Multiple sequence alignment - TraesCS2B01G378300

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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 TraesCS2B01G378300 chr2B 100.000 5843 0 0 1 5843 541091879 541097721 0.000000e+00 10791.0
1 TraesCS2B01G378300 chr2B 87.130 777 95 4 145 920 541018224 541018996 0.000000e+00 876.0
2 TraesCS2B01G378300 chr2B 87.500 296 33 3 3026 3319 421710615 421710322 7.250000e-89 339.0
3 TraesCS2B01G378300 chr2B 86.799 303 38 2 2203 2504 728190403 728190102 2.610000e-88 337.0
4 TraesCS2B01G378300 chr2B 91.000 200 15 3 1165 1363 541085884 541086081 3.470000e-67 267.0
5 TraesCS2B01G378300 chr2B 82.667 150 26 0 3394 3543 421709677 421709528 3.670000e-27 134.0
6 TraesCS2B01G378300 chr2D 93.174 5347 259 37 53 5364 459822863 459828138 0.000000e+00 7755.0
7 TraesCS2B01G378300 chr2D 90.232 1208 115 3 145 1351 459813366 459814571 0.000000e+00 1574.0
8 TraesCS2B01G378300 chr2D 87.667 300 32 4 3023 3319 354745965 354745668 1.560000e-90 344.0
9 TraesCS2B01G378300 chr2D 84.848 132 16 4 1718 1847 354747848 354747719 4.750000e-26 130.0
10 TraesCS2B01G378300 chr2D 82.000 150 27 0 3394 3543 354745185 354745036 1.710000e-25 128.0
11 TraesCS2B01G378300 chr2A 94.723 2729 108 13 2587 5291 602799677 602802393 0.000000e+00 4209.0
12 TraesCS2B01G378300 chr2A 92.049 1220 62 13 1398 2603 602797218 602798416 0.000000e+00 1683.0
13 TraesCS2B01G378300 chr2A 88.674 1086 103 6 1 1070 602776809 602777890 0.000000e+00 1306.0
14 TraesCS2B01G378300 chr2A 94.855 311 16 0 1066 1376 602796610 602796920 2.450000e-133 486.0
15 TraesCS2B01G378300 chr2A 80.585 479 66 19 5359 5831 572172607 572173064 1.560000e-90 344.0
16 TraesCS2B01G378300 chr2A 87.500 296 33 3 3026 3319 474312995 474312702 7.250000e-89 339.0
17 TraesCS2B01G378300 chr2A 82.000 150 27 0 3394 3543 474311878 474311729 1.710000e-25 128.0
18 TraesCS2B01G378300 chr2A 84.874 119 14 4 1718 1834 474315243 474315127 3.700000e-22 117.0
19 TraesCS2B01G378300 chr4A 83.191 470 71 8 5364 5829 251728662 251728197 1.950000e-114 424.0
20 TraesCS2B01G378300 chr4A 79.899 199 36 4 1109 1305 616238190 616238386 6.100000e-30 143.0
21 TraesCS2B01G378300 chr4A 78.846 208 41 3 1109 1314 632939501 632939295 2.840000e-28 137.0
22 TraesCS2B01G378300 chr1B 83.090 479 62 12 5370 5831 277270852 277270376 9.060000e-113 418.0
23 TraesCS2B01G378300 chr1B 82.292 480 68 8 5365 5829 412850922 412850445 3.280000e-107 399.0
24 TraesCS2B01G378300 chr1B 87.097 310 40 0 2203 2512 486310346 486310655 9.320000e-93 351.0
25 TraesCS2B01G378300 chr1B 83.060 183 26 4 1124 1305 22108943 22108765 1.690000e-35 161.0
26 TraesCS2B01G378300 chr1D 82.449 490 68 12 5365 5843 316892777 316892295 4.210000e-111 412.0
27 TraesCS2B01G378300 chr1D 83.110 373 53 8 5442 5811 212536751 212536386 1.210000e-86 331.0
28 TraesCS2B01G378300 chr1A 82.203 472 69 12 5365 5829 36859697 36860160 5.490000e-105 392.0
29 TraesCS2B01G378300 chr3B 80.754 504 72 13 5362 5843 307068083 307068583 2.570000e-98 370.0
30 TraesCS2B01G378300 chr3D 80.041 486 82 11 5365 5843 287940634 287940157 4.330000e-91 346.0
31 TraesCS2B01G378300 chr6D 84.091 352 52 3 5493 5843 43189086 43189434 2.610000e-88 337.0
32 TraesCS2B01G378300 chr4D 79.957 469 66 18 5365 5829 223612015 223612459 2.630000e-83 320.0
33 TraesCS2B01G378300 chr3A 83.282 323 46 6 5510 5829 377575653 377575336 2.060000e-74 291.0
34 TraesCS2B01G378300 chr7D 78.042 337 56 16 5512 5843 482283126 482282803 4.620000e-46 196.0
35 TraesCS2B01G378300 chr5D 80.282 213 34 7 1109 1314 552051447 552051658 2.820000e-33 154.0
36 TraesCS2B01G378300 chr6A 80.435 184 34 2 1116 1298 52118561 52118743 7.900000e-29 139.0
37 TraesCS2B01G378300 chr5A 77.895 95 15 3 230 318 546969242 546969148 3.000000e-03 54.7


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 TraesCS2B01G378300 chr2B 541091879 541097721 5842 False 10791.000000 10791 100.000000 1 5843 1 chr2B.!!$F3 5842
