Multiple sequence alignment - TraesCS3A01G351500

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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 TraesCS3A01G351500 chr3A 100.000 6188 0 0 1 6188 600003480 600009667 0.000000e+00 11428.0
1 TraesCS3A01G351500 chr3A 96.226 53 2 0 5760 5812 127843830 127843778 3.070000e-13 87.9
2 TraesCS3A01G351500 chr3D 94.306 5093 204 40 641 5695 457091377 457096421 0.000000e+00 7720.0
3 TraesCS3A01G351500 chr3D 88.889 387 35 2 5807 6185 457096536 457096922 2.610000e-128 470.0
4 TraesCS3A01G351500 chr3D 89.068 311 32 2 2 310 457090596 457090906 9.730000e-103 385.0
5 TraesCS3A01G351500 chr3B 91.736 3243 194 36 616 3822 603855717 603858921 0.000000e+00 4436.0
6 TraesCS3A01G351500 chr3B 94.006 1902 89 16 3833 5716 603859121 603861015 0.000000e+00 2857.0
7 TraesCS3A01G351500 chr3B 87.728 383 42 4 5807 6188 603861053 603861431 5.690000e-120 442.0
8 TraesCS3A01G351500 chr3B 83.142 261 34 6 5929 6188 78705958 78705707 4.820000e-56 230.0
9 TraesCS3A01G351500 chr3B 94.737 57 3 0 5754 5810 733549442 733549498 8.540000e-14 89.8
10 TraesCS3A01G351500 chr3B 91.525 59 3 2 5758 5814 105445035 105445093 5.140000e-11 80.5
11 TraesCS3A01G351500 chr5B 85.588 340 44 5 2 337 700911647 700911309 9.870000e-93 351.0
12 TraesCS3A01G351500 chr5B 89.753 283 10 7 641 920 700910862 700910596 1.650000e-90 344.0
13 TraesCS3A01G351500 chr5B 77.401 354 64 13 5813 6151 639614080 639613728 4.890000e-46 196.0
14 TraesCS3A01G351500 chr2D 80.000 130 24 2 6059 6188 609783623 609783496 1.840000e-15 95.3
15 TraesCS3A01G351500 chr2A 96.154 52 2 0 5758 5809 721829209 721829260 1.110000e-12 86.1
16 TraesCS3A01G351500 chrUn 96.078 51 2 0 5760 5810 343407056 343407106 3.970000e-12 84.2
17 TraesCS3A01G351500 chr6A 94.545 55 2 1 5760 5813 114840834 114840888 3.970000e-12 84.2
18 TraesCS3A01G351500 chr1A 94.545 55 2 1 5760 5813 14428799 14428745 3.970000e-12 84.2
19 TraesCS3A01G351500 chr7D 92.982 57 3 1 5760 5815 17773784 17773728 1.430000e-11 82.4
20 TraesCS3A01G351500 chr4D 94.340 53 3 0 5760 5812 197837239 197837291 1.430000e-11 82.4
21 TraesCS3A01G351500 chr6D 93.182 44 3 0 5590 5633 200485813 200485856 1.440000e-06 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G351500 chr3A 600003480 600009667 6187 False 11428.000000 11428 100.000000 1 6188 1 chr3A.!!$F1 6187
1 TraesCS3A01G351500 chr3D 457090596 457096922 6326 False 2858.333333 7720 90.754333 2 6185 3 chr3D.!!$F1 6183
2 TraesCS3A01G351500 chr3B 603855717 603861431 5714 False 2578.333333 4436 91.156667 616 6188 3 chr3B.!!$F3 5572
3 TraesCS3A01G351500 chr5B 700910596 700911647 1051 True 347.500000 351 87.670500 2 920 2 chr5B.!!$R2 918

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
468 705 0.100503 AAGATTACCGCGGCAAATGC 59.899 50.000 28.58 17.37 41.14 3.56 F
554 795 0.547075 TGGGACGGAGGAGAGAGTAG 59.453 60.000 0.00 0.00 0.00 2.57 F
1646 1917 0.322816 TTGGATCAGGCCTGCTGAAC 60.323 55.000 28.91 15.61 34.26 3.18 F
2007 2290 0.320771 TTTTCAGGAGCTCGAGGTGC 60.321 55.000 26.32 26.32 0.00 5.01 F
2132 2415 0.607489 GGGATGCTGTGCTTGAGTGT 60.607 55.000 0.00 0.00 0.00 3.55 F
3406 3695 1.211949 GGCAGTTGGCTAAGATACCCA 59.788 52.381 0.00 0.00 44.01 4.51 F
3538 3827 2.268298 CTTCATTTGCTTGCAGGCATC 58.732 47.619 25.18 0.00 42.09 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1521 1788 0.598065 AGAATTTTGTGGCAGGCGTC 59.402 50.000 0.00 0.00 0.00 5.19 R
1796 2067 0.814457 CCTCCTCCTTGTCTCTGTCG 59.186 60.000 0.00 0.00 0.00 4.35 R
2590 2874 1.065199 ACAGGCACTACATGACCCATG 60.065 52.381 0.00 5.48 42.18 3.66 R
3834 4313 1.062002 CAAATAAGGTGCGGCGTACAG 59.938 52.381 28.25 6.16 0.00 2.74 R
3935 4426 9.665719 TTATAACTGTGCTCAATCTGTTAATCA 57.334 29.630 3.43 0.00 33.93 2.57 R
4750 5242 0.454600 CAAGCATCATGGACACTGGC 59.545 55.000 0.00 0.00 0.00 4.85 R
5382 5878 0.746659 ACAGGCCAGTTCAACAAAGC 59.253 50.000 5.01 0.00 0.00 3.51 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
52 54 5.643777 GTGCTTGGACACAGTCTATGTATTT 59.356 40.000 0.00 0.00 41.41 1.40
55 57 6.183360 GCTTGGACACAGTCTATGTATTTGAC 60.183 42.308 0.00 0.00 41.41 3.18
69 71 4.693095 TGTATTTGACGCTTGAAGCATACA 59.307 37.500 18.22 17.99 42.58 2.29
75 77 6.710692 TGACGCTTGAAGCATACATATATG 57.289 37.500 18.22 11.29 42.58 1.78
88 90 9.970553 AGCATACATATATGGTTCATCTTTCAT 57.029 29.630 16.96 0.00 45.23 2.57
126 129 5.762711 TGACACTGTTTTAGCTGCAATCTAA 59.237 36.000 1.02 4.50 0.00 2.10
273 276 1.087501 GGGACGAGGCATTTCAACTC 58.912 55.000 0.00 0.00 0.00 3.01
276 279 2.003301 GACGAGGCATTTCAACTCTCC 58.997 52.381 0.00 0.00 0.00 3.71
278 281 1.373570 GAGGCATTTCAACTCTCCGG 58.626 55.000 0.00 0.00 0.00 5.14
