Multiple sequence alignment - TraesCS1A01G228500

Loading Multiple Alignment...

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 TraesCS1A01G228500 chr1A 100.000 2564 0 0 1 2564 399827359 399824796 0.000000e+00 4735
1 TraesCS1A01G228500 chr1A 86.063 1435 128 44 635 2038 405093042 405091649 0.000000e+00 1476
2 TraesCS1A01G228500 chr1A 81.517 211 29 7 2075 2283 405360129 405360331 5.680000e-37 165
3 TraesCS1A01G228500 chr1D 90.227 2333 153 32 1 2283 318499132 318496825 0.000000e+00 2976
4 TraesCS1A01G228500 chr1D 87.094 1418 125 31 654 2038 318722079 318723471 0.000000e+00 1552
5 TraesCS1A01G228500 chr1D 81.771 192 25 8 2306 2493 318560397 318560212 4.420000e-33 152
6 TraesCS1A01G228500 chr1B 92.295 1765 100 17 533 2283 430618556 430616814 0.000000e+00 2473
7 TraesCS1A01G228500 chr1B 86.066 1421 140 37 655 2038 431032634 431034033 0.000000e+00 1474
8 TraesCS1A01G228500 chr1B 78.638 323 32 16 1961 2283 430886977 430886692 2.030000e-41 180
9 TraesCS1A01G228500 chr1B 86.290 124 14 2 2301 2423 430886596 430886475 5.760000e-27 132
10 TraesCS1A01G228500 chr4D 80.117 342 55 12 10 344 28470800 28470465 2.550000e-60 243
11 TraesCS1A01G228500 chr2D 81.152 191 35 1 10 199 417548714 417548524 4.420000e-33 152


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 TraesCS1A01G228500 chr1A 399824796 399827359 2563 True 4735 4735 100.000 1 2564 1 chr1A.!!$R1 2563
1 TraesCS1A01G228500 chr1A 405091649 405093042 1393 True 1476 1476 86.063 635 2038 1 chr1A.!!$R2 1403
2 TraesCS1A01G228500 chr1D 318496825 318499132 2307 True 2976 2976 90.227 1 2283 1 chr1D.!!$R1 2282
3 TraesCS1A01G228500 chr1D 318722079 318723471 1392 False 1552 1552 87.094 654 2038 1 chr1D.!!$F1 1384
4 TraesCS1A01G228500 chr1B 430616814 430618556 1742 True 2473 2473 92.295 533 2283 1 chr1B.!!$R1 1750
5 TraesCS1A01G228500 chr1B 431032634 431034033 1399 False 1474 1474 86.066 655 2038 1 chr1B.!!$F1 1383

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
258 259 0.107945 GACTTCTTGAGGAGGCGCAT 60.108 55.0 10.83 0.0 0.0 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 1956 0.030773 CACGCGAGCCTAATCTAGCA 59.969 55.0 15.93 0.0 34.92 3.49 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
42 43 2.386064 GACCTGCCACCGGTTGTACA 62.386 60.000 2.97 0.00 34.19 2.90
45 46 1.302913 TGCCACCGGTTGTACATGG 60.303 57.895 2.97 1.56 0.00 3.66
49 50 1.848895 ACCGGTTGTACATGGGGGT 60.849 57.895 0.00 8.01 0.00 4.95
51 52 1.377987 CGGTTGTACATGGGGGTGG 60.378 63.158 0.00 0.00 0.00 4.61
94 95 0.443869 CCGAGCCAATTCTTCGTGTG 59.556 55.000 0.00 0.00 0.00 3.82
101 102 1.726791 CAATTCTTCGTGTGGGTCTCG 59.273 52.381 0.00 0.00 34.85 4.04
103 104 2.742710 TTCTTCGTGTGGGTCTCGCG 62.743 60.000 0.00 0.00 39.65 5.87
106 107 4.657824 CGTGTGGGTCTCGCGGTT 62.658 66.667 6.13 0.00 35.57 4.44
128 129 1.952102 TTATCTCCGCCACCCACGTC 61.952 60.000 0.00 0.00 0.00 4.34
168 169 0.872021 GCCGATGTACTTCCTCTGCG 60.872 60.000 3.35 0.00 0.00 5.18
170 171 0.456221 CGATGTACTTCCTCTGCGGT 59.544 55.000 3.35 0.00 0.00 5.68
172 173 2.098607 CGATGTACTTCCTCTGCGGTTA 59.901 50.000 3.35 0.00 0.00 2.85
199 200 1.946475 GAGGGAGGTCGGGAAAGTCG 61.946 65.000 0.00 0.00 0.00 4.18
207 208 1.218047 CGGGAAAGTCGGAGATGCA 59.782 57.895 0.00 0.00 40.67 3.96
211 212 1.363744 GAAAGTCGGAGATGCAGTGG 58.636 55.000 0.00 0.00 40.67 4.00
217 218 2.750657 GGAGATGCAGTGGGAGGGG 61.751 68.421 0.00 0.00 0.00 4.79
218 219 2.693864 AGATGCAGTGGGAGGGGG 60.694 66.667 0.00 0.00 0.00 5.40
225 226 4.256180 GTGGGAGGGGGCGCATAG 62.256 72.222 10.83 0.00 33.14 2.23
229 230 4.256180 GAGGGGGCGCATAGGTGG 62.256 72.222 10.83 0.00 0.00 4.61
237 238 3.845259 GCATAGGTGGGGCGACGA 61.845 66.667 0.00 0.00 0.00 4.20
240 241 4.720902 TAGGTGGGGCGACGACGA 62.721 66.667 12.29 0.00 42.66 4.20
254 255 0.456995 CGACGACTTCTTGAGGAGGC 60.457 60.000 0.00 0.00 0.00 4.70
257 258 1.293498 GACTTCTTGAGGAGGCGCA 59.707 57.895 10.83 0.00 0.00 6.09
258 259 0.107945 GACTTCTTGAGGAGGCGCAT 60.108 55.000 10.83 0.00 0.00 4.73
339 355 2.003548 GGCCATTGGGAGGAGAGGT 61.004 63.158 4.53 0.00 35.59 3.85
349 365 4.388499 GGAGAGGTGCGGCGGAAA 62.388 66.667 9.78 0.00 0.00 3.13
396 412 2.042230 GGGGACGGAGGAGGCTAA 60.042 66.667 0.00 0.00 0.00 3.09
397 413 2.134933 GGGGACGGAGGAGGCTAAG 61.135 68.421 0.00 0.00 0.00 2.18
400 416 1.110518 GGACGGAGGAGGCTAAGAGG 61.111 65.000 0.00 0.00 0.00 3.69
401 417 1.740332 GACGGAGGAGGCTAAGAGGC 61.740 65.000 0.00 0.00 41.73 4.70
403 419 2.503382 GGAGGAGGCTAAGAGGCGG 61.503 68.421 0.00 0.00 46.58 6.13
404 420 1.455959 GAGGAGGCTAAGAGGCGGA 60.456 63.158 0.00 0.00 46.58 5.54
406 422 2.503382 GGAGGCTAAGAGGCGGAGG 61.503 68.421 0.00 0.00 46.58 4.30
408 424 3.551407 GGCTAAGAGGCGGAGGGG 61.551 72.222 0.00 0.00 0.00 4.79
409 425 2.444140 GCTAAGAGGCGGAGGGGA 60.444 66.667 0.00 0.00 0.00 4.81
410 426 2.798364 GCTAAGAGGCGGAGGGGAC 61.798 68.421 0.00 0.00 0.00 4.46
411 427 1.381327 CTAAGAGGCGGAGGGGACA 60.381 63.158 0.00 0.00 0.00 4.02
414 430 1.842381 AAGAGGCGGAGGGGACAAAG 61.842 60.000 0.00 0.00 0.00 2.77
415 431 2.203938 AGGCGGAGGGGACAAAGA 60.204 61.111 0.00 0.00 0.00 2.52
416 432 1.838073 GAGGCGGAGGGGACAAAGAA 61.838 60.000 0.00 0.00 0.00 2.52
