Multiple sequence alignment - TraesCS7D01G514400

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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 TraesCS7D01G514400 chr7D 100.000 6579 0 0 1 6579 615467172 615460594 0.000000e+00 12150.0
1 TraesCS7D01G514400 chr7D 88.399 431 46 4 5093 5522 614703831 614704258 3.520000e-142 516.0
2 TraesCS7D01G514400 chr7D 77.273 528 70 24 1 522 2336728 2337211 1.410000e-66 265.0
3 TraesCS7D01G514400 chr7D 88.506 174 18 2 4930 5101 614702837 614703010 6.680000e-50 209.0
4 TraesCS7D01G514400 chr7D 88.571 140 16 0 2498 2637 615463026 615463165 3.150000e-38 171.0
5 TraesCS7D01G514400 chr7D 89.051 137 15 0 4008 4144 615464536 615464672 3.150000e-38 171.0
6 TraesCS7D01G514400 chr7D 95.146 103 4 1 5704 5805 618321362 618321464 1.900000e-35 161.0
7 TraesCS7D01G514400 chr7D 92.857 84 3 2 3363 3444 615463747 615463665 1.160000e-22 119.0
8 TraesCS7D01G514400 chr7D 92.857 84 3 2 3426 3508 615463810 615463729 1.160000e-22 119.0
9 TraesCS7D01G514400 chr7D 78.082 146 19 7 4009 4147 3596202 3596063 5.470000e-11 80.5
10 TraesCS7D01G514400 chr7D 100.000 28 0 0 2872 2899 554200370 554200343 1.200000e-02 52.8
11 TraesCS7D01G514400 chr1A 93.250 1674 56 22 2498 4144 557131551 557133194 0.000000e+00 2412.0
12 TraesCS7D01G514400 chr1A 81.057 454 66 13 1 439 339481877 339482325 1.760000e-90 344.0
13 TraesCS7D01G514400 chr1A 89.362 235 16 5 3099 3329 566468384 566468613 3.000000e-73 287.0
14 TraesCS7D01G514400 chr1A 83.268 257 30 4 3832 4077 566475156 566475410 2.390000e-54 224.0
15 TraesCS7D01G514400 chr1A 90.164 122 5 6 5707 5825 548772380 548772263 1.140000e-32 152.0
16 TraesCS7D01G514400 chr1A 93.902 82 4 1 3363 3444 557132467 557132547 8.960000e-24 122.0
17 TraesCS7D01G514400 chr1A 91.667 84 4 2 3426 3508 557132404 557132485 5.390000e-21 113.0
18 TraesCS7D01G514400 chr7B 88.591 2016 117 35 528 2497 708001346 707999398 0.000000e+00 2344.0
19 TraesCS7D01G514400 chr7B 99.360 781 4 1 4930 5709 707998596 707997816 0.000000e+00 1413.0
20 TraesCS7D01G514400 chr7B 98.855 786 7 1 4148 4933 707999406 707998623 0.000000e+00 1400.0
21 TraesCS7D01G514400 chr7B 96.888 482 13 2 6100 6579 707997410 707996929 0.000000e+00 806.0
22 TraesCS7D01G514400 chr7B 96.486 313 11 0 5789 6101 707997816 707997504 9.780000e-143 518.0
23 TraesCS7D01G514400 chr7B 81.818 484 53 21 1 455 256379878 256380355 2.240000e-99 374.0
24 TraesCS7D01G514400 chr7B 84.959 246 30 6 1 241 667293669 667293912 6.590000e-60 243.0
25 TraesCS7D01G514400 chr7B 80.243 329 51 3 6265 6579 712844769 712844441 1.100000e-57 235.0
26 TraesCS7D01G514400 chr7B 95.098 102 5 0 5700 5801 483787731 483787832 1.900000e-35 161.0
27 TraesCS7D01G514400 chr7B 83.108 148 15 5 2213 2356 708102590 708102449 6.930000e-25 126.0
28 TraesCS7D01G514400 chr7B 82.734 139 12 8 4557 4695 707958242 707958116 5.390000e-21 113.0
29 TraesCS7D01G514400 chr7B 93.333 45 2 1 3514 3558 525702577 525702620 1.530000e-06 65.8
30 TraesCS7D01G514400 chr7B 91.111 45 3 1 3514 3558 525625260 525625303 7.120000e-05 60.2
31 TraesCS7D01G514400 chr7A 88.441 1912 103 50 638 2470 707969599 707967727 0.000000e+00 2198.0
32 TraesCS7D01G514400 chr7A 94.381 783 36 7 4930 5709 707966767 707965990 0.000000e+00 1195.0
33 TraesCS7D01G514400 chr7A 91.625 800 40 15 4148 4933 707967722 707966936 0.000000e+00 1081.0
34 TraesCS7D01G514400 chr7A 94.882 508 21 4 6075 6579 707965734 707965229 0.000000e+00 789.0
35 TraesCS7D01G514400 chr7A 97.692 260 6 0 5789 6048 707965990 707965731 1.300000e-121 448.0
36 TraesCS7D01G514400 chr7A 82.803 314 38 12 7 310 610963895 610964202 3.910000e-67 267.0
37 TraesCS7D01G514400 chr7A 79.911 224 43 2 6333 6555 176986705 176986483 5.280000e-36 163.0
38 TraesCS7D01G514400 chr7A 85.938 128 14 3 523 647 707971556 707971430 4.140000e-27 134.0
39 TraesCS7D01G514400 chr7A 82.979 141 22 2 2498 2637 703096433 703096572 6.930000e-25 126.0
40 TraesCS7D01G514400 chr7A 95.082 61 2 1 4930 4989 707966909 707966849 1.950000e-15 95.3
41 TraesCS7D01G514400 chr5D 96.685 905 25 4 2953 3855 515677820 515676919 0.000000e+00 1500.0
42 TraesCS7D01G514400 chr5D 95.902 122 4 1 3959 4080 515676881 515676761 5.200000e-46 196.0
43 TraesCS7D01G514400 chr5D 93.204 103 5 2 5699 5799 551772454 551772352 4.110000e-32 150.0
44 TraesCS7D01G514400 chr5D 93.902 82 4 1 3363 3444 515677348 515677268 8.960000e-24 122.0
45 TraesCS7D01G514400 chr5D 86.111 108 5 9 2832 2932 526095994 526096098 2.510000e-19 108.0
46 TraesCS7D01G514400 chr5D 96.774 62 2 0 4079 4140 515676599 515676538 3.250000e-18 104.0
47 TraesCS7D01G514400 chr3D 88.937 461 37 4 3696 4144 11791294 11790836 2.070000e-154 556.0
