Multiple sequence alignment - TraesCS5D01G166200

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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 TraesCS5D01G166200 chr5D 100.000 9470 0 0 1 9470 258638506 258647975 0.000000e+00 17488.0
1 TraesCS5D01G166200 chr5D 89.889 1622 94 27 6531 8125 15676240 15674662 0.000000e+00 2023.0
2 TraesCS5D01G166200 chr5D 91.754 861 39 8 5662 6516 15677157 15676323 0.000000e+00 1168.0
3 TraesCS5D01G166200 chr5D 92.611 406 27 3 8140 8545 15674520 15674118 1.770000e-161 580.0
4 TraesCS5D01G166200 chr5D 94.783 345 14 4 5391 5733 15677500 15677158 1.400000e-147 534.0
5 TraesCS5D01G166200 chr5D 90.426 94 4 3 5260 5348 15723871 15723778 1.670000e-22 119.0
6 TraesCS5D01G166200 chr5B 97.971 7296 102 25 866 8125 292731894 292739179 0.000000e+00 12611.0
7 TraesCS5D01G166200 chr5B 95.816 1195 34 7 8128 9313 292739305 292740492 0.000000e+00 1916.0
8 TraesCS5D01G166200 chr5B 92.893 394 25 3 469 862 292728689 292729079 3.840000e-158 569.0
9 TraesCS5D01G166200 chr5B 86.869 396 41 2 1 385 292727978 292728373 5.250000e-117 433.0
10 TraesCS5D01G166200 chr5A 96.422 4220 117 16 896 5090 343449857 343454067 0.000000e+00 6926.0
11 TraesCS5D01G166200 chr5A 96.861 2899 45 17 5257 8125 343454066 343456948 0.000000e+00 4807.0
12 TraesCS5D01G166200 chr5A 93.894 606 25 4 8862 9466 343457974 343458568 0.000000e+00 904.0
13 TraesCS5D01G166200 chr5A 88.706 788 23 35 8134 8859 343457080 343457863 0.000000e+00 902.0
14 TraesCS5D01G166200 chr5A 86.028 501 51 8 370 853 343404487 343404985 3.920000e-143 520.0
15 TraesCS5D01G166200 chr5A 82.857 175 27 3 3059 3231 491048988 491049161 4.580000e-33 154.0
16 TraesCS5D01G166200 chrUn 89.889 1622 94 27 6531 8125 67699580 67698002 0.000000e+00 2023.0
17 TraesCS5D01G166200 chrUn 91.754 861 39 8 5662 6516 67700497 67699663 0.000000e+00 1168.0
18 TraesCS5D01G166200 chrUn 92.611 406 27 3 8140 8545 67697860 67697458 1.770000e-161 580.0
19 TraesCS5D01G166200 chrUn 94.783 345 14 4 5391 5733 67700840 67700498 1.400000e-147 534.0
20 TraesCS5D01G166200 chr4A 89.156 1623 96 26 6529 8125 586497197 586495629 0.000000e+00 1949.0
21 TraesCS5D01G166200 chr4A 94.774 1263 46 9 5260 6516 586498521 586497273 0.000000e+00 1949.0
22 TraesCS5D01G166200 chr4A 80.241 830 116 27 2421 3231 38680070 38679270 1.770000e-161 580.0
23 TraesCS5D01G166200 chr4A 93.316 374 24 1 8149 8522 586495475 586495103 1.390000e-152 551.0
24 TraesCS5D01G166200 chr3A 88.578 1646 101 29 6512 8125 670852589 670854179 0.000000e+00 1917.0
25 TraesCS5D01G166200 chr3A 93.946 859 35 6 5662 6516 670851711 670852556 0.000000e+00 1282.0
26 TraesCS5D01G166200 chr3A 95.810 358 11 4 5377 5733 670851356 670851710 8.250000e-160 575.0
27 TraesCS5D01G166200 chr3A 93.211 383 25 1 8140 8522 670854328 670854709 6.420000e-156 562.0
28 TraesCS5D01G166200 chr3A 96.183 131 3 1 5260 5388 670849812 670849942 7.450000e-51 213.0
29 TraesCS5D01G166200 chr3A 94.286 35 2 0 441 475 41598070 41598036 5.000000e-03 54.7
30 TraesCS5D01G166200 chr7B 93.395 863 35 8 5662 6516 639268031 639267183 0.000000e+00 1258.0
31 TraesCS5D01G166200 chr7B 95.388 477 17 4 5260 5733 639268506 639268032 0.000000e+00 754.0
32 TraesCS5D01G166200 chr7B 82.569 654 83 19 2485 3118 610330906 610331548 1.800000e-151 547.0
33 TraesCS5D01G166200 chr7B 80.097 206 31 9 3030 3231 213471084 213471283 2.760000e-30 145.0
34 TraesCS5D01G166200 chr2D 84.118 680 88 11 2496 3160 545957053 545956379 2.880000e-179 640.0
35 TraesCS5D01G166200 chr2D 90.604 149 14 0 9322 9470 22200798 22200946 2.090000e-46 198.0
36 TraesCS5D01G166200 chr2D 79.842 253 32 11 3007 3245 470381714 470381961 5.880000e-37 167.0
37 TraesCS5D01G166200 chr2B 80.845 757 110 18 2497 3226 652852439 652851691 6.420000e-156 562.0
38 TraesCS5D01G166200 chr1B 89.589 365 36 2 3704 4066 283904425 283904061 6.700000e-126 462.0
39 TraesCS5D01G166200 chr4D 94.631 149 7 1 9323 9470 362792000 362792148 7.400000e-56 230.0
40 TraesCS5D01G166200 chr6D 79.573 328 53 8 2445 2769 65602936 65602620 1.240000e-53 222.0
41 TraesCS5D01G166200 chr6D 82.105 190 31 3 3044 3231 296822367 296822555 9.840000e-35 159.0
42 TraesCS5D01G166200 chr6D 85.256 156 19 4 3078 3231 468812393 468812240 3.540000e-34 158.0
43 TraesCS5D01G166200 chr2A 91.275 149 13 0 9322 9470 680510160 680510012 4.480000e-48 204.0
44 TraesCS5D01G166200 chr1D 90.667 150 13 1 9322 9470 314506200 314506349 2.090000e-46 198.0
