Multiple sequence alignment - TraesCS1D01G155400

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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 TraesCS1D01G155400 chr1D 100.000 3230 0 0 1 3230 218411523 218408294 0.000000e+00 5965.0
1 TraesCS1D01G155400 chr1D 91.617 334 27 1 2372 2705 75466332 75466000 8.160000e-126 460.0
2 TraesCS1D01G155400 chr1D 88.889 45 5 0 1620 1664 430861090 430861046 4.500000e-04 56.5
3 TraesCS1D01G155400 chr1A 92.947 1588 52 27 832 2377 280604461 280602892 0.000000e+00 2257.0
4 TraesCS1D01G155400 chr1A 92.081 543 25 9 2699 3230 280602897 280602362 0.000000e+00 749.0
5 TraesCS1D01G155400 chr1A 82.353 68 10 2 1620 1686 529126357 529126291 1.250000e-04 58.4
6 TraesCS1D01G155400 chr1B 93.229 1536 43 17 855 2377 312250002 312248515 0.000000e+00 2204.0
7 TraesCS1D01G155400 chr1B 90.749 227 17 2 2874 3096 312248149 312247923 1.880000e-77 300.0
8 TraesCS1D01G155400 chr1B 96.648 179 4 2 2699 2876 312248520 312248343 2.440000e-76 296.0
9 TraesCS1D01G155400 chr1B 98.551 138 2 0 3093 3230 312246710 312246573 8.950000e-61 244.0
10 TraesCS1D01G155400 chr1B 82.353 68 10 2 1620 1686 582021884 582021818 1.250000e-04 58.4
11 TraesCS1D01G155400 chr3D 94.624 837 24 5 1 835 45553735 45554552 0.000000e+00 1277.0
12 TraesCS1D01G155400 chr3D 91.045 335 28 2 2371 2705 395307908 395307576 4.910000e-123 451.0
13 TraesCS1D01G155400 chr3D 83.858 254 24 14 1158 1395 288295777 288296029 3.240000e-55 226.0
14 TraesCS1D01G155400 chr3D 90.000 170 8 4 1156 1324 329686507 329686346 9.080000e-51 211.0
15 TraesCS1D01G155400 chr5A 92.270 815 48 9 1 811 666753864 666753061 0.000000e+00 1142.0
16 TraesCS1D01G155400 chr5A 82.105 95 15 2 1601 1694 283111203 283111110 2.670000e-11 80.5
17 TraesCS1D01G155400 chr4B 91.479 845 44 6 1 843 426599226 426598408 0.000000e+00 1136.0
18 TraesCS1D01G155400 chr4B 97.500 40 1 0 1215 1254 140587431 140587470 5.780000e-08 69.4
19 TraesCS1D01G155400 chr4A 89.870 849 62 11 1 842 682029253 682030084 0.000000e+00 1070.0
20 TraesCS1D01G155400 chr2D 86.799 856 73 20 1 833 543453250 543454088 0.000000e+00 918.0
21 TraesCS1D01G155400 chr2D 86.424 825 72 22 1 809 595530368 595531168 0.000000e+00 867.0
22 TraesCS1D01G155400 chr2D 81.776 856 105 26 4 835 177853724 177852896 0.000000e+00 669.0
23 TraesCS1D01G155400 chr2D 90.560 339 29 3 2371 2709 90603709 90604044 2.290000e-121 446.0
24 TraesCS1D01G155400 chr6A 91.814 623 39 7 214 835 30427756 30427145 0.000000e+00 857.0
25 TraesCS1D01G155400 chr6A 87.989 741 62 14 100 834 599916651 599917370 0.000000e+00 850.0
26 TraesCS1D01G155400 chr2B 84.831 857 75 26 1 843 723434986 723435801 0.000000e+00 811.0
27 TraesCS1D01G155400 chr2B 92.097 329 25 1 2374 2702 92499372 92499045 2.270000e-126 462.0
28 TraesCS1D01G155400 chr2B 90.164 122 10 2 1 120 82710278 82710399 1.200000e-34 158.0
29 TraesCS1D01G155400 chr2A 82.401 858 79 31 1 842 729572982 729573783 0.000000e+00 682.0
30 TraesCS1D01G155400 chr7D 92.097 329 24 2 2374 2702 545254128 545253802 2.270000e-126 462.0
31 TraesCS1D01G155400 chr7D 91.489 329 26 2 2374 2702 415151347 415151673 4.910000e-123 451.0
32 TraesCS1D01G155400 chr3A 91.818 330 23 4 2374 2702 522321615 522321289 1.060000e-124 457.0
33 TraesCS1D01G155400 chr3A 86.667 240 29 3 1156 1395 378305219 378305455 2.470000e-66 263.0
34 TraesCS1D01G155400 chr6D 91.541 331 26 2 2372 2702 462404739 462404411 3.800000e-124 455.0
35 TraesCS1D01G155400 chr5D 91.265 332 27 2 2374 2705 261309411 261309082 4.910000e-123 451.0
36 TraesCS1D01G155400 chr5D 97.917 48 1 0 1207 1254 564235257 564235210 2.060000e-12 84.2
37 TraesCS1D01G155400 chr5D 81.053 95 16 2 1601 1694 215256151 215256058 1.240000e-09 75.0
38 TraesCS1D01G155400 chr5B 85.507 207 22 2 1157 1363 60910160 60910358 3.270000e-50 209.0
39 TraesCS1D01G155400 chr5B 82.105 95 15 2 1601 1694 230782024 230781931 2.670000e-11 80.5


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 TraesCS1D01G155400 chr1D 218408294 218411523 3229 True 5965 5965 100.00000 1 3230 1 chr1D.!!$R2 3229
1 TraesCS1D01G155400 chr1A 280602362 280604461 2099 True 1503 2257 92.51400 832 3230 2 chr1A.!!$R2 2398
2 TraesCS1D01G155400 chr1B 312246573 312250002 3429 True 761 2204 94.79425 855 3230 4 chr1B.!!$R2 2375
3 TraesCS1D01G155400 chr3D 45553735 45554552 817 False 1277 1277 94.62400 1 835 1 chr3D.!!$F1 834
4 TraesCS1D01G155400 chr5A 666753061 666753864 803 True 1142 1142 92.27000 1 811 1 chr5A.!!$R2 810
5 TraesCS1D01G155400 chr4B 426598408 426599226 818 True 1136 1136 91.47900 1 843 1 chr4B.!!$R1 842
6 TraesCS1D01G155400 chr4A 682029253 682030084 831 False 1070 1070 89.87000 1 842 1 chr4A.!!$F1 841
7 TraesCS1D01G155400 chr2D 543453250 543454088 838 False 918 918 86.79900 1 833 1 chr2D.!!$F2 832
