Multiple sequence alignment - TraesCS2D01G275100

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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 TraesCS2D01G275100 chr2D 100.000 4028 0 0 1 4028 344795974 344800001 0.000000e+00 7439.0
1 TraesCS2D01G275100 chr2D 86.207 116 12 3 542 656 443245946 443246058 5.470000e-24 122.0
2 TraesCS2D01G275100 chr2A 92.446 2780 100 44 645 3371 456100954 456103676 0.000000e+00 3869.0
3 TraesCS2D01G275100 chr2A 89.937 318 19 9 224 529 456100640 456100956 8.110000e-107 398.0
4 TraesCS2D01G275100 chr2A 96.996 233 6 1 1 232 456081821 456082053 1.360000e-104 390.0
5 TraesCS2D01G275100 chr2A 96.567 233 7 1 1 232 456097242 456097474 6.320000e-103 385.0
6 TraesCS2D01G275100 chr2A 79.070 387 50 26 134 503 592426073 592425701 1.870000e-58 237.0
7 TraesCS2D01G275100 chr2A 85.246 122 16 2 527 648 113315775 113315656 1.520000e-24 124.0
8 TraesCS2D01G275100 chr2A 95.775 71 3 0 1011 1081 13961280 13961350 9.150000e-22 115.0
9 TraesCS2D01G275100 chr2B 90.097 1858 107 24 648 2478 410061055 410062862 0.000000e+00 2340.0
10 TraesCS2D01G275100 chr2B 92.500 960 53 10 2432 3373 410062864 410063822 0.000000e+00 1356.0
11 TraesCS2D01G275100 chr2B 92.704 466 22 8 1 463 410059785 410060241 0.000000e+00 662.0
12 TraesCS2D01G275100 chr2B 77.506 449 65 29 48 474 43049772 43049338 1.870000e-58 237.0
13 TraesCS2D01G275100 chr2B 89.781 137 6 5 3463 3598 410064368 410064497 6.920000e-38 169.0
14 TraesCS2D01G275100 chr2B 90.598 117 8 2 3756 3870 121367708 121367593 6.970000e-33 152.0
15 TraesCS2D01G275100 chr2B 91.935 62 2 3 3860 3921 410064982 410065040 2.580000e-12 84.2
16 TraesCS2D01G275100 chr1B 95.327 107 3 1 3756 3860 674074463 674074357 6.920000e-38 169.0
17 TraesCS2D01G275100 chr1B 97.059 34 1 0 263 296 368404350 368404383 1.560000e-04 58.4
18 TraesCS2D01G275100 chr4B 96.117 103 2 1 3756 3856 413734208 413734310 2.490000e-37 167.0
19 TraesCS2D01G275100 chr4B 91.304 115 6 2 3756 3868 398529230 398529342 1.940000e-33 154.0
20 TraesCS2D01G275100 chr7A 96.078 102 2 1 3756 3855 78506237 78506136 8.960000e-37 165.0
21 TraesCS2D01G275100 chr7A 86.585 82 9 1 566 647 679759005 679759084 5.540000e-14 89.8
22 TraesCS2D01G275100 chr6A 95.192 104 3 1 3756 3857 189553672 189553569 3.220000e-36 163.0
23 TraesCS2D01G275100 chr5A 95.192 104 3 1 3756 3857 560578052 560578155 3.220000e-36 163.0
24 TraesCS2D01G275100 chr5A 86.813 91 10 1 557 647 548474557 548474469 2.560000e-17 100.0
25 TraesCS2D01G275100 chrUn 90.083 121 7 4 3756 3873 10314578 10314460 6.970000e-33 152.0
26 TraesCS2D01G275100 chrUn 90.083 121 7 4 3756 3873 299762110 299761992 6.970000e-33 152.0
27 TraesCS2D01G275100 chr7B 83.333 168 24 4 2678 2843 743548271 743548436 6.970000e-33 152.0
28 TraesCS2D01G275100 chr4A 85.981 107 13 2 543 649 233453205 233453309 3.290000e-21 113.0
29 TraesCS2D01G275100 chr4D 90.141 71 7 0 533 603 133725491 133725421 4.290000e-15 93.5
30 TraesCS2D01G275100 chr6D 94.915 59 0 2 3859 3916 183387425 183387481 5.540000e-14 89.8
31 TraesCS2D01G275100 chr1A 82.022 89 10 5 213 297 313913405 313913319 2.010000e-08 71.3
32 TraesCS2D01G275100 chr3A 83.333 72 7 5 245 315 715482861 715482928 1.210000e-05 62.1
33 TraesCS2D01G275100 chr3D 96.970 33 0 1 263 294 81733414 81733446 2.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G275100 chr2D 344795974 344800001 4027 False 7439.000000 7439 100.000000 1 4028 1 chr2D.!!$F1 4027
1 TraesCS2D01G275100 chr2A 456097242 456103676 6434 False 1550.666667 3869 92.983333 1 3371 3 chr2A.!!$F3 3370
2 TraesCS2D01G275100 chr2B 410059785 410065040 5255 False 922.240000 2340 91.403400 1 3921 5 chr2B.!!$F1 3920

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
740 4671 0.107897 TGGGCCAACTATGTAGCGTG 60.108 55.0 2.13 0.0 0.00 5.34 F
2624 6660 0.107508 TCCCTGCTCACTGCTTATGC 60.108 55.0 0.00 0.0 43.37 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2647 6686 0.115152 TCAGCCTCTTGTCCCTGAGA 59.885 55.0 0.0 0.0 32.44 3.27 R
3958 8765 0.108585 TTTGAGGGCTTTGCTCGTCT 59.891 50.0 0.0 0.0 32.17 4.18 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
42 43 3.573967 TGAACAAAGCTCTCAAATTCCCC 59.426 43.478 0.00 0.00 0.00 4.81
55 56 0.614812 ATTCCCCCAAGCAAATGCAC 59.385 50.000 8.28 0.00 45.16 4.57
395 3573 5.778862 TGCTACCAACATTTTCTAAAAGCC 58.221 37.500 0.00 0.00 0.00 4.35
427 3605 2.181426 TTTTAACGCTGCACACACAC 57.819 45.000 0.00 0.00 0.00 3.82
531 3753 7.940178 AAAAACAAAATCCAGGAACGTAATC 57.060 32.000 0.00 0.00 0.00 1.75
532 3754 5.638596 AACAAAATCCAGGAACGTAATCC 57.361 39.130 0.00 0.00 39.96 3.01
533 3755 4.014406 ACAAAATCCAGGAACGTAATCCC 58.986 43.478 2.56 0.00 40.59 3.85
534 3756 4.263771 ACAAAATCCAGGAACGTAATCCCT 60.264 41.667 2.56 0.00 40.59 4.20
535 3757 4.586306 AAATCCAGGAACGTAATCCCTT 57.414 40.909 2.56 0.00 40.59 3.95
536 3758 3.840124 ATCCAGGAACGTAATCCCTTC 57.160 47.619 2.56 0.00 40.59 3.46
537 3759 1.479323 TCCAGGAACGTAATCCCTTCG 59.521 52.381 2.56 0.00 40.59 3.79
538 3760 1.206371 CCAGGAACGTAATCCCTTCGT 59.794 52.381 2.56 0.00 40.59 3.85
539 3761 2.537401 CAGGAACGTAATCCCTTCGTC 58.463 52.381 2.56 0.00 40.59 4.20
540 3762 2.165845 CAGGAACGTAATCCCTTCGTCT 59.834 50.000 2.56 0.00 40.59 4.18
541 3763 3.379372 CAGGAACGTAATCCCTTCGTCTA 59.621 47.826 2.56 0.00 40.59 2.59
542 3764 4.019174 AGGAACGTAATCCCTTCGTCTAA 58.981 43.478 2.56 0.00 40.59 2.10
