Multiple sequence alignment - TraesCS3D01G287900

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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 TraesCS3D01G287900 chr3D 100.000 3221 0 0 1 3221 397094689 397091469 0.000000e+00 5949
1 TraesCS3D01G287900 chr3D 89.783 646 44 10 2596 3221 31790294 31790937 0.000000e+00 808
2 TraesCS3D01G287900 chr3A 93.943 2295 75 23 125 2387 516546281 516544019 0.000000e+00 3410
3 TraesCS3D01G287900 chr3A 88.872 647 52 8 2595 3221 444446560 444445914 0.000000e+00 778
4 TraesCS3D01G287900 chr3A 88.136 649 55 7 2595 3221 483750399 483751047 0.000000e+00 752
5 TraesCS3D01G287900 chr3A 98.246 57 1 0 2505 2561 516543850 516543794 2.040000e-17 100
6 TraesCS3D01G287900 chr3B 94.803 1424 41 10 1150 2570 522321665 522320272 0.000000e+00 2189
7 TraesCS3D01G287900 chr3B 87.682 1031 47 23 130 1112 522322664 522321666 0.000000e+00 1127
8 TraesCS3D01G287900 chr3B 88.854 646 51 9 2596 3221 39640623 39639979 0.000000e+00 774
9 TraesCS3D01G287900 chr3B 88.924 632 56 9 2596 3219 677972762 677972137 0.000000e+00 767
10 TraesCS3D01G287900 chr4D 91.036 647 36 9 2596 3221 463695106 463695751 0.000000e+00 854
11 TraesCS3D01G287900 chr4D 90.263 647 42 9 2595 3221 494026356 494027001 0.000000e+00 826
12 TraesCS3D01G287900 chr7D 90.590 627 43 7 2604 3221 568977744 568978363 0.000000e+00 817
13 TraesCS3D01G287900 chr6D 89.335 647 49 7 2595 3221 456312452 456313098 0.000000e+00 795
14 TraesCS3D01G287900 chr5A 89.352 648 44 14 2596 3221 32051356 32050712 0.000000e+00 791
15 TraesCS3D01G287900 chr4B 89.181 647 48 10 2596 3221 312784956 312784311 0.000000e+00 787
16 TraesCS3D01G287900 chr7B 89.009 646 51 8 2596 3221 424542324 424541679 0.000000e+00 782
17 TraesCS3D01G287900 chr7B 88.235 646 56 8 2596 3221 372337045 372337690 0.000000e+00 754
18 TraesCS3D01G287900 chr4A 89.009 646 51 8 2596 3221 36323509 36322864 0.000000e+00 782
19 TraesCS3D01G287900 chr5B 88.872 647 50 10 2596 3221 311961639 311960994 0.000000e+00 776
20 TraesCS3D01G287900 chr5D 89.117 634 41 7 2596 3221 45353780 45353167 0.000000e+00 763
21 TraesCS3D01G287900 chr1A 88.390 646 55 8 2596 3221 237744560 237743915 0.000000e+00 760
22 TraesCS3D01G287900 chrUn 89.431 492 33 7 2749 3221 455619591 455619100 1.280000e-168 603


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 TraesCS3D01G287900 chr3D 397091469 397094689 3220 True 5949 5949 100.0000 1 3221 1 chr3D.!!$R1 3220
1 TraesCS3D01G287900 chr3D 31790294 31790937 643 False 808 808 89.7830 2596 3221 1 chr3D.!!$F1 625
2 TraesCS3D01G287900 chr3A 516543794 516546281 2487 True 1755 3410 96.0945 125 2561 2 chr3A.!!$R2 2436
3 TraesCS3D01G287900 chr3A 444445914 444446560 646 True 778 778 88.8720 2595 3221 1 chr3A.!!$R1 626
4 TraesCS3D01G287900 chr3A 483750399 483751047 648 False 752 752 88.1360 2595 3221 1 chr3A.!!$F1 626
5 TraesCS3D01G287900 chr3B 522320272 522322664 2392 True 1658 2189 91.2425 130 2570 2 chr3B.!!$R3 2440
6 TraesCS3D01G287900 chr3B 39639979 39640623 644 True 774 774 88.8540 2596 3221 1 chr3B.!!$R1 625
7 TraesCS3D01G287900 chr3B 677972137 677972762 625 True 767 767 88.9240 2596 3219 1 chr3B.!!$R2 623
8 TraesCS3D01G287900 chr4D 463695106 463695751 645 False 854 854 91.0360 2596 3221 1 chr4D.!!$F1 625
9 TraesCS3D01G287900 chr4D 494026356 494027001 645 False 826 826 90.2630 2595 3221 1 chr4D.!!$F2 626
10 TraesCS3D01G287900 chr7D 568977744 568978363 619 False 817 817 90.5900 2604 3221 1 chr7D.!!$F1 617
11 TraesCS3D01G287900 chr6D 456312452 456313098 646 False 795 795 89.3350 2595 3221 1 chr6D.!!$F1 626
12 TraesCS3D01G287900 chr5A 32050712 32051356 644 True 791 791 89.3520 2596 3221 1 chr5A.!!$R1 625
13 TraesCS3D01G287900 chr4B 312784311 312784956 645 True 787 787 89.1810 2596 3221 1 chr4B.!!$R1 625
14 TraesCS3D01G287900 chr7B 424541679 424542324 645 True 782 782 89.0090 2596 3221 1 chr7B.!!$R1 625
15 TraesCS3D01G287900 chr7B 372337045 372337690 645 False 754 754 88.2350 2596 3221 1 chr7B.!!$F1 625
16 TraesCS3D01G287900 chr4A 36322864 36323509 645 True 782 782 89.0090 2596 3221 1 chr4A.!!$R1 625
