
298 333 1.670674 CCTTGCGCAGTTGCATTTCAT 60.671 47.619 11.31 0.00 45.78 2.57
299 334 2.063266 CTTGCGCAGTTGCATTTCATT 58.937 42.857 11.31 0.00 45.78 2.57
300 335 1.700523 TGCGCAGTTGCATTTCATTC 58.299 45.000 5.66 0.00 40.62 2.67
301 336 1.000496 TGCGCAGTTGCATTTCATTCA 60.000 42.857 5.66 0.00 40.62 2.57
302 337 1.652124 GCGCAGTTGCATTTCATTCAG 59.348 47.619 0.30 0.00 42.21 3.02
303 338 1.652124 CGCAGTTGCATTTCATTCAGC 59.348 47.619 4.84 0.00 42.21 4.26
304 339 2.670229 CGCAGTTGCATTTCATTCAGCT 60.670 45.455 4.84 0.00 42.21 4.24
305 340 3.426560 CGCAGTTGCATTTCATTCAGCTA 60.427 43.478 4.84 0.00 42.21 3.32
306 341 4.487948 GCAGTTGCATTTCATTCAGCTAA 58.512 39.130 0.00 0.00 41.59 3.09
307 342 4.325472 GCAGTTGCATTTCATTCAGCTAAC 59.675 41.667 0.00 0.00 41.59 2.34
308 343 5.463286 CAGTTGCATTTCATTCAGCTAACA 58.537 37.500 0.00 0.00 0.00 2.41
309 344 5.344128 CAGTTGCATTTCATTCAGCTAACAC 59.656 40.000 0.00 0.00 0.00 3.32
310 345 4.082274 TGCATTTCATTCAGCTAACACG 57.918 40.909 0.00 0.00 0.00 4.49
311 346 2.848302 GCATTTCATTCAGCTAACACGC 59.152 45.455 0.00 0.00 0.00 5.34
312 347 3.429085 CATTTCATTCAGCTAACACGCC 58.571 45.455 0.00 0.00 0.00 5.68
313 348 2.472695 TTCATTCAGCTAACACGCCT 57.527 45.000 0.00 0.00 0.00 5.52
314 349 1.725641 TCATTCAGCTAACACGCCTG 58.274 50.000 0.00 0.00 0.00 4.85
315 350 0.097674 CATTCAGCTAACACGCCTGC 59.902 55.000 0.00 0.00 0.00 4.85
316 351 1.026718 ATTCAGCTAACACGCCTGCC 61.027 55.000 0.00 0.00 0.00 4.85
317 352 3.490759 CAGCTAACACGCCTGCCG 61.491 66.667 0.00 0.00 44.21 5.69
318 353 3.691342 AGCTAACACGCCTGCCGA 61.691 61.111 0.00 0.00 41.02 5.54
319 354 3.488090 GCTAACACGCCTGCCGAC 61.488 66.667 0.00 0.00 41.02 4.79
320 355 2.048597 CTAACACGCCTGCCGACA 60.049 61.111 0.00 0.00 41.02 4.35
321 356 2.356553 TAACACGCCTGCCGACAC 60.357 61.111 0.00 0.00 41.02 3.67
322 357 3.153270 TAACACGCCTGCCGACACA 62.153 57.895 0.00 0.00 41.02 3.72
323 358 2.443260 TAACACGCCTGCCGACACAT 62.443 55.000 0.00 0.00 41.02 3.21
324 359 3.049674 CACGCCTGCCGACACATT 61.050 61.111 0.00 0.00 41.02 2.71
325 360 2.281484 ACGCCTGCCGACACATTT 60.281 55.556 0.00 0.00 41.02 2.32
326 361 1.896660 ACGCCTGCCGACACATTTT 60.897 52.632 0.00 0.00 41.02 1.82
327 362 1.285641 CGCCTGCCGACACATTTTT 59.714 52.632 0.00 0.00 40.02 1.94
328 363 0.729140 CGCCTGCCGACACATTTTTC 60.729 55.000 0.00 0.00 40.02 2.29
329 364 0.598065 GCCTGCCGACACATTTTTCT 59.402 50.000 0.00 0.00 0.00 2.52
330 365 1.810151 GCCTGCCGACACATTTTTCTA 59.190 47.619 0.00 0.00 0.00 2.10
331 366 2.414161 GCCTGCCGACACATTTTTCTAC 60.414 50.000 0.00 0.00 0.00 2.59
332 367 3.074412 CCTGCCGACACATTTTTCTACT 58.926 45.455 0.00 0.00 0.00 2.57
333 368 4.250464 CCTGCCGACACATTTTTCTACTA 58.750 43.478 0.00 0.00 0.00 1.82
334 369 4.092968 CCTGCCGACACATTTTTCTACTAC 59.907 45.833 0.00 0.00 0.00 2.73
335 370 3.676172 TGCCGACACATTTTTCTACTACG 59.324 43.478 0.00 0.00 0.00 3.51
336 371 3.676646 GCCGACACATTTTTCTACTACGT 59.323 43.478 0.00 0.00 0.00 3.57
337 372 4.858692 GCCGACACATTTTTCTACTACGTA 59.141 41.667 0.00 0.00 0.00 3.57
338 373 5.220098 GCCGACACATTTTTCTACTACGTAC 60.220 44.000 0.00 0.00 0.00 3.67
339 374 6.088824 CCGACACATTTTTCTACTACGTACT 58.911 40.000 0.00 0.00 0.00 2.73
