Multiple sequence alignment - TraesCS1D01G205100

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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 TraesCS1D01G205100 chr1D 100.000 2678 0 0 1 2678 290507801 290505124 0.000000e+00 4946
1 TraesCS1D01G205100 chr1D 97.869 1689 33 3 612 2298 254477022 254475335 0.000000e+00 2916
2 TraesCS1D01G205100 chr1D 96.445 1688 59 1 612 2298 180356371 180358058 0.000000e+00 2784
3 TraesCS1D01G205100 chr1D 95.860 1691 59 6 612 2301 244768504 244766824 0.000000e+00 2724
4 TraesCS1D01G205100 chr1D 95.740 1690 71 1 612 2301 244201315 244199627 0.000000e+00 2721
5 TraesCS1D01G205100 chr1D 98.347 605 6 3 1 602 254524408 254523805 0.000000e+00 1059
6 TraesCS1D01G205100 chr1A 98.282 1688 28 1 612 2298 554447922 554449609 0.000000e+00 2955
7 TraesCS1D01G205100 chr3B 98.050 1692 31 1 612 2301 201493027 201491336 0.000000e+00 2940
8 TraesCS1D01G205100 chr3B 91.988 337 25 1 2344 2678 418301175 418300839 3.120000e-129 472
9 TraesCS1D01G205100 chr3B 91.124 338 28 2 2343 2678 57217615 57217278 8.740000e-125 457
10 TraesCS1D01G205100 chr3B 91.343 335 26 2 2346 2678 136503077 136502744 3.140000e-124 455
11 TraesCS1D01G205100 chr5D 97.931 1692 33 2 612 2301 503330935 503329244 0.000000e+00 2929
12 TraesCS1D01G205100 chr5D 97.747 1687 38 0 612 2298 6235877 6237563 0.000000e+00 2905
13 TraesCS1D01G205100 chr5D 98.176 603 10 1 1 602 329121770 329122372 0.000000e+00 1051
14 TraesCS1D01G205100 chr5D 97.360 606 12 2 1 602 503216555 503215950 0.000000e+00 1027
15 TraesCS1D01G205100 chr2D 98.432 1403 20 1 898 2298 33929969 33931371 0.000000e+00 2468
16 TraesCS1D01G205100 chr2D 98.185 606 7 2 1 602 272795557 272796162 0.000000e+00 1055
17 TraesCS1D01G205100 chr2D 91.420 338 26 2 2343 2678 520406644 520406980 6.760000e-126 460
18 TraesCS1D01G205100 chrUn 97.794 680 13 2 612 1289 426380361 426381040 0.000000e+00 1171
19 TraesCS1D01G205100 chrUn 98.188 607 6 3 1 602 93411294 93411900 0.000000e+00 1055
20 TraesCS1D01G205100 chrUn 90.504 337 30 2 2343 2678 335888107 335888442 6.800000e-121 444
21 TraesCS1D01G205100 chr3A 97.855 606 9 3 1 602 672911672 672912277 0.000000e+00 1044
22 TraesCS1D01G205100 chr6D 97.529 607 10 3 1 602 168249877 168249271 0.000000e+00 1033
23 TraesCS1D01G205100 chr6A 96.694 605 16 3 1 602 271188111 271187508 0.000000e+00 1003
24 TraesCS1D01G205100 chr7A 96.683 603 18 2 1 602 352183471 352184072 0.000000e+00 1002
25 TraesCS1D01G205100 chr4B 92.239 335 23 2 2346 2678 295540899 295540566 3.120000e-129 472
26 TraesCS1D01G205100 chr4B 91.098 337 26 3 2345 2678 157171328 157170993 1.130000e-123 453
27 TraesCS1D01G205100 chr4D 91.420 338 25 3 2343 2678 509554578 509554243 6.760000e-126 460
28 TraesCS1D01G205100 chr7D 90.801 337 29 2 2344 2678 365740069 365740405 1.460000e-122 449


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 TraesCS1D01G205100 chr1D 290505124 290507801 2677 True 4946 4946 100.000 1 2678 1 chr1D.!!$R5 2677
1 TraesCS1D01G205100 chr1D 254475335 254477022 1687 True 2916 2916 97.869 612 2298 1 chr1D.!!$R3 1686
2 TraesCS1D01G205100 chr1D 180356371 180358058 1687 False 2784 2784 96.445 612 2298 1 chr1D.!!$F1 1686
3 TraesCS1D01G205100 chr1D 244766824 244768504 1680 True 2724 2724 95.860 612 2301 1 chr1D.!!$R2 1689
4 TraesCS1D01G205100 chr1D 244199627 244201315 1688 True 2721 2721 95.740 612 2301 1 chr1D.!!$R1 1689
5 TraesCS1D01G205100 chr1D 254523805 254524408 603 True 1059 1059 98.347 1 602 1 chr1D.!!$R4 601
6 TraesCS1D01G205100 chr1A 554447922 554449609 1687 False 2955 2955 98.282 612 2298 1 chr1A.!!$F1 1686
7 TraesCS1D01G205100 chr3B 201491336 201493027 1691 True 2940 2940 98.050 612 2301 1 chr3B.!!$R3 1689
8 TraesCS1D01G205100 chr5D 503329244 503330935 1691 True 2929 2929 97.931 612 2301 1 chr5D.!!$R2 1689
9 TraesCS1D01G205100 chr5D 6235877 6237563 1686 False 2905 2905 97.747 612 2298 1 chr5D.!!$F1 1686
10 TraesCS1D01G205100 chr5D 329121770 329122372 602 False 1051 1051 98.176 1 602 1 chr5D.!!$F2 601
11 TraesCS1D01G205100 chr5D 503215950 503216555 605 True 1027 1027 97.360 1 602 1 chr5D.!!$R1 601
12 TraesCS1D01G205100 chr2D 33929969 33931371 1402 False 2468 2468 98.432 898 2298 1 chr2D.!!$F1 1400
13 TraesCS1D01G205100 chr2D 272795557 272796162 605 False 1055 1055 98.185 1 602 1 chr2D.!!$F2 601
14 TraesCS1D01G205100 chrUn 426380361 426381040 679 False 1171 1171 97.794 612 1289 1 chrUn.!!$F3 677
15 TraesCS1D01G205100 chrUn 93411294 93411900 606 False 1055 1055 98.188 1 602 1 chrUn.!!$F1 601
16 TraesCS1D01G205100 chr3A 672911672 672912277 605 False 1044 1044 97.855 1 602 1 chr3A.!!$F1 601
17 TraesCS1D01G205100 chr6D 168249271 168249877 606 True 1033 1033 97.529 1 602 1 chr6D.!!$R1 601
18 TraesCS1D01G205100 chr6A 271187508 271188111 603 True 1003 1003 96.694 1 602 1 chr6A.!!$R1 601
19 TraesCS1D01G205100 chr7A 352183471 352184072 601 False 1002 1002 96.683 1 602 1 chr7A.!!$F1 601

