Multiple sequence alignment - TraesCS2B01G584500

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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 TraesCS2B01G584500 chr2B 100.000 4725 0 0 297 5021 771420829 771416105 0.000000e+00 8726.0
1 TraesCS2B01G584500 chr2B 96.633 980 33 0 3313 4292 771488157 771487178 0.000000e+00 1628.0
2 TraesCS2B01G584500 chr2B 93.731 989 36 14 441 1411 771489492 771488512 0.000000e+00 1459.0
3 TraesCS2B01G584500 chr2B 95.777 734 24 5 4290 5021 771480868 771480140 0.000000e+00 1177.0
4 TraesCS2B01G584500 chr2B 97.802 364 8 0 2903 3266 771488519 771488156 3.300000e-176 628.0
5 TraesCS2B01G584500 chr2B 96.403 139 4 1 2760 2898 535579459 535579596 1.410000e-55 228.0
6 TraesCS2B01G584500 chr2B 100.000 62 0 0 1 62 771421125 771421064 1.140000e-21 115.0
7 TraesCS2B01G584500 chr2B 82.927 123 11 8 448 563 751582780 751582899 8.890000e-18 102.0
8 TraesCS2B01G584500 chr2B 80.180 111 17 5 447 556 752950011 752949905 1.500000e-10 78.7
9 TraesCS2B01G584500 chr6D 90.422 2182 144 38 2881 5021 459549230 459551387 0.000000e+00 2811.0
10 TraesCS2B01G584500 chr6D 86.344 1589 125 49 2881 4413 471274698 471276250 0.000000e+00 1648.0
11 TraesCS2B01G584500 chr6D 91.805 1025 44 13 3335 4326 471114096 471113079 0.000000e+00 1391.0
12 TraesCS2B01G584500 chr6D 86.386 404 46 4 2922 3325 471114546 471114152 2.780000e-117 433.0
13 TraesCS2B01G584500 chr6D 83.182 440 42 23 705 1126 471115148 471114723 1.710000e-99 374.0
14 TraesCS2B01G584500 chr6D 88.803 259 14 11 879 1126 471274197 471274451 2.270000e-78 303.0
15 TraesCS2B01G584500 chr6D 87.333 150 13 3 982 1125 459548504 459548653 3.110000e-37 167.0
16 TraesCS2B01G584500 chr6D 85.246 122 13 4 4669 4785 471276027 471276148 2.460000e-23 121.0
17 TraesCS2B01G584500 chr6D 82.143 112 11 6 740 851 471262532 471262634 2.490000e-13 87.9
18 TraesCS2B01G584500 chr1B 98.964 1351 12 2 1409 2758 641616881 641618230 0.000000e+00 2416.0
19 TraesCS2B01G584500 chr1B 99.180 1342 10 1 1416 2757 655769508 655770848 0.000000e+00 2416.0
20 TraesCS2B01G584500 chr1B 98.253 1374 18 6 1387 2758 405927343 405928712 0.000000e+00 2399.0
21 TraesCS2B01G584500 chr1B 97.059 136 3 1 2760 2895 39681512 39681646 1.410000e-55 228.0
22 TraesCS2B01G584500 chr3B 99.107 1344 10 2 1416 2758 695915044 695916386 0.000000e+00 2414.0
23 TraesCS2B01G584500 chr3B 99.194 124 1 0 2760 2883 695918229 695918352 1.820000e-54 224.0
24 TraesCS2B01G584500 chr1A 99.035 1347 11 2 1412 2758 517045160 517046504 0.000000e+00 2414.0
25 TraesCS2B01G584500 chr6B 99.034 1346 12 1 1413 2758 692135537 692136881 0.000000e+00 2412.0
26 TraesCS2B01G584500 chr6B 89.382 1441 108 21 2923 4326 719423221 719424653 0.000000e+00 1772.0
27 TraesCS2B01G584500 chr6B 82.127 442 40 21 3915 4326 719309221 719308789 4.810000e-90 342.0
28 TraesCS2B01G584500 chr6B 85.075 268 20 8 869 1126 719422786 719423043 6.450000e-64 255.0
29 TraesCS2B01G584500 chr6B 85.000 180 15 10 705 880 719422583 719422754 6.680000e-39 172.0
30 TraesCS2B01G584500 chr6B 94.118 51 1 1 4370 4420 719308790 719308742 5.390000e-10 76.8
31 TraesCS2B01G584500 chr2A 99.106 1343 11 1 1416 2758 748456864 748455523 0.000000e+00 2412.0
32 TraesCS2B01G584500 chr2A 98.961 1347 13 1 1412 2758 687328411 687327066 0.000000e+00 2409.0
33 TraesCS2B01G584500 chr6A 98.538 1368 13 7 1397 2758 104522007 104520641 0.000000e+00 2409.0
34 TraesCS2B01G584500 chr6A 88.575 1453 107 28 2881 4290 616054268 616055704 0.000000e+00 1709.0
35 TraesCS2B01G584500 chr6A 81.150 626 79 26 4426 5021 616055319 616055935 2.740000e-127 466.0
36 TraesCS2B01G584500 chr6A 90.323 186 13 3 945 1126 616053831 616054015 6.500000e-59 239.0
37 TraesCS2B01G584500 chr6A 98.473 131 2 0 2760 2890 110070183 110070053 1.090000e-56 231.0
38 TraesCS2B01G584500 chr3A 87.076 1532 133 36 2935 4420 574278797 574280309 0.000000e+00 1672.0
39 TraesCS2B01G584500 chr3A 88.518 1228 104 29 2888 4096 574320708 574319499 0.000000e+00 1452.0
40 TraesCS2B01G584500 chr3A 86.275 153 9 6 985 1125 574321913 574321761 6.730000e-34 156.0
41 TraesCS2B01G584500 chr3A 74.219 384 68 20 4426 4782 574279800 574280179 1.130000e-26 132.0
42 TraesCS2B01G584500 chr7B 81.844 1052 143 28 2929 3973 707884208 707883198 0.000000e+00 841.0
43 TraesCS2B01G584500 chr7B 88.689 389 27 10 4430 4808 680075351 680074970 4.580000e-125 459.0
44 TraesCS2B01G584500 chr7B 88.462 338 27 8 4426 4753 707881467 707881132 1.010000e-106 398.0
45 TraesCS2B01G584500 chr7B 96.429 140 2 3 2754 2893 254671690 254671554 1.410000e-55 228.0
46 TraesCS2B01G584500 chr7B 96.040 101 3 1 4922 5021 680074965 680074865 4.020000e-36 163.0
