Multiple sequence alignment - TraesCS3B01G140000

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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 TraesCS3B01G140000 chr3B 100.000 3380 0 0 1 3380 126311762 126308383 0.000000e+00 6242.0
1 TraesCS3B01G140000 chr3B 86.029 1360 161 18 1028 2365 126302843 126301491 0.000000e+00 1432.0
2 TraesCS3B01G140000 chr3B 83.091 1378 181 27 1019 2365 79979113 79980469 0.000000e+00 1206.0
3 TraesCS3B01G140000 chr3D 93.616 1817 97 10 787 2596 80569209 80567405 0.000000e+00 2695.0
4 TraesCS3B01G140000 chr3D 92.740 1832 112 9 860 2683 80262750 80264568 0.000000e+00 2627.0
5 TraesCS3B01G140000 chr3D 83.169 1622 197 43 793 2365 80478970 80477376 0.000000e+00 1413.0
6 TraesCS3B01G140000 chr3D 81.788 1510 208 43 882 2364 50424864 50426333 0.000000e+00 1203.0
7 TraesCS3B01G140000 chr3D 75.036 1378 259 58 1043 2364 80417934 80416586 8.190000e-156 560.0
8 TraesCS3B01G140000 chr3D 91.099 191 10 2 3190 3380 80564662 80564479 5.600000e-63 252.0
9 TraesCS3B01G140000 chr3D 90.840 131 4 2 3250 3380 80264586 80264708 5.800000e-38 169.0
10 TraesCS3B01G140000 chr3D 92.958 71 5 0 1 71 80230058 80230128 1.660000e-18 104.0
11 TraesCS3B01G140000 chr3A 95.396 1694 68 4 787 2478 94187638 94185953 0.000000e+00 2687.0
12 TraesCS3B01G140000 chr3A 84.413 1482 175 32 912 2365 94183605 94182152 0.000000e+00 1406.0
13 TraesCS3B01G140000 chr3A 91.601 1012 49 9 1395 2398 94102322 94103305 0.000000e+00 1365.0
14 TraesCS3B01G140000 chr3A 81.457 1510 209 41 882 2362 63485214 63486681 0.000000e+00 1171.0
15 TraesCS3B01G140000 chr3A 85.081 1106 139 17 1275 2365 94107016 94108110 0.000000e+00 1105.0
16 TraesCS3B01G140000 chr3A 85.859 297 34 5 89 384 94190144 94189855 3.280000e-80 309.0
17 TraesCS3B01G140000 chr3A 95.238 189 9 0 1121 1309 94101597 94101785 1.970000e-77 300.0
18 TraesCS3B01G140000 chr3A 82.267 344 45 13 442 770 94189703 94189361 1.990000e-72 283.0
19 TraesCS3B01G140000 chr3A 86.145 166 15 4 2445 2606 94104369 94104530 4.480000e-39 172.0
20 TraesCS3B01G140000 chr4B 92.941 510 35 1 2682 3190 37192060 37191551 0.000000e+00 741.0
21 TraesCS3B01G140000 chr4B 91.124 507 40 5 2688 3190 143321514 143321009 0.000000e+00 682.0
22 TraesCS3B01G140000 chr4B 83.333 90 12 3 347 434 462242578 462242666 2.800000e-11 80.5
23 TraesCS3B01G140000 chr5D 91.406 512 40 2 2683 3190 327606623 327606112 0.000000e+00 699.0
24 TraesCS3B01G140000 chr2B 88.258 511 55 3 2683 3192 482640017 482639511 1.040000e-169 606.0
25 TraesCS3B01G140000 chr2D 86.187 514 57 9 2683 3192 238156180 238155677 8.250000e-151 544.0
26 TraesCS3B01G140000 chr2D 82.635 501 78 8 2680 3176 387432069 387432564 5.180000e-118 435.0
27 TraesCS3B01G140000 chr2D 83.088 136 20 3 289 424 351362611 351362743 1.650000e-23 121.0
28 TraesCS3B01G140000 chr6A 88.136 413 49 0 2780 3192 563249444 563249032 3.030000e-135 492.0
29 TraesCS3B01G140000 chr4A 85.088 456 60 6 2721 3172 150668650 150669101 3.070000e-125 459.0
30 TraesCS3B01G140000 chr1B 92.013 313 24 1 2682 2993 5866072 5865760 4.000000e-119 438.0
31 TraesCS3B01G140000 chr2A 82.550 149 23 3 289 437 469094388 469094533 9.840000e-26 128.0
32 TraesCS3B01G140000 chr1D 80.392 153 28 2 293 444 366483531 366483682 7.660000e-22 115.0
33 TraesCS3B01G140000 chr4D 82.278 79 11 3 347 423 375378353 375378430 7.830000e-07 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 TraesCS3B01G140000 chr3B 126308383 126311762 3379 True 6242.00 6242 100.00000 1 3380 1 chr3B.!!$R2 3379
1 TraesCS3B01G140000 chr3B 126301491 126302843 1352 True 1432.00 1432 86.02900 1028 2365 1 chr3B.!!$R1 1337
2 TraesCS3B01G140000 chr3B 79979113 79980469 1356 False 1206.00 1206 83.09100 1019 2365 1 chr3B.!!$F1 1346
3 TraesCS3B01G140000 chr3D 80564479 80569209 4730 True 1473.50 2695 92.35750 787 3380 2 chr3D.!!$R3 2593
4 TraesCS3B01G140000 chr3D 80477376 80478970 1594 True 1413.00 1413 83.16900 793 2365 1 chr3D.!!$R2 1572
5 TraesCS3B01G140000 chr3D 80262750 80264708 1958 False 1398.00 2627 91.79000 860 3380 2 chr3D.!!$F3 2520
