Multiple sequence alignment - TraesCS6A01G125200

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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 TraesCS6A01G125200 chr6A 100.000 4772 0 0 1 4772 98814604 98809833 0.000000e+00 8813.0
1 TraesCS6A01G125200 chr6A 88.860 3815 375 34 507 4281 98324367 98320563 0.000000e+00 4645.0
2 TraesCS6A01G125200 chr6A 83.188 3331 514 38 841 4150 98256590 98253285 0.000000e+00 3007.0
3 TraesCS6A01G125200 chr6A 83.089 3205 501 28 983 4164 98250013 98246827 0.000000e+00 2878.0
4 TraesCS6A01G125200 chr6A 81.946 3423 555 48 897 4288 98316058 98312668 0.000000e+00 2839.0
5 TraesCS6A01G125200 chr6A 96.226 53 2 0 214 266 98888909 98888857 2.370000e-13 87.9
6 TraesCS6A01G125200 chr6A 87.143 70 8 1 224 292 98257196 98257127 1.420000e-10 78.7
7 TraesCS6A01G125200 chr6A 91.667 48 3 1 297 343 465213657 465213610 1.110000e-06 65.8
8 TraesCS6A01G125200 chr6D 91.352 3943 303 17 342 4267 82139790 82135869 0.000000e+00 5358.0
9 TraesCS6A01G125200 chr6D 89.335 3807 360 30 507 4274 81935898 81932099 0.000000e+00 4739.0
10 TraesCS6A01G125200 chr6D 80.904 3430 582 60 870 4261 82204107 82200713 0.000000e+00 2638.0
11 TraesCS6A01G125200 chr6D 82.521 2094 342 21 936 3015 83020905 83018822 0.000000e+00 1818.0
12 TraesCS6A01G125200 chr6D 90.681 279 23 3 29 306 82140065 82139789 7.540000e-98 368.0
13 TraesCS6A01G125200 chr6D 83.133 249 20 8 4540 4772 82135444 82135202 1.740000e-49 207.0
14 TraesCS6A01G125200 chr6D 89.041 73 7 1 221 292 81764736 81764664 6.580000e-14 89.8
15 TraesCS6A01G125200 chr6D 91.667 60 2 3 221 277 82970129 82970070 3.960000e-11 80.5
16 TraesCS6A01G125200 chr6B 91.098 3943 318 14 342 4267 157028063 157024137 0.000000e+00 5306.0
17 TraesCS6A01G125200 chr6B 89.069 3815 358 33 507 4281 156741503 156737708 0.000000e+00 4680.0
18 TraesCS6A01G125200 chr6B 82.961 3316 525 33 853 4150 156533335 156530042 0.000000e+00 2957.0
19 TraesCS6A01G125200 chr6B 81.204 3703 600 57 616 4288 157489639 157486003 0.000000e+00 2894.0
20 TraesCS6A01G125200 chr6B 84.406 2097 306 15 935 3020 157900247 157902333 0.000000e+00 2041.0
21 TraesCS6A01G125200 chr6B 88.356 292 20 3 29 306 157028353 157028062 5.920000e-89 339.0
22 TraesCS6A01G125200 chr6B 89.041 73 7 1 221 292 156533984 156533912 6.580000e-14 89.8
23 TraesCS6A01G125200 chr6B 96.078 51 2 0 216 266 157110266 157110216 3.060000e-12 84.2
24 TraesCS6A01G125200 chr6B 91.803 61 1 2 357 413 157133485 157133425 1.100000e-11 82.4
25 TraesCS6A01G125200 chr1D 97.436 39 1 0 299 337 79028601 79028639 3.080000e-07 67.6
26 TraesCS6A01G125200 chr1D 97.436 39 1 0 299 337 176206406 176206444 3.080000e-07 67.6
27 TraesCS6A01G125200 chr1D 91.667 48 3 1 297 343 113163811 113163764 1.110000e-06 65.8
28 TraesCS6A01G125200 chrUn 91.667 48 3 1 297 343 424750494 424750447 1.110000e-06 65.8
29 TraesCS6A01G125200 chr7A 90.196 51 4 1 297 346 352131440 352131390 1.110000e-06 65.8
30 TraesCS6A01G125200 chr7A 95.238 42 1 1 297 337 352626284 352626325 1.110000e-06 65.8
31 TraesCS6A01G125200 chr3B 91.667 48 3 1 297 343 268613402 268613355 1.110000e-06 65.8
32 TraesCS6A01G125200 chr3A 91.667 48 3 1 297 343 66008469 66008422 1.110000e-06 65.8


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 TraesCS6A01G125200 chr6A 98809833 98814604 4771 True 8813.000000 8813 100.000000 1 4772 1 chr6A.!!$R3 4771
1 TraesCS6A01G125200 chr6A 98320563 98324367 3804 True 4645.000000 4645 88.860000 507 4281 1 chr6A.!!$R2 3774
2 TraesCS6A01G125200 chr6A 98312668 98316058 3390 True 2839.000000 2839 81.946000 897 4288 1 chr6A.!!$R1 3391
3 TraesCS6A01G125200 chr6A 98246827 98257196 10369 True 1987.900000 3007 84.473333 224 4164 3 chr6A.!!$R6 3940
4 TraesCS6A01G125200 chr6D 81932099 81935898 3799 True 4739.000000 4739 89.335000 507 4274 1 chr6D.!!$R2 3767
5 TraesCS6A01G125200 chr6D 82200713 82204107 3394 True 2638.000000 2638 80.904000 870 4261 1 chr6D.!!$R3 3391
6 TraesCS6A01G125200 chr6D 82135202 82140065 4863 True 1977.666667 5358 88.388667 29 4772 3 chr6D.!!$R6 4743
7 TraesCS6A01G125200 chr6D 83018822 83020905 2083 True 1818.000000 1818 82.521000 936 3015 1 chr6D.!!$R5 2079
8 TraesCS6A01G125200 chr6B 156737708 156741503 3795 True 4680.000000 4680 89.069000 507 4281 1 chr6B.!!$R1 3774
9 TraesCS6A01G125200 chr6B 157486003 157489639 3636 True 2894.000000 2894 81.204000 616 4288 1 chr6B.!!$R4 3672
10 TraesCS6A01G125200 chr6B 157024137 157028353 4216 True 2822.500000 5306 89.727000 29 4267 2 chr6B.!!$R6 4238
