Multiple sequence alignment - TraesCS7A01G061000

Loading Multiple Alignment...

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 TraesCS7A01G061000 chr7A 100.000 3587 0 0 1 3587 30088604 30092190 0.000000e+00 6625.0
1 TraesCS7A01G061000 chr7A 82.068 619 86 18 5 619 718520768 718521365 4.130000e-139 505.0
2 TraesCS7A01G061000 chr7A 89.062 64 6 1 2666 2729 102571154 102571216 1.070000e-10 78.7
3 TraesCS7A01G061000 chr7D 90.670 2926 131 55 736 3587 29830303 29833160 0.000000e+00 3760.0
4 TraesCS7A01G061000 chr7D 82.143 616 99 10 8 620 82609655 82610262 5.310000e-143 518.0
5 TraesCS7A01G061000 chr7D 81.541 623 103 10 1 621 461201514 461202126 1.490000e-138 503.0
6 TraesCS7A01G061000 chr4A 88.278 3003 167 97 688 3587 699889419 699886499 0.000000e+00 3424.0
7 TraesCS7A01G061000 chr2D 84.530 627 83 13 1 623 604074441 604075057 3.060000e-170 608.0
8 TraesCS7A01G061000 chr2D 100.000 50 0 0 2667 2716 635627142 635627093 3.810000e-15 93.5
9 TraesCS7A01G061000 chr5B 83.094 627 95 10 1 625 54508288 54507671 8.700000e-156 560.0
10 TraesCS7A01G061000 chr5B 81.220 623 103 13 2 621 72077715 72078326 1.160000e-134 490.0
11 TraesCS7A01G061000 chr5B 98.077 52 1 0 2668 2719 285935693 285935642 1.370000e-14 91.6
12 TraesCS7A01G061000 chr5D 82.880 625 92 12 1 621 487270725 487270112 6.770000e-152 547.0
13 TraesCS7A01G061000 chr5D 98.077 52 1 0 2667 2718 565043138 565043087 1.370000e-14 91.6
14 TraesCS7A01G061000 chr6D 82.372 624 99 9 1 622 291218190 291218804 1.900000e-147 532.0
15 TraesCS7A01G061000 chr2B 82.010 617 95 14 7 619 5474913 5475517 8.880000e-141 510.0
16 TraesCS7A01G061000 chr4D 81.159 207 31 4 1503 1708 503451195 503451394 3.710000e-35 159.0
17 TraesCS7A01G061000 chr4D 80.583 206 34 2 1503 1708 503507119 503506920 1.720000e-33 154.0
18 TraesCS7A01G061000 chr4B 81.503 173 26 4 1503 1672 648572965 648573134 1.740000e-28 137.0
19 TraesCS7A01G061000 chr4B 81.699 153 26 2 1503 1654 648695243 648695092 3.760000e-25 126.0
20 TraesCS7A01G061000 chr1A 100.000 50 0 0 2667 2716 233008964 233009013 3.810000e-15 93.5
21 TraesCS7A01G061000 chr1D 100.000 48 0 0 2666 2713 421659392 421659439 4.930000e-14 89.8
22 TraesCS7A01G061000 chr6A 90.769 65 4 2 2668 2732 282145931 282145869 6.380000e-13 86.1


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 TraesCS7A01G061000 chr7A 30088604 30092190 3586 False 6625 6625 100.000 1 3587 1 chr7A.!!$F1 3586
1 TraesCS7A01G061000 chr7A 718520768 718521365 597 False 505 505 82.068 5 619 1 chr7A.!!$F3 614
2 TraesCS7A01G061000 chr7D 29830303 29833160 2857 False 3760 3760 90.670 736 3587 1 chr7D.!!$F1 2851
3 TraesCS7A01G061000 chr7D 82609655 82610262 607 False 518 518 82.143 8 620 1 chr7D.!!$F2 612
4 TraesCS7A01G061000 chr7D 461201514 461202126 612 False 503 503 81.541 1 621 1 chr7D.!!$F3 620
5 TraesCS7A01G061000 chr4A 699886499 699889419 2920 True 3424 3424 88.278 688 3587 1 chr4A.!!$R1 2899
6 TraesCS7A01G061000 chr2D 604074441 604075057 616 False 608 608 84.530 1 623 1 chr2D.!!$F1 622
7 TraesCS7A01G061000 chr5B 54507671 54508288 617 True 560 560 83.094 1 625 1 chr5B.!!$R1 624
8 TraesCS7A01G061000 chr5B 72077715 72078326 611 False 490 490 81.220 2 621 1 chr5B.!!$F1 619
9 TraesCS7A01G061000 chr5D 487270112 487270725 613 True 547 547 82.880 1 621 1 chr5D.!!$R1 620
10 TraesCS7A01G061000 chr6D 291218190 291218804 614 False 532 532 82.372 1 622 1 chr6D.!!$F1 621
11 TraesCS7A01G061000 chr2B 5474913 5475517 604 False 510 510 82.010 7 619 1 chr2B.!!$F1 612

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
778 782 0.029035 ACGGAGAAATCGGTCGATCG 59.971 55.0 12.98 12.98 33.08 3.69 F
961 999 0.040351 CCTCTCTCTCCCACCACTCA 59.960 60.0 0.00 0.00 0.00 3.41 F
1457 1506 0.179076 TGACCGATCGGCTCTACGTA 60.179 55.0 33.62 11.03 39.32 3.57 F
2028 2102 0.977395 CTCCTCCCCTCTTGTTTCGT 59.023 55.0 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 2354 0.320374 TCGGCCGAAGTGAATGAAGT 59.680 50.0 28.99 0.00 0.00 3.01 R
2277 2357 0.534873 TGATCGGCCGAAGTGAATGA 59.465 50.0 34.66 5.37 0.00 2.57 R
2280 2360 1.011968 CGTTGATCGGCCGAAGTGAA 61.012 55.0 34.66 14.91 35.71 3.18 R
3553 3717 0.729690 GCACAGGAATCTTCTTCGCC 59.270 55.0 0.00 0.00 0.00 5.54 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
103 104 3.746889 CATTGCCGCCGCCAGAAA 61.747 61.111 0.00 0.00 0.00 2.52
149 150 3.479203 CCCATACCGGAGCCAGCA 61.479 66.667 9.46 0.00 36.56 4.41
150 151 2.109799 CCATACCGGAGCCAGCAG 59.890 66.667 9.46 0.00 36.56 4.24
168 169 2.546795 GCAGGACCTTATCGATGACAGG 60.547 54.545 8.54 12.76 0.00 4.00
171 172 1.337071 GACCTTATCGATGACAGGCGA 59.663 52.381 8.54 5.77 41.14 5.54
