Multiple sequence alignment - TraesCS6B01G290500

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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 TraesCS6B01G290500 chr6B 100.000 4973 0 0 1 4973 522639089 522644061 0.000000e+00 9184.0
1 TraesCS6B01G290500 chr6B 81.369 628 72 18 4374 4970 187993666 187993053 2.100000e-128 470.0
2 TraesCS6B01G290500 chr6B 84.871 271 40 1 3469 3739 522681937 522682206 6.340000e-69 272.0
3 TraesCS6B01G290500 chr6B 80.000 300 58 2 3573 3871 553415735 553416033 2.330000e-53 220.0
4 TraesCS6B01G290500 chr6B 86.792 159 19 2 2654 2811 553414822 553414979 5.120000e-40 176.0
5 TraesCS6B01G290500 chr6B 100.000 53 0 0 3797 3849 522681358 522681410 1.140000e-16 99.0
6 TraesCS6B01G290500 chr6A 90.131 4114 191 80 390 4381 486546751 486550771 0.000000e+00 5149.0
7 TraesCS6B01G290500 chr6A 86.695 233 14 4 89 305 486546519 486546750 4.970000e-60 243.0
8 TraesCS6B01G290500 chr6A 82.721 272 36 6 3469 3740 486583782 486584042 1.080000e-56 231.0
9 TraesCS6B01G290500 chr6A 80.537 298 56 2 3575 3871 508714294 508713998 1.390000e-55 228.0
10 TraesCS6B01G290500 chr6A 80.417 240 41 6 2581 2817 508715282 508715046 1.420000e-40 178.0
11 TraesCS6B01G290500 chr6A 100.000 53 0 0 3797 3849 486554581 486554633 1.140000e-16 99.0
12 TraesCS6B01G290500 chr6A 92.157 51 4 0 13 63 486546493 486546543 6.910000e-09 73.1
13 TraesCS6B01G290500 chr6D 93.226 2849 102 41 1562 4377 355139126 355136336 0.000000e+00 4108.0
14 TraesCS6B01G290500 chr6D 89.577 921 49 21 618 1519 355140092 355139200 0.000000e+00 1125.0
15 TraesCS6B01G290500 chr6D 89.427 227 12 5 89 305 355140424 355140200 4.900000e-70 276.0
16 TraesCS6B01G290500 chr6D 79.940 334 59 5 3246 3576 67572107 67571779 6.430000e-59 239.0
17 TraesCS6B01G290500 chr6D 80.201 298 57 2 3575 3871 368109882 368109586 6.480000e-54 222.0
18 TraesCS6B01G290500 chr6D 81.277 235 38 6 2581 2812 368110870 368110639 8.500000e-43 185.0
19 TraesCS6B01G290500 chr6D 89.796 49 2 2 4376 4421 44416691 44416739 5.380000e-05 60.2
20 TraesCS6B01G290500 chr4D 94.118 595 21 7 4379 4973 77316877 77316297 0.000000e+00 893.0
21 TraesCS6B01G290500 chr4D 79.079 521 59 21 4381 4871 230641877 230641377 3.740000e-81 313.0
22 TraesCS6B01G290500 chr4D 92.381 105 6 1 4866 4970 230640535 230640433 1.120000e-31 148.0
23 TraesCS6B01G290500 chr2A 92.655 531 31 4 4381 4911 645302146 645301624 0.000000e+00 758.0
24 TraesCS6B01G290500 chr2A 95.775 71 3 0 4903 4973 645301227 645301157 1.130000e-21 115.0
25 TraesCS6B01G290500 chr7B 88.013 609 41 13 4374 4973 228142735 228142150 0.000000e+00 691.0
26 TraesCS6B01G290500 chr4A 84.746 177 23 4 2637 2811 590935306 590935132 1.840000e-39 174.0
27 TraesCS6B01G290500 chr1A 92.857 42 3 0 4373 4414 177489926 177489967 1.490000e-05 62.1
28 TraesCS6B01G290500 chr1A 94.872 39 2 0 4376 4414 289320925 289320963 1.490000e-05 62.1
29 TraesCS6B01G290500 chr3B 86.792 53 7 0 4372 4424 811767605 811767553 5.380000e-05 60.2
30 TraesCS6B01G290500 chr3A 100.000 30 0 0 314 343 666119446 666119417 6.950000e-04 56.5


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 TraesCS6B01G290500 chr6B 522639089 522644061 4972 False 9184.000000 9184 100.000000 1 4973 1 chr6B.!!$F1 4972
1 TraesCS6B01G290500 chr6B 187993053 187993666 613 True 470.000000 470 81.369000 4374 4970 1 chr6B.!!$R1 596
2 TraesCS6B01G290500 chr6A 486546493 486554633 8140 False 1391.025000 5149 92.245750 13 4381 4 chr6A.!!$F2 4368
3 TraesCS6B01G290500 chr6A 508713998 508715282 1284 True 203.000000 228 80.477000 2581 3871 2 chr6A.!!$R1 1290
4 TraesCS6B01G290500 chr6D 355136336 355140424 4088 True 1836.333333 4108 90.743333 89 4377 3 chr6D.!!$R2 4288
5 TraesCS6B01G290500 chr6D 368109586 368110870 1284 True 203.500000 222 80.739000 2581 3871 2 chr6D.!!$R3 1290
6 TraesCS6B01G290500 chr4D 77316297 77316877 580 True 893.000000 893 94.118000 4379 4973 1 chr4D.!!$R1 594
7 TraesCS6B01G290500 chr4D 230640433 230641877 1444 True 230.500000 313 85.730000 4381 4970 2 chr4D.!!$R2 589
8 TraesCS6B01G290500 chr2A 645301157 645302146 989 True 436.500000 758 94.215000 4381 4973 2 chr2A.!!$R1 592
9 TraesCS6B01G290500 chr7B 228142150 228142735 585 True 691.000000 691 88.013000 4374 4973 1 chr7B.!!$R1 599

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
315 327 0.175989 GCCGGGAGTGAGTAAAGGAG 59.824 60.0 2.18 0.00 0.00 3.69 F
524 545 0.179210 GACGACAGAGACGAGTGAGC 60.179 60.0 0.00 0.00 34.70 4.26 F
588 609 0.812811 CGATGATGGGCTGTGGTCTG 60.813 60.0 0.00 0.00 0.00 3.51 F
1607 1732 0.031178 CGTTTTGCCTCAAAGCAGCT 59.969 50.0 0.00 0.00 45.13 4.24 F
2011 2177 0.107116 TTGGCACTGTACCGGTTTGT 60.107 50.0 15.04 6.71 0.00 2.83 F
2372 2569 0.117340 AGCACTCCTACCCAACCTCT 59.883 55.0 0.00 0.00 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1185 1255 0.031314 CGATCACCCTCATCGTCAGG 59.969 60.0 0.00 0.00 38.67 3.86 R
1553 1678 0.107831 GGACTTGCACTACCACCACA 59.892 55.0 0.00 0.00 0.00 4.17 R
2250 2426 0.249398 AGAACATGTAGACGGTGCCC 59.751 55.0 0.00 0.00 0.00 5.36 R
2841 3042 0.251608 CCCAAAACCCGAGAACCCAT 60.252 55.0 0.00 0.00 0.00 4.00 R
