Multiple sequence alignment - TraesCS6B01G041200

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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 TraesCS6B01G041200 chr6B 100.000 5603 0 0 1 5603 25559190 25553588 0.000000e+00 10347.0
1 TraesCS6B01G041200 chr6A 91.670 2665 169 21 2976 5603 14608349 14605701 0.000000e+00 3642.0
2 TraesCS6B01G041200 chr6A 89.889 1711 131 27 1237 2928 14609954 14608267 0.000000e+00 2163.0
3 TraesCS6B01G041200 chr6D 91.329 2249 151 16 2930 5146 13976858 13979094 0.000000e+00 3033.0
4 TraesCS6B01G041200 chr6D 92.530 2142 106 27 804 2928 13974711 13976815 0.000000e+00 3020.0
5 TraesCS6B01G041200 chr6D 85.227 440 50 8 79 509 13973125 13973558 6.660000e-119 438.0
6 TraesCS6B01G041200 chr6D 87.624 202 24 1 5142 5343 13987526 13987726 3.380000e-57 233.0
7 TraesCS6B01G041200 chr6D 94.118 85 1 1 1 81 13972725 13972809 5.890000e-25 126.0
8 TraesCS6B01G041200 chrUn 82.492 634 100 9 1901 2527 32134356 32133727 3.820000e-151 545.0
9 TraesCS6B01G041200 chrUn 79.147 633 123 6 1904 2527 32089733 32089101 4.010000e-116 429.0
10 TraesCS6B01G041200 chrUn 75.000 252 46 17 1456 1702 32134964 32134725 3.570000e-17 100.0
11 TraesCS6B01G041200 chr1B 77.434 647 113 18 1905 2524 658714479 658713839 6.900000e-94 355.0
12 TraesCS6B01G041200 chr1B 74.736 851 164 36 3787 4602 658708643 658707809 3.230000e-87 333.0
13 TraesCS6B01G041200 chr1B 77.297 555 107 11 4059 4602 658712686 658712140 5.450000e-80 309.0
14 TraesCS6B01G041200 chr1B 75.556 630 138 13 1909 2527 658739045 658738421 4.240000e-76 296.0
15 TraesCS6B01G041200 chr1A 73.846 845 183 27 3787 4602 568026148 568025313 9.120000e-78 302.0
16 TraesCS6B01G041200 chr1D 73.095 840 190 28 3787 4602 473708724 473707897 3.330000e-67 267.0
17 TraesCS6B01G041200 chr1D 83.178 107 14 3 1621 1726 473762728 473762625 1.660000e-15 95.3
18 TraesCS6B01G041200 chr5A 86.813 182 21 3 326 505 656731609 656731789 3.420000e-47 200.0
19 TraesCS6B01G041200 chr5D 85.946 185 24 2 327 509 356690065 356689881 4.430000e-46 196.0
20 TraesCS6B01G041200 chr3D 77.225 382 54 20 1431 1812 3012292 3012640 5.730000e-45 193.0
21 TraesCS6B01G041200 chr2A 86.188 181 20 5 328 505 155766468 155766646 2.060000e-44 191.0
22 TraesCS6B01G041200 chr2A 85.475 179 24 2 332 508 585794760 585794582 9.590000e-43 185.0
23 TraesCS6B01G041200 chr2A 85.000 180 24 3 332 508 196508335 196508156 4.460000e-41 180.0
24 TraesCS6B01G041200 chr7B 85.246 183 24 3 329 508 717326007 717326189 9.590000e-43 185.0
25 TraesCS6B01G041200 chr7B 100.000 29 0 0 4704 4732 447971721 447971693 3.000000e-03 54.7
26 TraesCS6B01G041200 chr3B 86.047 172 19 4 332 500 529675423 529675592 4.460000e-41 180.0
27 TraesCS6B01G041200 chr3B 78.378 185 30 4 1638 1815 3043290 3043109 1.650000e-20 111.0
28 TraesCS6B01G041200 chr3A 85.227 176 23 3 332 504 11385482 11385307 1.600000e-40 178.0
29 TraesCS6B01G041200 chr7D 100.000 29 0 0 4704 4732 430160397 430160369 3.000000e-03 54.7


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 TraesCS6B01G041200 chr6B 25553588 25559190 5602 True 10347.000000 10347 100.0000 1 5603 1 chr6B.!!$R1 5602
1 TraesCS6B01G041200 chr6A 14605701 14609954 4253 True 2902.500000 3642 90.7795 1237 5603 2 chr6A.!!$R1 4366
2 TraesCS6B01G041200 chr6D 13972725 13979094 6369 False 1654.250000 3033 90.8010 1 5146 4 chr6D.!!$F2 5145
3 TraesCS6B01G041200 chrUn 32089101 32089733 632 True 429.000000 429 79.1470 1904 2527 1 chrUn.!!$R1 623
4 TraesCS6B01G041200 chrUn 32133727 32134964 1237 True 322.500000 545 78.7460 1456 2527 2 chrUn.!!$R2 1071
5 TraesCS6B01G041200 chr1B 658707809 658714479 6670 True 332.333333 355 76.4890 1905 4602 3 chr1B.!!$R2 2697
6 TraesCS6B01G041200 chr1B 658738421 658739045 624 True 296.000000 296 75.5560 1909 2527 1 chr1B.!!$R1 618
7 TraesCS6B01G041200 chr1A 568025313 568026148 835 True 302.000000 302 73.8460 3787 4602 1 chr1A.!!$R1 815
8 TraesCS6B01G041200 chr1D 473707897 473708724 827 True 267.000000 267 73.0950 3787 4602 1 chr1D.!!$R1 815

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
949 2160 0.033504 GTCTCTCCAGTCGGCAACAA 59.966 55.0 0.00 0.00 0.00 2.83 F
1942 3402 0.109504 GTCGAGAAGCTTCAGCGACT 60.110 55.0 38.85 20.36 45.33 4.18 F
2929 8862 0.181350 CTCACCCTGTTGCTATCCCC 59.819 60.0 0.00 0.00 0.00 4.81 F
4078 10204 0.037326 AACCGATGAGCACGACATGT 60.037 50.0 0.00 0.00 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2550 8473 0.464452 CCCTAAGTCAAGTAGGCCGG 59.536 60.0 0.00 0.0 37.41 6.13 R
3575 9686 0.397114 TCTTCGCCATGGGAGAGCTA 60.397 55.0 15.13 0.0 32.27 3.32 R
4338 10473 0.750182 CACCCCCAACGTTTGTCACT 60.750 55.0 0.00 0.0 0.00 3.41 R
4988 11127 0.480252 AAGCAGCAAGTTCTCCCCTT 59.520 50.0 0.00 0.0 0.00 3.95 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
