Multiple sequence alignment - TraesCS7D01G343100

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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 TraesCS7D01G343100 chr7D 100.000 3343 0 0 1 3343 439711650 439708308 0.000000e+00 6174.0
1 TraesCS7D01G343100 chr2D 91.677 2403 162 21 1 2374 574399745 574397352 0.000000e+00 3295.0
2 TraesCS7D01G343100 chr2D 84.330 619 44 11 2721 3334 163023960 163024530 1.050000e-154 556.0
3 TraesCS7D01G343100 chr2D 89.881 336 32 2 2998 3332 113482629 113482295 6.630000e-117 431.0
4 TraesCS7D01G343100 chr2D 88.630 343 39 0 2992 3334 472026407 472026749 5.160000e-113 418.0
5 TraesCS7D01G343100 chr2D 88.201 339 38 1 2998 3334 545782176 545782514 1.440000e-108 403.0
6 TraesCS7D01G343100 chr6D 89.717 2402 212 16 1 2373 48684509 48682114 0.000000e+00 3035.0
7 TraesCS7D01G343100 chr6D 89.564 1284 104 16 1 1256 32690340 32689059 0.000000e+00 1602.0
8 TraesCS7D01G343100 chr6D 89.674 184 17 2 2575 2757 10706912 10706730 2.010000e-57 233.0
9 TraesCS7D01G343100 chr6D 90.110 182 12 2 2570 2750 445803940 445803764 7.210000e-57 231.0
10 TraesCS7D01G343100 chr7B 89.550 2402 216 17 1 2373 651393917 651391522 0.000000e+00 3013.0
11 TraesCS7D01G343100 chr7B 85.283 761 95 6 2575 3334 742087605 742086861 0.000000e+00 769.0
12 TraesCS7D01G343100 chr7B 89.247 186 18 2 2573 2757 104010998 104010814 7.210000e-57 231.0
13 TraesCS7D01G343100 chr5A 88.824 2407 235 19 1 2378 592307915 592305514 0.000000e+00 2924.0
14 TraesCS7D01G343100 chr1D 87.116 2406 269 20 1 2376 216024950 216022556 0.000000e+00 2687.0
15 TraesCS7D01G343100 chr1D 80.723 581 80 15 2769 3334 382777134 382776571 1.110000e-114 424.0
16 TraesCS7D01G343100 chr3D 89.762 1846 154 15 548 2364 300564990 300566829 0.000000e+00 2329.0
17 TraesCS7D01G343100 chr3D 85.576 2177 275 19 1 2147 225356561 225358728 0.000000e+00 2244.0
18 TraesCS7D01G343100 chr3D 86.573 782 80 13 2571 3334 540946113 540945339 0.000000e+00 839.0
19 TraesCS7D01G343100 chr3D 91.083 314 26 2 3022 3334 548718229 548717917 1.110000e-114 424.0
20 TraesCS7D01G343100 chr3D 83.544 79 12 1 2214 2291 295808568 295808646 4.630000e-09 73.1
21 TraesCS7D01G343100 chr3A 87.892 1784 182 18 617 2372 211951278 211953055 0.000000e+00 2067.0
22 TraesCS7D01G343100 chr3A 88.462 338 35 4 2998 3334 629050383 629050049 4.020000e-109 405.0
23 TraesCS7D01G343100 chr3A 75.641 312 38 22 2767 3055 686613985 686613689 1.630000e-23 121.0
24 TraesCS7D01G343100 chr3B 89.004 1446 140 11 933 2373 1790865 1789434 0.000000e+00 1772.0
25 TraesCS7D01G343100 chr3B 89.785 1116 89 8 3 1094 420901191 420900077 0.000000e+00 1406.0
26 TraesCS7D01G343100 chr3B 88.270 341 35 3 2995 3334 829297112 829296776 1.440000e-108 403.0
27 TraesCS7D01G343100 chr4A 89.121 1388 145 6 930 2313 662511414 662512799 0.000000e+00 1722.0
28 TraesCS7D01G343100 chr4A 90.682 880 79 3 2 881 662467884 662468760 0.000000e+00 1168.0
29 TraesCS7D01G343100 chr4A 89.247 186 18 2 2573 2757 282085327 282085143 7.210000e-57 231.0
30 TraesCS7D01G343100 chr5D 85.418 1447 203 8 933 2373 117351050 117352494 0.000000e+00 1496.0
31 TraesCS7D01G343100 chr2A 84.211 779 67 27 2573 3343 382783797 382783067 0.000000e+00 706.0
32 TraesCS7D01G343100 chr2A 84.211 779 67 27 2573 3343 719483094 719482364 0.000000e+00 706.0
33 TraesCS7D01G343100 chr7A 83.051 767 74 18 2569 3334 732440982 732441693 0.000000e+00 645.0
34 TraesCS7D01G343100 chr4B 76.244 804 120 49 2575 3334 157959425 157960201 8.820000e-96 361.0


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 TraesCS7D01G343100 chr7D 439708308 439711650 3342 True 6174 6174 100.000 1 3343 1 chr7D.!!$R1 3342
1 TraesCS7D01G343100 chr2D 574397352 574399745 2393 True 3295 3295 91.677 1 2374 1 chr2D.!!$R2 2373
2 TraesCS7D01G343100 chr2D 163023960 163024530 570 False 556 556 84.330 2721 3334 1 chr2D.!!$F1 613
3 TraesCS7D01G343100 chr6D 48682114 48684509 2395 True 3035 3035 89.717 1 2373 1 chr6D.!!$R3 2372
4 TraesCS7D01G343100 chr6D 32689059 32690340 1281 True 1602 1602 89.564 1 1256 1 chr6D.!!$R2 1255
5 TraesCS7D01G343100 chr7B 651391522 651393917 2395 True 3013 3013 89.550 1 2373 1 chr7B.!!$R2 2372
6 TraesCS7D01G343100 chr7B 742086861 742087605 744 True 769 769 85.283 2575 3334 1 chr7B.!!$R3 759
7 TraesCS7D01G343100 chr5A 592305514 592307915 2401 True 2924 2924 88.824 1 2378 1 chr5A.!!$R1 2377
8 TraesCS7D01G343100 chr1D 216022556 216024950 2394 True 2687 2687 87.116 1 2376 1 chr1D.!!$R1 2375
9 TraesCS7D01G343100 chr1D 382776571 382777134 563 True 424 424 80.723 2769 3334 1 chr1D.!!$R2 565
10 TraesCS7D01G343100 chr3D 300564990 300566829 1839 False 2329 2329 89.762 548 2364 1 chr3D.!!$F3 1816
11 TraesCS7D01G343100 chr3D 225356561 225358728 2167 False 2244 2244 85.576 1 2147 1 chr3D.!!$F1 2146
12 TraesCS7D01G343100 chr3D 540945339 540946113 774 True 839 839 86.573 2571 3334 1 chr3D.!!$R1 763
13 TraesCS7D01G343100 chr3A 211951278 211953055 1777 False 2067 2067 87.892 617 2372 1 chr3A.!!$F1 1755
14 TraesCS7D01G343100 chr3B 1789434 1790865 1431 True 1772 1772 89.004 933 2373 1 chr3B.!!$R1 1440
15 TraesCS7D01G343100 chr3B 420900077 420901191 1114 True 1406 1406 89.785 3 1094 1 chr3B.!!$R2 1091
16 TraesCS7D01G343100 chr4A 662511414 662512799 1385 False 1722 1722 89.121 930 2313 1 chr4A.!!$F2 1383
