Multiple sequence alignment - TraesCS6B01G175700

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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 TraesCS6B01G175700 chr6B 100.000 4240 0 0 1 4240 191748564 191752803 0.000000e+00 7830.0
1 TraesCS6B01G175700 chr6B 92.257 452 35 0 1 452 496318624 496318173 3.570000e-180 641.0
2 TraesCS6B01G175700 chr6B 91.372 452 38 1 1 452 458901587 458901137 6.020000e-173 617.0
3 TraesCS6B01G175700 chr6A 92.473 2936 153 33 1325 4240 127568501 127571388 0.000000e+00 4135.0
4 TraesCS6B01G175700 chr6A 92.428 449 28 3 882 1327 127568029 127568474 1.660000e-178 636.0
5 TraesCS6B01G175700 chr6D 92.344 2926 130 24 1307 4177 105536980 105539866 0.000000e+00 4076.0
6 TraesCS6B01G175700 chr6D 96.567 466 14 2 865 1329 105536491 105536955 0.000000e+00 771.0
7 TraesCS6B01G175700 chr6D 87.500 64 7 1 825 887 4987380 4987317 5.880000e-09 73.1
8 TraesCS6B01G175700 chr6D 83.333 78 10 3 811 886 324173452 324173528 7.610000e-08 69.4
9 TraesCS6B01G175700 chr3B 92.478 452 34 0 1 452 598880484 598880033 0.000000e+00 647.0
10 TraesCS6B01G175700 chr3B 91.209 182 12 2 446 623 598879974 598879793 1.180000e-60 244.0
11 TraesCS6B01G175700 chr5B 92.257 452 35 0 1 452 349398843 349398392 3.570000e-180 641.0
12 TraesCS6B01G175700 chr5B 92.257 452 35 0 1 452 707532684 707533135 3.570000e-180 641.0
13 TraesCS6B01G175700 chr5B 92.070 454 31 4 1 452 163117985 163117535 5.980000e-178 634.0
14 TraesCS6B01G175700 chr5B 92.308 182 10 2 446 623 170161159 170160978 5.440000e-64 255.0
15 TraesCS6B01G175700 chr7B 92.274 453 32 3 1 452 45601681 45601231 1.290000e-179 640.0
16 TraesCS6B01G175700 chr7B 90.811 185 13 2 443 623 273904407 273904591 1.180000e-60 244.0
17 TraesCS6B01G175700 chr7B 90.217 184 15 1 443 623 194253567 194253750 1.970000e-58 237.0
18 TraesCS6B01G175700 chr7B 90.110 182 14 2 446 623 275095102 275094921 2.550000e-57 233.0
19 TraesCS6B01G175700 chr2B 92.035 452 36 0 1 452 88033808 88033357 1.660000e-178 636.0
20 TraesCS6B01G175700 chr2B 89.730 185 15 2 443 623 173876711 173876895 2.550000e-57 233.0
21 TraesCS6B01G175700 chr2B 90.323 62 5 1 826 886 129757401 129757462 3.510000e-11 80.5
22 TraesCS6B01G175700 chr4B 91.028 457 41 0 1 457 476679382 476679838 6.020000e-173 617.0
23 TraesCS6B01G175700 chr4B 90.110 182 14 2 446 623 256771754 256771573 2.550000e-57 233.0
24 TraesCS6B01G175700 chr1B 90.659 182 13 2 446 623 188584350 188584531 5.480000e-59 239.0
25 TraesCS6B01G175700 chr1B 90.270 185 14 2 443 623 219752021 219752205 5.480000e-59 239.0
26 TraesCS6B01G175700 chr7D 89.375 160 14 2 3971 4129 307213126 307213283 9.300000e-47 198.0
27 TraesCS6B01G175700 chr7D 88.889 63 6 1 826 887 562513015 562513077 4.550000e-10 76.8
28 TraesCS6B01G175700 chr7A 86.957 69 8 1 819 886 643889321 643889253 4.550000e-10 76.8
29 TraesCS6B01G175700 chr5A 88.889 63 6 1 826 887 332851604 332851542 4.550000e-10 76.8
30 TraesCS6B01G175700 chr3D 88.889 63 6 1 826 887 350489395 350489457 4.550000e-10 76.8
31 TraesCS6B01G175700 chr2D 86.111 72 9 1 816 886 581336062 581335991 4.550000e-10 76.8
32 TraesCS6B01G175700 chr1D 88.889 63 6 1 826 887 248598644 248598706 4.550000e-10 76.8
33 TraesCS6B01G175700 chr1D 87.500 56 7 0 4123 4178 244757168 244757113 9.840000e-07 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G175700 chr6B 191748564 191752803 4239 False 7830.0 7830 100.0000 1 4240 1 chr6B.!!$F1 4239
1 TraesCS6B01G175700 chr6A 127568029 127571388 3359 False 2385.5 4135 92.4505 882 4240 2 chr6A.!!$F1 3358
2 TraesCS6B01G175700 chr6D 105536491 105539866 3375 False 2423.5 4076 94.4555 865 4177 2 chr6D.!!$F2 3312
3 TraesCS6B01G175700 chr3B 598879793 598880484 691 True 445.5 647 91.8435 1 623 2 chr3B.!!$R1 622

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
758 828 0.107410 TTGAGGTGACGTGGCAACTT 60.107 50.000 0.0 0.0 35.57 2.66 F
759 829 0.107410 TGAGGTGACGTGGCAACTTT 60.107 50.000 0.0 0.0 35.57 2.66 F
1362 1513 1.063649 GCCATGATGAGCTTGCGTG 59.936 57.895 0.0 0.0 0.00 5.34 F
3002 3184 0.111061 TGCAGGACACCAATGCTCTT 59.889 50.000 0.0 0.0 40.62 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1601 1762 0.598065 GATGTGCACACCCAAAGGAC 59.402 55.000 24.37 1.74 36.73 3.85 R
1618 1779 0.810031 GCAGGTGCCACGAATACGAT 60.810 55.000 0.00 0.00 37.79 3.73 R
3103 3285 1.134367 CATCACCATCTTGCTTGCCTG 59.866 52.381 0.00 0.00 0.00 4.85 R
