Multiple sequence alignment - TraesCS2B01G310800

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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 TraesCS2B01G310800 chr2B 100.000 5368 0 0 1 5368 444496574 444501941 0.000000e+00 9913.0
1 TraesCS2B01G310800 chr2B 92.669 532 38 1 54 585 528281554 528281024 0.000000e+00 765.0
2 TraesCS2B01G310800 chr2B 99.293 283 2 0 4511 4793 444506069 444506351 3.710000e-141 512.0
3 TraesCS2B01G310800 chr2D 94.113 3720 135 33 818 4514 374071010 374074668 0.000000e+00 5579.0
4 TraesCS2B01G310800 chr2D 92.209 860 61 5 4509 5365 485475739 485474883 0.000000e+00 1212.0
5 TraesCS2B01G310800 chr2D 97.115 104 1 2 585 686 374070459 374070562 1.990000e-39 174.0
6 TraesCS2B01G310800 chr2D 91.429 70 2 3 760 829 374070590 374070655 5.720000e-15 93.5
7 TraesCS2B01G310800 chr2A 93.229 3781 176 33 760 4514 507027486 507031212 0.000000e+00 5491.0
8 TraesCS2B01G310800 chr2A 95.192 104 3 2 585 686 507027355 507027458 4.300000e-36 163.0
9 TraesCS2B01G310800 chr3B 94.529 859 46 1 4510 5368 192185650 192184793 0.000000e+00 1325.0
10 TraesCS2B01G310800 chr3D 91.977 860 62 6 4509 5365 133819901 133820756 0.000000e+00 1199.0
11 TraesCS2B01G310800 chr7D 91.385 859 68 5 4510 5365 2133189 2132334 0.000000e+00 1171.0
12 TraesCS2B01G310800 chr3A 85.134 861 115 11 4510 5362 218126564 218125709 0.000000e+00 869.0
13 TraesCS2B01G310800 chr1A 85.134 861 115 9 4511 5363 30403938 30404793 0.000000e+00 869.0
14 TraesCS2B01G310800 chr1A 78.772 570 93 20 3049 3605 463523084 463522530 1.840000e-94 357.0
15 TraesCS2B01G310800 chr1A 89.157 83 9 0 677 759 186714653 186714735 2.640000e-18 104.0
16 TraesCS2B01G310800 chr5B 93.576 576 37 0 4788 5363 102616022 102615447 0.000000e+00 859.0
17 TraesCS2B01G310800 chr5B 92.551 537 39 1 53 588 658390690 658390154 0.000000e+00 769.0
18 TraesCS2B01G310800 chr5B 91.573 534 44 1 51 584 545332377 545332909 0.000000e+00 736.0
19 TraesCS2B01G310800 chr5B 90.772 531 48 1 54 584 235240812 235241341 0.000000e+00 708.0
20 TraesCS2B01G310800 chr5B 92.000 75 6 0 685 759 622495351 622495425 7.350000e-19 106.0
21 TraesCS2B01G310800 chr5B 82.022 89 12 2 671 759 60588617 60588701 7.460000e-09 73.1
22 TraesCS2B01G310800 chr1B 84.615 858 118 12 4510 5362 303280132 303279284 0.000000e+00 841.0
23 TraesCS2B01G310800 chr1B 90.772 531 49 0 54 584 461614307 461614837 0.000000e+00 710.0
24 TraesCS2B01G310800 chr1B 90.772 531 48 1 54 584 582740452 582740981 0.000000e+00 708.0
25 TraesCS2B01G310800 chr1B 78.533 559 97 18 3050 3603 488038450 488037910 3.980000e-91 346.0
26 TraesCS2B01G310800 chr1B 91.139 79 7 0 684 762 641036522 641036444 2.040000e-19 108.0
27 TraesCS2B01G310800 chr1B 92.000 75 6 0 685 759 8776076 8776002 7.350000e-19 106.0
28 TraesCS2B01G310800 chr6B 91.241 548 47 1 45 592 40577489 40578035 0.000000e+00 745.0
29 TraesCS2B01G310800 chr6B 91.188 522 46 0 53 574 52003606 52003085 0.000000e+00 710.0
30 TraesCS2B01G310800 chr6B 83.772 228 35 2 3700 3926 224866332 224866558 1.170000e-51 215.0
31 TraesCS2B01G310800 chr4A 82.051 858 141 9 4511 5363 543084648 543083799 0.000000e+00 719.0
32 TraesCS2B01G310800 chr4D 91.082 527 47 0 57 583 434458583 434459109 0.000000e+00 713.0
33 TraesCS2B01G310800 chr4D 89.024 82 9 0 678 759 12518171 12518090 9.510000e-18 102.0
34 TraesCS2B01G310800 chr4D 95.122 41 2 0 685 725 505555308 505555268 1.250000e-06 65.8
35 TraesCS2B01G310800 chr6A 77.656 546 97 18 3385 3926 153679425 153678901 5.220000e-80 309.0
36 TraesCS2B01G310800 chr6A 80.851 282 52 2 4081 4361 153678731 153678451 2.520000e-53 220.0
37 TraesCS2B01G310800 chr6A 92.000 75 6 0 685 759 17303355 17303281 7.350000e-19 106.0
38 TraesCS2B01G310800 chr6A 92.000 75 6 0 685 759 616205756 616205830 7.350000e-19 106.0
39 TraesCS2B01G310800 chr1D 87.330 221 28 0 3385 3605 364696446 364696226 2.480000e-63 254.0
40 TraesCS2B01G310800 chr6D 81.004 279 51 2 4081 4358 126430434 126430711 2.520000e-53 220.0