543 3765 4.463891 AGGAACGTAATCCCTTCGTCTAAA 59.536 41.667 2.56 0.00 40.59 1.85
544 3766 5.047092 AGGAACGTAATCCCTTCGTCTAAAA 60.047 40.000 2.56 0.00 40.59 1.52
545 3767 5.639082 GGAACGTAATCCCTTCGTCTAAAAA 59.361 40.000 0.00 0.00 36.80 1.94
587 3809 9.529325 TGAATGTATGTAGTATCAAGTTAGTGC 57.471 33.333 0.00 0.00 0.00 4.40
588 3810 9.751542 GAATGTATGTAGTATCAAGTTAGTGCT 57.248 33.333 0.00 0.00 0.00 4.40
591 3813 9.623000 TGTATGTAGTATCAAGTTAGTGCTAGA 57.377 33.333 0.00 0.00 0.00 2.43
595 3817 9.623000 TGTAGTATCAAGTTAGTGCTAGATACA 57.377 33.333 11.52 0.00 39.94 2.29
619 3841 9.320295 ACATTTATTTGAGGAATAAGTTTGGGA 57.680 29.630 0.00 0.00 40.36 4.37
620 3842 9.586435 CATTTATTTGAGGAATAAGTTTGGGAC 57.414 33.333 0.00 0.00 40.36 4.46
621 3843 8.713708 TTTATTTGAGGAATAAGTTTGGGACA 57.286 30.769 0.00 0.00 40.36 4.02
622 3844 8.713708 TTATTTGAGGAATAAGTTTGGGACAA 57.286 30.769 0.00 0.00 38.19 3.18
623 3845 9.148879 TTATTTGAGGAATAAGTTTGGGACAAA 57.851 29.630 0.00 0.00 38.19 2.83
643 3865 3.888811 TTTTTCCGGACGGAGGGA 58.111 55.556 13.64 1.83 46.06 4.20
708 4639 8.023706 GGAGGTCTCAATGAAAAATGTACTTTC 58.976 37.037 0.00 0.00 34.09 2.62
740 4671 0.107897 TGGGCCAACTATGTAGCGTG 60.108 55.000 2.13 0.00 0.00 5.34
749 4680 3.014623 ACTATGTAGCGTGCTCTGTACA 58.985 45.455 0.00 0.00 0.00 2.90
897 4829 4.010349 CCGGATGCCTTCCTATTTAATCC 58.990 47.826 0.00 0.00 42.99 3.01
1021 4960 1.300233 GGTAAGCTCCGCCGATCTG 60.300 63.158 0.00 0.00 0.00 2.90
1180 5119 3.679083 CGAAAGTAAGAGCGAATCCCCTT 60.679 47.826 0.00 0.00 0.00 3.95
1183 5122 1.129058 TAAGAGCGAATCCCCTTCCC 58.871 55.000 0.00 0.00 0.00 3.97
1184 5123 1.636769 AAGAGCGAATCCCCTTCCCC 61.637 60.000 0.00 0.00 0.00 4.81
1185 5124 3.097162 AGCGAATCCCCTTCCCCC 61.097 66.667 0.00 0.00 0.00 5.40
1236 5175 4.499183 GTGAAGATGTGTGGAGGTTCTAG 58.501 47.826 0.00 0.00 0.00 2.43
1265 5204 6.636044 GGTTAGATCCGTGTTTACTTAGATCG 59.364 42.308 0.00 0.00 33.92 3.69
1330 5269 3.139603 TCATTTATTCGACGCGTCTGA 57.860 42.857 33.94 28.05 0.00 3.27
1446 5387 0.868406 CCGCTTTCTGGTGACTTGAC 59.132 55.000 0.00 0.00 0.00 3.18
1483 5424 1.531677 CGCACATCTATGGTTTTGGCG 60.532 52.381 0.00 0.00 35.87 5.69
1499 5440 1.421485 GCGACATGCGAACTTCTGG 59.579 57.895 12.67 0.00 44.57 3.86
1551 5504 4.794762 CGTGAACTTGATGTTGGCAATATG 59.205 41.667 14.51 2.92 39.30 1.78
1596 5551 5.340803 TGTAGTGATACTGCTGTTTCGATC 58.659 41.667 0.09 0.00 31.77 3.69
1709 5665 8.817100 CATGATGTTGTCTATACGTAAACATGT 58.183 33.333 21.32 10.92 40.55 3.21
1746 5702 5.784578 TCTGCGAGTTATTCTTAGCCATA 57.215 39.130 0.00 0.00 32.15 2.74
1826 5782 2.093235 ACTGATCAACTCTTAGGCTGGC 60.093 50.000 0.00 0.00 0.00 4.85
1851 5807 4.781934 AGACCTTGCAAGAACTTTACACT 58.218 39.130 28.05 9.52 0.00 3.55
1852 5808 5.193679 AGACCTTGCAAGAACTTTACACTT 58.806 37.500 28.05 0.40 0.00 3.16
2073 6029 3.433957 TGGATGTGGTTTACAATTCGTCG 59.566 43.478 0.00 0.00 43.77 5.12
2145 6101 1.344114 GTTGATGCAGCCCCTTTCAAA 59.656 47.619 0.00 0.00 0.00 2.69
2306 6264 4.938226 AGCTTGTTTAGGATGTGCTACTTC 59.062 41.667 0.00 0.00 0.00 3.01
2327 6312 8.955061 ACTTCGTTGAAATGATATTCAGTTTG 57.045 30.769 0.00 0.00 40.21 2.93
2340 6325 7.549134 TGATATTCAGTTTGGTAGTTGTAGCAG 59.451 37.037 0.00 0.00 37.92 4.24
2407 6392 5.412904 CCTTTCATTCTGGACTGTTAGTTCC 59.587 44.000 0.00 0.00 0.00 3.62
2421 6407 6.204108 ACTGTTAGTTCCAACTTGTTTATCCG 59.796 38.462 0.00 0.00 40.37 4.18
2543 6579 6.709397 TGCATTTTGCCAATAATGTTTCAAGA 59.291 30.769 11.36 0.00 44.23 3.02
2575 6611 9.279233 AGTTTATATTATGCCCTTTTTCCCTTT 57.721 29.630 0.00 0.00 0.00 3.11
2624 6660 0.107508 TCCCTGCTCACTGCTTATGC 60.108 55.000 0.00 0.00 43.37 3.14
2647 6686 6.985645 TGCTTGCTTTGTGTGATTTTCTTATT 59.014 30.769 0.00 0.00 0.00 1.40
2649 6688 7.383300 GCTTGCTTTGTGTGATTTTCTTATTCT 59.617 33.333 0.00 0.00 0.00 2.40
2875 6916 5.245531 TCATCTGTTCATCACCCTTTGTAC 58.754 41.667 0.00 0.00 0.00 2.90
2886 6927 9.967451 TCATCACCCTTTGTACATTAAATTCTA 57.033 29.630 0.00 0.00 0.00 2.10
2929 6981 9.953565 TTCTTGTTAGCTATGGTGTTAATACTT 57.046 29.630 2.17 0.00 0.00 2.24
2930 6982 9.953565 TCTTGTTAGCTATGGTGTTAATACTTT 57.046 29.630 2.17 0.00 0.00 2.66
3201 7257 9.499479 AAGCTATCCAGATTCTATTATGTGTTG 57.501 33.333 0.00 0.00 0.00 3.33
3202 7258 8.654997 AGCTATCCAGATTCTATTATGTGTTGT 58.345 33.333 0.00 0.00 0.00 3.32
3203 7259 9.277783 GCTATCCAGATTCTATTATGTGTTGTT 57.722 33.333 0.00 0.00 0.00 2.83
3229 7285 8.318412 TCTACCTTGCAGTATTTTCATCTGTTA 58.682 33.333 0.00 0.00 0.00 2.41
3297 7353 2.290896 TGCCTTCCAGGATGTAGTTTGG 60.291 50.000 0.00 0.00 37.67 3.28
3343 7399 6.457392 GCAAATGAGCTTCATCGTATCTGAAA 60.457 38.462 0.00 0.00 35.76 2.69
3347 7403 4.636249 AGCTTCATCGTATCTGAAATCCC 58.364 43.478 0.00 0.00 32.53 3.85
3349 7405 4.688413 GCTTCATCGTATCTGAAATCCCTC 59.312 45.833 0.00 0.00 32.53 4.30
3350 7406 4.505313 TCATCGTATCTGAAATCCCTCG 57.495 45.455 0.00 0.00 0.00 4.63
3373 7429 5.106157 CGTCATGGAAGTAAAGCAATTTCCT 60.106 40.000 8.69 0.00 39.80 3.36
3375 7431 6.808704 GTCATGGAAGTAAAGCAATTTCCTTC 59.191 38.462 8.69 3.45 39.80 3.46
3376 7432 6.721208 TCATGGAAGTAAAGCAATTTCCTTCT 59.279 34.615 6.16 0.00 39.80 2.85
3378 7434 6.306987 TGGAAGTAAAGCAATTTCCTTCTCT 58.693 36.000 6.16 0.00 39.80 3.10
3379 7435 6.777580 TGGAAGTAAAGCAATTTCCTTCTCTT 59.222 34.615 6.16 0.00 39.80 2.85
3380 7436 7.040409 TGGAAGTAAAGCAATTTCCTTCTCTTC 60.040 37.037 15.21 15.21 39.80 2.87