284 287 1.808411 TTTCAACTCTCCGGTGCATC 58.192 50.000 0.00 0.00 0.00 3.91
310 313 2.099098 CCCGTGGGTGAATAGCAAATTC 59.901 50.000 0.00 5.16 0.00 2.17
314 317 4.858692 CGTGGGTGAATAGCAAATTCAAAG 59.141 41.667 14.05 1.51 39.43 2.77
315 318 5.564651 CGTGGGTGAATAGCAAATTCAAAGT 60.565 40.000 14.05 0.00 39.43 2.66
318 321 7.328493 GTGGGTGAATAGCAAATTCAAAGTAAC 59.672 37.037 14.05 7.10 39.43 2.50
320 323 7.542130 GGGTGAATAGCAAATTCAAAGTAACAG 59.458 37.037 14.05 0.00 39.43 3.16
322 325 7.542130 GTGAATAGCAAATTCAAAGTAACAGGG 59.458 37.037 14.05 0.00 39.43 4.45
330 333 9.119418 CAAATTCAAAGTAACAGGGGAAAAATT 57.881 29.630 0.00 0.00 0.00 1.82
332 335 7.425224 TTCAAAGTAACAGGGGAAAAATTCA 57.575 32.000 0.00 0.00 0.00 2.57
397 634 4.207891 AGTTACTATTCACCAGGTGCAG 57.792 45.455 15.64 13.42 32.98 4.41
412 649 1.227205 GCAGATGAGCCTGGACTCG 60.227 63.158 0.00 0.00 39.68 4.18
426 663 5.368145 CCTGGACTCGGAATTGAATATTCA 58.632 41.667 14.23 14.23 34.92 2.57
428 665 6.148480 CCTGGACTCGGAATTGAATATTCATC 59.852 42.308 18.61 13.62 37.00 2.92
429 666 5.696270 TGGACTCGGAATTGAATATTCATCG 59.304 40.000 18.61 17.79 37.00 3.84
434 671 9.489084 ACTCGGAATTGAATATTCATCGATAAA 57.511 29.630 18.61 2.71 37.00 1.40
461 698 7.305763 GCATTTATTTTAACAAGATTACCGCGG 60.306 37.037 26.86 26.86 0.00 6.46
462 699 3.474693 TTTTAACAAGATTACCGCGGC 57.525 42.857 28.58 9.08 0.00 6.53
463 700 2.096220 TTAACAAGATTACCGCGGCA 57.904 45.000 28.58 10.63 0.00 5.69
464 701 2.096220 TAACAAGATTACCGCGGCAA 57.904 45.000 28.58 21.35 0.00 4.52
465 702 1.240256 AACAAGATTACCGCGGCAAA 58.760 45.000 28.58 20.89 0.00 3.68
468 705 0.100503 AAGATTACCGCGGCAAATGC 59.899 50.000 28.58 17.37 41.14 3.56
485 722 6.090088 GGCAAATGCGTAGAGTATTATCTCTG 59.910 42.308 6.50 0.00 42.17 3.35
487 724 7.169982 GCAAATGCGTAGAGTATTATCTCTGTT 59.830 37.037 6.50 0.00 43.54 3.16
488 725 9.035607 CAAATGCGTAGAGTATTATCTCTGTTT 57.964 33.333 6.50 0.00 43.54 2.83
496 733 7.504403 AGAGTATTATCTCTGTTTGTCCCATG 58.496 38.462 0.00 0.00 42.36 3.66
500 737 9.778741 GTATTATCTCTGTTTGTCCCATGATAA 57.221 33.333 0.00 0.00 32.24 1.75
505 742 9.699410 ATCTCTGTTTGTCCCATGATAAAATAA 57.301 29.630 0.00 0.00 34.01 1.40
506 743 9.177608 TCTCTGTTTGTCCCATGATAAAATAAG 57.822 33.333 0.00 0.00 34.01 1.73
507 744 9.177608 CTCTGTTTGTCCCATGATAAAATAAGA 57.822 33.333 0.00 0.00 34.01 2.10
508 745 9.699410 TCTGTTTGTCCCATGATAAAATAAGAT 57.301 29.630 0.00 0.00 34.01 2.40
509 746 9.956720 CTGTTTGTCCCATGATAAAATAAGATC 57.043 33.333 0.00 0.00 34.01 2.75
510 747 9.699410 TGTTTGTCCCATGATAAAATAAGATCT 57.301 29.630 0.00 0.00 34.01 2.75
547 788 7.425224 AATCTTATATTATGGGACGGAGGAG 57.575 40.000 0.00 0.00 0.00 3.69
550 791 4.676799 ATATTATGGGACGGAGGAGAGA 57.323 45.455 0.00 0.00 0.00 3.10
551 792 2.366640 TTATGGGACGGAGGAGAGAG 57.633 55.000 0.00 0.00 0.00 3.20
552 793 1.223501 TATGGGACGGAGGAGAGAGT 58.776 55.000 0.00 0.00 0.00 3.24
553 794 1.223501 ATGGGACGGAGGAGAGAGTA 58.776 55.000 0.00 0.00 0.00 2.59
554 795 0.547075 TGGGACGGAGGAGAGAGTAG 59.453 60.000 0.00 0.00 0.00 2.57
555 796 0.547553 GGGACGGAGGAGAGAGTAGT 59.452 60.000 0.00 0.00 0.00 2.73
556 797 1.064537 GGGACGGAGGAGAGAGTAGTT 60.065 57.143 0.00 0.00 0.00 2.24
557 798 2.621147 GGGACGGAGGAGAGAGTAGTTT 60.621 54.545 0.00 0.00 0.00 2.66
558 799 3.371380 GGGACGGAGGAGAGAGTAGTTTA 60.371 52.174 0.00 0.00 0.00 2.01
559 800 4.463070 GGACGGAGGAGAGAGTAGTTTAT 58.537 47.826 0.00 0.00 0.00 1.40
560 801 4.516321 GGACGGAGGAGAGAGTAGTTTATC 59.484 50.000 0.00 0.00 0.00 1.75
561 802 4.463070 ACGGAGGAGAGAGTAGTTTATCC 58.537 47.826 0.00 0.00 0.00 2.59
562 803 4.079901 ACGGAGGAGAGAGTAGTTTATCCA 60.080 45.833 4.71 0.00 0.00 3.41
563 804 4.888239 CGGAGGAGAGAGTAGTTTATCCAA 59.112 45.833 4.71 0.00 0.00 3.53
564 805 5.360144 CGGAGGAGAGAGTAGTTTATCCAAA 59.640 44.000 4.71 0.00 0.00 3.28
565 806 6.575267 GGAGGAGAGAGTAGTTTATCCAAAC 58.425 44.000 4.71 0.00 43.71 2.93
566 807 6.154706 GGAGGAGAGAGTAGTTTATCCAAACA 59.845 42.308 4.71 0.00 45.44 2.83
567 808 7.310485 GGAGGAGAGAGTAGTTTATCCAAACAA 60.310 40.741 4.71 0.00 45.44 2.83
568 809 7.387643 AGGAGAGAGTAGTTTATCCAAACAAC 58.612 38.462 4.71 0.00 45.44 3.32
569 810 7.235812 AGGAGAGAGTAGTTTATCCAAACAACT 59.764 37.037 4.71 0.00 45.44 3.16
570 811 7.878644 GGAGAGAGTAGTTTATCCAAACAACTT 59.121 37.037 0.00 0.00 45.44 2.66
571 812 8.834749 AGAGAGTAGTTTATCCAAACAACTTC 57.165 34.615 3.36 0.00 45.44 3.01
572 813 8.429641 AGAGAGTAGTTTATCCAAACAACTTCA 58.570 33.333 3.36 0.00 45.44 3.02
573 814 8.608844 AGAGTAGTTTATCCAAACAACTTCAG 57.391 34.615 3.36 0.00 45.44 3.02
574 815 8.429641 AGAGTAGTTTATCCAAACAACTTCAGA 58.570 33.333 3.36 0.00 45.44 3.27
