Multiple sequence alignment - TraesCS7B01G146700

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 TraesCS7B01G146700 chr7B 100.000 5083 0 0 1 5083 191779589 191774507 0.000000e+00 9387.0
1 TraesCS7B01G146700 chr7B 91.176 68 4 1 3586 3651 744075149 744075216 1.950000e-14 91.6
2 TraesCS7B01G146700 chr7B 90.000 70 5 1 3585 3652 342715020 342715089 7.010000e-14 89.8
3 TraesCS7B01G146700 chr7A 93.887 2274 85 24 23 2291 222496909 222499133 0.000000e+00 3380.0
4 TraesCS7B01G146700 chr7A 94.637 1212 45 9 2392 3591 222499129 222500332 0.000000e+00 1860.0
5 TraesCS7B01G146700 chr7A 94.097 559 27 4 3650 4202 222500317 222500875 0.000000e+00 845.0
6 TraesCS7B01G146700 chr7A 92.424 330 15 3 4200 4521 222500970 222501297 3.590000e-126 462.0
7 TraesCS7B01G146700 chr7A 78.517 391 27 19 4627 5005 222501478 222501823 2.400000e-48 204.0
8 TraesCS7B01G146700 chr7A 98.198 111 2 0 2287 2397 560407051 560407161 1.440000e-45 195.0
9 TraesCS7B01G146700 chr7D 93.133 2301 112 24 1 2288 209790098 209792365 0.000000e+00 3332.0
10 TraesCS7B01G146700 chr7D 96.167 1200 39 3 2392 3588 209792364 209793559 0.000000e+00 1954.0
11 TraesCS7B01G146700 chr7D 94.761 878 37 5 3650 4520 209793547 209794422 0.000000e+00 1358.0
12 TraesCS7B01G146700 chr7D 86.512 215 15 7 4627 4832 209794601 209794810 1.840000e-54 224.0
13 TraesCS7B01G146700 chr7D 91.549 71 4 1 3585 3653 28010178 28010248 4.190000e-16 97.1
14 TraesCS7B01G146700 chr5A 93.598 328 19 2 1655 1982 256223250 256222925 5.910000e-134 488.0
15 TraesCS7B01G146700 chr5A 76.423 492 102 11 2473 2956 476603933 476603448 2.350000e-63 254.0
16 TraesCS7B01G146700 chr5D 75.354 495 105 15 2471 2956 375193167 375192681 6.620000e-54 222.0
17 TraesCS7B01G146700 chr5D 75.802 343 74 9 3715 4054 375191978 375191642 1.130000e-36 165.0
18 TraesCS7B01G146700 chr5D 91.304 69 4 1 3585 3651 34073592 34073524 5.420000e-15 93.5
19 TraesCS7B01G146700 chr1A 99.099 111 1 0 2287 2397 134973595 134973485 3.100000e-47 200.0
20 TraesCS7B01G146700 chr6D 97.414 116 2 1 2284 2398 457693988 457694103 4.010000e-46 196.0
21 TraesCS7B01G146700 chr6B 97.414 116 1 2 2287 2401 299051451 299051565 4.010000e-46 196.0
22 TraesCS7B01G146700 chr4A 96.610 118 4 0 2286 2403 575976168 575976051 4.010000e-46 196.0
23 TraesCS7B01G146700 chr3B 96.610 118 4 0 2287 2404 214560158 214560275 4.010000e-46 196.0
24 TraesCS7B01G146700 chr3B 92.063 63 2 2 3592 3651 561182043 561182105 9.070000e-13 86.1
25 TraesCS7B01G146700 chr5B 96.610 118 2 2 2287 2403 697185041 697184925 1.440000e-45 195.0
26 TraesCS7B01G146700 chr5B 93.077 130 7 2 2265 2394 638765288 638765415 6.720000e-44 189.0
27 TraesCS7B01G146700 chr5B 89.041 73 5 2 3590 3660 484836948 484836877 2.520000e-13 87.9
28 TraesCS7B01G146700 chr3A 96.610 118 2 2 2276 2393 583676582 583676697 1.440000e-45 195.0
29 TraesCS7B01G146700 chr4B 91.176 68 4 1 3585 3650 427254556 427254489 1.950000e-14 91.6
30 TraesCS7B01G146700 chrUn 91.045 67 4 1 3585 3649 67772888 67772822 7.010000e-14 89.8
31 TraesCS7B01G146700 chr2D 88.732 71 5 2 3585 3653 592646809 592646878 3.260000e-12 84.2


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 TraesCS7B01G146700 chr7B 191774507 191779589 5082 True 9387.0 9387 100.00000 1 5083 1 chr7B.!!$R1 5082
1 TraesCS7B01G146700 chr7A 222496909 222501823 4914 False 1350.2 3380 90.71240 23 5005 5 chr7A.!!$F2 4982
2 TraesCS7B01G146700 chr7D 209790098 209794810 4712 False 1717.0 3332 92.64325 1 4832 4 chr7D.!!$F2 4831

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
53 57 0.963355 GCGTTTGGGGCTGTGGAATA 60.963 55.000 0.00 0.0 0.00 1.75 F
128 132 1.499056 CGTGAGCGCTTGATTTGCT 59.501 52.632 13.26 0.0 42.73 3.91 F
1103 1128 1.556911 ACAAGGTGAGGCTCATGGTAG 59.443 52.381 21.84 12.2 0.00 3.18 F
1668 1693 1.333619 GCACATAAGTTGCATACCCCG 59.666 52.381 0.00 0.0 0.00 5.73 F
3329 3363 0.680061 GGAAAGAGGTCAGTGTCCGT 59.320 55.000 0.48 0.0 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1080 1105 1.064906 CCATGAGCCTCACCTTGTGAT 60.065 52.381 0.00 0.00 41.94 3.06 R
1668 1693 1.227002 CCTAGAAAGACGCCGAGCC 60.227 63.158 0.00 0.00 0.00 4.70 R
2375 2400 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30 R
3599 3638 0.105593 CCTCTGCATGTACGAGGCAT 59.894 55.000 13.41 0.00 41.43 4.40 R
4411 4557 0.314578 GTCGCATTCGCATCTTCACG 60.315 55.000 0.00 0.00 38.40 4.35 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 39 1.134946 GTTTTCCTGATGGATTGGGCG 59.865 52.381 0.00 0.00 42.81 6.13
44 48 3.770040 GGATTGGGCGTTTGGGGC 61.770 66.667 0.00 0.00 0.00 5.80
51 55 2.909965 GCGTTTGGGGCTGTGGAA 60.910 61.111 0.00 0.00 0.00 3.53
53 57 0.963355 GCGTTTGGGGCTGTGGAATA 60.963 55.000 0.00 0.00 0.00 1.75
55 59 1.613255 CGTTTGGGGCTGTGGAATAGT 60.613 52.381 0.00 0.00 0.00 2.12
56 60 1.818674 GTTTGGGGCTGTGGAATAGTG 59.181 52.381 0.00 0.00 0.00 2.74
58 62 1.959710 TGGGGCTGTGGAATAGTGTA 58.040 50.000 0.00 0.00 0.00 2.90
59 63 2.487775 TGGGGCTGTGGAATAGTGTAT 58.512 47.619 0.00 0.00 0.00 2.29
61 65 4.041464 TGGGGCTGTGGAATAGTGTATTA 58.959 43.478 0.00 0.00 0.00 0.98
