Multiple sequence alignment - TraesCS2B01G198800

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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 TraesCS2B01G198800 chr2B 100.000 6319 0 0 1 6319 176413003 176406685 0.000000e+00 11670
1 TraesCS2B01G198800 chr2D 92.692 5747 233 79 682 6319 123809385 123803717 0.000000e+00 8113
2 TraesCS2B01G198800 chr2D 89.384 292 14 8 18 308 123809883 123809608 1.010000e-92 351
3 TraesCS2B01G198800 chr2A 93.077 2080 74 36 4289 6319 129099868 129097810 0.000000e+00 2979
4 TraesCS2B01G198800 chr2A 91.313 1934 90 31 2415 4288 129101822 129099907 0.000000e+00 2569
5 TraesCS2B01G198800 chr2A 91.365 1656 85 24 682 2302 129103507 129101875 0.000000e+00 2213
6 TraesCS2B01G198800 chr2A 84.795 513 41 16 24 531 129104082 129103602 1.230000e-131 481
7 TraesCS2B01G198800 chr3A 94.218 882 34 5 4864 5741 729020999 729020131 0.000000e+00 1330
8 TraesCS2B01G198800 chr7B 92.383 407 14 5 4864 5260 504225480 504225081 1.190000e-156 564
9 TraesCS2B01G198800 chr7B 91.136 361 14 8 5408 5766 504225081 504224737 2.060000e-129 473
10 TraesCS2B01G198800 chr1B 92.383 407 14 5 4864 5260 101250259 101250658 1.190000e-156 564
11 TraesCS2B01G198800 chr1B 91.690 361 12 8 5408 5766 101250658 101251002 9.520000e-133 484


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 TraesCS2B01G198800 chr2B 176406685 176413003 6318 True 11670.0 11670 100.0000 1 6319 1 chr2B.!!$R1 6318
1 TraesCS2B01G198800 chr2D 123803717 123809883 6166 True 4232.0 8113 91.0380 18 6319 2 chr2D.!!$R1 6301
2 TraesCS2B01G198800 chr2A 129097810 129104082 6272 True 2060.5 2979 90.1375 24 6319 4 chr2A.!!$R1 6295
3 TraesCS2B01G198800 chr3A 729020131 729020999 868 True 1330.0 1330 94.2180 4864 5741 1 chr3A.!!$R1 877
4 TraesCS2B01G198800 chr7B 504224737 504225480 743 True 518.5 564 91.7595 4864 5766 2 chr7B.!!$R1 902
5 TraesCS2B01G198800 chr1B 101250259 101251002 743 False 524.0 564 92.0365 4864 5766 2 chr1B.!!$F1 902

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
58 59 0.034283 TGCTTGGCTGTGCATCCATA 60.034 50.000 6.20 0.0 33.94 2.74 F
261 266 0.038599 ATCTGAAGCCACCACATGCA 59.961 50.000 0.00 0.0 0.00 3.96 F
884 949 0.179020 TTCCTTCTGCACCACACAGG 60.179 55.000 0.00 0.0 45.67 4.00 F
887 952 0.179048 CTTCTGCACCACACAGGACA 60.179 55.000 0.00 0.0 41.22 4.02 F
897 962 0.179073 ACACAGGACACAGCACTGAC 60.179 55.000 4.31 0.0 36.17 3.51 F
1383 1448 1.079503 GTTTCTGATCTCCGTGTGGC 58.920 55.000 0.00 0.0 34.14 5.01 F
1797 1873 1.273327 CTCCCAAGGGTTTTGTCATGC 59.727 52.381 4.80 0.0 36.47 4.06 F
1913 1989 1.962807 TCATCAGGGTTTGTTTGCTGG 59.037 47.619 0.00 0.0 0.00 4.85 F
3697 3866 0.469917 CTGGGATAATCAGGGTGCGT 59.530 55.000 0.00 0.0 0.00 5.24 F
4025 4206 0.744414 GTGCGCTCCTGATTAGCCAA 60.744 55.000 9.73 0.0 36.60 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1420 1485 0.970937 TGGAGAACCCTAGGTCGCTG 60.971 60.000 8.29 0.00 33.12 5.18 R
1597 1664 1.918293 CCAGCCCAGACCCACTACA 60.918 63.158 0.00 0.00 0.00 2.74 R
2842 2965 1.677576 CTGAGTGCAAGTTGAGGCAAA 59.322 47.619 7.16 0.00 42.45 3.68 R
2901 3024 5.584649 GGCTCTTACATTGTAGCAACATACA 59.415 40.000 11.16 0.00 36.68 2.29 R
2999 3122 2.186903 CGGCCTTGCGGTAGTCAT 59.813 61.111 0.00 0.00 0.00 3.06 R
3228 3351 2.373169 TGCCCTCAATATAGAAGGCCAG 59.627 50.000 5.01 0.00 43.12 4.85 R
3661 3830 0.467384 CAGAGATCGGAGTTGGGCAT 59.533 55.000 0.00 0.00 0.00 4.40 R
3799 3980 2.414994 ATCAGCTGGACCAAGACATG 57.585 50.000 15.13 0.00 0.00 3.21 R
4874 5129 1.000607 CCTGCCAATGCACATGATAGC 60.001 52.381 0.00 0.68 44.23 2.97 R
5986 6410 2.267174 AGCATCTGCAACAAGTGACT 57.733 45.000 4.79 0.00 45.16 3.41 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 53 0.464870 AAATTGTGCTTGGCTGTGCA 59.535 45.000 0.00 0.00 36.79 4.57
58 59 0.034283 TGCTTGGCTGTGCATCCATA 60.034 50.000 6.20 0.00 33.94 2.74
128 133 5.124936 GGTACAATCCAAAACCCAGTATGTC 59.875 44.000 0.00 0.00 0.00 3.06
157 162 0.617249 AGGAAGCAGCCAGTAGAGCT 60.617 55.000 0.00 0.00 42.70 4.09
171 176 3.579626 GAGCTGCGCCGTTTGTCAC 62.580 63.158 4.18 0.00 0.00 3.67
188 193 2.159627 GTCACCCGAAAGCTGTATTGTG 59.840 50.000 0.00 0.00 0.00 3.33
261 266 0.038599 ATCTGAAGCCACCACATGCA 59.961 50.000 0.00 0.00 0.00 3.96
262 267 0.038599 TCTGAAGCCACCACATGCAT 59.961 50.000 0.00 0.00 0.00 3.96
298 303 4.682860 GCCGCGTAGTGCTAGATATTTTAA 59.317 41.667 4.92 0.00 43.27 1.52
326 331 8.836959 ATCGTTAGTGAAAAACAGTTTCTTTC 57.163 30.769 0.00 1.44 33.78 2.62
327 332 7.245604 TCGTTAGTGAAAAACAGTTTCTTTCC 58.754 34.615 0.00 0.00 33.78 3.13
328 333 6.193959 CGTTAGTGAAAAACAGTTTCTTTCCG 59.806 38.462 0.00 0.00 33.78 4.30
329 334 5.890424 AGTGAAAAACAGTTTCTTTCCGA 57.110 34.783 0.00 0.00 0.00 4.55
