Multiple sequence alignment - TraesCS1A01G030600

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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 TraesCS1A01G030600 chr1A 100.000 3992 0 0 1 3992 14146849 14142858 0.000000e+00 7372.0
1 TraesCS1A01G030600 chr1A 100.000 62 0 0 1 62 24445926 24445865 9.070000e-22 115.0
2 TraesCS1A01G030600 chr1A 100.000 62 0 0 1 62 37708825 37708886 9.070000e-22 115.0
3 TraesCS1A01G030600 chr1A 100.000 62 0 0 1 62 96193099 96193038 9.070000e-22 115.0
4 TraesCS1A01G030600 chr1A 100.000 62 0 0 1 62 277019541 277019480 9.070000e-22 115.0
5 TraesCS1A01G030600 chr1A 100.000 62 0 0 1 62 376481350 376481289 9.070000e-22 115.0
6 TraesCS1A01G030600 chr1A 100.000 62 0 0 1 62 376488201 376488140 9.070000e-22 115.0
7 TraesCS1A01G030600 chr1A 100.000 62 0 0 1 62 390932935 390932996 9.070000e-22 115.0
8 TraesCS1A01G030600 chr1A 100.000 62 0 0 1 62 469514017 469513956 9.070000e-22 115.0
9 TraesCS1A01G030600 chr1A 89.231 65 7 0 1910 1974 94126740 94126676 9.190000e-12 82.4
10 TraesCS1A01G030600 chr1B 91.751 1188 61 17 2837 3992 17793091 17791909 0.000000e+00 1616.0
11 TraesCS1A01G030600 chr1B 90.931 816 45 19 2048 2841 17794058 17793250 0.000000e+00 1070.0
12 TraesCS1A01G030600 chr1B 82.660 842 72 44 625 1412 17795591 17794770 0.000000e+00 678.0
13 TraesCS1A01G030600 chr1B 86.469 606 61 12 1409 2011 17794740 17794153 0.000000e+00 645.0
14 TraesCS1A01G030600 chr1B 86.131 274 23 8 79 349 17795991 17795730 8.450000e-72 281.0
15 TraesCS1A01G030600 chr1D 84.451 1267 98 49 800 2011 12317644 12316422 0.000000e+00 1157.0
16 TraesCS1A01G030600 chr1D 92.663 736 36 8 3259 3992 12315003 12314284 0.000000e+00 1044.0
17 TraesCS1A01G030600 chr1D 91.204 648 43 10 2048 2690 12316338 12315700 0.000000e+00 869.0
18 TraesCS1A01G030600 chr1D 91.784 426 27 2 2876 3293 12315429 12315004 1.600000e-163 586.0
19 TraesCS1A01G030600 chr1D 76.505 515 71 26 217 711 12318369 12317885 6.670000e-58 235.0
20 TraesCS1A01G030600 chr1D 95.070 142 5 2 82 221 12318669 12318528 5.190000e-54 222.0
21 TraesCS1A01G030600 chr1D 91.549 71 6 0 1909 1979 10263812 10263742 9.130000e-17 99.0
22 TraesCS1A01G030600 chr2A 97.101 69 1 1 1 68 770224722 770224654 9.070000e-22 115.0
23 TraesCS1A01G030600 chr2A 84.146 82 6 1 2048 2122 277139508 277139427 5.530000e-09 73.1
24 TraesCS1A01G030600 chr2A 95.455 44 2 0 2048 2091 161944716 161944759 1.990000e-08 71.3
25 TraesCS1A01G030600 chr4D 92.000 75 6 0 1905 1979 18694653 18694727 5.460000e-19 106.0
26 TraesCS1A01G030600 chr4D 86.301 73 4 1 2048 2114 18694759 18694831 1.540000e-09 75.0
27 TraesCS1A01G030600 chr6A 91.429 70 6 0 1910 1979 31882287 31882356 3.280000e-16 97.1
28 TraesCS1A01G030600 chr6B 88.060 67 6 2 1913 1979 633905805 633905741 1.190000e-10 78.7
29 TraesCS1A01G030600 chr5B 97.674 43 1 0 2048 2090 701514677 701514635 1.540000e-09 75.0
30 TraesCS1A01G030600 chr3B 88.525 61 7 0 1913 1973 226088468 226088408 1.540000e-09 75.0
31 TraesCS1A01G030600 chrUn 84.146 82 6 1 2048 2122 477203811 477203730 5.530000e-09 73.1
32 TraesCS1A01G030600 chrUn 95.349 43 2 0 2048 2090 186910930 186910972 7.160000e-08 69.4
33 TraesCS1A01G030600 chrUn 95.349 43 2 0 2048 2090 400989461 400989419 7.160000e-08 69.4
34 TraesCS1A01G030600 chr7D 100.000 34 0 0 2015 2048 249642 249609 3.330000e-06 63.9
35 TraesCS1A01G030600 chr5D 100.000 34 0 0 1946 1979 391311505 391311472 3.330000e-06 63.9


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 TraesCS1A01G030600 chr1A 14142858 14146849 3991 True 7372.0 7372 100.000000 1 3992 1 chr1A.!!$R1 3991
1 TraesCS1A01G030600 chr1B 17791909 17795991 4082 True 858.0 1616 87.588400 79 3992 5 chr1B.!!$R1 3913
2 TraesCS1A01G030600 chr1D 12314284 12318669 4385 True 685.5 1157 88.612833 82 3992 6 chr1D.!!$R2 3910

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
495 678 0.035439 TCCAGGGAAATCGTTCTGCC 60.035 55.0 0.00 0.00 33.92 4.85 F
855 1252 0.179094 TTTCTAGGGGCATACACGCG 60.179 55.0 3.53 3.53 0.00 6.01 F
1838 2322 0.392461 GGGTGTGTGAGTGTGTGTGT 60.392 55.0 0.00 0.00 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2113 2685 0.035056 AGTTCTCCAATGAAGGGGCG 60.035 55.0 0.00 0.00 0.0 6.13 R
2470 3056 0.850784 ACAGGTAGCCAAAACAGGGT 59.149 50.0 0.00 0.00 43.0 4.34 R
3280 4239 0.038251 AGTGCTCGCTCGAAATCACA 60.038 50.0 15.73 0.61 0.0 3.58 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
23 24 6.025749 TCCACCTCGATTATATTGTAGCAG 57.974 41.667 0.00 0.00 0.00 4.24
24 25 5.538813 TCCACCTCGATTATATTGTAGCAGT 59.461 40.000 0.00 0.00 0.00 4.40
25 26 5.635280 CCACCTCGATTATATTGTAGCAGTG 59.365 44.000 0.00 0.00 0.00 3.66
26 27 5.119279 CACCTCGATTATATTGTAGCAGTGC 59.881 44.000 7.13 7.13 0.00 4.40
27 28 5.011125 ACCTCGATTATATTGTAGCAGTGCT 59.989 40.000 23.44 23.44 43.41 4.40
28 29 5.928839 CCTCGATTATATTGTAGCAGTGCTT 59.071 40.000 25.23 7.71 40.44 3.91
29 30 7.090808 CCTCGATTATATTGTAGCAGTGCTTA 58.909 38.462 25.23 10.00 40.44 3.09
30 31 7.274468 CCTCGATTATATTGTAGCAGTGCTTAG 59.726 40.741 25.23 2.05 40.44 2.18
31 32 7.090808 TCGATTATATTGTAGCAGTGCTTAGG 58.909 38.462 25.23 2.39 40.44 2.69
32 33 6.183360 CGATTATATTGTAGCAGTGCTTAGGC 60.183 42.308 25.23 11.82 40.44 3.93
