Multiple sequence alignment - TraesCS3B01G430900

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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 TraesCS3B01G430900 chr3B 100.000 6413 0 0 1 6413 669917039 669923451 0.000000e+00 11843.0
1 TraesCS3B01G430900 chr3B 93.046 604 31 10 1 593 789178564 789179167 0.000000e+00 872.0
2 TraesCS3B01G430900 chr3B 92.484 612 34 7 1 611 480337285 480336685 0.000000e+00 865.0
3 TraesCS3B01G430900 chr3B 91.993 612 44 4 1 611 828078886 828079493 0.000000e+00 854.0
4 TraesCS3B01G430900 chr3B 92.771 83 6 0 598 680 669766169 669766251 3.140000e-23 121.0
5 TraesCS3B01G430900 chr3A 93.980 3588 150 34 591 4155 645557797 645561341 0.000000e+00 5369.0
6 TraesCS3B01G430900 chr3A 94.857 1011 43 5 4500 5509 645561814 645562816 0.000000e+00 1570.0
7 TraesCS3B01G430900 chr3A 85.752 379 33 8 6043 6413 645563073 645563438 1.300000e-101 381.0
8 TraesCS3B01G430900 chr3A 90.722 194 16 1 4304 4497 645561588 645561779 2.290000e-64 257.0
9 TraesCS3B01G430900 chr3D 93.853 3579 134 27 598 4155 508055911 508059424 0.000000e+00 5312.0
10 TraesCS3B01G430900 chr3D 96.647 1014 34 0 4495 5508 508059721 508060734 0.000000e+00 1685.0
11 TraesCS3B01G430900 chr3D 89.972 359 31 3 5653 6009 590228738 590229093 5.860000e-125 459.0
12 TraesCS3B01G430900 chr3D 87.332 371 41 4 5643 6009 206057951 206057583 2.760000e-113 420.0
13 TraesCS3B01G430900 chr3D 88.169 355 38 4 5656 6009 590228348 590228699 2.760000e-113 420.0
14 TraesCS3B01G430900 chr3D 90.842 273 23 2 4226 4497 508059420 508059691 1.310000e-96 364.0
15 TraesCS3B01G430900 chr3D 90.244 82 4 3 4149 4229 395058038 395058116 3.160000e-18 104.0
16 TraesCS3B01G430900 chr5A 91.724 1015 51 9 1008 2006 398262861 398261864 0.000000e+00 1378.0
17 TraesCS3B01G430900 chr5A 85.517 145 18 2 3905 4049 162029982 162029841 1.440000e-31 148.0
18 TraesCS3B01G430900 chr5A 88.506 87 7 3 4146 4231 308461605 308461689 1.140000e-17 102.0
19 TraesCS3B01G430900 chr4A 90.345 1015 65 12 1008 2006 331464463 331465460 0.000000e+00 1301.0
20 TraesCS3B01G430900 chr4A 90.588 85 2 2 4150 4229 733665194 733665111 2.440000e-19 108.0
21 TraesCS3B01G430900 chr1B 93.434 594 35 3 1 593 575893754 575893164 0.000000e+00 878.0
22 TraesCS3B01G430900 chr2A 92.496 613 39 5 1 611 721915312 721914705 0.000000e+00 870.0
23 TraesCS3B01G430900 chr2A 84.397 141 20 2 3738 3877 260844024 260843885 3.120000e-28 137.0
24 TraesCS3B01G430900 chr6B 93.121 596 36 4 1 593 230768799 230769392 0.000000e+00 869.0
25 TraesCS3B01G430900 chrUn 92.977 598 32 8 1 593 48575597 48576189 0.000000e+00 863.0
26 TraesCS3B01G430900 chrUn 92.703 603 34 9 1 593 3215766 3216368 0.000000e+00 861.0
27 TraesCS3B01G430900 chr5B 93.109 595 31 5 1 593 217271863 217272449 0.000000e+00 863.0
28 TraesCS3B01G430900 chr5B 90.808 359 30 3 5653 6009 7316292 7316649 1.620000e-130 477.0
29 TraesCS3B01G430900 chr5B 88.022 359 35 8 5656 6012 531936977 531936625 9.940000e-113 418.0
30 TraesCS3B01G430900 chr5B 89.855 69 7 0 3809 3877 173246611 173246679 8.860000e-14 89.8
31 TraesCS3B01G430900 chr4D 88.889 351 34 3 5662 6009 484939305 484939653 1.650000e-115 427.0
32 TraesCS3B01G430900 chr4D 87.023 131 15 2 3738 3867 126505022 126505151 5.180000e-31 147.0
33 TraesCS3B01G430900 chr4D 83.465 127 18 2 3751 3877 194084084 194083961 1.460000e-21 115.0
34 TraesCS3B01G430900 chr7A 88.473 347 38 2 5653 5998 674358095 674358440 9.940000e-113 418.0
35 TraesCS3B01G430900 chr7A 83.916 143 20 2 3907 4049 310800720 310800581 4.030000e-27 134.0
36 TraesCS3B01G430900 chr7A 89.535 86 1 3 4153 4230 20293272 20293357 1.140000e-17 102.0
37 TraesCS3B01G430900 chr7A 84.466 103 6 4 4140 4232 705218010 705217908 6.850000e-15 93.5
38 TraesCS3B01G430900 chr5D 88.539 349 35 5 5652 5998 384197850 384197505 9.940000e-113 418.0
39 TraesCS3B01G430900 chr5D 84.138 145 20 2 3905 4049 423357898 423357757 3.120000e-28 137.0
40 TraesCS3B01G430900 chr5D 84.314 102 7 4 4149 4244 277244588 277244686 2.460000e-14 91.6
41 TraesCS3B01G430900 chr2D 87.228 368 41 6 5647 6012 8142374 8142737 1.290000e-111 414.0
42 TraesCS3B01G430900 chr6D 86.207 145 17 2 3905 4049 326409914 326409773 3.100000e-33 154.0
43 TraesCS3B01G430900 chr6D 91.566 83 1 2 4153 4230 26738821 26738740 6.800000e-20 110.0
44 TraesCS3B01G430900 chr6A 85.517 145 18 2 3905 4049 265779870 265779729 1.440000e-31 148.0
45 TraesCS3B01G430900 chr1D 85.517 145 18 2 3905 4049 42091896 42092037 1.440000e-31 148.0
46 TraesCS3B01G430900 chr7D 86.719 128 16 1 3750 3877 46355989 46355863 2.410000e-29 141.0
47 TraesCS3B01G430900 chr7D 89.535 86 1 3 4153 4230 20238976 20239061 1.140000e-17 102.0
48 TraesCS3B01G430900 chr7D 87.368 95 3 5 4144 4229 423531858 423531764 4.090000e-17 100.0
49 TraesCS3B01G430900 chr1A 84.722 144 19 2 3905 4048 560190095 560189955 2.410000e-29 141.0
50 TraesCS3B01G430900 chr1A 84.615 143 16 6 3738 3877 335997464 335997603 3.120000e-28 137.0


