Multiple sequence alignment - TraesCS6D01G311200

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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 TraesCS6D01G311200 chr6D 100.000 4651 0 0 1 4651 420757185 420761835 0.000000e+00 8589.0
1 TraesCS6D01G311200 chr6B 90.962 3939 198 53 1 3846 634042988 634046861 0.000000e+00 5156.0
2 TraesCS6D01G311200 chr6B 86.434 774 54 13 3917 4648 634046915 634047679 0.000000e+00 800.0
3 TraesCS6D01G311200 chr6A 91.231 3273 184 50 512 3745 563730783 563727575 0.000000e+00 4359.0
4 TraesCS6D01G311200 chr6A 88.786 758 46 18 3914 4648 563741858 563742599 0.000000e+00 893.0
5 TraesCS6D01G311200 chr6A 88.158 76 7 2 362 437 563730878 563730805 6.410000e-14 89.8
6 TraesCS6D01G311200 chr4D 78.673 211 43 2 1178 1387 475954415 475954206 6.280000e-29 139.0
7 TraesCS6D01G311200 chr4A 78.571 210 43 2 1179 1387 683258877 683258669 2.260000e-28 137.0
8 TraesCS6D01G311200 chr4A 78.075 187 41 0 1201 1387 682992080 682991894 8.180000e-23 119.0
9 TraesCS6D01G311200 chr4B 78.095 210 46 0 1178 1387 600433062 600432853 2.920000e-27 134.0
10 TraesCS6D01G311200 chr5A 75.806 186 39 5 1201 1383 413220355 413220537 6.410000e-14 89.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G311200 chr6D 420757185 420761835 4650 False 8589.0 8589 100.0000 1 4651 1 chr6D.!!$F1 4650
1 TraesCS6D01G311200 chr6B 634042988 634047679 4691 False 2978.0 5156 88.6980 1 4648 2 chr6B.!!$F1 4647
2 TraesCS6D01G311200 chr6A 563727575 563730878 3303 True 2224.4 4359 89.6945 362 3745 2 chr6A.!!$R1 3383
3 TraesCS6D01G311200 chr6A 563741858 563742599 741 False 893.0 893 88.7860 3914 4648 1 chr6A.!!$F1 734

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
506 528 0.104120 TCTCATAACCACGCCATCCG 59.896 55.000 0.00 0.0 44.21 4.18 F
793 849 0.532573 TCTGCTTCCACGTCCTCATC 59.467 55.000 0.00 0.0 0.00 2.92 F
981 1046 0.877743 GTGAAGCTCCTCAACCAAGC 59.122 55.000 0.00 0.0 36.27 4.01 F
992 1064 1.068474 CAACCAAGCTAAGACGACGG 58.932 55.000 0.00 0.0 0.00 4.79 F
1803 1887 1.449246 CTTCCTGCTGGAGAAGGCG 60.449 63.158 12.54 0.0 44.24 5.52 F
3078 3177 2.029623 TCTGCGTGATCCTACCTAACC 58.970 52.381 0.00 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 2016 0.528466 TGATGCCGTCGAAGATGCTC 60.528 55.000 0.00 0.00 43.31 4.26 R
2391 2478 0.606401 CGCAGTTGTCATGGTCCCTT 60.606 55.000 0.00 0.00 0.00 3.95 R
2472 2559 1.079543 CGGGTTGAGGAGCAGAGTG 60.080 63.158 0.00 0.00 0.00 3.51 R
2922 3009 1.296392 CACCCTCATGGCGTTGAGA 59.704 57.895 16.30 0.00 44.88 3.27 R
3224 3333 0.037882 ACCTGCAGATCTGTGTCGTG 60.038 55.000 23.38 9.34 0.00 4.35 R
3989 4137 1.557832 TGAATTTCCCCGATCCGAAGT 59.442 47.619 0.00 0.00 0.00 3.01 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
41 42 5.721000 TGGCCTCAAACCAAATCAAAGATAT 59.279 36.000 3.32 0.00 33.12 1.63
77 78 0.984230 TACTCCCTCACTTGCCCAAG 59.016 55.000 6.48 6.48 43.79 3.61
165 166 4.111375 TCTGTCTCTAATTCGCCTCAAC 57.889 45.455 0.00 0.00 0.00 3.18
166 167 3.119101 TCTGTCTCTAATTCGCCTCAACC 60.119 47.826 0.00 0.00 0.00 3.77
177 178 1.134098 CGCCTCAACCCCATCAACTAT 60.134 52.381 0.00 0.00 0.00 2.12
178 179 2.683742 CGCCTCAACCCCATCAACTATT 60.684 50.000 0.00 0.00 0.00 1.73
180 181 4.532834 GCCTCAACCCCATCAACTATTTA 58.467 43.478 0.00 0.00 0.00 1.40
182 183 5.241728 GCCTCAACCCCATCAACTATTTATC 59.758 44.000 0.00 0.00 0.00 1.75
183 184 6.605119 CCTCAACCCCATCAACTATTTATCT 58.395 40.000 0.00 0.00 0.00 1.98
184 185 7.691791 GCCTCAACCCCATCAACTATTTATCTA 60.692 40.741 0.00 0.00 0.00 1.98
250 261 2.534019 CGTGGCTGTGCTTTCACGT 61.534 57.895 6.55 0.00 46.01 4.49
253 264 1.008538 GGCTGTGCTTTCACGTTGG 60.009 57.895 0.00 0.00 46.01 3.77
269 280 2.095466 CGTTGGCACGTAATTTGTGGAT 60.095 45.455 11.18 0.00 41.84 3.41
270 281 3.241701 GTTGGCACGTAATTTGTGGATG 58.758 45.455 11.18 0.00 37.80 3.51
271 282 2.784347 TGGCACGTAATTTGTGGATGA 58.216 42.857 11.18 0.00 37.80 2.92
285 296 2.433970 GTGGATGAGAGGAAAGAGAGGG 59.566 54.545 0.00 0.00 0.00 4.30
306 328 2.534903 GGCGGCTACAGAAATCGGC 61.535 63.158 0.00 0.00 39.02 5.54
311 333 1.406887 GGCTACAGAAATCGGCTTCCA 60.407 52.381 0.00 0.00 0.00 3.53
316 338 1.747355 CAGAAATCGGCTTCCATTGCT 59.253 47.619 0.00 0.00 0.00 3.91