340 375 6.583806 CCGACACATTTTTCTACTACGTACTT 59.416 38.462 0.00 0.00 0.00 2.24
341 376 7.410087 CCGACACATTTTTCTACTACGTACTTG 60.410 40.741 0.00 0.00 0.00 3.16
342 377 7.324375 CGACACATTTTTCTACTACGTACTTGA 59.676 37.037 0.00 0.00 0.00 3.02
343 378 8.876275 ACACATTTTTCTACTACGTACTTGAA 57.124 30.769 0.00 0.00 0.00 2.69
344 379 9.485206 ACACATTTTTCTACTACGTACTTGAAT 57.515 29.630 0.00 0.00 0.00 2.57
398 433 4.681978 GGCGACACAACCCGAGCT 62.682 66.667 0.00 0.00 0.00 4.09
399 434 3.112709 GCGACACAACCCGAGCTC 61.113 66.667 2.73 2.73 0.00 4.09
400 435 2.805353 CGACACAACCCGAGCTCG 60.805 66.667 29.06 29.06 39.44 5.03
410 445 2.415010 CGAGCTCGGATCACCCTG 59.585 66.667 28.40 0.00 35.37 4.45
411 446 2.107953 GAGCTCGGATCACCCTGC 59.892 66.667 0.00 0.00 0.00 4.85
412 447 3.781770 GAGCTCGGATCACCCTGCG 62.782 68.421 0.00 0.00 36.50 5.18
413 448 4.899239 GCTCGGATCACCCTGCGG 62.899 72.222 0.00 0.00 0.00 5.69
414 449 4.899239 CTCGGATCACCCTGCGGC 62.899 72.222 0.00 0.00 0.00 6.53
418 453 4.451150 GATCACCCTGCGGCGACA 62.451 66.667 12.98 7.54 0.00 4.35
419 454 4.760047 ATCACCCTGCGGCGACAC 62.760 66.667 12.98 0.00 0.00 3.67
442 477 1.128015 GCTCGACGCTCGTGTTTTC 59.872 57.895 0.00 0.00 41.35 2.29
444 479 1.266786 CTCGACGCTCGTGTTTTCGT 61.267 55.000 0.00 0.00 41.35 3.85
446 481 0.713718 CGACGCTCGTGTTTTCGTTG 60.714 55.000 0.00 0.00 34.72 4.10
457 492 4.152402 CGTGTTTTCGTTGGATCTTGATCT 59.848 41.667 10.03 0.00 0.00 2.75
459 494 5.179368 GTGTTTTCGTTGGATCTTGATCTGA 59.821 40.000 10.03 0.00 0.00 3.27
460 495 5.409520 TGTTTTCGTTGGATCTTGATCTGAG 59.590 40.000 10.03 0.00 0.00 3.35
461 496 5.405935 TTTCGTTGGATCTTGATCTGAGA 57.594 39.130 10.03 0.00 0.00 3.27
462 497 5.405935 TTCGTTGGATCTTGATCTGAGAA 57.594 39.130 10.03 8.23 0.00 2.87
463 498 4.748892 TCGTTGGATCTTGATCTGAGAAC 58.251 43.478 10.03 7.52 0.00 3.01
464 499 3.549471 CGTTGGATCTTGATCTGAGAACG 59.451 47.826 10.03 13.42 0.00 3.95
465 500 3.808466 TGGATCTTGATCTGAGAACGG 57.192 47.619 10.03 0.00 0.00 4.44
468 503 3.243704 GGATCTTGATCTGAGAACGGGAG 60.244 52.174 10.03 0.00 0.00 4.30
469 504 1.478510 TCTTGATCTGAGAACGGGAGC 59.521 52.381 0.00 0.00 0.00 4.70
470 505 1.205655 CTTGATCTGAGAACGGGAGCA 59.794 52.381 0.00 0.00 0.00 4.26
471 506 0.820226 TGATCTGAGAACGGGAGCAG 59.180 55.000 0.00 0.00 0.00 4.24
472 507 0.529555 GATCTGAGAACGGGAGCAGC 60.530 60.000 0.00 0.00 0.00 5.25
473 508 1.260538 ATCTGAGAACGGGAGCAGCA 61.261 55.000 0.00 0.00 0.00 4.41
474 509 1.447489 CTGAGAACGGGAGCAGCAG 60.447 63.158 0.00 0.00 0.00 4.24
475 510 2.817396 GAGAACGGGAGCAGCAGC 60.817 66.667 0.00 0.00 42.56 5.25
476 511 4.400961 AGAACGGGAGCAGCAGCC 62.401 66.667 0.00 0.00 43.56 4.85
575 610 4.935630 CGGAAGGTCAAAAACGGC 57.064 55.556 0.00 0.00 0.00 5.68
576 611 1.082366 CGGAAGGTCAAAAACGGCG 60.082 57.895 4.80 4.80 0.00 6.46
577 612 1.500512 CGGAAGGTCAAAAACGGCGA 61.501 55.000 16.62 0.00 0.00 5.54
631 666 2.637025 CGGCCACGTCAAAACAGG 59.363 61.111 2.24 0.00 34.81 4.00
672 708 2.356553 GCGGCACCAACACGTAGA 60.357 61.111 0.00 0.00 0.00 2.59
673 709 2.380410 GCGGCACCAACACGTAGAG 61.380 63.158 0.00 0.00 0.00 2.43
674 710 1.287815 CGGCACCAACACGTAGAGA 59.712 57.895 0.00 0.00 0.00 3.10
675 711 0.108804 CGGCACCAACACGTAGAGAT 60.109 55.000 0.00 0.00 0.00 2.75