418 434 1.241990 GGCGGAGGGGACAAAGAAAC 61.242 60.000 0.00 0.00 0.00 2.78
420 436 0.953960 CGGAGGGGACAAAGAAACGG 60.954 60.000 0.00 0.00 0.00 4.44
463 483 3.056678 TCAACGAGCGGTGGAGTAAATAA 60.057 43.478 8.17 0.00 32.83 1.40
470 490 6.036300 CGAGCGGTGGAGTAAATAAATGTTAA 59.964 38.462 0.00 0.00 0.00 2.01
483 503 6.780706 ATAAATGTTAAGGATAAGCGACGG 57.219 37.500 0.00 0.00 0.00 4.79
484 504 4.395959 AATGTTAAGGATAAGCGACGGA 57.604 40.909 0.00 0.00 0.00 4.69
489 509 2.581216 AGGATAAGCGACGGAGGATA 57.419 50.000 0.00 0.00 0.00 2.59
514 534 7.878621 AATGATCCTCCTCTAACCATTATCA 57.121 36.000 0.00 0.00 0.00 2.15
516 536 5.782331 TGATCCTCCTCTAACCATTATCAGG 59.218 44.000 0.00 0.00 0.00 3.86
521 541 4.772624 TCCTCTAACCATTATCAGGGATCG 59.227 45.833 0.00 0.00 0.00 3.69
530 550 0.485099 ATCAGGGATCGGCTAGGTCT 59.515 55.000 0.00 0.00 0.00 3.85
551 589 5.862860 GTCTCAGGTTTTTACTCCTCTAACG 59.137 44.000 0.00 0.00 30.91 3.18
554 592 3.005554 GGTTTTTACTCCTCTAACGGGC 58.994 50.000 0.00 0.00 0.00 6.13
568 606 0.317479 ACGGGCTATAGGCGATCAAC 59.683 55.000 19.09 4.30 42.94 3.18
585 623 4.207891 TCAACTAGAAATGCCCTGAGAC 57.792 45.455 0.00 0.00 0.00 3.36
589 627 2.486472 AGAAATGCCCTGAGACAGTG 57.514 50.000 0.00 0.00 0.00 3.66
747 787 1.452108 CCCCCATTCGCTCCACTTC 60.452 63.158 0.00 0.00 0.00 3.01
1329 1404 1.803519 GTTCGACTCCAGCAGCGAG 60.804 63.158 0.00 0.00 33.88 5.03
1533 1608 2.434359 GAGCCCAAGAACGACCCG 60.434 66.667 0.00 0.00 0.00 5.28
1573 1648 2.105128 CGGTGTGAGGCGGATCTC 59.895 66.667 0.00 0.00 0.00 2.75
1574 1649 2.418910 CGGTGTGAGGCGGATCTCT 61.419 63.158 0.00 0.00 34.98 3.10
1636 1711 2.431942 AGCACGTAAACGGCGGAG 60.432 61.111 13.24 0.00 44.95 4.63
1716 1791 1.447314 CGAGGTACGGTTGGCTTCC 60.447 63.158 0.00 0.00 38.46 3.46
1718 1793 0.108281 GAGGTACGGTTGGCTTCCTC 60.108 60.000 0.00 0.00 35.45 3.71
1719 1794 1.447314 GGTACGGTTGGCTTCCTCG 60.447 63.158 0.00 0.00 0.00 4.63
1784 1861 1.462670 CTCGCTCTCTTCAGTTTTGGC 59.537 52.381 0.00 0.00 0.00 4.52
1828 1905 6.307776 TGGATCGGAGTCTTCTTCTATATGT 58.692 40.000 0.00 0.00 0.00 2.29
2056 2162 6.929606 GGTACCTAATTACATGGCTCTACAAG 59.070 42.308 4.06 0.00 0.00 3.16
2111 2217 4.515567 GGAAAGAAGTCCAATTGAACTCGT 59.484 41.667 7.12 0.00 37.65 4.18
2122 2228 7.009357 GTCCAATTGAACTCGTCTAGAATGTAC 59.991 40.741 7.12 0.00 0.00 2.90
2123 2229 6.811665 CCAATTGAACTCGTCTAGAATGTACA 59.188 38.462 7.12 0.00 0.00 2.90
2125 2231 4.966249 TGAACTCGTCTAGAATGTACACG 58.034 43.478 0.00 0.00 0.00 4.49
2126 2232 4.142752 TGAACTCGTCTAGAATGTACACGG 60.143 45.833 0.00 0.00 0.00 4.94
2127 2233 3.341823 ACTCGTCTAGAATGTACACGGT 58.658 45.455 0.00 0.00 0.00 4.83
2134 2240 6.090358 CGTCTAGAATGTACACGGTTGAAATT 59.910 38.462 0.00 0.00 0.00 1.82
2172 2278 3.614399 CACCCAAGTGGACTCAGAC 57.386 57.895 0.00 0.00 40.55 3.51
2173 2279 0.035458 CACCCAAGTGGACTCAGACC 59.965 60.000 0.00 0.00 40.55 3.85
2176 2282 0.987294 CCAAGTGGACTCAGACCCAT 59.013 55.000 0.00 0.00 37.39 4.00
2181 2287 2.834549 AGTGGACTCAGACCCATTGTAG 59.165 50.000 0.00 0.00 34.58 2.74
2183 2289 3.008049 GTGGACTCAGACCCATTGTAGTT 59.992 47.826 0.00 0.00 34.58 2.24
2199 2305 6.613755 TTGTAGTTGTAGGAAACTGCTTTC 57.386 37.500 6.70 0.00 44.33 2.62
2200 2306 5.925509 TGTAGTTGTAGGAAACTGCTTTCT 58.074 37.500 6.70 0.00 44.33 2.52
2269 2375 3.576932 TTTGCAAGCAGGCGCCATG 62.577 57.895 31.54 23.68 39.83 3.66
2283 2389 2.867429 CGCCATGGAAACTGAAATGTC 58.133 47.619 18.40 0.00 0.00 3.06
2284 2390 2.489329 CGCCATGGAAACTGAAATGTCT 59.511 45.455 18.40 0.00 0.00 3.41
2285 2391 3.057315 CGCCATGGAAACTGAAATGTCTT 60.057 43.478 18.40 0.00 0.00 3.01
2286 2392 4.559300 CGCCATGGAAACTGAAATGTCTTT 60.559 41.667 18.40 0.00 0.00 2.52
2287 2393 5.335583 CGCCATGGAAACTGAAATGTCTTTA 60.336 40.000 18.40 0.00 0.00 1.85
2288 2394 5.863935 GCCATGGAAACTGAAATGTCTTTAC 59.136 40.000 18.40 0.00 0.00 2.01
2289 2395 6.389906 CCATGGAAACTGAAATGTCTTTACC 58.610 40.000 5.56 0.00 0.00 2.85
2290 2396 6.209391 CCATGGAAACTGAAATGTCTTTACCT 59.791 38.462 5.56 0.00 0.00 3.08
2291 2397 7.255942 CCATGGAAACTGAAATGTCTTTACCTT 60.256 37.037 5.56 0.00 0.00 3.50
2292 2398 7.272037 TGGAAACTGAAATGTCTTTACCTTC 57.728 36.000 0.00 0.00 0.00 3.46
2293 2399 6.017440 TGGAAACTGAAATGTCTTTACCTTCG 60.017 38.462 0.00 0.00 0.00 3.79
2294 2400 6.204108 GGAAACTGAAATGTCTTTACCTTCGA 59.796 38.462 0.00 0.00 0.00 3.71
2295 2401 7.255001 GGAAACTGAAATGTCTTTACCTTCGAA 60.255 37.037 0.00 0.00 0.00 3.71
2296 2402 7.745620 AACTGAAATGTCTTTACCTTCGAAT 57.254 32.000 0.00 0.00 0.00 3.34
2297 2403 8.842358 AACTGAAATGTCTTTACCTTCGAATA 57.158 30.769 0.00 0.00 0.00 1.75
2298 2404 8.842358 ACTGAAATGTCTTTACCTTCGAATAA 57.158 30.769 0.00 0.00 0.00 1.40
2299 2405 8.718734 ACTGAAATGTCTTTACCTTCGAATAAC 58.281 33.333 0.00 0.00 0.00 1.89
2300 2406 8.036273 TGAAATGTCTTTACCTTCGAATAACC 57.964 34.615 0.00 0.00 0.00 2.85
2301 2407 7.662258 TGAAATGTCTTTACCTTCGAATAACCA 59.338 33.333 0.00 0.00 0.00 3.67
2302 2408 8.575649 AAATGTCTTTACCTTCGAATAACCAT 57.424 30.769 0.00 0.00 0.00 3.55
2303 2409 6.978343 TGTCTTTACCTTCGAATAACCATG 57.022 37.500 0.00 0.00 0.00 3.66
2304 2410 5.878116 TGTCTTTACCTTCGAATAACCATGG 59.122 40.000 11.19 11.19 0.00 3.66
