Multiple sequence alignment - TraesCS2A01G027800

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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 TraesCS2A01G027800 chr2A 100.000 6200 0 0 1 6200 12892213 12898412 0.000000e+00 11450
1 TraesCS2A01G027800 chr2A 89.415 1266 93 15 3970 5213 12977574 12978820 0.000000e+00 1557
2 TraesCS2A01G027800 chr2A 82.675 1241 154 27 1348 2556 12433559 12432348 0.000000e+00 1044
3 TraesCS2A01G027800 chr2A 83.705 1031 134 27 4214 5214 12364978 12363952 0.000000e+00 942
4 TraesCS2A01G027800 chr2A 83.317 1031 124 28 4214 5211 12427825 12426810 0.000000e+00 907
5 TraesCS2A01G027800 chr2A 92.212 565 18 7 5661 6200 70118658 70119221 0.000000e+00 776
6 TraesCS2A01G027800 chr2A 78.448 1276 190 42 997 2218 750266316 750267560 0.000000e+00 754
7 TraesCS2A01G027800 chr2A 87.621 622 64 8 1995 2612 12971818 12972430 0.000000e+00 710
8 TraesCS2A01G027800 chr2A 82.593 810 97 17 2922 3690 12366199 12365393 0.000000e+00 675
9 TraesCS2A01G027800 chr2A 83.422 754 97 18 4468 5199 750280536 750281283 0.000000e+00 675
10 TraesCS2A01G027800 chr2A 87.744 563 41 10 5663 6200 677215013 677215572 3.150000e-177 632
11 TraesCS2A01G027800 chr2A 83.306 599 85 7 1385 1978 12368057 12367469 7.070000e-149 538
12 TraesCS2A01G027800 chr2A 83.128 569 68 12 3158 3700 12972883 12973449 1.550000e-135 494
13 TraesCS2A01G027800 chr2A 81.081 629 86 20 1353 1978 12971175 12971773 7.270000e-129 472
14 TraesCS2A01G027800 chr2A 84.665 463 51 12 2653 3114 12972436 12972879 1.590000e-120 444
15 TraesCS2A01G027800 chr2A 83.034 501 66 14 3970 4462 750279955 750280444 2.650000e-118 436
16 TraesCS2A01G027800 chr2A 79.964 554 94 14 3158 3695 750279343 750279895 5.830000e-105 392
17 TraesCS2A01G027800 chr2A 88.172 279 9 5 5665 5919 70134652 70134930 1.680000e-80 311
18 TraesCS2A01G027800 chr2A 86.447 273 27 7 3883 4152 12965700 12965965 2.190000e-74 291
19 TraesCS2A01G027800 chr2A 85.663 279 7 7 5663 5919 12904580 12904847 4.770000e-66 263
20 TraesCS2A01G027800 chr2A 85.000 260 27 7 2917 3167 12431672 12431416 2.870000e-63 254
21 TraesCS2A01G027800 chr2A 88.750 160 14 3 2954 3111 537460155 537459998 6.340000e-45 193
22 TraesCS2A01G027800 chr2D 97.164 3667 74 7 1995 5632 12261842 12258177 0.000000e+00 6168
23 TraesCS2A01G027800 chr2D 97.187 1635 33 7 355 1985 12263506 12261881 0.000000e+00 2752
24 TraesCS2A01G027800 chr2D 89.388 1225 92 15 4010 5213 12400732 12401939 0.000000e+00 1507
25 TraesCS2A01G027800 chr2D 88.795 589 56 7 1995 2577 12393997 12394581 0.000000e+00 713
26 TraesCS2A01G027800 chr2D 79.661 767 108 31 2957 3687 619276289 619277043 5.540000e-140 508
27 TraesCS2A01G027800 chr2D 83.128 569 69 14 3158 3700 12395062 12395629 1.550000e-135 494
28 TraesCS2A01G027800 chr2D 81.329 632 80 24 1353 1978 12393348 12393947 4.350000e-131 479
29 TraesCS2A01G027800 chr2D 84.017 463 51 13 2653 3114 12394618 12395058 2.070000e-114 424
30 TraesCS2A01G027800 chr2D 86.905 252 24 4 2922 3167 11863020 11862772 2.200000e-69 274
31 TraesCS2A01G027800 chr2D 89.375 160 13 3 2954 3111 400301887 400301730 1.360000e-46 198
32 TraesCS2A01G027800 chr2D 89.222 167 5 2 147 300 12263686 12263520 4.900000e-46 196
33 TraesCS2A01G027800 chr2B 87.734 962 88 13 3970 4910 18703019 18703971 0.000000e+00 1096
34 TraesCS2A01G027800 chr2B 87.734 962 88 13 3970 4910 18766784 18767736 0.000000e+00 1096
35 TraesCS2A01G027800 chr2B 87.356 957 92 10 3975 4910 18733910 18734858 0.000000e+00 1070
36 TraesCS2A01G027800 chr2B 87.987 899 78 13 4033 4910 18794096 18794985 0.000000e+00 1035
37 TraesCS2A01G027800 chr2B 81.701 1317 162 48 1353 2633 18678630 18677357 0.000000e+00 1024
38 TraesCS2A01G027800 chr2B 82.073 1177 151 30 1394 2543 757529796 757530939 0.000000e+00 950
39 TraesCS2A01G027800 chr2B 83.874 1017 123 30 4218 5213 18307531 18306535 0.000000e+00 931
40 TraesCS2A01G027800 chr2B 88.734 719 57 6 4214 4910 18672622 18671906 0.000000e+00 857
41 TraesCS2A01G027800 chr2B 87.011 639 68 11 1995 2626 18762055 18762685 0.000000e+00 706
42 TraesCS2A01G027800 chr2B 86.854 639 69 11 1995 2626 18729378 18730008 0.000000e+00 701
43 TraesCS2A01G027800 chr2B 87.227 595 63 10 2037 2626 18737547 18738133 0.000000e+00 665
44 TraesCS2A01G027800 chr2B 81.290 775 118 15 4457 5209 757387924 757388693 2.470000e-168 603
45 TraesCS2A01G027800 chr2B 84.119 636 86 8 1348 1978 18310705 18310080 8.890000e-168 601
