Multiple sequence alignment - TraesCS7D01G095000

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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 TraesCS7D01G095000 chr7D 100.000 5466 0 0 1 5466 57094830 57089365 0.000000e+00 10094
1 TraesCS7D01G095000 chr7D 93.410 1214 67 4 2613 3818 57793943 57795151 0.000000e+00 1786
2 TraesCS7D01G095000 chr7D 88.657 670 46 11 872 1528 57777879 57778531 0.000000e+00 789
3 TraesCS7D01G095000 chr7D 89.320 103 11 0 3922 4024 57536851 57536953 4.440000e-26 130
4 TraesCS7D01G095000 chr4A 92.996 4640 201 49 872 5466 673956700 673961260 0.000000e+00 6654
5 TraesCS7D01G095000 chr4A 90.379 634 57 4 35 665 598418357 598417725 0.000000e+00 830
6 TraesCS7D01G095000 chr4A 79.702 537 66 25 3157 3670 674742901 674742385 1.130000e-91 348
7 TraesCS7D01G095000 chr4A 83.333 312 45 5 3052 3363 674621005 674621309 1.160000e-71 281
8 TraesCS7D01G095000 chr3D 92.110 4702 243 39 809 5466 545262098 545257481 0.000000e+00 6510
9 TraesCS7D01G095000 chr3D 89.465 636 61 5 34 666 136727844 136728476 0.000000e+00 798
10 TraesCS7D01G095000 chr7A 94.381 3328 171 12 1688 5008 61819335 61816017 0.000000e+00 5096
11 TraesCS7D01G095000 chr7A 91.437 2943 148 36 872 3808 62083098 62085942 0.000000e+00 3943
12 TraesCS7D01G095000 chr7A 90.553 1302 115 2 3229 4530 61887265 61888558 0.000000e+00 1716
13 TraesCS7D01G095000 chr7A 88.783 838 69 17 1743 2561 61882612 61883443 0.000000e+00 1003
14 TraesCS7D01G095000 chr7A 87.153 685 71 9 2558 3233 61883601 61884277 0.000000e+00 761
15 TraesCS7D01G095000 chr7A 92.072 391 11 4 1259 1649 61819703 61819333 2.900000e-147 532
16 TraesCS7D01G095000 chr7A 87.982 441 30 8 793 1210 61820452 61820012 2.940000e-137 499
17 TraesCS7D01G095000 chr7A 76.364 990 158 54 2136 3104 62743432 62742498 3.860000e-126 462
18 TraesCS7D01G095000 chr7A 82.178 505 71 7 3365 3868 62738862 62738376 3.050000e-112 416
19 TraesCS7D01G095000 chr7A 87.774 319 24 3 5163 5466 61815698 61815380 5.210000e-95 359
20 TraesCS7D01G095000 chr7A 84.477 277 29 5 872 1147 61882298 61882561 1.510000e-65 261
21 TraesCS7D01G095000 chr7A 81.544 298 37 10 1721 2003 62743936 62743642 4.260000e-56 230
22 TraesCS7D01G095000 chr7A 82.723 191 27 5 3157 3346 62739033 62738848 1.220000e-36 165
23 TraesCS7D01G095000 chr7A 94.624 93 5 0 5050 5142 61815898 61815806 1.590000e-30 145
24 TraesCS7D01G095000 chr1B 90.302 629 56 4 34 659 571442384 571443010 0.000000e+00 819
25 TraesCS7D01G095000 chr5B 89.172 628 63 5 35 659 485730801 485731426 0.000000e+00 778
26 TraesCS7D01G095000 chr5B 88.995 627 63 5 36 659 462178052 462178675 0.000000e+00 771
27 TraesCS7D01G095000 chr2A 88.661 635 64 7 36 665 592003004 592002373 0.000000e+00 767
28 TraesCS7D01G095000 chr6A 88.498 626 68 3 35 657 503936016 503935392 0.000000e+00 754
29 TraesCS7D01G095000 chr4D 88.567 621 66 4 41 657 82937348 82937967 0.000000e+00 749
30 TraesCS7D01G095000 chr4D 87.969 640 67 7 33 665 477515304 477514668 0.000000e+00 747
31 TraesCS7D01G095000 chrUn 80.754 504 66 15 3366 3861 91224372 91224852 1.120000e-96 364
32 TraesCS7D01G095000 chrUn 87.313 134 17 0 3106 3239 91224068 91224201 2.640000e-33 154


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 TraesCS7D01G095000 chr7D 57089365 57094830 5465 True 10094.00 10094 100.00000 1 5466 1 chr7D.!!$R1 5465
1 TraesCS7D01G095000 chr7D 57793943 57795151 1208 False 1786.00 1786 93.41000 2613 3818 1 chr7D.!!$F3 1205
2 TraesCS7D01G095000 chr7D 57777879 57778531 652 False 789.00 789 88.65700 872 1528 1 chr7D.!!$F2 656
3 TraesCS7D01G095000 chr4A 673956700 673961260 4560 False 6654.00 6654 92.99600 872 5466 1 chr4A.!!$F1 4594
4 TraesCS7D01G095000 chr4A 598417725 598418357 632 True 830.00 830 90.37900 35 665 1 chr4A.!!$R1 630
5 TraesCS7D01G095000 chr4A 674742385 674742901 516 True 348.00 348 79.70200 3157 3670 1 chr4A.!!$R2 513
6 TraesCS7D01G095000 chr3D 545257481 545262098 4617 True 6510.00 6510 92.11000 809 5466 1 chr3D.!!$R1 4657
7 TraesCS7D01G095000 chr3D 136727844 136728476 632 False 798.00 798 89.46500 34 666 1 chr3D.!!$F1 632
8 TraesCS7D01G095000 chr7A 62083098 62085942 2844 False 3943.00 3943 91.43700 872 3808 1 chr7A.!!$F1 2936