8 TraesCS1D01G155400 chr2D 595530368 595531168 800 False 867 867 86.42400 1 809 1 chr2D.!!$F3 808
9 TraesCS1D01G155400 chr2D 177852896 177853724 828 True 669 669 81.77600 4 835 1 chr2D.!!$R1 831
10 TraesCS1D01G155400 chr6A 30427145 30427756 611 True 857 857 91.81400 214 835 1 chr6A.!!$R1 621
11 TraesCS1D01G155400 chr6A 599916651 599917370 719 False 850 850 87.98900 100 834 1 chr6A.!!$F1 734
12 TraesCS1D01G155400 chr2B 723434986 723435801 815 False 811 811 84.83100 1 843 1 chr2B.!!$F2 842
13 TraesCS1D01G155400 chr2A 729572982 729573783 801 False 682 682 82.40100 1 842 1 chr2A.!!$F1 841

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
639 697 0.535102 CCAACACCTCACCACTCACC 60.535 60.0 0.00 0.0 0.00 4.02 F
761 827 0.730155 GTGACCGCAATGACGTACGA 60.730 55.0 24.41 0.0 0.00 3.43 F
1462 1531 0.914417 GGTCCAAGATCCTGGGGTCA 60.914 60.0 10.55 0.0 37.06 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1791 1863 0.249197 TCCGCTGCATCTCATTCTCG 60.249 55.0 0.0 0.0 0.0 4.04 R
1864 1940 0.317938 GTAGTACATCGAGCCAGCCG 60.318 60.0 0.0 0.0 0.0 5.52 R
2988 3299 0.318699 TCTCGAACAAGCCGTCTGTG 60.319 55.0 0.0 0.0 0.0 3.66 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
124 137 4.872124 ACCCGCGTAGTTTTCTTAAATAGG 59.128 41.667 4.92 0.00 0.00 2.57
313 351 6.583912 TTGAAACGTCACAAACAACAAAAA 57.416 29.167 5.17 0.00 31.90 1.94
455 494 9.897744 TTGTGAGTTTGATGTCAATTTATTCTC 57.102 29.630 0.00 0.00 35.55 2.87
496 543 6.166279 CAGTTATCTCTTAGTTTGCTGGACA 58.834 40.000 0.00 0.00 0.00 4.02
639 697 0.535102 CCAACACCTCACCACTCACC 60.535 60.000 0.00 0.00 0.00 4.02
755 821 3.747193 CAAGTTATGTGACCGCAATGAC 58.253 45.455 0.00 0.00 0.00 3.06
756 822 1.999735 AGTTATGTGACCGCAATGACG 59.000 47.619 0.00 0.00 0.00 4.35
757 823 1.730064 GTTATGTGACCGCAATGACGT 59.270 47.619 0.00 0.00 0.00 4.34
758 824 2.924926 GTTATGTGACCGCAATGACGTA 59.075 45.455 0.00 0.00 0.00 3.57
759 825 1.355971 ATGTGACCGCAATGACGTAC 58.644 50.000 0.00 0.00 0.00 3.67
760 826 1.004785 TGTGACCGCAATGACGTACG 61.005 55.000 15.01 15.01 0.00 3.67
761 827 0.730155 GTGACCGCAATGACGTACGA 60.730 55.000 24.41 0.00 0.00 3.43
789 855 7.780008 ATTTTACAACTTTTAGCACCAAACC 57.220 32.000 0.00 0.00 0.00 3.27
863 930 6.704289 AATGCAGTATTACTAGTACACCGA 57.296 37.500 0.91 0.00 0.00 4.69
1023 1092 2.932261 AGGAAGAAGAACAAAACGCCT 58.068 42.857 0.00 0.00 0.00 5.52
1024 1093 4.081322 AGGAAGAAGAACAAAACGCCTA 57.919 40.909 0.00 0.00 0.00 3.93
1120 1189 4.988598 CACGAGCCAACCGCACCT 62.989 66.667 0.00 0.00 41.38 4.00
1121 1190 4.681978 ACGAGCCAACCGCACCTC 62.682 66.667 0.00 0.00 41.38 3.85
1122 1191 4.680237 CGAGCCAACCGCACCTCA 62.680 66.667 0.00 0.00 41.38 3.86
1153 1222 4.560856 GAGCGCGAGACGATGGCT 62.561 66.667 12.10 0.00 43.08 4.75
1462 1531 0.914417 GGTCCAAGATCCTGGGGTCA 60.914 60.000 10.55 0.00 37.06 4.02
1791 1863 2.915463 CGAGTAGTTTGTGATCGGTGAC 59.085 50.000 0.00 0.00 0.00 3.67
1864 1940 2.045242 GTTTTCCCCGGAGAGGCC 60.045 66.667 0.73 0.00 39.21 5.19
2020 2096 1.139654 GATCTGCCATCACCAGCACTA 59.860 52.381 0.00 0.00 34.68 2.74
2027 2103 3.243569 GCCATCACCAGCACTAGTACTAG 60.244 52.174 25.30 25.30 39.04 2.57
2030 2106 5.008811 CCATCACCAGCACTAGTACTAGTAC 59.991 48.000 30.34 25.67 43.98 2.73
2353 2462 4.990257 TCGCATTAACTAGTTAGTTCGCT 58.010 39.130 19.95 0.00 44.77 4.93
2371 2480 2.093625 CGCTCGCATACTTAACTGCAAA 59.906 45.455 0.00 0.00 38.30 3.68
2372 2481 3.674423 GCTCGCATACTTAACTGCAAAG 58.326 45.455 0.00 0.00 38.30 2.77
2373 2482 3.125316 GCTCGCATACTTAACTGCAAAGT 59.875 43.478 7.39 7.39 40.25 2.66
2374 2483 4.328983 GCTCGCATACTTAACTGCAAAGTA 59.671 41.667 10.98 10.98 42.10 2.24
2375 2484 5.724223 GCTCGCATACTTAACTGCAAAGTAC 60.724 44.000 10.84 0.97 41.05 2.73
2376 2485 5.475719 TCGCATACTTAACTGCAAAGTACT 58.524 37.500 10.84 0.00 41.05 2.73
2377 2486 5.575606 TCGCATACTTAACTGCAAAGTACTC 59.424 40.000 10.84 6.05 41.05 2.59
2378 2487 5.220416 CGCATACTTAACTGCAAAGTACTCC 60.220 44.000 10.84 3.52 41.05 3.85
2379 2488 5.064834 GCATACTTAACTGCAAAGTACTCCC 59.935 44.000 10.84 0.00 41.05 4.30
2380 2489 4.976540 ACTTAACTGCAAAGTACTCCCT 57.023 40.909 0.00 0.00 35.44 4.20
2381 2490 4.895961 ACTTAACTGCAAAGTACTCCCTC 58.104 43.478 0.00 0.00 35.44 4.30
2382 2491 2.861147 AACTGCAAAGTACTCCCTCC 57.139 50.000 0.00 0.00 0.00 4.30
2383 2492 2.031495 ACTGCAAAGTACTCCCTCCT 57.969 50.000 0.00 0.00 0.00 3.69
2384 2493 2.339769 ACTGCAAAGTACTCCCTCCTT 58.660 47.619 0.00 0.00 0.00 3.36
2385 2494 2.711547 ACTGCAAAGTACTCCCTCCTTT 59.288 45.455 0.00 0.00 0.00 3.11
2386 2495 3.244596 ACTGCAAAGTACTCCCTCCTTTC 60.245 47.826 0.00 0.00 0.00 2.62
2387 2496 2.039879 TGCAAAGTACTCCCTCCTTTCC 59.960 50.000 0.00 0.00 0.00 3.13
2388 2497 2.935676 GCAAAGTACTCCCTCCTTTCCG 60.936 54.545 0.00 0.00 0.00 4.30