47 TraesCS2B01G584500 chr7B 93.182 88 4 2 4936 5021 707880919 707880832 1.470000e-25 128.0
48 TraesCS2B01G584500 chr7D 88.760 605 34 16 4426 5020 600865475 600864895 0.000000e+00 710.0
49 TraesCS2B01G584500 chr7D 82.550 298 41 3 2929 3226 600866201 600865915 8.340000e-63 252.0
50 TraesCS2B01G584500 chr7D 96.078 102 4 0 297 398 553369322 553369423 3.110000e-37 167.0
51 TraesCS2B01G584500 chr7D 98.387 62 1 0 1 62 553369184 553369245 5.310000e-20 110.0
52 TraesCS2B01G584500 chr7A 89.371 461 30 9 4426 4877 692785343 692784893 3.390000e-156 562.0
53 TraesCS2B01G584500 chr7A 96.667 90 2 1 4933 5021 692784897 692784808 1.130000e-31 148.0
54 TraesCS2B01G584500 chr5B 97.744 133 3 0 2760 2892 207036264 207036396 3.910000e-56 230.0
55 TraesCS2B01G584500 chr5B 98.387 62 1 0 1 62 412283210 412283271 5.310000e-20 110.0
56 TraesCS2B01G584500 chrUn 99.206 126 1 0 2760 2885 217442945 217443070 1.410000e-55 228.0
57 TraesCS2B01G584500 chrUn 99.206 126 1 0 2760 2885 217449742 217449867 1.410000e-55 228.0
58 TraesCS2B01G584500 chr2D 94.483 145 5 3 2760 2904 532677962 532678103 2.350000e-53 220.0
59 TraesCS2B01G584500 chr2D 82.609 115 17 3 441 553 23319760 23319647 1.150000e-16 99.0
60 TraesCS2B01G584500 chr2D 94.643 56 2 1 640 695 628573101 628573155 8.960000e-13 86.1
61 TraesCS2B01G584500 chr5D 85.366 123 12 4 438 558 9638497 9638615 6.830000e-24 122.0


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 TraesCS2B01G584500 chr2B 771416105 771421125 5020 True 4420.500000 8726 100.000000 1 5021 2 chr2B.!!$R3 5020
1 TraesCS2B01G584500 chr2B 771487178 771489492 2314 True 1238.333333 1628 96.055333 441 4292 3 chr2B.!!$R4 3851
2 TraesCS2B01G584500 chr2B 771480140 771480868 728 True 1177.000000 1177 95.777000 4290 5021 1 chr2B.!!$R2 731
3 TraesCS2B01G584500 chr6D 459548504 459551387 2883 False 1489.000000 2811 88.877500 982 5021 2 chr6D.!!$F2 4039
4 TraesCS2B01G584500 chr6D 471113079 471115148 2069 True 732.666667 1391 87.124333 705 4326 3 chr6D.!!$R1 3621
5 TraesCS2B01G584500 chr6D 471274197 471276250 2053 False 690.666667 1648 86.797667 879 4785 3 chr6D.!!$F3 3906
6 TraesCS2B01G584500 chr1B 641616881 641618230 1349 False 2416.000000 2416 98.964000 1409 2758 1 chr1B.!!$F3 1349
7 TraesCS2B01G584500 chr1B 655769508 655770848 1340 False 2416.000000 2416 99.180000 1416 2757 1 chr1B.!!$F4 1341
8 TraesCS2B01G584500 chr1B 405927343 405928712 1369 False 2399.000000 2399 98.253000 1387 2758 1 chr1B.!!$F2 1371
9 TraesCS2B01G584500 chr3B 695915044 695918352 3308 False 1319.000000 2414 99.150500 1416 2883 2 chr3B.!!$F1 1467
10 TraesCS2B01G584500 chr1A 517045160 517046504 1344 False 2414.000000 2414 99.035000 1412 2758 1 chr1A.!!$F1 1346
11 TraesCS2B01G584500 chr6B 692135537 692136881 1344 False 2412.000000 2412 99.034000 1413 2758 1 chr6B.!!$F1 1345
12 TraesCS2B01G584500 chr6B 719422583 719424653 2070 False 733.000000 1772 86.485667 705 4326 3 chr6B.!!$F2 3621
13 TraesCS2B01G584500 chr2A 748455523 748456864 1341 True 2412.000000 2412 99.106000 1416 2758 1 chr2A.!!$R2 1342
14 TraesCS2B01G584500 chr2A 687327066 687328411 1345 True 2409.000000 2409 98.961000 1412 2758 1 chr2A.!!$R1 1346
15 TraesCS2B01G584500 chr6A 104520641 104522007 1366 True 2409.000000 2409 98.538000 1397 2758 1 chr6A.!!$R1 1361
16 TraesCS2B01G584500 chr6A 616053831 616055935 2104 False 804.666667 1709 86.682667 945 5021 3 chr6A.!!$F1 4076
17 TraesCS2B01G584500 chr3A 574278797 574280309 1512 False 902.000000 1672 80.647500 2935 4782 2 chr3A.!!$F1 1847
18 TraesCS2B01G584500 chr3A 574319499 574321913 2414 True 804.000000 1452 87.396500 985 4096 2 chr3A.!!$R1 3111
19 TraesCS2B01G584500 chr7B 707880832 707884208 3376 True 455.666667 841 87.829333 2929 5021 3 chr7B.!!$R3 2092
20 TraesCS2B01G584500 chr7D 600864895 600866201 1306 True 481.000000 710 85.655000 2929 5020 2 chr7D.!!$R1 2091
21 TraesCS2B01G584500 chr7A 692784808 692785343 535 True 355.000000 562 93.019000 4426 5021 2 chr7A.!!$R1 595

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
60 61 0.037232 CCCCAACTGTTCCTCGAGAC 60.037 60.000 15.71 5.57 0.00 3.36 F
417 418 0.249073 CGAGCCTCTGGTCCGTATTG 60.249 60.000 0.00 0.00 35.55 1.90 F
418 419 0.530870 GAGCCTCTGGTCCGTATTGC 60.531 60.000 0.00 0.00 32.76 3.56 F
464 465 0.603569 TTCAGTCTCTCGAAGGTGCC 59.396 55.000 0.00 0.00 0.00 5.01 F
810 826 1.066587 CAGAGGGAAGCGATCGACC 59.933 63.158 21.57 17.42 0.00 4.79 F
904 965 1.108727 CCAGTGCCACCAGAAAGCAA 61.109 55.000 0.00 0.00 38.45 3.91 F
2924 5752 0.030235 GCGTTCCTGTGACCAAAACC 59.970 55.000 0.00 0.00 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1504 2093 1.206878 TGCTATCCATGTGCCAGAGT 58.793 50.000 0.00 0.0 0.00 3.24 R
