Multiple sequence alignment - TraesCS1A01G340800

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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 TraesCS1A01G340800 chr1A 100.000 3391 0 0 1 3391 530775955 530772565 0.000000e+00 6263.0
1 TraesCS1A01G340800 chr1A 97.721 2764 53 2 629 3391 241984780 241987534 0.000000e+00 4747.0
2 TraesCS1A01G340800 chr1A 97.118 2776 51 8 626 3391 13720042 13722798 0.000000e+00 4656.0
3 TraesCS1A01G340800 chr1A 88.235 85 6 3 478 562 530522737 530522657 7.740000e-17 99.0
4 TraesCS1A01G340800 chr2A 97.763 2772 52 3 630 3391 753951605 753954376 0.000000e+00 4767.0
5 TraesCS1A01G340800 chr2A 89.412 85 6 2 478 562 617072608 617072689 1.660000e-18 104.0
6 TraesCS1A01G340800 chr3A 97.763 2771 52 3 630 3391 713795703 713798472 0.000000e+00 4765.0
7 TraesCS1A01G340800 chr3A 97.548 2773 53 5 629 3391 725985799 725988566 0.000000e+00 4730.0
8 TraesCS1A01G340800 chr3A 96.807 2787 65 4 629 3391 699770274 699773060 0.000000e+00 4632.0
9 TraesCS1A01G340800 chr6A 97.690 2770 49 3 631 3391 369654872 369657635 0.000000e+00 4747.0
10 TraesCS1A01G340800 chr5D 93.538 2677 117 24 630 3283 525155548 525158191 0.000000e+00 3934.0
11 TraesCS1A01G340800 chr5D 92.706 1988 104 26 630 2609 474542533 474544487 0.000000e+00 2830.0
12 TraesCS1A01G340800 chr5D 90.984 1098 60 21 626 1701 423748934 423750014 0.000000e+00 1443.0
13 TraesCS1A01G340800 chr5D 89.412 85 6 3 478 562 331213954 331214035 1.660000e-18 104.0
14 TraesCS1A01G340800 chr7A 97.802 2275 41 2 1125 3391 107350010 107352283 0.000000e+00 3916.0
15 TraesCS1A01G340800 chr7A 88.235 85 7 3 478 562 620860055 620860136 7.740000e-17 99.0
16 TraesCS1A01G340800 chr7D 94.458 2003 97 9 630 2627 508795049 508797042 0.000000e+00 3072.0
17 TraesCS1A01G340800 chr1D 94.182 2011 101 10 630 2627 481961642 481959635 0.000000e+00 3051.0
18 TraesCS1A01G340800 chr1D 87.586 435 26 11 57 476 432314572 432314151 2.370000e-131 479.0
19 TraesCS1A01G340800 chr1D 88.506 261 22 5 20 275 432229466 432229209 3.290000e-80 309.0
20 TraesCS1A01G340800 chr1D 85.279 197 24 4 267 459 432221227 432221032 7.420000e-47 198.0
21 TraesCS1A01G340800 chr1D 85.207 169 13 10 477 639 432314108 432313946 2.710000e-36 163.0
22 TraesCS1A01G340800 chrUn 97.957 881 16 2 2512 3391 305973244 305972365 0.000000e+00 1526.0
23 TraesCS1A01G340800 chrUn 97.957 881 16 2 2512 3391 359036840 359035961 0.000000e+00 1526.0
24 TraesCS1A01G340800 chr1B 90.289 381 30 4 98 477 583751536 583751162 3.040000e-135 492.0
25 TraesCS1A01G340800 chr2D 89.157 83 6 2 478 560 634854276 634854355 2.150000e-17 100.0
26 TraesCS1A01G340800 chr5B 87.059 85 8 2 478 562 291999087 291999006 3.600000e-15 93.5
27 TraesCS1A01G340800 chr3D 87.059 85 8 2 478 562 552772414 552772495 3.600000e-15 93.5
28 TraesCS1A01G340800 chr2B 87.059 85 8 2 478 562 50021581 50021500 3.600000e-15 93.5


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 TraesCS1A01G340800 chr1A 530772565 530775955 3390 True 6263 6263 100.0000 1 3391 1 chr1A.!!$R2 3390
1 TraesCS1A01G340800 chr1A 241984780 241987534 2754 False 4747 4747 97.7210 629 3391 1 chr1A.!!$F2 2762
2 TraesCS1A01G340800 chr1A 13720042 13722798 2756 False 4656 4656 97.1180 626 3391 1 chr1A.!!$F1 2765
3 TraesCS1A01G340800 chr2A 753951605 753954376 2771 False 4767 4767 97.7630 630 3391 1 chr2A.!!$F2 2761
4 TraesCS1A01G340800 chr3A 713795703 713798472 2769 False 4765 4765 97.7630 630 3391 1 chr3A.!!$F2 2761
5 TraesCS1A01G340800 chr3A 725985799 725988566 2767 False 4730 4730 97.5480 629 3391 1 chr3A.!!$F3 2762
6 TraesCS1A01G340800 chr3A 699770274 699773060 2786 False 4632 4632 96.8070 629 3391 1 chr3A.!!$F1 2762
7 TraesCS1A01G340800 chr6A 369654872 369657635 2763 False 4747 4747 97.6900 631 3391 1 chr6A.!!$F1 2760
8 TraesCS1A01G340800 chr5D 525155548 525158191 2643 False 3934 3934 93.5380 630 3283 1 chr5D.!!$F4 2653
9 TraesCS1A01G340800 chr5D 474542533 474544487 1954 False 2830 2830 92.7060 630 2609 1 chr5D.!!$F3 1979
10 TraesCS1A01G340800 chr5D 423748934 423750014 1080 False 1443 1443 90.9840 626 1701 1 chr5D.!!$F2 1075