330 335 6.262193 AGTGAAAAACAGTTTCTTTCCGAA 57.738 33.333 0.00 0.00 0.00 4.30
331 336 6.863275 AGTGAAAAACAGTTTCTTTCCGAAT 58.137 32.000 0.00 0.00 0.00 3.34
332 337 7.320399 AGTGAAAAACAGTTTCTTTCCGAATT 58.680 30.769 0.00 0.00 0.00 2.17
333 338 7.488150 AGTGAAAAACAGTTTCTTTCCGAATTC 59.512 33.333 0.00 0.00 0.00 2.17
334 339 7.488150 GTGAAAAACAGTTTCTTTCCGAATTCT 59.512 33.333 3.52 0.00 0.00 2.40
335 340 7.487829 TGAAAAACAGTTTCTTTCCGAATTCTG 59.512 33.333 3.52 0.00 38.61 3.02
336 341 6.693315 AAACAGTTTCTTTCCGAATTCTGA 57.307 33.333 3.52 0.00 37.38 3.27
337 342 5.931441 ACAGTTTCTTTCCGAATTCTGAG 57.069 39.130 3.52 0.00 37.38 3.35
338 343 4.757149 ACAGTTTCTTTCCGAATTCTGAGG 59.243 41.667 3.52 0.00 37.38 3.86
339 344 4.997395 CAGTTTCTTTCCGAATTCTGAGGA 59.003 41.667 3.52 0.00 36.73 3.71
340 345 5.470098 CAGTTTCTTTCCGAATTCTGAGGAA 59.530 40.000 8.69 8.69 41.76 3.36
368 373 4.449131 ACTGAAGTGAGGATCGTCGTATA 58.551 43.478 10.63 0.00 38.61 1.47
379 384 3.982576 TCGTCGTATACATGCATGAGT 57.017 42.857 32.75 21.02 0.00 3.41
384 389 6.072673 TCGTCGTATACATGCATGAGTAATCT 60.073 38.462 32.75 11.20 0.00 2.40
385 390 6.032880 CGTCGTATACATGCATGAGTAATCTG 59.967 42.308 32.75 12.53 0.00 2.90
386 391 7.084486 GTCGTATACATGCATGAGTAATCTGA 58.916 38.462 32.75 15.50 0.00 3.27
387 392 7.757173 GTCGTATACATGCATGAGTAATCTGAT 59.243 37.037 32.75 8.94 0.00 2.90
388 393 7.756722 TCGTATACATGCATGAGTAATCTGATG 59.243 37.037 32.75 11.61 38.11 3.07
389 394 7.756722 CGTATACATGCATGAGTAATCTGATGA 59.243 37.037 32.75 2.56 37.45 2.92
390 395 9.428097 GTATACATGCATGAGTAATCTGATGAA 57.572 33.333 32.75 1.94 37.45 2.57
410 415 7.804600 TGATGAATTGAAGATCAACAACGAAAG 59.195 33.333 6.71 0.00 39.45 2.62
411 416 7.258022 TGAATTGAAGATCAACAACGAAAGA 57.742 32.000 6.71 0.00 39.45 2.52
412 417 7.702386 TGAATTGAAGATCAACAACGAAAGAA 58.298 30.769 6.71 0.00 39.45 2.52
413 418 7.857389 TGAATTGAAGATCAACAACGAAAGAAG 59.143 33.333 6.71 0.00 39.45 2.85
437 442 3.530265 TTGAATATGCCGAGTTACCGT 57.470 42.857 0.00 0.00 0.00 4.83
439 444 3.968649 TGAATATGCCGAGTTACCGTAC 58.031 45.455 0.00 0.00 0.00 3.67
442 447 2.008268 ATGCCGAGTTACCGTACCCG 62.008 60.000 0.00 0.00 0.00 5.28
475 480 8.306313 ACCTACAAGGAAGAAAAGTTGATTTT 57.694 30.769 0.00 0.00 39.86 1.82
476 481 8.197439 ACCTACAAGGAAGAAAAGTTGATTTTG 58.803 33.333 0.00 0.00 38.27 2.44
486 491 0.881118 GTTGATTTTGGCGCTCCAGA 59.119 50.000 7.64 0.00 44.53 3.86
487 492 0.881118 TTGATTTTGGCGCTCCAGAC 59.119 50.000 7.64 0.00 44.53 3.51
530 535 7.172868 TCACGTTGGTTTGAGATATTACCTA 57.827 36.000 0.00 0.00 0.00 3.08
531 536 7.037438 TCACGTTGGTTTGAGATATTACCTAC 58.963 38.462 0.00 0.00 34.47 3.18
532 537 7.039882 CACGTTGGTTTGAGATATTACCTACT 58.960 38.462 0.00 0.00 35.27 2.57
533 538 7.222224 CACGTTGGTTTGAGATATTACCTACTC 59.778 40.741 0.00 0.00 35.27 2.59
535 540 8.627403 CGTTGGTTTGAGATATTACCTACTCTA 58.373 37.037 0.00 0.00 35.27 2.43
543 548 9.624373 TGAGATATTACCTACTCTAAAACGTCT 57.376 33.333 0.00 0.00 0.00 4.18
545 550 9.624373 AGATATTACCTACTCTAAAACGTCTCA 57.376 33.333 0.00 0.00 0.00 3.27
552 557 9.406113 ACCTACTCTAAAACGTCTCATATTAGT 57.594 33.333 0.00 0.00 0.00 2.24
631 636 6.072893 GGAGTAGTAGATTCCATCGAGAAGAC 60.073 46.154 0.00 0.00 34.04 3.01
637 642 5.897050 AGATTCCATCGAGAAGACAGTAAC 58.103 41.667 0.00 0.00 0.00 2.50
643 648 4.659111 TCGAGAAGACAGTAACAAACCA 57.341 40.909 0.00 0.00 0.00 3.67
676 722 4.065321 TGACATGTCACACATACACACA 57.935 40.909 24.56 0.00 36.53 3.72
677 723 3.807071 TGACATGTCACACATACACACAC 59.193 43.478 24.56 0.00 36.53 3.82
678 724 4.058124 GACATGTCACACATACACACACT 58.942 43.478 21.07 0.00 36.53 3.55
679 725 4.450976 ACATGTCACACATACACACACTT 58.549 39.130 0.00 0.00 36.53 3.16
680 726 4.273235 ACATGTCACACATACACACACTTG 59.727 41.667 0.00 0.00 36.53 3.16
681 727 4.130286 TGTCACACATACACACACTTGA 57.870 40.909 0.00 0.00 0.00 3.02
682 728 3.868661 TGTCACACATACACACACTTGAC 59.131 43.478 0.00 0.00 34.09 3.18
683 729 3.868661 GTCACACATACACACACTTGACA 59.131 43.478 0.00 0.00 33.77 3.58
684 730 3.868661 TCACACATACACACACTTGACAC 59.131 43.478 0.00 0.00 0.00 3.67
692 738 5.734855 ACACACACTTGACACTTGTAATC 57.265 39.130 0.00 0.00 0.00 1.75
693 739 5.428253 ACACACACTTGACACTTGTAATCT 58.572 37.500 0.00 0.00 0.00 2.40
696 742 5.690409 ACACACTTGACACTTGTAATCTACG 59.310 40.000 0.00 0.00 0.00 3.51
746 794 5.620206 ACTATCCGCATGGTTGATTTGATA 58.380 37.500 0.00 0.00 36.30 2.15
776 830 4.040047 TGGATGATAGTCCAGATTGGTGT 58.960 43.478 0.00 0.00 43.20 4.16
780 834 7.179160 TGGATGATAGTCCAGATTGGTGTATAG 59.821 40.741 0.00 0.00 43.20 1.31
784 838 9.025041 TGATAGTCCAGATTGGTGTATAGTATG 57.975 37.037 0.00 0.00 39.03 2.39
785 839 8.958060 ATAGTCCAGATTGGTGTATAGTATGT 57.042 34.615 0.00 0.00 39.03 2.29