45 TraesCS5D01G166200 chr1A 90.667 150 13 1 9322 9470 330766042 330765893 2.090000e-46 198.0
46 TraesCS5D01G166200 chr1A 88.554 166 15 4 9307 9469 398058677 398058513 2.090000e-46 198.0
47 TraesCS5D01G166200 chr1A 85.621 153 20 2 3010 3161 373828072 373827921 9.840000e-35 159.0
48 TraesCS5D01G166200 chr1A 81.410 156 16 9 2496 2647 420393387 420393533 2.160000e-21 115.0
49 TraesCS5D01G166200 chr7A 86.782 174 19 4 9300 9470 30261866 30261694 3.490000e-44 191.0
50 TraesCS5D01G166200 chr7A 84.298 121 17 2 485 604 729891973 729891854 6.010000e-22 117.0
51 TraesCS5D01G166200 chr3B 89.610 154 9 6 9322 9470 757283285 757283134 1.260000e-43 189.0
52 TraesCS5D01G166200 chr3D 84.000 175 24 4 3060 3231 512220423 512220596 2.120000e-36 165.0


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 TraesCS5D01G166200 chr5D 258638506 258647975 9469 False 17488.00 17488 100.000000 1 9470 1 chr5D.!!$F1 9469
1 TraesCS5D01G166200 chr5D 15674118 15677500 3382 True 1076.25 2023 92.259250 5391 8545 4 chr5D.!!$R2 3154
2 TraesCS5D01G166200 chr5B 292727978 292740492 12514 False 3882.25 12611 93.387250 1 9313 4 chr5B.!!$F1 9312
3 TraesCS5D01G166200 chr5A 343449857 343458568 8711 False 3384.75 6926 93.970750 896 9466 4 chr5A.!!$F3 8570
4 TraesCS5D01G166200 chrUn 67697458 67700840 3382 True 1076.25 2023 92.259250 5391 8545 4 chrUn.!!$R1 3154
5 TraesCS5D01G166200 chr4A 586495103 586498521 3418 True 1483.00 1949 92.415333 5260 8522 3 chr4A.!!$R2 3262
6 TraesCS5D01G166200 chr4A 38679270 38680070 800 True 580.00 580 80.241000 2421 3231 1 chr4A.!!$R1 810
7 TraesCS5D01G166200 chr3A 670849812 670854709 4897 False 909.80 1917 93.545600 5260 8522 5 chr3A.!!$F1 3262
8 TraesCS5D01G166200 chr7B 639267183 639268506 1323 True 1006.00 1258 94.391500 5260 6516 2 chr7B.!!$R1 1256
9 TraesCS5D01G166200 chr7B 610330906 610331548 642 False 547.00 547 82.569000 2485 3118 1 chr7B.!!$F2 633
10 TraesCS5D01G166200 chr2D 545956379 545957053 674 True 640.00 640 84.118000 2496 3160 1 chr2D.!!$R1 664
11 TraesCS5D01G166200 chr2B 652851691 652852439 748 True 562.00 562 80.845000 2497 3226 1 chr2B.!!$R1 729

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
415 427 0.098200 TCTCGCATCGTACCAGTTCG 59.902 55.000 0.00 0.00 0.00 3.95 F
416 428 0.179171 CTCGCATCGTACCAGTTCGT 60.179 55.000 0.00 0.00 0.00 3.85 F
417 429 0.455464 TCGCATCGTACCAGTTCGTG 60.455 55.000 0.00 0.00 0.00 4.35 F
948 4003 0.525668 CCCGCAGATAGTGTGACGTC 60.526 60.000 9.11 9.11 39.20 4.34 F
1299 4372 0.918983 TGGGGATGTAGGCTCTTTGG 59.081 55.000 0.00 0.00 0.00 3.28 F
1323 4396 1.944676 CGACGCTATCTGTTCGGGC 60.945 63.158 0.00 0.00 0.00 6.13 F
1930 5009 7.060421 TCTCAAAAGAGTTTGTGATAGGGTTT 58.940 34.615 0.00 0.00 43.90 3.27 F
3319 6461 4.997395 GGCATTTTCTTTTCTTCCCTTTCC 59.003 41.667 0.00 0.00 0.00 3.13 F
4628 7778 4.323485 GGATTAGTGGATCTGGTGTTGACA 60.323 45.833 0.00 0.00 0.00 3.58 F
5949 10616 2.151502 TGGGCTGGTTGACAAGAAAA 57.848 45.000 0.00 0.00 0.00 2.29 F
6778 11523 0.252742 AGGTCGTCTTGGGGGATTCT 60.253 55.000 0.00 0.00 0.00 2.40 F
7510 12293 0.668706 CTGACAGCAGAACTCCCGTG 60.669 60.000 0.00 0.00 45.17 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1226 4296 1.752501 CGCCGAATCTACCGTGCAAG 61.753 60.000 0.0 0.0 0.00 4.01 R
1305 4378 1.944676 GCCCGAACAGATAGCGTCG 60.945 63.158 0.0 0.0 0.00 5.12 R
1323 4396 4.599047 TTGCCATACTTCCCAAAACAAG 57.401 40.909 0.0 0.0 0.00 3.16 R
2925 6021 3.921119 TGTCCGACTAGCTTTTTCGTA 57.079 42.857 0.0 0.0 0.00 3.43 R
2978 6074 0.953471 CCCGATTTCACTTGCACCGA 60.953 55.000 0.0 0.0 0.00 4.69 R
3319 6461 5.485209 AGTTAGGTCAACAAGGAAGTAGG 57.515 43.478 0.0 0.0 39.81 3.18 R
3642 6787 0.323178 AGCCATTGCCTCCAACTGAG 60.323 55.000 0.0 0.0 41.07 3.35 R
4844 8004 3.107601 AGAGCAGCACTTCCAATAGGTA 58.892 45.455 0.0 0.0 35.89 3.08 R
6097 10764 0.826062 TAGTGCCTTAGTAACCGCCC 59.174 55.000 0.0 0.0 0.00 6.13 R
6869 11614 0.323302 TACACATGCCTTTCTCCGCA 59.677 50.000 0.0 0.0 39.79 5.69 R
8333 13251 1.202639 TGGTCACACAAGTCAGCGAAT 60.203 47.619 0.0 0.0 0.00 3.34 R
8853 13831 2.625737 TGCTTCAGAGATAGCAACTGC 58.374 47.619 0.0 0.0 43.88 4.40 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
21 22 1.882623 GAAACAACCTGAAGGCTCCAG 59.117 52.381 0.00 0.00 39.32 3.86
31 32 1.684450 GAAGGCTCCAGCTACTAGACC 59.316 57.143 0.00 0.00 41.70 3.85
60 61 2.277373 GTCAGCTAGGTCGTCGCG 60.277 66.667 0.00 0.00 0.00 5.87
61 62 2.745100 TCAGCTAGGTCGTCGCGT 60.745 61.111 5.77 0.00 0.00 6.01
