Multiple sequence alignment - TraesCS4A01G356400

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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 TraesCS4A01G356400 chr4A 100.000 8357 0 0 1 8357 629910234 629918590 0.000000e+00 15433.0
1 TraesCS4A01G356400 chr4A 100.000 134 0 0 4500 4633 629914593 629914726 1.800000e-61 248.0
2 TraesCS4A01G356400 chr4A 100.000 134 0 0 4360 4493 629914733 629914866 1.800000e-61 248.0
3 TraesCS4A01G356400 chr5B 95.971 3078 65 14 1465 4496 680342459 680339395 0.000000e+00 4942.0
4 TraesCS4A01G356400 chr5B 95.659 2004 53 11 5702 7685 680338133 680336144 0.000000e+00 3188.0
5 TraesCS4A01G356400 chr5B 97.943 1118 21 2 4500 5617 680339531 680338416 0.000000e+00 1936.0
6 TraesCS4A01G356400 chr5B 89.387 848 34 22 653 1467 680343307 680342483 0.000000e+00 1016.0
7 TraesCS4A01G356400 chr5B 90.223 583 48 6 7777 8357 680323160 680322585 0.000000e+00 752.0
8 TraesCS4A01G356400 chr5B 86.752 234 25 2 5110 5338 471023210 471022978 1.080000e-63 255.0
9 TraesCS4A01G356400 chr5B 85.652 230 28 3 5110 5338 473116637 473116862 3.900000e-58 237.0
10 TraesCS4A01G356400 chr5B 78.025 405 59 22 18 414 680344050 680343668 2.350000e-55 228.0
11 TraesCS4A01G356400 chr5B 92.174 115 9 0 5610 5724 680338252 680338138 6.710000e-36 163.0
12 TraesCS4A01G356400 chr5D 97.474 1900 39 4 2607 4498 538769807 538767909 0.000000e+00 3234.0
13 TraesCS4A01G356400 chr5D 96.142 1633 48 9 938 2559 538771435 538769807 0.000000e+00 2652.0
14 TraesCS4A01G356400 chr5D 98.551 1311 16 2 4500 5808 538768048 538766739 0.000000e+00 2313.0
15 TraesCS4A01G356400 chr5D 96.264 1151 16 10 5741 6890 538766743 538765619 0.000000e+00 1862.0
16 TraesCS4A01G356400 chr5D 97.011 803 18 3 6889 7685 538765537 538764735 0.000000e+00 1345.0
17 TraesCS4A01G356400 chr5D 91.652 563 28 9 7686 8242 538763178 538762629 0.000000e+00 761.0
18 TraesCS4A01G356400 chr5D 88.446 502 43 6 1 491 538773202 538772705 7.220000e-165 592.0
19 TraesCS4A01G356400 chr5D 94.604 278 9 2 653 924 538772177 538771900 7.750000e-115 425.0
20 TraesCS4A01G356400 chr5D 88.646 229 26 0 5110 5338 393057977 393058205 6.390000e-71 279.0
21 TraesCS4A01G356400 chr5D 90.000 50 1 4 7817 7864 63614522 63614569 2.520000e-05 62.1
22 TraesCS4A01G356400 chr1A 85.664 572 52 10 7089 7640 590120829 590121390 7.270000e-160 575.0
23 TraesCS4A01G356400 chr1A 90.141 71 7 0 6141 6211 82716379 82716449 8.930000e-15 93.5
24 TraesCS4A01G356400 chr4B 82.292 384 53 11 2019 2394 624519924 624520300 1.350000e-82 318.0
25 TraesCS4A01G356400 chr5A 89.083 229 24 1 5110 5338 494231295 494231068 4.940000e-72 283.0
26 TraesCS4A01G356400 chr5A 83.333 126 20 1 6778 6903 680582606 680582482 1.910000e-21 115.0
27 TraesCS4A01G356400 chr2D 89.302 215 22 1 5125 5338 87754081 87754295 1.380000e-67 268.0
28 TraesCS4A01G356400 chr2A 87.225 227 29 0 5112 5338 88010000 88010226 8.320000e-65 259.0
29 TraesCS4A01G356400 chr2B 87.336 229 20 6 5112 5338 232785267 232785046 3.870000e-63 254.0
30 TraesCS4A01G356400 chr3D 90.000 60 5 1 6153 6211 421782121 421782062 8.990000e-10 76.8
31 TraesCS4A01G356400 chr6D 95.000 40 2 0 5335 5374 467812475 467812514 7.000000e-06 63.9
32 TraesCS4A01G356400 chr6A 95.000 40 2 0 5335 5374 613930054 613930015 7.000000e-06 63.9


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 TraesCS4A01G356400 chr4A 629910234 629918590 8356 False 5309.666667 15433 100.0000 1 8357 3 chr4A.!!$F1 8356
1 TraesCS4A01G356400 chr5B 680336144 680344050 7906 True 1912.166667 4942 91.5265 18 7685 6 chr5B.!!$R3 7667
2 TraesCS4A01G356400 chr5B 680322585 680323160 575 True 752.000000 752 90.2230 7777 8357 1 chr5B.!!$R2 580
3 TraesCS4A01G356400 chr5D 538762629 538773202 10573 True 1648.000000 3234 95.0180 1 8242 8 chr5D.!!$R1 8241
4 TraesCS4A01G356400 chr1A 590120829 590121390 561 False 575.000000 575 85.6640 7089 7640 1 chr1A.!!$F2 551

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
248 253 0.025513 GCACGCTTCTGCTTGTATCG 59.974 55.000 0.00 0.00 40.11 2.92 F
708 1169 1.066752 TCACTGGACCAACGTGTCG 59.933 57.895 12.29 0.00 36.07 4.35 F
1352 2278 0.179084 CCGGCTTCCATCGAGCTTAA 60.179 55.000 0.00 0.00 40.01 1.85 F
2401 3375 0.253044 TAGCTTGGACATGGAGGCAC 59.747 55.000 0.00 0.00 0.00 5.01 F
3498 4496 2.301583 GCCAAGTCCAGAGAAGTCTTCT 59.698 50.000 15.14 15.14 44.21 2.85 F
3855 4860 0.461548 CTCCGGTGCTTGCTGAGATA 59.538 55.000 0.00 0.00 0.00 1.98 F
5095 6107 1.134367 CATTCCGGCTCTTCTCGTACA 59.866 52.381 0.00 0.00 0.00 2.90 F
5732 6942 1.269936 GCAATGGCTCAAGCACTTGTT 60.270 47.619 10.05 0.00 44.36 2.83 F
