Multiple sequence alignment - TraesCS4D01G077300

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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 TraesCS4D01G077300 chr4D 100.000 2558 0 0 1 2558 51457023 51454466 0.000000e+00 4724.0
1 TraesCS4D01G077300 chr4D 87.147 957 73 21 696 1640 51348677 51347759 0.000000e+00 1040.0
2 TraesCS4D01G077300 chr4D 88.048 661 41 8 993 1644 51315335 51314704 0.000000e+00 749.0
3 TraesCS4D01G077300 chr4D 96.491 114 3 1 791 904 51315440 51315328 1.210000e-43 187.0
4 TraesCS4D01G077300 chr4A 91.184 794 50 11 697 1472 545192576 545193367 0.000000e+00 1061.0
5 TraesCS4D01G077300 chr4A 83.955 885 68 26 781 1644 545124144 545124975 0.000000e+00 780.0
6 TraesCS4D01G077300 chr4A 90.411 73 6 1 1568 1639 545193460 545193532 7.530000e-16 95.3
7 TraesCS4D01G077300 chr3D 87.568 917 103 7 1644 2550 460950804 460951719 0.000000e+00 1051.0
8 TraesCS4D01G077300 chr3D 98.039 102 2 0 1 102 380135821 380135922 7.270000e-41 178.0
9 TraesCS4D01G077300 chr3D 96.226 106 3 1 1 105 62086754 62086859 3.380000e-39 172.0
10 TraesCS4D01G077300 chr2B 87.500 920 104 7 1643 2552 619966357 619965439 0.000000e+00 1051.0
11 TraesCS4D01G077300 chr2B 86.174 528 60 12 124 641 795074630 795075154 2.220000e-155 558.0
12 TraesCS4D01G077300 chr2B 98.039 102 2 0 1 102 719429746 719429645 7.270000e-41 178.0
13 TraesCS4D01G077300 chr2B 98.020 101 2 0 2 102 733515017 733514917 2.620000e-40 176.0
14 TraesCS4D01G077300 chr3A 87.351 925 106 7 1644 2558 53190348 53189425 0.000000e+00 1050.0
15 TraesCS4D01G077300 chr7D 87.229 924 105 9 1639 2552 550639025 550639945 0.000000e+00 1040.0
16 TraesCS4D01G077300 chr7A 86.162 925 109 8 1644 2558 654213239 654212324 0.000000e+00 981.0
17 TraesCS4D01G077300 chr2D 86.588 850 99 7 1710 2552 478114803 478113962 0.000000e+00 924.0
18 TraesCS4D01G077300 chr2D 98.039 102 2 0 1 102 668419 668318 7.270000e-41 178.0
19 TraesCS4D01G077300 chr2D 98.039 102 2 0 1 102 35473270 35473169 7.270000e-41 178.0
20 TraesCS4D01G077300 chr1B 88.197 771 88 3 1785 2552 409699792 409699022 0.000000e+00 917.0
21 TraesCS4D01G077300 chr1B 84.775 578 68 15 124 685 192142025 192141452 1.720000e-156 562.0
22 TraesCS4D01G077300 chr4B 87.200 750 42 19 696 1428 75652889 75652177 0.000000e+00 804.0
23 TraesCS4D01G077300 chr4B 83.815 173 19 6 1477 1644 75652156 75651988 3.410000e-34 156.0
24 TraesCS4D01G077300 chr1D 86.413 736 86 7 1644 2370 29483710 29484440 0.000000e+00 793.0
25 TraesCS4D01G077300 chr7B 86.264 546 73 2 2007 2550 689233857 689234402 2.190000e-165 592.0
26 TraesCS4D01G077300 chr7B 85.052 582 68 12 124 688 380072738 380073317 2.210000e-160 575.0
27 TraesCS4D01G077300 chr7B 84.682 581 69 13 124 686 648274082 648273504 1.720000e-156 562.0
28 TraesCS4D01G077300 chr3B 84.880 582 68 14 124 687 463483594 463484173 1.030000e-158 569.0
29 TraesCS4D01G077300 chr3B 84.682 581 69 13 124 686 534159088 534159666 1.720000e-156 562.0
30 TraesCS4D01G077300 chr3B 85.878 524 62 11 124 638 778000364 778000884 4.810000e-152 547.0
31 TraesCS4D01G077300 chr3B 83.904 584 74 14 124 689 707027435 707026854 8.050000e-150 540.0
32 TraesCS4D01G077300 chr3B 99.020 102 1 0 1 102 738093300 738093199 1.560000e-42 183.0
33 TraesCS4D01G077300 chr6B 86.450 524 60 9 124 638 61211614 61212135 4.780000e-157 564.0
34 TraesCS4D01G077300 chr6B 98.039 102 2 0 1 102 706030901 706031002 7.270000e-41 178.0
35 TraesCS4D01G077300 chr6B 98.000 100 2 0 3 102 706601495 706601594 9.410000e-40 174.0
36 TraesCS4D01G077300 chr6A 84.418 584 71 13 124 690 591940880 591940300 8.000000e-155 556.0
37 TraesCS4D01G077300 chr6A 85.992 257 28 4 1644 1893 517660094 517660349 4.200000e-68 268.0
38 TraesCS4D01G077300 chr2A 86.256 422 49 5 1644 2057 50072548 50072968 1.400000e-122 449.0
39 TraesCS4D01G077300 chr5D 86.804 341 37 4 1644 1977 68209492 68209831 8.640000e-100 374.0
40 TraesCS4D01G077300 chrUn 85.145 276 22 4 696 954 249139693 249139420 5.430000e-67 265.0


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 TraesCS4D01G077300 chr4D 51454466 51457023 2557 True 4724.00 4724 100.0000 1 2558 1 chr4D.!!$R2 2557