63 67 4.102681 GGGGCTGTGGAATAGTGTATTAGT 59.897 45.833 0.00 0.00 0.00 2.24
64 68 5.397559 GGGGCTGTGGAATAGTGTATTAGTT 60.398 44.000 0.00 0.00 0.00 2.24
65 69 5.758784 GGGCTGTGGAATAGTGTATTAGTTC 59.241 44.000 0.00 0.00 0.00 3.01
79 83 8.812972 AGTGTATTAGTTCTAGTTTGTGATCCA 58.187 33.333 0.00 0.00 0.00 3.41
89 93 4.133820 AGTTTGTGATCCACATTCACGAA 58.866 39.130 0.27 3.04 44.16 3.85
95 99 5.009510 TGTGATCCACATTCACGAATTTTGT 59.990 36.000 0.00 0.00 45.14 2.83
115 119 1.966451 GCCCTGTTGTTCCCGTGAG 60.966 63.158 0.00 0.00 0.00 3.51
117 121 2.317609 CCTGTTGTTCCCGTGAGCG 61.318 63.158 0.00 0.00 37.95 5.03
128 132 1.499056 CGTGAGCGCTTGATTTGCT 59.501 52.632 13.26 0.00 42.73 3.91
175 179 4.500116 GTCCACGGCGAGCTCTCC 62.500 72.222 16.62 13.01 0.00 3.71
190 194 1.751351 CTCTCCCTGTGATACGAGCAA 59.249 52.381 0.00 0.00 0.00 3.91
220 224 7.224949 GGTTGCAGACTTGAATAGTATTAGGAC 59.775 40.741 0.00 0.00 37.17 3.85
260 264 3.057174 GGTTTGGTTGGCGATCATTTACA 60.057 43.478 0.00 0.00 0.00 2.41
382 386 5.688807 AGTCCTACGCCTATCTAGTTGTTA 58.311 41.667 0.00 0.00 0.00 2.41
455 470 3.926527 TCATGTGAAGTAGTTAAGCAGCG 59.073 43.478 0.00 0.00 0.00 5.18
499 517 9.607988 TTCGAGAATTTGGCTCTATTTATTACA 57.392 29.630 0.00 0.00 0.00 2.41
541 559 9.384764 AGATGAATTTTAGTTTACTCTGGTAGC 57.615 33.333 0.00 0.00 0.00 3.58
696 715 9.722184 ACATCACATCCTATATGAAAATGAGAG 57.278 33.333 0.00 0.00 0.00 3.20
823 843 1.647702 GTAGCGTTTCTTCTTCCGACG 59.352 52.381 0.00 0.00 36.85 5.12
861 881 5.663456 TCCTTTATGCCTGAATTTGAATGC 58.337 37.500 0.00 0.00 0.00 3.56
907 932 9.918630 ACATTTTCCTCATTTTTCAGTCTTATG 57.081 29.630 0.00 0.00 0.00 1.90
1014 1039 2.181975 CCTGAAATGGGTGCCAAAGAT 58.818 47.619 0.00 0.00 36.95 2.40
1020 1045 2.917713 TGGGTGCCAAAGATAATGGT 57.082 45.000 0.00 0.00 40.23 3.55
1080 1105 4.437682 ACCATCCAGAGTTTCTGTTTCA 57.562 40.909 5.46 0.00 42.80 2.69
1103 1128 1.556911 ACAAGGTGAGGCTCATGGTAG 59.443 52.381 21.84 12.20 0.00 3.18
1282 1307 2.627699 CCAAAACCTAGGAAAGCAGCAA 59.372 45.455 17.98 0.00 0.00 3.91
1326 1351 8.777865 TTGAAGTTAGAAGACCAGATATTGTG 57.222 34.615 0.00 0.00 0.00 3.33
1528 1553 7.789273 AAAATTGTTGATGATGACAAAGCAA 57.211 28.000 0.00 0.00 39.03 3.91
1554 1579 3.866651 ACATCGGAGAAATGAGGAACTG 58.133 45.455 0.00 0.00 43.58 3.16
1668 1693 1.333619 GCACATAAGTTGCATACCCCG 59.666 52.381 0.00 0.00 0.00 5.73
1881 1906 6.443832 AGAATAAAGCTTCCCCCATTAACAT 58.556 36.000 0.00 0.00 0.00 2.71
1964 1989 6.956299 ATTTCAAAATCTTTTGGCATCTCG 57.044 33.333 13.77 0.00 45.68 4.04
2014 2039 3.385193 AAACTTAAATGGCAGTGCACC 57.615 42.857 18.61 0.00 0.00 5.01
2129 2154 3.026694 AGCAGATAATTGGCAGGAAACC 58.973 45.455 0.00 0.00 0.00 3.27
2144 2169 2.956333 GGAAACCAGTACACTTTTGGCT 59.044 45.455 0.00 0.00 35.35 4.75
2186 2211 8.525290 AATCTTGGATATTTTCTCGGATTGTT 57.475 30.769 0.00 0.00 0.00 2.83
2227 2252 7.615757 GCAGGTAATATTTTCCTTAGGCCATAT 59.384 37.037 5.01 0.00 0.00 1.78
2268 2293 2.906389 ACTGGTCTTGCATTCCTAGTCA 59.094 45.455 0.00 0.00 0.00 3.41
2282 2307 7.651808 CATTCCTAGTCAAGTGTTTCACAAAT 58.348 34.615 2.80 0.00 36.74 2.32
2286 2311 9.349713 TCCTAGTCAAGTGTTTCACAAATAAAT 57.650 29.630 2.80 0.00 36.74 1.40
2291 2316 9.394477 GTCAAGTGTTTCACAAATAAATACTCC 57.606 33.333 2.80 0.00 37.31 3.85
2292 2317 8.573035 TCAAGTGTTTCACAAATAAATACTCCC 58.427 33.333 2.80 0.00 37.31 4.30
2293 2318 8.576442 CAAGTGTTTCACAAATAAATACTCCCT 58.424 33.333 2.80 0.00 37.31 4.20
2294 2319 8.336801 AGTGTTTCACAAATAAATACTCCCTC 57.663 34.615 2.80 0.00 34.41 4.30
2295 2320 7.393515 AGTGTTTCACAAATAAATACTCCCTCC 59.606 37.037 2.80 0.00 34.41 4.30
2296 2321 6.373216 TGTTTCACAAATAAATACTCCCTCCG 59.627 38.462 0.00 0.00 0.00 4.63
2297 2322 5.687166 TCACAAATAAATACTCCCTCCGT 57.313 39.130 0.00 0.00 0.00 4.69
2298 2323 6.057321 TCACAAATAAATACTCCCTCCGTT 57.943 37.500 0.00 0.00 0.00 4.44
2299 2324 6.110707 TCACAAATAAATACTCCCTCCGTTC 58.889 40.000 0.00 0.00 0.00 3.95
2300 2325 5.006358 CACAAATAAATACTCCCTCCGTTCG 59.994 44.000 0.00 0.00 0.00 3.95
2301 2326 4.332428 AATAAATACTCCCTCCGTTCGG 57.668 45.455 4.74 4.74 0.00 4.30
2302 2327 1.856629 AAATACTCCCTCCGTTCGGA 58.143 50.000 13.34 13.34 0.00 4.55
2303 2328 1.856629 AATACTCCCTCCGTTCGGAA 58.143 50.000 14.79 0.00 33.41 4.30
2304 2329 2.083628 ATACTCCCTCCGTTCGGAAT 57.916 50.000 14.79 2.14 33.41 3.01
2305 2330 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
2306 2331 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2307 2332 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2308 2333 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2309 2334 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2310 2335 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2311 2336 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2312 2337 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2313 2338 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
2314 2339 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
2315 2340 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
2316 2341 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