787 841 6.016192 AGTCCAGATTGGTGTATAGTATGTCG 60.016 42.308 0.00 0.00 39.03 4.35
789 843 6.206829 TCCAGATTGGTGTATAGTATGTCGAG 59.793 42.308 0.00 0.00 39.03 4.04
812 868 9.861138 CGAGCATTTTCTGATTAAAAGATCTAG 57.139 33.333 0.00 0.00 32.20 2.43
813 869 9.662545 GAGCATTTTCTGATTAAAAGATCTAGC 57.337 33.333 0.00 0.00 32.20 3.42
816 872 9.727627 CATTTTCTGATTAAAAGATCTAGCACC 57.272 33.333 0.00 0.00 32.20 5.01
824 880 9.346725 GATTAAAAGATCTAGCACCAAAGTTTG 57.653 33.333 8.73 8.73 0.00 2.93
827 883 7.817418 AAAGATCTAGCACCAAAGTTTGTAA 57.183 32.000 14.36 0.00 0.00 2.41
829 885 9.515226 AAAGATCTAGCACCAAAGTTTGTAATA 57.485 29.630 14.36 1.84 0.00 0.98
838 894 9.262358 GCACCAAAGTTTGTAATATAAAACCAA 57.738 29.630 14.36 0.00 37.04 3.67
884 949 0.179020 TTCCTTCTGCACCACACAGG 60.179 55.000 0.00 0.00 45.67 4.00
886 951 0.886490 CCTTCTGCACCACACAGGAC 60.886 60.000 0.00 0.00 41.22 3.85
887 952 0.179048 CTTCTGCACCACACAGGACA 60.179 55.000 0.00 0.00 41.22 4.02
888 953 0.463654 TTCTGCACCACACAGGACAC 60.464 55.000 0.00 0.00 41.22 3.67
889 954 1.153188 CTGCACCACACAGGACACA 60.153 57.895 0.00 0.00 41.22 3.72
890 955 1.153188 TGCACCACACAGGACACAG 60.153 57.895 0.00 0.00 41.22 3.66
891 956 2.546494 GCACCACACAGGACACAGC 61.546 63.158 0.00 0.00 41.22 4.40
892 957 1.153188 CACCACACAGGACACAGCA 60.153 57.895 0.00 0.00 41.22 4.41
893 958 1.153168 ACCACACAGGACACAGCAC 60.153 57.895 0.00 0.00 41.22 4.40
894 959 1.146930 CCACACAGGACACAGCACT 59.853 57.895 0.00 0.00 41.22 4.40
895 960 1.162181 CCACACAGGACACAGCACTG 61.162 60.000 0.00 0.00 41.22 3.66
896 961 0.179076 CACACAGGACACAGCACTGA 60.179 55.000 4.31 0.00 36.17 3.41
897 962 0.179073 ACACAGGACACAGCACTGAC 60.179 55.000 4.31 0.00 36.17 3.51
938 1003 3.544698 AGGGAGTGAAGTACAGAAGGA 57.455 47.619 0.00 0.00 0.00 3.36
942 1007 4.283722 GGGAGTGAAGTACAGAAGGAAGAA 59.716 45.833 0.00 0.00 0.00 2.52
949 1014 5.216614 AGTACAGAAGGAAGAAGTGAACC 57.783 43.478 0.00 0.00 0.00 3.62
1101 1166 2.127528 AAGACCCCCTTCCTCCCC 59.872 66.667 0.00 0.00 0.00 4.81
1102 1167 3.945064 AAGACCCCCTTCCTCCCCG 62.945 68.421 0.00 0.00 0.00 5.73
1344 1409 2.242670 CGATGATTCGCGCGGTTC 59.757 61.111 31.69 25.34 38.75 3.62
1383 1448 1.079503 GTTTCTGATCTCCGTGTGGC 58.920 55.000 0.00 0.00 34.14 5.01
1575 1640 2.036571 TGAATGCTGTGAGCTGCGG 61.037 57.895 0.00 0.00 42.97 5.69
1595 1662 3.677976 CGGACTGTACAGTTTGGTATCCC 60.678 52.174 28.49 20.05 42.66 3.85
1597 1664 2.901839 ACTGTACAGTTTGGTATCCCGT 59.098 45.455 22.95 0.00 38.83 5.28
1697 1769 2.180017 CGGAGCAAAGCACATGGC 59.820 61.111 0.00 0.00 45.30 4.40
1724 1797 6.581171 AATCAGACCTTTTCATCTTTGGAC 57.419 37.500 0.00 0.00 0.00 4.02
1797 1873 1.273327 CTCCCAAGGGTTTTGTCATGC 59.727 52.381 4.80 0.00 36.47 4.06
1913 1989 1.962807 TCATCAGGGTTTGTTTGCTGG 59.037 47.619 0.00 0.00 0.00 4.85
2019 2099 5.350633 TCAAATTCAAGCTTTGACCAACAG 58.649 37.500 0.00 0.00 39.87 3.16
2055 2135 9.793252 AAACTGATTTCATTGGATTCTTATTCG 57.207 29.630 0.00 0.00 0.00 3.34
2165 2247 7.174946 ACAGTCAAATATGCCTTATTTATCCGG 59.825 37.037 0.00 0.00 38.23 5.14
2208 2294 6.200878 ACCTCTCAAATTGGGAAGAGTTTA 57.799 37.500 0.00 0.00 0.00 2.01
2217 2304 4.316025 TGGGAAGAGTTTAAATGGAGGG 57.684 45.455 0.00 0.00 0.00 4.30
2326 2445 2.290641 TGCTTCTTTTCTTCTTCACGGC 59.709 45.455 0.00 0.00 0.00 5.68
2348 2467 3.557595 CGGACCTATCTGAATTTCAGTGC 59.442 47.826 22.44 10.64 44.58 4.40
2350 2469 5.189180 GGACCTATCTGAATTTCAGTGCTT 58.811 41.667 22.44 11.03 44.58 3.91
2413 2532 7.727331 TTTGGTTCCAATATTTTTGCTTCTG 57.273 32.000 5.06 0.00 0.00 3.02
2431 2550 6.542005 TGCTTCTGTTTTGTGATAGAGAACAA 59.458 34.615 0.00 0.00 34.57 2.83
2432 2551 7.229306 TGCTTCTGTTTTGTGATAGAGAACAAT 59.771 33.333 0.00 0.00 36.26 2.71
2433 2552 7.748241 GCTTCTGTTTTGTGATAGAGAACAATC 59.252 37.037 0.00 0.00 36.26 2.67
2435 2554 9.996554 TTCTGTTTTGTGATAGAGAACAATCTA 57.003 29.630 0.00 0.00 36.26 1.98
2436 2555 9.645059 TCTGTTTTGTGATAGAGAACAATCTAG 57.355 33.333 0.00 0.00 36.26 2.43
2437 2556 8.256611 TGTTTTGTGATAGAGAACAATCTAGC 57.743 34.615 0.00 0.00 38.41 3.42
2438 2557 8.097038 TGTTTTGTGATAGAGAACAATCTAGCT 58.903 33.333 0.00 0.00 38.67 3.32
2439 2558 9.587772 GTTTTGTGATAGAGAACAATCTAGCTA 57.412 33.333 0.00 0.00 38.67 3.32
2480 2599 3.773860 TGAAAATGTTGCAGAACACGT 57.226 38.095 0.00 0.00 44.90 4.49
2509 2629 7.781693 AGTTCTAGATCATTGCCATATGGTTTT 59.218 33.333 22.79 5.22 37.57 2.43
2545 2665 6.057533 TGATGTATGCTCTTGTTATTCAGGG 58.942 40.000 0.00 0.00 0.00 4.45
2738 2858 5.048224 CACAAGGTGATTTCATTCTTCAGCT 60.048 40.000 0.00 0.00 46.86 4.24
2762 2882 5.372373 AGGGCAAATACATTTCTCTAGCTC 58.628 41.667 0.00 0.00 0.00 4.09
2901 3024 2.513026 AAAGCGCGCATGGAGAGAGT 62.513 55.000 35.10 4.83 0.00 3.24