2389 2498 1.569653 AAGTACTCCCTCCTTTCCGG 58.430 55.000 0.00 0.00 0.00 5.14
2390 2499 0.412640 AGTACTCCCTCCTTTCCGGT 59.587 55.000 0.00 0.00 0.00 5.28
2391 2500 1.203275 AGTACTCCCTCCTTTCCGGTT 60.203 52.381 0.00 0.00 0.00 4.44
2392 2501 1.627329 GTACTCCCTCCTTTCCGGTTT 59.373 52.381 0.00 0.00 0.00 3.27
2393 2502 2.034436 ACTCCCTCCTTTCCGGTTTA 57.966 50.000 0.00 0.00 0.00 2.01
2394 2503 2.558974 ACTCCCTCCTTTCCGGTTTAT 58.441 47.619 0.00 0.00 0.00 1.40
2395 2504 3.727948 ACTCCCTCCTTTCCGGTTTATA 58.272 45.455 0.00 0.00 0.00 0.98
2396 2505 3.710165 ACTCCCTCCTTTCCGGTTTATAG 59.290 47.826 0.00 0.00 0.00 1.31
2397 2506 3.043418 TCCCTCCTTTCCGGTTTATAGG 58.957 50.000 0.00 4.62 0.00 2.57
2398 2507 2.105993 CCCTCCTTTCCGGTTTATAGGG 59.894 54.545 16.03 16.03 36.05 3.53
2399 2508 2.486727 CCTCCTTTCCGGTTTATAGGGC 60.487 54.545 0.00 0.00 0.00 5.19
2400 2509 2.438392 CTCCTTTCCGGTTTATAGGGCT 59.562 50.000 0.00 0.00 0.00 5.19
2401 2510 2.848071 TCCTTTCCGGTTTATAGGGCTT 59.152 45.455 0.00 0.00 0.00 4.35
2402 2511 4.039339 TCCTTTCCGGTTTATAGGGCTTA 58.961 43.478 0.00 0.00 0.00 3.09
2403 2512 4.661709 TCCTTTCCGGTTTATAGGGCTTAT 59.338 41.667 0.00 0.00 0.00 1.73
2404 2513 5.001874 CCTTTCCGGTTTATAGGGCTTATC 58.998 45.833 0.00 0.00 0.00 1.75
2405 2514 5.221864 CCTTTCCGGTTTATAGGGCTTATCT 60.222 44.000 0.00 0.00 0.00 1.98
2406 2515 5.899631 TTCCGGTTTATAGGGCTTATCTT 57.100 39.130 0.00 0.00 0.00 2.40
2407 2516 6.999705 TTCCGGTTTATAGGGCTTATCTTA 57.000 37.500 0.00 0.00 0.00 2.10
2408 2517 6.999705 TCCGGTTTATAGGGCTTATCTTAA 57.000 37.500 0.00 0.00 0.00 1.85
2409 2518 7.377696 TCCGGTTTATAGGGCTTATCTTAAA 57.622 36.000 0.00 0.00 0.00 1.52
2410 2519 7.804147 TCCGGTTTATAGGGCTTATCTTAAAA 58.196 34.615 0.00 0.00 0.00 1.52
2411 2520 8.442374 TCCGGTTTATAGGGCTTATCTTAAAAT 58.558 33.333 0.00 0.00 0.00 1.82
2412 2521 8.727910 CCGGTTTATAGGGCTTATCTTAAAATC 58.272 37.037 0.00 0.00 0.00 2.17
2413 2522 8.727910 CGGTTTATAGGGCTTATCTTAAAATCC 58.272 37.037 0.00 0.00 0.00 3.01
2414 2523 9.809395 GGTTTATAGGGCTTATCTTAAAATCCT 57.191 33.333 0.00 0.00 0.00 3.24
2421 2530 9.769677 AGGGCTTATCTTAAAATCCTAGTTTTT 57.230 29.630 6.07 6.07 33.62 1.94
2458 2567 8.519799 AGACTTAATTTGGTTGTTCTTCTTCA 57.480 30.769 0.00 0.00 0.00 3.02
2459 2568 8.406297 AGACTTAATTTGGTTGTTCTTCTTCAC 58.594 33.333 0.00 0.00 0.00 3.18
2460 2569 8.062065 ACTTAATTTGGTTGTTCTTCTTCACA 57.938 30.769 0.00 0.00 0.00 3.58
2461 2570 8.527810 ACTTAATTTGGTTGTTCTTCTTCACAA 58.472 29.630 0.00 0.00 0.00 3.33
2462 2571 8.925161 TTAATTTGGTTGTTCTTCTTCACAAG 57.075 30.769 0.00 0.00 33.55 3.16
2463 2572 5.975693 TTTGGTTGTTCTTCTTCACAAGT 57.024 34.783 0.00 0.00 33.55 3.16
2464 2573 5.975693 TTGGTTGTTCTTCTTCACAAGTT 57.024 34.783 0.00 0.00 33.55 2.66
2465 2574 5.560966 TGGTTGTTCTTCTTCACAAGTTC 57.439 39.130 0.00 0.00 33.55 3.01
2466 2575 5.007034 TGGTTGTTCTTCTTCACAAGTTCA 58.993 37.500 0.00 0.00 33.55 3.18
2467 2576 5.123820 TGGTTGTTCTTCTTCACAAGTTCAG 59.876 40.000 0.00 0.00 33.55 3.02
2468 2577 5.354234 GGTTGTTCTTCTTCACAAGTTCAGA 59.646 40.000 0.00 0.00 33.55 3.27
2469 2578 6.038714 GGTTGTTCTTCTTCACAAGTTCAGAT 59.961 38.462 0.00 0.00 33.55 2.90
2470 2579 7.415653 GGTTGTTCTTCTTCACAAGTTCAGATT 60.416 37.037 0.00 0.00 33.55 2.40
2471 2580 7.630242 TGTTCTTCTTCACAAGTTCAGATTT 57.370 32.000 0.00 0.00 0.00 2.17
2472 2581 7.697691 TGTTCTTCTTCACAAGTTCAGATTTC 58.302 34.615 0.00 0.00 0.00 2.17
2473 2582 7.336679 TGTTCTTCTTCACAAGTTCAGATTTCA 59.663 33.333 0.00 0.00 0.00 2.69
2474 2583 7.864108 TCTTCTTCACAAGTTCAGATTTCAA 57.136 32.000 0.00 0.00 0.00 2.69
2475 2584 7.923888 TCTTCTTCACAAGTTCAGATTTCAAG 58.076 34.615 0.00 0.00 0.00 3.02
2476 2585 6.624352 TCTTCACAAGTTCAGATTTCAAGG 57.376 37.500 0.00 0.00 0.00 3.61
2477 2586 6.122277 TCTTCACAAGTTCAGATTTCAAGGT 58.878 36.000 0.00 0.00 0.00 3.50
2478 2587 5.756195 TCACAAGTTCAGATTTCAAGGTG 57.244 39.130 0.00 0.00 0.00 4.00
2479 2588 4.036734 TCACAAGTTCAGATTTCAAGGTGC 59.963 41.667 0.00 0.00 0.00 5.01
2480 2589 3.953612 ACAAGTTCAGATTTCAAGGTGCA 59.046 39.130 0.00 0.00 0.00 4.57
2481 2590 4.202050 ACAAGTTCAGATTTCAAGGTGCAC 60.202 41.667 8.80 8.80 0.00 4.57
2482 2591 3.825328 AGTTCAGATTTCAAGGTGCACT 58.175 40.909 17.98 0.00 0.00 4.40
2483 2592 4.973168 AGTTCAGATTTCAAGGTGCACTA 58.027 39.130 17.98 0.00 0.00 2.74
2484 2593 5.376625 AGTTCAGATTTCAAGGTGCACTAA 58.623 37.500 17.98 3.68 0.00 2.24
2485 2594 5.471456 AGTTCAGATTTCAAGGTGCACTAAG 59.529 40.000 17.98 6.71 0.00 2.18
2486 2595 4.973168 TCAGATTTCAAGGTGCACTAAGT 58.027 39.130 17.98 3.38 0.00 2.24
2487 2596 6.109156 TCAGATTTCAAGGTGCACTAAGTA 57.891 37.500 17.98 0.00 0.00 2.24
2488 2597 6.530120 TCAGATTTCAAGGTGCACTAAGTAA 58.470 36.000 17.98 6.74 0.00 2.24
2489 2598 7.168219 TCAGATTTCAAGGTGCACTAAGTAAT 58.832 34.615 17.98 11.15 0.00 1.89
