Multiple sequence alignment - TraesCS3A01G210400

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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 TraesCS3A01G210400 chr3A 100.000 2824 0 0 3770 6593 376780031 376782854 0.000000e+00 5216.0
1 TraesCS3A01G210400 chr3A 100.000 2216 0 0 1 2216 376776262 376778477 0.000000e+00 4093.0
2 TraesCS3A01G210400 chr3A 100.000 1067 0 0 2424 3490 376778685 376779751 0.000000e+00 1971.0
3 TraesCS3A01G210400 chr3D 94.565 1527 41 15 707 2216 287287803 287289304 0.000000e+00 2322.0
4 TraesCS3A01G210400 chr3D 93.306 1225 39 15 3781 4990 287290637 287291833 0.000000e+00 1768.0
5 TraesCS3A01G210400 chr3D 95.700 1093 20 8 2424 3490 287289337 287290428 0.000000e+00 1733.0
6 TraesCS3A01G210400 chr3D 91.667 876 33 15 4981 5826 287292221 287293086 0.000000e+00 1177.0
7 TraesCS3A01G210400 chr3D 88.174 668 46 17 1 660 287287070 287287712 0.000000e+00 765.0
8 TraesCS3A01G210400 chr3D 83.897 621 25 36 5945 6538 287293102 287293674 2.110000e-144 523.0
9 TraesCS3A01G210400 chr3D 100.000 37 0 0 5862 5898 278515034 278514998 1.190000e-07 69.4
10 TraesCS3A01G210400 chr3D 89.474 57 2 2 5867 5919 380048779 380048723 1.190000e-07 69.4
11 TraesCS3A01G210400 chr3B 95.814 1314 41 8 3875 5176 380506008 380507319 0.000000e+00 2109.0
12 TraesCS3A01G210400 chr3B 93.483 1289 45 7 929 2216 380503284 380504534 0.000000e+00 1879.0
13 TraesCS3A01G210400 chr3B 95.438 1096 20 13 2424 3490 380504566 380505660 0.000000e+00 1720.0
14 TraesCS3A01G210400 chr3B 94.165 617 21 6 5200 5805 380507385 380507997 0.000000e+00 926.0
15 TraesCS3A01G210400 chr3B 89.655 406 36 5 1 401 380494074 380494478 4.560000e-141 512.0
16 TraesCS3A01G210400 chr3B 84.951 412 24 15 443 846 380502650 380503031 3.730000e-102 383.0
17 TraesCS3A01G210400 chr3B 81.844 347 27 18 6052 6389 380508058 380508377 6.560000e-65 259.0
18 TraesCS3A01G210400 chr3B 88.158 76 4 2 3770 3844 380505929 380506000 1.180000e-12 86.1
19 TraesCS3A01G210400 chr5D 79.496 278 37 12 22 296 433635863 433635603 5.250000e-41 180.0
20 TraesCS3A01G210400 chr1D 100.000 37 0 0 5862 5898 206041070 206041034 1.190000e-07 69.4
21 TraesCS3A01G210400 chr2A 100.000 36 0 0 5863 5898 703998935 703998900 4.270000e-07 67.6
22 TraesCS3A01G210400 chrUn 85.938 64 3 4 5862 5919 156526287 156526224 5.520000e-06 63.9
23 TraesCS3A01G210400 chr7A 86.667 60 2 4 5866 5919 567475365 567475424 1.990000e-05 62.1
24 TraesCS3A01G210400 chr5B 86.667 60 2 4 5866 5919 356213797 356213738 1.990000e-05 62.1
25 TraesCS3A01G210400 chr1B 85.714 63 3 4 5863 5919 342124820 342124882 1.990000e-05 62.1
26 TraesCS3A01G210400 chr4A 84.615 65 4 5 5861 5919 498135499 498135563 7.140000e-05 60.2


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 TraesCS3A01G210400 chr3A 376776262 376782854 6592 False 3760.000000 5216 100.000000 1 6593 3 chr3A.!!$F1 6592
1 TraesCS3A01G210400 chr3D 287287070 287293674 6604 False 1381.333333 2322 91.218167 1 6538 6 chr3D.!!$F1 6537
2 TraesCS3A01G210400 chr3B 380502650 380508377 5727 False 1051.728571 2109 90.550429 443 6389 7 chr3B.!!$F2 5946

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
242 244 0.178990 GATGTGCCCCCAATAGGACC 60.179 60.000 0.00 0.0 38.24 4.46 F
282 284 0.321671 CTGTGGACAACCGACCATCT 59.678 55.000 0.00 0.0 39.21 2.90 F
330 332 0.546598 ACCCAGACCCAATCCGAATC 59.453 55.000 0.00 0.0 0.00 2.52 F
457 465 0.814010 GATCCTACGCGGCCATTGTT 60.814 55.000 12.47 0.0 0.00 2.83 F
1666 1956 1.063174 GATTTCAGCCATCTGTGACGC 59.937 52.381 0.00 0.0 41.10 5.19 F
2015 2305 0.403655 TATCAAACCAGTGCAGGGCA 59.596 50.000 4.26 0.0 35.60 5.36 F
3166 3484 0.623723 TGACCAGGTTTATCCCCTGC 59.376 55.000 0.00 0.0 46.73 4.85 F
4050 4370 2.488153 GGCATAAGTCAAACTCGGCTTT 59.512 45.455 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1219 1497 0.469518 GGAGGTATGGGCCGTACTCT 60.470 60.000 29.75 24.64 0.00 3.24 R
1308 1588 0.875728 ACGGGATCGCGAATCTCTAG 59.124 55.000 35.09 7.35 40.63 2.43 R
1669 1959 0.958382 TTGGGCGAATTCGTCTTGGG 60.958 55.000 29.41 1.18 44.45 4.12 R
1670 1960 1.094785 ATTGGGCGAATTCGTCTTGG 58.905 50.000 29.41 1.92 44.45 3.61 R
3098 3416 2.027561 TGACCATACGGAAACCTGGAAG 60.028 50.000 0.00 0.00 35.59 3.46 R
3947 4267 1.003355 CCAGGCACACAGGTCGATT 60.003 57.895 0.00 0.00 0.00 3.34 R
4992 5723 1.860950 CACGCTGGTATGCATCAGTAC 59.139 52.381 14.82 3.38 33.81 2.73 R
5910 6702 0.176680 ACTATCACTTGCTCCCGCTG 59.823 55.000 0.00 0.00 36.97 5.18 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
55 56 0.603439 CGCCCCTTGCTGCAAAAATT 60.603 50.000 16.74 0.00 38.05 1.82
57 58 1.525941 CCCCTTGCTGCAAAAATTGG 58.474 50.000 16.74 12.90 0.00 3.16
91 92 2.677979 CGAGAGGCAGACGACGACA 61.678 63.158 0.00 0.00 0.00 4.35
94 95 2.983930 GAGGCAGACGACGACAGCT 61.984 63.158 13.43 1.50 0.00 4.24
162 163 1.067354 GGTAGGCGACGAAAGAAGGAA 60.067 52.381 0.00 0.00 0.00 3.36