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
851 859 1.134694 GGGCAATGAGTTTCGACGC 59.865 57.895 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2410 2424 0.102844 AAGTGCAGTGCATTTGCGTT 59.897 45.0 23.33 12.34 44.4 4.84 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
200 201 1.790838 CGAGCTCGAGGACGTAGTTTG 60.791 57.143 32.06 0.00 41.96 2.93
524 531 5.632347 ACTCAAGTTCCGAAGTAATTACACG 59.368 40.000 17.65 19.29 0.00 4.49
602 609 5.526111 TCCAAAAAGAAATCGATACGATCCC 59.474 40.000 0.00 3.14 46.30 3.85
603 610 5.527582 CCAAAAAGAAATCGATACGATCCCT 59.472 40.000 0.00 5.13 46.30 4.20
604 611 6.704493 CCAAAAAGAAATCGATACGATCCCTA 59.296 38.462 0.00 0.00 46.30 3.53
605 612 7.225931 CCAAAAAGAAATCGATACGATCCCTAA 59.774 37.037 0.00 0.00 46.30 2.69
606 613 8.774586 CAAAAAGAAATCGATACGATCCCTAAT 58.225 33.333 0.00 0.00 46.30 1.73
607 614 7.891183 AAAGAAATCGATACGATCCCTAATG 57.109 36.000 0.00 0.00 46.30 1.90
608 615 5.967088 AGAAATCGATACGATCCCTAATGG 58.033 41.667 0.00 0.00 46.30 3.16
609 616 5.715279 AGAAATCGATACGATCCCTAATGGA 59.285 40.000 0.00 0.00 46.30 3.41
672 679 6.122277 TCCTATTCTGGCATTTTCGATTTCT 58.878 36.000 0.00 0.00 0.00 2.52
681 688 5.119125 GGCATTTTCGATTTCTGGACTTTTG 59.881 40.000 0.00 0.00 0.00 2.44
705 712 2.561419 CTCGGTTAGTGAAGGACCAGAA 59.439 50.000 0.00 0.00 32.95 3.02
763 771 1.285078 GAGGGGCTTGGGTACAATTCT 59.715 52.381 0.00 0.00 35.73 2.40
851 859 1.134694 GGGCAATGAGTTTCGACGC 59.865 57.895 0.00 0.00 0.00 5.19
1048 1061 7.038154 CTTGACCAAACAAGTTCCAATTCTA 57.962 36.000 0.00 0.00 41.32 2.10
1081 1094 8.664798 CAACTACACCAAATGATCTTTCGAATA 58.335 33.333 0.00 0.00 0.00 1.75
1278 1291 7.019388 TGGCTCCCTCTTTAGTGAGATTATAT 58.981 38.462 0.00 0.00 36.23 0.86
1331 1344 5.941555 GCTATGGGAGCCTGTACTATTAT 57.058 43.478 0.00 0.00 46.41 1.28
1337 1350 4.264713 GGGAGCCTGTACTATTATAGGGGA 60.265 50.000 4.15 0.00 37.13 4.81
1698 1711 2.039879 GGAGAGGGGCTCTTTTGTGTAA 59.960 50.000 0.00 0.00 41.35 2.41
2097 2111 5.495640 GTCTGTCTTCTGGATTTGGAGAAT 58.504 41.667 0.00 0.00 0.00 2.40
2100 2114 5.879763 TGTCTTCTGGATTTGGAGAATTGA 58.120 37.500 0.00 0.00 0.00 2.57
2167 2181 3.937814 TGATAATCATCCGCGCCTTAAT 58.062 40.909 0.00 0.00 0.00 1.40
2229 2243 8.683776 TTACGTAAGGATTATATAACCCCCAT 57.316 34.615 3.29 0.00 46.39 4.00
2298 2312 5.643777 GCTCACTTATACAACACAACTCCAT 59.356 40.000 0.00 0.00 0.00 3.41
2325 2339 5.861222 ATATATGTGTGTGTGTGTGTGTG 57.139 39.130 0.00 0.00 0.00 3.82
2326 2340 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
2327 2341 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2328 2342 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2329 2343 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2330 2344 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2331 2345 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2332 2346 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2333 2347 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2334 2348 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2335 2349 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2336 2350 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2337 2351 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2338 2352 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2339 2353 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2340 2354 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2341 2355 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2342 2356 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2343 2357 2.070028 GTGTGTGTGTGTGTGTGTGTA 58.930 47.619 0.00 0.00 0.00 2.90
2344 2358 2.070028 TGTGTGTGTGTGTGTGTGTAC 58.930 47.619 0.00 0.00 0.00 2.90
2345 2359 2.070028 GTGTGTGTGTGTGTGTGTACA 58.930 47.619 0.00 0.00 0.00 2.90
2346 2360 2.093625 GTGTGTGTGTGTGTGTGTACAG 59.906 50.000 0.00 0.00 37.52 2.74
2347 2361 1.062002 GTGTGTGTGTGTGTGTACAGC 59.938 52.381 0.00 0.00 37.52 4.40
2348 2362 0.655733 GTGTGTGTGTGTGTACAGCC 59.344 55.000 0.00 0.00 37.52 4.85
2349 2363 0.808060 TGTGTGTGTGTGTACAGCCG 60.808 55.000 0.00 0.00 37.52 5.52
2350 2364 1.227409 TGTGTGTGTGTACAGCCGG 60.227 57.895 0.00 0.00 37.52 6.13
2351 2365 1.227438 GTGTGTGTGTACAGCCGGT 60.227 57.895 1.90 0.00 37.52 5.28
2352 2366 1.068417 TGTGTGTGTACAGCCGGTC 59.932 57.895 1.90 0.00 37.52 4.79
2353 2367 1.366366 GTGTGTGTACAGCCGGTCT 59.634 57.895 1.90 0.00 37.52 3.85
2354 2368 0.599558 GTGTGTGTACAGCCGGTCTA 59.400 55.000 1.90 0.00 37.52 2.59
2355 2369 1.203994 GTGTGTGTACAGCCGGTCTAT 59.796 52.381 1.90 0.00 37.52 1.98
2356 2370 1.897133 TGTGTGTACAGCCGGTCTATT 59.103 47.619 1.90 0.00 31.91 1.73
2357 2371 3.090790 TGTGTGTACAGCCGGTCTATTA 58.909 45.455 1.90 0.00 31.91 0.98
2358 2372 3.702548 TGTGTGTACAGCCGGTCTATTAT 59.297 43.478 1.90 0.00 31.91 1.28
2359 2373 4.049186 GTGTGTACAGCCGGTCTATTATG 58.951 47.826 1.90 0.00 0.00 1.90
2360 2374 3.057734 GTGTACAGCCGGTCTATTATGC 58.942 50.000 1.90 0.00 0.00 3.14
