Multiple sequence alignment - TraesCS5A01G132500

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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 TraesCS5A01G132500 chr5A 100.000 5195 0 0 1 5195 299070225 299065031 0.000000e+00 9594.0
1 TraesCS5A01G132500 chr5D 95.912 2128 63 10 730 2839 224329056 224326935 0.000000e+00 3426.0
2 TraesCS5A01G132500 chr5D 96.568 1719 44 6 2860 4567 224326948 224325234 0.000000e+00 2833.0
3 TraesCS5A01G132500 chr5D 91.608 286 17 4 4566 4845 224322033 224321749 6.310000e-104 388.0
4 TraesCS5A01G132500 chr5D 89.011 182 20 0 1 182 224347482 224347301 5.230000e-55 226.0
5 TraesCS5A01G132500 chr5D 89.375 160 17 0 5036 5195 224321215 224321056 8.820000e-48 202.0
6 TraesCS5A01G132500 chr5B 95.042 2138 72 13 716 2839 247057051 247059168 0.000000e+00 3330.0
7 TraesCS5A01G132500 chr5B 95.399 1391 37 12 3393 4764 247059630 247061012 0.000000e+00 2189.0
8 TraesCS5A01G132500 chr5B 94.239 486 17 9 2860 3338 247059155 247059636 0.000000e+00 732.0
9 TraesCS5A01G132500 chr5B 84.582 694 77 13 1 683 246988536 246989210 0.000000e+00 662.0
10 TraesCS5A01G132500 chr5B 91.166 283 19 3 4919 5195 247061142 247061424 3.800000e-101 379.0
11 TraesCS5A01G132500 chr5B 92.029 138 4 4 4743 4878 247061019 247061151 2.470000e-43 187.0
12 TraesCS5A01G132500 chr4B 85.752 765 100 5 1274 2029 172772307 172773071 0.000000e+00 800.0
13 TraesCS5A01G132500 chr4B 90.173 173 17 0 2399 2571 172773471 172773643 5.230000e-55 226.0
14 TraesCS5A01G132500 chr4B 84.158 202 32 0 3135 3336 172775235 172775436 4.100000e-46 196.0
15 TraesCS5A01G132500 chr4A 81.039 1039 162 18 1019 2029 464994451 464993420 0.000000e+00 795.0
16 TraesCS5A01G132500 chr4A 88.439 173 20 0 2399 2571 464993013 464992841 5.270000e-50 209.0
17 TraesCS5A01G132500 chr4A 86.441 177 24 0 2655 2831 464991639 464991463 1.480000e-45 195.0
18 TraesCS5A01G132500 chr4D 85.583 763 101 5 1276 2029 112192482 112193244 0.000000e+00 791.0
19 TraesCS5A01G132500 chr4D 87.861 173 21 0 2399 2571 112193683 112193855 2.450000e-48 204.0
20 TraesCS5A01G132500 chr4D 84.653 202 31 0 3135 3336 112195405 112195606 8.820000e-48 202.0
21 TraesCS5A01G132500 chr4D 83.258 221 28 9 4980 5193 102148053 102147835 1.480000e-45 195.0
22 TraesCS5A01G132500 chr4D 86.207 174 24 0 2655 2828 112194903 112195076 6.870000e-44 189.0
23 TraesCS5A01G132500 chr4D 85.246 122 18 0 2940 3061 112195192 112195313 5.460000e-25 126.0
24 TraesCS5A01G132500 chr4D 97.368 38 1 0 4878 4915 3003615 3003652 1.210000e-06 65.8
25 TraesCS5A01G132500 chr7D 80.631 222 31 9 4980 5193 152133912 152134129 1.500000e-35 161.0
26 TraesCS5A01G132500 chr7D 83.929 168 24 2 4968 5135 41697885 41698049 1.940000e-34 158.0
27 TraesCS5A01G132500 chr2B 82.199 191 23 9 5010 5192 305325551 305325364 2.510000e-33 154.0
28 TraesCS5A01G132500 chr2B 82.703 185 21 9 5010 5186 305325948 305325767 2.510000e-33 154.0
29 TraesCS5A01G132500 chr2B 89.286 84 9 0 2193 2276 119632779 119632696 7.110000e-19 106.0
30 TraesCS5A01G132500 chr2B 84.524 84 11 2 2194 2276 736108953 736109035 1.200000e-11 82.4
31 TraesCS5A01G132500 chr2B 94.872 39 2 0 2238 2276 14598958 14598920 1.560000e-05 62.1
32 TraesCS5A01G132500 chr1D 80.788 203 31 8 4997 5193 226827363 226827563 9.010000e-33 152.0
33 TraesCS5A01G132500 chr3D 78.924 223 33 9 4980 5193 581095194 581094977 7.010000e-29 139.0
34 TraesCS5A01G132500 chr2D 89.286 84 9 0 2193 2276 77382274 77382191 7.110000e-19 106.0
35 TraesCS5A01G132500 chr2A 97.674 43 1 0 4878 4920 674081991 674082033 2.010000e-09 75.0
36 TraesCS5A01G132500 chr7B 97.222 36 1 0 2238 2273 84060371 84060406 1.560000e-05 62.1


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 TraesCS5A01G132500 chr5A 299065031 299070225 5194 True 9594.000000 9594 100.000000 1 5195 1 chr5A.!!$R1 5194
1 TraesCS5A01G132500 chr5D 224321056 224329056 8000 True 1712.250000 3426 93.365750 730 5195 4 chr5D.!!$R2 4465
2 TraesCS5A01G132500 chr5B 247057051 247061424 4373 False 1363.400000 3330 93.575000 716 5195 5 chr5B.!!$F2 4479
3 TraesCS5A01G132500 chr5B 246988536 246989210 674 False 662.000000 662 84.582000 1 683 1 chr5B.!!$F1 682
4 TraesCS5A01G132500 chr4B 172772307 172775436 3129 False 407.333333 800 86.694333 1274 3336 3 chr4B.!!$F1 2062
5 TraesCS5A01G132500 chr4A 464991463 464994451 2988 True 399.666667 795 85.306333 1019 2831 3 chr4A.!!$R1 1812
6 TraesCS5A01G132500 chr4D 112192482 112195606 3124 False 302.400000 791 85.910000 1276 3336 5 chr4D.!!$F2 2060