163 164 2.611224 GGTAGGCGACGAAAGAAGGAAA 60.611 50.000 0.00 0.00 0.00 3.13
176 177 6.652900 CGAAAGAAGGAAAGAAGGAAGAAGAT 59.347 38.462 0.00 0.00 0.00 2.40
185 186 7.281999 GGAAAGAAGGAAGAAGATGTTATGGAG 59.718 40.741 0.00 0.00 0.00 3.86
186 187 7.502060 AAGAAGGAAGAAGATGTTATGGAGA 57.498 36.000 0.00 0.00 0.00 3.71
189 190 7.826744 AGAAGGAAGAAGATGTTATGGAGAAAC 59.173 37.037 0.00 0.00 0.00 2.78
190 191 6.109359 AGGAAGAAGATGTTATGGAGAAACG 58.891 40.000 0.00 0.00 0.00 3.60
191 192 6.070767 AGGAAGAAGATGTTATGGAGAAACGA 60.071 38.462 0.00 0.00 0.00 3.85
192 193 6.594159 GGAAGAAGATGTTATGGAGAAACGAA 59.406 38.462 0.00 0.00 0.00 3.85
229 231 4.220602 ACAAATAGGAAGGTTTGGATGTGC 59.779 41.667 0.00 0.00 39.12 4.57
234 236 2.029892 AAGGTTTGGATGTGCCCCCA 62.030 55.000 0.00 0.00 34.97 4.96
242 244 0.178990 GATGTGCCCCCAATAGGACC 60.179 60.000 0.00 0.00 38.24 4.46
246 248 2.070650 GCCCCCAATAGGACCTCGT 61.071 63.158 0.00 0.00 38.24 4.18
269 271 2.281484 GCAGGCCGAAACTGTGGA 60.281 61.111 0.00 0.00 38.22 4.02
272 274 0.817634 CAGGCCGAAACTGTGGACAA 60.818 55.000 0.00 0.00 34.89 3.18
273 275 0.818040 AGGCCGAAACTGTGGACAAC 60.818 55.000 0.00 0.00 34.89 3.32
282 284 0.321671 CTGTGGACAACCGACCATCT 59.678 55.000 0.00 0.00 39.21 2.90
299 301 4.164221 ACCATCTGGAATCGTTTACCATCT 59.836 41.667 2.55 0.00 38.94 2.90
313 315 2.330216 ACCATCTAGATGTGCCCTACC 58.670 52.381 27.03 0.00 37.11 3.18
323 325 1.230149 TGCCCTACCCAGACCCAAT 60.230 57.895 0.00 0.00 0.00 3.16
324 326 1.279025 TGCCCTACCCAGACCCAATC 61.279 60.000 0.00 0.00 0.00 2.67
326 328 1.696097 CCCTACCCAGACCCAATCCG 61.696 65.000 0.00 0.00 0.00 4.18
327 329 0.689745 CCTACCCAGACCCAATCCGA 60.690 60.000 0.00 0.00 0.00 4.55
329 331 1.768870 CTACCCAGACCCAATCCGAAT 59.231 52.381 0.00 0.00 0.00 3.34
330 332 0.546598 ACCCAGACCCAATCCGAATC 59.453 55.000 0.00 0.00 0.00 2.52
332 334 0.839946 CCAGACCCAATCCGAATCCT 59.160 55.000 0.00 0.00 0.00 3.24
349 352 9.349713 TCCGAATCCTTAGTGCATAAAAATAAT 57.650 29.630 0.00 0.00 0.00 1.28
457 465 0.814010 GATCCTACGCGGCCATTGTT 60.814 55.000 12.47 0.00 0.00 2.83
460 468 1.088306 CCTACGCGGCCATTGTTAAA 58.912 50.000 12.47 0.00 0.00 1.52
473 481 6.366061 GGCCATTGTTAAAAGTTTGCTTCTAG 59.634 38.462 0.00 0.00 33.01 2.43
474 482 6.923508 GCCATTGTTAAAAGTTTGCTTCTAGT 59.076 34.615 0.00 0.00 33.01 2.57
478 486 7.095695 TGTTAAAAGTTTGCTTCTAGTGCTT 57.904 32.000 10.68 0.00 33.01 3.91
489 497 5.639506 TGCTTCTAGTGCTTGTATCTTTGTC 59.360 40.000 10.68 0.00 0.00 3.18
490 498 5.220303 GCTTCTAGTGCTTGTATCTTTGTCG 60.220 44.000 3.84 0.00 0.00 4.35
491 499 4.744570 TCTAGTGCTTGTATCTTTGTCGG 58.255 43.478 0.00 0.00 0.00 4.79
492 500 2.076863 AGTGCTTGTATCTTTGTCGGC 58.923 47.619 0.00 0.00 0.00 5.54
493 501 2.076863 GTGCTTGTATCTTTGTCGGCT 58.923 47.619 0.00 0.00 0.00 5.52
494 502 2.076100 TGCTTGTATCTTTGTCGGCTG 58.924 47.619 0.00 0.00 0.00 4.85
495 503 2.076863 GCTTGTATCTTTGTCGGCTGT 58.923 47.619 0.00 0.00 0.00 4.40
496 504 2.094417 GCTTGTATCTTTGTCGGCTGTC 59.906 50.000 0.00 0.00 0.00 3.51
521 529 7.064847 TCGAGTTACTTCTGAAGAGAGTGTATC 59.935 40.741 23.36 8.99 0.00 2.24
575 583 9.566432 GACAAAACCTCCTCTATATTTGATGAT 57.434 33.333 0.00 0.00 33.30 2.45
597 605 5.909621 TGGTCGCTATATATGACTTACCC 57.090 43.478 12.45 0.94 33.21 3.69
613 621 1.600058 ACCCATCATCATGACCCAGT 58.400 50.000 0.00 0.00 30.57 4.00
616 624 3.527253 ACCCATCATCATGACCCAGTTTA 59.473 43.478 0.00 0.00 30.57 2.01
871 978 3.501458 GACGTGCCTAGCCCGGATC 62.501 68.421 0.73 0.00 0.00 3.36
1019 1297 4.880426 GGCTCCCCTCCCGATCCA 62.880 72.222 0.00 0.00 0.00 3.41
1043 1321 4.207281 CGCGGCGGAGATCCTTCA 62.207 66.667 15.84 0.00 0.00 3.02
1219 1497 3.315142 GATGCACCTCTCCGCCACA 62.315 63.158 0.00 0.00 0.00 4.17
1228 1506 3.701604 CTCCGCCACAGAGTACGGC 62.702 68.421 0.00 0.00 45.23 5.68
1308 1588 2.253452 CTGCTTGGTCTGCGTTGC 59.747 61.111 0.00 0.00 0.00 4.17
1372 1652 7.042523 CGATTGGCCAATTGGAGATTTATTTTC 60.043 37.037 31.13 14.45 37.39 2.29
1373 1653 6.872585 TGGCCAATTGGAGATTTATTTTCT 57.127 33.333 29.02 0.00 37.39 2.52
1374 1654 7.256494 TGGCCAATTGGAGATTTATTTTCTT 57.744 32.000 29.02 0.00 37.39 2.52
1375 1655 7.330262 TGGCCAATTGGAGATTTATTTTCTTC 58.670 34.615 29.02 3.92 37.39 2.87
1586 1866 1.734465 GTCATGGCAACTCTGTAGCAC 59.266 52.381 0.00 0.00 37.61 4.40
1647 1937 1.191535 CATCCACTCCCACCTTACGA 58.808 55.000 0.00 0.00 0.00 3.43
1666 1956 1.063174 GATTTCAGCCATCTGTGACGC 59.937 52.381 0.00 0.00 41.10 5.19
1669 1959 2.125912 AGCCATCTGTGACGCGTC 60.126 61.111 31.66 31.66 0.00 5.19
1670 1960 3.188786 GCCATCTGTGACGCGTCC 61.189 66.667 34.34 25.11 0.00 4.79
1738 2028 7.867909 GTGCTCTTGTGCTATGATATACAGTAA 59.132 37.037 0.00 0.00 0.00 2.24
1804 2094 9.034544 TCTGTATTGTGATCGTATTTCTGATTG 57.965 33.333 0.00 0.00 0.00 2.67
2015 2305 0.403655 TATCAAACCAGTGCAGGGCA 59.596 50.000 4.26 0.00 35.60 5.36
2538 2828 8.296713 GCATTACATCTGAGGTAAAAACTTTGA 58.703 33.333 17.45 0.00 34.67 2.69