74 79 0.467384 CATTCATCCGGAGAGTGCCT 59.533 55.000 11.34 0.00 0.00 4.75
99 422 5.967088 TCATAGGAGTTGCTCTAAACACTC 58.033 41.667 0.00 0.00 32.21 3.51
134 457 9.026074 TCAAATAAAAGTTTAGCCTTTCAAACG 57.974 29.630 0.00 0.00 39.18 3.60
147 470 5.751509 GCCTTTCAAACGTTAACCAGAAAAT 59.248 36.000 0.00 0.00 0.00 1.82
193 517 8.747538 ATAAATTTAAGTCGGCCATCTAAACT 57.252 30.769 2.24 0.00 0.00 2.66
194 518 9.841295 ATAAATTTAAGTCGGCCATCTAAACTA 57.159 29.630 2.24 0.00 0.00 2.24
198 523 7.605410 TTAAGTCGGCCATCTAAACTAAAAG 57.395 36.000 2.24 0.00 0.00 2.27
199 524 5.161943 AGTCGGCCATCTAAACTAAAAGT 57.838 39.130 2.24 0.00 0.00 2.66
203 528 8.648693 AGTCGGCCATCTAAACTAAAAGTATAT 58.351 33.333 2.24 0.00 0.00 0.86
204 529 8.709646 GTCGGCCATCTAAACTAAAAGTATATG 58.290 37.037 2.24 0.00 0.00 1.78
258 584 8.960591 ACAAATTTCAGAAGAAAAAGAGTCAGA 58.039 29.630 0.00 0.00 46.06 3.27
272 598 0.458716 GTCAGAGTAAGGGTCGCTGC 60.459 60.000 0.00 0.00 33.87 5.25
281 607 1.068250 GGGTCGCTGCCAGAGTATC 59.932 63.158 0.00 0.00 0.00 2.24
324 654 6.667007 CATGTTTCTACACATGCTGACATA 57.333 37.500 1.06 0.00 45.74 2.29
325 655 6.481134 CATGTTTCTACACATGCTGACATAC 58.519 40.000 1.06 0.00 45.74 2.39
326 656 4.625311 TGTTTCTACACATGCTGACATACG 59.375 41.667 0.00 0.00 33.67 3.06
327 657 4.712122 TTCTACACATGCTGACATACGA 57.288 40.909 0.00 0.00 33.67 3.43
328 658 4.918810 TCTACACATGCTGACATACGAT 57.081 40.909 0.00 0.00 33.67 3.73
329 659 5.262588 TCTACACATGCTGACATACGATT 57.737 39.130 0.00 0.00 33.67 3.34
330 660 6.385649 TCTACACATGCTGACATACGATTA 57.614 37.500 0.00 0.00 33.67 1.75
356 686 7.675962 TTTTTAACACAGTACAGACACAAGT 57.324 32.000 0.00 0.00 0.00 3.16
358 688 3.179443 ACACAGTACAGACACAAGTGG 57.821 47.619 5.08 0.00 33.55 4.00
362 692 3.388024 ACAGTACAGACACAAGTGGTCAT 59.612 43.478 5.08 0.00 37.74 3.06
370 700 6.096423 ACAGACACAAGTGGTCATATATACGT 59.904 38.462 5.08 0.00 37.74 3.57
372 702 6.096423 AGACACAAGTGGTCATATATACGTGT 59.904 38.462 0.00 0.00 37.74 4.49
373 703 6.270815 ACACAAGTGGTCATATATACGTGTC 58.729 40.000 0.00 0.00 34.41 3.67
393 723 3.086282 TCTACACTCACGCCTATGAACA 58.914 45.455 0.00 0.00 0.00 3.18
394 724 3.699538 TCTACACTCACGCCTATGAACAT 59.300 43.478 0.00 0.00 0.00 2.71
402 732 1.257936 CGCCTATGAACATACACACGC 59.742 52.381 0.00 0.00 0.00 5.34
404 734 2.030457 GCCTATGAACATACACACGCAC 59.970 50.000 0.00 0.00 0.00 5.34
405 735 3.258228 CCTATGAACATACACACGCACA 58.742 45.455 0.00 0.00 0.00 4.57
408 738 2.556257 TGAACATACACACGCACAACT 58.444 42.857 0.00 0.00 0.00 3.16
423 753 3.685550 GCACAACTTACCCCTATGAGCAT 60.686 47.826 0.00 0.00 0.00 3.79
429 759 2.088104 ACCCCTATGAGCATCTTCGA 57.912 50.000 0.00 0.00 34.92 3.71
440 770 1.405105 GCATCTTCGAGAGACTGAGCT 59.595 52.381 0.00 0.00 41.84 4.09
442 772 2.481289 TCTTCGAGAGACTGAGCTGA 57.519 50.000 0.00 0.00 41.84 4.26
451 781 5.456548 AGAGACTGAGCTGACATATCATG 57.543 43.478 0.00 0.00 33.22 3.07
456 786 5.737860 ACTGAGCTGACATATCATGTTGAA 58.262 37.500 0.00 0.00 45.03 2.69
485 816 1.532007 GTCATCGTAGGCTCCTCGTAG 59.468 57.143 0.00 0.00 0.00 3.51
490 821 0.936600 GTAGGCTCCTCGTAGTCGAC 59.063 60.000 7.70 7.70 41.35 4.20
505 836 0.037877 TCGACGGGAACTTCTCCTCT 59.962 55.000 0.00 0.00 44.68 3.69
509 840 2.100087 GACGGGAACTTCTCCTCTCATC 59.900 54.545 0.00 0.00 44.68 2.92
511 842 2.104170 GGGAACTTCTCCTCTCATCGT 58.896 52.381 0.00 0.00 44.68 3.73
513 844 3.316868 GGGAACTTCTCCTCTCATCGTAG 59.683 52.174 0.00 0.00 44.68 3.51
514 845 3.243267 GGAACTTCTCCTCTCATCGTAGC 60.243 52.174 0.00 0.00 41.61 3.58
516 847 2.302260 CTTCTCCTCTCATCGTAGCCA 58.698 52.381 0.00 0.00 0.00 4.75
517 848 1.974265 TCTCCTCTCATCGTAGCCAG 58.026 55.000 0.00 0.00 0.00 4.85
518 849 1.213182 TCTCCTCTCATCGTAGCCAGT 59.787 52.381 0.00 0.00 0.00 4.00
519 850 1.336440 CTCCTCTCATCGTAGCCAGTG 59.664 57.143 0.00 0.00 0.00 3.66
531 1708 2.208326 AGCCAGTGCGTTTTTCAAAG 57.792 45.000 0.00 0.00 44.33 2.77
546 1723 2.942804 TCAAAGTTTCTCACATGCCCA 58.057 42.857 0.00 0.00 0.00 5.36
547 1724 3.295093 TCAAAGTTTCTCACATGCCCAA 58.705 40.909 0.00 0.00 0.00 4.12
548 1725 3.703556 TCAAAGTTTCTCACATGCCCAAA 59.296 39.130 0.00 0.00 0.00 3.28
553 1730 5.058490 AGTTTCTCACATGCCCAAATTTTG 58.942 37.500 1.99 1.99 0.00 2.44
555 1732 4.686191 TCTCACATGCCCAAATTTTGTT 57.314 36.364 8.26 0.00 0.00 2.83
603 1780 7.147724 TGTCCAAACACCATAAAATTTGGTACA 60.148 33.333 12.88 12.39 45.71 2.90
606 1783 7.437748 CAAACACCATAAAATTTGGTACAGGA 58.562 34.615 0.00 0.00 45.71 3.86
607 1784 6.584185 ACACCATAAAATTTGGTACAGGAC 57.416 37.500 0.00 0.00 45.71 3.85
610 1787 5.646360 ACCATAAAATTTGGTACAGGACTCG 59.354 40.000 0.00 0.00 45.62 4.18
616 1793 1.153628 GGTACAGGACTCGCGCATT 60.154 57.895 8.75 0.00 0.00 3.56
617 1794 1.146358 GGTACAGGACTCGCGCATTC 61.146 60.000 8.75 0.00 0.00 2.67
