Multiple sequence alignment - TraesCS6D01G190100

Loading Multiple Alignment...

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 TraesCS6D01G190100 chr6D 100.000 3485 0 0 1 3485 262780240 262783724 0.000000e+00 6436.0
1 TraesCS6D01G190100 chr6D 97.872 47 1 0 75 121 262780268 262780314 8.020000e-12 82.4
2 TraesCS6D01G190100 chr6D 97.872 47 1 0 29 75 262780314 262780360 8.020000e-12 82.4
3 TraesCS6D01G190100 chr6A 92.839 2402 131 17 740 3108 357404493 357406886 0.000000e+00 3445.0
4 TraesCS6D01G190100 chr6A 81.277 689 67 27 77 726 357372604 357373269 5.190000e-138 501.0
5 TraesCS6D01G190100 chr6A 81.227 554 58 32 884 1410 299717270 299717804 4.190000e-109 405.0
6 TraesCS6D01G190100 chr6A 82.579 442 68 8 2049 2488 299718502 299718936 7.060000e-102 381.0
7 TraesCS6D01G190100 chr6A 93.923 181 10 1 3305 3485 357406973 357407152 4.430000e-69 272.0
8 TraesCS6D01G190100 chr6A 87.356 87 2 4 3229 3315 357406938 357407015 1.330000e-14 91.6
9 TraesCS6D01G190100 chr6B 91.495 2434 154 24 417 2811 347121571 347119152 0.000000e+00 3299.0
10 TraesCS6D01G190100 chr6B 91.071 56 5 0 2810 2865 82007390 82007445 3.730000e-10 76.8
11 TraesCS6D01G190100 chr2A 85.882 85 9 2 2810 2891 747597440 747597524 1.720000e-13 87.9
12 TraesCS6D01G190100 chr7D 90.164 61 6 0 2809 2869 563767639 563767579 2.880000e-11 80.5
13 TraesCS6D01G190100 chr7D 91.228 57 5 0 2809 2865 176573167 176573111 1.040000e-10 78.7
14 TraesCS6D01G190100 chrUn 91.071 56 5 0 2810 2865 134234986 134235041 3.730000e-10 76.8
15 TraesCS6D01G190100 chr5B 91.071 56 5 0 2810 2865 318403052 318403107 3.730000e-10 76.8
16 TraesCS6D01G190100 chr5A 91.071 56 5 0 2810 2865 371028488 371028433 3.730000e-10 76.8
17 TraesCS6D01G190100 chr1A 79.121 91 16 3 2803 2891 430616322 430616411 3.760000e-05 60.2


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 TraesCS6D01G190100 chr6D 262780240 262783724 3484 False 2200.266667 6436 98.581333 1 3485 3 chr6D.!!$F1 3484
1 TraesCS6D01G190100 chr6A 357404493 357407152 2659 False 1269.533333 3445 91.372667 740 3485 3 chr6A.!!$F3 2745
2 TraesCS6D01G190100 chr6A 357372604 357373269 665 False 501.000000 501 81.277000 77 726 1 chr6A.!!$F1 649
3 TraesCS6D01G190100 chr6A 299717270 299718936 1666 False 393.000000 405 81.903000 884 2488 2 chr6A.!!$F2 1604
4 TraesCS6D01G190100 chr6B 347119152 347121571 2419 True 3299.000000 3299 91.495000 417 2811 1 chr6B.!!$R1 2394

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
65 66 0.034574 ACACAAAGCACACCAGTGGA 60.035 50.0 18.4 0.0 45.98 4.02 F
253 268 0.166814 GTGTTGAGCTTGTCGCCATC 59.833 55.0 0.0 0.0 40.39 3.51 F
1452 1536 0.618458 TGCACCCACTCCTCATAACC 59.382 55.0 0.0 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 2112 0.401356 TGCAGAACCAGATGCCTGAA 59.599 50.0 0.0 0.0 43.02 3.02 R
1848 2113 0.622136 ATGCAGAACCAGATGCCTGA 59.378 50.0 0.0 0.0 43.02 3.86 R
3077 3379 0.035881 ATGCCTCATATCCGTGCAGG 59.964 55.0 0.0 0.0 42.97 4.85 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
19 20 1.866015 ATCCTGGAAGACATGTCGGA 58.134 50.000 19.85 18.89 34.07 4.55
20 21 1.186200 TCCTGGAAGACATGTCGGAG 58.814 55.000 19.85 13.28 34.07 4.63
21 22 1.186200 CCTGGAAGACATGTCGGAGA 58.814 55.000 19.85 5.48 34.07 3.71
32 33 4.571250 TCGGAGACACGATTGCAC 57.429 55.556 0.00 0.00 38.06 4.57
33 34 1.663173 TCGGAGACACGATTGCACA 59.337 52.632 0.00 0.00 38.06 4.57
34 35 0.666274 TCGGAGACACGATTGCACAC 60.666 55.000 0.00 0.00 38.06 3.82
35 36 1.781555 GGAGACACGATTGCACACG 59.218 57.895 9.65 9.65 0.00 4.49
36 37 1.130613 GAGACACGATTGCACACGC 59.869 57.895 10.89 0.00 39.24 5.34
37 38 2.173382 GACACGATTGCACACGCC 59.827 61.111 10.89 0.00 37.32 5.68
38 39 3.308878 GACACGATTGCACACGCCC 62.309 63.158 10.89 0.00 37.32 6.13
39 40 3.049674 CACGATTGCACACGCCCT 61.050 61.111 10.89 0.00 37.32 5.19
40 41 3.049674 ACGATTGCACACGCCCTG 61.050 61.111 10.89 0.00 37.32 4.45
41 42 4.465512 CGATTGCACACGCCCTGC 62.466 66.667 0.00 0.00 37.32 4.85
53 54 3.726517 CCCTGCGCCGACACAAAG 61.727 66.667 4.18 0.00 0.00 2.77
54 55 4.389576 CCTGCGCCGACACAAAGC 62.390 66.667 4.18 0.00 0.00 3.51
55 56 3.648982 CTGCGCCGACACAAAGCA 61.649 61.111 4.18 0.00 36.34 3.91
56 57 3.862063 CTGCGCCGACACAAAGCAC 62.862 63.158 4.18 0.00 33.92 4.40
57 58 3.947841 GCGCCGACACAAAGCACA 61.948 61.111 0.00 0.00 0.00 4.57
58 59 2.052237 CGCCGACACAAAGCACAC 60.052 61.111 0.00 0.00 0.00 3.82
59 60 2.331451 GCCGACACAAAGCACACC 59.669 61.111 0.00 0.00 0.00 4.16
60 61 2.477176 GCCGACACAAAGCACACCA 61.477 57.895 0.00 0.00 0.00 4.17
61 62 1.648720 CCGACACAAAGCACACCAG 59.351 57.895 0.00 0.00 0.00 4.00
62 63 1.095228 CCGACACAAAGCACACCAGT 61.095 55.000 0.00 0.00 0.00 4.00
64 65 0.381801 GACACAAAGCACACCAGTGG 59.618 55.000 7.91 7.91 45.98 4.00
65 66 0.034574 ACACAAAGCACACCAGTGGA 60.035 50.000 18.40 0.00 45.98 4.02
66 67 1.102154 CACAAAGCACACCAGTGGAA 58.898 50.000 18.40 0.00 45.98 3.53
67 68 1.476085 CACAAAGCACACCAGTGGAAA 59.524 47.619 18.40 0.00 45.98 3.13
