Multiple sequence alignment - TraesCS3B01G441200

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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 TraesCS3B01G441200 chr3B 100.000 3659 0 0 1 3659 680677971 680674313 0.000000e+00 6758.0
1 TraesCS3B01G441200 chr3B 92.406 2041 113 21 769 2796 680733073 680731062 0.000000e+00 2872.0
2 TraesCS3B01G441200 chr3B 91.782 1947 108 30 769 2684 680478265 680476340 0.000000e+00 2662.0
3 TraesCS3B01G441200 chr3B 90.476 504 46 2 1 504 567802337 567802838 0.000000e+00 664.0
4 TraesCS3B01G441200 chr3B 79.688 384 68 8 3271 3647 37640455 37640075 6.020000e-68 268.0
5 TraesCS3B01G441200 chr3B 86.301 73 9 1 3066 3138 736943518 736943447 1.090000e-10 78.7
6 TraesCS3B01G441200 chr3A 92.007 2915 147 36 769 3659 651648535 651651387 0.000000e+00 4013.0
7 TraesCS3B01G441200 chr3A 91.440 2909 173 36 769 3659 651961980 651964830 0.000000e+00 3923.0
8 TraesCS3B01G441200 chr3A 91.338 1928 96 31 769 2684 651996077 651997945 0.000000e+00 2569.0
9 TraesCS3B01G441200 chr3A 90.297 505 48 1 1 504 65351692 65351188 0.000000e+00 660.0
10 TraesCS3B01G441200 chr3D 91.841 2917 174 27 769 3659 516671008 516673886 0.000000e+00 4010.0
11 TraesCS3B01G441200 chr3D 95.401 848 38 1 1838 2684 516856631 516857478 0.000000e+00 1349.0
12 TraesCS3B01G441200 chr3D 88.322 1019 89 21 769 1778 516855450 516856447 0.000000e+00 1195.0
13 TraesCS3B01G441200 chr3D 81.383 188 23 6 2084 2268 497721644 497721466 3.810000e-30 143.0
14 TraesCS3B01G441200 chr3D 74.436 266 45 13 3386 3631 266668750 266668488 3.890000e-15 93.5
15 TraesCS3B01G441200 chr7D 89.013 1702 142 25 988 2684 502231425 502233086 0.000000e+00 2065.0
16 TraesCS3B01G441200 chr7D 79.009 424 78 9 2087 2506 141562228 141562644 2.780000e-71 279.0
17 TraesCS3B01G441200 chr7D 84.793 217 33 0 2087 2303 152219671 152219887 6.150000e-53 219.0
18 TraesCS3B01G441200 chr7D 76.751 357 66 8 3213 3569 212887876 212887537 2.240000e-42 183.0
19 TraesCS3B01G441200 chr7D 84.354 147 15 6 2919 3059 133328835 133328979 1.770000e-28 137.0
20 TraesCS3B01G441200 chr1A 85.340 764 105 6 1883 2641 460281706 460282467 0.000000e+00 784.0
21 TraesCS3B01G441200 chr1D 85.059 763 109 5 1883 2641 360467955 360468716 0.000000e+00 773.0
22 TraesCS3B01G441200 chr1D 82.517 143 18 3 2919 3056 379591520 379591660 6.420000e-23 119.0
23 TraesCS3B01G441200 chr1D 89.189 74 7 1 3066 3139 487907312 487907240 1.400000e-14 91.6
24 TraesCS3B01G441200 chr1B 84.797 763 111 4 1883 2641 482697686 482698447 0.000000e+00 761.0
25 TraesCS3B01G441200 chr1B 90.551 508 48 0 1 508 221330488 221330995 0.000000e+00 673.0
26 TraesCS3B01G441200 chr1B 89.764 508 51 1 1 507 380642032 380641525 0.000000e+00 649.0
27 TraesCS3B01G441200 chr1B 90.909 77 7 0 3572 3648 296681050 296680974 1.800000e-18 104.0
28 TraesCS3B01G441200 chr1B 89.706 68 6 1 3066 3133 287703865 287703799 6.510000e-13 86.1
29 TraesCS3B01G441200 chr4A 91.018 501 41 1 4 504 704158993 704158497 0.000000e+00 673.0
30 TraesCS3B01G441200 chr4A 77.207 623 121 18 2026 2642 513805349 513805956 9.730000e-91 344.0
31 TraesCS3B01G441200 chr5B 90.675 504 46 1 1 504 546424572 546424070 0.000000e+00 669.0
32 TraesCS3B01G441200 chr5B 89.320 515 53 2 1 514 631783894 631783381 0.000000e+00 645.0
33 TraesCS3B01G441200 chr5B 82.192 146 20 3 2919 3060 523710265 523710408 1.780000e-23 121.0
34 TraesCS3B01G441200 chr5B 93.846 65 4 0 3068 3132 496586949 496587013 8.360000e-17 99.0
35 TraesCS3B01G441200 chr5D 90.079 504 50 0 1 504 403558824 403558321 0.000000e+00 654.0
36 TraesCS3B01G441200 chr5D 82.176 533 91 4 1230 1760 192537909 192538439 4.310000e-124 455.0
37 TraesCS3B01G441200 chr7B 89.784 509 49 3 1 508 535818470 535817964 0.000000e+00 649.0
38 TraesCS3B01G441200 chr7B 82.000 150 18 4 2919 3060 21662540 21662688 6.420000e-23 119.0
39 TraesCS3B01G441200 chr7B 85.586 111 13 3 3550 3659 289229511 289229619 2.990000e-21 113.0
40 TraesCS3B01G441200 chr4B 77.760 634 116 22 2026 2651 106491947 106491331 2.080000e-97 366.0
41 TraesCS3B01G441200 chr4D 77.532 632 121 18 2026 2651 74159224 74158608 9.660000e-96 361.0
42 TraesCS3B01G441200 chr4D 82.993 147 20 4 2923 3067 295116107 295116250 1.070000e-25 128.0
43 TraesCS3B01G441200 chr5A 75.796 628 123 19 1892 2506 225242986 225243597 1.290000e-74 291.0
44 TraesCS3B01G441200 chr5A 81.481 108 19 1 3552 3659 693294887 693294781 1.810000e-13 87.9
45 TraesCS3B01G441200 chr2B 81.507 146 21 3 2918 3059 94038236 94038093 8.300000e-22 115.0
46 TraesCS3B01G441200 chr2B 91.045 67 6 0 3066 3132 546777241 546777175 1.400000e-14 91.6
47 TraesCS3B01G441200 chr2A 77.835 194 26 10 2953 3133 655281277 655281088 1.800000e-18 104.0
48 TraesCS3B01G441200 chr7A 76.214 206 42 5 3275 3474 732739882 732740086 6.460000e-18 102.0
49 TraesCS3B01G441200 chr2D 75.115 217 44 7 3450 3659 58849633 58849420 3.890000e-15 93.5
50 TraesCS3B01G441200 chr6A 88.889 72 6 2 3432 3502 60092891 60092821 1.810000e-13 87.9


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 TraesCS3B01G441200 chr3B 680674313 680677971 3658 True 6758 6758 100.0000 1 3659 1 chr3B.!!$R3 3658
1 TraesCS3B01G441200 chr3B 680731062 680733073 2011 True 2872 2872 92.4060 769 2796 1 chr3B.!!$R4 2027
2 TraesCS3B01G441200 chr3B 680476340 680478265 1925 True 2662 2662 91.7820 769 2684 1 chr3B.!!$R2 1915
3 TraesCS3B01G441200 chr3B 567802337 567802838 501 False 664 664 90.4760 1 504 1 chr3B.!!$F1 503
