Multiple sequence alignment - TraesCS6A01G182100

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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 TraesCS6A01G182100 chr6A 100.000 2480 0 0 1 2480 209784120 209781641 0.000000e+00 4580.0
1 TraesCS6A01G182100 chr6A 96.883 770 17 2 1711 2480 410851164 410851926 0.000000e+00 1282.0
2 TraesCS6A01G182100 chr6A 93.830 778 44 4 1706 2480 418614221 418613445 0.000000e+00 1168.0
3 TraesCS6A01G182100 chr6A 97.037 135 4 0 1577 1711 606611831 606611965 6.900000e-56 228.0
4 TraesCS6A01G182100 chr6B 92.959 1122 60 9 468 1583 279009089 279007981 0.000000e+00 1616.0
5 TraesCS6A01G182100 chr6B 84.677 124 13 1 279 402 279009217 279009100 4.330000e-23 119.0
6 TraesCS6A01G182100 chr6B 82.796 93 16 0 96 188 147958058 147958150 1.580000e-12 84.2
7 TraesCS6A01G182100 chr6D 94.944 890 29 8 581 1462 156429570 156428689 0.000000e+00 1380.0
8 TraesCS6A01G182100 chr3A 98.191 774 10 2 1708 2480 712364101 712364871 0.000000e+00 1349.0
9 TraesCS6A01G182100 chr3A 94.408 769 40 3 1712 2478 497190243 497191010 0.000000e+00 1179.0
10 TraesCS6A01G182100 chr3A 94.034 771 42 4 1712 2480 691685752 691686520 0.000000e+00 1166.0
11 TraesCS6A01G182100 chr3A 97.778 135 3 0 1577 1711 412693547 412693681 1.480000e-57 233.0
12 TraesCS6A01G182100 chr1A 98.179 769 14 0 1712 2480 474202936 474203704 0.000000e+00 1343.0
13 TraesCS6A01G182100 chr1A 94.315 774 37 6 1712 2480 580182432 580181661 0.000000e+00 1179.0
14 TraesCS6A01G182100 chr5A 97.919 769 16 0 1712 2480 77900003 77899235 0.000000e+00 1332.0
15 TraesCS6A01G182100 chr5A 97.778 135 3 0 1577 1711 635462411 635462277 1.480000e-57 233.0
16 TraesCS6A01G182100 chr5A 96.296 135 5 0 1577 1711 364681844 364681710 3.210000e-54 222.0
17 TraesCS6A01G182100 chr2A 94.201 776 42 3 1707 2480 770362130 770362904 0.000000e+00 1181.0
18 TraesCS6A01G182100 chr7A 97.037 135 4 0 1577 1711 91742076 91742210 6.900000e-56 228.0
19 TraesCS6A01G182100 chr7A 97.037 135 4 0 1577 1711 542451954 542452088 6.900000e-56 228.0
20 TraesCS6A01G182100 chr7A 95.139 144 6 1 1568 1711 401405153 401405295 2.480000e-55 226.0
21 TraesCS6A01G182100 chr4A 94.406 143 8 0 1569 1711 572504554 572504696 1.150000e-53 220.0
22 TraesCS6A01G182100 chr4A 93.243 148 9 1 1564 1711 96541240 96541094 1.490000e-52 217.0
23 TraesCS6A01G182100 chr5B 84.848 132 18 1 115 244 456273336 456273205 5.570000e-27 132.0
24 TraesCS6A01G182100 chr5D 91.111 45 4 0 53 97 28677180 28677136 7.410000e-06 62.1


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 TraesCS6A01G182100 chr6A 209781641 209784120 2479 True 4580.0 4580 100.000 1 2480 1 chr6A.!!$R1 2479
1 TraesCS6A01G182100 chr6A 410851164 410851926 762 False 1282.0 1282 96.883 1711 2480 1 chr6A.!!$F1 769
2 TraesCS6A01G182100 chr6A 418613445 418614221 776 True 1168.0 1168 93.830 1706 2480 1 chr6A.!!$R2 774
3 TraesCS6A01G182100 chr6B 279007981 279009217 1236 True 867.5 1616 88.818 279 1583 2 chr6B.!!$R1 1304
4 TraesCS6A01G182100 chr6D 156428689 156429570 881 True 1380.0 1380 94.944 581 1462 1 chr6D.!!$R1 881
5 TraesCS6A01G182100 chr3A 712364101 712364871 770 False 1349.0 1349 98.191 1708 2480 1 chr3A.!!$F4 772
6 TraesCS6A01G182100 chr3A 497190243 497191010 767 False 1179.0 1179 94.408 1712 2478 1 chr3A.!!$F2 766
7 TraesCS6A01G182100 chr3A 691685752 691686520 768 False 1166.0 1166 94.034 1712 2480 1 chr3A.!!$F3 768
8 TraesCS6A01G182100 chr1A 474202936 474203704 768 False 1343.0 1343 98.179 1712 2480 1 chr1A.!!$F1 768
9 TraesCS6A01G182100 chr1A 580181661 580182432 771 True 1179.0 1179 94.315 1712 2480 1 chr1A.!!$R1 768
10 TraesCS6A01G182100 chr5A 77899235 77900003 768 True 1332.0 1332 97.919 1712 2480 1 chr5A.!!$R1 768
11 TraesCS6A01G182100 chr2A 770362130 770362904 774 False 1181.0 1181 94.201 1707 2480 1 chr2A.!!$F1 773

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
464 465 0.26023 TGACTAGCCTGAGGGGAGAG 59.74 60.0 0.0 0.0 37.23 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1891 1906 0.17576 GACTCAGATGGCAACCGCTA 59.824 55.0 0.0 0.0 38.6 4.26 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.419154 AGACCTTCCCGGAAATCCT 57.581 52.632 0.73 0.00 36.31 3.24
19 20 2.563039 AGACCTTCCCGGAAATCCTA 57.437 50.000 0.73 0.00 36.31 2.94
20 21 3.061909 AGACCTTCCCGGAAATCCTAT 57.938 47.619 0.73 0.00 36.31 2.57
21 22 2.706190 AGACCTTCCCGGAAATCCTATG 59.294 50.000 0.73 0.00 36.31 2.23
22 23 2.438392 GACCTTCCCGGAAATCCTATGT 59.562 50.000 0.73 0.00 36.31 2.29
23 24 2.172717 ACCTTCCCGGAAATCCTATGTG 59.827 50.000 0.73 0.00 36.31 3.21
24 25 2.438021 CCTTCCCGGAAATCCTATGTGA 59.562 50.000 0.73 0.00 33.16 3.58
25 26 3.118038 CCTTCCCGGAAATCCTATGTGAA 60.118 47.826 0.73 0.00 33.16 3.18
26 27 4.523083 CTTCCCGGAAATCCTATGTGAAA 58.477 43.478 0.73 0.00 0.00 2.69