11 TraesCS6A01G125200 chr6B 157900247 157902333 2086 False 2041.000000 2041 84.406000 935 3020 1 chr6B.!!$F1 2085
12 TraesCS6A01G125200 chr6B 156530042 156533984 3942 True 1523.400000 2957 86.001000 221 4150 2 chr6B.!!$R5 3929

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
875 1053 0.036164 TACGGCTGCAAGTGGACAAT 59.964 50.000 0.5 0.0 35.30 2.71 F
1453 1659 0.392193 CGAGCTGCCATCTTCAACCT 60.392 55.000 0.0 0.0 0.00 3.50 F
1458 1664 1.004044 CTGCCATCTTCAACCTCTGGT 59.996 52.381 0.0 0.0 37.65 4.00 F
2820 9470 0.250338 ACCTCAGAAACTTGCGGGTC 60.250 55.000 0.0 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2799 9449 0.250295 CCCGCAAGTTTCTGAGGTCA 60.250 55.000 0.0 0.0 34.68 4.02 R
2800 9450 0.250338 ACCCGCAAGTTTCTGAGGTC 60.250 55.000 0.0 0.0 34.68 3.85 R
2906 9556 0.548510 AGGCCCTTCTAGGTCATTGC 59.451 55.000 0.0 0.0 32.23 3.56 R
4728 11596 1.202592 TCTCGCAGTTAGCCACAAACA 60.203 47.619 0.0 0.0 41.38 2.83 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
54 55 7.850935 ATAAAAGGTAATCTCGATGAGGGTA 57.149 36.000 0.00 0.00 0.00 3.69
62 63 3.087031 TCTCGATGAGGGTAAACGTTCT 58.913 45.455 0.00 0.00 0.00 3.01
71 72 3.008704 AGGGTAAACGTTCTGCTACCAAT 59.991 43.478 22.23 11.56 36.34 3.16
76 77 7.019418 GGTAAACGTTCTGCTACCAATTTAAG 58.981 38.462 17.98 0.00 34.99 1.85
80 81 8.556213 AACGTTCTGCTACCAATTTAAGATAA 57.444 30.769 0.00 0.00 0.00 1.75
81 82 8.556213 ACGTTCTGCTACCAATTTAAGATAAA 57.444 30.769 0.00 0.00 0.00 1.40
82 83 8.665685 ACGTTCTGCTACCAATTTAAGATAAAG 58.334 33.333 0.00 0.00 0.00 1.85
83 84 8.879759 CGTTCTGCTACCAATTTAAGATAAAGA 58.120 33.333 0.00 0.00 0.00 2.52
129 145 3.386726 TCCCTAAAGACCATGACCATACG 59.613 47.826 0.00 0.00 0.00 3.06
135 151 2.036475 AGACCATGACCATACGAGCATC 59.964 50.000 0.00 0.00 0.00 3.91
139 155 3.555586 CCATGACCATACGAGCATCATCA 60.556 47.826 0.00 0.00 33.17 3.07
202 218 4.051237 ACGTTACCCAGTTTACTTCGAAC 58.949 43.478 0.00 0.00 0.00 3.95
267 286 5.580297 GGAGAATGAAAAACAACAGCAAACA 59.420 36.000 0.00 0.00 0.00 2.83
277 296 7.840342 AAACAACAGCAAACATAAACATCAA 57.160 28.000 0.00 0.00 0.00 2.57
279 298 7.840342 ACAACAGCAAACATAAACATCAAAA 57.160 28.000 0.00 0.00 0.00 2.44
286 305 7.712205 AGCAAACATAAACATCAAAAGAAGCTT 59.288 29.630 0.00 0.00 0.00 3.74
304 331 2.564771 CTTGCTCGAATGATAAGGGCA 58.435 47.619 0.00 0.00 0.00 5.36
305 332 2.708216 TGCTCGAATGATAAGGGCAA 57.292 45.000 0.00 0.00 0.00 4.52
306 333 3.213206 TGCTCGAATGATAAGGGCAAT 57.787 42.857 0.00 0.00 0.00 3.56
307 334 3.141398 TGCTCGAATGATAAGGGCAATC 58.859 45.455 0.00 0.00 0.00 2.67
308 335 3.181451 TGCTCGAATGATAAGGGCAATCT 60.181 43.478 0.00 0.00 0.00 2.40
309 336 3.817647 GCTCGAATGATAAGGGCAATCTT 59.182 43.478 0.00 0.00 0.00 2.40
310 337 4.276926 GCTCGAATGATAAGGGCAATCTTT 59.723 41.667 0.00 0.00 0.00 2.52
311 338 5.755813 CTCGAATGATAAGGGCAATCTTTG 58.244 41.667 0.00 0.00 0.00 2.77
334 361 5.489792 CCTATTAGGCAAGAGGATAGCAA 57.510 43.478 0.00 0.00 44.57 3.91
335 362 5.486526 CCTATTAGGCAAGAGGATAGCAAG 58.513 45.833 0.00 0.00 44.57 4.01
336 363 5.012561 CCTATTAGGCAAGAGGATAGCAAGT 59.987 44.000 0.00 0.00 44.57 3.16
337 364 6.211584 CCTATTAGGCAAGAGGATAGCAAGTA 59.788 42.308 0.00 0.00 44.57 2.24
338 365 3.828875 AGGCAAGAGGATAGCAAGTAC 57.171 47.619 0.00 0.00 0.00 2.73
339 366 3.107601 AGGCAAGAGGATAGCAAGTACA 58.892 45.455 0.00 0.00 0.00 2.90
340 367 3.519510 AGGCAAGAGGATAGCAAGTACAA 59.480 43.478 0.00 0.00 0.00 2.41
407 436 1.465188 AGGTCAACCATCCACCCCA 60.465 57.895 1.33 0.00 38.89 4.96
426 455 4.222588 CCCCATCCATTAAGCAACAAAGAA 59.777 41.667 0.00 0.00 0.00 2.52
545 679 3.864003 GGCAAGGATACGTCAAGAAGTAC 59.136 47.826 0.00 0.00 46.39 2.73
582 716 2.223852 GCTAGCGGGAAGAAGTTAGAGG 60.224 54.545 0.00 0.00 0.00 3.69
597 733 1.172812 AGAGGTGTTTTGAAGCCGGC 61.173 55.000 21.89 21.89 0.00 6.13
745 914 4.471904 TTGTCAGTAGATTACAGCAGGG 57.528 45.455 0.00 0.00 0.00 4.45
746 915 2.168521 TGTCAGTAGATTACAGCAGGGC 59.831 50.000 0.00 0.00 0.00 5.19
747 916 1.409064 TCAGTAGATTACAGCAGGGCG 59.591 52.381 0.00 0.00 0.00 6.13
748 917 0.753262 AGTAGATTACAGCAGGGCGG 59.247 55.000 0.00 0.00 0.00 6.13
749 918 0.880718 GTAGATTACAGCAGGGCGGC 60.881 60.000 0.00 0.00 0.00 6.53
860 1038 3.328382 TTTCCTTCATGGTGACTACGG 57.672 47.619 0.00 0.00 37.07 4.02
875 1053 0.036164 TACGGCTGCAAGTGGACAAT 59.964 50.000 0.50 0.00 35.30 2.71
895 1073 6.767456 ACAATACAAAATGGGAGCAAAATCA 58.233 32.000 0.00 0.00 0.00 2.57
912 1092 6.714278 CAAAATCATCTTTCCTTTCCCCATT 58.286 36.000 0.00 0.00 0.00 3.16
921 1101 4.170468 TCCTTTCCCCATTATGCTCTTC 57.830 45.455 0.00 0.00 0.00 2.87