17 TraesCS3D01G287900 chr5B 311960994 311961639 645 True 776 776 88.8720 2596 3221 1 chr5B.!!$R1 625
18 TraesCS3D01G287900 chr5D 45353167 45353780 613 True 763 763 89.1170 2596 3221 1 chr5D.!!$R1 625
19 TraesCS3D01G287900 chr1A 237743915 237744560 645 True 760 760 88.3900 2596 3221 1 chr1A.!!$R1 625

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
853 905 0.108585 TCTGAACTTGTCCACTGCCC 59.891 55.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2458 2676 0.251297 TTGGACCCCTGATGTTGCTG 60.251 55.0 0.0 0.0 0.0 4.41 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
23 24 6.411630 TGAACCACACTTTATATGCGTTAC 57.588 37.500 0.00 0.00 0.00 2.50
24 25 5.062433 TGAACCACACTTTATATGCGTTACG 59.938 40.000 0.00 0.00 0.00 3.18
25 26 4.497300 ACCACACTTTATATGCGTTACGT 58.503 39.130 6.63 0.00 0.00 3.57
26 27 5.649557 ACCACACTTTATATGCGTTACGTA 58.350 37.500 6.63 1.27 0.00 3.57
27 28 5.745294 ACCACACTTTATATGCGTTACGTAG 59.255 40.000 6.63 0.00 0.00 3.51
28 29 5.174398 CCACACTTTATATGCGTTACGTAGG 59.826 44.000 6.63 0.00 0.00 3.18
29 30 4.741676 ACACTTTATATGCGTTACGTAGGC 59.258 41.667 6.63 12.27 38.13 3.93
30 31 4.980434 CACTTTATATGCGTTACGTAGGCT 59.020 41.667 17.87 0.00 38.45 4.58
31 32 4.980434 ACTTTATATGCGTTACGTAGGCTG 59.020 41.667 17.87 2.61 38.45 4.85
32 33 4.572985 TTATATGCGTTACGTAGGCTGT 57.427 40.909 17.87 11.14 38.45 4.40
33 34 2.480224 TATGCGTTACGTAGGCTGTC 57.520 50.000 17.87 0.00 38.45 3.51
34 35 0.528924 ATGCGTTACGTAGGCTGTCA 59.471 50.000 17.87 0.00 38.45 3.58
35 36 0.314618 TGCGTTACGTAGGCTGTCAA 59.685 50.000 17.87 0.00 38.45 3.18
36 37 1.067425 TGCGTTACGTAGGCTGTCAAT 60.067 47.619 17.87 0.00 38.45 2.57
37 38 2.164017 TGCGTTACGTAGGCTGTCAATA 59.836 45.455 17.87 0.00 38.45 1.90
38 39 2.533129 GCGTTACGTAGGCTGTCAATAC 59.467 50.000 6.63 0.00 34.83 1.89
39 40 2.780014 CGTTACGTAGGCTGTCAATACG 59.220 50.000 0.00 0.00 45.81 3.06
40 41 3.111098 GTTACGTAGGCTGTCAATACGG 58.889 50.000 9.72 0.00 44.91 4.02
41 42 1.180029 ACGTAGGCTGTCAATACGGT 58.820 50.000 9.72 0.00 44.91 4.83
42 43 1.135199 ACGTAGGCTGTCAATACGGTG 60.135 52.381 9.72 0.00 44.91 4.94
43 44 1.135199 CGTAGGCTGTCAATACGGTGT 60.135 52.381 0.00 0.00 38.82 4.16
44 45 2.268298 GTAGGCTGTCAATACGGTGTG 58.732 52.381 0.00 0.00 34.20 3.82
45 46 0.685097 AGGCTGTCAATACGGTGTGT 59.315 50.000 0.00 0.00 34.20 3.72
46 47 0.796312 GGCTGTCAATACGGTGTGTG 59.204 55.000 0.00 0.00 34.20 3.82
47 48 1.508632 GCTGTCAATACGGTGTGTGT 58.491 50.000 0.00 0.00 34.20 3.72
48 49 1.194547 GCTGTCAATACGGTGTGTGTG 59.805 52.381 0.00 0.00 34.20 3.82
49 50 1.194547 CTGTCAATACGGTGTGTGTGC 59.805 52.381 0.00 0.00 0.00 4.57
50 51 1.202592 TGTCAATACGGTGTGTGTGCT 60.203 47.619 0.00 0.00 0.00 4.40
51 52 2.036089 TGTCAATACGGTGTGTGTGCTA 59.964 45.455 0.00 0.00 0.00 3.49
52 53 2.666508 GTCAATACGGTGTGTGTGCTAG 59.333 50.000 0.00 0.00 0.00 3.42
53 54 2.559231 TCAATACGGTGTGTGTGCTAGA 59.441 45.455 0.00 0.00 0.00 2.43
54 55 2.923655 CAATACGGTGTGTGTGCTAGAG 59.076 50.000 0.00 0.00 0.00 2.43
55 56 1.612676 TACGGTGTGTGTGCTAGAGT 58.387 50.000 0.00 0.00 0.00 3.24
56 57 0.750850 ACGGTGTGTGTGCTAGAGTT 59.249 50.000 0.00 0.00 0.00 3.01
57 58 1.139989 CGGTGTGTGTGCTAGAGTTG 58.860 55.000 0.00 0.00 0.00 3.16
58 59 0.868406 GGTGTGTGTGCTAGAGTTGC 59.132 55.000 0.00 0.00 0.00 4.17
59 60 1.541233 GGTGTGTGTGCTAGAGTTGCT 60.541 52.381 0.00 0.00 0.00 3.91
60 61 1.795286 GTGTGTGTGCTAGAGTTGCTC 59.205 52.381 0.00 0.00 0.00 4.26
61 62 1.688735 TGTGTGTGCTAGAGTTGCTCT 59.311 47.619 4.02 4.02 43.83 4.09
62 63 2.103094 TGTGTGTGCTAGAGTTGCTCTT 59.897 45.455 3.87 0.00 41.50 2.85
63 64 3.320826 TGTGTGTGCTAGAGTTGCTCTTA 59.679 43.478 3.87 0.00 41.50 2.10
64 65 4.202212 TGTGTGTGCTAGAGTTGCTCTTAA 60.202 41.667 3.87 0.00 41.50 1.85
65 66 4.750098 GTGTGTGCTAGAGTTGCTCTTAAA 59.250 41.667 3.87 0.00 41.50 1.52
66 67 4.991056 TGTGTGCTAGAGTTGCTCTTAAAG 59.009 41.667 3.87 0.00 41.50 1.85
67 68 5.221441 TGTGTGCTAGAGTTGCTCTTAAAGA 60.221 40.000 3.87 0.00 41.50 2.52
68 69 5.696724 GTGTGCTAGAGTTGCTCTTAAAGAA 59.303 40.000 3.87 0.00 41.50 2.52
69 70 5.696724 TGTGCTAGAGTTGCTCTTAAAGAAC 59.303 40.000 3.87 2.01 41.50 3.01
70 71 5.696724 GTGCTAGAGTTGCTCTTAAAGAACA 59.303 40.000 3.87 0.00 41.50 3.18
