Multiple sequence alignment - TraesCS5B01G330500

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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 TraesCS5B01G330500 chr5B 100.000 3478 0 0 1 3478 514856101 514852624 0.000000e+00 6423
1 TraesCS5B01G330500 chr5B 84.337 1079 95 31 1450 2498 514929691 514928657 0.000000e+00 989
2 TraesCS5B01G330500 chr5B 86.082 388 44 3 990 1377 514930104 514929727 3.230000e-110 409
3 TraesCS5B01G330500 chr5D 97.449 980 25 0 2499 3478 425651837 425650858 0.000000e+00 1672
4 TraesCS5B01G330500 chr5D 92.168 881 58 5 990 1862 425653948 425653071 0.000000e+00 1234
5 TraesCS5B01G330500 chr5D 88.766 632 54 9 1871 2498 425653021 425652403 0.000000e+00 758
6 TraesCS5B01G330500 chr5D 82.270 925 80 34 47 962 425655073 425654224 0.000000e+00 723
7 TraesCS5B01G330500 chr5D 84.351 639 60 18 1862 2498 425717905 425717305 1.080000e-164 590
8 TraesCS5B01G330500 chr5D 90.073 413 34 3 1450 1862 425718443 425718038 2.380000e-146 529
9 TraesCS5B01G330500 chr5D 86.340 388 43 3 990 1377 425718856 425718479 6.950000e-112 414
10 TraesCS5B01G330500 chr5A 96.439 983 32 1 2499 3478 539945646 539944664 0.000000e+00 1618
11 TraesCS5B01G330500 chr5A 86.845 1087 89 15 1451 2498 539947319 539946248 0.000000e+00 1166
12 TraesCS5B01G330500 chr5A 85.640 766 66 27 1451 2187 539957883 539957133 0.000000e+00 765
13 TraesCS5B01G330500 chr5A 90.000 390 34 3 990 1377 539947736 539947350 1.860000e-137 499
14 TraesCS5B01G330500 chr5A 83.691 233 33 3 2271 2498 539957099 539956867 7.560000e-52 215
15 TraesCS5B01G330500 chr6D 79.545 220 25 11 241 441 352873316 352873534 4.680000e-29 139


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 TraesCS5B01G330500 chr5B 514852624 514856101 3477 True 6423.000000 6423 100.000000 1 3478 1 chr5B.!!$R1 3477
1 TraesCS5B01G330500 chr5B 514928657 514930104 1447 True 699.000000 989 85.209500 990 2498 2 chr5B.!!$R2 1508
2 TraesCS5B01G330500 chr5D 425650858 425655073 4215 True 1096.750000 1672 90.163250 47 3478 4 chr5D.!!$R1 3431
3 TraesCS5B01G330500 chr5D 425717305 425718856 1551 True 511.000000 590 86.921333 990 2498 3 chr5D.!!$R2 1508
4 TraesCS5B01G330500 chr5A 539944664 539947736 3072 True 1094.333333 1618 91.094667 990 3478 3 chr5A.!!$R1 2488
5 TraesCS5B01G330500 chr5A 539956867 539957883 1016 True 490.000000 765 84.665500 1451 2498 2 chr5A.!!$R2 1047

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
92 93 0.104120 GGACGCAAAAACCAAAGCCT 59.896 50.0 0.00 0.0 0.00 4.58 F
128 129 0.108585 GAGTTCTCCTGGCCACAACA 59.891 55.0 0.00 0.0 0.00 3.33 F
177 178 0.108615 CCCTTCTCGGTGCAGTAGTG 60.109 60.0 0.00 0.0 0.00 2.74 F
348 351 0.386352 CATGCGTTGGTGCTTGAGTG 60.386 55.0 0.00 0.0 41.18 3.51 F
738 748 0.391597 TCCACTTCCACTCGGTGAAC 59.608 55.0 5.71 0.0 35.23 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1718 1998 1.628340 CACCAGGTGGACCATTGTCTA 59.372 52.381 12.40 0.00 41.47 2.59 R
1884 2312 2.169330 TCAAGTGCCATAAAGCATGCA 58.831 42.857 21.98 0.00 46.24 3.96 R
2166 2599 2.373224 CTGGAATTTTGAGGCTCTCCC 58.627 52.381 16.72 8.02 0.00 4.30 R
2344 2792 3.140325 TGAAGCCTAAGGTTTCCTGTG 57.860 47.619 0.00 0.00 41.26 3.66 R
2639 3716 1.471327 GCTGCTGACCTGATGAGAGTC 60.471 57.143 0.00 0.00 0.00 3.36 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
17 18 3.214253 TCTCCGCTCTCATGCCAG 58.786 61.111 0.00 0.00 0.00 4.85
18 19 2.588314 CTCCGCTCTCATGCCAGC 60.588 66.667 5.80 5.80 0.00 4.85
19 20 3.381333 CTCCGCTCTCATGCCAGCA 62.381 63.158 14.06 0.00 35.15 4.41
20 21 3.200593 CCGCTCTCATGCCAGCAC 61.201 66.667 14.06 0.00 35.15 4.40
21 22 3.561213 CGCTCTCATGCCAGCACG 61.561 66.667 14.06 0.00 35.15 5.34
22 23 3.200593 GCTCTCATGCCAGCACGG 61.201 66.667 10.05 0.00 35.56 4.94
38 39 2.260434 GGCCGACGACAAGCACTA 59.740 61.111 0.00 0.00 0.00 2.74
39 40 2.092882 GGCCGACGACAAGCACTAC 61.093 63.158 0.00 0.00 0.00 2.73
40 41 1.372499 GCCGACGACAAGCACTACA 60.372 57.895 0.00 0.00 0.00 2.74
41 42 1.344942 GCCGACGACAAGCACTACAG 61.345 60.000 0.00 0.00 0.00 2.74
42 43 0.240145 CCGACGACAAGCACTACAGA 59.760 55.000 0.00 0.00 0.00 3.41
43 44 1.328439 CGACGACAAGCACTACAGAC 58.672 55.000 0.00 0.00 0.00 3.51
44 45 1.328439 GACGACAAGCACTACAGACG 58.672 55.000 0.00 0.00 0.00 4.18
45 46 0.949397 ACGACAAGCACTACAGACGA 59.051 50.000 0.00 0.00 0.00 4.20
49 50 1.954382 ACAAGCACTACAGACGACTCA 59.046 47.619 0.00 0.00 0.00 3.41
58 59 2.876645 GACGACTCAAGCTCGCCG 60.877 66.667 0.00 0.00 34.34 6.46