172 173 1.754803 ACCTTATCGATGACAGGCGAA 59.245 47.619 8.54 0.00 40.20 4.70
211 212 1.689233 ATAAGGACCAGCGCCCTGA 60.689 57.895 2.29 0.00 41.77 3.86
309 310 1.574263 GAGAAGCCCTAACCTCACCT 58.426 55.000 0.00 0.00 0.00 4.00
313 314 2.732619 GCCCTAACCTCACCTCCCG 61.733 68.421 0.00 0.00 0.00 5.14
324 325 2.685380 CCTCCCGGAAGAGCTGGT 60.685 66.667 0.73 0.00 41.87 4.00
325 326 2.581354 CTCCCGGAAGAGCTGGTG 59.419 66.667 0.73 0.00 41.87 4.17
382 383 5.404946 CAACGGACGAACTTAAGGAAGATA 58.595 41.667 7.53 0.00 36.45 1.98
383 384 5.848833 ACGGACGAACTTAAGGAAGATAT 57.151 39.130 7.53 0.00 36.45 1.63
386 387 6.040616 ACGGACGAACTTAAGGAAGATATGAT 59.959 38.462 7.53 0.00 36.45 2.45
387 388 6.363626 CGGACGAACTTAAGGAAGATATGATG 59.636 42.308 7.53 0.00 36.45 3.07
399 400 2.301296 AGATATGATGCCGGAAGACTGG 59.699 50.000 5.05 0.00 44.87 4.00
400 401 0.758734 TATGATGCCGGAAGACTGGG 59.241 55.000 5.05 0.00 42.48 4.45
418 419 1.443872 GTCGAAGAAGAAGCGCCGA 60.444 57.895 2.29 0.00 39.69 5.54
432 433 1.669760 GCCGACATCCGTCCAAACA 60.670 57.895 0.00 0.00 39.11 2.83
448 449 0.617820 AACACTACCCCTGCGAGGAT 60.618 55.000 4.00 0.00 37.67 3.24
450 451 1.342674 ACACTACCCCTGCGAGGATTA 60.343 52.381 4.00 0.00 37.67 1.75
451 452 1.971357 CACTACCCCTGCGAGGATTAT 59.029 52.381 4.00 0.00 37.67 1.28
452 453 3.162666 CACTACCCCTGCGAGGATTATA 58.837 50.000 4.00 0.00 37.67 0.98
458 460 2.806244 CCCTGCGAGGATTATAAAACCG 59.194 50.000 4.00 0.00 37.67 4.44
556 560 2.586357 GAATCCACGGGCTCGCTC 60.586 66.667 5.51 0.00 40.63 5.03
557 561 4.514577 AATCCACGGGCTCGCTCG 62.515 66.667 5.51 9.97 46.76 5.03
570 574 2.387445 CGCTCGCCGGTGAAAATCA 61.387 57.895 20.06 0.00 0.00 2.57
583 587 4.152647 GTGAAAATCAAAGGGAGGAAGGT 58.847 43.478 0.00 0.00 0.00 3.50
584 588 4.588951 GTGAAAATCAAAGGGAGGAAGGTT 59.411 41.667 0.00 0.00 0.00 3.50
625 629 2.889678 AGAGGGCAAAGAAAAGCTCTTG 59.110 45.455 0.00 0.00 44.00 3.02
626 630 2.625314 GAGGGCAAAGAAAAGCTCTTGT 59.375 45.455 0.00 0.00 44.00 3.16
627 631 3.033909 AGGGCAAAGAAAAGCTCTTGTT 58.966 40.909 0.00 0.00 44.00 2.83
628 632 3.126073 GGGCAAAGAAAAGCTCTTGTTG 58.874 45.455 0.00 0.00 44.00 3.33
629 633 2.541346 GGCAAAGAAAAGCTCTTGTTGC 59.459 45.455 8.60 8.60 44.00 4.17
630 634 2.541346 GCAAAGAAAAGCTCTTGTTGCC 59.459 45.455 6.53 0.00 44.00 4.52
631 635 3.739209 GCAAAGAAAAGCTCTTGTTGCCT 60.739 43.478 6.53 0.00 44.00 4.75
632 636 4.436332 CAAAGAAAAGCTCTTGTTGCCTT 58.564 39.130 0.00 0.00 44.00 4.35
633 637 5.591099 CAAAGAAAAGCTCTTGTTGCCTTA 58.409 37.500 0.00 0.00 44.00 2.69
634 638 4.837896 AGAAAAGCTCTTGTTGCCTTAC 57.162 40.909 0.00 0.00 0.00 2.34
635 639 4.464947 AGAAAAGCTCTTGTTGCCTTACT 58.535 39.130 0.00 0.00 0.00 2.24
636 640 4.276926 AGAAAAGCTCTTGTTGCCTTACTG 59.723 41.667 0.00 0.00 0.00 2.74
637 641 2.191128 AGCTCTTGTTGCCTTACTGG 57.809 50.000 0.00 0.00 39.35 4.00
638 642 1.421646 AGCTCTTGTTGCCTTACTGGT 59.578 47.619 0.00 0.00 38.35 4.00
639 643 2.637872 AGCTCTTGTTGCCTTACTGGTA 59.362 45.455 0.00 0.00 38.35 3.25
640 644 3.264450 AGCTCTTGTTGCCTTACTGGTAT 59.736 43.478 0.00 0.00 38.35 2.73
641 645 3.375299 GCTCTTGTTGCCTTACTGGTATG 59.625 47.826 0.00 0.00 38.35 2.39
642 646 4.832248 CTCTTGTTGCCTTACTGGTATGA 58.168 43.478 0.00 0.00 38.35 2.15
643 647 5.235850 TCTTGTTGCCTTACTGGTATGAA 57.764 39.130 0.00 0.00 38.35 2.57
644 648 5.626142 TCTTGTTGCCTTACTGGTATGAAA 58.374 37.500 0.00 0.00 38.35 2.69
645 649 5.472137 TCTTGTTGCCTTACTGGTATGAAAC 59.528 40.000 0.00 0.00 38.35 2.78
646 650 4.980573 TGTTGCCTTACTGGTATGAAACT 58.019 39.130 0.00 0.00 38.35 2.66
647 651 5.001232 TGTTGCCTTACTGGTATGAAACTC 58.999 41.667 0.00 0.00 38.35 3.01
648 652 5.221843 TGTTGCCTTACTGGTATGAAACTCT 60.222 40.000 0.00 0.00 38.35 3.24
649 653 4.832248 TGCCTTACTGGTATGAAACTCTG 58.168 43.478 0.00 0.00 38.35 3.35
650 654 4.530553 TGCCTTACTGGTATGAAACTCTGA 59.469 41.667 0.00 0.00 38.35 3.27
651 655 5.012664 TGCCTTACTGGTATGAAACTCTGAA 59.987 40.000 0.00 0.00 38.35 3.02
652 656 6.116126 GCCTTACTGGTATGAAACTCTGAAT 58.884 40.000 0.00 0.00 38.35 2.57
653 657 6.599638 GCCTTACTGGTATGAAACTCTGAATT 59.400 38.462 0.00 0.00 38.35 2.17
654 658 7.414540 GCCTTACTGGTATGAAACTCTGAATTG 60.415 40.741 0.00 0.00 38.35 2.32
655 659 7.824289 CCTTACTGGTATGAAACTCTGAATTGA 59.176 37.037 0.00 0.00 0.00 2.57
656 660 8.777865 TTACTGGTATGAAACTCTGAATTGAG 57.222 34.615 0.00 0.00 39.78 3.02
657 661 7.009179 ACTGGTATGAAACTCTGAATTGAGA 57.991 36.000 0.00 0.00 37.50 3.27
658 662 6.876257 ACTGGTATGAAACTCTGAATTGAGAC 59.124 38.462 0.00 0.00 37.50 3.36
659 663 5.869344 TGGTATGAAACTCTGAATTGAGACG 59.131 40.000 0.00 0.00 37.50 4.18
660 664 6.100004 GGTATGAAACTCTGAATTGAGACGA 58.900 40.000 0.00 0.00 37.50 4.20
