Multiple sequence alignment - TraesCS2D01G291300

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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 TraesCS2D01G291300 chr2D 100.000 3880 0 0 1 3880 373417632 373421511 0.000000e+00 7166
1 TraesCS2D01G291300 chr2D 79.492 551 72 22 10 533 160328545 160328009 1.710000e-93 353
2 TraesCS2D01G291300 chr2D 87.879 165 11 6 3347 3506 556927093 556926933 6.620000e-43 185
3 TraesCS2D01G291300 chr2D 85.906 149 21 0 3698 3846 325331702 325331554 4.010000e-35 159
4 TraesCS2D01G291300 chr2B 94.223 2683 104 26 913 3567 442914901 442917560 0.000000e+00 4048
5 TraesCS2D01G291300 chr2B 95.956 272 9 2 3610 3880 442917554 442917824 1.280000e-119 440
6 TraesCS2D01G291300 chr2B 88.095 168 12 5 3347 3509 608226725 608226889 3.960000e-45 193
7 TraesCS2D01G291300 chr2B 90.678 118 8 3 748 863 442914756 442914872 1.870000e-33 154
8 TraesCS2D01G291300 chr2A 92.843 2515 107 34 884 3370 504708968 504711437 0.000000e+00 3579
9 TraesCS2D01G291300 chr2A 96.175 183 7 0 3698 3880 504711849 504712031 2.270000e-77 300
10 TraesCS2D01G291300 chr2A 88.889 207 19 3 659 863 504708774 504708978 6.440000e-63 252
11 TraesCS2D01G291300 chr6B 81.900 663 81 23 3 629 671720371 671719712 1.240000e-144 523
12 TraesCS2D01G291300 chr6B 80.325 493 63 17 138 597 43061699 43061208 3.710000e-90 342
13 TraesCS2D01G291300 chr6B 85.185 162 23 1 3698 3859 157485759 157485599 8.620000e-37 165
14 TraesCS2D01G291300 chrUn 83.074 579 65 12 14 561 223002340 223001764 2.690000e-136 496
15 TraesCS2D01G291300 chrUn 84.400 500 50 12 14 488 17329413 17329909 2.110000e-127 466
16 TraesCS2D01G291300 chrUn 81.888 392 39 11 200 561 464287190 464286801 6.300000e-78 302
17 TraesCS2D01G291300 chrUn 87.719 171 14 5 3343 3510 96478222 96478388 3.960000e-45 193
18 TraesCS2D01G291300 chr1B 83.824 544 58 14 14 533 305248955 305249492 1.250000e-134 490
19 TraesCS2D01G291300 chr1B 81.445 609 70 20 26 597 15720307 15719705 3.530000e-125 459
20 TraesCS2D01G291300 chr3D 82.729 579 67 12 14 561 29493993 29493417 5.830000e-133 484
21 TraesCS2D01G291300 chr3D 82.383 579 69 12 14 561 29565862 29565286 1.260000e-129 473
22 TraesCS2D01G291300 chr3D 86.471 170 14 6 3347 3510 128214007 128214173 1.110000e-40 178
23 TraesCS2D01G291300 chr6D 83.457 538 61 13 14 525 82499741 82500276 3.510000e-130 475
24 TraesCS2D01G291300 chr6D 86.577 149 20 0 3698 3846 290949568 290949716 8.620000e-37 165
25 TraesCS2D01G291300 chr1D 82.601 546 67 14 14 533 443301950 443302493 1.270000e-124 457
26 TraesCS2D01G291300 chr1D 80.750 613 80 20 14 593 439108929 439108322 9.890000e-121 444
27 TraesCS2D01G291300 chr1A 80.480 625 83 19 5 593 535331276 535330655 3.560000e-120 442
28 TraesCS2D01G291300 chr4D 81.934 548 64 16 14 532 505502989 505502448 7.700000e-117 431
29 TraesCS2D01G291300 chr4D 87.248 149 19 0 3698 3846 269470277 269470425 1.850000e-38 171
30 TraesCS2D01G291300 chr7A 82.398 517 64 16 14 506 88035689 88035176 3.580000e-115 425
31 TraesCS2D01G291300 chr7D 81.190 521 70 13 5 499 54241284 54240766 1.010000e-105 394
32 TraesCS2D01G291300 chr7D 86.826 167 14 5 3345 3506 236831566 236831729 3.080000e-41 180
33 TraesCS2D01G291300 chr7D 88.095 84 10 0 450 533 77171434 77171351 2.470000e-17 100
34 TraesCS2D01G291300 chr5D 85.870 184 17 6 3335 3513 377987991 377988170 1.840000e-43 187
35 TraesCS2D01G291300 chr3A 86.982 169 14 5 3344 3507 510298650 510298815 2.380000e-42 183
36 TraesCS2D01G291300 chr3A 85.333 150 20 2 3698 3846 404654854 404655002 1.870000e-33 154
37 TraesCS2D01G291300 chr5A 87.273 165 13 5 3347 3506 653299440 653299601 8.560000e-42 182
38 TraesCS2D01G291300 chr4B 88.806 134 15 0 3698 3831 295702064 295702197 8.620000e-37 165
39 TraesCS2D01G291300 chr5B 86.047 129 18 0 3718 3846 656066657 656066529 5.230000e-29 139


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 TraesCS2D01G291300 chr2D 373417632 373421511 3879 False 7166.000000 7166 100.000000 1 3880 1 chr2D.!!$F1 3879
1 TraesCS2D01G291300 chr2D 160328009 160328545 536 True 353.000000 353 79.492000 10 533 1 chr2D.!!$R1 523
2 TraesCS2D01G291300 chr2B 442914756 442917824 3068 False 1547.333333 4048 93.619000 748 3880 3 chr2B.!!$F2 3132
3 TraesCS2D01G291300 chr2A 504708774 504712031 3257 False 1377.000000 3579 92.635667 659 3880 3 chr2A.!!$F1 3221
4 TraesCS2D01G291300 chr6B 671719712 671720371 659 True 523.000000 523 81.900000 3 629 1 chr6B.!!$R3 626
