Multiple sequence alignment - TraesCS3B01G535300

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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 TraesCS3B01G535300 chr3B 100.000 2776 0 0 1 2776 775446754 775443979 0.000000e+00 5127.0
1 TraesCS3B01G535300 chr3B 89.474 608 52 6 716 1322 775563115 775562519 0.000000e+00 758.0
2 TraesCS3B01G535300 chr3B 89.922 516 32 8 1383 1880 775562428 775561915 0.000000e+00 647.0
3 TraesCS3B01G535300 chr3B 79.613 775 142 14 1008 1769 778660256 778661027 2.430000e-150 542.0
4 TraesCS3B01G535300 chr3B 74.823 707 140 28 1029 1716 779303166 779303853 4.530000e-73 285.0
5 TraesCS3B01G535300 chr3B 74.003 627 134 26 1055 1664 779525040 779525654 7.730000e-56 228.0
6 TraesCS3B01G535300 chr3D 92.780 1385 58 12 716 2058 580318855 580317471 0.000000e+00 1965.0
7 TraesCS3B01G535300 chr3D 81.641 768 128 11 1011 1769 582620423 582619660 2.350000e-175 625.0
8 TraesCS3B01G535300 chr3D 93.484 353 14 7 119 462 580321809 580321457 1.470000e-142 516.0
9 TraesCS3B01G535300 chr3D 74.405 672 138 25 1055 1702 582056802 582056141 9.860000e-65 257.0
10 TraesCS3B01G535300 chr3A 90.190 683 30 10 1401 2046 715594434 715593752 0.000000e+00 856.0
11 TraesCS3B01G535300 chr3A 89.626 588 51 4 735 1322 715595122 715594545 0.000000e+00 739.0
12 TraesCS3B01G535300 chr3A 81.267 726 118 14 2056 2776 690982273 690982985 3.100000e-159 571.0
13 TraesCS3B01G535300 chr3A 87.937 315 29 6 156 463 715597067 715596755 2.030000e-96 363.0
14 TraesCS3B01G535300 chr3A 76.087 322 60 9 994 1299 696168164 696167844 4.790000e-33 152.0
15 TraesCS3B01G535300 chr3A 90.909 44 4 0 672 715 171180814 171180771 2.990000e-05 60.2
16 TraesCS3B01G535300 chr6A 80.360 723 126 12 2060 2776 4713546 4712834 4.070000e-148 534.0
17 TraesCS3B01G535300 chr6D 80.082 728 106 25 2056 2776 157154094 157154789 3.190000e-139 505.0
18 TraesCS3B01G535300 chr2D 79.570 744 123 15 2056 2776 612201696 612200959 3.190000e-139 505.0
19 TraesCS3B01G535300 chr4D 79.343 731 122 18 2056 2776 83271250 83270539 1.160000e-133 486.0
20 TraesCS3B01G535300 chr7D 80.000 620 95 18 2061 2656 159709121 159709735 5.490000e-117 431.0
21 TraesCS3B01G535300 chr2B 79.421 622 100 17 2061 2659 638763649 638763033 5.530000e-112 414.0
22 TraesCS3B01G535300 chr4B 81.988 483 75 8 2077 2553 649841024 649840548 1.550000e-107 399.0
23 TraesCS3B01G535300 chr4B 100.000 32 0 0 672 703 422035722 422035691 2.990000e-05 60.2
24 TraesCS3B01G535300 chr4A 81.856 485 78 7 2077 2558 660217895 660217418 1.550000e-107 399.0
25 TraesCS3B01G535300 chr4A 83.036 224 29 6 1055 1269 24758567 24758790 7.840000e-46 195.0
26 TraesCS3B01G535300 chr5A 79.362 533 84 16 2158 2683 680620819 680621332 4.400000e-93 351.0
27 TraesCS3B01G535300 chr5A 97.101 69 2 0 1 69 10291408 10291340 1.750000e-22 117.0
28 TraesCS3B01G535300 chr5B 83.613 238 29 5 479 715 263894745 263894517 6.020000e-52 215.0
29 TraesCS3B01G535300 chr5B 98.901 91 1 0 1 91 660697841 660697931 2.210000e-36 163.0
30 TraesCS3B01G535300 chr7A 82.949 217 31 5 1030 1244 48436915 48437127 1.010000e-44 191.0
31 TraesCS3B01G535300 chr7A 98.936 94 1 0 1 94 618104905 618104812 4.750000e-38 169.0
32 TraesCS3B01G535300 chr1B 86.550 171 21 2 545 715 595319883 595319715 1.310000e-43 187.0
33 TraesCS3B01G535300 chr1B 88.889 54 4 2 651 703 476075902 476075954 6.420000e-07 65.8
34 TraesCS3B01G535300 chr7B 78.873 213 31 11 1122 1324 645256259 645256467 6.240000e-27 132.0
35 TraesCS3B01G535300 chr6B 83.704 135 19 3 2642 2776 529876882 529877013 1.040000e-24 124.0
36 TraesCS3B01G535300 chr1A 88.636 44 5 0 672 715 321889711 321889668 1.000000e-03 54.7


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 TraesCS3B01G535300 chr3B 775443979 775446754 2775 True 5127.000000 5127 100.000 1 2776 1 chr3B.!!$R1 2775
1 TraesCS3B01G535300 chr3B 775561915 775563115 1200 True 702.500000 758 89.698 716 1880 2 chr3B.!!$R2 1164
2 TraesCS3B01G535300 chr3B 778660256 778661027 771 False 542.000000 542 79.613 1008 1769 1 chr3B.!!$F1 761
3 TraesCS3B01G535300 chr3B 779303166 779303853 687 False 285.000000 285 74.823 1029 1716 1 chr3B.!!$F2 687