33 34 1.656652 ATTGTAGCAGTGCTTAGGCG 58.343 50.000 25.23 0.00 40.44 5.52
34 35 0.606096 TTGTAGCAGTGCTTAGGCGA 59.394 50.000 25.23 8.56 40.44 5.54
35 36 0.606096 TGTAGCAGTGCTTAGGCGAA 59.394 50.000 25.23 0.00 40.44 4.70
36 37 1.281899 GTAGCAGTGCTTAGGCGAAG 58.718 55.000 25.23 2.68 40.44 3.79
49 50 4.124351 CGAAGCCCTGCGACGGTA 62.124 66.667 0.00 0.00 0.00 4.02
50 51 2.202756 GAAGCCCTGCGACGGTAG 60.203 66.667 0.00 0.00 0.00 3.18
51 52 2.678934 AAGCCCTGCGACGGTAGA 60.679 61.111 0.00 0.00 0.00 2.59
52 53 2.221906 GAAGCCCTGCGACGGTAGAA 62.222 60.000 0.00 0.00 0.00 2.10
53 54 2.502692 AAGCCCTGCGACGGTAGAAC 62.503 60.000 0.00 0.00 0.00 3.01
54 55 2.967397 CCCTGCGACGGTAGAACA 59.033 61.111 0.00 0.00 0.00 3.18
55 56 1.515954 CCCTGCGACGGTAGAACAT 59.484 57.895 0.00 0.00 0.00 2.71
56 57 0.527817 CCCTGCGACGGTAGAACATC 60.528 60.000 0.00 0.00 0.00 3.06
57 58 0.172578 CCTGCGACGGTAGAACATCA 59.827 55.000 0.00 0.00 0.00 3.07
58 59 1.403647 CCTGCGACGGTAGAACATCAA 60.404 52.381 0.00 0.00 0.00 2.57
59 60 1.920574 CTGCGACGGTAGAACATCAAG 59.079 52.381 0.00 0.00 0.00 3.02
60 61 1.542472 TGCGACGGTAGAACATCAAGA 59.458 47.619 0.00 0.00 0.00 3.02
61 62 2.165641 TGCGACGGTAGAACATCAAGAT 59.834 45.455 0.00 0.00 0.00 2.40
62 63 2.535984 GCGACGGTAGAACATCAAGATG 59.464 50.000 8.45 8.45 44.15 2.90
72 73 2.028420 CATCAAGATGTGGCCTTCGA 57.972 50.000 3.32 0.00 34.23 3.71
73 74 2.358957 CATCAAGATGTGGCCTTCGAA 58.641 47.619 3.32 0.00 34.23 3.71
74 75 2.099141 TCAAGATGTGGCCTTCGAAG 57.901 50.000 18.51 18.51 0.00 3.79
75 76 0.449388 CAAGATGTGGCCTTCGAAGC 59.551 55.000 19.99 14.36 0.00 3.86
76 77 1.021390 AAGATGTGGCCTTCGAAGCG 61.021 55.000 19.99 13.61 0.00 4.68
77 78 1.741770 GATGTGGCCTTCGAAGCGT 60.742 57.895 19.99 7.27 0.00 5.07
170 171 6.093357 GTGTGATTTTGGACATGGTTTTTGTT 59.907 34.615 0.00 0.00 0.00 2.83
210 214 3.761752 CGAAGGTGGATGTAATTTTGGGT 59.238 43.478 0.00 0.00 0.00 4.51
221 390 2.908688 ATTTTGGGTGTGGTTTGCTC 57.091 45.000 0.00 0.00 0.00 4.26
277 446 0.939106 GTGCCGTGCAATGTTGTTCC 60.939 55.000 0.00 0.00 41.47 3.62
279 448 1.805428 GCCGTGCAATGTTGTTCCCT 61.805 55.000 0.00 0.00 0.00 4.20
281 450 1.199097 CCGTGCAATGTTGTTCCCTAC 59.801 52.381 0.00 0.00 0.00 3.18
326 495 1.334869 CAGTTCATAGCCATTTCGCCC 59.665 52.381 0.00 0.00 0.00 6.13
327 496 0.307760 GTTCATAGCCATTTCGCCCG 59.692 55.000 0.00 0.00 0.00 6.13
328 497 1.444119 TTCATAGCCATTTCGCCCGC 61.444 55.000 0.00 0.00 0.00 6.13
366 535 3.065371 GCTAATGCCACCATACTTGTGTC 59.935 47.826 0.00 0.00 31.71 3.67
367 536 1.737838 ATGCCACCATACTTGTGTCG 58.262 50.000 0.00 0.00 31.71 4.35
368 537 0.394938 TGCCACCATACTTGTGTCGT 59.605 50.000 0.00 0.00 31.71 4.34
369 538 0.796312 GCCACCATACTTGTGTCGTG 59.204 55.000 0.00 0.00 31.71 4.35
370 539 0.796312 CCACCATACTTGTGTCGTGC 59.204 55.000 0.00 0.00 31.71 5.34
372 541 0.394938 ACCATACTTGTGTCGTGCCA 59.605 50.000 0.00 0.00 0.00 4.92
373 542 0.796312 CCATACTTGTGTCGTGCCAC 59.204 55.000 0.00 0.00 35.86 5.01
374 543 1.507562 CATACTTGTGTCGTGCCACA 58.492 50.000 0.00 2.10 43.32 4.17
375 544 1.194547 CATACTTGTGTCGTGCCACAC 59.805 52.381 0.00 4.19 44.60 3.82
376 545 0.462375 TACTTGTGTCGTGCCACACT 59.538 50.000 10.89 0.00 45.98 3.55
378 547 0.732571 CTTGTGTCGTGCCACACTTT 59.267 50.000 10.89 0.00 45.98 2.66
380 549 0.449786 TGTGTCGTGCCACACTTTTG 59.550 50.000 10.89 0.00 45.98 2.44
382 551 1.666700 GTGTCGTGCCACACTTTTGTA 59.333 47.619 0.00 0.00 43.00 2.41
383 552 1.937223 TGTCGTGCCACACTTTTGTAG 59.063 47.619 0.00 0.00 33.30 2.74
384 553 1.937899 GTCGTGCCACACTTTTGTAGT 59.062 47.619 0.00 0.00 37.68 2.73
385 554 3.125316 GTCGTGCCACACTTTTGTAGTA 58.875 45.455 0.00 0.00 34.56 1.82
386 555 3.183775 GTCGTGCCACACTTTTGTAGTAG 59.816 47.826 0.00 0.00 34.56 2.57
393 562 7.065324 GTGCCACACTTTTGTAGTAGCATATAA 59.935 37.037 0.00 0.00 38.24 0.98
394 563 7.608376 TGCCACACTTTTGTAGTAGCATATAAA 59.392 33.333 0.00 0.00 33.89 1.40
422 592 4.202295 TGTTATGCTTTGCCAAAATGGTGA 60.202 37.500 0.00 0.00 40.46 4.02
427 597 0.392336 TTGCCAAAATGGTGACCAGC 59.608 50.000 11.23 8.22 40.46 4.85
434 604 2.086610 AATGGTGACCAGCCTTTTGT 57.913 45.000 11.23 0.00 36.75 2.83
435 605 2.086610 ATGGTGACCAGCCTTTTGTT 57.913 45.000 11.23 0.00 36.75 2.83
439 609 2.481276 GGTGACCAGCCTTTTGTTGTTC 60.481 50.000 0.00 0.00 0.00 3.18
442 612 4.037446 GTGACCAGCCTTTTGTTGTTCATA 59.963 41.667 0.00 0.00 0.00 2.15
444 614 6.007076 TGACCAGCCTTTTGTTGTTCATATA 58.993 36.000 0.00 0.00 0.00 0.86
445 615 6.663093 TGACCAGCCTTTTGTTGTTCATATAT 59.337 34.615 0.00 0.00 0.00 0.86
478 661 2.386661 TCTGCAAGAACGGAATCTCC 57.613 50.000 0.00 0.00 42.31 3.71
483 666 1.555075 CAAGAACGGAATCTCCAGGGA 59.445 52.381 0.00 0.00 35.91 4.20
484 667 1.952621 AGAACGGAATCTCCAGGGAA 58.047 50.000 0.00 0.00 35.91 3.97
485 668 2.266279 AGAACGGAATCTCCAGGGAAA 58.734 47.619 0.00 0.00 35.91 3.13
486 669 2.846827 AGAACGGAATCTCCAGGGAAAT 59.153 45.455 0.00 0.00 35.91 2.17
487 670 3.118223 AGAACGGAATCTCCAGGGAAATC 60.118 47.826 0.00 0.00 35.91 2.17
488 671 1.139058 ACGGAATCTCCAGGGAAATCG 59.861 52.381 0.00 0.00 35.91 3.34
489 672 1.139058 CGGAATCTCCAGGGAAATCGT 59.861 52.381 0.00 0.00 35.91 3.73
490 673 2.420129 CGGAATCTCCAGGGAAATCGTT 60.420 50.000 0.00 0.00 35.91 3.85
491 674 3.206964 GGAATCTCCAGGGAAATCGTTC 58.793 50.000 0.00 0.00 36.28 3.95