2490 2599 7.665559 TCAGATTTCAAGGTGCACTAAGTAATT 59.334 33.333 17.98 2.28 0.00 1.40
2491 2600 7.752239 CAGATTTCAAGGTGCACTAAGTAATTG 59.248 37.037 17.98 10.23 0.00 2.32
2492 2601 5.371115 TTCAAGGTGCACTAAGTAATTGC 57.629 39.130 17.98 0.00 36.76 3.56
2493 2602 4.393834 TCAAGGTGCACTAAGTAATTGCA 58.606 39.130 17.98 0.00 43.89 4.08
2498 2607 4.780275 TGCACTAAGTAATTGCATGCAA 57.220 36.364 33.57 33.57 41.29 4.08
2499 2608 4.735985 TGCACTAAGTAATTGCATGCAAG 58.264 39.130 34.15 22.50 41.29 4.01
2500 2609 4.218200 TGCACTAAGTAATTGCATGCAAGT 59.782 37.500 34.15 33.44 41.29 3.16
2501 2610 5.414144 TGCACTAAGTAATTGCATGCAAGTA 59.586 36.000 34.15 32.38 41.29 2.24
2502 2611 6.095300 TGCACTAAGTAATTGCATGCAAGTAT 59.905 34.615 34.82 25.09 41.29 2.12
2503 2612 6.974622 GCACTAAGTAATTGCATGCAAGTATT 59.025 34.615 34.82 29.70 38.46 1.89
2504 2613 8.128582 GCACTAAGTAATTGCATGCAAGTATTA 58.871 33.333 34.82 28.55 38.46 0.98
2531 2640 9.715121 AAAAGAAAATTGATCAATGCATGTACT 57.285 25.926 21.39 10.93 0.00 2.73
2532 2641 9.715121 AAAGAAAATTGATCAATGCATGTACTT 57.285 25.926 21.39 15.21 0.00 2.24
2533 2642 9.715121 AAGAAAATTGATCAATGCATGTACTTT 57.285 25.926 21.39 14.42 0.00 2.66
2565 2674 7.485418 CATGCATTGCAATTAATACATTGGT 57.515 32.000 16.46 0.00 43.62 3.67
2566 2675 8.590719 CATGCATTGCAATTAATACATTGGTA 57.409 30.769 16.46 0.00 43.62 3.25
2567 2676 9.043079 CATGCATTGCAATTAATACATTGGTAA 57.957 29.630 16.46 0.00 43.62 2.85
2568 2677 9.610705 ATGCATTGCAATTAATACATTGGTAAA 57.389 25.926 16.46 0.00 43.62 2.01
2569 2678 8.877779 TGCATTGCAATTAATACATTGGTAAAC 58.122 29.630 9.83 0.00 34.76 2.01
2570 2679 8.877779 GCATTGCAATTAATACATTGGTAAACA 58.122 29.630 9.83 0.00 35.07 2.83
2632 2741 9.381027 GCTTTTGCAAATTACAAAAAGTATTCC 57.619 29.630 13.65 0.00 44.07 3.01
2635 2744 7.954788 TGCAAATTACAAAAAGTATTCCACC 57.045 32.000 0.00 0.00 31.53 4.61
2636 2745 7.500992 TGCAAATTACAAAAAGTATTCCACCA 58.499 30.769 0.00 0.00 31.53 4.17
2637 2746 7.439655 TGCAAATTACAAAAAGTATTCCACCAC 59.560 33.333 0.00 0.00 31.53 4.16
2638 2747 7.655732 GCAAATTACAAAAAGTATTCCACCACT 59.344 33.333 0.00 0.00 31.53 4.00
2639 2748 9.191995 CAAATTACAAAAAGTATTCCACCACTC 57.808 33.333 0.00 0.00 31.53 3.51
2640 2749 8.472007 AATTACAAAAAGTATTCCACCACTCA 57.528 30.769 0.00 0.00 31.53 3.41
2641 2750 8.650143 ATTACAAAAAGTATTCCACCACTCAT 57.350 30.769 0.00 0.00 31.53 2.90
2642 2751 6.575162 ACAAAAAGTATTCCACCACTCATC 57.425 37.500 0.00 0.00 0.00 2.92
2643 2752 6.068010 ACAAAAAGTATTCCACCACTCATCA 58.932 36.000 0.00 0.00 0.00 3.07
2644 2753 6.721208 ACAAAAAGTATTCCACCACTCATCAT 59.279 34.615 0.00 0.00 0.00 2.45
2645 2754 7.094205 ACAAAAAGTATTCCACCACTCATCATC 60.094 37.037 0.00 0.00 0.00 2.92
2646 2755 5.965033 AAGTATTCCACCACTCATCATCT 57.035 39.130 0.00 0.00 0.00 2.90
2647 2756 7.437713 AAAGTATTCCACCACTCATCATCTA 57.562 36.000 0.00 0.00 0.00 1.98
2648 2757 6.412362 AGTATTCCACCACTCATCATCTAC 57.588 41.667 0.00 0.00 0.00 2.59
2649 2758 4.696479 ATTCCACCACTCATCATCTACC 57.304 45.455 0.00 0.00 0.00 3.18
2650 2759 3.404869 TCCACCACTCATCATCTACCT 57.595 47.619 0.00 0.00 0.00 3.08
2651 2760 3.724478 TCCACCACTCATCATCTACCTT 58.276 45.455 0.00 0.00 0.00 3.50
2652 2761 3.452264 TCCACCACTCATCATCTACCTTG 59.548 47.826 0.00 0.00 0.00 3.61
2653 2762 3.452264 CCACCACTCATCATCTACCTTGA 59.548 47.826 0.00 0.00 0.00 3.02
2654 2763 4.102210 CCACCACTCATCATCTACCTTGAT 59.898 45.833 0.00 0.00 34.15 2.57
2655 2764 5.397221 CCACCACTCATCATCTACCTTGATT 60.397 44.000 0.00 0.00 31.50 2.57
2656 2765 5.526479 CACCACTCATCATCTACCTTGATTG 59.474 44.000 0.00 0.00 31.50 2.67
2657 2766 5.061853 CCACTCATCATCTACCTTGATTGG 58.938 45.833 0.00 0.00 34.10 3.16
2658 2767 5.397221 CCACTCATCATCTACCTTGATTGGT 60.397 44.000 0.00 0.00 43.66 3.67
2659 2768 5.526479 CACTCATCATCTACCTTGATTGGTG 59.474 44.000 0.00 0.00 41.05 4.17
2660 2769 5.426509 ACTCATCATCTACCTTGATTGGTGA 59.573 40.000 0.00 0.00 41.05 4.02
2661 2770 5.922053 TCATCATCTACCTTGATTGGTGAG 58.078 41.667 0.00 0.00 41.05 3.51
2662 2771 5.662657 TCATCATCTACCTTGATTGGTGAGA 59.337 40.000 0.00 0.00 41.05 3.27
2663 2772 6.328410 TCATCATCTACCTTGATTGGTGAGAT 59.672 38.462 0.00 0.00 41.05 2.75
2664 2773 6.566079 TCATCTACCTTGATTGGTGAGATT 57.434 37.500 0.00 0.00 41.05 2.40
2665 2774 6.962182 TCATCTACCTTGATTGGTGAGATTT 58.038 36.000 0.00 0.00 41.05 2.17
2666 2775 7.405292 TCATCTACCTTGATTGGTGAGATTTT 58.595 34.615 0.00 0.00 41.05 1.82
2667 2776 7.890127 TCATCTACCTTGATTGGTGAGATTTTT 59.110 33.333 0.00 0.00 41.05 1.94
2668 2777 7.452880 TCTACCTTGATTGGTGAGATTTTTG 57.547 36.000 0.00 0.00 41.05 2.44
2669 2778 7.230747 TCTACCTTGATTGGTGAGATTTTTGA 58.769 34.615 0.00 0.00 41.05 2.69
2670 2779 6.729690 ACCTTGATTGGTGAGATTTTTGAA 57.270 33.333 0.00 0.00 39.17 2.69