9 TraesCS7D01G095000 chr7A 61815380 61820452 5072 True 1326.20 5096 91.36660 793 5466 5 chr7A.!!$R1 4673
10 TraesCS7D01G095000 chr7A 61882298 61888558 6260 False 935.25 1716 87.74150 872 4530 4 chr7A.!!$F2 3658
11 TraesCS7D01G095000 chr7A 62738376 62743936 5560 True 318.25 462 80.70225 1721 3868 4 chr7A.!!$R2 2147
12 TraesCS7D01G095000 chr1B 571442384 571443010 626 False 819.00 819 90.30200 34 659 1 chr1B.!!$F1 625
13 TraesCS7D01G095000 chr5B 485730801 485731426 625 False 778.00 778 89.17200 35 659 1 chr5B.!!$F2 624
14 TraesCS7D01G095000 chr5B 462178052 462178675 623 False 771.00 771 88.99500 36 659 1 chr5B.!!$F1 623
15 TraesCS7D01G095000 chr2A 592002373 592003004 631 True 767.00 767 88.66100 36 665 1 chr2A.!!$R1 629
16 TraesCS7D01G095000 chr6A 503935392 503936016 624 True 754.00 754 88.49800 35 657 1 chr6A.!!$R1 622
17 TraesCS7D01G095000 chr4D 82937348 82937967 619 False 749.00 749 88.56700 41 657 1 chr4D.!!$F1 616
18 TraesCS7D01G095000 chr4D 477514668 477515304 636 True 747.00 747 87.96900 33 665 1 chr4D.!!$R1 632
19 TraesCS7D01G095000 chrUn 91224068 91224852 784 False 259.00 364 84.03350 3106 3861 2 chrUn.!!$F1 755

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
726 736 0.036388 TGCATGAGAAGGGTTCGGTC 60.036 55.000 0.00 0.00 34.02 4.79 F
890 917 0.326522 TCCAAGCCCATCTCCAGCTA 60.327 55.000 0.00 0.00 35.30 3.32 F
1573 1884 1.338389 GCAATGCTGCCACTTCCAAAT 60.338 47.619 0.00 0.00 43.26 2.32 F
2753 3348 0.588252 CACGGCCAAGTGAACTCTTG 59.412 55.000 2.24 8.92 44.43 3.02 F
3302 10412 0.110373 GGGTAAAACAAGCAGCGACG 60.110 55.000 0.00 0.00 0.00 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 2258 0.749454 GCGGGATTGAGCCATCACTT 60.749 55.000 0.00 0.00 34.35 3.16 R
2736 3331 1.593196 TTCAAGAGTTCACTTGGCCG 58.407 50.000 0.00 0.00 44.84 6.13 R
3273 10380 3.799963 GCTTGTTTTACCCAAGAAAACCG 59.200 43.478 4.43 2.28 43.21 4.44 R
3977 11113 1.208776 CACCCCTAAAGGAACCCGTAG 59.791 57.143 0.00 0.00 38.24 3.51 R
5124 12360 1.068895 CCAAATGCTTGCACTGGAACA 59.931 47.619 16.28 0.00 0.00 3.18 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
17 18 2.281070 CACGTCTTGGTGCTGCCT 60.281 61.111 0.00 0.00 38.35 4.75
18 19 2.031163 ACGTCTTGGTGCTGCCTC 59.969 61.111 0.00 0.00 38.35 4.70
19 20 3.114616 CGTCTTGGTGCTGCCTCG 61.115 66.667 0.00 0.00 38.35 4.63
20 21 2.031163 GTCTTGGTGCTGCCTCGT 59.969 61.111 0.00 0.00 38.35 4.18
21 22 1.292223 GTCTTGGTGCTGCCTCGTA 59.708 57.895 0.00 0.00 38.35 3.43
22 23 0.320421 GTCTTGGTGCTGCCTCGTAA 60.320 55.000 0.00 0.00 38.35 3.18
23 24 0.394938 TCTTGGTGCTGCCTCGTAAA 59.605 50.000 0.00 0.00 38.35 2.01
24 25 1.003118 TCTTGGTGCTGCCTCGTAAAT 59.997 47.619 0.00 0.00 38.35 1.40
25 26 1.131126 CTTGGTGCTGCCTCGTAAATG 59.869 52.381 0.00 0.00 38.35 2.32
26 27 1.305219 TGGTGCTGCCTCGTAAATGC 61.305 55.000 0.00 0.00 38.35 3.56
27 28 1.305219 GGTGCTGCCTCGTAAATGCA 61.305 55.000 0.00 0.00 0.00 3.96
28 29 0.179189 GTGCTGCCTCGTAAATGCAC 60.179 55.000 0.00 0.00 42.69 4.57
29 30 0.605050 TGCTGCCTCGTAAATGCACA 60.605 50.000 0.00 0.00 0.00 4.57
30 31 0.179189 GCTGCCTCGTAAATGCACAC 60.179 55.000 0.00 0.00 0.00 3.82
31 32 0.095245 CTGCCTCGTAAATGCACACG 59.905 55.000 10.24 10.24 39.48 4.49
32 33 1.226018 GCCTCGTAAATGCACACGC 60.226 57.895 11.36 0.00 38.05 5.34
158 159 0.179018 AAACCCACTGTGAGCACTCC 60.179 55.000 9.86 0.00 0.00 3.85
189 192 1.474332 TACTCACCGGGGCGAAAACT 61.474 55.000 6.32 0.00 0.00 2.66
250 253 2.962859 AGCCCCAAAAGAACACAAGAT 58.037 42.857 0.00 0.00 0.00 2.40
254 261 4.706962 GCCCCAAAAGAACACAAGATAGAT 59.293 41.667 0.00 0.00 0.00 1.98
282 289 3.111098 CAACAGCTGAGCAACAAAAGTC 58.889 45.455 23.35 0.00 0.00 3.01
286 293 2.961062 AGCTGAGCAACAAAAGTCCATT 59.039 40.909 7.39 0.00 0.00 3.16
307 315 1.978617 CGCACAGGGGGAAAGCAAT 60.979 57.895 0.00 0.00 0.00 3.56
344 353 2.734755 CCATGGGGTAGCATCTTCAA 57.265 50.000 2.85 0.00 0.00 2.69
351 360 3.065371 GGGGTAGCATCTTCAACAAATCG 59.935 47.826 0.00 0.00 0.00 3.34
459 468 1.865788 GCCACGCCATCTTGCTTCAA 61.866 55.000 0.00 0.00 0.00 2.69
465 474 2.157738 GCCATCTTGCTTCAACAGTCT 58.842 47.619 0.00 0.00 0.00 3.24
475 484 3.476552 CTTCAACAGTCTTGCCCAGTAA 58.523 45.455 0.00 0.00 0.00 2.24