6 TraesCS3B01G140000 chr3D 50424864 50426333 1469 False 1203.00 1203 81.78800 882 2364 1 chr3D.!!$F1 1482
7 TraesCS3B01G140000 chr3D 80416586 80417934 1348 True 560.00 560 75.03600 1043 2364 1 chr3D.!!$R1 1321
8 TraesCS3B01G140000 chr3A 94182152 94190144 7992 True 1171.25 2687 86.98375 89 2478 4 chr3A.!!$R1 2389
9 TraesCS3B01G140000 chr3A 63485214 63486681 1467 False 1171.00 1171 81.45700 882 2362 1 chr3A.!!$F1 1480
10 TraesCS3B01G140000 chr3A 94101597 94108110 6513 False 735.50 1365 89.51625 1121 2606 4 chr3A.!!$F2 1485
11 TraesCS3B01G140000 chr4B 37191551 37192060 509 True 741.00 741 92.94100 2682 3190 1 chr4B.!!$R1 508
12 TraesCS3B01G140000 chr4B 143321009 143321514 505 True 682.00 682 91.12400 2688 3190 1 chr4B.!!$R2 502
13 TraesCS3B01G140000 chr5D 327606112 327606623 511 True 699.00 699 91.40600 2683 3190 1 chr5D.!!$R1 507
14 TraesCS3B01G140000 chr2B 482639511 482640017 506 True 606.00 606 88.25800 2683 3192 1 chr2B.!!$R1 509
15 TraesCS3B01G140000 chr2D 238155677 238156180 503 True 544.00 544 86.18700 2683 3192 1 chr2D.!!$R1 509

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
774 885 0.370273 AAAGACTAAATCAGCGCGCG 59.630 50.0 28.44 28.44 0.0 6.86 F
1646 8828 0.322975 AGAGTCAACTTCGGCTGCAT 59.677 50.0 0.50 0.00 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2030 9215 0.392193 CTTCCGCTGGAGCTTGATGT 60.392 55.0 0.0 0.0 39.32 3.06 R
3152 15794 0.450482 GCGTGTCCGTTTTGTGATCG 60.450 55.0 0.0 0.0 36.15 3.69 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
36 37 6.930667 ATGGAATAAAAATTGCAGGAATGC 57.069 33.333 0.00 0.00 35.41 3.56
37 38 6.052405 TGGAATAAAAATTGCAGGAATGCT 57.948 33.333 1.53 0.00 35.49 3.79
38 39 7.180322 TGGAATAAAAATTGCAGGAATGCTA 57.820 32.000 1.53 0.00 35.49 3.49
39 40 7.267128 TGGAATAAAAATTGCAGGAATGCTAG 58.733 34.615 1.53 0.00 35.49 3.42
40 41 6.201615 GGAATAAAAATTGCAGGAATGCTAGC 59.798 38.462 8.10 8.10 35.49 3.42
41 42 4.813750 AAAAATTGCAGGAATGCTAGCT 57.186 36.364 17.23 0.00 35.49 3.32
42 43 5.920193 AAAAATTGCAGGAATGCTAGCTA 57.080 34.783 17.23 2.58 35.49 3.32
43 44 4.907879 AAATTGCAGGAATGCTAGCTAC 57.092 40.909 17.23 7.03 35.49 3.58
44 45 3.853355 ATTGCAGGAATGCTAGCTACT 57.147 42.857 17.23 0.00 35.49 2.57
45 46 4.963318 ATTGCAGGAATGCTAGCTACTA 57.037 40.909 17.23 0.00 35.49 1.82
46 47 3.735237 TGCAGGAATGCTAGCTACTAC 57.265 47.619 17.23 0.00 35.49 2.73
47 48 3.031013 TGCAGGAATGCTAGCTACTACA 58.969 45.455 17.23 0.23 35.49 2.74
48 49 3.068732 TGCAGGAATGCTAGCTACTACAG 59.931 47.826 17.23 1.93 35.49 2.74
49 50 3.319405 GCAGGAATGCTAGCTACTACAGA 59.681 47.826 17.23 0.00 0.00 3.41
50 51 4.021544 GCAGGAATGCTAGCTACTACAGAT 60.022 45.833 17.23 0.00 0.00 2.90
51 52 5.468592 CAGGAATGCTAGCTACTACAGATG 58.531 45.833 17.23 0.00 0.00 2.90
52 53 5.010516 CAGGAATGCTAGCTACTACAGATGT 59.989 44.000 17.23 0.00 0.00 3.06
53 54 6.207614 CAGGAATGCTAGCTACTACAGATGTA 59.792 42.308 17.23 0.00 0.00 2.29
75 76 9.750783 ATGTAGTATATATTAGAAGGGTCGTGT 57.249 33.333 0.00 0.00 0.00 4.49
76 77 9.224267 TGTAGTATATATTAGAAGGGTCGTGTC 57.776 37.037 0.00 0.00 0.00 3.67
77 78 9.224267 GTAGTATATATTAGAAGGGTCGTGTCA 57.776 37.037 0.00 0.00 0.00 3.58
78 79 8.108551 AGTATATATTAGAAGGGTCGTGTCAC 57.891 38.462 0.00 0.00 0.00 3.67
79 80 4.667519 ATATTAGAAGGGTCGTGTCACC 57.332 45.455 0.00 0.00 35.42 4.02
109 110 3.715628 AGGATTGTGTGCACTTTGTTC 57.284 42.857 19.41 8.41 0.00 3.18
112 113 3.181487 GGATTGTGTGCACTTTGTTCTGT 60.181 43.478 19.41 0.00 0.00 3.41
115 116 0.376852 TGTGCACTTTGTTCTGTCGC 59.623 50.000 19.41 0.00 0.00 5.19
116 117 0.657840 GTGCACTTTGTTCTGTCGCT 59.342 50.000 10.32 0.00 0.00 4.93
125 126 1.014352 GTTCTGTCGCTGGTGTTGTT 58.986 50.000 0.00 0.00 0.00 2.83
128 129 0.813610 CTGTCGCTGGTGTTGTTGGA 60.814 55.000 0.00 0.00 0.00 3.53
133 134 2.428890 TCGCTGGTGTTGTTGGAATTTT 59.571 40.909 0.00 0.00 0.00 1.82
134 135 2.794350 CGCTGGTGTTGTTGGAATTTTC 59.206 45.455 0.00 0.00 0.00 2.29
135 136 3.490761 CGCTGGTGTTGTTGGAATTTTCT 60.491 43.478 0.00 0.00 0.00 2.52
136 137 4.051237 GCTGGTGTTGTTGGAATTTTCTC 58.949 43.478 0.00 0.00 0.00 2.87
137 138 4.202151 GCTGGTGTTGTTGGAATTTTCTCT 60.202 41.667 0.00 0.00 0.00 3.10
