Multiple sequence alignment - TraesCS4A01G493000

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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 TraesCS4A01G493000 chr4A 100.000 2840 0 0 1 2840 741796798 741793959 0.000000e+00 5245
1 TraesCS4A01G493000 chr4A 92.247 2012 125 15 849 2840 741589005 741591005 0.000000e+00 2822
2 TraesCS4A01G493000 chr4A 91.880 1995 107 22 862 2840 741485613 741483658 0.000000e+00 2736
3 TraesCS4A01G493000 chr4A 90.752 1968 131 24 862 2794 739650643 739652594 0.000000e+00 2579
4 TraesCS4A01G493000 chr4A 90.396 1968 138 24 862 2794 742055922 742057873 0.000000e+00 2540
5 TraesCS4A01G493000 chr4A 90.025 2005 138 20 894 2840 740456805 740454805 0.000000e+00 2538
6 TraesCS4A01G493000 chr4A 88.042 2007 167 35 865 2840 739866234 739868198 0.000000e+00 2309
7 TraesCS4A01G493000 chr4A 88.262 1968 150 37 853 2796 740303692 740305602 0.000000e+00 2279
8 TraesCS4A01G493000 chr4A 87.414 1740 150 25 1162 2840 740577922 740579653 0.000000e+00 1936
9 TraesCS4A01G493000 chr4A 94.494 1235 52 9 825 2055 740022174 740020952 0.000000e+00 1890
10 TraesCS4A01G493000 chr4A 93.317 838 38 16 1386 2216 741817729 741816903 0.000000e+00 1221
11 TraesCS4A01G493000 chr4A 92.026 627 37 1 2227 2840 741815650 741815024 0.000000e+00 869
12 TraesCS4A01G493000 chr4A 91.549 568 35 3 2286 2840 740019075 740018508 0.000000e+00 771
13 TraesCS4A01G493000 chr4A 93.624 298 18 1 213 510 741588442 741588738 7.220000e-121 444
14 TraesCS4A01G493000 chr4A 91.497 294 25 0 213 506 740457180 740456887 3.410000e-109 405
15 TraesCS4A01G493000 chr4A 91.065 291 26 0 213 503 740269114 740269404 7.370000e-106 394
16 TraesCS4A01G493000 chr4A 91.065 291 23 3 213 503 740303267 740303554 9.540000e-105 390
17 TraesCS4A01G493000 chr4A 90.378 291 28 0 213 503 740346519 740346809 1.600000e-102 383
18 TraesCS4A01G493000 chr4A 88.424 311 28 4 213 519 740566765 740567071 4.470000e-98 368
19 TraesCS4A01G493000 chr7D 90.986 1997 122 16 862 2839 3788339 3786382 0.000000e+00 2638
20 TraesCS4A01G493000 chr7D 94.904 1413 40 8 782 2167 2611364 2609957 0.000000e+00 2182
21 TraesCS4A01G493000 chr7D 86.537 2050 186 34 865 2840 2567514 2565481 0.000000e+00 2174
22 TraesCS4A01G493000 chr7D 90.717 614 44 1 2240 2840 3633199 3632586 0.000000e+00 806
23 TraesCS4A01G493000 chr7D 89.498 638 53 2 2217 2840 2609960 2609323 0.000000e+00 795
24 TraesCS4A01G493000 chr7D 90.141 568 43 1 2286 2840 2357659 2357092 0.000000e+00 726
25 TraesCS4A01G493000 chr7D 88.111 614 47 8 2240 2840 3906951 3907551 0.000000e+00 706
26 TraesCS4A01G493000 chr7D 91.509 318 25 2 213 530 2611722 2611407 1.210000e-118 436
27 TraesCS4A01G493000 chr7D 94.521 219 11 1 569 787 231613137 231613354 1.260000e-88 337
28 TraesCS4A01G493000 chr7D 94.819 193 10 0 2 194 413875588 413875396 4.600000e-78 302
29 TraesCS4A01G493000 chr7A 86.637 2013 219 21 865 2840 3311244 3313243 0.000000e+00 2182
30 TraesCS4A01G493000 chr7A 91.696 566 47 0 2231 2796 3631638 3631073 0.000000e+00 785
31 TraesCS4A01G493000 chr7A 91.921 557 45 0 2240 2796 3208034 3207478 0.000000e+00 780
32 TraesCS4A01G493000 chr7A 85.789 760 72 5 2092 2838 2117697 2116961 0.000000e+00 773
33 TraesCS4A01G493000 chr7A 89.388 556 59 0 2240 2795 1996506 1995951 0.000000e+00 701
34 TraesCS4A01G493000 chr7A 90.278 288 28 0 213 500 3285530 3285817 7.430000e-101 377
35 TraesCS4A01G493000 chr7A 88.065 310 33 3 213 522 2002378 2002073 5.780000e-97 364
36 TraesCS4A01G493000 chr2D 77.878 556 118 5 2244 2796 603139957 603139404 9.740000e-90 340
37 TraesCS4A01G493000 chr2D 94.819 193 10 0 2 194 103077458 103077266 4.600000e-78 302
38 TraesCS4A01G493000 chr2D 95.263 190 9 0 2 191 381525387 381525576 4.600000e-78 302
39 TraesCS4A01G493000 chrUn 94.907 216 10 1 572 787 3311474 3311260 1.260000e-88 337
40 TraesCS4A01G493000 chrUn 75.944 503 108 5 2290 2790 112610827 112610336 2.190000e-61 246
41 TraesCS4A01G493000 chr5D 94.907 216 10 1 572 787 240133889 240133675 1.260000e-88 337
42 TraesCS4A01G493000 chr1D 94.907 216 10 1 572 787 254492397 254492183 1.260000e-88 337
43 TraesCS4A01G493000 chr1D 94.521 219 11 1 569 787 254493320 254493537 1.260000e-88 337
44 TraesCS4A01G493000 chr1D 94.521 219 11 1 569 787 483918416 483918633 1.260000e-88 337
45 TraesCS4A01G493000 chr1D 94.521 219 11 1 569 787 483920219 483920436 1.260000e-88 337
46 TraesCS4A01G493000 chr1D 94.444 216 11 1 572 787 254494197 254493983 5.860000e-87 331
47 TraesCS4A01G493000 chr1D 95.263 190 9 0 2 191 107139523 107139712 4.600000e-78 302
48 TraesCS4A01G493000 chr1D 94.819 193 10 0 2 194 359669838 359669646 4.600000e-78 302
49 TraesCS4A01G493000 chr3D 94.444 216 11 1 572 787 21900274 21900060 5.860000e-87 331
50 TraesCS4A01G493000 chr4D 95.337 193 9 0 2 194 370034494 370034302 9.880000e-80 307
51 TraesCS4A01G493000 chr6D 94.819 193 10 0 2 194 87507151 87506959 4.600000e-78 302
52 TraesCS4A01G493000 chr4B 95.263 190 9 0 2 191 386975210 386975399 4.600000e-78 302
53 TraesCS4A01G493000 chr4B 95.263 190 9 0 2 191 386980743 386980932 4.600000e-78 302
54 TraesCS4A01G493000 chr6A 74.603 504 113 7 2290 2790 45331907 45332398 1.030000e-49 207


