Multiple sequence alignment - TraesCS5B01G218800

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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 TraesCS5B01G218800 chr5B 100.000 3926 0 0 980 4905 392143054 392139129 0.000000e+00 7251.0
1 TraesCS5B01G218800 chr5B 98.605 932 13 0 981 1912 392153991 392153060 0.000000e+00 1650.0
2 TraesCS5B01G218800 chr5B 100.000 440 0 0 1 440 392144033 392143594 0.000000e+00 813.0
3 TraesCS5B01G218800 chr5B 89.141 396 29 9 47 440 392154510 392154127 9.550000e-132 481.0
4 TraesCS5B01G218800 chr5B 89.347 291 23 5 34 321 136056160 136056445 4.670000e-95 359.0
5 TraesCS5B01G218800 chr5A 92.007 2427 137 20 980 3383 436626864 436624472 0.000000e+00 3354.0
6 TraesCS5B01G218800 chr5A 91.769 1470 101 13 3448 4905 436624469 436623008 0.000000e+00 2026.0
7 TraesCS5B01G218800 chr5D 91.108 2418 142 26 985 3383 335137321 335134958 0.000000e+00 3206.0
8 TraesCS5B01G218800 chr5D 91.469 1477 96 18 3448 4905 335134955 335133490 0.000000e+00 2002.0
9 TraesCS5B01G218800 chr5D 86.679 533 26 8 985 1501 335225437 335224934 2.580000e-152 549.0
10 TraesCS5B01G218800 chr5D 88.421 285 26 5 44 322 451067424 451067141 2.190000e-88 337.0
11 TraesCS5B01G218800 chr5D 87.889 289 30 5 35 320 513917079 513917365 7.870000e-88 335.0
12 TraesCS5B01G218800 chr5D 87.889 289 28 7 34 318 7559994 7559709 2.830000e-87 333.0
13 TraesCS5B01G218800 chr5D 84.211 247 23 9 4238 4473 335223451 335223210 4.940000e-55 226.0
14 TraesCS5B01G218800 chr5D 87.302 189 23 1 1496 1684 335223658 335223471 1.070000e-51 215.0
15 TraesCS5B01G218800 chr5D 83.186 113 19 0 4576 4688 335221163 335221051 2.420000e-18 104.0
16 TraesCS5B01G218800 chr5D 90.385 52 4 1 3412 3462 405255730 405255679 3.170000e-07 67.6
17 TraesCS5B01G218800 chr7B 90.211 664 51 8 4248 4905 141006956 141007611 0.000000e+00 854.0
18 TraesCS5B01G218800 chr7B 87.956 631 43 17 2752 3379 141006058 141006658 0.000000e+00 713.0
19 TraesCS5B01G218800 chr7B 87.869 305 23 6 3449 3753 141006667 141006957 3.630000e-91 346.0
20 TraesCS5B01G218800 chr7A 91.339 635 37 9 2752 3380 177341629 177342251 0.000000e+00 852.0
21 TraesCS5B01G218800 chr7A 89.124 662 55 10 4248 4905 177342565 177343213 0.000000e+00 808.0
22 TraesCS5B01G218800 chr7A 88.710 310 28 4 3449 3753 177342259 177342566 6.000000e-99 372.0
23 TraesCS5B01G218800 chr7A 91.837 49 3 1 3405 3452 143359450 143359402 3.170000e-07 67.6
24 TraesCS5B01G218800 chr7D 87.264 636 44 16 2752 3380 175657882 175658487 0.000000e+00 691.0
25 TraesCS5B01G218800 chr7D 88.889 306 28 4 3449 3753 175658495 175658795 6.000000e-99 372.0
26 TraesCS5B01G218800 chr7D 91.200 250 18 2 4248 4493 175658794 175659043 2.190000e-88 337.0
27 TraesCS5B01G218800 chr7D 89.427 227 17 3 4681 4905 175660589 175660810 3.740000e-71 279.0
28 TraesCS5B01G218800 chr3B 88.814 295 26 7 29 320 377115115 377115405 6.040000e-94 355.0
29 TraesCS5B01G218800 chr3B 97.500 40 1 0 3414 3453 685063087 685063126 8.810000e-08 69.4
30 TraesCS5B01G218800 chr3D 88.475 295 28 6 29 320 255424387 255424678 7.810000e-93 351.0
31 TraesCS5B01G218800 chr3A 88.136 295 28 7 30 320 319962308 319962599 1.310000e-90 344.0
32 TraesCS5B01G218800 chr6A 86.792 318 28 9 27 335 374422651 374422963 4.700000e-90 342.0
33 TraesCS5B01G218800 chr1A 93.750 48 3 0 3403 3450 515590739 515590786 6.810000e-09 73.1
34 TraesCS5B01G218800 chr1A 100.000 30 0 0 3379 3408 29996535 29996564 6.860000e-04 56.5
35 TraesCS5B01G218800 chr4A 97.561 41 1 0 3410 3450 514413322 514413362 2.450000e-08 71.3
36 TraesCS5B01G218800 chr2B 85.507 69 6 1 3394 3458 513283046 513282978 8.810000e-08 69.4
37 TraesCS5B01G218800 chr4D 85.294 68 5 3 3388 3450 50885691 50885758 1.140000e-06 65.8
38 TraesCS5B01G218800 chr4B 86.154 65 4 4 3389 3453 74870995 74870936 1.140000e-06 65.8
39 TraesCS5B01G218800 chr2A 91.489 47 4 0 3412 3458 552492959 552493005 1.140000e-06 65.8


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 TraesCS5B01G218800 chr5B 392139129 392144033 4904 True 4032.000000 7251 100.000000 1 4905 2 chr5B.!!$R1 4904
1 TraesCS5B01G218800 chr5B 392153060 392154510 1450 True 1065.500000 1650 93.873000 47 1912 2 chr5B.!!$R2 1865
2 TraesCS5B01G218800 chr5A 436623008 436626864 3856 True 2690.000000 3354 91.888000 980 4905 2 chr5A.!!$R1 3925
3 TraesCS5B01G218800 chr5D 335133490 335137321 3831 True 2604.000000 3206 91.288500 985 4905 2 chr5D.!!$R4 3920
