Multiple sequence alignment - TraesCS4A01G475400

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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 TraesCS4A01G475400 chr4A 100.000 6263 0 0 1 6263 734383798 734390060 0.000000e+00 11566.0
1 TraesCS4A01G475400 chr4A 89.570 4324 371 43 1505 5780 736470575 736466284 0.000000e+00 5413.0
2 TraesCS4A01G475400 chr4A 89.843 4017 328 36 1204 5179 736896591 736900568 0.000000e+00 5084.0
3 TraesCS4A01G475400 chr4A 85.838 4173 518 47 1237 5361 735562866 735558719 0.000000e+00 4364.0
4 TraesCS4A01G475400 chr4A 84.442 4493 604 61 915 5361 735315845 735320288 0.000000e+00 4337.0
5 TraesCS4A01G475400 chr4A 82.479 4840 705 78 753 5506 735775790 735780572 0.000000e+00 4108.0
6 TraesCS4A01G475400 chr4A 85.016 4051 534 44 1347 5361 736413338 736409325 0.000000e+00 4050.0
7 TraesCS4A01G475400 chr4A 83.451 4405 642 53 975 5333 735368334 735363971 0.000000e+00 4015.0
8 TraesCS4A01G475400 chr4A 84.358 4002 565 35 1356 5332 736147261 736151226 0.000000e+00 3866.0
9 TraesCS4A01G475400 chr4A 83.619 4139 585 51 1362 5478 735487973 735483906 0.000000e+00 3801.0
10 TraesCS4A01G475400 chr4A 83.105 3948 580 54 1425 5344 736119768 736123656 0.000000e+00 3515.0
11 TraesCS4A01G475400 chr4A 82.257 4182 628 64 1362 5506 735818690 735822794 0.000000e+00 3507.0
12 TraesCS4A01G475400 chr4A 85.234 3183 417 36 1481 4624 735831766 735834934 0.000000e+00 3225.0
13 TraesCS4A01G475400 chr4A 84.212 3357 452 33 849 4147 734996194 734999530 0.000000e+00 3192.0
14 TraesCS4A01G475400 chr4A 82.653 3551 540 46 1829 5361 735662599 735659107 0.000000e+00 3075.0
15 TraesCS4A01G475400 chr4A 84.915 2592 355 25 1432 3999 736055980 736058559 0.000000e+00 2588.0
16 TraesCS4A01G475400 chr4A 87.951 2191 239 19 1425 3599 734480184 734482365 0.000000e+00 2560.0
17 TraesCS4A01G475400 chr4A 84.595 2603 343 37 1432 3996 735767159 735769741 0.000000e+00 2532.0
18 TraesCS4A01G475400 chr4A 84.220 2313 333 16 1425 3727 734876255 734878545 0.000000e+00 2220.0
19 TraesCS4A01G475400 chr4A 92.143 1260 57 17 559 1803 735663827 735662595 0.000000e+00 1740.0
20 TraesCS4A01G475400 chr4A 98.943 473 5 0 5791 6263 736907794 736908266 0.000000e+00 846.0
21 TraesCS4A01G475400 chr4A 83.805 883 107 14 623 1485 736471654 736470788 0.000000e+00 806.0
22 TraesCS4A01G475400 chr4A 95.983 473 16 1 5791 6260 735836210 735836682 0.000000e+00 765.0
23 TraesCS4A01G475400 chr4A 85.015 654 96 2 2665 3318 736611695 736612346 0.000000e+00 664.0
24 TraesCS4A01G475400 chr4A 84.266 661 64 18 559 1208 736895513 736896144 5.370000e-170 608.0
25 TraesCS4A01G475400 chr4A 95.509 334 2 3 5460 5780 736906444 736906777 7.190000e-144 521.0
26 TraesCS4A01G475400 chr4A 79.384 422 37 25 775 1170 734872838 734873235 1.040000e-62 252.0
27 TraesCS4A01G475400 chr4A 90.446 157 8 4 176 330 735811507 735811658 3.830000e-47 200.0
28 TraesCS4A01G475400 chr4A 87.952 166 13 3 753 911 735368512 735368347 8.290000e-44 189.0
29 TraesCS4A01G475400 chr4A 75.219 456 68 27 5797 6235 735001117 735001544 2.320000e-39 174.0
30 TraesCS4A01G475400 chr4A 76.190 378 55 22 727 1081 735019006 735019371 3.880000e-37 167.0
31 TraesCS4A01G475400 chr4A 89.764 127 12 1 559 685 735775662 735775787 1.810000e-35 161.0
32 TraesCS4A01G475400 chr4A 88.976 127 13 1 559 685 735368643 735368518 8.410000e-34 156.0
33 TraesCS4A01G475400 chr4A 90.909 99 7 2 234 330 734994680 734994778 1.420000e-26 132.0
34 TraesCS4A01G475400 chr4A 95.062 81 3 1 609 688 734996074 734996154 6.590000e-25 126.0
35 TraesCS4A01G475400 chr4A 87.879 99 9 3 58 155 619416560 619416656 5.130000e-21 113.0
36 TraesCS4A01G475400 chr4A 81.457 151 17 7 178 317 736054516 736054666 5.130000e-21 113.0
37 TraesCS4A01G475400 chr4A 79.000 100 20 1 5590 5688 736003802 736003703 4.050000e-07 67.6
38 TraesCS4A01G475400 chr7A 87.902 5199 497 63 647 5780 6929374 6924243 0.000000e+00 5995.0
39 TraesCS4A01G475400 chr7A 83.160 3931 573 53 1425 5314 7322285 7318403 0.000000e+00 3509.0
40 TraesCS4A01G475400 chr7A 87.342 158 17 2 176 330 6930256 6930099 1.790000e-40 178.0
41 TraesCS4A01G475400 chr7A 84.247 146 15 6 5881 6025 6968709 6968571 1.100000e-27 135.0
42 TraesCS4A01G475400 chr7D 88.010 4804 460 59 623 5361 5449885 5445133 0.000000e+00 5574.0
43 TraesCS4A01G475400 chr7D 83.035 5022 729 70 803 5756 5638669 5633703 0.000000e+00 4440.0
44 TraesCS4A01G475400 chr7D 79.276 304 40 18 731 1015 5566422 5566123 2.300000e-44 191.0
45 TraesCS4A01G475400 chr7D 74.946 467 69 34 5795 6253 5633869 5633443 3.000000e-38 171.0
46 TraesCS4A01G475400 chr7D 80.537 149 22 5 188 330 5450150 5450003 2.390000e-19 108.0
47 TraesCS4A01G475400 chr7D 93.651 63 2 1 270 330 5639253 5639191 6.690000e-15 93.5
48 TraesCS4A01G475400 chr3B 76.104 3871 821 74 1421 5244 559880967 559884780 0.000000e+00 1929.0
49 TraesCS4A01G475400 chr3B 92.800 125 7 2 31 155 243313533 243313655 4.990000e-41 180.0
50 TraesCS4A01G475400 chr3B 91.339 127 9 2 30 155 43335893 43336018 8.350000e-39 172.0