319 341 0.753111 AATCGGCTTCCATTGCTCCC 60.753 55.000 0.00 0.00 0.00 4.30
333 355 4.323477 TCCCTGCGTTCCCGTTGG 62.323 66.667 0.00 0.00 36.15 3.77
334 356 4.323477 CCCTGCGTTCCCGTTGGA 62.323 66.667 0.00 0.00 39.54 3.53
484 506 2.579738 GTCTTGGACGCTCCTCCC 59.420 66.667 5.77 0.00 37.46 4.30
485 507 2.683933 TCTTGGACGCTCCTCCCC 60.684 66.667 5.77 0.00 37.46 4.81
486 508 2.685380 CTTGGACGCTCCTCCCCT 60.685 66.667 5.77 0.00 37.46 4.79
487 509 2.203938 TTGGACGCTCCTCCCCTT 60.204 61.111 5.77 0.00 37.46 3.95
488 510 2.245438 CTTGGACGCTCCTCCCCTTC 62.245 65.000 5.77 0.00 37.46 3.46
489 511 2.364448 GGACGCTCCTCCCCTTCT 60.364 66.667 0.00 0.00 32.53 2.85
490 512 2.428085 GGACGCTCCTCCCCTTCTC 61.428 68.421 0.00 0.00 32.53 2.87
491 513 1.682684 GACGCTCCTCCCCTTCTCA 60.683 63.158 0.00 0.00 0.00 3.27
492 514 1.002274 ACGCTCCTCCCCTTCTCAT 59.998 57.895 0.00 0.00 0.00 2.90
493 515 0.261991 ACGCTCCTCCCCTTCTCATA 59.738 55.000 0.00 0.00 0.00 2.15
494 516 1.343075 ACGCTCCTCCCCTTCTCATAA 60.343 52.381 0.00 0.00 0.00 1.90
495 517 1.069358 CGCTCCTCCCCTTCTCATAAC 59.931 57.143 0.00 0.00 0.00 1.89
496 518 1.418264 GCTCCTCCCCTTCTCATAACC 59.582 57.143 0.00 0.00 0.00 2.85
497 519 2.764269 CTCCTCCCCTTCTCATAACCA 58.236 52.381 0.00 0.00 0.00 3.67
498 520 2.436173 CTCCTCCCCTTCTCATAACCAC 59.564 54.545 0.00 0.00 0.00 4.16
499 521 1.139058 CCTCCCCTTCTCATAACCACG 59.861 57.143 0.00 0.00 0.00 4.94
500 522 0.539986 TCCCCTTCTCATAACCACGC 59.460 55.000 0.00 0.00 0.00 5.34
501 523 0.463833 CCCCTTCTCATAACCACGCC 60.464 60.000 0.00 0.00 0.00 5.68
502 524 0.251916 CCCTTCTCATAACCACGCCA 59.748 55.000 0.00 0.00 0.00 5.69
503 525 1.134098 CCCTTCTCATAACCACGCCAT 60.134 52.381 0.00 0.00 0.00 4.40
504 526 2.213499 CCTTCTCATAACCACGCCATC 58.787 52.381 0.00 0.00 0.00 3.51
505 527 2.213499 CTTCTCATAACCACGCCATCC 58.787 52.381 0.00 0.00 0.00 3.51
506 528 0.104120 TCTCATAACCACGCCATCCG 59.896 55.000 0.00 0.00 44.21 4.18
507 529 1.498865 CTCATAACCACGCCATCCGC 61.499 60.000 0.00 0.00 41.76 5.54
508 530 1.523711 CATAACCACGCCATCCGCT 60.524 57.895 0.00 0.00 41.76 5.52
509 531 1.095228 CATAACCACGCCATCCGCTT 61.095 55.000 0.00 0.00 41.76 4.68
510 532 1.095228 ATAACCACGCCATCCGCTTG 61.095 55.000 0.00 0.00 41.76 4.01
528 550 0.609151 TGCCTCCGTTTCGATTGGTA 59.391 50.000 0.00 0.00 0.00 3.25
536 558 2.350498 CGTTTCGATTGGTATGTGTCCC 59.650 50.000 0.00 0.00 0.00 4.46
612 638 8.333186 GTTTTATCTACGAACACAACAAGAAGT 58.667 33.333 0.00 0.00 0.00 3.01
655 684 4.703897 TCAACATCGTTCTTCTTGTTCCT 58.296 39.130 0.00 0.00 30.23 3.36
674 703 5.628797 TCCTATGGATGCATACAAGTCAA 57.371 39.130 17.35 0.00 0.00 3.18
675 704 5.614308 TCCTATGGATGCATACAAGTCAAG 58.386 41.667 17.35 8.43 0.00 3.02
676 705 5.366477 TCCTATGGATGCATACAAGTCAAGA 59.634 40.000 17.35 4.61 0.00 3.02
677 706 5.699915 CCTATGGATGCATACAAGTCAAGAG 59.300 44.000 17.35 4.84 0.00 2.85
678 707 4.824479 TGGATGCATACAAGTCAAGAGA 57.176 40.909 9.85 0.00 0.00 3.10
679 708 5.363562 TGGATGCATACAAGTCAAGAGAT 57.636 39.130 9.85 0.00 0.00 2.75
680 709 6.484364 TGGATGCATACAAGTCAAGAGATA 57.516 37.500 9.85 0.00 0.00 1.98
681 710 7.071069 TGGATGCATACAAGTCAAGAGATAT 57.929 36.000 9.85 0.00 0.00 1.63
682 711 7.512130 TGGATGCATACAAGTCAAGAGATATT 58.488 34.615 9.85 0.00 0.00 1.28
683 712 7.443272 TGGATGCATACAAGTCAAGAGATATTG 59.557 37.037 9.85 0.00 32.59 1.90
707 745 3.055530 TGTTTCTTGCACCAACCACAAAT 60.056 39.130 0.00 0.00 0.00 2.32
708 746 2.886862 TCTTGCACCAACCACAAATG 57.113 45.000 0.00 0.00 0.00 2.32
710 748 2.499289 TCTTGCACCAACCACAAATGTT 59.501 40.909 0.00 0.00 0.00 2.71
769 825 1.559368 CCAATCATGGGCCACTTTGA 58.441 50.000 20.53 16.28 43.51 2.69
793 849 0.532573 TCTGCTTCCACGTCCTCATC 59.467 55.000 0.00 0.00 0.00 2.92
798 858 2.223618 GCTTCCACGTCCTCATCTACTC 60.224 54.545 0.00 0.00 0.00 2.59
801 861 2.025226 TCCACGTCCTCATCTACTCCTT 60.025 50.000 0.00 0.00 0.00 3.36
803 863 3.283751 CACGTCCTCATCTACTCCTTCT 58.716 50.000 0.00 0.00 0.00 2.85
804 864 4.452825 CACGTCCTCATCTACTCCTTCTA 58.547 47.826 0.00 0.00 0.00 2.10
805 865 4.273969 CACGTCCTCATCTACTCCTTCTAC 59.726 50.000 0.00 0.00 0.00 2.59
806 866 4.164604 ACGTCCTCATCTACTCCTTCTACT 59.835 45.833 0.00 0.00 0.00 2.57