4 TraesCS5B01G218800 chr5D 335221051 335225437 4386 True 273.500000 549 85.344500 985 4688 4 chr5D.!!$R5 3703
5 TraesCS5B01G218800 chr7B 141006058 141007611 1553 False 637.666667 854 88.678667 2752 4905 3 chr7B.!!$F1 2153
6 TraesCS5B01G218800 chr7A 177341629 177343213 1584 False 677.333333 852 89.724333 2752 4905 3 chr7A.!!$F1 2153
7 TraesCS5B01G218800 chr7D 175657882 175660810 2928 False 419.750000 691 89.195000 2752 4905 4 chr7D.!!$F1 2153

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
104 105 0.179001 CCACCCTTCGTCCAACCTTT 60.179 55.0 0.00 0.00 0.00 3.11 F
403 405 0.312102 TGCGACTCTGTGTGTCTCTG 59.688 55.0 0.00 0.00 32.70 3.35 F
404 406 0.312416 GCGACTCTGTGTGTCTCTGT 59.688 55.0 0.00 0.00 32.70 3.41 F
2271 3577 0.318441 TGTCCACACAGAGCTGCTAC 59.682 55.0 0.15 0.00 0.00 3.58 F
2582 3902 0.606944 TTGGTTGATGGCACGGTACC 60.607 55.0 0.16 0.16 0.00 3.34 F
3675 5018 0.109132 GACATTGAAAGCAAGGCCGG 60.109 55.0 0.00 0.00 39.28 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1765 3068 0.251341 AACCAGCTAAGGGCCAACAG 60.251 55.000 6.18 0.0 43.05 3.16 R
2251 3557 1.066573 GTAGCAGCTCTGTGTGGACAT 60.067 52.381 0.00 0.0 0.00 3.06 R
2340 3646 1.480789 TCCAGTCAGGCGCATTAGTA 58.519 50.000 10.83 0.0 37.29 1.82 R
3656 4999 0.109132 CCGGCCTTGCTTTCAATGTC 60.109 55.000 0.00 0.0 0.00 3.06 R
3814 5157 0.388659 GGGCTGCATTGTCAACAACA 59.611 50.000 0.50 0.0 38.86 3.33 R
4753 9413 0.833287 GCTCCCCTGTTATCTCAGCA 59.167 55.000 0.00 0.0 34.47 4.41 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
23 24 6.319229 CATGTTCACTACACGAGAATGTAC 57.681 41.667 0.00 0.00 40.19 2.90
24 25 5.441709 TGTTCACTACACGAGAATGTACA 57.558 39.130 0.00 0.00 33.85 2.90
25 26 5.834169 TGTTCACTACACGAGAATGTACAA 58.166 37.500 0.00 0.00 33.85 2.41
26 27 6.274579 TGTTCACTACACGAGAATGTACAAA 58.725 36.000 0.00 0.00 33.85 2.83
27 28 6.926826 TGTTCACTACACGAGAATGTACAAAT 59.073 34.615 0.00 0.00 33.85 2.32
28 29 8.083462 TGTTCACTACACGAGAATGTACAAATA 58.917 33.333 0.00 0.00 33.85 1.40
29 30 8.371053 GTTCACTACACGAGAATGTACAAATAC 58.629 37.037 0.00 0.00 33.85 1.89
30 31 7.595604 TCACTACACGAGAATGTACAAATACA 58.404 34.615 0.00 0.00 45.37 2.29
78 79 9.685276 AAAAAGAAGGTTCCAATTTCATCTTTT 57.315 25.926 0.00 0.00 43.71 2.27
101 102 1.599797 CACCACCCTTCGTCCAACC 60.600 63.158 0.00 0.00 0.00 3.77
104 105 0.179001 CCACCCTTCGTCCAACCTTT 60.179 55.000 0.00 0.00 0.00 3.11
271 272 9.953565 TTATTAACAGGTAAATCACAAGCTACT 57.046 29.630 0.00 0.00 0.00 2.57
275 276 6.164176 ACAGGTAAATCACAAGCTACTGTAC 58.836 40.000 0.00 0.00 0.00 2.90
282 283 8.934507 AAATCACAAGCTACTGTACTAGAATC 57.065 34.615 0.00 0.00 0.00 2.52
300 301 5.709966 AGAATCTTTATTTCCCGTTGCAAC 58.290 37.500 19.89 19.89 0.00 4.17
310 311 2.722188 GTTGCAACGCACGAGCAC 60.722 61.111 14.90 6.70 38.71 4.40
326 327 4.703575 ACGAGCACTGTTCTAGTTACCATA 59.296 41.667 0.00 0.00 37.60 2.74
327 328 5.163642 ACGAGCACTGTTCTAGTTACCATAG 60.164 44.000 0.00 0.00 37.60 2.23
333 335 7.817962 GCACTGTTCTAGTTACCATAGAAAAGA 59.182 37.037 16.21 0.00 43.16 2.52
395 397 2.623416 TGGGTAGATATGCGACTCTGTG 59.377 50.000 0.00 0.00 0.00 3.66
396 398 2.623889 GGGTAGATATGCGACTCTGTGT 59.376 50.000 0.00 0.00 0.00 3.72
397 399 3.551046 GGGTAGATATGCGACTCTGTGTG 60.551 52.174 0.00 0.00 0.00 3.82
398 400 3.066900 GGTAGATATGCGACTCTGTGTGT 59.933 47.826 0.00 0.00 0.00 3.72
399 401 3.428746 AGATATGCGACTCTGTGTGTC 57.571 47.619 0.00 0.00 0.00 3.67
400 402 3.020274 AGATATGCGACTCTGTGTGTCT 58.980 45.455 0.00 0.00 32.70 3.41
401 403 2.921634 TATGCGACTCTGTGTGTCTC 57.078 50.000 0.00 0.00 32.70 3.36
402 404 1.252175 ATGCGACTCTGTGTGTCTCT 58.748 50.000 0.00 0.00 32.70 3.10
403 405 0.312102 TGCGACTCTGTGTGTCTCTG 59.688 55.000 0.00 0.00 32.70 3.35
404 406 0.312416 GCGACTCTGTGTGTCTCTGT 59.688 55.000 0.00 0.00 32.70 3.41
413 415 4.811024 TCTGTGTGTCTCTGTTGCTTTAAG 59.189 41.667 0.00 0.00 0.00 1.85
417 419 6.150307 TGTGTGTCTCTGTTGCTTTAAGAAAA 59.850 34.615 0.00 0.00 0.00 2.29
1171 1187 1.586541 CTCTACAGACGCAGGTGCA 59.413 57.895 2.33 0.00 42.21 4.57
1760 3063 2.796593 CAAGCTAAAAGCAAAGGTGTGC 59.203 45.455 1.22 0.00 45.56 4.57
1920 3223 1.431243 TGGGGGTTTTGGCAACTAGAT 59.569 47.619 0.00 0.00 37.61 1.98
2066 3371 4.923068 AGTGGAGGTGTCACTCGA 57.077 55.556 2.35 0.00 41.10 4.04
2069 3374 1.971357 AGTGGAGGTGTCACTCGAAAT 59.029 47.619 2.35 0.00 41.10 2.17
2070 3375 2.069273 GTGGAGGTGTCACTCGAAATG 58.931 52.381 2.35 0.00 38.39 2.32
