Multiple sequence alignment - TraesCS1B01G455700

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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 TraesCS1B01G455700 chr1B 100.000 2762 0 0 1 2762 670716318 670713557 0.000000e+00 5101.0
1 TraesCS1B01G455700 chr1B 91.484 411 31 2 124 530 683745910 683745500 1.860000e-156 562.0
2 TraesCS1B01G455700 chr1B 94.611 167 7 2 944 1109 683693643 683693478 9.810000e-65 257.0
3 TraesCS1B01G455700 chr1B 89.175 194 8 4 749 934 683738537 683738349 2.140000e-56 230.0
4 TraesCS1B01G455700 chr1B 86.861 137 14 2 572 704 683739023 683738887 1.710000e-32 150.0
5 TraesCS1B01G455700 chr1B 90.476 42 4 0 511 552 597271641 597271682 3.840000e-04 56.5
6 TraesCS1B01G455700 chr1D 92.939 1048 45 10 725 1764 482209831 482208805 0.000000e+00 1498.0
7 TraesCS1B01G455700 chr1D 93.682 554 28 4 1770 2322 482208750 482208203 0.000000e+00 822.0
8 TraesCS1B01G455700 chr1D 91.629 442 27 9 2322 2762 482208243 482207811 1.090000e-168 603.0
9 TraesCS1B01G455700 chr1D 100.000 43 0 0 2107 2149 482207910 482207868 2.280000e-11 80.5
10 TraesCS1B01G455700 chr1D 90.000 40 4 0 2655 2694 482206201 482206162 5.000000e-03 52.8
11 TraesCS1B01G455700 chr1A 90.304 1052 66 13 721 1762 578912428 578911403 0.000000e+00 1345.0
12 TraesCS1B01G455700 chr1A 84.634 410 59 4 251 659 578913014 578912608 3.310000e-109 405.0
13 TraesCS1B01G455700 chr3A 71.850 508 101 36 71 557 23893016 23892530 1.050000e-19 108.0
14 TraesCS1B01G455700 chr3A 71.513 509 107 30 71 557 23880721 23880229 4.870000e-18 102.0
15 TraesCS1B01G455700 chr3A 82.353 119 17 4 469 584 716800589 716800472 1.750000e-17 100.0
16 TraesCS1B01G455700 chr4A 85.507 69 6 4 510 576 711225160 711225094 4.940000e-08 69.4


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 TraesCS1B01G455700 chr1B 670713557 670716318 2761 True 5101.00 5101 100.000 1 2762 1 chr1B.!!$R1 2761
1 TraesCS1B01G455700 chr1D 482206162 482209831 3669 True 611.26 1498 93.650 725 2762 5 chr1D.!!$R1 2037
2 TraesCS1B01G455700 chr1A 578911403 578913014 1611 True 875.00 1345 87.469 251 1762 2 chr1A.!!$R1 1511

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
686 688 0.035881 CTGAGGCTGCTTGAAGGTGA 59.964 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2365 2584 0.462759 ATCTTGTCTAAGCTGCGGCC 60.463 55.0 15.55 0.0 39.73 6.13 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
37 38 9.968870 TCATAAGCGGTTAAAACATTTTTAAGT 57.031 25.926 11.60 0.00 0.00 2.24
39 40 6.519353 AGCGGTTAAAACATTTTTAAGTGC 57.481 33.333 14.10 14.10 0.00 4.40
40 41 5.174216 AGCGGTTAAAACATTTTTAAGTGCG 59.826 36.000 15.10 0.00 33.78 5.34
41 42 5.359493 CGGTTAAAACATTTTTAAGTGCGC 58.641 37.500 0.00 0.00 0.00 6.09
42 43 5.051641 CGGTTAAAACATTTTTAAGTGCGCA 60.052 36.000 5.66 5.66 0.00 6.09
43 44 6.346199 CGGTTAAAACATTTTTAAGTGCGCAT 60.346 34.615 15.91 0.00 0.00 4.73
44 45 7.348956 GGTTAAAACATTTTTAAGTGCGCATT 58.651 30.769 15.91 6.43 0.00 3.56
45 46 7.320087 GGTTAAAACATTTTTAAGTGCGCATTG 59.680 33.333 15.91 0.00 0.00 2.82
46 47 4.988708 AACATTTTTAAGTGCGCATTGG 57.011 36.364 15.91 0.00 0.00 3.16
47 48 4.250116 ACATTTTTAAGTGCGCATTGGA 57.750 36.364 15.91 0.00 0.00 3.53
48 49 4.819769 ACATTTTTAAGTGCGCATTGGAT 58.180 34.783 15.91 0.00 0.00 3.41
49 50 5.960113 ACATTTTTAAGTGCGCATTGGATA 58.040 33.333 15.91 0.00 0.00 2.59
50 51 6.572519 ACATTTTTAAGTGCGCATTGGATAT 58.427 32.000 15.91 0.00 0.00 1.63
51 52 7.041107 ACATTTTTAAGTGCGCATTGGATATT 58.959 30.769 15.91 2.96 0.00 1.28
52 53 8.194104 ACATTTTTAAGTGCGCATTGGATATTA 58.806 29.630 15.91 1.97 0.00 0.98
53 54 9.195411 CATTTTTAAGTGCGCATTGGATATTAT 57.805 29.630 15.91 0.00 0.00 1.28
54 55 9.762933 ATTTTTAAGTGCGCATTGGATATTATT 57.237 25.926 15.91 0.00 0.00 1.40
55 56 9.593134 TTTTTAAGTGCGCATTGGATATTATTT 57.407 25.926 15.91 0.00 0.00 1.40
56 57 8.572828 TTTAAGTGCGCATTGGATATTATTTG 57.427 30.769 15.91 0.00 0.00 2.32
57 58 6.389830 AAGTGCGCATTGGATATTATTTGA 57.610 33.333 15.91 0.00 0.00 2.69
58 59 6.389830 AGTGCGCATTGGATATTATTTGAA 57.610 33.333 15.91 0.00 0.00 2.69
59 60 6.985117 AGTGCGCATTGGATATTATTTGAAT 58.015 32.000 15.91 0.00 0.00 2.57
60 61 8.109705 AGTGCGCATTGGATATTATTTGAATA 57.890 30.769 15.91 0.00 0.00 1.75
61 62 8.575589 AGTGCGCATTGGATATTATTTGAATAA 58.424 29.630 15.91 0.00 35.52 1.40