4045 4253 1.227973 GGCTATGGCAGGGCAGTAC 60.228 63.158 14.64 0.00 40.87 2.73 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
32 33 0.841961 TCCTTGAGGCCATGATGAGG 59.158 55.000 5.01 3.28 34.44 3.86
55 56 4.312443 CCAAAGATCAACTTTTGCATGCT 58.688 39.130 20.33 0.00 45.22 3.79
66 67 2.871182 TTGCATGCTAGAGTACCTCG 57.129 50.000 20.33 0.00 35.36 4.63
73 74 3.036819 TGCTAGAGTACCTCGACCTAGA 58.963 50.000 0.00 0.00 35.36 2.43
80 81 2.128507 CCTCGACCTAGACCCCTGC 61.129 68.421 0.00 0.00 0.00 4.85
83 84 1.218316 CGACCTAGACCCCTGCAAC 59.782 63.158 0.00 0.00 0.00 4.17
94 95 1.239968 CCCTGCAACAAGGAGCTGAC 61.240 60.000 0.00 0.00 40.02 3.51
136 137 0.818040 ACTTTCTTCCTTGCCGCGTT 60.818 50.000 4.92 0.00 0.00 4.84
158 159 0.601576 TGGGGTTGTCATCGTTGTCG 60.602 55.000 0.00 0.00 38.55 4.35
161 162 0.110823 GGTTGTCATCGTTGTCGTGC 60.111 55.000 0.00 0.00 38.33 5.34
167 168 1.067693 CATCGTTGTCGTGCTTGCTA 58.932 50.000 0.00 0.00 38.33 3.49
170 171 1.267533 TCGTTGTCGTGCTTGCTACTA 59.732 47.619 0.00 0.00 38.33 1.82
194 195 1.063183 GATCCTTATCTGGCCCTGCT 58.937 55.000 0.00 0.00 0.00 4.24
195 196 2.260822 GATCCTTATCTGGCCCTGCTA 58.739 52.381 0.00 0.00 0.00 3.49
251 252 1.302752 TGCTACCAAGGCTGCACTG 60.303 57.895 0.50 0.00 0.00 3.66
254 255 0.674895 CTACCAAGGCTGCACTGACC 60.675 60.000 0.50 0.00 0.00 4.02
295 296 1.933853 GTATAGCAACAACGGCTCCTG 59.066 52.381 0.00 0.00 42.62 3.86
299 300 3.175710 AACAACGGCTCCTGGGGT 61.176 61.111 0.00 0.00 0.00 4.95
319 320 3.712907 GGGCGCAACCAGGGTAGA 61.713 66.667 10.83 0.00 42.05 2.59
324 325 0.670546 CGCAACCAGGGTAGACACAG 60.671 60.000 0.00 0.00 0.00 3.66
335 336 3.018149 GGTAGACACAGAGGACAGGTAG 58.982 54.545 0.00 0.00 0.00 3.18
343 344 3.165875 CAGAGGACAGGTAGGTCTTCAA 58.834 50.000 7.93 0.00 43.93 2.69
344 345 3.772025 CAGAGGACAGGTAGGTCTTCAAT 59.228 47.826 7.93 0.00 43.93 2.57
357 358 5.072741 AGGTCTTCAATTCTTGCAAAGCTA 58.927 37.500 0.00 0.00 45.70 3.32
358 359 5.713861 AGGTCTTCAATTCTTGCAAAGCTAT 59.286 36.000 0.00 0.00 45.70 2.97
418 419 5.452078 TTCAAAATCTTGAAGAACGGCAT 57.548 34.783 0.00 0.00 44.76 4.40
427 428 4.166011 GAACGGCATGGCACGCTC 62.166 66.667 20.37 5.67 0.00 5.03
458 524 3.201487 TGGAGATGAATCTGCTCAATGGT 59.799 43.478 12.31 0.00 44.46 3.55
470 536 4.401022 TGCTCAATGGTCTTGATCTTGTT 58.599 39.130 0.00 0.00 0.00 2.83
482 548 3.509442 TGATCTTGTTGGGATTGGCTTT 58.491 40.909 0.00 0.00 0.00 3.51
491 557 1.109323 GGATTGGCTTTGATCCCCCG 61.109 60.000 0.00 0.00 36.61 5.73
514 581 3.153919 GGGACACAAAGTATCCAAGCAA 58.846 45.455 0.00 0.00 33.87 3.91
525 592 2.256461 CAAGCAACTTGCCGGAGC 59.744 61.111 5.05 0.00 46.52 4.70
600 670 3.959535 TTGCAAACATCTCCAAATCCC 57.040 42.857 0.00 0.00 0.00 3.85
623 693 3.608316 ATGAGAGTTGCTCTGTCCTTC 57.392 47.619 3.12 0.00 41.35 3.46
624 694 1.620819 TGAGAGTTGCTCTGTCCTTCC 59.379 52.381 3.12 0.00 41.35 3.46
625 695 1.899142 GAGAGTTGCTCTGTCCTTCCT 59.101 52.381 3.12 0.00 41.35 3.36
626 696 1.899142 AGAGTTGCTCTGTCCTTCCTC 59.101 52.381 0.00 0.00 39.62 3.71
627 697 0.605589 AGTTGCTCTGTCCTTCCTCG 59.394 55.000 0.00 0.00 0.00 4.63
628 698 0.318762 GTTGCTCTGTCCTTCCTCGT 59.681 55.000 0.00 0.00 0.00 4.18
629 699 1.544691 GTTGCTCTGTCCTTCCTCGTA 59.455 52.381 0.00 0.00 0.00 3.43
630 700 1.464734 TGCTCTGTCCTTCCTCGTAG 58.535 55.000 0.00 0.00 0.00 3.51
631 701 1.004394 TGCTCTGTCCTTCCTCGTAGA 59.996 52.381 0.00 0.00 0.00 2.59
646 716 4.750952 TCGTAGAGATCTTCTTATGGCG 57.249 45.455 0.00 0.00 37.36 5.69
647 717 4.386711 TCGTAGAGATCTTCTTATGGCGA 58.613 43.478 0.00 0.00 37.36 5.54
648 718 4.452795 TCGTAGAGATCTTCTTATGGCGAG 59.547 45.833 0.00 0.00 37.36 5.03
649 719 4.214545 CGTAGAGATCTTCTTATGGCGAGT 59.785 45.833 0.00 0.00 37.36 4.18
650 720 5.408909 CGTAGAGATCTTCTTATGGCGAGTA 59.591 44.000 0.00 0.00 37.36 2.59
651 721 6.073167 CGTAGAGATCTTCTTATGGCGAGTAA 60.073 42.308 0.00 0.00 37.36 2.24
652 722 6.716934 AGAGATCTTCTTATGGCGAGTAAA 57.283 37.500 0.00 0.00 29.61 2.01
653 723 7.296628 AGAGATCTTCTTATGGCGAGTAAAT 57.703 36.000 0.00 0.00 29.61 1.40
654 724 7.731054 AGAGATCTTCTTATGGCGAGTAAATT 58.269 34.615 0.00 0.00 29.61 1.82
655 725 8.207545 AGAGATCTTCTTATGGCGAGTAAATTT 58.792 33.333 0.00 0.00 29.61 1.82
656 726 9.477484 GAGATCTTCTTATGGCGAGTAAATTTA 57.523 33.333 0.00 0.00 0.00 1.40
663 733 9.796120 TCTTATGGCGAGTAAATTTATTTTTGG 57.204 29.630 0.31 0.00 0.00 3.28
664 734 9.796120 CTTATGGCGAGTAAATTTATTTTTGGA 57.204 29.630 0.31 0.00 0.00 3.53
665 735 9.575783 TTATGGCGAGTAAATTTATTTTTGGAC 57.424 29.630 0.31 0.00 0.00 4.02