2607 2897 2.671130 TGTCATGCGAGCTTCATGTA 57.329 45.000 21.63 13.53 41.40 2.29
2697 2987 7.708752 TCTTGAGGATTTTTACAAATTTTGCGT 59.291 29.630 9.04 0.00 32.35 5.24
2931 3248 2.462456 TTCACAGACATCTGACTGCC 57.538 50.000 15.76 0.00 46.59 4.85
2989 3306 1.008309 GACTAGAGATGACCGCCGC 60.008 63.158 0.00 0.00 0.00 6.53
3098 3416 6.427853 TGCATGTGGTTATAGTAATCTGATGC 59.572 38.462 0.00 0.00 0.00 3.91
3166 3484 0.623723 TGACCAGGTTTATCCCCTGC 59.376 55.000 0.00 0.00 46.73 4.85
3236 3554 7.633361 TCAGTTGTCTAAACACGAAGTTATC 57.367 36.000 0.00 0.00 41.61 1.75
3406 3724 6.322491 GTGAGGTCTTTTAAACATACCATGC 58.678 40.000 12.82 5.22 32.43 4.06
3799 4118 8.847196 TCGCTATGATAGTAACAACAGTCTATT 58.153 33.333 0.92 0.00 0.00 1.73
3800 4119 9.464714 CGCTATGATAGTAACAACAGTCTATTT 57.535 33.333 0.92 0.00 0.00 1.40
3832 4151 8.893219 TGTGTTGATAATTATTGCCAAAAACA 57.107 26.923 0.00 5.56 0.00 2.83
4050 4370 2.488153 GGCATAAGTCAAACTCGGCTTT 59.512 45.455 0.00 0.00 0.00 3.51
4139 4459 6.934645 TCATTCTGTCATACGGTTCTTTTCTT 59.065 34.615 0.00 0.00 0.00 2.52
4273 4593 5.868801 GCATTTGGCAAGCTAACATTTTAGA 59.131 36.000 0.00 0.00 43.97 2.10
4275 4595 7.464977 GCATTTGGCAAGCTAACATTTTAGATG 60.465 37.037 0.00 2.46 43.97 2.90
4471 4795 8.213518 TGTGGAGATGATAATAAAAAGAGCAC 57.786 34.615 0.00 0.00 0.00 4.40
4487 4811 4.583871 AGAGCACAGGGAAATCTTAACAG 58.416 43.478 0.00 0.00 0.00 3.16
4593 4917 3.814842 CCACGCATGAATTATTCTGGCTA 59.185 43.478 15.27 0.00 0.00 3.93
4798 5122 8.882415 AGGTTGACCTTATATGTATGTTTACG 57.118 34.615 0.00 0.00 46.09 3.18
4909 5233 4.902448 AGTTCTCTAGAAGGTCACTGGTTT 59.098 41.667 0.00 0.00 34.27 3.27
4962 5296 6.808321 ACTATTGGTAGGCTGATTTAGTCA 57.192 37.500 0.00 0.00 31.82 3.41
5084 5819 6.335777 TGCACATGATTCTATAGATCCATCG 58.664 40.000 2.58 7.63 0.00 3.84
5086 5821 6.815641 GCACATGATTCTATAGATCCATCGTT 59.184 38.462 2.58 0.00 0.00 3.85
5127 5864 2.038557 ACTTGTGAGTGCCCGATAGTTT 59.961 45.455 0.00 0.00 33.99 2.66
5191 5946 4.085357 TGTCTCTGTGTGCCACTATTTT 57.915 40.909 0.00 0.00 35.11 1.82
5211 5991 7.693969 ATTTTGGACCTCAACTCTAGAATTG 57.306 36.000 7.62 7.62 34.67 2.32
5216 5996 4.837972 ACCTCAACTCTAGAATTGAAGGC 58.162 43.478 21.84 0.00 34.52 4.35
5360 6143 0.759436 AGAACAGGGTCCACGACAGT 60.759 55.000 0.00 0.00 33.68 3.55
5385 6168 1.134220 TGCCGATCTTTTAATCGCCCT 60.134 47.619 0.91 0.00 45.56 5.19
5420 6205 1.269723 GGTTGTACAAAAGGCCTGCTC 59.730 52.381 5.69 0.00 0.00 4.26
5570 6356 1.081094 GGCGCAGTTGTACGGTAAAT 58.919 50.000 10.83 0.00 0.00 1.40
5715 6507 2.638480 TGGAACTTGTGCAGCTTAGT 57.362 45.000 0.00 0.00 0.00 2.24
5752 6544 2.741930 GGGCACCGTCGTTAACTAC 58.258 57.895 3.71 1.87 40.86 2.73
5765 6557 6.583806 CGTCGTTAACTACTGTGTATTTTCCT 59.416 38.462 8.45 0.00 0.00 3.36
5789 6581 2.987232 CCTCCTGGCTTTGTACCTTAC 58.013 52.381 0.00 0.00 0.00 2.34
5790 6582 2.304761 CCTCCTGGCTTTGTACCTTACA 59.695 50.000 0.00 0.00 36.79 2.41
5791 6583 3.054361 CCTCCTGGCTTTGTACCTTACAT 60.054 47.826 0.00 0.00 38.68 2.29
5792 6584 4.163458 CCTCCTGGCTTTGTACCTTACATA 59.837 45.833 0.00 0.00 38.68 2.29
5793 6585 5.338871 CCTCCTGGCTTTGTACCTTACATAA 60.339 44.000 0.00 0.00 38.68 1.90
5822 6614 9.947433 AAAGAAATAAATCATGAAAATGCAGGA 57.053 25.926 0.00 0.00 32.72 3.86
5829 6621 7.649533 AATCATGAAAATGCAGGACTATGAA 57.350 32.000 0.00 0.00 30.77 2.57
5830 6622 7.649533 ATCATGAAAATGCAGGACTATGAAA 57.350 32.000 0.00 0.00 30.77 2.69
5832 6624 7.894708 TCATGAAAATGCAGGACTATGAAAAA 58.105 30.769 0.00 0.00 0.00 1.94
5833 6625 8.533657 TCATGAAAATGCAGGACTATGAAAAAT 58.466 29.630 0.00 0.00 0.00 1.82
5834 6626 9.806203 CATGAAAATGCAGGACTATGAAAAATA 57.194 29.630 0.00 0.00 0.00 1.40
5836 6628 9.859427 TGAAAATGCAGGACTATGAAAAATAAG 57.141 29.630 0.00 0.00 0.00 1.73
5840 6632 7.572523 TGCAGGACTATGAAAAATAAGATGG 57.427 36.000 0.00 0.00 0.00 3.51
5841 6633 6.039717 TGCAGGACTATGAAAAATAAGATGGC 59.960 38.462 0.00 0.00 0.00 4.40
5842 6634 6.515696 GCAGGACTATGAAAAATAAGATGGCC 60.516 42.308 0.00 0.00 0.00 5.36
5843 6635 6.547141 CAGGACTATGAAAAATAAGATGGCCA 59.453 38.462 8.56 8.56 0.00 5.36
5845 6637 7.232127 AGGACTATGAAAAATAAGATGGCCATG 59.768 37.037 26.56 5.61 0.00 3.66
5846 6638 6.752168 ACTATGAAAAATAAGATGGCCATGC 58.248 36.000 26.56 14.84 0.00 4.06
5847 6639 4.044336 TGAAAAATAAGATGGCCATGCG 57.956 40.909 26.56 0.00 0.00 4.73
5849 6641 3.996150 AAAATAAGATGGCCATGCGAG 57.004 42.857 26.56 0.00 0.00 5.03
5850 6642 2.645838 AATAAGATGGCCATGCGAGT 57.354 45.000 26.56 3.45 0.00 4.18
5851 6643 3.769739 AATAAGATGGCCATGCGAGTA 57.230 42.857 26.56 7.89 0.00 2.59
5852 6644 3.988976 ATAAGATGGCCATGCGAGTAT 57.011 42.857 26.56 9.89 0.00 2.12
5853 6645 5.420725 AATAAGATGGCCATGCGAGTATA 57.579 39.130 26.56 5.61 0.00 1.47
5854 6646 3.988976 AAGATGGCCATGCGAGTATAT 57.011 42.857 26.56 0.00 0.00 0.86
5855 6647 3.988976 AGATGGCCATGCGAGTATATT 57.011 42.857 26.56 0.00 0.00 1.28