5 TraesCS2D01G291300 chrUn 223001764 223002340 576 True 496.000000 496 83.074000 14 561 1 chrUn.!!$R1 547
6 TraesCS2D01G291300 chr1B 305248955 305249492 537 False 490.000000 490 83.824000 14 533 1 chr1B.!!$F1 519
7 TraesCS2D01G291300 chr1B 15719705 15720307 602 True 459.000000 459 81.445000 26 597 1 chr1B.!!$R1 571
8 TraesCS2D01G291300 chr3D 29493417 29493993 576 True 484.000000 484 82.729000 14 561 1 chr3D.!!$R1 547
9 TraesCS2D01G291300 chr3D 29565286 29565862 576 True 473.000000 473 82.383000 14 561 1 chr3D.!!$R2 547
10 TraesCS2D01G291300 chr6D 82499741 82500276 535 False 475.000000 475 83.457000 14 525 1 chr6D.!!$F1 511
11 TraesCS2D01G291300 chr1D 443301950 443302493 543 False 457.000000 457 82.601000 14 533 1 chr1D.!!$F1 519
12 TraesCS2D01G291300 chr1D 439108322 439108929 607 True 444.000000 444 80.750000 14 593 1 chr1D.!!$R1 579
13 TraesCS2D01G291300 chr1A 535330655 535331276 621 True 442.000000 442 80.480000 5 593 1 chr1A.!!$R1 588
14 TraesCS2D01G291300 chr4D 505502448 505502989 541 True 431.000000 431 81.934000 14 532 1 chr4D.!!$R1 518
15 TraesCS2D01G291300 chr7A 88035176 88035689 513 True 425.000000 425 82.398000 14 506 1 chr7A.!!$R1 492
16 TraesCS2D01G291300 chr7D 54240766 54241284 518 True 394.000000 394 81.190000 5 499 1 chr7D.!!$R1 494

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
561 604 0.108898 CCACCTCTCAGCGTCAAGAG 60.109 60.0 3.88 3.88 39.00 2.85 F
656 699 0.111704 CGCGCGTCAAATAAGATCCG 60.112 55.0 24.19 0.00 0.00 4.18 F
860 903 0.179062 GAGCCCTGATTGCTCGTCAT 60.179 55.0 0.00 0.00 45.05 3.06 F
861 904 0.254178 AGCCCTGATTGCTCGTCATT 59.746 50.0 0.00 0.00 32.41 2.57 F
1335 1403 0.850883 TCCTGGGGCAAGAGGGATTT 60.851 55.0 0.00 0.00 0.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1510 1578 1.202545 GGAACAATAGGGAGAGACGCC 60.203 57.143 0.00 0.00 0.00 5.68 R
1607 1678 1.896660 GCCACGCCTTTTCCTGTCA 60.897 57.895 0.00 0.00 0.00 3.58 R
2342 2413 2.018515 AGACTAGCGAGACTAACAGCC 58.981 52.381 0.00 0.00 0.00 4.85 R
2770 2841 3.226346 TGCTGATCTTTTTCTGCATGC 57.774 42.857 11.82 11.82 43.09 4.06 R
3272 3349 1.002134 AGGGGGTCATTGCAGTTCG 60.002 57.895 0.00 0.00 0.00 3.95 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
65 67 8.512138 ACCTAAAATCCAAGAAAATACGAAGTG 58.488 33.333 0.00 0.00 45.73 3.16
69 71 8.842358 AAATCCAAGAAAATACGAAGTGACTA 57.158 30.769 0.00 0.00 45.73 2.59
108 110 8.909708 TTATAATGAAATTTCTTGGAAGCACG 57.090 30.769 18.64 0.00 37.87 5.34
129 132 5.466432 CGTCTTCACTACGTCAATCTCTA 57.534 43.478 0.00 0.00 35.66 2.43
145 148 8.617809 GTCAATCTCTACTCGAAGAAATACTCT 58.382 37.037 0.00 0.00 34.09 3.24
198 204 1.873591 GGAGCAACGATGTTGTCACTT 59.126 47.619 10.96 0.00 0.00 3.16
221 227 3.066291 TCACCCGCACAAACATTATCT 57.934 42.857 0.00 0.00 0.00 1.98
308 315 2.368192 TTGGGCCGGGGATGATCT 60.368 61.111 2.18 0.00 0.00 2.75
310 317 2.113986 GGGCCGGGGATGATCTTG 59.886 66.667 2.18 0.00 0.00 3.02
347 354 5.048643 CCGTCGAATCACTATATCTTCACCT 60.049 44.000 0.00 0.00 0.00 4.00
348 355 6.081049 CGTCGAATCACTATATCTTCACCTC 58.919 44.000 0.00 0.00 0.00 3.85
364 376 8.792830 TCTTCACCTCGATAAAAAGATTTCAT 57.207 30.769 0.00 0.00 0.00 2.57
427 460 7.386025 CACAACAACATAAACTCATCTGAGAGA 59.614 37.037 13.94 0.00 44.74 3.10
520 555 6.456795 TGATCACTAGACAATGACGAAGAT 57.543 37.500 0.00 0.00 0.00 2.40
528 563 5.527951 AGACAATGACGAAGATCATAGAGC 58.472 41.667 0.00 0.00 38.40 4.09
561 604 0.108898 CCACCTCTCAGCGTCAAGAG 60.109 60.000 3.88 3.88 39.00 2.85
562 605 0.884514 CACCTCTCAGCGTCAAGAGA 59.115 55.000 10.44 0.00 41.28 3.10
563 606 1.270826 CACCTCTCAGCGTCAAGAGAA 59.729 52.381 10.44 0.00 41.28 2.87
567 610 1.957177 TCTCAGCGTCAAGAGAACAGT 59.043 47.619 0.00 0.00 37.91 3.55
576 619 1.532868 CAAGAGAACAGTCAAAGGCGG 59.467 52.381 0.00 0.00 0.00 6.13
577 620 1.048601 AGAGAACAGTCAAAGGCGGA 58.951 50.000 0.00 0.00 0.00 5.54
578 621 1.149148 GAGAACAGTCAAAGGCGGAC 58.851 55.000 0.00 0.00 35.50 4.79
600 643 6.218108 ACGGACCTAAATTTCTTAGACGAT 57.782 37.500 0.00 0.00 0.00 3.73
601 644 6.040878 ACGGACCTAAATTTCTTAGACGATG 58.959 40.000 0.00 0.00 0.00 3.84
603 646 6.924060 CGGACCTAAATTTCTTAGACGATGAT 59.076 38.462 0.00 0.00 0.00 2.45
605 648 7.926555 GGACCTAAATTTCTTAGACGATGATGA 59.073 37.037 0.00 0.00 0.00 2.92
606 649 8.649973 ACCTAAATTTCTTAGACGATGATGAC 57.350 34.615 0.00 0.00 0.00 3.06