666 736 7.222000 TGGCGAGTAAATTTATTTTTGGACT 57.778 32.000 0.31 0.00 0.00 3.85
667 737 7.662897 TGGCGAGTAAATTTATTTTTGGACTT 58.337 30.769 0.31 0.00 0.00 3.01
668 738 7.810759 TGGCGAGTAAATTTATTTTTGGACTTC 59.189 33.333 0.31 0.00 0.00 3.01
669 739 7.274904 GGCGAGTAAATTTATTTTTGGACTTCC 59.725 37.037 0.31 0.00 0.00 3.46
670 740 7.810759 GCGAGTAAATTTATTTTTGGACTTCCA 59.189 33.333 0.31 0.00 45.94 3.53
671 741 9.855021 CGAGTAAATTTATTTTTGGACTTCCAT 57.145 29.630 0.31 0.00 46.97 3.41
683 753 9.709495 TTTTTGGACTTCCATAAATCTTGAATG 57.291 29.630 9.16 0.00 46.97 2.67
684 754 8.421249 TTTGGACTTCCATAAATCTTGAATGT 57.579 30.769 0.00 0.00 46.97 2.71
685 755 8.421249 TTGGACTTCCATAAATCTTGAATGTT 57.579 30.769 0.00 0.00 46.97 2.71
686 756 8.055279 TGGACTTCCATAAATCTTGAATGTTC 57.945 34.615 0.00 0.00 42.01 3.18
687 757 7.148255 TGGACTTCCATAAATCTTGAATGTTCG 60.148 37.037 0.00 0.00 42.01 3.95
688 758 7.088589 ACTTCCATAAATCTTGAATGTTCGG 57.911 36.000 0.00 0.00 0.00 4.30
689 759 6.095440 ACTTCCATAAATCTTGAATGTTCGGG 59.905 38.462 0.00 0.00 0.00 5.14
690 760 5.505780 TCCATAAATCTTGAATGTTCGGGT 58.494 37.500 0.00 0.00 0.00 5.28
691 761 5.949354 TCCATAAATCTTGAATGTTCGGGTT 59.051 36.000 0.00 0.00 0.00 4.11
692 762 6.094881 TCCATAAATCTTGAATGTTCGGGTTC 59.905 38.462 0.00 0.00 0.00 3.62
693 763 4.419522 AAATCTTGAATGTTCGGGTTCG 57.580 40.909 0.00 0.00 37.82 3.95
694 764 1.803334 TCTTGAATGTTCGGGTTCGG 58.197 50.000 0.00 0.00 36.95 4.30
695 765 1.345089 TCTTGAATGTTCGGGTTCGGA 59.655 47.619 0.00 0.00 36.95 4.55
696 766 2.027561 TCTTGAATGTTCGGGTTCGGAT 60.028 45.455 0.00 0.00 36.95 4.18
697 767 2.483014 TGAATGTTCGGGTTCGGATT 57.517 45.000 0.00 0.00 36.95 3.01
698 768 2.785562 TGAATGTTCGGGTTCGGATTT 58.214 42.857 0.00 0.00 36.95 2.17
699 769 3.150767 TGAATGTTCGGGTTCGGATTTT 58.849 40.909 0.00 0.00 36.95 1.82
700 770 4.325119 TGAATGTTCGGGTTCGGATTTTA 58.675 39.130 0.00 0.00 36.95 1.52
701 771 4.760715 TGAATGTTCGGGTTCGGATTTTAA 59.239 37.500 0.00 0.00 36.95 1.52
702 772 4.957759 ATGTTCGGGTTCGGATTTTAAG 57.042 40.909 0.00 0.00 36.95 1.85
703 773 2.485038 TGTTCGGGTTCGGATTTTAAGC 59.515 45.455 0.00 0.00 36.95 3.09
704 774 2.476126 TCGGGTTCGGATTTTAAGCA 57.524 45.000 0.00 0.00 36.95 3.91
705 775 2.993937 TCGGGTTCGGATTTTAAGCAT 58.006 42.857 0.00 0.00 36.95 3.79
706 776 2.680841 TCGGGTTCGGATTTTAAGCATG 59.319 45.455 0.00 0.00 36.95 4.06
707 777 2.422127 CGGGTTCGGATTTTAAGCATGT 59.578 45.455 0.00 0.00 0.00 3.21
708 778 3.486875 CGGGTTCGGATTTTAAGCATGTC 60.487 47.826 0.00 0.00 0.00 3.06
709 779 3.442273 GGGTTCGGATTTTAAGCATGTCA 59.558 43.478 0.00 0.00 0.00 3.58
710 780 4.412207 GGTTCGGATTTTAAGCATGTCAC 58.588 43.478 0.00 0.00 0.00 3.67
711 781 4.156008 GGTTCGGATTTTAAGCATGTCACT 59.844 41.667 0.00 0.00 0.00 3.41
712 782 5.324697 GTTCGGATTTTAAGCATGTCACTC 58.675 41.667 0.00 0.00 0.00 3.51
713 783 3.938963 TCGGATTTTAAGCATGTCACTCC 59.061 43.478 0.00 0.00 0.00 3.85
714 784 3.242413 CGGATTTTAAGCATGTCACTCCG 60.242 47.826 0.00 0.00 37.41 4.63
715 785 3.938963 GGATTTTAAGCATGTCACTCCGA 59.061 43.478 0.00 0.00 0.00 4.55
716 786 4.394920 GGATTTTAAGCATGTCACTCCGAA 59.605 41.667 0.00 0.00 0.00 4.30
717 787 4.742438 TTTTAAGCATGTCACTCCGAAC 57.258 40.909 0.00 0.00 0.00 3.95
718 788 3.678056 TTAAGCATGTCACTCCGAACT 57.322 42.857 0.00 0.00 0.00 3.01
719 789 1.800805 AAGCATGTCACTCCGAACTG 58.199 50.000 0.00 0.00 0.00 3.16
720 790 0.681733 AGCATGTCACTCCGAACTGT 59.318 50.000 0.00 0.00 0.00 3.55
721 791 1.070758 AGCATGTCACTCCGAACTGTT 59.929 47.619 0.00 0.00 0.00 3.16
722 792 1.873591 GCATGTCACTCCGAACTGTTT 59.126 47.619 0.00 0.00 0.00 2.83
723 793 2.290641 GCATGTCACTCCGAACTGTTTT 59.709 45.455 0.00 0.00 0.00 2.43
724 794 3.243068 GCATGTCACTCCGAACTGTTTTT 60.243 43.478 0.00 0.00 0.00 1.94
752 822 3.107642 ACTTTAGTTGAGGTGACGTGG 57.892 47.619 0.00 0.00 0.00 4.94
753 823 1.798813 CTTTAGTTGAGGTGACGTGGC 59.201 52.381 0.00 0.00 0.00 5.01
754 824 0.753867 TTAGTTGAGGTGACGTGGCA 59.246 50.000 0.00 0.00 0.00 4.92
755 825 0.753867 TAGTTGAGGTGACGTGGCAA 59.246 50.000 0.00 0.00 0.00 4.52
756 826 0.814010 AGTTGAGGTGACGTGGCAAC 60.814 55.000 0.00 0.00 39.17 4.17
757 827 0.814010 GTTGAGGTGACGTGGCAACT 60.814 55.000 0.00 0.00 38.85 3.16
758 828 0.107410 TTGAGGTGACGTGGCAACTT 60.107 50.000 0.00 0.00 35.57 2.66
759 829 0.107410 TGAGGTGACGTGGCAACTTT 60.107 50.000 0.00 0.00 35.57 2.66
760 830 1.139256 TGAGGTGACGTGGCAACTTTA 59.861 47.619 0.00 0.00 35.57 1.85
761 831 1.798813 GAGGTGACGTGGCAACTTTAG 59.201 52.381 0.00 0.00 35.57 1.85
