Multiple sequence alignment - TraesCS5D01G396400

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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 TraesCS5D01G396400 chr5D 100.000 5614 0 0 1 5614 464017515 464023128 0.000000e+00 10368.0
1 TraesCS5D01G396400 chr5D 92.708 96 7 0 3 98 92172991 92173086 7.580000e-29 139.0
2 TraesCS5D01G396400 chr5A 93.333 3300 151 40 760 4020 584415647 584418916 0.000000e+00 4811.0
3 TraesCS5D01G396400 chr5A 90.870 920 56 16 4094 4986 584419146 584420064 0.000000e+00 1208.0
4 TraesCS5D01G396400 chr5A 92.810 306 11 7 346 644 584415039 584415340 3.110000e-117 433.0
5 TraesCS5D01G396400 chr5A 90.000 160 13 2 5306 5462 584420493 584420652 2.650000e-48 204.0
6 TraesCS5D01G396400 chr5A 90.722 97 8 1 5 100 549221387 549221291 1.640000e-25 128.0
7 TraesCS5D01G396400 chr5A 88.889 63 6 1 4983 5044 584420151 584420213 6.030000e-10 76.8
8 TraesCS5D01G396400 chr5B 92.936 3256 162 37 1829 5042 570891677 570894906 0.000000e+00 4676.0
9 TraesCS5D01G396400 chr5B 92.308 1248 65 15 592 1826 570890409 570891638 0.000000e+00 1744.0
10 TraesCS5D01G396400 chr5B 92.105 342 22 4 256 596 570889753 570890090 1.420000e-130 477.0
11 TraesCS5D01G396400 chr5B 86.604 321 18 4 5306 5601 570895405 570895725 1.170000e-86 331.0
12 TraesCS5D01G396400 chr5B 92.308 169 11 2 42 208 570889309 570889477 7.270000e-59 239.0
13 TraesCS5D01G396400 chr5B 91.667 96 8 0 3 98 97515586 97515681 3.530000e-27 134.0
14 TraesCS5D01G396400 chr2B 92.481 133 9 1 2180 2311 579992243 579992111 7.420000e-44 189.0
15 TraesCS5D01G396400 chr2B 96.226 53 2 0 2299 2351 579992103 579992051 2.790000e-13 87.9
16 TraesCS5D01G396400 chr3A 83.108 148 19 4 92 239 108429095 108429236 4.560000e-26 130.0
17 TraesCS5D01G396400 chr6D 89.796 98 10 0 3 100 131683616 131683519 5.900000e-25 126.0
18 TraesCS5D01G396400 chr6D 90.526 95 9 0 4 98 248516034 248516128 5.900000e-25 126.0
19 TraesCS5D01G396400 chr3D 89.796 98 10 0 3 100 276508865 276508962 5.900000e-25 126.0
20 TraesCS5D01G396400 chr4D 84.615 130 15 4 1 127 344120133 344120006 2.120000e-24 124.0
21 TraesCS5D01G396400 chr6B 89.000 100 10 1 1 100 298532898 298532996 7.640000e-24 122.0
22 TraesCS5D01G396400 chr6A 83.333 120 17 3 95 212 52322779 52322661 2.140000e-19 108.0
23 TraesCS5D01G396400 chr6A 94.737 38 2 0 95 132 52328096 52328059 6.070000e-05 60.2
24 TraesCS5D01G396400 chr3B 79.470 151 26 4 95 244 341559280 341559134 9.950000e-18 102.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G396400 chr5D 464017515 464023128 5613 False 10368.00 10368 100.0000 1 5614 1 chr5D.!!$F2 5613
1 TraesCS5D01G396400 chr5A 584415039 584420652 5613 False 1346.56 4811 91.1804 346 5462 5 chr5A.!!$F1 5116
2 TraesCS5D01G396400 chr5B 570889309 570895725 6416 False 1493.40 4676 91.2522 42 5601 5 chr5B.!!$F2 5559

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
310 540 0.390860 CCGTTCCTGCTGGATAGAGG 59.609 60.000 13.72 10.33 42.81 3.69 F
638 1195 0.691748 TTATCCACCCCTACCACCCG 60.692 60.000 0.00 0.00 0.00 5.28 F
1219 2022 0.243636 ACTGCCGCCTTTGTAATTGC 59.756 50.000 0.00 0.00 0.00 3.56 F
1779 2583 1.004862 GAGCAGGGGTAGAAAGCCTTT 59.995 52.381 0.00 0.00 43.23 3.11 F
3168 4019 2.800250 CCTTCAGCTGGGAAACAAGAT 58.200 47.619 15.13 0.00 0.00 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1202 2005 0.243365 CTGCAATTACAAAGGCGGCA 59.757 50.000 13.08 0.00 0.00 5.69 R
1723 2527 0.679505 AGACAGACAACTAAGCGCCA 59.320 50.000 2.29 0.00 0.00 5.69 R
2214 3063 0.712222 GAAACTACCGTAGCACGTGC 59.288 55.000 32.79 32.79 40.58 5.34 R
3458 4309 2.582052 TGTGTTCACCTAAAAGGCCAG 58.418 47.619 5.01 0.00 39.63 4.85 R
5161 6334 0.036022 ACCTGGCAAGTTCTCTCAGC 59.964 55.000 0.00 0.00 0.00 4.26 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
80 81 9.729281 AATTTTTACATCTCCAAATTTGCATCT 57.271 25.926 12.92 0.00 0.00 2.90
147 148 8.035394 TGGTTGTCATTTAAGTTGTGCTAAAAA 58.965 29.630 0.00 0.00 0.00 1.94
148 149 9.040939 GGTTGTCATTTAAGTTGTGCTAAAAAT 57.959 29.630 0.00 0.00 0.00 1.82
151 154 9.462174 TGTCATTTAAGTTGTGCTAAAAATCTG 57.538 29.630 0.00 0.00 0.00 2.90
161 164 8.560374 GTTGTGCTAAAAATCTGTCTAAACTCT 58.440 33.333 0.00 0.00 0.00 3.24
222 249 4.420741 CCCCCTCCCCCTCTTTAG 57.579 66.667 0.00 0.00 0.00 1.85
237 264 4.211920 CTCTTTAGACCCCTCTTCTCGAT 58.788 47.826 0.00 0.00 0.00 3.59
240 267 2.358322 AGACCCCTCTTCTCGATCTC 57.642 55.000 0.00 0.00 0.00 2.75
243 270 1.566703 ACCCCTCTTCTCGATCTCTCA 59.433 52.381 0.00 0.00 0.00 3.27