1 TraesCS2B01G378300 chr2B 541018224 541018996 772 False 876.000000 876 87.130000 145 920 1 chr2B.!!$F1 775
2 TraesCS2B01G378300 chr2B 421709528 421710615 1087 True 236.500000 339 85.083500 3026 3543 2 chr2B.!!$R2 517
3 TraesCS2B01G378300 chr2D 459822863 459828138 5275 False 7755.000000 7755 93.174000 53 5364 1 chr2D.!!$F2 5311
4 TraesCS2B01G378300 chr2D 459813366 459814571 1205 False 1574.000000 1574 90.232000 145 1351 1 chr2D.!!$F1 1206
5 TraesCS2B01G378300 chr2D 354745036 354747848 2812 True 200.666667 344 84.838333 1718 3543 3 chr2D.!!$R1 1825
6 TraesCS2B01G378300 chr2A 602796610 602802393 5783 False 2126.000000 4209 93.875667 1066 5291 3 chr2A.!!$F3 4225
7 TraesCS2B01G378300 chr2A 602776809 602777890 1081 False 1306.000000 1306 88.674000 1 1070 1 chr2A.!!$F2 1069
8 TraesCS2B01G378300 chr3B 307068083 307068583 500 False 370.000000 370 80.754000 5362 5843 1 chr3B.!!$F1 481

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
431 447 0.110509 GTCGACGACTCTGCGTGTTA 60.111 55.000 20.52 0.0 45.72 2.41 F
448 464 2.107378 TGTTACCCATTTCACAGCTCCA 59.893 45.455 0.00 0.0 0.00 3.86 F
1396 1412 1.151450 CACAGGGTTGGGCTCAAGT 59.849 57.895 0.00 0.0 32.92 3.16 F
1881 2187 1.164411 CTCTCTCTCGCACACACTCT 58.836 55.000 0.00 0.0 0.00 3.24 F
2806 4982 0.042581 TGGACCCTGGCTGACATCTA 59.957 55.000 0.00 0.0 0.00 1.98 F
4047 7483 1.730064 GAGGAAAAGCGATACGTTGCA 59.270 47.619 0.00 0.0 37.19 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1382 1398 0.110486 TTGAGACTTGAGCCCAACCC 59.890 55.0 0.0 0.0 0.00 4.11 R
1943 2842 1.167851 ATGACAGAAACATGGTGGCG 58.832 50.0 0.0 0.0 0.00 5.69 R
2594 3493 1.837648 CACTCTAGCTCAGTGATGCG 58.162 55.0 17.3 0.0 43.54 4.73 R
3607 7043 2.136298 TGTGAGTTGGTTTTCAGGCA 57.864 45.0 0.0 0.0 0.00 4.75 R
4172 7608 2.009681 TGGTGTCTCCTGAACTGCTA 57.990 50.0 0.0 0.0 37.07 3.49 R
5027 8481 0.179100 ACTTCCGCATCCATGAGACG 60.179 55.0 0.0 0.0 0.00 4.18 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
21 22 1.079127 CGTCTTGGGCCGTCTCAAT 60.079 57.895 0.00 0.00 0.00 2.57
22 23 1.361668 CGTCTTGGGCCGTCTCAATG 61.362 60.000 0.00 0.00 0.00 2.82
37 38 4.022603 TCTCAATGTTCTCTGAGGAGGAG 58.977 47.826 4.59 1.77 39.67 3.69
71 87 9.935241 TTGATGGAGCTAGATCTGAAAATATAC 57.065 33.333 8.10 0.00 0.00 1.47
113 129 9.455847 GCTATATCCAATTTCACAAAGTCATTC 57.544 33.333 0.00 0.00 0.00 2.67
114 130 9.956720 CTATATCCAATTTCACAAAGTCATTCC 57.043 33.333 0.00 0.00 0.00 3.01
119 135 6.275335 CAATTTCACAAAGTCATTCCTGTGT 58.725 36.000 0.00 0.00 40.07 3.72
123 139 1.069022 CAAAGTCATTCCTGTGTGCCG 60.069 52.381 0.00 0.00 0.00 5.69
127 143 0.320683 TCATTCCTGTGTGCCGTCAG 60.321 55.000 0.00 0.00 0.00 3.51
128 144 0.603707 CATTCCTGTGTGCCGTCAGT 60.604 55.000 0.00 0.00 0.00 3.41
152 168 9.209175 AGTTAAACTTCATGTAGCTAACAGAAG 57.791 33.333 20.26 20.26 42.70 2.85
218 234 4.782822 GCAAACGTAAACGAGCTTGTACAA 60.783 41.667 7.13 8.28 43.02 2.41
271 287 3.722147 CCTCATGTAGGGAATGACTTCG 58.278 50.000 0.00 0.00 42.32 3.79
292 308 2.286872 CTGCTGCTGGATACCTTCTTG 58.713 52.381 0.00 0.00 0.00 3.02
339 355 1.280421 GAAGGTGCCAAGATCTGTCCT 59.720 52.381 0.00 0.00 0.00 3.85
358 374 3.813166 TCCTCACGAAAAAGACATGAACC 59.187 43.478 0.00 0.00 0.00 3.62
431 447 0.110509 GTCGACGACTCTGCGTGTTA 60.111 55.000 20.52 0.00 45.72 2.41
448 464 2.107378 TGTTACCCATTTCACAGCTCCA 59.893 45.455 0.00 0.00 0.00 3.86
449 465 2.488153 GTTACCCATTTCACAGCTCCAC 59.512 50.000 0.00 0.00 0.00 4.02
528 544 2.262915 CTCACCGTCCTCTGTGGC 59.737 66.667 0.00 0.00 35.26 5.01
541 557 4.219944 TCCTCTGTGGCCATAACGATATAC 59.780 45.833 9.72 0.00 35.26 1.47
682 698 3.207669 GCATTGGGCCGAGAGCTG 61.208 66.667 12.46 1.15 43.05 4.24
912 928 2.764314 CGAAATCCGGCAAGGGCAG 61.764 63.158 0.00 0.00 43.71 4.85
994 1010 2.807108 GCCGATGGTATTTGAGAGGACC 60.807 54.545 0.00 0.00 0.00 4.46
1330 1346 2.282887 GTGGGTTGTGGCCGGAAT 60.283 61.111 5.05 0.00 0.00 3.01
1382 1398 1.808945 GGTCATTTCACAGGCTCACAG 59.191 52.381 0.00 0.00 0.00 3.66