62 63 1.372997 GACTCAAGCTCGCCGTTGA 60.373 57.895 0.00 0.00 0.00 3.18
66 67 3.044305 AAGCTCGCCGTTGACAGC 61.044 61.111 0.00 0.00 0.00 4.40
67 68 3.807631 AAGCTCGCCGTTGACAGCA 62.808 57.895 0.00 0.00 34.08 4.41
77 78 1.672030 TTGACAGCAGCCATGGACG 60.672 57.895 18.40 6.15 0.00 4.79
92 93 0.104120 GGACGCAAAAACCAAAGCCT 59.896 50.000 0.00 0.00 0.00 4.58
93 94 1.208259 GACGCAAAAACCAAAGCCTG 58.792 50.000 0.00 0.00 0.00 4.85
101 102 1.122227 AACCAAAGCCTGCACACAAT 58.878 45.000 0.00 0.00 0.00 2.71
117 118 1.486726 ACAATGATCCCGGAGTTCTCC 59.513 52.381 0.73 8.66 0.00 3.71
128 129 0.108585 GAGTTCTCCTGGCCACAACA 59.891 55.000 0.00 0.00 0.00 3.33
132 133 2.672651 TCCTGGCCACAACATGCG 60.673 61.111 0.00 0.00 0.00 4.73
159 160 2.276869 AAAAATCCCGGAGCTTGCC 58.723 52.632 0.73 0.00 0.00 4.52
160 161 1.257750 AAAAATCCCGGAGCTTGCCC 61.258 55.000 0.73 0.00 0.00 5.36
161 162 2.155197 AAAATCCCGGAGCTTGCCCT 62.155 55.000 0.73 0.00 0.00 5.19
162 163 2.155197 AAATCCCGGAGCTTGCCCTT 62.155 55.000 0.73 0.00 0.00 3.95
163 164 2.558380 AATCCCGGAGCTTGCCCTTC 62.558 60.000 0.73 0.00 0.00 3.46
164 165 3.721706 CCCGGAGCTTGCCCTTCT 61.722 66.667 0.73 0.00 0.00 2.85
168 169 2.665603 GAGCTTGCCCTTCTCGGT 59.334 61.111 0.00 0.00 0.00 4.69
169 170 1.743252 GAGCTTGCCCTTCTCGGTG 60.743 63.158 0.00 0.00 0.00 4.94
171 172 2.032528 CTTGCCCTTCTCGGTGCA 59.967 61.111 0.00 0.00 37.24 4.57
172 173 2.032528 TTGCCCTTCTCGGTGCAG 59.967 61.111 0.00 0.00 39.22 4.41
173 174 2.738213 CTTGCCCTTCTCGGTGCAGT 62.738 60.000 0.00 0.00 39.22 4.40
174 175 1.476845 TTGCCCTTCTCGGTGCAGTA 61.477 55.000 0.00 0.00 39.22 2.74
175 176 1.153549 GCCCTTCTCGGTGCAGTAG 60.154 63.158 0.00 0.00 0.00 2.57
176 177 1.889530 GCCCTTCTCGGTGCAGTAGT 61.890 60.000 0.00 0.00 0.00 2.73
177 178 0.108615 CCCTTCTCGGTGCAGTAGTG 60.109 60.000 0.00 0.00 0.00 2.74
224 225 1.202533 CGTGGGATGGGTACAGATCAC 60.203 57.143 0.00 0.00 0.00 3.06
225 226 1.119684 TGGGATGGGTACAGATCACG 58.880 55.000 0.00 0.00 0.00 4.35
227 228 1.120530 GGATGGGTACAGATCACGGT 58.879 55.000 0.00 0.00 0.00 4.83
231 232 1.274167 TGGGTACAGATCACGGTGAAC 59.726 52.381 15.72 12.70 0.00 3.18
246 247 3.059597 CGGTGAACAAGTCTCACAATCAC 60.060 47.826 5.42 0.00 44.16 3.06
270 271 6.876257 ACTAGGAACAAATCTCTCAATCACAC 59.124 38.462 0.00 0.00 0.00 3.82
299 302 5.179045 ACTCTCAATCAAGTTGTTGCTTG 57.821 39.130 2.11 3.83 45.18 4.01
343 346 3.683937 GCCCATGCGTTGGTGCTT 61.684 61.111 4.93 0.00 44.83 3.91
344 347 2.259204 CCCATGCGTTGGTGCTTG 59.741 61.111 4.93 0.00 44.83 4.01
348 351 0.386352 CATGCGTTGGTGCTTGAGTG 60.386 55.000 0.00 0.00 41.18 3.51
366 369 3.772932 AGTGCACACAAAGTGTTTGATG 58.227 40.909 21.04 5.50 45.08 3.07
374 377 4.739228 CACAAAGTGTTTGATGAAATGCGA 59.261 37.500 6.40 0.00 43.26 5.10
375 378 4.739716 ACAAAGTGTTTGATGAAATGCGAC 59.260 37.500 6.40 0.00 43.26 5.19
376 379 4.566545 AAGTGTTTGATGAAATGCGACA 57.433 36.364 0.00 0.00 0.00 4.35
377 380 3.888934 AGTGTTTGATGAAATGCGACAC 58.111 40.909 0.00 0.00 36.94 3.67
378 381 2.651703 GTGTTTGATGAAATGCGACACG 59.348 45.455 0.00 0.00 0.00 4.49
379 382 2.545946 TGTTTGATGAAATGCGACACGA 59.454 40.909 0.00 0.00 0.00 4.35
381 384 2.873170 TGATGAAATGCGACACGAAC 57.127 45.000 0.00 0.00 0.00 3.95
382 385 1.125930 TGATGAAATGCGACACGAACG 59.874 47.619 0.00 0.00 0.00 3.95
426 436 1.808945 CTATGATTGAATGGCCGGCTC 59.191 52.381 28.56 17.20 0.00 4.70
429 439 2.909457 GATTGAATGGCCGGCTCCCA 62.909 60.000 28.56 17.00 36.66 4.37
432 442 3.721370 GAATGGCCGGCTCCCACAT 62.721 63.158 28.56 17.86 34.68 3.21
433 443 3.721370 AATGGCCGGCTCCCACATC 62.721 63.158 28.56 7.32 34.68 3.06
437 447 4.082523 CCGGCTCCCACATCGTGT 62.083 66.667 0.00 0.00 0.00 4.49
438 448 2.509336 CGGCTCCCACATCGTGTC 60.509 66.667 0.00 0.00 0.00 3.67
439 449 2.125106 GGCTCCCACATCGTGTCC 60.125 66.667 0.00 0.00 0.00 4.02
440 450 2.662596 GCTCCCACATCGTGTCCA 59.337 61.111 0.00 0.00 0.00 4.02
441 451 1.221840 GCTCCCACATCGTGTCCAT 59.778 57.895 0.00 0.00 0.00 3.41
442 452 1.091771 GCTCCCACATCGTGTCCATG 61.092 60.000 0.00 0.00 0.00 3.66
443 453 0.462581 CTCCCACATCGTGTCCATGG 60.463 60.000 4.97 4.97 0.00 3.66
444 454 0.907230 TCCCACATCGTGTCCATGGA 60.907 55.000 11.44 11.44 31.69 3.41
445 455 0.744414 CCCACATCGTGTCCATGGAC 60.744 60.000 33.97 33.97 44.77 4.02
454 464 2.159181 GTCCATGGACGTGTTTCGG 58.841 57.895 28.52 0.00 44.69 4.30
458 468 2.027929 TCCATGGACGTGTTTCGGTATT 60.028 45.455 11.44 0.00 44.69 1.89
460 470 4.124238 CCATGGACGTGTTTCGGTATTAT 58.876 43.478 5.56 0.00 44.69 1.28
