Multiple sequence alignment - TraesCS2B01G227800

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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 TraesCS2B01G227800 chr2B 100.000 8429 0 0 1 8429 221917951 221926379 0.000000e+00 15566
1 TraesCS2B01G227800 chr2B 86.638 696 89 4 1 694 340734835 340735528 0.000000e+00 767
2 TraesCS2B01G227800 chr2B 84.103 195 24 1 4936 5123 221921803 221921997 1.870000e-41 182
3 TraesCS2B01G227800 chr2B 84.103 195 24 1 3853 4047 221922886 221923073 1.870000e-41 182
4 TraesCS2B01G227800 chr2D 96.350 6137 141 19 760 6842 162499084 162505191 0.000000e+00 10015
5 TraesCS2B01G227800 chr2D 95.028 1066 41 6 6922 7981 162505188 162506247 0.000000e+00 1664
6 TraesCS2B01G227800 chr2D 87.050 695 86 4 2 694 508043764 508044456 0.000000e+00 782
7 TraesCS2B01G227800 chr2D 94.783 460 14 6 7973 8425 162506741 162507197 0.000000e+00 708
8 TraesCS2B01G227800 chr2D 89.431 246 26 0 5238 5483 53914869 53915114 2.280000e-80 311
9 TraesCS2B01G227800 chr2D 86.667 195 19 1 4936 5123 162502202 162502396 8.570000e-50 209
10 TraesCS2B01G227800 chr2D 85.128 195 22 1 3853 4047 162503284 162503471 8.630000e-45 193
11 TraesCS2B01G227800 chr2D 93.878 98 5 1 6836 6933 361405772 361405868 6.820000e-31 147
12 TraesCS2B01G227800 chr2A 91.686 3512 183 30 749 4192 173499926 173503396 0.000000e+00 4767
13 TraesCS2B01G227800 chr2A 95.883 1336 36 8 5518 6839 173504770 173506100 0.000000e+00 2145
14 TraesCS2B01G227800 chr2A 93.579 1059 43 6 6924 7977 173506102 173507140 0.000000e+00 1555
15 TraesCS2B01G227800 chr2A 93.981 432 17 5 7999 8422 173508086 173508516 0.000000e+00 645
16 TraesCS2B01G227800 chr2A 81.735 219 34 4 4452 4669 173503946 173504159 2.420000e-40 178
17 TraesCS2B01G227800 chr5D 88.362 696 74 6 1 694 507398814 507399504 0.000000e+00 830
18 TraesCS2B01G227800 chr3D 87.050 695 86 4 2 694 299917036 299917728 0.000000e+00 782
19 TraesCS2B01G227800 chr3D 86.638 696 88 5 2 694 312620102 312620795 0.000000e+00 765
20 TraesCS2B01G227800 chr3D 89.431 246 26 0 5238 5483 145418399 145418154 2.280000e-80 311
21 TraesCS2B01G227800 chr6B 86.676 698 85 7 1 694 259425312 259426005 0.000000e+00 767
22 TraesCS2B01G227800 chr4D 86.448 701 81 12 1 694 20683841 20684534 0.000000e+00 756
23 TraesCS2B01G227800 chr6D 86.207 696 92 4 1 694 145585360 145586053 0.000000e+00 750
24 TraesCS2B01G227800 chr1A 86.227 697 88 8 2 694 135485972 135486664 0.000000e+00 749
25 TraesCS2B01G227800 chr1A 92.233 103 6 2 6834 6934 418057813 418057711 2.450000e-30 145
26 TraesCS2B01G227800 chr7D 89.837 246 25 0 5238 5483 382103304 382103549 4.910000e-82 316
27 TraesCS2B01G227800 chr7D 94.000 100 5 1 6837 6936 1260947 1261045 5.270000e-32 150
28 TraesCS2B01G227800 chr7D 93.878 98 6 0 6837 6934 574289497 574289594 1.900000e-31 148
29 TraesCS2B01G227800 chr7B 89.837 246 25 0 5238 5483 644490460 644490215 4.910000e-82 316
30 TraesCS2B01G227800 chrUn 89.431 246 26 0 5238 5483 233530243 233530488 2.280000e-80 311
31 TraesCS2B01G227800 chrUn 89.431 246 26 0 5238 5483 257939655 257939410 2.280000e-80 311
32 TraesCS2B01G227800 chrUn 89.431 246 26 0 5238 5483 451663658 451663903 2.280000e-80 311
33 TraesCS2B01G227800 chr7A 89.431 246 26 0 5238 5483 60101447 60101692 2.280000e-80 311
34 TraesCS2B01G227800 chr7A 95.699 93 4 0 6838 6930 80994168 80994076 5.270000e-32 150
35 TraesCS2B01G227800 chr4B 96.703 91 3 0 6836 6926 29271834 29271924 1.470000e-32 152
36 TraesCS2B01G227800 chr5A 94.792 96 3 2 6837 6931 608605223 608605129 1.900000e-31 148
37 TraesCS2B01G227800 chr3B 94.737 95 5 0 6839 6933 818896674 818896580 1.900000e-31 148
38 TraesCS2B01G227800 chr3A 94.737 95 5 0 6839 6933 725517078 725517172 1.900000e-31 148


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 TraesCS2B01G227800 chr2B 221917951 221926379 8428 False 15566.0 15566 100.0000 1 8429 1 chr2B.!!$F1 8428
1 TraesCS2B01G227800 chr2B 340734835 340735528 693 False 767.0 767 86.6380 1 694 1 chr2B.!!$F2 693
2 TraesCS2B01G227800 chr2D 162499084 162507197 8113 False 2557.8 10015 91.5912 760 8425 5 chr2D.!!$F4 7665
3 TraesCS2B01G227800 chr2D 508043764 508044456 692 False 782.0 782 87.0500 2 694 1 chr2D.!!$F3 692
4 TraesCS2B01G227800 chr2A 173499926 173508516 8590 False 1858.0 4767 91.3728 749 8422 5 chr2A.!!$F1 7673
5 TraesCS2B01G227800 chr5D 507398814 507399504 690 False 830.0 830 88.3620 1 694 1 chr5D.!!$F1 693
6 TraesCS2B01G227800 chr3D 299917036 299917728 692 False 782.0 782 87.0500 2 694 1 chr3D.!!$F1 692
7 TraesCS2B01G227800 chr3D 312620102 312620795 693 False 765.0 765 86.6380 2 694 1 chr3D.!!$F2 692
8 TraesCS2B01G227800 chr6B 259425312 259426005 693 False 767.0 767 86.6760 1 694 1 chr6B.!!$F1 693
9 TraesCS2B01G227800 chr4D 20683841 20684534 693 False 756.0 756 86.4480 1 694 1 chr4D.!!$F1 693
10 TraesCS2B01G227800 chr6D 145585360 145586053 693 False 750.0 750 86.2070 1 694 1 chr6D.!!$F1 693
11 TraesCS2B01G227800 chr1A 135485972 135486664 692 False 749.0 749 86.2270 2 694 1 chr1A.!!$F1 692

