Multiple sequence alignment - TraesCS3B01G395400

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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 TraesCS3B01G395400 chr3B 100.000 4148 0 0 1 4148 623147800 623151947 0.000000e+00 7661
1 TraesCS3B01G395400 chr3D 89.275 3655 233 68 542 4148 469152685 469156228 0.000000e+00 4431
2 TraesCS3B01G395400 chr3D 90.909 385 26 6 1 376 469152297 469152681 3.700000e-140 508
3 TraesCS3B01G395400 chr3A 91.311 2532 141 31 1596 4114 611701463 611703928 0.000000e+00 3384
4 TraesCS3B01G395400 chr3A 92.635 706 28 11 913 1598 611700601 611701302 0.000000e+00 994
5 TraesCS3B01G395400 chr3A 93.048 187 9 4 371 556 362899676 362899859 1.900000e-68 270
6 TraesCS3B01G395400 chr2A 88.335 823 55 14 1146 1948 675938172 675938973 0.000000e+00 950
7 TraesCS3B01G395400 chr5A 91.008 645 41 12 1053 1688 503647191 503647827 0.000000e+00 854
8 TraesCS3B01G395400 chr5A 94.505 182 8 2 372 551 290391866 290391685 3.160000e-71 279
9 TraesCS3B01G395400 chr5D 94.944 178 8 1 365 541 274578000 274578177 1.140000e-70 278
10 TraesCS3B01G395400 chr4D 95.429 175 7 1 374 547 93338209 93338035 1.140000e-70 278
11 TraesCS3B01G395400 chr4D 92.593 189 11 3 373 559 377455674 377455487 6.840000e-68 268
12 TraesCS3B01G395400 chr4D 86.957 115 15 0 1342 1456 363661723 363661837 3.370000e-26 130
13 TraesCS3B01G395400 chr2D 96.450 169 5 1 373 540 571949912 571950080 1.140000e-70 278
14 TraesCS3B01G395400 chr6D 93.478 184 9 3 361 542 182340021 182339839 1.900000e-68 270
15 TraesCS3B01G395400 chr6D 89.806 206 15 5 342 542 164575460 164575256 4.110000e-65 259
16 TraesCS3B01G395400 chr4A 93.514 185 7 5 369 552 357678777 357678597 1.900000e-68 270
17 TraesCS3B01G395400 chr4A 86.087 115 16 0 1342 1456 101759026 101758912 1.570000e-24 124
18 TraesCS3B01G395400 chr7B 86.070 201 12 4 694 879 123738936 123738737 7.030000e-48 202
19 TraesCS3B01G395400 chr7B 93.162 117 6 2 761 876 630128042 630127927 1.980000e-38 171
20 TraesCS3B01G395400 chr7D 85.279 197 15 3 694 877 321045655 321045460 1.520000e-44 191
21 TraesCS3B01G395400 chr6B 84.848 198 16 2 694 878 620698796 620698992 1.970000e-43 187
22 TraesCS3B01G395400 chr6B 84.772 197 16 8 694 877 181494 181299 7.080000e-43 185
23 TraesCS3B01G395400 chr2B 84.772 197 15 3 694 876 723426015 723426210 2.550000e-42 183
24 TraesCS3B01G395400 chr1A 84.043 188 28 2 691 877 549277202 549277388 3.290000e-41 180
25 TraesCS3B01G395400 chr1B 83.756 197 17 3 694 876 11133526 11133331 5.510000e-39 172
26 TraesCS3B01G395400 chr4B 87.826 115 14 0 1342 1456 449014435 449014549 7.230000e-28 135


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 TraesCS3B01G395400 chr3B 623147800 623151947 4147 False 7661.0 7661 100.000 1 4148 1 chr3B.!!$F1 4147
1 TraesCS3B01G395400 chr3D 469152297 469156228 3931 False 2469.5 4431 90.092 1 4148 2 chr3D.!!$F1 4147
2 TraesCS3B01G395400 chr3A 611700601 611703928 3327 False 2189.0 3384 91.973 913 4114 2 chr3A.!!$F2 3201
3 TraesCS3B01G395400 chr2A 675938172 675938973 801 False 950.0 950 88.335 1146 1948 1 chr2A.!!$F1 802
4 TraesCS3B01G395400 chr5A 503647191 503647827 636 False 854.0 854 91.008 1053 1688 1 chr5A.!!$F1 635

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
142 152 0.320334 ATGACGTCGCAATGGACACA 60.320 50.0 11.62 0.0 36.73 3.72 F
1444 1494 1.031571 TCGCCAACAAGCCCATGATC 61.032 55.0 0.00 0.0 0.00 2.92 F
2623 2863 0.243907 TCACTGGCTTGCGTCTCTAC 59.756 55.0 0.00 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 2229 0.243907 CACGACAGTTGGACTCCGAT 59.756 55.0 0.00 0.00 0.0 4.18 R
2665 2905 0.184692 TCCCAACAACATGTGCTCCA 59.815 50.0 0.00 0.00 0.0 3.86 R
3695 3944 0.107654 AGCATGGCCTAGAACGGTTC 60.108 55.0 12.91 12.91 0.0 3.62 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
27 28 4.735369 ACAAGGTCATTTTATGGGTGACA 58.265 39.130 7.00 0.00 43.01 3.58
31 32 6.575244 AGGTCATTTTATGGGTGACATAGA 57.425 37.500 7.00 0.00 42.69 1.98
40 41 7.482169 TTATGGGTGACATAGAGACCATATC 57.518 40.000 0.00 0.00 42.69 1.63
79 80 9.387123 GATTTTATCCTCTCGTCATTTATTTGC 57.613 33.333 0.00 0.00 0.00 3.68
83 90 9.607988 TTATCCTCTCGTCATTTATTTGCTTAA 57.392 29.630 0.00 0.00 0.00 1.85