51 TraesCS4A01G475400 chr3A 92.857 126 6 3 31 155 653223048 653223171 4.990000e-41 180.0
52 TraesCS4A01G475400 chr1B 92.126 127 8 2 31 156 679226670 679226545 1.790000e-40 178.0
53 TraesCS4A01G475400 chr1B 90.323 124 12 0 31 154 638690 638567 5.020000e-36 163.0
54 TraesCS4A01G475400 chr1B 89.516 124 11 2 31 154 61313317 61313438 8.410000e-34 156.0
55 TraesCS4A01G475400 chr1A 92.800 125 6 3 31 155 13934023 13934144 1.790000e-40 178.0
56 TraesCS4A01G475400 chr2B 92.683 123 6 2 32 154 158906992 158907111 2.320000e-39 174.0
57 TraesCS4A01G475400 chr2B 92.063 126 6 3 31 155 759258219 759258341 2.320000e-39 174.0
58 TraesCS4A01G475400 chr2B 97.059 34 0 1 1 33 759258167 759258200 8.770000e-04 56.5
59 TraesCS4A01G475400 chr1D 92.000 125 8 2 31 155 107214737 107214859 2.320000e-39 174.0
60 TraesCS4A01G475400 chr6A 88.028 142 11 6 12 152 486591735 486591871 5.020000e-36 163.0
61 TraesCS4A01G475400 chr6D 87.356 87 9 2 70 155 1903779 1903694 1.440000e-16 99.0


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 TraesCS4A01G475400 chr4A 734383798 734390060 6262 False 11566.000000 11566 100.000000 1 6263 1 chr4A.!!$F2 6262
1 TraesCS4A01G475400 chr4A 735558719 735562866 4147 True 4364.000000 4364 85.838000 1237 5361 1 chr4A.!!$R2 4124
2 TraesCS4A01G475400 chr4A 735315845 735320288 4443 False 4337.000000 4337 84.442000 915 5361 1 chr4A.!!$F5 4446
3 TraesCS4A01G475400 chr4A 736409325 736413338 4013 True 4050.000000 4050 85.016000 1347 5361 1 chr4A.!!$R4 4014
4 TraesCS4A01G475400 chr4A 736147261 736151226 3965 False 3866.000000 3866 84.358000 1356 5332 1 chr4A.!!$F10 3976
5 TraesCS4A01G475400 chr4A 735483906 735487973 4067 True 3801.000000 3801 83.619000 1362 5478 1 chr4A.!!$R1 4116
6 TraesCS4A01G475400 chr4A 736119768 736123656 3888 False 3515.000000 3515 83.105000 1425 5344 1 chr4A.!!$F9 3919
7 TraesCS4A01G475400 chr4A 735818690 735822794 4104 False 3507.000000 3507 82.257000 1362 5506 1 chr4A.!!$F8 4144
8 TraesCS4A01G475400 chr4A 736466284 736471654 5370 True 3109.500000 5413 86.687500 623 5780 2 chr4A.!!$R7 5157
9 TraesCS4A01G475400 chr4A 736895513 736900568 5055 False 2846.000000 5084 87.054500 559 5179 2 chr4A.!!$F17 4620
10 TraesCS4A01G475400 chr4A 734480184 734482365 2181 False 2560.000000 2560 87.951000 1425 3599 1 chr4A.!!$F3 2174
11 TraesCS4A01G475400 chr4A 735767159 735769741 2582 False 2532.000000 2532 84.595000 1432 3996 1 chr4A.!!$F6 2564
12 TraesCS4A01G475400 chr4A 735659107 735663827 4720 True 2407.500000 3075 87.398000 559 5361 2 chr4A.!!$R6 4802
13 TraesCS4A01G475400 chr4A 735775662 735780572 4910 False 2134.500000 4108 86.121500 559 5506 2 chr4A.!!$F14 4947
14 TraesCS4A01G475400 chr4A 735831766 735836682 4916 False 1995.000000 3225 90.608500 1481 6260 2 chr4A.!!$F15 4779
15 TraesCS4A01G475400 chr4A 735363971 735368643 4672 True 1453.333333 4015 86.793000 559 5333 3 chr4A.!!$R5 4774
16 TraesCS4A01G475400 chr4A 736054516 736058559 4043 False 1350.500000 2588 83.186000 178 3999 2 chr4A.!!$F16 3821
17 TraesCS4A01G475400 chr4A 734872838 734878545 5707 False 1236.000000 2220 81.802000 775 3727 2 chr4A.!!$F12 2952
18 TraesCS4A01G475400 chr4A 734994680 735001544 6864 False 906.000000 3192 86.350500 234 6235 4 chr4A.!!$F13 6001
19 TraesCS4A01G475400 chr4A 736906444 736908266 1822 False 683.500000 846 97.226000 5460 6263 2 chr4A.!!$F18 803
20 TraesCS4A01G475400 chr4A 736611695 736612346 651 False 664.000000 664 85.015000 2665 3318 1 chr4A.!!$F11 653
21 TraesCS4A01G475400 chr7A 7318403 7322285 3882 True 3509.000000 3509 83.160000 1425 5314 1 chr7A.!!$R2 3889
22 TraesCS4A01G475400 chr7A 6924243 6930256 6013 True 3086.500000 5995 87.622000 176 5780 2 chr7A.!!$R3 5604
23 TraesCS4A01G475400 chr7D 5445133 5450150 5017 True 2841.000000 5574 84.273500 188 5361 2 chr7D.!!$R2 5173
24 TraesCS4A01G475400 chr7D 5633443 5639253 5810 True 1568.166667 4440 83.877333 270 6253 3 chr7D.!!$R3 5983
25 TraesCS4A01G475400 chr3B 559880967 559884780 3813 False 1929.000000 1929 76.104000 1421 5244 1 chr3B.!!$F3 3823

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
128 129 0.107993 TCTTTCTGATGCAGAGGCCG 60.108 55.0 0.0 0.0 41.75 6.13 F
1192 2473 0.250901 AGGTCATTCCACACTGCCAC 60.251 55.0 0.0 0.0 39.02 5.01 F
1492 6278 0.038892 TTCAACCTACCTCGACGTGC 60.039 55.0 0.0 0.0 0.00 5.34 F
2970 8038 0.247460 TGGCAGAATCACTCTCCACG 59.753 55.0 0.0 0.0 30.73 4.94 F
3439 8541 0.678048 AGCACCGCCTCAAATTCCTC 60.678 55.0 0.0 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1492 6278 1.826921 GGAGCTCATGGGCCATGTG 60.827 63.158 38.04 35.73 41.98 3.21 R
2712 7734 0.819259 GGAAGCACCTCTGCACACAA 60.819 55.000 0.00 0.00 46.97 3.33 R
3402 8486 0.110823 CTTTCCGCTCGTTTGTTCGG 60.111 55.000 0.00 0.00 42.96 4.30 R
4305 9429 1.197949 GAAAGAGAAAGCCCACGAAGC 59.802 52.381 0.00 0.00 0.00 3.86 R
5314 10471 4.240881 ACATACATCTTTGAGGGTGCAT 57.759 40.909 0.00 0.00 0.00 3.96 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
18 19 4.073052 CCAGCGGTTGTGGCTTTA 57.927 55.556 0.00 0.00 39.08 1.85