661 665 6.590292 GGTATGAAACTCTGAATTGAGACGAA 59.410 38.462 0.00 0.00 37.50 3.85
662 666 7.278868 GGTATGAAACTCTGAATTGAGACGAAT 59.721 37.037 0.00 0.00 37.50 3.34
663 667 6.471976 TGAAACTCTGAATTGAGACGAATG 57.528 37.500 0.00 0.00 37.50 2.67
664 668 4.935885 AACTCTGAATTGAGACGAATGC 57.064 40.909 0.00 0.00 37.50 3.56
665 669 3.930336 ACTCTGAATTGAGACGAATGCA 58.070 40.909 0.00 0.00 37.50 3.96
666 670 4.318332 ACTCTGAATTGAGACGAATGCAA 58.682 39.130 0.00 0.00 37.50 4.08
667 671 4.153117 ACTCTGAATTGAGACGAATGCAAC 59.847 41.667 0.00 0.00 37.50 4.17
668 672 3.436704 TCTGAATTGAGACGAATGCAACC 59.563 43.478 0.00 0.00 0.00 3.77
669 673 3.145286 TGAATTGAGACGAATGCAACCA 58.855 40.909 0.00 0.00 0.00 3.67
670 674 3.189080 TGAATTGAGACGAATGCAACCAG 59.811 43.478 0.00 0.00 0.00 4.00
671 675 2.254546 TTGAGACGAATGCAACCAGT 57.745 45.000 0.00 0.00 0.00 4.00
672 676 1.795768 TGAGACGAATGCAACCAGTC 58.204 50.000 0.00 0.00 32.96 3.51
679 683 2.898705 GAATGCAACCAGTCGATCTCT 58.101 47.619 0.00 0.00 0.00 3.10
680 684 3.265791 GAATGCAACCAGTCGATCTCTT 58.734 45.455 0.00 0.00 0.00 2.85
681 685 2.839486 TGCAACCAGTCGATCTCTTT 57.161 45.000 0.00 0.00 0.00 2.52
682 686 2.688507 TGCAACCAGTCGATCTCTTTC 58.311 47.619 0.00 0.00 0.00 2.62
683 687 2.300152 TGCAACCAGTCGATCTCTTTCT 59.700 45.455 0.00 0.00 0.00 2.52
684 688 3.244215 TGCAACCAGTCGATCTCTTTCTT 60.244 43.478 0.00 0.00 0.00 2.52
685 689 4.021456 TGCAACCAGTCGATCTCTTTCTTA 60.021 41.667 0.00 0.00 0.00 2.10
686 690 4.929808 GCAACCAGTCGATCTCTTTCTTAA 59.070 41.667 0.00 0.00 0.00 1.85
693 697 7.486551 CCAGTCGATCTCTTTCTTAAAGTACAG 59.513 40.741 0.00 0.00 39.52 2.74
703 707 7.497909 TCTTTCTTAAAGTACAGTTTGAGGGTG 59.502 37.037 0.00 0.00 39.52 4.61
709 713 6.391227 AAGTACAGTTTGAGGGTGAATTTG 57.609 37.500 0.00 0.00 0.00 2.32
718 722 5.584253 TGAGGGTGAATTTGTTTTCGAAA 57.416 34.783 6.47 6.47 0.00 3.46
720 724 5.358442 TGAGGGTGAATTTGTTTTCGAAAGA 59.642 36.000 10.98 0.00 39.20 2.52
757 761 7.822658 TGTGTAGCTACCAAATTTAATGAACC 58.177 34.615 21.01 0.00 0.00 3.62
771 775 1.803334 TGAACCAACGGAGAAATCGG 58.197 50.000 0.00 0.00 0.00 4.18
775 779 0.108992 CCAACGGAGAAATCGGTCGA 60.109 55.000 0.00 0.00 0.00 4.20
776 780 1.470979 CCAACGGAGAAATCGGTCGAT 60.471 52.381 0.00 0.00 36.23 3.59
777 781 1.852895 CAACGGAGAAATCGGTCGATC 59.147 52.381 6.32 0.00 33.08 3.69
778 782 0.029035 ACGGAGAAATCGGTCGATCG 59.971 55.000 12.98 12.98 33.08 3.69
823 827 0.603975 GTCGCTTTCCAGAGCACCTT 60.604 55.000 0.00 0.00 42.83 3.50
824 828 0.603707 TCGCTTTCCAGAGCACCTTG 60.604 55.000 0.00 0.00 42.83 3.61
825 829 1.583477 GCTTTCCAGAGCACCTTGC 59.417 57.895 0.00 0.00 45.46 4.01
935 948 0.989602 GCCGGCTATTTATACCCCCT 59.010 55.000 22.15 0.00 0.00 4.79
936 949 1.065636 GCCGGCTATTTATACCCCCTC 60.066 57.143 22.15 0.00 0.00 4.30
937 950 1.206371 CCGGCTATTTATACCCCCTCG 59.794 57.143 0.00 0.00 0.00 4.63
938 951 1.897802 CGGCTATTTATACCCCCTCGT 59.102 52.381 0.00 0.00 0.00 4.18
941 979 3.171528 GCTATTTATACCCCCTCGTCCT 58.828 50.000 0.00 0.00 0.00 3.85
943 981 2.092598 TTTATACCCCCTCGTCCTCC 57.907 55.000 0.00 0.00 0.00 4.30
954 992 0.914902 TCGTCCTCCTCTCTCTCCCA 60.915 60.000 0.00 0.00 0.00 4.37
957 995 0.851332 TCCTCCTCTCTCTCCCACCA 60.851 60.000 0.00 0.00 0.00 4.17
961 999 0.040351 CCTCTCTCTCCCACCACTCA 59.960 60.000 0.00 0.00 0.00 3.41
964 1002 1.943116 CTCTCTCCCACCACTCAGCG 61.943 65.000 0.00 0.00 0.00 5.18
965 1003 2.997315 TCTCCCACCACTCAGCGG 60.997 66.667 0.00 0.00 0.00 5.52
966 1004 4.767255 CTCCCACCACTCAGCGGC 62.767 72.222 0.00 0.00 0.00 6.53
970 1008 4.624364 CACCACTCAGCGGCACCA 62.624 66.667 1.45 0.00 0.00 4.17
971 1009 4.626081 ACCACTCAGCGGCACCAC 62.626 66.667 1.45 0.00 0.00 4.16
972 1010 4.320456 CCACTCAGCGGCACCACT 62.320 66.667 1.45 0.00 0.00 4.00
973 1011 2.740055 CACTCAGCGGCACCACTC 60.740 66.667 1.45 0.00 0.00 3.51
974 1012 2.919856 ACTCAGCGGCACCACTCT 60.920 61.111 1.45 0.00 0.00 3.24
975 1013 2.125753 CTCAGCGGCACCACTCTC 60.126 66.667 1.45 0.00 0.00 3.20
976 1014 2.601666 TCAGCGGCACCACTCTCT 60.602 61.111 1.45 0.00 0.00 3.10
977 1015 2.433838 CAGCGGCACCACTCTCTG 60.434 66.667 1.45 0.00 0.00 3.35
978 1016 4.385405 AGCGGCACCACTCTCTGC 62.385 66.667 1.45 0.00 0.00 4.26
1367 1414 1.825474 CCTCAACCTCCTCATGTACGT 59.175 52.381 0.00 0.00 0.00 3.57
1368 1415 2.159226 CCTCAACCTCCTCATGTACGTC 60.159 54.545 0.00 0.00 0.00 4.34
1370 1417 1.548719 CAACCTCCTCATGTACGTCCA 59.451 52.381 0.00 0.00 0.00 4.02
1393 1440 1.156330 TCCCCGATCCTCATCCTCC 59.844 63.158 0.00 0.00 0.00 4.30
1395 1442 2.279069 CCCGATCCTCATCCTCCCG 61.279 68.421 0.00 0.00 0.00 5.14
1396 1443 2.653702 CGATCCTCATCCTCCCGC 59.346 66.667 0.00 0.00 0.00 6.13