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 TraesCS4A01G493000 chr4A 741793959 741796798 2839 True 5245.000000 5245 100.000000 1 2840 1 chr4A.!!$R2 2839
1 TraesCS4A01G493000 chr4A 741483658 741485613 1955 True 2736.000000 2736 91.880000 862 2840 1 chr4A.!!$R1 1978
2 TraesCS4A01G493000 chr4A 739650643 739652594 1951 False 2579.000000 2579 90.752000 862 2794 1 chr4A.!!$F1 1932
3 TraesCS4A01G493000 chr4A 742055922 742057873 1951 False 2540.000000 2540 90.396000 862 2794 1 chr4A.!!$F7 1932
4 TraesCS4A01G493000 chr4A 739866234 739868198 1964 False 2309.000000 2309 88.042000 865 2840 1 chr4A.!!$F2 1975
5 TraesCS4A01G493000 chr4A 740577922 740579653 1731 False 1936.000000 1936 87.414000 1162 2840 1 chr4A.!!$F6 1678
6 TraesCS4A01G493000 chr4A 741588442 741591005 2563 False 1633.000000 2822 92.935500 213 2840 2 chr4A.!!$F9 2627
7 TraesCS4A01G493000 chr4A 740454805 740457180 2375 True 1471.500000 2538 90.761000 213 2840 2 chr4A.!!$R4 2627
8 TraesCS4A01G493000 chr4A 740303267 740305602 2335 False 1334.500000 2279 89.663500 213 2796 2 chr4A.!!$F8 2583
9 TraesCS4A01G493000 chr4A 740018508 740022174 3666 True 1330.500000 1890 93.021500 825 2840 2 chr4A.!!$R3 2015
10 TraesCS4A01G493000 chr4A 741815024 741817729 2705 True 1045.000000 1221 92.671500 1386 2840 2 chr4A.!!$R5 1454
11 TraesCS4A01G493000 chr7D 3786382 3788339 1957 True 2638.000000 2638 90.986000 862 2839 1 chr7D.!!$R4 1977
12 TraesCS4A01G493000 chr7D 2565481 2567514 2033 True 2174.000000 2174 86.537000 865 2840 1 chr7D.!!$R2 1975
13 TraesCS4A01G493000 chr7D 2609323 2611722 2399 True 1137.666667 2182 91.970333 213 2840 3 chr7D.!!$R6 2627
14 TraesCS4A01G493000 chr7D 3632586 3633199 613 True 806.000000 806 90.717000 2240 2840 1 chr7D.!!$R3 600
15 TraesCS4A01G493000 chr7D 2357092 2357659 567 True 726.000000 726 90.141000 2286 2840 1 chr7D.!!$R1 554
16 TraesCS4A01G493000 chr7D 3906951 3907551 600 False 706.000000 706 88.111000 2240 2840 1 chr7D.!!$F1 600
17 TraesCS4A01G493000 chr7A 3311244 3313243 1999 False 2182.000000 2182 86.637000 865 2840 1 chr7A.!!$F2 1975
18 TraesCS4A01G493000 chr7A 3631073 3631638 565 True 785.000000 785 91.696000 2231 2796 1 chr7A.!!$R5 565
19 TraesCS4A01G493000 chr7A 3207478 3208034 556 True 780.000000 780 91.921000 2240 2796 1 chr7A.!!$R4 556
20 TraesCS4A01G493000 chr7A 2116961 2117697 736 True 773.000000 773 85.789000 2092 2838 1 chr7A.!!$R3 746
21 TraesCS4A01G493000 chr7A 1995951 1996506 555 True 701.000000 701 89.388000 2240 2795 1 chr7A.!!$R1 555
22 TraesCS4A01G493000 chr2D 603139404 603139957 553 True 340.000000 340 77.878000 2244 2796 1 chr2D.!!$R2 552
23 TraesCS4A01G493000 chr1D 483918416 483920436 2020 False 337.000000 337 94.521000 569 787 2 chr1D.!!$F3 218
24 TraesCS4A01G493000 chr1D 254492183 254494197 2014 True 334.000000 337 94.675500 572 787 2 chr1D.!!$R2 215

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
557 800 0.036875 CTTATCTCCCCGGGCCAATC 59.963 60.0 17.73 0.0 0.00 2.67 F
998 1439 0.250295 TTCAGTGTTTCTCTGGGCGG 60.250 55.0 0.00 0.0 34.15 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 2275 1.800586 TGTGAAGTTCATCAGAAGCGC 59.199 47.619 9.18 0.0 33.63 5.92 R
2496 6466 2.181525 CAGCCAAAAATCCCGCCG 59.818 61.111 0.00 0.0 0.00 6.46 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
22 23 4.026356 ACTCCCAGTTCCATTTCAGAAG 57.974 45.455 0.00 0.00 0.00 2.85
23 24 2.751806 CTCCCAGTTCCATTTCAGAAGC 59.248 50.000 0.00 0.00 0.00 3.86
24 25 2.376518 TCCCAGTTCCATTTCAGAAGCT 59.623 45.455 0.00 0.00 0.00 3.74
25 26 3.160269 CCCAGTTCCATTTCAGAAGCTT 58.840 45.455 0.00 0.00 0.00 3.74
26 27 4.042809 TCCCAGTTCCATTTCAGAAGCTTA 59.957 41.667 0.00 0.00 0.00 3.09
27 28 4.952335 CCCAGTTCCATTTCAGAAGCTTAT 59.048 41.667 0.00 0.00 0.00 1.73
28 29 5.163581 CCCAGTTCCATTTCAGAAGCTTATG 60.164 44.000 14.99 14.99 0.00 1.90
29 30 5.338365 CAGTTCCATTTCAGAAGCTTATGC 58.662 41.667 16.28 0.00 40.05 3.14
30 31 5.012239 AGTTCCATTTCAGAAGCTTATGCA 58.988 37.500 16.28 2.26 42.74 3.96
31 32 5.655532 AGTTCCATTTCAGAAGCTTATGCAT 59.344 36.000 16.28 3.79 42.74 3.96
32 33 5.762825 TCCATTTCAGAAGCTTATGCATC 57.237 39.130 16.28 0.42 42.74 3.91
33 34 5.443283 TCCATTTCAGAAGCTTATGCATCT 58.557 37.500 16.28 2.76 46.58 2.90
34 35 5.530171 TCCATTTCAGAAGCTTATGCATCTC 59.470 40.000 16.28 0.00 44.23 2.75
35 36 5.531659 CCATTTCAGAAGCTTATGCATCTCT 59.468 40.000 16.28 0.00 44.23 3.10
36 37 6.431278 CATTTCAGAAGCTTATGCATCTCTG 58.569 40.000 16.28 8.70 44.23 3.35
37 38 4.069300 TCAGAAGCTTATGCATCTCTGG 57.931 45.455 16.28 6.49 44.23 3.86
38 39 3.708121 TCAGAAGCTTATGCATCTCTGGA 59.292 43.478 16.28 8.13 44.23 3.86
39 40 4.347292 TCAGAAGCTTATGCATCTCTGGAT 59.653 41.667 16.28 0.00 44.23 3.41
40 41 4.452795 CAGAAGCTTATGCATCTCTGGATG 59.547 45.833 8.36 2.05 44.23 3.51
50 51 3.979948 CATCTCTGGATGCTGACTACTG 58.020 50.000 0.00 0.00 42.12 2.74
51 52 2.382882 TCTCTGGATGCTGACTACTGG 58.617 52.381 0.00 0.00 0.00 4.00
52 53 2.024941 TCTCTGGATGCTGACTACTGGA 60.025 50.000 0.00 0.00 0.00 3.86
53 54 2.762887 CTCTGGATGCTGACTACTGGAA 59.237 50.000 0.00 0.00 0.00 3.53
54 55 2.762887 TCTGGATGCTGACTACTGGAAG 59.237 50.000 0.00 0.00 42.29 3.46