19 20 2.566824 CCAGCGGTTGTGGCTTTAT 58.433 52.632 0.00 0.00 39.08 1.40
20 21 0.171007 CCAGCGGTTGTGGCTTTATG 59.829 55.000 0.00 0.00 39.08 1.90
21 22 0.171007 CAGCGGTTGTGGCTTTATGG 59.829 55.000 0.00 0.00 39.08 2.74
22 23 1.153842 GCGGTTGTGGCTTTATGGC 60.154 57.895 0.00 0.00 42.18 4.40
36 37 4.805719 GCTTTATGGCCTTTTATTGTGAGC 59.194 41.667 3.32 0.00 0.00 4.26
37 38 5.394553 GCTTTATGGCCTTTTATTGTGAGCT 60.395 40.000 3.32 0.00 0.00 4.09
38 39 5.835113 TTATGGCCTTTTATTGTGAGCTC 57.165 39.130 6.82 6.82 0.00 4.09
39 40 2.083774 TGGCCTTTTATTGTGAGCTCG 58.916 47.619 9.64 0.00 0.00 5.03
40 41 1.202188 GGCCTTTTATTGTGAGCTCGC 60.202 52.381 20.51 20.51 0.00 5.03
41 42 1.202188 GCCTTTTATTGTGAGCTCGCC 60.202 52.381 23.96 10.40 0.00 5.54
42 43 2.359900 CCTTTTATTGTGAGCTCGCCT 58.640 47.619 23.96 13.84 0.00 5.52
43 44 2.749621 CCTTTTATTGTGAGCTCGCCTT 59.250 45.455 23.96 13.65 0.00 4.35
44 45 3.191371 CCTTTTATTGTGAGCTCGCCTTT 59.809 43.478 23.96 11.24 0.00 3.11
45 46 4.394920 CCTTTTATTGTGAGCTCGCCTTTA 59.605 41.667 23.96 10.28 0.00 1.85
46 47 5.066505 CCTTTTATTGTGAGCTCGCCTTTAT 59.933 40.000 23.96 13.88 0.00 1.40
47 48 6.404734 CCTTTTATTGTGAGCTCGCCTTTATT 60.405 38.462 23.96 5.08 0.00 1.40
48 49 6.509418 TTTATTGTGAGCTCGCCTTTATTT 57.491 33.333 23.96 4.25 0.00 1.40
49 50 6.509418 TTATTGTGAGCTCGCCTTTATTTT 57.491 33.333 23.96 3.28 0.00 1.82
50 51 3.829886 TGTGAGCTCGCCTTTATTTTG 57.170 42.857 23.96 0.00 0.00 2.44
51 52 3.146066 TGTGAGCTCGCCTTTATTTTGT 58.854 40.909 23.96 0.00 0.00 2.83
52 53 3.568007 TGTGAGCTCGCCTTTATTTTGTT 59.432 39.130 23.96 0.00 0.00 2.83
53 54 4.037446 TGTGAGCTCGCCTTTATTTTGTTT 59.963 37.500 23.96 0.00 0.00 2.83
54 55 4.982295 GTGAGCTCGCCTTTATTTTGTTTT 59.018 37.500 16.69 0.00 0.00 2.43
55 56 4.981674 TGAGCTCGCCTTTATTTTGTTTTG 59.018 37.500 9.64 0.00 0.00 2.44
56 57 3.740832 AGCTCGCCTTTATTTTGTTTTGC 59.259 39.130 0.00 0.00 0.00 3.68
57 58 3.421698 GCTCGCCTTTATTTTGTTTTGCG 60.422 43.478 0.00 0.00 41.90 4.85
58 59 3.966154 TCGCCTTTATTTTGTTTTGCGA 58.034 36.364 0.00 0.00 46.26 5.10
59 60 3.731717 TCGCCTTTATTTTGTTTTGCGAC 59.268 39.130 0.00 0.00 43.98 5.19
60 61 3.733727 CGCCTTTATTTTGTTTTGCGACT 59.266 39.130 0.00 0.00 43.07 4.18
61 62 4.208253 CGCCTTTATTTTGTTTTGCGACTT 59.792 37.500 0.00 0.00 43.07 3.01
62 63 5.276631 CGCCTTTATTTTGTTTTGCGACTTT 60.277 36.000 0.00 0.00 43.07 2.66
63 64 6.074782 CGCCTTTATTTTGTTTTGCGACTTTA 60.075 34.615 0.00 0.00 43.07 1.85
64 65 7.515371 CGCCTTTATTTTGTTTTGCGACTTTAA 60.515 33.333 0.00 0.00 43.07 1.52
65 66 7.792048 GCCTTTATTTTGTTTTGCGACTTTAAG 59.208 33.333 0.00 0.00 0.00 1.85
66 67 9.026074 CCTTTATTTTGTTTTGCGACTTTAAGA 57.974 29.630 0.00 0.00 0.00 2.10
67 68 9.829637 CTTTATTTTGTTTTGCGACTTTAAGAC 57.170 29.630 0.00 0.00 0.00 3.01
68 69 6.822073 ATTTTGTTTTGCGACTTTAAGACC 57.178 33.333 0.00 0.00 0.00 3.85
69 70 5.570234 TTTGTTTTGCGACTTTAAGACCT 57.430 34.783 0.00 0.00 0.00 3.85
70 71 5.570234 TTGTTTTGCGACTTTAAGACCTT 57.430 34.783 0.00 0.00 0.00 3.50
71 72 4.915704 TGTTTTGCGACTTTAAGACCTTG 58.084 39.130 0.00 0.00 0.00 3.61
72 73 4.396790 TGTTTTGCGACTTTAAGACCTTGT 59.603 37.500 0.00 0.00 0.00 3.16
73 74 5.106078 TGTTTTGCGACTTTAAGACCTTGTT 60.106 36.000 0.00 0.00 0.00 2.83
74 75 4.545823 TTGCGACTTTAAGACCTTGTTG 57.454 40.909 0.00 0.00 0.00 3.33
75 76 3.799366 TGCGACTTTAAGACCTTGTTGA 58.201 40.909 0.00 0.00 0.00 3.18
76 77 4.193090 TGCGACTTTAAGACCTTGTTGAA 58.807 39.130 0.00 0.00 0.00 2.69
77 78 4.034742 TGCGACTTTAAGACCTTGTTGAAC 59.965 41.667 0.00 0.00 0.00 3.18
78 79 4.554134 GCGACTTTAAGACCTTGTTGAACC 60.554 45.833 0.00 0.00 0.00 3.62
79 80 4.814771 CGACTTTAAGACCTTGTTGAACCT 59.185 41.667 0.00 0.00 0.00 3.50
80 81 5.987347 CGACTTTAAGACCTTGTTGAACCTA 59.013 40.000 0.00 0.00 0.00 3.08
81 82 6.649557 CGACTTTAAGACCTTGTTGAACCTAT 59.350 38.462 0.00 0.00 0.00 2.57
82 83 7.172703 CGACTTTAAGACCTTGTTGAACCTATT 59.827 37.037 0.00 0.00 0.00 1.73
83 84 8.762481 ACTTTAAGACCTTGTTGAACCTATTT 57.238 30.769 0.00 0.00 0.00 1.40
84 85 9.197306 ACTTTAAGACCTTGTTGAACCTATTTT 57.803 29.630 0.00 0.00 0.00 1.82
111 112 8.574251 TTTATAAAATATGGCCGTATGCATCT 57.426 30.769 18.38 0.00 43.89 2.90
112 113 8.574251 TTATAAAATATGGCCGTATGCATCTT 57.426 30.769 18.38 5.68 43.89 2.40
113 114 5.789643 AAAATATGGCCGTATGCATCTTT 57.210 34.783 18.38 11.31 43.89 2.52
114 115 5.376854 AAATATGGCCGTATGCATCTTTC 57.623 39.130 18.38 0.00 43.89 2.62
115 116 2.645838 ATGGCCGTATGCATCTTTCT 57.354 45.000 0.19 0.00 43.89 2.52
116 117 1.667236 TGGCCGTATGCATCTTTCTG 58.333 50.000 0.19 0.00 43.89 3.02
117 118 1.209261 TGGCCGTATGCATCTTTCTGA 59.791 47.619 0.19 0.00 43.89 3.27
118 119 2.158769 TGGCCGTATGCATCTTTCTGAT 60.159 45.455 0.19 0.00 43.89 2.90
127 128 1.948145 CATCTTTCTGATGCAGAGGCC 59.052 52.381 0.00 0.00 44.96 5.19
128 129 0.107993 TCTTTCTGATGCAGAGGCCG 60.108 55.000 0.00 0.00 41.75 6.13
129 130 1.078214 TTTCTGATGCAGAGGCCGG 60.078 57.895 0.00 0.00 41.75 6.13
130 131 2.541547 TTTCTGATGCAGAGGCCGGG 62.542 60.000 2.18 0.00 41.75 5.73
131 132 4.559063 CTGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