41 TraesCS2B01G310800 chr6D 83.260 227 38 0 3700 3926 126429991 126430217 5.450000e-50 209.0
42 TraesCS2B01G310800 chr5D 92.000 75 6 0 685 759 74461742 74461668 7.350000e-19 106.0
43 TraesCS2B01G310800 chr5A 87.234 94 7 5 669 759 586314452 586314361 9.510000e-18 102.0


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 TraesCS2B01G310800 chr2B 444496574 444501941 5367 False 9913.000000 9913 100.0000 1 5368 1 chr2B.!!$F1 5367
1 TraesCS2B01G310800 chr2B 528281024 528281554 530 True 765.000000 765 92.6690 54 585 1 chr2B.!!$R1 531
2 TraesCS2B01G310800 chr2D 374070459 374074668 4209 False 1948.833333 5579 94.2190 585 4514 3 chr2D.!!$F1 3929
3 TraesCS2B01G310800 chr2D 485474883 485475739 856 True 1212.000000 1212 92.2090 4509 5365 1 chr2D.!!$R1 856
4 TraesCS2B01G310800 chr2A 507027355 507031212 3857 False 2827.000000 5491 94.2105 585 4514 2 chr2A.!!$F1 3929
5 TraesCS2B01G310800 chr3B 192184793 192185650 857 True 1325.000000 1325 94.5290 4510 5368 1 chr3B.!!$R1 858
6 TraesCS2B01G310800 chr3D 133819901 133820756 855 False 1199.000000 1199 91.9770 4509 5365 1 chr3D.!!$F1 856
7 TraesCS2B01G310800 chr7D 2132334 2133189 855 True 1171.000000 1171 91.3850 4510 5365 1 chr7D.!!$R1 855
8 TraesCS2B01G310800 chr3A 218125709 218126564 855 True 869.000000 869 85.1340 4510 5362 1 chr3A.!!$R1 852
9 TraesCS2B01G310800 chr1A 30403938 30404793 855 False 869.000000 869 85.1340 4511 5363 1 chr1A.!!$F1 852
10 TraesCS2B01G310800 chr1A 463522530 463523084 554 True 357.000000 357 78.7720 3049 3605 1 chr1A.!!$R1 556
11 TraesCS2B01G310800 chr5B 102615447 102616022 575 True 859.000000 859 93.5760 4788 5363 1 chr5B.!!$R1 575
12 TraesCS2B01G310800 chr5B 658390154 658390690 536 True 769.000000 769 92.5510 53 588 1 chr5B.!!$R2 535
13 TraesCS2B01G310800 chr5B 545332377 545332909 532 False 736.000000 736 91.5730 51 584 1 chr5B.!!$F3 533
14 TraesCS2B01G310800 chr5B 235240812 235241341 529 False 708.000000 708 90.7720 54 584 1 chr5B.!!$F2 530
15 TraesCS2B01G310800 chr1B 303279284 303280132 848 True 841.000000 841 84.6150 4510 5362 1 chr1B.!!$R2 852
16 TraesCS2B01G310800 chr1B 461614307 461614837 530 False 710.000000 710 90.7720 54 584 1 chr1B.!!$F1 530
17 TraesCS2B01G310800 chr1B 582740452 582740981 529 False 708.000000 708 90.7720 54 584 1 chr1B.!!$F2 530
18 TraesCS2B01G310800 chr1B 488037910 488038450 540 True 346.000000 346 78.5330 3050 3603 1 chr1B.!!$R3 553
19 TraesCS2B01G310800 chr6B 40577489 40578035 546 False 745.000000 745 91.2410 45 592 1 chr6B.!!$F1 547
20 TraesCS2B01G310800 chr6B 52003085 52003606 521 True 710.000000 710 91.1880 53 574 1 chr6B.!!$R1 521
21 TraesCS2B01G310800 chr4A 543083799 543084648 849 True 719.000000 719 82.0510 4511 5363 1 chr4A.!!$R1 852
22 TraesCS2B01G310800 chr4D 434458583 434459109 526 False 713.000000 713 91.0820 57 583 1 chr4D.!!$F1 526
23 TraesCS2B01G310800 chr6A 153678451 153679425 974 True 264.500000 309 79.2535 3385 4361 2 chr6A.!!$R2 976
24 TraesCS2B01G310800 chr6D 126429991 126430711 720 False 214.500000 220 82.1320 3700 4358 2 chr6D.!!$F1 658

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
34 35 0.035881 CGCATCTGGGTCTGGCATAT 59.964 55.000 0.00 0.00 0.00 1.78 F
694 698 0.096628 CGTCACGAGTACTCCTTCCG 59.903 60.000 17.23 8.27 0.00 4.30 F
2112 2488 0.249398 GGGCTTACCTCGTGACATGT 59.751 55.000 0.00 0.00 35.85 3.21 F
3645 4045 1.202110 GCTGATCACCGTGCATCTTTG 60.202 52.381 0.00 0.00 0.00 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1194 1566 0.248661 CCACCACTACTCGCGATCAG 60.249 60.0 10.36 12.54 0.00 2.90 R
2285 2665 0.817634 CGTTTCCAGACACAAGGGCA 60.818 55.0 0.00 0.00 0.00 5.36 R
3989 4390 0.029834 GCTTAATCATGCCAGGTGCG 59.970 55.0 0.00 0.00 45.60 5.34 R
4763 5236 0.107945 ATCAAGAGGAGCGCCAAGAC 60.108 55.0 9.88 0.00 36.29 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 6.618287 TTAATGAAAAGATACGCATCTGGG 57.382 37.500 0.00 0.00 40.81 4.45
25 26 3.627395 TGAAAAGATACGCATCTGGGT 57.373 42.857 0.00 5.21 40.81 4.51