2071 3376 1.001974 TGGAGGTGTCACTCGAAATGG 59.998 52.381 2.35 0.00 38.39 3.16
2072 3377 1.079503 GAGGTGTCACTCGAAATGGC 58.920 55.000 2.35 0.00 0.00 4.40
2073 3378 0.687354 AGGTGTCACTCGAAATGGCT 59.313 50.000 2.35 0.00 0.00 4.75
2074 3379 1.079503 GGTGTCACTCGAAATGGCTC 58.920 55.000 2.35 0.00 0.00 4.70
2075 3380 1.608025 GGTGTCACTCGAAATGGCTCA 60.608 52.381 2.35 0.00 0.00 4.26
2077 3382 2.744202 GTGTCACTCGAAATGGCTCAAT 59.256 45.455 0.00 0.00 0.00 2.57
2078 3383 2.743664 TGTCACTCGAAATGGCTCAATG 59.256 45.455 2.94 0.00 0.00 2.82
2079 3384 1.739466 TCACTCGAAATGGCTCAATGC 59.261 47.619 0.00 0.00 41.94 3.56
2097 3403 7.148340 GCTCAATGCCTGTATCCAAATACTATC 60.148 40.741 0.00 0.00 36.21 2.08
2124 3430 7.123247 GCTATTTGGAACATATATTGATGGGCT 59.877 37.037 0.00 0.00 39.30 5.19
2177 3483 7.067494 GGACTGATAGCATATTTGGAACTTGTT 59.933 37.037 0.00 0.00 0.00 2.83
2192 3498 8.463930 TGGAACTTGTTGAAAGTAATCTGAAT 57.536 30.769 0.00 0.00 0.00 2.57
2215 3521 8.974060 AATGATAATACCTATCCGTTTGTTGT 57.026 30.769 0.00 0.00 36.33 3.32
2226 3532 7.431084 CCTATCCGTTTGTTGTTTATATTGTGC 59.569 37.037 0.00 0.00 0.00 4.57
2251 3557 4.623932 AGGACATCTTTTGCACTACAGA 57.376 40.909 0.00 0.00 0.00 3.41
2265 3571 2.232452 ACTACAGATGTCCACACAGAGC 59.768 50.000 0.00 0.00 35.41 4.09
2271 3577 0.318441 TGTCCACACAGAGCTGCTAC 59.682 55.000 0.15 0.00 0.00 3.58
2292 3598 4.899352 CCTGGAGAGGTTATATTCTGGG 57.101 50.000 0.00 0.00 34.16 4.45
2355 3661 4.392138 AGAAAACTTACTAATGCGCCTGAC 59.608 41.667 4.18 0.00 0.00 3.51
2366 3672 1.417517 TGCGCCTGACTGGATATTGAT 59.582 47.619 4.18 0.00 38.35 2.57
2470 3790 8.623903 TGGTTATTCTTGCTTAGCATTCTATTG 58.376 33.333 8.05 0.00 38.76 1.90
2541 3861 2.475466 GGCAGTGGATGGACATGCG 61.475 63.158 0.00 0.00 37.76 4.73
2582 3902 0.606944 TTGGTTGATGGCACGGTACC 60.607 55.000 0.16 0.16 0.00 3.34
2602 3922 6.982724 GGTACCGTATTAAGTGCTTATGTTCT 59.017 38.462 0.00 0.00 0.00 3.01
2624 3944 7.792374 TCTCCAGCATTATACAACTGATTTC 57.208 36.000 0.00 0.00 31.67 2.17
2644 3964 9.491675 TGATTTCAACAAATTCAGCAATGTTAT 57.508 25.926 0.00 0.00 34.45 1.89
2678 3998 8.150827 TCTTCCTAATATATTCCACCTCCATG 57.849 38.462 0.00 0.00 0.00 3.66
2728 4048 3.917988 TCTGCCATATTCTGATAGCGTG 58.082 45.455 0.00 0.00 0.00 5.34
2729 4049 3.573967 TCTGCCATATTCTGATAGCGTGA 59.426 43.478 0.00 0.00 0.00 4.35
2734 4054 5.300752 CCATATTCTGATAGCGTGAAAGGT 58.699 41.667 0.00 0.00 0.00 3.50
2789 4109 1.359848 GTGGCATGTTACTCCACTCG 58.640 55.000 11.06 0.00 45.04 4.18
2853 4176 6.985117 TGTTCTTCAGAGCATGCTTATTTTT 58.015 32.000 23.61 0.00 30.24 1.94
2905 4231 9.088512 GCCTTCGAGATTGTATATGTTTATAGG 57.911 37.037 0.00 0.00 0.00 2.57
2906 4232 9.088512 CCTTCGAGATTGTATATGTTTATAGGC 57.911 37.037 0.00 0.00 0.00 3.93
2910 4236 9.424319 CGAGATTGTATATGTTTATAGGCACTT 57.576 33.333 0.00 0.00 41.75 3.16
2916 4242 8.836413 TGTATATGTTTATAGGCACTTTTCTGC 58.164 33.333 0.00 0.00 41.75 4.26
2935 4261 6.862711 TCTGCATTCAGATGATGATTTCTC 57.137 37.500 0.00 0.00 43.95 2.87
2936 4262 6.354130 TCTGCATTCAGATGATGATTTCTCA 58.646 36.000 0.00 0.00 43.95 3.27
3036 4364 9.530633 TTCTTGTCTTACAAACTTCTCTACTTC 57.469 33.333 0.00 0.00 37.69 3.01
3149 4483 9.490663 GTGCTTTTGTCAAAGTATCACATATAC 57.509 33.333 0.00 0.00 41.51 1.47
3214 4549 3.266772 TGGACCTCTTATGGCAATGTTCT 59.733 43.478 0.00 0.00 0.00 3.01
3240 4575 4.163458 TCGGCTTACTCCTGGATTATTTGT 59.837 41.667 0.00 0.00 0.00 2.83
3246 4581 7.172361 GCTTACTCCTGGATTATTTGTCATCTC 59.828 40.741 0.00 0.00 0.00 2.75
3260 4595 6.692849 TTGTCATCTCCTAATGCTGGATAT 57.307 37.500 0.00 0.00 32.56 1.63
3277 4612 6.183360 GCTGGATATTTTTGTCCAAGTAGGTC 60.183 42.308 0.00 0.00 43.52 3.85
3304 4639 4.446371 GTGCATTAGCTGTGGAGTCTATT 58.554 43.478 0.00 0.00 42.74 1.73
3385 4720 9.965824 AGTGTTATGGTTGTTCAGAAAATTAAG 57.034 29.630 0.00 0.00 0.00 1.85
3386 4721 9.744468 GTGTTATGGTTGTTCAGAAAATTAAGT 57.256 29.630 0.00 0.00 0.00 2.24
3392 4727 8.626526 TGGTTGTTCAGAAAATTAAGTTACTCC 58.373 33.333 0.00 0.00 0.00 3.85
3393 4728 8.080417 GGTTGTTCAGAAAATTAAGTTACTCCC 58.920 37.037 0.00 0.00 0.00 4.30
3394 4729 8.847196 GTTGTTCAGAAAATTAAGTTACTCCCT 58.153 33.333 0.00 0.00 0.00 4.20
3395 4730 8.617290 TGTTCAGAAAATTAAGTTACTCCCTC 57.383 34.615 0.00 0.00 0.00 4.30
3396 4731 7.664318 TGTTCAGAAAATTAAGTTACTCCCTCC 59.336 37.037 0.00 0.00 0.00 4.30
3397 4732 6.403878 TCAGAAAATTAAGTTACTCCCTCCG 58.596 40.000 0.00 0.00 0.00 4.63