464 474 3.524541 GACGTGTTTCGGTATTATGGGT 58.475 45.455 0.00 0.00 44.69 4.51
465 475 3.524541 ACGTGTTTCGGTATTATGGGTC 58.475 45.455 0.00 0.00 44.69 4.46
466 476 3.055963 ACGTGTTTCGGTATTATGGGTCA 60.056 43.478 0.00 0.00 44.69 4.02
467 477 3.554324 CGTGTTTCGGTATTATGGGTCAG 59.446 47.826 0.00 0.00 35.71 3.51
468 478 4.678574 CGTGTTTCGGTATTATGGGTCAGA 60.679 45.833 0.00 0.00 35.71 3.27
469 479 4.809426 GTGTTTCGGTATTATGGGTCAGAG 59.191 45.833 0.00 0.00 0.00 3.35
470 480 4.712829 TGTTTCGGTATTATGGGTCAGAGA 59.287 41.667 0.00 0.00 0.00 3.10
471 481 4.931661 TTCGGTATTATGGGTCAGAGAC 57.068 45.455 0.00 0.00 0.00 3.36
472 482 2.882761 TCGGTATTATGGGTCAGAGACG 59.117 50.000 0.00 0.00 32.65 4.18
479 489 2.338984 GGTCAGAGACGCACCGTT 59.661 61.111 0.00 0.00 41.37 4.44
481 491 1.007734 GTCAGAGACGCACCGTTGA 60.008 57.895 0.00 0.00 41.37 3.18
493 503 2.528743 CCGTTGAGCAGCGCATAGG 61.529 63.158 11.47 2.77 33.61 2.57
494 504 2.711924 GTTGAGCAGCGCATAGGC 59.288 61.111 11.47 7.81 0.00 3.93
497 507 0.530650 TTGAGCAGCGCATAGGCTAC 60.531 55.000 11.47 7.81 42.53 3.58
506 516 2.476519 GCGCATAGGCTACGAGATACTC 60.477 54.545 0.30 0.00 38.10 2.59
509 519 4.515361 GCATAGGCTACGAGATACTCCTA 58.485 47.826 0.00 0.00 36.96 2.94
510 520 4.333372 GCATAGGCTACGAGATACTCCTAC 59.667 50.000 0.00 0.00 36.96 3.18
512 522 4.644163 AGGCTACGAGATACTCCTACAT 57.356 45.455 0.00 0.00 0.00 2.29
513 523 4.988029 AGGCTACGAGATACTCCTACATT 58.012 43.478 0.00 0.00 0.00 2.71
514 524 6.124316 AGGCTACGAGATACTCCTACATTA 57.876 41.667 0.00 0.00 0.00 1.90
516 526 5.939296 GGCTACGAGATACTCCTACATTACT 59.061 44.000 0.00 0.00 0.00 2.24
517 527 7.038445 AGGCTACGAGATACTCCTACATTACTA 60.038 40.741 0.00 0.00 0.00 1.82
518 528 7.064490 GGCTACGAGATACTCCTACATTACTAC 59.936 44.444 0.00 0.00 0.00 2.73
519 529 7.818930 GCTACGAGATACTCCTACATTACTACT 59.181 40.741 0.00 0.00 0.00 2.57
520 530 9.357652 CTACGAGATACTCCTACATTACTACTC 57.642 40.741 0.00 0.00 0.00 2.59
521 531 7.160726 ACGAGATACTCCTACATTACTACTCC 58.839 42.308 0.00 0.00 0.00 3.85
522 532 7.160049 CGAGATACTCCTACATTACTACTCCA 58.840 42.308 0.00 0.00 0.00 3.86
523 533 7.118101 CGAGATACTCCTACATTACTACTCCAC 59.882 44.444 0.00 0.00 0.00 4.02
524 534 7.813331 AGATACTCCTACATTACTACTCCACA 58.187 38.462 0.00 0.00 0.00 4.17
525 535 7.940137 AGATACTCCTACATTACTACTCCACAG 59.060 40.741 0.00 0.00 0.00 3.66
526 536 4.645588 ACTCCTACATTACTACTCCACAGC 59.354 45.833 0.00 0.00 0.00 4.40
527 537 4.868268 TCCTACATTACTACTCCACAGCT 58.132 43.478 0.00 0.00 0.00 4.24
533 543 0.409876 ACTACTCCACAGCTCCAGGA 59.590 55.000 0.00 0.00 0.00 3.86
540 550 1.561643 CACAGCTCCAGGAACTAGGA 58.438 55.000 0.00 0.00 36.02 2.94
561 571 3.403038 AGATGAAAGCGCTACAGTGTTT 58.597 40.909 12.05 0.00 0.00 2.83
570 580 3.365220 GCGCTACAGTGTTTTACAGAGAG 59.635 47.826 0.00 0.00 0.00 3.20
573 583 5.563085 CGCTACAGTGTTTTACAGAGAGACT 60.563 44.000 0.00 0.00 0.00 3.24
613 623 2.434359 GAAAGCGACGGGGGAGTG 60.434 66.667 0.00 0.00 0.00 3.51
641 651 3.128242 CAGCTAAAAAGCAGATCCACAGG 59.872 47.826 0.00 0.00 37.25 4.00
692 702 8.607713 TCCATGTTCTAGTAATCTGGGTAAAAA 58.392 33.333 0.00 0.00 0.00 1.94
738 748 0.391597 TCCACTTCCACTCGGTGAAC 59.608 55.000 5.71 0.00 35.23 3.18
768 778 2.352323 GCCTATAAGAGCTCTCCTTCGC 60.352 54.545 18.55 12.57 0.00 4.70
802 812 4.082463 GCGTGAACTCAATTCCCCAATTAA 60.082 41.667 0.00 0.00 36.36 1.40
831 841 3.505386 AGACCCCATATACTCTCTGCTG 58.495 50.000 0.00 0.00 0.00 4.41
840 850 6.239148 CCATATACTCTCTGCTGCTCTGTTAA 60.239 42.308 0.00 0.00 0.00 2.01
841 851 5.667539 ATACTCTCTGCTGCTCTGTTAAA 57.332 39.130 0.00 0.00 0.00 1.52
842 852 3.924144 ACTCTCTGCTGCTCTGTTAAAG 58.076 45.455 0.00 0.00 0.00 1.85
843 853 3.323403 ACTCTCTGCTGCTCTGTTAAAGT 59.677 43.478 0.00 0.00 0.00 2.66
844 854 3.919216 TCTCTGCTGCTCTGTTAAAGTC 58.081 45.455 0.00 0.00 0.00 3.01
845 855 2.999355 CTCTGCTGCTCTGTTAAAGTCC 59.001 50.000 0.00 0.00 0.00 3.85
846 856 1.728971 CTGCTGCTCTGTTAAAGTCCG 59.271 52.381 0.00 0.00 0.00 4.79
847 857 1.343142 TGCTGCTCTGTTAAAGTCCGA 59.657 47.619 0.00 0.00 0.00 4.55
848 858 1.727335 GCTGCTCTGTTAAAGTCCGAC 59.273 52.381 0.00 0.00 0.00 4.79
849 859 2.610727 GCTGCTCTGTTAAAGTCCGACT 60.611 50.000 0.00 0.00 0.00 4.18
850 860 2.989840 CTGCTCTGTTAAAGTCCGACTG 59.010 50.000 0.65 0.00 0.00 3.51
851 861 2.626266 TGCTCTGTTAAAGTCCGACTGA 59.374 45.455 0.65 0.00 0.00 3.41
852 862 3.258372 TGCTCTGTTAAAGTCCGACTGAT 59.742 43.478 0.65 0.00 0.00 2.90
853 863 4.461431 TGCTCTGTTAAAGTCCGACTGATA 59.539 41.667 0.65 0.00 0.00 2.15