248 275 4.499526 CCCTCTTCTCGATCTCTCAACATG 60.500 50.000 0.00 0.00 0.00 3.21
254 281 4.083590 TCTCGATCTCTCAACATGCTATCG 60.084 45.833 0.00 0.00 36.87 2.92
255 282 2.660715 CGATCTCTCAACATGCTATCGC 59.339 50.000 0.00 0.00 0.00 4.58
258 285 2.099098 TCTCTCAACATGCTATCGCGAA 59.901 45.455 15.24 0.00 39.65 4.70
261 288 3.682377 TCTCAACATGCTATCGCGAAAAA 59.318 39.130 15.24 0.08 39.65 1.94
262 289 3.742786 TCAACATGCTATCGCGAAAAAC 58.257 40.909 15.24 3.60 39.65 2.43
263 290 3.187432 TCAACATGCTATCGCGAAAAACA 59.813 39.130 15.24 10.07 39.65 2.83
264 291 3.822594 ACATGCTATCGCGAAAAACAA 57.177 38.095 15.24 0.00 39.65 2.83
266 293 4.541779 ACATGCTATCGCGAAAAACAAAA 58.458 34.783 15.24 0.00 39.65 2.44
268 295 4.939948 TGCTATCGCGAAAAACAAAAAC 57.060 36.364 15.24 0.00 39.65 2.43
269 296 4.602995 TGCTATCGCGAAAAACAAAAACT 58.397 34.783 15.24 0.00 39.65 2.66
277 507 6.033725 TCGCGAAAAACAAAAACTAAGAAACC 59.966 34.615 6.20 0.00 0.00 3.27
287 517 3.102052 ACTAAGAAACCGAAGCGAACA 57.898 42.857 0.00 0.00 0.00 3.18
310 540 0.390860 CCGTTCCTGCTGGATAGAGG 59.609 60.000 13.72 10.33 42.81 3.69
314 544 2.634940 GTTCCTGCTGGATAGAGGCATA 59.365 50.000 13.72 0.00 42.81 3.14
323 553 8.150827 TGCTGGATAGAGGCATAATAAGTTAT 57.849 34.615 0.00 0.00 0.00 1.89
326 556 9.737427 CTGGATAGAGGCATAATAAGTTATACG 57.263 37.037 0.00 0.00 0.00 3.06
392 623 3.139029 GGGTGTCCGTAGCAGAAAG 57.861 57.895 0.00 0.00 0.00 2.62
581 815 3.124088 CCCTCTCCTCCTCCCCTT 58.876 66.667 0.00 0.00 0.00 3.95
637 1194 1.213678 GTTTATCCACCCCTACCACCC 59.786 57.143 0.00 0.00 0.00 4.61
638 1195 0.691748 TTATCCACCCCTACCACCCG 60.692 60.000 0.00 0.00 0.00 5.28
639 1196 1.889010 TATCCACCCCTACCACCCGT 61.889 60.000 0.00 0.00 0.00 5.28
640 1197 3.712907 CCACCCCTACCACCCGTG 61.713 72.222 0.00 0.00 0.00 4.94
642 1199 4.651516 ACCCCTACCACCCGTGCT 62.652 66.667 0.00 0.00 0.00 4.40
643 1200 3.782443 CCCCTACCACCCGTGCTC 61.782 72.222 0.00 0.00 0.00 4.26
749 1307 2.905880 CGCCGGTCCTCGAGGTAT 60.906 66.667 30.17 0.00 42.43 2.73
797 1566 0.951558 CTTTGAACCCAGACCGGTTG 59.048 55.000 9.42 9.22 46.35 3.77
909 1678 6.487331 CCTCGTCTGTTCCTATGTTCTAGTAT 59.513 42.308 0.00 0.00 0.00 2.12
1120 1902 4.452733 ACGCGGCCAAGGTAGCTC 62.453 66.667 12.47 0.00 0.00 4.09
1202 2005 2.224646 GGAGGAGAGGTTGCTGAAAACT 60.225 50.000 0.00 0.00 39.06 2.66
1219 2022 0.243636 ACTGCCGCCTTTGTAATTGC 59.756 50.000 0.00 0.00 0.00 3.56
1242 2045 1.121407 CCTCCGGGATGCAGTATGGA 61.121 60.000 0.00 0.00 44.23 3.41
1495 2298 4.753107 ACTGACACGTTTCATTTCGGTATT 59.247 37.500 4.61 0.00 0.00 1.89
1496 2299 5.024768 TGACACGTTTCATTTCGGTATTG 57.975 39.130 0.00 0.00 0.00 1.90
1497 2300 4.512198 TGACACGTTTCATTTCGGTATTGT 59.488 37.500 0.00 0.00 0.00 2.71
1629 2432 5.428253 AGTCACAAGTGTGTAGTCATTGTT 58.572 37.500 11.06 0.00 45.76 2.83
1659 2462 8.609176 TGTAGTCTTAATAATCGCATGGTTTTC 58.391 33.333 0.00 0.00 0.00 2.29
1664 2467 5.659440 AATAATCGCATGGTTTTCAAGGT 57.341 34.783 0.00 0.00 0.00 3.50
1713 2517 1.138247 GGCAGCTGCTTGGAAATCG 59.862 57.895 35.82 0.00 41.70 3.34
1723 2527 1.182385 TTGGAAATCGGCCCGCTTTT 61.182 50.000 6.40 5.06 0.00 2.27
1738 2542 1.266989 GCTTTTGGCGCTTAGTTGTCT 59.733 47.619 7.64 0.00 0.00 3.41
1740 2544 1.961793 TTTGGCGCTTAGTTGTCTGT 58.038 45.000 7.64 0.00 0.00 3.41
1754 2558 2.443416 TGTCTGTCTTAGCGCTTAGGA 58.557 47.619 22.14 12.29 0.00 2.94
1773 2577 2.180276 GAGTCAGAGCAGGGGTAGAAA 58.820 52.381 0.00 0.00 0.00 2.52
1779 2583 1.004862 GAGCAGGGGTAGAAAGCCTTT 59.995 52.381 0.00 0.00 43.23 3.11
1891 2731 9.959721 AGGAGTAAGCATTAAGATAAAACTGAA 57.040 29.630 0.00 0.00 28.70 3.02
2617 3466 7.350382 TGACCTGCTTAATTAATCCCAACATA 58.650 34.615 0.00 0.00 0.00 2.29
2618 3467 7.836685 TGACCTGCTTAATTAATCCCAACATAA 59.163 33.333 0.00 0.00 0.00 1.90
2651 3500 8.243426 TGGTTCTAAGTGTTTTGCATATCATTC 58.757 33.333 0.00 0.00 0.00 2.67
2708 3559 3.081061 TGCTAACCTTACCGTACGAAGA 58.919 45.455 18.76 0.00 0.00 2.87
2709 3560 3.696051 TGCTAACCTTACCGTACGAAGAT 59.304 43.478 18.76 8.24 0.00 2.40
2784 3635 5.239306 TGTCCTTCATCAAAACTTAGCTGTG 59.761 40.000 0.00 0.00 0.00 3.66
3168 4019 2.800250 CCTTCAGCTGGGAAACAAGAT 58.200 47.619 15.13 0.00 0.00 2.40
3177 4028 4.335594 GCTGGGAAACAAGATAATAGCGTT 59.664 41.667 0.00 0.00 0.00 4.84
3243 4094 6.259550 ACATACAAGGATGCAAAGTTCTTC 57.740 37.500 0.00 0.00 0.00 2.87
3434 4285 7.347222 ACTGTATTGTATCACCCTTTCCTCATA 59.653 37.037 0.00 0.00 0.00 2.15
3458 4309 3.429410 GGCATTTGTATTGACCTTGAGCC 60.429 47.826 0.00 0.00 0.00 4.70
3703 4554 6.890293 AGAGGTACACTTTCTGAAAACTTCT 58.110 36.000 9.98 9.98 0.00 2.85