55 56 1.833630 TGGATGCTGACTACTGGAAGG 59.166 52.381 0.00 0.00 39.30 3.46
56 57 2.111384 GGATGCTGACTACTGGAAGGA 58.889 52.381 0.00 0.00 39.30 3.36
57 58 2.703007 GGATGCTGACTACTGGAAGGAT 59.297 50.000 0.00 0.00 39.30 3.24
58 59 3.494048 GGATGCTGACTACTGGAAGGATG 60.494 52.174 0.00 0.00 39.30 3.51
59 60 1.208052 TGCTGACTACTGGAAGGATGC 59.792 52.381 0.00 0.00 39.30 3.91
60 61 1.804372 GCTGACTACTGGAAGGATGCG 60.804 57.143 0.00 0.00 39.30 4.73
61 62 0.824109 TGACTACTGGAAGGATGCGG 59.176 55.000 0.00 0.00 39.30 5.69
62 63 0.824759 GACTACTGGAAGGATGCGGT 59.175 55.000 0.00 0.00 39.30 5.68
63 64 0.824759 ACTACTGGAAGGATGCGGTC 59.175 55.000 0.00 0.00 39.30 4.79
64 65 1.115467 CTACTGGAAGGATGCGGTCT 58.885 55.000 0.00 0.00 39.30 3.85
65 66 0.824109 TACTGGAAGGATGCGGTCTG 59.176 55.000 0.00 0.00 39.30 3.51
66 67 1.194781 ACTGGAAGGATGCGGTCTGT 61.195 55.000 0.00 0.00 39.30 3.41
67 68 0.824109 CTGGAAGGATGCGGTCTGTA 59.176 55.000 0.00 0.00 0.00 2.74
68 69 0.824109 TGGAAGGATGCGGTCTGTAG 59.176 55.000 0.00 0.00 0.00 2.74
69 70 0.530870 GGAAGGATGCGGTCTGTAGC 60.531 60.000 0.00 0.00 0.00 3.58
78 79 3.949031 GGTCTGTAGCGAGATGGAC 57.051 57.895 0.00 0.00 0.00 4.02
79 80 1.394618 GGTCTGTAGCGAGATGGACT 58.605 55.000 0.00 0.00 0.00 3.85
80 81 1.335496 GGTCTGTAGCGAGATGGACTC 59.665 57.143 0.00 0.00 41.79 3.36
81 82 1.335496 GTCTGTAGCGAGATGGACTCC 59.665 57.143 0.00 0.00 42.18 3.85
82 83 1.064685 TCTGTAGCGAGATGGACTCCA 60.065 52.381 0.00 0.00 42.18 3.86
99 100 2.473070 TCCATCTTGGATAACGGGACA 58.527 47.619 0.00 0.00 42.67 4.02
100 101 3.045634 TCCATCTTGGATAACGGGACAT 58.954 45.455 0.00 0.00 42.67 3.06
101 102 3.141398 CCATCTTGGATAACGGGACATG 58.859 50.000 0.00 0.00 40.96 3.21
102 103 3.141398 CATCTTGGATAACGGGACATGG 58.859 50.000 0.00 0.00 0.00 3.66
103 104 1.488812 TCTTGGATAACGGGACATGGG 59.511 52.381 0.00 0.00 0.00 4.00
104 105 1.488812 CTTGGATAACGGGACATGGGA 59.511 52.381 0.00 0.00 0.00 4.37
105 106 1.128200 TGGATAACGGGACATGGGAG 58.872 55.000 0.00 0.00 0.00 4.30
106 107 1.343580 TGGATAACGGGACATGGGAGA 60.344 52.381 0.00 0.00 0.00 3.71
107 108 1.978580 GGATAACGGGACATGGGAGAT 59.021 52.381 0.00 0.00 0.00 2.75
108 109 2.028020 GGATAACGGGACATGGGAGATC 60.028 54.545 0.00 0.00 0.00 2.75
109 110 2.168458 TAACGGGACATGGGAGATCA 57.832 50.000 0.00 0.00 0.00 2.92
110 111 1.511613 AACGGGACATGGGAGATCAT 58.488 50.000 0.00 0.00 0.00 2.45
111 112 1.511613 ACGGGACATGGGAGATCATT 58.488 50.000 0.00 0.00 0.00 2.57
112 113 1.141657 ACGGGACATGGGAGATCATTG 59.858 52.381 0.00 0.00 0.00 2.82
113 114 1.417517 CGGGACATGGGAGATCATTGA 59.582 52.381 0.00 0.00 0.00 2.57
114 115 2.039480 CGGGACATGGGAGATCATTGAT 59.961 50.000 0.00 0.00 0.00 2.57
115 116 3.683802 GGGACATGGGAGATCATTGATC 58.316 50.000 17.26 17.26 39.17 2.92
116 117 3.332919 GGACATGGGAGATCATTGATCG 58.667 50.000 18.52 7.90 43.17 3.69
117 118 3.244353 GGACATGGGAGATCATTGATCGT 60.244 47.826 18.52 10.66 43.17 3.73
118 119 3.993081 GACATGGGAGATCATTGATCGTC 59.007 47.826 18.52 14.71 43.17 4.20
119 120 3.244353 ACATGGGAGATCATTGATCGTCC 60.244 47.826 23.37 23.37 43.17 4.79
120 121 2.682594 TGGGAGATCATTGATCGTCCT 58.317 47.619 26.70 12.63 43.17 3.85
121 122 3.041211 TGGGAGATCATTGATCGTCCTT 58.959 45.455 26.70 12.36 43.17 3.36
122 123 4.223144 TGGGAGATCATTGATCGTCCTTA 58.777 43.478 26.70 19.53 43.17 2.69
123 124 4.039245 TGGGAGATCATTGATCGTCCTTAC 59.961 45.833 26.70 18.34 43.17 2.34
127 128 3.880047 TCATTGATCGTCCTTACGGTT 57.120 42.857 0.00 0.00 44.12 4.44
128 129 3.517602 TCATTGATCGTCCTTACGGTTG 58.482 45.455 0.00 0.00 44.12 3.77
129 130 1.717194 TTGATCGTCCTTACGGTTGC 58.283 50.000 0.00 0.00 44.12 4.17
130 131 0.108520 TGATCGTCCTTACGGTTGCC 60.109 55.000 0.00 0.00 44.12 4.52
131 132 0.108520 GATCGTCCTTACGGTTGCCA 60.109 55.000 0.00 0.00 44.12 4.92
132 133 1.673626 GATCGTCCTTACGGTTGCCAA 60.674 52.381 0.00 0.00 44.12 4.52
133 134 1.864176 CGTCCTTACGGTTGCCAAC 59.136 57.895 0.00 0.00 45.50 3.77
151 152 2.760092 CAACCATTGGGATGTAAGTGGG 59.240 50.000 7.78 0.00 38.05 4.61
152 153 2.000048 ACCATTGGGATGTAAGTGGGT 59.000 47.619 7.78 0.00 38.05 4.51
153 154 2.291540 ACCATTGGGATGTAAGTGGGTG 60.292 50.000 7.78 0.00 38.05 4.61
154 155 2.291540 CCATTGGGATGTAAGTGGGTGT 60.292 50.000 0.00 0.00 35.59 4.16
155 156 3.430453 CATTGGGATGTAAGTGGGTGTT 58.570 45.455 0.00 0.00 0.00 3.32
156 157 2.871096 TGGGATGTAAGTGGGTGTTC 57.129 50.000 0.00 0.00 0.00 3.18
157 158 2.058705 TGGGATGTAAGTGGGTGTTCA 58.941 47.619 0.00 0.00 0.00 3.18
158 159 2.443632 TGGGATGTAAGTGGGTGTTCAA 59.556 45.455 0.00 0.00 0.00 2.69
159 160 3.081804 GGGATGTAAGTGGGTGTTCAAG 58.918 50.000 0.00 0.00 0.00 3.02
160 161 3.244770 GGGATGTAAGTGGGTGTTCAAGA 60.245 47.826 0.00 0.00 0.00 3.02
161 162 4.394729 GGATGTAAGTGGGTGTTCAAGAA 58.605 43.478 0.00 0.00 0.00 2.52
162 163 4.455877 GGATGTAAGTGGGTGTTCAAGAAG 59.544 45.833 0.00 0.00 0.00 2.85
163 164 4.764050 TGTAAGTGGGTGTTCAAGAAGA 57.236 40.909 0.00 0.00 0.00 2.87
164 165 5.105567 TGTAAGTGGGTGTTCAAGAAGAA 57.894 39.130 0.00 0.00 0.00 2.52
165 166 5.123227 TGTAAGTGGGTGTTCAAGAAGAAG 58.877 41.667 0.00 0.00 36.78 2.85
166 167 2.576615 AGTGGGTGTTCAAGAAGAAGC 58.423 47.619 0.00 0.00 36.78 3.86