133 134 4.247380 GATGCAGAGGCCGGGGAG 62.247 72.222 2.18 0.00 40.13 4.30
169 170 2.978156 AAAAAGCTGGGTCAGATCCA 57.022 45.000 1.28 1.28 32.44 3.41
170 171 2.206576 AAAAGCTGGGTCAGATCCAC 57.793 50.000 0.00 0.00 32.44 4.02
171 172 1.366319 AAAGCTGGGTCAGATCCACT 58.634 50.000 0.00 0.00 32.44 4.00
172 173 1.366319 AAGCTGGGTCAGATCCACTT 58.634 50.000 0.00 5.10 32.44 3.16
173 174 0.617413 AGCTGGGTCAGATCCACTTG 59.383 55.000 0.00 0.00 32.44 3.16
174 175 0.615331 GCTGGGTCAGATCCACTTGA 59.385 55.000 0.00 0.00 32.44 3.02
185 186 1.444933 TCCACTTGACCACTTCCCAT 58.555 50.000 0.00 0.00 0.00 4.00
203 204 4.351054 CCGCCTTGTCCTTGCCCT 62.351 66.667 0.00 0.00 0.00 5.19
224 225 5.671493 CCTAGTGGGTTTATTCATTCTCGT 58.329 41.667 0.00 0.00 0.00 4.18
226 227 4.514401 AGTGGGTTTATTCATTCTCGTCC 58.486 43.478 0.00 0.00 0.00 4.79
253 263 1.099295 TGCGTAGTCGGATCGATGGT 61.099 55.000 0.54 0.00 38.42 3.55
262 272 1.746517 GATCGATGGTTACCCGCCT 59.253 57.895 0.54 0.00 0.00 5.52
313 325 8.264347 ACCACCAATTAATGATACCCAAATTTC 58.736 33.333 0.00 0.00 0.00 2.17
357 404 2.892784 ACGCTGGACTTTATAGAGGC 57.107 50.000 0.00 0.00 0.00 4.70
359 406 2.700897 ACGCTGGACTTTATAGAGGCAT 59.299 45.455 0.00 0.00 0.00 4.40
378 430 2.473530 TGCTTCGTGTTTTCTGCTTG 57.526 45.000 0.00 0.00 0.00 4.01
379 431 2.013400 TGCTTCGTGTTTTCTGCTTGA 58.987 42.857 0.00 0.00 0.00 3.02
381 433 3.119673 TGCTTCGTGTTTTCTGCTTGAAA 60.120 39.130 2.22 2.22 42.33 2.69
385 437 2.531508 CGTGTTTTCTGCTTGAAAGTGC 59.468 45.455 5.81 0.00 44.40 4.40
390 442 1.081641 CTGCTTGAAAGTGCGCAGG 60.082 57.895 12.22 0.00 44.48 4.85
391 443 1.509644 CTGCTTGAAAGTGCGCAGGA 61.510 55.000 12.22 0.00 44.48 3.86
434 486 3.245586 TGGGTAAAGCAGGGAATGACATT 60.246 43.478 0.00 0.00 0.00 2.71
450 538 7.388776 GGAATGACATTGATACAATAGCTGCTA 59.611 37.037 12.40 12.40 0.00 3.49
451 539 7.664082 ATGACATTGATACAATAGCTGCTAC 57.336 36.000 12.26 0.00 0.00 3.58
453 541 7.275183 TGACATTGATACAATAGCTGCTACTT 58.725 34.615 12.26 5.16 0.00 2.24
454 542 8.421002 TGACATTGATACAATAGCTGCTACTTA 58.579 33.333 12.26 4.02 0.00 2.24
459 547 8.183104 TGATACAATAGCTGCTACTTAGATGT 57.817 34.615 12.26 11.96 0.00 3.06
460 548 9.297037 TGATACAATAGCTGCTACTTAGATGTA 57.703 33.333 12.26 13.49 0.00 2.29
478 570 3.983821 TGTAAACCAAACCCAAGGAAGT 58.016 40.909 0.00 0.00 0.00 3.01
493 613 5.474876 CCAAGGAAGTGAAAAATGCTAGACT 59.525 40.000 0.00 0.00 0.00 3.24
496 616 7.246171 AGGAAGTGAAAAATGCTAGACTAGA 57.754 36.000 13.91 0.00 0.00 2.43
497 617 7.327214 AGGAAGTGAAAAATGCTAGACTAGAG 58.673 38.462 13.91 0.00 0.00 2.43
498 618 7.179338 AGGAAGTGAAAAATGCTAGACTAGAGA 59.821 37.037 13.91 0.00 0.00 3.10
503 623 7.819900 GTGAAAAATGCTAGACTAGAGAAAGGA 59.180 37.037 13.91 0.00 0.00 3.36
505 625 5.862678 AATGCTAGACTAGAGAAAGGACC 57.137 43.478 13.91 0.00 0.00 4.46
513 633 4.954089 ACTAGAGAAAGGACCAGGAGAAT 58.046 43.478 0.00 0.00 0.00 2.40
517 637 5.594777 AGAGAAAGGACCAGGAGAATAAGA 58.405 41.667 0.00 0.00 0.00 2.10
531 653 8.684520 CAGGAGAATAAGAAAAATGAGAAGCAT 58.315 33.333 0.00 0.00 39.43 3.79
549 671 5.584253 AGCATACACTAGTTCGTCAGATT 57.416 39.130 0.00 0.00 0.00 2.40
550 672 5.344066 AGCATACACTAGTTCGTCAGATTG 58.656 41.667 0.00 0.00 0.00 2.67
618 1811 4.082571 AGTTTTCTCATGATTTCCTTGCGG 60.083 41.667 0.00 0.00 0.00 5.69
621 1814 2.503765 TCTCATGATTTCCTTGCGGGTA 59.496 45.455 0.00 0.00 36.25 3.69
772 1969 1.589716 GAGCTGTGTCCATGTTGGCC 61.590 60.000 0.00 0.00 37.47 5.36
773 1970 1.604593 GCTGTGTCCATGTTGGCCT 60.605 57.895 3.32 0.00 37.47 5.19
819 2034 8.231161 GTCCATCTCAGCTAAACTTAAAGAAAC 58.769 37.037 0.00 0.00 0.00 2.78
960 2230 1.406205 GGCTCCTACAACTCTGCTTCC 60.406 57.143 0.00 0.00 0.00 3.46
961 2231 1.406205 GCTCCTACAACTCTGCTTCCC 60.406 57.143 0.00 0.00 0.00 3.97
962 2232 1.902508 CTCCTACAACTCTGCTTCCCA 59.097 52.381 0.00 0.00 0.00 4.37
963 2233 1.623811 TCCTACAACTCTGCTTCCCAC 59.376 52.381 0.00 0.00 0.00 4.61
964 2234 1.625818 CCTACAACTCTGCTTCCCACT 59.374 52.381 0.00 0.00 0.00 4.00
965 2235 2.039084 CCTACAACTCTGCTTCCCACTT 59.961 50.000 0.00 0.00 0.00 3.16
966 2236 2.262423 ACAACTCTGCTTCCCACTTC 57.738 50.000 0.00 0.00 0.00 3.01
967 2237 1.771255 ACAACTCTGCTTCCCACTTCT 59.229 47.619 0.00 0.00 0.00 2.85
968 2238 2.972713 ACAACTCTGCTTCCCACTTCTA 59.027 45.455 0.00 0.00 0.00 2.10
969 2239 3.244249 ACAACTCTGCTTCCCACTTCTAC 60.244 47.826 0.00 0.00 0.00 2.59
970 2240 2.609747 ACTCTGCTTCCCACTTCTACA 58.390 47.619 0.00 0.00 0.00 2.74
971 2241 3.177228 ACTCTGCTTCCCACTTCTACAT 58.823 45.455 0.00 0.00 0.00 2.29
972 2242 3.196685 ACTCTGCTTCCCACTTCTACATC 59.803 47.826 0.00 0.00 0.00 3.06
973 2243 2.501723 TCTGCTTCCCACTTCTACATCC 59.498 50.000 0.00 0.00 0.00 3.51
1143 2423 8.112822 TGGTTATTTCTACATCCATTCCAGAAA 58.887 33.333 0.00 0.00 38.99 2.52
1188 2469 4.378770 CGATTTTCAGGTCATTCCACACTG 60.379 45.833 0.00 0.00 39.02 3.66
1192 2473 0.250901 AGGTCATTCCACACTGCCAC 60.251 55.000 0.00 0.00 39.02 5.01
1257 5804 9.911788 ATCAGTAGGTTTCTGTTTTCATATCAT 57.088 29.630 0.00 0.00 34.86 2.45
1488 6274 2.094182 TGATGCTTCAACCTACCTCGAC 60.094 50.000 0.00 0.00 0.00 4.20