2305 2411 5.296035 GTCTTTACCTTCGAATAACCATGGG 59.704 44.000 18.09 0.00 0.00 4.00
2306 2412 2.729028 ACCTTCGAATAACCATGGGG 57.271 50.000 18.09 6.52 41.29 4.96
2307 2413 2.201830 ACCTTCGAATAACCATGGGGA 58.798 47.619 18.09 3.09 38.05 4.81
2308 2414 2.578940 ACCTTCGAATAACCATGGGGAA 59.421 45.455 18.09 8.31 38.05 3.97
2309 2415 3.204382 ACCTTCGAATAACCATGGGGAAT 59.796 43.478 18.09 3.15 38.05 3.01
2310 2416 4.414182 ACCTTCGAATAACCATGGGGAATA 59.586 41.667 18.09 4.00 38.05 1.75
2311 2417 5.103855 ACCTTCGAATAACCATGGGGAATAA 60.104 40.000 18.09 0.60 38.05 1.40
2312 2418 5.830991 CCTTCGAATAACCATGGGGAATAAA 59.169 40.000 18.09 1.28 38.05 1.40
2313 2419 6.016276 CCTTCGAATAACCATGGGGAATAAAG 60.016 42.308 18.09 10.68 38.05 1.85
2314 2420 5.381757 TCGAATAACCATGGGGAATAAAGG 58.618 41.667 18.09 0.00 38.05 3.11
2315 2421 4.022329 CGAATAACCATGGGGAATAAAGGC 60.022 45.833 18.09 0.00 38.05 4.35
2316 2422 1.775385 AACCATGGGGAATAAAGGCG 58.225 50.000 18.09 0.00 38.05 5.52
2317 2423 0.755327 ACCATGGGGAATAAAGGCGC 60.755 55.000 18.09 0.00 38.05 6.53
2318 2424 0.754957 CCATGGGGAATAAAGGCGCA 60.755 55.000 10.83 0.00 35.59 6.09
2319 2425 0.670162 CATGGGGAATAAAGGCGCAG 59.330 55.000 10.83 0.00 0.00 5.18
2320 2426 0.550914 ATGGGGAATAAAGGCGCAGA 59.449 50.000 10.83 0.00 0.00 4.26
2321 2427 0.550914 TGGGGAATAAAGGCGCAGAT 59.449 50.000 10.83 0.00 0.00 2.90
2322 2428 0.954452 GGGGAATAAAGGCGCAGATG 59.046 55.000 10.83 0.00 0.00 2.90
2323 2429 0.312102 GGGAATAAAGGCGCAGATGC 59.688 55.000 10.83 0.00 37.78 3.91
2324 2430 1.312815 GGAATAAAGGCGCAGATGCT 58.687 50.000 10.83 0.00 39.32 3.79
2325 2431 1.678101 GGAATAAAGGCGCAGATGCTT 59.322 47.619 10.83 0.00 39.32 3.91
2326 2432 2.878406 GGAATAAAGGCGCAGATGCTTA 59.122 45.455 10.83 0.00 39.32 3.09
2327 2433 3.058639 GGAATAAAGGCGCAGATGCTTAG 60.059 47.826 10.83 0.00 39.32 2.18
2328 2434 1.953559 TAAAGGCGCAGATGCTTAGG 58.046 50.000 10.83 0.00 39.32 2.69
2329 2435 0.749454 AAAGGCGCAGATGCTTAGGG 60.749 55.000 10.83 0.00 39.32 3.53
2330 2436 3.282920 GGCGCAGATGCTTAGGGC 61.283 66.667 10.83 0.00 39.32 5.19
2331 2437 2.203126 GCGCAGATGCTTAGGGCT 60.203 61.111 0.30 0.00 42.39 5.19
2332 2438 2.250237 GCGCAGATGCTTAGGGCTC 61.250 63.158 0.30 0.00 42.39 4.70
2333 2439 1.596477 CGCAGATGCTTAGGGCTCC 60.596 63.158 2.95 0.00 42.39 4.70
2334 2440 1.835693 GCAGATGCTTAGGGCTCCT 59.164 57.895 0.00 0.00 42.39 3.69
2335 2441 0.182299 GCAGATGCTTAGGGCTCCTT 59.818 55.000 0.00 0.00 42.39 3.36
2336 2442 1.409381 GCAGATGCTTAGGGCTCCTTT 60.409 52.381 0.00 0.00 42.39 3.11
2337 2443 2.295885 CAGATGCTTAGGGCTCCTTTG 58.704 52.381 0.00 0.00 42.39 2.77
2338 2444 2.092753 CAGATGCTTAGGGCTCCTTTGA 60.093 50.000 0.00 0.00 42.39 2.69
2339 2445 2.782341 AGATGCTTAGGGCTCCTTTGAT 59.218 45.455 0.00 0.00 42.39 2.57
2340 2446 3.203934 AGATGCTTAGGGCTCCTTTGATT 59.796 43.478 0.00 0.00 42.39 2.57
2341 2447 3.004752 TGCTTAGGGCTCCTTTGATTC 57.995 47.619 0.00 0.00 42.39 2.52
2342 2448 2.308570 TGCTTAGGGCTCCTTTGATTCA 59.691 45.455 0.00 0.00 42.39 2.57
2343 2449 2.685388 GCTTAGGGCTCCTTTGATTCAC 59.315 50.000 0.00 0.00 38.06 3.18
2344 2450 3.873801 GCTTAGGGCTCCTTTGATTCACA 60.874 47.826 0.00 0.00 38.06 3.58
2345 2451 4.530875 CTTAGGGCTCCTTTGATTCACAT 58.469 43.478 0.00 0.00 34.61 3.21
2346 2452 2.731572 AGGGCTCCTTTGATTCACATG 58.268 47.619 0.00 0.00 0.00 3.21
2347 2453 2.309755 AGGGCTCCTTTGATTCACATGA 59.690 45.455 0.00 0.00 0.00 3.07
2348 2454 3.053095 AGGGCTCCTTTGATTCACATGAT 60.053 43.478 0.00 0.00 0.00 2.45
2349 2455 4.166725 AGGGCTCCTTTGATTCACATGATA 59.833 41.667 0.00 0.00 0.00 2.15
2350 2456 4.518211 GGGCTCCTTTGATTCACATGATAG 59.482 45.833 0.00 0.00 0.00 2.08
2351 2457 4.518211 GGCTCCTTTGATTCACATGATAGG 59.482 45.833 0.00 0.00 0.00 2.57
2352 2458 5.371526 GCTCCTTTGATTCACATGATAGGA 58.628 41.667 0.00 0.00 0.00 2.94
2353 2459 5.824624 GCTCCTTTGATTCACATGATAGGAA 59.175 40.000 0.00 0.00 30.72 3.36
2354 2460 6.319658 GCTCCTTTGATTCACATGATAGGAAA 59.680 38.462 0.00 0.00 30.72 3.13
2355 2461 7.148018 GCTCCTTTGATTCACATGATAGGAAAA 60.148 37.037 0.00 0.00 30.72 2.29
2356 2462 8.827832 TCCTTTGATTCACATGATAGGAAAAT 57.172 30.769 0.00 0.00 0.00 1.82
2357 2463 9.919416 TCCTTTGATTCACATGATAGGAAAATA 57.081 29.630 0.00 0.00 0.00 1.40
2361 2467 9.565090 TTGATTCACATGATAGGAAAATAGAGG 57.435 33.333 0.00 0.00 0.00 3.69
2362 2468 8.937835 TGATTCACATGATAGGAAAATAGAGGA 58.062 33.333 0.00 0.00 0.00 3.71
2363 2469 9.956640 GATTCACATGATAGGAAAATAGAGGAT 57.043 33.333 0.00 0.00 0.00 3.24
2365 2471 9.565090 TTCACATGATAGGAAAATAGAGGATTG 57.435 33.333 0.00 0.00 0.00 2.67
2366 2472 7.663081 TCACATGATAGGAAAATAGAGGATTGC 59.337 37.037 0.00 0.00 0.00 3.56
2367 2473 7.664731 CACATGATAGGAAAATAGAGGATTGCT 59.335 37.037 0.00 0.00 0.00 3.91
2368 2474 8.884323 ACATGATAGGAAAATAGAGGATTGCTA 58.116 33.333 0.00 0.00 32.66 3.49
2369 2475 9.902684 CATGATAGGAAAATAGAGGATTGCTAT 57.097 33.333 0.00 0.00 39.45 2.97
2370 2476 9.902684 ATGATAGGAAAATAGAGGATTGCTATG 57.097 33.333 3.93 0.00 37.68 2.23
2371 2477 9.104713 TGATAGGAAAATAGAGGATTGCTATGA 57.895 33.333 3.93 0.00 37.68 2.15
2372 2478 9.377312 GATAGGAAAATAGAGGATTGCTATGAC 57.623 37.037 3.93 0.00 37.68 3.06