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 TraesCS3B01G430900 chr3B 669917039 669923451 6412 False 11843.000000 11843 100.000000 1 6413 1 chr3B.!!$F2 6412
1 TraesCS3B01G430900 chr3B 789178564 789179167 603 False 872.000000 872 93.046000 1 593 1 chr3B.!!$F3 592
2 TraesCS3B01G430900 chr3B 480336685 480337285 600 True 865.000000 865 92.484000 1 611 1 chr3B.!!$R1 610
3 TraesCS3B01G430900 chr3B 828078886 828079493 607 False 854.000000 854 91.993000 1 611 1 chr3B.!!$F4 610
4 TraesCS3B01G430900 chr3A 645557797 645563438 5641 False 1894.250000 5369 91.327750 591 6413 4 chr3A.!!$F1 5822
5 TraesCS3B01G430900 chr3D 508055911 508060734 4823 False 2453.666667 5312 93.780667 598 5508 3 chr3D.!!$F2 4910
6 TraesCS3B01G430900 chr3D 590228348 590229093 745 False 439.500000 459 89.070500 5653 6009 2 chr3D.!!$F3 356
7 TraesCS3B01G430900 chr5A 398261864 398262861 997 True 1378.000000 1378 91.724000 1008 2006 1 chr5A.!!$R2 998
8 TraesCS3B01G430900 chr4A 331464463 331465460 997 False 1301.000000 1301 90.345000 1008 2006 1 chr4A.!!$F1 998
9 TraesCS3B01G430900 chr1B 575893164 575893754 590 True 878.000000 878 93.434000 1 593 1 chr1B.!!$R1 592
10 TraesCS3B01G430900 chr2A 721914705 721915312 607 True 870.000000 870 92.496000 1 611 1 chr2A.!!$R2 610
11 TraesCS3B01G430900 chr6B 230768799 230769392 593 False 869.000000 869 93.121000 1 593 1 chr6B.!!$F1 592
12 TraesCS3B01G430900 chrUn 48575597 48576189 592 False 863.000000 863 92.977000 1 593 1 chrUn.!!$F2 592
13 TraesCS3B01G430900 chrUn 3215766 3216368 602 False 861.000000 861 92.703000 1 593 1 chrUn.!!$F1 592
14 TraesCS3B01G430900 chr5B 217271863 217272449 586 False 863.000000 863 93.109000 1 593 1 chr5B.!!$F3 592

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
331 337 0.333312 AGAGAGCGAGAGAAAGGGGA 59.667 55.000 0.00 0.0 0.0 4.81 F
348 374 0.560688 GGAGGGGGAGACAGAGAGAT 59.439 60.000 0.00 0.0 0.0 2.75 F
1949 2028 1.068333 CCAATTGTTGAAGAGGCCACG 60.068 52.381 5.01 0.0 0.0 4.94 F
2575 2654 1.400494 GCTTTGTCGTGTCCTTTGTGT 59.600 47.619 0.00 0.0 0.0 3.72 F
3462 3552 0.741221 CTTCGTAGTTCCCTGCCTGC 60.741 60.000 0.00 0.0 0.0 4.85 F
3573 3663 1.329292 CGCGTGAAAGAACTGAAACCA 59.671 47.619 0.00 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2125 0.752658 AACCTCCAAGCAAAACTGCC 59.247 50.000 0.00 0.0 34.90 4.85 R
2098 2177 4.765339 GCAGGAAAGGTACCAGTACAAAAT 59.235 41.667 15.94 0.0 37.78 1.82 R
3447 3537 1.379642 GCATGCAGGCAGGGAACTAC 61.380 60.000 20.11 0.0 40.21 2.73 R
3497 3587 1.549203 CAGGTAAGGTTGCTGCCATT 58.451 50.000 0.00 0.0 0.00 3.16 R
5105 5417 0.539438 TCGCCAGGCCAATCTTGTTT 60.539 50.000 5.01 0.0 0.00 2.83 R
5509 5821 1.968540 GCTTGCGCCACCTCTCTTT 60.969 57.895 4.18 0.0 0.00 2.52 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
158 160 9.796120 AAGCAAACTTATAATTTATAGCGCAAA 57.204 25.926 11.47 1.09 33.13 3.68
214 220 8.650143 ATTGCAAATAAATACCCCACTATAGG 57.350 34.615 1.71 0.00 0.00 2.57
284 290 1.698506 ATGTCGCAGGGGAAAACAAA 58.301 45.000 0.00 0.00 0.00 2.83
314 320 4.497173 CTCATCGCGAGAATGAGAGAAAGA 60.497 45.833 26.49 0.00 45.45 2.52
328 334 3.443681 AGAGAAAGAGAGCGAGAGAAAGG 59.556 47.826 0.00 0.00 0.00 3.11
330 336 1.190643 AAGAGAGCGAGAGAAAGGGG 58.809 55.000 0.00 0.00 0.00 4.79
331 337 0.333312 AGAGAGCGAGAGAAAGGGGA 59.667 55.000 0.00 0.00 0.00 4.81
332 338 0.744281 GAGAGCGAGAGAAAGGGGAG 59.256 60.000 0.00 0.00 0.00 4.30
333 339 0.686112 AGAGCGAGAGAAAGGGGAGG 60.686 60.000 0.00 0.00 0.00 4.30
340 366 0.983905 GAGAAAGGGGAGGGGGAGAC 60.984 65.000 0.00 0.00 0.00 3.36
348 374 0.560688 GGAGGGGGAGACAGAGAGAT 59.439 60.000 0.00 0.00 0.00 2.75
384 413 1.285373 AGAGGGAGAGAGACGCCTTAA 59.715 52.381 0.00 0.00 38.52 1.85
492 522 3.181497 GCAACACAAATATGATGCCTCGT 60.181 43.478 0.00 0.00 32.22 4.18
521 551 4.917906 AAGGAGATGGACCTATTATGGC 57.082 45.455 0.00 0.00 36.67 4.40
593 626 1.358759 CAACGCACGGGCTCTTTTT 59.641 52.632 8.62 0.00 38.10 1.94
755 789 3.692406 GACCGGAGCAACGAGGGT 61.692 66.667 9.46 0.00 35.47 4.34
1026 1064 1.302431 CACACCCGTCTGATGCCAA 60.302 57.895 0.00 0.00 0.00 4.52
1216 1254 2.363795 TCCGACTCCGCCATCCTT 60.364 61.111 0.00 0.00 0.00 3.36
1882 1945 5.360714 CCTTCAACAGGTATATTTGTGCCAT 59.639 40.000 0.00 0.00 37.99 4.40
1885 1948 5.356751 TCAACAGGTATATTTGTGCCATGTC 59.643 40.000 0.00 0.00 0.00 3.06
1887 1950 5.509498 ACAGGTATATTTGTGCCATGTCTT 58.491 37.500 0.00 0.00 0.00 3.01
1888 1951 5.590259 ACAGGTATATTTGTGCCATGTCTTC 59.410 40.000 0.00 0.00 0.00 2.87
1925 2004 7.321153 TCCTAGCAGTAAATCTGTAAACTGTC 58.679 38.462 3.55 0.00 45.23 3.51
1940 2019 2.571212 ACTGTCGAGCCAATTGTTGAA 58.429 42.857 4.43 0.00 0.00 2.69
1949 2028 1.068333 CCAATTGTTGAAGAGGCCACG 60.068 52.381 5.01 0.00 0.00 4.94
2046 2125 4.751098 CCAAGTGACCCAATTGTTCAATTG 59.249 41.667 25.70 25.70 37.68 2.32
2089 2168 6.557568 TCAACAACAATAGGGTAAAGGGAAT 58.442 36.000 0.00 0.00 0.00 3.01