2361 2375 2.963101 TGTACAGCCGGTCTATTATGCT 59.037 45.455 1.90 0.00 0.00 3.79
2362 2376 4.022589 GTGTACAGCCGGTCTATTATGCTA 60.023 45.833 1.90 0.00 0.00 3.49
2363 2377 4.585581 TGTACAGCCGGTCTATTATGCTAA 59.414 41.667 1.90 0.00 0.00 3.09
2364 2378 4.891992 ACAGCCGGTCTATTATGCTAAT 57.108 40.909 1.90 0.00 0.00 1.73
2365 2379 5.995565 ACAGCCGGTCTATTATGCTAATA 57.004 39.130 1.90 0.00 0.00 0.98
2366 2380 6.546428 ACAGCCGGTCTATTATGCTAATAT 57.454 37.500 1.90 0.00 0.00 1.28
2367 2381 6.947464 ACAGCCGGTCTATTATGCTAATATT 58.053 36.000 1.90 0.00 0.00 1.28
2368 2382 8.074613 ACAGCCGGTCTATTATGCTAATATTA 57.925 34.615 1.90 0.00 0.00 0.98
2369 2383 8.198109 ACAGCCGGTCTATTATGCTAATATTAG 58.802 37.037 16.79 16.79 0.00 1.73
2399 2413 9.890629 AATAACTATTCTGATAACACTTCTGCA 57.109 29.630 0.00 0.00 0.00 4.41
2400 2414 7.602517 AACTATTCTGATAACACTTCTGCAC 57.397 36.000 0.00 0.00 0.00 4.57
2401 2415 6.940739 ACTATTCTGATAACACTTCTGCACT 58.059 36.000 0.00 0.00 0.00 4.40
2402 2416 6.815641 ACTATTCTGATAACACTTCTGCACTG 59.184 38.462 0.00 0.00 0.00 3.66
2403 2417 3.329386 TCTGATAACACTTCTGCACTGC 58.671 45.455 0.00 0.00 0.00 4.40
2404 2418 3.069289 CTGATAACACTTCTGCACTGCA 58.931 45.455 3.11 3.11 36.92 4.41
2405 2419 2.807967 TGATAACACTTCTGCACTGCAC 59.192 45.455 0.00 0.00 33.79 4.57
2406 2420 1.217001 TAACACTTCTGCACTGCACG 58.783 50.000 0.00 0.00 33.79 5.34
2407 2421 2.051804 AACACTTCTGCACTGCACGC 62.052 55.000 0.00 0.00 33.79 5.34
2408 2422 2.109799 ACTTCTGCACTGCACGCT 59.890 55.556 0.00 0.00 33.79 5.07
2409 2423 1.524621 ACTTCTGCACTGCACGCTT 60.525 52.632 0.00 0.00 33.79 4.68
2410 2424 0.249868 ACTTCTGCACTGCACGCTTA 60.250 50.000 0.00 0.00 33.79 3.09
2411 2425 0.867746 CTTCTGCACTGCACGCTTAA 59.132 50.000 0.00 0.00 33.79 1.85
2412 2426 0.586319 TTCTGCACTGCACGCTTAAC 59.414 50.000 0.00 0.00 33.79 2.01
2423 2437 3.383026 CGCTTAACGCAAATGCACT 57.617 47.368 6.18 0.00 42.21 4.40
2424 2438 0.976963 CGCTTAACGCAAATGCACTG 59.023 50.000 6.18 0.00 42.21 3.66
2425 2439 0.710017 GCTTAACGCAAATGCACTGC 59.290 50.000 11.72 11.72 42.21 4.40
2426 2440 1.929926 GCTTAACGCAAATGCACTGCA 60.930 47.619 19.54 6.09 42.21 4.41
2427 2441 1.715519 CTTAACGCAAATGCACTGCAC 59.284 47.619 19.54 0.00 43.04 4.57
2428 2442 0.950836 TAACGCAAATGCACTGCACT 59.049 45.000 19.54 9.95 43.04 4.40
2429 2443 0.102844 AACGCAAATGCACTGCACTT 59.897 45.000 19.54 0.00 43.04 3.16
2430 2444 0.102844 ACGCAAATGCACTGCACTTT 59.897 45.000 19.54 5.83 43.04 2.66
2431 2445 0.780002 CGCAAATGCACTGCACTTTC 59.220 50.000 19.54 0.00 43.04 2.62
2432 2446 1.855513 GCAAATGCACTGCACTTTCA 58.144 45.000 15.89 0.00 43.04 2.69
2433 2447 1.790623 GCAAATGCACTGCACTTTCAG 59.209 47.619 15.89 0.00 43.04 3.02
2435 2449 3.550639 GCAAATGCACTGCACTTTCAGTA 60.551 43.478 15.89 0.00 44.81 2.74
2436 2450 4.224433 CAAATGCACTGCACTTTCAGTAG 58.776 43.478 5.67 0.00 44.81 2.57
2437 2451 1.229428 TGCACTGCACTTTCAGTAGC 58.771 50.000 0.00 4.33 44.81 3.58
2438 2452 1.229428 GCACTGCACTTTCAGTAGCA 58.771 50.000 0.00 0.00 44.81 3.49
2439 2453 1.069636 GCACTGCACTTTCAGTAGCAC 60.070 52.381 0.00 0.00 44.81 4.40
2440 2454 1.193203 CACTGCACTTTCAGTAGCACG 59.807 52.381 0.00 0.00 44.81 5.34
2441 2455 0.792640 CTGCACTTTCAGTAGCACGG 59.207 55.000 0.00 0.00 32.07 4.94
2442 2456 0.602638 TGCACTTTCAGTAGCACGGG 60.603 55.000 0.00 0.00 31.03 5.28
2443 2457 0.602905 GCACTTTCAGTAGCACGGGT 60.603 55.000 0.00 0.00 0.00 5.28
2444 2458 1.148310 CACTTTCAGTAGCACGGGTG 58.852 55.000 0.00 0.00 0.00 4.61
2454 2468 3.979789 CACGGGTGCTGCAATACA 58.020 55.556 2.77 0.00 0.00 2.29
2455 2469 1.501741 CACGGGTGCTGCAATACAC 59.498 57.895 2.77 5.78 36.03 2.90
2456 2470 1.072332 ACGGGTGCTGCAATACACA 59.928 52.632 2.77 0.00 38.57 3.72
2457 2471 1.234615 ACGGGTGCTGCAATACACAC 61.235 55.000 2.77 10.45 38.57 3.82
2458 2472 1.233950 CGGGTGCTGCAATACACACA 61.234 55.000 2.77 0.00 40.30 3.72
2459 2473 0.240945 GGGTGCTGCAATACACACAC 59.759 55.000 2.77 3.86 40.03 3.82
2460 2474 1.238439 GGTGCTGCAATACACACACT 58.762 50.000 2.77 0.00 38.57 3.55
2461 2475 2.422597 GGTGCTGCAATACACACACTA 58.577 47.619 2.77 0.00 38.57 2.74
2462 2476 2.416547 GGTGCTGCAATACACACACTAG 59.583 50.000 2.77 0.00 38.57 2.57
2463 2477 3.067106 GTGCTGCAATACACACACTAGT 58.933 45.455 2.77 0.00 36.77 2.57
2477 2491 3.914312 ACACTAGTGAACTTCATGTCGG 58.086 45.455 29.30 0.00 0.00 4.79
2478 2492 3.572682 ACACTAGTGAACTTCATGTCGGA 59.427 43.478 29.30 0.00 0.00 4.55
2479 2493 4.038763 ACACTAGTGAACTTCATGTCGGAA 59.961 41.667 29.30 0.00 0.00 4.30
2480 2494 4.988540 CACTAGTGAACTTCATGTCGGAAA 59.011 41.667 18.45 0.00 0.00 3.13
2481 2495 5.465390 CACTAGTGAACTTCATGTCGGAAAA 59.535 40.000 18.45 0.00 0.00 2.29
2482 2496 6.018262 CACTAGTGAACTTCATGTCGGAAAAA 60.018 38.462 18.45 0.00 0.00 1.94
2503 2517 2.228138 CTGCATGCAGTGTTTTTGGT 57.772 45.000 34.76 0.00 39.10 3.67
2504 2518 3.367992 CTGCATGCAGTGTTTTTGGTA 57.632 42.857 34.76 2.37 39.10 3.25
2505 2519 3.052036 CTGCATGCAGTGTTTTTGGTAC 58.948 45.455 34.76 0.00 39.10 3.34