4 TraesCS3B01G535300 chr3B 779525040 779525654 614 False 228.000000 228 74.003 1055 1664 1 chr3B.!!$F3 609
5 TraesCS3B01G535300 chr3D 580317471 580321809 4338 True 1240.500000 1965 93.132 119 2058 2 chr3D.!!$R3 1939
6 TraesCS3B01G535300 chr3D 582619660 582620423 763 True 625.000000 625 81.641 1011 1769 1 chr3D.!!$R2 758
7 TraesCS3B01G535300 chr3D 582056141 582056802 661 True 257.000000 257 74.405 1055 1702 1 chr3D.!!$R1 647
8 TraesCS3B01G535300 chr3A 715593752 715597067 3315 True 652.666667 856 89.251 156 2046 3 chr3A.!!$R3 1890
9 TraesCS3B01G535300 chr3A 690982273 690982985 712 False 571.000000 571 81.267 2056 2776 1 chr3A.!!$F1 720
10 TraesCS3B01G535300 chr6A 4712834 4713546 712 True 534.000000 534 80.360 2060 2776 1 chr6A.!!$R1 716
11 TraesCS3B01G535300 chr6D 157154094 157154789 695 False 505.000000 505 80.082 2056 2776 1 chr6D.!!$F1 720
12 TraesCS3B01G535300 chr2D 612200959 612201696 737 True 505.000000 505 79.570 2056 2776 1 chr2D.!!$R1 720
13 TraesCS3B01G535300 chr4D 83270539 83271250 711 True 486.000000 486 79.343 2056 2776 1 chr4D.!!$R1 720
14 TraesCS3B01G535300 chr7D 159709121 159709735 614 False 431.000000 431 80.000 2061 2656 1 chr7D.!!$F1 595
15 TraesCS3B01G535300 chr2B 638763033 638763649 616 True 414.000000 414 79.421 2061 2659 1 chr2B.!!$R1 598
16 TraesCS3B01G535300 chr5A 680620819 680621332 513 False 351.000000 351 79.362 2158 2683 1 chr5A.!!$F1 525

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
54 55 0.099968 TCGCCATCTCGGTAGTTTCG 59.900 55.0 0.00 0.00 36.97 3.46 F
668 2958 0.103572 TAATCGAACGGTGGCTAGGC 59.896 55.0 9.85 9.85 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1299 4025 0.456142 CCTTGTCGTCGATGAAGCGA 60.456 55.0 9.35 0.0 38.07 4.93 R
2636 5566 0.396417 CGTCCTCCTCATCCACCTCT 60.396 60.0 0.00 0.0 0.00 3.69 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
17 18 4.345286 AGAGGAGCTGCCCCTGGT 62.345 66.667 7.70 0.00 37.37 4.00
18 19 3.791586 GAGGAGCTGCCCCTGGTC 61.792 72.222 7.70 0.00 37.37 4.02
21 22 4.459089 GAGCTGCCCCTGGTCGTC 62.459 72.222 0.00 0.00 0.00 4.20
24 25 3.066190 CTGCCCCTGGTCGTCGTA 61.066 66.667 0.00 0.00 0.00 3.43
25 26 3.064987 CTGCCCCTGGTCGTCGTAG 62.065 68.421 0.00 0.00 0.00 3.51
26 27 4.509737 GCCCCTGGTCGTCGTAGC 62.510 72.222 0.00 0.00 0.00 3.58
27 28 3.834799 CCCCTGGTCGTCGTAGCC 61.835 72.222 0.00 0.00 0.00 3.93
28 29 3.834799 CCCTGGTCGTCGTAGCCC 61.835 72.222 0.00 0.00 0.00 5.19
29 30 3.066190 CCTGGTCGTCGTAGCCCA 61.066 66.667 0.00 0.00 0.00 5.36
30 31 2.642254 CCTGGTCGTCGTAGCCCAA 61.642 63.158 0.00 0.00 0.00 4.12
31 32 1.153823 CTGGTCGTCGTAGCCCAAG 60.154 63.158 0.00 0.00 0.00 3.61
32 33 2.183555 GGTCGTCGTAGCCCAAGG 59.816 66.667 0.00 0.00 0.00 3.61
49 50 4.327885 GCTTCGCCATCTCGGTAG 57.672 61.111 0.00 0.00 36.97 3.18
50 51 1.437986 GCTTCGCCATCTCGGTAGT 59.562 57.895 0.00 0.00 36.97 2.73
51 52 0.179108 GCTTCGCCATCTCGGTAGTT 60.179 55.000 0.00 0.00 36.97 2.24
52 53 1.739371 GCTTCGCCATCTCGGTAGTTT 60.739 52.381 0.00 0.00 36.97 2.66
53 54 2.194271 CTTCGCCATCTCGGTAGTTTC 58.806 52.381 0.00 0.00 36.97 2.78
54 55 0.099968 TCGCCATCTCGGTAGTTTCG 59.900 55.000 0.00 0.00 36.97 3.46
55 56 0.870307 CGCCATCTCGGTAGTTTCGG 60.870 60.000 0.00 0.00 36.97 4.30
56 57 0.529992 GCCATCTCGGTAGTTTCGGG 60.530 60.000 0.00 0.00 36.97 5.14
57 58 0.529992 CCATCTCGGTAGTTTCGGGC 60.530 60.000 0.00 0.00 0.00 6.13
58 59 0.529992 CATCTCGGTAGTTTCGGGCC 60.530 60.000 0.00 0.00 0.00 5.80
59 60 2.012902 ATCTCGGTAGTTTCGGGCCG 62.013 60.000 22.51 22.51 44.95 6.13
60 61 4.440127 TCGGTAGTTTCGGGCCGC 62.440 66.667 23.83 7.63 43.45 6.53
95 96 2.280628 GGAAACCCTAATCAGCTCACG 58.719 52.381 0.00 0.00 0.00 4.35
96 97 1.666189 GAAACCCTAATCAGCTCACGC 59.334 52.381 0.00 0.00 0.00 5.34
97 98 0.613260 AACCCTAATCAGCTCACGCA 59.387 50.000 0.00 0.00 39.10 5.24
98 99 0.613260 ACCCTAATCAGCTCACGCAA 59.387 50.000 0.00 0.00 39.10 4.85
100 101 0.654683 CCTAATCAGCTCACGCAAGC 59.345 55.000 1.52 1.52 45.62 4.01
101 102 1.362768 CTAATCAGCTCACGCAAGCA 58.637 50.000 11.69 0.00 45.00 3.91
102 103 1.938577 CTAATCAGCTCACGCAAGCAT 59.061 47.619 11.69 0.00 45.00 3.79