46 TraesCS2A01G027800 chr2B 80.602 830 97 20 2922 3690 18308799 18307973 3.220000e-162 582
47 TraesCS2A01G027800 chr2B 80.208 768 102 33 2957 3687 757386271 757387025 1.180000e-146 531
48 TraesCS2A01G027800 chr2B 79.843 764 103 27 2972 3687 757212893 757213653 1.540000e-140 510
49 TraesCS2A01G027800 chr2B 82.746 568 72 10 3158 3700 18699558 18700124 3.360000e-132 483
50 TraesCS2A01G027800 chr2B 84.538 498 61 10 3217 3700 18676856 18676361 4.350000e-131 479
51 TraesCS2A01G027800 chr2B 82.042 568 76 10 3158 3700 18730444 18731010 1.570000e-125 460
52 TraesCS2A01G027800 chr2B 82.042 568 76 10 3158 3700 18790544 18791110 1.570000e-125 460
53 TraesCS2A01G027800 chr2B 82.979 470 57 14 2653 3120 18677373 18676925 2.690000e-108 403
54 TraesCS2A01G027800 chr2B 82.974 464 56 15 2653 3114 18729998 18730440 1.250000e-106 398
55 TraesCS2A01G027800 chr2B 82.759 464 57 16 2653 3114 18699112 18699554 5.830000e-105 392
56 TraesCS2A01G027800 chr2B 84.138 290 34 9 2653 2940 18762675 18762954 2.850000e-68 270
57 TraesCS2A01G027800 chr2B 84.291 261 33 6 2653 2911 18738123 18738377 1.330000e-61 248
58 TraesCS2A01G027800 chr2B 87.302 126 16 0 1026 1151 757527568 757527693 1.800000e-30 145
59 TraesCS2A01G027800 chr2B 87.619 105 7 5 5463 5563 748078631 748078529 3.930000e-22 117
60 TraesCS2A01G027800 chr1A 92.705 562 16 7 5663 6200 327706105 327706665 0.000000e+00 787
61 TraesCS2A01G027800 chr1A 91.281 562 21 7 5663 6200 561407112 561407669 0.000000e+00 741
62 TraesCS2A01G027800 chr1A 91.103 562 22 7 5663 6200 561391448 561392005 0.000000e+00 736
63 TraesCS2A01G027800 chr1A 82.171 129 16 5 5423 5546 401405873 401405999 3.060000e-18 104
64 TraesCS2A01G027800 chr3D 92.168 549 19 5 5676 6200 35725013 35724465 0.000000e+00 754
65 TraesCS2A01G027800 chrUn 86.854 639 69 11 1995 2626 330381256 330381886 0.000000e+00 701
66 TraesCS2A01G027800 chrUn 86.542 587 67 9 1996 2580 387129134 387129710 2.440000e-178 636
67 TraesCS2A01G027800 chrUn 89.876 484 36 4 4440 4910 438497327 438496844 1.480000e-170 610
68 TraesCS2A01G027800 chrUn 88.514 444 48 3 1509 1951 387128619 387129060 9.150000e-148 534
69 TraesCS2A01G027800 chrUn 84.990 493 66 4 3216 3700 464195219 464194727 1.550000e-135 494
70 TraesCS2A01G027800 chrUn 96.642 268 9 0 4946 5213 438496837 438496570 4.410000e-121 446
71 TraesCS2A01G027800 chrUn 88.119 202 16 3 2654 2855 387129748 387129941 3.740000e-57 233
72 TraesCS2A01G027800 chr4A 88.319 565 39 9 5662 6200 713604420 713603857 0.000000e+00 652
73 TraesCS2A01G027800 chr4A 87.965 565 42 11 5661 6200 621726795 621726232 1.460000e-180 643
74 TraesCS2A01G027800 chr7D 94.175 412 19 4 5793 6200 168813670 168814080 1.900000e-174 623
75 TraesCS2A01G027800 chr7D 86.477 281 14 13 5663 5919 168817725 168818005 2.830000e-73 287
76 TraesCS2A01G027800 chr7D 88.000 125 10 3 5423 5542 532183853 532183977 6.480000e-30 143
77 TraesCS2A01G027800 chr7D 88.000 125 10 3 5423 5542 556524517 556524393 6.480000e-30 143
78 TraesCS2A01G027800 chr7D 87.200 125 10 4 5423 5542 55836393 55836270 3.010000e-28 137
79 TraesCS2A01G027800 chr7A 84.559 544 27 20 5659 6200 17118234 17117746 2.600000e-133 486
80 TraesCS2A01G027800 chr7A 81.720 279 17 23 5663 5919 17110870 17110604 1.050000e-47 202
81 TraesCS2A01G027800 chr7A 87.200 125 11 3 5423 5542 368955614 368955490 3.010000e-28 137
82 TraesCS2A01G027800 chr5B 89.655 116 9 2 5423 5535 554916667 554916552 1.800000e-30 145
83 TraesCS2A01G027800 chr4D 88.000 125 10 4 5423 5542 248451122 248451246 6.480000e-30 143
84 TraesCS2A01G027800 chr4D 87.200 125 11 3 5423 5542 295485449 295485325 3.010000e-28 137


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 TraesCS2A01G027800 chr2A 12892213 12898412 6199 False 11450.000000 11450 100.000000 1 6200 1 chr2A.!!$F1 6199
1 TraesCS2A01G027800 chr2A 12977574 12978820 1246 False 1557.000000 1557 89.415000 3970 5213 1 chr2A.!!$F4 1243
2 TraesCS2A01G027800 chr2A 70118658 70119221 563 False 776.000000 776 92.212000 5661 6200 1 chr2A.!!$F5 539
3 TraesCS2A01G027800 chr2A 750266316 750267560 1244 False 754.000000 754 78.448000 997 2218 1 chr2A.!!$F8 1221
4 TraesCS2A01G027800 chr2A 12426810 12433559 6749 True 735.000000 1044 83.664000 1348 5211 3 chr2A.!!$R3 3863
5 TraesCS2A01G027800 chr2A 12363952 12368057 4105 True 718.333333 942 83.201333 1385 5214 3 chr2A.!!$R2 3829
6 TraesCS2A01G027800 chr2A 677215013 677215572 559 False 632.000000 632 87.744000 5663 6200 1 chr2A.!!$F7 537