3108 3315 1.046472 TGGTGTCTTCGGTGGTGAGT 61.046 55.0 0.00 0.00 0.00 3.41 R
4254 4642 0.100861 GCAGACTAGTCAGCGGTACC 59.899 60.0 22.42 0.16 32.62 3.34 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
24 25 1.614903 CAATTCAGGAGCAAGCAACCA 59.385 47.619 10.01 0.00 0.00 3.67
63 64 3.492313 GTCCATTTACTGAAAGCAAGCG 58.508 45.455 0.00 0.00 37.60 4.68
64 65 3.188460 GTCCATTTACTGAAAGCAAGCGA 59.812 43.478 0.00 0.00 37.60 4.93
65 66 3.188460 TCCATTTACTGAAAGCAAGCGAC 59.812 43.478 0.00 0.00 37.60 5.19
66 67 3.492313 CATTTACTGAAAGCAAGCGACC 58.508 45.455 0.00 0.00 37.60 4.79
67 68 2.248280 TTACTGAAAGCAAGCGACCA 57.752 45.000 0.00 0.00 37.60 4.02
68 69 1.795768 TACTGAAAGCAAGCGACCAG 58.204 50.000 0.00 8.33 37.60 4.00
69 70 1.510480 ACTGAAAGCAAGCGACCAGC 61.510 55.000 9.35 0.00 42.69 4.85
70 71 4.752478 TACTGAAAGCAAGCGACCAGCA 62.752 50.000 9.35 0.00 44.45 4.41
99 100 2.435234 GGCGTGTGGCGTCCATTA 60.435 61.111 1.90 0.00 44.92 1.90
103 104 0.442310 CGTGTGGCGTCCATTAACTG 59.558 55.000 1.90 0.00 35.28 3.16
106 107 2.550606 GTGTGGCGTCCATTAACTGAAA 59.449 45.455 1.90 0.00 35.28 2.69
107 108 2.811431 TGTGGCGTCCATTAACTGAAAG 59.189 45.455 1.90 0.00 35.28 2.62
108 109 1.810151 TGGCGTCCATTAACTGAAAGC 59.190 47.619 0.00 0.00 37.60 3.51
119 120 2.472695 ACTGAAAGCAAGCGGATGTA 57.527 45.000 0.00 0.00 37.60 2.29
120 121 2.778299 ACTGAAAGCAAGCGGATGTAA 58.222 42.857 0.00 0.00 37.60 2.41
168 179 3.751479 TGATCACGGCTAAGCATACAT 57.249 42.857 0.00 0.00 0.00 2.29
226 237 8.571461 TGCCAATCATATTATGAGGAGATTTC 57.429 34.615 11.77 0.00 43.53 2.17
282 294 1.739667 GCACTTCTTGCCCCGTTTT 59.260 52.632 0.00 0.00 46.63 2.43
296 308 0.727793 CGTTTTGCGGACGAAATGGG 60.728 55.000 0.00 0.00 42.82 4.00
305 317 2.824041 CGAAATGGGCCGGGAGTG 60.824 66.667 2.18 0.00 0.00 3.51
306 318 2.674754 GAAATGGGCCGGGAGTGA 59.325 61.111 2.18 0.00 0.00 3.41
307 319 1.452108 GAAATGGGCCGGGAGTGAG 60.452 63.158 2.18 0.00 0.00 3.51
308 320 2.198304 GAAATGGGCCGGGAGTGAGT 62.198 60.000 2.18 0.00 0.00 3.41
309 321 0.912487 AAATGGGCCGGGAGTGAGTA 60.912 55.000 2.18 0.00 0.00 2.59
310 322 0.912487 AATGGGCCGGGAGTGAGTAA 60.912 55.000 2.18 0.00 0.00 2.24
311 323 0.912487 ATGGGCCGGGAGTGAGTAAA 60.912 55.000 2.18 0.00 0.00 2.01
312 324 1.221021 GGGCCGGGAGTGAGTAAAG 59.779 63.158 2.18 0.00 0.00 1.85
313 325 1.221021 GGCCGGGAGTGAGTAAAGG 59.779 63.158 2.18 0.00 0.00 3.11
314 326 1.262640 GGCCGGGAGTGAGTAAAGGA 61.263 60.000 2.18 0.00 0.00 3.36
315 327 0.175989 GCCGGGAGTGAGTAAAGGAG 59.824 60.000 2.18 0.00 0.00 3.69
316 328 0.175989 CCGGGAGTGAGTAAAGGAGC 59.824 60.000 0.00 0.00 0.00 4.70
317 329 0.895530 CGGGAGTGAGTAAAGGAGCA 59.104 55.000 0.00 0.00 0.00 4.26
318 330 1.275291 CGGGAGTGAGTAAAGGAGCAA 59.725 52.381 0.00 0.00 0.00 3.91
319 331 2.093447 CGGGAGTGAGTAAAGGAGCAAT 60.093 50.000 0.00 0.00 0.00 3.56
320 332 3.274288 GGGAGTGAGTAAAGGAGCAATG 58.726 50.000 0.00 0.00 0.00 2.82
321 333 2.680339 GGAGTGAGTAAAGGAGCAATGC 59.320 50.000 0.00 0.00 0.00 3.56
322 334 3.604582 GAGTGAGTAAAGGAGCAATGCT 58.395 45.455 7.79 7.79 43.88 3.79
323 335 4.383118 GGAGTGAGTAAAGGAGCAATGCTA 60.383 45.833 8.12 0.00 39.88 3.49
324 336 4.508662 AGTGAGTAAAGGAGCAATGCTAC 58.491 43.478 9.97 9.97 39.88 3.58
325 337 4.020218 AGTGAGTAAAGGAGCAATGCTACA 60.020 41.667 20.85 0.00 42.99 2.74
326 338 4.878397 GTGAGTAAAGGAGCAATGCTACAT 59.122 41.667 20.85 4.43 42.99 2.29
327 339 5.007136 GTGAGTAAAGGAGCAATGCTACATC 59.993 44.000 20.85 9.53 42.99 3.06
328 340 5.104776 TGAGTAAAGGAGCAATGCTACATCT 60.105 40.000 20.85 11.27 42.99 2.90
329 341 6.098266 TGAGTAAAGGAGCAATGCTACATCTA 59.902 38.462 20.85 4.72 42.99 1.98
330 342 6.284459 AGTAAAGGAGCAATGCTACATCTAC 58.716 40.000 20.85 15.98 42.99 2.59
331 343 5.365021 AAAGGAGCAATGCTACATCTACT 57.635 39.130 20.85 0.00 42.99 2.57
332 344 6.485830 AAAGGAGCAATGCTACATCTACTA 57.514 37.500 20.85 0.00 42.99 1.82
333 345 6.485830 AAGGAGCAATGCTACATCTACTAA 57.514 37.500 20.85 0.00 42.99 2.24
334 346 6.485830 AGGAGCAATGCTACATCTACTAAA 57.514 37.500 20.85 0.00 42.99 1.85
335 347 6.284459 AGGAGCAATGCTACATCTACTAAAC 58.716 40.000 20.85 0.00 42.99 2.01
336 348 5.467063 GGAGCAATGCTACATCTACTAAACC 59.533 44.000 13.46 0.00 39.71 3.27
337 349 6.240549 AGCAATGCTACATCTACTAAACCT 57.759 37.500 5.69 0.00 36.99 3.50
338 350 6.653989 AGCAATGCTACATCTACTAAACCTT 58.346 36.000 5.69 0.00 36.99 3.50
339 351 7.792032 AGCAATGCTACATCTACTAAACCTTA 58.208 34.615 5.69 0.00 36.99 2.69
340 352 7.711339 AGCAATGCTACATCTACTAAACCTTAC 59.289 37.037 5.69 0.00 36.99 2.34
341 353 7.306632 GCAATGCTACATCTACTAAACCTTACG 60.307 40.741 0.00 0.00 0.00 3.18
342 354 6.764308 TGCTACATCTACTAAACCTTACGT 57.236 37.500 0.00 0.00 0.00 3.57
343 355 7.864108 TGCTACATCTACTAAACCTTACGTA 57.136 36.000 0.00 0.00 0.00 3.57
344 356 8.279970 TGCTACATCTACTAAACCTTACGTAA 57.720 34.615 7.94 7.94 0.00 3.18
356 368 4.102035 CCTTACGTAAGGCTTCGTAACT 57.898 45.455 34.93 10.62 45.56 2.24
357 369 4.488879 CCTTACGTAAGGCTTCGTAACTT 58.511 43.478 34.93 10.02 45.56 2.66
358 370 4.925646 CCTTACGTAAGGCTTCGTAACTTT 59.074 41.667 34.93 9.88 45.56 2.66
