Multiple sequence alignment - TraesCS3D01G173500

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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 TraesCS3D01G173500 chr3D 100.000 5634 0 0 1 5634 154618797 154613164 0.000000e+00 10405.0
1 TraesCS3D01G173500 chr3D 85.542 83 11 1 5377 5458 170546942 170547024 1.010000e-12 86.1
2 TraesCS3D01G173500 chr3D 94.545 55 3 0 5384 5438 365921891 365921945 1.010000e-12 86.1
3 TraesCS3D01G173500 chr3A 96.420 3017 62 17 2450 5439 173946258 173943261 0.000000e+00 4931.0
4 TraesCS3D01G173500 chr3A 97.476 1902 33 7 387 2282 173948133 173946241 0.000000e+00 3232.0
5 TraesCS3D01G173500 chr3A 93.282 387 21 5 1 385 173948737 173948354 2.950000e-157 566.0
6 TraesCS3D01G173500 chr3A 95.500 200 8 1 5435 5634 173943234 173943036 9.110000e-83 318.0
7 TraesCS3D01G173500 chr3A 96.196 184 4 3 2287 2468 667700966 667701148 1.190000e-76 298.0
8 TraesCS3D01G173500 chr3A 92.982 57 2 2 5384 5439 549622794 549622849 1.300000e-11 82.4
9 TraesCS3D01G173500 chr3A 84.337 83 12 1 5377 5458 208074006 208074088 4.680000e-11 80.5
10 TraesCS3D01G173500 chr3A 84.211 76 11 1 5384 5458 83981311 83981236 7.830000e-09 73.1
11 TraesCS3D01G173500 chr3B 96.748 2952 79 14 2450 5389 226480571 226483517 0.000000e+00 4903.0
12 TraesCS3D01G173500 chr3B 95.128 1909 63 9 386 2282 226478698 226480588 0.000000e+00 2983.0
13 TraesCS3D01G173500 chrUn 100.000 401 0 0 4243 4643 478601153 478601553 0.000000e+00 741.0
14 TraesCS3D01G173500 chr4D 99.415 171 0 1 2281 2450 355283730 355283560 5.480000e-80 309.0
15 TraesCS3D01G173500 chr4D 94.231 52 3 0 4898 4949 85258483 85258432 4.680000e-11 80.5
16 TraesCS3D01G173500 chr4D 91.071 56 4 1 4898 4953 85165880 85165934 2.180000e-09 75.0
17 TraesCS3D01G173500 chr4A 98.837 172 1 1 2280 2450 658953760 658953931 7.090000e-79 305.0
18 TraesCS3D01G173500 chr4A 97.222 180 4 1 2273 2451 6935465 6935644 2.550000e-78 303.0
19 TraesCS3D01G173500 chr4A 94.118 51 3 0 4899 4949 618286323 618286373 1.680000e-10 78.7
20 TraesCS3D01G173500 chr4A 93.878 49 2 1 4899 4947 548788847 548788800 7.830000e-09 73.1
21 TraesCS3D01G173500 chr6A 98.276 174 2 1 2277 2449 135677233 135677060 2.550000e-78 303.0
22 TraesCS3D01G173500 chr6A 92.727 55 4 0 5384 5438 430338756 430338810 4.680000e-11 80.5
23 TraesCS3D01G173500 chr2A 98.276 174 2 1 2278 2450 691479345 691479518 2.550000e-78 303.0
24 TraesCS3D01G173500 chr1B 98.276 174 2 1 2279 2451 158536134 158536307 2.550000e-78 303.0
25 TraesCS3D01G173500 chr6B 97.191 178 2 3 2284 2460 432492963 432492788 1.190000e-76 298.0
26 TraesCS3D01G173500 chr5B 96.175 183 3 2 2272 2450 633962724 633962542 4.270000e-76 296.0
27 TraesCS3D01G173500 chr7B 85.526 76 10 1 5384 5458 505937314 505937389 1.680000e-10 78.7
28 TraesCS3D01G173500 chr7B 79.167 96 12 6 4855 4944 227279942 227279849 6.100000e-05 60.2
29 TraesCS3D01G173500 chr1A 92.727 55 3 1 4899 4953 61012562 61012509 1.680000e-10 78.7
30 TraesCS3D01G173500 chr6D 95.652 46 2 0 4899 4944 229431519 229431474 2.180000e-09 75.0


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 TraesCS3D01G173500 chr3D 154613164 154618797 5633 True 10405.00 10405 100.0000 1 5634 1 chr3D.!!$R1 5633
1 TraesCS3D01G173500 chr3A 173943036 173948737 5701 True 2261.75 4931 95.6695 1 5634 4 chr3A.!!$R2 5633
2 TraesCS3D01G173500 chr3B 226478698 226483517 4819 False 3943.00 4903 95.9380 386 5389 2 chr3B.!!$F1 5003

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
830 1058 0.455295 CACTCTGAGGTTCTCGACGC 60.455 60.0 9.85 0.00 32.35 5.19 F
2384 2621 0.037877 AAGTGCAATGCAGAGAGGCT 59.962 50.0 8.73 0.00 40.08 4.58 F
2400 2637 0.108281 GGCTGGTTCGAACTAGGACC 60.108 60.0 33.89 25.78 37.90 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2409 2646 0.036875 GGTGAAGTCCTCCCCACTTG 59.963 60.000 0.0 0.0 34.10 3.16 R
4241 4482 3.846588 TCTTTATCTCCTCCTGCCAACTT 59.153 43.478 0.0 0.0 0.00 2.66 R
4643 4884 5.921408 CCCTACTAGAGCTAATAAAACAGCG 59.079 44.000 0.0 0.0 42.74 5.18 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
43 44 2.659016 CTGTGCGAGAAGGAGGCA 59.341 61.111 0.00 0.00 0.00 4.75
47 48 0.809241 GTGCGAGAAGGAGGCATCAG 60.809 60.000 0.00 0.00 39.14 2.90
68 69 1.739338 CGAGGGGATGAGGGACGAAG 61.739 65.000 0.00 0.00 0.00 3.79
83 84 0.535335 CGAAGAAGGTCGATTGGGGA 59.465 55.000 0.00 0.00 43.86 4.81