2373 2479 6.538263 AGGAAAATAGAGGATTGCTATGACC 58.462 40.000 0.00 0.00 0.00 4.02
2374 2480 6.331307 AGGAAAATAGAGGATTGCTATGACCT 59.669 38.462 0.00 0.00 35.29 3.85
2375 2481 7.514127 AGGAAAATAGAGGATTGCTATGACCTA 59.486 37.037 0.00 0.00 31.08 3.08
2376 2482 7.604545 GGAAAATAGAGGATTGCTATGACCTAC 59.395 40.741 0.00 0.00 32.53 3.18
2377 2483 6.613153 AATAGAGGATTGCTATGACCTACC 57.387 41.667 0.00 0.00 32.53 3.18
2378 2484 3.928754 AGAGGATTGCTATGACCTACCA 58.071 45.455 0.00 0.00 32.53 3.25
2379 2485 3.900601 AGAGGATTGCTATGACCTACCAG 59.099 47.826 0.00 0.00 32.53 4.00
2380 2486 3.643792 GAGGATTGCTATGACCTACCAGT 59.356 47.826 0.00 0.00 32.53 4.00
2381 2487 3.643792 AGGATTGCTATGACCTACCAGTC 59.356 47.826 0.00 0.00 37.28 3.51
2382 2488 3.244249 GGATTGCTATGACCTACCAGTCC 60.244 52.174 0.00 0.00 35.83 3.85
2383 2489 2.543037 TGCTATGACCTACCAGTCCA 57.457 50.000 0.00 0.00 35.83 4.02
2384 2490 3.046283 TGCTATGACCTACCAGTCCAT 57.954 47.619 0.00 0.00 35.83 3.41
2385 2491 3.384168 TGCTATGACCTACCAGTCCATT 58.616 45.455 0.00 0.00 35.83 3.16
2386 2492 3.780294 TGCTATGACCTACCAGTCCATTT 59.220 43.478 0.00 0.00 35.83 2.32
2387 2493 4.130118 GCTATGACCTACCAGTCCATTTG 58.870 47.826 0.00 0.00 35.83 2.32
2388 2494 4.141711 GCTATGACCTACCAGTCCATTTGA 60.142 45.833 0.00 0.00 35.83 2.69
2389 2495 4.927267 ATGACCTACCAGTCCATTTGAA 57.073 40.909 0.00 0.00 35.83 2.69
2390 2496 4.927267 TGACCTACCAGTCCATTTGAAT 57.073 40.909 0.00 0.00 35.83 2.57
2391 2497 5.255397 TGACCTACCAGTCCATTTGAATT 57.745 39.130 0.00 0.00 35.83 2.17
2392 2498 5.253330 TGACCTACCAGTCCATTTGAATTC 58.747 41.667 0.00 0.00 35.83 2.17
2393 2499 5.014123 TGACCTACCAGTCCATTTGAATTCT 59.986 40.000 7.05 0.00 35.83 2.40
2394 2500 6.214615 TGACCTACCAGTCCATTTGAATTCTA 59.785 38.462 7.05 0.00 35.83 2.10
2395 2501 7.092444 TGACCTACCAGTCCATTTGAATTCTAT 60.092 37.037 7.05 0.00 35.83 1.98
2396 2502 7.056635 ACCTACCAGTCCATTTGAATTCTATG 58.943 38.462 7.05 9.98 0.00 2.23
2397 2503 6.488006 CCTACCAGTCCATTTGAATTCTATGG 59.512 42.308 23.44 23.44 40.14 2.74
2398 2504 6.078456 ACCAGTCCATTTGAATTCTATGGA 57.922 37.500 25.98 25.98 44.12 3.41
2399 2505 6.493166 ACCAGTCCATTTGAATTCTATGGAA 58.507 36.000 28.90 17.98 46.81 3.53
2400 2506 7.128077 ACCAGTCCATTTGAATTCTATGGAAT 58.872 34.615 28.90 26.75 46.81 3.01
2418 2524 9.846248 CTATGGAATTCTAAAACAAAGGAACTG 57.154 33.333 5.23 0.00 40.86 3.16
2419 2525 7.049799 TGGAATTCTAAAACAAAGGAACTGG 57.950 36.000 5.23 0.00 40.86 4.00
2420 2526 5.926542 GGAATTCTAAAACAAAGGAACTGGC 59.073 40.000 5.23 0.00 40.86 4.85
2421 2527 6.462347 GGAATTCTAAAACAAAGGAACTGGCA 60.462 38.462 5.23 0.00 40.86 4.92
2422 2528 4.911514 TCTAAAACAAAGGAACTGGCAC 57.088 40.909 0.00 0.00 40.86 5.01
2423 2529 2.979814 AAAACAAAGGAACTGGCACC 57.020 45.000 0.00 0.00 40.86 5.01
2424 2530 1.119684 AAACAAAGGAACTGGCACCC 58.880 50.000 0.00 0.00 40.86 4.61
2425 2531 0.032615 AACAAAGGAACTGGCACCCA 60.033 50.000 0.00 0.00 40.86 4.51
2426 2532 0.032615 ACAAAGGAACTGGCACCCAA 60.033 50.000 0.00 0.00 40.86 4.12
2427 2533 1.118838 CAAAGGAACTGGCACCCAAA 58.881 50.000 0.00 0.00 40.86 3.28
2428 2534 1.693606 CAAAGGAACTGGCACCCAAAT 59.306 47.619 0.00 0.00 40.86 2.32
2429 2535 1.341080 AAGGAACTGGCACCCAAATG 58.659 50.000 0.00 0.00 40.86 2.32
2430 2536 0.188342 AGGAACTGGCACCCAAATGT 59.812 50.000 0.00 0.00 37.18 2.71
2431 2537 0.318120 GGAACTGGCACCCAAATGTG 59.682 55.000 0.00 0.00 39.29 3.21
2432 2538 1.039856 GAACTGGCACCCAAATGTGT 58.960 50.000 0.00 0.00 38.52 3.72
2433 2539 0.752054 AACTGGCACCCAAATGTGTG 59.248 50.000 0.00 0.00 38.52 3.82
2434 2540 0.396974 ACTGGCACCCAAATGTGTGT 60.397 50.000 0.00 0.00 38.52 3.72
2435 2541 0.752054 CTGGCACCCAAATGTGTGTT 59.248 50.000 0.00 0.00 38.52 3.32
2436 2542 1.138661 CTGGCACCCAAATGTGTGTTT 59.861 47.619 0.00 0.00 38.52 2.83
2437 2543 1.134580 TGGCACCCAAATGTGTGTTTG 60.135 47.619 0.00 0.00 38.52 2.93
2438 2544 1.134551 GGCACCCAAATGTGTGTTTGT 60.135 47.619 0.00 0.00 37.37 2.83
2439 2545 1.932511 GCACCCAAATGTGTGTTTGTG 59.067 47.619 0.00 0.00 37.37 3.33
2440 2546 2.548875 CACCCAAATGTGTGTTTGTGG 58.451 47.619 0.00 0.00 37.37 4.17
2441 2547 1.484240 ACCCAAATGTGTGTTTGTGGG 59.516 47.619 4.98 4.98 37.37 4.61
2442 2548 1.202627 CCCAAATGTGTGTTTGTGGGG 60.203 52.381 0.00 0.00 37.37 4.96
2443 2549 1.202627 CCAAATGTGTGTTTGTGGGGG 60.203 52.381 0.00 0.00 37.37 5.40
2460 2566 3.713826 GGGGGCATAGGAATTATTCGA 57.286 47.619 0.00 0.00 0.00 3.71
2461 2567 4.028993 GGGGGCATAGGAATTATTCGAA 57.971 45.455 0.00 0.00 0.00 3.71
2462 2568 4.010349 GGGGGCATAGGAATTATTCGAAG 58.990 47.826 3.35 0.00 0.00 3.79
2463 2569 4.263331 GGGGGCATAGGAATTATTCGAAGA 60.263 45.833 3.35 0.00 0.00 2.87
2464 2570 4.938226 GGGGCATAGGAATTATTCGAAGAG 59.062 45.833 3.35 0.00 38.43 2.85
2465 2571 4.393371 GGGCATAGGAATTATTCGAAGAGC 59.607 45.833 3.35 0.00 38.43 4.09
2466 2572 5.241662 GGCATAGGAATTATTCGAAGAGCT 58.758 41.667 3.35 0.00 38.43 4.09
2467 2573 5.703130 GGCATAGGAATTATTCGAAGAGCTT 59.297 40.000 3.35 0.00 38.43 3.74
2468 2574 6.874134 GGCATAGGAATTATTCGAAGAGCTTA 59.126 38.462 3.35 0.00 38.43 3.09
2469 2575 7.064016 GGCATAGGAATTATTCGAAGAGCTTAG 59.936 40.741 3.35 0.00 38.43 2.18