977 1161 5.531287 AGGGTACAACTTTAGCTCTTGTTTG 59.469 40.000 0.00 0.00 30.76 2.93
1005 1193 2.362077 AGTTCACCAGAAAACCATGCAC 59.638 45.455 0.00 0.00 35.08 4.57
1008 1196 1.039856 ACCAGAAAACCATGCACACC 58.960 50.000 0.00 0.00 0.00 4.16
1017 1205 0.533491 CCATGCACACCCTCCATTTG 59.467 55.000 0.00 0.00 0.00 2.32
1296 1499 0.994247 AGGGGCACATCTCACAATCA 59.006 50.000 0.00 0.00 0.00 2.57
1362 1565 2.847234 TTGTCCGGTGGTCTGCCT 60.847 61.111 0.00 0.00 35.27 4.75
1375 1578 1.126488 TCTGCCTCTGGGATTGCTAG 58.874 55.000 0.00 0.00 33.58 3.42
1453 1659 0.392193 CGAGCTGCCATCTTCAACCT 60.392 55.000 0.00 0.00 0.00 3.50
1458 1664 1.004044 CTGCCATCTTCAACCTCTGGT 59.996 52.381 0.00 0.00 37.65 4.00
1461 1667 2.501723 GCCATCTTCAACCTCTGGTAGA 59.498 50.000 0.00 0.00 33.12 2.59
1572 1778 3.119388 TCAATGCCAGCAATAACAGCTTC 60.119 43.478 0.00 0.00 41.14 3.86
1808 2014 7.865706 ATGGTTTGTATGGAGTTCTTGATAC 57.134 36.000 0.00 0.00 0.00 2.24
1855 2061 5.779241 TCTTGTAACCCTTGATCTTGGAT 57.221 39.130 6.20 0.00 0.00 3.41
1905 2111 8.310382 CCAGATTATATAGGTCAACTCAAGAGG 58.690 40.741 1.73 0.00 0.00 3.69
1995 2201 7.599621 TGCAAAAATCTCATAACAATTGACCTG 59.400 33.333 13.59 6.05 0.00 4.00
2032 2238 3.679980 CAGTGGAGAACTTACCAATGTCG 59.320 47.826 0.00 0.00 44.00 4.35
2248 2454 2.819115 TCACAAACATTGCAAATGCGT 58.181 38.095 1.71 0.00 45.83 5.24
2300 2506 2.676342 CCACCCTGCTTATTTCGTACAC 59.324 50.000 0.00 0.00 0.00 2.90
2503 2709 5.491982 TCAACTCCTTAAGCCATCTCTTTC 58.508 41.667 0.00 0.00 0.00 2.62
2519 2725 9.205719 CCATCTCTTTCATATAGATGTGTCAAG 57.794 37.037 10.23 0.00 43.28 3.02
2603 2809 3.360867 ACAACACAACTCATTTGGACCA 58.639 40.909 0.00 0.00 39.84 4.02
2646 2852 6.064060 TCTTTATAATGGCCCATCACTTCAG 58.936 40.000 0.00 0.00 0.00 3.02
2671 2877 3.492656 CCGTGTGGTTACATCTATCCCAG 60.493 52.174 0.00 0.00 39.39 4.45
2698 2904 4.229876 GTTGAATCTAAGCAACAACAGCC 58.770 43.478 0.00 0.00 42.86 4.85
2700 2906 4.144297 TGAATCTAAGCAACAACAGCCTT 58.856 39.130 0.00 0.00 0.00 4.35
2736 2942 3.424703 CCCACAGATTGGTCAGTTGAAT 58.575 45.455 0.00 0.00 45.25 2.57
2747 2953 5.069318 TGGTCAGTTGAATATGCTTGTTGA 58.931 37.500 0.00 0.00 0.00 3.18
2748 2954 5.181811 TGGTCAGTTGAATATGCTTGTTGAG 59.818 40.000 0.00 0.00 0.00 3.02
2799 9449 2.242196 ACAGATCCCCCAATCGATTTGT 59.758 45.455 8.21 4.97 33.15 2.83
2800 9450 2.620115 CAGATCCCCCAATCGATTTGTG 59.380 50.000 8.21 0.00 33.15 3.33
2807 9457 2.679837 CCCAATCGATTTGTGACCTCAG 59.320 50.000 8.21 0.00 33.15 3.35
2816 9466 1.581934 TGTGACCTCAGAAACTTGCG 58.418 50.000 0.00 0.00 0.00 4.85
2820 9470 0.250338 ACCTCAGAAACTTGCGGGTC 60.250 55.000 0.00 0.00 0.00 4.46
2829 9479 3.434940 AACTTGCGGGTCCTAGATTTT 57.565 42.857 0.00 0.00 0.00 1.82
2856 9506 3.441572 GCAACAATCTCACAGGTGCTATT 59.558 43.478 0.00 0.00 0.00 1.73
2906 9556 6.218019 TCCTTTCAGCATTCAACATTTCAAG 58.782 36.000 0.00 0.00 0.00 3.02
2943 9593 1.776667 CCTATTCCATCTGGAGGCCAA 59.223 52.381 5.01 0.00 46.36 4.52
2997 9647 0.111061 ATCCAAAGCTGTGTGGCTCA 59.889 50.000 2.51 0.00 42.24 4.26
3156 9806 0.914644 TCTCAATCAGGCAGAAGGGG 59.085 55.000 0.00 0.00 0.00 4.79
3164 9814 0.477795 AGGCAGAAGGGGTTTAGGGT 60.478 55.000 0.00 0.00 0.00 4.34
3366 10016 2.981859 ATGGGTTAGTCTACAAGGCG 57.018 50.000 0.00 0.00 0.00 5.52
3590 10240 4.517832 GCTGCATAACAAGGATGATGATGA 59.482 41.667 0.00 0.00 0.00 2.92
3591 10241 5.183331 GCTGCATAACAAGGATGATGATGAT 59.817 40.000 0.00 0.00 0.00 2.45
3592 10242 6.569179 TGCATAACAAGGATGATGATGATG 57.431 37.500 0.00 0.00 0.00 3.07
3719 10370 6.118170 AGACATCAAATCCAGTAACATCCTG 58.882 40.000 0.00 0.00 0.00 3.86
3730 10381 1.915141 AACATCCTGCTGGACAAAGG 58.085 50.000 15.36 5.18 46.51 3.11
3761 10412 4.824289 CTTATGTTGCAGATTTTGGGCTT 58.176 39.130 0.00 0.00 0.00 4.35
3905 10556 1.552792 GGAGTAGTCCTGCTTGAGCTT 59.447 52.381 9.55 0.00 40.17 3.74
3920 10571 0.392193 AGCTTCTCACTGGAATGCGG 60.392 55.000 0.00 0.00 0.00 5.69
4011 10662 3.341823 CAAGTTGAGGTCTTGGATCCAG 58.658 50.000 15.53 9.55 38.70 3.86
4073 10724 0.945265 TTGAAGCCGCTTGCAAATGC 60.945 50.000 11.20 3.39 44.83 3.56
4178 10829 8.651391 TGCAAAGATCAGCAAAAATATAATGG 57.349 30.769 5.21 0.00 37.90 3.16
4288 10956 8.099364 AGAGTTTGTTTCATACATTGTACAGG 57.901 34.615 0.00 0.00 36.44 4.00
4289 10957 7.719633 AGAGTTTGTTTCATACATTGTACAGGT 59.280 33.333 0.00 1.44 36.44 4.00
4290 10958 8.232913 AGTTTGTTTCATACATTGTACAGGTT 57.767 30.769 7.45 0.00 36.44 3.50
4291 10959 8.349983 AGTTTGTTTCATACATTGTACAGGTTC 58.650 33.333 7.45 0.00 36.44 3.62
4292 10960 7.809546 TTGTTTCATACATTGTACAGGTTCA 57.190 32.000 7.45 0.00 36.44 3.18
