Multiple sequence alignment - TraesCS3D01G441300

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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 TraesCS3D01G441300 chr3D 100.000 3298 0 0 1 3298 551429291 551432588 0.000000e+00 6091.0
1 TraesCS3D01G441300 chr3D 91.485 1421 48 31 670 2035 551346700 551345298 0.000000e+00 1886.0
2 TraesCS3D01G441300 chr3D 92.161 472 30 5 2827 3295 459493891 459493424 0.000000e+00 660.0
3 TraesCS3D01G441300 chr3D 86.856 563 47 17 1 549 551351072 551350523 3.640000e-169 604.0
4 TraesCS3D01G441300 chr3B 89.872 1402 65 30 667 2035 731096203 731094846 0.000000e+00 1731.0
5 TraesCS3D01G441300 chr3B 85.124 363 37 9 193 548 731097259 731096907 4.050000e-94 355.0
6 TraesCS3D01G441300 chr3B 97.368 38 1 0 1 38 731097321 731097284 7.640000e-07 65.8
7 TraesCS3D01G441300 chr3A 92.510 1215 59 23 842 2035 688592214 688591011 0.000000e+00 1711.0
8 TraesCS3D01G441300 chr3A 93.151 803 51 4 2034 2832 661840278 661839476 0.000000e+00 1175.0
9 TraesCS3D01G441300 chr3A 87.758 825 32 9 2034 2831 669527664 669528446 0.000000e+00 900.0
10 TraesCS3D01G441300 chr3A 92.324 469 33 2 2827 3295 13266452 13266917 0.000000e+00 664.0
11 TraesCS3D01G441300 chr3A 91.525 472 39 1 2827 3298 621038121 621038591 0.000000e+00 649.0
12 TraesCS3D01G441300 chr3A 90.962 343 13 4 453 781 688592568 688592230 2.330000e-121 446.0
13 TraesCS3D01G441300 chr3A 88.251 366 21 9 41 386 688593484 688593121 5.090000e-113 418.0
14 TraesCS3D01G441300 chr4A 84.452 1505 85 53 662 2035 595442473 595443959 0.000000e+00 1345.0
15 TraesCS3D01G441300 chr4A 81.356 236 21 13 324 542 595442051 595442280 1.570000e-38 171.0
16 TraesCS3D01G441300 chr4D 83.153 1478 134 56 653 2035 7874502 7873045 0.000000e+00 1243.0
17 TraesCS3D01G441300 chr5D 93.672 806 41 4 2034 2832 470383083 470382281 0.000000e+00 1197.0
18 TraesCS3D01G441300 chr5D 92.946 808 48 7 2032 2833 291539562 291538758 0.000000e+00 1168.0
19 TraesCS3D01G441300 chr5D 93.540 774 37 5 2034 2796 56908843 56908072 0.000000e+00 1140.0
20 TraesCS3D01G441300 chr5D 90.382 811 64 11 2032 2832 264361226 264362032 0.000000e+00 1053.0
21 TraesCS3D01G441300 chr6D 93.416 805 40 6 2032 2832 414265282 414266077 0.000000e+00 1181.0
22 TraesCS3D01G441300 chr6D 91.775 766 46 7 2036 2791 322579935 322579177 0.000000e+00 1050.0
23 TraesCS3D01G441300 chr6D 92.111 469 34 2 2830 3298 445610846 445611311 0.000000e+00 658.0
24 TraesCS3D01G441300 chr7A 90.311 805 63 9 2032 2832 547547891 547547098 0.000000e+00 1040.0
25 TraesCS3D01G441300 chr7A 82.090 871 107 23 1198 2035 636629241 636630095 0.000000e+00 699.0
26 TraesCS3D01G441300 chr7A 92.178 473 32 4 2827 3298 632269109 632268641 0.000000e+00 664.0
27 TraesCS3D01G441300 chr7A 82.404 807 94 24 1270 2035 635860618 635861417 0.000000e+00 660.0
28 TraesCS3D01G441300 chr7A 76.898 303 25 23 249 532 636628284 636628560 2.670000e-26 130.0
29 TraesCS3D01G441300 chr7A 83.929 112 9 4 1027 1129 636629019 636629130 7.530000e-17 99.0
30 TraesCS3D01G441300 chr2A 91.316 760 55 8 2032 2788 89866589 89865838 0.000000e+00 1027.0
31 TraesCS3D01G441300 chr4B 88.734 861 60 16 1200 2023 14054840 14055700 0.000000e+00 1018.0
32 TraesCS3D01G441300 chr4B 81.526 249 25 15 913 1154 14054518 14054752 5.620000e-43 185.0
33 TraesCS3D01G441300 chr4B 84.810 158 10 9 693 845 14054242 14054390 2.650000e-31 147.0
34 TraesCS3D01G441300 chr7D 83.671 790 91 19 1270 2035 550800723 550801498 0.000000e+00 710.0
35 TraesCS3D01G441300 chr7D 85.042 722 74 14 1339 2035 550553393 550554105 0.000000e+00 704.0
36 TraesCS3D01G441300 chr7D 92.751 469 33 1 2827 3295 572593388 572593855 0.000000e+00 676.0
37 TraesCS3D01G441300 chr7D 82.353 799 93 26 1270 2035 550463253 550464036 0.000000e+00 651.0
38 TraesCS3D01G441300 chr7D 84.655 580 66 16 1466 2035 550655440 550656006 1.030000e-154 556.0
39 TraesCS3D01G441300 chr7D 85.849 106 9 2 1030 1129 550800432 550800537 1.250000e-19 108.0
40 TraesCS3D01G441300 chr7D 78.710 155 25 6 1041 1191 550553062 550553212 2.710000e-16 97.1
41 TraesCS3D01G441300 chr7D 83.636 110 9 4 1029 1129 550643228 550643337 9.740000e-16 95.3
42 TraesCS3D01G441300 chr7D 80.583 103 10 6 689 781 550800173 550800275 1.640000e-08 71.3
43 TraesCS3D01G441300 chr7D 80.208 96 3 7 689 781 550462690 550462772 1.280000e-04 58.4
44 TraesCS3D01G441300 chr7D 80.208 96 3 7 689 781 550642956 550643038 1.280000e-04 58.4
45 TraesCS3D01G441300 chr7B 83.437 803 89 23 1270 2035 595007713 595008508 0.000000e+00 706.0