1454 1503 0.739561 AACTGACCGATCGGCTCTAC 59.260 55.000 33.62 18.95 39.32 2.59
1455 1504 1.280142 CTGACCGATCGGCTCTACG 59.720 63.158 33.62 16.72 39.32 3.51
1456 1505 1.437772 CTGACCGATCGGCTCTACGT 61.438 60.000 33.62 12.81 39.32 3.57
1457 1506 0.179076 TGACCGATCGGCTCTACGTA 60.179 55.000 33.62 11.03 39.32 3.57
1725 1783 1.693083 GCAAGGCCACGTACGTCATC 61.693 60.000 19.94 10.42 0.00 2.92
1733 1795 2.681848 CCACGTACGTCATCTACCTTCT 59.318 50.000 19.94 0.00 0.00 2.85
1752 1814 5.756833 CCTTCTTATTAATCACCACCGTACC 59.243 44.000 0.00 0.00 0.00 3.34
1755 1817 6.285224 TCTTATTAATCACCACCGTACCATG 58.715 40.000 0.00 0.00 0.00 3.66
1756 1818 3.985019 TTAATCACCACCGTACCATGT 57.015 42.857 0.00 0.00 0.00 3.21
1757 1819 5.617528 ATTAATCACCACCGTACCATGTA 57.382 39.130 0.00 0.00 0.00 2.29
1758 1820 3.536956 AATCACCACCGTACCATGTAG 57.463 47.619 0.00 0.00 0.00 2.74
1759 1821 2.219080 TCACCACCGTACCATGTAGA 57.781 50.000 0.00 0.00 0.00 2.59
1998 2060 4.742201 CCGGCCTCGTCACCAGTG 62.742 72.222 0.00 0.00 33.95 3.66
2003 2065 1.587054 CCTCGTCACCAGTGAGTCC 59.413 63.158 0.00 0.00 40.75 3.85
2028 2102 0.977395 CTCCTCCCCTCTTGTTTCGT 59.023 55.000 0.00 0.00 0.00 3.85
2075 2150 1.663173 TCGTTGTCGATGTGAGGCA 59.337 52.632 0.00 0.00 41.35 4.75
2079 2154 2.887568 GTCGATGTGAGGCAGGCG 60.888 66.667 0.00 0.00 0.00 5.52
2102 2177 4.643387 GCCCAGGAGCCACGTGTT 62.643 66.667 15.65 1.64 33.18 3.32
2171 2251 4.698575 ACAAATAAACGTGGCAAATGGTT 58.301 34.783 0.00 0.00 0.00 3.67
2272 2352 1.071385 CAGGTCAGCCACTCTCACTTT 59.929 52.381 0.00 0.00 37.19 2.66
2273 2353 1.346068 AGGTCAGCCACTCTCACTTTC 59.654 52.381 0.00 0.00 37.19 2.62
2274 2354 1.070758 GGTCAGCCACTCTCACTTTCA 59.929 52.381 0.00 0.00 34.09 2.69
2275 2355 2.139118 GTCAGCCACTCTCACTTTCAC 58.861 52.381 0.00 0.00 0.00 3.18
2277 2357 2.435805 TCAGCCACTCTCACTTTCACTT 59.564 45.455 0.00 0.00 0.00 3.16
2279 2359 2.435805 AGCCACTCTCACTTTCACTTCA 59.564 45.455 0.00 0.00 0.00 3.02
2280 2360 3.072184 AGCCACTCTCACTTTCACTTCAT 59.928 43.478 0.00 0.00 0.00 2.57
2281 2361 3.817647 GCCACTCTCACTTTCACTTCATT 59.182 43.478 0.00 0.00 0.00 2.57
2282 2362 4.083590 GCCACTCTCACTTTCACTTCATTC 60.084 45.833 0.00 0.00 0.00 2.67
2283 2363 5.059161 CCACTCTCACTTTCACTTCATTCA 58.941 41.667 0.00 0.00 0.00 2.57
2327 2407 1.452108 CCGGAATCCTGACCCTTGC 60.452 63.158 0.00 0.00 0.00 4.01
2328 2408 1.299648 CGGAATCCTGACCCTTGCA 59.700 57.895 0.00 0.00 0.00 4.08
2512 2595 1.032657 CGCCGAGAAGGAGAAGGAGA 61.033 60.000 0.00 0.00 43.02 3.71
2513 2596 1.408969 GCCGAGAAGGAGAAGGAGAT 58.591 55.000 0.00 0.00 45.00 2.75
2518 2601 2.365293 GAGAAGGAGAAGGAGATGAGCC 59.635 54.545 0.00 0.00 0.00 4.70
2519 2602 2.023113 AGAAGGAGAAGGAGATGAGCCT 60.023 50.000 0.00 0.00 37.35 4.58
2520 2603 2.086610 AGGAGAAGGAGATGAGCCTC 57.913 55.000 0.00 0.00 33.76 4.70
2620 2711 6.797995 GCACCGTAAAATTAGTTTTGATCGAA 59.202 34.615 6.23 0.00 38.01 3.71
2637 2734 2.230508 TCGAAGAACGGCTACAAGATGT 59.769 45.455 0.00 0.00 42.82 3.06
2663 2760 2.808906 ACCTGAAATTGGAGGCTACC 57.191 50.000 0.00 0.00 31.90 3.18
2664 2761 1.992557 ACCTGAAATTGGAGGCTACCA 59.007 47.619 0.00 0.00 38.24 3.25
2665 2762 2.582636 ACCTGAAATTGGAGGCTACCAT 59.417 45.455 0.00 0.00 39.82 3.55
2821 2943 8.310406 TGTATACTGTCAGTGCAATATAATGC 57.690 34.615 16.03 5.79 46.58 3.56
2823 2945 8.993121 GTATACTGTCAGTGCAATATAATGCTT 58.007 33.333 16.03 0.04 46.54 3.91
2834 2958 6.601217 TGCAATATAATGCTTAGTGTGTTCCA 59.399 34.615 13.73 0.00 46.54 3.53
2835 2959 6.912591 GCAATATAATGCTTAGTGTGTTCCAC 59.087 38.462 5.49 0.00 43.06 4.02
2845 2969 0.836606 TGTGTTCCACTTCCAGAGCA 59.163 50.000 0.00 0.00 35.11 4.26
2846 2970 1.202687 TGTGTTCCACTTCCAGAGCAG 60.203 52.381 0.00 0.00 35.11 4.24
2869 2993 3.086282 TGAATCTTGCATGTCACATGCT 58.914 40.909 36.36 20.74 44.79 3.79
2870 2994 3.128068 TGAATCTTGCATGTCACATGCTC 59.872 43.478 36.36 26.73 44.79 4.26
2872 3000 2.718563 TCTTGCATGTCACATGCTCAT 58.281 42.857 36.36 0.00 44.79 2.90
2907 3035 2.106477 ATCACACACACACACACACA 57.894 45.000 0.00 0.00 0.00 3.72
2908 3036 1.152510 TCACACACACACACACACAC 58.847 50.000 0.00 0.00 0.00 3.82
2909 3037 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2910 3038 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2911 3039 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2912 3040 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2913 3041 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2914 3042 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2915 3043 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2916 3044 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2917 3045 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2918 3046 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2931 3059 7.384115 ACACACACACACACTAGATTACAATAC 59.616 37.037 0.00 0.00 0.00 1.89