2069 2659 2.912020 GGTGGTACCTCGGAAGGAT 58.088 57.895 14.36 0.0 46.67 3.24 R
2176 2766 2.971901 ACCTTGGAATCGAAAGGGTT 57.028 45.000 16.12 0.0 46.12 4.11 R
2676 3266 2.475155 TGGGAGAGAGTCATTGAGCAT 58.525 47.619 0.00 0.0 0.00 3.79 R
2898 5329 2.236146 TGGTCACAGGAACGCATAGATT 59.764 45.455 0.00 0.0 31.55 2.40 R
3107 5935 2.863740 GTTGCGATTGTGATCCGATGTA 59.136 45.455 0.00 0.0 0.00 2.29 R
4460 9246 0.463295 CCGCTCATTCACCATGCTCT 60.463 55.000 0.00 0.0 32.13 4.09 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
17 18 4.643387 AGGACCAGCGGTGTTGCC 62.643 66.667 14.40 11.26 35.25 4.52
18 19 4.643387 GGACCAGCGGTGTTGCCT 62.643 66.667 14.40 0.00 35.25 4.75
19 20 3.050275 GACCAGCGGTGTTGCCTC 61.050 66.667 14.40 0.00 35.25 4.70
20 21 3.537206 GACCAGCGGTGTTGCCTCT 62.537 63.158 14.40 0.00 35.25 3.69
21 22 2.281761 CCAGCGGTGTTGCCTCTT 60.282 61.111 14.40 0.00 34.65 2.85
22 23 2.328099 CCAGCGGTGTTGCCTCTTC 61.328 63.158 14.40 0.00 34.65 2.87
23 24 2.032681 AGCGGTGTTGCCTCTTCC 59.967 61.111 0.00 0.00 34.65 3.46
24 25 2.032681 GCGGTGTTGCCTCTTCCT 59.967 61.111 0.00 0.00 34.25 3.36
25 26 2.035442 GCGGTGTTGCCTCTTCCTC 61.035 63.158 0.00 0.00 34.25 3.71
26 27 1.674057 CGGTGTTGCCTCTTCCTCT 59.326 57.895 0.00 0.00 34.25 3.69
27 28 0.671781 CGGTGTTGCCTCTTCCTCTG 60.672 60.000 0.00 0.00 34.25 3.35
28 29 0.687354 GGTGTTGCCTCTTCCTCTGA 59.313 55.000 0.00 0.00 0.00 3.27
29 30 1.338579 GGTGTTGCCTCTTCCTCTGAG 60.339 57.143 0.00 0.00 0.00 3.35
30 31 1.620819 GTGTTGCCTCTTCCTCTGAGA 59.379 52.381 6.17 0.00 33.68 3.27
31 32 2.235898 GTGTTGCCTCTTCCTCTGAGAT 59.764 50.000 6.17 0.00 33.68 2.75
32 33 2.235650 TGTTGCCTCTTCCTCTGAGATG 59.764 50.000 6.17 0.00 33.68 2.90
33 34 2.235898 GTTGCCTCTTCCTCTGAGATGT 59.764 50.000 6.17 0.00 33.68 3.06
34 35 2.106566 TGCCTCTTCCTCTGAGATGTC 58.893 52.381 6.17 0.00 33.68 3.06
35 36 1.066908 GCCTCTTCCTCTGAGATGTCG 59.933 57.143 6.17 0.00 33.68 4.35
36 37 2.649190 CCTCTTCCTCTGAGATGTCGA 58.351 52.381 6.17 0.00 33.68 4.20
37 38 2.618241 CCTCTTCCTCTGAGATGTCGAG 59.382 54.545 6.17 4.70 33.68 4.04
38 39 3.278574 CTCTTCCTCTGAGATGTCGAGT 58.721 50.000 6.17 0.00 33.68 4.18
39 40 3.691575 TCTTCCTCTGAGATGTCGAGTT 58.308 45.455 6.17 0.00 0.00 3.01
40 41 4.082845 TCTTCCTCTGAGATGTCGAGTTT 58.917 43.478 6.17 0.00 0.00 2.66
41 42 4.156922 TCTTCCTCTGAGATGTCGAGTTTC 59.843 45.833 6.17 0.00 0.00 2.78
42 43 2.755655 TCCTCTGAGATGTCGAGTTTCC 59.244 50.000 6.17 0.00 0.00 3.13
43 44 2.159170 CCTCTGAGATGTCGAGTTTCCC 60.159 54.545 6.17 0.00 0.00 3.97
44 45 1.825474 TCTGAGATGTCGAGTTTCCCC 59.175 52.381 0.00 0.00 0.00 4.81
45 46 1.550524 CTGAGATGTCGAGTTTCCCCA 59.449 52.381 0.00 0.00 0.00 4.96
46 47 1.974957 TGAGATGTCGAGTTTCCCCAA 59.025 47.619 0.00 0.00 0.00 4.12
47 48 2.289444 TGAGATGTCGAGTTTCCCCAAC 60.289 50.000 0.00 0.00 35.32 3.77
49 50 2.076863 GATGTCGAGTTTCCCCAACTG 58.923 52.381 0.00 0.00 46.53 3.16
50 51 0.834612 TGTCGAGTTTCCCCAACTGT 59.165 50.000 0.00 0.00 46.53 3.55
51 52 1.210967 TGTCGAGTTTCCCCAACTGTT 59.789 47.619 0.00 0.00 46.53 3.16
52 53 1.871676 GTCGAGTTTCCCCAACTGTTC 59.128 52.381 0.00 0.00 46.53 3.18
53 54 1.202722 TCGAGTTTCCCCAACTGTTCC 60.203 52.381 0.00 0.00 46.53 3.62
54 55 1.202770 CGAGTTTCCCCAACTGTTCCT 60.203 52.381 0.00 0.00 46.53 3.36
55 56 2.505405 GAGTTTCCCCAACTGTTCCTC 58.495 52.381 0.00 0.00 46.53 3.71
56 57 1.202770 AGTTTCCCCAACTGTTCCTCG 60.203 52.381 0.00 0.00 44.70 4.63
57 58 1.133363 TTTCCCCAACTGTTCCTCGA 58.867 50.000 0.00 0.00 0.00 4.04
58 59 0.685097 TTCCCCAACTGTTCCTCGAG 59.315 55.000 5.13 5.13 0.00 4.04
59 60 0.178944 TCCCCAACTGTTCCTCGAGA 60.179 55.000 15.71 0.00 0.00 4.04
60 61 0.037232 CCCCAACTGTTCCTCGAGAC 60.037 60.000 15.71 5.57 0.00 3.36
61 62 0.388649 CCCAACTGTTCCTCGAGACG 60.389 60.000 15.71 0.00 0.00 4.18
313 314 3.564027 GATCTCAAACGCGCCCCG 61.564 66.667 5.73 0.00 44.21 5.73
326 327 3.781307 CCCCGTCGATCAAGCCCA 61.781 66.667 0.00 0.00 0.00 5.36
327 328 2.511600 CCCGTCGATCAAGCCCAC 60.512 66.667 0.00 0.00 0.00 4.61
328 329 2.885644 CCGTCGATCAAGCCCACG 60.886 66.667 0.00 0.00 0.00 4.94
329 330 2.885644 CGTCGATCAAGCCCACGG 60.886 66.667 0.00 0.00 0.00 4.94
330 331 2.511600 GTCGATCAAGCCCACGGG 60.512 66.667 0.00 0.00 38.57 5.28
348 349 4.215742 CGCCGCCAAGATCCGGTA 62.216 66.667 0.00 0.00 45.98 4.02
349 350 2.188469 GCCGCCAAGATCCGGTAA 59.812 61.111 0.00 0.00 45.98 2.85
350 351 1.450669 GCCGCCAAGATCCGGTAAA 60.451 57.895 0.00 0.00 45.98 2.01
351 352 1.712018 GCCGCCAAGATCCGGTAAAC 61.712 60.000 0.00 0.00 45.98 2.01
352 353 1.093496 CCGCCAAGATCCGGTAAACC 61.093 60.000 0.00 0.00 39.67 3.27
353 354 1.093496 CGCCAAGATCCGGTAAACCC 61.093 60.000 0.00 0.00 0.00 4.11