766 813 1.178534 GCGGAGAGGGAGGAGATCAG 61.179 65.000 0.00 0.00 0.00 2.90
826 882 3.868200 AAGGCGCCCTCAAACCCAG 62.868 63.158 26.15 0.00 30.89 4.45
827 883 4.344865 GGCGCCCTCAAACCCAGA 62.345 66.667 18.11 0.00 0.00 3.86
834 892 1.889170 CCCTCAAACCCAGAAAAGCTC 59.111 52.381 0.00 0.00 0.00 4.09
885 948 2.301583 GGAGGTAAGGGATGATCTCTGC 59.698 54.545 0.00 0.00 0.00 4.26
904 967 1.009389 CGTCTTCTCAACCGTGCTCC 61.009 60.000 0.00 0.00 0.00 4.70
953 1016 0.455005 GAGCTGCCAGAATTGCCTTC 59.545 55.000 0.00 0.00 0.00 3.46
984 1047 2.354259 AGCTGCATCACAAGTAGAAGC 58.646 47.619 1.02 0.00 0.00 3.86
1037 1100 2.543067 AATGCTTCCCCTGCTCGTCC 62.543 60.000 0.00 0.00 0.00 4.79
1042 1105 0.683504 TTCCCCTGCTCGTCCTACTC 60.684 60.000 0.00 0.00 0.00 2.59
1067 1130 6.180472 TCCTCTTTTACAATCCATCTCAACC 58.820 40.000 0.00 0.00 0.00 3.77
1188 1251 2.734079 GTCCAGAAAGAAAGCGACAGAG 59.266 50.000 0.00 0.00 0.00 3.35
1321 1402 4.344359 TGGCCCTTATTTTTGACCAAAC 57.656 40.909 0.00 0.00 0.00 2.93
1478 1559 2.990941 GCAATTCAGTGCATATCCACG 58.009 47.619 0.00 0.00 44.29 4.94
1552 1633 6.366332 CCTCGCATATCTGTAAAACCATACTC 59.634 42.308 0.00 0.00 0.00 2.59
1582 1663 3.080319 GCCATTCTCTGAATCATAGGGC 58.920 50.000 0.00 0.00 0.00 5.19
1639 1720 1.242076 AGCCAATGTCTGACAACAGC 58.758 50.000 15.31 16.18 43.17 4.40
1663 1744 2.305405 GCGAGCATTGCTACCTGAG 58.695 57.895 11.96 0.76 44.02 3.35
1810 1891 1.045407 AGGAGTTGTTCAGCGTGGTA 58.955 50.000 0.00 0.00 0.00 3.25
1816 1897 4.382320 TTCAGCGTGGTACGGCCC 62.382 66.667 0.00 0.00 42.82 5.80
1860 1941 5.134679 TCCTCCTATTTCTCTACCTGCTAGT 59.865 44.000 0.00 0.00 0.00 2.57
1861 1942 5.836358 CCTCCTATTTCTCTACCTGCTAGTT 59.164 44.000 0.00 0.00 0.00 2.24
1870 1951 1.246056 ACCTGCTAGTTGGCGTCGTA 61.246 55.000 0.00 0.00 34.52 3.43
1924 2005 2.805099 CAAGAGAACCAACAGAGTGCTC 59.195 50.000 0.00 0.00 39.84 4.26
1989 2070 4.559862 ATGGAGACCTTGTTCCTAACAG 57.440 45.455 0.00 0.00 43.27 3.16
1990 2071 2.038557 TGGAGACCTTGTTCCTAACAGC 59.961 50.000 0.00 0.00 43.27 4.40
1999 2080 0.669619 TTCCTAACAGCGACACGACA 59.330 50.000 0.00 0.00 0.00 4.35
2029 2110 2.716398 GCTTGTGTTTTCGTCTTCACC 58.284 47.619 0.00 0.00 0.00 4.02
2041 2122 2.045438 TTCACCGGCATGGCGATT 60.045 55.556 39.49 24.27 43.94 3.34
2065 2146 1.612156 CTCTCTTCGTGAGCAAGTCG 58.388 55.000 3.89 0.00 42.38 4.18
2182 2263 7.072177 TGAGACAAACAAGACAAAGTACAAG 57.928 36.000 0.00 0.00 0.00 3.16
2303 2384 1.977854 TCTGTGCCACAATCACTACCT 59.022 47.619 0.00 0.00 35.58 3.08
2336 2417 3.374367 GGATAAAAGCTTCTCGTCCCAAC 59.626 47.826 0.00 0.00 0.00 3.77
2392 2473 0.308993 GCACCATAATTCTGGCGCTC 59.691 55.000 13.93 0.00 40.45 5.03
2410 2491 2.815478 CTCTTCTTCATGTACCTCGCC 58.185 52.381 0.00 0.00 0.00 5.54
2505 2586 4.162888 TCTTGAAGCAGCTGATCTGGATAA 59.837 41.667 20.43 3.98 43.06 1.75
2566 2647 6.443206 CAGTATTCTTCCCTCCATCATATCCT 59.557 42.308 0.00 0.00 0.00 3.24
2567 2648 7.621285 CAGTATTCTTCCCTCCATCATATCCTA 59.379 40.741 0.00 0.00 0.00 2.94
2576 2659 7.295672 TCCCTCCATCATATCCTAAGATTTTGT 59.704 37.037 0.00 0.00 33.67 2.83
2727 2818 2.110213 GTTGACCAGTCCGGCACA 59.890 61.111 0.00 0.00 39.03 4.57
2783 2874 1.134521 TCAGTGACGAACATATGGGCC 60.135 52.381 7.80 0.00 0.00 5.80
