Multiple sequence alignment - TraesCS3B01G131800

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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 TraesCS3B01G131800 chr3B 100.000 2667 0 0 1 2667 114141594 114144260 0.000000e+00 4926.0
1 TraesCS3B01G131800 chr3B 95.937 443 17 1 1 443 191146390 191145949 0.000000e+00 717.0
2 TraesCS3B01G131800 chr3B 88.850 287 23 6 444 723 763247525 763247809 7.070000e-91 344.0
3 TraesCS3B01G131800 chr3B 100.000 30 0 0 1634 1663 114143197 114143226 3.710000e-04 56.5
4 TraesCS3B01G131800 chr3B 100.000 30 0 0 1604 1633 114143227 114143256 3.710000e-04 56.5
5 TraesCS3B01G131800 chr3D 90.544 1047 60 16 1634 2667 67713245 67712225 0.000000e+00 1349.0
6 TraesCS3B01G131800 chr3D 90.899 879 41 14 794 1633 67714094 67713216 0.000000e+00 1144.0
7 TraesCS3B01G131800 chr3D 95.034 443 22 0 1 443 583609509 583609951 0.000000e+00 697.0
8 TraesCS3B01G131800 chr3A 90.628 1035 64 14 1634 2657 79403114 79402102 0.000000e+00 1343.0
9 TraesCS3B01G131800 chr3A 95.272 698 30 3 938 1633 79403781 79403085 0.000000e+00 1103.0
10 TraesCS3B01G131800 chr2A 87.430 891 61 15 1735 2592 73554200 73555072 0.000000e+00 977.0
11 TraesCS3B01G131800 chr2B 90.579 743 39 6 1930 2651 113325565 113326297 0.000000e+00 955.0
12 TraesCS3B01G131800 chr2B 94.808 443 23 0 1 443 532003727 532003285 0.000000e+00 691.0
13 TraesCS3B01G131800 chr2B 87.900 281 31 2 444 721 608481164 608481444 7.120000e-86 327.0
14 TraesCS3B01G131800 chr2B 90.741 108 5 5 817 922 113325475 113325579 3.580000e-29 139.0
15 TraesCS3B01G131800 chr2D 90.122 739 42 6 1934 2651 74279191 74279919 0.000000e+00 931.0
16 TraesCS3B01G131800 chr2D 95.798 119 5 0 794 912 74279071 74279189 2.710000e-45 193.0
17 TraesCS3B01G131800 chr5B 95.485 443 20 0 1 443 653003156 653003598 0.000000e+00 708.0
18 TraesCS3B01G131800 chr4B 95.485 443 20 0 1 443 634193525 634193967 0.000000e+00 708.0
19 TraesCS3B01G131800 chr4B 95.260 443 21 0 1 443 171808686 171808244 0.000000e+00 702.0
20 TraesCS3B01G131800 chr4B 95.011 441 22 0 3 443 72841201 72841641 0.000000e+00 693.0
21 TraesCS3B01G131800 chr4B 89.416 274 23 4 449 719 634194931 634195201 9.140000e-90 340.0
22 TraesCS3B01G131800 chr4B 88.645 273 29 2 447 717 37924581 37924309 5.500000e-87 331.0
23 TraesCS3B01G131800 chr1B 94.808 443 23 0 1 443 40367094 40367536 0.000000e+00 691.0
24 TraesCS3B01G131800 chr1B 88.172 279 27 5 445 719 611320684 611320960 7.120000e-86 327.0
25 TraesCS3B01G131800 chr6D 94.808 443 20 1 1 443 465950496 465950935 0.000000e+00 688.0
26 TraesCS3B01G131800 chr1D 89.046 283 26 5 444 721 308447175 308447457 1.970000e-91 346.0
27 TraesCS3B01G131800 chr7B 88.612 281 29 2 447 724 15925649 15925369 3.290000e-89 339.0
28 TraesCS3B01G131800 chr5D 88.612 281 26 6 444 719 260845023 260845302 1.180000e-88 337.0
29 TraesCS3B01G131800 chr5D 88.768 276 28 3 447 719 481124754 481124479 4.250000e-88 335.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G131800 chr3B 114141594 114144260 2666 False 1679.666667 4926 100.0000 1 2667 3 chr3B.!!$F2 2666
1 TraesCS3B01G131800 chr3D 67712225 67714094 1869 True 1246.500000 1349 90.7215 794 2667 2 chr3D.!!$R1 1873
2 TraesCS3B01G131800 chr3A 79402102 79403781 1679 True 1223.000000 1343 92.9500 938 2657 2 chr3A.!!$R1 1719
3 TraesCS3B01G131800 chr2A 73554200 73555072 872 False 977.000000 977 87.4300 1735 2592 1 chr2A.!!$F1 857
4 TraesCS3B01G131800 chr2B 113325475 113326297 822 False 547.000000 955 90.6600 817 2651 2 chr2B.!!$F2 1834
5 TraesCS3B01G131800 chr2D 74279071 74279919 848 False 562.000000 931 92.9600 794 2651 2 chr2D.!!$F1 1857
6 TraesCS3B01G131800 chr4B 634193525 634195201 1676 False 524.000000 708 92.4505 1 719 2 chr4B.!!$F2 718

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
606 607 0.033504 ACCGCGCCCAACTCTATATG 59.966 55.0 0.00 0.00 0.00 1.78 F
771 772 0.034616 ATAGCTGCTTCCAGATCGCC 59.965 55.0 7.79 0.00 41.77 5.54 F
781 782 0.101759 CCAGATCGCCAAATGCAAGG 59.898 55.0 0.00 0.00 41.33 3.61 F
787 788 0.456653 CGCCAAATGCAAGGTACTGC 60.457 55.0 0.00 0.27 40.86 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 2148 0.036010 CCGTTCATGGAGGAGCTTGT 60.036 55.0 0.00 0.00 0.00 3.16 R
1661 2158 0.174845 TAGCTCGGTTCCGTTCATGG 59.825 55.0 11.04 0.00 0.00 3.66 R
1665 2162 0.175073 ACCATAGCTCGGTTCCGTTC 59.825 55.0 11.04 4.59 30.53 3.95 R
1667 2164 0.743097 GTACCATAGCTCGGTTCCGT 59.257 55.0 12.67 0.00 37.99 4.69 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
74 75 6.322969 TCCATAGCATTTTTGAGCTCATCATT 59.677 34.615 19.04 0.28 42.05 2.57
76 77 7.494625 CCATAGCATTTTTGAGCTCATCATTTT 59.505 33.333 19.04 3.91 42.05 1.82
135 136 0.596082 CATCCGGTCGTTTTGGCTTT 59.404 50.000 0.00 0.00 0.00 3.51
155 156 5.682943 TTTGAGTATGAAACCGAGTTTGG 57.317 39.130 6.73 0.00 35.77 3.28
166 167 1.515521 CGAGTTTGGTGTGGGGCTTC 61.516 60.000 0.00 0.00 0.00 3.86
191 192 5.361571 TCTTGCCATATTCACTTGATGCATT 59.638 36.000 0.00 0.00 0.00 3.56
198 199 3.986996 TCACTTGATGCATTCTCCTCA 57.013 42.857 0.00 0.00 0.00 3.86
201 202 4.080751 TCACTTGATGCATTCTCCTCATCA 60.081 41.667 0.00 0.00 43.17 3.07
203 204 5.299531 CACTTGATGCATTCTCCTCATCATT 59.700 40.000 0.00 0.00 43.94 2.57
209 210 7.942894 TGATGCATTCTCCTCATCATTATCTTT 59.057 33.333 0.00 0.00 40.91 2.52
230 231 5.493397 TTCAAATTAATTGTTCGCTTGCG 57.507 34.783 8.87 8.87 40.11 4.85