1 TraesCS4D01G077300 chr4D 51347759 51348677 918 True 1040.00 1040 87.1470 696 1640 1 chr4D.!!$R1 944
2 TraesCS4D01G077300 chr4D 51314704 51315440 736 True 468.00 749 92.2695 791 1644 2 chr4D.!!$R3 853
3 TraesCS4D01G077300 chr4A 545124144 545124975 831 False 780.00 780 83.9550 781 1644 1 chr4A.!!$F1 863
4 TraesCS4D01G077300 chr4A 545192576 545193532 956 False 578.15 1061 90.7975 697 1639 2 chr4A.!!$F2 942
5 TraesCS4D01G077300 chr3D 460950804 460951719 915 False 1051.00 1051 87.5680 1644 2550 1 chr3D.!!$F3 906
6 TraesCS4D01G077300 chr2B 619965439 619966357 918 True 1051.00 1051 87.5000 1643 2552 1 chr2B.!!$R1 909
7 TraesCS4D01G077300 chr2B 795074630 795075154 524 False 558.00 558 86.1740 124 641 1 chr2B.!!$F1 517
8 TraesCS4D01G077300 chr3A 53189425 53190348 923 True 1050.00 1050 87.3510 1644 2558 1 chr3A.!!$R1 914
9 TraesCS4D01G077300 chr7D 550639025 550639945 920 False 1040.00 1040 87.2290 1639 2552 1 chr7D.!!$F1 913
10 TraesCS4D01G077300 chr7A 654212324 654213239 915 True 981.00 981 86.1620 1644 2558 1 chr7A.!!$R1 914
11 TraesCS4D01G077300 chr2D 478113962 478114803 841 True 924.00 924 86.5880 1710 2552 1 chr2D.!!$R3 842
12 TraesCS4D01G077300 chr1B 409699022 409699792 770 True 917.00 917 88.1970 1785 2552 1 chr1B.!!$R2 767
13 TraesCS4D01G077300 chr1B 192141452 192142025 573 True 562.00 562 84.7750 124 685 1 chr1B.!!$R1 561
14 TraesCS4D01G077300 chr4B 75651988 75652889 901 True 480.00 804 85.5075 696 1644 2 chr4B.!!$R1 948
15 TraesCS4D01G077300 chr1D 29483710 29484440 730 False 793.00 793 86.4130 1644 2370 1 chr1D.!!$F1 726
16 TraesCS4D01G077300 chr7B 689233857 689234402 545 False 592.00 592 86.2640 2007 2550 1 chr7B.!!$F2 543
17 TraesCS4D01G077300 chr7B 380072738 380073317 579 False 575.00 575 85.0520 124 688 1 chr7B.!!$F1 564
18 TraesCS4D01G077300 chr7B 648273504 648274082 578 True 562.00 562 84.6820 124 686 1 chr7B.!!$R1 562
19 TraesCS4D01G077300 chr3B 463483594 463484173 579 False 569.00 569 84.8800 124 687 1 chr3B.!!$F1 563
20 TraesCS4D01G077300 chr3B 534159088 534159666 578 False 562.00 562 84.6820 124 686 1 chr3B.!!$F2 562
21 TraesCS4D01G077300 chr3B 778000364 778000884 520 False 547.00 547 85.8780 124 638 1 chr3B.!!$F3 514
22 TraesCS4D01G077300 chr3B 707026854 707027435 581 True 540.00 540 83.9040 124 689 1 chr3B.!!$R1 565
23 TraesCS4D01G077300 chr6B 61211614 61212135 521 False 564.00 564 86.4500 124 638 1 chr6B.!!$F1 514
24 TraesCS4D01G077300 chr6A 591940300 591940880 580 True 556.00 556 84.4180 124 690 1 chr6A.!!$R1 566

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
401 409 0.038892 GGCCTTCGTTCGTCTGTGTA 60.039 55.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2352 2501 0.18135 CCACATGGCCCCTAGACTTC 59.819 60.0 0.0 0.0 0.0 3.01 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
20 21 2.672714 GAATTTGTTGAGGAAACCGGC 58.327 47.619 0.00 0.00 38.06 6.13
21 22 0.596082 ATTTGTTGAGGAAACCGGCG 59.404 50.000 0.00 0.00 38.06 6.46
22 23 2.065906 TTTGTTGAGGAAACCGGCGC 62.066 55.000 0.00 0.00 38.06 6.53
23 24 3.733960 GTTGAGGAAACCGGCGCC 61.734 66.667 19.07 19.07 32.13 6.53
39 40 3.136123 CCGCTGGACTTGCCCATG 61.136 66.667 0.00 0.00 35.33 3.66
40 41 2.046023 CGCTGGACTTGCCCATGA 60.046 61.111 0.00 0.00 35.33 3.07
41 42 1.452651 CGCTGGACTTGCCCATGAT 60.453 57.895 0.00 0.00 35.33 2.45
42 43 1.033746 CGCTGGACTTGCCCATGATT 61.034 55.000 0.00 0.00 35.33 2.57
43 44 1.746861 CGCTGGACTTGCCCATGATTA 60.747 52.381 0.00 0.00 35.33 1.75
44 45 1.952296 GCTGGACTTGCCCATGATTAG 59.048 52.381 0.00 0.00 35.33 1.73
45 46 1.952296 CTGGACTTGCCCATGATTAGC 59.048 52.381 0.00 0.00 35.33 3.09
46 47 1.284491 TGGACTTGCCCATGATTAGCA 59.716 47.619 0.00 0.00 34.97 3.49
47 48 2.291475 TGGACTTGCCCATGATTAGCAA 60.291 45.455 0.00 3.31 43.83 3.91
48 49 2.760092 GGACTTGCCCATGATTAGCAAA 59.240 45.455 11.66 0.67 45.20 3.68
49 50 3.429410 GGACTTGCCCATGATTAGCAAAC 60.429 47.826 11.66 9.30 45.20 2.93
50 51 2.497273 ACTTGCCCATGATTAGCAAACC 59.503 45.455 11.66 0.00 45.20 3.27