17 TraesCS7D01G343100 chr4A 662467884 662468760 876 False 1168 1168 90.682 2 881 1 chr4A.!!$F1 879
18 TraesCS7D01G343100 chr5D 117351050 117352494 1444 False 1496 1496 85.418 933 2373 1 chr5D.!!$F1 1440
19 TraesCS7D01G343100 chr2A 382783067 382783797 730 True 706 706 84.211 2573 3343 1 chr2A.!!$R1 770
20 TraesCS7D01G343100 chr2A 719482364 719483094 730 True 706 706 84.211 2573 3343 1 chr2A.!!$R2 770
21 TraesCS7D01G343100 chr7A 732440982 732441693 711 False 645 645 83.051 2569 3334 1 chr7A.!!$F1 765
22 TraesCS7D01G343100 chr4B 157959425 157960201 776 False 361 361 76.244 2575 3334 1 chr4B.!!$F1 759

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
876 882 1.962807 CTTTCCAAACAGGCATGGTGA 59.037 47.619 2.31 0.0 37.94 4.02 F
1016 1048 1.264288 GTGGCTATATTTGGCGAGTGC 59.736 52.381 0.00 0.0 41.71 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 1876 0.173708 ACCTTCTTCATCGACGCCTC 59.826 55.0 0.0 0.00 0.00 4.70 R
2405 2452 0.179034 GGCCATGAGGTCTCACATCC 60.179 60.0 0.0 1.42 43.11 3.51 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
29 30 3.759815 AGAGTAGAGTGGCCTTTCCTA 57.240 47.619 3.32 0.00 35.26 2.94
71 72 2.519013 GGCTTCTGTCAAGAATGGGTT 58.481 47.619 0.00 0.00 41.60 4.11
118 119 7.152645 TCAACAGTTGAATACAGAGTTAGGAC 58.847 38.462 13.90 0.00 36.59 3.85
154 155 4.381411 AGTGAGAGTTTCAAGCCTACAAC 58.619 43.478 0.00 0.00 37.61 3.32
345 347 7.652909 TGATTCTTATGAAAGCCAACAAACAAG 59.347 33.333 0.00 0.00 35.63 3.16
477 479 8.314751 AGATTAGAGCACAACTTTGTACTACAT 58.685 33.333 0.00 0.00 39.91 2.29
517 519 4.287067 GGCCCTCAGTGATAAATATCTGGA 59.713 45.833 0.00 0.00 33.88 3.86
827 833 8.426569 AAAAATCAAGGAGGAATGAGATTTCA 57.573 30.769 0.00 0.00 35.38 2.69
858 864 6.378848 TCCACTGTTTTAACTTGGCTTTACTT 59.621 34.615 8.24 0.00 34.61 2.24
859 865 7.039270 CCACTGTTTTAACTTGGCTTTACTTT 58.961 34.615 0.00 0.00 0.00 2.66
874 880 2.086610 ACTTTCCAAACAGGCATGGT 57.913 45.000 2.31 0.00 37.94 3.55
876 882 1.962807 CTTTCCAAACAGGCATGGTGA 59.037 47.619 2.31 0.00 37.94 4.02
890 896 3.947196 GCATGGTGACTGTTGGATAATCA 59.053 43.478 0.00 0.00 0.00 2.57
926 932 4.713321 TGCTTCTATCCTACGGGTAAAGTT 59.287 41.667 0.00 0.00 0.00 2.66
927 933 5.893255 TGCTTCTATCCTACGGGTAAAGTTA 59.107 40.000 0.00 0.00 0.00 2.24
928 934 6.380846 TGCTTCTATCCTACGGGTAAAGTTAA 59.619 38.462 0.00 0.00 0.00 2.01
929 935 6.922407 GCTTCTATCCTACGGGTAAAGTTAAG 59.078 42.308 0.00 0.00 0.00 1.85
976 1005 5.782893 TTACATGGCAAAGTATTATGGCC 57.217 39.130 0.00 0.00 41.07 5.36
978 1007 2.719531 TGGCAAAGTATTATGGCCGA 57.280 45.000 0.00 0.00 41.20 5.54
982 1014 2.943033 GCAAAGTATTATGGCCGACACT 59.057 45.455 0.00 0.00 0.00 3.55
1016 1048 1.264288 GTGGCTATATTTGGCGAGTGC 59.736 52.381 0.00 0.00 41.71 4.40
1054 1086 7.068702 ACATTAATATTTGGGAAGATGCCTGA 58.931 34.615 0.00 0.00 0.00 3.86
1070 1102 2.034305 GCCTGAATTCCAAGCTATGCAG 59.966 50.000 2.27 0.00 29.68 4.41
1173 1205 7.405292 TGGGATGAAGACTTGATTAGACAAAT 58.595 34.615 0.00 0.00 0.00 2.32
1256 1288 6.628844 GCAAGATTTCATTGCCTGGAACTATT 60.629 38.462 0.00 0.00 45.79 1.73
1285 1319 8.567285 AAAATGGTATTTTCTCAGTTCGATCT 57.433 30.769 0.00 0.00 0.00 2.75
1304 1338 2.634940 TCTGCCTATTCTATGGAGTGGC 59.365 50.000 10.56 10.56 39.33 5.01
1379 1413 4.705023 CAGTTAACCCCATTTGGAGTAAGG 59.295 45.833 0.88 0.00 37.39 2.69
1443 1478 4.908481 TGGCATACCCTACATGGTACAATA 59.092 41.667 0.00 0.00 43.45 1.90
1479 1514 5.902681 ACGCTAGCTAACAGACATATGAAA 58.097 37.500 13.93 0.00 0.00 2.69
1527 1563 6.555463 TCGGAGGGTTTAGAAGATACAAAT 57.445 37.500 0.00 0.00 0.00 2.32
1563 1599 3.437049 GCTGTAGTAAAGCAAAGGAGGTG 59.563 47.826 7.50 0.00 40.52 4.00
1578 1615 1.908299 GGTGTGGAAAAGGCTGGGG 60.908 63.158 0.00 0.00 0.00 4.96
1667 1705 9.931698 TTACTACTCCTACCAGATCAAGATTTA 57.068 33.333 0.00 0.00 0.00 1.40
1680 1719 6.936900 AGATCAAGATTTACGGATATTGGGTG 59.063 38.462 0.00 0.00 31.05 4.61
1742 1781 6.990349 GGTATCTATGATGGGAAAGACGAAAA 59.010 38.462 0.00 0.00 0.00 2.29
1833 1876 1.979855 TGTTAATGCATCATCCCCCG 58.020 50.000 0.00 0.00 0.00 5.73
1891 1934 7.527457 CCTCCAAGAGGTTTCGTTAAATTTAG 58.473 38.462 2.28 0.00 44.25 1.85
1959 2002 1.601162 CGGTCCTTCGAGACGACAAAA 60.601 52.381 9.81 0.00 37.66 2.44
1983 2026 3.633986 CAGGTTTATTGCTGGAGGGAATC 59.366 47.826 0.00 0.00 37.22 2.52
2050 2094 2.673368 CTCTCAAATGCGGTCTAACACC 59.327 50.000 0.00 0.00 42.69 4.16
2301 2348 3.258123 TGGTTTGAGGAGCCTTTAAATGC 59.742 43.478 7.32 7.32 0.00 3.56
2327 2374 8.611757 CAATTGTAATGATCCTCACAAACGATA 58.388 33.333 0.00 0.00 34.79 2.92
2393 2440 8.757164 AAAAAGATCTGAACGACAAACTTTTT 57.243 26.923 0.00 0.00 38.53 1.94
2394 2441 9.849166 AAAAAGATCTGAACGACAAACTTTTTA 57.151 25.926 20.14 0.00 39.72 1.52
2395 2442 8.836959 AAAGATCTGAACGACAAACTTTTTAC 57.163 30.769 0.00 0.00 0.00 2.01
2396 2443 6.956047 AGATCTGAACGACAAACTTTTTACC 58.044 36.000 0.00 0.00 0.00 2.85
2397 2444 6.540914 AGATCTGAACGACAAACTTTTTACCA 59.459 34.615 0.00 0.00 0.00 3.25
2398 2445 6.497785 TCTGAACGACAAACTTTTTACCAA 57.502 33.333 0.00 0.00 0.00 3.67
2399 2446 6.548171 TCTGAACGACAAACTTTTTACCAAG 58.452 36.000 0.00 0.00 0.00 3.61
2400 2447 6.149807 TCTGAACGACAAACTTTTTACCAAGT 59.850 34.615 0.00 0.00 38.74 3.16
2401 2448 7.333921 TCTGAACGACAAACTTTTTACCAAGTA 59.666 33.333 0.00 0.00 35.87 2.24
