Multiple sequence alignment - TraesCS6A01G182300

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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 TraesCS6A01G182300 chr6A 100.000 6812 0 0 1 6812 209892865 209899676 0.000000e+00 12580.0
1 TraesCS6A01G182300 chr6A 100.000 30 0 0 1 30 521331146 521331117 1.000000e-03 56.5
2 TraesCS6A01G182300 chr6D 96.037 4340 126 18 853 5173 156443698 156448010 0.000000e+00 7020.0
3 TraesCS6A01G182300 chr6D 95.395 1216 35 13 5171 6375 156449578 156450783 0.000000e+00 1916.0
4 TraesCS6A01G182300 chr6D 85.932 789 72 13 5 783 156442877 156443636 0.000000e+00 806.0
5 TraesCS6A01G182300 chr6B 95.432 2802 109 13 853 3642 279044713 279047507 0.000000e+00 4447.0
6 TraesCS6A01G182300 chr6B 97.403 1540 31 5 3572 5111 279047508 279049038 0.000000e+00 2614.0
7 TraesCS6A01G182300 chr6B 95.451 1275 38 12 5109 6375 279049131 279050393 0.000000e+00 2015.0
8 TraesCS6A01G182300 chr6B 85.473 296 20 5 471 760 279035824 279036102 3.110000e-73 287.0
9 TraesCS6A01G182300 chr6B 100.000 28 0 0 4 31 64932233 64932206 1.200000e-02 52.8
10 TraesCS6A01G182300 chr1A 96.372 441 16 0 6372 6812 216861767 216862207 0.000000e+00 726.0
11 TraesCS6A01G182300 chr1A 96.154 442 17 0 6371 6812 202759589 202760030 0.000000e+00 723.0
12 TraesCS6A01G182300 chr1A 96.145 441 16 1 6372 6812 202763348 202763787 0.000000e+00 719.0
13 TraesCS6A01G182300 chr5A 95.937 443 16 2 6372 6812 214971682 214971240 0.000000e+00 717.0
14 TraesCS6A01G182300 chr5A 95.516 446 18 2 6369 6812 214976043 214975598 0.000000e+00 712.0
15 TraesCS6A01G182300 chr5A 85.057 87 9 3 4915 5001 398259142 398259060 1.220000e-12 86.1
16 TraesCS6A01G182300 chr2A 95.928 442 18 0 6371 6812 324888495 324888054 0.000000e+00 717.0
17 TraesCS6A01G182300 chr2A 95.918 441 18 0 6372 6812 356696295 356696735 0.000000e+00 715.0
18 TraesCS6A01G182300 chr2A 87.578 161 14 4 5940 6098 79316001 79316157 1.510000e-41 182.0
19 TraesCS6A01G182300 chr2A 100.000 30 0 0 1 30 157836164 157836193 1.000000e-03 56.5
20 TraesCS6A01G182300 chrUn 95.918 441 18 0 6372 6812 118543560 118544000 0.000000e+00 715.0
21 TraesCS6A01G182300 chrUn 83.247 388 65 0 37 424 68800863 68801250 2.340000e-94 357.0
22 TraesCS6A01G182300 chrUn 77.193 285 52 8 3242 3521 364972353 364972629 3.290000e-33 154.0
23 TraesCS6A01G182300 chr3A 95.143 453 20 2 6361 6812 314039634 314040085 0.000000e+00 713.0
24 TraesCS6A01G182300 chr3A 88.415 164 12 6 5937 6098 582283209 582283367 2.510000e-44 191.0
25 TraesCS6A01G182300 chr3A 83.908 87 10 4 4915 5001 714570387 714570305 5.660000e-11 80.5
26 TraesCS6A01G182300 chr2D 84.029 407 62 3 33 438 62067855 62067451 8.280000e-104 388.0
27 TraesCS6A01G182300 chr2D 88.199 161 13 4 5940 6098 79056163 79056319 3.240000e-43 187.0
28 TraesCS6A01G182300 chr1D 84.224 393 60 2 33 424 435361363 435361754 1.390000e-101 381.0
29 TraesCS6A01G182300 chr7D 83.000 400 64 4 38 435 80712623 80712226 6.500000e-95 359.0
30 TraesCS6A01G182300 chr7D 82.178 404 72 0 38 441 7568038 7568441 1.410000e-91 348.0
31 TraesCS6A01G182300 chr7D 83.721 86 10 4 4916 5001 38012248 38012167 2.040000e-10 78.7
32 TraesCS6A01G182300 chr2B 82.759 406 67 3 35 438 730178879 730179283 6.500000e-95 359.0
33 TraesCS6A01G182300 chr2B 83.041 171 27 2 3270 3439 42619506 42619337 3.290000e-33 154.0
34 TraesCS6A01G182300 chr2B 78.261 253 46 6 3270 3521 42759824 42759580 3.290000e-33 154.0
35 TraesCS6A01G182300 chr2B 77.866 253 47 6 3270 3521 42828317 42828073 1.530000e-31 148.0
36 TraesCS6A01G182300 chr1B 82.641 409 66 5 33 438 30713698 30713292 2.340000e-94 357.0
37 TraesCS6A01G182300 chr1B 75.391 447 64 25 3919 4343 684586611 684586189 2.530000e-39 174.0
38 TraesCS6A01G182300 chr3D 82.222 405 70 2 33 436 29810609 29810206 1.410000e-91 348.0
39 TraesCS6A01G182300 chr3D 89.441 161 12 5 5940 6097 315480420 315480578 1.500000e-46 198.0
40 TraesCS6A01G182300 chr3D 87.805 164 13 6 5937 6098 441388661 441388819 1.170000e-42 185.0
41 TraesCS6A01G182300 chr3D 89.231 65 6 1 4915 4978 65435280 65435216 5.660000e-11 80.5
42 TraesCS6A01G182300 chr4B 89.809 157 10 4 5944 6098 106227409 106227561 5.390000e-46 196.0
43 TraesCS6A01G182300 chr3B 88.820 161 14 4 5940 6097 404830477 404830318 1.940000e-45 195.0