610 653 1.337071 TCTTAGACGATGATGACGGCC 59.663 52.381 0.00 0.00 39.85 6.13
629 672 0.165944 CGCGCAAGAAACCCTAGTTG 59.834 55.000 8.75 0.00 43.02 3.16
630 673 1.519408 GCGCAAGAAACCCTAGTTGA 58.481 50.000 0.30 0.00 43.02 3.18
631 674 1.197036 GCGCAAGAAACCCTAGTTGAC 59.803 52.381 0.30 0.00 43.02 3.18
632 675 1.459592 CGCAAGAAACCCTAGTTGACG 59.540 52.381 0.00 0.00 43.02 4.35
633 676 2.762745 GCAAGAAACCCTAGTTGACGA 58.237 47.619 0.00 0.00 35.97 4.20
634 677 2.479275 GCAAGAAACCCTAGTTGACGAC 59.521 50.000 0.00 0.00 35.97 4.34
635 678 2.719426 AGAAACCCTAGTTGACGACG 57.281 50.000 0.00 0.00 35.97 5.12
636 679 1.271656 AGAAACCCTAGTTGACGACGG 59.728 52.381 0.00 0.00 35.97 4.79
637 680 0.320160 AAACCCTAGTTGACGACGGC 60.320 55.000 0.00 0.00 35.97 5.68
638 681 2.202570 CCCTAGTTGACGACGGCG 60.203 66.667 10.39 10.39 44.79 6.46
639 682 2.879462 CCTAGTTGACGACGGCGC 60.879 66.667 12.58 3.84 42.48 6.53
640 683 3.238241 CTAGTTGACGACGGCGCG 61.238 66.667 12.58 19.04 42.48 6.86
649 692 3.547313 GACGGCGCGCGTCAAATA 61.547 61.111 34.37 0.00 36.49 1.40
650 693 3.073874 GACGGCGCGCGTCAAATAA 62.074 57.895 34.37 0.00 36.49 1.40
651 694 2.349648 CGGCGCGCGTCAAATAAG 60.350 61.111 35.03 13.19 0.00 1.73
652 695 2.794355 CGGCGCGCGTCAAATAAGA 61.794 57.895 35.03 0.00 0.00 2.10
653 696 1.641677 GGCGCGCGTCAAATAAGAT 59.358 52.632 31.92 0.00 0.00 2.40
654 697 0.383124 GGCGCGCGTCAAATAAGATC 60.383 55.000 31.92 8.43 0.00 2.75
655 698 0.383124 GCGCGCGTCAAATAAGATCC 60.383 55.000 32.35 5.47 0.00 3.36
656 699 0.111704 CGCGCGTCAAATAAGATCCG 60.112 55.000 24.19 0.00 0.00 4.18
657 700 0.383124 GCGCGTCAAATAAGATCCGC 60.383 55.000 8.43 0.00 37.91 5.54
658 701 0.232303 CGCGTCAAATAAGATCCGCC 59.768 55.000 0.00 0.00 38.01 6.13
659 702 0.586802 GCGTCAAATAAGATCCGCCC 59.413 55.000 0.00 0.00 35.45 6.13
660 703 1.226746 CGTCAAATAAGATCCGCCCC 58.773 55.000 0.00 0.00 0.00 5.80
661 704 1.202651 CGTCAAATAAGATCCGCCCCT 60.203 52.381 0.00 0.00 0.00 4.79
662 705 2.745152 CGTCAAATAAGATCCGCCCCTT 60.745 50.000 0.00 0.00 0.00 3.95
663 706 3.493699 CGTCAAATAAGATCCGCCCCTTA 60.494 47.826 0.00 0.00 0.00 2.69
664 707 4.457466 GTCAAATAAGATCCGCCCCTTAA 58.543 43.478 0.00 0.00 0.00 1.85
665 708 4.275196 GTCAAATAAGATCCGCCCCTTAAC 59.725 45.833 0.00 0.00 0.00 2.01
666 709 4.080243 TCAAATAAGATCCGCCCCTTAACA 60.080 41.667 0.00 0.00 0.00 2.41
667 710 2.994186 TAAGATCCGCCCCTTAACAC 57.006 50.000 0.00 0.00 0.00 3.32
668 711 0.255033 AAGATCCGCCCCTTAACACC 59.745 55.000 0.00 0.00 0.00 4.16
669 712 0.912487 AGATCCGCCCCTTAACACCA 60.912 55.000 0.00 0.00 0.00 4.17
670 713 0.746923 GATCCGCCCCTTAACACCAC 60.747 60.000 0.00 0.00 0.00 4.16
671 714 2.530958 ATCCGCCCCTTAACACCACG 62.531 60.000 0.00 0.00 0.00 4.94
672 715 3.428282 CGCCCCTTAACACCACGC 61.428 66.667 0.00 0.00 0.00 5.34
673 716 3.428282 GCCCCTTAACACCACGCG 61.428 66.667 3.53 3.53 0.00 6.01
674 717 2.344500 CCCCTTAACACCACGCGA 59.656 61.111 15.93 0.00 0.00 5.87
675 718 1.301874 CCCCTTAACACCACGCGAA 60.302 57.895 15.93 0.00 0.00 4.70
676 719 1.296056 CCCCTTAACACCACGCGAAG 61.296 60.000 15.93 5.72 0.00 3.79
689 732 4.110493 CGAAGCGATGAAGGGTCC 57.890 61.111 0.00 0.00 0.00 4.46
697 740 1.003118 CGATGAAGGGTCCCTGTTTCA 59.997 52.381 12.53 12.43 32.13 2.69
698 741 2.437413 GATGAAGGGTCCCTGTTTCAC 58.563 52.381 12.53 3.42 32.13 3.18
706 749 2.268076 CCCTGTTTCACGGGCCAAG 61.268 63.158 4.39 0.00 43.40 3.61
719 762 2.115910 CCAAGACCAAGCAGGCCA 59.884 61.111 5.01 0.00 43.14 5.36
734 777 1.173913 GGCCACATTAACAGTCACCC 58.826 55.000 0.00 0.00 0.00 4.61
743 786 6.036083 CACATTAACAGTCACCCGAGAAATAG 59.964 42.308 0.00 0.00 0.00 1.73
749 792 2.232941 GTCACCCGAGAAATAGTCCACA 59.767 50.000 0.00 0.00 0.00 4.17
802 845 2.098117 CCCAAATGGCTGAGATCGTTTC 59.902 50.000 0.00 0.00 0.00 2.78
805 848 2.215907 ATGGCTGAGATCGTTTCGAG 57.784 50.000 0.00 0.00 39.91 4.04
854 897 3.424105 GGGGGAGCCCTGATTGCT 61.424 66.667 5.38 0.00 44.66 3.91
858 901 4.116878 GAGCCCTGATTGCTCGTC 57.883 61.111 0.00 0.00 45.05 4.20
859 902 1.219124 GAGCCCTGATTGCTCGTCA 59.781 57.895 0.00 0.00 45.05 4.35
860 903 0.179062 GAGCCCTGATTGCTCGTCAT 60.179 55.000 0.00 0.00 45.05 3.06
861 904 0.254178 AGCCCTGATTGCTCGTCATT 59.746 50.000 0.00 0.00 32.41 2.57
862 905 1.098050 GCCCTGATTGCTCGTCATTT 58.902 50.000 0.00 0.00 0.00 2.32
863 906 1.064654 GCCCTGATTGCTCGTCATTTC 59.935 52.381 0.00 0.00 0.00 2.17
864 907 2.636830 CCCTGATTGCTCGTCATTTCT 58.363 47.619 0.00 0.00 0.00 2.52