4293 10961 7.809546 TGTTTCATACATTGTACAGGTTCAA 57.190 32.000 7.45 0.00 0.00 2.69
4294 10962 8.226819 TGTTTCATACATTGTACAGGTTCAAA 57.773 30.769 7.45 3.28 0.00 2.69
4295 10963 8.687242 TGTTTCATACATTGTACAGGTTCAAAA 58.313 29.630 7.45 4.28 0.00 2.44
4296 10964 9.522804 GTTTCATACATTGTACAGGTTCAAAAA 57.477 29.630 7.45 0.00 0.00 1.94
4334 11002 2.428925 TAGTTCGGGCGGGGTCATC 61.429 63.158 0.00 0.00 0.00 2.92
4336 11004 3.781307 TTCGGGCGGGGTCATCTG 61.781 66.667 0.00 0.00 0.00 2.90
4383 11052 1.901159 AGCTGCCCATGTTTTGCATTA 59.099 42.857 0.00 0.00 35.19 1.90
4386 11055 3.064271 GCTGCCCATGTTTTGCATTAATG 59.936 43.478 11.27 11.27 35.19 1.90
4387 11056 4.505808 CTGCCCATGTTTTGCATTAATGA 58.494 39.130 19.73 1.75 35.19 2.57
4388 11057 5.100344 TGCCCATGTTTTGCATTAATGAT 57.900 34.783 19.73 0.00 35.19 2.45
4390 11059 6.647229 TGCCCATGTTTTGCATTAATGATTA 58.353 32.000 19.73 1.70 35.19 1.75
4413 11082 5.435686 TCATTATTAGTGTTCAGCCAGGT 57.564 39.130 0.00 0.00 0.00 4.00
4420 11089 2.079925 GTGTTCAGCCAGGTGATTCTC 58.920 52.381 0.00 0.00 0.00 2.87
4433 11102 3.305335 GGTGATTCTCGTGGCATGTTTTT 60.305 43.478 6.60 0.00 0.00 1.94
4459 11128 4.117685 GTTGTATTCCGCCGACTAATCTT 58.882 43.478 0.00 0.00 0.00 2.40
4460 11129 3.713288 TGTATTCCGCCGACTAATCTTG 58.287 45.455 0.00 0.00 0.00 3.02
4461 11130 2.981859 ATTCCGCCGACTAATCTTGT 57.018 45.000 0.00 0.00 0.00 3.16
4462 11131 4.338964 TGTATTCCGCCGACTAATCTTGTA 59.661 41.667 0.00 0.00 0.00 2.41
4463 11132 3.431922 TTCCGCCGACTAATCTTGTAG 57.568 47.619 0.00 0.00 0.00 2.74
4464 11133 2.646930 TCCGCCGACTAATCTTGTAGA 58.353 47.619 0.00 0.00 0.00 2.59
4465 11134 3.018856 TCCGCCGACTAATCTTGTAGAA 58.981 45.455 0.00 0.00 0.00 2.10
4466 11135 3.066342 TCCGCCGACTAATCTTGTAGAAG 59.934 47.826 0.00 0.00 0.00 2.85
4467 11136 3.066342 CCGCCGACTAATCTTGTAGAAGA 59.934 47.826 4.58 4.58 42.53 2.87
4468 11137 4.439700 CCGCCGACTAATCTTGTAGAAGAA 60.440 45.833 6.39 0.00 41.64 2.52
4469 11138 5.282510 CGCCGACTAATCTTGTAGAAGAAT 58.717 41.667 6.39 0.61 41.64 2.40
4470 11139 5.749109 CGCCGACTAATCTTGTAGAAGAATT 59.251 40.000 6.39 4.83 41.64 2.17
4471 11140 6.255887 CGCCGACTAATCTTGTAGAAGAATTT 59.744 38.462 6.39 0.32 41.64 1.82
4472 11141 7.201530 CGCCGACTAATCTTGTAGAAGAATTTT 60.202 37.037 6.39 0.00 41.64 1.82
4473 11142 8.451748 GCCGACTAATCTTGTAGAAGAATTTTT 58.548 33.333 6.39 0.00 41.64 1.94
4474 11143 9.974750 CCGACTAATCTTGTAGAAGAATTTTTC 57.025 33.333 6.39 0.46 41.64 2.29
4484 11153 9.997482 TTGTAGAAGAATTTTTCACTACAACAC 57.003 29.630 21.56 6.64 45.25 3.32
4485 11154 9.168451 TGTAGAAGAATTTTTCACTACAACACA 57.832 29.630 10.99 0.49 42.59 3.72
4486 11155 9.434559 GTAGAAGAATTTTTCACTACAACACAC 57.565 33.333 10.99 0.00 39.38 3.82
4487 11156 8.050778 AGAAGAATTTTTCACTACAACACACA 57.949 30.769 10.99 0.00 0.00 3.72
4488 11157 8.686334 AGAAGAATTTTTCACTACAACACACAT 58.314 29.630 10.99 0.00 0.00 3.21
4489 11158 8.633075 AAGAATTTTTCACTACAACACACATG 57.367 30.769 0.00 0.00 0.00 3.21
4490 11159 7.995289 AGAATTTTTCACTACAACACACATGA 58.005 30.769 0.00 0.00 0.00 3.07
4491 11160 8.465999 AGAATTTTTCACTACAACACACATGAA 58.534 29.630 0.00 0.00 0.00 2.57
4492 11161 7.985634 ATTTTTCACTACAACACACATGAAC 57.014 32.000 0.00 0.00 0.00 3.18
4493 11162 6.502136 TTTTCACTACAACACACATGAACA 57.498 33.333 0.00 0.00 0.00 3.18
4494 11163 6.502136 TTTCACTACAACACACATGAACAA 57.498 33.333 0.00 0.00 0.00 2.83
4495 11164 6.691754 TTCACTACAACACACATGAACAAT 57.308 33.333 0.00 0.00 0.00 2.71
4496 11165 6.691754 TCACTACAACACACATGAACAATT 57.308 33.333 0.00 0.00 0.00 2.32
4497 11166 6.724263 TCACTACAACACACATGAACAATTC 58.276 36.000 0.00 0.00 0.00 2.17
4498 11167 6.317391 TCACTACAACACACATGAACAATTCA 59.683 34.615 0.00 0.00 45.01 2.57
4499 11168 6.414694 CACTACAACACACATGAACAATTCAC 59.585 38.462 0.00 0.00 43.48 3.18
4500 11169 4.681744 ACAACACACATGAACAATTCACC 58.318 39.130 0.00 0.00 43.48 4.02
4501 11170 4.050553 CAACACACATGAACAATTCACCC 58.949 43.478 0.00 0.00 43.48 4.61
4502 11171 2.627699 ACACACATGAACAATTCACCCC 59.372 45.455 0.00 0.00 43.48 4.95
4503 11172 2.627221 CACACATGAACAATTCACCCCA 59.373 45.455 0.00 0.00 43.48 4.96
4504 11173 3.069300 CACACATGAACAATTCACCCCAA 59.931 43.478 0.00 0.00 43.48 4.12
4505 11174 3.708631 ACACATGAACAATTCACCCCAAA 59.291 39.130 0.00 0.00 43.48 3.28
4506 11175 4.163078 ACACATGAACAATTCACCCCAAAA 59.837 37.500 0.00 0.00 43.48 2.44
4507 11176 5.163216 ACACATGAACAATTCACCCCAAAAT 60.163 36.000 0.00 0.00 43.48 1.82
4508 11177 6.042552 ACACATGAACAATTCACCCCAAAATA 59.957 34.615 0.00 0.00 43.48 1.40
4509 11178 6.591062 CACATGAACAATTCACCCCAAAATAG 59.409 38.462 0.00 0.00 43.48 1.73