7 TraesCS2A01G027800 chr2A 12971175 12973449 2274 False 530.000000 710 84.123750 1353 3700 4 chr2A.!!$F9 2347
8 TraesCS2A01G027800 chr2A 750279343 750281283 1940 False 501.000000 675 82.140000 3158 5199 3 chr2A.!!$F10 2041
9 TraesCS2A01G027800 chr2D 12258177 12263686 5509 True 3038.666667 6168 94.524333 147 5632 3 chr2D.!!$R3 5485
10 TraesCS2A01G027800 chr2D 12400732 12401939 1207 False 1507.000000 1507 89.388000 4010 5213 1 chr2D.!!$F1 1203
11 TraesCS2A01G027800 chr2D 12393348 12395629 2281 False 527.500000 713 84.317250 1353 3700 4 chr2D.!!$F3 2347
12 TraesCS2A01G027800 chr2D 619276289 619277043 754 False 508.000000 508 79.661000 2957 3687 1 chr2D.!!$F2 730
13 TraesCS2A01G027800 chr2B 18790544 18794985 4441 False 747.500000 1035 85.014500 3158 4910 2 chr2B.!!$F5 1752
14 TraesCS2A01G027800 chr2B 18306535 18310705 4170 True 704.666667 931 82.865000 1348 5213 3 chr2B.!!$R2 3865
15 TraesCS2A01G027800 chr2B 18671906 18678630 6724 True 690.750000 1024 84.488000 1353 4910 4 chr2B.!!$R3 3557
16 TraesCS2A01G027800 chr2B 18762055 18767736 5681 False 690.666667 1096 86.294333 1995 4910 3 chr2B.!!$F4 2915
17 TraesCS2A01G027800 chr2B 18699112 18703971 4859 False 657.000000 1096 84.413000 2653 4910 3 chr2B.!!$F2 2257
18 TraesCS2A01G027800 chr2B 18729378 18738377 8999 False 590.333333 1070 85.124000 1995 4910 6 chr2B.!!$F3 2915
19 TraesCS2A01G027800 chr2B 757386271 757388693 2422 False 567.000000 603 80.749000 2957 5209 2 chr2B.!!$F6 2252
20 TraesCS2A01G027800 chr2B 757527568 757530939 3371 False 547.500000 950 84.687500 1026 2543 2 chr2B.!!$F7 1517
21 TraesCS2A01G027800 chr2B 757212893 757213653 760 False 510.000000 510 79.843000 2972 3687 1 chr2B.!!$F1 715
22 TraesCS2A01G027800 chr1A 327706105 327706665 560 False 787.000000 787 92.705000 5663 6200 1 chr1A.!!$F1 537
23 TraesCS2A01G027800 chr1A 561407112 561407669 557 False 741.000000 741 91.281000 5663 6200 1 chr1A.!!$F4 537
24 TraesCS2A01G027800 chr1A 561391448 561392005 557 False 736.000000 736 91.103000 5663 6200 1 chr1A.!!$F3 537
25 TraesCS2A01G027800 chr3D 35724465 35725013 548 True 754.000000 754 92.168000 5676 6200 1 chr3D.!!$R1 524
26 TraesCS2A01G027800 chrUn 330381256 330381886 630 False 701.000000 701 86.854000 1995 2626 1 chrUn.!!$F1 631
27 TraesCS2A01G027800 chrUn 438496570 438497327 757 True 528.000000 610 93.259000 4440 5213 2 chrUn.!!$R2 773
28 TraesCS2A01G027800 chrUn 387128619 387129941 1322 False 467.666667 636 87.725000 1509 2855 3 chrUn.!!$F2 1346
29 TraesCS2A01G027800 chr4A 713603857 713604420 563 True 652.000000 652 88.319000 5662 6200 1 chr4A.!!$R2 538
30 TraesCS2A01G027800 chr4A 621726232 621726795 563 True 643.000000 643 87.965000 5661 6200 1 chr4A.!!$R1 539
31 TraesCS2A01G027800 chr7D 168813670 168818005 4335 False 455.000000 623 90.326000 5663 6200 2 chr7D.!!$F2 537

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
417 431 1.191535 TGTCGCTAGCTACCAACCAT 58.808 50.000 16.05 0.0 0.00 3.55 F
1652 3545 0.173708 AAGGATGAACCGAGCGAGAC 59.826 55.000 0.00 0.0 44.74 3.36 F
1670 3563 1.852280 GACGCGACAAATGATCGATGA 59.148 47.619 15.93 0.0 42.25 2.92 F
3296 5696 2.027625 GGAGACCAACCACGCTTCG 61.028 63.158 0.00 0.0 0.00 3.79 F
4766 14307 0.599728 GCACCATCGAGATCTGCTCC 60.600 60.000 0.00 0.0 40.70 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 3817 0.043053 CTGTCACACAAGTTGTCGCG 60.043 55.000 5.27 0.0 35.67 5.87 R
3078 5424 1.878522 GACGTCGTAGCCATGCTGG 60.879 63.158 0.00 0.0 40.10 4.85 R
3597 8676 4.097135 TGTTTCAATTCTCGGCAAACTTGA 59.903 37.500 0.00 0.0 0.00 3.02 R
4782 14323 1.048601 AGGTTCAGTTTCTGCTCGGA 58.951 50.000 0.00 0.0 0.00 4.55 R
5623 15234 1.537202 GAGTCTTTGACATGCCACACC 59.463 52.381 0.00 0.0 34.60 4.16 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
37 38 9.384682 GTACACTACTCGAAAAGATTATCTAGC 57.615 37.037 0.00 0.00 0.00 3.42
38 39 7.427214 ACACTACTCGAAAAGATTATCTAGCC 58.573 38.462 0.00 0.00 0.00 3.93
39 40 7.068348 ACACTACTCGAAAAGATTATCTAGCCA 59.932 37.037 0.00 0.00 0.00 4.75
40 41 7.593273 CACTACTCGAAAAGATTATCTAGCCAG 59.407 40.741 0.00 0.00 0.00 4.85
41 42 6.472686 ACTCGAAAAGATTATCTAGCCAGT 57.527 37.500 0.00 0.00 0.00 4.00
42 43 6.879400 ACTCGAAAAGATTATCTAGCCAGTT 58.121 36.000 0.00 0.00 0.00 3.16
43 44 7.331791 ACTCGAAAAGATTATCTAGCCAGTTT 58.668 34.615 0.00 0.00 0.00 2.66
44 45 7.824779 ACTCGAAAAGATTATCTAGCCAGTTTT 59.175 33.333 0.00 0.00 0.00 2.43
45 46 7.974675 TCGAAAAGATTATCTAGCCAGTTTTG 58.025 34.615 0.00 0.00 0.00 2.44