2506 2520 2.223923 TGCATGCAGTGTTTTTGGTACC 60.224 45.455 18.46 4.43 0.00 3.34
2507 2521 2.035832 GCATGCAGTGTTTTTGGTACCT 59.964 45.455 14.21 0.00 0.00 3.08
2508 2522 3.492482 GCATGCAGTGTTTTTGGTACCTT 60.492 43.478 14.21 0.00 0.00 3.50
2509 2523 4.692228 CATGCAGTGTTTTTGGTACCTTT 58.308 39.130 14.36 0.00 0.00 3.11
2510 2524 4.810191 TGCAGTGTTTTTGGTACCTTTT 57.190 36.364 14.36 0.00 0.00 2.27
2511 2525 5.153950 TGCAGTGTTTTTGGTACCTTTTT 57.846 34.783 14.36 0.00 0.00 1.94
2537 2551 8.343974 TGCTCTAGTTTATTAACCGTTTATCG 57.656 34.615 0.00 0.00 34.71 2.92
2559 2573 3.725740 GGAACGATACGTGTAATACACCG 59.274 47.826 16.89 15.79 45.93 4.94
2560 2574 4.342772 GAACGATACGTGTAATACACCGT 58.657 43.478 16.89 16.36 45.93 4.83
2561 2575 4.355543 ACGATACGTGTAATACACCGTT 57.644 40.909 16.89 5.30 45.93 4.44
2562 2576 4.097714 ACGATACGTGTAATACACCGTTG 58.902 43.478 16.89 9.67 45.93 4.10
2563 2577 4.142708 ACGATACGTGTAATACACCGTTGA 60.143 41.667 16.89 5.91 45.93 3.18
2564 2578 4.435554 CGATACGTGTAATACACCGTTGAG 59.564 45.833 16.89 5.33 45.93 3.02
2565 2579 3.921119 ACGTGTAATACACCGTTGAGA 57.079 42.857 16.89 0.00 45.93 3.27
2566 2580 4.241590 ACGTGTAATACACCGTTGAGAA 57.758 40.909 16.89 0.00 45.93 2.87
2567 2581 4.232221 ACGTGTAATACACCGTTGAGAAG 58.768 43.478 16.89 3.35 45.93 2.85
2568 2582 3.060363 CGTGTAATACACCGTTGAGAAGC 59.940 47.826 16.89 0.00 45.93 3.86
2569 2583 4.243270 GTGTAATACACCGTTGAGAAGCT 58.757 43.478 12.26 0.00 43.05 3.74
2570 2584 5.404946 GTGTAATACACCGTTGAGAAGCTA 58.595 41.667 12.26 0.00 43.05 3.32
2571 2585 6.040878 GTGTAATACACCGTTGAGAAGCTAT 58.959 40.000 12.26 0.00 43.05 2.97
2572 2586 6.019801 GTGTAATACACCGTTGAGAAGCTATG 60.020 42.308 12.26 0.00 43.05 2.23
2573 2587 2.386661 ACACCGTTGAGAAGCTATGG 57.613 50.000 0.00 0.00 34.95 2.74
2574 2588 1.899814 ACACCGTTGAGAAGCTATGGA 59.100 47.619 0.00 0.00 33.32 3.41
2575 2589 2.501723 ACACCGTTGAGAAGCTATGGAT 59.498 45.455 0.00 0.00 33.32 3.41
2576 2590 3.055094 ACACCGTTGAGAAGCTATGGATT 60.055 43.478 0.00 0.00 33.32 3.01
2577 2591 4.161565 ACACCGTTGAGAAGCTATGGATTA 59.838 41.667 0.00 0.00 33.32 1.75
2578 2592 4.747108 CACCGTTGAGAAGCTATGGATTAG 59.253 45.833 0.00 0.00 33.32 1.73
2579 2593 4.202264 ACCGTTGAGAAGCTATGGATTAGG 60.202 45.833 0.00 0.00 33.32 2.69
2580 2594 3.743396 CGTTGAGAAGCTATGGATTAGGC 59.257 47.826 0.00 0.00 0.00 3.93
2581 2595 3.667497 TGAGAAGCTATGGATTAGGCG 57.333 47.619 0.00 0.00 0.00 5.52
2582 2596 2.289072 TGAGAAGCTATGGATTAGGCGC 60.289 50.000 0.00 0.00 0.00 6.53
2583 2597 1.694150 AGAAGCTATGGATTAGGCGCA 59.306 47.619 10.83 0.00 0.00 6.09
2584 2598 2.104792 AGAAGCTATGGATTAGGCGCAA 59.895 45.455 10.83 0.00 0.00 4.85
2585 2599 1.884235 AGCTATGGATTAGGCGCAAC 58.116 50.000 10.83 0.00 0.00 4.17
2586 2600 1.140852 AGCTATGGATTAGGCGCAACA 59.859 47.619 10.83 0.00 0.00 3.33
2587 2601 2.154462 GCTATGGATTAGGCGCAACAT 58.846 47.619 10.83 6.35 0.00 2.71
2588 2602 2.160417 GCTATGGATTAGGCGCAACATC 59.840 50.000 10.83 6.56 0.00 3.06
2589 2603 1.229428 ATGGATTAGGCGCAACATCG 58.771 50.000 10.83 0.00 0.00 3.84
2603 2617 1.896220 ACATCGCCATGTTGAACACT 58.104 45.000 0.00 0.00 40.66 3.55
2604 2618 2.229792 ACATCGCCATGTTGAACACTT 58.770 42.857 0.00 0.00 40.66 3.16
2605 2619 2.622942 ACATCGCCATGTTGAACACTTT 59.377 40.909 0.00 0.00 40.66 2.66
2606 2620 3.068024 ACATCGCCATGTTGAACACTTTT 59.932 39.130 0.00 0.00 40.66 2.27
2607 2621 3.347958 TCGCCATGTTGAACACTTTTC 57.652 42.857 0.00 0.00 0.00 2.29
2608 2622 2.043411 CGCCATGTTGAACACTTTTCG 58.957 47.619 0.00 0.00 0.00 3.46
2609 2623 2.286713 CGCCATGTTGAACACTTTTCGA 60.287 45.455 0.00 0.00 0.00 3.71
2610 2624 3.609175 CGCCATGTTGAACACTTTTCGAT 60.609 43.478 0.00 0.00 0.00 3.59
2611 2625 4.377943 CGCCATGTTGAACACTTTTCGATA 60.378 41.667 0.00 0.00 0.00 2.92
2612 2626 5.640732 GCCATGTTGAACACTTTTCGATAT 58.359 37.500 0.00 0.00 0.00 1.63
2613 2627 6.092748 GCCATGTTGAACACTTTTCGATATT 58.907 36.000 0.00 0.00 0.00 1.28
2614 2628 6.251376 GCCATGTTGAACACTTTTCGATATTC 59.749 38.462 0.00 0.00 0.00 1.75
2615 2629 7.530010 CCATGTTGAACACTTTTCGATATTCT 58.470 34.615 0.00 0.00 0.00 2.40
2616 2630 8.023128 CCATGTTGAACACTTTTCGATATTCTT 58.977 33.333 0.00 0.00 0.00 2.52
2617 2631 9.055248 CATGTTGAACACTTTTCGATATTCTTC 57.945 33.333 0.00 0.00 0.00 2.87
2618 2632 8.148807 TGTTGAACACTTTTCGATATTCTTCA 57.851 30.769 0.00 0.00 0.00 3.02
2619 2633 8.067784 TGTTGAACACTTTTCGATATTCTTCAC 58.932 33.333 0.00 0.00 0.00 3.18
2620 2634 6.817396 TGAACACTTTTCGATATTCTTCACG 58.183 36.000 0.00 0.00 0.00 4.35
2621 2635 5.779806 ACACTTTTCGATATTCTTCACGG 57.220 39.130 0.00 0.00 0.00 4.94
2622 2636 5.235516 ACACTTTTCGATATTCTTCACGGT 58.764 37.500 0.00 0.00 0.00 4.83
2623 2637 5.699458 ACACTTTTCGATATTCTTCACGGTT 59.301 36.000 0.00 0.00 0.00 4.44
2624 2638 6.204108 ACACTTTTCGATATTCTTCACGGTTT 59.796 34.615 0.00 0.00 0.00 3.27
2625 2639 7.385752 ACACTTTTCGATATTCTTCACGGTTTA 59.614 33.333 0.00 0.00 0.00 2.01