46 TraesCS3D01G441300 chr7B 86.275 102 5 6 689 781 595166242 595166343 5.820000e-18 102.0
47 TraesCS3D01G441300 chr7B 85.437 103 5 6 689 781 595306801 595306903 7.530000e-17 99.0
48 TraesCS3D01G441300 chr7B 84.404 109 8 4 1030 1129 595307322 595307430 7.530000e-17 99.0
49 TraesCS3D01G441300 chr7B 90.909 77 0 5 456 532 595306596 595306665 2.710000e-16 97.1
50 TraesCS3D01G441300 chr7B 83.178 107 9 3 1029 1126 595007418 595007524 4.530000e-14 89.8
51 TraesCS3D01G441300 chr2D 92.324 469 35 1 2827 3295 387195975 387196442 0.000000e+00 665.0
52 TraesCS3D01G441300 chr2D 96.429 84 3 0 2749 2832 629602191 629602274 4.440000e-29 139.0
53 TraesCS3D01G441300 chr1B 91.525 472 36 2 2827 3295 679180283 679180753 0.000000e+00 647.0
54 TraesCS3D01G441300 chr1B 91.332 473 39 2 2827 3298 56461942 56461471 0.000000e+00 645.0


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 TraesCS3D01G441300 chr3D 551429291 551432588 3297 False 6091.000000 6091 100.000000 1 3298 1 chr3D.!!$F1 3297
1 TraesCS3D01G441300 chr3D 551345298 551351072 5774 True 1245.000000 1886 89.170500 1 2035 2 chr3D.!!$R2 2034
2 TraesCS3D01G441300 chr3B 731094846 731097321 2475 True 717.266667 1731 90.788000 1 2035 3 chr3B.!!$R1 2034
3 TraesCS3D01G441300 chr3A 661839476 661840278 802 True 1175.000000 1175 93.151000 2034 2832 1 chr3A.!!$R1 798
4 TraesCS3D01G441300 chr3A 669527664 669528446 782 False 900.000000 900 87.758000 2034 2831 1 chr3A.!!$F3 797
5 TraesCS3D01G441300 chr3A 688591011 688593484 2473 True 858.333333 1711 90.574333 41 2035 3 chr3A.!!$R2 1994
6 TraesCS3D01G441300 chr4A 595442051 595443959 1908 False 758.000000 1345 82.904000 324 2035 2 chr4A.!!$F1 1711
7 TraesCS3D01G441300 chr4D 7873045 7874502 1457 True 1243.000000 1243 83.153000 653 2035 1 chr4D.!!$R1 1382
8 TraesCS3D01G441300 chr5D 470382281 470383083 802 True 1197.000000 1197 93.672000 2034 2832 1 chr5D.!!$R3 798
9 TraesCS3D01G441300 chr5D 291538758 291539562 804 True 1168.000000 1168 92.946000 2032 2833 1 chr5D.!!$R2 801
10 TraesCS3D01G441300 chr5D 56908072 56908843 771 True 1140.000000 1140 93.540000 2034 2796 1 chr5D.!!$R1 762
11 TraesCS3D01G441300 chr5D 264361226 264362032 806 False 1053.000000 1053 90.382000 2032 2832 1 chr5D.!!$F1 800
12 TraesCS3D01G441300 chr6D 414265282 414266077 795 False 1181.000000 1181 93.416000 2032 2832 1 chr6D.!!$F1 800
13 TraesCS3D01G441300 chr6D 322579177 322579935 758 True 1050.000000 1050 91.775000 2036 2791 1 chr6D.!!$R1 755
14 TraesCS3D01G441300 chr7A 547547098 547547891 793 True 1040.000000 1040 90.311000 2032 2832 1 chr7A.!!$R1 800
15 TraesCS3D01G441300 chr7A 635860618 635861417 799 False 660.000000 660 82.404000 1270 2035 1 chr7A.!!$F1 765
16 TraesCS3D01G441300 chr7A 636628284 636630095 1811 False 309.333333 699 80.972333 249 2035 3 chr7A.!!$F2 1786
17 TraesCS3D01G441300 chr2A 89865838 89866589 751 True 1027.000000 1027 91.316000 2032 2788 1 chr2A.!!$R1 756
18 TraesCS3D01G441300 chr4B 14054242 14055700 1458 False 450.000000 1018 85.023333 693 2023 3 chr4B.!!$F1 1330
19 TraesCS3D01G441300 chr7D 550655440 550656006 566 False 556.000000 556 84.655000 1466 2035 1 chr7D.!!$F1 569
20 TraesCS3D01G441300 chr7D 550553062 550554105 1043 False 400.550000 704 81.876000 1041 2035 2 chr7D.!!$F4 994
21 TraesCS3D01G441300 chr7D 550462690 550464036 1346 False 354.700000 651 81.280500 689 2035 2 chr7D.!!$F3 1346
22 TraesCS3D01G441300 chr7D 550800173 550801498 1325 False 296.433333 710 83.367667 689 2035 3 chr7D.!!$F6 1346
23 TraesCS3D01G441300 chr7B 595007418 595008508 1090 False 397.900000 706 83.307500 1029 2035 2 chr7B.!!$F2 1006

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
139 140 0.039180 TTGAGCCCTCGTCTCTACCA 59.961 55.0 0.00 0.00 0.00 3.25 F
140 141 0.039180 TGAGCCCTCGTCTCTACCAA 59.961 55.0 0.00 0.00 0.00 3.67 F
305 330 0.177373 TGAGCCTAGTGCATGCTGAG 59.823 55.0 20.33 12.59 44.83 3.35 F
483 1080 0.606401 CACCCCAAGATTCGTGCAGT 60.606 55.0 0.00 0.00 0.00 4.40 F
484 1081 0.981183 ACCCCAAGATTCGTGCAGTA 59.019 50.0 0.00 0.00 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 7437 1.141881 CGCGGATGTTAGAGCCAGT 59.858 57.895 0.00 0.0 0.00 4.00 R
2125 7445 2.010497 TGCATTTTAGCGCGGATGTTA 58.990 42.857 8.83 0.0 37.31 2.41 R
2130 7450 2.791256 GCTGCATTTTAGCGCGGA 59.209 55.556 8.83 0.0 36.59 5.54 R
2194 7515 2.974692 ATATGCAATGCCCCGGCGAA 62.975 55.000 9.30 0.0 45.51 4.70 R
2618 7951 0.609131 ACGGGAGGCATGAGTTTTGG 60.609 55.000 0.00 0.0 0.00 3.28 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