87 94 7.693951 CCTCTCGTCATTTATTTGCTTAAACAG 59.306 37.037 0.00 0.00 0.00 3.16
102 109 9.897744 TTGCTTAAACAGAAATCTTGTCATAAG 57.102 29.630 0.00 0.00 0.00 1.73
120 129 6.201806 GTCATAAGGCACATAGACAAGCTAAG 59.798 42.308 0.00 0.00 31.66 2.18
131 140 3.921021 AGACAAGCTAAGAAATGACGTCG 59.079 43.478 11.62 0.00 0.00 5.12
142 152 0.320334 ATGACGTCGCAATGGACACA 60.320 50.000 11.62 0.00 36.73 3.72
236 246 1.734163 CCATCGGTTAGACCAACACC 58.266 55.000 0.00 0.00 38.47 4.16
249 259 5.741011 AGACCAACACCGTATGATGTTTAT 58.259 37.500 0.00 0.00 36.92 1.40
255 265 6.578020 ACACCGTATGATGTTTATGTTACG 57.422 37.500 0.00 0.00 33.97 3.18
271 281 3.952323 TGTTACGGTCAAATTTGTTCCCA 59.048 39.130 17.47 11.15 0.00 4.37
358 368 8.635765 AATCTCATTTACTAGCCTGAAAAACA 57.364 30.769 0.00 0.00 0.00 2.83
382 392 9.561069 ACATCTTACATTTTGATATGTACTCCC 57.439 33.333 0.00 0.00 39.90 4.30
383 393 9.784531 CATCTTACATTTTGATATGTACTCCCT 57.215 33.333 0.00 0.00 39.90 4.20
385 395 8.429641 TCTTACATTTTGATATGTACTCCCTCC 58.570 37.037 0.00 0.00 39.90 4.30
386 396 5.611374 ACATTTTGATATGTACTCCCTCCG 58.389 41.667 0.00 0.00 36.99 4.63
387 397 5.130477 ACATTTTGATATGTACTCCCTCCGT 59.870 40.000 0.00 0.00 36.99 4.69
388 398 5.687166 TTTTGATATGTACTCCCTCCGTT 57.313 39.130 0.00 0.00 0.00 4.44
389 399 4.931661 TTGATATGTACTCCCTCCGTTC 57.068 45.455 0.00 0.00 0.00 3.95
390 400 3.228453 TGATATGTACTCCCTCCGTTCC 58.772 50.000 0.00 0.00 0.00 3.62
391 401 3.117246 TGATATGTACTCCCTCCGTTCCT 60.117 47.826 0.00 0.00 0.00 3.36
392 402 4.105217 TGATATGTACTCCCTCCGTTCCTA 59.895 45.833 0.00 0.00 0.00 2.94
393 403 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
394 404 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
395 405 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
396 406 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
397 407 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
398 408 5.901276 TGTACTCCCTCCGTTCCTAAATATT 59.099 40.000 0.00 0.00 0.00 1.28
399 409 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
400 410 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
401 411 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
402 412 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
403 413 4.820173 CCCTCCGTTCCTAAATATTTGTCC 59.180 45.833 11.05 0.00 0.00 4.02
404 414 5.397559 CCCTCCGTTCCTAAATATTTGTCCT 60.398 44.000 11.05 0.00 0.00 3.85
405 415 6.120220 CCTCCGTTCCTAAATATTTGTCCTT 58.880 40.000 11.05 0.00 0.00 3.36
406 416 6.602009 CCTCCGTTCCTAAATATTTGTCCTTT 59.398 38.462 11.05 0.00 0.00 3.11
407 417 7.122204 CCTCCGTTCCTAAATATTTGTCCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
408 418 9.169592 CTCCGTTCCTAAATATTTGTCCTTTTA 57.830 33.333 11.05 0.00 0.00 1.52
409 419 9.169592 TCCGTTCCTAAATATTTGTCCTTTTAG 57.830 33.333 11.05 0.00 33.47 1.85
410 420 9.169592 CCGTTCCTAAATATTTGTCCTTTTAGA 57.830 33.333 11.05 0.00 34.90 2.10
481 491 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
482 492 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
483 493 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
484 494 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
485 495 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
486 496 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
487 497 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
488 498 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
489 499 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
490 500 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
491 501 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
492 502 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
493 503 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
494 504 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
495 505 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
496 506 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
497 507 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
498 508 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
499 509 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
500 510 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
501 511 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