138 139 5.682212 GCTGGTGTTGTTGGAATTTTCTCTT 60.682 40.000 0.00 0.00 0.00 2.85
139 140 6.293004 TGGTGTTGTTGGAATTTTCTCTTT 57.707 33.333 0.00 0.00 0.00 2.52
165 166 5.514274 AATGTCTATTATTTGGGTTGGCG 57.486 39.130 0.00 0.00 0.00 5.69
170 171 1.550327 TTATTTGGGTTGGCGCATGA 58.450 45.000 10.83 0.00 37.40 3.07
178 179 1.956477 GGTTGGCGCATGAGGAATATT 59.044 47.619 10.83 0.00 0.00 1.28
179 180 2.362077 GGTTGGCGCATGAGGAATATTT 59.638 45.455 10.83 0.00 0.00 1.40
180 181 3.181476 GGTTGGCGCATGAGGAATATTTT 60.181 43.478 10.83 0.00 0.00 1.82
222 223 1.577328 TAGTGCGCTTTCTTGGCAGC 61.577 55.000 9.73 0.00 37.36 5.25
223 224 2.906388 TGCGCTTTCTTGGCAGCA 60.906 55.556 9.73 0.00 35.60 4.41
225 226 1.804326 GCGCTTTCTTGGCAGCATG 60.804 57.895 0.00 0.00 35.60 4.06
229 230 2.537401 GCTTTCTTGGCAGCATGATTC 58.463 47.619 0.00 0.00 39.69 2.52
244 245 7.465173 CAGCATGATTCTATGATGTGCTAATC 58.535 38.462 0.00 0.00 39.08 1.75
269 270 8.889717 TCAATTCATACTTATTTCGGGAAGTTC 58.110 33.333 0.00 0.00 37.16 3.01
284 286 4.589675 TTCCCGGTGTTGGTGGCC 62.590 66.667 0.00 0.00 0.00 5.36
290 292 4.054825 GTGTTGGTGGCCGCATGG 62.055 66.667 19.98 0.00 38.77 3.66
307 309 1.085893 TGGCGCTACAATGTCACATG 58.914 50.000 7.64 0.00 0.00 3.21
312 314 3.785505 GCGCTACAATGTCACATGTTAGC 60.786 47.826 16.33 16.33 0.00 3.09
321 323 3.186409 TGTCACATGTTAGCGCTTCTTTC 59.814 43.478 18.68 2.50 0.00 2.62
333 335 3.250040 GCGCTTCTTTCTTTAGGTGTTGA 59.750 43.478 0.00 0.00 0.00 3.18
346 348 1.386533 GTGTTGAGAGGATGCATGGG 58.613 55.000 2.46 0.00 0.00 4.00
349 351 1.211457 GTTGAGAGGATGCATGGGACT 59.789 52.381 2.46 0.00 0.00 3.85
353 355 2.902486 GAGAGGATGCATGGGACTGATA 59.098 50.000 2.46 0.00 0.00 2.15
354 356 2.905085 AGAGGATGCATGGGACTGATAG 59.095 50.000 2.46 0.00 0.00 2.08
384 386 2.094234 GGCTGGTTGTTGCCGATTAATT 60.094 45.455 0.00 0.00 39.71 1.40
386 388 3.367630 GCTGGTTGTTGCCGATTAATTTG 59.632 43.478 0.00 0.00 0.00 2.32
387 389 4.804108 CTGGTTGTTGCCGATTAATTTGA 58.196 39.130 0.00 0.00 0.00 2.69
388 390 4.804108 TGGTTGTTGCCGATTAATTTGAG 58.196 39.130 0.00 0.00 0.00 3.02
389 391 4.520874 TGGTTGTTGCCGATTAATTTGAGA 59.479 37.500 0.00 0.00 0.00 3.27
390 392 5.010112 TGGTTGTTGCCGATTAATTTGAGAA 59.990 36.000 0.00 0.00 0.00 2.87
391 393 5.923684 GGTTGTTGCCGATTAATTTGAGAAA 59.076 36.000 0.00 0.00 0.00 2.52
392 394 6.589907 GGTTGTTGCCGATTAATTTGAGAAAT 59.410 34.615 0.00 0.00 0.00 2.17
393 395 7.201435 GGTTGTTGCCGATTAATTTGAGAAATC 60.201 37.037 0.00 0.00 0.00 2.17
394 396 6.918626 TGTTGCCGATTAATTTGAGAAATCA 58.081 32.000 0.00 0.00 31.37 2.57
396 398 8.034215 TGTTGCCGATTAATTTGAGAAATCATT 58.966 29.630 0.00 0.00 31.37 2.57
397 399 7.990541 TGCCGATTAATTTGAGAAATCATTG 57.009 32.000 0.00 0.00 31.37 2.82
398 400 6.476380 TGCCGATTAATTTGAGAAATCATTGC 59.524 34.615 0.00 0.00 31.37 3.56
399 401 6.074142 GCCGATTAATTTGAGAAATCATTGCC 60.074 38.462 0.00 0.00 31.37 4.52
400 402 6.421801 CCGATTAATTTGAGAAATCATTGCCC 59.578 38.462 0.00 0.00 31.37 5.36
401 403 6.421801 CGATTAATTTGAGAAATCATTGCCCC 59.578 38.462 0.00 0.00 31.37 5.80
404 406 5.703730 ATTTGAGAAATCATTGCCCCAAT 57.296 34.783 0.00 0.00 34.04 3.16
405 407 4.741321 TTGAGAAATCATTGCCCCAATC 57.259 40.909 0.00 0.00 31.05 2.67
407 409 4.095211 TGAGAAATCATTGCCCCAATCAA 58.905 39.130 0.00 0.00 31.05 2.57
408 410 4.531339 TGAGAAATCATTGCCCCAATCAAA 59.469 37.500 0.00 0.00 31.05 2.69
411 413 6.486941 AGAAATCATTGCCCCAATCAAAATT 58.513 32.000 0.00 0.00 31.05 1.82
412 414 6.376018 AGAAATCATTGCCCCAATCAAAATTG 59.624 34.615 0.00 0.00 41.69 2.32
413 415 4.637387 TCATTGCCCCAATCAAAATTGT 57.363 36.364 0.00 0.00 40.63 2.71
415 417 4.041321 TCATTGCCCCAATCAAAATTGTGA 59.959 37.500 0.00 0.00 40.63 3.58
416 418 4.428294 TTGCCCCAATCAAAATTGTGAA 57.572 36.364 1.55 0.00 40.63 3.18
417 419 4.637387 TGCCCCAATCAAAATTGTGAAT 57.363 36.364 1.55 0.00 40.63 2.57
418 420 4.577875 TGCCCCAATCAAAATTGTGAATC 58.422 39.130 1.55 0.00 40.63 2.52
419 421 4.041321 TGCCCCAATCAAAATTGTGAATCA 59.959 37.500 1.55 0.00 40.63 2.57
420 422 5.002516 GCCCCAATCAAAATTGTGAATCAA 58.997 37.500 1.55 0.00 40.63 2.57