1492 6278 0.038892 TTCAACCTACCTCGACGTGC 60.039 55.000 0.00 0.00 0.00 5.34
1642 6621 2.609747 TCTACCTGGCTGAAGACTTGT 58.390 47.619 0.00 0.00 0.00 3.16
1937 6940 3.198635 ACCACATCAATACCACCTCTGAG 59.801 47.826 0.00 0.00 0.00 3.35
1999 7002 3.131396 CGACTTACCAAGACAACTGCTT 58.869 45.455 0.00 0.00 0.00 3.91
2162 7166 0.865111 CGCAAACTTGATGTCCGTCA 59.135 50.000 0.00 0.00 0.00 4.35
2329 7338 1.045350 CAGCGAGAGGGAATGGGAGA 61.045 60.000 0.00 0.00 0.00 3.71
2331 7340 0.761802 GCGAGAGGGAATGGGAGAAT 59.238 55.000 0.00 0.00 0.00 2.40
2347 7356 4.279922 GGGAGAATCTGTTAGCTCCTCTAC 59.720 50.000 0.00 0.00 44.91 2.59
2420 7430 1.694150 TCCAGCTGCTCTTTACTGTGT 59.306 47.619 8.66 0.00 0.00 3.72
2436 7446 4.726583 ACTGTGTAGAAGTGTGTCCTCTA 58.273 43.478 0.00 0.00 0.00 2.43
2454 7464 5.045651 TCCTCTAGAAAACATGGAAGATGCA 60.046 40.000 0.00 0.00 0.00 3.96
2541 7563 2.174360 GGAAGGCTGGAAGATTTTGCT 58.826 47.619 0.00 0.00 34.07 3.91
2663 7685 8.239314 TGCTCTAACTTTGATGATTGACAAATC 58.761 33.333 0.00 0.00 42.28 2.17
2712 7734 6.897966 TGTGGAGTTATGAGAAGTTAGATCCT 59.102 38.462 0.00 0.00 0.00 3.24
2716 7738 7.708752 GGAGTTATGAGAAGTTAGATCCTTGTG 59.291 40.741 0.00 0.00 0.00 3.33
2829 7851 4.297510 TCATTGATTCGTGCAACCAAAAG 58.702 39.130 0.00 0.00 0.00 2.27
2893 7922 6.918892 TGATCTCTGTTTCGTTCTTTCAAA 57.081 33.333 0.00 0.00 0.00 2.69
2894 7923 7.496529 TGATCTCTGTTTCGTTCTTTCAAAT 57.503 32.000 0.00 0.00 0.00 2.32
2895 7924 7.355017 TGATCTCTGTTTCGTTCTTTCAAATG 58.645 34.615 0.00 0.00 0.00 2.32
2969 8037 1.552337 TCTGGCAGAATCACTCTCCAC 59.448 52.381 16.28 0.00 31.77 4.02
2970 8038 0.247460 TGGCAGAATCACTCTCCACG 59.753 55.000 0.00 0.00 30.73 4.94
3016 8084 7.861629 AGATGATAAGGTGACAGAAATACCAA 58.138 34.615 0.00 0.00 36.94 3.67
3036 8104 4.750098 CCAACCACAGTTCGACATATATCC 59.250 45.833 0.00 0.00 32.45 2.59
3075 8143 5.956068 TGATGCAACACAAGCAAAGTATA 57.044 34.783 0.00 0.00 46.27 1.47
3080 8148 5.104374 GCAACACAAGCAAAGTATATGCAT 58.896 37.500 3.79 3.79 46.22 3.96
3180 8256 2.316119 ATTTGAAGAAGTTGCGCGTC 57.684 45.000 8.43 0.00 0.00 5.19
3187 8263 3.014604 AGAAGTTGCGCGTCCTATATC 57.985 47.619 8.43 0.00 0.00 1.63
3200 8276 6.087522 GCGTCCTATATCTGTCATCTTACAC 58.912 44.000 0.00 0.00 0.00 2.90
3246 8330 1.865865 GTGAGTTGAAGCACCTTCGA 58.134 50.000 1.07 0.00 42.78 3.71
3282 8366 8.335532 TCATAAGAACACTGATTTCCGAATTT 57.664 30.769 0.00 0.00 0.00 1.82
3291 8375 6.094603 CACTGATTTCCGAATTTCCAAGATCT 59.905 38.462 0.00 0.00 0.00 2.75
3335 8419 6.830912 TGCAGCTACTTCTGGTAAATGATAT 58.169 36.000 0.00 0.00 34.74 1.63
3402 8486 5.744345 ACGACATCTTGACTCGAATGATTAC 59.256 40.000 0.00 0.00 0.00 1.89
3439 8541 0.678048 AGCACCGCCTCAAATTCCTC 60.678 55.000 0.00 0.00 0.00 3.71
3512 8614 7.281549 GCAAAAGAAAATGGGATATGAATTGCT 59.718 33.333 0.00 0.00 35.36 3.91
3582 8684 4.705110 TCTTGAGAATGTCACTGGGAAA 57.295 40.909 0.00 0.00 33.71 3.13
3591 8693 2.106338 TGTCACTGGGAAAGATGAAGCA 59.894 45.455 0.00 0.00 0.00 3.91
3612 8714 5.355071 AGCATTAGAATCGAAGTTGCATCAA 59.645 36.000 4.91 0.00 0.00 2.57
4165 9286 2.093310 GCTGATGTCTCACGTGTTCATG 59.907 50.000 16.51 8.76 0.00 3.07
4386 9510 2.306805 TGATGGCCTCACTTCACTGAAT 59.693 45.455 3.32 0.00 0.00 2.57
5249 10403 3.104512 TCCGCTGGAAGGAATTTAGAGA 58.895 45.455 0.00 0.00 34.33 3.10
5251 10405 4.899457 TCCGCTGGAAGGAATTTAGAGATA 59.101 41.667 0.00 0.00 34.33 1.98
5252 10406 5.365605 TCCGCTGGAAGGAATTTAGAGATAA 59.634 40.000 0.00 0.00 34.33 1.75
5253 10407 6.055588 CCGCTGGAAGGAATTTAGAGATAAA 58.944 40.000 0.00 0.00 0.00 1.40
5254 10408 6.017852 CCGCTGGAAGGAATTTAGAGATAAAC 60.018 42.308 0.00 0.00 0.00 2.01
5314 10471 3.161450 GCTCCCATCGGCCACCTA 61.161 66.667 2.24 0.00 0.00 3.08
5434 10761 3.508744 ACTTCAAATTAATGGCAGGCG 57.491 42.857 0.00 0.00 0.00 5.52
5536 10882 2.437359 CACCAGCTAGCCAGTGCC 60.437 66.667 18.60 0.00 38.69 5.01
5537 10883 2.930019 ACCAGCTAGCCAGTGCCA 60.930 61.111 12.13 0.00 38.69 4.92
5670 11032 4.586421 TGCCAGTTACCATTTTGTTCATGA 59.414 37.500 0.00 0.00 0.00 3.07
5780 11148 6.483687 GGTTCGTGTGTATGGATTGTAATTC 58.516 40.000 0.00 0.00 0.00 2.17
5783 11151 7.997107 TCGTGTGTATGGATTGTAATTCTAC 57.003 36.000 0.00 0.00 0.00 2.59
5784 11152 6.982141 TCGTGTGTATGGATTGTAATTCTACC 59.018 38.462 0.00 0.00 0.00 3.18
5785 11153 6.759356 CGTGTGTATGGATTGTAATTCTACCA 59.241 38.462 0.00 0.00 0.00 3.25
5789 11157 7.441458 GTGTATGGATTGTAATTCTACCACCTC 59.559 40.741 0.00 0.00 0.00 3.85
5822 12249 1.556911 CTGTCCTCTGGTGCCACTATT 59.443 52.381 0.00 0.00 0.00 1.73
6212 12652 6.205784 TGTGTGCTCTGTTTATTTTTGTAGC 58.794 36.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.595093 GCCATAAAGCCACAACCGCT 61.595 55.000 0.00 0.00 38.53 5.52
4 5 1.153842 GCCATAAAGCCACAACCGC 60.154 57.895 0.00 0.00 0.00 5.68
13 14 4.805719 GCTCACAATAAAAGGCCATAAAGC 59.194 41.667 5.01 0.00 0.00 3.51
14 15 6.212888 AGCTCACAATAAAAGGCCATAAAG 57.787 37.500 5.01 0.00 0.00 1.85
15 16 5.163663 CGAGCTCACAATAAAAGGCCATAAA 60.164 40.000 15.40 0.00 0.00 1.40
16 17 4.335315 CGAGCTCACAATAAAAGGCCATAA 59.665 41.667 15.40 0.00 0.00 1.90