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
698 710 0.037017 TGACCCCCGTTGGTATTGTG 59.963 55.0 0.0 0.0 39.24 3.33 F
699 711 0.037160 GACCCCCGTTGGTATTGTGT 59.963 55.0 0.0 0.0 39.24 3.72 F
1974 2051 0.105593 TGCCATCGCAGAAGATCCTC 59.894 55.0 0.0 0.0 43.58 3.71 F
2602 3908 0.390998 GCTGTCTCTCACCTGCTTCC 60.391 60.0 0.0 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2301 2456 0.036010 GTGCAGTGATGGTGGTAGCT 60.036 55.000 0.00 0.0 0.00 3.32 R
2397 2682 1.609239 CCTTCCCACAGCATGCCTA 59.391 57.895 15.66 0.0 42.53 3.93 R
2871 4621 0.107654 GTGTGGGCTAGCTAAGGTGG 60.108 60.000 15.72 0.0 0.00 4.61 R
4257 6105 2.247358 GGATGGTGGGCAAAGAAGAAA 58.753 47.619 0.00 0.0 0.00 2.52 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
24 25 1.620589 ATCCCCACCCATGCACTCT 60.621 57.895 0.00 0.00 0.00 3.24
26 27 2.044650 CCCACCCATGCACTCTGG 60.045 66.667 0.00 0.00 0.00 3.86
37 38 1.202915 TGCACTCTGGCTGGATTTCAA 60.203 47.619 0.00 0.00 34.04 2.69
38 39 2.097825 GCACTCTGGCTGGATTTCAAT 58.902 47.619 0.00 0.00 0.00 2.57
45 46 3.271055 GGCTGGATTTCAATGCCATTT 57.729 42.857 0.00 0.00 42.79 2.32
46 47 2.940410 GGCTGGATTTCAATGCCATTTG 59.060 45.455 0.00 0.00 42.79 2.32
49 50 4.186159 CTGGATTTCAATGCCATTTGGAC 58.814 43.478 0.00 0.00 37.39 4.02
51 52 3.119173 GGATTTCAATGCCATTTGGACGA 60.119 43.478 0.00 0.00 37.39 4.20
56 57 1.091771 ATGCCATTTGGACGAGCTCG 61.092 55.000 33.45 33.45 39.60 5.03
59 60 1.699656 CCATTTGGACGAGCTCGCAG 61.700 60.000 34.83 16.22 44.43 5.18
60 61 2.103042 ATTTGGACGAGCTCGCAGC 61.103 57.895 34.83 23.30 44.43 5.25
78 79 3.204827 ACATGCCGCCTCAATCGC 61.205 61.111 0.00 0.00 0.00 4.58
80 81 2.898840 ATGCCGCCTCAATCGCTG 60.899 61.111 0.00 0.00 0.00 5.18
97 98 2.357760 GGCGAGGCCGTAACACAA 60.358 61.111 0.00 0.00 39.62 3.33
102 103 0.319297 GAGGCCGTAACACAAGTCGT 60.319 55.000 0.00 0.00 0.00 4.34
117 118 2.431771 CGTCGTGATTGCCGGTCA 60.432 61.111 1.90 0.00 0.00 4.02
140 141 2.124736 CCATGGTTCGCCCGTCAT 60.125 61.111 2.57 0.00 36.08 3.06
177 178 1.401539 GGACGAAGCAAAATGCCTCAC 60.402 52.381 0.00 0.00 46.52 3.51
179 180 0.454957 CGAAGCAAAATGCCTCACCG 60.455 55.000 0.00 0.00 46.52 4.94
184 185 2.625823 AAAATGCCTCACCGGTGCG 61.626 57.895 30.25 24.01 34.25 5.34
216 217 2.158959 GTCGGTCGCAACATCCTCG 61.159 63.158 0.00 0.00 0.00 4.63
217 218 2.180769 CGGTCGCAACATCCTCGA 59.819 61.111 0.00 0.00 0.00 4.04
226 227 0.737715 AACATCCTCGAAGCGTGCTC 60.738 55.000 0.00 0.00 0.00 4.26
227 228 1.153765 CATCCTCGAAGCGTGCTCA 60.154 57.895 0.00 0.00 0.00 4.26
254 255 3.138798 TGCTCGTCGTAGCTCCCC 61.139 66.667 14.74 0.00 43.19 4.81
264 265 3.949885 TAGCTCCCCTTGTCGCCGA 62.950 63.158 0.00 0.00 0.00 5.54
268 269 3.508840 CCCCTTGTCGCCGATTGC 61.509 66.667 0.00 0.00 0.00 3.56
276 277 4.465512 CGCCGATTGCAGCACACC 62.466 66.667 0.00 0.00 41.33 4.16
277 278 4.465512 GCCGATTGCAGCACACCG 62.466 66.667 0.00 0.00 40.77 4.94
299 300 1.101331 CCCAGATCAGCAAGGAAAGC 58.899 55.000 0.00 0.00 0.00 3.51
301 302 1.446907 CAGATCAGCAAGGAAAGCGT 58.553 50.000 0.00 0.00 37.01 5.07
306 307 1.066858 TCAGCAAGGAAAGCGTAGAGG 60.067 52.381 0.00 0.00 37.01 3.69
311 312 3.139077 CAAGGAAAGCGTAGAGGTTGTT 58.861 45.455 0.00 0.00 40.91 2.83
314 315 2.479275 GGAAAGCGTAGAGGTTGTTGAC 59.521 50.000 0.00 0.00 40.91 3.18
315 316 2.902705 AAGCGTAGAGGTTGTTGACA 57.097 45.000 0.00 0.00 39.39 3.58
319 320 4.134563 AGCGTAGAGGTTGTTGACATTTT 58.865 39.130 0.00 0.00 0.00 1.82
321 322 4.675114 GCGTAGAGGTTGTTGACATTTTTG 59.325 41.667 0.00 0.00 0.00 2.44
325 326 6.036577 AGAGGTTGTTGACATTTTTGTTGT 57.963 33.333 0.00 0.00 0.00 3.32
326 327 5.868801 AGAGGTTGTTGACATTTTTGTTGTG 59.131 36.000 0.00 0.00 0.00 3.33
328 329 4.094146 GGTTGTTGACATTTTTGTTGTGGG 59.906 41.667 0.00 0.00 0.00 4.61
329 330 3.866651 TGTTGACATTTTTGTTGTGGGG 58.133 40.909 0.00 0.00 0.00 4.96
330 331 3.261897 TGTTGACATTTTTGTTGTGGGGT 59.738 39.130 0.00 0.00 0.00 4.95
331 332 4.257731 GTTGACATTTTTGTTGTGGGGTT 58.742 39.130 0.00 0.00 0.00 4.11
334 335 6.049955 TGACATTTTTGTTGTGGGGTTTTA 57.950 33.333 0.00 0.00 0.00 1.52
335 336 5.875359 TGACATTTTTGTTGTGGGGTTTTAC 59.125 36.000 0.00 0.00 0.00 2.01
336 337 4.870991 ACATTTTTGTTGTGGGGTTTTACG 59.129 37.500 0.00 0.00 0.00 3.18
337 338 2.580966 TTTGTTGTGGGGTTTTACGC 57.419 45.000 0.00 0.00 0.00 4.42
377 378 0.759346 ACCACCTCTGACCTTGACAC 59.241 55.000 0.00 0.00 0.00 3.67
385 386 1.107945 TGACCTTGACACGTCAGACA 58.892 50.000 0.41 0.00 41.13 3.41
386 387 1.202371 TGACCTTGACACGTCAGACAC 60.202 52.381 0.41 0.00 41.13 3.67