6376 7626 0.817634 CGAGCACAAAGGACCAACCA 60.818 55.000 0.00 0.00 42.04 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1175 2100 2.122413 CCCGATCCCTGATCCCCA 60.122 66.667 0.00 0.00 35.83 4.96 R
1818 2791 3.054878 GGCAAACAACAGAGAAGCAATG 58.945 45.455 0.00 0.00 0.00 2.82 R
2525 3499 3.403968 TCAGCACCGCACTAATTTTACA 58.596 40.909 0.00 0.00 0.00 2.41 R
3674 4679 2.658285 TGATGATGTGAAAGATGGCCC 58.342 47.619 0.00 0.00 0.00 5.80 R
4942 5954 1.973812 GCCCTGCTGTTTGGGTCTC 60.974 63.158 0.00 0.00 45.06 3.36 R
5615 6798 2.674796 AACCATCTCGTAAGTGAGGC 57.325 50.000 0.00 0.00 43.81 4.70 R
6306 7556 0.036010 AGCATACACCTGTCCAGCAC 60.036 55.000 0.00 0.00 0.00 4.40 R
7335 8674 0.027716 ACGACGACTCGGAATCATCG 59.972 55.000 3.27 3.27 44.80 3.84 R
7737 10661 0.465097 TCAAACCGGCGTAAAACCCA 60.465 50.000 6.01 0.00 0.00 4.51 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
154 159 5.941733 CAAGACAATCGTCATGGAAAATCA 58.058 37.500 0.00 0.00 45.23 2.57
174 179 0.389426 ATCACGAACCGGAAAGGACG 60.389 55.000 9.46 6.80 45.00 4.79
176 181 1.007336 CACGAACCGGAAAGGACGAG 61.007 60.000 9.46 0.00 45.00 4.18
207 212 1.451504 CCACCTGGCTCTCAACACA 59.548 57.895 0.00 0.00 0.00 3.72
213 218 0.108585 TGGCTCTCAACACAACCCTC 59.891 55.000 0.00 0.00 0.00 4.30
214 219 0.398318 GGCTCTCAACACAACCCTCT 59.602 55.000 0.00 0.00 0.00 3.69
248 253 0.025513 GCACGCTTCTGCTTGTATCG 59.974 55.000 0.00 0.00 40.11 2.92
271 276 3.197766 AGACCTCGGATTGTAGCATGAAA 59.802 43.478 0.00 0.00 0.00 2.69
278 283 4.273318 GGATTGTAGCATGAAACCTCCTT 58.727 43.478 0.00 0.00 0.00 3.36
298 303 6.487828 TCCTTGAGTGAATTGATGGAAGAAT 58.512 36.000 0.00 0.00 0.00 2.40
323 328 5.681337 GCAAAGAGCACCTAATATCTTCC 57.319 43.478 0.00 0.00 44.79 3.46
347 352 2.504367 CAGGTGTTAGTTGGGGACTTG 58.496 52.381 0.00 0.00 39.86 3.16
349 354 1.477923 GGTGTTAGTTGGGGACTTGCA 60.478 52.381 0.00 0.00 39.86 4.08
352 358 2.890311 TGTTAGTTGGGGACTTGCAATG 59.110 45.455 0.00 0.00 39.86 2.82
360 366 2.161609 GGGGACTTGCAATGTTAACTCG 59.838 50.000 7.22 0.00 0.00 4.18
363 369 3.119849 GGACTTGCAATGTTAACTCGCAT 60.120 43.478 14.84 4.77 31.67 4.73
382 388 8.505625 ACTCGCATAAACTATAGTAGAGCTTAC 58.494 37.037 5.65 0.00 0.00 2.34
383 389 8.618702 TCGCATAAACTATAGTAGAGCTTACT 57.381 34.615 5.65 11.59 0.00 2.24
407 440 6.749139 TCTCGTTTGGTTCATAGGATATGAG 58.251 40.000 0.24 0.00 0.00 2.90
471 513 9.113838 GAAAAAGAGATGTTATCTGAGGCATAA 57.886 33.333 0.00 0.00 40.38 1.90
478 858 8.484575 AGATGTTATCTGAGGCATAAGATATGG 58.515 37.037 6.27 0.00 38.44 2.74
485 868 8.627208 TCTGAGGCATAAGATATGGATTTTTC 57.373 34.615 0.04 0.00 0.00 2.29
497 880 2.491693 TGGATTTTTCCATTGAGTCGGC 59.508 45.455 0.00 0.00 34.33 5.54
499 882 3.428045 GGATTTTTCCATTGAGTCGGCTG 60.428 47.826 0.00 0.00 0.00 4.85
502 888 2.028420 TTCCATTGAGTCGGCTGATG 57.972 50.000 0.00 0.00 0.00 3.07
504 890 1.278985 TCCATTGAGTCGGCTGATGTT 59.721 47.619 0.00 0.00 0.00 2.71
507 893 3.057315 CCATTGAGTCGGCTGATGTTTTT 60.057 43.478 0.00 0.00 0.00 1.94
579 965 7.115414 AGAATTCATTCTTAGGAACCAAGAGG 58.885 38.462 8.44 0.00 44.28 3.69
582 968 5.094387 TCATTCTTAGGAACCAAGAGGACT 58.906 41.667 0.00 0.00 38.69 3.85
585 971 7.236847 TCATTCTTAGGAACCAAGAGGACTAAA 59.763 37.037 0.00 0.00 38.69 1.85
586 972 7.383156 TTCTTAGGAACCAAGAGGACTAAAA 57.617 36.000 0.00 0.00 38.69 1.52
587 973 7.569599 TCTTAGGAACCAAGAGGACTAAAAT 57.430 36.000 0.00 0.00 38.69 1.82
590 991 9.734984 CTTAGGAACCAAGAGGACTAAAATAAA 57.265 33.333 0.00 0.00 38.69 1.40
593 994 9.244292 AGGAACCAAGAGGACTAAAATAAATTC 57.756 33.333 0.00 0.00 38.69 2.17
595 996 9.244292 GAACCAAGAGGACTAAAATAAATTCCT 57.756 33.333 0.00 0.00 39.51 3.36
637 1046 9.778741 AATTCATGTAAACTCTTCTTACTCACA 57.221 29.630 0.00 0.00 31.73 3.58
638 1047 9.778741 ATTCATGTAAACTCTTCTTACTCACAA 57.221 29.630 0.00 0.00 31.73 3.33
639 1048 9.607988 TTCATGTAAACTCTTCTTACTCACAAA 57.392 29.630 0.00 0.00 31.73 2.83
640 1049 9.778741 TCATGTAAACTCTTCTTACTCACAAAT 57.221 29.630 0.00 0.00 31.73 2.32
643 1052 9.391006 TGTAAACTCTTCTTACTCACAAATTGT 57.609 29.630 0.00 0.00 31.73 2.71
695 1156 2.203001 TGCACCACCACGTCACTG 60.203 61.111 0.00 0.00 0.00 3.66
708 1169 1.066752 TCACTGGACCAACGTGTCG 59.933 57.895 12.29 0.00 36.07 4.35
737 1198 4.715130 CCTCCCCCGTCCACCTCA 62.715 72.222 0.00 0.00 0.00 3.86
1175 2100 3.400599 CTAGGCCCGCCGAAATGGT 62.401 63.158 0.00 0.00 41.95 3.55
1200 2125 1.598130 CAGGGATCGGGAATTCGGC 60.598 63.158 0.00 0.00 0.00 5.54
1315 2241 1.212751 GCAAATGGACGAGGTTGGC 59.787 57.895 0.00 0.00 0.00 4.52
1352 2278 0.179084 CCGGCTTCCATCGAGCTTAA 60.179 55.000 0.00 0.00 40.01 1.85
1355 2281 2.546795 CGGCTTCCATCGAGCTTAAGAT 60.547 50.000 6.67 0.00 40.01 2.40