807 867 5.127491 CGTCCTCATCTACTCCTTCTACTT 58.873 45.833 0.00 0.00 0.00 2.24
808 868 5.008217 CGTCCTCATCTACTCCTTCTACTTG 59.992 48.000 0.00 0.00 0.00 3.16
833 893 3.196939 AGCCTTCATCTCTTCATGAGC 57.803 47.619 0.00 0.00 42.38 4.26
866 927 1.263217 CAGCCAAACTGTTCCACGTAC 59.737 52.381 0.00 0.00 41.86 3.67
936 1001 2.668279 GCATTCGCTTCAAATCCAACGT 60.668 45.455 0.00 0.00 34.30 3.99
946 1011 2.679837 CAAATCCAACGTCATCTCCTGG 59.320 50.000 0.00 0.00 0.00 4.45
974 1039 1.617018 CCCATCCGTGAAGCTCCTCA 61.617 60.000 0.00 0.00 0.00 3.86
981 1046 0.877743 GTGAAGCTCCTCAACCAAGC 59.122 55.000 0.00 0.00 36.27 4.01
983 1048 1.977854 TGAAGCTCCTCAACCAAGCTA 59.022 47.619 0.00 0.00 45.33 3.32
985 1050 2.777832 AGCTCCTCAACCAAGCTAAG 57.222 50.000 0.00 0.00 44.28 2.18
986 1051 2.260822 AGCTCCTCAACCAAGCTAAGA 58.739 47.619 0.00 0.00 44.28 2.10
992 1064 1.068474 CAACCAAGCTAAGACGACGG 58.932 55.000 0.00 0.00 0.00 4.79
1298 1370 1.959226 TCGCCAGCGACCTCAAAAC 60.959 57.895 11.27 0.00 44.01 2.43
1656 1740 2.596631 AACTGGCTGCAGGTGCTG 60.597 61.111 17.12 3.93 42.66 4.41
1700 1784 4.803426 GGTGACGCGGCTCTGGAG 62.803 72.222 15.80 0.00 0.00 3.86
1803 1887 1.449246 CTTCCTGCTGGAGAAGGCG 60.449 63.158 12.54 0.00 44.24 5.52
1839 1923 2.357881 TCCGTCTGCAAGCTGCTG 60.358 61.111 1.35 8.61 45.31 4.41
1842 1926 2.389020 CGTCTGCAAGCTGCTGGAG 61.389 63.158 8.57 10.78 45.31 3.86
1932 2016 4.147449 TCGCAGTGCATCGAGGGG 62.147 66.667 16.83 0.00 0.00 4.79
2022 2106 3.260483 GAGCAGCTCATCGGCGTG 61.260 66.667 18.17 4.88 40.93 5.34
2269 2353 3.390521 CCCTGCTCTACACCGGCA 61.391 66.667 0.00 0.00 34.66 5.69
2391 2478 2.703416 CACATACTCAAGAAGCTGGCA 58.297 47.619 0.00 0.00 0.00 4.92
2424 2511 2.438254 TGCGGCAAGATCGGCAAT 60.438 55.556 0.00 0.00 38.95 3.56
2469 2556 2.308039 GGAGTTCACGCACGTGTCC 61.308 63.158 21.28 17.02 45.55 4.02
2472 2559 4.612412 TTCACGCACGTGTCCCCC 62.612 66.667 21.28 0.00 45.55 5.40
3075 3174 5.138276 AGTATTTCTGCGTGATCCTACCTA 58.862 41.667 0.00 0.00 0.00 3.08
3076 3175 5.597182 AGTATTTCTGCGTGATCCTACCTAA 59.403 40.000 0.00 0.00 0.00 2.69
3077 3176 3.795623 TTCTGCGTGATCCTACCTAAC 57.204 47.619 0.00 0.00 0.00 2.34
3078 3177 2.029623 TCTGCGTGATCCTACCTAACC 58.970 52.381 0.00 0.00 0.00 2.85
3079 3178 2.032620 CTGCGTGATCCTACCTAACCT 58.967 52.381 0.00 0.00 0.00 3.50
3117 3216 8.876790 GCACAATCTTAAACCGTACTTACTTAT 58.123 33.333 0.00 0.00 0.00 1.73
3246 3355 1.354040 GACACAGATCTGCAGGTTCG 58.646 55.000 22.83 4.33 0.00 3.95
3252 3361 0.109272 GATCTGCAGGTTCGTCGACA 60.109 55.000 17.16 0.00 0.00 4.35
3394 3503 1.855213 TTCGTGGTGCAGCAGATTGC 61.855 55.000 20.85 6.08 45.46 3.56
3424 3533 4.778415 GAGCTCAACTCGCCGCGA 62.778 66.667 15.90 15.90 35.18 5.87
3425 3534 4.135153 AGCTCAACTCGCCGCGAT 62.135 61.111 17.22 0.00 34.61 4.58
3443 3558 3.670377 GGCGGTGGCTTTGTGGAC 61.670 66.667 0.00 0.00 39.81 4.02
3626 3741 4.996434 GACGCTGCTGGTGCTGGT 62.996 66.667 0.00 0.00 40.48 4.00
3645 3760 1.188219 TGCTGGAGGAGAAAGCGTCT 61.188 55.000 0.00 0.00 39.88 4.18
3658 3773 2.100605 AGCGTCTCCTGAATCAAACC 57.899 50.000 0.00 0.00 0.00 3.27
3669 3784 4.543692 CTGAATCAAACCAAAGACTGCAG 58.456 43.478 13.48 13.48 0.00 4.41
3699 3820 2.169352 CGAAGTGGGAGGAGTGAATCAT 59.831 50.000 0.00 0.00 0.00 2.45
3702 3823 3.184628 AGTGGGAGGAGTGAATCATGAA 58.815 45.455 0.00 0.00 0.00 2.57
3717 3838 9.669353 GTGAATCATGAAATGCGATTAGTTAAT 57.331 29.630 0.00 0.00 46.21 1.40
3739 3860 3.822735 TGGAGTTGAGCATTCTTTTCCTG 59.177 43.478 0.00 0.00 0.00 3.86
3747 3868 8.560374 GTTGAGCATTCTTTTCCTGGTATATAC 58.440 37.037 4.14 4.14 0.00 1.47
3756 3877 6.553953 TTTCCTGGTATATACTGCAAGACA 57.446 37.500 12.54 0.00 37.43 3.41
3757 3878 5.531122 TCCTGGTATATACTGCAAGACAC 57.469 43.478 12.54 0.00 37.43 3.67
3758 3879 4.959839 TCCTGGTATATACTGCAAGACACA 59.040 41.667 12.54 0.00 37.43 3.72
3762 3883 7.372451 TGGTATATACTGCAAGACACAAAAC 57.628 36.000 12.54 0.00 37.43 2.43
3763 3884 7.165485 TGGTATATACTGCAAGACACAAAACT 58.835 34.615 12.54 0.00 37.43 2.66
3764 3885 8.315482 TGGTATATACTGCAAGACACAAAACTA 58.685 33.333 12.54 0.00 37.43 2.24
3821 3948 6.166279 TGGTCAATGTGATTAGAGAGTTCAC 58.834 40.000 0.00 0.00 40.10 3.18
3822 3949 6.014242 TGGTCAATGTGATTAGAGAGTTCACT 60.014 38.462 4.19 0.00 40.29 3.41