51 52 2.530460 TGCCCATGATTAGCAAACCT 57.470 45.000 0.00 0.00 32.56 3.50
52 53 2.101783 TGCCCATGATTAGCAAACCTG 58.898 47.619 0.00 0.00 32.56 4.00
67 68 5.640189 CAAACCTGCATTGAGAAGAGAAT 57.360 39.130 0.00 0.00 0.00 2.40
68 69 6.748333 CAAACCTGCATTGAGAAGAGAATA 57.252 37.500 0.00 0.00 0.00 1.75
69 70 7.149569 CAAACCTGCATTGAGAAGAGAATAA 57.850 36.000 0.00 0.00 0.00 1.40
70 71 7.596494 CAAACCTGCATTGAGAAGAGAATAAA 58.404 34.615 0.00 0.00 0.00 1.40
71 72 6.749923 ACCTGCATTGAGAAGAGAATAAAC 57.250 37.500 0.00 0.00 0.00 2.01
72 73 6.240894 ACCTGCATTGAGAAGAGAATAAACA 58.759 36.000 0.00 0.00 0.00 2.83
73 74 6.716628 ACCTGCATTGAGAAGAGAATAAACAA 59.283 34.615 0.00 0.00 0.00 2.83
74 75 7.395489 ACCTGCATTGAGAAGAGAATAAACAAT 59.605 33.333 0.00 0.00 0.00 2.71
75 76 8.248945 CCTGCATTGAGAAGAGAATAAACAATT 58.751 33.333 0.00 0.00 0.00 2.32
100 101 7.759489 AGTAAGGACATCAAATAAACAAGCA 57.241 32.000 0.00 0.00 0.00 3.91
101 102 8.353423 AGTAAGGACATCAAATAAACAAGCAT 57.647 30.769 0.00 0.00 0.00 3.79
102 103 8.462016 AGTAAGGACATCAAATAAACAAGCATC 58.538 33.333 0.00 0.00 0.00 3.91
103 104 5.883661 AGGACATCAAATAAACAAGCATCG 58.116 37.500 0.00 0.00 0.00 3.84
104 105 5.647658 AGGACATCAAATAAACAAGCATCGA 59.352 36.000 0.00 0.00 0.00 3.59
105 106 5.967674 GGACATCAAATAAACAAGCATCGAG 59.032 40.000 0.00 0.00 0.00 4.04
106 107 5.335127 ACATCAAATAAACAAGCATCGAGC 58.665 37.500 0.00 0.00 46.19 5.03
112 113 1.956477 AAACAAGCATCGAGCCTTGTT 59.044 42.857 27.23 27.23 46.59 2.83
113 114 1.537202 AACAAGCATCGAGCCTTGTTC 59.463 47.619 27.23 0.00 44.05 3.18
114 115 3.708615 AACAAGCATCGAGCCTTGTTCC 61.709 50.000 27.23 0.00 44.05 3.62
115 116 3.093278 GCATCGAGCCTTGTTCCG 58.907 61.111 0.00 0.00 37.23 4.30
116 117 2.464459 GCATCGAGCCTTGTTCCGG 61.464 63.158 0.00 0.00 37.23 5.14
117 118 1.079127 CATCGAGCCTTGTTCCGGT 60.079 57.895 0.00 0.00 0.00 5.28
118 119 0.174845 CATCGAGCCTTGTTCCGGTA 59.825 55.000 0.00 0.00 0.00 4.02
119 120 0.460311 ATCGAGCCTTGTTCCGGTAG 59.540 55.000 0.00 0.00 0.00 3.18
120 121 0.896940 TCGAGCCTTGTTCCGGTAGT 60.897 55.000 0.00 0.00 0.00 2.73
121 122 0.736325 CGAGCCTTGTTCCGGTAGTG 60.736 60.000 0.00 0.00 0.00 2.74
122 123 0.320697 GAGCCTTGTTCCGGTAGTGT 59.679 55.000 0.00 0.00 0.00 3.55
128 129 4.202182 GCCTTGTTCCGGTAGTGTATCATA 60.202 45.833 0.00 0.00 0.00 2.15
134 135 2.161808 CCGGTAGTGTATCATAGAGGCG 59.838 54.545 0.00 0.00 0.00 5.52
178 179 1.221021 GGAGGGCTCCGTTTGTAGG 59.779 63.158 0.00 0.00 40.36 3.18
185 187 2.359848 GGCTCCGTTTGTAGGTGTTTTT 59.640 45.455 0.00 0.00 0.00 1.94
214 216 1.618343 GTTAGGGTTTGTGCCATGCTT 59.382 47.619 0.00 0.00 0.00 3.91
216 218 1.549203 AGGGTTTGTGCCATGCTTAG 58.451 50.000 0.00 0.00 0.00 2.18
220 222 2.298729 GGTTTGTGCCATGCTTAGGAAA 59.701 45.455 0.00 0.00 0.00 3.13
222 224 3.658757 TTGTGCCATGCTTAGGAAAAC 57.341 42.857 0.00 0.00 0.00 2.43
224 226 0.525761 TGCCATGCTTAGGAAAACGC 59.474 50.000 0.00 0.00 0.00 4.84
246 248 2.125350 GTGGCGGCTCTCTGAAGG 60.125 66.667 11.43 0.00 0.00 3.46
262 264 3.777522 CTGAAGGTGGAATAAGGTCCTCT 59.222 47.826 0.00 0.00 38.62 3.69
274 276 3.430497 TCCTCTCCGCCTAGCCCT 61.430 66.667 0.00 0.00 0.00 5.19
283 285 2.279073 CCTAGCCCTCGTCCTGGA 59.721 66.667 0.00 0.00 0.00 3.86
284 286 1.381327 CCTAGCCCTCGTCCTGGAA 60.381 63.158 0.00 0.00 0.00 3.53
285 287 1.395826 CCTAGCCCTCGTCCTGGAAG 61.396 65.000 0.00 0.00 0.00 3.46
286 288 0.395862 CTAGCCCTCGTCCTGGAAGA 60.396 60.000 11.82 11.82 34.07 2.87
288 290 2.896443 CCCTCGTCCTGGAAGAGC 59.104 66.667 27.71 3.25 36.97 4.09
292 294 1.181786 CTCGTCCTGGAAGAGCTTCT 58.818 55.000 23.40 0.00 39.45 2.85
305 307 1.297745 GCTTCTAGCGTCGTCGGAG 60.298 63.158 3.90 0.00 37.56 4.63
317 319 2.038813 TCGGAGGGCATGTGGAGA 59.961 61.111 0.00 0.00 0.00 3.71
319 321 1.227764 CGGAGGGCATGTGGAGATG 60.228 63.158 0.00 0.00 0.00 2.90
337 339 3.209812 TGTCTCCGGCGGATCTCG 61.210 66.667 31.23 18.07 42.76 4.04
351 353 2.619941 ATCTCGTGGGATCCGGTCGA 62.620 60.000 18.46 18.46 0.00 4.20
355 357 3.136123 TGGGATCCGGTCGACGTC 61.136 66.667 9.92 5.18 42.24 4.34
361 363 1.645704 ATCCGGTCGACGTCTGTCTG 61.646 60.000 14.70 9.68 43.21 3.51
362 364 2.322830 CCGGTCGACGTCTGTCTGA 61.323 63.158 14.70 0.00 43.21 3.27