62 63 2.277373 CAGCTAGGTCGTCGCGTC 60.277 66.667 5.77 0.00 0.00 5.19
65 66 4.233635 CTAGGTCGTCGCGTCGGG 62.234 72.222 24.30 2.31 0.00 5.14
79 80 3.636231 CGGGCCCAGTGTCCTTGA 61.636 66.667 24.92 0.00 0.00 3.02
105 106 2.050350 CGGAGGCTCTGGTCGGTTA 61.050 63.158 15.82 0.00 0.00 2.85
127 128 2.279120 GAGCTCGGTGATGGCTCG 60.279 66.667 0.00 0.00 42.03 5.03
133 134 3.083997 GGTGATGGCTCGGGTCCT 61.084 66.667 0.00 0.00 0.00 3.85
134 135 2.187946 GTGATGGCTCGGGTCCTG 59.812 66.667 0.00 0.00 0.00 3.86
146 147 1.895866 CGGGTCCTGGAGTTTCTAGGT 60.896 57.143 0.00 0.00 44.54 3.08
147 148 2.267192 GGGTCCTGGAGTTTCTAGGTT 58.733 52.381 0.00 0.00 44.54 3.50
148 149 2.027100 GGGTCCTGGAGTTTCTAGGTTG 60.027 54.545 0.00 0.00 44.54 3.77
149 150 2.904434 GGTCCTGGAGTTTCTAGGTTGA 59.096 50.000 0.00 0.00 44.54 3.18
150 151 3.326880 GGTCCTGGAGTTTCTAGGTTGAA 59.673 47.826 0.00 0.00 44.54 2.69
155 167 4.232091 TGGAGTTTCTAGGTTGAACTCCT 58.768 43.478 28.25 4.67 40.59 3.69
156 168 5.399991 TGGAGTTTCTAGGTTGAACTCCTA 58.600 41.667 28.25 19.84 40.59 2.94
163 175 5.590818 TCTAGGTTGAACTCCTATTGGACT 58.409 41.667 0.00 0.00 37.46 3.85
166 178 3.194968 GGTTGAACTCCTATTGGACTCGA 59.805 47.826 0.00 0.00 37.46 4.04
177 189 6.605995 TCCTATTGGACTCGAAGACTTTGATA 59.394 38.462 5.57 0.00 37.46 2.15
189 201 6.237595 CGAAGACTTTGATATCGACAAGGTTC 60.238 42.308 11.69 11.69 37.60 3.62
226 238 0.669625 ACGACGACTTAAGGCCAAGC 60.670 55.000 5.01 0.00 0.00 4.01
241 253 1.925455 AAGCCCAGCTAGAAGCCCA 60.925 57.895 0.00 0.00 43.77 5.36
242 254 1.284841 AAGCCCAGCTAGAAGCCCAT 61.285 55.000 0.00 0.00 43.77 4.00
248 260 1.152368 GCTAGAAGCCCATGCCCAT 59.848 57.895 0.00 0.00 38.69 4.00
279 291 2.338500 GGTCTGGTCAAGATCAACGAC 58.662 52.381 0.00 0.00 35.91 4.34
301 313 1.490490 GGGATATGCCACCAGTCAGAA 59.510 52.381 8.65 0.00 38.95 3.02
327 339 2.648059 GCTAGTCAGGGAACATGCATT 58.352 47.619 0.00 0.00 0.00 3.56
343 355 6.906659 ACATGCATTAGTGTTCTCTTTGAAG 58.093 36.000 0.00 0.00 35.01 3.02
357 369 1.808411 TTGAAGAGGTCCAACGCATC 58.192 50.000 0.00 0.00 0.00 3.91
362 374 2.358247 GGTCCAACGCATCGGTGT 60.358 61.111 0.00 0.00 43.64 4.16
380 392 7.688478 TCGGTGTTCGATATACATGTAAAAG 57.312 36.000 10.14 2.44 43.74 2.27
385 397 7.850982 GTGTTCGATATACATGTAAAAGCCTTG 59.149 37.037 10.14 0.00 0.00 3.61
386 398 7.551262 TGTTCGATATACATGTAAAAGCCTTGT 59.449 33.333 10.14 0.00 0.00 3.16
387 399 7.709269 TCGATATACATGTAAAAGCCTTGTC 57.291 36.000 10.14 0.00 0.00 3.18
388 400 6.419710 TCGATATACATGTAAAAGCCTTGTCG 59.580 38.462 10.14 10.78 0.00 4.35
389 401 6.346598 CGATATACATGTAAAAGCCTTGTCGG 60.347 42.308 10.14 0.00 0.00 4.79
390 402 2.159382 ACATGTAAAAGCCTTGTCGGG 58.841 47.619 0.00 0.00 0.00 5.14
391 403 1.472480 CATGTAAAAGCCTTGTCGGGG 59.528 52.381 0.00 0.00 0.00 5.73
397 409 3.056328 GCCTTGTCGGGGCTTGTC 61.056 66.667 0.00 0.00 45.57 3.18
398 410 2.750350 CCTTGTCGGGGCTTGTCT 59.250 61.111 0.00 0.00 0.00 3.41
399 411 1.376037 CCTTGTCGGGGCTTGTCTC 60.376 63.158 0.00 0.00 0.00 3.36
400 412 1.738099 CTTGTCGGGGCTTGTCTCG 60.738 63.158 0.00 0.00 0.00 4.04
401 413 3.876589 TTGTCGGGGCTTGTCTCGC 62.877 63.158 0.00 0.00 0.00 5.03
402 414 4.373116 GTCGGGGCTTGTCTCGCA 62.373 66.667 0.00 0.00 0.00 5.10
403 415 3.390521 TCGGGGCTTGTCTCGCAT 61.391 61.111 0.00 0.00 0.00 4.73
404 416 2.892425 CGGGGCTTGTCTCGCATC 60.892 66.667 0.00 0.00 0.00 3.91
405 417 2.892425 GGGGCTTGTCTCGCATCG 60.892 66.667 0.00 0.00 0.00 3.84
406 418 2.125512 GGGCTTGTCTCGCATCGT 60.126 61.111 0.00 0.00 0.00 3.73
407 419 1.141019 GGGCTTGTCTCGCATCGTA 59.859 57.895 0.00 0.00 0.00 3.43
408 420 1.146358 GGGCTTGTCTCGCATCGTAC 61.146 60.000 0.00 0.00 0.00 3.67
409 421 1.146358 GGCTTGTCTCGCATCGTACC 61.146 60.000 0.00 0.00 0.00 3.34
410 422 0.457853 GCTTGTCTCGCATCGTACCA 60.458 55.000 0.00 0.00 0.00 3.25
411 423 1.550065 CTTGTCTCGCATCGTACCAG 58.450 55.000 0.00 0.00 0.00 4.00
412 424 0.885879 TTGTCTCGCATCGTACCAGT 59.114 50.000 0.00 0.00 0.00 4.00
413 425 0.885879 TGTCTCGCATCGTACCAGTT 59.114 50.000 0.00 0.00 0.00 3.16
414 426 1.135489 TGTCTCGCATCGTACCAGTTC 60.135 52.381 0.00 0.00 0.00 3.01
415 427 0.098200 TCTCGCATCGTACCAGTTCG 59.902 55.000 0.00 0.00 0.00 3.95
416 428 0.179171 CTCGCATCGTACCAGTTCGT 60.179 55.000 0.00 0.00 0.00 3.85
417 429 0.455464 TCGCATCGTACCAGTTCGTG 60.455 55.000 0.00 0.00 0.00 4.35
429 441 3.313012 CAGTTCGTGGACATGTAGGAA 57.687 47.619 0.00 0.00 0.00 3.36
430 442 3.254060 CAGTTCGTGGACATGTAGGAAG 58.746 50.000 0.00 0.00 0.00 3.46