2402 2449 7.465989 TGAACGACAAACTTTTTACCAAGTAG 58.534 34.615 0.00 0.00 35.87 2.57
2403 2450 5.813717 ACGACAAACTTTTTACCAAGTAGC 58.186 37.500 0.00 0.00 35.87 3.58
2404 2451 5.354792 ACGACAAACTTTTTACCAAGTAGCA 59.645 36.000 0.00 0.00 35.87 3.49
2405 2452 5.907391 CGACAAACTTTTTACCAAGTAGCAG 59.093 40.000 0.00 0.00 35.87 4.24
2406 2453 6.144078 ACAAACTTTTTACCAAGTAGCAGG 57.856 37.500 0.00 0.00 35.87 4.85
2407 2454 5.889289 ACAAACTTTTTACCAAGTAGCAGGA 59.111 36.000 0.00 0.00 35.87 3.86
2408 2455 6.549736 ACAAACTTTTTACCAAGTAGCAGGAT 59.450 34.615 0.00 0.00 35.87 3.24
2409 2456 6.575162 AACTTTTTACCAAGTAGCAGGATG 57.425 37.500 0.00 0.00 35.87 3.51
2410 2457 5.631119 ACTTTTTACCAAGTAGCAGGATGT 58.369 37.500 0.00 0.00 34.93 3.06
2411 2458 5.473504 ACTTTTTACCAAGTAGCAGGATGTG 59.526 40.000 0.00 0.00 34.93 3.21
2412 2459 4.901197 TTTACCAAGTAGCAGGATGTGA 57.099 40.909 0.00 0.00 39.31 3.58
2413 2460 4.471904 TTACCAAGTAGCAGGATGTGAG 57.528 45.455 0.00 0.00 39.31 3.51
2414 2461 2.540383 ACCAAGTAGCAGGATGTGAGA 58.460 47.619 0.00 0.00 39.31 3.27
2415 2462 2.234908 ACCAAGTAGCAGGATGTGAGAC 59.765 50.000 0.00 0.00 39.31 3.36
2416 2463 2.419297 CCAAGTAGCAGGATGTGAGACC 60.419 54.545 0.00 0.00 39.31 3.85
2417 2464 2.499289 CAAGTAGCAGGATGTGAGACCT 59.501 50.000 0.00 0.00 39.31 3.85
2418 2465 2.383855 AGTAGCAGGATGTGAGACCTC 58.616 52.381 0.00 0.00 39.31 3.85
2419 2466 2.103373 GTAGCAGGATGTGAGACCTCA 58.897 52.381 0.00 0.00 39.31 3.86
2420 2467 1.876849 AGCAGGATGTGAGACCTCAT 58.123 50.000 2.78 0.00 42.18 2.90
2421 2468 1.485480 AGCAGGATGTGAGACCTCATG 59.515 52.381 2.78 0.00 42.18 3.07
2422 2469 1.474677 GCAGGATGTGAGACCTCATGG 60.475 57.143 2.78 0.00 42.18 3.66
2423 2470 0.835941 AGGATGTGAGACCTCATGGC 59.164 55.000 2.78 0.00 42.18 4.40
2424 2471 0.179034 GGATGTGAGACCTCATGGCC 60.179 60.000 0.00 0.00 42.18 5.36
2425 2472 0.835941 GATGTGAGACCTCATGGCCT 59.164 55.000 3.32 0.00 42.18 5.19
2426 2473 2.042464 GATGTGAGACCTCATGGCCTA 58.958 52.381 3.32 0.00 42.18 3.93
2427 2474 1.195115 TGTGAGACCTCATGGCCTAC 58.805 55.000 3.32 0.00 42.18 3.18
2428 2475 1.195115 GTGAGACCTCATGGCCTACA 58.805 55.000 3.32 0.00 42.18 2.74
2429 2476 1.555075 GTGAGACCTCATGGCCTACAA 59.445 52.381 3.32 0.00 42.18 2.41
2430 2477 2.171448 GTGAGACCTCATGGCCTACAAT 59.829 50.000 3.32 0.00 42.18 2.71
2431 2478 2.171237 TGAGACCTCATGGCCTACAATG 59.829 50.000 3.32 0.00 34.14 2.82
2432 2479 2.435805 GAGACCTCATGGCCTACAATGA 59.564 50.000 3.32 3.52 36.63 2.57
2433 2480 3.051581 AGACCTCATGGCCTACAATGAT 58.948 45.455 3.32 0.00 36.63 2.45
2434 2481 3.144506 GACCTCATGGCCTACAATGATG 58.855 50.000 3.32 4.42 36.63 3.07
2435 2482 2.511218 ACCTCATGGCCTACAATGATGT 59.489 45.455 3.32 5.10 39.22 3.06
2436 2483 2.882761 CCTCATGGCCTACAATGATGTG 59.117 50.000 3.32 0.00 40.84 3.21
2437 2484 3.548770 CTCATGGCCTACAATGATGTGT 58.451 45.455 3.32 0.00 40.84 3.72
2438 2485 3.544684 TCATGGCCTACAATGATGTGTC 58.455 45.455 3.32 0.00 40.84 3.67
2439 2486 3.200605 TCATGGCCTACAATGATGTGTCT 59.799 43.478 3.32 0.00 40.84 3.41
2440 2487 4.408596 TCATGGCCTACAATGATGTGTCTA 59.591 41.667 3.32 0.00 40.84 2.59
2441 2488 5.072193 TCATGGCCTACAATGATGTGTCTAT 59.928 40.000 3.32 0.00 40.84 1.98
2442 2489 4.960938 TGGCCTACAATGATGTGTCTATC 58.039 43.478 3.32 0.00 40.84 2.08
2443 2490 4.655649 TGGCCTACAATGATGTGTCTATCT 59.344 41.667 3.32 0.00 40.84 1.98
2444 2491 4.993584 GGCCTACAATGATGTGTCTATCTG 59.006 45.833 0.00 0.00 40.84 2.90
2445 2492 4.993584 GCCTACAATGATGTGTCTATCTGG 59.006 45.833 0.00 0.00 40.84 3.86
2446 2493 5.453903 GCCTACAATGATGTGTCTATCTGGT 60.454 44.000 0.00 0.00 40.84 4.00
2447 2494 6.239317 GCCTACAATGATGTGTCTATCTGGTA 60.239 42.308 0.00 0.00 40.84 3.25
2448 2495 7.148641 CCTACAATGATGTGTCTATCTGGTAC 58.851 42.308 0.00 0.00 40.84 3.34
2449 2496 6.544928 ACAATGATGTGTCTATCTGGTACA 57.455 37.500 0.00 0.00 38.69 2.90
2450 2497 6.946340 ACAATGATGTGTCTATCTGGTACAA 58.054 36.000 0.00 0.00 38.69 2.41
2451 2498 7.568349 ACAATGATGTGTCTATCTGGTACAAT 58.432 34.615 0.00 0.00 38.69 2.71
2452 2499 7.712639 ACAATGATGTGTCTATCTGGTACAATC 59.287 37.037 0.00 0.00 38.69 2.67
2453 2500 5.831997 TGATGTGTCTATCTGGTACAATCG 58.168 41.667 0.00 0.00 38.70 3.34
2454 2501 5.359860 TGATGTGTCTATCTGGTACAATCGT 59.640 40.000 0.00 0.00 38.70 3.73
2455 2502 4.993905 TGTGTCTATCTGGTACAATCGTG 58.006 43.478 0.00 0.00 38.70 4.35
2456 2503 4.703093 TGTGTCTATCTGGTACAATCGTGA 59.297 41.667 0.00 0.00 38.70 4.35
2457 2504 5.035443 GTGTCTATCTGGTACAATCGTGAC 58.965 45.833 0.00 0.00 38.70 3.67
2458 2505 4.703093 TGTCTATCTGGTACAATCGTGACA 59.297 41.667 0.00 0.00 38.70 3.58
2459 2506 5.035443 GTCTATCTGGTACAATCGTGACAC 58.965 45.833 0.00 0.00 38.70 3.67
2460 2507 3.953712 ATCTGGTACAATCGTGACACA 57.046 42.857 6.37 0.00 38.70 3.72
2461 2508 3.021269 TCTGGTACAATCGTGACACAC 57.979 47.619 6.37 0.00 38.70 3.82
2462 2509 2.362717 TCTGGTACAATCGTGACACACA 59.637 45.455 6.37 0.00 38.70 3.72
2463 2510 2.475111 CTGGTACAATCGTGACACACAC 59.525 50.000 6.37 0.00 41.74 3.82
2464 2511 2.159085 TGGTACAATCGTGACACACACA 60.159 45.455 6.37 0.00 42.55 3.72
2465 2512 3.679083 TGGTACAATCGTGACACACACAA 60.679 43.478 6.37 0.00 42.55 3.33
2466 2513 5.501011 TGGTACAATCGTGACACACACAAG 61.501 45.833 6.37 0.00 42.55 3.16
2467 2514 7.633054 TGGTACAATCGTGACACACACAAGA 62.633 44.000 6.37 0.00 42.55 3.02
2475 2522 4.944962 TGACACACACAAGAAGTTTGAG 57.055 40.909 0.00 0.00 32.28 3.02