1384 1400 1.171308 CATTTCACAGGCTCACAGGG 58.829 55.000 0.00 0.00 0.00 4.45
1396 1412 1.151450 CACAGGGTTGGGCTCAAGT 59.849 57.895 0.00 0.00 32.92 3.16
1409 1701 1.943507 GCTCAAGTCTCAACCAGCTCC 60.944 57.143 0.00 0.00 0.00 4.70
1413 1705 3.303135 TCTCAACCAGCTCCGCGT 61.303 61.111 4.92 0.00 0.00 6.01
1440 1738 1.549950 GGGGATTTCTGCCAAAGTGGA 60.550 52.381 0.00 0.00 40.96 4.02
1871 2177 1.401552 CTTCTGCAGGACTCTCTCTCG 59.598 57.143 15.13 0.00 0.00 4.04
1881 2187 1.164411 CTCTCTCTCGCACACACTCT 58.836 55.000 0.00 0.00 0.00 3.24
1925 2231 6.969043 ACCATACTTCCAATTCCTGAACATA 58.031 36.000 0.00 0.00 0.00 2.29
1943 2842 1.791103 TAGCAACGGGTGTTTGCTGC 61.791 55.000 17.59 0.00 40.34 5.25
1979 2878 7.703058 TCTGTCATTCTGTAGATTGTGAGTA 57.297 36.000 4.32 0.00 0.00 2.59
1983 2882 9.803315 TGTCATTCTGTAGATTGTGAGTATTAC 57.197 33.333 4.32 0.00 0.00 1.89
2033 2932 5.306937 ACCCCATATGTCGTAAAGATGATGA 59.693 40.000 1.24 0.00 0.00 2.92
2050 2949 8.324191 AGATGATGAAAACCTTATACTGGAGA 57.676 34.615 0.00 0.00 0.00 3.71
2073 2972 2.295349 AGAATTTGCTCTTGTGCTGGTG 59.705 45.455 0.00 0.00 0.00 4.17
2124 3023 1.210155 GATCAAGTGGCGTTGCACC 59.790 57.895 0.00 0.00 0.00 5.01
2251 3150 9.762381 CCTAGTCCTATGTAAAAGGAGATCTAT 57.238 37.037 0.00 0.00 43.81 1.98
2353 3252 3.724478 TGTTGGTCTCATCTCCTATGGT 58.276 45.455 0.00 0.00 0.00 3.55
2404 3303 4.036971 ACTGAAGCAGTATCGATACCTGTC 59.963 45.833 27.78 20.23 43.46 3.51
2470 3369 7.391833 GTCAAGAGGACAGTGAAAGGATTTATT 59.608 37.037 0.00 0.00 46.19 1.40
2605 4781 6.918022 TGTACATAAACTATCGCATCACTGAG 59.082 38.462 0.00 0.00 0.00 3.35
2806 4982 0.042581 TGGACCCTGGCTGACATCTA 59.957 55.000 0.00 0.00 0.00 1.98
2913 5091 8.907222 AAACATTCTATTTCCATTGCACTTTT 57.093 26.923 0.00 0.00 0.00 2.27
3077 5941 4.199310 CACAAGGAAGGAAAGTTGTCTCA 58.801 43.478 0.00 0.00 30.69 3.27
3333 6601 6.090483 TGGTTAGATCTACTCTAATGCAGC 57.910 41.667 0.67 0.00 45.78 5.25
3340 6608 5.914898 TCTACTCTAATGCAGCAGTGTTA 57.085 39.130 5.38 0.00 0.00 2.41
3387 6655 5.759059 TGGAAGATTTATGTCCTCAGCATT 58.241 37.500 0.00 0.00 32.28 3.56
3605 7041 9.162764 GCACACCAACTTAAGAGAGATAAAATA 57.837 33.333 10.09 0.00 0.00 1.40
3842 7278 4.022068 TCATGTGGGTTCAAAATCTTCTGC 60.022 41.667 0.00 0.00 0.00 4.26
3843 7279 3.295093 TGTGGGTTCAAAATCTTCTGCA 58.705 40.909 0.00 0.00 0.00 4.41
4017 7453 2.101415 GGATACGCTAGGGTTTAACCGT 59.899 50.000 18.45 13.96 39.83 4.83
4047 7483 1.730064 GAGGAAAAGCGATACGTTGCA 59.270 47.619 0.00 0.00 37.19 4.08
4069 7505 4.038271 TCACCAGCTCAATCATCCTTTT 57.962 40.909 0.00 0.00 0.00 2.27
4099 7535 5.460419 GGTGAGCATATTCTCTCGTAAACTG 59.540 44.000 3.99 0.00 34.29 3.16
4120 7556 6.924111 ACTGTGTTGAATATGGATGGTTTTC 58.076 36.000 0.00 0.00 0.00 2.29
4373 7809 5.368523 CAGGATACCTGTAGGAACCCATTTA 59.631 44.000 4.64 0.00 45.82 1.40
4382 7818 6.704310 TGTAGGAACCCATTTAACAGTCTAC 58.296 40.000 0.00 0.00 0.00 2.59
4447 7890 6.204688 TGAAATTGACACCATACTCAAGTGAC 59.795 38.462 0.00 0.00 35.47 3.67
4452 7895 5.527214 TGACACCATACTCAAGTGACTTTTG 59.473 40.000 0.00 0.00 35.47 2.44
4483 7926 9.582431 TTAGTAGTATCTGTGCAAATGTTCTAC 57.418 33.333 0.00 0.00 0.00 2.59
4580 8023 9.807921 TTCTTAGAAGGGATGACAAAAGTTATT 57.192 29.630 0.00 0.00 0.00 1.40
4588 8031 6.014584 GGGATGACAAAAGTTATTCCAGGTTT 60.015 38.462 0.00 0.00 0.00 3.27
4591 8034 7.883391 TGACAAAAGTTATTCCAGGTTTGTA 57.117 32.000 2.83 0.00 38.82 2.41
4595 8038 8.194769 ACAAAAGTTATTCCAGGTTTGTACTTG 58.805 33.333 1.20 0.00 37.41 3.16
4597 8040 7.506328 AAGTTATTCCAGGTTTGTACTTGTC 57.494 36.000 0.00 0.00 29.85 3.18
4602 8045 6.488769 TTCCAGGTTTGTACTTGTCTTCTA 57.511 37.500 0.00 0.00 29.85 2.10
4603 8046 6.488769 TCCAGGTTTGTACTTGTCTTCTAA 57.511 37.500 0.00 0.00 29.85 2.10
4605 8048 8.197592 TCCAGGTTTGTACTTGTCTTCTAATA 57.802 34.615 0.00 0.00 29.85 0.98
4606 8049 8.311836 TCCAGGTTTGTACTTGTCTTCTAATAG 58.688 37.037 0.00 0.00 29.85 1.73
4607 8050 8.311836 CCAGGTTTGTACTTGTCTTCTAATAGA 58.688 37.037 0.00 0.00 29.85 1.98
4624 8071 9.823647 TTCTAATAGAAGGAACATGAATCTGTC 57.176 33.333 0.00 0.00 29.50 3.51