88 89 0.765510 AAGGTCGATTGGGGATAGGC 59.234 55.000 0.00 0.00 0.00 3.93
119 120 2.906354 CAGGAACCCTAATCACCTTCG 58.094 52.381 0.00 0.00 29.64 3.79
128 129 2.279582 AATCACCTTCGTGTCGCTAG 57.720 50.000 0.00 0.00 41.09 3.42
135 136 2.445316 CTTCGTGTCGCTAGTCTCATG 58.555 52.381 0.00 0.00 0.00 3.07
155 156 0.812811 CCCGCTGGATGACATGACAG 60.813 60.000 0.00 10.84 0.00 3.51
172 173 5.130705 TGACAGGAGTATATGTGAGAGGT 57.869 43.478 0.00 0.00 0.00 3.85
173 174 6.262056 TGACAGGAGTATATGTGAGAGGTA 57.738 41.667 0.00 0.00 0.00 3.08
175 176 6.773200 TGACAGGAGTATATGTGAGAGGTAAG 59.227 42.308 0.00 0.00 0.00 2.34
195 197 2.094258 AGAATTGTTGCTATCGTGCGTG 59.906 45.455 0.00 0.00 35.36 5.34
202 204 1.813753 CTATCGTGCGTGGGGTTGG 60.814 63.158 0.00 0.00 0.00 3.77
214 216 1.988406 GGGTTGGGTCGCTCTAGGT 60.988 63.158 0.00 0.00 0.00 3.08
250 252 8.585018 AGTTTTGTAGAAATGATAAAACCAGGG 58.415 33.333 0.00 0.00 40.33 4.45
299 301 9.742144 GGAGCGGAATATAGAGGAGATATAATA 57.258 37.037 0.00 0.00 0.00 0.98
354 356 9.578576 AGAGAAAAATATTGCAGGATTAGCATA 57.421 29.630 0.00 0.00 42.33 3.14
377 380 0.890996 AAAAGGCCGGTGAAGCTCAG 60.891 55.000 1.90 0.00 0.00 3.35
385 388 2.271800 CGGTGAAGCTCAGGAACATAC 58.728 52.381 0.00 0.00 0.00 2.39
386 389 2.093973 CGGTGAAGCTCAGGAACATACT 60.094 50.000 0.00 0.00 0.00 2.12
387 390 3.130516 CGGTGAAGCTCAGGAACATACTA 59.869 47.826 0.00 0.00 0.00 1.82
388 391 4.688021 GGTGAAGCTCAGGAACATACTAG 58.312 47.826 0.00 0.00 0.00 2.57
389 392 4.160626 GGTGAAGCTCAGGAACATACTAGT 59.839 45.833 0.00 0.00 0.00 2.57
390 393 5.337652 GGTGAAGCTCAGGAACATACTAGTT 60.338 44.000 0.00 0.00 0.00 2.24
519 741 2.029470 GGGCAAATCGGTCAAATCAACA 60.029 45.455 0.00 0.00 0.00 3.33
821 1049 1.137872 GCGATTGATCCACTCTGAGGT 59.862 52.381 9.85 0.00 0.00 3.85
830 1058 0.455295 CACTCTGAGGTTCTCGACGC 60.455 60.000 9.85 0.00 32.35 5.19
1775 2007 1.272704 GCTTGGGAAGAAGGAATGGGT 60.273 52.381 0.00 0.00 0.00 4.51
1899 2131 3.267551 GGGGTTTGGTGGGAAGATACTTA 59.732 47.826 0.00 0.00 0.00 2.24
1908 2140 4.876679 GTGGGAAGATACTTAAGGAAGCAC 59.123 45.833 7.53 0.00 35.97 4.40
1978 2210 0.685458 GGGGAAGATTGTGGCAGCAT 60.685 55.000 0.00 0.00 0.00 3.79
2239 2476 6.385649 TGTTACTGAAACTTGATGAAACCC 57.614 37.500 0.00 0.00 38.99 4.11
2295 2532 9.511272 TCTTAAACTATTTAAAAGGACAGACCC 57.489 33.333 0.00 0.00 35.61 4.46
2296 2533 9.292195 CTTAAACTATTTAAAAGGACAGACCCA 57.708 33.333 0.00 0.00 35.61 4.51
2297 2534 7.761038 AAACTATTTAAAAGGACAGACCCAG 57.239 36.000 0.00 0.00 40.05 4.45
2298 2535 6.449830 ACTATTTAAAAGGACAGACCCAGT 57.550 37.500 0.00 0.00 40.05 4.00
2299 2536 6.238648 ACTATTTAAAAGGACAGACCCAGTG 58.761 40.000 0.00 0.00 40.05 3.66
2300 2537 2.561478 TAAAAGGACAGACCCAGTGC 57.439 50.000 0.00 0.00 40.05 4.40
2301 2538 0.550914 AAAAGGACAGACCCAGTGCA 59.449 50.000 0.00 0.00 40.05 4.57
2302 2539 0.773644 AAAGGACAGACCCAGTGCAT 59.226 50.000 0.00 0.00 40.05 3.96
2303 2540 1.656587 AAGGACAGACCCAGTGCATA 58.343 50.000 0.00 0.00 40.05 3.14
2304 2541 1.198713 AGGACAGACCCAGTGCATAG 58.801 55.000 0.00 0.00 40.05 2.23
2305 2542 1.195115 GGACAGACCCAGTGCATAGA 58.805 55.000 0.00 0.00 0.00 1.98
2306 2543 1.555075 GGACAGACCCAGTGCATAGAA 59.445 52.381 0.00 0.00 0.00 2.10
2307 2544 2.419297 GGACAGACCCAGTGCATAGAAG 60.419 54.545 0.00 0.00 0.00 2.85
2308 2545 1.065854 ACAGACCCAGTGCATAGAAGC 60.066 52.381 0.00 0.00 0.00 3.86
2309 2546 1.209019 CAGACCCAGTGCATAGAAGCT 59.791 52.381 0.00 0.00 34.99 3.74
2310 2547 1.484240 AGACCCAGTGCATAGAAGCTC 59.516 52.381 0.00 0.00 34.99 4.09
2311 2548 0.543749 ACCCAGTGCATAGAAGCTCC 59.456 55.000 0.00 0.00 34.99 4.70
2312 2549 0.179034 CCCAGTGCATAGAAGCTCCC 60.179 60.000 0.00 0.00 34.99 4.30
2313 2550 0.543277 CCAGTGCATAGAAGCTCCCA 59.457 55.000 0.00 0.00 34.99 4.37
2314 2551 1.661341 CAGTGCATAGAAGCTCCCAC 58.339 55.000 0.00 0.00 34.99 4.61
2315 2552 1.065926 CAGTGCATAGAAGCTCCCACA 60.066 52.381 0.00 0.00 34.99 4.17
2316 2553 1.065854 AGTGCATAGAAGCTCCCACAC 60.066 52.381 0.00 0.00 34.99 3.82
2317 2554 0.983467 TGCATAGAAGCTCCCACACA 59.017 50.000 0.00 0.00 34.99 3.72
2318 2555 1.350684 TGCATAGAAGCTCCCACACAA 59.649 47.619 0.00 0.00 34.99 3.33
2319 2556 2.012673 GCATAGAAGCTCCCACACAAG 58.987 52.381 0.00 0.00 0.00 3.16
2320 2557 2.636830 CATAGAAGCTCCCACACAAGG 58.363 52.381 0.00 0.00 0.00 3.61