17 18 3.876914 CGAGCTCACAATAAAAGGCCATA 59.123 43.478 15.40 0.00 0.00 2.74
18 19 2.684881 CGAGCTCACAATAAAAGGCCAT 59.315 45.455 15.40 0.00 0.00 4.40
19 20 2.083774 CGAGCTCACAATAAAAGGCCA 58.916 47.619 15.40 0.00 0.00 5.36
20 21 1.202188 GCGAGCTCACAATAAAAGGCC 60.202 52.381 15.40 0.00 0.00 5.19
21 22 1.202188 GGCGAGCTCACAATAAAAGGC 60.202 52.381 15.40 4.44 0.00 4.35
22 23 2.359900 AGGCGAGCTCACAATAAAAGG 58.640 47.619 15.40 0.00 0.00 3.11
23 24 4.425577 AAAGGCGAGCTCACAATAAAAG 57.574 40.909 15.40 0.00 0.00 2.27
24 25 6.509418 AATAAAGGCGAGCTCACAATAAAA 57.491 33.333 15.40 0.00 0.00 1.52
25 26 6.509418 AAATAAAGGCGAGCTCACAATAAA 57.491 33.333 15.40 0.00 0.00 1.40
26 27 6.072175 ACAAAATAAAGGCGAGCTCACAATAA 60.072 34.615 15.40 0.00 0.00 1.40
27 28 5.414454 ACAAAATAAAGGCGAGCTCACAATA 59.586 36.000 15.40 3.94 0.00 1.90
28 29 4.218417 ACAAAATAAAGGCGAGCTCACAAT 59.782 37.500 15.40 1.80 0.00 2.71
29 30 3.568007 ACAAAATAAAGGCGAGCTCACAA 59.432 39.130 15.40 0.00 0.00 3.33
30 31 3.146066 ACAAAATAAAGGCGAGCTCACA 58.854 40.909 15.40 0.00 0.00 3.58
31 32 3.831715 ACAAAATAAAGGCGAGCTCAC 57.168 42.857 15.40 3.30 0.00 3.51
32 33 4.846779 AAACAAAATAAAGGCGAGCTCA 57.153 36.364 15.40 0.00 0.00 4.26
33 34 4.143326 GCAAAACAAAATAAAGGCGAGCTC 60.143 41.667 2.73 2.73 0.00 4.09
34 35 3.740832 GCAAAACAAAATAAAGGCGAGCT 59.259 39.130 0.00 0.00 0.00 4.09
35 36 3.421698 CGCAAAACAAAATAAAGGCGAGC 60.422 43.478 0.00 0.00 45.42 5.03
36 37 3.978217 TCGCAAAACAAAATAAAGGCGAG 59.022 39.130 0.00 0.00 46.01 5.03
38 39 3.733727 AGTCGCAAAACAAAATAAAGGCG 59.266 39.130 0.00 0.00 44.09 5.52
39 40 5.651172 AAGTCGCAAAACAAAATAAAGGC 57.349 34.783 0.00 0.00 0.00 4.35
40 41 9.026074 TCTTAAAGTCGCAAAACAAAATAAAGG 57.974 29.630 0.00 0.00 0.00 3.11
41 42 9.829637 GTCTTAAAGTCGCAAAACAAAATAAAG 57.170 29.630 0.00 0.00 0.00 1.85
42 43 8.809478 GGTCTTAAAGTCGCAAAACAAAATAAA 58.191 29.630 0.00 0.00 0.00 1.40
43 44 8.192110 AGGTCTTAAAGTCGCAAAACAAAATAA 58.808 29.630 0.00 0.00 0.00 1.40
44 45 7.708998 AGGTCTTAAAGTCGCAAAACAAAATA 58.291 30.769 0.00 0.00 0.00 1.40
45 46 6.569780 AGGTCTTAAAGTCGCAAAACAAAAT 58.430 32.000 0.00 0.00 0.00 1.82
46 47 5.956642 AGGTCTTAAAGTCGCAAAACAAAA 58.043 33.333 0.00 0.00 0.00 2.44
47 48 5.570234 AGGTCTTAAAGTCGCAAAACAAA 57.430 34.783 0.00 0.00 0.00 2.83
48 49 5.106078 ACAAGGTCTTAAAGTCGCAAAACAA 60.106 36.000 0.00 0.00 0.00 2.83
49 50 4.396790 ACAAGGTCTTAAAGTCGCAAAACA 59.603 37.500 0.00 0.00 0.00 2.83
50 51 4.916870 ACAAGGTCTTAAAGTCGCAAAAC 58.083 39.130 0.00 0.00 0.00 2.43
51 52 5.124138 TCAACAAGGTCTTAAAGTCGCAAAA 59.876 36.000 0.00 0.00 0.00 2.44
52 53 4.636648 TCAACAAGGTCTTAAAGTCGCAAA 59.363 37.500 0.00 0.00 0.00 3.68
53 54 4.193090 TCAACAAGGTCTTAAAGTCGCAA 58.807 39.130 0.00 0.00 0.00 4.85
54 55 3.799366 TCAACAAGGTCTTAAAGTCGCA 58.201 40.909 0.00 0.00 0.00 5.10
55 56 4.524749 GTTCAACAAGGTCTTAAAGTCGC 58.475 43.478 0.00 0.00 0.00 5.19
56 57 4.814771 AGGTTCAACAAGGTCTTAAAGTCG 59.185 41.667 0.00 0.00 0.00 4.18
57 58 7.981102 ATAGGTTCAACAAGGTCTTAAAGTC 57.019 36.000 0.00 0.00 0.00 3.01
58 59 8.762481 AAATAGGTTCAACAAGGTCTTAAAGT 57.238 30.769 0.00 0.00 0.00 2.66
85 86 9.189156 AGATGCATACGGCCATATTTTATAAAT 57.811 29.630 2.24 0.00 43.89 1.40
86 87 8.574251 AGATGCATACGGCCATATTTTATAAA 57.426 30.769 2.24 0.00 43.89 1.40
87 88 8.574251 AAGATGCATACGGCCATATTTTATAA 57.426 30.769 2.24 0.00 43.89 0.98
88 89 8.574251 AAAGATGCATACGGCCATATTTTATA 57.426 30.769 2.24 0.00 43.89 0.98
89 90 7.394359 AGAAAGATGCATACGGCCATATTTTAT 59.606 33.333 2.24 0.00 43.89 1.40
90 91 6.714810 AGAAAGATGCATACGGCCATATTTTA 59.285 34.615 2.24 0.00 43.89 1.52
91 92 5.536161 AGAAAGATGCATACGGCCATATTTT 59.464 36.000 2.24 0.00 43.89 1.82
92 93 5.048504 CAGAAAGATGCATACGGCCATATTT 60.049 40.000 2.24 0.00 43.89 1.40
93 94 4.456911 CAGAAAGATGCATACGGCCATATT 59.543 41.667 2.24 0.00 43.89 1.28
94 95 4.005650 CAGAAAGATGCATACGGCCATAT 58.994 43.478 2.24 0.00 43.89 1.78
95 96 3.070878 TCAGAAAGATGCATACGGCCATA 59.929 43.478 2.24 0.00 43.89 2.74
96 97 2.158769 TCAGAAAGATGCATACGGCCAT 60.159 45.455 2.24 0.00 43.89 4.40
97 98 1.209261 TCAGAAAGATGCATACGGCCA 59.791 47.619 2.24 0.00 43.89 5.36
98 99 1.953559 TCAGAAAGATGCATACGGCC 58.046 50.000 0.00 0.00 43.89 6.13
99 100 3.532892 CATCAGAAAGATGCATACGGC 57.467 47.619 0.00 0.00 46.90 5.68
108 109 1.474677 CGGCCTCTGCATCAGAAAGAT 60.475 52.381 0.00 0.00 40.18 2.40
109 110 0.107993 CGGCCTCTGCATCAGAAAGA 60.108 55.000 0.00 0.00 40.18 2.52
110 111 1.094073 CCGGCCTCTGCATCAGAAAG 61.094 60.000 0.00 0.00 40.18 2.62
111 112 1.078214 CCGGCCTCTGCATCAGAAA 60.078 57.895 0.00 0.00 40.18 2.52
112 113 2.586245 CCGGCCTCTGCATCAGAA 59.414 61.111 0.00 0.00 40.18 3.02
113 114 3.473647 CCCGGCCTCTGCATCAGA 61.474 66.667 0.00 0.00 38.25 3.27
114 115 4.559063 CCCCGGCCTCTGCATCAG 62.559 72.222 0.00 0.00 40.13 2.90
116 117 4.247380 CTCCCCGGCCTCTGCATC 62.247 72.222 0.00 0.00 40.13 3.91
150 151 2.108952 AGTGGATCTGACCCAGCTTTTT 59.891 45.455 0.00 0.00 33.75 1.94
151 152 1.707427 AGTGGATCTGACCCAGCTTTT 59.293 47.619 0.00 0.00 33.75 2.27
152 153 1.366319 AGTGGATCTGACCCAGCTTT 58.634 50.000 0.00 0.00 33.75 3.51