4510 11179 6.496565 ACATGAACAATTCACCCCAAAATAGA 59.503 34.615 0.00 0.00 43.48 1.98
4511 11180 6.588719 TGAACAATTCACCCCAAAATAGAG 57.411 37.500 0.00 0.00 34.08 2.43
4512 11181 6.310941 TGAACAATTCACCCCAAAATAGAGA 58.689 36.000 0.00 0.00 34.08 3.10
4513 11182 6.780031 TGAACAATTCACCCCAAAATAGAGAA 59.220 34.615 0.00 0.00 34.08 2.87
4514 11183 7.288852 TGAACAATTCACCCCAAAATAGAGAAA 59.711 33.333 0.00 0.00 34.08 2.52
4515 11184 7.610580 ACAATTCACCCCAAAATAGAGAAAA 57.389 32.000 0.00 0.00 0.00 2.29
4516 11185 8.206126 ACAATTCACCCCAAAATAGAGAAAAT 57.794 30.769 0.00 0.00 0.00 1.82
4517 11186 8.314021 ACAATTCACCCCAAAATAGAGAAAATC 58.686 33.333 0.00 0.00 0.00 2.17
4518 11187 8.534496 CAATTCACCCCAAAATAGAGAAAATCT 58.466 33.333 0.00 0.00 42.47 2.40
4519 11188 7.466746 TTCACCCCAAAATAGAGAAAATCTG 57.533 36.000 0.00 0.00 39.20 2.90
4520 11189 6.552008 TCACCCCAAAATAGAGAAAATCTGT 58.448 36.000 0.00 0.00 39.20 3.41
4521 11190 6.434028 TCACCCCAAAATAGAGAAAATCTGTG 59.566 38.462 0.00 0.00 39.20 3.66
4522 11191 5.185828 ACCCCAAAATAGAGAAAATCTGTGC 59.814 40.000 0.00 0.00 39.20 4.57
4523 11192 5.185635 CCCCAAAATAGAGAAAATCTGTGCA 59.814 40.000 0.00 0.00 39.20 4.57
4524 11193 6.295236 CCCCAAAATAGAGAAAATCTGTGCAA 60.295 38.462 0.00 0.00 39.20 4.08
4525 11194 7.153985 CCCAAAATAGAGAAAATCTGTGCAAA 58.846 34.615 0.00 0.00 39.20 3.68
4526 11195 7.330208 CCCAAAATAGAGAAAATCTGTGCAAAG 59.670 37.037 0.00 0.00 39.20 2.77
4527 11196 8.084073 CCAAAATAGAGAAAATCTGTGCAAAGA 58.916 33.333 9.56 9.56 39.20 2.52
4528 11197 9.467258 CAAAATAGAGAAAATCTGTGCAAAGAA 57.533 29.630 11.47 0.00 39.20 2.52
4570 11422 7.781056 ACAATGACAAAAACAAGAACTGGTAT 58.219 30.769 0.00 0.00 0.00 2.73
4574 11426 9.965824 ATGACAAAAACAAGAACTGGTATAAAG 57.034 29.630 0.00 0.00 0.00 1.85
4575 11427 8.410141 TGACAAAAACAAGAACTGGTATAAAGG 58.590 33.333 0.00 0.00 0.00 3.11
4576 11428 8.301252 ACAAAAACAAGAACTGGTATAAAGGT 57.699 30.769 0.00 0.00 0.00 3.50
4577 11429 8.410912 ACAAAAACAAGAACTGGTATAAAGGTC 58.589 33.333 0.00 0.00 0.00 3.85
4578 11430 7.520451 AAAACAAGAACTGGTATAAAGGTCC 57.480 36.000 0.00 0.00 31.29 4.46
4579 11431 5.836024 ACAAGAACTGGTATAAAGGTCCA 57.164 39.130 0.00 0.00 31.29 4.02
4580 11432 6.388619 ACAAGAACTGGTATAAAGGTCCAT 57.611 37.500 0.00 0.00 31.29 3.41
4581 11433 6.790319 ACAAGAACTGGTATAAAGGTCCATT 58.210 36.000 0.00 0.00 31.29 3.16
4582 11434 6.884836 ACAAGAACTGGTATAAAGGTCCATTC 59.115 38.462 0.00 0.00 31.29 2.67
4584 11436 7.213178 AGAACTGGTATAAAGGTCCATTCAT 57.787 36.000 0.00 0.00 31.29 2.57
4625 11477 4.086457 AGAAAAACGCCAGGGATGTTATT 58.914 39.130 0.00 0.00 0.00 1.40
4662 11522 9.783256 GTTCCATAATTGTTGATAGTTTGTACC 57.217 33.333 0.00 0.00 0.00 3.34
4709 11577 4.055360 GGGTTGTTTTCTAACATTGGCAC 58.945 43.478 0.00 0.00 43.43 5.01
4710 11578 4.202212 GGGTTGTTTTCTAACATTGGCACT 60.202 41.667 0.00 0.00 43.43 4.40
4711 11579 5.010213 GGGTTGTTTTCTAACATTGGCACTA 59.990 40.000 0.00 0.00 43.43 2.74
4712 11580 6.149633 GGTTGTTTTCTAACATTGGCACTAG 58.850 40.000 0.00 0.00 43.43 2.57
4713 11581 5.957842 TGTTTTCTAACATTGGCACTAGG 57.042 39.130 0.00 0.00 39.29 3.02
4714 11582 5.381757 TGTTTTCTAACATTGGCACTAGGT 58.618 37.500 0.00 0.00 39.29 3.08
4715 11583 5.240623 TGTTTTCTAACATTGGCACTAGGTG 59.759 40.000 0.00 0.00 39.29 4.00
4728 11596 3.744660 CACTAGGTGCAGAAAACTCCTT 58.255 45.455 0.00 0.00 33.29 3.36
4742 11610 3.577805 ACTCCTTGTTTGTGGCTAACT 57.422 42.857 0.00 0.00 0.00 2.24
4745 11613 1.334960 CCTTGTTTGTGGCTAACTGCG 60.335 52.381 0.00 0.00 44.05 5.18
4754 11622 3.384789 TGTGGCTAACTGCGAGAGATTAT 59.615 43.478 0.00 0.00 44.05 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.726438 CCCTCATCGAGATTACCTTTTATTATT 57.274 33.333 0.00 0.00 0.00 1.40
27 28 8.881262 ACCCTCATCGAGATTACCTTTTATTAT 58.119 33.333 0.00 0.00 0.00 1.28
37 38 4.929781 ACGTTTACCCTCATCGAGATTAC 58.070 43.478 0.00 0.00 0.00 1.89
54 55 6.870971 TCTTAAATTGGTAGCAGAACGTTT 57.129 33.333 0.46 0.00 0.00 3.60
83 84 9.614792 GGACAGAACCATGTATTTATCTTACTT 57.385 33.333 0.00 0.00 32.25 2.24
84 85 8.211629 GGGACAGAACCATGTATTTATCTTACT 58.788 37.037 0.00 0.00 32.25 2.24
85 86 8.211629 AGGGACAGAACCATGTATTTATCTTAC 58.788 37.037 0.00 0.00 32.25 2.34
95 96 4.224370 GGTCTTTAGGGACAGAACCATGTA 59.776 45.833 0.00 0.00 37.91 2.29
129 145 1.941294 CAGTTGGCTCTGATGATGCTC 59.059 52.381 4.71 0.00 37.61 4.26
139 155 1.612726 GCTGGTTGATCAGTTGGCTCT 60.613 52.381 0.00 0.00 37.12 4.09
172 188 2.521105 ACTGGGTAACGTGTGAGTTC 57.479 50.000 0.00 0.00 35.70 3.01
202 218 7.517734 CACTATTATATTGTGGTTCGGAAACGG 60.518 40.741 0.70 0.00 41.92 4.44