46 47 7.822334 TCGAAAAGATTATCTAGCCAGTTTTGA 59.178 33.333 0.00 0.00 0.00 2.69
47 48 8.616076 CGAAAAGATTATCTAGCCAGTTTTGAT 58.384 33.333 0.00 0.00 0.00 2.57
48 49 9.727627 GAAAAGATTATCTAGCCAGTTTTGATG 57.272 33.333 0.00 0.00 0.00 3.07
49 50 7.814264 AAGATTATCTAGCCAGTTTTGATGG 57.186 36.000 0.00 0.00 41.04 3.51
50 51 7.141758 AGATTATCTAGCCAGTTTTGATGGA 57.858 36.000 0.00 0.00 40.51 3.41
51 52 7.577303 AGATTATCTAGCCAGTTTTGATGGAA 58.423 34.615 0.00 0.00 40.51 3.53
52 53 8.055181 AGATTATCTAGCCAGTTTTGATGGAAA 58.945 33.333 0.00 0.00 40.51 3.13
53 54 8.773033 ATTATCTAGCCAGTTTTGATGGAAAT 57.227 30.769 0.00 0.00 40.51 2.17
54 55 8.593945 TTATCTAGCCAGTTTTGATGGAAATT 57.406 30.769 0.00 0.00 40.51 1.82
55 56 9.693739 TTATCTAGCCAGTTTTGATGGAAATTA 57.306 29.630 0.00 0.00 40.51 1.40
56 57 8.593945 ATCTAGCCAGTTTTGATGGAAATTAA 57.406 30.769 0.00 0.00 40.51 1.40
57 58 8.415950 TCTAGCCAGTTTTGATGGAAATTAAA 57.584 30.769 0.00 0.00 40.51 1.52
58 59 8.303876 TCTAGCCAGTTTTGATGGAAATTAAAC 58.696 33.333 0.00 0.00 40.51 2.01
59 60 7.066307 AGCCAGTTTTGATGGAAATTAAACT 57.934 32.000 0.00 0.00 40.51 2.66
60 61 8.189119 AGCCAGTTTTGATGGAAATTAAACTA 57.811 30.769 0.00 0.00 40.51 2.24
61 62 8.088365 AGCCAGTTTTGATGGAAATTAAACTAC 58.912 33.333 0.00 0.00 40.51 2.73
62 63 7.870445 GCCAGTTTTGATGGAAATTAAACTACA 59.130 33.333 0.00 0.00 40.51 2.74
63 64 9.927668 CCAGTTTTGATGGAAATTAAACTACAT 57.072 29.630 0.00 0.00 40.51 2.29
73 74 9.513906 TGGAAATTAAACTACATTCATCACAGA 57.486 29.630 0.00 0.00 0.00 3.41
113 114 8.756486 AATGTGATCCATAAATCTGTGATCAA 57.244 30.769 0.00 0.00 31.97 2.57
114 115 8.756486 ATGTGATCCATAAATCTGTGATCAAA 57.244 30.769 0.00 0.00 30.76 2.69
115 116 8.756486 TGTGATCCATAAATCTGTGATCAAAT 57.244 30.769 0.00 0.00 30.76 2.32
116 117 9.192642 TGTGATCCATAAATCTGTGATCAAATT 57.807 29.630 0.00 0.00 30.76 1.82
139 140 9.825972 AATTAAACTACATTCATCACAGTTTCG 57.174 29.630 1.60 0.00 39.47 3.46
140 141 8.596271 TTAAACTACATTCATCACAGTTTCGA 57.404 30.769 1.60 0.00 39.47 3.71
141 142 7.672983 AAACTACATTCATCACAGTTTCGAT 57.327 32.000 0.00 0.00 35.13 3.59
142 143 6.653273 ACTACATTCATCACAGTTTCGATG 57.347 37.500 0.00 0.00 40.34 3.84
143 144 4.952262 ACATTCATCACAGTTTCGATGG 57.048 40.909 0.00 0.00 39.60 3.51
144 145 4.578871 ACATTCATCACAGTTTCGATGGA 58.421 39.130 0.00 0.00 39.60 3.41
145 146 4.633126 ACATTCATCACAGTTTCGATGGAG 59.367 41.667 0.00 0.00 39.60 3.86
314 328 9.267084 TGCTCGCTATGTTATTAAATACAATCA 57.733 29.630 0.00 0.00 0.00 2.57
315 329 9.530129 GCTCGCTATGTTATTAAATACAATCAC 57.470 33.333 0.00 0.00 0.00 3.06
316 330 9.727403 CTCGCTATGTTATTAAATACAATCACG 57.273 33.333 0.00 0.00 0.00 4.35
317 331 9.251792 TCGCTATGTTATTAAATACAATCACGT 57.748 29.630 0.00 0.00 0.00 4.49
328 342 7.609760 AAATACAATCACGTAGATTTGCTCA 57.390 32.000 9.56 0.00 44.48 4.26
329 343 4.928661 ACAATCACGTAGATTTGCTCAC 57.071 40.909 9.56 0.00 44.48 3.51
330 344 3.684788 ACAATCACGTAGATTTGCTCACC 59.315 43.478 9.56 0.00 44.48 4.02
331 345 3.610040 ATCACGTAGATTTGCTCACCA 57.390 42.857 0.00 0.00 31.20 4.17
332 346 3.610040 TCACGTAGATTTGCTCACCAT 57.390 42.857 0.00 0.00 0.00 3.55
333 347 4.729227 TCACGTAGATTTGCTCACCATA 57.271 40.909 0.00 0.00 0.00 2.74
334 348 5.079689 TCACGTAGATTTGCTCACCATAA 57.920 39.130 0.00 0.00 0.00 1.90
335 349 5.483811 TCACGTAGATTTGCTCACCATAAA 58.516 37.500 0.00 0.00 0.00 1.40
336 350 6.112734 TCACGTAGATTTGCTCACCATAAAT 58.887 36.000 0.00 0.00 0.00 1.40
337 351 7.269316 TCACGTAGATTTGCTCACCATAAATA 58.731 34.615 0.00 0.00 0.00 1.40
338 352 7.223971 TCACGTAGATTTGCTCACCATAAATAC 59.776 37.037 0.00 0.00 0.00 1.89
339 353 7.011016 CACGTAGATTTGCTCACCATAAATACA 59.989 37.037 0.00 0.00 0.00 2.29
340 354 7.551262 ACGTAGATTTGCTCACCATAAATACAA 59.449 33.333 0.00 0.00 0.00 2.41
341 355 8.559536 CGTAGATTTGCTCACCATAAATACAAT 58.440 33.333 0.00 0.00 0.00 2.71
342 356 9.884465 GTAGATTTGCTCACCATAAATACAATC 57.116 33.333 0.00 0.00 0.00 2.67
343 357 8.523915 AGATTTGCTCACCATAAATACAATCA 57.476 30.769 0.00 0.00 0.00 2.57
344 358 8.408601 AGATTTGCTCACCATAAATACAATCAC 58.591 33.333 0.00 0.00 0.00 3.06
345 359 5.733226 TGCTCACCATAAATACAATCACG 57.267 39.130 0.00 0.00 0.00 4.35
346 360 5.182487 TGCTCACCATAAATACAATCACGT 58.818 37.500 0.00 0.00 0.00 4.49
347 361 5.645929 TGCTCACCATAAATACAATCACGTT 59.354 36.000 0.00 0.00 0.00 3.99
348 362 6.819146 TGCTCACCATAAATACAATCACGTTA 59.181 34.615 0.00 0.00 0.00 3.18
349 363 7.497579 TGCTCACCATAAATACAATCACGTTAT 59.502 33.333 0.00 0.00 0.00 1.89