3398 4733 6.211986 TCAGAAAATTAAGTTACTCCCTCCGA 59.788 38.462 0.00 0.00 0.00 4.55
3399 4734 7.048512 CAGAAAATTAAGTTACTCCCTCCGAT 58.951 38.462 0.00 0.00 0.00 4.18
3400 4735 7.224949 CAGAAAATTAAGTTACTCCCTCCGATC 59.775 40.741 0.00 0.00 0.00 3.69
3401 4736 5.548181 AATTAAGTTACTCCCTCCGATCC 57.452 43.478 0.00 0.00 0.00 3.36
3402 4737 2.544844 AAGTTACTCCCTCCGATCCA 57.455 50.000 0.00 0.00 0.00 3.41
3403 4738 2.777459 AGTTACTCCCTCCGATCCAT 57.223 50.000 0.00 0.00 0.00 3.41
3404 4739 3.897657 AGTTACTCCCTCCGATCCATA 57.102 47.619 0.00 0.00 0.00 2.74
3405 4740 4.405756 AGTTACTCCCTCCGATCCATAT 57.594 45.455 0.00 0.00 0.00 1.78
3406 4741 4.753186 AGTTACTCCCTCCGATCCATATT 58.247 43.478 0.00 0.00 0.00 1.28
3407 4742 5.900437 AGTTACTCCCTCCGATCCATATTA 58.100 41.667 0.00 0.00 0.00 0.98
3408 4743 5.952947 AGTTACTCCCTCCGATCCATATTAG 59.047 44.000 0.00 0.00 0.00 1.73
3409 4744 4.405756 ACTCCCTCCGATCCATATTAGT 57.594 45.455 0.00 0.00 0.00 2.24
3410 4745 5.531753 ACTCCCTCCGATCCATATTAGTA 57.468 43.478 0.00 0.00 0.00 1.82
3411 4746 6.093617 ACTCCCTCCGATCCATATTAGTAT 57.906 41.667 0.00 0.00 0.00 2.12
3412 4747 7.222180 ACTCCCTCCGATCCATATTAGTATA 57.778 40.000 0.00 0.00 0.00 1.47
3413 4748 7.061688 ACTCCCTCCGATCCATATTAGTATAC 58.938 42.308 0.00 0.00 0.00 1.47
3414 4749 7.091902 ACTCCCTCCGATCCATATTAGTATACT 60.092 40.741 10.87 10.87 0.00 2.12
3415 4750 8.341022 TCCCTCCGATCCATATTAGTATACTA 57.659 38.462 8.59 8.59 0.00 1.82
3416 4751 8.784880 TCCCTCCGATCCATATTAGTATACTAA 58.215 37.037 24.01 24.01 42.04 2.24
3417 4752 9.417561 CCCTCCGATCCATATTAGTATACTAAA 57.582 37.037 25.21 16.14 41.27 1.85
3419 4754 9.953697 CTCCGATCCATATTAGTATACTAAAGC 57.046 37.037 25.21 12.75 41.27 3.51
3420 4755 9.696572 TCCGATCCATATTAGTATACTAAAGCT 57.303 33.333 25.21 14.01 41.27 3.74
3421 4756 9.737427 CCGATCCATATTAGTATACTAAAGCTG 57.263 37.037 25.21 20.57 41.27 4.24
3422 4757 9.239002 CGATCCATATTAGTATACTAAAGCTGC 57.761 37.037 25.21 12.70 41.27 5.25
3425 4760 9.706691 TCCATATTAGTATACTAAAGCTGCAAC 57.293 33.333 25.21 0.00 41.27 4.17
3426 4761 9.489084 CCATATTAGTATACTAAAGCTGCAACA 57.511 33.333 25.21 3.18 41.27 3.33
3437 4772 8.292444 ACTAAAGCTGCAACAATTAATATGGA 57.708 30.769 1.02 0.00 0.00 3.41
3438 4773 8.917088 ACTAAAGCTGCAACAATTAATATGGAT 58.083 29.630 1.02 0.00 0.00 3.41
3439 4774 9.403110 CTAAAGCTGCAACAATTAATATGGATC 57.597 33.333 1.02 0.00 0.00 3.36
3440 4775 6.005583 AGCTGCAACAATTAATATGGATCG 57.994 37.500 1.02 0.00 0.00 3.69
3441 4776 5.048504 AGCTGCAACAATTAATATGGATCGG 60.049 40.000 1.02 0.00 0.00 4.18
3442 4777 5.048782 GCTGCAACAATTAATATGGATCGGA 60.049 40.000 0.00 0.00 0.00 4.55
3443 4778 6.558771 TGCAACAATTAATATGGATCGGAG 57.441 37.500 0.00 0.00 0.00 4.63
3444 4779 5.473162 TGCAACAATTAATATGGATCGGAGG 59.527 40.000 0.00 0.00 0.00 4.30
3445 4780 5.106157 GCAACAATTAATATGGATCGGAGGG 60.106 44.000 0.00 0.00 0.00 4.30
3446 4781 6.237901 CAACAATTAATATGGATCGGAGGGA 58.762 40.000 0.00 0.00 0.00 4.20
3475 4811 7.788026 TCTTCTTTGTGTACTCTCTACCAAAA 58.212 34.615 0.00 0.00 0.00 2.44
3499 4841 8.964420 AATGTTGTTCTTTTGGTCAATATACG 57.036 30.769 0.00 0.00 0.00 3.06
3509 4851 5.100344 TGGTCAATATACGGTAAAGCCAA 57.900 39.130 0.00 0.00 36.97 4.52
3523 4866 7.142680 CGGTAAAGCCAATTTCTGACTTAAAA 58.857 34.615 0.00 0.00 36.97 1.52
3529 4872 9.783081 AAGCCAATTTCTGACTTAAAATTCATT 57.217 25.926 0.00 0.00 33.86 2.57
3673 5016 0.968405 TGGACATTGAAAGCAAGGCC 59.032 50.000 0.00 0.00 39.28 5.19
3675 5018 0.109132 GACATTGAAAGCAAGGCCGG 60.109 55.000 0.00 0.00 39.28 6.13
3698 5041 5.278169 GGTGATTATGGTAGCAAAGCTGATG 60.278 44.000 0.00 0.00 40.10 3.07
3712 5055 3.280295 AGCTGATGAGGATTGCAGAAAG 58.720 45.455 0.00 0.00 0.00 2.62
3731 5074 6.207417 CAGAAAGAAAGAAGATTACCAAGCCA 59.793 38.462 0.00 0.00 0.00 4.75
3808 5151 8.515473 GTGTCATACAAAATCGATGAAAATTCG 58.485 33.333 0.00 0.00 37.94 3.34
3872 5215 3.136009 ACCAAAACAGGTGTAGCTACC 57.864 47.619 21.01 9.61 41.30 3.18
3889 5232 4.841246 AGCTACCTAACATGGAGGGATAAG 59.159 45.833 17.59 11.06 38.52 1.73
3895 5238 3.778954 ACATGGAGGGATAAGCTTAGC 57.221 47.619 13.37 13.37 0.00 3.09
3916 5259 9.339850 CTTAGCACTTTGTAGGAGAGTAGTATA 57.660 37.037 0.00 0.00 0.00 1.47
3917 5260 7.571080 AGCACTTTGTAGGAGAGTAGTATAC 57.429 40.000 0.00 0.00 43.47 1.47
3918 5261 7.117397 AGCACTTTGTAGGAGAGTAGTATACA 58.883 38.462 5.50 0.00 46.26 2.29
3919 5262 7.283580 AGCACTTTGTAGGAGAGTAGTATACAG 59.716 40.741 5.50 0.00 46.26 2.74