68 69 2.101249 CACAAAGCACACCAGTGGAAAT 59.899 45.455 18.40 0.00 45.98 2.17
69 70 2.101249 ACAAAGCACACCAGTGGAAATG 59.899 45.455 18.40 11.67 45.98 2.32
87 88 3.534056 GGGATGCACATGCCCTGC 61.534 66.667 9.87 0.00 42.72 4.85
102 103 3.862063 CTGCGCCGACACAAAGCAC 62.862 63.158 4.18 0.00 33.92 4.40
107 108 1.648720 CCGACACAAAGCACACCAG 59.351 57.895 0.00 0.00 0.00 4.00
114 115 2.101249 CACAAAGCACACCAGTGGAAAT 59.899 45.455 18.40 0.00 45.98 2.17
126 127 0.555769 GTGGAAATGGGGATAGGGCA 59.444 55.000 0.00 0.00 0.00 5.36
138 139 3.562176 GGGATAGGGCAGGGATAACATTG 60.562 52.174 0.00 0.00 0.00 2.82
139 140 3.074538 GGATAGGGCAGGGATAACATTGT 59.925 47.826 0.00 0.00 0.00 2.71
141 142 3.018423 AGGGCAGGGATAACATTGTTC 57.982 47.619 5.07 0.00 0.00 3.18
142 143 2.311542 AGGGCAGGGATAACATTGTTCA 59.688 45.455 5.07 0.00 0.00 3.18
143 144 3.052642 AGGGCAGGGATAACATTGTTCAT 60.053 43.478 5.07 0.00 0.00 2.57
153 168 1.949525 ACATTGTTCATATGCCTCGCC 59.050 47.619 0.00 0.00 0.00 5.54
169 184 1.066752 GCCGTCCCAAACCAAACAC 59.933 57.895 0.00 0.00 0.00 3.32
180 195 0.253610 ACCAAACACGAAGACCCACA 59.746 50.000 0.00 0.00 0.00 4.17
183 198 2.478879 CCAAACACGAAGACCCACAAAC 60.479 50.000 0.00 0.00 0.00 2.93
184 199 2.116827 AACACGAAGACCCACAAACA 57.883 45.000 0.00 0.00 0.00 2.83
190 205 3.183754 CGAAGACCCACAAACAAAAACC 58.816 45.455 0.00 0.00 0.00 3.27
192 207 4.096682 CGAAGACCCACAAACAAAAACCTA 59.903 41.667 0.00 0.00 0.00 3.08
206 221 8.677871 AACAAAAACCTAAAAAGTAACACTCG 57.322 30.769 0.00 0.00 0.00 4.18
207 222 6.748658 ACAAAAACCTAAAAAGTAACACTCGC 59.251 34.615 0.00 0.00 0.00 5.03
210 225 3.737774 ACCTAAAAAGTAACACTCGCGAC 59.262 43.478 3.71 0.00 0.00 5.19
220 235 2.713011 ACACTCGCGACGATGTATAAC 58.287 47.619 3.71 0.00 34.61 1.89
238 253 7.620880 TGTATAACAGATTCAAGCCTAGTGTT 58.379 34.615 0.00 0.00 0.00 3.32
242 257 3.373439 CAGATTCAAGCCTAGTGTTGAGC 59.627 47.826 4.66 2.78 34.25 4.26
243 258 3.262915 AGATTCAAGCCTAGTGTTGAGCT 59.737 43.478 0.00 0.00 34.25 4.09
244 259 3.492102 TTCAAGCCTAGTGTTGAGCTT 57.508 42.857 0.00 1.01 46.10 3.74
246 261 2.938956 AAGCCTAGTGTTGAGCTTGT 57.061 45.000 1.46 0.00 43.63 3.16
248 263 1.071605 GCCTAGTGTTGAGCTTGTCG 58.928 55.000 0.00 0.00 0.00 4.35
253 268 0.166814 GTGTTGAGCTTGTCGCCATC 59.833 55.000 0.00 0.00 40.39 3.51
254 269 1.291184 TGTTGAGCTTGTCGCCATCG 61.291 55.000 0.00 0.00 40.39 3.84
255 270 2.390599 TTGAGCTTGTCGCCATCGC 61.391 57.895 0.00 0.00 40.39 4.58
256 271 2.815211 GAGCTTGTCGCCATCGCA 60.815 61.111 0.00 0.00 40.39 5.10
257 272 2.358615 AGCTTGTCGCCATCGCAA 60.359 55.556 0.00 0.00 40.39 4.85
258 273 1.911293 GAGCTTGTCGCCATCGCAAA 61.911 55.000 0.00 0.00 40.39 3.68
259 274 1.512734 GCTTGTCGCCATCGCAAAG 60.513 57.895 0.00 0.00 33.72 2.77
260 275 1.135315 CTTGTCGCCATCGCAAAGG 59.865 57.895 0.00 0.00 33.72 3.11
266 281 2.886610 CCATCGCAAAGGCATGCA 59.113 55.556 21.36 0.00 46.76 3.96
267 282 1.517694 CCATCGCAAAGGCATGCAC 60.518 57.895 21.36 9.10 46.76 4.57
268 283 1.509463 CATCGCAAAGGCATGCACT 59.491 52.632 21.36 11.46 46.76 4.40
269 284 0.800683 CATCGCAAAGGCATGCACTG 60.801 55.000 21.36 13.78 46.76 3.66
270 285 0.961857 ATCGCAAAGGCATGCACTGA 60.962 50.000 21.36 8.30 46.76 3.41
271 286 1.443194 CGCAAAGGCATGCACTGAC 60.443 57.895 21.36 4.57 46.76 3.51
280 295 2.630158 GCATGCACTGACATCTTCTCT 58.370 47.619 14.21 0.00 0.00 3.10
282 297 3.679361 GCATGCACTGACATCTTCTCTCT 60.679 47.826 14.21 0.00 0.00 3.10
283 298 3.589495 TGCACTGACATCTTCTCTCTG 57.411 47.619 0.00 0.00 0.00 3.35
292 307 5.827267 TGACATCTTCTCTCTGGTGATCTAG 59.173 44.000 0.00 0.00 0.00 2.43
294 309 3.561143 TCTTCTCTCTGGTGATCTAGCC 58.439 50.000 0.00 0.00 0.00 3.93
300 315 1.306911 TGGTGATCTAGCCAGGCCA 60.307 57.895 8.22 0.00 0.00 5.36
320 335 4.681978 GCACCCGGTGAAGAGCGT 62.682 66.667 22.37 0.00 41.62 5.07
327 342 1.060713 CGGTGAAGAGCGTTACACTG 58.939 55.000 0.00 0.00 38.30 3.66
328 343 1.429463 GGTGAAGAGCGTTACACTGG 58.571 55.000 0.00 0.00 34.28 4.00
355 370 2.851104 GTTTGACGAAGACCGCCG 59.149 61.111 0.00 0.00 43.32 6.46
388 403 2.959516 TCTCTTTCATCGTCGCACAAT 58.040 42.857 0.00 0.00 0.00 2.71
398 413 1.860950 CGTCGCACAATAATCCTCCAG 59.139 52.381 0.00 0.00 0.00 3.86
400 415 1.209261 TCGCACAATAATCCTCCAGCA 59.791 47.619 0.00 0.00 0.00 4.41
406 421 3.118112 ACAATAATCCTCCAGCACCTCTG 60.118 47.826 0.00 0.00 42.49 3.35
412 427 0.954449 CTCCAGCACCTCTGCAACAG 60.954 60.000 0.00 0.00 46.97 3.16
413 428 1.970114 CCAGCACCTCTGCAACAGG 60.970 63.158 9.45 9.45 46.97 4.00
415 430 2.282040 GCACCTCTGCAACAGGCT 60.282 61.111 10.74 0.00 43.62 4.58
439 454 1.705997 CCAATTAGGACCTCCCCCGG 61.706 65.000 0.00 0.00 41.22 5.73
462 477 3.348236 CCGCATGGGCTTATCAGC 58.652 61.111 3.80 0.00 46.52 4.26
494 509 1.229643 GGCGACTAGAGGGGTAGGT 59.770 63.158 0.00 0.00 0.00 3.08
497 512 1.970092 CGACTAGAGGGGTAGGTGAG 58.030 60.000 0.00 0.00 0.00 3.51
498 513 1.477195 CGACTAGAGGGGTAGGTGAGG 60.477 61.905 0.00 0.00 0.00 3.86