2956 3084 7.667219 ACATTAGATCAAATGTTCAACTCCACT 59.333 33.333 0.00 0.00 45.54 4.00
2957 3085 9.166173 CATTAGATCAAATGTTCAACTCCACTA 57.834 33.333 0.00 0.00 33.11 2.74
2958 3086 8.777865 TTAGATCAAATGTTCAACTCCACTAG 57.222 34.615 0.00 0.00 0.00 2.57
2959 3087 5.645497 AGATCAAATGTTCAACTCCACTAGC 59.355 40.000 0.00 0.00 0.00 3.42
2960 3088 4.713553 TCAAATGTTCAACTCCACTAGCA 58.286 39.130 0.00 0.00 0.00 3.49
3076 3209 1.655484 TGCACGTCAGCTAATCATGG 58.345 50.000 0.00 0.00 34.99 3.66
3089 3222 0.742505 ATCATGGCAGGCATCAAACG 59.257 50.000 6.47 0.00 0.00 3.60
3121 3254 5.365605 TGTCTGTAACTGAAGAGAAAAGGGA 59.634 40.000 0.00 0.00 0.00 4.20
3175 3317 5.460571 GCAGCTTGCAATTTCTTAAATCC 57.539 39.130 0.00 0.00 44.26 3.01
3291 3438 1.347320 GTTCCACTACGAGGAAAGCG 58.653 55.000 0.00 0.00 46.03 4.68
3336 3484 3.147629 CATCAGGAGATTGGCAGGATTC 58.852 50.000 0.00 0.00 30.20 2.52
3365 3518 3.174790 GCATTCGCCAGCAATCATC 57.825 52.632 0.00 0.00 0.00 2.92
3403 3559 8.771766 CCCTGCTGATCATAATCATAATAATCG 58.228 37.037 0.00 0.00 41.05 3.34
3454 3615 2.352127 GCTCGTAACCGAACCTACTGTT 60.352 50.000 0.00 0.00 43.69 3.16
3473 3634 4.053295 TGTTCGTACTTAACCAAGTGCTC 58.947 43.478 0.35 0.00 44.81 4.26
3521 3682 2.693591 CAAGATTGGCCTCATGATTGCT 59.306 45.455 3.32 0.00 0.00 3.91
3551 3715 9.905713 ATCAGTTGCAGGTTATAATTTAGAAGA 57.094 29.630 0.00 0.00 0.00 2.87
3552 3716 9.733556 TCAGTTGCAGGTTATAATTTAGAAGAA 57.266 29.630 0.00 0.00 0.00 2.52
3553 3717 9.994432 CAGTTGCAGGTTATAATTTAGAAGAAG 57.006 33.333 0.00 0.00 0.00 2.85
3555 3719 7.568199 TGCAGGTTATAATTTAGAAGAAGGC 57.432 36.000 0.00 0.00 0.00 4.35
3556 3720 6.260050 TGCAGGTTATAATTTAGAAGAAGGCG 59.740 38.462 0.00 0.00 0.00 5.52
3557 3721 6.482308 GCAGGTTATAATTTAGAAGAAGGCGA 59.518 38.462 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 147 2.363680 CTGTCATCGATAAGGTCCTGCT 59.636 50.000 0.00 0.00 0.00 4.24
149 150 1.689273 GCCTGTCATCGATAAGGTCCT 59.311 52.381 17.61 0.00 32.06 3.85
150 151 1.603172 CGCCTGTCATCGATAAGGTCC 60.603 57.143 17.61 5.97 32.06 4.46
168 169 0.967803 CGTGCACGAAGATTTTTCGC 59.032 50.000 34.93 0.00 44.98 4.70
171 172 1.599419 GGCACGTGCACGAAGATTTTT 60.599 47.619 42.94 17.58 44.36 1.94
172 173 0.040425 GGCACGTGCACGAAGATTTT 60.040 50.000 42.94 18.38 44.36 1.82
222 223 1.438651 TTCAAGGATTCAACGGCGAG 58.561 50.000 16.62 5.73 0.00 5.03
295 296 2.732619 CGGGAGGTGAGGTTAGGGC 61.733 68.421 0.00 0.00 0.00 5.19
309 310 2.203788 ACACCAGCTCTTCCGGGA 60.204 61.111 0.00 0.00 0.00 5.14
313 314 2.777832 AGATTCACACCAGCTCTTCC 57.222 50.000 0.00 0.00 0.00 3.46
324 325 1.141019 GCTCCGGCGTAGATTCACA 59.859 57.895 2.79 0.00 0.00 3.58
325 326 0.595310 GAGCTCCGGCGTAGATTCAC 60.595 60.000 2.79 0.00 44.37 3.18
373 374 3.648067 TCTTCCGGCATCATATCTTCCTT 59.352 43.478 0.00 0.00 0.00 3.36
382 383 1.274703 ACCCAGTCTTCCGGCATCAT 61.275 55.000 0.00 0.00 0.00 2.45
383 384 1.899437 GACCCAGTCTTCCGGCATCA 61.899 60.000 0.00 0.00 0.00 3.07
386 387 3.691342 CGACCCAGTCTTCCGGCA 61.691 66.667 0.00 0.00 0.00 5.69
387 388 2.837371 CTTCGACCCAGTCTTCCGGC 62.837 65.000 0.00 0.00 0.00 6.13
399 400 2.445438 CGGCGCTTCTTCTTCGACC 61.445 63.158 7.64 0.00 0.00 4.79
400 401 1.443872 TCGGCGCTTCTTCTTCGAC 60.444 57.895 7.64 0.00 0.00 4.20
418 419 1.002773 GGGTAGTGTTTGGACGGATGT 59.997 52.381 0.00 0.00 0.00 3.06
432 433 2.400467 ATAATCCTCGCAGGGGTAGT 57.600 50.000 2.86 0.00 35.59 2.73
450 451 8.854117 CCAACTAGTAGATAGGTACGGTTTTAT 58.146 37.037 3.59 0.00 35.63 1.40
451 452 7.285401 CCCAACTAGTAGATAGGTACGGTTTTA 59.715 40.741 3.59 0.00 35.63 1.52
452 453 6.097412 CCCAACTAGTAGATAGGTACGGTTTT 59.903 42.308 3.59 0.00 35.63 2.43
458 460 4.759183 CGGACCCAACTAGTAGATAGGTAC 59.241 50.000 3.59 0.37 35.63 3.34
527 531 3.561241 GGATTCGCCTCCCCTCCC 61.561 72.222 0.00 0.00 0.00 4.30
556 560 0.109319 CCCTTTGATTTTCACCGGCG 60.109 55.000 0.00 0.00 0.00 6.46
557 561 1.202348 CTCCCTTTGATTTTCACCGGC 59.798 52.381 0.00 0.00 0.00 6.13
558 562 1.818674 CCTCCCTTTGATTTTCACCGG 59.181 52.381 0.00 0.00 0.00 5.28
559 563 2.790433 TCCTCCCTTTGATTTTCACCG 58.210 47.619 0.00 0.00 0.00 4.94
566 570 4.593206 GGAAAAACCTTCCTCCCTTTGATT 59.407 41.667 0.00 0.00 35.73 2.57
570 574 2.972348 GGGAAAAACCTTCCTCCCTTT 58.028 47.619 3.66 0.00 43.74 3.11
583 587 1.530323 GCAAGGCGACTAGGGAAAAA 58.470 50.000 0.00 0.00 42.68 1.94
584 588 3.243128 GCAAGGCGACTAGGGAAAA 57.757 52.632 0.00 0.00 42.68 2.29
610 614 4.050852 AGGCAACAAGAGCTTTTCTTTG 57.949 40.909 0.00 0.00 43.68 2.77
