Multiple sequence alignment - TraesCS5D01G549100

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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 TraesCS5D01G549100 chr5D 100.000 3196 0 0 712 3907 556408289 556405094 0.000000e+00 5903.0
1 TraesCS5D01G549100 chr5D 97.068 648 19 0 2141 2788 524291032 524291679 0.000000e+00 1092.0
2 TraesCS5D01G549100 chr5D 100.000 474 0 0 1 474 556409000 556408527 0.000000e+00 876.0
3 TraesCS5D01G549100 chr5D 94.515 474 23 3 1 473 425212648 425213119 0.000000e+00 728.0
4 TraesCS5D01G549100 chr6D 96.604 1767 43 4 2141 3907 294670407 294668658 0.000000e+00 2915.0
5 TraesCS5D01G549100 chr7B 94.284 1767 71 16 2141 3907 601442959 601444695 0.000000e+00 2676.0
6 TraesCS5D01G549100 chr7B 93.910 509 30 1 958 1465 64765323 64764815 0.000000e+00 767.0
7 TraesCS5D01G549100 chr7B 94.105 475 24 4 1 473 27646855 27647327 0.000000e+00 719.0
8 TraesCS5D01G549100 chr7B 96.335 382 13 1 1464 1845 64764784 64764404 9.220000e-176 627.0
9 TraesCS5D01G549100 chr7B 94.444 144 8 0 712 855 603523190 603523047 5.080000e-54 222.0
10 TraesCS5D01G549100 chr7B 95.000 120 4 2 852 971 27647539 27647656 1.850000e-43 187.0
11 TraesCS5D01G549100 chr7B 95.614 114 4 1 852 965 603523015 603522903 8.620000e-42 182.0
12 TraesCS5D01G549100 chr2B 96.514 1463 49 1 2141 3603 707721532 707722992 0.000000e+00 2418.0
13 TraesCS5D01G549100 chr2B 96.648 1253 38 2 2395 3647 701140123 701141371 0.000000e+00 2078.0
14 TraesCS5D01G549100 chr2B 94.444 144 8 0 712 855 726406025 726406168 5.080000e-54 222.0
15 TraesCS5D01G549100 chr2D 96.856 1336 40 2 2573 3907 614005338 614006672 0.000000e+00 2233.0
16 TraesCS5D01G549100 chr2D 96.203 474 16 2 1 473 614003250 614003722 0.000000e+00 774.0
17 TraesCS5D01G549100 chr2D 94.351 478 16 4 1 473 638010018 638010489 0.000000e+00 723.0
18 TraesCS5D01G549100 chr5A 97.209 1254 33 2 2395 3647 649694647 649693395 0.000000e+00 2121.0
19 TraesCS5D01G549100 chr5A 94.824 483 25 0 3417 3899 10663410 10662928 0.000000e+00 754.0
20 TraesCS5D01G549100 chr5A 93.750 144 8 1 712 855 131653413 131653555 8.500000e-52 215.0
21 TraesCS5D01G549100 chr5A 98.165 109 2 0 852 960 131653587 131653695 1.430000e-44 191.0
22 TraesCS5D01G549100 chr7A 96.810 1254 38 2 2395 3647 107667671 107666419 0.000000e+00 2093.0
23 TraesCS5D01G549100 chr7A 95.137 473 18 2 1 473 512539291 512539758 0.000000e+00 741.0
24 TraesCS5D01G549100 chr7A 94.926 473 18 2 1 473 211063518 211063052 0.000000e+00 736.0
25 TraesCS5D01G549100 chr7A 95.506 445 18 2 3463 3907 88100997 88101439 0.000000e+00 710.0
26 TraesCS5D01G549100 chr7A 95.833 144 5 1 712 855 631782320 631782462 8.440000e-57 231.0
27 TraesCS5D01G549100 chr4A 96.571 1254 37 4 2395 3647 660153426 660152178 0.000000e+00 2073.0
28 TraesCS5D01G549100 chr1B 96.409 1253 41 2 2395 3647 622054538 622053290 0.000000e+00 2061.0
29 TraesCS5D01G549100 chr1B 94.303 509 28 1 958 1465 549465777 549465269 0.000000e+00 778.0
30 TraesCS5D01G549100 chr1B 91.833 502 39 2 1466 1966 633331571 633332071 0.000000e+00 699.0
31 TraesCS5D01G549100 chr1B 93.049 446 27 4 1006 1449 633330984 633331427 0.000000e+00 649.0
32 TraesCS5D01G549100 chr1B 96.859 382 11 1 1464 1845 549465238 549464858 4.260000e-179 638.0
33 TraesCS5D01G549100 chr1B 94.068 118 5 2 852 969 587847962 587848077 1.120000e-40 178.0
34 TraesCS5D01G549100 chr1A 92.110 1014 68 9 1006 2012 552211526 552212534 0.000000e+00 1419.0
35 TraesCS5D01G549100 chr1A 88.793 116 13 0 1006 1121 552201610 552201725 4.070000e-30 143.0
36 TraesCS5D01G549100 chr1D 91.124 1014 65 13 1006 2012 461138695 461139690 0.000000e+00 1351.0
37 TraesCS5D01G549100 chr7D 95.519 491 19 2 3417 3905 289818013 289818502 0.000000e+00 782.0
38 TraesCS5D01G549100 chr7D 97.464 276 7 0 3632 3907 592824693 592824418 4.570000e-129 472.0
39 TraesCS5D01G549100 chr7D 98.182 55 1 0 2141 2195 592850153 592850099 3.210000e-16 97.1
40 TraesCS5D01G549100 chr6B 94.106 509 29 1 958 1465 30365047 30364539 0.000000e+00 773.0
41 TraesCS5D01G549100 chr6B 96.073 382 14 1 1464 1845 30364508 30364128 4.290000e-174 621.0
42 TraesCS5D01G549100 chr6B 94.340 212 11 1 958 1168 655258080 655258291 1.350000e-84 324.0
43 TraesCS5D01G549100 chr3B 94.106 509 29 1 958 1465 769345154 769345662 0.000000e+00 773.0
44 TraesCS5D01G549100 chr3B 94.947 475 18 4 1 473 88182144 88181674 0.000000e+00 739.0
45 TraesCS5D01G549100 chr3B 96.859 382 11 1 1464 1845 769345693 769346073 4.260000e-179 638.0
46 TraesCS5D01G549100 chr3B 94.776 134 7 0 714 847 775130205 775130072 3.960000e-50 209.0
47 TraesCS5D01G549100 chr3B 94.872 117 4 2 852 968 775130032 775129918 8.620000e-42 182.0
48 TraesCS5D01G549100 chr3A 94.929 493 23 2 3417 3907 560634619 560634127 0.000000e+00 771.0
49 TraesCS5D01G549100 chr3A 95.775 142 5 1 712 853 8916958 8917098 1.090000e-55 228.0
50 TraesCS5D01G549100 chr2A 94.503 473 21 2 1 473 107733521 107733988 0.000000e+00 725.0