2321 2558 1.729586 TAGAAGCTCCCACACAAGGT 58.270 50.000 0.00 0.00 0.00 3.50
2329 2566 4.481195 CACACAAGGTGGGGTCTG 57.519 61.111 1.07 0.00 44.04 3.51
2330 2567 1.228245 CACACAAGGTGGGGTCTGG 60.228 63.158 1.07 0.00 44.04 3.86
2331 2568 2.436109 CACAAGGTGGGGTCTGGG 59.564 66.667 0.00 0.00 0.00 4.45
2332 2569 2.858974 ACAAGGTGGGGTCTGGGG 60.859 66.667 0.00 0.00 0.00 4.96
2333 2570 2.531685 CAAGGTGGGGTCTGGGGA 60.532 66.667 0.00 0.00 0.00 4.81
2334 2571 2.204151 AAGGTGGGGTCTGGGGAG 60.204 66.667 0.00 0.00 0.00 4.30
2335 2572 3.891432 AAGGTGGGGTCTGGGGAGG 62.891 68.421 0.00 0.00 0.00 4.30
2337 2574 4.348495 GTGGGGTCTGGGGAGGGA 62.348 72.222 0.00 0.00 0.00 4.20
2338 2575 3.300962 TGGGGTCTGGGGAGGGAT 61.301 66.667 0.00 0.00 0.00 3.85
2339 2576 2.044620 GGGGTCTGGGGAGGGATT 59.955 66.667 0.00 0.00 0.00 3.01
2340 2577 1.320512 GGGGTCTGGGGAGGGATTA 59.679 63.158 0.00 0.00 0.00 1.75
2341 2578 0.103876 GGGGTCTGGGGAGGGATTAT 60.104 60.000 0.00 0.00 0.00 1.28
2342 2579 1.153565 GGGGTCTGGGGAGGGATTATA 59.846 57.143 0.00 0.00 0.00 0.98
2343 2580 2.552367 GGGTCTGGGGAGGGATTATAG 58.448 57.143 0.00 0.00 0.00 1.31
2344 2581 2.552367 GGTCTGGGGAGGGATTATAGG 58.448 57.143 0.00 0.00 0.00 2.57
2345 2582 2.113777 GGTCTGGGGAGGGATTATAGGA 59.886 54.545 0.00 0.00 0.00 2.94
2346 2583 3.441054 GGTCTGGGGAGGGATTATAGGAA 60.441 52.174 0.00 0.00 0.00 3.36
2347 2584 3.583526 GTCTGGGGAGGGATTATAGGAAC 59.416 52.174 0.00 0.00 0.00 3.62
2348 2585 2.913617 CTGGGGAGGGATTATAGGAACC 59.086 54.545 0.00 0.00 0.00 3.62
2349 2586 2.531463 TGGGGAGGGATTATAGGAACCT 59.469 50.000 0.00 0.00 0.00 3.50
2350 2587 3.741438 TGGGGAGGGATTATAGGAACCTA 59.259 47.826 2.93 2.93 0.00 3.08
2351 2588 4.202901 TGGGGAGGGATTATAGGAACCTAG 60.203 50.000 6.72 0.00 31.45 3.02
2352 2589 4.202912 GGGGAGGGATTATAGGAACCTAGT 60.203 50.000 6.72 0.00 31.45 2.57
2353 2590 5.024785 GGGAGGGATTATAGGAACCTAGTC 58.975 50.000 6.72 4.93 31.45 2.59
2354 2591 5.222589 GGGAGGGATTATAGGAACCTAGTCT 60.223 48.000 6.72 0.00 31.45 3.24
2355 2592 6.324544 GGAGGGATTATAGGAACCTAGTCTT 58.675 44.000 6.72 0.00 31.45 3.01
2356 2593 7.477008 GGAGGGATTATAGGAACCTAGTCTTA 58.523 42.308 6.72 0.00 31.45 2.10
2357 2594 7.396907 GGAGGGATTATAGGAACCTAGTCTTAC 59.603 44.444 6.72 0.00 31.45 2.34
2358 2595 7.247500 AGGGATTATAGGAACCTAGTCTTACC 58.753 42.308 6.72 4.95 31.45 2.85
2359 2596 6.440010 GGGATTATAGGAACCTAGTCTTACCC 59.560 46.154 6.72 9.62 31.45 3.69
2360 2597 6.440010 GGATTATAGGAACCTAGTCTTACCCC 59.560 46.154 6.72 0.00 31.45 4.95
2361 2598 6.618836 TTATAGGAACCTAGTCTTACCCCT 57.381 41.667 6.72 0.00 31.45 4.79
2362 2599 3.117552 AGGAACCTAGTCTTACCCCTG 57.882 52.381 0.00 0.00 0.00 4.45
2363 2600 1.485480 GGAACCTAGTCTTACCCCTGC 59.515 57.143 0.00 0.00 0.00 4.85
2364 2601 2.185387 GAACCTAGTCTTACCCCTGCA 58.815 52.381 0.00 0.00 0.00 4.41
2365 2602 2.337359 ACCTAGTCTTACCCCTGCAA 57.663 50.000 0.00 0.00 0.00 4.08
2366 2603 2.627933 ACCTAGTCTTACCCCTGCAAA 58.372 47.619 0.00 0.00 0.00 3.68
2367 2604 2.572104 ACCTAGTCTTACCCCTGCAAAG 59.428 50.000 0.00 0.00 0.00 2.77
2368 2605 2.572104 CCTAGTCTTACCCCTGCAAAGT 59.428 50.000 0.00 0.00 0.00 2.66
2369 2606 2.568623 AGTCTTACCCCTGCAAAGTG 57.431 50.000 0.00 0.00 0.00 3.16
2370 2607 0.881796 GTCTTACCCCTGCAAAGTGC 59.118 55.000 0.00 0.00 45.29 4.40
2381 2618 1.978542 GCAAAGTGCAATGCAGAGAG 58.021 50.000 8.73 0.33 44.26 3.20
2382 2619 1.402456 GCAAAGTGCAATGCAGAGAGG 60.402 52.381 8.73 0.00 44.26 3.69
2383 2620 0.886563 AAAGTGCAATGCAGAGAGGC 59.113 50.000 8.73 0.00 40.08 4.70
2384 2621 0.037877 AAGTGCAATGCAGAGAGGCT 59.962 50.000 8.73 0.00 40.08 4.58
2386 2623 1.378119 TGCAATGCAGAGAGGCTGG 60.378 57.895 2.72 0.00 45.03 4.85
2387 2624 1.378250 GCAATGCAGAGAGGCTGGT 60.378 57.895 0.00 0.00 45.03 4.00
2388 2625 0.964358 GCAATGCAGAGAGGCTGGTT 60.964 55.000 0.00 0.00 45.03 3.67
2389 2626 1.093159 CAATGCAGAGAGGCTGGTTC 58.907 55.000 0.00 0.00 45.03 3.62
2390 2627 0.392193 AATGCAGAGAGGCTGGTTCG 60.392 55.000 0.00 0.00 45.03 3.95
2391 2628 1.260538 ATGCAGAGAGGCTGGTTCGA 61.261 55.000 0.00 0.00 45.03 3.71
2392 2629 1.293498 GCAGAGAGGCTGGTTCGAA 59.707 57.895 0.00 0.00 45.03 3.71
2393 2630 1.016653 GCAGAGAGGCTGGTTCGAAC 61.017 60.000 20.14 20.14 45.03 3.95
2394 2631 0.605589 CAGAGAGGCTGGTTCGAACT 59.394 55.000 26.32 7.49 41.07 3.01
2395 2632 1.819288 CAGAGAGGCTGGTTCGAACTA 59.181 52.381 26.32 20.42 41.07 2.24