48 TraesCS7D01G514400 chr3D 89.037 374 17 7 2816 3183 11792621 11792266 6.050000e-120 442.0
49 TraesCS7D01G514400 chr3D 95.473 243 9 1 3187 3429 11791956 11791716 2.880000e-103 387.0
50 TraesCS7D01G514400 chr3D 79.303 459 61 19 2483 2937 343317801 343317373 2.320000e-74 291.0
51 TraesCS7D01G514400 chr3D 92.398 171 11 1 3426 3596 11791457 11791289 6.590000e-60 243.0
52 TraesCS7D01G514400 chr3D 94.059 101 6 0 5704 5804 419904858 419904758 3.180000e-33 154.0
53 TraesCS7D01G514400 chr3D 77.434 226 31 14 313 522 544501730 544501951 4.170000e-22 117.0
54 TraesCS7D01G514400 chr2D 80.603 696 79 34 3429 4119 298291405 298290761 2.760000e-133 486.0
55 TraesCS7D01G514400 chr2D 85.000 440 45 9 2496 2934 298292317 298291898 1.700000e-115 427.0
56 TraesCS7D01G514400 chr2D 78.929 560 67 28 1 522 15108890 15108344 3.800000e-87 333.0
57 TraesCS7D01G514400 chr2D 81.955 399 53 10 2502 2897 351812315 351812697 2.960000e-83 320.0
58 TraesCS7D01G514400 chr2D 87.500 168 8 7 3286 3444 298291492 298291329 1.460000e-41 182.0
59 TraesCS7D01G514400 chr2B 79.886 701 77 36 3429 4116 363920733 363921382 7.780000e-124 455.0
60 TraesCS7D01G514400 chr2B 84.668 437 46 9 2496 2931 363919822 363920238 3.670000e-112 416.0
61 TraesCS7D01G514400 chr2B 80.633 537 63 26 4 522 487210267 487209754 1.730000e-100 377.0
62 TraesCS7D01G514400 chr2B 79.197 548 73 27 1 522 456054032 456053500 6.320000e-90 342.0
63 TraesCS7D01G514400 chr2B 79.197 548 73 27 1 522 456054895 456054363 6.320000e-90 342.0
64 TraesCS7D01G514400 chr2B 84.946 186 23 4 2524 2705 596083409 596083225 4.050000e-42 183.0
65 TraesCS7D01G514400 chr2B 80.749 187 21 8 349 522 46722219 46722035 1.490000e-26 132.0
66 TraesCS7D01G514400 chr2A 85.981 428 43 13 3427 3850 371336360 371335946 6.050000e-120 442.0
67 TraesCS7D01G514400 chr2A 84.545 440 47 9 2496 2934 371337314 371336895 3.670000e-112 416.0
68 TraesCS7D01G514400 chr2A 87.440 207 12 7 3248 3444 371336484 371336282 6.640000e-55 226.0
69 TraesCS7D01G514400 chr2A 88.732 142 15 1 4011 4151 371335830 371335689 8.770000e-39 172.0
70 TraesCS7D01G514400 chr1B 83.370 457 49 17 2531 2975 657163315 657163756 1.330000e-106 398.0
71 TraesCS7D01G514400 chr1B 80.674 564 61 25 1 522 549789742 549789185 1.720000e-105 394.0
72 TraesCS7D01G514400 chr1B 82.883 111 14 3 4008 4114 657163424 657163315 1.950000e-15 95.3
73 TraesCS7D01G514400 chr3A 80.674 564 61 25 1 522 351133539 351134096 1.720000e-105 394.0
74 TraesCS7D01G514400 chr3A 79.916 478 69 16 57 522 474414174 474413712 6.360000e-85 326.0
75 TraesCS7D01G514400 chr3A 81.481 162 25 4 3088 3249 657679748 657679904 1.930000e-25 128.0
76 TraesCS7D01G514400 chr3A 97.297 37 1 0 2512 2548 719135627 719135663 5.510000e-06 63.9
77 TraesCS7D01G514400 chr1D 80.488 533 67 21 1 516 362573566 362573054 2.240000e-99 374.0
78 TraesCS7D01G514400 chr1D 86.395 294 33 4 1 289 260985757 260985466 1.380000e-81 315.0
79 TraesCS7D01G514400 chr1D 77.155 232 30 17 313 526 234326598 234326824 5.390000e-21 113.0
80 TraesCS7D01G514400 chr6D 83.957 374 42 12 92 455 189424220 189424585 6.320000e-90 342.0
81 TraesCS7D01G514400 chr6D 89.375 160 14 3 3426 3584 439487955 439487798 1.450000e-46 198.0
82 TraesCS7D01G514400 chr6D 74.261 575 86 34 1 522 117554997 117555562 1.130000e-42 185.0
83 TraesCS7D01G514400 chr6D 87.302 126 11 4 2491 2614 439172297 439172419 8.900000e-29 139.0
84 TraesCS7D01G514400 chr4B 79.197 548 73 26 1 522 546639350 546638818 6.320000e-90 342.0
85 TraesCS7D01G514400 chr4B 78.723 188 24 11 349 522 574623029 574623214 1.940000e-20 111.0
86 TraesCS7D01G514400 chr3B 80.349 458 58 16 5 454 753958398 753958831 1.060000e-82 318.0
87 TraesCS7D01G514400 chr4D 78.676 544 67 20 1 522 208215509 208214993 3.830000e-82 316.0
88 TraesCS7D01G514400 chr4D 88.384 198 19 4 3 198 260715296 260715101 1.100000e-57 235.0
89 TraesCS7D01G514400 chr4D 80.000 330 44 15 6265 6579 393137294 393137616 2.390000e-54 224.0
90 TraesCS7D01G514400 chr4D 77.976 168 19 7 2652 2819 298907474 298907623 9.090000e-14 89.8
91 TraesCS7D01G514400 chr6B 78.188 298 53 11 6265 6555 421776487 421776195 5.240000e-41 180.0
92 TraesCS7D01G514400 chr4A 96.000 100 4 0 5700 5799 661959881 661959782 5.280000e-36 163.0
93 TraesCS7D01G514400 chr4A 95.050 101 3 2 5703 5803 422945196 422945098 2.460000e-34 158.0
94 TraesCS7D01G514400 chr6A 97.826 92 2 0 5704 5795 542602876 542602785 6.830000e-35 159.0
95 TraesCS7D01G514400 chr6A 79.000 200 26 12 349 534 29032935 29032738 8.960000e-24 122.0
96 TraesCS7D01G514400 chr5B 86.301 146 12 5 3248 3386 661120300 661120444 1.140000e-32 152.0
97 TraesCS7D01G514400 chr5A 88.983 118 9 3 5701 5815 641790209 641790093 6.880000e-30 143.0