512 521 5.987347 CAGGCAGAAAAGACACATTCAAAAT 59.013 36.000 0.00 0.00 0.00 1.82
609 618 4.523558 CCCCGTTGTATAAAACTTTTCCCA 59.476 41.667 4.29 0.00 0.00 4.37
610 619 5.186215 CCCCGTTGTATAAAACTTTTCCCAT 59.814 40.000 4.29 0.00 0.00 4.00
634 644 3.131396 GGGAAGAACGTATAGCACCATG 58.869 50.000 0.00 0.00 0.00 3.66
659 669 6.681120 GCATAAGCTTGCCAAATGTTATCAGA 60.681 38.462 9.86 0.00 36.60 3.27
666 676 6.343716 TGCCAAATGTTATCAGAACACATT 57.656 33.333 5.18 5.18 41.83 2.71
667 677 7.459795 TGCCAAATGTTATCAGAACACATTA 57.540 32.000 9.86 0.00 39.66 1.90
668 678 7.890515 TGCCAAATGTTATCAGAACACATTAA 58.109 30.769 9.86 0.00 39.66 1.40
669 679 8.363390 TGCCAAATGTTATCAGAACACATTAAA 58.637 29.630 9.86 0.00 39.66 1.52
670 680 9.369904 GCCAAATGTTATCAGAACACATTAAAT 57.630 29.630 9.86 0.00 39.66 1.40
673 683 9.926158 AAATGTTATCAGAACACATTAAATGCA 57.074 25.926 9.86 0.00 39.66 3.96
674 684 8.915871 ATGTTATCAGAACACATTAAATGCAC 57.084 30.769 0.00 0.00 32.37 4.57
675 685 7.020602 TGTTATCAGAACACATTAAATGCACG 58.979 34.615 0.00 0.00 0.00 5.34
676 686 3.820689 TCAGAACACATTAAATGCACGC 58.179 40.909 0.00 0.00 0.00 5.34
677 687 2.916716 CAGAACACATTAAATGCACGCC 59.083 45.455 0.00 0.00 0.00 5.68
678 688 2.819608 AGAACACATTAAATGCACGCCT 59.180 40.909 0.00 0.00 0.00 5.52
679 689 3.255642 AGAACACATTAAATGCACGCCTT 59.744 39.130 0.00 0.00 0.00 4.35
680 690 2.945278 ACACATTAAATGCACGCCTTG 58.055 42.857 0.00 0.00 0.00 3.61
689 699 3.114616 CACGCCTTGCTCGACCAG 61.115 66.667 0.00 0.00 0.00 4.00
690 700 3.616721 ACGCCTTGCTCGACCAGT 61.617 61.111 0.00 0.00 0.00 4.00
691 701 2.357517 CGCCTTGCTCGACCAGTT 60.358 61.111 0.00 0.00 0.00 3.16
692 702 2.671177 CGCCTTGCTCGACCAGTTG 61.671 63.158 0.00 0.00 0.00 3.16
693 703 1.598130 GCCTTGCTCGACCAGTTGT 60.598 57.895 0.00 0.00 0.00 3.32
694 704 1.569479 GCCTTGCTCGACCAGTTGTC 61.569 60.000 0.00 0.00 40.81 3.18
704 714 1.865340 GACCAGTTGTCGTCTTTCACC 59.135 52.381 0.00 0.00 33.49 4.02
705 715 1.208535 ACCAGTTGTCGTCTTTCACCA 59.791 47.619 0.00 0.00 0.00 4.17
706 716 2.285083 CCAGTTGTCGTCTTTCACCAA 58.715 47.619 0.00 0.00 0.00 3.67
707 717 2.878406 CCAGTTGTCGTCTTTCACCAAT 59.122 45.455 0.00 0.00 0.00 3.16
708 718 3.303990 CCAGTTGTCGTCTTTCACCAATG 60.304 47.826 0.00 0.00 0.00 2.82
709 719 2.290641 AGTTGTCGTCTTTCACCAATGC 59.709 45.455 0.00 0.00 0.00 3.56
710 720 1.960417 TGTCGTCTTTCACCAATGCA 58.040 45.000 0.00 0.00 0.00 3.96
711 721 2.503331 TGTCGTCTTTCACCAATGCAT 58.497 42.857 0.00 0.00 0.00 3.96
712 722 2.226200 TGTCGTCTTTCACCAATGCATG 59.774 45.455 0.00 0.00 0.00 4.06
713 723 2.483877 GTCGTCTTTCACCAATGCATGA 59.516 45.455 0.00 0.00 0.00 3.07
714 724 2.743664 TCGTCTTTCACCAATGCATGAG 59.256 45.455 0.00 0.00 0.00 2.90
715 725 2.743664 CGTCTTTCACCAATGCATGAGA 59.256 45.455 0.00 0.00 0.00 3.27
716 726 3.189080 CGTCTTTCACCAATGCATGAGAA 59.811 43.478 0.00 0.00 0.00 2.87
717 727 4.670992 CGTCTTTCACCAATGCATGAGAAG 60.671 45.833 0.00 2.37 0.00 2.85
718 728 3.760151 TCTTTCACCAATGCATGAGAAGG 59.240 43.478 0.00 3.43 0.00 3.46
719 729 2.133281 TCACCAATGCATGAGAAGGG 57.867 50.000 0.00 0.00 0.00 3.95
720 730 1.355381 TCACCAATGCATGAGAAGGGT 59.645 47.619 0.00 0.00 0.00 4.34
721 731 2.173519 CACCAATGCATGAGAAGGGTT 58.826 47.619 0.00 0.00 0.00 4.11
722 732 2.165030 CACCAATGCATGAGAAGGGTTC 59.835 50.000 0.00 0.00 0.00 3.62
723 733 1.402968 CCAATGCATGAGAAGGGTTCG 59.597 52.381 0.00 0.00 34.02 3.95
724 734 1.402968 CAATGCATGAGAAGGGTTCGG 59.597 52.381 0.00 0.00 34.02 4.30
725 735 0.620556 ATGCATGAGAAGGGTTCGGT 59.379 50.000 0.00 0.00 34.02 4.69
726 736 0.036388 TGCATGAGAAGGGTTCGGTC 60.036 55.000 0.00 0.00 34.02 4.79
727 737 0.036388 GCATGAGAAGGGTTCGGTCA 60.036 55.000 0.00 0.00 34.02 4.02
728 738 2.009042 GCATGAGAAGGGTTCGGTCAG 61.009 57.143 0.00 0.00 34.02 3.51
729 739 1.550524 CATGAGAAGGGTTCGGTCAGA 59.449 52.381 0.00 0.00 34.02 3.27
730 740 1.712056 TGAGAAGGGTTCGGTCAGAA 58.288 50.000 0.00 0.00 36.31 3.02
731 741 2.257207 TGAGAAGGGTTCGGTCAGAAT 58.743 47.619 0.00 0.00 41.49 2.40
732 742 2.233922 TGAGAAGGGTTCGGTCAGAATC 59.766 50.000 0.00 0.00 41.49 2.52
733 743 2.233922 GAGAAGGGTTCGGTCAGAATCA 59.766 50.000 0.00 0.00 41.70 2.57