2794 2885 5.408604 CGAACATATGGGCCTGTACTTAATC 59.591 44.000 4.53 0.00 0.00 1.75
2826 2917 8.662141 GCTTAAATACTTTAGTTGAATGGTCGA 58.338 33.333 0.00 0.00 0.00 4.20
2832 2923 7.972832 ACTTTAGTTGAATGGTCGATTAACA 57.027 32.000 0.00 0.00 0.00 2.41
2926 3019 4.393990 ACACAATGGATATGCTCATATGCG 59.606 41.667 13.96 0.00 42.71 4.73
3038 3131 5.594926 CCATGAAATATTTCCAGCTTCCAC 58.405 41.667 22.42 0.00 36.36 4.02
3059 3152 2.918712 ATGGTAGCCTGTGTAGATGC 57.081 50.000 0.00 0.00 0.00 3.91
3146 3239 3.019003 GCTCGGCAAGTGGAGGCTA 62.019 63.158 0.00 0.00 0.00 3.93
3167 3260 7.015779 AGGCTAAGATCTCAGGTAAATAGGAAC 59.984 40.741 0.00 0.00 0.00 3.62
3235 3328 4.414846 AGAGTTCCCTATTCAGGCATTCAT 59.585 41.667 0.00 0.00 41.08 2.57
3350 3453 5.163663 CGGTATACACCAATTGCAGTCAAAT 60.164 40.000 5.01 0.00 46.14 2.32
3407 3517 2.682856 ACAAGCAACTACAAGTGGTGTG 59.317 45.455 0.00 0.00 41.89 3.82
3426 3536 4.082463 GTGTGACCAAAACAAAAGGAGACA 60.082 41.667 0.00 0.00 0.00 3.41
3512 3622 1.580059 TCTGTTGGGGGATGTACTCC 58.420 55.000 0.00 0.00 44.11 3.85
3706 3816 5.388408 TTTTAAACACAAACCCGTTGACT 57.612 34.783 0.00 0.00 39.87 3.41
3750 3860 5.010012 AGCAGTCATAAACCTTTTGGAACAG 59.990 40.000 0.00 0.00 42.39 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.533318 GGTCAACAGGAGCACTTCG 58.467 57.895 0.00 0.00 43.54 3.79
6 7 3.209410 CCAAGATATGGTCAACAGGAGC 58.791 50.000 0.00 0.00 44.85 4.70
18 19 4.212847 CAGGATCTTCAACGCCAAGATATG 59.787 45.833 4.53 4.06 40.11 1.78
19 20 4.141620 ACAGGATCTTCAACGCCAAGATAT 60.142 41.667 4.53 0.00 40.11 1.63
20 21 3.197766 ACAGGATCTTCAACGCCAAGATA 59.802 43.478 4.53 0.00 40.11 1.98
21 22 2.026822 ACAGGATCTTCAACGCCAAGAT 60.027 45.455 4.25 4.25 42.25 2.40
22 23 1.347707 ACAGGATCTTCAACGCCAAGA 59.652 47.619 0.00 0.00 34.37 3.02
23 24 1.734465 GACAGGATCTTCAACGCCAAG 59.266 52.381 0.00 0.00 0.00 3.61
24 25 1.071542 TGACAGGATCTTCAACGCCAA 59.928 47.619 0.00 0.00 0.00 4.52
25 26 0.684535 TGACAGGATCTTCAACGCCA 59.315 50.000 0.00 0.00 0.00 5.69
26 27 2.029838 ATGACAGGATCTTCAACGCC 57.970 50.000 0.00 0.00 0.00 5.68
27 28 2.352960 GGAATGACAGGATCTTCAACGC 59.647 50.000 0.00 0.00 0.00 4.84
28 29 2.604914 CGGAATGACAGGATCTTCAACG 59.395 50.000 0.00 0.00 0.00 4.10
29 30 3.861840 TCGGAATGACAGGATCTTCAAC 58.138 45.455 0.00 0.00 0.00 3.18
30 31 3.679917 GCTCGGAATGACAGGATCTTCAA 60.680 47.826 0.00 0.00 0.00 2.69
31 32 2.159043 GCTCGGAATGACAGGATCTTCA 60.159 50.000 0.00 0.00 0.00 3.02
32 33 2.102252 AGCTCGGAATGACAGGATCTTC 59.898 50.000 0.00 0.00 0.00 2.87
33 34 2.114616 AGCTCGGAATGACAGGATCTT 58.885 47.619 0.00 0.00 0.00 2.40
34 35 1.786937 AGCTCGGAATGACAGGATCT 58.213 50.000 0.00 0.00 0.00 2.75
35 36 2.611225 AAGCTCGGAATGACAGGATC 57.389 50.000 0.00 0.00 0.00 3.36
36 37 2.636830 CAAAGCTCGGAATGACAGGAT 58.363 47.619 0.00 0.00 0.00 3.24
37 38 1.945819 GCAAAGCTCGGAATGACAGGA 60.946 52.381 0.00 0.00 0.00 3.86
38 39 0.449388 GCAAAGCTCGGAATGACAGG 59.551 55.000 0.00 0.00 0.00 4.00
39 40 0.449388 GGCAAAGCTCGGAATGACAG 59.551 55.000 0.00 0.00 0.00 3.51
40 41 0.250684 TGGCAAAGCTCGGAATGACA 60.251 50.000 0.00 0.00 0.00 3.58
41 42 0.881118 TTGGCAAAGCTCGGAATGAC 59.119 50.000 0.00 0.00 0.00 3.06