865 908 3.012518 CCCTGATTGCTCGTCATTTCTT 58.987 45.455 0.00 0.00 0.00 2.52
866 909 3.441572 CCCTGATTGCTCGTCATTTCTTT 59.558 43.478 0.00 0.00 0.00 2.52
867 910 4.082571 CCCTGATTGCTCGTCATTTCTTTT 60.083 41.667 0.00 0.00 0.00 2.27
868 911 5.464168 CCTGATTGCTCGTCATTTCTTTTT 58.536 37.500 0.00 0.00 0.00 1.94
888 931 1.503818 TTTCGGAACAAGGTGCTCGC 61.504 55.000 0.00 0.00 0.00 5.03
911 954 2.535934 TTTAGCGCCGCATAAACTTG 57.464 45.000 13.36 0.00 0.00 3.16
934 987 6.630131 TGGAAGGAGATAACAGGGACATATA 58.370 40.000 0.00 0.00 0.00 0.86
967 1027 4.991056 CGAACTCCTGAAACAATCAAGAGA 59.009 41.667 10.23 0.00 45.70 3.10
974 1034 5.484173 TGAAACAATCAAGAGACACACAC 57.516 39.130 0.00 0.00 34.30 3.82
975 1035 4.940654 TGAAACAATCAAGAGACACACACA 59.059 37.500 0.00 0.00 34.30 3.72
976 1036 5.065090 TGAAACAATCAAGAGACACACACAG 59.935 40.000 0.00 0.00 34.30 3.66
1322 1389 2.450320 CCTGGGATCTGCTCCTGGG 61.450 68.421 0.00 0.00 44.28 4.45
1335 1403 0.850883 TCCTGGGGCAAGAGGGATTT 60.851 55.000 0.00 0.00 0.00 2.17
1351 1419 3.181483 GGGATTTGCAGATCCATGAACAC 60.181 47.826 31.16 13.08 46.11 3.32
1504 1572 3.555966 GGGAATTTCTGGATGGATCGTT 58.444 45.455 0.00 0.00 0.00 3.85
1534 1604 4.462133 CGTCTCTCCCTATTGTTCCTCTA 58.538 47.826 0.00 0.00 0.00 2.43
1562 1633 8.044908 TCTTTGGTACATCTTACATTTACTCCC 58.955 37.037 0.00 0.00 39.30 4.30
1574 1645 6.205101 ACATTTACTCCCTGTAGAACTACG 57.795 41.667 7.36 3.23 38.85 3.51
1587 1658 7.802251 CCTGTAGAACTACGTATTCCTAAATCG 59.198 40.741 0.00 0.00 38.85 3.34
1591 1662 8.108551 AGAACTACGTATTCCTAAATCGCTAT 57.891 34.615 0.00 0.00 0.00 2.97
1598 1669 6.349944 CGTATTCCTAAATCGCTATACACCCT 60.350 42.308 0.00 0.00 0.00 4.34
1607 1678 6.912951 ATCGCTATACACCCTAACATTACT 57.087 37.500 0.00 0.00 0.00 2.24
1611 1682 6.460537 CGCTATACACCCTAACATTACTGACA 60.461 42.308 0.00 0.00 0.00 3.58
1620 1691 5.123979 CCTAACATTACTGACAGGAAAAGGC 59.876 44.000 3.70 0.00 32.15 4.35
1632 1703 2.897326 AGGAAAAGGCGTGGCTTATTTT 59.103 40.909 9.23 0.29 0.00 1.82
1675 1746 7.302524 AGCATTGATTTTGAACATGAAATTGC 58.697 30.769 0.00 2.53 31.51 3.56
1694 1765 2.945008 TGCAAACTCTTGTGAGGTTCTG 59.055 45.455 0.00 0.00 46.39 3.02
1695 1766 2.945668 GCAAACTCTTGTGAGGTTCTGT 59.054 45.455 0.00 0.00 46.39 3.41
1696 1767 3.002759 GCAAACTCTTGTGAGGTTCTGTC 59.997 47.826 0.00 0.00 46.39 3.51
1697 1768 4.446371 CAAACTCTTGTGAGGTTCTGTCT 58.554 43.478 0.00 0.00 46.39 3.41
1724 1795 2.490903 GAGGCATATGCATGGATGAACC 59.509 50.000 28.07 7.92 44.36 3.62
1780 1851 8.800332 TGTAAAGTTTAACCCTGTTTGTTTGTA 58.200 29.630 0.00 0.00 0.00 2.41
1792 1863 8.764287 CCCTGTTTGTTTGTAATCTTTGAATTC 58.236 33.333 0.00 0.00 0.00 2.17
1799 1870 9.868277 TGTTTGTAATCTTTGAATTCAACTTGT 57.132 25.926 20.35 9.17 35.28 3.16
1833 1904 7.663081 AGTCTTATGGCTACATATGAAACATGG 59.337 37.037 10.38 6.39 42.12 3.66
1859 1930 2.810274 CCATTTCTGGCATATCGACTGG 59.190 50.000 0.00 0.00 35.23 4.00
2600 2671 7.989741 TCTTCCATTCAGATCCTTATGAACTTC 59.010 37.037 0.00 0.00 38.19 3.01
2770 2841 7.974675 ACATTCATCCTAACATCTTGTTTACG 58.025 34.615 0.00 0.00 41.45 3.18
3127 3202 3.767902 AGAGGATTTCTGCTATGGCTC 57.232 47.619 1.68 0.00 39.59 4.70
3148 3223 3.517901 TCGATTCCTCCATGTACCTTGTT 59.482 43.478 0.00 0.00 0.00 2.83
3259 3336 4.153986 GTGCATTTCTGATGACTGAAACG 58.846 43.478 0.00 0.00 43.10 3.60
3272 3349 5.437263 TGACTGAAACGTTCTTAAATTCGC 58.563 37.500 0.00 0.00 0.00 4.70
3285 3362 2.247311 AATTCGCGAACTGCAATGAC 57.753 45.000 26.00 0.00 46.97 3.06
3286 3363 0.447801 ATTCGCGAACTGCAATGACC 59.552 50.000 26.00 0.00 46.97 4.02
3358 3435 3.704566 TGATGCATACTACTTCCTCCGTT 59.295 43.478 0.00 0.00 0.00 4.44
3359 3436 4.161565 TGATGCATACTACTTCCTCCGTTT 59.838 41.667 0.00 0.00 0.00 3.60
3402 3479 8.915057 AGAGATTTCAATAAGGACCACATATG 57.085 34.615 0.00 0.00 0.00 1.78
3444 3525 6.246420 AGTGTAGATTCACTCATTTTGTGC 57.754 37.500 0.00 0.00 44.07 4.57
3447 3528 7.013655 AGTGTAGATTCACTCATTTTGTGCTTT 59.986 33.333 0.00 0.00 44.07 3.51
3448 3529 7.649306 GTGTAGATTCACTCATTTTGTGCTTTT 59.351 33.333 0.00 0.00 35.58 2.27
3449 3530 7.648908 TGTAGATTCACTCATTTTGTGCTTTTG 59.351 33.333 0.00 0.00 35.58 2.44
3529 3610 1.364626 GGAGCGCTGACATGAACTGG 61.365 60.000 18.48 0.00 0.00 4.00
3549 3630 4.264253 TGGTGCTGTAAGAATTCCATCAG 58.736 43.478 0.65 9.04 34.07 2.90
3567 3648 9.642327 TTCCATCAGTGATTACAAATTTCAATG 57.358 29.630 1.86 0.00 36.94 2.82
3568 3649 8.805175 TCCATCAGTGATTACAAATTTCAATGT 58.195 29.630 1.86 0.00 36.94 2.71