73 74 0.593128 GATCAATCGGCCGGATTTGG 59.407 55.000 27.83 12.26 42.77 3.28
139 140 0.039180 TTGAGCCCTCGTCTCTACCA 59.961 55.000 0.00 0.00 0.00 3.25
140 141 0.039180 TGAGCCCTCGTCTCTACCAA 59.961 55.000 0.00 0.00 0.00 3.67
206 221 0.901580 TCCCCCTCAACCGTCTACAC 60.902 60.000 0.00 0.00 0.00 2.90
224 242 5.941647 TCTACACCTATAACCAGCCAAAAAC 59.058 40.000 0.00 0.00 0.00 2.43
237 258 4.574828 CAGCCAAAAACACGCCTATAGTAT 59.425 41.667 0.00 0.00 0.00 2.12
302 327 0.907486 TTCTGAGCCTAGTGCATGCT 59.093 50.000 20.33 1.26 44.83 3.79
305 330 0.177373 TGAGCCTAGTGCATGCTGAG 59.823 55.000 20.33 12.59 44.83 3.35
328 357 2.993220 TGCAGTGCATGAACTTACGTAG 59.007 45.455 15.37 0.00 31.71 3.51
383 936 1.198094 TCTCCGAATTGCCCTCCACA 61.198 55.000 0.00 0.00 0.00 4.17
387 940 1.247567 CGAATTGCCCTCCACAAACT 58.752 50.000 0.00 0.00 0.00 2.66
436 1025 7.139392 GGAGACCAGAGTAATTTGTTTTGTTC 58.861 38.462 0.00 0.00 0.00 3.18
437 1026 7.039313 AGACCAGAGTAATTTGTTTTGTTCC 57.961 36.000 0.00 0.00 0.00 3.62
438 1027 5.827666 ACCAGAGTAATTTGTTTTGTTCCG 58.172 37.500 0.00 0.00 0.00 4.30
439 1028 5.358725 ACCAGAGTAATTTGTTTTGTTCCGT 59.641 36.000 0.00 0.00 0.00 4.69
440 1029 6.127563 ACCAGAGTAATTTGTTTTGTTCCGTT 60.128 34.615 0.00 0.00 0.00 4.44
441 1030 6.416750 CCAGAGTAATTTGTTTTGTTCCGTTC 59.583 38.462 0.00 0.00 0.00 3.95
442 1031 6.140108 CAGAGTAATTTGTTTTGTTCCGTTCG 59.860 38.462 0.00 0.00 0.00 3.95
443 1032 6.037391 AGAGTAATTTGTTTTGTTCCGTTCGA 59.963 34.615 0.00 0.00 0.00 3.71
444 1033 5.967088 AGTAATTTGTTTTGTTCCGTTCGAC 59.033 36.000 0.00 0.00 0.00 4.20
445 1034 4.625972 ATTTGTTTTGTTCCGTTCGACT 57.374 36.364 0.00 0.00 0.00 4.18
446 1035 4.422546 TTTGTTTTGTTCCGTTCGACTT 57.577 36.364 0.00 0.00 0.00 3.01
447 1036 3.661758 TGTTTTGTTCCGTTCGACTTC 57.338 42.857 0.00 0.00 0.00 3.01
448 1037 2.029486 TGTTTTGTTCCGTTCGACTTCG 59.971 45.455 0.00 0.00 41.45 3.79
463 1057 3.003480 GACTTCGATCTGGGTTTCCTTG 58.997 50.000 0.00 0.00 0.00 3.61
483 1080 0.606401 CACCCCAAGATTCGTGCAGT 60.606 55.000 0.00 0.00 0.00 4.40
484 1081 0.981183 ACCCCAAGATTCGTGCAGTA 59.019 50.000 0.00 0.00 0.00 2.74
485 1082 1.066143 ACCCCAAGATTCGTGCAGTAG 60.066 52.381 0.00 0.00 0.00 2.57
486 1083 1.009829 CCCAAGATTCGTGCAGTAGC 58.990 55.000 0.00 0.00 42.57 3.58
553 1157 6.759497 ACCTACTAACTTGAATGATTTGGC 57.241 37.500 0.00 0.00 0.00 4.52
560 1183 5.813513 ACTTGAATGATTTGGCCTTCTTT 57.186 34.783 3.32 3.12 0.00 2.52
604 1787 2.738643 CGACCCCATATATGCATCCGTC 60.739 54.545 0.19 6.52 0.00 4.79
626 1814 3.007635 GGTTGCAGACCCTTGTGTATAC 58.992 50.000 6.76 0.00 43.06 1.47
1131 6237 2.360350 CACCACCAGCTCGCCAAT 60.360 61.111 0.00 0.00 0.00 3.16
1256 6458 4.467084 TCTGGCCGCGGTTGATCC 62.467 66.667 28.70 19.37 0.00 3.36
1291 6502 2.464459 GGCGCTCAGGAAATGACCG 61.464 63.158 7.64 0.00 39.52 4.79
1371 6591 3.341043 CACGCGCAACAGCAGACT 61.341 61.111 5.73 0.00 36.85 3.24
1416 6644 1.902508 AGACATGTGAGTCCCGTGATT 59.097 47.619 1.15 0.00 39.34 2.57
1443 6690 2.868196 GCCTCGTTTCCGGCTTTC 59.132 61.111 0.00 0.00 42.98 2.62
2024 7341 1.333702 GCGTCAACTTTTCGTGATGCA 60.334 47.619 11.86 0.00 41.43 3.96
2267 7589 4.453136 ACCTTCAAAATGCAATGAACATGC 59.547 37.500 8.39 0.00 44.08 4.06
2636 7969 0.609131 ACCAAAACTCATGCCTCCCG 60.609 55.000 0.00 0.00 0.00 5.14
2693 8026 2.446848 ATGCCTCCCATGGTCTCCG 61.447 63.158 11.73 0.00 31.48 4.63
2717 8050 1.304381 GCTCCAAAGCCACCCATGA 60.304 57.895 0.00 0.00 43.10 3.07
2833 8190 2.814280 TCAAGACTTCTTCACGGGAC 57.186 50.000 0.00 0.00 33.11 4.46
2835 8192 1.935300 CAAGACTTCTTCACGGGACGG 60.935 57.143 0.00 0.00 46.54 4.79
2937 8294 3.440415 GGCGGTGGCAAGGCTAAC 61.440 66.667 10.36 0.00 42.47 2.34
2939 8296 3.799755 CGGTGGCAAGGCTAACGC 61.800 66.667 0.00 0.00 43.87 4.84
2940 8297 2.359975 GGTGGCAAGGCTAACGCT 60.360 61.111 0.00 0.00 36.09 5.07
2941 8298 2.399356 GGTGGCAAGGCTAACGCTC 61.399 63.158 0.00 0.00 36.09 5.03
2942 8299 2.046314 TGGCAAGGCTAACGCTCC 60.046 61.111 0.00 0.00 36.09 4.70
2943 8300 2.824489 GGCAAGGCTAACGCTCCC 60.824 66.667 0.00 0.00 36.09 4.30
2944 8301 2.824489 GCAAGGCTAACGCTCCCC 60.824 66.667 0.00 0.00 36.09 4.81
2945 8302 2.511600 CAAGGCTAACGCTCCCCG 60.512 66.667 0.00 0.00 44.21 5.73
2946 8303 4.468689 AAGGCTAACGCTCCCCGC 62.469 66.667 0.00 0.00 41.76 6.13
2960 8317 4.446413 CCGCGCTAGGGTTTCCGT 62.446 66.667 5.56 0.00 38.33 4.69
2961 8318 2.884207 CGCGCTAGGGTTTCCGTC 60.884 66.667 5.56 0.00 38.33 4.79
2962 8319 2.884207 GCGCTAGGGTTTCCGTCG 60.884 66.667 8.77 0.00 38.33 5.12
2963 8320 2.202703 CGCTAGGGTTTCCGTCGG 60.203 66.667 4.39 4.39 38.33 4.79