762 832 1.140252 AGGTGACGTGGCAACTTTAGT 59.860 47.619 0.00 0.00 29.84 2.24
763 833 1.944709 GGTGACGTGGCAACTTTAGTT 59.055 47.619 0.00 0.00 39.12 2.24
785 855 8.460831 AGTTGTTAAAACATGTCAACTTTGAC 57.539 30.769 18.98 14.10 43.68 3.18
786 856 7.544217 AGTTGTTAAAACATGTCAACTTTGACC 59.456 33.333 18.98 4.73 44.36 4.02
787 857 6.925211 TGTTAAAACATGTCAACTTTGACCA 58.075 32.000 17.44 7.84 44.11 4.02
788 858 7.032580 TGTTAAAACATGTCAACTTTGACCAG 58.967 34.615 17.44 12.59 44.11 4.00
789 859 7.309499 TGTTAAAACATGTCAACTTTGACCAGT 60.309 33.333 17.44 13.13 44.11 4.00
800 870 8.974060 TCAACTTTGACCAGTTAGTTTTCTAT 57.026 30.769 0.00 0.00 35.10 1.98
801 871 9.403583 TCAACTTTGACCAGTTAGTTTTCTATT 57.596 29.630 0.00 0.00 35.10 1.73
850 920 2.817538 AAACGTTCAAGTTGTCACGG 57.182 45.000 24.38 12.88 36.95 4.94
851 921 1.729284 AACGTTCAAGTTGTCACGGT 58.271 45.000 24.38 19.30 36.95 4.83
852 922 1.729284 ACGTTCAAGTTGTCACGGTT 58.271 45.000 24.38 9.90 36.95 4.44
853 923 2.891112 ACGTTCAAGTTGTCACGGTTA 58.109 42.857 24.38 0.00 36.95 2.85
854 924 3.260740 ACGTTCAAGTTGTCACGGTTAA 58.739 40.909 24.38 1.46 36.95 2.01
855 925 3.683822 ACGTTCAAGTTGTCACGGTTAAA 59.316 39.130 24.38 0.85 36.95 1.52
856 926 4.153835 ACGTTCAAGTTGTCACGGTTAAAA 59.846 37.500 24.38 0.24 36.95 1.52
857 927 5.163733 ACGTTCAAGTTGTCACGGTTAAAAT 60.164 36.000 24.38 7.83 36.95 1.82
858 928 5.394322 CGTTCAAGTTGTCACGGTTAAAATC 59.606 40.000 17.39 0.00 0.00 2.17
859 929 5.427036 TCAAGTTGTCACGGTTAAAATCC 57.573 39.130 2.11 0.00 0.00 3.01
880 950 7.795482 ATCCGAACATTTATCATTTCCGTTA 57.205 32.000 0.00 0.00 0.00 3.18
898 968 7.868906 TCCGTTATTTTAGGGTCAAATAAGG 57.131 36.000 9.38 9.38 39.49 2.69
901 971 7.123098 CCGTTATTTTAGGGTCAAATAAGGGTT 59.877 37.037 19.53 0.00 45.99 4.11
923 993 4.957921 GGCAATTCGCACGACATCTTCG 62.958 54.545 0.00 0.00 45.67 3.79
967 1037 2.813908 CTTCCTACGCGCGCCTTT 60.814 61.111 32.58 13.56 0.00 3.11
1362 1513 1.063649 GCCATGATGAGCTTGCGTG 59.936 57.895 0.00 0.00 0.00 5.34
1418 1569 9.959721 AAACTCTTCATAGCTAATTTGGTCTTA 57.040 29.630 0.00 0.00 0.00 2.10
1422 1573 7.705325 TCTTCATAGCTAATTTGGTCTTACGAC 59.295 37.037 0.00 0.00 39.49 4.34
1514 1671 1.200020 AGCGGCCTTTTCTTTCATTCG 59.800 47.619 0.00 0.00 0.00 3.34
1517 1674 2.414161 CGGCCTTTTCTTTCATTCGTCC 60.414 50.000 0.00 0.00 0.00 4.79
1523 1680 5.432885 TTTTCTTTCATTCGTCCCTTGTC 57.567 39.130 0.00 0.00 0.00 3.18
1585 1746 3.833545 ACAGTCACACAGATCGTAGTC 57.166 47.619 0.00 0.00 0.00 2.59
1617 1778 1.040339 TTGGTCCTTTGGGTGTGCAC 61.040 55.000 10.75 10.75 0.00 4.57
1618 1779 1.454847 GGTCCTTTGGGTGTGCACA 60.455 57.895 17.42 17.42 0.00 4.57
1623 1784 1.518325 CTTTGGGTGTGCACATCGTA 58.482 50.000 24.69 12.28 0.00 3.43
1660 1821 3.501385 CCCCTTGGGTTTGGTTTCATCTA 60.501 47.826 4.84 0.00 38.25 1.98
1677 1838 5.289595 TCATCTACTTGTGTCATATTCCGC 58.710 41.667 0.00 0.00 0.00 5.54
1689 1858 3.748048 TCATATTCCGCTCTTGCTTATGC 59.252 43.478 0.00 0.00 36.97 3.14
1726 1895 4.536090 TGTCAAGATTACCTCCTGTTCCAT 59.464 41.667 0.00 0.00 0.00 3.41
1735 1904 2.091665 CCTCCTGTTCCATAGGGCAAAT 60.092 50.000 0.00 0.00 35.96 2.32
1771 1940 1.338105 TGACCAGTTCGAATGAGCAGG 60.338 52.381 0.00 0.00 37.88 4.85
1775 1944 2.093973 CCAGTTCGAATGAGCAGGTAGT 60.094 50.000 0.00 0.00 29.07 2.73
1806 1975 6.535865 TGATTGATAAATGCTTTGTTGATGCC 59.464 34.615 0.00 0.00 0.00 4.40
1894 2063 6.859112 AGCTTATGTTCGTATCCTATCCAT 57.141 37.500 0.00 0.00 0.00 3.41
1979 2148 8.565896 ACTTCTAATTGTCATTGTTGAGCATA 57.434 30.769 0.00 0.00 30.85 3.14
2121 2290 5.723295 CCCAAAGGTGAATACTGGATTTTG 58.277 41.667 0.00 0.00 0.00 2.44
2428 2600 9.640963 ACATATAACTGCTACTATCGGAATTTC 57.359 33.333 0.00 0.00 0.00 2.17
2576 2749 4.778534 ATGTTGCTGAGGTGAAATTCAG 57.221 40.909 0.00 0.00 42.87 3.02
2583 2756 2.037121 TGAGGTGAAATTCAGAGACGCA 59.963 45.455 0.00 0.00 0.00 5.24
2634 2807 7.201661 CGTGCTAAGGTTAATTTAGTTGGCATA 60.202 37.037 9.89 0.00 37.03 3.14
2666 2839 7.640616 TTACTTCGTCAAATTATCGTTCACA 57.359 32.000 0.00 0.00 0.00 3.58
2669 2842 5.369947 TCGTCAAATTATCGTTCACATCG 57.630 39.130 0.00 0.00 0.00 3.84
2876 3055 8.305046 TGCATACAAGCCTTTATTCCTATTTT 57.695 30.769 0.00 0.00 0.00 1.82
2978 3160 5.067805 CCTTTAAGTTCCTTTGTCTTGCTGT 59.932 40.000 0.00 0.00 0.00 4.40
3002 3184 0.111061 TGCAGGACACCAATGCTCTT 59.889 50.000 0.00 0.00 40.62 2.85
3082 3264 4.803329 AGGCAAGGATATTTGGACAGAT 57.197 40.909 0.00 0.00 0.00 2.90
