Multiple sequence alignment - TraesCS3A01G196200

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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 TraesCS3A01G196200 chr3A 100.000 4823 0 0 1 4823 295951609 295946787 0.000000e+00 8907.0
1 TraesCS3A01G196200 chr3A 94.602 389 19 1 1630 2016 18663048 18662660 6.910000e-168 601.0
2 TraesCS3A01G196200 chr3A 96.610 59 2 0 604 662 295950973 295950915 1.100000e-16 99.0
3 TraesCS3A01G196200 chr3A 96.610 59 2 0 637 695 295951006 295950948 1.100000e-16 99.0
4 TraesCS3A01G196200 chr1B 93.706 2113 99 10 2718 4823 632753801 632755886 0.000000e+00 3134.0
5 TraesCS3A01G196200 chr1B 95.579 1131 46 3 886 2013 632752057 632753186 0.000000e+00 1808.0
6 TraesCS3A01G196200 chr1B 95.974 621 25 0 1974 2594 632753182 632753802 0.000000e+00 1009.0
7 TraesCS3A01G196200 chr1B 84.293 382 49 10 999 1370 41449554 41449174 3.550000e-96 363.0
8 TraesCS3A01G196200 chr1B 85.993 307 15 11 1054 1335 41640782 41640479 2.180000e-78 303.0
9 TraesCS3A01G196200 chr1B 79.880 333 47 10 13 335 29019587 29019909 4.860000e-55 226.0
10 TraesCS3A01G196200 chr1B 82.759 87 13 2 1536 1621 528405099 528405014 5.180000e-10 76.8
11 TraesCS3A01G196200 chr7A 96.588 1817 59 2 637 2450 690659267 690661083 0.000000e+00 3009.0
12 TraesCS3A01G196200 chr7A 92.409 685 28 2 1 662 690658642 690659325 0.000000e+00 955.0
13 TraesCS3A01G196200 chr7A 95.116 389 17 1 1630 2016 107343365 107342977 3.190000e-171 612.0
14 TraesCS3A01G196200 chr7A 87.234 235 29 1 93 327 622260308 622260075 2.860000e-67 267.0
15 TraesCS3A01G196200 chr3B 95.213 1713 76 5 886 2594 569597239 569598949 0.000000e+00 2704.0
16 TraesCS3A01G196200 chr3B 92.559 1223 61 7 2718 3933 569598948 569600147 0.000000e+00 1727.0
17 TraesCS3A01G196200 chr3B 92.564 1022 56 11 2718 3725 784574104 784573089 0.000000e+00 1448.0
18 TraesCS3A01G196200 chr3B 89.536 1099 52 15 1363 2434 784575162 784574100 0.000000e+00 1334.0
19 TraesCS3A01G196200 chr3B 93.349 872 50 5 3955 4821 569600324 569601192 0.000000e+00 1282.0
20 TraesCS3A01G196200 chr3B 97.638 127 3 0 2593 2719 692220564 692220690 8.130000e-53 219.0
21 TraesCS3A01G196200 chr3B 92.053 151 9 3 2573 2722 578615301 578615449 4.890000e-50 209.0
22 TraesCS3A01G196200 chr2D 92.030 1719 124 10 886 2594 229311278 229312993 0.000000e+00 2403.0
23 TraesCS3A01G196200 chr2D 92.540 1059 74 4 3767 4823 229314134 229315189 0.000000e+00 1513.0
24 TraesCS3A01G196200 chr2D 91.501 1059 74 12 2718 3761 229312992 229314049 0.000000e+00 1443.0
25 TraesCS3A01G196200 chr2D 91.622 931 47 12 3893 4823 588835737 588836636 0.000000e+00 1258.0
26 TraesCS3A01G196200 chr6A 94.860 1498 65 9 3336 4823 463743481 463744976 0.000000e+00 2329.0
27 TraesCS3A01G196200 chr6A 94.712 1494 69 6 3336 4821 47592114 47590623 0.000000e+00 2313.0
28 TraesCS3A01G196200 chr6A 89.811 1060 88 12 2720 3764 4927838 4926784 0.000000e+00 1341.0
29 TraesCS3A01G196200 chr6A 95.620 548 24 0 2047 2594 463742414 463742961 0.000000e+00 880.0
30 TraesCS3A01G196200 chr6A 83.333 246 22 9 90 335 603769250 603769024 4.890000e-50 209.0
31 TraesCS3A01G196200 chr2A 94.519 1496 72 6 3336 4823 94387559 94386066 0.000000e+00 2300.0
32 TraesCS3A01G196200 chr2A 95.985 548 22 0 2047 2594 94388626 94388079 0.000000e+00 891.0
33 TraesCS3A01G196200 chr1A 94.834 1297 63 4 3528 4823 577673323 577672030 0.000000e+00 2021.0
34 TraesCS3A01G196200 chr1A 95.985 548 22 0 2047 2594 577674751 577674204 0.000000e+00 891.0
35 TraesCS3A01G196200 chr1A 94.087 389 21 1 1630 2016 585606368 585605980 1.500000e-164 590.0
36 TraesCS3A01G196200 chr1A 91.542 201 10 3 3336 3529 577673684 577673484 2.210000e-68 270.0
37 TraesCS3A01G196200 chr6B 94.306 966 44 7 3336 4293 713227482 713226520 0.000000e+00 1469.0
38 TraesCS3A01G196200 chr6B 93.463 979 41 9 3336 4293 302278968 302279944 0.000000e+00 1432.0
39 TraesCS3A01G196200 chr6B 91.149 1062 77 12 2718 3764 575573961 575572902 0.000000e+00 1424.0
40 TraesCS3A01G196200 chr6B 95.255 548 26 0 2047 2594 713228549 713228002 0.000000e+00 869.0
41 TraesCS3A01G196200 chr6B 81.818 88 12 4 1536 1621 71529 71444 2.410000e-08 71.3
42 TraesCS3A01G196200 chr4B 91.714 1062 69 13 2718 3764 342968278 342967221 0.000000e+00 1456.0
43 TraesCS3A01G196200 chr4B 93.361 979 42 9 3336 4293 186426830 186427806 0.000000e+00 1426.0
44 TraesCS3A01G196200 chr4B 94.021 485 28 1 886 1370 342969240 342968757 0.000000e+00 734.0
45 TraesCS3A01G196200 chr4B 94.531 256 14 0 2339 2594 342968532 342968277 3.500000e-106 396.0