44 TraesCS6A01G182300 chr4A 85.057 87 9 3 4915 5001 331467509 331467591 1.220000e-12 86.1
45 TraesCS6A01G182300 chr4A 87.143 70 8 1 4915 4983 38715198 38715267 2.040000e-10 78.7
46 TraesCS6A01G182300 chr7A 83.908 87 10 4 4915 5001 145452839 145452921 5.660000e-11 80.5
47 TraesCS6A01G182300 chr7A 89.231 65 6 1 4915 4978 676281908 676281844 5.660000e-11 80.5
48 TraesCS6A01G182300 chr5D 89.231 65 6 1 4915 4978 80213032 80213096 5.660000e-11 80.5
49 TraesCS6A01G182300 chr5B 89.231 65 6 1 4915 4978 382956045 382956109 5.660000e-11 80.5
50 TraesCS6A01G182300 chr5B 84.146 82 9 4 4920 5001 576798571 576798648 7.330000e-10 76.8
51 TraesCS6A01G182300 chr7B 100.000 30 0 0 1 30 454798953 454798924 1.000000e-03 56.5
52 TraesCS6A01G182300 chr4D 100.000 30 0 0 1 30 6144452 6144481 1.000000e-03 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G182300 chr6A 209892865 209899676 6811 False 12580.000000 12580 100.000000 1 6812 1 chr6A.!!$F1 6811
1 TraesCS6A01G182300 chr6D 156442877 156450783 7906 False 3247.333333 7020 92.454667 5 6375 3 chr6D.!!$F1 6370
2 TraesCS6A01G182300 chr6B 279044713 279050393 5680 False 3025.333333 4447 96.095333 853 6375 3 chr6B.!!$F2 5522
3 TraesCS6A01G182300 chr1A 202759589 202763787 4198 False 721.000000 723 96.149500 6371 6812 2 chr1A.!!$F2 441
4 TraesCS6A01G182300 chr5A 214971240 214976043 4803 True 714.500000 717 95.726500 6369 6812 2 chr5A.!!$R2 443

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
193 200 0.101040 TCTTCAACGTCGACGGTTGT 59.899 50.000 37.89 17.63 44.95 3.32 F
271 278 0.179086 CAACAAGTTTTGCCCGGCTT 60.179 50.000 11.61 0.00 0.00 4.35 F
1096 1129 0.394565 AATCGCTGTATGCTCCTCCC 59.605 55.000 0.00 0.00 40.11 4.30 F
2521 2572 0.036875 ACTTTCAAGAAGCTCCCCCG 59.963 55.000 0.00 0.00 0.00 5.73 F
2874 2929 2.980541 CATGGGACCATGCCAGTTT 58.019 52.632 17.57 0.00 42.59 2.66 F
3457 3514 1.512926 TGCTCTGAAACTTCGGCTTC 58.487 50.000 0.00 0.00 33.56 3.86 F
4871 4997 1.933853 GAGTCGTGTTGTGACTTTGCT 59.066 47.619 0.00 0.00 46.29 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1096 1129 0.246086 GCACCACACAGAGAGAGAGG 59.754 60.000 0.00 0.0 0.00 3.69 R
1105 1150 0.438445 CGAATACACGCACCACACAG 59.562 55.000 0.00 0.0 0.00 3.66 R
2980 3035 0.405585 CAGGTCAGTTCCCCACCAAT 59.594 55.000 0.00 0.0 31.99 3.16 R
3457 3514 1.465689 CGTCAACGCAAGCCTTATTGG 60.466 52.381 0.00 0.0 45.62 3.16 R
4326 4452 2.231716 TACTAAGAGCAGGTGCCTCA 57.768 50.000 0.00 0.0 43.38 3.86 R
5257 7048 5.771666 ACAAGGGATGGATGTTATAAGCATG 59.228 40.000 5.59 0.0 0.00 4.06 R
6176 7979 1.963338 GAGTGCAAGTTCCGCTGCT 60.963 57.895 0.00 0.0 0.00 4.24 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
35 42 1.681229 TTTGGTCCAGCCCTTATCCT 58.319 50.000 0.00 0.00 36.04 3.24
42 49 0.107017 CAGCCCTTATCCTGGTGGTG 60.107 60.000 0.00 0.00 34.23 4.17
56 63 2.166870 TGGTGGTGCGTCTAATATCGTT 59.833 45.455 0.00 0.00 0.00 3.85
62 69 2.427812 TGCGTCTAATATCGTTGGTGGA 59.572 45.455 0.00 0.00 0.00 4.02
68 75 5.815740 GTCTAATATCGTTGGTGGATGTGTT 59.184 40.000 0.00 0.00 0.00 3.32
69 76 4.963276 AATATCGTTGGTGGATGTGTTG 57.037 40.909 0.00 0.00 0.00 3.33
70 77 1.533625 ATCGTTGGTGGATGTGTTGG 58.466 50.000 0.00 0.00 0.00 3.77
71 78 0.536233 TCGTTGGTGGATGTGTTGGG 60.536 55.000 0.00 0.00 0.00 4.12
73 80 0.469144 GTTGGTGGATGTGTTGGGGT 60.469 55.000 0.00 0.00 0.00 4.95
74 81 0.468958 TTGGTGGATGTGTTGGGGTG 60.469 55.000 0.00 0.00 0.00 4.61
75 82 1.152830 GGTGGATGTGTTGGGGTGT 59.847 57.895 0.00 0.00 0.00 4.16
77 84 0.467290 GTGGATGTGTTGGGGTGTGT 60.467 55.000 0.00 0.00 0.00 3.72
78 85 0.179004 TGGATGTGTTGGGGTGTGTC 60.179 55.000 0.00 0.00 0.00 3.67
116 123 1.303309 GGTGGATTTGCTCGGATCTG 58.697 55.000 0.00 0.00 0.00 2.90
131 138 2.422832 GGATCTGGTCGTAGTTCGTCTT 59.577 50.000 0.00 0.00 40.80 3.01
136 143 2.237526 GGTCGTAGTTCGTCTTCGTTC 58.762 52.381 8.44 5.05 37.98 3.95
138 145 1.136252 TCGTAGTTCGTCTTCGTTCGG 60.136 52.381 8.44 0.00 37.98 4.30
142 149 0.595825 GTTCGTCTTCGTTCGGGTGT 60.596 55.000 0.00 0.00 38.33 4.16
143 150 0.318107 TTCGTCTTCGTTCGGGTGTC 60.318 55.000 0.00 0.00 38.33 3.67
144 151 1.168407 TCGTCTTCGTTCGGGTGTCT 61.168 55.000 0.00 0.00 38.33 3.41
154 161 1.227438 CGGGTGTCTTCACGTTGGT 60.227 57.895 0.00 0.00 44.68 3.67
160 167 2.681344 GTGTCTTCACGTTGGTTCCTTT 59.319 45.455 0.00 0.00 34.79 3.11