618 1795 1.226575 TACAGGACTCGCGCATTCG 60.227 57.895 8.75 0.00 39.07 3.34
619 1796 1.650314 TACAGGACTCGCGCATTCGA 61.650 55.000 8.75 0.00 38.10 3.71
625 1802 2.104928 TCGCGCATTCGAGCATCT 59.895 55.556 8.75 0.00 37.91 2.90
626 1803 1.519234 TCGCGCATTCGAGCATCTT 60.519 52.632 8.75 0.00 37.91 2.40
627 1804 1.367312 CGCGCATTCGAGCATCTTG 60.367 57.895 8.75 0.00 37.91 3.02
628 1805 1.653533 GCGCATTCGAGCATCTTGC 60.654 57.895 0.30 0.00 38.92 4.01
629 1806 2.313717 GCGCATTCGAGCATCTTGCA 62.314 55.000 0.30 0.00 40.25 4.08
630 1807 3.577462 GCGCATTCGAGCATCTTGCAT 62.577 52.381 0.30 0.00 40.25 3.96
690 1867 8.356657 ACCTTTTGATTTTATCGTTCATTCACA 58.643 29.630 0.00 0.00 0.00 3.58
695 1872 5.545658 TTTTATCGTTCATTCACAGGAGC 57.454 39.130 0.00 0.00 0.00 4.70
709 1886 4.106925 GAGCAGCTGGACCCAGGG 62.107 72.222 17.12 2.85 43.77 4.45
710 1887 4.664267 AGCAGCTGGACCCAGGGA 62.664 66.667 14.54 0.00 43.77 4.20
711 1888 4.106925 GCAGCTGGACCCAGGGAG 62.107 72.222 14.54 0.00 43.77 4.30
712 1889 4.106925 CAGCTGGACCCAGGGAGC 62.107 72.222 14.54 11.46 43.77 4.70
723 1900 4.489771 AGGGAGCCAAATCGCCGG 62.490 66.667 0.00 0.00 32.81 6.13
729 1906 4.418328 CCAAATCGCCGGGTCCCA 62.418 66.667 9.12 0.00 0.00 4.37
774 1951 5.280470 GCTTACAAAATGGGGGAATTCCTTT 60.280 40.000 23.63 13.24 35.95 3.11
776 1953 4.238669 ACAAAATGGGGGAATTCCTTTCA 58.761 39.130 23.63 18.08 35.94 2.69
783 1960 2.308866 GGGGAATTCCTTTCACTCTCCA 59.691 50.000 23.63 0.00 37.90 3.86
791 1968 3.903714 TCCTTTCACTCTCCATTGACTGA 59.096 43.478 0.00 0.00 0.00 3.41
802 1979 4.264253 TCCATTGACTGATCCACACAATC 58.736 43.478 0.00 0.00 0.00 2.67
806 1983 4.001618 TGACTGATCCACACAATCGAAA 57.998 40.909 0.00 0.00 0.00 3.46
807 1984 4.578871 TGACTGATCCACACAATCGAAAT 58.421 39.130 0.00 0.00 0.00 2.17
861 2071 1.851065 TTGCTATGCCTGGACAGCCA 61.851 55.000 0.00 0.00 43.47 4.75
864 2074 1.315690 CTATGCCTGGACAGCCATTG 58.684 55.000 0.88 0.00 44.91 2.82
885 2095 1.399714 CGTGCTGGGTCTGGACTATA 58.600 55.000 0.67 0.00 0.00 1.31
891 2101 2.879646 CTGGGTCTGGACTATAGACGAC 59.120 54.545 6.78 4.43 44.24 4.34
892 2102 2.508716 TGGGTCTGGACTATAGACGACT 59.491 50.000 6.78 0.00 44.24 4.18
894 2104 2.801679 GGTCTGGACTATAGACGACTCG 59.198 54.545 6.78 0.00 44.24 4.18
907 2118 1.130749 ACGACTCGAAGGTCAAGATCG 59.869 52.381 5.20 0.00 36.12 3.69
948 2159 1.112916 TGTCTCTCCAGTCGGCAACA 61.113 55.000 0.00 0.00 0.00 3.33
949 2160 0.033504 GTCTCTCCAGTCGGCAACAA 59.966 55.000 0.00 0.00 0.00 2.83
984 2195 1.257743 ATAGTATGACCGCGGCATCT 58.742 50.000 29.65 25.88 0.00 2.90
1013 2224 4.496336 GCCCATGAAGCGCCTCCT 62.496 66.667 2.29 0.00 0.00 3.69
1014 2225 2.203126 CCCATGAAGCGCCTCCTC 60.203 66.667 2.29 0.00 0.00 3.71
1015 2226 2.203126 CCATGAAGCGCCTCCTCC 60.203 66.667 2.29 0.00 0.00 4.30
1016 2227 2.203126 CATGAAGCGCCTCCTCCC 60.203 66.667 2.29 0.00 0.00 4.30
1017 2228 3.854669 ATGAAGCGCCTCCTCCCG 61.855 66.667 2.29 0.00 0.00 5.14
1065 2282 1.395826 ATTCTTCCTCCTCCCGCTCG 61.396 60.000 0.00 0.00 0.00 5.03
1085 2302 4.393155 CGTAGCCTGGGTGCTGCA 62.393 66.667 9.02 0.00 43.22 4.41
1131 2348 1.979155 CAGAGCACACGGAGGAGGA 60.979 63.158 0.00 0.00 0.00 3.71
1160 2377 8.822855 TCGCAAGGTAATTAATACTACATGTTG 58.177 33.333 2.30 4.29 34.74 3.33
1172 2389 4.828829 ACTACATGTTGCAGTAGTAACCC 58.171 43.478 13.22 0.00 46.56 4.11
1173 2390 2.695359 ACATGTTGCAGTAGTAACCCG 58.305 47.619 0.00 0.00 39.29 5.28
1185 2402 6.747739 GCAGTAGTAACCCGTACTAGTTTAAC 59.252 42.308 0.00 0.00 43.63 2.01
1217 2434 3.647636 ACTCTGGATCTGGCTAAGCTAA 58.352 45.455 0.00 0.00 0.00 3.09
1223 2440 5.621193 TGGATCTGGCTAAGCTAATTAACC 58.379 41.667 0.00 0.00 31.26 2.85
1228 2445 2.548480 GGCTAAGCTAATTAACCGCCTG 59.452 50.000 0.00 0.00 32.20 4.85
1229 2446 2.031944 GCTAAGCTAATTAACCGCCTGC 60.032 50.000 0.00 0.00 0.00 4.85
1230 2447 2.122783 AAGCTAATTAACCGCCTGCA 57.877 45.000 0.00 0.00 0.00 4.41
1231 2448 2.348411 AGCTAATTAACCGCCTGCAT 57.652 45.000 0.00 0.00 0.00 3.96
1232 2449 1.949525 AGCTAATTAACCGCCTGCATG 59.050 47.619 0.00 0.00 0.00 4.06
1233 2450 1.676006 GCTAATTAACCGCCTGCATGT 59.324 47.619 0.00 0.00 0.00 3.21
1234 2451 2.541588 GCTAATTAACCGCCTGCATGTG 60.542 50.000 0.00 0.00 0.00 3.21
1235 2452 1.544724 AATTAACCGCCTGCATGTGT 58.455 45.000 1.81 0.00 0.00 3.72
1269 2486 2.809119 GCGTCTCTAGCTCTACATAGCA 59.191 50.000 0.00 0.00 45.30 3.49
1383 2600 4.369182 CGATCTCTACGGCCTTAATTTGT 58.631 43.478 0.00 0.00 0.00 2.83
1450 2672 2.467880 AGTAAGGAAGGATCTTCGGCA 58.532 47.619 0.00 0.00 0.00 5.69
1454 2676 0.469917 GGAAGGATCTTCGGCATCCA 59.530 55.000 9.87 0.00 42.28 3.41
1604 2834 7.405469 TTGCATGTGTTGAATGTTGAATAAC 57.595 32.000 0.00 0.00 37.32 1.89
1620 2850 9.617523 TGTTGAATAACTATCATGTGATGTGAT 57.382 29.630 5.78 0.00 37.68 3.06
1621 2851 9.874215 GTTGAATAACTATCATGTGATGTGATG 57.126 33.333 5.78 0.00 36.96 3.07