492 675 3.118223 GGAATCTCCAGGGAAATCGTTCT 60.118 47.826 0.00 0.00 36.28 3.01
493 676 3.550437 ATCTCCAGGGAAATCGTTCTG 57.450 47.619 0.00 0.00 33.92 3.02
494 677 1.066143 TCTCCAGGGAAATCGTTCTGC 60.066 52.381 0.00 0.00 33.92 4.26
495 678 0.035439 TCCAGGGAAATCGTTCTGCC 60.035 55.000 0.00 0.00 33.92 4.85
496 679 0.322456 CCAGGGAAATCGTTCTGCCA 60.322 55.000 0.00 0.00 33.92 4.92
497 680 0.804989 CAGGGAAATCGTTCTGCCAC 59.195 55.000 0.00 0.00 33.92 5.01
498 681 0.693049 AGGGAAATCGTTCTGCCACT 59.307 50.000 0.00 0.00 33.92 4.00
499 682 1.087501 GGGAAATCGTTCTGCCACTC 58.912 55.000 0.00 0.00 33.92 3.51
500 683 1.339151 GGGAAATCGTTCTGCCACTCT 60.339 52.381 0.00 0.00 33.92 3.24
510 693 0.607489 CTGCCACTCTGTTTGGAGGG 60.607 60.000 2.10 0.00 36.02 4.30
515 698 3.500343 CCACTCTGTTTGGAGGGAAAAT 58.500 45.455 0.00 0.00 38.93 1.82
547 730 6.383415 GCACGGACATCTTGGTAAAAATTAA 58.617 36.000 0.00 0.00 0.00 1.40
570 753 9.798885 TTAATTTTTGTTTTTGTTCTTGTGTCG 57.201 25.926 0.00 0.00 0.00 4.35
613 796 9.190858 TCAAAATTCATGTGGTTTTCTAAATCG 57.809 29.630 0.00 0.00 0.00 3.34
618 801 9.787532 ATTCATGTGGTTTTCTAAATCGTATTG 57.212 29.630 0.00 0.00 0.00 1.90
619 802 8.554835 TCATGTGGTTTTCTAAATCGTATTGA 57.445 30.769 0.00 0.00 0.00 2.57
620 803 8.664798 TCATGTGGTTTTCTAAATCGTATTGAG 58.335 33.333 0.00 0.00 0.00 3.02
621 804 8.664798 CATGTGGTTTTCTAAATCGTATTGAGA 58.335 33.333 0.00 0.00 0.00 3.27
623 806 8.879759 TGTGGTTTTCTAAATCGTATTGAGATC 58.120 33.333 0.00 0.00 0.00 2.75
634 835 4.578928 TCGTATTGAGATCCACTTCGATCA 59.421 41.667 0.00 0.00 41.03 2.92
651 852 9.599866 ACTTCGATCATGTGTTCTTTATATTCA 57.400 29.630 0.00 0.00 0.00 2.57
657 858 5.198116 TGTGTTCTTTATATTCACGCGTG 57.802 39.130 32.76 32.76 32.55 5.34
665 866 9.828852 TTCTTTATATTCACGCGTGTTAAAAAT 57.171 25.926 35.74 27.89 0.00 1.82
675 880 2.653113 CGTGTTAAAAATCCCGCGAAAC 59.347 45.455 8.23 0.00 32.94 2.78
676 881 3.630101 GTGTTAAAAATCCCGCGAAACA 58.370 40.909 8.23 2.08 0.00 2.83
773 1162 3.244976 GAACCGAACAATGCCAATCAAG 58.755 45.455 0.00 0.00 0.00 3.02
774 1163 1.545582 ACCGAACAATGCCAATCAAGG 59.454 47.619 0.00 0.00 0.00 3.61
832 1228 3.959535 TGGGTCAATGATTTGCCTTTC 57.040 42.857 0.00 0.00 32.73 2.62
833 1229 2.230992 TGGGTCAATGATTTGCCTTTCG 59.769 45.455 0.00 0.00 32.73 3.46
835 1231 2.094545 GGTCAATGATTTGCCTTTCGCT 60.095 45.455 0.00 0.00 38.78 4.93
839 1236 4.685628 TCAATGATTTGCCTTTCGCTTTTC 59.314 37.500 0.00 0.00 38.78 2.29
850 1247 2.614829 TCGCTTTTCTAGGGGCATAC 57.385 50.000 0.00 0.00 37.41 2.39
855 1252 0.179094 TTTCTAGGGGCATACACGCG 60.179 55.000 3.53 3.53 0.00 6.01
877 1274 2.645838 ATTTGACATCATCCGAGGGG 57.354 50.000 0.00 0.00 0.00 4.79
907 1304 0.560688 AACTCCCAACCACCAACCAT 59.439 50.000 0.00 0.00 0.00 3.55
927 1324 2.440539 ACACGCACGAGATCTTCTTT 57.559 45.000 0.00 0.00 0.00 2.52
984 1404 2.784654 CCCCCTCCTCCCTCGATCT 61.785 68.421 0.00 0.00 0.00 2.75
1038 1476 2.126463 TCGTCGGCGAAGAAGCAG 60.126 61.111 22.65 3.65 44.92 4.24
1039 1477 3.181967 CGTCGGCGAAGAAGCAGG 61.182 66.667 17.97 0.00 41.33 4.85
1040 1478 3.491652 GTCGGCGAAGAAGCAGGC 61.492 66.667 12.92 0.00 39.27 4.85
1173 1611 3.127533 GTGCACTGGATCCGCCAC 61.128 66.667 10.32 7.61 43.33 5.01
1261 1699 2.061578 TAAGCGCCCCGAATCTCCA 61.062 57.895 2.29 0.00 0.00 3.86
1286 1728 4.948847 CCCCCTTTTTCTTTCTTTGTCTG 58.051 43.478 0.00 0.00 0.00 3.51
1287 1729 4.202253 CCCCCTTTTTCTTTCTTTGTCTGG 60.202 45.833 0.00 0.00 0.00 3.86
1288 1730 4.371786 CCCTTTTTCTTTCTTTGTCTGGC 58.628 43.478 0.00 0.00 0.00 4.85
1289 1731 4.100035 CCCTTTTTCTTTCTTTGTCTGGCT 59.900 41.667 0.00 0.00 0.00 4.75
1291 1733 6.108687 CCTTTTTCTTTCTTTGTCTGGCTTT 58.891 36.000 0.00 0.00 0.00 3.51
1292 1734 6.256539 CCTTTTTCTTTCTTTGTCTGGCTTTC 59.743 38.462 0.00 0.00 0.00 2.62
1313 1755 2.738521 CTTGCCCGTGGAGTCGTG 60.739 66.667 0.00 0.00 0.00 4.35
1314 1756 4.980805 TTGCCCGTGGAGTCGTGC 62.981 66.667 0.00 0.00 35.06 5.34
1362 1806 1.582610 GGCTATCCGCTCTCCTCGAG 61.583 65.000 5.13 5.13 42.88 4.04
1374 1824 2.190843 CTCGAGCTCCTCCTCCGA 59.809 66.667 8.47 0.00 0.00 4.55
1380 1830 2.364961 CTCCTCCTCCGACCCCTT 59.635 66.667 0.00 0.00 0.00 3.95
1498 1981 2.838693 GACCGGGGAGTAGAGGCC 60.839 72.222 6.32 0.00 0.00 5.19
1550 2033 1.078497 GTGGATGTGGTGGATGCGA 60.078 57.895 0.00 0.00 0.00 5.10
1605 2088 2.780094 CGGCGACAGAGGAGCAGAT 61.780 63.158 0.00 0.00 0.00 2.90
1639 2122 0.401738 AACTGTCATGGAGTGGTGGG 59.598 55.000 0.00 0.00 0.00 4.61
1770 2253 2.892425 GCTCATCTCGTTGCGGGG 60.892 66.667 0.00 0.00 0.00 5.73
1771 2254 2.892640 CTCATCTCGTTGCGGGGA 59.107 61.111 0.00 0.00 0.00 4.81
1772 2255 1.227089 CTCATCTCGTTGCGGGGAG 60.227 63.158 0.00 0.00 0.00 4.30
1773 2256 1.667154 CTCATCTCGTTGCGGGGAGA 61.667 60.000 3.34 3.34 42.96 3.71
1774 2257 1.519455 CATCTCGTTGCGGGGAGAC 60.519 63.158 2.96 0.00 41.71 3.36
1775 2258 1.982395 ATCTCGTTGCGGGGAGACA 60.982 57.895 2.96 0.00 41.71 3.41
1776 2259 1.541310 ATCTCGTTGCGGGGAGACAA 61.541 55.000 2.96 0.00 41.71 3.18
1781 2264 2.589157 TTGCGGGGAGACAACGGAT 61.589 57.895 0.00 0.00 33.25 4.18
1804 2287 1.317922 TGGGGAATGGGATGTGGAAT 58.682 50.000 0.00 0.00 0.00 3.01
1837 2321 1.095228 GGGGTGTGTGAGTGTGTGTG 61.095 60.000 0.00 0.00 0.00 3.82
1838 2322 0.392461 GGGTGTGTGAGTGTGTGTGT 60.392 55.000 0.00 0.00 0.00 3.72