62 63 9.190858 GTGCGCATTGGATATTATTTGAATAAA 57.809 29.630 15.91 0.00 34.79 1.40
63 64 9.926158 TGCGCATTGGATATTATTTGAATAAAT 57.074 25.926 5.66 0.00 39.69 1.40
86 87 9.512588 AAATGGTGGAAATATTTTTAACATGCA 57.487 25.926 13.59 0.00 0.00 3.96
87 88 9.683870 AATGGTGGAAATATTTTTAACATGCAT 57.316 25.926 13.59 0.00 0.00 3.96
88 89 9.683870 ATGGTGGAAATATTTTTAACATGCATT 57.316 25.926 12.61 0.00 0.00 3.56
89 90 9.512588 TGGTGGAAATATTTTTAACATGCATTT 57.487 25.926 0.00 0.00 0.00 2.32
143 144 9.932699 TTTTAAAAATGTGCAATCATTGAAGTG 57.067 25.926 0.00 0.00 37.96 3.16
144 145 8.659925 TTAAAAATGTGCAATCATTGAAGTGT 57.340 26.923 0.00 0.00 37.96 3.55
145 146 6.774354 AAAATGTGCAATCATTGAAGTGTC 57.226 33.333 0.00 0.00 37.96 3.67
146 147 5.456548 AATGTGCAATCATTGAAGTGTCA 57.543 34.783 0.00 0.00 36.78 3.58
148 149 5.259832 TGTGCAATCATTGAAGTGTCAAA 57.740 34.783 0.00 0.00 46.66 2.69
149 150 5.658468 TGTGCAATCATTGAAGTGTCAAAA 58.342 33.333 0.00 0.00 46.66 2.44
150 151 5.519566 TGTGCAATCATTGAAGTGTCAAAAC 59.480 36.000 0.00 0.00 46.66 2.43
151 152 5.519566 GTGCAATCATTGAAGTGTCAAAACA 59.480 36.000 0.00 0.00 46.66 2.83
152 153 6.201425 GTGCAATCATTGAAGTGTCAAAACAT 59.799 34.615 0.00 0.00 46.66 2.71
153 154 6.762187 TGCAATCATTGAAGTGTCAAAACATT 59.238 30.769 0.00 0.00 46.66 2.71
154 155 7.280428 TGCAATCATTGAAGTGTCAAAACATTT 59.720 29.630 0.00 0.00 46.66 2.32
155 156 8.124199 GCAATCATTGAAGTGTCAAAACATTTT 58.876 29.630 0.00 0.00 46.66 1.82
200 201 8.528044 TTTTTAGTGGTAGGAAACATTTCTGT 57.472 30.769 4.45 0.00 37.35 3.41
202 203 7.504924 TTAGTGGTAGGAAACATTTCTGTTG 57.495 36.000 4.45 0.00 44.83 3.33
203 204 5.690865 AGTGGTAGGAAACATTTCTGTTGA 58.309 37.500 4.45 0.00 44.83 3.18
204 205 6.126409 AGTGGTAGGAAACATTTCTGTTGAA 58.874 36.000 4.45 0.00 44.83 2.69
205 206 6.777580 AGTGGTAGGAAACATTTCTGTTGAAT 59.222 34.615 4.45 0.00 44.83 2.57
206 207 7.287696 AGTGGTAGGAAACATTTCTGTTGAATT 59.712 33.333 4.45 0.00 44.83 2.17
207 208 8.573035 GTGGTAGGAAACATTTCTGTTGAATTA 58.427 33.333 4.45 0.00 44.83 1.40
208 209 9.308000 TGGTAGGAAACATTTCTGTTGAATTAT 57.692 29.630 4.45 0.00 44.83 1.28
215 216 9.545105 AAACATTTCTGTTGAATTATTTGAGCA 57.455 25.926 0.00 0.00 44.83 4.26
216 217 9.715121 AACATTTCTGTTGAATTATTTGAGCAT 57.285 25.926 0.00 0.00 43.92 3.79
217 218 9.715121 ACATTTCTGTTGAATTATTTGAGCATT 57.285 25.926 0.00 0.00 28.70 3.56
220 221 9.545105 TTTCTGTTGAATTATTTGAGCATTTGT 57.455 25.926 0.00 0.00 31.56 2.83
221 222 9.545105 TTCTGTTGAATTATTTGAGCATTTGTT 57.455 25.926 0.00 0.00 0.00 2.83
222 223 8.980610 TCTGTTGAATTATTTGAGCATTTGTTG 58.019 29.630 0.00 0.00 0.00 3.33
317 318 8.355272 TGAACAATGTTTTTGAATGACATGAG 57.645 30.769 0.00 0.00 34.47 2.90
318 319 6.774354 ACAATGTTTTTGAATGACATGAGC 57.226 33.333 0.00 0.00 34.47 4.26
320 321 6.422701 ACAATGTTTTTGAATGACATGAGCAG 59.577 34.615 0.00 0.00 34.47 4.24
326 327 6.831727 TTTGAATGACATGAGCAGTTTTTG 57.168 33.333 0.00 0.00 0.00 2.44
340 341 4.279659 CAGTTTTTGCAACCTACTCGAAC 58.720 43.478 0.00 0.00 0.00 3.95
341 342 3.942748 AGTTTTTGCAACCTACTCGAACA 59.057 39.130 0.00 0.00 0.00 3.18
353 354 6.725246 ACCTACTCGAACAAAATTTTCACAG 58.275 36.000 0.00 0.00 0.00 3.66
358 359 8.305441 ACTCGAACAAAATTTTCACAGTTTTT 57.695 26.923 0.00 0.00 0.00 1.94
497 499 7.699566 TGCACTTCTTTAACTTTTCGTAATGT 58.300 30.769 0.00 0.00 0.00 2.71
499 501 7.357287 GCACTTCTTTAACTTTTCGTAATGTGC 60.357 37.037 0.00 0.00 37.10 4.57
503 505 6.913673 TCTTTAACTTTTCGTAATGTGCAACC 59.086 34.615 0.00 0.00 34.36 3.77
648 650 8.830580 TGAAGAATAATCGAATGGAAAGATCAC 58.169 33.333 0.00 0.00 0.00 3.06
659 661 2.222027 GAAAGATCACTAATGGGCCGG 58.778 52.381 0.00 0.00 0.00 6.13
660 662 0.179018 AAGATCACTAATGGGCCGGC 60.179 55.000 21.18 21.18 0.00 6.13
661 663 1.056700 AGATCACTAATGGGCCGGCT 61.057 55.000 28.56 9.11 0.00 5.52
662 664 0.179018 GATCACTAATGGGCCGGCTT 60.179 55.000 28.56 15.89 0.00 4.35
663 665 1.071699 GATCACTAATGGGCCGGCTTA 59.928 52.381 28.56 16.20 0.00 3.09
664 666 0.179468 TCACTAATGGGCCGGCTTAC 59.821 55.000 28.56 17.47 0.00 2.34
665 667 0.180406 CACTAATGGGCCGGCTTACT 59.820 55.000 28.56 11.58 0.00 2.24
666 668 1.414919 CACTAATGGGCCGGCTTACTA 59.585 52.381 28.56 8.23 0.00 1.82
667 669 1.415289 ACTAATGGGCCGGCTTACTAC 59.585 52.381 28.56 8.16 0.00 2.73
668 670 1.692519 CTAATGGGCCGGCTTACTACT 59.307 52.381 28.56 7.24 0.00 2.57