2317 2342 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
2318 2343 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
2319 2344 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
2320 2345 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
2321 2346 4.868171 TCGGAATTACTTGTCTCGGAAATG 59.132 41.667 0.00 0.00 0.00 2.32
2322 2347 4.868171 CGGAATTACTTGTCTCGGAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2323 2348 5.350365 CGGAATTACTTGTCTCGGAAATGAA 59.650 40.000 0.00 0.00 0.00 2.57
2324 2349 6.037172 CGGAATTACTTGTCTCGGAAATGAAT 59.963 38.462 0.00 0.00 0.00 2.57
2325 2350 7.189512 GGAATTACTTGTCTCGGAAATGAATG 58.810 38.462 0.00 0.00 0.00 2.67
2326 2351 7.148239 GGAATTACTTGTCTCGGAAATGAATGT 60.148 37.037 0.00 0.00 0.00 2.71
2327 2352 8.786826 AATTACTTGTCTCGGAAATGAATGTA 57.213 30.769 0.00 0.00 0.00 2.29
2328 2353 8.964476 ATTACTTGTCTCGGAAATGAATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
2329 2354 6.910536 ACTTGTCTCGGAAATGAATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
2330 2355 6.644347 ACTTGTCTCGGAAATGAATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
2331 2356 7.782049 ACTTGTCTCGGAAATGAATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
2332 2357 7.923344 ACTTGTCTCGGAAATGAATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
2333 2358 7.582667 TGTCTCGGAAATGAATGTATCTAGA 57.417 36.000 0.00 0.00 0.00 2.43
2334 2359 8.007405 TGTCTCGGAAATGAATGTATCTAGAA 57.993 34.615 0.00 0.00 0.00 2.10
2335 2360 7.921214 TGTCTCGGAAATGAATGTATCTAGAAC 59.079 37.037 0.00 0.00 0.00 3.01
2336 2361 8.138712 GTCTCGGAAATGAATGTATCTAGAACT 58.861 37.037 0.00 0.00 0.00 3.01
2337 2362 9.350951 TCTCGGAAATGAATGTATCTAGAACTA 57.649 33.333 0.00 0.00 0.00 2.24
2338 2363 9.967346 CTCGGAAATGAATGTATCTAGAACTAA 57.033 33.333 0.00 0.00 0.00 2.24
2365 2390 9.664332 AATATGTCTAGATACATCCATTTCTGC 57.336 33.333 0.00 0.00 40.52 4.26
2366 2391 5.532557 TGTCTAGATACATCCATTTCTGCG 58.467 41.667 0.00 0.00 0.00 5.18
2367 2392 5.301805 TGTCTAGATACATCCATTTCTGCGA 59.698 40.000 0.00 0.00 0.00 5.10
2368 2393 5.631512 GTCTAGATACATCCATTTCTGCGAC 59.368 44.000 0.00 0.00 0.00 5.19
2369 2394 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
2370 2395 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
2371 2396 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
2372 2397 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
2373 2398 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
2374 2399 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
2375 2400 4.943705 ACATCCATTTCTGCGACAAGTAAT 59.056 37.500 0.00 0.00 0.00 1.89
2376 2401 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
2377 2402 5.545658 TCCATTTCTGCGACAAGTAATTC 57.454 39.130 0.00 0.00 0.00 2.17
2378 2403 4.394920 TCCATTTCTGCGACAAGTAATTCC 59.605 41.667 0.00 0.00 0.00 3.01
2379 2404 4.334443 CATTTCTGCGACAAGTAATTCCG 58.666 43.478 0.00 0.00 0.00 4.30
2380 2405 3.306917 TTCTGCGACAAGTAATTCCGA 57.693 42.857 0.00 0.00 0.00 4.55
2381 2406 3.306917 TCTGCGACAAGTAATTCCGAA 57.693 42.857 0.00 0.00 0.00 4.30
2382 2407 2.991190 TCTGCGACAAGTAATTCCGAAC 59.009 45.455 0.00 0.00 0.00 3.95
2383 2408 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
2384 2409 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
2385 2410 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
2386 2411 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
2387 2412 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2388 2413 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2389 2414 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2390 2415 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2440 2465 8.834749 ACCTACTGTTCTCTAAATTTGTCTTC 57.165 34.615 0.00 0.00 0.00 2.87
2538 2563 2.223745 GTTCGTCAACCCCAAAAGCTA 58.776 47.619 0.00 0.00 0.00 3.32
2697 2722 5.410067 CAGTATTGGCAAAACTGGTATTGG 58.590 41.667 3.01 0.00 37.55 3.16
2707 2732 6.738453 GCAAAACTGGTATTGGTTGACATCTT 60.738 38.462 0.00 0.00 0.00 2.40
2759 2793 8.775220 TTCTAATTTGTGTATTTGACGTGTTG 57.225 30.769 0.00 0.00 0.00 3.33
2855 2889 4.399618 TCAGCTAGTGAGATACCAACTGAC 59.600 45.833 0.00 0.00 31.02 3.51
2858 2892 3.191888 AGTGAGATACCAACTGACCCT 57.808 47.619 0.00 0.00 0.00 4.34
2882 2916 1.004320 TGACCCAATCGTTGACCCG 60.004 57.895 0.15 0.00 0.00 5.28
3190 3224 1.279271 CCCTGAGGATGAAGGTTTCGT 59.721 52.381 0.00 0.00 33.47 3.85
3263 3297 5.551760 TTAAGCTGCTTAATGAACTGAGC 57.448 39.130 26.31 0.00 31.94 4.26
3329 3363 0.680061 GGAAAGAGGTCAGTGTCCGT 59.320 55.000 0.48 0.00 0.00 4.69
3346 3380 1.675714 CCGTGCATAGCTCCAGACAAA 60.676 52.381 0.00 0.00 0.00 2.83
3351 3385 5.008019 CGTGCATAGCTCCAGACAAATTTAT 59.992 40.000 0.00 0.00 0.00 1.40
3498 3532 2.230025 CGATCCTGTCCCTAGCATAGTG 59.770 54.545 0.00 0.00 36.82 2.74
3524 3558 2.027377 AGGAGCTGAATTCTGAGGTGTG 60.027 50.000 15.79 0.00 0.00 3.82
3525 3559 2.354259 GAGCTGAATTCTGAGGTGTGG 58.646 52.381 15.79 0.00 0.00 4.17
3538 3574 1.341531 AGGTGTGGTTTCTCTCTCACG 59.658 52.381 0.00 0.00 33.25 4.35