854 864 4.799428 GCTCTGTTAAAGTCCGACTGATAC 59.201 45.833 0.65 1.48 0.00 2.24
855 865 5.621555 GCTCTGTTAAAGTCCGACTGATACA 60.622 44.000 0.65 5.87 0.00 2.29
904 914 1.071542 TCGGGTTGCTCTTGTTGATCA 59.928 47.619 0.00 0.00 0.00 2.92
966 976 4.452733 CGGGGTTCTCGGCCTCAC 62.453 72.222 0.00 0.00 0.00 3.51
967 977 4.097361 GGGGTTCTCGGCCTCACC 62.097 72.222 0.00 0.61 0.00 4.02
978 988 4.003788 CCTCACCGGTGGCGAACT 62.004 66.667 33.40 0.00 0.00 3.01
1043 1313 3.347958 TGATCACTTTGCGGTTGTTTC 57.652 42.857 0.00 0.00 0.00 2.78
1058 1330 4.026886 GGTTGTTTCTGCAGCGTTTTTAAG 60.027 41.667 9.47 0.00 0.00 1.85
1124 1396 4.684485 CGAAGAGGCCTGTTGGAATTCTAT 60.684 45.833 21.75 0.00 34.57 1.98
1189 1467 5.018539 TGTTGGGTAGTAAATCAGATCCG 57.981 43.478 0.00 0.00 0.00 4.18
1239 1517 3.575687 AGGCTTCCATCCAAGAAAACAAG 59.424 43.478 0.00 0.00 0.00 3.16
1377 1655 3.507622 CCTTCCTTTGTTCATCAAGTCCC 59.492 47.826 0.00 0.00 37.35 4.46
1380 1658 3.888930 TCCTTTGTTCATCAAGTCCCAAC 59.111 43.478 0.00 0.00 37.35 3.77
1382 1660 4.261741 CCTTTGTTCATCAAGTCCCAACTG 60.262 45.833 0.00 0.00 37.35 3.16
1384 1662 2.441375 TGTTCATCAAGTCCCAACTGGA 59.559 45.455 0.00 0.00 39.82 3.86
1385 1663 3.074390 TGTTCATCAAGTCCCAACTGGAT 59.926 43.478 0.00 0.00 45.48 3.41
1420 1698 7.330208 CGTATACACTACCATATTAAACTGCCC 59.670 40.741 3.32 0.00 0.00 5.36
1428 1706 4.156922 CCATATTAAACTGCCCAAACGTCA 59.843 41.667 0.00 0.00 0.00 4.35
1429 1707 5.163561 CCATATTAAACTGCCCAAACGTCAT 60.164 40.000 0.00 0.00 0.00 3.06
1441 1721 4.215399 CCCAAACGTCATACATTTGTGAGT 59.785 41.667 0.00 0.00 32.53 3.41
1502 1782 9.085645 TCGATATATCTAGGTTGGTAAACATGT 57.914 33.333 10.93 0.00 38.10 3.21
1520 1800 2.874014 TGTGAAGATGGGCATGAACAA 58.126 42.857 0.00 0.00 0.00 2.83
1590 1870 6.698380 TCTTAACTTACTGAAGACCATGGAC 58.302 40.000 21.47 13.40 36.45 4.02
1615 1895 7.872483 ACCCAAATGATGTACAAAATGAGAAAC 59.128 33.333 0.00 0.00 0.00 2.78
1701 1981 4.574674 AGAAAGCATGGATGGTACTGAA 57.425 40.909 0.00 0.00 37.57 3.02
1706 1986 2.615912 GCATGGATGGTACTGAAGAAGC 59.384 50.000 0.00 0.00 0.00 3.86
1718 1998 3.181456 ACTGAAGAAGCACAGAAAGCTCT 60.181 43.478 0.00 0.00 42.53 4.09
1726 2006 4.252073 AGCACAGAAAGCTCTAGACAATG 58.748 43.478 0.00 0.00 38.01 2.82
1727 2007 3.373439 GCACAGAAAGCTCTAGACAATGG 59.627 47.826 0.00 0.00 0.00 3.16
1732 2012 3.618690 AAGCTCTAGACAATGGTCCAC 57.381 47.619 0.00 0.00 45.48 4.02
1752 2032 2.091102 CTGGTGGTGGGCTGCTTTTG 62.091 60.000 0.00 0.00 0.00 2.44
1911 2340 4.183865 GCTTTATGGCACTTGAATTTCCC 58.816 43.478 0.00 0.00 0.00 3.97
1912 2341 4.081476 GCTTTATGGCACTTGAATTTCCCT 60.081 41.667 0.00 0.00 0.00 4.20
2027 2456 6.554334 TGCATGTTGAAGTCCTAAGTAAAC 57.446 37.500 0.00 0.00 0.00 2.01
2083 2515 7.727181 AGGTACGATATTCTACAAGAAATGCT 58.273 34.615 0.00 0.00 37.82 3.79
2084 2516 8.204836 AGGTACGATATTCTACAAGAAATGCTT 58.795 33.333 0.00 0.00 37.82 3.91
2187 2620 1.747924 GGAGAGCCTCAAAATTCCAGC 59.252 52.381 0.00 0.00 31.08 4.85
2189 2622 3.087781 GAGAGCCTCAAAATTCCAGCTT 58.912 45.455 0.00 0.00 0.00 3.74
2234 2672 9.868277 TGCTTTTATTTCTTCTGTTTCTTTTGA 57.132 25.926 0.00 0.00 0.00 2.69
2262 2700 7.962441 TGATCATATGAATAAGAGGGTTCGAA 58.038 34.615 9.99 0.00 0.00 3.71
2263 2701 8.428852 TGATCATATGAATAAGAGGGTTCGAAA 58.571 33.333 9.99 0.00 0.00 3.46
2319 2759 3.181500 GCTGGATTGTACGAAATTGTCCC 60.181 47.826 0.00 0.00 0.00 4.46
2320 2760 3.004171 TGGATTGTACGAAATTGTCCCG 58.996 45.455 0.00 0.00 0.00 5.14
2336 2784 5.601583 TGTCCCGTCACTTTGCTTATATA 57.398 39.130 0.00 0.00 0.00 0.86
2344 2792 7.850982 CCGTCACTTTGCTTATATAATGTTGTC 59.149 37.037 0.00 0.00 0.00 3.18
2362 2810 2.441750 TGTCACAGGAAACCTTAGGCTT 59.558 45.455 0.00 0.00 0.00 4.35
2367 2815 4.524328 CACAGGAAACCTTAGGCTTCATTT 59.476 41.667 15.27 0.00 0.00 2.32
2383 2831 4.574674 TCATTTATATAGCCCTGGCAGG 57.425 45.455 27.04 27.04 44.88 4.85
2639 3716 1.376424 AGTGACCAGAGGCAATGCG 60.376 57.895 0.00 0.00 0.00 4.73
2773 3850 1.674651 GAAGACGTTGGGGAAGCCC 60.675 63.158 0.00 0.00 44.51 5.19
2845 3922 1.399504 GCTTGCTCTTCTCGTCGTCG 61.400 60.000 0.00 0.00 38.55 5.12
2881 3958 3.901797 CTCCACCTTCGCCCGCTTT 62.902 63.158 0.00 0.00 0.00 3.51
2887 3964 2.593148 TTCGCCCGCTTTTCTGCA 60.593 55.556 0.00 0.00 0.00 4.41
3130 4207 4.025858 GCCAGCTGCCACTCCTCA 62.026 66.667 8.66 0.00 0.00 3.86
3135 4212 1.227943 GCTGCCACTCCTCACACAA 60.228 57.895 0.00 0.00 0.00 3.33
3148 4225 3.306294 CCTCACACAAGCTGTAGATGTCA 60.306 47.826 0.00 0.00 0.00 3.58