387 388 1.067212 GACCTTGACACGTCAGACACT 59.933 52.381 0.41 0.00 41.13 3.55
388 389 1.480954 ACCTTGACACGTCAGACACTT 59.519 47.619 0.41 0.00 41.13 3.16
392 402 3.786516 TGACACGTCAGACACTTACAA 57.213 42.857 0.41 0.00 34.14 2.41
433 444 3.904717 ACACCATTGACCCTTGTGTTTA 58.095 40.909 0.00 0.00 36.84 2.01
434 445 4.479158 ACACCATTGACCCTTGTGTTTAT 58.521 39.130 0.00 0.00 36.84 1.40
443 454 9.866655 ATTGACCCTTGTGTTTATCATGTATAT 57.133 29.630 0.00 0.00 0.00 0.86
444 455 8.675705 TGACCCTTGTGTTTATCATGTATATG 57.324 34.615 0.00 0.00 35.57 1.78
445 456 7.719193 TGACCCTTGTGTTTATCATGTATATGG 59.281 37.037 0.00 0.00 34.97 2.74
486 497 7.578310 AAAGCACATCTCATAAGTATTGCAT 57.422 32.000 0.00 0.00 0.00 3.96
516 527 4.625028 TCCTATCTCATTGATCTTGCACG 58.375 43.478 0.00 0.00 36.65 5.34
534 545 3.246226 GCACGAAGATTCATGCGAGTATT 59.754 43.478 0.00 0.00 36.63 1.89
659 671 6.607019 TCAGGGTAAGTCCATTGTAAACTTT 58.393 36.000 0.00 0.00 38.11 2.66
662 674 6.940867 AGGGTAAGTCCATTGTAAACTTTCTC 59.059 38.462 0.00 0.00 38.11 2.87
675 687 6.995686 TGTAAACTTTCTCAGCAAGGTCAATA 59.004 34.615 0.00 0.00 0.00 1.90
691 703 3.093057 TCAATATTTTGACCCCCGTTGG 58.907 45.455 0.00 0.00 36.94 3.77
692 704 2.829120 CAATATTTTGACCCCCGTTGGT 59.171 45.455 0.00 0.00 42.79 3.67
693 705 4.017808 CAATATTTTGACCCCCGTTGGTA 58.982 43.478 0.00 0.00 39.24 3.25
694 706 2.911552 ATTTTGACCCCCGTTGGTAT 57.088 45.000 0.00 0.00 39.24 2.73
695 707 2.679429 TTTTGACCCCCGTTGGTATT 57.321 45.000 0.00 0.00 39.24 1.89
696 708 1.912417 TTTGACCCCCGTTGGTATTG 58.088 50.000 0.00 0.00 39.24 1.90
697 709 0.772384 TTGACCCCCGTTGGTATTGT 59.228 50.000 0.00 0.00 39.24 2.71
698 710 0.037017 TGACCCCCGTTGGTATTGTG 59.963 55.000 0.00 0.00 39.24 3.33
699 711 0.037160 GACCCCCGTTGGTATTGTGT 59.963 55.000 0.00 0.00 39.24 3.72
700 712 0.479378 ACCCCCGTTGGTATTGTGTT 59.521 50.000 0.00 0.00 36.67 3.32
701 713 0.885196 CCCCCGTTGGTATTGTGTTG 59.115 55.000 0.00 0.00 0.00 3.33
702 714 1.611519 CCCCGTTGGTATTGTGTTGT 58.388 50.000 0.00 0.00 0.00 3.32
703 715 1.268352 CCCCGTTGGTATTGTGTTGTG 59.732 52.381 0.00 0.00 0.00 3.33
704 716 1.950909 CCCGTTGGTATTGTGTTGTGT 59.049 47.619 0.00 0.00 0.00 3.72
705 717 2.359531 CCCGTTGGTATTGTGTTGTGTT 59.640 45.455 0.00 0.00 0.00 3.32
706 718 3.367607 CCGTTGGTATTGTGTTGTGTTG 58.632 45.455 0.00 0.00 0.00 3.33
707 719 3.367607 CGTTGGTATTGTGTTGTGTTGG 58.632 45.455 0.00 0.00 0.00 3.77
708 720 3.181495 CGTTGGTATTGTGTTGTGTTGGT 60.181 43.478 0.00 0.00 0.00 3.67
709 721 4.109050 GTTGGTATTGTGTTGTGTTGGTG 58.891 43.478 0.00 0.00 0.00 4.17
710 722 3.357203 TGGTATTGTGTTGTGTTGGTGT 58.643 40.909 0.00 0.00 0.00 4.16
711 723 3.378742 TGGTATTGTGTTGTGTTGGTGTC 59.621 43.478 0.00 0.00 0.00 3.67
712 724 3.243267 GGTATTGTGTTGTGTTGGTGTCC 60.243 47.826 0.00 0.00 0.00 4.02
713 725 1.178276 TTGTGTTGTGTTGGTGTCCC 58.822 50.000 0.00 0.00 0.00 4.46
714 726 0.329931 TGTGTTGTGTTGGTGTCCCT 59.670 50.000 0.00 0.00 0.00 4.20
724 736 2.427320 GTGTCCCTCTGCACTGCA 59.573 61.111 3.11 3.11 36.92 4.41
726 738 2.142761 TGTCCCTCTGCACTGCACT 61.143 57.895 0.00 0.00 33.79 4.40
746 758 5.393962 CACTCCTATTGTTTAGCAGCAAAC 58.606 41.667 11.41 11.41 38.60 2.93
753 765 4.486472 TTGTTTAGCAGCAAACACGGAGT 61.486 43.478 17.50 0.00 45.52 3.85
754 766 2.803956 GTTTAGCAGCAAACACGGAGTA 59.196 45.455 12.76 0.00 41.61 2.59
755 767 2.363788 TAGCAGCAAACACGGAGTAG 57.636 50.000 0.00 0.00 41.61 2.57
765 777 0.736053 CACGGAGTAGAGAGCAGACC 59.264 60.000 0.00 0.00 41.61 3.85
1082 1120 2.758089 GCATCCGCAAGCTCACCAG 61.758 63.158 0.00 0.00 38.36 4.00
1459 1527 3.020627 CTACCTACGAGGGCGACG 58.979 66.667 0.00 0.00 40.58 5.12
1950 2027 2.979649 GAGGGGAAGACGGTGTCC 59.020 66.667 0.00 0.00 32.18 4.02
1974 2051 0.105593 TGCCATCGCAGAAGATCCTC 59.894 55.000 0.00 0.00 43.58 3.71
2107 2184 1.048601 GGACCTTGACAGTCTCACCA 58.951 55.000 1.31 0.00 34.56 4.17
2297 2452 5.471797 GGTCTCTTTCCTTTTCCTCTTCTTG 59.528 44.000 0.00 0.00 0.00 3.02
2298 2453 5.471797 GTCTCTTTCCTTTTCCTCTTCTTGG 59.528 44.000 0.00 0.00 0.00 3.61
2299 2454 4.145052 TCTTTCCTTTTCCTCTTCTTGGC 58.855 43.478 0.00 0.00 0.00 4.52
2300 2455 3.884037 TTCCTTTTCCTCTTCTTGGCT 57.116 42.857 0.00 0.00 0.00 4.75
2301 2456 4.993705 TTCCTTTTCCTCTTCTTGGCTA 57.006 40.909 0.00 0.00 0.00 3.93
2321 2476 1.026718 GCTACCACCATCACTGCACC 61.027 60.000 0.00 0.00 0.00 5.01
2347 2502 2.686915 CCATTGCCATTTCCTCTCTGTC 59.313 50.000 0.00 0.00 0.00 3.51
2397 2682 2.887360 GCCGCCATTTCTGTGCAT 59.113 55.556 0.00 0.00 0.00 3.96
2595 3901 1.015109 CATGCATGCTGTCTCTCACC 58.985 55.000 20.33 0.00 0.00 4.02