3713 4564 8.956426 ACTTTCTGAAAACTTCTGTCAATAACA 58.044 29.630 4.18 0.00 36.18 2.41
3733 4587 4.376146 ACAAATTTTGGGTGGTGATTTCG 58.624 39.130 13.42 0.00 34.12 3.46
3742 4596 2.289444 GGTGGTGATTTCGTGAAGAGGA 60.289 50.000 0.00 0.00 0.00 3.71
3748 4602 3.007940 TGATTTCGTGAAGAGGACATGGT 59.992 43.478 0.00 0.00 0.00 3.55
3772 4626 5.069516 TCCACCAGGGATAACGTTAATACTC 59.930 44.000 12.81 5.11 42.15 2.59
3778 4632 9.017509 CCAGGGATAACGTTAATACTCTGTATA 57.982 37.037 24.64 1.66 0.00 1.47
3866 4723 1.716503 AGGTGCCTTCCCCAGTTAATT 59.283 47.619 0.00 0.00 0.00 1.40
3867 4724 2.923629 AGGTGCCTTCCCCAGTTAATTA 59.076 45.455 0.00 0.00 0.00 1.40
3868 4725 3.053619 AGGTGCCTTCCCCAGTTAATTAG 60.054 47.826 0.00 0.00 0.00 1.73
3870 4727 4.569015 GGTGCCTTCCCCAGTTAATTAGAA 60.569 45.833 0.00 0.00 0.00 2.10
3871 4728 4.398358 GTGCCTTCCCCAGTTAATTAGAAC 59.602 45.833 0.00 0.00 0.00 3.01
3872 4729 4.043561 TGCCTTCCCCAGTTAATTAGAACA 59.956 41.667 0.00 0.00 0.00 3.18
3873 4730 4.398358 GCCTTCCCCAGTTAATTAGAACAC 59.602 45.833 0.00 0.00 0.00 3.32
3874 4731 5.566469 CCTTCCCCAGTTAATTAGAACACA 58.434 41.667 0.00 0.00 0.00 3.72
3905 4767 5.581126 TGTTTCTCCATTATTGTCATGGC 57.419 39.130 0.00 0.00 41.10 4.40
3928 4790 4.574674 ATGCTAAAACTCAGGATGTGGA 57.425 40.909 0.00 0.00 37.40 4.02
3931 4793 2.185004 AAAACTCAGGATGTGGACCG 57.815 50.000 0.00 0.00 37.40 4.79
3932 4794 0.324943 AAACTCAGGATGTGGACCGG 59.675 55.000 0.00 0.00 37.40 5.28
3933 4795 0.836400 AACTCAGGATGTGGACCGGT 60.836 55.000 6.92 6.92 37.40 5.28
3934 4796 1.219124 CTCAGGATGTGGACCGGTG 59.781 63.158 14.63 0.00 37.40 4.94
3935 4797 1.535444 TCAGGATGTGGACCGGTGT 60.535 57.895 14.63 0.00 37.40 4.16
3943 4805 4.222145 GGATGTGGACCGGTGTGTATATAT 59.778 45.833 14.63 0.00 0.00 0.86
3945 4807 3.962063 TGTGGACCGGTGTGTATATATGT 59.038 43.478 14.63 0.00 0.00 2.29
3964 4826 4.188247 TGTGACTTAAGAATGTCCCTCG 57.812 45.455 10.09 0.00 32.67 4.63
3969 4831 2.306255 TAAGAATGTCCCTCGCGGCC 62.306 60.000 6.13 0.00 0.00 6.13
3971 4833 3.682292 GAATGTCCCTCGCGGCCTT 62.682 63.158 6.13 0.00 0.00 4.35
3989 4851 3.810373 CCTTGTTCGTATTTCTGTGCAC 58.190 45.455 10.75 10.75 0.00 4.57
4020 4882 3.717400 TTTTTGTTAATCGGTGCTGCA 57.283 38.095 0.00 0.00 0.00 4.41
4025 4887 2.161410 TGTTAATCGGTGCTGCAATGAC 59.839 45.455 2.77 0.00 0.00 3.06
4031 4893 1.672737 CGGTGCTGCAATGACTGACTA 60.673 52.381 2.77 0.00 0.00 2.59
4036 4898 3.706086 TGCTGCAATGACTGACTATAGGA 59.294 43.478 0.00 0.00 0.00 2.94
4040 4902 6.261826 GCTGCAATGACTGACTATAGGAAATT 59.738 38.462 4.43 0.00 0.00 1.82
4041 4903 7.558161 TGCAATGACTGACTATAGGAAATTG 57.442 36.000 4.43 6.59 0.00 2.32
4088 4951 9.513906 TGACCAAAATAACATTCAGATTCAGTA 57.486 29.630 0.00 0.00 0.00 2.74
4107 5128 8.731275 TTCAGTAGGGTGTCATTGTATTTATG 57.269 34.615 0.00 0.00 0.00 1.90
4114 5135 7.559533 AGGGTGTCATTGTATTTATGTAATGCA 59.440 33.333 0.00 0.00 37.11 3.96
4182 5205 6.115448 ACTTATTACTCAAAGCACTGGTCT 57.885 37.500 0.00 0.00 0.00 3.85
4192 5215 1.080230 CACTGGTCTGCTGTCTCCG 60.080 63.158 0.00 0.00 0.00 4.63
4194 5217 1.214062 CTGGTCTGCTGTCTCCGTC 59.786 63.158 0.00 0.00 0.00 4.79
4199 5222 1.812922 CTGCTGTCTCCGTCATGCC 60.813 63.158 0.00 0.00 0.00 4.40
4362 5385 1.228429 GGGGCAGGCAAGTGTTGTA 60.228 57.895 0.00 0.00 0.00 2.41
4363 5386 0.825840 GGGGCAGGCAAGTGTTGTAA 60.826 55.000 0.00 0.00 0.00 2.41
4370 5393 1.665735 GGCAAGTGTTGTAACCATGCG 60.666 52.381 9.06 0.00 33.98 4.73
4373 5396 1.156736 AGTGTTGTAACCATGCGCTC 58.843 50.000 9.73 0.00 0.00 5.03
4381 5415 1.568612 AACCATGCGCTCTGTTGACG 61.569 55.000 9.73 0.00 0.00 4.35
4389 5423 2.412089 GCGCTCTGTTGACGATTTTAGT 59.588 45.455 0.00 0.00 0.00 2.24
4395 5429 7.201444 CGCTCTGTTGACGATTTTAGTATTTCT 60.201 37.037 0.00 0.00 0.00 2.52
4404 5438 9.362539 GACGATTTTAGTATTTCTTGAGTACCA 57.637 33.333 0.00 0.00 0.00 3.25
4412 5446 3.975168 TTCTTGAGTACCAGTTAGGGC 57.025 47.619 0.00 0.00 43.89 5.19
4413 5447 2.897350 TCTTGAGTACCAGTTAGGGCA 58.103 47.619 0.00 0.00 43.89 5.36
4415 5449 0.902531 TGAGTACCAGTTAGGGCAGC 59.097 55.000 0.00 0.00 43.89 5.25
4418 5452 0.459759 GTACCAGTTAGGGCAGCGTC 60.460 60.000 0.00 0.00 43.89 5.19
4428 5463 1.171308 GGGCAGCGTCGATATAGGTA 58.829 55.000 0.00 0.00 0.00 3.08
4539 5575 2.659016 CGAGCAAGGAGAGCACCA 59.341 61.111 0.00 0.00 0.00 4.17
4684 5724 0.602905 AAAACTCGGTCAGGCTTCGG 60.603 55.000 0.00 0.00 0.00 4.30
4773 5820 7.785028 AGGTCTCTTATATACTTGGTGACATCA 59.215 37.037 0.00 0.00 42.32 3.07
4829 5879 3.349022 TGTTTCGGAGTCTTGTTGGTTT 58.651 40.909 0.00 0.00 0.00 3.27