2626 2640 8.225107 CACTTTTCGATATTCTTCACGGTTTAA 58.775 33.333 0.00 0.00 0.00 1.52
2627 2641 8.440833 ACTTTTCGATATTCTTCACGGTTTAAG 58.559 33.333 0.00 0.00 0.00 1.85
2628 2642 8.537049 TTTTCGATATTCTTCACGGTTTAAGA 57.463 30.769 0.00 0.00 0.00 2.10
2629 2643 7.751047 TTCGATATTCTTCACGGTTTAAGAG 57.249 36.000 0.00 0.00 33.49 2.85
2630 2644 5.747197 TCGATATTCTTCACGGTTTAAGAGC 59.253 40.000 3.67 0.00 33.49 4.09
2631 2645 5.518847 CGATATTCTTCACGGTTTAAGAGCA 59.481 40.000 3.67 0.00 33.49 4.26
2632 2646 6.291849 CGATATTCTTCACGGTTTAAGAGCAG 60.292 42.308 3.67 0.00 33.49 4.24
2633 2647 3.746045 TCTTCACGGTTTAAGAGCAGT 57.254 42.857 0.00 0.00 0.00 4.40
2634 2648 4.067972 TCTTCACGGTTTAAGAGCAGTT 57.932 40.909 0.00 0.00 0.00 3.16
2635 2649 4.448210 TCTTCACGGTTTAAGAGCAGTTT 58.552 39.130 0.00 0.00 0.00 2.66
2636 2650 4.879545 TCTTCACGGTTTAAGAGCAGTTTT 59.120 37.500 0.00 0.00 0.00 2.43
2637 2651 4.545823 TCACGGTTTAAGAGCAGTTTTG 57.454 40.909 0.00 0.00 0.00 2.44
2638 2652 4.193090 TCACGGTTTAAGAGCAGTTTTGA 58.807 39.130 0.00 0.00 0.00 2.69
2639 2653 4.636648 TCACGGTTTAAGAGCAGTTTTGAA 59.363 37.500 0.00 0.00 0.00 2.69
2640 2654 5.124138 TCACGGTTTAAGAGCAGTTTTGAAA 59.876 36.000 0.00 0.00 0.00 2.69
2641 2655 5.802956 CACGGTTTAAGAGCAGTTTTGAAAA 59.197 36.000 0.00 0.00 0.00 2.29
2642 2656 6.475402 CACGGTTTAAGAGCAGTTTTGAAAAT 59.525 34.615 0.00 0.00 0.00 1.82
2643 2657 6.475402 ACGGTTTAAGAGCAGTTTTGAAAATG 59.525 34.615 0.00 0.00 37.08 2.32
2644 2658 6.074356 CGGTTTAAGAGCAGTTTTGAAAATGG 60.074 38.462 6.12 0.00 34.79 3.16
2645 2659 6.761242 GGTTTAAGAGCAGTTTTGAAAATGGT 59.239 34.615 8.14 8.14 45.72 3.55
2646 2660 7.254421 GGTTTAAGAGCAGTTTTGAAAATGGTG 60.254 37.037 12.48 1.97 43.53 4.17
2647 2661 3.721035 AGAGCAGTTTTGAAAATGGTGC 58.279 40.909 12.48 12.07 43.53 5.01
2648 2662 2.472488 GAGCAGTTTTGAAAATGGTGCG 59.528 45.455 12.48 0.00 43.53 5.34
2649 2663 1.526464 GCAGTTTTGAAAATGGTGCGG 59.474 47.619 6.12 0.00 34.79 5.69
2650 2664 1.526464 CAGTTTTGAAAATGGTGCGGC 59.474 47.619 0.00 0.00 30.93 6.53
2651 2665 1.137872 AGTTTTGAAAATGGTGCGGCA 59.862 42.857 0.00 0.00 0.00 5.69
2652 2666 1.260297 GTTTTGAAAATGGTGCGGCAC 59.740 47.619 24.43 24.43 0.00 5.01
2653 2667 0.461548 TTTGAAAATGGTGCGGCACA 59.538 45.000 31.74 19.21 35.86 4.57
2669 2683 4.700365 CACGACGAGTGGCAGCGA 62.700 66.667 15.46 0.00 46.77 4.93
2670 2684 4.406173 ACGACGAGTGGCAGCGAG 62.406 66.667 15.46 11.05 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
325 330 7.021790 GTCTGAAACCGAGTGGATTTATTTTC 58.978 38.462 0.00 0.00 39.21 2.29
524 531 8.561738 TGAACCTGAGTCCATTTTTCTATTAC 57.438 34.615 0.00 0.00 0.00 1.89
655 662 3.441572 AGTCCAGAAATCGAAAATGCCAG 59.558 43.478 0.00 0.00 0.00 4.85
672 679 0.766131 TAACCGAGGCCAAAAGTCCA 59.234 50.000 5.01 0.00 0.00 4.02
681 688 0.108281 GTCCTTCACTAACCGAGGCC 60.108 60.000 0.00 0.00 0.00 5.19
685 692 2.297698 TCTGGTCCTTCACTAACCGA 57.702 50.000 0.00 0.00 35.76 4.69
705 712 6.415573 ACCCGATTCATAACTAGAAAGCTTT 58.584 36.000 12.53 12.53 0.00 3.51
763 771 6.367695 AGCGCAAACATATAATAGCGTATTCA 59.632 34.615 11.47 0.00 46.09 2.57
851 859 5.294799 TCGATAAAAACGGATACACCCAATG 59.705 40.000 0.00 0.00 34.64 2.82
1008 1021 6.442541 TGGTCAAGTAAGGGAAACTCAATA 57.557 37.500 0.00 0.00 0.00 1.90
1081 1094 5.128008 GCCATAAACTAGAGAGTCTTGACCT 59.872 44.000 0.00 0.00 33.58 3.85
1278 1291 1.702182 TTGGTTCAGGCATTTGCTCA 58.298 45.000 2.12 0.00 41.70 4.26
1331 1344 3.443052 TCCGTACTGAACATTTCCCCTA 58.557 45.455 0.00 0.00 0.00 3.53
1337 1350 8.019656 ACTATAGGAATCCGTACTGAACATTT 57.980 34.615 4.43 0.00 0.00 2.32
1962 1976 1.603172 CGCTAGCTAAAGATCCACCGG 60.603 57.143 13.93 0.00 0.00 5.28
2097 2111 2.540516 TCGCGTTCTTGAAAATCGTCAA 59.459 40.909 5.77 0.00 36.15 3.18
2100 2114 3.432252 AGATTCGCGTTCTTGAAAATCGT 59.568 39.130 5.77 0.00 0.00 3.73
2167 2181 5.116180 CAACTTTCAGGCATTAGGATACGA 58.884 41.667 0.00 0.00 46.39 3.43
2301 2315 7.064490 CACACACACACACACACACATATATAT 59.936 37.037 0.00 0.00 0.00 0.86
2302 2316 6.367422 CACACACACACACACACACATATATA 59.633 38.462 0.00 0.00 0.00 0.86
2303 2317 5.179182 CACACACACACACACACACATATAT 59.821 40.000 0.00 0.00 0.00 0.86
2304 2318 4.509600 CACACACACACACACACACATATA 59.490 41.667 0.00 0.00 0.00 0.86
2305 2319 3.312146 CACACACACACACACACACATAT 59.688 43.478 0.00 0.00 0.00 1.78
2306 2320 2.675348 CACACACACACACACACACATA 59.325 45.455 0.00 0.00 0.00 2.29
2307 2321 1.468127 CACACACACACACACACACAT 59.532 47.619 0.00 0.00 0.00 3.21