2396 2633 2.096248 AGAGAGGCTGGTTCGAACTAG 58.904 52.381 30.81 30.81 40.12 2.57
2397 2634 1.135333 GAGAGGCTGGTTCGAACTAGG 59.865 57.143 33.89 21.58 37.90 3.02
2398 2635 1.183549 GAGGCTGGTTCGAACTAGGA 58.816 55.000 33.89 14.36 37.90 2.94
2399 2636 0.896226 AGGCTGGTTCGAACTAGGAC 59.104 55.000 33.89 21.97 37.90 3.85
2400 2637 0.108281 GGCTGGTTCGAACTAGGACC 60.108 60.000 33.89 25.78 37.90 4.46
2401 2638 0.896226 GCTGGTTCGAACTAGGACCT 59.104 55.000 33.89 0.00 37.90 3.85
2402 2639 1.135053 GCTGGTTCGAACTAGGACCTC 60.135 57.143 33.89 18.51 37.90 3.85
2403 2640 2.448453 CTGGTTCGAACTAGGACCTCT 58.552 52.381 28.43 0.00 34.28 3.69
2404 2641 2.826725 CTGGTTCGAACTAGGACCTCTT 59.173 50.000 28.43 0.00 34.28 2.85
2405 2642 2.561419 TGGTTCGAACTAGGACCTCTTG 59.439 50.000 26.32 0.00 33.33 3.02
2406 2643 2.094130 GGTTCGAACTAGGACCTCTTGG 60.094 54.545 26.32 0.00 39.83 3.61
2407 2644 1.183549 TCGAACTAGGACCTCTTGGC 58.816 55.000 0.00 0.00 36.63 4.52
2408 2645 0.895530 CGAACTAGGACCTCTTGGCA 59.104 55.000 0.00 0.00 36.63 4.92
2409 2646 1.404315 CGAACTAGGACCTCTTGGCAC 60.404 57.143 0.00 0.00 36.63 5.01
2410 2647 1.623811 GAACTAGGACCTCTTGGCACA 59.376 52.381 0.00 0.00 36.63 4.57
2421 2658 2.449518 TGGCACAAGTGGGGAGGA 60.450 61.111 2.00 0.00 31.92 3.71
2422 2659 2.034221 GGCACAAGTGGGGAGGAC 59.966 66.667 2.00 0.00 0.00 3.85
2423 2660 2.529744 GGCACAAGTGGGGAGGACT 61.530 63.158 2.00 0.00 0.00 3.85
2424 2661 1.456287 GCACAAGTGGGGAGGACTT 59.544 57.895 2.00 0.00 33.82 3.01
2425 2662 0.606673 GCACAAGTGGGGAGGACTTC 60.607 60.000 2.00 0.00 31.05 3.01
2426 2663 0.764890 CACAAGTGGGGAGGACTTCA 59.235 55.000 0.00 0.00 31.05 3.02
2427 2664 0.765510 ACAAGTGGGGAGGACTTCAC 59.234 55.000 0.00 0.00 31.05 3.18
2433 2670 1.003233 GGGAGGACTTCACCACTGC 60.003 63.158 0.00 0.00 0.00 4.40
2434 2671 1.374758 GGAGGACTTCACCACTGCG 60.375 63.158 0.00 0.00 0.00 5.18
2435 2672 2.029844 GAGGACTTCACCACTGCGC 61.030 63.158 0.00 0.00 0.00 6.09
2436 2673 3.050275 GGACTTCACCACTGCGCC 61.050 66.667 4.18 0.00 0.00 6.53
2437 2674 2.280797 GACTTCACCACTGCGCCA 60.281 61.111 4.18 0.00 0.00 5.69
2438 2675 2.281070 ACTTCACCACTGCGCCAG 60.281 61.111 4.18 4.99 37.52 4.85
2439 2676 3.052082 CTTCACCACTGCGCCAGG 61.052 66.667 4.18 6.64 35.51 4.45
2451 2688 4.811364 GCCAGGCCTGCCCTCTTC 62.811 72.222 28.39 5.60 44.09 2.87
2452 2689 3.013932 CCAGGCCTGCCCTCTTCT 61.014 66.667 28.39 0.00 44.09 2.85
2453 2690 2.271497 CAGGCCTGCCCTCTTCTG 59.729 66.667 22.33 0.00 44.09 3.02
2454 2691 2.204059 AGGCCTGCCCTCTTCTGT 60.204 61.111 3.11 0.00 41.21 3.41
2455 2692 2.270527 GGCCTGCCCTCTTCTGTC 59.729 66.667 0.00 0.00 0.00 3.51
2456 2693 2.297129 GGCCTGCCCTCTTCTGTCT 61.297 63.158 0.00 0.00 0.00 3.41
2457 2694 1.682257 GCCTGCCCTCTTCTGTCTT 59.318 57.895 0.00 0.00 0.00 3.01
2458 2695 0.905357 GCCTGCCCTCTTCTGTCTTA 59.095 55.000 0.00 0.00 0.00 2.10
2459 2696 1.279271 GCCTGCCCTCTTCTGTCTTAA 59.721 52.381 0.00 0.00 0.00 1.85
2460 2697 2.290323 GCCTGCCCTCTTCTGTCTTAAA 60.290 50.000 0.00 0.00 0.00 1.52
2461 2698 3.339141 CCTGCCCTCTTCTGTCTTAAAC 58.661 50.000 0.00 0.00 0.00 2.01
2462 2699 3.008485 CCTGCCCTCTTCTGTCTTAAACT 59.992 47.826 0.00 0.00 0.00 2.66
2463 2700 4.223032 CCTGCCCTCTTCTGTCTTAAACTA 59.777 45.833 0.00 0.00 0.00 2.24
2464 2701 5.104735 CCTGCCCTCTTCTGTCTTAAACTAT 60.105 44.000 0.00 0.00 0.00 2.12
2465 2702 6.374417 TGCCCTCTTCTGTCTTAAACTATT 57.626 37.500 0.00 0.00 0.00 1.73
2466 2703 6.779860 TGCCCTCTTCTGTCTTAAACTATTT 58.220 36.000 0.00 0.00 0.00 1.40
2467 2704 6.655003 TGCCCTCTTCTGTCTTAAACTATTTG 59.345 38.462 0.00 0.00 0.00 2.32
2468 2705 6.403746 GCCCTCTTCTGTCTTAAACTATTTGC 60.404 42.308 0.00 0.00 0.00 3.68
2469 2706 6.881602 CCCTCTTCTGTCTTAAACTATTTGCT 59.118 38.462 0.00 0.00 0.00 3.91
2470 2707 8.041323 CCCTCTTCTGTCTTAAACTATTTGCTA 58.959 37.037 0.00 0.00 0.00 3.49
2471 2708 9.436957 CCTCTTCTGTCTTAAACTATTTGCTAA 57.563 33.333 0.00 0.00 0.00 3.09
2580 2818 8.897752 GGAGAAATAGTGCTCTTTGTTGATTAT 58.102 33.333 0.00 0.00 0.00 1.28
2621 2859 1.497286 ACCAGGACTTTTGTTGGCCTA 59.503 47.619 3.32 0.00 34.49 3.93
2789 3027 6.624352 ATGCAGCATCGTAATGAGTTTTAT 57.376 33.333 0.52 0.00 34.61 1.40
2951 3190 4.147321 AGTTGTCAGTTGAGAATGCCAAT 58.853 39.130 0.00 0.00 29.85 3.16
3011 3250 7.480810 AGCAAAAGGTAAACTAAAGAACTGTG 58.519 34.615 0.00 0.00 0.00 3.66