26 27 3.531538 TGAAAAGATACGCATCTGGGTC 58.468 45.455 0.00 0.00 40.81 4.46
27 28 3.197766 TGAAAAGATACGCATCTGGGTCT 59.802 43.478 0.00 0.00 40.81 3.85
28 29 2.898729 AAGATACGCATCTGGGTCTG 57.101 50.000 0.00 0.00 40.81 3.51
29 30 1.043816 AGATACGCATCTGGGTCTGG 58.956 55.000 0.00 0.00 40.15 3.86
30 31 0.601311 GATACGCATCTGGGTCTGGC 60.601 60.000 2.90 0.00 41.61 4.85
31 32 1.337384 ATACGCATCTGGGTCTGGCA 61.337 55.000 2.90 0.00 41.61 4.92
32 33 1.337384 TACGCATCTGGGTCTGGCAT 61.337 55.000 2.90 0.00 41.61 4.40
33 34 1.337384 ACGCATCTGGGTCTGGCATA 61.337 55.000 0.00 0.00 36.39 3.14
34 35 0.035881 CGCATCTGGGTCTGGCATAT 59.964 55.000 0.00 0.00 0.00 1.78
35 36 1.544093 CGCATCTGGGTCTGGCATATT 60.544 52.381 0.00 0.00 0.00 1.28
36 37 2.157738 GCATCTGGGTCTGGCATATTC 58.842 52.381 0.00 0.00 0.00 1.75
37 38 2.420642 CATCTGGGTCTGGCATATTCG 58.579 52.381 0.00 0.00 0.00 3.34
38 39 1.496060 TCTGGGTCTGGCATATTCGT 58.504 50.000 0.00 0.00 0.00 3.85
39 40 1.138859 TCTGGGTCTGGCATATTCGTG 59.861 52.381 0.00 0.00 0.00 4.35
40 41 1.138859 CTGGGTCTGGCATATTCGTGA 59.861 52.381 0.00 0.00 0.00 4.35
41 42 1.557371 TGGGTCTGGCATATTCGTGAA 59.443 47.619 0.00 0.00 0.00 3.18
42 43 2.026729 TGGGTCTGGCATATTCGTGAAA 60.027 45.455 0.00 0.00 0.00 2.69
43 44 3.013921 GGGTCTGGCATATTCGTGAAAA 58.986 45.455 0.00 0.00 0.00 2.29
47 48 3.616821 TCTGGCATATTCGTGAAAAGTCG 59.383 43.478 0.00 0.00 0.00 4.18
297 298 6.874134 CCAGGTAGTAGGATTCAATAAATCGG 59.126 42.308 0.00 0.00 44.08 4.18
331 332 6.058553 AGATGAGAAAGATGTGAATGTGGA 57.941 37.500 0.00 0.00 0.00 4.02
337 338 9.076781 TGAGAAAGATGTGAATGTGGAAAATAA 57.923 29.630 0.00 0.00 0.00 1.40
341 342 6.256053 AGATGTGAATGTGGAAAATAACCCT 58.744 36.000 0.00 0.00 0.00 4.34
357 358 6.997942 ATAACCCTTCCATAGACTTAGGAC 57.002 41.667 0.00 0.00 0.00 3.85
391 393 9.831737 AGTCATCGAAAAATTCTTTGTAATGAG 57.168 29.630 0.00 0.00 0.00 2.90
397 399 9.356929 CGAAAAATTCTTTGTAATGAGCAAAAC 57.643 29.630 0.00 0.00 35.71 2.43
418 420 2.034305 CCACGCTACTACCGAGCTTAAT 59.966 50.000 0.00 0.00 37.81 1.40
578 580 1.731720 GCTTCGAGCTTCTTGTCCAT 58.268 50.000 0.00 0.00 38.45 3.41
632 634 0.908180 AGTTTAGCTAGGGCGTGGGT 60.908 55.000 0.16 0.16 44.37 4.51
666 668 5.063817 CACATTTGTACATCGCATTCTGAGA 59.936 40.000 0.00 0.00 0.00 3.27
686 690 0.240411 AAGTCTGCCGTCACGAGTAC 59.760 55.000 0.00 0.00 0.00 2.73
688 692 0.179194 GTCTGCCGTCACGAGTACTC 60.179 60.000 13.18 13.18 0.00 2.59
689 693 1.136984 CTGCCGTCACGAGTACTCC 59.863 63.158 17.23 2.14 0.00 3.85
690 694 1.303074 TGCCGTCACGAGTACTCCT 60.303 57.895 17.23 2.73 0.00 3.69
692 696 0.179169 GCCGTCACGAGTACTCCTTC 60.179 60.000 17.23 4.89 0.00 3.46
693 697 0.450983 CCGTCACGAGTACTCCTTCC 59.549 60.000 17.23 2.64 0.00 3.46
694 698 0.096628 CGTCACGAGTACTCCTTCCG 59.903 60.000 17.23 8.27 0.00 4.30
695 699 1.163554 GTCACGAGTACTCCTTCCGT 58.836 55.000 17.23 8.94 0.00 4.69
696 700 1.538950 GTCACGAGTACTCCTTCCGTT 59.461 52.381 17.23 0.00 0.00 4.44
697 701 1.808945 TCACGAGTACTCCTTCCGTTC 59.191 52.381 17.23 0.00 0.00 3.95
698 702 1.135460 CACGAGTACTCCTTCCGTTCC 60.135 57.143 17.23 0.00 0.00 3.62
699 703 1.171308 CGAGTACTCCTTCCGTTCCA 58.829 55.000 17.23 0.00 0.00 3.53
701 705 2.029649 CGAGTACTCCTTCCGTTCCAAA 60.030 50.000 17.23 0.00 0.00 3.28
703 707 4.576879 GAGTACTCCTTCCGTTCCAAAAT 58.423 43.478 12.13 0.00 0.00 1.82
704 708 5.622914 CGAGTACTCCTTCCGTTCCAAAATA 60.623 44.000 17.23 0.00 0.00 1.40
705 709 5.731591 AGTACTCCTTCCGTTCCAAAATAG 58.268 41.667 0.00 0.00 0.00 1.73
707 711 5.437191 ACTCCTTCCGTTCCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
708 712 5.186198 ACTCCTTCCGTTCCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
709 713 5.045869 ACTCCTTCCGTTCCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
710 714 5.183228 TCCTTCCGTTCCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
711 715 4.335594 CCTTCCGTTCCAAAATAGATGACC 59.664 45.833 0.00 0.00 0.00 4.02
712 716 3.881220 TCCGTTCCAAAATAGATGACCC 58.119 45.455 0.00 0.00 0.00 4.46