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 TraesCS7D01G514400 chr7D 615460594 615467172 6578 True 4129.333333 12150 95.238000 1 6579 3 chr7D.!!$R3 6578
1 TraesCS7D01G514400 chr7D 614702837 614704258 1421 False 362.500000 516 88.452500 4930 5522 2 chr7D.!!$F3 592
2 TraesCS7D01G514400 chr1A 557131551 557133194 1643 False 882.333333 2412 92.939667 2498 4144 3 chr1A.!!$F4 1646
3 TraesCS7D01G514400 chr7B 707996929 708001346 4417 True 1296.200000 2344 96.036000 528 6579 5 chr7B.!!$R4 6051
4 TraesCS7D01G514400 chr7A 707965229 707971556 6327 True 848.614286 2198 92.577286 523 6579 7 chr7A.!!$R2 6056
5 TraesCS7D01G514400 chr5D 515676538 515677820 1282 True 480.500000 1500 95.815750 2953 4140 4 chr5D.!!$R2 1187
6 TraesCS7D01G514400 chr3D 11790836 11792621 1785 True 407.000000 556 91.461250 2816 4144 4 chr3D.!!$R3 1328
7 TraesCS7D01G514400 chr2D 298290761 298292317 1556 True 365.000000 486 84.367667 2496 4119 3 chr2D.!!$R2 1623
8 TraesCS7D01G514400 chr2D 15108344 15108890 546 True 333.000000 333 78.929000 1 522 1 chr2D.!!$R1 521
9 TraesCS7D01G514400 chr2B 363919822 363921382 1560 False 435.500000 455 82.277000 2496 4116 2 chr2B.!!$F1 1620
10 TraesCS7D01G514400 chr2B 487209754 487210267 513 True 377.000000 377 80.633000 4 522 1 chr2B.!!$R2 518
11 TraesCS7D01G514400 chr2B 456053500 456054895 1395 True 342.000000 342 79.197000 1 522 2 chr2B.!!$R4 521
12 TraesCS7D01G514400 chr2A 371335689 371337314 1625 True 314.000000 442 86.674500 2496 4151 4 chr2A.!!$R1 1655
13 TraesCS7D01G514400 chr1B 549789185 549789742 557 True 394.000000 394 80.674000 1 522 1 chr1B.!!$R1 521
14 TraesCS7D01G514400 chr3A 351133539 351134096 557 False 394.000000 394 80.674000 1 522 1 chr3A.!!$F1 521
15 TraesCS7D01G514400 chr1D 362573054 362573566 512 True 374.000000 374 80.488000 1 516 1 chr1D.!!$R2 515
16 TraesCS7D01G514400 chr4B 546638818 546639350 532 True 342.000000 342 79.197000 1 522 1 chr4B.!!$R1 521
17 TraesCS7D01G514400 chr4D 208214993 208215509 516 True 316.000000 316 78.676000 1 522 1 chr4D.!!$R1 521

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
543 1496 1.133823 TGTGCCGCCATGAGGAATTAT 60.134 47.619 10.78 0.00 36.89 1.28 F
821 3619 1.452145 ATTTTTCGCGCACCACCACT 61.452 50.000 8.75 0.00 0.00 4.00 F
1445 4286 0.034476 ATCATGCACGCGATCAGGAT 59.966 50.000 15.93 18.79 0.00 3.24 F
2343 5207 0.110678 CATCTGCTCCATGGAGGCAT 59.889 55.000 36.92 20.49 42.19 4.40 F
2688 5577 1.412710 TGTGAGTATCCCTTGGATCGC 59.587 52.381 0.00 0.00 42.11 4.58 F
2742 5631 1.599240 GGAGAATCATGCTCCGGGC 60.599 63.158 0.00 4.52 42.22 6.13 F
3863 7414 1.669760 GGTGCGTCCCGATGTTTCA 60.670 57.895 0.00 0.00 0.00 2.69 F
3873 7424 2.480419 CCCGATGTTTCAGTCAGTTGTC 59.520 50.000 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1347 4161 0.394938 TGGCAAAGCTGTAGGAACGA 59.605 50.000 0.00 0.0 0.00 3.85 R
1853 4713 0.788391 CCAAGAACCGTTACAGCGTC 59.212 55.000 0.00 0.0 0.00 5.19 R
2826 5715 1.596934 GAGGGAACGACATGGCTCA 59.403 57.895 0.00 0.0 0.00 4.26 R
3860 7411 0.596600 GGCGACGACAACTGACTGAA 60.597 55.000 0.00 0.0 0.00 3.02 R
4037 7599 1.070445 GTGGGATCCCTGAGCATCG 59.930 63.158 31.05 0.0 38.61 3.84 R
4144 7869 7.649533 TCATTTGCAAGATCTGAATAATGGT 57.350 32.000 15.29 0.0 0.00 3.55 R
4919 8806 5.090139 TGGGATATTGGGTCACAAAATTGT 58.910 37.500 0.00 0.0 43.46 2.71 R
5710 10462 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.0 34.63 4.20 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
108 110 6.713276 TGGAATTATATAACCCATACCCACG 58.287 40.000 12.16 0.00 0.00 4.94
200 210 8.816640 AATTTGTGAACTCAAAATGTATGACC 57.183 30.769 6.22 0.00 40.05 4.02
201 211 6.951062 TTGTGAACTCAAAATGTATGACCA 57.049 33.333 0.00 0.00 0.00 4.02
209 227 5.468592 TCAAAATGTATGACCATGTGTTGC 58.531 37.500 0.00 0.00 0.00 4.17
211 229 4.707030 AATGTATGACCATGTGTTGCTG 57.293 40.909 0.00 0.00 0.00 4.41
225 243 5.119694 TGTGTTGCTGTTTATGACTGTGTA 58.880 37.500 0.00 0.00 0.00 2.90
226 244 5.236263 TGTGTTGCTGTTTATGACTGTGTAG 59.764 40.000 0.00 0.00 0.00 2.74
250 268 6.070196 GTGTTGTTTTGATGTGTTGTTGTTG 58.930 36.000 0.00 0.00 0.00 3.33
252 270 6.258727 TGTTGTTTTGATGTGTTGTTGTTGTT 59.741 30.769 0.00 0.00 0.00 2.83
254 272 6.882072 TGTTTTGATGTGTTGTTGTTGTTTC 58.118 32.000 0.00 0.00 0.00 2.78
255 273 6.073548 TGTTTTGATGTGTTGTTGTTGTTTCC 60.074 34.615 0.00 0.00 0.00 3.13
352 427 8.627428 GCTGTTTATGATTACGAGTTTTTCAAC 58.373 33.333 0.00 0.00 0.00 3.18
393 468 3.785486 GGTAATTTTACCCGCGAGTACT 58.215 45.455 8.23 0.00 45.94 2.73
420 495 1.691196 CCTGTCGGGTAACGGGTATA 58.309 55.000 0.00 0.00 44.45 1.47
427 502 3.132111 TCGGGTAACGGGTATAGGAAAAC 59.868 47.826 0.00 0.00 44.45 2.43
431 508 4.877823 GGTAACGGGTATAGGAAAACTTGG 59.122 45.833 0.00 0.00 0.00 3.61