431 443 2.000447 GTTCGTGGACATGTAGGAAGC 59.000 52.381 0.00 0.00 0.00 3.86
432 444 1.262417 TCGTGGACATGTAGGAAGCA 58.738 50.000 0.00 0.00 0.00 3.91
433 445 1.067142 TCGTGGACATGTAGGAAGCAC 60.067 52.381 0.00 0.00 0.00 4.40
434 446 1.337728 CGTGGACATGTAGGAAGCACA 60.338 52.381 0.00 0.00 0.00 4.57
435 447 2.350522 GTGGACATGTAGGAAGCACAG 58.649 52.381 0.00 0.00 0.00 3.66
436 448 1.278985 TGGACATGTAGGAAGCACAGG 59.721 52.381 0.00 0.00 34.03 4.00
437 449 1.373570 GACATGTAGGAAGCACAGGC 58.626 55.000 0.00 0.00 41.61 4.85
438 450 0.692476 ACATGTAGGAAGCACAGGCA 59.308 50.000 0.00 0.00 44.61 4.75
439 451 1.073763 ACATGTAGGAAGCACAGGCAA 59.926 47.619 0.00 0.00 44.61 4.52
440 452 2.291153 ACATGTAGGAAGCACAGGCAAT 60.291 45.455 0.00 0.00 44.61 3.56
441 453 1.825090 TGTAGGAAGCACAGGCAATG 58.175 50.000 0.00 0.00 44.61 2.82
442 454 1.098050 GTAGGAAGCACAGGCAATGG 58.902 55.000 0.00 0.00 44.61 3.16
443 455 0.680921 TAGGAAGCACAGGCAATGGC 60.681 55.000 0.00 0.00 44.61 4.40
444 456 2.180017 GAAGCACAGGCAATGGCG 59.820 61.111 0.00 0.00 44.61 5.69
445 457 3.346631 GAAGCACAGGCAATGGCGG 62.347 63.158 5.29 5.29 44.61 6.13
446 458 3.866379 AAGCACAGGCAATGGCGGA 62.866 57.895 14.32 0.00 44.61 5.54
447 459 3.818787 GCACAGGCAATGGCGGAG 61.819 66.667 14.32 6.99 42.47 4.63
465 477 5.300969 CGGAGCTTGATGAAGATTTTTGA 57.699 39.130 0.00 0.00 0.00 2.69
466 478 5.330295 CGGAGCTTGATGAAGATTTTTGAG 58.670 41.667 0.00 0.00 0.00 3.02
467 479 5.648572 GGAGCTTGATGAAGATTTTTGAGG 58.351 41.667 0.00 0.00 0.00 3.86
491 735 5.106594 GGGGCAAAGAAAACAAATTATGCAG 60.107 40.000 0.00 0.00 34.37 4.41
497 741 8.490355 CAAAGAAAACAAATTATGCAGGAACTC 58.510 33.333 0.00 0.00 34.60 3.01
534 778 9.753674 TGAATATCCAAGGCTAATAATTTAGGG 57.246 33.333 0.00 0.00 36.18 3.53
563 807 7.603024 CACTTAAGAGTTTTTCTAGTGTAGGGG 59.397 40.741 10.09 0.00 37.57 4.79
572 816 2.017049 CTAGTGTAGGGGTGCAATTGC 58.983 52.381 23.69 23.69 42.50 3.56
581 825 1.003476 GTGCAATTGCCCCCTTTGG 60.003 57.895 26.94 0.00 41.18 3.28
603 847 3.114616 CGTGAAGCTCCGCCACTG 61.115 66.667 0.00 0.00 0.00 3.66
621 865 1.278985 CTGGACACAGGGCATTACTCA 59.721 52.381 0.00 0.00 41.13 3.41
628 872 4.041691 ACACAGGGCATTACTCAGTAACTT 59.958 41.667 0.00 0.00 30.49 2.66
632 876 3.694566 GGGCATTACTCAGTAACTTTGGG 59.305 47.826 0.00 0.00 30.49 4.12
633 877 3.694566 GGCATTACTCAGTAACTTTGGGG 59.305 47.826 0.00 0.00 30.49 4.96
648 892 2.282180 GGGCTCCAAGACCGCAAA 60.282 61.111 0.00 0.00 30.77 3.68
661 905 2.694760 CGCAAAGCTCAAGAGGGGC 61.695 63.158 0.00 0.00 0.00 5.80
698 942 0.810648 TGGCTAGGCATTTTTCGCTG 59.189 50.000 16.16 0.00 0.00 5.18
821 1065 4.569162 TCGCGCTAATACAAATAGCAAAGT 59.431 37.500 5.56 0.00 44.77 2.66
834 1078 8.454106 ACAAATAGCAAAGTGTATTTAGCTCTG 58.546 33.333 0.00 0.00 33.83 3.35
836 1080 9.667107 AAATAGCAAAGTGTATTTAGCTCTGTA 57.333 29.630 0.00 0.00 33.83 2.74
840 1084 9.319143 AGCAAAGTGTATTTAGCTCTGTATAAG 57.681 33.333 0.00 0.00 0.00 1.73
894 3949 1.758514 GCAGGGGTCGGATCTCTCA 60.759 63.158 0.00 0.00 0.00 3.27
903 3958 3.443037 GTCGGATCTCTCATGTTCAGTG 58.557 50.000 0.00 0.00 0.00 3.66
948 4003 0.525668 CCCGCAGATAGTGTGACGTC 60.526 60.000 9.11 9.11 39.20 4.34
1029 4090 2.954684 AAGATCGGCGGCAACCAGA 61.955 57.895 10.53 0.00 0.00 3.86
1226 4296 1.452833 GCTTGGGTGCCTCCTGATC 60.453 63.158 0.00 0.00 36.25 2.92
1299 4372 0.918983 TGGGGATGTAGGCTCTTTGG 59.081 55.000 0.00 0.00 0.00 3.28
1305 4378 4.109675 TAGGCTCTTTGGCGGCCC 62.110 66.667 17.97 0.00 46.31 5.80
1323 4396 1.944676 CGACGCTATCTGTTCGGGC 60.945 63.158 0.00 0.00 0.00 6.13
1392 4470 8.043113 ACAACAATGTAGATAGCTTCTCAATGA 58.957 33.333 0.00 0.00 38.24 2.57
1930 5009 7.060421 TCTCAAAAGAGTTTGTGATAGGGTTT 58.940 34.615 0.00 0.00 43.90 3.27
3319 6461 4.997395 GGCATTTTCTTTTCTTCCCTTTCC 59.003 41.667 0.00 0.00 0.00 3.13
3642 6787 5.240183 TGCAGATTATTCAAAGATGGCTAGC 59.760 40.000 6.04 6.04 0.00 3.42
3796 6941 6.208007 TGAACTTAGTTGATCGTCCTCTAACA 59.792 38.462 0.93 0.00 0.00 2.41
3881 7026 5.834460 TCTTCTGTTACCTACCCATACTGA 58.166 41.667 0.00 0.00 0.00 3.41
3936 7081 6.773685 ACTGTTGTTTTAAGTACTATTGGCCA 59.226 34.615 0.00 0.00 0.00 5.36
4089 7239 8.912988 ACCCAACGATGATGTTTTGATAATAAT 58.087 29.630 0.00 0.00 0.00 1.28
4373 7523 8.364894 TGTGCTTACATTTTAGTCTTGAGAGTA 58.635 33.333 0.00 0.00 0.00 2.59
4385 7535 7.296628 AGTCTTGAGAGTATTTTCTGTCTGT 57.703 36.000 0.00 0.00 0.00 3.41
4628 7778 4.323485 GGATTAGTGGATCTGGTGTTGACA 60.323 45.833 0.00 0.00 0.00 3.58