502 512 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
503 513 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
504 514 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
505 515 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
506 516 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
507 517 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
508 518 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
509 519 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
517 527 9.996554 TCACTTGTTGAAATCTCTATAAAGACA 57.003 29.630 0.00 0.00 0.00 3.41
535 545 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
536 546 6.555463 AGACAAATATTTAGGAACGGAGGA 57.445 37.500 0.00 0.00 0.00 3.71
537 547 6.583562 AGACAAATATTTAGGAACGGAGGAG 58.416 40.000 0.00 0.00 0.00 3.69
538 548 6.156429 AGACAAATATTTAGGAACGGAGGAGT 59.844 38.462 0.00 0.00 0.00 3.85
539 549 7.343833 AGACAAATATTTAGGAACGGAGGAGTA 59.656 37.037 0.00 0.00 0.00 2.59
540 550 8.030913 ACAAATATTTAGGAACGGAGGAGTAT 57.969 34.615 0.00 0.00 0.00 2.12
544 554 5.841957 TTTAGGAACGGAGGAGTATGTAC 57.158 43.478 0.00 0.00 0.00 2.90
676 686 1.692749 AGGGGAGTGGTGTGTGTGT 60.693 57.895 0.00 0.00 0.00 3.72
677 687 1.525995 GGGGAGTGGTGTGTGTGTG 60.526 63.158 0.00 0.00 0.00 3.82
678 688 1.223487 GGGAGTGGTGTGTGTGTGT 59.777 57.895 0.00 0.00 0.00 3.72
679 689 1.095228 GGGAGTGGTGTGTGTGTGTG 61.095 60.000 0.00 0.00 0.00 3.82
684 694 1.226660 GGTGTGTGTGTGTGCAAGC 60.227 57.895 0.00 0.00 0.00 4.01
688 698 4.629115 GTGTGTGTGCAAGCGGGC 62.629 66.667 0.00 0.00 0.00 6.13
707 717 1.901948 ACAGCGAGTTCGGGTGAGA 60.902 57.895 3.50 0.00 40.23 3.27
717 727 1.639722 TCGGGTGAGAAGGTGATTCA 58.360 50.000 0.00 0.00 40.67 2.57
720 730 2.169352 CGGGTGAGAAGGTGATTCATCT 59.831 50.000 0.00 0.00 40.67 2.90
745 755 2.084610 TTCTTCGATGACTGCTGTGG 57.915 50.000 0.00 0.00 0.00 4.17
747 757 2.167662 TCTTCGATGACTGCTGTGGTA 58.832 47.619 0.00 0.00 0.00 3.25
751 761 1.363744 GATGACTGCTGTGGTAGTGC 58.636 55.000 0.00 0.00 38.47 4.40
781 803 2.999355 GGTGTCAAGCTCAGAGATGTTC 59.001 50.000 0.00 0.00 0.00 3.18
800 822 9.507329 AGATGTTCTGCTATCTTTTCAGTTTTA 57.493 29.630 0.00 0.00 29.64 1.52
808 830 9.230122 TGCTATCTTTTCAGTTTTATGATGTCA 57.770 29.630 0.00 0.00 0.00 3.58
857 879 7.591426 TGATCTTTATGATATGAACGAGACACG 59.409 37.037 0.00 0.00 40.83 4.49
947 974 4.655762 TGATCCTTAATCTCTCGTGGTG 57.344 45.455 0.00 0.00 35.24 4.17
963 990 2.160813 GTGGTGTATTGCGACGGATTTT 59.839 45.455 0.00 0.00 0.00 1.82
982 1009 4.628963 TTTCCTATATAAAGGCGACCCC 57.371 45.455 0.00 0.00 36.51 4.95
1087 1121 3.181465 GCATATTCTCTTCCCGGTCTTGA 60.181 47.826 0.00 0.00 0.00 3.02
1296 1343 7.227910 AGTGTGATTTTAATTCTGTTACGGTGT 59.772 33.333 0.00 0.00 0.00 4.16
1315 1362 2.611800 TGGCCTGCAGGGATCAGT 60.612 61.111 33.46 0.00 37.23 3.41
1322 1369 1.997874 GCAGGGATCAGTGGGGAGT 60.998 63.158 0.00 0.00 0.00 3.85
1444 1494 1.031571 TCGCCAACAAGCCCATGATC 61.032 55.000 0.00 0.00 0.00 2.92
1510 1569 1.613925 GGTGCTGTGAGTCAGTGAGTA 59.386 52.381 0.00 0.00 45.23 2.59
1630 1852 8.440059 GCTTTAACTTTTATAACCAATTGCCAC 58.560 33.333 0.00 0.00 0.00 5.01
1653 1875 4.083581 AGTAGCATTTCAATGTGTTCGC 57.916 40.909 1.59 0.00 38.65 4.70
1818 2053 3.641648 ACAAATGCAGAACGATTTGTGG 58.358 40.909 11.89 0.00 46.25 4.17
1874 2109 4.460382 ACCTACCAATTTGTGCAGATTGAG 59.540 41.667 14.51 8.72 35.60 3.02
1904 2139 2.572104 AGATGTTGGGGTTACAGAGGTC 59.428 50.000 0.00 0.00 0.00 3.85
1951 2186 9.627123 CCCAGAGGTAAAACATGAGATAATTTA 57.373 33.333 0.00 0.00 0.00 1.40
1976 2216 4.635223 TCTGTTGTTCTCTCATGGAGTTG 58.365 43.478 9.98 0.00 42.40 3.16
1989 2229 7.676004 TCTCATGGAGTTGTCTGTATTTAACA 58.324 34.615 0.00 0.00 36.42 2.41
2005 2245 2.457366 AACATCGGAGTCCAACTGTC 57.543 50.000 10.49 0.00 0.00 3.51
2017 2257 1.003545 CCAACTGTCGTGCTTTGTCTG 60.004 52.381 0.00 0.00 0.00 3.51
2295 2535 3.797039 TCTTTGACCACTCTCTTGTGTG 58.203 45.455 0.00 0.00 36.30 3.82
2297 2537 2.602257 TGACCACTCTCTTGTGTGTG 57.398 50.000 0.00 0.00 36.33 3.82
2298 2538 1.831106 TGACCACTCTCTTGTGTGTGT 59.169 47.619 0.00 0.00 36.33 3.72
2301 2541 4.051922 GACCACTCTCTTGTGTGTGTAAG 58.948 47.826 0.00 0.00 36.33 2.34
2302 2542 2.802816 CCACTCTCTTGTGTGTGTAAGC 59.197 50.000 0.00 0.00 36.33 3.09
