Multiple sequence alignment - TraesCS4B01G331100

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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 TraesCS4B01G331100 chr4B 100.000 2966 0 0 1 2966 621715618 621712653 0.000000e+00 5478.0
1 TraesCS4B01G331100 chr4B 88.732 71 7 1 2290 2359 508978467 508978537 5.270000e-13 86.1
2 TraesCS4B01G331100 chr5A 91.834 2045 130 20 933 2964 667306224 667304204 0.000000e+00 2817.0
3 TraesCS4B01G331100 chr5A 95.238 42 2 0 723 764 416182706 416182747 1.910000e-07 67.6
4 TraesCS4B01G331100 chr4D 89.383 1620 111 30 1388 2964 486933120 486931519 0.000000e+00 1982.0
5 TraesCS4B01G331100 chr4D 89.784 509 28 10 909 1396 486933654 486933149 5.400000e-177 630.0
6 TraesCS4B01G331100 chr4D 78.906 512 75 13 23 526 486936166 486935680 1.720000e-82 316.0
7 TraesCS4B01G331100 chr4D 100.000 36 0 0 813 848 486935428 486935393 1.910000e-07 67.6
8 TraesCS4B01G331100 chr6D 95.455 44 1 1 722 764 31481096 31481053 5.300000e-08 69.4
9 TraesCS4B01G331100 chr6A 95.455 44 1 1 722 764 31744141 31744184 5.300000e-08 69.4
10 TraesCS4B01G331100 chr6B 80.899 89 13 4 726 813 696292169 696292254 1.910000e-07 67.6
11 TraesCS4B01G331100 chr2D 95.122 41 2 0 725 765 426932159 426932199 6.860000e-07 65.8
12 TraesCS4B01G331100 chr2A 95.122 41 2 0 725 765 562095058 562095098 6.860000e-07 65.8
13 TraesCS4B01G331100 chr1B 95.122 41 2 0 725 765 643168399 643168359 6.860000e-07 65.8
14 TraesCS4B01G331100 chr1B 93.023 43 3 0 724 766 621487508 621487466 2.470000e-06 63.9
15 TraesCS4B01G331100 chr2B 89.796 49 4 1 725 772 51108062 51108014 8.880000e-06 62.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G331100 chr4B 621712653 621715618 2965 True 5478.0 5478 100.00000 1 2966 1 chr4B.!!$R1 2965
1 TraesCS4B01G331100 chr5A 667304204 667306224 2020 True 2817.0 2817 91.83400 933 2964 1 chr5A.!!$R1 2031
2 TraesCS4B01G331100 chr4D 486931519 486936166 4647 True 748.9 1982 89.51825 23 2964 4 chr4D.!!$R1 2941


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
19 20 0.035343 GAGGAAAGCCACCACCTACC 60.035 60.0 0.0 0.0 36.29 3.18 F
273 275 0.037326 GACAGGGACTCGCATTGTCA 60.037 55.0 9.4 0.0 38.36 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 3737 1.271379 ACAACCTTCTTCCATGACGGG 60.271 52.381 0.00 0.0 34.36 5.28 R
2176 4008 0.617935 TGGGATGCAATCGAGTTCCA 59.382 50.000 4.62 0.0 46.86 3.53 R


All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.553109 GAGGAAAGCCACCACCTAC 57.447 57.895 0.00 0.00 36.29 3.18
19 20 0.035343 GAGGAAAGCCACCACCTACC 60.035 60.000 0.00 0.00 36.29 3.18
20 21 0.770557 AGGAAAGCCACCACCTACCA 60.771 55.000 0.00 0.00 36.29 3.25
21 22 0.608308 GGAAAGCCACCACCTACCAC 60.608 60.000 0.00 0.00 0.00 4.16
22 23 0.608308 GAAAGCCACCACCTACCACC 60.608 60.000 0.00 0.00 0.00 4.61
23 24 1.357272 AAAGCCACCACCTACCACCA 61.357 55.000 0.00 0.00 0.00 4.17
24 25 1.140134 AAGCCACCACCTACCACCAT 61.140 55.000 0.00 0.00 0.00 3.55
25 26 1.077716 GCCACCACCTACCACCATC 60.078 63.158 0.00 0.00 0.00 3.51
26 27 1.607612 CCACCACCTACCACCATCC 59.392 63.158 0.00 0.00 0.00 3.51
27 28 1.204786 CCACCACCTACCACCATCCA 61.205 60.000 0.00 0.00 0.00 3.41
28 29 0.918983 CACCACCTACCACCATCCAT 59.081 55.000 0.00 0.00 0.00 3.41
29 30 0.918983 ACCACCTACCACCATCCATG 59.081 55.000 0.00 0.00 0.00 3.66
30 31 0.466189 CCACCTACCACCATCCATGC 60.466 60.000 0.00 0.00 0.00 4.06
31 32 0.255604 CACCTACCACCATCCATGCA 59.744 55.000 0.00 0.00 0.00 3.96
32 33 0.255890 ACCTACCACCATCCATGCAC 59.744 55.000 0.00 0.00 0.00 4.57
33 34 0.466189 CCTACCACCATCCATGCACC 60.466 60.000 0.00 0.00 0.00 5.01
34 35 0.466189 CTACCACCATCCATGCACCC 60.466 60.000 0.00 0.00 0.00 4.61
35 36 1.932156 TACCACCATCCATGCACCCC 61.932 60.000 0.00 0.00 0.00 4.95
36 37 2.359797 CACCATCCATGCACCCCA 59.640 61.111 0.00 0.00 0.00 4.96
42 43 0.998928 ATCCATGCACCCCAGTACAA 59.001 50.000 0.00 0.00 0.00 2.41
55 56 3.193691 CCCAGTACAAAACACCAAACACA 59.806 43.478 0.00 0.00 0.00 3.72
72 73 2.618241 ACACAACTGCAACAATCGACAT 59.382 40.909 0.00 0.00 0.00 3.06
79 80 1.135972 GCAACAATCGACATCAACGCT 60.136 47.619 0.00 0.00 0.00 5.07
81 82 3.659735 CAACAATCGACATCAACGCTAC 58.340 45.455 0.00 0.00 0.00 3.58
82 83 1.917955 ACAATCGACATCAACGCTACG 59.082 47.619 0.00 0.00 0.00 3.51
84 85 0.100682 ATCGACATCAACGCTACGCT 59.899 50.000 0.00 0.00 0.00 5.07
85 86 0.109458 TCGACATCAACGCTACGCTT 60.109 50.000 0.00 0.00 0.00 4.68
88 89 1.321743 GACATCAACGCTACGCTTGAG 59.678 52.381 9.55 6.06 33.42 3.02
93 94 0.314302 AACGCTACGCTTGAGTGTCT 59.686 50.000 0.00 0.00 36.65 3.41
98 99 2.171940 CGCTTGAGTGTCTTGCGC 59.828 61.111 0.00 0.00 40.15 6.09
129 130 3.181475 GGACACAAATCTCGCTAGATCCA 60.181 47.826 0.55 0.00 41.81 3.41