1393 2319 4.261825 GCCACAACTCCTAGCTAGATAGTG 60.262 50.000 22.70 19.29 0.00 2.74
1415 2341 5.009631 TGCAATTTTCCTATATATGCCGCT 58.990 37.500 0.00 0.00 0.00 5.52
1417 2343 6.316140 TGCAATTTTCCTATATATGCCGCTAG 59.684 38.462 0.00 0.00 0.00 3.42
1419 2345 7.148239 GCAATTTTCCTATATATGCCGCTAGTT 60.148 37.037 0.00 0.00 0.00 2.24
1421 2347 6.599356 TTTCCTATATATGCCGCTAGTTCA 57.401 37.500 0.00 0.00 0.00 3.18
1778 2746 7.633621 AGATATTGAAATGCATGTAAGTCACG 58.366 34.615 0.00 0.00 0.00 4.35
2401 3375 0.253044 TAGCTTGGACATGGAGGCAC 59.747 55.000 0.00 0.00 0.00 5.01
2431 3405 6.922957 ACAAATTTTGTCGCATATTTGTCACT 59.077 30.769 8.97 5.94 43.81 3.41
2887 3885 5.163405 TGAGTATCTTCCACCTGATGCTAAC 60.163 44.000 0.00 0.00 36.15 2.34
2979 3977 5.045942 TCCATCTGACAGCATTACAGGTTTA 60.046 40.000 0.00 0.00 33.19 2.01
3184 4182 4.415596 ACCCATAGATCTGTGATCTCTCC 58.584 47.826 20.07 0.00 0.00 3.71
3405 4403 4.627467 GTGGTGAGTTATGTGCAGTTCTAG 59.373 45.833 0.00 0.00 0.00 2.43
3498 4496 2.301583 GCCAAGTCCAGAGAAGTCTTCT 59.698 50.000 15.14 15.14 44.21 2.85
3548 4546 4.842574 TGCAACATAGTCCAAAGAGCATA 58.157 39.130 0.00 0.00 0.00 3.14
3656 4654 6.347888 GCTTATGCGGTAGTTTTTGTTCAGTA 60.348 38.462 0.00 0.00 0.00 2.74
3674 4679 7.822334 TGTTCAGTATACCAGTATCAAACTTGG 59.178 37.037 0.00 0.00 35.76 3.61
3821 4826 4.460382 AGTTCATGGCCATGTCTAGTTTTG 59.540 41.667 38.18 16.53 39.72 2.44
3855 4860 0.461548 CTCCGGTGCTTGCTGAGATA 59.538 55.000 0.00 0.00 0.00 1.98
4120 5131 4.569966 GCAATGTGAGTACTGGAATCTCTG 59.430 45.833 0.00 0.00 0.00 3.35
4153 5164 8.780249 TCTCATGCATAATCTTTGTGATATGTG 58.220 33.333 0.00 0.00 34.45 3.21
4490 5502 4.657814 AGGGAAAAACAGAGAAGGCATA 57.342 40.909 0.00 0.00 0.00 3.14
4491 5503 5.198602 AGGGAAAAACAGAGAAGGCATAT 57.801 39.130 0.00 0.00 0.00 1.78
4492 5504 5.583932 AGGGAAAAACAGAGAAGGCATATT 58.416 37.500 0.00 0.00 0.00 1.28
4493 5505 6.019108 AGGGAAAAACAGAGAAGGCATATTT 58.981 36.000 0.00 0.00 0.00 1.40
4494 5506 6.071165 AGGGAAAAACAGAGAAGGCATATTTG 60.071 38.462 0.00 0.00 0.00 2.32
4495 5507 6.071391 GGGAAAAACAGAGAAGGCATATTTGA 60.071 38.462 0.00 0.00 0.00 2.69
4496 5508 7.378181 GGAAAAACAGAGAAGGCATATTTGAA 58.622 34.615 0.00 0.00 0.00 2.69
4497 5509 8.037166 GGAAAAACAGAGAAGGCATATTTGAAT 58.963 33.333 0.00 0.00 0.00 2.57
4498 5510 8.992835 AAAAACAGAGAAGGCATATTTGAATC 57.007 30.769 0.00 0.00 0.00 2.52
4499 5511 7.951347 AAACAGAGAAGGCATATTTGAATCT 57.049 32.000 0.00 0.00 0.00 2.40
4500 5512 7.565323 AACAGAGAAGGCATATTTGAATCTC 57.435 36.000 0.00 0.00 32.20 2.75
4501 5513 6.897986 ACAGAGAAGGCATATTTGAATCTCT 58.102 36.000 8.78 8.78 37.78 3.10
4502 5514 6.766944 ACAGAGAAGGCATATTTGAATCTCTG 59.233 38.462 24.58 24.58 46.86 3.35
4503 5515 6.990939 CAGAGAAGGCATATTTGAATCTCTGA 59.009 38.462 23.34 0.00 45.87 3.27
4504 5516 7.498239 CAGAGAAGGCATATTTGAATCTCTGAA 59.502 37.037 23.34 0.00 45.87 3.02
4505 5517 7.498570 AGAGAAGGCATATTTGAATCTCTGAAC 59.501 37.037 11.91 0.00 36.83 3.18
4506 5518 7.344913 AGAAGGCATATTTGAATCTCTGAACT 58.655 34.615 0.00 0.00 0.00 3.01
4507 5519 6.939132 AGGCATATTTGAATCTCTGAACTG 57.061 37.500 0.00 0.00 0.00 3.16
4508 5520 6.656902 AGGCATATTTGAATCTCTGAACTGA 58.343 36.000 0.00 0.00 0.00 3.41
4509 5521 7.114754 AGGCATATTTGAATCTCTGAACTGAA 58.885 34.615 0.00 0.00 0.00 3.02
4510 5522 7.282675 AGGCATATTTGAATCTCTGAACTGAAG 59.717 37.037 0.00 0.00 0.00 3.02
4511 5523 6.911511 GCATATTTGAATCTCTGAACTGAAGC 59.088 38.462 0.00 0.00 0.00 3.86
4512 5524 4.997905 TTTGAATCTCTGAACTGAAGCG 57.002 40.909 0.00 0.00 0.00 4.68
4513 5525 2.341257 TGAATCTCTGAACTGAAGCGC 58.659 47.619 0.00 0.00 0.00 5.92
4514 5526 2.028658 TGAATCTCTGAACTGAAGCGCT 60.029 45.455 2.64 2.64 0.00 5.92
4515 5527 2.758736 ATCTCTGAACTGAAGCGCTT 57.241 45.000 25.35 25.35 0.00 4.68
4516 5528 3.876274 ATCTCTGAACTGAAGCGCTTA 57.124 42.857 25.11 10.69 0.00 3.09
4517 5529 3.223423 TCTCTGAACTGAAGCGCTTAG 57.777 47.619 25.11 21.13 0.00 2.18
4518 5530 2.558795 TCTCTGAACTGAAGCGCTTAGT 59.441 45.455 25.11 21.76 0.00 2.24
4519 5531 3.005897 TCTCTGAACTGAAGCGCTTAGTT 59.994 43.478 28.91 28.91 37.36 2.24
4520 5532 3.059884 TCTGAACTGAAGCGCTTAGTTG 58.940 45.455 31.41 23.23 34.99 3.16
4521 5533 2.143122 TGAACTGAAGCGCTTAGTTGG 58.857 47.619 31.41 20.14 34.99 3.77
4522 5534 2.224185 TGAACTGAAGCGCTTAGTTGGA 60.224 45.455 31.41 21.48 34.99 3.53
4523 5535 2.770164 ACTGAAGCGCTTAGTTGGAT 57.230 45.000 25.11 0.00 0.00 3.41
4524 5536 3.059352 ACTGAAGCGCTTAGTTGGATT 57.941 42.857 25.11 0.00 0.00 3.01
4525 5537 4.202245 ACTGAAGCGCTTAGTTGGATTA 57.798 40.909 25.11 0.00 0.00 1.75
4526 5538 4.770795 ACTGAAGCGCTTAGTTGGATTAT 58.229 39.130 25.11 0.00 0.00 1.28
4527 5539 5.186198 ACTGAAGCGCTTAGTTGGATTATT 58.814 37.500 25.11 0.00 0.00 1.40