4875 8035 4.261825 GGAAGTGCTGCTCTCTATATCGTT 60.262 45.833 4.52 0.00 0.00 3.85
5233 8393 4.154942 GCATGGGGATATTGGAAATGACT 58.845 43.478 0.00 0.00 0.00 3.41
5949 10616 2.151502 TGGGCTGGTTGACAAGAAAA 57.848 45.000 0.00 0.00 0.00 2.29
6097 10764 9.743057 AGAAATATCTCTATTCGACTTCAGTTG 57.257 33.333 0.00 0.00 0.00 3.16
6373 11046 0.737219 GGATCAGATTGTGCTGGTGC 59.263 55.000 0.00 0.00 36.55 5.01
6778 11523 0.252742 AGGTCGTCTTGGGGGATTCT 60.253 55.000 0.00 0.00 0.00 2.40
6869 11614 3.642503 TTCGAACCCGCACCCCAT 61.643 61.111 0.00 0.00 35.37 4.00
7213 11985 6.867816 TGCTTTTTATTGTTTGGCTCTATGTG 59.132 34.615 0.00 0.00 0.00 3.21
7510 12293 0.668706 CTGACAGCAGAACTCCCGTG 60.669 60.000 0.00 0.00 45.17 4.94
8128 12912 3.036431 GCCACAGGCTTGGTAAACT 57.964 52.632 14.43 0.00 46.69 2.66
8129 12913 0.881796 GCCACAGGCTTGGTAAACTC 59.118 55.000 14.43 0.00 46.69 3.01
8130 12914 1.156736 CCACAGGCTTGGTAAACTCG 58.843 55.000 0.00 0.00 0.00 4.18
8131 12915 1.542547 CCACAGGCTTGGTAAACTCGT 60.543 52.381 0.00 0.00 0.00 4.18
8137 13055 2.876550 GGCTTGGTAAACTCGTGAACTT 59.123 45.455 0.00 0.00 0.00 2.66
8333 13251 7.429636 AATCCTCGATGTAAAAGAACGAAAA 57.570 32.000 0.00 0.00 32.85 2.29
8361 13279 3.880490 TGACTTGTGTGACCATTTACCAC 59.120 43.478 0.00 0.00 0.00 4.16
8383 13301 5.926542 CACTTCCTCTCGTACTGAATTTTGA 59.073 40.000 0.00 0.00 0.00 2.69
8488 13406 1.630369 AGGCAAACTGAGTAGATGGCA 59.370 47.619 17.31 0.00 39.97 4.92
8853 13831 4.217111 ACACACACACGCGCGTTG 62.217 61.111 35.90 32.08 0.00 4.10
8883 13973 7.374272 TGCTATCTCTGAAGCAACACTATATC 58.626 38.462 0.22 0.00 45.36 1.63
8930 14020 2.003301 GAGGCAGGACGATGTTCTTTC 58.997 52.381 0.00 0.00 0.00 2.62
8932 14022 1.610624 GGCAGGACGATGTTCTTTCCA 60.611 52.381 0.00 0.00 0.00 3.53
9045 14136 5.223382 AGATTAGATCGGCAACAGATTACG 58.777 41.667 0.00 0.00 31.55 3.18
9086 14177 5.896073 AGTCAGGAACCCAGGAATTATAG 57.104 43.478 0.00 0.00 0.00 1.31
9272 14370 5.295292 AGCTTTGTCATCATTCCATAACTCG 59.705 40.000 0.00 0.00 0.00 4.18
9281 14379 6.392625 TCATTCCATAACTCGACTAAGGAG 57.607 41.667 0.00 0.00 37.54 3.69
9321 14419 9.628500 GAACTATGATATTTTGAAGGGTTAGGT 57.372 33.333 0.00 0.00 0.00 3.08
9324 14422 9.726438 CTATGATATTTTGAAGGGTTAGGTAGG 57.274 37.037 0.00 0.00 0.00 3.18
9384 14482 6.705302 AGTCACTCAATCAAGCATAAGAAGA 58.295 36.000 0.00 0.00 0.00 2.87
9438 14537 5.174035 CGAATCTCCGTGTAAGATCAATGAC 59.826 44.000 0.00 0.00 32.29 3.06
9442 14541 7.348080 TCTCCGTGTAAGATCAATGACTTAT 57.652 36.000 0.00 0.00 32.48 1.73
9454 14553 9.761504 AGATCAATGACTTATGACTTAGATGTG 57.238 33.333 0.00 0.00 0.00 3.21
9460 14559 8.648557 TGACTTATGACTTAGATGTGCAATAC 57.351 34.615 0.00 0.00 0.00 1.89
9466 14565 8.613060 ATGACTTAGATGTGCAATACTTATGG 57.387 34.615 0.00 0.00 0.00 2.74
9467 14566 6.483307 TGACTTAGATGTGCAATACTTATGGC 59.517 38.462 0.00 0.00 33.16 4.40
9468 14567 6.356556 ACTTAGATGTGCAATACTTATGGCA 58.643 36.000 0.00 0.00 40.19 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.379972 GTCTAGTAGCTGGAGCCTTCA 58.620 52.381 0.00 0.00 43.38 3.02
21 22 2.412112 CGTGCCCGGTCTAGTAGC 59.588 66.667 0.00 0.00 0.00 3.58
47 48 4.883300 CCGACGCGACGACCTAGC 62.883 72.222 30.91 0.00 35.09 3.42
60 61 3.637273 AAGGACACTGGGCCCGAC 61.637 66.667 19.37 2.86 0.00 4.79
61 62 3.636231 CAAGGACACTGGGCCCGA 61.636 66.667 19.37 5.42 0.00 5.14
62 63 2.690653 TTTCAAGGACACTGGGCCCG 62.691 60.000 19.37 14.85 0.00 6.13
65 66 2.800881 CTTTTTCAAGGACACTGGGC 57.199 50.000 0.00 0.00 0.00 5.36
79 80 1.303643 CAGAGCCTCCGCCCTTTTT 60.304 57.895 0.00 0.00 34.57 1.94
96 97 2.978824 GCTCCTGCTAACCGACCA 59.021 61.111 0.00 0.00 36.03 4.02
109 110 2.107953 GAGCCATCACCGAGCTCC 59.892 66.667 8.47 0.00 45.83 4.70
127 128 1.954035 ACCTAGAAACTCCAGGACCC 58.046 55.000 0.00 0.00 33.44 4.46
133 134 4.232091 AGGAGTTCAACCTAGAAACTCCA 58.768 43.478 28.56 0.00 42.19 3.86
134 135 4.893829 AGGAGTTCAACCTAGAAACTCC 57.106 45.455 24.21 24.21 41.25 3.85
155 167 7.012989 TCGATATCAAAGTCTTCGAGTCCAATA 59.987 37.037 3.12 0.00 34.24 1.90
156 168 5.980116 CGATATCAAAGTCTTCGAGTCCAAT 59.020 40.000 3.12 0.00 31.74 3.16
163 175 5.105877 ACCTTGTCGATATCAAAGTCTTCGA 60.106 40.000 3.12 0.00 36.57 3.71
166 178 5.875359 GGAACCTTGTCGATATCAAAGTCTT 59.125 40.000 3.12 0.00 0.00 3.01
189 201 0.034477 GTGGGATACACTTGGTGGGG 60.034 60.000 2.75 0.00 46.72 4.96
203 215 1.588082 GCCTTAAGTCGTCGTGGGA 59.412 57.895 0.97 0.00 0.00 4.37
226 238 1.527844 GCATGGGCTTCTAGCTGGG 60.528 63.158 0.00 0.00 41.99 4.45