2476 2523 3.126858 TGACACACACAAGAAGTTTGAGC 59.873 43.478 0.00 0.00 32.28 4.26
2477 2524 2.423538 ACACACACAAGAAGTTTGAGCC 59.576 45.455 0.00 0.00 32.28 4.70
2478 2525 1.670811 ACACACAAGAAGTTTGAGCCG 59.329 47.619 0.00 0.00 32.28 5.52
2479 2526 1.939934 CACACAAGAAGTTTGAGCCGA 59.060 47.619 0.00 0.00 29.21 5.54
2480 2527 2.549754 CACACAAGAAGTTTGAGCCGAT 59.450 45.455 0.00 0.00 29.21 4.18
2481 2528 3.003689 CACACAAGAAGTTTGAGCCGATT 59.996 43.478 0.00 0.00 29.21 3.34
2482 2529 4.213270 CACACAAGAAGTTTGAGCCGATTA 59.787 41.667 0.00 0.00 29.21 1.75
2483 2530 5.003804 ACACAAGAAGTTTGAGCCGATTAT 58.996 37.500 0.00 0.00 0.00 1.28
2484 2531 6.092122 CACACAAGAAGTTTGAGCCGATTATA 59.908 38.462 0.00 0.00 29.21 0.98
2485 2532 6.823689 ACACAAGAAGTTTGAGCCGATTATAT 59.176 34.615 0.00 0.00 0.00 0.86
2486 2533 7.985184 ACACAAGAAGTTTGAGCCGATTATATA 59.015 33.333 0.00 0.00 0.00 0.86
2487 2534 8.276325 CACAAGAAGTTTGAGCCGATTATATAC 58.724 37.037 0.00 0.00 0.00 1.47
2488 2535 7.985184 ACAAGAAGTTTGAGCCGATTATATACA 59.015 33.333 0.00 0.00 0.00 2.29
2489 2536 7.948278 AGAAGTTTGAGCCGATTATATACAC 57.052 36.000 0.00 0.00 0.00 2.90
2490 2537 7.497595 AGAAGTTTGAGCCGATTATATACACA 58.502 34.615 0.00 0.00 0.00 3.72
2491 2538 8.150945 AGAAGTTTGAGCCGATTATATACACAT 58.849 33.333 0.00 0.00 0.00 3.21
2492 2539 7.658179 AGTTTGAGCCGATTATATACACATG 57.342 36.000 0.00 0.00 0.00 3.21
2493 2540 6.650807 AGTTTGAGCCGATTATATACACATGG 59.349 38.462 0.00 0.00 0.00 3.66
2494 2541 5.993748 TGAGCCGATTATATACACATGGA 57.006 39.130 0.00 0.00 0.00 3.41
2495 2542 5.965922 TGAGCCGATTATATACACATGGAG 58.034 41.667 0.00 0.00 0.00 3.86
2496 2543 5.714806 TGAGCCGATTATATACACATGGAGA 59.285 40.000 0.00 0.00 0.00 3.71
2497 2544 6.381133 TGAGCCGATTATATACACATGGAGAT 59.619 38.462 0.00 0.00 0.00 2.75
2498 2545 6.577103 AGCCGATTATATACACATGGAGATG 58.423 40.000 0.00 0.00 35.49 2.90
2499 2546 6.381133 AGCCGATTATATACACATGGAGATGA 59.619 38.462 0.00 0.00 33.36 2.92
2500 2547 7.070447 AGCCGATTATATACACATGGAGATGAT 59.930 37.037 0.00 0.00 33.36 2.45
2501 2548 7.170489 GCCGATTATATACACATGGAGATGATG 59.830 40.741 0.00 0.00 33.36 3.07
2502 2549 8.200120 CCGATTATATACACATGGAGATGATGT 58.800 37.037 0.00 0.00 34.24 3.06
2503 2550 9.242477 CGATTATATACACATGGAGATGATGTC 57.758 37.037 0.00 0.00 31.46 3.06
2504 2551 9.539825 GATTATATACACATGGAGATGATGTCC 57.460 37.037 0.93 0.93 31.46 4.02
2514 2561 5.757988 TGGAGATGATGTCCAAAATGATCA 58.242 37.500 9.09 0.00 41.32 2.92
2515 2562 6.370453 TGGAGATGATGTCCAAAATGATCAT 58.630 36.000 9.09 1.18 41.32 2.45
2516 2563 6.264518 TGGAGATGATGTCCAAAATGATCATG 59.735 38.462 9.09 0.00 41.32 3.07
2517 2564 6.294564 GGAGATGATGTCCAAAATGATCATGG 60.295 42.308 9.46 8.29 36.02 3.66
2518 2565 6.134055 AGATGATGTCCAAAATGATCATGGT 58.866 36.000 9.46 0.00 36.02 3.55
2519 2566 7.292319 AGATGATGTCCAAAATGATCATGGTA 58.708 34.615 9.46 2.87 36.02 3.25
2520 2567 7.781219 AGATGATGTCCAAAATGATCATGGTAA 59.219 33.333 9.46 1.73 36.02 2.85
2521 2568 7.715266 TGATGTCCAAAATGATCATGGTAAA 57.285 32.000 9.46 0.00 35.66 2.01
2522 2569 8.308851 TGATGTCCAAAATGATCATGGTAAAT 57.691 30.769 9.46 4.07 35.66 1.40
2523 2570 9.418839 TGATGTCCAAAATGATCATGGTAAATA 57.581 29.630 9.46 0.00 35.66 1.40
2524 2571 9.683069 GATGTCCAAAATGATCATGGTAAATAC 57.317 33.333 9.46 2.67 35.66 1.89
2525 2572 8.821686 TGTCCAAAATGATCATGGTAAATACT 57.178 30.769 9.46 0.00 35.66 2.12
2526 2573 8.685427 TGTCCAAAATGATCATGGTAAATACTG 58.315 33.333 9.46 0.00 35.66 2.74
2527 2574 8.902806 GTCCAAAATGATCATGGTAAATACTGA 58.097 33.333 9.46 0.00 35.66 3.41
2528 2575 9.645128 TCCAAAATGATCATGGTAAATACTGAT 57.355 29.630 9.46 0.00 35.66 2.90
2529 2576 9.687210 CCAAAATGATCATGGTAAATACTGATG 57.313 33.333 9.46 0.00 0.00 3.07
2530 2577 9.687210 CAAAATGATCATGGTAAATACTGATGG 57.313 33.333 9.46 0.00 0.00 3.51
2531 2578 9.425248 AAAATGATCATGGTAAATACTGATGGT 57.575 29.630 9.46 0.00 0.00 3.55
2532 2579 7.991084 ATGATCATGGTAAATACTGATGGTG 57.009 36.000 7.59 0.00 0.00 4.17
2533 2580 6.298361 TGATCATGGTAAATACTGATGGTGG 58.702 40.000 0.00 0.00 0.00 4.61
2534 2581 5.047566 TCATGGTAAATACTGATGGTGGG 57.952 43.478 0.00 0.00 0.00 4.61
2535 2582 3.290948 TGGTAAATACTGATGGTGGGC 57.709 47.619 0.00 0.00 0.00 5.36
2536 2583 2.092103 TGGTAAATACTGATGGTGGGCC 60.092 50.000 0.00 0.00 0.00 5.80
2545 2592 4.259694 TGGTGGGCCATCAAGGTA 57.740 55.556 19.25 0.00 40.46 3.08
2546 2593 1.998530 TGGTGGGCCATCAAGGTAG 59.001 57.895 19.25 0.00 40.46 3.18
2547 2594 1.453928 GGTGGGCCATCAAGGTAGC 60.454 63.158 13.13 0.00 40.61 3.58
2548 2595 1.609783 GTGGGCCATCAAGGTAGCT 59.390 57.895 10.70 0.00 40.61 3.32
2549 2596 0.749454 GTGGGCCATCAAGGTAGCTG 60.749 60.000 10.70 0.00 40.61 4.24
2550 2597 1.207488 TGGGCCATCAAGGTAGCTGT 61.207 55.000 0.00 0.00 40.61 4.40
2551 2598 0.749454 GGGCCATCAAGGTAGCTGTG 60.749 60.000 4.39 0.00 40.61 3.66
2552 2599 0.253044 GGCCATCAAGGTAGCTGTGA 59.747 55.000 0.00 2.32 40.61 3.58
2553 2600 1.340017 GGCCATCAAGGTAGCTGTGAA 60.340 52.381 0.00 0.00 40.61 3.18
2554 2601 2.648059 GCCATCAAGGTAGCTGTGAAT 58.352 47.619 0.00 0.00 40.61 2.57
2555 2602 3.433598 GGCCATCAAGGTAGCTGTGAATA 60.434 47.826 0.00 0.00 40.61 1.75
2556 2603 3.812053 GCCATCAAGGTAGCTGTGAATAG 59.188 47.826 0.00 0.00 40.61 1.73
2557 2604 3.812053 CCATCAAGGTAGCTGTGAATAGC 59.188 47.826 0.00 0.00 44.01 2.97