153 154 1.004044 CAAGTGGATCTGACCCAGCTT 59.996 52.381 0.00 0.00 33.75 3.74
154 155 0.617413 CAAGTGGATCTGACCCAGCT 59.383 55.000 0.00 0.00 33.75 4.24
155 156 0.615331 TCAAGTGGATCTGACCCAGC 59.385 55.000 0.00 0.00 33.75 4.85
156 157 1.065854 GGTCAAGTGGATCTGACCCAG 60.066 57.143 17.21 0.00 43.56 4.45
157 158 0.984230 GGTCAAGTGGATCTGACCCA 59.016 55.000 17.21 0.00 43.56 4.51
158 159 3.863407 GGTCAAGTGGATCTGACCC 57.137 57.895 17.21 3.97 43.56 4.46
160 161 3.330267 GAAGTGGTCAAGTGGATCTGAC 58.670 50.000 4.62 4.62 0.00 3.51
161 162 2.303022 GGAAGTGGTCAAGTGGATCTGA 59.697 50.000 0.00 0.00 0.00 3.27
162 163 2.616510 GGGAAGTGGTCAAGTGGATCTG 60.617 54.545 0.00 0.00 0.00 2.90
163 164 1.630878 GGGAAGTGGTCAAGTGGATCT 59.369 52.381 0.00 0.00 0.00 2.75
164 165 1.351017 TGGGAAGTGGTCAAGTGGATC 59.649 52.381 0.00 0.00 0.00 3.36
165 166 1.444933 TGGGAAGTGGTCAAGTGGAT 58.555 50.000 0.00 0.00 0.00 3.41
166 167 1.351017 GATGGGAAGTGGTCAAGTGGA 59.649 52.381 0.00 0.00 0.00 4.02
167 168 1.614317 GGATGGGAAGTGGTCAAGTGG 60.614 57.143 0.00 0.00 0.00 4.00
168 169 1.826385 GGATGGGAAGTGGTCAAGTG 58.174 55.000 0.00 0.00 0.00 3.16
169 170 0.324943 CGGATGGGAAGTGGTCAAGT 59.675 55.000 0.00 0.00 0.00 3.16
170 171 1.026718 GCGGATGGGAAGTGGTCAAG 61.027 60.000 0.00 0.00 0.00 3.02
171 172 1.002624 GCGGATGGGAAGTGGTCAA 60.003 57.895 0.00 0.00 0.00 3.18
172 173 2.668632 GCGGATGGGAAGTGGTCA 59.331 61.111 0.00 0.00 0.00 4.02
173 174 2.124695 GGCGGATGGGAAGTGGTC 60.125 66.667 0.00 0.00 0.00 4.02
174 175 2.231380 AAGGCGGATGGGAAGTGGT 61.231 57.895 0.00 0.00 0.00 4.16
185 186 4.344865 GGGCAAGGACAAGGCGGA 62.345 66.667 0.00 0.00 0.00 5.54
203 204 5.667466 GGACGAGAATGAATAAACCCACTA 58.333 41.667 0.00 0.00 0.00 2.74
217 218 0.928229 GCAATAACGCGGACGAGAAT 59.072 50.000 12.47 0.00 43.93 2.40
253 263 1.180029 GAGTGTCTGTAGGCGGGTAA 58.820 55.000 0.00 0.00 0.00 2.85
262 272 3.170991 AGTAAGCAGGGAGTGTCTGTA 57.829 47.619 0.00 0.00 34.89 2.74
351 398 2.472695 AAACACGAAGCATGCCTCTA 57.527 45.000 15.66 0.00 0.00 2.43
355 402 1.689959 CAGAAAACACGAAGCATGCC 58.310 50.000 15.66 0.00 0.00 4.40
356 403 1.055338 GCAGAAAACACGAAGCATGC 58.945 50.000 10.51 10.51 0.00 4.06
357 404 2.693797 AGCAGAAAACACGAAGCATG 57.306 45.000 0.00 0.00 0.00 4.06
359 406 2.013400 TCAAGCAGAAAACACGAAGCA 58.987 42.857 0.00 0.00 0.00 3.91
378 430 3.423154 CCCGTCCTGCGCACTTTC 61.423 66.667 5.66 0.00 39.71 2.62
379 431 3.883744 CTCCCGTCCTGCGCACTTT 62.884 63.158 5.66 0.00 39.71 2.66
390 442 1.480954 TGAATTACAGCCTCTCCCGTC 59.519 52.381 0.00 0.00 0.00 4.79
391 443 1.482593 CTGAATTACAGCCTCTCCCGT 59.517 52.381 0.00 0.00 39.86 5.28
402 454 4.331968 CCTGCTTTACCCACTGAATTACA 58.668 43.478 0.00 0.00 0.00 2.41
434 486 8.183104 ACATCTAAGTAGCAGCTATTGTATCA 57.817 34.615 5.14 0.00 0.00 2.15
450 538 5.773176 CCTTGGGTTTGGTTTACATCTAAGT 59.227 40.000 0.00 0.00 0.00 2.24
451 539 6.007703 TCCTTGGGTTTGGTTTACATCTAAG 58.992 40.000 0.00 0.00 0.00 2.18
453 541 5.586155 TCCTTGGGTTTGGTTTACATCTA 57.414 39.130 0.00 0.00 0.00 1.98
454 542 4.463050 TCCTTGGGTTTGGTTTACATCT 57.537 40.909 0.00 0.00 0.00 2.90
459 547 4.252570 TCACTTCCTTGGGTTTGGTTTA 57.747 40.909 0.00 0.00 0.00 2.01
460 548 3.108847 TCACTTCCTTGGGTTTGGTTT 57.891 42.857 0.00 0.00 0.00 3.27
478 570 7.819900 GTCCTTTCTCTAGTCTAGCATTTTTCA 59.180 37.037 1.60 0.00 0.00 2.69
493 613 6.742756 TCTTATTCTCCTGGTCCTTTCTCTA 58.257 40.000 0.00 0.00 0.00 2.43
496 616 6.704056 TTTCTTATTCTCCTGGTCCTTTCT 57.296 37.500 0.00 0.00 0.00 2.52
497 617 7.761038 TTTTTCTTATTCTCCTGGTCCTTTC 57.239 36.000 0.00 0.00 0.00 2.62
498 618 7.950124 TCATTTTTCTTATTCTCCTGGTCCTTT 59.050 33.333 0.00 0.00 0.00 3.11
503 623 7.121907 GCTTCTCATTTTTCTTATTCTCCTGGT 59.878 37.037 0.00 0.00 0.00 4.00
505 625 8.048534 TGCTTCTCATTTTTCTTATTCTCCTG 57.951 34.615 0.00 0.00 0.00 3.86
513 633 9.944376 ACTAGTGTATGCTTCTCATTTTTCTTA 57.056 29.630 0.00 0.00 36.63 2.10
517 637 7.387948 ACGAACTAGTGTATGCTTCTCATTTTT 59.612 33.333 0.00 0.00 36.63 1.94
531 653 3.762288 AGGCAATCTGACGAACTAGTGTA 59.238 43.478 0.00 0.00 0.00 2.90
550 672 5.997746 TCCATAAATTACATACTGCAGAGGC 59.002 40.000 23.35 0.00 41.68 4.70
556 678 9.480053 AAATTGCATCCATAAATTACATACTGC 57.520 29.630 0.00 0.00 0.00 4.40
583 1478 7.928307 TCATGAGAAAACTAGGAATTCCTTG 57.072 36.000 31.45 29.43 46.09 3.61
590 1485 7.094205 GCAAGGAAATCATGAGAAAACTAGGAA 60.094 37.037 0.09 0.00 0.00 3.36
605 1500 9.265434 ATAGATGTTCTACCCGCAAGGAAATCA 62.265 40.741 0.00 0.00 46.85 2.57
618 1811 7.387643 GGAACCATCCTTATAGATGTTCTACC 58.612 42.308 0.00 0.00 41.79 3.18
772 1969 7.103641 TGGACTTGCTAATAAACTAACCAGAG 58.896 38.462 0.00 0.00 0.00 3.35
773 1970 7.011499 TGGACTTGCTAATAAACTAACCAGA 57.989 36.000 0.00 0.00 0.00 3.86
819 2034 0.811616 GATGGTCCAGCTACTTGCCG 60.812 60.000 0.00 0.00 44.23 5.69
960 2230 3.119101 AGCTTACACGGATGTAGAAGTGG 60.119 47.826 0.00 0.00 42.29 4.00
961 2231 4.106197 GAGCTTACACGGATGTAGAAGTG 58.894 47.826 0.00 0.00 42.29 3.16
962 2232 3.762288 TGAGCTTACACGGATGTAGAAGT 59.238 43.478 0.00 0.00 42.29 3.01