2132 2211 4.071961 ACCTTTCCTGCATTTGGTTTTC 57.928 40.909 0.00 0.00 0.00 2.29
2134 2213 4.898861 ACCTTTCCTGCATTTGGTTTTCTA 59.101 37.500 0.00 0.00 0.00 2.10
2441 2520 7.025963 GTGTCATTCCTTGATTGCTTCTTAAG 58.974 38.462 0.00 0.00 36.54 1.85
2483 2562 1.699083 TCACTCATGTCCTGCCTTTGA 59.301 47.619 0.00 0.00 0.00 2.69
2484 2563 2.106338 TCACTCATGTCCTGCCTTTGAA 59.894 45.455 0.00 0.00 0.00 2.69
2485 2564 2.227388 CACTCATGTCCTGCCTTTGAAC 59.773 50.000 0.00 0.00 0.00 3.18
2486 2565 2.158623 ACTCATGTCCTGCCTTTGAACA 60.159 45.455 0.00 0.00 0.00 3.18
2487 2566 2.886523 CTCATGTCCTGCCTTTGAACAA 59.113 45.455 0.00 0.00 0.00 2.83
2488 2567 3.295093 TCATGTCCTGCCTTTGAACAAA 58.705 40.909 0.00 0.17 0.00 2.83
2489 2568 3.896888 TCATGTCCTGCCTTTGAACAAAT 59.103 39.130 0.44 0.00 0.00 2.32
2490 2569 4.344679 TCATGTCCTGCCTTTGAACAAATT 59.655 37.500 0.44 0.00 0.00 1.82
2491 2570 4.751767 TGTCCTGCCTTTGAACAAATTT 57.248 36.364 0.44 0.00 0.00 1.82
2492 2571 5.096443 TGTCCTGCCTTTGAACAAATTTT 57.904 34.783 0.44 0.00 0.00 1.82
2493 2572 5.495640 TGTCCTGCCTTTGAACAAATTTTT 58.504 33.333 0.44 0.00 0.00 1.94
2575 2654 1.400494 GCTTTGTCGTGTCCTTTGTGT 59.600 47.619 0.00 0.00 0.00 3.72
2578 2657 3.530265 TTGTCGTGTCCTTTGTGTAGT 57.470 42.857 0.00 0.00 0.00 2.73
2585 2664 4.384846 CGTGTCCTTTGTGTAGTACATGTC 59.615 45.833 0.00 0.00 39.48 3.06
2592 2671 6.650807 CCTTTGTGTAGTACATGTCACTGAAT 59.349 38.462 0.00 0.00 39.48 2.57
2688 2771 2.257207 TGTTCTGTAGGACTTGAGGGG 58.743 52.381 0.00 0.00 0.00 4.79
2740 2823 5.410746 TGCAGCTAGATCTAAATATGCAAGC 59.589 40.000 20.08 17.67 39.29 4.01
2780 2863 5.954296 ATGTCTGGTTTGAACTGAAGATG 57.046 39.130 0.00 0.00 0.00 2.90
2797 2880 6.759272 TGAAGATGTAGAGTGCTACTTGTTT 58.241 36.000 0.00 0.00 45.79 2.83
2821 2904 8.685838 TTCTCTCCTAATTCTAGAAGCTCTAC 57.314 38.462 11.53 0.00 0.00 2.59
2830 2913 7.719871 ATTCTAGAAGCTCTACTGTTTGGTA 57.280 36.000 11.53 0.00 0.00 3.25
2910 2994 3.071479 TCAGCTCCAAATTTGTACGTCC 58.929 45.455 16.73 0.00 0.00 4.79
2940 3024 9.478019 CGTAAAGATTAAAGCTGTTTCATGTAG 57.522 33.333 0.00 0.00 0.00 2.74
2942 3026 6.442513 AGATTAAAGCTGTTTCATGTAGCC 57.557 37.500 0.00 0.00 38.18 3.93
3037 3122 9.202273 CTTATGATCTATTAGCCACTTTGTCTC 57.798 37.037 0.00 0.00 0.00 3.36
3078 3163 9.566530 TGGTGAAATGACAAAACATATATTTCG 57.433 29.630 0.00 0.00 37.35 3.46
3079 3164 9.019764 GGTGAAATGACAAAACATATATTTCGG 57.980 33.333 0.00 0.00 37.35 4.30
3231 3316 4.924462 GGTACTTACTCTGTTTGACTGAGC 59.076 45.833 12.90 0.00 44.79 4.26
3332 3417 5.255397 TGTAGGGTGATTCAAAGGTCATT 57.745 39.130 0.00 0.00 0.00 2.57
3377 3462 2.715046 TCAAAGTCCATTGCTAGGCTG 58.285 47.619 0.00 0.00 0.00 4.85
3411 3496 2.167487 GGTGTTCAGGCAAGTTTTGGAA 59.833 45.455 0.00 0.00 0.00 3.53
3447 3537 8.285776 ACAATTTTTGTATGCTTCTTTCTTCG 57.714 30.769 0.00 0.00 43.27 3.79
3459 3549 2.028385 TCTTTCTTCGTAGTTCCCTGCC 60.028 50.000 0.00 0.00 0.00 4.85
3460 3550 1.640917 TTCTTCGTAGTTCCCTGCCT 58.359 50.000 0.00 0.00 0.00 4.75
3461 3551 0.895530 TCTTCGTAGTTCCCTGCCTG 59.104 55.000 0.00 0.00 0.00 4.85
3462 3552 0.741221 CTTCGTAGTTCCCTGCCTGC 60.741 60.000 0.00 0.00 0.00 4.85
3573 3663 1.329292 CGCGTGAAAGAACTGAAACCA 59.671 47.619 0.00 0.00 0.00 3.67
3624 3714 8.095452 AGGTAATAATTCACACCTGAGAATCT 57.905 34.615 4.45 0.00 39.93 2.40
3703 3794 8.862325 TTGTGACTGTAGTGGATTCATATTTT 57.138 30.769 0.00 0.00 0.00 1.82
3739 3832 9.964303 TGGTTGCATAATATATAAAAGTGCTTG 57.036 29.630 11.50 0.00 32.67 4.01
3740 3833 9.410556 GGTTGCATAATATATAAAAGTGCTTGG 57.589 33.333 11.50 0.00 32.67 3.61
3741 3834 9.965824 GTTGCATAATATATAAAAGTGCTTGGT 57.034 29.630 11.50 0.00 32.67 3.67
3742 3835 9.964303 TTGCATAATATATAAAAGTGCTTGGTG 57.036 29.630 11.50 0.00 32.67 4.17
3743 3836 9.130661 TGCATAATATATAAAAGTGCTTGGTGT 57.869 29.630 11.50 0.00 32.67 4.16
3759 3853 3.417101 TGGTGTAATGGTGTTGTCATCC 58.583 45.455 0.00 0.00 0.00 3.51
3771 3865 3.327464 TGTTGTCATCCCTCTCACATTCA 59.673 43.478 0.00 0.00 0.00 2.57
3786 3880 6.149973 TCTCACATTCAAGCCTTTTATCACTG 59.850 38.462 0.00 0.00 0.00 3.66
3880 3981 1.683441 CCCACCCCTACACTTGTCC 59.317 63.158 0.00 0.00 0.00 4.02
3888 3989 2.092914 CCCTACACTTGTCCTTGGATCC 60.093 54.545 4.20 4.20 0.00 3.36
3985 4087 2.318908 TGATTTCTTTTGTGCAGGGCT 58.681 42.857 0.00 0.00 0.00 5.19
4127 4229 1.442857 GGAGCTGTGACACTCGACG 60.443 63.158 7.20 0.00 33.55 5.12
4143 4248 4.022589 ACTCGACGAGGACAAATAGTTCAA 60.023 41.667 27.39 0.00 33.35 2.69
4155 4260 9.269453 GGACAAATAGTTCAAGTACAAAGTACT 57.731 33.333 4.09 4.09 0.00 2.73
4157 4262 9.269453 ACAAATAGTTCAAGTACAAAGTACTCC 57.731 33.333 9.98 0.77 0.00 3.85
4158 4263 8.718734 CAAATAGTTCAAGTACAAAGTACTCCC 58.281 37.037 9.98 0.48 0.00 4.30
4159 4264 7.793948 ATAGTTCAAGTACAAAGTACTCCCT 57.206 36.000 9.98 6.72 0.00 4.20
4160 4265 6.099159 AGTTCAAGTACAAAGTACTCCCTC 57.901 41.667 9.98 3.39 0.00 4.30
4161 4266 5.839606 AGTTCAAGTACAAAGTACTCCCTCT 59.160 40.000 9.98 5.23 0.00 3.69
4162 4267 5.723672 TCAAGTACAAAGTACTCCCTCTG 57.276 43.478 9.98 5.26 0.00 3.35
