Multiple sequence alignment - TraesCS1D01G091100

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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 TraesCS1D01G091100 chr1D 100.000 7497 0 0 709 8205 77386304 77378808 0.000000e+00 13845.0
1 TraesCS1D01G091100 chr1D 100.000 510 0 0 1 510 77387012 77386503 0.000000e+00 942.0
2 TraesCS1D01G091100 chr1D 83.069 189 16 6 7465 7637 212429120 212428932 3.070000e-34 158.0
3 TraesCS1D01G091100 chr1A 93.706 4639 207 42 732 5336 108766727 108762140 0.000000e+00 6870.0
4 TraesCS1D01G091100 chr1A 93.128 1426 72 12 6410 7821 108761269 108759856 0.000000e+00 2067.0
5 TraesCS1D01G091100 chr1A 97.101 828 20 2 5495 6321 108762144 108761320 0.000000e+00 1393.0
6 TraesCS1D01G091100 chr1A 89.451 237 8 6 7975 8204 108756375 108756149 4.850000e-72 283.0
7 TraesCS1D01G091100 chr1A 90.598 117 11 0 7518 7634 94748434 94748550 1.100000e-33 156.0
8 TraesCS1D01G091100 chr1A 89.899 99 10 0 1844 1942 108765540 108765442 2.400000e-25 128.0
9 TraesCS1D01G091100 chr1A 96.154 78 2 1 6234 6311 108761346 108761270 8.650000e-25 126.0
10 TraesCS1D01G091100 chr1B 96.633 3980 88 22 722 4687 121004175 121000228 0.000000e+00 6565.0
11 TraesCS1D01G091100 chr1B 94.915 1062 30 5 6226 7279 120993602 120992557 0.000000e+00 1640.0
12 TraesCS1D01G091100 chr1B 96.381 829 27 3 5495 6321 120994395 120993568 0.000000e+00 1362.0
13 TraesCS1D01G091100 chr1B 98.951 667 5 2 4670 5336 120995055 120994391 0.000000e+00 1192.0
14 TraesCS1D01G091100 chr1B 88.391 491 45 5 7281 7765 120992472 120991988 1.540000e-161 580.0
15 TraesCS1D01G091100 chr1B 98.141 269 5 0 1 269 121005216 121004948 3.470000e-128 470.0
16 TraesCS1D01G091100 chr1B 95.390 282 2 6 7932 8204 120991866 120991587 9.780000e-119 438.0
17 TraesCS1D01G091100 chr1B 98.770 244 3 0 267 510 121004866 121004623 1.260000e-117 435.0
18 TraesCS1D01G091100 chr1B 89.899 99 10 0 1844 1942 121002986 121002888 2.400000e-25 128.0
19 TraesCS1D01G091100 chr7A 88.482 764 71 11 2689 3449 477155488 477154739 0.000000e+00 907.0
20 TraesCS1D01G091100 chr7A 93.583 187 9 3 5331 5514 320981338 320981152 8.110000e-70 276.0
21 TraesCS1D01G091100 chr7A 86.567 134 9 4 7932 8061 571375848 571375976 1.110000e-28 139.0
22 TraesCS1D01G091100 chr7A 89.474 95 10 0 8101 8195 571382502 571382596 4.020000e-23 121.0
23 TraesCS1D01G091100 chr7D 87.712 765 72 16 2689 3449 414841503 414840757 0.000000e+00 872.0
24 TraesCS1D01G091100 chr7D 87.582 765 72 16 2689 3449 415114930 415114185 0.000000e+00 865.0
25 TraesCS1D01G091100 chr7D 88.142 253 23 5 7172 7420 511228012 511228261 2.240000e-75 294.0
26 TraesCS1D01G091100 chr7D 87.645 259 22 7 7172 7420 199607136 199606878 8.050000e-75 292.0
27 TraesCS1D01G091100 chr7D 88.000 250 21 6 7172 7412 485106460 485106709 3.750000e-73 287.0
28 TraesCS1D01G091100 chr7D 92.593 189 12 2 5332 5518 535309854 535309666 3.770000e-68 270.0
29 TraesCS1D01G091100 chr7D 84.109 258 31 7 7173 7420 194080715 194080972 2.960000e-59 241.0
30 TraesCS1D01G091100 chr7D 83.922 255 26 5 7942 8195 503760998 503761238 6.410000e-56 230.0
31 TraesCS1D01G091100 chr7D 82.418 273 23 13 7940 8195 503362162 503362426 1.790000e-51 215.0
32 TraesCS1D01G091100 chr7D 81.588 277 26 8 7932 8192 503635375 503635642 1.080000e-48 206.0
33 TraesCS1D01G091100 chr7D 87.705 122 14 1 2573 2694 415198039 415197919 3.090000e-29 141.0
34 TraesCS1D01G091100 chr7D 89.474 95 10 0 8101 8195 503361660 503361754 4.020000e-23 121.0
35 TraesCS1D01G091100 chr6D 98.788 165 2 0 5332 5496 389916622 389916786 2.240000e-75 294.0
36 TraesCS1D01G091100 chr6D 94.972 179 8 1 5321 5498 32865345 32865167 6.270000e-71 279.0
37 TraesCS1D01G091100 chr7B 87.259 259 23 7 7172 7420 540063199 540063457 3.750000e-73 287.0
38 TraesCS1D01G091100 chr7B 82.288 271 23 7 7941 8195 531824270 531824531 2.320000e-50 211.0
39 TraesCS1D01G091100 chr7B 82.192 146 17 2 8051 8195 532032696 532032833 5.200000e-22 117.0
40 TraesCS1D01G091100 chr6B 96.045 177 6 1 5321 5496 696483565 696483389 3.750000e-73 287.0
41 TraesCS1D01G091100 chr5A 94.211 190 8 3 5328 5517 651496990 651496804 3.750000e-73 287.0
42 TraesCS1D01G091100 chr5A 86.260 131 14 4 7642 7770 295079493 295079365 1.110000e-28 139.0
43 TraesCS1D01G091100 chr5D 97.041 169 5 0 5329 5497 368995526 368995358 1.350000e-72 285.0
44 TraesCS1D01G091100 chr2D 97.024 168 5 0 5328 5495 475088506 475088339 4.850000e-72 283.0