4 TraesCS3B01G441200 chr3A 651648535 651651387 2852 False 4013 4013 92.0070 769 3659 1 chr3A.!!$F1 2890
5 TraesCS3B01G441200 chr3A 651961980 651964830 2850 False 3923 3923 91.4400 769 3659 1 chr3A.!!$F2 2890
6 TraesCS3B01G441200 chr3A 651996077 651997945 1868 False 2569 2569 91.3380 769 2684 1 chr3A.!!$F3 1915
7 TraesCS3B01G441200 chr3A 65351188 65351692 504 True 660 660 90.2970 1 504 1 chr3A.!!$R1 503
8 TraesCS3B01G441200 chr3D 516671008 516673886 2878 False 4010 4010 91.8410 769 3659 1 chr3D.!!$F1 2890
9 TraesCS3B01G441200 chr3D 516855450 516857478 2028 False 1272 1349 91.8615 769 2684 2 chr3D.!!$F2 1915
10 TraesCS3B01G441200 chr7D 502231425 502233086 1661 False 2065 2065 89.0130 988 2684 1 chr7D.!!$F4 1696
11 TraesCS3B01G441200 chr1A 460281706 460282467 761 False 784 784 85.3400 1883 2641 1 chr1A.!!$F1 758
12 TraesCS3B01G441200 chr1D 360467955 360468716 761 False 773 773 85.0590 1883 2641 1 chr1D.!!$F1 758
13 TraesCS3B01G441200 chr1B 482697686 482698447 761 False 761 761 84.7970 1883 2641 1 chr1B.!!$F2 758
14 TraesCS3B01G441200 chr1B 221330488 221330995 507 False 673 673 90.5510 1 508 1 chr1B.!!$F1 507
15 TraesCS3B01G441200 chr1B 380641525 380642032 507 True 649 649 89.7640 1 507 1 chr1B.!!$R3 506
16 TraesCS3B01G441200 chr4A 513805349 513805956 607 False 344 344 77.2070 2026 2642 1 chr4A.!!$F1 616
17 TraesCS3B01G441200 chr5B 546424070 546424572 502 True 669 669 90.6750 1 504 1 chr5B.!!$R1 503
18 TraesCS3B01G441200 chr5B 631783381 631783894 513 True 645 645 89.3200 1 514 1 chr5B.!!$R2 513
19 TraesCS3B01G441200 chr5D 403558321 403558824 503 True 654 654 90.0790 1 504 1 chr5D.!!$R1 503
20 TraesCS3B01G441200 chr5D 192537909 192538439 530 False 455 455 82.1760 1230 1760 1 chr5D.!!$F1 530
21 TraesCS3B01G441200 chr7B 535817964 535818470 506 True 649 649 89.7840 1 508 1 chr7B.!!$R1 507
22 TraesCS3B01G441200 chr4B 106491331 106491947 616 True 366 366 77.7600 2026 2651 1 chr4B.!!$R1 625
23 TraesCS3B01G441200 chr4D 74158608 74159224 616 True 361 361 77.5320 2026 2651 1 chr4D.!!$R1 625
24 TraesCS3B01G441200 chr5A 225242986 225243597 611 False 291 291 75.7960 1892 2506 1 chr5A.!!$F1 614

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
688 690 0.028770 CGCCAGCTTTTCGTGTTTCA 59.971 50.0 0.0 0.0 0.0 2.69 F
709 711 0.038159 GTGTTGAGGAGACGAGGTGG 60.038 60.0 0.0 0.0 0.0 4.61 F
748 750 0.038526 AGGTACACTCTGTTTCGCCG 60.039 55.0 0.0 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 1744 2.332104 CGAAGATGATCATGTAGGGCG 58.668 52.381 14.30 7.79 0.0 6.13 R
2580 2857 3.606662 GCTGCGGCGAGGGAGATA 61.607 66.667 12.98 0.00 0.0 1.98 R
2694 2972 5.102953 TCCTACACCTTGAATCCTTGATG 57.897 43.478 0.00 0.00 0.0 3.07 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
142 143 9.695526 CACACTAATTTGGATCTTCAAAATGAA 57.304 29.630 1.91 0.00 39.64 2.57
330 332 7.578736 CGTGCAAACTTGTTTTGATATGAAAAC 59.421 33.333 19.79 19.79 46.76 2.43
331 333 7.578736 GTGCAAACTTGTTTTGATATGAAAACG 59.421 33.333 20.74 12.62 46.76 3.60
383 385 2.117206 AAACGGATGCAGCCCCAA 59.883 55.556 16.93 0.00 0.00 4.12
423 425 1.281925 ATCTTTGGACAGGCCCGGAT 61.282 55.000 0.73 0.00 34.97 4.18
442 444 3.899980 GGATACGACCCCATTACCTTACT 59.100 47.826 0.00 0.00 0.00 2.24
474 476 0.603439 ATACGGGCAAAACGGACGTT 60.603 50.000 3.99 3.99 40.45 3.99
488 490 2.247267 CGTTCGTTTGGTGTCGCC 59.753 61.111 0.00 0.00 37.90 5.54
527 529 4.758251 CAGCCGATCACCACCGCA 62.758 66.667 0.00 0.00 0.00 5.69
528 530 4.457496 AGCCGATCACCACCGCAG 62.457 66.667 0.00 0.00 0.00 5.18
530 532 4.758251 CCGATCACCACCGCAGCA 62.758 66.667 0.00 0.00 0.00 4.41
531 533 2.741985 CGATCACCACCGCAGCAA 60.742 61.111 0.00 0.00 0.00 3.91
532 534 2.870372 GATCACCACCGCAGCAAC 59.130 61.111 0.00 0.00 0.00 4.17
533 535 3.027170 GATCACCACCGCAGCAACG 62.027 63.158 0.00 0.00 0.00 4.10
534 536 3.529341 ATCACCACCGCAGCAACGA 62.529 57.895 0.00 0.00 34.06 3.85
535 537 3.716006 CACCACCGCAGCAACGAG 61.716 66.667 0.00 0.00 34.06 4.18
546 548 2.445274 GCAACGAGCGATCAGTTCA 58.555 52.632 0.00 0.00 0.00 3.18
547 549 0.093705 GCAACGAGCGATCAGTTCAC 59.906 55.000 0.00 0.00 0.00 3.18
548 550 1.418373 CAACGAGCGATCAGTTCACA 58.582 50.000 0.00 0.00 0.00 3.58
549 551 1.125021 CAACGAGCGATCAGTTCACAC 59.875 52.381 0.00 0.00 0.00 3.82
550 552 0.388649 ACGAGCGATCAGTTCACACC 60.389 55.000 0.00 0.00 0.00 4.16
551 553 1.406219 CGAGCGATCAGTTCACACCG 61.406 60.000 0.00 0.00 0.00 4.94
552 554 0.109272 GAGCGATCAGTTCACACCGA 60.109 55.000 0.00 0.00 0.00 4.69
553 555 0.109086 AGCGATCAGTTCACACCGAG 60.109 55.000 0.00 0.00 0.00 4.63
554 556 1.687494 GCGATCAGTTCACACCGAGC 61.687 60.000 0.00 0.00 0.00 5.03
555 557 1.078759 CGATCAGTTCACACCGAGCC 61.079 60.000 0.00 0.00 0.00 4.70
556 558 0.741221 GATCAGTTCACACCGAGCCC 60.741 60.000 0.00 0.00 0.00 5.19
557 559 1.194781 ATCAGTTCACACCGAGCCCT 61.195 55.000 0.00 0.00 0.00 5.19
558 560 1.374758 CAGTTCACACCGAGCCCTC 60.375 63.158 0.00 0.00 0.00 4.30
559 561 1.534235 AGTTCACACCGAGCCCTCT 60.534 57.895 0.00 0.00 0.00 3.69
560 562 1.079750 GTTCACACCGAGCCCTCTC 60.080 63.158 0.00 0.00 35.99 3.20
578 580 4.025401 GGCCGACCGTGCAACAAG 62.025 66.667 0.00 0.00 35.74 3.16
579 581 4.025401 GCCGACCGTGCAACAAGG 62.025 66.667 0.00 0.00 38.88 3.61
580 582 3.353836 CCGACCGTGCAACAAGGG 61.354 66.667 4.60 0.00 37.32 3.95
581 583 3.353836 CGACCGTGCAACAAGGGG 61.354 66.667 4.60 0.00 37.32 4.79
582 584 2.112297 GACCGTGCAACAAGGGGA 59.888 61.111 4.60 0.00 37.32 4.81
583 585 1.966451 GACCGTGCAACAAGGGGAG 60.966 63.158 4.60 0.00 37.32 4.30
584 586 2.391724 GACCGTGCAACAAGGGGAGA 62.392 60.000 4.60 0.00 37.32 3.71