2470 2576 7.815068 GCATAGGAATTATTCGAAGAGCTTAGA 59.185 37.037 3.35 0.00 38.43 2.10
2471 2577 9.134734 CATAGGAATTATTCGAAGAGCTTAGAC 57.865 37.037 3.35 0.00 38.43 2.59
2472 2578 7.354751 AGGAATTATTCGAAGAGCTTAGACT 57.645 36.000 3.35 0.00 38.43 3.24
2473 2579 7.787028 AGGAATTATTCGAAGAGCTTAGACTT 58.213 34.615 3.35 0.00 38.43 3.01
2474 2580 8.261522 AGGAATTATTCGAAGAGCTTAGACTTT 58.738 33.333 3.35 0.00 38.43 2.66
2475 2581 9.530633 GGAATTATTCGAAGAGCTTAGACTTTA 57.469 33.333 3.35 0.00 38.43 1.85
2479 2585 7.763172 ATTCGAAGAGCTTAGACTTTATGTG 57.237 36.000 3.35 0.00 38.43 3.21
2480 2586 6.510879 TCGAAGAGCTTAGACTTTATGTGA 57.489 37.500 0.00 0.00 0.00 3.58
2481 2587 6.920817 TCGAAGAGCTTAGACTTTATGTGAA 58.079 36.000 0.00 0.00 0.00 3.18
2482 2588 7.375834 TCGAAGAGCTTAGACTTTATGTGAAA 58.624 34.615 0.00 0.00 0.00 2.69
2483 2589 8.035394 TCGAAGAGCTTAGACTTTATGTGAAAT 58.965 33.333 0.00 0.00 0.00 2.17
2484 2590 8.660373 CGAAGAGCTTAGACTTTATGTGAAATT 58.340 33.333 0.00 0.00 0.00 1.82
2546 2652 5.818136 GATCACGATCCTTTGAAAATCCA 57.182 39.130 0.00 0.00 31.76 3.41
2547 2653 6.194796 GATCACGATCCTTTGAAAATCCAA 57.805 37.500 0.00 0.00 31.76 3.53
2548 2654 6.780457 ATCACGATCCTTTGAAAATCCAAT 57.220 33.333 0.00 0.00 0.00 3.16
2549 2655 5.953183 TCACGATCCTTTGAAAATCCAATG 58.047 37.500 0.00 0.00 0.00 2.82
2550 2656 5.709631 TCACGATCCTTTGAAAATCCAATGA 59.290 36.000 0.00 0.00 0.00 2.57
2551 2657 6.208402 TCACGATCCTTTGAAAATCCAATGAA 59.792 34.615 0.00 0.00 0.00 2.57
2552 2658 7.037438 CACGATCCTTTGAAAATCCAATGAAT 58.963 34.615 0.00 0.00 0.00 2.57
2553 2659 7.221452 CACGATCCTTTGAAAATCCAATGAATC 59.779 37.037 0.00 0.00 0.00 2.52
2554 2660 7.093814 ACGATCCTTTGAAAATCCAATGAATCA 60.094 33.333 0.00 0.00 0.00 2.57
2555 2661 7.760794 CGATCCTTTGAAAATCCAATGAATCAA 59.239 33.333 0.00 0.00 0.00 2.57
2556 2662 9.439500 GATCCTTTGAAAATCCAATGAATCAAA 57.561 29.630 0.00 0.00 33.92 2.69
2557 2663 8.836268 TCCTTTGAAAATCCAATGAATCAAAG 57.164 30.769 15.52 15.52 42.28 2.77
2558 2664 8.431222 TCCTTTGAAAATCCAATGAATCAAAGT 58.569 29.630 18.99 0.00 41.78 2.66
2559 2665 9.709495 CCTTTGAAAATCCAATGAATCAAAGTA 57.291 29.630 18.99 0.00 41.78 2.24
2561 2667 8.761575 TTGAAAATCCAATGAATCAAAGTAGC 57.238 30.769 0.00 0.00 0.00 3.58
2562 2668 8.125978 TGAAAATCCAATGAATCAAAGTAGCT 57.874 30.769 0.00 0.00 0.00 3.32
2563 2669 8.587608 TGAAAATCCAATGAATCAAAGTAGCTT 58.412 29.630 0.00 0.00 0.00 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 2.191786 CTCGCCACCCCCATGTACAA 62.192 60.000 0.00 0.00 0.00 2.41
37 38 2.608059 TCGCCACCCCCATGTACA 60.608 61.111 0.00 0.00 0.00 2.90
94 95 0.808847 GATAACCAACCGCGAGACCC 60.809 60.000 8.23 0.00 0.00 4.46
103 104 0.746923 GGTGGCGGAGATAACCAACC 60.747 60.000 0.00 0.00 34.98 3.77
106 107 1.613928 TGGGTGGCGGAGATAACCA 60.614 57.895 0.00 0.00 34.18 3.67
148 149 0.872021 GCAGAGGAAGTACATCGGCG 60.872 60.000 0.00 0.00 40.01 6.46
168 169 1.067582 CTCCCTCCGTGCGATAACC 59.932 63.158 0.00 0.00 0.00 2.85
170 171 1.380785 ACCTCCCTCCGTGCGATAA 60.381 57.895 0.00 0.00 0.00 1.75
172 173 3.148279 GACCTCCCTCCGTGCGAT 61.148 66.667 0.00 0.00 0.00 4.58
177 178 3.534704 TTTCCCGACCTCCCTCCGT 62.535 63.158 0.00 0.00 0.00 4.69
199 200 2.750657 CCCCTCCCACTGCATCTCC 61.751 68.421 0.00 0.00 0.00 3.71
207 208 4.815973 TATGCGCCCCCTCCCACT 62.816 66.667 4.18 0.00 0.00 4.00
211 212 4.256180 CACCTATGCGCCCCCTCC 62.256 72.222 4.18 0.00 0.00 4.30
226 227 4.353437 AAGTCGTCGTCGCCCCAC 62.353 66.667 0.00 0.00 36.96 4.61
227 228 4.047059 GAAGTCGTCGTCGCCCCA 62.047 66.667 0.00 0.00 36.96 4.96
229 230 2.087009 CAAGAAGTCGTCGTCGCCC 61.087 63.158 0.00 0.00 36.96 6.13
234 235 0.882474 CCTCCTCAAGAAGTCGTCGT 59.118 55.000 0.00 0.00 0.00 4.34
237 238 1.587054 CGCCTCCTCAAGAAGTCGT 59.413 57.895 0.00 0.00 0.00 4.34
240 241 0.107945 GATGCGCCTCCTCAAGAAGT 60.108 55.000 4.18 0.00 0.00 3.01
387 403 1.456705 CTCCGCCTCTTAGCCTCCT 60.457 63.158 0.00 0.00 0.00 3.69
389 405 2.503382 CCCTCCGCCTCTTAGCCTC 61.503 68.421 0.00 0.00 0.00 4.70
391 407 3.551407 CCCCTCCGCCTCTTAGCC 61.551 72.222 0.00 0.00 0.00 3.93
392 408 2.444140 TCCCCTCCGCCTCTTAGC 60.444 66.667 0.00 0.00 0.00 3.09
393 409 0.976073 TTGTCCCCTCCGCCTCTTAG 60.976 60.000 0.00 0.00 0.00 2.18
396 412 2.203938 TTTGTCCCCTCCGCCTCT 60.204 61.111 0.00 0.00 0.00 3.69
397 413 1.838073 TTCTTTGTCCCCTCCGCCTC 61.838 60.000 0.00 0.00 0.00 4.70
400 416 1.574702 CGTTTCTTTGTCCCCTCCGC 61.575 60.000 0.00 0.00 0.00 5.54
401 417 0.953960 CCGTTTCTTTGTCCCCTCCG 60.954 60.000 0.00 0.00 0.00 4.63
403 419 0.109913 ACCCGTTTCTTTGTCCCCTC 59.890 55.000 0.00 0.00 0.00 4.30
404 420 0.179001 CACCCGTTTCTTTGTCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
406 422 0.179012 TCCACCCGTTTCTTTGTCCC 60.179 55.000 0.00 0.00 0.00 4.46
408 424 2.249844 TCTCCACCCGTTTCTTTGTC 57.750 50.000 0.00 0.00 0.00 3.18
409 425 2.951229 ATCTCCACCCGTTTCTTTGT 57.049 45.000 0.00 0.00 0.00 2.83
410 426 4.584327 AAAATCTCCACCCGTTTCTTTG 57.416 40.909 0.00 0.00 0.00 2.77
439 455 2.191354 TACTCCACCGCTCGTTGACG 62.191 60.000 0.00 0.00 41.45 4.35
440 456 0.038892 TTACTCCACCGCTCGTTGAC 60.039 55.000 0.00 0.00 0.00 3.18
443 459 3.598019 TTATTTACTCCACCGCTCGTT 57.402 42.857 0.00 0.00 0.00 3.85