4872 5922 4.877378 TTGTTTAGACTAAAGGAGCCGA 57.123 40.909 7.93 0.00 0.00 5.54
4961 6017 8.622948 AAGTAATAAGAACAAAGAACTCCTGG 57.377 34.615 0.00 0.00 0.00 4.45
4981 6037 5.775195 CCTGGTTTTTCTAGTCCCTTGATTT 59.225 40.000 0.00 0.00 0.00 2.17
4986 6133 6.633500 TTTTCTAGTCCCTTGATTTGTGTG 57.367 37.500 0.00 0.00 0.00 3.82
4995 6142 4.805192 CCCTTGATTTGTGTGTTGTTTGAG 59.195 41.667 0.00 0.00 0.00 3.02
5012 6159 7.325660 TGTTTGAGATTTTATGCCTGATCTC 57.674 36.000 5.49 5.49 42.95 2.75
5014 6161 7.066645 TGTTTGAGATTTTATGCCTGATCTCTG 59.933 37.037 11.96 0.00 43.02 3.35
5064 6230 5.729510 GAGAATCTTTTGAGACTACTGCCT 58.270 41.667 0.00 0.00 0.00 4.75
5069 6235 3.667497 TTTGAGACTACTGCCTGTCTG 57.333 47.619 0.09 0.00 42.79 3.51
5072 6238 2.290960 TGAGACTACTGCCTGTCTGCTA 60.291 50.000 0.09 0.00 42.79 3.49
5073 6239 2.955660 GAGACTACTGCCTGTCTGCTAT 59.044 50.000 0.09 0.00 42.79 2.97
5077 6250 0.617413 ACTGCCTGTCTGCTATTGCT 59.383 50.000 0.00 0.00 40.48 3.91
5078 6251 1.297664 CTGCCTGTCTGCTATTGCTC 58.702 55.000 0.00 0.00 40.48 4.26
5087 6260 0.536724 TGCTATTGCTCGCAGGAAGA 59.463 50.000 0.00 0.00 40.48 2.87
5089 6262 1.328986 GCTATTGCTCGCAGGAAGAAC 59.671 52.381 0.00 0.00 36.03 3.01
5090 6263 1.936547 CTATTGCTCGCAGGAAGAACC 59.063 52.381 0.00 0.00 39.35 3.62
5091 6264 0.678048 ATTGCTCGCAGGAAGAACCC 60.678 55.000 0.00 0.00 40.05 4.11
5092 6265 2.815647 GCTCGCAGGAAGAACCCG 60.816 66.667 0.00 0.00 40.05 5.28
5102 6275 2.245438 GAAGAACCCGCCTCCCAGAG 62.245 65.000 0.00 0.00 0.00 3.35
5110 6283 2.935481 CCTCCCAGAGGTTGGCCA 60.935 66.667 0.00 0.00 46.32 5.36
5111 6284 2.673523 CTCCCAGAGGTTGGCCAG 59.326 66.667 5.11 0.00 46.32 4.85
5112 6285 1.920325 CTCCCAGAGGTTGGCCAGA 60.920 63.158 5.11 0.00 46.32 3.86
5114 6287 1.065410 TCCCAGAGGTTGGCCAGAAA 61.065 55.000 5.11 0.00 46.32 2.52
5115 6288 0.040204 CCCAGAGGTTGGCCAGAAAT 59.960 55.000 5.11 0.00 46.32 2.17
5116 6289 1.550869 CCCAGAGGTTGGCCAGAAATT 60.551 52.381 5.11 0.00 46.32 1.82
5117 6290 1.547372 CCAGAGGTTGGCCAGAAATTG 59.453 52.381 5.11 3.53 40.87 2.32
5131 6304 5.857268 CCAGAAATTGGTTTGGACTCATTT 58.143 37.500 0.00 0.00 42.41 2.32
5133 6306 5.178067 CAGAAATTGGTTTGGACTCATTTGC 59.822 40.000 0.00 0.00 0.00 3.68
5134 6307 4.961438 AATTGGTTTGGACTCATTTGCT 57.039 36.364 0.00 0.00 0.00 3.91
5135 6308 6.267471 AGAAATTGGTTTGGACTCATTTGCTA 59.733 34.615 0.00 0.00 0.00 3.49
5137 6310 6.610075 ATTGGTTTGGACTCATTTGCTATT 57.390 33.333 0.00 0.00 0.00 1.73
5138 6311 6.418057 TTGGTTTGGACTCATTTGCTATTT 57.582 33.333 0.00 0.00 0.00 1.40
5139 6312 5.782047 TGGTTTGGACTCATTTGCTATTTG 58.218 37.500 0.00 0.00 0.00 2.32
5140 6313 5.170748 GGTTTGGACTCATTTGCTATTTGG 58.829 41.667 0.00 0.00 0.00 3.28
5141 6314 4.454728 TTGGACTCATTTGCTATTTGGC 57.545 40.909 0.00 0.00 0.00 4.52
5143 6316 3.193267 TGGACTCATTTGCTATTTGGCAC 59.807 43.478 0.00 0.00 42.27 5.01
5146 6319 4.813027 ACTCATTTGCTATTTGGCACTTG 58.187 39.130 0.00 0.00 42.27 3.16
5147 6320 3.587923 TCATTTGCTATTTGGCACTTGC 58.412 40.909 0.00 0.00 42.27 4.01
5188 6361 1.963515 GAACTTGCCAGGTTTGATGGT 59.036 47.619 0.00 0.00 40.17 3.55
5195 6368 1.616159 CAGGTTTGATGGTTCGGGTT 58.384 50.000 0.00 0.00 0.00 4.11
5198 6371 1.539827 GGTTTGATGGTTCGGGTTGAG 59.460 52.381 0.00 0.00 0.00 3.02
5231 6404 2.269241 GCACCGGAGAAGGAAGGG 59.731 66.667 9.46 0.00 34.73 3.95
5248 6421 2.284405 GGGGAGTCTGGGGTTCGA 60.284 66.667 0.00 0.00 0.00 3.71
5250 6423 2.572284 GGAGTCTGGGGTTCGACG 59.428 66.667 0.00 0.00 35.38 5.12
5251 6424 2.572284 GAGTCTGGGGTTCGACGG 59.428 66.667 0.00 0.00 35.38 4.79
5252 6425 2.203596 AGTCTGGGGTTCGACGGT 60.204 61.111 0.00 0.00 35.38 4.83
5253 6426 1.813728 GAGTCTGGGGTTCGACGGTT 61.814 60.000 0.00 0.00 35.38 4.44
5254 6427 1.070275 GTCTGGGGTTCGACGGTTT 59.930 57.895 0.00 0.00 0.00 3.27
5255 6428 1.070105 TCTGGGGTTCGACGGTTTG 59.930 57.895 0.00 0.00 0.00 2.93
5256 6429 1.070105 CTGGGGTTCGACGGTTTGA 59.930 57.895 0.00 0.00 0.00 2.69
5257 6430 0.949105 CTGGGGTTCGACGGTTTGAG 60.949 60.000 0.00 0.00 0.00 3.02
5258 6431 1.670083 GGGGTTCGACGGTTTGAGG 60.670 63.158 0.00 0.00 0.00 3.86
5259 6432 1.070275 GGGTTCGACGGTTTGAGGT 59.930 57.895 0.00 0.00 0.00 3.85
5260 6433 0.533531 GGGTTCGACGGTTTGAGGTT 60.534 55.000 0.00 0.00 0.00 3.50
5261 6434 1.302366 GGTTCGACGGTTTGAGGTTT 58.698 50.000 0.00 0.00 0.00 3.27
5262 6435 1.672363 GGTTCGACGGTTTGAGGTTTT 59.328 47.619 0.00 0.00 0.00 2.43
5263 6436 2.540157 GGTTCGACGGTTTGAGGTTTTG 60.540 50.000 0.00 0.00 0.00 2.44
5264 6437 1.301423 TCGACGGTTTGAGGTTTTGG 58.699 50.000 0.00 0.00 0.00 3.28