2308 2322 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2309 2323 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2310 2324 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2311 2325 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2312 2326 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2313 2327 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2314 2328 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2315 2329 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2316 2330 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2317 2331 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2318 2332 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2319 2333 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2320 2334 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2321 2335 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2322 2336 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2323 2337 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2324 2338 2.070028 GTACACACACACACACACACA 58.930 47.619 0.00 0.00 0.00 3.72
2325 2339 2.070028 TGTACACACACACACACACAC 58.930 47.619 0.00 0.00 0.00 3.82
2326 2340 2.342179 CTGTACACACACACACACACA 58.658 47.619 0.00 0.00 0.00 3.72
2327 2341 1.062002 GCTGTACACACACACACACAC 59.938 52.381 0.00 0.00 0.00 3.82
2328 2342 1.364721 GCTGTACACACACACACACA 58.635 50.000 0.00 0.00 0.00 3.72
2329 2343 0.655733 GGCTGTACACACACACACAC 59.344 55.000 0.00 0.00 0.00 3.82
2330 2344 0.808060 CGGCTGTACACACACACACA 60.808 55.000 0.00 0.00 0.00 3.72
2331 2345 1.495584 CCGGCTGTACACACACACAC 61.496 60.000 0.00 0.00 0.00 3.82
2332 2346 1.227409 CCGGCTGTACACACACACA 60.227 57.895 0.00 0.00 0.00 3.72
2333 2347 1.219522 GACCGGCTGTACACACACAC 61.220 60.000 0.00 0.00 0.00 3.82
2334 2348 1.068417 GACCGGCTGTACACACACA 59.932 57.895 0.00 0.00 0.00 3.72
2335 2349 0.599558 TAGACCGGCTGTACACACAC 59.400 55.000 0.00 0.00 0.00 3.82
2336 2350 1.552578 ATAGACCGGCTGTACACACA 58.447 50.000 0.00 0.00 0.00 3.72
2337 2351 2.667473 AATAGACCGGCTGTACACAC 57.333 50.000 0.00 0.00 0.00 3.82
2338 2352 3.491964 GCATAATAGACCGGCTGTACACA 60.492 47.826 0.00 0.00 0.00 3.72
2339 2353 3.057734 GCATAATAGACCGGCTGTACAC 58.942 50.000 0.00 0.00 0.00 2.90
2340 2354 2.963101 AGCATAATAGACCGGCTGTACA 59.037 45.455 0.00 0.00 32.76 2.90
2341 2355 3.662247 AGCATAATAGACCGGCTGTAC 57.338 47.619 0.00 0.00 32.76 2.90
2342 2356 5.995565 ATTAGCATAATAGACCGGCTGTA 57.004 39.130 0.00 0.00 36.10 2.74
2343 2357 4.891992 ATTAGCATAATAGACCGGCTGT 57.108 40.909 0.00 0.00 36.10 4.40
2344 2358 8.581057 CTAATATTAGCATAATAGACCGGCTG 57.419 38.462 9.51 0.00 36.10 4.85
2373 2387 9.890629 TGCAGAAGTGTTATCAGAATAGTTATT 57.109 29.630 0.00 0.00 0.00 1.40
2374 2388 9.319143 GTGCAGAAGTGTTATCAGAATAGTTAT 57.681 33.333 0.00 0.00 0.00 1.89
2375 2389 8.531982 AGTGCAGAAGTGTTATCAGAATAGTTA 58.468 33.333 0.00 0.00 0.00 2.24
2376 2390 7.332926 CAGTGCAGAAGTGTTATCAGAATAGTT 59.667 37.037 0.00 0.00 0.00 2.24
2377 2391 6.815641 CAGTGCAGAAGTGTTATCAGAATAGT 59.184 38.462 0.00 0.00 0.00 2.12
2378 2392 6.238049 GCAGTGCAGAAGTGTTATCAGAATAG 60.238 42.308 11.09 0.00 0.00 1.73
2379 2393 5.582269 GCAGTGCAGAAGTGTTATCAGAATA 59.418 40.000 11.09 0.00 0.00 1.75
2380 2394 4.394300 GCAGTGCAGAAGTGTTATCAGAAT 59.606 41.667 11.09 0.00 0.00 2.40
2381 2395 3.748048 GCAGTGCAGAAGTGTTATCAGAA 59.252 43.478 11.09 0.00 0.00 3.02
2382 2396 3.244181 TGCAGTGCAGAAGTGTTATCAGA 60.244 43.478 15.37 0.00 33.32 3.27
2383 2397 3.069289 TGCAGTGCAGAAGTGTTATCAG 58.931 45.455 15.37 0.00 33.32 2.90
2384 2398 2.807967 GTGCAGTGCAGAAGTGTTATCA 59.192 45.455 20.42 0.00 40.08 2.15
2385 2399 2.159787 CGTGCAGTGCAGAAGTGTTATC 60.160 50.000 20.42 1.13 40.08 1.75
2386 2400 1.800586 CGTGCAGTGCAGAAGTGTTAT 59.199 47.619 20.42 0.00 40.08 1.89
2387 2401 1.217001 CGTGCAGTGCAGAAGTGTTA 58.783 50.000 20.42 0.00 40.08 2.41
2388 2402 2.016961 CGTGCAGTGCAGAAGTGTT 58.983 52.632 20.42 0.00 40.08 3.32
2389 2403 2.537560 GCGTGCAGTGCAGAAGTGT 61.538 57.895 20.42 0.00 40.08 3.55
2390 2404 1.779025 AAGCGTGCAGTGCAGAAGTG 61.779 55.000 20.42 7.43 40.08 3.16
2391 2405 0.249868 TAAGCGTGCAGTGCAGAAGT 60.250 50.000 20.42 7.29 40.08 3.01
2392 2406 0.867746 TTAAGCGTGCAGTGCAGAAG 59.132 50.000 20.42 14.11 40.08 2.85
2393 2407 0.586319 GTTAAGCGTGCAGTGCAGAA 59.414 50.000 20.42 5.18 40.08 3.02
2394 2408 1.556591 CGTTAAGCGTGCAGTGCAGA 61.557 55.000 20.42 0.00 40.08 4.26
2395 2409 1.154599 CGTTAAGCGTGCAGTGCAG 60.155 57.895 20.42 13.74 40.08 4.41
2396 2410 2.935191 CGTTAAGCGTGCAGTGCA 59.065 55.556 15.37 15.37 35.60 4.57
2397 2411 2.499732 GCGTTAAGCGTGCAGTGC 60.500 61.111 8.58 8.58 43.66 4.40
2406 2420 0.710017 GCAGTGCATTTGCGTTAAGC 59.290 50.000 11.09 0.00 45.83 3.09
2407 2421 1.715519 GTGCAGTGCATTTGCGTTAAG 59.284 47.619 22.87 0.00 44.40 1.85
2408 2422 1.336440 AGTGCAGTGCATTTGCGTTAA 59.664 42.857 22.87 0.00 44.40 2.01
2409 2423 0.950836 AGTGCAGTGCATTTGCGTTA 59.049 45.000 22.87 0.00 44.40 3.18
2410 2424 0.102844 AAGTGCAGTGCATTTGCGTT 59.897 45.000 23.33 12.34 44.40 4.84
2411 2425 0.102844 AAAGTGCAGTGCATTTGCGT 59.897 45.000 24.45 8.28 44.40 5.24
2412 2426 0.780002 GAAAGTGCAGTGCATTTGCG 59.220 50.000 24.45 0.00 44.40 4.85
2413 2427 1.790623 CTGAAAGTGCAGTGCATTTGC 59.209 47.619 24.45 22.89 41.91 3.68
2437 2451 1.233950 TGTGTATTGCAGCACCCGTG 61.234 55.000 13.16 0.00 34.94 4.94
2438 2452 1.072332 TGTGTATTGCAGCACCCGT 59.928 52.632 13.16 0.00 34.94 5.28