359 371 5.164022 CCTTACGTAAGGCTTCGTAACTTTG 60.164 44.000 34.93 19.97 45.56 2.77
360 372 3.721035 ACGTAAGGCTTCGTAACTTTGT 58.279 40.909 18.50 0.00 46.39 2.83
361 373 4.122046 ACGTAAGGCTTCGTAACTTTGTT 58.878 39.130 18.50 0.00 46.39 2.83
362 374 4.209911 ACGTAAGGCTTCGTAACTTTGTTC 59.790 41.667 18.50 0.00 46.39 3.18
363 375 3.872560 AAGGCTTCGTAACTTTGTTCG 57.127 42.857 0.00 0.00 0.00 3.95
364 376 2.830104 AGGCTTCGTAACTTTGTTCGT 58.170 42.857 0.00 0.00 0.00 3.85
365 377 3.981211 AGGCTTCGTAACTTTGTTCGTA 58.019 40.909 0.00 0.00 0.00 3.43
366 378 3.985925 AGGCTTCGTAACTTTGTTCGTAG 59.014 43.478 0.00 0.00 0.00 3.51
367 379 3.983344 GGCTTCGTAACTTTGTTCGTAGA 59.017 43.478 0.00 0.00 0.00 2.59
368 380 4.624452 GGCTTCGTAACTTTGTTCGTAGAT 59.376 41.667 0.00 0.00 35.04 1.98
369 381 5.444218 GGCTTCGTAACTTTGTTCGTAGATG 60.444 44.000 0.00 0.00 35.04 2.90
370 382 5.118203 GCTTCGTAACTTTGTTCGTAGATGT 59.882 40.000 0.00 0.00 35.04 3.06
371 383 6.306356 GCTTCGTAACTTTGTTCGTAGATGTA 59.694 38.462 0.00 0.00 35.04 2.29
372 384 7.461156 GCTTCGTAACTTTGTTCGTAGATGTAG 60.461 40.741 0.00 0.00 35.04 2.74
373 385 6.902341 TCGTAACTTTGTTCGTAGATGTAGT 58.098 36.000 0.00 0.00 35.04 2.73
374 386 8.028540 TCGTAACTTTGTTCGTAGATGTAGTA 57.971 34.615 0.00 0.00 35.04 1.82
375 387 8.668353 TCGTAACTTTGTTCGTAGATGTAGTAT 58.332 33.333 0.00 0.00 35.04 2.12
376 388 9.282247 CGTAACTTTGTTCGTAGATGTAGTATT 57.718 33.333 0.00 0.00 35.04 1.89
383 395 9.524106 TTGTTCGTAGATGTAGTATTATTGGTG 57.476 33.333 0.00 0.00 35.04 4.17
384 396 8.905850 TGTTCGTAGATGTAGTATTATTGGTGA 58.094 33.333 0.00 0.00 35.04 4.02
385 397 9.395707 GTTCGTAGATGTAGTATTATTGGTGAG 57.604 37.037 0.00 0.00 35.04 3.51
386 398 8.687292 TCGTAGATGTAGTATTATTGGTGAGT 57.313 34.615 0.00 0.00 0.00 3.41
387 399 9.783081 TCGTAGATGTAGTATTATTGGTGAGTA 57.217 33.333 0.00 0.00 0.00 2.59
418 431 1.872197 TTTTGCTGCGCGGGCTAAAT 61.872 50.000 25.62 0.00 40.82 1.40
420 433 1.711060 TTGCTGCGCGGGCTAAATAC 61.711 55.000 25.62 8.71 40.82 1.89
422 435 2.586635 TGCGCGGGCTAAATACGG 60.587 61.111 25.62 0.00 40.82 4.02
424 437 2.107546 CGCGGGCTAAATACGGGT 59.892 61.111 0.00 0.00 36.08 5.28
425 438 1.522130 CGCGGGCTAAATACGGGTT 60.522 57.895 0.00 0.00 36.08 4.11
454 469 1.529010 CCAACTGCTGAAGCCACCA 60.529 57.895 0.00 0.00 41.18 4.17
471 486 0.976641 CCACCTGCAGGAGTTACTGA 59.023 55.000 39.19 0.00 40.97 3.41
474 489 3.476552 CACCTGCAGGAGTTACTGAAAA 58.523 45.455 39.19 0.00 40.97 2.29
524 545 0.179210 GACGACAGAGACGAGTGAGC 60.179 60.000 0.00 0.00 34.70 4.26
525 546 0.885150 ACGACAGAGACGAGTGAGCA 60.885 55.000 0.00 0.00 34.70 4.26
531 552 1.950098 GAGACGAGTGAGCAAAGCGC 61.950 60.000 0.00 0.00 42.91 5.92
532 553 2.280119 ACGAGTGAGCAAAGCGCA 60.280 55.556 11.47 0.00 46.13 6.09
548 569 2.354188 CACACGACGCACGAGGAA 60.354 61.111 9.43 0.00 45.77 3.36
581 602 3.274586 CCGTGCGATGATGGGCTG 61.275 66.667 0.00 0.00 0.00 4.85
582 603 2.512286 CGTGCGATGATGGGCTGT 60.512 61.111 0.00 0.00 0.00 4.40
583 604 2.816360 CGTGCGATGATGGGCTGTG 61.816 63.158 0.00 0.00 0.00 3.66
584 605 2.124612 TGCGATGATGGGCTGTGG 60.125 61.111 0.00 0.00 0.00 4.17
585 606 2.124570 GCGATGATGGGCTGTGGT 60.125 61.111 0.00 0.00 0.00 4.16
586 607 2.182842 GCGATGATGGGCTGTGGTC 61.183 63.158 0.00 0.00 0.00 4.02
587 608 1.524002 CGATGATGGGCTGTGGTCT 59.476 57.895 0.00 0.00 0.00 3.85
588 609 0.812811 CGATGATGGGCTGTGGTCTG 60.813 60.000 0.00 0.00 0.00 3.51
609 630 2.686470 CCTCTGGGCTCTCTGGCA 60.686 66.667 0.00 0.00 43.83 4.92
610 631 2.733669 CCTCTGGGCTCTCTGGCAG 61.734 68.421 8.58 8.58 43.83 4.85
649 670 3.142174 GGGTCAGGTCAGAAGAACAAAG 58.858 50.000 0.00 0.00 32.39 2.77
671 695 2.844966 AGAGGAGCTAGGGGGTAAAAAC 59.155 50.000 0.00 0.00 0.00 2.43
689 719 7.112984 GGTAAAAACACAAAGAAATAGAGCGTG 59.887 37.037 0.00 0.00 0.00 5.34
690 720 5.751243 AAACACAAAGAAATAGAGCGTGT 57.249 34.783 0.00 0.00 37.71 4.49
693 723 3.745975 CACAAAGAAATAGAGCGTGTCCA 59.254 43.478 0.00 0.00 0.00 4.02
746 776 2.437651 TGAACCAGTGACCTCATGTGAA 59.562 45.455 0.00 0.00 0.00 3.18
954 1009 4.118410 CTCAGCTTCTCTCGTTGCATTAT 58.882 43.478 0.00 0.00 0.00 1.28
963 1018 1.921887 TCGTTGCATTATTCGACGGAC 59.078 47.619 4.95 0.00 40.65 4.79
1008 1063 4.156739 GCAAGGAAGTGAGAAATGGTTAGG 59.843 45.833 0.00 0.00 0.00 2.69
1059 1120 3.933332 AGTTATTTTCTCTACGTGGCTGC 59.067 43.478 0.00 0.00 0.00 5.25
1072 1136 3.790437 GCTGCAGCTAGCCAGGGA 61.790 66.667 31.33 7.67 44.83 4.20
1096 1160 5.593968 TCAGTTTCGTCTTGCTTTGTACTA 58.406 37.500 0.00 0.00 0.00 1.82
1097 1161 5.461078 TCAGTTTCGTCTTGCTTTGTACTAC 59.539 40.000 0.00 0.00 0.00 2.73
1098 1162 5.462398 CAGTTTCGTCTTGCTTTGTACTACT 59.538 40.000 0.00 0.00 0.00 2.57
1099 1163 5.690857 AGTTTCGTCTTGCTTTGTACTACTC 59.309 40.000 0.00 0.00 0.00 2.59
1100 1164 5.449107 TTCGTCTTGCTTTGTACTACTCT 57.551 39.130 0.00 0.00 0.00 3.24
1101 1165 5.044428 TCGTCTTGCTTTGTACTACTCTC 57.956 43.478 0.00 0.00 0.00 3.20
1102 1166 4.760715 TCGTCTTGCTTTGTACTACTCTCT 59.239 41.667 0.00 0.00 0.00 3.10
1103 1167 4.854291 CGTCTTGCTTTGTACTACTCTCTG 59.146 45.833 0.00 0.00 0.00 3.35
1104 1168 5.334957 CGTCTTGCTTTGTACTACTCTCTGA 60.335 44.000 0.00 0.00 0.00 3.27