3540 3576 2.223971 GGTGTGGTTTCTCTCTCACGAA 60.224 50.000 0.00 0.00 33.25 3.85
3593 3632 8.950403 CATTATCATGCTGACATATCAAAGTG 57.050 34.615 0.00 0.00 33.67 3.16
3594 3633 7.500720 TTATCATGCTGACATATCAAAGTGG 57.499 36.000 0.00 0.00 33.67 4.00
3595 3634 3.628942 TCATGCTGACATATCAAAGTGGC 59.371 43.478 0.00 0.00 33.67 5.01
3596 3635 2.368439 TGCTGACATATCAAAGTGGCC 58.632 47.619 0.00 0.00 33.30 5.36
3597 3636 1.331756 GCTGACATATCAAAGTGGCCG 59.668 52.381 0.00 0.00 33.30 6.13
3598 3637 2.632377 CTGACATATCAAAGTGGCCGT 58.368 47.619 0.00 0.00 33.30 5.68
3599 3638 3.792401 CTGACATATCAAAGTGGCCGTA 58.208 45.455 0.00 0.00 33.30 4.02
3600 3639 4.380531 CTGACATATCAAAGTGGCCGTAT 58.619 43.478 0.00 0.00 33.30 3.06
3601 3640 4.126437 TGACATATCAAAGTGGCCGTATG 58.874 43.478 0.00 0.97 0.00 2.39
3602 3641 2.878406 ACATATCAAAGTGGCCGTATGC 59.122 45.455 0.00 0.00 40.16 3.14
3612 3651 2.517598 GCCGTATGCCTCGTACATG 58.482 57.895 0.00 0.00 0.00 3.21
3613 3652 1.557443 GCCGTATGCCTCGTACATGC 61.557 60.000 0.00 0.00 0.00 4.06
3614 3653 0.249280 CCGTATGCCTCGTACATGCA 60.249 55.000 3.76 3.76 39.68 3.96
3615 3654 1.131771 CGTATGCCTCGTACATGCAG 58.868 55.000 7.00 0.00 38.58 4.41
3616 3655 1.269051 CGTATGCCTCGTACATGCAGA 60.269 52.381 7.00 0.28 38.58 4.26
3617 3656 2.398498 GTATGCCTCGTACATGCAGAG 58.602 52.381 7.00 0.00 38.58 3.35
3619 3658 4.427394 CCTCGTACATGCAGAGGC 57.573 61.111 15.75 0.00 44.09 4.70
3620 3659 1.227380 CCTCGTACATGCAGAGGCC 60.227 63.158 15.75 0.00 44.09 5.19
3621 3660 1.589993 CTCGTACATGCAGAGGCCG 60.590 63.158 0.00 0.00 40.13 6.13
3622 3661 2.586079 CGTACATGCAGAGGCCGG 60.586 66.667 0.00 0.00 40.13 6.13
3623 3662 2.203070 GTACATGCAGAGGCCGGG 60.203 66.667 2.18 0.00 40.13 5.73
3624 3663 3.479203 TACATGCAGAGGCCGGGG 61.479 66.667 2.18 0.00 40.13 5.73
3625 3664 3.993865 TACATGCAGAGGCCGGGGA 62.994 63.158 2.18 0.00 40.13 4.81
3626 3665 4.559063 CATGCAGAGGCCGGGGAG 62.559 72.222 2.18 0.00 40.13 4.30
3687 3726 1.819928 TTGCGCAACAGACATGGTAT 58.180 45.000 21.02 0.00 0.00 2.73
3690 3729 2.095314 TGCGCAACAGACATGGTATTTG 60.095 45.455 8.16 0.00 0.00 2.32
3696 3735 5.692814 CAACAGACATGGTATTTGACACTG 58.307 41.667 0.00 0.00 0.00 3.66
3725 3764 5.642491 TCATATTATGATGCAGAGCTTGCTC 59.358 40.000 14.16 14.16 43.15 4.26
3920 3959 3.117851 ACGATCTAGATGACCTGGACTCA 60.118 47.826 10.74 0.00 35.10 3.41
3928 3967 2.037367 CCTGGACTCACCCCTCGA 59.963 66.667 0.00 0.00 38.00 4.04
3964 4003 4.069232 CGCTCCACCTTCGCCAGA 62.069 66.667 0.00 0.00 0.00 3.86
4019 4058 1.003233 AGCTTCCTTGGAGAACGCC 60.003 57.895 0.00 0.00 0.00 5.68
4104 4146 8.053355 TGTGAAGATCACCTCTATAGTTACTCA 58.947 37.037 7.94 0.00 46.40 3.41
4203 4345 3.846588 ACTAGGGCCCCTTGTATGATATG 59.153 47.826 21.43 0.00 37.79 1.78
4388 4534 0.823769 TCGTGTGAGCTGTCTCCACT 60.824 55.000 0.00 0.00 37.87 4.00
4389 4535 0.881796 CGTGTGAGCTGTCTCCACTA 59.118 55.000 0.00 0.00 37.87 2.74
4411 4557 9.776158 CACTATAGTCTAAACATATCGATGGAC 57.224 37.037 8.54 0.00 37.39 4.02
4521 4671 1.004080 CCTCCGGATGCTGCATAGG 60.004 63.158 23.03 23.03 0.00 2.57
4522 4672 1.670406 CTCCGGATGCTGCATAGGC 60.670 63.158 23.78 10.54 41.68 3.93
4524 4674 3.046087 CGGATGCTGCATAGGCCG 61.046 66.667 21.66 21.66 40.13 6.13
4533 4683 2.901840 CATAGGCCGCCGCACAAT 60.902 61.111 3.05 0.00 36.38 2.71
4544 4703 1.584483 CGCACAATCGCATTGCTCC 60.584 57.895 7.12 0.00 43.98 4.70
4581 4761 3.138798 GCGGCGAGGGAGACTGTA 61.139 66.667 12.98 0.00 0.00 2.74
4606 4786 0.665670 CACGAGTGCACAGTGAGAGG 60.666 60.000 29.76 11.04 38.06 3.69
4607 4787 1.109920 ACGAGTGCACAGTGAGAGGT 61.110 55.000 21.04 1.64 0.00 3.85
4608 4788 0.387878 CGAGTGCACAGTGAGAGGTC 60.388 60.000 21.04 3.13 0.00 3.85
4609 4789 0.965439 GAGTGCACAGTGAGAGGTCT 59.035 55.000 21.04 0.00 0.00 3.85
4610 4790 0.678395 AGTGCACAGTGAGAGGTCTG 59.322 55.000 21.04 0.00 37.65 3.51
4611 4791 0.320247 GTGCACAGTGAGAGGTCTGG 60.320 60.000 13.17 0.00 36.17 3.86
4754 4986 4.028490 CCCCGCTACCACTGCCAA 62.028 66.667 0.00 0.00 0.00 4.52
4770 5020 4.923281 ACTGCCAAATCGCATTTTAGAAAC 59.077 37.500 0.00 0.00 38.30 2.78
4772 5022 4.683781 TGCCAAATCGCATTTTAGAAACAC 59.316 37.500 0.00 0.00 32.62 3.32
4805 5055 3.296854 TCTATCGGTACTCAAGCCACAT 58.703 45.455 0.00 0.00 0.00 3.21
4807 5057 4.891168 TCTATCGGTACTCAAGCCACATAA 59.109 41.667 0.00 0.00 0.00 1.90
4809 5059 3.857052 TCGGTACTCAAGCCACATAAAG 58.143 45.455 0.00 0.00 0.00 1.85
4810 5060 2.351726 CGGTACTCAAGCCACATAAAGC 59.648 50.000 0.00 0.00 0.00 3.51
4811 5061 3.343617 GGTACTCAAGCCACATAAAGCA 58.656 45.455 0.00 0.00 0.00 3.91
4882 5134 6.802608 AGAAAATTACCATCGTCGTCTCATA 58.197 36.000 0.00 0.00 0.00 2.15
4889 5141 4.174009 CCATCGTCGTCTCATACACTTTT 58.826 43.478 0.00 0.00 0.00 2.27
4925 5183 6.161381 AGGACAGCTTTATTGATTTGCAAAG 58.839 36.000 18.19 1.99 40.48 2.77
4937 5195 4.808364 TGATTTGCAAAGCAGTTTTACACC 59.192 37.500 25.24 0.00 40.61 4.16
4940 5198 2.164624 TGCAAAGCAGTTTTACACCGTT 59.835 40.909 0.00 0.00 33.32 4.44
4943 5201 3.685836 AAGCAGTTTTACACCGTTCAC 57.314 42.857 0.00 0.00 0.00 3.18
4949 5207 4.093703 CAGTTTTACACCGTTCACAAGACA 59.906 41.667 0.00 0.00 0.00 3.41