45 TraesCS1D01G091100 chr2D 97.674 43 1 0 7641 7683 155554437 155554395 3.180000e-09 75.0
46 TraesCS1D01G091100 chr3B 94.972 179 5 4 5332 5510 550322939 550322765 2.260000e-70 278.0
47 TraesCS1D01G091100 chr3B 80.992 121 21 2 7641 7760 793028779 793028898 2.440000e-15 95.3
48 TraesCS1D01G091100 chr2A 86.207 261 21 9 7172 7420 15610796 15611053 1.360000e-67 268.0
49 TraesCS1D01G091100 chr2B 85.115 262 28 7 7170 7420 438744184 438743923 2.940000e-64 257.0
50 TraesCS1D01G091100 chr5B 87.678 211 24 1 7172 7380 655285254 655285044 2.290000e-60 244.0
51 TraesCS1D01G091100 chr4A 84.556 259 23 9 7171 7420 352482006 352481756 2.960000e-59 241.0
52 TraesCS1D01G091100 chrUn 83.784 185 15 6 7465 7634 233525017 233525201 2.370000e-35 161.0
53 TraesCS1D01G091100 chrUn 83.511 188 16 6 7465 7637 257944363 257944176 2.370000e-35 161.0
54 TraesCS1D01G091100 chr4D 83.069 189 16 6 7465 7637 123689213 123689025 3.070000e-34 158.0
55 TraesCS1D01G091100 chr4D 90.000 120 12 0 7518 7637 241053890 241053771 1.100000e-33 156.0
56 TraesCS1D01G091100 chr4B 83.333 186 15 6 7465 7634 495537524 495537709 3.070000e-34 158.0


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 TraesCS1D01G091100 chr1D 77378808 77387012 8204 True 7393.500000 13845 100.000000 1 8205 2 chr1D.!!$R2 8204
1 TraesCS1D01G091100 chr1A 108756149 108766727 10578 True 1811.166667 6870 93.239833 732 8204 6 chr1A.!!$R1 7472
2 TraesCS1D01G091100 chr1B 121000228 121005216 4988 True 1899.500000 6565 95.860750 1 4687 4 chr1B.!!$R2 4686
3 TraesCS1D01G091100 chr1B 120991587 120995055 3468 True 1042.400000 1640 94.805600 4670 8204 5 chr1B.!!$R1 3534
4 TraesCS1D01G091100 chr7A 477154739 477155488 749 True 907.000000 907 88.482000 2689 3449 1 chr7A.!!$R2 760
5 TraesCS1D01G091100 chr7D 414840757 414841503 746 True 872.000000 872 87.712000 2689 3449 1 chr7D.!!$R2 760
6 TraesCS1D01G091100 chr7D 415114185 415114930 745 True 865.000000 865 87.582000 2689 3449 1 chr7D.!!$R3 760

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
937 1265 1.076438 TCCCACAGGAGAGAGAGACA 58.924 55.000 0.00 0.0 37.19 3.41 F
1708 2053 1.000385 GAGGACTCAGAGGATGATGCG 60.000 57.143 1.53 0.0 37.28 4.73 F
1752 2100 1.110518 GCGGTAGAGGAGGAAGAGGG 61.111 65.000 0.00 0.0 0.00 4.30 F
1798 2146 2.042301 GCTGGTGATGGGGATAGGACT 61.042 57.143 0.00 0.0 0.00 3.85 F
1840 2188 2.764128 GAGGATGGTGGGAGCGGA 60.764 66.667 0.00 0.0 0.00 5.54 F
4100 4457 0.472471 AGCCGAAGTTGAACCTCCAA 59.528 50.000 0.00 0.0 0.00 3.53 F
5451 5820 0.756294 CATCCGTATGTGGTAGCCCA 59.244 55.000 0.00 0.0 38.87 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 2242 1.279846 TGAACAGCAGCCTCATCATCA 59.720 47.619 0.0 0.0 0.00 3.07 R
3365 3722 0.101040 TCTTCGTTCGTTGTGTCGGT 59.899 50.000 0.0 0.0 0.00 4.69 R
3367 3724 1.750351 TCTCTTCGTTCGTTGTGTCG 58.250 50.000 0.0 0.0 0.00 4.35 R
4100 4457 8.000709 AGATACAACTCTCAGATCTCTCTTCAT 58.999 37.037 0.0 0.0 0.00 2.57 R
4238 4595 2.158449 GTCGCATGTCTTTCTGAGGTTG 59.842 50.000 0.0 0.0 0.00 3.77 R
5480 5849 0.702902 TGACTACTCCCTCCGTTCCT 59.297 55.000 0.0 0.0 0.00 3.36 R
7826 8370 0.474854 TCCTAAAGGGGTGGACTGCA 60.475 55.000 0.0 0.0 35.41 4.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 2.681706 CCGCAGACCAGATACATGATC 58.318 52.381 0.00 0.00 34.40 2.92
241 242 3.825328 AGCTCAACCAAAGTCTCACAAT 58.175 40.909 0.00 0.00 0.00 2.71
444 529 2.358737 CCTTGTGGCTCGTGGGAC 60.359 66.667 0.00 0.00 0.00 4.46
856 1178 2.315386 GCTTCGAAAACGGACGGCT 61.315 57.895 0.00 0.00 0.00 5.52
936 1264 3.989782 TCCCACAGGAGAGAGAGAC 57.010 57.895 0.00 0.00 37.19 3.36
937 1265 1.076438 TCCCACAGGAGAGAGAGACA 58.924 55.000 0.00 0.00 37.19 3.41
938 1266 1.181786 CCCACAGGAGAGAGAGACAC 58.818 60.000 0.00 0.00 33.47 3.67
939 1267 1.548809 CCCACAGGAGAGAGAGACACA 60.549 57.143 0.00 0.00 33.47 3.72
940 1268 1.543802 CCACAGGAGAGAGAGACACAC 59.456 57.143 0.00 0.00 0.00 3.82
1159 1493 1.571215 CCTGGTACGGCGGTTGTTTC 61.571 60.000 13.24 0.00 0.00 2.78
1174 1508 6.677913 CGGTTGTTTCTTTATTGTTCCATCT 58.322 36.000 0.00 0.00 0.00 2.90
1175 1509 7.145323 CGGTTGTTTCTTTATTGTTCCATCTT 58.855 34.615 0.00 0.00 0.00 2.40
1204 1538 1.464722 CCCCAAATGTGTGTCCCCT 59.535 57.895 0.00 0.00 0.00 4.79
1221 1555 8.050930 TGTGTCCCCTTTTATCTTTTATACTCC 58.949 37.037 0.00 0.00 0.00 3.85
1609 1954 4.704833 ACGCAGCCGCTGGACAAT 62.705 61.111 21.77 0.00 38.22 2.71
1628 1973 4.405671 ACGAGGAGACCGAGGCGA 62.406 66.667 0.00 0.00 0.00 5.54
1708 2053 1.000385 GAGGACTCAGAGGATGATGCG 60.000 57.143 1.53 0.00 37.28 4.73