51 TraesCS5D01G549100 chr2A 94.093 474 22 3 1 473 107524880 107525348 0.000000e+00 715.0
52 TraesCS5D01G549100 chr2A 97.183 142 3 1 714 855 24793481 24793341 5.050000e-59 239.0
53 TraesCS5D01G549100 chr2A 94.444 144 7 1 712 855 484063676 484063818 1.830000e-53 220.0
54 TraesCS5D01G549100 chr2A 94.444 144 7 1 712 855 644822187 644822329 1.830000e-53 220.0
55 TraesCS5D01G549100 chr2A 97.248 109 3 0 852 960 484063850 484063958 6.670000e-43 185.0
56 TraesCS5D01G549100 chr2A 96.330 109 4 0 852 960 24793309 24793201 3.100000e-41 180.0
57 TraesCS5D01G549100 chr4B 96.056 431 17 0 3477 3907 397238426 397237996 0.000000e+00 702.0
58 TraesCS5D01G549100 chr5B 97.131 244 7 0 2141 2384 532063748 532063991 2.810000e-111 412.0
59 TraesCS5D01G549100 chrUn 80.292 274 37 14 712 971 312658396 312658126 1.430000e-44 191.0
60 TraesCS5D01G549100 chrUn 80.292 274 37 14 712 971 312666030 312665760 1.430000e-44 191.0
61 TraesCS5D01G549100 chr4D 98.182 55 1 0 2141 2195 458010459 458010405 3.210000e-16 97.1
62 TraesCS5D01G549100 chr4D 98.182 55 1 0 2141 2195 481400642 481400588 3.210000e-16 97.1


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 TraesCS5D01G549100 chr5D 556405094 556409000 3906 True 3389.5 5903 100.0000 1 3907 2 chr5D.!!$R1 3906
1 TraesCS5D01G549100 chr5D 524291032 524291679 647 False 1092.0 1092 97.0680 2141 2788 1 chr5D.!!$F2 647
2 TraesCS5D01G549100 chr6D 294668658 294670407 1749 True 2915.0 2915 96.6040 2141 3907 1 chr6D.!!$R1 1766
3 TraesCS5D01G549100 chr7B 601442959 601444695 1736 False 2676.0 2676 94.2840 2141 3907 1 chr7B.!!$F1 1766
4 TraesCS5D01G549100 chr7B 64764404 64765323 919 True 697.0 767 95.1225 958 1845 2 chr7B.!!$R1 887
5 TraesCS5D01G549100 chr7B 27646855 27647656 801 False 453.0 719 94.5525 1 971 2 chr7B.!!$F2 970
6 TraesCS5D01G549100 chr2B 707721532 707722992 1460 False 2418.0 2418 96.5140 2141 3603 1 chr2B.!!$F2 1462
7 TraesCS5D01G549100 chr2B 701140123 701141371 1248 False 2078.0 2078 96.6480 2395 3647 1 chr2B.!!$F1 1252
8 TraesCS5D01G549100 chr2D 614003250 614006672 3422 False 1503.5 2233 96.5295 1 3907 2 chr2D.!!$F2 3906
9 TraesCS5D01G549100 chr5A 649693395 649694647 1252 True 2121.0 2121 97.2090 2395 3647 1 chr5A.!!$R2 1252
10 TraesCS5D01G549100 chr7A 107666419 107667671 1252 True 2093.0 2093 96.8100 2395 3647 1 chr7A.!!$R1 1252
11 TraesCS5D01G549100 chr4A 660152178 660153426 1248 True 2073.0 2073 96.5710 2395 3647 1 chr4A.!!$R1 1252
12 TraesCS5D01G549100 chr1B 622053290 622054538 1248 True 2061.0 2061 96.4090 2395 3647 1 chr1B.!!$R1 1252
13 TraesCS5D01G549100 chr1B 549464858 549465777 919 True 708.0 778 95.5810 958 1845 2 chr1B.!!$R2 887
14 TraesCS5D01G549100 chr1B 633330984 633332071 1087 False 674.0 699 92.4410 1006 1966 2 chr1B.!!$F2 960
15 TraesCS5D01G549100 chr1A 552211526 552212534 1008 False 1419.0 1419 92.1100 1006 2012 1 chr1A.!!$F2 1006
16 TraesCS5D01G549100 chr1D 461138695 461139690 995 False 1351.0 1351 91.1240 1006 2012 1 chr1D.!!$F1 1006
17 TraesCS5D01G549100 chr6B 30364128 30365047 919 True 697.0 773 95.0895 958 1845 2 chr6B.!!$R1 887
18 TraesCS5D01G549100 chr3B 769345154 769346073 919 False 705.5 773 95.4825 958 1845 2 chr3B.!!$F1 887

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
473 475 0.106469 CGTCTCCCTCCCTCAGATCA 60.106 60.000 0.00 0.00 0.00 2.92 F
782 784 0.327000 CCACCTCCTCCCTTCCAGAT 60.327 60.000 0.00 0.00 0.00 2.90 F
784 786 0.397816 ACCTCCTCCCTTCCAGATCG 60.398 60.000 0.00 0.00 0.00 3.69 F
914 916 1.152247 TCTCCCCTCGGATCCATGG 60.152 63.158 13.41 4.97 37.60 3.66 F
1449 1454 1.303236 TTTGGCCGCTGTATGCAGT 60.303 52.632 12.66 0.00 44.32 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1314 1318 0.314935 ATGCCAAGCAACTGAAACGG 59.685 50.000 0.00 0.0 43.62 4.44 R
2025 3631 1.076024 AGGGGACAACTGATGCATTGT 59.924 47.619 0.00 1.0 41.70 2.71 R
2026 3632 1.843368 AGGGGACAACTGATGCATTG 58.157 50.000 0.00 0.0 0.00 2.82 R
2027 3633 2.610438 AAGGGGACAACTGATGCATT 57.390 45.000 0.00 0.0 0.00 3.56 R
3224 4927 0.257039 AGGTTCCATCAGGCCATGAC 59.743 55.000 5.01 0.0 41.91 3.06 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
246 247 1.202405 TCACACGGATCGATGACATGG 60.202 52.381 0.54 0.00 0.00 3.66
249 250 1.007387 CGGATCGATGACATGGCGA 60.007 57.895 0.54 0.00 38.51 5.54
273 274 2.333069 TCCATCCATCCATCTCTCCAC 58.667 52.381 0.00 0.00 0.00 4.02
354 356 0.683179 GCATCCACCTACCCAAACCC 60.683 60.000 0.00 0.00 0.00 4.11
365 367 0.180406 CCCAAACCCTACCCAGATCG 59.820 60.000 0.00 0.00 0.00 3.69
423 425 2.164865 ATCTCCTCATCGCCGCCATC 62.165 60.000 0.00 0.00 0.00 3.51
424 426 4.284860 TCCTCATCGCCGCCATCG 62.285 66.667 0.00 0.00 0.00 3.84
425 427 4.284860 CCTCATCGCCGCCATCGA 62.285 66.667 0.00 0.00 40.45 3.59
426 428 3.032609 CTCATCGCCGCCATCGAC 61.033 66.667 0.00 0.00 38.88 4.20
427 429 4.923710 TCATCGCCGCCATCGACG 62.924 66.667 0.00 0.00 42.86 5.12
436 438 4.570663 CCATCGACGACGCTCCCC 62.571 72.222 0.00 0.00 39.58 4.81
437 439 3.518998 CATCGACGACGCTCCCCT 61.519 66.667 0.00 0.00 39.58 4.79