3381 7437 6.487689 AGTAAAGCAATTTCCTTCTCTTCG 57.512 37.500 0.00 0.00 0.00 3.79
3382 7438 4.773323 AAAGCAATTTCCTTCTCTTCGG 57.227 40.909 0.00 0.00 0.00 4.30
3383 7439 2.716217 AGCAATTTCCTTCTCTTCGGG 58.284 47.619 0.00 0.00 0.00 5.14
3385 7441 2.436417 CAATTTCCTTCTCTTCGGGCA 58.564 47.619 0.00 0.00 0.00 5.36
3412 7500 0.108138 CTCTCCGCAACTAACCCAGG 60.108 60.000 0.00 0.00 0.00 4.45
3416 7504 2.690778 CGCAACTAACCCAGGCTGC 61.691 63.158 9.56 0.00 35.12 5.25
3418 7506 2.359975 AACTAACCCAGGCTGCGC 60.360 61.111 9.56 0.00 0.00 6.09
3444 7846 3.413327 TGATTTTGTGCTAGGCGGTTTA 58.587 40.909 0.00 0.00 0.00 2.01
3445 7847 3.189702 TGATTTTGTGCTAGGCGGTTTAC 59.810 43.478 0.00 0.00 0.00 2.01
3568 8080 3.431415 ACTTGCCCCAACTCCTTTAATC 58.569 45.455 0.00 0.00 0.00 1.75
3576 8088 5.132816 CCCCAACTCCTTTAATCCTGACTAT 59.867 44.000 0.00 0.00 0.00 2.12
3618 8150 9.283768 GAAACCAATAAAAATCCAAATGAACCT 57.716 29.630 0.00 0.00 0.00 3.50
3629 8161 9.713684 AAATCCAAATGAACCTAATTATCCTGA 57.286 29.630 0.00 0.00 0.00 3.86
3631 8163 7.872138 TCCAAATGAACCTAATTATCCTGACT 58.128 34.615 0.00 0.00 0.00 3.41
3632 8164 8.998814 TCCAAATGAACCTAATTATCCTGACTA 58.001 33.333 0.00 0.00 0.00 2.59
3633 8165 9.799106 CCAAATGAACCTAATTATCCTGACTAT 57.201 33.333 0.00 0.00 0.00 2.12
3638 8174 5.415961 ACCTAATTATCCTGACTATGCCCT 58.584 41.667 0.00 0.00 0.00 5.19
3653 8189 3.478857 TGCCCTTCAAGAAACGACTTA 57.521 42.857 0.00 0.00 0.00 2.24
3654 8190 3.811083 TGCCCTTCAAGAAACGACTTAA 58.189 40.909 0.00 0.00 0.00 1.85
3662 8198 1.001293 AGAAACGACTTAACCGGGGTC 59.999 52.381 6.32 7.70 0.00 4.46
3664 8200 1.923356 AACGACTTAACCGGGGTCTA 58.077 50.000 6.32 0.00 0.00 2.59
3666 8202 0.743097 CGACTTAACCGGGGTCTAGG 59.257 60.000 6.32 0.00 0.00 3.02
3667 8203 1.857965 GACTTAACCGGGGTCTAGGT 58.142 55.000 6.32 0.00 43.68 3.08
3668 8204 1.479730 GACTTAACCGGGGTCTAGGTG 59.520 57.143 6.32 0.00 41.21 4.00
3669 8205 1.077663 ACTTAACCGGGGTCTAGGTGA 59.922 52.381 6.32 0.00 41.21 4.02
3670 8206 2.181975 CTTAACCGGGGTCTAGGTGAA 58.818 52.381 6.32 0.00 41.21 3.18
3671 8207 2.323999 TAACCGGGGTCTAGGTGAAA 57.676 50.000 6.32 0.00 41.21 2.69
3672 8208 0.981943 AACCGGGGTCTAGGTGAAAG 59.018 55.000 6.32 0.00 41.21 2.62
3673 8209 1.221021 CCGGGGTCTAGGTGAAAGC 59.779 63.158 0.00 0.00 0.00 3.51
3691 8246 7.716998 GGTGAAAGCTTCTCCATCTCATAATAA 59.283 37.037 0.00 0.00 41.71 1.40
3699 8254 6.574463 TCTCCATCTCATAATAATCCTCCCA 58.426 40.000 0.00 0.00 0.00 4.37
3725 8532 0.178990 GGGCAAGGTGGAAGAACTGT 60.179 55.000 0.00 0.00 0.00 3.55
3731 8538 3.425162 AGGTGGAAGAACTGTTGGATC 57.575 47.619 0.00 0.00 0.00 3.36
3757 8564 3.669251 GCTAGAGCTCCGGAAATACAT 57.331 47.619 10.93 0.00 38.21 2.29
3758 8565 3.580731 GCTAGAGCTCCGGAAATACATC 58.419 50.000 10.93 0.00 38.21 3.06
3759 8566 3.005897 GCTAGAGCTCCGGAAATACATCA 59.994 47.826 10.93 0.00 38.21 3.07
3763 8570 5.440610 AGAGCTCCGGAAATACATCAAAAT 58.559 37.500 10.93 0.00 0.00 1.82
3764 8571 5.297776 AGAGCTCCGGAAATACATCAAAATG 59.702 40.000 10.93 0.00 38.93 2.32
3765 8572 4.339247 AGCTCCGGAAATACATCAAAATGG 59.661 41.667 5.23 0.00 37.19 3.16
3766 8573 4.338118 GCTCCGGAAATACATCAAAATGGA 59.662 41.667 5.23 0.00 37.19 3.41
3767 8574 5.010012 GCTCCGGAAATACATCAAAATGGAT 59.990 40.000 5.23 0.00 38.13 3.41
3769 8576 7.255451 GCTCCGGAAATACATCAAAATGGATAA 60.255 37.037 5.23 0.00 35.22 1.75
3770 8577 8.526667 TCCGGAAATACATCAAAATGGATAAA 57.473 30.769 0.00 0.00 35.22 1.40
3771 8578 8.972127 TCCGGAAATACATCAAAATGGATAAAA 58.028 29.630 0.00 0.00 35.22 1.52
3772 8579 9.248291 CCGGAAATACATCAAAATGGATAAAAG 57.752 33.333 0.00 0.00 35.22 2.27
3773 8580 9.248291 CGGAAATACATCAAAATGGATAAAAGG 57.752 33.333 0.00 0.00 35.22 3.11
3774 8581 9.546428 GGAAATACATCAAAATGGATAAAAGGG 57.454 33.333 0.00 0.00 35.22 3.95
3775 8582 9.546428 GAAATACATCAAAATGGATAAAAGGGG 57.454 33.333 0.00 0.00 35.22 4.79
3776 8583 8.852671 AATACATCAAAATGGATAAAAGGGGA 57.147 30.769 0.00 0.00 35.22 4.81
3778 8585 7.128234 ACATCAAAATGGATAAAAGGGGATG 57.872 36.000 0.00 0.00 37.19 3.51
3782 8589 8.852671 TCAAAATGGATAAAAGGGGATGTATT 57.147 30.769 0.00 0.00 0.00 1.89
3783 8590 9.278011 TCAAAATGGATAAAAGGGGATGTATTT 57.722 29.630 0.00 0.00 0.00 1.40
3788 8595 9.759473 ATGGATAAAAGGGGATGTATTTAGATG 57.241 33.333 0.00 0.00 0.00 2.90
3789 8596 8.732854 TGGATAAAAGGGGATGTATTTAGATGT 58.267 33.333 0.00 0.00 0.00 3.06
3843 8650 8.883789 TTTATTTTGATGACGTATTTTCGGAC 57.116 30.769 0.00 0.00 34.94 4.79
3844 8651 4.571375 TTTGATGACGTATTTTCGGACG 57.429 40.909 0.00 0.00 44.57 4.79
3845 8652 2.532235 TGATGACGTATTTTCGGACGG 58.468 47.619 0.00 0.00 43.32 4.79
3846 8653 2.164017 TGATGACGTATTTTCGGACGGA 59.836 45.455 0.00 0.00 43.32 4.69
3847 8654 2.267188 TGACGTATTTTCGGACGGAG 57.733 50.000 0.00 0.00 43.32 4.63
3848 8655 1.135315 TGACGTATTTTCGGACGGAGG 60.135 52.381 0.00 0.00 43.32 4.30
3849 8656 0.174162 ACGTATTTTCGGACGGAGGG 59.826 55.000 0.00 0.00 43.32 4.30
3850 8657 0.457035 CGTATTTTCGGACGGAGGGA 59.543 55.000 0.00 0.00 35.43 4.20
3851 8658 1.535437 CGTATTTTCGGACGGAGGGAG 60.535 57.143 0.00 0.00 35.43 4.30
3852 8659 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
3853 8660 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
3854 8661 1.856629 TTTTCGGACGGAGGGAGTAT 58.143 50.000 0.00 0.00 0.00 2.12
3855 8662 2.734755 TTTCGGACGGAGGGAGTATA 57.265 50.000 0.00 0.00 0.00 1.47
3856 8663 2.965671 TTCGGACGGAGGGAGTATAT 57.034 50.000 0.00 0.00 0.00 0.86