1851 2335 2.881513 TGTGTGTGTGAGAGAGAGAGAC 59.118 50.000 0.00 0.00 0.00 3.36
1855 2339 5.182190 GTGTGTGTGAGAGAGAGAGACATAA 59.818 44.000 0.00 0.00 0.00 1.90
1859 2343 4.228438 TGTGAGAGAGAGAGACATAAGGGA 59.772 45.833 0.00 0.00 0.00 4.20
1881 2365 5.692204 GGAGATGAACTTGTGTATATGGACG 59.308 44.000 0.00 0.00 0.00 4.79
1882 2366 5.050490 AGATGAACTTGTGTATATGGACGC 58.950 41.667 0.00 0.00 0.00 5.19
1883 2367 4.195225 TGAACTTGTGTATATGGACGCA 57.805 40.909 0.00 0.00 38.04 5.24
1904 2388 3.487120 AAAACTAGCCGTTGGAGAACT 57.513 42.857 0.00 0.00 35.61 3.01
1905 2389 4.612264 AAAACTAGCCGTTGGAGAACTA 57.388 40.909 0.00 0.00 35.61 2.24
1930 2414 1.978455 AAAGGACAGACCGGTGCACA 61.978 55.000 14.63 0.00 44.74 4.57
1943 2427 2.358372 TGCACATAGCTCCCGCTCA 61.358 57.895 0.00 0.00 45.15 4.26
2026 2548 0.601046 ACGTGCTCACATGTCAGTGG 60.601 55.000 0.00 0.00 42.51 4.00
2061 2633 2.222027 GCAGTACAAGTGGCTGTTTCT 58.778 47.619 0.00 0.00 33.18 2.52
2080 2652 0.962356 TAGGACTCGAACCCGTGACC 60.962 60.000 4.92 0.00 41.75 4.02
2081 2653 2.273912 GGACTCGAACCCGTGACCT 61.274 63.158 0.00 0.00 39.62 3.85
2082 2654 1.212229 GACTCGAACCCGTGACCTC 59.788 63.158 0.00 0.00 37.05 3.85
2083 2655 1.521450 GACTCGAACCCGTGACCTCA 61.521 60.000 0.00 0.00 37.05 3.86
2084 2656 0.898789 ACTCGAACCCGTGACCTCAT 60.899 55.000 0.00 0.00 37.05 2.90
2085 2657 0.458543 CTCGAACCCGTGACCTCATG 60.459 60.000 0.00 0.00 37.05 3.07
2106 2678 0.948678 TCAACAGTTTTACCGCTGCC 59.051 50.000 0.00 0.00 36.26 4.85
2192 2764 0.514691 GCTGCTGGAGTTGAACGAAG 59.485 55.000 0.00 0.00 0.00 3.79
2279 2853 5.308497 TGTTCTTGTAGTACCTCAATTGGGA 59.692 40.000 6.97 0.00 0.00 4.37
2335 2915 4.546570 GCTCTTGCCGTTTCAGTTATTTT 58.453 39.130 0.00 0.00 0.00 1.82
2342 2922 6.153067 TGCCGTTTCAGTTATTTTTGGTATG 58.847 36.000 0.00 0.00 0.00 2.39
2343 2923 6.153756 GCCGTTTCAGTTATTTTTGGTATGT 58.846 36.000 0.00 0.00 0.00 2.29
2344 2924 7.040617 TGCCGTTTCAGTTATTTTTGGTATGTA 60.041 33.333 0.00 0.00 0.00 2.29
2345 2925 7.808856 GCCGTTTCAGTTATTTTTGGTATGTAA 59.191 33.333 0.00 0.00 0.00 2.41
2346 2926 9.337091 CCGTTTCAGTTATTTTTGGTATGTAAG 57.663 33.333 0.00 0.00 0.00 2.34
2347 2927 9.887406 CGTTTCAGTTATTTTTGGTATGTAAGT 57.113 29.630 0.00 0.00 0.00 2.24
2383 2965 1.464219 CAAATTTGGAATGCGGGCAAC 59.536 47.619 10.49 0.00 0.00 4.17
2470 3056 8.895737 GTTGGAATATGTTTTCGGTTATTAGGA 58.104 33.333 0.00 0.00 0.00 2.94
2493 3079 2.423538 CCTGTTTTGGCTACCTGTATGC 59.576 50.000 0.00 0.00 0.00 3.14
2512 3098 4.400529 TGCGAGCTCTTGATGGTTATAA 57.599 40.909 12.85 0.00 0.00 0.98
2664 3252 4.725490 TCTTTCACCCTTTTCCTGGTAAG 58.275 43.478 0.00 0.00 32.32 2.34
2665 3253 4.167307 TCTTTCACCCTTTTCCTGGTAAGT 59.833 41.667 0.00 0.00 32.32 2.24
2666 3254 3.502123 TCACCCTTTTCCTGGTAAGTG 57.498 47.619 0.00 0.00 32.32 3.16
2667 3255 3.050089 TCACCCTTTTCCTGGTAAGTGA 58.950 45.455 0.00 0.00 32.32 3.41
2709 3298 6.072508 TGTTTCATCAGTTCCAATCTAGTTGC 60.073 38.462 0.00 0.00 36.46 4.17
2710 3299 5.164620 TCATCAGTTCCAATCTAGTTGCA 57.835 39.130 0.00 0.00 36.46 4.08
2749 3339 7.004086 TGAAATCATTCTTAAACCCAGACTGT 58.996 34.615 0.93 0.00 36.48 3.55
2750 3340 6.824305 AATCATTCTTAAACCCAGACTGTG 57.176 37.500 0.93 0.00 0.00 3.66
2752 3342 5.305585 TCATTCTTAAACCCAGACTGTGTC 58.694 41.667 0.93 0.00 0.00 3.67
2772 3362 6.878923 TGTGTCTATTGGTTCTTTCTACCATG 59.121 38.462 0.00 0.00 44.70 3.66
2773 3363 5.880332 TGTCTATTGGTTCTTTCTACCATGC 59.120 40.000 0.00 0.00 44.70 4.06
2783 3373 2.042686 TCTACCATGCTGATGTTGCC 57.957 50.000 0.00 0.00 0.00 4.52
2785 3382 0.251634 TACCATGCTGATGTTGCCGA 59.748 50.000 0.00 0.00 0.00 5.54
2851 3611 6.612306 GCAGTAGCAAGTACATAAAAGCTTT 58.388 36.000 5.69 5.69 41.58 3.51
2867 3627 3.846360 AGCTTTAAGTAGTGGTAGCACG 58.154 45.455 18.73 3.92 0.00 5.34
2981 3897 3.137544 TGGATCCTTGTGTACAGTTTGGT 59.862 43.478 14.23 0.00 0.00 3.67
3018 3934 4.098914 AGCTCCTTTGTTGAACATACCA 57.901 40.909 0.00 0.00 0.00 3.25
3227 4151 9.494271 GTAACTATTGGATATCATTCTCTTGCA 57.506 33.333 4.83 0.00 0.00 4.08
3242 4166 8.740369 CATTCTCTTGCATCGATTCAATAAAAC 58.260 33.333 10.90 0.00 0.00 2.43
3323 4282 3.496884 GCTTCCAAACGTATGAACAGACA 59.503 43.478 0.00 0.00 0.00 3.41
3333 4292 3.708403 ATGAACAGACAAGCATGAGGA 57.292 42.857 0.00 0.00 0.00 3.71
3334 4293 3.708403 TGAACAGACAAGCATGAGGAT 57.292 42.857 0.00 0.00 0.00 3.24
3435 4402 7.201478 GCACAGTAAATTAGTTGTCTAGCTCTG 60.201 40.741 0.00 0.00 0.00 3.35
3494 4463 1.770658 TGATCCACCATCCATCAGGTC 59.229 52.381 0.00 0.00 35.52 3.85
3502 4471 2.113807 CATCCATCAGGTCCTGTCTCA 58.886 52.381 18.65 0.00 35.89 3.27
3533 4502 4.194640 CGATCTTCTATTGCCATATGGGG 58.805 47.826 23.30 0.00 37.04 4.96
3569 4538 2.631062 GGGGAATTTTCTCCGTTTGGTT 59.369 45.455 0.00 0.00 38.24 3.67
3578 4547 1.104577 TCCGTTTGGTTGGTCCTTGC 61.105 55.000 0.00 0.00 37.07 4.01
3658 4627 2.186384 CGAGGGCTGCTCCTTCAG 59.814 66.667 10.40 3.55 40.75 3.02
3680 4649 1.427020 GAAGCTTCTCGCCACATGC 59.573 57.895 19.44 0.00 40.39 4.06
3801 4770 3.517296 TTGTTGTGGCCTGGATAAGAA 57.483 42.857 3.32 0.00 0.00 2.52
3802 4771 3.517296 TGTTGTGGCCTGGATAAGAAA 57.483 42.857 3.32 0.00 0.00 2.52
3803 4772 3.420893 TGTTGTGGCCTGGATAAGAAAG 58.579 45.455 3.32 0.00 0.00 2.62
3804 4773 3.073798 TGTTGTGGCCTGGATAAGAAAGA 59.926 43.478 3.32 0.00 0.00 2.52