1622 2852 9.617523 TTGAATAACTATCATGTGATGTGATGT 57.382 29.630 5.78 0.00 36.96 3.06
1623 2853 9.048446 TGAATAACTATCATGTGATGTGATGTG 57.952 33.333 5.78 0.00 36.96 3.21
1624 2854 9.264719 GAATAACTATCATGTGATGTGATGTGA 57.735 33.333 5.78 0.00 36.96 3.58
1633 2863 4.213906 TGTGATGTGATGTGATGTGTTGTC 59.786 41.667 0.00 0.00 0.00 3.18
1855 3109 2.928116 GCATGACTTCGTAACCCTGTAC 59.072 50.000 0.00 0.00 0.00 2.90
1890 3342 3.281341 TGGAAACATTTCACGTCATGC 57.719 42.857 6.68 0.00 38.92 4.06
1891 3343 2.030363 TGGAAACATTTCACGTCATGCC 60.030 45.455 6.68 0.00 38.92 4.40
1892 3344 2.030363 GGAAACATTTCACGTCATGCCA 60.030 45.455 6.68 0.00 38.92 4.92
1893 3345 3.367292 GGAAACATTTCACGTCATGCCAT 60.367 43.478 6.68 0.00 38.92 4.40
1894 3346 3.492421 AACATTTCACGTCATGCCATC 57.508 42.857 0.00 0.00 0.00 3.51
1895 3347 2.435422 ACATTTCACGTCATGCCATCA 58.565 42.857 0.00 0.00 0.00 3.07
1896 3348 3.018856 ACATTTCACGTCATGCCATCAT 58.981 40.909 0.00 0.00 0.00 2.45
1942 3402 0.109504 GTCGAGAAGCTTCAGCGACT 60.110 55.000 38.85 20.36 45.33 4.18
2512 8435 3.731652 TCATGCTGGGAAACAAACAAG 57.268 42.857 0.00 0.00 0.00 3.16
2540 8463 4.810491 AGTGGTACGTTTTTATTCACACGT 59.190 37.500 0.00 1.48 46.97 4.49
2541 8464 4.899616 GTGGTACGTTTTTATTCACACGTG 59.100 41.667 15.48 15.48 45.13 4.49
2550 8473 0.320771 ATTCACACGTGACTGAGGGC 60.321 55.000 25.01 0.00 39.66 5.19
2551 8474 2.357517 CACACGTGACTGAGGGCC 60.358 66.667 25.01 0.00 0.00 5.80
2552 8475 3.991051 ACACGTGACTGAGGGCCG 61.991 66.667 25.01 0.00 0.00 6.13
2553 8476 4.742201 CACGTGACTGAGGGCCGG 62.742 72.222 10.90 0.00 0.00 6.13
2593 8516 7.175119 GGGGTCTTATTTATGCTTTCTGGTATC 59.825 40.741 0.00 0.00 0.00 2.24
2620 8543 6.017109 AGCTCAAGAATAAGAAGCGAACAAAA 60.017 34.615 0.00 0.00 0.00 2.44
2802 8729 7.067494 GCATTATTATTCTTTCCCCATCGCTAT 59.933 37.037 0.00 0.00 0.00 2.97
2828 8755 8.519526 TCCTAACAAAAACATGCTTACAATAGG 58.480 33.333 0.00 0.00 0.00 2.57
2835 8762 6.545504 AACATGCTTACAATAGGCTATTCG 57.454 37.500 16.70 14.05 0.00 3.34
2846 8778 2.480845 AGGCTATTCGTATTTCGTGGC 58.519 47.619 0.00 0.00 40.80 5.01
2852 8784 5.220605 GCTATTCGTATTTCGTGGCTTCTTT 60.221 40.000 0.00 0.00 40.80 2.52
2854 8786 6.730960 ATTCGTATTTCGTGGCTTCTTTTA 57.269 33.333 0.00 0.00 40.80 1.52
2855 8787 5.773239 TCGTATTTCGTGGCTTCTTTTAG 57.227 39.130 0.00 0.00 40.80 1.85
2858 8790 6.308766 TCGTATTTCGTGGCTTCTTTTAGTAC 59.691 38.462 0.00 0.00 40.80 2.73
2868 8801 7.806487 GTGGCTTCTTTTAGTACACCATTTTAC 59.194 37.037 0.00 0.00 0.00 2.01
2869 8802 7.722285 TGGCTTCTTTTAGTACACCATTTTACT 59.278 33.333 0.00 0.00 33.11 2.24
2876 8809 4.079253 AGTACACCATTTTACTGGGCAAG 58.921 43.478 0.00 0.00 40.85 4.01
2885 8818 3.517296 TTACTGGGCAAGTCCAAATCA 57.483 42.857 0.00 0.00 40.56 2.57
2897 8830 6.313658 GCAAGTCCAAATCAGACAAACTTTTT 59.686 34.615 0.00 0.00 36.68 1.94
2898 8831 7.674705 GCAAGTCCAAATCAGACAAACTTTTTG 60.675 37.037 0.00 0.00 36.68 2.44
2928 8861 1.204146 TCTCACCCTGTTGCTATCCC 58.796 55.000 0.00 0.00 0.00 3.85
2929 8862 0.181350 CTCACCCTGTTGCTATCCCC 59.819 60.000 0.00 0.00 0.00 4.81
2930 8863 0.548926 TCACCCTGTTGCTATCCCCA 60.549 55.000 0.00 0.00 0.00 4.96
2931 8864 0.552848 CACCCTGTTGCTATCCCCAT 59.447 55.000 0.00 0.00 0.00 4.00
2932 8865 1.063717 CACCCTGTTGCTATCCCCATT 60.064 52.381 0.00 0.00 0.00 3.16
2957 8931 0.722676 TCTTCCCCCATCACTACCCT 59.277 55.000 0.00 0.00 0.00 4.34
2962 8936 2.201830 CCCCCATCACTACCCTAACAA 58.798 52.381 0.00 0.00 0.00 2.83
2970 8944 6.293955 CCATCACTACCCTAACAAAAACACAG 60.294 42.308 0.00 0.00 0.00 3.66
3003 8977 7.357303 TCTTCTTTTAGTACCATTTTCGTTGC 58.643 34.615 0.00 0.00 0.00 4.17
3020 8994 3.066064 CGTTGCCAATTCCAAATCCGATA 59.934 43.478 0.00 0.00 0.00 2.92
3054 9028 3.068873 ACTCAATATTCTCTCCTGTCGCC 59.931 47.826 0.00 0.00 0.00 5.54
3062 9036 1.271934 CTCTCCTGTCGCCATCCTATG 59.728 57.143 0.00 0.00 0.00 2.23
3075 9049 4.142093 GCCATCCTATGAAGCAAAACACAT 60.142 41.667 0.00 0.00 0.00 3.21
3108 9082 9.474920 TCTTACATCATTTTTGTTGTCAATTCC 57.525 29.630 0.00 0.00 33.32 3.01
3173 9177 7.571026 CCATAGCAATTCGATCTAAACAAGAG 58.429 38.462 0.00 0.00 37.74 2.85
3313 9331 2.357034 CAGGCGGCACAGTACGTT 60.357 61.111 13.08 0.00 0.00 3.99
3323 9341 1.732259 CACAGTACGTTCAAGATGGCC 59.268 52.381 0.00 0.00 0.00 5.36
3433 9451 3.181449 TGGACCTTGACATCGGAAAGAAA 60.181 43.478 0.00 0.00 0.00 2.52
3507 9525 5.149977 GTGCAATGAGAGTTTGAGTTTAGC 58.850 41.667 0.00 0.00 0.00 3.09
3510 9528 5.105997 GCAATGAGAGTTTGAGTTTAGCCAT 60.106 40.000 0.00 0.00 0.00 4.40
3514 9532 5.012664 TGAGAGTTTGAGTTTAGCCATGGTA 59.987 40.000 14.67 1.63 0.00 3.25
3515 9533 5.876357 AGAGTTTGAGTTTAGCCATGGTAA 58.124 37.500 14.67 8.05 0.00 2.85
3528 9546 3.542046 TGGTAACATGCAAGCGCTA 57.458 47.368 12.05 0.00 46.17 4.26
3575 9686 7.778470 TCTTGTTTTGTTTTGTTTTGTGAGT 57.222 28.000 0.00 0.00 0.00 3.41