734 744 2.637872 AGAAGGGTTCGGTCAGAATCAA 59.362 45.455 0.00 0.00 41.70 2.57
735 745 3.072476 AGAAGGGTTCGGTCAGAATCAAA 59.928 43.478 0.00 0.00 41.70 2.69
736 746 3.502123 AGGGTTCGGTCAGAATCAAAA 57.498 42.857 0.00 0.00 41.70 2.44
737 747 4.034285 AGGGTTCGGTCAGAATCAAAAT 57.966 40.909 0.00 0.00 41.70 1.82
738 748 3.758554 AGGGTTCGGTCAGAATCAAAATG 59.241 43.478 0.00 0.00 41.70 2.32
739 749 3.119495 GGGTTCGGTCAGAATCAAAATGG 60.119 47.826 0.00 0.00 41.70 3.16
740 750 3.756434 GGTTCGGTCAGAATCAAAATGGA 59.244 43.478 0.00 0.00 41.49 3.41
741 751 4.217550 GGTTCGGTCAGAATCAAAATGGAA 59.782 41.667 0.00 0.00 41.49 3.53
742 752 5.278758 GGTTCGGTCAGAATCAAAATGGAAA 60.279 40.000 0.00 0.00 41.49 3.13
743 753 6.389906 GTTCGGTCAGAATCAAAATGGAAAT 58.610 36.000 0.00 0.00 41.49 2.17
744 754 6.194796 TCGGTCAGAATCAAAATGGAAATC 57.805 37.500 0.00 0.00 0.00 2.17
745 755 5.945784 TCGGTCAGAATCAAAATGGAAATCT 59.054 36.000 0.00 0.00 0.00 2.40
746 756 7.109501 TCGGTCAGAATCAAAATGGAAATCTA 58.890 34.615 0.00 0.00 0.00 1.98
747 757 7.775093 TCGGTCAGAATCAAAATGGAAATCTAT 59.225 33.333 0.00 0.00 0.00 1.98
748 758 8.408601 CGGTCAGAATCAAAATGGAAATCTATT 58.591 33.333 0.00 0.00 0.00 1.73
807 817 1.144969 TGACGCTTAAGGCACGAAAG 58.855 50.000 4.29 0.00 41.91 2.62
830 840 3.618351 AGGACTTCAGGCAAATGATGAG 58.382 45.455 5.93 0.00 0.00 2.90
890 917 0.326522 TCCAAGCCCATCTCCAGCTA 60.327 55.000 0.00 0.00 35.30 3.32
1523 1834 3.246350 TGGTGAGATTTCTCCCCTTCCTA 60.246 47.826 9.96 0.00 40.58 2.94
1573 1884 1.338389 GCAATGCTGCCACTTCCAAAT 60.338 47.619 0.00 0.00 43.26 2.32
1575 1886 1.927487 ATGCTGCCACTTCCAAATGA 58.073 45.000 0.00 0.00 0.00 2.57
1576 1887 1.702182 TGCTGCCACTTCCAAATGAA 58.298 45.000 0.00 0.00 0.00 2.57
1577 1888 2.037901 TGCTGCCACTTCCAAATGAAA 58.962 42.857 0.00 0.00 31.06 2.69
1578 1889 2.224018 TGCTGCCACTTCCAAATGAAAC 60.224 45.455 0.00 0.00 31.06 2.78
1579 1890 2.036346 GCTGCCACTTCCAAATGAAACT 59.964 45.455 0.00 0.00 31.06 2.66
1580 1891 3.645884 CTGCCACTTCCAAATGAAACTG 58.354 45.455 0.00 0.00 31.06 3.16
1581 1892 2.224018 TGCCACTTCCAAATGAAACTGC 60.224 45.455 0.00 0.00 31.06 4.40
1582 1893 2.867647 GCCACTTCCAAATGAAACTGCC 60.868 50.000 0.00 0.00 31.06 4.85
1583 1894 2.364970 CCACTTCCAAATGAAACTGCCA 59.635 45.455 0.00 0.00 31.06 4.92
1584 1895 3.383761 CACTTCCAAATGAAACTGCCAC 58.616 45.455 0.00 0.00 31.06 5.01
1585 1896 3.068590 CACTTCCAAATGAAACTGCCACT 59.931 43.478 0.00 0.00 31.06 4.00
1586 1897 3.706086 ACTTCCAAATGAAACTGCCACTT 59.294 39.130 0.00 0.00 31.06 3.16
1587 1898 4.202151 ACTTCCAAATGAAACTGCCACTTC 60.202 41.667 0.00 0.00 31.06 3.01
1588 1899 2.627699 TCCAAATGAAACTGCCACTTCC 59.372 45.455 0.00 0.00 0.00 3.46
1589 1900 2.364970 CCAAATGAAACTGCCACTTCCA 59.635 45.455 0.00 0.00 0.00 3.53
1590 1901 3.181467 CCAAATGAAACTGCCACTTCCAA 60.181 43.478 0.00 0.00 0.00 3.53
1591 1902 4.440880 CAAATGAAACTGCCACTTCCAAA 58.559 39.130 0.00 0.00 0.00 3.28
1592 1903 3.733443 ATGAAACTGCCACTTCCAAAC 57.267 42.857 0.00 0.00 0.00 2.93
1593 1904 2.451490 TGAAACTGCCACTTCCAAACA 58.549 42.857 0.00 0.00 0.00 2.83
1609 1920 3.888930 CCAAACAAACTTTAGGAGGCTGA 59.111 43.478 0.00 0.00 0.00 4.26
1681 1992 3.320541 TCATGAAATTTTGTGTTCGCCCT 59.679 39.130 0.00 0.00 0.00 5.19
1746 2058 6.499234 TCTGTTGATGTTCATGTATTGTGG 57.501 37.500 0.00 0.00 0.00 4.17
1934 2258 4.842531 TCCATCTTATCAAGTGCTTCCA 57.157 40.909 0.00 0.00 0.00 3.53
1985 2309 4.384208 GCTTGGGACAGTTATACATGGACT 60.384 45.833 0.00 0.00 42.39 3.85
2081 2450 3.917988 TGGCTGCGAACATGATATAGAG 58.082 45.455 0.00 0.00 0.00 2.43
2177 2591 9.953697 AAAATAATTGTACTGTTTTGCGAGTAA 57.046 25.926 0.00 0.00 0.00 2.24
2184 2598 7.735500 TGTACTGTTTTGCGAGTAATACAATC 58.264 34.615 0.00 0.00 0.00 2.67
2236 2653 4.811557 GTCTGTGCTTACATTAGGTGATCC 59.188 45.833 0.00 0.00 0.00 3.36
2298 2718 9.434559 GCCATTCTTTTACGTATTTTACTGATC 57.565 33.333 0.00 0.00 0.00 2.92
2753 3348 0.588252 CACGGCCAAGTGAACTCTTG 59.412 55.000 2.24 8.92 44.43 3.02
2780 3382 7.215719 AGCTTGGATTTAAACTACCTCAAAC 57.784 36.000 0.00 0.00 0.00 2.93
3302 10412 0.110373 GGGTAAAACAAGCAGCGACG 60.110 55.000 0.00 0.00 0.00 5.12
3390 10508 7.107542 CCATCAAAAGGATTGGTCAAATTCAT 58.892 34.615 0.00 0.00 32.57 2.57