1752 2100 1.110518 GCGGTAGAGGAGGAAGAGGG 61.111 65.000 0.00 0.00 0.00 4.30
1798 2146 2.042301 GCTGGTGATGGGGATAGGACT 61.042 57.143 0.00 0.00 0.00 3.85
1840 2188 2.764128 GAGGATGGTGGGAGCGGA 60.764 66.667 0.00 0.00 0.00 5.54
1894 2242 6.372931 AGAGGAGAGAGTAAATGATAGCAGT 58.627 40.000 0.00 0.00 0.00 4.40
2096 2444 2.802247 CAAGTGCAAAGTGACGATGAGA 59.198 45.455 0.00 0.00 0.00 3.27
2118 2466 3.019564 GCCTGCCAAATAATGAGACAGT 58.980 45.455 0.00 0.00 0.00 3.55
2339 2688 7.050377 CAGTGGTTATCCTTGAATAGATGTGT 58.950 38.462 0.00 0.00 34.23 3.72
2630 2980 5.393027 CGCTTTCATTGGTTTAGCCTTACAT 60.393 40.000 0.00 0.00 38.35 2.29
2684 3034 3.515901 AGTTCTAGCTACTTCCAAGGGTG 59.484 47.826 0.00 0.00 0.00 4.61
2730 3080 6.486248 CACTTCATTTATTCGGTACACATGG 58.514 40.000 0.00 0.00 0.00 3.66
2865 3218 8.887036 TCTTGTTATACATATGCGATGTTCTT 57.113 30.769 9.13 0.00 33.76 2.52
2924 3277 6.801539 TGTGAGTAAAGGCTTGTAAATCAG 57.198 37.500 0.00 0.00 0.00 2.90
3203 3560 7.078031 AGGCATGATTTGACCAATGGAACAG 62.078 44.000 6.16 0.00 35.87 3.16
3365 3722 5.043248 GCTCAACAGCAAAGAAGCTTTTTA 58.957 37.500 0.00 0.00 43.70 1.52
3367 3724 5.348164 TCAACAGCAAAGAAGCTTTTTACC 58.652 37.500 0.00 0.00 43.70 2.85
4100 4457 0.472471 AGCCGAAGTTGAACCTCCAA 59.528 50.000 0.00 0.00 0.00 3.53
4238 4595 7.923414 ATAAAAGTAACTGAGATGAACCACC 57.077 36.000 0.00 0.00 0.00 4.61
4523 4880 4.023980 ACCGATGATTAGTGAGAGAACCA 58.976 43.478 0.00 0.00 0.00 3.67
5049 5418 5.765182 CACCAAAATGTAACTCTCCAGTTCT 59.235 40.000 0.00 0.00 42.27 3.01
5335 5704 7.907214 ATTTCTGTGTTGGTACATTCTACTC 57.093 36.000 0.00 0.00 39.30 2.59
5336 5705 5.401531 TCTGTGTTGGTACATTCTACTCC 57.598 43.478 0.00 0.00 39.30 3.85
5337 5706 4.222145 TCTGTGTTGGTACATTCTACTCCC 59.778 45.833 0.00 0.00 39.30 4.30
5338 5707 4.164981 TGTGTTGGTACATTCTACTCCCT 58.835 43.478 0.00 0.00 39.30 4.20
5339 5708 4.222145 TGTGTTGGTACATTCTACTCCCTC 59.778 45.833 0.00 0.00 39.30 4.30
5340 5709 3.773119 TGTTGGTACATTCTACTCCCTCC 59.227 47.826 0.00 0.00 39.30 4.30
5341 5710 2.662866 TGGTACATTCTACTCCCTCCG 58.337 52.381 0.00 0.00 0.00 4.63
5342 5711 2.024655 TGGTACATTCTACTCCCTCCGT 60.025 50.000 0.00 0.00 0.00 4.69
5343 5712 3.029570 GGTACATTCTACTCCCTCCGTT 58.970 50.000 0.00 0.00 0.00 4.44
5344 5713 3.067883 GGTACATTCTACTCCCTCCGTTC 59.932 52.174 0.00 0.00 0.00 3.95
5345 5714 2.108970 ACATTCTACTCCCTCCGTTCC 58.891 52.381 0.00 0.00 0.00 3.62
5346 5715 2.292323 ACATTCTACTCCCTCCGTTCCT 60.292 50.000 0.00 0.00 0.00 3.36
5347 5716 3.053095 ACATTCTACTCCCTCCGTTCCTA 60.053 47.826 0.00 0.00 0.00 2.94
5348 5717 3.744940 TTCTACTCCCTCCGTTCCTAA 57.255 47.619 0.00 0.00 0.00 2.69
5349 5718 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
5350 5719 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
5351 5720 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
5352 5721 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
5353 5722 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
5354 5723 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
5355 5724 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
5356 5725 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
5357 5726 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
5358 5727 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
5359 5728 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
5360 5729 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
5361 5730 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
5362 5731 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
5363 5732 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
5364 5733 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
5365 5734 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
5393 5762 6.939551 TTAACAAGTGACTACATACGAAGC 57.060 37.500 0.00 0.00 0.00 3.86
5394 5763 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
5395 5764 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
5396 5765 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
5397 5766 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
5398 5767 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
5399 5768 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
5400 5769 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
5401 5770 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
5402 5771 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
5403 5772 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