4163 4268 5.145564 TCAAGTACAAAGTACTCCCTCTGT 58.854 41.667 9.98 0.00 0.00 3.41
4164 4269 6.309357 TCAAGTACAAAGTACTCCCTCTGTA 58.691 40.000 9.98 0.00 0.00 2.74
4165 4270 6.779049 TCAAGTACAAAGTACTCCCTCTGTAA 59.221 38.462 9.98 0.00 0.00 2.41
4166 4271 7.288389 TCAAGTACAAAGTACTCCCTCTGTAAA 59.712 37.037 9.98 0.00 0.00 2.01
4167 4272 6.990798 AGTACAAAGTACTCCCTCTGTAAAC 58.009 40.000 4.09 0.00 0.00 2.01
4168 4273 6.781507 AGTACAAAGTACTCCCTCTGTAAACT 59.218 38.462 4.09 0.00 0.00 2.66
4169 4274 7.946776 AGTACAAAGTACTCCCTCTGTAAACTA 59.053 37.037 4.09 0.00 0.00 2.24
4170 4275 7.607615 ACAAAGTACTCCCTCTGTAAACTAA 57.392 36.000 0.00 0.00 0.00 2.24
4171 4276 8.203681 ACAAAGTACTCCCTCTGTAAACTAAT 57.796 34.615 0.00 0.00 0.00 1.73
4172 4277 9.317827 ACAAAGTACTCCCTCTGTAAACTAATA 57.682 33.333 0.00 0.00 0.00 0.98
4225 4330 9.543231 TCTAAAAGATCTTAGTTTACAGAGGGA 57.457 33.333 8.75 0.00 31.86 4.20
4226 4331 9.810545 CTAAAAGATCTTAGTTTACAGAGGGAG 57.189 37.037 8.75 0.00 0.00 4.30
4227 4332 7.800300 AAAGATCTTAGTTTACAGAGGGAGT 57.200 36.000 8.75 0.00 0.00 3.85
4228 4333 8.896722 AAAGATCTTAGTTTACAGAGGGAGTA 57.103 34.615 8.75 0.00 0.00 2.59
4229 4334 7.885009 AGATCTTAGTTTACAGAGGGAGTAC 57.115 40.000 0.00 0.00 0.00 2.73
4245 4350 4.262617 GGAGTACAAGGGAATGGTCTTTC 58.737 47.826 0.00 0.00 0.00 2.62
4255 4360 7.425224 AGGGAATGGTCTTTCGGATATATAG 57.575 40.000 0.00 0.00 0.00 1.31
4347 4625 8.738645 AATTAAGAAGGTATTGCTTAGTGGAG 57.261 34.615 0.00 0.00 0.00 3.86
4378 4657 7.550551 TGCAGTTAAACATCATTTTGAAAACCA 59.449 29.630 0.00 0.00 0.00 3.67
4380 4659 8.055402 CAGTTAAACATCATTTTGAAAACCACG 58.945 33.333 0.00 0.00 0.00 4.94
4409 4688 8.458575 TCCATTACCTGGTATATACTGTCCTTA 58.541 37.037 7.50 0.00 46.08 2.69
4414 4693 8.562949 ACCTGGTATATACTGTCCTTATGTTT 57.437 34.615 12.54 0.00 0.00 2.83
4435 4714 6.617879 GTTTAGCATCGACCTAAACCATTTT 58.382 36.000 25.52 0.00 44.28 1.82
4441 4720 5.890424 TCGACCTAAACCATTTTCCATTC 57.110 39.130 0.00 0.00 0.00 2.67
4443 4722 5.646360 TCGACCTAAACCATTTTCCATTCTC 59.354 40.000 0.00 0.00 0.00 2.87
4490 4769 2.367894 TGTGCATCATTGGCCTTTTTGA 59.632 40.909 3.32 1.89 0.00 2.69
4497 4776 6.406849 GCATCATTGGCCTTTTTGACCTAATA 60.407 38.462 3.32 0.00 0.00 0.98
4561 4872 9.520515 ACTACTTTTTGATGAATTGACTATGGT 57.479 29.630 0.00 0.00 0.00 3.55
4615 4926 4.460034 TGCAGTACATCGGTGTTCTTAGTA 59.540 41.667 6.64 0.00 39.77 1.82
4678 4989 9.599322 GCACATAGCATATTTATTGTTCTGTAC 57.401 33.333 0.00 0.00 44.79 2.90
4708 5019 8.407832 TGTACATCATGATTGGATAAAAGCAAG 58.592 33.333 5.16 0.00 0.00 4.01
4722 5033 3.715628 AAGCAAGGTAAGTTTGTGCAG 57.284 42.857 0.00 0.00 37.68 4.41
4748 5059 7.935338 TTTCTACTACCGTCAACTACAAAAG 57.065 36.000 0.00 0.00 0.00 2.27
4749 5060 5.464168 TCTACTACCGTCAACTACAAAAGC 58.536 41.667 0.00 0.00 0.00 3.51
4821 5133 6.245408 TGCCACCTGATATTTTTCTACTGTT 58.755 36.000 0.00 0.00 0.00 3.16
4968 5280 6.544197 TGTAGTTCAGGTGTTTTAAGATTGCA 59.456 34.615 0.00 0.00 0.00 4.08
4984 5296 3.781079 TTGCAACTGTTCAAACCTCAG 57.219 42.857 0.00 0.00 35.60 3.35
5443 5755 1.980765 AGTCTCATTGCCTCTCACCAA 59.019 47.619 0.00 0.00 0.00 3.67
5509 5821 0.538584 TGCCACACCATGCACAAAAA 59.461 45.000 0.00 0.00 31.31 1.94
5557 5899 6.610075 ATTCTGTGGTTAAGAATGGCAATT 57.390 33.333 0.00 0.00 41.67 2.32
5573 5915 6.252967 TGGCAATTTGTGTGTCATACTTAG 57.747 37.500 1.16 0.00 0.00 2.18
5588 5930 2.718563 ACTTAGTGGCCCGTATTTTGG 58.281 47.619 0.00 0.00 0.00 3.28
5596 5938 1.463674 CCCGTATTTTGGCAGCTTCT 58.536 50.000 0.00 0.00 0.00 2.85
5601 5943 3.684788 CGTATTTTGGCAGCTTCTAGTGT 59.315 43.478 0.00 0.00 0.00 3.55
5614 5956 1.427753 TCTAGTGTGGTGAGTCAGGGA 59.572 52.381 0.00 0.00 0.00 4.20
5647 5990 5.043356 ACCCCTTTCCTTTCCAATATAGCTT 60.043 40.000 0.00 0.00 0.00 3.74
5650 5993 6.488344 CCCTTTCCTTTCCAATATAGCTTCTC 59.512 42.308 0.00 0.00 0.00 2.87
5652 5995 5.215252 TCCTTTCCAATATAGCTTCTCGG 57.785 43.478 0.00 0.00 0.00 4.63
5654 5997 5.544176 TCCTTTCCAATATAGCTTCTCGGAT 59.456 40.000 0.00 0.00 0.00 4.18
5655 5998 6.724441 TCCTTTCCAATATAGCTTCTCGGATA 59.276 38.462 0.00 0.00 0.00 2.59
5656 5999 7.038659 CCTTTCCAATATAGCTTCTCGGATAG 58.961 42.308 0.00 0.00 0.00 2.08
5681 6024 0.469705 TTTTGGCACATGGGAGCACT 60.470 50.000 0.00 0.00 39.30 4.40
5682 6025 0.469705 TTTGGCACATGGGAGCACTT 60.470 50.000 0.00 0.00 39.30 3.16
5684 6027 1.604593 GGCACATGGGAGCACTTGT 60.605 57.895 0.00 0.00 31.64 3.16
5690 6033 1.067295 ATGGGAGCACTTGTTCCTGA 58.933 50.000 11.44 0.47 43.85 3.86
5699 6042 7.154656 GGAGCACTTGTTCCTGATTTTTAAAT 58.845 34.615 4.93 0.00 41.53 1.40
5701 6044 8.962884 AGCACTTGTTCCTGATTTTTAAATTT 57.037 26.923 0.00 0.00 0.00 1.82
5752 6095 7.559835 AAAAATTTCAAACAAAAACTTGGCG 57.440 28.000 0.00 0.00 0.00 5.69
5757 6100 2.785713 AACAAAAACTTGGCGCGTAT 57.214 40.000 8.43 0.00 0.00 3.06
5760 6103 3.753842 ACAAAAACTTGGCGCGTATATG 58.246 40.909 8.43 0.00 0.00 1.78
5769 6112 4.619437 TGGCGCGTATATGTCGATATTA 57.381 40.909 8.43 0.00 0.00 0.98