2303 2543 3.493350 CCACTCTCTTGTGTGTGTAAGCT 60.493 47.826 0.00 0.00 36.33 3.74
2306 2546 3.982475 TCTCTTGTGTGTGTAAGCTCTG 58.018 45.455 0.00 0.00 0.00 3.35
2317 2557 7.330946 GTGTGTGTAAGCTCTGATGTATGTAAA 59.669 37.037 0.00 0.00 0.00 2.01
2419 2659 6.207417 TGGAAAGATTTGTAGAGAAGCCAAAG 59.793 38.462 0.00 0.00 32.17 2.77
2456 2696 7.318141 CAACAAGATCAATGCAGGAATTTACT 58.682 34.615 0.00 0.00 0.00 2.24
2473 2713 7.749126 GGAATTTACTTGTTAAATCCGTCTGTG 59.251 37.037 0.00 0.00 39.14 3.66
2533 2773 0.984230 AGGTCTTCCCTCGAATTGCA 59.016 50.000 0.00 0.00 40.71 4.08
2620 2860 0.671781 ACATCACTGGCTTGCGTCTC 60.672 55.000 0.00 0.00 0.00 3.36
2623 2863 0.243907 TCACTGGCTTGCGTCTCTAC 59.756 55.000 0.00 0.00 0.00 2.59
2635 2875 4.270834 TGCGTCTCTACCTAGATTCACTT 58.729 43.478 0.00 0.00 0.00 3.16
2644 2884 9.191479 CTCTACCTAGATTCACTTAGGAAGAAA 57.809 37.037 4.66 0.00 34.01 2.52
2869 3109 2.746277 GGCTGGCATTCGACGGTT 60.746 61.111 0.00 0.00 0.00 4.44
2944 3184 1.669211 GGTGACGAGGTCTACAGCAAC 60.669 57.143 0.00 0.00 33.15 4.17
2962 3202 2.112297 GGCGGTGTTGTTCTCCCA 59.888 61.111 0.00 0.00 0.00 4.37
3125 3365 5.061560 GCGAGACTTGTTAAACTGATGAGAG 59.938 44.000 0.00 0.00 0.00 3.20
3145 3385 6.758416 TGAGAGTGTATGTGCATTAGTCATTC 59.242 38.462 0.00 0.00 0.00 2.67
3170 3410 5.391950 CCAGTGTTGTTTCCCATTAAGATCG 60.392 44.000 0.00 0.00 0.00 3.69
3300 3540 7.254761 CCTTTGAAGGTGAATTTTAACTTTGCC 60.255 37.037 1.49 0.00 41.41 4.52
3326 3566 6.991938 AGTATGAAGCTCCTGATTCTGATAC 58.008 40.000 0.00 0.00 39.16 2.24
3327 3567 4.313277 TGAAGCTCCTGATTCTGATACG 57.687 45.455 0.00 0.00 39.16 3.06
3328 3568 3.701542 TGAAGCTCCTGATTCTGATACGT 59.298 43.478 0.00 0.00 39.16 3.57
3329 3569 4.887655 TGAAGCTCCTGATTCTGATACGTA 59.112 41.667 0.00 0.00 39.16 3.57
3330 3570 5.359860 TGAAGCTCCTGATTCTGATACGTAA 59.640 40.000 0.00 0.00 39.16 3.18
3331 3571 6.040955 TGAAGCTCCTGATTCTGATACGTAAT 59.959 38.462 0.00 0.00 39.16 1.89
3332 3572 6.412362 AGCTCCTGATTCTGATACGTAATT 57.588 37.500 0.00 0.00 0.00 1.40
3333 3573 6.821388 AGCTCCTGATTCTGATACGTAATTT 58.179 36.000 0.00 0.00 0.00 1.82
3334 3574 6.703607 AGCTCCTGATTCTGATACGTAATTTG 59.296 38.462 0.00 0.00 0.00 2.32
3335 3575 6.564873 GCTCCTGATTCTGATACGTAATTTGC 60.565 42.308 0.00 0.00 0.00 3.68
3360 3603 0.381089 GCTATCAGCCTTGCAGCAAG 59.619 55.000 26.03 26.03 40.75 4.01
3364 3607 2.035312 AGCCTTGCAGCAAGAGGG 59.965 61.111 32.94 20.17 43.42 4.30
3376 3619 1.740025 GCAAGAGGGTATGAACAGCAC 59.260 52.381 0.00 0.00 0.00 4.40
3377 3620 2.875672 GCAAGAGGGTATGAACAGCACA 60.876 50.000 0.00 0.00 0.00 4.57
3387 3630 5.048782 GGTATGAACAGCACATTCTGAAACA 60.049 40.000 0.00 0.00 37.51 2.83
3393 3636 2.046313 GCACATTCTGAAACACGCTTG 58.954 47.619 0.00 0.00 0.00 4.01
3424 3667 2.258013 TGTAGGCTGCAAACGTGGC 61.258 57.895 1.69 5.57 0.00 5.01
3432 3675 2.671619 CAAACGTGGCCGATGGGT 60.672 61.111 0.00 0.00 37.88 4.51
3442 3686 0.663153 GCCGATGGGTATTGCTCAAC 59.337 55.000 0.00 0.00 34.97 3.18
3507 3751 4.141642 TGGTGTGTTATCATGAGATCTGGG 60.142 45.833 0.00 0.00 35.67 4.45
3513 3757 0.749049 TCATGAGATCTGGGCGAGTG 59.251 55.000 0.00 0.00 0.00 3.51
3538 3782 0.654683 CGCTAGTTTGCTCATCCTGC 59.345 55.000 0.00 0.00 0.00 4.85
3610 3856 1.369692 CCAACGACTGTGGGCTGTA 59.630 57.895 0.00 0.00 30.66 2.74
3613 3859 0.317479 AACGACTGTGGGCTGTAGAC 59.683 55.000 0.00 0.00 0.00 2.59
3694 3943 3.118702 AGCAGACACAGATGAGAAGATGG 60.119 47.826 0.00 0.00 0.00 3.51
3695 3944 3.794717 CAGACACAGATGAGAAGATGGG 58.205 50.000 0.00 0.00 0.00 4.00
3745 3994 4.379603 CCTCTGTGTACCTCTTGTAACTCG 60.380 50.000 0.00 0.00 0.00 4.18
3746 3995 4.392047 TCTGTGTACCTCTTGTAACTCGA 58.608 43.478 0.00 0.00 0.00 4.04
3748 3997 3.058708 TGTGTACCTCTTGTAACTCGACG 60.059 47.826 0.00 0.00 0.00 5.12
3750 3999 0.243095 ACCTCTTGTAACTCGACGGC 59.757 55.000 0.00 0.00 0.00 5.68
3770 4019 1.052124 TTCTGTGGACGGGACTGGTT 61.052 55.000 0.00 0.00 0.00 3.67
3783 4032 4.663334 GGGACTGGTTAGATTGTTTTCCT 58.337 43.478 0.00 0.00 0.00 3.36
3785 4034 5.048013 GGGACTGGTTAGATTGTTTTCCTTG 60.048 44.000 0.00 0.00 0.00 3.61
3788 4037 7.094762 GGACTGGTTAGATTGTTTTCCTTGTAG 60.095 40.741 0.00 0.00 0.00 2.74
3789 4038 7.514721 ACTGGTTAGATTGTTTTCCTTGTAGA 58.485 34.615 0.00 0.00 0.00 2.59
3790 4039 7.996644 ACTGGTTAGATTGTTTTCCTTGTAGAA 59.003 33.333 0.00 0.00 0.00 2.10