3182 4259 4.074970 GTCTTTCATGAGTGGGTTGTGAT 58.925 43.478 0.00 0.00 0.00 3.06
3385 4462 0.253044 CCATGTGGGTCTGTACCTGG 59.747 60.000 0.00 0.00 45.95 4.45
3416 4493 3.411114 ATGCCCCTCCACATGCTCG 62.411 63.158 0.00 0.00 0.00 5.03
3441 4518 5.105106 TCAAGCTGAAATGGAATGCATTCAT 60.105 36.000 34.08 23.71 38.53 2.57
3471 4548 2.486982 ACATGCATGAGAACAGAGCAAC 59.513 45.455 32.75 0.00 41.62 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.086391 GCTGGCATGAGAGCGGAGA 62.086 63.158 0.00 0.00 34.64 3.71
1 2 2.588314 GCTGGCATGAGAGCGGAG 60.588 66.667 0.00 0.00 34.64 4.63
2 3 3.393106 TGCTGGCATGAGAGCGGA 61.393 61.111 0.00 0.00 38.09 5.54
3 4 3.200593 GTGCTGGCATGAGAGCGG 61.201 66.667 0.00 0.00 38.09 5.52
4 5 3.561213 CGTGCTGGCATGAGAGCG 61.561 66.667 8.93 0.00 38.09 5.03
5 6 3.200593 CCGTGCTGGCATGAGAGC 61.201 66.667 15.37 8.98 35.09 4.09
20 21 3.620300 TAGTGCTTGTCGTCGGCCG 62.620 63.158 22.12 22.12 38.13 6.13
21 22 2.092882 GTAGTGCTTGTCGTCGGCC 61.093 63.158 0.00 0.00 0.00 6.13
22 23 1.344942 CTGTAGTGCTTGTCGTCGGC 61.345 60.000 0.00 0.00 0.00 5.54
23 24 0.240145 TCTGTAGTGCTTGTCGTCGG 59.760 55.000 0.00 0.00 0.00 4.79
24 25 1.328439 GTCTGTAGTGCTTGTCGTCG 58.672 55.000 0.00 0.00 0.00 5.12
25 26 1.069432 TCGTCTGTAGTGCTTGTCGTC 60.069 52.381 0.00 0.00 0.00 4.20
26 27 0.949397 TCGTCTGTAGTGCTTGTCGT 59.051 50.000 0.00 0.00 0.00 4.34
27 28 1.069159 AGTCGTCTGTAGTGCTTGTCG 60.069 52.381 0.00 0.00 0.00 4.35
28 29 2.031069 TGAGTCGTCTGTAGTGCTTGTC 60.031 50.000 0.00 0.00 0.00 3.18
29 30 1.954382 TGAGTCGTCTGTAGTGCTTGT 59.046 47.619 0.00 0.00 0.00 3.16
30 31 2.706555 TGAGTCGTCTGTAGTGCTTG 57.293 50.000 0.00 0.00 0.00 4.01
31 32 2.608261 GCTTGAGTCGTCTGTAGTGCTT 60.608 50.000 0.00 0.00 0.00 3.91
32 33 1.068194 GCTTGAGTCGTCTGTAGTGCT 60.068 52.381 0.00 0.00 0.00 4.40
33 34 1.068194 AGCTTGAGTCGTCTGTAGTGC 60.068 52.381 0.00 0.00 0.00 4.40
34 35 2.726373 CGAGCTTGAGTCGTCTGTAGTG 60.726 54.545 0.00 0.00 32.62 2.74
35 36 1.465387 CGAGCTTGAGTCGTCTGTAGT 59.535 52.381 0.00 0.00 32.62 2.73
36 37 1.792273 GCGAGCTTGAGTCGTCTGTAG 60.792 57.143 4.70 0.00 39.69 2.74
37 38 0.168348 GCGAGCTTGAGTCGTCTGTA 59.832 55.000 4.70 0.00 39.69 2.74
38 39 1.081108 GCGAGCTTGAGTCGTCTGT 60.081 57.895 4.70 0.00 39.69 3.41
39 40 1.803519 GGCGAGCTTGAGTCGTCTG 60.804 63.158 4.70 0.00 38.99 3.51
40 41 2.569134 GGCGAGCTTGAGTCGTCT 59.431 61.111 4.70 0.00 38.99 4.18
41 42 2.876645 CGGCGAGCTTGAGTCGTC 60.877 66.667 4.70 0.00 39.69 4.20
42 43 3.208884 AACGGCGAGCTTGAGTCGT 62.209 57.895 16.62 8.41 39.69 4.34
43 44 2.430921 AACGGCGAGCTTGAGTCG 60.431 61.111 16.62 7.71 40.50 4.18
44 45 1.372997 TCAACGGCGAGCTTGAGTC 60.373 57.895 16.62 0.00 0.00 3.36
45 46 1.664965 GTCAACGGCGAGCTTGAGT 60.665 57.895 16.62 0.45 0.00 3.41
49 50 3.044305 GCTGTCAACGGCGAGCTT 61.044 61.111 16.62 0.00 38.61 3.74
58 59 1.878775 GTCCATGGCTGCTGTCAAC 59.121 57.895 6.96 0.00 0.00 3.18
62 63 3.848301 TTGCGTCCATGGCTGCTGT 62.848 57.895 23.14 0.00 0.00 4.40
66 67 0.667184 GGTTTTTGCGTCCATGGCTG 60.667 55.000 6.96 2.36 0.00 4.85
67 68 1.112315 TGGTTTTTGCGTCCATGGCT 61.112 50.000 6.96 0.00 0.00 4.75
77 78 0.657312 GTGCAGGCTTTGGTTTTTGC 59.343 50.000 0.00 0.00 0.00 3.68
92 93 0.392863 CTCCGGGATCATTGTGTGCA 60.393 55.000 0.00 0.00 0.00 4.57
93 94 0.392998 ACTCCGGGATCATTGTGTGC 60.393 55.000 0.00 0.00 0.00 4.57
117 118 2.256158 CACGCATGTTGTGGCCAG 59.744 61.111 5.11 0.00 33.69 4.85
145 146 3.017581 AAGGGCAAGCTCCGGGAT 61.018 61.111 0.00 0.00 0.00 3.85
146 147 3.717294 GAAGGGCAAGCTCCGGGA 61.717 66.667 0.00 0.00 0.00 5.14
149 150 2.510238 CGAGAAGGGCAAGCTCCG 60.510 66.667 0.00 0.00 0.00 4.63
151 152 1.743252 CACCGAGAAGGGCAAGCTC 60.743 63.158 0.00 0.00 46.96 4.09
152 153 2.348998 CACCGAGAAGGGCAAGCT 59.651 61.111 0.00 0.00 46.96 3.74
153 154 3.435186 GCACCGAGAAGGGCAAGC 61.435 66.667 0.00 0.00 46.96 4.01
154 155 2.032528 TGCACCGAGAAGGGCAAG 59.967 61.111 0.00 0.00 46.96 4.01
155 156 1.476845 TACTGCACCGAGAAGGGCAA 61.477 55.000 0.00 0.00 46.96 4.52
156 157 1.888436 CTACTGCACCGAGAAGGGCA 61.888 60.000 0.00 0.00 46.96 5.36
157 158 1.153549 CTACTGCACCGAGAAGGGC 60.154 63.158 0.00 0.00 46.96 5.19
159 160 0.737715 GCACTACTGCACCGAGAAGG 60.738 60.000 0.00 0.00 43.62 3.46
160 161 0.737715 GGCACTACTGCACCGAGAAG 60.738 60.000 0.00 0.00 46.28 2.85
161 162 1.292223 GGCACTACTGCACCGAGAA 59.708 57.895 0.00 0.00 46.28 2.87
162 163 2.646175 GGGCACTACTGCACCGAGA 61.646 63.158 0.00 0.00 46.28 4.04
163 164 2.125512 GGGCACTACTGCACCGAG 60.126 66.667 0.00 0.00 46.28 4.63