669 671 0.180406 AATGGGCCGGCTTACTACTG 59.820 55.000 28.56 0.00 0.00 2.74
670 672 0.689745 ATGGGCCGGCTTACTACTGA 60.690 55.000 28.56 1.08 0.00 3.41
671 673 1.327690 TGGGCCGGCTTACTACTGAG 61.328 60.000 28.56 0.00 0.00 3.35
672 674 1.442148 GGCCGGCTTACTACTGAGG 59.558 63.158 28.56 0.00 0.00 3.86
673 675 1.227292 GCCGGCTTACTACTGAGGC 60.227 63.158 22.15 0.00 36.08 4.70
674 676 1.677637 GCCGGCTTACTACTGAGGCT 61.678 60.000 22.15 0.00 39.92 4.58
675 677 0.103208 CCGGCTTACTACTGAGGCTG 59.897 60.000 0.00 0.00 36.40 4.85
676 678 0.528684 CGGCTTACTACTGAGGCTGC 60.529 60.000 0.00 0.00 36.40 5.25
677 679 0.827368 GGCTTACTACTGAGGCTGCT 59.173 55.000 0.00 0.00 35.73 4.24
678 680 1.208293 GGCTTACTACTGAGGCTGCTT 59.792 52.381 0.00 0.00 35.73 3.91
679 681 2.275318 GCTTACTACTGAGGCTGCTTG 58.725 52.381 0.00 0.00 0.00 4.01
680 682 2.093973 GCTTACTACTGAGGCTGCTTGA 60.094 50.000 0.00 0.00 0.00 3.02
681 683 3.617531 GCTTACTACTGAGGCTGCTTGAA 60.618 47.826 0.00 0.00 0.00 2.69
682 684 2.758736 ACTACTGAGGCTGCTTGAAG 57.241 50.000 0.00 0.00 0.00 3.02
683 685 1.277557 ACTACTGAGGCTGCTTGAAGG 59.722 52.381 0.00 0.00 0.00 3.46
684 686 1.277557 CTACTGAGGCTGCTTGAAGGT 59.722 52.381 0.00 0.00 0.00 3.50
685 687 0.250640 ACTGAGGCTGCTTGAAGGTG 60.251 55.000 0.00 0.00 0.00 4.00
686 688 0.035881 CTGAGGCTGCTTGAAGGTGA 59.964 55.000 0.00 0.00 0.00 4.02
687 689 0.035881 TGAGGCTGCTTGAAGGTGAG 59.964 55.000 0.00 0.00 0.00 3.51
688 690 1.303155 AGGCTGCTTGAAGGTGAGC 60.303 57.895 0.00 0.00 39.33 4.26
689 691 1.303155 GGCTGCTTGAAGGTGAGCT 60.303 57.895 0.00 0.00 39.60 4.09
690 692 1.584380 GGCTGCTTGAAGGTGAGCTG 61.584 60.000 0.00 0.00 39.60 4.24
691 693 0.888285 GCTGCTTGAAGGTGAGCTGT 60.888 55.000 0.00 0.00 39.25 4.40
692 694 1.609061 GCTGCTTGAAGGTGAGCTGTA 60.609 52.381 0.00 0.00 39.25 2.74
697 699 1.324383 TGAAGGTGAGCTGTACGTCA 58.676 50.000 0.00 0.00 0.00 4.35
704 706 0.456995 GAGCTGTACGTCAGTCTGGC 60.457 60.000 13.91 0.00 45.23 4.85
705 707 1.179174 AGCTGTACGTCAGTCTGGCA 61.179 55.000 5.10 0.00 45.23 4.92
706 708 1.009389 GCTGTACGTCAGTCTGGCAC 61.009 60.000 5.10 0.00 45.23 5.01
707 709 0.729478 CTGTACGTCAGTCTGGCACG 60.729 60.000 11.40 11.40 39.17 5.34
708 710 2.087009 GTACGTCAGTCTGGCACGC 61.087 63.158 12.58 0.00 37.02 5.34
709 711 2.557372 TACGTCAGTCTGGCACGCA 61.557 57.895 12.58 0.00 37.02 5.24
710 712 2.472232 TACGTCAGTCTGGCACGCAG 62.472 60.000 12.58 0.00 37.02 5.18
711 713 2.740055 GTCAGTCTGGCACGCAGG 60.740 66.667 0.00 0.00 0.00 4.85
712 714 2.917227 TCAGTCTGGCACGCAGGA 60.917 61.111 0.00 0.00 0.00 3.86
713 715 2.031012 CAGTCTGGCACGCAGGAA 59.969 61.111 0.00 0.00 0.00 3.36
714 716 2.031163 AGTCTGGCACGCAGGAAC 59.969 61.111 0.00 0.00 0.00 3.62
715 717 3.414700 GTCTGGCACGCAGGAACG 61.415 66.667 0.00 0.00 39.50 3.95
718 720 2.356553 TGGCACGCAGGAACGTAC 60.357 61.111 0.00 0.00 46.34 3.67
719 721 2.048503 GGCACGCAGGAACGTACT 60.049 61.111 0.00 0.00 46.34 2.73
723 877 1.614385 CACGCAGGAACGTACTGTAG 58.386 55.000 18.01 14.99 46.34 2.74
749 906 1.005394 GTCCATGTCAACCCGTCGT 60.005 57.895 0.00 0.00 0.00 4.34
750 907 1.012486 GTCCATGTCAACCCGTCGTC 61.012 60.000 0.00 0.00 0.00 4.20
751 908 2.092291 CCATGTCAACCCGTCGTCG 61.092 63.158 0.00 0.00 0.00 5.12
820 977 1.261619 GAATTCAAGCTCGCCATACGG 59.738 52.381 0.00 0.00 43.89 4.02
821 978 0.464036 ATTCAAGCTCGCCATACGGA 59.536 50.000 0.00 0.00 43.89 4.69
822 979 0.248012 TTCAAGCTCGCCATACGGAA 59.752 50.000 0.00 0.00 43.89 4.30
823 980 0.248012 TCAAGCTCGCCATACGGAAA 59.752 50.000 0.00 0.00 43.89 3.13
824 981 1.134521 TCAAGCTCGCCATACGGAAAT 60.135 47.619 0.00 0.00 43.89 2.17
825 982 1.261619 CAAGCTCGCCATACGGAAATC 59.738 52.381 0.00 0.00 43.89 2.17
840 999 0.808755 AAATCAAATGGCGTCCCGAC 59.191 50.000 0.00 0.00 34.27 4.79
867 1026 2.756760 CCTCCAACCACCAGATCAATTG 59.243 50.000 0.00 0.00 0.00 2.32
868 1027 2.165030 CTCCAACCACCAGATCAATTGC 59.835 50.000 0.00 0.00 0.00 3.56
869 1028 1.894466 CCAACCACCAGATCAATTGCA 59.106 47.619 0.00 0.00 0.00 4.08
870 1029 2.353011 CCAACCACCAGATCAATTGCAC 60.353 50.000 0.00 0.00 0.00 4.57
871 1030 1.549203 ACCACCAGATCAATTGCACC 58.451 50.000 0.00 0.00 0.00 5.01
872 1031 1.076024 ACCACCAGATCAATTGCACCT 59.924 47.619 0.00 0.00 0.00 4.00
873 1032 1.475280 CCACCAGATCAATTGCACCTG 59.525 52.381 0.00 7.46 0.00 4.00