350 364 8.342634 GCTCACCATAAATACAATCACGTTATT 58.657 33.333 0.00 0.00 0.00 1.40
364 378 8.697067 CAATCACGTTATTAAATACTAGTCCCG 58.303 37.037 0.00 0.00 0.00 5.14
381 395 1.681264 CCCGCAAACAGGAAGAAACTT 59.319 47.619 0.00 0.00 0.00 2.66
417 431 1.191535 TGTCGCTAGCTACCAACCAT 58.808 50.000 16.05 0.00 0.00 3.55
470 484 2.158534 AGATAGACTGCTCCGATGACCT 60.159 50.000 0.00 0.00 0.00 3.85
514 528 2.100605 AAACTTCGGAGAGTGGCATC 57.899 50.000 0.00 0.00 38.43 3.91
593 608 2.533942 CGTTTTTGGACCTCGCAAAAAG 59.466 45.455 9.82 3.47 37.04 2.27
596 611 4.457834 TTTTGGACCTCGCAAAAAGAAA 57.542 36.364 0.00 0.00 0.00 2.52
610 625 6.023410 CGCAAAAAGAAAATGACACGTTTTTG 60.023 34.615 11.79 11.79 43.14 2.44
611 626 6.248210 GCAAAAAGAAAATGACACGTTTTTGG 59.752 34.615 15.87 2.82 41.71 3.28
612 627 7.513968 CAAAAAGAAAATGACACGTTTTTGGA 58.486 30.769 9.26 0.00 39.51 3.53
613 628 6.641176 AAAGAAAATGACACGTTTTTGGAC 57.359 33.333 0.62 0.00 0.00 4.02
614 629 5.576447 AGAAAATGACACGTTTTTGGACT 57.424 34.783 0.62 0.00 0.00 3.85
615 630 5.961272 AGAAAATGACACGTTTTTGGACTT 58.039 33.333 0.62 0.00 0.00 3.01
616 631 6.394809 AGAAAATGACACGTTTTTGGACTTT 58.605 32.000 0.62 0.00 0.00 2.66
617 632 7.540299 AGAAAATGACACGTTTTTGGACTTTA 58.460 30.769 0.62 0.00 0.00 1.85
630 645 2.554893 TGGACTTTAATGGTTCCGCAAC 59.445 45.455 0.00 0.00 0.00 4.17
649 664 5.452777 GCAACTTAACAATCCTCTGTGTTC 58.547 41.667 0.00 0.00 38.80 3.18
676 691 5.209977 TGGTCATCTTCGTAAATATCGTCG 58.790 41.667 0.00 0.00 0.00 5.12
680 695 6.847792 GTCATCTTCGTAAATATCGTCGTACA 59.152 38.462 0.00 0.00 0.00 2.90
686 701 6.999456 TCGTAAATATCGTCGTACACTTGTA 58.001 36.000 0.00 0.00 0.00 2.41
696 711 5.230726 CGTCGTACACTTGTAACATATTCCC 59.769 44.000 0.00 0.00 31.52 3.97
815 832 2.486636 CTTCCGTCGTGGTGCAGCTA 62.487 60.000 18.08 0.37 39.52 3.32
995 1013 2.435805 ACAAAGAGACACAGAGAAGGCA 59.564 45.455 0.00 0.00 0.00 4.75
1217 2081 8.091449 ACTGTTTTGATGGAAACTTTTGTTACA 58.909 29.630 2.68 0.00 42.67 2.41
1225 2178 9.132521 GATGGAAACTTTTGTTACATCTTCATG 57.867 33.333 13.94 0.00 44.50 3.07
1652 3545 0.173708 AAGGATGAACCGAGCGAGAC 59.826 55.000 0.00 0.00 44.74 3.36
1670 3563 1.852280 GACGCGACAAATGATCGATGA 59.148 47.619 15.93 0.00 42.25 2.92
1863 3756 4.517285 GTGATCCTGCTTTCTTCATGGTA 58.483 43.478 0.00 0.00 0.00 3.25
1924 3817 4.023707 CAGTGAAGTCTTGGAACATTGACC 60.024 45.833 0.00 0.00 40.99 4.02
2122 4050 2.327325 ACTTCCCAGCACTCCTAGAA 57.673 50.000 0.00 0.00 0.00 2.10
2234 4172 4.588490 TGCATACTTAGCTACATGCGTGC 61.588 47.826 20.73 14.61 45.31 5.34
2629 4568 5.415701 GCCTCTTCAATTGGTCAATACTGAA 59.584 40.000 5.42 9.22 31.88 3.02
2635 4574 7.815840 TCAATTGGTCAATACTGAAACAGAA 57.184 32.000 5.42 0.00 35.18 3.02
3078 5424 2.125633 GGTTTCCGTCTCCTCCGC 60.126 66.667 0.00 0.00 0.00 5.54
3296 5696 2.027625 GGAGACCAACCACGCTTCG 61.028 63.158 0.00 0.00 0.00 3.79
3597 8676 3.443681 CACGCTAAACTTCCCATGGAAAT 59.556 43.478 15.22 0.00 41.54 2.17
3609 8688 2.230992 CCATGGAAATCAAGTTTGCCGA 59.769 45.455 5.56 0.00 37.34 5.54
3813 8894 9.967451 TTTAATCCTAAACTTGATCCATGTGTA 57.033 29.630 0.00 0.00 0.00 2.90
3899 12446 6.016276 GGAACTTCTCATGTACAAAATGTGGT 60.016 38.462 0.00 0.00 0.00 4.16
3962 12848 8.664798 TCAACTAACATGTGACACTATAAATGC 58.335 33.333 7.20 0.00 0.00 3.56
3989 12999 6.648725 GCTTCTAGAGAATTTATGGTAGCCAG 59.351 42.308 0.00 0.00 33.00 4.85
4083 13111 4.725790 AAATGGCTAAGGCTGATTTCAC 57.274 40.909 0.00 0.00 38.73 3.18
4218 13615 7.397476 ACCACTAGATTCTTACATGAGACTTGA 59.603 37.037 0.00 0.00 0.00 3.02
4285 13682 2.430921 CGACTCCAAAGAGCGCGT 60.431 61.111 8.43 0.00 44.65 6.01
4766 14307 0.599728 GCACCATCGAGATCTGCTCC 60.600 60.000 0.00 0.00 40.70 4.70
4811 14352 5.564848 GCAGAAACTGAACCTTTGGGATTAC 60.565 44.000 2.81 0.00 32.44 1.89
5018 14603 3.305720 AGAACACAGAGGACTTACACCA 58.694 45.455 0.00 0.00 0.00 4.17
5169 14754 4.460382 CCTGAAACAGTTGATAGCCACATT 59.540 41.667 0.00 0.00 0.00 2.71
5352 14937 8.837788 CAAGGACTGCACATGAATATATAGAA 57.162 34.615 0.00 0.00 0.00 2.10
5375 14960 7.344612 AGAAAGAAAGGTAACAAGGTTCCAAAT 59.655 33.333 0.00 0.00 41.41 2.32
5430 15015 8.097662 AGTTTGCTGCTATAAATATACTCCCTC 58.902 37.037 0.00 0.00 0.00 4.30
5503 15112 4.827692 AGCAAAATGTCTACGTACATCCA 58.172 39.130 4.49 0.00 39.16 3.41
5572 15183 0.179092 GGGAGTACATGTACACGCCC 60.179 60.000 32.02 30.73 38.48 6.13
5654 15337 0.439985 CAAAGACTCGACATGGCACG 59.560 55.000 0.00 0.81 0.00 5.34
5655 15338 0.033504 AAAGACTCGACATGGCACGT 59.966 50.000 0.00 0.00 0.00 4.49