1105 1169 6.090129 GTCTTGCTTTGTACTACTCTCTGAG 58.910 44.000 0.00 0.00 35.52 3.35
1106 1170 5.770663 TCTTGCTTTGTACTACTCTCTGAGT 59.229 40.000 4.32 5.53 45.54 3.41
1109 1173 5.770663 TGCTTTGTACTACTCTCTGAGTCTT 59.229 40.000 4.32 0.00 42.40 3.01
1130 1195 7.768120 AGTCTTTGTTAGATAAGAATCTGCTGG 59.232 37.037 0.00 0.00 42.60 4.85
1185 1255 1.153997 GTCTGCGAACGAGGGAGAC 60.154 63.158 9.83 9.83 43.86 3.36
1317 1387 3.056328 GCGGTGAAGGGCAAGTCC 61.056 66.667 0.00 0.00 0.00 3.85
1398 1469 2.731451 GCGAAAAACAGCAAGGATTTCC 59.269 45.455 0.00 0.00 0.00 3.13
1439 1512 1.142748 CTGCTGATCACCGTCTCCC 59.857 63.158 0.00 0.00 0.00 4.30
1467 1554 4.733972 AGAAAAGCTAGCAGAACGAAAC 57.266 40.909 18.83 0.00 0.00 2.78
1468 1555 3.184581 AGAAAAGCTAGCAGAACGAAACG 59.815 43.478 18.83 0.00 0.00 3.60
1472 1559 3.128349 AGCTAGCAGAACGAAACGAAAA 58.872 40.909 18.83 0.00 0.00 2.29
1473 1560 3.184581 AGCTAGCAGAACGAAACGAAAAG 59.815 43.478 18.83 0.00 0.00 2.27
1475 1562 3.587403 AGCAGAACGAAACGAAAAGAC 57.413 42.857 0.00 0.00 0.00 3.01
1542 1667 2.617308 TGATACGTAGGAGTAGTGCAGC 59.383 50.000 0.08 0.00 0.00 5.25
1544 1669 1.064296 CGTAGGAGTAGTGCAGCGG 59.936 63.158 0.00 0.00 0.00 5.52
1545 1670 1.227002 GTAGGAGTAGTGCAGCGGC 60.227 63.158 0.31 0.31 41.68 6.53
1555 1680 3.578456 GCAGCGGCACATACTTGT 58.422 55.556 3.18 0.00 40.72 3.16
1607 1732 0.031178 CGTTTTGCCTCAAAGCAGCT 59.969 50.000 0.00 0.00 45.13 4.24
1736 1862 2.292267 CGAATGCTAATTCAGGGCAGT 58.708 47.619 0.00 0.00 42.08 4.40
1985 2151 6.400579 TTCGTTTTCGTTGTACAGTTTACA 57.599 33.333 0.00 0.00 44.46 2.41
2002 2168 5.416326 AGTTTACACTTTTGTTGGCACTGTA 59.584 36.000 0.00 0.00 37.15 2.74
2011 2177 0.107116 TTGGCACTGTACCGGTTTGT 60.107 50.000 15.04 6.71 0.00 2.83
2015 2181 1.658994 CACTGTACCGGTTTGTGTGT 58.341 50.000 15.04 0.59 0.00 3.72
2016 2182 2.823984 CACTGTACCGGTTTGTGTGTA 58.176 47.619 15.04 0.00 0.00 2.90
2036 2202 3.672447 TCGTCGCGTGGTTAGCCA 61.672 61.111 5.77 0.00 43.73 4.75
2062 2228 8.295569 GCCATTAGCATTTAGTAGTGTAGTAC 57.704 38.462 0.00 0.00 42.97 2.73
2063 2229 7.384387 GCCATTAGCATTTAGTAGTGTAGTACC 59.616 40.741 0.00 0.00 42.97 3.34
2064 2230 7.594015 CCATTAGCATTTAGTAGTGTAGTACCG 59.406 40.741 0.00 0.00 0.00 4.02
2065 2231 7.864108 TTAGCATTTAGTAGTGTAGTACCGA 57.136 36.000 0.00 0.00 0.00 4.69
2066 2232 6.129053 AGCATTTAGTAGTGTAGTACCGAC 57.871 41.667 0.00 0.00 0.00 4.79
2067 2233 5.884792 AGCATTTAGTAGTGTAGTACCGACT 59.115 40.000 0.00 4.22 39.92 4.18
2068 2234 5.970023 GCATTTAGTAGTGTAGTACCGACTG 59.030 44.000 11.87 2.22 36.28 3.51
2069 2235 6.183360 GCATTTAGTAGTGTAGTACCGACTGA 60.183 42.308 11.87 4.60 36.28 3.41
2070 2236 7.468357 GCATTTAGTAGTGTAGTACCGACTGAT 60.468 40.741 11.87 6.16 36.28 2.90
2073 2239 5.494724 AGTAGTGTAGTACCGACTGATGAA 58.505 41.667 0.00 0.00 36.28 2.57
2074 2240 6.120905 AGTAGTGTAGTACCGACTGATGAAT 58.879 40.000 0.00 0.00 36.28 2.57
2075 2241 5.250235 AGTGTAGTACCGACTGATGAATG 57.750 43.478 0.00 0.00 36.28 2.67
2076 2242 4.948004 AGTGTAGTACCGACTGATGAATGA 59.052 41.667 0.00 0.00 36.28 2.57
2077 2243 5.417894 AGTGTAGTACCGACTGATGAATGAA 59.582 40.000 0.00 0.00 36.28 2.57
2078 2244 5.515626 GTGTAGTACCGACTGATGAATGAAC 59.484 44.000 0.00 0.00 36.28 3.18
2080 2246 2.010145 ACCGACTGATGAATGAACCG 57.990 50.000 0.00 0.00 0.00 4.44
2081 2247 1.548719 ACCGACTGATGAATGAACCGA 59.451 47.619 0.00 0.00 0.00 4.69
2082 2248 1.927174 CCGACTGATGAATGAACCGAC 59.073 52.381 0.00 0.00 0.00 4.79
2083 2249 1.927174 CGACTGATGAATGAACCGACC 59.073 52.381 0.00 0.00 0.00 4.79
2085 2251 1.909302 ACTGATGAATGAACCGACCCT 59.091 47.619 0.00 0.00 0.00 4.34
2086 2252 2.305927 ACTGATGAATGAACCGACCCTT 59.694 45.455 0.00 0.00 0.00 3.95
2087 2253 2.679837 CTGATGAATGAACCGACCCTTG 59.320 50.000 0.00 0.00 0.00 3.61
2088 2254 1.401905 GATGAATGAACCGACCCTTGC 59.598 52.381 0.00 0.00 0.00 4.01
2089 2255 0.608035 TGAATGAACCGACCCTTGCC 60.608 55.000 0.00 0.00 0.00 4.52
2097 2263 3.948719 GACCCTTGCCGGTGGTCA 61.949 66.667 21.85 2.96 46.29 4.02
2098 2264 3.256960 ACCCTTGCCGGTGGTCAT 61.257 61.111 1.90 0.00 33.77 3.06
2099 2265 2.751436 CCCTTGCCGGTGGTCATG 60.751 66.667 1.90 0.00 0.00 3.07
2100 2266 3.443045 CCTTGCCGGTGGTCATGC 61.443 66.667 1.90 0.00 0.00 4.06
2103 2269 1.996786 CTTGCCGGTGGTCATGCATC 61.997 60.000 1.90 0.00 33.08 3.91
2105 2271 1.146041 GCCGGTGGTCATGCATCTA 59.854 57.895 1.90 0.00 0.00 1.98
2250 2426 1.151777 ACAACGTGAGCAAGTGGACG 61.152 55.000 0.00 0.00 37.82 4.79
2340 2516 3.851955 GCCATCTTCCAGGCCATG 58.148 61.111 5.01 0.00 45.18 3.66
2360 2557 0.524862 TTCGTCCTCGTAAGCACTCC 59.475 55.000 0.00 0.00 38.33 3.85
2361 2558 0.322277 TCGTCCTCGTAAGCACTCCT 60.322 55.000 0.00 0.00 38.33 3.69
2362 2559 1.065926 TCGTCCTCGTAAGCACTCCTA 60.066 52.381 0.00 0.00 38.33 2.94
2363 2560 1.063764 CGTCCTCGTAAGCACTCCTAC 59.936 57.143 0.00 0.00 37.18 3.18
2364 2561 1.404748 GTCCTCGTAAGCACTCCTACC 59.595 57.143 0.00 0.00 37.18 3.18
2365 2562 0.745468 CCTCGTAAGCACTCCTACCC 59.255 60.000 0.00 0.00 37.18 3.69
2366 2563 1.471119 CTCGTAAGCACTCCTACCCA 58.529 55.000 0.00 0.00 37.18 4.51