575 816 8.379457 AGTAGTTTATCCAAACAACTTCAGAC 57.621 34.615 3.36 0.00 45.44 3.51
576 817 8.211629 AGTAGTTTATCCAAACAACTTCAGACT 58.788 33.333 3.36 0.00 45.44 3.24
577 818 7.881775 AGTTTATCCAAACAACTTCAGACTT 57.118 32.000 3.36 0.00 45.44 3.01
578 819 8.293699 AGTTTATCCAAACAACTTCAGACTTT 57.706 30.769 3.36 0.00 45.44 2.66
579 820 9.403583 AGTTTATCCAAACAACTTCAGACTTTA 57.596 29.630 3.36 0.00 45.44 1.85
624 865 8.608844 AAGAAACACCTCATACTTTTAGTCAG 57.391 34.615 0.00 0.00 0.00 3.51
636 877 0.895530 TTAGTCAGTTGCTCGGGGAG 59.104 55.000 0.00 0.00 0.00 4.30
639 880 0.670854 GTCAGTTGCTCGGGGAGAAC 60.671 60.000 0.00 0.00 0.00 3.01
754 997 3.521529 ATCCTATGCGGCCTCGTGC 62.522 63.158 0.00 0.00 38.89 5.34
765 1008 3.151022 CTCGTGCTCTCCCCTCCC 61.151 72.222 0.00 0.00 0.00 4.30
791 1034 0.608640 TTCCTCTGACTTCTTCGCCC 59.391 55.000 0.00 0.00 0.00 6.13
820 1073 2.835895 GTCCTCGCCTCCTCCTCC 60.836 72.222 0.00 0.00 0.00 4.30
821 1074 3.024356 TCCTCGCCTCCTCCTCCT 61.024 66.667 0.00 0.00 0.00 3.69
822 1075 2.520741 CCTCGCCTCCTCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
823 1076 2.520741 CTCGCCTCCTCCTCCTCC 60.521 72.222 0.00 0.00 0.00 4.30
824 1077 3.024356 TCGCCTCCTCCTCCTCCT 61.024 66.667 0.00 0.00 0.00 3.69
825 1078 2.520741 CGCCTCCTCCTCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
826 1079 2.123033 GCCTCCTCCTCCTCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
827 1080 2.710826 GCCTCCTCCTCCTCCTCCT 61.711 68.421 0.00 0.00 0.00 3.69
828 1081 1.541672 CCTCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
829 1082 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
830 1083 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
831 1084 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
871 1124 3.760035 CCCGACCCGACCTGACTG 61.760 72.222 0.00 0.00 0.00 3.51
872 1125 2.675423 CCGACCCGACCTGACTGA 60.675 66.667 0.00 0.00 0.00 3.41
873 1126 2.567049 CGACCCGACCTGACTGAC 59.433 66.667 0.00 0.00 0.00 3.51
874 1127 1.972223 CGACCCGACCTGACTGACT 60.972 63.158 0.00 0.00 0.00 3.41
925 1178 1.497722 GCAACTGCTTACCTCACGC 59.502 57.895 0.00 0.00 38.21 5.34
1310 1575 1.665137 GTTAAACCCCTCCTCCTCCA 58.335 55.000 0.00 0.00 0.00 3.86
1329 1595 2.593956 GGCCCCTCTCTGTTTCCGT 61.594 63.158 0.00 0.00 0.00 4.69
1440 1707 5.414454 CGACCCAATATGTTTCTTCTTGGAA 59.586 40.000 1.31 0.00 38.92 3.53
1557 1827 0.404812 TCTATCTCCCCGCCTAGTCC 59.595 60.000 0.00 0.00 0.00 3.85
1573 1843 0.972883 GTCCAGTGCTCTGTTCTCCT 59.027 55.000 14.31 0.00 39.82 3.69
1646 1917 0.322816 TTGGATCAGGCCTGCTGAAC 60.323 55.000 28.91 15.61 34.26 3.18
1649 1920 1.919600 GATCAGGCCTGCTGAACCCT 61.920 60.000 28.91 4.37 34.26 4.34
1796 2067 1.823899 CTTCCATACCAAGCCGGGC 60.824 63.158 12.11 12.11 40.22 6.13
1869 2152 2.241880 CCGGCAGAAACGTTCGTGT 61.242 57.895 0.00 0.00 34.02 4.49
1974 2257 4.560743 TCTGCGGTTGCTGTGCCA 62.561 61.111 0.00 0.00 43.34 4.92
1982 2265 1.845664 TTGCTGTGCCAGGGGACTA 60.846 57.895 11.37 0.00 40.21 2.59
1992 2275 4.082190 GTGCCAGGGGACTAAAGAATTTTC 60.082 45.833 2.37 0.00 40.09 2.29
2004 2287 3.258971 AGAATTTTCAGGAGCTCGAGG 57.741 47.619 15.58 0.00 0.00 4.63
2007 2290 0.320771 TTTTCAGGAGCTCGAGGTGC 60.321 55.000 26.32 26.32 0.00 5.01
2027 2310 2.806382 GCTCAGGAATTCTAGCTCTGCC 60.806 54.545 15.97 0.00 32.18 4.85
2132 2415 0.607489 GGGATGCTGTGCTTGAGTGT 60.607 55.000 0.00 0.00 0.00 3.55
2165 2448 2.674796 ATTCTGGGCAAGTAGACGAC 57.325 50.000 0.00 0.00 0.00 4.34
2272 2555 9.436957 AAGTAAGTATCAGTACTCCATTTGTTG 57.563 33.333 0.00 0.00 40.24 3.33
2332 2615 9.938280 TTTCTCCTCTTAAATCACTTATTCGAA 57.062 29.630 0.00 0.00 0.00 3.71
2362 2645 8.695456 AGACAGTTTGAAATTGTTTACTGGATT 58.305 29.630 7.50 0.00 37.80 3.01
2395 2678 5.197806 AGGGGGAGTGGGAATAAATTACAAT 59.802 40.000 0.00 0.00 0.00 2.71
2398 2681 7.396339 GGGGGAGTGGGAATAAATTACAATATC 59.604 40.741 0.00 0.00 0.00 1.63
2417 2700 8.828751 ACAATATCTAAAAGGTTGGGTACTGTA 58.171 33.333 0.00 0.00 21.68 2.74
2474 2757 4.185394 TCTGCTGCCATTTTGCAAATATG 58.815 39.130 13.65 17.26 41.51 1.78
2491 2775 1.648116 ATGCAAGGCAGGGAAAATGT 58.352 45.000 0.00 0.00 43.65 2.71
2522 2806 2.811431 CAGTGACGGCCATTTTCAGTAA 59.189 45.455 2.24 0.00 0.00 2.24
2679 2966 8.813282 GTTTGTTTCGGTTCTAATTTCAAATGT 58.187 29.630 0.00 0.00 0.00 2.71
2724 3011 1.746615 GGTGCGCCATGTCACTGAT 60.747 57.895 12.58 0.00 33.91 2.90
2740 3027 7.492524 TGTCACTGATAATGTAGAGTTGGATC 58.507 38.462 0.00 0.00 0.00 3.36
2852 3139 4.801330 ATGATGACACCTACGAGTTTGA 57.199 40.909 0.00 0.00 0.00 2.69
2928 3215 6.226787 TGAGAAAGAAGATCCAGAGTCAAAC 58.773 40.000 0.00 0.00 0.00 2.93
2958 3245 3.134458 GGCCGTCTCTAATTTCCATCAG 58.866 50.000 0.00 0.00 0.00 2.90