371 373 1.272203 ACGTCTGTCTGAGGTGGATCT 60.272 52.381 4.49 0.00 41.58 2.75
373 375 1.134848 GTCTGTCTGAGGTGGATCTGC 60.135 57.143 0.00 0.00 0.00 4.26
374 376 1.193323 CTGTCTGAGGTGGATCTGCT 58.807 55.000 0.00 0.00 0.00 4.24
384 386 4.055654 GATCTGCTTGGATCCGGC 57.944 61.111 18.89 18.89 36.91 6.13
390 392 2.584608 CTTGGATCCGGCCTTCGT 59.415 61.111 7.39 0.00 37.11 3.85
401 409 0.038892 GGCCTTCGTTCGTCTGTGTA 60.039 55.000 0.00 0.00 0.00 2.90
402 410 1.058404 GCCTTCGTTCGTCTGTGTAC 58.942 55.000 0.00 0.00 0.00 2.90
403 411 1.324718 CCTTCGTTCGTCTGTGTACG 58.675 55.000 0.00 0.00 44.19 3.67
407 415 1.764967 GTTCGTCTGTGTACGTGCG 59.235 57.895 0.00 0.00 43.31 5.34
423 431 1.078708 GCGGGTTGGATCCTTTCGA 60.079 57.895 14.23 0.00 0.00 3.71
425 433 1.202604 GCGGGTTGGATCCTTTCGATA 60.203 52.381 14.23 0.00 0.00 2.92
428 436 4.243270 CGGGTTGGATCCTTTCGATATAC 58.757 47.826 14.23 0.00 0.00 1.47
446 454 1.226688 CGCTTCTCTTCATCGGCGA 60.227 57.895 13.87 13.87 44.36 5.54
466 474 2.186826 GGTTGCTGTTCTGGTGCGT 61.187 57.895 0.00 0.00 0.00 5.24
480 488 2.192175 GCGTTGGTCCTATGGGGG 59.808 66.667 0.00 0.00 35.33 5.40
526 534 7.272978 ACTGTCTACTACAACAATGTTTGTCT 58.727 34.615 0.00 0.00 44.59 3.41
532 540 3.290710 ACAACAATGTTTGTCTGGCTCT 58.709 40.909 0.00 0.00 44.59 4.09
535 543 3.759581 ACAATGTTTGTCTGGCTCTGAT 58.240 40.909 0.00 0.00 40.56 2.90
552 560 1.151943 ATGAGGGAGGGGCGATGAT 60.152 57.895 0.00 0.00 0.00 2.45
556 564 3.877450 GGAGGGGCGATGATGGCA 61.877 66.667 1.08 0.00 35.84 4.92
579 587 3.764466 CCTTCGGCTCGCTCCAGT 61.764 66.667 0.00 0.00 0.00 4.00
581 589 4.742201 TTCGGCTCGCTCCAGTGC 62.742 66.667 0.00 0.00 0.00 4.40
597 605 1.538512 AGTGCTTGTAGTCGTCGCTAA 59.461 47.619 0.00 0.00 0.00 3.09
632 640 8.019669 CAGACCTGAATGTAATTTTCACTTCTG 58.980 37.037 8.62 8.62 36.07 3.02
641 649 8.740123 TGTAATTTTCACTTCTGGTGTTCTTA 57.260 30.769 0.00 0.00 45.50 2.10
642 650 9.349713 TGTAATTTTCACTTCTGGTGTTCTTAT 57.650 29.630 0.00 0.00 45.50 1.73
712 728 9.249457 GAAAAGATTGAAGGAAGAAAACGAAAT 57.751 29.630 0.00 0.00 0.00 2.17
738 755 3.750639 TTTGTTTCACACGACCTGTTC 57.249 42.857 0.00 0.00 0.00 3.18
746 765 3.764972 TCACACGACCTGTTCCACATATA 59.235 43.478 0.00 0.00 0.00 0.86
747 766 4.112634 CACACGACCTGTTCCACATATAG 58.887 47.826 0.00 0.00 0.00 1.31
750 769 4.037565 CACGACCTGTTCCACATATAGCTA 59.962 45.833 0.00 0.00 0.00 3.32
754 773 3.306088 CCTGTTCCACATATAGCTACCGG 60.306 52.174 0.00 0.00 0.00 5.28
878 912 1.743321 AACCAACGTGCAACATGGGG 61.743 55.000 15.11 3.89 45.06 4.96
910 944 1.874019 CAGACCGATCGACCAAGCG 60.874 63.158 18.66 0.00 0.00 4.68
911 945 2.181021 GACCGATCGACCAAGCGT 59.819 61.111 18.66 3.31 0.00 5.07
1064 1131 2.168521 GCTGAGCTACCTACCATCACAA 59.831 50.000 0.00 0.00 0.00 3.33
1087 1161 4.446994 TTCACAACACACATTTTGCAGA 57.553 36.364 0.00 0.00 0.00 4.26
1428 1502 1.654954 CTGACTTGCATCCAGCCAGC 61.655 60.000 0.00 0.00 44.83 4.85
1499 1584 1.136774 GACGGGCTTTGGATTTCGC 59.863 57.895 0.00 0.00 0.00 4.70
1504 1589 1.153765 GCTTTGGATTTCGCCTGCC 60.154 57.895 0.00 0.00 0.00 4.85
1505 1590 1.137404 CTTTGGATTTCGCCTGCCG 59.863 57.895 0.00 0.00 38.61 5.69
1517 1602 1.199097 CGCCTGCCGACTATTTTGTTT 59.801 47.619 0.00 0.00 40.02 2.83
1525 1620 5.477291 TGCCGACTATTTTGTTTTATTCCCA 59.523 36.000 0.00 0.00 0.00 4.37
1539 1634 9.413048 TGTTTTATTCCCAAATTACATTTCGTC 57.587 29.630 0.00 0.00 0.00 4.20
1553 1649 2.833631 TTCGTCCCCTCTGTTTTCTC 57.166 50.000 0.00 0.00 0.00 2.87
1559 1689 3.053077 TCCCCTCTGTTTTCTCAGGAAA 58.947 45.455 0.00 0.00 39.38 3.13
1628 1764 0.036105 AGTTCATCGCCATGTCAGCA 60.036 50.000 0.00 0.00 0.00 4.41
1648 1784 4.810491 AGCATTGCTGTGTAAACCTTTTTG 59.190 37.500 11.09 0.00 37.57 2.44
1652 1788 5.899120 TGCTGTGTAAACCTTTTTGTACA 57.101 34.783 0.00 0.00 0.00 2.90
1706 1849 1.134995 TCGATTACACTCAGCCTGCTG 60.135 52.381 12.91 12.91 44.86 4.41
1719 1862 1.340017 GCCTGCTGACAATGAAGGGTA 60.340 52.381 0.00 0.00 0.00 3.69
1746 1889 2.617308 GCATCCATCCAACACTCAGATG 59.383 50.000 0.00 0.00 37.69 2.90
1755 1898 2.472695 ACACTCAGATGCCGCTAAAA 57.527 45.000 0.00 0.00 0.00 1.52