3818 10954 0.317479 ACTGCGAGTACCCACAGTTC 59.683 55.000 6.47 0.00 40.35 3.01
3977 11113 4.581824 TCTCATGCCCTAATTTTCTGCATC 59.418 41.667 0.00 0.00 40.46 3.91
4152 11288 4.452825 TCATCTAGTCGTGGAGGTTCTAG 58.547 47.826 0.00 0.00 0.00 2.43
4330 11466 0.819259 TATTGCTGAATGAGGCGGGC 60.819 55.000 0.00 0.00 0.00 6.13
4365 11501 3.139603 TGTAATCGATCTTCGCGACAA 57.860 42.857 9.15 0.00 40.94 3.18
4426 11562 2.143122 TGTGAGGCATTCAAAGACGTC 58.857 47.619 7.70 7.70 37.61 4.34
4537 11676 3.380479 TCTCCTTTTGGTGACTGTACG 57.620 47.619 0.00 0.00 41.38 3.67
4587 11726 3.726557 ATCCATTCAGCTCTTGGTCAA 57.273 42.857 6.11 0.00 0.00 3.18
4621 11760 5.392767 TTCTGTACAAGAAGTCCTAGCTG 57.607 43.478 0.00 0.00 40.09 4.24
4666 11805 4.225942 AGCAATTCTGATCAGTTCTACCCA 59.774 41.667 21.92 0.00 0.00 4.51
4743 11882 6.096141 ACATCTGTCAGGTCTTGATAGTGTAG 59.904 42.308 8.29 1.59 43.38 2.74
4754 11893 7.013846 GGTCTTGATAGTGTAGAGTAGCATCTT 59.986 40.741 0.00 0.00 0.00 2.40
4755 11894 9.058174 GTCTTGATAGTGTAGAGTAGCATCTTA 57.942 37.037 0.00 0.00 0.00 2.10
4758 11897 8.840833 TGATAGTGTAGAGTAGCATCTTAGAG 57.159 38.462 0.00 0.00 0.00 2.43
4774 11913 7.609532 GCATCTTAGAGACATAAATTAGGCCAT 59.390 37.037 5.01 0.00 0.00 4.40
4792 11931 4.881850 GGCCATGCAAAGTAGTAATACTGT 59.118 41.667 3.18 0.00 0.00 3.55
4828 11967 1.489481 ATCTGTCGGCTCCATTCTGA 58.511 50.000 0.00 0.00 0.00 3.27
4959 12100 8.761689 TCAGTTACTATAAATTTCCTACCCGTT 58.238 33.333 0.00 0.00 0.00 4.44
4980 12121 7.301054 CCGTTTGCAGGAGATATTTGATATTC 58.699 38.462 0.00 0.00 0.00 1.75
4981 12122 7.173907 CCGTTTGCAGGAGATATTTGATATTCT 59.826 37.037 0.00 0.00 0.00 2.40
4996 12137 9.842775 ATTTGATATTCTTATCTTGACTGAGCA 57.157 29.630 0.00 0.00 36.07 4.26
5026 12262 9.949174 GATGTATATTTTACATGACATGCACAA 57.051 29.630 15.49 2.50 38.18 3.33
5046 12282 4.219070 ACAATTGCACATGTTACTCTGCAT 59.781 37.500 5.05 0.00 39.32 3.96
5047 12283 4.627611 ATTGCACATGTTACTCTGCATC 57.372 40.909 7.18 0.00 39.32 3.91
5048 12284 3.339253 TGCACATGTTACTCTGCATCT 57.661 42.857 0.00 0.00 34.73 2.90
5049 12285 3.264947 TGCACATGTTACTCTGCATCTC 58.735 45.455 0.00 0.00 34.73 2.75
5050 12286 3.055602 TGCACATGTTACTCTGCATCTCT 60.056 43.478 0.00 0.00 34.73 3.10
5051 12287 3.555139 GCACATGTTACTCTGCATCTCTC 59.445 47.826 0.00 0.00 0.00 3.20
5052 12288 4.680172 GCACATGTTACTCTGCATCTCTCT 60.680 45.833 0.00 0.00 0.00 3.10
5053 12289 5.451103 GCACATGTTACTCTGCATCTCTCTA 60.451 44.000 0.00 0.00 0.00 2.43
5054 12290 5.976534 CACATGTTACTCTGCATCTCTCTAC 59.023 44.000 0.00 0.00 0.00 2.59
5055 12291 5.890985 ACATGTTACTCTGCATCTCTCTACT 59.109 40.000 0.00 0.00 0.00 2.57
5124 12360 4.831155 TGCACTAACTACTTCACTGTACCT 59.169 41.667 0.00 0.00 0.00 3.08
5137 12373 2.146342 CTGTACCTGTTCCAGTGCAAG 58.854 52.381 0.00 0.00 0.00 4.01
5182 12513 2.887568 GAGCTGCGTGGGTGATCG 60.888 66.667 0.00 0.00 0.00 3.69
5198 12529 5.088739 GGTGATCGAACTGCTTTTGTAATG 58.911 41.667 0.00 0.00 0.00 1.90
5281 12617 6.948886 TGGTCCTATAAAGCAATTTGTAACCA 59.051 34.615 0.00 0.00 0.00 3.67
5285 12621 7.175293 TCCTATAAAGCAATTTGTAACCACGTT 59.825 33.333 0.00 0.00 0.00 3.99
5339 12679 0.875059 GCAGACCACCGAGAAAAAGG 59.125 55.000 0.00 0.00 0.00 3.11
5343 12683 3.630312 CAGACCACCGAGAAAAAGGAAAA 59.370 43.478 0.00 0.00 0.00 2.29
5350 12690 5.515270 CACCGAGAAAAAGGAAAAGTCAAAC 59.485 40.000 0.00 0.00 0.00 2.93
5351 12691 5.184287 ACCGAGAAAAAGGAAAAGTCAAACA 59.816 36.000 0.00 0.00 0.00 2.83
5451 12809 8.303876 GCAGTTCCAGGTAATTTATTTCTGAAA 58.696 33.333 5.15 5.15 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.031163 GAGGCAGCACCAAGACGT 59.969 61.111 0.00 0.00 43.14 4.34
2 3 2.486636 TACGAGGCAGCACCAAGACG 62.487 60.000 0.00 0.00 43.14 4.18
3 4 0.320421 TTACGAGGCAGCACCAAGAC 60.320 55.000 0.00 0.00 43.14 3.01
5 6 1.131126 CATTTACGAGGCAGCACCAAG 59.869 52.381 0.00 0.00 43.14 3.61
6 7 1.164411 CATTTACGAGGCAGCACCAA 58.836 50.000 0.00 0.00 43.14 3.67
7 8 1.305219 GCATTTACGAGGCAGCACCA 61.305 55.000 0.00 0.00 43.14 4.17
8 9 1.305219 TGCATTTACGAGGCAGCACC 61.305 55.000 0.00 0.00 39.61 5.01
9 10 0.179189 GTGCATTTACGAGGCAGCAC 60.179 55.000 10.15 10.15 44.31 4.40
10 11 0.605050 TGTGCATTTACGAGGCAGCA 60.605 50.000 0.00 0.00 38.38 4.41