3243 3425 0.601057 TCGGCGTCTTGACTGATTCA 59.399 50.000 6.85 0.00 0.00 2.57
3333 3515 4.340381 AGAGGCTTTATTGAATGTGGCATC 59.660 41.667 0.00 0.00 0.00 3.91
3343 3527 1.586422 ATGTGGCATCGAGAAATCCG 58.414 50.000 0.00 0.00 0.00 4.18
3360 3544 8.970691 AGAAATCCGTAAAATTTGTTCAGATG 57.029 30.769 0.00 0.00 0.00 2.90
3404 3588 9.113838 AGAAGTGATATAACTGCAATGTTAAGG 57.886 33.333 0.62 0.00 36.22 2.69
3411 3595 2.094675 CTGCAATGTTAAGGACCCCTG 58.905 52.381 0.00 0.00 32.13 4.45
3546 3730 3.211045 GACCAAAACCAACTCTGTAGCA 58.789 45.455 0.00 0.00 0.00 3.49
3579 3763 4.906618 TCAGTAACCTCCTTTGATGGTTC 58.093 43.478 0.00 0.00 42.38 3.62
3623 3807 4.574013 GCGAAGTCTGGATGATTGATCTTT 59.426 41.667 0.00 0.00 0.00 2.52
3635 3819 6.272822 TGATTGATCTTTGACTTCTCGAGA 57.727 37.500 12.08 12.08 0.00 4.04
3666 3850 1.294138 CCCAGCAAAGCATTGGGTG 59.706 57.895 3.55 0.21 45.31 4.61
3679 3865 3.841643 CATTGGGTGCAAAATGTCTCTC 58.158 45.455 8.98 0.00 0.00 3.20
3680 3866 2.957402 TGGGTGCAAAATGTCTCTCT 57.043 45.000 0.00 0.00 0.00 3.10
3690 3876 7.695618 GTGCAAAATGTCTCTCTTGATAATGTC 59.304 37.037 0.00 0.00 0.00 3.06
3703 3889 8.833231 TCTTGATAATGTCGTTTCTCTTTTCT 57.167 30.769 0.00 0.00 0.00 2.52
3803 3989 4.021916 ACCACAGAGCTAGTATAAACCGT 58.978 43.478 0.00 0.00 0.00 4.83
3888 4096 5.348997 GTGCTACTTAGTGTCATTTCTGGAC 59.651 44.000 0.00 0.00 35.83 4.02
3907 4115 7.788026 TCTGGACGTTGTTATAAGGATGTAAT 58.212 34.615 0.00 0.00 0.00 1.89
3973 4181 1.549203 AACCATCATGGGTGCAAGTC 58.451 50.000 9.04 0.00 43.37 3.01
3993 4201 4.704057 AGTCATGCCTTTTTCATCTTCCTC 59.296 41.667 0.00 0.00 0.00 3.71
3999 4207 4.623171 GCCTTTTTCATCTTCCTCGTAGGA 60.623 45.833 0.00 0.11 44.10 2.94
4022 4230 4.940654 AGCCTTCAGTCTTTTGATTAGAGC 59.059 41.667 0.00 0.00 0.00 4.09
4024 4232 5.391416 GCCTTCAGTCTTTTGATTAGAGCAC 60.391 44.000 0.00 0.00 0.00 4.40
4056 4264 2.510238 CAGAGCGTACTGCCCTGC 60.510 66.667 7.90 0.00 42.83 4.85
4062 4270 1.595382 CGTACTGCCCTGCCATAGC 60.595 63.158 0.00 0.00 40.48 2.97
4085 4293 2.287487 GCGAGGGTCTTAATAGTCGGTC 60.287 54.545 0.00 0.00 0.00 4.79
4090 4298 2.031333 GGTCTTAATAGTCGGTCGCGAT 60.031 50.000 14.06 0.00 0.00 4.58
4135 4343 3.154710 GGAACTTCCAGGAAATTTCGGT 58.845 45.455 11.95 0.00 36.28 4.69
4136 4344 3.572682 GGAACTTCCAGGAAATTTCGGTT 59.427 43.478 11.95 2.66 36.28 4.44
4143 4351 7.503230 ACTTCCAGGAAATTTCGGTTTAAGTTA 59.497 33.333 11.95 0.00 0.00 2.24
4148 4356 9.471084 CAGGAAATTTCGGTTTAAGTTATTTGT 57.529 29.630 11.95 0.00 0.00 2.83
4218 4426 2.548875 TGTTGCACAAATTTCAGTGGC 58.451 42.857 9.85 4.36 36.29 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.600916 GGCCTCAAGGAAACTGCGT 60.601 57.895 0.00 0.00 42.68 5.24
7 8 0.529378 CATGGCCTCAAGGAAACTGC 59.471 55.000 3.32 0.00 42.68 4.40
66 67 0.690762 TTGTTGCAGGGGTCTAGGTC 59.309 55.000 0.00 0.00 0.00 3.85
73 74 2.116125 GCTCCTTGTTGCAGGGGT 59.884 61.111 0.00 0.00 36.67 4.95
80 81 1.871080 ACTTCGTCAGCTCCTTGTTG 58.129 50.000 0.00 0.00 0.00 3.33
83 84 2.029828 AGTGTACTTCGTCAGCTCCTTG 60.030 50.000 0.00 0.00 0.00 3.61
94 95 2.094659 CAGCGCCCAGTGTACTTCG 61.095 63.158 2.29 0.00 0.00 3.79
109 110 1.000938 CAAGGAAGAAAGTGGTGCAGC 60.001 52.381 9.47 9.47 0.00 5.25
136 137 1.142060 ACAACGATGACAACCCCAAGA 59.858 47.619 0.00 0.00 0.00 3.02
158 159 4.954875 AGGATCAGAATAGTAGCAAGCAC 58.045 43.478 0.00 0.00 0.00 4.40
161 162 8.034215 CCAGATAAGGATCAGAATAGTAGCAAG 58.966 40.741 0.00 0.00 34.17 4.01
167 168 4.534103 GGGCCAGATAAGGATCAGAATAGT 59.466 45.833 4.39 0.00 34.17 2.12
170 171 3.330110 CAGGGCCAGATAAGGATCAGAAT 59.670 47.826 6.18 0.00 34.17 2.40
200 201 3.195182 TGGATGAGAAAGAGAGTGAGCAG 59.805 47.826 0.00 0.00 0.00 4.24
254 255 1.169661 TAGCGGCAACCAACCAAGTG 61.170 55.000 1.45 0.00 0.00 3.16
299 300 3.134703 TACCCTGGTTGCGCCCAAA 62.135 57.895 4.18 0.00 33.07 3.28
305 306 0.670546 CTGTGTCTACCCTGGTTGCG 60.671 60.000 0.00 0.00 0.00 4.85
319 320 1.429687 AGACCTACCTGTCCTCTGTGT 59.570 52.381 0.00 0.00 35.83 3.72
324 325 4.468153 AGAATTGAAGACCTACCTGTCCTC 59.532 45.833 0.00 0.00 35.83 3.71
343 344 4.015084 AGCAGACATAGCTTTGCAAGAAT 58.985 39.130 3.86 0.00 39.87 2.40
344 345 3.415212 AGCAGACATAGCTTTGCAAGAA 58.585 40.909 3.86 0.00 39.87 2.52
357 358 0.842030 TGGACCCCTGAAGCAGACAT 60.842 55.000 0.00 0.00 32.44 3.06
358 359 1.461268 TGGACCCCTGAAGCAGACA 60.461 57.895 0.00 0.00 32.44 3.41
427 428 2.158986 AGATTCATCTCCAAGTCTGCCG 60.159 50.000 0.00 0.00 29.30 5.69
458 524 3.091545 GCCAATCCCAACAAGATCAAGA 58.908 45.455 0.00 0.00 0.00 3.02