169 176 2.928116 CGTTGGTTCCTTTCGATCTACC 59.072 50.000 0.00 0.00 0.00 3.18
175 182 5.070047 TGGTTCCTTTCGATCTACCCTATTC 59.930 44.000 0.00 0.00 0.00 1.75
181 188 6.702282 CCTTTCGATCTACCCTATTCTTCAAC 59.298 42.308 0.00 0.00 0.00 3.18
186 193 4.264253 TCTACCCTATTCTTCAACGTCGA 58.736 43.478 0.00 0.00 0.00 4.20
193 200 0.101040 TCTTCAACGTCGACGGTTGT 59.899 50.000 37.89 17.63 44.95 3.32
200 207 0.228742 CGTCGACGGTTGTTGTTCTG 59.771 55.000 29.70 0.00 35.37 3.02
201 208 0.580104 GTCGACGGTTGTTGTTCTGG 59.420 55.000 0.00 0.00 0.00 3.86
238 245 2.817844 GGGCCTTAACACGATGACTTTT 59.182 45.455 0.84 0.00 0.00 2.27
239 246 3.119955 GGGCCTTAACACGATGACTTTTC 60.120 47.826 0.84 0.00 0.00 2.29
240 247 3.500680 GGCCTTAACACGATGACTTTTCA 59.499 43.478 0.00 0.00 35.73 2.69
245 252 3.609103 ACACGATGACTTTTCAAGTGC 57.391 42.857 11.26 0.00 43.10 4.40
252 259 5.062308 CGATGACTTTTCAAGTGCCTACTAC 59.938 44.000 0.00 0.00 43.03 2.73
254 261 5.676552 TGACTTTTCAAGTGCCTACTACAA 58.323 37.500 0.00 0.00 43.03 2.41
271 278 0.179086 CAACAAGTTTTGCCCGGCTT 60.179 50.000 11.61 0.00 0.00 4.35
311 318 2.035442 GGCGGCACACCTTCTTCTC 61.035 63.158 3.07 0.00 0.00 2.87
313 320 1.569479 GCGGCACACCTTCTTCTCAC 61.569 60.000 0.00 0.00 0.00 3.51
320 327 4.501571 GCACACCTTCTTCTCACTTCAGTA 60.502 45.833 0.00 0.00 0.00 2.74
330 337 7.426410 TCTTCTCACTTCAGTACTTGTACTTG 58.574 38.462 10.38 7.21 0.00 3.16
332 339 6.736123 TCTCACTTCAGTACTTGTACTTGTC 58.264 40.000 10.38 0.00 0.00 3.18
340 347 3.299340 ACTTGTACTTGTCGCTAGGTG 57.701 47.619 0.00 0.00 0.00 4.00
344 351 0.806868 TACTTGTCGCTAGGTGGTCG 59.193 55.000 0.00 0.00 0.00 4.79
351 358 1.134310 TCGCTAGGTGGTCGACAGATA 60.134 52.381 18.91 3.54 0.00 1.98
458 467 7.672983 AACATGACAATTTATCTGTTCTCGT 57.327 32.000 0.00 0.00 0.00 4.18
460 469 8.948631 ACATGACAATTTATCTGTTCTCGTAT 57.051 30.769 0.00 0.00 0.00 3.06
461 470 9.383519 ACATGACAATTTATCTGTTCTCGTATT 57.616 29.630 0.00 0.00 0.00 1.89
546 555 2.039818 TGCTTTACCACGTTGAACCA 57.960 45.000 0.00 0.00 0.00 3.67
555 564 5.217978 ACCACGTTGAACCACTAGAATAA 57.782 39.130 0.00 0.00 0.00 1.40
556 565 5.613329 ACCACGTTGAACCACTAGAATAAA 58.387 37.500 0.00 0.00 0.00 1.40
557 566 6.056884 ACCACGTTGAACCACTAGAATAAAA 58.943 36.000 0.00 0.00 0.00 1.52
558 567 6.713450 ACCACGTTGAACCACTAGAATAAAAT 59.287 34.615 0.00 0.00 0.00 1.82
559 568 7.229907 ACCACGTTGAACCACTAGAATAAAATT 59.770 33.333 0.00 0.00 0.00 1.82
560 569 7.537306 CCACGTTGAACCACTAGAATAAAATTG 59.463 37.037 0.00 0.00 0.00 2.32
561 570 8.073768 CACGTTGAACCACTAGAATAAAATTGT 58.926 33.333 0.00 0.00 0.00 2.71
562 571 8.287503 ACGTTGAACCACTAGAATAAAATTGTC 58.712 33.333 0.00 0.00 0.00 3.18
563 572 8.504005 CGTTGAACCACTAGAATAAAATTGTCT 58.496 33.333 0.00 0.00 0.00 3.41
566 575 9.349713 TGAACCACTAGAATAAAATTGTCTTGT 57.650 29.630 0.00 0.00 0.00 3.16
568 577 9.965824 AACCACTAGAATAAAATTGTCTTGTTG 57.034 29.630 0.00 0.00 0.00 3.33
607 617 4.154556 TGGCTAATGTTTTTACTACACGGC 59.845 41.667 0.00 0.00 0.00 5.68
632 642 9.392259 GCTAAAACCTAATGTTTGTACTATCCT 57.608 33.333 0.00 0.00 46.39 3.24
637 647 7.727181 ACCTAATGTTTGTACTATCCTGCTAG 58.273 38.462 0.00 0.00 0.00 3.42
720 731 3.245122 GGGGTGATTAGGACCAAAGTGAA 60.245 47.826 0.00 0.00 34.89 3.18
731 742 4.340617 GACCAAAGTGAACATGGGGATAA 58.659 43.478 0.00 0.00 38.58 1.75
737 748 7.981225 CCAAAGTGAACATGGGGATAAATTTAG 59.019 37.037 3.94 0.00 0.00 1.85
748 759 5.297029 GGGGATAAATTTAGGATATGCGAGC 59.703 44.000 3.94 0.00 0.00 5.03
750 761 3.813529 AAATTTAGGATATGCGAGCGC 57.186 42.857 8.08 8.08 42.35 5.92
810 821 2.702592 TTTGAGTGGTCGGAACAAGT 57.297 45.000 0.00 0.00 0.00 3.16
811 822 2.702592 TTGAGTGGTCGGAACAAGTT 57.297 45.000 0.00 0.00 0.00 2.66
812 823 2.234300 TGAGTGGTCGGAACAAGTTC 57.766 50.000 0.00 4.39 38.80 3.01
813 824 1.760613 TGAGTGGTCGGAACAAGTTCT 59.239 47.619 12.22 0.00 39.45 3.01
824 835 3.933332 GGAACAAGTTCTCGTATCCCTTG 59.067 47.826 12.22 0.00 39.45 3.61
834 845 2.026729 TCGTATCCCTTGGTGCATTTCA 60.027 45.455 0.00 0.00 0.00 2.69
838 849 1.144708 TCCCTTGGTGCATTTCACTCA 59.855 47.619 0.00 0.00 44.98 3.41
881 912 4.956085 AGTACAAAAACCCAAATTCAGGC 58.044 39.130 0.00 0.00 0.00 4.85
887 919 2.713967 CCCAAATTCAGGCCCAGCG 61.714 63.158 0.00 0.00 0.00 5.18
901 933 2.125106 AGCGACATCTTTCGGCCC 60.125 61.111 0.00 0.00 39.50 5.80