11 12 0.179189 GTGTGCATTTACGAGGCAGC 60.179 55.000 0.00 0.00 38.38 5.25
12 13 0.095245 CGTGTGCATTTACGAGGCAG 59.905 55.000 13.62 0.00 42.54 4.85
13 14 1.906994 GCGTGTGCATTTACGAGGCA 61.907 55.000 20.41 0.00 42.54 4.75
14 15 1.226018 GCGTGTGCATTTACGAGGC 60.226 57.895 20.41 4.09 42.54 4.70
15 16 0.796312 AAGCGTGTGCATTTACGAGG 59.204 50.000 20.41 0.00 46.23 4.63
16 17 2.594529 AAAGCGTGTGCATTTACGAG 57.405 45.000 20.41 0.00 46.23 4.18
17 18 3.341857 AAAAAGCGTGTGCATTTACGA 57.658 38.095 20.41 0.00 40.81 3.43
50 51 6.071616 TGTTGCAGTAATGGAAAAGGGTAATC 60.072 38.462 0.00 0.00 0.00 1.75
58 59 5.473846 TCCGTTATGTTGCAGTAATGGAAAA 59.526 36.000 19.17 0.00 40.96 2.29
158 159 2.602456 CCGGTGAGTAATCTCGATGACG 60.602 54.545 0.00 0.00 43.09 4.35
189 192 2.708051 ACTGAGATTAGGTGTCGTCGA 58.292 47.619 0.00 0.00 0.00 4.20
250 253 0.460811 CAGCTGTTGCGAGCCATCTA 60.461 55.000 5.25 0.00 45.42 1.98
254 261 2.357881 CTCAGCTGTTGCGAGCCA 60.358 61.111 14.67 0.00 45.42 4.75
307 315 5.652014 CCCATGGTTTAGCTAGATGTTTGAA 59.348 40.000 11.73 0.00 0.00 2.69
351 360 0.242825 CCATGATGAATCGGCATGCC 59.757 55.000 27.67 27.67 38.40 4.40
446 455 3.611057 GCAAGACTGTTGAAGCAAGATGG 60.611 47.826 0.00 0.00 0.00 3.51
459 468 1.488812 TGTGTTACTGGGCAAGACTGT 59.511 47.619 0.00 0.00 0.00 3.55
465 474 3.244735 TGCTCTAATGTGTTACTGGGCAA 60.245 43.478 0.00 0.00 0.00 4.52
475 484 1.625315 TCTGCCTGTGCTCTAATGTGT 59.375 47.619 0.00 0.00 38.71 3.72
512 521 7.789273 TCGAGTTTAAACCACTTACAAATCA 57.211 32.000 14.72 0.00 0.00 2.57
529 538 4.434520 GCAATAGAGCTACCTTCGAGTTT 58.565 43.478 0.00 0.00 0.00 2.66
609 618 3.069729 GGTGCTATACGTTCTTCCCTGAT 59.930 47.826 0.00 0.00 0.00 2.90
610 619 2.429610 GGTGCTATACGTTCTTCCCTGA 59.570 50.000 0.00 0.00 0.00 3.86
634 644 5.350633 TGATAACATTTGGCAAGCTTATGC 58.649 37.500 0.00 0.00 45.67 3.14
659 669 3.316283 CAAGGCGTGCATTTAATGTGTT 58.684 40.909 6.81 0.00 0.00 3.32
672 682 3.114616 CTGGTCGAGCAAGGCGTG 61.115 66.667 19.16 1.62 0.00 5.34
673 683 3.165160 AACTGGTCGAGCAAGGCGT 62.165 57.895 19.16 10.01 0.00 5.68
674 684 2.357517 AACTGGTCGAGCAAGGCG 60.358 61.111 19.16 9.33 0.00 5.52
675 685 1.569479 GACAACTGGTCGAGCAAGGC 61.569 60.000 19.16 9.94 36.65 4.35
676 686 2.533318 GACAACTGGTCGAGCAAGG 58.467 57.895 19.16 10.45 36.65 3.61
684 694 1.865340 GGTGAAAGACGACAACTGGTC 59.135 52.381 0.00 0.00 43.36 4.02
685 695 1.208535 TGGTGAAAGACGACAACTGGT 59.791 47.619 0.00 0.00 0.00 4.00
686 696 1.948104 TGGTGAAAGACGACAACTGG 58.052 50.000 0.00 0.00 0.00 4.00
687 697 3.849645 GCATTGGTGAAAGACGACAACTG 60.850 47.826 0.00 0.00 0.00 3.16
688 698 2.290641 GCATTGGTGAAAGACGACAACT 59.709 45.455 0.00 0.00 0.00 3.16
689 699 2.032799 TGCATTGGTGAAAGACGACAAC 59.967 45.455 0.00 0.00 0.00 3.32
690 700 2.293170 TGCATTGGTGAAAGACGACAA 58.707 42.857 0.00 0.00 0.00 3.18
691 701 1.960417 TGCATTGGTGAAAGACGACA 58.040 45.000 0.00 0.00 0.00 4.35
692 702 2.483877 TCATGCATTGGTGAAAGACGAC 59.516 45.455 0.00 0.00 0.00 4.34
693 703 2.743664 CTCATGCATTGGTGAAAGACGA 59.256 45.455 0.00 0.00 0.00 4.20
694 704 2.743664 TCTCATGCATTGGTGAAAGACG 59.256 45.455 0.00 0.00 0.00 4.18
695 705 4.380233 CCTTCTCATGCATTGGTGAAAGAC 60.380 45.833 0.00 0.00 0.00 3.01
696 706 3.760151 CCTTCTCATGCATTGGTGAAAGA 59.240 43.478 0.00 0.00 0.00 2.52
697 707 3.119245 CCCTTCTCATGCATTGGTGAAAG 60.119 47.826 0.00 0.48 0.00 2.62
698 708 2.827322 CCCTTCTCATGCATTGGTGAAA 59.173 45.455 0.00 0.00 0.00 2.69
699 709 2.225091 ACCCTTCTCATGCATTGGTGAA 60.225 45.455 0.00 0.00 0.00 3.18
700 710 1.355381 ACCCTTCTCATGCATTGGTGA 59.645 47.619 0.00 0.00 0.00 4.02
701 711 1.843368 ACCCTTCTCATGCATTGGTG 58.157 50.000 0.00 0.00 0.00 4.17
702 712 2.450476 GAACCCTTCTCATGCATTGGT 58.550 47.619 0.00 0.00 0.00 3.67
703 713 1.402968 CGAACCCTTCTCATGCATTGG 59.597 52.381 0.00 0.00 0.00 3.16
704 714 1.402968 CCGAACCCTTCTCATGCATTG 59.597 52.381 0.00 0.00 0.00 2.82
705 715 1.004745 ACCGAACCCTTCTCATGCATT 59.995 47.619 0.00 0.00 0.00 3.56
706 716 0.620556 ACCGAACCCTTCTCATGCAT 59.379 50.000 0.00 0.00 0.00 3.96
707 717 0.036388 GACCGAACCCTTCTCATGCA 60.036 55.000 0.00 0.00 0.00 3.96
708 718 0.036388 TGACCGAACCCTTCTCATGC 60.036 55.000 0.00 0.00 0.00 4.06
709 719 1.550524 TCTGACCGAACCCTTCTCATG 59.449 52.381 0.00 0.00 0.00 3.07