523 538 1.349259 CGGCTAGGGTTTTGTCGTCG 61.349 60.000 0.00 0.00 0.00 5.12
536 551 2.809601 CGTCGCCCACCTTTCTCG 60.810 66.667 0.00 0.00 0.00 4.04
597 639 4.941263 TCCACCATCAAAAGATAACGGAAG 59.059 41.667 0.00 0.00 0.00 3.46
699 741 7.646130 TCGAAGTTTGAATTAATGTTTTCGCTT 59.354 29.630 0.00 0.00 36.00 4.68
700 742 7.731302 CGAAGTTTGAATTAATGTTTTCGCTTG 59.269 33.333 0.00 0.00 0.00 4.01
701 743 8.419076 AAGTTTGAATTAATGTTTTCGCTTGT 57.581 26.923 0.00 0.00 0.00 3.16
800 844 3.888930 CGATGTACAAATGGGCCCTAAAT 59.111 43.478 25.70 6.88 0.00 1.40
874 933 1.893137 GGCCCAGAAAGTTAGGGTTTG 59.107 52.381 0.00 0.00 44.69 2.93
1023 1082 2.190578 CCGACCTCCAAGATGGCC 59.809 66.667 0.00 0.00 37.47 5.36
1242 1325 4.577246 CTACCGCCTCGCAGCTCC 62.577 72.222 0.00 0.00 0.00 4.70
1255 1339 3.844090 GCTCCCTCTGTCCTCCGC 61.844 72.222 0.00 0.00 0.00 5.54
1412 1496 2.093658 TCTCTGGTAAATCTCGTTGGCC 60.094 50.000 0.00 0.00 0.00 5.36
1441 1525 2.988010 TGATACTGAGATGCACCCAC 57.012 50.000 0.00 0.00 0.00 4.61
1452 1536 0.618458 TGCACCCACTCCTCATAACC 59.382 55.000 0.00 0.00 0.00 2.85
1470 1554 1.005687 ACCCAGTAGCGTAGGTCTTCT 59.994 52.381 0.00 0.00 40.68 2.85
1472 1556 2.099427 CCCAGTAGCGTAGGTCTTCTTC 59.901 54.545 0.00 0.00 40.68 2.87
1539 1648 5.938710 AGTAGCTATTCATGGATTGATGCAG 59.061 40.000 4.80 0.00 33.34 4.41
1602 1713 1.544691 TCTAGTTCCAGCCTGTTCGTC 59.455 52.381 0.00 0.00 0.00 4.20
1604 1715 1.300697 GTTCCAGCCTGTTCGTCGT 60.301 57.895 0.00 0.00 0.00 4.34
1615 1726 4.174009 CCTGTTCGTCGTGTAAATCAGAT 58.826 43.478 0.00 0.00 0.00 2.90
1651 1794 4.648651 ACCATATGGGGTTCGCTATTTAC 58.351 43.478 25.55 0.00 42.91 2.01
1654 1797 6.106673 CCATATGGGGTTCGCTATTTACTAG 58.893 44.000 14.52 0.00 0.00 2.57
1655 1798 6.070995 CCATATGGGGTTCGCTATTTACTAGA 60.071 42.308 14.52 0.00 0.00 2.43
1741 1905 5.193679 GGGAACTACACTAAAATGCCATCT 58.806 41.667 0.00 0.00 0.00 2.90
1745 1909 7.224949 GGAACTACACTAAAATGCCATCTAGTC 59.775 40.741 0.00 0.00 0.00 2.59
1780 1944 8.478066 AGTGACATGTTTCTATCTGTTAGCATA 58.522 33.333 0.00 0.00 0.00 3.14
1864 2129 1.938577 CGATTCAGGCATCTGGTTCTG 59.061 52.381 0.00 0.00 41.23 3.02
1865 2130 1.674962 GATTCAGGCATCTGGTTCTGC 59.325 52.381 0.00 0.00 41.23 4.26
1955 2243 1.043022 CCTGGGAATTTAGCATGCCC 58.957 55.000 15.66 6.99 39.29 5.36
1959 2247 3.921104 TGGGAATTTAGCATGCCCAATA 58.079 40.909 15.66 0.00 45.35 1.90
1968 2256 9.586732 AATTTAGCATGCCCAATACTTCTAATA 57.413 29.630 15.66 0.00 0.00 0.98
2011 2299 4.382901 GGCCAATTGCTTATTTCATGGTCA 60.383 41.667 0.00 0.00 40.92 4.02
2247 2535 3.532232 ACTGAGAAGGAGGTACATCCCTA 59.468 47.826 22.53 4.55 40.53 3.53
2282 2570 8.887036 ACGATCAGCTTATGTTTATGTCATTA 57.113 30.769 0.00 0.00 0.00 1.90
2290 2578 9.956720 GCTTATGTTTATGTCATTATTTGCTCT 57.043 29.630 0.00 0.00 0.00 4.09
2349 2638 3.450457 AGACTACCAAGAATCTGCCAGAG 59.550 47.826 0.00 0.00 0.00 3.35
2581 2870 3.901222 TCCTATGTCAGTTGAAGTGACCA 59.099 43.478 25.47 16.00 45.57 4.02
2631 2920 3.330701 TCCTTATCTGCTTTGGTGGTTCT 59.669 43.478 0.00 0.00 0.00 3.01
2703 2993 6.579583 TGCGATTTGTTTTCATTTTCATTCG 58.420 32.000 0.00 0.00 0.00 3.34
2757 3048 9.378551 TGTTGTGATTTAGGTCAATATAGTGTC 57.621 33.333 0.00 0.00 0.00 3.67
2768 3059 6.924060 GGTCAATATAGTGTCGATGTTTAGCT 59.076 38.462 0.00 0.00 0.00 3.32
2803 3094 2.765699 GGGATTTCAGCCATTTGCCTTA 59.234 45.455 0.00 0.00 42.71 2.69
2815 3106 4.157840 CCATTTGCCTTAAGTGTTACTCCC 59.842 45.833 0.97 0.00 0.00 4.30
2823 3114 0.886563 AGTGTTACTCCCTCCGTTCG 59.113 55.000 0.00 0.00 0.00 3.95
2826 3117 2.086869 TGTTACTCCCTCCGTTCGTAG 58.913 52.381 0.00 0.00 0.00 3.51
2857 3151 6.539103 AGACCTTTTAGAGATTTCAATACCGC 59.461 38.462 0.00 0.00 0.00 5.68
2867 3161 7.004555 AGATTTCAATACCGCCTACATATGA 57.995 36.000 10.38 0.00 0.00 2.15
2869 3163 7.936847 AGATTTCAATACCGCCTACATATGAAA 59.063 33.333 10.38 0.00 0.00 2.69
2964 3258 4.911610 CCTGTGAATTTCGTTGTAGCAAAG 59.088 41.667 0.00 0.00 0.00 2.77
2991 3285 5.686159 ACCGATTACTATTCTGACGTAGG 57.314 43.478 0.00 0.00 0.00 3.18
3002 3296 4.252971 TCTGACGTAGGAAAACTCCAAG 57.747 45.455 0.00 0.00 0.00 3.61
3003 3297 3.893200 TCTGACGTAGGAAAACTCCAAGA 59.107 43.478 0.00 0.00 0.00 3.02
3004 3298 4.022242 TCTGACGTAGGAAAACTCCAAGAG 60.022 45.833 0.00 0.00 35.52 2.85
3006 3300 2.970640 ACGTAGGAAAACTCCAAGAGGT 59.029 45.455 0.00 0.00 33.35 3.85
3010 3306 5.337330 CGTAGGAAAACTCCAAGAGGTACAT 60.337 44.000 0.00 0.00 33.35 2.29
3013 3309 3.788227 AAACTCCAAGAGGTACATGCA 57.212 42.857 0.00 0.00 33.35 3.96
3018 3314 1.406539 CCAAGAGGTACATGCATTGCC 59.593 52.381 6.12 2.08 0.00 4.52
3077 3379 2.887568 CTCGATGGCGCTGTGTCC 60.888 66.667 7.64 0.00 37.46 4.02
3079 3381 4.457496 CGATGGCGCTGTGTCCCT 62.457 66.667 7.64 0.00 0.00 4.20
3088 3390 1.897423 CTGTGTCCCTGCACGGATA 59.103 57.895 7.74 2.31 45.85 2.59
3099 3403 1.140652 TGCACGGATATGAGGCATCAA 59.859 47.619 4.62 0.00 39.39 2.57
3100 3404 1.802960 GCACGGATATGAGGCATCAAG 59.197 52.381 4.62 0.00 39.39 3.02