2439 2453 1.233950 TGTGTGTATTGCAGCACCCG 61.234 55.000 13.16 0.00 34.94 5.28
2440 2454 0.240945 GTGTGTGTATTGCAGCACCC 59.759 55.000 13.16 5.14 34.94 4.61
2441 2455 1.238439 AGTGTGTGTATTGCAGCACC 58.762 50.000 13.16 7.32 35.86 5.01
2442 2456 3.067106 ACTAGTGTGTGTATTGCAGCAC 58.933 45.455 0.00 10.07 35.64 4.40
2443 2457 3.066380 CACTAGTGTGTGTATTGCAGCA 58.934 45.455 15.06 0.00 39.24 4.41
2444 2458 3.325870 TCACTAGTGTGTGTATTGCAGC 58.674 45.455 21.99 0.00 44.14 5.25
2445 2459 4.991056 AGTTCACTAGTGTGTGTATTGCAG 59.009 41.667 21.99 0.00 44.14 4.41
2446 2460 4.956085 AGTTCACTAGTGTGTGTATTGCA 58.044 39.130 21.99 0.00 44.14 4.08
2447 2461 5.465390 TGAAGTTCACTAGTGTGTGTATTGC 59.535 40.000 21.99 5.55 44.14 3.56
2448 2462 7.171508 ACATGAAGTTCACTAGTGTGTGTATTG 59.828 37.037 21.99 14.99 44.14 1.90
2449 2463 7.217200 ACATGAAGTTCACTAGTGTGTGTATT 58.783 34.615 21.99 9.79 44.14 1.89
2450 2464 6.759272 ACATGAAGTTCACTAGTGTGTGTAT 58.241 36.000 21.99 8.66 44.14 2.29
2451 2465 6.156748 ACATGAAGTTCACTAGTGTGTGTA 57.843 37.500 21.99 6.82 44.14 2.90
2452 2466 5.023533 ACATGAAGTTCACTAGTGTGTGT 57.976 39.130 21.99 13.43 44.14 3.72
2453 2467 4.148871 CGACATGAAGTTCACTAGTGTGTG 59.851 45.833 21.99 12.90 44.14 3.82
2454 2468 4.299155 CGACATGAAGTTCACTAGTGTGT 58.701 43.478 21.99 16.32 44.14 3.72
2455 2469 3.675225 CCGACATGAAGTTCACTAGTGTG 59.325 47.826 21.99 13.33 45.07 3.82
2456 2470 3.572682 TCCGACATGAAGTTCACTAGTGT 59.427 43.478 21.99 8.64 0.00 3.55
2457 2471 4.174411 TCCGACATGAAGTTCACTAGTG 57.826 45.455 17.17 17.17 0.00 2.74
2458 2472 4.866508 TTCCGACATGAAGTTCACTAGT 57.133 40.909 7.96 7.41 0.00 2.57
2459 2473 6.539649 TTTTTCCGACATGAAGTTCACTAG 57.460 37.500 7.96 4.05 0.00 2.57
2485 2499 2.223923 GGTACCAAAAACACTGCATGCA 60.224 45.455 21.29 21.29 0.00 3.96
2486 2500 2.035832 AGGTACCAAAAACACTGCATGC 59.964 45.455 15.94 11.82 0.00 4.06
2487 2501 4.320608 AAGGTACCAAAAACACTGCATG 57.679 40.909 15.94 0.00 0.00 4.06
2488 2502 5.351948 AAAAGGTACCAAAAACACTGCAT 57.648 34.783 15.94 0.00 0.00 3.96
2489 2503 4.810191 AAAAGGTACCAAAAACACTGCA 57.190 36.364 15.94 0.00 0.00 4.41
2511 2525 8.810427 CGATAAACGGTTAATAAACTAGAGCAA 58.190 33.333 0.00 0.00 38.46 3.91
2512 2526 8.343974 CGATAAACGGTTAATAAACTAGAGCA 57.656 34.615 0.00 0.00 38.46 4.26
2531 2545 7.375808 GTGTATTACACGTATCGTTCCGATAAA 59.624 37.037 11.00 0.19 43.08 1.40
2532 2546 6.850823 GTGTATTACACGTATCGTTCCGATAA 59.149 38.462 11.00 0.00 43.08 1.75
2533 2547 6.362686 GTGTATTACACGTATCGTTCCGATA 58.637 40.000 11.00 2.42 41.00 2.92
2534 2548 5.207768 GTGTATTACACGTATCGTTCCGAT 58.792 41.667 11.00 4.42 43.22 4.18
2535 2549 4.587306 GTGTATTACACGTATCGTTCCGA 58.413 43.478 11.00 0.00 39.53 4.55
2536 2550 4.918755 GTGTATTACACGTATCGTTCCG 57.081 45.455 11.00 0.00 39.53 4.30
2548 2562 4.530710 AGCTTCTCAACGGTGTATTACA 57.469 40.909 0.00 0.00 0.00 2.41
2549 2563 5.462398 CCATAGCTTCTCAACGGTGTATTAC 59.538 44.000 0.00 0.00 0.00 1.89
2550 2564 5.361571 TCCATAGCTTCTCAACGGTGTATTA 59.638 40.000 0.00 0.00 0.00 0.98
2551 2565 4.161565 TCCATAGCTTCTCAACGGTGTATT 59.838 41.667 0.00 0.00 0.00 1.89
2552 2566 3.704566 TCCATAGCTTCTCAACGGTGTAT 59.295 43.478 0.00 0.00 0.00 2.29
2553 2567 3.093814 TCCATAGCTTCTCAACGGTGTA 58.906 45.455 0.00 0.00 0.00 2.90
2554 2568 1.899814 TCCATAGCTTCTCAACGGTGT 59.100 47.619 0.00 0.00 0.00 4.16
2555 2569 2.672961 TCCATAGCTTCTCAACGGTG 57.327 50.000 0.00 0.00 0.00 4.94
2556 2570 3.914426 AATCCATAGCTTCTCAACGGT 57.086 42.857 0.00 0.00 0.00 4.83
2557 2571 4.310769 CCTAATCCATAGCTTCTCAACGG 58.689 47.826 0.00 0.00 0.00 4.44
2558 2572 3.743396 GCCTAATCCATAGCTTCTCAACG 59.257 47.826 0.00 0.00 0.00 4.10
2559 2573 3.743396 CGCCTAATCCATAGCTTCTCAAC 59.257 47.826 0.00 0.00 0.00 3.18
2560 2574 3.803715 GCGCCTAATCCATAGCTTCTCAA 60.804 47.826 0.00 0.00 0.00 3.02
2561 2575 2.289072 GCGCCTAATCCATAGCTTCTCA 60.289 50.000 0.00 0.00 0.00 3.27
2562 2576 2.289072 TGCGCCTAATCCATAGCTTCTC 60.289 50.000 4.18 0.00 0.00 2.87
2563 2577 1.694150 TGCGCCTAATCCATAGCTTCT 59.306 47.619 4.18 0.00 0.00 2.85
2564 2578 2.169832 TGCGCCTAATCCATAGCTTC 57.830 50.000 4.18 0.00 0.00 3.86
2565 2579 2.222027 GTTGCGCCTAATCCATAGCTT 58.778 47.619 4.18 0.00 0.00 3.74
2566 2580 1.140852 TGTTGCGCCTAATCCATAGCT 59.859 47.619 4.18 0.00 0.00 3.32
2567 2581 1.593196 TGTTGCGCCTAATCCATAGC 58.407 50.000 4.18 0.00 0.00 2.97
2568 2582 2.413112 CGATGTTGCGCCTAATCCATAG 59.587 50.000 4.18 0.00 0.00 2.23
2569 2583 2.412870 CGATGTTGCGCCTAATCCATA 58.587 47.619 4.18 0.00 0.00 2.74
2570 2584 1.229428 CGATGTTGCGCCTAATCCAT 58.771 50.000 4.18 0.00 0.00 3.41
2571 2585 2.689083 CGATGTTGCGCCTAATCCA 58.311 52.632 4.18 0.00 0.00 3.41
2584 2598 1.896220 AGTGTTCAACATGGCGATGT 58.104 45.000 8.73 8.73 45.24 3.06
2585 2599 2.995466 AAGTGTTCAACATGGCGATG 57.005 45.000 7.21 7.21 35.49 3.84
2586 2600 3.609175 CGAAAAGTGTTCAACATGGCGAT 60.609 43.478 0.00 0.00 0.00 4.58
2587 2601 2.286713 CGAAAAGTGTTCAACATGGCGA 60.287 45.455 0.00 0.00 0.00 5.54