46 TraesCS3A01G196200 chr6D 89.736 1062 93 12 2718 3764 225662986 225661926 0.000000e+00 1343.0
47 TraesCS3A01G196200 chr6D 90.693 505 43 4 3762 4266 225661848 225661348 0.000000e+00 669.0
48 TraesCS3A01G196200 chr7B 91.515 931 53 12 3893 4823 697731549 697730645 0.000000e+00 1258.0
49 TraesCS3A01G196200 chr7B 87.521 593 52 5 91 662 128811039 128810448 0.000000e+00 665.0
50 TraesCS3A01G196200 chr7B 94.400 250 13 1 637 886 128810506 128810258 2.720000e-102 383.0
51 TraesCS3A01G196200 chr7B 80.060 331 46 11 15 335 748687942 748688262 1.350000e-55 228.0
52 TraesCS3A01G196200 chr7B 92.517 147 10 1 2573 2719 118126188 118126333 4.890000e-50 209.0
53 TraesCS3A01G196200 chr7B 87.730 163 19 1 173 335 114568972 114569133 6.370000e-44 189.0
54 TraesCS3A01G196200 chr5D 94.158 582 34 0 2718 3299 524292270 524292851 0.000000e+00 887.0
55 TraesCS3A01G196200 chr5D 91.652 587 42 4 2716 3299 289583303 289582721 0.000000e+00 806.0
56 TraesCS3A01G196200 chr3D 91.795 585 45 1 2718 3299 34546203 34546787 0.000000e+00 811.0
57 TraesCS3A01G196200 chr5A 94.859 389 18 1 1630 2016 415814962 415814574 1.480000e-169 606.0
58 TraesCS3A01G196200 chr5A 90.650 246 22 1 90 335 608641267 608641023 4.660000e-85 326.0
59 TraesCS3A01G196200 chr1D 90.591 372 30 3 1001 1370 25954045 25953677 5.610000e-134 488.0
60 TraesCS3A01G196200 chr1D 94.141 256 15 0 2339 2594 2853145 2853400 1.630000e-104 390.0
61 TraesCS3A01G196200 chr5B 97.638 127 3 0 2593 2719 711836952 711837078 8.130000e-53 219.0
62 TraesCS3A01G196200 chr5B 95.420 131 6 0 2590 2720 670073686 670073816 4.890000e-50 209.0
63 TraesCS3A01G196200 chr5B 91.026 156 10 4 2573 2726 710627677 710627524 1.760000e-49 207.0
64 TraesCS3A01G196200 chr5B 88.571 105 10 2 3269 3373 711784707 711784605 5.070000e-25 126.0
65 TraesCS3A01G196200 chr5B 81.928 83 13 2 1537 1618 567702446 567702365 8.660000e-08 69.4
66 TraesCS3A01G196200 chr4A 96.899 129 4 0 2591 2719 589667166 589667294 2.920000e-52 217.0
67 TraesCS3A01G196200 chr4A 91.026 156 10 4 2573 2726 604081688 604081841 1.760000e-49 207.0
68 TraesCS3A01G196200 chrUn 91.026 156 10 4 2573 2726 332269312 332269465 1.760000e-49 207.0
69 TraesCS3A01G196200 chrUn 87.342 79 7 2 659 737 112971047 112970972 2.390000e-13 87.9
70 TraesCS3A01G196200 chr2B 77.477 333 55 11 13 335 80319764 80319442 1.070000e-41 182.0
71 TraesCS3A01G196200 chr7D 93.103 87 6 0 1278 1364 292420101 292420187 1.410000e-25 128.0
72 TraesCS3A01G196200 chr7D 87.500 88 9 2 1536 1622 404156006 404156092 3.070000e-17 100.0


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 TraesCS3A01G196200 chr3A 295946787 295951609 4822 True 3035.000000 8907 97.740000 1 4823 3 chr3A.!!$R2 4822
1 TraesCS3A01G196200 chr1B 632752057 632755886 3829 False 1983.666667 3134 95.086333 886 4823 3 chr1B.!!$F2 3937
2 TraesCS3A01G196200 chr7A 690658642 690661083 2441 False 1982.000000 3009 94.498500 1 2450 2 chr7A.!!$F1 2449
3 TraesCS3A01G196200 chr3B 569597239 569601192 3953 False 1904.333333 2704 93.707000 886 4821 3 chr3B.!!$F3 3935
4 TraesCS3A01G196200 chr3B 784573089 784575162 2073 True 1391.000000 1448 91.050000 1363 3725 2 chr3B.!!$R1 2362
5 TraesCS3A01G196200 chr2D 229311278 229315189 3911 False 1786.333333 2403 92.023667 886 4823 3 chr2D.!!$F2 3937
6 TraesCS3A01G196200 chr2D 588835737 588836636 899 False 1258.000000 1258 91.622000 3893 4823 1 chr2D.!!$F1 930
7 TraesCS3A01G196200 chr6A 47590623 47592114 1491 True 2313.000000 2313 94.712000 3336 4821 1 chr6A.!!$R2 1485
8 TraesCS3A01G196200 chr6A 463742414 463744976 2562 False 1604.500000 2329 95.240000 2047 4823 2 chr6A.!!$F1 2776
9 TraesCS3A01G196200 chr6A 4926784 4927838 1054 True 1341.000000 1341 89.811000 2720 3764 1 chr6A.!!$R1 1044
10 TraesCS3A01G196200 chr2A 94386066 94388626 2560 True 1595.500000 2300 95.252000 2047 4823 2 chr2A.!!$R1 2776
11 TraesCS3A01G196200 chr1A 577672030 577674751 2721 True 1060.666667 2021 94.120333 2047 4823 3 chr1A.!!$R2 2776
12 TraesCS3A01G196200 chr6B 302278968 302279944 976 False 1432.000000 1432 93.463000 3336 4293 1 chr6B.!!$F1 957
13 TraesCS3A01G196200 chr6B 575572902 575573961 1059 True 1424.000000 1424 91.149000 2718 3764 1 chr6B.!!$R2 1046
14 TraesCS3A01G196200 chr6B 713226520 713228549 2029 True 1169.000000 1469 94.780500 2047 4293 2 chr6B.!!$R3 2246
15 TraesCS3A01G196200 chr4B 186426830 186427806 976 False 1426.000000 1426 93.361000 3336 4293 1 chr4B.!!$F1 957