5265 6438 0.309612 CGACGGTTTGAGGTTTTGGG 59.690 55.000 0.00 0.00 0.00 4.12
5266 6439 1.395635 GACGGTTTGAGGTTTTGGGT 58.604 50.000 0.00 0.00 0.00 4.51
5277 6796 2.090999 AGGTTTTGGGTGGGCTTTCTTA 60.091 45.455 0.00 0.00 0.00 2.10
5278 6797 2.701423 GGTTTTGGGTGGGCTTTCTTAA 59.299 45.455 0.00 0.00 0.00 1.85
5279 6798 3.134985 GGTTTTGGGTGGGCTTTCTTAAA 59.865 43.478 0.00 0.00 0.00 1.52
5284 6803 4.227197 TGGGTGGGCTTTCTTAAATTTGA 58.773 39.130 0.00 0.00 0.00 2.69
5293 6812 7.173047 GGGCTTTCTTAAATTTGAGAAATGCAA 59.827 33.333 31.64 18.71 40.51 4.08
5333 6869 1.205655 TCGAGGGAGAAGATTGCACTG 59.794 52.381 0.00 0.00 0.00 3.66
5334 6870 1.205655 CGAGGGAGAAGATTGCACTGA 59.794 52.381 0.00 0.00 0.00 3.41
5406 6942 3.690460 AGCACCTCGATTTCCAAATTCT 58.310 40.909 0.00 0.00 0.00 2.40
5445 6983 5.050634 TCTCGAACTAAAACCACGACAATTG 60.051 40.000 3.24 3.24 0.00 2.32
5490 7049 2.493675 CACGGTTGATGAGGAAGAGAGA 59.506 50.000 0.00 0.00 0.00 3.10
5504 7063 2.571212 AGAGAGATGCTAGACCGTGAG 58.429 52.381 0.00 0.00 0.00 3.51
5536 7095 1.112315 TTGTGGTTGTGGCATGGTCC 61.112 55.000 0.00 0.00 0.00 4.46
5539 7098 1.978617 GGTTGTGGCATGGTCCTGG 60.979 63.158 0.00 0.00 0.00 4.45
5561 7120 1.669115 CTGAAGCAGGACACCACCG 60.669 63.158 0.00 0.00 34.73 4.94
5563 7122 4.988598 AAGCAGGACACCACCGCG 62.989 66.667 0.00 0.00 35.71 6.46
5585 7147 4.025730 CGATGGTGATGTATAACACACAGC 60.026 45.833 2.46 10.78 40.86 4.40
5601 7163 0.301687 CAGCGGACGCATGATTGTAC 59.698 55.000 19.48 0.00 44.88 2.90
5602 7164 0.108377 AGCGGACGCATGATTGTACA 60.108 50.000 19.48 0.00 44.88 2.90
5603 7165 0.301687 GCGGACGCATGATTGTACAG 59.698 55.000 12.31 0.00 41.49 2.74
5604 7166 1.640428 CGGACGCATGATTGTACAGT 58.360 50.000 0.00 0.00 0.00 3.55
5605 7167 1.999735 CGGACGCATGATTGTACAGTT 59.000 47.619 0.00 0.00 0.00 3.16
5606 7168 3.183754 CGGACGCATGATTGTACAGTTA 58.816 45.455 0.00 0.00 0.00 2.24
5607 7169 3.802139 CGGACGCATGATTGTACAGTTAT 59.198 43.478 0.00 0.00 0.00 1.89
5608 7170 4.270084 CGGACGCATGATTGTACAGTTATT 59.730 41.667 0.00 0.00 0.00 1.40
5609 7171 5.460748 CGGACGCATGATTGTACAGTTATTA 59.539 40.000 0.00 0.00 0.00 0.98
5610 7172 6.561533 CGGACGCATGATTGTACAGTTATTAC 60.562 42.308 0.00 0.00 0.00 1.89
5611 7173 6.479001 GGACGCATGATTGTACAGTTATTACT 59.521 38.462 0.00 0.00 34.00 2.24
5612 7174 7.011109 GGACGCATGATTGTACAGTTATTACTT 59.989 37.037 0.00 0.00 30.26 2.24
5613 7175 7.684670 ACGCATGATTGTACAGTTATTACTTG 58.315 34.615 0.00 0.00 30.26 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.065019 TCTTCAAAACGTGCTTTCTGC 57.935 42.857 0.00 0.00 43.25 4.26
30 31 4.601019 ACATCTTCAAAACGTGCTTTCTG 58.399 39.130 0.00 0.00 0.00 3.02
31 32 4.900635 ACATCTTCAAAACGTGCTTTCT 57.099 36.364 0.00 0.00 0.00 2.52
32 33 7.623268 ATTTACATCTTCAAAACGTGCTTTC 57.377 32.000 0.00 0.00 0.00 2.62
33 34 8.419076 AAATTTACATCTTCAAAACGTGCTTT 57.581 26.923 0.00 0.00 0.00 3.51
34 35 8.419076 AAAATTTACATCTTCAAAACGTGCTT 57.581 26.923 0.00 0.00 0.00 3.91
35 36 8.419076 AAAAATTTACATCTTCAAAACGTGCT 57.581 26.923 0.00 0.00 0.00 4.40
36 37 9.562752 GTAAAAATTTACATCTTCAAAACGTGC 57.437 29.630 10.40 0.00 41.93 5.34
135 136 8.560374 AGAGTTTAGACAGATTTTTAGCACAAC 58.440 33.333 0.00 0.00 0.00 3.32
147 148 9.871238 TTTAATTCGCTTAGAGTTTAGACAGAT 57.129 29.630 0.00 0.00 31.03 2.90
148 149 9.701098 TTTTAATTCGCTTAGAGTTTAGACAGA 57.299 29.630 0.00 0.00 31.03 3.41
158 161 5.795441 GGTGCAGTTTTTAATTCGCTTAGAG 59.205 40.000 0.00 0.00 0.00 2.43
161 164 5.699097 AGGTGCAGTTTTTAATTCGCTTA 57.301 34.783 0.00 0.00 0.00 3.09
208 211 0.694783 GGGGTCTAAAGAGGGGGAGG 60.695 65.000 0.00 0.00 0.00 4.30
210 213 0.342313 GAGGGGTCTAAAGAGGGGGA 59.658 60.000 0.00 0.00 0.00 4.81
213 216 3.035363 GAGAAGAGGGGTCTAAAGAGGG 58.965 54.545 0.00 0.00 0.00 4.30
214 217 2.691011 CGAGAAGAGGGGTCTAAAGAGG 59.309 54.545 0.00 0.00 0.00 3.69
215 218 3.622630 TCGAGAAGAGGGGTCTAAAGAG 58.377 50.000 0.00 0.00 0.00 2.85
216 219 3.733883 TCGAGAAGAGGGGTCTAAAGA 57.266 47.619 0.00 0.00 0.00 2.52
218 221 4.079672 AGAGATCGAGAAGAGGGGTCTAAA 60.080 45.833 0.00 0.00 0.00 1.85
219 222 3.460340 AGAGATCGAGAAGAGGGGTCTAA 59.540 47.826 0.00 0.00 0.00 2.10
222 249 2.227194 GAGAGATCGAGAAGAGGGGTC 58.773 57.143 0.00 0.00 0.00 4.46
254 281 6.033725 TCGGTTTCTTAGTTTTTGTTTTTCGC 59.966 34.615 0.00 0.00 0.00 4.70
255 282 7.495339 TCGGTTTCTTAGTTTTTGTTTTTCG 57.505 32.000 0.00 0.00 0.00 3.46
258 285 6.034150 CGCTTCGGTTTCTTAGTTTTTGTTTT 59.966 34.615 0.00 0.00 0.00 2.43
261 288 4.333372 TCGCTTCGGTTTCTTAGTTTTTGT 59.667 37.500 0.00 0.00 0.00 2.83