3469 3709 6.518493 AGGTATTGAACACTTCTAAACGTGA 58.482 36.000 0.00 0.00 35.23 4.35
3685 3926 3.371063 TCGGTGCTCGACCTGGAC 61.371 66.667 0.00 0.00 43.55 4.02
4010 4251 1.634702 GTACTGCTCCTTTCTCTGCG 58.365 55.000 0.00 0.00 0.00 5.18
4823 5064 2.482374 CTTTGGCTGCTAGCGTGC 59.518 61.111 20.05 20.05 43.62 5.34
4860 5105 7.498900 TGCAGGTGTATATTACCTCTCAAATTG 59.501 37.037 8.29 0.00 45.19 2.32
4885 5146 3.198635 TGTCTTAGATTTGGCTGCTAGCT 59.801 43.478 17.23 0.00 41.99 3.32
4886 5147 4.405680 TGTCTTAGATTTGGCTGCTAGCTA 59.594 41.667 17.23 1.31 41.99 3.32
4887 5148 4.987912 GTCTTAGATTTGGCTGCTAGCTAG 59.012 45.833 16.84 16.84 41.99 3.42
4991 5256 2.335316 TGTTGTGAGTTGTGGTACCC 57.665 50.000 10.07 1.05 0.00 3.69
5017 5282 1.002366 GTTGCGACATCTTCAGCGAT 58.998 50.000 0.00 0.00 0.00 4.58
5150 5415 8.434733 AAGAGAAGGTACTGAAAACAAGTTAC 57.565 34.615 0.00 0.00 40.86 2.50
5174 5439 2.594131 GGAACTTTGCTGGGTAAGGTT 58.406 47.619 0.00 0.00 31.38 3.50
5183 5448 2.355716 GCTGGGTAAGGTTACTGATGCA 60.356 50.000 0.00 0.00 34.16 3.96
5329 5595 6.950860 TGGGATATTCATGGCACTAGATAA 57.049 37.500 0.00 0.00 0.00 1.75
5392 5659 5.216622 TGCACCTTATATGTTACTCCCTCT 58.783 41.667 0.00 0.00 0.00 3.69
5393 5660 5.070446 TGCACCTTATATGTTACTCCCTCTG 59.930 44.000 0.00 0.00 0.00 3.35
5522 5820 6.949715 TGTGGACGTAGGGAGTATTTTTAAT 58.050 36.000 0.00 0.00 0.00 1.40
5555 5853 9.139174 TCTTCATGAAAAGTTTGTGTTTCTTTC 57.861 29.630 9.88 0.00 35.26 2.62
5598 5896 4.890158 TGTCTCACAGCCAAAGAAGATA 57.110 40.909 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.454573 TTCCCGTCCCGACCATCG 61.455 66.667 0.00 0.00 40.07 3.84
43 44 1.840650 CCTCATCCCCTCGCCTGAT 60.841 63.158 0.00 0.00 0.00 2.90
47 48 3.551407 GTCCCTCATCCCCTCGCC 61.551 72.222 0.00 0.00 0.00 5.54
68 69 1.270893 GCCTATCCCCAATCGACCTTC 60.271 57.143 0.00 0.00 0.00 3.46
99 100 2.236395 ACGAAGGTGATTAGGGTTCCTG 59.764 50.000 0.00 0.00 34.61 3.86
119 120 0.528684 GGGCATGAGACTAGCGACAC 60.529 60.000 0.00 0.00 0.00 3.67
128 129 1.890979 CATCCAGCGGGCATGAGAC 60.891 63.158 0.00 0.00 0.00 3.36
135 136 2.182842 GTCATGTCATCCAGCGGGC 61.183 63.158 0.00 0.00 0.00 6.13
155 156 8.643324 ACAATTCTTACCTCTCACATATACTCC 58.357 37.037 0.00 0.00 0.00 3.85
172 173 3.930229 ACGCACGATAGCAACAATTCTTA 59.070 39.130 0.00 0.00 42.67 2.10
173 174 2.742053 ACGCACGATAGCAACAATTCTT 59.258 40.909 0.00 0.00 42.67 2.52
175 176 2.430956 CACGCACGATAGCAACAATTC 58.569 47.619 0.00 0.00 42.67 2.17
195 197 2.732619 CCTAGAGCGACCCAACCCC 61.733 68.421 0.00 0.00 0.00 4.95
202 204 4.062991 TGAAAGAAAAACCTAGAGCGACC 58.937 43.478 0.00 0.00 0.00 4.79
206 208 7.258441 ACAAAACTGAAAGAAAAACCTAGAGC 58.742 34.615 0.00 0.00 37.43 4.09
250 252 3.054361 TCTTGCTTCCCACCTCCTTTATC 60.054 47.826 0.00 0.00 0.00 1.75
330 332 9.578576 TCTATGCTAATCCTGCAATATTTTTCT 57.421 29.630 0.00 0.00 44.01 2.52
373 376 7.976734 CCACTTCTTAACTAGTATGTTCCTGAG 59.023 40.741 0.00 0.00 0.00 3.35
377 380 6.403878 TGCCACTTCTTAACTAGTATGTTCC 58.596 40.000 0.00 0.00 0.00 3.62
385 388 2.415512 GCCGTTGCCACTTCTTAACTAG 59.584 50.000 0.00 0.00 0.00 2.57
386 389 2.224329 TGCCGTTGCCACTTCTTAACTA 60.224 45.455 0.00 0.00 36.33 2.24
387 390 1.235724 GCCGTTGCCACTTCTTAACT 58.764 50.000 0.00 0.00 0.00 2.24
388 391 0.948678 TGCCGTTGCCACTTCTTAAC 59.051 50.000 0.00 0.00 36.33 2.01
389 392 0.948678 GTGCCGTTGCCACTTCTTAA 59.051 50.000 0.00 0.00 36.33 1.85
390 393 1.225376 CGTGCCGTTGCCACTTCTTA 61.225 55.000 0.00 0.00 36.33 2.10
477 699 7.001674 TGCCCTGACTCTTAAGACAATTTTAA 58.998 34.615 0.00 0.00 0.00 1.52
487 709 2.939103 CCGATTTGCCCTGACTCTTAAG 59.061 50.000 0.00 0.00 0.00 1.85
489 711 1.906574 ACCGATTTGCCCTGACTCTTA 59.093 47.619 0.00 0.00 0.00 2.10
495 717 2.091541 GATTTGACCGATTTGCCCTGA 58.908 47.619 0.00 0.00 0.00 3.86
519 741 2.367486 GTAAGCGGAGACAGGACTAGT 58.633 52.381 0.00 0.00 0.00 2.57
821 1049 0.251916 ATCAAATGGGGCGTCGAGAA 59.748 50.000 0.00 0.00 0.00 2.87
830 1058 1.439353 CGACGCTGGATCAAATGGGG 61.439 60.000 0.00 0.00 0.00 4.96
978 1210 2.360483 TGTCGGATCAGAGATTCAGCTC 59.640 50.000 0.00 0.00 35.11 4.09
979 1211 2.382882 TGTCGGATCAGAGATTCAGCT 58.617 47.619 0.00 0.00 0.00 4.24
980 1212 2.879002 TGTCGGATCAGAGATTCAGC 57.121 50.000 0.00 0.00 0.00 4.26
981 1213 4.056740 CCATTGTCGGATCAGAGATTCAG 58.943 47.826 0.00 0.00 0.00 3.02
1775 2007 1.529010 CCACAACTGCTCCTTGCCA 60.529 57.895 0.00 0.00 42.00 4.92