4528 5540 6.346096 ACTGAAGCGCTTAGTTGGATTATTA 58.654 36.000 25.11 0.00 0.00 0.98
4529 5541 6.258068 ACTGAAGCGCTTAGTTGGATTATTAC 59.742 38.462 25.11 5.67 0.00 1.89
4530 5542 6.346096 TGAAGCGCTTAGTTGGATTATTACT 58.654 36.000 25.11 0.00 0.00 2.24
4531 5543 6.257849 TGAAGCGCTTAGTTGGATTATTACTG 59.742 38.462 25.11 0.00 0.00 2.74
4532 5544 5.057149 AGCGCTTAGTTGGATTATTACTGG 58.943 41.667 2.64 0.00 0.00 4.00
4533 5545 4.814771 GCGCTTAGTTGGATTATTACTGGT 59.185 41.667 0.00 0.00 0.00 4.00
4534 5546 5.296035 GCGCTTAGTTGGATTATTACTGGTT 59.704 40.000 0.00 0.00 0.00 3.67
4535 5547 6.183360 GCGCTTAGTTGGATTATTACTGGTTT 60.183 38.462 0.00 0.00 0.00 3.27
4536 5548 7.011669 GCGCTTAGTTGGATTATTACTGGTTTA 59.988 37.037 0.00 0.00 0.00 2.01
4537 5549 8.333186 CGCTTAGTTGGATTATTACTGGTTTAC 58.667 37.037 0.00 0.00 0.00 2.01
4538 5550 9.392259 GCTTAGTTGGATTATTACTGGTTTACT 57.608 33.333 0.00 0.00 0.00 2.24
4571 5583 9.618890 TTTTTCTCAATTAGATGGGACTGATAG 57.381 33.333 0.00 0.00 33.05 2.08
4572 5584 8.553085 TTTCTCAATTAGATGGGACTGATAGA 57.447 34.615 0.00 0.00 33.05 1.98
4573 5585 8.553085 TTCTCAATTAGATGGGACTGATAGAA 57.447 34.615 0.00 0.00 33.05 2.10
4574 5586 8.187913 TCTCAATTAGATGGGACTGATAGAAG 57.812 38.462 0.00 0.00 0.00 2.85
4575 5587 7.786943 TCTCAATTAGATGGGACTGATAGAAGT 59.213 37.037 0.00 0.00 0.00 3.01
4576 5588 9.083422 CTCAATTAGATGGGACTGATAGAAGTA 57.917 37.037 0.00 0.00 0.00 2.24
4577 5589 8.861086 TCAATTAGATGGGACTGATAGAAGTAC 58.139 37.037 0.00 0.00 0.00 2.73
4578 5590 8.865090 CAATTAGATGGGACTGATAGAAGTACT 58.135 37.037 0.00 0.00 31.08 2.73
4581 5593 9.931698 TTAGATGGGACTGATAGAAGTACTAAA 57.068 33.333 0.00 0.00 34.56 1.85
4583 5595 9.440761 AGATGGGACTGATAGAAGTACTAAATT 57.559 33.333 0.00 0.00 34.56 1.82
4584 5596 9.482627 GATGGGACTGATAGAAGTACTAAATTG 57.517 37.037 0.00 0.00 34.56 2.32
4585 5597 8.603898 TGGGACTGATAGAAGTACTAAATTGA 57.396 34.615 0.00 0.00 34.56 2.57
4586 5598 9.213777 TGGGACTGATAGAAGTACTAAATTGAT 57.786 33.333 0.00 0.00 34.56 2.57
4611 5623 8.876275 TTGAAAGAGACAAATGAAATGAAAGG 57.124 30.769 0.00 0.00 0.00 3.11
4612 5624 7.436118 TGAAAGAGACAAATGAAATGAAAGGG 58.564 34.615 0.00 0.00 0.00 3.95
4613 5625 7.287466 TGAAAGAGACAAATGAAATGAAAGGGA 59.713 33.333 0.00 0.00 0.00 4.20
4614 5626 7.601705 AAGAGACAAATGAAATGAAAGGGAA 57.398 32.000 0.00 0.00 0.00 3.97
4615 5627 7.601705 AGAGACAAATGAAATGAAAGGGAAA 57.398 32.000 0.00 0.00 0.00 3.13
4616 5628 8.021898 AGAGACAAATGAAATGAAAGGGAAAA 57.978 30.769 0.00 0.00 0.00 2.29
4617 5629 8.485392 AGAGACAAATGAAATGAAAGGGAAAAA 58.515 29.630 0.00 0.00 0.00 1.94
4618 5630 8.437360 AGACAAATGAAATGAAAGGGAAAAAC 57.563 30.769 0.00 0.00 0.00 2.43
4619 5631 8.046107 AGACAAATGAAATGAAAGGGAAAAACA 58.954 29.630 0.00 0.00 0.00 2.83
4620 5632 8.212317 ACAAATGAAATGAAAGGGAAAAACAG 57.788 30.769 0.00 0.00 0.00 3.16
4621 5633 8.046107 ACAAATGAAATGAAAGGGAAAAACAGA 58.954 29.630 0.00 0.00 0.00 3.41
4622 5634 8.553696 CAAATGAAATGAAAGGGAAAAACAGAG 58.446 33.333 0.00 0.00 0.00 3.35
4623 5635 7.601705 ATGAAATGAAAGGGAAAAACAGAGA 57.398 32.000 0.00 0.00 0.00 3.10
4624 5636 7.416964 TGAAATGAAAGGGAAAAACAGAGAA 57.583 32.000 0.00 0.00 0.00 2.87
4625 5637 7.491682 TGAAATGAAAGGGAAAAACAGAGAAG 58.508 34.615 0.00 0.00 0.00 2.85
4626 5638 6.410942 AATGAAAGGGAAAAACAGAGAAGG 57.589 37.500 0.00 0.00 0.00 3.46
4627 5639 3.636764 TGAAAGGGAAAAACAGAGAAGGC 59.363 43.478 0.00 0.00 0.00 4.35
4942 5954 3.801698 AGAATCACAGATGGAATGGTCG 58.198 45.455 0.00 0.00 0.00 4.79
5044 6056 3.034635 TGGTGGTGGCAATAACAAAAGT 58.965 40.909 0.00 0.00 0.00 2.66
5095 6107 1.134367 CATTCCGGCTCTTCTCGTACA 59.866 52.381 0.00 0.00 0.00 2.90
5615 6798 2.610232 GGTATTGGCTTGCAACTTGGTG 60.610 50.000 0.00 0.00 0.00 4.17
5663 6846 7.756272 TCACATTATGTTGAGAAATCACAATGC 59.244 33.333 0.00 0.00 0.00 3.56
5671 6854 6.198650 TGAGAAATCACAATGCCACATAAG 57.801 37.500 0.00 0.00 0.00 1.73
5732 6942 1.269936 GCAATGGCTCAAGCACTTGTT 60.270 47.619 10.05 0.00 44.36 2.83
6051 7301 3.335579 GGTTGTTAGCACTGTAGAAGGG 58.664 50.000 0.00 0.00 0.00 3.95
6376 7626 0.817634 CGAGCACAAAGGACCAACCA 60.818 55.000 0.00 0.00 42.04 3.67
6388 7638 2.633488 GACCAACCAACCTCAGATAGC 58.367 52.381 0.00 0.00 0.00 2.97
6556 7806 5.758570 GCAGAAAGCATTTGTTGAATCTC 57.241 39.130 0.00 0.00 39.27 2.75
6683 7935 6.633500 TTTGGAAGATGTACTTGAAACTGG 57.367 37.500 0.00 0.00 39.13 4.00
6860 8112 1.310933 AAGCAGAGGCCAGAAATGCG 61.311 55.000 5.01 0.00 41.69 4.73
6938 8274 2.925563 ACGTACGGCATAGTTAGTTTGC 59.074 45.455 21.06 0.00 35.64 3.68
7087 8426 5.364778 TGCGCATCTATGTATGTAAAACCT 58.635 37.500 5.66 0.00 0.00 3.50
7335 8674 2.979649 GGAACCCCTCCAGACGAC 59.020 66.667 0.00 0.00 44.67 4.34