3826 3953 4.560128 TGTGATTAGAGAGTTCACTGTGC 58.440 43.478 2.12 0.00 40.29 4.57
3839 3966 5.359576 AGTTCACTGTGCATAGTTCCAAAAA 59.640 36.000 14.10 0.00 0.00 1.94
3840 3967 6.040842 AGTTCACTGTGCATAGTTCCAAAAAT 59.959 34.615 14.10 0.74 0.00 1.82
3841 3968 7.230510 AGTTCACTGTGCATAGTTCCAAAAATA 59.769 33.333 14.10 0.00 0.00 1.40
3843 3970 6.150976 TCACTGTGCATAGTTCCAAAAATAGG 59.849 38.462 14.10 0.00 0.00 2.57
3844 3971 6.150976 CACTGTGCATAGTTCCAAAAATAGGA 59.849 38.462 14.10 0.00 0.00 2.94
3845 3972 6.891908 ACTGTGCATAGTTCCAAAAATAGGAT 59.108 34.615 10.73 0.00 34.56 3.24
3846 3973 7.099266 TGTGCATAGTTCCAAAAATAGGATG 57.901 36.000 0.00 0.00 34.56 3.51
3848 3975 6.096846 GTGCATAGTTCCAAAAATAGGATGGT 59.903 38.462 0.00 0.00 34.56 3.55
3849 3976 6.096705 TGCATAGTTCCAAAAATAGGATGGTG 59.903 38.462 0.00 0.00 34.56 4.17
3850 3977 6.096846 GCATAGTTCCAAAAATAGGATGGTGT 59.903 38.462 0.00 0.00 34.56 4.16
3851 3978 7.284489 GCATAGTTCCAAAAATAGGATGGTGTA 59.716 37.037 0.00 0.00 34.56 2.90
3852 3979 9.354673 CATAGTTCCAAAAATAGGATGGTGTAT 57.645 33.333 0.00 0.00 34.56 2.29
3884 4011 9.188588 ACGTATATATAGTTCCAAAACATGACG 57.811 33.333 0.00 0.00 37.88 4.35
3885 4012 8.160342 CGTATATATAGTTCCAAAACATGACGC 58.840 37.037 0.00 0.00 37.88 5.19
3886 4013 8.984764 GTATATATAGTTCCAAAACATGACGCA 58.015 33.333 0.00 0.00 37.88 5.24
3887 4014 4.685169 ATAGTTCCAAAACATGACGCAG 57.315 40.909 0.00 0.00 37.88 5.18
3888 4015 2.571212 AGTTCCAAAACATGACGCAGA 58.429 42.857 0.00 0.00 37.88 4.26
3889 4016 2.948979 AGTTCCAAAACATGACGCAGAA 59.051 40.909 0.00 0.00 37.88 3.02
3890 4017 3.380004 AGTTCCAAAACATGACGCAGAAA 59.620 39.130 0.00 0.00 37.88 2.52
3891 4018 4.109050 GTTCCAAAACATGACGCAGAAAA 58.891 39.130 0.00 0.00 35.36 2.29
3920 4068 4.641094 AGACCGAACAGATTAGGAGTACAG 59.359 45.833 0.00 0.00 34.78 2.74
3926 4074 7.140048 CGAACAGATTAGGAGTACAGGATTAC 58.860 42.308 0.00 0.00 0.00 1.89
3941 4089 2.683362 GGATTACAGCCTGGTTAACAGC 59.317 50.000 8.10 7.14 46.14 4.40
3978 4126 8.848474 AGATCCTATCCATGTTTTATTTACCG 57.152 34.615 0.00 0.00 0.00 4.02
3979 4127 8.656806 AGATCCTATCCATGTTTTATTTACCGA 58.343 33.333 0.00 0.00 0.00 4.69
3989 4137 5.008415 TGTTTTATTTACCGACTTTCCGCAA 59.992 36.000 0.00 0.00 0.00 4.85
3990 4138 4.666928 TTATTTACCGACTTTCCGCAAC 57.333 40.909 0.00 0.00 0.00 4.17
4016 4164 3.490348 GATCGGGGAAATTCATCCACAT 58.510 45.455 0.00 0.00 43.53 3.21
4033 4181 3.124636 CCACATAACTTCGAGAAAACGGG 59.875 47.826 0.00 0.00 0.00 5.28
4034 4182 2.740447 ACATAACTTCGAGAAAACGGGC 59.260 45.455 0.00 0.00 0.00 6.13
4040 4188 1.741770 CGAGAAAACGGGCTCTGGG 60.742 63.158 0.00 0.00 0.00 4.45
4055 4203 5.006386 GGCTCTGGGACCTAATCATTATTG 58.994 45.833 0.00 0.00 0.00 1.90
4057 4205 6.064717 GCTCTGGGACCTAATCATTATTGTT 58.935 40.000 0.00 0.00 0.00 2.83
4058 4206 6.547510 GCTCTGGGACCTAATCATTATTGTTT 59.452 38.462 0.00 0.00 0.00 2.83
4059 4207 7.068716 GCTCTGGGACCTAATCATTATTGTTTT 59.931 37.037 0.00 0.00 0.00 2.43
4060 4208 8.519799 TCTGGGACCTAATCATTATTGTTTTC 57.480 34.615 0.00 0.00 0.00 2.29
4061 4209 8.112822 TCTGGGACCTAATCATTATTGTTTTCA 58.887 33.333 0.00 0.00 0.00 2.69
4062 4210 8.062065 TGGGACCTAATCATTATTGTTTTCAC 57.938 34.615 0.00 0.00 0.00 3.18
4064 4212 7.193595 GGACCTAATCATTATTGTTTTCACGG 58.806 38.462 0.00 0.00 0.00 4.94
4068 4216 9.418045 CCTAATCATTATTGTTTTCACGGTTTT 57.582 29.630 0.00 0.00 0.00 2.43
4071 4219 7.839438 TCATTATTGTTTTCACGGTTTTACG 57.161 32.000 0.00 0.00 40.31 3.18
4072 4220 7.637229 TCATTATTGTTTTCACGGTTTTACGA 58.363 30.769 0.00 0.00 37.61 3.43
4073 4221 7.587028 TCATTATTGTTTTCACGGTTTTACGAC 59.413 33.333 0.00 0.00 37.61 4.34
4074 4222 3.672028 TGTTTTCACGGTTTTACGACC 57.328 42.857 0.00 0.00 37.61 4.79
4075 4223 3.269178 TGTTTTCACGGTTTTACGACCT 58.731 40.909 0.00 0.00 37.56 3.85
4076 4224 3.063725 TGTTTTCACGGTTTTACGACCTG 59.936 43.478 0.00 0.00 37.56 4.00
4077 4225 2.886862 TTCACGGTTTTACGACCTGA 57.113 45.000 0.00 0.00 37.56 3.86
4078 4226 2.427232 TCACGGTTTTACGACCTGAG 57.573 50.000 0.00 0.00 37.56 3.35
4098 4246 5.868454 TGAGAAGTTCATCCAAATGACTCA 58.132 37.500 5.50 0.00 41.62 3.41
4196 4348 2.867109 TGAAGCCTTCTCCCTTGAAG 57.133 50.000 5.96 0.00 42.10 3.02