267 286 6.072508 TCGAGCAAGCTTCTTTTGATGTTTAT 60.073 34.615 0.00 0.00 0.00 1.40
277 296 5.065731 CCTTATCATTCGAGCAAGCTTCTTT 59.934 40.000 0.00 0.00 0.00 2.52
279 298 4.125703 CCTTATCATTCGAGCAAGCTTCT 58.874 43.478 0.00 0.00 0.00 2.85
286 305 2.708216 TTGCCCTTATCATTCGAGCA 57.292 45.000 0.00 0.00 0.00 4.26
312 339 5.012561 ACTTGCTATCCTCTTGCCTAATAGG 59.987 44.000 0.99 0.99 38.80 2.57
313 340 6.107901 ACTTGCTATCCTCTTGCCTAATAG 57.892 41.667 0.00 0.00 0.00 1.73
314 341 6.553476 TGTACTTGCTATCCTCTTGCCTAATA 59.447 38.462 0.00 0.00 0.00 0.98
315 342 5.366768 TGTACTTGCTATCCTCTTGCCTAAT 59.633 40.000 0.00 0.00 0.00 1.73
316 343 4.714802 TGTACTTGCTATCCTCTTGCCTAA 59.285 41.667 0.00 0.00 0.00 2.69
317 344 4.286707 TGTACTTGCTATCCTCTTGCCTA 58.713 43.478 0.00 0.00 0.00 3.93
318 345 3.107601 TGTACTTGCTATCCTCTTGCCT 58.892 45.455 0.00 0.00 0.00 4.75
319 346 3.543680 TGTACTTGCTATCCTCTTGCC 57.456 47.619 0.00 0.00 0.00 4.52
320 347 5.412904 ACTTTTGTACTTGCTATCCTCTTGC 59.587 40.000 0.00 0.00 0.00 4.01
321 348 8.443937 GTTACTTTTGTACTTGCTATCCTCTTG 58.556 37.037 0.00 0.00 34.15 3.02
322 349 7.606839 GGTTACTTTTGTACTTGCTATCCTCTT 59.393 37.037 0.00 0.00 34.15 2.85
323 350 7.104290 GGTTACTTTTGTACTTGCTATCCTCT 58.896 38.462 0.00 0.00 34.15 3.69
324 351 6.315642 GGGTTACTTTTGTACTTGCTATCCTC 59.684 42.308 0.00 0.00 34.15 3.71
325 352 6.178324 GGGTTACTTTTGTACTTGCTATCCT 58.822 40.000 0.00 0.00 34.15 3.24
326 353 5.356190 GGGGTTACTTTTGTACTTGCTATCC 59.644 44.000 0.00 0.00 34.15 2.59
327 354 6.178324 AGGGGTTACTTTTGTACTTGCTATC 58.822 40.000 0.00 0.00 34.15 2.08
328 355 6.135819 AGGGGTTACTTTTGTACTTGCTAT 57.864 37.500 0.00 0.00 34.15 2.97
329 356 5.072058 TGAGGGGTTACTTTTGTACTTGCTA 59.928 40.000 0.00 0.00 34.15 3.49
330 357 4.141344 TGAGGGGTTACTTTTGTACTTGCT 60.141 41.667 0.00 0.00 34.15 3.91
331 358 4.139038 TGAGGGGTTACTTTTGTACTTGC 58.861 43.478 0.00 0.00 34.15 4.01
332 359 4.760204 CCTGAGGGGTTACTTTTGTACTTG 59.240 45.833 0.00 0.00 34.15 3.16
333 360 4.981812 CCTGAGGGGTTACTTTTGTACTT 58.018 43.478 0.00 0.00 34.15 2.24
334 361 4.635699 CCTGAGGGGTTACTTTTGTACT 57.364 45.455 0.00 0.00 34.15 2.73
407 436 6.103997 CAGCATTCTTTGTTGCTTAATGGAT 58.896 36.000 0.00 0.00 46.71 3.41
472 601 5.701224 TGAAAGGAAAGAACAGTTGGGTAT 58.299 37.500 0.00 0.00 0.00 2.73
545 679 3.425359 CGCTAGCACTTGACCAGAAAATG 60.425 47.826 16.45 0.00 0.00 2.32
582 716 0.383949 TCTTGCCGGCTTCAAAACAC 59.616 50.000 29.70 0.00 0.00 3.32
597 733 6.634805 TGCCTTAATCTACTCACTTCTCTTG 58.365 40.000 0.00 0.00 0.00 3.02
745 914 3.146066 TCATTATTCCACTATTGGCCGC 58.854 45.455 0.00 0.00 43.56 6.53
746 915 5.519722 GTTTCATTATTCCACTATTGGCCG 58.480 41.667 0.00 0.00 43.56 6.13
747 916 5.067283 ACGTTTCATTATTCCACTATTGGCC 59.933 40.000 0.00 0.00 43.56 5.36
748 917 6.131544 ACGTTTCATTATTCCACTATTGGC 57.868 37.500 0.00 0.00 43.56 4.52
749 918 6.418956 CGACGTTTCATTATTCCACTATTGG 58.581 40.000 0.00 0.00 45.56 3.16
809 987 8.083462 GGTCATGAAATTTGGAATTTGCAAAAT 58.917 29.630 17.19 7.91 40.92 1.82
812 990 6.297582 AGGTCATGAAATTTGGAATTTGCAA 58.702 32.000 0.00 0.00 0.00 4.08
815 993 7.966246 TCAAGGTCATGAAATTTGGAATTTG 57.034 32.000 0.00 0.26 0.00 2.32
819 997 7.016465 AGGAAATCAAGGTCATGAAATTTGGAA 59.984 33.333 0.00 0.00 32.06 3.53
825 1003 7.364408 CCATGAAGGAAATCAAGGTCATGAAAT 60.364 37.037 11.91 0.00 43.14 2.17
860 1038 3.641437 TTTGTATTGTCCACTTGCAGC 57.359 42.857 0.00 0.00 0.00 5.25
875 1053 6.855763 AGATGATTTTGCTCCCATTTTGTA 57.144 33.333 0.00 0.00 0.00 2.41
895 1073 5.103344 AGAGCATAATGGGGAAAGGAAAGAT 60.103 40.000 0.00 0.00 0.00 2.40
912 1092 4.037222 TGGTCTAACCATGGAAGAGCATA 58.963 43.478 31.62 19.89 44.79 3.14
977 1161 3.366374 GGTTTTCTGGTGAACTAGCATGC 60.366 47.826 10.51 10.51 35.99 4.06
1005 1193 1.993956 TGTTGGACAAATGGAGGGTG 58.006 50.000 0.00 0.00 0.00 4.61
1008 1196 4.935352 TTTCTTGTTGGACAAATGGAGG 57.065 40.909 0.00 0.00 37.69 4.30
1017 1205 2.798976 TGCTGCATTTCTTGTTGGAC 57.201 45.000 0.00 0.00 0.00 4.02
1252 1455 0.393537 CCCTTCGAAGGCAGCAAGAT 60.394 55.000 34.54 0.00 45.10 2.40
1296 1499 1.995626 CCCGGTGAGGATCCCAAGT 60.996 63.158 8.55 0.00 45.00 3.16
1362 1565 1.419012 CTGGATGCTAGCAATCCCAGA 59.581 52.381 36.05 21.38 40.84 3.86
1375 1578 1.876156 GGTAGTAATGCTGCTGGATGC 59.124 52.381 0.00 0.00 43.25 3.91
1453 1659 3.289797 CCTGCAGAGGTCTACCAGA 57.710 57.895 17.39 0.00 38.89 3.86
1572 1778 1.278985 TGAGTTGGTATCTGCCCACTG 59.721 52.381 0.00 0.00 35.03 3.66
1808 2014 3.128764 TCTGAGGTTGACTATGCGTGTAG 59.871 47.826 0.00 0.00 0.00 2.74
1855 2061 4.177537 TCTTTCCACTGAATTGGTTCCA 57.822 40.909 0.00 0.00 37.93 3.53