2964 8321 2.976356 GCTAGGGTTTCCGTCGGT 59.024 61.111 11.88 0.00 38.33 4.69
2965 8322 1.447314 GCTAGGGTTTCCGTCGGTG 60.447 63.158 11.88 0.00 38.33 4.94
2966 8323 1.217244 CTAGGGTTTCCGTCGGTGG 59.783 63.158 11.88 0.00 38.33 4.61
2967 8324 2.847435 CTAGGGTTTCCGTCGGTGGC 62.847 65.000 11.88 2.30 38.33 5.01
2968 8325 4.324991 GGGTTTCCGTCGGTGGCT 62.325 66.667 11.88 0.00 0.00 4.75
2969 8326 3.047877 GGTTTCCGTCGGTGGCTG 61.048 66.667 11.88 0.00 0.00 4.85
2970 8327 3.723348 GTTTCCGTCGGTGGCTGC 61.723 66.667 11.88 0.00 0.00 5.25
2992 8349 4.208686 GAGGGGTCGCGGCTGTAG 62.209 72.222 11.94 0.00 0.00 2.74
2995 8352 3.537874 GGGTCGCGGCTGTAGGAT 61.538 66.667 11.94 0.00 0.00 3.24
2996 8353 2.279517 GGTCGCGGCTGTAGGATG 60.280 66.667 11.94 0.00 0.00 3.51
2997 8354 2.279517 GTCGCGGCTGTAGGATGG 60.280 66.667 1.90 0.00 0.00 3.51
2998 8355 3.536917 TCGCGGCTGTAGGATGGG 61.537 66.667 6.13 0.00 0.00 4.00
2999 8356 4.609018 CGCGGCTGTAGGATGGGG 62.609 72.222 0.00 0.00 0.00 4.96
3000 8357 3.480133 GCGGCTGTAGGATGGGGT 61.480 66.667 0.00 0.00 0.00 4.95
3001 8358 2.505982 CGGCTGTAGGATGGGGTG 59.494 66.667 0.00 0.00 0.00 4.61
3002 8359 2.063979 CGGCTGTAGGATGGGGTGA 61.064 63.158 0.00 0.00 0.00 4.02
3003 8360 1.832912 GGCTGTAGGATGGGGTGAG 59.167 63.158 0.00 0.00 0.00 3.51
3004 8361 0.983378 GGCTGTAGGATGGGGTGAGT 60.983 60.000 0.00 0.00 0.00 3.41
3005 8362 0.179000 GCTGTAGGATGGGGTGAGTG 59.821 60.000 0.00 0.00 0.00 3.51
3006 8363 0.833287 CTGTAGGATGGGGTGAGTGG 59.167 60.000 0.00 0.00 0.00 4.00
3007 8364 0.620410 TGTAGGATGGGGTGAGTGGG 60.620 60.000 0.00 0.00 0.00 4.61
3008 8365 1.004230 TAGGATGGGGTGAGTGGGG 59.996 63.158 0.00 0.00 0.00 4.96
3009 8366 1.833055 TAGGATGGGGTGAGTGGGGT 61.833 60.000 0.00 0.00 0.00 4.95
3010 8367 2.677228 GATGGGGTGAGTGGGGTG 59.323 66.667 0.00 0.00 0.00 4.61
3011 8368 3.645268 GATGGGGTGAGTGGGGTGC 62.645 68.421 0.00 0.00 0.00 5.01
3028 8385 3.576356 CCGGCGTGTGCATCCATC 61.576 66.667 6.01 0.00 45.35 3.51
3029 8386 3.928769 CGGCGTGTGCATCCATCG 61.929 66.667 0.00 0.00 45.35 3.84
3030 8387 3.576356 GGCGTGTGCATCCATCGG 61.576 66.667 0.00 0.00 45.35 4.18
3031 8388 3.576356 GCGTGTGCATCCATCGGG 61.576 66.667 0.00 0.00 42.15 5.14
3032 8389 2.125147 CGTGTGCATCCATCGGGT 60.125 61.111 0.00 0.00 34.93 5.28
3033 8390 2.173669 CGTGTGCATCCATCGGGTC 61.174 63.158 0.00 0.00 34.93 4.46
3034 8391 1.078497 GTGTGCATCCATCGGGTCA 60.078 57.895 0.00 0.00 34.93 4.02
3035 8392 0.676466 GTGTGCATCCATCGGGTCAA 60.676 55.000 0.00 0.00 34.93 3.18
3036 8393 0.392863 TGTGCATCCATCGGGTCAAG 60.393 55.000 0.00 0.00 34.93 3.02
3037 8394 0.392998 GTGCATCCATCGGGTCAAGT 60.393 55.000 0.00 0.00 34.93 3.16
3038 8395 0.327924 TGCATCCATCGGGTCAAGTT 59.672 50.000 0.00 0.00 34.93 2.66
3039 8396 1.017387 GCATCCATCGGGTCAAGTTC 58.983 55.000 0.00 0.00 34.93 3.01
3040 8397 1.290203 CATCCATCGGGTCAAGTTCG 58.710 55.000 0.00 0.00 34.93 3.95
3041 8398 0.462047 ATCCATCGGGTCAAGTTCGC 60.462 55.000 0.00 0.00 34.93 4.70
3042 8399 2.106683 CCATCGGGTCAAGTTCGCC 61.107 63.158 0.00 0.00 0.00 5.54
3043 8400 2.125673 ATCGGGTCAAGTTCGCCG 60.126 61.111 0.00 0.00 0.00 6.46
3044 8401 3.659089 ATCGGGTCAAGTTCGCCGG 62.659 63.158 0.00 0.00 0.00 6.13
3080 8437 3.781307 CGATGGTGGCGGGGAAGA 61.781 66.667 0.00 0.00 0.00 2.87
3081 8438 2.190578 GATGGTGGCGGGGAAGAG 59.809 66.667 0.00 0.00 0.00 2.85
3082 8439 2.285368 ATGGTGGCGGGGAAGAGA 60.285 61.111 0.00 0.00 0.00 3.10
3083 8440 2.317149 GATGGTGGCGGGGAAGAGAG 62.317 65.000 0.00 0.00 0.00 3.20
3084 8441 2.683933 GGTGGCGGGGAAGAGAGA 60.684 66.667 0.00 0.00 0.00 3.10
3085 8442 2.726351 GGTGGCGGGGAAGAGAGAG 61.726 68.421 0.00 0.00 0.00 3.20
3086 8443 1.985116 GTGGCGGGGAAGAGAGAGT 60.985 63.158 0.00 0.00 0.00 3.24
3087 8444 1.984570 TGGCGGGGAAGAGAGAGTG 60.985 63.158 0.00 0.00 0.00 3.51
3088 8445 2.185608 GCGGGGAAGAGAGAGTGC 59.814 66.667 0.00 0.00 0.00 4.40
3089 8446 2.492090 CGGGGAAGAGAGAGTGCG 59.508 66.667 0.00 0.00 0.00 5.34
3090 8447 2.896443 GGGGAAGAGAGAGTGCGG 59.104 66.667 0.00 0.00 0.00 5.69
3091 8448 2.185608 GGGAAGAGAGAGTGCGGC 59.814 66.667 0.00 0.00 0.00 6.53
3092 8449 2.202676 GGAAGAGAGAGTGCGGCG 60.203 66.667 0.51 0.51 0.00 6.46
3093 8450 2.883253 GAAGAGAGAGTGCGGCGC 60.883 66.667 27.44 27.44 0.00 6.53
3094 8451 4.785512 AAGAGAGAGTGCGGCGCG 62.786 66.667 28.09 0.00 0.00 6.86
3136 8493 4.434354 AAGCCGGCGCCCCAAATA 62.434 61.111 23.46 0.00 34.57 1.40
3139 8496 3.514362 CCGGCGCCCCAAATACAC 61.514 66.667 23.46 0.00 0.00 2.90
3140 8497 2.748251 CGGCGCCCCAAATACACA 60.748 61.111 23.46 0.00 0.00 3.72
3141 8498 2.760159 CGGCGCCCCAAATACACAG 61.760 63.158 23.46 0.00 0.00 3.66