2367 2564 1.822990 CTCGTAAGCACTCCTACCCAA 59.177 52.381 0.00 0.00 37.18 4.12
2368 2565 1.547372 TCGTAAGCACTCCTACCCAAC 59.453 52.381 0.00 0.00 37.18 3.77
2369 2566 1.405121 CGTAAGCACTCCTACCCAACC 60.405 57.143 0.00 0.00 0.00 3.77
2370 2567 1.907255 GTAAGCACTCCTACCCAACCT 59.093 52.381 0.00 0.00 0.00 3.50
2371 2568 0.984995 AAGCACTCCTACCCAACCTC 59.015 55.000 0.00 0.00 0.00 3.85
2372 2569 0.117340 AGCACTCCTACCCAACCTCT 59.883 55.000 0.00 0.00 0.00 3.69
2373 2570 0.250513 GCACTCCTACCCAACCTCTG 59.749 60.000 0.00 0.00 0.00 3.35
2374 2571 1.645710 CACTCCTACCCAACCTCTGT 58.354 55.000 0.00 0.00 0.00 3.41
2375 2572 2.816411 CACTCCTACCCAACCTCTGTA 58.184 52.381 0.00 0.00 0.00 2.74
2376 2573 2.761208 CACTCCTACCCAACCTCTGTAG 59.239 54.545 0.00 0.00 33.38 2.74
2394 2591 8.148999 CCTCTGTAGGTTTTTCTAGTTTGTACT 58.851 37.037 0.00 0.00 38.19 2.73
2395 2592 8.882415 TCTGTAGGTTTTTCTAGTTTGTACTG 57.118 34.615 0.00 0.00 35.78 2.74
2397 2594 8.428186 TGTAGGTTTTTCTAGTTTGTACTGTG 57.572 34.615 0.00 0.00 35.78 3.66
2401 2598 7.395206 AGGTTTTTCTAGTTTGTACTGTGGTTT 59.605 33.333 0.00 0.00 35.78 3.27
2403 2600 8.856247 GTTTTTCTAGTTTGTACTGTGGTTTTG 58.144 33.333 0.00 0.00 35.78 2.44
2404 2601 7.690952 TTTCTAGTTTGTACTGTGGTTTTGT 57.309 32.000 0.00 0.00 35.78 2.83
2451 2651 2.436646 GGTGCACATCAGGGACGG 60.437 66.667 20.43 0.00 0.00 4.79
2452 2652 2.436646 GTGCACATCAGGGACGGG 60.437 66.667 13.17 0.00 0.00 5.28
2703 2904 2.275380 GCCCAACATCGCCACCTTT 61.275 57.895 0.00 0.00 0.00 3.11
2835 3036 0.339859 TCAGCTACCTCCAGGACCAT 59.660 55.000 0.00 0.00 38.94 3.55
2841 3042 1.383799 CCTCCAGGACCATGGCAAA 59.616 57.895 13.04 0.00 40.41 3.68
2856 3057 0.966179 GCAAATGGGTTCTCGGGTTT 59.034 50.000 0.00 0.00 0.00 3.27
3042 3249 2.403987 CTGTACGAGGGCGACGAG 59.596 66.667 0.00 0.00 41.64 4.18
3078 3285 1.141657 TCAAGGAAGCTTCTGCACACT 59.858 47.619 25.05 10.34 42.74 3.55
3128 3335 0.105964 CTCACCACCGAAGACACCAA 59.894 55.000 0.00 0.00 0.00 3.67
3378 3747 2.125106 GACATCCTCACCGTGGCC 60.125 66.667 0.00 0.00 0.00 5.36
3849 4224 0.106469 TCCTGCTCGCCATACTCTCT 60.106 55.000 0.00 0.00 0.00 3.10
3939 4314 1.744368 CGACGACGAGGAGGAAGGA 60.744 63.158 0.00 0.00 42.66 3.36
4240 4628 1.137513 GTGACGCTGTAACTGACCAC 58.862 55.000 0.00 0.00 0.00 4.16
4241 4629 1.037493 TGACGCTGTAACTGACCACT 58.963 50.000 0.00 0.00 0.00 4.00
4242 4630 2.030540 GTGACGCTGTAACTGACCACTA 60.031 50.000 0.00 0.00 0.00 2.74
4254 4642 4.806330 ACTGACCACTACTTATGTTCACG 58.194 43.478 0.00 0.00 0.00 4.35
4287 4675 6.436218 TGACTAGTCTGCTACCACTTCATTTA 59.564 38.462 23.01 0.00 0.00 1.40
4305 4699 4.508461 TTTATATGCATGCATGGACAGC 57.492 40.909 37.43 13.57 37.82 4.40
4403 4831 2.964438 GATGATACCCCGCGCGTTGA 62.964 60.000 29.95 11.32 0.00 3.18
4404 4832 3.259751 GATACCCCGCGCGTTGAC 61.260 66.667 29.95 10.87 0.00 3.18
4487 7380 8.958119 TGAATATACTTGTTAACCAGTCATCC 57.042 34.615 15.09 0.67 0.00 3.51
4489 7382 9.561069 GAATATACTTGTTAACCAGTCATCCAT 57.439 33.333 15.09 6.47 0.00 3.41
4490 7383 9.561069 AATATACTTGTTAACCAGTCATCCATC 57.439 33.333 15.09 0.00 0.00 3.51
4492 7385 6.620877 ACTTGTTAACCAGTCATCCATCTA 57.379 37.500 6.52 0.00 0.00 1.98
4836 8028 6.366340 AGAAGATTTGCATGATGGAGAGAAT 58.634 36.000 0.00 0.00 0.00 2.40
4871 9138 8.768397 ACCAGTTCAGGTTGTATCATAATTCTA 58.232 33.333 0.00 0.00 39.34 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.610038 TGCTTGCTCCTGAATTGTGTG 59.390 47.619 0.00 0.00 0.00 3.82
1 2 1.985473 TGCTTGCTCCTGAATTGTGT 58.015 45.000 0.00 0.00 0.00 3.72
2 3 2.608752 GGTTGCTTGCTCCTGAATTGTG 60.609 50.000 0.00 0.00 0.00 3.33
3 4 1.615392 GGTTGCTTGCTCCTGAATTGT 59.385 47.619 0.00 0.00 0.00 2.71
4 5 1.614903 TGGTTGCTTGCTCCTGAATTG 59.385 47.619 0.00 0.00 0.00 2.32
5 6 1.891150 CTGGTTGCTTGCTCCTGAATT 59.109 47.619 8.26 0.00 0.00 2.17
6 7 1.542492 CTGGTTGCTTGCTCCTGAAT 58.458 50.000 8.26 0.00 0.00 2.57
7 8 1.174712 GCTGGTTGCTTGCTCCTGAA 61.175 55.000 13.99 0.00 38.95 3.02
8 9 1.601759 GCTGGTTGCTTGCTCCTGA 60.602 57.895 13.99 0.00 38.95 3.86
9 10 1.900016 TGCTGGTTGCTTGCTCCTG 60.900 57.895 8.26 8.50 43.37 3.86
10 11 1.900498 GTGCTGGTTGCTTGCTCCT 60.900 57.895 8.26 0.00 43.37 3.69
11 12 2.647297 GTGCTGGTTGCTTGCTCC 59.353 61.111 0.00 0.00 43.37 4.70
85 86 1.803334 TCAGTTAATGGACGCCACAC 58.197 50.000 0.50 0.00 35.80 3.82
86 87 2.552599 TTCAGTTAATGGACGCCACA 57.447 45.000 0.50 0.00 35.80 4.17
87 88 2.414161 GCTTTCAGTTAATGGACGCCAC 60.414 50.000 0.50 0.00 35.80 5.01
99 100 1.609208 ACATCCGCTTGCTTTCAGTT 58.391 45.000 0.00 0.00 0.00 3.16
103 104 3.853671 CACATTTACATCCGCTTGCTTTC 59.146 43.478 0.00 0.00 0.00 2.62
106 107 2.710377 TCACATTTACATCCGCTTGCT 58.290 42.857 0.00 0.00 0.00 3.91
107 108 3.698029 ATCACATTTACATCCGCTTGC 57.302 42.857 0.00 0.00 0.00 4.01
108 109 6.117911 TGTAATCACATTTACATCCGCTTG 57.882 37.500 0.00 0.00 37.20 4.01
226 237 3.359950 CCCAATCTTTCCCTTTCTCTGG 58.640 50.000 0.00 0.00 0.00 3.86
296 308 0.175989 CTCCTTTACTCACTCCCGGC 59.824 60.000 0.00 0.00 0.00 6.13
305 317 5.363939 AGATGTAGCATTGCTCCTTTACTC 58.636 41.667 15.81 7.04 40.44 2.59
306 318 5.365021 AGATGTAGCATTGCTCCTTTACT 57.635 39.130 15.81 5.89 40.44 2.24