230 242 1.152368 ATGGGCATGGGCTTCTAGC 59.848 57.895 0.00 0.00 41.46 3.42
241 253 2.173569 GACCCTTAGTCTTCATGGGCAT 59.826 50.000 0.00 0.00 42.69 4.40
242 254 1.559682 GACCCTTAGTCTTCATGGGCA 59.440 52.381 0.00 0.00 42.69 5.36
279 291 0.839277 TGACTGGTGGCATATCCCTG 59.161 55.000 0.00 0.00 0.00 4.45
301 313 2.551270 TGTTCCCTGACTAGCCTTCAT 58.449 47.619 0.00 0.00 0.00 2.57
309 321 4.225042 ACACTAATGCATGTTCCCTGACTA 59.775 41.667 0.00 0.00 0.00 2.59
340 352 1.084370 CCGATGCGTTGGACCTCTTC 61.084 60.000 6.30 0.00 0.00 2.87
343 355 2.100631 CACCGATGCGTTGGACCTC 61.101 63.158 19.72 0.00 32.70 3.85
357 369 6.352526 GCTTTTACATGTATATCGAACACCG 58.647 40.000 6.36 0.00 40.25 4.94
362 374 7.042992 CGACAAGGCTTTTACATGTATATCGAA 60.043 37.037 6.36 0.00 0.00 3.71
363 375 6.419710 CGACAAGGCTTTTACATGTATATCGA 59.580 38.462 6.36 0.00 0.00 3.59
385 397 3.665675 ATGCGAGACAAGCCCCGAC 62.666 63.158 0.00 0.00 0.00 4.79
386 398 3.371097 GATGCGAGACAAGCCCCGA 62.371 63.158 0.00 0.00 0.00 5.14
387 399 2.892425 GATGCGAGACAAGCCCCG 60.892 66.667 0.00 0.00 0.00 5.73
388 400 2.292794 TACGATGCGAGACAAGCCCC 62.293 60.000 0.00 0.00 0.00 5.80
389 401 1.141019 TACGATGCGAGACAAGCCC 59.859 57.895 0.00 0.00 0.00 5.19
390 402 1.146358 GGTACGATGCGAGACAAGCC 61.146 60.000 0.00 0.00 0.00 4.35
391 403 0.457853 TGGTACGATGCGAGACAAGC 60.458 55.000 0.00 0.00 0.00 4.01
392 404 1.135373 ACTGGTACGATGCGAGACAAG 60.135 52.381 0.00 0.00 0.00 3.16
393 405 0.885879 ACTGGTACGATGCGAGACAA 59.114 50.000 0.00 0.00 0.00 3.18
394 406 0.885879 AACTGGTACGATGCGAGACA 59.114 50.000 0.00 0.00 0.00 3.41
395 407 1.546834 GAACTGGTACGATGCGAGAC 58.453 55.000 0.00 0.00 0.00 3.36
396 408 0.098200 CGAACTGGTACGATGCGAGA 59.902 55.000 0.00 0.00 0.00 4.04
397 409 0.179171 ACGAACTGGTACGATGCGAG 60.179 55.000 0.00 0.00 0.00 5.03
398 410 0.455464 CACGAACTGGTACGATGCGA 60.455 55.000 0.00 0.00 0.00 5.10
399 411 1.410737 CCACGAACTGGTACGATGCG 61.411 60.000 0.00 0.00 34.90 4.73
400 412 0.108992 TCCACGAACTGGTACGATGC 60.109 55.000 0.00 0.00 41.52 3.91
401 413 1.068125 TGTCCACGAACTGGTACGATG 60.068 52.381 0.00 0.00 41.52 3.84
402 414 1.250328 TGTCCACGAACTGGTACGAT 58.750 50.000 0.00 0.00 41.52 3.73
403 415 1.068125 CATGTCCACGAACTGGTACGA 60.068 52.381 0.00 0.00 41.52 3.43
404 416 1.336517 ACATGTCCACGAACTGGTACG 60.337 52.381 0.00 0.00 41.52 3.67
405 417 2.450609 ACATGTCCACGAACTGGTAC 57.549 50.000 0.00 0.00 41.52 3.34
406 418 2.494471 CCTACATGTCCACGAACTGGTA 59.506 50.000 0.00 0.00 41.52 3.25
407 419 1.275291 CCTACATGTCCACGAACTGGT 59.725 52.381 0.00 0.00 41.52 4.00
408 420 1.548719 TCCTACATGTCCACGAACTGG 59.451 52.381 0.00 0.00 42.29 4.00
409 421 3.254060 CTTCCTACATGTCCACGAACTG 58.746 50.000 0.00 0.00 0.00 3.16
410 422 2.353803 GCTTCCTACATGTCCACGAACT 60.354 50.000 0.00 0.00 0.00 3.01
411 423 2.000447 GCTTCCTACATGTCCACGAAC 59.000 52.381 0.00 0.00 0.00 3.95
412 424 1.621317 TGCTTCCTACATGTCCACGAA 59.379 47.619 0.00 0.00 0.00 3.85
413 425 1.067142 GTGCTTCCTACATGTCCACGA 60.067 52.381 0.00 0.00 0.00 4.35
414 426 1.337728 TGTGCTTCCTACATGTCCACG 60.338 52.381 0.00 0.00 0.00 4.94
415 427 2.350522 CTGTGCTTCCTACATGTCCAC 58.649 52.381 0.00 2.45 0.00 4.02
416 428 1.278985 CCTGTGCTTCCTACATGTCCA 59.721 52.381 0.00 0.00 0.00 4.02
417 429 2.014068 GCCTGTGCTTCCTACATGTCC 61.014 57.143 0.00 0.00 33.53 4.02
418 430 1.339055 TGCCTGTGCTTCCTACATGTC 60.339 52.381 0.00 0.00 38.71 3.06
419 431 0.692476 TGCCTGTGCTTCCTACATGT 59.308 50.000 2.69 2.69 38.71 3.21
420 432 1.825090 TTGCCTGTGCTTCCTACATG 58.175 50.000 0.00 0.00 38.71 3.21
421 433 2.372264 CATTGCCTGTGCTTCCTACAT 58.628 47.619 0.00 0.00 38.71 2.29
422 434 1.614051 CCATTGCCTGTGCTTCCTACA 60.614 52.381 0.00 0.00 38.71 2.74
423 435 1.098050 CCATTGCCTGTGCTTCCTAC 58.902 55.000 0.00 0.00 38.71 3.18
424 436 0.680921 GCCATTGCCTGTGCTTCCTA 60.681 55.000 0.00 0.00 38.71 2.94
425 437 1.980772 GCCATTGCCTGTGCTTCCT 60.981 57.895 0.00 0.00 38.71 3.36
426 438 2.575461 GCCATTGCCTGTGCTTCC 59.425 61.111 0.00 0.00 38.71 3.46
427 439 2.180017 CGCCATTGCCTGTGCTTC 59.820 61.111 0.00 0.00 38.71 3.86
428 440 3.376078 CCGCCATTGCCTGTGCTT 61.376 61.111 0.00 0.00 38.71 3.91
429 441 4.349503 TCCGCCATTGCCTGTGCT 62.350 61.111 0.00 0.00 38.71 4.40
430 442 3.818787 CTCCGCCATTGCCTGTGC 61.819 66.667 0.00 0.00 38.26 4.57
431 443 3.818787 GCTCCGCCATTGCCTGTG 61.819 66.667 0.00 0.00 0.00 3.66
432 444 3.574074 AAGCTCCGCCATTGCCTGT 62.574 57.895 0.00 0.00 0.00 4.00
433 445 2.753043 AAGCTCCGCCATTGCCTG 60.753 61.111 0.00 0.00 0.00 4.85