27 28 3.881220 TCCCGGAAATCCTATGTGAAAC 58.119 45.455 0.73 0.00 37.35 2.78
28 29 3.521937 TCCCGGAAATCCTATGTGAAACT 59.478 43.478 0.73 0.00 38.04 2.66
29 30 3.627577 CCCGGAAATCCTATGTGAAACTG 59.372 47.826 0.73 0.00 38.04 3.16
30 31 3.065371 CCGGAAATCCTATGTGAAACTGC 59.935 47.826 0.00 0.00 38.04 4.40
31 32 3.941483 CGGAAATCCTATGTGAAACTGCT 59.059 43.478 0.00 0.00 38.04 4.24
32 33 4.396166 CGGAAATCCTATGTGAAACTGCTT 59.604 41.667 0.00 0.00 38.04 3.91
33 34 5.106157 CGGAAATCCTATGTGAAACTGCTTT 60.106 40.000 0.00 0.00 38.04 3.51
34 35 6.093495 CGGAAATCCTATGTGAAACTGCTTTA 59.907 38.462 0.00 0.00 38.04 1.85
35 36 7.361713 CGGAAATCCTATGTGAAACTGCTTTAA 60.362 37.037 0.00 0.00 38.04 1.52
36 37 8.303876 GGAAATCCTATGTGAAACTGCTTTAAA 58.696 33.333 0.00 0.00 38.04 1.52
37 38 9.346725 GAAATCCTATGTGAAACTGCTTTAAAG 57.653 33.333 11.02 11.02 38.04 1.85
38 39 8.409358 AATCCTATGTGAAACTGCTTTAAAGT 57.591 30.769 16.38 0.00 38.04 2.66
39 40 7.202016 TCCTATGTGAAACTGCTTTAAAGTG 57.798 36.000 16.38 11.81 38.04 3.16
40 41 6.995686 TCCTATGTGAAACTGCTTTAAAGTGA 59.004 34.615 16.38 3.35 38.04 3.41
41 42 7.500892 TCCTATGTGAAACTGCTTTAAAGTGAA 59.499 33.333 16.38 2.68 38.04 3.18
42 43 8.299570 CCTATGTGAAACTGCTTTAAAGTGAAT 58.700 33.333 16.38 0.40 38.04 2.57
43 44 9.683069 CTATGTGAAACTGCTTTAAAGTGAATT 57.317 29.630 16.38 7.45 38.04 2.17
44 45 8.947055 ATGTGAAACTGCTTTAAAGTGAATTT 57.053 26.923 16.38 11.46 38.04 1.82
45 46 8.770438 TGTGAAACTGCTTTAAAGTGAATTTT 57.230 26.923 16.38 9.12 38.04 1.82
46 47 8.655092 TGTGAAACTGCTTTAAAGTGAATTTTG 58.345 29.630 16.38 1.94 38.04 2.44
47 48 8.655970 GTGAAACTGCTTTAAAGTGAATTTTGT 58.344 29.630 16.38 2.47 32.01 2.83
48 49 8.655092 TGAAACTGCTTTAAAGTGAATTTTGTG 58.345 29.630 16.38 0.00 32.01 3.33
49 50 8.770438 AAACTGCTTTAAAGTGAATTTTGTGA 57.230 26.923 16.38 0.00 32.01 3.58
50 51 8.770438 AACTGCTTTAAAGTGAATTTTGTGAA 57.230 26.923 16.38 0.00 32.01 3.18
51 52 8.947055 ACTGCTTTAAAGTGAATTTTGTGAAT 57.053 26.923 16.38 0.00 32.01 2.57
52 53 9.382275 ACTGCTTTAAAGTGAATTTTGTGAATT 57.618 25.926 16.38 0.00 32.01 2.17
53 54 9.640974 CTGCTTTAAAGTGAATTTTGTGAATTG 57.359 29.630 16.38 0.00 32.01 2.32
54 55 9.376075 TGCTTTAAAGTGAATTTTGTGAATTGA 57.624 25.926 16.38 0.00 32.01 2.57
60 61 9.434420 AAAGTGAATTTTGTGAATTGAAACTGA 57.566 25.926 0.00 0.00 0.00 3.41
61 62 9.603921 AAGTGAATTTTGTGAATTGAAACTGAT 57.396 25.926 0.00 0.00 0.00 2.90
62 63 9.603921 AGTGAATTTTGTGAATTGAAACTGATT 57.396 25.926 0.00 0.00 0.00 2.57
69 70 7.949903 TGTGAATTGAAACTGATTTTGATGG 57.050 32.000 0.00 0.00 0.00 3.51
70 71 7.724287 TGTGAATTGAAACTGATTTTGATGGA 58.276 30.769 0.00 0.00 0.00 3.41
71 72 7.868922 TGTGAATTGAAACTGATTTTGATGGAG 59.131 33.333 0.00 0.00 0.00 3.86
72 73 6.869913 TGAATTGAAACTGATTTTGATGGAGC 59.130 34.615 0.00 0.00 0.00 4.70
73 74 4.424061 TGAAACTGATTTTGATGGAGCG 57.576 40.909 0.00 0.00 0.00 5.03
74 75 3.191162 TGAAACTGATTTTGATGGAGCGG 59.809 43.478 0.00 0.00 0.00 5.52
75 76 2.787473 ACTGATTTTGATGGAGCGGA 57.213 45.000 0.00 0.00 0.00 5.54
76 77 2.636830 ACTGATTTTGATGGAGCGGAG 58.363 47.619 0.00 0.00 0.00 4.63
89 90 3.972227 CGGAGCAGTCCCAAACAG 58.028 61.111 0.00 0.00 40.20 3.16
90 91 1.371183 CGGAGCAGTCCCAAACAGA 59.629 57.895 0.00 0.00 40.20 3.41
91 92 0.951040 CGGAGCAGTCCCAAACAGAC 60.951 60.000 0.00 0.00 40.20 3.51
92 93 0.398318 GGAGCAGTCCCAAACAGACT 59.602 55.000 0.00 0.00 45.45 3.24
93 94 1.202818 GGAGCAGTCCCAAACAGACTT 60.203 52.381 0.00 0.00 41.87 3.01
94 95 2.576615 GAGCAGTCCCAAACAGACTTT 58.423 47.619 0.00 0.00 41.87 2.66
95 96 2.952310 GAGCAGTCCCAAACAGACTTTT 59.048 45.455 0.00 0.00 41.87 2.27
96 97 4.134563 GAGCAGTCCCAAACAGACTTTTA 58.865 43.478 0.00 0.00 41.87 1.52
97 98 4.729868 AGCAGTCCCAAACAGACTTTTAT 58.270 39.130 0.00 0.00 41.87 1.40
98 99 5.876357 AGCAGTCCCAAACAGACTTTTATA 58.124 37.500 0.00 0.00 41.87 0.98
99 100 6.485171 AGCAGTCCCAAACAGACTTTTATAT 58.515 36.000 0.00 0.00 41.87 0.86
100 101 7.630082 AGCAGTCCCAAACAGACTTTTATATA 58.370 34.615 0.00 0.00 41.87 0.86
101 102 8.275040 AGCAGTCCCAAACAGACTTTTATATAT 58.725 33.333 0.00 0.00 41.87 0.86
102 103 9.555727 GCAGTCCCAAACAGACTTTTATATATA 57.444 33.333 0.00 0.00 41.87 0.86
255 256 7.953158 TTTATATGCACTATGTCAAGAGAGC 57.047 36.000 0.00 1.95 32.57 4.09
256 257 2.284263 TGCACTATGTCAAGAGAGCG 57.716 50.000 0.00 0.00 34.40 5.03
257 258 1.818674 TGCACTATGTCAAGAGAGCGA 59.181 47.619 0.00 0.00 34.40 4.93
258 259 2.189342 GCACTATGTCAAGAGAGCGAC 58.811 52.381 0.00 0.00 0.00 5.19
259 260 2.159310 GCACTATGTCAAGAGAGCGACT 60.159 50.000 0.00 0.00 33.18 4.18
260 261 3.690422 CACTATGTCAAGAGAGCGACTC 58.310 50.000 5.96 5.96 45.22 3.36
267 268 4.946411 GAGAGCGACTCACACGTT 57.054 55.556 9.09 0.00 44.36 3.99
268 269 2.425278 GAGAGCGACTCACACGTTG 58.575 57.895 9.09 0.00 44.36 4.10
269 270 1.609840 GAGAGCGACTCACACGTTGC 61.610 60.000 9.09 0.00 44.36 4.17
270 271 2.988549 GAGCGACTCACACGTTGCG 61.989 63.158 0.00 0.00 46.55 4.85