1899 2131 4.757149 GTCTTAATGTCAGTGTGCTTCCTT 59.243 41.667 0.00 0.00 0.00 3.36
1908 2140 7.720442 TCTCATCTATGGTCTTAATGTCAGTG 58.280 38.462 0.00 0.00 0.00 3.66
1978 2210 1.004560 CCTCGAGCTGAGTTGCCAA 60.005 57.895 6.99 0.00 43.64 4.52
2239 2476 3.254060 CAAGGTACCGACTGAATCACTG 58.746 50.000 6.18 0.00 0.00 3.66
2282 2519 0.550914 TGCACTGGGTCTGTCCTTTT 59.449 50.000 0.00 0.00 36.25 2.27
2283 2520 0.773644 ATGCACTGGGTCTGTCCTTT 59.226 50.000 0.00 0.00 36.25 3.11
2284 2521 1.556911 CTATGCACTGGGTCTGTCCTT 59.443 52.381 0.00 0.00 36.25 3.36
2285 2522 1.198713 CTATGCACTGGGTCTGTCCT 58.801 55.000 0.00 0.00 36.25 3.85
2286 2523 1.195115 TCTATGCACTGGGTCTGTCC 58.805 55.000 0.00 0.00 0.00 4.02
2287 2524 2.898705 CTTCTATGCACTGGGTCTGTC 58.101 52.381 0.00 0.00 0.00 3.51
2288 2525 1.065854 GCTTCTATGCACTGGGTCTGT 60.066 52.381 0.00 0.00 0.00 3.41
2289 2526 1.209019 AGCTTCTATGCACTGGGTCTG 59.791 52.381 0.00 0.00 34.99 3.51
2290 2527 1.484240 GAGCTTCTATGCACTGGGTCT 59.516 52.381 0.00 0.00 34.99 3.85
2291 2528 1.474143 GGAGCTTCTATGCACTGGGTC 60.474 57.143 0.00 0.00 34.99 4.46
2292 2529 0.543749 GGAGCTTCTATGCACTGGGT 59.456 55.000 0.00 0.00 34.99 4.51
2293 2530 0.179034 GGGAGCTTCTATGCACTGGG 60.179 60.000 0.00 0.00 34.99 4.45
2294 2531 0.543277 TGGGAGCTTCTATGCACTGG 59.457 55.000 0.00 0.00 34.99 4.00
2295 2532 1.065926 TGTGGGAGCTTCTATGCACTG 60.066 52.381 0.00 0.00 34.99 3.66
2296 2533 1.065854 GTGTGGGAGCTTCTATGCACT 60.066 52.381 0.00 0.00 34.99 4.40
2297 2534 1.339055 TGTGTGGGAGCTTCTATGCAC 60.339 52.381 0.00 0.00 34.99 4.57
2298 2535 0.983467 TGTGTGGGAGCTTCTATGCA 59.017 50.000 0.00 0.00 34.99 3.96
2299 2536 2.012673 CTTGTGTGGGAGCTTCTATGC 58.987 52.381 0.00 0.00 0.00 3.14
2300 2537 2.026822 ACCTTGTGTGGGAGCTTCTATG 60.027 50.000 0.00 0.00 0.00 2.23
2301 2538 2.026822 CACCTTGTGTGGGAGCTTCTAT 60.027 50.000 0.00 0.00 41.52 1.98
2302 2539 1.347707 CACCTTGTGTGGGAGCTTCTA 59.652 52.381 0.00 0.00 41.52 2.10
2303 2540 0.109342 CACCTTGTGTGGGAGCTTCT 59.891 55.000 0.00 0.00 41.52 2.85
2304 2541 2.633860 CACCTTGTGTGGGAGCTTC 58.366 57.895 0.00 0.00 41.52 3.86
2305 2542 4.907457 CACCTTGTGTGGGAGCTT 57.093 55.556 0.00 0.00 41.52 3.74
2312 2549 1.228245 CCAGACCCCACCTTGTGTG 60.228 63.158 0.00 0.00 45.01 3.82
2313 2550 2.460853 CCCAGACCCCACCTTGTGT 61.461 63.158 0.00 0.00 0.00 3.72
2314 2551 2.436109 CCCAGACCCCACCTTGTG 59.564 66.667 0.00 0.00 0.00 3.33
2315 2552 2.858974 CCCCAGACCCCACCTTGT 60.859 66.667 0.00 0.00 0.00 3.16
2316 2553 2.531685 TCCCCAGACCCCACCTTG 60.532 66.667 0.00 0.00 0.00 3.61
2317 2554 2.204151 CTCCCCAGACCCCACCTT 60.204 66.667 0.00 0.00 0.00 3.50
2318 2555 4.354943 CCTCCCCAGACCCCACCT 62.355 72.222 0.00 0.00 0.00 4.00
2320 2557 3.660092 ATCCCTCCCCAGACCCCAC 62.660 68.421 0.00 0.00 0.00 4.61
2321 2558 1.542093 TAATCCCTCCCCAGACCCCA 61.542 60.000 0.00 0.00 0.00 4.96
2322 2559 0.103876 ATAATCCCTCCCCAGACCCC 60.104 60.000 0.00 0.00 0.00 4.95
2323 2560 2.552367 CTATAATCCCTCCCCAGACCC 58.448 57.143 0.00 0.00 0.00 4.46
2324 2561 2.113777 TCCTATAATCCCTCCCCAGACC 59.886 54.545 0.00 0.00 0.00 3.85
2325 2562 3.562108 TCCTATAATCCCTCCCCAGAC 57.438 52.381 0.00 0.00 0.00 3.51
2326 2563 3.441054 GGTTCCTATAATCCCTCCCCAGA 60.441 52.174 0.00 0.00 0.00 3.86
2327 2564 2.913617 GGTTCCTATAATCCCTCCCCAG 59.086 54.545 0.00 0.00 0.00 4.45
2328 2565 2.531463 AGGTTCCTATAATCCCTCCCCA 59.469 50.000 0.00 0.00 0.00 4.96
2329 2566 3.293215 AGGTTCCTATAATCCCTCCCC 57.707 52.381 0.00 0.00 0.00 4.81
2330 2567 5.024785 GACTAGGTTCCTATAATCCCTCCC 58.975 50.000 0.00 0.00 0.00 4.30
2331 2568 5.906254 AGACTAGGTTCCTATAATCCCTCC 58.094 45.833 0.00 0.00 0.00 4.30
2332 2569 7.396907 GGTAAGACTAGGTTCCTATAATCCCTC 59.603 44.444 0.00 0.00 0.00 4.30
2333 2570 7.247500 GGTAAGACTAGGTTCCTATAATCCCT 58.753 42.308 0.00 0.00 0.00 4.20
2334 2571 6.440010 GGGTAAGACTAGGTTCCTATAATCCC 59.560 46.154 0.00 4.36 0.00 3.85
2335 2572 6.440010 GGGGTAAGACTAGGTTCCTATAATCC 59.560 46.154 0.00 0.00 0.00 3.01
2336 2573 7.178805 CAGGGGTAAGACTAGGTTCCTATAATC 59.821 44.444 0.00 0.00 0.00 1.75
2337 2574 7.017531 CAGGGGTAAGACTAGGTTCCTATAAT 58.982 42.308 0.00 0.00 0.00 1.28
2338 2575 6.379579 CAGGGGTAAGACTAGGTTCCTATAA 58.620 44.000 0.00 0.00 0.00 0.98
2339 2576 5.694949 GCAGGGGTAAGACTAGGTTCCTATA 60.695 48.000 0.00 0.00 0.00 1.31