5856 6648 4.292186 AGATGGCCATGCGAGTATATTT 57.708 40.909 26.56 0.00 0.00 1.40
5857 6649 4.655963 AGATGGCCATGCGAGTATATTTT 58.344 39.130 26.56 0.00 0.00 1.82
5858 6650 5.804639 AGATGGCCATGCGAGTATATTTTA 58.195 37.500 26.56 0.00 0.00 1.52
5859 6651 5.643777 AGATGGCCATGCGAGTATATTTTAC 59.356 40.000 26.56 1.96 0.00 2.01
5860 6652 3.743911 TGGCCATGCGAGTATATTTTACG 59.256 43.478 0.00 0.00 0.00 3.18
5868 6660 6.686130 GCGAGTATATTTTACGCATGTACT 57.314 37.500 0.00 0.00 46.75 2.73
5869 6661 6.739561 GCGAGTATATTTTACGCATGTACTC 58.260 40.000 0.00 7.45 46.75 2.59
5870 6662 6.183359 GCGAGTATATTTTACGCATGTACTCC 60.183 42.308 0.00 3.34 46.75 3.85
5871 6663 6.307318 CGAGTATATTTTACGCATGTACTCCC 59.693 42.308 10.38 0.00 40.03 4.30
5872 6664 7.299246 AGTATATTTTACGCATGTACTCCCT 57.701 36.000 0.00 0.00 0.00 4.20
5873 6665 7.732996 AGTATATTTTACGCATGTACTCCCTT 58.267 34.615 0.00 0.00 0.00 3.95
5874 6666 7.871463 AGTATATTTTACGCATGTACTCCCTTC 59.129 37.037 0.00 0.00 0.00 3.46
5875 6667 2.572191 TTACGCATGTACTCCCTTCG 57.428 50.000 0.00 0.00 0.00 3.79
5876 6668 1.466856 TACGCATGTACTCCCTTCGT 58.533 50.000 0.00 0.00 0.00 3.85
5913 6705 5.458015 AGCGTTTACCAATTTCTTTACAGC 58.542 37.500 0.00 0.00 0.00 4.40
5914 6706 4.319901 GCGTTTACCAATTTCTTTACAGCG 59.680 41.667 0.00 0.00 0.00 5.18
5915 6707 4.849383 CGTTTACCAATTTCTTTACAGCGG 59.151 41.667 0.00 0.00 0.00 5.52
5916 6708 5.158494 GTTTACCAATTTCTTTACAGCGGG 58.842 41.667 0.00 0.00 0.00 6.13
5917 6709 3.149005 ACCAATTTCTTTACAGCGGGA 57.851 42.857 0.00 0.00 0.00 5.14
5918 6710 3.081804 ACCAATTTCTTTACAGCGGGAG 58.918 45.455 0.00 0.00 0.00 4.30
5932 6724 2.510768 CGGGAGCAAGTGATAGTACC 57.489 55.000 0.00 0.00 0.00 3.34
5933 6725 1.754803 CGGGAGCAAGTGATAGTACCA 59.245 52.381 0.00 0.00 0.00 3.25
5934 6726 2.365617 CGGGAGCAAGTGATAGTACCAT 59.634 50.000 0.00 0.00 0.00 3.55
5935 6727 3.181465 CGGGAGCAAGTGATAGTACCATT 60.181 47.826 0.00 0.00 0.00 3.16
5936 6728 4.683400 CGGGAGCAAGTGATAGTACCATTT 60.683 45.833 0.00 0.00 0.00 2.32
5937 6729 5.193679 GGGAGCAAGTGATAGTACCATTTT 58.806 41.667 0.00 0.00 0.00 1.82
5938 6730 6.354130 GGGAGCAAGTGATAGTACCATTTTA 58.646 40.000 0.00 0.00 0.00 1.52
5939 6731 6.998673 GGGAGCAAGTGATAGTACCATTTTAT 59.001 38.462 0.00 0.00 0.00 1.40
5940 6732 7.502561 GGGAGCAAGTGATAGTACCATTTTATT 59.497 37.037 0.00 0.00 0.00 1.40
5941 6733 8.903820 GGAGCAAGTGATAGTACCATTTTATTT 58.096 33.333 0.00 0.00 0.00 1.40
5996 6790 7.795734 ACGTACGTGATAGTATCATTAAACTCG 59.204 37.037 22.14 14.02 42.04 4.18
6044 6838 9.544314 CGTATATATATTTATCTCGGCAGCTAC 57.456 37.037 0.00 0.00 0.00 3.58
6045 6839 9.544314 GTATATATATTTATCTCGGCAGCTACG 57.456 37.037 0.00 3.77 0.00 3.51
6046 6840 2.440539 ATTTATCTCGGCAGCTACGG 57.559 50.000 9.72 0.00 0.00 4.02
6047 6841 1.108776 TTTATCTCGGCAGCTACGGT 58.891 50.000 9.72 0.00 0.00 4.83
6048 6842 0.666913 TTATCTCGGCAGCTACGGTC 59.333 55.000 9.72 0.00 0.00 4.79
6117 6914 0.726827 ACGGACGCTGCATTTACATG 59.273 50.000 0.00 0.00 0.00 3.21
6247 7056 1.296715 CCACTTGAACCCCTCCTCG 59.703 63.158 0.00 0.00 0.00 4.63
6326 7147 1.280421 GCTTCTCCTTGTGGTCCTGAT 59.720 52.381 0.00 0.00 34.23 2.90
6354 7184 2.294512 CTCCTTTCACCACCTTTTCTGC 59.705 50.000 0.00 0.00 0.00 4.26
6389 7219 2.093394 TGTTTCCTGTCGTCCACTTTCA 60.093 45.455 0.00 0.00 0.00 2.69
6409 7239 3.723922 GCCGGGGGTTCCTTGCTA 61.724 66.667 2.18 0.00 0.00 3.49
6410 7240 2.271173 CCGGGGGTTCCTTGCTAC 59.729 66.667 0.00 0.00 0.00 3.58
6411 7241 2.298661 CCGGGGGTTCCTTGCTACT 61.299 63.158 0.00 0.00 0.00 2.57
6412 7242 1.221021 CGGGGGTTCCTTGCTACTC 59.779 63.158 0.00 0.00 0.00 2.59
6413 7243 1.221021 GGGGGTTCCTTGCTACTCG 59.779 63.158 0.00 0.00 0.00 4.18
6414 7244 1.449778 GGGGTTCCTTGCTACTCGC 60.450 63.158 0.00 0.00 39.77 5.03
6415 7245 1.597461 GGGTTCCTTGCTACTCGCT 59.403 57.895 0.00 0.00 40.11 4.93
6416 7246 0.741221 GGGTTCCTTGCTACTCGCTG 60.741 60.000 0.00 0.00 40.11 5.18
6417 7247 1.362406 GGTTCCTTGCTACTCGCTGC 61.362 60.000 0.00 0.00 40.11 5.25
6418 7248 0.670546 GTTCCTTGCTACTCGCTGCA 60.671 55.000 0.00 0.00 40.11 4.41
6419 7249 0.390340 TTCCTTGCTACTCGCTGCAG 60.390 55.000 10.11 10.11 40.46 4.41
6420 7250 1.079543 CCTTGCTACTCGCTGCAGT 60.080 57.895 16.64 5.27 40.46 4.40
6421 7251 0.671781 CCTTGCTACTCGCTGCAGTT 60.672 55.000 16.64 0.00 40.46 3.16
6422 7252 1.151668 CTTGCTACTCGCTGCAGTTT 58.848 50.000 16.64 0.00 40.46 2.66
6423 7253 0.867746 TTGCTACTCGCTGCAGTTTG 59.132 50.000 16.64 7.93 40.46 2.93
6424 7254 0.950555 TGCTACTCGCTGCAGTTTGG 60.951 55.000 16.64 6.11 40.11 3.28
6425 7255 0.951040 GCTACTCGCTGCAGTTTGGT 60.951 55.000 16.64 11.54 35.14 3.67
6426 7256 1.071605 CTACTCGCTGCAGTTTGGTC 58.928 55.000 16.64 0.00 0.00 4.02
6427 7257 0.320421 TACTCGCTGCAGTTTGGTCC 60.320 55.000 16.64 0.00 0.00 4.46
6428 7258 1.302033 CTCGCTGCAGTTTGGTCCT 60.302 57.895 16.64 0.00 0.00 3.85
6429 7259 0.886490 CTCGCTGCAGTTTGGTCCTT 60.886 55.000 16.64 0.00 0.00 3.36