4830 8278 1.876473 AGGGGAGATAGGATCCAGGTT 59.124 52.381 15.82 0.00 38.70 3.50
4868 8316 1.146957 TGTTCGTTGTTGTCGTCCCG 61.147 55.000 0.00 0.00 0.00 5.14
4893 8341 0.651031 CGATACTCAGACGAGCGTCA 59.349 55.000 22.96 4.32 46.76 4.35
4900 8349 1.154016 AGACGAGCGTCATGTTCCG 60.154 57.895 22.96 0.00 46.76 4.30
4912 8361 5.100259 CGTCATGTTCCGTTTGAGTAGTAT 58.900 41.667 0.00 0.00 0.00 2.12
5027 8481 5.018149 ACTAGTCTTCCTGTAACCTTCCTC 58.982 45.833 0.00 0.00 0.00 3.71
5145 8602 7.276658 CACTAGAAAATACACACTCTAGGCTTG 59.723 40.741 0.00 0.00 41.06 4.01
5164 8621 0.955428 GACTTCCGTTGCCATGCTGA 60.955 55.000 0.00 0.00 0.00 4.26
5180 8637 4.554036 GAGAGGGACGCCATGGGC 62.554 72.222 15.13 4.92 46.75 5.36
5202 8659 3.115556 CTCGGGGAGAGCGAAGAG 58.884 66.667 0.00 0.00 40.54 2.85
5203 8660 1.751162 CTCGGGGAGAGCGAAGAGT 60.751 63.158 0.00 0.00 40.54 3.24
5204 8661 0.464013 CTCGGGGAGAGCGAAGAGTA 60.464 60.000 0.00 0.00 40.54 2.59
5319 8800 2.203549 CTGGGCCACCTCTTCCTTCC 62.204 65.000 0.00 0.00 37.76 3.46
5381 8862 1.144936 CTGTCGGAATCAGGGCTCC 59.855 63.158 0.00 0.00 0.00 4.70
5387 8868 2.039405 AATCAGGGCTCCGGGGAT 60.039 61.111 4.80 0.00 0.00 3.85
5393 8874 2.768344 GGCTCCGGGGATCCAAGA 60.768 66.667 15.23 5.76 31.27 3.02
5402 8883 2.554344 CGGGGATCCAAGAAAAGGTTCA 60.554 50.000 15.23 0.00 36.09 3.18
5408 8889 5.536538 GGATCCAAGAAAAGGTTCAAACTCT 59.463 40.000 6.95 0.00 36.09 3.24
5424 8905 2.046892 CTGGGGTGTGCTCGAAGG 60.047 66.667 0.00 0.00 0.00 3.46
5425 8906 2.525629 TGGGGTGTGCTCGAAGGA 60.526 61.111 0.00 0.00 0.00 3.36
5428 8909 2.584391 GGGTGTGCTCGAAGGACCT 61.584 63.158 0.00 0.00 35.52 3.85
5429 8910 1.079750 GGTGTGCTCGAAGGACCTC 60.080 63.158 0.00 0.00 35.52 3.85
5431 8912 1.901948 TGTGCTCGAAGGACCTCGT 60.902 57.895 0.00 0.00 39.84 4.18
5435 8916 0.456995 GCTCGAAGGACCTCGTCAAG 60.457 60.000 0.00 0.00 39.84 3.02
5436 8917 0.882474 CTCGAAGGACCTCGTCAAGT 59.118 55.000 0.00 0.00 39.84 3.16
5442 8923 1.819903 AGGACCTCGTCAAGTTCTAGC 59.180 52.381 0.00 0.00 33.68 3.42
5445 8926 2.750712 GACCTCGTCAAGTTCTAGCTCT 59.249 50.000 0.00 0.00 32.09 4.09
5446 8927 2.750712 ACCTCGTCAAGTTCTAGCTCTC 59.249 50.000 0.00 0.00 0.00 3.20
5449 8930 2.162608 TCGTCAAGTTCTAGCTCTCTGC 59.837 50.000 0.00 0.00 43.29 4.26
5453 8934 1.190643 AGTTCTAGCTCTCTGCCCAC 58.809 55.000 0.00 0.00 44.23 4.61
5454 8935 1.190643 GTTCTAGCTCTCTGCCCACT 58.809 55.000 0.00 0.00 44.23 4.00
5483 8964 2.338015 AATGCTCCAGCGTGCTTGG 61.338 57.895 0.00 0.00 45.83 3.61
5494 8975 2.688666 TGCTTGGGCGAGGAGGAT 60.689 61.111 0.00 0.00 42.25 3.24
5497 8978 1.907739 CTTGGGCGAGGAGGATGAA 59.092 57.895 0.00 0.00 0.00 2.57
5498 8979 0.462759 CTTGGGCGAGGAGGATGAAC 60.463 60.000 0.00 0.00 0.00 3.18
5500 8981 1.144936 GGGCGAGGAGGATGAACAG 59.855 63.158 0.00 0.00 0.00 3.16
5502 8983 1.880340 GCGAGGAGGATGAACAGCG 60.880 63.158 0.00 0.00 0.00 5.18
5503 8984 1.227089 CGAGGAGGATGAACAGCGG 60.227 63.158 0.00 0.00 0.00 5.52
5504 8985 1.667154 CGAGGAGGATGAACAGCGGA 61.667 60.000 0.00 0.00 0.00 5.54
5505 8986 0.179097 GAGGAGGATGAACAGCGGAC 60.179 60.000 0.00 0.00 0.00 4.79
5506 8987 1.153349 GGAGGATGAACAGCGGACC 60.153 63.158 0.00 0.00 0.00 4.46
5507 8988 1.153349 GAGGATGAACAGCGGACCC 60.153 63.158 0.00 0.00 0.00 4.46
5508 8989 2.511600 GGATGAACAGCGGACCCG 60.512 66.667 3.73 3.73 43.09 5.28
5509 8990 2.511600 GATGAACAGCGGACCCGG 60.512 66.667 10.70 0.00 40.19 5.73
5558 9042 2.380932 TGGTGTAAGACCCTACTCCTGA 59.619 50.000 0.00 0.00 45.45 3.86
5575 9060 2.165030 CCTGATTTGTGTGGATTGCCTC 59.835 50.000 0.00 0.00 34.31 4.70
5609 9094 5.644977 TGAGTATGAGTGTGTACAAGGAG 57.355 43.478 0.00 0.00 0.00 3.69
5612 9097 3.963428 ATGAGTGTGTACAAGGAGGAC 57.037 47.619 0.00 0.00 0.00 3.85
5615 9100 2.367567 GAGTGTGTACAAGGAGGACCAA 59.632 50.000 0.00 0.00 38.94 3.67
5624 9109 2.266055 GAGGACCAACTGCCTCGG 59.734 66.667 0.00 0.00 41.10 4.63
5638 9123 4.124943 TCGGGAGGCTCGGCTAGT 62.125 66.667 8.69 0.00 0.00 2.57