2340 2577 4.817286 CAGGGGTAAGACTAGGTTCCTAT 58.183 47.826 0.00 0.00 0.00 2.57
2341 2578 3.629282 GCAGGGGTAAGACTAGGTTCCTA 60.629 52.174 0.00 0.00 0.00 2.94
2342 2579 2.893153 GCAGGGGTAAGACTAGGTTCCT 60.893 54.545 0.00 0.00 0.00 3.36
2343 2580 1.485480 GCAGGGGTAAGACTAGGTTCC 59.515 57.143 0.00 0.00 0.00 3.62
2344 2581 2.185387 TGCAGGGGTAAGACTAGGTTC 58.815 52.381 0.00 0.00 0.00 3.62
2345 2582 2.337359 TGCAGGGGTAAGACTAGGTT 57.663 50.000 0.00 0.00 0.00 3.50
2346 2583 2.337359 TTGCAGGGGTAAGACTAGGT 57.663 50.000 0.00 0.00 0.00 3.08
2347 2584 2.572104 ACTTTGCAGGGGTAAGACTAGG 59.428 50.000 2.16 0.00 0.00 3.02
2348 2585 3.600388 CACTTTGCAGGGGTAAGACTAG 58.400 50.000 2.16 0.00 0.00 2.57
2349 2586 2.290071 GCACTTTGCAGGGGTAAGACTA 60.290 50.000 2.16 0.00 44.26 2.59
2350 2587 1.545651 GCACTTTGCAGGGGTAAGACT 60.546 52.381 2.16 0.00 44.26 3.24
2351 2588 0.881796 GCACTTTGCAGGGGTAAGAC 59.118 55.000 2.16 0.00 44.26 3.01
2352 2589 3.339547 GCACTTTGCAGGGGTAAGA 57.660 52.632 2.16 0.00 44.26 2.10
2362 2599 1.402456 CCTCTCTGCATTGCACTTTGC 60.402 52.381 7.38 8.20 45.29 3.68
2363 2600 1.402456 GCCTCTCTGCATTGCACTTTG 60.402 52.381 7.38 0.00 33.79 2.77
2364 2601 0.886563 GCCTCTCTGCATTGCACTTT 59.113 50.000 7.38 0.00 33.79 2.66
2365 2602 0.037877 AGCCTCTCTGCATTGCACTT 59.962 50.000 7.38 0.00 33.79 3.16
2366 2603 0.677098 CAGCCTCTCTGCATTGCACT 60.677 55.000 7.38 0.00 35.78 4.40
2367 2604 1.654954 CCAGCCTCTCTGCATTGCAC 61.655 60.000 7.38 0.00 41.50 4.57
2368 2605 1.378119 CCAGCCTCTCTGCATTGCA 60.378 57.895 11.50 11.50 41.50 4.08
2369 2606 0.964358 AACCAGCCTCTCTGCATTGC 60.964 55.000 0.46 0.46 41.50 3.56
2370 2607 1.093159 GAACCAGCCTCTCTGCATTG 58.907 55.000 0.00 0.00 41.50 2.82
2371 2608 0.392193 CGAACCAGCCTCTCTGCATT 60.392 55.000 0.00 0.00 41.50 3.56
2372 2609 1.220206 CGAACCAGCCTCTCTGCAT 59.780 57.895 0.00 0.00 41.50 3.96
2373 2610 1.471829 TTCGAACCAGCCTCTCTGCA 61.472 55.000 0.00 0.00 41.50 4.41
2374 2611 1.016653 GTTCGAACCAGCCTCTCTGC 61.017 60.000 17.68 0.00 41.50 4.26
2375 2612 0.605589 AGTTCGAACCAGCCTCTCTG 59.394 55.000 24.22 0.00 42.49 3.35
2376 2613 2.096248 CTAGTTCGAACCAGCCTCTCT 58.904 52.381 24.22 5.45 0.00 3.10
2377 2614 1.135333 CCTAGTTCGAACCAGCCTCTC 59.865 57.143 24.22 0.00 0.00 3.20
2378 2615 1.187087 CCTAGTTCGAACCAGCCTCT 58.813 55.000 24.22 6.92 0.00 3.69
2379 2616 1.135053 GTCCTAGTTCGAACCAGCCTC 60.135 57.143 24.22 9.39 0.00 4.70
2380 2617 0.896226 GTCCTAGTTCGAACCAGCCT 59.104 55.000 24.22 8.40 0.00 4.58
2381 2618 0.108281 GGTCCTAGTTCGAACCAGCC 60.108 60.000 24.22 13.64 0.00 4.85
2382 2619 0.896226 AGGTCCTAGTTCGAACCAGC 59.104 55.000 24.22 14.78 34.09 4.85
2383 2620 2.448453 AGAGGTCCTAGTTCGAACCAG 58.552 52.381 24.22 19.81 34.09 4.00
2384 2621 2.561419 CAAGAGGTCCTAGTTCGAACCA 59.439 50.000 24.22 10.67 34.09 3.67
2385 2622 2.094130 CCAAGAGGTCCTAGTTCGAACC 60.094 54.545 24.22 9.20 0.00 3.62
2386 2623 2.674462 GCCAAGAGGTCCTAGTTCGAAC 60.674 54.545 20.71 20.71 37.19 3.95
2387 2624 1.549170 GCCAAGAGGTCCTAGTTCGAA 59.451 52.381 0.00 0.00 37.19 3.71
2388 2625 1.183549 GCCAAGAGGTCCTAGTTCGA 58.816 55.000 0.00 0.00 37.19 3.71
2389 2626 0.895530 TGCCAAGAGGTCCTAGTTCG 59.104 55.000 0.00 0.00 37.19 3.95
2390 2627 1.623811 TGTGCCAAGAGGTCCTAGTTC 59.376 52.381 0.00 0.00 37.19 3.01
2391 2628 1.729586 TGTGCCAAGAGGTCCTAGTT 58.270 50.000 0.00 0.00 37.19 2.24
2392 2629 1.625818 CTTGTGCCAAGAGGTCCTAGT 59.374 52.381 8.72 0.00 37.19 2.57
2393 2630 1.625818 ACTTGTGCCAAGAGGTCCTAG 59.374 52.381 18.22 0.00 37.19 3.02
2394 2631 1.347707 CACTTGTGCCAAGAGGTCCTA 59.652 52.381 18.22 0.00 37.19 2.94
2395 2632 0.109342 CACTTGTGCCAAGAGGTCCT 59.891 55.000 18.22 0.00 37.19 3.85
2396 2633 0.890996 CCACTTGTGCCAAGAGGTCC 60.891 60.000 18.22 0.00 37.19 4.46
2397 2634 0.890996 CCCACTTGTGCCAAGAGGTC 60.891 60.000 21.11 0.00 37.19 3.85
2398 2635 1.151450 CCCACTTGTGCCAAGAGGT 59.849 57.895 21.11 2.99 37.19 3.85
2399 2636 1.604593 CCCCACTTGTGCCAAGAGG 60.605 63.158 18.22 18.17 38.23 3.69
2400 2637 0.607489 CTCCCCACTTGTGCCAAGAG 60.607 60.000 18.22 11.85 0.00 2.85
2401 2638 1.455849 CTCCCCACTTGTGCCAAGA 59.544 57.895 18.22 0.00 0.00 3.02
2402 2639 1.604593 CCTCCCCACTTGTGCCAAG 60.605 63.158 11.87 11.87 0.00 3.61
2403 2640 2.081787 TCCTCCCCACTTGTGCCAA 61.082 57.895 0.00 0.00 0.00 4.52
2404 2641 2.449518 TCCTCCCCACTTGTGCCA 60.450 61.111 0.00 0.00 0.00 4.92