3817 4786 9.729023 CTGGATAAGAAAGAGTATATGATAGCG 57.271 37.037 0.00 0.00 0.00 4.26
3831 4800 4.541085 TGATAGCGCATTTGTTGAGATG 57.459 40.909 11.47 0.00 0.00 2.90
3836 4805 1.067706 CGCATTTGTTGAGATGGGCAA 60.068 47.619 0.00 0.00 30.98 4.52
3842 4811 1.340889 TGTTGAGATGGGCAAAAGCAC 59.659 47.619 0.00 0.00 0.00 4.40
3843 4812 1.340889 GTTGAGATGGGCAAAAGCACA 59.659 47.619 0.00 0.00 0.00 4.57
3893 4863 5.099575 GCTGTTCTTCTAGCTACTCAAGAC 58.900 45.833 5.03 3.15 36.99 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.538813 ACTGCTACAATATAATCGAGGTGGA 59.461 40.000 0.00 0.00 0.00 4.02
1 2 5.635280 CACTGCTACAATATAATCGAGGTGG 59.365 44.000 0.00 0.00 0.00 4.61
2 3 5.119279 GCACTGCTACAATATAATCGAGGTG 59.881 44.000 0.00 0.00 0.00 4.00
3 4 5.011125 AGCACTGCTACAATATAATCGAGGT 59.989 40.000 0.21 0.00 36.99 3.85
4 5 5.473931 AGCACTGCTACAATATAATCGAGG 58.526 41.667 0.21 0.00 36.99 4.63
5 6 7.274468 CCTAAGCACTGCTACAATATAATCGAG 59.726 40.741 3.33 0.00 38.25 4.04
6 7 7.090808 CCTAAGCACTGCTACAATATAATCGA 58.909 38.462 3.33 0.00 38.25 3.59
7 8 6.183360 GCCTAAGCACTGCTACAATATAATCG 60.183 42.308 3.33 0.00 38.25 3.34
8 9 6.183360 CGCCTAAGCACTGCTACAATATAATC 60.183 42.308 3.33 0.00 38.25 1.75
9 10 5.639506 CGCCTAAGCACTGCTACAATATAAT 59.360 40.000 3.33 0.00 38.25 1.28
10 11 4.988540 CGCCTAAGCACTGCTACAATATAA 59.011 41.667 3.33 0.00 38.25 0.98
11 12 4.279922 TCGCCTAAGCACTGCTACAATATA 59.720 41.667 3.33 0.00 38.25 0.86
12 13 3.069586 TCGCCTAAGCACTGCTACAATAT 59.930 43.478 3.33 0.00 38.25 1.28
13 14 2.429250 TCGCCTAAGCACTGCTACAATA 59.571 45.455 3.33 0.00 38.25 1.90
14 15 1.207089 TCGCCTAAGCACTGCTACAAT 59.793 47.619 3.33 0.00 38.25 2.71
15 16 0.606096 TCGCCTAAGCACTGCTACAA 59.394 50.000 3.33 0.00 38.25 2.41
16 17 0.606096 TTCGCCTAAGCACTGCTACA 59.394 50.000 3.33 0.00 38.25 2.74
17 18 1.281899 CTTCGCCTAAGCACTGCTAC 58.718 55.000 3.33 0.00 38.25 3.58
18 19 3.741029 CTTCGCCTAAGCACTGCTA 57.259 52.632 3.33 0.00 38.25 3.49
19 20 4.606071 CTTCGCCTAAGCACTGCT 57.394 55.556 0.00 0.00 42.56 4.24
32 33 4.124351 TACCGTCGCAGGGCTTCG 62.124 66.667 1.26 0.00 35.02 3.79
33 34 2.202756 CTACCGTCGCAGGGCTTC 60.203 66.667 1.26 0.00 35.02 3.86
34 35 2.280552 TTCTACCGTCGCAGGGCTT 61.281 57.895 1.26 0.00 35.02 4.35
35 36 2.678934 TTCTACCGTCGCAGGGCT 60.679 61.111 1.26 0.00 35.02 5.19
36 37 2.508663 GTTCTACCGTCGCAGGGC 60.509 66.667 1.26 0.00 35.02 5.19
37 38 0.527817 GATGTTCTACCGTCGCAGGG 60.528 60.000 1.26 0.00 35.02 4.45
38 39 0.172578 TGATGTTCTACCGTCGCAGG 59.827 55.000 0.00 0.00 37.30 4.85
39 40 1.920574 CTTGATGTTCTACCGTCGCAG 59.079 52.381 0.00 0.00 0.00 5.18
40 41 1.542472 TCTTGATGTTCTACCGTCGCA 59.458 47.619 0.00 0.00 0.00 5.10
41 42 2.273370 TCTTGATGTTCTACCGTCGC 57.727 50.000 0.00 0.00 0.00 5.19
42 43 3.547868 CACATCTTGATGTTCTACCGTCG 59.452 47.826 12.95 0.00 31.37 5.12
43 44 3.865745 CCACATCTTGATGTTCTACCGTC 59.134 47.826 12.95 0.00 31.37 4.79
44 45 3.861840 CCACATCTTGATGTTCTACCGT 58.138 45.455 12.95 0.00 31.37 4.83
45 46 2.609459 GCCACATCTTGATGTTCTACCG 59.391 50.000 12.95 2.33 31.37 4.02
46 47 2.945668 GGCCACATCTTGATGTTCTACC 59.054 50.000 12.95 8.77 31.37 3.18
47 48 3.878778 AGGCCACATCTTGATGTTCTAC 58.121 45.455 12.95 5.31 31.37 2.59
48 49 4.517285 GAAGGCCACATCTTGATGTTCTA 58.483 43.478 12.95 0.00 31.37 2.10
49 50 3.350833 GAAGGCCACATCTTGATGTTCT 58.649 45.455 12.95 8.71 31.37 3.01
50 51 2.096496 CGAAGGCCACATCTTGATGTTC 59.904 50.000 12.95 7.65 31.37 3.18
51 52 2.086869 CGAAGGCCACATCTTGATGTT 58.913 47.619 12.95 0.00 31.37 2.71
52 53 1.278985 TCGAAGGCCACATCTTGATGT 59.721 47.619 5.01 10.15 34.64 3.06
53 54 2.028420 TCGAAGGCCACATCTTGATG 57.972 50.000 5.01 8.87 0.00 3.07
54 55 2.636830 CTTCGAAGGCCACATCTTGAT 58.363 47.619 17.70 0.00 0.00 2.57
55 56 1.945819 GCTTCGAAGGCCACATCTTGA 60.946 52.381 25.77 0.00 0.00 3.02
56 57 0.449388 GCTTCGAAGGCCACATCTTG 59.551 55.000 25.77 0.00 0.00 3.02
57 58 1.021390 CGCTTCGAAGGCCACATCTT 61.021 55.000 25.77 0.00 0.00 2.40
58 59 1.448540 CGCTTCGAAGGCCACATCT 60.449 57.895 25.77 0.00 0.00 2.90
59 60 1.741770 ACGCTTCGAAGGCCACATC 60.742 57.895 25.77 6.94 0.00 3.06
60 61 2.034879 CACGCTTCGAAGGCCACAT 61.035 57.895 25.77 0.00 0.00 3.21
61 62 2.664851 CACGCTTCGAAGGCCACA 60.665 61.111 25.77 0.00 0.00 4.17
62 63 4.090057 GCACGCTTCGAAGGCCAC 62.090 66.667 25.77 8.72 0.00 5.01
66 67 2.227968 CTTTCCGCACGCTTCGAAGG 62.228 60.000 25.77 17.63 0.00 3.46
67 68 1.130613 CTTTCCGCACGCTTCGAAG 59.869 57.895 21.02 21.02 0.00 3.79
68 69 2.950172 GCTTTCCGCACGCTTCGAA 61.950 57.895 0.00 0.00 38.92 3.71
69 70 3.411351 GCTTTCCGCACGCTTCGA 61.411 61.111 0.00 0.00 38.92 3.71
70 71 4.445545 GGCTTTCCGCACGCTTCG 62.446 66.667 0.00 0.00 41.67 3.79
71 72 3.050275 AGGCTTTCCGCACGCTTC 61.050 61.111 0.00 0.00 41.67 3.86
72 73 3.357079 CAGGCTTTCCGCACGCTT 61.357 61.111 0.00 0.00 41.67 4.68
205 209 0.033601 ACAGAGCAAACCACACCCAA 60.034 50.000 0.00 0.00 0.00 4.12
210 214 0.107263 TGCAGACAGAGCAAACCACA 60.107 50.000 0.00 0.00 39.39 4.17
221 390 6.286758 ACAATAGATCCTACATTGCAGACAG 58.713 40.000 6.78 0.00 33.82 3.51
297 466 4.729227 TGGCTATGAACTGAACATACGA 57.271 40.909 0.00 0.00 0.00 3.43
326 495 1.402968 AGCCATAAACAGATGCAAGCG 59.597 47.619 0.00 0.00 0.00 4.68