4004 5350 3.334583 TTCAGTGGCAATCAGTACTCC 57.665 47.619 0.00 0.00 0.00 3.85
4022 5368 6.891908 AGTACTCCATAATGCACCTGAATTTT 59.108 34.615 0.00 0.00 0.00 1.82
4024 5370 7.716799 ACTCCATAATGCACCTGAATTTTTA 57.283 32.000 0.00 0.00 0.00 1.52
4069 5415 9.971922 GCCATATAATTGTTGCTCTTTCTAAAT 57.028 29.630 0.00 0.00 0.00 1.40
4177 5529 8.406297 GTTGACAAGTAGAAAGTTCAAGGATTT 58.594 33.333 0.00 0.00 0.00 2.17
4211 5563 4.629200 GGATCAGATATTCATCGTGGAAGC 59.371 45.833 0.00 0.00 36.20 3.86
4219 5571 3.239587 TCATCGTGGAAGCGTAAATCA 57.760 42.857 0.00 0.00 0.00 2.57
4273 5625 6.088616 GCAAAACTGTTATCTTCAATGCTGAC 59.911 38.462 0.00 0.00 0.00 3.51
4302 5655 4.399303 AGAAGGTTTTCACTGTGAAGGTTG 59.601 41.667 21.13 0.00 37.70 3.77
4343 5700 7.884354 AGGTATGCATCTACTAGGTTACTACTC 59.116 40.741 0.19 0.00 0.00 2.59
4349 5706 6.324601 TCTACTAGGTTACTACTCCAGCTT 57.675 41.667 0.00 0.00 0.00 3.74
4466 5840 7.656707 TCAATCAATATATCATGACACCACG 57.343 36.000 0.00 0.00 0.00 4.94
4526 7827 5.581126 TGTTGATTTGCAGGGATCATAAC 57.419 39.130 9.41 7.21 32.73 1.89
4668 8166 9.301153 CTGCAGTTCTAATTGTTTACAAGTTTT 57.699 29.630 5.25 0.00 39.47 2.43
4677 8175 4.794334 TGTTTACAAGTTTTAGCCCTGGA 58.206 39.130 0.00 0.00 0.00 3.86
4679 9337 2.586648 ACAAGTTTTAGCCCTGGAGG 57.413 50.000 0.00 0.00 39.47 4.30
4688 9346 1.376649 AGCCCTGGAGGAAATGACTT 58.623 50.000 0.00 0.00 38.24 3.01
4689 9347 1.283321 AGCCCTGGAGGAAATGACTTC 59.717 52.381 0.00 0.00 38.24 3.01
4727 9387 4.400567 GCTCAAGAATGCTAATTTCCAGGT 59.599 41.667 0.00 0.00 0.00 4.00
4732 9392 6.521151 AGAATGCTAATTTCCAGGTTTGAG 57.479 37.500 0.00 0.00 0.00 3.02
4748 9408 6.203723 CAGGTTTGAGCATATTAGCTTAGGTC 59.796 42.308 0.00 0.00 46.75 3.85
4889 9552 2.033801 ACAATGCTTGTCTGTCAGTTGC 59.966 45.455 0.00 1.62 40.56 4.17
4895 9558 0.394192 TGTCTGTCAGTTGCCTCAGG 59.606 55.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.861787 TGTACATTCTCGTGTAGTGAACATG 59.138 40.000 0.00 0.00 45.08 3.21
1 2 6.020971 TGTACATTCTCGTGTAGTGAACAT 57.979 37.500 0.00 0.00 41.10 2.71
2 3 5.441709 TGTACATTCTCGTGTAGTGAACA 57.558 39.130 0.00 0.00 35.40 3.18
3 4 6.758593 TTTGTACATTCTCGTGTAGTGAAC 57.241 37.500 0.00 0.00 35.40 3.18
4 5 8.083462 TGTATTTGTACATTCTCGTGTAGTGAA 58.917 33.333 0.00 0.00 35.40 3.18
5 6 7.595604 TGTATTTGTACATTCTCGTGTAGTGA 58.404 34.615 0.00 0.00 35.40 3.41
6 7 7.806149 TGTATTTGTACATTCTCGTGTAGTG 57.194 36.000 0.00 0.00 35.40 2.74
7 8 8.033038 ACATGTATTTGTACATTCTCGTGTAGT 58.967 33.333 0.00 0.00 38.51 2.73
8 9 8.407457 ACATGTATTTGTACATTCTCGTGTAG 57.593 34.615 0.00 0.00 38.51 2.74
10 11 8.942338 ATACATGTATTTGTACATTCTCGTGT 57.058 30.769 12.75 15.42 38.51 4.49
11 12 9.249457 AGATACATGTATTTGTACATTCTCGTG 57.751 33.333 19.19 3.21 38.51 4.35
12 13 9.464714 GAGATACATGTATTTGTACATTCTCGT 57.535 33.333 19.19 0.00 38.51 4.18
13 14 9.684448 AGAGATACATGTATTTGTACATTCTCG 57.316 33.333 19.19 3.99 41.75 4.04
78 79 1.452801 GACGAAGGGTGGTGGGAAA 59.547 57.895 0.00 0.00 0.00 3.13
81 82 2.824880 TTGGACGAAGGGTGGTGGG 61.825 63.158 0.00 0.00 0.00 4.61
88 89 1.880027 CAAGAAAGGTTGGACGAAGGG 59.120 52.381 0.00 0.00 0.00 3.95
93 94 8.657074 TTATCATATACAAGAAAGGTTGGACG 57.343 34.615 0.00 0.00 0.00 4.79
267 268 9.680315 CGGGAAATAAAGATTCTAGTACAGTAG 57.320 37.037 0.00 0.00 0.00 2.57
268 269 9.193806 ACGGGAAATAAAGATTCTAGTACAGTA 57.806 33.333 0.00 0.00 0.00 2.74
270 271 8.818057 CAACGGGAAATAAAGATTCTAGTACAG 58.182 37.037 0.00 0.00 0.00 2.74
271 272 7.279313 GCAACGGGAAATAAAGATTCTAGTACA 59.721 37.037 0.00 0.00 0.00 2.90
275 276 6.677781 TGCAACGGGAAATAAAGATTCTAG 57.322 37.500 0.00 0.00 0.00 2.43
300 301 0.387367 ACTAGAACAGTGCTCGTGCG 60.387 55.000 4.84 0.00 43.34 5.34
310 311 8.532819 ACCTCTTTTCTATGGTAACTAGAACAG 58.467 37.037 0.00 6.74 35.50 3.16
326 327 4.335594 GCGGCAACATAATACCTCTTTTCT 59.664 41.667 0.00 0.00 0.00 2.52
327 328 4.095782 TGCGGCAACATAATACCTCTTTTC 59.904 41.667 0.00 0.00 0.00 2.29
333 335 4.792521 TTTTTGCGGCAACATAATACCT 57.207 36.364 16.15 0.00 0.00 3.08
358 360 6.274322 TCTACCCAAATTGCATAATACCCT 57.726 37.500 0.00 0.00 0.00 4.34
395 397 7.472543 TCTTTTTCTTAAAGCAACAGAGACAC 58.527 34.615 0.00 0.00 0.00 3.67
396 398 7.624360 TCTTTTTCTTAAAGCAACAGAGACA 57.376 32.000 0.00 0.00 0.00 3.41
397 399 8.962111 CAATCTTTTTCTTAAAGCAACAGAGAC 58.038 33.333 0.00 0.00 0.00 3.36
398 400 8.137437 CCAATCTTTTTCTTAAAGCAACAGAGA 58.863 33.333 0.00 0.00 0.00 3.10