2999 3122 2.104792 CTGTTGGAACCCTCACTGAGAA 59.895 50.000 7.69 0.00 0.00 2.87
3156 3279 6.598525 TGTAAATTGATGTTGTGTCGCTAAG 58.401 36.000 0.00 0.00 0.00 2.18
3215 3338 4.141620 TGAGATATTTGAGGCCAGAACTCC 60.142 45.833 5.01 0.00 34.06 3.85
3219 3342 3.312736 TTTGAGGCCAGAACTCCTTTT 57.687 42.857 5.01 0.00 34.06 2.27
3256 3384 7.830099 CCTTCTATATTGAGGGCAGAATTTT 57.170 36.000 2.53 0.00 0.00 1.82
3281 3409 7.479980 TCATTTGCCAGTAACTAATATGCAAC 58.520 34.615 0.00 0.00 37.01 4.17
3283 3411 3.874543 TGCCAGTAACTAATATGCAACCG 59.125 43.478 0.00 0.00 0.00 4.44
3295 3423 9.787435 ACTAATATGCAACCGATTTATTCCTAA 57.213 29.630 0.00 0.00 0.00 2.69
3361 3498 5.154215 GCTGATGAGCATTGAAACTAGAC 57.846 43.478 0.00 0.00 45.46 2.59
3362 3499 4.260132 GCTGATGAGCATTGAAACTAGACG 60.260 45.833 0.00 0.00 45.46 4.18
3363 3500 5.072040 TGATGAGCATTGAAACTAGACGA 57.928 39.130 0.00 0.00 0.00 4.20
3364 3501 5.105063 TGATGAGCATTGAAACTAGACGAG 58.895 41.667 0.00 0.00 0.00 4.18
3365 3502 3.254060 TGAGCATTGAAACTAGACGAGC 58.746 45.455 0.00 0.00 0.00 5.03
3367 3504 3.866651 AGCATTGAAACTAGACGAGCAT 58.133 40.909 0.00 0.00 0.00 3.79
3368 3505 4.256920 AGCATTGAAACTAGACGAGCATT 58.743 39.130 0.00 0.00 0.00 3.56
3465 3629 3.507233 TGTTTCAGAAGCCCAATGTGATC 59.493 43.478 0.00 0.00 0.00 2.92
3476 3640 3.318839 CCCAATGTGATCTGTGTTTGTGT 59.681 43.478 0.00 0.00 0.00 3.72
3490 3654 4.562394 GTGTTTGTGTCAAGTCACCAAATG 59.438 41.667 0.00 0.00 37.51 2.32
3518 3687 5.990386 TGCAAAATGTGATACAAAGTTGCAT 59.010 32.000 18.18 0.00 42.65 3.96
3555 3724 5.146482 CAAACAAGGTTGCAAAGTTGATG 57.854 39.130 22.58 17.28 0.00 3.07
3566 3735 3.488310 GCAAAGTTGATGAACTGCAACAG 59.512 43.478 0.00 0.00 45.08 3.16
3572 3741 2.885894 TGATGAACTGCAACAGCATTCA 59.114 40.909 13.48 13.48 38.67 2.57
3579 3748 3.250744 CTGCAACAGCATTCATCAAAGG 58.749 45.455 0.00 0.00 37.69 3.11
3601 3770 4.908601 TTGAGGCTCAACCATCTCTTAA 57.091 40.909 25.38 0.00 43.14 1.85
3602 3771 4.478206 TGAGGCTCAACCATCTCTTAAG 57.522 45.455 16.28 0.00 43.14 1.85
3605 3774 5.105310 TGAGGCTCAACCATCTCTTAAGTAC 60.105 44.000 16.28 0.00 43.14 2.73
3627 3796 5.168569 ACAGTACCAGATACATTCACAACG 58.831 41.667 0.00 0.00 36.09 4.10
3686 3855 2.965831 CCAACTCCGATCTCTGGGATAA 59.034 50.000 0.00 0.00 34.33 1.75
3697 3866 0.469917 CTGGGATAATCAGGGTGCGT 59.530 55.000 0.00 0.00 0.00 5.24
3793 3974 8.647796 TCAACTAGATGAAACTCAAAAGGACTA 58.352 33.333 0.00 0.00 0.00 2.59
3799 3980 9.232473 AGATGAAACTCAAAAGGACTAATAACC 57.768 33.333 0.00 0.00 0.00 2.85
3933 4114 4.041917 CGCTGGTGCATGCCGTTT 62.042 61.111 16.68 0.00 39.64 3.60
4025 4206 0.744414 GTGCGCTCCTGATTAGCCAA 60.744 55.000 9.73 0.00 36.60 4.52
4056 4237 6.039616 GGTTGTTGAAAAGCTTGACATGTTA 58.960 36.000 0.00 0.00 0.00 2.41
4088 4269 4.735132 CGAAGGTGCGAAGGCGGA 62.735 66.667 0.00 0.00 44.10 5.54
4149 4330 2.924105 GCTTGCACCACCTGAAGCC 61.924 63.158 0.00 0.00 35.76 4.35
4150 4331 1.228367 CTTGCACCACCTGAAGCCT 60.228 57.895 0.00 0.00 0.00 4.58
4151 4332 1.521450 CTTGCACCACCTGAAGCCTG 61.521 60.000 0.00 0.00 0.00 4.85
4152 4333 3.368571 GCACCACCTGAAGCCTGC 61.369 66.667 0.00 0.00 0.00 4.85
4153 4334 2.433446 CACCACCTGAAGCCTGCT 59.567 61.111 0.00 0.00 0.00 4.24
4154 4335 1.228367 CACCACCTGAAGCCTGCTT 60.228 57.895 3.62 3.62 39.23 3.91
4260 4447 5.549228 AGATTCATGAAGGTATGGCTGGATA 59.451 40.000 14.54 0.00 0.00 2.59
4324 4548 8.388484 ACTTATAGTTGTACGTAGATGGGTAG 57.612 38.462 0.00 0.00 0.00 3.18
4340 4564 2.093394 GGGTAGAAGCCTTCAGGAACTC 60.093 54.545 7.29 0.00 37.39 3.01
4361 4585 5.407387 ACTCAAATGCTGAACAAATGAATGC 59.593 36.000 0.00 0.00 32.17 3.56
4413 4657 5.046304 CCAGAGGTTCTCATCAAGGTTTAGA 60.046 44.000 0.00 0.00 32.06 2.10
4447 4697 1.409427 CACGGGTCAGATTAGTCCTCC 59.591 57.143 0.00 0.00 0.00 4.30
4525 4775 4.666237 GCATTCAGCAAATACCAGAGAAC 58.334 43.478 0.00 0.00 44.79 3.01
4579 4829 7.227049 TCAGGACCAAATAACAAATTCTTCC 57.773 36.000 0.00 0.00 0.00 3.46
4777 5027 6.204108 GGATGAACCTGGGTAAATAATACACG 59.796 42.308 0.00 0.00 35.41 4.49
4778 5028 6.052405 TGAACCTGGGTAAATAATACACGT 57.948 37.500 0.00 0.00 0.00 4.49
4779 5029 6.474630 TGAACCTGGGTAAATAATACACGTT 58.525 36.000 0.00 0.00 0.00 3.99
4780 5030 6.372103 TGAACCTGGGTAAATAATACACGTTG 59.628 38.462 0.00 0.00 0.00 4.10
4781 5031 6.052405 ACCTGGGTAAATAATACACGTTGA 57.948 37.500 0.00 0.00 0.00 3.18
4782 5032 6.655930 ACCTGGGTAAATAATACACGTTGAT 58.344 36.000 0.00 0.00 0.00 2.57
4783 5033 7.794041 ACCTGGGTAAATAATACACGTTGATA 58.206 34.615 0.00 0.00 0.00 2.15
4784 5034 7.712205 ACCTGGGTAAATAATACACGTTGATAC 59.288 37.037 0.00 0.00 0.00 2.24
4785 5035 7.711772 CCTGGGTAAATAATACACGTTGATACA 59.288 37.037 0.00 0.00 0.00 2.29