3792 4041 9.362151 TGGTTAGATTGTTTTCCTTGTAGAATT 57.638 29.630 0.00 0.00 0.00 2.17
3800 4049 9.567776 TTGTTTTCCTTGTAGAATTGTAGATCA 57.432 29.630 0.00 0.00 0.00 2.92
3806 4055 8.762645 TCCTTGTAGAATTGTAGATCACTGAAT 58.237 33.333 0.00 0.00 0.00 2.57
3807 4056 9.388506 CCTTGTAGAATTGTAGATCACTGAATT 57.611 33.333 0.00 0.00 0.00 2.17
3856 4105 0.878416 TGGAATGCGGCTGTGTAAAC 59.122 50.000 0.00 0.00 0.00 2.01
3889 4138 9.139174 CTGTTACTTTCTTTCTTTTCTGCAAAA 57.861 29.630 0.00 0.00 0.00 2.44
3890 4139 9.651913 TGTTACTTTCTTTCTTTTCTGCAAAAT 57.348 25.926 0.00 0.00 30.91 1.82
3925 4174 0.679640 TGCGCTGTAATTTCCAGGGG 60.680 55.000 9.73 5.89 41.64 4.79
3927 4176 1.384222 CGCTGTAATTTCCAGGGGGC 61.384 60.000 11.70 0.00 38.73 5.80
3929 4178 0.631212 CTGTAATTTCCAGGGGGCCT 59.369 55.000 0.84 0.00 0.00 5.19
3951 4202 0.946221 GGTCGTGCAACTGGTGAGAG 60.946 60.000 0.00 0.00 31.75 3.20
3963 4214 5.543507 ACTGGTGAGAGCTGGAATTATAG 57.456 43.478 0.00 0.00 0.00 1.31
3979 4230 6.539103 GGAATTATAGCACTTTCGGAGTTTCT 59.461 38.462 0.00 0.00 36.10 2.52
3997 4248 1.872952 TCTGTTGCAAGTCATTGTCCG 59.127 47.619 0.00 0.00 38.76 4.79
4007 4258 1.327764 GTCATTGTCCGCGGATTCTTC 59.672 52.381 33.58 18.74 0.00 2.87
4012 4263 2.028876 TGTCCGCGGATTCTTCAGATA 58.971 47.619 33.58 0.00 0.00 1.98
4030 4281 7.517614 TCAGATAAAGAGCTGTTCGATATCT 57.482 36.000 9.43 9.43 40.16 1.98
4043 4294 7.234187 TGTTCGATATCTGTATGCTTTTCAC 57.766 36.000 0.34 0.00 0.00 3.18
4079 4330 2.035066 AGACTTTTGCAATGCCTGACAC 59.965 45.455 1.53 0.00 0.00 3.67
4085 4336 1.073763 TGCAATGCCTGACACTAGGTT 59.926 47.619 1.53 0.00 40.11 3.50
4097 4348 6.535508 CCTGACACTAGGTTAGATAGTTTTGC 59.464 42.308 0.00 0.00 35.20 3.68
4118 4369 0.321346 TCTCGCAATCCTTGTGCTCA 59.679 50.000 0.00 0.00 40.84 4.26
4119 4370 0.725686 CTCGCAATCCTTGTGCTCAG 59.274 55.000 0.00 0.00 40.84 3.35
4126 4377 0.111061 TCCTTGTGCTCAGCCATTGT 59.889 50.000 0.00 0.00 0.00 2.71
4127 4378 0.963962 CCTTGTGCTCAGCCATTGTT 59.036 50.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.483640 GGTCTCTATGTCACCCATAAAATGAC 59.516 42.308 0.00 0.00 42.54 3.06
77 78 8.514594 CCTTATGACAAGATTTCTGTTTAAGCA 58.485 33.333 0.00 0.00 0.00 3.91
78 79 7.486232 GCCTTATGACAAGATTTCTGTTTAAGC 59.514 37.037 0.00 0.00 0.00 3.09
79 80 8.514594 TGCCTTATGACAAGATTTCTGTTTAAG 58.485 33.333 0.00 0.00 0.00 1.85
83 90 5.769662 TGTGCCTTATGACAAGATTTCTGTT 59.230 36.000 0.00 0.00 0.00 3.16
87 94 7.280876 TGTCTATGTGCCTTATGACAAGATTTC 59.719 37.037 0.00 0.00 32.50 2.17
102 109 5.586243 TCATTTCTTAGCTTGTCTATGTGCC 59.414 40.000 0.00 0.00 0.00 5.01
120 129 1.463056 TGTCCATTGCGACGTCATTTC 59.537 47.619 17.16 1.84 35.40 2.17
131 140 2.352127 GCCTCTTTTCTGTGTCCATTGC 60.352 50.000 0.00 0.00 0.00 3.56
142 152 2.859165 TCATCCAACGCCTCTTTTCT 57.141 45.000 0.00 0.00 0.00 2.52
203 213 1.210967 CCGATGGCTAAACCCAACCTA 59.789 52.381 0.00 0.00 38.61 3.08
210 220 2.093341 TGGTCTAACCGATGGCTAAACC 60.093 50.000 0.00 0.00 42.58 3.27
236 246 6.815672 TGACCGTAACATAAACATCATACG 57.184 37.500 0.00 0.00 36.73 3.06
249 259 3.952323 TGGGAACAAATTTGACCGTAACA 59.048 39.130 24.64 15.17 37.44 2.41
376 386 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
378 388 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
379 389 5.397109 GGACAAATATTTAGGAACGGAGGGA 60.397 44.000 0.00 0.00 0.00 4.20
380 390 4.820173 GGACAAATATTTAGGAACGGAGGG 59.180 45.833 0.00 0.00 0.00 4.30
381 391 5.681639 AGGACAAATATTTAGGAACGGAGG 58.318 41.667 0.00 0.00 0.00 4.30
382 392 7.625828 AAAGGACAAATATTTAGGAACGGAG 57.374 36.000 0.00 0.00 0.00 4.63
383 393 9.169592 CTAAAAGGACAAATATTTAGGAACGGA 57.830 33.333 0.00 0.00 33.69 4.69
384 394 9.169592 TCTAAAAGGACAAATATTTAGGAACGG 57.830 33.333 0.00 0.00 36.48 4.44
423 433 9.990868 TGTCTATATACATCCATATGTGGTAGT 57.009 33.333 8.51 10.44 45.99 2.73
459 469 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
460 470 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
461 471 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
462 472 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
463 473 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
464 474 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