3857 8664 2.486472 TCGGACGGAGGGAGTATATC 57.514 55.000 0.00 0.00 0.00 1.63
3893 8700 3.740115 TGAGGAAGTTGTGCCTTTACTC 58.260 45.455 0.00 0.00 33.84 2.59
3894 8701 3.391296 TGAGGAAGTTGTGCCTTTACTCT 59.609 43.478 0.00 0.00 33.84 3.24
3895 8702 3.997681 GAGGAAGTTGTGCCTTTACTCTC 59.002 47.826 0.00 0.00 33.84 3.20
3903 8710 1.476891 TGCCTTTACTCTCGCTCGAAT 59.523 47.619 0.00 0.00 0.00 3.34
3909 8716 5.007823 CCTTTACTCTCGCTCGAATTAGAGA 59.992 44.000 18.55 13.60 40.57 3.10
3916 8723 5.068234 TCGCTCGAATTAGAGAAAAAGGA 57.932 39.130 18.55 3.58 40.57 3.36
3919 8726 4.572795 GCTCGAATTAGAGAAAAAGGAGGG 59.427 45.833 18.55 0.00 40.57 4.30
3920 8727 5.627040 GCTCGAATTAGAGAAAAAGGAGGGA 60.627 44.000 18.55 0.00 40.57 4.20
3921 8728 6.561519 TCGAATTAGAGAAAAAGGAGGGAT 57.438 37.500 0.00 0.00 0.00 3.85
3922 8729 7.670605 TCGAATTAGAGAAAAAGGAGGGATA 57.329 36.000 0.00 0.00 0.00 2.59
3923 8730 8.263854 TCGAATTAGAGAAAAAGGAGGGATAT 57.736 34.615 0.00 0.00 0.00 1.63
3924 8731 8.150945 TCGAATTAGAGAAAAAGGAGGGATATG 58.849 37.037 0.00 0.00 0.00 1.78
3925 8732 7.095017 CGAATTAGAGAAAAAGGAGGGATATGC 60.095 40.741 0.00 0.00 0.00 3.14
3926 8733 4.078639 AGAGAAAAAGGAGGGATATGCG 57.921 45.455 0.00 0.00 0.00 4.73
3927 8734 2.550180 GAGAAAAAGGAGGGATATGCGC 59.450 50.000 0.00 0.00 0.00 6.09
3928 8735 2.092429 AGAAAAAGGAGGGATATGCGCA 60.092 45.455 14.96 14.96 0.00 6.09
3929 8736 2.664402 AAAAGGAGGGATATGCGCAT 57.336 45.000 28.23 28.23 0.00 4.73
3930 8737 2.664402 AAAGGAGGGATATGCGCATT 57.336 45.000 30.42 16.25 0.00 3.56
3931 8738 2.664402 AAGGAGGGATATGCGCATTT 57.336 45.000 30.42 21.71 0.00 2.32
3932 8739 2.191128 AGGAGGGATATGCGCATTTC 57.809 50.000 30.42 28.22 0.00 2.17
3933 8740 1.168714 GGAGGGATATGCGCATTTCC 58.831 55.000 37.35 37.35 37.95 3.13
3934 8741 1.271597 GGAGGGATATGCGCATTTCCT 60.272 52.381 40.26 33.98 38.48 3.36
3935 8742 2.508526 GAGGGATATGCGCATTTCCTT 58.491 47.619 40.26 37.24 38.48 3.36
3936 8743 3.559171 GGAGGGATATGCGCATTTCCTTA 60.559 47.826 40.26 21.82 38.48 2.69
3937 8744 4.265073 GAGGGATATGCGCATTTCCTTAT 58.735 43.478 40.26 31.12 38.48 1.73
3938 8745 4.666512 AGGGATATGCGCATTTCCTTATT 58.333 39.130 40.26 27.34 38.48 1.40
3939 8746 5.079643 AGGGATATGCGCATTTCCTTATTT 58.920 37.500 40.26 25.58 38.48 1.40
3940 8747 5.183904 AGGGATATGCGCATTTCCTTATTTC 59.816 40.000 40.26 28.99 38.48 2.17
3941 8748 5.048083 GGGATATGCGCATTTCCTTATTTCA 60.048 40.000 40.26 18.75 38.48 2.69
3942 8749 5.858581 GGATATGCGCATTTCCTTATTTCAC 59.141 40.000 37.50 17.91 36.42 3.18
3943 8750 4.717233 ATGCGCATTTCCTTATTTCACA 57.283 36.364 19.28 0.00 0.00 3.58
3944 8751 4.511617 TGCGCATTTCCTTATTTCACAA 57.488 36.364 5.66 0.00 0.00 3.33
3945 8752 5.070770 TGCGCATTTCCTTATTTCACAAT 57.929 34.783 5.66 0.00 0.00 2.71
3946 8753 4.863689 TGCGCATTTCCTTATTTCACAATG 59.136 37.500 5.66 0.00 0.00 2.82
3947 8754 5.101628 GCGCATTTCCTTATTTCACAATGA 58.898 37.500 0.30 0.00 0.00 2.57
3948 8755 5.576384 GCGCATTTCCTTATTTCACAATGAA 59.424 36.000 0.30 0.00 34.03 2.57
3963 8770 8.996024 TTCACAATGAAATAAGTGATAGACGA 57.004 30.769 0.00 0.00 39.94 4.20
3964 8771 8.634475 TCACAATGAAATAAGTGATAGACGAG 57.366 34.615 0.00 0.00 36.82 4.18
3965 8772 7.222805 TCACAATGAAATAAGTGATAGACGAGC 59.777 37.037 0.00 0.00 36.82 5.03
3966 8773 7.010460 CACAATGAAATAAGTGATAGACGAGCA 59.990 37.037 0.00 0.00 35.29 4.26
3967 8774 7.549134 ACAATGAAATAAGTGATAGACGAGCAA 59.451 33.333 0.00 0.00 0.00 3.91
3968 8775 8.390354 CAATGAAATAAGTGATAGACGAGCAAA 58.610 33.333 0.00 0.00 0.00 3.68
3969 8776 7.525688 TGAAATAAGTGATAGACGAGCAAAG 57.474 36.000 0.00 0.00 0.00 2.77
3970 8777 5.975410 AATAAGTGATAGACGAGCAAAGC 57.025 39.130 0.00 0.00 0.00 3.51
3971 8778 2.301577 AGTGATAGACGAGCAAAGCC 57.698 50.000 0.00 0.00 0.00 4.35
3972 8779 1.134670 AGTGATAGACGAGCAAAGCCC 60.135 52.381 0.00 0.00 0.00 5.19
3973 8780 1.134670 GTGATAGACGAGCAAAGCCCT 60.135 52.381 0.00 0.00 0.00 5.19
3974 8781 1.137086 TGATAGACGAGCAAAGCCCTC 59.863 52.381 0.00 0.00 0.00 4.30
3975 8782 1.137086 GATAGACGAGCAAAGCCCTCA 59.863 52.381 0.00 0.00 0.00 3.86
3976 8783 0.973632 TAGACGAGCAAAGCCCTCAA 59.026 50.000 0.00 0.00 0.00 3.02
3977 8784 0.108585 AGACGAGCAAAGCCCTCAAA 59.891 50.000 0.00 0.00 0.00 2.69
3978 8785 1.168714 GACGAGCAAAGCCCTCAAAT 58.831 50.000 0.00 0.00 0.00 2.32
3979 8786 2.027192 AGACGAGCAAAGCCCTCAAATA 60.027 45.455 0.00 0.00 0.00 1.40
3980 8787 2.352960 GACGAGCAAAGCCCTCAAATAG 59.647 50.000 0.00 0.00 0.00 1.73
3981 8788 2.290323 ACGAGCAAAGCCCTCAAATAGT 60.290 45.455 0.00 0.00 0.00 2.12
3982 8789 2.749621 CGAGCAAAGCCCTCAAATAGTT 59.250 45.455 0.00 0.00 0.00 2.24
3983 8790 3.181506 CGAGCAAAGCCCTCAAATAGTTC 60.182 47.826 0.00 0.00 0.00 3.01
3984 8791 4.013050 GAGCAAAGCCCTCAAATAGTTCT 58.987 43.478 0.00 0.00 0.00 3.01
3985 8792 4.411013 AGCAAAGCCCTCAAATAGTTCTT 58.589 39.130 0.00 0.00 0.00 2.52
3986 8793 5.570320 AGCAAAGCCCTCAAATAGTTCTTA 58.430 37.500 0.00 0.00 0.00 2.10
3987 8794 6.190587 AGCAAAGCCCTCAAATAGTTCTTAT 58.809 36.000 0.00 0.00 0.00 1.73
3988 8795 6.096001 AGCAAAGCCCTCAAATAGTTCTTATG 59.904 38.462 0.00 0.00 0.00 1.90
3989 8796 6.268566 CAAAGCCCTCAAATAGTTCTTATGC 58.731 40.000 0.00 0.00 0.00 3.14
3990 8797 5.379706 AGCCCTCAAATAGTTCTTATGCT 57.620 39.130 0.00 0.00 0.00 3.79
3991 8798 5.760131 AGCCCTCAAATAGTTCTTATGCTT 58.240 37.500 0.00 0.00 0.00 3.91
3992 8799 6.190587 AGCCCTCAAATAGTTCTTATGCTTT 58.809 36.000 0.00 0.00 0.00 3.51