354 355 0.255033 GCCAAGATCCGGTAAACCCT 59.745 55.000 0.00 0.00 0.00 4.34
355 356 1.487558 GCCAAGATCCGGTAAACCCTA 59.512 52.381 0.00 0.00 0.00 3.53
356 357 2.484947 GCCAAGATCCGGTAAACCCTAG 60.485 54.545 0.00 0.00 0.00 3.02
357 358 2.770232 CCAAGATCCGGTAAACCCTAGT 59.230 50.000 0.00 0.00 0.00 2.57
358 359 3.181468 CCAAGATCCGGTAAACCCTAGTC 60.181 52.174 0.00 0.00 0.00 2.59
359 360 2.305009 AGATCCGGTAAACCCTAGTCG 58.695 52.381 0.00 0.00 0.00 4.18
360 361 0.749049 ATCCGGTAAACCCTAGTCGC 59.251 55.000 0.00 0.00 0.00 5.19
361 362 1.142531 CCGGTAAACCCTAGTCGCC 59.857 63.158 0.00 0.00 0.00 5.54
362 363 1.142531 CGGTAAACCCTAGTCGCCC 59.857 63.158 0.00 0.00 0.00 6.13
363 364 1.524002 GGTAAACCCTAGTCGCCCC 59.476 63.158 0.00 0.00 0.00 5.80
364 365 1.266867 GGTAAACCCTAGTCGCCCCA 61.267 60.000 0.00 0.00 0.00 4.96
365 366 0.614812 GTAAACCCTAGTCGCCCCAA 59.385 55.000 0.00 0.00 0.00 4.12
366 367 1.211212 GTAAACCCTAGTCGCCCCAAT 59.789 52.381 0.00 0.00 0.00 3.16
367 368 0.255033 AAACCCTAGTCGCCCCAATC 59.745 55.000 0.00 0.00 0.00 2.67
368 369 1.968050 AACCCTAGTCGCCCCAATCG 61.968 60.000 0.00 0.00 0.00 3.34
369 370 2.280186 CCTAGTCGCCCCAATCGC 60.280 66.667 0.00 0.00 0.00 4.58
370 371 2.280186 CTAGTCGCCCCAATCGCC 60.280 66.667 0.00 0.00 0.00 5.54
371 372 2.762459 TAGTCGCCCCAATCGCCT 60.762 61.111 0.00 0.00 0.00 5.52
372 373 2.311688 CTAGTCGCCCCAATCGCCTT 62.312 60.000 0.00 0.00 0.00 4.35
373 374 1.906105 TAGTCGCCCCAATCGCCTTT 61.906 55.000 0.00 0.00 0.00 3.11
374 375 2.749839 TCGCCCCAATCGCCTTTG 60.750 61.111 0.00 0.00 0.00 2.77
375 376 3.825611 CGCCCCAATCGCCTTTGG 61.826 66.667 5.51 5.51 44.82 3.28
387 388 4.016706 CTTTGGGAGGACCGCGGT 62.017 66.667 34.89 34.89 44.64 5.68
388 389 3.546714 CTTTGGGAGGACCGCGGTT 62.547 63.158 34.65 18.89 44.64 4.44
389 390 3.122727 TTTGGGAGGACCGCGGTTT 62.123 57.895 34.65 23.95 44.64 3.27
390 391 3.540367 TTGGGAGGACCGCGGTTTC 62.540 63.158 34.65 29.70 44.64 2.78
391 392 4.772687 GGGAGGACCGCGGTTTCC 62.773 72.222 36.23 36.23 36.97 3.13
403 404 1.577922 GGTTTCCGGAAAACGAGCC 59.422 57.895 30.49 22.20 46.85 4.70
404 405 0.887836 GGTTTCCGGAAAACGAGCCT 60.888 55.000 30.49 0.00 46.85 4.58
405 406 2.801993 GGTTTCCGGAAAACGAGCCTC 61.802 57.143 30.49 15.29 46.85 4.70
410 411 2.842320 GGAAAACGAGCCTCTGGTC 58.158 57.895 0.00 0.00 35.63 4.02
411 412 0.673956 GGAAAACGAGCCTCTGGTCC 60.674 60.000 0.00 0.00 35.55 4.46
412 413 1.004918 AAAACGAGCCTCTGGTCCG 60.005 57.895 0.00 0.00 35.55 4.79
413 414 1.755393 AAAACGAGCCTCTGGTCCGT 61.755 55.000 0.00 0.00 35.55 4.69
414 415 0.896940 AAACGAGCCTCTGGTCCGTA 60.897 55.000 0.00 0.00 35.55 4.02
415 416 0.683504 AACGAGCCTCTGGTCCGTAT 60.684 55.000 0.00 0.00 35.55 3.06
416 417 0.683504 ACGAGCCTCTGGTCCGTATT 60.684 55.000 0.00 0.00 35.55 1.89
417 418 0.249073 CGAGCCTCTGGTCCGTATTG 60.249 60.000 0.00 0.00 35.55 1.90
418 419 0.530870 GAGCCTCTGGTCCGTATTGC 60.531 60.000 0.00 0.00 32.76 3.56
419 420 1.523938 GCCTCTGGTCCGTATTGCC 60.524 63.158 0.00 0.00 0.00 4.52
420 421 1.904771 CCTCTGGTCCGTATTGCCA 59.095 57.895 0.00 0.00 0.00 4.92
422 423 4.540153 CTGGTCCGTATTGCCAGG 57.460 61.111 0.00 0.00 44.36 4.45
423 424 1.602237 CTGGTCCGTATTGCCAGGT 59.398 57.895 0.00 0.00 44.36 4.00
424 425 0.828022 CTGGTCCGTATTGCCAGGTA 59.172 55.000 0.00 0.00 44.36 3.08
425 426 1.416401 CTGGTCCGTATTGCCAGGTAT 59.584 52.381 0.00 0.00 44.36 2.73
426 427 1.841277 TGGTCCGTATTGCCAGGTATT 59.159 47.619 0.00 0.00 0.00 1.89
427 428 2.158871 TGGTCCGTATTGCCAGGTATTC 60.159 50.000 0.00 0.00 0.00 1.75
428 429 2.104281 GGTCCGTATTGCCAGGTATTCT 59.896 50.000 0.00 0.00 0.00 2.40
429 430 3.322828 GGTCCGTATTGCCAGGTATTCTA 59.677 47.826 0.00 0.00 0.00 2.10
430 431 4.020485 GGTCCGTATTGCCAGGTATTCTAT 60.020 45.833 0.00 0.00 0.00 1.98
431 432 5.169295 GTCCGTATTGCCAGGTATTCTATC 58.831 45.833 0.00 0.00 0.00 2.08
432 433 4.222145 TCCGTATTGCCAGGTATTCTATCC 59.778 45.833 0.00 0.00 0.00 2.59
433 434 4.223032 CCGTATTGCCAGGTATTCTATCCT 59.777 45.833 0.00 0.00 33.96 3.24
434 435 5.421056 CCGTATTGCCAGGTATTCTATCCTA 59.579 44.000 0.00 0.00 32.26 2.94
435 436 6.098409 CCGTATTGCCAGGTATTCTATCCTAT 59.902 42.308 0.00 0.00 32.26 2.57
436 437 7.203910 CGTATTGCCAGGTATTCTATCCTATC 58.796 42.308 0.00 0.00 32.26 2.08
437 438 6.567602 ATTGCCAGGTATTCTATCCTATCC 57.432 41.667 0.00 0.00 32.26 2.59
438 439 5.023514 TGCCAGGTATTCTATCCTATCCA 57.976 43.478 0.00 0.00 32.26 3.41
439 440 5.026121 TGCCAGGTATTCTATCCTATCCAG 58.974 45.833 0.00 0.00 32.26 3.86
440 441 4.407296 GCCAGGTATTCTATCCTATCCAGG 59.593 50.000 0.00 0.00 44.17 4.45
441 442 4.407296 CCAGGTATTCTATCCTATCCAGGC 59.593 50.000 0.00 0.00 42.30 4.85