946 978 2.048127 GCGCTCCGACCAAGTCTT 60.048 61.111 0.00 0.00 0.00 3.01
1096 1129 0.394565 AATCGCTGTATGCTCCTCCC 59.605 55.000 0.00 0.00 40.11 4.30
1105 1150 0.188342 ATGCTCCTCCCCTCTCTCTC 59.812 60.000 0.00 0.00 0.00 3.20
1107 1152 0.468029 GCTCCTCCCCTCTCTCTCTG 60.468 65.000 0.00 0.00 0.00 3.35
1139 1184 1.321474 ATTCGGACTCGGGCGTATAA 58.679 50.000 0.00 0.00 36.95 0.98
1170 1215 0.250252 TTGCCGCTGACATCAAGTGA 60.250 50.000 0.00 0.00 0.00 3.41
1192 1237 0.918983 AGGGGAGCGATGAAATTCCA 59.081 50.000 0.00 0.00 0.00 3.53
1266 1311 1.202698 ACTGAGAAGTTGAGCCACACC 60.203 52.381 0.00 0.00 0.00 4.16
1294 1339 8.183104 TCCATCAGATCGATATAGTTTTCTGT 57.817 34.615 0.00 0.00 33.88 3.41
1368 1416 9.725019 ACTAAATGTTGAGTGATGTAAAGATGA 57.275 29.630 0.00 0.00 0.00 2.92
1401 1449 9.533253 AAGAAACATGACAATTTTAACCTTCTG 57.467 29.630 0.00 0.00 0.00 3.02
1414 1462 6.466885 TTAACCTTCTGAGAGCACTATACC 57.533 41.667 0.00 0.00 0.00 2.73
1448 1496 7.038941 TCACTACTCCTTTTCTTCTTCTTAGGG 60.039 40.741 0.00 0.00 0.00 3.53
1478 1526 1.602191 GCGTTTGCTAATGACCAACG 58.398 50.000 4.18 0.00 38.39 4.10
1547 1595 7.223584 TGGATCTTGTGAAATTAGAACTGTCA 58.776 34.615 0.00 0.00 0.00 3.58
1551 1599 8.506168 TCTTGTGAAATTAGAACTGTCAAACT 57.494 30.769 0.00 0.00 0.00 2.66
1723 1771 5.107837 CGCTATGAATTTAAGTACTCCGCTG 60.108 44.000 0.00 0.00 0.00 5.18
1819 1867 1.179152 TCAATCGAACGCTGGTCCTA 58.821 50.000 0.00 0.00 0.00 2.94
1820 1868 1.754803 TCAATCGAACGCTGGTCCTAT 59.245 47.619 0.00 0.00 0.00 2.57
1860 1908 2.964464 AGAGATCATTCAGACGGAGCAT 59.036 45.455 0.00 0.00 0.00 3.79
1869 1917 1.134699 CAGACGGAGCATAGGAAAGCA 60.135 52.381 0.00 0.00 0.00 3.91
1920 1968 2.996249 ATGATCCGAGCATTCACAGT 57.004 45.000 0.00 0.00 0.00 3.55
2013 2061 2.478335 TTAAGTGGCGGGGCTCCTTG 62.478 60.000 0.00 0.00 0.00 3.61
2085 2136 6.899393 TGCACTGGAATAAGACAGAAATTT 57.101 33.333 0.00 0.00 38.09 1.82
2202 2253 4.478843 ACTAATGCAGCTATGAAATGCG 57.521 40.909 0.00 0.00 42.92 4.73
2362 2413 6.573434 TCACATCGAAGCTGTTATCTTGTAT 58.427 36.000 0.00 0.00 0.00 2.29
2407 2458 6.183360 ACACTCATTTTGGTGTCTTCTTCTTG 60.183 38.462 0.00 0.00 42.09 3.02
2449 2500 2.798976 TCATTTCTTTGTGCAGTGCC 57.201 45.000 13.72 4.57 0.00 5.01
2521 2572 0.036875 ACTTTCAAGAAGCTCCCCCG 59.963 55.000 0.00 0.00 0.00 5.73
2560 2611 3.258872 GCTCCTCTAGTCATGATGATGCT 59.741 47.826 0.00 0.00 0.00 3.79
2564 2615 7.550597 TCCTCTAGTCATGATGATGCTTAAT 57.449 36.000 0.00 0.00 0.00 1.40
2610 2661 3.550437 TGGTTTGGTTTGGATTTGGTG 57.450 42.857 0.00 0.00 0.00 4.17
2624 2675 4.333926 GGATTTGGTGACTATCTCAACTGC 59.666 45.833 0.00 0.00 37.51 4.40
2625 2676 4.350368 TTTGGTGACTATCTCAACTGCA 57.650 40.909 0.00 0.00 37.51 4.41
2626 2677 4.350368 TTGGTGACTATCTCAACTGCAA 57.650 40.909 0.00 0.00 37.51 4.08
2627 2678 4.350368 TGGTGACTATCTCAACTGCAAA 57.650 40.909 0.00 0.00 37.51 3.68
2741 2796 9.807649 CATTTACTAAAGCCTAAAATTCAGCAT 57.192 29.630 0.00 0.00 0.00 3.79
2874 2929 2.980541 CATGGGACCATGCCAGTTT 58.019 52.632 17.57 0.00 42.59 2.66
2899 2954 3.838317 ACCATACTAGTTCTCCAGCACAA 59.162 43.478 0.00 0.00 0.00 3.33
2972 3027 6.122277 TGTCTTTCTTTTGATGACCTTCTGT 58.878 36.000 0.00 0.00 34.01 3.41
2974 3029 7.122650 TGTCTTTCTTTTGATGACCTTCTGTTT 59.877 33.333 0.00 0.00 34.01 2.83
3176 3232 7.450074 TCCTTATACAGTGAGTGAATGTGTTT 58.550 34.615 0.00 0.00 0.00 2.83
3396 3453 9.613428 CTTTTGAGTATGAATATTGACCCTGTA 57.387 33.333 0.00 0.00 0.00 2.74
3457 3514 1.512926 TGCTCTGAAACTTCGGCTTC 58.487 50.000 0.00 0.00 33.56 3.86
3745 3871 6.763610 GGATCTCCCTTCAGTTGTTTATACTG 59.236 42.308 0.00 0.00 43.41 2.74
3757 3883 9.973450 CAGTTGTTTATACTGTAGCTCATAGAT 57.027 33.333 0.00 0.00 38.51 1.98
3768 3894 6.730175 TGTAGCTCATAGATCGAGAACTTTC 58.270 40.000 0.00 0.00 31.84 2.62
4014 4140 2.969821 TAAGTTCCATTGGCAGGTGT 57.030 45.000 0.00 0.00 0.00 4.16
4066 4192 8.371571 TCTATATTATGCATGGTCATGTCTCT 57.628 34.615 10.16 0.00 40.80 3.10
4082 4208 8.665685 GTCATGTCTCTTACCGTTGATATTTTT 58.334 33.333 0.00 0.00 0.00 1.94
4198 4324 7.069950 GCATGGGGTTTCTTAGAAATCCTAAAT 59.930 37.037 29.27 19.78 36.95 1.40
4326 4452 7.095017 GCTTCTTTAGCTGTAGAATCAAGTGTT 60.095 37.037 11.37 0.00 46.77 3.32
4564 4690 9.914131 AGGTAATAAAGTTCTCAATTTTTCAGC 57.086 29.630 0.00 0.00 0.00 4.26
4868 4994 3.520290 TGAGAGTCGTGTTGTGACTTT 57.480 42.857 0.00 0.00 46.29 2.66