103 104 2.028420 AATCAGCTCACGCAAGCATA 57.972 45.000 11.69 0.36 45.00 3.14
104 105 1.579698 ATCAGCTCACGCAAGCATAG 58.420 50.000 11.69 2.36 45.00 2.23
105 106 0.532115 TCAGCTCACGCAAGCATAGA 59.468 50.000 11.69 4.41 45.00 1.98
106 107 1.137675 TCAGCTCACGCAAGCATAGAT 59.862 47.619 11.69 0.00 45.00 1.98
107 108 1.260825 CAGCTCACGCAAGCATAGATG 59.739 52.381 11.69 0.00 45.00 2.90
108 109 1.137675 AGCTCACGCAAGCATAGATGA 59.862 47.619 11.69 0.00 45.00 2.92
109 110 2.141517 GCTCACGCAAGCATAGATGAT 58.858 47.619 4.85 0.00 42.05 2.45
110 111 3.006217 AGCTCACGCAAGCATAGATGATA 59.994 43.478 11.69 0.00 45.00 2.15
111 112 3.367327 GCTCACGCAAGCATAGATGATAG 59.633 47.826 4.85 0.00 42.05 2.08
112 113 3.917988 TCACGCAAGCATAGATGATAGG 58.082 45.455 0.00 0.00 45.62 2.57
113 114 3.573967 TCACGCAAGCATAGATGATAGGA 59.426 43.478 0.00 0.00 45.62 2.94
114 115 4.221482 TCACGCAAGCATAGATGATAGGAT 59.779 41.667 0.00 0.00 45.62 3.24
115 116 5.418840 TCACGCAAGCATAGATGATAGGATA 59.581 40.000 0.00 0.00 45.62 2.59
116 117 6.097412 TCACGCAAGCATAGATGATAGGATAT 59.903 38.462 0.00 0.00 45.62 1.63
117 118 6.420306 CACGCAAGCATAGATGATAGGATATC 59.580 42.308 0.00 0.00 45.62 1.63
212 213 1.360820 GCTCTGTAGGGCGAAACTTC 58.639 55.000 0.00 0.00 0.00 3.01
277 284 9.459640 CCTTCAAATCATCATAGCAAAGTATTG 57.540 33.333 0.00 0.00 39.65 1.90
286 293 7.320443 TCATAGCAAAGTATTGGCAAAGTAG 57.680 36.000 3.01 0.00 37.02 2.57
290 297 4.622740 GCAAAGTATTGGCAAAGTAGCAAG 59.377 41.667 3.01 0.00 37.02 4.01
410 421 2.098770 GCAATCCCTCTTGTCATTGCTC 59.901 50.000 7.98 0.00 45.09 4.26
420 431 5.569355 TCTTGTCATTGCTCCTTATTCCAA 58.431 37.500 0.00 0.00 0.00 3.53
463 474 1.595311 ATCCCTCTGTGTGGCCATAA 58.405 50.000 9.72 0.00 0.00 1.90
465 476 1.004277 TCCCTCTGTGTGGCCATAAAC 59.996 52.381 9.72 9.11 0.00 2.01
466 477 1.004745 CCCTCTGTGTGGCCATAAACT 59.995 52.381 9.72 0.00 0.00 2.66
469 480 1.621317 TCTGTGTGGCCATAAACTCGA 59.379 47.619 9.72 6.68 0.00 4.04
472 483 0.739462 TGTGGCCATAAACTCGAGCG 60.739 55.000 9.72 0.00 0.00 5.03
475 486 1.491505 GGCCATAAACTCGAGCGAGC 61.492 60.000 18.80 7.11 45.54 5.03
476 487 1.812214 GCCATAAACTCGAGCGAGCG 61.812 60.000 18.80 0.00 45.54 5.03
544 2326 3.992641 TGGAGCGTGAGGGGAGGA 61.993 66.667 0.00 0.00 0.00 3.71
545 2327 3.151022 GGAGCGTGAGGGGAGGAG 61.151 72.222 0.00 0.00 0.00 3.69
546 2328 3.844090 GAGCGTGAGGGGAGGAGC 61.844 72.222 0.00 0.00 0.00 4.70
567 2349 3.582120 CACCGCGGTGTGTTTGCT 61.582 61.111 42.92 11.99 40.91 3.91
568 2350 3.582120 ACCGCGGTGTGTTTGCTG 61.582 61.111 33.75 0.00 0.00 4.41
569 2351 3.582120 CCGCGGTGTGTTTGCTGT 61.582 61.111 19.50 0.00 0.00 4.40
570 2352 2.407210 CGCGGTGTGTTTGCTGTT 59.593 55.556 0.00 0.00 0.00 3.16
571 2353 1.938814 CGCGGTGTGTTTGCTGTTG 60.939 57.895 0.00 0.00 0.00 3.33
572 2354 1.138671 GCGGTGTGTTTGCTGTTGT 59.861 52.632 0.00 0.00 0.00 3.32
573 2355 1.139226 GCGGTGTGTTTGCTGTTGTG 61.139 55.000 0.00 0.00 0.00 3.33
574 2356 0.449786 CGGTGTGTTTGCTGTTGTGA 59.550 50.000 0.00 0.00 0.00 3.58
575 2357 1.065401 CGGTGTGTTTGCTGTTGTGAT 59.935 47.619 0.00 0.00 0.00 3.06
576 2358 2.462889 GGTGTGTTTGCTGTTGTGATG 58.537 47.619 0.00 0.00 0.00 3.07
577 2359 1.854126 GTGTGTTTGCTGTTGTGATGC 59.146 47.619 0.00 0.00 0.00 3.91
578 2360 1.122849 GTGTTTGCTGTTGTGATGCG 58.877 50.000 0.00 0.00 0.00 4.73
579 2361 1.020437 TGTTTGCTGTTGTGATGCGA 58.980 45.000 0.00 0.00 0.00 5.10
580 2362 1.002576 TGTTTGCTGTTGTGATGCGAG 60.003 47.619 0.00 0.00 0.00 5.03
581 2363 0.592637 TTTGCTGTTGTGATGCGAGG 59.407 50.000 0.00 0.00 0.00 4.63
582 2364 1.236616 TTGCTGTTGTGATGCGAGGG 61.237 55.000 0.00 0.00 0.00 4.30
583 2365 1.375908 GCTGTTGTGATGCGAGGGA 60.376 57.895 0.00 0.00 0.00 4.20
584 2366 1.639298 GCTGTTGTGATGCGAGGGAC 61.639 60.000 0.00 0.00 0.00 4.46
585 2367 0.320683 CTGTTGTGATGCGAGGGACA 60.321 55.000 0.00 0.00 0.00 4.02
586 2368 0.320683 TGTTGTGATGCGAGGGACAG 60.321 55.000 0.00 0.00 0.00 3.51
587 2369 1.021390 GTTGTGATGCGAGGGACAGG 61.021 60.000 0.00 0.00 0.00 4.00
588 2370 2.184020 TTGTGATGCGAGGGACAGGG 62.184 60.000 0.00 0.00 0.00 4.45
589 2371 3.083349 TGATGCGAGGGACAGGGG 61.083 66.667 0.00 0.00 0.00 4.79
590 2372 2.764128 GATGCGAGGGACAGGGGA 60.764 66.667 0.00 0.00 0.00 4.81