6430 7260 1.165907 TCGCTGCAGTTTGGTCCTTG 61.166 55.000 16.64 0.00 0.00 3.61
6441 7271 2.266055 GTCCTTGGCCGTCTCCTG 59.734 66.667 0.00 0.00 0.00 3.86
6443 7273 1.841556 TCCTTGGCCGTCTCCTGTT 60.842 57.895 0.00 0.00 0.00 3.16
6516 7349 3.333680 TCCTGGCTAACCTTGGATTTCTT 59.666 43.478 0.00 0.00 35.38 2.52
6523 7356 5.236695 GCTAACCTTGGATTTCTTATCCGTC 59.763 44.000 0.00 0.00 41.03 4.79
6528 7361 3.788937 TGGATTTCTTATCCGTCGGTTC 58.211 45.455 11.88 0.00 41.03 3.62
6552 7385 4.500116 GACAGCGTCCGAGGCCTC 62.500 72.222 23.79 23.79 0.00 4.70
6554 7387 3.842923 CAGCGTCCGAGGCCTCAT 61.843 66.667 31.67 7.60 0.00 2.90
6555 7388 3.077556 AGCGTCCGAGGCCTCATT 61.078 61.111 31.67 7.63 0.00 2.57
6556 7389 2.586357 GCGTCCGAGGCCTCATTC 60.586 66.667 31.67 18.58 0.00 2.67
6557 7390 3.082579 GCGTCCGAGGCCTCATTCT 62.083 63.158 31.67 0.00 0.00 2.40
6558 7391 1.066587 CGTCCGAGGCCTCATTCTC 59.933 63.158 31.67 15.25 0.00 2.87
6559 7392 1.667154 CGTCCGAGGCCTCATTCTCA 61.667 60.000 31.67 5.91 0.00 3.27
6560 7393 0.179097 GTCCGAGGCCTCATTCTCAC 60.179 60.000 31.67 14.02 0.00 3.51
6561 7394 0.324738 TCCGAGGCCTCATTCTCACT 60.325 55.000 31.67 0.00 0.00 3.41
6562 7395 0.179089 CCGAGGCCTCATTCTCACTG 60.179 60.000 31.67 12.17 0.00 3.66
6563 7396 0.179089 CGAGGCCTCATTCTCACTGG 60.179 60.000 31.67 8.04 0.00 4.00
6564 7397 0.179936 GAGGCCTCATTCTCACTGGG 59.820 60.000 28.43 0.00 0.00 4.45
6565 7398 1.452833 GGCCTCATTCTCACTGGGC 60.453 63.158 0.00 0.00 38.92 5.36
6566 7399 1.817099 GCCTCATTCTCACTGGGCG 60.817 63.158 0.00 0.00 0.00 6.13
6567 7400 1.153289 CCTCATTCTCACTGGGCGG 60.153 63.158 0.00 0.00 0.00 6.13
6568 7401 1.153289 CTCATTCTCACTGGGCGGG 60.153 63.158 0.00 0.00 0.00 6.13
6569 7402 2.124570 CATTCTCACTGGGCGGGG 60.125 66.667 0.00 0.00 0.00 5.73
6570 7403 3.411517 ATTCTCACTGGGCGGGGG 61.412 66.667 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 1.139163 GTCCGCACCAATTTTTGCAG 58.861 50.000 8.41 0.00 38.76 4.41
55 56 4.386951 CCCGACATGTCCGCACCA 62.387 66.667 20.03 0.00 0.00 4.17
74 75 1.135731 CTGTCGTCGTCTGCCTCTC 59.864 63.158 0.00 0.00 0.00 3.20
91 92 1.670406 CTCCACTCGCTGCAAAGCT 60.670 57.895 0.00 0.00 0.00 3.74
94 95 0.884704 GTTCCTCCACTCGCTGCAAA 60.885 55.000 0.00 0.00 0.00 3.68
162 163 7.502060 TCTCCATAACATCTTCTTCCTTCTT 57.498 36.000 0.00 0.00 0.00 2.52
163 164 7.502060 TTCTCCATAACATCTTCTTCCTTCT 57.498 36.000 0.00 0.00 0.00 2.85
176 177 4.069304 CAACCCTTCGTTTCTCCATAACA 58.931 43.478 0.00 0.00 29.93 2.41
185 186 2.940410 TGTCTTCACAACCCTTCGTTTC 59.060 45.455 0.00 0.00 29.93 2.78
186 187 2.681344 GTGTCTTCACAACCCTTCGTTT 59.319 45.455 0.00 0.00 43.37 3.60
229 231 1.830145 CACGAGGTCCTATTGGGGG 59.170 63.158 0.00 0.00 35.33 5.40
234 236 2.104331 CGCGCACGAGGTCCTATT 59.896 61.111 8.75 0.00 43.93 1.73
253 255 0.817634 TTGTCCACAGTTTCGGCCTG 60.818 55.000 0.00 0.00 36.01 4.85
269 271 1.405526 CGATTCCAGATGGTCGGTTGT 60.406 52.381 0.00 0.00 32.18 3.32
272 274 0.902531 AACGATTCCAGATGGTCGGT 59.097 50.000 14.20 6.70 37.82 4.69
273 275 2.024176 AAACGATTCCAGATGGTCGG 57.976 50.000 14.20 0.33 37.82 4.79
282 284 6.280643 CACATCTAGATGGTAAACGATTCCA 58.719 40.000 31.19 0.00 42.91 3.53
299 301 1.691482 GGTCTGGGTAGGGCACATCTA 60.691 57.143 0.00 0.00 0.00 1.98
313 315 0.839946 AGGATTCGGATTGGGTCTGG 59.160 55.000 0.00 0.00 33.78 3.86
323 325 8.740123 TTATTTTTATGCACTAAGGATTCGGA 57.260 30.769 0.00 0.00 0.00 4.55
324 326 9.612620 GATTATTTTTATGCACTAAGGATTCGG 57.387 33.333 0.00 0.00 0.00 4.30
326 328 9.612620 CCGATTATTTTTATGCACTAAGGATTC 57.387 33.333 0.00 0.00 0.00 2.52
327 329 9.131791 ACCGATTATTTTTATGCACTAAGGATT 57.868 29.630 0.00 0.00 0.00 3.01
329 331 8.514330 AACCGATTATTTTTATGCACTAAGGA 57.486 30.769 0.00 0.00 0.00 3.36
349 352 8.761575 AGTCGATACAAAATTTAGTAAACCGA 57.238 30.769 0.00 0.00 0.00 4.69
412 419 9.709387 CCTCCCTTTCCTTCCTTTATAATTTTA 57.291 33.333 0.00 0.00 0.00 1.52
413 420 8.406643 TCCTCCCTTTCCTTCCTTTATAATTTT 58.593 33.333 0.00 0.00 0.00 1.82
414 421 7.950803 TCCTCCCTTTCCTTCCTTTATAATTT 58.049 34.615 0.00 0.00 0.00 1.82
415 422 7.539798 TCCTCCCTTTCCTTCCTTTATAATT 57.460 36.000 0.00 0.00 0.00 1.40
416 423 7.202326 GGATCCTCCCTTTCCTTCCTTTATAAT 60.202 40.741 3.84 0.00 0.00 1.28
417 424 6.102762 GGATCCTCCCTTTCCTTCCTTTATAA 59.897 42.308 3.84 0.00 0.00 0.98
446 453 2.096466 GCAAACTTTTAACAATGGCCGC 60.096 45.455 0.00 0.00 0.00 6.53
447 454 3.389221 AGCAAACTTTTAACAATGGCCG 58.611 40.909 0.00 0.00 0.00 6.13
457 465 6.693315 ACAAGCACTAGAAGCAAACTTTTA 57.307 33.333 12.97 0.00 35.82 1.52
460 468 6.234177 AGATACAAGCACTAGAAGCAAACTT 58.766 36.000 12.97 0.00 39.43 2.66
473 481 2.076863 AGCCGACAAAGATACAAGCAC 58.923 47.619 0.00 0.00 0.00 4.40
474 482 2.076100 CAGCCGACAAAGATACAAGCA 58.924 47.619 0.00 0.00 0.00 3.91
478 486 1.542472 TCGACAGCCGACAAAGATACA 59.458 47.619 0.00 0.00 43.23 2.29