2602 3908 0.390998 GCTGTCTCTCACCTGCTTCC 60.391 60.000 0.00 0.00 0.00 3.46
2604 3910 0.471780 TGTCTCTCACCTGCTTCCCA 60.472 55.000 0.00 0.00 0.00 4.37
2729 4479 2.512896 GGGGATGATGCGCTCCTT 59.487 61.111 9.73 0.00 0.00 3.36
2840 4590 4.158949 GTCAAGGTAGGTTCTTCTCTCCTC 59.841 50.000 0.00 0.00 33.34 3.71
2842 4592 4.685513 AGGTAGGTTCTTCTCTCCTCTT 57.314 45.455 0.00 0.00 33.34 2.85
2845 4595 5.847265 AGGTAGGTTCTTCTCTCCTCTTTTT 59.153 40.000 0.00 0.00 33.34 1.94
2893 4645 0.460284 CCTTAGCTAGCCCACACACG 60.460 60.000 12.13 0.00 0.00 4.49
2922 4674 5.619132 TTAAGCATGTCTGAGATGGATCA 57.381 39.130 15.55 0.00 0.00 2.92
2986 4740 4.551410 GCCTATTATAAACACGTCCGCAAC 60.551 45.833 0.00 0.00 0.00 4.17
3061 4815 1.550524 GGGGGCATTCAGAAAAAGGTC 59.449 52.381 0.00 0.00 0.00 3.85
3098 4854 7.067372 CAGAAATTGGCCAGTGTATTGAGATTA 59.933 37.037 5.11 0.00 0.00 1.75
3223 4997 1.453155 TGAAAGGATCTTCGCTTGGC 58.547 50.000 0.00 0.00 0.00 4.52
3338 5173 2.265367 TCCAGGAATTCTGCAGGTACA 58.735 47.619 15.13 0.00 42.05 2.90
3339 5174 2.846206 TCCAGGAATTCTGCAGGTACAT 59.154 45.455 15.13 0.00 42.05 2.29
3340 5175 3.118261 TCCAGGAATTCTGCAGGTACATC 60.118 47.826 15.13 5.69 42.05 3.06
3341 5176 3.118112 CCAGGAATTCTGCAGGTACATCT 60.118 47.826 15.13 2.36 42.05 2.90
3342 5177 4.125703 CAGGAATTCTGCAGGTACATCTC 58.874 47.826 15.13 1.47 36.60 2.75
3343 5178 3.135530 AGGAATTCTGCAGGTACATCTCC 59.864 47.826 15.13 10.26 0.00 3.71
3344 5179 3.471680 GAATTCTGCAGGTACATCTCCC 58.528 50.000 15.13 0.00 0.00 4.30
3345 5180 1.951209 TTCTGCAGGTACATCTCCCA 58.049 50.000 15.13 0.00 0.00 4.37
3346 5181 2.180946 TCTGCAGGTACATCTCCCAT 57.819 50.000 15.13 0.00 0.00 4.00
3347 5182 2.042464 TCTGCAGGTACATCTCCCATC 58.958 52.381 15.13 0.00 0.00 3.51
3348 5183 2.045524 CTGCAGGTACATCTCCCATCT 58.954 52.381 5.57 0.00 0.00 2.90
3349 5184 1.764723 TGCAGGTACATCTCCCATCTG 59.235 52.381 0.00 0.00 0.00 2.90
3350 5185 1.542108 GCAGGTACATCTCCCATCTGC 60.542 57.143 0.00 0.00 39.13 4.26
3351 5186 1.071385 CAGGTACATCTCCCATCTGCC 59.929 57.143 0.00 0.00 0.00 4.85
3352 5187 0.034059 GGTACATCTCCCATCTGCCG 59.966 60.000 0.00 0.00 0.00 5.69
3353 5188 0.034059 GTACATCTCCCATCTGCCGG 59.966 60.000 0.00 0.00 0.00 6.13
3354 5189 0.105709 TACATCTCCCATCTGCCGGA 60.106 55.000 5.05 0.00 0.00 5.14
3355 5190 0.765903 ACATCTCCCATCTGCCGGAT 60.766 55.000 5.05 0.00 34.51 4.18
3356 5191 0.399454 CATCTCCCATCTGCCGGATT 59.601 55.000 5.05 0.00 31.27 3.01
3357 5192 0.399454 ATCTCCCATCTGCCGGATTG 59.601 55.000 5.05 0.00 31.27 2.67
3358 5193 1.895707 CTCCCATCTGCCGGATTGC 60.896 63.158 5.05 0.00 31.27 3.56
3359 5194 2.124193 CCCATCTGCCGGATTGCA 60.124 61.111 5.05 0.00 39.37 4.08
3360 5195 2.484062 CCCATCTGCCGGATTGCAC 61.484 63.158 5.05 0.00 36.04 4.57
3361 5196 1.750018 CCATCTGCCGGATTGCACA 60.750 57.895 5.05 0.00 36.04 4.57
3362 5197 1.721664 CCATCTGCCGGATTGCACAG 61.722 60.000 5.05 0.96 36.04 3.66
3363 5198 1.452651 ATCTGCCGGATTGCACAGG 60.453 57.895 5.05 0.00 36.04 4.00
3364 5199 1.913951 ATCTGCCGGATTGCACAGGA 61.914 55.000 5.05 0.00 36.04 3.86
3365 5200 1.452651 CTGCCGGATTGCACAGGAT 60.453 57.895 5.05 0.00 36.04 3.24
3366 5201 1.001020 TGCCGGATTGCACAGGATT 60.001 52.632 5.05 0.00 36.04 3.01
3367 5202 1.031571 TGCCGGATTGCACAGGATTC 61.032 55.000 5.05 0.00 36.04 2.52
3368 5203 0.749454 GCCGGATTGCACAGGATTCT 60.749 55.000 5.05 0.00 0.00 2.40
3369 5204 1.019673 CCGGATTGCACAGGATTCTG 58.980 55.000 0.00 0.00 46.10 3.02
3383 5218 6.830873 CAGGATTCTGTTTCCTCTCATTTT 57.169 37.500 0.00 0.00 41.78 1.82
3384 5219 6.618811 CAGGATTCTGTTTCCTCTCATTTTG 58.381 40.000 0.00 0.00 41.78 2.44
3385 5220 6.208204 CAGGATTCTGTTTCCTCTCATTTTGT 59.792 38.462 0.00 0.00 41.78 2.83
3386 5221 6.779539 AGGATTCTGTTTCCTCTCATTTTGTT 59.220 34.615 0.00 0.00 39.46 2.83
3387 5222 7.944554 AGGATTCTGTTTCCTCTCATTTTGTTA 59.055 33.333 0.00 0.00 39.46 2.41
3388 5223 8.023706 GGATTCTGTTTCCTCTCATTTTGTTAC 58.976 37.037 0.00 0.00 0.00 2.50
3389 5224 8.697507 ATTCTGTTTCCTCTCATTTTGTTACT 57.302 30.769 0.00 0.00 0.00 2.24
3390 5225 8.519799 TTCTGTTTCCTCTCATTTTGTTACTT 57.480 30.769 0.00 0.00 0.00 2.24
3391 5226 9.621629 TTCTGTTTCCTCTCATTTTGTTACTTA 57.378 29.630 0.00 0.00 0.00 2.24
3392 5227 9.052759 TCTGTTTCCTCTCATTTTGTTACTTAC 57.947 33.333 0.00 0.00 0.00 2.34
3393 5228 8.740123 TGTTTCCTCTCATTTTGTTACTTACA 57.260 30.769 0.00 0.00 34.12 2.41
3394 5229 9.349713 TGTTTCCTCTCATTTTGTTACTTACAT 57.650 29.630 0.00 0.00 36.44 2.29
3395 5230 9.612620 GTTTCCTCTCATTTTGTTACTTACATG 57.387 33.333 0.00 0.00 36.44 3.21