7416 8755 7.456902 TCTCCTTCTTTACCCCCATACATATAC 59.543 40.741 0.00 0.00 0.00 1.47
7417 8756 7.318401 TCCTTCTTTACCCCCATACATATACT 58.682 38.462 0.00 0.00 0.00 2.12
7418 8757 8.466797 TCCTTCTTTACCCCCATACATATACTA 58.533 37.037 0.00 0.00 0.00 1.82
7419 8758 9.280456 CCTTCTTTACCCCCATACATATACTAT 57.720 37.037 0.00 0.00 0.00 2.12
7591 8959 2.483877 GTGTGTTTCCTTGCGATGATCA 59.516 45.455 0.00 0.00 0.00 2.92
7593 8961 3.758023 TGTGTTTCCTTGCGATGATCAAT 59.242 39.130 0.00 0.00 0.00 2.57
7609 8977 8.654215 CGATGATCAATCATTAGTTATCTGGTG 58.346 37.037 0.00 0.00 46.84 4.17
7657 9025 4.109050 GTGTTTCCGCACAAAATTCTCAA 58.891 39.130 0.00 0.00 39.07 3.02
7658 9026 4.026886 GTGTTTCCGCACAAAATTCTCAAC 60.027 41.667 0.00 0.00 39.07 3.18
7663 9031 2.032030 CGCACAAAATTCTCAACGGTCT 60.032 45.455 0.00 0.00 0.00 3.85
7705 10629 1.045911 GGAGACTGGCAGGTAGGAGG 61.046 65.000 20.34 0.00 0.00 4.30
7737 10661 2.159707 CGGATGACGTGCGAAATCTTTT 60.160 45.455 1.86 0.00 45.38 2.27
7746 10670 4.147479 CGTGCGAAATCTTTTGGGTTTTAC 59.853 41.667 0.00 0.00 0.00 2.01
7764 10688 1.652930 CGCCGGTTTGAAACGTGTG 60.653 57.895 1.90 0.00 0.00 3.82
7765 10689 1.942223 GCCGGTTTGAAACGTGTGC 60.942 57.895 1.90 0.00 0.00 4.57
7777 10704 2.728690 ACGTGTGCTAACCATTACGA 57.271 45.000 0.00 0.00 39.00 3.43
7791 10718 5.844004 ACCATTACGACAACATATCTCCTC 58.156 41.667 0.00 0.00 0.00 3.71
7792 10719 5.598830 ACCATTACGACAACATATCTCCTCT 59.401 40.000 0.00 0.00 0.00 3.69
7793 10720 6.098409 ACCATTACGACAACATATCTCCTCTT 59.902 38.462 0.00 0.00 0.00 2.85
7794 10721 6.986817 CCATTACGACAACATATCTCCTCTTT 59.013 38.462 0.00 0.00 0.00 2.52
7795 10722 7.495934 CCATTACGACAACATATCTCCTCTTTT 59.504 37.037 0.00 0.00 0.00 2.27
7880 10807 9.787532 AACATGTATTTTACCAAATCAATCTCG 57.212 29.630 0.00 0.00 34.29 4.04
7934 10861 7.556275 AGAGTGTTCAGTTGGTATCAAGAAAAA 59.444 33.333 0.00 0.00 32.92 1.94
7959 10886 8.771521 ATGTTCATCCCATATCAAGAAATTGA 57.228 30.769 0.00 0.00 35.15 2.57
8324 11254 9.617975 GCTTTTTATAATATGACATGAGCCTTC 57.382 33.333 0.00 0.00 0.00 3.46
8338 11268 8.353423 ACATGAGCCTTCTTTAAATACACAAT 57.647 30.769 0.00 0.00 0.00 2.71
8350 11280 9.680315 CTTTAAATACACAATAACGTTTTGGGA 57.320 29.630 23.23 12.34 31.81 4.37
8352 11282 9.680315 TTAAATACACAATAACGTTTTGGGAAG 57.320 29.630 23.23 13.92 31.81 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.685097 GATGGGTCGGCCTGCTATTA 59.315 55.000 5.77 0.00 34.45 0.98
13 14 2.069273 CTTATTCGATGATGGGTCGGC 58.931 52.381 0.00 0.00 39.45 5.54
54 58 4.530161 ACTCTGGTGTTGCTTCTTCTATCT 59.470 41.667 0.00 0.00 0.00 1.98
55 59 4.629200 CACTCTGGTGTTGCTTCTTCTATC 59.371 45.833 0.00 0.00 38.54 2.08
154 159 1.804601 GTCCTTTCCGGTTCGTGATT 58.195 50.000 0.00 0.00 0.00 2.57
174 179 1.570024 AGGTGGGAGTAGGTAGTCCTC 59.430 57.143 10.17 5.00 43.79 3.71
176 181 1.688627 CCAGGTGGGAGTAGGTAGTCC 60.689 61.905 2.57 2.57 43.62 3.85
207 212 1.730851 AACGGGAAGAAGAGAGGGTT 58.269 50.000 0.00 0.00 0.00 4.11
213 218 2.688364 GTGCAAAACGGGAAGAAGAG 57.312 50.000 0.00 0.00 0.00 2.85
248 253 2.362397 TCATGCTACAATCCGAGGTCTC 59.638 50.000 0.00 0.00 0.00 3.36
256 261 3.891049 AGGAGGTTTCATGCTACAATCC 58.109 45.455 10.15 10.15 0.00 3.01
264 269 2.783135 TCACTCAAGGAGGTTTCATGC 58.217 47.619 0.00 0.00 33.35 4.06
271 276 3.588842 TCCATCAATTCACTCAAGGAGGT 59.411 43.478 0.00 0.00 33.35 3.85
278 283 6.885918 TGCTAATTCTTCCATCAATTCACTCA 59.114 34.615 0.00 0.00 0.00 3.41
298 303 6.992715 GGAAGATATTAGGTGCTCTTTGCTAA 59.007 38.462 0.00 0.00 43.37 3.09
316 321 2.829720 ACTAACACCTGCGTGGAAGATA 59.170 45.455 2.38 0.00 44.86 1.98
323 328 1.234615 CCCCAACTAACACCTGCGTG 61.235 60.000 0.00 0.00 46.11 5.34
347 352 8.548721 ACTATAGTTTATGCGAGTTAACATTGC 58.451 33.333 8.61 8.89 0.00 3.56
352 358 9.116054 GCTCTACTATAGTTTATGCGAGTTAAC 57.884 37.037 11.40 0.00 0.00 2.01
382 388 6.749139 TCATATCCTATGAACCAAACGAGAG 58.251 40.000 0.00 0.00 0.00 3.20
383 389 6.323996 ACTCATATCCTATGAACCAAACGAGA 59.676 38.462 0.00 0.00 0.00 4.04
451 493 9.531942 CATATCTTATGCCTCAGATAACATCTC 57.468 37.037 0.00 0.00 37.58 2.75
453 495 8.481314 TCCATATCTTATGCCTCAGATAACATC 58.519 37.037 0.00 0.00 35.96 3.06
461 503 7.449395 TGGAAAAATCCATATCTTATGCCTCAG 59.551 37.037 0.00 0.00 34.33 3.35
478 858 3.440173 TCAGCCGACTCAATGGAAAAATC 59.560 43.478 0.00 0.00 0.00 2.17
485 868 1.742761 AACATCAGCCGACTCAATGG 58.257 50.000 0.00 0.00 0.00 3.16
555 941 7.066404 GTCCTCTTGGTTCCTAAGAATGAATTC 59.934 40.741 0.00 0.00 34.07 2.17
557 943 6.216456 AGTCCTCTTGGTTCCTAAGAATGAAT 59.784 38.462 0.00 0.00 34.07 2.57
559 945 5.094387 AGTCCTCTTGGTTCCTAAGAATGA 58.906 41.667 0.00 0.00 34.07 2.57