710 720 1.938585 TCTGACCGAACCCTTCTCAT 58.061 50.000 0.00 0.00 0.00 2.90
711 721 1.712056 TTCTGACCGAACCCTTCTCA 58.288 50.000 0.00 0.00 0.00 3.27
712 722 2.233922 TGATTCTGACCGAACCCTTCTC 59.766 50.000 0.00 0.00 33.72 2.87
713 723 2.257207 TGATTCTGACCGAACCCTTCT 58.743 47.619 0.00 0.00 33.72 2.85
714 724 2.762535 TGATTCTGACCGAACCCTTC 57.237 50.000 0.00 0.00 33.72 3.46
715 725 3.502123 TTTGATTCTGACCGAACCCTT 57.498 42.857 0.00 0.00 33.72 3.95
716 726 3.502123 TTTTGATTCTGACCGAACCCT 57.498 42.857 0.00 0.00 33.72 4.34
717 727 3.119495 CCATTTTGATTCTGACCGAACCC 60.119 47.826 0.00 0.00 33.72 4.11
718 728 3.756434 TCCATTTTGATTCTGACCGAACC 59.244 43.478 0.00 0.00 33.72 3.62
719 729 5.371115 TTCCATTTTGATTCTGACCGAAC 57.629 39.130 0.00 0.00 33.72 3.95
720 730 6.434028 AGATTTCCATTTTGATTCTGACCGAA 59.566 34.615 0.00 0.00 35.78 4.30
721 731 5.945784 AGATTTCCATTTTGATTCTGACCGA 59.054 36.000 0.00 0.00 0.00 4.69
722 732 6.199937 AGATTTCCATTTTGATTCTGACCG 57.800 37.500 0.00 0.00 0.00 4.79
772 782 9.388346 CTTAAGCGTCATATATATGCTACTAGC 57.612 37.037 16.59 13.78 38.24 3.42
773 783 9.885934 CCTTAAGCGTCATATATATGCTACTAG 57.114 37.037 16.59 9.06 38.24 2.57
774 784 8.350722 GCCTTAAGCGTCATATATATGCTACTA 58.649 37.037 16.59 0.00 38.24 1.82
775 785 7.203910 GCCTTAAGCGTCATATATATGCTACT 58.796 38.462 16.59 10.52 38.24 2.57
776 786 7.396190 GCCTTAAGCGTCATATATATGCTAC 57.604 40.000 16.59 10.32 38.24 3.58
807 817 4.517285 TCATCATTTGCCTGAAGTCCTAC 58.483 43.478 0.00 0.00 0.00 3.18
817 827 2.097825 GAGCCAACTCATCATTTGCCT 58.902 47.619 0.00 0.00 42.93 4.75
830 840 1.522580 GGCCATCTCTCGAGCCAAC 60.523 63.158 7.81 0.00 45.07 3.77
860 871 2.653115 GCTTGGAAGCCCAACTGC 59.347 61.111 0.00 0.00 46.94 4.40
890 917 0.104120 GGGCTTTTGTGCTTCGGTTT 59.896 50.000 0.00 0.00 0.00 3.27
981 1010 2.506472 TTTTTGGGTTTGCCGCCC 59.494 55.556 0.83 0.83 46.26 6.13
1004 1048 3.528370 CGTGTAGGGGAGGAGGCG 61.528 72.222 0.00 0.00 0.00 5.52
1005 1049 2.043248 TCGTGTAGGGGAGGAGGC 60.043 66.667 0.00 0.00 0.00 4.70
1018 1066 2.734723 CAGGTGCGTGAGGTCGTG 60.735 66.667 0.00 0.00 0.00 4.35
1523 1834 2.811873 GCATGCTATTCGGGGAGAACAT 60.812 50.000 11.37 0.00 42.39 2.71
1573 1884 2.451490 TGTTTGGAAGTGGCAGTTTCA 58.549 42.857 12.09 12.09 0.00 2.69
1575 1886 3.260632 AGTTTGTTTGGAAGTGGCAGTTT 59.739 39.130 9.30 0.00 0.00 2.66
1576 1887 2.831526 AGTTTGTTTGGAAGTGGCAGTT 59.168 40.909 7.41 7.41 0.00 3.16
1577 1888 2.456577 AGTTTGTTTGGAAGTGGCAGT 58.543 42.857 0.00 0.00 0.00 4.40
1578 1889 3.525268 AAGTTTGTTTGGAAGTGGCAG 57.475 42.857 0.00 0.00 0.00 4.85
1579 1890 3.971245 AAAGTTTGTTTGGAAGTGGCA 57.029 38.095 0.00 0.00 0.00 4.92
1580 1891 4.098807 TCCTAAAGTTTGTTTGGAAGTGGC 59.901 41.667 0.00 0.00 30.76 5.01
1581 1892 5.221244 CCTCCTAAAGTTTGTTTGGAAGTGG 60.221 44.000 0.00 0.00 32.97 4.00
1582 1893 5.736207 GCCTCCTAAAGTTTGTTTGGAAGTG 60.736 44.000 0.00 0.00 32.97 3.16
1583 1894 4.341235 GCCTCCTAAAGTTTGTTTGGAAGT 59.659 41.667 0.00 0.00 32.97 3.01
1584 1895 4.584743 AGCCTCCTAAAGTTTGTTTGGAAG 59.415 41.667 0.00 0.00 32.97 3.46
1585 1896 4.340950 CAGCCTCCTAAAGTTTGTTTGGAA 59.659 41.667 0.00 0.00 32.97 3.53
1586 1897 3.888930 CAGCCTCCTAAAGTTTGTTTGGA 59.111 43.478 0.00 0.53 32.49 3.53
1587 1898 3.888930 TCAGCCTCCTAAAGTTTGTTTGG 59.111 43.478 0.00 0.00 0.00 3.28
1588 1899 5.010012 ACATCAGCCTCCTAAAGTTTGTTTG 59.990 40.000 0.00 0.00 0.00 2.93
1589 1900 5.140454 ACATCAGCCTCCTAAAGTTTGTTT 58.860 37.500 0.00 0.00 0.00 2.83
1590 1901 4.729868 ACATCAGCCTCCTAAAGTTTGTT 58.270 39.130 0.00 0.00 0.00 2.83
1591 1902 4.373156 ACATCAGCCTCCTAAAGTTTGT 57.627 40.909 0.00 0.00 0.00 2.83
1592 1903 8.682936 ATAATACATCAGCCTCCTAAAGTTTG 57.317 34.615 0.00 0.00 0.00 2.93
1681 1992 2.451490 CTACAGCCTGAGGAAGTGAGA 58.549 52.381 0.65 0.00 0.00 3.27
1746 2058 1.256117 CGCAACTGCACAAAAGAAAGC 59.744 47.619 2.12 0.00 42.21 3.51
1934 2258 0.749454 GCGGGATTGAGCCATCACTT 60.749 55.000 0.00 0.00 34.35 3.16
2113 2488 8.956426 GTTAAGATCAATGTACATTTCTGGGAA 58.044 33.333 18.50 11.61 0.00 3.97
2150 2564 8.865590 ACTCGCAAAACAGTACAATTATTTTT 57.134 26.923 0.00 0.00 0.00 1.94
2155 2569 9.205719 TGTATTACTCGCAAAACAGTACAATTA 57.794 29.630 0.00 0.00 0.00 1.40