3396 5231 8.918202 TTCCTCTCATTTTGTTACTTACATGT 57.082 30.769 2.69 2.69 36.44 3.21
3398 5233 9.431887 TCCTCTCATTTTGTTACTTACATGTAC 57.568 33.333 4.68 0.00 36.44 2.90
3399 5234 8.665685 CCTCTCATTTTGTTACTTACATGTACC 58.334 37.037 4.68 0.00 36.44 3.34
3456 5291 5.740290 TTTGAAGAGACCTAAGTACCCAG 57.260 43.478 0.00 0.00 0.00 4.45
3458 5293 4.342359 TGAAGAGACCTAAGTACCCAGTC 58.658 47.826 0.00 0.00 0.00 3.51
3465 5300 2.166664 CCTAAGTACCCAGTCTGCTCAC 59.833 54.545 0.00 0.00 0.00 3.51
3472 5307 0.170116 CCAGTCTGCTCACGACTCTC 59.830 60.000 0.00 0.00 39.59 3.20
3668 5515 5.007136 CACGAGCCTGATTTATTCTTCTTCC 59.993 44.000 0.00 0.00 0.00 3.46
3674 5522 8.526978 AGCCTGATTTATTCTTCTTCCTTTTTC 58.473 33.333 0.00 0.00 0.00 2.29
3814 5662 3.729217 GCTTTACGTTGCAGTTTTCCTTC 59.271 43.478 0.00 0.00 0.00 3.46
3876 5724 6.811954 TGCATTGCATTCATCTTGATATTGT 58.188 32.000 7.38 0.00 31.71 2.71
3877 5725 6.699642 TGCATTGCATTCATCTTGATATTGTG 59.300 34.615 7.38 0.00 31.71 3.33
4257 6105 1.214424 ACCTTAACAGTTGGCTGGTGT 59.786 47.619 0.00 0.00 43.57 4.16
4374 6222 8.932945 TCTTCTTCATGTATGTGTTCATAGAC 57.067 34.615 0.00 0.00 37.23 2.59
4577 9627 9.305555 TCACTATCAGTTTACCTAGTTACAACT 57.694 33.333 0.00 0.00 42.91 3.16
4578 9628 9.924650 CACTATCAGTTTACCTAGTTACAACTT 57.075 33.333 0.00 0.00 40.37 2.66
4614 9668 6.208797 GCCTTTTTACCTTAACCATCAGAAGT 59.791 38.462 0.00 0.00 0.00 3.01
4648 9702 9.023962 ACCAAAATTAATCATTAGAAGCTCACA 57.976 29.630 0.00 0.00 0.00 3.58
4772 9857 3.295973 AGAGATACTCCCTTGTCTGAGC 58.704 50.000 0.00 0.00 31.65 4.26
4899 10411 1.170442 TTTTCGAAAAGGGGGATCGC 58.830 50.000 19.08 0.06 36.56 4.58
4900 10412 0.678684 TTTCGAAAAGGGGGATCGCC 60.679 55.000 20.31 20.31 36.56 5.54
4910 10422 4.247380 GGATCGCCCCAGCCTCTG 62.247 72.222 0.00 0.00 34.57 3.35
4911 10423 4.925861 GATCGCCCCAGCCTCTGC 62.926 72.222 0.00 0.00 34.57 4.26
4916 10428 3.790437 CCCCAGCCTCTGCATCGT 61.790 66.667 0.00 0.00 41.13 3.73
4917 10429 2.434843 CCCCAGCCTCTGCATCGTA 61.435 63.158 0.00 0.00 41.13 3.43
4918 10430 1.522092 CCCAGCCTCTGCATCGTAA 59.478 57.895 0.00 0.00 41.13 3.18
4919 10431 0.107456 CCCAGCCTCTGCATCGTAAT 59.893 55.000 0.00 0.00 41.13 1.89
4920 10432 1.475751 CCCAGCCTCTGCATCGTAATT 60.476 52.381 0.00 0.00 41.13 1.40
4921 10433 2.224281 CCCAGCCTCTGCATCGTAATTA 60.224 50.000 0.00 0.00 41.13 1.40
4922 10434 2.802816 CCAGCCTCTGCATCGTAATTAC 59.197 50.000 5.47 5.47 41.13 1.89
4923 10435 3.493350 CCAGCCTCTGCATCGTAATTACT 60.493 47.826 13.56 0.00 41.13 2.24
4924 10436 3.738282 CAGCCTCTGCATCGTAATTACTC 59.262 47.826 13.56 1.51 41.13 2.59
4925 10437 3.639094 AGCCTCTGCATCGTAATTACTCT 59.361 43.478 13.56 0.00 41.13 3.24
4926 10438 4.100189 AGCCTCTGCATCGTAATTACTCTT 59.900 41.667 13.56 0.00 41.13 2.85
4927 10439 4.811557 GCCTCTGCATCGTAATTACTCTTT 59.188 41.667 13.56 0.00 37.47 2.52
4928 10440 5.983720 GCCTCTGCATCGTAATTACTCTTTA 59.016 40.000 13.56 0.00 37.47 1.85
4973 10489 4.273318 AGTTTTAACATGCTCCATCTCCC 58.727 43.478 0.00 0.00 0.00 4.30
5071 10587 6.595772 TGTCACCAAAAATTGTATTGTTGC 57.404 33.333 0.00 0.00 0.00 4.17
5076 10592 7.496920 TCACCAAAAATTGTATTGTTGCATTCA 59.503 29.630 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.044650 CAGAGTGCATGGGTGGGG 60.045 66.667 0.00 0.00 0.00 4.96
26 27 2.940410 CCAAATGGCATTGAAATCCAGC 59.060 45.455 14.47 0.00 32.78 4.85
37 38 1.091771 CGAGCTCGTCCAAATGGCAT 61.092 55.000 27.79 0.00 34.44 4.40
38 39 1.741401 CGAGCTCGTCCAAATGGCA 60.741 57.895 27.79 0.00 34.44 4.92
45 46 4.724602 GTGCTGCGAGCTCGTCCA 62.725 66.667 34.46 24.98 42.97 4.02
46 47 3.997064 ATGTGCTGCGAGCTCGTCC 62.997 63.158 34.46 22.92 42.97 4.79
49 50 4.219846 GCATGTGCTGCGAGCTCG 62.220 66.667 31.37 31.37 42.97 5.03
59 60 2.410469 GATTGAGGCGGCATGTGC 59.590 61.111 13.08 3.76 41.14 4.57
60 61 2.711311 CGATTGAGGCGGCATGTG 59.289 61.111 13.08 0.00 0.00 3.21
80 81 2.357760 TTGTGTTACGGCCTCGCC 60.358 61.111 0.00 0.00 46.75 5.54
87 88 0.774098 CACGACGACTTGTGTTACGG 59.226 55.000 0.00 0.00 0.00 4.02
88 89 1.745566 TCACGACGACTTGTGTTACG 58.254 50.000 0.00 0.00 37.38 3.18
90 91 2.473609 GCAATCACGACGACTTGTGTTA 59.526 45.455 0.00 0.00 37.38 2.41
97 98 2.126071 CCGGCAATCACGACGACT 60.126 61.111 0.00 0.00 41.00 4.18
102 103 0.529773 GCTATGACCGGCAATCACGA 60.530 55.000 0.00 0.00 0.00 4.35
117 118 1.152963 GGGCGAACCATGGTGCTAT 60.153 57.895 20.60 1.23 39.85 2.97
177 178 1.003262 CACATTTTTGCTCGCACCGG 61.003 55.000 0.00 0.00 0.00 5.28
179 180 1.608093 CGCACATTTTTGCTCGCACC 61.608 55.000 0.00 0.00 40.62 5.01