625 629 5.122396 CAGAGTTTCATACCAGTAAGGCAAC 59.878 44.000 0.00 0.00 43.14 4.17
626 630 5.012664 TCAGAGTTTCATACCAGTAAGGCAA 59.987 40.000 0.00 0.00 43.14 4.52
627 631 4.530553 TCAGAGTTTCATACCAGTAAGGCA 59.469 41.667 0.00 0.00 43.14 4.75
628 632 5.086104 TCAGAGTTTCATACCAGTAAGGC 57.914 43.478 0.00 0.00 43.14 4.35
629 633 7.824289 TCAATTCAGAGTTTCATACCAGTAAGG 59.176 37.037 0.00 0.00 45.67 2.69
630 634 8.777865 TCAATTCAGAGTTTCATACCAGTAAG 57.222 34.615 0.00 0.00 0.00 2.34
631 635 8.593679 TCTCAATTCAGAGTTTCATACCAGTAA 58.406 33.333 0.00 0.00 36.97 2.24
632 636 8.035394 GTCTCAATTCAGAGTTTCATACCAGTA 58.965 37.037 0.00 0.00 36.97 2.74
633 637 6.876257 GTCTCAATTCAGAGTTTCATACCAGT 59.124 38.462 0.00 0.00 36.97 4.00
634 638 6.035435 CGTCTCAATTCAGAGTTTCATACCAG 59.965 42.308 0.00 0.00 36.97 4.00
635 639 5.869344 CGTCTCAATTCAGAGTTTCATACCA 59.131 40.000 0.00 0.00 36.97 3.25
636 640 6.100004 TCGTCTCAATTCAGAGTTTCATACC 58.900 40.000 0.00 0.00 36.97 2.73
637 641 7.582435 TTCGTCTCAATTCAGAGTTTCATAC 57.418 36.000 0.00 0.00 36.97 2.39
638 642 7.201556 GCATTCGTCTCAATTCAGAGTTTCATA 60.202 37.037 0.00 0.00 36.97 2.15
639 643 6.402983 GCATTCGTCTCAATTCAGAGTTTCAT 60.403 38.462 0.00 0.00 36.97 2.57
640 644 5.106948 GCATTCGTCTCAATTCAGAGTTTCA 60.107 40.000 0.00 0.00 36.97 2.69
641 645 5.106948 TGCATTCGTCTCAATTCAGAGTTTC 60.107 40.000 0.00 0.00 36.97 2.78
642 646 4.756642 TGCATTCGTCTCAATTCAGAGTTT 59.243 37.500 0.00 0.00 36.97 2.66
643 647 4.318332 TGCATTCGTCTCAATTCAGAGTT 58.682 39.130 0.00 0.00 36.97 3.01
644 648 3.930336 TGCATTCGTCTCAATTCAGAGT 58.070 40.909 0.00 0.00 36.97 3.24
645 649 4.436584 GGTTGCATTCGTCTCAATTCAGAG 60.437 45.833 0.00 0.00 36.97 3.35
646 650 3.436704 GGTTGCATTCGTCTCAATTCAGA 59.563 43.478 0.00 0.00 0.00 3.27
647 651 3.189080 TGGTTGCATTCGTCTCAATTCAG 59.811 43.478 0.00 0.00 0.00 3.02
648 652 3.145286 TGGTTGCATTCGTCTCAATTCA 58.855 40.909 0.00 0.00 0.00 2.57
649 653 3.189287 ACTGGTTGCATTCGTCTCAATTC 59.811 43.478 0.00 0.00 0.00 2.17
650 654 3.149196 ACTGGTTGCATTCGTCTCAATT 58.851 40.909 0.00 0.00 0.00 2.32
651 655 2.744202 GACTGGTTGCATTCGTCTCAAT 59.256 45.455 0.00 0.00 0.00 2.57
652 656 2.143122 GACTGGTTGCATTCGTCTCAA 58.857 47.619 0.00 0.00 0.00 3.02
653 657 1.795768 GACTGGTTGCATTCGTCTCA 58.204 50.000 0.00 0.00 0.00 3.27
654 658 0.716108 CGACTGGTTGCATTCGTCTC 59.284 55.000 0.00 0.00 0.00 3.36
655 659 0.317160 TCGACTGGTTGCATTCGTCT 59.683 50.000 0.00 0.00 33.20 4.18
656 660 1.324736 GATCGACTGGTTGCATTCGTC 59.675 52.381 0.00 0.00 33.20 4.20
657 661 1.066858 AGATCGACTGGTTGCATTCGT 60.067 47.619 0.00 0.00 33.20 3.85
658 662 1.590238 GAGATCGACTGGTTGCATTCG 59.410 52.381 0.00 0.00 0.00 3.34
659 663 2.898705 AGAGATCGACTGGTTGCATTC 58.101 47.619 0.00 0.00 0.00 2.67
660 664 3.340814 AAGAGATCGACTGGTTGCATT 57.659 42.857 0.00 0.00 0.00 3.56
661 665 3.055530 AGAAAGAGATCGACTGGTTGCAT 60.056 43.478 0.00 0.00 0.00 3.96
662 666 2.300152 AGAAAGAGATCGACTGGTTGCA 59.700 45.455 0.00 0.00 0.00 4.08
663 667 2.966050 AGAAAGAGATCGACTGGTTGC 58.034 47.619 0.00 0.00 0.00 4.17
664 668 6.647067 ACTTTAAGAAAGAGATCGACTGGTTG 59.353 38.462 5.98 0.00 41.02 3.77
665 669 6.760291 ACTTTAAGAAAGAGATCGACTGGTT 58.240 36.000 5.98 0.00 41.02 3.67
666 670 6.347859 ACTTTAAGAAAGAGATCGACTGGT 57.652 37.500 5.98 0.00 41.02 4.00
667 671 7.313646 TGTACTTTAAGAAAGAGATCGACTGG 58.686 38.462 5.98 0.00 41.02 4.00
668 672 8.024285 ACTGTACTTTAAGAAAGAGATCGACTG 58.976 37.037 5.98 2.10 41.02 3.51
669 673 8.113173 ACTGTACTTTAAGAAAGAGATCGACT 57.887 34.615 5.98 0.00 41.02 4.18
670 674 8.745464 AACTGTACTTTAAGAAAGAGATCGAC 57.255 34.615 5.98 0.00 41.02 4.20
671 675 9.193133 CAAACTGTACTTTAAGAAAGAGATCGA 57.807 33.333 5.98 0.00 41.02 3.59
672 676 9.193133 TCAAACTGTACTTTAAGAAAGAGATCG 57.807 33.333 5.98 0.00 41.02 3.69
674 678 9.495572 CCTCAAACTGTACTTTAAGAAAGAGAT 57.504 33.333 5.98 0.00 41.02 2.75
675 679 7.931948 CCCTCAAACTGTACTTTAAGAAAGAGA 59.068 37.037 5.98 0.00 41.02 3.10
676 680 7.715686 ACCCTCAAACTGTACTTTAAGAAAGAG 59.284 37.037 5.98 0.00 41.02 2.85
677 681 7.497909 CACCCTCAAACTGTACTTTAAGAAAGA 59.502 37.037 5.98 0.00 41.02 2.52
678 682 7.497909 TCACCCTCAAACTGTACTTTAAGAAAG 59.502 37.037 0.00 0.00 44.10 2.62
679 683 7.340256 TCACCCTCAAACTGTACTTTAAGAAA 58.660 34.615 0.00 0.00 0.00 2.52
680 684 6.891388 TCACCCTCAAACTGTACTTTAAGAA 58.109 36.000 0.00 0.00 0.00 2.52
681 685 6.488769 TCACCCTCAAACTGTACTTTAAGA 57.511 37.500 0.00 0.00 0.00 2.10
682 686 7.745620 ATTCACCCTCAAACTGTACTTTAAG 57.254 36.000 0.00 0.00 0.00 1.85
683 687 8.410141 CAAATTCACCCTCAAACTGTACTTTAA 58.590 33.333 0.00 0.00 0.00 1.52
684 688 7.558444 ACAAATTCACCCTCAAACTGTACTTTA 59.442 33.333 0.00 0.00 0.00 1.85