271 272 4.702826 GCGACTCACACGTTGCGC 62.703 66.667 0.00 0.00 34.85 6.09
273 274 4.702826 GACTCACACGTTGCGCGC 62.703 66.667 27.26 27.26 46.11 6.86
288 289 2.600731 CGCCCCCTCTCTCTCTCT 59.399 66.667 0.00 0.00 0.00 3.10
289 290 1.528309 CGCCCCCTCTCTCTCTCTC 60.528 68.421 0.00 0.00 0.00 3.20
290 291 1.930520 GCCCCCTCTCTCTCTCTCT 59.069 63.158 0.00 0.00 0.00 3.10
299 300 5.707298 CCCTCTCTCTCTCTCTTAATGCTAG 59.293 48.000 0.00 0.00 0.00 3.42
349 350 0.534652 GCCTAAGCTGAGATGGGCTG 60.535 60.000 0.00 0.00 38.91 4.85
353 354 3.072184 CCTAAGCTGAGATGGGCTGTTAT 59.928 47.826 0.00 0.00 38.91 1.89
354 355 2.634815 AGCTGAGATGGGCTGTTATG 57.365 50.000 0.00 0.00 37.41 1.90
355 356 2.121948 AGCTGAGATGGGCTGTTATGA 58.878 47.619 0.00 0.00 37.41 2.15
356 357 2.709934 AGCTGAGATGGGCTGTTATGAT 59.290 45.455 0.00 0.00 37.41 2.45
357 358 3.137913 AGCTGAGATGGGCTGTTATGATT 59.862 43.478 0.00 0.00 37.41 2.57
358 359 3.252701 GCTGAGATGGGCTGTTATGATTG 59.747 47.826 0.00 0.00 0.00 2.67
374 375 4.214986 TGATTGGTTAAGGATGAAGCGA 57.785 40.909 0.00 0.00 26.25 4.93
380 381 0.980754 TAAGGATGAAGCGAGGCCCA 60.981 55.000 0.00 0.00 0.00 5.36
381 382 2.514824 GGATGAAGCGAGGCCCAC 60.515 66.667 0.00 0.00 0.00 4.61
385 386 3.081409 GAAGCGAGGCCCACCCTA 61.081 66.667 0.00 0.00 46.60 3.53
395 396 1.006639 GGCCCACCCTAAAAATCAGGA 59.993 52.381 0.00 0.00 34.91 3.86
402 403 4.471386 CACCCTAAAAATCAGGAGGAGAGA 59.529 45.833 0.00 0.00 34.91 3.10
403 404 5.131809 CACCCTAAAAATCAGGAGGAGAGAT 59.868 44.000 0.00 0.00 34.91 2.75
404 405 5.733647 ACCCTAAAAATCAGGAGGAGAGATT 59.266 40.000 0.00 0.00 34.91 2.40
405 406 6.909158 ACCCTAAAAATCAGGAGGAGAGATTA 59.091 38.462 0.00 0.00 34.91 1.75
406 407 7.406151 ACCCTAAAAATCAGGAGGAGAGATTAA 59.594 37.037 0.00 0.00 34.91 1.40
407 408 7.936301 CCCTAAAAATCAGGAGGAGAGATTAAG 59.064 40.741 0.00 0.00 34.91 1.85
410 411 7.996758 AAAATCAGGAGGAGAGATTAAGGTA 57.003 36.000 0.00 0.00 32.11 3.08
411 412 7.996758 AAATCAGGAGGAGAGATTAAGGTAA 57.003 36.000 0.00 0.00 32.11 2.85
412 413 7.610580 AATCAGGAGGAGAGATTAAGGTAAG 57.389 40.000 0.00 0.00 30.70 2.34
413 414 6.093617 TCAGGAGGAGAGATTAAGGTAAGT 57.906 41.667 0.00 0.00 0.00 2.24
414 415 6.130569 TCAGGAGGAGAGATTAAGGTAAGTC 58.869 44.000 0.00 0.00 0.00 3.01
415 416 5.303333 CAGGAGGAGAGATTAAGGTAAGTCC 59.697 48.000 0.00 0.00 0.00 3.85
416 417 4.278919 GGAGGAGAGATTAAGGTAAGTCCG 59.721 50.000 0.00 0.00 41.99 4.79
417 418 4.869451 AGGAGAGATTAAGGTAAGTCCGT 58.131 43.478 0.00 0.00 41.99 4.69
418 419 6.011122 AGGAGAGATTAAGGTAAGTCCGTA 57.989 41.667 0.00 0.00 41.99 4.02
419 420 6.430007 AGGAGAGATTAAGGTAAGTCCGTAA 58.570 40.000 0.00 0.00 42.44 3.18
420 421 6.546772 AGGAGAGATTAAGGTAAGTCCGTAAG 59.453 42.308 0.00 0.00 41.79 2.34
421 422 6.320926 GGAGAGATTAAGGTAAGTCCGTAAGT 59.679 42.308 0.00 0.00 41.79 2.24
422 423 7.147932 GGAGAGATTAAGGTAAGTCCGTAAGTT 60.148 40.741 0.00 0.00 41.79 2.66
423 424 8.814038 AGAGATTAAGGTAAGTCCGTAAGTTA 57.186 34.615 0.00 0.00 41.79 2.24
424 425 8.681806 AGAGATTAAGGTAAGTCCGTAAGTTAC 58.318 37.037 2.72 2.72 41.79 2.50
425 426 8.586879 AGATTAAGGTAAGTCCGTAAGTTACT 57.413 34.615 11.17 0.00 41.79 2.24
426 427 9.029368 AGATTAAGGTAAGTCCGTAAGTTACTT 57.971 33.333 11.17 2.32 41.79 2.24
427 428 8.992835 ATTAAGGTAAGTCCGTAAGTTACTTG 57.007 34.615 8.00 2.76 41.79 3.16
428 429 4.814147 AGGTAAGTCCGTAAGTTACTTGC 58.186 43.478 8.00 5.44 41.61 4.01
429 430 4.525874 AGGTAAGTCCGTAAGTTACTTGCT 59.474 41.667 8.00 3.47 41.61 3.91
430 431 5.711976 AGGTAAGTCCGTAAGTTACTTGCTA 59.288 40.000 8.00 0.00 41.61 3.49
431 432 6.209391 AGGTAAGTCCGTAAGTTACTTGCTAA 59.791 38.462 8.00 0.00 41.61 3.09
432 433 6.529477 GGTAAGTCCGTAAGTTACTTGCTAAG 59.471 42.308 8.00 0.00 41.61 2.18
433 434 5.718724 AGTCCGTAAGTTACTTGCTAAGT 57.281 39.130 8.00 6.74 45.40 2.24
434 435 6.094193 AGTCCGTAAGTTACTTGCTAAGTT 57.906 37.500 8.00 0.00 42.81 2.66
435 436 7.219484 AGTCCGTAAGTTACTTGCTAAGTTA 57.781 36.000 8.00 0.00 42.81 2.24
436 437 7.087007 AGTCCGTAAGTTACTTGCTAAGTTAC 58.913 38.462 8.00 8.63 42.81 2.50
453 454 9.628746 GCTAAGTTACTCTTATTATGACTAGCC 57.371 37.037 0.00 0.00 37.89 3.93
456 457 8.998277 AGTTACTCTTATTATGACTAGCCTGA 57.002 34.615 0.00 0.00 0.00 3.86
457 458 9.073475 AGTTACTCTTATTATGACTAGCCTGAG 57.927 37.037 0.00 0.00 0.00 3.35
458 459 6.909550 ACTCTTATTATGACTAGCCTGAGG 57.090 41.667 0.00 0.00 0.00 3.86
459 460 5.777732 ACTCTTATTATGACTAGCCTGAGGG 59.222 44.000 0.00 0.00 0.00 4.30
460 461 5.087323 TCTTATTATGACTAGCCTGAGGGG 58.913 45.833 0.00 0.00 38.36 4.79
461 462 3.637821 ATTATGACTAGCCTGAGGGGA 57.362 47.619 0.00 0.00 37.23 4.81
462 463 2.685106 TATGACTAGCCTGAGGGGAG 57.315 55.000 0.00 0.00 37.23 4.30
463 464 0.937441 ATGACTAGCCTGAGGGGAGA 59.063 55.000 0.00 0.00 37.23 3.71
464 465 0.260230 TGACTAGCCTGAGGGGAGAG 59.740 60.000 0.00 0.00 37.23 3.20
465 466 0.469144 GACTAGCCTGAGGGGAGAGG 60.469 65.000 0.00 0.00 37.23 3.69