438 440 3.210528 ATCGACGACGCTCCCCTC 61.211 66.667 0.00 0.00 39.58 4.30
441 443 3.210528 GACGACGCTCCCCTCGAT 61.211 66.667 0.00 0.00 33.96 3.59
442 444 3.183776 GACGACGCTCCCCTCGATC 62.184 68.421 0.00 0.00 33.96 3.69
443 445 3.967335 CGACGCTCCCCTCGATCC 61.967 72.222 0.00 0.00 31.24 3.36
444 446 3.607661 GACGCTCCCCTCGATCCC 61.608 72.222 0.00 0.00 0.00 3.85
445 447 4.144727 ACGCTCCCCTCGATCCCT 62.145 66.667 0.00 0.00 0.00 4.20
446 448 3.299190 CGCTCCCCTCGATCCCTC 61.299 72.222 0.00 0.00 0.00 4.30
447 449 2.920384 GCTCCCCTCGATCCCTCC 60.920 72.222 0.00 0.00 0.00 4.30
448 450 2.203714 CTCCCCTCGATCCCTCCC 60.204 72.222 0.00 0.00 0.00 4.30
449 451 3.033773 TCCCCTCGATCCCTCCCA 61.034 66.667 0.00 0.00 0.00 4.37
450 452 2.844839 CCCCTCGATCCCTCCCAC 60.845 72.222 0.00 0.00 0.00 4.61
451 453 2.844839 CCCTCGATCCCTCCCACC 60.845 72.222 0.00 0.00 0.00 4.61
452 454 3.227276 CCTCGATCCCTCCCACCG 61.227 72.222 0.00 0.00 0.00 4.94
453 455 3.917760 CTCGATCCCTCCCACCGC 61.918 72.222 0.00 0.00 0.00 5.68
469 471 3.151022 GCCGTCTCCCTCCCTCAG 61.151 72.222 0.00 0.00 0.00 3.35
470 472 2.684104 CCGTCTCCCTCCCTCAGA 59.316 66.667 0.00 0.00 0.00 3.27
471 473 1.231641 CCGTCTCCCTCCCTCAGAT 59.768 63.158 0.00 0.00 0.00 2.90
472 474 0.825840 CCGTCTCCCTCCCTCAGATC 60.826 65.000 0.00 0.00 0.00 2.75
473 475 0.106469 CGTCTCCCTCCCTCAGATCA 60.106 60.000 0.00 0.00 0.00 2.92
728 730 4.385405 ACCGTGCTCCTCTGCAGC 62.385 66.667 9.47 0.00 44.20 5.25
729 731 4.079850 CCGTGCTCCTCTGCAGCT 62.080 66.667 9.47 0.00 44.20 4.24
730 732 2.047465 CGTGCTCCTCTGCAGCTT 60.047 61.111 9.47 0.00 44.20 3.74
731 733 2.099431 CGTGCTCCTCTGCAGCTTC 61.099 63.158 9.47 0.00 44.20 3.86
732 734 1.296068 GTGCTCCTCTGCAGCTTCT 59.704 57.895 9.47 0.00 44.20 2.85
733 735 1.020333 GTGCTCCTCTGCAGCTTCTG 61.020 60.000 9.47 0.00 44.20 3.02
765 767 4.063967 CCGCTGACTACCACGCCA 62.064 66.667 0.00 0.00 0.00 5.69
766 768 2.809601 CGCTGACTACCACGCCAC 60.810 66.667 0.00 0.00 0.00 5.01
767 769 2.434359 GCTGACTACCACGCCACC 60.434 66.667 0.00 0.00 0.00 4.61
768 770 2.943978 GCTGACTACCACGCCACCT 61.944 63.158 0.00 0.00 0.00 4.00
769 771 1.215647 CTGACTACCACGCCACCTC 59.784 63.158 0.00 0.00 0.00 3.85
770 772 2.227089 CTGACTACCACGCCACCTCC 62.227 65.000 0.00 0.00 0.00 4.30
771 773 1.982938 GACTACCACGCCACCTCCT 60.983 63.158 0.00 0.00 0.00 3.69
772 774 1.946475 GACTACCACGCCACCTCCTC 61.946 65.000 0.00 0.00 0.00 3.71
773 775 2.682494 TACCACGCCACCTCCTCC 60.682 66.667 0.00 0.00 0.00 4.30
776 778 3.322466 CACGCCACCTCCTCCCTT 61.322 66.667 0.00 0.00 0.00 3.95
777 779 3.003763 ACGCCACCTCCTCCCTTC 61.004 66.667 0.00 0.00 0.00 3.46
778 780 3.787001 CGCCACCTCCTCCCTTCC 61.787 72.222 0.00 0.00 0.00 3.46
779 781 2.610859 GCCACCTCCTCCCTTCCA 60.611 66.667 0.00 0.00 0.00 3.53
780 782 2.674220 GCCACCTCCTCCCTTCCAG 61.674 68.421 0.00 0.00 0.00 3.86
781 783 1.081092 CCACCTCCTCCCTTCCAGA 59.919 63.158 0.00 0.00 0.00 3.86
782 784 0.327000 CCACCTCCTCCCTTCCAGAT 60.327 60.000 0.00 0.00 0.00 2.90
783 785 1.127343 CACCTCCTCCCTTCCAGATC 58.873 60.000 0.00 0.00 0.00 2.75
784 786 0.397816 ACCTCCTCCCTTCCAGATCG 60.398 60.000 0.00 0.00 0.00 3.69
785 787 1.745264 CTCCTCCCTTCCAGATCGC 59.255 63.158 0.00 0.00 0.00 4.58
786 788 2.081425 CTCCTCCCTTCCAGATCGCG 62.081 65.000 0.00 0.00 0.00 5.87
787 789 2.419198 CTCCCTTCCAGATCGCGG 59.581 66.667 6.13 0.00 0.00 6.46
788 790 3.798954 CTCCCTTCCAGATCGCGGC 62.799 68.421 6.13 0.00 0.00 6.53
789 791 4.918201 CCCTTCCAGATCGCGGCC 62.918 72.222 6.13 0.00 0.00 6.13
834 836 4.586235 CCGTCCATGGCATCCCCC 62.586 72.222 6.96 0.00 0.00 5.40
835 837 3.807839 CGTCCATGGCATCCCCCA 61.808 66.667 6.96 0.00 39.65 4.96
836 838 2.123726 GTCCATGGCATCCCCCAC 60.124 66.667 6.96 0.00 37.79 4.61
837 839 3.807839 TCCATGGCATCCCCCACG 61.808 66.667 6.96 0.00 37.79 4.94
843 845 4.564110 GCATCCCCCACGCCCTAC 62.564 72.222 0.00 0.00 0.00 3.18
844 846 2.768344 CATCCCCCACGCCCTACT 60.768 66.667 0.00 0.00 0.00 2.57
845 847 2.446036 ATCCCCCACGCCCTACTC 60.446 66.667 0.00 0.00 0.00 2.59
846 848 4.791069 TCCCCCACGCCCTACTCC 62.791 72.222 0.00 0.00 0.00 3.85
847 849 4.798682 CCCCCACGCCCTACTCCT 62.799 72.222 0.00 0.00 0.00 3.69
848 850 3.155167 CCCCACGCCCTACTCCTC 61.155 72.222 0.00 0.00 0.00 3.71
849 851 2.042843 CCCACGCCCTACTCCTCT 60.043 66.667 0.00 0.00 0.00 3.69
850 852 2.128507 CCCACGCCCTACTCCTCTC 61.129 68.421 0.00 0.00 0.00 3.20
851 853 2.482333 CCACGCCCTACTCCTCTCG 61.482 68.421 0.00 0.00 0.00 4.04
852 854 2.829458 ACGCCCTACTCCTCTCGC 60.829 66.667 0.00 0.00 0.00 5.03
853 855 3.597728 CGCCCTACTCCTCTCGCC 61.598 72.222 0.00 0.00 0.00 5.54
854 856 3.228017 GCCCTACTCCTCTCGCCC 61.228 72.222 0.00 0.00 0.00 6.13
855 857 2.279073 CCCTACTCCTCTCGCCCA 59.721 66.667 0.00 0.00 0.00 5.36
856 858 2.128507 CCCTACTCCTCTCGCCCAC 61.129 68.421 0.00 0.00 0.00 4.61
857 859 2.128507 CCTACTCCTCTCGCCCACC 61.129 68.421 0.00 0.00 0.00 4.61
858 860 2.043248 TACTCCTCTCGCCCACCC 60.043 66.667 0.00 0.00 0.00 4.61