130 131 4.433615 GACACAAATCTCGCTAGATCCAA 58.566 43.478 0.55 0.00 41.81 3.53
131 132 4.437239 ACACAAATCTCGCTAGATCCAAG 58.563 43.478 0.55 0.00 41.81 3.61
132 133 4.160439 ACACAAATCTCGCTAGATCCAAGA 59.840 41.667 0.55 0.00 41.81 3.02
133 134 4.505922 CACAAATCTCGCTAGATCCAAGAC 59.494 45.833 0.55 0.00 41.81 3.01
134 135 4.054671 CAAATCTCGCTAGATCCAAGACC 58.945 47.826 0.55 0.00 41.81 3.85
135 136 1.309950 TCTCGCTAGATCCAAGACCG 58.690 55.000 0.00 0.00 0.00 4.79
136 137 0.312416 CTCGCTAGATCCAAGACCGG 59.688 60.000 0.00 0.00 0.00 5.28
137 138 1.300233 CGCTAGATCCAAGACCGGC 60.300 63.158 0.00 0.00 0.00 6.13
138 139 1.823295 GCTAGATCCAAGACCGGCA 59.177 57.895 0.00 0.00 0.00 5.69
139 140 0.178068 GCTAGATCCAAGACCGGCAA 59.822 55.000 0.00 0.00 0.00 4.52
153 154 1.675641 GGCAAGAAGACCGCACCAT 60.676 57.895 0.00 0.00 0.00 3.55
154 155 1.244019 GGCAAGAAGACCGCACCATT 61.244 55.000 0.00 0.00 0.00 3.16
179 180 3.186613 GGCACCTCTGAAAGAAAACTACG 59.813 47.826 0.00 0.00 46.34 3.51
181 182 3.186613 CACCTCTGAAAGAAAACTACGCC 59.813 47.826 0.00 0.00 46.34 5.68
182 183 2.742589 CCTCTGAAAGAAAACTACGCCC 59.257 50.000 0.00 0.00 46.34 6.13
194 195 2.249139 ACTACGCCCATCCTATCTTCC 58.751 52.381 0.00 0.00 0.00 3.46
195 196 1.202582 CTACGCCCATCCTATCTTCCG 59.797 57.143 0.00 0.00 0.00 4.30
221 223 0.768221 TGAAACTGCTGAGGTCCCCT 60.768 55.000 0.00 0.00 36.03 4.79
253 255 0.941542 CTAGAGAGGCGGACGAAGAG 59.058 60.000 0.00 0.00 0.00 2.85
259 261 2.182030 GCGGACGAAGAGGACAGG 59.818 66.667 0.00 0.00 0.00 4.00
268 270 0.616111 AAGAGGACAGGGACTCGCAT 60.616 55.000 0.00 0.00 34.60 4.73
273 275 0.037326 GACAGGGACTCGCATTGTCA 60.037 55.000 9.40 0.00 38.36 3.58
275 277 1.021390 CAGGGACTCGCATTGTCACC 61.021 60.000 0.00 0.00 38.52 4.02
276 278 1.003839 GGGACTCGCATTGTCACCA 60.004 57.895 0.00 0.00 36.26 4.17
282 284 2.158300 CGCATTGTCACCAGCGTTA 58.842 52.632 0.00 0.00 44.67 3.18
290 292 2.626266 TGTCACCAGCGTTAAGAGAAGA 59.374 45.455 0.00 0.00 0.00 2.87
300 302 6.034470 CAGCGTTAAGAGAAGACAAGAAGATC 59.966 42.308 0.00 0.00 0.00 2.75
301 303 5.864474 GCGTTAAGAGAAGACAAGAAGATCA 59.136 40.000 0.00 0.00 0.00 2.92
303 305 6.863645 CGTTAAGAGAAGACAAGAAGATCACA 59.136 38.462 0.00 0.00 0.00 3.58
304 306 7.543868 CGTTAAGAGAAGACAAGAAGATCACAT 59.456 37.037 0.00 0.00 0.00 3.21
305 307 8.868916 GTTAAGAGAAGACAAGAAGATCACATC 58.131 37.037 0.00 0.00 0.00 3.06
306 308 5.976458 AGAGAAGACAAGAAGATCACATCC 58.024 41.667 0.00 0.00 0.00 3.51
307 309 5.096443 AGAAGACAAGAAGATCACATCCC 57.904 43.478 0.00 0.00 0.00 3.85
308 310 4.782156 AGAAGACAAGAAGATCACATCCCT 59.218 41.667 0.00 0.00 0.00 4.20
309 311 5.960811 AGAAGACAAGAAGATCACATCCCTA 59.039 40.000 0.00 0.00 0.00 3.53
310 312 6.441924 AGAAGACAAGAAGATCACATCCCTAA 59.558 38.462 0.00 0.00 0.00 2.69
311 313 5.983540 AGACAAGAAGATCACATCCCTAAC 58.016 41.667 0.00 0.00 0.00 2.34
312 314 5.485353 AGACAAGAAGATCACATCCCTAACA 59.515 40.000 0.00 0.00 0.00 2.41
313 315 5.491982 ACAAGAAGATCACATCCCTAACAC 58.508 41.667 0.00 0.00 0.00 3.32
314 316 4.762289 AGAAGATCACATCCCTAACACC 57.238 45.455 0.00 0.00 0.00 4.16
315 317 4.366267 AGAAGATCACATCCCTAACACCT 58.634 43.478 0.00 0.00 0.00 4.00
316 318 4.785376 AGAAGATCACATCCCTAACACCTT 59.215 41.667 0.00 0.00 0.00 3.50
330 332 0.310854 CACCTTGCTGGAACGGTTTC 59.689 55.000 0.00 0.00 39.71 2.78
341 343 0.883370 AACGGTTTCCAGGAGCGAAC 60.883 55.000 6.74 0.62 40.15 3.95
345 347 2.774687 GGTTTCCAGGAGCGAACTAAA 58.225 47.619 3.05 0.00 0.00 1.85
347 349 3.400255 GTTTCCAGGAGCGAACTAAACT 58.600 45.455 0.00 0.00 0.00 2.66
356 358 4.451096 GGAGCGAACTAAACTGTTGATTCA 59.549 41.667 0.00 0.00 0.00 2.57
359 361 5.470098 AGCGAACTAAACTGTTGATTCACAT 59.530 36.000 0.00 0.00 0.00 3.21
362 364 7.351981 CGAACTAAACTGTTGATTCACATGAA 58.648 34.615 0.00 0.00 38.56 2.57
363 365 7.321271 CGAACTAAACTGTTGATTCACATGAAC 59.679 37.037 0.00 0.00 36.80 3.18
366 368 8.131100 ACTAAACTGTTGATTCACATGAACTTG 58.869 33.333 0.00 0.00 36.80 3.16
389 391 9.993881 CTTGAAAGTACATGAAAAATAAAAGCG 57.006 29.630 0.00 0.00 0.00 4.68
484 487 4.102524 ACAATGAGGTTTAGCGGATGGATA 59.897 41.667 0.00 0.00 0.00 2.59
511 518 7.598759 TTTACCAAAATAGGGTGCAAAGTAA 57.401 32.000 0.00 0.00 39.48 2.24
512 519 7.784470 TTACCAAAATAGGGTGCAAAGTAAT 57.216 32.000 0.00 0.00 39.48 1.89
514 521 6.016555 ACCAAAATAGGGTGCAAAGTAATCT 58.983 36.000 0.00 0.00 37.23 2.40
521 528 9.528489 AATAGGGTGCAAAGTAATCTTAGAAAA 57.472 29.630 0.00 0.00 33.09 2.29
541 548 3.701205 AAATGCAAAGGTTCCAATCCC 57.299 42.857 0.00 0.00 0.00 3.85
542 549 1.185315 ATGCAAAGGTTCCAATCCCG 58.815 50.000 0.00 0.00 0.00 5.14
544 551 0.243636 GCAAAGGTTCCAATCCCGTG 59.756 55.000 0.00 0.00 0.00 4.94
555 591 5.070770 TCCAATCCCGTGAATCAAATTTG 57.929 39.130 12.15 12.15 0.00 2.32