5650 9135 1.107538 CGGCTAGTTCGAGGGATCCA 61.108 60.000 15.23 0.00 0.00 3.41
5653 9138 2.483889 GGCTAGTTCGAGGGATCCAAAG 60.484 54.545 15.23 3.56 0.00 2.77
5655 9140 1.657804 AGTTCGAGGGATCCAAAGGT 58.342 50.000 15.23 0.00 0.00 3.50
5660 9145 3.153919 TCGAGGGATCCAAAGGTTTTTG 58.846 45.455 15.23 0.00 42.66 2.44
5661 9146 3.153919 CGAGGGATCCAAAGGTTTTTGA 58.846 45.455 15.23 0.00 45.21 2.69
5679 9180 3.199442 TGACCCTTCTCTATGGTGGAA 57.801 47.619 0.00 0.00 30.97 3.53
5686 9187 4.407296 CCTTCTCTATGGTGGAAACTAGCT 59.593 45.833 0.00 0.00 0.00 3.32
5703 9204 6.854091 ACTAGCTTATACTTATACTGGCCC 57.146 41.667 0.00 0.00 0.00 5.80
5704 9205 6.563163 ACTAGCTTATACTTATACTGGCCCT 58.437 40.000 0.00 0.00 0.00 5.19
5716 9217 2.285743 GGCCCTGGTCCTCTTCCT 60.286 66.667 0.00 0.00 0.00 3.36
5766 9267 0.250989 AACGGCCGATTTTGAAGGGA 60.251 50.000 35.90 0.00 0.00 4.20
5771 9272 2.159382 GCCGATTTTGAAGGGAGACAA 58.841 47.619 0.00 0.00 0.00 3.18
5781 9282 4.678256 TGAAGGGAGACAAGAGTACATCT 58.322 43.478 0.00 0.00 41.27 2.90
5799 9300 9.036980 AGTACATCTTATCTTGACTAAAGGTGT 57.963 33.333 5.30 5.30 43.68 4.16
5815 9316 0.927537 GTGTTTTTCGCCTGCCAAAC 59.072 50.000 0.00 0.00 0.00 2.93
5817 9318 0.104120 GTTTTTCGCCTGCCAAACCT 59.896 50.000 0.00 0.00 0.00 3.50
5818 9319 0.387565 TTTTTCGCCTGCCAAACCTC 59.612 50.000 0.00 0.00 0.00 3.85
5830 9331 1.002134 AAACCTCCCTGCCATGACG 60.002 57.895 0.00 0.00 0.00 4.35
5833 9334 2.665000 CTCCCTGCCATGACGTGT 59.335 61.111 0.00 0.00 0.00 4.49
5834 9335 1.448540 CTCCCTGCCATGACGTGTC 60.449 63.158 0.00 0.00 0.00 3.67
5838 9339 1.667830 CTGCCATGACGTGTCGGTT 60.668 57.895 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.493675 TCCTCAGAGAACATTGAGACGG 59.506 50.000 0.00 0.00 42.67 4.79
21 22 0.616111 GGCCTCCTCCTCAGAGAACA 60.616 60.000 0.00 0.00 43.39 3.18
22 23 0.616111 TGGCCTCCTCCTCAGAGAAC 60.616 60.000 3.32 0.00 43.39 3.01
79 95 7.706159 TGTGAAATTGGATATAGCAATGTCAC 58.294 34.615 19.11 19.11 46.14 3.67
85 101 8.347004 TGACTTTGTGAAATTGGATATAGCAA 57.653 30.769 0.00 0.00 0.00 3.91
92 108 6.268387 ACAGGAATGACTTTGTGAAATTGGAT 59.732 34.615 0.00 0.00 0.00 3.41
113 129 1.263217 GTTTAACTGACGGCACACAGG 59.737 52.381 0.00 0.00 36.88 4.00
114 130 2.210116 AGTTTAACTGACGGCACACAG 58.790 47.619 0.00 0.00 38.11 3.66
119 135 3.472652 ACATGAAGTTTAACTGACGGCA 58.527 40.909 0.00 0.00 0.00 5.69
120 136 4.435651 GCTACATGAAGTTTAACTGACGGC 60.436 45.833 0.00 0.00 0.00 5.68
123 139 8.306680 TGTTAGCTACATGAAGTTTAACTGAC 57.693 34.615 0.00 0.00 0.00 3.51
127 143 8.989980 ACTTCTGTTAGCTACATGAAGTTTAAC 58.010 33.333 19.99 5.10 44.08 2.01
218 234 3.119101 CCAGGTACTAGCATCGTCAAACT 60.119 47.826 0.00 0.00 36.02 2.66
271 287 0.179936 AGAAGGTATCCAGCAGCAGC 59.820 55.000 0.00 0.00 42.56 5.25
292 308 2.205911 GAGCTTAATTCAGGCCGAGTC 58.794 52.381 0.00 0.00 0.00 3.36
339 355 2.882137 GGGGTTCATGTCTTTTTCGTGA 59.118 45.455 0.00 0.00 0.00 4.35
358 374 3.818787 GTCTGCTGCGCCAATGGG 61.819 66.667 4.18 0.00 37.18 4.00
431 447 0.251341 GGTGGAGCTGTGAAATGGGT 60.251 55.000 0.00 0.00 0.00 4.51
448 464 3.005539 ATGGAGGCTGACGCAGGT 61.006 61.111 0.00 0.00 38.10 4.00
449 465 2.202987 GATGGAGGCTGACGCAGG 60.203 66.667 0.00 0.00 38.10 4.85
512 528 3.311110 GGCCACAGAGGACGGTGA 61.311 66.667 0.00 0.00 42.97 4.02
541 557 1.455786 CCAAAGTGTAAGTGCGACGAG 59.544 52.381 0.00 0.00 0.00 4.18
646 662 2.864114 CCTTGTGGGAGATGCAGTG 58.136 57.895 0.00 0.00 37.23 3.66
1134 1150 1.226323 CTCTACCGCGAGTTCCACG 60.226 63.158 8.23 0.00 0.00 4.94
1192 1208 2.347490 GCCTCCCTCGTCTGCAAA 59.653 61.111 0.00 0.00 0.00 3.68
1382 1398 0.110486 TTGAGACTTGAGCCCAACCC 59.890 55.000 0.00 0.00 0.00 4.11
1384 1400 1.239347 GGTTGAGACTTGAGCCCAAC 58.761 55.000 0.00 0.00 37.10 3.77
1625 1931 4.680237 CGCGCACAGACAGGGGAA 62.680 66.667 8.75 0.00 0.00 3.97
1871 2177 5.052481 TGCTATTATGATGAGAGTGTGTGC 58.948 41.667 0.00 0.00 0.00 4.57
1925 2231 3.119193 CAGCAAACACCCGTTGCT 58.881 55.556 5.85 5.85 38.90 3.91
1943 2842 1.167851 ATGACAGAAACATGGTGGCG 58.832 50.000 0.00 0.00 0.00 5.69