2671 2780 7.307131 ACCTTGATTGGTGAGATTTTTGAAT 57.693 32.000 0.00 0.00 39.17 2.57
2672 2781 7.738847 ACCTTGATTGGTGAGATTTTTGAATT 58.261 30.769 0.00 0.00 39.17 2.17
2673 2782 7.658575 ACCTTGATTGGTGAGATTTTTGAATTG 59.341 33.333 0.00 0.00 39.17 2.32
2674 2783 7.874016 CCTTGATTGGTGAGATTTTTGAATTGA 59.126 33.333 0.00 0.00 0.00 2.57
2675 2784 8.821147 TTGATTGGTGAGATTTTTGAATTGAG 57.179 30.769 0.00 0.00 0.00 3.02
2676 2785 6.869913 TGATTGGTGAGATTTTTGAATTGAGC 59.130 34.615 0.00 0.00 0.00 4.26
2677 2786 5.138125 TGGTGAGATTTTTGAATTGAGCC 57.862 39.130 0.00 0.00 0.00 4.70
2678 2787 4.021192 TGGTGAGATTTTTGAATTGAGCCC 60.021 41.667 0.00 0.00 0.00 5.19
2679 2788 4.221482 GGTGAGATTTTTGAATTGAGCCCT 59.779 41.667 0.00 0.00 0.00 5.19
2680 2789 5.418840 GGTGAGATTTTTGAATTGAGCCCTA 59.581 40.000 0.00 0.00 0.00 3.53
2681 2790 6.097412 GGTGAGATTTTTGAATTGAGCCCTAT 59.903 38.462 0.00 0.00 0.00 2.57
2682 2791 7.285401 GGTGAGATTTTTGAATTGAGCCCTATA 59.715 37.037 0.00 0.00 0.00 1.31
2683 2792 8.686334 GTGAGATTTTTGAATTGAGCCCTATAA 58.314 33.333 0.00 0.00 0.00 0.98
2684 2793 9.253832 TGAGATTTTTGAATTGAGCCCTATAAA 57.746 29.630 0.00 0.00 0.00 1.40
2685 2794 9.521503 GAGATTTTTGAATTGAGCCCTATAAAC 57.478 33.333 0.00 0.00 0.00 2.01
2686 2795 8.478066 AGATTTTTGAATTGAGCCCTATAAACC 58.522 33.333 0.00 0.00 0.00 3.27
2687 2796 5.828299 TTTGAATTGAGCCCTATAAACCG 57.172 39.130 0.00 0.00 0.00 4.44
2688 2797 4.764050 TGAATTGAGCCCTATAAACCGA 57.236 40.909 0.00 0.00 0.00 4.69
2689 2798 5.105567 TGAATTGAGCCCTATAAACCGAA 57.894 39.130 0.00 0.00 0.00 4.30
2690 2799 5.502079 TGAATTGAGCCCTATAAACCGAAA 58.498 37.500 0.00 0.00 0.00 3.46
2691 2800 5.946972 TGAATTGAGCCCTATAAACCGAAAA 59.053 36.000 0.00 0.00 0.00 2.29
2692 2801 6.094881 TGAATTGAGCCCTATAAACCGAAAAG 59.905 38.462 0.00 0.00 0.00 2.27
2694 2803 3.520317 TGAGCCCTATAAACCGAAAAGGA 59.480 43.478 0.00 0.00 45.00 3.36
2695 2804 4.127907 GAGCCCTATAAACCGAAAAGGAG 58.872 47.826 0.00 0.00 45.00 3.69
2696 2805 3.118000 AGCCCTATAAACCGAAAAGGAGG 60.118 47.826 0.00 0.00 45.00 4.30
2697 2806 3.816994 CCCTATAAACCGAAAAGGAGGG 58.183 50.000 0.00 0.00 45.00 4.30
2832 2944 2.890945 TCACGACTGATGAAGACTCCAA 59.109 45.455 0.00 0.00 0.00 3.53
2847 2959 2.901839 ACTCCAAAGAAAGCTACCGGTA 59.098 45.455 14.95 14.95 0.00 4.02
2848 2960 3.325716 ACTCCAAAGAAAGCTACCGGTAA 59.674 43.478 16.65 0.00 0.00 2.85
2932 3241 1.655484 TGCAGCATGTATCACTTCGG 58.345 50.000 0.00 0.00 39.31 4.30
2962 3271 5.012239 TGCTGGCTCACATTTCTTCTAATT 58.988 37.500 0.00 0.00 0.00 1.40
2970 3279 3.694566 ACATTTCTTCTAATTGACCGCCC 59.305 43.478 0.00 0.00 0.00 6.13
2998 3309 2.158957 TCTTTTGAGAACACAGACGGCT 60.159 45.455 0.00 0.00 0.00 5.52
3041 3352 8.417106 TCAGTGCTAGATAGACTAATTTTGGAG 58.583 37.037 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 45 4.512657 GAATCATTCTGTTTGAGCGATCG 58.487 43.478 11.69 11.69 0.00 3.69
124 137 9.472995 CGTGTGTATGTTGTTATTAATCTTGTC 57.527 33.333 0.00 0.00 0.00 3.18
378 417 3.576550 TCAGCCCAACAAAGGAATAAACC 59.423 43.478 0.00 0.00 0.00 3.27
455 494 2.202623 GCACTAGCCACTCGACCG 60.203 66.667 0.00 0.00 33.58 4.79
496 543 1.049289 GCCAGGGGACTAGAACGGAT 61.049 60.000 0.00 0.00 40.21 4.18
756 822 8.213812 TGCTAAAAGTTGTAAAATACGTCGTAC 58.786 33.333 7.36 0.00 0.00 3.67
757 823 8.213812 GTGCTAAAAGTTGTAAAATACGTCGTA 58.786 33.333 7.69 7.69 0.00 3.43
758 824 7.065283 GTGCTAAAAGTTGTAAAATACGTCGT 58.935 34.615 2.21 2.21 0.00 4.34
759 825 6.517374 GGTGCTAAAAGTTGTAAAATACGTCG 59.483 38.462 0.00 0.00 0.00 5.12
760 826 7.354257 TGGTGCTAAAAGTTGTAAAATACGTC 58.646 34.615 0.00 0.00 0.00 4.34
761 827 7.261829 TGGTGCTAAAAGTTGTAAAATACGT 57.738 32.000 0.00 0.00 0.00 3.57
789 855 8.929746 AGTCATATAACTTGCATATGATGTTCG 58.070 33.333 6.97 0.00 43.63 3.95
843 910 5.490139 TGTCGGTGTACTAGTAATACTGC 57.510 43.478 16.90 13.68 0.00 4.40
844 911 5.065602 TGCTGTCGGTGTACTAGTAATACTG 59.934 44.000 16.08 16.08 0.00 2.74
845 912 5.188434 TGCTGTCGGTGTACTAGTAATACT 58.812 41.667 3.61 0.00 0.00 2.12
846 913 5.490139 TGCTGTCGGTGTACTAGTAATAC 57.510 43.478 3.61 7.05 0.00 1.89
847 914 5.447683 CGTTGCTGTCGGTGTACTAGTAATA 60.448 44.000 3.61 0.00 0.00 0.98
848 915 4.673580 CGTTGCTGTCGGTGTACTAGTAAT 60.674 45.833 3.61 0.00 0.00 1.89
849 916 3.365264 CGTTGCTGTCGGTGTACTAGTAA 60.365 47.826 3.61 0.00 0.00 2.24
863 930 2.029288 CGTCTGCCATCGTTGCTGT 61.029 57.895 0.00 0.00 0.00 4.40
1023 1092 2.728690 AAGTGTATGTGAACCGCGTA 57.271 45.000 4.92 0.00 0.00 4.42
1024 1093 1.873698 AAAGTGTATGTGAACCGCGT 58.126 45.000 4.92 0.00 0.00 6.01
1087 1156 4.458829 TGATCCGGCGGAGGAGGT 62.459 66.667 33.82 17.34 44.55 3.85
1121 1190 4.530857 CTCTTACCCCGCCGGCTG 62.531 72.222 26.68 19.17 33.26 4.85
1331 1400 2.283966 CCTGGAGGGAGTGGACGT 60.284 66.667 0.00 0.00 37.23 4.34