559 648 4.497473 TCCCGTGAATCAAATTTGTGAC 57.503 40.909 17.47 10.24 0.00 3.67
564 653 6.410038 CCGTGAATCAAATTTGTGACAAAAC 58.590 36.000 15.31 5.13 0.00 2.43
565 654 6.035435 CCGTGAATCAAATTTGTGACAAAACA 59.965 34.615 15.31 4.63 0.00 2.83
572 661 8.334016 TCAAATTTGTGACAAAACATCTTACG 57.666 30.769 15.31 0.63 0.00 3.18
578 667 8.775220 TTGTGACAAAACATCTTACGTTAATG 57.225 30.769 0.00 0.00 0.00 1.90
586 675 8.603242 AAACATCTTACGTTAATGAACAGAGT 57.397 30.769 0.58 0.00 35.06 3.24
646 741 7.888250 GGGAAATACTTTCTCTGATCCAAAT 57.112 36.000 0.00 0.00 37.18 2.32
647 742 7.935520 GGGAAATACTTTCTCTGATCCAAATC 58.064 38.462 0.00 0.00 37.18 2.17
648 743 7.557719 GGGAAATACTTTCTCTGATCCAAATCA 59.442 37.037 0.00 0.00 37.18 2.57
649 744 8.960591 GGAAATACTTTCTCTGATCCAAATCAA 58.039 33.333 0.00 0.00 39.22 2.57
653 748 9.690913 ATACTTTCTCTGATCCAAATCAATTGA 57.309 29.630 11.26 11.26 41.33 2.57
654 749 7.824672 ACTTTCTCTGATCCAAATCAATTGAC 58.175 34.615 11.07 0.00 41.33 3.18
655 750 6.426980 TTCTCTGATCCAAATCAATTGACG 57.573 37.500 11.07 2.30 41.33 4.35
656 751 4.333649 TCTCTGATCCAAATCAATTGACGC 59.666 41.667 11.07 0.00 41.33 5.19
657 752 4.009002 TCTGATCCAAATCAATTGACGCA 58.991 39.130 11.07 1.05 41.33 5.24
658 753 4.095334 TCTGATCCAAATCAATTGACGCAG 59.905 41.667 11.07 10.16 41.33 5.18
659 754 2.634982 TCCAAATCAATTGACGCAGC 57.365 45.000 11.07 0.00 41.85 5.25
660 755 1.202114 TCCAAATCAATTGACGCAGCC 59.798 47.619 11.07 0.00 41.85 4.85
661 756 1.203052 CCAAATCAATTGACGCAGCCT 59.797 47.619 11.07 0.00 41.85 4.58
662 757 2.423185 CCAAATCAATTGACGCAGCCTA 59.577 45.455 11.07 0.00 41.85 3.93
663 758 3.067180 CCAAATCAATTGACGCAGCCTAT 59.933 43.478 11.07 0.00 41.85 2.57
664 759 4.440525 CCAAATCAATTGACGCAGCCTATT 60.441 41.667 11.07 0.00 41.85 1.73
665 760 5.221028 CCAAATCAATTGACGCAGCCTATTA 60.221 40.000 11.07 0.00 41.85 0.98
670 765 2.706555 TGACGCAGCCTATTAGATCG 57.293 50.000 0.00 0.00 0.00 3.69
683 778 6.606395 GCCTATTAGATCGGAGGGAGTATAAA 59.394 42.308 7.18 0.00 0.00 1.40
689 784 7.619512 AGATCGGAGGGAGTATAAAATTTCT 57.380 36.000 0.00 0.00 0.00 2.52
693 788 7.399634 TCGGAGGGAGTATAAAATTTCTTTGT 58.600 34.615 0.00 0.00 0.00 2.83
702 797 9.916397 AGTATAAAATTTCTTTGTATCGAAGCG 57.084 29.630 0.00 0.00 0.00 4.68
703 798 9.698617 GTATAAAATTTCTTTGTATCGAAGCGT 57.301 29.630 0.00 0.00 0.00 5.07
706 801 3.587797 TTCTTTGTATCGAAGCGTCCT 57.412 42.857 0.00 0.00 0.00 3.85
707 802 3.587797 TCTTTGTATCGAAGCGTCCTT 57.412 42.857 0.00 0.00 0.00 3.36
709 804 4.418392 TCTTTGTATCGAAGCGTCCTTAC 58.582 43.478 0.00 0.00 0.00 2.34
724 819 5.519722 CGTCCTTACAAAGAATTGCAAACT 58.480 37.500 1.71 3.20 40.34 2.66
725 820 6.664515 CGTCCTTACAAAGAATTGCAAACTA 58.335 36.000 1.71 0.00 40.34 2.24
726 821 6.577427 CGTCCTTACAAAGAATTGCAAACTAC 59.423 38.462 1.71 0.00 40.34 2.73
727 822 7.519970 CGTCCTTACAAAGAATTGCAAACTACT 60.520 37.037 1.71 0.00 40.34 2.57
728 823 8.135529 GTCCTTACAAAGAATTGCAAACTACTT 58.864 33.333 1.71 4.20 40.34 2.24
729 824 8.349983 TCCTTACAAAGAATTGCAAACTACTTC 58.650 33.333 1.71 2.00 40.34 3.01
730 825 7.595130 CCTTACAAAGAATTGCAAACTACTTCC 59.405 37.037 1.71 0.00 40.34 3.46
731 826 6.715347 ACAAAGAATTGCAAACTACTTCCT 57.285 33.333 1.71 0.00 40.34 3.36
732 827 6.739112 ACAAAGAATTGCAAACTACTTCCTC 58.261 36.000 1.71 0.00 40.34 3.71
733 828 5.966742 AAGAATTGCAAACTACTTCCTCC 57.033 39.130 1.71 0.00 0.00 4.30
734 829 5.248380 AGAATTGCAAACTACTTCCTCCT 57.752 39.130 1.71 0.00 0.00 3.69
735 830 5.635120 AGAATTGCAAACTACTTCCTCCTT 58.365 37.500 1.71 0.00 0.00 3.36
736 831 5.707764 AGAATTGCAAACTACTTCCTCCTTC 59.292 40.000 1.71 0.00 0.00 3.46
737 832 4.706842 TTGCAAACTACTTCCTCCTTCT 57.293 40.909 0.00 0.00 0.00 2.85
738 833 4.273148 TGCAAACTACTTCCTCCTTCTC 57.727 45.455 0.00 0.00 0.00 2.87
739 834 3.646162 TGCAAACTACTTCCTCCTTCTCA 59.354 43.478 0.00 0.00 0.00 3.27
740 835 4.287067 TGCAAACTACTTCCTCCTTCTCAT 59.713 41.667 0.00 0.00 0.00 2.90
741 836 5.483937 TGCAAACTACTTCCTCCTTCTCATA 59.516 40.000 0.00 0.00 0.00 2.15
742 837 6.013725 TGCAAACTACTTCCTCCTTCTCATAA 60.014 38.462 0.00 0.00 0.00 1.90
743 838 7.051000 GCAAACTACTTCCTCCTTCTCATAAT 58.949 38.462 0.00 0.00 0.00 1.28
744 839 8.204836 GCAAACTACTTCCTCCTTCTCATAATA 58.795 37.037 0.00 0.00 0.00 0.98
751 846 8.811994 ACTTCCTCCTTCTCATAATATAAGAGC 58.188 37.037 0.00 0.00 0.00 4.09
752 847 7.397892 TCCTCCTTCTCATAATATAAGAGCG 57.602 40.000 0.00 0.00 0.00 5.03
753 848 6.948886 TCCTCCTTCTCATAATATAAGAGCGT 59.051 38.462 0.00 0.00 0.00 5.07
754 849 7.451877 TCCTCCTTCTCATAATATAAGAGCGTT 59.548 37.037 0.00 0.00 0.00 4.84
755 850 8.091449 CCTCCTTCTCATAATATAAGAGCGTTT 58.909 37.037 0.00 0.00 0.00 3.60