11 TraesCS1A01G340800 chr7A 107350010 107352283 2273 False 3916 3916 97.8020 1125 3391 1 chr7A.!!$F1 2266
12 TraesCS1A01G340800 chr7D 508795049 508797042 1993 False 3072 3072 94.4580 630 2627 1 chr7D.!!$F1 1997
13 TraesCS1A01G340800 chr1D 481959635 481961642 2007 True 3051 3051 94.1820 630 2627 1 chr1D.!!$R3 1997
14 TraesCS1A01G340800 chr1D 432313946 432314572 626 True 321 479 86.3965 57 639 2 chr1D.!!$R4 582
15 TraesCS1A01G340800 chrUn 305972365 305973244 879 True 1526 1526 97.9570 2512 3391 1 chrUn.!!$R1 879
16 TraesCS1A01G340800 chrUn 359035961 359036840 879 True 1526 1526 97.9570 2512 3391 1 chrUn.!!$R2 879

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
83 84 0.029700 TGCACCGATGGATACGTACG 59.970 55.0 15.01 15.01 42.51 3.67 F
412 423 0.037975 CATGCTTTGGCGCCTTCTTT 60.038 50.0 29.70 5.19 42.25 2.52 F
415 426 0.109551 GCTTTGGCGCCTTCTTTCTC 60.110 55.0 29.70 4.71 0.00 2.87 F
449 460 0.318699 CGCTTTCACGTCCACAGAGA 60.319 55.0 0.00 0.00 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1437 1494 6.572519 ACTAACATTTGATTGTTGCAACTGT 58.427 32.000 28.61 19.47 39.73 3.55 R
2245 2348 3.695357 TCATCTCATCCCTCTCCTTCA 57.305 47.619 0.00 0.00 0.00 3.02 R
2315 2418 4.521146 CAGCTTTCATAAGATCACCCACT 58.479 43.478 0.00 0.00 32.92 4.00 R
2432 2535 3.825328 CCAGCTATATTGTTCCAAGGCT 58.175 45.455 0.00 0.00 0.00 4.58 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
20 21 3.194005 TCGGCCTGGTTTTATCATCTC 57.806 47.619 0.00 0.00 0.00 2.75
21 22 2.503765 TCGGCCTGGTTTTATCATCTCA 59.496 45.455 0.00 0.00 0.00 3.27
22 23 3.136443 TCGGCCTGGTTTTATCATCTCAT 59.864 43.478 0.00 0.00 0.00 2.90
23 24 3.499918 CGGCCTGGTTTTATCATCTCATC 59.500 47.826 0.00 0.00 0.00 2.92
24 25 4.723309 GGCCTGGTTTTATCATCTCATCT 58.277 43.478 0.00 0.00 0.00 2.90
25 26 4.759183 GGCCTGGTTTTATCATCTCATCTC 59.241 45.833 0.00 0.00 0.00 2.75
26 27 4.450419 GCCTGGTTTTATCATCTCATCTCG 59.550 45.833 0.00 0.00 0.00 4.04
27 28 5.605534 CCTGGTTTTATCATCTCATCTCGT 58.394 41.667 0.00 0.00 0.00 4.18
28 29 5.464722 CCTGGTTTTATCATCTCATCTCGTG 59.535 44.000 0.00 0.00 0.00 4.35
29 30 4.811024 TGGTTTTATCATCTCATCTCGTGC 59.189 41.667 0.00 0.00 0.00 5.34
30 31 4.811024 GGTTTTATCATCTCATCTCGTGCA 59.189 41.667 0.00 0.00 0.00 4.57
31 32 5.294306 GGTTTTATCATCTCATCTCGTGCAA 59.706 40.000 0.00 0.00 0.00 4.08
32 33 6.417327 GTTTTATCATCTCATCTCGTGCAAG 58.583 40.000 0.00 0.00 0.00 4.01
33 34 1.931906 TCATCTCATCTCGTGCAAGC 58.068 50.000 0.00 0.00 0.00 4.01
34 35 0.575859 CATCTCATCTCGTGCAAGCG 59.424 55.000 0.00 0.00 0.00 4.68
35 36 1.150567 ATCTCATCTCGTGCAAGCGC 61.151 55.000 0.00 0.00 39.24 5.92
36 37 2.806856 CTCATCTCGTGCAAGCGCC 61.807 63.158 2.29 0.00 37.32 6.53
37 38 4.214383 CATCTCGTGCAAGCGCCG 62.214 66.667 2.29 0.00 37.32 6.46
48 49 4.065110 AGCGCCGCTTTCTCTTTT 57.935 50.000 5.39 0.00 33.89 2.27
49 50 2.331265 AGCGCCGCTTTCTCTTTTT 58.669 47.368 5.39 0.00 33.89 1.94
73 74 2.733227 GCCATCTCTTTTTGCACCGATG 60.733 50.000 0.00 0.00 0.00 3.84
80 81 2.102070 TTTTGCACCGATGGATACGT 57.898 45.000 0.00 0.00 42.51 3.57
81 82 2.963548 TTTGCACCGATGGATACGTA 57.036 45.000 0.00 0.00 42.51 3.57
82 83 2.212869 TTGCACCGATGGATACGTAC 57.787 50.000 0.00 0.00 42.51 3.67
83 84 0.029700 TGCACCGATGGATACGTACG 59.970 55.000 15.01 15.01 42.51 3.67
84 85 0.662374 GCACCGATGGATACGTACGG 60.662 60.000 21.06 17.17 45.67 4.02
113 114 1.598601 GGTTTACACGTCCGAAAGCAA 59.401 47.619 9.48 0.00 32.26 3.91
120 121 0.586319 CGTCCGAAAGCAAAGCAGAA 59.414 50.000 0.00 0.00 0.00 3.02
121 122 1.398960 CGTCCGAAAGCAAAGCAGAAG 60.399 52.381 0.00 0.00 0.00 2.85
124 125 1.603802 CCGAAAGCAAAGCAGAAGACA 59.396 47.619 0.00 0.00 0.00 3.41
126 127 3.231965 CGAAAGCAAAGCAGAAGACATG 58.768 45.455 0.00 0.00 0.00 3.21
128 129 4.555313 CGAAAGCAAAGCAGAAGACATGAA 60.555 41.667 0.00 0.00 0.00 2.57
130 131 2.555757 AGCAAAGCAGAAGACATGAACC 59.444 45.455 0.00 0.00 0.00 3.62
131 132 2.294233 GCAAAGCAGAAGACATGAACCA 59.706 45.455 0.00 0.00 0.00 3.67
137 138 1.648467 GAAGACATGAACCAGCGGCC 61.648 60.000 0.00 0.00 0.00 6.13
177 178 0.394216 TGGCACTGTGGGCATATGAC 60.394 55.000 6.97 2.47 38.55 3.06