543 1496 1.133823 TGTGCCGCCATGAGGAATTAT 60.134 47.619 10.78 0.00 36.89 1.28
551 1504 4.142752 CGCCATGAGGAATTATGCACTATG 60.143 45.833 0.00 0.00 36.89 2.23
584 1539 3.296322 TTTCTGCGCCTTTTGGTTATG 57.704 42.857 4.18 0.00 42.99 1.90
624 1580 6.945938 TTCAAGGTATTTTTCGGTTCTCAA 57.054 33.333 0.00 0.00 0.00 3.02
628 1584 7.447238 TCAAGGTATTTTTCGGTTCTCAAAGAT 59.553 33.333 0.00 0.00 0.00 2.40
631 1587 7.021790 GGTATTTTTCGGTTCTCAAAGATGTC 58.978 38.462 0.00 0.00 0.00 3.06
661 3459 8.268878 AGACATAAGCAATTTATACTCCCTCT 57.731 34.615 0.00 0.00 30.75 3.69
665 3463 6.567602 AAGCAATTTATACTCCCTCTGTCT 57.432 37.500 0.00 0.00 0.00 3.41
678 3476 6.841229 ACTCCCTCTGTCTCATAATATGACAA 59.159 38.462 0.00 0.00 39.74 3.18
699 3497 9.897744 TGACAATGTTATAGCAGAAAAGAAAAG 57.102 29.630 0.00 0.00 0.00 2.27
772 3570 9.229784 CAAAAGAAATGAGATAACGATTGATGG 57.770 33.333 0.00 0.00 0.00 3.51
821 3619 1.452145 ATTTTTCGCGCACCACCACT 61.452 50.000 8.75 0.00 0.00 4.00
903 3702 9.860898 AAATAGATTTTACAGTGGATGCTTTTC 57.139 29.630 0.00 0.00 0.00 2.29
904 3703 6.899393 AGATTTTACAGTGGATGCTTTTCA 57.101 33.333 0.00 0.00 0.00 2.69
905 3704 7.472334 AGATTTTACAGTGGATGCTTTTCAT 57.528 32.000 0.00 0.00 38.32 2.57
938 3738 4.220602 AGAAATAGCACCAAATTCACCCAC 59.779 41.667 0.00 0.00 0.00 4.61
985 3785 4.405680 ACCAAGGGGACAAGAAAAGAAAAG 59.594 41.667 0.00 0.00 38.05 2.27
988 3788 6.351796 CCAAGGGGACAAGAAAAGAAAAGAAA 60.352 38.462 0.00 0.00 35.59 2.52
989 3789 6.867519 AGGGGACAAGAAAAGAAAAGAAAA 57.132 33.333 0.00 0.00 0.00 2.29
991 3791 7.103641 AGGGGACAAGAAAAGAAAAGAAAAAC 58.896 34.615 0.00 0.00 0.00 2.43
994 3794 8.227791 GGGACAAGAAAAGAAAAGAAAAACAAC 58.772 33.333 0.00 0.00 0.00 3.32
996 3796 7.792925 ACAAGAAAAGAAAAGAAAAACAACCG 58.207 30.769 0.00 0.00 0.00 4.44
998 3798 6.163476 AGAAAAGAAAAGAAAAACAACCGCT 58.837 32.000 0.00 0.00 0.00 5.52
999 3799 5.778161 AAAGAAAAGAAAAACAACCGCTG 57.222 34.783 0.00 0.00 0.00 5.18
1352 4166 3.839432 CGCCCTCCCCTCTCGTTC 61.839 72.222 0.00 0.00 0.00 3.95
1371 4185 1.974957 TCCTACAGCTTTGCCACTGTA 59.025 47.619 3.15 3.15 45.09 2.74
1372 4186 2.571653 TCCTACAGCTTTGCCACTGTAT 59.428 45.455 3.55 0.00 45.63 2.29
1373 4187 2.939103 CCTACAGCTTTGCCACTGTATC 59.061 50.000 3.55 0.00 45.63 2.24
1403 4244 4.594970 TGGTAGTAAATTGGTGATGGTGG 58.405 43.478 0.00 0.00 0.00 4.61
1407 4248 2.692709 AAATTGGTGATGGTGGTGGA 57.307 45.000 0.00 0.00 0.00 4.02
1445 4286 0.034476 ATCATGCACGCGATCAGGAT 59.966 50.000 15.93 18.79 0.00 3.24
1615 4475 1.534476 TGTCAGAGCCGGTGGGTTA 60.534 57.895 1.90 0.00 31.55 2.85
1626 4486 3.423749 CCGGTGGGTTAGGTAAATGTTT 58.576 45.455 0.00 0.00 0.00 2.83
1627 4487 3.191791 CCGGTGGGTTAGGTAAATGTTTG 59.808 47.826 0.00 0.00 0.00 2.93
1662 4522 3.979495 GCTCTGTTCTGAAAGCATGTTTG 59.021 43.478 7.50 0.00 34.86 2.93
1682 4542 7.708998 TGTTTGTCATGGAAACTAACTTTACC 58.291 34.615 17.06 0.00 34.72 2.85
1683 4543 7.339721 TGTTTGTCATGGAAACTAACTTTACCA 59.660 33.333 17.06 0.00 34.72 3.25
1684 4544 7.883391 TTGTCATGGAAACTAACTTTACCAA 57.117 32.000 0.00 0.00 0.00 3.67
1685 4545 7.504924 TGTCATGGAAACTAACTTTACCAAG 57.495 36.000 0.00 0.00 35.92 3.61
1686 4546 6.016610 TGTCATGGAAACTAACTTTACCAAGC 60.017 38.462 0.00 0.00 32.57 4.01
1687 4547 6.016610 GTCATGGAAACTAACTTTACCAAGCA 60.017 38.462 0.00 0.00 32.57 3.91
1688 4548 6.206634 TCATGGAAACTAACTTTACCAAGCAG 59.793 38.462 0.00 0.00 32.57 4.24
1689 4549 5.686753 TGGAAACTAACTTTACCAAGCAGA 58.313 37.500 0.00 0.00 32.57 4.26
1692 4552 7.286775 TGGAAACTAACTTTACCAAGCAGATTT 59.713 33.333 0.00 0.00 32.57 2.17
1698 4558 6.648879 ACTTTACCAAGCAGATTTAAAGCA 57.351 33.333 6.19 0.00 34.47 3.91
1729 4589 8.074972 ACGATGAGTAAATTATCTCGGAACTAC 58.925 37.037 0.00 0.00 33.88 2.73
1730 4590 8.074370 CGATGAGTAAATTATCTCGGAACTACA 58.926 37.037 5.67 0.00 33.88 2.74
1731 4591 9.915629 GATGAGTAAATTATCTCGGAACTACAT 57.084 33.333 5.67 0.00 33.88 2.29
1745 4605 7.952671 TCGGAACTACATATAAGAATTGCTCT 58.047 34.615 0.00 0.00 35.13 4.09
1747 4607 9.862371 CGGAACTACATATAAGAATTGCTCTAT 57.138 33.333 0.00 0.00 32.46 1.98
1863 4723 0.974836 GCAATTTGCGACGCTGTAAC 59.025 50.000 22.08 2.53 31.71 2.50
1872 4732 0.788391 GACGCTGTAACGGTTCTTGG 59.212 55.000 0.00 0.00 37.37 3.61
2001 4863 4.082354 AGCAGAACTTGAAATTCCTGATGC 60.082 41.667 0.00 0.00 0.00 3.91
2008 4870 7.565323 ACTTGAAATTCCTGATGCTAGAATC 57.435 36.000 3.43 3.43 30.06 2.52
2039 4901 3.959535 ACTTATGGTGCCATTGGTTTG 57.040 42.857 9.19 0.00 37.82 2.93
2343 5207 0.110678 CATCTGCTCCATGGAGGCAT 59.889 55.000 36.92 20.49 42.19 4.40
2571 5460 5.478332 ACGTGAGCCATCAGATCTATAATGA 59.522 40.000 11.56 0.00 35.66 2.57
2594 5483 3.139077 CGCCATAGATTAAAGGTGGGAC 58.861 50.000 0.00 0.00 0.00 4.46
2688 5577 1.412710 TGTGAGTATCCCTTGGATCGC 59.587 52.381 0.00 0.00 42.11 4.58