591 2373 2.040464 ATGCGAGGGACAGGGGAT 60.040 61.111 0.00 0.00 0.00 3.85
592 2374 2.388890 GATGCGAGGGACAGGGGATG 62.389 65.000 0.00 0.00 0.00 3.51
593 2375 4.554036 GCGAGGGACAGGGGATGC 62.554 72.222 0.00 0.00 0.00 3.91
594 2376 4.227134 CGAGGGACAGGGGATGCG 62.227 72.222 0.00 0.00 0.00 4.73
604 2386 3.849951 GGGATGCGCGAGGAGGAA 61.850 66.667 12.10 0.00 32.19 3.36
608 2390 2.284798 GATGCGCGAGGAGGAAGACA 62.285 60.000 12.10 0.00 32.19 3.41
610 2392 1.807573 GCGCGAGGAGGAAGACAAG 60.808 63.158 12.10 0.00 0.00 3.16
611 2393 1.883732 CGCGAGGAGGAAGACAAGA 59.116 57.895 0.00 0.00 0.00 3.02
612 2394 0.456995 CGCGAGGAGGAAGACAAGAC 60.457 60.000 0.00 0.00 0.00 3.01
616 2398 1.474879 GAGGAGGAAGACAAGACTCGG 59.525 57.143 0.00 0.00 0.00 4.63
617 2399 0.533032 GGAGGAAGACAAGACTCGGG 59.467 60.000 0.00 0.00 0.00 5.14
619 2401 0.905337 AGGAAGACAAGACTCGGGGG 60.905 60.000 0.00 0.00 0.00 5.40
635 2417 2.841442 GGGGGATAAGATCTGAACGG 57.159 55.000 0.00 0.00 0.00 4.44
639 2929 1.416401 GGATAAGATCTGAACGGCCCA 59.584 52.381 0.00 0.00 0.00 5.36
641 2931 0.830648 TAAGATCTGAACGGCCCAGG 59.169 55.000 7.54 0.00 32.73 4.45
646 2936 4.424711 TGAACGGCCCAGGGATGC 62.425 66.667 10.89 0.00 0.00 3.91
651 2941 2.274104 GGCCCAGGGATGCGTTAA 59.726 61.111 10.89 0.00 0.00 2.01
653 2943 1.172812 GGCCCAGGGATGCGTTAATC 61.173 60.000 10.89 0.00 0.00 1.75
655 2945 0.105964 CCCAGGGATGCGTTAATCGA 59.894 55.000 0.00 0.00 42.86 3.59
667 2957 2.199236 GTTAATCGAACGGTGGCTAGG 58.801 52.381 0.00 0.00 0.00 3.02
668 2958 0.103572 TAATCGAACGGTGGCTAGGC 59.896 55.000 9.85 9.85 0.00 3.93
669 2959 2.901051 AATCGAACGGTGGCTAGGCG 62.901 60.000 12.19 0.00 0.00 5.52
672 2962 4.078516 AACGGTGGCTAGGCGTCC 62.079 66.667 12.19 14.84 0.00 4.79
684 2974 2.564458 GCGTCCGGCCGAAAAATT 59.436 55.556 30.73 0.00 34.80 1.82
686 2976 1.154112 CGTCCGGCCGAAAAATTGG 60.154 57.895 30.73 7.15 0.00 3.16
692 2982 2.125713 CCGAAAAATTGGGCCGGC 60.126 61.111 21.18 21.18 33.47 6.13
694 2984 2.813474 GAAAAATTGGGCCGGCGC 60.813 61.111 34.64 34.64 0.00 6.53
695 2985 4.733371 AAAAATTGGGCCGGCGCG 62.733 61.111 34.63 0.00 35.02 6.86
824 3547 3.199727 ACTTGTGCTGGGGAAACAAAAAT 59.800 39.130 0.00 0.00 33.67 1.82
828 3551 6.672266 TGTGCTGGGGAAACAAAAATAATA 57.328 33.333 0.00 0.00 0.00 0.98
942 3665 2.375345 ACCGGCCATTACCCAGAGG 61.375 63.158 0.00 0.00 40.04 3.69
1248 3974 4.144703 GAGGCCTTCGACGGACCC 62.145 72.222 10.79 3.19 29.81 4.46
1260 3986 2.688538 GGACCCCGACTCCTACCT 59.311 66.667 0.00 0.00 0.00 3.08
1381 4185 0.389426 ACTCGTGGTTATGCACGGAC 60.389 55.000 0.00 0.00 44.03 4.79
1383 4187 0.389296 TCGTGGTTATGCACGGACTG 60.389 55.000 0.00 0.00 44.03 3.51
1384 4188 0.389296 CGTGGTTATGCACGGACTGA 60.389 55.000 0.00 0.00 40.67 3.41
1388 4192 3.936453 GTGGTTATGCACGGACTGATTTA 59.064 43.478 0.00 0.00 0.00 1.40
1498 4305 3.764466 CTTCGCGCTCCTGGAGGT 61.764 66.667 24.43 0.00 36.34 3.85
1508 4318 2.729479 CCTGGAGGTGCAGCTCGAT 61.729 63.158 32.99 7.48 0.00 3.59
1664 4477 2.606519 TGGGCCAAGGAGTACGCT 60.607 61.111 2.13 0.00 0.00 5.07
1880 4722 3.997021 CCAGTATTAATCAGCCATCGGAC 59.003 47.826 0.00 0.00 0.00 4.79
1886 4728 0.882042 ATCAGCCATCGGACGAATGC 60.882 55.000 0.00 4.67 0.00 3.56
1888 4730 1.815421 AGCCATCGGACGAATGCAC 60.815 57.895 17.09 5.17 0.00 4.57
1939 4781 1.920574 CACATTACTCCTCTCGCAACG 59.079 52.381 0.00 0.00 0.00 4.10
1950 4800 0.581529 CTCGCAACGCTTGACAGAAA 59.418 50.000 2.51 0.00 0.00 2.52
1984 4837 1.669760 TTTAAGGAGCACACCGGCG 60.670 57.895 0.00 0.00 39.27 6.46
2007 4860 2.716017 GCTCCACTCCTCCGGTCAG 61.716 68.421 0.00 0.00 0.00 3.51
2026 4879 1.707427 AGGAAGGTCACAGAATGGCTT 59.293 47.619 0.00 0.00 43.62 4.35
2034 4887 3.064545 GTCACAGAATGGCTTATGCTGAC 59.935 47.826 14.09 7.82 44.17 3.51
2040 4893 1.191535 TGGCTTATGCTGACGGTAGT 58.808 50.000 0.13 0.00 39.59 2.73
2041 4894 1.553248 TGGCTTATGCTGACGGTAGTT 59.447 47.619 0.13 0.00 39.59 2.24
2046 4899 2.295253 ATGCTGACGGTAGTTGTAGC 57.705 50.000 0.00 0.00 34.73 3.58
2054 4907 0.893447 GGTAGTTGTAGCTGACCGGT 59.107 55.000 6.92 6.92 0.00 5.28
2058 4911 3.975168 AGTTGTAGCTGACCGGTTTAT 57.025 42.857 9.42 0.00 0.00 1.40