442 443 4.407296 CAGGTATTCTATCCTATCCAGGCC 59.593 50.000 0.00 0.00 42.30 5.19
443 444 3.385111 GGTATTCTATCCTATCCAGGCCG 59.615 52.174 0.00 0.00 42.30 6.13
444 445 1.938585 TTCTATCCTATCCAGGCCGG 58.061 55.000 0.00 0.00 42.30 6.13
445 446 0.784495 TCTATCCTATCCAGGCCGGT 59.216 55.000 1.90 4.37 42.30 5.28
446 447 1.149288 TCTATCCTATCCAGGCCGGTT 59.851 52.381 1.90 7.73 42.30 4.44
464 465 0.603569 TTCAGTCTCTCGAAGGTGCC 59.396 55.000 0.00 0.00 0.00 5.01
486 487 5.426689 CCATAGGGATAGTATGTGCATGT 57.573 43.478 0.00 0.00 35.59 3.21
547 549 1.607713 CTCGCTCTGTACTGTGTTCG 58.392 55.000 0.00 0.00 0.00 3.95
575 584 4.143333 CGTACCCGGCTGACCCTG 62.143 72.222 0.00 0.00 0.00 4.45
589 600 3.207778 TGACCCTGAAAAACGTAACCTG 58.792 45.455 0.00 0.00 0.00 4.00
624 635 1.685765 GCCCCTCCCCAATTTCACC 60.686 63.158 0.00 0.00 0.00 4.02
719 730 1.388837 GGCCGTTTGGTTTGGTGACT 61.389 55.000 0.00 0.00 37.67 3.41
734 745 1.087202 TGACTGCGTGCGTGTTTTCT 61.087 50.000 0.00 0.00 0.00 2.52
809 825 1.590259 GCAGAGGGAAGCGATCGAC 60.590 63.158 21.57 10.46 0.00 4.20
810 826 1.066587 CAGAGGGAAGCGATCGACC 59.933 63.158 21.57 17.42 0.00 4.79
811 827 2.026301 GAGGGAAGCGATCGACCG 59.974 66.667 21.57 0.00 0.00 4.79
812 828 2.439701 AGGGAAGCGATCGACCGA 60.440 61.111 21.57 0.00 0.00 4.69
904 965 1.108727 CCAGTGCCACCAGAAAGCAA 61.109 55.000 0.00 0.00 38.45 3.91
909 970 1.667722 CCACCAGAAAGCAAAGGGC 59.332 57.895 0.00 0.00 45.30 5.19
918 979 3.579685 GCAAAGGGCGGAGAAGAC 58.420 61.111 0.00 0.00 0.00 3.01
1138 1230 7.067859 ACGACCAGAGTAATAACAATGCTACTA 59.932 37.037 0.00 0.00 0.00 1.82
1223 1320 5.533528 TCATTCATTGGATTGTGCTCATAGG 59.466 40.000 0.00 0.00 0.00 2.57
1227 1324 6.057533 TCATTGGATTGTGCTCATAGGTTAG 58.942 40.000 0.00 0.00 0.00 2.34
1248 1345 2.380084 TGTGGCTACGGATGAGAAAC 57.620 50.000 0.00 0.00 0.00 2.78
1409 1997 7.041780 GCTTTATTTATCATGGATGTGTCTCGT 60.042 37.037 0.00 0.00 0.00 4.18
1412 2000 9.825109 TTATTTATCATGGATGTGTCTCGTTTA 57.175 29.630 0.00 0.00 0.00 2.01
1413 2001 7.534085 TTTATCATGGATGTGTCTCGTTTAC 57.466 36.000 0.00 0.00 0.00 2.01
1414 2002 4.801330 TCATGGATGTGTCTCGTTTACT 57.199 40.909 0.00 0.00 0.00 2.24
1504 2093 2.234661 AGATCTCGCAACCAACTCATGA 59.765 45.455 0.00 0.00 0.00 3.07
1549 2138 1.305802 ACGCACCCCTGTCCATAGA 60.306 57.895 0.00 0.00 0.00 1.98
1690 2280 2.932194 AGCTTCTGGAGGCCTGCA 60.932 61.111 26.78 26.78 33.44 4.41
2176 2766 7.895759 TCGGTTTTAGTTCTACTAAGCCTAAA 58.104 34.615 14.49 0.00 41.23 1.85
2676 3266 4.928661 GCTTGTCATTCTTCTTAAGCGA 57.071 40.909 0.00 0.00 32.41 4.93
2728 3318 7.286087 TCATTGTATGGCTCATCAGCTTAATTT 59.714 33.333 0.00 0.00 46.03 1.82
2758 3348 8.258708 GGTAATTAGTACAACTCTGAACATCCT 58.741 37.037 0.00 0.00 34.01 3.24
2801 5232 6.721318 TCCATAAGAGTGGCTGAGTTTTTAT 58.279 36.000 0.00 0.00 39.19 1.40
2898 5329 5.049267 GGCGGAGTTTACTGATAACAACAAA 60.049 40.000 0.00 0.00 0.00 2.83
2924 5752 0.030235 GCGTTCCTGTGACCAAAACC 59.970 55.000 0.00 0.00 0.00 3.27
2931 5759 2.554032 CCTGTGACCAAAACCTAGCTTG 59.446 50.000 0.00 0.00 0.00 4.01
3059 5887 1.874345 GAGTGGCCGACCTCGAAGAA 61.874 60.000 0.00 0.00 43.02 2.52
3279 6111 3.591527 TGGACATTTGGATGGACCTACTT 59.408 43.478 0.00 0.00 37.60 2.24
3280 6112 3.947834 GGACATTTGGATGGACCTACTTG 59.052 47.826 0.00 0.00 37.60 3.16
3282 6114 5.440610 GACATTTGGATGGACCTACTTGAT 58.559 41.667 0.00 0.00 37.60 2.57
3284 6116 6.256053 ACATTTGGATGGACCTACTTGATTT 58.744 36.000 0.00 0.00 37.60 2.17
3301 6133 0.111061 TTTGACTGGCTGGAGCATGT 59.889 50.000 0.20 0.00 44.36 3.21
3305 6137 2.216898 GACTGGCTGGAGCATGTATTC 58.783 52.381 0.20 0.00 44.36 1.75
3657 8315 3.103911 GTCGCCGAGGTCACAACG 61.104 66.667 0.00 0.00 0.00 4.10
3675 8333 0.905337 CGGTGAGGGAAGGAGAGGTT 60.905 60.000 0.00 0.00 0.00 3.50
3835 8496 1.656652 CAAAGAAGACGGCGATGGAT 58.343 50.000 16.62 0.00 0.00 3.41
4460 9246 1.215673 TGTTGCCTGGTCCCTTGTTTA 59.784 47.619 0.00 0.00 0.00 2.01
4558 9348 1.304381 TGCTCCACCCAAGCATTCC 60.304 57.895 0.00 0.00 44.51 3.01
4559 9349 1.304381 GCTCCACCCAAGCATTCCA 60.304 57.895 0.00 0.00 39.61 3.53
4582 9374 6.127619 CCAGGTGTTCTTTGTTTTTCTCTCTT 60.128 38.462 0.00 0.00 0.00 2.85
4702 9518 5.235616 TCTTTGCTCAGTTGTAAGTAAACCG 59.764 40.000 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.643387 GGCAACACCGCTGGTCCT 62.643 66.667 0.00 0.00 31.02 3.85
7 8 2.032681 AGGAAGAGGCAACACCGC 59.967 61.111 0.00 0.00 46.52 5.68
10 11 1.620819 TCTCAGAGGAAGAGGCAACAC 59.379 52.381 0.00 0.00 41.41 3.32
11 12 2.015456 TCTCAGAGGAAGAGGCAACA 57.985 50.000 0.00 0.00 41.41 3.33
12 13 2.235898 ACATCTCAGAGGAAGAGGCAAC 59.764 50.000 0.00 0.00 33.92 4.17
13 14 2.499289 GACATCTCAGAGGAAGAGGCAA 59.501 50.000 0.00 0.00 33.92 4.52