2705 5594 2.876091 TCGCTTCACGTTCCAATCTAG 58.124 47.619 0.00 0.00 44.19 2.43
2716 5605 4.919168 CGTTCCAATCTAGTACGTCACAAA 59.081 41.667 0.00 0.00 0.00 2.83
2717 5606 5.575606 CGTTCCAATCTAGTACGTCACAAAT 59.424 40.000 0.00 0.00 0.00 2.32
2718 5607 6.237490 CGTTCCAATCTAGTACGTCACAAATC 60.237 42.308 0.00 0.00 0.00 2.17
2719 5608 6.275494 TCCAATCTAGTACGTCACAAATCA 57.725 37.500 0.00 0.00 0.00 2.57
2720 5609 6.097356 TCCAATCTAGTACGTCACAAATCAC 58.903 40.000 0.00 0.00 0.00 3.06
2721 5610 5.867174 CCAATCTAGTACGTCACAAATCACA 59.133 40.000 0.00 0.00 0.00 3.58
2722 5611 6.367695 CCAATCTAGTACGTCACAAATCACAA 59.632 38.462 0.00 0.00 0.00 3.33
2732 5621 5.106594 CGTCACAAATCACAATGGAGAATCA 60.107 40.000 0.00 0.00 36.25 2.57
2735 5624 5.518847 CACAAATCACAATGGAGAATCATGC 59.481 40.000 0.00 0.00 36.25 4.06
2736 5625 5.421056 ACAAATCACAATGGAGAATCATGCT 59.579 36.000 0.00 0.00 36.25 3.79
2737 5626 5.769484 AATCACAATGGAGAATCATGCTC 57.231 39.130 0.00 0.00 36.25 4.26
2741 5630 4.787871 GGAGAATCATGCTCCGGG 57.212 61.111 0.00 0.00 42.22 5.73
2742 5631 1.599240 GGAGAATCATGCTCCGGGC 60.599 63.158 0.00 4.52 42.22 6.13
2826 5715 2.920912 TTCCTCCGGTGGCGACTT 60.921 61.111 18.03 0.00 0.00 3.01
2899 5788 4.113815 CGAGCCATGCCCTTCCCA 62.114 66.667 0.00 0.00 0.00 4.37
2900 5789 2.360191 GAGCCATGCCCTTCCCAA 59.640 61.111 0.00 0.00 0.00 4.12
2934 5824 4.383861 CCTCTGTCGGCTGCTGCA 62.384 66.667 17.89 0.88 41.91 4.41
3118 6030 6.791303 ACAAGTTCGTGTGTTACATGATTTT 58.209 32.000 0.00 1.24 43.00 1.82
3157 6069 8.748412 TGTGCCAATATTTTATTAAGCTGAAGT 58.252 29.630 0.00 0.00 0.00 3.01
3288 6551 3.973206 ATCACCACCGAACAGTAATCA 57.027 42.857 0.00 0.00 0.00 2.57
3488 7021 4.779489 TCAGAGAAATTGGATCACTGAGGA 59.221 41.667 0.00 0.00 38.86 3.71
3489 7022 5.105023 TCAGAGAAATTGGATCACTGAGGAG 60.105 44.000 0.00 0.00 38.86 3.69
3592 7134 2.585247 GTGATGGACGCGGCTACC 60.585 66.667 13.91 0.00 0.00 3.18
3616 7158 3.918977 TCACACCCACCGTCACCG 61.919 66.667 0.00 0.00 0.00 4.94
3860 7411 2.358247 GTGGTGCGTCCCGATGTT 60.358 61.111 0.00 0.00 34.77 2.71
3863 7414 1.669760 GGTGCGTCCCGATGTTTCA 60.670 57.895 0.00 0.00 0.00 2.69
3873 7424 2.480419 CCCGATGTTTCAGTCAGTTGTC 59.520 50.000 0.00 0.00 0.00 3.18
3990 7552 2.667969 GGCAATCCTCAAACGATTTTGC 59.332 45.455 3.87 3.87 41.78 3.68
4037 7599 7.216881 GGGTTATTTGTTAATCGCGTTTAAGTC 59.783 37.037 19.72 11.46 0.00 3.01
4144 7869 8.463930 AAAAGACATTTTCACTGGATACTTCA 57.536 30.769 0.00 0.00 33.21 3.02
4148 7873 6.248433 ACATTTTCACTGGATACTTCACCAT 58.752 36.000 0.00 0.00 35.54 3.55
4229 7955 7.902920 AGCAGGAACCATAATTTACATGATT 57.097 32.000 0.00 0.00 0.00 2.57
4230 7956 8.995027 AGCAGGAACCATAATTTACATGATTA 57.005 30.769 0.00 0.00 0.00 1.75
5663 10415 5.001232 ACAACACTTATAAAGACGCCATGT 58.999 37.500 0.00 0.00 0.00 3.21
5714 10466 8.911018 TTATGGCTACATATTATGTACTCCCT 57.089 34.615 11.64 10.85 44.38 4.20
5715 10467 6.852420 TGGCTACATATTATGTACTCCCTC 57.148 41.667 11.64 1.46 44.38 4.30
5716 10468 5.720041 TGGCTACATATTATGTACTCCCTCC 59.280 44.000 11.64 7.54 44.38 4.30
5717 10469 5.163540 GGCTACATATTATGTACTCCCTCCG 60.164 48.000 11.64 2.80 44.38 4.63
5718 10470 5.418209 GCTACATATTATGTACTCCCTCCGT 59.582 44.000 11.64 0.00 44.38 4.69
5719 10471 6.600822 GCTACATATTATGTACTCCCTCCGTA 59.399 42.308 11.64 0.00 44.38 4.02
5720 10472 7.121759 GCTACATATTATGTACTCCCTCCGTAA 59.878 40.741 11.64 0.00 44.38 3.18
5721 10473 7.844493 ACATATTATGTACTCCCTCCGTAAA 57.156 36.000 7.55 0.00 42.78 2.01
5722 10474 7.664758 ACATATTATGTACTCCCTCCGTAAAC 58.335 38.462 7.55 0.00 42.78 2.01
5723 10475 7.508296 ACATATTATGTACTCCCTCCGTAAACT 59.492 37.037 7.55 0.00 42.78 2.66
5724 10476 9.017509 CATATTATGTACTCCCTCCGTAAACTA 57.982 37.037 0.00 0.00 0.00 2.24
5725 10477 7.902920 ATTATGTACTCCCTCCGTAAACTAA 57.097 36.000 0.00 0.00 0.00 2.24
5726 10478 7.902920 TTATGTACTCCCTCCGTAAACTAAT 57.097 36.000 0.00 0.00 0.00 1.73
5727 10479 8.995027 TTATGTACTCCCTCCGTAAACTAATA 57.005 34.615 0.00 0.00 0.00 0.98
5728 10480 9.592196 TTATGTACTCCCTCCGTAAACTAATAT 57.408 33.333 0.00 0.00 0.00 1.28
5730 10482 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
5731 10483 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
5732 10484 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
5733 10485 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
5734 10486 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
5735 10487 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
5736 10488 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
5737 10489 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
5738 10490 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
5739 10491 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