2086 4940 4.768448 TCTACAACCGTATCTCTCAAACCA 59.232 41.667 0.00 0.00 0.00 3.67
2091 4945 2.093447 CCGTATCTCTCAAACCAGCCTT 60.093 50.000 0.00 0.00 0.00 4.35
2156 5012 1.307343 CACCCAGATGGACCCCTCT 60.307 63.158 0.00 0.00 37.39 3.69
2157 5013 1.307343 ACCCAGATGGACCCCTCTG 60.307 63.158 12.58 12.58 38.88 3.35
2182 5038 0.036010 CCTCAAACGCCCAGACTGAT 60.036 55.000 3.32 0.00 0.00 2.90
2183 5039 1.207089 CCTCAAACGCCCAGACTGATA 59.793 52.381 3.32 0.00 0.00 2.15
2274 5134 2.203625 GCAAAAGGGTCCCAGCCA 60.204 61.111 11.55 0.00 38.48 4.75
2283 5143 1.194121 GGTCCCAGCCAAAAATGCCT 61.194 55.000 0.00 0.00 0.00 4.75
2317 5178 0.452585 CCGAAACTCGTCTCCTCCTC 59.547 60.000 0.00 0.00 38.40 3.71
2323 5184 2.045242 CGTCTCCTCCTCCGGACA 60.045 66.667 0.00 0.00 0.00 4.02
2384 5248 3.625764 GCATTGTCCGGCTATTTAAGTCA 59.374 43.478 0.00 0.00 0.00 3.41
2387 5251 4.546829 TGTCCGGCTATTTAAGTCAACT 57.453 40.909 0.00 0.00 0.00 3.16
2397 5261 0.320374 TAAGTCAACTGGAGGCACCG 59.680 55.000 0.00 0.00 42.61 4.94
2398 5262 1.407656 AAGTCAACTGGAGGCACCGA 61.408 55.000 0.00 0.00 42.61 4.69
2413 5278 0.251073 ACCGAAAACCCTACCATCCG 59.749 55.000 0.00 0.00 0.00 4.18
2418 5283 1.364269 AAACCCTACCATCCGTCCAA 58.636 50.000 0.00 0.00 0.00 3.53
2428 5293 2.097466 CCATCCGTCCAAATTTTCCTCG 59.903 50.000 0.00 0.00 0.00 4.63
2463 5328 1.003355 CGCCACATTCCACTCCACT 60.003 57.895 0.00 0.00 0.00 4.00
2464 5329 0.249120 CGCCACATTCCACTCCACTA 59.751 55.000 0.00 0.00 0.00 2.74
2474 5339 2.100989 CCACTCCACTAGTCCACCTAC 58.899 57.143 0.00 0.00 35.76 3.18
2483 5348 1.794714 AGTCCACCTACTAGCCATGG 58.205 55.000 7.63 7.63 0.00 3.66
2485 5350 0.326143 TCCACCTACTAGCCATGGCA 60.326 55.000 37.18 21.91 44.88 4.92
2490 5356 0.179045 CTACTAGCCATGGCACCACC 60.179 60.000 37.18 8.17 44.88 4.61
2558 5425 1.984570 CTCCTTGAGCAGACCCGGA 60.985 63.158 0.73 0.00 0.00 5.14
2560 5427 2.266055 CTTGAGCAGACCCGGACC 59.734 66.667 0.73 0.00 0.00 4.46
2561 5428 3.649277 CTTGAGCAGACCCGGACCG 62.649 68.421 6.99 6.99 0.00 4.79
2633 5563 0.330431 AGGAGGAGGAGGAGGAGGAT 60.330 60.000 0.00 0.00 0.00 3.24
2636 5566 1.219213 GAGGAGGAGGAGGAGGATGAA 59.781 57.143 0.00 0.00 0.00 2.57
2641 5571 1.062505 GGAGGAGGAGGATGAAGAGGT 60.063 57.143 0.00 0.00 0.00 3.85
2642 5572 2.038659 GAGGAGGAGGATGAAGAGGTG 58.961 57.143 0.00 0.00 0.00 4.00
2645 5575 2.688477 GAGGAGGATGAAGAGGTGGAT 58.312 52.381 0.00 0.00 0.00 3.41
2655 5585 0.396417 AGAGGTGGATGAGGAGGACG 60.396 60.000 0.00 0.00 0.00 4.79
2656 5586 0.395862 GAGGTGGATGAGGAGGACGA 60.396 60.000 0.00 0.00 0.00 4.20
2658 5588 0.390860 GGTGGATGAGGAGGACGATG 59.609 60.000 0.00 0.00 0.00 3.84
2659 5589 1.403814 GTGGATGAGGAGGACGATGA 58.596 55.000 0.00 0.00 0.00 2.92
2660 5590 1.339610 GTGGATGAGGAGGACGATGAG 59.660 57.143 0.00 0.00 0.00 2.90
2661 5591 1.215423 TGGATGAGGAGGACGATGAGA 59.785 52.381 0.00 0.00 0.00 3.27
2662 5592 2.311463 GGATGAGGAGGACGATGAGAA 58.689 52.381 0.00 0.00 0.00 2.87
2663 5593 2.035321 GGATGAGGAGGACGATGAGAAC 59.965 54.545 0.00 0.00 0.00 3.01
2664 5594 1.095600 TGAGGAGGACGATGAGAACG 58.904 55.000 0.00 0.00 0.00 3.95
2665 5595 1.339727 TGAGGAGGACGATGAGAACGA 60.340 52.381 0.00 0.00 34.70 3.85
2666 5596 1.332375 GAGGAGGACGATGAGAACGAG 59.668 57.143 0.00 0.00 34.70 4.18
2681 5638 2.284151 GAGGAGGAGGAGGGGGAC 59.716 72.222 0.00 0.00 0.00 4.46
2729 5689 1.913951 TTGGCGACAGGGATCTGCAT 61.914 55.000 0.00 0.00 44.59 3.96
2760 5720 1.133009 AGGCCATACTCGATTCCCTCT 60.133 52.381 5.01 0.00 0.00 3.69
2761 5721 1.694696 GGCCATACTCGATTCCCTCTT 59.305 52.381 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.791586 GACCAGGGGCAGCTCCTC 61.792 72.222 12.48 0.00 34.66 3.71
7 8 3.064987 CTACGACGACCAGGGGCAG 62.065 68.421 0.00 0.00 0.00 4.85
8 9 3.066190 CTACGACGACCAGGGGCA 61.066 66.667 0.00 0.00 0.00 5.36
9 10 4.509737 GCTACGACGACCAGGGGC 62.510 72.222 0.00 0.00 0.00 5.80
10 11 3.834799 GGCTACGACGACCAGGGG 61.835 72.222 0.00 0.00 0.00 4.79
11 12 3.834799 GGGCTACGACGACCAGGG 61.835 72.222 0.00 0.00 0.00 4.45
12 13 2.558554 CTTGGGCTACGACGACCAGG 62.559 65.000 0.00 1.22 33.96 4.45
13 14 1.153823 CTTGGGCTACGACGACCAG 60.154 63.158 0.00 0.00 33.96 4.00
14 15 2.642254 CCTTGGGCTACGACGACCA 61.642 63.158 0.00 1.33 0.00 4.02