4394 4557 0.473694 TGGCTCCAGGAAGTCCTTCA 60.474 55.000 9.12 0.00 46.09 3.02
4424 4587 2.745698 CAGCCACAGCCAGAGTCA 59.254 61.111 0.00 0.00 41.25 3.41
4439 4602 3.828451 CAGAGTCAAATTTGGTGGTGGAT 59.172 43.478 17.90 0.00 0.00 3.41
4526 4689 2.114411 GTTCCCGGCAACCTGGAA 59.886 61.111 0.00 5.50 43.02 3.53
4527 4690 1.304134 GTTCCCGGCAACCTGGAAT 60.304 57.895 11.97 0.00 45.86 3.01
4538 4701 2.821378 CAACCTGGAATGCAATGTGAGA 59.179 45.455 0.00 0.00 0.00 3.27
4553 4742 6.626623 GCAATGTGAGATTAGTTTGAAGGCAT 60.627 38.462 0.00 0.00 0.00 4.40
4603 4793 5.067153 CAGGTACAAACAAAGGTTGTCATGA 59.933 40.000 3.38 0.00 44.59 3.07
4606 4796 5.850557 ACAAACAAAGGTTGTCATGATGA 57.149 34.783 0.00 0.00 44.59 2.92
4640 4830 2.275466 AGCTCCCTTTGGGCTAACTTA 58.725 47.619 0.00 0.00 43.94 2.24
4648 4838 5.280317 CCCTTTGGGCTAACTTAGTTCAGTA 60.280 44.000 0.00 0.00 35.35 2.74
4649 4839 6.415573 CCTTTGGGCTAACTTAGTTCAGTAT 58.584 40.000 0.00 0.00 0.00 2.12
4650 4840 6.539103 CCTTTGGGCTAACTTAGTTCAGTATC 59.461 42.308 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.362355 GGTTTGAGGCCAACGGTTG 59.638 57.895 13.86 13.86 30.88 3.77
19 20 8.000780 ACTATATCTTTGATTTGGTTTGAGGC 57.999 34.615 0.00 0.00 0.00 4.70
25 26 9.753674 TGAAGGAACTATATCTTTGATTTGGTT 57.246 29.630 0.00 0.00 38.49 3.67
41 42 6.023603 AGGGAGTAAGACAATGAAGGAACTA 58.976 40.000 0.00 0.00 38.49 2.24
77 78 9.003112 CGAGTTGAAATGTTCATATGATTTGAC 57.997 33.333 6.17 2.21 39.84 3.18
78 79 8.729756 ACGAGTTGAAATGTTCATATGATTTGA 58.270 29.630 6.17 0.00 39.84 2.69
79 80 8.900511 ACGAGTTGAAATGTTCATATGATTTG 57.099 30.769 6.17 0.00 39.84 2.32
80 81 8.729756 TGACGAGTTGAAATGTTCATATGATTT 58.270 29.630 6.17 4.36 39.84 2.17
122 123 5.514204 AGATACTTGCGTACAACGTTCATAC 59.486 40.000 0.00 3.41 44.73 2.39
127 128 3.645884 ACAGATACTTGCGTACAACGTT 58.354 40.909 0.00 0.00 44.73 3.99
142 143 5.221263 GGTTGAGGCGAATTAGAGACAGATA 60.221 44.000 0.00 0.00 0.00 1.98
153 154 0.331278 TGATGGGGTTGAGGCGAATT 59.669 50.000 0.00 0.00 0.00 2.17
205 206 2.225019 CACAACTCACCAACAGATGCTC 59.775 50.000 0.00 0.00 0.00 4.26
211 212 1.095228 ACGCCACAACTCACCAACAG 61.095 55.000 0.00 0.00 0.00 3.16
217 218 2.279918 ACGGACGCCACAACTCAC 60.280 61.111 0.00 0.00 0.00 3.51
240 251 2.712539 CGTGCCAACGTGAAAGCA 59.287 55.556 0.00 0.00 44.93 3.91
250 261 3.149981 TCATCCACAAATTACGTGCCAA 58.850 40.909 0.00 0.00 32.85 4.52
253 264 3.063997 CCTCTCATCCACAAATTACGTGC 59.936 47.826 0.00 0.00 32.85 5.34
269 280 0.972983 CGCCCCTCTCTTTCCTCTCA 60.973 60.000 0.00 0.00 0.00 3.27
270 281 1.681486 CCGCCCCTCTCTTTCCTCTC 61.681 65.000 0.00 0.00 0.00 3.20
271 282 1.687493 CCGCCCCTCTCTTTCCTCT 60.687 63.158 0.00 0.00 0.00 3.69
285 296 2.513897 ATTTCTGTAGCCGCCGCC 60.514 61.111 0.00 0.00 34.57 6.13
306 328 0.962356 AACGCAGGGAGCAATGGAAG 60.962 55.000 0.00 0.00 46.13 3.46
311 333 2.044946 GGGAACGCAGGGAGCAAT 60.045 61.111 0.00 0.00 46.13 3.56
333 355 0.806492 GGGTCGATCTTCCGCTGTTC 60.806 60.000 0.00 0.00 0.00 3.18
334 356 1.218316 GGGTCGATCTTCCGCTGTT 59.782 57.895 0.00 0.00 0.00 3.16
339 361 4.587189 GCCCGGGTCGATCTTCCG 62.587 72.222 24.63 10.93 43.05 4.30
340 362 4.237207 GGCCCGGGTCGATCTTCC 62.237 72.222 24.63 8.21 0.00 3.46
391 413 2.844146 CAAACGACGGACTGCGAC 59.156 61.111 0.00 0.00 0.00 5.19
400 422 2.425124 CCGTGCAAGCAAACGACG 60.425 61.111 6.63 0.00 42.32 5.12
472 494 2.364448 AGAAGGGGAGGAGCGTCC 60.364 66.667 0.67 0.67 36.58 4.79
481 503 0.539986 GCGTGGTTATGAGAAGGGGA 59.460 55.000 0.00 0.00 0.00 4.81
482 504 0.463833 GGCGTGGTTATGAGAAGGGG 60.464 60.000 0.00 0.00 0.00 4.79
484 506 2.213499 GATGGCGTGGTTATGAGAAGG 58.787 52.381 0.00 0.00 0.00 3.46
485 507 2.213499 GGATGGCGTGGTTATGAGAAG 58.787 52.381 0.00 0.00 0.00 2.85
486 508 1.472552 CGGATGGCGTGGTTATGAGAA 60.473 52.381 0.00 0.00 0.00 2.87
487 509 0.104120 CGGATGGCGTGGTTATGAGA 59.896 55.000 0.00 0.00 0.00 3.27
488 510 1.498865 GCGGATGGCGTGGTTATGAG 61.499 60.000 0.00 0.00 0.00 2.90
489 511 1.522806 GCGGATGGCGTGGTTATGA 60.523 57.895 0.00 0.00 0.00 2.15
490 512 3.022287 GCGGATGGCGTGGTTATG 58.978 61.111 0.00 0.00 0.00 1.90
500 522 3.976701 AACGGAGGCAAGCGGATGG 62.977 63.158 0.00 0.00 0.00 3.51
501 523 1.982073 GAAACGGAGGCAAGCGGATG 61.982 60.000 0.00 0.00 0.00 3.51