5740 10492 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
5741 10493 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
5755 10507 9.570488 AAGAGCGTTTAGATTACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
5756 10508 8.954350 AGAGCGTTTAGATTACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
5757 10509 9.733219 GAGCGTTTAGATTACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
5758 10510 9.733219 AGCGTTTAGATTACTAAAGTAGTGATC 57.267 33.333 10.62 10.62 46.38 2.92
5766 10518 9.733219 GATTACTAAAGTAGTGATCTAAACGCT 57.267 33.333 11.11 0.00 44.10 5.07
5768 10520 9.918630 TTACTAAAGTAGTGATCTAAACGCTTT 57.081 29.630 0.00 3.97 39.81 3.51
5769 10521 8.828688 ACTAAAGTAGTGATCTAAACGCTTTT 57.171 30.769 10.23 0.00 37.69 2.27
5770 10522 9.918630 ACTAAAGTAGTGATCTAAACGCTTTTA 57.081 29.630 10.23 0.00 37.69 1.52
5787 10539 8.658499 ACGCTTTTATATTAGTTTACAGAGGG 57.342 34.615 0.00 0.00 0.00 4.30
5863 10615 3.992643 AGAGACTGCATATGACATCAGC 58.007 45.455 6.97 0.00 0.00 4.26
5972 10724 4.384846 CGTTTGTAGAAGAATGTACGTGCT 59.615 41.667 4.97 0.00 0.00 4.40
6012 10764 1.001181 GAGTGTGTGCATGCCCAAAAT 59.999 47.619 16.68 3.54 0.00 1.82
6075 10827 4.570874 GATGGGGAAGAGGCGGCC 62.571 72.222 12.11 12.11 0.00 6.13
6094 10846 2.841215 CCGTTGTTCTTCCCAACTACA 58.159 47.619 0.00 0.00 39.98 2.74
6184 11032 5.661056 TTCTACCTAGTCCAAGTGTCATG 57.339 43.478 0.00 0.00 0.00 3.07
6295 11144 7.884816 TGCAACACTAAGTAACTCTACAATC 57.115 36.000 0.00 0.00 0.00 2.67
6381 11230 9.317936 CAGTAAGCAATAGTTCACAAGATCATA 57.682 33.333 0.00 0.00 0.00 2.15
6384 11233 8.743085 AAGCAATAGTTCACAAGATCATATGT 57.257 30.769 1.90 0.00 0.00 2.29
6424 11273 8.947055 ACTTGTTTTTCACTAAATTCATTGCT 57.053 26.923 0.00 0.00 0.00 3.91
6544 11394 9.708092 CTTCAATCAAGCATAATAGAGAGATCA 57.292 33.333 0.00 0.00 0.00 2.92
6551 11401 9.887629 CAAGCATAATAGAGAGATCACCAATAT 57.112 33.333 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 89 7.311234 GGGTACGTGGGTATGGGTTATATAATT 60.311 40.741 0.00 0.00 0.00 1.40
90 92 5.022787 GGGTACGTGGGTATGGGTTATATA 58.977 45.833 0.00 0.00 0.00 0.86
174 184 9.260002 GGTCATACATTTTGAGTTCACAAATTT 57.740 29.630 0.00 0.00 39.09 1.82
199 209 4.022935 ACAGTCATAAACAGCAACACATGG 60.023 41.667 0.00 0.00 0.00 3.66
200 210 4.913345 CACAGTCATAAACAGCAACACATG 59.087 41.667 0.00 0.00 0.00 3.21
201 211 4.580167 ACACAGTCATAAACAGCAACACAT 59.420 37.500 0.00 0.00 0.00 3.21
209 227 6.844696 ACAACACTACACAGTCATAAACAG 57.155 37.500 0.00 0.00 30.46 3.16
211 229 8.178964 TCAAAACAACACTACACAGTCATAAAC 58.821 33.333 0.00 0.00 30.46 2.01
225 243 5.537188 ACAACAACACATCAAAACAACACT 58.463 33.333 0.00 0.00 0.00 3.55
226 244 5.837586 ACAACAACACATCAAAACAACAC 57.162 34.783 0.00 0.00 0.00 3.32
250 268 9.620660 ACATTTAATAAACAACATCTCGGAAAC 57.379 29.630 0.00 0.00 0.00 2.78
252 270 8.788806 ACACATTTAATAAACAACATCTCGGAA 58.211 29.630 0.00 0.00 0.00 4.30
254 272 8.849490 CAACACATTTAATAAACAACATCTCGG 58.151 33.333 0.00 0.00 0.00 4.63
255 273 9.393249 ACAACACATTTAATAAACAACATCTCG 57.607 29.630 0.00 0.00 0.00 4.04
322 395 7.435068 AAACTCGTAATCATAAACAGCAACT 57.565 32.000 0.00 0.00 0.00 3.16
340 413 5.555069 GCAAAGCATCAAGTTGAAAAACTCG 60.555 40.000 10.14 0.00 31.53 4.18
352 427 2.739913 CCCATGTTTGCAAAGCATCAAG 59.260 45.455 13.26 4.02 44.89 3.02
420 495 1.213430 TCAACGGGTCCAAGTTTTCCT 59.787 47.619 0.00 0.00 0.00 3.36
449 526 1.224592 CGCCCCCATTGAGCTTACT 59.775 57.895 0.00 0.00 0.00 2.24
460 550 3.350621 ATACCCTTACCCGCCCCCA 62.351 63.158 0.00 0.00 0.00 4.96
492 1445 2.279918 CGCAGGGTATGGGTACGC 60.280 66.667 2.35 2.35 42.36 4.42
565 1520 2.227865 GACATAACCAAAAGGCGCAGAA 59.772 45.455 10.83 0.00 0.00 3.02
566 1521 1.810151 GACATAACCAAAAGGCGCAGA 59.190 47.619 10.83 0.00 0.00 4.26
578 1533 8.995220 TGAATATAAAAGCCATACGACATAACC 58.005 33.333 0.00 0.00 0.00 2.85
584 1539 7.492352 ACCTTGAATATAAAAGCCATACGAC 57.508 36.000 0.00 0.00 0.00 4.34
643 3439 5.663106 TGAGACAGAGGGAGTATAAATTGCT 59.337 40.000 0.00 0.00 0.00 3.91
821 3619 5.538053 TGTCCAGTGGAAAAAGATATTTGCA 59.462 36.000 15.09 0.00 38.14 4.08
903 3702 7.034685 TGGTGCTATTTCTTTCATCATGATG 57.965 36.000 26.79 26.79 40.09 3.07
904 3703 7.649533 TTGGTGCTATTTCTTTCATCATGAT 57.350 32.000 1.18 1.18 0.00 2.45
905 3704 7.465353 TTTGGTGCTATTTCTTTCATCATGA 57.535 32.000 0.00 0.00 0.00 3.07
909 3708 7.276438 GGTGAATTTGGTGCTATTTCTTTCATC 59.724 37.037 0.00 0.00 0.00 2.92
923 3722 4.881019 TTATTGGTGGGTGAATTTGGTG 57.119 40.909 0.00 0.00 0.00 4.17
925 3724 6.939163 TGAATTTTATTGGTGGGTGAATTTGG 59.061 34.615 0.00 0.00 0.00 3.28
938 3738 5.720371 TGTGTGGGTCTGAATTTTATTGG 57.280 39.130 0.00 0.00 0.00 3.16
1306 4120 0.112025 TGTGGGTGATGATGTGGCAA 59.888 50.000 0.00 0.00 0.00 4.52