3386 3675 2.966516 GGTATACTCACTTGAGGGAGGG 59.033 54.545 14.36 0.00 46.13 4.30
3406 3695 1.211949 GGCAGTTGGCTAAGATACCCA 59.788 52.381 0.00 0.00 44.01 4.51
3415 3704 5.437060 TGGCTAAGATACCCATTTTCTGTC 58.563 41.667 0.00 0.00 0.00 3.51
3433 3722 4.067896 CTGTCAACTCCATACTGCAAACT 58.932 43.478 0.00 0.00 0.00 2.66
3434 3723 5.011635 TCTGTCAACTCCATACTGCAAACTA 59.988 40.000 0.00 0.00 0.00 2.24
3435 3724 5.237815 TGTCAACTCCATACTGCAAACTAG 58.762 41.667 0.00 0.00 0.00 2.57
3498 3787 9.396022 GACTTGGTCCTTATGAATATCTCAAAA 57.604 33.333 0.00 0.00 37.67 2.44
3531 3820 4.572950 GCAACATACTTCATTTGCTTGC 57.427 40.909 0.00 0.00 40.97 4.01
3538 3827 2.268298 CTTCATTTGCTTGCAGGCATC 58.732 47.619 25.18 0.00 42.09 3.91
3594 3883 5.163663 CCTTTCGCATTCTACCTTGCATAAA 60.164 40.000 0.00 0.00 38.80 1.40
3623 3913 8.028354 TGATTGCTGACAGTAAACAAATATTGG 58.972 33.333 12.65 0.00 34.12 3.16
3748 4038 7.567250 TCCTAGGATACAGGTATGTTGAATTGA 59.433 37.037 7.62 0.00 41.01 2.57
3830 4124 8.583810 AATTATGCATTCACATAAGAACATGC 57.416 30.769 3.54 0.00 43.70 4.06
3834 4313 4.675510 CATTCACATAAGAACATGCCACC 58.324 43.478 0.00 0.00 0.00 4.61
3918 4409 9.857957 ACTCCAAACTTATTGTTTTCGTAAAAA 57.142 25.926 0.00 0.00 45.69 1.94
4441 4932 9.489084 TTGCAATACATGGACTTCATAGTATAC 57.511 33.333 0.00 0.00 33.33 1.47
4450 4941 8.112016 TGGACTTCATAGTATACTAGCATGTC 57.888 38.462 17.31 18.78 33.84 3.06
4498 4989 5.070001 TGTAAATCTGTGGTCCTCCAAAAG 58.930 41.667 0.00 0.00 46.15 2.27
4608 5099 3.581332 TGGAGGACGTGGATAGTCTTTTT 59.419 43.478 0.00 0.00 38.58 1.94
4614 5105 8.302515 AGGACGTGGATAGTCTTTTTATCTTA 57.697 34.615 0.00 0.00 38.58 2.10
4688 5180 8.443953 TGTTTTACCATTTAAAAGCAGCAAAT 57.556 26.923 0.00 0.00 0.00 2.32
4750 5242 8.424918 ACATGACAGGTACTATTTCCTAATGAG 58.575 37.037 0.00 0.00 36.02 2.90
4828 5320 4.993705 AATGTTAGAGTTGGGACAGGAA 57.006 40.909 0.00 0.00 42.39 3.36
4921 5413 3.073798 TGTTTCAAGCCCCTATCAGTCAA 59.926 43.478 0.00 0.00 0.00 3.18
4931 5423 5.068987 GCCCCTATCAGTCAAATGCATTAAA 59.931 40.000 13.39 0.55 0.00 1.52
5032 5526 3.133721 CCAGGAGACAGGTCAATTAGAGG 59.866 52.174 1.84 0.00 31.08 3.69
5034 5528 4.099266 CAGGAGACAGGTCAATTAGAGGAG 59.901 50.000 1.84 0.00 0.00 3.69
5037 5531 5.657302 GGAGACAGGTCAATTAGAGGAGTTA 59.343 44.000 1.84 0.00 0.00 2.24
5038 5532 6.183360 GGAGACAGGTCAATTAGAGGAGTTAG 60.183 46.154 1.84 0.00 0.00 2.34
5052 5546 3.703921 GGAGTTAGTCCCAGAGAAGTCT 58.296 50.000 0.00 0.00 39.88 3.24
5085 5579 1.153107 CTTGCGATGCCCTGATCCA 60.153 57.895 0.00 0.00 0.00 3.41
5365 5861 2.907042 CCTTGAGGTGTAGAGGGTCTTT 59.093 50.000 0.00 0.00 0.00 2.52
5388 5884 0.105408 CTTTTGGCTGCAGGCTTTGT 59.895 50.000 36.39 0.00 41.69 2.83
5415 5911 2.268076 CCTGTGGCCCGGTTTCTTG 61.268 63.158 0.00 0.00 0.00 3.02
5601 6101 6.640518 GTCCAGTGTTTGATAAGGACATCTA 58.359 40.000 0.00 0.00 43.74 1.98
5645 6145 1.228003 ACCAAACATCGGCGGACAA 60.228 52.632 7.21 0.00 0.00 3.18
5680 6180 1.526575 CCATCAACCTGGTGCACCAC 61.527 60.000 34.74 10.57 42.01 4.16
5692 6226 2.815211 CACCACATGTCCGCTCCG 60.815 66.667 0.00 0.00 0.00 4.63
5742 6285 8.260270 TGATGCATACATAGATCAATAGCAAC 57.740 34.615 0.00 0.00 36.35 4.17
5744 6287 7.895975 TGCATACATAGATCAATAGCAACTC 57.104 36.000 0.00 0.00 0.00 3.01
5747 6290 7.601886 GCATACATAGATCAATAGCAACTCAGT 59.398 37.037 0.00 0.00 0.00 3.41
5748 6291 8.923683 CATACATAGATCAATAGCAACTCAGTG 58.076 37.037 0.00 0.00 0.00 3.66
5750 6293 6.983307 ACATAGATCAATAGCAACTCAGTGAC 59.017 38.462 0.00 0.00 0.00 3.67
5751 6294 5.411831 AGATCAATAGCAACTCAGTGACA 57.588 39.130 0.00 0.00 0.00 3.58
5752 6295 5.798132 AGATCAATAGCAACTCAGTGACAA 58.202 37.500 0.00 0.00 0.00 3.18
5754 6297 5.868043 TCAATAGCAACTCAGTGACAATG 57.132 39.130 0.00 0.00 0.00 2.82
5756 6299 5.764686 TCAATAGCAACTCAGTGACAATGTT 59.235 36.000 2.39 0.00 0.00 2.71
5757 6300 5.869753 ATAGCAACTCAGTGACAATGTTC 57.130 39.130 2.39 0.00 0.00 3.18
5758 6301 3.544684 AGCAACTCAGTGACAATGTTCA 58.455 40.909 2.39 0.00 0.00 3.18
5761 6304 5.942236 AGCAACTCAGTGACAATGTTCATAT 59.058 36.000 2.39 0.00 0.00 1.78
5762 6305 6.025896 GCAACTCAGTGACAATGTTCATATG 58.974 40.000 2.39 0.00 0.00 1.78
5763 6306 5.808042 ACTCAGTGACAATGTTCATATGC 57.192 39.130 2.39 0.00 0.00 3.14
5765 6308 5.884232 ACTCAGTGACAATGTTCATATGCAT 59.116 36.000 3.79 3.79 0.00 3.96
5766 6309 6.037940 ACTCAGTGACAATGTTCATATGCATC 59.962 38.462 0.19 0.00 0.00 3.91
5767 6310 5.881443 TCAGTGACAATGTTCATATGCATCA 59.119 36.000 0.19 0.00 0.00 3.07
5768 6311 6.544564 TCAGTGACAATGTTCATATGCATCAT 59.455 34.615 0.19 0.00 0.00 2.45
5769 6312 7.067737 TCAGTGACAATGTTCATATGCATCATT 59.932 33.333 0.19 3.37 0.00 2.57