265 266 8.853126 TCAAATCCAAATCATCAATATCCTCAC 58.147 33.333 0.00 0.00 0.00 3.51
279 280 3.140325 TCCTCACGCTTCTTCCATTTT 57.860 42.857 0.00 0.00 0.00 1.82
307 308 7.792374 TCATCCTTCAATACTTCATAGCAAC 57.208 36.000 0.00 0.00 0.00 4.17
425 426 7.111353 TGAAAACAAAACAAGTTAGCACAAC 57.889 32.000 0.00 0.00 0.00 3.32
443 444 1.989430 ACAAACACCAACAACAAGCG 58.011 45.000 0.00 0.00 0.00 4.68
444 445 0.644843 CAAACACCAACAACAAGCGC 59.355 50.000 0.00 0.00 0.00 5.92
445 446 0.530288 AAACACCAACAACAAGCGCT 59.470 45.000 2.64 2.64 0.00 5.92
446 447 0.100503 AACACCAACAACAAGCGCTC 59.899 50.000 12.06 0.00 0.00 5.03
447 448 1.369209 CACCAACAACAAGCGCTCG 60.369 57.895 12.06 0.00 0.00 5.03
448 449 1.817941 ACCAACAACAAGCGCTCGT 60.818 52.632 12.06 0.82 0.00 4.18
449 450 1.369209 CCAACAACAAGCGCTCGTG 60.369 57.895 12.06 9.39 0.00 4.35
450 451 2.005537 CAACAACAAGCGCTCGTGC 61.006 57.895 12.06 0.00 0.00 5.34
461 462 4.129737 CTCGTGCGTCCATCGGGT 62.130 66.667 0.00 0.00 40.26 5.28
462 463 4.124351 TCGTGCGTCCATCGGGTC 62.124 66.667 0.00 0.00 40.26 4.46
463 464 4.429212 CGTGCGTCCATCGGGTCA 62.429 66.667 0.00 0.00 40.26 4.02
464 465 2.047655 GTGCGTCCATCGGGTCAA 60.048 61.111 0.00 0.00 40.26 3.18
465 466 2.047655 TGCGTCCATCGGGTCAAC 60.048 61.111 0.00 0.00 40.26 3.18
466 467 2.264794 GCGTCCATCGGGTCAACT 59.735 61.111 0.00 0.00 40.26 3.16
467 468 1.810030 GCGTCCATCGGGTCAACTC 60.810 63.158 0.00 0.00 40.26 3.01
468 469 1.516386 CGTCCATCGGGTCAACTCG 60.516 63.158 0.00 0.00 35.71 4.18
469 470 1.810030 GTCCATCGGGTCAACTCGC 60.810 63.158 0.00 0.00 34.93 5.03
470 471 2.511600 CCATCGGGTCAACTCGCC 60.512 66.667 0.00 0.00 0.00 5.54
471 472 2.885644 CATCGGGTCAACTCGCCG 60.886 66.667 0.00 0.00 0.00 6.46
472 473 4.143333 ATCGGGTCAACTCGCCGG 62.143 66.667 0.00 0.00 0.00 6.13
518 519 3.827898 CGGGGGAGAGAGTGCGAC 61.828 72.222 0.00 0.00 0.00 5.19
519 520 3.827898 GGGGGAGAGAGTGCGACG 61.828 72.222 0.00 0.00 0.00 5.12
520 521 4.500116 GGGGAGAGAGTGCGACGC 62.500 72.222 14.19 14.19 0.00 5.19
521 522 4.838486 GGGAGAGAGTGCGACGCG 62.838 72.222 16.14 3.53 0.00 6.01
522 523 3.800863 GGAGAGAGTGCGACGCGA 61.801 66.667 15.93 1.28 0.00 5.87
523 524 2.276994 GAGAGAGTGCGACGCGAG 60.277 66.667 15.93 7.68 0.00 5.03
524 525 4.468615 AGAGAGTGCGACGCGAGC 62.469 66.667 15.93 18.93 0.00 5.03
560 561 4.659172 CGGAAGCAGGTGCCCCAA 62.659 66.667 10.48 0.00 43.38 4.12
561 562 2.677875 GGAAGCAGGTGCCCCAAG 60.678 66.667 0.00 0.00 43.38 3.61
562 563 2.116125 GAAGCAGGTGCCCCAAGT 59.884 61.111 0.00 0.00 43.38 3.16
563 564 1.378762 GAAGCAGGTGCCCCAAGTA 59.621 57.895 0.00 0.00 43.38 2.24
564 565 0.960861 GAAGCAGGTGCCCCAAGTAC 60.961 60.000 0.00 0.00 43.38 2.73
565 566 2.746277 GCAGGTGCCCCAAGTACG 60.746 66.667 0.00 0.00 34.31 3.67
566 567 2.746277 CAGGTGCCCCAAGTACGC 60.746 66.667 0.00 0.00 30.59 4.42
567 568 3.246112 AGGTGCCCCAAGTACGCA 61.246 61.111 0.00 0.00 30.59 5.24
568 569 2.746277 GGTGCCCCAAGTACGCAG 60.746 66.667 0.00 0.00 32.08 5.18
569 570 2.746277 GTGCCCCAAGTACGCAGG 60.746 66.667 0.00 0.00 32.08 4.85
570 571 4.028490 TGCCCCAAGTACGCAGGG 62.028 66.667 11.58 11.58 42.94 4.45
583 584 2.586079 CAGGGCGCGATGACGATT 60.586 61.111 12.10 0.00 42.66 3.34
584 585 2.279517 AGGGCGCGATGACGATTC 60.280 61.111 12.10 0.00 42.66 2.52
585 586 2.584970 GGGCGCGATGACGATTCA 60.585 61.111 12.10 0.00 42.66 2.57
586 587 2.171079 GGGCGCGATGACGATTCAA 61.171 57.895 12.10 0.00 42.66 2.69
587 588 1.701545 GGGCGCGATGACGATTCAAA 61.702 55.000 12.10 0.00 42.66 2.69
588 589 0.586502 GGCGCGATGACGATTCAAAC 60.587 55.000 12.10 0.00 42.66 2.93
589 590 0.586502 GCGCGATGACGATTCAAACC 60.587 55.000 12.10 0.00 42.66 3.27
590 591 0.314259 CGCGATGACGATTCAAACCG 60.314 55.000 0.00 0.00 42.66 4.44
591 592 0.586502 GCGATGACGATTCAAACCGC 60.587 55.000 0.00 0.00 42.66 5.68
592 593 0.314259 CGATGACGATTCAAACCGCG 60.314 55.000 0.00 0.00 42.66 6.46
593 594 0.586502 GATGACGATTCAAACCGCGC 60.587 55.000 0.00 0.00 34.61 6.86
594 595 1.977594 ATGACGATTCAAACCGCGCC 61.978 55.000 0.00 0.00 34.61 6.53
595 596 3.376914 GACGATTCAAACCGCGCCC 62.377 63.158 0.00 0.00 0.00 6.13
596 597 3.427425 CGATTCAAACCGCGCCCA 61.427 61.111 0.00 0.00 0.00 5.36
597 598 2.958576 GATTCAAACCGCGCCCAA 59.041 55.556 0.00 0.00 0.00 4.12
598 599 1.443702 GATTCAAACCGCGCCCAAC 60.444 57.895 0.00 0.00 0.00 3.77
599 600 1.862602 GATTCAAACCGCGCCCAACT 61.863 55.000 0.00 0.00 0.00 3.16
600 601 1.862602 ATTCAAACCGCGCCCAACTC 61.863 55.000 0.00 0.00 0.00 3.01
601 602 2.951475 TTCAAACCGCGCCCAACTCT 62.951 55.000 0.00 0.00 0.00 3.24
602 603 1.669760 CAAACCGCGCCCAACTCTA 60.670 57.895 0.00 0.00 0.00 2.43
603 604 1.024579 CAAACCGCGCCCAACTCTAT 61.025 55.000 0.00 0.00 0.00 1.98
604 605 0.538118 AAACCGCGCCCAACTCTATA 59.462 50.000 0.00 0.00 0.00 1.31
605 606 0.756903 AACCGCGCCCAACTCTATAT 59.243 50.000 0.00 0.00 0.00 0.86
606 607 0.033504 ACCGCGCCCAACTCTATATG 59.966 55.000 0.00 0.00 0.00 1.78
607 608 1.291877 CCGCGCCCAACTCTATATGC 61.292 60.000 0.00 0.00 0.00 3.14
608 609 1.291877 CGCGCCCAACTCTATATGCC 61.292 60.000 0.00 0.00 0.00 4.40
609 610 0.250295 GCGCCCAACTCTATATGCCA 60.250 55.000 0.00 0.00 0.00 4.92
610 611 1.512926 CGCCCAACTCTATATGCCAC 58.487 55.000 0.00 0.00 0.00 5.01
611 612 1.512926 GCCCAACTCTATATGCCACG 58.487 55.000 0.00 0.00 0.00 4.94
612 613 1.512926 CCCAACTCTATATGCCACGC 58.487 55.000 0.00 0.00 0.00 5.34
613 614 1.139989 CCAACTCTATATGCCACGCG 58.860 55.000 3.53 3.53 0.00 6.01