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
719 725 0.108424 CTGACTGCTCTGCTGTACCC 60.108 60.000 2.26 0.00 40.59 3.69 F
1202 1227 0.549169 CTTCCCCTAACACCCCTCCA 60.549 60.000 0.00 0.00 0.00 3.86 F
1984 2025 0.475906 AACTCTTGCAGCTGGTCCTT 59.524 50.000 17.12 0.00 0.00 3.36 F
2937 3016 1.075542 TATTCTGCAACCTTGTCGCG 58.924 50.000 0.00 0.00 0.00 5.87 F
3310 3389 0.243907 TCGCTCCTCAAGAAGGTTCG 59.756 55.000 0.00 0.00 46.32 3.95 F
4382 4736 0.246635 CCTGAACTGGGTCTACACGG 59.753 60.000 0.00 0.00 0.00 4.94 F
4838 5283 1.140452 CACCCACTGATCAGCTAGCAT 59.860 52.381 22.83 1.68 0.00 3.79 F
4912 5358 1.613437 TCTGCATCGTCTCTGACAACA 59.387 47.619 0.00 0.00 32.09 3.33 F
4943 5389 2.046604 GGCGGGGTGTTAGTGACC 60.047 66.667 0.00 0.00 0.00 4.02 F
6850 7310 2.537143 ACTTTGATGTACTCCCTCCGT 58.463 47.619 0.00 0.00 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 2001 1.177256 CCAGCTGCAAGAGTTTGGCT 61.177 55.000 8.66 0.0 33.74 4.75 R
2920 2999 1.227409 TCGCGACAAGGTTGCAGAA 60.227 52.632 3.71 0.0 42.60 3.02 R
3310 3389 0.379669 CAACTGAATCAGATGGCGGC 59.620 55.000 18.20 0.0 35.18 6.53 R
4601 4989 0.031721 GTCGTTGGACTTGAGGACGT 59.968 55.000 0.00 0.0 40.15 4.34 R
4725 5166 0.909610 CTGGGAAGCTACCTGGGTGA 60.910 60.000 8.65 0.0 0.00 4.02 R
5256 5703 3.265221 AGTTCAATCTCCAAGCCAGATGA 59.735 43.478 0.00 0.0 30.62 2.92 R
5811 6268 6.942576 TCAGCTTTTAATTCTACAGGCTCTTT 59.057 34.615 0.00 0.0 0.00 2.52 R
6874 7334 4.033587 GCGTTTAGATCACCAAAATAGCGA 59.966 41.667 0.00 0.0 0.00 4.93 R
6917 7377 3.014623 GGCACCTTTAACATGTACTCCC 58.985 50.000 0.00 0.0 0.00 4.30 R
8208 9622 0.886490 CTTCTTCTTGCTGGCGTGGT 60.886 55.000 0.00 0.0 0.00 4.16 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
29 31 0.896923 TCCCTTGCATGCATCCAAAC 59.103 50.000 23.37 0.00 0.00 2.93
109 112 8.503458 ACAAATATCTTCTCATCAAGAGGTTG 57.497 34.615 0.00 0.00 44.81 3.77
140 143 1.285641 CGCCAATTGCTTGTCGGTT 59.714 52.632 0.00 0.00 38.05 4.44
146 149 0.511221 ATTGCTTGTCGGTTCGAACG 59.489 50.000 21.34 16.21 37.72 3.95
278 282 4.285292 CACTCTCATTGTCACAAAGCAAC 58.715 43.478 0.00 0.00 0.00 4.17
320 324 9.942850 TGTATCACATAATCTTTGAGAGTTTGA 57.057 29.630 3.55 0.00 28.60 2.69
331 335 6.828273 TCTTTGAGAGTTTGAGTCATCCAAAA 59.172 34.615 0.00 0.00 35.57 2.44
359 363 0.371301 CACAACATGATCCTGCGACG 59.629 55.000 0.00 0.00 0.00 5.12
408 412 7.504924 AATGATACCGAGTTTTGTTTCTTGA 57.495 32.000 0.00 0.00 0.00 3.02
412 416 5.638596 ACCGAGTTTTGTTTCTTGAAAGT 57.361 34.783 0.00 0.00 0.00 2.66
450 454 6.828785 GGACCTACCAAGAAATTGACATGTAT 59.171 38.462 0.00 0.00 38.79 2.29
454 458 4.640201 ACCAAGAAATTGACATGTATCCGG 59.360 41.667 0.00 0.00 0.00 5.14
457 461 5.614324 AGAAATTGACATGTATCCGGAGA 57.386 39.130 11.34 0.75 0.00 3.71
476 480 5.105064 CGGAGAGGATTTTCTACCAACCTTA 60.105 44.000 0.00 0.00 0.00 2.69
477 481 6.114089 GGAGAGGATTTTCTACCAACCTTAC 58.886 44.000 0.00 0.00 0.00 2.34
511 515 4.073293 CCGAGTAGGAATAGCCAACAAT 57.927 45.455 0.00 0.00 45.00 2.71
552 557 9.137459 TCTTAAGGTACCAATGTCAAAATTTGA 57.863 29.630 15.94 4.03 37.33 2.69
589 595 8.460317 AATATCTCATTATCCTTCCCATGACT 57.540 34.615 0.00 0.00 0.00 3.41
604 610 7.786178 TCCCATGACTTTAAGATAACATTCG 57.214 36.000 0.00 0.00 0.00 3.34
623 629 1.406903 GCTTGGGGCTGCTTGATATT 58.593 50.000 0.00 0.00 38.06 1.28
629 635 1.684983 GGGCTGCTTGATATTGTGCAT 59.315 47.619 0.00 0.00 34.79 3.96
652 658 8.962857 CATACATGCACACACTTAACATAAAA 57.037 30.769 0.00 0.00 0.00 1.52
665 671 7.384115 CACTTAACATAAAAGTCAGGACGAGAA 59.616 37.037 0.00 0.00 34.99 2.87
672 678 1.620819 AGTCAGGACGAGAAGCACAAT 59.379 47.619 0.00 0.00 36.20 2.71
678 684 4.210746 CAGGACGAGAAGCACAATGATATG 59.789 45.833 0.00 0.00 0.00 1.78
681 687 5.468072 GGACGAGAAGCACAATGATATGATT 59.532 40.000 0.00 0.00 0.00 2.57
700 706 6.992063 TGATTAGAGAACCAATCTTTCAGC 57.008 37.500 0.00 0.00 38.96 4.26
701 707 6.715280 TGATTAGAGAACCAATCTTTCAGCT 58.285 36.000 0.00 0.00 38.96 4.24
702 708 6.596888 TGATTAGAGAACCAATCTTTCAGCTG 59.403 38.462 7.63 7.63 38.96 4.24
703 709 4.630644 AGAGAACCAATCTTTCAGCTGA 57.369 40.909 13.74 13.74 38.96 4.26
704 710 4.322567 AGAGAACCAATCTTTCAGCTGAC 58.677 43.478 18.03 0.15 38.96 3.51
705 711 4.041444 AGAGAACCAATCTTTCAGCTGACT 59.959 41.667 18.03 5.84 38.96 3.41
706 712 4.070716 AGAACCAATCTTTCAGCTGACTG 58.929 43.478 18.03 12.28 39.40 3.51
707 713 2.157738 ACCAATCTTTCAGCTGACTGC 58.842 47.619 18.03 0.00 44.10 4.40
708 714 7.726409 AGAACCAATCTTTCAGCTGACTGCT 62.726 44.000 18.03 0.21 44.87 4.24
717 723 2.748268 GCTGACTGCTCTGCTGTAC 58.252 57.895 2.26 0.00 40.59 2.90
718 724 0.739112 GCTGACTGCTCTGCTGTACC 60.739 60.000 2.26 0.00 40.59 3.34
719 725 0.108424 CTGACTGCTCTGCTGTACCC 60.108 60.000 2.26 0.00 40.59 3.69
720 726 0.831711 TGACTGCTCTGCTGTACCCA 60.832 55.000 2.26 0.00 40.59 4.51
721 727 0.108424 GACTGCTCTGCTGTACCCAG 60.108 60.000 2.26 4.68 40.59 4.45
729 735 4.291047 CTGTACCCAGCTGCACAG 57.709 61.111 20.15 20.15 33.11 3.66
730 736 1.372683 CTGTACCCAGCTGCACAGT 59.627 57.895 23.08 14.33 34.91 3.55