3101 3405 2.420642 CACGGATATGAGGCATCAAGG 58.579 52.381 4.62 0.00 39.39 3.61
3102 3406 2.037641 CACGGATATGAGGCATCAAGGA 59.962 50.000 4.62 0.00 39.39 3.36
3103 3407 2.037772 ACGGATATGAGGCATCAAGGAC 59.962 50.000 4.62 0.00 39.39 3.85
3104 3408 2.693069 GGATATGAGGCATCAAGGACG 58.307 52.381 4.62 0.00 39.39 4.79
3105 3409 2.072298 GATATGAGGCATCAAGGACGC 58.928 52.381 4.62 0.00 39.39 5.19
3106 3410 1.123077 TATGAGGCATCAAGGACGCT 58.877 50.000 4.62 0.00 39.39 5.07
3107 3411 0.179062 ATGAGGCATCAAGGACGCTC 60.179 55.000 4.62 0.00 39.39 5.03
3108 3412 1.880340 GAGGCATCAAGGACGCTCG 60.880 63.158 0.00 0.00 0.00 5.03
3109 3413 2.892425 GGCATCAAGGACGCTCGG 60.892 66.667 0.00 0.00 0.00 4.63
3110 3414 2.892425 GCATCAAGGACGCTCGGG 60.892 66.667 0.00 0.00 0.00 5.14
3111 3415 2.892425 CATCAAGGACGCTCGGGC 60.892 66.667 0.00 0.00 0.00 6.13
3112 3416 3.077556 ATCAAGGACGCTCGGGCT 61.078 61.111 5.36 0.00 36.09 5.19
3113 3417 3.082579 ATCAAGGACGCTCGGGCTC 62.083 63.158 5.36 1.41 36.09 4.70
3125 3429 4.882396 GGGCTCGCGAGAAGCTCC 62.882 72.222 38.74 27.52 45.59 4.70
3152 3456 1.153823 AGCGACATCCGTGCACTAC 60.154 57.895 16.19 0.00 41.15 2.73
3188 3492 3.425713 CAGCGCTGTTCCGTGCAT 61.426 61.111 29.24 0.00 42.62 3.96
3189 3493 3.121030 AGCGCTGTTCCGTGCATC 61.121 61.111 10.39 0.00 42.62 3.91
3190 3494 3.121030 GCGCTGTTCCGTGCATCT 61.121 61.111 0.00 0.00 40.04 2.90
3191 3495 3.084579 CGCTGTTCCGTGCATCTC 58.915 61.111 0.00 0.00 0.00 2.75
3192 3496 1.446792 CGCTGTTCCGTGCATCTCT 60.447 57.895 0.00 0.00 0.00 3.10
3193 3497 0.179137 CGCTGTTCCGTGCATCTCTA 60.179 55.000 0.00 0.00 0.00 2.43
3194 3498 1.735700 CGCTGTTCCGTGCATCTCTAA 60.736 52.381 0.00 0.00 0.00 2.10
3195 3499 1.929836 GCTGTTCCGTGCATCTCTAAG 59.070 52.381 0.00 0.00 0.00 2.18
3196 3500 2.417379 GCTGTTCCGTGCATCTCTAAGA 60.417 50.000 0.00 0.00 0.00 2.10
3197 3501 3.443037 CTGTTCCGTGCATCTCTAAGAG 58.557 50.000 0.00 0.00 0.00 2.85
3198 3502 2.166459 TGTTCCGTGCATCTCTAAGAGG 59.834 50.000 0.00 0.00 0.00 3.69
3199 3503 1.403814 TCCGTGCATCTCTAAGAGGG 58.596 55.000 0.00 0.00 0.00 4.30
3200 3504 0.249657 CCGTGCATCTCTAAGAGGGC 60.250 60.000 0.00 3.98 33.42 5.19
3201 3505 0.749649 CGTGCATCTCTAAGAGGGCT 59.250 55.000 12.07 0.00 33.76 5.19
3202 3506 1.957177 CGTGCATCTCTAAGAGGGCTA 59.043 52.381 12.07 0.87 33.76 3.93
3203 3507 2.030363 CGTGCATCTCTAAGAGGGCTAG 60.030 54.545 12.07 0.00 33.76 3.42
3204 3508 2.962421 GTGCATCTCTAAGAGGGCTAGT 59.038 50.000 12.07 0.00 33.76 2.57
3205 3509 3.386402 GTGCATCTCTAAGAGGGCTAGTT 59.614 47.826 12.07 0.00 33.76 2.24
3206 3510 3.386078 TGCATCTCTAAGAGGGCTAGTTG 59.614 47.826 12.07 0.00 33.76 3.16
3207 3511 3.386402 GCATCTCTAAGAGGGCTAGTTGT 59.614 47.826 0.00 0.00 31.38 3.32
3208 3512 4.585162 GCATCTCTAAGAGGGCTAGTTGTA 59.415 45.833 0.00 0.00 31.38 2.41
3209 3513 5.508320 GCATCTCTAAGAGGGCTAGTTGTAC 60.508 48.000 0.00 0.00 31.38 2.90
3210 3514 5.453866 TCTCTAAGAGGGCTAGTTGTACT 57.546 43.478 0.00 0.00 0.00 2.73
3211 3515 5.194432 TCTCTAAGAGGGCTAGTTGTACTG 58.806 45.833 0.00 0.00 0.00 2.74
3212 3516 3.700038 TCTAAGAGGGCTAGTTGTACTGC 59.300 47.826 0.00 0.00 0.00 4.40
3213 3517 2.239681 AGAGGGCTAGTTGTACTGCT 57.760 50.000 0.00 0.00 0.00 4.24
3214 3518 1.827969 AGAGGGCTAGTTGTACTGCTG 59.172 52.381 0.00 0.00 0.00 4.41
3215 3519 0.250513 AGGGCTAGTTGTACTGCTGC 59.749 55.000 0.00 0.00 0.00 5.25
3216 3520 0.250513 GGGCTAGTTGTACTGCTGCT 59.749 55.000 0.00 0.00 0.00 4.24
3217 3521 1.646189 GGCTAGTTGTACTGCTGCTC 58.354 55.000 0.00 0.00 0.00 4.26
3218 3522 1.205893 GGCTAGTTGTACTGCTGCTCT 59.794 52.381 0.00 0.00 0.00 4.09
3219 3523 2.266554 GCTAGTTGTACTGCTGCTCTG 58.733 52.381 0.00 0.00 0.00 3.35
3220 3524 2.266554 CTAGTTGTACTGCTGCTCTGC 58.733 52.381 0.00 0.00 0.00 4.26
3221 3525 0.321122 AGTTGTACTGCTGCTCTGCC 60.321 55.000 0.00 0.00 0.00 4.85
3222 3526 1.003355 TTGTACTGCTGCTCTGCCC 60.003 57.895 0.00 0.00 0.00 5.36
3223 3527 1.767654 TTGTACTGCTGCTCTGCCCA 61.768 55.000 0.00 0.00 0.00 5.36
3224 3528 1.449246 GTACTGCTGCTCTGCCCAG 60.449 63.158 0.00 0.00 34.59 4.45
3225 3529 1.610379 TACTGCTGCTCTGCCCAGA 60.610 57.895 0.00 0.00 33.35 3.86
3270 3574 2.104132 TGATGTCGACGGCCATCG 59.896 61.111 16.57 16.57 40.25 3.84
3281 3585 2.110006 GCCATCGCCTCTTCCTCC 59.890 66.667 0.00 0.00 0.00 4.30
3282 3586 2.439104 GCCATCGCCTCTTCCTCCT 61.439 63.158 0.00 0.00 0.00 3.69
3283 3587 1.745264 CCATCGCCTCTTCCTCCTC 59.255 63.158 0.00 0.00 0.00 3.71
3284 3588 1.361993 CATCGCCTCTTCCTCCTCG 59.638 63.158 0.00 0.00 0.00 4.63
3285 3589 2.494530 ATCGCCTCTTCCTCCTCGC 61.495 63.158 0.00 0.00 0.00 5.03
3286 3590 2.920076 ATCGCCTCTTCCTCCTCGCT 62.920 60.000 0.00 0.00 0.00 4.93
3287 3591 2.498726 GCCTCTTCCTCCTCGCTG 59.501 66.667 0.00 0.00 0.00 5.18
3288 3592 2.055042 GCCTCTTCCTCCTCGCTGA 61.055 63.158 0.00 0.00 0.00 4.26
3289 3593 1.813192 CCTCTTCCTCCTCGCTGAC 59.187 63.158 0.00 0.00 0.00 3.51
3290 3594 1.671901 CCTCTTCCTCCTCGCTGACC 61.672 65.000 0.00 0.00 0.00 4.02