489 497 1.199327 TCAGAAGTAACTCGACAGCCG 59.801 52.381 0.00 0.00 40.25 5.52
490 498 3.057456 TCTTCAGAAGTAACTCGACAGCC 60.057 47.826 10.09 0.00 0.00 4.85
491 499 4.083217 TCTCTTCAGAAGTAACTCGACAGC 60.083 45.833 10.09 0.00 0.00 4.40
492 500 5.180492 ACTCTCTTCAGAAGTAACTCGACAG 59.820 44.000 10.09 0.00 0.00 3.51
493 501 5.049336 CACTCTCTTCAGAAGTAACTCGACA 60.049 44.000 10.09 0.00 0.00 4.35
494 502 5.049267 ACACTCTCTTCAGAAGTAACTCGAC 60.049 44.000 10.09 0.00 0.00 4.20
495 503 5.064558 ACACTCTCTTCAGAAGTAACTCGA 58.935 41.667 10.09 0.00 0.00 4.04
496 504 5.365403 ACACTCTCTTCAGAAGTAACTCG 57.635 43.478 10.09 0.00 0.00 4.18
575 583 5.326900 TGGGTAAGTCATATATAGCGACCA 58.673 41.667 10.15 0.00 0.00 4.02
590 598 3.122480 TGGGTCATGATGATGGGTAAGT 58.878 45.455 0.00 0.00 0.00 2.24
597 605 8.324306 AGGTATATAAACTGGGTCATGATGATG 58.676 37.037 0.00 0.00 0.00 3.07
699 800 9.883142 TTTTAGTTGATCAATGTGAACCTTTTT 57.117 25.926 12.12 0.00 0.00 1.94
700 801 9.883142 TTTTTAGTTGATCAATGTGAACCTTTT 57.117 25.926 12.12 0.00 0.00 2.27
777 878 3.445096 CCAGCCAGGAGACAAAAATTAGG 59.555 47.826 0.00 0.00 41.22 2.69
779 880 2.825532 GCCAGCCAGGAGACAAAAATTA 59.174 45.455 0.00 0.00 41.22 1.40
781 882 1.260544 GCCAGCCAGGAGACAAAAAT 58.739 50.000 0.00 0.00 41.22 1.82
903 1010 1.251251 CCTTCTCACAAGCCAAAGGG 58.749 55.000 0.00 0.00 34.19 3.95
904 1011 0.600057 GCCTTCTCACAAGCCAAAGG 59.400 55.000 0.00 0.00 39.59 3.11
905 1012 0.239347 CGCCTTCTCACAAGCCAAAG 59.761 55.000 0.00 0.00 0.00 2.77
916 1023 3.426829 GCCAGAAAAGAATTCGCCTTCTC 60.427 47.826 13.53 4.51 34.40 2.87
917 1024 2.489722 GCCAGAAAAGAATTCGCCTTCT 59.510 45.455 11.62 11.62 37.06 2.85
1032 1310 2.829741 CGGAGGAATGAAGGATCTCC 57.170 55.000 0.00 0.00 40.28 3.71
1219 1497 0.469518 GGAGGTATGGGCCGTACTCT 60.470 60.000 29.75 24.64 0.00 3.24
1228 1506 1.784358 TACCGTTCTGGAGGTATGGG 58.216 55.000 0.00 0.00 42.00 4.00
1308 1588 0.875728 ACGGGATCGCGAATCTCTAG 59.124 55.000 35.09 7.35 40.63 2.43
1372 1652 7.526359 GCAGTCTCCCTTATTATCCCTAAGAAG 60.526 44.444 0.00 0.00 36.40 2.85
1373 1653 6.270231 GCAGTCTCCCTTATTATCCCTAAGAA 59.730 42.308 0.00 0.00 0.00 2.52
1374 1654 5.780793 GCAGTCTCCCTTATTATCCCTAAGA 59.219 44.000 0.00 0.00 0.00 2.10
1375 1655 5.544176 TGCAGTCTCCCTTATTATCCCTAAG 59.456 44.000 0.00 0.00 0.00 2.18
1380 1660 3.555168 CGGTGCAGTCTCCCTTATTATCC 60.555 52.174 0.00 0.00 0.00 2.59
1388 1668 4.008933 GCACGGTGCAGTCTCCCT 62.009 66.667 27.10 0.00 44.26 4.20
1537 1817 5.433526 GGCTGTGGGAAATACAGTATAACA 58.566 41.667 6.95 0.00 45.60 2.41
1586 1866 1.773391 ATCAGGGGGATCAGGCTGG 60.773 63.158 15.73 0.00 0.00 4.85
1647 1937 1.089920 GCGTCACAGATGGCTGAAAT 58.910 50.000 0.00 0.00 45.17 2.17
1669 1959 0.958382 TTGGGCGAATTCGTCTTGGG 60.958 55.000 29.41 1.18 44.45 4.12
1670 1960 1.094785 ATTGGGCGAATTCGTCTTGG 58.905 50.000 29.41 1.92 44.45 3.61
1683 1973 6.463995 TGGAACTGATGTAATAAATTGGGC 57.536 37.500 0.00 0.00 0.00 5.36
1738 2028 5.220662 GCATAGAACAAACATACACAGCGAT 60.221 40.000 0.00 0.00 0.00 4.58
1804 2094 2.751806 CAAGGGAGAAGGTTCTGCAATC 59.248 50.000 12.61 0.00 46.10 2.67
1939 2229 1.602851 GCATCCTAGCAGTGCTTCATG 59.397 52.381 25.23 21.38 40.44 3.07
2015 2305 3.368116 CCGTTAGGATCAAACCGAAGTCT 60.368 47.826 0.00 0.00 41.02 3.24
2538 2828 4.420522 AAAATGGACAGCACAATGGTTT 57.579 36.364 0.00 0.00 0.00 3.27
2607 2897 7.236225 TCATGTCATCCAGATCCTACACAATAT 59.764 37.037 0.00 0.00 0.00 1.28
2697 2987 7.450074 ACATTTTCAGTCAGAAGTACATACCA 58.550 34.615 0.00 0.00 37.57 3.25
3069 3387 9.237187 TCAGATTACTATAACCACATGCAAAAA 57.763 29.630 0.00 0.00 0.00 1.94
3098 3416 2.027561 TGACCATACGGAAACCTGGAAG 60.028 50.000 0.00 0.00 35.59 3.46
3832 4151 3.255642 GCACCATCAACAAAGTGGTACAT 59.744 43.478 0.00 0.00 44.09 2.29
3873 4192 1.276989 ACTTGCAGGCAAATTGATGGG 59.723 47.619 8.20 0.00 35.33 4.00
3947 4267 1.003355 CCAGGCACACAGGTCGATT 60.003 57.895 0.00 0.00 0.00 3.34
4050 4370 4.384056 GCTGATATAAAAGAGCAGCCAGA 58.616 43.478 0.00 0.00 44.50 3.86
4139 4459 4.694982 ACACATGATGTTAATCTTCGTGCA 59.305 37.500 0.00 0.00 38.98 4.57
4273 4593 6.426937 GGACTGTGTAAATGTGTTACTGTCAT 59.573 38.462 0.00 0.00 40.05 3.06
4275 4595 5.989777 AGGACTGTGTAAATGTGTTACTGTC 59.010 40.000 0.00 0.00 38.61 3.51
4471 4795 4.019174 ACATGCCTGTTAAGATTTCCCTG 58.981 43.478 0.00 0.00 28.70 4.45
4487 4811 5.036117 TCCCTCTTGAAATACTACATGCC 57.964 43.478 0.00 0.00 0.00 4.40
4745 5069 5.633830 ATTGTACCTGCTGTTCAAATGAG 57.366 39.130 3.88 0.00 37.71 2.90
4823 5147 5.003160 TGACCATCTGTTGTTATTCCTGTG 58.997 41.667 0.00 0.00 0.00 3.66
4962 5296 2.365582 CTGGGCGTGTTATAGGCTTTT 58.634 47.619 0.00 0.00 40.00 2.27
4992 5723 1.860950 CACGCTGGTATGCATCAGTAC 59.139 52.381 14.82 3.38 33.81 2.73
5093 5828 6.426937 GGCACTCACAAGTTTCAAATAGAGTA 59.573 38.462 0.00 0.00 33.72 2.59
5191 5946 5.046304 CCTTCAATTCTAGAGTTGAGGTCCA 60.046 44.000 27.27 15.27 38.11 4.02
5211 5991 1.227497 CATCAGAGCTCCCGCCTTC 60.227 63.158 10.93 0.00 36.60 3.46