1775 1922 3.648339 AAAGTAGCATGTTTGGCACAG 57.352 42.857 0.00 0.00 42.39 3.66
1780 1927 2.522185 AGCATGTTTGGCACAGAGATT 58.478 42.857 0.00 0.00 42.39 2.40
1782 1929 2.602878 CATGTTTGGCACAGAGATTGC 58.397 47.619 0.00 0.00 42.39 3.56
1850 1997 6.295249 AGCAAAATTTATAGCTCTCTCCCTC 58.705 40.000 0.00 0.00 30.05 4.30
1862 2009 2.761208 TCTCTCCCTCATTTCCTCGAAC 59.239 50.000 0.00 0.00 0.00 3.95
1884 2031 6.650427 ACATAGGCGTCACAATAGATCTTA 57.350 37.500 0.00 0.00 0.00 2.10
1945 2092 1.153823 CGACCTCCATCACCACGTC 60.154 63.158 0.00 0.00 0.00 4.34
1978 2125 4.264253 CTCAGTTGGGCAAATATGACTCA 58.736 43.478 0.00 0.00 33.84 3.41
1979 2126 4.858850 TCAGTTGGGCAAATATGACTCAT 58.141 39.130 0.00 0.00 33.84 2.90
1988 2135 5.334105 GGCAAATATGACTCATTCGCGTAAT 60.334 40.000 5.77 1.63 0.00 1.89
1999 2147 0.442310 TCGCGTAATGCAAGCACTTC 59.558 50.000 5.77 0.00 46.97 3.01
2009 2157 2.288334 TGCAAGCACTTCGCAATGAAAT 60.288 40.909 0.00 0.00 46.13 2.17
2049 2197 3.515286 CTTGCTCCATGCGCCCTG 61.515 66.667 4.18 1.86 46.63 4.45
2063 2211 4.680237 CCTGAACGGAGTGGCGCA 62.680 66.667 10.83 0.00 45.00 6.09
2095 2243 1.311747 GCCTCCTCCTCCTACCTGT 59.688 63.158 0.00 0.00 0.00 4.00
2111 2259 2.308570 ACCTGTATCAAAGCATCCACCA 59.691 45.455 0.00 0.00 0.00 4.17
2139 2287 6.071391 CCATCAGTGTTAATTTTAACCCAGCT 60.071 38.462 9.96 0.00 41.72 4.24
2159 2307 2.188161 GGTTTCGGTGGTCGCCAAA 61.188 57.895 0.00 0.00 34.18 3.28
2162 2310 1.716826 TTTCGGTGGTCGCCAAACAC 61.717 55.000 0.00 0.00 34.18 3.32
2221 2369 2.696893 GGAGCCAGGTCCTCCCTA 59.303 66.667 8.65 0.00 43.86 3.53
2303 2452 3.994204 TGACCATATTGCATGCATGAC 57.006 42.857 30.64 20.41 0.00 3.06
2324 2473 3.190079 CCGTGATGATCTGACATCGTTT 58.810 45.455 12.36 0.00 46.49 3.60
2338 2487 3.813166 ACATCGTTTCATCGTGGAAAACT 59.187 39.130 5.97 0.00 38.41 2.66
2339 2488 3.870723 TCGTTTCATCGTGGAAAACTG 57.129 42.857 5.97 1.58 38.41 3.16
2347 2496 3.048337 TCGTGGAAAACTGTGTATCCC 57.952 47.619 4.84 0.00 0.00 3.85
2352 2501 2.081462 GAAAACTGTGTATCCCCCACG 58.919 52.381 0.00 0.00 35.56 4.94
2359 2508 2.291735 TGTGTATCCCCCACGAAGTCTA 60.292 50.000 0.00 0.00 41.61 2.59
2385 2534 2.755469 GTGGCCGGATGCAATGGT 60.755 61.111 5.05 0.00 43.89 3.55
2405 2554 0.034670 GGCAGCTTCAGGTCCAAGAT 60.035 55.000 0.00 0.00 0.00 2.40
2415 2564 0.833949 GGTCCAAGATCTCCCTCACC 59.166 60.000 0.00 0.00 0.00 4.02
2419 2568 0.539051 CAAGATCTCCCTCACCGCTT 59.461 55.000 0.00 0.00 0.00 4.68
2495 2645 8.650490 TCATCCATAGCTTTACATAGATCACAA 58.350 33.333 0.00 0.00 0.00 3.33
2532 2682 4.675976 ATGTGCCAATATTTCATGGTGG 57.324 40.909 0.00 0.00 39.00 4.61
2533 2683 3.439154 TGTGCCAATATTTCATGGTGGT 58.561 40.909 0.00 0.00 39.00 4.16
2552 2706 5.395611 GTGGTATAGTCAGGGAGAATACCT 58.604 45.833 10.29 0.00 41.67 3.08
2553 2707 5.839606 GTGGTATAGTCAGGGAGAATACCTT 59.160 44.000 10.29 0.00 41.67 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.000717 CGCCGGTTTCCTCAACAAATT 60.001 47.619 1.90 0.00 37.07 1.82
5 6 2.975799 GCGCCGGTTTCCTCAACA 60.976 61.111 1.90 0.00 37.07 3.33
6 7 3.733960 GGCGCCGGTTTCCTCAAC 61.734 66.667 12.58 0.00 34.18 3.18
22 23 2.898920 ATCATGGGCAAGTCCAGCGG 62.899 60.000 0.00 0.00 40.56 5.52
23 24 1.033746 AATCATGGGCAAGTCCAGCG 61.034 55.000 0.00 0.00 40.56 5.18
24 25 1.952296 CTAATCATGGGCAAGTCCAGC 59.048 52.381 0.00 0.00 40.56 4.85
25 26 1.952296 GCTAATCATGGGCAAGTCCAG 59.048 52.381 0.00 0.00 40.56 3.86
26 27 1.284491 TGCTAATCATGGGCAAGTCCA 59.716 47.619 0.00 0.00 41.60 4.02
27 28 2.057137 TGCTAATCATGGGCAAGTCC 57.943 50.000 0.00 0.00 32.79 3.85
28 29 3.429410 GGTTTGCTAATCATGGGCAAGTC 60.429 47.826 12.90 11.04 44.83 3.01
29 30 2.497273 GGTTTGCTAATCATGGGCAAGT 59.503 45.455 12.90 0.00 44.83 3.16
30 31 2.762327 AGGTTTGCTAATCATGGGCAAG 59.238 45.455 12.90 0.62 44.83 4.01
31 32 2.496871 CAGGTTTGCTAATCATGGGCAA 59.503 45.455 10.49 10.49 42.97 4.52
32 33 2.101783 CAGGTTTGCTAATCATGGGCA 58.898 47.619 0.00 0.00 0.00 5.36
33 34 1.202452 GCAGGTTTGCTAATCATGGGC 60.202 52.381 0.00 0.00 46.95 5.36
34 35 2.877043 GCAGGTTTGCTAATCATGGG 57.123 50.000 0.00 0.00 46.95 4.00
45 46 5.640189 ATTCTCTTCTCAATGCAGGTTTG 57.360 39.130 0.00 0.00 0.00 2.93