184 185 0.040425 ACCGACGCACATTTTTGCTC 60.040 50.000 0.00 0.00 40.62 4.26
187 188 2.695087 CGACCGACGCACATTTTTG 58.305 52.632 0.00 0.00 34.51 2.44
248 249 3.682292 AATCGGCGACAAGGGGAGC 62.682 63.158 13.76 0.00 0.00 4.70
276 277 3.570638 CTTGCTGATCTGGGCGCG 61.571 66.667 0.00 0.00 0.00 6.86
277 278 3.207669 CCTTGCTGATCTGGGCGC 61.208 66.667 0.00 0.00 0.00 6.53
286 287 1.066858 CCTCTACGCTTTCCTTGCTGA 60.067 52.381 0.00 0.00 0.00 4.26
299 300 5.816919 ACAAAAATGTCAACAACCTCTACG 58.183 37.500 0.00 0.00 0.00 3.51
301 302 7.032580 CACAACAAAAATGTCAACAACCTCTA 58.967 34.615 0.00 0.00 0.00 2.43
306 307 4.094146 CCCCACAACAAAAATGTCAACAAC 59.906 41.667 0.00 0.00 0.00 3.32
311 312 4.559862 AAACCCCACAACAAAAATGTCA 57.440 36.364 0.00 0.00 0.00 3.58
314 315 4.260415 GCGTAAAACCCCACAACAAAAATG 60.260 41.667 0.00 0.00 0.00 2.32
315 316 3.872182 GCGTAAAACCCCACAACAAAAAT 59.128 39.130 0.00 0.00 0.00 1.82
319 320 0.745468 GGCGTAAAACCCCACAACAA 59.255 50.000 0.00 0.00 0.00 2.83
321 322 1.283487 CGGCGTAAAACCCCACAAC 59.717 57.895 0.00 0.00 0.00 3.32
325 326 2.357275 CGACGGCGTAAAACCCCA 60.357 61.111 14.74 0.00 0.00 4.96
342 343 1.130186 GTGGTTAGAGACGTCGAGGAC 59.870 57.143 12.85 5.73 0.00 3.85
343 344 1.446907 GTGGTTAGAGACGTCGAGGA 58.553 55.000 12.85 0.00 0.00 3.71
344 345 0.450983 GGTGGTTAGAGACGTCGAGG 59.549 60.000 10.46 3.03 0.00 4.63
345 346 1.397692 GAGGTGGTTAGAGACGTCGAG 59.602 57.143 10.46 0.00 0.00 4.04
346 347 1.002888 AGAGGTGGTTAGAGACGTCGA 59.997 52.381 10.46 0.00 33.26 4.20
347 348 1.130749 CAGAGGTGGTTAGAGACGTCG 59.869 57.143 10.46 0.00 33.26 5.12
348 349 2.162008 GTCAGAGGTGGTTAGAGACGTC 59.838 54.545 7.70 7.70 0.00 4.34
349 350 2.161030 GTCAGAGGTGGTTAGAGACGT 58.839 52.381 0.00 0.00 0.00 4.34
350 351 1.473278 GGTCAGAGGTGGTTAGAGACG 59.527 57.143 0.00 0.00 0.00 4.18
377 378 5.103000 CCCTTATCTTGTAAGTGTCTGACG 58.897 45.833 2.98 0.00 0.00 4.35
385 386 4.436079 ACCCTCACCCTTATCTTGTAAGT 58.564 43.478 0.00 0.00 0.00 2.24
386 387 5.897824 TCTACCCTCACCCTTATCTTGTAAG 59.102 44.000 0.00 0.00 0.00 2.34
387 388 5.845734 TCTACCCTCACCCTTATCTTGTAA 58.154 41.667 0.00 0.00 0.00 2.41
388 389 5.476950 TCTACCCTCACCCTTATCTTGTA 57.523 43.478 0.00 0.00 0.00 2.41
392 402 4.470304 GTGTTTCTACCCTCACCCTTATCT 59.530 45.833 0.00 0.00 0.00 1.98
433 444 7.828508 AAAGCAATCACACCATATACATGAT 57.171 32.000 0.00 0.00 33.67 2.45
434 445 7.482474 CAAAAGCAATCACACCATATACATGA 58.518 34.615 0.00 0.00 33.67 3.07
443 454 4.619973 CTTTAGCAAAAGCAATCACACCA 58.380 39.130 0.00 0.00 35.98 4.17
496 507 5.981915 TCTTCGTGCAAGATCAATGAGATAG 59.018 40.000 2.36 0.00 36.08 2.08
550 561 8.579850 TGCAAATATAAAGGACTCAATCAAGT 57.420 30.769 0.00 0.00 0.00 3.16
597 608 9.753674 TTTGATTTTTCAGGTATGTCTAGGAAT 57.246 29.630 0.00 0.00 0.00 3.01
629 641 5.990668 ACAATGGACTTACCCTGAGTATTC 58.009 41.667 0.00 0.00 38.00 1.75
640 652 7.041372 TGCTGAGAAAGTTTACAATGGACTTAC 60.041 37.037 0.00 0.00 33.54 2.34
642 654 5.827797 TGCTGAGAAAGTTTACAATGGACTT 59.172 36.000 0.00 0.00 35.27 3.01
675 687 2.829120 CAATACCAACGGGGGTCAAAAT 59.171 45.455 3.31 0.00 42.42 1.82
683 695 1.268352 CACAACACAATACCAACGGGG 59.732 52.381 0.00 0.00 44.81 5.73
684 696 1.950909 ACACAACACAATACCAACGGG 59.049 47.619 0.00 0.00 41.29 5.28
685 697 3.367607 CAACACAACACAATACCAACGG 58.632 45.455 0.00 0.00 0.00 4.44
686 698 3.181495 ACCAACACAACACAATACCAACG 60.181 43.478 0.00 0.00 0.00 4.10
687 699 4.109050 CACCAACACAACACAATACCAAC 58.891 43.478 0.00 0.00 0.00 3.77
688 700 3.764434 ACACCAACACAACACAATACCAA 59.236 39.130 0.00 0.00 0.00 3.67
689 701 3.357203 ACACCAACACAACACAATACCA 58.643 40.909 0.00 0.00 0.00 3.25
690 702 3.243267 GGACACCAACACAACACAATACC 60.243 47.826 0.00 0.00 0.00 2.73
691 703 3.243267 GGGACACCAACACAACACAATAC 60.243 47.826 0.00 0.00 36.50 1.89
692 704 2.952978 GGGACACCAACACAACACAATA 59.047 45.455 0.00 0.00 36.50 1.90
693 705 1.754226 GGGACACCAACACAACACAAT 59.246 47.619 0.00 0.00 36.50 2.71
694 706 1.178276 GGGACACCAACACAACACAA 58.822 50.000 0.00 0.00 36.50 3.33
695 707 0.329931 AGGGACACCAACACAACACA 59.670 50.000 0.00 0.00 40.13 3.72
696 708 1.021968 GAGGGACACCAACACAACAC 58.978 55.000 0.00 0.00 40.13 3.32
697 709 0.916086 AGAGGGACACCAACACAACA 59.084 50.000 0.00 0.00 40.13 3.33
698 710 1.308998 CAGAGGGACACCAACACAAC 58.691 55.000 0.00 0.00 40.13 3.32
699 711 0.465460 GCAGAGGGACACCAACACAA 60.465 55.000 0.00 0.00 40.13 3.33
700 712 1.148273 GCAGAGGGACACCAACACA 59.852 57.895 0.00 0.00 40.13 3.72
701 713 1.148273 TGCAGAGGGACACCAACAC 59.852 57.895 0.00 0.00 40.13 3.32