167 168 2.173569 AGTGGGTGTTCAAGAAGAAGCT 59.826 45.455 0.00 0.00 36.78 3.74
168 169 2.952310 GTGGGTGTTCAAGAAGAAGCTT 59.048 45.455 0.00 0.00 36.78 3.74
169 170 4.134563 GTGGGTGTTCAAGAAGAAGCTTA 58.865 43.478 0.00 0.00 36.78 3.09
170 171 4.214332 GTGGGTGTTCAAGAAGAAGCTTAG 59.786 45.833 0.00 0.00 36.78 2.18
171 172 3.753797 GGGTGTTCAAGAAGAAGCTTAGG 59.246 47.826 0.00 0.00 36.78 2.69
172 173 3.189495 GGTGTTCAAGAAGAAGCTTAGGC 59.811 47.826 0.00 0.00 36.78 3.93
173 174 3.189495 GTGTTCAAGAAGAAGCTTAGGCC 59.811 47.826 0.00 0.00 36.78 5.19
174 175 2.750166 GTTCAAGAAGAAGCTTAGGCCC 59.250 50.000 0.00 0.00 36.78 5.80
175 176 1.066143 TCAAGAAGAAGCTTAGGCCCG 60.066 52.381 0.00 0.00 39.73 6.13
176 177 1.066143 CAAGAAGAAGCTTAGGCCCGA 60.066 52.381 0.00 0.00 39.73 5.14
177 178 1.501582 AGAAGAAGCTTAGGCCCGAT 58.498 50.000 0.00 0.00 39.73 4.18
178 179 1.139853 AGAAGAAGCTTAGGCCCGATG 59.860 52.381 0.00 0.00 39.73 3.84
179 180 0.181350 AAGAAGCTTAGGCCCGATGG 59.819 55.000 0.00 0.00 39.73 3.51
180 181 0.983378 AGAAGCTTAGGCCCGATGGT 60.983 55.000 0.00 0.00 39.73 3.55
181 182 0.756903 GAAGCTTAGGCCCGATGGTA 59.243 55.000 0.00 0.00 39.73 3.25
182 183 0.468648 AAGCTTAGGCCCGATGGTAC 59.531 55.000 0.00 0.00 39.73 3.34
183 184 0.398664 AGCTTAGGCCCGATGGTACT 60.399 55.000 0.00 0.00 39.73 2.73
184 185 0.249911 GCTTAGGCCCGATGGTACTG 60.250 60.000 0.00 0.00 0.00 2.74
185 186 1.120530 CTTAGGCCCGATGGTACTGT 58.879 55.000 0.00 0.00 0.00 3.55
186 187 1.485066 CTTAGGCCCGATGGTACTGTT 59.515 52.381 0.00 0.00 0.00 3.16
187 188 0.828022 TAGGCCCGATGGTACTGTTG 59.172 55.000 0.00 0.00 0.00 3.33
188 189 0.907704 AGGCCCGATGGTACTGTTGA 60.908 55.000 0.00 0.00 0.00 3.18
189 190 0.462047 GGCCCGATGGTACTGTTGAG 60.462 60.000 0.00 0.00 0.00 3.02
190 191 0.535335 GCCCGATGGTACTGTTGAGA 59.465 55.000 0.00 0.00 0.00 3.27
191 192 1.471676 GCCCGATGGTACTGTTGAGAG 60.472 57.143 0.00 0.00 0.00 3.20
192 193 1.137086 CCCGATGGTACTGTTGAGAGG 59.863 57.143 0.00 0.00 0.00 3.69
193 194 1.825474 CCGATGGTACTGTTGAGAGGT 59.175 52.381 0.00 0.00 0.00 3.85
194 195 2.417379 CCGATGGTACTGTTGAGAGGTG 60.417 54.545 0.00 0.00 0.00 4.00
195 196 2.231478 CGATGGTACTGTTGAGAGGTGT 59.769 50.000 0.00 0.00 0.00 4.16
196 197 3.306088 CGATGGTACTGTTGAGAGGTGTT 60.306 47.826 0.00 0.00 0.00 3.32
197 198 3.746045 TGGTACTGTTGAGAGGTGTTC 57.254 47.619 0.00 0.00 0.00 3.18
198 199 3.035363 TGGTACTGTTGAGAGGTGTTCA 58.965 45.455 0.00 0.00 0.00 3.18
199 200 3.452990 TGGTACTGTTGAGAGGTGTTCAA 59.547 43.478 0.00 0.00 32.44 2.69
200 201 4.058817 GGTACTGTTGAGAGGTGTTCAAG 58.941 47.826 0.00 0.00 35.39 3.02
201 202 4.202223 GGTACTGTTGAGAGGTGTTCAAGA 60.202 45.833 0.00 0.00 35.39 3.02
202 203 4.487714 ACTGTTGAGAGGTGTTCAAGAA 57.512 40.909 0.00 0.00 35.39 2.52
203 204 4.446371 ACTGTTGAGAGGTGTTCAAGAAG 58.554 43.478 0.00 0.00 35.39 2.85
204 205 4.162320 ACTGTTGAGAGGTGTTCAAGAAGA 59.838 41.667 5.22 0.00 35.39 2.87
205 206 5.097742 TGTTGAGAGGTGTTCAAGAAGAA 57.902 39.130 0.00 0.00 35.39 2.52
206 207 5.118990 TGTTGAGAGGTGTTCAAGAAGAAG 58.881 41.667 0.00 0.00 36.78 2.85
207 208 3.733337 TGAGAGGTGTTCAAGAAGAAGC 58.267 45.455 0.00 0.00 36.78 3.86
208 209 3.389329 TGAGAGGTGTTCAAGAAGAAGCT 59.611 43.478 0.00 0.00 36.78 3.74
209 210 4.141620 TGAGAGGTGTTCAAGAAGAAGCTT 60.142 41.667 0.00 0.00 36.78 3.74
210 211 5.070446 TGAGAGGTGTTCAAGAAGAAGCTTA 59.930 40.000 0.00 0.00 36.78 3.09
211 212 5.301555 AGAGGTGTTCAAGAAGAAGCTTAC 58.698 41.667 0.00 0.00 36.78 2.34
486 490 1.032014 CCAACCCAAGGTGACACTTG 58.968 55.000 5.39 7.95 45.71 3.16
506 681 4.762289 TGGCTTCTCTCCTTCCTAATTC 57.238 45.455 0.00 0.00 0.00 2.17
522 697 7.865347 TCCTAATTCCCTATCCCTCTACTAT 57.135 40.000 0.00 0.00 0.00 2.12
541 784 6.786967 ACTATAAAGAGAGCCGTTTCCTTA 57.213 37.500 0.00 0.00 0.00 2.69
544 787 4.828072 AAAGAGAGCCGTTTCCTTATCT 57.172 40.909 0.00 0.00 0.00 1.98
545 788 4.394439 AAGAGAGCCGTTTCCTTATCTC 57.606 45.455 0.00 0.00 34.69 2.75
546 789 2.696187 AGAGAGCCGTTTCCTTATCTCC 59.304 50.000 0.00 0.00 34.97 3.71
547 790 1.763545 AGAGCCGTTTCCTTATCTCCC 59.236 52.381 0.00 0.00 0.00 4.30
548 791 0.837940 AGCCGTTTCCTTATCTCCCC 59.162 55.000 0.00 0.00 0.00 4.81
549 792 0.532196 GCCGTTTCCTTATCTCCCCG 60.532 60.000 0.00 0.00 0.00 5.73
550 793 0.106149 CCGTTTCCTTATCTCCCCGG 59.894 60.000 0.00 0.00 0.00 5.73
551 794 0.106149 CGTTTCCTTATCTCCCCGGG 59.894 60.000 15.80 15.80 0.00 5.73
552 795 0.179026 GTTTCCTTATCTCCCCGGGC 60.179 60.000 17.73 0.00 0.00 6.13
553 796 1.350310 TTTCCTTATCTCCCCGGGCC 61.350 60.000 17.73 0.00 0.00 5.80
554 797 2.447765 CCTTATCTCCCCGGGCCA 60.448 66.667 17.73 1.73 0.00 5.36
555 798 2.076184 CCTTATCTCCCCGGGCCAA 61.076 63.158 17.73 1.32 0.00 4.52
556 799 1.427072 CCTTATCTCCCCGGGCCAAT 61.427 60.000 17.73 10.03 0.00 3.16
557 800 0.036875 CTTATCTCCCCGGGCCAATC 59.963 60.000 17.73 0.00 0.00 2.67
558 801 1.423794 TTATCTCCCCGGGCCAATCC 61.424 60.000 17.73 0.00 0.00 3.01
568 811 4.162690 GCCAATCCGAGGACGCCT 62.163 66.667 0.00 0.00 38.29 5.52
569 812 2.792947 GCCAATCCGAGGACGCCTA 61.793 63.158 0.00 0.00 38.29 3.93
570 813 2.050269 CCAATCCGAGGACGCCTAT 58.950 57.895 0.00 0.00 38.29 2.57
577 820 1.571919 CGAGGACGCCTATGAAAAGG 58.428 55.000 0.00 0.00 39.87 3.11