14 15 2.106566 GACATCTCAGAGGAAGAGGCA 58.893 52.381 0.00 0.00 33.92 4.75
15 16 1.066908 CGACATCTCAGAGGAAGAGGC 59.933 57.143 0.00 0.00 33.92 4.70
16 17 2.618241 CTCGACATCTCAGAGGAAGAGG 59.382 54.545 0.00 0.00 33.92 3.69
17 18 3.278574 ACTCGACATCTCAGAGGAAGAG 58.721 50.000 12.04 12.04 36.40 2.85
18 19 3.358111 ACTCGACATCTCAGAGGAAGA 57.642 47.619 0.00 0.00 36.40 2.87
19 20 4.420168 GAAACTCGACATCTCAGAGGAAG 58.580 47.826 0.00 0.00 36.40 3.46
20 21 3.193691 GGAAACTCGACATCTCAGAGGAA 59.806 47.826 0.00 0.00 36.40 3.36
21 22 2.755655 GGAAACTCGACATCTCAGAGGA 59.244 50.000 0.00 0.00 36.40 3.71
22 23 2.159170 GGGAAACTCGACATCTCAGAGG 60.159 54.545 0.00 0.00 36.40 3.69
23 24 2.159170 GGGGAAACTCGACATCTCAGAG 60.159 54.545 0.00 0.00 37.96 3.35
24 25 1.825474 GGGGAAACTCGACATCTCAGA 59.175 52.381 0.00 0.00 0.00 3.27
25 26 1.550524 TGGGGAAACTCGACATCTCAG 59.449 52.381 0.00 0.00 0.00 3.35
26 27 1.639722 TGGGGAAACTCGACATCTCA 58.360 50.000 0.00 0.00 0.00 3.27
27 28 2.347731 GTTGGGGAAACTCGACATCTC 58.652 52.381 0.00 0.00 45.36 2.75
28 29 2.474410 GTTGGGGAAACTCGACATCT 57.526 50.000 0.00 0.00 45.36 2.90
32 33 1.871676 GAACAGTTGGGGAAACTCGAC 59.128 52.381 0.00 0.00 46.60 4.20
33 34 1.202722 GGAACAGTTGGGGAAACTCGA 60.203 52.381 0.00 0.00 46.60 4.04
34 35 1.202770 AGGAACAGTTGGGGAAACTCG 60.203 52.381 0.00 0.00 46.60 4.18
35 36 2.505405 GAGGAACAGTTGGGGAAACTC 58.495 52.381 0.00 0.00 46.60 3.01
37 38 1.202722 TCGAGGAACAGTTGGGGAAAC 60.203 52.381 0.00 0.00 39.24 2.78
38 39 1.071699 CTCGAGGAACAGTTGGGGAAA 59.928 52.381 3.91 0.00 0.00 3.13
39 40 0.685097 CTCGAGGAACAGTTGGGGAA 59.315 55.000 3.91 0.00 0.00 3.97
40 41 0.178944 TCTCGAGGAACAGTTGGGGA 60.179 55.000 13.56 0.00 0.00 4.81
41 42 0.037232 GTCTCGAGGAACAGTTGGGG 60.037 60.000 13.56 0.00 0.00 4.96
42 43 0.388649 CGTCTCGAGGAACAGTTGGG 60.389 60.000 13.56 0.00 0.00 4.12
43 44 3.108521 CGTCTCGAGGAACAGTTGG 57.891 57.895 13.56 0.00 0.00 3.77
296 297 3.564027 CGGGGCGCGTTTGAGATC 61.564 66.667 16.48 0.00 0.00 2.75
297 298 4.388499 ACGGGGCGCGTTTGAGAT 62.388 61.111 24.56 0.00 0.00 2.75
309 310 3.781307 TGGGCTTGATCGACGGGG 61.781 66.667 0.00 0.00 0.00 5.73
310 311 2.511600 GTGGGCTTGATCGACGGG 60.512 66.667 0.00 0.00 0.00 5.28
311 312 2.885644 CGTGGGCTTGATCGACGG 60.886 66.667 0.00 0.00 33.77 4.79
312 313 2.885644 CCGTGGGCTTGATCGACG 60.886 66.667 0.00 0.00 36.39 5.12
313 314 2.511600 CCCGTGGGCTTGATCGAC 60.512 66.667 0.00 0.00 0.00 4.20
331 332 3.726595 TTACCGGATCTTGGCGGCG 62.727 63.158 9.46 0.51 0.00 6.46
332 333 1.450669 TTTACCGGATCTTGGCGGC 60.451 57.895 9.46 0.00 0.00 6.53
333 334 1.093496 GGTTTACCGGATCTTGGCGG 61.093 60.000 9.46 6.59 0.00 6.13
334 335 1.093496 GGGTTTACCGGATCTTGGCG 61.093 60.000 9.46 0.00 36.71 5.69
335 336 0.255033 AGGGTTTACCGGATCTTGGC 59.745 55.000 9.46 0.00 46.96 4.52
336 337 2.770232 ACTAGGGTTTACCGGATCTTGG 59.230 50.000 9.46 3.37 46.96 3.61
337 338 3.490419 CGACTAGGGTTTACCGGATCTTG 60.490 52.174 9.46 0.00 46.96 3.02
338 339 2.692041 CGACTAGGGTTTACCGGATCTT 59.308 50.000 9.46 0.00 46.96 2.40
339 340 2.305009 CGACTAGGGTTTACCGGATCT 58.695 52.381 9.46 0.00 46.96 2.75
340 341 1.269465 GCGACTAGGGTTTACCGGATC 60.269 57.143 9.46 0.00 46.96 3.36
341 342 0.749049 GCGACTAGGGTTTACCGGAT 59.251 55.000 9.46 0.00 46.96 4.18
342 343 1.322538 GGCGACTAGGGTTTACCGGA 61.323 60.000 9.46 0.00 46.96 5.14
343 344 1.142531 GGCGACTAGGGTTTACCGG 59.857 63.158 0.00 0.00 46.96 5.28
344 345 1.142531 GGGCGACTAGGGTTTACCG 59.857 63.158 0.00 0.00 46.96 4.02
345 346 1.266867 TGGGGCGACTAGGGTTTACC 61.267 60.000 0.00 0.00 40.67 2.85
346 347 0.614812 TTGGGGCGACTAGGGTTTAC 59.385 55.000 0.00 0.00 0.00 2.01
347 348 1.487558 GATTGGGGCGACTAGGGTTTA 59.512 52.381 0.00 0.00 0.00 2.01
348 349 0.255033 GATTGGGGCGACTAGGGTTT 59.745 55.000 0.00 0.00 0.00 3.27
349 350 1.912971 GATTGGGGCGACTAGGGTT 59.087 57.895 0.00 0.00 0.00 4.11
350 351 2.432300 CGATTGGGGCGACTAGGGT 61.432 63.158 0.00 0.00 0.00 4.34
351 352 2.421739 CGATTGGGGCGACTAGGG 59.578 66.667 0.00 0.00 0.00 3.53
352 353 2.280186 GCGATTGGGGCGACTAGG 60.280 66.667 0.00 0.00 0.00 3.02
353 354 2.280186 GGCGATTGGGGCGACTAG 60.280 66.667 0.00 0.00 33.04 2.57
354 355 2.762459 AGGCGATTGGGGCGACTA 60.762 61.111 0.00 0.00 46.97 2.59
356 357 2.750237 AAAGGCGATTGGGGCGAC 60.750 61.111 0.00 0.00 37.59 5.19
357 358 2.749839 CAAAGGCGATTGGGGCGA 60.750 61.111 0.00 0.00 37.59 5.54
358 359 3.825611 CCAAAGGCGATTGGGGCG 61.826 66.667 14.93 0.00 45.03 6.13
363 364 1.032114 GGTCCTCCCAAAGGCGATTG 61.032 60.000 0.00 0.00 45.78 2.67
364 365 1.303282 GGTCCTCCCAAAGGCGATT 59.697 57.895 0.00 0.00 45.78 3.34
365 366 2.998949 GGTCCTCCCAAAGGCGAT 59.001 61.111 0.00 0.00 45.78 4.58
366 367 3.702048 CGGTCCTCCCAAAGGCGA 61.702 66.667 0.00 0.00 45.78 5.54