422 424 6.151480 GCCCCAATCAAAATTGTGAATCAAAT 59.849 34.615 1.55 0.00 40.63 2.32
423 425 7.626876 GCCCCAATCAAAATTGTGAATCAAATC 60.627 37.037 1.55 0.00 40.63 2.17
424 426 7.148205 CCCCAATCAAAATTGTGAATCAAATCC 60.148 37.037 1.55 0.00 40.63 3.01
425 427 7.390996 CCCAATCAAAATTGTGAATCAAATCCA 59.609 33.333 1.55 0.00 40.63 3.41
426 428 8.784994 CCAATCAAAATTGTGAATCAAATCCAA 58.215 29.630 1.55 0.00 40.63 3.53
461 557 6.797033 CCTTAACTTTATGCTGAGTGTTTTCG 59.203 38.462 0.00 0.00 0.00 3.46
462 558 7.307751 CCTTAACTTTATGCTGAGTGTTTTCGA 60.308 37.037 0.00 0.00 0.00 3.71
471 567 1.126846 GAGTGTTTTCGAGTCATGCCG 59.873 52.381 0.00 0.00 0.00 5.69
474 570 1.666553 TTTTCGAGTCATGCCGCGT 60.667 52.632 4.92 0.00 0.00 6.01
475 571 0.388778 TTTTCGAGTCATGCCGCGTA 60.389 50.000 4.92 0.00 0.00 4.42
476 572 1.074319 TTTCGAGTCATGCCGCGTAC 61.074 55.000 4.92 0.00 0.00 3.67
477 573 3.312504 CGAGTCATGCCGCGTACG 61.313 66.667 11.84 11.84 39.67 3.67
478 574 2.202570 GAGTCATGCCGCGTACGT 60.203 61.111 17.90 0.00 37.70 3.57
479 575 1.063006 GAGTCATGCCGCGTACGTA 59.937 57.895 17.90 0.00 37.70 3.57
485 581 1.375853 ATGCCGCGTACGTAGTGGTA 61.376 55.000 17.90 13.22 45.73 3.25
486 582 1.356624 GCCGCGTACGTAGTGGTAT 59.643 57.895 17.90 0.00 45.73 2.73
487 583 0.931662 GCCGCGTACGTAGTGGTATG 60.932 60.000 17.90 0.00 45.73 2.39
488 584 0.931662 CCGCGTACGTAGTGGTATGC 60.932 60.000 17.90 6.81 46.82 3.14
491 587 0.657312 CGTACGTAGTGGTATGCCGA 59.343 55.000 7.22 0.00 45.73 5.54
492 588 1.333524 CGTACGTAGTGGTATGCCGAG 60.334 57.143 7.22 0.00 45.73 4.63
496 597 1.337071 CGTAGTGGTATGCCGAGACAT 59.663 52.381 0.00 0.00 37.67 3.06
513 614 1.060713 CATCGTCTTGGTGTCGACAC 58.939 55.000 35.26 35.26 45.72 3.67
544 645 1.445942 GCCATAAGCCGAGTAGCCA 59.554 57.895 0.00 0.00 34.35 4.75
551 652 6.349300 CCATAAGCCGAGTAGCCAATATAAT 58.651 40.000 0.00 0.00 0.00 1.28
554 655 5.340439 AGCCGAGTAGCCAATATAATACC 57.660 43.478 0.00 0.00 0.00 2.73
560 661 6.812160 CGAGTAGCCAATATAATACCCTTGAC 59.188 42.308 0.00 0.00 0.00 3.18
641 745 8.665643 TTCACAAGGAAAACGTAAGAGAATTA 57.334 30.769 0.00 0.00 34.70 1.40
643 747 8.717821 TCACAAGGAAAACGTAAGAGAATTATG 58.282 33.333 0.00 0.00 43.62 1.90
662 766 9.838339 GAATTATGAAATAAGGTCAGAGGAGAA 57.162 33.333 0.00 0.00 42.97 2.87
663 767 9.620259 AATTATGAAATAAGGTCAGAGGAGAAC 57.380 33.333 0.00 0.00 42.97 3.01
664 768 6.627087 ATGAAATAAGGTCAGAGGAGAACA 57.373 37.500 0.00 0.00 0.00 3.18
668 772 6.821616 AATAAGGTCAGAGGAGAACATGAT 57.178 37.500 0.00 0.00 0.00 2.45
669 773 7.921041 AATAAGGTCAGAGGAGAACATGATA 57.079 36.000 0.00 0.00 0.00 2.15
671 775 6.627087 AAGGTCAGAGGAGAACATGATAAA 57.373 37.500 0.00 0.00 0.00 1.40
672 776 6.232581 AGGTCAGAGGAGAACATGATAAAG 57.767 41.667 0.00 0.00 0.00 1.85
678 788 9.224267 TCAGAGGAGAACATGATAAAGAAAAAG 57.776 33.333 0.00 0.00 0.00 2.27
705 815 6.272822 AGGAGAAAATCATGCAGTTTAACC 57.727 37.500 0.00 0.00 0.00 2.85
706 816 5.774690 AGGAGAAAATCATGCAGTTTAACCA 59.225 36.000 0.00 0.00 0.00 3.67
709 819 7.063780 GGAGAAAATCATGCAGTTTAACCATTG 59.936 37.037 0.00 0.00 0.00 2.82
712 822 2.094803 TCATGCAGTTTAACCATTGCCG 60.095 45.455 5.56 0.00 35.75 5.69
721 831 4.920640 TTAACCATTGCCGTTTCTGAAA 57.079 36.364 0.00 0.00 0.00 2.69
723 833 2.582052 ACCATTGCCGTTTCTGAAAGA 58.418 42.857 2.48 0.00 44.68 2.52
732 842 6.378582 TGCCGTTTCTGAAAGATTTAATGTC 58.621 36.000 2.48 0.00 46.36 3.06
744 854 6.225981 AGATTTAATGTCCCTGCCATTTTC 57.774 37.500 0.00 0.00 34.51 2.29
760 871 1.892209 TTTCTGGCGGAGGAAAAGAC 58.108 50.000 0.00 0.00 0.00 3.01
762 873 1.933021 TCTGGCGGAGGAAAAGACTA 58.067 50.000 0.00 0.00 0.00 2.59
770 881 3.307242 CGGAGGAAAAGACTAAATCAGCG 59.693 47.826 0.00 0.00 0.00 5.18
771 882 3.064134 GGAGGAAAAGACTAAATCAGCGC 59.936 47.826 0.00 0.00 0.00 5.92
772 883 2.673368 AGGAAAAGACTAAATCAGCGCG 59.327 45.455 0.00 0.00 0.00 6.86
774 885 0.370273 AAAGACTAAATCAGCGCGCG 59.630 50.000 28.44 28.44 0.00 6.86
775 886 2.025359 AAGACTAAATCAGCGCGCGC 62.025 55.000 45.10 45.10 42.33 6.86
776 887 3.492980 GACTAAATCAGCGCGCGCC 62.493 63.158 46.98 30.60 43.17 6.53
789 900 2.581354 GCGCCCTGTCTCACTGAT 59.419 61.111 0.00 0.00 0.00 2.90