466 467 1.152355 CTAGCCTGAGGGGAGAGGG 60.152 68.421 0.00 0.00 37.23 4.30
506 507 4.650754 TCCTCCGTAAGTCTAGCATTTC 57.349 45.455 0.00 0.00 0.00 2.17
516 517 7.201696 CGTAAGTCTAGCATTTCTCTCTCTCTT 60.202 40.741 0.00 0.00 0.00 2.85
522 523 6.549433 AGCATTTCTCTCTCTCTTTCTGAT 57.451 37.500 0.00 0.00 0.00 2.90
542 543 8.280258 TCTGATGAGGAACCCATCTATTATTT 57.720 34.615 16.81 0.00 44.26 1.40
543 544 8.727149 TCTGATGAGGAACCCATCTATTATTTT 58.273 33.333 16.81 0.00 44.26 1.82
549 550 5.705905 GGAACCCATCTATTATTTTCCCTCG 59.294 44.000 0.00 0.00 0.00 4.63
555 556 7.093992 CCATCTATTATTTTCCCTCGTCTCTC 58.906 42.308 0.00 0.00 0.00 3.20
579 580 4.035558 TGTTGAGAGCAAATGTGACACTTC 59.964 41.667 7.20 0.00 35.42 3.01
634 635 3.345737 ACATGACCGCGTGTCTATG 57.654 52.632 22.40 22.42 44.75 2.23
827 834 2.742372 GCCACCACCACGCAGTAG 60.742 66.667 0.00 0.00 41.61 2.57
828 835 2.741092 CCACCACCACGCAGTAGT 59.259 61.111 0.00 0.00 41.61 2.73
829 836 1.969085 CCACCACCACGCAGTAGTA 59.031 57.895 0.00 0.00 41.61 1.82
950 958 0.681564 GGCTTCTCGTCTCCTCCTCA 60.682 60.000 0.00 0.00 0.00 3.86
1275 1290 2.104132 TGGATGCGGATCGTCACG 59.896 61.111 11.02 0.00 32.27 4.35
1441 1456 0.757561 TGGGATGGCGTTCTCGGATA 60.758 55.000 0.00 0.00 37.56 2.59
1506 1521 1.867233 CTTGTGAGGAGTTTGTGGACG 59.133 52.381 0.00 0.00 0.00 4.79
1555 1570 1.474879 GGTGTAGCTCAGACTGGTCTC 59.525 57.143 1.81 0.00 37.98 3.36
1556 1571 2.442413 GTGTAGCTCAGACTGGTCTCT 58.558 52.381 1.81 0.00 37.98 3.10
1557 1572 3.611970 GTGTAGCTCAGACTGGTCTCTA 58.388 50.000 1.81 0.00 37.98 2.43
1558 1573 4.204012 GTGTAGCTCAGACTGGTCTCTAT 58.796 47.826 1.81 0.00 37.98 1.98
1559 1574 4.274950 GTGTAGCTCAGACTGGTCTCTATC 59.725 50.000 1.81 0.00 37.98 2.08
1562 1577 4.609301 AGCTCAGACTGGTCTCTATCTTT 58.391 43.478 1.81 0.00 37.98 2.52
1563 1578 4.402155 AGCTCAGACTGGTCTCTATCTTTG 59.598 45.833 1.81 0.00 37.98 2.77
1564 1579 4.400884 GCTCAGACTGGTCTCTATCTTTGA 59.599 45.833 1.81 0.00 37.98 2.69
1565 1580 5.105554 GCTCAGACTGGTCTCTATCTTTGAA 60.106 44.000 1.81 0.00 37.98 2.69
1571 1586 8.432805 AGACTGGTCTCTATCTTTGAAGAAAAA 58.567 33.333 0.00 0.00 35.14 1.94
1592 1607 7.683437 AAAAAGAATACTACCTCCTTTTCGG 57.317 36.000 0.00 0.00 36.42 4.30
1593 1608 6.370186 AAAGAATACTACCTCCTTTTCGGT 57.630 37.500 0.00 0.00 37.31 4.69
1594 1609 6.370186 AAGAATACTACCTCCTTTTCGGTT 57.630 37.500 0.00 0.00 34.76 4.44
1595 1610 6.370186 AGAATACTACCTCCTTTTCGGTTT 57.630 37.500 0.00 0.00 34.76 3.27
1596 1611 7.486407 AGAATACTACCTCCTTTTCGGTTTA 57.514 36.000 0.00 0.00 34.76 2.01
1597 1612 7.326454 AGAATACTACCTCCTTTTCGGTTTAC 58.674 38.462 0.00 0.00 34.76 2.01
1598 1613 4.961438 ACTACCTCCTTTTCGGTTTACA 57.039 40.909 0.00 0.00 34.76 2.41
1599 1614 5.294734 ACTACCTCCTTTTCGGTTTACAA 57.705 39.130 0.00 0.00 34.76 2.41
1600 1615 5.303165 ACTACCTCCTTTTCGGTTTACAAG 58.697 41.667 0.00 0.00 34.76 3.16
1601 1616 4.160642 ACCTCCTTTTCGGTTTACAAGT 57.839 40.909 0.00 0.00 0.00 3.16
1602 1617 4.132336 ACCTCCTTTTCGGTTTACAAGTC 58.868 43.478 0.00 0.00 0.00 3.01
1603 1618 3.501062 CCTCCTTTTCGGTTTACAAGTCC 59.499 47.826 0.00 0.00 0.00 3.85
1604 1619 4.386711 CTCCTTTTCGGTTTACAAGTCCT 58.613 43.478 0.00 0.00 0.00 3.85
1605 1620 5.511888 CCTCCTTTTCGGTTTACAAGTCCTA 60.512 44.000 0.00 0.00 0.00 2.94
1606 1621 5.299949 TCCTTTTCGGTTTACAAGTCCTAC 58.700 41.667 0.00 0.00 0.00 3.18
1607 1622 4.151157 CCTTTTCGGTTTACAAGTCCTACG 59.849 45.833 0.00 0.00 0.00 3.51
1608 1623 2.352503 TCGGTTTACAAGTCCTACGC 57.647 50.000 0.00 0.00 0.00 4.42
1609 1624 0.986992 CGGTTTACAAGTCCTACGCG 59.013 55.000 3.53 3.53 0.00 6.01
1610 1625 1.666888 CGGTTTACAAGTCCTACGCGT 60.667 52.381 19.17 19.17 0.00 6.01
1611 1626 2.414029 CGGTTTACAAGTCCTACGCGTA 60.414 50.000 19.40 19.40 0.00 4.42
1612 1627 3.731867 CGGTTTACAAGTCCTACGCGTAT 60.732 47.826 20.91 5.41 0.00 3.06
1613 1628 4.495679 CGGTTTACAAGTCCTACGCGTATA 60.496 45.833 20.91 8.44 0.00 1.47
1614 1629 4.735338 GGTTTACAAGTCCTACGCGTATAC 59.265 45.833 20.91 19.74 0.00 1.47
1615 1630 4.552166 TTACAAGTCCTACGCGTATACC 57.448 45.455 20.91 10.04 0.00 2.73
1616 1631 2.648059 ACAAGTCCTACGCGTATACCT 58.352 47.619 20.91 12.19 0.00 3.08
1617 1632 3.808728 ACAAGTCCTACGCGTATACCTA 58.191 45.455 20.91 0.00 0.00 3.08
1618 1633 3.812053 ACAAGTCCTACGCGTATACCTAG 59.188 47.826 20.91 8.56 0.00 3.02
1619 1634 3.051081 AGTCCTACGCGTATACCTAGG 57.949 52.381 20.91 18.03 0.00 3.02
1620 1635 2.370189 AGTCCTACGCGTATACCTAGGT 59.630 50.000 20.91 20.57 0.00 3.08
1621 1636 3.142174 GTCCTACGCGTATACCTAGGTT 58.858 50.000 22.11 10.62 0.00 3.50
1622 1637 3.058639 GTCCTACGCGTATACCTAGGTTG 60.059 52.174 22.11 9.15 0.00 3.77
1623 1638 2.880890 CCTACGCGTATACCTAGGTTGT 59.119 50.000 22.11 12.13 0.00 3.32
1624 1639 3.058639 CCTACGCGTATACCTAGGTTGTC 60.059 52.174 22.11 9.56 0.00 3.18
1625 1640 2.368439 ACGCGTATACCTAGGTTGTCA 58.632 47.619 22.11 1.21 0.00 3.58