4871 4997 1.933853 GAGTCGTGTTGTGACTTTGCT 59.066 47.619 0.00 0.00 46.29 3.91
5028 5154 5.741388 AAATGTCACCATCGATCTAAAGC 57.259 39.130 0.00 0.00 0.00 3.51
5131 5352 4.627611 AGCATGCAACTGACATTACATC 57.372 40.909 21.98 0.00 0.00 3.06
5132 5353 3.064408 AGCATGCAACTGACATTACATCG 59.936 43.478 21.98 0.00 0.00 3.84
5202 6993 5.643777 CCTGAATCAAAGTAACGTCCATCTT 59.356 40.000 0.00 0.00 0.00 2.40
5224 7015 6.319658 TCTTGTTTTCAGCAAGAAGTCTCATT 59.680 34.615 5.41 0.00 46.21 2.57
5232 7023 7.810658 TCAGCAAGAAGTCTCATTTATGAAAC 58.189 34.615 0.00 0.00 36.18 2.78
5257 7048 7.809806 ACATTTATGTAGCAAAGCTGAAGTTTC 59.190 33.333 1.04 0.00 40.10 2.78
5418 7209 2.616842 AGTTGCTTTTGGAGGTTACACG 59.383 45.455 0.00 0.00 0.00 4.49
5633 7424 7.646922 GCATTATCACCAGAAATTAAAGCTCAG 59.353 37.037 0.00 0.00 0.00 3.35
5680 7471 0.032952 TCCGAGGTGTGTTTTCTCCG 59.967 55.000 0.00 0.00 0.00 4.63
5697 7488 7.548196 TTTCTCCGATTGTTGTATCCATAAC 57.452 36.000 0.00 0.00 0.00 1.89
5842 7637 7.482169 TTTGAGCAGTAAGAAGAGGAAGATA 57.518 36.000 0.00 0.00 0.00 1.98
5864 7659 5.813080 ATACCGAGAACTAAAAACCATGC 57.187 39.130 0.00 0.00 0.00 4.06
5926 7721 5.484715 CCATTGATTTCTTGCCATTGTCTT 58.515 37.500 0.00 0.00 0.00 3.01
6204 8007 4.690748 CGGAACTTGCACTCTTTTCTGATA 59.309 41.667 0.00 0.00 0.00 2.15
6205 8008 5.352569 CGGAACTTGCACTCTTTTCTGATAT 59.647 40.000 0.00 0.00 0.00 1.63
6278 8081 2.761786 AGGCATGGCATATCAAAGGT 57.238 45.000 22.64 0.00 0.00 3.50
6348 8151 4.582869 AGCTAGCATGACAATTTCTGACA 58.417 39.130 18.83 0.00 34.18 3.58
6349 8152 4.634883 AGCTAGCATGACAATTTCTGACAG 59.365 41.667 18.83 0.00 33.16 3.51
6350 8153 4.633126 GCTAGCATGACAATTTCTGACAGA 59.367 41.667 10.63 0.00 33.16 3.41
6386 8189 0.249657 CAAGTGATAGAGGCGAGGGC 60.250 60.000 0.00 0.00 38.90 5.19
6422 8227 8.811378 TCGATGAGATGATAATTATCGATTTGC 58.189 33.333 18.35 7.97 40.71 3.68
6484 12676 7.168137 GACGTTGTGTCTTAGCAATCGCTAG 62.168 48.000 0.00 0.00 45.44 3.42
6674 12866 1.397692 GGTCGTTGGACACAAACGAAA 59.602 47.619 14.23 0.00 45.28 3.46
6716 12908 9.138596 TGGCTAACTTTTAACTAAACAAATCCT 57.861 29.630 0.00 0.00 0.00 3.24
6717 12909 9.622004 GGCTAACTTTTAACTAAACAAATCCTC 57.378 33.333 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.228552 GGGCTGGACCAAAAGCTCA 60.229 57.895 0.00 0.00 39.82 4.26
23 24 0.107017 CACCACCAGGATAAGGGCTG 60.107 60.000 0.00 0.00 38.69 4.85
35 42 1.752498 ACGATATTAGACGCACCACCA 59.248 47.619 0.00 0.00 0.00 4.17
42 49 3.088194 TCCACCAACGATATTAGACGC 57.912 47.619 0.00 0.00 0.00 5.19
56 63 1.152599 CACCCCAACACATCCACCA 59.847 57.895 0.00 0.00 0.00 4.17
62 69 4.920828 GGACACACCCCAACACAT 57.079 55.556 0.00 0.00 0.00 3.21
78 85 3.758554 CACCAAGAACAAATCCACTAGGG 59.241 47.826 0.00 0.00 34.83 3.53
80 87 4.651778 TCCACCAAGAACAAATCCACTAG 58.348 43.478 0.00 0.00 0.00 2.57
81 88 4.715534 TCCACCAAGAACAAATCCACTA 57.284 40.909 0.00 0.00 0.00 2.74
82 89 3.593442 TCCACCAAGAACAAATCCACT 57.407 42.857 0.00 0.00 0.00 4.00
83 90 4.871933 AATCCACCAAGAACAAATCCAC 57.128 40.909 0.00 0.00 0.00 4.02
84 91 4.502950 GCAAATCCACCAAGAACAAATCCA 60.503 41.667 0.00 0.00 0.00 3.41
85 92 3.996363 GCAAATCCACCAAGAACAAATCC 59.004 43.478 0.00 0.00 0.00 3.01
86 93 4.886579 AGCAAATCCACCAAGAACAAATC 58.113 39.130 0.00 0.00 0.00 2.17
87 94 4.559300 CGAGCAAATCCACCAAGAACAAAT 60.559 41.667 0.00 0.00 0.00 2.32
88 95 3.243367 CGAGCAAATCCACCAAGAACAAA 60.243 43.478 0.00 0.00 0.00 2.83
89 96 2.293122 CGAGCAAATCCACCAAGAACAA 59.707 45.455 0.00 0.00 0.00 2.83
90 97 1.879380 CGAGCAAATCCACCAAGAACA 59.121 47.619 0.00 0.00 0.00 3.18
91 98 1.200020 CCGAGCAAATCCACCAAGAAC 59.800 52.381 0.00 0.00 0.00 3.01
92 99 1.073125 TCCGAGCAAATCCACCAAGAA 59.927 47.619 0.00 0.00 0.00 2.52
93 100 0.690192 TCCGAGCAAATCCACCAAGA 59.310 50.000 0.00 0.00 0.00 3.02
116 123 2.237526 GAACGAAGACGAACTACGACC 58.762 52.381 0.00 0.00 45.77 4.79
131 138 1.008194 CGTGAAGACACCCGAACGA 60.008 57.895 0.00 0.00 43.34 3.85
136 143 0.812412 AACCAACGTGAAGACACCCG 60.812 55.000 0.00 0.00 43.34 5.28
138 145 0.942252 GGAACCAACGTGAAGACACC 59.058 55.000 0.00 0.00 43.34 4.16
142 149 2.159071 TCGAAAGGAACCAACGTGAAGA 60.159 45.455 0.00 0.00 0.00 2.87
143 150 2.206750 TCGAAAGGAACCAACGTGAAG 58.793 47.619 0.00 0.00 0.00 3.02
144 151 2.312722 TCGAAAGGAACCAACGTGAA 57.687 45.000 0.00 0.00 0.00 3.18