16 TraesCS3A01G196200 chr4B 342967221 342969240 2019 True 862.000000 1456 93.422000 886 3764 3 chr4B.!!$R1 2878
17 TraesCS3A01G196200 chr6D 225661348 225662986 1638 True 1006.000000 1343 90.214500 2718 4266 2 chr6D.!!$R1 1548
18 TraesCS3A01G196200 chr7B 697730645 697731549 904 True 1258.000000 1258 91.515000 3893 4823 1 chr7B.!!$R1 930
19 TraesCS3A01G196200 chr7B 128810258 128811039 781 True 524.000000 665 90.960500 91 886 2 chr7B.!!$R2 795
20 TraesCS3A01G196200 chr5D 524292270 524292851 581 False 887.000000 887 94.158000 2718 3299 1 chr5D.!!$F1 581
21 TraesCS3A01G196200 chr5D 289582721 289583303 582 True 806.000000 806 91.652000 2716 3299 1 chr5D.!!$R1 583
22 TraesCS3A01G196200 chr3D 34546203 34546787 584 False 811.000000 811 91.795000 2718 3299 1 chr3D.!!$F1 581

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
665 689 0.419865 TCCTGTTAGGGGGACATGGA 59.580 55.000 0.0 0.0 35.59 3.41 F
2053 2152 1.067071 GTAAGTAGGTGCCGCTGAGTT 60.067 52.381 0.0 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2592 2692 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.0 46.06 2.59 R
3838 4374 1.061131 CAGTCGCCAATTCTAACTGCG 59.939 52.381 0.00 0.0 46.09 5.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 3.526430 CGAGCTGGATCCTCGGAA 58.474 61.111 14.23 0.00 46.15 4.30
202 203 2.881539 TAGCAGTCGATCCCGGTCGT 62.882 60.000 13.47 0.00 42.07 4.34
229 230 0.710588 TTCACCAGCCTCCTCCTCTA 59.289 55.000 0.00 0.00 0.00 2.43
311 312 1.194121 TGTGCTGCTCCTTCTGCCTA 61.194 55.000 0.00 0.00 0.00 3.93
316 317 0.612174 TGCTCCTTCTGCCTACGTCT 60.612 55.000 0.00 0.00 0.00 4.18
382 383 1.153745 CCTCCTCAACTTCGCTCCG 60.154 63.158 0.00 0.00 0.00 4.63
428 429 5.194473 ACTGACTCCATCTGGTAGAACTA 57.806 43.478 0.00 0.00 36.34 2.24
469 493 6.467723 GTGTATAGAACAACAACACCTGAG 57.532 41.667 0.00 0.00 40.63 3.35
474 498 5.304686 AGAACAACAACACCTGAGGATTA 57.695 39.130 4.99 0.00 0.00 1.75
664 688 3.021356 TCCTGTTAGGGGGACATGG 57.979 57.895 0.00 0.00 35.59 3.66
665 689 0.419865 TCCTGTTAGGGGGACATGGA 59.580 55.000 0.00 0.00 35.59 3.41
666 690 1.203505 TCCTGTTAGGGGGACATGGAA 60.204 52.381 0.00 0.00 35.59 3.53
667 691 1.638589 CCTGTTAGGGGGACATGGAAA 59.361 52.381 0.00 0.00 0.00 3.13
668 692 2.042433 CCTGTTAGGGGGACATGGAAAA 59.958 50.000 0.00 0.00 0.00 2.29
669 693 3.309848 CCTGTTAGGGGGACATGGAAAAT 60.310 47.826 0.00 0.00 0.00 1.82
670 694 4.352893 CTGTTAGGGGGACATGGAAAATT 58.647 43.478 0.00 0.00 0.00 1.82
671 695 4.349365 TGTTAGGGGGACATGGAAAATTC 58.651 43.478 0.00 0.00 0.00 2.17
672 696 4.202727 TGTTAGGGGGACATGGAAAATTCA 60.203 41.667 0.00 0.00 0.00 2.57
673 697 3.105959 AGGGGGACATGGAAAATTCAG 57.894 47.619 0.00 0.00 0.00 3.02
674 698 2.383338 AGGGGGACATGGAAAATTCAGT 59.617 45.455 0.00 0.00 0.00 3.41
675 699 3.173151 GGGGGACATGGAAAATTCAGTT 58.827 45.455 0.00 0.00 0.00 3.16
676 700 4.045334 AGGGGGACATGGAAAATTCAGTTA 59.955 41.667 0.00 0.00 0.00 2.24
677 701 4.962362 GGGGGACATGGAAAATTCAGTTAT 59.038 41.667 0.00 0.00 0.00 1.89
678 702 5.163416 GGGGGACATGGAAAATTCAGTTATG 60.163 44.000 0.00 0.00 0.00 1.90
679 703 5.422012 GGGGACATGGAAAATTCAGTTATGT 59.578 40.000 0.00 0.00 0.00 2.29
680 704 6.405842 GGGGACATGGAAAATTCAGTTATGTC 60.406 42.308 15.75 15.75 41.12 3.06
682 706 7.156876 GACATGGAAAATTCAGTTATGTCCA 57.843 36.000 0.00 0.00 37.84 4.02
683 707 7.161773 ACATGGAAAATTCAGTTATGTCCAG 57.838 36.000 0.00 0.00 37.13 3.86
684 708 6.721208 ACATGGAAAATTCAGTTATGTCCAGT 59.279 34.615 0.00 0.00 37.13 4.00
685 709 7.233348 ACATGGAAAATTCAGTTATGTCCAGTT 59.767 33.333 0.00 0.00 37.13 3.16
686 710 8.739039 CATGGAAAATTCAGTTATGTCCAGTTA 58.261 33.333 0.00 0.00 37.13 2.24
687 711 8.335532 TGGAAAATTCAGTTATGTCCAGTTAG 57.664 34.615 0.00 0.00 0.00 2.34
688 712 7.393234 TGGAAAATTCAGTTATGTCCAGTTAGG 59.607 37.037 0.00 0.00 39.47 2.69
689 713 7.148069 GGAAAATTCAGTTATGTCCAGTTAGGG 60.148 40.741 0.00 0.00 38.24 3.53
690 714 4.837093 TTCAGTTATGTCCAGTTAGGGG 57.163 45.455 0.00 0.00 38.24 4.79
691 715 3.798515 TCAGTTATGTCCAGTTAGGGGT 58.201 45.455 0.00 0.00 38.24 4.95
692 716 4.950361 TCAGTTATGTCCAGTTAGGGGTA 58.050 43.478 0.00 0.00 38.24 3.69
693 717 4.713321 TCAGTTATGTCCAGTTAGGGGTAC 59.287 45.833 0.00 0.00 38.24 3.34
694 718 4.468510 CAGTTATGTCCAGTTAGGGGTACA 59.531 45.833 0.00 0.00 38.24 2.90
758 782 7.277760 GGTGTCTATACAAATGCCCAAAAATTC 59.722 37.037 0.00 0.00 37.36 2.17
818 842 2.361119 TCTATAGTTCAATGCGCGAGGT 59.639 45.455 12.10 0.00 0.00 3.85
844 868 1.873591 AGGCACGATTCAGTCAACAAC 59.126 47.619 0.00 0.00 0.00 3.32
888 912 3.694072 GCCCTGTACATGACAAGCATTTA 59.306 43.478 0.00 0.00 37.70 1.40