874 1033 1.135199 CACCAGATCAATTGCACCTGC 60.135 52.381 0.00 0.00 42.50 4.85
949 1116 2.180204 CCCGCCGTTCCTGCTATTG 61.180 63.158 0.00 0.00 0.00 1.90
1010 1179 3.632080 ACAACCCATGGCGGACGA 61.632 61.111 6.09 0.00 36.56 4.20
1062 1231 4.509737 GAGCCCGCCGTCCACTAC 62.510 72.222 0.00 0.00 0.00 2.73
1162 1331 2.659016 CGAGTCTTGCTCCTGCCA 59.341 61.111 0.00 0.00 41.10 4.92
1296 1465 1.153823 GACCATGGACTCCGTCACG 60.154 63.158 21.47 0.00 33.68 4.35
1764 1933 2.167861 GGAGTTCGGTCGCTGATGC 61.168 63.158 0.00 0.00 0.00 3.91
1766 1935 0.807667 GAGTTCGGTCGCTGATGCAT 60.808 55.000 0.00 0.00 39.64 3.96
1768 1986 0.807667 GTTCGGTCGCTGATGCATCT 60.808 55.000 26.32 0.00 39.64 2.90
1775 1993 2.004733 TCGCTGATGCATCTGTTTCTG 58.995 47.619 27.86 16.04 39.64 3.02
1787 2006 3.706698 TCTGTTTCTGTTCTGTCGTCAG 58.293 45.455 3.03 3.03 42.54 3.51
1793 2012 2.809119 TCTGTTCTGTCGTCAGTCTCTC 59.191 50.000 9.48 0.00 41.91 3.20
1799 2018 1.001746 TGTCGTCAGTCTCTCTACCGT 59.998 52.381 0.00 0.00 0.00 4.83
1802 2021 1.166129 GTCAGTCTCTCTACCGTGCA 58.834 55.000 0.00 0.00 0.00 4.57
1875 2094 4.460948 TTCTAACTTCGGCGGAGTAATT 57.539 40.909 23.14 8.91 0.00 1.40
1913 2132 7.835181 TCGTATTATTTACCATCAACCCCTTTT 59.165 33.333 0.00 0.00 0.00 2.27
1924 2143 3.444388 TCAACCCCTTTTGTACACACAAC 59.556 43.478 0.00 0.00 44.28 3.32
1996 2215 3.206150 CAATCAAAGGATGGTAGGTCCG 58.794 50.000 0.00 0.00 40.76 4.79
2012 2231 7.880195 TGGTAGGTCCGACTAGATAAGTATAAC 59.120 40.741 0.00 0.00 39.07 1.89
2056 2275 9.679661 ACTTCATGACACCATTATTACAATACA 57.320 29.630 0.00 0.00 0.00 2.29
2058 2277 9.679661 TTCATGACACCATTATTACAATACAGT 57.320 29.630 0.00 0.00 0.00 3.55
2152 2371 9.476202 CGTCAATTGAGATAGTATAACAATGGA 57.524 33.333 8.80 11.87 32.66 3.41
2180 2399 1.521010 CACTCTGCCGGCTGATCAG 60.521 63.158 32.72 23.93 0.00 2.90
2193 2412 0.820226 TGATCAGGCAGAGAGTTCCG 59.180 55.000 0.00 0.00 0.00 4.30
2201 2420 2.047179 GAGAGTTCCGCCACCCAC 60.047 66.667 0.00 0.00 0.00 4.61
2303 2522 4.340617 CCCCTTACCTTATCTTGCAACAA 58.659 43.478 0.00 0.00 0.00 2.83
2304 2523 4.157840 CCCCTTACCTTATCTTGCAACAAC 59.842 45.833 0.00 0.00 0.00 3.32
2305 2524 4.764823 CCCTTACCTTATCTTGCAACAACA 59.235 41.667 0.00 0.00 0.00 3.33
2306 2525 5.242838 CCCTTACCTTATCTTGCAACAACAA 59.757 40.000 0.00 0.00 0.00 2.83
2307 2526 6.239176 CCCTTACCTTATCTTGCAACAACAAA 60.239 38.462 0.00 0.00 0.00 2.83
2308 2527 6.640907 CCTTACCTTATCTTGCAACAACAAAC 59.359 38.462 0.00 0.00 0.00 2.93
2309 2528 4.944048 ACCTTATCTTGCAACAACAAACC 58.056 39.130 0.00 0.00 0.00 3.27
2310 2529 4.404073 ACCTTATCTTGCAACAACAAACCA 59.596 37.500 0.00 0.00 0.00 3.67
2311 2530 4.744631 CCTTATCTTGCAACAACAAACCAC 59.255 41.667 0.00 0.00 0.00 4.16
2312 2531 3.883830 ATCTTGCAACAACAAACCACA 57.116 38.095 0.00 0.00 0.00 4.17
2313 2532 3.667497 TCTTGCAACAACAAACCACAA 57.333 38.095 0.00 0.00 0.00 3.33
2314 2533 4.199432 TCTTGCAACAACAAACCACAAT 57.801 36.364 0.00 0.00 0.00 2.71
2315 2534 5.330455 TCTTGCAACAACAAACCACAATA 57.670 34.783 0.00 0.00 0.00 1.90
2316 2535 5.347342 TCTTGCAACAACAAACCACAATAG 58.653 37.500 0.00 0.00 0.00 1.73
2317 2536 4.727507 TGCAACAACAAACCACAATAGT 57.272 36.364 0.00 0.00 0.00 2.12
2318 2537 4.428209 TGCAACAACAAACCACAATAGTG 58.572 39.130 0.00 0.00 45.47 2.74
2333 2552 6.903340 ACAATAGTGAACCCCTTACCTTAT 57.097 37.500 0.00 0.00 0.00 1.73
2334 2553 6.659824 ACAATAGTGAACCCCTTACCTTATG 58.340 40.000 0.00 0.00 0.00 1.90
2335 2554 6.216868 ACAATAGTGAACCCCTTACCTTATGT 59.783 38.462 0.00 0.00 0.00 2.29
2336 2555 6.903340 ATAGTGAACCCCTTACCTTATGTT 57.097 37.500 0.00 0.00 0.00 2.71
2337 2556 4.918588 AGTGAACCCCTTACCTTATGTTG 58.081 43.478 0.00 0.00 0.00 3.33
2338 2557 3.442625 GTGAACCCCTTACCTTATGTTGC 59.557 47.826 0.00 0.00 0.00 4.17
2339 2558 3.074687 TGAACCCCTTACCTTATGTTGCA 59.925 43.478 0.00 0.00 0.00 4.08
2340 2559 3.818295 ACCCCTTACCTTATGTTGCAA 57.182 42.857 0.00 0.00 0.00 4.08
2341 2560 3.427573 ACCCCTTACCTTATGTTGCAAC 58.572 45.455 22.83 22.83 0.00 4.17
2342 2561 3.181427 ACCCCTTACCTTATGTTGCAACA 60.181 43.478 32.78 32.78 44.06 3.33
2365 2584 1.065358 AACCACAATAGCGAACGACG 58.935 50.000 0.00 0.00 45.66 5.12
2368 2587 1.808390 ACAATAGCGAACGACGGCC 60.808 57.895 0.00 0.00 42.83 6.13
2392 2611 5.166398 GCAGCTTAGACAAGATTTTGCAAT 58.834 37.500 0.00 0.00 37.85 3.56