4961 5219 5.337554 GTTCACAAGACAGGGTAACAAAAC 58.662 41.667 0.00 0.00 39.74 2.43
4964 5222 4.881850 CACAAGACAGGGTAACAAAACTCT 59.118 41.667 0.00 0.00 39.74 3.24
4974 5232 5.221783 GGGTAACAAAACTCTAGGAGGTTCA 60.222 44.000 0.00 0.00 38.80 3.18
4981 5239 1.957877 CTCTAGGAGGTTCATCGACCC 59.042 57.143 0.00 0.00 40.73 4.46
4983 5241 2.091278 TCTAGGAGGTTCATCGACCCAT 60.091 50.000 0.00 0.00 40.73 4.00
4998 5256 6.288941 TCGACCCATTTACAATCAGTTCTA 57.711 37.500 0.00 0.00 0.00 2.10
5005 5263 8.265055 CCCATTTACAATCAGTTCTAGAGGTAA 58.735 37.037 0.00 0.00 0.00 2.85
5006 5264 9.099454 CCATTTACAATCAGTTCTAGAGGTAAC 57.901 37.037 0.00 0.00 0.00 2.50
5019 5277 2.810486 GGTAACTAGCTATGCCGCG 58.190 57.895 0.00 0.00 34.40 6.46
5020 5278 1.282930 GGTAACTAGCTATGCCGCGC 61.283 60.000 0.00 0.00 34.40 6.86
5021 5279 1.371267 TAACTAGCTATGCCGCGCG 60.371 57.895 25.67 25.67 34.40 6.86
5049 5307 3.680786 CGCCGCCCCTCATCGATA 61.681 66.667 0.00 0.00 0.00 2.92
5050 5308 2.048127 GCCGCCCCTCATCGATAC 60.048 66.667 0.00 0.00 0.00 2.24
5051 5309 2.258591 CCGCCCCTCATCGATACG 59.741 66.667 0.00 0.00 0.00 3.06
5052 5310 2.561956 CCGCCCCTCATCGATACGT 61.562 63.158 0.00 0.00 0.00 3.57
5053 5311 1.362717 CGCCCCTCATCGATACGTT 59.637 57.895 0.00 0.00 0.00 3.99
5054 5312 0.594602 CGCCCCTCATCGATACGTTA 59.405 55.000 0.00 0.00 0.00 3.18
5055 5313 1.201647 CGCCCCTCATCGATACGTTAT 59.798 52.381 0.00 0.00 0.00 1.89
5056 5314 2.421073 CGCCCCTCATCGATACGTTATA 59.579 50.000 0.00 0.00 0.00 0.98
5057 5315 3.066342 CGCCCCTCATCGATACGTTATAT 59.934 47.826 0.00 0.00 0.00 0.86
5058 5316 4.360563 GCCCCTCATCGATACGTTATATG 58.639 47.826 0.00 0.00 0.00 1.78
5059 5317 4.142227 GCCCCTCATCGATACGTTATATGT 60.142 45.833 0.00 0.00 0.00 2.29
5060 5318 5.066893 GCCCCTCATCGATACGTTATATGTA 59.933 44.000 0.00 0.00 0.00 2.29
5061 5319 6.238953 GCCCCTCATCGATACGTTATATGTAT 60.239 42.308 0.00 0.00 33.27 2.29
5062 5320 7.683704 GCCCCTCATCGATACGTTATATGTATT 60.684 40.741 0.00 0.00 30.89 1.89
5063 5321 8.843262 CCCCTCATCGATACGTTATATGTATTA 58.157 37.037 0.00 0.00 30.89 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.182001 CCATCAGGAAAACAGAAGGTTAGTG 59.818 44.000 0.00 0.00 36.22 2.74
8 9 4.453480 TCCATCAGGAAAACAGAAGGTT 57.547 40.909 0.00 0.00 42.23 3.50
36 39 1.818674 CACTATTCCACAGCCCCAAAC 59.181 52.381 0.00 0.00 0.00 2.93
53 57 8.812972 TGGATCACAAACTAGAACTAATACACT 58.187 33.333 0.00 0.00 0.00 3.55
55 59 8.590204 TGTGGATCACAAACTAGAACTAATACA 58.410 33.333 0.00 0.00 41.69 2.29
56 60 8.997621 TGTGGATCACAAACTAGAACTAATAC 57.002 34.615 0.00 0.00 41.69 1.89
73 77 5.703978 ACAAAATTCGTGAATGTGGATCA 57.296 34.783 0.00 0.00 0.00 2.92
79 83 4.079253 AGGGCTACAAAATTCGTGAATGT 58.921 39.130 0.00 0.00 0.00 2.71
89 93 2.897326 GGGAACAACAGGGCTACAAAAT 59.103 45.455 0.00 0.00 0.00 1.82
95 99 1.122632 TCACGGGAACAACAGGGCTA 61.123 55.000 0.00 0.00 0.00 3.93
115 119 2.090524 GCACCAGCAAATCAAGCGC 61.091 57.895 0.00 0.00 41.58 5.92
142 146 1.314730 GGACGACAAGGAAAAGGCAA 58.685 50.000 0.00 0.00 0.00 4.52
175 179 2.002586 CCAACTTGCTCGTATCACAGG 58.997 52.381 0.00 0.00 0.00 4.00
190 194 4.718961 ACTATTCAAGTCTGCAACCAACT 58.281 39.130 0.00 0.00 30.33 3.16
220 224 2.667199 AAACCGCCGACCCGAAAG 60.667 61.111 0.00 0.00 0.00 2.62
260 264 7.310237 GGCAATATTCCTCCATAAATGCAGATT 60.310 37.037 0.00 0.00 31.69 2.40
541 559 2.146724 TGTGGAGGACAGGGGTGTG 61.147 63.158 0.00 0.00 0.00 3.82
696 715 4.813296 ACTTTCTGAACCAAATCGTCAC 57.187 40.909 0.00 0.00 0.00 3.67
793 813 3.915437 AGAAACGCTACACAAAATGGG 57.085 42.857 0.00 0.00 0.00 4.00
823 843 9.051679 AGGCATAAAGGAATTAAAAACAAACAC 57.948 29.630 0.00 0.00 0.00 3.32
861 881 4.183865 TGTCGATGCCAGAAGAAATACAG 58.816 43.478 0.00 0.00 0.00 2.74
907 932 0.459489 TGCAAAACAAGCCTGTCCAC 59.541 50.000 0.00 0.00 33.45 4.02
1014 1039 6.127225 CCTTCTCATCTCTCACTTCACCATTA 60.127 42.308 0.00 0.00 0.00 1.90
1020 1045 4.022603 CTCCCTTCTCATCTCTCACTTCA 58.977 47.826 0.00 0.00 0.00 3.02
1080 1105 1.064906 CCATGAGCCTCACCTTGTGAT 60.065 52.381 0.00 0.00 41.94 3.06
1103 1128 5.062809 CCTCTTTTCGCTCTATTGTCTTCAC 59.937 44.000 0.00 0.00 0.00 3.18
1326 1351 1.669604 GAGGGCGAGAAGGGATTTTC 58.330 55.000 0.00 0.00 0.00 2.29
1506 1531 7.972832 AATTGCTTTGTCATCATCAACAATT 57.027 28.000 0.00 0.00 35.46 2.32
1528 1553 7.066284 CAGTTCCTCATTTCTCCGATGTAAAAT 59.934 37.037 0.00 0.00 0.00 1.82
1554 1579 4.516698 TCCATCTTCTCAAGTTTTGACTGC 59.483 41.667 0.00 0.00 35.46 4.40
1668 1693 1.227002 CCTAGAAAGACGCCGAGCC 60.227 63.158 0.00 0.00 0.00 4.70
1752 1777 2.540101 CACAACGAGAACAAGACCAGAC 59.460 50.000 0.00 0.00 0.00 3.51
1826 1851 6.685828 CACATCTCATACGCTGAATTCAAAAG 59.314 38.462 9.88 6.29 32.14 2.27
1830 1855 4.122046 CCACATCTCATACGCTGAATTCA 58.878 43.478 8.12 8.12 32.14 2.57
1881 1906 9.865321 GTATGTTAACCTACATCAACAGTAGAA 57.135 33.333 14.10 0.00 41.07 2.10
1964 1989 1.234821 TGGTTGGAGTTGATTGACGC 58.765 50.000 0.00 0.00 0.00 5.19
2036 2061 1.611419 CACTGGCATGGATCTGGGT 59.389 57.895 0.00 0.00 0.00 4.51
2129 2154 3.648339 AATGCAGCCAAAAGTGTACTG 57.352 42.857 0.00 0.00 32.67 2.74