399 401 7.095899 GCCAATCTTTTTCTTAAAGCAACAGAG 60.096 37.037 0.00 0.00 0.00 3.35
400 402 6.701400 GCCAATCTTTTTCTTAAAGCAACAGA 59.299 34.615 0.00 0.00 0.00 3.41
401 403 6.703165 AGCCAATCTTTTTCTTAAAGCAACAG 59.297 34.615 0.00 0.00 0.00 3.16
402 404 6.581712 AGCCAATCTTTTTCTTAAAGCAACA 58.418 32.000 0.00 0.00 0.00 3.33
403 405 6.146184 GGAGCCAATCTTTTTCTTAAAGCAAC 59.854 38.462 0.00 0.00 0.00 4.17
404 406 6.223120 GGAGCCAATCTTTTTCTTAAAGCAA 58.777 36.000 0.00 0.00 0.00 3.91
413 415 0.817654 CGGGGGAGCCAATCTTTTTC 59.182 55.000 0.00 0.00 0.00 2.29
417 419 2.439553 TTTGCGGGGGAGCCAATCTT 62.440 55.000 0.00 0.00 36.02 2.40
1760 3063 1.028868 GCTAAGGGCCAACAGCAGAG 61.029 60.000 16.35 0.00 46.50 3.35
1765 3068 0.251341 AACCAGCTAAGGGCCAACAG 60.251 55.000 6.18 0.00 43.05 3.16
1949 3252 6.715264 ACTTATTGCTTACCTTTGCTACACTT 59.285 34.615 0.00 0.00 0.00 3.16
2023 3328 3.756963 TCCTTATGCGACGCAGACTATAT 59.243 43.478 28.10 11.78 43.65 0.86
2073 3378 8.483202 GCGATAGTATTTGGATACAGGCATTGA 61.483 40.741 0.00 0.00 45.26 2.57
2074 3379 6.402550 GCGATAGTATTTGGATACAGGCATTG 60.403 42.308 0.00 0.00 45.26 2.82
2075 3380 5.643777 GCGATAGTATTTGGATACAGGCATT 59.356 40.000 0.00 0.00 45.26 3.56
2077 3382 4.283467 AGCGATAGTATTTGGATACAGGCA 59.717 41.667 0.00 0.00 45.26 4.75
2078 3383 4.822026 AGCGATAGTATTTGGATACAGGC 58.178 43.478 0.00 0.00 45.26 4.85
2079 3384 8.873830 CAAATAGCGATAGTATTTGGATACAGG 58.126 37.037 7.25 0.00 45.26 4.00
2097 3403 7.475015 CCCATCAATATATGTTCCAAATAGCG 58.525 38.462 0.00 0.00 0.00 4.26
2157 3463 8.806146 ACTTTCAACAAGTTCCAAATATGCTAT 58.194 29.630 0.00 0.00 0.00 2.97
2164 3470 8.912988 TCAGATTACTTTCAACAAGTTCCAAAT 58.087 29.630 0.00 0.00 0.00 2.32
2166 3472 7.873719 TCAGATTACTTTCAACAAGTTCCAA 57.126 32.000 0.00 0.00 0.00 3.53
2192 3498 8.795842 AAACAACAAACGGATAGGTATTATCA 57.204 30.769 0.00 0.00 40.02 2.15
2200 3506 7.431084 GCACAATATAAACAACAAACGGATAGG 59.569 37.037 0.00 0.00 0.00 2.57
2201 3507 7.163520 CGCACAATATAAACAACAAACGGATAG 59.836 37.037 0.00 0.00 0.00 2.08
2206 3512 5.147865 TCCGCACAATATAAACAACAAACG 58.852 37.500 0.00 0.00 0.00 3.60
2215 3521 5.680619 AGATGTCCTTCCGCACAATATAAA 58.319 37.500 0.00 0.00 0.00 1.40
2219 3525 3.627395 AAGATGTCCTTCCGCACAATA 57.373 42.857 0.00 0.00 0.00 1.90
2226 3532 2.154462 AGTGCAAAAGATGTCCTTCCG 58.846 47.619 0.00 0.00 33.02 4.30
2251 3557 1.066573 GTAGCAGCTCTGTGTGGACAT 60.067 52.381 0.00 0.00 0.00 3.06
2271 3577 3.008485 GCCCAGAATATAACCTCTCCAGG 59.992 52.174 0.00 0.00 46.87 4.45
2324 3630 9.634300 GCGCATTAGTAAGTTTTCTTATAGTTC 57.366 33.333 0.30 0.00 43.18 3.01
2338 3644 2.159099 TCCAGTCAGGCGCATTAGTAAG 60.159 50.000 10.83 0.00 37.29 2.34
2340 3646 1.480789 TCCAGTCAGGCGCATTAGTA 58.519 50.000 10.83 0.00 37.29 1.82
2355 3661 7.713942 TGTGATTCAGTTCTCATCAATATCCAG 59.286 37.037 0.00 0.00 0.00 3.86
2366 3672 3.262660 AGAGGCATGTGATTCAGTTCTCA 59.737 43.478 0.00 0.00 0.00 3.27
2448 3768 7.255242 GGCACAATAGAATGCTAAGCAAGAATA 60.255 37.037 0.00 0.00 43.62 1.75
2490 3810 7.426410 AGAAAAGGCTCAAGTAAAAGTTAAGC 58.574 34.615 0.00 0.00 0.00 3.09
2541 3861 7.031975 CCAAATCTACTCCAGAAAGCAAAATC 58.968 38.462 0.00 0.00 36.67 2.17
2582 3902 6.292381 GCTGGAGAACATAAGCACTTAATACG 60.292 42.308 0.00 0.00 35.69 3.06
2584 3904 6.649155 TGCTGGAGAACATAAGCACTTAATA 58.351 36.000 0.00 0.00 40.59 0.98
2602 3922 7.392953 TGTTGAAATCAGTTGTATAATGCTGGA 59.607 33.333 0.00 0.00 0.00 3.86
2644 3964 8.208224 TGGAATATATTAGGAAGAGTTCGCAAA 58.792 33.333 0.00 0.00 0.00 3.68
2668 3988 0.107508 CAGGCTGTACATGGAGGTGG 60.108 60.000 6.28 0.00 0.00 4.61
2728 4048 5.007724 CCAATTAGGAATAGTCGCACCTTTC 59.992 44.000 0.00 0.00 41.22 2.62
2729 4049 4.881850 CCAATTAGGAATAGTCGCACCTTT 59.118 41.667 0.00 0.00 41.22 3.11
2734 4054 6.462487 CCTCTAACCAATTAGGAATAGTCGCA 60.462 42.308 1.54 0.00 41.22 5.10
2786 4106 6.470877 GCTGTAAAGATCAAGAGAGTAACGAG 59.529 42.308 0.00 0.00 0.00 4.18
2789 4109 7.316640 TGAGCTGTAAAGATCAAGAGAGTAAC 58.683 38.462 0.00 0.00 30.72 2.50
2853 4176 7.326063 CGCACTATCATGTATTTCGACTCATAA 59.674 37.037 0.00 0.00 0.00 1.90
2874 4199 0.530744 TACAATCTCGAAGGCGCACT 59.469 50.000 10.83 0.02 37.46 4.40
2877 4202 3.318017 ACATATACAATCTCGAAGGCGC 58.682 45.455 0.00 0.00 37.46 6.53
2931 4257 9.449719 GGATGTTTAGGTAAGAGAAAATGAGAA 57.550 33.333 0.00 0.00 0.00 2.87
2932 4258 8.047310 GGGATGTTTAGGTAAGAGAAAATGAGA 58.953 37.037 0.00 0.00 0.00 3.27