179 180 0.744414 GCACTGTGGGCATATGACGT 60.744 55.000 6.97 0.00 0.00 4.34
217 228 1.400500 CCACGCGCCGAACTTATTTTT 60.400 47.619 5.73 0.00 0.00 1.94
310 321 0.538057 CATGGCATGATACCCGGCTT 60.538 55.000 22.91 0.00 0.00 4.35
313 324 2.896801 GCATGATACCCGGCTTGCG 61.897 63.158 0.00 0.00 0.00 4.85
339 350 2.577059 CCTGGCGCTCGGAGTTTA 59.423 61.111 7.64 0.00 0.00 2.01
340 351 1.810030 CCTGGCGCTCGGAGTTTAC 60.810 63.158 7.64 0.00 0.00 2.01
341 352 2.126228 TGGCGCTCGGAGTTTACG 60.126 61.111 7.64 2.73 0.00 3.18
344 355 3.374330 CGCTCGGAGTTTACGCAG 58.626 61.111 6.90 0.00 0.00 5.18
345 356 2.789203 CGCTCGGAGTTTACGCAGC 61.789 63.158 6.90 0.00 33.96 5.25
346 357 1.736645 GCTCGGAGTTTACGCAGCA 60.737 57.895 6.90 0.00 35.82 4.41
347 358 1.687494 GCTCGGAGTTTACGCAGCAG 61.687 60.000 6.90 0.00 35.82 4.24
348 359 1.078759 CTCGGAGTTTACGCAGCAGG 61.079 60.000 0.00 0.00 0.00 4.85
349 360 2.100631 CGGAGTTTACGCAGCAGGG 61.101 63.158 0.00 0.00 0.00 4.45
350 361 2.399356 GGAGTTTACGCAGCAGGGC 61.399 63.158 0.00 0.00 0.00 5.19
367 378 4.003011 CGCGACGAAACGGGCAAA 62.003 61.111 0.00 0.00 39.08 3.68
368 379 2.426261 GCGACGAAACGGGCAAAC 60.426 61.111 0.00 0.00 32.43 2.93
369 380 2.127906 CGACGAAACGGGCAAACG 60.128 61.111 0.00 0.00 40.31 3.60
370 381 2.426261 GACGAAACGGGCAAACGC 60.426 61.111 0.00 0.00 37.37 4.84
385 396 2.851104 CGCCGGACGTCAACTTTC 59.149 61.111 18.91 0.00 36.87 2.62
386 397 2.851104 GCCGGACGTCAACTTTCG 59.149 61.111 18.91 10.20 0.00 3.46
387 398 2.664436 GCCGGACGTCAACTTTCGG 61.664 63.158 18.91 19.60 40.33 4.30
388 399 1.300388 CCGGACGTCAACTTTCGGT 60.300 57.895 18.91 0.00 33.63 4.69
389 400 1.554042 CCGGACGTCAACTTTCGGTG 61.554 60.000 18.91 0.00 33.63 4.94
390 401 1.568025 GGACGTCAACTTTCGGTGC 59.432 57.895 18.91 0.00 0.00 5.01
391 402 0.878961 GGACGTCAACTTTCGGTGCT 60.879 55.000 18.91 0.00 0.00 4.40
392 403 0.935196 GACGTCAACTTTCGGTGCTT 59.065 50.000 11.55 0.00 0.00 3.91
393 404 0.935196 ACGTCAACTTTCGGTGCTTC 59.065 50.000 0.00 0.00 0.00 3.86
394 405 0.934496 CGTCAACTTTCGGTGCTTCA 59.066 50.000 0.00 0.00 0.00 3.02
395 406 1.531149 CGTCAACTTTCGGTGCTTCAT 59.469 47.619 0.00 0.00 0.00 2.57
396 407 2.662791 CGTCAACTTTCGGTGCTTCATG 60.663 50.000 0.00 0.00 0.00 3.07
397 408 1.266718 TCAACTTTCGGTGCTTCATGC 59.733 47.619 0.00 0.00 43.25 4.06
398 409 1.267806 CAACTTTCGGTGCTTCATGCT 59.732 47.619 0.00 0.00 43.37 3.79
399 410 1.609208 ACTTTCGGTGCTTCATGCTT 58.391 45.000 0.00 0.00 43.37 3.91
400 411 1.956477 ACTTTCGGTGCTTCATGCTTT 59.044 42.857 0.00 0.00 43.37 3.51
401 412 2.287788 ACTTTCGGTGCTTCATGCTTTG 60.288 45.455 0.00 0.00 43.37 2.77
402 413 0.597568 TTCGGTGCTTCATGCTTTGG 59.402 50.000 0.00 0.00 43.37 3.28
403 414 1.444895 CGGTGCTTCATGCTTTGGC 60.445 57.895 0.00 0.00 43.37 4.52
404 415 1.444895 GGTGCTTCATGCTTTGGCG 60.445 57.895 0.00 0.00 43.37 5.69
405 416 2.090524 GTGCTTCATGCTTTGGCGC 61.091 57.895 0.00 0.00 43.37 6.53
406 417 2.507769 GCTTCATGCTTTGGCGCC 60.508 61.111 22.73 22.73 42.25 6.53
407 418 2.998279 GCTTCATGCTTTGGCGCCT 61.998 57.895 29.70 1.94 42.25 5.52
408 419 1.588082 CTTCATGCTTTGGCGCCTT 59.412 52.632 29.70 2.20 42.25 4.35
409 420 0.457337 CTTCATGCTTTGGCGCCTTC 60.457 55.000 29.70 13.96 42.25 3.46
410 421 0.895100 TTCATGCTTTGGCGCCTTCT 60.895 50.000 29.70 3.19 42.25 2.85
411 422 0.895100 TCATGCTTTGGCGCCTTCTT 60.895 50.000 29.70 8.97 42.25 2.52
412 423 0.037975 CATGCTTTGGCGCCTTCTTT 60.038 50.000 29.70 5.19 42.25 2.52
413 424 0.244721 ATGCTTTGGCGCCTTCTTTC 59.755 50.000 29.70 12.13 42.25 2.62
414 425 0.823356 TGCTTTGGCGCCTTCTTTCT 60.823 50.000 29.70 0.00 42.25 2.52
415 426 0.109551 GCTTTGGCGCCTTCTTTCTC 60.110 55.000 29.70 4.71 0.00 2.87
416 427 1.238439 CTTTGGCGCCTTCTTTCTCA 58.762 50.000 29.70 0.00 0.00 3.27
417 428 1.608590 CTTTGGCGCCTTCTTTCTCAA 59.391 47.619 29.70 7.02 0.00 3.02
418 429 1.909700 TTGGCGCCTTCTTTCTCAAT 58.090 45.000 29.70 0.00 0.00 2.57
419 430 1.167851 TGGCGCCTTCTTTCTCAATG 58.832 50.000 29.70 0.00 0.00 2.82
420 431 0.453390 GGCGCCTTCTTTCTCAATGG 59.547 55.000 22.15 0.00 0.00 3.16
421 432 1.168714 GCGCCTTCTTTCTCAATGGT 58.831 50.000 0.00 0.00 0.00 3.55