42 43 1.541147 CTTTGGCAAAGCTCGGAATGA 59.459 47.619 25.46 0.00 0.00 2.57
43 44 1.403249 CCTTTGGCAAAGCTCGGAATG 60.403 52.381 30.00 13.08 37.18 2.67
44 45 0.890683 CCTTTGGCAAAGCTCGGAAT 59.109 50.000 30.00 0.00 37.18 3.01
45 46 1.178534 CCCTTTGGCAAAGCTCGGAA 61.179 55.000 30.00 0.00 37.18 4.30
46 47 1.603455 CCCTTTGGCAAAGCTCGGA 60.603 57.895 30.00 0.00 37.18 4.55
47 48 2.964978 CCCTTTGGCAAAGCTCGG 59.035 61.111 30.00 22.60 37.18 4.63
57 58 1.671054 ATGTGTCGTCGCCCTTTGG 60.671 57.895 0.00 0.00 0.00 3.28
58 59 1.497278 CATGTGTCGTCGCCCTTTG 59.503 57.895 0.00 0.00 0.00 2.77
59 60 2.325082 GCATGTGTCGTCGCCCTTT 61.325 57.895 0.00 0.00 0.00 3.11
60 61 2.742372 GCATGTGTCGTCGCCCTT 60.742 61.111 0.00 0.00 0.00 3.95
66 67 3.071459 CTTCGCCGCATGTGTCGTC 62.071 63.158 9.72 0.00 0.00 4.20
67 68 3.112075 CTTCGCCGCATGTGTCGT 61.112 61.111 9.72 0.00 0.00 4.34
68 69 2.809174 TCTTCGCCGCATGTGTCG 60.809 61.111 2.78 2.78 0.00 4.35
69 70 2.740714 GGTCTTCGCCGCATGTGTC 61.741 63.158 5.38 0.00 0.00 3.67
70 71 2.742372 GGTCTTCGCCGCATGTGT 60.742 61.111 5.38 0.00 0.00 3.72
71 72 2.741985 TGGTCTTCGCCGCATGTG 60.742 61.111 0.00 0.00 0.00 3.21
72 73 2.742372 GTGGTCTTCGCCGCATGT 60.742 61.111 0.00 0.00 38.79 3.21
73 74 2.741985 TGTGGTCTTCGCCGCATG 60.742 61.111 0.00 0.00 43.32 4.06
75 76 4.228567 TGTGTGGTCTTCGCCGCA 62.229 61.111 0.00 0.00 45.66 5.69
76 77 3.414700 CTGTGTGGTCTTCGCCGC 61.415 66.667 0.00 0.00 39.37 6.53
77 78 3.414700 GCTGTGTGGTCTTCGCCG 61.415 66.667 0.00 0.00 0.00 6.46
78 79 3.050275 GGCTGTGTGGTCTTCGCC 61.050 66.667 0.00 0.00 0.00 5.54
79 80 3.050275 GGGCTGTGTGGTCTTCGC 61.050 66.667 0.00 0.00 0.00 4.70
80 81 0.249120 TATGGGCTGTGTGGTCTTCG 59.751 55.000 0.00 0.00 0.00 3.79
81 82 2.014068 GCTATGGGCTGTGTGGTCTTC 61.014 57.143 0.00 0.00 38.06 2.87
82 83 0.035056 GCTATGGGCTGTGTGGTCTT 60.035 55.000 0.00 0.00 38.06 3.01
83 84 1.200760 TGCTATGGGCTGTGTGGTCT 61.201 55.000 0.00 0.00 42.39 3.85
84 85 0.322456 TTGCTATGGGCTGTGTGGTC 60.322 55.000 0.00 0.00 42.39 4.02
85 86 0.112218 TTTGCTATGGGCTGTGTGGT 59.888 50.000 0.00 0.00 42.39 4.16
86 87 1.067635 GTTTTGCTATGGGCTGTGTGG 60.068 52.381 0.00 0.00 42.39 4.17
87 88 1.067635 GGTTTTGCTATGGGCTGTGTG 60.068 52.381 0.00 0.00 42.39 3.82
88 89 1.256812 GGTTTTGCTATGGGCTGTGT 58.743 50.000 0.00 0.00 42.39 3.72
89 90 0.532115 GGGTTTTGCTATGGGCTGTG 59.468 55.000 0.00 0.00 42.39 3.66
90 91 0.114168 TGGGTTTTGCTATGGGCTGT 59.886 50.000 0.00 0.00 42.39 4.40
91 92 1.066929 GTTGGGTTTTGCTATGGGCTG 60.067 52.381 0.00 0.00 42.39 4.85
92 93 1.266178 GTTGGGTTTTGCTATGGGCT 58.734 50.000 0.00 0.00 42.39 5.19
93 94 0.249120 GGTTGGGTTTTGCTATGGGC 59.751 55.000 0.00 0.00 42.22 5.36
94 95 0.901827 GGGTTGGGTTTTGCTATGGG 59.098 55.000 0.00 0.00 0.00 4.00
95 96 1.638529 TGGGTTGGGTTTTGCTATGG 58.361 50.000 0.00 0.00 0.00 2.74
96 97 3.598299 CAATGGGTTGGGTTTTGCTATG 58.402 45.455 0.00 0.00 0.00 2.23
97 98 3.979101 CAATGGGTTGGGTTTTGCTAT 57.021 42.857 0.00 0.00 0.00 2.97
123 124 4.215908 TGTGGTGTGGGTAAGCATTTAAA 58.784 39.130 0.00 0.00 0.00 1.52
133 134 0.108774 TTTGCGATGTGGTGTGGGTA 59.891 50.000 0.00 0.00 0.00 3.69
134 135 1.152860 TTTGCGATGTGGTGTGGGT 60.153 52.632 0.00 0.00 0.00 4.51
146 147 0.673644 GTCCCTAGCTTGCTTTGCGA 60.674 55.000 0.00 0.00 35.28 5.10