5404 5773 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
5405 5774 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
5406 5775 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
5407 5776 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
5408 5777 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
5409 5778 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
5410 5779 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
5411 5780 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
5412 5781 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
5448 5817 7.563888 TCTATATACATCCGTATGTGGTAGC 57.436 40.000 3.56 0.00 45.99 3.58
5449 5818 3.955650 ATACATCCGTATGTGGTAGCC 57.044 47.619 3.56 0.00 45.99 3.93
5450 5819 0.756903 ACATCCGTATGTGGTAGCCC 59.243 55.000 0.00 0.00 44.79 5.19
5451 5820 0.756294 CATCCGTATGTGGTAGCCCA 59.244 55.000 0.00 0.00 38.87 5.36
5452 5821 1.347707 CATCCGTATGTGGTAGCCCAT 59.652 52.381 0.00 0.00 44.35 4.00
5453 5822 1.502690 TCCGTATGTGGTAGCCCATT 58.497 50.000 0.00 0.00 44.35 3.16
5454 5823 1.841277 TCCGTATGTGGTAGCCCATTT 59.159 47.619 0.00 0.00 44.35 2.32
5455 5824 3.039743 TCCGTATGTGGTAGCCCATTTA 58.960 45.455 0.00 0.00 44.35 1.40
5456 5825 3.455177 TCCGTATGTGGTAGCCCATTTAA 59.545 43.478 0.00 0.00 44.35 1.52
5457 5826 4.080469 TCCGTATGTGGTAGCCCATTTAAA 60.080 41.667 0.00 0.00 44.35 1.52
5458 5827 4.641094 CCGTATGTGGTAGCCCATTTAAAA 59.359 41.667 0.00 0.00 44.35 1.52
5459 5828 5.300792 CCGTATGTGGTAGCCCATTTAAAAT 59.699 40.000 0.00 0.00 44.35 1.82
5460 5829 6.435428 CGTATGTGGTAGCCCATTTAAAATC 58.565 40.000 0.00 0.00 44.35 2.17
5461 5830 6.262273 CGTATGTGGTAGCCCATTTAAAATCT 59.738 38.462 0.00 0.00 44.35 2.40
5462 5831 6.715347 ATGTGGTAGCCCATTTAAAATCTC 57.285 37.500 0.00 0.00 44.35 2.75
5463 5832 5.826643 TGTGGTAGCCCATTTAAAATCTCT 58.173 37.500 0.00 0.00 44.35 3.10
5464 5833 6.964464 TGTGGTAGCCCATTTAAAATCTCTA 58.036 36.000 0.00 0.00 44.35 2.43
5465 5834 7.406916 TGTGGTAGCCCATTTAAAATCTCTAA 58.593 34.615 0.00 0.00 44.35 2.10
5466 5835 7.891183 TGTGGTAGCCCATTTAAAATCTCTAAA 59.109 33.333 0.00 0.00 44.35 1.85
5467 5836 8.745590 GTGGTAGCCCATTTAAAATCTCTAAAA 58.254 33.333 0.00 0.00 44.35 1.52
5468 5837 9.315363 TGGTAGCCCATTTAAAATCTCTAAAAA 57.685 29.630 0.00 0.00 35.17 1.94
5469 5838 9.803315 GGTAGCCCATTTAAAATCTCTAAAAAG 57.197 33.333 0.00 0.00 0.00 2.27
5472 5841 9.088987 AGCCCATTTAAAATCTCTAAAAAGACA 57.911 29.630 0.00 0.00 0.00 3.41
5473 5842 9.705290 GCCCATTTAAAATCTCTAAAAAGACAA 57.295 29.630 0.00 0.00 0.00 3.18
5490 5859 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
5491 5860 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
5492 5861 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
5493 5862 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
5494 5863 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
5804 6173 1.271271 CCTCAGCTTGCAAGAGTCCTT 60.271 52.381 30.39 4.57 0.00 3.36
5859 6228 7.690256 TCTTTTGCCTAAGTCTTTCCTAGATT 58.310 34.615 0.00 0.00 34.79 2.40
6290 6723 4.639135 AAGTTCCAGAAAACTGCAGAAC 57.361 40.909 23.35 11.79 39.40 3.01
6327 6760 8.579682 TTTAGGTACTCTGTTTTTACGAACTC 57.420 34.615 0.00 0.00 41.75 3.01
6329 6762 4.143452 GGTACTCTGTTTTTACGAACTCGC 60.143 45.833 0.00 0.00 44.43 5.03
6396 6829 7.148507 GGGATCTTAACTTCTCATAATCATGCG 60.149 40.741 0.00 0.00 31.73 4.73
6460 6893 5.417580 TGCAGTTCTGTCCTTTAACTTTGTT 59.582 36.000 1.78 0.00 31.21 2.83
6557 6990 4.646945 TCATCTCATGTGAAGAGGACTACC 59.353 45.833 0.90 0.00 33.92 3.18
6575 7008 1.236616 CCAAACATGCGCTCCACTCA 61.237 55.000 9.73 0.00 0.00 3.41
6774 7207 1.899814 TGACGAAACCCTGATGCTAGT 59.100 47.619 0.00 0.00 0.00 2.57
6826 7259 4.999310 TCCCTTGATAGATAGACCGATGT 58.001 43.478 0.00 0.00 0.00 3.06
6995 7433 1.000896 GGTACAGCCCATGCCTGTT 60.001 57.895 18.47 7.05 38.69 3.16
6996 7434 0.611896 GGTACAGCCCATGCCTGTTT 60.612 55.000 18.47 2.51 38.69 2.83
6997 7435 1.256812 GTACAGCCCATGCCTGTTTT 58.743 50.000 18.47 1.94 38.69 2.43
6998 7436 2.442413 GTACAGCCCATGCCTGTTTTA 58.558 47.619 18.47 3.10 38.69 1.52
6999 7437 2.236489 ACAGCCCATGCCTGTTTTAT 57.764 45.000 10.42 0.00 38.69 1.40
7011 7449 1.949525 CTGTTTTATGCCCATCCTCGG 59.050 52.381 0.00 0.00 0.00 4.63
7167 7613 0.388659 CTGCCTTGATCCTCCTCTCG 59.611 60.000 0.00 0.00 0.00 4.04
7195 7641 9.682465 AATACTCCCTCTGTTTTTATTTACTCC 57.318 33.333 0.00 0.00 0.00 3.85
7262 7708 8.410141 ACCAAGTTCATCGAAAACAATCTAAAA 58.590 29.630 14.29 0.00 0.00 1.52