5792 6135 4.717233 ACATGCTCACAAAGTTGTTTCA 57.283 36.364 0.00 0.00 39.91 2.69
5793 6136 4.423732 ACATGCTCACAAAGTTGTTTCAC 58.576 39.130 0.00 0.00 39.91 3.18
5804 6147 3.750512 AGTTGTTTCACGAAAAACCGAC 58.249 40.909 12.52 11.22 38.16 4.79
5807 6150 3.490399 TGTTTCACGAAAAACCGACAAC 58.510 40.909 12.52 0.00 38.16 3.32
5811 6154 4.519191 TCACGAAAAACCGACAACTTAC 57.481 40.909 0.00 0.00 0.00 2.34
5817 6160 2.582728 AACCGACAACTTACGTGTCA 57.417 45.000 0.00 0.00 33.20 3.58
5833 6176 3.413558 GTGTCACGTGTGAAAAAGACAC 58.586 45.455 16.51 15.32 45.79 3.67
5889 6234 9.139174 CACATTCTTTTGTCTTTTTACACAAGT 57.861 29.630 0.00 0.00 38.02 3.16
5945 6290 4.681483 CGTGCACACATATAATGTCGAGAT 59.319 41.667 18.64 0.00 42.70 2.75
5958 6303 3.780902 TGTCGAGATGTATGCGTCAAAT 58.219 40.909 5.77 0.00 33.18 2.32
5959 6304 4.180817 TGTCGAGATGTATGCGTCAAATT 58.819 39.130 5.77 0.00 33.18 1.82
5963 6308 7.148557 TGTCGAGATGTATGCGTCAAATTTTTA 60.149 33.333 5.77 0.00 33.18 1.52
5968 6313 9.086336 AGATGTATGCGTCAAATTTTTATTTGG 57.914 29.630 5.77 0.00 40.79 3.28
6002 6347 9.828852 TCGCACTTTAAAATATATTTTTCGTGT 57.171 25.926 24.53 16.21 40.24 4.49
6003 6348 9.865642 CGCACTTTAAAATATATTTTTCGTGTG 57.134 29.630 24.53 25.07 40.24 3.82
6004 6349 9.670180 GCACTTTAAAATATATTTTTCGTGTGC 57.330 29.630 28.97 28.97 40.06 4.57
6014 6359 1.165907 TTTCGTGTGCAGGAAGCCAG 61.166 55.000 7.27 0.00 44.83 4.85
6018 6363 1.826385 GTGTGCAGGAAGCCAGTATT 58.174 50.000 0.00 0.00 44.83 1.89
6038 6383 6.830324 AGTATTGGTCATGTTTCAGTATGCAT 59.170 34.615 3.79 3.79 34.76 3.96
6039 6384 5.981088 TTGGTCATGTTTCAGTATGCATT 57.019 34.783 3.54 0.00 34.76 3.56
6040 6385 7.643569 ATTGGTCATGTTTCAGTATGCATTA 57.356 32.000 3.54 0.00 34.76 1.90
6042 6387 5.589855 TGGTCATGTTTCAGTATGCATTAGG 59.410 40.000 3.54 0.00 34.76 2.69
6045 6390 6.488006 GTCATGTTTCAGTATGCATTAGGGAT 59.512 38.462 3.54 0.00 34.76 3.85
6046 6391 6.487668 TCATGTTTCAGTATGCATTAGGGATG 59.512 38.462 3.54 0.00 38.85 3.51
6049 6394 6.487668 TGTTTCAGTATGCATTAGGGATGATG 59.512 38.462 3.54 0.00 37.49 3.07
6050 6395 5.830799 TCAGTATGCATTAGGGATGATGT 57.169 39.130 3.54 0.00 37.49 3.06
6051 6396 5.554070 TCAGTATGCATTAGGGATGATGTG 58.446 41.667 3.54 0.00 37.49 3.21
6053 6398 4.598807 AGTATGCATTAGGGATGATGTGGA 59.401 41.667 3.54 0.00 38.03 4.02
6054 6399 3.497103 TGCATTAGGGATGATGTGGAG 57.503 47.619 0.00 0.00 38.03 3.86
6055 6400 2.157738 GCATTAGGGATGATGTGGAGC 58.842 52.381 0.00 0.00 38.03 4.70
6056 6401 2.487805 GCATTAGGGATGATGTGGAGCA 60.488 50.000 0.00 0.00 38.03 4.26
6057 6402 3.824133 CATTAGGGATGATGTGGAGCAA 58.176 45.455 0.00 0.00 38.03 3.91
6068 6430 2.517959 TGTGGAGCAAGGGAGATTTTG 58.482 47.619 0.00 0.00 0.00 2.44
6074 6436 5.418840 TGGAGCAAGGGAGATTTTGTATTTC 59.581 40.000 0.00 0.00 0.00 2.17
6078 6440 7.966812 AGCAAGGGAGATTTTGTATTTCTTTT 58.033 30.769 0.00 0.00 0.00 2.27
6122 6484 6.000219 TGCCTCATCCATTAATTAAGAGAGC 59.000 40.000 11.18 12.03 0.00 4.09
6167 6537 8.197439 AGAAAAGGTCTCCAAACAAAATACAAG 58.803 33.333 0.00 0.00 0.00 3.16
6170 6540 6.365520 AGGTCTCCAAACAAAATACAAGAGT 58.634 36.000 0.00 0.00 0.00 3.24
6197 6567 6.887376 TTACTCTCTCGACATTATTTGTGC 57.113 37.500 0.00 0.00 39.18 4.57
6202 6572 5.041951 TCTCGACATTATTTGTGCCAAAC 57.958 39.130 2.96 0.00 39.18 2.93
6213 6583 1.153549 TGCCAAACGTTTTGCACCC 60.154 52.632 29.54 7.85 34.40 4.61
6214 6584 2.234335 GCCAAACGTTTTGCACCCG 61.234 57.895 26.80 8.47 0.00 5.28
6255 6625 4.785301 CTTCCTTCTTGATGCCCTCAATA 58.215 43.478 0.00 0.00 42.87 1.90
6269 6639 1.949525 CTCAATAAGGATTGCCCGTGG 59.050 52.381 0.00 0.00 42.01 4.94
6270 6640 1.283613 TCAATAAGGATTGCCCGTGGT 59.716 47.619 0.00 0.00 42.01 4.16
6271 6641 1.405105 CAATAAGGATTGCCCGTGGTG 59.595 52.381 0.00 0.00 40.87 4.17
6272 6642 0.106719 ATAAGGATTGCCCGTGGTGG 60.107 55.000 0.00 0.00 40.87 4.61
6289 6659 4.012895 GCGTGGTGCGGACTTGTG 62.013 66.667 7.11 0.00 41.69 3.33
6294 6664 1.593209 GGTGCGGACTTGTGACGAA 60.593 57.895 7.11 0.00 0.00 3.85
6296 6666 0.865769 GTGCGGACTTGTGACGAAAT 59.134 50.000 0.00 0.00 0.00 2.17
6309 6679 4.279671 TGTGACGAAATACCCTTGCATTTT 59.720 37.500 0.00 0.00 0.00 1.82
6345 6715 2.623416 GGTCCAACTTATAAGCATGGCC 59.377 50.000 23.72 22.58 36.67 5.36
6352 6722 6.463331 CCAACTTATAAGCATGGCCATTGATT 60.463 38.462 17.92 18.16 32.00 2.57
6369 6739 6.183360 CCATTGATTCCATGGCACTTCTATTT 60.183 38.462 6.96 0.00 0.00 1.40
6396 6766 1.737838 TGGCTTCGGACATGTTGATC 58.262 50.000 0.00 0.00 0.00 2.92
6398 6768 1.678728 GGCTTCGGACATGTTGATCCA 60.679 52.381 0.00 0.00 34.35 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
314 320 0.686112 CCTCCCCTTTCTCTCGCTCT 60.686 60.000 0.00 0.00 0.00 4.09
328 334 1.075600 CTCTCTGTCTCCCCCTCCC 60.076 68.421 0.00 0.00 0.00 4.30
330 336 1.703411 CATCTCTCTGTCTCCCCCTC 58.297 60.000 0.00 0.00 0.00 4.30
331 337 0.264359 CCATCTCTCTGTCTCCCCCT 59.736 60.000 0.00 0.00 0.00 4.79
332 338 0.263172 TCCATCTCTCTGTCTCCCCC 59.737 60.000 0.00 0.00 0.00 5.40