756 851 9.482627 CTCCTTCTCATAATATAAGAGCGTTTT 57.517 33.333 0.00 0.00 0.00 2.43
757 852 9.832445 TCCTTCTCATAATATAAGAGCGTTTTT 57.168 29.630 0.00 0.00 0.00 1.94
810 905 9.683870 ACTTATATTATACTAAGACGGAGGGAG 57.316 37.037 0.00 0.00 0.00 4.30
811 906 9.683870 CTTATATTATACTAAGACGGAGGGAGT 57.316 37.037 0.00 0.00 0.00 3.85
848 943 5.815233 TGAAACAAATTTGCCATAGGGAA 57.185 34.783 18.12 0.00 35.59 3.97
849 944 5.792741 TGAAACAAATTTGCCATAGGGAAG 58.207 37.500 18.12 0.00 33.87 3.46
850 945 5.541868 TGAAACAAATTTGCCATAGGGAAGA 59.458 36.000 18.12 0.00 33.87 2.87
851 946 6.213195 TGAAACAAATTTGCCATAGGGAAGAT 59.787 34.615 18.12 0.00 33.87 2.40
853 948 4.651045 ACAAATTTGCCATAGGGAAGATCC 59.349 41.667 18.12 0.00 33.87 3.36
880 996 0.329261 CCTTGCCCCATCTGTCAGAA 59.671 55.000 6.64 0.00 0.00 3.02
881 997 1.272092 CCTTGCCCCATCTGTCAGAAA 60.272 52.381 6.64 0.00 0.00 2.52
883 999 2.425143 TGCCCCATCTGTCAGAAATC 57.575 50.000 6.64 0.00 0.00 2.17
885 1001 2.295885 GCCCCATCTGTCAGAAATCAG 58.704 52.381 6.64 0.00 0.00 2.90
891 1007 3.685139 TCTGTCAGAAATCAGGGACAC 57.315 47.619 0.00 0.00 35.51 3.67
902 1018 2.507484 TCAGGGACACAGAAATGCAAG 58.493 47.619 0.00 0.00 0.00 4.01
903 1019 2.158623 TCAGGGACACAGAAATGCAAGT 60.159 45.455 0.00 0.00 0.00 3.16
904 1020 2.227388 CAGGGACACAGAAATGCAAGTC 59.773 50.000 0.00 0.00 0.00 3.01
905 1021 1.197721 GGGACACAGAAATGCAAGTCG 59.802 52.381 0.00 0.00 0.00 4.18
906 1022 2.143122 GGACACAGAAATGCAAGTCGA 58.857 47.619 0.00 0.00 0.00 4.20
907 1023 2.096218 GGACACAGAAATGCAAGTCGAC 60.096 50.000 7.70 7.70 0.00 4.20
909 1025 2.802816 ACACAGAAATGCAAGTCGACTC 59.197 45.455 20.33 8.01 0.00 3.36
911 1027 2.802816 ACAGAAATGCAAGTCGACTCAC 59.197 45.455 20.33 14.39 0.00 3.51
925 2699 1.957695 CTCACGCTCTTGCTGTGCA 60.958 57.895 0.00 0.00 40.62 4.57
944 2718 0.457851 AGTAGCATCTGACACTCGCC 59.542 55.000 0.00 0.00 0.00 5.54
946 2720 0.173481 TAGCATCTGACACTCGCCAC 59.827 55.000 0.00 0.00 0.00 5.01
960 2734 2.368011 GCCACCTCCTACCCACCTC 61.368 68.421 0.00 0.00 0.00 3.85
961 2735 1.689582 CCACCTCCTACCCACCTCC 60.690 68.421 0.00 0.00 0.00 4.30
962 2736 1.392534 CACCTCCTACCCACCTCCT 59.607 63.158 0.00 0.00 0.00 3.69
963 2737 0.635009 CACCTCCTACCCACCTCCTA 59.365 60.000 0.00 0.00 0.00 2.94
964 2738 1.220750 CACCTCCTACCCACCTCCTAT 59.779 57.143 0.00 0.00 0.00 2.57
967 2741 0.865362 TCCTACCCACCTCCTATCCC 59.135 60.000 0.00 0.00 0.00 3.85
968 2742 0.178900 CCTACCCACCTCCTATCCCC 60.179 65.000 0.00 0.00 0.00 4.81
969 2743 0.868186 CTACCCACCTCCTATCCCCT 59.132 60.000 0.00 0.00 0.00 4.79
970 2744 1.223337 CTACCCACCTCCTATCCCCTT 59.777 57.143 0.00 0.00 0.00 3.95
992 2769 1.096386 CGTCCGTCTAGGTCTGGAGG 61.096 65.000 0.00 0.00 41.99 4.30
1221 3010 0.816373 GTCGGTACCCACCTCTTCTC 59.184 60.000 6.25 0.00 43.33 2.87
1224 3013 1.196012 GGTACCCACCTCTTCTCCTG 58.804 60.000 0.00 0.00 42.11 3.86
1229 3018 0.251634 CCACCTCTTCTCCTGCTTCC 59.748 60.000 0.00 0.00 0.00 3.46
1252 3041 4.435253 CGCAGCTAGTTTCTTCACATCTTG 60.435 45.833 0.00 0.00 0.00 3.02
1262 3051 6.455360 TTCTTCACATCTTGTTTTGCTTCT 57.545 33.333 0.00 0.00 0.00 2.85
1265 3054 5.428496 TCACATCTTGTTTTGCTTCTCTG 57.572 39.130 0.00 0.00 0.00 3.35
1308 3097 9.849166 TTCGTTGATAAAGATGGAAATTTTACC 57.151 29.630 0.00 0.00 0.00 2.85
1357 3149 6.705863 ATTATCCAGTTTCTGAATTGAGGC 57.294 37.500 0.00 0.00 32.44 4.70
1396 3188 6.600427 TGGCATGTTCATATGTATGGATGATC 59.400 38.462 1.90 0.00 32.27 2.92
1629 3458 0.617535 AAGGCCAGGCATTTAACCCC 60.618 55.000 15.19 0.00 0.00 4.95
1830 3659 2.957402 TGCCCAACACTGATCTTCTT 57.043 45.000 0.00 0.00 0.00 2.52
1902 3731 0.761802 GATGGTGGGATGAGGTCTCC 59.238 60.000 0.00 0.00 0.00 3.71
1905 3734 2.764128 TGGGATGAGGTCTCCGCC 60.764 66.667 0.00 0.00 33.29 6.13
1908 3737 4.593864 GATGAGGTCTCCGCCCGC 62.594 72.222 0.00 0.00 0.00 6.13
2034 3864 2.289547 ACGTTCTGTTATGTGTTGCCAC 59.710 45.455 0.00 0.00 42.19 5.01
2176 4008 1.696063 ATTCTGTGCTGTTGCCTGTT 58.304 45.000 0.00 0.00 38.71 3.16
2257 4089 3.139077 CCTGTTACTTTCAGTGGGTCAC 58.861 50.000 0.00 0.00 34.10 3.67
2317 4150 8.534496 CCTCCATTCCAAATTATTGAAGTTCTT 58.466 33.333 4.17 0.00 38.94 2.52
2336 4169 6.547510 AGTTCTTGCTTTGTCCTAAGTCAAAT 59.452 34.615 0.00 0.00 31.96 2.32
2342 4175 9.691362 TTGCTTTGTCCTAAGTCAAATTTATTC 57.309 29.630 0.00 0.00 31.96 1.75
2470 4308 9.626045 CACATCTTGATTCAATATTGATCCATG 57.374 33.333 18.61 18.10 37.00 3.66
2553 4391 6.203915 TGCGAGTTGTCATTTGTAGTATTTGT 59.796 34.615 0.00 0.00 0.00 2.83
2629 4467 5.904362 AACAAATAGAGTCCTGGCAAATC 57.096 39.130 0.00 0.00 0.00 2.17
2639 4477 2.951269 TGGCAAATCTGAGGCAGTG 58.049 52.632 0.00 0.00 35.21 3.66
2658 4496 5.234757 GCAGTGCAAATGTTCAAAGAATTCA 59.765 36.000 11.09 0.00 32.28 2.57