422 433 2.356135 GCGCCTTCTTTCTCAATGGTA 58.644 47.619 0.00 0.00 0.00 3.25
423 434 2.747446 GCGCCTTCTTTCTCAATGGTAA 59.253 45.455 0.00 0.00 0.00 2.85
424 435 3.426292 GCGCCTTCTTTCTCAATGGTAAC 60.426 47.826 0.00 0.00 0.00 2.50
437 448 2.605837 TGGTAACACTGACGCTTTCA 57.394 45.000 0.00 0.00 46.17 2.69
438 449 2.206750 TGGTAACACTGACGCTTTCAC 58.793 47.619 0.00 0.00 46.17 3.18
439 450 1.191647 GGTAACACTGACGCTTTCACG 59.808 52.381 0.00 0.00 39.50 4.35
446 457 4.027755 ACGCTTTCACGTCCACAG 57.972 55.556 0.00 0.00 44.43 3.66
447 458 1.440060 ACGCTTTCACGTCCACAGA 59.560 52.632 0.00 0.00 44.43 3.41
448 459 0.597637 ACGCTTTCACGTCCACAGAG 60.598 55.000 0.00 0.00 44.43 3.35
449 460 0.318699 CGCTTTCACGTCCACAGAGA 60.319 55.000 0.00 0.00 0.00 3.10
450 461 1.865865 GCTTTCACGTCCACAGAGAA 58.134 50.000 0.00 0.00 0.00 2.87
451 462 2.417719 GCTTTCACGTCCACAGAGAAT 58.582 47.619 0.00 0.00 0.00 2.40
452 463 2.158449 GCTTTCACGTCCACAGAGAATG 59.842 50.000 0.00 0.00 0.00 2.67
453 464 2.455674 TTCACGTCCACAGAGAATGG 57.544 50.000 0.00 0.00 38.71 3.16
454 465 1.627864 TCACGTCCACAGAGAATGGA 58.372 50.000 0.00 0.00 44.20 3.41
462 473 5.860941 TCCACAGAGAATGGAATCTAGTC 57.139 43.478 0.00 0.00 43.43 2.59
463 474 5.523588 TCCACAGAGAATGGAATCTAGTCT 58.476 41.667 0.00 0.00 43.43 3.24
464 475 5.960811 TCCACAGAGAATGGAATCTAGTCTT 59.039 40.000 0.00 0.00 43.43 3.01
465 476 6.441924 TCCACAGAGAATGGAATCTAGTCTTT 59.558 38.462 0.00 0.00 43.43 2.52
466 477 6.760770 CCACAGAGAATGGAATCTAGTCTTTC 59.239 42.308 0.00 0.00 39.87 2.62
467 478 6.760770 CACAGAGAATGGAATCTAGTCTTTCC 59.239 42.308 0.00 12.20 41.51 3.13
468 479 5.982516 CAGAGAATGGAATCTAGTCTTTCCG 59.017 44.000 0.00 0.00 43.61 4.30
469 480 5.659079 AGAGAATGGAATCTAGTCTTTCCGT 59.341 40.000 0.00 11.48 43.61 4.69
472 483 4.467198 TGGAATCTAGTCTTTCCGTTCC 57.533 45.455 13.44 0.00 43.61 3.62
473 484 4.094476 TGGAATCTAGTCTTTCCGTTCCT 58.906 43.478 13.44 0.00 43.61 3.36
474 485 5.266788 TGGAATCTAGTCTTTCCGTTCCTA 58.733 41.667 13.44 0.00 43.61 2.94
475 486 5.718130 TGGAATCTAGTCTTTCCGTTCCTAA 59.282 40.000 13.44 0.00 43.61 2.69
476 487 6.211986 TGGAATCTAGTCTTTCCGTTCCTAAA 59.788 38.462 13.44 0.00 43.61 1.85
477 488 7.101700 GGAATCTAGTCTTTCCGTTCCTAAAA 58.898 38.462 6.25 0.00 32.65 1.52
478 489 7.769507 GGAATCTAGTCTTTCCGTTCCTAAAAT 59.230 37.037 6.25 0.00 32.65 1.82
479 490 8.494016 AATCTAGTCTTTCCGTTCCTAAAATG 57.506 34.615 0.00 0.00 0.00 2.32
480 491 7.001099 TCTAGTCTTTCCGTTCCTAAAATGT 57.999 36.000 0.00 0.00 0.00 2.71
481 492 8.125978 TCTAGTCTTTCCGTTCCTAAAATGTA 57.874 34.615 0.00 0.00 0.00 2.29
482 493 8.755977 TCTAGTCTTTCCGTTCCTAAAATGTAT 58.244 33.333 0.00 0.00 0.00 2.29
536 547 7.986085 ACTCATTTTGCTTTGTATGTAGTCT 57.014 32.000 0.00 0.00 0.00 3.24
538 549 9.672673 ACTCATTTTGCTTTGTATGTAGTCTAT 57.327 29.630 0.00 0.00 0.00 1.98
571 582 9.825109 ATATCTAAAAAGACTTAGAACTGAGGC 57.175 33.333 0.00 0.00 40.42 4.70
572 583 7.062749 TCTAAAAAGACTTAGAACTGAGGCA 57.937 36.000 2.49 0.00 35.45 4.75
573 584 7.506114 TCTAAAAAGACTTAGAACTGAGGCAA 58.494 34.615 2.49 0.00 35.45 4.52
574 585 8.157476 TCTAAAAAGACTTAGAACTGAGGCAAT 58.843 33.333 2.49 0.00 35.45 3.56
575 586 9.436957 CTAAAAAGACTTAGAACTGAGGCAATA 57.563 33.333 2.49 0.00 31.59 1.90
576 587 7.674471 AAAAGACTTAGAACTGAGGCAATAC 57.326 36.000 2.49 0.00 0.00 1.89
577 588 6.360370 AAGACTTAGAACTGAGGCAATACA 57.640 37.500 2.49 0.00 0.00 2.29
578 589 6.552445 AGACTTAGAACTGAGGCAATACAT 57.448 37.500 2.49 0.00 0.00 2.29
579 590 6.344500 AGACTTAGAACTGAGGCAATACATG 58.656 40.000 2.49 0.00 0.00 3.21
593 604 5.568482 GCAATACATGCGTACAATTTCTCA 58.432 37.500 0.00 0.00 46.87 3.27
594 605 6.027131 GCAATACATGCGTACAATTTCTCAA 58.973 36.000 0.00 0.00 46.87 3.02
595 606 6.692681 GCAATACATGCGTACAATTTCTCAAT 59.307 34.615 0.00 0.00 46.87 2.57
596 607 7.855409 GCAATACATGCGTACAATTTCTCAATA 59.145 33.333 0.00 0.00 46.87 1.90
597 608 9.715123 CAATACATGCGTACAATTTCTCAATAA 57.285 29.630 0.00 0.00 0.00 1.40
598 609 9.716507 AATACATGCGTACAATTTCTCAATAAC 57.283 29.630 0.00 0.00 0.00 1.89
599 610 7.139896 ACATGCGTACAATTTCTCAATAACA 57.860 32.000 0.00 0.00 0.00 2.41