198 199 1.687840 TACCCATCCCACGGACCAG 60.688 63.158 0.00 0.00 32.98 4.00
199 200 1.991167 GTACCCATCCCACGGACCA 60.991 63.158 0.00 0.00 32.98 4.02
203 204 0.393077 GATCTGTACCCATCCCACGG 59.607 60.000 0.00 0.00 0.00 4.94
224 225 3.059597 GTGATTGTGAGACTTGTTCACCG 60.060 47.826 3.24 0.00 43.32 4.94
225 226 4.130118 AGTGATTGTGAGACTTGTTCACC 58.870 43.478 3.24 0.00 43.32 4.02
227 228 5.304357 TCCTAGTGATTGTGAGACTTGTTCA 59.696 40.000 0.00 0.00 0.00 3.18
231 232 5.541845 TGTTCCTAGTGATTGTGAGACTTG 58.458 41.667 0.00 0.00 0.00 3.16
246 247 6.035435 CGTGTGATTGAGAGATTTGTTCCTAG 59.965 42.308 0.00 0.00 0.00 3.02
270 271 4.776743 CAACTTGATTGAGAGTTGTTCCG 58.223 43.478 7.80 0.00 44.73 4.30
330 333 1.951510 CACTCAAGCACCAACGCAT 59.048 52.632 0.00 0.00 0.00 4.73
331 334 2.833533 GCACTCAAGCACCAACGCA 61.834 57.895 0.00 0.00 0.00 5.24
332 335 2.050985 GCACTCAAGCACCAACGC 60.051 61.111 0.00 0.00 0.00 4.84
333 336 3.419828 TGCACTCAAGCACCAACG 58.580 55.556 0.00 0.00 40.11 4.10
343 346 2.816672 TCAAACACTTTGTGTGCACTCA 59.183 40.909 19.41 18.25 46.79 3.41
344 347 3.485947 TCAAACACTTTGTGTGCACTC 57.514 42.857 19.41 15.51 46.79 3.51
348 351 5.730269 CATTTCATCAAACACTTTGTGTGC 58.270 37.500 4.01 0.00 46.79 4.57
366 369 1.057636 TCTCGTTCGTGTCGCATTTC 58.942 50.000 0.00 0.00 0.00 2.17
374 377 3.928727 TCCTATTTGTCTCGTTCGTGT 57.071 42.857 0.00 0.00 0.00 4.49
375 378 5.585500 TTTTCCTATTTGTCTCGTTCGTG 57.415 39.130 0.00 0.00 0.00 4.35
376 379 6.796705 ATTTTTCCTATTTGTCTCGTTCGT 57.203 33.333 0.00 0.00 0.00 3.85
377 380 7.295201 TCAATTTTTCCTATTTGTCTCGTTCG 58.705 34.615 0.00 0.00 0.00 3.95
405 415 1.143684 AGCCGGCCATTCAATCATAGT 59.856 47.619 26.15 0.00 0.00 2.12
426 436 0.744414 GTCCATGGACACGATGTGGG 60.744 60.000 35.21 0.00 44.02 4.61
429 439 0.389817 CACGTCCATGGACACGATGT 60.390 55.000 37.42 25.99 44.77 3.06
432 442 0.105224 AAACACGTCCATGGACACGA 59.895 50.000 37.42 5.79 44.77 4.35
433 443 0.511221 GAAACACGTCCATGGACACG 59.489 55.000 37.42 29.84 44.77 4.49
435 445 0.601576 CCGAAACACGTCCATGGACA 60.602 55.000 37.42 7.42 44.77 4.02
436 446 0.601841 ACCGAAACACGTCCATGGAC 60.602 55.000 31.59 31.59 40.78 4.02
437 447 0.967662 TACCGAAACACGTCCATGGA 59.032 50.000 11.44 11.44 40.78 3.41
438 448 2.018542 ATACCGAAACACGTCCATGG 57.981 50.000 4.97 4.97 40.78 3.66
439 449 4.025229 CCATAATACCGAAACACGTCCATG 60.025 45.833 0.00 0.00 40.78 3.66
440 450 4.124238 CCATAATACCGAAACACGTCCAT 58.876 43.478 0.00 0.00 40.78 3.41
441 451 3.523547 CCATAATACCGAAACACGTCCA 58.476 45.455 0.00 0.00 40.78 4.02
442 452 2.867975 CCCATAATACCGAAACACGTCC 59.132 50.000 0.00 0.00 40.78 4.79
443 453 3.524541 ACCCATAATACCGAAACACGTC 58.475 45.455 0.00 0.00 40.78 4.34
444 454 3.055963 TGACCCATAATACCGAAACACGT 60.056 43.478 0.00 0.00 40.78 4.49
445 455 3.523547 TGACCCATAATACCGAAACACG 58.476 45.455 0.00 0.00 42.18 4.49
453 463 2.364324 TGCGTCTCTGACCCATAATACC 59.636 50.000 0.00 0.00 0.00 2.73
454 464 3.381949 GTGCGTCTCTGACCCATAATAC 58.618 50.000 0.00 0.00 0.00 1.89
458 468 1.663379 CGGTGCGTCTCTGACCCATA 61.663 60.000 0.00 0.00 0.00 2.74
460 470 3.680786 CGGTGCGTCTCTGACCCA 61.681 66.667 0.00 0.00 0.00 4.51
464 474 1.285950 CTCAACGGTGCGTCTCTGA 59.714 57.895 0.00 0.00 39.99 3.27
465 475 2.375766 GCTCAACGGTGCGTCTCTG 61.376 63.158 0.00 0.00 39.99 3.35
466 476 2.049063 GCTCAACGGTGCGTCTCT 60.049 61.111 0.00 0.00 39.99 3.10
467 477 2.355837 TGCTCAACGGTGCGTCTC 60.356 61.111 0.00 0.00 39.99 3.36
468 478 2.356313 CTGCTCAACGGTGCGTCT 60.356 61.111 0.00 0.00 39.99 4.18
469 479 4.077188 GCTGCTCAACGGTGCGTC 62.077 66.667 0.00 0.00 39.99 5.19
479 489 1.068083 GTAGCCTATGCGCTGCTCA 59.932 57.895 9.73 0.00 44.33 4.26
481 491 2.028190 CGTAGCCTATGCGCTGCT 59.972 61.111 9.73 13.82 44.33 4.24
493 503 7.818930 AGTAGTAATGTAGGAGTATCTCGTAGC 59.181 40.741 0.41 0.00 32.61 3.58
494 504 9.357652 GAGTAGTAATGTAGGAGTATCTCGTAG 57.642 40.741 0.41 0.00 32.61 3.51
497 507 7.118101 GTGGAGTAGTAATGTAGGAGTATCTCG 59.882 44.444 0.00 0.00 33.73 4.04
506 516 4.038162 GGAGCTGTGGAGTAGTAATGTAGG 59.962 50.000 0.00 0.00 0.00 3.18
509 519 3.441101 TGGAGCTGTGGAGTAGTAATGT 58.559 45.455 0.00 0.00 0.00 2.71
510 520 3.181471 CCTGGAGCTGTGGAGTAGTAATG 60.181 52.174 0.00 0.00 0.00 1.90
512 522 2.042569 TCCTGGAGCTGTGGAGTAGTAA 59.957 50.000 0.00 0.00 0.00 2.24
513 523 1.639108 TCCTGGAGCTGTGGAGTAGTA 59.361 52.381 0.00 0.00 0.00 1.82
514 524 0.409876 TCCTGGAGCTGTGGAGTAGT 59.590 55.000 0.00 0.00 0.00 2.73