3569 3650 8.865978 CCATCAGTGATTACAAATTTCAATGTG 58.134 33.333 1.86 3.68 36.94 3.21
3570 3651 9.628746 CATCAGTGATTACAAATTTCAATGTGA 57.371 29.630 1.86 3.96 36.94 3.58
3571 3652 9.630098 ATCAGTGATTACAAATTTCAATGTGAC 57.370 29.630 0.00 0.00 36.94 3.67
3572 3653 8.849168 TCAGTGATTACAAATTTCAATGTGACT 58.151 29.630 4.89 0.96 36.94 3.41
3573 3654 8.908678 CAGTGATTACAAATTTCAATGTGACTG 58.091 33.333 0.00 0.00 32.46 3.51
3574 3655 8.084073 AGTGATTACAAATTTCAATGTGACTGG 58.916 33.333 0.00 0.00 0.00 4.00
3575 3656 7.867403 GTGATTACAAATTTCAATGTGACTGGT 59.133 33.333 0.00 0.00 0.00 4.00
3576 3657 7.866898 TGATTACAAATTTCAATGTGACTGGTG 59.133 33.333 0.00 0.00 0.00 4.17
3577 3658 4.370917 ACAAATTTCAATGTGACTGGTGC 58.629 39.130 0.00 0.00 0.00 5.01
3578 3659 3.665745 AATTTCAATGTGACTGGTGCC 57.334 42.857 0.00 0.00 0.00 5.01
3579 3660 0.950836 TTTCAATGTGACTGGTGCCG 59.049 50.000 0.00 0.00 0.00 5.69
3580 3661 0.179032 TTCAATGTGACTGGTGCCGT 60.179 50.000 0.00 0.00 0.00 5.68
3581 3662 0.179032 TCAATGTGACTGGTGCCGTT 60.179 50.000 0.00 0.00 0.00 4.44
3582 3663 0.238289 CAATGTGACTGGTGCCGTTC 59.762 55.000 0.00 0.00 0.00 3.95
3583 3664 0.889186 AATGTGACTGGTGCCGTTCC 60.889 55.000 0.00 0.00 0.00 3.62
3584 3665 2.050836 ATGTGACTGGTGCCGTTCCA 62.051 55.000 0.00 0.00 0.00 3.53
3589 3670 4.713946 TGGTGCCGTTCCAGAATC 57.286 55.556 0.00 0.00 0.00 2.52
3590 3671 1.757949 TGGTGCCGTTCCAGAATCA 59.242 52.632 0.00 0.00 0.00 2.57
3591 3672 0.109532 TGGTGCCGTTCCAGAATCAA 59.890 50.000 0.00 0.00 0.00 2.57
3592 3673 1.271871 TGGTGCCGTTCCAGAATCAAT 60.272 47.619 0.00 0.00 0.00 2.57
3593 3674 1.133025 GGTGCCGTTCCAGAATCAATG 59.867 52.381 0.00 0.00 0.00 2.82
3594 3675 1.812571 GTGCCGTTCCAGAATCAATGT 59.187 47.619 0.00 0.00 0.00 2.71
3595 3676 2.228822 GTGCCGTTCCAGAATCAATGTT 59.771 45.455 0.00 0.00 0.00 2.71
3596 3677 2.487762 TGCCGTTCCAGAATCAATGTTC 59.512 45.455 0.00 0.00 0.00 3.18
3597 3678 2.487762 GCCGTTCCAGAATCAATGTTCA 59.512 45.455 0.00 0.00 0.00 3.18
3598 3679 3.426695 GCCGTTCCAGAATCAATGTTCAG 60.427 47.826 0.00 0.00 0.00 3.02
3599 3680 3.753272 CCGTTCCAGAATCAATGTTCAGT 59.247 43.478 0.00 0.00 0.00 3.41
3600 3681 4.378770 CCGTTCCAGAATCAATGTTCAGTG 60.379 45.833 0.00 0.00 0.00 3.66
3601 3682 4.452114 CGTTCCAGAATCAATGTTCAGTGA 59.548 41.667 5.47 5.47 0.00 3.41
3602 3683 5.390251 CGTTCCAGAATCAATGTTCAGTGAG 60.390 44.000 8.75 0.00 0.00 3.51
3603 3684 5.488262 TCCAGAATCAATGTTCAGTGAGA 57.512 39.130 8.75 0.00 0.00 3.27
3604 3685 5.240891 TCCAGAATCAATGTTCAGTGAGAC 58.759 41.667 8.75 5.56 0.00 3.36
3605 3686 4.092529 CCAGAATCAATGTTCAGTGAGACG 59.907 45.833 8.75 0.00 0.00 4.18
3606 3687 4.092529 CAGAATCAATGTTCAGTGAGACGG 59.907 45.833 8.75 3.29 0.00 4.79
3607 3688 3.685139 ATCAATGTTCAGTGAGACGGT 57.315 42.857 8.75 0.00 0.00 4.83
3608 3689 2.754472 TCAATGTTCAGTGAGACGGTG 58.246 47.619 0.00 0.00 0.00 4.94
3609 3690 1.800586 CAATGTTCAGTGAGACGGTGG 59.199 52.381 0.00 0.00 0.00 4.61
3610 3691 1.048601 ATGTTCAGTGAGACGGTGGT 58.951 50.000 0.00 0.00 0.00 4.16
3611 3692 0.828022 TGTTCAGTGAGACGGTGGTT 59.172 50.000 0.00 0.00 0.00 3.67
3612 3693 1.202486 TGTTCAGTGAGACGGTGGTTC 60.202 52.381 0.00 0.00 0.00 3.62
3613 3694 0.391597 TTCAGTGAGACGGTGGTTCC 59.608 55.000 0.00 0.00 0.00 3.62
3614 3695 0.757561 TCAGTGAGACGGTGGTTCCA 60.758 55.000 0.00 0.00 35.57 3.53
3615 3696 0.105964 CAGTGAGACGGTGGTTCCAA 59.894 55.000 0.00 0.00 35.57 3.53
3616 3697 1.056660 AGTGAGACGGTGGTTCCAAT 58.943 50.000 0.00 0.00 35.57 3.16
3617 3698 2.028476 CAGTGAGACGGTGGTTCCAATA 60.028 50.000 0.00 0.00 35.57 1.90
3618 3699 2.028385 AGTGAGACGGTGGTTCCAATAC 60.028 50.000 0.00 0.00 35.57 1.89
3668 3749 0.966179 ATTTCCGCTTGTTTGGGTCC 59.034 50.000 0.00 0.00 0.00 4.46
3672 3809 1.377229 CGCTTGTTTGGGTCCCCTA 59.623 57.895 5.13 0.00 36.94 3.53
3747 3910 1.073763 TCATGTTTGGCTGGCACTACT 59.926 47.619 2.29 0.00 0.00 2.57
3748 3911 1.200716 CATGTTTGGCTGGCACTACTG 59.799 52.381 2.29 2.83 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 119 6.732531 TTTCTTCGAGTAGAGATTGACGTA 57.267 37.500 0.00 0.00 0.00 3.57
117 120 5.624344 TTTCTTCGAGTAGAGATTGACGT 57.376 39.130 0.00 0.00 0.00 4.34
145 148 4.817517 CAGCCTCTTTACCGAAGTCTTTA 58.182 43.478 0.00 0.00 36.70 1.85
198 204 2.969628 AATGTTTGTGCGGGTGAAAA 57.030 40.000 0.00 0.00 0.00 2.29
308 315 0.320421 GACGGCCTGCACTTCTACAA 60.320 55.000 0.00 0.00 0.00 2.41
310 317 1.805945 CGACGGCCTGCACTTCTAC 60.806 63.158 0.00 0.00 0.00 2.59