2558 2605 3.543680 TCAAGGTAGCTGTGAATAGCC 57.456 47.619 0.00 0.00 44.76 3.93
2559 2606 2.837591 TCAAGGTAGCTGTGAATAGCCA 59.162 45.455 0.00 0.00 44.76 4.75
2560 2607 3.455910 TCAAGGTAGCTGTGAATAGCCAT 59.544 43.478 0.00 0.00 44.76 4.40
2561 2608 3.760580 AGGTAGCTGTGAATAGCCATC 57.239 47.619 0.00 0.00 44.76 3.51
2562 2609 2.036475 AGGTAGCTGTGAATAGCCATCG 59.964 50.000 0.00 0.00 44.76 3.84
2563 2610 2.035961 GGTAGCTGTGAATAGCCATCGA 59.964 50.000 0.00 0.00 44.76 3.59
2564 2611 2.231215 AGCTGTGAATAGCCATCGAC 57.769 50.000 0.00 0.00 44.76 4.20
2565 2612 0.855349 GCTGTGAATAGCCATCGACG 59.145 55.000 0.00 0.00 37.73 5.12
2566 2613 1.536072 GCTGTGAATAGCCATCGACGA 60.536 52.381 0.00 0.00 37.73 4.20
2567 2614 2.864097 GCTGTGAATAGCCATCGACGAT 60.864 50.000 4.05 4.05 37.73 3.73
2568 2615 2.983136 CTGTGAATAGCCATCGACGATC 59.017 50.000 7.54 0.00 0.00 3.69
2569 2616 2.288213 TGTGAATAGCCATCGACGATCC 60.288 50.000 7.54 2.11 0.00 3.36
2570 2617 1.960689 TGAATAGCCATCGACGATCCA 59.039 47.619 7.54 0.00 0.00 3.41
2571 2618 2.562738 TGAATAGCCATCGACGATCCAT 59.437 45.455 7.54 0.00 0.00 3.41
2640 2687 4.642429 GGAGATGTAAAATATGGACCGCT 58.358 43.478 0.00 0.00 0.00 5.52
2678 2725 3.674997 AGCTCCGAAAAATGCTCAACTA 58.325 40.909 0.00 0.00 0.00 2.24
2697 2744 5.241403 ACTACAACAGATGGTCCAAATCA 57.759 39.130 0.00 0.00 0.00 2.57
2701 2748 4.042062 ACAACAGATGGTCCAAATCAGAGA 59.958 41.667 0.00 0.00 0.00 3.10
2702 2749 5.191426 CAACAGATGGTCCAAATCAGAGAT 58.809 41.667 0.00 0.00 0.00 2.75
2703 2750 4.778579 ACAGATGGTCCAAATCAGAGATG 58.221 43.478 0.00 0.00 0.00 2.90
2704 2751 4.226846 ACAGATGGTCCAAATCAGAGATGT 59.773 41.667 0.00 0.00 0.00 3.06
2705 2752 5.426509 ACAGATGGTCCAAATCAGAGATGTA 59.573 40.000 0.00 0.00 0.00 2.29
2706 2753 6.070021 ACAGATGGTCCAAATCAGAGATGTAA 60.070 38.462 0.00 0.00 0.00 2.41
2726 2774 9.780413 GATGTAAATTAAAAGAGCTTCTCCAAG 57.220 33.333 0.00 0.00 0.00 3.61
2750 2799 7.177878 AGAGATGGTCCAAAACAAGATGTAAT 58.822 34.615 0.00 0.00 0.00 1.89
2763 2853 0.179045 ATGTAATCGACCAGCAGCCC 60.179 55.000 0.00 0.00 0.00 5.19
2765 2855 1.992834 TAATCGACCAGCAGCCCCA 60.993 57.895 0.00 0.00 0.00 4.96
2780 2881 1.821759 CCCACGAACACCTTGTGCA 60.822 57.895 0.00 0.00 36.98 4.57
2782 2883 1.095228 CCACGAACACCTTGTGCACT 61.095 55.000 19.41 0.00 36.98 4.40
2815 2916 2.828549 GCCGCCGATTGGATTGGT 60.829 61.111 1.98 0.00 37.49 3.67
2818 2919 1.312371 CCGCCGATTGGATTGGTTGT 61.312 55.000 1.98 0.00 37.49 3.32
2822 2923 1.271934 CCGATTGGATTGGTTGTTGCA 59.728 47.619 0.00 0.00 37.49 4.08
2863 3017 0.753111 TGATGAGAGCTAGCTCGGCA 60.753 55.000 33.31 32.29 46.90 5.69
2883 3038 2.492090 CGGTGAAGAGGAGCTCGG 59.508 66.667 7.83 0.00 35.36 4.63
2926 3106 4.753662 CCGACGGGGAGGAGGTCA 62.754 72.222 5.81 0.00 38.47 4.02
2927 3107 2.442272 CGACGGGGAGGAGGTCAT 60.442 66.667 0.00 0.00 0.00 3.06
2979 3159 2.120718 AAGGTCGTGGAGAGGCCT 59.879 61.111 3.86 3.86 37.63 5.19
3020 3219 3.083997 CGGCAGCCTAAGGACCCT 61.084 66.667 10.54 0.00 0.00 4.34
3024 3223 2.038975 AGCCTAAGGACCCTGCGA 59.961 61.111 0.00 0.00 0.00 5.10
3203 3433 4.794439 GGATTTTGGCGGTGGCGC 62.794 66.667 0.00 0.00 41.24 6.53
3334 3565 6.625520 TTGCATCTCGTGATGTAAATTTGCAT 60.626 34.615 22.90 20.00 46.80 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 6.494835 AGCCCAGTCTCAACATAATTTCTTTT 59.505 34.615 0.00 0.00 0.00 2.27
71 72 7.546778 TGAGACGCATTGCATAATAAAGTTA 57.453 32.000 9.69 0.00 0.00 2.24
118 119 8.307483 TGAAACTCTCACTTTCCTCTGTATTAG 58.693 37.037 0.00 0.00 0.00 1.73
154 155 0.248843 GTCTCCCTGTCTCAAGCCTG 59.751 60.000 0.00 0.00 0.00 4.85
345 347 3.793465 GCAACTTTCAGAGTTTCTGCACC 60.793 47.826 1.23 0.00 46.34 5.01
477 479 5.369404 TGAGGGCCTCAGTCATTATATTCAA 59.631 40.000 32.01 3.38 35.39 2.69
517 519 0.974010 CCCCACATTTGCTGGCAGAT 60.974 55.000 20.86 0.00 0.00 2.90
568 570 2.140065 TCTCTTGACAACACGCTCAG 57.860 50.000 0.00 0.00 0.00 3.35
827 833 5.278957 GCCAAGTTAAAACAGTGGATGTCAT 60.279 40.000 15.84 0.00 43.00 3.06
858 864 1.133513 AGTCACCATGCCTGTTTGGAA 60.134 47.619 0.00 0.00 38.35 3.53
859 865 0.478072 AGTCACCATGCCTGTTTGGA 59.522 50.000 0.00 0.00 38.35 3.53
874 880 6.903516 AGGAATCATGATTATCCAACAGTCA 58.096 36.000 22.77 0.00 0.00 3.41
876 882 7.067859 CACAAGGAATCATGATTATCCAACAGT 59.932 37.037 22.77 14.27 0.00 3.55
890 896 5.104193 AGGATAGAAGCACACAAGGAATCAT 60.104 40.000 0.00 0.00 0.00 2.45
929 935 4.520874 AGAAGAGCCTTTCTTTAACTTGGC 59.479 41.667 0.00 0.00 46.12 4.52
976 1005 4.089493 CCACGTTTCAGTGTATTAGTGTCG 59.911 45.833 0.00 0.00 40.33 4.35
978 1007 3.744426 GCCACGTTTCAGTGTATTAGTGT 59.256 43.478 0.00 0.00 40.33 3.55
982 1014 8.822855 CAAATATAGCCACGTTTCAGTGTATTA 58.177 33.333 0.00 0.00 40.33 0.98
1016 1048 7.254387 CCAAATATTAATGTTGTTGCCATTCCG 60.254 37.037 0.00 0.00 34.51 4.30
1024 1056 8.819974 GCATCTTCCCAAATATTAATGTTGTTG 58.180 33.333 0.00 0.00 0.00 3.33
1025 1057 7.986889 GGCATCTTCCCAAATATTAATGTTGTT 59.013 33.333 0.00 0.00 0.00 2.83
1070 1102 6.255950 CCTTAGGCGTTACAATTTTTCTAGC 58.744 40.000 0.00 0.00 0.00 3.42
1173 1205 4.143986 TGTACATCGATTGGCCACATAA 57.856 40.909 3.88 0.00 0.00 1.90
1304 1338 2.198827 TTGCTTCCATACTGGTGGTG 57.801 50.000 2.01 0.00 39.03 4.17
1379 1413 4.081642 TGCTGGACAGACTAACTTCCATAC 60.082 45.833 3.00 0.00 36.24 2.39
1443 1478 2.233922 AGCTAGCGTAACTCAACATGGT 59.766 45.455 9.55 0.00 0.00 3.55