3142 8499 2.489751 GCGCCCCAAATACACAGC 59.510 61.111 0.00 0.00 0.00 4.40
3143 8500 2.791256 CGCCCCAAATACACAGCG 59.209 61.111 0.00 0.00 37.39 5.18
3144 8501 2.489751 GCCCCAAATACACAGCGC 59.510 61.111 0.00 0.00 0.00 5.92
3145 8502 2.791256 CCCCAAATACACAGCGCG 59.209 61.111 0.00 0.00 0.00 6.86
3146 8503 1.743623 CCCCAAATACACAGCGCGA 60.744 57.895 12.10 0.00 0.00 5.87
3147 8504 1.705337 CCCCAAATACACAGCGCGAG 61.705 60.000 12.10 3.23 0.00 5.03
3148 8505 1.019278 CCCAAATACACAGCGCGAGT 61.019 55.000 12.10 4.06 0.00 4.18
3149 8506 0.796312 CCAAATACACAGCGCGAGTT 59.204 50.000 12.10 1.40 0.00 3.01
3160 8517 3.039588 GCGAGTTGGCGTTTCGGA 61.040 61.111 6.50 0.00 35.05 4.55
3161 8518 2.851104 CGAGTTGGCGTTTCGGAC 59.149 61.111 0.00 0.00 0.00 4.79
3162 8519 2.664436 CGAGTTGGCGTTTCGGACC 61.664 63.158 0.00 0.00 0.00 4.46
3163 8520 2.663852 AGTTGGCGTTTCGGACCG 60.664 61.111 7.84 7.84 0.00 4.79
3177 8534 3.778360 GACCGCGCGCCCAACTATA 62.778 63.158 27.36 0.00 0.00 1.31
3178 8535 2.357034 CCGCGCGCCCAACTATAT 60.357 61.111 27.36 0.00 0.00 0.86
3179 8536 1.080366 CCGCGCGCCCAACTATATA 60.080 57.895 27.36 0.00 0.00 0.86
3180 8537 0.459585 CCGCGCGCCCAACTATATAT 60.460 55.000 27.36 0.00 0.00 0.86
3181 8538 0.645355 CGCGCGCCCAACTATATATG 59.355 55.000 27.72 1.87 0.00 1.78
3182 8539 0.373716 GCGCGCCCAACTATATATGC 59.626 55.000 23.24 0.00 0.00 3.14
3183 8540 1.006832 CGCGCCCAACTATATATGCC 58.993 55.000 0.00 0.00 0.00 4.40
3184 8541 1.006832 GCGCCCAACTATATATGCCG 58.993 55.000 0.00 0.00 0.00 5.69
3185 8542 1.006832 CGCCCAACTATATATGCCGC 58.993 55.000 0.00 0.00 0.00 6.53
3186 8543 1.006832 GCCCAACTATATATGCCGCG 58.993 55.000 0.00 0.00 0.00 6.46
3187 8544 1.006832 CCCAACTATATATGCCGCGC 58.993 55.000 0.00 0.00 0.00 6.86
3188 8545 0.645355 CCAACTATATATGCCGCGCG 59.355 55.000 25.67 25.67 0.00 6.86
3189 8546 1.346365 CAACTATATATGCCGCGCGT 58.654 50.000 29.95 13.36 0.00 6.01
3190 8547 1.059122 CAACTATATATGCCGCGCGTG 59.941 52.381 29.95 20.72 0.00 5.34
3191 8548 1.076533 ACTATATATGCCGCGCGTGC 61.077 55.000 29.95 29.10 37.91 5.34
3220 8577 4.400961 GCCCGCTGGAGCTTGTCT 62.401 66.667 0.00 0.00 39.32 3.41
3221 8578 3.019003 GCCCGCTGGAGCTTGTCTA 62.019 63.158 0.00 0.00 39.32 2.59
3222 8579 1.153549 CCCGCTGGAGCTTGTCTAC 60.154 63.158 0.00 0.00 39.32 2.59
3223 8580 1.591703 CCGCTGGAGCTTGTCTACA 59.408 57.895 0.00 0.00 39.32 2.74
3228 8585 2.839486 TGGAGCTTGTCTACAGGTTG 57.161 50.000 0.00 0.00 30.44 3.77
3229 8586 1.270839 TGGAGCTTGTCTACAGGTTGC 60.271 52.381 0.00 0.00 30.44 4.17
3230 8587 1.071605 GAGCTTGTCTACAGGTTGCG 58.928 55.000 0.00 0.00 0.00 4.85
3231 8588 0.951040 AGCTTGTCTACAGGTTGCGC 60.951 55.000 0.00 0.00 0.00 6.09
3232 8589 1.781555 CTTGTCTACAGGTTGCGCG 59.218 57.895 0.00 0.00 0.00 6.86
3233 8590 2.227968 CTTGTCTACAGGTTGCGCGC 62.228 60.000 27.26 27.26 0.00 6.86
3234 8591 2.736995 GTCTACAGGTTGCGCGCA 60.737 61.111 33.09 33.09 0.00 6.09
3235 8592 2.736995 TCTACAGGTTGCGCGCAC 60.737 61.111 36.72 27.03 0.00 5.34
3236 8593 4.134187 CTACAGGTTGCGCGCACG 62.134 66.667 36.72 23.94 44.07 5.34
3246 8603 2.944049 CGCGCACGCTAAAATGGC 60.944 61.111 13.70 0.00 39.32 4.40
3247 8604 2.178025 GCGCACGCTAAAATGGCA 59.822 55.556 7.96 0.00 38.26 4.92
3248 8605 1.443533 GCGCACGCTAAAATGGCAA 60.444 52.632 7.96 0.00 38.26 4.52
3249 8606 1.006314 GCGCACGCTAAAATGGCAAA 61.006 50.000 7.96 0.00 38.26 3.68
3250 8607 1.413382 CGCACGCTAAAATGGCAAAA 58.587 45.000 0.00 0.00 0.00 2.44
3251 8608 1.991965 CGCACGCTAAAATGGCAAAAT 59.008 42.857 0.00 0.00 0.00 1.82
3252 8609 2.411409 CGCACGCTAAAATGGCAAAATT 59.589 40.909 0.00 0.00 0.00 1.82
3253 8610 3.120718 CGCACGCTAAAATGGCAAAATTT 60.121 39.130 0.00 0.00 0.00 1.82
3254 8611 4.150343 GCACGCTAAAATGGCAAAATTTG 58.850 39.130 0.57 0.57 30.21 2.32
3274 8631 1.154469 GGCACGACGCTTGTTTAGC 60.154 57.895 0.00 0.00 46.83 3.09
3281 8638 4.130857 GCTTGTTTAGCGCGGTTG 57.869 55.556 19.09 1.47 40.71 3.77
3282 8639 1.281656 GCTTGTTTAGCGCGGTTGT 59.718 52.632 19.09 0.00 40.71 3.32
3283 8640 0.317519 GCTTGTTTAGCGCGGTTGTT 60.318 50.000 19.09 0.00 40.71 2.83
3284 8641 1.394697 CTTGTTTAGCGCGGTTGTTG 58.605 50.000 19.09 0.00 0.00 3.33
3285 8642 0.029567 TTGTTTAGCGCGGTTGTTGG 59.970 50.000 19.09 0.00 0.00 3.77
3286 8643 0.814410 TGTTTAGCGCGGTTGTTGGA 60.814 50.000 19.09 0.00 0.00 3.53
3287 8644 0.110373 GTTTAGCGCGGTTGTTGGAG 60.110 55.000 19.09 0.00 0.00 3.86
3288 8645 0.249953 TTTAGCGCGGTTGTTGGAGA 60.250 50.000 19.09 0.00 0.00 3.71
3289 8646 0.036765 TTAGCGCGGTTGTTGGAGAT 60.037 50.000 19.09 0.00 0.00 2.75