444 460 3.598019 TTTATTTACTCCACCGCTCGT 57.402 42.857 0.00 0.00 0.00 4.18
445 461 3.869246 ACATTTATTTACTCCACCGCTCG 59.131 43.478 0.00 0.00 0.00 5.03
446 462 5.813080 AACATTTATTTACTCCACCGCTC 57.187 39.130 0.00 0.00 0.00 5.03
463 483 4.369182 CTCCGTCGCTTATCCTTAACATT 58.631 43.478 0.00 0.00 0.00 2.71
470 490 2.581216 TATCCTCCGTCGCTTATCCT 57.419 50.000 0.00 0.00 0.00 3.24
489 509 8.280258 TGATAATGGTTAGAGGAGGATCATTT 57.720 34.615 0.00 0.00 36.25 2.32
497 517 5.105554 CGATCCCTGATAATGGTTAGAGGAG 60.106 48.000 0.00 0.00 0.00 3.69
502 522 3.261897 AGCCGATCCCTGATAATGGTTAG 59.738 47.826 0.00 0.00 0.00 2.34
503 523 3.248024 AGCCGATCCCTGATAATGGTTA 58.752 45.455 0.00 0.00 0.00 2.85
507 527 2.834549 ACCTAGCCGATCCCTGATAATG 59.165 50.000 0.00 0.00 0.00 1.90
508 528 3.100671 GACCTAGCCGATCCCTGATAAT 58.899 50.000 0.00 0.00 0.00 1.28
514 534 0.178975 CTGAGACCTAGCCGATCCCT 60.179 60.000 0.00 0.00 0.00 4.20
516 536 0.468400 ACCTGAGACCTAGCCGATCC 60.468 60.000 0.00 0.00 0.00 3.36
521 541 4.505808 GAGTAAAAACCTGAGACCTAGCC 58.494 47.826 0.00 0.00 0.00 3.93
530 550 4.020839 CCCGTTAGAGGAGTAAAAACCTGA 60.021 45.833 0.00 0.00 36.57 3.86
551 589 3.090037 TCTAGTTGATCGCCTATAGCCC 58.910 50.000 0.00 0.00 38.78 5.19
554 592 5.578727 GGCATTTCTAGTTGATCGCCTATAG 59.421 44.000 0.00 0.00 33.46 1.31
568 606 3.529533 CACTGTCTCAGGGCATTTCTAG 58.470 50.000 1.90 0.00 35.51 2.43
585 623 2.093447 CCTAGGTTGGCTCTTACCACTG 60.093 54.545 0.00 0.00 40.19 3.66
589 627 3.516700 TGTAACCTAGGTTGGCTCTTACC 59.483 47.826 33.19 12.02 38.92 2.85
747 787 1.584724 AGGATGAAGGTGGTGTAGGG 58.415 55.000 0.00 0.00 0.00 3.53
1533 1608 2.430244 TCTGCGCCGTCGTCTTTC 60.430 61.111 4.18 0.00 38.14 2.62
1548 1623 3.314331 CCTCACACCGGGCACTCT 61.314 66.667 6.32 0.00 0.00 3.24
1590 1665 3.195698 GCTTTGGTAGCTCGCGGG 61.196 66.667 6.13 2.60 46.77 6.13
1716 1791 2.470821 ACAAAACAGAAGACGACCGAG 58.529 47.619 0.00 0.00 0.00 4.63
1718 1793 2.350498 ACAACAAAACAGAAGACGACCG 59.650 45.455 0.00 0.00 0.00 4.79
1719 1794 3.126343 ACACAACAAAACAGAAGACGACC 59.874 43.478 0.00 0.00 0.00 4.79
1784 1861 3.124128 CCAAATATGCATCTCACCGATCG 59.876 47.826 8.51 8.51 0.00 3.69
1828 1905 5.049267 CCAATCATACGCACATCATCATCAA 60.049 40.000 0.00 0.00 0.00 2.57
1879 1956 0.030773 CACGCGAGCCTAATCTAGCA 59.969 55.000 15.93 0.00 34.92 3.49
1880 1957 0.030908 ACACGCGAGCCTAATCTAGC 59.969 55.000 15.93 0.00 0.00 3.42
1881 1958 1.333931 TCACACGCGAGCCTAATCTAG 59.666 52.381 15.93 0.00 0.00 2.43
2042 2148 2.826128 TCTCGTTCTTGTAGAGCCATGT 59.174 45.455 0.00 0.00 32.42 3.21
2048 2154 4.785511 TCCCTTTCTCGTTCTTGTAGAG 57.214 45.455 0.00 0.00 0.00 2.43
2080 2186 3.771577 TGGACTTCTTTCCTTCCTGAC 57.228 47.619 0.00 0.00 36.51 3.51
2083 2189 5.324832 TCAATTGGACTTCTTTCCTTCCT 57.675 39.130 5.42 0.00 36.51 3.36
2090 2196 5.368989 AGACGAGTTCAATTGGACTTCTTT 58.631 37.500 20.50 5.62 0.00 2.52
2091 2197 4.962155 AGACGAGTTCAATTGGACTTCTT 58.038 39.130 20.50 8.04 0.00 2.52
2111 2217 9.146984 CTTAATTTCAACCGTGTACATTCTAGA 57.853 33.333 0.00 0.00 0.00 2.43
2122 2228 5.746245 TGCTTGTTTCTTAATTTCAACCGTG 59.254 36.000 0.00 0.00 0.00 4.94
2123 2229 5.897050 TGCTTGTTTCTTAATTTCAACCGT 58.103 33.333 0.00 0.00 0.00 4.83
2125 2231 7.203218 AGTCTGCTTGTTTCTTAATTTCAACC 58.797 34.615 0.00 0.00 0.00 3.77
2126 2232 7.915397 TGAGTCTGCTTGTTTCTTAATTTCAAC 59.085 33.333 0.00 0.00 0.00 3.18
2127 2233 7.995289 TGAGTCTGCTTGTTTCTTAATTTCAA 58.005 30.769 0.00 0.00 0.00 2.69
2134 2240 4.574828 GGTGTTGAGTCTGCTTGTTTCTTA 59.425 41.667 0.00 0.00 0.00 2.10
2166 2272 4.466370 TCCTACAACTACAATGGGTCTGAG 59.534 45.833 0.00 0.00 0.00 3.35
2167 2273 4.422057 TCCTACAACTACAATGGGTCTGA 58.578 43.478 0.00 0.00 0.00 3.27
2168 2274 4.819105 TCCTACAACTACAATGGGTCTG 57.181 45.455 0.00 0.00 0.00 3.51
2169 2275 5.309806 AGTTTCCTACAACTACAATGGGTCT 59.690 40.000 0.00 0.00 35.10 3.85
2170 2276 5.411669 CAGTTTCCTACAACTACAATGGGTC 59.588 44.000 0.00 0.00 35.10 4.46
2171 2277 5.313712 CAGTTTCCTACAACTACAATGGGT 58.686 41.667 0.00 0.00 35.10 4.51
2172 2278 4.156008 GCAGTTTCCTACAACTACAATGGG 59.844 45.833 0.00 0.00 35.10 4.00
2173 2279 5.003804 AGCAGTTTCCTACAACTACAATGG 58.996 41.667 0.00 0.00 35.10 3.16
2176 2282 6.354130 AGAAAGCAGTTTCCTACAACTACAA 58.646 36.000 0.00 0.00 42.84 2.41
2181 2287 6.862711 AGTAAGAAAGCAGTTTCCTACAAC 57.137 37.500 8.90 0.00 42.84 3.32
2183 2289 6.016024 TCGTAGTAAGAAAGCAGTTTCCTACA 60.016 38.462 8.90 0.00 42.84 2.74
2199 2305 6.754209 AGAGAATTCAAGCATGTCGTAGTAAG 59.246 38.462 8.44 0.00 0.00 2.34
2200 2306 6.631016 AGAGAATTCAAGCATGTCGTAGTAA 58.369 36.000 8.44 0.00 0.00 2.24
2269 2375 6.204108 TCGAAGGTAAAGACATTTCAGTTTCC 59.796 38.462 0.00 0.00 27.45 3.13
2283 2389 4.578928 CCCCATGGTTATTCGAAGGTAAAG 59.421 45.833 11.73 0.00 0.00 1.85
2284 2390 4.227754 TCCCCATGGTTATTCGAAGGTAAA 59.772 41.667 11.73 0.00 0.00 2.01
2285 2391 3.781407 TCCCCATGGTTATTCGAAGGTAA 59.219 43.478 11.73 0.00 0.00 2.85
2286 2392 3.386063 TCCCCATGGTTATTCGAAGGTA 58.614 45.455 11.73 0.00 0.00 3.08
2287 2393 2.201830 TCCCCATGGTTATTCGAAGGT 58.798 47.619 11.73 0.00 0.00 3.50
2288 2394 3.290948 TTCCCCATGGTTATTCGAAGG 57.709 47.619 11.73 0.93 0.00 3.46