1479 1514 1.075536 GTGGGGAAGATGGGTGAAACT 59.924 52.381 0.00 0.00 36.74 2.66
1527 1563 6.894339 TTACTACAGCGGAAGATCATATGA 57.106 37.500 8.10 8.10 0.00 2.15
1563 1599 1.908299 CCACCCCAGCCTTTTCCAC 60.908 63.158 0.00 0.00 0.00 4.02
1667 1705 1.281419 TGTGGTCACCCAATATCCGT 58.719 50.000 0.00 0.00 44.15 4.69
1680 1719 1.983605 CATCTCACGTACGTTGTGGTC 59.016 52.381 20.23 0.00 37.91 4.02
1688 1727 5.458779 TGAAATAGCAATCATCTCACGTACG 59.541 40.000 15.01 15.01 0.00 3.67
1833 1876 0.173708 ACCTTCTTCATCGACGCCTC 59.826 55.000 0.00 0.00 0.00 4.70
1887 1930 7.862372 GTGATCAAAAGAAGCATCAACACTAAA 59.138 33.333 0.00 0.00 0.00 1.85
1891 1934 4.614284 CGTGATCAAAAGAAGCATCAACAC 59.386 41.667 0.00 0.00 0.00 3.32
1983 2026 4.411327 TCCGCGCAAAAATCTATTTTCTG 58.589 39.130 8.75 4.35 38.92 3.02
2107 2152 6.351711 TGTCCTCCATCATTCATAGTTTCAG 58.648 40.000 0.00 0.00 0.00 3.02
2141 2186 3.729906 GAAGATTGCTGCTGCCGCG 62.730 63.158 13.47 0.00 39.65 6.46
2374 2421 6.687081 TGGTAAAAAGTTTGTCGTTCAGAT 57.313 33.333 0.00 0.00 0.00 2.90
2375 2422 6.149807 ACTTGGTAAAAAGTTTGTCGTTCAGA 59.850 34.615 0.00 0.00 37.05 3.27
2376 2423 6.319399 ACTTGGTAAAAAGTTTGTCGTTCAG 58.681 36.000 0.00 0.00 37.05 3.02
2377 2424 6.256912 ACTTGGTAAAAAGTTTGTCGTTCA 57.743 33.333 0.00 0.00 37.05 3.18
2378 2425 6.412943 GCTACTTGGTAAAAAGTTTGTCGTTC 59.587 38.462 0.00 0.00 40.77 3.95
2379 2426 6.127952 TGCTACTTGGTAAAAAGTTTGTCGTT 60.128 34.615 0.00 0.00 40.77 3.85
2380 2427 5.354792 TGCTACTTGGTAAAAAGTTTGTCGT 59.645 36.000 0.00 0.00 40.77 4.34
2381 2428 5.812652 TGCTACTTGGTAAAAAGTTTGTCG 58.187 37.500 0.00 0.00 40.77 4.35
2382 2429 6.038936 TCCTGCTACTTGGTAAAAAGTTTGTC 59.961 38.462 0.00 0.00 40.77 3.18
2383 2430 5.889289 TCCTGCTACTTGGTAAAAAGTTTGT 59.111 36.000 0.00 0.00 40.77 2.83
2384 2431 6.385649 TCCTGCTACTTGGTAAAAAGTTTG 57.614 37.500 0.00 0.00 40.77 2.93
2385 2432 6.549736 ACATCCTGCTACTTGGTAAAAAGTTT 59.450 34.615 0.00 0.00 40.77 2.66
2386 2433 6.016276 CACATCCTGCTACTTGGTAAAAAGTT 60.016 38.462 0.00 0.00 40.77 2.66
2387 2434 5.473504 CACATCCTGCTACTTGGTAAAAAGT 59.526 40.000 0.00 0.00 42.89 2.66
2388 2435 5.705441 TCACATCCTGCTACTTGGTAAAAAG 59.295 40.000 0.00 0.00 0.00 2.27
2389 2436 5.626142 TCACATCCTGCTACTTGGTAAAAA 58.374 37.500 0.00 0.00 0.00 1.94
2390 2437 5.012664 TCTCACATCCTGCTACTTGGTAAAA 59.987 40.000 0.00 0.00 0.00 1.52
2391 2438 4.530553 TCTCACATCCTGCTACTTGGTAAA 59.469 41.667 0.00 0.00 0.00 2.01
2392 2439 4.081642 GTCTCACATCCTGCTACTTGGTAA 60.082 45.833 0.00 0.00 0.00 2.85
2393 2440 3.447586 GTCTCACATCCTGCTACTTGGTA 59.552 47.826 0.00 0.00 0.00 3.25
2394 2441 2.234908 GTCTCACATCCTGCTACTTGGT 59.765 50.000 0.00 0.00 0.00 3.67
2395 2442 2.419297 GGTCTCACATCCTGCTACTTGG 60.419 54.545 0.00 0.00 0.00 3.61
2396 2443 2.499289 AGGTCTCACATCCTGCTACTTG 59.501 50.000 0.00 0.00 32.29 3.16
2397 2444 2.763448 GAGGTCTCACATCCTGCTACTT 59.237 50.000 0.00 0.00 33.83 2.24
2398 2445 2.291865 TGAGGTCTCACATCCTGCTACT 60.292 50.000 0.00 0.00 34.14 2.57
2399 2446 2.103373 TGAGGTCTCACATCCTGCTAC 58.897 52.381 0.00 0.00 34.14 3.58
2400 2447 2.532250 TGAGGTCTCACATCCTGCTA 57.468 50.000 0.00 0.00 34.14 3.49
2401 2448 1.485480 CATGAGGTCTCACATCCTGCT 59.515 52.381 2.46 0.00 43.11 4.24
2402 2449 1.474677 CCATGAGGTCTCACATCCTGC 60.475 57.143 2.46 0.00 43.11 4.85
2403 2450 1.474677 GCCATGAGGTCTCACATCCTG 60.475 57.143 2.46 0.00 43.11 3.86
2404 2451 0.835941 GCCATGAGGTCTCACATCCT 59.164 55.000 2.46 0.00 43.11 3.24
2405 2452 0.179034 GGCCATGAGGTCTCACATCC 60.179 60.000 0.00 1.42 43.11 3.51
2406 2453 3.393472 GGCCATGAGGTCTCACATC 57.607 57.895 0.00 0.00 43.11 3.06
2413 2460 3.144506 CATCATTGTAGGCCATGAGGTC 58.855 50.000 5.01 0.00 40.92 3.85
2414 2461 2.511218 ACATCATTGTAGGCCATGAGGT 59.489 45.455 13.57 13.57 33.43 3.85
2415 2462 2.882761 CACATCATTGTAGGCCATGAGG 59.117 50.000 5.01 9.81 33.76 3.86
2416 2463 3.548770 ACACATCATTGTAGGCCATGAG 58.451 45.455 5.01 0.00 33.76 2.90
2417 2464 3.200605 AGACACATCATTGTAGGCCATGA 59.799 43.478 5.01 5.61 33.76 3.07
2418 2465 3.548770 AGACACATCATTGTAGGCCATG 58.451 45.455 5.01 0.00 33.76 3.66
2419 2466 3.939740 AGACACATCATTGTAGGCCAT 57.060 42.857 5.01 0.00 33.76 4.40
2420 2467 4.655649 AGATAGACACATCATTGTAGGCCA 59.344 41.667 5.01 0.00 33.76 5.36
2421 2468 4.993584 CAGATAGACACATCATTGTAGGCC 59.006 45.833 0.00 0.00 33.76 5.19
2422 2469 4.993584 CCAGATAGACACATCATTGTAGGC 59.006 45.833 0.00 0.00 33.76 3.93
2423 2470 6.166984 ACCAGATAGACACATCATTGTAGG 57.833 41.667 0.00 0.00 33.76 3.18
2424 2471 7.716612 TGTACCAGATAGACACATCATTGTAG 58.283 38.462 0.00 0.00 33.76 2.74
2425 2472 7.654022 TGTACCAGATAGACACATCATTGTA 57.346 36.000 0.00 0.00 33.76 2.41
2426 2473 6.544928 TGTACCAGATAGACACATCATTGT 57.455 37.500 0.00 0.00 36.15 2.71
2427 2474 7.095899 CGATTGTACCAGATAGACACATCATTG 60.096 40.741 0.00 0.00 0.00 2.82
2428 2475 6.925718 CGATTGTACCAGATAGACACATCATT 59.074 38.462 0.00 0.00 0.00 2.57
2429 2476 6.040955 ACGATTGTACCAGATAGACACATCAT 59.959 38.462 0.00 0.00 0.00 2.45
2430 2477 5.359860 ACGATTGTACCAGATAGACACATCA 59.640 40.000 0.00 0.00 0.00 3.07
2431 2478 5.687730 CACGATTGTACCAGATAGACACATC 59.312 44.000 0.00 0.00 0.00 3.06
2432 2479 5.359860 TCACGATTGTACCAGATAGACACAT 59.640 40.000 0.00 0.00 0.00 3.21
2433 2480 4.703093 TCACGATTGTACCAGATAGACACA 59.297 41.667 0.00 0.00 0.00 3.72