702 714 1.148273 GTGCAGAGGGACACCAACA 59.852 57.895 0.00 0.00 40.13 3.33
703 715 0.886490 CAGTGCAGAGGGACACCAAC 60.886 60.000 0.00 0.00 37.91 3.77
704 716 1.451504 CAGTGCAGAGGGACACCAA 59.548 57.895 0.00 0.00 37.91 3.67
705 717 3.150949 CAGTGCAGAGGGACACCA 58.849 61.111 0.00 0.00 37.91 4.17
706 718 2.359230 GCAGTGCAGAGGGACACC 60.359 66.667 11.09 0.00 37.91 4.16
707 719 1.963338 GTGCAGTGCAGAGGGACAC 60.963 63.158 20.42 0.00 40.08 3.67
708 720 2.104572 GAGTGCAGTGCAGAGGGACA 62.105 60.000 20.42 0.00 40.08 4.02
709 721 1.375268 GAGTGCAGTGCAGAGGGAC 60.375 63.158 20.42 5.44 40.08 4.46
710 722 2.587247 GGAGTGCAGTGCAGAGGGA 61.587 63.158 20.42 0.00 40.08 4.20
711 723 1.260538 TAGGAGTGCAGTGCAGAGGG 61.261 60.000 20.42 0.00 40.08 4.30
712 724 0.829333 ATAGGAGTGCAGTGCAGAGG 59.171 55.000 20.42 0.00 40.08 3.69
713 725 2.277969 CAATAGGAGTGCAGTGCAGAG 58.722 52.381 20.42 0.00 40.08 3.35
714 726 1.625315 ACAATAGGAGTGCAGTGCAGA 59.375 47.619 20.42 2.93 40.08 4.26
724 736 5.070001 TGTTTGCTGCTAAACAATAGGAGT 58.930 37.500 20.22 0.00 44.84 3.85
746 758 0.736053 GGTCTGCTCTCTACTCCGTG 59.264 60.000 0.00 0.00 0.00 4.94
753 765 1.454111 GGAGGCGGTCTGCTCTCTA 60.454 63.158 16.82 0.00 45.43 2.43
754 766 2.757917 GGAGGCGGTCTGCTCTCT 60.758 66.667 16.82 2.20 45.43 3.10
755 767 4.200283 CGGAGGCGGTCTGCTCTC 62.200 72.222 3.10 8.38 45.43 3.20
985 1023 2.475466 CCATTGGCGCTACAGGCTG 61.475 63.158 14.16 14.16 39.13 4.85
1220 1267 3.402681 CACCCTCCTCGGCACCAT 61.403 66.667 0.00 0.00 0.00 3.55
1221 1268 4.631740 TCACCCTCCTCGGCACCA 62.632 66.667 0.00 0.00 0.00 4.17
1224 1271 4.671590 TCGTCACCCTCCTCGGCA 62.672 66.667 0.00 0.00 0.00 5.69
1629 1697 2.586079 CCGTGGCGCCAGATGTAG 60.586 66.667 33.73 16.45 0.00 2.74
1650 1718 0.613572 TCCAGGTGCCGATGTACTCA 60.614 55.000 0.00 0.00 0.00 3.41
2045 2122 3.324099 CTCGACACCGACACCCTCG 62.324 68.421 0.00 0.00 40.30 4.63
2297 2452 1.123928 AGTGATGGTGGTAGCTAGCC 58.876 55.000 19.78 12.11 0.00 3.93
2298 2453 1.808133 GCAGTGATGGTGGTAGCTAGC 60.808 57.143 16.08 16.08 0.00 3.42
2299 2454 1.482182 TGCAGTGATGGTGGTAGCTAG 59.518 52.381 0.00 0.00 0.00 3.42
2300 2455 1.207089 GTGCAGTGATGGTGGTAGCTA 59.793 52.381 0.00 0.00 0.00 3.32
2301 2456 0.036010 GTGCAGTGATGGTGGTAGCT 60.036 55.000 0.00 0.00 0.00 3.32
2397 2682 1.609239 CCTTCCCACAGCATGCCTA 59.391 57.895 15.66 0.00 42.53 3.93
2595 3901 3.300388 TGGAGACTACTATGGGAAGCAG 58.700 50.000 0.00 0.00 0.00 4.24
2602 3908 3.782046 CCGTGTTTGGAGACTACTATGG 58.218 50.000 0.00 0.00 0.00 2.74
2604 3910 2.159282 CGCCGTGTTTGGAGACTACTAT 60.159 50.000 0.00 0.00 0.00 2.12
2729 4479 1.377202 GCCGGGTGATGAAAGCTCA 60.377 57.895 2.18 0.00 35.56 4.26
2735 4485 0.958091 CACTTTTGCCGGGTGATGAA 59.042 50.000 2.18 0.00 33.32 2.57
2855 4605 4.797912 AGGTGGAGAGAAGAACCTTTTT 57.202 40.909 0.00 0.00 40.14 1.94
2860 4610 2.835156 AGCTAAGGTGGAGAGAAGAACC 59.165 50.000 0.00 0.00 0.00 3.62
2861 4611 4.440940 GCTAGCTAAGGTGGAGAGAAGAAC 60.441 50.000 7.70 0.00 0.00 3.01
2862 4612 3.702045 GCTAGCTAAGGTGGAGAGAAGAA 59.298 47.826 7.70 0.00 0.00 2.52
2863 4613 3.292460 GCTAGCTAAGGTGGAGAGAAGA 58.708 50.000 7.70 0.00 0.00 2.87
2864 4614 2.364002 GGCTAGCTAAGGTGGAGAGAAG 59.636 54.545 15.72 0.00 0.00 2.85
2866 4616 1.411787 GGGCTAGCTAAGGTGGAGAGA 60.412 57.143 15.72 0.00 0.00 3.10
2867 4617 1.044611 GGGCTAGCTAAGGTGGAGAG 58.955 60.000 15.72 0.00 0.00 3.20
2868 4618 0.338467 TGGGCTAGCTAAGGTGGAGA 59.662 55.000 15.72 0.00 0.00 3.71
2869 4619 0.466124 GTGGGCTAGCTAAGGTGGAG 59.534 60.000 15.72 0.00 0.00 3.86
2870 4620 0.252513 TGTGGGCTAGCTAAGGTGGA 60.253 55.000 15.72 0.00 0.00 4.02
2871 4621 0.107654 GTGTGGGCTAGCTAAGGTGG 60.108 60.000 15.72 0.00 0.00 4.61
2893 4645 5.362556 TCTCAGACATGCTTAAAACTTGC 57.637 39.130 0.00 0.00 0.00 4.01
2922 4674 2.289444 ACCTGTCGATGATCAAAACCGT 60.289 45.455 0.00 0.00 0.00 4.83
2986 4740 8.516811 ACTTTGTTATTAGAGTGTTGTCGTAG 57.483 34.615 0.00 0.00 0.00 3.51
3061 4815 3.518590 GCCAATTTCTGAAAGCATCCTG 58.481 45.455 8.95 0.09 0.00 3.86
3223 4997 2.401766 GGGCTTGTCTGTCATGCGG 61.402 63.158 6.67 0.00 44.70 5.69
3338 5173 0.399454 CAATCCGGCAGATGGGAGAT 59.601 55.000 0.00 0.00 35.40 2.75
3339 5174 1.832219 CAATCCGGCAGATGGGAGA 59.168 57.895 0.00 0.00 35.40 3.71
3340 5175 1.895707 GCAATCCGGCAGATGGGAG 60.896 63.158 0.00 0.00 35.40 4.30
3341 5176 2.192979 GCAATCCGGCAGATGGGA 59.807 61.111 0.00 0.00 34.56 4.37
3342 5177 2.124193 TGCAATCCGGCAGATGGG 60.124 61.111 0.00 0.00 39.25 4.00
3343 5178 1.721664 CTGTGCAATCCGGCAGATGG 61.722 60.000 0.00 0.00 45.96 3.51