5770 6313 7.378728 CAGTGACAATGTTCATATGCATCATTC 59.621 37.037 0.19 0.00 0.00 2.67
5771 6314 7.067737 AGTGACAATGTTCATATGCATCATTCA 59.932 33.333 0.19 0.00 0.00 2.57
5772 6315 7.378728 GTGACAATGTTCATATGCATCATTCAG 59.621 37.037 0.19 0.00 0.00 3.02
5773 6316 7.283580 TGACAATGTTCATATGCATCATTCAGA 59.716 33.333 0.19 0.00 0.00 3.27
5774 6317 8.178313 ACAATGTTCATATGCATCATTCAGAT 57.822 30.769 0.19 0.00 37.48 2.90
5783 6326 2.852449 CATCATTCAGATGCAGAGGCT 58.148 47.619 0.00 0.00 46.90 4.58
5784 6327 2.327200 TCATTCAGATGCAGAGGCTG 57.673 50.000 0.00 0.00 41.91 4.85
5785 6328 1.134189 TCATTCAGATGCAGAGGCTGG 60.134 52.381 0.00 0.00 41.91 4.85
5786 6329 0.183014 ATTCAGATGCAGAGGCTGGG 59.817 55.000 0.00 0.00 41.91 4.45
5787 6330 1.918467 TTCAGATGCAGAGGCTGGGG 61.918 60.000 0.00 0.00 41.91 4.96
5788 6331 3.806667 AGATGCAGAGGCTGGGGC 61.807 66.667 0.00 0.00 41.91 5.80
5789 6332 4.119363 GATGCAGAGGCTGGGGCA 62.119 66.667 6.76 6.76 41.91 5.36
5790 6333 3.426836 ATGCAGAGGCTGGGGCAT 61.427 61.111 10.35 10.35 41.81 4.40
5791 6334 2.060567 GATGCAGAGGCTGGGGCATA 62.061 60.000 14.71 0.00 46.17 3.14
5792 6335 2.203266 GCAGAGGCTGGGGCATAC 60.203 66.667 0.00 0.00 40.87 2.39
5793 6336 2.512896 CAGAGGCTGGGGCATACC 59.487 66.667 0.00 0.00 40.87 2.73
5835 6378 7.733402 AATGCAATCACAACTAAAAAGCATT 57.267 28.000 0.00 0.00 43.06 3.56
5861 6404 6.645003 GGATCAACAAGTTTTTACATCCAACC 59.355 38.462 0.00 0.00 0.00 3.77
5866 6409 5.768164 ACAAGTTTTTACATCCAACCGATCT 59.232 36.000 0.00 0.00 0.00 2.75
5875 6418 5.805728 ACATCCAACCGATCTAAAAAGAGT 58.194 37.500 0.00 0.00 0.00 3.24
5876 6419 5.875359 ACATCCAACCGATCTAAAAAGAGTC 59.125 40.000 0.00 0.00 0.00 3.36
5877 6420 5.477607 TCCAACCGATCTAAAAAGAGTCA 57.522 39.130 0.00 0.00 0.00 3.41
5882 6425 6.110411 ACCGATCTAAAAAGAGTCAAGGAA 57.890 37.500 0.00 0.00 0.00 3.36
5884 6427 5.582665 CCGATCTAAAAAGAGTCAAGGAAGG 59.417 44.000 0.00 0.00 0.00 3.46
5919 6462 3.508845 TTTTGCCTCCTAGTTCAGCTT 57.491 42.857 0.00 0.00 0.00 3.74
5936 6479 4.338118 TCAGCTTTCCGTGTCAAATTCTTT 59.662 37.500 0.00 0.00 0.00 2.52
5945 6488 4.684703 CGTGTCAAATTCTTTACTCCTCGT 59.315 41.667 0.00 0.00 0.00 4.18
5947 6490 5.927115 GTGTCAAATTCTTTACTCCTCGTCT 59.073 40.000 0.00 0.00 0.00 4.18
5965 6508 1.684386 CTGGCTCCTCCGAAGCATCT 61.684 60.000 0.00 0.00 41.66 2.90
5967 6510 1.680522 GGCTCCTCCGAAGCATCTGA 61.681 60.000 0.00 0.00 41.66 3.27
5980 6523 1.539929 GCATCTGAGTAGCGCTCCAAT 60.540 52.381 16.34 0.00 43.48 3.16
6018 6561 1.301677 TGCACAATGTTCGCCGCATA 61.302 50.000 0.00 0.00 0.00 3.14
6020 6563 1.006086 CACAATGTTCGCCGCATAGA 58.994 50.000 0.00 0.00 0.00 1.98
6048 6591 3.198635 AGTCCGACATCTTCATGGTCAAT 59.801 43.478 0.40 0.00 33.82 2.57
6122 6673 4.792068 TCCATGAACTTGTCAAACCTCTT 58.208 39.130 0.00 0.00 40.50 2.85
6151 6702 4.834496 TCTTTTCCTCCTTTGCATCATTGT 59.166 37.500 0.00 0.00 0.00 2.71
6152 6703 4.524316 TTTCCTCCTTTGCATCATTGTG 57.476 40.909 0.00 0.00 0.00 3.33
6158 6709 3.512329 TCCTTTGCATCATTGTGCTTGAT 59.488 39.130 10.93 0.00 45.27 2.57
6167 6718 4.779696 TCATTGTGCTTGATGTATGCCTA 58.220 39.130 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.945033 AAACTTAGTGCAACCAAATAATGTG 57.055 32.000 0.00 0.00 37.80 3.21
3 4 7.984617 ACAAAACTTAGTGCAACCAAATAATGT 59.015 29.630 0.00 0.00 37.80 2.71
4 5 8.274939 CACAAAACTTAGTGCAACCAAATAATG 58.725 33.333 0.00 0.00 37.80 1.90
5 6 8.364129 CACAAAACTTAGTGCAACCAAATAAT 57.636 30.769 0.00 0.00 37.80 1.28
41 42 5.063438 TGCTTCAAGCGTCAAATACATAGAC 59.937 40.000 4.57 0.00 46.26 2.59
42 43 5.175127 TGCTTCAAGCGTCAAATACATAGA 58.825 37.500 4.57 0.00 46.26 1.98
43 44 5.469373 TGCTTCAAGCGTCAAATACATAG 57.531 39.130 4.57 0.00 46.26 2.23
46 48 4.693095 TGTATGCTTCAAGCGTCAAATACA 59.307 37.500 7.58 11.04 46.26 2.29
52 54 5.639082 CCATATATGTATGCTTCAAGCGTCA 59.361 40.000 7.58 6.78 46.26 4.35
55 57 6.147656 TGAACCATATATGTATGCTTCAAGCG 59.852 38.462 14.43 0.00 46.26 4.68
99 101 4.916983 TGCAGCTAAAACAGTGTCATTT 57.083 36.364 0.00 0.00 0.00 2.32
126 129 4.338682 GCATGCATGAAGGAGAGAGAAAAT 59.661 41.667 30.64 0.00 0.00 1.82
236 239 4.397103 CGTCCCGCTATTAGGTGATATGTA 59.603 45.833 0.00 0.00 0.00 2.29
242 245 1.315690 CTCGTCCCGCTATTAGGTGA 58.684 55.000 0.00 0.00 0.00 4.02
264 267 2.026822 AGATGCACCGGAGAGTTGAAAT 60.027 45.455 9.46 0.00 0.00 2.17
269 272 1.078848 GCAGATGCACCGGAGAGTT 60.079 57.895 9.46 0.00 41.59 3.01
270 273 2.581354 GCAGATGCACCGGAGAGT 59.419 61.111 9.46 0.00 41.59 3.24
304 307 8.675705 ATTTTTCCCCTGTTACTTTGAATTTG 57.324 30.769 0.00 0.00 0.00 2.32
310 313 8.499403 TTTTGAATTTTTCCCCTGTTACTTTG 57.501 30.769 0.00 0.00 0.00 2.77
345 348 9.906660 AAACATAGCATAAGAAATCGAAAAACA 57.093 25.926 0.00 0.00 0.00 2.83