2144 2169 5.510349 CCAAGATTCGATCCTCTCTAATGCA 60.510 44.000 0.00 0.00 0.00 3.96
2186 2211 1.447217 CTGCCACCACACTGTCTCA 59.553 57.895 0.00 0.00 0.00 3.27
2227 2252 7.573710 ACCAGTTTGGAGCAAGTGATTATATA 58.426 34.615 1.40 0.00 40.96 0.86
2228 2253 6.426587 ACCAGTTTGGAGCAAGTGATTATAT 58.573 36.000 1.40 0.00 40.96 0.86
2229 2254 5.815581 ACCAGTTTGGAGCAAGTGATTATA 58.184 37.500 1.40 0.00 40.96 0.98
2230 2255 4.666512 ACCAGTTTGGAGCAAGTGATTAT 58.333 39.130 1.40 0.00 40.96 1.28
2236 2261 2.301346 CAAGACCAGTTTGGAGCAAGT 58.699 47.619 1.40 0.00 40.96 3.16
2282 2307 3.017048 TCCGAACGGAGGGAGTATTTA 57.983 47.619 12.04 0.00 39.76 1.40
2286 2311 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
2287 2312 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
2288 2313 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2289 2314 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2290 2315 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2291 2316 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2292 2317 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
2293 2318 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
2294 2319 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
2295 2320 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
2296 2321 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
2297 2322 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
2298 2323 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
2299 2324 4.868171 TCATTTCCGAGACAAGTAATTCCG 59.132 41.667 0.00 0.00 0.00 4.30
2300 2325 6.737254 TTCATTTCCGAGACAAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
2301 2326 7.752695 ACATTCATTTCCGAGACAAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
2302 2327 7.687941 ACATTCATTTCCGAGACAAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
2303 2328 8.964476 ATACATTCATTTCCGAGACAAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
2304 2329 8.258007 AGATACATTCATTTCCGAGACAAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
2305 2330 7.782049 AGATACATTCATTTCCGAGACAAGTA 58.218 34.615 0.00 0.00 0.00 2.24
2306 2331 6.644347 AGATACATTCATTTCCGAGACAAGT 58.356 36.000 0.00 0.00 0.00 3.16
2307 2332 8.138074 TCTAGATACATTCATTTCCGAGACAAG 58.862 37.037 0.00 0.00 0.00 3.16
2308 2333 8.007405 TCTAGATACATTCATTTCCGAGACAA 57.993 34.615 0.00 0.00 0.00 3.18
2309 2334 7.582667 TCTAGATACATTCATTTCCGAGACA 57.417 36.000 0.00 0.00 0.00 3.41
2310 2335 8.138712 AGTTCTAGATACATTCATTTCCGAGAC 58.861 37.037 0.00 0.00 0.00 3.36
2311 2336 8.239038 AGTTCTAGATACATTCATTTCCGAGA 57.761 34.615 0.00 0.00 0.00 4.04
2312 2337 9.967346 TTAGTTCTAGATACATTCATTTCCGAG 57.033 33.333 0.00 0.00 0.00 4.63
2339 2364 9.664332 GCAGAAATGGATGTATCTAGACATATT 57.336 33.333 0.00 0.00 40.18 1.28
2340 2365 7.978414 CGCAGAAATGGATGTATCTAGACATAT 59.022 37.037 0.00 0.00 40.18 1.78
2341 2366 7.176690 TCGCAGAAATGGATGTATCTAGACATA 59.823 37.037 0.00 0.00 40.18 2.29
2342 2367 6.015095 TCGCAGAAATGGATGTATCTAGACAT 60.015 38.462 0.00 0.00 42.82 3.06
2343 2368 5.301805 TCGCAGAAATGGATGTATCTAGACA 59.698 40.000 0.00 0.00 0.00 3.41
2344 2369 5.631512 GTCGCAGAAATGGATGTATCTAGAC 59.368 44.000 0.00 0.00 39.69 2.59
2345 2370 5.301805 TGTCGCAGAAATGGATGTATCTAGA 59.698 40.000 0.00 0.00 39.69 2.43
2346 2371 5.532557 TGTCGCAGAAATGGATGTATCTAG 58.467 41.667 0.00 0.00 39.69 2.43
2347 2372 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
2348 2373 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
2349 2374 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
2350 2375 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
2351 2376 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
2352 2377 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
2353 2378 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
2354 2379 5.066505 GGAATTACTTGTCGCAGAAATGGAT 59.933 40.000 0.00 0.00 39.69 3.41
2355 2380 4.394920 GGAATTACTTGTCGCAGAAATGGA 59.605 41.667 0.00 0.00 39.69 3.41
2356 2381 4.662145 GGAATTACTTGTCGCAGAAATGG 58.338 43.478 0.00 0.00 39.69 3.16
2357 2382 4.092821 TCGGAATTACTTGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
2358 2383 4.250464 TCGGAATTACTTGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
2359 2384 3.655486 TCGGAATTACTTGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
2360 2385 3.306917 TCGGAATTACTTGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
2361 2386 2.991190 GTTCGGAATTACTTGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
2362 2387 2.222508 CGTTCGGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
2363 2388 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
2364 2389 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
2365 2390 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2366 2391 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2367 2392 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2368 2393 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2369 2394 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2370 2395 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2371 2396 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2372 2397 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2373 2398 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