327 496 4.637483 TTAGCCATAAACAGATGCAAGC 57.363 40.909 0.00 0.00 0.00 4.01
328 497 4.980434 GCATTAGCCATAAACAGATGCAAG 59.020 41.667 0.00 0.00 38.52 4.01
354 523 0.796312 GTGGCACGACACAAGTATGG 59.204 55.000 0.00 0.00 40.99 2.74
366 535 2.096417 GCTACTACAAAAGTGTGGCACG 60.096 50.000 13.77 0.00 39.75 5.34
367 536 2.875933 TGCTACTACAAAAGTGTGGCAC 59.124 45.455 11.55 11.55 39.75 5.01
368 537 3.201353 TGCTACTACAAAAGTGTGGCA 57.799 42.857 0.00 0.00 39.75 4.92
369 538 7.548196 TTATATGCTACTACAAAAGTGTGGC 57.452 36.000 0.00 0.00 39.75 5.01
386 555 8.063630 GGCAAAGCATAACACAAATTTATATGC 58.936 33.333 19.45 19.45 45.69 3.14
393 562 6.690194 TTTTGGCAAAGCATAACACAAATT 57.310 29.167 13.04 0.00 0.00 1.82
394 563 6.294065 CCATTTTGGCAAAGCATAACACAAAT 60.294 34.615 13.04 0.00 0.00 2.32
422 592 6.437162 ACATATATGAACAACAAAAGGCTGGT 59.563 34.615 19.63 0.00 0.00 4.00
427 597 9.225201 CGATCAACATATATGAACAACAAAAGG 57.775 33.333 19.63 0.00 0.00 3.11
435 605 9.546428 AGATCAAACGATCAACATATATGAACA 57.454 29.630 19.63 2.56 41.60 3.18
439 609 7.799784 TGCAGATCAAACGATCAACATATATG 58.200 34.615 11.29 11.29 41.60 1.78
442 612 6.539826 TCTTGCAGATCAAACGATCAACATAT 59.460 34.615 5.33 0.00 41.60 1.78
444 614 4.696877 TCTTGCAGATCAAACGATCAACAT 59.303 37.500 5.33 0.00 41.60 2.71
445 615 4.064388 TCTTGCAGATCAAACGATCAACA 58.936 39.130 5.33 0.34 41.60 3.33
460 643 2.005451 CTGGAGATTCCGTTCTTGCAG 58.995 52.381 0.00 0.00 40.17 4.41
461 644 1.339055 CCTGGAGATTCCGTTCTTGCA 60.339 52.381 0.00 0.00 40.17 4.08
463 646 1.555075 TCCCTGGAGATTCCGTTCTTG 59.445 52.381 0.00 0.00 40.17 3.02
467 650 2.420129 CGATTTCCCTGGAGATTCCGTT 60.420 50.000 0.00 0.00 40.17 4.44
472 655 3.878778 CAGAACGATTTCCCTGGAGATT 58.121 45.455 0.00 0.00 31.28 2.40
478 661 0.804989 GTGGCAGAACGATTTCCCTG 59.195 55.000 0.00 0.00 31.28 4.45
483 666 2.550830 ACAGAGTGGCAGAACGATTT 57.449 45.000 0.00 0.00 0.00 2.17
484 667 2.549754 CAAACAGAGTGGCAGAACGATT 59.450 45.455 0.00 0.00 0.00 3.34
485 668 2.146342 CAAACAGAGTGGCAGAACGAT 58.854 47.619 0.00 0.00 0.00 3.73
486 669 1.581934 CAAACAGAGTGGCAGAACGA 58.418 50.000 0.00 0.00 0.00 3.85
487 670 0.588252 CCAAACAGAGTGGCAGAACG 59.412 55.000 0.00 0.00 0.00 3.95
488 671 1.876156 CTCCAAACAGAGTGGCAGAAC 59.124 52.381 0.00 0.00 35.99 3.01
489 672 1.202806 CCTCCAAACAGAGTGGCAGAA 60.203 52.381 0.00 0.00 35.99 3.02
490 673 0.397941 CCTCCAAACAGAGTGGCAGA 59.602 55.000 0.00 0.00 35.99 4.26
491 674 0.607489 CCCTCCAAACAGAGTGGCAG 60.607 60.000 0.00 0.00 35.99 4.85
492 675 1.059584 TCCCTCCAAACAGAGTGGCA 61.060 55.000 0.00 0.00 35.99 4.92
493 676 0.110486 TTCCCTCCAAACAGAGTGGC 59.890 55.000 0.00 0.00 35.99 5.01
494 677 2.656947 TTTCCCTCCAAACAGAGTGG 57.343 50.000 0.00 0.00 37.51 4.00
495 678 5.068987 TGAAATTTTCCCTCCAAACAGAGTG 59.931 40.000 6.68 0.00 31.53 3.51
496 679 5.208121 TGAAATTTTCCCTCCAAACAGAGT 58.792 37.500 6.68 0.00 31.53 3.24
497 680 5.789643 TGAAATTTTCCCTCCAAACAGAG 57.210 39.130 6.68 0.00 0.00 3.35
498 681 5.048083 CGATGAAATTTTCCCTCCAAACAGA 60.048 40.000 6.68 0.00 0.00 3.41
499 682 5.163513 CGATGAAATTTTCCCTCCAAACAG 58.836 41.667 6.68 0.00 0.00 3.16
500 683 4.021544 CCGATGAAATTTTCCCTCCAAACA 60.022 41.667 6.68 0.00 0.00 2.83
510 693 2.095466 TGTCCGTGCCGATGAAATTTTC 60.095 45.455 2.05 2.05 0.00 2.29
515 698 0.249120 AGATGTCCGTGCCGATGAAA 59.751 50.000 0.00 0.00 0.00 2.69
547 730 7.169982 TGACGACACAAGAACAAAAACAAAAAT 59.830 29.630 0.00 0.00 0.00 1.82
565 748 1.413382 CAGAGAGTGCTTGACGACAC 58.587 55.000 0.00 0.00 37.05 3.67
566 749 0.315251 CCAGAGAGTGCTTGACGACA 59.685 55.000 0.00 0.00 0.00 4.35
567 750 0.315568 ACCAGAGAGTGCTTGACGAC 59.684 55.000 0.00 0.00 0.00 4.34
568 751 1.000163 GAACCAGAGAGTGCTTGACGA 60.000 52.381 0.00 0.00 0.00 4.20
569 752 1.269778 TGAACCAGAGAGTGCTTGACG 60.270 52.381 0.00 0.00 0.00 4.35
570 753 2.533266 TGAACCAGAGAGTGCTTGAC 57.467 50.000 0.00 0.00 0.00 3.18
613 796 6.145209 CACATGATCGAAGTGGATCTCAATAC 59.855 42.308 0.00 0.00 42.63 1.89
617 800 3.448660 ACACATGATCGAAGTGGATCTCA 59.551 43.478 0.00 0.50 42.63 3.27
618 801 4.052159 ACACATGATCGAAGTGGATCTC 57.948 45.455 0.00 0.00 42.63 2.75
619 802 4.161189 AGAACACATGATCGAAGTGGATCT 59.839 41.667 0.00 13.19 42.63 2.75
620 803 4.437239 AGAACACATGATCGAAGTGGATC 58.563 43.478 0.00 11.72 42.52 3.36
621 804 4.478206 AGAACACATGATCGAAGTGGAT 57.522 40.909 0.00 5.15 37.58 3.41
623 806 6.668541 ATAAAGAACACATGATCGAAGTGG 57.331 37.500 0.00 0.00 37.58 4.00
634 835 5.350365 ACACGCGTGAATATAAAGAACACAT 59.650 36.000 42.94 13.64 0.00 3.21
657 858 5.638660 TTTTGTTTCGCGGGATTTTTAAC 57.361 34.783 6.13 5.02 0.00 2.01
665 866 1.287503 GCCATTTTGTTTCGCGGGA 59.712 52.632 6.13 0.00 0.00 5.14
675 880 6.718454 TGTTTTTCGATAATGGCCATTTTG 57.282 33.333 34.85 23.38 32.50 2.44
676 881 7.158021 TCTTGTTTTTCGATAATGGCCATTTT 58.842 30.769 34.85 27.22 32.50 1.82
725 1114 2.215363 CGGATTTTGCAACAACAACGAC 59.785 45.455 0.00 0.00 0.00 4.34
727 1116 1.520590 CCGGATTTTGCAACAACAACG 59.479 47.619 0.00 0.00 0.00 4.10
728 1117 1.260297 GCCGGATTTTGCAACAACAAC 59.740 47.619 5.05 0.00 0.00 3.32
806 1202 3.385433 GGCAAATCATTGACCCATCATGA 59.615 43.478 0.00 0.00 38.75 3.07
832 1228 1.940613 GTGTATGCCCCTAGAAAAGCG 59.059 52.381 0.00 0.00 0.00 4.68
833 1229 1.940613 CGTGTATGCCCCTAGAAAAGC 59.059 52.381 0.00 0.00 0.00 3.51