262 289 4.839796 TCGCTTCGGTTTCTTAGTTTTTG 58.160 39.130 0.00 0.00 0.00 2.44
263 290 5.163733 TGTTCGCTTCGGTTTCTTAGTTTTT 60.164 36.000 0.00 0.00 0.00 1.94
264 291 4.333372 TGTTCGCTTCGGTTTCTTAGTTTT 59.667 37.500 0.00 0.00 0.00 2.43
266 293 3.246936 GTGTTCGCTTCGGTTTCTTAGTT 59.753 43.478 0.00 0.00 0.00 2.24
268 295 2.798283 TGTGTTCGCTTCGGTTTCTTAG 59.202 45.455 0.00 0.00 0.00 2.18
269 296 2.798283 CTGTGTTCGCTTCGGTTTCTTA 59.202 45.455 0.00 0.00 0.00 2.10
277 507 2.480426 GAACGGCTGTGTTCGCTTCG 62.480 60.000 0.00 0.00 38.91 3.79
342 572 3.219281 GCAACCCACCAAAAAGAGTAGA 58.781 45.455 0.00 0.00 0.00 2.59
344 574 1.950909 CGCAACCCACCAAAAAGAGTA 59.049 47.619 0.00 0.00 0.00 2.59
379 610 1.601419 CCGGACCTTTCTGCTACGGA 61.601 60.000 0.00 0.00 42.19 4.69
392 623 0.249363 GCTCGTTTATCTCCCGGACC 60.249 60.000 0.73 0.00 0.00 4.46
489 723 4.741239 GGAGGGGAGGAGGCCACA 62.741 72.222 5.01 0.00 32.19 4.17
777 1546 1.228154 ACCGGTCTGGGTTCAAAGC 60.228 57.895 0.00 0.00 44.64 3.51
797 1566 3.554692 CAATCTGCGCCGTCGGTC 61.555 66.667 13.94 5.94 35.95 4.79
909 1678 6.046593 CACAACTAGAACCAGTACTGACAAA 58.953 40.000 24.68 4.77 0.00 2.83
1142 1924 1.387084 GCTAGAACAGAGCAACGAACG 59.613 52.381 0.00 0.00 39.84 3.95
1202 2005 0.243365 CTGCAATTACAAAGGCGGCA 59.757 50.000 13.08 0.00 0.00 5.69
1239 2042 2.350895 CCGGTGTTGGCAGATCCA 59.649 61.111 0.00 0.00 44.85 3.41
1495 2298 3.627123 CCATCATAACCTGATTCGCAACA 59.373 43.478 0.00 0.00 42.07 3.33
1496 2299 3.548818 GCCATCATAACCTGATTCGCAAC 60.549 47.826 0.00 0.00 42.07 4.17
1497 2300 2.618241 GCCATCATAACCTGATTCGCAA 59.382 45.455 0.00 0.00 42.07 4.85
1629 2432 8.803235 ACCATGCGATTATTAAGACTACATAGA 58.197 33.333 0.00 0.00 0.00 1.98
1648 2451 1.335872 GGACACCTTGAAAACCATGCG 60.336 52.381 0.00 0.00 0.00 4.73
1664 2467 2.598787 CCCTAACCCAAGGCGGACA 61.599 63.158 0.00 0.00 36.56 4.02
1701 2505 2.749839 CGGGCCGATTTCCAAGCA 60.750 61.111 24.41 0.00 0.00 3.91
1723 2527 0.679505 AGACAGACAACTAAGCGCCA 59.320 50.000 2.29 0.00 0.00 5.69
1733 2537 2.823747 TCCTAAGCGCTAAGACAGACAA 59.176 45.455 12.05 0.00 0.00 3.18
1738 2542 2.423892 CTGACTCCTAAGCGCTAAGACA 59.576 50.000 12.05 11.59 0.00 3.41
1740 2544 2.946329 CTCTGACTCCTAAGCGCTAAGA 59.054 50.000 12.05 7.10 0.00 2.10
1754 2558 2.183679 CTTTCTACCCCTGCTCTGACT 58.816 52.381 0.00 0.00 0.00 3.41
1773 2577 1.002502 GGTAAGGCGTCCAAAGGCT 60.003 57.895 0.00 0.00 46.93 4.58
1840 2680 3.363341 TTCAAACGCAGGTGGAAAATC 57.637 42.857 0.00 0.00 0.00 2.17
1846 2686 1.197721 CTAGCTTTCAAACGCAGGTGG 59.802 52.381 0.00 0.00 0.00 4.61
1851 2691 2.543777 ACTCCTAGCTTTCAAACGCA 57.456 45.000 0.00 0.00 0.00 5.24
1890 2730 4.032960 TCATCTACATGGGCACAGTTTT 57.967 40.909 0.00 0.00 0.00 2.43
1891 2731 3.719268 TCATCTACATGGGCACAGTTT 57.281 42.857 0.00 0.00 0.00 2.66
2214 3063 0.712222 GAAACTACCGTAGCACGTGC 59.288 55.000 32.79 32.79 40.58 5.34
2617 3466 7.230510 TGCAAAACACTTAGAACCAGTCATATT 59.769 33.333 0.00 0.00 0.00 1.28
2618 3467 6.714810 TGCAAAACACTTAGAACCAGTCATAT 59.285 34.615 0.00 0.00 0.00 1.78
2708 3559 8.576442 CAAAACTGGTCATTTTGTTACCTCTAT 58.424 33.333 2.72 0.00 40.57 1.98
2709 3560 7.469456 GCAAAACTGGTCATTTTGTTACCTCTA 60.469 37.037 10.82 0.00 45.03 2.43
3243 4094 5.041287 TCCTCGCTGTAAGATTTGATAACG 58.959 41.667 0.00 0.00 34.07 3.18
3434 4285 4.142093 GCTCAAGGTCAATACAAATGCCAT 60.142 41.667 0.00 0.00 0.00 4.40
3458 4309 2.582052 TGTGTTCACCTAAAAGGCCAG 58.418 47.619 5.01 0.00 39.63 4.85
3703 4554 6.051717 CACCACCCAAAATTTGTTATTGACA 58.948 36.000 4.92 0.00 36.19 3.58
3713 4564 4.100189 TCACGAAATCACCACCCAAAATTT 59.900 37.500 0.00 0.00 0.00 1.82
3905 4767 5.525378 GTCCACATCCTGAGTTTTAGCATAG 59.475 44.000 0.00 0.00 0.00 2.23
3928 4790 5.864418 AAGTCACATATATACACACCGGT 57.136 39.130 0.00 0.00 0.00 5.28
3943 4805 3.616560 GCGAGGGACATTCTTAAGTCACA 60.617 47.826 1.63 0.00 40.60 3.58
3945 4807 2.416836 CGCGAGGGACATTCTTAAGTCA 60.417 50.000 0.00 0.00 36.50 3.41
3964 4826 1.084289 AGAAATACGAACAAGGCCGC 58.916 50.000 0.00 0.00 0.00 6.53
3969 4831 4.466567 TGTGCACAGAAATACGAACAAG 57.533 40.909 17.42 0.00 0.00 3.16
3971 4833 4.991687 TGTATGTGCACAGAAATACGAACA 59.008 37.500 25.84 9.26 0.00 3.18
4048 4910 8.835439 GTTATTTTGGTCAATTTGTGAATGGTT 58.165 29.630 0.00 0.00 38.23 3.67
4072 4935 5.013079 TGACACCCTACTGAATCTGAATGTT 59.987 40.000 0.00 0.00 0.00 2.71
4077 4940 4.532126 ACAATGACACCCTACTGAATCTGA 59.468 41.667 0.00 0.00 0.00 3.27
4082 4945 8.325787 ACATAAATACAATGACACCCTACTGAA 58.674 33.333 0.00 0.00 0.00 3.02