560 946 5.428184 AGTCCTCTTGGTTCCTAAGAATG 57.572 43.478 0.00 0.00 34.07 2.67
562 948 7.383156 TTTTAGTCCTCTTGGTTCCTAAGAA 57.617 36.000 0.00 0.00 34.07 2.52
563 949 7.569599 ATTTTAGTCCTCTTGGTTCCTAAGA 57.430 36.000 0.00 0.00 33.44 2.10
564 950 9.734984 TTTATTTTAGTCCTCTTGGTTCCTAAG 57.265 33.333 0.00 0.00 34.23 2.18
568 954 8.467598 GGAATTTATTTTAGTCCTCTTGGTTCC 58.532 37.037 0.00 0.00 34.23 3.62
569 955 9.244292 AGGAATTTATTTTAGTCCTCTTGGTTC 57.756 33.333 0.00 0.00 33.26 3.62
571 957 9.601810 AAAGGAATTTATTTTAGTCCTCTTGGT 57.398 29.630 0.00 0.00 37.75 3.67
637 1046 0.586319 CGCTCCGTGTCACACAATTT 59.414 50.000 9.06 0.00 33.40 1.82
638 1047 0.249699 TCGCTCCGTGTCACACAATT 60.250 50.000 9.06 0.00 33.40 2.32
639 1048 0.667487 CTCGCTCCGTGTCACACAAT 60.667 55.000 9.06 0.00 33.40 2.71
640 1049 1.299850 CTCGCTCCGTGTCACACAA 60.300 57.895 9.06 0.00 33.40 3.33
642 1051 3.106407 GCTCGCTCCGTGTCACAC 61.106 66.667 0.00 0.00 0.00 3.82
643 1052 3.145422 TTGCTCGCTCCGTGTCACA 62.145 57.895 3.42 0.00 0.00 3.58
644 1053 2.355837 TTGCTCGCTCCGTGTCAC 60.356 61.111 0.00 0.00 0.00 3.67
645 1054 2.049156 CTTGCTCGCTCCGTGTCA 60.049 61.111 0.00 0.00 0.00 3.58
646 1055 3.482783 GCTTGCTCGCTCCGTGTC 61.483 66.667 0.00 0.00 0.00 3.67
647 1056 3.807631 TTGCTTGCTCGCTCCGTGT 62.808 57.895 0.00 0.00 0.00 4.49
648 1057 3.043713 TTGCTTGCTCGCTCCGTG 61.044 61.111 0.00 0.00 0.00 4.94
649 1058 3.044305 GTTGCTTGCTCGCTCCGT 61.044 61.111 0.00 0.00 0.00 4.69
650 1059 3.793144 GGTTGCTTGCTCGCTCCG 61.793 66.667 0.00 0.00 0.00 4.63
737 1198 4.382320 TCCTTTAACGCGGCCGCT 62.382 61.111 43.60 30.70 39.32 5.52
907 1374 4.143333 GGCTAGGGTTCGCTGCGA 62.143 66.667 22.24 22.24 0.00 5.10
1077 2002 4.467084 GAGATGGCGGCGGTGGAA 62.467 66.667 9.78 0.00 0.00 3.53
1175 2100 2.122413 CCCGATCCCTGATCCCCA 60.122 66.667 0.00 0.00 35.83 4.96
1200 2125 2.262915 GAGGTCAGTCGCCACCAG 59.737 66.667 0.00 0.00 34.80 4.00
1327 2253 2.721167 CGATGGAAGCCGGGAGTCA 61.721 63.158 2.18 0.00 0.00 3.41
1373 2299 4.537751 TGCACTATCTAGCTAGGAGTTGT 58.462 43.478 20.58 10.90 0.00 3.32
1393 2319 5.567138 AGCGGCATATATAGGAAAATTGC 57.433 39.130 1.45 0.00 0.00 3.56
1415 2341 4.825085 CCAAAAGGCCAAACTAGTGAACTA 59.175 41.667 5.01 0.00 0.00 2.24
1417 2343 3.634910 TCCAAAAGGCCAAACTAGTGAAC 59.365 43.478 5.01 0.00 0.00 3.18
1419 2345 3.586470 TCCAAAAGGCCAAACTAGTGA 57.414 42.857 5.01 0.00 0.00 3.41
1421 2347 3.637769 TGTTCCAAAAGGCCAAACTAGT 58.362 40.909 5.01 0.00 0.00 2.57
1450 2386 5.658634 TCACTGGGCATCTATCTATATGGAC 59.341 44.000 0.00 0.00 0.00 4.02
1818 2791 3.054878 GGCAAACAACAGAGAAGCAATG 58.945 45.455 0.00 0.00 0.00 2.82
2401 3375 5.990745 ATATGCGACAAAATTTGTTCGTG 57.009 34.783 21.74 11.91 45.52 4.35
2525 3499 3.403968 TCAGCACCGCACTAATTTTACA 58.596 40.909 0.00 0.00 0.00 2.41
2857 3855 5.211973 TCAGGTGGAAGATACTCATTAGCT 58.788 41.667 0.00 0.00 0.00 3.32
2979 3977 5.880332 TGCAGACTGAAAAGTGACTTTTAGT 59.120 36.000 21.90 21.70 42.72 2.24
3174 4172 8.815565 TGATATAATAGGACAGGAGAGATCAC 57.184 38.462 0.00 0.00 0.00 3.06
3405 4403 5.948992 AGTTCATAGTTGCCAGAGAAAAC 57.051 39.130 0.00 0.00 0.00 2.43
3548 4546 6.716628 TGTTTCATAATTCCAAAGCTGAGAGT 59.283 34.615 0.00 0.00 0.00 3.24
3656 4654 3.372675 GGCCCCAAGTTTGATACTGGTAT 60.373 47.826 0.00 0.00 37.12 2.73
3674 4679 2.658285 TGATGATGTGAAAGATGGCCC 58.342 47.619 0.00 0.00 0.00 5.80
3733 4738 7.473511 GCCCTCACTTAGTATCATAAATGGACT 60.474 40.741 0.00 4.55 0.00 3.85
3821 4826 4.165779 CACCGGAGAATTATTGCAACAAC 58.834 43.478 9.46 0.00 0.00 3.32
3855 4860 5.654650 TCATTCACTTAAGGGTGTTTGTGTT 59.345 36.000 4.27 0.00 38.28 3.32
4120 5131 8.710551 CACAAAGATTATGCATGAGAGATCTAC 58.289 37.037 10.16 0.00 0.00 2.59
4153 5164 3.981211 ACAATGTCACCAAATGAACAGC 58.019 40.909 0.00 0.00 39.72 4.40
4286 5298 4.908601 TGGAGCATCTCACTAGGAAAAA 57.091 40.909 0.00 0.00 33.73 1.94
4490 5502 4.142730 GCGCTTCAGTTCAGAGATTCAAAT 60.143 41.667 0.00 0.00 0.00 2.32
4491 5503 3.187227 GCGCTTCAGTTCAGAGATTCAAA 59.813 43.478 0.00 0.00 0.00 2.69
4492 5504 2.738846 GCGCTTCAGTTCAGAGATTCAA 59.261 45.455 0.00 0.00 0.00 2.69
4493 5505 2.028658 AGCGCTTCAGTTCAGAGATTCA 60.029 45.455 2.64 0.00 0.00 2.57
4494 5506 2.615869 AGCGCTTCAGTTCAGAGATTC 58.384 47.619 2.64 0.00 0.00 2.52
4495 5507 2.758736 AGCGCTTCAGTTCAGAGATT 57.241 45.000 2.64 0.00 0.00 2.40
4496 5508 2.758736 AAGCGCTTCAGTTCAGAGAT 57.241 45.000 18.98 0.00 0.00 2.75
4497 5509 2.558795 ACTAAGCGCTTCAGTTCAGAGA 59.441 45.455 28.82 3.55 0.00 3.10
4498 5510 2.953020 ACTAAGCGCTTCAGTTCAGAG 58.047 47.619 28.82 17.89 0.00 3.35
4499 5511 3.059884 CAACTAAGCGCTTCAGTTCAGA 58.940 45.455 28.82 5.23 30.20 3.27
4500 5512 2.158449 CCAACTAAGCGCTTCAGTTCAG 59.842 50.000 28.82 19.43 30.20 3.02