2405 2642 2.034221 GTCCTCCCCACTTGTGCC 59.966 66.667 0.00 0.00 0.00 5.01
2406 2643 0.606673 GAAGTCCTCCCCACTTGTGC 60.607 60.000 0.00 0.00 34.10 4.57
2407 2644 0.764890 TGAAGTCCTCCCCACTTGTG 59.235 55.000 0.00 0.00 34.10 3.33
2408 2645 0.765510 GTGAAGTCCTCCCCACTTGT 59.234 55.000 0.00 0.00 34.10 3.16
2409 2646 0.036875 GGTGAAGTCCTCCCCACTTG 59.963 60.000 0.00 0.00 34.10 3.16
2410 2647 0.401395 TGGTGAAGTCCTCCCCACTT 60.401 55.000 0.00 0.00 36.77 3.16
2411 2648 1.128188 GTGGTGAAGTCCTCCCCACT 61.128 60.000 0.00 0.00 41.83 4.00
2412 2649 1.128188 AGTGGTGAAGTCCTCCCCAC 61.128 60.000 0.00 0.00 44.69 4.61
2413 2650 1.127567 CAGTGGTGAAGTCCTCCCCA 61.128 60.000 0.00 0.00 0.00 4.96
2414 2651 1.679898 CAGTGGTGAAGTCCTCCCC 59.320 63.158 0.00 0.00 0.00 4.81
2415 2652 1.003233 GCAGTGGTGAAGTCCTCCC 60.003 63.158 0.00 0.00 0.00 4.30
2416 2653 1.374758 CGCAGTGGTGAAGTCCTCC 60.375 63.158 0.00 0.00 0.00 4.30
2417 2654 2.029844 GCGCAGTGGTGAAGTCCTC 61.030 63.158 0.30 0.00 0.00 3.71
2418 2655 2.031163 GCGCAGTGGTGAAGTCCT 59.969 61.111 0.30 0.00 0.00 3.85
2419 2656 3.050275 GGCGCAGTGGTGAAGTCC 61.050 66.667 10.83 0.00 0.00 3.85
2420 2657 2.280797 TGGCGCAGTGGTGAAGTC 60.281 61.111 10.83 0.00 0.00 3.01
2421 2658 2.281070 CTGGCGCAGTGGTGAAGT 60.281 61.111 10.83 0.00 0.00 3.01
2422 2659 3.052082 CCTGGCGCAGTGGTGAAG 61.052 66.667 10.83 0.00 0.00 3.02
2435 2672 3.013932 AGAAGAGGGCAGGCCTGG 61.014 66.667 33.46 15.81 36.10 4.45
2436 2673 2.271497 CAGAAGAGGGCAGGCCTG 59.729 66.667 29.34 29.34 36.10 4.85
2437 2674 2.204059 ACAGAAGAGGGCAGGCCT 60.204 61.111 17.36 17.36 36.10 5.19
2438 2675 1.846712 AAGACAGAAGAGGGCAGGCC 61.847 60.000 4.33 4.33 0.00 5.19
2439 2676 0.905357 TAAGACAGAAGAGGGCAGGC 59.095 55.000 0.00 0.00 0.00 4.85
2440 2677 3.008485 AGTTTAAGACAGAAGAGGGCAGG 59.992 47.826 0.00 0.00 0.00 4.85
2441 2678 4.278975 AGTTTAAGACAGAAGAGGGCAG 57.721 45.455 0.00 0.00 0.00 4.85
2442 2679 6.374417 AATAGTTTAAGACAGAAGAGGGCA 57.626 37.500 0.00 0.00 0.00 5.36
2443 2680 6.403746 GCAAATAGTTTAAGACAGAAGAGGGC 60.404 42.308 0.00 0.00 0.00 5.19
2444 2681 6.881602 AGCAAATAGTTTAAGACAGAAGAGGG 59.118 38.462 0.00 0.00 0.00 4.30
2445 2682 7.913674 AGCAAATAGTTTAAGACAGAAGAGG 57.086 36.000 0.00 0.00 0.00 3.69
2580 2818 2.176314 CTGCACTCCTGCTGCCTGTA 62.176 60.000 0.00 0.00 44.57 2.74
2644 2882 6.942532 TGTTAAAGCAGACAAGAGACAAAT 57.057 33.333 0.00 0.00 0.00 2.32
2789 3027 1.885887 CGCATTTCTGAAGGGGAAACA 59.114 47.619 3.24 0.00 35.84 2.83
3011 3250 4.113354 GCATAGCTTAGTACCTCACACAC 58.887 47.826 0.00 0.00 0.00 3.82
3207 3447 6.648879 AAATGTAGAAAGCAGCAGGTAAAA 57.351 33.333 0.00 0.00 0.00 1.52
3208 3448 6.648879 AAAATGTAGAAAGCAGCAGGTAAA 57.351 33.333 0.00 0.00 0.00 2.01
3469 3709 9.850628 GCACTTGTGCAATCATATCATATATTT 57.149 29.630 19.36 0.00 34.41 1.40
3685 3926 4.503910 TGTTCCCACGATTAGTTCTCATG 58.496 43.478 0.00 0.00 0.00 3.07
4241 4482 3.846588 TCTTTATCTCCTCCTGCCAACTT 59.153 43.478 0.00 0.00 0.00 2.66
4643 4884 5.921408 CCCTACTAGAGCTAATAAAACAGCG 59.079 44.000 0.00 0.00 42.74 5.18
4823 5064 1.795768 ACACCTGCACAATCTACACG 58.204 50.000 0.00 0.00 0.00 4.49
4860 5105 2.751806 AGCAGCCAAATCTAAGACAAGC 59.248 45.455 0.00 0.00 0.00 4.01
4885 5146 9.451002 AATTTGTCTAGATAGATACTAGCGCTA 57.549 33.333 17.75 17.75 37.73 4.26
4886 5147 7.931578 ATTTGTCTAGATAGATACTAGCGCT 57.068 36.000 17.26 17.26 37.73 5.92
4887 5148 8.973835 AAATTTGTCTAGATAGATACTAGCGC 57.026 34.615 0.00 0.00 37.73 5.92
4991 5256 2.667969 TGAAGATGTCGCAACAAGATCG 59.332 45.455 0.00 0.00 39.30 3.69
5017 5282 3.807553 TCAAACTGACACATGCTCAAGA 58.192 40.909 0.00 0.00 0.00 3.02
5150 5415 2.286365 TACCCAGCAAAGTTCCCTTG 57.714 50.000 0.00 0.00 0.00 3.61
5174 5439 1.901833 TCAGAAGTGCCTGCATCAGTA 59.098 47.619 0.00 0.00 34.28 2.74
5183 5448 2.089980 GTCAATGCATCAGAAGTGCCT 58.910 47.619 0.00 0.00 41.83 4.75
5329 5595 5.010922 TGCAAAACATCCTAGAGCATTTTGT 59.989 36.000 16.61 0.00 38.61 2.83
5522 5820 9.337396 ACACAAACTTTTCATGAAGATACAGTA 57.663 29.630 8.41 0.00 0.00 2.74
5529 5827 9.139174 GAAAGAAACACAAACTTTTCATGAAGA 57.861 29.630 8.41 3.12 34.68 2.87
5544 5842 6.429791 TTTCAATGTCTCGAAAGAAACACA 57.570 33.333 0.00 0.00 44.97 3.72
5555 5853 6.258160 ACAACAGAAACTTTTCAATGTCTCG 58.742 36.000 4.58 0.00 39.61 4.04


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

AutoCloner maintained by Alex Coulton.