713 717 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
714 718 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
715 719 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
716 720 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
717 721 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
718 722 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
719 723 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
720 724 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
721 725 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
722 726 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
723 727 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
724 728 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
725 729 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
726 730 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
727 731 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
728 732 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
729 733 7.287810 AGATGACCCAACTTTGTACTAACTTT 58.712 34.615 0.00 0.00 0.00 2.66
730 734 8.434392 AGATGACCCAACTTTGTACTAACTTTA 58.566 33.333 0.00 0.00 0.00 1.85
731 735 8.983702 ATGACCCAACTTTGTACTAACTTTAA 57.016 30.769 0.00 0.00 0.00 1.52
732 736 8.983702 TGACCCAACTTTGTACTAACTTTAAT 57.016 30.769 0.00 0.00 0.00 1.40
820 1188 3.000819 TACAGACGTGGGGCCCTG 61.001 66.667 25.93 18.77 0.00 4.45
830 1198 4.778143 GGGCCCTGGTGTACAGCG 62.778 72.222 17.04 13.73 46.14 5.18
879 1247 2.008268 TTACCACTAGTAGCGGCCGC 62.008 60.000 42.34 42.34 42.33 6.53
961 1333 0.947244 CTCGTGGAACTTGCTTGCTT 59.053 50.000 0.00 0.00 31.75 3.91
976 1348 2.115266 CTTGCCACCCCGTCCTTT 59.885 61.111 0.00 0.00 0.00 3.11
1086 1458 2.360980 CACCCCTCCGTCCTCTCT 59.639 66.667 0.00 0.00 0.00 3.10
1175 1547 1.830145 GGTACCATGTGATCCGCCT 59.170 57.895 7.15 0.00 0.00 5.52
1194 1566 2.030451 CCTGGTTGCTTTCTTGCTTCTC 60.030 50.000 0.00 0.00 0.00 2.87
1315 1687 5.593010 CCTCCAACTGCATAGTAGTAGTTC 58.407 45.833 0.00 0.00 41.53 3.01
1320 1692 6.311445 CCAACTGCATAGTAGTAGTTCTTGTG 59.689 42.308 0.00 0.00 41.53 3.33
1325 1697 5.292101 GCATAGTAGTAGTTCTTGTGCCTTG 59.708 44.000 4.10 0.00 0.00 3.61
1388 1761 4.188462 TGTTACAAATCCCTAGCATCGTG 58.812 43.478 0.00 0.00 0.00 4.35
1393 1766 5.482908 ACAAATCCCTAGCATCGTGATATC 58.517 41.667 0.00 0.00 0.00 1.63
1420 1793 1.524008 CCCCGTCCTTGCCACTTTTC 61.524 60.000 0.00 0.00 0.00 2.29
1428 1801 2.227388 CCTTGCCACTTTTCAGCAGTAG 59.773 50.000 0.00 0.00 37.89 2.57
1466 1839 9.891828 CCAAGCAAGTTATTCGCATATATAAAA 57.108 29.630 0.00 0.00 0.00 1.52
1500 1873 5.026121 AGACAATAGGTGAAGGAGTCATCA 58.974 41.667 0.00 0.00 40.16 3.07
1567 1940 6.263344 GGAATAAAATAGTTGCTCGGTTTCC 58.737 40.000 0.00 0.00 0.00 3.13
1805 2181 7.821846 AGAGTTGGTTATCTTTTCAGATCTGTC 59.178 37.037 21.92 6.66 40.53 3.51
1908 2284 7.044836 CCAAAGTTTTGTCGCAAAATTTTCATG 60.045 33.333 22.65 16.99 36.45 3.07
1914 2290 3.058450 TCGCAAAATTTTCATGCCACTG 58.942 40.909 0.00 0.00 36.75 3.66
1915 2291 2.411806 CGCAAAATTTTCATGCCACTGC 60.412 45.455 0.00 0.00 36.75 4.40
2004 2380 4.885907 AGCATATGGTGTCATTTTCTCAGG 59.114 41.667 6.62 0.00 34.96 3.86
2078 2454 2.030412 TGTTGCGTGGTGCTCGAT 59.970 55.556 0.00 0.00 46.63 3.59
2112 2488 0.249398 GGGCTTACCTCGTGACATGT 59.751 55.000 0.00 0.00 35.85 3.21
2114 2490 2.537401 GGCTTACCTCGTGACATGTAC 58.463 52.381 0.00 0.00 0.00 2.90
2285 2665 8.364142 TCGTCAGATTTAAAATTTGGGATTTGT 58.636 29.630 0.00 0.00 0.00 2.83
2292 2672 3.421919 AATTTGGGATTTGTGCCCTTG 57.578 42.857 0.00 0.00 46.19 3.61
2585 2965 8.200120 ACTTAATTATTTCGTGGGACCTACTAC 58.800 37.037 6.41 0.00 0.00 2.73
2587 2967 2.198827 TTTCGTGGGACCTACTACGA 57.801 50.000 6.41 7.86 42.94 3.43
2606 2986 7.837863 ACTACGATTTCCTTCAGACTTCATTA 58.162 34.615 0.00 0.00 0.00 1.90
2643 3023 8.844244 CATTTGGGAGATTTTCTCTTGGTATAG 58.156 37.037 4.65 0.00 42.95 1.31
2644 3024 7.510675 TTGGGAGATTTTCTCTTGGTATAGT 57.489 36.000 4.65 0.00 42.95 2.12
2645 3025 8.618240 TTGGGAGATTTTCTCTTGGTATAGTA 57.382 34.615 4.65 0.00 42.95 1.82