614 615 0.508641 CAACTCTATATGCCACGCGC 59.491 55.000 5.73 0.00 38.31 6.86
615 616 0.939577 AACTCTATATGCCACGCGCG 60.940 55.000 30.96 30.96 42.08 6.86
616 617 2.720758 CTCTATATGCCACGCGCGC 61.721 63.158 32.58 23.91 42.08 6.86
632 633 4.886925 GCGGTTATTGCGCGCCTG 62.887 66.667 30.77 18.51 0.00 4.85
633 634 4.886925 CGGTTATTGCGCGCCTGC 62.887 66.667 30.77 13.82 37.91 4.85
634 635 3.508840 GGTTATTGCGCGCCTGCT 61.509 61.111 30.77 12.78 39.65 4.24
635 636 2.485122 GTTATTGCGCGCCTGCTT 59.515 55.556 30.77 11.03 39.65 3.91
636 637 1.869132 GTTATTGCGCGCCTGCTTG 60.869 57.895 30.77 0.00 39.65 4.01
637 638 2.037702 TTATTGCGCGCCTGCTTGA 61.038 52.632 30.77 4.37 39.65 3.02
638 639 1.980951 TTATTGCGCGCCTGCTTGAG 61.981 55.000 30.77 0.00 39.65 3.02
639 640 2.850806 TATTGCGCGCCTGCTTGAGA 62.851 55.000 30.77 2.53 39.65 3.27
642 643 3.782244 CGCGCCTGCTTGAGACAC 61.782 66.667 0.00 0.00 39.65 3.67
643 644 2.358003 GCGCCTGCTTGAGACACT 60.358 61.111 0.00 0.00 38.39 3.55
644 645 2.386660 GCGCCTGCTTGAGACACTC 61.387 63.158 0.00 0.00 38.39 3.51
645 646 1.291588 CGCCTGCTTGAGACACTCT 59.708 57.895 0.00 0.00 0.00 3.24
646 647 0.528017 CGCCTGCTTGAGACACTCTA 59.472 55.000 0.00 0.00 0.00 2.43
647 648 1.734047 CGCCTGCTTGAGACACTCTAC 60.734 57.143 0.00 0.00 0.00 2.59
648 649 1.404851 GCCTGCTTGAGACACTCTACC 60.405 57.143 0.00 0.00 0.00 3.18
649 650 1.135257 CCTGCTTGAGACACTCTACCG 60.135 57.143 0.00 0.00 0.00 4.02
650 651 1.813178 CTGCTTGAGACACTCTACCGA 59.187 52.381 0.00 0.00 0.00 4.69
651 652 2.425312 CTGCTTGAGACACTCTACCGAT 59.575 50.000 0.00 0.00 0.00 4.18
652 653 2.826128 TGCTTGAGACACTCTACCGATT 59.174 45.455 0.00 0.00 0.00 3.34
653 654 3.182967 GCTTGAGACACTCTACCGATTG 58.817 50.000 0.00 0.00 0.00 2.67
654 655 2.941453 TGAGACACTCTACCGATTGC 57.059 50.000 0.00 0.00 0.00 3.56
655 656 1.132453 TGAGACACTCTACCGATTGCG 59.868 52.381 0.00 0.00 37.24 4.85
665 666 2.096782 CGATTGCGGCGCGTTAAA 59.903 55.556 28.09 16.28 0.00 1.52
666 667 1.510204 CGATTGCGGCGCGTTAAAA 60.510 52.632 28.09 15.87 0.00 1.52
667 668 0.859788 CGATTGCGGCGCGTTAAAAT 60.860 50.000 28.09 20.10 0.00 1.82
668 669 0.565679 GATTGCGGCGCGTTAAAATG 59.434 50.000 28.09 0.00 0.00 2.32
669 670 0.169230 ATTGCGGCGCGTTAAAATGA 59.831 45.000 28.09 2.47 0.00 2.57
670 671 0.453615 TTGCGGCGCGTTAAAATGAG 60.454 50.000 28.09 0.00 0.00 2.90
671 672 2.214948 GCGGCGCGTTAAAATGAGC 61.215 57.895 19.09 2.44 39.57 4.26
672 673 1.133664 CGGCGCGTTAAAATGAGCA 59.866 52.632 8.43 0.00 41.66 4.26
673 674 0.453615 CGGCGCGTTAAAATGAGCAA 60.454 50.000 8.43 0.00 41.66 3.91
674 675 1.692296 GGCGCGTTAAAATGAGCAAA 58.308 45.000 8.43 0.00 41.66 3.68
675 676 2.258755 GGCGCGTTAAAATGAGCAAAT 58.741 42.857 8.43 0.00 41.66 2.32
676 677 2.666022 GGCGCGTTAAAATGAGCAAATT 59.334 40.909 8.43 0.00 41.66 1.82
677 678 3.122780 GGCGCGTTAAAATGAGCAAATTT 59.877 39.130 8.43 0.00 41.66 1.82
678 679 4.074272 GCGCGTTAAAATGAGCAAATTTG 58.926 39.130 14.03 14.03 39.97 2.32
697 698 3.810896 GGCCCGGCGCTTGTTTAG 61.811 66.667 7.64 0.00 37.74 1.85
698 699 4.476410 GCCCGGCGCTTGTTTAGC 62.476 66.667 7.64 0.00 46.83 3.09
705 706 2.202349 GCTTGTTTAGCGCGGCTG 60.202 61.111 8.83 0.00 40.71 4.85
706 707 2.966309 GCTTGTTTAGCGCGGCTGT 61.966 57.895 8.83 0.00 40.71 4.40
707 708 1.574428 CTTGTTTAGCGCGGCTGTT 59.426 52.632 8.83 0.00 40.10 3.16
708 709 0.725784 CTTGTTTAGCGCGGCTGTTG 60.726 55.000 8.83 0.00 40.10 3.33
709 710 2.123988 TTGTTTAGCGCGGCTGTTGG 62.124 55.000 8.83 0.00 40.10 3.77
710 711 2.031314 TTTAGCGCGGCTGTTGGA 59.969 55.556 8.83 0.00 40.10 3.53
711 712 2.032634 TTTAGCGCGGCTGTTGGAG 61.033 57.895 8.83 0.00 40.10 3.86
712 713 2.443260 TTTAGCGCGGCTGTTGGAGA 62.443 55.000 8.83 0.00 40.10 3.71
713 714 2.238847 TTAGCGCGGCTGTTGGAGAT 62.239 55.000 8.83 0.00 40.10 2.75
714 715 2.906182 TAGCGCGGCTGTTGGAGATG 62.906 60.000 8.83 0.00 40.10 2.90
715 716 3.869272 CGCGGCTGTTGGAGATGC 61.869 66.667 0.00 0.00 0.00 3.91
716 717 2.437359 GCGGCTGTTGGAGATGCT 60.437 61.111 0.00 0.00 0.00 3.79
717 718 2.467826 GCGGCTGTTGGAGATGCTC 61.468 63.158 0.00 0.00 0.00 4.26
718 719 1.220206 CGGCTGTTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
719 720 0.392193 CGGCTGTTGGAGATGCTCTT 60.392 55.000 0.00 0.00 0.00 2.85
720 721 1.134699 CGGCTGTTGGAGATGCTCTTA 60.135 52.381 0.00 0.00 0.00 2.10
721 722 2.559440 GGCTGTTGGAGATGCTCTTAG 58.441 52.381 0.00 0.00 0.00 2.18
722 723 1.939255 GCTGTTGGAGATGCTCTTAGC 59.061 52.381 0.00 0.00 42.82 3.09
744 745 5.574815 CAAGAATTGCGTTTAAAGGGTTG 57.425 39.130 9.76 0.00 40.39 3.77
745 746 4.929819 AGAATTGCGTTTAAAGGGTTGT 57.070 36.364 9.76 0.00 0.00 3.32
746 747 6.210078 CAAGAATTGCGTTTAAAGGGTTGTA 58.790 36.000 9.76 0.00 40.39 2.41
747 748 6.394025 AGAATTGCGTTTAAAGGGTTGTAA 57.606 33.333 9.76 0.00 0.00 2.41
748 749 6.988522 AGAATTGCGTTTAAAGGGTTGTAAT 58.011 32.000 9.76 0.00 0.00 1.89
749 750 7.088272 AGAATTGCGTTTAAAGGGTTGTAATC 58.912 34.615 9.76 0.00 0.00 1.75
750 751 4.769859 TGCGTTTAAAGGGTTGTAATCC 57.230 40.909 9.76 0.00 0.00 3.01
751 752 3.506844 TGCGTTTAAAGGGTTGTAATCCC 59.493 43.478 9.76 0.00 44.90 3.85
752 753 3.506844 GCGTTTAAAGGGTTGTAATCCCA 59.493 43.478 9.76 0.00 46.82 4.37
753 754 4.158949 GCGTTTAAAGGGTTGTAATCCCAT 59.841 41.667 9.76 0.00 46.82 4.00
754 755 5.357596 GCGTTTAAAGGGTTGTAATCCCATA 59.642 40.000 9.76 0.00 46.82 2.74
755 756 6.459161 GCGTTTAAAGGGTTGTAATCCCATAG 60.459 42.308 9.76 0.00 46.82 2.23