2393 2612 5.061808 GCAGCTTAGACAAGATTTTGCAATG 59.938 40.000 0.00 0.00 37.85 2.82
2401 2620 4.586001 ACAAGATTTTGCAATGTCACCTCT 59.414 37.500 0.00 0.00 37.85 3.69
2431 2650 3.754188 AAATCTGCAACAAGATCTCGC 57.246 42.857 0.00 0.00 35.83 5.03
2432 2651 2.391616 ATCTGCAACAAGATCTCGCA 57.608 45.000 0.00 2.30 30.91 5.10
2544 2763 6.925165 ACCTCTGTTGAAAATGTTTATGCAAG 59.075 34.615 0.00 0.00 0.00 4.01
2548 2767 7.652909 TCTGTTGAAAATGTTTATGCAAGAAGG 59.347 33.333 0.00 0.00 0.00 3.46
2550 2769 7.224362 TGTTGAAAATGTTTATGCAAGAAGGTG 59.776 33.333 0.00 0.00 0.00 4.00
2551 2770 6.815089 TGAAAATGTTTATGCAAGAAGGTGT 58.185 32.000 0.00 0.00 0.00 4.16
2552 2771 7.271511 TGAAAATGTTTATGCAAGAAGGTGTT 58.728 30.769 0.00 0.00 0.00 3.32
2596 2815 3.201290 CTCAGCGCTAGTCAAATCCAAT 58.799 45.455 10.99 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.968870 ACTTAAAAATGTTTTAACCGCTTATGA 57.031 25.926 2.55 0.00 0.00 2.15
13 14 8.705134 GCACTTAAAAATGTTTTAACCGCTTAT 58.295 29.630 2.55 0.00 0.00 1.73
14 15 7.096558 CGCACTTAAAAATGTTTTAACCGCTTA 60.097 33.333 14.19 0.00 0.00 3.09
15 16 6.291902 CGCACTTAAAAATGTTTTAACCGCTT 60.292 34.615 14.19 0.00 0.00 4.68
16 17 5.174216 CGCACTTAAAAATGTTTTAACCGCT 59.826 36.000 14.19 0.00 0.00 5.52
17 18 5.359493 CGCACTTAAAAATGTTTTAACCGC 58.641 37.500 2.55 6.83 0.00 5.68
18 19 5.051641 TGCGCACTTAAAAATGTTTTAACCG 60.052 36.000 5.66 6.75 0.00 4.44
19 20 6.275305 TGCGCACTTAAAAATGTTTTAACC 57.725 33.333 5.66 0.00 0.00 2.85
20 21 7.320087 CCAATGCGCACTTAAAAATGTTTTAAC 59.680 33.333 14.90 0.00 0.00 2.01
21 22 7.224753 TCCAATGCGCACTTAAAAATGTTTTAA 59.775 29.630 14.90 5.94 0.00 1.52
22 23 6.701841 TCCAATGCGCACTTAAAAATGTTTTA 59.298 30.769 14.90 0.00 0.00 1.52
23 24 5.525378 TCCAATGCGCACTTAAAAATGTTTT 59.475 32.000 14.90 0.00 0.00 2.43
24 25 5.053145 TCCAATGCGCACTTAAAAATGTTT 58.947 33.333 14.90 0.00 0.00 2.83
25 26 4.626042 TCCAATGCGCACTTAAAAATGTT 58.374 34.783 14.90 0.00 0.00 2.71
26 27 4.250116 TCCAATGCGCACTTAAAAATGT 57.750 36.364 14.90 0.00 0.00 2.71
27 28 7.467557 AATATCCAATGCGCACTTAAAAATG 57.532 32.000 14.90 1.73 0.00 2.32
28 29 9.762933 AATAATATCCAATGCGCACTTAAAAAT 57.237 25.926 14.90 2.82 0.00 1.82
29 30 9.593134 AAATAATATCCAATGCGCACTTAAAAA 57.407 25.926 14.90 0.00 0.00 1.94
30 31 9.029243 CAAATAATATCCAATGCGCACTTAAAA 57.971 29.630 14.90 0.00 0.00 1.52
31 32 8.409371 TCAAATAATATCCAATGCGCACTTAAA 58.591 29.630 14.90 0.00 0.00 1.52
32 33 7.935520 TCAAATAATATCCAATGCGCACTTAA 58.064 30.769 14.90 0.00 0.00 1.85
33 34 7.503521 TCAAATAATATCCAATGCGCACTTA 57.496 32.000 14.90 0.00 0.00 2.24
34 35 6.389830 TCAAATAATATCCAATGCGCACTT 57.610 33.333 14.90 5.65 0.00 3.16
35 36 6.389830 TTCAAATAATATCCAATGCGCACT 57.610 33.333 14.90 0.00 0.00 4.40
36 37 8.741101 TTATTCAAATAATATCCAATGCGCAC 57.259 30.769 14.90 0.00 0.00 5.34
37 38 9.926158 ATTTATTCAAATAATATCCAATGCGCA 57.074 25.926 14.96 14.96 32.46 6.09
60 61 9.512588 TGCATGTTAAAAATATTTCCACCATTT 57.487 25.926 0.10 0.00 0.00 2.32
61 62 9.683870 ATGCATGTTAAAAATATTTCCACCATT 57.316 25.926 0.00 0.00 0.00 3.16
62 63 9.683870 AATGCATGTTAAAAATATTTCCACCAT 57.316 25.926 0.00 0.17 0.00 3.55
63 64 9.512588 AAATGCATGTTAAAAATATTTCCACCA 57.487 25.926 0.00 0.00 0.00 4.17
117 118 9.932699 CACTTCAATGATTGCACATTTTTAAAA 57.067 25.926 0.00 0.00 38.25 1.52
118 119 9.107177 ACACTTCAATGATTGCACATTTTTAAA 57.893 25.926 0.00 0.00 38.25 1.52
119 120 8.659925 ACACTTCAATGATTGCACATTTTTAA 57.340 26.923 0.00 0.00 38.25 1.52
120 121 7.924947 TGACACTTCAATGATTGCACATTTTTA 59.075 29.630 0.00 0.00 38.25 1.52
121 122 6.762187 TGACACTTCAATGATTGCACATTTTT 59.238 30.769 0.00 0.00 38.25 1.94
122 123 6.282167 TGACACTTCAATGATTGCACATTTT 58.718 32.000 0.00 0.00 38.25 1.82
123 124 5.845103 TGACACTTCAATGATTGCACATTT 58.155 33.333 0.00 0.00 38.25 2.32
124 125 5.456548 TGACACTTCAATGATTGCACATT 57.543 34.783 0.00 0.00 40.50 2.71
125 126 5.456548 TTGACACTTCAATGATTGCACAT 57.543 34.783 0.00 0.00 36.79 3.21
126 127 4.915158 TTGACACTTCAATGATTGCACA 57.085 36.364 0.00 0.00 36.79 4.57
127 128 5.519566 TGTTTTGACACTTCAATGATTGCAC 59.480 36.000 0.00 0.00 41.50 4.57
128 129 5.658468 TGTTTTGACACTTCAATGATTGCA 58.342 33.333 0.00 0.00 41.50 4.08
129 130 6.774354 ATGTTTTGACACTTCAATGATTGC 57.226 33.333 0.00 0.00 41.50 3.56
175 176 8.528044 ACAGAAATGTTTCCTACCACTAAAAA 57.472 30.769 2.04 0.00 37.92 1.94