71 72 6.370166 GTGCTAGAGTTGCTCTTAAAGAACAT 59.630 38.462 3.87 0.00 41.50 2.71
72 73 7.545965 GTGCTAGAGTTGCTCTTAAAGAACATA 59.454 37.037 3.87 0.00 41.50 2.29
73 74 8.260818 TGCTAGAGTTGCTCTTAAAGAACATAT 58.739 33.333 3.87 0.00 41.50 1.78
74 75 8.547069 GCTAGAGTTGCTCTTAAAGAACATATG 58.453 37.037 0.00 0.00 41.50 1.78
75 76 9.809096 CTAGAGTTGCTCTTAAAGAACATATGA 57.191 33.333 10.38 0.00 41.50 2.15
76 77 8.715191 AGAGTTGCTCTTAAAGAACATATGAG 57.285 34.615 10.38 0.00 37.60 2.90
77 78 8.317679 AGAGTTGCTCTTAAAGAACATATGAGT 58.682 33.333 10.38 0.00 37.60 3.41
78 79 8.854614 AGTTGCTCTTAAAGAACATATGAGTT 57.145 30.769 10.38 0.00 30.96 3.01
79 80 8.725148 AGTTGCTCTTAAAGAACATATGAGTTG 58.275 33.333 10.38 0.00 30.96 3.16
80 81 8.721478 GTTGCTCTTAAAGAACATATGAGTTGA 58.279 33.333 10.38 0.00 30.96 3.18
81 82 8.484641 TGCTCTTAAAGAACATATGAGTTGAG 57.515 34.615 10.38 6.79 30.96 3.02
82 83 8.097038 TGCTCTTAAAGAACATATGAGTTGAGT 58.903 33.333 10.38 0.00 30.96 3.41
83 84 9.587772 GCTCTTAAAGAACATATGAGTTGAGTA 57.412 33.333 10.38 0.00 30.96 2.59
89 90 9.646427 AAAGAACATATGAGTTGAGTAAGAGAC 57.354 33.333 10.38 0.00 0.00 3.36
90 91 8.354711 AGAACATATGAGTTGAGTAAGAGACA 57.645 34.615 10.38 0.00 0.00 3.41
91 92 8.976353 AGAACATATGAGTTGAGTAAGAGACAT 58.024 33.333 10.38 0.00 0.00 3.06
92 93 9.243637 GAACATATGAGTTGAGTAAGAGACATC 57.756 37.037 10.38 0.00 0.00 3.06
93 94 8.298729 ACATATGAGTTGAGTAAGAGACATCA 57.701 34.615 10.38 0.00 0.00 3.07
94 95 8.753133 ACATATGAGTTGAGTAAGAGACATCAA 58.247 33.333 10.38 0.00 0.00 2.57
95 96 9.247126 CATATGAGTTGAGTAAGAGACATCAAG 57.753 37.037 0.00 0.00 32.64 3.02
96 97 6.656632 TGAGTTGAGTAAGAGACATCAAGT 57.343 37.500 0.00 0.00 37.88 3.16
97 98 6.450545 TGAGTTGAGTAAGAGACATCAAGTG 58.549 40.000 0.00 0.00 35.89 3.16
98 99 6.040955 TGAGTTGAGTAAGAGACATCAAGTGT 59.959 38.462 0.00 0.00 45.83 3.55
99 100 6.821388 AGTTGAGTAAGAGACATCAAGTGTT 58.179 36.000 0.00 0.00 42.36 3.32
100 101 7.952671 AGTTGAGTAAGAGACATCAAGTGTTA 58.047 34.615 0.00 0.00 42.36 2.41
101 102 8.421784 AGTTGAGTAAGAGACATCAAGTGTTAA 58.578 33.333 0.00 0.00 42.36 2.01
102 103 8.704234 GTTGAGTAAGAGACATCAAGTGTTAAG 58.296 37.037 0.00 0.00 42.36 1.85
103 104 8.178313 TGAGTAAGAGACATCAAGTGTTAAGA 57.822 34.615 0.00 0.00 42.36 2.10
104 105 8.300286 TGAGTAAGAGACATCAAGTGTTAAGAG 58.700 37.037 0.00 0.00 42.36 2.85
105 106 8.410673 AGTAAGAGACATCAAGTGTTAAGAGA 57.589 34.615 0.00 0.00 42.36 3.10
106 107 9.030452 AGTAAGAGACATCAAGTGTTAAGAGAT 57.970 33.333 0.00 0.00 42.36 2.75
107 108 9.296400 GTAAGAGACATCAAGTGTTAAGAGATC 57.704 37.037 0.00 0.00 42.36 2.75
108 109 7.473735 AGAGACATCAAGTGTTAAGAGATCA 57.526 36.000 0.00 0.00 42.36 2.92
109 110 8.076910 AGAGACATCAAGTGTTAAGAGATCAT 57.923 34.615 0.00 0.00 42.36 2.45
110 111 8.196771 AGAGACATCAAGTGTTAAGAGATCATC 58.803 37.037 0.00 0.00 42.36 2.92
111 112 7.271511 AGACATCAAGTGTTAAGAGATCATCC 58.728 38.462 0.00 0.00 42.36 3.51
112 113 6.352516 ACATCAAGTGTTAAGAGATCATCCC 58.647 40.000 0.00 0.00 38.01 3.85
113 114 6.157645 ACATCAAGTGTTAAGAGATCATCCCT 59.842 38.462 0.00 0.00 38.01 4.20
114 115 6.627087 TCAAGTGTTAAGAGATCATCCCTT 57.373 37.500 0.00 0.00 0.00 3.95
115 116 6.644347 TCAAGTGTTAAGAGATCATCCCTTC 58.356 40.000 0.00 0.00 0.00 3.46
116 117 6.441924 TCAAGTGTTAAGAGATCATCCCTTCT 59.558 38.462 0.00 0.00 0.00 2.85
117 118 6.478512 AGTGTTAAGAGATCATCCCTTCTC 57.521 41.667 0.00 0.00 38.93 2.87
151 153 7.398332 AGAGAATGCATACCCTTTTCTGATTTT 59.602 33.333 0.00 0.00 0.00 1.82
158 160 8.659491 GCATACCCTTTTCTGATTTTTCAATTC 58.341 33.333 0.00 0.00 0.00 2.17
171 173 6.409524 TTTTTCAATTCTCCAAGTCAGCAT 57.590 33.333 0.00 0.00 0.00 3.79
178 180 3.198068 TCTCCAAGTCAGCATTTATCGC 58.802 45.455 0.00 0.00 0.00 4.58
210 215 6.722590 TCGGCACTATATCTCCCTGTTTTATA 59.277 38.462 0.00 0.00 0.00 0.98
212 217 7.876068 CGGCACTATATCTCCCTGTTTTATAAA 59.124 37.037 0.00 0.00 0.00 1.40
213 218 9.220767 GGCACTATATCTCCCTGTTTTATAAAG 57.779 37.037 0.00 0.00 0.00 1.85
255 263 5.486735 TCCAAACTTGCATCCAATCATTT 57.513 34.783 0.00 0.00 0.00 2.32
261 285 8.653338 CAAACTTGCATCCAATCATTTAAAGAG 58.347 33.333 0.00 0.00 0.00 2.85
321 345 1.035139 CATCCAAGCATTACCCAGCC 58.965 55.000 0.00 0.00 0.00 4.85