352 589 9.559958 ACTTCAAAAACATAGCATAAGAAATCG 57.440 29.630 0.00 0.00 0.00 3.34
368 605 7.860872 CACCTGGTGAATAGTAACTTCAAAAAC 59.139 37.037 22.33 0.00 35.23 2.43
376 613 3.838317 TCTGCACCTGGTGAATAGTAACT 59.162 43.478 30.23 0.00 35.23 2.24
379 616 4.030216 TCATCTGCACCTGGTGAATAGTA 58.970 43.478 30.23 13.46 35.23 1.82
397 634 0.755686 ATTCCGAGTCCAGGCTCATC 59.244 55.000 10.44 0.00 35.33 2.92
434 671 7.431084 CGCGGTAATCTTGTTAAAATAAATGCT 59.569 33.333 0.00 0.00 0.00 3.79
461 698 6.642950 ACAGAGATAATACTCTACGCATTTGC 59.357 38.462 0.00 0.00 44.18 3.68
462 699 8.581057 AACAGAGATAATACTCTACGCATTTG 57.419 34.615 0.00 0.00 44.18 2.32
463 700 9.035607 CAAACAGAGATAATACTCTACGCATTT 57.964 33.333 0.00 0.00 44.18 2.32
464 701 8.198109 ACAAACAGAGATAATACTCTACGCATT 58.802 33.333 0.00 0.00 44.18 3.56
465 702 7.717568 ACAAACAGAGATAATACTCTACGCAT 58.282 34.615 0.00 0.00 44.18 4.73
468 705 7.140048 GGGACAAACAGAGATAATACTCTACG 58.860 42.308 0.00 0.00 44.18 3.51
469 706 8.008513 TGGGACAAACAGAGATAATACTCTAC 57.991 38.462 0.00 0.00 39.51 2.59
522 759 8.341513 TCTCCTCCGTCCCATAATATAAGATTA 58.658 37.037 0.00 0.00 0.00 1.75
530 771 3.398292 ACTCTCTCCTCCGTCCCATAATA 59.602 47.826 0.00 0.00 0.00 0.98
541 782 6.154706 TGTTTGGATAAACTACTCTCTCCTCC 59.845 42.308 4.76 0.00 45.06 4.30
551 792 8.379457 AGTCTGAAGTTGTTTGGATAAACTAC 57.621 34.615 8.66 8.66 46.13 2.73
552 793 8.974060 AAGTCTGAAGTTGTTTGGATAAACTA 57.026 30.769 4.76 0.00 45.06 2.24
553 794 7.881775 AAGTCTGAAGTTGTTTGGATAAACT 57.118 32.000 4.76 0.00 45.06 2.66
598 839 8.974060 TGACTAAAAGTATGAGGTGTTTCTTT 57.026 30.769 0.00 0.00 0.00 2.52
599 840 8.211629 ACTGACTAAAAGTATGAGGTGTTTCTT 58.788 33.333 0.00 0.00 0.00 2.52
600 841 7.736893 ACTGACTAAAAGTATGAGGTGTTTCT 58.263 34.615 0.00 0.00 0.00 2.52
601 842 7.964604 ACTGACTAAAAGTATGAGGTGTTTC 57.035 36.000 0.00 0.00 0.00 2.78
602 843 7.255139 GCAACTGACTAAAAGTATGAGGTGTTT 60.255 37.037 0.00 0.00 0.00 2.83
603 844 6.204882 GCAACTGACTAAAAGTATGAGGTGTT 59.795 38.462 0.00 0.00 0.00 3.32
604 845 5.701290 GCAACTGACTAAAAGTATGAGGTGT 59.299 40.000 0.00 0.00 0.00 4.16
605 846 5.934625 AGCAACTGACTAAAAGTATGAGGTG 59.065 40.000 0.00 0.00 0.00 4.00
606 847 6.115448 AGCAACTGACTAAAAGTATGAGGT 57.885 37.500 0.00 0.00 0.00 3.85
607 848 5.289675 CGAGCAACTGACTAAAAGTATGAGG 59.710 44.000 0.00 0.00 0.00 3.86
608 849 5.289675 CCGAGCAACTGACTAAAAGTATGAG 59.710 44.000 0.00 0.00 0.00 2.90
609 850 5.168569 CCGAGCAACTGACTAAAAGTATGA 58.831 41.667 0.00 0.00 0.00 2.15
610 851 4.330074 CCCGAGCAACTGACTAAAAGTATG 59.670 45.833 0.00 0.00 0.00 2.39
611 852 4.504858 CCCGAGCAACTGACTAAAAGTAT 58.495 43.478 0.00 0.00 0.00 2.12
612 853 3.306502 CCCCGAGCAACTGACTAAAAGTA 60.307 47.826 0.00 0.00 0.00 2.24
613 854 2.550208 CCCCGAGCAACTGACTAAAAGT 60.550 50.000 0.00 0.00 0.00 2.66
614 855 2.076863 CCCCGAGCAACTGACTAAAAG 58.923 52.381 0.00 0.00 0.00 2.27
615 856 1.695242 TCCCCGAGCAACTGACTAAAA 59.305 47.619 0.00 0.00 0.00 1.52
616 857 1.275291 CTCCCCGAGCAACTGACTAAA 59.725 52.381 0.00 0.00 0.00 1.85
617 858 0.895530 CTCCCCGAGCAACTGACTAA 59.104 55.000 0.00 0.00 0.00 2.24
618 859 0.039180 TCTCCCCGAGCAACTGACTA 59.961 55.000 0.00 0.00 0.00 2.59
619 860 0.832135 TTCTCCCCGAGCAACTGACT 60.832 55.000 0.00 0.00 0.00 3.41
754 997 0.341609 AAAGAGAGGGGAGGGGAGAG 59.658 60.000 0.00 0.00 0.00 3.20
765 1008 4.380444 CGAAGAAGTCAGAGGAAAGAGAGG 60.380 50.000 0.00 0.00 0.00 3.69
791 1034 1.671901 GCGAGGACTGGAGAAGGAGG 61.672 65.000 0.00 0.00 0.00 4.30
820 1073 0.179029 GAGAGGACGAGGAGGAGGAG 60.179 65.000 0.00 0.00 0.00 3.69
821 1074 1.637724 GGAGAGGACGAGGAGGAGGA 61.638 65.000 0.00 0.00 0.00 3.71
822 1075 1.152839 GGAGAGGACGAGGAGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
823 1076 0.179029 GAGGAGAGGACGAGGAGGAG 60.179 65.000 0.00 0.00 0.00 3.69
824 1077 1.637724 GGAGGAGAGGACGAGGAGGA 61.638 65.000 0.00 0.00 0.00 3.71
825 1078 1.152839 GGAGGAGAGGACGAGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
826 1079 1.152839 GGGAGGAGAGGACGAGGAG 60.153 68.421 0.00 0.00 0.00 3.69
827 1080 2.691779 GGGGAGGAGAGGACGAGGA 61.692 68.421 0.00 0.00 0.00 3.71
828 1081 2.123640 GGGGAGGAGAGGACGAGG 60.124 72.222 0.00 0.00 0.00 4.63
829 1082 2.123640 GGGGGAGGAGAGGACGAG 60.124 72.222 0.00 0.00 0.00 4.18
830 1083 4.124943 CGGGGGAGGAGAGGACGA 62.125 72.222 0.00 0.00 0.00 4.20
1310 1575 2.294078 CGGAAACAGAGAGGGGCCT 61.294 63.158 0.84 0.00 0.00 5.19
1350 1616 1.299165 CGGATCGAGATTTCGCGGT 60.299 57.895 6.13 0.00 46.28 5.68
1454 1721 8.086522 CAGGATCAATTTCAATTCTTTGACAGT 58.913 33.333 0.00 0.00 41.50 3.55
1457 1724 6.815142 CCCAGGATCAATTTCAATTCTTTGAC 59.185 38.462 0.00 0.00 41.50 3.18