731 737 0.608130 CTGTACCCAGCTGCACAGTA 59.392 55.000 23.08 13.55 34.91 2.74
732 738 1.001974 CTGTACCCAGCTGCACAGTAA 59.998 52.381 23.08 8.46 34.91 2.24
733 739 1.418264 TGTACCCAGCTGCACAGTAAA 59.582 47.619 8.66 0.00 0.00 2.01
734 740 2.158740 TGTACCCAGCTGCACAGTAAAA 60.159 45.455 8.66 0.00 0.00 1.52
735 741 1.318576 ACCCAGCTGCACAGTAAAAC 58.681 50.000 8.66 0.00 0.00 2.43
736 742 1.317613 CCCAGCTGCACAGTAAAACA 58.682 50.000 8.66 0.00 0.00 2.83
737 743 1.001378 CCCAGCTGCACAGTAAAACAC 60.001 52.381 8.66 0.00 0.00 3.32
738 744 1.001378 CCAGCTGCACAGTAAAACACC 60.001 52.381 8.66 0.00 0.00 4.16
739 745 1.949525 CAGCTGCACAGTAAAACACCT 59.050 47.619 0.00 0.00 0.00 4.00
740 746 2.031682 CAGCTGCACAGTAAAACACCTC 60.032 50.000 0.00 0.00 0.00 3.85
741 747 1.946768 GCTGCACAGTAAAACACCTCA 59.053 47.619 0.00 0.00 0.00 3.86
742 748 2.357637 GCTGCACAGTAAAACACCTCAA 59.642 45.455 0.00 0.00 0.00 3.02
743 749 3.181491 GCTGCACAGTAAAACACCTCAAA 60.181 43.478 0.00 0.00 0.00 2.69
744 750 4.601019 CTGCACAGTAAAACACCTCAAAG 58.399 43.478 0.00 0.00 0.00 2.77
745 751 4.265893 TGCACAGTAAAACACCTCAAAGA 58.734 39.130 0.00 0.00 0.00 2.52
746 752 4.702612 TGCACAGTAAAACACCTCAAAGAA 59.297 37.500 0.00 0.00 0.00 2.52
747 753 5.163663 TGCACAGTAAAACACCTCAAAGAAG 60.164 40.000 0.00 0.00 0.00 2.85
786 792 1.270252 ACCGCAAAAATGGGCAGAAAG 60.270 47.619 0.00 0.00 0.00 2.62
792 799 4.815846 GCAAAAATGGGCAGAAAGAAAAGA 59.184 37.500 0.00 0.00 0.00 2.52
956 981 2.978010 CGCCCGCAAACTCCAAGT 60.978 61.111 0.00 0.00 0.00 3.16
1196 1221 1.608154 GCCCTCTTCCCCTAACACC 59.392 63.158 0.00 0.00 0.00 4.16
1202 1227 0.549169 CTTCCCCTAACACCCCTCCA 60.549 60.000 0.00 0.00 0.00 3.86
1230 1255 2.514205 TTGCTGGCTTCTTTTCTTGC 57.486 45.000 0.00 0.00 0.00 4.01
1357 1383 4.176752 GGGGCAGTCGCTTAGGGG 62.177 72.222 0.00 0.00 38.60 4.79
1427 1453 7.014326 GGGGATTGGTAACTAAAAATCTGATCC 59.986 40.741 0.00 0.00 37.61 3.36
1468 1494 4.653893 TGCTGTTCTGTGGCACAA 57.346 50.000 22.31 9.90 44.16 3.33
1476 1502 2.618241 GTTCTGTGGCACAATCTGTTCA 59.382 45.455 22.31 0.00 44.16 3.18
1483 1509 1.270550 GCACAATCTGTTCAACTGGGG 59.729 52.381 0.00 0.00 0.00 4.96
1504 1530 2.230992 GCCCATCACAGCACAATTACAA 59.769 45.455 0.00 0.00 0.00 2.41
1505 1531 3.674138 GCCCATCACAGCACAATTACAAG 60.674 47.826 0.00 0.00 0.00 3.16
1506 1532 3.507233 CCCATCACAGCACAATTACAAGT 59.493 43.478 0.00 0.00 0.00 3.16
1534 1560 4.107363 ACGTAAGCTAGCTTGACCTTAC 57.893 45.455 34.98 23.64 45.62 2.34
1637 1663 2.354103 CCGAACCATCTCATCAGTGTGT 60.354 50.000 0.00 0.00 0.00 3.72
1741 1767 1.161563 TCGAAAACCTGTGCGGGAAC 61.162 55.000 3.74 0.00 36.97 3.62
1775 1801 4.475016 AGTACCATGCTTTCCTCAGGTAAT 59.525 41.667 0.00 0.00 33.80 1.89
1805 1844 6.992063 TCTGGATTAGAAAAATGTCTCTGC 57.008 37.500 0.00 0.00 30.84 4.26
1913 1954 3.130693 GGTCTAGTAGTTGTACCTGCCTG 59.869 52.174 0.00 0.00 0.00 4.85
1934 1975 5.734720 CTGGATTAGGACTTGCAACTAAGA 58.265 41.667 12.04 1.52 31.02 2.10
1945 1986 2.869801 TGCAACTAAGACTGTTTGGTCG 59.130 45.455 0.00 0.00 40.76 4.79
1960 2001 2.302260 TGGTCGCCTCATTGACAAAAA 58.698 42.857 0.00 0.00 36.83 1.94
1984 2025 0.475906 AACTCTTGCAGCTGGTCCTT 59.524 50.000 17.12 0.00 0.00 3.36
1999 2040 3.181469 TGGTCCTTACACACTTGACACTC 60.181 47.826 0.00 0.00 0.00 3.51
2074 2116 1.544246 AGTATCTGCGTGTGTGTGCTA 59.456 47.619 0.00 0.00 0.00 3.49
2131 2173 5.271625 CACTACGAGTACATAAGCACGATT 58.728 41.667 0.00 0.00 0.00 3.34
2209 2266 4.024048 ACCGAACTTTTGTCTAAGTGCATG 60.024 41.667 0.00 0.00 38.33 4.06
2213 2270 7.360861 CCGAACTTTTGTCTAAGTGCATGAATA 60.361 37.037 0.00 0.00 38.33 1.75
2214 2271 7.478667 CGAACTTTTGTCTAAGTGCATGAATAC 59.521 37.037 0.00 0.00 38.33 1.89
2215 2272 7.986085 ACTTTTGTCTAAGTGCATGAATACT 57.014 32.000 0.00 0.00 37.00 2.12
2216 2273 8.034058 ACTTTTGTCTAAGTGCATGAATACTC 57.966 34.615 0.00 0.00 37.00 2.59
2217 2274 7.880195 ACTTTTGTCTAAGTGCATGAATACTCT 59.120 33.333 0.00 0.00 37.00 3.24
2218 2275 9.371136 CTTTTGTCTAAGTGCATGAATACTCTA 57.629 33.333 0.00 0.00 0.00 2.43
2219 2276 8.703604 TTTGTCTAAGTGCATGAATACTCTAC 57.296 34.615 0.00 0.00 0.00 2.59
2220 2277 6.806751 TGTCTAAGTGCATGAATACTCTACC 58.193 40.000 0.00 0.00 0.00 3.18
2221 2278 6.607600 TGTCTAAGTGCATGAATACTCTACCT 59.392 38.462 0.00 0.00 0.00 3.08
2222 2279 6.920758 GTCTAAGTGCATGAATACTCTACCTG 59.079 42.308 0.00 0.00 0.00 4.00
2229 2296 7.330454 GTGCATGAATACTCTACCTGATACATG 59.670 40.741 0.00 0.00 35.85 3.21
2299 2366 5.122519 TGTCTTGTGTTTCTATTCTGCACA 58.877 37.500 0.00 0.00 38.15 4.57
2491 2570 8.946085 CAAAAGTATAGTAAGGAAGAACATGCA 58.054 33.333 0.00 0.00 0.00 3.96
2673 2752 4.074970 ACAGACGATTCAGGCAAAGAATT 58.925 39.130 0.00 0.00 35.93 2.17
2911 2990 1.336887 CCCACCTGTTCAGTCTACACG 60.337 57.143 0.00 0.00 0.00 4.49
2920 2999 6.092955 TGTTCAGTCTACACGGAAACTTAT 57.907 37.500 0.00 0.00 38.29 1.73
2937 3016 1.075542 TATTCTGCAACCTTGTCGCG 58.924 50.000 0.00 0.00 0.00 5.87
3057 3136 7.697710 CGAATATGAAATAGAAGCTTTTGCACA 59.302 33.333 0.00 0.00 39.40 4.57
3241 3320 7.807977 AGTGCTTGAACTGAATTTTAGAAGA 57.192 32.000 0.00 0.00 0.00 2.87