3291 3595 0.682855 CTCTTCCTCCTCGCTGACCT 60.683 60.000 0.00 0.00 0.00 3.85
3292 3596 0.681564 TCTTCCTCCTCGCTGACCTC 60.682 60.000 0.00 0.00 0.00 3.85
3293 3597 0.967887 CTTCCTCCTCGCTGACCTCA 60.968 60.000 0.00 0.00 0.00 3.86
3294 3598 0.967887 TTCCTCCTCGCTGACCTCAG 60.968 60.000 0.00 0.00 46.40 3.35
3302 3606 2.672908 CTGACCTCAGCCATGCCA 59.327 61.111 0.00 0.00 37.15 4.92
3303 3607 1.226542 CTGACCTCAGCCATGCCAT 59.773 57.895 0.00 0.00 37.15 4.40
3304 3608 1.077285 TGACCTCAGCCATGCCATG 60.077 57.895 0.00 0.00 0.00 3.66
3312 3616 3.829226 CCATGCCATGGCCCTCCT 61.829 66.667 33.44 10.45 44.70 3.69
3313 3617 2.203451 CATGCCATGGCCCTCCTC 60.203 66.667 33.44 5.22 41.09 3.71
3314 3618 3.505773 ATGCCATGGCCCTCCTCC 61.506 66.667 33.44 4.41 41.09 4.30
3315 3619 4.765970 TGCCATGGCCCTCCTCCT 62.766 66.667 33.44 0.00 41.09 3.69
3316 3620 3.883549 GCCATGGCCCTCCTCCTC 61.884 72.222 27.24 0.00 34.56 3.71
3317 3621 3.554342 CCATGGCCCTCCTCCTCG 61.554 72.222 0.00 0.00 0.00 4.63
3318 3622 4.247380 CATGGCCCTCCTCCTCGC 62.247 72.222 0.00 0.00 0.00 5.03
3400 3704 1.532298 GCTCGAAGGTTAGCTCGTCTC 60.532 57.143 0.00 0.00 36.46 3.36
3404 3708 2.854777 CGAAGGTTAGCTCGTCTCAATG 59.145 50.000 0.00 0.00 0.00 2.82
3406 3710 1.827969 AGGTTAGCTCGTCTCAATGCT 59.172 47.619 0.00 0.00 39.30 3.79
3417 3721 1.303561 TCAATGCTGGCCTGGTGAC 60.304 57.895 12.06 0.00 0.00 3.67
3446 3750 2.018542 TGCGAACTAGGGATTTTCGG 57.981 50.000 12.60 0.00 41.89 4.30
3476 3780 1.757306 CTGCTTGGACAGTGGGAGT 59.243 57.895 0.00 0.00 32.78 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.759445 CTCCGACATGTCTTCCAGGAT 59.241 52.381 22.95 0.00 0.00 3.24
1 2 1.186200 CTCCGACATGTCTTCCAGGA 58.814 55.000 22.95 18.98 0.00 3.86
3 4 1.546029 TGTCTCCGACATGTCTTCCAG 59.454 52.381 22.95 12.69 37.67 3.86
4 5 1.272490 GTGTCTCCGACATGTCTTCCA 59.728 52.381 22.95 9.76 44.63 3.53
5 6 1.732732 CGTGTCTCCGACATGTCTTCC 60.733 57.143 22.95 7.45 44.63 3.46
6 7 1.199327 TCGTGTCTCCGACATGTCTTC 59.801 52.381 22.95 9.32 46.18 2.87
7 8 1.244816 TCGTGTCTCCGACATGTCTT 58.755 50.000 22.95 0.00 46.18 3.01
8 9 1.464734 ATCGTGTCTCCGACATGTCT 58.535 50.000 22.95 0.00 46.18 3.41
9 10 1.920574 CAATCGTGTCTCCGACATGTC 59.079 52.381 16.21 16.21 46.18 3.06
10 11 1.996292 CAATCGTGTCTCCGACATGT 58.004 50.000 13.93 0.00 46.18 3.21
12 13 0.246360 TGCAATCGTGTCTCCGACAT 59.754 50.000 0.00 0.00 44.63 3.06
13 14 0.666274 GTGCAATCGTGTCTCCGACA 60.666 55.000 0.00 0.00 40.50 4.35
14 15 0.666274 TGTGCAATCGTGTCTCCGAC 60.666 55.000 0.00 0.00 40.08 4.79
15 16 0.666274 GTGTGCAATCGTGTCTCCGA 60.666 55.000 0.00 0.00 41.73 4.55
16 17 1.781555 GTGTGCAATCGTGTCTCCG 59.218 57.895 0.00 0.00 0.00 4.63
17 18 1.781555 CGTGTGCAATCGTGTCTCC 59.218 57.895 0.00 0.00 0.00 3.71
18 19 1.130613 GCGTGTGCAATCGTGTCTC 59.869 57.895 12.16 0.00 42.15 3.36
19 20 2.317609 GGCGTGTGCAATCGTGTCT 61.318 57.895 12.16 0.00 45.35 3.41
20 21 2.173382 GGCGTGTGCAATCGTGTC 59.827 61.111 12.16 1.64 45.35 3.67
21 22 3.353836 GGGCGTGTGCAATCGTGT 61.354 61.111 12.16 0.00 45.35 4.49
22 23 3.049674 AGGGCGTGTGCAATCGTG 61.050 61.111 12.16 0.00 45.35 4.35
23 24 3.049674 CAGGGCGTGTGCAATCGT 61.050 61.111 12.16 0.00 45.35 3.73
24 25 4.465512 GCAGGGCGTGTGCAATCG 62.466 66.667 9.16 7.31 45.35 3.34
36 37 3.726517 CTTTGTGTCGGCGCAGGG 61.727 66.667 10.83 0.00 36.39 4.45
37 38 4.389576 GCTTTGTGTCGGCGCAGG 62.390 66.667 10.83 0.00 36.39 4.85
38 39 3.648982 TGCTTTGTGTCGGCGCAG 61.649 61.111 10.83 5.07 36.39 5.18
39 40 3.947841 GTGCTTTGTGTCGGCGCA 61.948 61.111 10.83 0.00 36.61 6.09
40 41 3.947841 TGTGCTTTGTGTCGGCGC 61.948 61.111 0.00 0.00 37.05 6.53
41 42 2.052237 GTGTGCTTTGTGTCGGCG 60.052 61.111 0.00 0.00 0.00 6.46
42 43 2.331451 GGTGTGCTTTGTGTCGGC 59.669 61.111 0.00 0.00 0.00 5.54
43 44 1.095228 ACTGGTGTGCTTTGTGTCGG 61.095 55.000 0.00 0.00 0.00 4.79
44 45 0.027979 CACTGGTGTGCTTTGTGTCG 59.972 55.000 0.00 0.00 37.38 4.35
45 46 0.381801 CCACTGGTGTGCTTTGTGTC 59.618 55.000 0.00 0.00 42.54 3.67
46 47 0.034574 TCCACTGGTGTGCTTTGTGT 60.035 50.000 0.00 0.00 42.54 3.72
47 48 1.102154 TTCCACTGGTGTGCTTTGTG 58.898 50.000 0.00 0.00 42.54 3.33
48 49 1.846007 TTTCCACTGGTGTGCTTTGT 58.154 45.000 0.00 0.00 42.54 2.83
49 50 2.546373 CCATTTCCACTGGTGTGCTTTG 60.546 50.000 0.00 0.00 42.54 2.77
50 51 1.688197 CCATTTCCACTGGTGTGCTTT 59.312 47.619 0.00 0.00 42.54 3.51
51 52 1.331214 CCATTTCCACTGGTGTGCTT 58.669 50.000 0.00 0.00 42.54 3.91
52 53 0.540365 CCCATTTCCACTGGTGTGCT 60.540 55.000 0.00 0.00 42.54 4.40
53 54 1.535204 CCCCATTTCCACTGGTGTGC 61.535 60.000 0.00 0.00 42.54 4.57
54 55 0.112218 TCCCCATTTCCACTGGTGTG 59.888 55.000 0.00 0.00 43.45 3.82
55 56 1.084018 ATCCCCATTTCCACTGGTGT 58.916 50.000 0.00 0.00 31.44 4.16
56 57 1.477553 CATCCCCATTTCCACTGGTG 58.522 55.000 0.00 0.00 31.44 4.17
57 58 0.324645 GCATCCCCATTTCCACTGGT 60.325 55.000 0.00 0.00 31.44 4.00
58 59 0.324552 TGCATCCCCATTTCCACTGG 60.325 55.000 0.00 0.00 0.00 4.00
59 60 0.819582 GTGCATCCCCATTTCCACTG 59.180 55.000 0.00 0.00 0.00 3.66