585 587 1.228124 CCGTGCAACAAGGGGAGAA 60.228 57.895 0.00 0.00 35.74 2.87
586 588 0.821711 CCGTGCAACAAGGGGAGAAA 60.822 55.000 0.00 0.00 35.74 2.52
587 589 0.593128 CGTGCAACAAGGGGAGAAAG 59.407 55.000 0.00 0.00 35.74 2.62
588 590 0.315251 GTGCAACAAGGGGAGAAAGC 59.685 55.000 0.00 0.00 36.32 3.51
589 591 0.185901 TGCAACAAGGGGAGAAAGCT 59.814 50.000 0.00 0.00 0.00 3.74
590 592 1.423541 TGCAACAAGGGGAGAAAGCTA 59.576 47.619 0.00 0.00 0.00 3.32
591 593 2.087646 GCAACAAGGGGAGAAAGCTAG 58.912 52.381 0.00 0.00 0.00 3.42
592 594 2.290323 GCAACAAGGGGAGAAAGCTAGA 60.290 50.000 0.00 0.00 0.00 2.43
593 595 3.604582 CAACAAGGGGAGAAAGCTAGAG 58.395 50.000 0.00 0.00 0.00 2.43
594 596 2.192263 ACAAGGGGAGAAAGCTAGAGG 58.808 52.381 0.00 0.00 0.00 3.69
595 597 2.225650 ACAAGGGGAGAAAGCTAGAGGA 60.226 50.000 0.00 0.00 0.00 3.71
596 598 2.433970 CAAGGGGAGAAAGCTAGAGGAG 59.566 54.545 0.00 0.00 0.00 3.69
613 615 2.869101 GAGCTCCTCCAAAGAAAGGT 57.131 50.000 0.87 0.00 34.12 3.50
614 616 3.983044 GAGCTCCTCCAAAGAAAGGTA 57.017 47.619 0.87 0.00 34.12 3.08
615 617 3.601435 GAGCTCCTCCAAAGAAAGGTAC 58.399 50.000 0.87 0.00 34.12 3.34
617 619 3.262151 AGCTCCTCCAAAGAAAGGTACTC 59.738 47.826 0.00 0.00 38.49 2.59
618 620 3.620226 GCTCCTCCAAAGAAAGGTACTCC 60.620 52.174 0.00 0.00 38.49 3.85
620 622 3.838903 TCCTCCAAAGAAAGGTACTCCTC 59.161 47.826 0.00 0.00 44.35 3.71
621 623 3.841255 CCTCCAAAGAAAGGTACTCCTCT 59.159 47.826 0.00 0.00 44.35 3.69
622 624 5.024118 CCTCCAAAGAAAGGTACTCCTCTA 58.976 45.833 0.00 0.00 44.35 2.43
623 625 5.128008 CCTCCAAAGAAAGGTACTCCTCTAG 59.872 48.000 0.00 0.00 44.35 2.43
624 626 4.466726 TCCAAAGAAAGGTACTCCTCTAGC 59.533 45.833 0.00 0.00 44.35 3.42
625 627 4.468153 CCAAAGAAAGGTACTCCTCTAGCT 59.532 45.833 0.00 0.00 44.35 3.32
626 628 5.046231 CCAAAGAAAGGTACTCCTCTAGCTT 60.046 44.000 0.00 0.00 44.35 3.74
627 629 6.468543 CAAAGAAAGGTACTCCTCTAGCTTT 58.531 40.000 0.00 3.65 44.35 3.51
628 630 6.689663 AAGAAAGGTACTCCTCTAGCTTTT 57.310 37.500 0.00 0.00 44.35 2.27
629 631 6.288941 AGAAAGGTACTCCTCTAGCTTTTC 57.711 41.667 0.00 0.00 44.35 2.29
630 632 4.722361 AAGGTACTCCTCTAGCTTTTCG 57.278 45.455 0.00 0.00 44.35 3.46
631 633 3.699413 AGGTACTCCTCTAGCTTTTCGT 58.301 45.455 0.00 0.00 40.58 3.85
632 634 3.444388 AGGTACTCCTCTAGCTTTTCGTG 59.556 47.826 0.00 0.00 40.58 4.35
633 635 3.193056 GGTACTCCTCTAGCTTTTCGTGT 59.807 47.826 0.00 0.00 0.00 4.49
634 636 4.321824 GGTACTCCTCTAGCTTTTCGTGTT 60.322 45.833 0.00 0.00 0.00 3.32
635 637 4.338379 ACTCCTCTAGCTTTTCGTGTTT 57.662 40.909 0.00 0.00 0.00 2.83
636 638 4.308265 ACTCCTCTAGCTTTTCGTGTTTC 58.692 43.478 0.00 0.00 0.00 2.78
637 639 4.202223 ACTCCTCTAGCTTTTCGTGTTTCA 60.202 41.667 0.00 0.00 0.00 2.69
638 640 4.699637 TCCTCTAGCTTTTCGTGTTTCAA 58.300 39.130 0.00 0.00 0.00 2.69
639 641 5.305585 TCCTCTAGCTTTTCGTGTTTCAAT 58.694 37.500 0.00 0.00 0.00 2.57
640 642 5.408604 TCCTCTAGCTTTTCGTGTTTCAATC 59.591 40.000 0.00 0.00 0.00 2.67
641 643 5.390991 CCTCTAGCTTTTCGTGTTTCAATCC 60.391 44.000 0.00 0.00 0.00 3.01
642 644 5.305585 TCTAGCTTTTCGTGTTTCAATCCT 58.694 37.500 0.00 0.00 0.00 3.24
643 645 4.489679 AGCTTTTCGTGTTTCAATCCTC 57.510 40.909 0.00 0.00 0.00 3.71
644 646 3.058914 AGCTTTTCGTGTTTCAATCCTCG 60.059 43.478 0.00 0.00 0.00 4.63
645 647 3.303791 GCTTTTCGTGTTTCAATCCTCGT 60.304 43.478 0.00 0.00 0.00 4.18
646 648 4.084223 GCTTTTCGTGTTTCAATCCTCGTA 60.084 41.667 0.00 0.00 0.00 3.43
647 649 5.585500 TTTTCGTGTTTCAATCCTCGTAG 57.415 39.130 0.00 0.00 0.00 3.51
648 650 3.226346 TCGTGTTTCAATCCTCGTAGG 57.774 47.619 0.00 0.00 36.46 3.18
660 662 3.768632 CGTAGGAGACGCTGTTGC 58.231 61.111 0.00 0.00 46.27 4.17
661 663 1.080772 CGTAGGAGACGCTGTTGCA 60.081 57.895 0.00 0.00 46.27 4.08
662 664 0.666274 CGTAGGAGACGCTGTTGCAA 60.666 55.000 0.00 0.00 46.27 4.08
663 665 1.726853 GTAGGAGACGCTGTTGCAAT 58.273 50.000 0.59 0.00 39.64 3.56
664 666 1.661112 GTAGGAGACGCTGTTGCAATC 59.339 52.381 0.59 0.00 39.64 2.67
665 667 0.674895 AGGAGACGCTGTTGCAATCC 60.675 55.000 0.59 3.35 39.64 3.01
666 668 0.674895 GGAGACGCTGTTGCAATCCT 60.675 55.000 0.59 0.00 39.64 3.24
667 669 0.445436 GAGACGCTGTTGCAATCCTG 59.555 55.000 0.59 0.00 39.64 3.86
668 670 0.250467 AGACGCTGTTGCAATCCTGT 60.250 50.000 0.59 0.00 39.64 4.00
669 671 0.166814 GACGCTGTTGCAATCCTGTC 59.833 55.000 0.59 5.78 39.64 3.51
670 672 1.133253 CGCTGTTGCAATCCTGTCG 59.867 57.895 0.59 0.00 39.64 4.35
671 673 1.154150 GCTGTTGCAATCCTGTCGC 60.154 57.895 0.59 0.00 39.41 5.19
672 674 1.503542 CTGTTGCAATCCTGTCGCC 59.496 57.895 0.59 0.00 0.00 5.54
673 675 1.228094 TGTTGCAATCCTGTCGCCA 60.228 52.632 0.59 0.00 0.00 5.69
674 676 1.236616 TGTTGCAATCCTGTCGCCAG 61.237 55.000 0.59 0.00 38.50 4.85
675 677 2.334946 TTGCAATCCTGTCGCCAGC 61.335 57.895 0.00 0.00 37.38 4.85
676 678 2.437359 GCAATCCTGTCGCCAGCT 60.437 61.111 0.00 0.00 37.38 4.24
677 679 2.042831 GCAATCCTGTCGCCAGCTT 61.043 57.895 0.00 0.00 37.38 3.74
678 680 1.589716 GCAATCCTGTCGCCAGCTTT 61.590 55.000 0.00 0.00 37.38 3.51
679 681 0.883833 CAATCCTGTCGCCAGCTTTT 59.116 50.000 0.00 0.00 37.38 2.27
680 682 1.135575 CAATCCTGTCGCCAGCTTTTC 60.136 52.381 0.00 0.00 37.38 2.29
681 683 1.021390 ATCCTGTCGCCAGCTTTTCG 61.021 55.000 0.00 0.00 37.38 3.46
682 684 1.961277 CCTGTCGCCAGCTTTTCGT 60.961 57.895 0.00 0.00 37.38 3.85
683 685 1.205064 CTGTCGCCAGCTTTTCGTG 59.795 57.895 0.00 0.00 0.00 4.35
684 686 1.498865 CTGTCGCCAGCTTTTCGTGT 61.499 55.000 0.00 0.00 0.00 4.49
685 687 1.092921 TGTCGCCAGCTTTTCGTGTT 61.093 50.000 0.00 0.00 0.00 3.32