1404 1428 5.565592 TCGGACGCTGATTTAACTAGTTA 57.434 39.130 11.38 11.38 0.00 2.24
1430 1454 6.645884 ACCTGTCCATTATTAACTAACCCA 57.354 37.500 0.00 0.00 0.00 4.51
1447 1471 3.575805 ACCCATGTTTCTTGATGGTGTT 58.424 40.909 0.00 0.00 37.96 3.32
1534 1558 5.178809 GCGTTAGTTACCTTCTTGTCACATT 59.821 40.000 0.00 0.00 0.00 2.71
1547 1571 1.123077 TCACATTCTCCCTCCATCCG 58.877 55.000 0.00 0.00 0.00 4.18
1579 1603 4.513692 AGACGTTTGTGCAAGCTAACATTA 59.486 37.500 0.00 0.00 0.00 1.90
1592 1616 8.296799 CAAGCTAACATTACTTGCAAAAATGA 57.703 30.769 28.06 14.09 34.90 2.57
1863 1890 4.660789 ATGCCAAAGCCAGAAATATGAC 57.339 40.909 0.00 0.00 38.69 3.06
1911 1951 2.245546 TCCCTCCCATGCAAAATCATCT 59.754 45.455 0.00 0.00 0.00 2.90
1965 2005 5.231702 TCCAATCGACACTTCATTTCGTTA 58.768 37.500 0.00 0.00 34.35 3.18
2053 2152 1.067071 GTAAGTAGGTGCCGCTGAGTT 60.067 52.381 0.00 0.00 0.00 3.01
2288 2387 7.696453 GTGATCTCGTTATACAATTTTGGGTTG 59.304 37.037 0.00 0.00 0.00 3.77
2436 2536 9.391006 TGGTACAAAATTGGTCTGATATTAGTC 57.609 33.333 0.00 0.00 31.92 2.59
2480 2580 4.686554 GGTTCCTGCTGCTTATTAGTATCG 59.313 45.833 0.00 0.00 0.00 2.92
2537 2637 6.283694 TGTACTGATTATCTTGGTGAGCATC 58.716 40.000 0.00 0.00 0.00 3.91
2572 2672 4.210331 GGAATACATTGTCTGCTGGGAAT 58.790 43.478 0.00 0.00 0.00 3.01
2592 2692 6.541278 GGGAATTCTATTTACCTTTGCGTACT 59.459 38.462 5.23 0.00 0.00 2.73
2593 2693 7.712205 GGGAATTCTATTTACCTTTGCGTACTA 59.288 37.037 5.23 0.00 0.00 1.82
2594 2694 8.546244 GGAATTCTATTTACCTTTGCGTACTAC 58.454 37.037 5.23 0.00 0.00 2.73
2595 2695 9.310716 GAATTCTATTTACCTTTGCGTACTACT 57.689 33.333 0.00 0.00 0.00 2.57
2596 2696 8.868635 ATTCTATTTACCTTTGCGTACTACTC 57.131 34.615 0.00 0.00 0.00 2.59
2597 2697 6.799512 TCTATTTACCTTTGCGTACTACTCC 58.200 40.000 0.00 0.00 0.00 3.85
2598 2698 3.874392 TTACCTTTGCGTACTACTCCC 57.126 47.619 0.00 0.00 0.00 4.30
2599 2699 1.934410 ACCTTTGCGTACTACTCCCT 58.066 50.000 0.00 0.00 0.00 4.20
2600 2700 1.823610 ACCTTTGCGTACTACTCCCTC 59.176 52.381 0.00 0.00 0.00 4.30
2601 2701 1.136500 CCTTTGCGTACTACTCCCTCC 59.864 57.143 0.00 0.00 0.00 4.30
2602 2702 0.813184 TTTGCGTACTACTCCCTCCG 59.187 55.000 0.00 0.00 0.00 4.63
2603 2703 0.322816 TTGCGTACTACTCCCTCCGT 60.323 55.000 0.00 0.00 0.00 4.69
2604 2704 0.745845 TGCGTACTACTCCCTCCGTC 60.746 60.000 0.00 0.00 0.00 4.79
2605 2705 1.443322 GCGTACTACTCCCTCCGTCC 61.443 65.000 0.00 0.00 0.00 4.79
2606 2706 1.156645 CGTACTACTCCCTCCGTCCG 61.157 65.000 0.00 0.00 0.00 4.79
2607 2707 0.817229 GTACTACTCCCTCCGTCCGG 60.817 65.000 0.00 0.00 0.00 5.14
2608 2708 0.982852 TACTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
2609 2709 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
2610 2710 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
2611 2711 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2612 2712 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2613 2713 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2614 2714 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2615 2715 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2616 2716 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2617 2717 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2618 2718 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2619 2719 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2620 2720 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
2621 2721 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
2622 2722 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
2623 2723 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
2624 2724 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
2625 2725 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
2626 2726 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
2627 2727 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
2628 2728 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
2629 2729 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
2630 2730 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
2638 2738 9.918630 ACTTGTCATCAAAATGAATAAAAGGAG 57.081 29.630 0.00 0.00 43.42 3.69
2683 2783 8.672823 AGTTTTATATACATCCCTTTTCGTCC 57.327 34.615 0.00 0.00 0.00 4.79
2684 2784 8.269317 AGTTTTATATACATCCCTTTTCGTCCA 58.731 33.333 0.00 0.00 0.00 4.02
2685 2785 9.063615 GTTTTATATACATCCCTTTTCGTCCAT 57.936 33.333 0.00 0.00 0.00 3.41
2686 2786 9.635404 TTTTATATACATCCCTTTTCGTCCATT 57.365 29.630 0.00 0.00 0.00 3.16