1721 1791 1.876714 CGTAAGGGCACGGACGATG 60.877 63.158 9.78 0.00 38.26 3.84
1731 1801 6.619801 ACTCATCAAATTAATCGTAAGGGC 57.380 37.500 0.00 0.00 38.47 5.19
1791 1863 0.249197 TCCGCTGCATCTCATTCTCG 60.249 55.000 0.00 0.00 0.00 4.04
1864 1940 0.317938 GTAGTACATCGAGCCAGCCG 60.318 60.000 0.00 0.00 0.00 5.52
2027 2103 7.652507 GGTGGCAGATCATTTTAGTACTAGTAC 59.347 40.741 23.03 23.03 36.35 2.73
2030 2106 6.703607 CAGGTGGCAGATCATTTTAGTACTAG 59.296 42.308 2.23 0.00 0.00 2.57
2033 2109 4.035675 GCAGGTGGCAGATCATTTTAGTAC 59.964 45.833 0.00 0.00 43.97 2.73
2353 2462 5.475719 AGTACTTTGCAGTTAAGTATGCGA 58.524 37.500 11.59 0.00 45.54 5.10
2371 2480 0.412640 ACCGGAAAGGAGGGAGTACT 59.587 55.000 9.46 0.00 45.00 2.73
2372 2481 1.273759 AACCGGAAAGGAGGGAGTAC 58.726 55.000 9.46 0.00 45.00 2.73
2373 2482 2.034436 AAACCGGAAAGGAGGGAGTA 57.966 50.000 9.46 0.00 45.00 2.59
2374 2483 2.034436 TAAACCGGAAAGGAGGGAGT 57.966 50.000 9.46 0.00 45.00 3.85
2375 2484 3.071167 CCTATAAACCGGAAAGGAGGGAG 59.929 52.174 9.46 0.00 45.00 4.30
2376 2485 3.043418 CCTATAAACCGGAAAGGAGGGA 58.957 50.000 9.46 0.00 45.00 4.20
2377 2486 2.105993 CCCTATAAACCGGAAAGGAGGG 59.894 54.545 9.46 14.71 45.00 4.30
2378 2487 2.486727 GCCCTATAAACCGGAAAGGAGG 60.487 54.545 9.46 9.03 45.00 4.30
2379 2488 2.438392 AGCCCTATAAACCGGAAAGGAG 59.562 50.000 9.46 0.00 45.00 3.69
2380 2489 2.484602 AGCCCTATAAACCGGAAAGGA 58.515 47.619 9.46 0.00 45.00 3.36
2382 2491 5.866207 AGATAAGCCCTATAAACCGGAAAG 58.134 41.667 9.46 0.00 0.00 2.62
2383 2492 5.899631 AGATAAGCCCTATAAACCGGAAA 57.100 39.130 9.46 0.00 0.00 3.13
2384 2493 5.899631 AAGATAAGCCCTATAAACCGGAA 57.100 39.130 9.46 0.00 0.00 4.30
2385 2494 6.999705 TTAAGATAAGCCCTATAAACCGGA 57.000 37.500 9.46 0.00 0.00 5.14
2386 2495 8.631480 ATTTTAAGATAAGCCCTATAAACCGG 57.369 34.615 0.00 0.00 0.00 5.28
2387 2496 8.727910 GGATTTTAAGATAAGCCCTATAAACCG 58.272 37.037 0.00 0.00 0.00 4.44
2388 2497 9.809395 AGGATTTTAAGATAAGCCCTATAAACC 57.191 33.333 0.00 0.00 31.45 3.27
2395 2504 9.769677 AAAAACTAGGATTTTAAGATAAGCCCT 57.230 29.630 6.70 0.00 31.45 5.19
2432 2541 8.966868 TGAAGAAGAACAACCAAATTAAGTCTT 58.033 29.630 0.00 0.00 0.00 3.01
2433 2542 8.406297 GTGAAGAAGAACAACCAAATTAAGTCT 58.594 33.333 0.00 0.00 0.00 3.24
2434 2543 8.188139 TGTGAAGAAGAACAACCAAATTAAGTC 58.812 33.333 0.00 0.00 0.00 3.01
2435 2544 8.062065 TGTGAAGAAGAACAACCAAATTAAGT 57.938 30.769 0.00 0.00 0.00 2.24
2436 2545 8.925161 TTGTGAAGAAGAACAACCAAATTAAG 57.075 30.769 0.00 0.00 31.52 1.85
2437 2546 8.527810 ACTTGTGAAGAAGAACAACCAAATTAA 58.472 29.630 0.00 0.00 32.98 1.40
2438 2547 8.062065 ACTTGTGAAGAAGAACAACCAAATTA 57.938 30.769 0.00 0.00 32.98 1.40
2439 2548 6.935167 ACTTGTGAAGAAGAACAACCAAATT 58.065 32.000 0.00 0.00 32.98 1.82
2440 2549 6.530019 ACTTGTGAAGAAGAACAACCAAAT 57.470 33.333 0.00 0.00 32.98 2.32
2441 2550 5.975693 ACTTGTGAAGAAGAACAACCAAA 57.024 34.783 0.00 0.00 32.98 3.28
2442 2551 5.475220 TGAACTTGTGAAGAAGAACAACCAA 59.525 36.000 0.00 0.00 32.98 3.67
2443 2552 5.007034 TGAACTTGTGAAGAAGAACAACCA 58.993 37.500 0.00 0.00 32.98 3.67
2444 2553 5.354234 TCTGAACTTGTGAAGAAGAACAACC 59.646 40.000 0.00 0.00 32.98 3.77
2445 2554 6.422776 TCTGAACTTGTGAAGAAGAACAAC 57.577 37.500 0.00 0.00 32.98 3.32
2446 2555 7.630242 AATCTGAACTTGTGAAGAAGAACAA 57.370 32.000 0.00 0.00 35.14 2.83
2447 2556 7.336679 TGAAATCTGAACTTGTGAAGAAGAACA 59.663 33.333 0.00 0.00 0.00 3.18
2448 2557 7.697691 TGAAATCTGAACTTGTGAAGAAGAAC 58.302 34.615 0.00 0.00 0.00 3.01
2449 2558 7.864108 TGAAATCTGAACTTGTGAAGAAGAA 57.136 32.000 0.00 0.00 0.00 2.52
2450 2559 7.012704 CCTTGAAATCTGAACTTGTGAAGAAGA 59.987 37.037 0.00 0.00 0.00 2.87
2451 2560 7.137426 CCTTGAAATCTGAACTTGTGAAGAAG 58.863 38.462 0.00 0.00 0.00 2.85
2452 2561 6.603201 ACCTTGAAATCTGAACTTGTGAAGAA 59.397 34.615 0.00 0.00 0.00 2.52
2453 2562 6.038603 CACCTTGAAATCTGAACTTGTGAAGA 59.961 38.462 0.00 0.00 0.00 2.87
2454 2563 6.204359 CACCTTGAAATCTGAACTTGTGAAG 58.796 40.000 0.00 0.00 0.00 3.02
2455 2564 5.450412 GCACCTTGAAATCTGAACTTGTGAA 60.450 40.000 0.00 0.00 0.00 3.18
2456 2565 4.036734 GCACCTTGAAATCTGAACTTGTGA 59.963 41.667 0.00 0.00 0.00 3.58
2457 2566 4.202040 TGCACCTTGAAATCTGAACTTGTG 60.202 41.667 0.00 0.00 0.00 3.33
2458 2567 3.953612 TGCACCTTGAAATCTGAACTTGT 59.046 39.130 0.00 0.00 0.00 3.16
2459 2568 4.037208 AGTGCACCTTGAAATCTGAACTTG 59.963 41.667 14.63 0.00 0.00 3.16
2460 2569 4.210331 AGTGCACCTTGAAATCTGAACTT 58.790 39.130 14.63 0.00 0.00 2.66
2461 2570 3.825328 AGTGCACCTTGAAATCTGAACT 58.175 40.909 14.63 0.00 0.00 3.01
2462 2571 5.239525 ACTTAGTGCACCTTGAAATCTGAAC 59.760 40.000 14.63 0.00 0.00 3.18
2463 2572 5.376625 ACTTAGTGCACCTTGAAATCTGAA 58.623 37.500 14.63 0.00 0.00 3.02
2464 2573 4.973168 ACTTAGTGCACCTTGAAATCTGA 58.027 39.130 14.63 0.00 0.00 3.27