4786 5036 8.651391 TGGGTAAATAATACACGTTGATACAG 57.349 34.615 0.00 0.00 0.00 2.74
4787 5037 8.476447 TGGGTAAATAATACACGTTGATACAGA 58.524 33.333 0.00 0.00 0.00 3.41
4788 5038 8.758715 GGGTAAATAATACACGTTGATACAGAC 58.241 37.037 0.00 0.00 0.00 3.51
4791 5041 7.766219 AATAATACACGTTGATACAGACCAC 57.234 36.000 0.00 0.00 0.00 4.16
4792 5042 5.401531 AATACACGTTGATACAGACCACT 57.598 39.130 0.00 0.00 0.00 4.00
4794 5044 4.436242 ACACGTTGATACAGACCACTAG 57.564 45.455 0.00 0.00 0.00 2.57
4795 5045 3.825014 ACACGTTGATACAGACCACTAGT 59.175 43.478 0.00 0.00 0.00 2.57
4796 5046 4.082895 ACACGTTGATACAGACCACTAGTC 60.083 45.833 0.00 0.00 46.71 2.59
4874 5129 9.161629 TGAAACTATATGCCATAAATATGACCG 57.838 33.333 1.98 0.00 35.75 4.79
5138 5405 7.039923 CCAAGCCATAGCAGAATGAATAAGATT 60.040 37.037 0.00 0.00 43.56 2.40
5340 5756 7.559486 TCAGCAGTATAAGGAATATATGCCTG 58.441 38.462 13.49 1.65 34.72 4.85
5344 5760 9.838339 GCAGTATAAGGAATATATGCCTGTAAT 57.162 33.333 13.49 9.77 34.00 1.89
5610 6027 2.837031 AATGGGGCTTCGGCGATGTT 62.837 55.000 21.59 7.12 42.91 2.71
5752 6170 8.399529 TGGTAAGAGCATAGTAATAGGATAGGT 58.600 37.037 0.00 0.00 0.00 3.08
5851 6273 4.476846 TCCCTCTGCCCAAAATATAAGACA 59.523 41.667 0.00 0.00 0.00 3.41
5986 6410 4.994852 GGTGTGTTGCTCATTTAGACTACA 59.005 41.667 0.00 0.00 0.00 2.74
6043 6467 2.027377 CAGACTTGGCTGATGAGGAGTT 60.027 50.000 0.00 0.00 38.14 3.01
6287 6714 4.216257 TCACTTAGCTCCAAGCAACATTTC 59.784 41.667 0.00 0.00 45.56 2.17
6302 6729 3.359950 ACATTTCTCTGCAGGGATTTCC 58.640 45.455 19.11 0.00 0.00 3.13
6312 6739 4.095946 TGCAGGGATTTCCAATTAGCTTT 58.904 39.130 0.00 0.00 38.24 3.51
6313 6740 5.268387 TGCAGGGATTTCCAATTAGCTTTA 58.732 37.500 0.00 0.00 38.24 1.85
6314 6741 5.360714 TGCAGGGATTTCCAATTAGCTTTAG 59.639 40.000 0.00 0.00 38.24 1.85
6316 6743 6.127338 GCAGGGATTTCCAATTAGCTTTAGTT 60.127 38.462 0.00 0.00 38.24 2.24
6317 6744 7.260603 CAGGGATTTCCAATTAGCTTTAGTTG 58.739 38.462 0.00 0.00 38.24 3.16
6318 6745 7.122650 CAGGGATTTCCAATTAGCTTTAGTTGA 59.877 37.037 0.00 0.00 38.24 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.565455 ATTTGCCTCTTTTTCCATTTGGA 57.435 34.783 0.00 0.00 43.73 3.53
15 16 5.532032 ACAATTTGCCTCTTTTTCCATTTGG 59.468 36.000 0.00 0.00 0.00 3.28
16 17 6.432107 CACAATTTGCCTCTTTTTCCATTTG 58.568 36.000 0.00 0.00 0.00 2.32
17 18 5.008911 GCACAATTTGCCTCTTTTTCCATTT 59.991 36.000 0.00 0.00 46.63 2.32
18 19 4.516321 GCACAATTTGCCTCTTTTTCCATT 59.484 37.500 0.00 0.00 46.63 3.16
19 20 4.067192 GCACAATTTGCCTCTTTTTCCAT 58.933 39.130 0.00 0.00 46.63 3.41
20 21 3.465871 GCACAATTTGCCTCTTTTTCCA 58.534 40.909 0.00 0.00 46.63 3.53
49 50 1.447217 CGGTCTGGCTATGGATGCA 59.553 57.895 0.00 0.00 0.00 3.96
52 53 2.520536 GGGCGGTCTGGCTATGGAT 61.521 63.158 5.05 0.00 44.11 3.41
88 90 1.683917 GTACCAGCTGATCGTCAGGAT 59.316 52.381 17.39 0.00 44.43 3.24
128 133 2.032528 TGCTTCCTTGCCGTGGAG 59.967 61.111 0.00 0.00 34.76 3.86
171 176 0.451783 GGCACAATACAGCTTTCGGG 59.548 55.000 0.00 0.00 0.00 5.14
188 193 1.564348 TGGAAGGACTTTGGGATAGGC 59.436 52.381 0.00 0.00 0.00 3.93
261 266 1.587054 GCGGCGAGTCAGGCTATAT 59.413 57.895 12.98 0.00 34.19 0.86
262 267 2.904676 CGCGGCGAGTCAGGCTATA 61.905 63.158 19.16 0.00 34.19 1.31
306 311 6.988622 TCGGAAAGAAACTGTTTTTCACTA 57.011 33.333 15.65 2.72 33.57 2.74
311 316 7.543756 TCAGAATTCGGAAAGAAACTGTTTTT 58.456 30.769 7.28 0.00 42.91 1.94
315 320 4.757149 CCTCAGAATTCGGAAAGAAACTGT 59.243 41.667 9.61 0.00 42.91 3.55
316 321 4.997395 TCCTCAGAATTCGGAAAGAAACTG 59.003 41.667 9.61 10.04 42.91 3.16
317 322 5.228945 TCCTCAGAATTCGGAAAGAAACT 57.771 39.130 9.61 0.00 42.91 2.66
318 323 5.941948 TTCCTCAGAATTCGGAAAGAAAC 57.058 39.130 9.61 0.00 42.91 2.78
330 335 8.924511 TCACTTCAGTTTTAATTCCTCAGAAT 57.075 30.769 0.00 0.00 44.86 2.40
331 336 7.445402 CCTCACTTCAGTTTTAATTCCTCAGAA 59.555 37.037 0.00 0.00 36.15 3.02
332 337 6.936900 CCTCACTTCAGTTTTAATTCCTCAGA 59.063 38.462 0.00 0.00 0.00 3.27
333 338 6.936900 TCCTCACTTCAGTTTTAATTCCTCAG 59.063 38.462 0.00 0.00 0.00 3.35
334 339 6.837312 TCCTCACTTCAGTTTTAATTCCTCA 58.163 36.000 0.00 0.00 0.00 3.86
335 340 7.201565 CGATCCTCACTTCAGTTTTAATTCCTC 60.202 40.741 0.00 0.00 0.00 3.71
336 341 6.595716 CGATCCTCACTTCAGTTTTAATTCCT 59.404 38.462 0.00 0.00 0.00 3.36
337 342 6.371825 ACGATCCTCACTTCAGTTTTAATTCC 59.628 38.462 0.00 0.00 0.00 3.01
338 343 7.365840 ACGATCCTCACTTCAGTTTTAATTC 57.634 36.000 0.00 0.00 0.00 2.17
339 344 6.090898 CGACGATCCTCACTTCAGTTTTAATT 59.909 38.462 0.00 0.00 0.00 1.40
340 345 5.577164 CGACGATCCTCACTTCAGTTTTAAT 59.423 40.000 0.00 0.00 0.00 1.40
368 373 7.501225 TCAATTCATCAGATTACTCATGCATGT 59.499 33.333 25.43 10.70 0.00 3.21
384 389 6.799926 TCGTTGTTGATCTTCAATTCATCA 57.200 33.333 0.00 0.00 38.79 3.07