1521 1788 0.598065 AGAATTTTGTGGCAGGCGTC 59.402 50.000 0.00 0.00 0.00 5.19
1523 1790 2.684881 AGATAGAATTTTGTGGCAGGCG 59.315 45.455 0.00 0.00 0.00 5.52
1529 1796 2.618709 GCGGGGAGATAGAATTTTGTGG 59.381 50.000 0.00 0.00 0.00 4.17
1646 1917 1.813753 CGACCACACGCCATAAGGG 60.814 63.158 0.00 0.00 40.85 3.95
1649 1920 1.444724 CGACGACCACACGCCATAA 60.445 57.895 0.00 0.00 36.70 1.90
1796 2067 0.814457 CCTCCTCCTTGTCTCTGTCG 59.186 60.000 0.00 0.00 0.00 4.35
1845 2128 2.742372 CGTTTCTGCCGGTCCTGG 60.742 66.667 1.90 0.00 0.00 4.45
1869 2152 2.221299 AGTAGTCGCCAGGGCCAAA 61.221 57.895 6.18 0.00 37.98 3.28
1907 2190 1.746615 CCCCTCACAGCCGTCATTG 60.747 63.158 0.00 0.00 0.00 2.82
1974 2257 5.808050 GCTCCTGAAAATTCTTTAGTCCCCT 60.808 44.000 0.00 0.00 0.00 4.79
1982 2265 4.006319 CCTCGAGCTCCTGAAAATTCTTT 58.994 43.478 6.99 0.00 0.00 2.52
2004 2287 3.456280 CAGAGCTAGAATTCCTGAGCAC 58.544 50.000 20.59 16.11 37.40 4.40
2007 2290 2.545532 CGGCAGAGCTAGAATTCCTGAG 60.546 54.545 11.47 4.52 0.00 3.35
2010 2293 1.137872 CACGGCAGAGCTAGAATTCCT 59.862 52.381 0.65 0.00 0.00 3.36
2012 2295 2.301577 ACACGGCAGAGCTAGAATTC 57.698 50.000 0.00 0.00 0.00 2.17
2027 2310 3.383505 TGATCTTGTACCTCCCATACACG 59.616 47.826 0.00 0.00 32.30 4.49
2165 2448 2.352651 CACAACATTCAGCTCCATACGG 59.647 50.000 0.00 0.00 0.00 4.02
2326 2609 8.137437 ACAATTTCAAACTGTCTTCATTCGAAT 58.863 29.630 4.39 4.39 0.00 3.34
2332 2615 9.520204 CAGTAAACAATTTCAAACTGTCTTCAT 57.480 29.630 0.00 0.00 31.82 2.57
2362 2645 2.319747 TCCCACTCCCCCTCTACATTAA 59.680 50.000 0.00 0.00 0.00 1.40
2395 2678 8.117956 TCTCTACAGTACCCAACCTTTTAGATA 58.882 37.037 0.00 0.00 0.00 1.98
2398 2681 6.600882 TCTCTACAGTACCCAACCTTTTAG 57.399 41.667 0.00 0.00 0.00 1.85
2417 2700 8.655935 ATTTACAATTCAACCTGGAAATCTCT 57.344 30.769 0.00 0.00 31.71 3.10
2474 2757 3.893326 ATAACATTTTCCCTGCCTTGC 57.107 42.857 0.00 0.00 0.00 4.01
2515 2799 4.821260 TGCAGCTCTGAAAATGTTACTGAA 59.179 37.500 0.29 0.00 0.00 3.02
2522 2806 6.927416 TGATTATTTGCAGCTCTGAAAATGT 58.073 32.000 20.68 12.09 45.72 2.71
2590 2874 1.065199 ACAGGCACTACATGACCCATG 60.065 52.381 0.00 5.48 42.18 3.66
2679 2966 2.568062 TGGACCTATGCAAGACGGTAAA 59.432 45.455 0.00 0.00 0.00 2.01
2740 3027 9.801714 GCTTTTCAGATTGTTTTCATTGTTATG 57.198 29.630 0.00 0.00 0.00 1.90
2852 3139 4.352009 TGTATTCAATGGCCCAACATCTT 58.648 39.130 0.00 0.00 0.00 2.40
2928 3215 3.459232 TTAGAGACGGCCTGATCAATG 57.541 47.619 0.00 0.00 0.00 2.82
2958 3245 8.433421 TTCTCAATTCAAATACCTCGTATTCC 57.567 34.615 0.00 0.00 37.69 3.01
3104 3393 9.927668 GAATTCAAGACAATGGGAAAATCTTTA 57.072 29.630 0.00 0.00 0.00 1.85
3386 3675 1.968704 GGGTATCTTAGCCAACTGCC 58.031 55.000 0.00 0.00 45.50 4.85
3406 3695 5.316167 TGCAGTATGGAGTTGACAGAAAAT 58.684 37.500 0.00 0.00 35.86 1.82
3415 3704 6.398918 AGTACTAGTTTGCAGTATGGAGTTG 58.601 40.000 0.00 0.00 38.09 3.16
3498 3787 7.170393 TGAAGTATGTTGCTACAGTACATCT 57.830 36.000 7.16 0.00 37.77 2.90
3531 3820 1.202065 CGACAATCAAACGGATGCCTG 60.202 52.381 0.00 0.00 36.02 4.85
3538 3827 1.927174 CTAGGCTCGACAATCAAACGG 59.073 52.381 0.00 0.00 0.00 4.44
3623 3913 4.919754 GTGACAATGAAAAGATGTTCCTGC 59.080 41.667 0.00 0.00 0.00 4.85
3815 4105 3.244875 ACAGGTGGCATGTTCTTATGTGA 60.245 43.478 0.00 0.00 0.00 3.58
3823 4113 1.644786 GGCGTACAGGTGGCATGTTC 61.645 60.000 0.00 0.00 32.02 3.18
3824 4114 1.674322 GGCGTACAGGTGGCATGTT 60.674 57.895 0.00 0.00 32.02 2.71
3834 4313 1.062002 CAAATAAGGTGCGGCGTACAG 59.938 52.381 28.25 6.16 0.00 2.74
3935 4426 9.665719 TTATAACTGTGCTCAATCTGTTAATCA 57.334 29.630 3.43 0.00 33.93 2.57
4353 4844 9.586435 TCGACCATTATGTGCTTATTATCATAG 57.414 33.333 0.00 0.00 0.00 2.23
4355 4846 8.886719 CATCGACCATTATGTGCTTATTATCAT 58.113 33.333 0.00 0.00 0.00 2.45
4356 4847 7.334171 CCATCGACCATTATGTGCTTATTATCA 59.666 37.037 0.00 0.00 0.00 2.15
4357 4848 7.334421 ACCATCGACCATTATGTGCTTATTATC 59.666 37.037 0.00 0.00 0.00 1.75
4358 4849 7.168219 ACCATCGACCATTATGTGCTTATTAT 58.832 34.615 0.00 0.00 0.00 1.28
4359 4850 6.530120 ACCATCGACCATTATGTGCTTATTA 58.470 36.000 0.00 0.00 0.00 0.98
4360 4851 5.376625 ACCATCGACCATTATGTGCTTATT 58.623 37.500 0.00 0.00 0.00 1.40
4478 4969 2.893489 GCTTTTGGAGGACCACAGATTT 59.107 45.455 0.00 0.00 46.80 2.17
4488 4979 2.050144 ACTCACTCTGCTTTTGGAGGA 58.950 47.619 0.00 0.00 38.51 3.71
4489 4980 2.557920 ACTCACTCTGCTTTTGGAGG 57.442 50.000 0.00 0.00 38.51 4.30
4498 4989 6.102663 TCAAGCTCTATTTTACTCACTCTGC 58.897 40.000 0.00 0.00 0.00 4.26
4614 5105 6.995686 TGTGTTTGTGTGAGTTGAGGTTATAT 59.004 34.615 0.00 0.00 0.00 0.86
4688 5180 8.969260 ACATTATGAGTTTTATGAGCAGATGA 57.031 30.769 0.00 0.00 0.00 2.92
4722 5214 4.770795 AGGAAATAGTACCTGTCATGTGC 58.229 43.478 0.00 0.00 34.99 4.57