871 873 4.410400 CACCCGGCACCCTTCCTC 62.410 72.222 0.00 0.00 0.00 3.71
874 876 3.787001 CCGGCACCCTTCCTCCTC 61.787 72.222 0.00 0.00 0.00 3.71
875 877 3.787001 CGGCACCCTTCCTCCTCC 61.787 72.222 0.00 0.00 0.00 4.30
876 878 2.610859 GGCACCCTTCCTCCTCCA 60.611 66.667 0.00 0.00 0.00 3.86
877 879 2.231380 GGCACCCTTCCTCCTCCAA 61.231 63.158 0.00 0.00 0.00 3.53
878 880 1.301293 GCACCCTTCCTCCTCCAAG 59.699 63.158 0.00 0.00 0.00 3.61
879 881 1.201429 GCACCCTTCCTCCTCCAAGA 61.201 60.000 0.00 0.00 0.00 3.02
880 882 1.362224 CACCCTTCCTCCTCCAAGAA 58.638 55.000 0.00 0.00 0.00 2.52
881 883 1.705186 CACCCTTCCTCCTCCAAGAAA 59.295 52.381 0.00 0.00 0.00 2.52
882 884 1.988846 ACCCTTCCTCCTCCAAGAAAG 59.011 52.381 0.00 0.00 0.00 2.62
883 885 1.340502 CCCTTCCTCCTCCAAGAAAGC 60.341 57.143 0.00 0.00 0.00 3.51
884 886 1.352352 CCTTCCTCCTCCAAGAAAGCA 59.648 52.381 0.00 0.00 0.00 3.91
885 887 2.224867 CCTTCCTCCTCCAAGAAAGCAA 60.225 50.000 0.00 0.00 0.00 3.91
886 888 3.490348 CTTCCTCCTCCAAGAAAGCAAA 58.510 45.455 0.00 0.00 0.00 3.68
887 889 3.146104 TCCTCCTCCAAGAAAGCAAAG 57.854 47.619 0.00 0.00 0.00 2.77
888 890 1.543358 CCTCCTCCAAGAAAGCAAAGC 59.457 52.381 0.00 0.00 0.00 3.51
889 891 2.512705 CTCCTCCAAGAAAGCAAAGCT 58.487 47.619 0.00 0.00 42.56 3.74
890 892 2.228343 CTCCTCCAAGAAAGCAAAGCTG 59.772 50.000 0.00 0.00 39.62 4.24
900 902 3.993535 CAAAGCTGCACCCTCTCC 58.006 61.111 1.02 0.00 0.00 3.71
901 903 1.676967 CAAAGCTGCACCCTCTCCC 60.677 63.158 1.02 0.00 0.00 4.30
902 904 2.911926 AAAGCTGCACCCTCTCCCC 61.912 63.158 1.02 0.00 0.00 4.81
903 905 3.880033 AAGCTGCACCCTCTCCCCT 62.880 63.158 1.02 0.00 0.00 4.79
904 906 3.791586 GCTGCACCCTCTCCCCTC 61.792 72.222 0.00 0.00 0.00 4.30
905 907 3.465403 CTGCACCCTCTCCCCTCG 61.465 72.222 0.00 0.00 0.00 4.63
907 909 4.779733 GCACCCTCTCCCCTCGGA 62.780 72.222 0.00 0.00 36.45 4.55
908 910 2.283809 CACCCTCTCCCCTCGGAT 59.716 66.667 0.00 0.00 37.60 4.18
909 911 1.834822 CACCCTCTCCCCTCGGATC 60.835 68.421 0.00 0.00 37.60 3.36
910 912 2.203714 CCCTCTCCCCTCGGATCC 60.204 72.222 0.00 0.00 37.60 3.36
911 913 2.609339 CCTCTCCCCTCGGATCCA 59.391 66.667 13.41 0.00 37.60 3.41
912 914 1.157276 CCTCTCCCCTCGGATCCAT 59.843 63.158 13.41 0.00 37.60 3.41
913 915 1.190833 CCTCTCCCCTCGGATCCATG 61.191 65.000 13.41 3.13 37.60 3.66
914 916 1.152247 TCTCCCCTCGGATCCATGG 60.152 63.158 13.41 4.97 37.60 3.66
915 917 2.849162 TCCCCTCGGATCCATGGC 60.849 66.667 13.41 0.00 31.13 4.40
916 918 4.320456 CCCCTCGGATCCATGGCG 62.320 72.222 13.41 5.26 0.00 5.69
917 919 4.996434 CCCTCGGATCCATGGCGC 62.996 72.222 13.41 0.00 0.00 6.53
918 920 3.933722 CCTCGGATCCATGGCGCT 61.934 66.667 13.41 0.00 0.00 5.92
919 921 2.664185 CTCGGATCCATGGCGCTG 60.664 66.667 13.41 6.51 0.00 5.18
920 922 4.916293 TCGGATCCATGGCGCTGC 62.916 66.667 13.41 0.00 0.00 5.25
921 923 4.923942 CGGATCCATGGCGCTGCT 62.924 66.667 13.41 0.00 0.00 4.24
922 924 2.976903 GGATCCATGGCGCTGCTC 60.977 66.667 6.96 0.00 0.00 4.26
923 925 2.203112 GATCCATGGCGCTGCTCA 60.203 61.111 6.96 0.00 0.00 4.26
924 926 2.203167 ATCCATGGCGCTGCTCAG 60.203 61.111 6.96 0.00 0.00 3.35
952 954 4.292178 CGCGGGCTCTCTCCCATC 62.292 72.222 0.00 0.00 46.92 3.51
953 955 4.292178 GCGGGCTCTCTCCCATCG 62.292 72.222 0.00 0.00 46.92 3.84
954 956 3.610669 CGGGCTCTCTCCCATCGG 61.611 72.222 0.00 0.00 46.92 4.18
955 957 3.934962 GGGCTCTCTCCCATCGGC 61.935 72.222 0.00 0.00 45.82 5.54
956 958 4.292178 GGCTCTCTCCCATCGGCG 62.292 72.222 0.00 0.00 0.00 6.46
1075 1079 2.193248 GCGGCCCTAATCCTGCTT 59.807 61.111 0.00 0.00 0.00 3.91
1296 1300 3.620966 GCATTCAGAGCTGTTAGGGTCTT 60.621 47.826 0.00 0.00 41.37 3.01
1314 1318 3.619038 GTCTTTCTGGGTGATCGTTGATC 59.381 47.826 0.00 0.00 39.31 2.92
1449 1454 1.303236 TTTGGCCGCTGTATGCAGT 60.303 52.632 12.66 0.00 44.32 4.40
1574 1707 2.952978 TGGCCGTGTTCACTTATTGTTT 59.047 40.909 0.00 0.00 0.00 2.83
1934 3469 8.999220 TTGCTGATCTAATCTTCATATAGCTG 57.001 34.615 0.00 0.00 0.00 4.24
1954 3560 5.992217 AGCTGAAGTGGAAACTAGTAACTTG 59.008 40.000 14.40 6.06 31.45 3.16
1984 3590 6.380274 TCTGGTGGTATTGGTTGTTTGTTTTA 59.620 34.615 0.00 0.00 0.00 1.52
1996 3602 9.003658 TGGTTGTTTGTTTTATTGTGATTTTGT 57.996 25.926 0.00 0.00 0.00 2.83
2012 3618 7.065443 TGTGATTTTGTTTCATGAATGTGCAAA 59.935 29.630 9.40 14.29 0.00 3.68
2015 3621 6.922247 TTTGTTTCATGAATGTGCAAATGT 57.078 29.167 9.40 0.00 0.00 2.71
2016 3622 5.908916 TGTTTCATGAATGTGCAAATGTG 57.091 34.783 9.40 0.00 0.00 3.21
2017 3623 5.358090 TGTTTCATGAATGTGCAAATGTGT 58.642 33.333 9.40 0.00 0.00 3.72
2018 3624 5.816258 TGTTTCATGAATGTGCAAATGTGTT 59.184 32.000 9.40 0.00 0.00 3.32
2019 3625 6.018913 TGTTTCATGAATGTGCAAATGTGTTC 60.019 34.615 9.40 0.00 0.00 3.18
2020 3626 4.558178 TCATGAATGTGCAAATGTGTTCC 58.442 39.130 0.00 0.00 0.00 3.62
2021 3627 4.281435 TCATGAATGTGCAAATGTGTTCCT 59.719 37.500 0.00 0.00 0.00 3.36
2022 3628 4.669206 TGAATGTGCAAATGTGTTCCTT 57.331 36.364 0.00 0.00 0.00 3.36
2023 3629 5.781210 TGAATGTGCAAATGTGTTCCTTA 57.219 34.783 0.00 0.00 0.00 2.69