581 824 2.039879 AGGACGCCTATGAAAAGGTTGT 59.960 45.455 0.00 0.00 39.02 3.32
584 827 4.456566 GGACGCCTATGAAAAGGTTGTTTA 59.543 41.667 0.00 0.00 39.02 2.01
606 849 9.308318 GTTTAGATTTACAAAAAGGTTGCTTGA 57.692 29.630 0.00 0.00 0.00 3.02
613 856 6.582437 ACAAAAAGGTTGCTTGAATTTACG 57.418 33.333 0.00 0.00 0.00 3.18
641 884 6.075315 AGTTTGCTTGGATTTACTAAAGGGT 58.925 36.000 0.00 0.00 0.00 4.34
642 885 6.553476 AGTTTGCTTGGATTTACTAAAGGGTT 59.447 34.615 0.00 0.00 0.00 4.11
643 886 5.975693 TGCTTGGATTTACTAAAGGGTTG 57.024 39.130 0.00 0.00 0.00 3.77
644 887 4.219725 TGCTTGGATTTACTAAAGGGTTGC 59.780 41.667 0.00 0.00 0.00 4.17
645 888 4.462834 GCTTGGATTTACTAAAGGGTTGCT 59.537 41.667 0.00 0.00 0.00 3.91
646 889 5.047306 GCTTGGATTTACTAAAGGGTTGCTT 60.047 40.000 0.00 0.00 0.00 3.91
647 890 6.152154 GCTTGGATTTACTAAAGGGTTGCTTA 59.848 38.462 0.00 0.00 0.00 3.09
648 891 7.628580 GCTTGGATTTACTAAAGGGTTGCTTAG 60.629 40.741 0.00 0.00 0.00 2.18
649 892 7.023171 TGGATTTACTAAAGGGTTGCTTAGA 57.977 36.000 0.00 0.00 0.00 2.10
650 893 7.639378 TGGATTTACTAAAGGGTTGCTTAGAT 58.361 34.615 0.00 0.00 0.00 1.98
651 894 8.113462 TGGATTTACTAAAGGGTTGCTTAGATT 58.887 33.333 0.00 0.00 0.00 2.40
652 895 8.967918 GGATTTACTAAAGGGTTGCTTAGATTT 58.032 33.333 0.00 0.00 0.00 2.17
658 901 9.582648 ACTAAAGGGTTGCTTAGATTTAAGAAA 57.417 29.630 7.19 0.00 38.88 2.52
661 904 7.468141 AGGGTTGCTTAGATTTAAGAAAAGG 57.532 36.000 7.19 0.00 36.42 3.11
662 905 7.010771 AGGGTTGCTTAGATTTAAGAAAAGGT 58.989 34.615 7.19 0.00 36.42 3.50
663 906 7.509318 AGGGTTGCTTAGATTTAAGAAAAGGTT 59.491 33.333 7.19 0.00 36.42 3.50
664 907 7.598869 GGGTTGCTTAGATTTAAGAAAAGGTTG 59.401 37.037 7.19 0.00 36.42 3.77
665 908 8.141909 GGTTGCTTAGATTTAAGAAAAGGTTGT 58.858 33.333 7.19 0.00 36.42 3.32
666 909 9.529325 GTTGCTTAGATTTAAGAAAAGGTTGTT 57.471 29.630 7.19 0.00 36.42 2.83
764 1007 9.503399 TTTAGGATCCAGAAGAAGTAGTTTTTC 57.497 33.333 15.82 5.61 0.00 2.29
765 1008 7.323052 AGGATCCAGAAGAAGTAGTTTTTCT 57.677 36.000 15.82 9.69 36.49 2.52
766 1009 7.750655 AGGATCCAGAAGAAGTAGTTTTTCTT 58.249 34.615 15.82 0.00 45.05 2.52
767 1010 8.221251 AGGATCCAGAAGAAGTAGTTTTTCTTT 58.779 33.333 15.82 2.84 43.07 2.52
768 1011 8.293157 GGATCCAGAAGAAGTAGTTTTTCTTTG 58.707 37.037 12.24 7.96 43.07 2.77
769 1012 8.980481 ATCCAGAAGAAGTAGTTTTTCTTTGA 57.020 30.769 12.24 11.99 43.07 2.69
770 1013 8.980481 TCCAGAAGAAGTAGTTTTTCTTTGAT 57.020 30.769 12.24 0.00 43.07 2.57
771 1014 9.057089 TCCAGAAGAAGTAGTTTTTCTTTGATC 57.943 33.333 12.24 0.00 43.07 2.92
772 1015 8.293157 CCAGAAGAAGTAGTTTTTCTTTGATCC 58.707 37.037 12.24 0.00 43.07 3.36
773 1016 8.840321 CAGAAGAAGTAGTTTTTCTTTGATCCA 58.160 33.333 12.24 0.00 43.07 3.41
774 1017 9.579932 AGAAGAAGTAGTTTTTCTTTGATCCAT 57.420 29.630 9.69 0.00 43.07 3.41
809 1067 4.627035 TGCTGACATAACTCGATCTTGTTG 59.373 41.667 9.51 0.00 0.00 3.33
810 1068 4.493220 GCTGACATAACTCGATCTTGTTGC 60.493 45.833 9.51 1.44 0.00 4.17
811 1069 4.565022 TGACATAACTCGATCTTGTTGCA 58.435 39.130 9.51 0.00 0.00 4.08
812 1070 4.388773 TGACATAACTCGATCTTGTTGCAC 59.611 41.667 9.51 0.00 0.00 4.57
813 1071 4.569943 ACATAACTCGATCTTGTTGCACT 58.430 39.130 9.51 0.00 0.00 4.40
814 1072 5.720202 ACATAACTCGATCTTGTTGCACTA 58.280 37.500 9.51 0.00 0.00 2.74
815 1073 6.341316 ACATAACTCGATCTTGTTGCACTAT 58.659 36.000 9.51 0.00 0.00 2.12
816 1074 7.489160 ACATAACTCGATCTTGTTGCACTATA 58.511 34.615 9.51 0.00 0.00 1.31
817 1075 7.649705 ACATAACTCGATCTTGTTGCACTATAG 59.350 37.037 0.00 0.00 0.00 1.31
818 1076 4.938080 ACTCGATCTTGTTGCACTATAGG 58.062 43.478 4.43 0.00 0.00 2.57
819 1077 3.717707 TCGATCTTGTTGCACTATAGGC 58.282 45.455 4.43 5.55 0.00 3.93
820 1078 3.132111 TCGATCTTGTTGCACTATAGGCA 59.868 43.478 10.69 10.69 40.00 4.75
821 1079 3.492383 CGATCTTGTTGCACTATAGGCAG 59.508 47.826 13.38 5.42 43.05 4.85
822 1080 3.981071 TCTTGTTGCACTATAGGCAGT 57.019 42.857 13.38 0.00 43.05 4.40
823 1081 5.601662 GATCTTGTTGCACTATAGGCAGTA 58.398 41.667 13.38 6.66 43.05 2.74
953 1394 4.771114 TTTCAGAAGTTTCAGTGGGAGA 57.229 40.909 0.00 0.00 0.00 3.71
971 1412 3.091545 GAGATAGAGGCAGAGAGATGGG 58.908 54.545 0.00 0.00 0.00 4.00
975 1416 1.306825 AGGCAGAGAGATGGGTGCT 60.307 57.895 0.00 0.00 36.15 4.40
998 1439 0.250295 TTCAGTGTTTCTCTGGGCGG 60.250 55.000 0.00 0.00 34.15 6.13
1234 1675 0.467290 TGACAACTTTGTGCCCCCTC 60.467 55.000 0.00 0.00 42.43 4.30
1236 1677 0.755327 ACAACTTTGTGCCCCCTCAC 60.755 55.000 0.00 0.00 40.49 3.51
1366 1807 4.658063 TGTTATCTCCAAAACCATCCGTT 58.342 39.130 0.00 0.00 35.70 4.44
1830 2275 0.393537 AGCATCCCCAAGAAGCGAAG 60.394 55.000 0.00 0.00 44.02 3.79
1988 2574 2.708861 TCCCTACAGGTTGCTCTTTTGA 59.291 45.455 0.00 0.00 36.75 2.69
2330 5988 7.804600 CGTTGTTGATGATTTATGGGATACATG 59.195 37.037 0.00 0.00 40.82 3.21
2368 6338 2.452600 TCAGCTTTTCCCCAAGTGTT 57.547 45.000 0.00 0.00 0.00 3.32
2600 6585 1.886313 CGCTAGCCACCATCAGCAG 60.886 63.158 9.66 0.00 33.55 4.24
2683 6962 3.120792 TCGCTAGTGTCTTGTTTGTCAC 58.879 45.455 2.66 0.00 0.00 3.67
2790 7069 3.318313 ACTTGGTATGTATCCAGAGGGG 58.682 50.000 0.00 0.00 36.28 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.376518 AGCTTCTGAAATGGAACTGGGA 59.623 45.455 0.00 0.00 0.00 4.37