835 1231 1.741055 CGCGTGTATGCCCCTAGAAAA 60.741 52.381 0.00 0.00 0.00 2.29
839 1236 0.885879 TATCGCGTGTATGCCCCTAG 59.114 55.000 5.77 0.00 0.00 3.02
850 1247 3.422214 CGGATGATGTCAAATATCGCGTG 60.422 47.826 5.77 0.00 0.00 5.34
855 1252 4.256920 CCCCTCGGATGATGTCAAATATC 58.743 47.826 0.00 0.00 0.00 1.63
891 1288 1.149986 TGTATGGTTGGTGGTTGGGA 58.850 50.000 0.00 0.00 0.00 4.37
907 1304 3.570926 AAAGAAGATCTCGTGCGTGTA 57.429 42.857 0.00 0.00 0.00 2.90
927 1324 1.423921 GGTTCCCTCCTTTGGACTGAA 59.576 52.381 0.00 0.00 0.00 3.02
966 1383 2.203714 GATCGAGGGAGGAGGGGG 60.204 72.222 0.00 0.00 0.00 5.40
968 1385 1.602323 CGAGATCGAGGGAGGAGGG 60.602 68.421 0.00 0.00 43.02 4.30
971 1388 2.203365 GGCGAGATCGAGGGAGGA 60.203 66.667 6.39 0.00 43.02 3.71
997 1417 3.880846 CTTCGCCTTCGCCATGGC 61.881 66.667 27.67 27.67 45.25 4.40
1030 1468 2.743928 CTTCGCCGCCTGCTTCTT 60.744 61.111 0.00 0.00 38.05 2.52
1031 1469 3.655810 CTCTTCGCCGCCTGCTTCT 62.656 63.158 0.00 0.00 38.05 2.85
1228 1666 0.105039 GCTTACAGGACGATCCAGGG 59.895 60.000 6.78 0.00 39.61 4.45
1269 1711 6.935167 AGAAAGCCAGACAAAGAAAGAAAAA 58.065 32.000 0.00 0.00 0.00 1.94
1270 1712 6.378280 AGAGAAAGCCAGACAAAGAAAGAAAA 59.622 34.615 0.00 0.00 0.00 2.29
1271 1713 5.888161 AGAGAAAGCCAGACAAAGAAAGAAA 59.112 36.000 0.00 0.00 0.00 2.52
1272 1714 5.440610 AGAGAAAGCCAGACAAAGAAAGAA 58.559 37.500 0.00 0.00 0.00 2.52
1273 1715 5.041191 AGAGAAAGCCAGACAAAGAAAGA 57.959 39.130 0.00 0.00 0.00 2.52
1274 1716 5.062528 AGAGAGAAAGCCAGACAAAGAAAG 58.937 41.667 0.00 0.00 0.00 2.62
1275 1717 5.041191 AGAGAGAAAGCCAGACAAAGAAA 57.959 39.130 0.00 0.00 0.00 2.52
1276 1718 4.696479 AGAGAGAAAGCCAGACAAAGAA 57.304 40.909 0.00 0.00 0.00 2.52
1277 1719 4.384056 CAAGAGAGAAAGCCAGACAAAGA 58.616 43.478 0.00 0.00 0.00 2.52
1282 1724 1.447945 GGCAAGAGAGAAAGCCAGAC 58.552 55.000 0.00 0.00 46.26 3.51
1286 1728 1.003233 ACGGGCAAGAGAGAAAGCC 60.003 57.895 0.00 0.00 46.28 4.35
1287 1729 1.301677 CCACGGGCAAGAGAGAAAGC 61.302 60.000 0.00 0.00 0.00 3.51
1288 1730 0.321671 TCCACGGGCAAGAGAGAAAG 59.678 55.000 0.00 0.00 0.00 2.62
1289 1731 0.321671 CTCCACGGGCAAGAGAGAAA 59.678 55.000 0.00 0.00 0.00 2.52
1291 1733 1.228894 ACTCCACGGGCAAGAGAGA 60.229 57.895 0.00 0.00 0.00 3.10
1292 1734 1.216710 GACTCCACGGGCAAGAGAG 59.783 63.158 0.00 0.00 0.00 3.20
1362 1806 3.986116 AAGGGGTCGGAGGAGGAGC 62.986 68.421 0.00 0.00 0.00 4.70
1366 1810 2.764547 GGGAAGGGGTCGGAGGAG 60.765 72.222 0.00 0.00 0.00 3.69
1390 1840 3.427425 CCGGCCGAATTCGTTGCA 61.427 61.111 30.73 0.00 37.74 4.08
1393 1843 2.125269 CCTCCGGCCGAATTCGTT 60.125 61.111 30.73 0.00 37.74 3.85
1420 1903 4.316823 ACCACCTCTCCCGCTCCA 62.317 66.667 0.00 0.00 0.00 3.86
1479 1962 2.128507 GCCTCTACTCCCCGGTCAG 61.129 68.421 0.00 0.00 0.00 3.51
1521 2004 1.913262 ACATCCACTGCGACCTCCA 60.913 57.895 0.00 0.00 0.00 3.86
1605 2088 0.602638 CAGTTCTGTGCCGGCAAGTA 60.603 55.000 34.66 20.49 0.00 2.24
1759 2242 2.027625 GTTGTCTCCCCGCAACGAG 61.028 63.158 0.00 0.00 36.15 4.18
1770 2253 2.317040 TCCCCATCTATCCGTTGTCTC 58.683 52.381 0.00 0.00 0.00 3.36
1771 2254 2.471815 TCCCCATCTATCCGTTGTCT 57.528 50.000 0.00 0.00 0.00 3.41
1772 2255 3.403038 CATTCCCCATCTATCCGTTGTC 58.597 50.000 0.00 0.00 0.00 3.18
1773 2256 2.106511 CCATTCCCCATCTATCCGTTGT 59.893 50.000 0.00 0.00 0.00 3.32
1774 2257 2.553028 CCCATTCCCCATCTATCCGTTG 60.553 54.545 0.00 0.00 0.00 4.10
1775 2258 1.705186 CCCATTCCCCATCTATCCGTT 59.295 52.381 0.00 0.00 0.00 4.44
1776 2259 1.132527 TCCCATTCCCCATCTATCCGT 60.133 52.381 0.00 0.00 0.00 4.69
1781 2264 2.065007 CCACATCCCATTCCCCATCTA 58.935 52.381 0.00 0.00 0.00 1.98
1804 2287 2.284921 CCCCTGGCTCTGTCTCCA 60.285 66.667 0.00 0.00 0.00 3.86
1820 2304 0.726827 CACACACACACTCACACACC 59.273 55.000 0.00 0.00 0.00 4.16
1837 2321 4.787551 TCCCTTATGTCTCTCTCTCTCAC 58.212 47.826 0.00 0.00 0.00 3.51
1838 2322 4.724293 TCTCCCTTATGTCTCTCTCTCTCA 59.276 45.833 0.00 0.00 0.00 3.27
1851 2335 9.212641 CATATACACAAGTTCATCTCCCTTATG 57.787 37.037 0.00 0.00 0.00 1.90
1855 2339 5.905331 TCCATATACACAAGTTCATCTCCCT 59.095 40.000 0.00 0.00 0.00 4.20
1859 2343 5.050490 GCGTCCATATACACAAGTTCATCT 58.950 41.667 0.00 0.00 0.00 2.90
1881 2365 1.877443 TCTCCAACGGCTAGTTTTTGC 59.123 47.619 0.00 0.00 42.02 3.68
1882 2366 3.564225 AGTTCTCCAACGGCTAGTTTTTG 59.436 43.478 0.00 0.00 42.02 2.44
1883 2367 3.816994 AGTTCTCCAACGGCTAGTTTTT 58.183 40.909 0.00 0.00 42.02 1.94
1916 2400 1.079127 GCTATGTGCACCGGTCTGT 60.079 57.895 15.69 0.00 42.31 3.41
1920 2404 2.584608 GGAGCTATGTGCACCGGT 59.415 61.111 15.69 0.00 42.21 5.28
1956 2452 3.205851 AAAGTGGTCGGGCCCTTCC 62.206 63.158 22.43 21.52 36.04 3.46
1957 2453 1.971695 CAAAGTGGTCGGGCCCTTC 60.972 63.158 22.43 12.49 36.04 3.46
1958 2454 2.115266 CAAAGTGGTCGGGCCCTT 59.885 61.111 22.43 2.34 36.04 3.95
1959 2455 3.966543 CCAAAGTGGTCGGGCCCT 61.967 66.667 22.43 0.00 36.04 5.19
1961 2457 4.280019 ACCCAAAGTGGTCGGGCC 62.280 66.667 0.00 0.00 44.49 5.80
1962 2458 2.983592 CACCCAAAGTGGTCGGGC 60.984 66.667 0.00 0.00 44.49 6.13
2013 2535 0.537143 GTTGGGCCACTGACATGTGA 60.537 55.000 5.23 0.00 40.12 3.58
2043 2565 3.901844 TCCTAGAAACAGCCACTTGTACT 59.098 43.478 0.00 0.00 0.00 2.73