2687 2787 9.635404 TTTATATACATCCCTTTTCGTCCATTT 57.365 29.630 0.00 0.00 0.00 2.32
2688 2788 9.635404 TTATATACATCCCTTTTCGTCCATTTT 57.365 29.630 0.00 0.00 0.00 1.82
2689 2789 4.519540 ACATCCCTTTTCGTCCATTTTG 57.480 40.909 0.00 0.00 0.00 2.44
2690 2790 4.148838 ACATCCCTTTTCGTCCATTTTGA 58.851 39.130 0.00 0.00 0.00 2.69
2691 2791 4.218417 ACATCCCTTTTCGTCCATTTTGAG 59.782 41.667 0.00 0.00 0.00 3.02
2692 2792 3.153919 TCCCTTTTCGTCCATTTTGAGG 58.846 45.455 0.00 0.00 0.00 3.86
2693 2793 3.153919 CCCTTTTCGTCCATTTTGAGGA 58.846 45.455 0.00 0.00 0.00 3.71
2705 2805 6.908825 TCCATTTTGAGGACAAGTATTTTCG 58.091 36.000 0.00 0.00 37.32 3.46
2706 2806 6.072175 TCCATTTTGAGGACAAGTATTTTCGG 60.072 38.462 0.00 0.00 37.32 4.30
2707 2807 6.072175 CCATTTTGAGGACAAGTATTTTCGGA 60.072 38.462 0.00 0.00 37.32 4.55
2708 2808 5.934935 TTTGAGGACAAGTATTTTCGGAC 57.065 39.130 0.00 0.00 37.32 4.79
2709 2809 3.581755 TGAGGACAAGTATTTTCGGACG 58.418 45.455 0.00 0.00 0.00 4.79
2710 2810 2.928116 GAGGACAAGTATTTTCGGACGG 59.072 50.000 0.00 0.00 0.00 4.79
2711 2811 2.564062 AGGACAAGTATTTTCGGACGGA 59.436 45.455 0.00 0.00 0.00 4.69
2712 2812 2.928116 GGACAAGTATTTTCGGACGGAG 59.072 50.000 0.00 0.00 0.00 4.63
2713 2813 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2714 2814 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2753 2853 2.832129 TGAGGGTCCTTTGTGCTACTAG 59.168 50.000 0.00 0.00 0.00 2.57
2829 2929 3.859627 GCTTGTGCATGAATCTGTTTGCT 60.860 43.478 0.00 0.00 39.41 3.91
2834 2934 3.068448 TGCATGAATCTGTTTGCTGTTGT 59.932 39.130 0.00 0.00 36.10 3.32
2948 3048 1.385915 CCCTCCTGGATGGGGCTTA 60.386 63.158 18.40 0.00 39.76 3.09
2949 3049 0.773700 CCCTCCTGGATGGGGCTTAT 60.774 60.000 18.40 0.00 39.76 1.73
3143 3246 7.232910 TGTGATTGGATTATTGGATATCTGCA 58.767 34.615 2.05 0.00 0.00 4.41
3248 3351 7.589958 TCTGGATTAGTCTATTGTTCTCCTC 57.410 40.000 0.00 0.00 0.00 3.71
3265 3368 1.705186 CCTCAGACCCTCCTTTTTCCA 59.295 52.381 0.00 0.00 0.00 3.53
3305 3408 4.344102 GGATGGGCCGCTATCATTATAGTA 59.656 45.833 13.26 0.00 37.90 1.82
3400 3600 7.875554 TCTGGGTTATTTTTATTGAACTTTGGC 59.124 33.333 0.00 0.00 0.00 4.52
3404 3604 7.360861 GGTTATTTTTATTGAACTTTGGCCTGC 60.361 37.037 3.32 0.00 0.00 4.85
3405 3605 4.953940 TTTTATTGAACTTTGGCCTGCT 57.046 36.364 3.32 0.00 0.00 4.24
3406 3606 4.519540 TTTATTGAACTTTGGCCTGCTC 57.480 40.909 3.32 0.00 0.00 4.26
3407 3607 1.999648 ATTGAACTTTGGCCTGCTCA 58.000 45.000 3.32 0.00 0.00 4.26
3408 3608 1.999648 TTGAACTTTGGCCTGCTCAT 58.000 45.000 3.32 0.00 0.00 2.90
3409 3609 1.250328 TGAACTTTGGCCTGCTCATG 58.750 50.000 3.32 0.00 0.00 3.07
3412 3612 1.304713 CTTTGGCCTGCTCATGGGT 60.305 57.895 3.32 0.00 0.00 4.51
3426 3633 4.026052 CTCATGGGTAGGCCTTCATTTTT 58.974 43.478 12.58 0.00 34.45 1.94
3475 3682 9.314321 CCTACAGTTCTACAAAATTGATACGAT 57.686 33.333 0.00 0.00 0.00 3.73
3501 3708 9.743057 TTGATTGTTTTGTTACTTGGACAATAG 57.257 29.630 0.00 0.00 37.71 1.73
3697 4074 1.028330 CATCATCACCAAGCGCAGGT 61.028 55.000 17.61 17.61 44.60 4.00
3739 4116 0.460987 GACCTCTTCTGGCATGTCGG 60.461 60.000 0.00 0.00 0.00 4.79
3764 4221 4.393062 CCTTCGACATGAAACTGTATGCTT 59.607 41.667 0.00 0.00 35.79 3.91
3838 4374 3.003480 AGGTAAAGCTTGCAAGTCGATC 58.997 45.455 26.55 14.48 0.00 3.69
3923 4462 4.237724 CGAGCATTGTTCTTCTAGTGTGA 58.762 43.478 0.00 0.00 0.00 3.58
4024 4724 1.139853 GTTGCTGCTGCTAGGATAGGT 59.860 52.381 17.00 0.00 39.70 3.08
4069 4769 4.637534 AGCTAGTGTATGTTGAATTGCTGG 59.362 41.667 0.00 0.00 0.00 4.85
4078 4778 3.893720 GTTGAATTGCTGGTCAACTCAG 58.106 45.455 15.36 0.00 46.57 3.35
4103 4816 1.700042 GGGCCTGGCTGCTAGTACAT 61.700 60.000 19.68 0.00 0.00 2.29
4158 4875 1.601162 GGCGCATGCAGTGGATTATTG 60.601 52.381 19.57 0.00 45.35 1.90
4356 5073 4.003648 ACAGTAGTGATGGTTTTGCTAGC 58.996 43.478 8.10 8.10 0.00 3.42
4357 5074 3.062639 CAGTAGTGATGGTTTTGCTAGCG 59.937 47.826 10.77 0.00 0.00 4.26
4366 5083 7.587757 GTGATGGTTTTGCTAGCGAAAATATAG 59.412 37.037 27.83 0.00 31.84 1.31
4389 5106 7.818997 AGCAGCACTTACATAGTATACACTA 57.181 36.000 5.50 0.00 41.47 2.74
4514 5231 1.619332 GAGGTCCTGAACGTTTCTCCT 59.381 52.381 0.46 6.70 0.00 3.69
4528 5245 3.443099 TTCTCCTGCACATCGTAGATG 57.557 47.619 8.33 8.33 45.12 2.90
4652 5371 6.114187 TCTTGTGAGTATTTGACTGGATGT 57.886 37.500 0.00 0.00 39.06 3.06
4758 5477 6.795399 ACACCAAATGTTCTACTTGACAAAG 58.205 36.000 0.00 0.00 38.98 2.77
4786 5505 1.094785 GGGCTCTAAAAATGCTGCGA 58.905 50.000 0.00 0.00 0.00 5.10
4787 5506 1.202188 GGGCTCTAAAAATGCTGCGAC 60.202 52.381 0.00 0.00 0.00 5.19