2646 3026 8.019656 TGGGAGATTTTCTCTTGGTATAGTAC 57.980 38.462 4.65 0.00 42.95 2.73
2647 3027 7.844779 TGGGAGATTTTCTCTTGGTATAGTACT 59.155 37.037 0.00 0.00 42.95 2.73
2648 3028 9.364653 GGGAGATTTTCTCTTGGTATAGTACTA 57.635 37.037 4.77 4.77 42.95 1.82
2708 3088 2.418628 CTGTCCACAACAACAAGACGTT 59.581 45.455 0.00 0.00 37.45 3.99
2710 3090 3.120130 TGTCCACAACAACAAGACGTTTC 60.120 43.478 0.00 0.00 34.86 2.78
2733 3113 7.124573 TCCAGAAATTCTAATGCTAGTGCTA 57.875 36.000 0.00 0.00 40.48 3.49
2798 3178 5.227805 CGCATATTGAAAATGTCACGAAAGG 59.772 40.000 0.00 0.00 35.39 3.11
2818 3198 1.468520 GATTGGTGTCATGTTGGACCG 59.531 52.381 0.00 0.00 36.97 4.79
2824 3209 2.418628 GTGTCATGTTGGACCGGTAATG 59.581 50.000 7.34 7.21 36.97 1.90
2853 3238 7.934855 ACCTTCTAGTAGAACTTTATGACGA 57.065 36.000 8.59 0.00 29.89 4.20
2910 3305 5.885912 TCAAAAGCTAAGTTGAAACAGTCCT 59.114 36.000 5.23 0.00 30.93 3.85
2932 3327 5.104982 CCTTCTCTTAAGCCAGAAGACATCT 60.105 44.000 25.03 0.00 45.93 2.90
2968 3363 5.408604 ACACTAATTTAAACGAGGTGCAGAG 59.591 40.000 0.00 0.00 0.00 3.35
3062 3457 4.299155 TCTCTTTAGCTCTGTTCGTGTTG 58.701 43.478 0.00 0.00 0.00 3.33
3369 3764 2.271800 GTGATTCTCACGTCATGGACC 58.728 52.381 0.00 0.00 37.67 4.46
3645 4045 1.202110 GCTGATCACCGTGCATCTTTG 60.202 52.381 0.00 0.00 0.00 2.77
3983 4384 4.814234 ACATGGTATGTATGGTAACAAGCG 59.186 41.667 0.00 0.00 43.49 4.68
3984 4385 5.628200 ACATGGTATGTATGGTAACAAGCGT 60.628 40.000 0.00 0.00 43.49 5.07
3985 4386 7.398494 ACATGGTATGTATGGTAACAAGCGTC 61.398 42.308 0.00 0.00 43.49 5.19
4024 4425 1.029947 AAGCCGGCTACAAAATCCCG 61.030 55.000 33.07 0.00 40.39 5.14
4050 4456 0.596577 CTGACCGTTCGTTCCTCTGA 59.403 55.000 0.00 0.00 0.00 3.27
4053 4459 1.473278 GACCGTTCGTTCCTCTGATCT 59.527 52.381 0.00 0.00 0.00 2.75
4322 4785 3.179339 TTCCCCGTTGCCCAGGAA 61.179 61.111 0.00 0.00 36.05 3.36
4379 4842 0.608640 AGCAGTAACCTTCCACTCCG 59.391 55.000 0.00 0.00 0.00 4.63
4419 4883 2.867109 ATGCTTCTTGTGCAGTACCT 57.133 45.000 0.00 0.00 44.04 3.08
4700 5173 1.221021 CTCGGTTTAGGCCCACTCC 59.779 63.158 0.00 0.00 0.00 3.85
4763 5236 0.039165 GGCCTTCCTTTTGAACTGCG 60.039 55.000 0.00 0.00 30.08 5.18
4880 5353 5.233083 TCTTATCTTCCCATGTAGCCATG 57.767 43.478 0.00 0.00 46.65 3.66
4889 5362 1.626356 ATGTAGCCATGTCCAGCGGT 61.626 55.000 0.00 0.00 0.00 5.68
4892 5365 1.337384 TAGCCATGTCCAGCGGTGAT 61.337 55.000 17.83 0.00 0.00 3.06
4976 5450 1.072331 AGTACTTGTTCTGGCACCTGG 59.928 52.381 0.00 0.00 0.00 4.45
5021 5495 2.920645 CGAGAGCACCTGGTCGTGT 61.921 63.158 0.00 0.00 46.33 4.49
5261 5736 1.153369 TGAGCGGTGCTTATCAGCC 60.153 57.895 0.00 0.00 46.74 4.85
5325 5800 1.762957 CCGACTCCATAACCACCAGAT 59.237 52.381 0.00 0.00 0.00 2.90
5333 5808 6.329986 ACTCCATAACCACCAGATGATCATTA 59.670 38.462 10.14 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.772716 ACCCAGATGCGTATCTTTTCATTAAT 59.227 34.615 13.80 0.00 41.71 1.40
1 2 6.119536 ACCCAGATGCGTATCTTTTCATTAA 58.880 36.000 13.80 0.00 41.71 1.40
2 3 5.680619 ACCCAGATGCGTATCTTTTCATTA 58.319 37.500 13.80 0.00 41.71 1.90
3 4 4.526970 ACCCAGATGCGTATCTTTTCATT 58.473 39.130 13.80 0.00 41.71 2.57
4 5 4.130118 GACCCAGATGCGTATCTTTTCAT 58.870 43.478 13.80 0.00 41.71 2.57
5 6 3.197766 AGACCCAGATGCGTATCTTTTCA 59.802 43.478 13.80 0.00 41.71 2.69
6 7 3.557595 CAGACCCAGATGCGTATCTTTTC 59.442 47.826 13.80 9.92 41.71 2.29
7 8 3.535561 CAGACCCAGATGCGTATCTTTT 58.464 45.455 13.80 0.64 41.71 2.27
8 9 2.158900 CCAGACCCAGATGCGTATCTTT 60.159 50.000 13.80 1.02 41.71 2.52
9 10 1.414181 CCAGACCCAGATGCGTATCTT 59.586 52.381 13.80 0.00 41.71 2.40
10 11 1.043816 CCAGACCCAGATGCGTATCT 58.956 55.000 10.51 10.51 44.45 1.98
11 12 0.601311 GCCAGACCCAGATGCGTATC 60.601 60.000 5.22 5.22 0.00 2.24
12 13 1.337384 TGCCAGACCCAGATGCGTAT 61.337 55.000 0.00 0.00 0.00 3.06
13 14 1.337384 ATGCCAGACCCAGATGCGTA 61.337 55.000 0.00 0.00 0.00 4.42
14 15 1.337384 TATGCCAGACCCAGATGCGT 61.337 55.000 0.00 0.00 0.00 5.24