502 524 1.745489 GAAACGGAGGCAAGCGGAT 60.745 57.895 0.00 0.00 0.00 4.18
503 525 2.358247 GAAACGGAGGCAAGCGGA 60.358 61.111 0.00 0.00 0.00 5.54
504 526 3.788766 CGAAACGGAGGCAAGCGG 61.789 66.667 0.00 0.00 0.00 5.52
505 527 1.635663 AATCGAAACGGAGGCAAGCG 61.636 55.000 0.00 0.00 0.00 4.68
506 528 0.179189 CAATCGAAACGGAGGCAAGC 60.179 55.000 0.00 0.00 0.00 4.01
507 529 0.447801 CCAATCGAAACGGAGGCAAG 59.552 55.000 0.00 0.00 0.00 4.01
508 530 0.250553 ACCAATCGAAACGGAGGCAA 60.251 50.000 5.24 0.00 0.00 4.52
509 531 0.609151 TACCAATCGAAACGGAGGCA 59.391 50.000 5.24 0.00 0.00 4.75
510 532 1.597663 CATACCAATCGAAACGGAGGC 59.402 52.381 5.24 0.00 0.00 4.70
556 578 1.588139 CCGGAGAATCGGTGTACGC 60.588 63.158 0.00 0.00 44.60 4.42
585 611 7.181143 TCTTGTTGTGTTCGTAGATAAAACC 57.819 36.000 0.00 0.00 35.04 3.27
612 638 4.849810 TGAGAGAGGAAGGTAAATGGGAAA 59.150 41.667 0.00 0.00 0.00 3.13
655 684 6.484364 TCTCTTGACTTGTATGCATCCATA 57.516 37.500 0.19 0.00 32.85 2.74
674 703 5.769662 TGGTGCAAGAAACAACAATATCTCT 59.230 36.000 0.00 0.00 30.09 3.10
675 704 6.012658 TGGTGCAAGAAACAACAATATCTC 57.987 37.500 0.00 0.00 30.09 2.75
676 705 6.215845 GTTGGTGCAAGAAACAACAATATCT 58.784 36.000 4.08 0.00 45.76 1.98
677 706 5.405269 GGTTGGTGCAAGAAACAACAATATC 59.595 40.000 10.91 0.00 45.76 1.63
678 707 5.163364 TGGTTGGTGCAAGAAACAACAATAT 60.163 36.000 10.91 0.00 45.76 1.28
679 708 4.160439 TGGTTGGTGCAAGAAACAACAATA 59.840 37.500 10.91 0.00 45.76 1.90
680 709 3.055530 TGGTTGGTGCAAGAAACAACAAT 60.056 39.130 10.91 0.00 45.76 2.71
681 710 2.300152 TGGTTGGTGCAAGAAACAACAA 59.700 40.909 10.91 0.00 42.24 2.83
682 711 1.895798 TGGTTGGTGCAAGAAACAACA 59.104 42.857 10.91 0.00 43.61 3.33
683 712 2.267426 GTGGTTGGTGCAAGAAACAAC 58.733 47.619 0.08 0.08 41.71 3.32
707 745 5.502079 ACGTATTATTCCATTCCACCAACA 58.498 37.500 0.00 0.00 0.00 3.33
708 746 5.008316 GGACGTATTATTCCATTCCACCAAC 59.992 44.000 0.00 0.00 0.00 3.77
710 748 4.410883 AGGACGTATTATTCCATTCCACCA 59.589 41.667 0.00 0.00 33.92 4.17
803 863 6.890268 TGAAGAGATGAAGGCTACTACAAGTA 59.110 38.462 0.00 0.00 0.00 2.24
804 864 5.717178 TGAAGAGATGAAGGCTACTACAAGT 59.283 40.000 0.00 0.00 0.00 3.16
805 865 6.214191 TGAAGAGATGAAGGCTACTACAAG 57.786 41.667 0.00 0.00 0.00 3.16
806 866 6.381133 TCATGAAGAGATGAAGGCTACTACAA 59.619 38.462 0.00 0.00 29.11 2.41
807 867 5.893824 TCATGAAGAGATGAAGGCTACTACA 59.106 40.000 0.00 0.00 29.11 2.74
808 868 6.398234 TCATGAAGAGATGAAGGCTACTAC 57.602 41.667 0.00 0.00 29.11 2.73
833 893 3.414700 GGCTGCGTCAACGGTCAG 61.415 66.667 4.54 5.39 40.23 3.51
866 927 0.453950 CTTCCACAGGTCGACGTACG 60.454 60.000 15.01 15.01 44.09 3.67
936 1001 1.617536 AAGCCAGGCCAGGAGATGA 60.618 57.895 20.27 0.00 0.00 2.92
946 1011 4.115199 ACGGATGGGAAGCCAGGC 62.115 66.667 1.84 1.84 0.00 4.85
974 1039 0.669625 GCCGTCGTCTTAGCTTGGTT 60.670 55.000 0.00 0.00 0.00 3.67
981 1046 2.879462 GTGCCGCCGTCGTCTTAG 60.879 66.667 0.00 0.00 0.00 2.18
982 1047 4.424566 GGTGCCGCCGTCGTCTTA 62.425 66.667 0.00 0.00 0.00 2.10
992 1064 0.169009 GTTCTTCTTCATGGTGCCGC 59.831 55.000 0.00 0.00 0.00 6.53
997 1069 0.322546 GGCGGGTTCTTCTTCATGGT 60.323 55.000 0.00 0.00 0.00 3.55
1298 1370 1.293924 GATGCACCAGAAGTCGATGG 58.706 55.000 1.14 1.14 42.60 3.51
1524 1608 2.125512 ACGATCTGCCGCTGGAAC 60.126 61.111 0.00 0.00 0.00 3.62
1533 1617 1.890979 CATCAGGGCCACGATCTGC 60.891 63.158 6.18 0.00 0.00 4.26
1608 1692 1.993370 CCGATCTTCTTGGACACGAAC 59.007 52.381 0.00 0.00 0.00 3.95
1710 1794 2.435234 TTGGCCCCGTCGAAATCG 60.435 61.111 0.00 0.00 41.45 3.34
1721 1805 4.133796 GCCGCATGTTCTTGGCCC 62.134 66.667 0.00 0.00 41.70 5.80
1747 1831 2.161486 CCAGCGCGTAGAAGAGCAC 61.161 63.158 8.43 0.00 39.42 4.40
1803 1887 2.416972 GGACATCTTCCACGTCCAGTAC 60.417 54.545 2.98 0.00 46.98 2.73
1929 2013 2.107141 CCGTCGAAGATGCTCCCC 59.893 66.667 0.00 0.00 43.31 4.81
1932 2016 0.528466 TGATGCCGTCGAAGATGCTC 60.528 55.000 0.00 0.00 43.31 4.26
2391 2478 0.606401 CGCAGTTGTCATGGTCCCTT 60.606 55.000 0.00 0.00 0.00 3.95
2469 2556 1.298014 GTTGAGGAGCAGAGTGGGG 59.702 63.158 0.00 0.00 0.00 4.96
2472 2559 1.079543 CGGGTTGAGGAGCAGAGTG 60.080 63.158 0.00 0.00 0.00 3.51