2171 2585 8.276325 GCCAATAACTCAAGATTGTATTACTCG 58.724 37.037 0.00 0.00 32.22 4.18
2177 2591 7.944729 AAGTGCCAATAACTCAAGATTGTAT 57.055 32.000 0.00 0.00 32.22 2.29
2213 2630 4.811557 GGATCACCTAATGTAAGCACAGAC 59.188 45.833 0.00 0.00 38.30 3.51
2236 2653 7.630242 TCTCAAATTAGGCAACAGGATAAAG 57.370 36.000 0.00 0.00 41.41 1.85
2298 2718 5.568296 CACACAAACCAAAAATGCAAAACAG 59.432 36.000 0.00 0.00 0.00 3.16
2660 3255 7.062255 GGCTCAAGACATAACACTTTTAATTGC 59.938 37.037 0.00 0.00 0.00 3.56
2736 3331 1.593196 TTCAAGAGTTCACTTGGCCG 58.407 50.000 0.00 0.00 44.84 6.13
2753 3348 7.448748 TGAGGTAGTTTAAATCCAAGCTTTC 57.551 36.000 0.00 0.00 0.00 2.62
3032 3645 8.172741 ACCCCTGCAATCAGAAATAATATACAT 58.827 33.333 0.00 0.00 42.95 2.29
3273 10380 3.799963 GCTTGTTTTACCCAAGAAAACCG 59.200 43.478 4.43 2.28 43.21 4.44
3302 10412 8.514594 TGATTGTATGTTTTTCCATGAAGAGTC 58.485 33.333 0.00 0.00 0.00 3.36
3390 10508 5.614324 AGCATACCAAGCAGAACTGTATA 57.386 39.130 3.77 0.00 0.00 1.47
3818 10954 6.106673 ACACATTAAGTTTCTCTGTATCCCG 58.893 40.000 0.00 0.00 0.00 5.14
3977 11113 1.208776 CACCCCTAAAGGAACCCGTAG 59.791 57.143 0.00 0.00 38.24 3.51
4152 11288 3.826729 ACCACTTAAAGCCCATCTTTCAC 59.173 43.478 0.00 0.00 43.55 3.18
4365 11501 8.528643 GCCCTTTATTAGTCCAGTTTAACAATT 58.471 33.333 0.00 0.00 0.00 2.32
4537 11676 1.961277 CCACAGTTCACGTCCAGCC 60.961 63.158 0.00 0.00 0.00 4.85
4754 11893 6.186420 TGCATGGCCTAATTTATGTCTCTA 57.814 37.500 3.32 0.00 0.00 2.43
4755 11894 5.052693 TGCATGGCCTAATTTATGTCTCT 57.947 39.130 3.32 0.00 0.00 3.10
4758 11897 5.906073 ACTTTGCATGGCCTAATTTATGTC 58.094 37.500 3.32 0.00 0.00 3.06
4768 11907 5.126067 CAGTATTACTACTTTGCATGGCCT 58.874 41.667 3.32 0.00 35.99 5.19
4774 11913 9.884636 ACATGAATACAGTATTACTACTTTGCA 57.115 29.630 5.75 0.00 35.99 4.08
4792 11931 7.416817 CCGACAGATAAATTTGCACATGAATA 58.583 34.615 0.00 0.00 0.00 1.75
4810 11949 1.266178 TTCAGAATGGAGCCGACAGA 58.734 50.000 0.00 0.00 36.16 3.41
4828 11967 7.068593 TGACAGAAGAAATGAACTGGAAACATT 59.931 33.333 0.00 0.00 41.51 2.71
4944 12085 2.560981 CCTGCAAACGGGTAGGAAATTT 59.439 45.455 2.72 0.00 42.63 1.82
4980 12121 5.873712 ACATCAGTTGCTCAGTCAAGATAAG 59.126 40.000 0.00 0.00 0.00 1.73
4981 12122 5.798132 ACATCAGTTGCTCAGTCAAGATAA 58.202 37.500 0.00 0.00 0.00 1.75
4987 12128 9.098355 GTAAAATATACATCAGTTGCTCAGTCA 57.902 33.333 0.00 0.00 0.00 3.41
5029 12265 3.529533 AGAGATGCAGAGTAACATGTGC 58.470 45.455 0.00 0.00 39.78 4.57
5030 12266 5.008619 AGAGAGATGCAGAGTAACATGTG 57.991 43.478 0.00 0.00 0.00 3.21
5031 12267 5.890985 AGTAGAGAGATGCAGAGTAACATGT 59.109 40.000 0.00 0.00 0.00 3.21
5032 12268 6.389830 AGTAGAGAGATGCAGAGTAACATG 57.610 41.667 0.00 0.00 0.00 3.21
5033 12269 6.833416 AGAAGTAGAGAGATGCAGAGTAACAT 59.167 38.462 0.00 0.00 0.00 2.71
5046 12282 3.443329 CAGCAGCAAGAGAAGTAGAGAGA 59.557 47.826 0.00 0.00 0.00 3.10
5047 12283 3.772932 CAGCAGCAAGAGAAGTAGAGAG 58.227 50.000 0.00 0.00 0.00 3.20
5048 12284 2.094286 GCAGCAGCAAGAGAAGTAGAGA 60.094 50.000 0.00 0.00 41.58 3.10
5049 12285 2.270047 GCAGCAGCAAGAGAAGTAGAG 58.730 52.381 0.00 0.00 41.58 2.43
5050 12286 2.376808 GCAGCAGCAAGAGAAGTAGA 57.623 50.000 0.00 0.00 41.58 2.59
5075 12311 6.360370 TCAAGAATAGTTGGCTCAGTAACT 57.640 37.500 0.00 0.00 40.09 2.24
5124 12360 1.068895 CCAAATGCTTGCACTGGAACA 59.931 47.619 16.28 0.00 0.00 3.18
5172 12503 1.523758 AAAGCAGTTCGATCACCCAC 58.476 50.000 0.00 0.00 0.00 4.61
5182 12513 6.366061 GGTCATTTCCATTACAAAAGCAGTTC 59.634 38.462 0.00 0.00 0.00 3.01
5285 12621 9.474920 CAGCAAAGAAAATGATAAAGTTTACCA 57.525 29.630 0.00 0.00 0.00 3.25
5343 12683 9.366216 GTGAAGTTTCCTTAATTTTGTTTGACT 57.634 29.630 0.00 0.00 0.00 3.41
5350 12690 7.550906 TGTTTGGGTGAAGTTTCCTTAATTTTG 59.449 33.333 0.00 0.00 0.00 2.44
5351 12691 7.625469 TGTTTGGGTGAAGTTTCCTTAATTTT 58.375 30.769 0.00 0.00 0.00 1.82
5369 12713 4.605640 AACTGTGATTCCATTGTTTGGG 57.394 40.909 0.00 0.00 46.45 4.12
5370 12714 6.225318 ATCAAACTGTGATTCCATTGTTTGG 58.775 36.000 13.84 0.00 45.13 3.28
5397 12755 4.582656 TGGCACAAATAGCACTAACAAACT 59.417 37.500 0.00 0.00 31.92 2.66


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

AutoCloner maintained by Alex Coulton.