465 475 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
466 476 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
467 477 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
468 478 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
469 479 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
470 480 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
471 481 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
472 482 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
473 483 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
474 484 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
475 485 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
476 486 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
477 487 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
478 488 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
479 489 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
480 490 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
481 491 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
482 492 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
483 493 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
491 501 9.996554 TGTCTTTATAGAGATTTCAACAAGTGA 57.003 29.630 0.00 0.00 0.00 3.41
509 519 9.338622 CCTCCGTTCCTAAATATTTGTCTTTAT 57.661 33.333 11.05 0.00 0.00 1.40
510 520 8.542080 TCCTCCGTTCCTAAATATTTGTCTTTA 58.458 33.333 11.05 0.00 0.00 1.85
511 521 7.399634 TCCTCCGTTCCTAAATATTTGTCTTT 58.600 34.615 11.05 0.00 0.00 2.52
512 522 6.954232 TCCTCCGTTCCTAAATATTTGTCTT 58.046 36.000 11.05 0.00 0.00 3.01
513 523 6.156429 ACTCCTCCGTTCCTAAATATTTGTCT 59.844 38.462 11.05 0.00 0.00 3.41
514 524 6.346896 ACTCCTCCGTTCCTAAATATTTGTC 58.653 40.000 11.05 0.00 0.00 3.18
515 525 6.309389 ACTCCTCCGTTCCTAAATATTTGT 57.691 37.500 11.05 0.00 0.00 2.83
516 526 7.931948 ACATACTCCTCCGTTCCTAAATATTTG 59.068 37.037 11.05 1.40 0.00 2.32
517 527 8.030913 ACATACTCCTCCGTTCCTAAATATTT 57.969 34.615 5.89 5.89 0.00 1.40
518 528 7.613551 ACATACTCCTCCGTTCCTAAATATT 57.386 36.000 0.00 0.00 0.00 1.28
519 529 7.949006 AGTACATACTCCTCCGTTCCTAAATAT 59.051 37.037 0.00 0.00 0.00 1.28
520 530 7.293073 AGTACATACTCCTCCGTTCCTAAATA 58.707 38.462 0.00 0.00 0.00 1.40
521 531 6.134754 AGTACATACTCCTCCGTTCCTAAAT 58.865 40.000 0.00 0.00 0.00 1.40
522 532 5.513233 AGTACATACTCCTCCGTTCCTAAA 58.487 41.667 0.00 0.00 0.00 1.85
523 533 5.121380 AGTACATACTCCTCCGTTCCTAA 57.879 43.478 0.00 0.00 0.00 2.69
524 534 4.785346 AGTACATACTCCTCCGTTCCTA 57.215 45.455 0.00 0.00 0.00 2.94
525 535 3.666345 AGTACATACTCCTCCGTTCCT 57.334 47.619 0.00 0.00 0.00 3.36
526 536 7.700022 ATAATAGTACATACTCCTCCGTTCC 57.300 40.000 0.00 0.00 37.73 3.62
607 617 5.106475 ACAGCAGAAGTACGTTTTTGTTCAA 60.106 36.000 0.00 0.00 0.00 2.69
608 618 4.393680 ACAGCAGAAGTACGTTTTTGTTCA 59.606 37.500 0.00 0.00 0.00 3.18
618 628 5.502153 AGACCTAATACAGCAGAAGTACG 57.498 43.478 0.00 0.00 0.00 3.67
649 659 1.225704 CCACTCCCCTCCATCAAGC 59.774 63.158 0.00 0.00 0.00 4.01
650 660 0.254178 CACCACTCCCCTCCATCAAG 59.746 60.000 0.00 0.00 0.00 3.02
652 662 1.160870 ACACCACTCCCCTCCATCA 59.839 57.895 0.00 0.00 0.00 3.07
688 698 1.734477 CTCACCCGAACTCGCTGTG 60.734 63.158 11.52 11.52 39.93 3.66
689 699 1.461091 TTCTCACCCGAACTCGCTGT 61.461 55.000 0.00 0.00 38.18 4.40
691 701 1.587054 CTTCTCACCCGAACTCGCT 59.413 57.895 0.00 0.00 38.18 4.93
692 702 1.446272 CCTTCTCACCCGAACTCGC 60.446 63.158 0.00 0.00 38.18 5.03
740 750 2.579201 CCTCCGGCACTACCACAG 59.421 66.667 0.00 0.00 39.03 3.66
751 761 2.046892 CTTGACACCTGCCTCCGG 60.047 66.667 0.00 0.00 0.00 5.14
781 803 9.713740 GACATCATAAAACTGAAAAGATAGCAG 57.286 33.333 0.00 0.00 35.81 4.24
800 822 5.392767 AGTCACGTAAAGACTGACATCAT 57.607 39.130 6.25 0.00 44.23 2.45
802 824 4.982916 ACAAGTCACGTAAAGACTGACATC 59.017 41.667 7.70 0.00 45.11 3.06
947 974 6.963049 ATATAGGAAAATCCGTCGCAATAC 57.037 37.500 0.00 0.00 42.75 1.89
963 990 2.173519 CGGGGTCGCCTTTATATAGGA 58.826 52.381 12.96 0.00 37.50 2.94
987 1014 2.365582 GTTGGCACGAGGAAATACCAT 58.634 47.619 0.00 0.00 42.04 3.55
1019 1052 4.570874 GATGAAGGGCTCGGGGGC 62.571 72.222 0.00 0.00 40.05 5.80
1020 1053 2.378634 AAGATGAAGGGCTCGGGGG 61.379 63.158 0.00 0.00 0.00 5.40