393 406 8.627487 TGAGTTTATGTTGTTGTGTCAAAATC 57.373 30.769 0.00 0.00 0.00 2.17
561 604 1.566018 CCGTCCGCCTTTGACTGTTC 61.566 60.000 0.00 0.00 0.00 3.18
562 605 1.597027 CCGTCCGCCTTTGACTGTT 60.597 57.895 0.00 0.00 0.00 3.16
563 606 2.030562 CCGTCCGCCTTTGACTGT 59.969 61.111 0.00 0.00 0.00 3.55
567 610 1.186917 TTAGGTCCGTCCGCCTTTGA 61.187 55.000 0.00 0.00 41.99 2.69
576 619 5.644644 TCGTCTAAGAAATTTAGGTCCGTC 58.355 41.667 0.00 0.00 0.00 4.79
577 620 5.649782 TCGTCTAAGAAATTTAGGTCCGT 57.350 39.130 0.00 0.00 0.00 4.69
578 621 6.270815 TCATCGTCTAAGAAATTTAGGTCCG 58.729 40.000 0.00 0.00 0.00 4.79
610 653 0.165944 CAACTAGGGTTTCTTGCGCG 59.834 55.000 0.00 0.00 32.73 6.86
619 662 1.291272 GCCGTCGTCAACTAGGGTT 59.709 57.895 0.00 0.00 35.86 4.11
634 677 2.089433 ATCTTATTTGACGCGCGCCG 62.089 55.000 32.58 22.51 44.21 6.46
635 678 0.383124 GATCTTATTTGACGCGCGCC 60.383 55.000 32.58 21.99 0.00 6.53
636 679 0.383124 GGATCTTATTTGACGCGCGC 60.383 55.000 32.58 23.91 0.00 6.86
637 680 0.111704 CGGATCTTATTTGACGCGCG 60.112 55.000 30.96 30.96 0.00 6.86
638 681 0.383124 GCGGATCTTATTTGACGCGC 60.383 55.000 5.73 0.00 37.60 6.86
639 682 3.710233 GCGGATCTTATTTGACGCG 57.290 52.632 3.53 3.53 37.60 6.01
640 683 0.586802 GGGCGGATCTTATTTGACGC 59.413 55.000 0.00 0.00 45.53 5.19
641 684 1.202651 AGGGGCGGATCTTATTTGACG 60.203 52.381 0.00 0.00 0.00 4.35
642 685 2.640316 AGGGGCGGATCTTATTTGAC 57.360 50.000 0.00 0.00 0.00 3.18
643 686 4.080243 TGTTAAGGGGCGGATCTTATTTGA 60.080 41.667 0.00 0.00 0.00 2.69
644 687 4.036380 GTGTTAAGGGGCGGATCTTATTTG 59.964 45.833 0.00 0.00 0.00 2.32
645 688 4.204799 GTGTTAAGGGGCGGATCTTATTT 58.795 43.478 0.00 0.00 0.00 1.40
646 689 3.434596 GGTGTTAAGGGGCGGATCTTATT 60.435 47.826 0.00 0.00 0.00 1.40
647 690 2.105993 GGTGTTAAGGGGCGGATCTTAT 59.894 50.000 0.00 0.00 0.00 1.73
648 691 1.487558 GGTGTTAAGGGGCGGATCTTA 59.512 52.381 0.00 0.00 0.00 2.10
649 692 0.255033 GGTGTTAAGGGGCGGATCTT 59.745 55.000 0.00 0.00 0.00 2.40
650 693 0.912487 TGGTGTTAAGGGGCGGATCT 60.912 55.000 0.00 0.00 0.00 2.75
651 694 0.746923 GTGGTGTTAAGGGGCGGATC 60.747 60.000 0.00 0.00 0.00 3.36
652 695 1.301954 GTGGTGTTAAGGGGCGGAT 59.698 57.895 0.00 0.00 0.00 4.18
653 696 2.751688 GTGGTGTTAAGGGGCGGA 59.248 61.111 0.00 0.00 0.00 5.54
654 697 2.744709 CGTGGTGTTAAGGGGCGG 60.745 66.667 0.00 0.00 0.00 6.13
655 698 3.428282 GCGTGGTGTTAAGGGGCG 61.428 66.667 0.00 0.00 0.00 6.13
656 699 3.428282 CGCGTGGTGTTAAGGGGC 61.428 66.667 0.00 0.00 0.00 5.80
657 700 1.296056 CTTCGCGTGGTGTTAAGGGG 61.296 60.000 5.77 0.00 0.00 4.79
658 701 1.908066 GCTTCGCGTGGTGTTAAGGG 61.908 60.000 5.77 0.00 0.00 3.95
659 702 1.495951 GCTTCGCGTGGTGTTAAGG 59.504 57.895 5.77 0.00 0.00 2.69
671 714 2.174319 GGACCCTTCATCGCTTCGC 61.174 63.158 0.00 0.00 0.00 4.70
672 715 1.521681 GGGACCCTTCATCGCTTCG 60.522 63.158 2.09 0.00 0.00 3.79
673 716 0.462759 CAGGGACCCTTCATCGCTTC 60.463 60.000 11.56 0.00 37.26 3.86
674 717 1.201429 ACAGGGACCCTTCATCGCTT 61.201 55.000 11.56 0.00 37.26 4.68
675 718 1.201429 AACAGGGACCCTTCATCGCT 61.201 55.000 11.56 0.00 39.76 4.93
676 719 0.322546 AAACAGGGACCCTTCATCGC 60.323 55.000 11.56 0.00 0.00 4.58
677 720 1.003118 TGAAACAGGGACCCTTCATCG 59.997 52.381 11.56 1.01 0.00 3.84
689 732 1.228124 TCTTGGCCCGTGAAACAGG 60.228 57.895 0.00 0.00 37.49 4.00
697 740 3.850098 CTGCTTGGTCTTGGCCCGT 62.850 63.158 0.00 0.00 0.00 5.28
698 741 3.058160 CTGCTTGGTCTTGGCCCG 61.058 66.667 0.00 0.00 0.00 6.13
706 749 1.202348 GTTAATGTGGCCTGCTTGGTC 59.798 52.381 3.32 0.00 41.87 4.02
719 762 4.345859 TTTCTCGGGTGACTGTTAATGT 57.654 40.909 0.00 0.00 38.16 2.71
734 777 1.207089 TGGGCTGTGGACTATTTCTCG 59.793 52.381 0.00 0.00 0.00 4.04
743 786 1.002502 GTTACCCTGGGCTGTGGAC 60.003 63.158 14.08 0.00 0.00 4.02
749 792 1.683441 CTTTCCGTTACCCTGGGCT 59.317 57.895 14.08 2.62 0.00 5.19
802 845 1.880340 GCCGCCAGATCTTCACTCG 60.880 63.158 0.00 0.00 0.00 4.18
805 848 0.391661 TTCAGCCGCCAGATCTTCAC 60.392 55.000 0.00 0.00 0.00 3.18
867 910 1.332375 CGAGCACCTTGTTCCGAAAAA 59.668 47.619 0.00 0.00 0.00 1.94
868 911 0.941542 CGAGCACCTTGTTCCGAAAA 59.058 50.000 0.00 0.00 0.00 2.29
869 912 1.503818 GCGAGCACCTTGTTCCGAAA 61.504 55.000 0.00 0.00 0.00 3.46
870 913 1.959226 GCGAGCACCTTGTTCCGAA 60.959 57.895 0.00 0.00 0.00 4.30
871 914 2.357034 GCGAGCACCTTGTTCCGA 60.357 61.111 0.00 0.00 0.00 4.55
872 915 3.423154 GGCGAGCACCTTGTTCCG 61.423 66.667 0.00 0.00 0.00 4.30