307 319 6.284459 AGTAGATGTAGCATTGCTCCTTTAC 58.716 40.000 15.81 7.99 40.44 2.01
308 320 6.485830 AGTAGATGTAGCATTGCTCCTTTA 57.514 37.500 15.81 0.00 40.44 1.85
309 321 5.365021 AGTAGATGTAGCATTGCTCCTTT 57.635 39.130 15.81 0.00 40.44 3.11
310 322 6.485830 TTAGTAGATGTAGCATTGCTCCTT 57.514 37.500 15.81 1.32 40.44 3.36
311 323 6.284459 GTTTAGTAGATGTAGCATTGCTCCT 58.716 40.000 15.81 10.59 40.44 3.69
312 324 5.467063 GGTTTAGTAGATGTAGCATTGCTCC 59.533 44.000 15.81 3.99 40.44 4.70
313 325 6.284459 AGGTTTAGTAGATGTAGCATTGCTC 58.716 40.000 15.81 7.72 40.44 4.26
314 326 6.240549 AGGTTTAGTAGATGTAGCATTGCT 57.759 37.500 16.63 16.63 43.41 3.91
315 327 6.927294 AAGGTTTAGTAGATGTAGCATTGC 57.073 37.500 0.00 0.00 0.00 3.56
316 328 7.705325 ACGTAAGGTTTAGTAGATGTAGCATTG 59.295 37.037 0.00 0.00 46.39 2.82
317 329 7.779073 ACGTAAGGTTTAGTAGATGTAGCATT 58.221 34.615 0.00 0.00 46.39 3.56
318 330 7.344095 ACGTAAGGTTTAGTAGATGTAGCAT 57.656 36.000 0.00 0.00 46.39 3.79
319 331 6.764308 ACGTAAGGTTTAGTAGATGTAGCA 57.236 37.500 0.00 0.00 46.39 3.49
320 332 7.859875 CCTTACGTAAGGTTTAGTAGATGTAGC 59.140 40.741 36.16 0.00 46.11 3.58
338 350 4.870363 ACAAAGTTACGAAGCCTTACGTA 58.130 39.130 0.00 0.00 42.61 3.57
339 351 3.721035 ACAAAGTTACGAAGCCTTACGT 58.279 40.909 0.00 0.00 44.72 3.57
340 352 4.662394 CGAACAAAGTTACGAAGCCTTACG 60.662 45.833 0.00 0.00 0.00 3.18
341 353 4.209911 ACGAACAAAGTTACGAAGCCTTAC 59.790 41.667 0.00 0.00 0.00 2.34
342 354 4.370917 ACGAACAAAGTTACGAAGCCTTA 58.629 39.130 0.00 0.00 0.00 2.69
343 355 3.200483 ACGAACAAAGTTACGAAGCCTT 58.800 40.909 0.00 0.00 0.00 4.35
344 356 2.830104 ACGAACAAAGTTACGAAGCCT 58.170 42.857 0.00 0.00 0.00 4.58
345 357 3.983344 TCTACGAACAAAGTTACGAAGCC 59.017 43.478 0.00 0.00 0.00 4.35
346 358 5.118203 ACATCTACGAACAAAGTTACGAAGC 59.882 40.000 0.00 0.00 0.00 3.86
347 359 6.686130 ACATCTACGAACAAAGTTACGAAG 57.314 37.500 0.00 0.00 0.00 3.79
348 360 7.362662 ACTACATCTACGAACAAAGTTACGAA 58.637 34.615 0.00 0.00 0.00 3.85
349 361 6.902341 ACTACATCTACGAACAAAGTTACGA 58.098 36.000 0.00 0.00 0.00 3.43
350 362 8.832487 ATACTACATCTACGAACAAAGTTACG 57.168 34.615 0.00 0.00 0.00 3.18
357 369 9.524106 CACCAATAATACTACATCTACGAACAA 57.476 33.333 0.00 0.00 0.00 2.83
358 370 8.905850 TCACCAATAATACTACATCTACGAACA 58.094 33.333 0.00 0.00 0.00 3.18
359 371 9.395707 CTCACCAATAATACTACATCTACGAAC 57.604 37.037 0.00 0.00 0.00 3.95
360 372 9.128404 ACTCACCAATAATACTACATCTACGAA 57.872 33.333 0.00 0.00 0.00 3.85
361 373 8.687292 ACTCACCAATAATACTACATCTACGA 57.313 34.615 0.00 0.00 0.00 3.43
383 395 5.626955 GCAGCAAAAGTGAGTGATTTTACTC 59.373 40.000 0.00 0.00 45.71 2.59
384 396 5.523369 GCAGCAAAAGTGAGTGATTTTACT 58.477 37.500 0.00 0.00 0.00 2.24
385 397 4.379793 CGCAGCAAAAGTGAGTGATTTTAC 59.620 41.667 0.00 0.00 0.00 2.01
386 398 4.536065 CGCAGCAAAAGTGAGTGATTTTA 58.464 39.130 0.00 0.00 0.00 1.52
387 399 3.374745 CGCAGCAAAAGTGAGTGATTTT 58.625 40.909 0.00 0.00 0.00 1.82
388 400 3.004024 CGCAGCAAAAGTGAGTGATTT 57.996 42.857 0.00 0.00 0.00 2.17
418 431 1.203112 TGGTGGTACCAGTAACCCGTA 60.203 52.381 16.93 0.00 44.79 4.02
420 433 2.364353 TGGTGGTACCAGTAACCCG 58.636 57.895 16.93 0.00 44.79 5.28
454 469 3.118038 TGTTTTCAGTAACTCCTGCAGGT 60.118 43.478 31.58 16.00 36.34 4.00
471 486 3.066621 TGAAATTCAGCACGCTCTGTTTT 59.933 39.130 0.00 6.28 35.63 2.43
474 489 1.882912 TGAAATTCAGCACGCTCTGT 58.117 45.000 0.00 0.00 35.63 3.41
531 552 2.354188 TTCCTCGTGCGTCGTGTG 60.354 61.111 0.00 0.00 40.80 3.82
532 553 2.354305 GTTCCTCGTGCGTCGTGT 60.354 61.111 0.00 0.00 40.80 4.49
535 556 2.870161 CTCGTTCCTCGTGCGTCG 60.870 66.667 0.00 0.00 40.80 5.12
581 602 2.348998 CCAGAGGCCACAGACCAC 59.651 66.667 5.01 0.00 0.00 4.16
582 603 2.930019 CCCAGAGGCCACAGACCA 60.930 66.667 5.01 0.00 0.00 4.02
604 625 4.031129 AGCCAGCCAGACTGCCAG 62.031 66.667 0.00 0.00 45.78 4.85
605 626 4.340246 CAGCCAGCCAGACTGCCA 62.340 66.667 0.00 0.00 45.78 4.92
607 628 3.972971 CTCCAGCCAGCCAGACTGC 62.973 68.421 0.00 0.00 45.78 4.40
608 629 2.268280 CTCCAGCCAGCCAGACTG 59.732 66.667 0.00 0.00 46.77 3.51
609 630 2.121385 TCTCCAGCCAGCCAGACT 59.879 61.111 0.00 0.00 0.00 3.24
610 631 2.267324 GTCTCCAGCCAGCCAGAC 59.733 66.667 0.00 0.00 0.00 3.51
649 670 2.473576 TTTACCCCCTAGCTCCTCTC 57.526 55.000 0.00 0.00 0.00 3.20
671 695 3.745975 TGGACACGCTCTATTTCTTTGTG 59.254 43.478 0.00 0.00 0.00 3.33
689 719 4.430765 ACGTCACGGCCGATGGAC 62.431 66.667 35.90 30.39 0.00 4.02
690 720 4.124351 GACGTCACGGCCGATGGA 62.124 66.667 35.90 22.73 0.00 3.41
987 1042 5.515008 GGTCCTAACCATTTCTCACTTCCTT 60.515 44.000 0.00 0.00 45.68 3.36
1008 1063 1.964933 GGTAGAGGTGGAGCATAGGTC 59.035 57.143 0.00 0.00 0.00 3.85
1059 1120 0.835941 AACTGATCCCTGGCTAGCTG 59.164 55.000 15.72 7.95 0.00 4.24
1072 1136 5.057149 AGTACAAAGCAAGACGAAACTGAT 58.943 37.500 0.00 0.00 0.00 2.90
1096 1160 8.871629 TCTTATCTAACAAAGACTCAGAGAGT 57.128 34.615 3.79 0.12 46.42 3.24
1101 1165 8.816144 GCAGATTCTTATCTAACAAAGACTCAG 58.184 37.037 0.00 0.00 39.11 3.35
1102 1166 8.535335 AGCAGATTCTTATCTAACAAAGACTCA 58.465 33.333 0.00 0.00 39.11 3.41