2374 2399 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
2375 2400 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
2376 2401 0.393537 GAGTACTCCCTCCGTTCGGA 60.394 60.000 12.13 13.34 0.00 4.55
2377 2402 0.394080 AGAGTACTCCCTCCGTTCGG 60.394 60.000 19.38 4.74 31.53 4.30
2378 2403 0.733729 CAGAGTACTCCCTCCGTTCG 59.266 60.000 19.38 0.00 31.53 3.95
2379 2404 0.456628 GCAGAGTACTCCCTCCGTTC 59.543 60.000 19.38 0.00 31.53 3.95
2380 2405 0.251653 TGCAGAGTACTCCCTCCGTT 60.252 55.000 19.38 0.00 31.53 4.44
2381 2406 0.681564 CTGCAGAGTACTCCCTCCGT 60.682 60.000 19.38 0.00 31.53 4.69
2382 2407 0.681564 ACTGCAGAGTACTCCCTCCG 60.682 60.000 23.35 7.69 31.53 4.63
2383 2408 0.820871 CACTGCAGAGTACTCCCTCC 59.179 60.000 23.35 6.06 31.53 4.30
2384 2409 1.840737 TCACTGCAGAGTACTCCCTC 58.159 55.000 23.35 9.16 0.00 4.30
2385 2410 2.541233 ATCACTGCAGAGTACTCCCT 57.459 50.000 23.35 0.00 0.00 4.20
2386 2411 2.763448 AGAATCACTGCAGAGTACTCCC 59.237 50.000 23.35 11.28 0.00 4.30
2387 2412 3.699038 AGAGAATCACTGCAGAGTACTCC 59.301 47.826 23.35 5.74 37.82 3.85
2388 2413 4.397730 TGAGAGAATCACTGCAGAGTACTC 59.602 45.833 23.35 15.41 37.82 2.59
2389 2414 4.339748 TGAGAGAATCACTGCAGAGTACT 58.660 43.478 23.35 13.10 37.82 2.73
2390 2415 4.710423 TGAGAGAATCACTGCAGAGTAC 57.290 45.455 23.35 8.59 37.82 2.73
2538 2563 1.354705 GGAAGGGCCTAACACTTTCCT 59.645 52.381 6.41 0.00 0.00 3.36
2759 2793 6.346477 TGCTCCATCACCTGATAATAGTAC 57.654 41.667 0.00 0.00 32.63 2.73
2855 2889 4.283467 TCAACGATTGGGTCAGATATAGGG 59.717 45.833 0.00 0.00 0.00 3.53
2858 2892 4.039973 GGGTCAACGATTGGGTCAGATATA 59.960 45.833 0.00 0.00 0.00 0.86
2882 2916 0.466124 CTGGGATCGGGAGGACTTTC 59.534 60.000 0.00 0.00 0.00 2.62
3020 3054 4.849813 TCTCAACCACAATCATCATCCT 57.150 40.909 0.00 0.00 0.00 3.24
3190 3224 7.585440 TCTTTCATCATTCCCATTTCCTATGA 58.415 34.615 0.00 0.00 0.00 2.15
3263 3297 0.823769 TCGGGGTCATCAGGAGATCG 60.824 60.000 0.00 0.00 30.20 3.69
3329 3363 5.237127 CGATAAATTTGTCTGGAGCTATGCA 59.763 40.000 12.41 0.00 0.00 3.96
3346 3380 7.972832 TCCAACAGAAAACAGTACGATAAAT 57.027 32.000 0.00 0.00 0.00 1.40
3351 3385 5.361427 TCAATCCAACAGAAAACAGTACGA 58.639 37.500 0.00 0.00 0.00 3.43
3498 3532 4.161377 ACCTCAGAATTCAGCTCCTCTAAC 59.839 45.833 8.44 0.00 0.00 2.34
3524 3558 5.674933 AACATTTTCGTGAGAGAGAAACC 57.325 39.130 0.00 0.00 43.69 3.27
3525 3559 6.414987 CCAAAACATTTTCGTGAGAGAGAAAC 59.585 38.462 0.00 0.00 43.69 2.78
3575 3614 2.954318 GGCCACTTTGATATGTCAGCAT 59.046 45.455 0.00 0.00 39.03 3.79
3576 3615 2.368439 GGCCACTTTGATATGTCAGCA 58.632 47.619 0.00 0.00 35.39 4.41
3577 3616 1.331756 CGGCCACTTTGATATGTCAGC 59.668 52.381 2.24 0.00 35.39 4.26
3578 3617 2.632377 ACGGCCACTTTGATATGTCAG 58.368 47.619 2.24 0.00 35.39 3.51
3579 3618 2.779755 ACGGCCACTTTGATATGTCA 57.220 45.000 2.24 0.00 0.00 3.58
3580 3619 3.058914 GCATACGGCCACTTTGATATGTC 60.059 47.826 2.24 0.00 36.11 3.06
3581 3620 2.878406 GCATACGGCCACTTTGATATGT 59.122 45.455 2.24 0.00 36.11 2.29
3582 3621 3.542712 GCATACGGCCACTTTGATATG 57.457 47.619 2.24 0.09 36.11 1.78
3594 3633 1.557443 GCATGTACGAGGCATACGGC 61.557 60.000 0.00 0.00 43.74 5.68
3595 3634 0.249280 TGCATGTACGAGGCATACGG 60.249 55.000 2.24 0.00 36.14 4.02
3596 3635 1.131771 CTGCATGTACGAGGCATACG 58.868 55.000 6.40 0.00 41.43 3.06
3597 3636 2.398498 CTCTGCATGTACGAGGCATAC 58.602 52.381 6.40 0.00 41.43 2.39
3598 3637 1.341209 CCTCTGCATGTACGAGGCATA 59.659 52.381 13.41 0.09 41.43 3.14
3599 3638 0.105593 CCTCTGCATGTACGAGGCAT 59.894 55.000 13.41 0.00 41.43 4.40
3600 3639 1.517361 CCTCTGCATGTACGAGGCA 59.483 57.895 13.41 5.89 39.61 4.75
3601 3640 4.427394 CCTCTGCATGTACGAGGC 57.573 61.111 13.41 0.00 38.05 4.70
3602 3641 1.227380 GGCCTCTGCATGTACGAGG 60.227 63.158 18.42 18.42 45.59 4.63
3603 3642 1.589993 CGGCCTCTGCATGTACGAG 60.590 63.158 0.00 0.00 40.13 4.18
3604 3643 2.494445 CGGCCTCTGCATGTACGA 59.506 61.111 0.00 0.00 40.13 3.43
3605 3644 2.586079 CCGGCCTCTGCATGTACG 60.586 66.667 0.00 0.00 40.13 3.67
3606 3645 2.203070 CCCGGCCTCTGCATGTAC 60.203 66.667 0.00 0.00 40.13 2.90
3607 3646 3.479203 CCCCGGCCTCTGCATGTA 61.479 66.667 0.00 0.00 40.13 2.29
3609 3648 4.559063 CTCCCCGGCCTCTGCATG 62.559 72.222 0.00 0.00 40.13 4.06
3645 3684 8.231837 GCAAATGTTTGATATGTCAGCATTTTT 58.768 29.630 22.22 10.51 42.40 1.94
3646 3685 7.412129 CGCAAATGTTTGATATGTCAGCATTTT 60.412 33.333 22.22 12.58 42.40 1.82
3647 3686 6.035220 CGCAAATGTTTGATATGTCAGCATTT 59.965 34.615 20.56 20.56 43.87 2.32
3648 3687 5.517411 CGCAAATGTTTGATATGTCAGCATT 59.483 36.000 9.53 14.18 40.35 3.56
3687 3726 7.920160 TCATAATATGAAGTGCAGTGTCAAA 57.080 32.000 0.00 0.00 36.11 2.69
3690 3729 6.017687 TGCATCATAATATGAAGTGCAGTGTC 60.018 38.462 21.07 6.43 45.28 3.67
3696 3735 5.411977 AGCTCTGCATCATAATATGAAGTGC 59.588 40.000 17.39 17.39 45.97 4.40