3993 8800 6.319911 AGCCCTCAAATAGTTCTTATGCTTTC 59.680 38.462 0.00 0.00 0.00 2.62
3994 8801 6.095440 GCCCTCAAATAGTTCTTATGCTTTCA 59.905 38.462 0.00 0.00 0.00 2.69
3995 8802 7.201857 GCCCTCAAATAGTTCTTATGCTTTCAT 60.202 37.037 0.00 0.00 36.73 2.57
3996 8803 9.342308 CCCTCAAATAGTTCTTATGCTTTCATA 57.658 33.333 0.00 0.00 34.22 2.15
4000 8807 9.736023 CAAATAGTTCTTATGCTTTCATAACCC 57.264 33.333 0.00 0.00 39.52 4.11
4001 8808 9.700831 AAATAGTTCTTATGCTTTCATAACCCT 57.299 29.630 0.00 0.00 39.52 4.34
4005 8812 9.528489 AGTTCTTATGCTTTCATAACCCTAAAA 57.472 29.630 0.00 0.00 39.52 1.52
4012 8819 8.415950 TGCTTTCATAACCCTAAAAATTGAGA 57.584 30.769 0.00 0.00 0.00 3.27
4013 8820 9.034800 TGCTTTCATAACCCTAAAAATTGAGAT 57.965 29.630 0.00 0.00 0.00 2.75
4014 8821 9.305925 GCTTTCATAACCCTAAAAATTGAGATG 57.694 33.333 0.00 0.00 0.00 2.90
4015 8822 9.305925 CTTTCATAACCCTAAAAATTGAGATGC 57.694 33.333 0.00 0.00 0.00 3.91
4016 8823 7.953005 TCATAACCCTAAAAATTGAGATGCA 57.047 32.000 0.00 0.00 0.00 3.96
4017 8824 7.771183 TCATAACCCTAAAAATTGAGATGCAC 58.229 34.615 0.00 0.00 0.00 4.57
4018 8825 4.701956 ACCCTAAAAATTGAGATGCACG 57.298 40.909 0.00 0.00 0.00 5.34
4019 8826 4.331968 ACCCTAAAAATTGAGATGCACGA 58.668 39.130 0.00 0.00 0.00 4.35
4020 8827 4.764823 ACCCTAAAAATTGAGATGCACGAA 59.235 37.500 0.00 0.00 0.00 3.85
4021 8828 5.242838 ACCCTAAAAATTGAGATGCACGAAA 59.757 36.000 0.00 0.00 0.00 3.46
4022 8829 6.071391 ACCCTAAAAATTGAGATGCACGAAAT 60.071 34.615 0.00 0.00 0.00 2.17
4023 8830 7.122055 ACCCTAAAAATTGAGATGCACGAAATA 59.878 33.333 0.00 0.00 0.00 1.40
4024 8831 8.137437 CCCTAAAAATTGAGATGCACGAAATAT 58.863 33.333 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 9.843334 AAAAATATTAATTGTGCATTTGCTTGG 57.157 25.926 3.94 0.00 42.66 3.61
260 3438 5.175856 TCGGGCATTTGAAAAATGTTAAACG 59.824 36.000 12.82 10.43 0.00 3.60
377 3555 3.428534 GTGCGGCTTTTAGAAAATGTTGG 59.571 43.478 0.00 0.00 0.00 3.77
395 3573 4.030083 CAGCGTTAAAAATATGTTGGTGCG 59.970 41.667 0.00 0.00 0.00 5.34
513 3735 4.586306 AGGGATTACGTTCCTGGATTTT 57.414 40.909 6.26 0.00 35.97 1.82
561 3783 9.529325 GCACTAACTTGATACTACATACATTCA 57.471 33.333 0.00 0.00 0.00 2.57
562 3784 9.751542 AGCACTAACTTGATACTACATACATTC 57.248 33.333 0.00 0.00 0.00 2.67
565 3787 9.623000 TCTAGCACTAACTTGATACTACATACA 57.377 33.333 0.00 0.00 0.00 2.29
569 3791 9.623000 TGTATCTAGCACTAACTTGATACTACA 57.377 33.333 19.43 6.76 46.52 2.74
593 3815 9.320295 TCCCAAACTTATTCCTCAAATAAATGT 57.680 29.630 0.00 0.00 38.92 2.71
594 3816 9.586435 GTCCCAAACTTATTCCTCAAATAAATG 57.414 33.333 0.00 0.00 38.92 2.32
595 3817 9.320295 TGTCCCAAACTTATTCCTCAAATAAAT 57.680 29.630 0.00 0.00 38.92 1.40
596 3818 8.713708 TGTCCCAAACTTATTCCTCAAATAAA 57.286 30.769 0.00 0.00 38.92 1.40
597 3819 8.713708 TTGTCCCAAACTTATTCCTCAAATAA 57.286 30.769 0.00 0.00 37.46 1.40
598 3820 8.581578 GTTTGTCCCAAACTTATTCCTCAAATA 58.418 33.333 11.53 0.00 0.00 1.40
599 3821 7.290014 AGTTTGTCCCAAACTTATTCCTCAAAT 59.710 33.333 14.80 0.00 37.18 2.32
600 3822 6.609616 AGTTTGTCCCAAACTTATTCCTCAAA 59.390 34.615 14.80 0.00 37.18 2.69
601 3823 6.133356 AGTTTGTCCCAAACTTATTCCTCAA 58.867 36.000 14.80 0.00 37.18 3.02
602 3824 5.701224 AGTTTGTCCCAAACTTATTCCTCA 58.299 37.500 14.80 0.00 37.18 3.86
603 3825 6.650427 AAGTTTGTCCCAAACTTATTCCTC 57.350 37.500 25.50 0.00 45.51 3.71
604 3826 7.432148 AAAAGTTTGTCCCAAACTTATTCCT 57.568 32.000 26.42 13.71 46.33 3.36
626 3848 1.123246 ACTCCCTCCGTCCGGAAAAA 61.123 55.000 5.23 0.00 44.66 1.94
627 3849 0.251742 TACTCCCTCCGTCCGGAAAA 60.252 55.000 5.23 0.00 44.66 2.29
628 3850 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
629 3851 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
630 3852 0.982852 TAGTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
631 3853 0.107017 TTAGTACTCCCTCCGTCCGG 60.107 60.000 0.00 0.00 0.00 5.14
632 3854 1.307097 CTTAGTACTCCCTCCGTCCG 58.693 60.000 0.00 0.00 0.00 4.79
633 3855 1.213926 TCCTTAGTACTCCCTCCGTCC 59.786 57.143 0.00 0.00 0.00 4.79
634 3856 2.725221 TCCTTAGTACTCCCTCCGTC 57.275 55.000 0.00 0.00 0.00 4.79
635 3857 2.949508 GCTTCCTTAGTACTCCCTCCGT 60.950 54.545 0.00 0.00 0.00 4.69
636 3858 1.682323 GCTTCCTTAGTACTCCCTCCG 59.318 57.143 0.00 0.00 0.00 4.63
637 3859 1.682323 CGCTTCCTTAGTACTCCCTCC 59.318 57.143 0.00 0.00 0.00 4.30
638 3860 2.619646 CTCGCTTCCTTAGTACTCCCTC 59.380 54.545 0.00 0.00 0.00 4.30
639 3861 2.657143 CTCGCTTCCTTAGTACTCCCT 58.343 52.381 0.00 0.00 0.00 4.20
640 3862 1.067364 GCTCGCTTCCTTAGTACTCCC 59.933 57.143 0.00 0.00 0.00 4.30
641 3863 1.268640 CGCTCGCTTCCTTAGTACTCC 60.269 57.143 0.00 0.00 0.00 3.85
642 3864 1.268640 CCGCTCGCTTCCTTAGTACTC 60.269 57.143 0.00 0.00 0.00 2.59
643 3865 0.739561 CCGCTCGCTTCCTTAGTACT 59.260 55.000 0.00 0.00 0.00 2.73
712 4643 3.245229 ACATAGTTGGCCCATGTCAGAAA 60.245 43.478 0.00 0.00 0.00 2.52
713 4644 2.308570 ACATAGTTGGCCCATGTCAGAA 59.691 45.455 0.00 0.00 0.00 3.02
714 4645 1.915489 ACATAGTTGGCCCATGTCAGA 59.085 47.619 0.00 0.00 0.00 3.27
715 4646 2.425143 ACATAGTTGGCCCATGTCAG 57.575 50.000 0.00 0.00 0.00 3.51
716 4647 2.421388 GCTACATAGTTGGCCCATGTCA 60.421 50.000 11.36 1.55 34.78 3.58
757 4688 1.891060 GCAGACAGGACGCAACTTCG 61.891 60.000 0.00 0.00 0.00 3.79
918 4850 0.108567 GTCTCGCAAGGAGGAAGGAC 60.109 60.000 0.00 0.00 43.34 3.85
987 4926 4.715523 CCCATGGTGGCGTCGGTT 62.716 66.667 11.73 0.00 35.79 4.44