600 611 7.589395 ACATGCGTACAATTTCTCAATAACAA 58.411 30.769 0.00 0.00 0.00 2.83
601 612 7.750458 ACATGCGTACAATTTCTCAATAACAAG 59.250 33.333 0.00 0.00 0.00 3.16
602 613 6.083630 TGCGTACAATTTCTCAATAACAAGC 58.916 36.000 0.00 0.00 0.00 4.01
603 614 6.072728 TGCGTACAATTTCTCAATAACAAGCT 60.073 34.615 0.00 0.00 0.00 3.74
604 615 6.466097 GCGTACAATTTCTCAATAACAAGCTC 59.534 38.462 0.00 0.00 0.00 4.09
605 616 7.624344 GCGTACAATTTCTCAATAACAAGCTCT 60.624 37.037 0.00 0.00 0.00 4.09
606 617 7.900352 CGTACAATTTCTCAATAACAAGCTCTC 59.100 37.037 0.00 0.00 0.00 3.20
607 618 7.992754 ACAATTTCTCAATAACAAGCTCTCT 57.007 32.000 0.00 0.00 0.00 3.10
608 619 8.038492 ACAATTTCTCAATAACAAGCTCTCTC 57.962 34.615 0.00 0.00 0.00 3.20
609 620 7.882271 ACAATTTCTCAATAACAAGCTCTCTCT 59.118 33.333 0.00 0.00 0.00 3.10
610 621 8.728833 CAATTTCTCAATAACAAGCTCTCTCTT 58.271 33.333 0.00 0.00 0.00 2.85
611 622 8.860780 ATTTCTCAATAACAAGCTCTCTCTTT 57.139 30.769 0.00 0.00 0.00 2.52
612 623 8.682936 TTTCTCAATAACAAGCTCTCTCTTTT 57.317 30.769 0.00 0.00 0.00 2.27
613 624 8.682936 TTCTCAATAACAAGCTCTCTCTTTTT 57.317 30.769 0.00 0.00 0.00 1.94
693 704 0.538584 TTGCCACCACATTTGTTGCA 59.461 45.000 0.00 0.00 0.00 4.08
844 855 2.030862 TGGGTTGACGGCCGTTAC 59.969 61.111 34.65 29.99 0.00 2.50
864 875 1.724581 GCACGCGGTACAAAACAGC 60.725 57.895 12.47 0.00 44.79 4.40
889 900 4.767255 CTCCCCGCTGCTCACACC 62.767 72.222 0.00 0.00 0.00 4.16
1164 1199 4.222124 TGGAGCAGTTCCTATCTTTTCC 57.778 45.455 4.73 0.00 46.92 3.13
1601 1694 9.778741 AGTCTGTAGTAAATTCAGTCATTTTGA 57.221 29.630 0.00 0.00 0.00 2.69
2129 2232 4.222336 ACATGGAGAAGCTAGCTATCAGT 58.778 43.478 19.70 14.73 0.00 3.41
2242 2345 3.072184 CAGGGGGAGATCATTAGGAACAG 59.928 52.174 0.00 0.00 0.00 3.16
2245 2348 4.352298 GGGGGAGATCATTAGGAACAGAAT 59.648 45.833 0.00 0.00 0.00 2.40
2315 2418 5.046950 GGAGAAGAAGAAGCTGGAGTTTCTA 60.047 44.000 6.22 0.00 43.31 2.10
2925 3056 4.481280 ACTCCACCTCATCCTAGTAACCTA 59.519 45.833 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.917933 TGAGATGATAAAACCAGGCCG 58.082 47.619 0.00 0.00 0.00 6.13
4 5 5.464722 CACGAGATGAGATGATAAAACCAGG 59.535 44.000 0.00 0.00 0.00 4.45
6 7 4.811024 GCACGAGATGAGATGATAAAACCA 59.189 41.667 0.00 0.00 0.00 3.67
7 8 4.811024 TGCACGAGATGAGATGATAAAACC 59.189 41.667 0.00 0.00 0.00 3.27
8 9 5.973651 TGCACGAGATGAGATGATAAAAC 57.026 39.130 0.00 0.00 0.00 2.43
9 10 5.007039 GCTTGCACGAGATGAGATGATAAAA 59.993 40.000 0.00 0.00 0.00 1.52
10 11 4.509230 GCTTGCACGAGATGAGATGATAAA 59.491 41.667 0.00 0.00 0.00 1.40
11 12 4.053983 GCTTGCACGAGATGAGATGATAA 58.946 43.478 0.00 0.00 0.00 1.75
12 13 3.646946 GCTTGCACGAGATGAGATGATA 58.353 45.455 0.00 0.00 0.00 2.15
13 14 2.481854 GCTTGCACGAGATGAGATGAT 58.518 47.619 0.00 0.00 0.00 2.45
14 15 1.800286 CGCTTGCACGAGATGAGATGA 60.800 52.381 0.00 0.00 34.06 2.92
15 16 0.575859 CGCTTGCACGAGATGAGATG 59.424 55.000 0.00 0.00 34.06 2.90
16 17 1.150567 GCGCTTGCACGAGATGAGAT 61.151 55.000 0.00 0.00 38.92 2.75
17 18 1.807165 GCGCTTGCACGAGATGAGA 60.807 57.895 0.00 0.00 38.92 3.27
18 19 2.699809 GCGCTTGCACGAGATGAG 59.300 61.111 0.00 0.00 38.92 2.90
19 20 2.815211 GGCGCTTGCACGAGATGA 60.815 61.111 7.64 0.00 41.71 2.92
20 21 4.214383 CGGCGCTTGCACGAGATG 62.214 66.667 7.64 0.00 41.71 2.90
31 32 2.331265 AAAAAGAGAAAGCGGCGCT 58.669 47.368 31.35 31.35 42.56 5.92
32 33 4.944249 AAAAAGAGAAAGCGGCGC 57.056 50.000 26.86 26.86 0.00 6.53
47 48 3.876320 GGTGCAAAAAGAGATGGCAAAAA 59.124 39.130 0.00 0.00 36.08 1.94
48 49 3.465871 GGTGCAAAAAGAGATGGCAAAA 58.534 40.909 0.00 0.00 36.08 2.44
49 50 2.545532 CGGTGCAAAAAGAGATGGCAAA 60.546 45.455 0.00 0.00 36.08 3.68
50 51 1.000385 CGGTGCAAAAAGAGATGGCAA 60.000 47.619 0.00 0.00 36.08 4.52
51 52 0.597568 CGGTGCAAAAAGAGATGGCA 59.402 50.000 0.00 0.00 0.00 4.92
52 53 0.881118 TCGGTGCAAAAAGAGATGGC 59.119 50.000 0.00 0.00 0.00 4.40
53 54 2.159338 CCATCGGTGCAAAAAGAGATGG 60.159 50.000 14.50 14.50 45.83 3.51
54 55 2.749076 TCCATCGGTGCAAAAAGAGATG 59.251 45.455 0.00 0.00 36.27 2.90
55 56 3.071874 TCCATCGGTGCAAAAAGAGAT 57.928 42.857 0.00 0.00 0.00 2.75
73 74 1.083144 CTCGTCGCCGTACGTATCC 60.083 63.158 15.21 0.00 43.31 2.59