685 689 6.379988 ACAAATTCACCCTCAAACTGTACTTT 59.620 34.615 0.00 0.00 0.00 2.66
686 690 5.891551 ACAAATTCACCCTCAAACTGTACTT 59.108 36.000 0.00 0.00 0.00 2.24
693 697 5.344884 TCGAAAACAAATTCACCCTCAAAC 58.655 37.500 0.00 0.00 0.00 2.93
718 722 1.335182 CTACACAGATGGCGATCGTCT 59.665 52.381 21.85 11.07 42.17 4.18
720 724 0.249073 GCTACACAGATGGCGATCGT 60.249 55.000 17.81 0.00 33.34 3.73
726 730 2.691409 TTGGTAGCTACACAGATGGC 57.309 50.000 24.75 5.94 0.00 4.40
757 761 1.852895 GATCGACCGATTTCTCCGTTG 59.147 52.381 6.36 0.00 34.60 4.10
777 781 1.886861 GCAGACTGCACGTACCAACG 61.887 60.000 22.62 0.00 44.26 4.10
778 782 1.860078 GCAGACTGCACGTACCAAC 59.140 57.895 22.62 0.00 44.26 3.77
802 806 1.569479 GGTGCTCTGGAAAGCGACAC 61.569 60.000 0.00 0.00 45.54 3.67
823 827 0.467804 TGAGTTGCACTACCACTGCA 59.532 50.000 0.00 0.00 42.95 4.41
824 828 1.151668 CTGAGTTGCACTACCACTGC 58.848 55.000 0.00 0.00 35.03 4.40
825 829 1.151668 GCTGAGTTGCACTACCACTG 58.848 55.000 0.00 0.00 0.00 3.66
826 830 0.319900 CGCTGAGTTGCACTACCACT 60.320 55.000 0.00 0.00 0.00 4.00
827 831 0.319555 TCGCTGAGTTGCACTACCAC 60.320 55.000 0.00 0.00 0.00 4.16
828 832 0.319555 GTCGCTGAGTTGCACTACCA 60.320 55.000 0.00 0.00 0.00 3.25
829 833 1.344942 CGTCGCTGAGTTGCACTACC 61.345 60.000 0.00 0.00 0.00 3.18
830 834 1.945776 GCGTCGCTGAGTTGCACTAC 61.946 60.000 10.68 0.00 0.00 2.73
877 884 3.669036 CTCCTCCGTCGAGTGCACG 62.669 68.421 12.01 0.00 33.93 5.34
898 911 0.248702 GCCGGAGAGACGATGAAGAC 60.249 60.000 5.05 0.00 35.47 3.01
935 948 0.914902 TGGGAGAGAGAGGAGGACGA 60.915 60.000 0.00 0.00 0.00 4.20
936 949 0.750182 GTGGGAGAGAGAGGAGGACG 60.750 65.000 0.00 0.00 0.00 4.79
937 950 0.396556 GGTGGGAGAGAGAGGAGGAC 60.397 65.000 0.00 0.00 0.00 3.85
938 951 0.851332 TGGTGGGAGAGAGAGGAGGA 60.851 60.000 0.00 0.00 0.00 3.71
941 979 0.333312 GAGTGGTGGGAGAGAGAGGA 59.667 60.000 0.00 0.00 0.00 3.71
943 981 1.473258 CTGAGTGGTGGGAGAGAGAG 58.527 60.000 0.00 0.00 0.00 3.20
954 992 4.626081 GTGGTGCCGCTGAGTGGT 62.626 66.667 14.33 0.00 35.34 4.16
957 995 2.919856 AGAGTGGTGCCGCTGAGT 60.920 61.111 9.24 0.00 36.86 3.41
961 999 4.385405 GCAGAGAGTGGTGCCGCT 62.385 66.667 3.67 3.67 39.77 5.52
965 1003 1.376553 GGAAGGCAGAGAGTGGTGC 60.377 63.158 0.00 0.00 39.08 5.01
966 1004 0.248843 GAGGAAGGCAGAGAGTGGTG 59.751 60.000 0.00 0.00 0.00 4.17
967 1005 0.907230 GGAGGAAGGCAGAGAGTGGT 60.907 60.000 0.00 0.00 0.00 4.16
968 1006 1.621672 GGGAGGAAGGCAGAGAGTGG 61.622 65.000 0.00 0.00 0.00 4.00
969 1007 0.617249 AGGGAGGAAGGCAGAGAGTG 60.617 60.000 0.00 0.00 0.00 3.51
970 1008 0.325203 GAGGGAGGAAGGCAGAGAGT 60.325 60.000 0.00 0.00 0.00 3.24
971 1009 1.048160 GGAGGGAGGAAGGCAGAGAG 61.048 65.000 0.00 0.00 0.00 3.20
972 1010 1.002274 GGAGGGAGGAAGGCAGAGA 59.998 63.158 0.00 0.00 0.00 3.10
973 1011 0.693767 ATGGAGGGAGGAAGGCAGAG 60.694 60.000 0.00 0.00 0.00 3.35
974 1012 0.984961 CATGGAGGGAGGAAGGCAGA 60.985 60.000 0.00 0.00 0.00 4.26
975 1013 0.984961 TCATGGAGGGAGGAAGGCAG 60.985 60.000 0.00 0.00 0.00 4.85
976 1014 0.984961 CTCATGGAGGGAGGAAGGCA 60.985 60.000 0.00 0.00 0.00 4.75
977 1015 1.835693 CTCATGGAGGGAGGAAGGC 59.164 63.158 0.00 0.00 0.00 4.35
978 1016 1.835693 GCTCATGGAGGGAGGAAGG 59.164 63.158 0.00 0.00 32.96 3.46
979 1017 1.445095 CGCTCATGGAGGGAGGAAG 59.555 63.158 4.46 0.00 43.87 3.46
980 1018 2.735772 GCGCTCATGGAGGGAGGAA 61.736 63.158 13.64 0.00 43.87 3.36
1432 1479 0.721718 GAGCCGATCGGTCAGTTTTG 59.278 55.000 33.33 6.93 38.92 2.44
1632 1681 1.372997 CACGGTGGAGGAGACGTTG 60.373 63.158 0.00 0.00 37.48 4.10
1725 1783 6.579865 ACGGTGGTGATTAATAAGAAGGTAG 58.420 40.000 0.00 0.00 0.00 3.18
1733 1795 5.991861 ACATGGTACGGTGGTGATTAATAA 58.008 37.500 0.00 0.00 0.00 1.40
1798 1860 0.968405 GGCCATCAAGTTTCCAGCAA 59.032 50.000 0.00 0.00 0.00 3.91
1998 2060 1.231928 GGGAGGAGGAGGAGGACTC 59.768 68.421 0.00 0.00 45.84 3.36
2003 2065 0.398381 CAAGAGGGGAGGAGGAGGAG 60.398 65.000 0.00 0.00 0.00 3.69
2060 2134 1.375908 GCCTGCCTCACATCGACAA 60.376 57.895 0.00 0.00 0.00 3.18
2102 2177 4.758251 CGATGCGGTGTGAGGCCA 62.758 66.667 5.01 0.00 0.00 5.36
2141 2216 3.003897 GCCACGTTTATTTGTTGACTCCA 59.996 43.478 0.00 0.00 0.00 3.86
2171 2251 5.895534 AGTCGTTCCAGGGTACAATAAGATA 59.104 40.000 0.00 0.00 0.00 1.98
2260 2340 5.049818 GTGAATGAAGTGAAAGTGAGAGTGG 60.050 44.000 0.00 0.00 0.00 4.00
2272 2352 1.808411 GGCCGAAGTGAATGAAGTGA 58.192 50.000 0.00 0.00 0.00 3.41
2273 2353 0.443869 CGGCCGAAGTGAATGAAGTG 59.556 55.000 24.07 0.00 0.00 3.16
2274 2354 0.320374 TCGGCCGAAGTGAATGAAGT 59.680 50.000 28.99 0.00 0.00 3.01
2275 2355 1.594862 GATCGGCCGAAGTGAATGAAG 59.405 52.381 34.66 0.00 0.00 3.02