15 16 2.183555 CCTTGGGCTACGACGACC 59.816 66.667 0.00 0.00 0.00 4.79
16 17 2.508663 GCCTTGGGCTACGACGAC 60.509 66.667 0.00 0.00 46.69 4.34
33 34 2.194271 GAAACTACCGAGATGGCGAAG 58.806 52.381 0.00 0.00 43.94 3.79
34 35 1.468565 CGAAACTACCGAGATGGCGAA 60.469 52.381 0.00 0.00 43.94 4.70
35 36 0.099968 CGAAACTACCGAGATGGCGA 59.900 55.000 0.00 0.00 43.94 5.54
36 37 0.870307 CCGAAACTACCGAGATGGCG 60.870 60.000 0.00 0.00 43.94 5.69
37 38 0.529992 CCCGAAACTACCGAGATGGC 60.530 60.000 0.00 0.00 43.94 4.40
38 39 0.529992 GCCCGAAACTACCGAGATGG 60.530 60.000 0.00 0.00 46.41 3.51
39 40 0.529992 GGCCCGAAACTACCGAGATG 60.530 60.000 0.00 0.00 0.00 2.90
40 41 1.821258 GGCCCGAAACTACCGAGAT 59.179 57.895 0.00 0.00 0.00 2.75
41 42 3.291611 GGCCCGAAACTACCGAGA 58.708 61.111 0.00 0.00 0.00 4.04
74 75 2.644676 GTGAGCTGATTAGGGTTTCCC 58.355 52.381 0.00 0.00 45.90 3.97
75 76 2.280628 CGTGAGCTGATTAGGGTTTCC 58.719 52.381 0.00 0.00 0.00 3.13
90 91 3.925299 CCTATCATCTATGCTTGCGTGAG 59.075 47.826 0.00 0.00 0.00 3.51
91 92 3.573967 TCCTATCATCTATGCTTGCGTGA 59.426 43.478 0.00 0.00 0.00 4.35
92 93 3.917988 TCCTATCATCTATGCTTGCGTG 58.082 45.455 0.00 0.00 0.00 5.34
93 94 4.815533 ATCCTATCATCTATGCTTGCGT 57.184 40.909 0.00 0.00 0.00 5.24
94 95 6.747125 AGATATCCTATCATCTATGCTTGCG 58.253 40.000 0.00 0.00 29.66 4.85
95 96 9.474920 GTTAGATATCCTATCATCTATGCTTGC 57.525 37.037 0.00 0.00 34.55 4.01
96 97 9.979578 GGTTAGATATCCTATCATCTATGCTTG 57.020 37.037 0.00 0.00 34.55 4.01
97 98 9.720874 TGGTTAGATATCCTATCATCTATGCTT 57.279 33.333 0.00 0.00 34.55 3.91
98 99 9.895507 ATGGTTAGATATCCTATCATCTATGCT 57.104 33.333 0.00 0.00 34.55 3.79
116 117 9.337396 GGATGTTGTCATGTAATTATGGTTAGA 57.663 33.333 0.00 0.00 34.06 2.10
117 118 9.119418 TGGATGTTGTCATGTAATTATGGTTAG 57.881 33.333 0.00 0.00 34.06 2.34
131 132 5.475220 TCACCGTAAAAATGGATGTTGTCAT 59.525 36.000 0.00 0.00 36.95 3.06
133 134 5.048991 ACTCACCGTAAAAATGGATGTTGTC 60.049 40.000 0.00 0.00 0.00 3.18
237 239 3.749665 TTGAAGGGTGAGGCAAATTTG 57.250 42.857 14.03 14.03 0.00 2.32
242 244 2.673775 TGATTTGAAGGGTGAGGCAA 57.326 45.000 0.00 0.00 0.00 4.52
277 284 7.227512 AGTGATTATGTATCTTGCTACTTTGCC 59.772 37.037 0.00 0.00 34.17 4.52
410 421 4.023193 GGACGTATTGGCATTGGAATAAGG 60.023 45.833 0.00 0.00 0.00 2.69
420 431 2.170397 TCAGACATGGACGTATTGGCAT 59.830 45.455 0.00 0.00 0.00 4.40
526 2308 3.775654 CCTCCCCTCACGCTCCAC 61.776 72.222 0.00 0.00 0.00 4.02
551 2333 3.582120 CAGCAAACACACCGCGGT 61.582 61.111 28.70 28.70 0.00 5.68
552 2334 3.119709 AACAGCAAACACACCGCGG 62.120 57.895 26.86 26.86 0.00 6.46
556 2338 2.462889 CATCACAACAGCAAACACACC 58.537 47.619 0.00 0.00 0.00 4.16
560 2342 1.002576 CTCGCATCACAACAGCAAACA 60.003 47.619 0.00 0.00 0.00 2.83
561 2343 1.664016 CCTCGCATCACAACAGCAAAC 60.664 52.381 0.00 0.00 0.00 2.93
562 2344 0.592637 CCTCGCATCACAACAGCAAA 59.407 50.000 0.00 0.00 0.00 3.68
563 2345 1.236616 CCCTCGCATCACAACAGCAA 61.237 55.000 0.00 0.00 0.00 3.91
564 2346 1.672030 CCCTCGCATCACAACAGCA 60.672 57.895 0.00 0.00 0.00 4.41
565 2347 1.375908 TCCCTCGCATCACAACAGC 60.376 57.895 0.00 0.00 0.00 4.40
566 2348 0.320683 TGTCCCTCGCATCACAACAG 60.321 55.000 0.00 0.00 0.00 3.16
567 2349 0.320683 CTGTCCCTCGCATCACAACA 60.321 55.000 0.00 0.00 0.00 3.33
568 2350 1.021390 CCTGTCCCTCGCATCACAAC 61.021 60.000 0.00 0.00 0.00 3.32
569 2351 1.296392 CCTGTCCCTCGCATCACAA 59.704 57.895 0.00 0.00 0.00 3.33
570 2352 2.659063 CCCTGTCCCTCGCATCACA 61.659 63.158 0.00 0.00 0.00 3.58
571 2353 2.187946 CCCTGTCCCTCGCATCAC 59.812 66.667 0.00 0.00 0.00 3.06
572 2354 2.896677 ATCCCCTGTCCCTCGCATCA 62.897 60.000 0.00 0.00 0.00 3.07
573 2355 2.143419 ATCCCCTGTCCCTCGCATC 61.143 63.158 0.00 0.00 0.00 3.91
574 2356 2.040464 ATCCCCTGTCCCTCGCAT 60.040 61.111 0.00 0.00 0.00 4.73
575 2357 3.083349 CATCCCCTGTCCCTCGCA 61.083 66.667 0.00 0.00 0.00 5.10
576 2358 4.554036 GCATCCCCTGTCCCTCGC 62.554 72.222 0.00 0.00 0.00 5.03
577 2359 4.227134 CGCATCCCCTGTCCCTCG 62.227 72.222 0.00 0.00 0.00 4.63
578 2360 4.554036 GCGCATCCCCTGTCCCTC 62.554 72.222 0.30 0.00 0.00 4.30
581 2363 4.899239 CTCGCGCATCCCCTGTCC 62.899 72.222 8.75 0.00 0.00 4.02