491 557 2.488153 GCTTGGATACTTTGTGTCCCAC 59.512 50.000 10.24 0.00 42.06 4.61
497 564 3.983344 GCAAGTTGCTTGGATACTTTGTG 59.017 43.478 20.71 0.00 41.31 3.33
500 567 2.228822 CGGCAAGTTGCTTGGATACTTT 59.771 45.455 26.16 0.00 44.28 2.66
525 592 1.711060 AAGTGTGTGTTTGGCGTCCG 61.711 55.000 0.00 0.00 0.00 4.79
537 604 2.706190 AGCTAAACCCAGAGAAGTGTGT 59.294 45.455 0.00 0.00 0.00 3.72
574 641 4.933400 ATTTGGAGATGTTTGCAAATCTGC 59.067 37.500 21.01 21.01 42.94 4.26
599 669 2.266554 GACAGAGCAACTCTCATTCGG 58.733 52.381 0.00 0.00 44.35 4.30
600 670 2.094286 AGGACAGAGCAACTCTCATTCG 60.094 50.000 0.00 0.00 44.35 3.34
623 693 4.378978 CGCCATAAGAAGATCTCTACGAGG 60.379 50.000 0.00 0.00 32.46 4.63
624 694 4.452795 TCGCCATAAGAAGATCTCTACGAG 59.547 45.833 0.00 0.00 32.46 4.18
625 695 4.386711 TCGCCATAAGAAGATCTCTACGA 58.613 43.478 0.00 0.00 32.46 3.43
626 696 4.214545 ACTCGCCATAAGAAGATCTCTACG 59.785 45.833 0.00 0.00 32.46 3.51
627 697 5.699097 ACTCGCCATAAGAAGATCTCTAC 57.301 43.478 0.00 0.00 32.46 2.59
628 698 7.818997 TTTACTCGCCATAAGAAGATCTCTA 57.181 36.000 0.00 0.00 32.46 2.43
629 699 6.716934 TTTACTCGCCATAAGAAGATCTCT 57.283 37.500 0.00 0.00 35.13 3.10
630 700 7.954788 AATTTACTCGCCATAAGAAGATCTC 57.045 36.000 0.00 0.00 0.00 2.75
637 707 9.796120 CCAAAAATAAATTTACTCGCCATAAGA 57.204 29.630 0.00 0.00 0.00 2.10
638 708 9.796120 TCCAAAAATAAATTTACTCGCCATAAG 57.204 29.630 0.00 0.00 0.00 1.73
639 709 9.575783 GTCCAAAAATAAATTTACTCGCCATAA 57.424 29.630 0.00 0.00 0.00 1.90
640 710 8.962679 AGTCCAAAAATAAATTTACTCGCCATA 58.037 29.630 0.00 0.00 0.00 2.74
641 711 7.836842 AGTCCAAAAATAAATTTACTCGCCAT 58.163 30.769 0.00 0.00 0.00 4.40
642 712 7.222000 AGTCCAAAAATAAATTTACTCGCCA 57.778 32.000 0.00 0.00 0.00 5.69
643 713 7.274904 GGAAGTCCAAAAATAAATTTACTCGCC 59.725 37.037 0.00 0.00 35.64 5.54
644 714 7.810759 TGGAAGTCCAAAAATAAATTTACTCGC 59.189 33.333 0.00 0.00 44.35 5.03
662 732 7.189512 CGAACATTCAAGATTTATGGAAGTCC 58.810 38.462 0.00 0.00 0.00 3.85
663 733 7.189512 CCGAACATTCAAGATTTATGGAAGTC 58.810 38.462 0.00 0.00 0.00 3.01
664 734 6.095440 CCCGAACATTCAAGATTTATGGAAGT 59.905 38.462 0.00 0.00 0.00 3.01
665 735 6.095440 ACCCGAACATTCAAGATTTATGGAAG 59.905 38.462 0.00 0.00 0.00 3.46
666 736 5.949354 ACCCGAACATTCAAGATTTATGGAA 59.051 36.000 0.00 0.00 0.00 3.53
667 737 5.505780 ACCCGAACATTCAAGATTTATGGA 58.494 37.500 0.00 0.00 0.00 3.41
668 738 5.835113 ACCCGAACATTCAAGATTTATGG 57.165 39.130 0.00 0.00 0.00 2.74
669 739 5.965334 CGAACCCGAACATTCAAGATTTATG 59.035 40.000 0.00 0.00 38.22 1.90
670 740 5.065988 CCGAACCCGAACATTCAAGATTTAT 59.934 40.000 0.00 0.00 38.22 1.40
671 741 4.393680 CCGAACCCGAACATTCAAGATTTA 59.606 41.667 0.00 0.00 38.22 1.40
672 742 3.190535 CCGAACCCGAACATTCAAGATTT 59.809 43.478 0.00 0.00 38.22 2.17
673 743 2.747446 CCGAACCCGAACATTCAAGATT 59.253 45.455 0.00 0.00 38.22 2.40
674 744 2.027561 TCCGAACCCGAACATTCAAGAT 60.028 45.455 0.00 0.00 38.22 2.40
675 745 1.345089 TCCGAACCCGAACATTCAAGA 59.655 47.619 0.00 0.00 38.22 3.02
676 746 1.803334 TCCGAACCCGAACATTCAAG 58.197 50.000 0.00 0.00 38.22 3.02
677 747 2.483014 ATCCGAACCCGAACATTCAA 57.517 45.000 0.00 0.00 38.22 2.69
678 748 2.483014 AATCCGAACCCGAACATTCA 57.517 45.000 0.00 0.00 38.22 2.57
679 749 3.842732 AAAATCCGAACCCGAACATTC 57.157 42.857 0.00 0.00 38.22 2.67
680 750 4.380128 GCTTAAAATCCGAACCCGAACATT 60.380 41.667 0.00 0.00 38.22 2.71
681 751 3.128068 GCTTAAAATCCGAACCCGAACAT 59.872 43.478 0.00 0.00 38.22 2.71
682 752 2.485038 GCTTAAAATCCGAACCCGAACA 59.515 45.455 0.00 0.00 38.22 3.18
683 753 2.485038 TGCTTAAAATCCGAACCCGAAC 59.515 45.455 0.00 0.00 38.22 3.95
684 754 2.780714 TGCTTAAAATCCGAACCCGAA 58.219 42.857 0.00 0.00 38.22 4.30
685 755 2.476126 TGCTTAAAATCCGAACCCGA 57.524 45.000 0.00 0.00 38.22 5.14
686 756 2.422127 ACATGCTTAAAATCCGAACCCG 59.578 45.455 0.00 0.00 0.00 5.28
687 757 3.442273 TGACATGCTTAAAATCCGAACCC 59.558 43.478 0.00 0.00 0.00 4.11
688 758 4.156008 AGTGACATGCTTAAAATCCGAACC 59.844 41.667 0.00 0.00 0.00 3.62
689 759 5.296813 AGTGACATGCTTAAAATCCGAAC 57.703 39.130 0.00 0.00 0.00 3.95
690 760 4.394920 GGAGTGACATGCTTAAAATCCGAA 59.605 41.667 0.00 0.00 0.00 4.30
691 761 3.938963 GGAGTGACATGCTTAAAATCCGA 59.061 43.478 0.00 0.00 0.00 4.55
692 762 3.242413 CGGAGTGACATGCTTAAAATCCG 60.242 47.826 7.75 7.75 40.89 4.18
693 763 3.938963 TCGGAGTGACATGCTTAAAATCC 59.061 43.478 0.00 0.00 0.00 3.01
694 764 5.122396 AGTTCGGAGTGACATGCTTAAAATC 59.878 40.000 0.00 0.00 0.00 2.17