333 339 1.216678 TCTCCATCTCTCTGTCTCCCC 59.783 57.143 0.00 0.00 0.00 4.81
340 366 1.498576 TCCTCCCTCTCCATCTCTCTG 59.501 57.143 0.00 0.00 0.00 3.35
348 374 1.221635 CTCTCTCTCCTCCCTCTCCA 58.778 60.000 0.00 0.00 0.00 3.86
421 451 0.605319 GATGGCCTCGGTGTTGACAA 60.605 55.000 3.32 0.00 0.00 3.18
521 551 5.505173 AACTCAACAACCATCACTCAAAG 57.495 39.130 0.00 0.00 0.00 2.77
596 629 9.914834 TGCATGGGAGTACTTTATTTTAACTAT 57.085 29.630 0.00 0.00 0.00 2.12
850 885 4.270376 GGGATTGCGCGGATTGGC 62.270 66.667 8.83 0.00 0.00 4.52
879 914 0.533755 GGGATTCGGTGATCTGCAGG 60.534 60.000 15.13 0.00 0.00 4.85
954 989 2.597510 GAGTGGGGTGGTTGGTGC 60.598 66.667 0.00 0.00 0.00 5.01
955 990 2.281484 CGAGTGGGGTGGTTGGTG 60.281 66.667 0.00 0.00 0.00 4.17
956 991 2.770904 ACGAGTGGGGTGGTTGGT 60.771 61.111 0.00 0.00 0.00 3.67
1240 1278 3.599285 GAACCCCCGCACGATGTCA 62.599 63.158 0.00 0.00 0.00 3.58
1690 1746 4.023193 ACAACAATTGCCTTCCTAAGAACG 60.023 41.667 5.05 0.00 0.00 3.95
1885 1948 3.769844 TGCTAGGAGTGTCTTAAGGGAAG 59.230 47.826 1.85 0.00 36.38 3.46
1887 1950 3.245658 ACTGCTAGGAGTGTCTTAAGGGA 60.246 47.826 17.00 0.00 0.00 4.20
1888 1951 3.100671 ACTGCTAGGAGTGTCTTAAGGG 58.899 50.000 17.00 0.00 0.00 3.95
1925 2004 1.135575 GCCTCTTCAACAATTGGCTCG 60.136 52.381 10.83 0.00 37.58 5.03
1940 2019 3.199946 TCAGAATATTTTCCGTGGCCTCT 59.800 43.478 3.32 0.00 31.84 3.69
1949 2028 6.278363 AGCATTGCATGTCAGAATATTTTCC 58.722 36.000 11.91 0.00 31.84 3.13
2046 2125 0.752658 AACCTCCAAGCAAAACTGCC 59.247 50.000 0.00 0.00 34.90 4.85
2098 2177 4.765339 GCAGGAAAGGTACCAGTACAAAAT 59.235 41.667 15.94 0.00 37.78 1.82
2113 2192 6.986231 ACTTTAGAAAACCAAATGCAGGAAAG 59.014 34.615 0.00 0.00 0.00 2.62
2132 2211 9.965824 ACAATGTTACAAAATTCAGGACTTTAG 57.034 29.630 0.00 0.00 0.00 1.85
2134 2213 9.965824 CTACAATGTTACAAAATTCAGGACTTT 57.034 29.630 0.00 0.00 0.00 2.66
2344 2423 9.504708 TTTGCAAAAATATCATGAACCAGATTT 57.495 25.926 10.02 0.00 0.00 2.17
2441 2520 7.064728 AGTGAAGAACTTGACAGTAAAGTGTTC 59.935 37.037 3.82 10.62 37.90 3.18
2514 2593 6.119536 ACCGATGGATGCTTCACTAAAAATA 58.880 36.000 1.64 0.00 0.00 1.40
2535 2614 2.481449 GCCATACAGACCTTCAGTACCG 60.481 54.545 0.00 0.00 0.00 4.02
2688 2771 4.242336 AGGTCAGGAATTCCATCTTTCC 57.758 45.455 26.22 17.13 41.46 3.13
2780 2863 5.184287 AGGAGAGAAACAAGTAGCACTCTAC 59.816 44.000 0.00 0.00 44.27 2.59
2797 2880 7.936847 CAGTAGAGCTTCTAGAATTAGGAGAGA 59.063 40.741 5.44 0.00 34.84 3.10
2830 2913 8.839310 AGTGAGCGCTTGAATAGATATAATTT 57.161 30.769 13.26 0.00 0.00 1.82
2910 2994 7.526608 TGAAACAGCTTTAATCTTTACGGATG 58.473 34.615 0.00 0.00 0.00 3.51
3332 3417 5.249622 TCGGGTTCCATTAGCATCCATAATA 59.750 40.000 0.00 0.00 0.00 0.98
3426 3516 8.149973 ACTACGAAGAAAGAAGCATACAAAAA 57.850 30.769 0.00 0.00 0.00 1.94
3447 3537 1.379642 GCATGCAGGCAGGGAACTAC 61.380 60.000 20.11 0.00 40.21 2.73
3459 3549 4.190001 AGACAGAAGAATAGTGCATGCAG 58.810 43.478 23.41 7.71 0.00 4.41
3460 3550 4.212143 AGACAGAAGAATAGTGCATGCA 57.788 40.909 18.46 18.46 0.00 3.96
3461 3551 6.857777 ATTAGACAGAAGAATAGTGCATGC 57.142 37.500 11.82 11.82 0.00 4.06
3497 3587 1.549203 CAGGTAAGGTTGCTGCCATT 58.451 50.000 0.00 0.00 0.00 3.16
3573 3663 8.043113 TCATTTATTACTGTCAATGCAGTCTCT 58.957 33.333 12.21 3.91 45.63 3.10
3624 3714 7.148440 CCAAAAAGTGAAGAAAATTGCACAGAA 60.148 33.333 0.00 0.00 33.85 3.02
3676 3767 9.466497 AAATATGAATCCACTACAGTCACAAAT 57.534 29.630 0.00 0.00 0.00 2.32
3725 3818 7.396055 ACACCATTACACCAAGCACTTTTATAT 59.604 33.333 0.00 0.00 0.00 0.86
3734 3827 2.621055 GACAACACCATTACACCAAGCA 59.379 45.455 0.00 0.00 0.00 3.91
3738 3831 3.417101 GGATGACAACACCATTACACCA 58.583 45.455 0.00 0.00 0.00 4.17
3739 3832 2.752903 GGGATGACAACACCATTACACC 59.247 50.000 0.00 0.00 0.00 4.16
3740 3833 3.686016 AGGGATGACAACACCATTACAC 58.314 45.455 0.00 0.00 0.00 2.90
3741 3834 3.587061 AGAGGGATGACAACACCATTACA 59.413 43.478 0.00 0.00 0.00 2.41
3742 3835 4.192317 GAGAGGGATGACAACACCATTAC 58.808 47.826 0.00 0.00 0.00 1.89
3743 3836 3.843619 TGAGAGGGATGACAACACCATTA 59.156 43.478 0.00 0.00 0.00 1.90
3744 3837 2.644299 TGAGAGGGATGACAACACCATT 59.356 45.455 0.00 0.00 0.00 3.16
3745 3838 2.026822 GTGAGAGGGATGACAACACCAT 60.027 50.000 0.00 0.00 0.00 3.55
3759 3853 5.649395 TGATAAAAGGCTTGAATGTGAGAGG 59.351 40.000 0.00 0.00 0.00 3.69
3771 3865 7.448469 ACACTATTTGACAGTGATAAAAGGCTT 59.552 33.333 9.33 0.00 45.10 4.35
3880 3981 4.408921 TGTATGTACCAGAAGGGATCCAAG 59.591 45.833 15.23 0.00 41.15 3.61
3888 3989 3.118261 AGTGGCATGTATGTACCAGAAGG 60.118 47.826 0.00 0.00 42.21 3.46
3978 4080 2.039405 CACTGCTGAGAAGCCCTGC 61.039 63.158 0.00 0.00 0.00 4.85
3985 4087 3.969287 AGCATAAGTCACTGCTGAGAA 57.031 42.857 0.00 0.00 46.55 2.87
4127 4229 8.379457 ACTTTGTACTTGAACTATTTGTCCTC 57.621 34.615 0.00 0.00 0.00 3.71
4143 4248 6.781507 AGTTTACAGAGGGAGTACTTTGTACT 59.218 38.462 9.77 9.77 37.66 2.73
4199 4304 9.543231 TCCCTCTGTAAACTAAGATCTTTTAGA 57.457 33.333 14.36 4.35 35.20 2.10