2933 4259 8.049721 AGGGATGTTTAGGTAAGAGAAAATGAG 58.950 37.037 0.00 0.00 0.00 2.90
2934 4260 7.928873 AGGGATGTTTAGGTAAGAGAAAATGA 58.071 34.615 0.00 0.00 0.00 2.57
2935 4261 9.110502 GTAGGGATGTTTAGGTAAGAGAAAATG 57.889 37.037 0.00 0.00 0.00 2.32
2936 4262 8.832735 TGTAGGGATGTTTAGGTAAGAGAAAAT 58.167 33.333 0.00 0.00 0.00 1.82
3054 4385 8.762645 TCTATTGGATTTGTCAAGATACTGAGT 58.237 33.333 0.00 0.00 0.00 3.41
3214 4549 6.681729 AATAATCCAGGAGTAAGCCGATTA 57.318 37.500 0.00 0.00 30.26 1.75
3240 4575 8.000709 ACAAAAATATCCAGCATTAGGAGATGA 58.999 33.333 0.00 0.00 37.19 2.92
3246 4581 6.713762 TGGACAAAAATATCCAGCATTAGG 57.286 37.500 0.00 0.00 40.17 2.69
3260 4595 4.069304 CCATCGACCTACTTGGACAAAAA 58.931 43.478 0.00 0.00 39.71 1.94
3277 4612 0.659427 CCACAGCTAATGCACCATCG 59.341 55.000 0.00 0.00 42.74 3.84
3304 4639 5.824624 AGAAATGAAGTGCTCAGAAAAGTGA 59.175 36.000 0.00 0.00 37.52 3.41
3383 4718 2.544844 TGGATCGGAGGGAGTAACTT 57.455 50.000 0.00 0.00 0.00 2.66
3384 4719 2.777459 ATGGATCGGAGGGAGTAACT 57.223 50.000 0.00 0.00 0.00 2.24
3385 4720 5.715753 ACTAATATGGATCGGAGGGAGTAAC 59.284 44.000 0.00 0.00 0.00 2.50
3386 4721 5.900437 ACTAATATGGATCGGAGGGAGTAA 58.100 41.667 0.00 0.00 0.00 2.24
3387 4722 5.531753 ACTAATATGGATCGGAGGGAGTA 57.468 43.478 0.00 0.00 0.00 2.59
3388 4723 4.405756 ACTAATATGGATCGGAGGGAGT 57.594 45.455 0.00 0.00 0.00 3.85
3389 4724 7.291566 AGTATACTAATATGGATCGGAGGGAG 58.708 42.308 2.75 0.00 0.00 4.30
3390 4725 7.222180 AGTATACTAATATGGATCGGAGGGA 57.778 40.000 2.75 0.00 0.00 4.20
3391 4726 8.991783 TTAGTATACTAATATGGATCGGAGGG 57.008 38.462 19.30 0.00 33.83 4.30
3393 4728 9.953697 GCTTTAGTATACTAATATGGATCGGAG 57.046 37.037 22.80 14.76 38.16 4.63
3394 4729 9.696572 AGCTTTAGTATACTAATATGGATCGGA 57.303 33.333 22.80 6.25 38.16 4.55
3395 4730 9.737427 CAGCTTTAGTATACTAATATGGATCGG 57.263 37.037 22.80 4.18 38.16 4.18
3396 4731 9.239002 GCAGCTTTAGTATACTAATATGGATCG 57.761 37.037 22.80 9.80 38.16 3.69
3399 4734 9.706691 GTTGCAGCTTTAGTATACTAATATGGA 57.293 33.333 22.80 18.80 38.16 3.41
3400 4735 9.489084 TGTTGCAGCTTTAGTATACTAATATGG 57.511 33.333 22.80 14.96 38.16 2.74
3411 4746 9.402320 TCCATATTAATTGTTGCAGCTTTAGTA 57.598 29.630 1.17 2.53 0.00 1.82
3412 4747 8.292444 TCCATATTAATTGTTGCAGCTTTAGT 57.708 30.769 1.17 0.43 0.00 2.24
3413 4748 9.403110 GATCCATATTAATTGTTGCAGCTTTAG 57.597 33.333 1.17 0.00 0.00 1.85
3414 4749 8.075574 CGATCCATATTAATTGTTGCAGCTTTA 58.924 33.333 1.17 0.00 0.00 1.85
3415 4750 6.919662 CGATCCATATTAATTGTTGCAGCTTT 59.080 34.615 1.17 0.00 0.00 3.51
3416 4751 6.441274 CGATCCATATTAATTGTTGCAGCTT 58.559 36.000 1.17 0.00 0.00 3.74
3417 4752 5.048504 CCGATCCATATTAATTGTTGCAGCT 60.049 40.000 1.17 0.00 0.00 4.24
3418 4753 5.048782 TCCGATCCATATTAATTGTTGCAGC 60.049 40.000 0.00 0.00 0.00 5.25
3419 4754 6.348786 CCTCCGATCCATATTAATTGTTGCAG 60.349 42.308 0.00 0.00 0.00 4.41
3420 4755 5.473162 CCTCCGATCCATATTAATTGTTGCA 59.527 40.000 0.00 0.00 0.00 4.08
3421 4756 5.106157 CCCTCCGATCCATATTAATTGTTGC 60.106 44.000 0.00 0.00 0.00 4.17
3422 4757 6.237901 TCCCTCCGATCCATATTAATTGTTG 58.762 40.000 0.00 0.00 0.00 3.33
3423 4758 6.044404 ACTCCCTCCGATCCATATTAATTGTT 59.956 38.462 0.00 0.00 0.00 2.83
3424 4759 5.548056 ACTCCCTCCGATCCATATTAATTGT 59.452 40.000 0.00 0.00 0.00 2.71
3425 4760 6.054860 ACTCCCTCCGATCCATATTAATTG 57.945 41.667 0.00 0.00 0.00 2.32
3426 4761 7.846823 AGATACTCCCTCCGATCCATATTAATT 59.153 37.037 0.00 0.00 0.00 1.40
3427 4762 7.366226 AGATACTCCCTCCGATCCATATTAAT 58.634 38.462 0.00 0.00 0.00 1.40
3428 4763 6.742756 AGATACTCCCTCCGATCCATATTAA 58.257 40.000 0.00 0.00 0.00 1.40
3429 4764 6.342819 AGATACTCCCTCCGATCCATATTA 57.657 41.667 0.00 0.00 0.00 0.98
3430 4765 5.213868 AGATACTCCCTCCGATCCATATT 57.786 43.478 0.00 0.00 0.00 1.28
3431 4766 4.890499 AGATACTCCCTCCGATCCATAT 57.110 45.455 0.00 0.00 0.00 1.78
3432 4767 4.292571 AGAAGATACTCCCTCCGATCCATA 59.707 45.833 0.00 0.00 0.00 2.74
3433 4768 3.076785 AGAAGATACTCCCTCCGATCCAT 59.923 47.826 0.00 0.00 0.00 3.41
3434 4769 2.447429 AGAAGATACTCCCTCCGATCCA 59.553 50.000 0.00 0.00 0.00 3.41
3435 4770 3.163616 AGAAGATACTCCCTCCGATCC 57.836 52.381 0.00 0.00 0.00 3.36
3436 4771 4.342665 ACAAAGAAGATACTCCCTCCGATC 59.657 45.833 0.00 0.00 0.00 3.69
3437 4772 4.100189 CACAAAGAAGATACTCCCTCCGAT 59.900 45.833 0.00 0.00 0.00 4.18
3438 4773 3.447586 CACAAAGAAGATACTCCCTCCGA 59.552 47.826 0.00 0.00 0.00 4.55
3439 4774 3.195825 ACACAAAGAAGATACTCCCTCCG 59.804 47.826 0.00 0.00 0.00 4.63