4501 5513 2.143122 CCAACTAAGCGCTTCAGTTCA 58.857 47.619 28.82 6.93 30.20 3.18
4502 5514 2.413837 TCCAACTAAGCGCTTCAGTTC 58.586 47.619 28.82 0.00 30.20 3.01
4503 5515 2.543777 TCCAACTAAGCGCTTCAGTT 57.456 45.000 28.82 26.84 32.82 3.16
4504 5516 2.770164 ATCCAACTAAGCGCTTCAGT 57.230 45.000 28.82 23.12 0.00 3.41
4505 5517 5.741388 AATAATCCAACTAAGCGCTTCAG 57.259 39.130 28.82 22.49 0.00 3.02
4506 5518 6.257849 CAGTAATAATCCAACTAAGCGCTTCA 59.742 38.462 28.82 12.24 0.00 3.02
4507 5519 6.292919 CCAGTAATAATCCAACTAAGCGCTTC 60.293 42.308 28.82 6.77 0.00 3.86
4508 5520 5.527582 CCAGTAATAATCCAACTAAGCGCTT 59.472 40.000 27.97 27.97 0.00 4.68
4509 5521 5.057149 CCAGTAATAATCCAACTAAGCGCT 58.943 41.667 2.64 2.64 0.00 5.92
4510 5522 4.814771 ACCAGTAATAATCCAACTAAGCGC 59.185 41.667 0.00 0.00 0.00 5.92
4511 5523 6.920569 AACCAGTAATAATCCAACTAAGCG 57.079 37.500 0.00 0.00 0.00 4.68
4512 5524 9.392259 AGTAAACCAGTAATAATCCAACTAAGC 57.608 33.333 0.00 0.00 0.00 3.09
4545 5557 9.618890 CTATCAGTCCCATCTAATTGAGAAAAA 57.381 33.333 0.00 0.00 37.85 1.94
4546 5558 8.992349 TCTATCAGTCCCATCTAATTGAGAAAA 58.008 33.333 0.00 0.00 37.85 2.29
4547 5559 8.553085 TCTATCAGTCCCATCTAATTGAGAAA 57.447 34.615 0.00 0.00 37.85 2.52
4548 5560 8.553085 TTCTATCAGTCCCATCTAATTGAGAA 57.447 34.615 0.00 0.00 37.85 2.87
4549 5561 7.786943 ACTTCTATCAGTCCCATCTAATTGAGA 59.213 37.037 0.00 0.00 39.01 3.27
4550 5562 7.961351 ACTTCTATCAGTCCCATCTAATTGAG 58.039 38.462 0.00 0.00 0.00 3.02
4551 5563 7.921041 ACTTCTATCAGTCCCATCTAATTGA 57.079 36.000 0.00 0.00 0.00 2.57
4552 5564 8.865090 AGTACTTCTATCAGTCCCATCTAATTG 58.135 37.037 0.00 0.00 0.00 2.32
4555 5567 9.931698 TTTAGTACTTCTATCAGTCCCATCTAA 57.068 33.333 0.00 0.00 0.00 2.10
4557 5569 9.440761 AATTTAGTACTTCTATCAGTCCCATCT 57.559 33.333 0.00 0.00 0.00 2.90
4558 5570 9.482627 CAATTTAGTACTTCTATCAGTCCCATC 57.517 37.037 0.00 0.00 0.00 3.51
4559 5571 9.213777 TCAATTTAGTACTTCTATCAGTCCCAT 57.786 33.333 0.00 0.00 0.00 4.00
4560 5572 8.603898 TCAATTTAGTACTTCTATCAGTCCCA 57.396 34.615 0.00 0.00 0.00 4.37
4585 5597 9.485206 CCTTTCATTTCATTTGTCTCTTTCAAT 57.515 29.630 0.00 0.00 0.00 2.57
4586 5598 7.927629 CCCTTTCATTTCATTTGTCTCTTTCAA 59.072 33.333 0.00 0.00 0.00 2.69
4587 5599 7.287466 TCCCTTTCATTTCATTTGTCTCTTTCA 59.713 33.333 0.00 0.00 0.00 2.69
4588 5600 7.661040 TCCCTTTCATTTCATTTGTCTCTTTC 58.339 34.615 0.00 0.00 0.00 2.62
4589 5601 7.601705 TCCCTTTCATTTCATTTGTCTCTTT 57.398 32.000 0.00 0.00 0.00 2.52
4590 5602 7.601705 TTCCCTTTCATTTCATTTGTCTCTT 57.398 32.000 0.00 0.00 0.00 2.85
4591 5603 7.601705 TTTCCCTTTCATTTCATTTGTCTCT 57.398 32.000 0.00 0.00 0.00 3.10
4592 5604 8.551205 GTTTTTCCCTTTCATTTCATTTGTCTC 58.449 33.333 0.00 0.00 0.00 3.36
4593 5605 8.046107 TGTTTTTCCCTTTCATTTCATTTGTCT 58.954 29.630 0.00 0.00 0.00 3.41
4594 5606 8.207521 TGTTTTTCCCTTTCATTTCATTTGTC 57.792 30.769 0.00 0.00 0.00 3.18
4595 5607 8.046107 TCTGTTTTTCCCTTTCATTTCATTTGT 58.954 29.630 0.00 0.00 0.00 2.83
4596 5608 8.436046 TCTGTTTTTCCCTTTCATTTCATTTG 57.564 30.769 0.00 0.00 0.00 2.32
4597 5609 8.485392 TCTCTGTTTTTCCCTTTCATTTCATTT 58.515 29.630 0.00 0.00 0.00 2.32
4598 5610 8.021898 TCTCTGTTTTTCCCTTTCATTTCATT 57.978 30.769 0.00 0.00 0.00 2.57
4599 5611 7.601705 TCTCTGTTTTTCCCTTTCATTTCAT 57.398 32.000 0.00 0.00 0.00 2.57
4600 5612 7.416964 TTCTCTGTTTTTCCCTTTCATTTCA 57.583 32.000 0.00 0.00 0.00 2.69
4601 5613 6.925718 CCTTCTCTGTTTTTCCCTTTCATTTC 59.074 38.462 0.00 0.00 0.00 2.17
4602 5614 6.686378 GCCTTCTCTGTTTTTCCCTTTCATTT 60.686 38.462 0.00 0.00 0.00 2.32
4603 5615 5.221521 GCCTTCTCTGTTTTTCCCTTTCATT 60.222 40.000 0.00 0.00 0.00 2.57
4604 5616 4.281941 GCCTTCTCTGTTTTTCCCTTTCAT 59.718 41.667 0.00 0.00 0.00 2.57
4605 5617 3.636764 GCCTTCTCTGTTTTTCCCTTTCA 59.363 43.478 0.00 0.00 0.00 2.69
4606 5618 3.636764 TGCCTTCTCTGTTTTTCCCTTTC 59.363 43.478 0.00 0.00 0.00 2.62
4607 5619 3.642141 TGCCTTCTCTGTTTTTCCCTTT 58.358 40.909 0.00 0.00 0.00 3.11
4608 5620 3.312736 TGCCTTCTCTGTTTTTCCCTT 57.687 42.857 0.00 0.00 0.00 3.95
4609 5621 3.532641 ATGCCTTCTCTGTTTTTCCCT 57.467 42.857 0.00 0.00 0.00 4.20
4610 5622 5.394553 CCAATATGCCTTCTCTGTTTTTCCC 60.395 44.000 0.00 0.00 0.00 3.97
4611 5623 5.418840 TCCAATATGCCTTCTCTGTTTTTCC 59.581 40.000 0.00 0.00 0.00 3.13
4612 5624 6.515272 TCCAATATGCCTTCTCTGTTTTTC 57.485 37.500 0.00 0.00 0.00 2.29
4613 5625 6.438425 ACATCCAATATGCCTTCTCTGTTTTT 59.562 34.615 0.00 0.00 0.00 1.94
4614 5626 5.954150 ACATCCAATATGCCTTCTCTGTTTT 59.046 36.000 0.00 0.00 0.00 2.43
4615 5627 5.359009 CACATCCAATATGCCTTCTCTGTTT 59.641 40.000 0.00 0.00 0.00 2.83