5216 5996 1.110442 AGAGAACATCAGAGCTCCCG 58.890 55.000 10.93 1.67 0.00 5.14
5385 6168 6.043854 TGTACAACCATATGCACAGTAAGA 57.956 37.500 0.00 0.00 0.00 2.10
5420 6205 3.852205 GCAATCGATTGTGCCATCATCAG 60.852 47.826 32.52 9.04 39.88 2.90
5582 6368 5.413213 CCACCCACTACGAAAATAAACATCA 59.587 40.000 0.00 0.00 0.00 3.07
5583 6369 5.675323 GCCACCCACTACGAAAATAAACATC 60.675 44.000 0.00 0.00 0.00 3.06
5584 6370 4.157105 GCCACCCACTACGAAAATAAACAT 59.843 41.667 0.00 0.00 0.00 2.71
5679 6471 8.246180 ACAAGTTCCATTTGATAATGCAGTAAG 58.754 33.333 0.00 0.00 39.87 2.34
5715 6507 3.513515 GCCCAACAATTTCCATGTCCTTA 59.486 43.478 0.00 0.00 0.00 2.69
5752 6544 4.878397 CAGGAGGCTTAGGAAAATACACAG 59.122 45.833 0.00 0.00 0.00 3.66
5799 6591 8.937634 AGTCCTGCATTTTCATGATTTATTTC 57.062 30.769 0.00 0.00 31.07 2.17
5805 6597 7.649533 TTCATAGTCCTGCATTTTCATGATT 57.350 32.000 0.00 0.00 31.07 2.57
5822 6614 6.515531 CGCATGGCCATCTTATTTTTCATAGT 60.516 38.462 17.61 0.00 0.00 2.12
5826 6618 3.698539 TCGCATGGCCATCTTATTTTTCA 59.301 39.130 17.61 0.00 0.00 2.69
5829 6621 3.290710 ACTCGCATGGCCATCTTATTTT 58.709 40.909 17.61 0.00 0.00 1.82
5830 6622 2.936202 ACTCGCATGGCCATCTTATTT 58.064 42.857 17.61 0.00 0.00 1.40
5832 6624 3.988976 ATACTCGCATGGCCATCTTAT 57.011 42.857 17.61 5.33 0.00 1.73
5833 6625 5.420725 AATATACTCGCATGGCCATCTTA 57.579 39.130 17.61 2.47 0.00 2.10
5834 6626 3.988976 ATATACTCGCATGGCCATCTT 57.011 42.857 17.61 0.00 0.00 2.40
5835 6627 3.988976 AATATACTCGCATGGCCATCT 57.011 42.857 17.61 0.00 0.00 2.90
5836 6628 5.445939 CGTAAAATATACTCGCATGGCCATC 60.446 44.000 17.61 10.14 0.00 3.51
5837 6629 4.391830 CGTAAAATATACTCGCATGGCCAT 59.608 41.667 14.09 14.09 0.00 4.40
5838 6630 3.743911 CGTAAAATATACTCGCATGGCCA 59.256 43.478 8.56 8.56 0.00 5.36
5840 6632 3.732943 GCGTAAAATATACTCGCATGGC 58.267 45.455 0.00 0.00 45.01 4.40
5845 6637 6.183359 GGAGTACATGCGTAAAATATACTCGC 60.183 42.308 0.00 0.00 45.70 5.03
5846 6638 6.307318 GGGAGTACATGCGTAAAATATACTCG 59.693 42.308 0.00 0.00 38.51 4.18
5847 6639 7.376615 AGGGAGTACATGCGTAAAATATACTC 58.623 38.462 0.00 0.00 37.43 2.59
5849 6641 7.148853 CGAAGGGAGTACATGCGTAAAATATAC 60.149 40.741 0.00 0.00 0.00 1.47
5850 6642 6.864685 CGAAGGGAGTACATGCGTAAAATATA 59.135 38.462 0.00 0.00 0.00 0.86
5851 6643 5.694910 CGAAGGGAGTACATGCGTAAAATAT 59.305 40.000 0.00 0.00 0.00 1.28
5852 6644 5.045215 CGAAGGGAGTACATGCGTAAAATA 58.955 41.667 0.00 0.00 0.00 1.40
5853 6645 3.869246 CGAAGGGAGTACATGCGTAAAAT 59.131 43.478 0.00 0.00 0.00 1.82
5854 6646 3.255725 CGAAGGGAGTACATGCGTAAAA 58.744 45.455 0.00 0.00 0.00 1.52
5855 6647 2.231964 ACGAAGGGAGTACATGCGTAAA 59.768 45.455 0.00 0.00 0.00 2.01
5856 6648 1.820519 ACGAAGGGAGTACATGCGTAA 59.179 47.619 0.00 0.00 0.00 3.18
5857 6649 1.466856 ACGAAGGGAGTACATGCGTA 58.533 50.000 0.00 0.00 0.00 4.42
5858 6650 1.466856 TACGAAGGGAGTACATGCGT 58.533 50.000 0.00 0.00 0.00 5.24
5859 6651 2.572191 TTACGAAGGGAGTACATGCG 57.428 50.000 0.00 0.00 0.00 4.73
5860 6652 4.119442 TCTTTACGAAGGGAGTACATGC 57.881 45.455 0.00 0.00 33.56 4.06
5861 6653 8.888579 ATATTTCTTTACGAAGGGAGTACATG 57.111 34.615 0.00 0.00 33.56 3.21
5866 6658 7.927092 GCTCTTATATTTCTTTACGAAGGGAGT 59.073 37.037 0.00 0.00 33.56 3.85
5867 6659 7.115095 CGCTCTTATATTTCTTTACGAAGGGAG 59.885 40.741 0.00 0.00 33.56 4.30
5868 6660 6.921857 CGCTCTTATATTTCTTTACGAAGGGA 59.078 38.462 0.00 0.00 33.56 4.20
5869 6661 6.700520 ACGCTCTTATATTTCTTTACGAAGGG 59.299 38.462 0.00 0.00 33.56 3.95
5870 6662 7.695869 ACGCTCTTATATTTCTTTACGAAGG 57.304 36.000 0.00 0.00 33.56 3.46
5873 6665 9.023967 GGTAAACGCTCTTATATTTCTTTACGA 57.976 33.333 0.00 0.00 0.00 3.43
5874 6666 8.810427 TGGTAAACGCTCTTATATTTCTTTACG 58.190 33.333 0.00 0.00 0.00 3.18
5888 6680 6.567891 GCTGTAAAGAAATTGGTAAACGCTCT 60.568 38.462 0.00 0.00 0.00 4.09
5898 6690 2.159379 GCTCCCGCTGTAAAGAAATTGG 60.159 50.000 0.00 0.00 0.00 3.16
5905 6697 0.798776 CACTTGCTCCCGCTGTAAAG 59.201 55.000 0.00 0.00 36.97 1.85
5906 6698 0.394938 TCACTTGCTCCCGCTGTAAA 59.605 50.000 0.00 0.00 36.97 2.01
5908 6700 1.409064 CTATCACTTGCTCCCGCTGTA 59.591 52.381 0.00 0.00 36.97 2.74
5910 6702 0.176680 ACTATCACTTGCTCCCGCTG 59.823 55.000 0.00 0.00 36.97 5.18
5913 6705 1.754803 TGGTACTATCACTTGCTCCCG 59.245 52.381 0.00 0.00 0.00 5.14
5914 6706 4.423625 AATGGTACTATCACTTGCTCCC 57.576 45.455 0.00 0.00 0.00 4.30
5915 6707 8.451908 AATAAAATGGTACTATCACTTGCTCC 57.548 34.615 0.00 0.00 0.00 4.70
5952 6744 9.437045 CACGTACGTACATGACTAAAATATACA 57.563 33.333 22.34 0.00 0.00 2.29
5953 6745 9.650371 TCACGTACGTACATGACTAAAATATAC 57.350 33.333 22.34 0.00 0.00 1.47
5958 6750 7.751732 ACTATCACGTACGTACATGACTAAAA 58.248 34.615 25.00 3.92 30.73 1.52
5965 6757 9.815936 TTAATGATACTATCACGTACGTACATG 57.184 33.333 22.34 20.13 43.01 3.21
5996 6790 5.347907 ACGTGAGGAATAAATTCTCGTCAAC 59.652 40.000 2.91 4.59 37.00 3.18