1997 2896 7.737869 ACGACATATGGGGTATTACAATTACA 58.262 34.615 7.80 0.00 0.00 2.41
2000 2899 9.280174 CTTTACGACATATGGGGTATTACAATT 57.720 33.333 7.80 0.00 0.00 2.32
2001 2900 8.653191 TCTTTACGACATATGGGGTATTACAAT 58.347 33.333 7.80 0.00 0.00 2.71
2002 2901 8.020777 TCTTTACGACATATGGGGTATTACAA 57.979 34.615 7.80 0.22 0.00 2.41
2003 2902 7.600231 TCTTTACGACATATGGGGTATTACA 57.400 36.000 7.80 0.00 0.00 2.41
2004 2903 8.308931 TCATCTTTACGACATATGGGGTATTAC 58.691 37.037 7.80 0.00 0.00 1.89
2005 2904 8.425237 TCATCTTTACGACATATGGGGTATTA 57.575 34.615 7.80 0.57 0.00 0.98
2006 2905 7.311092 TCATCTTTACGACATATGGGGTATT 57.689 36.000 7.80 0.00 0.00 1.89
2011 2910 7.728847 TTTCATCATCTTTACGACATATGGG 57.271 36.000 7.80 0.96 0.00 4.00
2033 2932 9.454859 CAAATTCTCTCTCCAGTATAAGGTTTT 57.545 33.333 0.00 0.00 0.00 2.43
2050 2949 2.818432 CCAGCACAAGAGCAAATTCTCT 59.182 45.455 0.00 0.00 44.78 3.10
2088 2987 4.858850 TGATCAAAGTGCCCTGAACATAT 58.141 39.130 0.00 0.00 0.00 1.78
2090 2989 3.159213 TGATCAAAGTGCCCTGAACAT 57.841 42.857 0.00 0.00 0.00 2.71
2117 3016 3.505680 TGTGGTGATTTGATAGGTGCAAC 59.494 43.478 0.00 0.00 0.00 4.17
2124 3023 7.651808 AGAACAAACTTGTGGTGATTTGATAG 58.348 34.615 2.78 0.00 41.31 2.08
2353 3252 4.422073 ACGCCCTTGATCTATCATTTCA 57.578 40.909 0.00 0.00 36.56 2.69
2404 3303 5.524971 AACCATTATCAGCATCACCAATG 57.475 39.130 0.00 0.00 38.50 2.82
2470 3369 4.888326 AATTCCAGCAAAACCAGCATTA 57.112 36.364 0.00 0.00 0.00 1.90
2581 3480 6.129062 GCTCAGTGATGCGATAGTTTATGTAC 60.129 42.308 0.00 0.00 39.35 2.90
2586 3485 4.655762 AGCTCAGTGATGCGATAGTTTA 57.344 40.909 0.00 0.00 39.35 2.01
2594 3493 1.837648 CACTCTAGCTCAGTGATGCG 58.162 55.000 17.30 0.00 43.54 4.73
2605 4781 2.751166 TGAAGGTGAAGCACTCTAGC 57.249 50.000 0.00 0.00 34.40 3.42
2665 4841 6.854496 ACTCTCGCAAAACATAAACTACAA 57.146 33.333 0.00 0.00 0.00 2.41
3077 5941 3.118629 TGTGCATAATCGCTTCCTCTCTT 60.119 43.478 0.00 0.00 0.00 2.85
3333 6601 8.237267 GGTCAGAAATAGTTTGGAATAACACTG 58.763 37.037 0.00 0.00 0.00 3.66
3340 6608 3.694566 GGCGGTCAGAAATAGTTTGGAAT 59.305 43.478 0.00 0.00 0.00 3.01
3387 6655 2.617276 CCTGCAGAAAGAAGCATGGAGA 60.617 50.000 17.39 0.00 40.42 3.71
3549 6985 8.792830 ATAACACAAGTACTTGAAGCATGTAT 57.207 30.769 36.14 21.30 42.93 2.29
3605 7041 3.030291 TGTGAGTTGGTTTTCAGGCATT 58.970 40.909 0.00 0.00 0.00 3.56
3606 7042 2.665165 TGTGAGTTGGTTTTCAGGCAT 58.335 42.857 0.00 0.00 0.00 4.40
3607 7043 2.136298 TGTGAGTTGGTTTTCAGGCA 57.864 45.000 0.00 0.00 0.00 4.75
3842 7278 7.431960 CGTGGTACCAAATTGAACATGAATATG 59.568 37.037 18.31 0.00 40.24 1.78
3843 7279 7.479980 CGTGGTACCAAATTGAACATGAATAT 58.520 34.615 18.31 0.00 0.00 1.28
4017 7453 7.924412 ACGTATCGCTTTTCCTCTTCATAATAA 59.076 33.333 0.00 0.00 0.00 1.40
4047 7483 3.947612 AAGGATGATTGAGCTGGTGAT 57.052 42.857 0.00 0.00 0.00 3.06
4069 7505 3.378512 AGAGAATATGCTCACCACTCCA 58.621 45.455 13.47 0.00 37.37 3.86
4099 7535 6.530019 AGGAAAACCATCCATATTCAACAC 57.470 37.500 0.00 0.00 42.27 3.32
4120 7556 7.807977 ATAATTGTGTTGTAGCAGGATAAGG 57.192 36.000 0.00 0.00 0.00 2.69
4172 7608 2.009681 TGGTGTCTCCTGAACTGCTA 57.990 50.000 0.00 0.00 37.07 3.49
4362 7798 6.128363 CGAAAGTAGACTGTTAAATGGGTTCC 60.128 42.308 0.00 0.00 0.00 3.62
4432 7875 3.821033 GCCAAAAGTCACTTGAGTATGGT 59.179 43.478 15.27 0.00 37.14 3.55
4433 7876 4.074970 AGCCAAAAGTCACTTGAGTATGG 58.925 43.478 11.79 11.79 37.51 2.74
4434 7877 6.992063 ATAGCCAAAAGTCACTTGAGTATG 57.008 37.500 0.00 0.00 0.00 2.39
4435 7878 8.322091 ACTAATAGCCAAAAGTCACTTGAGTAT 58.678 33.333 0.00 0.00 0.00 2.12
4436 7879 7.676947 ACTAATAGCCAAAAGTCACTTGAGTA 58.323 34.615 0.00 0.00 0.00 2.59
4447 7890 7.710907 TGCACAGATACTACTAATAGCCAAAAG 59.289 37.037 0.00 0.00 30.75 2.27
4452 7895 7.657761 ACATTTGCACAGATACTACTAATAGCC 59.342 37.037 0.00 0.00 30.75 3.93
4580 8023 6.488769 TTAGAAGACAAGTACAAACCTGGA 57.511 37.500 0.00 0.00 0.00 3.86
4602 8045 7.628234 AGTGACAGATTCATGTTCCTTCTATT 58.372 34.615 0.00 0.00 36.32 1.73