2025 3631 6.577103 TGAATGTGCAAATGTGTTCCTTAAA 58.423 32.000 0.00 0.00 0.00 1.52
2026 3632 6.478344 TGAATGTGCAAATGTGTTCCTTAAAC 59.522 34.615 0.00 0.00 38.43 2.01
2027 3633 5.330455 TGTGCAAATGTGTTCCTTAAACA 57.670 34.783 0.00 0.00 45.60 2.83
2038 3644 6.403866 TGTTCCTTAAACAATGCATCAGTT 57.596 33.333 0.00 5.61 44.83 3.16
2039 3645 6.215121 TGTTCCTTAAACAATGCATCAGTTG 58.785 36.000 15.62 7.16 44.83 3.16
2040 3646 6.183360 TGTTCCTTAAACAATGCATCAGTTGT 60.183 34.615 15.62 7.76 44.83 3.32
2042 3648 5.048083 TCCTTAAACAATGCATCAGTTGTCC 60.048 40.000 15.62 0.00 37.56 4.02
2043 3649 3.665745 AAACAATGCATCAGTTGTCCC 57.334 42.857 15.62 0.00 37.56 4.46
2044 3650 1.549203 ACAATGCATCAGTTGTCCCC 58.451 50.000 0.00 0.00 33.53 4.81
2046 3721 2.173519 CAATGCATCAGTTGTCCCCTT 58.826 47.619 0.00 0.00 0.00 3.95
2049 3724 3.517296 TGCATCAGTTGTCCCCTTAAA 57.483 42.857 0.00 0.00 0.00 1.52
2050 3725 3.153919 TGCATCAGTTGTCCCCTTAAAC 58.846 45.455 0.00 0.00 0.00 2.01
2053 3728 4.038642 GCATCAGTTGTCCCCTTAAACAAA 59.961 41.667 0.00 0.00 37.15 2.83
2054 3729 5.452636 GCATCAGTTGTCCCCTTAAACAAAA 60.453 40.000 0.00 0.00 37.15 2.44
2079 3754 8.706322 AAAGGAAGTGTTGGTTTCATAATACT 57.294 30.769 0.00 0.00 30.87 2.12
2080 3755 7.923414 AGGAAGTGTTGGTTTCATAATACTC 57.077 36.000 0.00 0.00 29.61 2.59
2081 3756 7.458397 AGGAAGTGTTGGTTTCATAATACTCA 58.542 34.615 0.00 0.00 29.61 3.41
2083 3758 7.174253 GGAAGTGTTGGTTTCATAATACTCACA 59.826 37.037 0.00 0.00 29.61 3.58
2084 3759 8.458573 AAGTGTTGGTTTCATAATACTCACAA 57.541 30.769 0.00 0.00 29.61 3.33
2085 3760 8.635765 AGTGTTGGTTTCATAATACTCACAAT 57.364 30.769 0.00 0.00 0.00 2.71
2088 3763 9.072375 TGTTGGTTTCATAATACTCACAATCAA 57.928 29.630 0.00 0.00 0.00 2.57
2089 3764 9.341899 GTTGGTTTCATAATACTCACAATCAAC 57.658 33.333 0.00 0.00 0.00 3.18
2091 3766 8.729756 TGGTTTCATAATACTCACAATCAACAG 58.270 33.333 0.00 0.00 0.00 3.16
2092 3767 8.946085 GGTTTCATAATACTCACAATCAACAGA 58.054 33.333 0.00 0.00 0.00 3.41
2095 3770 9.889128 TTCATAATACTCACAATCAACAGATCA 57.111 29.630 0.00 0.00 0.00 2.92
2096 3771 9.889128 TCATAATACTCACAATCAACAGATCAA 57.111 29.630 0.00 0.00 0.00 2.57
2103 3778 9.071276 ACTCACAATCAACAGATCAATTTTAGT 57.929 29.630 0.00 0.00 0.00 2.24
2111 3786 9.778741 TCAACAGATCAATTTTAGTACTTCTGT 57.221 29.630 14.09 14.09 43.08 3.41
2126 3801 8.095937 AGTACTTCTGTTTGTTACTATTTGCC 57.904 34.615 0.00 0.00 0.00 4.52
2127 3802 6.952773 ACTTCTGTTTGTTACTATTTGCCA 57.047 33.333 0.00 0.00 0.00 4.92
2128 3803 6.735130 ACTTCTGTTTGTTACTATTTGCCAC 58.265 36.000 0.00 0.00 0.00 5.01
2129 3804 5.699097 TCTGTTTGTTACTATTTGCCACC 57.301 39.130 0.00 0.00 0.00 4.61
2130 3805 5.133941 TCTGTTTGTTACTATTTGCCACCA 58.866 37.500 0.00 0.00 0.00 4.17
2131 3806 5.240623 TCTGTTTGTTACTATTTGCCACCAG 59.759 40.000 0.00 0.00 0.00 4.00
2133 3808 6.062749 TGTTTGTTACTATTTGCCACCAGTA 58.937 36.000 0.00 0.00 0.00 2.74
2134 3809 6.546403 TGTTTGTTACTATTTGCCACCAGTAA 59.454 34.615 0.00 0.00 32.51 2.24
2135 3810 6.811253 TTGTTACTATTTGCCACCAGTAAG 57.189 37.500 0.00 0.00 34.93 2.34
2136 3811 6.116711 TGTTACTATTTGCCACCAGTAAGA 57.883 37.500 0.00 0.00 34.93 2.10
2137 3812 6.535540 TGTTACTATTTGCCACCAGTAAGAA 58.464 36.000 0.00 0.00 34.93 2.52
2138 3813 6.428771 TGTTACTATTTGCCACCAGTAAGAAC 59.571 38.462 0.00 0.00 34.93 3.01
2328 4030 2.670934 CTTCTGCCTGGCGCTTGT 60.671 61.111 14.98 0.00 38.78 3.16
2415 4117 7.231519 AGACTTCCCATTTCTTTTTCTACCTTG 59.768 37.037 0.00 0.00 0.00 3.61
2485 4187 6.204359 CAAGCTACTCATAAATCCAACATGC 58.796 40.000 0.00 0.00 0.00 4.06
2569 4271 7.221067 CGTTACTTAGCTTGGAAGAATGACTAG 59.779 40.741 1.70 0.00 0.00 2.57
3224 4927 2.890311 TGCAATGGTTTGGAGTACTTGG 59.110 45.455 0.00 0.00 33.22 3.61
3325 5028 2.583024 TGGTCATGGCATCACTTTGA 57.417 45.000 0.43 0.00 0.00 2.69
3544 5247 6.656632 TCTTGTATGAGTGGGTATCTCATC 57.343 41.667 10.95 5.49 45.78 2.92
3715 5419 1.540146 GGAAGCCATGTTGCCGTTTTT 60.540 47.619 0.00 0.00 0.00 1.94
3739 5443 0.255890 TTCCCAGCCTTGACTATGGC 59.744 55.000 0.00 0.00 45.08 4.40
3806 5510 5.722021 TTGTATCACACTTGTAGAGCTCA 57.278 39.130 17.77 0.00 0.00 4.26
3870 5574 4.754618 TCATATGTATTGGCAACGTGATCC 59.245 41.667 0.00 0.00 42.51 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 6.700960 TCAAATGCCAAACAATGTTGTCTAAG 59.299 34.615 0.00 0.00 41.31 2.18
84 85 5.426504 TCTTCAAATGCCAAACAATGTTGT 58.573 33.333 0.00 0.00 44.72 3.32
85 86 5.987777 TCTTCAAATGCCAAACAATGTTG 57.012 34.783 0.00 0.00 0.00 3.33
191 192 6.475504 CACCAATGGGAATAGAGCACATATA 58.524 40.000 3.55 0.00 38.05 0.86
246 247 0.037303 ATGGATGGATGGATGGTCGC 59.963 55.000 0.00 0.00 0.00 5.19
249 250 2.911636 GAGAGATGGATGGATGGATGGT 59.088 50.000 0.00 0.00 0.00 3.55
273 274 2.670019 ATGGATGGATGGATGTGGTG 57.330 50.000 0.00 0.00 0.00 4.17
317 319 0.032952 GCGGGTGGGGTTTTCTTTTC 59.967 55.000 0.00 0.00 0.00 2.29
322 324 2.348104 GGATGCGGGTGGGGTTTTC 61.348 63.158 0.00 0.00 0.00 2.29
365 367 2.588201 GGGAGGAGGGGATCGATGC 61.588 68.421 8.63 8.63 0.00 3.91
409 411 3.032609 GTCGATGGCGGCGATGAG 61.033 66.667 12.98 0.00 40.19 2.90