1626 1641 2.754552 ACGCGTATACCTAGGTTGTCAA 59.245 45.455 22.11 0.75 0.00 3.18
1627 1642 3.382546 ACGCGTATACCTAGGTTGTCAAT 59.617 43.478 22.11 9.64 0.00 2.57
1628 1643 4.142093 ACGCGTATACCTAGGTTGTCAATT 60.142 41.667 22.11 0.00 0.00 2.32
1629 1644 4.807304 CGCGTATACCTAGGTTGTCAATTT 59.193 41.667 22.11 0.00 0.00 1.82
1630 1645 5.292589 CGCGTATACCTAGGTTGTCAATTTT 59.707 40.000 22.11 0.00 0.00 1.82
1631 1646 6.476380 CGCGTATACCTAGGTTGTCAATTTTA 59.524 38.462 22.11 0.00 0.00 1.52
1632 1647 7.170320 CGCGTATACCTAGGTTGTCAATTTTAT 59.830 37.037 22.11 5.71 0.00 1.40
1633 1648 8.493547 GCGTATACCTAGGTTGTCAATTTTATC 58.506 37.037 22.11 0.00 0.00 1.75
1634 1649 9.537192 CGTATACCTAGGTTGTCAATTTTATCA 57.463 33.333 22.11 0.00 0.00 2.15
1690 1705 8.786826 ATACGGTTTGAAAATAGAACATCTGA 57.213 30.769 0.00 0.00 0.00 3.27
1691 1706 7.504924 ACGGTTTGAAAATAGAACATCTGAA 57.495 32.000 0.00 0.00 0.00 3.02
1692 1707 7.584987 ACGGTTTGAAAATAGAACATCTGAAG 58.415 34.615 0.00 0.00 0.00 3.02
1693 1708 7.228706 ACGGTTTGAAAATAGAACATCTGAAGT 59.771 33.333 0.00 0.00 0.00 3.01
1694 1709 8.076178 CGGTTTGAAAATAGAACATCTGAAGTT 58.924 33.333 0.00 0.00 0.00 2.66
1695 1710 9.750125 GGTTTGAAAATAGAACATCTGAAGTTT 57.250 29.630 0.00 0.00 0.00 2.66
1771 1786 2.174107 CCACACGCAAGCATCACG 59.826 61.111 0.00 0.00 45.62 4.35
1794 1809 1.654220 GCAGGTGTGTGCACGAATT 59.346 52.632 13.13 0.00 46.13 2.17
1839 1854 3.077519 GCCACGTAGGATGAGGCGT 62.078 63.158 8.04 0.00 41.22 5.68
2421 2446 2.407562 TGCCTATGGATTGAGCAGGTA 58.592 47.619 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.563039 TAGGATTTCCGGGAAGGTCT 57.437 50.000 9.80 10.49 42.08 3.85
1 2 2.438392 ACATAGGATTTCCGGGAAGGTC 59.562 50.000 9.80 11.76 42.08 3.85
2 3 2.172717 CACATAGGATTTCCGGGAAGGT 59.827 50.000 9.80 3.03 42.08 3.50
6 7 3.521937 AGTTTCACATAGGATTTCCGGGA 59.478 43.478 0.00 0.00 42.08 5.14
7 8 3.627577 CAGTTTCACATAGGATTTCCGGG 59.372 47.826 0.00 0.00 42.08 5.73
8 9 3.065371 GCAGTTTCACATAGGATTTCCGG 59.935 47.826 0.00 0.00 42.08 5.14
9 10 3.941483 AGCAGTTTCACATAGGATTTCCG 59.059 43.478 0.00 0.00 42.08 4.30
10 11 5.904362 AAGCAGTTTCACATAGGATTTCC 57.096 39.130 0.00 0.00 0.00 3.13
11 12 9.346725 CTTTAAAGCAGTTTCACATAGGATTTC 57.653 33.333 1.47 0.00 0.00 2.17
12 13 8.860088 ACTTTAAAGCAGTTTCACATAGGATTT 58.140 29.630 15.24 0.00 0.00 2.17
13 14 8.299570 CACTTTAAAGCAGTTTCACATAGGATT 58.700 33.333 15.24 0.00 0.00 3.01
14 15 7.665559 TCACTTTAAAGCAGTTTCACATAGGAT 59.334 33.333 15.24 0.00 0.00 3.24
15 16 6.995686 TCACTTTAAAGCAGTTTCACATAGGA 59.004 34.615 15.24 0.00 0.00 2.94
16 17 7.202016 TCACTTTAAAGCAGTTTCACATAGG 57.798 36.000 15.24 0.00 0.00 2.57
17 18 9.683069 AATTCACTTTAAAGCAGTTTCACATAG 57.317 29.630 15.24 0.00 0.00 2.23
19 20 8.947055 AAATTCACTTTAAAGCAGTTTCACAT 57.053 26.923 15.24 0.00 0.00 3.21
20 21 8.655092 CAAAATTCACTTTAAAGCAGTTTCACA 58.345 29.630 15.24 0.00 0.00 3.58
21 22 8.655970 ACAAAATTCACTTTAAAGCAGTTTCAC 58.344 29.630 15.24 0.00 0.00 3.18
22 23 8.655092 CACAAAATTCACTTTAAAGCAGTTTCA 58.345 29.630 15.24 0.00 0.00 2.69
23 24 8.868916 TCACAAAATTCACTTTAAAGCAGTTTC 58.131 29.630 15.24 0.00 0.00 2.78
24 25 8.770438 TCACAAAATTCACTTTAAAGCAGTTT 57.230 26.923 15.24 8.41 0.00 2.66
25 26 8.770438 TTCACAAAATTCACTTTAAAGCAGTT 57.230 26.923 15.24 2.80 0.00 3.16
26 27 8.947055 ATTCACAAAATTCACTTTAAAGCAGT 57.053 26.923 15.24 0.00 0.00 4.40
27 28 9.640974 CAATTCACAAAATTCACTTTAAAGCAG 57.359 29.630 15.24 8.37 0.00 4.24
28 29 9.376075 TCAATTCACAAAATTCACTTTAAAGCA 57.624 25.926 15.24 0.00 0.00 3.91
34 35 9.434420 TCAGTTTCAATTCACAAAATTCACTTT 57.566 25.926 0.00 0.00 0.00 2.66
35 36 9.603921 ATCAGTTTCAATTCACAAAATTCACTT 57.396 25.926 0.00 0.00 0.00 3.16
36 37 9.603921 AATCAGTTTCAATTCACAAAATTCACT 57.396 25.926 0.00 0.00 0.00 3.41
43 44 8.828644 CCATCAAAATCAGTTTCAATTCACAAA 58.171 29.630 0.00 0.00 0.00 2.83
44 45 8.202811 TCCATCAAAATCAGTTTCAATTCACAA 58.797 29.630 0.00 0.00 0.00 3.33
45 46 7.724287 TCCATCAAAATCAGTTTCAATTCACA 58.276 30.769 0.00 0.00 0.00 3.58
46 47 7.148689 GCTCCATCAAAATCAGTTTCAATTCAC 60.149 37.037 0.00 0.00 0.00 3.18
47 48 6.869913 GCTCCATCAAAATCAGTTTCAATTCA 59.130 34.615 0.00 0.00 0.00 2.57
48 49 6.034256 CGCTCCATCAAAATCAGTTTCAATTC 59.966 38.462 0.00 0.00 0.00 2.17
49 50 5.865552 CGCTCCATCAAAATCAGTTTCAATT 59.134 36.000 0.00 0.00 0.00 2.32
50 51 5.404946 CGCTCCATCAAAATCAGTTTCAAT 58.595 37.500 0.00 0.00 0.00 2.57
51 52 4.321156 CCGCTCCATCAAAATCAGTTTCAA 60.321 41.667 0.00 0.00 0.00 2.69
52 53 3.191162 CCGCTCCATCAAAATCAGTTTCA 59.809 43.478 0.00 0.00 0.00 2.69
53 54 3.440173 TCCGCTCCATCAAAATCAGTTTC 59.560 43.478 0.00 0.00 0.00 2.78
54 55 3.420893 TCCGCTCCATCAAAATCAGTTT 58.579 40.909 0.00 0.00 0.00 2.66
55 56 3.012518 CTCCGCTCCATCAAAATCAGTT 58.987 45.455 0.00 0.00 0.00 3.16
56 57 2.636830 CTCCGCTCCATCAAAATCAGT 58.363 47.619 0.00 0.00 0.00 3.41