1337 4151 0.756070 GTAGGAACGAGAGGGGAGGG 60.756 65.000 0.00 0.00 0.00 4.30
1347 4161 0.394938 TGGCAAAGCTGTAGGAACGA 59.605 50.000 0.00 0.00 0.00 3.85
1348 4162 0.517316 GTGGCAAAGCTGTAGGAACG 59.483 55.000 0.00 0.00 0.00 3.95
1349 4163 1.537202 CAGTGGCAAAGCTGTAGGAAC 59.463 52.381 0.00 0.00 0.00 3.62
1350 4164 1.142870 ACAGTGGCAAAGCTGTAGGAA 59.857 47.619 7.40 0.00 43.30 3.36
1351 4165 0.764890 ACAGTGGCAAAGCTGTAGGA 59.235 50.000 7.40 0.00 43.30 2.94
1352 4166 2.472695 TACAGTGGCAAAGCTGTAGG 57.527 50.000 11.21 0.00 43.30 3.18
1371 4185 8.333235 TCACCAATTTACTACCATACCAAAGAT 58.667 33.333 0.00 0.00 0.00 2.40
1372 4186 7.691213 TCACCAATTTACTACCATACCAAAGA 58.309 34.615 0.00 0.00 0.00 2.52
1373 4187 7.931578 TCACCAATTTACTACCATACCAAAG 57.068 36.000 0.00 0.00 0.00 2.77
1403 4244 2.224018 TGCAAAACAGCCAAGAATCCAC 60.224 45.455 0.00 0.00 0.00 4.02
1407 4248 3.575256 TGATCTGCAAAACAGCCAAGAAT 59.425 39.130 0.00 0.00 46.76 2.40
1455 4296 2.032681 AGGCCGCACTTGAACTCC 59.967 61.111 0.00 0.00 0.00 3.85
1564 4420 8.129211 AGCGCCATAAAACTTACTGATAATTTC 58.871 33.333 2.29 0.00 0.00 2.17
1615 4475 4.040217 TCCAATGCAAGCAAACATTTACCT 59.960 37.500 0.00 0.00 34.32 3.08
1627 4487 0.886563 ACAGAGCTTCCAATGCAAGC 59.113 50.000 0.00 0.00 45.71 4.01
1662 4522 6.016610 TGCTTGGTAAAGTTAGTTTCCATGAC 60.017 38.462 14.63 0.00 35.69 3.06
1676 4536 8.538409 AAATGCTTTAAATCTGCTTGGTAAAG 57.462 30.769 0.00 0.00 35.71 1.85
1677 4537 9.988815 TTAAATGCTTTAAATCTGCTTGGTAAA 57.011 25.926 0.00 0.00 32.53 2.01
1678 4538 9.418045 GTTAAATGCTTTAAATCTGCTTGGTAA 57.582 29.630 0.00 0.00 36.91 2.85
1679 4539 7.753132 CGTTAAATGCTTTAAATCTGCTTGGTA 59.247 33.333 0.00 0.00 36.91 3.25
1680 4540 6.586082 CGTTAAATGCTTTAAATCTGCTTGGT 59.414 34.615 0.00 0.00 36.91 3.67
1681 4541 6.806249 TCGTTAAATGCTTTAAATCTGCTTGG 59.194 34.615 0.00 0.00 36.91 3.61
1682 4542 7.795431 TCGTTAAATGCTTTAAATCTGCTTG 57.205 32.000 0.00 0.00 36.91 4.01
1683 4543 8.243426 TCATCGTTAAATGCTTTAAATCTGCTT 58.757 29.630 0.00 0.00 36.91 3.91
1684 4544 7.761409 TCATCGTTAAATGCTTTAAATCTGCT 58.239 30.769 0.00 0.00 36.91 4.24
1685 4545 7.698130 ACTCATCGTTAAATGCTTTAAATCTGC 59.302 33.333 0.00 0.00 36.91 4.26
1698 4558 9.976511 TCCGAGATAATTTACTCATCGTTAAAT 57.023 29.630 10.60 0.00 33.86 1.40
1732 4592 9.512588 CCCAATTCTACATAGAGCAATTCTTAT 57.487 33.333 0.00 0.00 37.36 1.73
1745 4605 9.645128 AATGTGATGATTTCCCAATTCTACATA 57.355 29.630 0.00 0.00 0.00 2.29
1747 4607 7.959658 AATGTGATGATTTCCCAATTCTACA 57.040 32.000 0.00 0.00 0.00 2.74
1853 4713 0.788391 CCAAGAACCGTTACAGCGTC 59.212 55.000 0.00 0.00 0.00 5.19
1854 4714 1.226030 GCCAAGAACCGTTACAGCGT 61.226 55.000 0.00 0.00 0.00 5.07
1863 4723 1.626654 CTACGCACAGCCAAGAACCG 61.627 60.000 0.00 0.00 0.00 4.44
1872 4732 2.351726 CCTAATTTGACCTACGCACAGC 59.648 50.000 0.00 0.00 0.00 4.40
1948 4808 3.462982 ACTGTACATTTTGTGCACTCGA 58.537 40.909 19.41 3.67 38.04 4.04
1949 4809 3.878086 ACTGTACATTTTGTGCACTCG 57.122 42.857 19.41 4.30 38.04 4.18
2001 4863 7.032580 CCATAAGTTCTGCGGATAGATTCTAG 58.967 42.308 0.00 0.00 0.00 2.43
2008 4870 2.802816 GCACCATAAGTTCTGCGGATAG 59.197 50.000 0.00 0.00 0.00 2.08
2039 4901 6.367422 CAGATACTCTCACTTCACTCAAAACC 59.633 42.308 0.00 0.00 0.00 3.27
2118 4981 4.143030 GCACTGCAGAGCATATATAAACCG 60.143 45.833 28.20 0.00 38.13 4.44
2280 5144 9.303116 GACAGAGATTAGGAGACCAATCTAATA 57.697 37.037 11.99 0.00 40.68 0.98
2343 5207 4.431378 TCAGACCCTAACCTTCAATGGTA 58.569 43.478 0.00 0.00 39.83 3.25
2396 5285 3.183172 GTGCAGCAGTATACATGACGATG 59.817 47.826 5.50 0.00 35.49 3.84
2490 5379 4.346709 TCATTGGATACTTCGCCCTGAATA 59.653 41.667 0.00 0.00 35.63 1.75
2491 5380 3.136443 TCATTGGATACTTCGCCCTGAAT 59.864 43.478 0.00 0.00 35.63 2.57
2492 5381 2.503765 TCATTGGATACTTCGCCCTGAA 59.496 45.455 0.00 0.00 34.74 3.02
2493 5382 2.115427 TCATTGGATACTTCGCCCTGA 58.885 47.619 0.00 0.00 37.61 3.86
2494 5383 2.620251 TCATTGGATACTTCGCCCTG 57.380 50.000 0.00 0.00 37.61 4.45
2571 5460 3.201266 TCCCACCTTTAATCTATGGCGTT 59.799 43.478 0.00 0.00 0.00 4.84
2594 5483 4.883585 TGCATTTAAGTGGATGCTTAGGAG 59.116 41.667 10.37 0.00 46.68 3.69
2627 5516 4.788925 TGATGGATAAGTTAGGGGGTTG 57.211 45.455 0.00 0.00 0.00 3.77
2688 5577 4.730657 ACGTACTAGATTGGAACGTGAAG 58.269 43.478 0.00 0.00 44.34 3.02
2705 5594 4.688879 TCTCCATTGTGATTTGTGACGTAC 59.311 41.667 0.00 0.00 0.00 3.67
2741 5630 3.279875 CTAATGGCCGCCGGAAGC 61.280 66.667 7.68 6.62 38.52 3.86
2742 5631 1.887707 GACTAATGGCCGCCGGAAG 60.888 63.158 7.68 4.10 0.00 3.46
2826 5715 1.596934 GAGGGAACGACATGGCTCA 59.403 57.895 0.00 0.00 0.00 4.26
2934 5824 5.010719 TGAGTAATCTGAAGGTTGAGACGTT 59.989 40.000 0.00 0.00 36.64 3.99
3157 6069 9.862371 TTAACATCTTTGTAAAGTTTTGCAGAA 57.138 25.926 0.00 0.00 37.31 3.02