332 356 1.830145 ACCCAGCCGGTGTATCATC 59.170 57.895 1.90 0.00 46.09 2.92
362 386 8.663025 AGAAGATGCATATCAAGTAATATTGCG 58.337 33.333 0.00 0.00 35.70 4.85
434 484 1.450312 GCGCCCAGCTGTACAAGAT 60.450 57.895 13.81 0.00 44.04 2.40
500 550 6.348868 CCTCTTCAAGCACCATTTCTTAACTC 60.349 42.308 0.00 0.00 0.00 3.01
556 607 2.877168 CCAATCAGTTAGATGCTCTGGC 59.123 50.000 0.00 0.00 36.96 4.85
688 739 2.816777 ATCTTCTGCCTCCCTTTTCC 57.183 50.000 0.00 0.00 0.00 3.13
782 833 3.181506 GGGATCGAGTGACTTCATTTTGC 60.182 47.826 0.00 0.00 0.00 3.68
830 881 5.662657 ACCTTGGGATGCTTTGCTTATATTT 59.337 36.000 0.00 0.00 0.00 1.40
852 904 1.517242 CTCTGAACTTGTCCACTGCC 58.483 55.000 0.00 0.00 0.00 4.85
853 905 0.108585 TCTGAACTTGTCCACTGCCC 59.891 55.000 0.00 0.00 0.00 5.36
989 1041 3.135530 ACCTTCTGGCTAATCTGATCCAC 59.864 47.826 0.00 0.00 36.63 4.02
998 1050 1.002069 ATCTGATCCACTGGGGCAAA 58.998 50.000 0.00 0.00 36.21 3.68
1065 1117 5.910614 GGTCCTACCTATTTGACATACGTT 58.089 41.667 0.00 0.00 34.73 3.99
1144 1196 6.421801 GGCATCATGATTTTGCTATGGTTTAC 59.578 38.462 17.01 0.00 36.62 2.01
1145 1197 7.205297 GCATCATGATTTTGCTATGGTTTACT 58.795 34.615 5.16 0.00 33.61 2.24
1149 1201 9.625747 TCATGATTTTGCTATGGTTTACTATGA 57.374 29.630 0.00 0.00 0.00 2.15
1150 1202 9.888878 CATGATTTTGCTATGGTTTACTATGAG 57.111 33.333 0.00 0.00 0.00 2.90
1240 1292 2.099592 GCCATTTGATGATTTGCTCCGA 59.900 45.455 0.00 0.00 0.00 4.55
1311 1363 2.960170 GTGTACGTCCTGGAGCGT 59.040 61.111 21.62 21.62 44.02 5.07
1321 1373 4.980805 TGGAGCGTGACCGGCAAC 62.981 66.667 0.00 0.00 33.68 4.17
1467 1519 1.317431 CGTACCACCTCATCGACCCA 61.317 60.000 0.00 0.00 0.00 4.51
1533 1585 1.738099 CGTCACCAAGAAGGCCTCG 60.738 63.158 5.23 0.00 43.14 4.63
1870 1922 1.069090 GTCACCGTCCTGCACAAGA 59.931 57.895 0.00 0.00 0.00 3.02
2154 2206 2.434359 CCGGACTTCAAGTCGGCC 60.434 66.667 17.61 1.88 45.96 6.13
2229 2290 1.437573 CTACGCTTGATCGGCTGGA 59.562 57.895 8.48 0.00 0.00 3.86
2230 2291 0.179111 CTACGCTTGATCGGCTGGAA 60.179 55.000 8.48 0.00 0.00 3.53
2231 2292 0.464036 TACGCTTGATCGGCTGGAAT 59.536 50.000 8.48 0.00 0.00 3.01
2232 2293 0.464036 ACGCTTGATCGGCTGGAATA 59.536 50.000 8.48 0.00 0.00 1.75
2233 2294 1.070758 ACGCTTGATCGGCTGGAATAT 59.929 47.619 8.48 0.00 0.00 1.28
2234 2295 2.299013 ACGCTTGATCGGCTGGAATATA 59.701 45.455 8.48 0.00 0.00 0.86
2235 2296 3.244078 ACGCTTGATCGGCTGGAATATAA 60.244 43.478 8.48 0.00 0.00 0.98
2236 2297 3.369147 CGCTTGATCGGCTGGAATATAAG 59.631 47.826 8.48 0.00 0.00 1.73
2237 2298 3.686726 GCTTGATCGGCTGGAATATAAGG 59.313 47.826 0.00 0.00 0.00 2.69
2298 2362 3.429543 CGAAAATGATTTGTGTTGGCTGG 59.570 43.478 0.00 0.00 0.00 4.85
2409 2627 4.133078 GAGCAGAGATCATAAACCTTGGG 58.867 47.826 0.00 0.00 0.00 4.12
2444 2662 0.104855 GCCTGGATGCATAGTCGACA 59.895 55.000 19.50 4.13 0.00 4.35
2445 2663 1.270518 GCCTGGATGCATAGTCGACAT 60.271 52.381 19.50 6.50 0.00 3.06
2446 2664 2.808202 GCCTGGATGCATAGTCGACATT 60.808 50.000 19.50 0.76 0.00 2.71
2447 2665 3.470709 CCTGGATGCATAGTCGACATTT 58.529 45.455 19.50 0.00 0.00 2.32
2448 2666 3.496130 CCTGGATGCATAGTCGACATTTC 59.504 47.826 19.50 4.69 0.00 2.17
2449 2667 3.466836 TGGATGCATAGTCGACATTTCC 58.533 45.455 19.50 14.21 0.00 3.13
2450 2668 3.134623 TGGATGCATAGTCGACATTTCCT 59.865 43.478 19.50 0.00 0.00 3.36
2451 2669 3.743396 GGATGCATAGTCGACATTTCCTC 59.257 47.826 19.50 7.40 0.00 3.71
2452 2670 3.885724 TGCATAGTCGACATTTCCTCA 57.114 42.857 19.50 3.22 0.00 3.86
2453 2671 4.406648 TGCATAGTCGACATTTCCTCAT 57.593 40.909 19.50 0.00 0.00 2.90
2454 2672 4.122046 TGCATAGTCGACATTTCCTCATG 58.878 43.478 19.50 8.33 0.00 3.07
2455 2673 4.141959 TGCATAGTCGACATTTCCTCATGA 60.142 41.667 19.50 0.00 0.00 3.07
2456 2674 4.993584 GCATAGTCGACATTTCCTCATGAT 59.006 41.667 19.50 0.00 0.00 2.45
2457 2675 5.119898 GCATAGTCGACATTTCCTCATGATC 59.880 44.000 19.50 0.00 0.00 2.92
2458 2676 4.065321 AGTCGACATTTCCTCATGATCC 57.935 45.455 19.50 0.00 0.00 3.36
2459 2677 3.452264 AGTCGACATTTCCTCATGATCCA 59.548 43.478 19.50 0.00 0.00 3.41
2460 2678 3.806521 GTCGACATTTCCTCATGATCCAG 59.193 47.826 11.55 0.00 0.00 3.86
2461 2679 2.547211 CGACATTTCCTCATGATCCAGC 59.453 50.000 0.00 0.00 0.00 4.85