7332 7861 7.553334 TGAGTCTAATGGTATTGACTTGGTAC 58.447 38.462 0.00 0.00 39.53 3.34
7345 7874 5.197451 TGACTTGGTACTGTGGATGTTTTT 58.803 37.500 0.00 0.00 0.00 1.94
7383 7919 6.693315 TGGTCAAAGTTTAGAAAGTTGAGG 57.307 37.500 0.00 0.00 32.20 3.86
7388 7924 7.706607 GTCAAAGTTTAGAAAGTTGAGGCAAAT 59.293 33.333 0.00 0.00 32.20 2.32
7398 7934 7.340232 AGAAAGTTGAGGCAAATCTAATATGCA 59.660 33.333 0.00 0.00 41.80 3.96
7405 7941 8.623903 TGAGGCAAATCTAATATGCAAAGTAAG 58.376 33.333 0.00 0.00 41.80 2.34
7439 7975 5.428253 GGAGCAGTTATTATGGTGAAGTGA 58.572 41.667 0.00 0.00 0.00 3.41
7485 8021 8.890718 ACTGATAACTCATTCATCTTGATGTTG 58.109 33.333 10.01 9.28 0.00 3.33
7508 8044 8.709646 GTTGTCATTGATACCTAATCGATAACC 58.290 37.037 0.00 0.00 36.68 2.85
7528 8064 4.467769 ACCAAGCTGATAATTCCATCCAG 58.532 43.478 0.00 0.00 0.00 3.86
7532 8068 6.460676 CCAAGCTGATAATTCCATCCAGTTTC 60.461 42.308 0.00 0.00 0.00 2.78
7634 8171 1.135333 GTCTTCTCGGCTGGAACCTAG 59.865 57.143 0.00 0.00 0.00 3.02
7639 8176 2.025605 TCTCGGCTGGAACCTAGAAGTA 60.026 50.000 0.00 0.00 29.13 2.24
7647 8184 5.510861 GCTGGAACCTAGAAGTACTTGTTCA 60.511 44.000 25.67 16.34 39.11 3.18
7682 8219 4.541714 TCTCAAAGGGATTGGAGAGGATTT 59.458 41.667 0.00 0.00 39.62 2.17
7687 8224 2.780010 GGGATTGGAGAGGATTTGAGGA 59.220 50.000 0.00 0.00 0.00 3.71
7690 8227 4.202346 GGATTGGAGAGGATTTGAGGAGAG 60.202 50.000 0.00 0.00 0.00 3.20
7696 8233 6.272324 TGGAGAGGATTTGAGGAGAGTTTAAA 59.728 38.462 0.00 0.00 0.00 1.52
7728 8272 7.298070 AGGAGATTTAATCCCCTTCAATCCATA 59.702 37.037 1.95 0.00 33.10 2.74
7737 8281 2.785857 CCTTCAATCCATACCCTTCCCT 59.214 50.000 0.00 0.00 0.00 4.20
7770 8314 2.884639 TCAACTGAACAAGGCCTTAAGC 59.115 45.455 20.00 10.59 42.60 3.09
7775 8319 2.622942 TGAACAAGGCCTTAAGCTTGTG 59.377 45.455 20.00 6.46 40.44 3.33
7778 8322 1.541588 CAAGGCCTTAAGCTTGTGTCC 59.458 52.381 20.00 5.41 43.05 4.02
7779 8323 0.038310 AGGCCTTAAGCTTGTGTCCC 59.962 55.000 9.86 3.14 43.05 4.46
7788 8332 0.310854 GCTTGTGTCCCGAACCAAAG 59.689 55.000 0.00 0.00 0.00 2.77
7812 8356 4.774726 ACTATATCACTCGGGAATGCATCT 59.225 41.667 0.00 0.00 0.00 2.90
7813 8357 2.251409 ATCACTCGGGAATGCATCTG 57.749 50.000 0.00 0.00 0.00 2.90
7814 8358 1.194218 TCACTCGGGAATGCATCTGA 58.806 50.000 0.00 0.00 0.00 3.27
7816 8360 0.467384 ACTCGGGAATGCATCTGAGG 59.533 55.000 21.90 9.34 35.88 3.86
7818 8362 1.139654 CTCGGGAATGCATCTGAGGAA 59.860 52.381 13.91 0.00 31.21 3.36
7819 8363 1.134401 TCGGGAATGCATCTGAGGAAC 60.134 52.381 0.00 0.00 0.00 3.62
7821 8365 2.295885 GGGAATGCATCTGAGGAACTG 58.704 52.381 0.00 0.00 41.55 3.16
7822 8366 2.092753 GGGAATGCATCTGAGGAACTGA 60.093 50.000 0.00 0.00 41.55 3.41
7825 8369 1.942776 TGCATCTGAGGAACTGAGGA 58.057 50.000 0.00 0.00 41.03 3.71
7826 8370 2.475155 TGCATCTGAGGAACTGAGGAT 58.525 47.619 0.00 0.00 41.03 3.24
7827 8371 2.169978 TGCATCTGAGGAACTGAGGATG 59.830 50.000 0.00 0.00 41.03 3.51
7828 8372 2.836262 CATCTGAGGAACTGAGGATGC 58.164 52.381 0.00 0.00 41.03 3.91
7829 8373 1.942776 TCTGAGGAACTGAGGATGCA 58.057 50.000 0.00 0.00 41.03 3.96
7830 8374 1.829849 TCTGAGGAACTGAGGATGCAG 59.170 52.381 0.00 0.00 41.03 4.41
7886 9859 8.433421 TCTCTTTCACTTACATTTTCTTTCGT 57.567 30.769 0.00 0.00 0.00 3.85
7895 9868 5.941948 ACATTTTCTTTCGTTCGAGGAAT 57.058 34.783 11.06 1.67 0.00 3.01
7897 9870 7.429636 ACATTTTCTTTCGTTCGAGGAATTA 57.570 32.000 11.06 6.04 0.00 1.40
7912 9885 0.719465 AATTAAGAACTGCGGACGCG 59.281 50.000 3.53 3.53 45.51 6.01
7947 9948 5.272397 GCTACGAGTACATAGACCTTGAAC 58.728 45.833 0.00 0.00 0.00 3.18
7948 9949 5.163683 GCTACGAGTACATAGACCTTGAACA 60.164 44.000 0.00 0.00 0.00 3.18
7950 9951 5.008331 ACGAGTACATAGACCTTGAACAGA 58.992 41.667 0.00 0.00 0.00 3.41
8195 12098 9.567776 TGGTTTATCAAATCTTACTGTTCAAGA 57.432 29.630 0.00 0.00 36.50 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 189 4.571919 ACGCTTTGCCAAATACTGTAGTA 58.428 39.130 0.00 0.00 34.67 1.82
416 501 2.352805 CACAAGGTGAGCCTCCCC 59.647 66.667 0.00 0.00 46.33 4.81
711 796 2.325082 TTTCTCTTTGCTCGCCGCC 61.325 57.895 0.00 0.00 38.05 6.13
712 797 1.154395 GTTTCTCTTTGCTCGCCGC 60.154 57.895 0.00 0.00 39.77 6.53
713 798 1.497722 GGTTTCTCTTTGCTCGCCG 59.502 57.895 0.00 0.00 0.00 6.46
714 799 0.606673 AGGGTTTCTCTTTGCTCGCC 60.607 55.000 0.00 0.00 0.00 5.54
715 800 0.799393 GAGGGTTTCTCTTTGCTCGC 59.201 55.000 0.00 0.00 39.38 5.03
716 801 1.002544 AGGAGGGTTTCTCTTTGCTCG 59.997 52.381 0.00 0.00 42.10 5.03
717 802 2.869101 AGGAGGGTTTCTCTTTGCTC 57.131 50.000 0.00 0.00 42.10 4.26