5656 15339 0.033504 AAGACTCGACATGGCACGTT 59.966 50.000 0.00 0.00 0.00 3.99
5657 15340 0.885879 AGACTCGACATGGCACGTTA 59.114 50.000 0.00 0.00 0.00 3.18
5658 15341 1.271379 AGACTCGACATGGCACGTTAA 59.729 47.619 0.00 0.00 0.00 2.01
5659 15342 2.094182 AGACTCGACATGGCACGTTAAT 60.094 45.455 0.00 0.00 0.00 1.40
5748 15469 3.071479 GGAGCGGTTACAAATCTGTGAA 58.929 45.455 0.00 0.00 36.96 3.18
5790 15511 0.370273 GGTTGCTAATGCGTGAGACG 59.630 55.000 0.00 0.00 45.88 4.18
5919 15778 7.442666 CCAAGTGCTCTAATTCTATTCCTAACC 59.557 40.741 0.00 0.00 0.00 2.85
6006 15895 9.868277 CATCATCTAGTCCTTCTTGTATAATCC 57.132 37.037 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.384682 GCTAGATAATCTTTTCGAGTAGTGTAC 57.615 37.037 0.00 0.00 0.00 2.90
12 13 8.566260 GGCTAGATAATCTTTTCGAGTAGTGTA 58.434 37.037 0.00 0.00 0.00 2.90
13 14 7.068348 TGGCTAGATAATCTTTTCGAGTAGTGT 59.932 37.037 0.00 0.00 0.00 3.55
14 15 7.426410 TGGCTAGATAATCTTTTCGAGTAGTG 58.574 38.462 0.00 0.00 0.00 2.74
15 16 7.285858 ACTGGCTAGATAATCTTTTCGAGTAGT 59.714 37.037 3.17 0.00 0.00 2.73
16 17 7.653647 ACTGGCTAGATAATCTTTTCGAGTAG 58.346 38.462 3.17 0.00 0.00 2.57
17 18 7.584122 ACTGGCTAGATAATCTTTTCGAGTA 57.416 36.000 3.17 0.00 0.00 2.59
18 19 6.472686 ACTGGCTAGATAATCTTTTCGAGT 57.527 37.500 3.17 0.00 0.00 4.18
19 20 7.778470 AAACTGGCTAGATAATCTTTTCGAG 57.222 36.000 3.17 0.00 0.00 4.04
20 21 7.822334 TCAAAACTGGCTAGATAATCTTTTCGA 59.178 33.333 3.17 0.00 0.00 3.71
21 22 7.974675 TCAAAACTGGCTAGATAATCTTTTCG 58.025 34.615 3.17 0.00 0.00 3.46
22 23 9.727627 CATCAAAACTGGCTAGATAATCTTTTC 57.272 33.333 3.17 0.00 0.00 2.29
23 24 8.689972 CCATCAAAACTGGCTAGATAATCTTTT 58.310 33.333 3.17 0.00 0.00 2.27
24 25 8.055181 TCCATCAAAACTGGCTAGATAATCTTT 58.945 33.333 3.17 0.00 33.56 2.52
25 26 7.577303 TCCATCAAAACTGGCTAGATAATCTT 58.423 34.615 3.17 0.00 33.56 2.40
26 27 7.141758 TCCATCAAAACTGGCTAGATAATCT 57.858 36.000 3.17 0.00 33.56 2.40
27 28 7.807977 TTCCATCAAAACTGGCTAGATAATC 57.192 36.000 3.17 0.00 33.56 1.75
28 29 8.773033 ATTTCCATCAAAACTGGCTAGATAAT 57.227 30.769 3.17 0.00 33.56 1.28
29 30 8.593945 AATTTCCATCAAAACTGGCTAGATAA 57.406 30.769 3.17 0.00 33.56 1.75
30 31 9.693739 TTAATTTCCATCAAAACTGGCTAGATA 57.306 29.630 3.17 0.00 33.56 1.98
31 32 8.593945 TTAATTTCCATCAAAACTGGCTAGAT 57.406 30.769 3.17 0.00 33.56 1.98
32 33 8.303876 GTTTAATTTCCATCAAAACTGGCTAGA 58.696 33.333 3.17 0.00 33.56 2.43
33 34 8.306761 AGTTTAATTTCCATCAAAACTGGCTAG 58.693 33.333 0.00 0.00 38.57 3.42
34 35 8.189119 AGTTTAATTTCCATCAAAACTGGCTA 57.811 30.769 0.00 0.00 38.57 3.93
35 36 7.066307 AGTTTAATTTCCATCAAAACTGGCT 57.934 32.000 0.00 0.00 38.57 4.75
36 37 7.870445 TGTAGTTTAATTTCCATCAAAACTGGC 59.130 33.333 9.48 4.78 39.86 4.85
37 38 9.927668 ATGTAGTTTAATTTCCATCAAAACTGG 57.072 29.630 9.48 0.00 39.86 4.00
47 48 9.513906 TCTGTGATGAATGTAGTTTAATTTCCA 57.486 29.630 0.00 0.00 0.00 3.53
87 88 9.850198 TTGATCACAGATTTATGGATCACATTA 57.150 29.630 0.00 0.00 42.73 1.90
88 89 8.756486 TTGATCACAGATTTATGGATCACATT 57.244 30.769 0.00 0.00 42.73 2.71
89 90 8.756486 TTTGATCACAGATTTATGGATCACAT 57.244 30.769 0.00 0.00 42.73 3.21
90 91 8.756486 ATTTGATCACAGATTTATGGATCACA 57.244 30.769 0.00 0.00 42.73 3.58
113 114 9.825972 CGAAACTGTGATGAATGTAGTTTAATT 57.174 29.630 0.00 0.00 40.50 1.40
114 115 9.214957 TCGAAACTGTGATGAATGTAGTTTAAT 57.785 29.630 0.00 0.00 40.50 1.40
115 116 8.596271 TCGAAACTGTGATGAATGTAGTTTAA 57.404 30.769 0.00 0.00 40.50 1.52
116 117 8.655970 CATCGAAACTGTGATGAATGTAGTTTA 58.344 33.333 0.00 0.00 43.68 2.01
117 118 7.361201 CCATCGAAACTGTGATGAATGTAGTTT 60.361 37.037 7.86 0.00 43.68 2.66
118 119 6.092670 CCATCGAAACTGTGATGAATGTAGTT 59.907 38.462 7.86 0.00 43.68 2.24
119 120 5.582269 CCATCGAAACTGTGATGAATGTAGT 59.418 40.000 7.86 0.00 43.68 2.73
120 121 5.812127 TCCATCGAAACTGTGATGAATGTAG 59.188 40.000 7.86 0.00 43.68 2.74
121 122 5.729510 TCCATCGAAACTGTGATGAATGTA 58.270 37.500 7.86 0.00 43.68 2.29
122 123 4.578871 TCCATCGAAACTGTGATGAATGT 58.421 39.130 7.86 0.00 43.68 2.71
123 124 4.633126 ACTCCATCGAAACTGTGATGAATG 59.367 41.667 7.86 2.07 43.68 2.67
124 125 4.836825 ACTCCATCGAAACTGTGATGAAT 58.163 39.130 7.86 0.00 43.68 2.57
125 126 4.271696 ACTCCATCGAAACTGTGATGAA 57.728 40.909 7.86 0.00 43.68 2.57
126 127 3.961480 ACTCCATCGAAACTGTGATGA 57.039 42.857 7.86 0.00 43.68 2.92
127 128 5.812127 TGAATACTCCATCGAAACTGTGATG 59.188 40.000 0.00 0.88 41.27 3.07
128 129 5.977635 TGAATACTCCATCGAAACTGTGAT 58.022 37.500 0.00 0.00 0.00 3.06