1021 1054 1.153086 CAAGATGAAGGGCTCGGGG 60.153 63.158 0.00 0.00 0.00 5.73
1022 1055 1.153086 CCAAGATGAAGGGCTCGGG 60.153 63.158 0.00 0.00 0.00 5.14
1023 1056 1.821332 GCCAAGATGAAGGGCTCGG 60.821 63.158 0.00 0.00 44.32 4.63
1087 1121 1.073199 CCTGTTTCTTGCCCCTCGT 59.927 57.895 0.00 0.00 0.00 4.18
1168 1203 1.419387 GGATCACCTGGATGAGGAAGG 59.581 57.143 0.00 0.00 46.33 3.46
1169 1204 1.419387 GGGATCACCTGGATGAGGAAG 59.581 57.143 0.00 0.00 46.33 3.46
1170 1205 1.511613 GGGATCACCTGGATGAGGAA 58.488 55.000 0.00 0.00 46.33 3.36
1296 1343 2.285592 TGATCCCTGCAGGCCAGA 60.286 61.111 28.39 19.45 44.64 3.86
1315 1362 0.253020 GTCCCCCTTCTTACTCCCCA 60.253 60.000 0.00 0.00 0.00 4.96
1322 1369 2.056223 CGAGGCGTCCCCCTTCTTA 61.056 63.158 0.00 0.00 34.69 2.10
1384 1434 3.753434 CTGAGCGTGAGAGGCCGT 61.753 66.667 0.00 0.00 0.00 5.68
1510 1569 3.676324 GCAGTAGGATTAACTCGCACACT 60.676 47.826 0.00 0.00 0.00 3.55
1630 1852 5.163864 TGCGAACACATTGAAATGCTACTAG 60.164 40.000 2.92 0.00 40.04 2.57
1653 1875 5.033589 AGATTTCTTAGCTCCCATCAGTG 57.966 43.478 0.00 0.00 0.00 3.66
1738 1968 1.040339 AGGTTTTTCCCAAGCACGCA 61.040 50.000 0.00 0.00 36.75 5.24
1745 1975 3.578716 TGACACACAAAGGTTTTTCCCAA 59.421 39.130 0.00 0.00 36.75 4.12
1818 2053 9.548208 CAATAAACTTTTCTTTCCTCGAATCTC 57.452 33.333 0.00 0.00 0.00 2.75
1874 2109 0.897621 CCCCAACATCTTTCAAGGCC 59.102 55.000 0.00 0.00 0.00 5.19
1904 2139 3.243068 GGCGGTAGTTGATGGCTAAAATG 60.243 47.826 0.00 0.00 0.00 2.32
1951 2186 4.776837 ACTCCATGAGAGAACAACAGAGAT 59.223 41.667 15.51 0.00 46.50 2.75
1955 2190 4.384056 ACAACTCCATGAGAGAACAACAG 58.616 43.478 15.51 3.21 46.50 3.16
1976 2216 5.657474 TGGACTCCGATGTTAAATACAGAC 58.343 41.667 0.00 0.00 40.83 3.51
1989 2229 0.243907 CACGACAGTTGGACTCCGAT 59.756 55.000 0.00 0.00 0.00 4.18
2005 2245 1.670811 ACCTGAAACAGACAAAGCACG 59.329 47.619 0.00 0.00 32.44 5.34
2017 2257 9.912634 TTCAAGAAATTAATCATGACCTGAAAC 57.087 29.630 0.00 0.00 37.44 2.78
2125 2365 0.825010 CCACAAGCTTGTCCCTTGCT 60.825 55.000 28.97 2.32 42.57 3.91
2271 2511 5.297776 CACACAAGAGAGTGGTCAAAGAAAT 59.702 40.000 0.00 0.00 43.72 2.17
2279 2519 2.604046 ACACACACAAGAGAGTGGTC 57.396 50.000 0.00 0.00 43.72 4.02
2295 2535 7.759886 TCAGTTTACATACATCAGAGCTTACAC 59.240 37.037 0.00 0.00 0.00 2.90
2297 2537 7.976734 AGTCAGTTTACATACATCAGAGCTTAC 59.023 37.037 0.00 0.00 0.00 2.34
2298 2538 7.976175 CAGTCAGTTTACATACATCAGAGCTTA 59.024 37.037 0.00 0.00 0.00 3.09
2301 2541 5.006165 GCAGTCAGTTTACATACATCAGAGC 59.994 44.000 0.00 0.00 0.00 4.09
2302 2542 5.521735 GGCAGTCAGTTTACATACATCAGAG 59.478 44.000 0.00 0.00 0.00 3.35
2303 2543 5.187772 AGGCAGTCAGTTTACATACATCAGA 59.812 40.000 0.00 0.00 0.00 3.27
2306 2546 5.665459 AGAGGCAGTCAGTTTACATACATC 58.335 41.667 0.00 0.00 0.00 3.06
2317 2557 6.183361 CCACCTATATTTAAGAGGCAGTCAGT 60.183 42.308 0.00 0.00 33.28 3.41
2419 2659 7.380602 GCATTGATCTTGTTGCCTACAAATATC 59.619 37.037 12.32 12.32 45.69 1.63
2456 2696 2.811431 CCAGCACAGACGGATTTAACAA 59.189 45.455 0.00 0.00 0.00 2.83
2473 2713 0.459585 TTAACTCGATGCGGTCCAGC 60.460 55.000 0.00 0.00 37.71 4.85
2521 2761 0.942962 GATCAGCTGCAATTCGAGGG 59.057 55.000 9.47 0.00 0.00 4.30
2620 2860 9.974980 GATTTCTTCCTAAGTGAATCTAGGTAG 57.025 37.037 0.00 0.00 33.51 3.18
2623 2863 7.440856 GCTGATTTCTTCCTAAGTGAATCTAGG 59.559 40.741 13.91 0.00 35.35 3.02
2635 2875 3.614092 CTTGGCAGCTGATTTCTTCCTA 58.386 45.455 20.43 3.02 0.00 2.94
2665 2905 0.184692 TCCCAACAACATGTGCTCCA 59.815 50.000 0.00 0.00 0.00 3.86
2806 3046 0.521242 GCTTCTTAATGCGCACACCG 60.521 55.000 14.90 1.58 40.75 4.94
2869 3109 0.747644 CTATGCGTGCCCATTGTCCA 60.748 55.000 0.00 0.00 0.00 4.02
2944 3184 3.047877 GGGAGAACAACACCGCCG 61.048 66.667 0.00 0.00 0.00 6.46
2962 3202 3.181451 TGCTTGACTTGATCTCCTTGTGT 60.181 43.478 0.00 0.00 0.00 3.72
3125 3365 4.881273 TGGGAATGACTAATGCACATACAC 59.119 41.667 0.00 0.00 0.00 2.90
3145 3385 4.148838 TCTTAATGGGAAACAACACTGGG 58.851 43.478 0.00 0.00 0.00 4.45
3170 3410 4.934515 ACGCTATACTAAAGCTGGAAGTC 58.065 43.478 0.00 0.00 37.85 3.01
3238 3478 8.862325 ATTTATCCTTTCTGTGACATTACACA 57.138 30.769 0.00 0.00 46.45 3.72
3300 3540 4.037327 TCAGAATCAGGAGCTTCATACTCG 59.963 45.833 0.00 0.00 34.87 4.18