176 177 8.410141 CAACAGAAATGTTTCCTACCACTAAAA 58.590 33.333 2.04 0.00 37.92 1.52
177 178 7.776030 TCAACAGAAATGTTTCCTACCACTAAA 59.224 33.333 2.04 0.00 37.92 1.85
178 179 7.284074 TCAACAGAAATGTTTCCTACCACTAA 58.716 34.615 2.04 0.00 37.92 2.24
179 180 6.833041 TCAACAGAAATGTTTCCTACCACTA 58.167 36.000 2.04 0.00 37.92 2.74
180 181 5.690865 TCAACAGAAATGTTTCCTACCACT 58.309 37.500 2.04 0.00 37.92 4.00
181 182 6.385649 TTCAACAGAAATGTTTCCTACCAC 57.614 37.500 2.04 0.00 37.92 4.16
182 183 7.595819 AATTCAACAGAAATGTTTCCTACCA 57.404 32.000 2.04 0.00 37.92 3.25
189 190 9.545105 TGCTCAAATAATTCAACAGAAATGTTT 57.455 25.926 0.00 0.00 0.00 2.83
190 191 9.715121 ATGCTCAAATAATTCAACAGAAATGTT 57.285 25.926 0.00 0.00 0.00 2.71
191 192 9.715121 AATGCTCAAATAATTCAACAGAAATGT 57.285 25.926 0.00 0.00 0.00 2.71
194 195 9.545105 ACAAATGCTCAAATAATTCAACAGAAA 57.455 25.926 0.00 0.00 0.00 2.52
195 196 9.545105 AACAAATGCTCAAATAATTCAACAGAA 57.455 25.926 0.00 0.00 0.00 3.02
196 197 8.980610 CAACAAATGCTCAAATAATTCAACAGA 58.019 29.630 0.00 0.00 0.00 3.41
296 297 6.422701 ACTGCTCATGTCATTCAAAAACATTG 59.577 34.615 0.00 0.00 31.43 2.82
318 319 4.201871 TGTTCGAGTAGGTTGCAAAAACTG 60.202 41.667 12.76 7.05 0.00 3.16
320 321 4.281525 TGTTCGAGTAGGTTGCAAAAAC 57.718 40.909 0.00 0.00 0.00 2.43
326 327 5.974751 TGAAAATTTTGTTCGAGTAGGTTGC 59.025 36.000 8.47 0.00 0.00 4.17
327 328 6.970043 TGTGAAAATTTTGTTCGAGTAGGTTG 59.030 34.615 8.47 0.00 0.00 3.77
332 333 8.973835 AAAACTGTGAAAATTTTGTTCGAGTA 57.026 26.923 8.47 0.00 0.00 2.59
473 474 7.357287 GCACATTACGAAAAGTTAAAGAAGTGC 60.357 37.037 0.00 0.00 38.34 4.40
478 479 6.913673 GGTTGCACATTACGAAAAGTTAAAGA 59.086 34.615 0.00 0.00 0.00 2.52
482 483 5.752892 TGGTTGCACATTACGAAAAGTTA 57.247 34.783 0.00 0.00 0.00 2.24
490 491 1.511887 GCGCTGGTTGCACATTACG 60.512 57.895 0.00 0.00 43.06 3.18
497 499 2.586258 TTTTAAAAGCGCTGGTTGCA 57.414 40.000 12.58 0.00 43.06 4.08
499 501 5.649602 TCAAATTTTAAAAGCGCTGGTTG 57.350 34.783 12.58 6.97 0.00 3.77
503 505 9.862585 AATTTACTTCAAATTTTAAAAGCGCTG 57.137 25.926 12.58 0.00 42.93 5.18
601 603 9.825972 TCTTCATTCGTTCATATGTTCTTTTTC 57.174 29.630 1.90 0.00 0.00 2.29
609 611 9.476202 TCGATTATTCTTCATTCGTTCATATGT 57.524 29.630 1.90 0.00 0.00 2.29
613 615 8.285394 CCATTCGATTATTCTTCATTCGTTCAT 58.715 33.333 0.00 0.00 0.00 2.57
614 616 7.494298 TCCATTCGATTATTCTTCATTCGTTCA 59.506 33.333 0.00 0.00 0.00 3.18
615 617 7.851508 TCCATTCGATTATTCTTCATTCGTTC 58.148 34.615 0.00 0.00 0.00 3.95
617 619 7.786178 TTCCATTCGATTATTCTTCATTCGT 57.214 32.000 0.00 0.00 0.00 3.85
618 620 8.551205 TCTTTCCATTCGATTATTCTTCATTCG 58.449 33.333 0.00 0.00 0.00 3.34
622 624 8.830580 GTGATCTTTCCATTCGATTATTCTTCA 58.169 33.333 0.00 0.00 0.00 3.02
629 631 7.661437 CCCATTAGTGATCTTTCCATTCGATTA 59.339 37.037 0.00 0.00 0.00 1.75
634 636 4.279420 GGCCCATTAGTGATCTTTCCATTC 59.721 45.833 0.00 0.00 0.00 2.67
648 650 1.692519 AGTAGTAAGCCGGCCCATTAG 59.307 52.381 26.15 0.00 0.00 1.73
650 652 0.180406 CAGTAGTAAGCCGGCCCATT 59.820 55.000 26.15 14.32 0.00 3.16
659 661 2.093973 TCAAGCAGCCTCAGTAGTAAGC 60.094 50.000 0.00 0.00 0.00 3.09
660 662 3.876274 TCAAGCAGCCTCAGTAGTAAG 57.124 47.619 0.00 0.00 0.00 2.34
661 663 3.055819 CCTTCAAGCAGCCTCAGTAGTAA 60.056 47.826 0.00 0.00 0.00 2.24
662 664 2.497675 CCTTCAAGCAGCCTCAGTAGTA 59.502 50.000 0.00 0.00 0.00 1.82
663 665 1.277557 CCTTCAAGCAGCCTCAGTAGT 59.722 52.381 0.00 0.00 0.00 2.73
664 666 1.277557 ACCTTCAAGCAGCCTCAGTAG 59.722 52.381 0.00 0.00 0.00 2.57
665 667 1.002430 CACCTTCAAGCAGCCTCAGTA 59.998 52.381 0.00 0.00 0.00 2.74
666 668 0.250640 CACCTTCAAGCAGCCTCAGT 60.251 55.000 0.00 0.00 0.00 3.41
667 669 0.035881 TCACCTTCAAGCAGCCTCAG 59.964 55.000 0.00 0.00 0.00 3.35
668 670 0.035881 CTCACCTTCAAGCAGCCTCA 59.964 55.000 0.00 0.00 0.00 3.86
669 671 1.304509 GCTCACCTTCAAGCAGCCTC 61.305 60.000 0.00 0.00 38.42 4.70
670 672 1.303155 GCTCACCTTCAAGCAGCCT 60.303 57.895 0.00 0.00 38.42 4.58
671 673 1.303155 AGCTCACCTTCAAGCAGCC 60.303 57.895 0.00 0.00 41.06 4.85
672 674 0.888285 ACAGCTCACCTTCAAGCAGC 60.888 55.000 0.00 0.00 41.06 5.25
673 675 2.072298 GTACAGCTCACCTTCAAGCAG 58.928 52.381 0.00 0.00 41.06 4.24
674 676 1.605457 CGTACAGCTCACCTTCAAGCA 60.605 52.381 0.00 0.00 41.06 3.91
675 677 1.071605 CGTACAGCTCACCTTCAAGC 58.928 55.000 0.00 0.00 38.84 4.01