60 61 0.409092 TGTGCATCCCCATTTCCACT 59.591 50.000 0.00 0.00 0.00 4.00
61 62 1.137479 CATGTGCATCCCCATTTCCAC 59.863 52.381 0.00 0.00 0.00 4.02
62 63 1.487300 CATGTGCATCCCCATTTCCA 58.513 50.000 0.00 0.00 0.00 3.53
63 64 0.105408 GCATGTGCATCCCCATTTCC 59.895 55.000 0.00 0.00 41.59 3.13
64 65 0.105408 GGCATGTGCATCCCCATTTC 59.895 55.000 7.36 0.00 44.36 2.17
65 66 1.339644 GGGCATGTGCATCCCCATTT 61.340 55.000 6.30 0.00 44.36 2.32
66 67 1.763256 GGGCATGTGCATCCCCATT 60.763 57.895 6.30 0.00 44.36 3.16
67 68 2.123164 GGGCATGTGCATCCCCAT 60.123 61.111 6.30 0.00 44.36 4.00
68 69 3.349304 AGGGCATGTGCATCCCCA 61.349 61.111 13.24 0.00 44.36 4.96
69 70 2.836360 CAGGGCATGTGCATCCCC 60.836 66.667 2.94 2.94 44.36 4.81
70 71 3.534056 GCAGGGCATGTGCATCCC 61.534 66.667 7.36 7.87 44.36 3.85
71 72 3.896133 CGCAGGGCATGTGCATCC 61.896 66.667 7.36 0.00 44.36 3.51
87 88 2.052237 GTGTGCTTTGTGTCGGCG 60.052 61.111 0.00 0.00 0.00 6.46
102 103 2.423373 CCTATCCCCATTTCCACTGGTG 60.423 54.545 0.00 0.00 31.44 4.17
107 108 0.555769 TGCCCTATCCCCATTTCCAC 59.444 55.000 0.00 0.00 0.00 4.02
114 115 0.575848 TTATCCCTGCCCTATCCCCA 59.424 55.000 0.00 0.00 0.00 4.96
117 118 3.074538 ACAATGTTATCCCTGCCCTATCC 59.925 47.826 0.00 0.00 0.00 2.59
126 127 5.957132 AGGCATATGAACAATGTTATCCCT 58.043 37.500 6.97 0.00 0.00 4.20
138 139 1.222115 GGACGGCGAGGCATATGAAC 61.222 60.000 16.62 0.00 0.00 3.18
139 140 1.069090 GGACGGCGAGGCATATGAA 59.931 57.895 16.62 0.00 0.00 2.57
141 142 2.357517 GGGACGGCGAGGCATATG 60.358 66.667 16.62 0.00 0.00 1.78
142 143 1.978455 TTTGGGACGGCGAGGCATAT 61.978 55.000 16.62 0.00 0.00 1.78
143 144 2.661066 TTTGGGACGGCGAGGCATA 61.661 57.895 16.62 0.00 0.00 3.14
153 168 0.733729 TTCGTGTTTGGTTTGGGACG 59.266 50.000 0.00 0.00 0.00 4.79
169 184 3.119280 AGGTTTTTGTTTGTGGGTCTTCG 60.119 43.478 0.00 0.00 0.00 3.79
180 195 9.131416 CGAGTGTTACTTTTTAGGTTTTTGTTT 57.869 29.630 0.00 0.00 0.00 2.83
183 198 6.075780 CGCGAGTGTTACTTTTTAGGTTTTTG 60.076 38.462 0.00 0.00 0.00 2.44
184 199 5.967088 CGCGAGTGTTACTTTTTAGGTTTTT 59.033 36.000 0.00 0.00 0.00 1.94
190 205 3.665409 TCGTCGCGAGTGTTACTTTTTAG 59.335 43.478 10.24 0.00 0.00 1.85
192 207 2.462889 TCGTCGCGAGTGTTACTTTTT 58.537 42.857 10.24 0.00 0.00 1.94
206 221 5.610552 GCTTGAATCTGTTATACATCGTCGC 60.611 44.000 0.00 0.00 0.00 5.19
207 222 5.107837 GGCTTGAATCTGTTATACATCGTCG 60.108 44.000 0.00 0.00 0.00 5.12
210 225 7.115520 CACTAGGCTTGAATCTGTTATACATCG 59.884 40.741 2.20 0.00 0.00 3.84
220 235 3.373439 GCTCAACACTAGGCTTGAATCTG 59.627 47.826 2.20 0.00 0.00 2.90
248 263 3.359515 TGCATGCCTTTGCGATGGC 62.360 57.895 21.42 21.42 45.77 4.40
253 268 1.443194 GTCAGTGCATGCCTTTGCG 60.443 57.895 16.68 0.46 45.77 4.85
254 269 0.245539 ATGTCAGTGCATGCCTTTGC 59.754 50.000 16.68 3.46 43.07 3.68
255 270 1.816835 AGATGTCAGTGCATGCCTTTG 59.183 47.619 16.68 10.85 0.00 2.77
256 271 2.211250 AGATGTCAGTGCATGCCTTT 57.789 45.000 16.68 0.00 0.00 3.11
257 272 2.089980 GAAGATGTCAGTGCATGCCTT 58.910 47.619 16.68 8.27 0.00 4.35
258 273 1.281287 AGAAGATGTCAGTGCATGCCT 59.719 47.619 16.68 9.12 0.00 4.75
259 274 1.669779 GAGAAGATGTCAGTGCATGCC 59.330 52.381 16.68 6.65 0.00 4.40
260 275 2.608546 GAGAGAAGATGTCAGTGCATGC 59.391 50.000 11.82 11.82 0.00 4.06
261 276 3.866327 CAGAGAGAAGATGTCAGTGCATG 59.134 47.826 5.01 0.00 0.00 4.06
262 277 3.118702 CCAGAGAGAAGATGTCAGTGCAT 60.119 47.826 0.00 0.44 0.00 3.96
263 278 2.233186 CCAGAGAGAAGATGTCAGTGCA 59.767 50.000 0.00 0.00 0.00 4.57
264 279 2.233431 ACCAGAGAGAAGATGTCAGTGC 59.767 50.000 0.00 0.00 0.00 4.40
265 280 3.509184 TCACCAGAGAGAAGATGTCAGTG 59.491 47.826 0.00 0.00 32.30 3.66
266 281 3.772387 TCACCAGAGAGAAGATGTCAGT 58.228 45.455 0.00 0.00 0.00 3.41
267 282 4.646040 AGATCACCAGAGAGAAGATGTCAG 59.354 45.833 0.00 0.00 0.00 3.51
268 283 4.608269 AGATCACCAGAGAGAAGATGTCA 58.392 43.478 0.00 0.00 0.00 3.58
269 284 5.278463 GCTAGATCACCAGAGAGAAGATGTC 60.278 48.000 0.00 0.00 0.00 3.06
270 285 4.584325 GCTAGATCACCAGAGAGAAGATGT 59.416 45.833 0.00 0.00 0.00 3.06
271 286 4.022068 GGCTAGATCACCAGAGAGAAGATG 60.022 50.000 0.00 0.00 0.00 2.90
282 297 1.306911 TGGCCTGGCTAGATCACCA 60.307 57.895 19.68 1.97 0.00 4.17
283 298 1.449353 CTGGCCTGGCTAGATCACC 59.551 63.158 26.11 3.17 39.54 4.02
300 315 3.322466 CTCTTCACCGGGTGCCCT 61.322 66.667 22.42 0.00 32.98 5.19
338 353 2.851104 CGGCGGTCTTCGTCAAAC 59.149 61.111 0.00 0.00 44.96 2.93
355 370 1.742268 GAAAGAGATGGGTGCTTGAGC 59.258 52.381 0.00 0.00 42.50 4.26
400 415 2.282040 GCAGCCTGTTGCAGAGGT 60.282 61.111 13.80 0.97 44.83 3.85
412 427 1.455773 GTCCTAATTGGGGGCAGCC 60.456 63.158 8.14 1.26 36.20 4.85
413 428 1.455773 GGTCCTAATTGGGGGCAGC 60.456 63.158 8.14 0.00 36.20 5.25
415 430 1.286305 GGAGGTCCTAATTGGGGGCA 61.286 60.000 8.14 0.00 36.20 5.36
447 462 0.520404 CATCGCTGATAAGCCCATGC 59.480 55.000 0.00 0.00 37.95 4.06
451 466 3.248029 CGCATCGCTGATAAGCCC 58.752 61.111 0.00 0.00 0.00 5.19