424 426 3.183776 GATCGAGGGGAGCGTCGTC 62.184 68.421 0.00 0.00 37.46 4.20
425 427 3.210528 GATCGAGGGGAGCGTCGT 61.211 66.667 0.00 0.00 37.46 4.34
426 428 3.967335 GGATCGAGGGGAGCGTCG 61.967 72.222 0.00 0.00 37.54 5.12
427 429 3.607661 GGGATCGAGGGGAGCGTC 61.608 72.222 0.00 0.00 0.00 5.19
428 430 4.144727 AGGGATCGAGGGGAGCGT 62.145 66.667 0.00 0.00 0.00 5.07
429 431 3.299190 GAGGGATCGAGGGGAGCG 61.299 72.222 0.00 0.00 0.00 5.03
430 432 2.920384 GGAGGGATCGAGGGGAGC 60.920 72.222 0.00 0.00 0.00 4.70
431 433 2.203714 GGGAGGGATCGAGGGGAG 60.204 72.222 0.00 0.00 0.00 4.30
432 434 3.033773 TGGGAGGGATCGAGGGGA 61.034 66.667 0.00 0.00 0.00 4.81
433 435 2.844839 GTGGGAGGGATCGAGGGG 60.845 72.222 0.00 0.00 0.00 4.79
434 436 2.844839 GGTGGGAGGGATCGAGGG 60.845 72.222 0.00 0.00 0.00 4.30
435 437 3.227276 CGGTGGGAGGGATCGAGG 61.227 72.222 0.00 0.00 0.00 4.63
436 438 3.917760 GCGGTGGGAGGGATCGAG 61.918 72.222 0.00 0.00 0.00 4.04
452 454 2.937959 ATCTGAGGGAGGGAGACGGC 62.938 65.000 0.00 0.00 0.00 5.68
453 455 0.825840 GATCTGAGGGAGGGAGACGG 60.826 65.000 0.00 0.00 0.00 4.79
454 456 0.106469 TGATCTGAGGGAGGGAGACG 60.106 60.000 0.00 0.00 0.00 4.18
455 457 3.935371 TGATCTGAGGGAGGGAGAC 57.065 57.895 0.00 0.00 0.00 3.36
711 713 4.385405 GCTGCAGAGGAGCACGGT 62.385 66.667 20.43 0.00 40.11 4.83
712 714 3.602513 AAGCTGCAGAGGAGCACGG 62.603 63.158 20.43 0.00 40.11 4.94
713 715 2.047465 AAGCTGCAGAGGAGCACG 60.047 61.111 20.43 0.00 40.11 5.34
714 716 1.020333 CAGAAGCTGCAGAGGAGCAC 61.020 60.000 20.43 6.48 40.11 4.40
715 717 1.295746 CAGAAGCTGCAGAGGAGCA 59.704 57.895 20.43 0.00 43.35 4.26
716 718 4.205287 CAGAAGCTGCAGAGGAGC 57.795 61.111 20.43 1.38 36.65 4.70
748 750 4.063967 TGGCGTGGTAGTCAGCGG 62.064 66.667 0.00 0.00 0.00 5.52
749 751 2.809601 GTGGCGTGGTAGTCAGCG 60.810 66.667 0.00 0.00 0.00 5.18
750 752 2.434359 GGTGGCGTGGTAGTCAGC 60.434 66.667 0.00 0.00 37.07 4.26
751 753 1.215647 GAGGTGGCGTGGTAGTCAG 59.784 63.158 0.00 0.00 0.00 3.51
752 754 2.280552 GGAGGTGGCGTGGTAGTCA 61.281 63.158 0.00 0.00 0.00 3.41
753 755 1.946475 GAGGAGGTGGCGTGGTAGTC 61.946 65.000 0.00 0.00 0.00 2.59
754 756 1.982938 GAGGAGGTGGCGTGGTAGT 60.983 63.158 0.00 0.00 0.00 2.73
755 757 2.722201 GGAGGAGGTGGCGTGGTAG 61.722 68.421 0.00 0.00 0.00 3.18
756 758 2.682494 GGAGGAGGTGGCGTGGTA 60.682 66.667 0.00 0.00 0.00 3.25
759 761 3.316573 GAAGGGAGGAGGTGGCGTG 62.317 68.421 0.00 0.00 0.00 5.34
760 762 3.003763 GAAGGGAGGAGGTGGCGT 61.004 66.667 0.00 0.00 0.00 5.68
761 763 3.787001 GGAAGGGAGGAGGTGGCG 61.787 72.222 0.00 0.00 0.00 5.69
762 764 2.610859 TGGAAGGGAGGAGGTGGC 60.611 66.667 0.00 0.00 0.00 5.01
763 765 0.327000 ATCTGGAAGGGAGGAGGTGG 60.327 60.000 0.00 0.00 0.00 4.61
764 766 1.127343 GATCTGGAAGGGAGGAGGTG 58.873 60.000 0.00 0.00 0.00 4.00
765 767 0.397816 CGATCTGGAAGGGAGGAGGT 60.398 60.000 0.00 0.00 0.00 3.85
766 768 1.753368 GCGATCTGGAAGGGAGGAGG 61.753 65.000 0.00 0.00 0.00 4.30
767 769 1.745264 GCGATCTGGAAGGGAGGAG 59.255 63.158 0.00 0.00 0.00 3.69
768 770 2.127869 CGCGATCTGGAAGGGAGGA 61.128 63.158 0.00 0.00 0.00 3.71
769 771 2.419198 CGCGATCTGGAAGGGAGG 59.581 66.667 0.00 0.00 0.00 4.30
770 772 2.419198 CCGCGATCTGGAAGGGAG 59.581 66.667 8.23 0.00 0.00 4.30
771 773 3.849951 GCCGCGATCTGGAAGGGA 61.850 66.667 8.23 0.00 0.00 4.20
772 774 4.918201 GGCCGCGATCTGGAAGGG 62.918 72.222 8.23 0.00 0.00 3.95
817 819 4.586235 GGGGGATGCCATGGACGG 62.586 72.222 18.40 0.00 0.00 4.79
818 820 3.807839 TGGGGGATGCCATGGACG 61.808 66.667 18.40 0.00 0.00 4.79
819 821 2.123726 GTGGGGGATGCCATGGAC 60.124 66.667 18.40 7.64 0.00 4.02
820 822 3.807839 CGTGGGGGATGCCATGGA 61.808 66.667 18.40 0.31 0.00 3.41
826 828 4.564110 GTAGGGCGTGGGGGATGC 62.564 72.222 0.00 0.00 35.63 3.91
827 829 2.768344 AGTAGGGCGTGGGGGATG 60.768 66.667 0.00 0.00 0.00 3.51
828 830 2.446036 GAGTAGGGCGTGGGGGAT 60.446 66.667 0.00 0.00 0.00 3.85
829 831 4.791069 GGAGTAGGGCGTGGGGGA 62.791 72.222 0.00 0.00 0.00 4.81
830 832 4.798682 AGGAGTAGGGCGTGGGGG 62.799 72.222 0.00 0.00 0.00 5.40
831 833 3.155167 GAGGAGTAGGGCGTGGGG 61.155 72.222 0.00 0.00 0.00 4.96
832 834 2.042843 AGAGGAGTAGGGCGTGGG 60.043 66.667 0.00 0.00 0.00 4.61
833 835 2.482333 CGAGAGGAGTAGGGCGTGG 61.482 68.421 0.00 0.00 0.00 4.94
834 836 3.111939 CGAGAGGAGTAGGGCGTG 58.888 66.667 0.00 0.00 0.00 5.34
835 837 2.829458 GCGAGAGGAGTAGGGCGT 60.829 66.667 0.00 0.00 0.00 5.68
836 838 3.597728 GGCGAGAGGAGTAGGGCG 61.598 72.222 0.00 0.00 0.00 6.13
837 839 3.228017 GGGCGAGAGGAGTAGGGC 61.228 72.222 0.00 0.00 0.00 5.19
838 840 2.128507 GTGGGCGAGAGGAGTAGGG 61.129 68.421 0.00 0.00 0.00 3.53
839 841 2.128507 GGTGGGCGAGAGGAGTAGG 61.129 68.421 0.00 0.00 0.00 3.18
840 842 2.128507 GGGTGGGCGAGAGGAGTAG 61.129 68.421 0.00 0.00 0.00 2.57
841 843 2.043248 GGGTGGGCGAGAGGAGTA 60.043 66.667 0.00 0.00 0.00 2.59
854 856 4.410400 GAGGAAGGGTGCCGGGTG 62.410 72.222 2.18 0.00 0.00 4.61
857 859 3.787001 GAGGAGGAAGGGTGCCGG 61.787 72.222 0.00 0.00 0.00 6.13