2588 2602 2.043411 CGAAAAGTGTTCAACATGGCG 58.957 47.619 0.00 0.00 0.00 5.69
2589 2603 3.347958 TCGAAAAGTGTTCAACATGGC 57.652 42.857 0.00 0.00 0.00 4.40
2590 2604 7.530010 AGAATATCGAAAAGTGTTCAACATGG 58.470 34.615 0.00 0.00 0.00 3.66
2591 2605 8.955061 AAGAATATCGAAAAGTGTTCAACATG 57.045 30.769 0.00 0.00 0.00 3.21
2592 2606 8.783093 TGAAGAATATCGAAAAGTGTTCAACAT 58.217 29.630 8.16 0.00 0.00 2.71
2593 2607 8.067784 GTGAAGAATATCGAAAAGTGTTCAACA 58.932 33.333 11.07 0.00 0.00 3.33
2594 2608 7.266335 CGTGAAGAATATCGAAAAGTGTTCAAC 59.734 37.037 11.07 6.76 0.00 3.18
2595 2609 7.287950 CGTGAAGAATATCGAAAAGTGTTCAA 58.712 34.615 11.07 0.00 0.00 2.69
2596 2610 6.128661 CCGTGAAGAATATCGAAAAGTGTTCA 60.129 38.462 6.95 6.95 0.00 3.18
2597 2611 6.128634 ACCGTGAAGAATATCGAAAAGTGTTC 60.129 38.462 0.00 0.00 0.00 3.18
2598 2612 5.699458 ACCGTGAAGAATATCGAAAAGTGTT 59.301 36.000 0.00 0.00 0.00 3.32
2599 2613 5.235516 ACCGTGAAGAATATCGAAAAGTGT 58.764 37.500 0.00 0.00 0.00 3.55
2600 2614 5.779806 ACCGTGAAGAATATCGAAAAGTG 57.220 39.130 0.00 0.00 0.00 3.16
2601 2615 6.796705 AAACCGTGAAGAATATCGAAAAGT 57.203 33.333 0.00 0.00 0.00 2.66
2602 2616 8.653338 TCTTAAACCGTGAAGAATATCGAAAAG 58.347 33.333 0.00 0.00 0.00 2.27
2603 2617 8.537049 TCTTAAACCGTGAAGAATATCGAAAA 57.463 30.769 0.00 0.00 0.00 2.29
2604 2618 7.201496 GCTCTTAAACCGTGAAGAATATCGAAA 60.201 37.037 0.00 0.00 31.46 3.46
2605 2619 6.255020 GCTCTTAAACCGTGAAGAATATCGAA 59.745 38.462 0.00 0.00 31.46 3.71
2606 2620 5.747197 GCTCTTAAACCGTGAAGAATATCGA 59.253 40.000 0.00 0.00 31.46 3.59
2607 2621 5.518847 TGCTCTTAAACCGTGAAGAATATCG 59.481 40.000 0.00 0.00 31.46 2.92
2608 2622 6.535508 ACTGCTCTTAAACCGTGAAGAATATC 59.464 38.462 0.00 0.00 31.46 1.63
2609 2623 6.407202 ACTGCTCTTAAACCGTGAAGAATAT 58.593 36.000 0.00 0.00 31.46 1.28
2610 2624 5.790593 ACTGCTCTTAAACCGTGAAGAATA 58.209 37.500 0.00 0.00 31.46 1.75
2611 2625 4.642429 ACTGCTCTTAAACCGTGAAGAAT 58.358 39.130 0.00 0.00 31.46 2.40
2612 2626 4.067972 ACTGCTCTTAAACCGTGAAGAA 57.932 40.909 0.00 0.00 31.46 2.52
2613 2627 3.746045 ACTGCTCTTAAACCGTGAAGA 57.254 42.857 0.00 0.00 0.00 2.87
2614 2628 4.813296 AAACTGCTCTTAAACCGTGAAG 57.187 40.909 0.00 0.00 0.00 3.02
2615 2629 4.636648 TCAAAACTGCTCTTAAACCGTGAA 59.363 37.500 0.00 0.00 0.00 3.18
2616 2630 4.193090 TCAAAACTGCTCTTAAACCGTGA 58.807 39.130 0.00 0.00 0.00 4.35
2617 2631 4.545823 TCAAAACTGCTCTTAAACCGTG 57.454 40.909 0.00 0.00 0.00 4.94
2618 2632 5.570234 TTTCAAAACTGCTCTTAAACCGT 57.430 34.783 0.00 0.00 0.00 4.83
2619 2633 6.074356 CCATTTTCAAAACTGCTCTTAAACCG 60.074 38.462 0.00 0.00 0.00 4.44
2620 2634 6.761242 ACCATTTTCAAAACTGCTCTTAAACC 59.239 34.615 0.00 0.00 0.00 3.27
2621 2635 7.621102 CACCATTTTCAAAACTGCTCTTAAAC 58.379 34.615 0.00 0.00 0.00 2.01
2622 2636 6.257630 GCACCATTTTCAAAACTGCTCTTAAA 59.742 34.615 2.93 0.00 0.00 1.52
2623 2637 5.752955 GCACCATTTTCAAAACTGCTCTTAA 59.247 36.000 2.93 0.00 0.00 1.85
2624 2638 5.288804 GCACCATTTTCAAAACTGCTCTTA 58.711 37.500 2.93 0.00 0.00 2.10
2625 2639 4.122046 GCACCATTTTCAAAACTGCTCTT 58.878 39.130 2.93 0.00 0.00 2.85
2626 2640 3.721035 GCACCATTTTCAAAACTGCTCT 58.279 40.909 2.93 0.00 0.00 4.09
2627 2641 2.472488 CGCACCATTTTCAAAACTGCTC 59.528 45.455 7.20 0.00 0.00 4.26
2628 2642 2.472816 CGCACCATTTTCAAAACTGCT 58.527 42.857 7.20 0.00 0.00 4.24
2629 2643 1.526464 CCGCACCATTTTCAAAACTGC 59.474 47.619 0.00 0.00 0.00 4.40
2630 2644 1.526464 GCCGCACCATTTTCAAAACTG 59.474 47.619 0.00 0.00 0.00 3.16
2631 2645 1.137872 TGCCGCACCATTTTCAAAACT 59.862 42.857 0.00 0.00 0.00 2.66
2632 2646 1.260297 GTGCCGCACCATTTTCAAAAC 59.740 47.619 12.80 0.00 0.00 2.43
2633 2647 1.134699 TGTGCCGCACCATTTTCAAAA 60.135 42.857 20.67 0.00 32.73 2.44
2634 2648 0.461548 TGTGCCGCACCATTTTCAAA 59.538 45.000 20.67 0.00 32.73 2.69
2635 2649 0.249238 GTGTGCCGCACCATTTTCAA 60.249 50.000 20.67 0.00 42.10 2.69
2636 2650 1.361993 GTGTGCCGCACCATTTTCA 59.638 52.632 20.67 0.00 42.10 2.69
2637 2651 1.729131 CGTGTGCCGCACCATTTTC 60.729 57.895 20.67 3.97 44.97 2.29
2638 2652 2.190170 TCGTGTGCCGCACCATTTT 61.190 52.632 20.67 0.00 44.97 1.82
2639 2653 2.593148 TCGTGTGCCGCACCATTT 60.593 55.556 20.67 0.00 44.97 2.32
2640 2654 3.353836 GTCGTGTGCCGCACCATT 61.354 61.111 20.67 0.00 44.97 3.16
2648 2662 4.961511 TGCCACTCGTCGTGTGCC 62.962 66.667 19.37 11.10 42.20 5.01
2649 2663 3.406361 CTGCCACTCGTCGTGTGC 61.406 66.667 19.37 15.26 42.20 4.57
2650 2664 3.406361 GCTGCCACTCGTCGTGTG 61.406 66.667 18.17 18.17 42.20 3.82
2652 2666 4.700365 TCGCTGCCACTCGTCGTG 62.700 66.667 0.00 0.00 43.41 4.35
2653 2667 4.406173 CTCGCTGCCACTCGTCGT 62.406 66.667 0.00 0.00 0.00 4.34
2658 2672 2.117941 AAAAACGCTCGCTGCCACTC 62.118 55.000 0.00 0.00 38.78 3.51
2659 2673 2.186826 AAAAACGCTCGCTGCCACT 61.187 52.632 0.00 0.00 38.78 4.00
2660 2674 2.331451 AAAAACGCTCGCTGCCAC 59.669 55.556 0.00 0.00 38.78 5.01


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

AutoCloner maintained by Alex Coulton.