3267 6530 5.128008 TGATGATTACTGTTCGGTGGTGATA 59.872 40.000 0.00 0.00 0.00 2.15
3288 6551 3.826729 GCAACTCCCCTGTAGTTTTTGAT 59.173 43.478 0.00 0.00 34.99 2.57
3592 7134 2.281761 GGTGGGTGTGACCTGCAG 60.282 66.667 6.78 6.78 38.64 4.41
3616 7158 2.757099 CACCAAGCTGATGCCCCC 60.757 66.667 0.00 0.00 40.80 5.40
3619 7161 3.455469 GGCCACCAAGCTGATGCC 61.455 66.667 0.00 0.00 40.80 4.40
3823 7374 1.098869 GTCAGAGCTCCGTCTCATCA 58.901 55.000 10.93 0.00 35.59 3.07
3855 7406 3.121328 CGACGACAACTGACTGAAACATC 60.121 47.826 0.00 0.00 0.00 3.06
3856 7407 2.794910 CGACGACAACTGACTGAAACAT 59.205 45.455 0.00 0.00 0.00 2.71
3860 7411 0.596600 GGCGACGACAACTGACTGAA 60.597 55.000 0.00 0.00 0.00 3.02
3948 7499 1.246056 TACCCAACTCTCCCACGTCG 61.246 60.000 0.00 0.00 0.00 5.12
3990 7552 5.484290 ACCCCCTATTCTCGTAATGATTAGG 59.516 44.000 0.00 0.00 37.33 2.69
4037 7599 1.070445 GTGGGATCCCTGAGCATCG 59.930 63.158 31.05 0.00 38.61 3.84
4144 7869 7.649533 TCATTTGCAAGATCTGAATAATGGT 57.350 32.000 15.29 0.00 0.00 3.55
4148 7873 8.741841 TGTGATTCATTTGCAAGATCTGAATAA 58.258 29.630 19.65 14.08 36.85 1.40
4919 8806 5.090139 TGGGATATTGGGTCACAAAATTGT 58.910 37.500 0.00 0.00 43.46 2.71
5291 10042 9.073587 AGAGCCATATACCCTGGAAATAATAAT 57.926 33.333 0.00 0.00 35.70 1.28
5708 10460 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
5709 10461 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
5710 10462 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
5711 10463 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
5712 10464 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
5713 10465 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
5714 10466 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
5715 10467 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
5729 10481 9.570488 CACTACTTTAGTAATCTAAACGCTCTT 57.430 33.333 0.00 0.00 40.05 2.85
5730 10482 8.954350 TCACTACTTTAGTAATCTAAACGCTCT 58.046 33.333 0.00 0.00 40.05 4.09
5731 10483 9.733219 ATCACTACTTTAGTAATCTAAACGCTC 57.267 33.333 0.00 0.00 40.05 5.03
5732 10484 9.733219 GATCACTACTTTAGTAATCTAAACGCT 57.267 33.333 0.00 0.00 40.05 5.07
5733 10485 9.733219 AGATCACTACTTTAGTAATCTAAACGC 57.267 33.333 0.00 0.00 40.05 4.84
5739 10491 9.733219 GCGTTTAGATCACTACTTTAGTAATCT 57.267 33.333 4.72 4.72 37.23 2.40
5740 10492 9.733219 AGCGTTTAGATCACTACTTTAGTAATC 57.267 33.333 0.00 0.00 37.23 1.75
5742 10494 9.918630 AAAGCGTTTAGATCACTACTTTAGTAA 57.081 29.630 0.00 0.00 37.23 2.24
5743 10495 9.918630 AAAAGCGTTTAGATCACTACTTTAGTA 57.081 29.630 0.00 0.00 37.23 1.82
5744 10496 8.828688 AAAAGCGTTTAGATCACTACTTTAGT 57.171 30.769 0.00 0.00 40.28 2.24
5761 10513 9.106070 CCCTCTGTAAACTAATATAAAAGCGTT 57.894 33.333 0.00 0.00 0.00 4.84
5762 10514 8.480501 TCCCTCTGTAAACTAATATAAAAGCGT 58.519 33.333 0.00 0.00 0.00 5.07
5763 10515 8.882415 TCCCTCTGTAAACTAATATAAAAGCG 57.118 34.615 0.00 0.00 0.00 4.68
5764 10516 9.833917 ACTCCCTCTGTAAACTAATATAAAAGC 57.166 33.333 0.00 0.00 0.00 3.51
5770 10522 9.490083 ACAACTACTCCCTCTGTAAACTAATAT 57.510 33.333 0.00 0.00 0.00 1.28
5771 10523 8.890410 ACAACTACTCCCTCTGTAAACTAATA 57.110 34.615 0.00 0.00 0.00 0.98
5772 10524 7.793948 ACAACTACTCCCTCTGTAAACTAAT 57.206 36.000 0.00 0.00 0.00 1.73
5773 10525 7.607615 AACAACTACTCCCTCTGTAAACTAA 57.392 36.000 0.00 0.00 0.00 2.24
5774 10526 8.890410 ATAACAACTACTCCCTCTGTAAACTA 57.110 34.615 0.00 0.00 0.00 2.24
5775 10527 7.453752 TGATAACAACTACTCCCTCTGTAAACT 59.546 37.037 0.00 0.00 0.00 2.66
5776 10528 7.609056 TGATAACAACTACTCCCTCTGTAAAC 58.391 38.462 0.00 0.00 0.00 2.01
5777 10529 7.786046 TGATAACAACTACTCCCTCTGTAAA 57.214 36.000 0.00 0.00 0.00 2.01
5778 10530 7.973048 ATGATAACAACTACTCCCTCTGTAA 57.027 36.000 0.00 0.00 0.00 2.41
5779 10531 7.973048 AATGATAACAACTACTCCCTCTGTA 57.027 36.000 0.00 0.00 0.00 2.74
5780 10532 6.875972 AATGATAACAACTACTCCCTCTGT 57.124 37.500 0.00 0.00 0.00 3.41
5781 10533 8.258007 TGTTAATGATAACAACTACTCCCTCTG 58.742 37.037 0.00 0.00 46.34 3.35
5782 10534 8.375493 TGTTAATGATAACAACTACTCCCTCT 57.625 34.615 0.00 0.00 46.34 3.69
5972 10724 0.673644 GCAACTTTGCGAGCCTCCTA 60.674 55.000 0.00 0.00 45.11 2.94
6012 10764 8.523915 AGATGACTATTCAACCAAATGCATTA 57.476 30.769 13.39 0.00 34.61 1.90
6184 11032 6.625873 TTTGTGTTTTTCCCCAAATATTGC 57.374 33.333 0.00 0.00 0.00 3.56
6295 11144 3.006110 TGAAGCTTTCATGGCAAAGGAAG 59.994 43.478 0.00 6.91 34.42 3.46
6424 11273 9.787435 ACCACAAGTGTTATAAGAGTATTTTCA 57.213 29.630 0.00 0.00 0.00 2.69
6466 11315 8.682710 GTCCACTTGCTTATGAAATTGGTATTA 58.317 33.333 5.83 0.00 34.26 0.98
6544 11394 7.619302 AGGTTCAAATCCATGTGTAATATTGGT 59.381 33.333 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.