5 6 5.678107 GCATAAGCTTCTGAAATGGAACTGG 60.678 44.000 15.47 0.00 37.91 4.00
6 7 5.106038 TGCATAAGCTTCTGAAATGGAACTG 60.106 40.000 15.47 0.00 42.74 3.16
7 8 5.012239 TGCATAAGCTTCTGAAATGGAACT 58.988 37.500 15.47 0.00 42.74 3.01
8 9 5.314923 TGCATAAGCTTCTGAAATGGAAC 57.685 39.130 15.47 0.00 42.74 3.62
9 10 6.140303 GATGCATAAGCTTCTGAAATGGAA 57.860 37.500 15.47 0.00 40.64 3.53
10 11 5.762825 GATGCATAAGCTTCTGAAATGGA 57.237 39.130 15.47 9.17 40.64 3.41
30 31 2.964464 CCAGTAGTCAGCATCCAGAGAT 59.036 50.000 0.00 0.00 0.00 2.75
31 32 2.024941 TCCAGTAGTCAGCATCCAGAGA 60.025 50.000 0.00 0.00 0.00 3.10
32 33 2.382882 TCCAGTAGTCAGCATCCAGAG 58.617 52.381 0.00 0.00 0.00 3.35
33 34 2.532250 TCCAGTAGTCAGCATCCAGA 57.468 50.000 0.00 0.00 0.00 3.86
34 35 2.158986 CCTTCCAGTAGTCAGCATCCAG 60.159 54.545 0.00 0.00 0.00 3.86
35 36 1.833630 CCTTCCAGTAGTCAGCATCCA 59.166 52.381 0.00 0.00 0.00 3.41
36 37 2.111384 TCCTTCCAGTAGTCAGCATCC 58.889 52.381 0.00 0.00 0.00 3.51
37 38 3.726607 CATCCTTCCAGTAGTCAGCATC 58.273 50.000 0.00 0.00 0.00 3.91
38 39 2.158842 GCATCCTTCCAGTAGTCAGCAT 60.159 50.000 0.00 0.00 0.00 3.79
39 40 1.208052 GCATCCTTCCAGTAGTCAGCA 59.792 52.381 0.00 0.00 0.00 4.41
40 41 1.804372 CGCATCCTTCCAGTAGTCAGC 60.804 57.143 0.00 0.00 0.00 4.26
41 42 1.202463 CCGCATCCTTCCAGTAGTCAG 60.202 57.143 0.00 0.00 0.00 3.51
42 43 0.824109 CCGCATCCTTCCAGTAGTCA 59.176 55.000 0.00 0.00 0.00 3.41
43 44 0.824759 ACCGCATCCTTCCAGTAGTC 59.175 55.000 0.00 0.00 0.00 2.59
44 45 0.824759 GACCGCATCCTTCCAGTAGT 59.175 55.000 0.00 0.00 0.00 2.73
45 46 1.115467 AGACCGCATCCTTCCAGTAG 58.885 55.000 0.00 0.00 0.00 2.57
46 47 0.824109 CAGACCGCATCCTTCCAGTA 59.176 55.000 0.00 0.00 0.00 2.74
47 48 1.194781 ACAGACCGCATCCTTCCAGT 61.195 55.000 0.00 0.00 0.00 4.00
48 49 0.824109 TACAGACCGCATCCTTCCAG 59.176 55.000 0.00 0.00 0.00 3.86
49 50 0.824109 CTACAGACCGCATCCTTCCA 59.176 55.000 0.00 0.00 0.00 3.53
50 51 0.530870 GCTACAGACCGCATCCTTCC 60.531 60.000 0.00 0.00 0.00 3.46
51 52 0.872021 CGCTACAGACCGCATCCTTC 60.872 60.000 0.00 0.00 0.00 3.46
52 53 1.141881 CGCTACAGACCGCATCCTT 59.858 57.895 0.00 0.00 0.00 3.36
53 54 1.729470 CTCGCTACAGACCGCATCCT 61.729 60.000 0.00 0.00 0.00 3.24
54 55 1.299468 CTCGCTACAGACCGCATCC 60.299 63.158 0.00 0.00 0.00 3.51
55 56 0.312416 ATCTCGCTACAGACCGCATC 59.688 55.000 0.00 0.00 0.00 3.91
56 57 0.031314 CATCTCGCTACAGACCGCAT 59.969 55.000 0.00 0.00 0.00 4.73
57 58 1.433471 CATCTCGCTACAGACCGCA 59.567 57.895 0.00 0.00 0.00 5.69
58 59 1.299468 CCATCTCGCTACAGACCGC 60.299 63.158 0.00 0.00 0.00 5.68
59 60 0.029567 GTCCATCTCGCTACAGACCG 59.970 60.000 0.00 0.00 0.00 4.79
60 61 1.335496 GAGTCCATCTCGCTACAGACC 59.665 57.143 0.00 0.00 33.25 3.85
61 62 1.335496 GGAGTCCATCTCGCTACAGAC 59.665 57.143 3.60 0.00 43.60 3.51
62 63 1.064685 TGGAGTCCATCTCGCTACAGA 60.065 52.381 8.12 0.00 43.60 3.41
63 64 1.393603 TGGAGTCCATCTCGCTACAG 58.606 55.000 8.12 0.00 43.60 2.74
64 65 2.073252 ATGGAGTCCATCTCGCTACA 57.927 50.000 19.53 0.00 40.74 2.74
80 81 3.141398 CATGTCCCGTTATCCAAGATGG 58.859 50.000 0.00 0.00 39.43 3.51
81 82 3.141398 CCATGTCCCGTTATCCAAGATG 58.859 50.000 0.00 0.00 0.00 2.90
82 83 2.106511 CCCATGTCCCGTTATCCAAGAT 59.893 50.000 0.00 0.00 0.00 2.40
83 84 1.488812 CCCATGTCCCGTTATCCAAGA 59.511 52.381 0.00 0.00 0.00 3.02
84 85 1.488812 TCCCATGTCCCGTTATCCAAG 59.511 52.381 0.00 0.00 0.00 3.61
85 86 1.488812 CTCCCATGTCCCGTTATCCAA 59.511 52.381 0.00 0.00 0.00 3.53
86 87 1.128200 CTCCCATGTCCCGTTATCCA 58.872 55.000 0.00 0.00 0.00 3.41
87 88 1.420430 TCTCCCATGTCCCGTTATCC 58.580 55.000 0.00 0.00 0.00 2.59
88 89 2.632996 TGATCTCCCATGTCCCGTTATC 59.367 50.000 0.00 0.00 0.00 1.75
89 90 2.689658 TGATCTCCCATGTCCCGTTAT 58.310 47.619 0.00 0.00 0.00 1.89
90 91 2.168458 TGATCTCCCATGTCCCGTTA 57.832 50.000 0.00 0.00 0.00 3.18
91 92 1.511613 ATGATCTCCCATGTCCCGTT 58.488 50.000 0.00 0.00 0.00 4.44
92 93 1.141657 CAATGATCTCCCATGTCCCGT 59.858 52.381 0.00 0.00 0.00 5.28
93 94 1.417517 TCAATGATCTCCCATGTCCCG 59.582 52.381 0.00 0.00 0.00 5.14
94 95 3.683802 GATCAATGATCTCCCATGTCCC 58.316 50.000 15.48 0.00 36.27 4.46
95 96 3.244353 ACGATCAATGATCTCCCATGTCC 60.244 47.826 19.62 0.00 36.96 4.02
96 97 3.993081 GACGATCAATGATCTCCCATGTC 59.007 47.826 19.62 14.13 36.96 3.06
97 98 3.244353 GGACGATCAATGATCTCCCATGT 60.244 47.826 19.62 9.76 36.96 3.21
98 99 3.007723 AGGACGATCAATGATCTCCCATG 59.992 47.826 24.73 12.41 37.22 3.66
99 100 3.246301 AGGACGATCAATGATCTCCCAT 58.754 45.455 24.73 13.45 37.22 4.00
100 101 2.682594 AGGACGATCAATGATCTCCCA 58.317 47.619 24.73 0.00 37.22 4.37
101 102 3.760580 AAGGACGATCAATGATCTCCC 57.239 47.619 24.73 21.30 37.22 4.30
130 131 2.760092 CCCACTTACATCCCAATGGTTG 59.240 50.000 0.00 0.00 37.19 3.77
131 132 2.381961 ACCCACTTACATCCCAATGGTT 59.618 45.455 0.00 0.00 37.19 3.67
132 133 2.000048 ACCCACTTACATCCCAATGGT 59.000 47.619 0.00 0.00 37.19 3.55
133 134 2.291540 ACACCCACTTACATCCCAATGG 60.292 50.000 0.00 0.00 37.19 3.16
134 135 3.085952 ACACCCACTTACATCCCAATG 57.914 47.619 0.00 0.00 38.93 2.82
135 136 3.075283 TGAACACCCACTTACATCCCAAT 59.925 43.478 0.00 0.00 0.00 3.16
136 137 2.443632 TGAACACCCACTTACATCCCAA 59.556 45.455 0.00 0.00 0.00 4.12