147 148 0.955428 TGTCCCTAGCTTGCTTTGCG 60.955 55.000 0.00 0.00 35.28 4.85
200 235 1.004394 TCACTCTCTCCTCGTGCCTTA 59.996 52.381 0.00 0.00 0.00 2.69
202 237 0.963355 GTCACTCTCTCCTCGTGCCT 60.963 60.000 0.00 0.00 0.00 4.75
224 259 1.688269 CGGGATAACGTAGGGCCCAA 61.688 60.000 27.56 1.51 38.75 4.12
232 267 5.178252 CGAACTAGAGAATCGGGATAACGTA 59.822 44.000 0.00 0.00 42.67 3.57
235 270 5.213675 CACGAACTAGAGAATCGGGATAAC 58.786 45.833 0.00 0.00 42.38 1.89
285 320 5.344128 GTGTTAGCTGAATGAAATGCAACTG 59.656 40.000 0.00 0.00 27.40 3.16
292 327 3.127548 CAGGCGTGTTAGCTGAATGAAAT 59.872 43.478 0.00 0.00 37.29 2.17
293 328 2.483877 CAGGCGTGTTAGCTGAATGAAA 59.516 45.455 0.00 0.00 37.29 2.69
294 329 2.076100 CAGGCGTGTTAGCTGAATGAA 58.924 47.619 0.00 0.00 37.29 2.57
295 330 1.725641 CAGGCGTGTTAGCTGAATGA 58.274 50.000 0.00 0.00 37.29 2.57
296 331 0.097674 GCAGGCGTGTTAGCTGAATG 59.902 55.000 8.40 0.00 37.29 2.67
297 332 1.026718 GGCAGGCGTGTTAGCTGAAT 61.027 55.000 8.40 0.00 37.29 2.57
298 333 1.671054 GGCAGGCGTGTTAGCTGAA 60.671 57.895 8.40 0.00 37.29 3.02
299 334 2.047274 GGCAGGCGTGTTAGCTGA 60.047 61.111 8.40 0.00 37.29 4.26
300 335 3.490759 CGGCAGGCGTGTTAGCTG 61.491 66.667 8.53 0.00 37.29 4.24
301 336 3.691342 TCGGCAGGCGTGTTAGCT 61.691 61.111 17.01 0.00 37.29 3.32
302 337 3.488090 GTCGGCAGGCGTGTTAGC 61.488 66.667 17.01 0.00 0.00 3.09
303 338 2.048597 TGTCGGCAGGCGTGTTAG 60.049 61.111 17.01 0.26 0.00 2.34
304 339 2.356553 GTGTCGGCAGGCGTGTTA 60.357 61.111 17.01 0.00 0.00 2.41
305 340 3.825160 ATGTGTCGGCAGGCGTGTT 62.825 57.895 17.01 0.00 0.00 3.32
306 341 3.825160 AATGTGTCGGCAGGCGTGT 62.825 57.895 17.01 0.00 0.00 4.49
307 342 2.128853 AAAATGTGTCGGCAGGCGTG 62.129 55.000 17.01 1.01 0.00 5.34
308 343 1.452145 AAAAATGTGTCGGCAGGCGT 61.452 50.000 17.01 0.00 0.00 5.68
309 344 0.729140 GAAAAATGTGTCGGCAGGCG 60.729 55.000 10.80 10.80 0.00 5.52
310 345 0.598065 AGAAAAATGTGTCGGCAGGC 59.402 50.000 0.00 0.00 0.00 4.85
311 346 3.074412 AGTAGAAAAATGTGTCGGCAGG 58.926 45.455 0.00 0.00 0.00 4.85
312 347 4.201589 CGTAGTAGAAAAATGTGTCGGCAG 60.202 45.833 0.00 0.00 0.00 4.85
313 348 3.676172 CGTAGTAGAAAAATGTGTCGGCA 59.324 43.478 0.00 0.00 0.00 5.69
314 349 3.676646 ACGTAGTAGAAAAATGTGTCGGC 59.323 43.478 0.00 0.00 41.94 5.54
352 387 1.017387 GCGGATCAGGCGATCTTTTT 58.983 50.000 15.39 0.00 46.30 1.94
353 388 0.815615 GGCGGATCAGGCGATCTTTT 60.816 55.000 3.22 0.00 46.30 2.27
354 389 1.227674 GGCGGATCAGGCGATCTTT 60.228 57.895 3.22 0.00 46.30 2.52
355 390 2.423446 GGCGGATCAGGCGATCTT 59.577 61.111 3.22 0.00 46.30 2.40
381 416 4.681978 AGCTCGGGTTGTGTCGCC 62.682 66.667 0.00 0.00 0.00 5.54
382 417 3.112709 GAGCTCGGGTTGTGTCGC 61.113 66.667 0.00 0.00 0.00 5.19
383 418 2.805353 CGAGCTCGGGTTGTGTCG 60.805 66.667 28.40 0.00 35.37 4.35
393 428 2.415010 CAGGGTGATCCGAGCTCG 59.585 66.667 29.06 29.06 41.52 5.03
394 429 2.107953 GCAGGGTGATCCGAGCTC 59.892 66.667 2.73 2.73 41.52 4.09
395 430 3.842923 CGCAGGGTGATCCGAGCT 61.843 66.667 1.07 0.00 41.52 4.09
424 459 1.128015 GAAAACACGAGCGTCGAGC 59.872 57.895 13.06 0.00 43.74 5.03
425 460 1.266786 ACGAAAACACGAGCGTCGAG 61.267 55.000 13.06 8.40 43.74 4.04