686 688 0.028902 GTCGCCAGCTTTTCGTGTTT 59.971 50.000 0.00 0.00 0.00 2.83
687 689 0.306533 TCGCCAGCTTTTCGTGTTTC 59.693 50.000 0.00 0.00 0.00 2.78
688 690 0.028770 CGCCAGCTTTTCGTGTTTCA 59.971 50.000 0.00 0.00 0.00 2.69
689 691 1.477105 GCCAGCTTTTCGTGTTTCAC 58.523 50.000 0.00 0.00 0.00 3.18
701 703 2.546778 GTGTTTCACGTGTTGAGGAGA 58.453 47.619 16.51 0.00 34.94 3.71
702 704 2.284417 GTGTTTCACGTGTTGAGGAGAC 59.716 50.000 16.51 0.86 34.94 3.36
704 706 1.026584 TTCACGTGTTGAGGAGACGA 58.973 50.000 16.51 0.00 47.00 4.20
705 707 0.591659 TCACGTGTTGAGGAGACGAG 59.408 55.000 16.51 0.00 47.00 4.18
706 708 0.387367 CACGTGTTGAGGAGACGAGG 60.387 60.000 7.58 0.00 47.00 4.63
707 709 0.822532 ACGTGTTGAGGAGACGAGGT 60.823 55.000 2.70 0.00 47.00 3.85
708 710 0.387367 CGTGTTGAGGAGACGAGGTG 60.387 60.000 0.00 0.00 47.00 4.00
709 711 0.038159 GTGTTGAGGAGACGAGGTGG 60.038 60.000 0.00 0.00 0.00 4.61
710 712 1.185618 TGTTGAGGAGACGAGGTGGG 61.186 60.000 0.00 0.00 0.00 4.61
711 713 2.283529 TTGAGGAGACGAGGTGGGC 61.284 63.158 0.00 0.00 0.00 5.36
712 714 2.363147 GAGGAGACGAGGTGGGCT 60.363 66.667 0.00 0.00 0.00 5.19
713 715 2.681778 AGGAGACGAGGTGGGCTG 60.682 66.667 0.00 0.00 0.00 4.85
714 716 2.680352 GGAGACGAGGTGGGCTGA 60.680 66.667 0.00 0.00 0.00 4.26
715 717 2.716017 GGAGACGAGGTGGGCTGAG 61.716 68.421 0.00 0.00 0.00 3.35
716 718 3.363844 GAGACGAGGTGGGCTGAGC 62.364 68.421 0.00 0.00 0.00 4.26
717 719 3.695606 GACGAGGTGGGCTGAGCA 61.696 66.667 6.82 0.00 0.00 4.26
718 720 3.655810 GACGAGGTGGGCTGAGCAG 62.656 68.421 6.82 0.00 0.00 4.24
719 721 3.699894 CGAGGTGGGCTGAGCAGT 61.700 66.667 6.82 0.00 0.00 4.40
720 722 2.046507 GAGGTGGGCTGAGCAGTG 60.047 66.667 6.82 0.00 0.00 3.66
721 723 2.851102 AGGTGGGCTGAGCAGTGT 60.851 61.111 6.82 0.00 0.00 3.55
722 724 2.670934 GGTGGGCTGAGCAGTGTG 60.671 66.667 6.82 0.00 0.00 3.82
723 725 3.360340 GTGGGCTGAGCAGTGTGC 61.360 66.667 6.82 0.00 45.46 4.57
732 734 4.675404 GCAGTGTGCGAAGTAGGT 57.325 55.556 0.00 0.00 31.71 3.08
733 735 3.806591 GCAGTGTGCGAAGTAGGTA 57.193 52.632 0.00 0.00 31.71 3.08
734 736 1.347320 GCAGTGTGCGAAGTAGGTAC 58.653 55.000 0.00 0.00 31.71 3.34
735 737 1.336517 GCAGTGTGCGAAGTAGGTACA 60.337 52.381 0.00 0.00 31.71 2.90
736 738 2.325761 CAGTGTGCGAAGTAGGTACAC 58.674 52.381 5.23 5.23 46.92 2.90
737 739 2.719426 GTGTGCGAAGTAGGTACACT 57.281 50.000 6.01 0.00 44.36 3.55
738 740 2.593257 GTGTGCGAAGTAGGTACACTC 58.407 52.381 6.01 0.00 44.36 3.51
739 741 2.228343 GTGTGCGAAGTAGGTACACTCT 59.772 50.000 6.01 0.00 44.36 3.24
740 742 2.228103 TGTGCGAAGTAGGTACACTCTG 59.772 50.000 0.00 0.00 32.49 3.35
741 743 2.228343 GTGCGAAGTAGGTACACTCTGT 59.772 50.000 0.00 0.00 0.00 3.41
742 744 2.889045 TGCGAAGTAGGTACACTCTGTT 59.111 45.455 0.00 0.00 0.00 3.16
743 745 3.319972 TGCGAAGTAGGTACACTCTGTTT 59.680 43.478 0.00 0.00 0.00 2.83
744 746 3.919197 GCGAAGTAGGTACACTCTGTTTC 59.081 47.826 0.00 0.00 0.00 2.78
745 747 4.156915 CGAAGTAGGTACACTCTGTTTCG 58.843 47.826 0.00 0.56 0.00 3.46
746 748 3.572604 AGTAGGTACACTCTGTTTCGC 57.427 47.619 0.00 0.00 0.00 4.70
747 749 2.230750 AGTAGGTACACTCTGTTTCGCC 59.769 50.000 0.00 0.00 0.00 5.54
748 750 0.038526 AGGTACACTCTGTTTCGCCG 60.039 55.000 0.00 0.00 0.00 6.46
749 751 1.623973 GGTACACTCTGTTTCGCCGC 61.624 60.000 0.00 0.00 0.00 6.53
750 752 0.666577 GTACACTCTGTTTCGCCGCT 60.667 55.000 0.00 0.00 0.00 5.52
751 753 0.666274 TACACTCTGTTTCGCCGCTG 60.666 55.000 0.00 0.00 0.00 5.18
752 754 1.664649 CACTCTGTTTCGCCGCTGA 60.665 57.895 0.00 0.00 0.00 4.26
753 755 1.016130 CACTCTGTTTCGCCGCTGAT 61.016 55.000 0.00 0.00 0.00 2.90
754 756 0.320771 ACTCTGTTTCGCCGCTGATT 60.321 50.000 0.00 0.00 0.00 2.57
755 757 0.371645 CTCTGTTTCGCCGCTGATTC 59.628 55.000 0.00 0.00 0.00 2.52
756 758 1.059369 CTGTTTCGCCGCTGATTCG 59.941 57.895 0.00 0.00 0.00 3.34
757 759 2.276680 GTTTCGCCGCTGATTCGC 60.277 61.111 0.00 0.00 0.00 4.70
765 767 3.706140 GCTGATTCGCGTAGTGGG 58.294 61.111 5.77 0.00 39.32 4.61
766 768 2.526120 GCTGATTCGCGTAGTGGGC 61.526 63.158 5.77 1.34 39.32 5.36
767 769 1.141881 CTGATTCGCGTAGTGGGCT 59.858 57.895 5.77 0.00 39.32 5.19
869 897 4.864916 AATTTACTATCACGCTGCACAG 57.135 40.909 0.00 0.00 0.00 3.66
883 911 1.756538 TGCACAGGATCGCATCTCTAA 59.243 47.619 0.00 0.00 31.95 2.10
921 953 0.976641 CTTACTGTGGTCTGGCCTCA 59.023 55.000 3.32 0.53 38.32 3.86
928 960 2.642311 TGTGGTCTGGCCTCATCTTAAA 59.358 45.455 3.32 0.00 35.98 1.52
962 994 1.133407 CACGCCTACTCTCTCTGTTCC 59.867 57.143 0.00 0.00 0.00 3.62
1005 1040 2.443952 AGGTCGATCGGGATGGCA 60.444 61.111 16.41 0.00 0.00 4.92
1189 1303 7.541091 CGTACAGTATCAGTACTTGATTGTTGT 59.459 37.037 11.43 13.60 44.14 3.32
1217 1338 1.004185 CTCTGACGTACGTACCGATGG 60.004 57.143 22.87 7.97 0.00 3.51
1351 1472 1.339824 CCTGCTGTCATGCTCCTCTTT 60.340 52.381 0.00 0.00 0.00 2.52
1623 1744 3.123620 CTGCAAGGTCTCCAGCGC 61.124 66.667 0.00 0.00 31.12 5.92
1796 2059 4.423625 AGGGGACTCTTATACACATTGC 57.576 45.455 0.00 0.00 32.90 3.56
1797 2060 3.780294 AGGGGACTCTTATACACATTGCA 59.220 43.478 0.00 0.00 32.90 4.08
1798 2061 4.227300 AGGGGACTCTTATACACATTGCAA 59.773 41.667 0.00 0.00 32.90 4.08
1799 2062 4.947388 GGGGACTCTTATACACATTGCAAA 59.053 41.667 1.71 0.00 0.00 3.68
1800 2063 5.594317 GGGGACTCTTATACACATTGCAAAT 59.406 40.000 1.71 0.00 0.00 2.32
1801 2064 6.096846 GGGGACTCTTATACACATTGCAAATT 59.903 38.462 1.71 0.00 0.00 1.82
1802 2065 6.974622 GGGACTCTTATACACATTGCAAATTG 59.025 38.462 1.71 6.14 0.00 2.32
1887 2154 2.740826 GCAGCAAACGGAGGCGTA 60.741 61.111 0.00 0.00 34.54 4.42