57 58 1.332997 GCTCCGCTCCATCAAAATCAG 59.667 52.381 0.00 0.00 0.00 2.90
58 59 1.339920 TGCTCCGCTCCATCAAAATCA 60.340 47.619 0.00 0.00 0.00 2.57
59 60 1.332997 CTGCTCCGCTCCATCAAAATC 59.667 52.381 0.00 0.00 0.00 2.17
60 61 1.340405 ACTGCTCCGCTCCATCAAAAT 60.340 47.619 0.00 0.00 0.00 1.82
61 62 0.036732 ACTGCTCCGCTCCATCAAAA 59.963 50.000 0.00 0.00 0.00 2.44
62 63 0.391661 GACTGCTCCGCTCCATCAAA 60.392 55.000 0.00 0.00 0.00 2.69
63 64 1.219124 GACTGCTCCGCTCCATCAA 59.781 57.895 0.00 0.00 0.00 2.57
64 65 2.725312 GGACTGCTCCGCTCCATCA 61.725 63.158 0.00 0.00 0.00 3.07
65 66 2.107953 GGACTGCTCCGCTCCATC 59.892 66.667 0.00 0.00 0.00 3.51
66 67 3.474570 GGGACTGCTCCGCTCCAT 61.475 66.667 0.00 0.00 37.46 3.41
68 69 3.254024 TTTGGGACTGCTCCGCTCC 62.254 63.158 0.00 0.00 37.46 4.70
69 70 2.035442 GTTTGGGACTGCTCCGCTC 61.035 63.158 0.00 0.00 37.46 5.03
70 71 2.032681 GTTTGGGACTGCTCCGCT 59.967 61.111 0.00 0.00 37.46 5.52
71 72 2.281484 TGTTTGGGACTGCTCCGC 60.281 61.111 0.00 0.00 37.46 5.54
72 73 0.951040 GTCTGTTTGGGACTGCTCCG 60.951 60.000 0.00 0.00 37.46 4.63
73 74 0.398318 AGTCTGTTTGGGACTGCTCC 59.602 55.000 0.00 0.00 41.76 4.70
74 75 2.262423 AAGTCTGTTTGGGACTGCTC 57.738 50.000 0.00 0.00 42.39 4.26
75 76 2.736670 AAAGTCTGTTTGGGACTGCT 57.263 45.000 0.00 0.00 42.39 4.24
76 77 6.759497 ATATAAAAGTCTGTTTGGGACTGC 57.241 37.500 0.00 0.00 42.39 4.40
229 230 8.997323 GCTCTCTTGACATAGTGCATATAAATT 58.003 33.333 0.00 0.00 33.53 1.82
230 231 7.330454 CGCTCTCTTGACATAGTGCATATAAAT 59.670 37.037 0.00 0.00 33.02 1.40
231 232 6.642540 CGCTCTCTTGACATAGTGCATATAAA 59.357 38.462 0.00 0.00 33.02 1.40
232 233 6.016276 TCGCTCTCTTGACATAGTGCATATAA 60.016 38.462 0.00 0.00 33.02 0.98
233 234 5.473504 TCGCTCTCTTGACATAGTGCATATA 59.526 40.000 0.00 0.00 33.02 0.86
234 235 4.279420 TCGCTCTCTTGACATAGTGCATAT 59.721 41.667 0.00 0.00 33.02 1.78
235 236 3.632145 TCGCTCTCTTGACATAGTGCATA 59.368 43.478 0.00 0.00 33.02 3.14
236 237 2.428530 TCGCTCTCTTGACATAGTGCAT 59.571 45.455 0.00 0.00 33.02 3.96
237 238 1.818674 TCGCTCTCTTGACATAGTGCA 59.181 47.619 10.94 0.00 33.02 4.57
238 239 2.159310 AGTCGCTCTCTTGACATAGTGC 60.159 50.000 0.00 3.48 37.58 4.40
239 240 3.127721 TGAGTCGCTCTCTTGACATAGTG 59.872 47.826 8.07 0.00 43.13 2.74
240 241 3.127895 GTGAGTCGCTCTCTTGACATAGT 59.872 47.826 8.07 0.00 43.13 2.12
241 242 3.127721 TGTGAGTCGCTCTCTTGACATAG 59.872 47.826 5.11 0.00 43.13 2.23
242 243 3.081804 TGTGAGTCGCTCTCTTGACATA 58.918 45.455 5.11 0.00 43.13 2.29
243 244 1.889170 TGTGAGTCGCTCTCTTGACAT 59.111 47.619 5.11 0.00 43.13 3.06
244 245 1.001268 GTGTGAGTCGCTCTCTTGACA 60.001 52.381 5.11 2.94 43.13 3.58
245 246 1.692296 GTGTGAGTCGCTCTCTTGAC 58.308 55.000 5.11 0.00 43.13 3.18
246 247 0.238553 CGTGTGAGTCGCTCTCTTGA 59.761 55.000 5.11 0.00 43.13 3.02
247 248 0.039978 ACGTGTGAGTCGCTCTCTTG 60.040 55.000 5.11 4.76 43.13 3.02
248 249 0.669077 AACGTGTGAGTCGCTCTCTT 59.331 50.000 5.11 0.00 43.13 2.85
249 250 0.039978 CAACGTGTGAGTCGCTCTCT 60.040 55.000 5.11 0.00 43.13 3.10
250 251 1.609840 GCAACGTGTGAGTCGCTCTC 61.610 60.000 5.11 4.83 43.03 3.20
251 252 1.661821 GCAACGTGTGAGTCGCTCT 60.662 57.895 5.11 0.00 0.00 4.09
252 253 2.846918 GCAACGTGTGAGTCGCTC 59.153 61.111 5.11 0.08 0.00 5.03
253 254 3.030308 CGCAACGTGTGAGTCGCT 61.030 61.111 5.11 0.00 0.00 4.93
254 255 4.702826 GCGCAACGTGTGAGTCGC 62.703 66.667 0.30 0.00 35.82 5.19
255 256 4.394941 CGCGCAACGTGTGAGTCG 62.395 66.667 8.75 0.00 36.87 4.18
256 257 4.702826 GCGCGCAACGTGTGAGTC 62.703 66.667 29.10 0.00 46.11 3.36
270 271 3.223589 GAGAGAGAGAGGGGGCGC 61.224 72.222 0.00 0.00 0.00 6.53
271 272 1.528309 GAGAGAGAGAGAGGGGGCG 60.528 68.421 0.00 0.00 0.00 6.13
272 273 0.261696 AAGAGAGAGAGAGAGGGGGC 59.738 60.000 0.00 0.00 0.00 5.80
273 274 3.963476 TTAAGAGAGAGAGAGAGGGGG 57.037 52.381 0.00 0.00 0.00 5.40
274 275 3.573967 GCATTAAGAGAGAGAGAGAGGGG 59.426 52.174 0.00 0.00 0.00 4.79
275 276 4.473444 AGCATTAAGAGAGAGAGAGAGGG 58.527 47.826 0.00 0.00 0.00 4.30
276 277 6.533730 TCTAGCATTAAGAGAGAGAGAGAGG 58.466 44.000 0.00 0.00 0.00 3.69
277 278 7.716998 AGTTCTAGCATTAAGAGAGAGAGAGAG 59.283 40.741 0.00 0.00 0.00 3.20
284 285 5.531659 CCCGTAGTTCTAGCATTAAGAGAGA 59.468 44.000 0.00 0.00 0.00 3.10
288 289 4.539726 TCCCCGTAGTTCTAGCATTAAGA 58.460 43.478 0.00 0.00 0.00 2.10
289 290 4.341520 ACTCCCCGTAGTTCTAGCATTAAG 59.658 45.833 0.00 0.00 0.00 1.85
290 291 4.284178 ACTCCCCGTAGTTCTAGCATTAA 58.716 43.478 0.00 0.00 0.00 1.40
299 300 3.259123 TCCTGTAAAACTCCCCGTAGTTC 59.741 47.826 0.00 0.00 38.76 3.01
331 332 0.835941 ACAGCCCATCTCAGCTTAGG 59.164 55.000 0.00 0.00 37.18 2.69
337 338 3.819337 CCAATCATAACAGCCCATCTCAG 59.181 47.826 0.00 0.00 0.00 3.35
349 350 6.260050 TCGCTTCATCCTTAACCAATCATAAC 59.740 38.462 0.00 0.00 0.00 1.89
353 354 4.191544 CTCGCTTCATCCTTAACCAATCA 58.808 43.478 0.00 0.00 0.00 2.57