1021 4960 1.134907 TCCGAGGGAACAACGAATAGC 60.135 52.381 0.00 0.00 35.12 2.97
1082 5021 0.179137 CACGCGAGATACCTGCAGAA 60.179 55.000 17.39 2.75 0.00 3.02
1236 5175 5.588958 AGTAAACACGGATCTAACCTACC 57.411 43.478 0.00 0.00 0.00 3.18
1265 5204 1.375551 ACGACAATTTATCCACGCCC 58.624 50.000 0.00 0.00 0.00 6.13
1318 5257 0.385598 CAAGAGTTCAGACGCGTCGA 60.386 55.000 31.56 26.87 34.09 4.20
1330 5269 6.321690 AGTTACCGAGCTATCATACAAGAGTT 59.678 38.462 0.00 0.00 0.00 3.01
1446 5387 3.223157 GTGCGTAAACGAATGAAGGTTG 58.777 45.455 6.71 0.00 43.02 3.77
1483 5424 1.195448 CACACCAGAAGTTCGCATGTC 59.805 52.381 0.00 0.00 0.00 3.06
1499 5440 7.647715 AGTTACAGCAAATTAACATGAACACAC 59.352 33.333 0.00 0.00 31.66 3.82
1551 5504 0.608640 AATGAGTGACGGACCCAGTC 59.391 55.000 0.00 0.00 38.98 3.51
1582 5537 1.865865 ACAACGATCGAAACAGCAGT 58.134 45.000 24.34 5.04 0.00 4.40
1596 5551 7.113684 TCACAAAACTTGTACTTCAAAACAACG 59.886 33.333 0.00 0.00 43.23 4.10
1728 5684 4.563184 GCGGATATGGCTAAGAATAACTCG 59.437 45.833 0.00 0.00 0.00 4.18
1746 5702 1.880027 GAAACAGAACCAAGTGCGGAT 59.120 47.619 0.00 0.00 0.00 4.18
1826 5782 4.816385 TGTAAAGTTCTTGCAAGGTCTCAG 59.184 41.667 25.73 0.00 0.00 3.35
1852 5808 9.567776 TGAAGGACAAAGTAAGATTCATAACAA 57.432 29.630 0.00 0.00 0.00 2.83
2133 6089 0.261696 ACCACTGTTTGAAAGGGGCT 59.738 50.000 0.00 0.00 42.47 5.19
2145 6101 4.162320 CCATAATGAGTCAGGTACCACTGT 59.838 45.833 15.94 0.00 39.48 3.55
2172 6128 4.935808 GCTTTCTTCTTCCTACCGATTTCA 59.064 41.667 0.00 0.00 0.00 2.69
2306 6264 8.450964 ACTACCAAACTGAATATCATTTCAACG 58.549 33.333 0.00 0.00 35.31 4.10
2327 6312 4.796038 TGGTACTTCTGCTACAACTACC 57.204 45.455 0.00 0.00 0.00 3.18
2363 6348 4.494350 GGATACTAATGCATGCAACCAG 57.506 45.455 26.68 22.15 0.00 4.00
2407 6392 1.743394 GGAGGCCGGATAAACAAGTTG 59.257 52.381 5.05 0.00 0.00 3.16
2421 6407 2.355010 ATACAATGAGCAAGGAGGCC 57.645 50.000 0.00 0.00 0.00 5.19
2543 6579 7.416407 AAAGGGCATAATATAAACTAGGGGT 57.584 36.000 0.00 0.00 0.00 4.95
2624 6660 8.807667 AGAATAAGAAAATCACACAAAGCAAG 57.192 30.769 0.00 0.00 0.00 4.01
2647 6686 0.115152 TCAGCCTCTTGTCCCTGAGA 59.885 55.000 0.00 0.00 32.44 3.27
2649 6688 0.906756 CCTCAGCCTCTTGTCCCTGA 60.907 60.000 0.00 0.00 33.65 3.86
2887 6928 8.989980 GCTAACAAGAAATTGTAGAGTACTGTT 58.010 33.333 0.00 0.00 34.24 3.16
2929 6981 6.408035 TGTACCTGTAGTTTCAAGACACAAA 58.592 36.000 0.00 0.00 0.00 2.83
2930 6982 5.979993 TGTACCTGTAGTTTCAAGACACAA 58.020 37.500 0.00 0.00 0.00 3.33
3030 7083 1.061711 GTAACATGCAGCAGCTCTTCG 59.938 52.381 0.00 0.00 42.74 3.79
3201 7257 7.119846 ACAGATGAAAATACTGCAAGGTAGAAC 59.880 37.037 0.00 0.00 39.30 3.01
3202 7258 7.168219 ACAGATGAAAATACTGCAAGGTAGAA 58.832 34.615 0.00 0.00 39.30 2.10
3203 7259 6.711277 ACAGATGAAAATACTGCAAGGTAGA 58.289 36.000 0.00 0.00 39.30 2.59
3229 7285 4.035208 AGACGCGAGAACAAAATTTCACTT 59.965 37.500 15.93 0.00 0.00 3.16
3297 7353 3.666638 GCAACTGCAAAAACCACACAAAC 60.667 43.478 0.00 0.00 41.59 2.93
3326 7382 4.636249 AGGGATTTCAGATACGATGAAGC 58.364 43.478 0.00 0.00 37.91 3.86
3343 7399 3.432326 GCTTTACTTCCATGACGAGGGAT 60.432 47.826 0.00 0.00 30.33 3.85
3347 7403 5.551760 AATTGCTTTACTTCCATGACGAG 57.448 39.130 0.00 0.00 0.00 4.18
3349 7405 5.095490 GGAAATTGCTTTACTTCCATGACG 58.905 41.667 0.00 0.00 37.79 4.35
3350 7406 6.272822 AGGAAATTGCTTTACTTCCATGAC 57.727 37.500 0.00 0.00 39.91 3.06
3381 7437 2.936912 CGGAGAGATCGGGATGCCC 61.937 68.421 0.00 0.00 41.09 5.36
3382 7438 2.653702 CGGAGAGATCGGGATGCC 59.346 66.667 0.00 0.00 0.00 4.40
3383 7439 2.048690 GCGGAGAGATCGGGATGC 60.049 66.667 0.00 0.00 0.00 3.91
3385 7441 0.757188 AGTTGCGGAGAGATCGGGAT 60.757 55.000 0.00 0.00 0.00 3.85
3391 7479 1.482593 CTGGGTTAGTTGCGGAGAGAT 59.517 52.381 0.00 0.00 0.00 2.75
3394 7482 1.980052 CCTGGGTTAGTTGCGGAGA 59.020 57.895 0.00 0.00 0.00 3.71
3395 7483 1.745489 GCCTGGGTTAGTTGCGGAG 60.745 63.158 0.00 0.00 0.00 4.63
3416 7504 3.548818 GCCTAGCACAAAATCAATAGGCG 60.549 47.826 5.38 0.00 44.06 5.52
3418 7506 3.003689 CCGCCTAGCACAAAATCAATAGG 59.996 47.826 0.00 0.00 34.23 2.57
3421 7509 2.446435 ACCGCCTAGCACAAAATCAAT 58.554 42.857 0.00 0.00 0.00 2.57
3422 7510 1.904287 ACCGCCTAGCACAAAATCAA 58.096 45.000 0.00 0.00 0.00 2.57
3473 7985 6.653020 TCCAAGCAACACAGATGTATATTCT 58.347 36.000 0.00 0.00 38.45 2.40
3476 7988 5.766670 CCATCCAAGCAACACAGATGTATAT 59.233 40.000 0.00 0.00 38.45 0.86
3477 7989 5.104569 TCCATCCAAGCAACACAGATGTATA 60.105 40.000 0.00 0.00 38.45 1.47
3478 7990 3.949754 CCATCCAAGCAACACAGATGTAT 59.050 43.478 0.00 0.00 38.45 2.29
3491 8003 1.760192 AGCAAGACATCCATCCAAGC 58.240 50.000 0.00 0.00 0.00 4.01
3538 8050 4.640647 GGAGTTGGGGCAAGTTAATTAGAG 59.359 45.833 0.00 0.00 0.00 2.43
3540 8052 4.600062 AGGAGTTGGGGCAAGTTAATTAG 58.400 43.478 0.00 0.00 0.00 1.73
3541 8053 4.668138 AGGAGTTGGGGCAAGTTAATTA 57.332 40.909 0.00 0.00 0.00 1.40
3543 8055 3.542969 AAGGAGTTGGGGCAAGTTAAT 57.457 42.857 0.00 0.00 0.00 1.40
3546 8058 3.322191 TTAAAGGAGTTGGGGCAAGTT 57.678 42.857 0.00 0.00 0.00 2.66
3548 8060 2.760650 GGATTAAAGGAGTTGGGGCAAG 59.239 50.000 0.00 0.00 0.00 4.01
3549 8061 2.381961 AGGATTAAAGGAGTTGGGGCAA 59.618 45.455 0.00 0.00 0.00 4.52
3550 8062 2.000048 AGGATTAAAGGAGTTGGGGCA 59.000 47.619 0.00 0.00 0.00 5.36
3551 8063 2.025321 TCAGGATTAAAGGAGTTGGGGC 60.025 50.000 0.00 0.00 0.00 5.80
3552 8064 3.267031 AGTCAGGATTAAAGGAGTTGGGG 59.733 47.826 0.00 0.00 0.00 4.96