4791 5511 2.083774 TCTAAAAATGCTGCGACCCAG 58.916 47.619 0.00 0.00 44.67 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 1.745264 CCTTCCGAGGATCCAGCTC 59.255 63.158 15.82 1.51 46.74 4.09
229 230 3.720601 TGCCCTTGCGGAGATGCT 61.721 61.111 0.00 0.00 41.78 3.79
254 255 4.039357 CGTCGACGACCTGCCTGT 62.039 66.667 33.35 0.00 43.02 4.00
311 312 0.383231 ACGTTGTCGAGGAAAGACGT 59.617 50.000 0.00 0.00 41.24 4.34
316 317 1.368579 GGGGACGTTGTCGAGGAAA 59.631 57.895 0.00 0.00 40.62 3.13
382 383 1.205893 CTCACCTACAGAAGCTCACCC 59.794 57.143 0.00 0.00 0.00 4.61
428 429 0.843984 ACCCAACCTACAACAGCAGT 59.156 50.000 0.00 0.00 0.00 4.40
464 488 5.533903 CCCTGAACATCAAATAATCCTCAGG 59.466 44.000 7.64 7.64 45.46 3.86
469 493 5.656416 TGAACCCCTGAACATCAAATAATCC 59.344 40.000 0.00 0.00 0.00 3.01
474 498 4.708421 CAGATGAACCCCTGAACATCAAAT 59.292 41.667 0.00 0.00 40.74 2.32
542 566 0.033781 AGGCAAAACTACCGTACGCA 59.966 50.000 10.49 0.00 0.00 5.24
662 686 7.393234 CCTAACTGGACATAACTGAATTTTCCA 59.607 37.037 0.00 0.00 38.35 3.53
663 687 7.148069 CCCTAACTGGACATAACTGAATTTTCC 60.148 40.741 0.00 0.00 38.35 3.13
664 688 7.148069 CCCCTAACTGGACATAACTGAATTTTC 60.148 40.741 0.00 0.00 38.35 2.29
665 689 6.663523 CCCCTAACTGGACATAACTGAATTTT 59.336 38.462 0.00 0.00 38.35 1.82
666 690 6.187682 CCCCTAACTGGACATAACTGAATTT 58.812 40.000 0.00 0.00 38.35 1.82
667 691 5.253096 ACCCCTAACTGGACATAACTGAATT 59.747 40.000 0.00 0.00 38.35 2.17
668 692 4.788617 ACCCCTAACTGGACATAACTGAAT 59.211 41.667 0.00 0.00 38.35 2.57
669 693 4.172807 ACCCCTAACTGGACATAACTGAA 58.827 43.478 0.00 0.00 38.35 3.02
670 694 3.798515 ACCCCTAACTGGACATAACTGA 58.201 45.455 0.00 0.00 38.35 3.41
671 695 4.468510 TGTACCCCTAACTGGACATAACTG 59.531 45.833 0.00 0.00 38.35 3.16
672 696 4.691238 TGTACCCCTAACTGGACATAACT 58.309 43.478 0.00 0.00 38.35 2.24
673 697 5.425196 TTGTACCCCTAACTGGACATAAC 57.575 43.478 0.00 0.00 38.35 1.89
674 698 4.080751 GCTTGTACCCCTAACTGGACATAA 60.081 45.833 0.00 0.00 38.35 1.90
675 699 3.453353 GCTTGTACCCCTAACTGGACATA 59.547 47.826 0.00 0.00 38.35 2.29
676 700 2.238898 GCTTGTACCCCTAACTGGACAT 59.761 50.000 0.00 0.00 38.35 3.06
677 701 1.626825 GCTTGTACCCCTAACTGGACA 59.373 52.381 0.00 0.00 38.35 4.02
678 702 1.626825 TGCTTGTACCCCTAACTGGAC 59.373 52.381 0.00 0.00 38.35 4.02
679 703 2.032965 TGCTTGTACCCCTAACTGGA 57.967 50.000 0.00 0.00 38.35 3.86
680 704 2.039879 ACTTGCTTGTACCCCTAACTGG 59.960 50.000 0.00 0.00 0.00 4.00
681 705 3.074412 CACTTGCTTGTACCCCTAACTG 58.926 50.000 0.00 0.00 0.00 3.16
682 706 2.709397 ACACTTGCTTGTACCCCTAACT 59.291 45.455 0.00 0.00 0.00 2.24
683 707 3.136009 ACACTTGCTTGTACCCCTAAC 57.864 47.619 0.00 0.00 0.00 2.34
684 708 3.746940 GAACACTTGCTTGTACCCCTAA 58.253 45.455 0.00 0.00 0.00 2.69
685 709 2.289195 CGAACACTTGCTTGTACCCCTA 60.289 50.000 0.00 0.00 0.00 3.53
686 710 1.542547 CGAACACTTGCTTGTACCCCT 60.543 52.381 0.00 0.00 0.00 4.79
687 711 0.872388 CGAACACTTGCTTGTACCCC 59.128 55.000 0.00 0.00 0.00 4.95
688 712 0.872388 CCGAACACTTGCTTGTACCC 59.128 55.000 0.00 0.00 0.00 3.69
689 713 1.263217 CACCGAACACTTGCTTGTACC 59.737 52.381 0.00 0.00 0.00 3.34
690 714 2.206750 TCACCGAACACTTGCTTGTAC 58.793 47.619 0.00 0.00 0.00 2.90
691 715 2.159014 ACTCACCGAACACTTGCTTGTA 60.159 45.455 0.00 0.00 0.00 2.41
692 716 1.299541 CTCACCGAACACTTGCTTGT 58.700 50.000 0.00 0.00 0.00 3.16
693 717 1.261619 GACTCACCGAACACTTGCTTG 59.738 52.381 0.00 0.00 0.00 4.01
694 718 1.134521 TGACTCACCGAACACTTGCTT 60.135 47.619 0.00 0.00 0.00 3.91
758 782 7.221067 CCGAGCTCTATTTCTACTTTTGTACAG 59.779 40.741 12.85 0.00 0.00 2.74
844 868 6.347321 GGGCACAAAATTTGTATTCCGAAAAG 60.347 38.462 11.33 0.00 43.23 2.27
888 912 9.331282 GTCTTATAAATGTGCAGAAGGTCTTAT 57.669 33.333 0.00 0.00 0.00 1.73
1159 1183 8.063200 TGTACTGCACAGACTAACATATACTT 57.937 34.615 4.31 0.00 31.89 2.24
1174 1198 1.300311 CGTCCCGTTGTACTGCACA 60.300 57.895 0.00 0.00 34.51 4.57
1224 1248 2.851102 CCCCCAGGATGCCGAGAT 60.851 66.667 0.00 0.00 33.47 2.75
1304 1328 2.993264 GGGGCAGCAGCAACACAT 60.993 61.111 2.65 0.00 44.61 3.21
1347 1371 1.821759 CACTTGGACGGTGTTGGCA 60.822 57.895 0.00 0.00 0.00 4.92
1404 1428 7.951245 TGGGTTAGTTAATAATGGACAGGTTTT 59.049 33.333 0.00 0.00 0.00 2.43
1430 1454 6.947733 TGGAGATAAACACCATCAAGAAACAT 59.052 34.615 0.00 0.00 34.50 2.71
1447 1471 9.739276 GACACATTTTATATCCCATGGAGATAA 57.261 33.333 15.22 10.68 42.03 1.75
1491 1515 1.972872 CCAACAGAGCAACAAGGACT 58.027 50.000 0.00 0.00 0.00 3.85
1534 1558 2.767644 TATTGTCGGATGGAGGGAGA 57.232 50.000 0.00 0.00 0.00 3.71