2462 2680 3.548770 GACATTTCCTCATGATCCAGCA 58.451 45.455 0.00 0.00 0.00 4.41
2463 2681 3.949754 GACATTTCCTCATGATCCAGCAA 59.050 43.478 0.00 0.00 0.00 3.91
2480 2698 1.993956 CAACATCAGGGGTCCAACAA 58.006 50.000 0.00 0.00 0.00 2.83
2570 2788 6.939622 TCAGAAATAGATTCAGACTGCAGAA 58.060 36.000 23.35 4.37 40.72 3.02
2571 2789 7.563020 TCAGAAATAGATTCAGACTGCAGAAT 58.437 34.615 23.35 9.86 40.72 2.40
2572 2790 8.699130 TCAGAAATAGATTCAGACTGCAGAATA 58.301 33.333 23.35 0.00 40.72 1.75
2573 2791 8.763356 CAGAAATAGATTCAGACTGCAGAATAC 58.237 37.037 23.35 8.67 40.72 1.89
2574 2792 8.703743 AGAAATAGATTCAGACTGCAGAATACT 58.296 33.333 23.35 10.86 40.72 2.12
2575 2793 8.885494 AAATAGATTCAGACTGCAGAATACTC 57.115 34.615 23.35 6.97 34.79 2.59
2576 2794 5.929058 AGATTCAGACTGCAGAATACTCA 57.071 39.130 23.35 0.00 34.79 3.41
2577 2795 6.482898 AGATTCAGACTGCAGAATACTCAT 57.517 37.500 23.35 7.98 34.79 2.90
2578 2796 6.514947 AGATTCAGACTGCAGAATACTCATC 58.485 40.000 23.35 14.87 34.79 2.92
2579 2797 5.929058 TTCAGACTGCAGAATACTCATCT 57.071 39.130 23.35 7.08 0.00 2.90
2580 2798 7.505248 AGATTCAGACTGCAGAATACTCATCTA 59.495 37.037 23.35 0.00 34.79 1.98
2581 2799 7.410120 TTCAGACTGCAGAATACTCATCTAA 57.590 36.000 23.35 0.00 0.00 2.10
2582 2800 6.800543 TCAGACTGCAGAATACTCATCTAAC 58.199 40.000 23.35 0.00 0.00 2.34
2583 2801 5.982516 CAGACTGCAGAATACTCATCTAACC 59.017 44.000 23.35 0.00 0.00 2.85
2584 2802 5.069781 AGACTGCAGAATACTCATCTAACCC 59.930 44.000 23.35 0.00 0.00 4.11
2585 2803 4.101741 ACTGCAGAATACTCATCTAACCCC 59.898 45.833 23.35 0.00 0.00 4.95
2586 2804 4.298626 TGCAGAATACTCATCTAACCCCT 58.701 43.478 0.00 0.00 0.00 4.79
2587 2805 4.721776 TGCAGAATACTCATCTAACCCCTT 59.278 41.667 0.00 0.00 0.00 3.95
2588 2806 5.191722 TGCAGAATACTCATCTAACCCCTTT 59.808 40.000 0.00 0.00 0.00 3.11
2589 2807 6.122964 GCAGAATACTCATCTAACCCCTTTT 58.877 40.000 0.00 0.00 0.00 2.27
2590 2808 7.092623 TGCAGAATACTCATCTAACCCCTTTTA 60.093 37.037 0.00 0.00 0.00 1.52
2591 2809 7.773690 GCAGAATACTCATCTAACCCCTTTTAA 59.226 37.037 0.00 0.00 0.00 1.52
2592 2810 9.853177 CAGAATACTCATCTAACCCCTTTTAAT 57.147 33.333 0.00 0.00 0.00 1.40
2647 2865 1.543650 CGGTGGTGGTGAATTGGTACA 60.544 52.381 0.00 0.00 0.00 2.90
2709 2928 1.732259 ACCGTTGCAAATCGAGCTAAG 59.268 47.619 10.71 0.00 0.00 2.18
2804 3026 4.880537 CTGCCCGCTCGCTCGATT 62.881 66.667 0.00 0.00 0.00 3.34
2823 3045 2.125512 GTGCAGTCCGGCTCGAAT 60.126 61.111 0.00 0.00 34.04 3.34
2854 3083 1.379176 TGCTCCACTCTCTCCCTCG 60.379 63.158 0.00 0.00 0.00 4.63
2958 3201 0.598562 GACGAAGCAGTGAGGAGACA 59.401 55.000 0.00 0.00 0.00 3.41
2972 3215 2.821366 GACATCCAGCCTGCCGTG 60.821 66.667 0.00 0.00 0.00 4.94
3164 3413 1.153005 CAGGGGCTTGAGCTGGATC 60.153 63.158 0.00 0.00 41.70 3.36
3169 3418 1.133853 GGGCTTGAGCTGGATCTGATT 60.134 52.381 0.00 0.00 41.70 2.57
3211 3460 0.694771 TGGCATCTGAGAGGCTTGTT 59.305 50.000 19.01 0.00 39.44 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.062433 CGTAACGCATATAAAGTGTGGTTCA 59.938 40.000 0.00 0.00 0.00 3.18
1 2 5.062558 ACGTAACGCATATAAAGTGTGGTTC 59.937 40.000 0.00 0.00 0.00 3.62
2 3 4.931002 ACGTAACGCATATAAAGTGTGGTT 59.069 37.500 0.00 0.00 0.00 3.67
3 4 4.497300 ACGTAACGCATATAAAGTGTGGT 58.503 39.130 0.00 0.00 0.00 4.16
4 5 5.174398 CCTACGTAACGCATATAAAGTGTGG 59.826 44.000 0.00 0.00 0.00 4.17
5 6 5.332055 GCCTACGTAACGCATATAAAGTGTG 60.332 44.000 8.95 0.00 0.00 3.82
6 7 4.741676 GCCTACGTAACGCATATAAAGTGT 59.258 41.667 8.95 0.00 0.00 3.55
7 8 4.980434 AGCCTACGTAACGCATATAAAGTG 59.020 41.667 14.71 0.00 0.00 3.16
8 9 4.980434 CAGCCTACGTAACGCATATAAAGT 59.020 41.667 14.71 0.00 0.00 2.66
9 10 4.980434 ACAGCCTACGTAACGCATATAAAG 59.020 41.667 14.71 0.00 0.00 1.85
10 11 4.935702 ACAGCCTACGTAACGCATATAAA 58.064 39.130 14.71 0.00 0.00 1.40
11 12 4.036616 TGACAGCCTACGTAACGCATATAA 59.963 41.667 14.71 0.00 0.00 0.98
12 13 3.565063 TGACAGCCTACGTAACGCATATA 59.435 43.478 14.71 0.00 0.00 0.86
13 14 2.359848 TGACAGCCTACGTAACGCATAT 59.640 45.455 14.71 2.14 0.00 1.78
14 15 1.744522 TGACAGCCTACGTAACGCATA 59.255 47.619 14.71 0.00 0.00 3.14
15 16 0.528924 TGACAGCCTACGTAACGCAT 59.471 50.000 14.71 4.51 0.00 4.73
16 17 0.314618 TTGACAGCCTACGTAACGCA 59.685 50.000 14.71 2.19 0.00 5.24