790 901 1.520342 GCGCCCTGTCTCACTGATC 60.520 63.158 0.00 0.00 0.00 2.92
801 2618 7.201947 CCCTGTCTCACTGATCACTAATAATCA 60.202 40.741 0.00 0.00 0.00 2.57
840 2658 7.881775 AATTACCGCCTTCAAATCTCTAATT 57.118 32.000 0.00 0.00 0.00 1.40
841 2659 8.974060 AATTACCGCCTTCAAATCTCTAATTA 57.026 30.769 0.00 0.00 0.00 1.40
842 2660 8.974060 ATTACCGCCTTCAAATCTCTAATTAA 57.026 30.769 0.00 0.00 0.00 1.40
843 2661 8.974060 TTACCGCCTTCAAATCTCTAATTAAT 57.026 30.769 0.00 0.00 0.00 1.40
880 2714 6.944234 AGTTACTATTGCAGGAAATTAGCC 57.056 37.500 0.00 0.00 0.00 3.93
906 2740 1.278238 GCTTACCACATTCGTCTCCG 58.722 55.000 0.00 0.00 0.00 4.63
954 2792 1.673168 CAGAGGAGGCCATTAGCAAC 58.327 55.000 5.01 0.00 46.50 4.17
974 2813 0.813184 CGACCGGGTGTAGAGCTAAA 59.187 55.000 3.30 0.00 0.00 1.85
975 2814 1.407979 CGACCGGGTGTAGAGCTAAAT 59.592 52.381 3.30 0.00 0.00 1.40
982 2825 4.623002 GGGTGTAGAGCTAAATACTGAGC 58.377 47.826 0.00 0.00 39.08 4.26
989 2832 5.901552 AGAGCTAAATACTGAGCAGAAGAC 58.098 41.667 4.21 0.00 41.36 3.01
1020 2867 4.501714 GCGGGTACGACATGGCGA 62.502 66.667 31.27 8.69 44.60 5.54
1023 2870 2.954868 GGTACGACATGGCGAGCG 60.955 66.667 31.27 10.19 34.83 5.03
1134 2987 2.361992 TCTCCCAAGTCGCCGCTA 60.362 61.111 0.00 0.00 0.00 4.26
1646 8828 0.322975 AGAGTCAACTTCGGCTGCAT 59.677 50.000 0.50 0.00 0.00 3.96
1649 8831 0.874390 GTCAACTTCGGCTGCATCAA 59.126 50.000 0.50 0.00 0.00 2.57
1737 8919 2.586079 ATCAACCAGATCGGCGCG 60.586 61.111 0.00 0.00 39.03 6.86
1935 9120 1.101331 GGAACTCGACCATCGTACCT 58.899 55.000 0.00 0.00 41.35 3.08
2030 9215 0.603569 GTGGGAGAGCTCACGAAGAA 59.396 55.000 17.77 0.00 35.45 2.52
2175 9369 1.375396 CGCCGTGATCACCCTGAAA 60.375 57.895 20.03 0.00 0.00 2.69
2370 9573 0.965439 CTCCTCCCGCCTCTAATCAG 59.035 60.000 0.00 0.00 0.00 2.90
2372 9575 1.118356 CCTCCCGCCTCTAATCAGCT 61.118 60.000 0.00 0.00 0.00 4.24
2474 9679 3.126343 CCCTACGTCTAATGTTTTGCCAC 59.874 47.826 0.00 0.00 0.00 5.01
2507 9712 1.741528 ATGCATGCGTGACTTGATGA 58.258 45.000 12.68 0.00 0.00 2.92
2562 10146 5.065090 TGCAACATGTAATTTCATCTCCGAG 59.935 40.000 0.00 0.00 0.00 4.63
2571 10155 3.685139 TTCATCTCCGAGACTGCTTTT 57.315 42.857 0.00 0.00 0.00 2.27
2598 12855 3.490759 CATGACCTGCACGACGGC 61.491 66.667 0.00 0.10 0.00 5.68
2631 12893 4.081917 TGTCCGCTACACTTTGATGACATA 60.082 41.667 0.00 0.00 31.43 2.29
2643 12905 4.322080 TGATGACATAGATGGACGAACC 57.678 45.455 0.00 0.00 39.54 3.62
2659 12921 3.067601 ACGAACCGATATGCACTGTCATA 59.932 43.478 0.00 3.57 33.89 2.15
2665 12927 5.645929 ACCGATATGCACTGTCATACAAAAA 59.354 36.000 0.00 0.00 32.36 1.94
2666 12928 6.318648 ACCGATATGCACTGTCATACAAAAAT 59.681 34.615 0.00 0.00 32.36 1.82
2668 12930 7.254898 CCGATATGCACTGTCATACAAAAATCT 60.255 37.037 0.00 0.00 32.36 2.40
2669 12931 7.795734 CGATATGCACTGTCATACAAAAATCTC 59.204 37.037 0.00 0.00 32.36 2.75
2670 12932 5.281693 TGCACTGTCATACAAAAATCTCG 57.718 39.130 0.00 0.00 0.00 4.04
2671 12933 4.091424 GCACTGTCATACAAAAATCTCGC 58.909 43.478 0.00 0.00 0.00 5.03
2672 12934 4.378356 GCACTGTCATACAAAAATCTCGCA 60.378 41.667 0.00 0.00 0.00 5.10
2673 12935 5.319139 CACTGTCATACAAAAATCTCGCAG 58.681 41.667 0.00 0.00 0.00 5.18
2674 12936 4.393062 ACTGTCATACAAAAATCTCGCAGG 59.607 41.667 0.00 0.00 0.00 4.85
2675 12937 4.323417 TGTCATACAAAAATCTCGCAGGT 58.677 39.130 0.00 0.00 0.00 4.00
2676 12938 4.759693 TGTCATACAAAAATCTCGCAGGTT 59.240 37.500 0.00 0.00 0.00 3.50
2677 12939 5.935206 TGTCATACAAAAATCTCGCAGGTTA 59.065 36.000 0.00 0.00 0.00 2.85
2678 12940 6.428465 TGTCATACAAAAATCTCGCAGGTTAA 59.572 34.615 0.00 0.00 0.00 2.01
2818 13649 1.204467 CACCGTGCCAGCCAATTAAAT 59.796 47.619 0.00 0.00 0.00 1.40
2822 13653 3.380004 CCGTGCCAGCCAATTAAATAAGA 59.620 43.478 0.00 0.00 0.00 2.10
2978 13915 9.756571 CCCACATAGTTAGTCCTAGAATAGTAT 57.243 37.037 0.00 0.00 36.82 2.12
3020 13990 3.181487 GCTGTTCAGTCCATGTTTGTTGT 60.181 43.478 1.78 0.00 0.00 3.32
3152 15794 1.546029 GGTTGATTGTTTCCTGCTCCC 59.454 52.381 0.00 0.00 0.00 4.30
3154 15796 0.690192 TGATTGTTTCCTGCTCCCGA 59.310 50.000 0.00 0.00 0.00 5.14