2678 4539 0.732538 GCGGTGTGTTAATGCAAGCC 60.733 55.000 0.00 0.00 0.00 4.35
2728 4590 7.506971 AGAATGAGATGCTGATTATCACTTGA 58.493 34.615 0.00 0.00 0.00 3.02
2829 4693 8.408043 TGAATTCATCTTGTCATTTTACAGGT 57.592 30.769 3.38 0.00 0.00 4.00
2832 4696 7.681939 TTCATCTTGTCATTTTACAGGTACC 57.318 36.000 2.73 2.73 0.00 3.34
2906 4770 6.830873 AAGCTAAGCACATTCAAAGATTCT 57.169 33.333 0.00 0.00 0.00 2.40
2923 4800 2.315925 TCTTCCATCAGATGAACGGC 57.684 50.000 12.41 0.00 0.00 5.68
2932 4809 5.240183 CCATCAGATGAACGGCTCAATTATT 59.760 40.000 12.41 0.00 37.67 1.40
2964 4841 1.799933 TGGGGGATGTTGCTTTTGTT 58.200 45.000 0.00 0.00 0.00 2.83
2965 4842 1.415659 TGGGGGATGTTGCTTTTGTTG 59.584 47.619 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.035343 GGTAGGTGGTGGCTTTCCTC 60.035 60.000 0.00 0.00 0.00 3.71
2 3 0.608308 GTGGTAGGTGGTGGCTTTCC 60.608 60.000 0.00 0.00 0.00 3.13
3 4 0.608308 GGTGGTAGGTGGTGGCTTTC 60.608 60.000 0.00 0.00 0.00 2.62
4 5 1.357272 TGGTGGTAGGTGGTGGCTTT 61.357 55.000 0.00 0.00 0.00 3.51
6 7 1.541368 ATGGTGGTAGGTGGTGGCT 60.541 57.895 0.00 0.00 0.00 4.75
8 9 1.204786 TGGATGGTGGTAGGTGGTGG 61.205 60.000 0.00 0.00 0.00 4.61
9 10 0.918983 ATGGATGGTGGTAGGTGGTG 59.081 55.000 0.00 0.00 0.00 4.17
10 11 0.918983 CATGGATGGTGGTAGGTGGT 59.081 55.000 0.00 0.00 0.00 4.16
13 14 0.255890 GTGCATGGATGGTGGTAGGT 59.744 55.000 0.00 0.00 0.00 3.08
14 15 0.466189 GGTGCATGGATGGTGGTAGG 60.466 60.000 0.00 0.00 0.00 3.18
15 16 0.466189 GGGTGCATGGATGGTGGTAG 60.466 60.000 0.00 0.00 0.00 3.18
16 17 1.612513 GGGTGCATGGATGGTGGTA 59.387 57.895 0.00 0.00 0.00 3.25
17 18 2.360191 GGGTGCATGGATGGTGGT 59.640 61.111 0.00 0.00 0.00 4.16
18 19 2.442643 GGGGTGCATGGATGGTGG 60.443 66.667 0.00 0.00 0.00 4.61
19 20 1.755395 CTGGGGTGCATGGATGGTG 60.755 63.158 0.00 0.00 0.00 4.17
20 21 0.918799 TACTGGGGTGCATGGATGGT 60.919 55.000 0.00 0.00 0.00 3.55
21 22 0.466189 GTACTGGGGTGCATGGATGG 60.466 60.000 0.00 0.00 0.00 3.51
22 23 0.255604 TGTACTGGGGTGCATGGATG 59.744 55.000 0.00 0.00 33.35 3.51
23 24 0.998928 TTGTACTGGGGTGCATGGAT 59.001 50.000 0.00 0.00 37.84 3.41
24 25 0.774276 TTTGTACTGGGGTGCATGGA 59.226 50.000 0.00 0.00 37.84 3.41
25 26 1.272212 GTTTTGTACTGGGGTGCATGG 59.728 52.381 0.00 0.00 37.84 3.66
26 27 1.959985 TGTTTTGTACTGGGGTGCATG 59.040 47.619 0.00 0.00 37.84 4.06
27 28 1.960689 GTGTTTTGTACTGGGGTGCAT 59.039 47.619 0.00 0.00 37.84 3.96
28 29 1.394618 GTGTTTTGTACTGGGGTGCA 58.605 50.000 0.00 0.00 36.33 4.57
29 30 0.671796 GGTGTTTTGTACTGGGGTGC 59.328 55.000 0.00 0.00 0.00 5.01
30 31 2.060050 TGGTGTTTTGTACTGGGGTG 57.940 50.000 0.00 0.00 0.00 4.61
31 32 2.761767 GTTTGGTGTTTTGTACTGGGGT 59.238 45.455 0.00 0.00 0.00 4.95
32 33 2.761208 TGTTTGGTGTTTTGTACTGGGG 59.239 45.455 0.00 0.00 0.00 4.96
33 34 3.193691 TGTGTTTGGTGTTTTGTACTGGG 59.806 43.478 0.00 0.00 0.00 4.45
34 35 4.442375 TGTGTTTGGTGTTTTGTACTGG 57.558 40.909 0.00 0.00 0.00 4.00
35 36 5.344665 CAGTTGTGTTTGGTGTTTTGTACTG 59.655 40.000 0.00 0.00 0.00 2.74
36 37 5.465935 CAGTTGTGTTTGGTGTTTTGTACT 58.534 37.500 0.00 0.00 0.00 2.73
42 43 3.063485 GTTGCAGTTGTGTTTGGTGTTT 58.937 40.909 0.00 0.00 0.00 2.83
55 56 3.606846 CGTTGATGTCGATTGTTGCAGTT 60.607 43.478 0.00 0.00 0.00 3.16
79 80 2.809181 CGCAAGACACTCAAGCGTA 58.191 52.632 0.00 0.00 43.08 4.42
129 130 1.004918 CGGTCTTCTTGCCGGTCTT 60.005 57.895 1.90 0.00 43.85 3.01
130 131 2.657237 CGGTCTTCTTGCCGGTCT 59.343 61.111 1.90 0.00 43.85 3.85
135 136 1.244019 AATGGTGCGGTCTTCTTGCC 61.244 55.000 0.00 0.00 0.00 4.52
136 137 0.598065 AAATGGTGCGGTCTTCTTGC 59.402 50.000 0.00 0.00 0.00 4.01
137 138 1.068333 CCAAATGGTGCGGTCTTCTTG 60.068 52.381 0.00 0.00 0.00 3.02
138 139 1.247567 CCAAATGGTGCGGTCTTCTT 58.752 50.000 0.00 0.00 0.00 2.52
139 140 0.609131 CCCAAATGGTGCGGTCTTCT 60.609 55.000 0.00 0.00 0.00 2.85
153 154 2.746279 TTCTTTCAGAGGTGCCCAAA 57.254 45.000 0.00 0.00 0.00 3.28
154 155 2.693074 GTTTTCTTTCAGAGGTGCCCAA 59.307 45.455 0.00 0.00 0.00 4.12
165 166 3.078837 GGATGGGCGTAGTTTTCTTTCA 58.921 45.455 0.00 0.00 0.00 2.69
171 172 4.444449 GGAAGATAGGATGGGCGTAGTTTT 60.444 45.833 0.00 0.00 0.00 2.43
176 177 1.202964 TCGGAAGATAGGATGGGCGTA 60.203 52.381 0.00 0.00 33.31 4.42
194 195 1.998315 CTCAGCAGTTTCACTCCATCG 59.002 52.381 0.00 0.00 0.00 3.84
195 196 2.289945 ACCTCAGCAGTTTCACTCCATC 60.290 50.000 0.00 0.00 0.00 3.51
221 223 2.043953 TCTAGCAGCAGGAGCCGA 60.044 61.111 0.00 0.00 43.56 5.54
222 224 2.074230 CTCTCTAGCAGCAGGAGCCG 62.074 65.000 9.09 1.47 43.56 5.52
223 225 1.741525 CTCTCTAGCAGCAGGAGCC 59.258 63.158 9.09 0.00 43.56 4.70
232 234 1.377366 CTTCGTCCGCCTCTCTAGCA 61.377 60.000 0.00 0.00 0.00 3.49
235 237 0.464013 CCTCTTCGTCCGCCTCTCTA 60.464 60.000 0.00 0.00 0.00 2.43