582 2364 4.899239 CCTCGCGCATCCCCTGTC 62.899 72.222 8.75 0.00 0.00 3.51
584 2366 4.598894 CTCCTCGCGCATCCCCTG 62.599 72.222 8.75 0.00 0.00 4.45
587 2369 3.798954 CTTCCTCCTCGCGCATCCC 62.799 68.421 8.75 0.00 0.00 3.85
588 2370 2.279784 CTTCCTCCTCGCGCATCC 60.280 66.667 8.75 0.00 0.00 3.51
589 2371 1.590259 GTCTTCCTCCTCGCGCATC 60.590 63.158 8.75 0.00 0.00 3.91
590 2372 1.888436 TTGTCTTCCTCCTCGCGCAT 61.888 55.000 8.75 0.00 0.00 4.73
591 2373 2.492449 CTTGTCTTCCTCCTCGCGCA 62.492 60.000 8.75 0.00 0.00 6.09
592 2374 1.807573 CTTGTCTTCCTCCTCGCGC 60.808 63.158 0.00 0.00 0.00 6.86
593 2375 0.456995 GTCTTGTCTTCCTCCTCGCG 60.457 60.000 0.00 0.00 0.00 5.87
594 2376 0.892063 AGTCTTGTCTTCCTCCTCGC 59.108 55.000 0.00 0.00 0.00 5.03
616 2398 1.270893 GCCGTTCAGATCTTATCCCCC 60.271 57.143 0.00 0.00 0.00 5.40
617 2399 1.270893 GGCCGTTCAGATCTTATCCCC 60.271 57.143 0.00 0.00 0.00 4.81
619 2401 1.416401 TGGGCCGTTCAGATCTTATCC 59.584 52.381 0.00 0.00 0.00 2.59
620 2402 2.548920 CCTGGGCCGTTCAGATCTTATC 60.549 54.545 8.90 0.00 34.36 1.75
621 2403 1.417890 CCTGGGCCGTTCAGATCTTAT 59.582 52.381 8.90 0.00 34.36 1.73
622 2404 0.830648 CCTGGGCCGTTCAGATCTTA 59.169 55.000 8.90 0.00 34.36 2.10
624 2406 2.370445 CCCTGGGCCGTTCAGATCT 61.370 63.158 8.90 0.00 34.36 2.75
625 2407 1.700042 ATCCCTGGGCCGTTCAGATC 61.700 60.000 8.22 0.00 34.36 2.75
627 2409 2.285368 ATCCCTGGGCCGTTCAGA 60.285 61.111 8.22 0.00 34.36 3.27
629 2411 4.424711 GCATCCCTGGGCCGTTCA 62.425 66.667 8.22 0.00 0.00 3.18
634 2416 1.152756 ATTAACGCATCCCTGGGCC 60.153 57.895 8.22 0.00 38.84 5.80
635 2417 1.507141 CGATTAACGCATCCCTGGGC 61.507 60.000 8.22 0.00 38.84 5.36
648 2938 1.472026 GCCTAGCCACCGTTCGATTAA 60.472 52.381 0.00 0.00 0.00 1.40
651 2941 2.499685 GCCTAGCCACCGTTCGAT 59.500 61.111 0.00 0.00 0.00 3.59
653 2943 4.430765 ACGCCTAGCCACCGTTCG 62.431 66.667 0.00 0.00 0.00 3.95
655 2945 4.078516 GGACGCCTAGCCACCGTT 62.079 66.667 0.00 0.00 35.06 4.44
667 2957 1.799916 CAATTTTTCGGCCGGACGC 60.800 57.895 29.18 0.00 0.00 5.19
668 2958 1.154112 CCAATTTTTCGGCCGGACG 60.154 57.895 27.95 27.95 0.00 4.79
669 2959 1.214325 CCCAATTTTTCGGCCGGAC 59.786 57.895 27.83 0.00 0.00 4.79
675 2965 2.125713 GCCGGCCCAATTTTTCGG 60.126 61.111 18.11 0.00 43.13 4.30
677 2967 2.813474 GCGCCGGCCCAATTTTTC 60.813 61.111 23.46 0.00 0.00 2.29
699 2989 1.580845 CTATGGGCATTGCTAGGCGC 61.581 60.000 14.30 14.30 43.37 6.53
700 2990 0.957395 CCTATGGGCATTGCTAGGCG 60.957 60.000 8.82 0.00 30.13 5.52
701 2991 2.952714 CCTATGGGCATTGCTAGGC 58.047 57.895 8.82 0.00 0.00 3.93
731 3454 9.468532 CAGACAGAGTGATCGATAAAATAATGA 57.531 33.333 0.00 0.00 0.00 2.57
781 3504 3.670055 GTCAAATGTTGATGTCTTTGCGG 59.330 43.478 0.00 0.00 42.47 5.69
942 3665 2.408271 TGATGGTGAGATTGTGAGGC 57.592 50.000 0.00 0.00 0.00 4.70
1018 3741 2.748058 AAAGCGCCGACAACCCTGAT 62.748 55.000 2.29 0.00 0.00 2.90
1248 3974 2.439701 TCGGCAGGTAGGAGTCGG 60.440 66.667 0.00 0.00 0.00 4.79
1260 3986 2.818841 CGGTCATATGGGTCGGCA 59.181 61.111 2.13 0.00 0.00 5.69
1299 4025 0.456142 CCTTGTCGTCGATGAAGCGA 60.456 55.000 9.35 0.00 38.07 4.93
1381 4185 2.211806 GCTCTGCCTCAGCTAAATCAG 58.788 52.381 0.00 0.00 40.80 2.90
1383 4187 2.211806 CTGCTCTGCCTCAGCTAAATC 58.788 52.381 0.00 0.00 40.80 2.17
1384 4188 1.558756 ACTGCTCTGCCTCAGCTAAAT 59.441 47.619 0.00 0.00 40.80 1.40
1388 4192 2.663796 CACTGCTCTGCCTCAGCT 59.336 61.111 0.91 0.00 40.80 4.24
1498 4305 1.519246 CTCTTCCCATCGAGCTGCA 59.481 57.895 1.02 0.00 0.00 4.41
1565 4375 3.345808 GTGAGCCAGTGCGCGAAA 61.346 61.111 12.10 0.00 44.33 3.46
1664 4477 2.338015 CCGGACCTTCTCGTCGGAA 61.338 63.158 0.00 0.00 35.67 4.30
1795 4608 1.138036 CCATGCACGCATCCACTTG 59.862 57.895 0.44 0.00 33.90 3.16
1880 4722 3.566273 TGCAAAGTTGGTGCATTCG 57.434 47.368 0.00 0.00 46.76 3.34
1886 4728 6.092092 TCAATTCGATATTGCAAAGTTGGTG 58.908 36.000 1.71 0.00 0.00 4.17
1888 4730 6.324819 ACTCAATTCGATATTGCAAAGTTGG 58.675 36.000 1.71 0.00 0.00 3.77
1898 4740 4.804139 GTGACGGTGACTCAATTCGATATT 59.196 41.667 0.00 0.00 0.00 1.28
1939 4781 4.351192 ACGACAACAAATTTCTGTCAAGC 58.649 39.130 21.43 4.52 39.56 4.01