516 526 1.203187 AGTTCCTGGAGCTGTGGAGTA 60.203 52.381 12.62 0.00 0.00 2.59
517 527 0.472734 AGTTCCTGGAGCTGTGGAGT 60.473 55.000 12.62 0.00 0.00 3.85
518 528 1.480137 CTAGTTCCTGGAGCTGTGGAG 59.520 57.143 21.67 8.30 0.00 3.86
519 529 1.561643 CTAGTTCCTGGAGCTGTGGA 58.438 55.000 21.67 2.18 0.00 4.02
520 530 0.539051 CCTAGTTCCTGGAGCTGTGG 59.461 60.000 21.67 18.27 0.00 4.17
521 531 1.480137 CTCCTAGTTCCTGGAGCTGTG 59.520 57.143 21.67 13.96 42.62 3.66
522 532 1.359474 TCTCCTAGTTCCTGGAGCTGT 59.641 52.381 21.67 0.52 46.90 4.40
523 533 2.151502 TCTCCTAGTTCCTGGAGCTG 57.848 55.000 21.67 11.88 46.90 4.24
524 534 2.246067 TCATCTCCTAGTTCCTGGAGCT 59.754 50.000 17.44 17.44 46.90 4.09
525 535 2.672098 TCATCTCCTAGTTCCTGGAGC 58.328 52.381 1.81 1.81 46.90 4.70
527 537 3.452627 GCTTTCATCTCCTAGTTCCTGGA 59.547 47.826 0.00 0.00 0.00 3.86
533 543 3.447586 TGTAGCGCTTTCATCTCCTAGTT 59.552 43.478 18.68 0.00 0.00 2.24
540 550 2.751166 ACACTGTAGCGCTTTCATCT 57.249 45.000 18.68 1.18 0.00 2.90
541 551 3.813529 AAACACTGTAGCGCTTTCATC 57.186 42.857 18.68 2.12 0.00 2.92
546 556 3.724374 TCTGTAAAACACTGTAGCGCTT 58.276 40.909 18.68 0.00 0.00 4.68
613 623 1.608590 TCTGCTTTTTAGCTGGTGCAC 59.391 47.619 8.80 8.80 42.74 4.57
620 630 3.350833 CCTGTGGATCTGCTTTTTAGCT 58.649 45.455 0.00 0.00 35.49 3.32
653 663 0.767375 ACATGGAGCACACTGGACTT 59.233 50.000 0.00 0.00 0.00 3.01
656 666 1.059098 AGAACATGGAGCACACTGGA 58.941 50.000 0.00 0.00 0.00 3.86
658 668 3.325293 ACTAGAACATGGAGCACACTG 57.675 47.619 0.00 0.00 0.00 3.66
725 735 0.888619 CTAGCTGTTCACCGAGTGGA 59.111 55.000 0.00 0.00 39.21 4.02
726 736 0.737715 GCTAGCTGTTCACCGAGTGG 60.738 60.000 7.70 0.00 42.84 4.00
727 737 0.244994 AGCTAGCTGTTCACCGAGTG 59.755 55.000 18.57 0.00 34.45 3.51
728 738 0.244994 CAGCTAGCTGTTCACCGAGT 59.755 55.000 32.46 0.00 39.10 4.18
729 739 1.080995 GCAGCTAGCTGTTCACCGAG 61.081 60.000 37.91 16.12 45.24 4.63
730 740 1.079819 GCAGCTAGCTGTTCACCGA 60.080 57.895 37.91 0.00 45.24 4.69
738 748 2.562298 AGCTCTTATAGGCAGCTAGCTG 59.438 50.000 35.54 35.54 41.84 4.24
802 812 5.800653 AGAGTATATGGGGTCTAGGGTTTT 58.199 41.667 0.00 0.00 0.00 2.43
831 841 3.299340 TCAGTCGGACTTTAACAGAGC 57.701 47.619 8.18 0.00 0.00 4.09
840 850 3.430929 GGATGCTTGTATCAGTCGGACTT 60.431 47.826 8.18 0.00 0.00 3.01
841 851 2.101582 GGATGCTTGTATCAGTCGGACT 59.898 50.000 4.45 4.45 0.00 3.85
842 852 2.474816 GGATGCTTGTATCAGTCGGAC 58.525 52.381 0.00 0.00 0.00 4.79
843 853 1.067060 CGGATGCTTGTATCAGTCGGA 59.933 52.381 1.55 0.00 0.00 4.55
844 854 1.202417 ACGGATGCTTGTATCAGTCGG 60.202 52.381 1.55 0.00 31.27 4.79
845 855 1.854743 CACGGATGCTTGTATCAGTCG 59.145 52.381 2.20 0.00 34.05 4.18
846 856 3.119291 CTCACGGATGCTTGTATCAGTC 58.881 50.000 2.20 0.00 34.05 3.51
847 857 2.760650 TCTCACGGATGCTTGTATCAGT 59.239 45.455 1.55 0.59 36.19 3.41
848 858 3.379240 CTCTCACGGATGCTTGTATCAG 58.621 50.000 1.55 0.00 0.00 2.90
849 859 2.101415 CCTCTCACGGATGCTTGTATCA 59.899 50.000 1.55 0.00 0.00 2.15
850 860 2.362397 TCCTCTCACGGATGCTTGTATC 59.638 50.000 0.00 0.00 0.00 2.24
851 861 2.388735 TCCTCTCACGGATGCTTGTAT 58.611 47.619 0.00 0.00 0.00 2.29
852 862 1.847328 TCCTCTCACGGATGCTTGTA 58.153 50.000 0.00 0.00 0.00 2.41
853 863 1.137872 GATCCTCTCACGGATGCTTGT 59.862 52.381 0.00 0.00 43.71 3.16
854 864 1.863267 GATCCTCTCACGGATGCTTG 58.137 55.000 0.00 0.00 43.71 4.01
855 865 0.387202 CGATCCTCTCACGGATGCTT 59.613 55.000 0.00 0.00 43.71 3.91
961 971 4.003788 AGTTCGCCACCGGTGAGG 62.004 66.667 36.07 24.95 43.44 3.86
962 972 2.738521 CAGTTCGCCACCGGTGAG 60.739 66.667 36.07 26.82 43.44 3.51
963 973 4.980805 GCAGTTCGCCACCGGTGA 62.981 66.667 36.07 13.84 40.77 4.02
965 975 4.988598 CTGCAGTTCGCCACCGGT 62.989 66.667 0.00 0.00 41.33 5.28
968 978 3.730761 CTGCTGCAGTTCGCCACC 61.731 66.667 21.21 0.00 41.33 4.61
969 979 4.395583 GCTGCTGCAGTTCGCCAC 62.396 66.667 28.50 8.34 41.33 5.01
988 998 2.217776 AGGATCCATTACAGGGGCTTT 58.782 47.619 15.82 0.00 0.00 3.51
992 1262 3.951563 TTGAAGGATCCATTACAGGGG 57.048 47.619 15.82 0.00 0.00 4.79
1043 1313 4.153986 CAGACATCTTAAAAACGCTGCAG 58.846 43.478 10.11 10.11 0.00 4.41
1058 1330 2.544267 GCCGCCATTAGTAACAGACATC 59.456 50.000 0.00 0.00 0.00 3.06
1124 1396 4.776349 TGAGCTCTTACAACCTTCACAAA 58.224 39.130 16.19 0.00 0.00 2.83
1189 1467 5.156355 TCCGACATCTTAAGTTTCACGTAC 58.844 41.667 1.63 0.00 0.00 3.67
1239 1517 2.002586 TGAGATTGCTGCGCTTTACTC 58.997 47.619 9.73 10.48 0.00 2.59
1296 1574 4.130857 CAGCGACTGGTTCTCTAGATCTA 58.869 47.826 1.69 1.69 0.00 1.98