1547 1571 5.508224 GCTTGCACAAACGTCTTATATTGTC 59.492 40.000 0.00 0.00 33.97 3.18
1579 1603 7.818930 CCCATAATGTAAGTCATTTTTGCAAGT 59.181 33.333 0.00 0.00 43.33 3.16
1592 1616 2.704065 CCCTCCGTCCCATAATGTAAGT 59.296 50.000 0.00 0.00 0.00 2.24
1863 1890 3.945285 AGTGGTGAAAAGTGTAGTGTTGG 59.055 43.478 0.00 0.00 0.00 3.77
1911 1951 1.587043 CGACGGGTGAGAGCTGAGAA 61.587 60.000 0.00 0.00 0.00 2.87
1965 2005 6.032094 GCATGTGTGTGTAATACGTACTAGT 58.968 40.000 0.00 0.00 33.46 2.57
2053 2152 7.577046 GCTCTATACTGTTTACCACTCACTCAA 60.577 40.741 0.00 0.00 0.00 3.02
2220 2319 8.888716 CAAAAAGTTAACTAAGGCCAACAAAAT 58.111 29.630 8.92 0.00 0.00 1.82
2288 2387 7.602753 AGGCTTTCCAAACTATTAATTGACAC 58.397 34.615 3.83 0.00 33.74 3.67
2436 2536 7.715686 GGAACCTCCCTACTTTTGTGATATAAG 59.284 40.741 0.00 0.00 0.00 1.73
2480 2580 6.099341 CCAAACACTGTAATAATCCAAAGCC 58.901 40.000 0.00 0.00 0.00 4.35
2572 2672 7.260603 GGAGTAGTACGCAAAGGTAAATAGAA 58.739 38.462 6.37 0.00 0.00 2.10
2592 2692 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
2593 2693 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
2594 2694 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2595 2695 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2596 2696 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2597 2697 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2598 2698 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
2599 2699 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
2600 2700 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
2601 2701 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
2602 2702 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
2603 2703 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
2604 2704 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
2605 2705 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
2612 2712 9.918630 CTCCTTTTATTCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
2657 2757 9.768662 GGACGAAAAGGGATGTATATAAAACTA 57.231 33.333 0.00 0.00 0.00 2.24
2658 2758 8.269317 TGGACGAAAAGGGATGTATATAAAACT 58.731 33.333 0.00 0.00 0.00 2.66
2659 2759 8.441312 TGGACGAAAAGGGATGTATATAAAAC 57.559 34.615 0.00 0.00 0.00 2.43
2660 2760 9.635404 AATGGACGAAAAGGGATGTATATAAAA 57.365 29.630 0.00 0.00 0.00 1.52
2661 2761 9.635404 AAATGGACGAAAAGGGATGTATATAAA 57.365 29.630 0.00 0.00 0.00 1.40
2662 2762 9.635404 AAAATGGACGAAAAGGGATGTATATAA 57.365 29.630 0.00 0.00 0.00 0.98
2663 2763 9.062524 CAAAATGGACGAAAAGGGATGTATATA 57.937 33.333 0.00 0.00 0.00 0.86
2664 2764 7.777910 TCAAAATGGACGAAAAGGGATGTATAT 59.222 33.333 0.00 0.00 0.00 0.86
2665 2765 7.113437 TCAAAATGGACGAAAAGGGATGTATA 58.887 34.615 0.00 0.00 0.00 1.47
2666 2766 5.949354 TCAAAATGGACGAAAAGGGATGTAT 59.051 36.000 0.00 0.00 0.00 2.29
2667 2767 5.317808 TCAAAATGGACGAAAAGGGATGTA 58.682 37.500 0.00 0.00 0.00 2.29
2668 2768 4.148838 TCAAAATGGACGAAAAGGGATGT 58.851 39.130 0.00 0.00 0.00 3.06
2669 2769 4.380867 CCTCAAAATGGACGAAAAGGGATG 60.381 45.833 0.00 0.00 0.00 3.51
2670 2770 3.763897 CCTCAAAATGGACGAAAAGGGAT 59.236 43.478 0.00 0.00 0.00 3.85
2671 2771 3.153919 CCTCAAAATGGACGAAAAGGGA 58.846 45.455 0.00 0.00 0.00 4.20
2672 2772 3.057526 GTCCTCAAAATGGACGAAAAGGG 60.058 47.826 0.00 0.00 43.55 3.95
2673 2773 4.160736 GTCCTCAAAATGGACGAAAAGG 57.839 45.455 0.00 0.00 43.55 3.11
2681 2781 6.072175 CCGAAAATACTTGTCCTCAAAATGGA 60.072 38.462 0.00 0.00 32.87 3.41
2682 2782 6.072175 TCCGAAAATACTTGTCCTCAAAATGG 60.072 38.462 0.00 0.00 32.87 3.16
2683 2783 6.801862 GTCCGAAAATACTTGTCCTCAAAATG 59.198 38.462 0.00 0.00 32.87 2.32
2684 2784 6.348213 CGTCCGAAAATACTTGTCCTCAAAAT 60.348 38.462 0.00 0.00 32.87 1.82
2685 2785 5.049954 CGTCCGAAAATACTTGTCCTCAAAA 60.050 40.000 0.00 0.00 32.87 2.44
2686 2786 4.449743 CGTCCGAAAATACTTGTCCTCAAA 59.550 41.667 0.00 0.00 32.87 2.69
2687 2787 3.991773 CGTCCGAAAATACTTGTCCTCAA 59.008 43.478 0.00 0.00 0.00 3.02
2688 2788 3.581755 CGTCCGAAAATACTTGTCCTCA 58.418 45.455 0.00 0.00 0.00 3.86
2689 2789 2.928116 CCGTCCGAAAATACTTGTCCTC 59.072 50.000 0.00 0.00 0.00 3.71
2690 2790 2.564062 TCCGTCCGAAAATACTTGTCCT 59.436 45.455 0.00 0.00 0.00 3.85
2691 2791 2.928116 CTCCGTCCGAAAATACTTGTCC 59.072 50.000 0.00 0.00 0.00 4.02