154 161 6.610020 TGAAGAATAGGGTAGATCGAAAGGAA 59.390 38.462 0.00 0.00 0.00 3.36
160 167 4.885907 ACGTTGAAGAATAGGGTAGATCGA 59.114 41.667 0.00 0.00 0.00 3.59
169 176 2.182825 CCGTCGACGTTGAAGAATAGG 58.817 52.381 33.49 12.11 37.74 2.57
175 182 0.925466 AACAACCGTCGACGTTGAAG 59.075 50.000 36.51 25.78 37.74 3.02
181 188 0.228742 CAGAACAACAACCGTCGACG 59.771 55.000 30.33 30.33 39.44 5.12
186 193 1.711060 CGCACCAGAACAACAACCGT 61.711 55.000 0.00 0.00 0.00 4.83
193 200 1.891919 GACCAGCGCACCAGAACAA 60.892 57.895 11.47 0.00 0.00 2.83
200 207 2.203070 CCATAGGACCAGCGCACC 60.203 66.667 11.47 7.54 0.00 5.01
201 208 2.203070 CCCATAGGACCAGCGCAC 60.203 66.667 11.47 0.00 33.47 5.34
238 245 4.682778 ACTTGTTGTAGTAGGCACTTGA 57.317 40.909 0.00 0.00 41.75 3.02
239 246 5.751243 AAACTTGTTGTAGTAGGCACTTG 57.249 39.130 0.00 0.00 41.75 3.16
240 247 5.449999 GCAAAACTTGTTGTAGTAGGCACTT 60.450 40.000 0.00 0.00 41.75 3.16
245 252 3.058501 CGGGCAAAACTTGTTGTAGTAGG 60.059 47.826 0.00 0.00 0.00 3.18
252 259 0.179086 AAGCCGGGCAAAACTTGTTG 60.179 50.000 23.09 0.00 0.00 3.33
254 261 1.739667 GAAGCCGGGCAAAACTTGT 59.260 52.632 23.09 0.00 0.00 3.16
274 281 3.399181 TCATCGCCCCACCCTCAC 61.399 66.667 0.00 0.00 0.00 3.51
275 282 3.399181 GTCATCGCCCCACCCTCA 61.399 66.667 0.00 0.00 0.00 3.86
296 303 2.147150 GAAGTGAGAAGAAGGTGTGCC 58.853 52.381 0.00 0.00 0.00 5.01
299 306 4.896482 AGTACTGAAGTGAGAAGAAGGTGT 59.104 41.667 0.00 0.00 0.00 4.16
301 308 5.364157 ACAAGTACTGAAGTGAGAAGAAGGT 59.636 40.000 0.00 0.00 0.00 3.50
311 318 4.148348 GCGACAAGTACAAGTACTGAAGTG 59.852 45.833 13.18 10.12 44.96 3.16
313 320 4.547532 AGCGACAAGTACAAGTACTGAAG 58.452 43.478 13.18 9.20 44.96 3.02
320 327 2.029290 CCACCTAGCGACAAGTACAAGT 60.029 50.000 0.00 0.00 0.00 3.16
332 339 1.306148 TATCTGTCGACCACCTAGCG 58.694 55.000 14.12 0.00 0.00 4.26
340 347 7.730364 AAAATTACATCCATATCTGTCGACC 57.270 36.000 14.12 0.00 0.00 4.79
385 392 9.552695 TCTATCCATCTTCAATCATGGTACTAT 57.447 33.333 0.00 0.00 40.59 2.12
431 438 9.055248 CGAGAACAGATAAATTGTCATGTTTTC 57.945 33.333 11.40 11.40 31.44 2.29
442 451 7.849804 ACTGCAATACGAGAACAGATAAATT 57.150 32.000 0.00 0.00 32.67 1.82
454 463 2.610433 TGCTCAGAACTGCAATACGAG 58.390 47.619 0.00 0.00 36.15 4.18
458 467 2.352651 GCGAATGCTCAGAACTGCAATA 59.647 45.455 0.00 0.00 42.74 1.90
460 469 0.518636 GCGAATGCTCAGAACTGCAA 59.481 50.000 0.00 0.00 42.74 4.08
461 470 2.165380 GCGAATGCTCAGAACTGCA 58.835 52.632 0.00 0.00 43.67 4.41
527 536 1.671845 GTGGTTCAACGTGGTAAAGCA 59.328 47.619 0.00 0.00 0.00 3.91
529 538 4.624015 TCTAGTGGTTCAACGTGGTAAAG 58.376 43.478 0.00 0.00 0.00 1.85
530 539 4.669206 TCTAGTGGTTCAACGTGGTAAA 57.331 40.909 0.00 0.00 0.00 2.01
535 544 8.073768 ACAATTTTATTCTAGTGGTTCAACGTG 58.926 33.333 0.00 0.00 0.00 4.49
555 564 4.111916 CCTGCGTTTCAACAAGACAATTT 58.888 39.130 0.00 0.00 0.00 1.82
556 565 3.490761 CCCTGCGTTTCAACAAGACAATT 60.491 43.478 0.00 0.00 0.00 2.32
557 566 2.034558 CCCTGCGTTTCAACAAGACAAT 59.965 45.455 0.00 0.00 0.00 2.71
558 567 1.403679 CCCTGCGTTTCAACAAGACAA 59.596 47.619 0.00 0.00 0.00 3.18
559 568 1.021202 CCCTGCGTTTCAACAAGACA 58.979 50.000 0.00 0.00 0.00 3.41
560 569 0.310854 CCCCTGCGTTTCAACAAGAC 59.689 55.000 0.00 0.00 0.00 3.01
561 570 0.106918 ACCCCTGCGTTTCAACAAGA 60.107 50.000 0.00 0.00 0.00 3.02
562 571 1.600023 TACCCCTGCGTTTCAACAAG 58.400 50.000 0.00 0.00 0.00 3.16
563 572 2.279935 ATACCCCTGCGTTTCAACAA 57.720 45.000 0.00 0.00 0.00 2.83
564 573 2.279935 AATACCCCTGCGTTTCAACA 57.720 45.000 0.00 0.00 0.00 3.33
565 574 2.352323 CCAAATACCCCTGCGTTTCAAC 60.352 50.000 0.00 0.00 0.00 3.18
566 575 1.889829 CCAAATACCCCTGCGTTTCAA 59.110 47.619 0.00 0.00 0.00 2.69
567 576 1.540267 CCAAATACCCCTGCGTTTCA 58.460 50.000 0.00 0.00 0.00 2.69
568 577 0.172578 GCCAAATACCCCTGCGTTTC 59.827 55.000 0.00 0.00 0.00 2.78
632 642 0.965866 CGTGAGAGGGTGGTCTAGCA 60.966 60.000 0.00 0.00 0.00 3.49
637 647 1.275291 TGATTTCGTGAGAGGGTGGTC 59.725 52.381 0.00 0.00 43.69 4.02
720 731 6.603201 CGCATATCCTAAATTTATCCCCATGT 59.397 38.462 0.00 0.00 0.00 3.21
731 742 1.726791 CGCGCTCGCATATCCTAAATT 59.273 47.619 14.80 0.00 42.06 1.82
737 748 3.406361 CCACGCGCTCGCATATCC 61.406 66.667 5.73 0.00 42.06 2.59
748 759 2.740714 GCTCACTTTAGCCCACGCG 61.741 63.158 3.53 3.53 41.18 6.01
750 761 1.933853 GTATGCTCACTTTAGCCCACG 59.066 52.381 0.00 0.00 42.05 4.94