480 495 0.935194 CCCTCACCTACCCCTCTAGT 59.065 60.000 0.00 0.00 0.00 2.57
482 497 0.556888 ACCCCTCACCTACCCCTCTA 60.557 60.000 0.00 0.00 0.00 2.43
498 513 3.578968 AAAACCCTAGCCGCCACCC 62.579 63.158 0.00 0.00 0.00 4.61
523 538 0.673956 GTCTTCCGAGAAAGGTGGGC 60.674 60.000 0.00 0.00 32.66 5.36
579 621 9.793252 ATTGATTTCTTCCGTTATCTTTTGATG 57.207 29.630 0.00 0.00 39.88 3.07
612 654 7.552687 AGTCGCTAATGTTTCATTCTCCAATAA 59.447 33.333 0.00 0.00 0.00 1.40
735 777 7.866393 CCTAAGTTCGACTGTTCTCTTCTAAAA 59.134 37.037 0.00 0.00 0.00 1.52
800 844 1.672441 GCCCGTGTGGAATTGTACGTA 60.672 52.381 0.00 0.00 37.49 3.57
984 1043 0.339510 CCATTGGGATCCCTTGGGTT 59.660 55.000 31.26 11.84 36.83 4.11
1242 1325 3.522731 CTCCGCGGAGGACAGAGG 61.523 72.222 41.47 19.14 45.98 3.69
1255 1339 3.777465 TCGATCTCAACCTAAACTCCG 57.223 47.619 0.00 0.00 0.00 4.63
1412 1496 1.889170 TCTCAGTATCATAGCGCAGGG 59.111 52.381 11.47 0.00 0.00 4.45
1441 1525 2.032620 ACGCTACTGGGTTATGAGGAG 58.967 52.381 0.00 0.00 35.78 3.69
1452 1536 2.753452 TGAAGAAGACCTACGCTACTGG 59.247 50.000 0.00 0.00 0.00 4.00
1472 1556 7.769272 ACTAAATTCACAAACCAACAATGTG 57.231 32.000 0.00 0.00 44.45 3.21
1505 1610 5.241949 CCATGAATAGCTACTCCGAGTAAGT 59.758 44.000 9.54 2.77 29.00 2.24
1514 1619 5.936372 TGCATCAATCCATGAATAGCTACTC 59.064 40.000 0.00 0.00 42.54 2.59
1557 1668 5.568620 ACCAAACAAGAGAGAACCTACAT 57.431 39.130 0.00 0.00 0.00 2.29
1558 1669 5.123227 CAACCAAACAAGAGAGAACCTACA 58.877 41.667 0.00 0.00 0.00 2.74
1569 1680 5.105567 TGGAACTAGACAACCAAACAAGA 57.894 39.130 0.00 0.00 0.00 3.02
1602 1713 9.314321 AGTTATAGTCCAAATCTGATTTACACG 57.686 33.333 14.78 3.67 0.00 4.49
1615 1726 6.852908 ACCCCATATGGTAGTTATAGTCCAAA 59.147 38.462 20.46 0.00 36.67 3.28
1687 1847 5.736486 TTTCTACGCATTTACAACACACA 57.264 34.783 0.00 0.00 0.00 3.72
1766 1930 6.986231 TGACACCAACATATGCTAACAGATAG 59.014 38.462 1.58 0.00 34.52 2.08
1780 1944 6.418057 AACCAATAACAATGACACCAACAT 57.582 33.333 0.00 0.00 0.00 2.71
1847 2112 0.401356 TGCAGAACCAGATGCCTGAA 59.599 50.000 0.00 0.00 43.02 3.02
1848 2113 0.622136 ATGCAGAACCAGATGCCTGA 59.378 50.000 0.00 0.00 43.02 3.86
1896 2166 1.999648 AGCCAAACATGCAAGAAGGA 58.000 45.000 0.00 0.00 0.00 3.36
1925 2195 1.534729 ATTCCCAGGTTTCGCAGAAC 58.465 50.000 0.00 0.00 45.90 3.01
1926 2196 2.286365 AATTCCCAGGTTTCGCAGAA 57.714 45.000 0.00 0.00 45.90 3.02
2022 2310 9.507280 AGAAACATCAGCGTTAAAATATGAATG 57.493 29.630 0.00 0.00 0.00 2.67
2025 2313 8.492673 AGAGAAACATCAGCGTTAAAATATGA 57.507 30.769 0.00 0.00 0.00 2.15
2247 2535 2.496899 AGCTGATCGTCCAATGGTTT 57.503 45.000 0.00 0.00 0.00 3.27
2290 2578 5.023533 ACAAGAGACAGAACTAAGTTGCA 57.976 39.130 0.00 0.00 0.00 4.08
2331 2620 3.582647 TGAACTCTGGCAGATTCTTGGTA 59.417 43.478 25.75 12.74 0.00 3.25
2361 2650 0.877649 CATCGATGGCCTTCTGGTCG 60.878 60.000 17.96 10.13 41.88 4.79
2664 2954 0.588737 TCGCAGCACAAATAACGCAA 59.411 45.000 0.00 0.00 0.00 4.85
2757 3048 2.226437 ACAACCAGCAAGCTAAACATCG 59.774 45.455 0.00 0.00 0.00 3.84
2768 3059 2.380064 AATCCCAGAACAACCAGCAA 57.620 45.000 0.00 0.00 0.00 3.91
2803 3094 1.271656 CGAACGGAGGGAGTAACACTT 59.728 52.381 0.00 0.00 29.26 3.16
2815 3106 6.557291 AAGGTCTTATATCTACGAACGGAG 57.443 41.667 0.00 0.00 0.00 4.63
2855 3149 7.914871 TCAATCATTTTGTTTCATATGTAGGCG 59.085 33.333 1.90 0.00 0.00 5.52
2891 3185 7.049754 TCAATATGAGCAACATACAGATGTGT 58.950 34.615 0.00 0.00 45.93 3.72
2905 3199 8.055181 ACCCTTTTAGAGATTTCAATATGAGCA 58.945 33.333 0.00 0.00 0.00 4.26
2964 3258 4.738740 CGTCAGAATAGTAATCGGTTGTCC 59.261 45.833 0.00 0.00 0.00 4.02
2991 3285 4.072131 TGCATGTACCTCTTGGAGTTTTC 58.928 43.478 0.00 0.00 37.04 2.29
3002 3296 1.406539 CCAAGGCAATGCATGTACCTC 59.593 52.381 14.02 0.00 0.00 3.85
3003 3297 1.005805 TCCAAGGCAATGCATGTACCT 59.994 47.619 7.79 4.62 0.00 3.08
3004 3298 1.406539 CTCCAAGGCAATGCATGTACC 59.593 52.381 7.79 1.91 0.00 3.34
3006 3300 2.646930 CTCTCCAAGGCAATGCATGTA 58.353 47.619 7.79 0.00 0.00 2.29
3010 3306 4.749323 CCTCTCCAAGGCAATGCA 57.251 55.556 7.79 0.00 38.67 3.96
3077 3379 0.035881 ATGCCTCATATCCGTGCAGG 59.964 55.000 0.00 0.00 42.97 4.85
3079 3381 0.758123 TGATGCCTCATATCCGTGCA 59.242 50.000 0.00 0.00 36.23 4.57
3081 3383 2.037641 TCCTTGATGCCTCATATCCGTG 59.962 50.000 0.00 0.00 0.00 4.94
3088 3390 0.179062 GAGCGTCCTTGATGCCTCAT 60.179 55.000 4.74 0.00 44.75 2.90
3108 3412 4.882396 GGAGCTTCTCGCGAGCCC 62.882 72.222 30.97 20.20 45.59 5.19
3110 3414 4.180946 TCGGAGCTTCTCGCGAGC 62.181 66.667 30.97 20.61 45.59 5.03
3111 3415 2.277628 GTCGGAGCTTCTCGCGAG 60.278 66.667 30.03 30.03 45.59 5.03
3112 3416 3.053896 TGTCGGAGCTTCTCGCGA 61.054 61.111 9.26 9.26 45.59 5.87
3113 3417 2.876645 GTGTCGGAGCTTCTCGCG 60.877 66.667 0.00 0.00 45.59 5.87
3114 3418 2.876645 CGTGTCGGAGCTTCTCGC 60.877 66.667 0.00 0.00 39.57 5.03
3125 3429 3.545481 GATGTCGCTGCCGTGTCG 61.545 66.667 0.00 0.00 35.54 4.35
3154 3458 1.078214 TGGCTGGCTCAAATCGAGG 60.078 57.895 2.00 0.00 42.55 4.63