354 355 3.561725 CCTCGCTTCATCCTTAACCAATC 59.438 47.826 0.00 0.00 0.00 2.67
355 356 3.545703 CCTCGCTTCATCCTTAACCAAT 58.454 45.455 0.00 0.00 0.00 3.16
356 357 2.939640 GCCTCGCTTCATCCTTAACCAA 60.940 50.000 0.00 0.00 0.00 3.67
357 358 1.406887 GCCTCGCTTCATCCTTAACCA 60.407 52.381 0.00 0.00 0.00 3.67
358 359 1.300481 GCCTCGCTTCATCCTTAACC 58.700 55.000 0.00 0.00 0.00 2.85
374 375 1.007118 CCTGATTTTTAGGGTGGGCCT 59.993 52.381 4.53 0.00 34.45 5.19
380 381 4.699994 TCTCTCCTCCTGATTTTTAGGGT 58.300 43.478 0.00 0.00 35.96 4.34
381 382 5.903198 ATCTCTCCTCCTGATTTTTAGGG 57.097 43.478 0.00 0.00 35.96 3.53
385 386 7.277405 ACCTTAATCTCTCCTCCTGATTTTT 57.723 36.000 0.00 0.00 33.24 1.94
395 396 4.869451 ACGGACTTACCTTAATCTCTCCT 58.131 43.478 0.00 0.00 36.31 3.69
402 403 7.547019 GCAAGTAACTTACGGACTTACCTTAAT 59.453 37.037 0.00 0.00 33.06 1.40
403 404 6.868339 GCAAGTAACTTACGGACTTACCTTAA 59.132 38.462 0.00 0.00 36.31 1.85
404 405 6.209391 AGCAAGTAACTTACGGACTTACCTTA 59.791 38.462 0.00 0.00 36.31 2.69
405 406 5.011431 AGCAAGTAACTTACGGACTTACCTT 59.989 40.000 0.00 0.00 36.31 3.50
406 407 4.525874 AGCAAGTAACTTACGGACTTACCT 59.474 41.667 0.00 0.00 36.31 3.08
407 408 4.814147 AGCAAGTAACTTACGGACTTACC 58.186 43.478 0.00 0.00 32.22 2.85
410 411 6.094193 ACTTAGCAAGTAACTTACGGACTT 57.906 37.500 0.44 0.00 40.69 3.01
411 412 5.718724 ACTTAGCAAGTAACTTACGGACT 57.281 39.130 0.44 0.00 40.69 3.85
412 413 7.087007 AGTAACTTAGCAAGTAACTTACGGAC 58.913 38.462 2.60 0.00 41.91 4.79
413 414 7.175641 AGAGTAACTTAGCAAGTAACTTACGGA 59.824 37.037 2.60 0.00 41.91 4.69
414 415 7.311408 AGAGTAACTTAGCAAGTAACTTACGG 58.689 38.462 2.60 0.00 41.91 4.02
415 416 8.739649 AAGAGTAACTTAGCAAGTAACTTACG 57.260 34.615 2.60 0.00 41.91 3.18
427 428 9.628746 GGCTAGTCATAATAAGAGTAACTTAGC 57.371 37.037 0.00 0.00 43.16 3.09
430 431 9.422681 TCAGGCTAGTCATAATAAGAGTAACTT 57.577 33.333 0.00 0.00 42.04 2.66
431 432 8.998277 TCAGGCTAGTCATAATAAGAGTAACT 57.002 34.615 0.00 0.00 0.00 2.24
432 433 8.301002 CCTCAGGCTAGTCATAATAAGAGTAAC 58.699 40.741 0.00 0.00 0.00 2.50
433 434 7.451877 CCCTCAGGCTAGTCATAATAAGAGTAA 59.548 40.741 0.00 0.00 0.00 2.24
434 435 6.948886 CCCTCAGGCTAGTCATAATAAGAGTA 59.051 42.308 0.00 0.00 0.00 2.59
435 436 5.777732 CCCTCAGGCTAGTCATAATAAGAGT 59.222 44.000 0.00 0.00 0.00 3.24
436 437 5.186797 CCCCTCAGGCTAGTCATAATAAGAG 59.813 48.000 0.00 0.00 0.00 2.85
437 438 5.087323 CCCCTCAGGCTAGTCATAATAAGA 58.913 45.833 0.00 0.00 0.00 2.10
438 439 5.087323 TCCCCTCAGGCTAGTCATAATAAG 58.913 45.833 0.00 0.00 34.51 1.73
439 440 5.087323 CTCCCCTCAGGCTAGTCATAATAA 58.913 45.833 0.00 0.00 34.51 1.40
440 441 4.357097 TCTCCCCTCAGGCTAGTCATAATA 59.643 45.833 0.00 0.00 34.51 0.98
441 442 3.142977 TCTCCCCTCAGGCTAGTCATAAT 59.857 47.826 0.00 0.00 34.51 1.28
442 443 2.518407 TCTCCCCTCAGGCTAGTCATAA 59.482 50.000 0.00 0.00 34.51 1.90
443 444 2.109128 CTCTCCCCTCAGGCTAGTCATA 59.891 54.545 0.00 0.00 34.51 2.15
444 445 0.937441 TCTCCCCTCAGGCTAGTCAT 59.063 55.000 0.00 0.00 34.51 3.06
445 446 0.260230 CTCTCCCCTCAGGCTAGTCA 59.740 60.000 0.00 0.00 34.51 3.41
446 447 0.469144 CCTCTCCCCTCAGGCTAGTC 60.469 65.000 0.00 0.00 34.51 2.59
447 448 1.623625 CCTCTCCCCTCAGGCTAGT 59.376 63.158 0.00 0.00 34.51 2.57
448 449 1.152355 CCCTCTCCCCTCAGGCTAG 60.152 68.421 0.00 0.00 34.51 3.42
449 450 2.716203 CCCCTCTCCCCTCAGGCTA 61.716 68.421 0.00 0.00 34.51 3.93
450 451 4.101077 CCCCTCTCCCCTCAGGCT 62.101 72.222 0.00 0.00 34.51 4.58
451 452 2.547123 TAACCCCTCTCCCCTCAGGC 62.547 65.000 0.00 0.00 34.51 4.85
452 453 0.044244 TTAACCCCTCTCCCCTCAGG 59.956 60.000 0.00 0.00 0.00 3.86
453 454 1.560146 GTTTAACCCCTCTCCCCTCAG 59.440 57.143 0.00 0.00 0.00 3.35
454 455 1.153565 AGTTTAACCCCTCTCCCCTCA 59.846 52.381 0.00 0.00 0.00 3.86
455 456 1.838715 GAGTTTAACCCCTCTCCCCTC 59.161 57.143 0.00 0.00 0.00 4.30
456 457 1.441553 AGAGTTTAACCCCTCTCCCCT 59.558 52.381 0.00 0.00 32.65 4.79
457 458 1.560146 CAGAGTTTAACCCCTCTCCCC 59.440 57.143 0.00 0.00 35.90 4.81
458 459 2.267192 ACAGAGTTTAACCCCTCTCCC 58.733 52.381 0.00 0.00 35.90 4.30
459 460 5.494390 TTTACAGAGTTTAACCCCTCTCC 57.506 43.478 0.00 0.00 35.90 3.71
506 507 5.163519 GGTTCCTCATCAGAAAGAGAGAGAG 60.164 48.000 5.10 0.00 35.48 3.20
516 517 7.878621 ATAATAGATGGGTTCCTCATCAGAA 57.121 36.000 16.52 7.31 42.38 3.02
522 523 6.392842 AGGGAAAATAATAGATGGGTTCCTCA 59.607 38.462 0.00 0.00 34.70 3.86
542 543 2.163509 CTCAACAGAGAGACGAGGGAA 58.836 52.381 0.00 0.00 37.87 3.97
543 544 1.351350 TCTCAACAGAGAGACGAGGGA 59.649 52.381 0.00 0.00 39.62 4.20
555 556 3.562973 AGTGTCACATTTGCTCTCAACAG 59.437 43.478 5.62 0.00 30.75 3.16
569 570 3.797039 CTTCTGACCTTGAAGTGTCACA 58.203 45.455 5.62 1.52 36.62 3.58
579 580 0.886490 AAGCCACGCTTCTGACCTTG 60.886 55.000 0.00 0.00 46.77 3.61
634 635 4.808364 GTCAAGCTTGGATGATGTAGAGTC 59.192 45.833 25.73 0.00 0.00 3.36