2289 2395 6.016276 CCTTTATTCCCCATGGTTATTCGAAG 60.016 42.308 11.73 6.47 0.00 3.79
2290 2396 5.830991 CCTTTATTCCCCATGGTTATTCGAA 59.169 40.000 11.73 0.00 0.00 3.71
2291 2397 5.381757 CCTTTATTCCCCATGGTTATTCGA 58.618 41.667 11.73 0.00 0.00 3.71
2292 2398 4.022329 GCCTTTATTCCCCATGGTTATTCG 60.022 45.833 11.73 0.00 0.00 3.34
2293 2399 4.022329 CGCCTTTATTCCCCATGGTTATTC 60.022 45.833 11.73 0.00 0.00 1.75
2294 2400 3.895041 CGCCTTTATTCCCCATGGTTATT 59.105 43.478 11.73 0.00 0.00 1.40
2295 2401 3.496331 CGCCTTTATTCCCCATGGTTAT 58.504 45.455 11.73 3.43 0.00 1.89
2296 2402 2.938838 CGCCTTTATTCCCCATGGTTA 58.061 47.619 11.73 0.00 0.00 2.85
2297 2403 1.775385 CGCCTTTATTCCCCATGGTT 58.225 50.000 11.73 0.00 0.00 3.67
2298 2404 0.755327 GCGCCTTTATTCCCCATGGT 60.755 55.000 11.73 0.00 0.00 3.55
2299 2405 0.754957 TGCGCCTTTATTCCCCATGG 60.755 55.000 4.18 4.14 0.00 3.66
2300 2406 0.670162 CTGCGCCTTTATTCCCCATG 59.330 55.000 4.18 0.00 0.00 3.66
2301 2407 0.550914 TCTGCGCCTTTATTCCCCAT 59.449 50.000 4.18 0.00 0.00 4.00
2302 2408 0.550914 ATCTGCGCCTTTATTCCCCA 59.449 50.000 4.18 0.00 0.00 4.96
2303 2409 0.954452 CATCTGCGCCTTTATTCCCC 59.046 55.000 4.18 0.00 0.00 4.81
2304 2410 0.312102 GCATCTGCGCCTTTATTCCC 59.688 55.000 4.18 0.00 0.00 3.97
2305 2411 3.853623 GCATCTGCGCCTTTATTCC 57.146 52.632 4.18 0.00 0.00 3.01
2322 2428 2.685388 GTGAATCAAAGGAGCCCTAAGC 59.315 50.000 0.00 0.00 44.25 3.09
2323 2429 3.955471 TGTGAATCAAAGGAGCCCTAAG 58.045 45.455 0.00 0.00 31.13 2.18
2324 2430 4.018506 TCATGTGAATCAAAGGAGCCCTAA 60.019 41.667 0.00 0.00 31.13 2.69
2325 2431 3.523157 TCATGTGAATCAAAGGAGCCCTA 59.477 43.478 0.00 0.00 31.13 3.53
2326 2432 2.309755 TCATGTGAATCAAAGGAGCCCT 59.690 45.455 0.00 0.00 33.87 5.19
2327 2433 2.726821 TCATGTGAATCAAAGGAGCCC 58.273 47.619 0.00 0.00 0.00 5.19
2328 2434 4.518211 CCTATCATGTGAATCAAAGGAGCC 59.482 45.833 0.00 0.00 0.00 4.70
2329 2435 5.371526 TCCTATCATGTGAATCAAAGGAGC 58.628 41.667 0.00 0.00 0.00 4.70
2330 2436 7.870509 TTTCCTATCATGTGAATCAAAGGAG 57.129 36.000 0.00 0.00 33.64 3.69
2331 2437 8.827832 ATTTTCCTATCATGTGAATCAAAGGA 57.172 30.769 0.00 0.00 0.00 3.36
2335 2441 9.565090 CCTCTATTTTCCTATCATGTGAATCAA 57.435 33.333 0.00 0.00 0.00 2.57
2336 2442 8.937835 TCCTCTATTTTCCTATCATGTGAATCA 58.062 33.333 0.00 0.00 0.00 2.57
2337 2443 9.956640 ATCCTCTATTTTCCTATCATGTGAATC 57.043 33.333 0.00 0.00 0.00 2.52
2339 2445 9.565090 CAATCCTCTATTTTCCTATCATGTGAA 57.435 33.333 0.00 0.00 0.00 3.18
2340 2446 7.663081 GCAATCCTCTATTTTCCTATCATGTGA 59.337 37.037 0.00 0.00 0.00 3.58
2341 2447 7.664731 AGCAATCCTCTATTTTCCTATCATGTG 59.335 37.037 0.00 0.00 0.00 3.21
2342 2448 7.753630 AGCAATCCTCTATTTTCCTATCATGT 58.246 34.615 0.00 0.00 0.00 3.21
2343 2449 9.902684 ATAGCAATCCTCTATTTTCCTATCATG 57.097 33.333 0.00 0.00 0.00 3.07
2344 2450 9.902684 CATAGCAATCCTCTATTTTCCTATCAT 57.097 33.333 0.00 0.00 0.00 2.45
2345 2451 9.104713 TCATAGCAATCCTCTATTTTCCTATCA 57.895 33.333 0.00 0.00 0.00 2.15
2346 2452 9.377312 GTCATAGCAATCCTCTATTTTCCTATC 57.623 37.037 0.00 0.00 0.00 2.08
2347 2453 8.325046 GGTCATAGCAATCCTCTATTTTCCTAT 58.675 37.037 0.00 0.00 0.00 2.57
2348 2454 7.514127 AGGTCATAGCAATCCTCTATTTTCCTA 59.486 37.037 0.00 0.00 0.00 2.94
2349 2455 6.331307 AGGTCATAGCAATCCTCTATTTTCCT 59.669 38.462 0.00 0.00 0.00 3.36
2350 2456 6.538263 AGGTCATAGCAATCCTCTATTTTCC 58.462 40.000 0.00 0.00 0.00 3.13
2351 2457 7.604545 GGTAGGTCATAGCAATCCTCTATTTTC 59.395 40.741 0.00 0.00 0.00 2.29
2352 2458 7.072454 TGGTAGGTCATAGCAATCCTCTATTTT 59.928 37.037 0.00 0.00 38.90 1.82
2353 2459 6.558775 TGGTAGGTCATAGCAATCCTCTATTT 59.441 38.462 0.00 0.00 38.90 1.40
2354 2460 6.084738 TGGTAGGTCATAGCAATCCTCTATT 58.915 40.000 0.00 0.00 38.90 1.73
2355 2461 5.655394 TGGTAGGTCATAGCAATCCTCTAT 58.345 41.667 0.00 0.00 38.90 1.98
2356 2462 5.074746 TGGTAGGTCATAGCAATCCTCTA 57.925 43.478 0.00 0.00 38.90 2.43
2357 2463 3.900601 CTGGTAGGTCATAGCAATCCTCT 59.099 47.826 0.00 0.00 41.20 3.69
2358 2464 3.643792 ACTGGTAGGTCATAGCAATCCTC 59.356 47.826 0.00 0.00 41.20 3.71
2359 2465 3.643792 GACTGGTAGGTCATAGCAATCCT 59.356 47.826 0.00 0.00 41.20 3.24
2360 2466 3.996480 GACTGGTAGGTCATAGCAATCC 58.004 50.000 0.00 0.00 41.20 3.01
2361 2467 3.388024 TGGACTGGTAGGTCATAGCAATC 59.612 47.826 0.00 0.00 41.20 2.67
2362 2468 3.384168 TGGACTGGTAGGTCATAGCAAT 58.616 45.455 0.00 0.00 41.20 3.56
2363 2469 2.827755 TGGACTGGTAGGTCATAGCAA 58.172 47.619 0.00 0.00 41.20 3.91
2364 2470 2.543037 TGGACTGGTAGGTCATAGCA 57.457 50.000 0.00 0.00 39.54 3.49
2365 2471 4.130118 CAAATGGACTGGTAGGTCATAGC 58.870 47.826 0.00 0.00 37.91 2.97
2366 2472 5.614324 TCAAATGGACTGGTAGGTCATAG 57.386 43.478 0.00 0.00 37.91 2.23
2367 2473 6.575244 ATTCAAATGGACTGGTAGGTCATA 57.425 37.500 0.00 0.00 37.91 2.15
2368 2474 4.927267 TTCAAATGGACTGGTAGGTCAT 57.073 40.909 0.00 0.00 37.91 3.06
2369 2475 4.927267 ATTCAAATGGACTGGTAGGTCA 57.073 40.909 0.00 0.00 37.91 4.02
2370 2476 5.501156 AGAATTCAAATGGACTGGTAGGTC 58.499 41.667 8.44 0.00 35.66 3.85
2371 2477 5.520748 AGAATTCAAATGGACTGGTAGGT 57.479 39.130 8.44 0.00 0.00 3.08
2372 2478 6.488006 CCATAGAATTCAAATGGACTGGTAGG 59.512 42.308 25.08 4.61 42.36 3.18