789 800 3.349022 ACTTGTTCCGACCACTCAAAAA 58.651 40.909 0.00 0.00 0.00 1.94
790 801 2.993937 ACTTGTTCCGACCACTCAAAA 58.006 42.857 0.00 0.00 0.00 2.44
791 802 2.702592 ACTTGTTCCGACCACTCAAA 57.297 45.000 0.00 0.00 0.00 2.69
792 803 2.169769 AGAACTTGTTCCGACCACTCAA 59.830 45.455 9.58 0.00 0.00 3.02
793 804 1.760613 AGAACTTGTTCCGACCACTCA 59.239 47.619 9.58 0.00 0.00 3.41
794 805 2.405172 GAGAACTTGTTCCGACCACTC 58.595 52.381 9.58 0.00 0.00 3.51
795 806 1.269621 CGAGAACTTGTTCCGACCACT 60.270 52.381 9.58 0.00 0.00 4.00
796 807 1.137513 CGAGAACTTGTTCCGACCAC 58.862 55.000 9.58 0.00 0.00 4.16
797 808 0.748450 ACGAGAACTTGTTCCGACCA 59.252 50.000 21.60 0.00 0.00 4.02
798 809 2.712057 TACGAGAACTTGTTCCGACC 57.288 50.000 21.60 6.91 0.00 4.79
799 810 3.177487 GGATACGAGAACTTGTTCCGAC 58.823 50.000 21.60 14.83 0.00 4.79
800 811 2.165030 GGGATACGAGAACTTGTTCCGA 59.835 50.000 21.60 11.60 31.06 4.55
801 812 2.165845 AGGGATACGAGAACTTGTTCCG 59.834 50.000 16.63 16.63 31.06 4.30
802 813 3.889520 AGGGATACGAGAACTTGTTCC 57.110 47.619 9.58 7.23 37.60 3.62
803 814 3.933332 CCAAGGGATACGAGAACTTGTTC 59.067 47.826 5.44 5.44 37.44 3.18
804 815 3.326880 ACCAAGGGATACGAGAACTTGTT 59.673 43.478 0.00 0.00 37.44 2.83
805 816 2.904434 ACCAAGGGATACGAGAACTTGT 59.096 45.455 0.00 0.32 37.44 3.16
806 817 3.262420 CACCAAGGGATACGAGAACTTG 58.738 50.000 0.00 0.00 38.52 3.16
807 818 2.354805 GCACCAAGGGATACGAGAACTT 60.355 50.000 0.00 0.00 37.60 2.66
808 819 1.207329 GCACCAAGGGATACGAGAACT 59.793 52.381 0.00 0.00 37.60 3.01
809 820 1.066430 TGCACCAAGGGATACGAGAAC 60.066 52.381 0.00 0.00 37.60 3.01
810 821 1.271856 TGCACCAAGGGATACGAGAA 58.728 50.000 0.00 0.00 37.60 2.87
811 822 1.496060 ATGCACCAAGGGATACGAGA 58.504 50.000 0.00 0.00 37.60 4.04
812 823 2.332063 AATGCACCAAGGGATACGAG 57.668 50.000 0.00 0.00 37.60 4.18
813 824 2.026729 TGAAATGCACCAAGGGATACGA 60.027 45.455 0.00 0.00 37.60 3.43
845 856 9.850628 GGGTTTTTGTACTTAATGGTAATTCTC 57.149 33.333 0.00 0.00 0.00 2.87
847 858 9.984190 TTGGGTTTTTGTACTTAATGGTAATTC 57.016 29.630 0.00 0.00 0.00 2.17
851 862 9.984190 GAATTTGGGTTTTTGTACTTAATGGTA 57.016 29.630 0.00 0.00 0.00 3.25
853 864 8.894768 TGAATTTGGGTTTTTGTACTTAATGG 57.105 30.769 0.00 0.00 0.00 3.16
854 865 8.987890 CCTGAATTTGGGTTTTTGTACTTAATG 58.012 33.333 0.00 0.00 0.00 1.90
855 866 7.659799 GCCTGAATTTGGGTTTTTGTACTTAAT 59.340 33.333 0.00 0.00 0.00 1.40
857 868 6.463190 GGCCTGAATTTGGGTTTTTGTACTTA 60.463 38.462 0.00 0.00 0.00 2.24
858 869 5.364778 GCCTGAATTTGGGTTTTTGTACTT 58.635 37.500 0.00 0.00 0.00 2.24
859 870 4.202315 GGCCTGAATTTGGGTTTTTGTACT 60.202 41.667 0.00 0.00 0.00 2.73
860 871 4.062293 GGCCTGAATTTGGGTTTTTGTAC 58.938 43.478 0.00 0.00 0.00 2.90
862 873 2.158682 GGGCCTGAATTTGGGTTTTTGT 60.159 45.455 0.84 0.00 0.00 2.83
865 896 1.699083 CTGGGCCTGAATTTGGGTTTT 59.301 47.619 4.53 0.00 0.00 2.43
876 907 1.841302 AAAGATGTCGCTGGGCCTGA 61.841 55.000 15.36 1.81 0.00 3.86
881 912 2.464459 GCCGAAAGATGTCGCTGGG 61.464 63.158 0.00 0.00 39.74 4.45
887 919 3.564027 CGCGGGCCGAAAGATGTC 61.564 66.667 33.44 8.12 40.02 3.06
946 978 4.612412 GTCCACGTTGGGCCGTCA 62.612 66.667 0.00 0.00 35.72 4.35
1096 1129 0.246086 GCACCACACAGAGAGAGAGG 59.754 60.000 0.00 0.00 0.00 3.69
1105 1150 0.438445 CGAATACACGCACCACACAG 59.562 55.000 0.00 0.00 0.00 3.66
1107 1152 0.668096 TCCGAATACACGCACCACAC 60.668 55.000 0.00 0.00 0.00 3.82
1139 1184 1.600916 GCGGCAAAGAGGGTTGTCT 60.601 57.895 0.00 0.00 30.68 3.41
1170 1215 2.422093 GGAATTTCATCGCTCCCCTCTT 60.422 50.000 0.00 0.00 0.00 2.85
1266 1311 9.650539 AGAAAACTATATCGATCTGATGGATTG 57.349 33.333 18.29 12.15 37.99 2.67
1294 1339 9.862371 GCTATATCGATTTTCCATCTAGAGAAA 57.138 33.333 1.71 0.71 0.00 2.52
1381 1429 7.025963 GCTCTCAGAAGGTTAAAATTGTCATG 58.974 38.462 0.00 0.00 0.00 3.07
1401 1449 7.044798 AGTGAAATTCAAGGTATAGTGCTCTC 58.955 38.462 0.00 0.00 0.00 3.20
1414 1462 9.061435 AGAAGAAAAGGAGTAGTGAAATTCAAG 57.939 33.333 0.00 0.00 0.00 3.02
1448 1496 2.732094 CAAACGCTGCAGCAAGGC 60.732 61.111 36.03 12.30 42.21 4.35
1478 1526 6.646439 GTGATGAACACCACAGTATACTGCC 61.646 48.000 28.88 12.12 43.93 4.85
1551 1599 8.564574 GGTCAAACATGAACTAGTTTTATCACA 58.435 33.333 10.02 2.14 35.90 3.58
1819 1867 1.529226 TTCCGCCGTGAAAATGACAT 58.471 45.000 0.00 0.00 0.00 3.06