2465 2574 6.801539 TTACTTAGTGCACCTTGAAATCTG 57.198 37.500 14.63 0.00 0.00 2.90
2466 2575 7.575720 GCAATTACTTAGTGCACCTTGAAATCT 60.576 37.037 14.63 0.00 38.19 2.40
2467 2576 6.528072 GCAATTACTTAGTGCACCTTGAAATC 59.472 38.462 14.63 0.00 38.19 2.17
2468 2577 6.015519 TGCAATTACTTAGTGCACCTTGAAAT 60.016 34.615 14.63 5.89 43.09 2.17
2469 2578 5.300539 TGCAATTACTTAGTGCACCTTGAAA 59.699 36.000 14.63 3.52 43.09 2.69
2470 2579 4.824537 TGCAATTACTTAGTGCACCTTGAA 59.175 37.500 14.63 2.10 43.09 2.69
2471 2580 4.393834 TGCAATTACTTAGTGCACCTTGA 58.606 39.130 14.63 0.00 43.09 3.02
2472 2581 4.764679 TGCAATTACTTAGTGCACCTTG 57.235 40.909 14.63 6.12 43.09 3.61
2478 2587 4.737054 ACTTGCATGCAATTACTTAGTGC 58.263 39.130 31.96 0.00 38.78 4.40
2505 2614 9.715121 AGTACATGCATTGATCAATTTTCTTTT 57.285 25.926 18.41 3.13 0.00 2.27
2506 2615 9.715121 AAGTACATGCATTGATCAATTTTCTTT 57.285 25.926 18.41 4.62 0.00 2.52
2507 2616 9.715121 AAAGTACATGCATTGATCAATTTTCTT 57.285 25.926 18.41 12.15 0.00 2.52
2511 2620 9.037737 GCATAAAGTACATGCATTGATCAATTT 57.962 29.630 18.41 10.08 46.47 1.82
2512 2621 8.583810 GCATAAAGTACATGCATTGATCAATT 57.416 30.769 18.41 6.51 46.47 2.32
2541 2650 7.485418 ACCAATGTATTAATTGCAATGCATG 57.515 32.000 13.82 0.00 39.41 4.06
2542 2651 9.610705 TTTACCAATGTATTAATTGCAATGCAT 57.389 25.926 13.82 10.48 41.27 3.96
2543 2652 8.877779 GTTTACCAATGTATTAATTGCAATGCA 58.122 29.630 13.82 2.72 36.42 3.96
2544 2653 8.877779 TGTTTACCAATGTATTAATTGCAATGC 58.122 29.630 13.82 0.00 36.42 3.56
2605 2714 9.928236 GAATACTTTTTGTAATTTGCAAAAGCA 57.072 25.926 17.19 12.17 43.70 3.91
2606 2715 9.381027 GGAATACTTTTTGTAATTTGCAAAAGC 57.619 29.630 17.19 9.70 43.70 3.51
2609 2718 8.831550 GGTGGAATACTTTTTGTAATTTGCAAA 58.168 29.630 15.44 15.44 34.45 3.68
2610 2719 7.987458 TGGTGGAATACTTTTTGTAATTTGCAA 59.013 29.630 0.00 0.00 34.45 4.08
2611 2720 7.439655 GTGGTGGAATACTTTTTGTAATTTGCA 59.560 33.333 0.00 0.00 34.45 4.08
2612 2721 7.655732 AGTGGTGGAATACTTTTTGTAATTTGC 59.344 33.333 0.00 0.00 34.45 3.68
2613 2722 9.191995 GAGTGGTGGAATACTTTTTGTAATTTG 57.808 33.333 0.00 0.00 34.45 2.32
2614 2723 8.919145 TGAGTGGTGGAATACTTTTTGTAATTT 58.081 29.630 0.00 0.00 34.45 1.82
2615 2724 8.472007 TGAGTGGTGGAATACTTTTTGTAATT 57.528 30.769 0.00 0.00 34.45 1.40
2616 2725 8.650143 ATGAGTGGTGGAATACTTTTTGTAAT 57.350 30.769 0.00 0.00 34.45 1.89
2617 2726 7.721842 TGATGAGTGGTGGAATACTTTTTGTAA 59.278 33.333 0.00 0.00 34.45 2.41
2618 2727 7.227873 TGATGAGTGGTGGAATACTTTTTGTA 58.772 34.615 0.00 0.00 35.37 2.41
2619 2728 6.068010 TGATGAGTGGTGGAATACTTTTTGT 58.932 36.000 0.00 0.00 0.00 2.83
2620 2729 6.573664 TGATGAGTGGTGGAATACTTTTTG 57.426 37.500 0.00 0.00 0.00 2.44
2621 2730 7.177878 AGATGATGAGTGGTGGAATACTTTTT 58.822 34.615 0.00 0.00 0.00 1.94
2622 2731 6.725364 AGATGATGAGTGGTGGAATACTTTT 58.275 36.000 0.00 0.00 0.00 2.27
2623 2732 6.319048 AGATGATGAGTGGTGGAATACTTT 57.681 37.500 0.00 0.00 0.00 2.66
2624 2733 5.965033 AGATGATGAGTGGTGGAATACTT 57.035 39.130 0.00 0.00 0.00 2.24
2625 2734 5.305644 GGTAGATGATGAGTGGTGGAATACT 59.694 44.000 0.00 0.00 0.00 2.12
2626 2735 5.305644 AGGTAGATGATGAGTGGTGGAATAC 59.694 44.000 0.00 0.00 0.00 1.89
2627 2736 5.467738 AGGTAGATGATGAGTGGTGGAATA 58.532 41.667 0.00 0.00 0.00 1.75
2628 2737 4.302067 AGGTAGATGATGAGTGGTGGAAT 58.698 43.478 0.00 0.00 0.00 3.01
2629 2738 3.724478 AGGTAGATGATGAGTGGTGGAA 58.276 45.455 0.00 0.00 0.00 3.53
2630 2739 3.404869 AGGTAGATGATGAGTGGTGGA 57.595 47.619 0.00 0.00 0.00 4.02
2631 2740 3.452264 TCAAGGTAGATGATGAGTGGTGG 59.548 47.826 0.00 0.00 0.00 4.61
2632 2741 4.743057 TCAAGGTAGATGATGAGTGGTG 57.257 45.455 0.00 0.00 0.00 4.17
2633 2742 5.678583 CAATCAAGGTAGATGATGAGTGGT 58.321 41.667 0.00 0.00 37.58 4.16
2635 2744 5.526479 CACCAATCAAGGTAGATGATGAGTG 59.474 44.000 0.00 0.00 40.77 3.51
2636 2745 5.426509 TCACCAATCAAGGTAGATGATGAGT 59.573 40.000 0.00 0.00 40.77 3.41
2637 2746 5.922053 TCACCAATCAAGGTAGATGATGAG 58.078 41.667 0.00 0.00 40.77 2.90
2638 2747 5.662657 TCTCACCAATCAAGGTAGATGATGA 59.337 40.000 0.00 0.00 40.77 2.92
2639 2748 5.922053 TCTCACCAATCAAGGTAGATGATG 58.078 41.667 0.00 0.00 40.77 3.07
2640 2749 6.760440 ATCTCACCAATCAAGGTAGATGAT 57.240 37.500 0.00 0.00 40.77 2.45
2641 2750 6.566079 AATCTCACCAATCAAGGTAGATGA 57.434 37.500 0.00 0.00 40.77 2.92
2642 2751 7.636150 AAAATCTCACCAATCAAGGTAGATG 57.364 36.000 0.00 0.00 40.77 2.90
2643 2752 7.890127 TCAAAAATCTCACCAATCAAGGTAGAT 59.110 33.333 0.00 0.00 40.77 1.98
2644 2753 7.230747 TCAAAAATCTCACCAATCAAGGTAGA 58.769 34.615 0.00 0.00 40.77 2.59
2645 2754 7.452880 TCAAAAATCTCACCAATCAAGGTAG 57.547 36.000 0.00 0.00 40.77 3.18
2646 2755 7.831691 TTCAAAAATCTCACCAATCAAGGTA 57.168 32.000 0.00 0.00 40.77 3.08
2647 2756 6.729690 TTCAAAAATCTCACCAATCAAGGT 57.270 33.333 0.00 0.00 44.48 3.50