426 461 0.866906 AACGAAAACACGAGCGTCGA 60.867 50.000 13.06 0.00 43.74 4.20
427 462 0.713718 CAACGAAAACACGAGCGTCG 60.714 55.000 5.97 5.97 46.93 5.12
428 463 0.382636 CCAACGAAAACACGAGCGTC 60.383 55.000 0.00 0.00 35.74 5.19
429 464 0.806884 TCCAACGAAAACACGAGCGT 60.807 50.000 0.00 0.00 38.81 5.07
430 465 0.511221 ATCCAACGAAAACACGAGCG 59.489 50.000 0.00 0.00 37.03 5.03
431 466 1.798813 AGATCCAACGAAAACACGAGC 59.201 47.619 0.00 0.00 37.03 5.03
433 468 3.459145 TCAAGATCCAACGAAAACACGA 58.541 40.909 0.00 0.00 37.03 4.35
435 470 5.179368 TCAGATCAAGATCCAACGAAAACAC 59.821 40.000 6.45 0.00 38.58 3.32
437 472 5.639506 TCTCAGATCAAGATCCAACGAAAAC 59.360 40.000 6.45 0.00 38.58 2.43
442 477 3.549471 CGTTCTCAGATCAAGATCCAACG 59.451 47.826 6.45 11.35 38.58 4.10
444 479 3.118629 CCCGTTCTCAGATCAAGATCCAA 60.119 47.826 6.45 0.00 38.58 3.53
446 481 2.695666 TCCCGTTCTCAGATCAAGATCC 59.304 50.000 6.45 0.00 38.58 3.36
457 492 2.659016 CTGCTGCTCCCGTTCTCA 59.341 61.111 0.00 0.00 0.00 3.27
459 494 4.400961 GGCTGCTGCTCCCGTTCT 62.401 66.667 15.64 0.00 39.59 3.01
474 509 3.376918 GGCAAAGTCCAGCAGGGC 61.377 66.667 0.00 0.00 40.92 5.19
475 510 1.975407 CAGGCAAAGTCCAGCAGGG 60.975 63.158 0.00 0.00 34.83 4.45
476 511 2.633509 GCAGGCAAAGTCCAGCAGG 61.634 63.158 0.00 0.00 38.37 4.85
477 512 2.960170 GCAGGCAAAGTCCAGCAG 59.040 61.111 0.00 0.00 38.37 4.24
478 513 2.979676 CGCAGGCAAAGTCCAGCA 60.980 61.111 0.00 0.00 38.39 4.41
479 514 2.980233 ACGCAGGCAAAGTCCAGC 60.980 61.111 0.00 0.00 35.55 4.85
480 515 2.949106 CACGCAGGCAAAGTCCAG 59.051 61.111 0.00 0.00 0.00 3.86
481 516 3.286751 GCACGCAGGCAAAGTCCA 61.287 61.111 0.00 0.00 0.00 4.02
482 517 3.286751 TGCACGCAGGCAAAGTCC 61.287 61.111 0.00 0.00 41.65 3.85
483 518 2.050985 GTGCACGCAGGCAAAGTC 60.051 61.111 0.00 0.00 46.93 3.01
484 519 3.595758 GGTGCACGCAGGCAAAGT 61.596 61.111 11.45 0.00 46.93 2.66
485 520 4.688419 CGGTGCACGCAGGCAAAG 62.688 66.667 11.45 0.00 46.93 2.77
524 559 4.814294 GAATCGACGTGGCGGGCT 62.814 66.667 0.00 0.00 0.00 5.19
574 609 3.894547 TTGGAACCCTTCGCCTCGC 62.895 63.158 0.00 0.00 0.00 5.03
575 610 2.033194 GTTGGAACCCTTCGCCTCG 61.033 63.158 0.00 0.00 0.00 4.63
576 611 0.250770 AAGTTGGAACCCTTCGCCTC 60.251 55.000 0.00 0.00 0.00 4.70
577 612 0.537371 CAAGTTGGAACCCTTCGCCT 60.537 55.000 0.00 0.00 0.00 5.52
624 659 1.228154 GTGGAGGTCGCCCTGTTTT 60.228 57.895 0.00 0.00 42.86 2.43
660 696 3.564644 CGGATCTATCTCTACGTGTTGGT 59.435 47.826 0.00 0.00 0.00 3.67
672 708 2.920645 CGCCACGCCGGATCTATCT 61.921 63.158 5.05 0.00 36.56 1.98
673 709 2.430921 CGCCACGCCGGATCTATC 60.431 66.667 5.05 0.00 36.56 2.08
766 813 1.142314 CTCTCCTGCTCTGCTCAGC 59.858 63.158 0.00 0.00 40.13 4.26
885 948 1.009389 GGAGCACGGTTGAGAAGACG 61.009 60.000 0.00 0.00 0.00 4.18
904 967 0.162507 CACGAAGCAAGCAGAGAACG 59.837 55.000 0.00 0.00 0.00 3.95
953 1016 2.286294 GTGATGCAGCTACAGAATTCGG 59.714 50.000 2.53 3.87 0.00 4.30
984 1047 1.170919 GCATACAGCAGGGCCATCTG 61.171 60.000 19.37 19.37 44.79 2.90
1037 1100 8.017418 AGATGGATTGTAAAAGAGGAGAGTAG 57.983 38.462 0.00 0.00 0.00 2.57
1042 1105 6.317391 GGTTGAGATGGATTGTAAAAGAGGAG 59.683 42.308 0.00 0.00 0.00 3.69
1250 1330 3.222603 TCTTTTTGACTTTCTGGGCCTC 58.777 45.455 4.53 0.00 0.00 4.70