129 130 5.400066 TGAATACTCCATCGAAACTGTGA 57.600 39.130 0.00 0.00 0.00 3.58
130 131 6.668541 ATTGAATACTCCATCGAAACTGTG 57.331 37.500 0.00 0.00 0.00 3.66
131 132 8.964476 AATATTGAATACTCCATCGAAACTGT 57.036 30.769 0.00 0.00 0.00 3.55
236 250 3.915437 AAATCAACAAGGCTAACGTGG 57.085 42.857 0.00 0.00 32.45 4.94
304 318 7.414098 GGTGAGCAAATCTACGTGATTGTATTT 60.414 37.037 12.06 1.56 43.99 1.40
305 319 6.037172 GGTGAGCAAATCTACGTGATTGTATT 59.963 38.462 12.06 2.44 43.99 1.89
306 320 5.523916 GGTGAGCAAATCTACGTGATTGTAT 59.476 40.000 12.06 3.95 43.99 2.29
307 321 4.868171 GGTGAGCAAATCTACGTGATTGTA 59.132 41.667 12.06 0.00 43.99 2.41
308 322 3.684788 GGTGAGCAAATCTACGTGATTGT 59.315 43.478 12.06 3.46 43.99 2.71
309 323 3.684305 TGGTGAGCAAATCTACGTGATTG 59.316 43.478 12.06 6.93 43.99 2.67
310 324 3.937814 TGGTGAGCAAATCTACGTGATT 58.062 40.909 0.00 2.74 46.49 2.57
311 325 3.610040 TGGTGAGCAAATCTACGTGAT 57.390 42.857 0.00 0.00 36.89 3.06
312 326 3.610040 ATGGTGAGCAAATCTACGTGA 57.390 42.857 0.00 0.00 0.00 4.35
313 327 5.794687 TTTATGGTGAGCAAATCTACGTG 57.205 39.130 0.00 0.00 0.00 4.49
314 328 7.045416 TGTATTTATGGTGAGCAAATCTACGT 58.955 34.615 0.00 0.00 0.00 3.57
315 329 7.477144 TGTATTTATGGTGAGCAAATCTACG 57.523 36.000 0.00 0.00 0.00 3.51
316 330 9.884465 GATTGTATTTATGGTGAGCAAATCTAC 57.116 33.333 0.00 0.00 0.00 2.59
317 331 9.625747 TGATTGTATTTATGGTGAGCAAATCTA 57.374 29.630 0.00 0.00 0.00 1.98
318 332 8.408601 GTGATTGTATTTATGGTGAGCAAATCT 58.591 33.333 0.00 0.00 0.00 2.40
319 333 7.376866 CGTGATTGTATTTATGGTGAGCAAATC 59.623 37.037 0.00 0.00 0.00 2.17
320 334 7.148086 ACGTGATTGTATTTATGGTGAGCAAAT 60.148 33.333 0.00 0.00 0.00 2.32
321 335 6.150307 ACGTGATTGTATTTATGGTGAGCAAA 59.850 34.615 0.00 0.00 0.00 3.68
322 336 5.645929 ACGTGATTGTATTTATGGTGAGCAA 59.354 36.000 0.00 0.00 0.00 3.91
323 337 5.182487 ACGTGATTGTATTTATGGTGAGCA 58.818 37.500 0.00 0.00 0.00 4.26
324 338 5.734855 ACGTGATTGTATTTATGGTGAGC 57.265 39.130 0.00 0.00 0.00 4.26
337 351 9.538508 GGGACTAGTATTTAATAACGTGATTGT 57.461 33.333 8.51 0.00 0.00 2.71
338 352 8.697067 CGGGACTAGTATTTAATAACGTGATTG 58.303 37.037 8.51 0.00 0.00 2.67
339 353 7.383300 GCGGGACTAGTATTTAATAACGTGATT 59.617 37.037 3.06 3.06 0.00 2.57
340 354 6.865205 GCGGGACTAGTATTTAATAACGTGAT 59.135 38.462 0.00 0.00 0.00 3.06
341 355 6.183360 TGCGGGACTAGTATTTAATAACGTGA 60.183 38.462 0.00 0.00 0.00 4.35
342 356 5.978919 TGCGGGACTAGTATTTAATAACGTG 59.021 40.000 0.00 0.00 0.00 4.49
343 357 6.147864 TGCGGGACTAGTATTTAATAACGT 57.852 37.500 0.00 0.00 0.00 3.99
344 358 7.010367 TGTTTGCGGGACTAGTATTTAATAACG 59.990 37.037 0.00 0.00 0.00 3.18
345 359 8.200364 TGTTTGCGGGACTAGTATTTAATAAC 57.800 34.615 0.00 0.00 0.00 1.89
346 360 7.496591 CCTGTTTGCGGGACTAGTATTTAATAA 59.503 37.037 0.00 0.00 43.97 1.40
347 361 6.987992 CCTGTTTGCGGGACTAGTATTTAATA 59.012 38.462 0.00 0.00 43.97 0.98
348 362 5.820947 CCTGTTTGCGGGACTAGTATTTAAT 59.179 40.000 0.00 0.00 43.97 1.40
349 363 5.046448 TCCTGTTTGCGGGACTAGTATTTAA 60.046 40.000 0.00 0.00 44.85 1.52
350 364 4.467082 TCCTGTTTGCGGGACTAGTATTTA 59.533 41.667 0.00 0.00 44.85 1.40
351 365 3.262405 TCCTGTTTGCGGGACTAGTATTT 59.738 43.478 0.00 0.00 44.85 1.40
352 366 2.835764 TCCTGTTTGCGGGACTAGTATT 59.164 45.455 0.00 0.00 44.85 1.89
353 367 2.463752 TCCTGTTTGCGGGACTAGTAT 58.536 47.619 0.00 0.00 44.85 2.12
364 378 2.033424 AGCGAAGTTTCTTCCTGTTTGC 59.967 45.455 4.28 1.65 0.00 3.68
381 395 3.550561 CGACAAAATTTTGCAGTAGCGA 58.449 40.909 26.94 0.00 46.23 4.93
417 431 1.961793 CCGTTGGAAAGTGAGGTCAA 58.038 50.000 0.00 0.00 0.00 3.18
486 500 6.514376 GCCACTCTCCGAAGTTTTCAAAATAA 60.514 38.462 0.00 0.00 0.00 1.40
508 522 3.195610 AGTCTAAGTCAACATCGATGCCA 59.804 43.478 25.11 6.38 0.00 4.92
514 528 4.029704 GCGACTAGTCTAAGTCAACATCG 58.970 47.826 20.34 4.51 45.13 3.84
593 608 6.641176 AAAGTCCAAAAACGTGTCATTTTC 57.359 33.333 0.00 0.00 0.00 2.29
596 611 6.699642 CCATTAAAGTCCAAAAACGTGTCATT 59.300 34.615 0.00 0.00 0.00 2.57
610 625 2.817844 AGTTGCGGAACCATTAAAGTCC 59.182 45.455 16.78 0.00 31.81 3.85
611 626 4.499037 AAGTTGCGGAACCATTAAAGTC 57.501 40.909 16.78 0.00 31.81 3.01
612 627 5.299782 TGTTAAGTTGCGGAACCATTAAAGT 59.700 36.000 16.78 0.00 31.81 2.66
613 628 5.764131 TGTTAAGTTGCGGAACCATTAAAG 58.236 37.500 16.78 0.00 31.81 1.85
614 629 5.769484 TGTTAAGTTGCGGAACCATTAAA 57.231 34.783 16.78 1.33 31.81 1.52
615 630 5.769484 TTGTTAAGTTGCGGAACCATTAA 57.231 34.783 16.78 12.37 31.81 1.40