137 138 2.058705 TGAACACCCACTTACATCCCA 58.941 47.619 0.00 0.00 0.00 4.37
138 139 2.871096 TGAACACCCACTTACATCCC 57.129 50.000 0.00 0.00 0.00 3.85
139 140 4.015872 TCTTGAACACCCACTTACATCC 57.984 45.455 0.00 0.00 0.00 3.51
140 141 5.305585 TCTTCTTGAACACCCACTTACATC 58.694 41.667 0.00 0.00 0.00 3.06
141 142 5.304686 TCTTCTTGAACACCCACTTACAT 57.695 39.130 0.00 0.00 0.00 2.29
142 143 4.764050 TCTTCTTGAACACCCACTTACA 57.236 40.909 0.00 0.00 0.00 2.41
143 144 4.023963 GCTTCTTCTTGAACACCCACTTAC 60.024 45.833 0.00 0.00 0.00 2.34
144 145 4.134563 GCTTCTTCTTGAACACCCACTTA 58.865 43.478 0.00 0.00 0.00 2.24
145 146 2.952310 GCTTCTTCTTGAACACCCACTT 59.048 45.455 0.00 0.00 0.00 3.16
146 147 2.173569 AGCTTCTTCTTGAACACCCACT 59.826 45.455 0.00 0.00 0.00 4.00
147 148 2.576615 AGCTTCTTCTTGAACACCCAC 58.423 47.619 0.00 0.00 0.00 4.61
148 149 3.297134 AAGCTTCTTCTTGAACACCCA 57.703 42.857 0.00 0.00 0.00 4.51
149 150 3.753797 CCTAAGCTTCTTCTTGAACACCC 59.246 47.826 0.00 0.00 0.00 4.61
150 151 3.189495 GCCTAAGCTTCTTCTTGAACACC 59.811 47.826 0.00 0.00 35.50 4.16
151 152 3.189495 GGCCTAAGCTTCTTCTTGAACAC 59.811 47.826 0.00 0.00 39.73 3.32
152 153 3.412386 GGCCTAAGCTTCTTCTTGAACA 58.588 45.455 0.00 0.00 39.73 3.18
153 154 2.750166 GGGCCTAAGCTTCTTCTTGAAC 59.250 50.000 0.00 0.00 39.73 3.18
154 155 2.615493 CGGGCCTAAGCTTCTTCTTGAA 60.615 50.000 0.00 0.00 39.73 2.69
155 156 1.066143 CGGGCCTAAGCTTCTTCTTGA 60.066 52.381 0.00 0.00 39.73 3.02
156 157 1.066143 TCGGGCCTAAGCTTCTTCTTG 60.066 52.381 0.00 0.00 39.73 3.02
157 158 1.276622 TCGGGCCTAAGCTTCTTCTT 58.723 50.000 0.00 0.00 39.73 2.52
158 159 1.139853 CATCGGGCCTAAGCTTCTTCT 59.860 52.381 0.00 0.00 39.73 2.85
159 160 1.587547 CATCGGGCCTAAGCTTCTTC 58.412 55.000 0.00 0.00 39.73 2.87
160 161 0.181350 CCATCGGGCCTAAGCTTCTT 59.819 55.000 0.00 0.00 39.73 2.52
161 162 0.983378 ACCATCGGGCCTAAGCTTCT 60.983 55.000 0.00 0.00 39.73 2.85
162 163 0.756903 TACCATCGGGCCTAAGCTTC 59.243 55.000 0.00 0.00 39.73 3.86
163 164 0.468648 GTACCATCGGGCCTAAGCTT 59.531 55.000 3.48 3.48 39.73 3.74
164 165 0.398664 AGTACCATCGGGCCTAAGCT 60.399 55.000 0.84 0.00 39.73 3.74
165 166 0.249911 CAGTACCATCGGGCCTAAGC 60.250 60.000 0.84 0.00 37.90 3.09
166 167 1.120530 ACAGTACCATCGGGCCTAAG 58.879 55.000 0.84 0.00 37.90 2.18
167 168 1.208535 CAACAGTACCATCGGGCCTAA 59.791 52.381 0.84 0.00 37.90 2.69
168 169 0.828022 CAACAGTACCATCGGGCCTA 59.172 55.000 0.84 0.00 37.90 3.93
169 170 0.907704 TCAACAGTACCATCGGGCCT 60.908 55.000 0.84 0.00 37.90 5.19
170 171 0.462047 CTCAACAGTACCATCGGGCC 60.462 60.000 0.00 0.00 37.90 5.80
171 172 0.535335 TCTCAACAGTACCATCGGGC 59.465 55.000 0.00 0.00 37.90 6.13
172 173 1.137086 CCTCTCAACAGTACCATCGGG 59.863 57.143 0.00 0.00 41.29 5.14
173 174 1.825474 ACCTCTCAACAGTACCATCGG 59.175 52.381 0.00 0.00 0.00 4.18
174 175 2.231478 ACACCTCTCAACAGTACCATCG 59.769 50.000 0.00 0.00 0.00 3.84
175 176 3.963428 ACACCTCTCAACAGTACCATC 57.037 47.619 0.00 0.00 0.00 3.51
176 177 3.646162 TGAACACCTCTCAACAGTACCAT 59.354 43.478 0.00 0.00 0.00 3.55
177 178 3.035363 TGAACACCTCTCAACAGTACCA 58.965 45.455 0.00 0.00 0.00 3.25
178 179 3.746045 TGAACACCTCTCAACAGTACC 57.254 47.619 0.00 0.00 0.00 3.34
179 180 4.945246 TCTTGAACACCTCTCAACAGTAC 58.055 43.478 0.00 0.00 0.00 2.73
180 181 5.362717 TCTTCTTGAACACCTCTCAACAGTA 59.637 40.000 0.00 0.00 0.00 2.74
181 182 4.162320 TCTTCTTGAACACCTCTCAACAGT 59.838 41.667 0.00 0.00 0.00 3.55
182 183 4.697514 TCTTCTTGAACACCTCTCAACAG 58.302 43.478 0.00 0.00 0.00 3.16
183 184 4.753516 TCTTCTTGAACACCTCTCAACA 57.246 40.909 0.00 0.00 0.00 3.33
184 185 4.024472 GCTTCTTCTTGAACACCTCTCAAC 60.024 45.833 0.00 0.00 0.00 3.18
185 186 4.130118 GCTTCTTCTTGAACACCTCTCAA 58.870 43.478 0.00 0.00 0.00 3.02
186 187 3.389329 AGCTTCTTCTTGAACACCTCTCA 59.611 43.478 0.00 0.00 0.00 3.27
187 188 4.001618 AGCTTCTTCTTGAACACCTCTC 57.998 45.455 0.00 0.00 0.00 3.20
188 189 4.429854 AAGCTTCTTCTTGAACACCTCT 57.570 40.909 0.00 0.00 0.00 3.69
189 190 4.150804 CGTAAGCTTCTTCTTGAACACCTC 59.849 45.833 0.00 0.00 0.00 3.85
190 191 4.058817 CGTAAGCTTCTTCTTGAACACCT 58.941 43.478 0.00 0.00 0.00 4.00
191 192 3.186613 CCGTAAGCTTCTTCTTGAACACC 59.813 47.826 0.00 0.00 0.00 4.16
192 193 3.364068 GCCGTAAGCTTCTTCTTGAACAC 60.364 47.826 0.00 0.00 38.99 3.32
193 194 2.806244 GCCGTAAGCTTCTTCTTGAACA 59.194 45.455 0.00 0.00 38.99 3.18
194 195 3.457198 GCCGTAAGCTTCTTCTTGAAC 57.543 47.619 0.00 0.00 38.99 3.18
253 254 1.284785 TCTTTAGGGCCACCAATGAGG 59.715 52.381 6.18 0.00 45.67 3.86
262 263 1.919654 TGCCTAACATCTTTAGGGCCA 59.080 47.619 6.18 0.57 41.38 5.36
486 490 3.181449 GGGAATTAGGAAGGAGAGAAGCC 60.181 52.174 0.00 0.00 0.00 4.35
506 681 6.831868 GCTCTCTTTATAGTAGAGGGATAGGG 59.168 46.154 14.75 0.00 41.82 3.53
522 697 5.163437 GGAGATAAGGAAACGGCTCTCTTTA 60.163 44.000 0.00 0.00 34.92 1.85
541 784 3.178611 GGATTGGCCCGGGGAGAT 61.179 66.667 25.28 6.61 0.00 2.75
551 794 2.100879 ATAGGCGTCCTCGGATTGGC 62.101 60.000 1.46 6.61 34.61 4.52
552 795 0.319900 CATAGGCGTCCTCGGATTGG 60.320 60.000 1.46 0.00 34.61 3.16
553 796 0.673985 TCATAGGCGTCCTCGGATTG 59.326 55.000 1.46 0.00 34.61 2.67
554 797 1.410004 TTCATAGGCGTCCTCGGATT 58.590 50.000 1.46 0.00 34.61 3.01