1103 1167 8.816144 CAGCAGATTCTTATCTAACAAAGACTC 58.184 37.037 0.00 0.00 39.11 3.36
1104 1168 7.768120 CCAGCAGATTCTTATCTAACAAAGACT 59.232 37.037 0.00 0.00 39.11 3.24
1105 1169 7.466590 GCCAGCAGATTCTTATCTAACAAAGAC 60.467 40.741 0.00 0.00 39.11 3.01
1106 1170 6.540189 GCCAGCAGATTCTTATCTAACAAAGA 59.460 38.462 0.00 0.00 39.11 2.52
1109 1173 5.744171 TGCCAGCAGATTCTTATCTAACAA 58.256 37.500 0.00 0.00 39.11 2.83
1130 1195 4.559251 CGAGACACATACTGTTAGACTTGC 59.441 45.833 0.00 0.00 31.03 4.01
1159 1229 3.782244 GTTCGCAGACTGCAGCCG 61.782 66.667 26.32 11.74 45.36 5.52
1185 1255 0.031314 CGATCACCCTCATCGTCAGG 59.969 60.000 0.00 0.00 38.67 3.86
1190 1260 0.947660 CATGGCGATCACCCTCATCG 60.948 60.000 0.00 0.00 44.94 3.84
1398 1469 5.367937 AGATAATATATGCAGCTGGTAGGGG 59.632 44.000 17.12 0.00 0.00 4.79
1439 1512 4.727507 TCTGCTAGCTTTTCTAGTGGAG 57.272 45.455 17.23 0.00 45.22 3.86
1467 1554 7.023575 CCTGGTTATCAAATCTTGTCTTTTCG 58.976 38.462 0.00 0.00 0.00 3.46
1468 1555 6.808704 GCCTGGTTATCAAATCTTGTCTTTTC 59.191 38.462 0.00 0.00 0.00 2.29
1472 1559 5.184892 AGCCTGGTTATCAAATCTTGTCT 57.815 39.130 0.00 0.00 0.00 3.41
1473 1560 5.904362 AAGCCTGGTTATCAAATCTTGTC 57.096 39.130 0.00 0.00 0.00 3.18
1475 1562 6.591448 GGAAAAAGCCTGGTTATCAAATCTTG 59.409 38.462 0.00 0.00 0.00 3.02
1546 1671 2.370519 TGCACTACCACCACAAGTATGT 59.629 45.455 0.00 0.00 41.61 2.29
1547 1672 3.052455 TGCACTACCACCACAAGTATG 57.948 47.619 0.00 0.00 0.00 2.39
1548 1673 3.072476 ACTTGCACTACCACCACAAGTAT 59.928 43.478 4.97 0.00 46.66 2.12
1549 1674 2.436542 ACTTGCACTACCACCACAAGTA 59.563 45.455 4.97 0.00 46.66 2.24
1550 1675 1.211949 ACTTGCACTACCACCACAAGT 59.788 47.619 0.00 0.00 44.47 3.16
1551 1676 1.873591 GACTTGCACTACCACCACAAG 59.126 52.381 0.00 0.00 42.63 3.16
1552 1677 1.476110 GGACTTGCACTACCACCACAA 60.476 52.381 0.00 0.00 0.00 3.33
1553 1678 0.107831 GGACTTGCACTACCACCACA 59.892 55.000 0.00 0.00 0.00 4.17
1554 1679 0.107831 TGGACTTGCACTACCACCAC 59.892 55.000 0.00 0.00 0.00 4.16
1555 1680 1.003118 GATGGACTTGCACTACCACCA 59.997 52.381 7.01 0.00 35.19 4.17
1556 1681 1.739067 GATGGACTTGCACTACCACC 58.261 55.000 7.01 0.00 35.19 4.61
1557 1682 1.067142 TCGATGGACTTGCACTACCAC 60.067 52.381 7.01 2.46 35.19 4.16
1558 1683 1.262417 TCGATGGACTTGCACTACCA 58.738 50.000 7.26 7.26 36.83 3.25
1736 1862 2.096980 CGTCTGCTGTCTCGTAATGGTA 59.903 50.000 0.00 0.00 0.00 3.25
1961 2106 6.735957 GTGTAAACTGTACAACGAAAACGAAA 59.264 34.615 0.00 0.00 0.00 3.46
1985 2151 1.673920 CGGTACAGTGCCAACAAAAGT 59.326 47.619 8.59 0.00 0.00 2.66
2002 2168 1.202557 ACGACATACACACAAACCGGT 60.203 47.619 0.00 0.00 0.00 5.28
2011 2177 1.443025 CCACGCGACGACATACACA 60.443 57.895 15.93 0.00 0.00 3.72
2015 2181 0.523968 GCTAACCACGCGACGACATA 60.524 55.000 15.93 0.00 0.00 2.29
2016 2182 1.804326 GCTAACCACGCGACGACAT 60.804 57.895 15.93 0.00 0.00 3.06
2036 2202 7.125792 ACTACACTACTAAATGCTAATGGCT 57.874 36.000 0.00 0.00 42.39 4.75
2041 2207 7.554118 AGTCGGTACTACACTACTAAATGCTAA 59.446 37.037 0.00 0.00 32.84 3.09
2042 2208 7.011763 CAGTCGGTACTACACTACTAAATGCTA 59.988 40.741 0.00 0.00 33.48 3.49
2044 2210 5.970023 CAGTCGGTACTACACTACTAAATGC 59.030 44.000 0.00 0.00 33.48 3.56
2046 2212 7.772292 TCATCAGTCGGTACTACACTACTAAAT 59.228 37.037 0.00 0.00 33.48 1.40
2047 2213 7.105588 TCATCAGTCGGTACTACACTACTAAA 58.894 38.462 0.00 0.00 33.48 1.85
2052 2218 6.117488 TCATTCATCAGTCGGTACTACACTA 58.883 40.000 0.00 0.00 33.48 2.74
2053 2219 4.948004 TCATTCATCAGTCGGTACTACACT 59.052 41.667 0.00 0.00 33.48 3.55
2054 2220 5.244785 TCATTCATCAGTCGGTACTACAC 57.755 43.478 0.00 0.00 33.48 2.90
2056 2222 5.041940 GGTTCATTCATCAGTCGGTACTAC 58.958 45.833 0.00 0.00 33.48 2.73
2057 2223 4.201980 CGGTTCATTCATCAGTCGGTACTA 60.202 45.833 0.00 0.00 33.48 1.82
2058 2224 3.428999 CGGTTCATTCATCAGTCGGTACT 60.429 47.826 0.00 0.00 35.91 2.73
2059 2225 2.858344 CGGTTCATTCATCAGTCGGTAC 59.142 50.000 0.00 0.00 0.00 3.34
2061 2227 1.548719 TCGGTTCATTCATCAGTCGGT 59.451 47.619 0.00 0.00 0.00 4.69
2062 2228 1.927174 GTCGGTTCATTCATCAGTCGG 59.073 52.381 0.00 0.00 0.00 4.79
2063 2229 1.927174 GGTCGGTTCATTCATCAGTCG 59.073 52.381 0.00 0.00 0.00 4.18
2064 2230 2.093447 AGGGTCGGTTCATTCATCAGTC 60.093 50.000 0.00 0.00 0.00 3.51
2065 2231 1.909302 AGGGTCGGTTCATTCATCAGT 59.091 47.619 0.00 0.00 0.00 3.41
2066 2232 2.679837 CAAGGGTCGGTTCATTCATCAG 59.320 50.000 0.00 0.00 0.00 2.90
2067 2233 2.710377 CAAGGGTCGGTTCATTCATCA 58.290 47.619 0.00 0.00 0.00 3.07
2068 2234 1.401905 GCAAGGGTCGGTTCATTCATC 59.598 52.381 0.00 0.00 0.00 2.92
2069 2235 1.463674 GCAAGGGTCGGTTCATTCAT 58.536 50.000 0.00 0.00 0.00 2.57
2070 2236 0.608035 GGCAAGGGTCGGTTCATTCA 60.608 55.000 0.00 0.00 0.00 2.57
2073 2239 2.046314 CGGCAAGGGTCGGTTCAT 60.046 61.111 0.00 0.00 38.79 2.57
2081 2247 3.256960 ATGACCACCGGCAAGGGT 61.257 61.111 0.00 3.98 46.96 4.34
2082 2248 2.751436 CATGACCACCGGCAAGGG 60.751 66.667 0.00 0.00 46.96 3.95
2085 2251 2.035469 ATGCATGACCACCGGCAA 59.965 55.556 0.00 0.00 40.02 4.52
2086 2252 1.621672 TAGATGCATGACCACCGGCA 61.622 55.000 2.46 0.00 41.00 5.69