718 803 2.713708 AGAAGGAGGGTTTCTCTTTGCT 59.286 45.455 0.00 0.00 41.16 3.91
719 804 2.816672 CAGAAGGAGGGTTTCTCTTTGC 59.183 50.000 0.00 0.00 41.16 3.68
720 805 4.092116 ACAGAAGGAGGGTTTCTCTTTG 57.908 45.455 0.00 0.00 41.16 2.77
779 1100 1.620822 GTGGAGACTGCCAAATGGTT 58.379 50.000 0.71 0.00 40.20 3.67
827 1149 1.214367 TTTCGAAGCAACGGTCAGAC 58.786 50.000 0.00 0.00 0.00 3.51
881 1203 4.664677 ACTGCCGAAACTCGCGCT 62.665 61.111 5.56 0.00 38.82 5.92
936 1264 4.962122 GCGCCGCTTGTGTGTGTG 62.962 66.667 0.00 0.00 0.00 3.82
939 1267 3.818121 TTAGGCGCCGCTTGTGTGT 62.818 57.895 23.20 1.83 0.00 3.72
940 1268 2.612567 TTTAGGCGCCGCTTGTGTG 61.613 57.895 23.20 0.00 0.00 3.82
1140 1473 1.571215 GAAACAACCGCCGTACCAGG 61.571 60.000 0.00 0.00 0.00 4.45
1141 1474 0.601841 AGAAACAACCGCCGTACCAG 60.602 55.000 0.00 0.00 0.00 4.00
1142 1475 0.179051 AAGAAACAACCGCCGTACCA 60.179 50.000 0.00 0.00 0.00 3.25
1143 1476 0.946528 AAAGAAACAACCGCCGTACC 59.053 50.000 0.00 0.00 0.00 3.34
1144 1477 4.153256 CAATAAAGAAACAACCGCCGTAC 58.847 43.478 0.00 0.00 0.00 3.67
1145 1478 3.814283 ACAATAAAGAAACAACCGCCGTA 59.186 39.130 0.00 0.00 0.00 4.02
1174 1508 4.226168 ACACATTTGGGGGAAAAGAACAAA 59.774 37.500 0.00 0.00 35.76 2.83
1175 1509 3.777522 ACACATTTGGGGGAAAAGAACAA 59.222 39.130 0.00 0.00 0.00 2.83
1229 1568 5.008613 CCCTCATCCGTTTAATAACACCATG 59.991 44.000 0.00 0.00 33.75 3.66
1607 1952 1.668101 GCCTCGGTCTCCTCGTCATT 61.668 60.000 0.00 0.00 0.00 2.57
1609 1954 2.750637 GCCTCGGTCTCCTCGTCA 60.751 66.667 0.00 0.00 0.00 4.35
1628 1973 5.145564 CTCCCCCTCAAATTCATCATCAAT 58.854 41.667 0.00 0.00 0.00 2.57
1752 2100 2.821366 CCGTGCTGCCACCATCTC 60.821 66.667 0.00 0.00 38.79 2.75
1798 2146 3.686241 CCTCGCATTCTTCAATCAACTGA 59.314 43.478 0.00 0.00 0.00 3.41
1847 2195 2.611518 CTGACATTCCTCGACCAACTC 58.388 52.381 0.00 0.00 0.00 3.01
1894 2242 1.279846 TGAACAGCAGCCTCATCATCA 59.720 47.619 0.00 0.00 0.00 3.07
1939 2287 2.100584 CCTCTCCTCTTCCTGACATTCG 59.899 54.545 0.00 0.00 0.00 3.34
2096 2444 3.285484 CTGTCTCATTATTTGGCAGGCT 58.715 45.455 0.00 0.00 0.00 4.58
2118 2466 2.503765 TCCTCGGCATAATCCTTCACAA 59.496 45.455 0.00 0.00 0.00 3.33
2339 2688 4.398988 CCAAATGTATGGCTGCTTACTTCA 59.601 41.667 0.00 0.00 32.78 3.02
2564 2914 7.456902 TGTGAAACTAGAGGTATTAAGAACCCT 59.543 37.037 0.00 6.23 36.07 4.34
2630 2980 3.237746 AGCATAGGCAAGATCTCTAGCA 58.762 45.455 14.33 0.00 44.61 3.49
2684 3034 4.276678 TGCCTAATTGCTGATACTTGCATC 59.723 41.667 0.00 0.00 39.07 3.91
2730 3080 3.677596 CACCTTGTGTGTCCAAAAACAAC 59.322 43.478 0.00 0.00 40.26 3.32
2832 3183 8.745590 TCGCATATGTATAACAAGAGCCTATAA 58.254 33.333 4.29 0.00 0.00 0.98
2865 3218 3.084039 CAGGACTTAGCATGCTTTCCAA 58.916 45.455 29.97 18.52 0.00 3.53
3031 3384 6.810888 AGACATCAACAAAAATGTTGTTCG 57.189 33.333 18.13 11.65 46.55 3.95
3203 3560 4.091075 GTCTACAATTTCCGTTCGGAGAAC 59.909 45.833 13.56 3.04 45.90 3.01
3365 3722 0.101040 TCTTCGTTCGTTGTGTCGGT 59.899 50.000 0.00 0.00 0.00 4.69
3367 3724 1.750351 TCTCTTCGTTCGTTGTGTCG 58.250 50.000 0.00 0.00 0.00 4.35
4100 4457 8.000709 AGATACAACTCTCAGATCTCTCTTCAT 58.999 37.037 0.00 0.00 0.00 2.57
4238 4595 2.158449 GTCGCATGTCTTTCTGAGGTTG 59.842 50.000 0.00 0.00 0.00 3.77
4342 4699 7.169308 GGTGTACTGTCATACTTATTTCCATCG 59.831 40.741 0.00 0.00 0.00 3.84
4523 4880 3.873910 CAGAACCCGAACCATATTCTGT 58.126 45.455 4.49 0.00 40.79 3.41
5049 5418 4.922206 AGATGTTTTCAGGGCACTATTCA 58.078 39.130 0.00 0.00 0.00 2.57
5332 5701 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
5333 5702 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
5334 5703 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
5335 5704 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
5336 5705 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
5337 5706 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
5338 5707 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
5339 5708 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
5367 5736 8.440833 GCTTCGTATGTAGTCACTTGTTAAAAT 58.559 33.333 0.00 0.00 0.00 1.82
5368 5737 7.438757 TGCTTCGTATGTAGTCACTTGTTAAAA 59.561 33.333 0.00 0.00 0.00 1.52
5369 5738 6.924612 TGCTTCGTATGTAGTCACTTGTTAAA 59.075 34.615 0.00 0.00 0.00 1.52
5370 5739 6.448852 TGCTTCGTATGTAGTCACTTGTTAA 58.551 36.000 0.00 0.00 0.00 2.01
5371 5740 6.016213 TGCTTCGTATGTAGTCACTTGTTA 57.984 37.500 0.00 0.00 0.00 2.41
5372 5741 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
5373 5742 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