1820 1868 1.265635 CTTTCCGCCGTGAAAATGACA 59.734 47.619 3.14 0.00 34.06 3.58
1920 1968 7.383029 GCAAAGAAATTGATCACAATGAAGTCA 59.617 33.333 0.00 0.00 44.67 3.41
2013 2061 5.739161 CACAACTTGTAGCTGAAACTTGAAC 59.261 40.000 0.00 0.00 0.00 3.18
2085 2136 4.762956 TTCGACATCAATTGTGCATCAA 57.237 36.364 5.13 0.00 39.18 2.57
2362 2413 5.716228 AGTGTGCAATCCCTCATAAAATCAA 59.284 36.000 0.00 0.00 0.00 2.57
2407 2458 2.870411 AGCACGTAAACAAACAGGAGTC 59.130 45.455 0.00 0.00 0.00 3.36
2521 2572 3.746492 AGGAGCGAATTTGTACTGTGTTC 59.254 43.478 0.00 0.00 0.00 3.18
2564 2615 9.699410 AAACAATAATTCAAGAGGGATGTATGA 57.301 29.630 0.00 0.00 0.00 2.15
2569 2620 7.174107 ACCAAACAATAATTCAAGAGGGATG 57.826 36.000 0.00 0.00 0.00 3.51
2741 2796 6.257849 GCAGTTTATTCTTCCATGACATACGA 59.742 38.462 0.00 0.00 0.00 3.43
2798 2853 9.911788 AAGAATCTGGTTAACATACTGATCAAT 57.088 29.630 8.10 0.00 0.00 2.57
2874 2929 4.888239 GTGCTGGAGAACTAGTATGGTAGA 59.112 45.833 0.00 0.00 0.00 2.59
2899 2954 0.608640 ACTCGAGAACCCGCAATCTT 59.391 50.000 21.68 0.00 0.00 2.40
2980 3035 0.405585 CAGGTCAGTTCCCCACCAAT 59.594 55.000 0.00 0.00 31.99 3.16
3433 3490 4.072131 AGCCGAAGTTTCAGAGCATAAAA 58.928 39.130 0.00 0.00 0.00 1.52
3457 3514 1.465689 CGTCAACGCAAGCCTTATTGG 60.466 52.381 0.00 0.00 45.62 3.16
3745 3871 6.146898 GGAAAGTTCTCGATCTATGAGCTAC 58.853 44.000 0.00 0.00 33.41 3.58
3757 3883 7.617225 TGGAAATTAGTATGGAAAGTTCTCGA 58.383 34.615 0.00 0.00 32.02 4.04
4054 4180 2.894765 TCAACGGTAAGAGACATGACCA 59.105 45.455 0.00 0.00 31.89 4.02
4198 4324 8.579850 ACAGCTTTAATCACCATTAGAAATGA 57.420 30.769 1.23 0.00 0.00 2.57
4326 4452 2.231716 TACTAAGAGCAGGTGCCTCA 57.768 50.000 0.00 0.00 43.38 3.86
4564 4690 9.751542 AGACTATATTATTCAGAAACTTGGTCG 57.248 33.333 0.00 0.00 0.00 4.79
4868 4994 7.646130 CCAGTCGTTGTTCTTAATTAAAAAGCA 59.354 33.333 0.00 0.00 0.00 3.91
5038 5164 6.009589 TCCTTATTTTTCATTGTGCTCAGGA 58.990 36.000 0.00 0.00 0.00 3.86
5131 5352 7.543868 TGTTATCAAAAAGGATAAATGCCAACG 59.456 33.333 0.00 0.00 40.41 4.10
5132 5353 8.770438 TGTTATCAAAAAGGATAAATGCCAAC 57.230 30.769 0.00 0.00 40.41 3.77
5202 6993 6.455360 AAATGAGACTTCTTGCTGAAAACA 57.545 33.333 0.00 0.00 33.79 2.83
5224 7015 9.571810 CAGCTTTGCTACATAAATGTTTCATAA 57.428 29.630 0.12 0.00 41.97 1.90
5232 7023 7.809331 TGAAACTTCAGCTTTGCTACATAAATG 59.191 33.333 0.00 0.00 36.40 2.32
5257 7048 5.771666 ACAAGGGATGGATGTTATAAGCATG 59.228 40.000 5.59 0.00 0.00 4.06
5588 7379 2.367894 TGCTGATCTGATAGCTCCAAGG 59.632 50.000 3.42 0.00 40.52 3.61
5697 7488 7.517259 GCCTTTCTAAAACAAAGTGCTCAAATG 60.517 37.037 0.00 0.00 30.53 2.32
5737 7532 5.471116 CCTGGAATGATATCAATGCGAGAAA 59.529 40.000 9.99 0.00 0.00 2.52
5743 7538 4.401519 CCCATCCTGGAATGATATCAATGC 59.598 45.833 9.99 7.46 40.96 3.56
5842 7637 5.250200 TGCATGGTTTTTAGTTCTCGGTAT 58.750 37.500 0.00 0.00 0.00 2.73
5864 7659 9.620660 AATCTACGCTTGGTAAAACTATTTTTG 57.379 29.630 1.32 0.00 35.62 2.44
6075 7877 4.004196 ACTCCCTCCGTTTACAAAAGAG 57.996 45.455 0.00 0.00 0.00 2.85
6076 7878 5.299949 GTTACTCCCTCCGTTTACAAAAGA 58.700 41.667 0.00 0.00 0.00 2.52
6077 7879 4.151157 CGTTACTCCCTCCGTTTACAAAAG 59.849 45.833 0.00 0.00 0.00 2.27
6078 7880 4.057432 CGTTACTCCCTCCGTTTACAAAA 58.943 43.478 0.00 0.00 0.00 2.44
6119 7921 3.859386 GCAGTCCAAGTTCTGTTTTTGTG 59.141 43.478 0.00 0.00 34.57 3.33
6176 7979 1.963338 GAGTGCAAGTTCCGCTGCT 60.963 57.895 0.00 0.00 0.00 4.24
6204 8007 5.962433 GCATTCCATCATTTATGCTGCTAT 58.038 37.500 0.00 0.00 40.08 2.97
6205 8008 5.381174 GCATTCCATCATTTATGCTGCTA 57.619 39.130 0.00 0.00 40.08 3.49
6303 8106 4.354893 AAAGAAAATTGCCATCCTTGCA 57.645 36.364 0.00 0.00 36.84 4.08
6306 8109 6.364568 AGCTAAAAGAAAATTGCCATCCTT 57.635 33.333 0.00 0.00 0.00 3.36
6411 8216 3.130516 AGTCGTCTCCAGCAAATCGATAA 59.869 43.478 0.00 0.00 0.00 1.75
6422 8227 2.520979 GATCGTCAAAGTCGTCTCCAG 58.479 52.381 0.00 0.00 0.00 3.86
6484 12676 2.108970 AGTAACCTCGGGAGATTGGTC 58.891 52.381 0.00 0.00 36.51 4.02
6674 12866 2.436417 AGCCATTGCAACTTCGTGTAT 58.564 42.857 0.00 0.00 41.13 2.29
6716 12908 8.540507 AGATCCATCTAGTAGCTTTTTACTGA 57.459 34.615 0.00 0.00 35.57 3.41
6717 12909 9.685828 GTAGATCCATCTAGTAGCTTTTTACTG 57.314 37.037 0.00 0.00 39.87 2.74


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

AutoCloner maintained by Alex Coulton.