963 2233 4.106197 GTGAGCTTACACGGATGTAGAAG 58.894 47.826 3.32 0.00 42.29 2.85
964 2234 3.119245 GGTGAGCTTACACGGATGTAGAA 60.119 47.826 11.15 0.00 42.29 2.10
965 2235 2.426024 GGTGAGCTTACACGGATGTAGA 59.574 50.000 11.15 0.00 42.29 2.59
966 2236 2.165641 TGGTGAGCTTACACGGATGTAG 59.834 50.000 11.15 0.00 42.29 2.74
967 2237 2.094390 GTGGTGAGCTTACACGGATGTA 60.094 50.000 11.15 0.00 40.48 2.29
968 2238 0.973632 TGGTGAGCTTACACGGATGT 59.026 50.000 11.15 0.00 43.30 3.06
969 2239 1.066858 AGTGGTGAGCTTACACGGATG 60.067 52.381 11.15 0.00 41.12 3.51
970 2240 1.204941 GAGTGGTGAGCTTACACGGAT 59.795 52.381 11.15 0.00 41.12 4.18
971 2241 0.601558 GAGTGGTGAGCTTACACGGA 59.398 55.000 11.15 0.00 41.12 4.69
972 2242 0.603569 AGAGTGGTGAGCTTACACGG 59.396 55.000 11.15 0.00 41.12 4.94
973 2243 3.784701 ATAGAGTGGTGAGCTTACACG 57.215 47.619 11.15 0.00 41.12 4.49
1143 2423 2.440539 AGACGAGCAATCGAAAGTGT 57.559 45.000 4.44 0.00 36.85 3.55
1169 2450 2.229792 GCAGTGTGGAATGACCTGAAA 58.770 47.619 0.00 0.00 39.86 2.69
1188 2469 7.114953 GCAAAGACTAAGAAAACTATTTGTGGC 59.885 37.037 0.00 0.00 0.00 5.01
1192 2473 9.346725 GATGGCAAAGACTAAGAAAACTATTTG 57.653 33.333 0.00 0.00 0.00 2.32
1257 5804 2.743636 AAGTTAGCTAGCTGCAACGA 57.256 45.000 27.68 2.54 45.94 3.85
1492 6278 1.826921 GGAGCTCATGGGCCATGTG 60.827 63.158 38.04 35.73 41.98 3.21
1642 6621 2.611971 GGTTGTACTCATGCTCGTCCAA 60.612 50.000 0.00 0.00 0.00 3.53
1820 6814 2.095461 GATGGAAGTCCTTGGCTTTCC 58.905 52.381 12.18 12.18 39.59 3.13
1865 6865 3.244596 GGGGCTCTCTCCATTATAACCAC 60.245 52.174 0.00 0.00 0.00 4.16
1937 6940 2.158957 TCCTTATCACGGCCAATCACTC 60.159 50.000 2.24 0.00 0.00 3.51
2061 7064 2.846193 TGTTGTGCTAAGGTGGACTTC 58.154 47.619 0.00 0.00 40.64 3.01
2162 7166 4.590647 ACTCAATGATCTCCCGTGTATGAT 59.409 41.667 0.00 0.00 0.00 2.45
2329 7338 5.137551 GGAGAGTAGAGGAGCTAACAGATT 58.862 45.833 0.00 0.00 0.00 2.40
2331 7340 3.117813 GGGAGAGTAGAGGAGCTAACAGA 60.118 52.174 0.00 0.00 0.00 3.41
2420 7430 6.971726 TGTTTTCTAGAGGACACACTTCTA 57.028 37.500 6.25 0.00 36.38 2.10
2436 7446 8.302515 AGAAATATGCATCTTCCATGTTTTCT 57.697 30.769 0.19 3.14 35.20 2.52
2454 7464 6.294731 GGTGTTTGAAGAGTGCCAAGAAATAT 60.295 38.462 0.00 0.00 0.00 1.28
2541 7563 4.460382 CCAAGCCTTTTAGCAATCTTCTCA 59.540 41.667 0.00 0.00 34.23 3.27
2612 7634 9.559732 CATCCTTCCATGTAGATATGTTTGTTA 57.440 33.333 0.00 0.00 0.00 2.41
2663 7685 2.005451 GTGCTGTCATAGGCTCACTTG 58.995 52.381 0.00 0.00 0.00 3.16
2712 7734 0.819259 GGAAGCACCTCTGCACACAA 60.819 55.000 0.00 0.00 46.97 3.33
2829 7851 5.221621 CCTCCCAATATCTTCCACTCTCTTC 60.222 48.000 0.00 0.00 0.00 2.87
2893 7922 5.184864 TGCAACCGAATTTCTTATCAACCAT 59.815 36.000 0.00 0.00 0.00 3.55
2894 7923 4.520874 TGCAACCGAATTTCTTATCAACCA 59.479 37.500 0.00 0.00 0.00 3.67
2895 7924 4.857037 GTGCAACCGAATTTCTTATCAACC 59.143 41.667 0.00 0.00 0.00 3.77
2969 8037 1.204941 CCAACCTGAAGTAGTCCTCCG 59.795 57.143 0.00 0.00 0.00 4.63
2970 8038 2.537143 TCCAACCTGAAGTAGTCCTCC 58.463 52.381 0.00 0.00 0.00 4.30
3016 8084 3.635373 ACGGATATATGTCGAACTGTGGT 59.365 43.478 10.79 0.00 0.00 4.16
3036 8104 3.425525 GCATCATACTATCAACACGGACG 59.574 47.826 0.00 0.00 0.00 4.79
3075 8143 3.565063 TGCGTAAATGATGTAGCATGCAT 59.435 39.130 21.98 4.29 46.79 3.96
3080 8148 8.088365 AGATAATAGTGCGTAAATGATGTAGCA 58.912 33.333 0.00 0.00 0.00 3.49
3180 8256 7.531857 ACTGGTGTAAGATGACAGATATAGG 57.468 40.000 0.00 0.00 33.57 2.57
3187 8263 7.159322 ACTTACTACTGGTGTAAGATGACAG 57.841 40.000 20.70 0.00 45.65 3.51
3200 8276 4.872691 CAGATTCTGGCAACTTACTACTGG 59.127 45.833 5.73 0.00 37.61 4.00
3282 8366 7.159372 GGTAAAGAGTACACAAAGATCTTGGA 58.841 38.462 17.08 0.00 30.90 3.53
3291 8375 5.186942 TGCAAGTGGTAAAGAGTACACAAA 58.813 37.500 0.00 0.00 36.35 2.83
3402 8486 0.110823 CTTTCCGCTCGTTTGTTCGG 60.111 55.000 0.00 0.00 42.96 4.30
3439 8541 3.254166 AGTGAAGTTAGCTTGCCAATGTG 59.746 43.478 0.00 0.00 34.61 3.21
3512 8614 5.397360 TCTCATTCATATCCCTCAGCTGTA 58.603 41.667 14.67 0.00 0.00 2.74
3582 8684 6.238320 GCAACTTCGATTCTAATGCTTCATCT 60.238 38.462 0.00 0.00 0.00 2.90
3612 8714 4.320494 CGCAAGCTACCAAGATGACTTTTT 60.320 41.667 0.00 0.00 33.70 1.94
4165 9286 1.420138 TCCAAGGACACTTCCAAGGTC 59.580 52.381 0.00 0.00 45.72 3.85
4305 9429 1.197949 GAAAGAGAAAGCCCACGAAGC 59.802 52.381 0.00 0.00 0.00 3.86
5251 10405 8.934023 TTGTAGGTGGAAATCTAAATCAGTTT 57.066 30.769 0.00 0.00 0.00 2.66
5252 10406 8.934023 TTTGTAGGTGGAAATCTAAATCAGTT 57.066 30.769 0.00 0.00 0.00 3.16
5283 10438 4.526970 GATGGGAGCTCATTTACCTTTCA 58.473 43.478 17.19 0.00 0.00 2.69
5295 10452 4.554036 GGTGGCCGATGGGAGCTC 62.554 72.222 4.71 4.71 34.06 4.09
5314 10471 4.240881 ACATACATCTTTGAGGGTGCAT 57.759 40.909 0.00 0.00 0.00 3.96
5784 11152 2.294078 GGAGGTGGTCCAGGAGGTG 61.294 68.421 0.00 0.00 46.10 4.00
5785 11153 2.122954 GGAGGTGGTCCAGGAGGT 59.877 66.667 0.00 0.00 46.10 3.85
5793 12220 1.261238 CCAGAGGACAGGAGGTGGTC 61.261 65.000 0.00 0.00 0.00 4.02
6212 12652 2.676632 ACAGAGCAGAGAATGAGCAG 57.323 50.000 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.