873 916 1.244019 AATGGCGAGCACCTTGTTCC 61.244 55.000 0.00 0.00 0.00 3.62
874 917 0.598065 AAATGGCGAGCACCTTGTTC 59.402 50.000 0.00 0.00 0.00 3.18
875 918 1.039856 AAAATGGCGAGCACCTTGTT 58.960 45.000 0.00 0.00 0.00 2.83
876 919 1.812571 CTAAAATGGCGAGCACCTTGT 59.187 47.619 0.00 0.00 0.00 3.16
877 920 1.468054 GCTAAAATGGCGAGCACCTTG 60.468 52.381 0.00 0.00 36.20 3.61
878 921 0.811281 GCTAAAATGGCGAGCACCTT 59.189 50.000 0.00 0.00 36.20 3.50
879 922 2.482326 GCTAAAATGGCGAGCACCT 58.518 52.632 0.00 0.00 36.20 4.00
888 931 2.116366 GTTTATGCGGCGCTAAAATGG 58.884 47.619 33.26 0.00 0.00 3.16
911 954 7.235812 AGTTATATGTCCCTGTTATCTCCTTCC 59.764 40.741 0.00 0.00 0.00 3.46
934 987 0.969894 CAGGAGTTCGGTCCAGAGTT 59.030 55.000 2.77 0.00 39.34 3.01
967 1027 1.704641 TCTGCTAGACCTGTGTGTGT 58.295 50.000 0.00 0.00 0.00 3.72
974 1034 1.340889 GCTCTGGATCTGCTAGACCTG 59.659 57.143 0.00 0.00 30.22 4.00
975 1035 1.703411 GCTCTGGATCTGCTAGACCT 58.297 55.000 0.00 0.00 30.22 3.85
976 1036 0.678950 GGCTCTGGATCTGCTAGACC 59.321 60.000 0.00 0.00 30.22 3.85
1190 1257 2.775856 GCGCGAGACAGGGATGAGA 61.776 63.158 12.10 0.00 0.00 3.27
1322 1389 1.680207 GATCTGCAAATCCCTCTTGCC 59.320 52.381 5.19 0.00 46.98 4.52
1335 1403 0.392863 CCCGTGTTCATGGATCTGCA 60.393 55.000 12.10 0.00 0.00 4.41
1351 1419 2.024176 ACCGAGATTTGATTGTCCCG 57.976 50.000 0.00 0.00 0.00 5.14
1504 1572 1.991339 TAGGGAGAGACGCCGGATGA 61.991 60.000 5.05 0.00 0.00 2.92
1510 1578 1.202545 GGAACAATAGGGAGAGACGCC 60.203 57.143 0.00 0.00 0.00 5.68
1512 1580 3.292460 AGAGGAACAATAGGGAGAGACG 58.708 50.000 0.00 0.00 0.00 4.18
1562 1633 7.323177 GCGATTTAGGAATACGTAGTTCTACAG 59.677 40.741 10.51 4.38 37.78 2.74
1574 1645 6.932947 AGGGTGTATAGCGATTTAGGAATAC 58.067 40.000 0.00 0.00 0.00 1.89
1587 1658 6.812998 TGTCAGTAATGTTAGGGTGTATAGC 58.187 40.000 0.00 0.00 0.00 2.97
1591 1662 5.335261 TCCTGTCAGTAATGTTAGGGTGTA 58.665 41.667 12.92 0.00 0.00 2.90
1598 1669 4.693566 CGCCTTTTCCTGTCAGTAATGTTA 59.306 41.667 0.00 0.00 0.00 2.41
1607 1678 1.896660 GCCACGCCTTTTCCTGTCA 60.897 57.895 0.00 0.00 0.00 3.58
1611 1682 2.215942 AATAAGCCACGCCTTTTCCT 57.784 45.000 0.00 0.00 0.00 3.36
1620 1691 6.910536 ACAAGAGAGATAAAATAAGCCACG 57.089 37.500 0.00 0.00 0.00 4.94
1657 1728 8.441312 AGAGTTTGCAATTTCATGTTCAAAAT 57.559 26.923 0.00 0.00 0.00 1.82
1675 1746 4.446371 AGACAGAACCTCACAAGAGTTTG 58.554 43.478 0.00 0.00 40.40 2.93
1694 1765 4.634883 CCATGCATATGCCTCTATTGAGAC 59.365 45.833 24.54 0.00 39.69 3.36
1695 1766 4.533311 TCCATGCATATGCCTCTATTGAGA 59.467 41.667 24.54 2.30 39.69 3.27
1696 1767 4.840271 TCCATGCATATGCCTCTATTGAG 58.160 43.478 24.54 1.61 41.18 3.02
1697 1768 4.914177 TCCATGCATATGCCTCTATTGA 57.086 40.909 24.54 9.87 41.18 2.57
1708 1779 4.763793 GCTACTTGGTTCATCCATGCATAT 59.236 41.667 0.00 0.00 46.60 1.78
1709 1780 4.136796 GCTACTTGGTTCATCCATGCATA 58.863 43.478 0.00 0.00 46.60 3.14
1780 1851 8.641541 ACCATACACAAGTTGAATTCAAAGATT 58.358 29.630 22.07 14.05 37.63 2.40
1792 1863 6.037172 GCCATAAGACTACCATACACAAGTTG 59.963 42.308 0.00 0.00 0.00 3.16
1799 1870 8.749354 CATATGTAGCCATAAGACTACCATACA 58.251 37.037 0.00 0.00 38.38 2.29
1805 1876 9.712305 ATGTTTCATATGTAGCCATAAGACTAC 57.288 33.333 1.90 0.00 37.12 2.73
1990 2061 5.663106 TCCTAGAAATGCAAGTAGATGGAGT 59.337 40.000 0.00 0.00 0.00 3.85
2234 2305 8.314021 CACTATCATACAACATATTGCTAGGGA 58.686 37.037 0.00 0.00 39.66 4.20
2342 2413 2.018515 AGACTAGCGAGACTAACAGCC 58.981 52.381 0.00 0.00 0.00 4.85
2623 2694 4.999950 GTCTTCTCTGCTTCCTTCATTTCA 59.000 41.667 0.00 0.00 0.00 2.69
2770 2841 3.226346 TGCTGATCTTTTTCTGCATGC 57.774 42.857 11.82 11.82 43.09 4.06
3083 3154 6.861065 TGTACAAAGGAGCAGAAGTTAAAG 57.139 37.500 0.00 0.00 0.00 1.85
3092 3167 3.685139 TCCTCTTGTACAAAGGAGCAG 57.315 47.619 24.04 12.10 34.26 4.24
3127 3202 3.543680 ACAAGGTACATGGAGGAATCG 57.456 47.619 0.00 0.00 0.00 3.34
3148 3223 3.489355 AGGATGAGCACATTGACAAACA 58.511 40.909 0.00 0.00 36.82 2.83
3259 3336 3.805823 TGCAGTTCGCGAATTTAAGAAC 58.194 40.909 26.23 10.16 46.97 3.01
3272 3349 1.002134 AGGGGGTCATTGCAGTTCG 60.002 57.895 0.00 0.00 0.00 3.95
3285 3362 4.305956 AAGCCAGCCAACAGGGGG 62.306 66.667 0.00 0.00 37.04 5.40
3286 3363 2.677875 GAAGCCAGCCAACAGGGG 60.678 66.667 0.00 0.00 37.04 4.79
3301 3378 2.833338 CTGGATGCCATTTTCTTGGGAA 59.167 45.455 0.00 0.00 40.78 3.97
3422 3499 6.246420 AGCACAAAATGAGTGAATCTACAC 57.754 37.500 0.00 0.00 39.30 2.90