17 18 1.636988 ATTGACAGCCTACGTAACGC 58.363 50.000 6.25 6.25 0.00 4.84
18 19 2.780014 CGTATTGACAGCCTACGTAACG 59.220 50.000 0.00 0.00 34.91 3.18
19 20 3.111098 CCGTATTGACAGCCTACGTAAC 58.889 50.000 0.00 0.00 37.20 2.50
20 21 2.754552 ACCGTATTGACAGCCTACGTAA 59.245 45.455 0.00 0.00 37.20 3.18
21 22 2.097954 CACCGTATTGACAGCCTACGTA 59.902 50.000 0.00 0.00 37.20 3.57
22 23 1.135199 CACCGTATTGACAGCCTACGT 60.135 52.381 0.00 0.00 37.20 3.57
23 24 1.135199 ACACCGTATTGACAGCCTACG 60.135 52.381 7.11 7.11 38.31 3.51
24 25 2.268298 CACACCGTATTGACAGCCTAC 58.732 52.381 0.00 0.00 0.00 3.18
25 26 1.897133 ACACACCGTATTGACAGCCTA 59.103 47.619 0.00 0.00 0.00 3.93
26 27 0.685097 ACACACCGTATTGACAGCCT 59.315 50.000 0.00 0.00 0.00 4.58
27 28 0.796312 CACACACCGTATTGACAGCC 59.204 55.000 0.00 0.00 0.00 4.85
28 29 1.194547 CACACACACCGTATTGACAGC 59.805 52.381 0.00 0.00 0.00 4.40
29 30 1.194547 GCACACACACCGTATTGACAG 59.805 52.381 0.00 0.00 0.00 3.51
30 31 1.202592 AGCACACACACCGTATTGACA 60.203 47.619 0.00 0.00 0.00 3.58
31 32 1.508632 AGCACACACACCGTATTGAC 58.491 50.000 0.00 0.00 0.00 3.18
32 33 2.559231 TCTAGCACACACACCGTATTGA 59.441 45.455 0.00 0.00 0.00 2.57
33 34 2.923655 CTCTAGCACACACACCGTATTG 59.076 50.000 0.00 0.00 0.00 1.90
34 35 2.561419 ACTCTAGCACACACACCGTATT 59.439 45.455 0.00 0.00 0.00 1.89
35 36 2.168496 ACTCTAGCACACACACCGTAT 58.832 47.619 0.00 0.00 0.00 3.06
36 37 1.612676 ACTCTAGCACACACACCGTA 58.387 50.000 0.00 0.00 0.00 4.02
37 38 0.750850 AACTCTAGCACACACACCGT 59.249 50.000 0.00 0.00 0.00 4.83
38 39 1.139989 CAACTCTAGCACACACACCG 58.860 55.000 0.00 0.00 0.00 4.94
39 40 0.868406 GCAACTCTAGCACACACACC 59.132 55.000 0.00 0.00 0.00 4.16
40 41 1.795286 GAGCAACTCTAGCACACACAC 59.205 52.381 0.00 0.00 0.00 3.82
41 42 1.688735 AGAGCAACTCTAGCACACACA 59.311 47.619 0.00 0.00 39.28 3.72
42 43 2.447244 AGAGCAACTCTAGCACACAC 57.553 50.000 0.00 0.00 39.28 3.82
43 44 4.600692 TTAAGAGCAACTCTAGCACACA 57.399 40.909 0.00 0.00 40.28 3.72
44 45 5.230942 TCTTTAAGAGCAACTCTAGCACAC 58.769 41.667 0.00 0.00 40.28 3.82
45 46 5.468540 TCTTTAAGAGCAACTCTAGCACA 57.531 39.130 0.00 0.00 40.28 4.57
46 47 5.696724 TGTTCTTTAAGAGCAACTCTAGCAC 59.303 40.000 9.01 0.00 40.28 4.40
47 48 5.853936 TGTTCTTTAAGAGCAACTCTAGCA 58.146 37.500 9.01 0.00 40.28 3.49
48 49 6.976636 ATGTTCTTTAAGAGCAACTCTAGC 57.023 37.500 14.94 0.00 40.28 3.42
49 50 9.809096 TCATATGTTCTTTAAGAGCAACTCTAG 57.191 33.333 14.94 3.91 40.28 2.43
50 51 9.809096 CTCATATGTTCTTTAAGAGCAACTCTA 57.191 33.333 14.94 4.32 40.28 2.43
51 52 8.317679 ACTCATATGTTCTTTAAGAGCAACTCT 58.682 33.333 14.94 2.24 43.37 3.24
52 53 8.485976 ACTCATATGTTCTTTAAGAGCAACTC 57.514 34.615 14.94 0.00 38.90 3.01
53 54 8.725148 CAACTCATATGTTCTTTAAGAGCAACT 58.275 33.333 14.94 3.25 38.90 3.16
54 55 8.721478 TCAACTCATATGTTCTTTAAGAGCAAC 58.279 33.333 14.94 2.25 38.90 4.17
55 56 8.846943 TCAACTCATATGTTCTTTAAGAGCAA 57.153 30.769 14.94 6.01 38.90 3.91
56 57 8.097038 ACTCAACTCATATGTTCTTTAAGAGCA 58.903 33.333 13.49 13.49 39.73 4.26
57 58 8.485976 ACTCAACTCATATGTTCTTTAAGAGC 57.514 34.615 1.90 1.79 0.00 4.09
63 64 9.646427 GTCTCTTACTCAACTCATATGTTCTTT 57.354 33.333 1.90 0.00 0.00 2.52
64 65 8.807118 TGTCTCTTACTCAACTCATATGTTCTT 58.193 33.333 1.90 0.00 0.00 2.52
65 66 8.354711 TGTCTCTTACTCAACTCATATGTTCT 57.645 34.615 1.90 0.00 0.00 3.01
66 67 9.243637 GATGTCTCTTACTCAACTCATATGTTC 57.756 37.037 1.90 0.00 0.00 3.18
67 68 8.753133 TGATGTCTCTTACTCAACTCATATGTT 58.247 33.333 1.90 0.00 0.00 2.71
68 69 8.298729 TGATGTCTCTTACTCAACTCATATGT 57.701 34.615 1.90 0.00 0.00 2.29
69 70 9.247126 CTTGATGTCTCTTACTCAACTCATATG 57.753 37.037 0.00 0.00 0.00 1.78
70 71 8.976353 ACTTGATGTCTCTTACTCAACTCATAT 58.024 33.333 0.00 0.00 0.00 1.78
71 72 8.246871 CACTTGATGTCTCTTACTCAACTCATA 58.753 37.037 0.00 0.00 0.00 2.15
72 73 7.095910 CACTTGATGTCTCTTACTCAACTCAT 58.904 38.462 0.00 0.00 0.00 2.90
73 74 6.040955 ACACTTGATGTCTCTTACTCAACTCA 59.959 38.462 0.00 0.00 36.54 3.41
74 75 6.451393 ACACTTGATGTCTCTTACTCAACTC 58.549 40.000 0.00 0.00 36.54 3.01
75 76 6.412362 ACACTTGATGTCTCTTACTCAACT 57.588 37.500 0.00 0.00 36.54 3.16