46 47 7.231317 TGTTTATTCTCTTCTCAATGCAGGTTT 59.769 33.333 0.00 0.00 0.00 3.27
47 48 6.716628 TGTTTATTCTCTTCTCAATGCAGGTT 59.283 34.615 0.00 0.00 0.00 3.50
48 49 6.240894 TGTTTATTCTCTTCTCAATGCAGGT 58.759 36.000 0.00 0.00 0.00 4.00
49 50 6.748333 TGTTTATTCTCTTCTCAATGCAGG 57.252 37.500 0.00 0.00 0.00 4.85
74 75 9.290988 TGCTTGTTTATTTGATGTCCTTACTAA 57.709 29.630 0.00 0.00 0.00 2.24
75 76 8.856153 TGCTTGTTTATTTGATGTCCTTACTA 57.144 30.769 0.00 0.00 0.00 1.82
76 77 7.759489 TGCTTGTTTATTTGATGTCCTTACT 57.241 32.000 0.00 0.00 0.00 2.24
77 78 7.429340 CGATGCTTGTTTATTTGATGTCCTTAC 59.571 37.037 0.00 0.00 0.00 2.34
78 79 7.335673 TCGATGCTTGTTTATTTGATGTCCTTA 59.664 33.333 0.00 0.00 0.00 2.69
79 80 6.150976 TCGATGCTTGTTTATTTGATGTCCTT 59.849 34.615 0.00 0.00 0.00 3.36
80 81 5.647658 TCGATGCTTGTTTATTTGATGTCCT 59.352 36.000 0.00 0.00 0.00 3.85
81 82 5.879237 TCGATGCTTGTTTATTTGATGTCC 58.121 37.500 0.00 0.00 0.00 4.02
82 83 5.453587 GCTCGATGCTTGTTTATTTGATGTC 59.546 40.000 0.00 0.00 38.95 3.06
83 84 5.335127 GCTCGATGCTTGTTTATTTGATGT 58.665 37.500 0.00 0.00 38.95 3.06
84 85 4.736793 GGCTCGATGCTTGTTTATTTGATG 59.263 41.667 6.78 0.00 42.39 3.07
85 86 4.641989 AGGCTCGATGCTTGTTTATTTGAT 59.358 37.500 6.78 0.00 42.39 2.57
86 87 4.009675 AGGCTCGATGCTTGTTTATTTGA 58.990 39.130 6.78 0.00 42.39 2.69
87 88 4.361451 AGGCTCGATGCTTGTTTATTTG 57.639 40.909 6.78 0.00 42.39 2.32
88 89 4.218417 ACAAGGCTCGATGCTTGTTTATTT 59.782 37.500 0.00 0.00 38.73 1.40
89 90 3.758554 ACAAGGCTCGATGCTTGTTTATT 59.241 39.130 0.00 0.00 38.73 1.40
90 91 3.347216 ACAAGGCTCGATGCTTGTTTAT 58.653 40.909 0.00 0.00 38.73 1.40
91 92 2.778299 ACAAGGCTCGATGCTTGTTTA 58.222 42.857 0.00 0.00 38.73 2.01
92 93 1.609208 ACAAGGCTCGATGCTTGTTT 58.391 45.000 0.00 2.47 38.73 2.83
93 94 1.537202 GAACAAGGCTCGATGCTTGTT 59.463 47.619 21.70 21.70 45.84 2.83
94 95 1.160137 GAACAAGGCTCGATGCTTGT 58.840 50.000 0.00 0.00 41.33 3.16
95 96 0.449388 GGAACAAGGCTCGATGCTTG 59.551 55.000 6.78 0.00 42.39 4.01
96 97 1.021390 CGGAACAAGGCTCGATGCTT 61.021 55.000 6.78 0.00 42.39 3.91
97 98 1.448540 CGGAACAAGGCTCGATGCT 60.449 57.895 6.78 0.00 42.39 3.79
98 99 2.464459 CCGGAACAAGGCTCGATGC 61.464 63.158 0.00 0.00 41.94 3.91
99 100 0.174845 TACCGGAACAAGGCTCGATG 59.825 55.000 9.46 0.00 0.00 3.84
100 101 0.460311 CTACCGGAACAAGGCTCGAT 59.540 55.000 9.46 0.00 0.00 3.59
101 102 0.896940 ACTACCGGAACAAGGCTCGA 60.897 55.000 9.46 0.00 0.00 4.04
102 103 0.736325 CACTACCGGAACAAGGCTCG 60.736 60.000 9.46 0.00 0.00 5.03
103 104 0.320697 ACACTACCGGAACAAGGCTC 59.679 55.000 9.46 0.00 0.00 4.70
104 105 1.636148 TACACTACCGGAACAAGGCT 58.364 50.000 9.46 0.00 0.00 4.58
105 106 2.093869 TGATACACTACCGGAACAAGGC 60.094 50.000 9.46 0.00 0.00 4.35
106 107 3.880047 TGATACACTACCGGAACAAGG 57.120 47.619 9.46 0.00 0.00 3.61
107 108 6.387041 TCTATGATACACTACCGGAACAAG 57.613 41.667 9.46 2.00 0.00 3.16
108 109 5.301045 CCTCTATGATACACTACCGGAACAA 59.699 44.000 9.46 0.00 0.00 2.83
109 110 4.825634 CCTCTATGATACACTACCGGAACA 59.174 45.833 9.46 0.00 0.00 3.18
110 111 4.321082 GCCTCTATGATACACTACCGGAAC 60.321 50.000 9.46 0.00 0.00 3.62
111 112 3.825014 GCCTCTATGATACACTACCGGAA 59.175 47.826 9.46 0.00 0.00 4.30
112 113 3.418995 GCCTCTATGATACACTACCGGA 58.581 50.000 9.46 0.00 0.00 5.14
113 114 2.161808 CGCCTCTATGATACACTACCGG 59.838 54.545 0.00 0.00 0.00 5.28
114 115 2.414293 GCGCCTCTATGATACACTACCG 60.414 54.545 0.00 0.00 0.00 4.02
115 116 2.414293 CGCGCCTCTATGATACACTACC 60.414 54.545 0.00 0.00 0.00 3.18
116 117 2.414293 CCGCGCCTCTATGATACACTAC 60.414 54.545 0.00 0.00 0.00 2.73
117 118 1.810755 CCGCGCCTCTATGATACACTA 59.189 52.381 0.00 0.00 0.00 2.74
118 119 0.598562 CCGCGCCTCTATGATACACT 59.401 55.000 0.00 0.00 0.00 3.55
119 120 0.314302 ACCGCGCCTCTATGATACAC 59.686 55.000 0.00 0.00 0.00 2.90
120 121 0.313987 CACCGCGCCTCTATGATACA 59.686 55.000 0.00 0.00 0.00 2.29
121 122 0.388649 CCACCGCGCCTCTATGATAC 60.389 60.000 0.00 0.00 0.00 2.24
122 123 0.538746 TCCACCGCGCCTCTATGATA 60.539 55.000 0.00 0.00 0.00 2.15
185 187 5.187186 TGGCACAAACCCTAACAAAACTTAA 59.813 36.000 0.00 0.00 31.92 1.85