80 81 0.109781 GTAAACCACTCGTCGCCGTA 60.110 55.000 0.00 0.00 35.01 4.02
81 82 1.372128 GTAAACCACTCGTCGCCGT 60.372 57.895 0.00 0.00 35.01 5.68
82 83 1.372004 TGTAAACCACTCGTCGCCG 60.372 57.895 0.00 0.00 0.00 6.46
83 84 1.611592 CGTGTAAACCACTCGTCGCC 61.612 60.000 0.00 0.00 42.20 5.54
84 85 1.771044 CGTGTAAACCACTCGTCGC 59.229 57.895 0.00 0.00 42.20 5.19
113 114 2.157738 GCTGGTTCATGTCTTCTGCTT 58.842 47.619 0.00 0.00 0.00 3.91
120 121 2.045926 GGCCGCTGGTTCATGTCT 60.046 61.111 0.00 0.00 0.00 3.41
121 122 3.499737 CGGCCGCTGGTTCATGTC 61.500 66.667 14.67 0.00 0.00 3.06
130 131 3.755526 TTGATCATCCCGGCCGCTG 62.756 63.158 22.85 16.69 0.00 5.18
131 132 2.738213 GATTGATCATCCCGGCCGCT 62.738 60.000 22.85 2.90 0.00 5.52
137 138 1.000843 TGCTACCGATTGATCATCCCG 59.999 52.381 0.00 0.43 0.00 5.14
141 142 2.224597 TGCCATGCTACCGATTGATCAT 60.225 45.455 0.00 0.00 0.00 2.45
200 211 2.166007 CAGAAAAATAAGTTCGGCGCG 58.834 47.619 0.00 0.00 0.00 6.86
260 271 3.650950 AGGCCATGTTCCCGCTGT 61.651 61.111 5.01 0.00 0.00 4.40
264 275 2.438434 GGACAGGCCATGTTCCCG 60.438 66.667 5.01 0.00 44.17 5.14
265 276 2.438434 CGGACAGGCCATGTTCCC 60.438 66.667 5.01 4.40 44.17 3.97
295 306 2.896801 CGCAAGCCGGGTATCATGC 61.897 63.158 16.26 16.26 0.00 4.06
296 307 3.333414 CGCAAGCCGGGTATCATG 58.667 61.111 6.57 1.84 0.00 3.07
324 335 2.126228 CGTAAACTCCGAGCGCCA 60.126 61.111 2.29 0.00 0.00 5.69
327 338 2.789203 GCTGCGTAAACTCCGAGCG 61.789 63.158 0.00 0.00 0.00 5.03
350 361 4.003011 TTTGCCCGTTTCGTCGCG 62.003 61.111 0.00 0.00 0.00 5.87
351 362 2.426261 GTTTGCCCGTTTCGTCGC 60.426 61.111 0.00 0.00 0.00 5.19
352 363 2.127906 CGTTTGCCCGTTTCGTCG 60.128 61.111 0.00 0.00 0.00 5.12
353 364 2.426261 GCGTTTGCCCGTTTCGTC 60.426 61.111 0.00 0.00 33.98 4.20
369 380 2.664436 CCGAAAGTTGACGTCCGGC 61.664 63.158 14.12 2.98 0.00 6.13
370 381 1.300388 ACCGAAAGTTGACGTCCGG 60.300 57.895 21.91 21.91 42.30 5.14
371 382 1.850640 CACCGAAAGTTGACGTCCG 59.149 57.895 14.12 7.89 0.00 4.79
372 383 0.878961 AGCACCGAAAGTTGACGTCC 60.879 55.000 14.12 0.00 0.00 4.79
373 384 0.935196 AAGCACCGAAAGTTGACGTC 59.065 50.000 9.11 9.11 0.00 4.34
374 385 0.935196 GAAGCACCGAAAGTTGACGT 59.065 50.000 0.00 0.00 0.00 4.34
375 386 0.934496 TGAAGCACCGAAAGTTGACG 59.066 50.000 0.00 0.00 0.00 4.35
376 387 2.918131 GCATGAAGCACCGAAAGTTGAC 60.918 50.000 0.00 0.00 44.79 3.18
377 388 1.266718 GCATGAAGCACCGAAAGTTGA 59.733 47.619 0.00 0.00 44.79 3.18
378 389 1.689959 GCATGAAGCACCGAAAGTTG 58.310 50.000 0.00 0.00 44.79 3.16
389 400 2.496828 AAGGCGCCAAAGCATGAAGC 62.497 55.000 31.54 0.00 46.19 3.86
390 401 0.457337 GAAGGCGCCAAAGCATGAAG 60.457 55.000 31.54 0.00 39.83 3.02
391 402 0.895100 AGAAGGCGCCAAAGCATGAA 60.895 50.000 31.54 0.00 39.83 2.57
392 403 0.895100 AAGAAGGCGCCAAAGCATGA 60.895 50.000 31.54 0.00 39.83 3.07
393 404 0.037975 AAAGAAGGCGCCAAAGCATG 60.038 50.000 31.54 0.00 39.83 4.06
394 405 0.244721 GAAAGAAGGCGCCAAAGCAT 59.755 50.000 31.54 10.04 39.83 3.79
395 406 0.823356 AGAAAGAAGGCGCCAAAGCA 60.823 50.000 31.54 0.00 39.83 3.91
396 407 0.109551 GAGAAAGAAGGCGCCAAAGC 60.110 55.000 31.54 14.48 0.00 3.51
397 408 1.238439 TGAGAAAGAAGGCGCCAAAG 58.762 50.000 31.54 0.00 0.00 2.77
398 409 1.686355 TTGAGAAAGAAGGCGCCAAA 58.314 45.000 31.54 5.37 0.00 3.28
399 410 1.541147 CATTGAGAAAGAAGGCGCCAA 59.459 47.619 31.54 11.21 0.00 4.52
400 411 1.167851 CATTGAGAAAGAAGGCGCCA 58.832 50.000 31.54 3.13 0.00 5.69
401 412 0.453390 CCATTGAGAAAGAAGGCGCC 59.547 55.000 21.89 21.89 0.00 6.53
402 413 1.168714 ACCATTGAGAAAGAAGGCGC 58.831 50.000 0.00 0.00 0.00 6.53
403 414 3.751175 TGTTACCATTGAGAAAGAAGGCG 59.249 43.478 0.00 0.00 0.00 5.52
404 415 4.762251 AGTGTTACCATTGAGAAAGAAGGC 59.238 41.667 0.00 0.00 0.00 4.35
405 416 5.997746 TCAGTGTTACCATTGAGAAAGAAGG 59.002 40.000 0.00 0.00 32.94 3.46
406 417 6.346919 CGTCAGTGTTACCATTGAGAAAGAAG 60.347 42.308 0.00 0.00 37.91 2.85
407 418 5.465390 CGTCAGTGTTACCATTGAGAAAGAA 59.535 40.000 0.00 0.00 37.91 2.52
408 419 4.988540 CGTCAGTGTTACCATTGAGAAAGA 59.011 41.667 0.00 0.00 37.91 2.52
409 420 4.377431 GCGTCAGTGTTACCATTGAGAAAG 60.377 45.833 0.00 0.00 37.91 2.62