3334 3574 0.795085 CAAGGCTGATAGCGCATAGC 59.205 55.000 11.47 13.25 43.62 2.97
3335 3575 0.795085 GCAAGGCTGATAGCGCATAG 59.205 55.000 11.47 2.75 43.62 2.23
3360 3603 3.624861 CAGAATGTGCTGTTCATACCCTC 59.375 47.826 0.00 0.00 0.00 4.30
3364 3607 5.853282 GTGTTTCAGAATGTGCTGTTCATAC 59.147 40.000 0.00 0.00 37.20 2.39
3376 3619 2.031769 TCAGCAAGCGTGTTTCAGAATG 60.032 45.455 0.59 0.00 37.54 2.67
3377 3620 2.221169 TCAGCAAGCGTGTTTCAGAAT 58.779 42.857 0.59 0.00 0.00 2.40
3387 3630 3.520569 ACACAAAATTTTCAGCAAGCGT 58.479 36.364 0.00 0.00 0.00 5.07
3393 3636 3.429881 GCAGCCTACACAAAATTTTCAGC 59.570 43.478 0.00 0.00 0.00 4.26
3424 3667 2.158900 AGAGTTGAGCAATACCCATCGG 60.159 50.000 0.00 0.00 0.00 4.18
3432 3675 0.250234 AGCGGCAGAGTTGAGCAATA 59.750 50.000 1.45 0.00 33.68 1.90
3442 3686 0.725686 CTGATTTGTCAGCGGCAGAG 59.274 55.000 1.45 0.00 0.00 3.35
3471 3715 1.070786 ACACCAACTGCTGTACCCG 59.929 57.895 0.00 0.00 0.00 5.28
3513 3757 0.388134 TGAGCAAACTAGCGGTCGAC 60.388 55.000 7.13 7.13 40.15 4.20
3538 3782 1.614903 TGCAAAAGAATCCCAGCACAG 59.385 47.619 0.00 0.00 0.00 3.66
3610 3856 1.202758 TGCACAAGAACATTCGGGTCT 60.203 47.619 0.00 0.00 0.00 3.85
3613 3859 0.523072 CCTGCACAAGAACATTCGGG 59.477 55.000 0.00 0.00 0.00 5.14
3694 3943 1.095807 GCATGGCCTAGAACGGTTCC 61.096 60.000 16.84 3.05 0.00 3.62
3695 3944 0.107654 AGCATGGCCTAGAACGGTTC 60.108 55.000 12.91 12.91 0.00 3.62
3701 3950 2.170607 GGACAAGTAGCATGGCCTAGAA 59.829 50.000 3.32 0.00 43.09 2.10
3745 3994 2.432628 CCGTCCACAGAAGCCGTC 60.433 66.667 0.00 0.00 0.00 4.79
3746 3995 4.003788 CCCGTCCACAGAAGCCGT 62.004 66.667 0.00 0.00 0.00 5.68
3748 3997 2.047179 GTCCCGTCCACAGAAGCC 60.047 66.667 0.00 0.00 0.00 4.35
3750 3999 1.293498 CCAGTCCCGTCCACAGAAG 59.707 63.158 0.00 0.00 0.00 2.85
3783 4032 9.166173 CCAATTCAGTGATCTACAATTCTACAA 57.834 33.333 0.00 0.00 0.00 2.41
3785 4034 8.723942 ACCAATTCAGTGATCTACAATTCTAC 57.276 34.615 0.00 0.00 0.00 2.59
3788 4037 8.616076 CCTAACCAATTCAGTGATCTACAATTC 58.384 37.037 0.00 0.00 0.00 2.17
3789 4038 7.067494 GCCTAACCAATTCAGTGATCTACAATT 59.933 37.037 0.00 0.00 0.00 2.32
3790 4039 6.543831 GCCTAACCAATTCAGTGATCTACAAT 59.456 38.462 0.00 0.00 0.00 2.71
3792 4041 5.189736 AGCCTAACCAATTCAGTGATCTACA 59.810 40.000 0.00 0.00 0.00 2.74
3800 4049 2.171003 GCCAAGCCTAACCAATTCAGT 58.829 47.619 0.00 0.00 0.00 3.41
3827 4076 0.171007 CCGCATTCCACATTCACACC 59.829 55.000 0.00 0.00 0.00 4.16
3856 4105 9.717892 GAAAAGAAAGAAAGTAACAGGTACAAG 57.282 33.333 0.00 0.00 34.88 3.16
3889 4138 2.923605 GCGCAAGATGCAACTTTGTCAT 60.924 45.455 6.47 0.39 45.36 3.06
3890 4139 1.600164 GCGCAAGATGCAACTTTGTCA 60.600 47.619 6.47 0.00 45.36 3.58
3925 4174 3.050275 GTTGCACGACCTCAGGCC 61.050 66.667 0.00 0.00 0.00 5.19
3927 4176 1.669115 CCAGTTGCACGACCTCAGG 60.669 63.158 0.00 0.00 0.00 3.86
3929 4178 1.227527 CACCAGTTGCACGACCTCA 60.228 57.895 0.00 0.00 0.00 3.86
3930 4179 0.946221 CTCACCAGTTGCACGACCTC 60.946 60.000 0.00 0.00 0.00 3.85
3931 4180 1.069765 CTCACCAGTTGCACGACCT 59.930 57.895 0.00 0.00 0.00 3.85
3932 4181 0.946221 CTCTCACCAGTTGCACGACC 60.946 60.000 0.00 0.00 0.00 4.79
3951 4202 4.127171 TCCGAAAGTGCTATAATTCCAGC 58.873 43.478 4.61 4.61 38.31 4.85
3963 4214 2.854805 GCAACAGAAACTCCGAAAGTGC 60.855 50.000 0.00 0.00 38.58 4.40
3979 4230 0.310543 GCGGACAATGACTTGCAACA 59.689 50.000 0.00 0.00 35.69 3.33
3997 4248 4.210955 CAGCTCTTTATCTGAAGAATCCGC 59.789 45.833 0.00 0.00 35.38 5.54
4007 4258 7.144661 ACAGATATCGAACAGCTCTTTATCTG 58.855 38.462 18.51 18.51 42.45 2.90
4012 4263 5.694006 GCATACAGATATCGAACAGCTCTTT 59.306 40.000 0.00 0.00 0.00 2.52
4030 4281 7.039434 TGGGTAATTCAATGTGAAAAGCATACA 60.039 33.333 0.00 0.00 40.12 2.29
4043 4294 6.095377 GCAAAAGTCTCTGGGTAATTCAATG 58.905 40.000 0.00 0.00 0.00 2.82
4079 4330 6.210078 CGAGAGGCAAAACTATCTAACCTAG 58.790 44.000 0.00 0.00 0.00 3.02
4109 4360 3.829948 CTTAACAATGGCTGAGCACAAG 58.170 45.455 6.82 2.42 0.00 3.16
4118 4369 2.236489 ATGGTGGCTTAACAATGGCT 57.764 45.000 0.00 0.00 0.00 4.75
4119 4370 3.055891 AGAAATGGTGGCTTAACAATGGC 60.056 43.478 0.00 0.00 0.00 4.40
4126 4377 4.599047 CCAAACAGAAATGGTGGCTTAA 57.401 40.909 0.00 0.00 31.84 1.85


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

AutoCloner maintained by Alex Coulton.