3290 8647 0.818938 TAGCGCGGTTGTTGGAGATA 59.181 50.000 19.09 0.00 0.00 1.98
3291 8648 0.739813 AGCGCGGTTGTTGGAGATAC 60.740 55.000 4.23 0.00 0.00 2.24
3292 8649 0.739813 GCGCGGTTGTTGGAGATACT 60.740 55.000 8.83 0.00 0.00 2.12
3293 8650 1.278238 CGCGGTTGTTGGAGATACTC 58.722 55.000 0.00 0.00 0.00 2.59
3294 8651 1.135083 CGCGGTTGTTGGAGATACTCT 60.135 52.381 0.00 0.00 0.00 3.24
3295 8652 2.674177 CGCGGTTGTTGGAGATACTCTT 60.674 50.000 0.00 0.00 0.00 2.85
3296 8653 3.428452 CGCGGTTGTTGGAGATACTCTTA 60.428 47.826 0.00 0.00 0.00 2.10
3297 8654 4.113354 GCGGTTGTTGGAGATACTCTTAG 58.887 47.826 0.00 0.00 0.00 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 1.757118 TGCCTATACTGTGCTCTGGTC 59.243 52.381 0.00 0.00 0.00 4.02
188 199 1.595357 GTGTAGACGGTTGAGGGGG 59.405 63.158 0.00 0.00 0.00 5.40
190 201 1.843368 TAGGTGTAGACGGTTGAGGG 58.157 55.000 0.00 0.00 0.00 4.30
191 202 4.202090 GGTTATAGGTGTAGACGGTTGAGG 60.202 50.000 0.00 0.00 0.00 3.86
206 221 3.672241 GCGTGTTTTTGGCTGGTTATAGG 60.672 47.826 0.00 0.00 0.00 2.57
224 242 8.961294 ATACTCCTACTAATACTATAGGCGTG 57.039 38.462 4.43 0.00 35.37 5.34
237 258 7.549842 GTGCTGATCGAGATATACTCCTACTAA 59.450 40.741 0.00 0.00 42.18 2.24
361 404 0.464554 GGAGGGCAATTCGGAGAAGG 60.465 60.000 0.00 0.00 45.90 3.46
383 936 1.802365 CTTGGTAAAGCGCCGTAGTTT 59.198 47.619 2.29 0.00 0.00 2.66
387 940 0.390209 GGACTTGGTAAAGCGCCGTA 60.390 55.000 2.29 0.00 36.84 4.02
418 984 6.037391 TCGAACGGAACAAAACAAATTACTCT 59.963 34.615 0.00 0.00 0.00 3.24
441 1030 1.204941 AGGAAACCCAGATCGAAGTCG 59.795 52.381 0.00 0.00 41.45 4.18
442 1031 3.003480 CAAGGAAACCCAGATCGAAGTC 58.997 50.000 0.00 0.00 0.00 3.01
443 1032 2.876079 GCAAGGAAACCCAGATCGAAGT 60.876 50.000 0.00 0.00 0.00 3.01
444 1033 1.740025 GCAAGGAAACCCAGATCGAAG 59.260 52.381 0.00 0.00 0.00 3.79
445 1034 1.073125 TGCAAGGAAACCCAGATCGAA 59.927 47.619 0.00 0.00 0.00 3.71
446 1035 0.690192 TGCAAGGAAACCCAGATCGA 59.310 50.000 0.00 0.00 0.00 3.59
447 1036 0.804989 GTGCAAGGAAACCCAGATCG 59.195 55.000 0.00 0.00 0.00 3.69
448 1037 1.177401 GGTGCAAGGAAACCCAGATC 58.823 55.000 0.00 0.00 0.00 2.75
449 1038 3.363787 GGTGCAAGGAAACCCAGAT 57.636 52.632 0.00 0.00 0.00 2.90
450 1039 4.920828 GGTGCAAGGAAACCCAGA 57.079 55.556 0.00 0.00 0.00 3.86
483 1080 1.556451 TGAGGCTGCTTTGATCTGCTA 59.444 47.619 0.00 0.00 0.00 3.49
484 1081 0.327259 TGAGGCTGCTTTGATCTGCT 59.673 50.000 0.00 0.00 0.00 4.24
485 1082 1.135460 GTTGAGGCTGCTTTGATCTGC 60.135 52.381 0.00 0.00 0.00 4.26
486 1083 1.129998 CGTTGAGGCTGCTTTGATCTG 59.870 52.381 0.00 0.00 0.00 2.90
487 1084 1.002430 TCGTTGAGGCTGCTTTGATCT 59.998 47.619 0.00 0.00 0.00 2.75
560 1183 4.619973 AGTTCATCGCTTGATTTGCAAAA 58.380 34.783 17.19 0.00 35.74 2.44
626 1814 2.552315 ACCAAGAATATATTTGGCCGCG 59.448 45.455 13.84 0.00 46.16 6.46
687 5597 4.712122 TTTATGCCTTCCGTTTCAATCC 57.288 40.909 0.00 0.00 0.00 3.01
1221 6423 2.202756 GCCAACCGCTCCGAGTAG 60.203 66.667 0.00 0.00 0.00 2.57
2024 7341 3.627041 TGGAGATGCTCTAATCCTCCT 57.373 47.619 0.00 0.00 32.79 3.69
2117 7437 1.141881 CGCGGATGTTAGAGCCAGT 59.858 57.895 0.00 0.00 0.00 4.00
2125 7445 2.010497 TGCATTTTAGCGCGGATGTTA 58.990 42.857 8.83 0.00 37.31 2.41
2130 7450 2.791256 GCTGCATTTTAGCGCGGA 59.209 55.556 8.83 0.00 36.59 5.54
2194 7515 2.974692 ATATGCAATGCCCCGGCGAA 62.975 55.000 9.30 0.00 45.51 4.70
2618 7951 0.609131 ACGGGAGGCATGAGTTTTGG 60.609 55.000 0.00 0.00 0.00 3.28
2717 8050 2.031465 CGTGGGCGGTTTAGGTGT 59.969 61.111 0.00 0.00 0.00 4.16
2920 8277 3.440415 GTTAGCCTTGCCACCGCC 61.440 66.667 0.00 0.00 0.00 6.13
2921 8278 3.799755 CGTTAGCCTTGCCACCGC 61.800 66.667 0.00 0.00 0.00 5.68
2922 8279 3.799755 GCGTTAGCCTTGCCACCG 61.800 66.667 0.00 0.00 37.42 4.94
2923 8280 2.359975 AGCGTTAGCCTTGCCACC 60.360 61.111 0.00 0.00 46.67 4.61
2924 8281 2.399356 GGAGCGTTAGCCTTGCCAC 61.399 63.158 0.00 0.00 46.67 5.01
2925 8282 2.046314 GGAGCGTTAGCCTTGCCA 60.046 61.111 0.00 0.00 46.67 4.92
2926 8283 2.824489 GGGAGCGTTAGCCTTGCC 60.824 66.667 0.00 0.00 46.67 4.52
2927 8284 2.824489 GGGGAGCGTTAGCCTTGC 60.824 66.667 0.00 0.00 46.67 4.01
2928 8285 2.511600 CGGGGAGCGTTAGCCTTG 60.512 66.667 0.00 0.00 46.67 3.61
2929 8286 4.468689 GCGGGGAGCGTTAGCCTT 62.469 66.667 0.00 0.00 46.67 4.35
2943 8300 4.446413 ACGGAAACCCTAGCGCGG 62.446 66.667 8.83 0.00 0.00 6.46
2944 8301 2.884207 GACGGAAACCCTAGCGCG 60.884 66.667 0.00 0.00 0.00 6.86
2945 8302 2.884207 CGACGGAAACCCTAGCGC 60.884 66.667 0.00 0.00 0.00 5.92
2946 8303 2.202703 CCGACGGAAACCCTAGCG 60.203 66.667 8.64 0.00 0.00 4.26