3155 3459 1.712977 GCTGGCTGGCTCAAATCGAG 61.713 60.000 2.00 0.00 45.37 4.04
3156 3460 1.746615 GCTGGCTGGCTCAAATCGA 60.747 57.895 2.00 0.00 0.00 3.59
3157 3461 2.796651 GCTGGCTGGCTCAAATCG 59.203 61.111 2.00 0.00 0.00 3.34
3158 3462 2.796651 CGCTGGCTGGCTCAAATC 59.203 61.111 2.00 0.00 0.00 2.17
3185 3489 3.386402 ACAACTAGCCCTCTTAGAGATGC 59.614 47.826 11.32 12.53 0.00 3.91
3186 3490 5.830991 AGTACAACTAGCCCTCTTAGAGATG 59.169 44.000 11.32 2.70 0.00 2.90
3187 3491 5.830991 CAGTACAACTAGCCCTCTTAGAGAT 59.169 44.000 11.32 0.00 0.00 2.75
3188 3492 5.194432 CAGTACAACTAGCCCTCTTAGAGA 58.806 45.833 11.32 0.00 0.00 3.10
3189 3493 4.202070 GCAGTACAACTAGCCCTCTTAGAG 60.202 50.000 1.56 1.56 0.00 2.43
3190 3494 3.700038 GCAGTACAACTAGCCCTCTTAGA 59.300 47.826 0.00 0.00 0.00 2.10
3191 3495 3.702045 AGCAGTACAACTAGCCCTCTTAG 59.298 47.826 0.00 0.00 0.00 2.18
3192 3496 3.447586 CAGCAGTACAACTAGCCCTCTTA 59.552 47.826 0.00 0.00 0.00 2.10
3193 3497 2.234908 CAGCAGTACAACTAGCCCTCTT 59.765 50.000 0.00 0.00 0.00 2.85
3194 3498 1.827969 CAGCAGTACAACTAGCCCTCT 59.172 52.381 0.00 0.00 0.00 3.69
3195 3499 1.740718 GCAGCAGTACAACTAGCCCTC 60.741 57.143 0.00 0.00 0.00 4.30
3196 3500 0.250513 GCAGCAGTACAACTAGCCCT 59.749 55.000 0.00 0.00 0.00 5.19
3197 3501 0.250513 AGCAGCAGTACAACTAGCCC 59.749 55.000 0.00 0.00 0.00 5.19
3198 3502 1.205893 AGAGCAGCAGTACAACTAGCC 59.794 52.381 0.00 0.00 0.00 3.93
3199 3503 2.266554 CAGAGCAGCAGTACAACTAGC 58.733 52.381 0.00 0.00 0.00 3.42
3200 3504 2.266554 GCAGAGCAGCAGTACAACTAG 58.733 52.381 0.00 0.00 0.00 2.57
3201 3505 1.066858 GGCAGAGCAGCAGTACAACTA 60.067 52.381 0.00 0.00 35.83 2.24
3202 3506 0.321122 GGCAGAGCAGCAGTACAACT 60.321 55.000 0.00 0.00 35.83 3.16
3203 3507 1.301677 GGGCAGAGCAGCAGTACAAC 61.302 60.000 0.00 0.00 35.83 3.32
3204 3508 1.003355 GGGCAGAGCAGCAGTACAA 60.003 57.895 0.00 0.00 35.83 2.41
3205 3509 2.176314 CTGGGCAGAGCAGCAGTACA 62.176 60.000 0.00 0.00 35.83 2.90
3206 3510 1.449246 CTGGGCAGAGCAGCAGTAC 60.449 63.158 0.00 0.00 35.83 2.73
3207 3511 1.610379 TCTGGGCAGAGCAGCAGTA 60.610 57.895 0.00 0.00 35.83 2.74
3208 3512 2.926779 TCTGGGCAGAGCAGCAGT 60.927 61.111 0.00 0.00 35.83 4.40
3216 3520 1.754745 GGTTCACACTCTGGGCAGA 59.245 57.895 0.00 0.00 35.85 4.26
3217 3521 1.302832 GGGTTCACACTCTGGGCAG 60.303 63.158 0.00 0.00 0.00 4.85
3218 3522 1.770110 AGGGTTCACACTCTGGGCA 60.770 57.895 0.00 0.00 29.67 5.36
3219 3523 1.302832 CAGGGTTCACACTCTGGGC 60.303 63.158 0.00 0.00 46.70 5.36
3223 3527 1.056700 AGTGGCAGGGTTCACACTCT 61.057 55.000 0.00 0.00 39.84 3.24
3224 3528 0.685097 TAGTGGCAGGGTTCACACTC 59.315 55.000 0.00 0.00 42.66 3.51
3225 3529 0.396811 GTAGTGGCAGGGTTCACACT 59.603 55.000 0.00 0.00 45.32 3.55
3226 3530 0.949105 CGTAGTGGCAGGGTTCACAC 60.949 60.000 0.00 0.00 36.43 3.82
3227 3531 1.116536 TCGTAGTGGCAGGGTTCACA 61.117 55.000 0.00 0.00 36.43 3.58
3228 3532 0.389948 CTCGTAGTGGCAGGGTTCAC 60.390 60.000 0.00 0.00 0.00 3.18
3229 3533 0.830444 ACTCGTAGTGGCAGGGTTCA 60.830 55.000 0.00 0.00 0.00 3.18
3270 3574 2.055042 TCAGCGAGGAGGAAGAGGC 61.055 63.158 0.00 0.00 0.00 4.70
3275 3579 0.967887 CTGAGGTCAGCGAGGAGGAA 60.968 60.000 0.00 0.00 37.15 3.36
3285 3589 1.101635 CATGGCATGGCTGAGGTCAG 61.102 60.000 19.80 2.37 46.40 3.51
3286 3590 1.077285 CATGGCATGGCTGAGGTCA 60.077 57.895 19.80 0.00 0.00 4.02
3287 3591 1.826921 CCATGGCATGGCTGAGGTC 60.827 63.158 31.96 0.00 44.70 3.85
3288 3592 2.277737 CCATGGCATGGCTGAGGT 59.722 61.111 31.96 0.00 44.70 3.85
3296 3600 2.203451 GAGGAGGGCCATGGCATG 60.203 66.667 36.56 20.56 44.11 4.06
3297 3601 3.505773 GGAGGAGGGCCATGGCAT 61.506 66.667 36.56 25.10 44.11 4.40
3298 3602 4.765970 AGGAGGAGGGCCATGGCA 62.766 66.667 36.56 0.00 44.11 4.92
3299 3603 3.883549 GAGGAGGAGGGCCATGGC 61.884 72.222 29.47 29.47 41.06 4.40
3300 3604 3.554342 CGAGGAGGAGGGCCATGG 61.554 72.222 7.63 7.63 36.29 3.66
3301 3605 4.247380 GCGAGGAGGAGGGCCATG 62.247 72.222 6.18 0.00 36.29 3.66
3307 3611 4.824515 AGGTCGGCGAGGAGGAGG 62.825 72.222 11.20 0.00 0.00 4.30
3308 3612 3.213402 GAGGTCGGCGAGGAGGAG 61.213 72.222 11.20 0.00 0.00 3.69
3309 3613 3.997400 CTGAGGTCGGCGAGGAGGA 62.997 68.421 11.20 0.00 0.00 3.71
3310 3614 3.522731 CTGAGGTCGGCGAGGAGG 61.523 72.222 11.20 0.00 0.00 4.30
3311 3615 4.200283 GCTGAGGTCGGCGAGGAG 62.200 72.222 11.20 4.88 38.61 3.69
3318 3622 3.411114 ATGGCATGGCTGAGGTCGG 62.411 63.158 21.08 0.00 0.00 4.79
3319 3623 2.184830 CATGGCATGGCTGAGGTCG 61.185 63.158 19.80 0.00 0.00 4.79
3320 3624 1.826921 CCATGGCATGGCTGAGGTC 60.827 63.158 31.96 0.00 44.70 3.85
3321 3625 2.277737 CCATGGCATGGCTGAGGT 59.722 61.111 31.96 0.00 44.70 3.85
3400 3704 2.693762 CGTCACCAGGCCAGCATTG 61.694 63.158 5.01 0.00 0.00 2.82
3432 3736 2.165845 CTGTCGTCCGAAAATCCCTAGT 59.834 50.000 0.00 0.00 0.00 2.57
3446 3750 1.364626 CCAAGCAGCCATCTGTCGTC 61.365 60.000 0.00 0.00 42.29 4.20


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

AutoCloner maintained by Alex Coulton.