2595 2872 3.606662 GCTATCTCCCTCGCCGCA 61.607 66.667 0.00 0.00 0.00 5.69
2687 2965 1.083080 CGATCGTGCACGCACAAAA 60.083 52.632 33.63 16.50 46.47 2.44
2689 2967 0.770008 GATCGTGCACGCACAAAAAC 59.230 50.000 33.63 11.00 46.47 2.43
2690 2968 0.099613 ATCGTGCACGCACAAAAACA 59.900 45.000 33.63 14.14 46.47 2.83
2692 2970 0.919981 CGTGCACGCACAAAAACAAT 59.080 45.000 28.16 0.00 46.47 2.71
2694 2972 2.098116 CGTGCACGCACAAAAACAATAC 60.098 45.455 28.16 0.00 46.47 1.89
2695 2973 2.854777 GTGCACGCACAAAAACAATACA 59.145 40.909 17.03 0.00 45.53 2.29
2696 2974 3.489047 GTGCACGCACAAAAACAATACAT 59.511 39.130 17.03 0.00 45.53 2.29
2697 2975 3.733224 TGCACGCACAAAAACAATACATC 59.267 39.130 0.00 0.00 0.00 3.06
2698 2976 3.733224 GCACGCACAAAAACAATACATCA 59.267 39.130 0.00 0.00 0.00 3.07
2699 2977 4.208047 GCACGCACAAAAACAATACATCAA 59.792 37.500 0.00 0.00 0.00 2.57
2700 2978 5.610124 GCACGCACAAAAACAATACATCAAG 60.610 40.000 0.00 0.00 0.00 3.02
2701 2979 4.981674 ACGCACAAAAACAATACATCAAGG 59.018 37.500 0.00 0.00 0.00 3.61
2702 2980 5.218885 CGCACAAAAACAATACATCAAGGA 58.781 37.500 0.00 0.00 0.00 3.36
2703 2981 5.863397 CGCACAAAAACAATACATCAAGGAT 59.137 36.000 0.00 0.00 0.00 3.24
2763 3042 7.543520 GGCCTTCAAACAATTCAAAGAAGATAG 59.456 37.037 0.00 0.00 35.67 2.08
2811 3090 4.063998 TGTAGTCATGCATGAGATCCAC 57.936 45.455 29.38 20.28 37.51 4.02
2814 3093 2.158798 AGTCATGCATGAGATCCACAGG 60.159 50.000 29.38 0.00 37.51 4.00
2815 3094 1.142262 TCATGCATGAGATCCACAGGG 59.858 52.381 25.42 0.00 32.11 4.45
2816 3095 3.227548 TCATGCATGAGATCCACAGGGA 61.228 50.000 25.42 0.00 38.82 4.20
2817 3096 4.714870 TCATGCATGAGATCCACAGGGAA 61.715 47.826 25.42 0.00 38.33 3.97
3013 3303 1.294068 TCCTACCCCTATGAGCACCTT 59.706 52.381 0.00 0.00 0.00 3.50
3015 3305 2.398588 CTACCCCTATGAGCACCTTCA 58.601 52.381 0.00 0.00 0.00 3.02
3024 3314 1.902508 TGAGCACCTTCAAGGGACTAG 59.097 52.381 8.75 0.00 40.58 2.57
3029 3319 0.976073 CCTTCAAGGGACTAGGCCGA 60.976 60.000 9.03 0.00 38.49 5.54
3073 3365 2.496817 GCCAGACGCCTAGGACTG 59.503 66.667 14.75 16.96 0.00 3.51
3081 3373 1.908483 GCCTAGGACTGGAACCCTG 59.092 63.158 14.75 0.00 34.11 4.45
3088 3380 2.125766 GACTGGAACCCTGGTGGACC 62.126 65.000 0.00 0.00 38.00 4.46
3103 3395 1.192428 GGACCGAGGATACCACTGTT 58.808 55.000 0.00 0.00 37.17 3.16
3189 3481 3.591527 TGGGTGATGGAGATTGTAACCTT 59.408 43.478 0.00 0.00 0.00 3.50
3225 3517 1.229131 ATGGTCAGGGCATCTCCAAT 58.771 50.000 0.00 0.00 36.21 3.16
3291 3588 2.276116 GCCAGTCCGAGGACACTGA 61.276 63.158 22.66 0.00 46.76 3.41
3297 3594 2.093288 AGTCCGAGGACACTGATACGTA 60.093 50.000 22.66 0.00 46.76 3.57
3348 3645 3.942748 TGTCCGTTAGTATGGGCAATTTC 59.057 43.478 0.00 0.00 42.02 2.17
3362 3659 4.437255 GGGCAATTTCAAATTCAAATCCGC 60.437 41.667 0.00 0.00 0.00 5.54
3379 3676 2.736995 CCCGATCACAACACGCGT 60.737 61.111 5.58 5.58 0.00 6.01
3419 3716 0.827368 GTCACAACCAAAAAGGGGCA 59.173 50.000 0.00 0.00 43.89 5.36
3429 3726 3.132824 CCAAAAAGGGGCAACTATCCATC 59.867 47.826 0.00 0.00 0.00 3.51
3430 3727 3.756082 AAAAGGGGCAACTATCCATCA 57.244 42.857 0.00 0.00 0.00 3.07
3507 3804 0.112995 ATTTTCTGCCCTGCTGGACA 59.887 50.000 11.88 4.60 35.39 4.02
3536 3833 1.941294 CAGACTCCATGCTCAATCTGC 59.059 52.381 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 9.577222 AACCAATTCATTTTGAAGATCCAAATT 57.423 25.926 0.00 0.00 40.05 1.82
142 143 2.933573 TCCCACACGTGTTTAACCAAT 58.066 42.857 20.79 0.00 0.00 3.16
204 205 8.356657 ACAACCAAATCGAAATTGTCTTGAATA 58.643 29.630 18.66 0.00 0.00 1.75
301 303 3.840890 TCAAAACAAGTTTGCACGTCT 57.159 38.095 0.00 0.00 45.38 4.18
407 409 1.605453 GTATCCGGGCCTGTCCAAA 59.395 57.895 11.58 0.00 36.21 3.28
408 410 2.727392 CGTATCCGGGCCTGTCCAA 61.727 63.158 11.58 0.00 36.21 3.53
409 411 3.151710 CGTATCCGGGCCTGTCCA 61.152 66.667 11.58 0.00 36.21 4.02
423 425 3.979911 TGAGTAAGGTAATGGGGTCGTA 58.020 45.455 0.00 0.00 0.00 3.43
435 437 7.442656 CCGTATTCTATCCATTTGAGTAAGGT 58.557 38.462 0.00 0.00 0.00 3.50
438 440 6.183361 TGCCCGTATTCTATCCATTTGAGTAA 60.183 38.462 0.00 0.00 0.00 2.24
442 444 4.698201 TGCCCGTATTCTATCCATTTGA 57.302 40.909 0.00 0.00 0.00 2.69
451 453 2.620242 GTCCGTTTTGCCCGTATTCTA 58.380 47.619 0.00 0.00 0.00 2.10
457 459 2.514360 AACGTCCGTTTTGCCCGT 60.514 55.556 0.00 0.00 34.22 5.28
474 476 3.229156 ATCGGGCGACACCAAACGA 62.229 57.895 0.00 0.00 42.05 3.85
482 484 1.375396 CCAACTTCATCGGGCGACA 60.375 57.895 0.00 0.00 0.00 4.35
488 490 1.668419 CCTTAGGCCAACTTCATCGG 58.332 55.000 5.01 0.00 0.00 4.18
510 512 4.758251 TGCGGTGGTGATCGGCTG 62.758 66.667 0.00 0.00 33.41 4.85
511 513 4.457496 CTGCGGTGGTGATCGGCT 62.457 66.667 0.00 0.00 33.41 5.52
513 515 4.758251 TGCTGCGGTGGTGATCGG 62.758 66.667 0.00 0.00 0.00 4.18
514 516 2.741985 TTGCTGCGGTGGTGATCG 60.742 61.111 0.00 0.00 0.00 3.69
515 517 2.870372 GTTGCTGCGGTGGTGATC 59.130 61.111 0.00 0.00 0.00 2.92
516 518 3.049674 CGTTGCTGCGGTGGTGAT 61.050 61.111 0.00 0.00 0.00 3.06
517 519 4.228567 TCGTTGCTGCGGTGGTGA 62.229 61.111 0.00 0.00 0.00 4.02
518 520 3.716006 CTCGTTGCTGCGGTGGTG 61.716 66.667 0.00 0.00 0.00 4.17
525 527 1.630244 AACTGATCGCTCGTTGCTGC 61.630 55.000 0.00 0.00 40.11 5.25
526 528 0.368227 GAACTGATCGCTCGTTGCTG 59.632 55.000 2.20 0.00 40.11 4.41
527 529 0.038251 TGAACTGATCGCTCGTTGCT 60.038 50.000 2.20 0.00 40.11 3.91
528 530 0.093705 GTGAACTGATCGCTCGTTGC 59.906 55.000 2.20 0.00 35.60 4.17
529 531 1.125021 GTGTGAACTGATCGCTCGTTG 59.875 52.381 0.26 0.00 39.38 4.10
530 532 1.419374 GTGTGAACTGATCGCTCGTT 58.581 50.000 0.26 0.00 39.38 3.85