2692 2792 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2693 2793 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2694 2794 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2695 2795 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2696 2796 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2697 2797 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2698 2798 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2699 2799 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2700 2800 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
2701 2801 1.856629 AATACTCCCTCCGTCCGAAA 58.143 50.000 0.00 0.00 0.00 3.46
2702 2802 2.301346 GTAATACTCCCTCCGTCCGAA 58.699 52.381 0.00 0.00 0.00 4.30
2703 2803 1.212688 TGTAATACTCCCTCCGTCCGA 59.787 52.381 0.00 0.00 0.00 4.55
2704 2804 1.683943 TGTAATACTCCCTCCGTCCG 58.316 55.000 0.00 0.00 0.00 4.79
2705 2805 4.141779 ACATTTGTAATACTCCCTCCGTCC 60.142 45.833 0.00 0.00 0.00 4.79
2706 2806 5.019785 ACATTTGTAATACTCCCTCCGTC 57.980 43.478 0.00 0.00 0.00 4.79
2707 2807 4.715297 AGACATTTGTAATACTCCCTCCGT 59.285 41.667 0.00 0.00 0.00 4.69
2708 2808 5.050490 CAGACATTTGTAATACTCCCTCCG 58.950 45.833 0.00 0.00 0.00 4.63
2709 2809 5.817816 CACAGACATTTGTAATACTCCCTCC 59.182 44.000 0.00 0.00 0.00 4.30
2710 2810 6.640518 TCACAGACATTTGTAATACTCCCTC 58.359 40.000 0.00 0.00 0.00 4.30
2711 2811 6.352222 CCTCACAGACATTTGTAATACTCCCT 60.352 42.308 0.00 0.00 0.00 4.20
2712 2812 5.817816 CCTCACAGACATTTGTAATACTCCC 59.182 44.000 0.00 0.00 0.00 4.30
2713 2813 5.817816 CCCTCACAGACATTTGTAATACTCC 59.182 44.000 0.00 0.00 0.00 3.85
2714 2814 6.407202 ACCCTCACAGACATTTGTAATACTC 58.593 40.000 0.00 0.00 0.00 2.59
2815 2915 6.262944 TGACTAACAACAGCAAACAGATTCAT 59.737 34.615 0.00 0.00 0.00 2.57
2829 2929 9.350357 GTAATAATCGACTTCTGACTAACAACA 57.650 33.333 0.00 0.00 0.00 3.33
2834 2934 8.188799 CACCAGTAATAATCGACTTCTGACTAA 58.811 37.037 0.00 0.00 0.00 2.24
2948 3048 2.996631 GCTCAATCAGAGGTCCAACAT 58.003 47.619 0.00 0.00 44.86 2.71
2949 3049 2.479566 GCTCAATCAGAGGTCCAACA 57.520 50.000 0.00 0.00 44.86 3.33
3248 3351 2.944129 TGTTGGAAAAAGGAGGGTCTG 58.056 47.619 0.00 0.00 0.00 3.51
3265 3368 3.006110 CCATCCAAACAGCAGACAATGTT 59.994 43.478 0.00 0.00 41.28 2.71
3400 3600 1.639635 AAGGCCTACCCATGAGCAGG 61.640 60.000 5.16 0.00 36.11 4.85
3404 3604 3.303351 AAATGAAGGCCTACCCATGAG 57.697 47.619 5.16 0.00 36.11 2.90
3405 3605 3.756082 AAAATGAAGGCCTACCCATGA 57.244 42.857 5.16 0.00 36.11 3.07
3426 3633 5.163499 GGTACACAAATTCAGAACCACCAAA 60.163 40.000 0.00 0.00 0.00 3.28
3475 3682 9.743057 CTATTGTCCAAGTAACAAAACAATCAA 57.257 29.630 2.14 0.00 39.84 2.57
3501 3708 7.711339 AGAACTGTAGGTACATAAATAGCAAGC 59.289 37.037 0.00 0.00 35.36 4.01
3697 4074 1.683011 GCCACCGAGGTACAGGTACTA 60.683 57.143 9.26 0.00 39.00 1.82
3739 4116 4.201724 GCATACAGTTTCATGTCGAAGGAC 60.202 45.833 0.00 0.00 43.71 3.85
3764 4221 4.644685 CACCAAAAGGAAGAGAAGAAACCA 59.355 41.667 0.00 0.00 0.00 3.67
3838 4374 1.061131 CAGTCGCCAATTCTAACTGCG 59.939 52.381 0.00 0.00 46.09 5.18
3909 4448 3.526534 GCCTGGATCACACTAGAAGAAC 58.473 50.000 0.00 0.00 0.00 3.01
3962 4662 6.504398 CATGTAAAGAAATGCATGCATCTCT 58.496 36.000 32.25 29.61 35.47 3.10
3988 4688 3.917380 CAGCAACGACTTTTGTTTGTCAA 59.083 39.130 0.00 0.00 33.18 3.18
4080 4780 1.751927 CTAGCAGCCAGGCCCAAAG 60.752 63.158 8.22 0.00 0.00 2.77
4081 4781 1.204786 TACTAGCAGCCAGGCCCAAA 61.205 55.000 8.22 0.00 0.00 3.28
4084 4784 1.700042 ATGTACTAGCAGCCAGGCCC 61.700 60.000 8.22 0.00 0.00 5.80
4087 4787 3.576118 ACATAGATGTACTAGCAGCCAGG 59.424 47.826 0.00 0.00 39.68 4.45
4103 4816 7.905649 ACTCCTACCTAGGTAGCTATACATAGA 59.094 40.741 34.91 23.68 45.09 1.98
4205 4922 1.264020 CGTGCGCATGCCAGTATAAAT 59.736 47.619 18.03 0.00 41.78 1.40
4356 5073 8.299262 ACTATGTAAGTGCTGCTATATTTTCG 57.701 34.615 0.00 0.00 36.93 3.46
4366 5083 7.085116 CCTAGTGTATACTATGTAAGTGCTGC 58.915 42.308 4.17 0.00 38.65 5.25
4389 5106 2.030007 CGAATCACAAATGTTGGCACCT 60.030 45.455 0.00 0.00 34.12 4.00
4514 5231 0.461870 GGTGGCATCTACGATGTGCA 60.462 55.000 5.81 0.00 40.53 4.57
4600 5317 1.710013 CGTATGCACGTCCAACTTCT 58.290 50.000 0.00 0.00 43.31 2.85
4719 5438 6.534793 ACATTTGGTGTTTTTCATTCACAGAC 59.465 34.615 0.00 0.00 38.01 3.51
4735 5454 6.795399 ACTTTGTCAAGTAGAACATTTGGTG 58.205 36.000 0.00 0.00 41.81 4.17
4758 5477 7.169813 GCAGCATTTTTAGAGCCCAAATATTAC 59.830 37.037 0.00 0.00 0.00 1.89
4779 5498 1.032794 CTATAGTCTGGGTCGCAGCA 58.967 55.000 11.94 0.70 0.00 4.41
4786 5505 4.816048 TCTGATCCACTATAGTCTGGGT 57.184 45.455 1.26 0.00 0.00 4.51
4787 5506 4.282195 GGTTCTGATCCACTATAGTCTGGG 59.718 50.000 1.26 1.70 0.00 4.45
4791 5511 6.276847 CACAAGGTTCTGATCCACTATAGTC 58.723 44.000 1.26 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.