3251 3330 9.487790 AACTGAATTTTAGAAGAGTGAGAAGAG 57.512 33.333 0.00 0.00 0.00 2.85
3310 3389 0.243907 TCGCTCCTCAAGAAGGTTCG 59.756 55.000 0.00 0.00 46.32 3.95
3351 3430 5.252547 TGCACCTAAGATGATGCTTACAAA 58.747 37.500 0.00 0.00 38.90 2.83
3395 3474 3.859961 AGTTATCAATGTGAGTTCTCGCG 59.140 43.478 0.00 0.00 0.00 5.87
3408 3487 7.865889 TGTGAGTTCTCGCGTTATTGATTATAT 59.134 33.333 5.77 0.00 0.00 0.86
3458 3537 8.683615 GGATATACCATATTCTCATCGTGTGTA 58.316 37.037 0.00 0.00 38.79 2.90
3497 3576 6.513806 TGAGTTCCATGTAATGTTGGATTG 57.486 37.500 0.00 0.00 44.81 2.67
3876 3965 2.675317 GCAACTAAGTCCTGCTCACGAT 60.675 50.000 0.00 0.00 33.20 3.73
3964 4053 1.224592 CAGGTTCTTAGCCCCGCAT 59.775 57.895 0.00 0.00 0.00 4.73
4129 4227 2.637383 GGCCGACGACAACTCCTCT 61.637 63.158 0.00 0.00 0.00 3.69
4141 4239 2.370189 CAACTCCTCTGTCTCCTTTGGT 59.630 50.000 0.00 0.00 0.00 3.67
4200 4542 0.904865 TCCTCCATCCACGCTGTTCT 60.905 55.000 0.00 0.00 0.00 3.01
4364 4718 2.240500 GCCATCGACTCGTGCATCC 61.241 63.158 0.00 0.00 0.00 3.51
4382 4736 0.246635 CCTGAACTGGGTCTACACGG 59.753 60.000 0.00 0.00 0.00 4.94
4392 4746 1.379443 TCTACACGGCCATCTCGGT 60.379 57.895 2.24 0.00 36.97 4.69
4447 4801 2.675423 ACGCACTCGGTCTGGCTA 60.675 61.111 0.00 0.00 40.69 3.93
4563 4951 1.664965 GCTTTGTGACGTCGGCTCT 60.665 57.895 11.62 0.00 0.00 4.09
4601 4989 3.620286 CGTCCTCAACGCGTTTCA 58.380 55.556 24.21 11.11 45.76 2.69
4615 5003 1.537348 CGTTTCACGTCCTCAAGTCCA 60.537 52.381 0.00 0.00 36.74 4.02
4725 5166 2.125512 GAGGCTTCACGCATCGGT 60.126 61.111 0.00 0.00 39.87 4.69
4750 5191 3.400054 GTAGCTTCCCAGGGCGGT 61.400 66.667 0.00 2.32 0.00 5.68
4759 5203 2.677228 CAGGGCGGTTCCTCCAAT 59.323 61.111 0.21 0.00 34.31 3.16
4784 5228 1.227999 GCAGAGCCGTAACAACAGCA 61.228 55.000 0.00 0.00 0.00 4.41
4838 5283 1.140452 CACCCACTGATCAGCTAGCAT 59.860 52.381 22.83 1.68 0.00 3.79
4912 5358 1.613437 TCTGCATCGTCTCTGACAACA 59.387 47.619 0.00 0.00 32.09 3.33
4943 5389 2.046604 GGCGGGGTGTTAGTGACC 60.047 66.667 0.00 0.00 0.00 4.02
4988 5434 3.767309 AGTCTCCCTGTACATCTCCTT 57.233 47.619 0.00 0.00 0.00 3.36
5011 5457 3.366476 GCGTAGGCCTAGTCATACAGATG 60.366 52.174 14.38 0.00 0.00 2.90
5129 5575 3.367498 CCTCTTGAGTCTTACAACCTCGG 60.367 52.174 0.00 0.00 0.00 4.63
5178 5625 4.427312 GAGATTGCATTTGCCCTTAACTG 58.573 43.478 0.00 0.00 41.18 3.16
5179 5626 3.196254 AGATTGCATTTGCCCTTAACTGG 59.804 43.478 0.00 0.00 41.18 4.00
5540 5987 6.041523 ACTGGCTAAGCACCTATTTTTGAAAA 59.958 34.615 0.00 0.00 0.00 2.29
5811 6268 8.078060 TGAAGATGATAATGTAGTGGAGTCAA 57.922 34.615 0.00 0.00 0.00 3.18
6048 6505 4.387026 TCATTGGACAAACTGAGGGATT 57.613 40.909 0.00 0.00 0.00 3.01
6838 7298 9.357652 CATACCAAATTTCCTGTTACTTTGATG 57.642 33.333 0.00 0.00 0.00 3.07
6839 7299 7.360113 ACCAAATTTCCTGTTACTTTGATGT 57.640 32.000 0.00 0.00 0.00 3.06
6840 7300 8.472007 ACCAAATTTCCTGTTACTTTGATGTA 57.528 30.769 0.00 0.00 0.00 2.29
6841 7301 8.357402 ACCAAATTTCCTGTTACTTTGATGTAC 58.643 33.333 0.00 0.00 0.00 2.90
6842 7302 8.576442 CCAAATTTCCTGTTACTTTGATGTACT 58.424 33.333 0.00 0.00 0.00 2.73
6843 7303 9.612620 CAAATTTCCTGTTACTTTGATGTACTC 57.387 33.333 0.00 0.00 0.00 2.59
6844 7304 7.923414 ATTTCCTGTTACTTTGATGTACTCC 57.077 36.000 0.00 0.00 0.00 3.85
6845 7305 5.416271 TCCTGTTACTTTGATGTACTCCC 57.584 43.478 0.00 0.00 0.00 4.30
6846 7306 5.091552 TCCTGTTACTTTGATGTACTCCCT 58.908 41.667 0.00 0.00 0.00 4.20
6847 7307 5.187186 TCCTGTTACTTTGATGTACTCCCTC 59.813 44.000 0.00 0.00 0.00 4.30
6848 7308 5.416271 TGTTACTTTGATGTACTCCCTCC 57.584 43.478 0.00 0.00 0.00 4.30
6849 7309 4.081862 TGTTACTTTGATGTACTCCCTCCG 60.082 45.833 0.00 0.00 0.00 4.63
6850 7310 2.537143 ACTTTGATGTACTCCCTCCGT 58.463 47.619 0.00 0.00 0.00 4.69
6851 7311 3.705051 ACTTTGATGTACTCCCTCCGTA 58.295 45.455 0.00 0.00 0.00 4.02
6852 7312 4.091549 ACTTTGATGTACTCCCTCCGTAA 58.908 43.478 0.00 0.00 0.00 3.18
6853 7313 4.529377 ACTTTGATGTACTCCCTCCGTAAA 59.471 41.667 0.00 0.00 0.00 2.01
6854 7314 4.460948 TTGATGTACTCCCTCCGTAAAC 57.539 45.455 0.00 0.00 0.00 2.01
6855 7315 3.705051 TGATGTACTCCCTCCGTAAACT 58.295 45.455 0.00 0.00 0.00 2.66
6856 7316 4.858850 TGATGTACTCCCTCCGTAAACTA 58.141 43.478 0.00 0.00 0.00 2.24
6857 7317 5.263599 TGATGTACTCCCTCCGTAAACTAA 58.736 41.667 0.00 0.00 0.00 2.24
6858 7318 5.895534 TGATGTACTCCCTCCGTAAACTAAT 59.104 40.000 0.00 0.00 0.00 1.73
6859 7319 7.062322 TGATGTACTCCCTCCGTAAACTAATA 58.938 38.462 0.00 0.00 0.00 0.98
6860 7320 7.727186 TGATGTACTCCCTCCGTAAACTAATAT 59.273 37.037 0.00 0.00 0.00 1.28
6861 7321 9.236006 GATGTACTCCCTCCGTAAACTAATATA 57.764 37.037 0.00 0.00 0.00 0.86
6862 7322 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
6863 7323 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
6864 7324 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
6865 7325 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
6866 7326 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
6867 7327 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
6868 7328 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