3659 9770 0.976641 AAGTGGCGATGTTCTCCTCA 59.023 50.000 0.00 0.00 0.00 3.86
3727 9838 4.025647 CAGCCGCTAAGCTAAAATGTACTC 60.026 45.833 0.00 0.00 42.61 2.59
3925 10036 1.897560 CTCTTCACCCAAACTGGTCC 58.102 55.000 0.00 0.00 36.12 4.46
4073 10199 2.029380 CCCATATAACCGATGAGCACGA 60.029 50.000 0.00 0.00 0.00 4.35
4078 10204 0.037326 AACCGATGAGCACGACATGT 60.037 50.000 0.00 0.00 0.00 3.21
4113 10239 1.451028 GCTGCCTCGGAAGATTGCT 60.451 57.895 0.00 0.00 40.84 3.91
4151 10277 1.971167 GCGGCAACATCAACCCTCA 60.971 57.895 0.00 0.00 0.00 3.86
4167 10293 4.193893 CATGGGGCGGCTGATCCA 62.194 66.667 9.56 8.17 34.01 3.41
4251 10386 3.058160 GCCTCCGTGCACTGCAAT 61.058 61.111 16.19 0.00 41.47 3.56
4327 10462 1.263356 CCTAAGAAGTCCGGTCACCA 58.737 55.000 0.00 0.00 0.00 4.17
4338 10473 0.034756 CGGTCACCATGTCAAGGACA 59.965 55.000 0.00 1.05 46.90 4.02
4355 10490 0.750182 ACAGTGACAAACGTTGGGGG 60.750 55.000 7.76 0.00 34.12 5.40
4362 10497 1.524393 AAACGTTGGGGGTGTCGAC 60.524 57.895 9.11 9.11 0.00 4.20
4530 10665 1.389555 GCAGCCTTACATGGGGTAAC 58.610 55.000 0.00 0.00 37.05 2.50
4622 10757 2.560542 AGTTAATTGGGCGAAACATGCA 59.439 40.909 0.00 0.00 0.00 3.96
4634 10769 5.348451 GGCGAAACATGCAAAACATAAGATT 59.652 36.000 0.00 0.00 36.64 2.40
4677 10812 6.572167 TTATTCACTTTCACATGCACATGA 57.428 33.333 17.19 0.00 41.20 3.07
4734 10869 5.041940 GCTACTAGTGAACTTATGAACCGG 58.958 45.833 5.39 0.00 0.00 5.28
4735 10870 4.467198 ACTAGTGAACTTATGAACCGGG 57.533 45.455 6.32 0.00 0.00 5.73
4736 10871 2.109425 AGTGAACTTATGAACCGGGC 57.891 50.000 6.32 0.00 0.00 6.13
4752 10887 0.034896 GGGCCGACTCAACTTTCTCA 59.965 55.000 0.00 0.00 0.00 3.27
4988 11127 9.098355 CGAATTAATGACCTTGATTCTTCACTA 57.902 33.333 6.46 0.00 37.58 2.74
5025 11164 4.147219 GCTTCTGCAAAATGACTTACGT 57.853 40.909 0.00 0.00 39.41 3.57
5090 11229 3.019564 AGTAATAGGCGGTCGTGTAGTT 58.980 45.455 0.00 0.00 0.00 2.24
5154 11293 3.339093 GGTGGTGGGAGGGAAGGG 61.339 72.222 0.00 0.00 0.00 3.95
5155 11294 2.204090 GTGGTGGGAGGGAAGGGA 60.204 66.667 0.00 0.00 0.00 4.20
5236 11375 2.203625 GGCCCACCACCAACACAT 60.204 61.111 0.00 0.00 35.26 3.21
5249 11388 2.621407 CCAACACATAGAAGGCCCACAT 60.621 50.000 0.00 0.00 0.00 3.21
5271 11410 2.013400 ACAAATGTCACACACGAGCAA 58.987 42.857 0.00 0.00 0.00 3.91
5277 11416 0.529773 TCACACACGAGCAAGGACAC 60.530 55.000 0.00 0.00 0.00 3.67
5309 11448 5.436175 CCCACCATCAACAACATAGACATA 58.564 41.667 0.00 0.00 0.00 2.29
5459 11601 3.452990 TGAAAATGGATGAGCATGGCAAT 59.547 39.130 0.00 0.00 0.00 3.56
5460 11602 4.650131 TGAAAATGGATGAGCATGGCAATA 59.350 37.500 0.00 0.00 0.00 1.90
5463 11605 0.239347 GGATGAGCATGGCAATACGC 59.761 55.000 0.00 0.00 41.28 4.42
5474 11616 1.720894 CAATACGCGCCTTCATGCA 59.279 52.632 5.73 0.00 0.00 3.96
5478 11620 0.804544 TACGCGCCTTCATGCACTAC 60.805 55.000 5.73 0.00 0.00 2.73
5489 11631 7.065923 CGCCTTCATGCACTACTATACTATAGA 59.934 40.741 6.78 0.00 0.00 1.98
5516 11658 3.953775 CCACGGCCTCACCCACTT 61.954 66.667 0.00 0.00 33.26 3.16
5517 11659 2.113139 CACGGCCTCACCCACTTT 59.887 61.111 0.00 0.00 33.26 2.66
5520 11662 2.359975 GGCCTCACCCACTTTCCG 60.360 66.667 0.00 0.00 0.00 4.30
5522 11664 2.742372 CCTCACCCACTTTCCGCG 60.742 66.667 0.00 0.00 0.00 6.46
5523 11665 3.423154 CTCACCCACTTTCCGCGC 61.423 66.667 0.00 0.00 0.00 6.86
5572 11717 3.685835 GCCAGGATCTAGGAAAGGGAAAC 60.686 52.174 7.97 0.00 0.00 2.78
5583 11728 4.079385 AGGAAAGGGAAACAAACCTACACT 60.079 41.667 0.00 0.00 35.64 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 79 7.561722 AGAGTGTTTAGAGCAACTCCTATGATA 59.438 37.037 0.00 0.00 0.00 2.15
123 446 3.974871 TCTGGTTAACGTTTGAAAGGC 57.025 42.857 5.91 0.00 0.00 4.35
168 491 8.747538 AGTTTAGATGGCCGACTTAAATTTAT 57.252 30.769 6.81 0.00 0.00 1.40
179 503 8.426489 ACATATACTTTTAGTTTAGATGGCCGA 58.574 33.333 0.00 0.00 0.00 5.54
216 541 9.734620 CTGAAATTTGTTAGTTGAATCTGTTCA 57.265 29.630 0.00 0.00 42.41 3.18
258 584 1.608717 CTCTGGCAGCGACCCTTACT 61.609 60.000 10.34 0.00 0.00 2.24
272 598 6.398095 TGTCACAACATTGTAGATACTCTGG 58.602 40.000 0.00 0.00 39.91 3.86
289 619 6.317391 TGTGTAGAAACATGTTGATGTCACAA 59.683 34.615 22.29 13.03 42.30 3.33
304 634 4.862574 TCGTATGTCAGCATGTGTAGAAAC 59.137 41.667 0.00 0.00 37.40 2.78
341 671 3.452755 TGACCACTTGTGTCTGTACTG 57.547 47.619 0.00 0.00 33.83 2.74
348 678 6.270815 ACACGTATATATGACCACTTGTGTC 58.729 40.000 8.98 0.00 31.82 3.67
351 681 6.710597 AGACACGTATATATGACCACTTGT 57.289 37.500 8.98 1.62 0.00 3.16
370 700 2.718563 TCATAGGCGTGAGTGTAGACA 58.281 47.619 0.00 0.00 0.00 3.41
372 702 3.086282 TGTTCATAGGCGTGAGTGTAGA 58.914 45.455 0.00 0.00 0.00 2.59
373 703 3.503827 TGTTCATAGGCGTGAGTGTAG 57.496 47.619 0.00 0.00 0.00 2.74
393 723 2.419667 GGGTAAGTTGTGCGTGTGTAT 58.580 47.619 0.00 0.00 0.00 2.29
394 724 1.540797 GGGGTAAGTTGTGCGTGTGTA 60.541 52.381 0.00 0.00 0.00 2.90