2505 2592 4.680237 TTCACGGAGCGCACCTGG 62.680 66.667 21.78 13.13 0.00 4.45
2862 2949 3.991536 GAGCACGTCGGCCCTCTTC 62.992 68.421 0.00 0.00 0.00 2.87
2922 3009 1.296392 CACCCTCATGGCGTTGAGA 59.704 57.895 16.30 0.00 44.88 3.27
3025 3115 6.743575 ATAACATGACCAAGCAAGTAAGAC 57.256 37.500 0.00 0.00 0.00 3.01
3034 3124 9.765795 AGAAATACTAGTATAACATGACCAAGC 57.234 33.333 15.74 0.00 0.00 4.01
3091 3190 6.716898 AGTAAGTACGGTTTAAGATTGTGC 57.283 37.500 0.00 0.00 0.00 4.57
3117 3216 4.405548 TGTCATCCACATGTCATTTCCAA 58.594 39.130 0.00 0.00 0.00 3.53
3119 3218 4.095483 GTCTGTCATCCACATGTCATTTCC 59.905 45.833 0.00 0.00 33.23 3.13
3122 3227 4.005650 GTGTCTGTCATCCACATGTCATT 58.994 43.478 0.00 0.00 33.23 2.57
3224 3333 0.037882 ACCTGCAGATCTGTGTCGTG 60.038 55.000 23.38 9.34 0.00 4.35
3252 3361 1.736645 CGGCGGTGAACTGTTCGAT 60.737 57.895 15.18 0.00 0.00 3.59
3257 3366 3.616721 AGCTCGGCGGTGAACTGT 61.617 61.111 7.21 0.00 0.00 3.55
3424 3533 2.990967 CCACAAAGCCACCGCCAT 60.991 61.111 0.00 0.00 34.57 4.40
3425 3534 4.196778 TCCACAAAGCCACCGCCA 62.197 61.111 0.00 0.00 34.57 5.69
3431 3546 0.823356 GGAGCAAGTCCACAAAGCCA 60.823 55.000 0.00 0.00 46.10 4.75
3606 3721 2.667536 AGCACCAGCAGCGTCTTG 60.668 61.111 0.00 0.00 45.49 3.02
3626 3741 1.188219 AGACGCTTTCTCCTCCAGCA 61.188 55.000 0.00 0.00 32.71 4.41
3627 3742 0.459411 GAGACGCTTTCTCCTCCAGC 60.459 60.000 1.56 0.00 44.74 4.85
3628 3743 3.731295 GAGACGCTTTCTCCTCCAG 57.269 57.895 1.56 0.00 44.74 3.86
3645 3760 3.569701 GCAGTCTTTGGTTTGATTCAGGA 59.430 43.478 0.00 0.00 0.00 3.86
3646 3761 3.318839 TGCAGTCTTTGGTTTGATTCAGG 59.681 43.478 0.00 0.00 0.00 3.86
3658 3773 0.510359 GAGCGTCACTGCAGTCTTTG 59.490 55.000 18.64 5.99 37.31 2.77
3669 3784 2.432628 CCCACTTCGGAGCGTCAC 60.433 66.667 0.00 0.00 36.56 3.67
3691 3812 9.669353 ATTAACTAATCGCATTTCATGATTCAC 57.331 29.630 0.00 0.00 34.40 3.18
3699 3820 7.335673 TCAACTCCATTAACTAATCGCATTTCA 59.664 33.333 0.00 0.00 0.00 2.69
3702 3823 6.238484 GCTCAACTCCATTAACTAATCGCATT 60.238 38.462 0.00 0.00 0.00 3.56
3717 3838 3.822735 CAGGAAAAGAATGCTCAACTCCA 59.177 43.478 0.00 0.00 0.00 3.86
3739 3860 7.611213 AGTTTTGTGTCTTGCAGTATATACC 57.389 36.000 9.32 0.00 0.00 2.73
3821 3948 6.757897 TCCTATTTTTGGAACTATGCACAG 57.242 37.500 0.00 0.00 0.00 3.66
3822 3949 6.096705 CCATCCTATTTTTGGAACTATGCACA 59.903 38.462 0.00 0.00 37.13 4.57
3826 3953 7.645058 ACACCATCCTATTTTTGGAACTATG 57.355 36.000 0.00 0.00 37.13 2.23
3858 3985 9.188588 CGTCATGTTTTGGAACTATATATACGT 57.811 33.333 0.00 0.00 36.70 3.57
3859 3986 8.160342 GCGTCATGTTTTGGAACTATATATACG 58.840 37.037 0.00 0.00 36.70 3.06
3860 3987 8.984764 TGCGTCATGTTTTGGAACTATATATAC 58.015 33.333 0.00 0.00 36.70 1.47
3861 3988 9.203421 CTGCGTCATGTTTTGGAACTATATATA 57.797 33.333 0.00 0.00 36.70 0.86
3862 3989 7.931407 TCTGCGTCATGTTTTGGAACTATATAT 59.069 33.333 0.00 0.00 36.70 0.86
3863 3990 7.269316 TCTGCGTCATGTTTTGGAACTATATA 58.731 34.615 0.00 0.00 36.70 0.86
3864 3991 6.112734 TCTGCGTCATGTTTTGGAACTATAT 58.887 36.000 0.00 0.00 36.70 0.86
3865 3992 5.483811 TCTGCGTCATGTTTTGGAACTATA 58.516 37.500 0.00 0.00 36.70 1.31
3866 3993 4.323417 TCTGCGTCATGTTTTGGAACTAT 58.677 39.130 0.00 0.00 36.70 2.12
3867 3994 3.734463 TCTGCGTCATGTTTTGGAACTA 58.266 40.909 0.00 0.00 36.70 2.24
3868 3995 2.571212 TCTGCGTCATGTTTTGGAACT 58.429 42.857 0.00 0.00 36.70 3.01
3869 3996 3.347958 TTCTGCGTCATGTTTTGGAAC 57.652 42.857 0.00 0.00 36.29 3.62
3870 3997 4.109050 GTTTTCTGCGTCATGTTTTGGAA 58.891 39.130 0.00 0.00 0.00 3.53
3871 3998 3.380004 AGTTTTCTGCGTCATGTTTTGGA 59.620 39.130 0.00 0.00 0.00 3.53
3872 3999 3.705604 AGTTTTCTGCGTCATGTTTTGG 58.294 40.909 0.00 0.00 0.00 3.28
3873 4000 5.288232 TGAAAGTTTTCTGCGTCATGTTTTG 59.712 36.000 6.21 0.00 38.02 2.44
3874 4001 5.406649 TGAAAGTTTTCTGCGTCATGTTTT 58.593 33.333 6.21 0.00 38.02 2.43
3875 4002 4.992688 TGAAAGTTTTCTGCGTCATGTTT 58.007 34.783 6.21 0.00 38.02 2.83
3876 4003 4.335315 TCTGAAAGTTTTCTGCGTCATGTT 59.665 37.500 6.21 0.00 38.02 2.71
3877 4004 3.876914 TCTGAAAGTTTTCTGCGTCATGT 59.123 39.130 6.21 0.00 38.02 3.21
3878 4005 4.214437 GTCTGAAAGTTTTCTGCGTCATG 58.786 43.478 6.21 0.00 38.02 3.07
3879 4006 3.251004 GGTCTGAAAGTTTTCTGCGTCAT 59.749 43.478 6.21 0.00 38.02 3.06