3187 15829 2.584608 GCATCCTGGTGCGGTAGT 59.415 61.111 5.69 0.00 35.10 2.73
3208 15851 8.867097 GGTAGTCCTCAGGTTAATTGTGATATA 58.133 37.037 0.00 0.00 0.00 0.86
3238 15881 9.427127 GTTCTTCGATGTTGCTAAATCTAAATC 57.573 33.333 0.00 0.00 0.00 2.17
3242 15885 7.618442 TCGATGTTGCTAAATCTAAATCGTTC 58.382 34.615 0.00 0.00 37.51 3.95
3286 15929 6.422776 AATTGATACACTAAAGCGGTCAAG 57.577 37.500 0.00 0.00 0.00 3.02
3299 15942 1.935873 CGGTCAAGCATGTGATGGTAG 59.064 52.381 0.00 0.00 40.65 3.18
3300 15943 2.677902 CGGTCAAGCATGTGATGGTAGT 60.678 50.000 0.00 0.00 40.65 2.73
3301 15944 3.430236 CGGTCAAGCATGTGATGGTAGTA 60.430 47.826 0.00 0.00 40.65 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 5.010516 ACATCTGTAGTAGCTAGCATTCCTG 59.989 44.000 18.83 4.96 0.00 3.86
29 30 5.144100 ACATCTGTAGTAGCTAGCATTCCT 58.856 41.667 18.83 8.92 0.00 3.36
30 31 5.461032 ACATCTGTAGTAGCTAGCATTCC 57.539 43.478 18.83 1.00 0.00 3.01
49 50 9.750783 ACACGACCCTTCTAATATATACTACAT 57.249 33.333 0.00 0.00 0.00 2.29
50 51 9.224267 GACACGACCCTTCTAATATATACTACA 57.776 37.037 0.00 0.00 0.00 2.74
51 52 9.224267 TGACACGACCCTTCTAATATATACTAC 57.776 37.037 0.00 0.00 0.00 2.73
52 53 9.224267 GTGACACGACCCTTCTAATATATACTA 57.776 37.037 0.00 0.00 0.00 1.82
53 54 7.176340 GGTGACACGACCCTTCTAATATATACT 59.824 40.741 0.00 0.00 0.00 2.12
54 55 7.311408 GGTGACACGACCCTTCTAATATATAC 58.689 42.308 0.00 0.00 0.00 1.47
55 56 7.458409 GGTGACACGACCCTTCTAATATATA 57.542 40.000 0.00 0.00 0.00 0.86
56 57 6.342338 GGTGACACGACCCTTCTAATATAT 57.658 41.667 0.00 0.00 0.00 0.86
57 58 5.779529 GGTGACACGACCCTTCTAATATA 57.220 43.478 0.00 0.00 0.00 0.86
58 59 4.667519 GGTGACACGACCCTTCTAATAT 57.332 45.455 0.00 0.00 0.00 1.28
85 86 4.831107 ACAAAGTGCACACAATCCTTTTT 58.169 34.783 21.04 4.32 0.00 1.94
86 87 4.470334 ACAAAGTGCACACAATCCTTTT 57.530 36.364 21.04 5.09 0.00 2.27
87 88 4.160252 AGAACAAAGTGCACACAATCCTTT 59.840 37.500 21.04 5.87 0.00 3.11
92 93 3.487376 CGACAGAACAAAGTGCACACAAT 60.487 43.478 21.04 0.23 0.00 2.71
105 106 0.107897 ACAACACCAGCGACAGAACA 60.108 50.000 0.00 0.00 0.00 3.18
109 110 0.813610 TCCAACAACACCAGCGACAG 60.814 55.000 0.00 0.00 0.00 3.51
112 113 1.686355 AATTCCAACAACACCAGCGA 58.314 45.000 0.00 0.00 0.00 4.93
115 116 5.520376 AGAGAAAATTCCAACAACACCAG 57.480 39.130 0.00 0.00 0.00 4.00
116 117 5.930837 AAGAGAAAATTCCAACAACACCA 57.069 34.783 0.00 0.00 0.00 4.17
138 139 9.660180 GCCAACCCAAATAATAGACATTTTTAA 57.340 29.630 0.00 0.00 0.00 1.52
139 140 7.976734 CGCCAACCCAAATAATAGACATTTTTA 59.023 33.333 0.00 0.00 0.00 1.52
144 145 3.317993 GCGCCAACCCAAATAATAGACAT 59.682 43.478 0.00 0.00 0.00 3.06
148 149 3.317711 TCATGCGCCAACCCAAATAATAG 59.682 43.478 4.18 0.00 0.00 1.73
193 194 2.755836 AAGCGCACTAAAACACTGTG 57.244 45.000 11.47 6.19 35.08 3.66
244 245 8.129211 GGAACTTCCCGAAATAAGTATGAATTG 58.871 37.037 0.00 0.00 34.91 2.32
290 292 2.900122 AACATGTGACATTGTAGCGC 57.100 45.000 0.00 0.00 0.00 5.92
307 309 4.451435 ACACCTAAAGAAAGAAGCGCTAAC 59.549 41.667 12.05 8.57 0.00 2.34
312 314 4.750098 TCTCAACACCTAAAGAAAGAAGCG 59.250 41.667 0.00 0.00 0.00 4.68
321 323 3.942829 TGCATCCTCTCAACACCTAAAG 58.057 45.455 0.00 0.00 0.00 1.85
333 335 1.817087 ATCAGTCCCATGCATCCTCT 58.183 50.000 0.00 0.00 0.00 3.69
384 386 4.095211 TGATTGGGGCAATGATTTCTCAA 58.905 39.130 0.00 0.00 33.90 3.02
386 388 4.741321 TTGATTGGGGCAATGATTTCTC 57.259 40.909 0.00 0.00 33.90 2.87
387 389 5.502089 TTTTGATTGGGGCAATGATTTCT 57.498 34.783 0.00 0.00 33.90 2.52
388 390 6.151480 ACAATTTTGATTGGGGCAATGATTTC 59.849 34.615 0.00 0.00 33.90 2.17
389 391 6.011481 ACAATTTTGATTGGGGCAATGATTT 58.989 32.000 0.00 0.00 33.90 2.17
390 392 5.416326 CACAATTTTGATTGGGGCAATGATT 59.584 36.000 0.00 0.00 33.90 2.57
391 393 4.944930 CACAATTTTGATTGGGGCAATGAT 59.055 37.500 0.00 0.00 33.90 2.45
392 394 4.041321 TCACAATTTTGATTGGGGCAATGA 59.959 37.500 1.93 0.00 35.72 2.57
393 395 4.325119 TCACAATTTTGATTGGGGCAATG 58.675 39.130 1.93 0.00 35.72 2.82
394 396 4.637387 TCACAATTTTGATTGGGGCAAT 57.363 36.364 1.93 0.00 35.72 3.56
396 398 4.041321 TGATTCACAATTTTGATTGGGGCA 59.959 37.500 0.00 0.00 35.72 5.36