15 16 0.035881 ATATGCCAGACCCAGATGCG 59.964 55.000 0.00 0.00 0.00 4.73
16 17 2.157738 GAATATGCCAGACCCAGATGC 58.842 52.381 0.00 0.00 0.00 3.91
17 18 2.224378 ACGAATATGCCAGACCCAGATG 60.224 50.000 0.00 0.00 0.00 2.90
18 19 2.050144 ACGAATATGCCAGACCCAGAT 58.950 47.619 0.00 0.00 0.00 2.90
19 20 1.138859 CACGAATATGCCAGACCCAGA 59.861 52.381 0.00 0.00 0.00 3.86
20 21 1.138859 TCACGAATATGCCAGACCCAG 59.861 52.381 0.00 0.00 0.00 4.45
21 22 1.199615 TCACGAATATGCCAGACCCA 58.800 50.000 0.00 0.00 0.00 4.51
22 23 2.325583 TTCACGAATATGCCAGACCC 57.674 50.000 0.00 0.00 0.00 4.46
23 24 3.689649 ACTTTTCACGAATATGCCAGACC 59.310 43.478 0.00 0.00 0.00 3.85
24 25 4.492570 CGACTTTTCACGAATATGCCAGAC 60.493 45.833 0.00 0.00 0.00 3.51
25 26 3.616821 CGACTTTTCACGAATATGCCAGA 59.383 43.478 0.00 0.00 0.00 3.86
26 27 3.616821 TCGACTTTTCACGAATATGCCAG 59.383 43.478 0.00 0.00 35.62 4.85
27 28 3.591023 TCGACTTTTCACGAATATGCCA 58.409 40.909 0.00 0.00 35.62 4.92
28 29 3.001330 CCTCGACTTTTCACGAATATGCC 59.999 47.826 0.00 0.00 38.05 4.40
29 30 3.863424 TCCTCGACTTTTCACGAATATGC 59.137 43.478 0.00 0.00 38.05 3.14
30 31 5.103000 ACTCCTCGACTTTTCACGAATATG 58.897 41.667 0.00 0.00 38.05 1.78
31 32 5.326200 ACTCCTCGACTTTTCACGAATAT 57.674 39.130 0.00 0.00 38.05 1.28
32 33 4.778534 ACTCCTCGACTTTTCACGAATA 57.221 40.909 0.00 0.00 38.05 1.75
33 34 3.662247 ACTCCTCGACTTTTCACGAAT 57.338 42.857 0.00 0.00 38.05 3.34
34 35 3.057736 CCTACTCCTCGACTTTTCACGAA 60.058 47.826 0.00 0.00 38.05 3.85
35 36 2.486982 CCTACTCCTCGACTTTTCACGA 59.513 50.000 0.00 0.00 37.03 4.35
36 37 2.415625 CCCTACTCCTCGACTTTTCACG 60.416 54.545 0.00 0.00 0.00 4.35
37 38 2.674462 GCCCTACTCCTCGACTTTTCAC 60.674 54.545 0.00 0.00 0.00 3.18
38 39 1.549170 GCCCTACTCCTCGACTTTTCA 59.451 52.381 0.00 0.00 0.00 2.69
39 40 1.826096 AGCCCTACTCCTCGACTTTTC 59.174 52.381 0.00 0.00 0.00 2.29
40 41 1.550976 CAGCCCTACTCCTCGACTTTT 59.449 52.381 0.00 0.00 0.00 2.27
41 42 1.187087 CAGCCCTACTCCTCGACTTT 58.813 55.000 0.00 0.00 0.00 2.66
42 43 0.684805 CCAGCCCTACTCCTCGACTT 60.685 60.000 0.00 0.00 0.00 3.01
43 44 1.076632 CCAGCCCTACTCCTCGACT 60.077 63.158 0.00 0.00 0.00 4.18
47 48 2.033372 GTTAGTCCAGCCCTACTCCTC 58.967 57.143 0.00 0.00 0.00 3.71
297 298 8.991026 CACATCTTTCTCATCTTCTCATATTCC 58.009 37.037 0.00 0.00 0.00 3.01
331 332 8.272889 GTCCTAAGTCTATGGAAGGGTTATTTT 58.727 37.037 0.00 0.00 0.00 1.82
337 338 4.016479 TCAGTCCTAAGTCTATGGAAGGGT 60.016 45.833 0.00 0.00 0.00 4.34
341 342 5.691896 TCGATCAGTCCTAAGTCTATGGAA 58.308 41.667 0.00 0.00 0.00 3.53
391 393 0.441145 CGGTAGTAGCGTGGTTTTGC 59.559 55.000 13.49 0.00 33.95 3.68
397 399 1.019673 TAAGCTCGGTAGTAGCGTGG 58.980 55.000 20.20 15.00 44.87 4.94
418 420 3.860641 TGCGAATTTCATGAGCTACTCA 58.139 40.909 0.00 0.00 44.99 3.41
570 572 2.560542 CTCCTCGATAGGGATGGACAAG 59.439 54.545 0.00 0.00 43.84 3.16
666 668 0.956633 TACTCGTGACGGCAGACTTT 59.043 50.000 4.70 0.00 0.00 2.66
686 690 5.294552 GTCATCTATTTTGGAACGGAAGGAG 59.705 44.000 0.00 0.00 0.00 3.69
688 692 4.335594 GGTCATCTATTTTGGAACGGAAGG 59.664 45.833 0.00 0.00 0.00 3.46
689 693 4.335594 GGGTCATCTATTTTGGAACGGAAG 59.664 45.833 0.00 0.00 0.00 3.46
690 694 4.263550 TGGGTCATCTATTTTGGAACGGAA 60.264 41.667 0.00 0.00 0.00 4.30
692 696 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
693 697 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
694 698 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
695 699 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
696 700 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
697 701 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
698 702 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
699 703 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
701 705 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
703 707 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
704 708 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
705 709 7.506328 AAAGTTAGTACAAAGTTGGGTCATC 57.494 36.000 0.00 0.00 0.00 2.92