4088 4951 7.559533 TGCATTACATAAATACAATGACACCCT 59.440 33.333 0.00 0.00 31.44 4.34
4107 5128 4.136796 TCATACTGCCAAGGATGCATTAC 58.863 43.478 0.00 0.00 43.62 1.89
4114 5135 5.057843 ACATCAATCATACTGCCAAGGAT 57.942 39.130 0.00 0.00 0.00 3.24
4151 5172 8.376270 AGTGCTTTGAGTAATAAGTTTAGAGGT 58.624 33.333 0.00 0.00 0.00 3.85
4182 5205 2.265739 GGCATGACGGAGACAGCA 59.734 61.111 0.00 0.00 34.76 4.41
4192 5215 1.026718 AGCTTAACCTGCGGCATGAC 61.027 55.000 12.29 0.00 35.28 3.06
4194 5217 0.179156 CAAGCTTAACCTGCGGCATG 60.179 55.000 1.75 2.81 35.28 4.06
4199 5222 0.874390 TTGCTCAAGCTTAACCTGCG 59.126 50.000 0.00 0.00 42.66 5.18
4362 5385 1.568612 CGTCAACAGAGCGCATGGTT 61.569 55.000 11.47 7.53 0.00 3.67
4363 5386 2.029288 CGTCAACAGAGCGCATGGT 61.029 57.895 11.47 3.10 0.00 3.55
4370 5393 7.965045 AGAAATACTAAAATCGTCAACAGAGC 58.035 34.615 0.00 0.00 0.00 4.09
4373 5396 9.746711 CTCAAGAAATACTAAAATCGTCAACAG 57.253 33.333 0.00 0.00 0.00 3.16
4389 5423 5.486063 TGCCCTAACTGGTACTCAAGAAATA 59.514 40.000 0.00 0.00 0.00 1.40
4395 5429 1.278127 GCTGCCCTAACTGGTACTCAA 59.722 52.381 0.00 0.00 0.00 3.02
4404 5438 1.329256 ATATCGACGCTGCCCTAACT 58.671 50.000 0.00 0.00 0.00 2.24
4409 5443 1.135460 GTACCTATATCGACGCTGCCC 60.135 57.143 0.00 0.00 0.00 5.36
4412 5446 5.029014 GCATTAGTACCTATATCGACGCTG 58.971 45.833 0.00 0.00 0.00 5.18
4413 5447 4.096081 GGCATTAGTACCTATATCGACGCT 59.904 45.833 0.00 0.00 0.00 5.07
4415 5449 5.570344 CAGGCATTAGTACCTATATCGACG 58.430 45.833 0.00 0.00 33.38 5.12
4418 5452 5.584253 AGCAGGCATTAGTACCTATATCG 57.416 43.478 0.00 0.00 33.38 2.92
4442 5477 5.144100 ACACCCTGGACAATGTGAATAAAA 58.856 37.500 6.98 0.00 33.08 1.52
4445 5480 4.078537 CAACACCCTGGACAATGTGAATA 58.921 43.478 6.98 0.00 33.08 1.75
4446 5481 2.892852 CAACACCCTGGACAATGTGAAT 59.107 45.455 6.98 0.00 33.08 2.57
4447 5482 2.092158 TCAACACCCTGGACAATGTGAA 60.092 45.455 6.98 0.00 33.08 3.18
4448 5483 1.492599 TCAACACCCTGGACAATGTGA 59.507 47.619 6.98 0.00 33.08 3.58
4449 5484 1.979855 TCAACACCCTGGACAATGTG 58.020 50.000 0.00 0.00 34.92 3.21
4450 5485 2.108075 TCATCAACACCCTGGACAATGT 59.892 45.455 0.00 0.00 0.00 2.71
4451 5486 2.751259 CTCATCAACACCCTGGACAATG 59.249 50.000 0.00 0.00 0.00 2.82
4463 5499 3.367806 CGCTCTTCTCCTTCTCATCAACA 60.368 47.826 0.00 0.00 0.00 3.33
4684 5724 3.001634 CCATGTATGATCCGCGCATATTC 59.998 47.826 8.75 0.00 31.54 1.75
4773 5820 3.140332 GGAAAGGGGCCATATAAGAACCT 59.860 47.826 4.39 0.00 0.00 3.50
4961 6017 6.918022 CACACAAATCAAGGGACTAGAAAAAC 59.082 38.462 0.00 0.00 38.49 2.43
4981 6037 5.982516 GGCATAAAATCTCAAACAACACACA 59.017 36.000 0.00 0.00 0.00 3.72
4986 6133 7.542025 AGATCAGGCATAAAATCTCAAACAAC 58.458 34.615 0.00 0.00 0.00 3.32
4995 6142 6.545298 AGGAAACAGAGATCAGGCATAAAATC 59.455 38.462 0.00 0.00 0.00 2.17
5012 6159 7.693969 ACCAAAAGATTCTCATAGGAAACAG 57.306 36.000 0.00 0.00 0.00 3.16
5044 6192 5.012561 AGACAGGCAGTAGTCTCAAAAGATT 59.987 40.000 0.00 0.00 40.96 2.40
5047 6195 3.993081 CAGACAGGCAGTAGTCTCAAAAG 59.007 47.826 0.00 0.00 42.87 2.27
5050 6198 1.273606 GCAGACAGGCAGTAGTCTCAA 59.726 52.381 0.00 0.00 42.87 3.02
5051 6199 0.891373 GCAGACAGGCAGTAGTCTCA 59.109 55.000 0.00 0.00 42.87 3.27
5052 6200 1.181786 AGCAGACAGGCAGTAGTCTC 58.818 55.000 0.00 0.00 42.87 3.36
5053 6201 2.516227 TAGCAGACAGGCAGTAGTCT 57.484 50.000 0.00 0.00 45.46 3.24
5069 6235 1.328986 GTTCTTCCTGCGAGCAATAGC 59.671 52.381 0.00 0.00 42.56 2.97
5072 6238 0.678048 GGGTTCTTCCTGCGAGCAAT 60.678 55.000 0.00 0.00 36.25 3.56
5073 6239 1.302511 GGGTTCTTCCTGCGAGCAA 60.303 57.895 0.00 0.00 36.25 3.91
5084 6257 2.203938 TCTGGGAGGCGGGTTCTT 60.204 61.111 0.00 0.00 0.00 2.52
5109 6282 5.178067 GCAAATGAGTCCAAACCAATTTCTG 59.822 40.000 0.00 0.00 0.00 3.02
5110 6283 5.070847 AGCAAATGAGTCCAAACCAATTTCT 59.929 36.000 0.00 0.00 0.00 2.52
5111 6284 5.299949 AGCAAATGAGTCCAAACCAATTTC 58.700 37.500 0.00 0.00 0.00 2.17
5112 6285 5.294734 AGCAAATGAGTCCAAACCAATTT 57.705 34.783 0.00 0.00 0.00 1.82
5114 6287 6.610075 AATAGCAAATGAGTCCAAACCAAT 57.390 33.333 0.00 0.00 0.00 3.16
5115 6288 6.222389 CAAATAGCAAATGAGTCCAAACCAA 58.778 36.000 0.00 0.00 0.00 3.67
5116 6289 5.279406 CCAAATAGCAAATGAGTCCAAACCA 60.279 40.000 0.00 0.00 0.00 3.67
5117 6290 5.170748 CCAAATAGCAAATGAGTCCAAACC 58.829 41.667 0.00 0.00 0.00 3.27
5118 6291 4.627035 GCCAAATAGCAAATGAGTCCAAAC 59.373 41.667 0.00 0.00 0.00 2.93
5119 6292 4.282957 TGCCAAATAGCAAATGAGTCCAAA 59.717 37.500 0.00 0.00 40.56 3.28
5120 6293 3.831333 TGCCAAATAGCAAATGAGTCCAA 59.169 39.130 0.00 0.00 40.56 3.53