2046 2568 2.706190 AGTCCTAGAAACAGCCACTTGT 59.294 45.455 0.00 0.00 0.00 3.16
2061 2633 0.962356 GGTCACGGGTTCGAGTCCTA 60.962 60.000 8.28 0.00 40.11 2.94
2080 2652 3.364964 GCGGTAAAACTGTTGACCATGAG 60.365 47.826 19.29 8.49 38.10 2.90
2081 2653 2.550606 GCGGTAAAACTGTTGACCATGA 59.449 45.455 19.29 0.00 38.10 3.07
2082 2654 2.552315 AGCGGTAAAACTGTTGACCATG 59.448 45.455 19.29 9.26 38.10 3.66
2083 2655 2.552315 CAGCGGTAAAACTGTTGACCAT 59.448 45.455 19.29 8.75 38.10 3.55
2084 2656 1.944024 CAGCGGTAAAACTGTTGACCA 59.056 47.619 19.29 0.00 38.10 4.02
2085 2657 1.334689 GCAGCGGTAAAACTGTTGACC 60.335 52.381 12.62 12.62 37.83 4.02
2086 2658 1.334689 GGCAGCGGTAAAACTGTTGAC 60.335 52.381 6.88 0.06 37.83 3.18
2087 2659 0.948678 GGCAGCGGTAAAACTGTTGA 59.051 50.000 6.88 0.00 37.83 3.18
2094 2666 1.605165 CCTTGGGGCAGCGGTAAAA 60.605 57.895 0.00 0.00 0.00 1.52
2106 2678 3.963124 AATGAAGGGGCGCCTTGGG 62.963 63.158 37.05 0.00 0.00 4.12
2113 2685 0.035056 AGTTCTCCAATGAAGGGGCG 60.035 55.000 0.00 0.00 0.00 6.13
2114 2686 2.924421 CTAGTTCTCCAATGAAGGGGC 58.076 52.381 0.00 0.00 0.00 5.80
2122 2694 6.942576 ACATTTGTAACAGCTAGTTCTCCAAT 59.057 34.615 5.04 3.02 41.64 3.16
2192 2764 6.127451 CCTGAACAAACATATTCCCCCTAAAC 60.127 42.308 0.00 0.00 0.00 2.01
2208 2781 1.214175 TCCAGCAACTCCCTGAACAAA 59.786 47.619 0.00 0.00 32.03 2.83
2293 2873 1.341531 CCATACACTCCATCGAGTCCC 59.658 57.143 0.00 0.00 46.90 4.46
2299 2879 2.477825 CAAGAGCCATACACTCCATCG 58.522 52.381 0.00 0.00 34.56 3.84
2301 2881 2.338577 GCAAGAGCCATACACTCCAT 57.661 50.000 0.00 0.00 34.56 3.41
2302 2882 3.861341 GCAAGAGCCATACACTCCA 57.139 52.632 0.00 0.00 34.56 3.86
2314 2894 5.402270 CCAAAAATAACTGAAACGGCAAGAG 59.598 40.000 0.00 0.00 0.00 2.85
2350 2930 8.934825 GCATTCCAAATTTGAAAACAGCTATTA 58.065 29.630 19.86 0.00 0.00 0.98
2351 2931 7.360269 CGCATTCCAAATTTGAAAACAGCTATT 60.360 33.333 19.86 0.00 0.00 1.73
2383 2965 4.907582 GGGTCTCAATTTTGTACGAAAACG 59.092 41.667 12.26 6.79 0.00 3.60
2394 2976 3.068590 CAGCAACACTGGGTCTCAATTTT 59.931 43.478 0.00 0.00 43.19 1.82
2470 3056 0.850784 ACAGGTAGCCAAAACAGGGT 59.149 50.000 0.00 0.00 43.00 4.34
2493 3079 4.153117 GGCATTATAACCATCAAGAGCTCG 59.847 45.833 8.37 0.00 0.00 5.03
2709 3298 5.333299 TGATTTCAGATTTGCTTGGGATG 57.667 39.130 0.00 0.00 0.00 3.51
2710 3299 6.383147 AGAATGATTTCAGATTTGCTTGGGAT 59.617 34.615 0.00 0.00 34.08 3.85
2772 3362 0.935898 CAGAGATCGGCAACATCAGC 59.064 55.000 0.00 0.00 0.00 4.26
2773 3363 2.306341 ACAGAGATCGGCAACATCAG 57.694 50.000 0.00 0.00 0.00 2.90
2783 3373 6.201806 GGATTTCAGAATGGTTACAGAGATCG 59.798 42.308 0.00 0.00 36.16 3.69
2785 3382 6.962182 TGGATTTCAGAATGGTTACAGAGAT 58.038 36.000 0.00 0.00 36.16 2.75
2851 3611 3.346315 TGCTACGTGCTACCACTACTTA 58.654 45.455 0.00 0.00 43.37 2.24
2867 3627 5.973565 GCCAAATAAGTCATGTGATTGCTAC 59.026 40.000 0.00 0.00 0.00 3.58
2874 3777 4.220163 TGCATTGCCAAATAAGTCATGTGA 59.780 37.500 6.12 0.00 0.00 3.58
2880 3783 8.597662 ATTGAATATGCATTGCCAAATAAGTC 57.402 30.769 3.54 0.00 0.00 3.01
2981 3897 4.978099 AGGAGCTTCTCATCAAAAGTGAA 58.022 39.130 0.00 0.00 37.30 3.18
3018 3934 2.242043 GCCAATCCGATCCCAAATCAT 58.758 47.619 0.00 0.00 0.00 2.45
3058 3980 7.952930 TCTAGGGCTCTTTGATAATCTACAGAT 59.047 37.037 0.00 0.00 36.07 2.90
3071 3993 2.479566 TGCTGTTCTAGGGCTCTTTG 57.520 50.000 0.00 0.00 0.00 2.77
3072 3994 3.245052 ACAATGCTGTTCTAGGGCTCTTT 60.245 43.478 0.00 0.00 28.57 2.52
3242 4166 7.216920 TCACGATGATCTACATGTTAAAACG 57.783 36.000 2.30 4.96 39.56 3.60
3280 4239 0.038251 AGTGCTCGCTCGAAATCACA 60.038 50.000 15.73 0.61 0.00 3.58
3312 4271 4.824479 TCCTCATGCTTGTCTGTTCATA 57.176 40.909 0.00 0.00 0.00 2.15
3323 4282 5.302568 TCTTGTTTGTCAAATCCTCATGCTT 59.697 36.000 0.40 0.00 35.48 3.91
3334 4293 9.734620 CTTTGATCATAACTCTTGTTTGTCAAA 57.265 29.630 0.00 0.00 37.59 2.69
3376 4342 3.907894 TTGTTACGTTTCCTTGGATGC 57.092 42.857 0.00 0.00 0.00 3.91
3435 4402 2.726241 GCGATTTTGCAAGAAACTCACC 59.274 45.455 0.00 0.00 34.15 4.02
3494 4463 0.668535 TCGTCACACAGTGAGACAGG 59.331 55.000 25.19 13.52 43.57 4.00
3502 4471 4.177026 GCAATAGAAGATCGTCACACAGT 58.823 43.478 11.35 0.00 0.00 3.55
3533 4502 2.879103 TCCCCACCAAGAAGTGAATC 57.121 50.000 0.00 0.00 40.34 2.52
3569 4538 4.697756 CGCGAAGGGCAAGGACCA 62.698 66.667 0.00 0.00 43.84 4.02
3674 4643 2.044650 CTCCACCTGGGGCATGTG 60.045 66.667 0.00 0.00 37.22 3.21
3680 4649 1.301293 GAAGAAGCTCCACCTGGGG 59.699 63.158 0.00 0.00 39.22 4.96
3707 4676 1.851658 GAGGCGAGCTGAAGAAGATC 58.148 55.000 0.00 0.00 37.99 2.75
3801 4770 7.657354 TCAACAAATGCGCTATCATATACTCTT 59.343 33.333 9.73 0.00 0.00 2.85
3802 4771 7.154656 TCAACAAATGCGCTATCATATACTCT 58.845 34.615 9.73 0.00 0.00 3.24
3803 4772 7.329471 TCTCAACAAATGCGCTATCATATACTC 59.671 37.037 9.73 0.00 0.00 2.59
3804 4773 7.154656 TCTCAACAAATGCGCTATCATATACT 58.845 34.615 9.73 0.00 0.00 2.12
3817 4786 2.747396 TTGCCCATCTCAACAAATGC 57.253 45.000 0.00 0.00 0.00 3.56
3831 4800 6.983474 ATTGTAAATATTGTGCTTTTGCCC 57.017 33.333 0.00 0.00 46.87 5.36
3889 4859 1.371558 GGTGGACTCTTGCCGTCTT 59.628 57.895 0.00 0.00 0.00 3.01
3893 4863 1.738099 CTTCGGTGGACTCTTGCCG 60.738 63.158 0.00 0.00 44.95 5.69


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

AutoCloner maintained by Alex Coulton.