2648 2757 7.874016 TCAATTCAAAAATCTCACCAATCAAGG 59.126 33.333 0.00 0.00 0.00 3.61
2649 2758 8.821147 TCAATTCAAAAATCTCACCAATCAAG 57.179 30.769 0.00 0.00 0.00 3.02
2650 2759 7.385752 GCTCAATTCAAAAATCTCACCAATCAA 59.614 33.333 0.00 0.00 0.00 2.57
2651 2760 6.869913 GCTCAATTCAAAAATCTCACCAATCA 59.130 34.615 0.00 0.00 0.00 2.57
2652 2761 6.312180 GGCTCAATTCAAAAATCTCACCAATC 59.688 38.462 0.00 0.00 0.00 2.67
2653 2762 6.168389 GGCTCAATTCAAAAATCTCACCAAT 58.832 36.000 0.00 0.00 0.00 3.16
2654 2763 5.511202 GGGCTCAATTCAAAAATCTCACCAA 60.511 40.000 0.00 0.00 0.00 3.67
2655 2764 4.021192 GGGCTCAATTCAAAAATCTCACCA 60.021 41.667 0.00 0.00 0.00 4.17
2656 2765 4.221482 AGGGCTCAATTCAAAAATCTCACC 59.779 41.667 0.00 0.00 0.00 4.02
2657 2766 5.397142 AGGGCTCAATTCAAAAATCTCAC 57.603 39.130 0.00 0.00 0.00 3.51
2658 2767 8.821686 TTATAGGGCTCAATTCAAAAATCTCA 57.178 30.769 0.00 0.00 0.00 3.27
2659 2768 9.521503 GTTTATAGGGCTCAATTCAAAAATCTC 57.478 33.333 0.00 0.00 0.00 2.75
2660 2769 8.478066 GGTTTATAGGGCTCAATTCAAAAATCT 58.522 33.333 0.00 0.00 0.00 2.40
2661 2770 7.435192 CGGTTTATAGGGCTCAATTCAAAAATC 59.565 37.037 0.00 0.00 0.00 2.17
2662 2771 7.123547 TCGGTTTATAGGGCTCAATTCAAAAAT 59.876 33.333 0.00 0.00 0.00 1.82
2663 2772 6.434652 TCGGTTTATAGGGCTCAATTCAAAAA 59.565 34.615 0.00 0.00 0.00 1.94
2664 2773 5.946972 TCGGTTTATAGGGCTCAATTCAAAA 59.053 36.000 0.00 0.00 0.00 2.44
2665 2774 5.502079 TCGGTTTATAGGGCTCAATTCAAA 58.498 37.500 0.00 0.00 0.00 2.69
2666 2775 5.105567 TCGGTTTATAGGGCTCAATTCAA 57.894 39.130 0.00 0.00 0.00 2.69
2667 2776 4.764050 TCGGTTTATAGGGCTCAATTCA 57.236 40.909 0.00 0.00 0.00 2.57
2668 2777 6.445357 TTTTCGGTTTATAGGGCTCAATTC 57.555 37.500 0.00 0.00 0.00 2.17
2669 2778 5.359860 CCTTTTCGGTTTATAGGGCTCAATT 59.640 40.000 0.00 0.00 0.00 2.32
2670 2779 4.887655 CCTTTTCGGTTTATAGGGCTCAAT 59.112 41.667 0.00 0.00 0.00 2.57
2671 2780 4.019141 TCCTTTTCGGTTTATAGGGCTCAA 60.019 41.667 0.00 0.00 0.00 3.02
2672 2781 3.520317 TCCTTTTCGGTTTATAGGGCTCA 59.480 43.478 0.00 0.00 0.00 4.26
2673 2782 4.127907 CTCCTTTTCGGTTTATAGGGCTC 58.872 47.826 0.00 0.00 0.00 4.70
2674 2783 3.118000 CCTCCTTTTCGGTTTATAGGGCT 60.118 47.826 0.00 0.00 0.00 5.19
2675 2784 3.211865 CCTCCTTTTCGGTTTATAGGGC 58.788 50.000 0.00 0.00 0.00 5.19
2676 2785 3.457012 TCCCTCCTTTTCGGTTTATAGGG 59.543 47.826 0.00 0.00 41.33 3.53
2677 2786 4.163649 ACTCCCTCCTTTTCGGTTTATAGG 59.836 45.833 0.00 0.00 0.00 2.57
2678 2787 5.354842 ACTCCCTCCTTTTCGGTTTATAG 57.645 43.478 0.00 0.00 0.00 1.31
2679 2788 5.960202 AGTACTCCCTCCTTTTCGGTTTATA 59.040 40.000 0.00 0.00 0.00 0.98
2680 2789 4.781621 AGTACTCCCTCCTTTTCGGTTTAT 59.218 41.667 0.00 0.00 0.00 1.40
2681 2790 4.162651 AGTACTCCCTCCTTTTCGGTTTA 58.837 43.478 0.00 0.00 0.00 2.01
2682 2791 2.977580 AGTACTCCCTCCTTTTCGGTTT 59.022 45.455 0.00 0.00 0.00 3.27
2683 2792 2.617658 AGTACTCCCTCCTTTTCGGTT 58.382 47.619 0.00 0.00 0.00 4.44
2684 2793 2.322339 AGTACTCCCTCCTTTTCGGT 57.678 50.000 0.00 0.00 0.00 4.69
2685 2794 2.101082 GCTAGTACTCCCTCCTTTTCGG 59.899 54.545 0.00 0.00 0.00 4.30
2686 2795 2.758979 TGCTAGTACTCCCTCCTTTTCG 59.241 50.000 0.00 0.00 0.00 3.46
2687 2796 5.119694 CAATGCTAGTACTCCCTCCTTTTC 58.880 45.833 0.00 0.00 0.00 2.29
2688 2797 4.626529 GCAATGCTAGTACTCCCTCCTTTT 60.627 45.833 0.00 0.00 0.00 2.27
2689 2798 3.118223 GCAATGCTAGTACTCCCTCCTTT 60.118 47.826 0.00 0.00 0.00 3.11
2690 2799 2.436173 GCAATGCTAGTACTCCCTCCTT 59.564 50.000 0.00 0.00 0.00 3.36
2691 2800 2.043227 GCAATGCTAGTACTCCCTCCT 58.957 52.381 0.00 0.00 0.00 3.69
2692 2801 1.070914 GGCAATGCTAGTACTCCCTCC 59.929 57.143 4.82 0.00 0.00 4.30
2693 2802 2.036604 GAGGCAATGCTAGTACTCCCTC 59.963 54.545 4.82 6.70 0.00 4.30
2694 2803 2.043227 GAGGCAATGCTAGTACTCCCT 58.957 52.381 4.82 0.00 0.00 4.20
2695 2804 1.070914 GGAGGCAATGCTAGTACTCCC 59.929 57.143 14.07 0.00 38.80 4.30
2696 2805 1.762957 TGGAGGCAATGCTAGTACTCC 59.237 52.381 16.99 16.99 43.63 3.85
2697 2806 3.543680 TTGGAGGCAATGCTAGTACTC 57.456 47.619 4.82 2.41 0.00 2.59
2932 3241 1.747709 ATGTGAGCCAGCATGAGTTC 58.252 50.000 0.00 0.00 39.69 3.01
2988 3299 0.318699 TCTCGAACAAGCCGTCTGTG 60.319 55.000 0.00 0.00 0.00 3.66
2990 3301 0.784778 GTTCTCGAACAAGCCGTCTG 59.215 55.000 4.99 0.00 40.84 3.51
2991 3302 0.663568 CGTTCTCGAACAAGCCGTCT 60.664 55.000 10.10 0.00 41.20 4.18
2995 3306 3.430895 TGAAATACGTTCTCGAACAAGCC 59.569 43.478 10.10 0.00 41.20 4.35
2998 3309 4.084745 GCACTGAAATACGTTCTCGAACAA 60.085 41.667 10.10 0.00 41.20 2.83
3037 3348 3.309296 AGGCGATCTATTTCTTCCTCCA 58.691 45.455 0.00 0.00 0.00 3.86
3041 3352 5.208463 AGAAGAGGCGATCTATTTCTTCC 57.792 43.478 16.10 5.65 42.85 3.46


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

AutoCloner maintained by Alex Coulton.