5374 5743 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
5375 5744 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
5376 5745 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
5377 5746 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
5378 5747 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
5379 5748 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
5380 5749 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
5381 5750 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
5382 5751 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
5383 5752 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
5384 5753 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
5385 5754 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
5386 5755 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
5387 5756 5.700832 TGTAGATTCACTCATTTTGCTTCGT 59.299 36.000 0.00 0.00 0.00 3.85
5388 5757 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
5389 5758 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
5422 5791 9.281371 GCTACCACATACGGATGTATATAGATA 57.719 37.037 14.23 0.00 44.82 1.98
5423 5792 7.230913 GGCTACCACATACGGATGTATATAGAT 59.769 40.741 14.23 0.00 44.82 1.98
5424 5793 6.544931 GGCTACCACATACGGATGTATATAGA 59.455 42.308 14.23 0.00 44.82 1.98
5425 5794 6.238953 GGGCTACCACATACGGATGTATATAG 60.239 46.154 14.23 15.27 44.82 1.31
5426 5795 5.595542 GGGCTACCACATACGGATGTATATA 59.404 44.000 14.23 5.36 44.82 0.86
5427 5796 4.404715 GGGCTACCACATACGGATGTATAT 59.595 45.833 14.23 4.37 44.82 0.86
5428 5797 3.765511 GGGCTACCACATACGGATGTATA 59.234 47.826 14.23 8.27 44.82 1.47
5429 5798 2.565834 GGGCTACCACATACGGATGTAT 59.434 50.000 14.23 7.46 44.82 2.29
5430 5799 1.965643 GGGCTACCACATACGGATGTA 59.034 52.381 14.23 0.00 44.82 2.29
5432 5801 0.756294 TGGGCTACCACATACGGATG 59.244 55.000 5.94 5.94 43.37 3.51
5433 5802 3.233953 TGGGCTACCACATACGGAT 57.766 52.632 0.00 0.00 43.37 4.18
5434 5803 4.789899 TGGGCTACCACATACGGA 57.210 55.556 0.00 0.00 43.37 4.69
5443 5812 9.803315 CTTTTTAGAGATTTTAAATGGGCTACC 57.197 33.333 0.00 0.00 37.24 3.18
5446 5815 9.088987 TGTCTTTTTAGAGATTTTAAATGGGCT 57.911 29.630 0.00 0.00 0.00 5.19
5447 5816 9.705290 TTGTCTTTTTAGAGATTTTAAATGGGC 57.295 29.630 0.00 0.00 0.00 5.36
5464 5833 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
5465 5834 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
5466 5835 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
5467 5836 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
5468 5837 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
5469 5838 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
5470 5839 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
5471 5840 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
5472 5841 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
5473 5842 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
5474 5843 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
5475 5844 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
5476 5845 3.959449 GACTACTCCCTCCGTTCCTAAAT 59.041 47.826 0.00 0.00 0.00 1.40
5477 5846 3.245371 TGACTACTCCCTCCGTTCCTAAA 60.245 47.826 0.00 0.00 0.00 1.85
5478 5847 2.309755 TGACTACTCCCTCCGTTCCTAA 59.690 50.000 0.00 0.00 0.00 2.69
5479 5848 1.918262 TGACTACTCCCTCCGTTCCTA 59.082 52.381 0.00 0.00 0.00 2.94
5480 5849 0.702902 TGACTACTCCCTCCGTTCCT 59.297 55.000 0.00 0.00 0.00 3.36
5481 5850 1.777941 ATGACTACTCCCTCCGTTCC 58.222 55.000 0.00 0.00 0.00 3.62
5482 5851 4.996788 TTAATGACTACTCCCTCCGTTC 57.003 45.455 0.00 0.00 0.00 3.95
5483 5852 5.952347 AATTAATGACTACTCCCTCCGTT 57.048 39.130 0.00 0.00 0.00 4.44
5484 5853 7.613551 AATAATTAATGACTACTCCCTCCGT 57.386 36.000 0.00 0.00 0.00 4.69
5485 5854 8.148351 TCAAATAATTAATGACTACTCCCTCCG 58.852 37.037 0.00 0.00 0.00 4.63
5486 5855 9.847224 TTCAAATAATTAATGACTACTCCCTCC 57.153 33.333 4.34 0.00 0.00 4.30
5804 6173 5.590530 ACAATTCACTTTACCAACAGCAA 57.409 34.783 0.00 0.00 0.00 3.91
6460 6893 1.969208 TCCAATGGCTGCACAAAATCA 59.031 42.857 0.50 0.00 0.00 2.57
6557 6990 0.806868 ATGAGTGGAGCGCATGTTTG 59.193 50.000 11.47 0.00 36.26 2.93
6826 7259 1.606668 GCAGATCAACAAACAACGGGA 59.393 47.619 0.00 0.00 0.00 5.14
6935 7368 7.177568 ACTGCTATGGTATCAACTCTTCGATAT 59.822 37.037 0.00 0.00 0.00 1.63
7011 7449 2.674796 ATCACAACCGAGCTAGAACC 57.325 50.000 0.00 0.00 0.00 3.62