858 860 3.787001 GGAGGAGGAAGGGTGCCG 61.787 72.222 0.00 0.00 0.00 5.69
859 861 2.203549 CTTGGAGGAGGAAGGGTGCC 62.204 65.000 0.00 0.00 0.00 5.01
860 862 1.201429 TCTTGGAGGAGGAAGGGTGC 61.201 60.000 0.00 0.00 0.00 5.01
861 863 1.362224 TTCTTGGAGGAGGAAGGGTG 58.638 55.000 0.00 0.00 0.00 4.61
862 864 1.988846 CTTTCTTGGAGGAGGAAGGGT 59.011 52.381 0.00 0.00 30.03 4.34
863 865 1.340502 GCTTTCTTGGAGGAGGAAGGG 60.341 57.143 0.00 0.00 33.60 3.95
864 866 1.352352 TGCTTTCTTGGAGGAGGAAGG 59.648 52.381 0.00 0.00 33.60 3.46
865 867 2.867109 TGCTTTCTTGGAGGAGGAAG 57.133 50.000 0.00 0.00 35.68 3.46
866 868 3.490348 CTTTGCTTTCTTGGAGGAGGAA 58.510 45.455 0.00 0.00 0.00 3.36
867 869 2.815589 GCTTTGCTTTCTTGGAGGAGGA 60.816 50.000 0.00 0.00 0.00 3.71
868 870 1.543358 GCTTTGCTTTCTTGGAGGAGG 59.457 52.381 0.00 0.00 0.00 4.30
869 871 2.228343 CAGCTTTGCTTTCTTGGAGGAG 59.772 50.000 0.00 0.00 36.40 3.69
870 872 2.233271 CAGCTTTGCTTTCTTGGAGGA 58.767 47.619 0.00 0.00 36.40 3.71
871 873 1.336609 GCAGCTTTGCTTTCTTGGAGG 60.337 52.381 0.00 0.00 36.40 4.30
872 874 1.338973 TGCAGCTTTGCTTTCTTGGAG 59.661 47.619 0.00 0.00 36.40 3.86
873 875 1.067516 GTGCAGCTTTGCTTTCTTGGA 59.932 47.619 0.00 0.00 36.40 3.53
874 876 1.494824 GTGCAGCTTTGCTTTCTTGG 58.505 50.000 0.00 0.00 36.40 3.61
875 877 1.494824 GGTGCAGCTTTGCTTTCTTG 58.505 50.000 9.07 0.00 36.40 3.02
876 878 0.390492 GGGTGCAGCTTTGCTTTCTT 59.610 50.000 16.65 0.00 36.40 2.52
877 879 0.468771 AGGGTGCAGCTTTGCTTTCT 60.469 50.000 16.65 0.00 36.40 2.52
878 880 0.038801 GAGGGTGCAGCTTTGCTTTC 60.039 55.000 16.65 0.00 36.40 2.62
879 881 0.468771 AGAGGGTGCAGCTTTGCTTT 60.469 50.000 16.65 0.00 36.40 3.51
880 882 0.892814 GAGAGGGTGCAGCTTTGCTT 60.893 55.000 16.65 0.00 36.40 3.91
881 883 1.303155 GAGAGGGTGCAGCTTTGCT 60.303 57.895 16.65 3.78 40.77 3.91
882 884 2.338785 GGAGAGGGTGCAGCTTTGC 61.339 63.158 16.65 4.26 0.00 3.68
883 885 1.676967 GGGAGAGGGTGCAGCTTTG 60.677 63.158 16.65 0.00 0.00 2.77
884 886 2.759795 GGGAGAGGGTGCAGCTTT 59.240 61.111 16.65 4.41 0.00 3.51
885 887 3.334054 GGGGAGAGGGTGCAGCTT 61.334 66.667 16.65 8.36 0.00 3.74
886 888 4.345286 AGGGGAGAGGGTGCAGCT 62.345 66.667 16.65 1.37 0.00 4.24
887 889 3.791586 GAGGGGAGAGGGTGCAGC 61.792 72.222 7.55 7.55 0.00 5.25
888 890 3.465403 CGAGGGGAGAGGGTGCAG 61.465 72.222 0.00 0.00 0.00 4.41
890 892 4.779733 TCCGAGGGGAGAGGGTGC 62.780 72.222 0.00 0.00 37.43 5.01
899 901 4.320456 CGCCATGGATCCGAGGGG 62.320 72.222 18.40 20.21 0.00 4.79
900 902 4.996434 GCGCCATGGATCCGAGGG 62.996 72.222 18.40 15.80 0.00 4.30
901 903 3.933722 AGCGCCATGGATCCGAGG 61.934 66.667 18.40 16.05 0.00 4.63
902 904 2.664185 CAGCGCCATGGATCCGAG 60.664 66.667 18.40 1.38 0.00 4.63
903 905 4.916293 GCAGCGCCATGGATCCGA 62.916 66.667 18.40 0.00 0.00 4.55
904 906 4.923942 AGCAGCGCCATGGATCCG 62.924 66.667 18.40 11.19 0.00 4.18
905 907 2.976903 GAGCAGCGCCATGGATCC 60.977 66.667 18.40 4.20 0.00 3.36
906 908 2.203112 TGAGCAGCGCCATGGATC 60.203 61.111 18.40 5.66 0.00 3.36
907 909 2.203167 CTGAGCAGCGCCATGGAT 60.203 61.111 18.40 0.00 0.00 3.41
939 941 4.292178 CGCCGATGGGAGAGAGCC 62.292 72.222 0.00 0.00 34.61 4.70
940 942 4.959596 GCGCCGATGGGAGAGAGC 62.960 72.222 0.62 0.00 34.61 4.09
941 943 3.531207 TGCGCCGATGGGAGAGAG 61.531 66.667 4.18 0.00 34.61 3.20
942 944 3.838271 GTGCGCCGATGGGAGAGA 61.838 66.667 4.18 0.00 34.61 3.10
943 945 4.899239 GGTGCGCCGATGGGAGAG 62.899 72.222 4.18 0.00 34.61 3.20
1075 1079 0.832135 AGTCAAACGAGGGAGCTCCA 60.832 55.000 33.29 8.15 38.24 3.86
1149 1153 1.587054 GACCTCCGACCACTCTGTG 59.413 63.158 0.00 0.00 0.00 3.66
1296 1300 1.134818 CGGATCAACGATCACCCAGAA 60.135 52.381 6.33 0.00 40.50 3.02
1314 1318 0.314935 ATGCCAAGCAACTGAAACGG 59.685 50.000 0.00 0.00 43.62 4.44
1416 1420 2.426738 GGCCAAAGCATATGTACTGCAA 59.573 45.455 0.00 0.00 42.15 4.08
1449 1454 9.715121 AAACAAAATACAGATAACTTACCTCGA 57.285 29.630 0.00 0.00 0.00 4.04
1578 1714 2.483877 CAGCTACATCGAAAACAGGCAA 59.516 45.455 0.00 0.00 0.00 4.52
1790 3187 5.423931 TCACATACCATAGGTAGAAACAGCA 59.576 40.000 2.07 0.00 41.83 4.41
1934 3469 6.803154 ATGCAAGTTACTAGTTTCCACTTC 57.197 37.500 0.00 1.46 34.06 3.01
1954 3560 4.207165 ACAACCAATACCACCAGATATGC 58.793 43.478 0.00 0.00 0.00 3.14
1984 3590 7.226918 TGCACATTCATGAAACAAAATCACAAT 59.773 29.630 13.09 0.00 0.00 2.71
1993 3599 5.816258 ACACATTTGCACATTCATGAAACAA 59.184 32.000 13.09 11.56 0.00 2.83
1996 3602 5.466058 GGAACACATTTGCACATTCATGAAA 59.534 36.000 13.09 0.00 0.00 2.69
2015 3621 6.183360 ACAACTGATGCATTGTTTAAGGAACA 60.183 34.615 13.90 0.00 46.19 3.18
2016 3622 6.215845 ACAACTGATGCATTGTTTAAGGAAC 58.784 36.000 13.90 0.00 35.51 3.62
2017 3623 6.403866 ACAACTGATGCATTGTTTAAGGAA 57.596 33.333 13.90 0.00 35.51 3.36
2018 3624 5.048083 GGACAACTGATGCATTGTTTAAGGA 60.048 40.000 13.90 0.00 39.13 3.36
2019 3625 5.163513 GGACAACTGATGCATTGTTTAAGG 58.836 41.667 13.90 7.68 39.13 2.69
2020 3626 5.163513 GGGACAACTGATGCATTGTTTAAG 58.836 41.667 13.90 7.95 39.13 1.85