3344 5179 1.721664 CCTGTGCAATCCGGCAGATG 61.722 60.000 0.00 0.00 45.96 2.90
3345 5180 1.452651 CCTGTGCAATCCGGCAGAT 60.453 57.895 0.00 0.00 45.96 2.90
3346 5181 1.913951 ATCCTGTGCAATCCGGCAGA 61.914 55.000 0.00 0.00 45.96 4.26
3347 5182 1.033746 AATCCTGTGCAATCCGGCAG 61.034 55.000 0.00 0.00 45.96 4.85
3348 5183 1.001020 AATCCTGTGCAATCCGGCA 60.001 52.632 0.00 0.00 42.53 5.69
3349 5184 0.749454 AGAATCCTGTGCAATCCGGC 60.749 55.000 0.00 0.00 0.00 6.13
3350 5185 1.019673 CAGAATCCTGTGCAATCCGG 58.980 55.000 0.00 0.00 35.70 5.14
3362 5197 6.581171 ACAAAATGAGAGGAAACAGAATCC 57.419 37.500 0.00 0.00 37.22 3.01
3363 5198 8.787852 AGTAACAAAATGAGAGGAAACAGAATC 58.212 33.333 0.00 0.00 0.00 2.52
3364 5199 8.697507 AGTAACAAAATGAGAGGAAACAGAAT 57.302 30.769 0.00 0.00 0.00 2.40
3365 5200 8.519799 AAGTAACAAAATGAGAGGAAACAGAA 57.480 30.769 0.00 0.00 0.00 3.02
3366 5201 9.052759 GTAAGTAACAAAATGAGAGGAAACAGA 57.947 33.333 0.00 0.00 0.00 3.41
3367 5202 8.836413 TGTAAGTAACAAAATGAGAGGAAACAG 58.164 33.333 0.00 0.00 34.29 3.16
3368 5203 8.740123 TGTAAGTAACAAAATGAGAGGAAACA 57.260 30.769 0.00 0.00 34.29 2.83
3369 5204 9.612620 CATGTAAGTAACAAAATGAGAGGAAAC 57.387 33.333 0.00 0.00 42.70 2.78
3370 5205 9.349713 ACATGTAAGTAACAAAATGAGAGGAAA 57.650 29.630 0.00 0.00 42.70 3.13
3371 5206 8.918202 ACATGTAAGTAACAAAATGAGAGGAA 57.082 30.769 0.00 0.00 42.70 3.36
3372 5207 9.431887 GTACATGTAAGTAACAAAATGAGAGGA 57.568 33.333 7.25 0.00 42.70 3.71
3373 5208 8.665685 GGTACATGTAAGTAACAAAATGAGAGG 58.334 37.037 7.25 0.00 42.70 3.69
3374 5209 9.214957 TGGTACATGTAAGTAACAAAATGAGAG 57.785 33.333 7.25 0.00 42.70 3.20
3425 5260 6.651225 ACTTAGGTCTCTTCAAATACAGTTGC 59.349 38.462 0.00 0.00 0.00 4.17
3456 5291 5.682943 AATATAGAGAGTCGTGAGCAGAC 57.317 43.478 0.00 0.00 38.81 3.51
3458 5293 6.312399 AGAAATATAGAGAGTCGTGAGCAG 57.688 41.667 0.00 0.00 0.00 4.24
3465 5300 6.016192 TGCCTGGTAAGAAATATAGAGAGTCG 60.016 42.308 0.00 0.00 0.00 4.18
3472 5307 6.483640 GTCCACTTGCCTGGTAAGAAATATAG 59.516 42.308 27.95 10.03 32.50 1.31
3799 5647 3.793465 GCTGAGTGAAGGAAAACTGCAAC 60.793 47.826 0.00 0.00 36.18 4.17
3876 5724 3.073678 CCAATGAGGTCGATGTTTGTCA 58.926 45.455 0.00 0.00 0.00 3.58
3877 5725 3.747099 CCAATGAGGTCGATGTTTGTC 57.253 47.619 0.00 0.00 0.00 3.18
4149 5997 3.437049 CCCTGAAAATGAAGTCTCGGAAC 59.563 47.826 0.00 0.00 0.00 3.62
4257 6105 2.247358 GGATGGTGGGCAAAGAAGAAA 58.753 47.619 0.00 0.00 0.00 2.52
4374 6222 9.299963 CAGAGAAGATTCAGTAGATGTACAAAG 57.700 37.037 0.00 0.00 0.00 2.77
4530 6378 3.949586 TGGATGAATTGACCCTATGCA 57.050 42.857 0.00 0.00 0.00 3.96
4580 9630 9.310449 TGGTTAAGGTAAAAAGGCATATGTTTA 57.690 29.630 4.29 0.00 0.00 2.01
4590 9640 7.761038 ACTTCTGATGGTTAAGGTAAAAAGG 57.239 36.000 0.00 0.00 0.00 3.11
4592 9642 9.416284 AGAAACTTCTGATGGTTAAGGTAAAAA 57.584 29.630 0.00 0.00 35.89 1.94
4601 9651 8.754991 TTGGTAAAAGAAACTTCTGATGGTTA 57.245 30.769 0.00 0.00 37.65 2.85
4633 9687 5.299028 TGCAAGTTTTGTGAGCTTCTAATGA 59.701 36.000 0.00 0.00 0.00 2.57
4648 9702 8.210265 TCTTTTGGGATCTAAAATGCAAGTTTT 58.790 29.630 4.28 3.97 34.98 2.43
4772 9857 7.038941 ACCCTAAATACGAGGAGATCCAATAAG 60.039 40.741 0.92 0.00 35.99 1.73
4879 10391 1.542472 GCGATCCCCCTTTTCGAAAAA 59.458 47.619 22.67 9.34 34.92 1.94
4880 10392 1.170442 GCGATCCCCCTTTTCGAAAA 58.830 50.000 21.35 21.35 34.92 2.29
4881 10393 0.678684 GGCGATCCCCCTTTTCGAAA 60.679 55.000 6.47 6.47 34.92 3.46
4882 10394 1.078001 GGCGATCCCCCTTTTCGAA 60.078 57.895 0.00 0.00 34.92 3.71
4883 10395 2.587889 GGCGATCCCCCTTTTCGA 59.412 61.111 0.00 0.00 34.92 3.71
4893 10405 4.247380 CAGAGGCTGGGGCGATCC 62.247 72.222 0.00 0.00 39.81 3.36
4894 10406 4.925861 GCAGAGGCTGGGGCGATC 62.926 72.222 0.00 0.00 39.81 3.69
4899 10411 1.971505 TTACGATGCAGAGGCTGGGG 61.972 60.000 0.00 0.00 41.91 4.96
4900 10412 0.107456 ATTACGATGCAGAGGCTGGG 59.893 55.000 0.00 0.00 41.91 4.45
4901 10413 1.959042 AATTACGATGCAGAGGCTGG 58.041 50.000 0.00 0.00 41.91 4.85
4902 10414 3.722147 AGTAATTACGATGCAGAGGCTG 58.278 45.455 9.91 0.00 41.91 4.85
4903 10415 3.639094 AGAGTAATTACGATGCAGAGGCT 59.361 43.478 9.91 0.00 41.91 4.58
4904 10416 3.983741 AGAGTAATTACGATGCAGAGGC 58.016 45.455 9.91 0.00 41.68 4.70
4905 10417 8.420374 TTTAAAGAGTAATTACGATGCAGAGG 57.580 34.615 9.91 0.00 0.00 3.69
4928 10440 9.723601 AACTTGCCAATATTCAATGTGTATTTT 57.276 25.926 0.00 0.00 0.00 1.82
5029 10545 6.589523 GGTGACATGCATTAACATTTTGCTAA 59.410 34.615 0.00 0.00 37.28 3.09


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

AutoCloner maintained by Alex Coulton.