756 757 6.459161 CGTTTAAAGGGTTGTAATCCCATAGC 60.459 42.308 3.79 0.00 46.82 2.97
757 758 4.881157 AAAGGGTTGTAATCCCATAGCT 57.119 40.909 3.79 0.00 46.82 3.32
758 759 3.864789 AGGGTTGTAATCCCATAGCTG 57.135 47.619 0.00 0.00 46.82 4.24
759 760 2.158608 AGGGTTGTAATCCCATAGCTGC 60.159 50.000 0.00 0.00 46.82 5.25
760 761 2.158608 GGGTTGTAATCCCATAGCTGCT 60.159 50.000 7.57 7.57 44.05 4.24
761 762 3.555966 GGTTGTAATCCCATAGCTGCTT 58.444 45.455 7.79 0.00 0.00 3.91
762 763 3.565902 GGTTGTAATCCCATAGCTGCTTC 59.434 47.826 7.79 0.00 0.00 3.86
763 764 3.492102 TGTAATCCCATAGCTGCTTCC 57.508 47.619 7.79 0.00 0.00 3.46
764 765 2.777114 TGTAATCCCATAGCTGCTTCCA 59.223 45.455 7.79 0.00 0.00 3.53
765 766 2.653234 AATCCCATAGCTGCTTCCAG 57.347 50.000 7.79 0.00 42.13 3.86
766 767 1.811778 ATCCCATAGCTGCTTCCAGA 58.188 50.000 7.79 0.76 41.77 3.86
767 768 1.811778 TCCCATAGCTGCTTCCAGAT 58.188 50.000 7.79 0.00 41.77 2.90
768 769 1.696336 TCCCATAGCTGCTTCCAGATC 59.304 52.381 7.79 0.00 41.77 2.75
769 770 1.607509 CCCATAGCTGCTTCCAGATCG 60.608 57.143 7.79 0.00 41.77 3.69
770 771 1.146637 CATAGCTGCTTCCAGATCGC 58.853 55.000 7.79 0.00 41.77 4.58
771 772 0.034616 ATAGCTGCTTCCAGATCGCC 59.965 55.000 7.79 0.00 41.77 5.54
772 773 1.329913 TAGCTGCTTCCAGATCGCCA 61.330 55.000 7.79 0.00 41.77 5.69
773 774 1.746615 GCTGCTTCCAGATCGCCAA 60.747 57.895 0.00 0.00 41.77 4.52
774 775 1.308069 GCTGCTTCCAGATCGCCAAA 61.308 55.000 0.00 0.00 41.77 3.28
775 776 1.386533 CTGCTTCCAGATCGCCAAAT 58.613 50.000 0.00 0.00 41.77 2.32
776 777 1.065102 CTGCTTCCAGATCGCCAAATG 59.935 52.381 0.00 0.00 41.77 2.32
777 778 0.248784 GCTTCCAGATCGCCAAATGC 60.249 55.000 0.00 0.00 0.00 3.56
778 779 1.097232 CTTCCAGATCGCCAAATGCA 58.903 50.000 0.00 0.00 41.33 3.96
779 780 1.473677 CTTCCAGATCGCCAAATGCAA 59.526 47.619 0.00 0.00 41.33 4.08
780 781 1.097232 TCCAGATCGCCAAATGCAAG 58.903 50.000 0.00 0.00 41.33 4.01
781 782 0.101759 CCAGATCGCCAAATGCAAGG 59.898 55.000 0.00 0.00 41.33 3.61
782 783 0.813184 CAGATCGCCAAATGCAAGGT 59.187 50.000 0.00 0.00 41.33 3.50
783 784 2.016318 CAGATCGCCAAATGCAAGGTA 58.984 47.619 0.00 0.00 41.33 3.08
784 785 2.017049 AGATCGCCAAATGCAAGGTAC 58.983 47.619 0.00 0.00 41.33 3.34
786 787 1.164411 TCGCCAAATGCAAGGTACTG 58.836 50.000 0.00 0.00 40.86 2.74
787 788 0.456653 CGCCAAATGCAAGGTACTGC 60.457 55.000 0.00 0.27 40.86 4.40
788 789 0.890683 GCCAAATGCAAGGTACTGCT 59.109 50.000 8.39 0.00 40.86 4.24
789 790 1.273327 GCCAAATGCAAGGTACTGCTT 59.727 47.619 8.39 0.00 40.86 3.91
790 791 2.927871 GCCAAATGCAAGGTACTGCTTG 60.928 50.000 8.39 7.84 40.86 4.01
791 792 2.557924 CCAAATGCAAGGTACTGCTTGA 59.442 45.455 14.00 2.67 40.86 3.02
792 793 3.194116 CCAAATGCAAGGTACTGCTTGAT 59.806 43.478 14.00 4.42 40.86 2.57
807 808 9.243637 GTACTGCTTGATGTGTTTTAATTTTGA 57.756 29.630 0.00 0.00 0.00 2.69
836 841 2.417933 GCCTCATGTGAGCTTACACTTG 59.582 50.000 14.24 13.26 42.93 3.16
841 846 1.217882 GTGAGCTTACACTTGCACGT 58.782 50.000 3.32 0.00 37.73 4.49
877 882 2.282407 ACGCTTTCACGTGGTTTACTT 58.718 42.857 17.00 0.00 46.28 2.24
922 929 8.556517 AAATTTTCGCAAAGTTAACTACAGAC 57.443 30.769 8.92 0.00 28.44 3.51
984 1118 2.750237 GCCAAACTAGCACCGGGG 60.750 66.667 6.32 0.84 0.00 5.73
1202 1699 2.580815 CATCCAGGCAGAGCACGA 59.419 61.111 0.00 0.00 0.00 4.35
1230 1727 2.103042 CCTCTTCGCCTTCAAGCCG 61.103 63.158 0.00 0.00 0.00 5.52
1340 1837 2.189521 CGGCGAGCCCAAGGTAAT 59.810 61.111 0.00 0.00 0.00 1.89
1369 1866 1.227118 CCTGCCCGTTTTGCGTTTT 60.227 52.632 0.00 0.00 39.32 2.43
1428 1925 2.629051 GGATTGGATTTTCCTCGTCGT 58.371 47.619 0.00 0.00 37.46 4.34
1459 1956 4.329545 TCGTGGACCAAGCCTGCC 62.330 66.667 2.02 0.00 0.00 4.85
1461 1958 2.360475 GTGGACCAAGCCTGCCTC 60.360 66.667 0.00 0.00 0.00 4.70
1488 1985 4.363990 CGTCGGTCTGCTGGTGCT 62.364 66.667 0.00 0.00 40.48 4.40
1493 1990 4.996434 GTCTGCTGGTGCTGGCGT 62.996 66.667 0.00 0.00 40.48 5.68
1555 2052 0.587768 TGTCGTCGAGCGTAGTCAAA 59.412 50.000 0.00 0.00 42.13 2.69
1633 2130 4.785453 CGGCCACAAGCTCCTCCC 62.785 72.222 2.24 0.00 43.05 4.30
1634 2131 4.432741 GGCCACAAGCTCCTCCCC 62.433 72.222 0.00 0.00 43.05 4.81
1635 2132 4.785453 GCCACAAGCTCCTCCCCG 62.785 72.222 0.00 0.00 38.99 5.73
1636 2133 3.322466 CCACAAGCTCCTCCCCGT 61.322 66.667 0.00 0.00 0.00 5.28
1637 2134 2.266055 CACAAGCTCCTCCCCGTC 59.734 66.667 0.00 0.00 0.00 4.79
1638 2135 2.120718 ACAAGCTCCTCCCCGTCT 59.879 61.111 0.00 0.00 0.00 4.18
1639 2136 1.985116 ACAAGCTCCTCCCCGTCTC 60.985 63.158 0.00 0.00 0.00 3.36
1640 2137 1.984570 CAAGCTCCTCCCCGTCTCA 60.985 63.158 0.00 0.00 0.00 3.27
1641 2138 1.684049 AAGCTCCTCCCCGTCTCAG 60.684 63.158 0.00 0.00 0.00 3.35
1642 2139 3.151022 GCTCCTCCCCGTCTCAGG 61.151 72.222 0.00 0.00 0.00 3.86
1643 2140 2.684104 CTCCTCCCCGTCTCAGGA 59.316 66.667 0.00 0.00 34.97 3.86
1644 2141 1.231641 CTCCTCCCCGTCTCAGGAT 59.768 63.158 0.00 0.00 35.70 3.24
1645 2142 1.075970 TCCTCCCCGTCTCAGGATG 60.076 63.158 0.00 0.00 30.92 3.51
1646 2143 2.801631 CCTCCCCGTCTCAGGATGC 61.802 68.421 0.00 0.00 34.76 3.91
1647 2144 3.144120 CTCCCCGTCTCAGGATGCG 62.144 68.421 0.00 0.00 34.76 4.73
1648 2145 4.227134 CCCCGTCTCAGGATGCGG 62.227 72.222 0.00 0.00 43.40 5.69
1649 2146 4.899239 CCCGTCTCAGGATGCGGC 62.899 72.222 0.00 0.00 42.54 6.53
1650 2147 4.899239 CCGTCTCAGGATGCGGCC 62.899 72.222 0.00 0.00 37.69 6.13
1651 2148 4.147449 CGTCTCAGGATGCGGCCA 62.147 66.667 2.24 0.00 34.76 5.36