695 765 5.003804 AGTTCGGAGTGACATGCTTAAAAT 58.996 37.500 0.00 0.00 0.00 1.82
696 766 4.213270 CAGTTCGGAGTGACATGCTTAAAA 59.787 41.667 0.00 0.00 0.00 1.52
697 767 3.745975 CAGTTCGGAGTGACATGCTTAAA 59.254 43.478 0.00 0.00 0.00 1.52
698 768 3.244078 ACAGTTCGGAGTGACATGCTTAA 60.244 43.478 5.27 0.00 0.00 1.85
699 769 2.299013 ACAGTTCGGAGTGACATGCTTA 59.701 45.455 5.27 0.00 0.00 3.09
700 770 1.070758 ACAGTTCGGAGTGACATGCTT 59.929 47.619 5.27 0.00 0.00 3.91
701 771 0.681733 ACAGTTCGGAGTGACATGCT 59.318 50.000 5.27 0.00 0.00 3.79
702 772 1.512926 AACAGTTCGGAGTGACATGC 58.487 50.000 5.27 0.00 0.00 4.06
703 773 4.552166 AAAAACAGTTCGGAGTGACATG 57.448 40.909 5.27 0.00 0.00 3.21
731 801 3.463944 CCACGTCACCTCAACTAAAGTT 58.536 45.455 0.00 0.00 39.12 2.66
732 802 2.805657 GCCACGTCACCTCAACTAAAGT 60.806 50.000 0.00 0.00 0.00 2.66
733 803 1.798813 GCCACGTCACCTCAACTAAAG 59.201 52.381 0.00 0.00 0.00 1.85
734 804 1.139256 TGCCACGTCACCTCAACTAAA 59.861 47.619 0.00 0.00 0.00 1.85
735 805 0.753867 TGCCACGTCACCTCAACTAA 59.246 50.000 0.00 0.00 0.00 2.24
736 806 0.753867 TTGCCACGTCACCTCAACTA 59.246 50.000 0.00 0.00 0.00 2.24
737 807 0.814010 GTTGCCACGTCACCTCAACT 60.814 55.000 0.00 0.00 35.46 3.16
738 808 0.814010 AGTTGCCACGTCACCTCAAC 60.814 55.000 0.00 0.00 37.78 3.18
739 809 0.107410 AAGTTGCCACGTCACCTCAA 60.107 50.000 0.00 0.00 0.00 3.02
740 810 0.107410 AAAGTTGCCACGTCACCTCA 60.107 50.000 0.00 0.00 0.00 3.86
741 811 1.798813 CTAAAGTTGCCACGTCACCTC 59.201 52.381 0.00 0.00 0.00 3.85
742 812 1.140252 ACTAAAGTTGCCACGTCACCT 59.860 47.619 0.00 0.00 0.00 4.00
743 813 1.589803 ACTAAAGTTGCCACGTCACC 58.410 50.000 0.00 0.00 0.00 4.02
775 845 8.974060 ATAGAAAACTAACTGGTCAAAGTTGA 57.026 30.769 0.00 0.00 40.58 3.18
829 899 3.058085 ACCGTGACAACTTGAACGTTTTT 60.058 39.130 0.46 0.00 32.25 1.94
830 900 2.485038 ACCGTGACAACTTGAACGTTTT 59.515 40.909 0.46 0.00 32.25 2.43
831 901 2.078392 ACCGTGACAACTTGAACGTTT 58.922 42.857 0.46 0.00 32.25 3.60
832 902 1.729284 ACCGTGACAACTTGAACGTT 58.271 45.000 0.00 0.00 32.25 3.99
833 903 1.729284 AACCGTGACAACTTGAACGT 58.271 45.000 15.61 0.00 32.25 3.99
834 904 3.929417 TTAACCGTGACAACTTGAACG 57.071 42.857 12.10 12.10 33.30 3.95
835 905 5.684184 GGATTTTAACCGTGACAACTTGAAC 59.316 40.000 0.00 0.00 0.00 3.18
836 906 5.504337 CGGATTTTAACCGTGACAACTTGAA 60.504 40.000 0.00 0.00 44.57 2.69
837 907 4.024725 CGGATTTTAACCGTGACAACTTGA 60.025 41.667 0.00 0.00 44.57 3.02
838 908 4.215965 CGGATTTTAACCGTGACAACTTG 58.784 43.478 0.00 0.00 44.57 3.16
839 909 4.477302 CGGATTTTAACCGTGACAACTT 57.523 40.909 0.00 0.00 44.57 2.66
851 921 9.509855 CGGAAATGATAAATGTTCGGATTTTAA 57.490 29.630 0.00 0.00 0.00 1.52
852 922 8.679100 ACGGAAATGATAAATGTTCGGATTTTA 58.321 29.630 0.00 0.00 0.00 1.52
853 923 7.543756 ACGGAAATGATAAATGTTCGGATTTT 58.456 30.769 0.00 0.00 0.00 1.82
854 924 7.095695 ACGGAAATGATAAATGTTCGGATTT 57.904 32.000 0.00 0.00 0.00 2.17
855 925 6.693315 ACGGAAATGATAAATGTTCGGATT 57.307 33.333 0.00 0.00 0.00 3.01
856 926 6.693315 AACGGAAATGATAAATGTTCGGAT 57.307 33.333 0.00 0.00 0.00 4.18
857 927 7.795482 ATAACGGAAATGATAAATGTTCGGA 57.205 32.000 0.00 0.00 0.00 4.55
858 928 8.850454 AAATAACGGAAATGATAAATGTTCGG 57.150 30.769 0.00 0.00 0.00 4.30
880 950 5.188948 GCCAACCCTTATTTGACCCTAAAAT 59.811 40.000 0.00 0.00 0.00 1.82
898 968 1.442017 GTCGTGCGAATTGCCAACC 60.442 57.895 0.00 0.00 45.60 3.77
901 971 0.673333 AGATGTCGTGCGAATTGCCA 60.673 50.000 0.00 0.00 45.60 4.92
923 993 1.219522 CGTCGTGGTCAAGTGGTTCC 61.220 60.000 0.00 0.00 0.00 3.62
924 994 1.828331 GCGTCGTGGTCAAGTGGTTC 61.828 60.000 0.00 0.00 0.00 3.62
926 996 2.279918 GCGTCGTGGTCAAGTGGT 60.280 61.111 0.00 0.00 0.00 4.16
967 1037 1.766864 TCGGGTGTGGGGAAAGTGA 60.767 57.895 0.00 0.00 0.00 3.41
1229 1302 2.069273 CAACTGTGTCAATCTCCGGAC 58.931 52.381 0.00 0.00 34.63 4.79
1362 1513 2.048603 GCCAGAACTCCACATGCCC 61.049 63.158 0.00 0.00 0.00 5.36
1389 1540 7.175104 ACCAAATTAGCTATGAAGAGTTTCCA 58.825 34.615 0.00 0.00 32.09 3.53
1418 1569 3.004106 GCCTATATAGGTGAACGTGTCGT 59.996 47.826 26.27 0.00 45.42 4.34
1422 1573 3.243737 TGCTGCCTATATAGGTGAACGTG 60.244 47.826 26.27 11.92 45.42 4.49
1514 1671 3.744660 ACAAAGATGACTGACAAGGGAC 58.255 45.455 0.00 0.00 0.00 4.46
1517 1674 4.999311 TGATGACAAAGATGACTGACAAGG 59.001 41.667 0.00 0.00 0.00 3.61
1596 1757 2.041153 CACACCCAAAGGACCAAGC 58.959 57.895 0.00 0.00 36.73 4.01
1601 1762 0.598065 GATGTGCACACCCAAAGGAC 59.402 55.000 24.37 1.74 36.73 3.85