676 678 2.288213 TGACGTACAGCTCACCTTCAAG 60.288 50.000 0.00 0.00 0.00 3.02
677 679 1.684450 TGACGTACAGCTCACCTTCAA 59.316 47.619 0.00 0.00 0.00 2.69
678 680 1.269723 CTGACGTACAGCTCACCTTCA 59.730 52.381 0.00 0.00 39.86 3.02
679 681 1.983972 CTGACGTACAGCTCACCTTC 58.016 55.000 0.00 0.00 39.86 3.46
689 691 1.284715 CGTGCCAGACTGACGTACA 59.715 57.895 3.32 0.00 0.00 2.90
690 692 2.087009 GCGTGCCAGACTGACGTAC 61.087 63.158 15.58 4.68 35.52 3.67
691 693 2.257371 GCGTGCCAGACTGACGTA 59.743 61.111 15.58 0.00 35.52 3.57
692 694 3.848347 CTGCGTGCCAGACTGACGT 62.848 63.158 15.58 0.00 44.64 4.34
697 699 2.031163 GTTCCTGCGTGCCAGACT 59.969 61.111 0.00 0.00 44.64 3.24
704 706 1.068748 ACTACAGTACGTTCCTGCGTG 60.069 52.381 13.13 7.48 45.33 5.34
706 708 1.614385 CACTACAGTACGTTCCTGCG 58.386 55.000 13.13 8.37 33.09 5.18
707 709 1.271656 ACCACTACAGTACGTTCCTGC 59.728 52.381 13.13 0.00 33.09 4.85
708 710 2.413765 CGACCACTACAGTACGTTCCTG 60.414 54.545 11.98 11.98 36.01 3.86
709 711 1.808945 CGACCACTACAGTACGTTCCT 59.191 52.381 0.00 0.00 0.00 3.36
710 712 1.537202 ACGACCACTACAGTACGTTCC 59.463 52.381 0.00 0.00 31.56 3.62
711 713 2.031682 ACACGACCACTACAGTACGTTC 60.032 50.000 0.00 0.00 32.58 3.95
712 714 1.949525 ACACGACCACTACAGTACGTT 59.050 47.619 0.00 0.00 32.58 3.99
713 715 1.532868 GACACGACCACTACAGTACGT 59.467 52.381 0.00 0.00 34.11 3.57
714 716 1.135859 GGACACGACCACTACAGTACG 60.136 57.143 0.00 0.00 0.00 3.67
715 717 1.881973 TGGACACGACCACTACAGTAC 59.118 52.381 0.00 0.00 34.77 2.73
716 718 2.275134 TGGACACGACCACTACAGTA 57.725 50.000 0.00 0.00 34.77 2.74
718 720 1.272490 ACATGGACACGACCACTACAG 59.728 52.381 0.00 0.00 43.03 2.74
719 721 1.271379 GACATGGACACGACCACTACA 59.729 52.381 0.00 0.00 43.03 2.74
723 877 0.865769 GTTGACATGGACACGACCAC 59.134 55.000 0.00 0.00 43.03 4.16
780 937 1.026718 GGTCAATGAAGAGCGGTGGG 61.027 60.000 0.00 0.00 0.00 4.61
788 945 4.326826 AGCTTGAATTCGGTCAATGAAGA 58.673 39.130 0.04 0.00 36.92 2.87
790 947 3.125146 CGAGCTTGAATTCGGTCAATGAA 59.875 43.478 11.45 0.00 36.92 2.57
840 999 2.358737 GGTGGTTGGAGGTCGCAG 60.359 66.667 0.00 0.00 0.00 5.18
941 1100 1.723870 GGCGAAGTGGCAATAGCAG 59.276 57.895 15.19 0.00 44.61 4.24
942 1101 3.903783 GGCGAAGTGGCAATAGCA 58.096 55.556 15.19 0.00 44.61 3.49
1010 1179 4.178169 TGGGTTTCGTGGGCGTGT 62.178 61.111 0.00 0.00 39.49 4.49
1058 1227 4.430765 CCTTGGCGCCGTCGTAGT 62.431 66.667 23.90 0.00 38.14 2.73
1083 1252 1.301479 GACGACGGCCTTGGACTTT 60.301 57.895 0.00 0.00 0.00 2.66
1146 1315 0.957888 GGTTGGCAGGAGCAAGACTC 60.958 60.000 0.00 0.00 45.45 3.36
1147 1316 1.073897 GGTTGGCAGGAGCAAGACT 59.926 57.895 0.00 0.00 44.61 3.24
1151 1320 3.565214 TCCGGTTGGCAGGAGCAA 61.565 61.111 0.00 0.00 44.61 3.91
1272 1441 1.908483 GGAGTCCATGGTCAGGTCC 59.092 63.158 12.58 5.83 0.00 4.46
1730 1899 2.813474 CCGCGACGCATGAAGGAA 60.813 61.111 21.35 0.00 0.00 3.36
1764 1933 4.051237 TGACGACAGAACAGAAACAGATG 58.949 43.478 0.00 0.00 0.00 2.90
1766 1935 3.130516 ACTGACGACAGAACAGAAACAGA 59.869 43.478 21.50 0.00 46.03 3.41
1768 1986 3.130516 AGACTGACGACAGAACAGAAACA 59.869 43.478 21.50 0.00 46.03 2.83
1775 1993 3.125658 GGTAGAGAGACTGACGACAGAAC 59.874 52.174 21.50 13.74 46.03 3.01
1787 2006 1.466024 CGTCTTGCACGGTAGAGAGAC 60.466 57.143 1.60 1.60 45.46 3.36
1799 2018 1.069978 TGGTGTGAGATTCGTCTTGCA 59.930 47.619 0.00 0.00 0.00 4.08
1802 2021 4.543590 AAGATGGTGTGAGATTCGTCTT 57.456 40.909 0.00 0.00 32.53 3.01
1848 2067 4.178540 CTCCGCCGAAGTTAGAATAAACA 58.821 43.478 0.00 0.00 0.00 2.83
1898 2117 3.227614 GTGTACAAAAGGGGTTGATGGT 58.772 45.455 0.00 0.00 32.59 3.55
1913 2132 4.944317 TGAAAACATCCAGTTGTGTGTACA 59.056 37.500 0.00 0.00 41.19 2.90
1924 2143 3.424703 ACCAGGTCATGAAAACATCCAG 58.575 45.455 0.00 0.00 0.00 3.86
1980 2199 2.249309 AGTCGGACCTACCATCCTTT 57.751 50.000 4.14 0.00 38.90 3.11
2112 2331 7.500992 TCTCAATTGACGGAGAATTAGCTAAT 58.499 34.615 13.37 13.37 37.23 1.73
2125 2344 8.712363 CCATTGTTATACTATCTCAATTGACGG 58.288 37.037 3.38 0.00 0.00 4.79
2152 2371 0.865769 CGGCAGAGTGTTAGCGTTTT 59.134 50.000 0.00 0.00 0.00 2.43
2183 2402 2.203788 TGGGTGGCGGAACTCTCT 60.204 61.111 0.00 0.00 0.00 3.10
2184 2403 2.047179 GTGGGTGGCGGAACTCTC 60.047 66.667 0.00 0.00 0.00 3.20
2201 2420 2.456119 GGACGATCCAACAGCTGCG 61.456 63.158 15.27 10.71 36.28 5.18