4200 4305 9.810545 CTCCCTCTGTAAACTAAGATCTTTTAG 57.189 37.037 14.36 8.49 36.83 1.85
4201 4306 9.322769 ACTCCCTCTGTAAACTAAGATCTTTTA 57.677 33.333 14.36 3.63 0.00 1.52
4202 4307 8.208575 ACTCCCTCTGTAAACTAAGATCTTTT 57.791 34.615 14.36 4.67 0.00 2.27
4203 4308 7.800300 ACTCCCTCTGTAAACTAAGATCTTT 57.200 36.000 14.36 0.00 0.00 2.52
4204 4309 7.894364 TGTACTCCCTCTGTAAACTAAGATCTT 59.106 37.037 13.56 13.56 0.00 2.40
4205 4310 7.411808 TGTACTCCCTCTGTAAACTAAGATCT 58.588 38.462 0.00 0.00 0.00 2.75
4206 4311 7.642082 TGTACTCCCTCTGTAAACTAAGATC 57.358 40.000 0.00 0.00 0.00 2.75
4207 4312 7.124448 CCTTGTACTCCCTCTGTAAACTAAGAT 59.876 40.741 0.00 0.00 0.00 2.40
4208 4313 6.436532 CCTTGTACTCCCTCTGTAAACTAAGA 59.563 42.308 0.00 0.00 0.00 2.10
4209 4314 6.351117 CCCTTGTACTCCCTCTGTAAACTAAG 60.351 46.154 0.00 0.00 0.00 2.18
4210 4315 5.482878 CCCTTGTACTCCCTCTGTAAACTAA 59.517 44.000 0.00 0.00 0.00 2.24
4211 4316 5.021458 CCCTTGTACTCCCTCTGTAAACTA 58.979 45.833 0.00 0.00 0.00 2.24
4212 4317 3.838903 CCCTTGTACTCCCTCTGTAAACT 59.161 47.826 0.00 0.00 0.00 2.66
4213 4318 3.836562 TCCCTTGTACTCCCTCTGTAAAC 59.163 47.826 0.00 0.00 0.00 2.01
4214 4319 4.136341 TCCCTTGTACTCCCTCTGTAAA 57.864 45.455 0.00 0.00 0.00 2.01
4215 4320 3.839323 TCCCTTGTACTCCCTCTGTAA 57.161 47.619 0.00 0.00 0.00 2.41
4216 4321 3.839323 TTCCCTTGTACTCCCTCTGTA 57.161 47.619 0.00 0.00 0.00 2.74
4217 4322 2.715763 TTCCCTTGTACTCCCTCTGT 57.284 50.000 0.00 0.00 0.00 3.41
4218 4323 2.171448 CCATTCCCTTGTACTCCCTCTG 59.829 54.545 0.00 0.00 0.00 3.35
4219 4324 2.225908 ACCATTCCCTTGTACTCCCTCT 60.226 50.000 0.00 0.00 0.00 3.69
4220 4325 2.170817 GACCATTCCCTTGTACTCCCTC 59.829 54.545 0.00 0.00 0.00 4.30
4221 4326 2.197465 GACCATTCCCTTGTACTCCCT 58.803 52.381 0.00 0.00 0.00 4.20
4222 4327 2.197465 AGACCATTCCCTTGTACTCCC 58.803 52.381 0.00 0.00 0.00 4.30
4223 4328 4.262617 GAAAGACCATTCCCTTGTACTCC 58.737 47.826 0.00 0.00 0.00 3.85
4224 4329 3.933332 CGAAAGACCATTCCCTTGTACTC 59.067 47.826 0.00 0.00 0.00 2.59
4225 4330 3.307480 CCGAAAGACCATTCCCTTGTACT 60.307 47.826 0.00 0.00 0.00 2.73
4226 4331 3.007635 CCGAAAGACCATTCCCTTGTAC 58.992 50.000 0.00 0.00 0.00 2.90
4227 4332 2.907696 TCCGAAAGACCATTCCCTTGTA 59.092 45.455 0.00 0.00 0.00 2.41
4228 4333 1.702957 TCCGAAAGACCATTCCCTTGT 59.297 47.619 0.00 0.00 0.00 3.16
4229 4334 2.489938 TCCGAAAGACCATTCCCTTG 57.510 50.000 0.00 0.00 0.00 3.61
4364 4642 3.948473 TGGAGACGTGGTTTTCAAAATGA 59.052 39.130 0.00 0.00 0.00 2.57
4409 4688 4.839121 TGGTTTAGGTCGATGCTAAACAT 58.161 39.130 6.22 0.00 42.21 2.71
4414 4693 4.879545 GGAAAATGGTTTAGGTCGATGCTA 59.120 41.667 0.00 0.00 0.00 3.49
4432 4711 7.905265 TGGCAAATAAATCAGAGAATGGAAAA 58.095 30.769 0.00 0.00 0.00 2.29
4435 4714 7.664552 AATGGCAAATAAATCAGAGAATGGA 57.335 32.000 0.00 0.00 0.00 3.41
4441 4720 6.870769 AGGTGAAATGGCAAATAAATCAGAG 58.129 36.000 0.00 0.00 0.00 3.35
4443 4722 9.603921 ATTTAGGTGAAATGGCAAATAAATCAG 57.396 29.630 0.00 0.00 36.35 2.90
4518 4829 4.703897 AGTAGTTTGAAGTGCTTGCAGTA 58.296 39.130 3.18 0.00 0.00 2.74
4561 4872 6.592607 GTCTCCCATTCTACAATCACGTAAAA 59.407 38.462 0.00 0.00 0.00 1.52
4563 4874 5.657474 GTCTCCCATTCTACAATCACGTAA 58.343 41.667 0.00 0.00 0.00 3.18
4615 4926 4.172807 TGGAGAGTACTTACCAACCCAAT 58.827 43.478 16.16 0.00 0.00 3.16
4708 5019 6.373186 AGTAGAAAACTGCACAAACTTACC 57.627 37.500 0.00 0.00 36.93 2.85
4722 5033 7.698836 TTTGTAGTTGACGGTAGTAGAAAAC 57.301 36.000 0.00 0.00 0.00 2.43
4748 5059 4.114794 GACAAATGGCCACATATTTGAGC 58.885 43.478 28.06 18.19 43.51 4.26
4749 5060 5.327616 TGACAAATGGCCACATATTTGAG 57.672 39.130 28.06 9.96 43.51 3.02
4968 5280 2.024414 GTGCCTGAGGTTTGAACAGTT 58.976 47.619 0.00 0.00 0.00 3.16
4984 5296 4.782019 TGTGATGGTTCTAATTTGTGCC 57.218 40.909 0.00 0.00 0.00 5.01
5105 5417 0.539438 TCGCCAGGCCAATCTTGTTT 60.539 50.000 5.01 0.00 0.00 2.83
5176 5488 2.048597 ACGGCTTCGATTCGTGCA 60.049 55.556 20.96 0.00 35.70 4.57
5314 5626 6.517697 CGGCTCATGGTACCATTACTAACATA 60.518 42.308 25.25 0.00 33.90 2.29
5392 5704 5.993106 AACTGAAGACTTCTGCTAACAAC 57.007 39.130 18.89 0.00 32.51 3.32
5443 5755 8.046107 AGTTCTGCTAGCATTTCTCTCTATTTT 58.954 33.333 19.72 0.00 0.00 1.82
5509 5821 1.968540 GCTTGCGCCACCTCTCTTT 60.969 57.895 4.18 0.00 0.00 2.52
5511 5823 3.602513 CTGCTTGCGCCACCTCTCT 62.603 63.158 4.18 0.00 34.43 3.10
5540 5882 5.163364 ACACACAAATTGCCATTCTTAACCA 60.163 36.000 0.00 0.00 0.00 3.67
5555 5897 4.700213 GGCCACTAAGTATGACACACAAAT 59.300 41.667 0.00 0.00 0.00 2.32
5557 5899 3.558321 GGGCCACTAAGTATGACACACAA 60.558 47.826 4.39 0.00 0.00 3.33
5588 5930 1.001406 ACTCACCACACTAGAAGCTGC 59.999 52.381 0.00 0.00 0.00 5.25
5596 5938 1.968493 GTTCCCTGACTCACCACACTA 59.032 52.381 0.00 0.00 0.00 2.74
5601 5943 1.208706 TGTTGTTCCCTGACTCACCA 58.791 50.000 0.00 0.00 0.00 4.17
5614 5956 4.591498 GGAAAGGAAAGGGGTAATGTTGTT 59.409 41.667 0.00 0.00 0.00 2.83
5647 5990 1.404986 CCAAAACGCCACTATCCGAGA 60.405 52.381 0.00 0.00 0.00 4.04