6027 6821 1.687123 ACCGTAGCTGCCGAGATAAAT 59.313 47.619 8.96 0.00 0.00 1.40
6028 6822 1.066605 GACCGTAGCTGCCGAGATAAA 59.933 52.381 8.96 0.00 0.00 1.40
6029 6823 0.666913 GACCGTAGCTGCCGAGATAA 59.333 55.000 8.96 0.00 0.00 1.75
6030 6824 1.504647 CGACCGTAGCTGCCGAGATA 61.505 60.000 8.96 0.00 0.00 1.98
6031 6825 2.835705 CGACCGTAGCTGCCGAGAT 61.836 63.158 8.96 0.00 0.00 2.75
6032 6826 2.857575 TACGACCGTAGCTGCCGAGA 62.858 60.000 8.96 0.00 0.00 4.04
6044 6838 0.379669 AAGCGGATGTACTACGACCG 59.620 55.000 15.22 15.22 40.44 4.79
6045 6839 1.133790 ACAAGCGGATGTACTACGACC 59.866 52.381 8.25 0.00 0.00 4.79
6046 6840 2.556534 ACAAGCGGATGTACTACGAC 57.443 50.000 8.25 1.45 0.00 4.34
6047 6841 3.059393 CGATACAAGCGGATGTACTACGA 60.059 47.826 8.25 0.00 38.53 3.43
6048 6842 3.223953 CGATACAAGCGGATGTACTACG 58.776 50.000 0.00 0.00 38.53 3.51
6117 6914 4.400884 TCTCCAGAAACTAGAGATCACTGC 59.599 45.833 2.56 0.00 31.80 4.40
6125 6922 4.023291 AGGCTCTTCTCCAGAAACTAGAG 58.977 47.826 0.00 0.00 33.07 2.43
6126 6923 4.054359 AGGCTCTTCTCCAGAAACTAGA 57.946 45.455 0.00 0.00 33.07 2.43
6127 6924 5.221422 CCATAGGCTCTTCTCCAGAAACTAG 60.221 48.000 0.00 0.00 33.07 2.57
6128 6925 4.651503 CCATAGGCTCTTCTCCAGAAACTA 59.348 45.833 0.00 0.00 33.07 2.24
6326 7147 3.184628 AGGTGGTGAAAGGAGATGATGA 58.815 45.455 0.00 0.00 0.00 2.92
6389 7219 4.060667 CAAGGAACCCCCGGCCAT 62.061 66.667 2.24 0.00 40.87 4.40
6407 7237 1.071605 GACCAAACTGCAGCGAGTAG 58.928 55.000 15.27 0.21 35.87 2.57
6408 7238 0.320421 GGACCAAACTGCAGCGAGTA 60.320 55.000 15.27 0.00 0.00 2.59
6409 7239 1.598130 GGACCAAACTGCAGCGAGT 60.598 57.895 15.27 6.28 0.00 4.18
6410 7240 0.886490 AAGGACCAAACTGCAGCGAG 60.886 55.000 15.27 3.01 0.00 5.03
6411 7241 1.148273 AAGGACCAAACTGCAGCGA 59.852 52.632 15.27 0.00 0.00 4.93
6412 7242 1.283793 CAAGGACCAAACTGCAGCG 59.716 57.895 15.27 2.10 0.00 5.18
6413 7243 1.662044 CCAAGGACCAAACTGCAGC 59.338 57.895 15.27 0.00 0.00 5.25
6414 7244 1.662044 GCCAAGGACCAAACTGCAG 59.338 57.895 13.48 13.48 0.00 4.41
6415 7245 1.832167 GGCCAAGGACCAAACTGCA 60.832 57.895 0.00 0.00 0.00 4.41
6416 7246 2.919494 CGGCCAAGGACCAAACTGC 61.919 63.158 2.24 0.00 0.00 4.40
6417 7247 1.515521 GACGGCCAAGGACCAAACTG 61.516 60.000 2.24 0.00 0.00 3.16
6418 7248 1.228154 GACGGCCAAGGACCAAACT 60.228 57.895 2.24 0.00 0.00 2.66
6419 7249 1.228154 AGACGGCCAAGGACCAAAC 60.228 57.895 2.24 0.00 0.00 2.93
6420 7250 1.072505 GAGACGGCCAAGGACCAAA 59.927 57.895 2.24 0.00 0.00 3.28
6421 7251 2.747686 GAGACGGCCAAGGACCAA 59.252 61.111 2.24 0.00 0.00 3.67
6422 7252 3.319198 GGAGACGGCCAAGGACCA 61.319 66.667 2.24 0.00 0.00 4.02
6423 7253 3.003763 AGGAGACGGCCAAGGACC 61.004 66.667 2.24 0.00 0.00 4.46
6424 7254 2.113243 AACAGGAGACGGCCAAGGAC 62.113 60.000 2.24 0.00 0.00 3.85
6425 7255 1.415672 AAACAGGAGACGGCCAAGGA 61.416 55.000 2.24 0.00 0.00 3.36
6426 7256 1.073199 AAACAGGAGACGGCCAAGG 59.927 57.895 2.24 0.00 0.00 3.61
6427 7257 0.535102 ACAAACAGGAGACGGCCAAG 60.535 55.000 2.24 0.00 0.00 3.61
6428 7258 0.817634 CACAAACAGGAGACGGCCAA 60.818 55.000 2.24 0.00 0.00 4.52
6429 7259 1.227823 CACAAACAGGAGACGGCCA 60.228 57.895 2.24 0.00 0.00 5.36
6430 7260 2.617274 GCACAAACAGGAGACGGCC 61.617 63.158 0.00 0.00 0.00 6.13
6441 7271 1.832167 TTGCAGGGGAGGCACAAAC 60.832 57.895 0.00 0.00 41.75 2.93
6443 7273 2.203480 GTTGCAGGGGAGGCACAA 60.203 61.111 0.00 0.00 41.75 3.33
6497 7330 5.445964 GGATAAGAAATCCAAGGTTAGCCA 58.554 41.667 0.00 0.00 38.09 4.75
6500 7333 5.462398 CGACGGATAAGAAATCCAAGGTTAG 59.538 44.000 4.98 0.00 38.08 2.34
6516 7349 2.404789 GCGACGAACCGACGGATA 59.595 61.111 23.38 0.00 43.80 2.59
6538 7371 3.077556 AATGAGGCCTCGGACGCT 61.078 61.111 27.43 5.32 0.00 5.07
6539 7372 2.586357 GAATGAGGCCTCGGACGC 60.586 66.667 27.43 11.25 0.00 5.19
6540 7373 1.066587 GAGAATGAGGCCTCGGACG 59.933 63.158 27.43 0.00 0.00 4.79
6541 7374 0.179097 GTGAGAATGAGGCCTCGGAC 60.179 60.000 27.43 19.29 32.30 4.79
6542 7375 0.324738 AGTGAGAATGAGGCCTCGGA 60.325 55.000 27.43 12.01 32.30 4.55
6543 7376 0.179089 CAGTGAGAATGAGGCCTCGG 60.179 60.000 27.43 4.76 32.30 4.63
6544 7377 0.179089 CCAGTGAGAATGAGGCCTCG 60.179 60.000 27.43 9.74 32.30 4.63
6545 7378 0.179936 CCCAGTGAGAATGAGGCCTC 59.820 60.000 26.78 26.78 0.00 4.70
6546 7379 1.919600 GCCCAGTGAGAATGAGGCCT 61.920 60.000 3.86 3.86 34.23 5.19
6547 7380 1.452833 GCCCAGTGAGAATGAGGCC 60.453 63.158 0.00 0.00 34.23 5.19
6548 7381 1.817099 CGCCCAGTGAGAATGAGGC 60.817 63.158 0.00 0.00 37.03 4.70
6549 7382 1.153289 CCGCCCAGTGAGAATGAGG 60.153 63.158 0.00 0.00 0.00 3.86
6550 7383 1.153289 CCCGCCCAGTGAGAATGAG 60.153 63.158 0.00 0.00 0.00 2.90
6551 7384 2.669133 CCCCGCCCAGTGAGAATGA 61.669 63.158 0.00 0.00 0.00 2.57
6552 7385 2.124570 CCCCGCCCAGTGAGAATG 60.125 66.667 0.00 0.00 0.00 2.67
6553 7386 3.411517 CCCCCGCCCAGTGAGAAT 61.412 66.667 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.