2087 2253 0.463654 TTAGATGCATGACCACCGGC 60.464 55.000 2.46 0.00 0.00 6.13
2088 2254 2.260844 ATTAGATGCATGACCACCGG 57.739 50.000 2.46 0.00 0.00 5.28
2089 2255 3.627123 TCAAATTAGATGCATGACCACCG 59.373 43.478 2.46 0.00 0.00 4.94
2092 2258 7.407393 TCAAATCAAATTAGATGCATGACCA 57.593 32.000 2.46 0.00 0.00 4.02
2103 2269 9.485591 GCAAATCAAAGCATCAAATCAAATTAG 57.514 29.630 0.00 0.00 0.00 1.73
2105 2271 7.877003 TGCAAATCAAAGCATCAAATCAAATT 58.123 26.923 0.00 0.00 35.51 1.82
2118 2284 3.054878 CTGGTTCACTGCAAATCAAAGC 58.945 45.455 0.00 0.00 0.00 3.51
2119 2285 3.553508 CCCTGGTTCACTGCAAATCAAAG 60.554 47.826 0.00 0.00 0.00 2.77
2250 2426 0.249398 AGAACATGTAGACGGTGCCC 59.751 55.000 0.00 0.00 0.00 5.36
2368 2565 8.148999 AGTACAAACTAGAAAAACCTACAGAGG 58.851 37.037 0.00 0.00 40.86 3.69
2369 2566 8.979574 CAGTACAAACTAGAAAAACCTACAGAG 58.020 37.037 0.00 0.00 33.48 3.35
2370 2567 8.480501 ACAGTACAAACTAGAAAAACCTACAGA 58.519 33.333 0.00 0.00 33.48 3.41
2371 2568 8.548721 CACAGTACAAACTAGAAAAACCTACAG 58.451 37.037 0.00 0.00 33.48 2.74
2372 2569 7.496591 CCACAGTACAAACTAGAAAAACCTACA 59.503 37.037 0.00 0.00 33.48 2.74
2373 2570 7.496920 ACCACAGTACAAACTAGAAAAACCTAC 59.503 37.037 0.00 0.00 33.48 3.18
2374 2571 7.567458 ACCACAGTACAAACTAGAAAAACCTA 58.433 34.615 0.00 0.00 33.48 3.08
2375 2572 6.420638 ACCACAGTACAAACTAGAAAAACCT 58.579 36.000 0.00 0.00 33.48 3.50
2376 2573 6.688637 ACCACAGTACAAACTAGAAAAACC 57.311 37.500 0.00 0.00 33.48 3.27
2377 2574 8.856247 CAAAACCACAGTACAAACTAGAAAAAC 58.144 33.333 0.00 0.00 33.48 2.43
2378 2575 8.578151 ACAAAACCACAGTACAAACTAGAAAAA 58.422 29.630 0.00 0.00 33.48 1.94
2379 2576 8.113173 ACAAAACCACAGTACAAACTAGAAAA 57.887 30.769 0.00 0.00 33.48 2.29
2380 2577 7.690952 ACAAAACCACAGTACAAACTAGAAA 57.309 32.000 0.00 0.00 33.48 2.52
2381 2578 7.010367 CGTACAAAACCACAGTACAAACTAGAA 59.990 37.037 0.00 0.00 38.35 2.10
2382 2579 6.476380 CGTACAAAACCACAGTACAAACTAGA 59.524 38.462 0.00 0.00 38.35 2.43
2383 2580 6.642917 CGTACAAAACCACAGTACAAACTAG 58.357 40.000 0.00 0.00 38.35 2.57
2384 2581 5.006552 GCGTACAAAACCACAGTACAAACTA 59.993 40.000 0.00 0.00 38.35 2.24
2385 2582 4.201841 GCGTACAAAACCACAGTACAAACT 60.202 41.667 0.00 0.00 38.35 2.66
2386 2583 4.030366 GCGTACAAAACCACAGTACAAAC 58.970 43.478 0.00 0.00 38.35 2.93
2394 2591 1.222766 ATCGCGCGTACAAAACCACA 61.223 50.000 30.98 5.67 0.00 4.17
2395 2592 0.517742 GATCGCGCGTACAAAACCAC 60.518 55.000 30.98 6.23 0.00 4.16
2397 2594 1.295645 CGATCGCGCGTACAAAACC 60.296 57.895 30.98 0.00 0.00 3.27
2401 2598 1.942223 CCATCGATCGCGCGTACAA 60.942 57.895 30.98 11.14 37.46 2.41
2403 2600 3.097728 CCCATCGATCGCGCGTAC 61.098 66.667 30.98 22.23 37.46 3.67
2404 2601 4.994201 GCCCATCGATCGCGCGTA 62.994 66.667 30.98 17.05 37.46 4.42
2461 2661 1.062525 CGCGGTACCACCTACGTAC 59.937 63.158 13.54 0.00 35.66 3.67
2462 2662 2.760159 GCGCGGTACCACCTACGTA 61.760 63.158 13.54 0.00 37.65 3.57
2835 3036 1.304052 CCCGAGAACCCATTTGCCA 60.304 57.895 0.00 0.00 0.00 4.92
2841 3042 0.251608 CCCAAAACCCGAGAACCCAT 60.252 55.000 0.00 0.00 0.00 4.00
3042 3249 2.808321 GAACCGGCGTCCGTCTTC 60.808 66.667 15.38 11.73 46.80 2.87
3057 3264 1.949525 GTGTGCAGAAGCTTCCTTGAA 59.050 47.619 22.81 7.57 42.74 2.69
3078 3285 3.497942 GGTCCAAGAACCTGAAGCCTTTA 60.498 47.826 0.00 0.00 36.32 1.85
3108 3315 1.046472 TGGTGTCTTCGGTGGTGAGT 61.046 55.000 0.00 0.00 0.00 3.41
3128 3335 2.925170 AGGTGGCGAGCTTGGAGT 60.925 61.111 2.37 0.00 0.00 3.85
3195 3564 1.066573 CGGAGGATGCTCTTCACTTGT 60.067 52.381 14.40 0.00 0.00 3.16
3378 3747 1.405526 CGGTACAGGAAGATGGTGGTG 60.406 57.143 0.00 0.00 0.00 4.17
3414 3783 1.303317 GGTGAACCGTGCCAGGAAT 60.303 57.895 1.23 0.00 34.73 3.01
3453 3822 2.108566 CCCATCCTCTGCAGCTCG 59.891 66.667 9.47 0.00 0.00 5.03
3519 3894 1.743252 GGCCTTCCTGAAGTGCTCG 60.743 63.158 15.27 0.17 36.72 5.03
4124 4504 3.312421 TGGCATGCTTATTCTTTAGTCGC 59.688 43.478 18.92 0.00 0.00 5.19
4223 4611 2.228343 AGTAGTGGTCAGTTACAGCGTC 59.772 50.000 0.00 0.00 0.00 5.19
4240 4628 3.111098 GCGGTACCGTGAACATAAGTAG 58.889 50.000 33.34 2.73 42.09 2.57
4241 4629 2.754552 AGCGGTACCGTGAACATAAGTA 59.245 45.455 33.34 0.00 42.09 2.24
4242 4630 1.547372 AGCGGTACCGTGAACATAAGT 59.453 47.619 33.34 4.86 42.09 2.24
4254 4642 0.100861 GCAGACTAGTCAGCGGTACC 59.899 60.000 22.42 0.16 32.62 3.34
4287 4675 0.879090 CGCTGTCCATGCATGCATAT 59.121 50.000 31.73 10.77 34.91 1.78
4305 4699 5.572211 AGTTATGCATACAAATGAAGTGCG 58.428 37.500 5.74 0.00 38.58 5.34
4403 4831 2.754946 TCTTTCTACAATTCCCGCGT 57.245 45.000 4.92 0.00 0.00 6.01
4404 4832 4.616181 ATTTCTTTCTACAATTCCCGCG 57.384 40.909 0.00 0.00 0.00 6.46
4489 7382 9.733556 TGAAATGATTTTACTTTAGCTGGTAGA 57.266 29.630 0.00 0.00 0.00 2.59
4522 7684 3.888930 TCTTCCCAGTTGTGAATTGTTCC 59.111 43.478 0.00 0.00 0.00 3.62
4567 7729 7.964559 CACCGGCAAACATTGATATGATATAAG 59.035 37.037 0.00 0.00 35.65 1.73
4830 8022 4.705507 TGAACTGGTACGCTTCTATTCTCT 59.294 41.667 0.00 0.00 0.00 3.10
4836 8028 2.522185 ACCTGAACTGGTACGCTTCTA 58.478 47.619 1.65 0.00 38.79 2.10


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

AutoCloner maintained by Alex Coulton.