214 216 1.022451 GCCACCATCGCGTTTTCCTA 61.022 55.000 5.77 0.00 0.00 2.94
216 218 2.178273 GCCACCATCGCGTTTTCC 59.822 61.111 5.77 0.00 0.00 3.13
224 226 3.842923 AGAGAGCCGCCACCATCG 61.843 66.667 0.00 0.00 0.00 3.84
238 240 3.777522 AGGACCTTATTCCACCTTCAGAG 59.222 47.826 0.00 0.00 38.25 3.35
239 241 3.775316 GAGGACCTTATTCCACCTTCAGA 59.225 47.826 0.00 0.00 38.25 3.27
240 242 3.777522 AGAGGACCTTATTCCACCTTCAG 59.222 47.826 0.00 0.00 38.25 3.02
246 248 1.202545 GCGGAGAGGACCTTATTCCAC 60.203 57.143 16.46 7.02 38.25 4.02
274 276 2.370349 CTAGAAGCTCTTCCAGGACGA 58.630 52.381 6.04 0.00 40.33 4.20
283 285 0.097325 CGACGACGCTAGAAGCTCTT 59.903 55.000 0.00 0.00 39.60 2.85
284 286 1.707239 CCGACGACGCTAGAAGCTCT 61.707 60.000 0.64 0.00 39.60 4.09
285 287 1.297745 CCGACGACGCTAGAAGCTC 60.298 63.158 0.64 0.00 39.60 4.09
286 288 1.707239 CTCCGACGACGCTAGAAGCT 61.707 60.000 0.64 0.00 39.60 3.74
288 290 1.352404 CCTCCGACGACGCTAGAAG 59.648 63.158 0.64 0.00 38.29 2.85
296 298 2.509336 CACATGCCCTCCGACGAC 60.509 66.667 0.00 0.00 0.00 4.34
305 307 0.254178 AGACACATCTCCACATGCCC 59.746 55.000 0.00 0.00 0.00 5.36
317 319 1.739338 GAGATCCGCCGGAGACACAT 61.739 60.000 13.12 0.00 34.05 3.21
319 321 2.413765 GAGATCCGCCGGAGACAC 59.586 66.667 13.12 3.39 34.05 3.67
337 339 3.407046 GACGTCGACCGGATCCCAC 62.407 68.421 9.46 0.00 42.24 4.61
351 353 1.178276 GATCCACCTCAGACAGACGT 58.822 55.000 0.00 0.00 0.00 4.34
355 357 1.193323 AGCAGATCCACCTCAGACAG 58.807 55.000 0.00 0.00 0.00 3.51
361 363 2.252976 GATCCAAGCAGATCCACCTC 57.747 55.000 0.00 0.00 37.31 3.85
371 373 2.272146 GAAGGCCGGATCCAAGCA 59.728 61.111 21.82 0.00 0.00 3.91
373 375 1.078426 AACGAAGGCCGGATCCAAG 60.078 57.895 13.41 3.20 43.93 3.61
374 376 1.078708 GAACGAAGGCCGGATCCAA 60.079 57.895 13.41 0.00 43.93 3.53
384 386 1.324718 CGTACACAGACGAACGAAGG 58.675 55.000 0.14 0.00 45.82 3.46
390 392 1.370778 CCGCACGTACACAGACGAA 60.371 57.895 2.55 0.00 45.82 3.85
401 409 2.406002 AAAGGATCCAACCCGCACGT 62.406 55.000 15.82 0.00 0.00 4.49
402 410 1.644786 GAAAGGATCCAACCCGCACG 61.645 60.000 15.82 0.00 0.00 5.34
403 411 1.644786 CGAAAGGATCCAACCCGCAC 61.645 60.000 15.82 0.00 0.00 5.34
407 415 4.243270 CGTATATCGAAAGGATCCAACCC 58.757 47.826 15.82 0.00 42.86 4.11
423 431 3.670895 CGCCGATGAAGAGAAGCGTATAT 60.671 47.826 0.00 0.00 38.81 0.86
425 433 1.600663 CGCCGATGAAGAGAAGCGTAT 60.601 52.381 0.00 0.00 38.81 3.06
428 436 1.226688 TCGCCGATGAAGAGAAGCG 60.227 57.895 0.00 0.00 44.61 4.68
446 454 2.186826 GCACCAGAACAGCAACCGT 61.187 57.895 0.00 0.00 0.00 4.83
466 474 1.518367 CTAAGCCCCCATAGGACCAA 58.482 55.000 0.00 0.00 38.24 3.67
480 488 0.714439 GGAAAGTCGTCGTGCTAAGC 59.286 55.000 0.00 0.00 0.00 3.09
526 534 1.383664 CCCTCCCTCATCAGAGCCA 60.384 63.158 0.00 0.00 40.68 4.75
532 540 2.142761 CATCGCCCCTCCCTCATCA 61.143 63.158 0.00 0.00 0.00 3.07
535 543 2.142761 CATCATCGCCCCTCCCTCA 61.143 63.158 0.00 0.00 0.00 3.86
579 587 1.538512 ACTTAGCGACGACTACAAGCA 59.461 47.619 0.00 0.00 0.00 3.91
581 589 2.095364 ACCACTTAGCGACGACTACAAG 60.095 50.000 0.00 0.12 0.00 3.16
625 633 8.499162 CAACTCTTAATAAGAACACCAGAAGTG 58.501 37.037 4.13 0.00 41.81 3.16
690 706 6.294731 CCCATTTCGTTTTCTTCCTTCAATCT 60.295 38.462 0.00 0.00 0.00 2.40
691 707 5.863935 CCCATTTCGTTTTCTTCCTTCAATC 59.136 40.000 0.00 0.00 0.00 2.67
692 708 5.783111 CCCATTTCGTTTTCTTCCTTCAAT 58.217 37.500 0.00 0.00 0.00 2.57
693 709 4.500716 GCCCATTTCGTTTTCTTCCTTCAA 60.501 41.667 0.00 0.00 0.00 2.69
694 710 3.005367 GCCCATTTCGTTTTCTTCCTTCA 59.995 43.478 0.00 0.00 0.00 3.02
738 755 0.108804 CGCCCGGTAGCTATATGTGG 60.109 60.000 0.00 0.00 0.00 4.17
746 765 3.459063 GTTCTCCGCCCGGTAGCT 61.459 66.667 6.61 0.00 36.47 3.32
747 766 3.427598 GAGTTCTCCGCCCGGTAGC 62.428 68.421 6.61 0.00 36.47 3.58
750 769 3.382832 CAGAGTTCTCCGCCCGGT 61.383 66.667 6.61 0.00 36.47 5.28
754 773 0.733223 GTCGAACAGAGTTCTCCGCC 60.733 60.000 8.11 0.00 0.00 6.13
878 912 2.033141 TCTGTGCCAGCTTGAGCC 59.967 61.111 0.00 0.00 43.38 4.70
910 944 5.973565 ACGCACGGTAGTAAAGTCAATATAC 59.026 40.000 0.00 0.00 0.00 1.47