4603 8046 7.192852 AGTGACAGATTCATGTTCCTTCTAT 57.807 36.000 0.00 0.00 36.32 1.98
4605 8048 5.495926 AGTGACAGATTCATGTTCCTTCT 57.504 39.130 0.00 0.00 36.32 2.85
4606 8049 6.166279 TGTAGTGACAGATTCATGTTCCTTC 58.834 40.000 0.00 0.00 36.32 3.46
4607 8050 6.114187 TGTAGTGACAGATTCATGTTCCTT 57.886 37.500 0.00 0.00 36.32 3.36
4652 8099 5.249393 ACATACACAGACCAAGATCCTTTCT 59.751 40.000 0.00 0.00 35.70 2.52
4653 8100 5.491982 ACATACACAGACCAAGATCCTTTC 58.508 41.667 0.00 0.00 0.00 2.62
4658 8105 6.992063 ATGAAACATACACAGACCAAGATC 57.008 37.500 0.00 0.00 0.00 2.75
4695 8143 2.202395 GCCTGCAAAGTGCCAAGGA 61.202 57.895 10.03 0.00 44.23 3.36
4893 8341 6.636705 TGCTTATACTACTCAAACGGAACAT 58.363 36.000 0.00 0.00 0.00 2.71
4912 8361 6.970452 ACTACCAAGTAACAGCCATTTGCTTA 60.970 38.462 0.00 0.00 41.00 3.09
4926 8375 4.467438 GGCCTACCAACTACTACCAAGTAA 59.533 45.833 0.00 0.00 35.24 2.24
5027 8481 0.179100 ACTTCCGCATCCATGAGACG 60.179 55.000 0.00 0.00 0.00 4.18
5145 8602 0.955428 TCAGCATGGCAACGGAAGTC 60.955 55.000 0.00 0.00 39.95 3.01
5185 8642 0.464013 TACTCTTCGCTCTCCCCGAG 60.464 60.000 0.00 0.00 42.88 4.63
5186 8643 0.747283 GTACTCTTCGCTCTCCCCGA 60.747 60.000 0.00 0.00 0.00 5.14
5187 8644 1.726533 GGTACTCTTCGCTCTCCCCG 61.727 65.000 0.00 0.00 0.00 5.73
5188 8645 0.683504 TGGTACTCTTCGCTCTCCCC 60.684 60.000 0.00 0.00 0.00 4.81
5189 8646 1.183549 TTGGTACTCTTCGCTCTCCC 58.816 55.000 0.00 0.00 0.00 4.30
5190 8647 2.541999 CGATTGGTACTCTTCGCTCTCC 60.542 54.545 0.00 0.00 0.00 3.71
5191 8648 2.541999 CCGATTGGTACTCTTCGCTCTC 60.542 54.545 0.00 0.00 0.00 3.20
5192 8649 1.405821 CCGATTGGTACTCTTCGCTCT 59.594 52.381 0.00 0.00 0.00 4.09
5193 8650 1.404391 TCCGATTGGTACTCTTCGCTC 59.596 52.381 0.00 0.00 36.30 5.03
5194 8651 1.471119 TCCGATTGGTACTCTTCGCT 58.529 50.000 0.00 0.00 36.30 4.93
5195 8652 2.128035 CATCCGATTGGTACTCTTCGC 58.872 52.381 0.00 0.00 36.30 4.70
5196 8653 3.181490 TGTCATCCGATTGGTACTCTTCG 60.181 47.826 0.00 0.00 36.30 3.79
5197 8654 4.363999 CTGTCATCCGATTGGTACTCTTC 58.636 47.826 0.00 0.00 36.30 2.87
5198 8655 3.133003 CCTGTCATCCGATTGGTACTCTT 59.867 47.826 0.00 0.00 36.30 2.85
5199 8656 2.695666 CCTGTCATCCGATTGGTACTCT 59.304 50.000 0.00 0.00 36.30 3.24
5200 8657 2.224066 CCCTGTCATCCGATTGGTACTC 60.224 54.545 0.00 0.00 36.30 2.59
5201 8658 1.762957 CCCTGTCATCCGATTGGTACT 59.237 52.381 0.00 0.00 36.30 2.73
5202 8659 1.810412 GCCCTGTCATCCGATTGGTAC 60.810 57.143 0.00 0.00 36.30 3.34
5203 8660 0.468226 GCCCTGTCATCCGATTGGTA 59.532 55.000 0.00 0.00 36.30 3.25
5204 8661 1.224592 GCCCTGTCATCCGATTGGT 59.775 57.895 0.00 0.00 36.30 3.67
5236 8711 3.115390 CCCCAAGTTCATCCTTCTCCTA 58.885 50.000 0.00 0.00 0.00 2.94
5334 8815 0.773014 CATAGGTCCATCATGGCCCA 59.227 55.000 6.51 0.00 38.22 5.36
5343 8824 4.008453 CCTGGGGCATAGGTCCAT 57.992 61.111 0.00 0.00 42.08 3.41
5381 8862 2.092323 GAACCTTTTCTTGGATCCCCG 58.908 52.381 9.90 0.00 34.29 5.73
5382 8863 3.169512 TGAACCTTTTCTTGGATCCCC 57.830 47.619 9.90 0.00 32.36 4.81
5383 8864 4.588951 AGTTTGAACCTTTTCTTGGATCCC 59.411 41.667 9.90 0.00 32.36 3.85
5387 8868 4.644685 CCAGAGTTTGAACCTTTTCTTGGA 59.355 41.667 0.00 0.00 32.36 3.53
5390 8871 3.960755 CCCCAGAGTTTGAACCTTTTCTT 59.039 43.478 0.00 0.00 32.36 2.52
5393 8874 3.031013 CACCCCAGAGTTTGAACCTTTT 58.969 45.455 0.00 0.00 0.00 2.27
5402 8883 1.071471 CGAGCACACCCCAGAGTTT 59.929 57.895 0.00 0.00 0.00 2.66
5408 8889 2.525629 TCCTTCGAGCACACCCCA 60.526 61.111 0.00 0.00 0.00 4.96
5424 8905 2.750712 AGAGCTAGAACTTGACGAGGTC 59.249 50.000 0.00 0.00 42.76 3.85
5425 8906 2.750712 GAGAGCTAGAACTTGACGAGGT 59.249 50.000 0.00 0.00 0.00 3.85
5428 8909 2.162608 GCAGAGAGCTAGAACTTGACGA 59.837 50.000 0.00 0.00 41.15 4.20
5429 8910 2.525055 GCAGAGAGCTAGAACTTGACG 58.475 52.381 0.00 0.00 41.15 4.35
5431 8912 1.827969 GGGCAGAGAGCTAGAACTTGA 59.172 52.381 0.00 0.00 44.79 3.02
5435 8916 1.134848 CAGTGGGCAGAGAGCTAGAAC 60.135 57.143 0.00 0.00 44.79 3.01
5436 8917 1.189752 CAGTGGGCAGAGAGCTAGAA 58.810 55.000 0.00 0.00 44.79 2.10