531 533 0.388649 GGTGTGAACTGATCGCTCGT 60.389 55.000 0.26 0.00 39.38 4.18
532 534 1.406219 CGGTGTGAACTGATCGCTCG 61.406 60.000 0.26 1.38 39.38 5.03
533 535 0.109272 TCGGTGTGAACTGATCGCTC 60.109 55.000 0.26 0.00 39.38 5.03
534 536 0.109086 CTCGGTGTGAACTGATCGCT 60.109 55.000 0.26 0.00 39.38 4.93
535 537 1.687494 GCTCGGTGTGAACTGATCGC 61.687 60.000 0.00 0.00 39.09 4.58
536 538 1.078759 GGCTCGGTGTGAACTGATCG 61.079 60.000 0.00 0.00 0.00 3.69
537 539 0.741221 GGGCTCGGTGTGAACTGATC 60.741 60.000 0.00 0.00 0.00 2.92
538 540 1.194781 AGGGCTCGGTGTGAACTGAT 61.195 55.000 0.00 0.00 0.00 2.90
539 541 1.816863 GAGGGCTCGGTGTGAACTGA 61.817 60.000 0.00 0.00 0.00 3.41
540 542 1.374758 GAGGGCTCGGTGTGAACTG 60.375 63.158 0.00 0.00 0.00 3.16
541 543 1.534235 AGAGGGCTCGGTGTGAACT 60.534 57.895 0.00 0.00 34.09 3.01
542 544 1.079750 GAGAGGGCTCGGTGTGAAC 60.080 63.158 0.00 0.00 34.09 3.18
543 545 3.377656 GAGAGGGCTCGGTGTGAA 58.622 61.111 0.00 0.00 34.09 3.18
561 563 4.025401 CTTGTTGCACGGTCGGCC 62.025 66.667 0.00 0.00 0.00 6.13
562 564 4.025401 CCTTGTTGCACGGTCGGC 62.025 66.667 0.00 0.00 0.00 5.54
563 565 3.353836 CCCTTGTTGCACGGTCGG 61.354 66.667 0.00 0.00 0.00 4.79
564 566 3.353836 CCCCTTGTTGCACGGTCG 61.354 66.667 0.00 0.00 0.00 4.79
565 567 1.966451 CTCCCCTTGTTGCACGGTC 60.966 63.158 0.00 0.00 0.00 4.79
566 568 1.990160 TTCTCCCCTTGTTGCACGGT 61.990 55.000 0.00 0.00 0.00 4.83
567 569 0.821711 TTTCTCCCCTTGTTGCACGG 60.822 55.000 0.00 0.00 0.00 4.94
568 570 0.593128 CTTTCTCCCCTTGTTGCACG 59.407 55.000 0.00 0.00 0.00 5.34
569 571 0.315251 GCTTTCTCCCCTTGTTGCAC 59.685 55.000 0.00 0.00 0.00 4.57
570 572 0.185901 AGCTTTCTCCCCTTGTTGCA 59.814 50.000 0.00 0.00 0.00 4.08
571 573 2.087646 CTAGCTTTCTCCCCTTGTTGC 58.912 52.381 0.00 0.00 0.00 4.17
572 574 3.604582 CTCTAGCTTTCTCCCCTTGTTG 58.395 50.000 0.00 0.00 0.00 3.33
573 575 2.573915 CCTCTAGCTTTCTCCCCTTGTT 59.426 50.000 0.00 0.00 0.00 2.83
574 576 2.192263 CCTCTAGCTTTCTCCCCTTGT 58.808 52.381 0.00 0.00 0.00 3.16
575 577 2.433970 CTCCTCTAGCTTTCTCCCCTTG 59.566 54.545 0.00 0.00 0.00 3.61
576 578 2.758130 CTCCTCTAGCTTTCTCCCCTT 58.242 52.381 0.00 0.00 0.00 3.95
577 579 2.470057 CTCCTCTAGCTTTCTCCCCT 57.530 55.000 0.00 0.00 0.00 4.79
594 596 2.869101 ACCTTTCTTTGGAGGAGCTC 57.131 50.000 4.71 4.71 36.84 4.09
595 597 3.252351 AGTACCTTTCTTTGGAGGAGCT 58.748 45.455 0.00 0.00 36.84 4.09
596 598 3.601435 GAGTACCTTTCTTTGGAGGAGC 58.399 50.000 0.00 0.00 36.84 4.70
597 599 3.841255 AGGAGTACCTTTCTTTGGAGGAG 59.159 47.826 0.00 0.00 45.36 3.69
598 600 3.870559 AGGAGTACCTTTCTTTGGAGGA 58.129 45.455 0.00 0.00 45.36 3.71
611 613 3.193056 ACACGAAAAGCTAGAGGAGTACC 59.807 47.826 0.00 0.00 0.00 3.34
612 614 4.437772 ACACGAAAAGCTAGAGGAGTAC 57.562 45.455 0.00 0.00 0.00 2.73
613 615 5.010314 TGAAACACGAAAAGCTAGAGGAGTA 59.990 40.000 0.00 0.00 0.00 2.59
614 616 4.202223 TGAAACACGAAAAGCTAGAGGAGT 60.202 41.667 0.00 0.00 0.00 3.85
615 617 4.307432 TGAAACACGAAAAGCTAGAGGAG 58.693 43.478 0.00 0.00 0.00 3.69
616 618 4.330944 TGAAACACGAAAAGCTAGAGGA 57.669 40.909 0.00 0.00 0.00 3.71
617 619 5.390991 GGATTGAAACACGAAAAGCTAGAGG 60.391 44.000 0.00 0.00 0.00 3.69
618 620 5.409826 AGGATTGAAACACGAAAAGCTAGAG 59.590 40.000 0.00 0.00 0.00 2.43
619 621 5.305585 AGGATTGAAACACGAAAAGCTAGA 58.694 37.500 0.00 0.00 0.00 2.43
620 622 5.613358 AGGATTGAAACACGAAAAGCTAG 57.387 39.130 0.00 0.00 0.00 3.42
621 623 4.151689 CGAGGATTGAAACACGAAAAGCTA 59.848 41.667 0.00 0.00 0.00 3.32
622 624 3.058914 CGAGGATTGAAACACGAAAAGCT 60.059 43.478 0.00 0.00 0.00 3.74
623 625 3.226347 CGAGGATTGAAACACGAAAAGC 58.774 45.455 0.00 0.00 0.00 3.51
624 626 4.468095 ACGAGGATTGAAACACGAAAAG 57.532 40.909 0.00 0.00 0.00 2.27
625 627 4.449743 CCTACGAGGATTGAAACACGAAAA 59.550 41.667 0.00 0.00 37.67 2.29
626 628 3.991773 CCTACGAGGATTGAAACACGAAA 59.008 43.478 0.00 0.00 37.67 3.46
627 629 3.256383 TCCTACGAGGATTGAAACACGAA 59.744 43.478 0.00 0.00 40.06 3.85
628 630 2.821378 TCCTACGAGGATTGAAACACGA 59.179 45.455 0.00 0.00 40.06 4.35
629 631 3.119602 TCTCCTACGAGGATTGAAACACG 60.120 47.826 4.39 0.00 44.81 4.49
630 632 4.174762 GTCTCCTACGAGGATTGAAACAC 58.825 47.826 4.39 0.00 44.81 3.32
631 633 4.451629 GTCTCCTACGAGGATTGAAACA 57.548 45.455 4.39 0.00 44.81 2.83
644 646 1.661112 GATTGCAACAGCGTCTCCTAC 59.339 52.381 0.00 0.00 0.00 3.18
645 647 1.405526 GGATTGCAACAGCGTCTCCTA 60.406 52.381 0.00 0.00 0.00 2.94
646 648 0.674895 GGATTGCAACAGCGTCTCCT 60.675 55.000 0.00 0.00 0.00 3.69
647 649 0.674895 AGGATTGCAACAGCGTCTCC 60.675 55.000 0.00 2.62 0.00 3.71
648 650 0.445436 CAGGATTGCAACAGCGTCTC 59.555 55.000 0.00 0.00 0.00 3.36
649 651 0.250467 ACAGGATTGCAACAGCGTCT 60.250 50.000 0.00 0.00 0.00 4.18
650 652 0.166814 GACAGGATTGCAACAGCGTC 59.833 55.000 0.00 3.10 0.00 5.19
651 653 1.568612 CGACAGGATTGCAACAGCGT 61.569 55.000 0.00 0.00 0.00 5.07
652 654 1.133253 CGACAGGATTGCAACAGCG 59.867 57.895 0.00 0.00 0.00 5.18
653 655 1.154150 GCGACAGGATTGCAACAGC 60.154 57.895 0.00 0.00 37.69 4.40
654 656 1.236616 TGGCGACAGGATTGCAACAG 61.237 55.000 0.00 0.00 39.86 3.16
655 657 1.228094 TGGCGACAGGATTGCAACA 60.228 52.632 0.00 0.00 39.86 3.33
656 658 3.667087 TGGCGACAGGATTGCAAC 58.333 55.556 0.00 0.00 39.86 4.17
666 668 1.092921 AACACGAAAAGCTGGCGACA 61.093 50.000 9.68 0.00 39.59 4.35
667 669 0.028902 AAACACGAAAAGCTGGCGAC 59.971 50.000 9.68 0.00 0.00 5.19
668 670 0.306533 GAAACACGAAAAGCTGGCGA 59.693 50.000 9.68 0.00 0.00 5.54
669 671 0.028770 TGAAACACGAAAAGCTGGCG 59.971 50.000 0.00 0.00 0.00 5.69