911 945 6.135290 ACGCACGGTAGTAAAGTCAATATA 57.865 37.500 0.00 0.00 0.00 0.86
1064 1131 5.417811 TCTGCAAAATGTGTGTTGTGAATT 58.582 33.333 0.00 0.00 0.00 2.17
1290 1364 2.049433 CGTGGTGACCGTCCTCAC 60.049 66.667 0.00 9.87 40.02 3.51
1367 1441 1.210931 CAACACCAATGAGCAGCCG 59.789 57.895 0.00 0.00 0.00 5.52
1428 1502 3.708734 GTTCGGCCACCAACGACG 61.709 66.667 2.24 0.00 39.04 5.12
1499 1584 6.033966 GGAATAAAACAAAATAGTCGGCAGG 58.966 40.000 0.00 0.00 0.00 4.85
1539 1634 3.508845 TTTCCTGAGAAAACAGAGGGG 57.491 47.619 0.00 0.00 39.05 4.79
1563 1693 2.158726 TGAAACTACCGGCAAAGACCTT 60.159 45.455 0.00 0.00 0.00 3.50
1564 1694 1.418637 TGAAACTACCGGCAAAGACCT 59.581 47.619 0.00 0.00 0.00 3.85
1565 1695 1.886886 TGAAACTACCGGCAAAGACC 58.113 50.000 0.00 0.00 0.00 3.85
1566 1696 3.974871 TTTGAAACTACCGGCAAAGAC 57.025 42.857 0.00 0.00 0.00 3.01
1628 1764 6.868622 TGTACAAAAAGGTTTACACAGCAAT 58.131 32.000 0.00 0.00 0.00 3.56
1648 1784 7.275560 GCAATAAAACTCCCATGTTTCATGTAC 59.724 37.037 8.57 0.00 38.98 2.90
1652 1788 6.357579 TGCAATAAAACTCCCATGTTTCAT 57.642 33.333 0.00 0.00 38.98 2.57
1706 1849 3.674997 TGCTTGTCTACCCTTCATTGTC 58.325 45.455 0.00 0.00 0.00 3.18
1719 1862 2.040813 AGTGTTGGATGGATGCTTGTCT 59.959 45.455 0.00 0.00 0.00 3.41
1755 1898 3.221771 TCTGTGCCAAACATGCTACTTT 58.778 40.909 0.00 0.00 38.39 2.66
1850 1997 2.540101 GACGCCTATGTTCGAGGAAATG 59.460 50.000 0.00 0.00 35.99 2.32
1862 2009 9.809096 AATATAAGATCTATTGTGACGCCTATG 57.191 33.333 0.00 0.00 0.00 2.23
1884 2031 9.717942 GAACCTCTAGCTTTCACATCATAATAT 57.282 33.333 0.00 0.00 0.00 1.28
1895 2042 2.038557 GGTGGTGAACCTCTAGCTTTCA 59.961 50.000 0.00 0.00 46.55 2.69
1978 2125 1.086696 AGTGCTTGCATTACGCGAAT 58.913 45.000 15.93 5.44 46.97 3.34
1979 2126 0.871722 AAGTGCTTGCATTACGCGAA 59.128 45.000 15.93 2.74 46.97 4.70
1988 2135 0.667453 TTCATTGCGAAGTGCTTGCA 59.333 45.000 0.00 0.00 46.63 4.08
1999 2147 5.065859 TGGTATCACTAACCATTTCATTGCG 59.934 40.000 0.00 0.00 42.10 4.85
2009 2157 3.631605 CCCCTACCTGGTATCACTAACCA 60.632 52.174 7.07 0.00 44.75 3.67
2048 2196 2.970324 GTTGCGCCACTCCGTTCA 60.970 61.111 4.18 0.00 0.00 3.18
2049 2197 3.723348 GGTTGCGCCACTCCGTTC 61.723 66.667 11.78 0.00 37.17 3.95
2063 2211 3.584868 GAGGCGGTGTAGCACGGTT 62.585 63.158 8.26 0.00 37.10 4.44
2095 2243 4.248174 TGGATTGGTGGATGCTTTGATA 57.752 40.909 0.00 0.00 0.00 2.15
2111 2259 8.429237 TGGGTTAAAATTAACACTGATGGATT 57.571 30.769 16.75 0.00 45.12 3.01
2139 2287 1.756408 TTGGCGACCACCGAAACCTA 61.756 55.000 0.00 0.00 41.76 3.08
2145 2293 2.589442 GTGTTTGGCGACCACCGA 60.589 61.111 0.00 0.00 41.76 4.69
2159 2307 0.681733 AGCACTCATGAAGGTCGTGT 59.318 50.000 12.14 0.00 35.03 4.49
2162 2310 1.478510 ACCTAGCACTCATGAAGGTCG 59.521 52.381 9.79 1.83 38.66 4.79
2221 2369 1.130054 TTCAGGCAGTCAAGAGGGCT 61.130 55.000 0.00 0.00 38.02 5.19
2303 2452 2.498807 ACGATGTCAGATCATCACGG 57.501 50.000 0.00 1.81 42.82 4.94
2324 2473 4.250464 GGATACACAGTTTTCCACGATGA 58.750 43.478 0.00 0.00 0.00 2.92
2339 2488 1.192428 AGACTTCGTGGGGGATACAC 58.808 55.000 0.00 0.00 42.03 2.90
2347 2496 2.732619 GGCCCCTAGACTTCGTGGG 61.733 68.421 0.00 0.00 39.37 4.61
2352 2501 0.181350 CCACATGGCCCCTAGACTTC 59.819 60.000 0.00 0.00 0.00 3.01
2372 2521 2.755064 TGCCACCATTGCATCCGG 60.755 61.111 0.00 0.00 32.85 5.14
2373 2522 2.802792 CTGCCACCATTGCATCCG 59.197 61.111 0.00 0.00 38.22 4.18
2385 2534 1.073722 CTTGGACCTGAAGCTGCCA 59.926 57.895 0.00 0.00 0.00 4.92
2405 2554 2.683933 GGGAAGCGGTGAGGGAGA 60.684 66.667 0.00 0.00 0.00 3.71
2415 2564 2.552315 TGCTAAGAGTTTTTGGGAAGCG 59.448 45.455 0.00 0.00 0.00 4.68
2419 2568 5.241403 TCTCATGCTAAGAGTTTTTGGGA 57.759 39.130 0.00 0.00 34.73 4.37
2495 2645 6.237901 TTGGCACATAAGAACTACATCAGTT 58.762 36.000 0.00 0.00 45.20 3.16
2501 2651 8.800370 TGAAATATTGGCACATAAGAACTACA 57.200 30.769 0.00 0.00 39.30 2.74
2532 2682 7.598759 TTCAAGGTATTCTCCCTGACTATAC 57.401 40.000 0.00 0.00 30.99 1.47
2533 2683 7.841282 CTTCAAGGTATTCTCCCTGACTATA 57.159 40.000 0.00 0.00 30.99 1.31


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

AutoCloner maintained by Alex Coulton.