3568 8080 0.681733 CGATGGGACCCATAGTCAGG 59.318 60.000 26.61 7.74 45.26 3.86
3618 8150 7.292356 TCTTGAAGGGCATAGTCAGGATAATTA 59.708 37.037 0.00 0.00 0.00 1.40
3619 8151 5.912149 TGAAGGGCATAGTCAGGATAATT 57.088 39.130 0.00 0.00 0.00 1.40
3623 8155 3.387962 TCTTGAAGGGCATAGTCAGGAT 58.612 45.455 0.00 0.00 0.00 3.24
3624 8156 2.832838 TCTTGAAGGGCATAGTCAGGA 58.167 47.619 0.00 0.00 0.00 3.86
3625 8157 3.634397 TTCTTGAAGGGCATAGTCAGG 57.366 47.619 0.00 0.00 0.00 3.86
3626 8158 3.372206 CGTTTCTTGAAGGGCATAGTCAG 59.628 47.826 0.00 0.00 0.00 3.51
3628 8160 3.371285 GTCGTTTCTTGAAGGGCATAGTC 59.629 47.826 0.00 0.00 0.00 2.59
3629 8161 3.008049 AGTCGTTTCTTGAAGGGCATAGT 59.992 43.478 0.00 0.00 30.37 2.12
3631 8163 3.695830 AGTCGTTTCTTGAAGGGCATA 57.304 42.857 0.00 0.00 30.37 3.14
3632 8164 2.568623 AGTCGTTTCTTGAAGGGCAT 57.431 45.000 0.00 0.00 30.37 4.40
3633 8165 2.341846 AAGTCGTTTCTTGAAGGGCA 57.658 45.000 0.00 0.00 30.37 5.36
3634 8166 3.058432 GGTTAAGTCGTTTCTTGAAGGGC 60.058 47.826 0.00 0.00 0.00 5.19
3638 8174 3.132925 CCCGGTTAAGTCGTTTCTTGAA 58.867 45.455 0.00 0.00 0.00 2.69
3653 8189 0.981943 CTTTCACCTAGACCCCGGTT 59.018 55.000 0.00 0.00 0.00 4.44
3654 8190 1.551019 GCTTTCACCTAGACCCCGGT 61.551 60.000 0.00 0.00 0.00 5.28
3662 8198 4.161189 TGAGATGGAGAAGCTTTCACCTAG 59.839 45.833 0.00 0.00 40.56 3.02
3664 8200 2.909006 TGAGATGGAGAAGCTTTCACCT 59.091 45.455 0.00 0.00 40.56 4.00
3666 8202 8.668510 TTATTATGAGATGGAGAAGCTTTCAC 57.331 34.615 0.00 0.00 0.00 3.18
3667 8203 9.499479 GATTATTATGAGATGGAGAAGCTTTCA 57.501 33.333 0.00 0.00 0.00 2.69
3668 8204 8.945057 GGATTATTATGAGATGGAGAAGCTTTC 58.055 37.037 0.00 0.04 0.00 2.62
3669 8205 8.667737 AGGATTATTATGAGATGGAGAAGCTTT 58.332 33.333 0.00 0.00 0.00 3.51
3670 8206 8.217188 AGGATTATTATGAGATGGAGAAGCTT 57.783 34.615 0.00 0.00 0.00 3.74
3671 8207 7.092935 GGAGGATTATTATGAGATGGAGAAGCT 60.093 40.741 0.00 0.00 0.00 3.74
3672 8208 7.047271 GGAGGATTATTATGAGATGGAGAAGC 58.953 42.308 0.00 0.00 0.00 3.86
3673 8209 7.181665 TGGGAGGATTATTATGAGATGGAGAAG 59.818 40.741 0.00 0.00 0.00 2.85
3674 8210 7.024994 TGGGAGGATTATTATGAGATGGAGAA 58.975 38.462 0.00 0.00 0.00 2.87
3699 8254 2.361610 CCACCTTGCCCGCAATCT 60.362 61.111 1.98 0.00 35.20 2.40
3748 8555 9.546428 CCCTTTTATCCATTTTGATGTATTTCC 57.454 33.333 0.00 0.00 0.00 3.13
3749 8556 9.546428 CCCCTTTTATCCATTTTGATGTATTTC 57.454 33.333 0.00 0.00 0.00 2.17
3753 8560 7.843760 ACATCCCCTTTTATCCATTTTGATGTA 59.156 33.333 0.00 0.00 37.80 2.29
3755 8562 7.128234 ACATCCCCTTTTATCCATTTTGATG 57.872 36.000 0.00 0.00 33.80 3.07
3757 8564 8.852671 AATACATCCCCTTTTATCCATTTTGA 57.147 30.769 0.00 0.00 0.00 2.69
3763 8570 8.732854 ACATCTAAATACATCCCCTTTTATCCA 58.267 33.333 0.00 0.00 0.00 3.41
3817 8624 9.498307 GTCCGAAAATACGTCATCAAAATAAAT 57.502 29.630 0.00 0.00 0.00 1.40
3818 8625 7.688989 CGTCCGAAAATACGTCATCAAAATAAA 59.311 33.333 0.00 0.00 34.48 1.40
3819 8626 7.174746 CGTCCGAAAATACGTCATCAAAATAA 58.825 34.615 0.00 0.00 34.48 1.40
3820 8627 6.237888 CCGTCCGAAAATACGTCATCAAAATA 60.238 38.462 0.00 0.00 37.40 1.40
3821 8628 5.446741 CCGTCCGAAAATACGTCATCAAAAT 60.447 40.000 0.00 0.00 37.40 1.82
3822 8629 4.143073 CCGTCCGAAAATACGTCATCAAAA 60.143 41.667 0.00 0.00 37.40 2.44
3823 8630 3.368539 CCGTCCGAAAATACGTCATCAAA 59.631 43.478 0.00 0.00 37.40 2.69
3824 8631 2.924926 CCGTCCGAAAATACGTCATCAA 59.075 45.455 0.00 0.00 37.40 2.57
3825 8632 2.164017 TCCGTCCGAAAATACGTCATCA 59.836 45.455 0.00 0.00 37.40 3.07
3826 8633 2.787680 CTCCGTCCGAAAATACGTCATC 59.212 50.000 0.00 0.00 37.40 2.92
3827 8634 2.480759 CCTCCGTCCGAAAATACGTCAT 60.481 50.000 0.00 0.00 37.40 3.06
3828 8635 1.135315 CCTCCGTCCGAAAATACGTCA 60.135 52.381 0.00 0.00 37.40 4.35
3829 8636 1.553308 CCTCCGTCCGAAAATACGTC 58.447 55.000 0.00 0.00 37.40 4.34
3830 8637 0.174162 CCCTCCGTCCGAAAATACGT 59.826 55.000 0.00 0.00 37.40 3.57
3831 8638 0.457035 TCCCTCCGTCCGAAAATACG 59.543 55.000 0.00 0.00 38.80 3.06
3832 8639 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
3833 8640 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
3834 8641 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
3835 8642 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
3836 8643 2.734755 TATACTCCCTCCGTCCGAAA 57.265 50.000 0.00 0.00 0.00 3.46
3837 8644 2.553904 GGATATACTCCCTCCGTCCGAA 60.554 54.545 0.00 0.00 38.19 4.30
3838 8645 1.004044 GGATATACTCCCTCCGTCCGA 59.996 57.143 0.00 0.00 38.19 4.55
3839 8646 1.004511 AGGATATACTCCCTCCGTCCG 59.995 57.143 0.00 0.00 46.27 4.79
3840 8647 2.903375 AGGATATACTCCCTCCGTCC 57.097 55.000 0.00 0.00 46.27 4.79
3841 8648 6.039605 GCTTTATAGGATATACTCCCTCCGTC 59.960 46.154 0.00 0.00 46.27 4.79
3842 8649 5.892686 GCTTTATAGGATATACTCCCTCCGT 59.107 44.000 0.00 0.00 46.27 4.69
3843 8650 5.892119 TGCTTTATAGGATATACTCCCTCCG 59.108 44.000 0.00 0.00 46.27 4.63
3844 8651 7.735326 TTGCTTTATAGGATATACTCCCTCC 57.265 40.000 0.00 0.00 46.27 4.30
3845 8652 9.036980 TCTTTGCTTTATAGGATATACTCCCTC 57.963 37.037 0.00 0.00 46.27 4.30
3846 8653 8.974292 TCTTTGCTTTATAGGATATACTCCCT 57.026 34.615 0.00 0.00 46.27 4.20
3847 8654 9.606631 CATCTTTGCTTTATAGGATATACTCCC 57.393 37.037 0.00 0.00 46.27 4.30
3853 8660 9.956640 CTTCCTCATCTTTGCTTTATAGGATAT 57.043 33.333 0.00 0.00 32.21 1.63
3854 8661 8.938883 ACTTCCTCATCTTTGCTTTATAGGATA 58.061 33.333 0.00 0.00 32.21 2.59