707 711 8.983702 ATTAAAGTTAGTACAAAGTTGGGTCA 57.016 30.769 0.00 0.00 0.00 4.02
739 743 9.386122 AGGCCTCTTCTAAAATAGATGATCTAA 57.614 33.333 6.22 0.00 38.03 2.10
740 744 8.964533 AGGCCTCTTCTAAAATAGATGATCTA 57.035 34.615 0.00 4.40 38.03 1.98
741 745 7.870426 AGGCCTCTTCTAAAATAGATGATCT 57.130 36.000 0.00 0.00 38.03 2.75
742 746 8.782144 CAAAGGCCTCTTCTAAAATAGATGATC 58.218 37.037 5.23 0.00 38.03 2.92
743 747 8.497745 TCAAAGGCCTCTTCTAAAATAGATGAT 58.502 33.333 5.23 0.00 38.03 2.45
744 748 7.861629 TCAAAGGCCTCTTCTAAAATAGATGA 58.138 34.615 5.23 3.78 36.85 2.92
745 749 8.511604 TTCAAAGGCCTCTTCTAAAATAGATG 57.488 34.615 5.23 0.00 34.22 2.90
746 750 9.706529 ATTTCAAAGGCCTCTTCTAAAATAGAT 57.293 29.630 5.23 0.00 34.22 1.98
747 751 9.178758 GATTTCAAAGGCCTCTTCTAAAATAGA 57.821 33.333 5.23 0.00 31.82 1.98
748 752 8.125448 CGATTTCAAAGGCCTCTTCTAAAATAG 58.875 37.037 5.23 4.03 31.82 1.73
749 753 7.827236 TCGATTTCAAAGGCCTCTTCTAAAATA 59.173 33.333 5.23 0.00 31.82 1.40
750 754 6.659242 TCGATTTCAAAGGCCTCTTCTAAAAT 59.341 34.615 5.23 6.95 31.82 1.82
751 755 6.001460 TCGATTTCAAAGGCCTCTTCTAAAA 58.999 36.000 5.23 1.84 31.82 1.52
752 756 5.411669 GTCGATTTCAAAGGCCTCTTCTAAA 59.588 40.000 5.23 3.35 31.82 1.85
753 757 4.935808 GTCGATTTCAAAGGCCTCTTCTAA 59.064 41.667 5.23 0.00 31.82 2.10
754 758 4.223032 AGTCGATTTCAAAGGCCTCTTCTA 59.777 41.667 5.23 0.00 31.82 2.10
755 759 3.008485 AGTCGATTTCAAAGGCCTCTTCT 59.992 43.478 5.23 0.00 31.82 2.85
756 760 3.339141 AGTCGATTTCAAAGGCCTCTTC 58.661 45.455 5.23 0.00 31.82 2.87
757 761 3.008485 AGAGTCGATTTCAAAGGCCTCTT 59.992 43.478 5.23 0.00 34.07 2.85
758 762 2.569404 AGAGTCGATTTCAAAGGCCTCT 59.431 45.455 5.23 0.00 0.00 3.69
820 1188 1.153353 TTAAAGCAGCGCTGTACACC 58.847 50.000 35.80 20.28 39.62 4.16
830 1198 3.443681 TCTTGGCCTTGTATTAAAGCAGC 59.556 43.478 3.32 0.00 0.00 5.25
879 1247 0.825010 AACTTGGCTGTGCTTCCTGG 60.825 55.000 0.00 0.00 0.00 4.45
961 1333 4.966787 GCAAAGGACGGGGTGGCA 62.967 66.667 0.00 0.00 0.00 4.92
1016 1388 4.103103 GCGTTGGAGGCCGCTTTC 62.103 66.667 6.40 0.00 46.08 2.62
1086 1458 6.870971 AGGCGTAAACAACAAAGAGATTAA 57.129 33.333 0.00 0.00 0.00 1.40
1175 1547 2.620115 CAGAGAAGCAAGAAAGCAACCA 59.380 45.455 0.00 0.00 36.85 3.67
1194 1566 0.248661 CCACCACTACTCGCGATCAG 60.249 60.000 10.36 12.54 0.00 2.90
1320 1692 0.880278 TCAGACGAGTGCAACAAGGC 60.880 55.000 0.00 0.00 41.43 4.35
1325 1697 0.861837 CTGGTTCAGACGAGTGCAAC 59.138 55.000 0.00 0.00 32.44 4.17
1388 1761 1.555533 GGACGGGGAATCAGGGATATC 59.444 57.143 0.00 0.00 0.00 1.63
1393 1766 1.224592 CAAGGACGGGGAATCAGGG 59.775 63.158 0.00 0.00 0.00 4.45
1420 1793 6.749118 GCTTGGTGAATAAATTTCTACTGCTG 59.251 38.462 0.00 0.00 0.00 4.41
1466 1839 8.971073 CCTTCACCTATTGTCTTTATTTGGATT 58.029 33.333 0.00 0.00 0.00 3.01
1467 1840 8.336235 TCCTTCACCTATTGTCTTTATTTGGAT 58.664 33.333 0.00 0.00 0.00 3.41
1500 1873 6.549433 ACACATATTTTGCAAGGAATCCAT 57.451 33.333 0.61 0.00 0.00 3.41
1567 1940 2.222508 CGACAAAGTGGCGTAGATTTCG 60.223 50.000 0.00 0.00 45.41 3.46
1787 2163 8.035394 AGTTTAGCGACAGATCTGAAAAGATAA 58.965 33.333 29.27 19.52 0.00 1.75
1792 2168 4.152402 GCAGTTTAGCGACAGATCTGAAAA 59.848 41.667 29.27 16.00 0.00 2.29
1805 2181 3.926527 TCTGAACACTATGCAGTTTAGCG 59.073 43.478 0.00 0.00 37.31 4.26
1908 2284 2.034685 TCTACGACAGATATGCAGTGGC 59.965 50.000 0.00 0.00 41.68 5.01
1914 2290 8.551205 TCAATGAAATTTCTACGACAGATATGC 58.449 33.333 18.64 0.00 31.22 3.14
1915 2291 9.855361 GTCAATGAAATTTCTACGACAGATATG 57.145 33.333 18.64 0.00 31.22 1.78
2004 2380 7.657354 AGTTTTGAATGCAGTAATTCTTTTCCC 59.343 33.333 0.00 0.00 37.44 3.97
2285 2665 0.817634 CGTTTCCAGACACAAGGGCA 60.818 55.000 0.00 0.00 0.00 5.36
2292 2672 2.835027 ACTCCTTTCGTTTCCAGACAC 58.165 47.619 0.00 0.00 0.00 3.67
2585 2965 8.333908 CAGATTAATGAAGTCTGAAGGAAATCG 58.666 37.037 0.00 0.00 41.38 3.34
2587 2967 7.067981 GGCAGATTAATGAAGTCTGAAGGAAAT 59.932 37.037 7.12 0.00 41.38 2.17
2606 2986 3.985127 TCTCCCAAATGATTGGCAGATT 58.015 40.909 0.00 0.00 46.45 2.40