2947 8304 1.447314 CACCGACGGAAACCCTAGC 60.447 63.158 23.38 0.00 0.00 3.42
2948 8305 1.217244 CCACCGACGGAAACCCTAG 59.783 63.158 23.38 0.00 0.00 3.02
2949 8306 2.946346 GCCACCGACGGAAACCCTA 61.946 63.158 23.38 0.00 0.00 3.53
2950 8307 4.324991 GCCACCGACGGAAACCCT 62.325 66.667 23.38 0.00 0.00 4.34
2951 8308 4.324991 AGCCACCGACGGAAACCC 62.325 66.667 23.38 3.84 0.00 4.11
2952 8309 3.047877 CAGCCACCGACGGAAACC 61.048 66.667 23.38 5.70 0.00 3.27
2953 8310 3.723348 GCAGCCACCGACGGAAAC 61.723 66.667 23.38 8.80 0.00 2.78
2975 8332 4.208686 CTACAGCCGCGACCCCTC 62.209 72.222 8.23 0.00 0.00 4.30
2978 8335 3.537874 ATCCTACAGCCGCGACCC 61.538 66.667 8.23 0.00 0.00 4.46
2979 8336 2.279517 CATCCTACAGCCGCGACC 60.280 66.667 8.23 0.00 0.00 4.79
2980 8337 2.279517 CCATCCTACAGCCGCGAC 60.280 66.667 8.23 0.00 0.00 5.19
2981 8338 3.536917 CCCATCCTACAGCCGCGA 61.537 66.667 8.23 0.00 0.00 5.87
2982 8339 4.609018 CCCCATCCTACAGCCGCG 62.609 72.222 0.00 0.00 0.00 6.46
2983 8340 3.480133 ACCCCATCCTACAGCCGC 61.480 66.667 0.00 0.00 0.00 6.53
2984 8341 2.032860 CTCACCCCATCCTACAGCCG 62.033 65.000 0.00 0.00 0.00 5.52
2985 8342 0.983378 ACTCACCCCATCCTACAGCC 60.983 60.000 0.00 0.00 0.00 4.85
2986 8343 0.179000 CACTCACCCCATCCTACAGC 59.821 60.000 0.00 0.00 0.00 4.40
2987 8344 0.833287 CCACTCACCCCATCCTACAG 59.167 60.000 0.00 0.00 0.00 2.74
2988 8345 0.620410 CCCACTCACCCCATCCTACA 60.620 60.000 0.00 0.00 0.00 2.74
2989 8346 1.345715 CCCCACTCACCCCATCCTAC 61.346 65.000 0.00 0.00 0.00 3.18
2990 8347 1.004230 CCCCACTCACCCCATCCTA 59.996 63.158 0.00 0.00 0.00 2.94
2991 8348 2.286425 CCCCACTCACCCCATCCT 60.286 66.667 0.00 0.00 0.00 3.24
2992 8349 2.614013 ACCCCACTCACCCCATCC 60.614 66.667 0.00 0.00 0.00 3.51
2993 8350 2.677228 CACCCCACTCACCCCATC 59.323 66.667 0.00 0.00 0.00 3.51
2994 8351 3.661648 GCACCCCACTCACCCCAT 61.662 66.667 0.00 0.00 0.00 4.00
3011 8368 3.576356 GATGGATGCACACGCCGG 61.576 66.667 0.00 0.00 37.32 6.13
3012 8369 3.928769 CGATGGATGCACACGCCG 61.929 66.667 0.00 0.00 37.32 6.46
3013 8370 3.576356 CCGATGGATGCACACGCC 61.576 66.667 9.44 0.00 37.32 5.68
3014 8371 3.576356 CCCGATGGATGCACACGC 61.576 66.667 9.44 0.00 39.24 5.34
3015 8372 2.125147 ACCCGATGGATGCACACG 60.125 61.111 8.26 8.26 34.81 4.49
3016 8373 0.676466 TTGACCCGATGGATGCACAC 60.676 55.000 0.00 0.00 34.81 3.82
3017 8374 0.392863 CTTGACCCGATGGATGCACA 60.393 55.000 0.00 0.00 34.81 4.57
3018 8375 0.392998 ACTTGACCCGATGGATGCAC 60.393 55.000 0.00 0.00 34.81 4.57
3019 8376 0.327924 AACTTGACCCGATGGATGCA 59.672 50.000 0.00 0.00 34.81 3.96
3020 8377 1.017387 GAACTTGACCCGATGGATGC 58.983 55.000 0.00 0.00 34.81 3.91
3021 8378 1.290203 CGAACTTGACCCGATGGATG 58.710 55.000 0.00 0.00 34.81 3.51
3022 8379 0.462047 GCGAACTTGACCCGATGGAT 60.462 55.000 0.00 0.00 34.81 3.41
3023 8380 1.079405 GCGAACTTGACCCGATGGA 60.079 57.895 0.00 0.00 34.81 3.41
3024 8381 2.106683 GGCGAACTTGACCCGATGG 61.107 63.158 0.00 0.00 37.80 3.51
3025 8382 2.452813 CGGCGAACTTGACCCGATG 61.453 63.158 0.00 0.00 43.20 3.84
3026 8383 2.125673 CGGCGAACTTGACCCGAT 60.126 61.111 0.00 0.00 43.20 4.18
3027 8384 4.367023 CCGGCGAACTTGACCCGA 62.367 66.667 9.30 0.00 43.20 5.14
3063 8420 3.740128 CTCTTCCCCGCCACCATCG 62.740 68.421 0.00 0.00 0.00 3.84
3064 8421 2.190578 CTCTTCCCCGCCACCATC 59.809 66.667 0.00 0.00 0.00 3.51
3065 8422 2.285368 TCTCTTCCCCGCCACCAT 60.285 61.111 0.00 0.00 0.00 3.55
3066 8423 3.003173 CTCTCTTCCCCGCCACCA 61.003 66.667 0.00 0.00 0.00 4.17
3067 8424 2.683933 TCTCTCTTCCCCGCCACC 60.684 66.667 0.00 0.00 0.00 4.61
3068 8425 1.985116 ACTCTCTCTTCCCCGCCAC 60.985 63.158 0.00 0.00 0.00 5.01
3069 8426 1.984570 CACTCTCTCTTCCCCGCCA 60.985 63.158 0.00 0.00 0.00 5.69
3070 8427 2.896443 CACTCTCTCTTCCCCGCC 59.104 66.667 0.00 0.00 0.00 6.13
3071 8428 2.185608 GCACTCTCTCTTCCCCGC 59.814 66.667 0.00 0.00 0.00 6.13
3072 8429 2.492090 CGCACTCTCTCTTCCCCG 59.508 66.667 0.00 0.00 0.00 5.73
3073 8430 2.896443 CCGCACTCTCTCTTCCCC 59.104 66.667 0.00 0.00 0.00 4.81
3074 8431 2.185608 GCCGCACTCTCTCTTCCC 59.814 66.667 0.00 0.00 0.00 3.97
3075 8432 2.202676 CGCCGCACTCTCTCTTCC 60.203 66.667 0.00 0.00 0.00 3.46
3076 8433 2.883253 GCGCCGCACTCTCTCTTC 60.883 66.667 3.15 0.00 0.00 2.87
3077 8434 4.785512 CGCGCCGCACTCTCTCTT 62.786 66.667 10.75 0.00 0.00 2.85
3119 8476 4.434354 TATTTGGGGCGCCGGCTT 62.434 61.111 26.68 6.55 39.81 4.35
3122 8479 3.514362 GTGTATTTGGGGCGCCGG 61.514 66.667 22.54 0.00 0.00 6.13
3123 8480 2.748251 TGTGTATTTGGGGCGCCG 60.748 61.111 22.54 0.00 0.00 6.46
3124 8481 3.063743 GCTGTGTATTTGGGGCGCC 62.064 63.158 21.18 21.18 0.00 6.53