6869 7329 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
6870 7330 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
6885 7345 6.910536 AGAGTGTTTAGATCGCTATTTTGG 57.089 37.500 0.00 0.00 0.00 3.28
6886 7346 6.407202 AGAGTGTTTAGATCGCTATTTTGGT 58.593 36.000 0.00 0.00 0.00 3.67
6887 7347 6.313905 AGAGTGTTTAGATCGCTATTTTGGTG 59.686 38.462 0.00 0.00 0.00 4.17
6888 7348 6.170506 AGTGTTTAGATCGCTATTTTGGTGA 58.829 36.000 0.00 0.00 0.00 4.02
6889 7349 6.823689 AGTGTTTAGATCGCTATTTTGGTGAT 59.176 34.615 0.00 0.00 36.74 3.06
6890 7350 7.011482 AGTGTTTAGATCGCTATTTTGGTGATC 59.989 37.037 8.60 8.60 45.56 2.92
6896 7356 5.712217 TCGCTATTTTGGTGATCTAAACG 57.288 39.130 0.00 0.00 0.00 3.60
6897 7357 4.033587 TCGCTATTTTGGTGATCTAAACGC 59.966 41.667 0.00 0.00 0.00 4.84
6898 7358 4.034048 CGCTATTTTGGTGATCTAAACGCT 59.966 41.667 0.00 0.00 0.00 5.07
6899 7359 5.502606 GCTATTTTGGTGATCTAAACGCTC 58.497 41.667 0.00 0.00 0.00 5.03
6900 7360 5.294552 GCTATTTTGGTGATCTAAACGCTCT 59.705 40.000 0.00 0.00 0.00 4.09
6901 7361 6.183360 GCTATTTTGGTGATCTAAACGCTCTT 60.183 38.462 0.00 0.00 0.00 2.85
6902 7362 7.011109 GCTATTTTGGTGATCTAAACGCTCTTA 59.989 37.037 0.00 0.00 0.00 2.10
6903 7363 7.865706 ATTTTGGTGATCTAAACGCTCTTAT 57.134 32.000 0.00 0.00 0.00 1.73
6904 7364 8.958119 ATTTTGGTGATCTAAACGCTCTTATA 57.042 30.769 0.00 0.00 0.00 0.98
6905 7365 8.958119 TTTTGGTGATCTAAACGCTCTTATAT 57.042 30.769 0.00 0.00 0.00 0.86
6906 7366 8.958119 TTTGGTGATCTAAACGCTCTTATATT 57.042 30.769 0.00 0.00 0.00 1.28
6908 7368 9.692749 TTGGTGATCTAAACGCTCTTATATTAG 57.307 33.333 0.00 0.00 0.00 1.73
6909 7369 8.857098 TGGTGATCTAAACGCTCTTATATTAGT 58.143 33.333 0.00 0.00 0.00 2.24
6910 7370 9.694137 GGTGATCTAAACGCTCTTATATTAGTT 57.306 33.333 0.00 0.00 0.00 2.24
6918 7378 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
6919 7379 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
6920 7380 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
6951 7411 0.883833 AGGTGCCAATCTTTTGCTCG 59.116 50.000 0.00 0.00 0.00 5.03
7148 7608 1.795872 TCTATCCGTTGCGTGTTTGTG 59.204 47.619 0.00 0.00 0.00 3.33
7165 7625 2.345876 TGTGTACGGCTGAACATCATG 58.654 47.619 0.00 0.00 0.00 3.07
7166 7626 2.289382 TGTGTACGGCTGAACATCATGT 60.289 45.455 0.00 0.00 0.00 3.21
7302 7765 0.941463 CGCCTATCGCTCCACATGAC 60.941 60.000 0.00 0.00 34.21 3.06
7440 7903 2.829003 TCGTAGAGAGCTGGCCCG 60.829 66.667 0.00 0.00 0.00 6.13
7441 7904 3.141488 CGTAGAGAGCTGGCCCGT 61.141 66.667 0.00 0.00 0.00 5.28
7506 7971 4.705023 TGTACTTCTCGGAGATGTCATCAA 59.295 41.667 24.57 8.97 34.84 2.57
7513 7978 8.818141 TTCTCGGAGATGTCATCAATAATTAC 57.182 34.615 15.20 0.00 33.89 1.89
7570 8035 3.003275 TGTTTGTCCTGAAATCGTTGCTC 59.997 43.478 0.00 0.00 0.00 4.26
7643 8108 6.884280 AAGCAAGAATACAAGTTGTAGCTT 57.116 33.333 23.47 23.47 36.14 3.74
7683 8148 0.177604 CTCTAGGCACAAGAGGGCTG 59.822 60.000 0.00 0.00 41.71 4.85
7684 8149 0.252239 TCTAGGCACAAGAGGGCTGA 60.252 55.000 0.00 0.00 41.71 4.26
7685 8150 0.107945 CTAGGCACAAGAGGGCTGAC 60.108 60.000 0.00 0.00 41.71 3.51
7686 8151 0.545309 TAGGCACAAGAGGGCTGACT 60.545 55.000 0.00 0.00 41.71 3.41
7732 8197 5.484173 ACACATGGATGTATAAGCAAACG 57.516 39.130 0.00 0.00 39.39 3.60
7807 8272 1.812922 GCACATGTCGAGGAGGCAG 60.813 63.158 0.00 0.00 38.18 4.85
7875 8340 8.530311 ACAGATGATGAATATCTCAGTGTATCC 58.470 37.037 0.00 0.00 37.52 2.59
8009 9420 2.094762 TAGCGAGAAAAAGGTGAGGC 57.905 50.000 0.00 0.00 0.00 4.70
8042 9453 2.685388 GCTTACCATCCTTCCAAGAAGC 59.315 50.000 0.00 0.00 0.00 3.86
8208 9622 3.398310 TGGGTATGCTGCTCGCCA 61.398 61.111 0.00 0.00 38.05 5.69
8232 9646 1.731160 CGCCAGCAAGAAGAAGAAGAG 59.269 52.381 0.00 0.00 0.00 2.85
8263 9680 0.110238 CCAAACCATCAGTTCACGCG 60.110 55.000 3.53 3.53 37.88 6.01
8377 9797 4.287781 TCGACCGGACGCAGCAAA 62.288 61.111 21.57 0.00 0.00 3.68
8413 9836 1.599797 CGGGTGTTGGGAACTGGAC 60.600 63.158 0.00 0.00 0.00 4.02
8425 9848 4.436998 CTGGACGGACCTGACGGC 62.437 72.222 0.00 0.00 39.52 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 52 6.124340 AGTGAGTTGAATATCATTGATGCCA 58.876 36.000 9.46 2.05 0.00 4.92
109 112 2.554032 CAATTGGCGGATATCTTCACCC 59.446 50.000 2.05 0.00 0.00 4.61
140 143 7.359431 GGTGACATAAATCTTAAACACGTTCGA 60.359 37.037 0.00 0.00 0.00 3.71
171 174 7.039270 CACCATTTCATTCATGATCATGTTGT 58.961 34.615 30.01 16.92 39.72 3.32
288 292 9.889128 TCTCAAAGATTATGTGATACATGTGAA 57.111 29.630 9.11 0.00 39.53 3.18
320 324 6.839124 TGTGCTCAATTATTTTGGATGACT 57.161 33.333 0.00 0.00 0.00 3.41
331 335 5.221185 GCAGGATCATGTTGTGCTCAATTAT 60.221 40.000 9.42 0.50 35.92 1.28
408 412 2.422945 GGTCCCTTGTGTCTTGGACTTT 60.423 50.000 7.40 0.00 45.29 2.66
412 416 1.975680 GTAGGTCCCTTGTGTCTTGGA 59.024 52.381 0.00 0.00 0.00 3.53
454 458 6.114089 GGTAAGGTTGGTAGAAAATCCTCTC 58.886 44.000 0.00 0.00 0.00 3.20
457 461 5.516062 GGTGGTAAGGTTGGTAGAAAATCCT 60.516 44.000 0.00 0.00 0.00 3.24
468 472 0.253610 TATGCCGGTGGTAAGGTTGG 59.746 55.000 1.90 0.00 0.00 3.77
496 500 8.636213 CATCTTTTGATATTGTTGGCTATTCCT 58.364 33.333 0.00 0.00 37.40 3.36