2643 3023 7.654520 TCAGGCGTATTGAAACCATTATAGTAC 59.345 37.037 0.00 0.00 0.00 2.73
2644 3024 7.728148 TCAGGCGTATTGAAACCATTATAGTA 58.272 34.615 0.00 0.00 0.00 1.82
2645 3025 6.588204 TCAGGCGTATTGAAACCATTATAGT 58.412 36.000 0.00 0.00 0.00 2.12
2646 3026 7.490962 TTCAGGCGTATTGAAACCATTATAG 57.509 36.000 0.00 0.00 31.98 1.31
2647 3027 7.521423 GCATTCAGGCGTATTGAAACCATTATA 60.521 37.037 3.24 0.00 38.01 0.98
2648 3028 6.735694 GCATTCAGGCGTATTGAAACCATTAT 60.736 38.462 3.24 0.00 38.01 1.28
2649 3029 5.449862 GCATTCAGGCGTATTGAAACCATTA 60.450 40.000 3.24 0.00 38.01 1.90
2650 3030 4.677779 GCATTCAGGCGTATTGAAACCATT 60.678 41.667 3.24 0.00 38.01 3.16
2708 3088 6.418101 AGCACTAGCATTAGAATTTCTGGAA 58.582 36.000 9.22 0.00 45.49 3.53
2710 3090 7.658982 TGATAGCACTAGCATTAGAATTTCTGG 59.341 37.037 9.22 0.42 45.49 3.86
2754 3134 4.887655 TGCGAGATTGTAGAACCTATCTCA 59.112 41.667 0.00 0.00 41.86 3.27
2755 3135 5.440234 TGCGAGATTGTAGAACCTATCTC 57.560 43.478 0.00 0.00 39.71 2.75
2798 3178 1.468520 CGGTCCAACATGACACCAATC 59.531 52.381 0.00 0.00 36.97 2.67
2818 3198 8.312564 AGTTCTACTAGAAGGTTTGTCATTACC 58.687 37.037 0.00 0.00 34.42 2.85
2824 3209 9.924650 TCATAAAGTTCTACTAGAAGGTTTGTC 57.075 33.333 0.00 0.00 34.42 3.18
2853 3238 1.963515 GGAAGGTTTGAACATGCACCT 59.036 47.619 0.00 0.00 41.71 4.00
2910 3305 6.365970 AAGATGTCTTCTGGCTTAAGAGAA 57.634 37.500 6.67 6.56 33.75 2.87
2968 3363 3.374745 CTGTGTCACTGCAATTTGAACC 58.625 45.455 4.27 0.00 0.00 3.62
3105 3500 2.399611 CGGCGAGCCAACGATTTC 59.600 61.111 15.03 0.00 35.37 2.17
3316 3711 5.879223 AGCTTGAAGTAGATTGTTCCATCTG 59.121 40.000 0.00 0.00 0.00 2.90
3317 3712 5.879223 CAGCTTGAAGTAGATTGTTCCATCT 59.121 40.000 0.00 0.00 0.00 2.90
3355 3750 0.455815 TCATCGGTCCATGACGTGAG 59.544 55.000 0.00 0.00 32.65 3.51
3369 3764 3.126831 GCTCCTGTACCAGATTTCATCG 58.873 50.000 0.00 0.00 32.44 3.84
3645 4045 1.336240 GCCTTGGATGTTGCAGTGAAC 60.336 52.381 0.00 0.00 0.00 3.18
3733 4134 1.736645 CGACCACCAGTAGTTGCCG 60.737 63.158 0.00 0.00 0.00 5.69
3968 4369 3.581755 GAGTGACGCTTGTTACCATACA 58.418 45.455 0.00 0.00 32.81 2.29
3983 4384 2.046892 ATGCCAGGTGCGAGTGAC 60.047 61.111 0.00 0.00 45.60 3.67
3984 4385 1.902765 ATCATGCCAGGTGCGAGTGA 61.903 55.000 0.00 0.00 45.60 3.41
3985 4386 1.028330 AATCATGCCAGGTGCGAGTG 61.028 55.000 0.00 0.00 45.60 3.51
3987 4388 1.600957 CTTAATCATGCCAGGTGCGAG 59.399 52.381 0.00 0.00 45.60 5.03
3989 4390 0.029834 GCTTAATCATGCCAGGTGCG 59.970 55.000 0.00 0.00 45.60 5.34
3990 4391 3.953201 GCTTAATCATGCCAGGTGC 57.047 52.632 0.00 0.00 41.77 5.01
4009 4410 0.675522 ACACCGGGATTTTGTAGCCG 60.676 55.000 6.32 0.00 0.00 5.52
4024 4425 1.788886 GAACGAACGGTCAGTTACACC 59.211 52.381 9.98 0.00 44.35 4.16
4036 4442 2.638556 ACAGATCAGAGGAACGAACG 57.361 50.000 0.00 0.00 0.00 3.95
4041 4447 2.158449 CGCACAAACAGATCAGAGGAAC 59.842 50.000 0.00 0.00 0.00 3.62
4366 4829 2.472029 AGATGATCGGAGTGGAAGGTT 58.528 47.619 0.00 0.00 0.00 3.50
4419 4883 2.048597 CTAACCACACGGCGCTGA 60.049 61.111 25.98 0.00 34.57 4.26
4461 4925 1.873591 CCAGACCGAAAGAAACACCTG 59.126 52.381 0.00 0.00 0.00 4.00
4463 4927 2.249844 TCCAGACCGAAAGAAACACC 57.750 50.000 0.00 0.00 0.00 4.16
4492 4956 7.176865 GCCCTCACAGATATATACAAGTGTCTA 59.823 40.741 9.01 0.00 0.00 2.59
4611 5080 3.787001 TGGGTGCGTGTGTGGTGA 61.787 61.111 0.00 0.00 0.00 4.02
4763 5236 0.107945 ATCAAGAGGAGCGCCAAGAC 60.108 55.000 9.88 0.00 36.29 3.01
4880 5353 1.520342 GAGCTCATCACCGCTGGAC 60.520 63.158 9.40 0.00 36.45 4.02
4889 5362 4.880120 GTCTTGATCAAATGGAGCTCATCA 59.120 41.667 17.19 11.78 34.44 3.07
4892 5365 4.564782 AGTCTTGATCAAATGGAGCTCA 57.435 40.909 17.19 1.87 31.67 4.26
4976 5450 5.104982 ACTTCCTTCTCCTGATGATCAGTTC 60.105 44.000 20.06 0.00 42.80 3.01
5261 5736 2.095768 CCAACAGCGTATGAAACACCAG 60.096 50.000 0.00 0.00 0.00 4.00
5325 5800 3.419943 TGCAACAGTGGCTTAATGATCA 58.580 40.909 0.43 0.00 0.00 2.92
5333 5808 1.001378 GACGATTTGCAACAGTGGCTT 60.001 47.619 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.