2277 2357 0.534873 TGATCGGCCGAAGTGAATGA 59.465 50.000 34.66 5.37 0.00 2.57
2279 2359 1.369625 GTTGATCGGCCGAAGTGAAT 58.630 50.000 34.66 15.34 0.00 2.57
2280 2360 1.011968 CGTTGATCGGCCGAAGTGAA 61.012 55.000 34.66 14.91 35.71 3.18
2281 2361 1.445410 CGTTGATCGGCCGAAGTGA 60.445 57.895 34.66 15.76 35.71 3.41
2282 2362 3.081133 CGTTGATCGGCCGAAGTG 58.919 61.111 34.66 16.46 35.71 3.16
2327 2407 1.893808 GCCGCCTGGGACATACATG 60.894 63.158 0.00 0.00 38.20 3.21
2328 2408 2.510906 GCCGCCTGGGACATACAT 59.489 61.111 0.00 0.00 38.20 2.29
2486 2569 2.892425 CCTTCTCGGCGGTGATGC 60.892 66.667 7.21 0.00 0.00 3.91
2512 2595 3.083997 GGTGACGGGGAGGCTCAT 61.084 66.667 17.69 0.00 0.00 2.90
2513 2596 4.631740 TGGTGACGGGGAGGCTCA 62.632 66.667 17.69 0.00 0.00 4.26
2518 2601 2.266055 GAAGCTGGTGACGGGGAG 59.734 66.667 0.00 0.00 37.13 4.30
2519 2602 2.525629 TGAAGCTGGTGACGGGGA 60.526 61.111 0.00 0.00 37.13 4.81
2520 2603 2.046892 CTGAAGCTGGTGACGGGG 60.047 66.667 0.00 0.00 37.13 5.73
2620 2711 1.736032 GCGACATCTTGTAGCCGTTCT 60.736 52.381 1.83 0.00 42.06 3.01
2637 2734 2.426522 CTCCAATTTCAGGTTCTGCGA 58.573 47.619 0.00 0.00 0.00 5.10
2663 2760 6.498304 ACTCAACTTTGCACTAACTTTGATG 58.502 36.000 0.00 0.00 0.00 3.07
2664 2761 6.318648 TGACTCAACTTTGCACTAACTTTGAT 59.681 34.615 0.00 0.00 0.00 2.57
2665 2762 5.645929 TGACTCAACTTTGCACTAACTTTGA 59.354 36.000 0.00 0.00 0.00 2.69
2834 2958 1.907936 AGATTCAGCTGCTCTGGAAGT 59.092 47.619 9.47 0.00 43.06 3.01
2835 2959 2.678836 CAAGATTCAGCTGCTCTGGAAG 59.321 50.000 9.47 2.12 43.06 3.46
2836 2960 2.708051 CAAGATTCAGCTGCTCTGGAA 58.292 47.619 9.47 0.68 43.06 3.53
2837 2961 1.678123 GCAAGATTCAGCTGCTCTGGA 60.678 52.381 19.30 0.00 43.06 3.86
2839 2963 1.450025 TGCAAGATTCAGCTGCTCTG 58.550 50.000 9.47 9.32 44.21 3.35
2840 2964 2.017782 CATGCAAGATTCAGCTGCTCT 58.982 47.619 9.47 10.76 0.00 4.09
2841 2965 1.743958 ACATGCAAGATTCAGCTGCTC 59.256 47.619 9.47 8.43 0.00 4.26
2842 2966 1.743958 GACATGCAAGATTCAGCTGCT 59.256 47.619 9.47 0.00 0.00 4.24
2843 2967 1.471287 TGACATGCAAGATTCAGCTGC 59.529 47.619 9.47 0.00 0.00 5.25
2845 2969 2.786777 TGTGACATGCAAGATTCAGCT 58.213 42.857 0.00 0.00 0.00 4.24
2846 2970 3.435566 CATGTGACATGCAAGATTCAGC 58.564 45.455 13.15 0.00 0.00 4.26
2854 2978 2.718563 AGATGAGCATGTGACATGCAA 58.281 42.857 41.04 31.66 46.77 4.08
2869 2993 3.781965 TGATTGATGGACAGGGAAGATGA 59.218 43.478 0.00 0.00 0.00 2.92
2870 2994 3.881688 GTGATTGATGGACAGGGAAGATG 59.118 47.826 0.00 0.00 0.00 2.90
2872 3000 2.912295 TGTGATTGATGGACAGGGAAGA 59.088 45.455 0.00 0.00 0.00 2.87
2907 3035 7.438564 TGTATTGTAATCTAGTGTGTGTGTGT 58.561 34.615 0.00 0.00 0.00 3.72
2908 3036 7.883229 TGTATTGTAATCTAGTGTGTGTGTG 57.117 36.000 0.00 0.00 0.00 3.82
2931 3059 8.048534 AGTGGAGTTGAACATTTGATCTAATG 57.951 34.615 22.97 22.97 40.53 1.90
2937 3065 5.316167 TGCTAGTGGAGTTGAACATTTGAT 58.684 37.500 0.00 0.00 0.00 2.57
2956 3084 7.500227 GGCTGGATAATTATTCATGCTATGCTA 59.500 37.037 19.20 0.00 0.00 3.49
2957 3085 6.320672 GGCTGGATAATTATTCATGCTATGCT 59.679 38.462 19.20 0.00 0.00 3.79
2958 3086 6.460676 GGGCTGGATAATTATTCATGCTATGC 60.461 42.308 19.20 13.11 0.00 3.14
2959 3087 6.604396 TGGGCTGGATAATTATTCATGCTATG 59.396 38.462 19.20 6.25 0.00 2.23
2960 3088 6.734532 TGGGCTGGATAATTATTCATGCTAT 58.265 36.000 19.20 0.00 0.00 2.97
3076 3209 1.154225 CGGTTCGTTTGATGCCTGC 60.154 57.895 0.00 0.00 0.00 4.85
3089 3222 2.750948 TCAGTTACAGACAAGCGGTTC 58.249 47.619 0.00 0.00 0.00 3.62
3247 3394 2.356135 AGCGGATGATTAACAAGCGTT 58.644 42.857 0.00 0.00 39.24 4.84
3248 3395 2.024176 AGCGGATGATTAACAAGCGT 57.976 45.000 0.00 0.00 34.49 5.07
3249 3396 3.405170 AAAGCGGATGATTAACAAGCG 57.595 42.857 0.00 0.00 34.49 4.68
3250 3397 4.201783 ACGTAAAGCGGATGATTAACAAGC 60.202 41.667 0.00 0.00 46.52 4.01
3336 3484 2.842256 GCGAATGCCCATCCAGCTG 61.842 63.158 6.78 6.78 33.98 4.24
3403 3559 2.041244 CGAAAGCCGCTTTGTGTTTAC 58.959 47.619 22.93 5.81 33.49 2.01
3409 3565 1.155424 TTCGTCGAAAGCCGCTTTGT 61.155 50.000 22.93 0.00 33.49 2.83
3454 3615 2.352030 CCGAGCACTTGGTTAAGTACGA 60.352 50.000 0.00 0.00 45.12 3.43
3473 3634 7.043125 CGCTAATCATATCCTAACATCATTCCG 60.043 40.741 0.00 0.00 0.00 4.30
3551 3715 2.704572 CACAGGAATCTTCTTCGCCTT 58.295 47.619 0.00 0.00 0.00 4.35
3552 3716 1.677217 GCACAGGAATCTTCTTCGCCT 60.677 52.381 0.00 0.00 0.00 5.52
3553 3717 0.729690 GCACAGGAATCTTCTTCGCC 59.270 55.000 0.00 0.00 0.00 5.54
3555 3719 1.396301 GCAGCACAGGAATCTTCTTCG 59.604 52.381 0.00 0.00 0.00 3.79
3556 3720 2.430465 TGCAGCACAGGAATCTTCTTC 58.570 47.619 0.00 0.00 0.00 2.87
3557 3721 2.574006 TGCAGCACAGGAATCTTCTT 57.426 45.000 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.