581 587 6.260936 AGCGAATGTTATCTTAAAGTCATGGG 59.739 38.462 0.00 0.00 0.00 4.00
582 588 7.251704 AGCGAATGTTATCTTAAAGTCATGG 57.748 36.000 0.00 0.00 0.00 3.66
589 595 4.097286 GCCCCAAGCGAATGTTATCTTAAA 59.903 41.667 0.00 0.00 0.00 1.52
604 610 1.068127 CAATATCAAGCAGCCCCAAGC 59.932 52.381 0.00 0.00 44.25 4.01
629 635 8.160521 ACTTTTATGTTAAGTGTGTGCATGTA 57.839 30.769 0.00 0.00 34.68 2.29
651 657 1.040646 TGTGCTTCTCGTCCTGACTT 58.959 50.000 0.00 0.00 0.00 3.01
652 658 1.040646 TTGTGCTTCTCGTCCTGACT 58.959 50.000 0.00 0.00 0.00 3.41
665 671 7.512130 TGGTTCTCTAATCATATCATTGTGCT 58.488 34.615 0.00 0.00 0.00 4.40
678 684 6.820656 TCAGCTGAAAGATTGGTTCTCTAATC 59.179 38.462 15.67 0.00 40.36 1.75
681 687 5.247110 AGTCAGCTGAAAGATTGGTTCTCTA 59.753 40.000 20.19 0.00 34.07 2.43
699 705 0.739112 GGTACAGCAGAGCAGTCAGC 60.739 60.000 0.00 0.00 46.19 4.26
700 706 0.108424 GGGTACAGCAGAGCAGTCAG 60.108 60.000 0.00 0.00 29.63 3.51
701 707 0.831711 TGGGTACAGCAGAGCAGTCA 60.832 55.000 0.00 0.00 29.63 3.41
702 708 0.108424 CTGGGTACAGCAGAGCAGTC 60.108 60.000 0.00 0.00 38.01 3.51
703 709 1.978473 CTGGGTACAGCAGAGCAGT 59.022 57.895 0.00 0.00 38.01 4.40
704 710 4.928398 CTGGGTACAGCAGAGCAG 57.072 61.111 0.00 0.00 38.01 4.24
713 719 1.052617 TTACTGTGCAGCTGGGTACA 58.947 50.000 17.12 5.29 32.39 2.90
714 720 2.178912 TTTACTGTGCAGCTGGGTAC 57.821 50.000 17.12 0.00 0.00 3.34
715 721 2.158740 TGTTTTACTGTGCAGCTGGGTA 60.159 45.455 17.12 0.00 0.00 3.69
716 722 1.318576 GTTTTACTGTGCAGCTGGGT 58.681 50.000 17.12 0.00 0.00 4.51
717 723 1.001378 GTGTTTTACTGTGCAGCTGGG 60.001 52.381 17.12 0.00 0.00 4.45
718 724 1.001378 GGTGTTTTACTGTGCAGCTGG 60.001 52.381 17.12 0.31 0.00 4.85
719 725 1.949525 AGGTGTTTTACTGTGCAGCTG 59.050 47.619 10.11 10.11 38.12 4.24
720 726 2.222027 GAGGTGTTTTACTGTGCAGCT 58.778 47.619 0.00 0.00 41.56 4.24
721 727 1.946768 TGAGGTGTTTTACTGTGCAGC 59.053 47.619 0.00 0.00 0.00 5.25
722 728 4.335315 TCTTTGAGGTGTTTTACTGTGCAG 59.665 41.667 0.00 0.00 0.00 4.41
723 729 4.265893 TCTTTGAGGTGTTTTACTGTGCA 58.734 39.130 0.00 0.00 0.00 4.57
724 730 4.893424 TCTTTGAGGTGTTTTACTGTGC 57.107 40.909 0.00 0.00 0.00 4.57
725 731 6.677781 TCTTCTTTGAGGTGTTTTACTGTG 57.322 37.500 0.00 0.00 0.00 3.66
726 732 7.110155 TCTTCTTCTTTGAGGTGTTTTACTGT 58.890 34.615 0.00 0.00 0.00 3.55
727 733 7.553881 TCTTCTTCTTTGAGGTGTTTTACTG 57.446 36.000 0.00 0.00 0.00 2.74
728 734 8.575649 TTTCTTCTTCTTTGAGGTGTTTTACT 57.424 30.769 0.00 0.00 0.00 2.24
729 735 9.634163 TTTTTCTTCTTCTTTGAGGTGTTTTAC 57.366 29.630 0.00 0.00 0.00 2.01
786 792 2.484651 GTCTCGGGGCTTTCTTCTTTTC 59.515 50.000 0.00 0.00 0.00 2.29
792 799 2.047179 GCGTCTCGGGGCTTTCTT 60.047 61.111 0.00 0.00 0.00 2.52
983 1008 0.671251 CATGGCCTACGAGTCTCCTC 59.329 60.000 3.32 0.00 0.00 3.71
1196 1221 2.484062 GCAATGCGTGGATGGAGGG 61.484 63.158 0.00 0.00 0.00 4.30
1202 1227 1.660560 GAAGCCAGCAATGCGTGGAT 61.661 55.000 21.89 15.55 35.67 3.41
1230 1255 0.460987 CGGCAGAAGCAAGAGGTAGG 60.461 60.000 0.00 0.00 44.61 3.18
1357 1383 6.382869 ACTGAATGCTGCATAGGTAATTTC 57.617 37.500 16.58 8.37 0.00 2.17
1468 1494 1.384191 GGGCCCCAGTTGAACAGAT 59.616 57.895 12.23 0.00 0.00 2.90
1476 1502 2.765969 CTGTGATGGGCCCCAGTT 59.234 61.111 22.27 0.25 36.75 3.16
1483 1509 1.818060 TGTAATTGTGCTGTGATGGGC 59.182 47.619 0.00 0.00 0.00 5.36
1504 1530 5.413833 TCAAGCTAGCTTACGTTGTACTACT 59.586 40.000 28.87 0.00 34.50 2.57
1505 1531 5.511025 GTCAAGCTAGCTTACGTTGTACTAC 59.489 44.000 28.87 8.18 34.50 2.73
1506 1532 5.392380 GGTCAAGCTAGCTTACGTTGTACTA 60.392 44.000 28.87 0.00 34.50 1.82
1534 1560 4.348656 CGTCTCATTCAATTCCATTGCAG 58.651 43.478 0.00 0.00 40.05 4.41
1741 1767 1.328680 GCATGGTACTTCGACTGCATG 59.671 52.381 0.00 0.00 0.00 4.06
1775 1801 6.478129 ACATTTTTCTAATCCAGAACGGGTA 58.522 36.000 0.00 0.00 43.09 3.69
1913 1954 5.582665 CAGTCTTAGTTGCAAGTCCTAATCC 59.417 44.000 10.78 3.73 0.00 3.01
1934 1975 1.202758 TCAATGAGGCGACCAAACAGT 60.203 47.619 0.00 0.00 0.00 3.55
1945 1986 2.818130 TGGCTTTTTGTCAATGAGGC 57.182 45.000 12.58 12.58 0.00 4.70
1960 2001 1.177256 CCAGCTGCAAGAGTTTGGCT 61.177 55.000 8.66 0.00 33.74 4.75
1984 2025 2.102420 CAGTGGGAGTGTCAAGTGTGTA 59.898 50.000 0.00 0.00 0.00 2.90
1999 2040 1.813092 GCTATGCATGACCTCAGTGGG 60.813 57.143 10.16 0.00 41.11 4.61
2131 2173 8.461222 CAACATAATCTGCACTGGAAAGAATAA 58.539 33.333 0.00 0.00 0.00 1.40
2213 2270 7.667575 AGTTGAATCATGTATCAGGTAGAGT 57.332 36.000 0.00 0.00 0.00 3.24
2214 2271 8.200120 TGAAGTTGAATCATGTATCAGGTAGAG 58.800 37.037 0.00 0.00 0.00 2.43
2215 2272 8.078060 TGAAGTTGAATCATGTATCAGGTAGA 57.922 34.615 0.00 0.00 0.00 2.59
2216 2273 8.899427 ATGAAGTTGAATCATGTATCAGGTAG 57.101 34.615 0.00 0.00 36.21 3.18
2217 2274 9.330063 GAATGAAGTTGAATCATGTATCAGGTA 57.670 33.333 0.00 0.00 37.58 3.08
2218 2275 7.830697 TGAATGAAGTTGAATCATGTATCAGGT 59.169 33.333 0.00 0.00 37.58 4.00
2219 2276 8.217131 TGAATGAAGTTGAATCATGTATCAGG 57.783 34.615 0.00 0.00 37.58 3.86
2220 2277 8.890718 ACTGAATGAAGTTGAATCATGTATCAG 58.109 33.333 12.00 12.00 41.29 2.90