76 77 8.589335 TTAACACTTGATGTCTCTTACTCAAC 57.411 34.615 0.00 0.00 42.31 3.18
77 78 8.638873 TCTTAACACTTGATGTCTCTTACTCAA 58.361 33.333 0.00 0.00 42.31 3.02
78 79 8.178313 TCTTAACACTTGATGTCTCTTACTCA 57.822 34.615 0.00 0.00 42.31 3.41
79 80 8.516234 TCTCTTAACACTTGATGTCTCTTACTC 58.484 37.037 0.00 0.00 42.31 2.59
80 81 8.410673 TCTCTTAACACTTGATGTCTCTTACT 57.589 34.615 0.00 0.00 42.31 2.24
81 82 9.296400 GATCTCTTAACACTTGATGTCTCTTAC 57.704 37.037 0.00 0.00 42.31 2.34
82 83 9.025041 TGATCTCTTAACACTTGATGTCTCTTA 57.975 33.333 0.00 0.00 42.31 2.10
83 84 7.901029 TGATCTCTTAACACTTGATGTCTCTT 58.099 34.615 0.00 0.00 42.31 2.85
84 85 7.473735 TGATCTCTTAACACTTGATGTCTCT 57.526 36.000 0.00 0.00 42.31 3.10
85 86 7.437862 GGATGATCTCTTAACACTTGATGTCTC 59.562 40.741 0.00 0.00 42.31 3.36
86 87 7.271511 GGATGATCTCTTAACACTTGATGTCT 58.728 38.462 0.00 0.00 42.31 3.41
87 88 6.481644 GGGATGATCTCTTAACACTTGATGTC 59.518 42.308 0.00 0.00 42.31 3.06
88 89 6.157645 AGGGATGATCTCTTAACACTTGATGT 59.842 38.462 0.00 0.00 46.42 3.06
89 90 6.590068 AGGGATGATCTCTTAACACTTGATG 58.410 40.000 0.00 0.00 0.00 3.07
90 91 6.821616 AGGGATGATCTCTTAACACTTGAT 57.178 37.500 0.00 0.00 0.00 2.57
91 92 6.441924 AGAAGGGATGATCTCTTAACACTTGA 59.558 38.462 7.69 0.00 37.31 3.02
92 93 6.648192 AGAAGGGATGATCTCTTAACACTTG 58.352 40.000 7.69 0.00 37.31 3.16
93 94 6.671779 AGAGAAGGGATGATCTCTTAACACTT 59.328 38.462 7.69 0.00 37.31 3.16
94 95 6.201591 AGAGAAGGGATGATCTCTTAACACT 58.798 40.000 7.69 0.39 37.31 3.55
95 96 6.478512 AGAGAAGGGATGATCTCTTAACAC 57.521 41.667 7.69 0.00 37.31 3.32
96 97 7.841729 ACTAAGAGAAGGGATGATCTCTTAACA 59.158 37.037 19.85 6.54 45.42 2.41
97 98 8.245195 ACTAAGAGAAGGGATGATCTCTTAAC 57.755 38.462 19.85 5.31 45.42 2.01
98 99 8.846423 AACTAAGAGAAGGGATGATCTCTTAA 57.154 34.615 19.85 9.16 45.42 1.85
99 100 9.937876 TTAACTAAGAGAAGGGATGATCTCTTA 57.062 33.333 7.69 18.85 44.69 2.10
101 102 8.285891 TCTTAACTAAGAGAAGGGATGATCTCT 58.714 37.037 0.00 0.00 40.85 3.10
102 103 8.472007 TCTTAACTAAGAGAAGGGATGATCTC 57.528 38.462 0.00 0.00 37.40 2.75
116 117 7.676683 AGGGTATGCATTCTCTTAACTAAGA 57.323 36.000 3.54 0.00 39.82 2.10
117 118 8.738645 AAAGGGTATGCATTCTCTTAACTAAG 57.261 34.615 17.69 0.00 34.65 2.18
118 119 9.174166 GAAAAGGGTATGCATTCTCTTAACTAA 57.826 33.333 17.69 0.00 0.00 2.24
119 120 8.548877 AGAAAAGGGTATGCATTCTCTTAACTA 58.451 33.333 17.69 0.00 0.00 2.24
120 121 7.337942 CAGAAAAGGGTATGCATTCTCTTAACT 59.662 37.037 17.69 15.76 0.00 2.24
121 122 7.336931 TCAGAAAAGGGTATGCATTCTCTTAAC 59.663 37.037 17.69 14.09 0.00 2.01
122 123 7.402054 TCAGAAAAGGGTATGCATTCTCTTAA 58.598 34.615 17.69 1.04 0.00 1.85
123 124 6.957631 TCAGAAAAGGGTATGCATTCTCTTA 58.042 36.000 17.69 0.49 0.00 2.10
151 153 7.414429 CGATAAATGCTGACTTGGAGAATTGAA 60.414 37.037 0.00 0.00 0.00 2.69
158 160 2.289002 GGCGATAAATGCTGACTTGGAG 59.711 50.000 0.00 0.00 0.00 3.86
187 190 9.220767 CTTTATAAAACAGGGAGATATAGTGCC 57.779 37.037 0.00 0.00 0.00 5.01
210 215 7.039082 TGGATTGCCTCTTTAAATGCTTACTTT 60.039 33.333 0.00 0.00 34.31 2.66
212 217 5.951747 TGGATTGCCTCTTTAAATGCTTACT 59.048 36.000 0.00 0.00 34.31 2.24
213 218 6.207691 TGGATTGCCTCTTTAAATGCTTAC 57.792 37.500 0.00 0.00 34.31 2.34
294 318 4.100808 GGGTAATGCTTGGATGCCAATTTA 59.899 41.667 0.00 0.00 43.07 1.40
321 345 4.084849 GCATCTTCTTTCGATGATACACCG 60.085 45.833 4.35 0.00 40.47 4.94
434 484 1.919240 TAGGAGCACGAAGTCTTCCA 58.081 50.000 7.01 0.00 41.61 3.53
688 739 4.436332 TGAGAGTGTGAATCATGAATCCG 58.564 43.478 8.30 0.00 0.00 4.18
782 833 9.490663 GGTACATTTTCAGATTTATTCAGAACG 57.509 33.333 0.00 0.00 30.41 3.95
830 881 2.485479 GCAGTGGACAAGTTCAGAGGAA 60.485 50.000 0.00 0.00 0.00 3.36
852 904 6.432162 CCAACCATGATACTCTTGGAATATGG 59.568 42.308 14.06 11.85 42.46 2.74
853 905 7.226441 TCCAACCATGATACTCTTGGAATATG 58.774 38.462 14.06 8.17 42.46 1.78
922 974 4.623002 TGTGCATACTAAACGTGAGACAA 58.377 39.130 4.81 0.00 0.00 3.18
989 1041 1.193462 TTTGCCCATCTTTGCCCCAG 61.193 55.000 0.00 0.00 0.00 4.45
1014 1066 3.262915 CCTCAAAGAGGTCCTTCTGTGAT 59.737 47.826 10.11 0.00 44.25 3.06
1044 1096 9.537192 CAATTAACGTATGTCAAATAGGTAGGA 57.463 33.333 0.00 0.00 0.00 2.94