402 732 3.627395 TGCTCATAGGGGTAAGTTGTG 57.373 47.619 0.00 0.00 0.00 3.33
404 734 4.696479 AGATGCTCATAGGGGTAAGTTG 57.304 45.455 0.00 0.00 0.00 3.16
405 735 4.202264 CGAAGATGCTCATAGGGGTAAGTT 60.202 45.833 0.00 0.00 0.00 2.66
408 738 3.572642 TCGAAGATGCTCATAGGGGTAA 58.427 45.455 0.00 0.00 0.00 2.85
423 753 2.080693 GTCAGCTCAGTCTCTCGAAGA 58.919 52.381 0.00 0.00 0.00 2.87
429 759 4.894705 ACATGATATGTCAGCTCAGTCTCT 59.105 41.667 0.00 0.00 39.92 3.10
440 770 9.161629 ACTTCGTAATTTCAACATGATATGTCA 57.838 29.630 0.00 0.00 44.07 3.58
469 800 0.529337 CGACTACGAGGAGCCTACGA 60.529 60.000 12.88 0.73 42.66 3.43
471 802 3.376218 TCGACTACGAGGAGCCTAC 57.624 57.895 0.00 0.00 43.81 3.18
485 816 4.885157 GGAGAAGTTCCCGTCGAC 57.115 61.111 5.18 5.18 40.37 4.20
497 828 2.302260 CTGGCTACGATGAGAGGAGAA 58.698 52.381 0.00 0.00 0.00 2.87
505 836 0.037697 AAACGCACTGGCTACGATGA 60.038 50.000 0.00 0.00 38.10 2.92
509 840 0.584396 TGAAAAACGCACTGGCTACG 59.416 50.000 0.00 0.00 38.10 3.51
511 842 2.685897 ACTTTGAAAAACGCACTGGCTA 59.314 40.909 0.00 0.00 38.10 3.93
513 844 1.921243 ACTTTGAAAAACGCACTGGC 58.079 45.000 0.00 0.00 0.00 4.85
514 845 4.173256 AGAAACTTTGAAAAACGCACTGG 58.827 39.130 0.00 0.00 0.00 4.00
516 847 4.857037 GTGAGAAACTTTGAAAAACGCACT 59.143 37.500 0.00 0.00 0.00 4.40
517 848 4.619336 TGTGAGAAACTTTGAAAAACGCAC 59.381 37.500 0.00 0.00 0.00 5.34
518 849 4.799678 TGTGAGAAACTTTGAAAAACGCA 58.200 34.783 0.00 0.00 0.00 5.24
519 850 5.717251 CATGTGAGAAACTTTGAAAAACGC 58.283 37.500 0.00 0.00 0.00 4.84
531 1708 4.815846 ACAAAATTTGGGCATGTGAGAAAC 59.184 37.500 10.71 0.00 34.12 2.78
561 1738 0.376852 GACACTTGCGTTGCACTCAA 59.623 50.000 0.00 0.00 38.71 3.02
566 1743 0.179150 GTTTGGACACTTGCGTTGCA 60.179 50.000 0.00 0.00 36.47 4.08
591 1768 2.482721 CGCGAGTCCTGTACCAAATTTT 59.517 45.455 0.00 0.00 0.00 1.82
600 1777 1.226575 CGAATGCGCGAGTCCTGTA 60.227 57.895 12.10 0.00 0.00 2.74
610 1787 1.653533 GCAAGATGCTCGAATGCGC 60.654 57.895 0.00 0.00 40.96 6.09
656 1833 9.819267 AACGATAAAATCAAAAGGTACCAAAAA 57.181 25.926 15.94 0.00 0.00 1.94
666 1843 8.853345 CCTGTGAATGAACGATAAAATCAAAAG 58.147 33.333 0.00 0.00 0.00 2.27
669 1846 7.626240 GCTCCTGTGAATGAACGATAAAATCAA 60.626 37.037 0.00 0.00 0.00 2.57
678 1855 1.941209 GCTGCTCCTGTGAATGAACGA 60.941 52.381 0.00 0.00 0.00 3.85
679 1856 0.445436 GCTGCTCCTGTGAATGAACG 59.555 55.000 0.00 0.00 0.00 3.95
690 1867 3.007920 CTGGGTCCAGCTGCTCCT 61.008 66.667 19.70 0.00 37.24 3.69
695 1872 4.106925 GCTCCCTGGGTCCAGCTG 62.107 72.222 13.56 6.78 42.35 4.24
709 1886 3.202706 GACCCGGCGATTTGGCTC 61.203 66.667 9.30 0.00 42.02 4.70
710 1887 4.796495 GGACCCGGCGATTTGGCT 62.796 66.667 9.30 0.00 42.02 4.75
712 1889 3.714487 ATGGGACCCGGCGATTTGG 62.714 63.158 9.30 2.75 0.00 3.28
713 1890 2.124320 ATGGGACCCGGCGATTTG 60.124 61.111 9.30 0.00 0.00 2.32
755 1932 4.286808 AGTGAAAGGAATTCCCCCATTTTG 59.713 41.667 21.22 0.00 37.22 2.44
756 1933 4.502415 AGTGAAAGGAATTCCCCCATTTT 58.498 39.130 21.22 13.94 37.22 1.82
762 1939 2.308866 TGGAGAGTGAAAGGAATTCCCC 59.691 50.000 21.22 11.73 37.22 4.81
767 1944 5.013495 TCAGTCAATGGAGAGTGAAAGGAAT 59.987 40.000 0.00 0.00 43.13 3.01
776 1953 3.055530 GTGTGGATCAGTCAATGGAGAGT 60.056 47.826 0.00 0.00 0.00 3.24
783 1960 4.206477 TCGATTGTGTGGATCAGTCAAT 57.794 40.909 0.00 0.00 0.00 2.57
791 1968 5.469479 GGAAACAATTTCGATTGTGTGGAT 58.531 37.500 5.21 0.00 43.29 3.41
802 1979 5.897377 AATGGTCTAGGGAAACAATTTCG 57.103 39.130 0.00 0.00 40.57 3.46
806 1983 5.789574 TGGTAATGGTCTAGGGAAACAAT 57.210 39.130 0.00 0.00 0.00 2.71
807 1984 5.789574 ATGGTAATGGTCTAGGGAAACAA 57.210 39.130 0.00 0.00 0.00 2.83
810 1987 5.789574 ACAATGGTAATGGTCTAGGGAAA 57.210 39.130 0.00 0.00 0.00 3.13
811 1988 5.789574 AACAATGGTAATGGTCTAGGGAA 57.210 39.130 0.00 0.00 0.00 3.97
813 1990 5.714806 ACAAAACAATGGTAATGGTCTAGGG 59.285 40.000 0.00 0.00 0.00 3.53
814 1991 6.659242 AGACAAAACAATGGTAATGGTCTAGG 59.341 38.462 0.00 0.00 0.00 3.02
820 2030 6.586082 GCAACTAGACAAAACAATGGTAATGG 59.414 38.462 0.00 0.00 0.00 3.16
861 2071 2.360350 CAGACCCAGCACGCCAAT 60.360 61.111 0.00 0.00 0.00 3.16
867 2077 2.362717 GTCTATAGTCCAGACCCAGCAC 59.637 54.545 0.00 0.00 37.11 4.40
872 2082 3.140623 GAGTCGTCTATAGTCCAGACCC 58.859 54.545 0.00 0.00 39.43 4.46
885 2095 1.893544 TCTTGACCTTCGAGTCGTCT 58.106 50.000 13.12 0.00 39.77 4.18
891 2101 1.554392 CTGCGATCTTGACCTTCGAG 58.446 55.000 0.00 0.00 34.92 4.04
892 2102 0.173481 CCTGCGATCTTGACCTTCGA 59.827 55.000 0.00 0.00 34.92 3.71
894 2104 1.424493 CGCCTGCGATCTTGACCTTC 61.424 60.000 5.43 0.00 42.83 3.46
948 2159 4.222124 ACTATTCTTCCTTCATGCCGTT 57.778 40.909 0.00 0.00 0.00 4.44
949 2160 3.914426 ACTATTCTTCCTTCATGCCGT 57.086 42.857 0.00 0.00 0.00 5.68
984 2195 5.419542 CGCTTCATGGGCTTAGCTTATATA 58.580 41.667 3.59 0.00 0.00 0.86