3920 3959 1.609794 GAACAGGGACTCGAGGGGT 60.610 63.158 18.41 4.20 34.60 4.95
3928 3967 0.318762 GCTCTTGTCGAACAGGGACT 59.681 55.000 0.00 0.00 43.88 3.85
4008 4047 0.181587 TCAAACCTGGCGTTCTCCAA 59.818 50.000 0.00 0.00 35.36 3.53
4064 4103 0.531090 TTCACAAGTTCACCGGACCG 60.531 55.000 9.46 6.99 0.00 4.79
4066 4105 2.234300 TCTTCACAAGTTCACCGGAC 57.766 50.000 9.46 0.00 0.00 4.79
4282 4428 6.183360 GGACATAGACCAAATCTTTTTAGCCC 60.183 42.308 0.00 0.00 39.04 5.19
4341 4487 1.003759 CGTCAGATTCGTCGGTAGGAG 60.004 57.143 0.00 0.00 0.00 3.69
4388 4534 8.448615 CACGTCCATCGATATGTTTAGACTATA 58.551 37.037 0.00 0.00 42.86 1.31
4389 4535 7.174426 TCACGTCCATCGATATGTTTAGACTAT 59.826 37.037 0.00 0.00 42.86 2.12
4411 4557 0.314578 GTCGCATTCGCATCTTCACG 60.315 55.000 0.00 0.00 38.40 4.35
4522 4672 4.178214 AATGCGATTGTGCGGCGG 62.178 61.111 9.78 0.00 37.81 6.13
4524 4674 3.249605 GCAATGCGATTGTGCGGC 61.250 61.111 9.58 0.00 42.20 6.53
4525 4675 1.584483 GAGCAATGCGATTGTGCGG 60.584 57.895 0.00 0.00 43.16 5.69
4526 4676 1.584483 GGAGCAATGCGATTGTGCG 60.584 57.895 0.00 0.00 43.16 5.34
4527 4677 0.524816 CAGGAGCAATGCGATTGTGC 60.525 55.000 0.00 0.00 42.20 4.57
4528 4678 0.524816 GCAGGAGCAATGCGATTGTG 60.525 55.000 0.00 0.00 42.20 3.33
4529 4679 1.805254 GCAGGAGCAATGCGATTGT 59.195 52.632 0.00 0.00 42.20 2.71
4544 4703 0.961857 TGCACCCATTACTGCTGCAG 60.962 55.000 27.02 27.02 32.55 4.41
4550 4709 2.764314 GCCGCTGCACCCATTACTG 61.764 63.158 0.00 0.00 37.47 2.74
4552 4711 3.876198 CGCCGCTGCACCCATTAC 61.876 66.667 0.00 0.00 37.32 1.89
4595 4775 1.271934 CAGACCAGACCTCTCACTGTG 59.728 57.143 0.17 0.17 32.93 3.66
4600 4780 1.133167 TCAACCAGACCAGACCTCTCA 60.133 52.381 0.00 0.00 0.00 3.27
4601 4781 1.633774 TCAACCAGACCAGACCTCTC 58.366 55.000 0.00 0.00 0.00 3.20
4606 4786 2.154462 CAACCATCAACCAGACCAGAC 58.846 52.381 0.00 0.00 0.00 3.51
4607 4787 1.073763 CCAACCATCAACCAGACCAGA 59.926 52.381 0.00 0.00 0.00 3.86
4608 4788 1.538047 CCAACCATCAACCAGACCAG 58.462 55.000 0.00 0.00 0.00 4.00
4609 4789 0.539438 GCCAACCATCAACCAGACCA 60.539 55.000 0.00 0.00 0.00 4.02
4610 4790 1.250840 GGCCAACCATCAACCAGACC 61.251 60.000 0.00 0.00 35.26 3.85
4611 4791 1.586154 CGGCCAACCATCAACCAGAC 61.586 60.000 2.24 0.00 34.57 3.51
4644 4874 2.746277 GACGCGGCCATCTTTGGT 60.746 61.111 12.47 0.00 45.57 3.67
4754 4986 3.672241 GCCGGTGTTTCTAAAATGCGATT 60.672 43.478 1.90 0.00 0.00 3.34
4770 5020 1.867233 CGATAGATTCCAAAGCCGGTG 59.133 52.381 1.90 0.00 39.76 4.94
4772 5022 1.202651 ACCGATAGATTCCAAAGCCGG 60.203 52.381 0.00 0.00 41.24 6.13
4807 5057 9.710900 CCTCTAAAAATCCTTTAAACATTGCTT 57.289 29.630 0.00 0.00 0.00 3.91
4809 5059 9.140286 GTCCTCTAAAAATCCTTTAAACATTGC 57.860 33.333 0.00 0.00 0.00 3.56
4851 5102 8.314143 ACGACGATGGTAATTTTCTTTAGAAA 57.686 30.769 0.00 0.89 41.77 2.52
4852 5103 7.816031 AGACGACGATGGTAATTTTCTTTAGAA 59.184 33.333 0.00 0.00 0.00 2.10
4853 5104 7.318141 AGACGACGATGGTAATTTTCTTTAGA 58.682 34.615 0.00 0.00 0.00 2.10
4854 5105 7.274904 TGAGACGACGATGGTAATTTTCTTTAG 59.725 37.037 0.00 0.00 0.00 1.85
4855 5106 7.092079 TGAGACGACGATGGTAATTTTCTTTA 58.908 34.615 0.00 0.00 0.00 1.85
4856 5107 5.929992 TGAGACGACGATGGTAATTTTCTTT 59.070 36.000 0.00 0.00 0.00 2.52
4864 5115 3.943381 AGTGTATGAGACGACGATGGTAA 59.057 43.478 0.00 0.00 0.00 2.85
4867 5118 3.422417 AAGTGTATGAGACGACGATGG 57.578 47.619 0.00 0.00 0.00 3.51
4895 5147 7.386025 GCAAATCAATAAAGCTGTCCTTTTTCT 59.614 33.333 0.00 0.00 40.85 2.52
4901 5153 5.726980 TTGCAAATCAATAAAGCTGTCCT 57.273 34.783 0.00 0.00 0.00 3.85
4902 5154 5.163923 GCTTTGCAAATCAATAAAGCTGTCC 60.164 40.000 13.23 0.00 46.90 4.02
4925 5183 3.064271 TCTTGTGAACGGTGTAAAACTGC 59.936 43.478 0.00 0.00 38.92 4.40
4928 5186 4.495184 CCTGTCTTGTGAACGGTGTAAAAC 60.495 45.833 0.00 0.00 0.00 2.43
4930 5188 3.199677 CCTGTCTTGTGAACGGTGTAAA 58.800 45.455 0.00 0.00 0.00 2.01
4937 5195 2.828877 TGTTACCCTGTCTTGTGAACG 58.171 47.619 0.00 0.00 0.00 3.95
4940 5198 4.850680 AGTTTTGTTACCCTGTCTTGTGA 58.149 39.130 0.00 0.00 0.00 3.58
4943 5201 5.701290 CCTAGAGTTTTGTTACCCTGTCTTG 59.299 44.000 0.00 0.00 0.00 3.02
4949 5207 4.500452 ACCTCCTAGAGTTTTGTTACCCT 58.500 43.478 0.00 0.00 0.00 4.34
4961 5219 1.957877 GGGTCGATGAACCTCCTAGAG 59.042 57.143 0.00 0.00 36.31 2.43
4964 5222 2.471815 ATGGGTCGATGAACCTCCTA 57.528 50.000 2.11 0.00 40.68 2.94
4974 5232 5.745227 AGAACTGATTGTAAATGGGTCGAT 58.255 37.500 0.00 0.00 0.00 3.59
4981 5239 9.877178 AGTTACCTCTAGAACTGATTGTAAATG 57.123 33.333 0.00 0.00 34.61 2.32
4998 5256 1.614413 GCGGCATAGCTAGTTACCTCT 59.386 52.381 0.00 0.00 0.00 3.69
5032 5290 3.680786 TATCGATGAGGGGCGGCG 61.681 66.667 8.54 0.51 0.00 6.46
5033 5291 2.048127 GTATCGATGAGGGGCGGC 60.048 66.667 8.54 0.00 0.00 6.53
5034 5292 2.083835 AACGTATCGATGAGGGGCGG 62.084 60.000 8.54 0.00 0.00 6.13
5035 5293 0.594602 TAACGTATCGATGAGGGGCG 59.405 55.000 8.54 5.60 0.00 6.13
5036 5294 4.142227 ACATATAACGTATCGATGAGGGGC 60.142 45.833 8.54 0.00 0.00 5.80
5037 5295 5.578005 ACATATAACGTATCGATGAGGGG 57.422 43.478 8.54 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.