1144 1196 3.808728 TCCCGGAATCTTTTGCTCATAG 58.191 45.455 0.73 0.00 0.00 2.23
1145 1197 3.924114 TCCCGGAATCTTTTGCTCATA 57.076 42.857 0.73 0.00 0.00 2.15
1147 1199 2.159382 GTTCCCGGAATCTTTTGCTCA 58.841 47.619 0.73 0.00 0.00 4.26
1148 1200 2.159382 TGTTCCCGGAATCTTTTGCTC 58.841 47.619 0.73 0.00 0.00 4.26
1149 1201 2.162681 CTGTTCCCGGAATCTTTTGCT 58.837 47.619 0.73 0.00 0.00 3.91
1150 1202 2.159382 TCTGTTCCCGGAATCTTTTGC 58.841 47.619 0.73 0.00 0.00 3.68
1240 1292 1.380302 GGTGTGGGCAGTTCCTGAT 59.620 57.895 0.00 0.00 32.44 2.90
1853 1905 1.367471 CTCTTGTGCAGGACGGTGA 59.633 57.895 0.00 0.00 0.00 4.02
2055 2107 4.802051 GGCTTGCCGATGCCCAGA 62.802 66.667 0.00 0.00 43.11 3.86
2154 2206 2.268920 CACTGGTGGATCCCGTGG 59.731 66.667 9.90 0.00 44.24 4.94
2236 2297 1.186200 GGATCCAAAGGAGGTTTGCC 58.814 55.000 6.95 0.00 43.82 4.52
2237 2298 1.821136 CAGGATCCAAAGGAGGTTTGC 59.179 52.381 15.82 0.00 43.82 3.68
2298 2362 1.795286 CGTTGACAGTTTCAGGCTCTC 59.205 52.381 0.00 0.00 34.94 3.20
2345 2417 7.520937 GCATGCCTTGAATCAAAAGTTCAAAAT 60.521 33.333 6.36 0.00 42.91 1.82
2444 2662 3.972133 TGTTGCTGGATCATGAGGAAAT 58.028 40.909 0.09 0.00 0.00 2.17
2445 2663 3.438216 TGTTGCTGGATCATGAGGAAA 57.562 42.857 0.09 0.00 0.00 3.13
2446 2664 3.054213 TGATGTTGCTGGATCATGAGGAA 60.054 43.478 0.09 0.00 0.00 3.36
2447 2665 2.506644 TGATGTTGCTGGATCATGAGGA 59.493 45.455 0.09 0.00 0.00 3.71
2448 2666 2.879026 CTGATGTTGCTGGATCATGAGG 59.121 50.000 0.09 0.00 0.00 3.86
2449 2667 2.879026 CCTGATGTTGCTGGATCATGAG 59.121 50.000 0.09 0.00 0.00 2.90
2450 2668 2.422377 CCCTGATGTTGCTGGATCATGA 60.422 50.000 0.00 0.00 0.00 3.07
2451 2669 1.954382 CCCTGATGTTGCTGGATCATG 59.046 52.381 0.00 0.00 0.00 3.07
2452 2670 1.133575 CCCCTGATGTTGCTGGATCAT 60.134 52.381 0.00 0.00 0.00 2.45
2453 2671 0.256752 CCCCTGATGTTGCTGGATCA 59.743 55.000 0.00 0.00 0.00 2.92
2454 2672 0.257039 ACCCCTGATGTTGCTGGATC 59.743 55.000 0.00 0.00 0.00 3.36
2455 2673 0.257039 GACCCCTGATGTTGCTGGAT 59.743 55.000 0.00 0.00 0.00 3.41
2456 2674 1.685224 GACCCCTGATGTTGCTGGA 59.315 57.895 0.00 0.00 0.00 3.86
2457 2675 1.379044 GGACCCCTGATGTTGCTGG 60.379 63.158 0.00 0.00 0.00 4.85
2458 2676 0.251297 TTGGACCCCTGATGTTGCTG 60.251 55.000 0.00 0.00 0.00 4.41
2459 2677 0.251341 GTTGGACCCCTGATGTTGCT 60.251 55.000 0.00 0.00 0.00 3.91
2460 2678 0.539438 TGTTGGACCCCTGATGTTGC 60.539 55.000 0.00 0.00 0.00 4.17
2461 2679 1.888512 CTTGTTGGACCCCTGATGTTG 59.111 52.381 0.00 0.00 0.00 3.33
2462 2680 1.499007 ACTTGTTGGACCCCTGATGTT 59.501 47.619 0.00 0.00 0.00 2.71
2463 2681 1.149101 ACTTGTTGGACCCCTGATGT 58.851 50.000 0.00 0.00 0.00 3.06
2480 2698 2.370189 AGCTCTGCTTTGAGGTTGTACT 59.630 45.455 0.00 0.00 41.36 2.73
2570 2788 9.225682 TCAGATTAAAAGGGGTTAGATGAGTAT 57.774 33.333 0.00 0.00 0.00 2.12
2571 2789 8.618240 TCAGATTAAAAGGGGTTAGATGAGTA 57.382 34.615 0.00 0.00 0.00 2.59
2572 2790 7.403231 TCTCAGATTAAAAGGGGTTAGATGAGT 59.597 37.037 0.00 0.00 32.96 3.41
2573 2791 7.796054 TCTCAGATTAAAAGGGGTTAGATGAG 58.204 38.462 0.00 0.00 0.00 2.90
2574 2792 7.749377 TCTCAGATTAAAAGGGGTTAGATGA 57.251 36.000 0.00 0.00 0.00 2.92
2581 2799 9.628500 GTGTAATTATCTCAGATTAAAAGGGGT 57.372 33.333 0.00 0.00 0.00 4.95
2582 2800 8.774586 CGTGTAATTATCTCAGATTAAAAGGGG 58.225 37.037 0.00 0.00 0.00 4.79
2583 2801 9.542462 TCGTGTAATTATCTCAGATTAAAAGGG 57.458 33.333 0.00 0.00 0.00 3.95
2591 2809 9.516546 TGGTACTATCGTGTAATTATCTCAGAT 57.483 33.333 0.00 0.00 0.00 2.90
2592 2810 8.781196 GTGGTACTATCGTGTAATTATCTCAGA 58.219 37.037 0.00 0.00 0.00 3.27
2593 2811 8.565416 TGTGGTACTATCGTGTAATTATCTCAG 58.435 37.037 0.00 0.00 0.00 3.35
2709 2928 5.876597 CGTCAATACGTAGAAATACGAAGC 58.123 41.667 14.13 0.00 45.45 3.86
2854 3083 4.500116 GAGGGAGGCACGAGCGAC 62.500 72.222 0.00 0.00 43.41 5.19
2958 3201 4.119363 ATGCACGGCAGGCTGGAT 62.119 61.111 17.64 0.00 43.65 3.41
2972 3215 1.156645 GGATGAGGTCGAGTGCATGC 61.157 60.000 11.82 11.82 0.00 4.06
3164 3413 2.686915 GCTTCTCACATGGGGAAATCAG 59.313 50.000 0.00 0.00 0.00 2.90
3169 3418 0.321564 CGTGCTTCTCACATGGGGAA 60.322 55.000 0.00 0.00 45.92 3.97
3192 3441 0.694771 AACAAGCCTCTCAGATGCCA 59.305 50.000 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.