1037 2254 4.263771 GGGAGGAGGAAGAATGGTGTAAAA 60.264 45.833 0.00 0.00 0.00 1.52
1085 2302 2.926779 TCCACAGGCAGAGCAGCT 60.927 61.111 0.00 0.00 34.17 4.24
1090 2307 2.433838 CAGCGTCCACAGGCAGAG 60.434 66.667 0.00 0.00 35.75 3.35
1149 2366 5.393352 CGGGTTACTACTGCAACATGTAGTA 60.393 44.000 15.87 15.87 44.97 1.82
1160 2377 4.972514 AACTAGTACGGGTTACTACTGC 57.027 45.455 0.00 0.00 41.60 4.40
1185 2402 5.988561 GCCAGATCCAGAGTTAACTAATCAG 59.011 44.000 8.42 6.64 0.00 2.90
1196 2413 2.173126 AGCTTAGCCAGATCCAGAGT 57.827 50.000 0.00 0.00 0.00 3.24
1199 2416 5.703130 GGTTAATTAGCTTAGCCAGATCCAG 59.297 44.000 0.00 0.00 39.74 3.86
1204 2421 3.463944 GCGGTTAATTAGCTTAGCCAGA 58.536 45.455 0.00 0.00 39.90 3.86
1217 2434 0.810648 CACACATGCAGGCGGTTAAT 59.189 50.000 0.00 0.00 0.00 1.40
1229 2446 2.425610 CGCACACACGCACACATG 60.426 61.111 0.00 0.00 0.00 3.21
1230 2447 2.894879 ACGCACACACGCACACAT 60.895 55.556 0.00 0.00 36.19 3.21
1231 2448 3.858989 CACGCACACACGCACACA 61.859 61.111 0.00 0.00 36.19 3.72
1241 2458 2.126463 GCTAGAGACGCACGCACA 60.126 61.111 0.00 0.00 0.00 4.57
1450 2672 4.261801 GCTTGTAGTTGTACACCATGGAT 58.738 43.478 21.47 8.74 38.95 3.41
1454 2676 4.009675 CCATGCTTGTAGTTGTACACCAT 58.990 43.478 0.00 0.00 38.95 3.55
1604 2834 6.482308 ACACATCACATCACATCACATGATAG 59.518 38.462 0.00 0.00 34.99 2.08
1620 2850 4.937201 ACTCTACAGACAACACATCACA 57.063 40.909 0.00 0.00 0.00 3.58
1621 2851 5.177696 GGAAACTCTACAGACAACACATCAC 59.822 44.000 0.00 0.00 0.00 3.06
1622 2852 5.297547 GGAAACTCTACAGACAACACATCA 58.702 41.667 0.00 0.00 0.00 3.07
1623 2853 4.386049 CGGAAACTCTACAGACAACACATC 59.614 45.833 0.00 0.00 0.00 3.06
1624 2854 4.307432 CGGAAACTCTACAGACAACACAT 58.693 43.478 0.00 0.00 0.00 3.21
1633 2863 5.962433 TGATTACTTCCGGAAACTCTACAG 58.038 41.667 19.39 6.14 0.00 2.74
1872 3315 3.281341 TGGCATGACGTGAAATGTTTC 57.719 42.857 0.00 0.00 35.18 2.78
1889 3341 9.638176 AGATCCCTAATTAATTGATATGATGGC 57.362 33.333 11.05 0.00 0.00 4.40
1892 3344 9.638176 GCCAGATCCCTAATTAATTGATATGAT 57.362 33.333 16.99 9.93 28.65 2.45
1893 3345 8.055181 GGCCAGATCCCTAATTAATTGATATGA 58.945 37.037 16.99 6.66 28.65 2.15
1894 3346 7.286316 GGGCCAGATCCCTAATTAATTGATATG 59.714 40.741 11.05 11.48 43.13 1.78
1895 3347 7.357471 GGGCCAGATCCCTAATTAATTGATAT 58.643 38.462 11.05 0.21 43.13 1.63
1896 3348 6.578238 CGGGCCAGATCCCTAATTAATTGATA 60.578 42.308 11.05 0.00 44.30 2.15
1920 3380 1.131037 CGCTGAAGCTTCTCGACTCG 61.131 60.000 26.09 15.39 39.32 4.18
2495 8418 3.011566 TCTCTTGTTTGTTTCCCAGCA 57.988 42.857 0.00 0.00 0.00 4.41
2512 8435 8.378421 GTGTGAATAAAAACGTACCACTATCTC 58.622 37.037 0.00 0.00 0.00 2.75
2540 8463 4.392166 TAGGCCGGCCCTCAGTCA 62.392 66.667 41.72 15.33 44.96 3.41
2541 8464 3.851128 GTAGGCCGGCCCTCAGTC 61.851 72.222 41.72 20.78 44.96 3.51
2550 8473 0.464452 CCCTAAGTCAAGTAGGCCGG 59.536 60.000 0.00 0.00 37.41 6.13
2551 8474 0.464452 CCCCTAAGTCAAGTAGGCCG 59.536 60.000 0.00 0.00 37.41 6.13
2552 8475 1.485480 GACCCCTAAGTCAAGTAGGCC 59.515 57.143 0.00 0.00 37.41 5.19
2553 8476 2.468915 AGACCCCTAAGTCAAGTAGGC 58.531 52.381 0.00 0.00 39.34 3.93
2593 8516 5.807520 TGTTCGCTTCTTATTCTTGAGCTAG 59.192 40.000 0.00 0.00 0.00 3.42
2620 8543 3.381590 GTCCCTGCAAGAAGAAACAAAGT 59.618 43.478 0.00 0.00 34.07 2.66
2629 8553 1.622811 AGAGACTGTCCCTGCAAGAAG 59.377 52.381 3.76 0.00 34.07 2.85
2631 8555 1.203112 AGAGAGACTGTCCCTGCAAGA 60.203 52.381 3.76 0.00 34.07 3.02
2676 8600 1.677576 CTTTGAAACCACTGCTGCTCA 59.322 47.619 0.00 0.00 0.00 4.26
2802 8729 8.519526 CCTATTGTAAGCATGTTTTTGTTAGGA 58.480 33.333 0.00 0.00 0.00 2.94
2828 8755 3.802685 AGAAGCCACGAAATACGAATAGC 59.197 43.478 0.00 0.00 45.77 2.97
2835 8762 7.232300 GTGTACTAAAAGAAGCCACGAAATAC 58.768 38.462 0.00 0.00 0.00 1.89
2846 8778 8.512138 CCCAGTAAAATGGTGTACTAAAAGAAG 58.488 37.037 0.00 0.00 38.81 2.85
2852 8784 5.244189 TGCCCAGTAAAATGGTGTACTAA 57.756 39.130 0.00 0.00 38.81 2.24
2854 8786 3.799432 TGCCCAGTAAAATGGTGTACT 57.201 42.857 0.00 0.00 38.81 2.73
2855 8787 3.824443 ACTTGCCCAGTAAAATGGTGTAC 59.176 43.478 0.00 0.00 38.81 2.90
2858 8790 2.231235 GGACTTGCCCAGTAAAATGGTG 59.769 50.000 0.00 0.00 38.81 4.17
2868 8801 1.815003 GTCTGATTTGGACTTGCCCAG 59.185 52.381 0.00 0.00 37.53 4.45
2869 8802 1.144708 TGTCTGATTTGGACTTGCCCA 59.855 47.619 0.00 0.00 35.04 5.36
2876 8809 5.580297 TGCAAAAAGTTTGTCTGATTTGGAC 59.420 36.000 2.92 0.00 35.83 4.02
2885 8818 8.416329 AGAATAATGAGTGCAAAAAGTTTGTCT 58.584 29.630 0.00 2.48 0.00 3.41
2897 8830 3.264193 ACAGGGTGAGAATAATGAGTGCA 59.736 43.478 0.00 0.00 0.00 4.57
2898 8831 3.878778 ACAGGGTGAGAATAATGAGTGC 58.121 45.455 0.00 0.00 0.00 4.40
2928 8861 0.918983 TGGGGGAAGACTGCTAATGG 59.081 55.000 0.00 0.00 0.00 3.16
2929 8862 2.173356 TGATGGGGGAAGACTGCTAATG 59.827 50.000 0.00 0.00 0.00 1.90