1652 2149 2.512515 GTCTCAGGATGCGGCCAC 60.513 66.667 2.24 0.00 34.76 5.01
1653 2150 3.002583 TCTCAGGATGCGGCCACA 61.003 61.111 2.24 0.00 34.76 4.17
1654 2151 2.046023 CTCAGGATGCGGCCACAA 60.046 61.111 2.24 0.00 34.76 3.33
1655 2152 2.046023 TCAGGATGCGGCCACAAG 60.046 61.111 2.24 0.00 34.76 3.16
1656 2153 3.818787 CAGGATGCGGCCACAAGC 61.819 66.667 2.24 0.00 42.60 4.01
1657 2154 4.039092 AGGATGCGGCCACAAGCT 62.039 61.111 2.24 0.00 43.05 3.74
1658 2155 3.512516 GGATGCGGCCACAAGCTC 61.513 66.667 2.24 0.00 43.05 4.09
1659 2156 3.512516 GATGCGGCCACAAGCTCC 61.513 66.667 2.24 0.00 43.05 4.70
1660 2157 3.984193 GATGCGGCCACAAGCTCCT 62.984 63.158 2.24 0.00 43.05 3.69
1661 2158 3.984193 ATGCGGCCACAAGCTCCTC 62.984 63.158 2.24 0.00 43.05 3.71
1663 2160 4.020617 CGGCCACAAGCTCCTCCA 62.021 66.667 2.24 0.00 43.05 3.86
1664 2161 2.679716 GGCCACAAGCTCCTCCAT 59.320 61.111 0.00 0.00 43.05 3.41
1665 2162 1.751927 GGCCACAAGCTCCTCCATG 60.752 63.158 0.00 0.00 43.05 3.66
1666 2163 1.300963 GCCACAAGCTCCTCCATGA 59.699 57.895 0.00 0.00 38.99 3.07
1667 2164 0.322816 GCCACAAGCTCCTCCATGAA 60.323 55.000 0.00 0.00 38.99 2.57
1668 2165 1.457346 CCACAAGCTCCTCCATGAAC 58.543 55.000 0.00 0.00 0.00 3.18
1672 2169 0.984230 AAGCTCCTCCATGAACGGAA 59.016 50.000 0.00 0.00 33.65 4.30
1681 2178 1.202533 CCATGAACGGAACCGAGCTAT 60.203 52.381 20.14 5.88 42.83 2.97
1682 2179 1.860950 CATGAACGGAACCGAGCTATG 59.139 52.381 20.14 13.13 42.83 2.23
1686 2183 0.743097 ACGGAACCGAGCTATGGTAC 59.257 55.000 20.14 6.40 39.29 3.34
1694 2194 6.239120 GGAACCGAGCTATGGTACTGTAATAA 60.239 42.308 10.36 0.00 39.29 1.40
1706 2206 7.383687 TGGTACTGTAATAACTCTCCTTTGTG 58.616 38.462 0.00 0.00 0.00 3.33
1707 2207 7.233962 TGGTACTGTAATAACTCTCCTTTGTGA 59.766 37.037 0.00 0.00 0.00 3.58
1712 2212 9.482627 CTGTAATAACTCTCCTTTGTGATATCC 57.517 37.037 0.00 0.00 0.00 2.59
1721 2222 4.133078 CCTTTGTGATATCCAGAGAAGCC 58.867 47.826 0.00 0.00 0.00 4.35
1723 2224 3.051940 TGTGATATCCAGAGAAGCCCT 57.948 47.619 0.00 0.00 0.00 5.19
1725 2226 3.389329 TGTGATATCCAGAGAAGCCCTTC 59.611 47.826 0.00 0.00 39.78 3.46
1745 2246 4.881019 TCTTCTCTGGTTTCTCTTCAGG 57.119 45.455 0.00 0.00 0.00 3.86
1786 2289 9.132521 GAGACAAAATTCCAGAATAAATGTGTG 57.867 33.333 9.16 0.00 0.00 3.82
1787 2290 8.641541 AGACAAAATTCCAGAATAAATGTGTGT 58.358 29.630 9.16 0.00 0.00 3.72
1805 2308 1.298264 TGCAGTTTGCTTCAACGCG 60.298 52.632 3.53 3.53 45.31 6.01
1839 2344 5.460646 TCTGCTGACGAAATTTTCCATTTC 58.539 37.500 3.61 0.00 35.34 2.17
1914 2419 7.709269 GATACATTACAACCACGTGTATCAT 57.291 36.000 15.65 0.00 45.38 2.45
1966 2476 2.031682 CCTCGTCAAAACAGCTTTCAGG 60.032 50.000 0.00 0.00 0.00 3.86
1980 2490 4.021544 AGCTTTCAGGTTTTTCACACACAA 60.022 37.500 0.00 0.00 0.00 3.33
2004 2514 6.840780 ACAACCAAATAAGATCAGGAAAGG 57.159 37.500 0.00 0.00 0.00 3.11
2018 2534 3.132289 CAGGAAAGGCAAGACTATCCGTA 59.868 47.826 0.00 0.00 32.22 4.02
2063 2581 5.186992 ACCAAAACAAAACTAGCAGAAAGGT 59.813 36.000 0.00 0.00 0.00 3.50
2068 2586 7.399245 AACAAAACTAGCAGAAAGGTGTAAA 57.601 32.000 0.00 0.00 0.00 2.01
2341 2889 6.258287 TCAAGAAAAATCCGTTGTCGTTTCTA 59.742 34.615 0.00 0.00 37.54 2.10
2480 3034 3.574284 TGATGCAAGGCAAACATACAC 57.426 42.857 0.00 0.00 43.62 2.90
2499 3053 2.978978 CACCAGGACCATATATCCACCA 59.021 50.000 0.00 0.00 38.86 4.17
2661 3224 7.611855 ACTGGCTAATTGCAACTTTAAGATAGT 59.388 33.333 0.00 0.00 45.15 2.12
2664 3227 7.910683 GGCTAATTGCAACTTTAAGATAGTCAC 59.089 37.037 0.00 0.00 45.15 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.618709 CAAGAAAAGAAGCCAACGAGGT 59.381 45.455 0.00 0.00 40.61 3.85
76 77 7.275560 CGCAAAAGAAAAGAAGAAGAGGAAAAA 59.724 33.333 0.00 0.00 0.00 1.94
135 136 4.062293 CACCAAACTCGGTTTCATACTCA 58.938 43.478 0.00 0.00 37.07 3.41
155 156 1.973812 GGCAAGAGAAGCCCCACAC 60.974 63.158 0.00 0.00 46.50 3.82
166 167 4.337274 TGCATCAAGTGAATATGGCAAGAG 59.663 41.667 0.00 0.00 0.00 2.85
176 177 4.851843 TGAGGAGAATGCATCAAGTGAAT 58.148 39.130 0.00 0.00 0.00 2.57
203 204 8.859156 GCAAGCGAACAATTAATTTGAAAGATA 58.141 29.630 0.00 0.00 38.76 1.98
209 210 4.541779 ACGCAAGCGAACAATTAATTTGA 58.458 34.783 22.30 0.00 42.83 2.69
265 266 5.039333 GGATGATGAAAAATGGAAGAAGCG 58.961 41.667 0.00 0.00 0.00 4.68
279 280 8.212995 TGCTATGAAGTATTGAAGGATGATGAA 58.787 33.333 0.00 0.00 0.00 2.57
396 397 8.531530 GTGCTAACTTGTTTTGTTTTCATGTAG 58.468 33.333 0.00 0.00 0.00 2.74
425 426 0.644843 GCGCTTGTTGTTGGTGTTTG 59.355 50.000 0.00 0.00 0.00 2.93
444 445 4.129737 ACCCGATGGACGCACGAG 62.130 66.667 0.00 0.00 41.07 4.18
445 446 4.124351 GACCCGATGGACGCACGA 62.124 66.667 0.00 0.00 41.07 4.35
446 447 3.925362 TTGACCCGATGGACGCACG 62.925 63.158 0.00 0.00 41.07 5.34
447 448 2.047655 TTGACCCGATGGACGCAC 60.048 61.111 0.00 0.00 41.07 5.34
448 449 2.047655 GTTGACCCGATGGACGCA 60.048 61.111 0.00 0.00 41.07 5.24
449 450 1.810030 GAGTTGACCCGATGGACGC 60.810 63.158 0.00 0.00 41.07 5.19
450 451 1.516386 CGAGTTGACCCGATGGACG 60.516 63.158 0.00 0.00 42.18 4.79
451 452 1.810030 GCGAGTTGACCCGATGGAC 60.810 63.158 0.00 0.00 34.81 4.02
452 453 2.577059 GCGAGTTGACCCGATGGA 59.423 61.111 0.00 0.00 34.81 3.41
453 454 2.511600 GGCGAGTTGACCCGATGG 60.512 66.667 0.00 0.00 37.80 3.51
454 455 2.885644 CGGCGAGTTGACCCGATG 60.886 66.667 0.00 0.00 44.55 3.84
501 502 3.827898 GTCGCACTCTCTCCCCCG 61.828 72.222 0.00 0.00 0.00 5.73