1962 2168 7.354025 TGTTATGAGATTTTTGCAATTGCTG 57.646 32.000 29.37 0.00 42.66 4.41
1973 2179 9.300681 TCTTCAGGTCAATTGTTATGAGATTTT 57.699 29.630 5.13 0.00 0.00 1.82
1995 2201 3.206150 TCCACTGAGTTTGTTGCTCTTC 58.794 45.455 0.00 0.00 34.30 2.87
2032 2238 1.923356 TTGGGCAGGTTGGAGAAATC 58.077 50.000 0.00 0.00 0.00 2.17
2248 2454 4.558226 TGCTGCTCTTAAGGATCTGAAA 57.442 40.909 1.85 0.00 0.00 2.69
2300 2506 2.015587 GCATGAGCTCTCCCTTGAAAG 58.984 52.381 16.19 0.00 37.91 2.62
2416 2622 8.856490 AAAATTAACATCTTCAGTTGTGTCAC 57.144 30.769 0.00 0.00 0.00 3.67
2519 2725 4.393371 GGATTTCTCCTGTAAGAGTGTTGC 59.607 45.833 0.00 0.00 38.65 4.17
2603 2809 0.480252 AGGCAGCTCAAAGACCCTTT 59.520 50.000 0.00 0.00 0.00 3.11
2665 2871 4.340381 GCTTAGATTCAACATTGCTGGGAT 59.660 41.667 0.00 0.00 0.00 3.85
2698 2904 1.633432 TGGGGGAATCACACCTGTAAG 59.367 52.381 0.00 0.00 42.76 2.34
2700 2906 0.988832 GTGGGGGAATCACACCTGTA 59.011 55.000 0.00 0.00 42.76 2.74
2751 2957 7.025963 CAGATAACTTGTTGAAGCTGAAATCC 58.974 38.462 0.00 0.00 31.68 3.01
2799 9449 0.250295 CCCGCAAGTTTCTGAGGTCA 60.250 55.000 0.00 0.00 34.68 4.02
2800 9450 0.250338 ACCCGCAAGTTTCTGAGGTC 60.250 55.000 0.00 0.00 34.68 3.85
2807 9457 2.693267 ATCTAGGACCCGCAAGTTTC 57.307 50.000 0.00 0.00 0.00 2.78
2816 9466 3.366052 TGCTGGAAAAATCTAGGACCC 57.634 47.619 0.00 0.00 0.00 4.46
2820 9470 6.151648 TGAGATTGTTGCTGGAAAAATCTAGG 59.848 38.462 22.41 0.00 37.63 3.02
2829 9479 2.158623 ACCTGTGAGATTGTTGCTGGAA 60.159 45.455 0.00 0.00 0.00 3.53
2856 9506 0.895100 GGGTGTTCAATGCAGCTGGA 60.895 55.000 17.12 14.45 35.03 3.86
2906 9556 0.548510 AGGCCCTTCTAGGTCATTGC 59.451 55.000 0.00 0.00 32.23 3.56
2997 9647 4.924305 ACAACATTTGTGAGTGAGCATT 57.076 36.364 0.00 0.00 43.48 3.56
3156 9806 9.175312 CTTTCCCTTCTATTCTTTACCCTAAAC 57.825 37.037 0.00 0.00 0.00 2.01
3164 9814 8.137745 TCCGTTACTTTCCCTTCTATTCTTTA 57.862 34.615 0.00 0.00 0.00 1.85
3253 9903 1.613925 GTTTTCTTCACCCTGGCCTTC 59.386 52.381 3.32 0.00 0.00 3.46
3590 10240 3.069872 CCAGTCAAGAGATGAGCTAGCAT 59.930 47.826 18.83 1.68 39.19 3.79
3591 10241 2.429971 CCAGTCAAGAGATGAGCTAGCA 59.570 50.000 18.83 0.00 39.19 3.49
3592 10242 2.802774 GCCAGTCAAGAGATGAGCTAGC 60.803 54.545 6.62 6.62 39.19 3.42
3719 10370 4.790765 AGCTTTAAATCCTTTGTCCAGC 57.209 40.909 0.00 0.00 0.00 4.85
3730 10381 9.962759 CAAAATCTGCAACATAAGCTTTAAATC 57.037 29.630 3.20 0.00 0.00 2.17
3761 10412 3.091545 GTTGGGAAGAATCAATCTGGCA 58.908 45.455 0.00 0.00 38.79 4.92
3905 10556 2.268920 GGCCGCATTCCAGTGAGA 59.731 61.111 0.00 0.00 0.00 3.27
4011 10662 2.541556 GTATCCTGTTCCTCGAAGTGC 58.458 52.381 0.00 0.00 0.00 4.40
4073 10724 4.718858 TGTAAACTGATTTTGGTCGACG 57.281 40.909 9.92 0.00 0.00 5.12
4307 10975 1.607251 CCGCCCGAACTACAACTTCTT 60.607 52.381 0.00 0.00 0.00 2.52
4318 10986 3.782443 AGATGACCCCGCCCGAAC 61.782 66.667 0.00 0.00 0.00 3.95
4386 11055 8.725148 CCTGGCTGAACACTAATAATGATAATC 58.275 37.037 0.00 0.00 0.00 1.75
4387 11056 8.220559 ACCTGGCTGAACACTAATAATGATAAT 58.779 33.333 0.00 0.00 0.00 1.28
4388 11057 7.498900 CACCTGGCTGAACACTAATAATGATAA 59.501 37.037 0.00 0.00 0.00 1.75
4390 11059 5.824624 CACCTGGCTGAACACTAATAATGAT 59.175 40.000 0.00 0.00 0.00 2.45
4433 11102 3.598019 AGTCGGCGGAATACAACTAAA 57.402 42.857 7.21 0.00 0.00 1.85
4443 11112 3.018856 TCTACAAGATTAGTCGGCGGAA 58.981 45.455 7.21 0.00 0.00 4.30
4446 11115 4.288670 TCTTCTACAAGATTAGTCGGCG 57.711 45.455 0.00 0.00 33.38 6.46
4459 11128 9.168451 TGTGTTGTAGTGAAAAATTCTTCTACA 57.832 29.630 16.50 16.50 41.21 2.74
4460 11129 9.434559 GTGTGTTGTAGTGAAAAATTCTTCTAC 57.565 33.333 13.54 13.54 37.80 2.59
4461 11130 9.168451 TGTGTGTTGTAGTGAAAAATTCTTCTA 57.832 29.630 0.00 0.00 0.00 2.10
4462 11131 8.050778 TGTGTGTTGTAGTGAAAAATTCTTCT 57.949 30.769 0.00 0.00 0.00 2.85
4463 11132 8.745837 CATGTGTGTTGTAGTGAAAAATTCTTC 58.254 33.333 0.00 0.00 0.00 2.87
4464 11133 8.465999 TCATGTGTGTTGTAGTGAAAAATTCTT 58.534 29.630 0.00 0.00 0.00 2.52
4465 11134 7.995289 TCATGTGTGTTGTAGTGAAAAATTCT 58.005 30.769 0.00 0.00 0.00 2.40
4466 11135 8.531530 GTTCATGTGTGTTGTAGTGAAAAATTC 58.468 33.333 0.00 0.00 0.00 2.17
4467 11136 8.031864 TGTTCATGTGTGTTGTAGTGAAAAATT 58.968 29.630 0.00 0.00 0.00 1.82
4468 11137 7.542890 TGTTCATGTGTGTTGTAGTGAAAAAT 58.457 30.769 0.00 0.00 0.00 1.82
4469 11138 6.914259 TGTTCATGTGTGTTGTAGTGAAAAA 58.086 32.000 0.00 0.00 0.00 1.94
4470 11139 6.502136 TGTTCATGTGTGTTGTAGTGAAAA 57.498 33.333 0.00 0.00 0.00 2.29
4471 11140 6.502136 TTGTTCATGTGTGTTGTAGTGAAA 57.498 33.333 0.00 0.00 0.00 2.69