4750 5242 0.454600 CAAGCATCATGGACACTGGC 59.545 55.000 0.00 0.00 0.00 4.85
4786 5278 6.669154 ACATTTCCATGTCTATTGGACCAATT 59.331 34.615 24.48 9.36 39.69 2.32
4891 5383 1.070601 GGGGCTTGAAACAGCAAACAT 59.929 47.619 0.00 0.00 42.10 2.71
4921 5413 9.730420 GTGGTTATCGAATACTTTTAATGCATT 57.270 29.630 17.56 17.56 0.00 3.56
5032 5526 5.014202 AGAAGACTTCTCTGGGACTAACTC 58.986 45.833 12.12 0.00 34.07 3.01
5034 5528 5.731957 AAGAAGACTTCTCTGGGACTAAC 57.268 43.478 17.97 0.00 39.61 2.34
5037 5531 3.244387 GCAAAGAAGACTTCTCTGGGACT 60.244 47.826 17.97 0.00 39.61 3.85
5038 5532 3.070748 GCAAAGAAGACTTCTCTGGGAC 58.929 50.000 17.97 0.00 39.61 4.46
5052 5546 1.069973 CGCAAGTGATGTCGCAAAGAA 60.070 47.619 0.00 0.00 0.00 2.52
5085 5579 9.965902 AGATAAGATAGAAAATCCACAAACTGT 57.034 29.630 0.00 0.00 0.00 3.55
5157 5651 1.091771 ATGAAAGCCACGGATGCTCG 61.092 55.000 0.00 0.00 38.34 5.03
5382 5878 0.746659 ACAGGCCAGTTCAACAAAGC 59.253 50.000 5.01 0.00 0.00 3.51
5383 5879 1.067516 CCACAGGCCAGTTCAACAAAG 59.932 52.381 5.01 0.00 0.00 2.77
5415 5911 1.226746 CTGAAAGACCGACACCAACC 58.773 55.000 0.00 0.00 34.07 3.77
5601 6101 0.109781 GATTTGATGCACGGCGTTGT 60.110 50.000 11.19 0.00 0.00 3.32
5645 6145 3.480133 GGCCGGCTCCACTACCAT 61.480 66.667 28.56 0.00 0.00 3.55
5742 6285 5.806366 TGCATATGAACATTGTCACTGAG 57.194 39.130 6.97 0.00 0.00 3.35
5744 6287 6.126568 TGATGCATATGAACATTGTCACTG 57.873 37.500 6.97 0.00 0.00 3.66
5747 6290 7.283580 TCTGAATGATGCATATGAACATTGTCA 59.716 33.333 19.38 13.96 32.50 3.58
5748 6291 7.645402 TCTGAATGATGCATATGAACATTGTC 58.355 34.615 19.38 11.40 32.50 3.18
5750 6293 8.452989 CATCTGAATGATGCATATGAACATTG 57.547 34.615 19.38 11.05 44.96 2.82
5765 6308 1.134189 CCAGCCTCTGCATCTGAATGA 60.134 52.381 6.89 0.00 41.13 2.57
5766 6309 1.309950 CCAGCCTCTGCATCTGAATG 58.690 55.000 6.89 0.00 41.13 2.67
5767 6310 0.183014 CCCAGCCTCTGCATCTGAAT 59.817 55.000 6.89 0.00 41.13 2.57
5768 6311 1.605992 CCCAGCCTCTGCATCTGAA 59.394 57.895 6.89 0.00 41.13 3.02
5769 6312 2.372890 CCCCAGCCTCTGCATCTGA 61.373 63.158 6.89 0.00 41.13 3.27
5770 6313 2.192443 CCCCAGCCTCTGCATCTG 59.808 66.667 0.00 0.00 41.13 2.90
5771 6314 3.806667 GCCCCAGCCTCTGCATCT 61.807 66.667 0.00 0.00 41.13 2.90
5772 6315 2.060567 TATGCCCCAGCCTCTGCATC 62.061 60.000 4.85 0.00 43.01 3.91
5773 6316 2.080536 TATGCCCCAGCCTCTGCAT 61.081 57.895 6.61 6.61 45.67 3.96
5774 6317 2.691996 TATGCCCCAGCCTCTGCA 60.692 61.111 0.00 0.00 41.13 4.41
5775 6318 2.203266 GTATGCCCCAGCCTCTGC 60.203 66.667 0.00 0.00 38.69 4.26
5776 6319 2.512896 GGTATGCCCCAGCCTCTG 59.487 66.667 0.00 0.00 38.69 3.35
5809 6352 7.551035 TGCTTTTTAGTTGTGATTGCATTTT 57.449 28.000 0.00 0.00 0.00 1.82
5811 6354 7.308109 CCAATGCTTTTTAGTTGTGATTGCATT 60.308 33.333 0.00 0.00 45.52 3.56
5835 6378 6.968263 TGGATGTAAAAACTTGTTGATCCA 57.032 33.333 0.00 0.00 36.59 3.41
5861 6404 6.398918 TCCTTCCTTGACTCTTTTTAGATCG 58.601 40.000 0.00 0.00 0.00 3.69
5866 6409 8.683615 GTCTTTTTCCTTCCTTGACTCTTTTTA 58.316 33.333 0.00 0.00 0.00 1.52
5875 6418 4.145365 TGACGTCTTTTTCCTTCCTTGA 57.855 40.909 17.92 0.00 0.00 3.02
5876 6419 4.893424 TTGACGTCTTTTTCCTTCCTTG 57.107 40.909 17.92 0.00 0.00 3.61
5877 6420 6.465439 AAATTGACGTCTTTTTCCTTCCTT 57.535 33.333 17.92 0.00 0.00 3.36
5882 6425 4.808895 GGCAAAAATTGACGTCTTTTTCCT 59.191 37.500 19.59 9.26 33.49 3.36
5884 6427 5.051039 GGAGGCAAAAATTGACGTCTTTTTC 60.051 40.000 19.59 11.88 45.70 2.29
5919 6462 5.617252 AGGAGTAAAGAATTTGACACGGAA 58.383 37.500 0.00 0.00 39.63 4.30
5936 6479 0.107116 GAGGAGCCAGACGAGGAGTA 60.107 60.000 0.00 0.00 0.00 2.59
5945 6488 1.680522 GATGCTTCGGAGGAGCCAGA 61.681 60.000 0.00 0.00 35.94 3.86
5947 6490 1.687146 AGATGCTTCGGAGGAGCCA 60.687 57.895 0.00 0.00 35.94 4.75
5967 6510 2.353208 GCTAGCATATTGGAGCGCTACT 60.353 50.000 22.67 3.45 35.93 2.57
6007 6550 1.261619 CTTGGATTCTATGCGGCGAAC 59.738 52.381 12.98 0.00 0.00 3.95
6018 6561 3.515502 TGAAGATGTCGGACTTGGATTCT 59.484 43.478 9.88 0.15 0.00 2.40
6020 6563 3.981071 TGAAGATGTCGGACTTGGATT 57.019 42.857 9.88 0.00 0.00 3.01
6048 6591 7.134362 AGAGAAGAAGATTGATGCCAAGATA 57.866 36.000 0.00 0.00 35.48 1.98
6122 6673 3.222603 GCAAAGGAGGAAAAGAAGACCA 58.777 45.455 0.00 0.00 0.00 4.02
6151 6702 3.041211 AGGAGTAGGCATACATCAAGCA 58.959 45.455 11.63 0.00 34.07 3.91
6152 6703 3.760580 AGGAGTAGGCATACATCAAGC 57.239 47.619 11.63 0.00 34.07 4.01
6158 6709 3.370527 GGCAAAGAAGGAGTAGGCATACA 60.371 47.826 11.63 0.00 34.07 2.29
6160 6711 2.843730 TGGCAAAGAAGGAGTAGGCATA 59.156 45.455 0.00 0.00 0.00 3.14
6167 6718 3.446442 ACATCATGGCAAAGAAGGAGT 57.554 42.857 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.