3529 3610 4.937620 TCACTGATGGAATTCTTACAGCAC 59.062 41.667 18.45 0.00 0.00 4.40
3549 3630 7.867403 ACCAGTCACATTGAAATTTGTAATCAC 59.133 33.333 0.00 0.00 0.00 3.06
3560 3641 0.950836 CGGCACCAGTCACATTGAAA 59.049 50.000 0.00 0.00 0.00 2.69
3567 3648 1.961277 CTGGAACGGCACCAGTCAC 60.961 63.158 13.92 0.00 46.71 3.67
3568 3649 2.425592 CTGGAACGGCACCAGTCA 59.574 61.111 13.92 0.00 46.71 3.41
3572 3653 0.109532 TTGATTCTGGAACGGCACCA 59.890 50.000 0.00 0.00 35.96 4.17
3573 3654 1.133025 CATTGATTCTGGAACGGCACC 59.867 52.381 0.00 0.00 32.53 5.01
3574 3655 1.812571 ACATTGATTCTGGAACGGCAC 59.187 47.619 0.00 0.00 32.53 5.01
3575 3656 2.198827 ACATTGATTCTGGAACGGCA 57.801 45.000 0.00 0.00 32.53 5.69
3576 3657 2.487762 TGAACATTGATTCTGGAACGGC 59.512 45.455 0.00 0.00 32.53 5.68
3577 3658 3.753272 ACTGAACATTGATTCTGGAACGG 59.247 43.478 0.00 0.00 33.20 4.44
3578 3659 4.452114 TCACTGAACATTGATTCTGGAACG 59.548 41.667 0.00 0.00 33.20 3.95
3579 3660 5.702670 TCTCACTGAACATTGATTCTGGAAC 59.297 40.000 0.00 0.00 33.20 3.62
3580 3661 5.702670 GTCTCACTGAACATTGATTCTGGAA 59.297 40.000 0.00 0.00 33.20 3.53
3581 3662 5.240891 GTCTCACTGAACATTGATTCTGGA 58.759 41.667 0.00 0.00 33.20 3.86
3582 3663 4.092529 CGTCTCACTGAACATTGATTCTGG 59.907 45.833 0.00 0.00 33.20 3.86
3583 3664 4.092529 CCGTCTCACTGAACATTGATTCTG 59.907 45.833 0.00 0.00 34.62 3.02
3584 3665 4.248859 CCGTCTCACTGAACATTGATTCT 58.751 43.478 0.00 0.00 0.00 2.40
3585 3666 3.997021 ACCGTCTCACTGAACATTGATTC 59.003 43.478 0.00 0.00 0.00 2.52
3586 3667 3.748048 CACCGTCTCACTGAACATTGATT 59.252 43.478 0.00 0.00 0.00 2.57
3587 3668 3.329386 CACCGTCTCACTGAACATTGAT 58.671 45.455 0.00 0.00 0.00 2.57
3588 3669 2.547855 CCACCGTCTCACTGAACATTGA 60.548 50.000 0.00 0.00 0.00 2.57
3589 3670 1.800586 CCACCGTCTCACTGAACATTG 59.199 52.381 0.00 0.00 0.00 2.82
3590 3671 1.416401 ACCACCGTCTCACTGAACATT 59.584 47.619 0.00 0.00 0.00 2.71
3591 3672 1.048601 ACCACCGTCTCACTGAACAT 58.951 50.000 0.00 0.00 0.00 2.71
3592 3673 0.828022 AACCACCGTCTCACTGAACA 59.172 50.000 0.00 0.00 0.00 3.18
3593 3674 1.499049 GAACCACCGTCTCACTGAAC 58.501 55.000 0.00 0.00 0.00 3.18
3594 3675 0.391597 GGAACCACCGTCTCACTGAA 59.608 55.000 0.00 0.00 0.00 3.02
3595 3676 0.757561 TGGAACCACCGTCTCACTGA 60.758 55.000 0.00 0.00 42.61 3.41
3596 3677 0.105964 TTGGAACCACCGTCTCACTG 59.894 55.000 0.00 0.00 42.61 3.66
3597 3678 1.056660 ATTGGAACCACCGTCTCACT 58.943 50.000 0.00 0.00 42.61 3.41
3598 3679 2.289195 TGTATTGGAACCACCGTCTCAC 60.289 50.000 0.00 0.00 42.61 3.51
3599 3680 1.972075 TGTATTGGAACCACCGTCTCA 59.028 47.619 0.00 0.00 42.61 3.27
3600 3681 2.754946 TGTATTGGAACCACCGTCTC 57.245 50.000 0.00 0.00 42.61 3.36
3601 3682 2.093128 GGATGTATTGGAACCACCGTCT 60.093 50.000 0.00 0.00 42.61 4.18
3602 3683 2.285977 GGATGTATTGGAACCACCGTC 58.714 52.381 0.00 0.00 42.61 4.79
3603 3684 1.631388 TGGATGTATTGGAACCACCGT 59.369 47.619 0.00 0.00 42.61 4.83
3604 3685 2.014128 GTGGATGTATTGGAACCACCG 58.986 52.381 0.00 0.00 43.29 4.94
3606 3687 2.291282 TGGGTGGATGTATTGGAACCAC 60.291 50.000 0.00 0.00 46.79 4.16
3607 3688 1.996291 TGGGTGGATGTATTGGAACCA 59.004 47.619 0.00 0.00 0.00 3.67
3608 3689 2.818751 TGGGTGGATGTATTGGAACC 57.181 50.000 0.00 0.00 0.00 3.62
3609 3690 6.207417 CAGAATATGGGTGGATGTATTGGAAC 59.793 42.308 0.00 0.00 0.00 3.62
3610 3691 6.102468 TCAGAATATGGGTGGATGTATTGGAA 59.898 38.462 0.00 0.00 0.00 3.53
3611 3692 5.610557 TCAGAATATGGGTGGATGTATTGGA 59.389 40.000 0.00 0.00 0.00 3.53
3612 3693 5.879763 TCAGAATATGGGTGGATGTATTGG 58.120 41.667 0.00 0.00 0.00 3.16
3613 3694 5.413833 GCTCAGAATATGGGTGGATGTATTG 59.586 44.000 0.00 0.00 0.00 1.90
3614 3695 5.311649 AGCTCAGAATATGGGTGGATGTATT 59.688 40.000 0.00 0.00 0.00 1.89
3615 3696 4.848660 AGCTCAGAATATGGGTGGATGTAT 59.151 41.667 0.00 0.00 0.00 2.29
3616 3697 4.234550 AGCTCAGAATATGGGTGGATGTA 58.765 43.478 0.00 0.00 0.00 2.29
3617 3698 3.051581 AGCTCAGAATATGGGTGGATGT 58.948 45.455 0.00 0.00 0.00 3.06
3618 3699 3.072038 TGAGCTCAGAATATGGGTGGATG 59.928 47.826 13.74 0.00 0.00 3.51
3652 3733 2.114411 GGGACCCAAACAAGCGGA 59.886 61.111 5.33 0.00 0.00 5.54
3668 3749 7.344352 TCCCTACCAAATGAAATGAAATTAGGG 59.656 37.037 0.00 0.00 33.67 3.53
3747 3910 4.079253 GGCAAGGATTTCACCTCTAAACA 58.921 43.478 0.00 0.00 39.62 2.83
3748 3911 4.079253 TGGCAAGGATTTCACCTCTAAAC 58.921 43.478 0.00 0.00 39.62 2.01


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

AutoCloner maintained by Alex Coulton.