2205 2424 2.872858 GGATAAAGGACGATCCAACAGC 59.127 50.000 6.78 0.00 41.24 4.40
2303 2522 3.117284 AGGGGTTCACTATTGTGGTTTGT 60.117 43.478 7.45 0.00 43.94 2.83
2304 2523 3.496331 AGGGGTTCACTATTGTGGTTTG 58.504 45.455 7.45 0.00 43.94 2.93
2305 2524 3.895704 AGGGGTTCACTATTGTGGTTT 57.104 42.857 7.45 0.00 43.94 3.27
2306 2525 3.895704 AAGGGGTTCACTATTGTGGTT 57.104 42.857 7.45 0.00 43.94 3.67
2307 2526 3.009805 GGTAAGGGGTTCACTATTGTGGT 59.990 47.826 7.45 0.00 43.94 4.16
2308 2527 3.265995 AGGTAAGGGGTTCACTATTGTGG 59.734 47.826 7.45 0.00 43.94 4.17
2309 2528 4.569719 AGGTAAGGGGTTCACTATTGTG 57.430 45.455 0.36 0.36 45.07 3.33
2310 2529 6.216868 ACATAAGGTAAGGGGTTCACTATTGT 59.783 38.462 0.00 0.00 0.00 2.71
2311 2530 6.659824 ACATAAGGTAAGGGGTTCACTATTG 58.340 40.000 0.00 0.00 0.00 1.90
2312 2531 6.903340 ACATAAGGTAAGGGGTTCACTATT 57.097 37.500 0.00 0.00 0.00 1.73
2313 2532 6.659824 CAACATAAGGTAAGGGGTTCACTAT 58.340 40.000 0.00 0.00 0.00 2.12
2314 2533 5.572066 GCAACATAAGGTAAGGGGTTCACTA 60.572 44.000 0.00 0.00 0.00 2.74
2315 2534 4.809691 GCAACATAAGGTAAGGGGTTCACT 60.810 45.833 0.00 0.00 0.00 3.41
2316 2535 3.442625 GCAACATAAGGTAAGGGGTTCAC 59.557 47.826 0.00 0.00 0.00 3.18
2317 2536 3.074687 TGCAACATAAGGTAAGGGGTTCA 59.925 43.478 0.00 0.00 0.00 3.18
2318 2537 3.692690 TGCAACATAAGGTAAGGGGTTC 58.307 45.455 0.00 0.00 0.00 3.62
2319 2538 3.818295 TGCAACATAAGGTAAGGGGTT 57.182 42.857 0.00 0.00 0.00 4.11
2320 2539 3.181427 TGTTGCAACATAAGGTAAGGGGT 60.181 43.478 27.96 0.00 33.17 4.95
2321 2540 3.426615 TGTTGCAACATAAGGTAAGGGG 58.573 45.455 27.96 0.00 33.17 4.79
2333 2552 3.599730 TTGTGGTTTGATGTTGCAACA 57.400 38.095 32.78 32.78 44.06 3.33
2334 2553 4.150451 GCTATTGTGGTTTGATGTTGCAAC 59.850 41.667 22.83 22.83 0.00 4.17
2335 2554 4.305769 GCTATTGTGGTTTGATGTTGCAA 58.694 39.130 0.00 0.00 0.00 4.08
2336 2555 3.611293 CGCTATTGTGGTTTGATGTTGCA 60.611 43.478 0.00 0.00 0.00 4.08
2337 2556 2.916716 CGCTATTGTGGTTTGATGTTGC 59.083 45.455 0.00 0.00 0.00 4.17
2338 2557 4.418013 TCGCTATTGTGGTTTGATGTTG 57.582 40.909 0.00 0.00 0.00 3.33
2339 2558 4.612712 CGTTCGCTATTGTGGTTTGATGTT 60.613 41.667 0.00 0.00 0.00 2.71
2340 2559 3.120338 CGTTCGCTATTGTGGTTTGATGT 60.120 43.478 0.00 0.00 0.00 3.06
2341 2560 3.124466 TCGTTCGCTATTGTGGTTTGATG 59.876 43.478 0.00 0.00 0.00 3.07
2342 2561 3.124636 GTCGTTCGCTATTGTGGTTTGAT 59.875 43.478 0.00 0.00 0.00 2.57
2343 2562 2.477375 GTCGTTCGCTATTGTGGTTTGA 59.523 45.455 0.00 0.00 0.00 2.69
2365 2584 0.462759 ATCTTGTCTAAGCTGCGGCC 60.463 55.000 15.55 0.00 39.73 6.13
2368 2587 3.166657 GCAAAATCTTGTCTAAGCTGCG 58.833 45.455 0.00 0.00 34.79 5.18
2413 2632 2.391616 TGCGAGATCTTGTTGCAGAT 57.608 45.000 11.71 0.00 36.12 2.90
2414 2633 2.004733 CATGCGAGATCTTGTTGCAGA 58.995 47.619 11.71 0.00 39.17 4.26
2499 2718 6.536224 AGAGGTTTTGTTGCAGATTTCTTTTG 59.464 34.615 0.00 0.00 0.00 2.44
2517 2736 7.271511 TGCATAAACATTTTCAACAGAGGTTT 58.728 30.769 0.00 0.00 34.21 3.27
2538 2757 2.168106 TGCAACAAACACCTTCTTGCAT 59.832 40.909 0.00 0.00 41.67 3.96
2544 2763 4.798387 CACTACTTTGCAACAAACACCTTC 59.202 41.667 0.00 0.00 0.00 3.46
2548 2767 4.364415 TCCACTACTTTGCAACAAACAC 57.636 40.909 0.00 0.00 0.00 3.32
2550 2769 6.704819 CATTTTCCACTACTTTGCAACAAAC 58.295 36.000 0.00 0.00 0.00 2.93
2551 2770 5.293079 GCATTTTCCACTACTTTGCAACAAA 59.707 36.000 0.00 0.00 0.00 2.83
2552 2771 4.808364 GCATTTTCCACTACTTTGCAACAA 59.192 37.500 0.00 0.00 0.00 2.83
2596 2815 0.909610 AGATCCGCCCCTTCAAGTCA 60.910 55.000 0.00 0.00 0.00 3.41
2601 2820 3.443145 TTTAAAAGATCCGCCCCTTCA 57.557 42.857 0.00 0.00 0.00 3.02
2603 2822 6.041637 GGATATTTTTAAAAGATCCGCCCCTT 59.958 38.462 22.82 0.00 29.96 3.95
2604 2823 5.538813 GGATATTTTTAAAAGATCCGCCCCT 59.461 40.000 22.82 0.00 29.96 4.79
2605 2824 5.564063 CGGATATTTTTAAAAGATCCGCCCC 60.564 44.000 36.38 17.09 44.08 5.80
2606 2825 5.458015 CGGATATTTTTAAAAGATCCGCCC 58.542 41.667 36.38 17.37 44.08 6.13
2694 2913 9.208022 TGAAGTGAATTATCAGTTGTTCTACAG 57.792 33.333 3.77 0.00 46.72 2.74
2695 2914 9.725019 ATGAAGTGAATTATCAGTTGTTCTACA 57.275 29.630 3.77 0.00 46.72 2.74
2699 2918 8.506437 TGTCATGAAGTGAATTATCAGTTGTTC 58.494 33.333 0.00 0.00 46.72 3.18


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

AutoCloner maintained by Alex Coulton.