1617 1778 0.930310 CAGGTGCCACGAATACGATG 59.070 55.000 0.00 0.00 42.66 3.84
1618 1779 0.810031 GCAGGTGCCACGAATACGAT 60.810 55.000 0.00 0.00 37.79 3.73
1653 1814 5.753438 GCGGAATATGACACAAGTAGATGAA 59.247 40.000 0.00 0.00 0.00 2.57
1660 1821 3.895232 AGAGCGGAATATGACACAAGT 57.105 42.857 0.00 0.00 0.00 3.16
1689 1858 7.012421 GGTAATCTTGACAATTAGCTAACCCTG 59.988 40.741 8.70 9.16 35.32 4.45
1726 1895 7.122650 CAGATTTCAGGTTCTTTATTTGCCCTA 59.877 37.037 0.00 0.00 0.00 3.53
1735 1904 6.187727 ACTGGTCAGATTTCAGGTTCTTTA 57.812 37.500 4.84 0.00 33.19 1.85
1848 2017 7.945109 AGCTATGAAGTCCTAAAATATTTCCCC 59.055 37.037 0.10 0.00 0.00 4.81
1894 2063 8.408043 AAGTTTGAATGTTTCATAGGATGTCA 57.592 30.769 0.00 0.00 39.84 3.58
1957 2126 8.510243 ACATATGCTCAACAATGACAATTAGA 57.490 30.769 1.58 0.00 0.00 2.10
1979 2148 8.090831 ACAGATGTAATTAGATCACGCATACAT 58.909 33.333 21.06 3.97 35.76 2.29
2410 2582 6.910536 AAACAGAAATTCCGATAGTAGCAG 57.089 37.500 0.00 0.00 0.00 4.24
2487 2659 4.256110 TCAACGCATTTCACTGATCTCAT 58.744 39.130 0.00 0.00 0.00 2.90
2550 2723 7.669427 TGAATTTCACCTCAGCAACATATTTT 58.331 30.769 0.00 0.00 0.00 1.82
2576 2749 3.984633 GCTATAATCTTGAGGTGCGTCTC 59.015 47.826 0.00 0.00 0.00 3.36
2583 2756 3.393687 TGGTGGGCTATAATCTTGAGGT 58.606 45.455 0.00 0.00 0.00 3.85
2649 2822 9.939047 GATATACGATGTGAACGATAATTTGAC 57.061 33.333 0.00 0.00 34.70 3.18
2876 3055 6.620678 GCTTAACATGGAAAGCACTTCAATA 58.379 36.000 22.36 0.00 45.89 1.90
2978 3160 1.273048 GCATTGGTGTCCTGCATTGAA 59.727 47.619 0.00 0.00 35.96 2.69
3002 3184 6.399743 TGCCGTGAATGTTAGTAAGTTCATA 58.600 36.000 11.67 1.41 33.65 2.15
3082 3264 1.688735 CACTGTCCTCCAGAGTGACAA 59.311 52.381 15.31 5.23 44.49 3.18
3103 3285 1.134367 CATCACCATCTTGCTTGCCTG 59.866 52.381 0.00 0.00 0.00 4.85
3333 3515 7.295201 TCTGAACAAATTTTACGGATTTCTCG 58.705 34.615 0.00 0.00 0.00 4.04
3360 3544 8.201554 TCACTTCTCATAGTTGTTTCATATGC 57.798 34.615 0.00 0.00 0.00 3.14
3404 3588 1.284785 TGGAATCACCAATCAGGGGTC 59.715 52.381 0.00 0.00 46.75 4.46
3428 3612 2.753055 TTCACACGGATTCGGAATGA 57.247 45.000 8.18 0.00 41.39 2.57
3513 3697 1.335810 GTTTTGGTCCGTTCCAAGTCC 59.664 52.381 8.22 0.00 46.27 3.85
3546 3730 5.782925 AGGAGGTTACTGAGGTGATAGATT 58.217 41.667 0.00 0.00 0.00 2.40
3579 3763 1.924524 ACGAACACAGAACACGTTCAG 59.075 47.619 12.21 6.72 41.84 3.02
3623 3807 1.270826 CAACAGGCTCTCGAGAAGTCA 59.729 52.381 17.36 0.00 0.00 3.41
3635 3819 0.112995 TGCTGGGAATTCAACAGGCT 59.887 50.000 22.91 0.00 32.98 4.58
3666 3850 6.904011 CGACATTATCAAGAGAGACATTTTGC 59.096 38.462 0.00 0.00 0.00 3.68
3679 3865 9.884465 AAAGAAAAGAGAAACGACATTATCAAG 57.116 29.630 0.00 0.00 0.00 3.02
3726 3912 8.702163 AATGGAAAATAATTTGATGACGGAAC 57.298 30.769 0.00 0.00 0.00 3.62
3803 3989 3.230134 ACTAACCAGATTTTGCAAGGCA 58.770 40.909 0.00 0.00 36.47 4.75
3907 4115 9.733556 AACTCAGTTATTGTGACAATGGTATTA 57.266 29.630 20.29 0.00 0.00 0.98
3929 4137 9.871238 TTATCACTTCCAGACTATACAAAACTC 57.129 33.333 0.00 0.00 0.00 3.01
3973 4181 3.441572 ACGAGGAAGATGAAAAAGGCATG 59.558 43.478 0.00 0.00 0.00 4.06
3993 4201 2.996621 CAAAAGACTGAAGGCTCCTACG 59.003 50.000 0.00 0.00 0.00 3.51
3999 4207 4.940654 GCTCTAATCAAAAGACTGAAGGCT 59.059 41.667 0.00 0.00 0.00 4.58
4022 4230 2.202544 GCTCTCTCGCGACCTGTG 60.203 66.667 3.71 0.00 0.00 3.66
4024 4232 2.101965 CTGCTCTCTCGCGACCTG 59.898 66.667 3.71 0.00 0.00 4.00
4045 4253 1.227973 GGCTATGGCAGGGCAGTAC 60.228 63.158 14.64 0.00 40.87 2.73
4051 4259 4.976925 CTCGCGGCTATGGCAGGG 62.977 72.222 11.59 11.59 44.84 4.45
4056 4264 1.461091 TAAGACCCTCGCGGCTATGG 61.461 60.000 6.13 2.30 33.26 2.74
4062 4270 1.334779 CGACTATTAAGACCCTCGCGG 60.335 57.143 6.13 0.00 37.81 6.46
4085 4293 3.659735 GTTGACTATGACAACAATCGCG 58.340 45.455 0.00 0.00 44.49 5.87
4133 4341 8.198778 TCCTGTCCAAAACAAATAACTTAAACC 58.801 33.333 0.00 0.00 37.45 3.27
4135 4343 8.750298 TGTCCTGTCCAAAACAAATAACTTAAA 58.250 29.630 0.00 0.00 37.45 1.52
4136 4344 8.294954 TGTCCTGTCCAAAACAAATAACTTAA 57.705 30.769 0.00 0.00 37.45 1.85
4143 4351 7.360113 ACTAAATGTCCTGTCCAAAACAAAT 57.640 32.000 0.00 0.00 37.45 2.32
4148 4356 6.549364 ACATGAACTAAATGTCCTGTCCAAAA 59.451 34.615 0.00 0.00 32.83 2.44
4149 4357 6.068010 ACATGAACTAAATGTCCTGTCCAAA 58.932 36.000 0.00 0.00 32.83 3.28
4218 4426 4.635833 TGCAACTTGGCATGTACATATG 57.364 40.909 8.32 0.00 39.25 1.78


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

AutoCloner maintained by Alex Coulton.