397 399 4.577875 TGATTCACAATTTTGATTGGGGC 58.422 39.130 0.00 0.00 35.72 5.80
398 400 7.148205 GGATTTGATTCACAATTTTGATTGGGG 60.148 37.037 0.00 0.00 38.36 4.96
399 401 7.390996 TGGATTTGATTCACAATTTTGATTGGG 59.609 33.333 0.00 0.00 38.36 4.12
400 402 8.325421 TGGATTTGATTCACAATTTTGATTGG 57.675 30.769 0.00 0.00 38.36 3.16
428 430 9.686683 ACTCAGCATAAAGTTAAGGTATTCAAT 57.313 29.630 0.00 0.00 0.00 2.57
430 432 8.100791 ACACTCAGCATAAAGTTAAGGTATTCA 58.899 33.333 0.00 0.00 0.00 2.57
432 434 8.863872 AACACTCAGCATAAAGTTAAGGTATT 57.136 30.769 0.00 0.00 0.00 1.89
433 435 8.863872 AAACACTCAGCATAAAGTTAAGGTAT 57.136 30.769 0.00 0.00 0.00 2.73
434 436 8.685838 AAAACACTCAGCATAAAGTTAAGGTA 57.314 30.769 0.00 0.00 0.00 3.08
435 437 7.519970 CGAAAACACTCAGCATAAAGTTAAGGT 60.520 37.037 0.00 0.00 0.00 3.50
437 439 7.572759 TCGAAAACACTCAGCATAAAGTTAAG 58.427 34.615 0.00 0.00 0.00 1.85
438 440 7.225931 ACTCGAAAACACTCAGCATAAAGTTAA 59.774 33.333 0.00 0.00 0.00 2.01
440 442 5.527582 ACTCGAAAACACTCAGCATAAAGTT 59.472 36.000 0.00 0.00 0.00 2.66
444 540 4.627058 TGACTCGAAAACACTCAGCATAA 58.373 39.130 0.00 0.00 0.00 1.90
461 557 0.928908 CTACGTACGCGGCATGACTC 60.929 60.000 16.72 0.00 43.45 3.36
462 558 1.063649 CTACGTACGCGGCATGACT 59.936 57.895 16.72 0.00 43.45 3.41
471 567 0.931662 CGGCATACCACTACGTACGC 60.932 60.000 16.72 0.00 34.57 4.42
474 570 1.942657 GTCTCGGCATACCACTACGTA 59.057 52.381 0.00 0.00 34.57 3.57
475 571 0.737219 GTCTCGGCATACCACTACGT 59.263 55.000 0.00 0.00 34.57 3.57
476 572 0.736636 TGTCTCGGCATACCACTACG 59.263 55.000 0.00 0.00 34.57 3.51
477 573 2.604855 CGATGTCTCGGCATACCACTAC 60.605 54.545 0.00 0.00 41.27 2.73
478 574 1.607148 CGATGTCTCGGCATACCACTA 59.393 52.381 0.00 0.00 41.27 2.74
479 575 0.385751 CGATGTCTCGGCATACCACT 59.614 55.000 0.00 0.00 41.27 4.00
491 587 1.068472 GTCGACACCAAGACGATGTCT 60.068 52.381 11.55 0.00 45.29 3.41
492 588 1.335597 TGTCGACACCAAGACGATGTC 60.336 52.381 15.76 0.00 45.29 3.06
496 597 0.248743 GTGTGTCGACACCAAGACGA 60.249 55.000 38.12 20.18 45.96 4.20
513 614 3.471680 GCTTATGGCCCTCTAAGAAGTG 58.528 50.000 16.80 0.00 34.27 3.16
540 641 5.562298 ACGTCAAGGGTATTATATTGGCT 57.438 39.130 0.00 0.00 0.00 4.75
633 737 9.218525 TCCTCTGACCTTATTTCATAATTCTCT 57.781 33.333 0.00 0.00 0.00 3.10
641 745 6.627087 TGTTCTCCTCTGACCTTATTTCAT 57.373 37.500 0.00 0.00 0.00 2.57
643 747 6.644347 TCATGTTCTCCTCTGACCTTATTTC 58.356 40.000 0.00 0.00 0.00 2.17
654 758 9.799106 TTCTTTTTCTTTATCATGTTCTCCTCT 57.201 29.630 0.00 0.00 0.00 3.69
671 775 9.028284 TGCATGATTTTCTCCTATTCTTTTTCT 57.972 29.630 0.00 0.00 0.00 2.52
672 776 9.298774 CTGCATGATTTTCTCCTATTCTTTTTC 57.701 33.333 0.00 0.00 0.00 2.29
678 788 9.508567 GTTAAACTGCATGATTTTCTCCTATTC 57.491 33.333 0.00 0.00 0.00 1.75
687 797 5.412286 GGCAATGGTTAAACTGCATGATTTT 59.588 36.000 7.02 0.00 36.50 1.82
705 815 7.329226 ACATTAAATCTTTCAGAAACGGCAATG 59.671 33.333 0.00 2.21 0.00 2.82
706 816 7.378181 ACATTAAATCTTTCAGAAACGGCAAT 58.622 30.769 0.00 0.00 0.00 3.56
709 819 5.800438 GGACATTAAATCTTTCAGAAACGGC 59.200 40.000 0.00 0.00 0.00 5.68
712 822 6.808704 GCAGGGACATTAAATCTTTCAGAAAC 59.191 38.462 0.00 0.00 0.00 2.78
721 831 5.960202 AGAAAATGGCAGGGACATTAAATCT 59.040 36.000 0.00 0.71 40.81 2.40
723 833 5.104817 CCAGAAAATGGCAGGGACATTAAAT 60.105 40.000 0.00 0.00 40.81 1.40
744 854 2.762535 TTAGTCTTTTCCTCCGCCAG 57.237 50.000 0.00 0.00 0.00 4.85
771 882 3.362399 ATCAGTGAGACAGGGCGCG 62.362 63.158 0.00 0.00 0.00 6.86
772 883 1.520342 GATCAGTGAGACAGGGCGC 60.520 63.158 0.00 0.00 0.00 6.53
774 885 0.901124 AGTGATCAGTGAGACAGGGC 59.099 55.000 1.14 0.00 0.00 5.19
775 886 6.471233 TTATTAGTGATCAGTGAGACAGGG 57.529 41.667 13.54 0.00 0.00 4.45
776 887 7.720442 TGATTATTAGTGATCAGTGAGACAGG 58.280 38.462 13.54 0.00 0.00 4.00
784 895 8.982685 CGTGCTAAATGATTATTAGTGATCAGT 58.017 33.333 8.40 8.40 34.32 3.41
785 896 9.196552 TCGTGCTAAATGATTATTAGTGATCAG 57.803 33.333 0.00 0.00 34.32 2.90
786 897 9.541143 TTCGTGCTAAATGATTATTAGTGATCA 57.459 29.630 0.00 0.00 35.18 2.92
789 900 7.985184 AGGTTCGTGCTAAATGATTATTAGTGA 59.015 33.333 0.00 0.00 33.77 3.41