385 390 8.017373 TCTTTCGTTGTTGATCTTCAATTCATC 58.983 33.333 0.00 0.00 38.79 2.92
386 391 7.874940 TCTTTCGTTGTTGATCTTCAATTCAT 58.125 30.769 0.00 0.00 38.79 2.57
387 392 7.258022 TCTTTCGTTGTTGATCTTCAATTCA 57.742 32.000 0.00 0.00 38.79 2.57
388 393 8.070171 TCTTCTTTCGTTGTTGATCTTCAATTC 58.930 33.333 0.00 0.00 38.79 2.17
389 394 7.930217 TCTTCTTTCGTTGTTGATCTTCAATT 58.070 30.769 0.00 0.00 38.79 2.32
390 395 7.496529 TCTTCTTTCGTTGTTGATCTTCAAT 57.503 32.000 0.00 0.00 38.79 2.57
391 396 6.918892 TCTTCTTTCGTTGTTGATCTTCAA 57.081 33.333 0.00 0.00 33.32 2.69
410 415 7.132863 GGTAACTCGGCATATTCAAATTCTTC 58.867 38.462 0.00 0.00 0.00 2.87
411 416 6.238374 CGGTAACTCGGCATATTCAAATTCTT 60.238 38.462 0.00 0.00 0.00 2.52
412 417 5.236478 CGGTAACTCGGCATATTCAAATTCT 59.764 40.000 0.00 0.00 0.00 2.40
413 418 5.007332 ACGGTAACTCGGCATATTCAAATTC 59.993 40.000 0.00 0.00 0.00 2.17
453 458 6.983890 GCCAAAATCAACTTTTCTTCCTTGTA 59.016 34.615 0.00 0.00 34.80 2.41
454 459 5.817296 GCCAAAATCAACTTTTCTTCCTTGT 59.183 36.000 0.00 0.00 34.80 3.16
486 491 1.003580 AGGGAAATGTGTGATCTGCGT 59.996 47.619 0.00 0.00 0.00 5.24
487 492 1.667724 GAGGGAAATGTGTGATCTGCG 59.332 52.381 0.00 0.00 0.00 5.18
598 603 9.848710 CGATGGAATCTACTACTCCCTATATAA 57.151 37.037 0.00 0.00 42.58 0.98
599 604 9.222098 TCGATGGAATCTACTACTCCCTATATA 57.778 37.037 0.00 0.00 42.58 0.86
600 605 8.103660 TCGATGGAATCTACTACTCCCTATAT 57.896 38.462 0.00 0.00 42.58 0.86
601 606 7.402361 TCTCGATGGAATCTACTACTCCCTATA 59.598 40.741 0.00 0.00 42.58 1.31
602 607 6.215841 TCTCGATGGAATCTACTACTCCCTAT 59.784 42.308 0.00 0.00 42.58 2.57
603 608 5.546887 TCTCGATGGAATCTACTACTCCCTA 59.453 44.000 0.00 0.00 42.58 3.53
604 609 4.351407 TCTCGATGGAATCTACTACTCCCT 59.649 45.833 0.00 0.00 42.58 4.20
605 610 4.653868 TCTCGATGGAATCTACTACTCCC 58.346 47.826 0.00 0.00 42.58 4.30
606 611 5.998981 TCTTCTCGATGGAATCTACTACTCC 59.001 44.000 0.00 0.00 42.58 3.85
607 612 6.483974 TGTCTTCTCGATGGAATCTACTACTC 59.516 42.308 0.00 0.00 42.58 2.59
608 613 6.358178 TGTCTTCTCGATGGAATCTACTACT 58.642 40.000 0.00 0.00 42.58 2.57
609 614 6.261381 ACTGTCTTCTCGATGGAATCTACTAC 59.739 42.308 0.00 0.00 42.58 2.73
610 615 6.358178 ACTGTCTTCTCGATGGAATCTACTA 58.642 40.000 0.00 0.00 42.58 1.82
611 616 5.197451 ACTGTCTTCTCGATGGAATCTACT 58.803 41.667 0.00 0.00 42.58 2.57
612 617 5.508200 ACTGTCTTCTCGATGGAATCTAC 57.492 43.478 0.00 0.00 42.58 2.59
631 636 8.356657 TCACTGGATTTTTATGGTTTGTTACTG 58.643 33.333 0.00 0.00 0.00 2.74
637 642 7.153985 ACATGTCACTGGATTTTTATGGTTTG 58.846 34.615 0.00 0.00 0.00 2.93
669 715 6.578944 AGATTACAAGTGTCAAGTGTGTGTA 58.421 36.000 0.85 0.00 0.00 2.90
672 718 5.690409 CGTAGATTACAAGTGTCAAGTGTGT 59.310 40.000 0.85 0.00 0.00 3.72
673 719 5.118664 CCGTAGATTACAAGTGTCAAGTGTG 59.881 44.000 0.85 0.00 0.00 3.82
674 720 5.227908 CCGTAGATTACAAGTGTCAAGTGT 58.772 41.667 0.00 0.00 0.00 3.55
675 721 4.091509 GCCGTAGATTACAAGTGTCAAGTG 59.908 45.833 0.00 0.00 0.00 3.16
676 722 4.021368 AGCCGTAGATTACAAGTGTCAAGT 60.021 41.667 0.00 0.00 0.00 3.16
677 723 4.495422 AGCCGTAGATTACAAGTGTCAAG 58.505 43.478 0.00 0.00 0.00 3.02
678 724 4.219944 AGAGCCGTAGATTACAAGTGTCAA 59.780 41.667 0.00 0.00 0.00 3.18
679 725 3.762288 AGAGCCGTAGATTACAAGTGTCA 59.238 43.478 0.00 0.00 0.00 3.58
680 726 4.373348 AGAGCCGTAGATTACAAGTGTC 57.627 45.455 0.00 0.00 0.00 3.67
681 727 4.803098 AAGAGCCGTAGATTACAAGTGT 57.197 40.909 0.00 0.00 0.00 3.55
682 728 5.921408 GGATAAGAGCCGTAGATTACAAGTG 59.079 44.000 0.00 0.00 0.00 3.16
683 729 5.597182 TGGATAAGAGCCGTAGATTACAAGT 59.403 40.000 0.00 0.00 0.00 3.16
684 730 6.085555 TGGATAAGAGCCGTAGATTACAAG 57.914 41.667 0.00 0.00 0.00 3.16
692 738 2.864343 CCGTTTTGGATAAGAGCCGTAG 59.136 50.000 0.00 0.00 42.00 3.51
693 739 2.496871 TCCGTTTTGGATAAGAGCCGTA 59.503 45.455 0.00 0.00 43.74 4.02
742 790 7.232910 TGGACTATCATCCAAATGCAATATCA 58.767 34.615 0.00 0.00 46.08 2.15
780 834 9.214953 CTTTTAATCAGAAAATGCTCGACATAC 57.785 33.333 1.73 0.00 38.34 2.39
784 838 8.394121 AGATCTTTTAATCAGAAAATGCTCGAC 58.606 33.333 0.00 0.00 0.00 4.20
785 839 8.498054 AGATCTTTTAATCAGAAAATGCTCGA 57.502 30.769 0.00 0.00 0.00 4.04
787 841 9.662545 GCTAGATCTTTTAATCAGAAAATGCTC 57.337 33.333 0.00 0.00 0.00 4.26
789 843 9.230932 GTGCTAGATCTTTTAATCAGAAAATGC 57.769 33.333 0.00 0.00 0.00 3.56
812 868 8.819643 TGGTTTTATATTACAAACTTTGGTGC 57.180 30.769 6.47 0.00 34.00 5.01
829 885 8.738645 AAGCGAGAAAGAGATATTGGTTTTAT 57.261 30.769 0.00 0.00 0.00 1.40
833 889 5.983540 AGAAGCGAGAAAGAGATATTGGTT 58.016 37.500 0.00 0.00 0.00 3.67
835 891 4.987912 GGAGAAGCGAGAAAGAGATATTGG 59.012 45.833 0.00 0.00 0.00 3.16
836 892 5.841810 AGGAGAAGCGAGAAAGAGATATTG 58.158 41.667 0.00 0.00 0.00 1.90