5463 8944 2.986306 AAGCACGCTGGAGCATTGC 61.986 57.895 12.34 12.34 45.14 3.56
5464 8945 1.154093 CAAGCACGCTGGAGCATTG 60.154 57.895 0.00 0.00 42.21 2.82
5465 8946 2.338015 CCAAGCACGCTGGAGCATT 61.338 57.895 0.00 0.00 42.21 3.56
5466 8947 2.749044 CCAAGCACGCTGGAGCAT 60.749 61.111 0.00 0.00 42.21 3.79
5483 8964 1.522580 GCTGTTCATCCTCCTCGCC 60.523 63.158 0.00 0.00 0.00 5.54
5487 8968 1.617947 GGTCCGCTGTTCATCCTCCT 61.618 60.000 0.00 0.00 0.00 3.69
5488 8969 1.153349 GGTCCGCTGTTCATCCTCC 60.153 63.158 0.00 0.00 0.00 4.30
5489 8970 1.153349 GGGTCCGCTGTTCATCCTC 60.153 63.158 0.00 0.00 0.00 3.71
5498 8979 3.599285 TAAACTGCCGGGTCCGCTG 62.599 63.158 2.18 6.54 38.24 5.18
5500 8981 3.122971 GTAAACTGCCGGGTCCGC 61.123 66.667 2.18 0.67 38.24 5.54
5502 8983 2.045634 GGGTAAACTGCCGGGTCC 60.046 66.667 2.18 0.00 0.00 4.46
5503 8984 1.376812 CTGGGTAAACTGCCGGGTC 60.377 63.158 2.18 0.00 0.00 4.46
5504 8985 2.754375 CTGGGTAAACTGCCGGGT 59.246 61.111 2.18 0.00 0.00 5.28
5505 8986 2.045340 CCTGGGTAAACTGCCGGG 60.045 66.667 2.18 0.00 0.00 5.73
5506 8987 0.958876 GAACCTGGGTAAACTGCCGG 60.959 60.000 0.00 0.00 0.00 6.13
5507 8988 1.296056 CGAACCTGGGTAAACTGCCG 61.296 60.000 0.00 0.00 0.00 5.69
5508 8989 0.958876 CCGAACCTGGGTAAACTGCC 60.959 60.000 0.00 0.00 0.00 4.85
5509 8990 0.958876 CCCGAACCTGGGTAAACTGC 60.959 60.000 0.00 0.00 44.76 4.40
5558 9042 0.527565 GCGAGGCAATCCACACAAAT 59.472 50.000 0.00 0.00 33.74 2.32
5575 9060 1.609072 TCATACTCATCCTTCCTCGCG 59.391 52.381 0.00 0.00 0.00 5.87
5582 9067 6.351371 CCTTGTACACACTCATACTCATCCTT 60.351 42.308 0.00 0.00 0.00 3.36
5585 9070 6.208988 TCCTTGTACACACTCATACTCATC 57.791 41.667 0.00 0.00 0.00 2.92
5590 9075 4.381718 GGTCCTCCTTGTACACACTCATAC 60.382 50.000 0.00 0.00 0.00 2.39
5609 9094 3.316573 CTCCCGAGGCAGTTGGTCC 62.317 68.421 0.00 0.00 0.00 4.46
5624 9109 2.065906 CTCGAACTAGCCGAGCCTCC 62.066 65.000 18.19 0.00 45.37 4.30
5631 9116 1.107538 TGGATCCCTCGAACTAGCCG 61.108 60.000 9.90 0.00 0.00 5.52
5638 9123 3.518992 AAAACCTTTGGATCCCTCGAA 57.481 42.857 9.90 0.00 0.00 3.71
5655 9140 4.352595 TCCACCATAGAGAAGGGTCAAAAA 59.647 41.667 0.00 0.00 31.03 1.94
5660 9145 3.519913 AGTTTCCACCATAGAGAAGGGTC 59.480 47.826 0.00 0.00 31.03 4.46
5661 9146 3.532102 AGTTTCCACCATAGAGAAGGGT 58.468 45.455 0.00 0.00 34.59 4.34
5663 9148 4.407296 AGCTAGTTTCCACCATAGAGAAGG 59.593 45.833 0.00 0.00 0.00 3.46
5664 9149 5.606348 AGCTAGTTTCCACCATAGAGAAG 57.394 43.478 0.00 0.00 0.00 2.85
5665 9150 7.676683 ATAAGCTAGTTTCCACCATAGAGAA 57.323 36.000 0.00 0.00 0.00 2.87
5679 9180 7.017531 AGGGCCAGTATAAGTATAAGCTAGTT 58.982 38.462 6.18 0.00 0.00 2.24
5686 9187 4.842380 GGACCAGGGCCAGTATAAGTATAA 59.158 45.833 6.40 0.00 0.00 0.98
5697 9198 2.674220 GGAAGAGGACCAGGGCCAG 61.674 68.421 16.27 0.00 0.00 4.85
5703 9204 1.267121 TTTCGGAGGAAGAGGACCAG 58.733 55.000 0.00 0.00 32.80 4.00
5704 9205 1.346722 GTTTTCGGAGGAAGAGGACCA 59.653 52.381 0.00 0.00 32.80 4.02
5716 9217 0.612732 TCCCGCCTAGAGTTTTCGGA 60.613 55.000 0.07 0.00 42.43 4.55
5753 9254 4.319177 ACTCTTGTCTCCCTTCAAAATCG 58.681 43.478 0.00 0.00 0.00 3.34
5754 9255 6.231211 TGTACTCTTGTCTCCCTTCAAAATC 58.769 40.000 0.00 0.00 0.00 2.17
5756 9257 5.623956 TGTACTCTTGTCTCCCTTCAAAA 57.376 39.130 0.00 0.00 0.00 2.44
5771 9272 9.482175 ACCTTTAGTCAAGATAAGATGTACTCT 57.518 33.333 0.00 0.00 33.80 3.24
5781 9282 7.357303 GCGAAAAACACCTTTAGTCAAGATAA 58.643 34.615 0.00 0.00 33.80 1.75
5786 9287 3.949113 AGGCGAAAAACACCTTTAGTCAA 59.051 39.130 0.00 0.00 0.00 3.18
5799 9300 0.387565 GAGGTTTGGCAGGCGAAAAA 59.612 50.000 3.00 0.00 0.00 1.94
5801 9302 1.901464 GGAGGTTTGGCAGGCGAAA 60.901 57.895 0.00 0.00 0.00 3.46
5815 9316 2.124983 CACGTCATGGCAGGGAGG 60.125 66.667 0.00 4.74 0.00 4.30
5817 9318 2.662596 GACACGTCATGGCAGGGA 59.337 61.111 0.00 0.00 35.73 4.20
5818 9319 2.815211 CGACACGTCATGGCAGGG 60.815 66.667 0.00 0.00 35.12 4.45


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

AutoCloner maintained by Alex Coulton.