410 421 3.496884 GCGTCAGTGTTACCATTGAGAAA 59.503 43.478 0.00 0.00 37.91 2.52
411 422 3.064207 GCGTCAGTGTTACCATTGAGAA 58.936 45.455 0.00 0.00 37.91 2.87
412 423 2.299013 AGCGTCAGTGTTACCATTGAGA 59.701 45.455 0.00 0.00 37.91 3.27
413 424 2.688507 AGCGTCAGTGTTACCATTGAG 58.311 47.619 0.00 0.00 37.91 3.02
414 425 2.831685 AGCGTCAGTGTTACCATTGA 57.168 45.000 0.00 0.00 35.23 2.57
415 426 3.249799 TGAAAGCGTCAGTGTTACCATTG 59.750 43.478 0.00 0.00 0.00 2.82
416 427 3.250040 GTGAAAGCGTCAGTGTTACCATT 59.750 43.478 0.00 0.00 36.74 3.16
417 428 2.806244 GTGAAAGCGTCAGTGTTACCAT 59.194 45.455 0.00 0.00 36.74 3.55
418 429 2.206750 GTGAAAGCGTCAGTGTTACCA 58.793 47.619 0.00 0.00 36.74 3.25
419 430 1.191647 CGTGAAAGCGTCAGTGTTACC 59.808 52.381 0.00 0.00 36.74 2.85
420 431 1.856597 ACGTGAAAGCGTCAGTGTTAC 59.143 47.619 0.00 0.00 41.71 2.50
421 432 2.212869 ACGTGAAAGCGTCAGTGTTA 57.787 45.000 0.00 0.00 41.71 2.41
422 433 3.059603 ACGTGAAAGCGTCAGTGTT 57.940 47.368 0.00 0.00 41.71 3.32
423 434 4.827481 ACGTGAAAGCGTCAGTGT 57.173 50.000 0.00 0.00 41.71 3.55
430 441 0.318699 TCTCTGTGGACGTGAAAGCG 60.319 55.000 0.00 0.00 37.94 4.68
431 442 1.865865 TTCTCTGTGGACGTGAAAGC 58.134 50.000 0.00 0.00 0.00 3.51
432 443 2.738846 CCATTCTCTGTGGACGTGAAAG 59.261 50.000 0.00 0.00 39.12 2.62
433 444 2.367241 TCCATTCTCTGTGGACGTGAAA 59.633 45.455 0.00 0.00 40.72 2.69
434 445 1.967779 TCCATTCTCTGTGGACGTGAA 59.032 47.619 0.00 0.00 40.72 3.18
435 446 1.627864 TCCATTCTCTGTGGACGTGA 58.372 50.000 0.00 0.00 40.72 4.35
436 447 2.455674 TTCCATTCTCTGTGGACGTG 57.544 50.000 0.00 0.00 45.05 4.49
437 448 2.834549 AGATTCCATTCTCTGTGGACGT 59.165 45.455 0.00 0.00 45.05 4.34
438 449 3.533606 AGATTCCATTCTCTGTGGACG 57.466 47.619 0.00 0.00 45.05 4.79
439 450 5.362430 AGACTAGATTCCATTCTCTGTGGAC 59.638 44.000 0.00 0.00 45.05 4.02
440 451 5.523588 AGACTAGATTCCATTCTCTGTGGA 58.476 41.667 0.00 0.00 43.77 4.02
441 452 5.867903 AGACTAGATTCCATTCTCTGTGG 57.132 43.478 0.00 0.00 38.11 4.17
442 453 6.760770 GGAAAGACTAGATTCCATTCTCTGTG 59.239 42.308 16.55 0.00 43.73 3.66
443 454 6.406400 CGGAAAGACTAGATTCCATTCTCTGT 60.406 42.308 19.42 0.00 44.35 3.41
444 455 5.982516 CGGAAAGACTAGATTCCATTCTCTG 59.017 44.000 19.42 5.15 44.35 3.35
445 456 5.659079 ACGGAAAGACTAGATTCCATTCTCT 59.341 40.000 19.42 0.00 44.35 3.10
446 457 5.908341 ACGGAAAGACTAGATTCCATTCTC 58.092 41.667 19.42 0.00 44.35 2.87
447 458 5.941555 ACGGAAAGACTAGATTCCATTCT 57.058 39.130 19.42 0.61 44.35 2.40
448 459 5.524281 GGAACGGAAAGACTAGATTCCATTC 59.476 44.000 18.43 18.43 43.59 2.67
449 460 5.189934 AGGAACGGAAAGACTAGATTCCATT 59.810 40.000 19.42 13.90 44.35 3.16
450 461 4.717280 AGGAACGGAAAGACTAGATTCCAT 59.283 41.667 19.42 11.62 44.35 3.41
451 462 4.094476 AGGAACGGAAAGACTAGATTCCA 58.906 43.478 19.42 0.00 44.35 3.53
452 463 4.739587 AGGAACGGAAAGACTAGATTCC 57.260 45.455 13.33 13.33 41.39 3.01
453 464 8.604890 CATTTTAGGAACGGAAAGACTAGATTC 58.395 37.037 0.00 0.00 0.00 2.52
454 465 8.101419 ACATTTTAGGAACGGAAAGACTAGATT 58.899 33.333 0.00 0.00 0.00 2.40
455 466 7.621796 ACATTTTAGGAACGGAAAGACTAGAT 58.378 34.615 0.00 0.00 0.00 1.98
456 467 7.001099 ACATTTTAGGAACGGAAAGACTAGA 57.999 36.000 0.00 0.00 0.00 2.43
457 468 8.943909 ATACATTTTAGGAACGGAAAGACTAG 57.056 34.615 0.00 0.00 0.00 2.57
510 521 9.502091 AGACTACATACAAAGCAAAATGAGTAA 57.498 29.630 0.00 0.00 0.00 2.24
512 523 7.986085 AGACTACATACAAAGCAAAATGAGT 57.014 32.000 0.00 0.00 0.00 3.41
545 556 9.825109 GCCTCAGTTCTAAGTCTTTTTAGATAT 57.175 33.333 0.00 0.00 38.92 1.63
546 557 8.812972 TGCCTCAGTTCTAAGTCTTTTTAGATA 58.187 33.333 0.00 0.00 38.92 1.98
547 558 7.680730 TGCCTCAGTTCTAAGTCTTTTTAGAT 58.319 34.615 0.00 0.00 38.92 1.98
548 559 7.062749 TGCCTCAGTTCTAAGTCTTTTTAGA 57.937 36.000 0.00 0.00 37.76 2.10
549 560 7.730364 TTGCCTCAGTTCTAAGTCTTTTTAG 57.270 36.000 0.00 0.00 32.99 1.85
550 561 9.216117 GTATTGCCTCAGTTCTAAGTCTTTTTA 57.784 33.333 0.00 0.00 0.00 1.52
551 562 7.719633 TGTATTGCCTCAGTTCTAAGTCTTTTT 59.280 33.333 0.00 0.00 0.00 1.94
552 563 7.224297 TGTATTGCCTCAGTTCTAAGTCTTTT 58.776 34.615 0.00 0.00 0.00 2.27