2021 3627 4.021544 GGGGACAACTGATGCATTGTTTAA 60.022 41.667 13.90 0.00 39.13 1.52
2022 3628 3.509575 GGGGACAACTGATGCATTGTTTA 59.490 43.478 13.90 0.00 39.13 2.01
2023 3629 2.299867 GGGGACAACTGATGCATTGTTT 59.700 45.455 13.90 7.95 39.13 2.83
2025 3631 1.076024 AGGGGACAACTGATGCATTGT 59.924 47.619 0.00 1.00 41.70 2.71
2026 3632 1.843368 AGGGGACAACTGATGCATTG 58.157 50.000 0.00 0.00 0.00 2.82
2027 3633 2.610438 AAGGGGACAACTGATGCATT 57.390 45.000 0.00 0.00 0.00 3.56
2029 3635 3.153919 GTTTAAGGGGACAACTGATGCA 58.846 45.455 0.00 0.00 0.00 3.96
2030 3636 3.153919 TGTTTAAGGGGACAACTGATGC 58.846 45.455 0.00 0.00 0.00 3.91
2031 3637 5.782893 TTTGTTTAAGGGGACAACTGATG 57.217 39.130 0.00 0.00 35.66 3.07
2032 3638 6.800072 TTTTTGTTTAAGGGGACAACTGAT 57.200 33.333 0.00 0.00 35.66 2.90
2053 3728 9.143155 AGTATTATGAAACCAACACTTCCTTTT 57.857 29.630 0.00 0.00 0.00 2.27
2054 3729 8.706322 AGTATTATGAAACCAACACTTCCTTT 57.294 30.769 0.00 0.00 0.00 3.11
2056 3731 7.390718 GTGAGTATTATGAAACCAACACTTCCT 59.609 37.037 0.00 0.00 0.00 3.36
2058 3733 8.094798 TGTGAGTATTATGAAACCAACACTTC 57.905 34.615 0.00 0.00 0.00 3.01
2064 3739 9.072375 TGTTGATTGTGAGTATTATGAAACCAA 57.928 29.630 0.00 0.00 0.00 3.67
2066 3741 8.946085 TCTGTTGATTGTGAGTATTATGAAACC 58.054 33.333 0.00 0.00 0.00 3.27
2069 3744 9.889128 TGATCTGTTGATTGTGAGTATTATGAA 57.111 29.630 0.00 0.00 32.19 2.57
2085 3760 9.778741 ACAGAAGTACTAAAATTGATCTGTTGA 57.221 29.630 14.09 0.00 42.47 3.18
2100 3775 9.211485 GGCAAATAGTAACAAACAGAAGTACTA 57.789 33.333 0.00 0.00 0.00 1.82
2101 3776 7.717875 TGGCAAATAGTAACAAACAGAAGTACT 59.282 33.333 0.00 0.00 0.00 2.73
2102 3777 7.801783 GTGGCAAATAGTAACAAACAGAAGTAC 59.198 37.037 0.00 0.00 0.00 2.73
2103 3778 7.040961 GGTGGCAAATAGTAACAAACAGAAGTA 60.041 37.037 0.00 0.00 0.00 2.24
2104 3779 6.238925 GGTGGCAAATAGTAACAAACAGAAGT 60.239 38.462 0.00 0.00 0.00 3.01
2105 3780 6.149633 GGTGGCAAATAGTAACAAACAGAAG 58.850 40.000 0.00 0.00 0.00 2.85
2108 3783 5.009610 ACTGGTGGCAAATAGTAACAAACAG 59.990 40.000 0.00 0.00 0.00 3.16
2109 3784 4.890581 ACTGGTGGCAAATAGTAACAAACA 59.109 37.500 0.00 0.00 0.00 2.83
2110 3785 5.447624 ACTGGTGGCAAATAGTAACAAAC 57.552 39.130 0.00 0.00 0.00 2.93
2111 3786 6.999272 TCTTACTGGTGGCAAATAGTAACAAA 59.001 34.615 12.62 3.35 33.48 2.83
2113 3788 6.116711 TCTTACTGGTGGCAAATAGTAACA 57.883 37.500 12.62 4.08 33.48 2.41
2114 3789 6.428771 TGTTCTTACTGGTGGCAAATAGTAAC 59.571 38.462 12.62 8.69 33.48 2.50
2115 3790 6.535540 TGTTCTTACTGGTGGCAAATAGTAA 58.464 36.000 14.70 14.70 35.18 2.24
2116 3791 6.116711 TGTTCTTACTGGTGGCAAATAGTA 57.883 37.500 0.00 0.00 0.00 1.82
2117 3792 4.980573 TGTTCTTACTGGTGGCAAATAGT 58.019 39.130 0.00 0.00 0.00 2.12
2118 3793 5.957842 TTGTTCTTACTGGTGGCAAATAG 57.042 39.130 0.00 0.00 0.00 1.73
2119 3794 6.007076 TGATTGTTCTTACTGGTGGCAAATA 58.993 36.000 0.00 0.00 0.00 1.40
2120 3795 4.832266 TGATTGTTCTTACTGGTGGCAAAT 59.168 37.500 0.00 0.00 0.00 2.32
2121 3796 4.037446 GTGATTGTTCTTACTGGTGGCAAA 59.963 41.667 0.00 0.00 0.00 3.68
2124 3799 3.146066 TGTGATTGTTCTTACTGGTGGC 58.854 45.455 0.00 0.00 0.00 5.01
2125 3800 5.241506 ACATTGTGATTGTTCTTACTGGTGG 59.758 40.000 0.00 0.00 0.00 4.61
2126 3801 6.317789 ACATTGTGATTGTTCTTACTGGTG 57.682 37.500 0.00 0.00 0.00 4.17
2127 3802 8.635765 AATACATTGTGATTGTTCTTACTGGT 57.364 30.769 0.00 0.00 0.00 4.00
2128 3803 9.912634 AAAATACATTGTGATTGTTCTTACTGG 57.087 29.630 0.00 0.00 0.00 4.00
2130 3805 9.410556 GCAAAATACATTGTGATTGTTCTTACT 57.589 29.630 0.00 0.00 32.80 2.24
2131 3806 9.190858 TGCAAAATACATTGTGATTGTTCTTAC 57.809 29.630 0.00 0.00 32.80 2.34
2133 3808 7.096106 CGTGCAAAATACATTGTGATTGTTCTT 60.096 33.333 0.00 0.00 32.80 2.52
2134 3809 6.363088 CGTGCAAAATACATTGTGATTGTTCT 59.637 34.615 0.00 0.00 32.80 3.01
2135 3810 6.515882 CGTGCAAAATACATTGTGATTGTTC 58.484 36.000 0.00 0.55 32.80 3.18
2136 3811 5.107530 GCGTGCAAAATACATTGTGATTGTT 60.108 36.000 0.00 0.00 32.80 2.83
2137 3812 4.385447 GCGTGCAAAATACATTGTGATTGT 59.615 37.500 0.00 0.00 32.80 2.71
2138 3813 4.622313 AGCGTGCAAAATACATTGTGATTG 59.378 37.500 0.00 3.52 32.80 2.67
2290 3992 6.490381 AGAAGGGACCTATTGAAAAAGTTGAC 59.510 38.462 0.00 0.00 0.00 3.18
2328 4030 6.489700 TCATGAAAGCAACTGGTAGAAATCAA 59.510 34.615 0.00 0.00 0.00 2.57
2415 4117 9.413048 GAGTACAATGTAGCCAGATATTAGAAC 57.587 37.037 0.00 0.00 0.00 3.01
2569 4271 6.200854 TGTGATCATTAGAATGCATACGTGTC 59.799 38.462 0.00 0.00 36.36 3.67
3224 4927 0.257039 AGGTTCCATCAGGCCATGAC 59.743 55.000 5.01 0.00 41.91 3.06
3325 5028 9.097257 CAACCAGATTTAAAACAAACAGAACAT 57.903 29.630 0.00 0.00 0.00 2.71
3367 5070 8.463607 CCAAAAACGTAAGATAATGGTTATGGT 58.536 33.333 0.00 0.00 43.62 3.55
3386 5089 3.058777 CACCAATGCTCAATGCCAAAAAC 60.059 43.478 0.00 0.00 42.00 2.43
3544 5247 7.703328 TGCTTTTTGTTCTCCAACTAGTTAAG 58.297 34.615 8.04 9.12 33.17 1.85
3739 5443 4.803426 GCCGGACTCGCTGGACAG 62.803 72.222 5.05 0.00 46.81 3.51
3870 5574 6.662414 TGATACTTCAAATAAGAGCAACCG 57.338 37.500 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.