434 446 2.563013 ATCAAGCTCCGCCATTGCCT 62.563 55.000 0.00 0.00 0.00 4.75
435 447 2.123428 ATCAAGCTCCGCCATTGCC 61.123 57.895 0.00 0.00 0.00 4.52
436 448 1.065273 CATCAAGCTCCGCCATTGC 59.935 57.895 0.00 0.00 0.00 3.56
437 449 1.065102 CTTCATCAAGCTCCGCCATTG 59.935 52.381 0.00 0.00 0.00 2.82
438 450 1.065199 TCTTCATCAAGCTCCGCCATT 60.065 47.619 0.00 0.00 0.00 3.16
439 451 0.543277 TCTTCATCAAGCTCCGCCAT 59.457 50.000 0.00 0.00 0.00 4.40
440 452 0.543277 ATCTTCATCAAGCTCCGCCA 59.457 50.000 0.00 0.00 0.00 5.69
441 453 1.673168 AATCTTCATCAAGCTCCGCC 58.327 50.000 0.00 0.00 0.00 6.13
442 454 3.772060 AAAATCTTCATCAAGCTCCGC 57.228 42.857 0.00 0.00 0.00 5.54
443 455 5.300969 TCAAAAATCTTCATCAAGCTCCG 57.699 39.130 0.00 0.00 0.00 4.63
444 456 5.393896 CCCTCAAAAATCTTCATCAAGCTCC 60.394 44.000 0.00 0.00 0.00 4.70
445 457 5.393896 CCCCTCAAAAATCTTCATCAAGCTC 60.394 44.000 0.00 0.00 0.00 4.09
446 458 4.465305 CCCCTCAAAAATCTTCATCAAGCT 59.535 41.667 0.00 0.00 0.00 3.74
447 459 4.382362 CCCCCTCAAAAATCTTCATCAAGC 60.382 45.833 0.00 0.00 0.00 4.01
448 460 4.382362 GCCCCCTCAAAAATCTTCATCAAG 60.382 45.833 0.00 0.00 0.00 3.02
449 461 3.515104 GCCCCCTCAAAAATCTTCATCAA 59.485 43.478 0.00 0.00 0.00 2.57
450 462 3.099141 GCCCCCTCAAAAATCTTCATCA 58.901 45.455 0.00 0.00 0.00 3.07
451 463 3.099141 TGCCCCCTCAAAAATCTTCATC 58.901 45.455 0.00 0.00 0.00 2.92
452 464 3.188880 TGCCCCCTCAAAAATCTTCAT 57.811 42.857 0.00 0.00 0.00 2.57
453 465 2.692709 TGCCCCCTCAAAAATCTTCA 57.307 45.000 0.00 0.00 0.00 3.02
454 466 3.578282 TCTTTGCCCCCTCAAAAATCTTC 59.422 43.478 0.00 0.00 35.75 2.87
455 467 3.586429 TCTTTGCCCCCTCAAAAATCTT 58.414 40.909 0.00 0.00 35.75 2.40
456 468 3.258722 TCTTTGCCCCCTCAAAAATCT 57.741 42.857 0.00 0.00 35.75 2.40
457 469 4.350368 TTTCTTTGCCCCCTCAAAAATC 57.650 40.909 0.00 0.00 35.75 2.17
458 470 4.080072 TGTTTTCTTTGCCCCCTCAAAAAT 60.080 37.500 0.00 0.00 35.75 1.82
459 471 3.264450 TGTTTTCTTTGCCCCCTCAAAAA 59.736 39.130 0.00 0.00 35.75 1.94
460 472 2.840651 TGTTTTCTTTGCCCCCTCAAAA 59.159 40.909 0.00 0.00 35.75 2.44
461 473 2.472029 TGTTTTCTTTGCCCCCTCAAA 58.528 42.857 0.00 0.00 35.01 2.69
462 474 2.166907 TGTTTTCTTTGCCCCCTCAA 57.833 45.000 0.00 0.00 0.00 3.02
463 475 2.166907 TTGTTTTCTTTGCCCCCTCA 57.833 45.000 0.00 0.00 0.00 3.86
464 476 3.769739 ATTTGTTTTCTTTGCCCCCTC 57.230 42.857 0.00 0.00 0.00 4.30
465 477 5.559770 CATAATTTGTTTTCTTTGCCCCCT 58.440 37.500 0.00 0.00 0.00 4.79
466 478 4.155826 GCATAATTTGTTTTCTTTGCCCCC 59.844 41.667 0.00 0.00 0.00 5.40
467 479 4.759183 TGCATAATTTGTTTTCTTTGCCCC 59.241 37.500 0.00 0.00 0.00 5.80
491 735 7.989741 TGGATATTCAAGATTTCTCAGAGTTCC 59.010 37.037 0.00 0.00 0.00 3.62
497 741 6.771749 AGCCTTGGATATTCAAGATTTCTCAG 59.228 38.462 23.22 6.66 44.98 3.35
549 793 4.331968 CAATTGCACCCCTACACTAGAAA 58.668 43.478 0.00 0.00 0.00 2.52
552 796 2.017049 GCAATTGCACCCCTACACTAG 58.983 52.381 25.36 0.00 41.59 2.57
563 807 1.003476 CCAAAGGGGGCAATTGCAC 60.003 57.895 30.32 27.77 45.53 4.57
572 816 4.740822 CACGGAGGCCAAAGGGGG 62.741 72.222 5.01 0.00 37.04 5.40
598 842 0.327924 TAATGCCCTGTGTCCAGTGG 59.672 55.000 1.40 1.40 36.95 4.00
603 847 1.279271 ACTGAGTAATGCCCTGTGTCC 59.721 52.381 0.00 0.00 0.00 4.02
610 854 3.694566 CCCAAAGTTACTGAGTAATGCCC 59.305 47.826 8.46 0.00 30.49 5.36
632 876 2.982744 GCTTTGCGGTCTTGGAGCC 61.983 63.158 0.00 0.00 0.00 4.70
633 877 1.916697 GAGCTTTGCGGTCTTGGAGC 61.917 60.000 0.00 0.00 37.18 4.70
648 892 1.419387 GATGTATGCCCCTCTTGAGCT 59.581 52.381 0.00 0.00 0.00 4.09
661 905 2.998670 GCCAGATGGACATCGATGTATG 59.001 50.000 30.04 20.92 41.95 2.39
698 942 8.140677 TCATTCACAATTGATTTTTCACCAAC 57.859 30.769 13.59 0.00 0.00 3.77
777 1021 8.218441 GCGCGAATAATATTATCACTTTACACA 58.782 33.333 12.10 0.00 0.00 3.72
778 1022 8.433126 AGCGCGAATAATATTATCACTTTACAC 58.567 33.333 12.10 0.00 0.00 2.90
811 1055 9.838339 ATACAGAGCTAAATACACTTTGCTATT 57.162 29.630 0.00 0.00 37.48 1.73
831 1075 9.727859 TGTTAAGGTACATTTTGCTTATACAGA 57.272 29.630 0.00 0.00 0.00 3.41
862 1106 5.053811 CGACCCCTGCAATTTTAAGTTTTT 58.946 37.500 0.00 0.00 0.00 1.94
863 1107 4.502431 CCGACCCCTGCAATTTTAAGTTTT 60.502 41.667 0.00 0.00 0.00 2.43
864 1108 3.006430 CCGACCCCTGCAATTTTAAGTTT 59.994 43.478 0.00 0.00 0.00 2.66
881 3936 2.428890 ACTGAACATGAGAGATCCGACC 59.571 50.000 0.00 0.00 0.00 4.79
894 3949 8.006298 TCAAAGTTGGAAAATACACTGAACAT 57.994 30.769 0.00 0.00 0.00 2.71
903 3958 6.265577 CGGATCCATCAAAGTTGGAAAATAC 58.734 40.000 13.41 0.00 45.99 1.89