670 672 1.477105 GTGAAACACGAAAAGCTGGC 58.523 50.000 0.00 0.00 36.32 4.85
681 683 2.284417 GTCTCCTCAACACGTGAAACAC 59.716 50.000 25.01 3.71 35.22 3.32
682 684 2.546778 GTCTCCTCAACACGTGAAACA 58.453 47.619 25.01 1.69 35.22 2.83
683 685 1.521423 CGTCTCCTCAACACGTGAAAC 59.479 52.381 25.01 6.89 35.22 2.78
684 686 1.406180 TCGTCTCCTCAACACGTGAAA 59.594 47.619 25.01 5.82 35.22 2.69
685 687 1.001706 CTCGTCTCCTCAACACGTGAA 60.002 52.381 25.01 6.21 35.22 3.18
686 688 0.591659 CTCGTCTCCTCAACACGTGA 59.408 55.000 25.01 0.00 35.05 4.35
687 689 0.387367 CCTCGTCTCCTCAACACGTG 60.387 60.000 15.48 15.48 35.05 4.49
688 690 0.822532 ACCTCGTCTCCTCAACACGT 60.823 55.000 0.00 0.00 35.05 4.49
689 691 0.387367 CACCTCGTCTCCTCAACACG 60.387 60.000 0.00 0.00 34.78 4.49
690 692 0.038159 CCACCTCGTCTCCTCAACAC 60.038 60.000 0.00 0.00 0.00 3.32
691 693 1.185618 CCCACCTCGTCTCCTCAACA 61.186 60.000 0.00 0.00 0.00 3.33
692 694 1.592223 CCCACCTCGTCTCCTCAAC 59.408 63.158 0.00 0.00 0.00 3.18
693 695 2.283529 GCCCACCTCGTCTCCTCAA 61.284 63.158 0.00 0.00 0.00 3.02
694 696 2.680352 GCCCACCTCGTCTCCTCA 60.680 66.667 0.00 0.00 0.00 3.86
695 697 2.363147 AGCCCACCTCGTCTCCTC 60.363 66.667 0.00 0.00 0.00 3.71
696 698 2.681778 CAGCCCACCTCGTCTCCT 60.682 66.667 0.00 0.00 0.00 3.69
697 699 2.680352 TCAGCCCACCTCGTCTCC 60.680 66.667 0.00 0.00 0.00 3.71
698 700 2.888863 CTCAGCCCACCTCGTCTC 59.111 66.667 0.00 0.00 0.00 3.36
699 701 3.386237 GCTCAGCCCACCTCGTCT 61.386 66.667 0.00 0.00 0.00 4.18
700 702 3.655810 CTGCTCAGCCCACCTCGTC 62.656 68.421 0.00 0.00 0.00 4.20
701 703 3.699894 CTGCTCAGCCCACCTCGT 61.700 66.667 0.00 0.00 0.00 4.18
702 704 3.699894 ACTGCTCAGCCCACCTCG 61.700 66.667 0.00 0.00 0.00 4.63
703 705 2.046507 CACTGCTCAGCCCACCTC 60.047 66.667 0.00 0.00 0.00 3.85
704 706 2.851102 ACACTGCTCAGCCCACCT 60.851 61.111 0.00 0.00 0.00 4.00
705 707 2.670934 CACACTGCTCAGCCCACC 60.671 66.667 0.00 0.00 0.00 4.61
706 708 3.360340 GCACACTGCTCAGCCCAC 61.360 66.667 0.00 0.00 40.96 4.61
707 709 4.994471 CGCACACTGCTCAGCCCA 62.994 66.667 0.00 0.00 42.25 5.36
708 710 4.687215 TCGCACACTGCTCAGCCC 62.687 66.667 0.00 0.00 42.25 5.19
709 711 2.666190 TTCGCACACTGCTCAGCC 60.666 61.111 0.00 0.00 42.25 4.85
710 712 0.667487 TACTTCGCACACTGCTCAGC 60.667 55.000 0.00 0.00 42.25 4.26
711 713 1.344458 CTACTTCGCACACTGCTCAG 58.656 55.000 0.00 0.00 42.25 3.35
712 714 0.038251 CCTACTTCGCACACTGCTCA 60.038 55.000 0.00 0.00 42.25 4.26
713 715 0.038159 ACCTACTTCGCACACTGCTC 60.038 55.000 0.00 0.00 42.25 4.26
714 716 1.067776 GTACCTACTTCGCACACTGCT 60.068 52.381 0.00 0.00 42.25 4.24
715 717 1.336517 TGTACCTACTTCGCACACTGC 60.337 52.381 0.00 0.00 40.69 4.40
716 718 2.030185 AGTGTACCTACTTCGCACACTG 60.030 50.000 4.97 0.00 45.96 3.66
717 719 2.236766 AGTGTACCTACTTCGCACACT 58.763 47.619 0.03 0.03 43.68 3.55
718 720 2.228343 AGAGTGTACCTACTTCGCACAC 59.772 50.000 0.00 0.00 39.78 3.82
719 721 2.228103 CAGAGTGTACCTACTTCGCACA 59.772 50.000 0.00 0.00 32.99 4.57
720 722 2.228343 ACAGAGTGTACCTACTTCGCAC 59.772 50.000 0.00 0.00 0.00 5.34
721 723 2.511659 ACAGAGTGTACCTACTTCGCA 58.488 47.619 0.00 0.00 0.00 5.10
722 724 3.572604 AACAGAGTGTACCTACTTCGC 57.427 47.619 0.00 0.00 0.00 4.70
723 725 4.156915 CGAAACAGAGTGTACCTACTTCG 58.843 47.826 0.00 0.00 0.00 3.79
724 726 3.919197 GCGAAACAGAGTGTACCTACTTC 59.081 47.826 0.00 0.00 0.00 3.01
725 727 3.305881 GGCGAAACAGAGTGTACCTACTT 60.306 47.826 0.00 0.00 0.00 2.24
726 728 2.230750 GGCGAAACAGAGTGTACCTACT 59.769 50.000 0.00 0.00 0.00 2.57
727 729 2.603953 GGCGAAACAGAGTGTACCTAC 58.396 52.381 0.00 0.00 0.00 3.18
728 730 1.200716 CGGCGAAACAGAGTGTACCTA 59.799 52.381 0.00 0.00 0.00 3.08
729 731 0.038526 CGGCGAAACAGAGTGTACCT 60.039 55.000 0.00 0.00 0.00 3.08
730 732 1.623973 GCGGCGAAACAGAGTGTACC 61.624 60.000 12.98 0.00 0.00 3.34
731 733 0.666577 AGCGGCGAAACAGAGTGTAC 60.667 55.000 12.98 0.00 0.00 2.90
732 734 0.666274 CAGCGGCGAAACAGAGTGTA 60.666 55.000 12.98 0.00 0.00 2.90
733 735 1.956170 CAGCGGCGAAACAGAGTGT 60.956 57.895 12.98 0.00 0.00 3.55
734 736 1.016130 ATCAGCGGCGAAACAGAGTG 61.016 55.000 12.98 0.00 0.00 3.51
735 737 0.320771 AATCAGCGGCGAAACAGAGT 60.321 50.000 12.98 0.00 0.00 3.24
736 738 0.371645 GAATCAGCGGCGAAACAGAG 59.628 55.000 12.98 0.00 0.00 3.35
737 739 1.351430 CGAATCAGCGGCGAAACAGA 61.351 55.000 12.98 0.00 0.00 3.41
738 740 1.059369 CGAATCAGCGGCGAAACAG 59.941 57.895 12.98 0.00 0.00 3.16
739 741 3.022401 GCGAATCAGCGGCGAAACA 62.022 57.895 12.98 0.00 0.00 2.83
740 742 2.276680 GCGAATCAGCGGCGAAAC 60.277 61.111 12.98 0.00 0.00 2.78
748 750 2.526120 GCCCACTACGCGAATCAGC 61.526 63.158 15.93 4.37 0.00 4.26
749 751 0.460284 AAGCCCACTACGCGAATCAG 60.460 55.000 15.93 6.68 0.00 2.90
750 752 0.818938 TAAGCCCACTACGCGAATCA 59.181 50.000 15.93 0.00 0.00 2.57
751 753 2.150397 ATAAGCCCACTACGCGAATC 57.850 50.000 15.93 0.00 0.00 2.52
752 754 3.738830 TTATAAGCCCACTACGCGAAT 57.261 42.857 15.93 0.00 0.00 3.34
753 755 3.523606 TTTATAAGCCCACTACGCGAA 57.476 42.857 15.93 0.00 0.00 4.70
754 756 3.738830 ATTTATAAGCCCACTACGCGA 57.261 42.857 15.93 0.00 0.00 5.87
755 757 3.606153 GCAATTTATAAGCCCACTACGCG 60.606 47.826 3.53 3.53 0.00 6.01
756 758 3.314080 TGCAATTTATAAGCCCACTACGC 59.686 43.478 0.00 0.00 0.00 4.42
757 759 4.261031 GGTGCAATTTATAAGCCCACTACG 60.261 45.833 0.00 0.00 0.00 3.51
758 760 4.037565 GGGTGCAATTTATAAGCCCACTAC 59.962 45.833 0.00 0.00 34.95 2.73
759 761 4.211920 GGGTGCAATTTATAAGCCCACTA 58.788 43.478 0.00 0.00 34.95 2.74