616 631 5.106078 GGATTGTTAAGTTGCGGAACCATTA 60.106 40.000 16.78 6.79 31.81 1.90
617 632 4.321675 GGATTGTTAAGTTGCGGAACCATT 60.322 41.667 16.78 7.81 31.81 3.16
630 645 7.554118 ACCATATGAACACAGAGGATTGTTAAG 59.446 37.037 3.65 0.00 36.06 1.85
649 664 8.689251 ACGATATTTACGAAGATGACCATATG 57.311 34.615 0.00 0.00 34.70 1.78
676 691 5.422145 ACCGGGAATATGTTACAAGTGTAC 58.578 41.667 6.32 0.00 0.00 2.90
680 695 4.829872 TGACCGGGAATATGTTACAAGT 57.170 40.909 6.32 0.00 0.00 3.16
686 701 4.229304 TGACATTGACCGGGAATATGTT 57.771 40.909 6.32 0.00 30.14 2.71
696 711 4.327982 AGATCCTGTATGACATTGACCG 57.672 45.455 0.00 0.00 0.00 4.79
995 1013 2.680221 GCAGTGAATGTCAGCATCCTCT 60.680 50.000 0.00 0.00 33.50 3.69
1652 3545 1.587946 TGTCATCGATCATTTGTCGCG 59.412 47.619 0.00 0.00 38.88 5.87
1659 3552 4.449068 GCCGTTCTTATGTCATCGATCATT 59.551 41.667 5.05 0.00 0.00 2.57
1670 3563 1.077716 GCCAGGGCCGTTCTTATGT 60.078 57.895 0.00 0.00 34.56 2.29
1924 3817 0.043053 CTGTCACACAAGTTGTCGCG 60.043 55.000 5.27 0.00 35.67 5.87
1985 3882 6.203723 GTCCAATCTACATTAGAATCAGTGGC 59.796 42.308 0.00 0.00 38.50 5.01
1989 3886 8.970859 AAAGGTCCAATCTACATTAGAATCAG 57.029 34.615 0.00 0.00 38.50 2.90
1993 3890 8.383175 ACAGAAAAGGTCCAATCTACATTAGAA 58.617 33.333 0.00 0.00 38.50 2.10
2122 4050 1.068352 AGTCCAGGTCCTTGGCCTTT 61.068 55.000 3.32 0.00 34.19 3.11
2292 4231 7.099764 TCCTACAATTTCAGAGTGAGATTGAC 58.900 38.462 20.88 0.00 46.06 3.18
2629 4568 7.012232 CCAATGCTGTTTTGGTAAAATTCTGTT 59.988 33.333 0.00 0.00 39.05 3.16
3078 5424 1.878522 GACGTCGTAGCCATGCTGG 60.879 63.158 0.00 0.00 40.10 4.85
3140 5490 5.005779 GCGCTTCTCAAATTTCGAATCTAGA 59.994 40.000 0.00 0.00 0.00 2.43
3597 8676 4.097135 TGTTTCAATTCTCGGCAAACTTGA 59.903 37.500 0.00 0.00 0.00 3.02
3609 8688 7.405292 TCCAGATACATCCTTGTTTCAATTCT 58.595 34.615 0.00 0.00 36.58 2.40
3813 8894 5.049198 CACTCAATGTATGTCACTTTGCTGT 60.049 40.000 0.00 0.00 40.43 4.40
3899 12446 9.422681 GATGGTTATTACCTATAGAGCCTCATA 57.577 37.037 0.00 0.00 45.27 2.15
3962 12848 6.648725 GGCTACCATAAATTCTCTAGAAGCTG 59.351 42.308 0.00 0.00 37.48 4.24
3989 12999 7.591426 GTCAGAAACAAAGGTGTGACAAATATC 59.409 37.037 0.00 0.00 38.27 1.63
4083 13111 5.521906 TCGGGAGAGTCTTTGATATTCTG 57.478 43.478 0.00 0.00 0.00 3.02
4152 13182 6.325993 TGATTGAATTTGGGGATAGAGACA 57.674 37.500 0.00 0.00 0.00 3.41
4218 13615 6.099701 TGAAATACCACCTGTGCATATACTCT 59.900 38.462 0.00 0.00 0.00 3.24
4285 13682 7.512705 GCTGAAGCTAAGAAGTAAGCCTTCAA 61.513 42.308 5.02 0.00 43.89 2.69
4766 14307 2.609459 CTCGGATGAAACAATCCTTCCG 59.391 50.000 0.00 0.00 46.38 4.30
4782 14323 1.048601 AGGTTCAGTTTCTGCTCGGA 58.951 50.000 0.00 0.00 0.00 4.55
4832 14373 1.074405 AGCTTGTGGCAGATGGAAGAA 59.926 47.619 0.00 0.00 44.79 2.52
5018 14603 2.097825 GCATCTCCAAATCCACTTGCT 58.902 47.619 0.00 0.00 0.00 3.91
5169 14754 5.263599 ACATCCTGAAATATGACCTTTGCA 58.736 37.500 0.00 0.00 0.00 4.08
5352 14937 6.609616 TCATTTGGAACCTTGTTACCTTTCTT 59.390 34.615 0.00 0.00 0.00 2.52
5375 14960 5.616270 ACAACTTACACATGTACCATGTCA 58.384 37.500 6.88 0.00 0.00 3.58
5503 15112 9.911788 AGACATTTCAAATGGACTAGAACATAT 57.088 29.630 14.70 0.00 0.00 1.78
5533 15144 8.582891 ACTCCCTCCATTCCTAAATATAAGTT 57.417 34.615 0.00 0.00 0.00 2.66
5546 15157 4.694339 GTGTACATGTACTCCCTCCATTC 58.306 47.826 30.69 6.22 37.00 2.67
5549 15160 2.097036 CGTGTACATGTACTCCCTCCA 58.903 52.381 30.69 11.06 37.00 3.86
5550 15161 1.202382 GCGTGTACATGTACTCCCTCC 60.202 57.143 30.69 14.18 37.00 4.30
5623 15234 1.537202 GAGTCTTTGACATGCCACACC 59.463 52.381 0.00 0.00 34.60 4.16
5648 15331 5.057819 TCACTTTACAAGATTAACGTGCCA 58.942 37.500 0.00 0.00 33.40 4.92
5650 15333 7.901874 TTTTCACTTTACAAGATTAACGTGC 57.098 32.000 0.00 0.00 33.40 5.34
5658 15341 9.034544 GCAAATCACTTTTTCACTTTACAAGAT 57.965 29.630 0.00 0.00 0.00 2.40
5659 15342 7.491048 GGCAAATCACTTTTTCACTTTACAAGA 59.509 33.333 0.00 0.00 0.00 3.02
5748 15469 3.127030 GCTGCTTGCGGTTAGAAATACTT 59.873 43.478 3.26 0.00 0.00 2.24
5790 15511 5.275067 ACTTCCTCTCTCATGTTAGCATC 57.725 43.478 0.00 0.00 31.99 3.91
5838 15581 3.243002 CCGACTTAGGAACCGACTATGTC 60.243 52.174 0.00 0.00 39.92 3.06
5893 15637 7.442666 GGTTAGGAATAGAATTAGAGCACTTGG 59.557 40.741 0.00 0.00 0.00 3.61
5991 15880 5.936956 GCAGGATGAGGATTATACAAGAAGG 59.063 44.000 0.00 0.00 39.69 3.46
6006 15895 5.237561 CAGAAATGATCTCAAGCAGGATGAG 59.762 44.000 0.00 0.00 44.53 2.90


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

AutoCloner maintained by Alex Coulton.