2930 8863 2.173569 GTGATGGGGGAAGACTGCTAAT 59.826 50.000 0.00 0.00 0.00 1.73
2931 8864 1.559682 GTGATGGGGGAAGACTGCTAA 59.440 52.381 0.00 0.00 0.00 3.09
2932 8865 1.204146 GTGATGGGGGAAGACTGCTA 58.796 55.000 0.00 0.00 0.00 3.49
2937 8870 0.837940 GGGTAGTGATGGGGGAAGAC 59.162 60.000 0.00 0.00 0.00 3.01
3003 8977 6.699575 AAGTCTTATCGGATTTGGAATTGG 57.300 37.500 0.00 0.00 0.00 3.16
3020 8994 6.876257 AGAGAATATTGAGTGCGAAAAGTCTT 59.124 34.615 0.00 0.00 0.00 3.01
3054 9028 7.894376 AAAATGTGTTTTGCTTCATAGGATG 57.106 32.000 0.00 0.00 36.24 3.51
3099 9073 8.869109 AGGTAAAAGATTGAATTGGAATTGACA 58.131 29.630 0.00 0.00 0.00 3.58
3103 9077 8.037166 GCAGAGGTAAAAGATTGAATTGGAATT 58.963 33.333 0.00 0.00 0.00 2.17
3104 9078 7.178983 TGCAGAGGTAAAAGATTGAATTGGAAT 59.821 33.333 0.00 0.00 0.00 3.01
3105 9079 6.493115 TGCAGAGGTAAAAGATTGAATTGGAA 59.507 34.615 0.00 0.00 0.00 3.53
3106 9080 6.009589 TGCAGAGGTAAAAGATTGAATTGGA 58.990 36.000 0.00 0.00 0.00 3.53
3107 9081 6.271488 TGCAGAGGTAAAAGATTGAATTGG 57.729 37.500 0.00 0.00 0.00 3.16
3108 9082 7.541162 TGATGCAGAGGTAAAAGATTGAATTG 58.459 34.615 0.00 0.00 0.00 2.32
3248 9257 2.719739 CATGGTGCAGAACAGGATCTT 58.280 47.619 0.00 0.00 0.00 2.40
3275 9284 2.625737 CTGGAACACATCTTGATCGCT 58.374 47.619 0.00 0.00 0.00 4.93
3313 9331 3.407967 GACCCCCGGCCATCTTGA 61.408 66.667 2.24 0.00 0.00 3.02
3323 9341 4.530857 GATGACGCCAGACCCCCG 62.531 72.222 0.00 0.00 0.00 5.73
3334 9352 2.607282 GGTATACTGGGCGAAGATGACG 60.607 54.545 2.25 0.00 0.00 4.35
3433 9451 0.530650 CGTCCATGTAGCTGGCGATT 60.531 55.000 0.00 0.00 37.74 3.34
3510 9528 2.036958 ATAGCGCTTGCATGTTACCA 57.963 45.000 18.68 0.00 42.66 3.25
3514 9532 2.358957 TCAGAATAGCGCTTGCATGTT 58.641 42.857 18.68 1.07 42.66 2.71
3515 9533 2.028420 TCAGAATAGCGCTTGCATGT 57.972 45.000 18.68 0.00 42.66 3.21
3528 9546 3.283751 AGTTCTCTCCGACGATCAGAAT 58.716 45.455 0.00 0.00 0.00 2.40
3575 9686 0.397114 TCTTCGCCATGGGAGAGCTA 60.397 55.000 15.13 0.00 32.27 3.32
3727 9838 1.933853 GCCACGGAGCATGTTAAGTAG 59.066 52.381 0.00 0.00 0.00 2.57
3758 9869 4.399004 AGATGTATCAAGGCACTGAGAC 57.601 45.455 7.26 7.26 40.86 3.36
3868 9979 2.676608 CCTGCTACATGTGGGGCA 59.323 61.111 9.11 14.55 0.00 5.36
4073 10199 0.821517 TTCCGCCAGTATCGACATGT 59.178 50.000 0.00 0.00 0.00 3.21
4078 10204 2.792947 GCCCTTCCGCCAGTATCGA 61.793 63.158 0.00 0.00 0.00 3.59
4151 10277 3.882326 CTGGATCAGCCGCCCCAT 61.882 66.667 0.00 0.00 40.66 4.00
4167 10293 1.349688 TCAATGTCGTAAACCAGGCCT 59.650 47.619 0.00 0.00 0.00 5.19
4251 10386 1.727511 CCGGTAGCATTCCCGTCGTA 61.728 60.000 0.00 0.00 42.67 3.43
4314 10449 0.762418 TTGACATGGTGACCGGACTT 59.238 50.000 9.46 0.00 0.00 3.01
4338 10473 0.750182 CACCCCCAACGTTTGTCACT 60.750 55.000 0.00 0.00 0.00 3.41
4355 10490 1.951510 TGGTACACGGAGTCGACAC 59.048 57.895 19.50 11.89 41.61 3.67
4473 10608 0.912486 GTAGCTTCCACACAGGGGAT 59.088 55.000 0.00 0.00 38.24 3.85
4530 10665 1.186200 TCCTCACCACCTTCTGATCG 58.814 55.000 0.00 0.00 0.00 3.69
4677 10812 8.609176 GTCAACACGGTGACACATAATAATAAT 58.391 33.333 16.29 0.00 46.00 1.28
4734 10869 1.531578 GTTGAGAAAGTTGAGTCGGCC 59.468 52.381 0.00 0.00 0.00 6.13
4735 10870 2.210116 TGTTGAGAAAGTTGAGTCGGC 58.790 47.619 0.00 0.00 0.00 5.54
4736 10871 4.119862 TCTTGTTGAGAAAGTTGAGTCGG 58.880 43.478 0.00 0.00 0.00 4.79
4752 10887 8.753497 AATGAGAGTTTAGAGGTTTTCTTGTT 57.247 30.769 0.00 0.00 37.36 2.83
4790 10925 6.526674 GTCCTGTATTTTTGCATAACCGAAAG 59.473 38.462 0.00 0.00 0.00 2.62
4882 11021 7.920682 CCTATACTTTTGTTTGCAGTTCTTGTT 59.079 33.333 0.00 0.00 0.00 2.83
4988 11127 0.480252 AAGCAGCAAGTTCTCCCCTT 59.520 50.000 0.00 0.00 0.00 3.95
5025 11164 3.197766 CAGCTAGTTGTTGGACCCTCATA 59.802 47.826 0.00 0.00 0.00 2.15
5183 11322 6.446318 CAAATAGCAGTTGTGTGGTGTTATT 58.554 36.000 0.00 0.00 31.30 1.40
5236 11375 3.245229 ACATTTGTCATGTGGGCCTTCTA 60.245 43.478 4.53 0.00 0.00 2.10
5264 11403 0.681733 ATGAGTGTGTCCTTGCTCGT 59.318 50.000 0.00 0.00 0.00 4.18
5266 11405 1.446907 CCATGAGTGTGTCCTTGCTC 58.553 55.000 0.00 0.00 0.00 4.26
5271 11410 1.847506 TGGGCCATGAGTGTGTCCT 60.848 57.895 0.00 0.00 0.00 3.85
5438 11580 3.530265 TTGCCATGCTCATCCATTTTC 57.470 42.857 0.00 0.00 0.00 2.29
5463 11605 4.244425 AGTATAGTAGTGCATGAAGGCG 57.756 45.455 0.00 0.00 36.28 5.52
5474 11616 6.952938 GGTGGGCCTTTCTATAGTATAGTAGT 59.047 42.308 15.34 0.00 0.00 2.73
5478 11620 5.046520 GTGGGTGGGCCTTTCTATAGTATAG 60.047 48.000 10.50 10.50 34.45 1.31
5523 11665 3.758088 CTCCACTCATCGGGCGACG 62.758 68.421 0.00 0.00 46.11 5.12
5557 11702 5.370289 TGTAGGTTTGTTTCCCTTTCCTAGA 59.630 40.000 0.00 0.00 32.08 2.43
5572 11717 7.849804 AGCACAATATAAGAGTGTAGGTTTG 57.150 36.000 0.00 0.00 32.99 2.93


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

AutoCloner maintained by Alex Coulton.