1252 1332 3.573967 TGATCTTTTTGACTTTCTGGGCC 59.426 43.478 0.00 0.00 0.00 5.80
1256 1336 8.355169 TGAATTCCTGATCTTTTTGACTTTCTG 58.645 33.333 2.27 0.00 0.00 3.02
1321 1402 4.460382 TCAAAGAGAGGCAGGCAAAATAAG 59.540 41.667 0.00 0.00 0.00 1.73
1639 1720 1.003116 GGTAGCAATGCTCGCTGAATG 60.003 52.381 12.53 0.00 40.73 2.67
1663 1744 1.809207 CACATTGGCATCGGGGTTC 59.191 57.895 0.00 0.00 0.00 3.62
1720 1801 2.586792 GGAGCCGACCTGCATCTT 59.413 61.111 0.00 0.00 0.00 2.40
1810 1891 1.608717 CTAGTCTGAAGCTGGGCCGT 61.609 60.000 0.00 0.00 0.00 5.68
1816 1897 3.131400 GGAACCCTACTAGTCTGAAGCTG 59.869 52.174 0.00 0.00 0.00 4.24
1860 1941 2.297033 AGGTAAAAGACTACGACGCCAA 59.703 45.455 0.00 0.00 0.00 4.52
1861 1942 1.888512 AGGTAAAAGACTACGACGCCA 59.111 47.619 0.00 0.00 0.00 5.69
1870 1951 6.126863 TGATCCATGACAAGGTAAAAGACT 57.873 37.500 0.00 0.00 0.00 3.24
1924 2005 0.663269 TGCAGAAGTACAGTGCGTCG 60.663 55.000 8.91 0.00 40.23 5.12
1963 2044 1.134068 GGAACAAGGTCTCCATAGCCC 60.134 57.143 0.00 0.00 0.00 5.19
1989 2070 2.127609 GCAGCTTTGTCGTGTCGC 60.128 61.111 0.00 0.00 0.00 5.19
1990 2071 1.488957 GAGCAGCTTTGTCGTGTCG 59.511 57.895 0.00 0.00 0.00 4.35
2011 2092 1.666700 CCGGTGAAGACGAAAACACAA 59.333 47.619 0.00 0.00 35.33 3.33
2029 2110 0.110056 GAGCAATAATCGCCATGCCG 60.110 55.000 0.00 0.00 39.59 5.69
2065 2146 1.584175 TCTCGACGAGATAGTCTGCC 58.416 55.000 23.27 0.00 38.90 4.85
2142 2223 5.618056 TGTCTCAATTTGTCTGAGCATTC 57.382 39.130 0.00 0.00 40.18 2.67
2182 2263 1.805945 CAGAGCGGCCGTGTAGAAC 60.806 63.158 28.70 7.91 0.00 3.01
2303 2384 4.618378 AGCTTTTATCCCCATAACCCAA 57.382 40.909 0.00 0.00 0.00 4.12
2392 2473 1.134367 TCGGCGAGGTACATGAAGAAG 59.866 52.381 4.99 0.00 0.00 2.85
2410 2491 0.042013 GTCGCTCGGTGTAGATCTCG 60.042 60.000 0.00 0.00 0.00 4.04
2434 2515 0.906775 CCCATTTGGCCAGCATCTTT 59.093 50.000 5.11 0.00 0.00 2.52
2505 2586 2.421529 GCTTACCCCACTTTCCGATCAT 60.422 50.000 0.00 0.00 0.00 2.45
2567 2648 8.918202 TCAACACTCATTACCTACAAAATCTT 57.082 30.769 0.00 0.00 0.00 2.40
2576 2659 7.936847 AGTTCACAAATCAACACTCATTACCTA 59.063 33.333 0.00 0.00 0.00 3.08
2727 2818 5.519808 TGAGTAAGGTCATATGTGGAGAGT 58.480 41.667 1.90 0.00 0.00 3.24
2813 2904 5.305585 ACAGTGTTAATCGACCATTCAACT 58.694 37.500 0.00 0.00 0.00 3.16
2914 3007 0.604780 GTCCAGGCGCATATGAGCAT 60.605 55.000 28.92 21.83 42.80 3.79
2926 3019 3.674997 TCTTTCTTACACATGTCCAGGC 58.325 45.455 0.00 0.00 0.00 4.85
3038 3131 3.321968 TGCATCTACACAGGCTACCATAG 59.678 47.826 0.00 0.00 0.00 2.23
3146 3239 7.051000 GCAAGTTCCTATTTACCTGAGATCTT 58.949 38.462 0.00 0.00 0.00 2.40
3179 3272 6.127793 TCTTAGTTCTACTAGGTCACCATCC 58.872 44.000 0.00 0.00 31.47 3.51
3235 3328 2.360801 GTGCAAGGCAACCTGTTAGAAA 59.639 45.455 0.00 0.00 41.47 2.52
3350 3453 5.441500 TCACCTTGGTATTCACAACAAGAA 58.558 37.500 2.52 0.00 42.07 2.52
3407 3517 4.983671 AGTGTCTCCTTTTGTTTTGGTC 57.016 40.909 0.00 0.00 0.00 4.02
3426 3536 3.274288 GCAGAATTGTGCTAGGCTAAGT 58.726 45.455 19.63 0.00 40.54 2.24
3512 3622 1.798223 TCCATTTCGTTTCTGTCGCAG 59.202 47.619 1.02 1.02 0.00 5.18
3706 3816 4.134563 GCTTTCACCTGGTCAGTTCTAAA 58.865 43.478 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.