760 762 3.031013 GGGTGCAATTTATAAGCCCACT 58.969 45.455 0.00 0.00 34.95 4.00
761 763 2.223711 CGGGTGCAATTTATAAGCCCAC 60.224 50.000 4.34 0.00 34.52 4.61
762 764 2.028130 CGGGTGCAATTTATAAGCCCA 58.972 47.619 4.34 0.00 34.52 5.36
763 765 2.028876 ACGGGTGCAATTTATAAGCCC 58.971 47.619 0.00 0.00 0.00 5.19
764 766 3.004002 GGTACGGGTGCAATTTATAAGCC 59.996 47.826 0.00 0.00 0.00 4.35
765 767 3.004002 GGGTACGGGTGCAATTTATAAGC 59.996 47.826 0.00 0.00 0.00 3.09
766 768 4.457466 AGGGTACGGGTGCAATTTATAAG 58.543 43.478 0.00 0.00 0.00 1.73
767 769 4.453751 GAGGGTACGGGTGCAATTTATAA 58.546 43.478 0.00 0.00 0.00 0.98
810 815 3.556306 CGAGGTGGTGGTGGGTGT 61.556 66.667 0.00 0.00 0.00 4.16
839 849 6.363626 CAGCGTGATAGTAAATTACTGCTAGG 59.636 42.308 15.34 7.90 39.81 3.02
841 851 5.690409 GCAGCGTGATAGTAAATTACTGCTA 59.310 40.000 15.34 0.00 43.46 3.49
847 857 4.808895 CCTGTGCAGCGTGATAGTAAATTA 59.191 41.667 0.00 0.00 0.00 1.40
848 858 3.623060 CCTGTGCAGCGTGATAGTAAATT 59.377 43.478 0.00 0.00 0.00 1.82
921 953 5.812642 CGTGCAGGTGAGAACTATTTAAGAT 59.187 40.000 0.00 0.00 0.00 2.40
928 960 0.108138 GGCGTGCAGGTGAGAACTAT 60.108 55.000 8.40 0.00 0.00 2.12
962 994 1.210155 GGCTTAACTGCTGCCAACG 59.790 57.895 0.00 0.00 45.46 4.10
1005 1040 2.426023 GTGGCCACGACCTTGTCT 59.574 61.111 22.49 0.00 0.00 3.41
1161 1238 4.627611 TCAAGTACTGATACTGTACGCC 57.372 45.455 0.00 0.00 41.00 5.68
1172 1249 6.701841 GTGAGAGAACAACAATCAAGTACTGA 59.298 38.462 0.00 0.00 38.81 3.41
1189 1303 2.763933 ACGTACGTCAGAGTGAGAGAA 58.236 47.619 16.72 0.00 0.00 2.87
1217 1338 4.450122 CGTGCCTGCACACATCGC 62.450 66.667 21.01 0.00 46.47 4.58
1333 1454 2.430465 GAAAAGAGGAGCATGACAGCA 58.570 47.619 0.00 0.00 36.85 4.41
1351 1472 1.068748 GTGAAGTAGGTGACGAGCGAA 60.069 52.381 0.00 0.00 0.00 4.70
1623 1744 2.332104 CGAAGATGATCATGTAGGGCG 58.668 52.381 14.30 7.79 0.00 6.13
1800 2063 6.664816 AGGGATTGCTTTTGTTGATCTATCAA 59.335 34.615 1.23 1.23 43.94 2.57
1801 2064 6.189859 AGGGATTGCTTTTGTTGATCTATCA 58.810 36.000 0.00 0.00 34.44 2.15
1802 2065 6.705863 AGGGATTGCTTTTGTTGATCTATC 57.294 37.500 0.00 0.00 0.00 2.08
1813 2076 6.189859 TCAACATGATCTAGGGATTGCTTTT 58.810 36.000 0.00 0.00 31.46 2.27
1887 2154 4.351054 CCGGTCAGGCTGCCCTTT 62.351 66.667 16.57 0.00 40.33 3.11
2580 2857 3.606662 GCTGCGGCGAGGGAGATA 61.607 66.667 12.98 0.00 0.00 1.98
2687 2965 6.721208 ACACCTTGAATCCTTGATGTATTGTT 59.279 34.615 0.00 0.00 0.00 2.83
2689 2967 6.764308 ACACCTTGAATCCTTGATGTATTG 57.236 37.500 0.00 0.00 0.00 1.90
2690 2968 7.056635 CCTACACCTTGAATCCTTGATGTATT 58.943 38.462 0.00 0.00 0.00 1.89
2692 2970 5.724370 TCCTACACCTTGAATCCTTGATGTA 59.276 40.000 0.00 0.00 0.00 2.29
2694 2972 5.102953 TCCTACACCTTGAATCCTTGATG 57.897 43.478 0.00 0.00 0.00 3.07
2695 2973 5.983333 ATCCTACACCTTGAATCCTTGAT 57.017 39.130 0.00 0.00 0.00 2.57
2696 2974 5.250543 TGAATCCTACACCTTGAATCCTTGA 59.749 40.000 0.00 0.00 0.00 3.02
2697 2975 5.500234 TGAATCCTACACCTTGAATCCTTG 58.500 41.667 0.00 0.00 0.00 3.61
2698 2976 5.779241 TGAATCCTACACCTTGAATCCTT 57.221 39.130 0.00 0.00 0.00 3.36
2699 2977 5.488919 TCTTGAATCCTACACCTTGAATCCT 59.511 40.000 0.00 0.00 0.00 3.24
2700 2978 5.586643 GTCTTGAATCCTACACCTTGAATCC 59.413 44.000 0.00 0.00 0.00 3.01
2701 2979 6.173339 TGTCTTGAATCCTACACCTTGAATC 58.827 40.000 0.00 0.00 0.00 2.52
2702 2980 6.126863 TGTCTTGAATCCTACACCTTGAAT 57.873 37.500 0.00 0.00 0.00 2.57
2703 2981 5.560722 TGTCTTGAATCCTACACCTTGAA 57.439 39.130 0.00 0.00 0.00 2.69
2946 3230 8.806146 TGAGTGTATGTGCATATGTATATGACT 58.194 33.333 14.41 12.69 42.05 3.41
2950 3234 7.819415 GGTGTGAGTGTATGTGCATATGTATAT 59.181 37.037 6.16 8.06 0.00 0.86
2951 3235 7.015195 AGGTGTGAGTGTATGTGCATATGTATA 59.985 37.037 6.16 0.00 0.00 1.47
3013 3303 1.077805 TGTCGGCCTAGTCCCTTGA 59.922 57.895 0.00 0.00 0.00 3.02
3015 3305 0.617820 ATGTGTCGGCCTAGTCCCTT 60.618 55.000 0.00 0.00 0.00 3.95
3024 3314 1.134699 TCTCAAGATGATGTGTCGGCC 60.135 52.381 0.00 0.00 0.00 6.13
3029 3319 5.077134 TCGTCAATCTCAAGATGATGTGT 57.923 39.130 0.00 0.00 34.49 3.72
3060 3350 1.516423 GGTTCCAGTCCTAGGCGTC 59.484 63.158 2.96 0.00 0.00 5.19
3073 3365 2.926242 TCGGTCCACCAGGGTTCC 60.926 66.667 0.00 0.00 38.11 3.62
3081 3373 1.821258 GTGGTATCCTCGGTCCACC 59.179 63.158 12.75 6.50 42.90 4.61
3088 3380 2.379972 AGGAGAACAGTGGTATCCTCG 58.620 52.381 18.92 0.00 38.38 4.63
3103 3395 2.626785 TGTGGTTGGATGGTTAGGAGA 58.373 47.619 0.00 0.00 0.00 3.71
3130 3422 4.582656 TCAGGAAATCCTTTTCTCGCAAAA 59.417 37.500 0.00 0.00 46.09 2.44
3189 3481 6.653320 CCTGACCATTACAACTACTTTGCTAA 59.347 38.462 0.00 0.00 39.01 3.09
3291 3588 1.405872 TGGATGGTCGGCTTACGTAT 58.594 50.000 0.00 0.00 44.69 3.06
3297 3594 3.636764 GGATAATTTTGGATGGTCGGCTT 59.363 43.478 0.00 0.00 0.00 4.35
3348 3645 2.098934 TGATCGGGCGGATTTGAATTTG 59.901 45.455 9.06 0.00 34.82 2.32
3362 3659 2.736995 ACGCGTGTTGTGATCGGG 60.737 61.111 12.93 0.00 41.79 5.14
3379 3676 1.522092 GGGCTGATGTGATCCGTCA 59.478 57.895 6.11 6.11 37.52 4.35
3419 3716 7.560991 TCAGGCATGTAAAAATGATGGATAGTT 59.439 33.333 0.00 0.00 0.00 2.24
3429 3726 7.599621 TCTTTTGTGATCAGGCATGTAAAAATG 59.400 33.333 0.00 0.00 0.00 2.32
3430 3727 7.669427 TCTTTTGTGATCAGGCATGTAAAAAT 58.331 30.769 0.00 0.00 0.00 1.82
3483 3780 2.094545 CCAGCAGGGCAGAAAATACAAC 60.095 50.000 0.00 0.00 0.00 3.32
3507 3804 1.211457 GCATGGAGTCTGGGATTGTCT 59.789 52.381 0.00 0.00 0.00 3.41
3516 3813 1.941294 GCAGATTGAGCATGGAGTCTG 59.059 52.381 0.00 0.00 36.92 3.51


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

AutoCloner maintained by Alex Coulton.