4616 5628 4.885907 CACATCCAATATGCCTTCTCTGTT 59.114 41.667 0.00 0.00 0.00 3.16
4617 5629 4.164796 TCACATCCAATATGCCTTCTCTGT 59.835 41.667 0.00 0.00 0.00 3.41
4618 5630 4.711399 TCACATCCAATATGCCTTCTCTG 58.289 43.478 0.00 0.00 0.00 3.35
4619 5631 5.378230 TTCACATCCAATATGCCTTCTCT 57.622 39.130 0.00 0.00 0.00 3.10
4620 5632 6.645790 ATTTCACATCCAATATGCCTTCTC 57.354 37.500 0.00 0.00 0.00 2.87
4621 5633 7.124599 TCAAATTTCACATCCAATATGCCTTCT 59.875 33.333 0.00 0.00 0.00 2.85
4622 5634 7.267128 TCAAATTTCACATCCAATATGCCTTC 58.733 34.615 0.00 0.00 0.00 3.46
4623 5635 7.185318 TCAAATTTCACATCCAATATGCCTT 57.815 32.000 0.00 0.00 0.00 4.35
4624 5636 6.795144 TCAAATTTCACATCCAATATGCCT 57.205 33.333 0.00 0.00 0.00 4.75
4625 5637 7.929785 AGATTCAAATTTCACATCCAATATGCC 59.070 33.333 0.00 0.00 0.00 4.40
4626 5638 8.882415 AGATTCAAATTTCACATCCAATATGC 57.118 30.769 0.00 0.00 0.00 3.14
4942 5954 1.973812 GCCCTGCTGTTTGGGTCTC 60.974 63.158 0.00 0.00 45.06 3.36
5044 6056 4.440826 TCAGGCACTTAAAAACCTACCA 57.559 40.909 0.00 0.00 34.60 3.25
5095 6107 9.355916 GAGGCAATCTAGGGTTTTTCTAATATT 57.644 33.333 0.00 0.00 0.00 1.28
5615 6798 2.674796 AACCATCTCGTAAGTGAGGC 57.325 50.000 0.00 0.00 43.81 4.70
5732 6942 8.143193 AGACAATACAATTTGCATTTCAAGACA 58.857 29.630 0.00 0.00 35.84 3.41
6051 7301 1.598130 ACTGGCAAGAGGAACACGC 60.598 57.895 0.00 0.00 0.00 5.34
6305 7555 0.321564 GCATACACCTGTCCAGCACA 60.322 55.000 0.00 0.00 0.00 4.57
6306 7556 0.036010 AGCATACACCTGTCCAGCAC 60.036 55.000 0.00 0.00 0.00 4.40
6376 7626 2.952978 CCTAGACGTGCTATCTGAGGTT 59.047 50.000 0.00 0.00 0.00 3.50
6388 7638 0.389948 GTTCCAGCACCCTAGACGTG 60.390 60.000 0.00 5.75 0.00 4.49
6514 7764 5.932303 TCTGCTGTATTCAAGTTAGGTCAAC 59.068 40.000 0.00 0.00 37.41 3.18
6556 7806 2.613691 ACGGCATTTCTACAGTAACCG 58.386 47.619 0.00 0.00 44.70 4.44
6683 7935 4.553429 GCACAACACAATGACGTATAAAGC 59.447 41.667 0.00 0.00 0.00 3.51
6860 8112 1.004440 ACTCGCCTTTGTCAGCTCC 60.004 57.895 0.00 0.00 0.00 4.70
6938 8274 1.915141 ATGCAGGACAAAAGGACAGG 58.085 50.000 0.00 0.00 0.00 4.00
7003 8339 9.708092 GGTTTAGACTTCTCTTACTTATTGTGT 57.292 33.333 0.00 0.00 0.00 3.72
7012 8351 8.146412 TGGTTTACTGGTTTAGACTTCTCTTAC 58.854 37.037 0.00 0.00 0.00 2.34
7087 8426 3.740115 GGACAGCTTGAAGTTCCTACAA 58.260 45.455 0.00 0.00 0.00 2.41
7335 8674 0.027716 ACGACGACTCGGAATCATCG 59.972 55.000 3.27 3.27 44.80 3.84
7416 8755 4.809673 TGATCGCTGCCTGTGTAATATAG 58.190 43.478 0.00 0.00 0.00 1.31
7417 8756 4.280929 ACTGATCGCTGCCTGTGTAATATA 59.719 41.667 0.00 0.00 0.00 0.86
7418 8757 3.070159 ACTGATCGCTGCCTGTGTAATAT 59.930 43.478 0.00 0.00 0.00 1.28
7419 8758 2.430694 ACTGATCGCTGCCTGTGTAATA 59.569 45.455 0.00 0.00 0.00 0.98
7420 8759 1.208052 ACTGATCGCTGCCTGTGTAAT 59.792 47.619 0.00 0.00 0.00 1.89
7591 8959 7.931407 TGCGTATTCACCAGATAACTAATGATT 59.069 33.333 0.00 0.00 0.00 2.57
7593 8961 6.811954 TGCGTATTCACCAGATAACTAATGA 58.188 36.000 0.00 0.00 0.00 2.57
7609 8977 9.253275 CAAACATTCAAATGAAATTGCGTATTC 57.747 29.630 9.62 0.00 36.10 1.75
7657 9025 2.363680 CCTGATGATAAGAGCAGACCGT 59.636 50.000 0.00 0.00 0.00 4.83
7658 9026 2.288702 CCCTGATGATAAGAGCAGACCG 60.289 54.545 0.00 0.00 0.00 4.79
7663 9031 2.968574 GAGGACCCTGATGATAAGAGCA 59.031 50.000 0.00 0.00 0.00 4.26
7713 10637 3.867700 TTTCGCACGTCATCCGCCA 62.868 57.895 0.00 0.00 41.42 5.69
7714 10638 2.361427 GATTTCGCACGTCATCCGCC 62.361 60.000 0.00 0.00 41.42 6.13
7715 10639 1.012234 GATTTCGCACGTCATCCGC 60.012 57.895 0.00 0.00 41.42 5.54
7716 10640 0.999406 AAGATTTCGCACGTCATCCG 59.001 50.000 0.00 0.00 44.03 4.18
7717 10641 3.163594 CAAAAGATTTCGCACGTCATCC 58.836 45.455 0.00 0.00 0.00 3.51
7728 10652 3.671459 CGGCGTAAAACCCAAAAGATTTC 59.329 43.478 0.00 0.00 0.00 2.17
7737 10661 0.465097 TCAAACCGGCGTAAAACCCA 60.465 50.000 6.01 0.00 0.00 4.51
7746 10670 1.652930 CACACGTTTCAAACCGGCG 60.653 57.895 0.00 0.00 0.00 6.46
7764 10688 6.145696 GGAGATATGTTGTCGTAATGGTTAGC 59.854 42.308 0.00 0.00 0.00 3.09
7765 10689 7.434492 AGGAGATATGTTGTCGTAATGGTTAG 58.566 38.462 0.00 0.00 0.00 2.34
7892 10819 3.322254 ACACTCTCTTCAATTCACGGACT 59.678 43.478 0.00 0.00 0.00 3.85
7897 10824 6.425504 CAACTGAACACTCTCTTCAATTCAC 58.574 40.000 0.00 0.00 0.00 3.18
7934 10861 8.771521 TCAATTTCTTGATATGGGATGAACAT 57.228 30.769 0.00 0.00 36.46 2.71
8116 11046 6.895607 TCATCGCGTATTTCAGAAATGTTA 57.104 33.333 17.38 0.00 32.38 2.41
8296 11226 9.305555 AGGCTCATGTCATATTATAAAAAGCAT 57.694 29.630 0.00 0.00 0.00 3.79
8311 11241 6.939730 TGTGTATTTAAAGAAGGCTCATGTCA 59.060 34.615 0.00 0.00 0.00 3.58
8324 11254 9.680315 TCCCAAAACGTTATTGTGTATTTAAAG 57.320 29.630 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.