3880 4007 2.612212 GGTCTGAAAGTTTTCTGCGTCA 59.388 45.455 6.21 0.00 38.02 4.35
3881 4008 2.348591 CGGTCTGAAAGTTTTCTGCGTC 60.349 50.000 6.21 1.44 38.02 5.19
3882 4009 1.597663 CGGTCTGAAAGTTTTCTGCGT 59.402 47.619 6.21 0.00 38.02 5.24
3883 4010 1.864711 TCGGTCTGAAAGTTTTCTGCG 59.135 47.619 6.21 5.91 38.02 5.18
3884 4011 3.064820 TGTTCGGTCTGAAAGTTTTCTGC 59.935 43.478 6.21 3.02 38.60 4.26
3885 4012 4.570772 TCTGTTCGGTCTGAAAGTTTTCTG 59.429 41.667 6.21 5.81 38.60 3.02
3886 4013 4.766375 TCTGTTCGGTCTGAAAGTTTTCT 58.234 39.130 6.21 0.00 38.60 2.52
3887 4014 5.674933 ATCTGTTCGGTCTGAAAGTTTTC 57.325 39.130 0.00 0.00 38.60 2.29
3888 4015 6.204882 CCTAATCTGTTCGGTCTGAAAGTTTT 59.795 38.462 0.00 0.00 38.60 2.43
3889 4016 5.701290 CCTAATCTGTTCGGTCTGAAAGTTT 59.299 40.000 0.00 0.00 38.60 2.66
3890 4017 5.011738 TCCTAATCTGTTCGGTCTGAAAGTT 59.988 40.000 0.00 0.00 38.60 2.66
3891 4018 4.527038 TCCTAATCTGTTCGGTCTGAAAGT 59.473 41.667 0.00 0.00 38.60 2.66
3920 4068 2.683362 GCTGTTAACCAGGCTGTAATCC 59.317 50.000 14.43 0.00 41.81 3.01
3926 4074 1.896220 TTCTGCTGTTAACCAGGCTG 58.104 50.000 7.75 7.75 41.81 4.85
3941 4089 5.188434 TGGATAGGATCTTGCAAGTTTCTG 58.812 41.667 25.19 0.15 0.00 3.02
3989 4137 1.557832 TGAATTTCCCCGATCCGAAGT 59.442 47.619 0.00 0.00 0.00 3.01
3990 4138 2.325583 TGAATTTCCCCGATCCGAAG 57.674 50.000 0.00 0.00 0.00 3.79
3999 4147 5.221048 CGAAGTTATGTGGATGAATTTCCCC 60.221 44.000 0.00 0.00 34.67 4.81
4016 4164 2.298163 AGAGCCCGTTTTCTCGAAGTTA 59.702 45.455 0.00 0.00 34.66 2.24
4033 4181 5.625150 ACAATAATGATTAGGTCCCAGAGC 58.375 41.667 0.00 0.00 0.00 4.09
4034 4182 8.525290 AAAACAATAATGATTAGGTCCCAGAG 57.475 34.615 0.00 0.00 0.00 3.35
4040 4188 7.758495 ACCGTGAAAACAATAATGATTAGGTC 58.242 34.615 0.00 0.00 0.00 3.85
4055 4203 3.309410 TCAGGTCGTAAAACCGTGAAAAC 59.691 43.478 0.00 0.00 44.49 2.43
4057 4205 3.125316 CTCAGGTCGTAAAACCGTGAAA 58.875 45.455 0.00 0.00 44.49 2.69
4058 4206 2.361757 TCTCAGGTCGTAAAACCGTGAA 59.638 45.455 0.00 0.00 44.49 3.18
4059 4207 1.955778 TCTCAGGTCGTAAAACCGTGA 59.044 47.619 0.00 0.00 44.49 4.35
4060 4208 2.427232 TCTCAGGTCGTAAAACCGTG 57.573 50.000 0.00 0.00 44.49 4.94
4061 4209 2.363359 ACTTCTCAGGTCGTAAAACCGT 59.637 45.455 0.00 0.00 44.49 4.83
4062 4210 3.022607 ACTTCTCAGGTCGTAAAACCG 57.977 47.619 0.00 0.00 44.49 4.44
4064 4212 5.120363 GGATGAACTTCTCAGGTCGTAAAAC 59.880 44.000 0.00 0.00 40.03 2.43
4068 4216 3.427573 TGGATGAACTTCTCAGGTCGTA 58.572 45.455 0.00 0.00 40.03 3.43
4071 4219 5.123027 GTCATTTGGATGAACTTCTCAGGTC 59.877 44.000 0.00 0.00 43.58 3.85
4072 4220 5.006386 GTCATTTGGATGAACTTCTCAGGT 58.994 41.667 0.00 0.00 43.58 4.00
4073 4221 5.251764 AGTCATTTGGATGAACTTCTCAGG 58.748 41.667 0.00 0.00 43.58 3.86
4074 4222 5.936372 TGAGTCATTTGGATGAACTTCTCAG 59.064 40.000 0.00 0.00 43.58 3.35
4075 4223 5.868454 TGAGTCATTTGGATGAACTTCTCA 58.132 37.500 0.00 4.35 43.58 3.27
4076 4224 6.652481 TCTTGAGTCATTTGGATGAACTTCTC 59.348 38.462 0.00 0.00 43.58 2.87
4077 4225 6.537355 TCTTGAGTCATTTGGATGAACTTCT 58.463 36.000 0.00 0.00 43.58 2.85
4078 4226 6.808008 TCTTGAGTCATTTGGATGAACTTC 57.192 37.500 0.00 0.00 43.58 3.01
4098 4246 2.843113 CCTCCTCCTGAATCCAGTTCTT 59.157 50.000 0.00 0.00 38.74 2.52
4226 4378 3.697190 AGGAGGGTAGAGATCACATGT 57.303 47.619 0.00 0.00 0.00 3.21
4418 4581 3.593442 TCCACCACCAAATTTGACTCT 57.407 42.857 19.86 0.00 0.00 3.24
4424 4587 5.221621 CCTGTACAAATCCACCACCAAATTT 60.222 40.000 0.00 0.00 0.00 1.82
4439 4602 4.804806 GGAACGCCCCTGTACAAA 57.195 55.556 0.00 0.00 0.00 2.83
4469 4632 1.813753 CGGTGATGGGGCGTACAAG 60.814 63.158 0.00 0.00 0.00 3.16
4481 4644 5.464030 AGTACAACAAGTTCTACGGTGAT 57.536 39.130 0.00 0.00 0.00 3.06
4526 4689 6.626623 GCCTTCAAACTAATCTCACATTGCAT 60.627 38.462 0.00 0.00 0.00 3.96
4527 4690 5.335897 GCCTTCAAACTAATCTCACATTGCA 60.336 40.000 0.00 0.00 0.00 4.08
4538 4701 8.125978 TCTGAAAATGATGCCTTCAAACTAAT 57.874 30.769 0.00 0.00 38.03 1.73
4573 4762 3.199677 CCTTTGTTTGTACCTGACGTGA 58.800 45.455 0.00 0.00 0.00 4.35
4606 4796 7.415646 CCAAAGGGAGCTAAACTCTGAAGTTT 61.416 42.308 8.45 8.45 46.25 2.66


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

AutoCloner maintained by Alex Coulton.