553 564 6.769512 TGTATTGCCTCAGTTCTAAGTCTTT 58.230 36.000 0.00 0.00 0.00 2.52
554 565 6.360370 TGTATTGCCTCAGTTCTAAGTCTT 57.640 37.500 0.00 0.00 0.00 3.01
555 566 6.344500 CATGTATTGCCTCAGTTCTAAGTCT 58.656 40.000 0.00 0.00 0.00 3.24
556 567 5.007136 GCATGTATTGCCTCAGTTCTAAGTC 59.993 44.000 0.00 0.00 46.15 3.01
557 568 4.878397 GCATGTATTGCCTCAGTTCTAAGT 59.122 41.667 0.00 0.00 46.15 2.24
558 569 5.415415 GCATGTATTGCCTCAGTTCTAAG 57.585 43.478 0.00 0.00 46.15 2.18
571 582 9.715123 TTATTGAGAAATTGTACGCATGTATTG 57.285 29.630 0.00 0.00 32.11 1.90
572 583 9.716507 GTTATTGAGAAATTGTACGCATGTATT 57.283 29.630 0.00 0.00 32.11 1.89
573 584 8.888716 TGTTATTGAGAAATTGTACGCATGTAT 58.111 29.630 0.00 0.00 32.11 2.29
574 585 8.257830 TGTTATTGAGAAATTGTACGCATGTA 57.742 30.769 0.00 0.00 0.00 2.29
575 586 7.139896 TGTTATTGAGAAATTGTACGCATGT 57.860 32.000 0.00 0.00 0.00 3.21
576 587 7.253420 GCTTGTTATTGAGAAATTGTACGCATG 60.253 37.037 0.00 0.00 0.00 4.06
577 588 6.747280 GCTTGTTATTGAGAAATTGTACGCAT 59.253 34.615 0.00 0.00 0.00 4.73
578 589 6.072728 AGCTTGTTATTGAGAAATTGTACGCA 60.073 34.615 0.00 0.00 0.00 5.24
579 590 6.314784 AGCTTGTTATTGAGAAATTGTACGC 58.685 36.000 0.00 0.00 0.00 4.42
580 591 7.743104 AGAGCTTGTTATTGAGAAATTGTACG 58.257 34.615 0.00 0.00 0.00 3.67
581 592 8.940952 AGAGAGCTTGTTATTGAGAAATTGTAC 58.059 33.333 0.00 0.00 0.00 2.90
582 593 9.155975 GAGAGAGCTTGTTATTGAGAAATTGTA 57.844 33.333 0.00 0.00 0.00 2.41
583 594 7.882271 AGAGAGAGCTTGTTATTGAGAAATTGT 59.118 33.333 0.00 0.00 0.00 2.71
584 595 8.266392 AGAGAGAGCTTGTTATTGAGAAATTG 57.734 34.615 0.00 0.00 0.00 2.32
585 596 8.860780 AAGAGAGAGCTTGTTATTGAGAAATT 57.139 30.769 0.00 0.00 0.00 1.82
586 597 8.860780 AAAGAGAGAGCTTGTTATTGAGAAAT 57.139 30.769 0.00 0.00 0.00 2.17
587 598 8.682936 AAAAGAGAGAGCTTGTTATTGAGAAA 57.317 30.769 0.00 0.00 0.00 2.52
588 599 8.682936 AAAAAGAGAGAGCTTGTTATTGAGAA 57.317 30.769 0.00 0.00 0.00 2.87
610 621 4.384247 CACTCGCTCAAAAACACACAAAAA 59.616 37.500 0.00 0.00 0.00 1.94
611 622 3.917380 CACTCGCTCAAAAACACACAAAA 59.083 39.130 0.00 0.00 0.00 2.44
612 623 3.189495 TCACTCGCTCAAAAACACACAAA 59.811 39.130 0.00 0.00 0.00 2.83
613 624 2.744741 TCACTCGCTCAAAAACACACAA 59.255 40.909 0.00 0.00 0.00 3.33
614 625 2.351455 TCACTCGCTCAAAAACACACA 58.649 42.857 0.00 0.00 0.00 3.72
615 626 3.398954 TTCACTCGCTCAAAAACACAC 57.601 42.857 0.00 0.00 0.00 3.82
616 627 4.350346 CAATTCACTCGCTCAAAAACACA 58.650 39.130 0.00 0.00 0.00 3.72
617 628 3.180387 GCAATTCACTCGCTCAAAAACAC 59.820 43.478 0.00 0.00 0.00 3.32
618 629 3.181492 TGCAATTCACTCGCTCAAAAACA 60.181 39.130 0.00 0.00 0.00 2.83
619 630 3.371168 TGCAATTCACTCGCTCAAAAAC 58.629 40.909 0.00 0.00 0.00 2.43
620 631 3.706802 TGCAATTCACTCGCTCAAAAA 57.293 38.095 0.00 0.00 0.00 1.94
621 632 3.706802 TTGCAATTCACTCGCTCAAAA 57.293 38.095 0.00 0.00 0.00 2.44
622 633 3.706802 TTTGCAATTCACTCGCTCAAA 57.293 38.095 0.00 0.00 0.00 2.69
623 634 3.706802 TTTTGCAATTCACTCGCTCAA 57.293 38.095 0.00 0.00 0.00 3.02
624 635 3.706802 TTTTTGCAATTCACTCGCTCA 57.293 38.095 0.00 0.00 0.00 4.26
693 704 1.133606 AGTGGTGGATTTTTGGGACGT 60.134 47.619 0.00 0.00 0.00 4.34
844 855 2.127534 GTTTTGTACCGCGTGCCG 60.128 61.111 4.92 0.00 0.00 5.69
880 891 2.447572 TGGAGTGGGGTGTGAGCA 60.448 61.111 0.00 0.00 0.00 4.26
889 900 2.357517 GTGTGCGAGTGGAGTGGG 60.358 66.667 0.00 0.00 0.00 4.61
1437 1494 6.572519 ACTAACATTTGATTGTTGCAACTGT 58.427 32.000 28.61 19.47 39.73 3.55
1601 1694 6.767902 ACATGTTTCATCAACTACAGACAGTT 59.232 34.615 0.00 0.00 39.34 3.16
2129 2232 4.873010 AGTCAGCACTATCCTTCTCCTTA 58.127 43.478 0.00 0.00 0.00 2.69
2242 2345 4.592351 TCATCTCATCCCTCTCCTTCATTC 59.408 45.833 0.00 0.00 0.00 2.67
2245 2348 3.695357 TCATCTCATCCCTCTCCTTCA 57.305 47.619 0.00 0.00 0.00 3.02
2315 2418 4.521146 CAGCTTTCATAAGATCACCCACT 58.479 43.478 0.00 0.00 32.92 4.00
2432 2535 3.825328 CCAGCTATATTGTTCCAAGGCT 58.175 45.455 0.00 0.00 0.00 4.58
2880 3011 7.040271 GGAGTAGGATTCTGTACCTAGATGAAC 60.040 44.444 0.00 0.00 39.10 3.18
2925 3056 3.259328 AGGGCCAATTTCCATCCTTTTT 58.741 40.909 6.18 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.