790 901 8.142994 AGGTTCGTGCTAAATGATTATTAGTG 57.857 34.615 0.00 0.00 33.77 2.74
801 2618 4.271776 GCGGTAATTAGGTTCGTGCTAAAT 59.728 41.667 0.00 0.00 0.00 1.40
841 2659 9.829507 CAATAGTAACTTGATTGGAGAGAGATT 57.170 33.333 0.00 0.00 0.00 2.40
842 2660 7.930865 GCAATAGTAACTTGATTGGAGAGAGAT 59.069 37.037 0.00 0.00 32.33 2.75
843 2661 7.093333 TGCAATAGTAACTTGATTGGAGAGAGA 60.093 37.037 0.00 0.00 32.33 3.10
858 2676 6.693315 TGGCTAATTTCCTGCAATAGTAAC 57.307 37.500 0.00 0.00 0.00 2.50
862 2680 6.645790 AGAATGGCTAATTTCCTGCAATAG 57.354 37.500 0.00 0.00 0.00 1.73
863 2681 6.683610 GCAAGAATGGCTAATTTCCTGCAATA 60.684 38.462 3.02 0.00 32.14 1.90
864 2682 5.667466 CAAGAATGGCTAATTTCCTGCAAT 58.333 37.500 0.00 0.00 0.00 3.56
880 2714 4.393062 AGACGAATGTGGTAAGCAAGAATG 59.607 41.667 0.00 0.00 0.00 2.67
906 2740 3.191371 GTGCAGTATTAATAGGGGCATGC 59.809 47.826 9.90 9.90 31.92 4.06
954 2792 1.033746 TTAGCTCTACACCCGGTCGG 61.034 60.000 0.00 1.86 37.81 4.79
974 2813 5.126384 GTGTCCTAAGTCTTCTGCTCAGTAT 59.874 44.000 0.00 0.00 0.00 2.12
975 2814 4.459685 GTGTCCTAAGTCTTCTGCTCAGTA 59.540 45.833 0.00 0.00 0.00 2.74
982 2825 3.686726 GCCATTGTGTCCTAAGTCTTCTG 59.313 47.826 0.00 0.00 0.00 3.02
989 2832 0.035439 ACCCGCCATTGTGTCCTAAG 60.035 55.000 0.00 0.00 0.00 2.18
1023 2870 2.970974 GACGCCAAGGAGCAACAGC 61.971 63.158 0.00 0.00 0.00 4.40
1646 8828 1.952133 CCGCCGTTCGTGTTCTTGA 60.952 57.895 0.00 0.00 36.19 3.02
1649 8831 4.595538 TGCCGCCGTTCGTGTTCT 62.596 61.111 0.00 0.00 36.19 3.01
2016 9201 3.583806 CTTGATGTTCTTCGTGAGCTCT 58.416 45.455 16.19 0.00 0.00 4.09
2025 9210 1.396301 CGCTGGAGCTTGATGTTCTTC 59.604 52.381 0.00 0.00 39.32 2.87
2030 9215 0.392193 CTTCCGCTGGAGCTTGATGT 60.392 55.000 0.00 0.00 39.32 3.06
2055 9240 3.393970 TCCAGCAGCTTCTCCGGG 61.394 66.667 0.00 0.00 0.00 5.73
2124 9315 2.027625 CAGCGTCACTTCCGGGAAC 61.028 63.158 5.09 0.00 0.00 3.62
2370 9573 7.831753 TGGTGATTAGCTATATCTACTCAAGC 58.168 38.462 5.52 0.00 32.45 4.01
2372 9575 9.533831 TCATGGTGATTAGCTATATCTACTCAA 57.466 33.333 5.52 0.00 32.45 3.02
2499 9704 2.230025 CAGACACCGAGACTCATCAAGT 59.770 50.000 2.82 0.00 42.42 3.16
2500 9705 2.416566 CCAGACACCGAGACTCATCAAG 60.417 54.545 2.82 0.00 0.00 3.02
2507 9712 1.645710 ATTTCCCAGACACCGAGACT 58.354 50.000 0.00 0.00 0.00 3.24
2562 10146 1.800586 TGCATCGTCTGAAAAGCAGTC 59.199 47.619 0.00 0.00 45.14 3.51
2571 10155 3.746900 CAGGTCATGCATCGTCTGA 57.253 52.632 11.98 0.00 0.00 3.27
2612 12869 5.176406 CCATCTATGTCATCAAAGTGTAGCG 59.824 44.000 0.00 0.00 0.00 4.26
2631 12893 1.686587 TGCATATCGGTTCGTCCATCT 59.313 47.619 0.00 0.00 35.57 2.90
2643 12905 7.633621 AGATTTTTGTATGACAGTGCATATCG 58.366 34.615 9.49 0.00 33.67 2.92
2659 12921 6.084326 ACAATTAACCTGCGAGATTTTTGT 57.916 33.333 0.00 0.00 0.00 2.83
2715 13052 9.468532 CTTTTGCCCTTCTTCTTTAATATATGC 57.531 33.333 0.00 0.00 0.00 3.14
2748 13089 8.171164 TGTAATTGAACATTGTAACATGGTGA 57.829 30.769 0.00 0.00 0.00 4.02
2777 13124 2.573369 GGATAGACGTGAGGAGTAGCA 58.427 52.381 0.00 0.00 0.00 3.49
2822 13653 2.279173 ACTGAAAGGGGATGTAAGCCT 58.721 47.619 0.00 0.00 39.68 4.58
3020 13990 2.509548 ACATCCTTGCACCTTGGCTATA 59.490 45.455 0.00 0.00 34.04 1.31
3081 15723 1.198713 GGTCTGGAAGGAGATCTGCA 58.801 55.000 17.24 0.00 0.00 4.41
3152 15794 0.450482 GCGTGTCCGTTTTGTGATCG 60.450 55.000 0.00 0.00 36.15 3.69
3154 15796 1.196808 GATGCGTGTCCGTTTTGTGAT 59.803 47.619 0.00 0.00 36.15 3.06
3187 15829 8.713971 ACACATATATCACAATTAACCTGAGGA 58.286 33.333 4.99 0.00 0.00 3.71
3208 15851 5.940192 TTTAGCAACATCGAAGAACACAT 57.060 34.783 0.00 0.00 43.58 3.21
3222 15865 8.822105 ATTTCGAACGATTTAGATTTAGCAAC 57.178 30.769 0.00 0.00 0.00 4.17
3286 15929 3.732212 TGATGCTACTACCATCACATGC 58.268 45.455 0.00 0.00 42.88 4.06
3299 15942 7.088589 ACCAACTAAATTGTGATGATGCTAC 57.911 36.000 0.00 0.00 36.47 3.58
3300 15943 6.037062 CGACCAACTAAATTGTGATGATGCTA 59.963 38.462 0.00 0.00 36.47 3.49
3301 15944 5.163723 CGACCAACTAAATTGTGATGATGCT 60.164 40.000 0.00 0.00 36.47 3.79
3343 15986 0.546598 CGGTTCTTATCCAGGCCCTT 59.453 55.000 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.