502 503 3.827898 CGTCGCACTCTCTCCCCC 61.828 72.222 0.00 0.00 0.00 5.40
503 504 4.500116 GCGTCGCACTCTCTCCCC 62.500 72.222 13.44 0.00 0.00 4.81
504 505 4.838486 CGCGTCGCACTCTCTCCC 62.838 72.222 18.75 0.00 0.00 4.30
505 506 3.726631 CTCGCGTCGCACTCTCTCC 62.727 68.421 18.75 0.00 0.00 3.71
506 507 2.276994 CTCGCGTCGCACTCTCTC 60.277 66.667 18.75 0.00 0.00 3.20
507 508 4.468615 GCTCGCGTCGCACTCTCT 62.469 66.667 18.75 0.00 0.00 3.10
552 553 2.746277 CCTGCGTACTTGGGGCAC 60.746 66.667 0.00 0.00 32.46 5.01
553 554 4.028490 CCCTGCGTACTTGGGGCA 62.028 66.667 6.76 0.40 37.37 5.36
566 567 2.586079 AATCGTCATCGCGCCCTG 60.586 61.111 0.00 0.00 36.96 4.45
567 568 2.279517 GAATCGTCATCGCGCCCT 60.280 61.111 0.00 0.00 36.96 5.19
568 569 1.701545 TTTGAATCGTCATCGCGCCC 61.702 55.000 0.00 0.00 36.96 6.13
569 570 0.586502 GTTTGAATCGTCATCGCGCC 60.587 55.000 0.00 0.00 36.96 6.53
570 571 0.586502 GGTTTGAATCGTCATCGCGC 60.587 55.000 0.00 0.00 36.96 6.86
571 572 0.314259 CGGTTTGAATCGTCATCGCG 60.314 55.000 0.00 0.00 36.96 5.87
572 573 0.586502 GCGGTTTGAATCGTCATCGC 60.587 55.000 0.00 0.00 39.23 4.58
573 574 0.314259 CGCGGTTTGAATCGTCATCG 60.314 55.000 0.00 0.00 34.38 3.84
574 575 0.586502 GCGCGGTTTGAATCGTCATC 60.587 55.000 8.83 0.00 34.38 2.92
575 576 1.423845 GCGCGGTTTGAATCGTCAT 59.576 52.632 8.83 0.00 34.38 3.06
576 577 2.673114 GGCGCGGTTTGAATCGTCA 61.673 57.895 8.83 0.00 34.38 4.35
577 578 2.097728 GGCGCGGTTTGAATCGTC 59.902 61.111 8.83 0.00 34.38 4.20
578 579 3.428282 GGGCGCGGTTTGAATCGT 61.428 61.111 8.83 0.00 34.38 3.73
579 580 2.972144 TTGGGCGCGGTTTGAATCG 61.972 57.895 8.83 0.00 35.16 3.34
580 581 1.443702 GTTGGGCGCGGTTTGAATC 60.444 57.895 8.83 0.00 0.00 2.52
581 582 1.862602 GAGTTGGGCGCGGTTTGAAT 61.863 55.000 8.83 0.00 0.00 2.57
582 583 2.517402 AGTTGGGCGCGGTTTGAA 60.517 55.556 8.83 0.00 0.00 2.69
583 584 2.102109 TAGAGTTGGGCGCGGTTTGA 62.102 55.000 8.83 0.00 0.00 2.69
584 585 1.024579 ATAGAGTTGGGCGCGGTTTG 61.025 55.000 8.83 0.00 0.00 2.93
585 586 0.538118 TATAGAGTTGGGCGCGGTTT 59.462 50.000 8.83 0.00 0.00 3.27
586 587 0.756903 ATATAGAGTTGGGCGCGGTT 59.243 50.000 8.83 0.00 0.00 4.44
587 588 0.033504 CATATAGAGTTGGGCGCGGT 59.966 55.000 8.83 0.00 0.00 5.68
588 589 1.291877 GCATATAGAGTTGGGCGCGG 61.292 60.000 8.83 0.00 0.00 6.46
589 590 1.291877 GGCATATAGAGTTGGGCGCG 61.292 60.000 0.00 0.00 0.00 6.86
590 591 0.250295 TGGCATATAGAGTTGGGCGC 60.250 55.000 0.00 0.00 0.00 6.53
591 592 1.512926 GTGGCATATAGAGTTGGGCG 58.487 55.000 0.00 0.00 0.00 6.13
592 593 1.512926 CGTGGCATATAGAGTTGGGC 58.487 55.000 0.00 0.00 0.00 5.36
593 594 1.512926 GCGTGGCATATAGAGTTGGG 58.487 55.000 0.00 0.00 0.00 4.12
594 595 1.139989 CGCGTGGCATATAGAGTTGG 58.860 55.000 0.00 0.00 0.00 3.77
595 596 0.508641 GCGCGTGGCATATAGAGTTG 59.491 55.000 8.43 0.00 42.87 3.16
596 597 0.939577 CGCGCGTGGCATATAGAGTT 60.940 55.000 24.19 0.00 43.84 3.01
597 598 1.371758 CGCGCGTGGCATATAGAGT 60.372 57.895 24.19 0.00 43.84 3.24
598 599 2.720758 GCGCGCGTGGCATATAGAG 61.721 63.158 32.35 0.00 43.84 2.43
599 600 2.733218 GCGCGCGTGGCATATAGA 60.733 61.111 32.35 0.00 43.84 1.98
600 601 4.121227 CGCGCGCGTGGCATATAG 62.121 66.667 42.49 13.34 43.84 1.31
616 617 4.886925 GCAGGCGCGCAATAACCG 62.887 66.667 34.42 12.93 0.00 4.44
617 618 3.051392 AAGCAGGCGCGCAATAACC 62.051 57.895 34.42 14.51 45.49 2.85
618 619 1.869132 CAAGCAGGCGCGCAATAAC 60.869 57.895 34.42 15.34 45.49 1.89
619 620 1.980951 CTCAAGCAGGCGCGCAATAA 61.981 55.000 34.42 9.89 45.49 1.40
620 621 2.435762 TCAAGCAGGCGCGCAATA 60.436 55.556 34.42 7.44 45.49 1.90
621 622 3.807538 CTCAAGCAGGCGCGCAAT 61.808 61.111 34.42 18.60 45.49 3.56
622 623 4.986645 TCTCAAGCAGGCGCGCAA 62.987 61.111 34.42 7.45 45.49 4.85
625 626 3.782244 GTGTCTCAAGCAGGCGCG 61.782 66.667 0.00 0.00 45.49 6.86
626 627 2.358003 AGTGTCTCAAGCAGGCGC 60.358 61.111 0.00 0.00 37.52 6.53
627 628 0.528017 TAGAGTGTCTCAAGCAGGCG 59.472 55.000 0.00 0.00 32.06 5.52
628 629 1.404851 GGTAGAGTGTCTCAAGCAGGC 60.405 57.143 0.00 0.00 32.06 4.85
629 630 1.135257 CGGTAGAGTGTCTCAAGCAGG 60.135 57.143 0.00 0.00 32.06 4.85
630 631 1.813178 TCGGTAGAGTGTCTCAAGCAG 59.187 52.381 0.00 0.00 32.06 4.24
631 632 1.905637 TCGGTAGAGTGTCTCAAGCA 58.094 50.000 0.00 0.00 32.06 3.91
632 633 3.182967 CAATCGGTAGAGTGTCTCAAGC 58.817 50.000 0.00 0.00 37.65 4.01
633 634 3.182967 GCAATCGGTAGAGTGTCTCAAG 58.817 50.000 0.00 0.00 43.66 3.02
634 635 2.415491 CGCAATCGGTAGAGTGTCTCAA 60.415 50.000 0.00 0.00 43.66 3.02
635 636 1.132453 CGCAATCGGTAGAGTGTCTCA 59.868 52.381 0.00 0.00 43.66 3.27
636 637 1.828832 CGCAATCGGTAGAGTGTCTC 58.171 55.000 0.00 0.00 43.66 3.36
648 649 0.859788 ATTTTAACGCGCCGCAATCG 60.860 50.000 10.75 0.00 0.00 3.34
649 650 0.565679 CATTTTAACGCGCCGCAATC 59.434 50.000 10.75 0.00 0.00 2.67
650 651 0.169230 TCATTTTAACGCGCCGCAAT 59.831 45.000 10.75 0.00 0.00 3.56
651 652 0.453615 CTCATTTTAACGCGCCGCAA 60.454 50.000 10.75 0.00 0.00 4.85
652 653 1.133664 CTCATTTTAACGCGCCGCA 59.866 52.632 10.75 0.00 0.00 5.69
653 654 2.214948 GCTCATTTTAACGCGCCGC 61.215 57.895 5.73 0.00 0.00 6.53
654 655 0.453615 TTGCTCATTTTAACGCGCCG 60.454 50.000 5.73 0.00 0.00 6.46
655 656 1.692296 TTTGCTCATTTTAACGCGCC 58.308 45.000 5.73 0.00 0.00 6.53
656 657 3.970828 AATTTGCTCATTTTAACGCGC 57.029 38.095 5.73 0.00 0.00 6.86
680 681 3.810896 CTAAACAAGCGCCGGGCC 61.811 66.667 14.55 6.41 45.17 5.80
681 682 4.476410 GCTAAACAAGCGCCGGGC 62.476 66.667 9.54 9.54 42.53 6.13