555 798 1.410004 TTTCATAGGCGTCCTCGGAT 58.590 50.000 1.46 0.00 34.61 4.18
556 799 1.136305 CTTTTCATAGGCGTCCTCGGA 59.864 52.381 1.46 0.00 34.61 4.55
557 800 1.571919 CTTTTCATAGGCGTCCTCGG 58.428 55.000 1.46 0.00 34.61 4.63
558 801 1.134788 ACCTTTTCATAGGCGTCCTCG 60.135 52.381 1.46 0.00 38.99 4.63
559 802 2.678336 CAACCTTTTCATAGGCGTCCTC 59.322 50.000 1.46 0.00 38.99 3.71
560 803 2.039879 ACAACCTTTTCATAGGCGTCCT 59.960 45.455 3.87 3.87 38.99 3.85
561 804 2.433436 ACAACCTTTTCATAGGCGTCC 58.567 47.619 0.00 0.00 38.99 4.79
562 805 4.499037 AAACAACCTTTTCATAGGCGTC 57.501 40.909 0.00 0.00 38.99 5.19
563 806 5.310451 TCTAAACAACCTTTTCATAGGCGT 58.690 37.500 0.00 0.00 38.99 5.68
564 807 5.873179 TCTAAACAACCTTTTCATAGGCG 57.127 39.130 0.00 0.00 38.99 5.52
565 808 9.569167 GTAAATCTAAACAACCTTTTCATAGGC 57.431 33.333 0.00 0.00 38.99 3.93
577 820 9.093970 AGCAACCTTTTTGTAAATCTAAACAAC 57.906 29.630 0.00 0.00 35.43 3.32
581 824 9.877178 TTCAAGCAACCTTTTTGTAAATCTAAA 57.123 25.926 0.00 0.00 0.00 1.85
584 827 8.962884 AATTCAAGCAACCTTTTTGTAAATCT 57.037 26.923 0.00 0.00 0.00 2.40
592 835 7.835634 TTTCGTAAATTCAAGCAACCTTTTT 57.164 28.000 0.00 0.00 0.00 1.94
596 839 6.144078 ACTTTTCGTAAATTCAAGCAACCT 57.856 33.333 0.00 0.00 0.00 3.50
606 849 8.432110 AAATCCAAGCAAACTTTTCGTAAATT 57.568 26.923 0.00 0.00 32.29 1.82
612 855 8.568732 TTTAGTAAATCCAAGCAAACTTTTCG 57.431 30.769 0.00 0.00 32.29 3.46
613 856 8.978539 CCTTTAGTAAATCCAAGCAAACTTTTC 58.021 33.333 0.00 0.00 32.29 2.29
738 981 9.503399 GAAAAACTACTTCTTCTGGATCCTAAA 57.497 33.333 14.23 6.27 0.00 1.85
739 982 8.881262 AGAAAAACTACTTCTTCTGGATCCTAA 58.119 33.333 14.23 6.62 28.46 2.69
740 983 8.437274 AGAAAAACTACTTCTTCTGGATCCTA 57.563 34.615 14.23 0.00 28.46 2.94
741 984 7.323052 AGAAAAACTACTTCTTCTGGATCCT 57.677 36.000 14.23 0.00 28.46 3.24
742 985 7.987750 AAGAAAAACTACTTCTTCTGGATCC 57.012 36.000 4.20 4.20 38.47 3.36
743 986 9.057089 TCAAAGAAAAACTACTTCTTCTGGATC 57.943 33.333 0.00 0.00 41.24 3.36
744 987 8.980481 TCAAAGAAAAACTACTTCTTCTGGAT 57.020 30.769 0.00 0.00 41.24 3.41
745 988 8.980481 ATCAAAGAAAAACTACTTCTTCTGGA 57.020 30.769 0.00 0.00 41.24 3.86
746 989 8.293157 GGATCAAAGAAAAACTACTTCTTCTGG 58.707 37.037 0.00 0.00 41.24 3.86
747 990 8.840321 TGGATCAAAGAAAAACTACTTCTTCTG 58.160 33.333 0.00 1.50 41.24 3.02
748 991 8.980481 TGGATCAAAGAAAAACTACTTCTTCT 57.020 30.769 0.00 0.00 41.24 2.85
763 1006 9.803507 AGCATCAAATAAGATATGGATCAAAGA 57.196 29.630 0.00 0.00 34.17 2.52
764 1007 9.841880 CAGCATCAAATAAGATATGGATCAAAG 57.158 33.333 0.00 0.00 34.17 2.77
765 1008 9.577222 TCAGCATCAAATAAGATATGGATCAAA 57.423 29.630 0.00 0.00 34.17 2.69
766 1009 9.006839 GTCAGCATCAAATAAGATATGGATCAA 57.993 33.333 0.00 0.00 34.17 2.57
767 1010 8.158789 TGTCAGCATCAAATAAGATATGGATCA 58.841 33.333 0.00 0.00 34.17 2.92
768 1011 8.557592 TGTCAGCATCAAATAAGATATGGATC 57.442 34.615 0.00 0.00 0.00 3.36
774 1017 9.196552 CGAGTTATGTCAGCATCAAATAAGATA 57.803 33.333 0.00 0.00 36.58 1.98
775 1018 7.928167 TCGAGTTATGTCAGCATCAAATAAGAT 59.072 33.333 0.00 0.00 36.58 2.40
776 1019 7.264947 TCGAGTTATGTCAGCATCAAATAAGA 58.735 34.615 0.00 0.00 36.58 2.10
777 1020 7.468922 TCGAGTTATGTCAGCATCAAATAAG 57.531 36.000 0.00 0.00 36.58 1.73
778 1021 7.928167 AGATCGAGTTATGTCAGCATCAAATAA 59.072 33.333 0.00 0.00 36.58 1.40
779 1022 7.436933 AGATCGAGTTATGTCAGCATCAAATA 58.563 34.615 0.00 0.00 36.58 1.40
780 1023 6.286758 AGATCGAGTTATGTCAGCATCAAAT 58.713 36.000 0.00 0.00 36.58 2.32
781 1024 5.664457 AGATCGAGTTATGTCAGCATCAAA 58.336 37.500 0.00 0.00 36.58 2.69
939 1380 2.769095 GCCTCTATCTCCCACTGAAACT 59.231 50.000 0.00 0.00 0.00 2.66
953 1394 2.607499 CACCCATCTCTCTGCCTCTAT 58.393 52.381 0.00 0.00 0.00 1.98
971 1412 4.212214 CCAGAGAAACACTGAAACTAGCAC 59.788 45.833 0.00 0.00 37.54 4.40
975 1416 3.740115 GCCCAGAGAAACACTGAAACTA 58.260 45.455 0.00 0.00 37.54 2.24
998 1439 3.914426 TCTTAAGAAGGGGTCTCATGC 57.086 47.619 1.68 0.00 34.56 4.06
1234 1675 2.839486 TTGTAGCCAAGAGACTGGTG 57.161 50.000 0.00 0.00 38.86 4.17
1236 1677 4.761739 TCAAATTTGTAGCCAAGAGACTGG 59.238 41.667 17.47 0.00 39.71 4.00
1366 1807 4.220382 CCTGGGAGCACAAATTACATCAAA 59.780 41.667 0.00 0.00 0.00 2.69
1830 2275 1.800586 TGTGAAGTTCATCAGAAGCGC 59.199 47.619 9.18 0.00 33.63 5.92
2330 5988 5.709164 AGCTGATTAATAACATCCCATGCTC 59.291 40.000 0.00 0.00 0.00 4.26
2368 6338 7.665559 AGTTGTTATTATTCTGCTTCCTTGACA 59.334 33.333 0.00 0.00 0.00 3.58
2477 6447 3.623510 GCCGAAGAATAAGTTCCTTGAGG 59.376 47.826 0.00 0.00 34.81 3.86
2487 6457 4.351192 CAAAAATCCCGCCGAAGAATAAG 58.649 43.478 0.00 0.00 0.00 1.73
2488 6458 3.129638 CCAAAAATCCCGCCGAAGAATAA 59.870 43.478 0.00 0.00 0.00 1.40
2496 6466 2.181525 CAGCCAAAAATCCCGCCG 59.818 61.111 0.00 0.00 0.00 6.46
2500 6470 3.069443 TCACTTTCACAGCCAAAAATCCC 59.931 43.478 0.00 0.00 0.00 3.85
2619 6604 5.391312 AATCCACTGATACAAAAGGCAAC 57.609 39.130 0.00 0.00 0.00 4.17
2620 6605 7.716799 ATAAATCCACTGATACAAAAGGCAA 57.283 32.000 0.00 0.00 0.00 4.52
2683 6962 6.494842 TCGTTCTTTCTGAAGTTGAATTTGG 58.505 36.000 0.00 0.00 35.01 3.28


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

AutoCloner maintained by Alex Coulton.