2373 2479 7.282585 TCCATAGAATTCAAATGGACTGGTAG 58.717 38.462 26.69 9.32 43.27 3.18
2374 2480 7.206789 TCCATAGAATTCAAATGGACTGGTA 57.793 36.000 26.69 12.50 43.27 3.25
2375 2481 6.078456 TCCATAGAATTCAAATGGACTGGT 57.922 37.500 26.69 0.77 43.27 4.00
2376 2482 7.592885 ATTCCATAGAATTCAAATGGACTGG 57.407 36.000 28.76 14.84 46.77 4.00
2391 2497 9.807921 AGTTCCTTTGTTTTAGAATTCCATAGA 57.192 29.630 0.65 0.00 0.00 1.98
2392 2498 9.846248 CAGTTCCTTTGTTTTAGAATTCCATAG 57.154 33.333 0.65 0.00 0.00 2.23
2393 2499 8.802267 CCAGTTCCTTTGTTTTAGAATTCCATA 58.198 33.333 0.65 0.00 0.00 2.74
2394 2500 7.670364 CCAGTTCCTTTGTTTTAGAATTCCAT 58.330 34.615 0.65 0.00 0.00 3.41
2395 2501 6.462347 GCCAGTTCCTTTGTTTTAGAATTCCA 60.462 38.462 0.65 0.00 0.00 3.53
2396 2502 5.926542 GCCAGTTCCTTTGTTTTAGAATTCC 59.073 40.000 0.65 0.00 0.00 3.01
2397 2503 6.420903 GTGCCAGTTCCTTTGTTTTAGAATTC 59.579 38.462 0.00 0.00 0.00 2.17
2398 2504 6.280643 GTGCCAGTTCCTTTGTTTTAGAATT 58.719 36.000 0.00 0.00 0.00 2.17
2399 2505 5.221441 GGTGCCAGTTCCTTTGTTTTAGAAT 60.221 40.000 0.00 0.00 0.00 2.40
2400 2506 4.098807 GGTGCCAGTTCCTTTGTTTTAGAA 59.901 41.667 0.00 0.00 0.00 2.10
2401 2507 3.634910 GGTGCCAGTTCCTTTGTTTTAGA 59.365 43.478 0.00 0.00 0.00 2.10
2402 2508 3.243737 GGGTGCCAGTTCCTTTGTTTTAG 60.244 47.826 0.00 0.00 0.00 1.85
2403 2509 2.696187 GGGTGCCAGTTCCTTTGTTTTA 59.304 45.455 0.00 0.00 0.00 1.52
2404 2510 1.484653 GGGTGCCAGTTCCTTTGTTTT 59.515 47.619 0.00 0.00 0.00 2.43
2405 2511 1.119684 GGGTGCCAGTTCCTTTGTTT 58.880 50.000 0.00 0.00 0.00 2.83
2406 2512 0.032615 TGGGTGCCAGTTCCTTTGTT 60.033 50.000 0.00 0.00 0.00 2.83
2407 2513 0.032615 TTGGGTGCCAGTTCCTTTGT 60.033 50.000 0.00 0.00 33.81 2.83
2408 2514 1.118838 TTTGGGTGCCAGTTCCTTTG 58.881 50.000 0.00 0.00 33.81 2.77
2409 2515 1.693606 CATTTGGGTGCCAGTTCCTTT 59.306 47.619 0.00 0.00 33.81 3.11
2410 2516 1.341080 CATTTGGGTGCCAGTTCCTT 58.659 50.000 0.00 0.00 33.81 3.36
2411 2517 0.188342 ACATTTGGGTGCCAGTTCCT 59.812 50.000 0.00 0.00 33.81 3.36
2412 2518 0.318120 CACATTTGGGTGCCAGTTCC 59.682 55.000 0.00 0.00 33.81 3.62
2413 2519 1.039856 ACACATTTGGGTGCCAGTTC 58.960 50.000 0.00 0.00 42.55 3.01
2414 2520 0.752054 CACACATTTGGGTGCCAGTT 59.248 50.000 0.00 0.00 43.10 3.16
2415 2521 2.428834 CACACATTTGGGTGCCAGT 58.571 52.632 0.00 0.00 43.10 4.00
2421 2527 1.484240 CCCACAAACACACATTTGGGT 59.516 47.619 3.52 0.00 43.21 4.51
2422 2528 1.202627 CCCCACAAACACACATTTGGG 60.203 52.381 0.00 0.00 42.74 4.12
2423 2529 1.202627 CCCCCACAAACACACATTTGG 60.203 52.381 3.52 0.00 42.74 3.28
2424 2530 2.237393 CCCCCACAAACACACATTTG 57.763 50.000 0.00 0.00 43.81 2.32
2440 2546 3.713826 TCGAATAATTCCTATGCCCCC 57.286 47.619 0.00 0.00 0.00 5.40
2441 2547 4.906618 TCTTCGAATAATTCCTATGCCCC 58.093 43.478 0.00 0.00 0.00 5.80
2442 2548 4.393371 GCTCTTCGAATAATTCCTATGCCC 59.607 45.833 0.00 0.00 0.00 5.36
2443 2549 5.241662 AGCTCTTCGAATAATTCCTATGCC 58.758 41.667 0.00 0.00 0.00 4.40
2444 2550 6.793492 AAGCTCTTCGAATAATTCCTATGC 57.207 37.500 0.00 0.00 0.00 3.14
2445 2551 9.134734 GTCTAAGCTCTTCGAATAATTCCTATG 57.865 37.037 0.00 0.00 0.00 2.23
2446 2552 9.084533 AGTCTAAGCTCTTCGAATAATTCCTAT 57.915 33.333 0.00 0.00 0.00 2.57
2447 2553 8.466617 AGTCTAAGCTCTTCGAATAATTCCTA 57.533 34.615 0.00 0.00 0.00 2.94
2448 2554 7.354751 AGTCTAAGCTCTTCGAATAATTCCT 57.645 36.000 0.00 0.00 0.00 3.36
2449 2555 8.426881 AAAGTCTAAGCTCTTCGAATAATTCC 57.573 34.615 0.00 0.00 0.00 3.01
2453 2559 9.302345 CACATAAAGTCTAAGCTCTTCGAATAA 57.698 33.333 0.00 0.00 0.00 1.40
2454 2560 8.683615 TCACATAAAGTCTAAGCTCTTCGAATA 58.316 33.333 0.00 0.00 0.00 1.75
2455 2561 7.548097 TCACATAAAGTCTAAGCTCTTCGAAT 58.452 34.615 0.00 0.00 0.00 3.34
2456 2562 6.920817 TCACATAAAGTCTAAGCTCTTCGAA 58.079 36.000 0.00 0.00 0.00 3.71
2457 2563 6.510879 TCACATAAAGTCTAAGCTCTTCGA 57.489 37.500 0.00 0.00 0.00 3.71
2458 2564 7.582435 TTTCACATAAAGTCTAAGCTCTTCG 57.418 36.000 0.00 0.00 0.00 3.79
2524 2630 5.818136 TGGATTTTCAAAGGATCGTGATC 57.182 39.130 1.11 1.11 37.11 2.92
2525 2631 6.377996 TCATTGGATTTTCAAAGGATCGTGAT 59.622 34.615 0.00 0.00 0.00 3.06
2526 2632 5.709631 TCATTGGATTTTCAAAGGATCGTGA 59.290 36.000 0.00 0.00 0.00 4.35
2527 2633 5.953183 TCATTGGATTTTCAAAGGATCGTG 58.047 37.500 0.00 0.00 0.00 4.35
2528 2634 6.588719 TTCATTGGATTTTCAAAGGATCGT 57.411 33.333 0.00 0.00 0.00 3.73
2529 2635 7.259882 TGATTCATTGGATTTTCAAAGGATCG 58.740 34.615 0.00 0.00 34.70 3.69
2530 2636 9.439500 TTTGATTCATTGGATTTTCAAAGGATC 57.561 29.630 0.00 0.00 33.38 3.36
2531 2637 9.444600 CTTTGATTCATTGGATTTTCAAAGGAT 57.555 29.630 12.93 0.00 39.11 3.24
2532 2638 8.431222 ACTTTGATTCATTGGATTTTCAAAGGA 58.569 29.630 20.77 0.00 43.84 3.36
2533 2639 8.611654 ACTTTGATTCATTGGATTTTCAAAGG 57.388 30.769 20.77 8.59 43.84 3.11
2535 2641 9.206870 GCTACTTTGATTCATTGGATTTTCAAA 57.793 29.630 0.00 0.00 0.00 2.69
2536 2642 8.587608 AGCTACTTTGATTCATTGGATTTTCAA 58.412 29.630 0.00 0.00 0.00 2.69
2537 2643 8.125978 AGCTACTTTGATTCATTGGATTTTCA 57.874 30.769 0.00 0.00 0.00 2.69
2538 2644 8.992835 AAGCTACTTTGATTCATTGGATTTTC 57.007 30.769 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.