689 690 0.725784 CAACAGCCGCGCTAAACAAG 60.726 55.000 5.56 0.00 36.40 3.16
690 691 1.281353 CAACAGCCGCGCTAAACAA 59.719 52.632 5.56 0.00 36.40 2.83
691 692 2.612567 CCAACAGCCGCGCTAAACA 61.613 57.895 5.56 0.00 36.40 2.83
692 693 2.175811 CCAACAGCCGCGCTAAAC 59.824 61.111 5.56 0.00 36.40 2.01
693 694 2.031314 TCCAACAGCCGCGCTAAA 59.969 55.556 5.56 0.00 36.40 1.85
694 695 2.238847 ATCTCCAACAGCCGCGCTAA 62.239 55.000 5.56 0.00 36.40 3.09
695 696 2.721167 ATCTCCAACAGCCGCGCTA 61.721 57.895 5.56 0.00 36.40 4.26
696 697 4.087892 ATCTCCAACAGCCGCGCT 62.088 61.111 5.56 0.00 40.77 5.92
697 698 3.869272 CATCTCCAACAGCCGCGC 61.869 66.667 0.00 0.00 0.00 6.86
698 699 3.869272 GCATCTCCAACAGCCGCG 61.869 66.667 0.00 0.00 0.00 6.46
699 700 2.437359 AGCATCTCCAACAGCCGC 60.437 61.111 0.00 0.00 0.00 6.53
700 701 3.805267 GAGCATCTCCAACAGCCG 58.195 61.111 0.00 0.00 0.00 5.52
722 723 5.047188 ACAACCCTTTAAACGCAATTCTTG 58.953 37.500 0.00 0.00 0.00 3.02
723 724 5.270893 ACAACCCTTTAAACGCAATTCTT 57.729 34.783 0.00 0.00 0.00 2.52
724 725 4.929819 ACAACCCTTTAAACGCAATTCT 57.070 36.364 0.00 0.00 0.00 2.40
725 726 6.309494 GGATTACAACCCTTTAAACGCAATTC 59.691 38.462 0.00 0.00 0.00 2.17
726 727 6.160684 GGATTACAACCCTTTAAACGCAATT 58.839 36.000 0.00 0.00 0.00 2.32
727 728 5.336929 GGGATTACAACCCTTTAAACGCAAT 60.337 40.000 0.00 0.00 43.65 3.56
728 729 4.022155 GGGATTACAACCCTTTAAACGCAA 60.022 41.667 0.00 0.00 43.65 4.85
729 730 3.506844 GGGATTACAACCCTTTAAACGCA 59.493 43.478 0.00 0.00 43.65 5.24
730 731 3.506844 TGGGATTACAACCCTTTAAACGC 59.493 43.478 0.00 0.00 46.82 4.84
731 732 5.907866 ATGGGATTACAACCCTTTAAACG 57.092 39.130 0.00 0.00 46.82 3.60
732 733 6.605995 AGCTATGGGATTACAACCCTTTAAAC 59.394 38.462 0.00 0.00 46.82 2.01
733 734 6.605594 CAGCTATGGGATTACAACCCTTTAAA 59.394 38.462 0.00 0.00 46.82 1.52
734 735 6.126409 CAGCTATGGGATTACAACCCTTTAA 58.874 40.000 0.00 0.00 46.82 1.52
735 736 5.690865 CAGCTATGGGATTACAACCCTTTA 58.309 41.667 0.00 0.00 46.82 1.85
736 737 4.536765 CAGCTATGGGATTACAACCCTTT 58.463 43.478 0.00 0.00 46.82 3.11
737 738 3.688414 GCAGCTATGGGATTACAACCCTT 60.688 47.826 0.00 0.00 46.82 3.95
738 739 2.158608 GCAGCTATGGGATTACAACCCT 60.159 50.000 0.00 0.00 46.82 4.34
739 740 2.158608 AGCAGCTATGGGATTACAACCC 60.159 50.000 0.00 0.00 46.87 4.11
740 741 3.214696 AGCAGCTATGGGATTACAACC 57.785 47.619 0.00 0.00 0.00 3.77
741 742 3.565902 GGAAGCAGCTATGGGATTACAAC 59.434 47.826 0.00 0.00 0.00 3.32
742 743 3.201930 TGGAAGCAGCTATGGGATTACAA 59.798 43.478 0.00 0.00 0.00 2.41
743 744 2.777114 TGGAAGCAGCTATGGGATTACA 59.223 45.455 0.00 0.00 0.00 2.41
744 745 3.071602 TCTGGAAGCAGCTATGGGATTAC 59.928 47.826 0.00 0.00 0.00 1.89
745 746 3.317406 TCTGGAAGCAGCTATGGGATTA 58.683 45.455 0.00 0.00 0.00 1.75
746 747 2.130193 TCTGGAAGCAGCTATGGGATT 58.870 47.619 0.00 0.00 0.00 3.01
747 748 1.811778 TCTGGAAGCAGCTATGGGAT 58.188 50.000 0.00 0.00 0.00 3.85
748 749 1.696336 GATCTGGAAGCAGCTATGGGA 59.304 52.381 0.00 0.00 0.00 4.37
749 750 1.607509 CGATCTGGAAGCAGCTATGGG 60.608 57.143 0.00 0.00 0.00 4.00
750 751 1.793258 CGATCTGGAAGCAGCTATGG 58.207 55.000 0.00 0.00 0.00 2.74
751 752 1.146637 GCGATCTGGAAGCAGCTATG 58.853 55.000 0.00 0.00 0.00 2.23
752 753 0.034616 GGCGATCTGGAAGCAGCTAT 59.965 55.000 0.00 0.00 0.00 2.97
753 754 1.329913 TGGCGATCTGGAAGCAGCTA 61.330 55.000 0.00 0.00 0.00 3.32
754 755 2.188994 GGCGATCTGGAAGCAGCT 59.811 61.111 0.00 0.00 0.00 4.24
755 756 1.308069 TTTGGCGATCTGGAAGCAGC 61.308 55.000 0.00 0.00 0.00 5.25
756 757 1.065102 CATTTGGCGATCTGGAAGCAG 59.935 52.381 0.00 0.00 0.00 4.24
757 758 1.097232 CATTTGGCGATCTGGAAGCA 58.903 50.000 0.00 0.00 0.00 3.91
758 759 0.248784 GCATTTGGCGATCTGGAAGC 60.249 55.000 0.00 0.00 0.00 3.86
759 760 3.932459 GCATTTGGCGATCTGGAAG 57.068 52.632 0.00 0.00 0.00 3.46
769 770 0.890683 AGCAGTACCTTGCATTTGGC 59.109 50.000 9.50 0.00 46.47 4.52
770 771 2.557924 TCAAGCAGTACCTTGCATTTGG 59.442 45.455 9.50 0.00 46.47 3.28
771 772 3.921119 TCAAGCAGTACCTTGCATTTG 57.079 42.857 9.50 6.37 46.47 2.32
772 773 3.828451 ACATCAAGCAGTACCTTGCATTT 59.172 39.130 9.50 0.00 46.47 2.32
773 774 3.192001 CACATCAAGCAGTACCTTGCATT 59.808 43.478 9.50 0.00 46.47 3.56
774 775 2.751259 CACATCAAGCAGTACCTTGCAT 59.249 45.455 9.50 0.00 46.47 3.96
775 776 2.153645 CACATCAAGCAGTACCTTGCA 58.846 47.619 9.50 0.00 46.47 4.08
776 777 2.154462 ACACATCAAGCAGTACCTTGC 58.846 47.619 6.92 3.36 41.47 4.01
777 778 4.836125 AAACACATCAAGCAGTACCTTG 57.164 40.909 5.72 5.72 42.73 3.61
778 779 6.952773 TTAAAACACATCAAGCAGTACCTT 57.047 33.333 0.00 0.00 0.00 3.50
779 780 7.524717 AATTAAAACACATCAAGCAGTACCT 57.475 32.000 0.00 0.00 0.00 3.08
780 781 8.487176 CAAAATTAAAACACATCAAGCAGTACC 58.513 33.333 0.00 0.00 0.00 3.34
781 782 9.243637 TCAAAATTAAAACACATCAAGCAGTAC 57.756 29.630 0.00 0.00 0.00 2.73
782 783 9.243637 GTCAAAATTAAAACACATCAAGCAGTA 57.756 29.630 0.00 0.00 0.00 2.74
783 784 7.981225 AGTCAAAATTAAAACACATCAAGCAGT 59.019 29.630 0.00 0.00 0.00 4.40
784 785 8.270799 CAGTCAAAATTAAAACACATCAAGCAG 58.729 33.333 0.00 0.00 0.00 4.24
785 786 7.978414 TCAGTCAAAATTAAAACACATCAAGCA 59.022 29.630 0.00 0.00 0.00 3.91
786 787 8.351495 TCAGTCAAAATTAAAACACATCAAGC 57.649 30.769 0.00 0.00 0.00 4.01
791 792 9.423061 GGCTAATCAGTCAAAATTAAAACACAT 57.577 29.630 0.00 0.00 0.00 3.21
792 793 8.637986 AGGCTAATCAGTCAAAATTAAAACACA 58.362 29.630 0.00 0.00 0.00 3.72