2221 2278 8.797350 ACTGAATGAAGTTGAATCATGTATCA 57.203 30.769 0.00 0.00 37.58 2.15
2222 2279 8.886719 TGACTGAATGAAGTTGAATCATGTATC 58.113 33.333 0.00 0.00 37.58 2.24
2229 2296 8.539770 TTCTACTGACTGAATGAAGTTGAATC 57.460 34.615 0.00 0.00 32.19 2.52
2281 2348 5.769662 AGGAATTGTGCAGAATAGAAACACA 59.230 36.000 9.82 0.00 39.35 3.72
2491 2570 6.790232 TCACTTTGAAAATCCTTTTCCACT 57.210 33.333 9.24 0.00 46.49 4.00
2569 2648 5.247862 TCTGCAAGCAAAATGTCTATCTCA 58.752 37.500 0.00 0.00 0.00 3.27
2804 2883 5.437191 ACAGGACCTTTACCAATCCTAAG 57.563 43.478 0.00 0.00 39.66 2.18
2911 2990 5.453567 ACAAGGTTGCAGAATAAGTTTCC 57.546 39.130 0.00 0.00 0.00 3.13
2920 2999 1.227409 TCGCGACAAGGTTGCAGAA 60.227 52.632 3.71 0.00 42.60 3.02
2937 3016 7.360776 CCTTTGAGATAGCTGAGAAAACAAGTC 60.361 40.741 0.00 0.00 0.00 3.01
3057 3136 9.056005 GCAAAGGAGATTTTTCTTTAACCAAAT 57.944 29.630 0.00 0.00 0.00 2.32
3196 3275 5.122239 CACTTCTTCAATATGAGGTCGCAAA 59.878 40.000 0.00 0.00 0.00 3.68
3241 3320 7.927629 GCTGAATCAATAATCTCTCTTCTCACT 59.072 37.037 0.00 0.00 0.00 3.41
3251 3330 6.765036 TCAGTCCTTGCTGAATCAATAATCTC 59.235 38.462 0.00 0.00 41.93 2.75
3310 3389 0.379669 CAACTGAATCAGATGGCGGC 59.620 55.000 18.20 0.00 35.18 6.53
3351 3430 6.357367 ACTGACATAAACTTCTTTCCACTGT 58.643 36.000 0.00 0.00 0.00 3.55
3408 3487 8.646004 TCCAGAATGAAAATATCAACAAAACCA 58.354 29.630 0.00 0.00 42.54 3.67
3458 3537 9.770097 CATGGAACTCAACTCATATATACAGTT 57.230 33.333 3.89 3.89 0.00 3.16
3497 3576 3.740832 GGCTACTCAAAACCAAATTGTGC 59.259 43.478 0.00 0.00 0.00 4.57
3857 3946 2.826128 TGATCGTGAGCAGGACTTAGTT 59.174 45.455 0.00 0.00 0.00 2.24
3860 3949 4.499865 GCTAATGATCGTGAGCAGGACTTA 60.500 45.833 18.15 0.00 34.96 2.24
3964 4053 2.166459 GCATGTACAGACTACAGAGGCA 59.834 50.000 0.33 0.00 30.20 4.75
4017 4106 3.002791 TCAAGAGAGTAATTTGCCGCAG 58.997 45.455 0.00 0.00 0.00 5.18
4102 4200 4.758251 TCGTCGGCCATGGCACTG 62.758 66.667 36.56 24.99 44.11 3.66
4129 4227 2.639065 GTGTTGTGACCAAAGGAGACA 58.361 47.619 0.00 0.00 30.94 3.41
4141 4239 1.606668 GCGAAAGGATTGGTGTTGTGA 59.393 47.619 0.00 0.00 0.00 3.58
4200 4542 2.185867 GGACGTGCTGCCGGATAA 59.814 61.111 5.05 0.00 0.00 1.75
4364 4718 0.389948 GCCGTGTAGACCCAGTTCAG 60.390 60.000 0.00 0.00 0.00 3.02
4392 4746 5.072741 TCACGATGATCATGAGTATCTCCA 58.927 41.667 14.30 1.65 34.92 3.86
4563 4951 1.983119 GCCCCTCATTGGTGATCGGA 61.983 60.000 0.00 0.00 32.98 4.55
4601 4989 0.031721 GTCGTTGGACTTGAGGACGT 59.968 55.000 0.00 0.00 40.15 4.34
4725 5166 0.909610 CTGGGAAGCTACCTGGGTGA 60.910 60.000 8.65 0.00 0.00 4.02
4750 5191 2.355513 GCTCTGCTCAGAATTGGAGGAA 60.356 50.000 0.93 0.00 36.94 3.36
4759 5203 0.966179 TGTTACGGCTCTGCTCAGAA 59.034 50.000 0.93 0.00 36.94 3.02
4784 5228 1.515020 GATGTCGCTGAGAGCCACT 59.485 57.895 0.00 0.00 38.18 4.00
4838 5283 6.321821 AGGTAGGCCTTTTGTCATAACATA 57.678 37.500 12.58 0.00 44.18 2.29
4912 5358 4.379243 CGCCGCAGACTCAGGGTT 62.379 66.667 0.00 0.00 0.00 4.11
4988 5434 1.954382 CTGTATGACTAGGCCTACGCA 59.046 52.381 8.91 10.32 36.38 5.24
5011 5457 3.003480 CCTGAGCTACAAAACCTGCTAC 58.997 50.000 0.00 0.00 35.76 3.58
5142 5589 0.924823 AATCTCCAAGCCAGCTGGAT 59.075 50.000 37.21 29.54 37.39 3.41
5178 5625 7.829706 ACCAATAGAGATTGAAAGGAGTTAACC 59.170 37.037 0.88 0.00 44.59 2.85
5179 5626 8.794335 ACCAATAGAGATTGAAAGGAGTTAAC 57.206 34.615 0.00 0.00 44.59 2.01
5256 5703 3.265221 AGTTCAATCTCCAAGCCAGATGA 59.735 43.478 0.00 0.00 30.62 2.92
5540 5987 8.323567 ACTTCCAGCAAAATATTCAATCCAAAT 58.676 29.630 0.00 0.00 0.00 2.32
5610 6067 7.386025 TGCTTTAAATGATCAGATATCCAGTCG 59.614 37.037 0.09 0.00 0.00 4.18
5811 6268 6.942576 TCAGCTTTTAATTCTACAGGCTCTTT 59.057 34.615 0.00 0.00 0.00 2.52
6838 7298 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
6839 7299 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
6840 7300 8.003629 ACTCTTATATTAGTTTACGGAGGGAGT 58.996 37.037 0.00 0.00 0.00 3.85
6841 7301 8.298140 CACTCTTATATTAGTTTACGGAGGGAG 58.702 40.741 0.00 0.00 0.00 4.30
6842 7302 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
6843 7303 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
6844 7304 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
6859 7319 9.046296 CCAAAATAGCGATCTAAACACTCTTAT 57.954 33.333 0.00 0.00 0.00 1.73
6860 7320 8.038944 ACCAAAATAGCGATCTAAACACTCTTA 58.961 33.333 0.00 0.00 0.00 2.10
6861 7321 6.879458 ACCAAAATAGCGATCTAAACACTCTT 59.121 34.615 0.00 0.00 0.00 2.85
6862 7322 6.313905 CACCAAAATAGCGATCTAAACACTCT 59.686 38.462 0.00 0.00 0.00 3.24
6863 7323 6.312918 TCACCAAAATAGCGATCTAAACACTC 59.687 38.462 0.00 0.00 0.00 3.51
6864 7324 6.170506 TCACCAAAATAGCGATCTAAACACT 58.829 36.000 0.00 0.00 0.00 3.55
6865 7325 6.417191 TCACCAAAATAGCGATCTAAACAC 57.583 37.500 0.00 0.00 0.00 3.32
6866 7326 7.047891 AGATCACCAAAATAGCGATCTAAACA 58.952 34.615 0.00 0.00 40.70 2.83
6867 7327 7.484035 AGATCACCAAAATAGCGATCTAAAC 57.516 36.000 0.00 0.00 40.70 2.01
6869 7329 9.042008 GTTTAGATCACCAAAATAGCGATCTAA 57.958 33.333 13.44 13.44 46.35 2.10
6870 7330 7.381408 CGTTTAGATCACCAAAATAGCGATCTA 59.619 37.037 0.00 0.00 42.12 1.98