7195 7641 6.216750 GACTTAGGTCAAAGCTAATATGCG 57.783 41.667 0.00 0.00 37.52 4.73
7222 7668 9.672086 CGATGAACTTGGTCAAACTTTATAAAA 57.328 29.630 0.00 0.00 0.00 1.52
7224 7670 8.610248 TCGATGAACTTGGTCAAACTTTATAA 57.390 30.769 0.00 0.00 0.00 0.98
7225 7671 8.610248 TTCGATGAACTTGGTCAAACTTTATA 57.390 30.769 0.00 0.00 0.00 0.98
7226 7672 7.504924 TTCGATGAACTTGGTCAAACTTTAT 57.495 32.000 0.00 0.00 0.00 1.40
7227 7673 6.928979 TTCGATGAACTTGGTCAAACTTTA 57.071 33.333 0.00 0.00 0.00 1.85
7228 7674 5.828299 TTCGATGAACTTGGTCAAACTTT 57.172 34.783 0.00 0.00 0.00 2.66
7229 7675 5.828299 TTTCGATGAACTTGGTCAAACTT 57.172 34.783 0.00 0.00 0.00 2.66
7230 7676 5.124776 TGTTTTCGATGAACTTGGTCAAACT 59.875 36.000 11.85 0.00 0.00 2.66
7231 7677 5.336744 TGTTTTCGATGAACTTGGTCAAAC 58.663 37.500 11.85 4.47 0.00 2.93
7234 7680 5.530915 AGATTGTTTTCGATGAACTTGGTCA 59.469 36.000 11.85 0.00 0.00 4.02
7345 7874 7.130681 ACTTTGACCAAATTCATACCCAAAA 57.869 32.000 0.00 0.00 0.00 2.44
7349 7878 8.117813 TCTAAACTTTGACCAAATTCATACCC 57.882 34.615 0.00 0.00 0.00 3.69
7350 7879 9.974980 TTTCTAAACTTTGACCAAATTCATACC 57.025 29.630 0.00 0.00 0.00 2.73
7355 7885 9.581099 TCAACTTTCTAAACTTTGACCAAATTC 57.419 29.630 0.00 0.00 0.00 2.17
7358 7888 7.543756 CCTCAACTTTCTAAACTTTGACCAAA 58.456 34.615 0.00 0.00 0.00 3.28
7398 7934 4.291249 TGCTCCCCCATTTCTACTTACTTT 59.709 41.667 0.00 0.00 0.00 2.66
7405 7941 2.808906 AACTGCTCCCCCATTTCTAC 57.191 50.000 0.00 0.00 0.00 2.59
7439 7975 5.469760 TCAGTGAATGTTTTCATGTGATCGT 59.530 36.000 0.00 0.00 43.49 3.73
7456 7992 9.106070 CATCAAGATGAATGAGTTATCAGTGAA 57.894 33.333 4.01 0.00 41.20 3.18
7485 8021 8.827177 TTGGTTATCGATTAGGTATCAATGAC 57.173 34.615 1.71 0.00 32.45 3.06
7508 8044 6.461110 AAACTGGATGGAATTATCAGCTTG 57.539 37.500 0.00 0.00 0.00 4.01
7528 8064 3.038017 GTTAAAACGGCCTCAACGAAAC 58.962 45.455 0.00 0.00 34.93 2.78
7532 8068 2.032426 ACAAGTTAAAACGGCCTCAACG 59.968 45.455 0.00 0.00 37.36 4.10
7634 8171 4.753610 GGGGTGTAACTGAACAAGTACTTC 59.246 45.833 4.77 0.00 38.56 3.01
7639 8176 3.458487 AGAAGGGGTGTAACTGAACAAGT 59.542 43.478 0.00 0.00 42.60 3.16
7682 8219 6.781014 TCTCCTACAAGTTTAAACTCTCCTCA 59.219 38.462 20.78 4.43 38.57 3.86
7728 8272 1.359130 CAGGGAATTCAAGGGAAGGGT 59.641 52.381 7.93 0.00 36.25 4.34
7737 8281 4.531854 TGTTCAGTTGACAGGGAATTCAA 58.468 39.130 7.93 0.00 0.00 2.69
7770 8314 1.602377 GTCTTTGGTTCGGGACACAAG 59.398 52.381 0.00 0.00 0.00 3.16
7775 8319 5.048507 GTGATATAGTCTTTGGTTCGGGAC 58.951 45.833 0.00 0.00 0.00 4.46
7778 8322 4.976731 CGAGTGATATAGTCTTTGGTTCGG 59.023 45.833 0.00 0.00 0.00 4.30
7779 8323 4.976731 CCGAGTGATATAGTCTTTGGTTCG 59.023 45.833 0.00 0.00 0.00 3.95
7788 8332 4.521130 TGCATTCCCGAGTGATATAGTC 57.479 45.455 0.00 0.00 0.00 2.59
7812 8356 1.552337 GACTGCATCCTCAGTTCCTCA 59.448 52.381 0.00 0.00 46.40 3.86
7813 8357 1.134551 GGACTGCATCCTCAGTTCCTC 60.135 57.143 7.65 0.00 46.40 3.71
7814 8358 0.908198 GGACTGCATCCTCAGTTCCT 59.092 55.000 7.65 0.00 46.40 3.36
7825 8369 0.625849 CCTAAAGGGGTGGACTGCAT 59.374 55.000 0.00 0.00 0.00 3.96
7826 8370 0.474854 TCCTAAAGGGGTGGACTGCA 60.475 55.000 0.00 0.00 35.41 4.41
7827 8371 0.696501 TTCCTAAAGGGGTGGACTGC 59.303 55.000 0.00 0.00 35.41 4.40
7828 8372 3.518992 TTTTCCTAAAGGGGTGGACTG 57.481 47.619 0.00 0.00 35.41 3.51
7829 8373 5.871324 TTATTTTCCTAAAGGGGTGGACT 57.129 39.130 0.00 0.00 35.41 3.85
7830 8374 5.186409 GGTTTATTTTCCTAAAGGGGTGGAC 59.814 44.000 0.00 0.00 35.41 4.02
7832 8376 5.338632 AGGTTTATTTTCCTAAAGGGGTGG 58.661 41.667 0.00 0.00 35.41 4.61
7833 8377 6.949463 TGTAGGTTTATTTTCCTAAAGGGGTG 59.051 38.462 0.00 0.00 37.94 4.61
7834 8378 7.106204 TGTAGGTTTATTTTCCTAAAGGGGT 57.894 36.000 0.00 0.00 37.94 4.95
7835 8379 8.603898 ATTGTAGGTTTATTTTCCTAAAGGGG 57.396 34.615 0.00 0.00 37.94 4.79
7873 9846 5.941948 ATTCCTCGAACGAAAGAAAATGT 57.058 34.783 11.35 0.00 0.00 2.71
7884 9857 3.241678 CGCAGTTCTTAATTCCTCGAACG 60.242 47.826 0.00 0.00 40.36 3.95
7886 9859 3.056393 TCCGCAGTTCTTAATTCCTCGAA 60.056 43.478 0.00 0.00 0.00 3.71
7895 9868 1.735198 CCGCGTCCGCAGTTCTTAA 60.735 57.895 12.58 0.00 42.06 1.85
7897 9870 4.295119 ACCGCGTCCGCAGTTCTT 62.295 61.111 12.58 0.00 42.06 2.52
7912 9885 0.527817 CTCGTAGCCACATTCGGACC 60.528 60.000 0.00 0.00 0.00 4.46
7947 9948 1.070577 GCGTAGTGTGCTTGTGTTCTG 60.071 52.381 0.00 0.00 0.00 3.02
7948 9949 1.217882 GCGTAGTGTGCTTGTGTTCT 58.782 50.000 0.00 0.00 0.00 3.01
7950 9951 0.179056 AGGCGTAGTGTGCTTGTGTT 60.179 50.000 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.