3125 8482 2.489751 GCTGTGTATTTGGGGCGC 59.510 61.111 0.00 0.00 0.00 6.53
3126 8483 2.791256 CGCTGTGTATTTGGGGCG 59.209 61.111 0.00 0.00 36.89 6.13
3127 8484 2.489751 GCGCTGTGTATTTGGGGC 59.510 61.111 0.00 0.00 0.00 5.80
3128 8485 1.705337 CTCGCGCTGTGTATTTGGGG 61.705 60.000 5.56 0.00 0.00 4.96
3129 8486 1.019278 ACTCGCGCTGTGTATTTGGG 61.019 55.000 5.56 0.00 0.00 4.12
3130 8487 0.796312 AACTCGCGCTGTGTATTTGG 59.204 50.000 5.56 0.00 0.00 3.28
3131 8488 1.464023 CCAACTCGCGCTGTGTATTTG 60.464 52.381 5.56 2.32 0.00 2.32
3132 8489 0.796312 CCAACTCGCGCTGTGTATTT 59.204 50.000 5.56 0.00 0.00 1.40
3133 8490 1.635663 GCCAACTCGCGCTGTGTATT 61.636 55.000 5.56 0.00 0.00 1.89
3134 8491 2.100631 GCCAACTCGCGCTGTGTAT 61.101 57.895 5.56 0.00 0.00 2.29
3135 8492 2.736995 GCCAACTCGCGCTGTGTA 60.737 61.111 5.56 0.00 0.00 2.90
3143 8500 3.039588 TCCGAAACGCCAACTCGC 61.040 61.111 0.00 0.00 0.00 5.03
3144 8501 2.664436 GGTCCGAAACGCCAACTCG 61.664 63.158 0.00 0.00 0.00 4.18
3145 8502 2.664436 CGGTCCGAAACGCCAACTC 61.664 63.158 4.91 0.00 0.00 3.01
3146 8503 2.663852 CGGTCCGAAACGCCAACT 60.664 61.111 4.91 0.00 0.00 3.16
3159 8516 3.667542 TATATAGTTGGGCGCGCGGTC 62.668 57.143 33.06 15.97 0.00 4.79
3160 8517 1.808531 TATATAGTTGGGCGCGCGGT 61.809 55.000 33.06 9.75 0.00 5.68
3161 8518 0.459585 ATATATAGTTGGGCGCGCGG 60.460 55.000 33.06 13.66 0.00 6.46
3162 8519 0.645355 CATATATAGTTGGGCGCGCG 59.355 55.000 28.44 28.44 0.00 6.86
3163 8520 0.373716 GCATATATAGTTGGGCGCGC 59.626 55.000 25.94 25.94 0.00 6.86
3164 8521 1.006832 GGCATATATAGTTGGGCGCG 58.993 55.000 0.00 0.00 0.00 6.86
3165 8522 1.006832 CGGCATATATAGTTGGGCGC 58.993 55.000 0.00 0.00 40.52 6.53
3167 8524 1.006832 CGCGGCATATATAGTTGGGC 58.993 55.000 0.00 0.00 0.00 5.36
3168 8525 1.006832 GCGCGGCATATATAGTTGGG 58.993 55.000 8.83 0.00 0.00 4.12
3169 8526 0.645355 CGCGCGGCATATATAGTTGG 59.355 55.000 24.84 0.00 0.00 3.77
3170 8527 1.059122 CACGCGCGGCATATATAGTTG 59.941 52.381 35.22 14.52 0.00 3.16
3171 8528 1.346365 CACGCGCGGCATATATAGTT 58.654 50.000 35.22 4.80 0.00 2.24
3172 8529 1.076533 GCACGCGCGGCATATATAGT 61.077 55.000 35.22 5.42 0.00 2.12
3173 8530 1.631072 GCACGCGCGGCATATATAG 59.369 57.895 35.22 12.26 0.00 1.31
3174 8531 3.775314 GCACGCGCGGCATATATA 58.225 55.556 35.22 0.00 0.00 0.86
3207 8564 0.610687 ACCTGTAGACAAGCTCCAGC 59.389 55.000 0.00 0.00 42.49 4.85
3208 8565 2.693069 CAACCTGTAGACAAGCTCCAG 58.307 52.381 0.00 0.00 30.87 3.86
3209 8566 1.270839 GCAACCTGTAGACAAGCTCCA 60.271 52.381 0.00 0.00 0.00 3.86
3210 8567 1.443802 GCAACCTGTAGACAAGCTCC 58.556 55.000 0.00 0.00 0.00 4.70
3211 8568 1.071605 CGCAACCTGTAGACAAGCTC 58.928 55.000 0.00 0.00 0.00 4.09
3212 8569 0.951040 GCGCAACCTGTAGACAAGCT 60.951 55.000 0.30 0.00 0.00 3.74
3213 8570 1.497722 GCGCAACCTGTAGACAAGC 59.502 57.895 0.30 0.00 0.00 4.01
3214 8571 1.781555 CGCGCAACCTGTAGACAAG 59.218 57.895 8.75 0.00 0.00 3.16
3215 8572 2.314647 GCGCGCAACCTGTAGACAA 61.315 57.895 29.10 0.00 0.00 3.18
3216 8573 2.736995 GCGCGCAACCTGTAGACA 60.737 61.111 29.10 0.00 0.00 3.41
3217 8574 2.736995 TGCGCGCAACCTGTAGAC 60.737 61.111 34.66 0.00 0.00 2.59
3218 8575 2.736995 GTGCGCGCAACCTGTAGA 60.737 61.111 38.24 6.62 0.00 2.59
3219 8576 4.134187 CGTGCGCGCAACCTGTAG 62.134 66.667 38.24 16.58 0.00 2.74
3230 8587 1.006314 TTTGCCATTTTAGCGTGCGC 61.006 50.000 8.67 8.67 42.33 6.09
3231 8588 1.413382 TTTTGCCATTTTAGCGTGCG 58.587 45.000 0.00 0.00 0.00 5.34
3232 8589 4.150343 CAAATTTTGCCATTTTAGCGTGC 58.850 39.130 0.00 0.00 0.00 5.34
3246 8603 1.766176 CGTCGTGCCGCAAATTTTG 59.234 52.632 4.72 4.72 0.00 2.44
3247 8604 4.220234 CGTCGTGCCGCAAATTTT 57.780 50.000 0.00 0.00 0.00 1.82
3257 8614 4.417240 GCTAAACAAGCGTCGTGC 57.583 55.556 0.00 0.00 42.53 5.34
3265 8622 1.394697 CAACAACCGCGCTAAACAAG 58.605 50.000 5.56 0.00 0.00 3.16
3266 8623 0.029567 CCAACAACCGCGCTAAACAA 59.970 50.000 5.56 0.00 0.00 2.83
3267 8624 0.814410 TCCAACAACCGCGCTAAACA 60.814 50.000 5.56 0.00 0.00 2.83
3268 8625 0.110373 CTCCAACAACCGCGCTAAAC 60.110 55.000 5.56 0.00 0.00 2.01
3269 8626 0.249953 TCTCCAACAACCGCGCTAAA 60.250 50.000 5.56 0.00 0.00 1.85
3270 8627 0.036765 ATCTCCAACAACCGCGCTAA 60.037 50.000 5.56 0.00 0.00 3.09
3271 8628 0.818938 TATCTCCAACAACCGCGCTA 59.181 50.000 5.56 0.00 0.00 4.26
3272 8629 0.739813 GTATCTCCAACAACCGCGCT 60.740 55.000 5.56 0.00 0.00 5.92
3273 8630 0.739813 AGTATCTCCAACAACCGCGC 60.740 55.000 0.00 0.00 0.00 6.86
3274 8631 1.278238 GAGTATCTCCAACAACCGCG 58.722 55.000 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.