807 808 2.770802 AGCTCACATGAGGCTAATCAGT 59.229 45.455 10.81 0.00 42.29 3.41
921 928 3.687125 TGCTACTCTACACTAGCACTGT 58.313 45.455 0.00 0.00 40.35 3.55
922 929 4.336713 TGATGCTACTCTACACTAGCACTG 59.663 45.833 1.59 0.00 46.24 3.66
946 980 2.661537 CGGTGCGCAGTGAACTGA 60.662 61.111 12.22 0.00 46.59 3.41
1340 1837 3.092511 GGGCAGGGATCAGCTCCA 61.093 66.667 0.00 0.00 46.98 3.86
1375 1872 1.145156 CAATATCCCCACACCGCGA 59.855 57.895 8.23 0.00 0.00 5.87
1459 1956 0.383246 GACCGACGACGATCATCGAG 60.383 60.000 19.21 10.91 45.13 4.04
1477 1974 4.254709 AACGCCAGCACCAGCAGA 62.255 61.111 0.00 0.00 45.49 4.26
1493 1990 2.992817 AAAGCCACCACCGCCATCAA 62.993 55.000 0.00 0.00 0.00 2.57
1555 2052 3.764466 CACGGCGAGAAGAGGGCT 61.764 66.667 16.62 0.00 0.00 5.19
1591 2088 1.931841 CTGAGACGGACGAAGACGATA 59.068 52.381 0.00 0.00 42.66 2.92
1634 2131 4.147449 TGGCCGCATCCTGAGACG 62.147 66.667 0.00 0.00 0.00 4.18
1635 2132 2.512515 GTGGCCGCATCCTGAGAC 60.513 66.667 12.58 0.00 0.00 3.36
1636 2133 2.526450 CTTGTGGCCGCATCCTGAGA 62.526 60.000 21.95 1.53 0.00 3.27
1637 2134 2.046023 TTGTGGCCGCATCCTGAG 60.046 61.111 21.95 0.00 0.00 3.35
1638 2135 2.046023 CTTGTGGCCGCATCCTGA 60.046 61.111 21.95 3.22 0.00 3.86
1639 2136 3.818787 GCTTGTGGCCGCATCCTG 61.819 66.667 21.95 11.81 34.27 3.86
1640 2137 3.984193 GAGCTTGTGGCCGCATCCT 62.984 63.158 21.95 18.69 43.05 3.24
1641 2138 3.512516 GAGCTTGTGGCCGCATCC 61.513 66.667 21.95 13.99 43.05 3.51
1642 2139 3.512516 GGAGCTTGTGGCCGCATC 61.513 66.667 21.95 14.89 43.05 3.91
1643 2140 3.984193 GAGGAGCTTGTGGCCGCAT 62.984 63.158 21.95 4.92 43.05 4.73
1644 2141 4.704833 GAGGAGCTTGTGGCCGCA 62.705 66.667 16.89 16.89 43.05 5.69
1646 2143 3.335356 ATGGAGGAGCTTGTGGCCG 62.335 63.158 0.00 0.00 43.05 6.13
1647 2144 1.751927 CATGGAGGAGCTTGTGGCC 60.752 63.158 0.00 0.00 43.05 5.36
1648 2145 0.322816 TTCATGGAGGAGCTTGTGGC 60.323 55.000 0.00 0.00 42.19 5.01
1649 2146 1.457346 GTTCATGGAGGAGCTTGTGG 58.543 55.000 0.00 0.00 0.00 4.17
1650 2147 1.081892 CGTTCATGGAGGAGCTTGTG 58.918 55.000 0.00 0.00 0.00 3.33
1651 2148 0.036010 CCGTTCATGGAGGAGCTTGT 60.036 55.000 0.00 0.00 0.00 3.16
1652 2149 0.250234 TCCGTTCATGGAGGAGCTTG 59.750 55.000 0.00 0.00 33.05 4.01
1653 2150 0.984230 TTCCGTTCATGGAGGAGCTT 59.016 50.000 0.00 0.00 39.72 3.74
1654 2151 0.250513 GTTCCGTTCATGGAGGAGCT 59.749 55.000 0.00 0.00 39.72 4.09
1655 2152 0.744771 GGTTCCGTTCATGGAGGAGC 60.745 60.000 0.00 3.14 39.72 4.70
1656 2153 0.460284 CGGTTCCGTTCATGGAGGAG 60.460 60.000 2.82 0.00 39.72 3.69
1657 2154 0.901114 TCGGTTCCGTTCATGGAGGA 60.901 55.000 11.04 0.00 39.72 3.71
1658 2155 0.460284 CTCGGTTCCGTTCATGGAGG 60.460 60.000 11.04 0.00 39.72 4.30
1659 2156 1.084370 GCTCGGTTCCGTTCATGGAG 61.084 60.000 11.04 0.87 39.72 3.86
1660 2157 1.079405 GCTCGGTTCCGTTCATGGA 60.079 57.895 11.04 0.00 35.83 3.41
1661 2158 0.174845 TAGCTCGGTTCCGTTCATGG 59.825 55.000 11.04 0.00 0.00 3.66
1662 2159 1.860950 CATAGCTCGGTTCCGTTCATG 59.139 52.381 11.04 7.15 0.00 3.07
1663 2160 1.202533 CCATAGCTCGGTTCCGTTCAT 60.203 52.381 11.04 0.00 0.00 2.57
1664 2161 0.174845 CCATAGCTCGGTTCCGTTCA 59.825 55.000 11.04 0.00 0.00 3.18
1665 2162 0.175073 ACCATAGCTCGGTTCCGTTC 59.825 55.000 11.04 4.59 30.53 3.95
1666 2163 1.135721 GTACCATAGCTCGGTTCCGTT 59.864 52.381 12.67 1.80 37.99 4.44
1667 2164 0.743097 GTACCATAGCTCGGTTCCGT 59.257 55.000 12.67 0.00 37.99 4.69
1668 2165 1.030457 AGTACCATAGCTCGGTTCCG 58.970 55.000 12.67 4.74 37.99 4.30
1672 2169 5.832060 AGTTATTACAGTACCATAGCTCGGT 59.168 40.000 12.14 12.14 40.73 4.69
1681 2178 7.233962 TCACAAAGGAGAGTTATTACAGTACCA 59.766 37.037 0.00 0.00 0.00 3.25
1682 2179 7.609056 TCACAAAGGAGAGTTATTACAGTACC 58.391 38.462 0.00 0.00 0.00 3.34
1686 2183 9.482627 GGATATCACAAAGGAGAGTTATTACAG 57.517 37.037 4.83 0.00 0.00 2.74
1694 2194 5.523588 TCTCTGGATATCACAAAGGAGAGT 58.476 41.667 4.83 0.00 0.00 3.24
1721 2222 5.220710 TGAAGAGAAACCAGAGAAGAAGG 57.779 43.478 0.00 0.00 0.00 3.46
1723 2224 4.901849 TCCTGAAGAGAAACCAGAGAAGAA 59.098 41.667 0.00 0.00 0.00 2.52
1725 2226 4.881019 TCCTGAAGAGAAACCAGAGAAG 57.119 45.455 0.00 0.00 0.00 2.85
1728 2229 7.065563 CACATAATTCCTGAAGAGAAACCAGAG 59.934 40.741 0.00 0.00 0.00 3.35
1732 2233 5.415701 TGCACATAATTCCTGAAGAGAAACC 59.584 40.000 0.00 0.00 0.00 3.27
1733 2234 6.500684 TGCACATAATTCCTGAAGAGAAAC 57.499 37.500 0.00 0.00 0.00 2.78
1745 2246 8.483307 AATTTTGTCTCCATTGCACATAATTC 57.517 30.769 0.00 0.00 30.53 2.17
1805 2308 6.834959 TTTCGTCAGCAGAGATGATTATTC 57.165 37.500 0.00 0.00 33.81 1.75
1839 2344 6.889301 ATGGAATATGGAACTTGCATACTG 57.111 37.500 5.22 0.00 33.52 2.74
1966 2476 5.659048 TTGGTTGTTTGTGTGTGAAAAAC 57.341 34.783 0.00 0.00 34.97 2.43
1980 2490 6.295292 GCCTTTCCTGATCTTATTTGGTTGTT 60.295 38.462 0.00 0.00 0.00 2.83
2004 2514 4.585955 TTGGATCTACGGATAGTCTTGC 57.414 45.455 0.00 0.00 31.46 4.01
2018 2534 6.903516 TGGTTCAGTGATATCATTTGGATCT 58.096 36.000 9.02 0.00 37.44 2.75
2063 2581 8.752254 CGAAGATGATAGCGACTAAAATTTACA 58.248 33.333 0.00 0.00 0.00 2.41
2068 2586 6.740110 AGACGAAGATGATAGCGACTAAAAT 58.260 36.000 0.00 0.00 0.00 1.82
2458 3012 4.107622 GTGTATGTTTGCCTTGCATCATC 58.892 43.478 9.38 4.95 38.76 2.92
2480 3034 5.129485 GTCTATGGTGGATATATGGTCCTGG 59.871 48.000 9.56 0.00 36.68 4.45


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

AutoCloner maintained by Alex Coulton.