838 894 6.478512 AAAGGAGAAGCGAGAAAGAGATAT 57.521 37.500 0.00 0.00 0.00 1.63
864 929 1.679139 CTGTGTGGTGCAGAAGGAAA 58.321 50.000 0.00 0.00 36.12 3.13
880 945 1.068083 CGTCAGTGCTGTGTCCTGT 59.932 57.895 0.00 0.00 0.00 4.00
884 949 0.594028 TTCGTCGTCAGTGCTGTGTC 60.594 55.000 0.00 0.00 0.00 3.67
886 951 1.278172 CCTTCGTCGTCAGTGCTGTG 61.278 60.000 0.00 0.00 0.00 3.66
887 952 1.007271 CCTTCGTCGTCAGTGCTGT 60.007 57.895 0.00 0.00 0.00 4.40
888 953 1.007271 ACCTTCGTCGTCAGTGCTG 60.007 57.895 0.00 0.00 0.00 4.41
889 954 1.007271 CACCTTCGTCGTCAGTGCT 60.007 57.895 0.00 0.00 0.00 4.40
890 955 2.022129 CCACCTTCGTCGTCAGTGC 61.022 63.158 0.00 0.00 0.00 4.40
891 956 2.022129 GCCACCTTCGTCGTCAGTG 61.022 63.158 0.00 0.00 0.00 3.66
892 957 2.023414 TTGCCACCTTCGTCGTCAGT 62.023 55.000 0.00 0.00 0.00 3.41
893 958 0.878523 TTTGCCACCTTCGTCGTCAG 60.879 55.000 0.00 0.00 0.00 3.51
894 959 1.144276 TTTGCCACCTTCGTCGTCA 59.856 52.632 0.00 0.00 0.00 4.35
895 960 1.568025 GTTTGCCACCTTCGTCGTC 59.432 57.895 0.00 0.00 0.00 4.20
896 961 1.890510 GGTTTGCCACCTTCGTCGT 60.891 57.895 0.00 0.00 43.29 4.34
897 962 2.943653 GGTTTGCCACCTTCGTCG 59.056 61.111 0.00 0.00 43.29 5.12
938 1003 2.251642 GCGCGTGGGTTCACTTCTT 61.252 57.895 8.43 0.00 41.53 2.52
1344 1409 1.029947 CCATTTCCCTTCCCGAACCG 61.030 60.000 0.00 0.00 0.00 4.44
1383 1448 1.416813 GCCTCGAATCTCTGCACACG 61.417 60.000 0.00 0.00 0.00 4.49
1420 1485 0.970937 TGGAGAACCCTAGGTCGCTG 60.971 60.000 8.29 0.00 33.12 5.18
1595 1662 2.264794 GCCCAGACCCACTACACG 59.735 66.667 0.00 0.00 0.00 4.49
1597 1664 1.918293 CCAGCCCAGACCCACTACA 60.918 63.158 0.00 0.00 0.00 2.74
1697 1769 7.280876 TCCAAAGATGAAAAGGTCTGATTATCG 59.719 37.037 0.00 0.00 0.00 2.92
1705 1777 4.319177 CTCGTCCAAAGATGAAAAGGTCT 58.681 43.478 0.00 0.00 37.58 3.85
1706 1778 3.437049 CCTCGTCCAAAGATGAAAAGGTC 59.563 47.826 0.00 0.00 37.58 3.85
1747 1820 5.070313 ACACACAAAATGCTTCCACCTTATT 59.930 36.000 0.00 0.00 0.00 1.40
1797 1873 3.181470 ACAAAATTTCCCCACAAACTCCG 60.181 43.478 0.00 0.00 0.00 4.63
1913 1989 8.341173 GGTGAAATATTCTCATTCTCATGTCAC 58.659 37.037 0.00 0.00 0.00 3.67
2019 2099 8.522830 TCCAATGAAATCAGTTTTAGGATCAAC 58.477 33.333 0.00 0.00 0.00 3.18
2208 2294 7.027874 TCTAGATTACACAAACCCTCCATTT 57.972 36.000 0.00 0.00 0.00 2.32
2278 2367 3.449918 TGGTCAGTATCCTCCACATCAA 58.550 45.455 0.00 0.00 0.00 2.57
2413 2532 8.485976 AGCTAGATTGTTCTCTATCACAAAAC 57.514 34.615 0.00 0.00 36.50 2.43
2459 2578 4.043750 CACGTGTTCTGCAACATTTTCAT 58.956 39.130 7.58 0.00 44.47 2.57
2467 2586 3.234596 GAACTACACGTGTTCTGCAAC 57.765 47.619 28.55 8.59 40.23 4.17
2480 2599 7.016563 ACCATATGGCAATGATCTAGAACTACA 59.983 37.037 22.18 0.00 39.32 2.74
2491 2610 9.311676 TCATGTATAAAACCATATGGCAATGAT 57.688 29.630 22.18 11.10 39.32 2.45
2509 2629 7.237209 AGAGCATACATCAGCTTCATGTATA 57.763 36.000 20.54 4.73 42.91 1.47
2545 2665 3.282885 CTTATCCTGGCCTTCTTTGTCC 58.717 50.000 3.32 0.00 0.00 4.02
2738 2858 6.464465 GGAGCTAGAGAAATGTATTTGCCCTA 60.464 42.308 0.00 0.00 0.00 3.53
2784 2904 3.539604 ACATGCCTAACATCTCAGCTTC 58.460 45.455 0.00 0.00 36.64 3.86
2787 2907 4.892433 AGATACATGCCTAACATCTCAGC 58.108 43.478 0.00 0.00 36.64 4.26
2842 2965 1.677576 CTGAGTGCAAGTTGAGGCAAA 59.322 47.619 7.16 0.00 42.45 3.68
2901 3024 5.584649 GGCTCTTACATTGTAGCAACATACA 59.415 40.000 11.16 0.00 36.68 2.29
2999 3122 2.186903 CGGCCTTGCGGTAGTCAT 59.813 61.111 0.00 0.00 0.00 3.06
3219 3342 7.402054 TCAATATAGAAGGCCAGTCAGAAAAA 58.598 34.615 5.01 0.00 0.00 1.94
3224 3347 4.262808 CCCTCAATATAGAAGGCCAGTCAG 60.263 50.000 5.01 0.00 0.00 3.51
3227 3350 2.373502 GCCCTCAATATAGAAGGCCAGT 59.626 50.000 5.01 0.00 38.85 4.00
3228 3351 2.373169 TGCCCTCAATATAGAAGGCCAG 59.627 50.000 5.01 0.00 43.12 4.85
3229 3352 2.373169 CTGCCCTCAATATAGAAGGCCA 59.627 50.000 5.01 0.00 43.12 5.36
3230 3353 2.639839 TCTGCCCTCAATATAGAAGGCC 59.360 50.000 0.00 0.00 43.12 5.19
3231 3354 4.357918 TTCTGCCCTCAATATAGAAGGC 57.642 45.455 0.00 0.00 43.87 4.35
3232 3355 7.503566 TGAAAATTCTGCCCTCAATATAGAAGG 59.496 37.037 0.00 0.00 31.67 3.46
3234 3357 9.425248 AATGAAAATTCTGCCCTCAATATAGAA 57.575 29.630 0.00 0.00 32.57 2.10
3235 3358 9.425248 AAATGAAAATTCTGCCCTCAATATAGA 57.575 29.630 0.00 0.00 0.00 1.98
3236 3359 9.472361 CAAATGAAAATTCTGCCCTCAATATAG 57.528 33.333 0.00 0.00 0.00 1.31
3237 3360 7.927629 GCAAATGAAAATTCTGCCCTCAATATA 59.072 33.333 0.00 0.00 0.00 0.86
3256 3384 7.416213 GGTTGCATATTAGTTACTGGCAAATGA 60.416 37.037 0.00 0.00 40.87 2.57
3356 3493 3.510388 TGAGGAACAATGCTCGTCTAG 57.490 47.619 7.68 0.00 46.23 2.43
3357 3494 4.081697 TCAATGAGGAACAATGCTCGTCTA 60.082 41.667 7.68 0.00 46.23 2.59