691 692 2.807967 TGATGTTCTTTCTGTTCCTGCG 59.192 45.455 0.00 0.00 0.00 5.18
742 743 1.198867 TGTATTGTCCATTGTGTGCGC 59.801 47.619 0.00 0.00 0.00 6.09
870 877 3.833645 CTTCGGGATGGCGACGGA 61.834 66.667 0.00 0.00 0.00 4.69
891 898 5.688621 TGATTATATAGCACGTTGGTTCGAC 59.311 40.000 0.00 0.00 34.70 4.20
990 1002 2.878406 CGAGGTTTCCATCGGCAATAAT 59.122 45.455 0.00 0.00 35.33 1.28
1087 1099 0.535102 AAGAAGGCGGACACAACAGG 60.535 55.000 0.00 0.00 0.00 4.00
1164 1176 1.379843 CCCAACCTTCCCAATCCCG 60.380 63.158 0.00 0.00 0.00 5.14
1165 1177 1.685765 GCCCAACCTTCCCAATCCC 60.686 63.158 0.00 0.00 0.00 3.85
1166 1178 1.078347 TGCCCAACCTTCCCAATCC 59.922 57.895 0.00 0.00 0.00 3.01
1167 1179 1.257750 GGTGCCCAACCTTCCCAATC 61.258 60.000 0.00 0.00 46.55 2.67
1168 1180 1.229177 GGTGCCCAACCTTCCCAAT 60.229 57.895 0.00 0.00 46.55 3.16
1169 1181 2.200092 GGTGCCCAACCTTCCCAA 59.800 61.111 0.00 0.00 46.55 4.12
1275 1290 1.144936 CCTCCGGCTCATCACCTTC 59.855 63.158 0.00 0.00 0.00 3.46
1519 1534 1.141881 ACCCATGAGTCGATGACGC 59.858 57.895 0.00 0.00 37.67 5.19
1571 1586 6.370186 AACCGAAAAGGAGGTAGTATTCTT 57.630 37.500 0.00 0.00 45.00 2.52
1573 1588 7.099120 TGTAAACCGAAAAGGAGGTAGTATTC 58.901 38.462 0.00 0.00 45.00 1.75
1579 1594 5.294734 ACTTGTAAACCGAAAAGGAGGTA 57.705 39.130 0.00 0.00 45.00 3.08
1583 1598 4.426736 AGGACTTGTAAACCGAAAAGGA 57.573 40.909 0.00 0.00 45.00 3.36
1585 1600 4.376717 GCGTAGGACTTGTAAACCGAAAAG 60.377 45.833 0.00 0.00 0.00 2.27
1586 1601 3.494251 GCGTAGGACTTGTAAACCGAAAA 59.506 43.478 0.00 0.00 0.00 2.29
1587 1602 3.059166 GCGTAGGACTTGTAAACCGAAA 58.941 45.455 0.00 0.00 0.00 3.46
1588 1603 2.676076 GCGTAGGACTTGTAAACCGAA 58.324 47.619 0.00 0.00 0.00 4.30
1589 1604 1.401409 CGCGTAGGACTTGTAAACCGA 60.401 52.381 0.00 0.00 0.00 4.69
1590 1605 0.986992 CGCGTAGGACTTGTAAACCG 59.013 55.000 0.00 0.00 0.00 4.44
1591 1606 2.070262 ACGCGTAGGACTTGTAAACC 57.930 50.000 11.67 0.00 0.00 3.27
1592 1607 4.735338 GGTATACGCGTAGGACTTGTAAAC 59.265 45.833 24.78 6.78 0.00 2.01
1593 1608 4.640201 AGGTATACGCGTAGGACTTGTAAA 59.360 41.667 24.78 0.00 0.00 2.01
1594 1609 4.199310 AGGTATACGCGTAGGACTTGTAA 58.801 43.478 24.78 0.00 0.00 2.41
1595 1610 3.808728 AGGTATACGCGTAGGACTTGTA 58.191 45.455 24.78 7.25 0.00 2.41
1596 1611 2.648059 AGGTATACGCGTAGGACTTGT 58.352 47.619 24.78 8.30 0.00 3.16
1597 1612 3.188048 CCTAGGTATACGCGTAGGACTTG 59.812 52.174 24.78 19.23 45.08 3.16
1598 1613 3.181450 ACCTAGGTATACGCGTAGGACTT 60.181 47.826 25.95 21.88 45.08 3.01
1599 1614 2.370189 ACCTAGGTATACGCGTAGGACT 59.630 50.000 25.95 22.11 45.08 3.85
1600 1615 2.772287 ACCTAGGTATACGCGTAGGAC 58.228 52.381 25.95 22.99 45.08 3.85
1601 1616 3.141398 CAACCTAGGTATACGCGTAGGA 58.859 50.000 25.95 14.03 45.08 2.94
1602 1617 2.880890 ACAACCTAGGTATACGCGTAGG 59.119 50.000 24.78 21.85 46.64 3.18
1603 1618 3.561310 TGACAACCTAGGTATACGCGTAG 59.439 47.826 24.78 11.28 0.00 3.51
1604 1619 3.540617 TGACAACCTAGGTATACGCGTA 58.459 45.455 22.94 22.94 0.00 4.42
1605 1620 2.368439 TGACAACCTAGGTATACGCGT 58.632 47.619 19.17 19.17 0.00 6.01
1606 1621 3.425577 TTGACAACCTAGGTATACGCG 57.574 47.619 16.67 3.53 0.00 6.01
1607 1622 6.673154 AAAATTGACAACCTAGGTATACGC 57.327 37.500 16.67 4.11 0.00 4.42
1608 1623 9.537192 TGATAAAATTGACAACCTAGGTATACG 57.463 33.333 16.67 6.92 0.00 3.06
1664 1679 9.878667 TCAGATGTTCTATTTTCAAACCGTATA 57.121 29.630 0.00 0.00 0.00 1.47
1665 1680 8.786826 TCAGATGTTCTATTTTCAAACCGTAT 57.213 30.769 0.00 0.00 0.00 3.06
1666 1681 8.610248 TTCAGATGTTCTATTTTCAAACCGTA 57.390 30.769 0.00 0.00 0.00 4.02
1667 1682 7.228706 ACTTCAGATGTTCTATTTTCAAACCGT 59.771 33.333 0.00 0.00 0.00 4.83
1668 1683 7.584987 ACTTCAGATGTTCTATTTTCAAACCG 58.415 34.615 0.00 0.00 0.00 4.44
1669 1684 9.750125 AAACTTCAGATGTTCTATTTTCAAACC 57.250 29.630 2.28 0.00 0.00 3.27
1699 1714 9.440784 GCGTTAACATTTCCGAAAATATATCAA 57.559 29.630 6.39 0.00 33.27 2.57
1700 1715 8.071368 GGCGTTAACATTTCCGAAAATATATCA 58.929 33.333 6.39 0.00 33.27 2.15
1701 1716 7.536281 GGGCGTTAACATTTCCGAAAATATATC 59.464 37.037 6.39 0.00 33.27 1.63
1702 1717 7.013464 TGGGCGTTAACATTTCCGAAAATATAT 59.987 33.333 6.39 0.00 33.27 0.86
1703 1718 6.318144 TGGGCGTTAACATTTCCGAAAATATA 59.682 34.615 6.39 0.00 33.27 0.86
1704 1719 5.125739 TGGGCGTTAACATTTCCGAAAATAT 59.874 36.000 6.39 0.00 33.27 1.28
1705 1720 4.458295 TGGGCGTTAACATTTCCGAAAATA 59.542 37.500 6.39 0.00 33.27 1.40
1771 1786 2.832661 TGCACACACCTGCCAACC 60.833 61.111 0.00 0.00 36.21 3.77
1839 1854 3.140225 TACTCGCACACCGCACACA 62.140 57.895 0.00 0.00 42.60 3.72
1891 1906 0.175760 GACTCAGATGGCAACCGCTA 59.824 55.000 0.00 0.00 38.60 4.26
2084 2099 1.878522 CCGTCGATTCTTCCGCCTG 60.879 63.158 0.00 0.00 0.00 4.85
2421 2446 1.146152 TCAAAAACAACCCCGGGAGAT 59.854 47.619 26.32 3.49 0.00 2.75


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

AutoCloner maintained by Alex Coulton.