3855 8662 7.810260 ACTTCCTCATCTTTGCTTTATAGGAT 58.190 34.615 0.00 0.00 32.21 3.24
3856 8663 7.200434 ACTTCCTCATCTTTGCTTTATAGGA 57.800 36.000 0.00 0.00 0.00 2.94
3857 8664 7.337942 ACAACTTCCTCATCTTTGCTTTATAGG 59.662 37.037 0.00 0.00 0.00 2.57
3858 8665 8.180267 CACAACTTCCTCATCTTTGCTTTATAG 58.820 37.037 0.00 0.00 0.00 1.31
3893 8700 5.103000 TCCTTTTTCTCTAATTCGAGCGAG 58.897 41.667 2.13 0.00 0.00 5.03
3894 8701 5.068234 TCCTTTTTCTCTAATTCGAGCGA 57.932 39.130 2.13 0.00 0.00 4.93
3895 8702 4.268884 CCTCCTTTTTCTCTAATTCGAGCG 59.731 45.833 2.13 0.00 0.00 5.03
3903 8710 5.611374 CGCATATCCCTCCTTTTTCTCTAA 58.389 41.667 0.00 0.00 0.00 2.10
3909 8716 2.435372 TGCGCATATCCCTCCTTTTT 57.565 45.000 5.66 0.00 0.00 1.94
3916 8723 2.664402 AAGGAAATGCGCATATCCCT 57.336 45.000 25.61 24.61 32.15 4.20
3919 8726 6.437928 TGTGAAATAAGGAAATGCGCATATC 58.562 36.000 25.61 15.65 0.00 1.63
3920 8727 6.389830 TGTGAAATAAGGAAATGCGCATAT 57.610 33.333 25.61 9.48 0.00 1.78
3921 8728 5.826601 TGTGAAATAAGGAAATGCGCATA 57.173 34.783 25.61 7.09 0.00 3.14
3922 8729 4.717233 TGTGAAATAAGGAAATGCGCAT 57.283 36.364 19.28 19.28 0.00 4.73
3923 8730 4.511617 TTGTGAAATAAGGAAATGCGCA 57.488 36.364 14.96 14.96 0.00 6.09
3924 8731 5.101628 TCATTGTGAAATAAGGAAATGCGC 58.898 37.500 0.00 0.00 0.00 6.09
3925 8732 7.579589 TTTCATTGTGAAATAAGGAAATGCG 57.420 32.000 1.24 0.00 41.51 4.73
3938 8745 8.996024 TCGTCTATCACTTATTTCATTGTGAA 57.004 30.769 0.00 0.00 41.78 3.18
3939 8746 7.222805 GCTCGTCTATCACTTATTTCATTGTGA 59.777 37.037 0.00 0.00 42.50 3.58
3940 8747 7.010460 TGCTCGTCTATCACTTATTTCATTGTG 59.990 37.037 0.00 0.00 0.00 3.33
3941 8748 7.041721 TGCTCGTCTATCACTTATTTCATTGT 58.958 34.615 0.00 0.00 0.00 2.71
3942 8749 7.468922 TGCTCGTCTATCACTTATTTCATTG 57.531 36.000 0.00 0.00 0.00 2.82
3943 8750 8.492673 TTTGCTCGTCTATCACTTATTTCATT 57.507 30.769 0.00 0.00 0.00 2.57
3944 8751 7.254590 GCTTTGCTCGTCTATCACTTATTTCAT 60.255 37.037 0.00 0.00 0.00 2.57
3945 8752 6.036083 GCTTTGCTCGTCTATCACTTATTTCA 59.964 38.462 0.00 0.00 0.00 2.69
3946 8753 6.414890 GCTTTGCTCGTCTATCACTTATTTC 58.585 40.000 0.00 0.00 0.00 2.17
3947 8754 5.294552 GGCTTTGCTCGTCTATCACTTATTT 59.705 40.000 0.00 0.00 0.00 1.40
3948 8755 4.811557 GGCTTTGCTCGTCTATCACTTATT 59.188 41.667 0.00 0.00 0.00 1.40
3949 8756 4.372656 GGCTTTGCTCGTCTATCACTTAT 58.627 43.478 0.00 0.00 0.00 1.73
3950 8757 3.430374 GGGCTTTGCTCGTCTATCACTTA 60.430 47.826 0.00 0.00 0.00 2.24
3951 8758 2.622436 GGCTTTGCTCGTCTATCACTT 58.378 47.619 0.00 0.00 0.00 3.16
3952 8759 1.134670 GGGCTTTGCTCGTCTATCACT 60.135 52.381 0.00 0.00 0.00 3.41
3953 8760 1.134670 AGGGCTTTGCTCGTCTATCAC 60.135 52.381 0.00 0.00 32.17 3.06
3954 8761 1.137086 GAGGGCTTTGCTCGTCTATCA 59.863 52.381 0.00 0.00 32.17 2.15
3955 8762 1.137086 TGAGGGCTTTGCTCGTCTATC 59.863 52.381 0.00 0.00 32.17 2.08
3956 8763 1.195115 TGAGGGCTTTGCTCGTCTAT 58.805 50.000 0.00 0.00 32.17 1.98
3957 8764 0.973632 TTGAGGGCTTTGCTCGTCTA 59.026 50.000 0.00 0.00 32.17 2.59
3958 8765 0.108585 TTTGAGGGCTTTGCTCGTCT 59.891 50.000 0.00 0.00 32.17 4.18
3959 8766 1.168714 ATTTGAGGGCTTTGCTCGTC 58.831 50.000 0.00 0.00 32.17 4.20
3960 8767 2.290323 ACTATTTGAGGGCTTTGCTCGT 60.290 45.455 0.00 0.00 32.17 4.18
3961 8768 2.359900 ACTATTTGAGGGCTTTGCTCG 58.640 47.619 0.00 0.00 32.17 5.03
3962 8769 4.013050 AGAACTATTTGAGGGCTTTGCTC 58.987 43.478 0.00 0.00 0.00 4.26
3963 8770 4.039603 AGAACTATTTGAGGGCTTTGCT 57.960 40.909 0.00 0.00 0.00 3.91
3964 8771 4.790765 AAGAACTATTTGAGGGCTTTGC 57.209 40.909 0.00 0.00 0.00 3.68
3965 8772 6.096001 AGCATAAGAACTATTTGAGGGCTTTG 59.904 38.462 0.00 0.00 0.00 2.77
3966 8773 6.190587 AGCATAAGAACTATTTGAGGGCTTT 58.809 36.000 0.00 0.00 0.00 3.51
3967 8774 5.760131 AGCATAAGAACTATTTGAGGGCTT 58.240 37.500 0.00 0.00 0.00 4.35
3968 8775 5.379706 AGCATAAGAACTATTTGAGGGCT 57.620 39.130 0.00 0.00 0.00 5.19
3969 8776 6.095440 TGAAAGCATAAGAACTATTTGAGGGC 59.905 38.462 0.00 0.00 0.00 5.19
3970 8777 7.630242 TGAAAGCATAAGAACTATTTGAGGG 57.370 36.000 0.00 0.00 0.00 4.30
3974 8781 9.736023 GGGTTATGAAAGCATAAGAACTATTTG 57.264 33.333 0.00 0.00 45.08 2.32
3975 8782 9.700831 AGGGTTATGAAAGCATAAGAACTATTT 57.299 29.630 0.00 0.00 45.08 1.40
3979 8786 9.528489 TTTTAGGGTTATGAAAGCATAAGAACT 57.472 29.630 0.00 0.00 45.08 3.01
3986 8793 9.034800 TCTCAATTTTTAGGGTTATGAAAGCAT 57.965 29.630 0.00 0.00 38.54 3.79
3987 8794 8.415950 TCTCAATTTTTAGGGTTATGAAAGCA 57.584 30.769 0.00 0.00 34.70 3.91
3988 8795 9.305925 CATCTCAATTTTTAGGGTTATGAAAGC 57.694 33.333 0.00 0.00 0.00 3.51
3989 8796 9.305925 GCATCTCAATTTTTAGGGTTATGAAAG 57.694 33.333 0.00 0.00 0.00 2.62
3990 8797 8.811017 TGCATCTCAATTTTTAGGGTTATGAAA 58.189 29.630 0.00 0.00 0.00 2.69
3991 8798 8.250332 GTGCATCTCAATTTTTAGGGTTATGAA 58.750 33.333 0.00 0.00 0.00 2.57
3992 8799 7.415095 CGTGCATCTCAATTTTTAGGGTTATGA 60.415 37.037 0.00 0.00 0.00 2.15
3993 8800 6.692681 CGTGCATCTCAATTTTTAGGGTTATG 59.307 38.462 0.00 0.00 0.00 1.90
3994 8801 6.601613 TCGTGCATCTCAATTTTTAGGGTTAT 59.398 34.615 0.00 0.00 0.00 1.89
3995 8802 5.941058 TCGTGCATCTCAATTTTTAGGGTTA 59.059 36.000 0.00 0.00 0.00 2.85
3996 8803 4.764823 TCGTGCATCTCAATTTTTAGGGTT 59.235 37.500 0.00 0.00 0.00 4.11
3997 8804 4.331968 TCGTGCATCTCAATTTTTAGGGT 58.668 39.130 0.00 0.00 0.00 4.34
3998 8805 4.963276 TCGTGCATCTCAATTTTTAGGG 57.037 40.909 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.