5121 6294 3.193267 GTGCCAAATAGCAAATGAGTCCA 59.807 43.478 0.00 0.00 46.19 4.02
5123 6296 4.708726 AGTGCCAAATAGCAAATGAGTC 57.291 40.909 0.00 0.00 46.19 3.36
5125 6298 3.615496 GCAAGTGCCAAATAGCAAATGAG 59.385 43.478 0.00 0.00 46.19 2.90
5126 6299 3.587923 GCAAGTGCCAAATAGCAAATGA 58.412 40.909 0.00 0.00 46.19 2.57
5154 6327 2.679349 GCAAGTTCTCTCAGCCTAAGGG 60.679 54.545 0.00 0.00 0.00 3.95
5155 6328 2.626840 GCAAGTTCTCTCAGCCTAAGG 58.373 52.381 0.00 0.00 0.00 2.69
5156 6329 2.027745 TGGCAAGTTCTCTCAGCCTAAG 60.028 50.000 0.00 0.00 41.91 2.18
5157 6330 1.977854 TGGCAAGTTCTCTCAGCCTAA 59.022 47.619 0.00 0.00 41.91 2.69
5158 6331 1.552337 CTGGCAAGTTCTCTCAGCCTA 59.448 52.381 0.00 0.00 41.91 3.93
5159 6332 0.324285 CTGGCAAGTTCTCTCAGCCT 59.676 55.000 0.00 0.00 41.91 4.58
5160 6333 0.676151 CCTGGCAAGTTCTCTCAGCC 60.676 60.000 0.00 0.00 41.82 4.85
5161 6334 0.036022 ACCTGGCAAGTTCTCTCAGC 59.964 55.000 0.00 0.00 0.00 4.26
5162 6335 2.551459 CAAACCTGGCAAGTTCTCTCAG 59.449 50.000 1.27 0.00 0.00 3.35
5163 6336 2.172505 TCAAACCTGGCAAGTTCTCTCA 59.827 45.455 1.27 0.00 0.00 3.27
5165 6338 3.152341 CATCAAACCTGGCAAGTTCTCT 58.848 45.455 1.27 0.00 0.00 3.10
5167 6340 2.242043 CCATCAAACCTGGCAAGTTCT 58.758 47.619 1.27 0.00 0.00 3.01
5168 6341 1.963515 ACCATCAAACCTGGCAAGTTC 59.036 47.619 1.27 0.00 37.27 3.01
5169 6342 2.086610 ACCATCAAACCTGGCAAGTT 57.913 45.000 0.00 0.00 37.27 2.66
5170 6343 1.963515 GAACCATCAAACCTGGCAAGT 59.036 47.619 0.00 0.00 37.27 3.16
5231 6404 2.284405 TCGAACCCCAGACTCCCC 60.284 66.667 0.00 0.00 0.00 4.81
5234 6407 1.813728 AACCGTCGAACCCCAGACTC 61.814 60.000 0.00 0.00 35.38 3.36
5239 6412 1.070105 CTCAAACCGTCGAACCCCA 59.930 57.895 0.00 0.00 0.00 4.96
5243 6416 2.540157 CCAAAACCTCAAACCGTCGAAC 60.540 50.000 0.00 0.00 0.00 3.95
5246 6419 0.309612 CCCAAAACCTCAAACCGTCG 59.690 55.000 0.00 0.00 0.00 5.12
5248 6421 1.107945 CACCCAAAACCTCAAACCGT 58.892 50.000 0.00 0.00 0.00 4.83
5250 6423 0.756294 CCCACCCAAAACCTCAAACC 59.244 55.000 0.00 0.00 0.00 3.27
5251 6424 0.105964 GCCCACCCAAAACCTCAAAC 59.894 55.000 0.00 0.00 0.00 2.93
5252 6425 0.031616 AGCCCACCCAAAACCTCAAA 60.032 50.000 0.00 0.00 0.00 2.69
5253 6426 0.031616 AAGCCCACCCAAAACCTCAA 60.032 50.000 0.00 0.00 0.00 3.02
5254 6427 0.031616 AAAGCCCACCCAAAACCTCA 60.032 50.000 0.00 0.00 0.00 3.86
5255 6428 0.679505 GAAAGCCCACCCAAAACCTC 59.320 55.000 0.00 0.00 0.00 3.85
5256 6429 0.264657 AGAAAGCCCACCCAAAACCT 59.735 50.000 0.00 0.00 0.00 3.50
5257 6430 1.128200 AAGAAAGCCCACCCAAAACC 58.872 50.000 0.00 0.00 0.00 3.27
5258 6431 4.409718 TTTAAGAAAGCCCACCCAAAAC 57.590 40.909 0.00 0.00 0.00 2.43
5259 6432 5.638530 AATTTAAGAAAGCCCACCCAAAA 57.361 34.783 0.00 0.00 0.00 2.44
5260 6433 5.131142 TCAAATTTAAGAAAGCCCACCCAAA 59.869 36.000 0.00 0.00 0.00 3.28
5261 6434 4.656112 TCAAATTTAAGAAAGCCCACCCAA 59.344 37.500 0.00 0.00 0.00 4.12
5262 6435 4.227197 TCAAATTTAAGAAAGCCCACCCA 58.773 39.130 0.00 0.00 0.00 4.51
5263 6436 4.526650 TCTCAAATTTAAGAAAGCCCACCC 59.473 41.667 0.00 0.00 0.00 4.61
5264 6437 5.722021 TCTCAAATTTAAGAAAGCCCACC 57.278 39.130 0.00 0.00 0.00 4.61
5265 6438 7.360353 GCATTTCTCAAATTTAAGAAAGCCCAC 60.360 37.037 18.93 5.89 42.86 4.61
5266 6439 6.650390 GCATTTCTCAAATTTAAGAAAGCCCA 59.350 34.615 18.93 0.00 42.86 5.36
5277 6796 5.050837 GCTCAACGTTGCATTTCTCAAATTT 60.051 36.000 23.47 0.00 0.00 1.82
5278 6797 4.445385 GCTCAACGTTGCATTTCTCAAATT 59.555 37.500 23.47 0.00 0.00 1.82
5279 6798 3.983344 GCTCAACGTTGCATTTCTCAAAT 59.017 39.130 23.47 0.00 0.00 2.32
5284 6803 3.316308 AGAAAGCTCAACGTTGCATTTCT 59.684 39.130 29.41 29.41 34.80 2.52
5293 6812 3.491267 CGAGAAAGAAGAAAGCTCAACGT 59.509 43.478 0.00 0.00 0.00 3.99
5445 6983 0.956633 GGTTCCCTCCGTTCCAAAAC 59.043 55.000 0.00 0.00 0.00 2.43
5490 7049 1.683917 GACATCCTCACGGTCTAGCAT 59.316 52.381 0.00 0.00 0.00 3.79
5504 7063 5.163622 CCACAACCACAATCAATAGACATCC 60.164 44.000 0.00 0.00 0.00 3.51
5518 7077 1.530419 GGACCATGCCACAACCACA 60.530 57.895 0.00 0.00 0.00 4.17
5520 7079 1.228521 CAGGACCATGCCACAACCA 60.229 57.895 0.00 0.00 0.00 3.67
5561 7120 3.868661 TGTGTGTTATACATCACCATCGC 59.131 43.478 0.00 0.00 42.24 4.58
5563 7122 4.025730 CGCTGTGTGTTATACATCACCATC 60.026 45.833 0.00 0.00 42.24 3.51
5564 7123 3.871006 CGCTGTGTGTTATACATCACCAT 59.129 43.478 0.00 0.00 42.24 3.55
5575 7137 1.005512 ATGCGTCCGCTGTGTGTTA 60.006 52.632 13.31 0.00 42.51 2.41
5585 7147 1.640428 ACTGTACAATCATGCGTCCG 58.360 50.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.