3358 3495 3.005554 CAATGAGGAACAATGCTCGTCT 58.994 45.455 7.68 0.00 46.23 4.18
3361 3498 3.005554 AGTCAATGAGGAACAATGCTCG 58.994 45.455 0.00 0.00 46.23 5.03
3362 3499 4.005650 TGAGTCAATGAGGAACAATGCTC 58.994 43.478 0.00 0.00 43.77 4.26
3363 3500 4.025040 TGAGTCAATGAGGAACAATGCT 57.975 40.909 0.00 0.00 30.26 3.79
3364 3501 4.157289 ACATGAGTCAATGAGGAACAATGC 59.843 41.667 0.00 0.00 30.26 3.56
3365 3502 5.892160 ACATGAGTCAATGAGGAACAATG 57.108 39.130 0.00 0.00 0.00 2.82
3367 3504 6.295249 TGTTACATGAGTCAATGAGGAACAA 58.705 36.000 0.00 0.56 31.58 2.83
3368 3505 5.863965 TGTTACATGAGTCAATGAGGAACA 58.136 37.500 0.00 4.55 31.81 3.18
3413 3577 5.556915 TCCAAACGAACCTGAAAGTGATAT 58.443 37.500 0.00 0.00 0.00 1.63
3414 3578 4.963373 TCCAAACGAACCTGAAAGTGATA 58.037 39.130 0.00 0.00 0.00 2.15
3465 3629 2.746904 TGGTGACTTGACACAAACACAG 59.253 45.455 16.30 0.00 41.88 3.66
3476 3640 4.933505 TGCATTTCATTTGGTGACTTGA 57.066 36.364 0.00 0.00 36.32 3.02
3490 3654 7.531534 GCAACTTTGTATCACATTTTGCATTTC 59.468 33.333 11.88 0.00 37.39 2.17
3518 3687 4.278170 CCTTGTTTGCCTGATTTCAGTACA 59.722 41.667 6.81 2.29 42.27 2.90
3537 3706 4.505191 CAGTTCATCAACTTTGCAACCTTG 59.495 41.667 0.00 3.66 41.24 3.61
3538 3707 4.685924 CAGTTCATCAACTTTGCAACCTT 58.314 39.130 0.00 0.00 41.24 3.50
3566 3735 2.494870 AGCCTCAACCTTTGATGAATGC 59.505 45.455 0.00 0.00 39.30 3.56
3599 3768 8.584063 TGTGAATGTATCTGGTACTGTACTTA 57.416 34.615 16.79 6.60 34.27 2.24
3601 3770 7.321153 GTTGTGAATGTATCTGGTACTGTACT 58.679 38.462 16.79 0.73 34.27 2.73
3602 3771 6.252869 CGTTGTGAATGTATCTGGTACTGTAC 59.747 42.308 9.46 9.46 34.27 2.90
3605 3774 4.566759 CCGTTGTGAATGTATCTGGTACTG 59.433 45.833 0.00 0.00 34.27 2.74
3627 3796 2.119939 AGGCCTATCCTTCCTTACCC 57.880 55.000 1.29 0.00 44.75 3.69
3661 3830 0.467384 CAGAGATCGGAGTTGGGCAT 59.533 55.000 0.00 0.00 0.00 4.40
3686 3855 3.627395 TCAAATAAGACGCACCCTGAT 57.373 42.857 0.00 0.00 0.00 2.90
3799 3980 2.414994 ATCAGCTGGACCAAGACATG 57.585 50.000 15.13 0.00 0.00 3.21
3813 3994 4.114794 GGAAATGTGGTTGCAATATCAGC 58.885 43.478 0.59 0.00 0.00 4.26
3887 4068 4.418392 CATGATGAGGTAAAGCAAAGCAC 58.582 43.478 0.00 0.00 0.00 4.40
3974 4155 3.552384 TTGGCTTCCGTCCCACGT 61.552 61.111 0.00 0.00 40.58 4.49
4025 4206 1.537990 GCTTTTCAACAACCGGCATGT 60.538 47.619 0.00 4.07 0.00 3.21
4056 4237 1.684386 CTTCGGCATCAGCTCCCTCT 61.684 60.000 0.00 0.00 41.70 3.69
4094 4275 3.582647 TGGCAAGAATACACTCCTTCAGA 59.417 43.478 0.00 0.00 0.00 3.27
4149 4330 0.036199 AGGAGCAGAAGCAGAAGCAG 60.036 55.000 0.00 0.00 45.49 4.24
4150 4331 0.036577 GAGGAGCAGAAGCAGAAGCA 60.037 55.000 0.00 0.00 45.49 3.91
4151 4332 1.083242 CGAGGAGCAGAAGCAGAAGC 61.083 60.000 0.00 0.00 45.49 3.86
4152 4333 0.529833 TCGAGGAGCAGAAGCAGAAG 59.470 55.000 0.00 0.00 45.49 2.85
4153 4334 0.529833 CTCGAGGAGCAGAAGCAGAA 59.470 55.000 3.91 0.00 45.49 3.02
4154 4335 0.610509 ACTCGAGGAGCAGAAGCAGA 60.611 55.000 18.41 0.00 45.49 4.26
4260 4447 2.304761 TGTTTCTAACATCGCCCCTTCT 59.695 45.455 0.00 0.00 36.25 2.85
4309 4533 3.220940 AGGCTTCTACCCATCTACGTAC 58.779 50.000 0.00 0.00 0.00 3.67
4312 4536 2.693591 TGAAGGCTTCTACCCATCTACG 59.306 50.000 26.26 0.00 0.00 3.51
4324 4548 3.366781 GCATTTGAGTTCCTGAAGGCTTC 60.367 47.826 20.27 20.27 34.44 3.86
4340 4564 5.617609 CAGCATTCATTTGTTCAGCATTTG 58.382 37.500 0.00 0.00 0.00 2.32
4413 4657 4.200874 TGACCCGTGAGTACATTTTTGTT 58.799 39.130 0.00 0.00 0.00 2.83
4447 4697 2.851195 AGGCTGCCTTGGTAATATTCG 58.149 47.619 17.22 0.00 0.00 3.34
4506 4756 4.713553 TGTGTTCTCTGGTATTTGCTGAA 58.286 39.130 0.00 0.00 0.00 3.02
4561 4811 8.980143 ACAATACGGAAGAATTTGTTATTTGG 57.020 30.769 0.00 0.00 31.02 3.28
4568 4818 9.457436 AAGGTAATACAATACGGAAGAATTTGT 57.543 29.630 0.00 0.00 35.99 2.83
4569 4819 9.931210 GAAGGTAATACAATACGGAAGAATTTG 57.069 33.333 0.00 0.00 0.00 2.32
4802 5056 8.305046 CCCCCTTCTTGTCATATTTATCAAAA 57.695 34.615 0.00 0.00 0.00 2.44
4874 5129 1.000607 CCTGCCAATGCACATGATAGC 60.001 52.381 0.00 0.68 44.23 2.97
5138 5405 6.469595 CGTTTACGATTTGTTGAGTTTTGGAA 59.530 34.615 0.00 0.00 43.02 3.53
5610 6027 4.958581 TGGCTCTTCTCTCTGATGATGTTA 59.041 41.667 0.00 0.00 0.00 2.41
5714 6131 4.662278 TGCTCTTACCAATGCCTAAACTT 58.338 39.130 0.00 0.00 0.00 2.66
5752 6170 5.009210 GCCTGTATTTTAATTATCGGCCACA 59.991 40.000 2.24 0.00 0.00 4.17
5986 6410 2.267174 AGCATCTGCAACAAGTGACT 57.733 45.000 4.79 0.00 45.16 3.41
5993 6417 2.689471 ACAACAAGAAGCATCTGCAACA 59.311 40.909 4.79 0.00 45.16 3.33
6193 6619 4.520492 GGCCATCCTATTTCCAACTATGTG 59.480 45.833 0.00 0.00 0.00 3.21
6287 6714 3.317430 GCTAATTGGAAATCCCTGCAGAG 59.683 47.826 17.39 0.39 35.38 3.35


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

AutoCloner maintained by Alex Coulton.