1377 1655 8.504005 AGTGTATACGAAAAGAAAATCCAGTTG 58.496 33.333 0.00 0.00 0.00 3.16
1380 1658 8.601476 GGTAGTGTATACGAAAAGAAAATCCAG 58.399 37.037 0.00 0.00 0.00 3.86
1382 1660 8.483307 TGGTAGTGTATACGAAAAGAAAATCC 57.517 34.615 0.00 0.00 0.00 3.01
1428 1706 7.490657 TTACACCCTCTACTCACAAATGTAT 57.509 36.000 0.00 0.00 0.00 2.29
1429 1707 6.921486 TTACACCCTCTACTCACAAATGTA 57.079 37.500 0.00 0.00 0.00 2.29
1441 1721 5.279506 GCTTAGCTGCATATTACACCCTCTA 60.280 44.000 1.02 0.00 0.00 2.43
1502 1782 2.225091 ACCTTGTTCATGCCCATCTTCA 60.225 45.455 0.00 0.00 0.00 3.02
1590 1870 7.331687 GGTTTCTCATTTTGTACATCATTTGGG 59.668 37.037 0.00 0.00 0.00 4.12
1615 1895 3.056107 TCCAAAGTAATCTGACCACGAGG 60.056 47.826 0.00 0.00 42.21 4.63
1701 1981 3.576118 TGTCTAGAGCTTTCTGTGCTTCT 59.424 43.478 0.00 0.00 41.30 2.85
1706 1986 4.573900 ACCATTGTCTAGAGCTTTCTGTG 58.426 43.478 0.00 0.00 0.00 3.66
1718 1998 1.628340 CACCAGGTGGACCATTGTCTA 59.372 52.381 12.40 0.00 41.47 2.59
1732 2012 3.815407 AAAGCAGCCCACCACCAGG 62.815 63.158 0.00 0.00 42.21 4.45
1884 2312 2.169330 TCAAGTGCCATAAAGCATGCA 58.831 42.857 21.98 0.00 46.24 3.96
1885 2313 2.945447 TCAAGTGCCATAAAGCATGC 57.055 45.000 10.51 10.51 46.24 4.06
1911 2340 7.338196 TCTTCTTGATCACCTAGTACAGAGAAG 59.662 40.741 15.55 15.55 38.32 2.85
1912 2341 7.175797 TCTTCTTGATCACCTAGTACAGAGAA 58.824 38.462 0.00 0.00 0.00 2.87
2027 2456 9.813826 ATGTAATATTCCTCCTATTTTTCCAGG 57.186 33.333 0.00 0.00 0.00 4.45
2083 2515 3.518705 ACATCAATTAAGGGCCAATGCAA 59.481 39.130 6.18 0.00 40.13 4.08
2084 2516 3.106054 ACATCAATTAAGGGCCAATGCA 58.894 40.909 6.18 0.00 40.13 3.96
2085 2517 3.825143 ACATCAATTAAGGGCCAATGC 57.175 42.857 6.18 0.00 0.00 3.56
2086 2518 7.581213 TTACTACATCAATTAAGGGCCAATG 57.419 36.000 6.18 0.00 0.00 2.82
2087 2519 8.782137 AATTACTACATCAATTAAGGGCCAAT 57.218 30.769 6.18 0.00 0.00 3.16
2160 2593 3.652057 TTTTGAGGCTCTCCCTTATGG 57.348 47.619 16.72 0.00 46.60 2.74
2166 2599 2.373224 CTGGAATTTTGAGGCTCTCCC 58.627 52.381 16.72 8.02 0.00 4.30
2187 2620 7.024340 AGCAGTATCAAATATCTGTTGCAAG 57.976 36.000 0.00 0.00 0.00 4.01
2189 2622 7.395190 AAAGCAGTATCAAATATCTGTTGCA 57.605 32.000 0.00 0.00 0.00 4.08
2234 2672 8.256605 CGAACCCTCTTATTCATATGATCAGAT 58.743 37.037 6.17 0.00 0.00 2.90
2235 2673 7.451566 TCGAACCCTCTTATTCATATGATCAGA 59.548 37.037 6.17 7.42 0.00 3.27
2236 2674 7.606349 TCGAACCCTCTTATTCATATGATCAG 58.394 38.462 6.17 3.34 0.00 2.90
2237 2675 7.539034 TCGAACCCTCTTATTCATATGATCA 57.461 36.000 6.17 0.00 0.00 2.92
2238 2676 8.713271 GTTTCGAACCCTCTTATTCATATGATC 58.287 37.037 6.17 0.00 0.00 2.92
2239 2677 8.432805 AGTTTCGAACCCTCTTATTCATATGAT 58.567 33.333 6.17 0.00 0.00 2.45
2240 2678 7.792032 AGTTTCGAACCCTCTTATTCATATGA 58.208 34.615 0.00 0.00 0.00 2.15
2241 2679 9.712305 ATAGTTTCGAACCCTCTTATTCATATG 57.288 33.333 0.00 0.00 0.00 1.78
2253 2691 8.368668 CCATTAAGAGATATAGTTTCGAACCCT 58.631 37.037 0.00 0.00 0.00 4.34
2319 2759 8.387354 TGACAACATTATATAAGCAAAGTGACG 58.613 33.333 1.02 0.00 0.00 4.35
2320 2760 9.490663 GTGACAACATTATATAAGCAAAGTGAC 57.509 33.333 1.02 0.00 0.00 3.67
2336 2784 4.827284 CCTAAGGTTTCCTGTGACAACATT 59.173 41.667 0.00 0.00 35.22 2.71
2344 2792 3.140325 TGAAGCCTAAGGTTTCCTGTG 57.860 47.619 0.00 0.00 41.26 3.66
2362 2810 4.574674 CCTGCCAGGGCTATATAAATGA 57.425 45.455 12.19 0.00 42.51 2.57
2383 2831 2.482374 GCCTGTTGCTGATCACGC 59.518 61.111 9.41 9.41 36.87 5.34
2404 2852 2.746269 TGAGACGGTACTTTTCGTTGG 58.254 47.619 0.00 0.00 39.88 3.77
2428 2876 2.164219 TGAATCTGCCCATTTTTCGAGC 59.836 45.455 0.00 0.00 0.00 5.03
2639 3716 1.471327 GCTGCTGACCTGATGAGAGTC 60.471 57.143 0.00 0.00 0.00 3.36
2773 3850 0.320771 CCCTGAACAACCTCCAGACG 60.321 60.000 0.00 0.00 0.00 4.18
2817 3894 1.342819 AGAAGAGCAAGCACGAGAAGT 59.657 47.619 0.00 0.00 0.00 3.01
2881 3958 0.534203 GGAAGACACCGGTTGCAGAA 60.534 55.000 2.97 0.00 0.00 3.02
3130 4207 3.576118 ACTCTGACATCTACAGCTTGTGT 59.424 43.478 0.00 0.00 43.86 3.72
3135 4212 3.446873 CCAGAACTCTGACATCTACAGCT 59.553 47.826 8.33 0.00 46.59 4.24
3148 4225 5.248020 ACTCATGAAAGACATCCAGAACTCT 59.752 40.000 0.00 0.00 37.07 3.24
3182 4259 0.329261 CTCTCCCTGTTCCAATGCCA 59.671 55.000 0.00 0.00 0.00 4.92
3416 4493 3.581024 TGCATTCCATTTCAGCTTGAC 57.419 42.857 0.00 0.00 0.00 3.18
3441 4518 5.559770 TGTTCTCATGCATGTTTCCTCTTA 58.440 37.500 25.43 2.73 0.00 2.10


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

AutoCloner maintained by Alex Coulton.