253 255 0.741221 GACAATGCGAGTCCCTGTCC 60.741 60.000 0.00 0.00 32.10 4.02
259 261 1.639298 GCTGGTGACAATGCGAGTCC 61.639 60.000 0.00 0.00 42.06 3.85
268 270 3.069016 TCTTCTCTTAACGCTGGTGACAA 59.931 43.478 0.00 0.00 42.06 3.18
273 275 3.321111 TCTTGTCTTCTCTTAACGCTGGT 59.679 43.478 0.00 0.00 0.00 4.00
275 277 5.223382 TCTTCTTGTCTTCTCTTAACGCTG 58.777 41.667 0.00 0.00 0.00 5.18
276 278 5.455056 TCTTCTTGTCTTCTCTTAACGCT 57.545 39.130 0.00 0.00 0.00 5.07
282 284 6.405538 GGATGTGATCTTCTTGTCTTCTCTT 58.594 40.000 0.00 0.00 0.00 2.85
290 292 5.491982 GTGTTAGGGATGTGATCTTCTTGT 58.508 41.667 0.00 0.00 0.00 3.16
300 302 2.086869 CAGCAAGGTGTTAGGGATGTG 58.913 52.381 0.00 0.00 0.00 3.21
301 303 1.004745 CCAGCAAGGTGTTAGGGATGT 59.995 52.381 0.00 0.00 0.00 3.06
303 305 1.668826 TCCAGCAAGGTGTTAGGGAT 58.331 50.000 0.00 0.00 39.02 3.85
304 306 1.073284 GTTCCAGCAAGGTGTTAGGGA 59.927 52.381 0.00 0.00 39.02 4.20
305 307 1.534729 GTTCCAGCAAGGTGTTAGGG 58.465 55.000 0.00 0.00 39.02 3.53
306 308 1.156736 CGTTCCAGCAAGGTGTTAGG 58.843 55.000 0.00 0.00 39.02 2.69
307 309 1.156736 CCGTTCCAGCAAGGTGTTAG 58.843 55.000 0.00 0.00 39.02 2.34
308 310 0.470766 ACCGTTCCAGCAAGGTGTTA 59.529 50.000 0.00 0.00 39.02 2.41
309 311 0.395173 AACCGTTCCAGCAAGGTGTT 60.395 50.000 0.00 0.00 37.03 3.32
310 312 0.395173 AAACCGTTCCAGCAAGGTGT 60.395 50.000 0.00 0.00 37.03 4.16
311 313 0.310854 GAAACCGTTCCAGCAAGGTG 59.689 55.000 0.00 0.00 37.03 4.00
312 314 2.715536 GAAACCGTTCCAGCAAGGT 58.284 52.632 0.00 0.00 39.02 3.50
330 332 2.457366 ACAGTTTAGTTCGCTCCTGG 57.543 50.000 0.00 0.00 0.00 4.45
333 335 4.451096 TGAATCAACAGTTTAGTTCGCTCC 59.549 41.667 0.00 0.00 0.00 4.70
341 343 8.344831 TCAAGTTCATGTGAATCAACAGTTTAG 58.655 33.333 0.00 0.00 36.33 1.85
345 347 6.698008 TTCAAGTTCATGTGAATCAACAGT 57.302 33.333 0.00 0.00 36.33 3.55
347 349 7.099266 ACTTTCAAGTTCATGTGAATCAACA 57.901 32.000 0.00 0.00 35.21 3.33
363 365 9.993881 CGCTTTTATTTTTCATGTACTTTCAAG 57.006 29.630 0.00 0.00 0.00 3.02
454 457 5.531659 TCCGCTAAACCTCATTGTACAAAAA 59.468 36.000 13.23 2.77 0.00 1.94
455 458 5.064558 TCCGCTAAACCTCATTGTACAAAA 58.935 37.500 13.23 3.15 0.00 2.44
456 459 4.643463 TCCGCTAAACCTCATTGTACAAA 58.357 39.130 13.23 0.00 0.00 2.83
457 460 4.274602 TCCGCTAAACCTCATTGTACAA 57.725 40.909 11.41 11.41 0.00 2.41
463 466 3.864789 ATCCATCCGCTAAACCTCATT 57.135 42.857 0.00 0.00 0.00 2.57
484 487 7.513856 ACTTTGCACCCTATTTTGGTAAAAAT 58.486 30.769 0.00 2.36 45.70 1.82
521 528 2.028203 CGGGATTGGAACCTTTGCATTT 60.028 45.455 0.00 0.00 0.00 2.32
526 533 1.904287 TCACGGGATTGGAACCTTTG 58.096 50.000 0.00 0.00 0.00 2.77
527 534 2.668144 TTCACGGGATTGGAACCTTT 57.332 45.000 0.00 0.00 0.00 3.11
529 536 1.633432 TGATTCACGGGATTGGAACCT 59.367 47.619 0.00 0.00 0.00 3.50
532 539 5.011533 ACAAATTTGATTCACGGGATTGGAA 59.988 36.000 24.64 0.00 0.00 3.53
534 541 4.626604 CACAAATTTGATTCACGGGATTGG 59.373 41.667 24.64 0.00 0.00 3.16
536 543 5.010516 TGTCACAAATTTGATTCACGGGATT 59.989 36.000 24.64 0.00 0.00 3.01
537 544 4.522405 TGTCACAAATTTGATTCACGGGAT 59.478 37.500 24.64 0.00 0.00 3.85
538 545 3.885901 TGTCACAAATTTGATTCACGGGA 59.114 39.130 24.64 0.00 0.00 5.14
540 547 6.035435 TGTTTTGTCACAAATTTGATTCACGG 59.965 34.615 24.64 5.19 0.00 4.94
541 548 6.987223 TGTTTTGTCACAAATTTGATTCACG 58.013 32.000 24.64 5.82 0.00 4.35
542 549 8.819974 AGATGTTTTGTCACAAATTTGATTCAC 58.180 29.630 24.64 13.93 0.00 3.18
555 591 8.889000 GTTCATTAACGTAAGATGTTTTGTCAC 58.111 33.333 0.00 0.00 43.62 3.67
559 648 9.318041 CTCTGTTCATTAACGTAAGATGTTTTG 57.682 33.333 0.00 0.00 38.53 2.44
564 653 9.318041 CAAAACTCTGTTCATTAACGTAAGATG 57.682 33.333 0.00 0.00 38.53 2.90
565 654 8.504005 CCAAAACTCTGTTCATTAACGTAAGAT 58.496 33.333 0.00 0.00 38.53 2.40
622 717 7.557719 TGATTTGGATCAGAGAAAGTATTTCCC 59.442 37.037 0.00 0.00 45.25 3.97
623 718 8.511604 TGATTTGGATCAGAGAAAGTATTTCC 57.488 34.615 0.00 0.00 45.25 3.13
627 722 9.690913 TCAATTGATTTGGATCAGAGAAAGTAT 57.309 29.630 3.38 0.00 42.90 2.12
628 723 8.950210 GTCAATTGATTTGGATCAGAGAAAGTA 58.050 33.333 12.12 0.00 42.90 2.24
629 724 7.361542 CGTCAATTGATTTGGATCAGAGAAAGT 60.362 37.037 12.12 0.00 42.90 2.66
630 725 6.965500 CGTCAATTGATTTGGATCAGAGAAAG 59.035 38.462 12.12 0.00 42.90 2.62
631 726 6.623549 GCGTCAATTGATTTGGATCAGAGAAA 60.624 38.462 12.12 0.00 42.90 2.52
632 727 5.163723 GCGTCAATTGATTTGGATCAGAGAA 60.164 40.000 12.12 0.00 42.90 2.87
633 728 4.333649 GCGTCAATTGATTTGGATCAGAGA 59.666 41.667 12.12 0.00 42.90 3.10
634 729 4.095334 TGCGTCAATTGATTTGGATCAGAG 59.905 41.667 12.12 0.00 42.90 3.35
635 730 4.009002 TGCGTCAATTGATTTGGATCAGA 58.991 39.130 12.12 0.00 42.90 3.27
636 731 4.348656 CTGCGTCAATTGATTTGGATCAG 58.651 43.478 12.12 7.54 42.90 2.90