370 371 3.546714 AACCGCGGTCCTCCCAAAG 62.547 63.158 34.29 0.00 0.00 2.77
371 372 3.122727 AAACCGCGGTCCTCCCAAA 62.123 57.895 34.29 0.00 0.00 3.28
372 373 3.540367 GAAACCGCGGTCCTCCCAA 62.540 63.158 34.29 0.00 0.00 4.12
373 374 4.011517 GAAACCGCGGTCCTCCCA 62.012 66.667 34.29 0.00 0.00 4.37
374 375 4.772687 GGAAACCGCGGTCCTCCC 62.773 72.222 34.01 26.40 0.00 4.30
378 379 4.685467 TTCCGGAAACCGCGGTCC 62.685 66.667 34.29 27.74 46.86 4.46
379 380 2.253051 TTTTCCGGAAACCGCGGTC 61.253 57.895 34.29 20.55 46.86 4.79
380 381 2.203181 TTTTCCGGAAACCGCGGT 60.203 55.556 28.97 28.70 46.86 5.68
381 382 2.253154 GTTTTCCGGAAACCGCGG 59.747 61.111 28.97 26.86 46.86 6.46
382 383 2.127534 CGTTTTCCGGAAACCGCG 60.128 61.111 29.82 26.37 46.86 6.46
383 384 1.205820 CTCGTTTTCCGGAAACCGC 59.794 57.895 34.02 22.84 46.86 5.68
385 386 0.887836 AGGCTCGTTTTCCGGAAACC 60.888 55.000 28.97 24.16 43.80 3.27
386 387 0.516001 GAGGCTCGTTTTCCGGAAAC 59.484 55.000 28.97 20.96 43.36 2.78
387 388 0.395312 AGAGGCTCGTTTTCCGGAAA 59.605 50.000 25.67 25.67 37.11 3.13
388 389 0.320421 CAGAGGCTCGTTTTCCGGAA 60.320 55.000 14.35 14.35 37.11 4.30
389 390 1.292223 CAGAGGCTCGTTTTCCGGA 59.708 57.895 9.22 0.00 37.11 5.14
390 391 1.741770 CCAGAGGCTCGTTTTCCGG 60.742 63.158 9.22 0.00 37.11 5.14
391 392 1.004918 ACCAGAGGCTCGTTTTCCG 60.005 57.895 9.22 0.00 38.13 4.30
392 393 0.673956 GGACCAGAGGCTCGTTTTCC 60.674 60.000 9.22 9.95 0.00 3.13
393 394 1.014564 CGGACCAGAGGCTCGTTTTC 61.015 60.000 9.22 4.52 0.00 2.29
394 395 1.004918 CGGACCAGAGGCTCGTTTT 60.005 57.895 9.22 0.00 0.00 2.43
395 396 0.896940 TACGGACCAGAGGCTCGTTT 60.897 55.000 9.22 0.00 36.44 3.60
396 397 0.683504 ATACGGACCAGAGGCTCGTT 60.684 55.000 9.22 0.00 36.44 3.85
397 398 0.683504 AATACGGACCAGAGGCTCGT 60.684 55.000 9.22 5.35 38.02 4.18
398 399 0.249073 CAATACGGACCAGAGGCTCG 60.249 60.000 9.22 4.13 0.00 5.03
399 400 0.530870 GCAATACGGACCAGAGGCTC 60.531 60.000 6.34 6.34 0.00 4.70
400 401 1.522569 GCAATACGGACCAGAGGCT 59.477 57.895 0.00 0.00 0.00 4.58
401 402 1.523938 GGCAATACGGACCAGAGGC 60.524 63.158 0.00 0.00 0.00 4.70
402 403 1.904771 TGGCAATACGGACCAGAGG 59.095 57.895 0.00 0.00 0.00 3.69
406 407 1.502690 ATACCTGGCAATACGGACCA 58.497 50.000 0.00 0.00 0.00 4.02
407 408 2.104281 AGAATACCTGGCAATACGGACC 59.896 50.000 0.00 0.00 0.00 4.46
408 409 3.470645 AGAATACCTGGCAATACGGAC 57.529 47.619 0.00 0.00 0.00 4.79
409 410 4.222145 GGATAGAATACCTGGCAATACGGA 59.778 45.833 0.00 0.00 0.00 4.69
410 411 4.223032 AGGATAGAATACCTGGCAATACGG 59.777 45.833 0.00 0.00 34.99 4.02
411 412 5.407407 AGGATAGAATACCTGGCAATACG 57.593 43.478 0.00 0.00 34.99 3.06
412 413 7.125811 TGGATAGGATAGAATACCTGGCAATAC 59.874 40.741 0.00 0.00 37.68 1.89
413 414 7.196187 TGGATAGGATAGAATACCTGGCAATA 58.804 38.462 0.00 0.00 37.68 1.90
414 415 6.032039 TGGATAGGATAGAATACCTGGCAAT 58.968 40.000 0.00 0.00 37.68 3.56
415 416 5.411493 TGGATAGGATAGAATACCTGGCAA 58.589 41.667 0.00 0.00 37.68 4.52
416 417 5.023514 TGGATAGGATAGAATACCTGGCA 57.976 43.478 0.00 0.00 37.68 4.92
417 418 5.606348 CTGGATAGGATAGAATACCTGGC 57.394 47.826 0.00 0.00 37.68 4.85
432 433 0.105039 GACTGAACCGGCCTGGATAG 59.895 60.000 18.74 14.43 42.00 2.08
433 434 0.325296 AGACTGAACCGGCCTGGATA 60.325 55.000 18.74 5.24 42.00 2.59
434 435 1.613630 AGACTGAACCGGCCTGGAT 60.614 57.895 18.74 8.23 42.00 3.41
435 436 2.203788 AGACTGAACCGGCCTGGA 60.204 61.111 18.74 0.00 42.00 3.86
436 437 2.232298 GAGAGACTGAACCGGCCTGG 62.232 65.000 0.00 11.48 46.41 4.45
437 438 1.216710 GAGAGACTGAACCGGCCTG 59.783 63.158 0.00 0.00 0.00 4.85
438 439 2.344203 CGAGAGACTGAACCGGCCT 61.344 63.158 0.00 0.00 0.00 5.19
439 440 1.874345 TTCGAGAGACTGAACCGGCC 61.874 60.000 0.00 0.00 41.84 6.13
440 441 0.456995 CTTCGAGAGACTGAACCGGC 60.457 60.000 0.00 0.00 41.84 6.13
441 442 0.171455 CCTTCGAGAGACTGAACCGG 59.829 60.000 0.00 0.00 41.84 5.28
442 443 0.882474 ACCTTCGAGAGACTGAACCG 59.118 55.000 0.00 0.00 41.84 4.44
443 444 1.670380 GCACCTTCGAGAGACTGAACC 60.670 57.143 0.00 0.00 41.84 3.62
444 445 1.670380 GGCACCTTCGAGAGACTGAAC 60.670 57.143 0.00 0.00 41.84 3.18
445 446 0.603569 GGCACCTTCGAGAGACTGAA 59.396 55.000 0.00 0.00 41.84 3.02
446 447 2.268022 GGCACCTTCGAGAGACTGA 58.732 57.895 0.00 0.00 41.84 3.41
464 465 5.181009 CACATGCACATACTATCCCTATGG 58.819 45.833 0.00 0.00 0.00 2.74
486 487 3.329520 ACACTCACCCCTATAAAAGCACA 59.670 43.478 0.00 0.00 0.00 4.57
491 492 4.141344 GCCCATACACTCACCCCTATAAAA 60.141 45.833 0.00 0.00 0.00 1.52
498 499 1.332144 TACGCCCATACACTCACCCC 61.332 60.000 0.00 0.00 0.00 4.95
501 502 2.596904 ACATACGCCCATACACTCAC 57.403 50.000 0.00 0.00 0.00 3.51