1950 4800 6.349033 GCTCCTTAAACCATACGACAACAAAT 60.349 38.462 0.00 0.00 0.00 2.32
2007 4860 2.206576 AAGCCATTCTGTGACCTTCC 57.793 50.000 0.00 0.00 0.00 3.46
2012 4865 3.064545 GTCAGCATAAGCCATTCTGTGAC 59.935 47.826 0.00 0.00 43.56 3.67
2026 4879 3.021695 AGCTACAACTACCGTCAGCATA 58.978 45.455 0.00 0.00 0.00 3.14
2034 4887 3.324170 CGGTCAGCTACAACTACCG 57.676 57.895 0.00 0.00 46.04 4.02
2040 4893 3.196039 TGCTATAAACCGGTCAGCTACAA 59.804 43.478 22.95 7.63 33.38 2.41
2041 4894 2.761767 TGCTATAAACCGGTCAGCTACA 59.238 45.455 22.95 11.16 33.38 2.74
2046 4899 5.196341 TGTAGATGCTATAAACCGGTCAG 57.804 43.478 8.04 4.19 0.00 3.51
2054 4907 8.405418 AGAGATACGGTTGTAGATGCTATAAA 57.595 34.615 0.00 0.00 33.17 1.40
2058 4911 5.374071 TGAGAGATACGGTTGTAGATGCTA 58.626 41.667 0.00 0.00 33.17 3.49
2073 4927 5.509163 GCGTATAAGGCTGGTTTGAGAGATA 60.509 44.000 0.00 0.00 0.00 1.98
2075 4929 3.430374 GCGTATAAGGCTGGTTTGAGAGA 60.430 47.826 0.00 0.00 0.00 3.10
2086 4940 3.937447 GCCCGGGCGTATAAGGCT 61.937 66.667 33.60 0.00 40.57 4.58
2138 4993 1.307343 AGAGGGGTCCATCTGGGTG 60.307 63.158 3.15 0.00 38.11 4.61
2256 5112 3.373565 GGCTGGGACCCTTTTGCG 61.374 66.667 13.00 0.00 0.00 4.85
2259 5115 1.886422 TTTTTGGCTGGGACCCTTTT 58.114 45.000 13.00 0.00 0.00 2.27
2274 5134 2.542020 CCGGGTTTGAAGGCATTTTT 57.458 45.000 0.00 0.00 0.00 1.94
2297 5158 0.966370 AGGAGGAGACGAGTTTCGGG 60.966 60.000 3.37 0.00 45.59 5.14
2384 5248 0.822121 GGTTTTCGGTGCCTCCAGTT 60.822 55.000 0.00 0.00 35.57 3.16
2387 5251 1.128809 TAGGGTTTTCGGTGCCTCCA 61.129 55.000 0.00 0.00 35.57 3.86
2397 5261 1.279846 TGGACGGATGGTAGGGTTTTC 59.720 52.381 0.00 0.00 0.00 2.29
2398 5262 1.364269 TGGACGGATGGTAGGGTTTT 58.636 50.000 0.00 0.00 0.00 2.43
2413 5278 3.146847 ACAGGACGAGGAAAATTTGGAC 58.853 45.455 0.00 0.00 0.00 4.02
2418 5283 1.804748 GCGAACAGGACGAGGAAAATT 59.195 47.619 0.00 0.00 0.00 1.82
2451 5316 2.188817 GGTGGACTAGTGGAGTGGAAT 58.811 52.381 0.00 0.00 39.06 3.01
2463 5328 2.958818 CCATGGCTAGTAGGTGGACTA 58.041 52.381 0.00 0.00 31.59 2.59
2464 5329 1.794714 CCATGGCTAGTAGGTGGACT 58.205 55.000 0.00 0.00 31.59 3.85
2474 5339 2.124151 GGGTGGTGCCATGGCTAG 60.124 66.667 35.53 0.00 42.51 3.42
2581 5466 0.977395 CCTCCTCCGGATCCAATACC 59.023 60.000 13.41 0.00 0.00 2.73
2585 5470 1.075226 CTCCCTCCTCCGGATCCAA 60.075 63.158 13.41 0.00 0.00 3.53
2596 5484 0.689412 CTCCTCCTCCAACTCCCTCC 60.689 65.000 0.00 0.00 0.00 4.30
2597 5485 0.689412 CCTCCTCCTCCAACTCCCTC 60.689 65.000 0.00 0.00 0.00 4.30
2598 5486 1.156322 TCCTCCTCCTCCAACTCCCT 61.156 60.000 0.00 0.00 0.00 4.20
2599 5487 0.689412 CTCCTCCTCCTCCAACTCCC 60.689 65.000 0.00 0.00 0.00 4.30
2633 5563 1.362584 TCCTCCTCATCCACCTCTTCA 59.637 52.381 0.00 0.00 0.00 3.02
2636 5566 0.396417 CGTCCTCCTCATCCACCTCT 60.396 60.000 0.00 0.00 0.00 3.69
2641 5571 1.215423 TCTCATCGTCCTCCTCATCCA 59.785 52.381 0.00 0.00 0.00 3.41
2642 5572 1.988293 TCTCATCGTCCTCCTCATCC 58.012 55.000 0.00 0.00 0.00 3.51
2645 5575 1.095600 CGTTCTCATCGTCCTCCTCA 58.904 55.000 0.00 0.00 0.00 3.86
2655 5585 1.953686 CTCCTCCTCCTCGTTCTCATC 59.046 57.143 0.00 0.00 0.00 2.92
2656 5586 1.410932 CCTCCTCCTCCTCGTTCTCAT 60.411 57.143 0.00 0.00 0.00 2.90
2658 5588 0.753848 CCCTCCTCCTCCTCGTTCTC 60.754 65.000 0.00 0.00 0.00 2.87
2659 5589 1.308326 CCCTCCTCCTCCTCGTTCT 59.692 63.158 0.00 0.00 0.00 3.01
2660 5590 1.758906 CCCCTCCTCCTCCTCGTTC 60.759 68.421 0.00 0.00 0.00 3.95
2661 5591 2.364961 CCCCTCCTCCTCCTCGTT 59.635 66.667 0.00 0.00 0.00 3.85
2662 5592 3.756783 CCCCCTCCTCCTCCTCGT 61.757 72.222 0.00 0.00 0.00 4.18
2663 5593 3.430497 TCCCCCTCCTCCTCCTCG 61.430 72.222 0.00 0.00 0.00 4.63
2664 5594 2.284151 GTCCCCCTCCTCCTCCTC 59.716 72.222 0.00 0.00 0.00 3.71
2665 5595 3.756783 CGTCCCCCTCCTCCTCCT 61.757 72.222 0.00 0.00 0.00 3.69
2666 5596 3.742248 CTCGTCCCCCTCCTCCTCC 62.742 73.684 0.00 0.00 0.00 4.30
2689 5646 2.774351 CCCCCACATCCTCCTCCC 60.774 72.222 0.00 0.00 0.00 4.30
2718 5678 2.827423 CTCCGCATGCAGATCCCT 59.173 61.111 19.57 0.00 0.00 4.20
2747 5707 0.818296 CCGACAAGAGGGAATCGAGT 59.182 55.000 0.00 0.00 36.70 4.18


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

AutoCloner maintained by Alex Coulton.