637 732 3.427909 GCTGCGTCAATTGATTTGGATCA 60.428 43.478 12.12 2.02 40.46 2.92
638 733 3.111098 GCTGCGTCAATTGATTTGGATC 58.889 45.455 12.12 0.00 35.92 3.36
639 734 2.159198 GGCTGCGTCAATTGATTTGGAT 60.159 45.455 12.12 0.00 35.92 3.41
640 735 1.202114 GGCTGCGTCAATTGATTTGGA 59.798 47.619 12.12 5.47 35.92 3.53
641 736 1.203052 AGGCTGCGTCAATTGATTTGG 59.797 47.619 12.12 4.48 35.92 3.28
642 737 2.642139 AGGCTGCGTCAATTGATTTG 57.358 45.000 12.12 6.20 36.61 2.32
643 738 4.989279 AATAGGCTGCGTCAATTGATTT 57.011 36.364 12.12 0.00 0.00 2.17
644 739 5.368145 TCTAATAGGCTGCGTCAATTGATT 58.632 37.500 12.12 0.98 0.00 2.57
645 740 4.960938 TCTAATAGGCTGCGTCAATTGAT 58.039 39.130 12.12 0.00 0.00 2.57
646 741 4.400529 TCTAATAGGCTGCGTCAATTGA 57.599 40.909 3.38 3.38 0.00 2.57
647 742 4.143242 CGATCTAATAGGCTGCGTCAATTG 60.143 45.833 0.00 0.00 0.00 2.32
648 743 3.990469 CGATCTAATAGGCTGCGTCAATT 59.010 43.478 0.00 0.00 0.00 2.32
649 744 3.579709 CGATCTAATAGGCTGCGTCAAT 58.420 45.455 0.00 0.00 0.00 2.57
650 745 2.288213 CCGATCTAATAGGCTGCGTCAA 60.288 50.000 0.00 0.00 0.00 3.18
651 746 1.269723 CCGATCTAATAGGCTGCGTCA 59.730 52.381 0.00 0.00 0.00 4.35
652 747 1.540267 TCCGATCTAATAGGCTGCGTC 59.460 52.381 0.00 0.00 0.00 5.19
653 748 1.542030 CTCCGATCTAATAGGCTGCGT 59.458 52.381 0.00 0.00 0.00 5.24
654 749 1.135257 CCTCCGATCTAATAGGCTGCG 60.135 57.143 0.00 0.00 0.00 5.18
655 750 1.205893 CCCTCCGATCTAATAGGCTGC 59.794 57.143 0.00 0.00 0.00 5.25
656 751 2.757868 CTCCCTCCGATCTAATAGGCTG 59.242 54.545 0.00 0.00 0.00 4.85
657 752 2.380590 ACTCCCTCCGATCTAATAGGCT 59.619 50.000 0.00 0.00 0.00 4.58
658 753 2.810164 ACTCCCTCCGATCTAATAGGC 58.190 52.381 0.00 0.00 0.00 3.93
659 754 8.591114 TTTTATACTCCCTCCGATCTAATAGG 57.409 38.462 0.00 0.00 0.00 2.57
662 757 9.945904 GAAATTTTATACTCCCTCCGATCTAAT 57.054 33.333 0.00 0.00 0.00 1.73
663 758 9.155785 AGAAATTTTATACTCCCTCCGATCTAA 57.844 33.333 0.00 0.00 0.00 2.10
664 759 8.722622 AGAAATTTTATACTCCCTCCGATCTA 57.277 34.615 0.00 0.00 0.00 1.98
665 760 7.619512 AGAAATTTTATACTCCCTCCGATCT 57.380 36.000 0.00 0.00 0.00 2.75
683 778 4.935808 AGGACGCTTCGATACAAAGAAATT 59.064 37.500 0.00 0.00 0.00 1.82
689 784 4.177165 TGTAAGGACGCTTCGATACAAA 57.823 40.909 4.81 0.00 0.00 2.83
693 788 4.707030 TCTTTGTAAGGACGCTTCGATA 57.293 40.909 0.00 0.00 0.00 2.92
697 792 4.159120 GCAATTCTTTGTAAGGACGCTTC 58.841 43.478 0.00 0.00 35.17 3.86
700 795 3.552604 TGCAATTCTTTGTAAGGACGC 57.447 42.857 0.00 0.00 35.17 5.19
701 796 5.519722 AGTTTGCAATTCTTTGTAAGGACG 58.480 37.500 0.00 0.00 38.43 4.79
702 797 7.649057 AGTAGTTTGCAATTCTTTGTAAGGAC 58.351 34.615 0.00 0.00 38.43 3.85
703 798 7.817418 AGTAGTTTGCAATTCTTTGTAAGGA 57.183 32.000 0.00 0.00 38.43 3.36
706 801 8.232913 AGGAAGTAGTTTGCAATTCTTTGTAA 57.767 30.769 0.00 0.00 35.92 2.41
707 802 7.040686 GGAGGAAGTAGTTTGCAATTCTTTGTA 60.041 37.037 0.00 0.00 35.17 2.41
709 804 6.015940 AGGAGGAAGTAGTTTGCAATTCTTTG 60.016 38.462 0.00 0.00 35.85 2.77
725 820 8.811994 GCTCTTATATTATGAGAAGGAGGAAGT 58.188 37.037 0.47 0.00 33.20 3.01
726 821 7.973388 CGCTCTTATATTATGAGAAGGAGGAAG 59.027 40.741 0.47 0.00 33.20 3.46
727 822 7.451877 ACGCTCTTATATTATGAGAAGGAGGAA 59.548 37.037 0.47 0.00 33.20 3.36
728 823 6.948886 ACGCTCTTATATTATGAGAAGGAGGA 59.051 38.462 0.47 0.00 33.20 3.71
729 824 7.164230 ACGCTCTTATATTATGAGAAGGAGG 57.836 40.000 0.47 0.00 33.20 4.30
730 825 9.482627 AAAACGCTCTTATATTATGAGAAGGAG 57.517 33.333 0.47 0.00 33.20 3.69
731 826 9.832445 AAAAACGCTCTTATATTATGAGAAGGA 57.168 29.630 0.47 0.00 33.20 3.36
784 879 9.683870 CTCCCTCCGTCTTAGTATAATATAAGT 57.316 37.037 0.00 0.00 32.09 2.24
785 880 9.683870 ACTCCCTCCGTCTTAGTATAATATAAG 57.316 37.037 0.00 0.00 0.00 1.73
790 885 8.953223 ATTTACTCCCTCCGTCTTAGTATAAT 57.047 34.615 0.00 0.00 0.00 1.28
791 886 8.773033 AATTTACTCCCTCCGTCTTAGTATAA 57.227 34.615 0.00 0.00 0.00 0.98
792 887 8.773033 AAATTTACTCCCTCCGTCTTAGTATA 57.227 34.615 0.00 0.00 0.00 1.47
793 888 7.564292 AGAAATTTACTCCCTCCGTCTTAGTAT 59.436 37.037 0.00 0.00 0.00 2.12
794 889 6.894103 AGAAATTTACTCCCTCCGTCTTAGTA 59.106 38.462 0.00 0.00 0.00 1.82
795 890 5.720520 AGAAATTTACTCCCTCCGTCTTAGT 59.279 40.000 0.00 0.00 0.00 2.24
796 891 6.223351 AGAAATTTACTCCCTCCGTCTTAG 57.777 41.667 0.00 0.00 0.00 2.18
797 892 7.722949 TTAGAAATTTACTCCCTCCGTCTTA 57.277 36.000 0.00 0.00 0.00 2.10
798 893 6.616237 TTAGAAATTTACTCCCTCCGTCTT 57.384 37.500 0.00 0.00 0.00 3.01
799 894 6.616237 TTTAGAAATTTACTCCCTCCGTCT 57.384 37.500 0.00 0.00 0.00 4.18
800 895 7.860918 AATTTAGAAATTTACTCCCTCCGTC 57.139 36.000 0.00 0.00 35.16 4.79
801 896 8.520351 CAAAATTTAGAAATTTACTCCCTCCGT 58.480 33.333 12.18 0.00 45.16 4.69