2434 2481 5.035443 GTCACGATTGTACCAGATAGACAC 58.965 45.833 0.00 0.00 0.00 3.67
2435 2482 4.703093 TGTCACGATTGTACCAGATAGACA 59.297 41.667 0.00 0.00 0.00 3.41
2436 2483 5.035443 GTGTCACGATTGTACCAGATAGAC 58.965 45.833 0.00 0.00 0.00 2.59
2437 2484 4.703093 TGTGTCACGATTGTACCAGATAGA 59.297 41.667 0.00 0.00 0.00 1.98
2438 2485 4.798907 GTGTGTCACGATTGTACCAGATAG 59.201 45.833 0.00 0.00 0.00 2.08
2439 2486 4.218852 TGTGTGTCACGATTGTACCAGATA 59.781 41.667 0.00 0.00 37.14 1.98
2440 2487 3.006430 TGTGTGTCACGATTGTACCAGAT 59.994 43.478 0.00 0.00 37.14 2.90
2441 2488 2.362717 TGTGTGTCACGATTGTACCAGA 59.637 45.455 0.00 0.00 37.14 3.86
2442 2489 2.475111 GTGTGTGTCACGATTGTACCAG 59.525 50.000 0.00 0.00 37.14 4.00
2443 2490 2.475818 GTGTGTGTCACGATTGTACCA 58.524 47.619 0.00 0.00 37.14 3.25
2453 2500 4.651994 CTCAAACTTCTTGTGTGTGTCAC 58.348 43.478 0.00 0.00 46.31 3.67
2454 2501 3.126858 GCTCAAACTTCTTGTGTGTGTCA 59.873 43.478 0.00 0.00 35.43 3.58
2455 2502 3.487544 GGCTCAAACTTCTTGTGTGTGTC 60.488 47.826 0.00 0.00 35.43 3.67
2456 2503 2.423538 GGCTCAAACTTCTTGTGTGTGT 59.576 45.455 0.00 0.00 35.43 3.72
2457 2504 2.539547 CGGCTCAAACTTCTTGTGTGTG 60.540 50.000 0.00 0.00 35.43 3.82
2458 2505 1.670811 CGGCTCAAACTTCTTGTGTGT 59.329 47.619 0.00 0.00 35.43 3.72
2459 2506 1.939934 TCGGCTCAAACTTCTTGTGTG 59.060 47.619 0.00 0.00 35.23 3.82
2460 2507 2.325583 TCGGCTCAAACTTCTTGTGT 57.674 45.000 0.00 0.00 0.00 3.72
2461 2508 3.904136 AATCGGCTCAAACTTCTTGTG 57.096 42.857 0.00 0.00 0.00 3.33
2462 2509 7.985184 TGTATATAATCGGCTCAAACTTCTTGT 59.015 33.333 0.00 0.00 0.00 3.16
2463 2510 8.276325 GTGTATATAATCGGCTCAAACTTCTTG 58.724 37.037 0.00 0.00 0.00 3.02
2464 2511 7.985184 TGTGTATATAATCGGCTCAAACTTCTT 59.015 33.333 0.00 0.00 0.00 2.52
2465 2512 7.497595 TGTGTATATAATCGGCTCAAACTTCT 58.502 34.615 0.00 0.00 0.00 2.85
2466 2513 7.709269 TGTGTATATAATCGGCTCAAACTTC 57.291 36.000 0.00 0.00 0.00 3.01
2467 2514 7.173218 CCATGTGTATATAATCGGCTCAAACTT 59.827 37.037 0.00 0.00 0.00 2.66
2468 2515 6.650807 CCATGTGTATATAATCGGCTCAAACT 59.349 38.462 0.00 0.00 0.00 2.66
2469 2516 6.649141 TCCATGTGTATATAATCGGCTCAAAC 59.351 38.462 0.00 0.00 0.00 2.93
2470 2517 6.764379 TCCATGTGTATATAATCGGCTCAAA 58.236 36.000 0.00 0.00 0.00 2.69
2471 2518 6.210584 TCTCCATGTGTATATAATCGGCTCAA 59.789 38.462 0.00 0.00 0.00 3.02
2472 2519 5.714806 TCTCCATGTGTATATAATCGGCTCA 59.285 40.000 0.00 0.00 0.00 4.26
2473 2520 6.208988 TCTCCATGTGTATATAATCGGCTC 57.791 41.667 0.00 0.00 0.00 4.70
2474 2521 6.381133 TCATCTCCATGTGTATATAATCGGCT 59.619 38.462 0.00 0.00 0.00 5.52
2475 2522 6.573434 TCATCTCCATGTGTATATAATCGGC 58.427 40.000 0.00 0.00 0.00 5.54
2476 2523 8.200120 ACATCATCTCCATGTGTATATAATCGG 58.800 37.037 0.00 0.00 33.04 4.18
2477 2524 9.242477 GACATCATCTCCATGTGTATATAATCG 57.758 37.037 0.00 0.00 34.49 3.34
2478 2525 9.539825 GGACATCATCTCCATGTGTATATAATC 57.460 37.037 0.00 0.00 34.49 1.75
2479 2526 9.050154 TGGACATCATCTCCATGTGTATATAAT 57.950 33.333 0.00 0.00 34.49 1.28
2480 2527 8.434589 TGGACATCATCTCCATGTGTATATAA 57.565 34.615 0.00 0.00 34.49 0.98
2481 2528 8.434589 TTGGACATCATCTCCATGTGTATATA 57.565 34.615 0.00 0.00 37.65 0.86
2482 2529 6.940430 TGGACATCATCTCCATGTGTATAT 57.060 37.500 0.00 0.00 34.49 0.86
2483 2530 6.745794 TTGGACATCATCTCCATGTGTATA 57.254 37.500 0.00 0.00 37.65 1.47
2484 2531 5.635278 TTGGACATCATCTCCATGTGTAT 57.365 39.130 0.00 0.00 37.65 2.29
2485 2532 5.434182 TTTGGACATCATCTCCATGTGTA 57.566 39.130 0.00 0.00 37.65 2.90
2486 2533 4.305539 TTTGGACATCATCTCCATGTGT 57.694 40.909 0.00 0.00 37.65 3.72
2487 2534 5.358725 TCATTTTGGACATCATCTCCATGTG 59.641 40.000 0.00 0.00 37.65 3.21
2488 2535 5.512298 TCATTTTGGACATCATCTCCATGT 58.488 37.500 0.00 0.00 37.65 3.21
2489 2536 6.264518 TGATCATTTTGGACATCATCTCCATG 59.735 38.462 0.00 0.00 37.65 3.66
2490 2537 6.370453 TGATCATTTTGGACATCATCTCCAT 58.630 36.000 0.00 0.00 37.65 3.41
2491 2538 5.757988 TGATCATTTTGGACATCATCTCCA 58.242 37.500 0.00 0.00 35.91 3.86
2492 2539 6.294564 CCATGATCATTTTGGACATCATCTCC 60.295 42.308 5.16 0.00 34.40 3.71
2493 2540 6.264744 ACCATGATCATTTTGGACATCATCTC 59.735 38.462 18.64 0.00 34.40 2.75
2494 2541 6.134055 ACCATGATCATTTTGGACATCATCT 58.866 36.000 18.64 0.00 34.40 2.90
2495 2542 6.401047 ACCATGATCATTTTGGACATCATC 57.599 37.500 18.64 0.00 34.40 2.92
2496 2543 7.901283 TTACCATGATCATTTTGGACATCAT 57.099 32.000 18.64 0.29 36.59 2.45
2497 2544 7.715266 TTTACCATGATCATTTTGGACATCA 57.285 32.000 18.64 0.00 34.52 3.07
2498 2545 9.683069 GTATTTACCATGATCATTTTGGACATC 57.317 33.333 18.64 3.05 34.52 3.06
2499 2546 9.425248 AGTATTTACCATGATCATTTTGGACAT 57.575 29.630 18.64 10.18 34.52 3.06
2500 2547 8.685427 CAGTATTTACCATGATCATTTTGGACA 58.315 33.333 18.64 5.15 34.52 4.02
2501 2548 8.902806 TCAGTATTTACCATGATCATTTTGGAC 58.097 33.333 18.64 7.45 34.52 4.02
2502 2549 9.645128 ATCAGTATTTACCATGATCATTTTGGA 57.355 29.630 18.64 0.00 34.52 3.53
2503 2550 9.687210 CATCAGTATTTACCATGATCATTTTGG 57.313 33.333 5.16 8.95 36.56 3.28
2504 2551 9.687210 CCATCAGTATTTACCATGATCATTTTG 57.313 33.333 5.16 0.00 30.09 2.44
2505 2552 9.425248 ACCATCAGTATTTACCATGATCATTTT 57.575 29.630 5.16 0.00 30.09 1.82
2506 2553 8.853126 CACCATCAGTATTTACCATGATCATTT 58.147 33.333 5.16 0.00 30.09 2.32
2507 2554 7.449395 CCACCATCAGTATTTACCATGATCATT 59.551 37.037 5.16 0.00 30.09 2.57