6871 7331 6.201044 CGTTTAGATCACCAAAATAGCGATCT 59.799 38.462 0.00 0.00 43.84 2.75
6872 7332 6.355638 CGTTTAGATCACCAAAATAGCGATC 58.644 40.000 0.00 0.00 34.08 3.69
6873 7333 5.277345 GCGTTTAGATCACCAAAATAGCGAT 60.277 40.000 0.00 0.00 0.00 4.58
6874 7334 4.033587 GCGTTTAGATCACCAAAATAGCGA 59.966 41.667 0.00 0.00 0.00 4.93
6875 7335 4.034048 AGCGTTTAGATCACCAAAATAGCG 59.966 41.667 0.00 0.00 0.00 4.26
6876 7336 5.294552 AGAGCGTTTAGATCACCAAAATAGC 59.705 40.000 0.00 1.43 37.82 2.97
6877 7337 6.910536 AGAGCGTTTAGATCACCAAAATAG 57.089 37.500 0.00 0.00 37.82 1.73
6878 7338 8.958119 ATAAGAGCGTTTAGATCACCAAAATA 57.042 30.769 0.00 0.00 37.82 1.40
6879 7339 7.865706 ATAAGAGCGTTTAGATCACCAAAAT 57.134 32.000 0.00 0.00 37.82 1.82
6880 7340 8.958119 ATATAAGAGCGTTTAGATCACCAAAA 57.042 30.769 0.00 0.00 37.82 2.44
6881 7341 8.958119 AATATAAGAGCGTTTAGATCACCAAA 57.042 30.769 0.00 0.00 37.82 3.28
6882 7342 9.692749 CTAATATAAGAGCGTTTAGATCACCAA 57.307 33.333 0.00 0.00 37.82 3.67
6883 7343 8.857098 ACTAATATAAGAGCGTTTAGATCACCA 58.143 33.333 0.00 0.00 37.82 4.17
6884 7344 9.694137 AACTAATATAAGAGCGTTTAGATCACC 57.306 33.333 0.00 0.00 37.82 4.02
6892 7352 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
6893 7353 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
6894 7354 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
6895 7355 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
6896 7356 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
6902 7362 9.435570 ACATGTACTCCCTCTGTAAACTAATAT 57.564 33.333 0.00 0.00 0.00 1.28
6903 7363 8.834004 ACATGTACTCCCTCTGTAAACTAATA 57.166 34.615 0.00 0.00 0.00 0.98
6904 7364 7.735326 ACATGTACTCCCTCTGTAAACTAAT 57.265 36.000 0.00 0.00 0.00 1.73
6905 7365 7.549147 AACATGTACTCCCTCTGTAAACTAA 57.451 36.000 0.00 0.00 0.00 2.24
6906 7366 8.654485 TTAACATGTACTCCCTCTGTAAACTA 57.346 34.615 0.00 0.00 0.00 2.24
6907 7367 7.549147 TTAACATGTACTCCCTCTGTAAACT 57.451 36.000 0.00 0.00 0.00 2.66
6908 7368 7.333672 CCTTTAACATGTACTCCCTCTGTAAAC 59.666 40.741 0.00 0.00 0.00 2.01
6909 7369 7.016858 ACCTTTAACATGTACTCCCTCTGTAAA 59.983 37.037 0.00 0.00 0.00 2.01
6910 7370 6.499350 ACCTTTAACATGTACTCCCTCTGTAA 59.501 38.462 0.00 0.00 0.00 2.41
6911 7371 6.021030 ACCTTTAACATGTACTCCCTCTGTA 58.979 40.000 0.00 0.00 0.00 2.74
6912 7372 4.844655 ACCTTTAACATGTACTCCCTCTGT 59.155 41.667 0.00 0.00 0.00 3.41
6913 7373 5.178797 CACCTTTAACATGTACTCCCTCTG 58.821 45.833 0.00 0.00 0.00 3.35
6914 7374 4.323562 GCACCTTTAACATGTACTCCCTCT 60.324 45.833 0.00 0.00 0.00 3.69
6915 7375 3.939592 GCACCTTTAACATGTACTCCCTC 59.060 47.826 0.00 0.00 0.00 4.30
6916 7376 3.308188 GGCACCTTTAACATGTACTCCCT 60.308 47.826 0.00 0.00 0.00 4.20
6917 7377 3.014623 GGCACCTTTAACATGTACTCCC 58.985 50.000 0.00 0.00 0.00 4.30
6918 7378 3.681593 TGGCACCTTTAACATGTACTCC 58.318 45.455 0.00 0.00 0.00 3.85
6919 7379 5.648092 AGATTGGCACCTTTAACATGTACTC 59.352 40.000 0.00 0.00 0.00 2.59
6920 7380 5.570320 AGATTGGCACCTTTAACATGTACT 58.430 37.500 0.00 0.00 0.00 2.73
6951 7411 7.701445 AGTGCATATCAAGAATAAGCTGAAAC 58.299 34.615 0.00 0.00 35.92 2.78
7110 7570 5.123979 GGATAGACTGAAGCAACGGATTTTT 59.876 40.000 0.00 0.00 0.00 1.94
7111 7571 4.636206 GGATAGACTGAAGCAACGGATTTT 59.364 41.667 0.00 0.00 0.00 1.82
7112 7572 4.192317 GGATAGACTGAAGCAACGGATTT 58.808 43.478 0.00 0.00 0.00 2.17
7113 7573 3.738281 CGGATAGACTGAAGCAACGGATT 60.738 47.826 0.00 0.00 0.00 3.01
7114 7574 2.223829 CGGATAGACTGAAGCAACGGAT 60.224 50.000 0.00 0.00 0.00 4.18
7148 7608 2.742053 ACAACATGATGTTCAGCCGTAC 59.258 45.455 8.03 0.00 38.77 3.67
7257 7720 1.028905 GGTCGGACTCAGATCCAGAG 58.971 60.000 8.23 10.38 38.87 3.35
7296 7759 4.338400 TCTTCTGATATTCCGTCGTCATGT 59.662 41.667 0.00 0.00 0.00 3.21
7302 7765 5.763088 TCTGAATCTTCTGATATTCCGTCG 58.237 41.667 9.47 0.00 32.25 5.12
7433 7896 1.656652 CATCTACAAGAACGGGCCAG 58.343 55.000 4.39 1.85 0.00 4.85
7440 7903 8.804688 ATATTTAGACTCGCATCTACAAGAAC 57.195 34.615 0.00 0.00 30.75 3.01
7441 7904 9.817809 AAATATTTAGACTCGCATCTACAAGAA 57.182 29.630 0.00 0.00 30.75 2.52
7544 8009 5.332506 GCAACGATTTCAGGACAAACAAATG 60.333 40.000 0.00 0.00 0.00 2.32
7643 8108 6.939622 AGAGAACTGTGTGATGATCAATACA 58.060 36.000 0.00 5.35 0.00 2.29
7683 8148 2.897969 TGTGGAGTTGTAAGGGAGAGTC 59.102 50.000 0.00 0.00 0.00 3.36
7684 8149 2.633481 GTGTGGAGTTGTAAGGGAGAGT 59.367 50.000 0.00 0.00 0.00 3.24
7685 8150 2.900546 AGTGTGGAGTTGTAAGGGAGAG 59.099 50.000 0.00 0.00 0.00 3.20
7686 8151 2.972348 AGTGTGGAGTTGTAAGGGAGA 58.028 47.619 0.00 0.00 0.00 3.71
7875 8340 8.190784 CCTGCAAAAACACTAGGGATATTAAAG 58.809 37.037 0.00 0.00 0.00 1.85
8009 9420 2.060326 TGGTAAGCTTTCACGTCTCG 57.940 50.000 3.20 0.00 0.00 4.04
8188 9602 2.203070 CGAGCAGCATACCCACCC 60.203 66.667 0.00 0.00 0.00 4.61
8208 9622 0.886490 CTTCTTCTTGCTGGCGTGGT 60.886 55.000 0.00 0.00 0.00 4.16
8263 9680 2.125673 TGCTCGCCGCTTACCTTC 60.126 61.111 0.00 0.00 40.11 3.46


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

AutoCloner maintained by Alex Coulton.