802 897 8.736244 TCAAAATTTAGAAATTTACTCCCTCCG 58.264 33.333 12.18 0.00 45.16 4.63
848 943 1.342374 GGGCAAGGTTGGATTGGATCT 60.342 52.381 0.00 0.00 0.00 2.75
849 944 1.114627 GGGCAAGGTTGGATTGGATC 58.885 55.000 0.00 0.00 0.00 3.36
850 945 0.325577 GGGGCAAGGTTGGATTGGAT 60.326 55.000 0.00 0.00 0.00 3.41
851 946 1.078347 GGGGCAAGGTTGGATTGGA 59.922 57.895 0.00 0.00 0.00 3.53
853 948 0.826062 GATGGGGCAAGGTTGGATTG 59.174 55.000 0.00 0.00 0.00 2.67
880 996 3.159213 TGCATTTCTGTGTCCCTGATT 57.841 42.857 0.00 0.00 0.00 2.57
881 997 2.885135 TGCATTTCTGTGTCCCTGAT 57.115 45.000 0.00 0.00 0.00 2.90
883 999 2.227388 GACTTGCATTTCTGTGTCCCTG 59.773 50.000 0.00 0.00 0.00 4.45
885 1001 1.197721 CGACTTGCATTTCTGTGTCCC 59.802 52.381 0.00 0.00 0.00 4.46
891 1007 2.159920 CGTGAGTCGACTTGCATTTCTG 60.160 50.000 21.08 0.00 42.86 3.02
902 1018 3.453465 GCAAGAGCGTGAGTCGAC 58.547 61.111 7.70 7.70 42.86 4.20
911 1027 1.964290 GCTACTGCACAGCAAGAGCG 61.964 60.000 10.08 0.00 41.99 5.03
925 2699 0.457851 GGCGAGTGTCAGATGCTACT 59.542 55.000 0.00 0.00 0.00 2.57
944 2718 0.635009 TAGGAGGTGGGTAGGAGGTG 59.365 60.000 0.00 0.00 0.00 4.00
946 2720 1.203199 GGATAGGAGGTGGGTAGGAGG 60.203 61.905 0.00 0.00 0.00 4.30
960 2734 1.047034 ACGGACGGAAAGGGGATAGG 61.047 60.000 0.00 0.00 0.00 2.57
961 2735 0.388294 GACGGACGGAAAGGGGATAG 59.612 60.000 0.00 0.00 0.00 2.08
962 2736 0.032813 AGACGGACGGAAAGGGGATA 60.033 55.000 0.00 0.00 0.00 2.59
963 2737 0.032813 TAGACGGACGGAAAGGGGAT 60.033 55.000 0.00 0.00 0.00 3.85
964 2738 0.682209 CTAGACGGACGGAAAGGGGA 60.682 60.000 0.00 0.00 0.00 4.81
967 2741 0.455005 GACCTAGACGGACGGAAAGG 59.545 60.000 0.00 2.13 36.31 3.11
968 2742 1.132643 CAGACCTAGACGGACGGAAAG 59.867 57.143 0.00 0.00 36.31 2.62
969 2743 1.171308 CAGACCTAGACGGACGGAAA 58.829 55.000 0.00 0.00 36.31 3.13
970 2744 0.679002 CCAGACCTAGACGGACGGAA 60.679 60.000 0.00 0.00 36.31 4.30
1011 2788 4.747529 GGCCCGTACACCGTCACC 62.748 72.222 0.00 0.00 33.66 4.02
1229 3018 3.257393 AGATGTGAAGAAACTAGCTGCG 58.743 45.455 0.00 0.00 0.00 5.18
1252 3041 4.362279 TGCAATTGACAGAGAAGCAAAAC 58.638 39.130 10.34 0.00 0.00 2.43
1262 3051 1.689984 TGGCACTTGCAATTGACAGA 58.310 45.000 20.45 0.00 44.36 3.41
1265 3054 1.987770 CGAATGGCACTTGCAATTGAC 59.012 47.619 19.89 17.69 44.25 3.18
1357 3149 4.789012 ACATGCCAACACTGGAATTTAG 57.211 40.909 0.00 0.00 46.92 1.85
1396 3188 1.812571 CATTCAGGGGAAAGTCAACCG 59.187 52.381 0.00 0.00 36.43 4.44
1581 3410 2.886610 CATTGCTCAATGGCGGCA 59.113 55.556 16.34 16.34 43.25 5.69
1590 3419 2.820178 TCAGACTCTACCCATTGCTCA 58.180 47.619 0.00 0.00 0.00 4.26
1632 3461 1.669999 GGAATGCGATGGCCAAGCTT 61.670 55.000 28.95 22.62 38.85 3.74
1722 3551 3.923864 ACGTCGAGCACCTTGGCA 61.924 61.111 0.00 0.00 35.83 4.92
1830 3659 1.597854 CTTGCCGGTCTTGCTCACA 60.598 57.895 1.90 0.00 0.00 3.58
1905 3734 1.815421 CTTCTTCCATGACGGGCGG 60.815 63.158 0.00 0.00 34.36 6.13
1908 3737 1.271379 ACAACCTTCTTCCATGACGGG 60.271 52.381 0.00 0.00 34.36 5.28
1984 3814 4.400961 ACCAGAAGCTGCTCGGCC 62.401 66.667 1.00 0.00 0.00 6.13
2034 3864 7.594758 CACAACACAATTAACATTTAGGAGTGG 59.405 37.037 0.00 0.00 0.00 4.00
2176 4008 0.617935 TGGGATGCAATCGAGTTCCA 59.382 50.000 4.62 0.00 46.86 3.53
2257 4089 7.397892 TCAGTAGGTAAAGAGATTGTCAGAG 57.602 40.000 0.00 0.00 0.00 3.35
2288 4120 6.381133 ACTTCAATAATTTGGAATGGAGGGAC 59.619 38.462 0.00 0.00 33.44 4.46
2317 4150 8.855110 TGAATAAATTTGACTTAGGACAAAGCA 58.145 29.630 8.28 0.00 39.50 3.91
2342 4175 8.925161 TTTTTCTACAGAATTGGTCAAACTTG 57.075 30.769 0.00 0.00 33.54 3.16
2355 4188 9.719355 TGTAGATAAGCACATTTTTCTACAGAA 57.281 29.630 12.08 0.00 38.81 3.02
2428 4264 5.108187 AGATGTGTCATCTTGCATTACCT 57.892 39.130 6.45 0.00 0.00 3.08
2588 4426 5.652744 TGTTTCTCAACTTTTCTCGTAGC 57.347 39.130 0.00 0.00 33.58 3.58
2629 4467 1.610038 TGAACATTTGCACTGCCTCAG 59.390 47.619 0.00 0.00 37.52 3.35
2638 4476 4.445052 CGCTGAATTCTTTGAACATTTGCA 59.555 37.500 7.05 0.00 0.00 4.08
2639 4477 4.143263 CCGCTGAATTCTTTGAACATTTGC 60.143 41.667 7.05 0.00 0.00 3.68
2658 4496 0.240945 GCTTGCATTAACACACCGCT 59.759 50.000 0.00 0.00 0.00 5.52
2728 4590 2.662866 AGCTGCCAATATGCATTCACT 58.337 42.857 3.54 0.00 41.16 3.41
2787 4649 8.712285 ATGAATTCATGCTTAAGTTTTCCATG 57.288 30.769 20.11 11.62 34.83 3.66
2791 4653 9.415544 ACAAGATGAATTCATGCTTAAGTTTTC 57.584 29.630 25.37 7.36 36.57 2.29
2906 4770 1.554617 TGAGCCGTTCATCTGATGGAA 59.445 47.619 17.06 7.87 0.00 3.53
2923 4800 6.883217 CCCATATGGAGTCAGGAATAATTGAG 59.117 42.308 24.00 0.00 37.39 3.02
2932 4809 0.948816 TCCCCCATATGGAGTCAGGA 59.051 55.000 24.00 16.30 37.39 3.86



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

AutoCloner maintained by Alex Coulton.