1029 4090 3.367498 GGAATAGCGAAGAGTGTGTGAGT 60.367 47.826 0.00 0.00 0.00 3.41
1226 4296 1.752501 CGCCGAATCTACCGTGCAAG 61.753 60.000 0.00 0.00 0.00 4.01
1305 4378 1.944676 GCCCGAACAGATAGCGTCG 60.945 63.158 0.00 0.00 0.00 5.12
1323 4396 4.599047 TTGCCATACTTCCCAAAACAAG 57.401 40.909 0.00 0.00 0.00 3.16
1392 4470 9.392259 GGCATTAACTAGGTTAAGAGTAACATT 57.608 33.333 8.48 0.00 40.58 2.71
1845 4924 7.511268 ACTTCACAGGTACATTACTTTGGTAA 58.489 34.615 0.00 0.00 41.42 2.85
1977 5056 6.171213 GTTTATAGCCCAGACTACACAAGTT 58.829 40.000 0.00 0.00 39.07 2.66
2136 5217 8.916062 TCATGGTTTATGCATGATCTGTTATTT 58.084 29.630 10.16 0.00 36.70 1.40
2144 5225 8.525316 TGGAATATTCATGGTTTATGCATGATC 58.475 33.333 17.07 0.00 35.58 2.92
2925 6021 3.921119 TGTCCGACTAGCTTTTTCGTA 57.079 42.857 0.00 0.00 0.00 3.43
2978 6074 0.953471 CCCGATTTCACTTGCACCGA 60.953 55.000 0.00 0.00 0.00 4.69
3319 6461 5.485209 AGTTAGGTCAACAAGGAAGTAGG 57.515 43.478 0.00 0.00 39.81 3.18
3642 6787 0.323178 AGCCATTGCCTCCAACTGAG 60.323 55.000 0.00 0.00 41.07 3.35
3881 7026 3.009916 AGTTCTGAAGATGCCTCACCATT 59.990 43.478 0.00 0.00 0.00 3.16
4373 7523 6.319658 ACAGTCACATTTCACAGACAGAAAAT 59.680 34.615 0.00 0.00 38.36 1.82
4385 7535 8.073467 TCCTACATGTATACAGTCACATTTCA 57.927 34.615 11.91 0.00 33.12 2.69
4844 8004 3.107601 AGAGCAGCACTTCCAATAGGTA 58.892 45.455 0.00 0.00 35.89 3.08
4875 8035 5.993055 TGAATGTTCATCAATAGGAGCTCA 58.007 37.500 17.19 0.00 31.01 4.26
5008 8168 4.690748 GCTCGCCTACTTCATATTTGCATA 59.309 41.667 0.00 0.00 0.00 3.14
5233 8393 7.343357 CCAGGGTGGAATGTTTTAGAATACTA 58.657 38.462 0.00 0.00 40.96 1.82
5949 10616 4.533815 TCGTACATATCTTCTGGACCACT 58.466 43.478 0.00 0.00 0.00 4.00
6097 10764 0.826062 TAGTGCCTTAGTAACCGCCC 59.174 55.000 0.00 0.00 0.00 6.13
6869 11614 0.323302 TACACATGCCTTTCTCCGCA 59.677 50.000 0.00 0.00 39.79 5.69
7982 12766 7.653311 GTGCTAGTTTTGTTTGGAAAGATGATT 59.347 33.333 0.00 0.00 0.00 2.57
8125 12909 4.881850 AGGAAAATCACAAGTTCACGAGTT 59.118 37.500 0.00 0.00 0.00 3.01
8126 12910 4.451900 AGGAAAATCACAAGTTCACGAGT 58.548 39.130 0.00 0.00 0.00 4.18
8127 12911 5.207768 CAAGGAAAATCACAAGTTCACGAG 58.792 41.667 0.00 0.00 0.00 4.18
8128 12912 4.638421 ACAAGGAAAATCACAAGTTCACGA 59.362 37.500 0.00 0.00 0.00 4.35
8129 12913 4.734854 CACAAGGAAAATCACAAGTTCACG 59.265 41.667 0.00 0.00 0.00 4.35
8130 12914 5.043248 CCACAAGGAAAATCACAAGTTCAC 58.957 41.667 0.00 0.00 36.89 3.18
8131 12915 4.952957 TCCACAAGGAAAATCACAAGTTCA 59.047 37.500 0.00 0.00 42.23 3.18
8333 13251 1.202639 TGGTCACACAAGTCAGCGAAT 60.203 47.619 0.00 0.00 0.00 3.34
8361 13279 7.009999 CAGATCAAAATTCAGTACGAGAGGAAG 59.990 40.741 0.00 0.00 0.00 3.46
8783 13761 4.347876 CCAAGGAATTTTCACTTCCCCTTT 59.652 41.667 0.00 0.00 42.68 3.11
8786 13764 3.506398 TCCAAGGAATTTTCACTTCCCC 58.494 45.455 0.00 0.00 42.68 4.81
8853 13831 2.625737 TGCTTCAGAGATAGCAACTGC 58.374 47.619 0.00 0.00 43.88 4.40
8879 13969 5.472301 AATTCACCCACCAAAGAGGATAT 57.528 39.130 0.00 0.00 41.22 1.63
8883 13973 3.193479 GCTAAATTCACCCACCAAAGAGG 59.807 47.826 0.00 0.00 45.67 3.69
9014 14105 8.807118 TCTGTTGCCGATCTAATCTAATCTAAT 58.193 33.333 0.00 0.00 0.00 1.73
9015 14106 8.178313 TCTGTTGCCGATCTAATCTAATCTAA 57.822 34.615 0.00 0.00 0.00 2.10
9016 14107 7.761038 TCTGTTGCCGATCTAATCTAATCTA 57.239 36.000 0.00 0.00 0.00 1.98
9017 14108 6.656632 TCTGTTGCCGATCTAATCTAATCT 57.343 37.500 0.00 0.00 0.00 2.40
9018 14109 7.897575 AATCTGTTGCCGATCTAATCTAATC 57.102 36.000 0.00 0.00 0.00 1.75
9045 14136 4.142359 TGACTAGAATTCTTCGGTCAGAGC 60.142 45.833 22.82 10.52 39.94 4.09
9086 14177 6.857964 GGTACTGATATATGCATGTGTTTTGC 59.142 38.462 10.16 0.00 40.55 3.68
9272 14370 5.055812 CCATCAGATTGCTTCTCCTTAGTC 58.944 45.833 0.00 0.00 29.93 2.59
9281 14379 8.789825 ATATCATAGTTCCATCAGATTGCTTC 57.210 34.615 0.00 0.00 0.00 3.86
9340 14438 7.336931 AGTGACTTAAATGTGCAATAACTAGGG 59.663 37.037 0.00 0.00 0.00 3.53
9342 14440 8.935844 TGAGTGACTTAAATGTGCAATAACTAG 58.064 33.333 0.00 0.00 0.00 2.57
9345 14443 8.970691 ATTGAGTGACTTAAATGTGCAATAAC 57.029 30.769 0.00 0.00 0.00 1.89
9357 14455 8.846943 TTCTTATGCTTGATTGAGTGACTTAA 57.153 30.769 0.00 0.00 0.00 1.85
9401 14500 5.183228 ACGGAGATTCGTGTGGATATTTTT 58.817 37.500 0.00 0.00 42.21 1.94
9433 14532 8.743085 ATTGCACATCTAAGTCATAAGTCATT 57.257 30.769 0.00 0.00 0.00 2.57
9442 14541 6.483307 GCCATAAGTATTGCACATCTAAGTCA 59.517 38.462 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.