5650 5993 1.302383 TGCCAAAACGCCACTATCCG 61.302 55.000 0.00 0.00 0.00 4.18
5652 5995 0.878416 TGTGCCAAAACGCCACTATC 59.122 50.000 0.00 0.00 0.00 2.08
5654 5997 0.595588 CATGTGCCAAAACGCCACTA 59.404 50.000 0.00 0.00 0.00 2.74
5655 5998 1.363443 CATGTGCCAAAACGCCACT 59.637 52.632 0.00 0.00 0.00 4.00
5656 5999 1.664333 CCATGTGCCAAAACGCCAC 60.664 57.895 0.00 0.00 0.00 5.01
5752 6095 8.729529 AGCATGTATAATATCGACATATACGC 57.270 34.615 14.44 12.97 35.99 4.42
5757 6100 9.921637 TTTGTGAGCATGTATAATATCGACATA 57.078 29.630 0.00 0.00 32.58 2.29
5760 6103 8.299262 ACTTTGTGAGCATGTATAATATCGAC 57.701 34.615 0.00 0.00 0.00 4.20
5769 6112 6.208644 GTGAAACAACTTTGTGAGCATGTAT 58.791 36.000 0.00 0.00 41.31 2.29
5792 6135 3.574216 CGTAAGTTGTCGGTTTTTCGT 57.426 42.857 0.00 0.00 0.00 3.85
5817 6160 3.242608 CGGATTGTGTCTTTTTCACACGT 60.243 43.478 0.00 0.00 46.12 4.49
5863 6206 9.139174 ACTTGTGTAAAAAGACAAAAGAATGTG 57.861 29.630 12.32 0.00 33.78 3.21
5868 6211 7.877003 TGTGACTTGTGTAAAAAGACAAAAGA 58.123 30.769 12.32 0.00 37.57 2.52
5912 6257 1.443802 TGTGTGCACGTCAAGTTTCA 58.556 45.000 13.13 0.00 0.00 2.69
5945 6290 8.818141 TTCCAAATAAAAATTTGACGCATACA 57.182 26.923 11.43 0.00 42.47 2.29
5978 6323 9.670180 GCACACGAAAAATATATTTTAAAGTGC 57.330 29.630 29.61 29.61 41.35 4.40
5985 6330 7.275560 GCTTCCTGCACACGAAAAATATATTTT 59.724 33.333 16.15 16.15 40.44 1.82
5992 6337 1.000274 GGCTTCCTGCACACGAAAAAT 60.000 47.619 0.00 0.00 45.15 1.82
5997 6342 1.468506 TACTGGCTTCCTGCACACGA 61.469 55.000 0.00 0.00 45.15 4.35
5998 6343 0.391661 ATACTGGCTTCCTGCACACG 60.392 55.000 0.00 0.00 45.15 4.49
5999 6344 1.470098 CAATACTGGCTTCCTGCACAC 59.530 52.381 0.00 0.00 45.15 3.82
6000 6345 1.614051 CCAATACTGGCTTCCTGCACA 60.614 52.381 0.00 0.00 45.15 4.57
6001 6346 1.098050 CCAATACTGGCTTCCTGCAC 58.902 55.000 0.00 0.00 45.15 4.57
6002 6347 3.575506 CCAATACTGGCTTCCTGCA 57.424 52.632 0.00 0.00 45.15 4.41
6014 6359 6.435430 TGCATACTGAAACATGACCAATAC 57.565 37.500 0.00 0.00 0.00 1.89
6018 6363 5.589855 CCTAATGCATACTGAAACATGACCA 59.410 40.000 0.00 0.00 0.00 4.02
6038 6383 2.173356 CCTTGCTCCACATCATCCCTAA 59.827 50.000 0.00 0.00 0.00 2.69
6039 6384 1.770658 CCTTGCTCCACATCATCCCTA 59.229 52.381 0.00 0.00 0.00 3.53
6040 6385 0.549950 CCTTGCTCCACATCATCCCT 59.450 55.000 0.00 0.00 0.00 4.20
6042 6387 0.548031 TCCCTTGCTCCACATCATCC 59.452 55.000 0.00 0.00 0.00 3.51
6045 6390 1.588239 ATCTCCCTTGCTCCACATCA 58.412 50.000 0.00 0.00 0.00 3.07
6046 6391 2.725221 AATCTCCCTTGCTCCACATC 57.275 50.000 0.00 0.00 0.00 3.06
6049 6394 2.519013 ACAAAATCTCCCTTGCTCCAC 58.481 47.619 0.00 0.00 0.00 4.02
6050 6395 2.978156 ACAAAATCTCCCTTGCTCCA 57.022 45.000 0.00 0.00 0.00 3.86
6051 6396 5.654209 AGAAATACAAAATCTCCCTTGCTCC 59.346 40.000 0.00 0.00 0.00 4.70
6053 6398 7.544804 AAAGAAATACAAAATCTCCCTTGCT 57.455 32.000 0.00 0.00 0.00 3.91
6054 6399 7.872483 TCAAAAGAAATACAAAATCTCCCTTGC 59.128 33.333 0.00 0.00 0.00 4.01
6055 6400 9.762933 TTCAAAAGAAATACAAAATCTCCCTTG 57.237 29.630 0.00 0.00 0.00 3.61
6057 6402 9.764363 GTTTCAAAAGAAATACAAAATCTCCCT 57.236 29.630 0.00 0.00 0.00 4.20
6068 6430 5.116069 TGCCTCCGTTTCAAAAGAAATAC 57.884 39.130 0.00 0.00 0.00 1.89
6074 6436 3.506067 AGGTTATGCCTCCGTTTCAAAAG 59.494 43.478 0.00 0.00 46.96 2.27
6092 6454 7.619302 TCTTAATTAATGGATGAGGCAAAGGTT 59.381 33.333 0.00 0.00 0.00 3.50
6127 6489 7.866898 GGAGACCTTTTCTATAACCGAATACTC 59.133 40.741 0.00 0.00 33.22 2.59
6131 6493 6.555463 TGGAGACCTTTTCTATAACCGAAT 57.445 37.500 0.00 0.00 33.22 3.34
6149 6511 6.361433 TGGACTCTTGTATTTTGTTTGGAGA 58.639 36.000 0.00 0.00 0.00 3.71
6170 6540 7.706607 CACAAATAATGTCGAGAGAGTAATGGA 59.293 37.037 0.00 0.00 41.46 3.41
6197 6567 1.139947 ACGGGTGCAAAACGTTTGG 59.860 52.632 15.46 13.24 37.61 3.28
6213 6583 1.502231 CAAGACTTCTGTCCACCACG 58.498 55.000 0.00 0.00 43.91 4.94
6214 6584 1.202698 AGCAAGACTTCTGTCCACCAC 60.203 52.381 0.00 0.00 43.91 4.16
6255 6625 2.035626 CCACCACGGGCAATCCTT 59.964 61.111 0.00 0.00 0.00 3.36
6272 6642 4.012895 CACAAGTCCGCACCACGC 62.013 66.667 0.00 0.00 41.76 5.34
6273 6643 2.279851 TCACAAGTCCGCACCACG 60.280 61.111 0.00 0.00 43.15 4.94
6314 6684 9.249053 TGCTTATAAGTTGGACCATTTGAAATA 57.751 29.630 13.91 0.00 0.00 1.40
6315 6685 8.133024 TGCTTATAAGTTGGACCATTTGAAAT 57.867 30.769 13.91 0.00 0.00 2.17
6317 6687 7.363705 CCATGCTTATAAGTTGGACCATTTGAA 60.364 37.037 22.41 0.00 35.03 2.69
6318 6688 6.096705 CCATGCTTATAAGTTGGACCATTTGA 59.903 38.462 22.41 0.00 35.03 2.69
6328 6698 5.518848 TCAATGGCCATGCTTATAAGTTG 57.481 39.130 21.63 10.58 0.00 3.16
6345 6715 6.401047 AATAGAAGTGCCATGGAATCAATG 57.599 37.500 18.40 0.00 0.00 2.82
6352 6722 4.016444 GTTCCAAATAGAAGTGCCATGGA 58.984 43.478 18.40 0.00 33.88 3.41
6360 6730 5.106157 CGAAGCCAATGTTCCAAATAGAAGT 60.106 40.000 0.00 0.00 0.00 3.01
6369 6739 0.109532 TGTCCGAAGCCAATGTTCCA 59.890 50.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.