4472 11141 6.691754 ATTGTTCATGTGTGTTGTAGTGAA 57.308 33.333 0.00 0.00 0.00 3.18
4473 11142 6.317391 TGAATTGTTCATGTGTGTTGTAGTGA 59.683 34.615 0.00 0.00 34.08 3.41
4474 11143 6.414694 GTGAATTGTTCATGTGTGTTGTAGTG 59.585 38.462 0.00 0.00 42.47 2.74
4475 11144 6.459573 GGTGAATTGTTCATGTGTGTTGTAGT 60.460 38.462 0.00 0.00 42.47 2.73
4476 11145 5.914635 GGTGAATTGTTCATGTGTGTTGTAG 59.085 40.000 0.00 0.00 42.47 2.74
4477 11146 5.221145 GGGTGAATTGTTCATGTGTGTTGTA 60.221 40.000 0.00 0.00 42.47 2.41
4478 11147 4.441356 GGGTGAATTGTTCATGTGTGTTGT 60.441 41.667 0.00 0.00 42.47 3.32
4479 11148 4.050553 GGGTGAATTGTTCATGTGTGTTG 58.949 43.478 0.00 0.00 42.47 3.33
4480 11149 3.069443 GGGGTGAATTGTTCATGTGTGTT 59.931 43.478 0.00 0.00 42.47 3.32
4481 11150 2.627699 GGGGTGAATTGTTCATGTGTGT 59.372 45.455 0.00 0.00 42.47 3.72
4482 11151 2.627221 TGGGGTGAATTGTTCATGTGTG 59.373 45.455 0.00 0.00 42.47 3.82
4483 11152 2.956132 TGGGGTGAATTGTTCATGTGT 58.044 42.857 0.00 0.00 42.47 3.72
4484 11153 4.333913 TTTGGGGTGAATTGTTCATGTG 57.666 40.909 0.00 0.00 42.47 3.21
4485 11154 5.565455 ATTTTGGGGTGAATTGTTCATGT 57.435 34.783 0.00 0.00 42.47 3.21
4486 11155 6.934056 TCTATTTTGGGGTGAATTGTTCATG 58.066 36.000 0.00 0.00 42.47 3.07
4487 11156 6.953520 TCTCTATTTTGGGGTGAATTGTTCAT 59.046 34.615 0.00 0.00 42.47 2.57
4488 11157 6.310941 TCTCTATTTTGGGGTGAATTGTTCA 58.689 36.000 0.00 0.00 37.33 3.18
4489 11158 6.834168 TCTCTATTTTGGGGTGAATTGTTC 57.166 37.500 0.00 0.00 0.00 3.18
4490 11159 7.610580 TTTCTCTATTTTGGGGTGAATTGTT 57.389 32.000 0.00 0.00 0.00 2.83
4491 11160 7.610580 TTTTCTCTATTTTGGGGTGAATTGT 57.389 32.000 0.00 0.00 0.00 2.71
4492 11161 8.534496 AGATTTTCTCTATTTTGGGGTGAATTG 58.466 33.333 0.00 0.00 30.26 2.32
4493 11162 8.534496 CAGATTTTCTCTATTTTGGGGTGAATT 58.466 33.333 0.00 0.00 31.13 2.17
4494 11163 7.675619 ACAGATTTTCTCTATTTTGGGGTGAAT 59.324 33.333 0.00 0.00 31.13 2.57
4495 11164 7.010160 ACAGATTTTCTCTATTTTGGGGTGAA 58.990 34.615 0.00 0.00 31.13 3.18
4496 11165 6.434028 CACAGATTTTCTCTATTTTGGGGTGA 59.566 38.462 0.00 0.00 31.13 4.02
4497 11166 6.624423 CACAGATTTTCTCTATTTTGGGGTG 58.376 40.000 0.00 0.00 31.13 4.61
4498 11167 5.185828 GCACAGATTTTCTCTATTTTGGGGT 59.814 40.000 0.00 0.00 31.13 4.95
4499 11168 5.185635 TGCACAGATTTTCTCTATTTTGGGG 59.814 40.000 0.00 0.00 31.13 4.96
4500 11169 6.271488 TGCACAGATTTTCTCTATTTTGGG 57.729 37.500 0.00 0.00 31.13 4.12
4501 11170 8.084073 TCTTTGCACAGATTTTCTCTATTTTGG 58.916 33.333 0.00 0.00 31.13 3.28
4502 11171 9.467258 TTCTTTGCACAGATTTTCTCTATTTTG 57.533 29.630 2.84 0.00 31.13 2.44
4534 11203 8.768957 TGTTTTTGTCATTGTTCAAATCTGAA 57.231 26.923 9.25 0.00 39.30 3.02
4535 11204 8.768957 TTGTTTTTGTCATTGTTCAAATCTGA 57.231 26.923 9.25 0.00 34.30 3.27
4538 11390 9.476761 GTTCTTGTTTTTGTCATTGTTCAAATC 57.523 29.630 9.25 7.53 34.30 2.17
4554 11406 7.064229 TGGACCTTTATACCAGTTCTTGTTTT 58.936 34.615 0.00 0.00 0.00 2.43
4570 11422 7.393234 CCTCTAAACAACATGAATGGACCTTTA 59.607 37.037 0.00 0.00 0.00 1.85
4574 11426 5.010282 ACCTCTAAACAACATGAATGGACC 58.990 41.667 0.00 0.00 0.00 4.46
4575 11427 5.705441 TCACCTCTAAACAACATGAATGGAC 59.295 40.000 0.00 0.00 0.00 4.02
4576 11428 5.875224 TCACCTCTAAACAACATGAATGGA 58.125 37.500 0.00 0.00 0.00 3.41
4577 11429 6.016360 TGTTCACCTCTAAACAACATGAATGG 60.016 38.462 0.00 0.00 32.69 3.16
4578 11430 6.969366 TGTTCACCTCTAAACAACATGAATG 58.031 36.000 0.00 0.09 32.69 2.67
4579 11431 7.502226 TCTTGTTCACCTCTAAACAACATGAAT 59.498 33.333 0.00 0.00 39.70 2.57
4580 11432 6.826231 TCTTGTTCACCTCTAAACAACATGAA 59.174 34.615 0.00 0.00 39.70 2.57
4581 11433 6.353323 TCTTGTTCACCTCTAAACAACATGA 58.647 36.000 0.00 0.00 39.70 3.07
4582 11434 6.618287 TCTTGTTCACCTCTAAACAACATG 57.382 37.500 0.00 0.00 39.70 3.21
4584 11436 7.455641 TTTTCTTGTTCACCTCTAAACAACA 57.544 32.000 0.00 0.00 39.70 3.33
4709 11577 3.744660 ACAAGGAGTTTTCTGCACCTAG 58.255 45.455 0.00 0.00 40.83 3.02
4710 11578 3.857157 ACAAGGAGTTTTCTGCACCTA 57.143 42.857 0.00 0.00 40.83 3.08
4711 11579 2.736670 ACAAGGAGTTTTCTGCACCT 57.263 45.000 0.00 0.00 40.83 4.00
4728 11596 1.202592 TCTCGCAGTTAGCCACAAACA 60.203 47.619 0.00 0.00 41.38 2.83
4733 11601 2.301577 AATCTCTCGCAGTTAGCCAC 57.698 50.000 0.00 0.00 41.38 5.01
4737 11605 5.763088 TGTGCTATAATCTCTCGCAGTTAG 58.237 41.667 0.00 0.00 0.00 2.34
4738 11606 5.767816 TGTGCTATAATCTCTCGCAGTTA 57.232 39.130 0.00 0.00 0.00 2.24
4742 11610 3.742882 GCATTGTGCTATAATCTCTCGCA 59.257 43.478 0.00 0.00 40.96 5.10


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

AutoCloner maintained by Alex Coulton.