3440 4775 4.828072 ACACAAAGAAGATACTCCCTCC 57.172 45.455 0.00 0.00 0.00 4.30
3441 4776 6.378848 AGAGTACACAAAGAAGATACTCCCTC 59.621 42.308 6.18 0.00 41.71 4.30
3442 4777 6.257586 AGAGTACACAAAGAAGATACTCCCT 58.742 40.000 6.18 0.00 41.71 4.20
3443 4778 6.378848 AGAGAGTACACAAAGAAGATACTCCC 59.621 42.308 6.18 0.00 41.71 4.30
3444 4779 7.399245 AGAGAGTACACAAAGAAGATACTCC 57.601 40.000 6.18 0.12 41.71 3.85
3445 4780 8.400186 GGTAGAGAGTACACAAAGAAGATACTC 58.600 40.741 0.00 0.00 41.29 2.59
3446 4781 7.889073 TGGTAGAGAGTACACAAAGAAGATACT 59.111 37.037 0.00 0.00 0.00 2.12
3475 4811 7.175990 ACCGTATATTGACCAAAAGAACAACAT 59.824 33.333 0.00 0.00 0.00 2.71
3656 4999 0.109132 CCGGCCTTGCTTTCAATGTC 60.109 55.000 0.00 0.00 0.00 3.06
3657 5000 0.827507 ACCGGCCTTGCTTTCAATGT 60.828 50.000 0.00 0.00 0.00 2.71
3673 5016 3.002656 CAGCTTTGCTACCATAATCACCG 59.997 47.826 0.00 0.00 36.40 4.94
3675 5018 5.528690 TCATCAGCTTTGCTACCATAATCAC 59.471 40.000 0.00 0.00 36.40 3.06
3698 5041 6.756299 ATCTTCTTTCTTTCTGCAATCCTC 57.244 37.500 0.00 0.00 0.00 3.71
3712 5055 5.003804 TCAGTGGCTTGGTAATCTTCTTTC 58.996 41.667 0.00 0.00 0.00 2.62
3731 5074 2.418910 CGATCGGGCAGGAGTCAGT 61.419 63.158 7.38 0.00 0.00 3.41
3814 5157 0.388659 GGGCTGCATTGTCAACAACA 59.611 50.000 0.50 0.00 38.86 3.33
3815 5158 0.675633 AGGGCTGCATTGTCAACAAC 59.324 50.000 0.50 0.00 38.86 3.32
3872 5215 5.221722 TGCTAAGCTTATCCCTCCATGTTAG 60.222 44.000 6.64 0.00 0.00 2.34
3889 5232 4.195225 ACTCTCCTACAAAGTGCTAAGC 57.805 45.455 0.00 0.00 0.00 3.09
3895 5238 8.734218 TCTGTATACTACTCTCCTACAAAGTG 57.266 38.462 4.17 0.00 0.00 3.16
3916 5259 3.537580 TGCGACTTACCAAAAGTTCTGT 58.462 40.909 0.00 0.00 0.00 3.41
3917 5260 3.058914 CCTGCGACTTACCAAAAGTTCTG 60.059 47.826 0.00 0.00 0.00 3.02
3918 5261 3.139077 CCTGCGACTTACCAAAAGTTCT 58.861 45.455 0.00 0.00 0.00 3.01
3919 5262 3.135994 TCCTGCGACTTACCAAAAGTTC 58.864 45.455 0.00 0.00 0.00 3.01
3956 5302 3.750130 CAGCCTCATGATATTGTACAGCC 59.250 47.826 0.00 0.00 0.00 4.85
3990 5336 4.023707 GTGCATTATGGAGTACTGATTGCC 60.024 45.833 0.00 0.00 0.00 4.52
4038 5384 9.101655 GAAAGAGCAACAATTATATGGCAAATT 57.898 29.630 0.00 0.00 0.00 1.82
4090 5436 9.606631 TGACACATGTTTATGCTACATAATACA 57.393 29.630 0.00 12.97 37.85 2.29
4145 5493 6.657541 TGAACTTTCTACTTGTCAACCACTTT 59.342 34.615 0.00 0.00 0.00 2.66
4196 5548 5.353111 TGATTTACGCTTCCACGATGAATA 58.647 37.500 0.00 0.00 36.70 1.75
4198 5550 3.591023 TGATTTACGCTTCCACGATGAA 58.409 40.909 0.00 0.00 36.70 2.57
4199 5551 3.186909 CTGATTTACGCTTCCACGATGA 58.813 45.455 0.00 0.00 36.70 2.92
4200 5552 2.285834 GCTGATTTACGCTTCCACGATG 60.286 50.000 0.00 0.00 36.70 3.84
4201 5553 1.933853 GCTGATTTACGCTTCCACGAT 59.066 47.619 0.00 0.00 36.70 3.73
4202 5554 1.337354 TGCTGATTTACGCTTCCACGA 60.337 47.619 0.00 0.00 36.70 4.35
4211 5563 6.198966 GCCTTAATTCCATTTGCTGATTTACG 59.801 38.462 0.00 0.00 0.00 3.18
4219 5571 5.394553 GCTGTTAGCCTTAATTCCATTTGCT 60.395 40.000 0.00 0.00 34.48 3.91
4273 5625 3.499918 CACAGTGAAAACCTTCTAGCTGG 59.500 47.826 0.00 0.00 34.18 4.85
4288 5641 3.199946 AGGAACTTCAACCTTCACAGTGA 59.800 43.478 0.00 0.00 27.25 3.41
4302 5655 5.488341 TGCATACCTTCTTACAGGAACTTC 58.512 41.667 0.00 0.00 34.60 3.01
4343 5700 1.540267 GATAGCATGCATCCAAGCTGG 59.460 52.381 21.98 0.00 44.85 4.85
4349 5706 3.151554 GGTGAATGATAGCATGCATCCA 58.848 45.455 21.98 13.99 42.00 3.41
4419 5793 4.727507 TGCCACTCATCTTCTAAGAGAC 57.272 45.455 0.00 0.00 38.66 3.36
4424 5798 6.417258 TGATTGAATGCCACTCATCTTCTAA 58.583 36.000 0.00 0.00 33.40 2.10
4510 7810 2.682856 GCTTCGTTATGATCCCTGCAAA 59.317 45.455 0.00 0.00 0.00 3.68
4526 7827 2.053627 GTGCATTTCCAAACTGCTTCG 58.946 47.619 0.00 0.00 36.84 3.79
4668 8166 2.270434 AGTCATTTCCTCCAGGGCTA 57.730 50.000 0.00 0.00 35.41 3.93
4670 8168 1.283321 AGAAGTCATTTCCTCCAGGGC 59.717 52.381 0.00 0.00 36.40 5.19
4688 9346 9.702494 CATTCTTGAGCTCATGTGTAATATAGA 57.298 33.333 24.31 14.52 0.00 1.98
4689 9347 8.441608 GCATTCTTGAGCTCATGTGTAATATAG 58.558 37.037 24.31 12.64 0.00 1.31
4727 9387 5.760253 GCTGACCTAAGCTAATATGCTCAAA 59.240 40.000 0.00 0.00 43.24 2.69
4748 9408 2.286872 CCCTGTTATCTCAGCAAGCTG 58.713 52.381 15.67 15.67 44.86 4.24
4753 9413 0.833287 GCTCCCCTGTTATCTCAGCA 59.167 55.000 0.00 0.00 34.47 4.41
4827 9490 1.539827 CTGCCGTTTTCAGGGGTAAAG 59.460 52.381 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.