530 531 2.046283 TTCGAACACAGTACAGAGCG 57.954 50.000 0.00 0.00 0.00 5.03
556 558 3.698820 GGGTCAGCCGGGTACGTT 61.699 66.667 5.47 0.00 38.78 3.99
558 560 4.143333 CAGGGTCAGCCGGGTACG 62.143 72.222 5.47 0.00 40.55 3.67
559 561 1.833787 TTTCAGGGTCAGCCGGGTAC 61.834 60.000 5.47 5.24 34.97 3.34
562 571 1.228429 TTTTTCAGGGTCAGCCGGG 60.228 57.895 2.18 0.00 34.97 5.73
565 574 1.886886 TACGTTTTTCAGGGTCAGCC 58.113 50.000 0.00 0.00 0.00 4.85
575 584 0.599558 GGGGGCAGGTTACGTTTTTC 59.400 55.000 0.00 0.00 0.00 2.29
589 600 1.478837 GGGCTAATTAGTTGAGGGGGC 60.479 57.143 13.91 0.00 0.00 5.80
643 654 7.227116 TGGCCTGATTTGATTTGAAAGAAAAAG 59.773 33.333 3.32 0.00 0.00 2.27
719 730 0.042880 CGTAAGAAAACACGCACGCA 60.043 50.000 0.00 0.00 43.02 5.24
734 745 4.876679 TGTTGACAGTTGGATCAAACGTAA 59.123 37.500 7.34 0.00 36.62 3.18
779 791 1.087501 CCCTCTGCCGCTTTACTTTC 58.912 55.000 0.00 0.00 0.00 2.62
811 827 3.629058 TCGAGGAATCAAACGATCGATC 58.371 45.455 24.34 15.68 34.57 3.69
812 828 3.710326 TCGAGGAATCAAACGATCGAT 57.290 42.857 24.34 7.21 34.57 3.59
872 888 2.039624 ACTGGCGTCCTCCATCCT 59.960 61.111 0.00 0.00 35.22 3.24
904 965 1.878656 CTCACGTCTTCTCCGCCCTT 61.879 60.000 0.00 0.00 0.00 3.95
909 970 1.658686 CCCTCCTCACGTCTTCTCCG 61.659 65.000 0.00 0.00 0.00 4.63
918 979 0.247736 CTTGGTTCTCCCTCCTCACG 59.752 60.000 0.00 0.00 0.00 4.35
1138 1230 2.043227 GGGAGCTAGAGGTGTTGCTAT 58.957 52.381 0.00 0.00 35.76 2.97
1223 1320 3.119245 TCTCATCCGTAGCCACAACTAAC 60.119 47.826 0.00 0.00 0.00 2.34
1227 1324 2.380084 TTCTCATCCGTAGCCACAAC 57.620 50.000 0.00 0.00 0.00 3.32
1248 1345 5.990996 AGGTTGATTAATTTGTGGCTGTTTG 59.009 36.000 0.00 0.00 0.00 2.93
1409 1997 8.867112 TTGTTGTTGTTGTTGTTGTTAGTAAA 57.133 26.923 0.00 0.00 0.00 2.01
1412 2000 6.074034 GCTTTGTTGTTGTTGTTGTTGTTAGT 60.074 34.615 0.00 0.00 0.00 2.24
1413 2001 6.295857 GCTTTGTTGTTGTTGTTGTTGTTAG 58.704 36.000 0.00 0.00 0.00 2.34
1414 2002 5.177696 GGCTTTGTTGTTGTTGTTGTTGTTA 59.822 36.000 0.00 0.00 0.00 2.41
1504 2093 1.206878 TGCTATCCATGTGCCAGAGT 58.793 50.000 0.00 0.00 0.00 3.24
1549 2138 5.854010 TTGGAGTATCGACAAAGAGCTAT 57.146 39.130 0.00 0.00 34.37 2.97
1690 2280 4.210331 GAGATGGTTTGGGCATATTCAGT 58.790 43.478 0.00 0.00 0.00 3.41
2069 2659 2.912020 GGTGGTACCTCGGAAGGAT 58.088 57.895 14.36 0.00 46.67 3.24
2176 2766 2.971901 ACCTTGGAATCGAAAGGGTT 57.028 45.000 16.12 0.00 46.12 4.11
2676 3266 2.475155 TGGGAGAGAGTCATTGAGCAT 58.525 47.619 0.00 0.00 0.00 3.79
2728 3318 6.822667 TCAGAGTTGTACTAATTACCGTGA 57.177 37.500 0.00 0.00 0.00 4.35
2758 3348 9.189156 CTTATGGAGATGAAACCCAAAAGATTA 57.811 33.333 0.00 0.00 33.15 1.75
2898 5329 2.236146 TGGTCACAGGAACGCATAGATT 59.764 45.455 0.00 0.00 31.55 2.40
2924 5752 3.789756 CGCATGAAGCAAAATCAAGCTAG 59.210 43.478 0.00 0.00 46.13 3.42
2931 5759 3.241868 GCAATGTCGCATGAAGCAAAATC 60.242 43.478 0.00 0.00 46.13 2.17
3059 5887 3.560251 AGCGGCCACTTGACACCT 61.560 61.111 2.24 0.00 0.00 4.00
3107 5935 2.863740 GTTGCGATTGTGATCCGATGTA 59.136 45.455 0.00 0.00 0.00 2.29
3279 6111 0.401356 TGCTCCAGCCAGTCAAATCA 59.599 50.000 0.00 0.00 41.18 2.57
3280 6112 1.404391 CATGCTCCAGCCAGTCAAATC 59.596 52.381 0.00 0.00 41.18 2.17
3282 6114 0.111061 ACATGCTCCAGCCAGTCAAA 59.889 50.000 0.00 0.00 41.18 2.69
3284 6116 1.206878 ATACATGCTCCAGCCAGTCA 58.793 50.000 0.00 0.00 41.18 3.41
3657 8315 0.906066 GAACCTCTCCTTCCCTCACC 59.094 60.000 0.00 0.00 0.00 4.02
3675 8333 3.443925 CGGGAGTCGAGCAGCAGA 61.444 66.667 0.00 0.00 42.43 4.26
3849 8513 4.072088 CCTCGCGCAACAACGACC 62.072 66.667 8.75 0.00 34.08 4.79
4141 8906 3.949754 ACGGTCATACGGAGAATCAGTTA 59.050 43.478 0.00 0.00 42.04 2.24
4460 9246 0.463295 CCGCTCATTCACCATGCTCT 60.463 55.000 0.00 0.00 32.13 4.09
4558 9348 6.442513 AGAGAGAAAAACAAAGAACACCTG 57.557 37.500 0.00 0.00 0.00 4.00
4559 9349 7.039714 ACAAAGAGAGAAAAACAAAGAACACCT 60.040 33.333 0.00 0.00 0.00 4.00
4582 9374 4.036734 CAGCTCTGAAACAAGGCTAAACAA 59.963 41.667 0.00 0.00 0.00 2.83
4702 9518 1.532604 GCCCAAAGTAGGCCAACACC 61.533 60.000 5.01 0.00 45.16 4.16
4737 9553 7.346751 TGCATCTTTCAGGTTTTACTTCTTT 57.653 32.000 0.00 0.00 0.00 2.52
4808 9625 3.221771 TGCTGTAACACAAGGCAGAATT 58.778 40.909 0.00 0.00 28.07 2.17
4809 9626 2.862541 TGCTGTAACACAAGGCAGAAT 58.137 42.857 0.00 0.00 28.07 2.40
4810 9627 2.340210 TGCTGTAACACAAGGCAGAA 57.660 45.000 0.00 0.00 28.07 3.02
4811 9628 2.340210 TTGCTGTAACACAAGGCAGA 57.660 45.000 0.00 0.00 32.15 4.26
4892 9712 4.581824 CACATGTGATTTATCTCTTGGGGG 59.418 45.833 21.64 0.00 32.85 5.40
4903 9723 1.433534 TGCGCGACACATGTGATTTA 58.566 45.000 31.94 10.05 0.00 1.40


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

AutoCloner maintained by Alex Coulton.