2508 2555 6.944290 CCACCATCAGTATTTACCATGATCAT 59.056 38.462 1.18 1.18 30.09 2.45
2509 2556 6.298361 CCACCATCAGTATTTACCATGATCA 58.702 40.000 0.00 0.00 30.09 2.92
2510 2557 5.707298 CCCACCATCAGTATTTACCATGATC 59.293 44.000 0.00 0.00 30.09 2.92
2511 2558 5.634118 CCCACCATCAGTATTTACCATGAT 58.366 41.667 0.00 0.00 32.70 2.45
2512 2559 4.688597 GCCCACCATCAGTATTTACCATGA 60.689 45.833 0.00 0.00 0.00 3.07
2513 2560 3.569701 GCCCACCATCAGTATTTACCATG 59.430 47.826 0.00 0.00 0.00 3.66
2514 2561 3.436470 GGCCCACCATCAGTATTTACCAT 60.436 47.826 0.00 0.00 35.26 3.55
2515 2562 2.092103 GGCCCACCATCAGTATTTACCA 60.092 50.000 0.00 0.00 35.26 3.25
2516 2563 2.092103 TGGCCCACCATCAGTATTTACC 60.092 50.000 0.00 0.00 42.67 2.85
2517 2564 3.290948 TGGCCCACCATCAGTATTTAC 57.709 47.619 0.00 0.00 42.67 2.01
2529 2576 1.453928 GCTACCTTGATGGCCCACC 60.454 63.158 0.00 0.00 40.22 4.61
2530 2577 0.749454 CAGCTACCTTGATGGCCCAC 60.749 60.000 0.00 0.00 40.22 4.61
2531 2578 1.207488 ACAGCTACCTTGATGGCCCA 61.207 55.000 0.00 0.00 40.22 5.36
2532 2579 0.749454 CACAGCTACCTTGATGGCCC 60.749 60.000 0.00 0.00 40.22 5.80
2533 2580 0.253044 TCACAGCTACCTTGATGGCC 59.747 55.000 0.00 0.00 40.22 5.36
2534 2581 2.113860 TTCACAGCTACCTTGATGGC 57.886 50.000 0.00 0.00 40.22 4.40
2535 2582 3.812053 GCTATTCACAGCTACCTTGATGG 59.188 47.826 0.00 0.00 38.57 3.51
2536 2583 3.812053 GGCTATTCACAGCTACCTTGATG 59.188 47.826 0.00 0.00 41.50 3.07
2537 2584 3.455910 TGGCTATTCACAGCTACCTTGAT 59.544 43.478 0.00 0.00 41.50 2.57
2538 2585 2.837591 TGGCTATTCACAGCTACCTTGA 59.162 45.455 0.00 0.00 41.50 3.02
2539 2586 3.266510 TGGCTATTCACAGCTACCTTG 57.733 47.619 0.00 0.00 41.50 3.61
2540 2587 3.493350 CGATGGCTATTCACAGCTACCTT 60.493 47.826 0.00 0.00 41.50 3.50
2541 2588 2.036475 CGATGGCTATTCACAGCTACCT 59.964 50.000 0.00 0.00 41.50 3.08
2542 2589 2.035961 TCGATGGCTATTCACAGCTACC 59.964 50.000 0.00 0.00 41.50 3.18
2543 2590 3.053455 GTCGATGGCTATTCACAGCTAC 58.947 50.000 0.00 0.00 41.50 3.58
2544 2591 2.287608 CGTCGATGGCTATTCACAGCTA 60.288 50.000 0.00 0.00 41.50 3.32
2545 2592 1.536922 CGTCGATGGCTATTCACAGCT 60.537 52.381 0.00 0.00 41.50 4.24
2546 2593 0.855349 CGTCGATGGCTATTCACAGC 59.145 55.000 0.00 0.00 41.02 4.40
2547 2594 2.492019 TCGTCGATGGCTATTCACAG 57.508 50.000 4.48 0.00 0.00 3.66
2548 2595 2.288213 GGATCGTCGATGGCTATTCACA 60.288 50.000 13.54 0.00 0.00 3.58
2549 2596 2.288213 TGGATCGTCGATGGCTATTCAC 60.288 50.000 13.54 0.00 0.00 3.18
2550 2597 1.960689 TGGATCGTCGATGGCTATTCA 59.039 47.619 13.54 0.00 0.00 2.57
2551 2598 2.724977 TGGATCGTCGATGGCTATTC 57.275 50.000 13.54 0.00 0.00 1.75
2552 2599 3.685139 AATGGATCGTCGATGGCTATT 57.315 42.857 13.54 6.11 0.00 1.73
2553 2600 4.462834 TCTTAATGGATCGTCGATGGCTAT 59.537 41.667 13.54 0.00 0.00 2.97
2554 2601 3.824443 TCTTAATGGATCGTCGATGGCTA 59.176 43.478 13.54 0.00 0.00 3.93
2555 2602 2.628178 TCTTAATGGATCGTCGATGGCT 59.372 45.455 13.54 0.00 0.00 4.75
2556 2603 2.989840 CTCTTAATGGATCGTCGATGGC 59.010 50.000 13.54 0.00 0.00 4.40
2557 2604 2.989840 GCTCTTAATGGATCGTCGATGG 59.010 50.000 13.54 0.00 0.00 3.51
2558 2605 3.642705 TGCTCTTAATGGATCGTCGATG 58.357 45.455 13.54 0.00 0.00 3.84
2559 2606 4.219507 AGATGCTCTTAATGGATCGTCGAT 59.780 41.667 7.63 7.63 37.35 3.59
2560 2607 3.570125 AGATGCTCTTAATGGATCGTCGA 59.430 43.478 0.00 0.00 37.35 4.20
2561 2608 3.906998 AGATGCTCTTAATGGATCGTCG 58.093 45.455 5.09 0.00 37.35 5.12
2562 2609 4.241681 GGAGATGCTCTTAATGGATCGTC 58.758 47.826 0.00 0.00 37.35 4.20
2563 2610 3.643320 TGGAGATGCTCTTAATGGATCGT 59.357 43.478 0.00 0.00 37.35 3.73
2564 2611 4.263018 TGGAGATGCTCTTAATGGATCG 57.737 45.455 0.00 0.00 37.35 3.69
2565 2612 7.619050 TCTATTGGAGATGCTCTTAATGGATC 58.381 38.462 0.00 3.14 33.36 3.36
2566 2613 7.565190 TCTATTGGAGATGCTCTTAATGGAT 57.435 36.000 0.00 0.00 28.85 3.41
2567 2614 7.565190 ATCTATTGGAGATGCTCTTAATGGA 57.435 36.000 0.00 0.00 43.71 3.41
2640 2687 3.128589 GGAGCTCCAAAACGCATCATTTA 59.871 43.478 28.43 0.00 35.64 1.40
2678 2725 4.042062 TCTCTGATTTGGACCATCTGTTGT 59.958 41.667 0.00 0.00 0.00 3.32
2697 2744 9.389755 GGAGAAGCTCTTTTAATTTACATCTCT 57.610 33.333 0.00 0.00 31.50 3.10
2701 2748 9.520515 TCTTGGAGAAGCTCTTTTAATTTACAT 57.479 29.630 0.00 0.00 0.00 2.29
2702 2749 8.918202 TCTTGGAGAAGCTCTTTTAATTTACA 57.082 30.769 0.00 0.00 0.00 2.41
2703 2750 9.220767 TCTCTTGGAGAAGCTCTTTTAATTTAC 57.779 33.333 0.00 0.00 35.59 2.01
2704 2751 9.965902 ATCTCTTGGAGAAGCTCTTTTAATTTA 57.034 29.630 1.26 0.00 42.27 1.40
2705 2752 8.738106 CATCTCTTGGAGAAGCTCTTTTAATTT 58.262 33.333 1.26 0.00 42.27 1.82
2706 2753 8.278729 CATCTCTTGGAGAAGCTCTTTTAATT 57.721 34.615 1.26 0.00 42.27 1.40
2726 2774 6.817765 TTACATCTTGTTTTGGACCATCTC 57.182 37.500 0.00 0.00 0.00 2.75
2753 2843 4.643387 GTTCGTGGGGCTGCTGGT 62.643 66.667 0.00 0.00 0.00 4.00
2763 2853 1.095228 AGTGCACAAGGTGTTCGTGG 61.095 55.000 21.04 0.00 35.75 4.94
2765 2855 0.732571 CAAGTGCACAAGGTGTTCGT 59.267 50.000 21.04 0.00 35.75 3.85
2780 2881 1.272147 GGCCATCTTCTTCCACCAAGT 60.272 52.381 0.00 0.00 33.27 3.16
2782 2883 0.322456 CGGCCATCTTCTTCCACCAA 60.322 55.000 2.24 0.00 0.00 3.67
2841 2962 1.028130 CGAGCTAGCTCTCATCACCA 58.972 55.000 35.36 0.00 40.69 4.17
2863 3017 2.284258 AGCTCCTCTTCACCGGCT 60.284 61.111 0.00 0.00 0.00 5.52
2869 3024 3.452786 CCGCCGAGCTCCTCTTCA 61.453 66.667 8.47 0.00 0.00 3.02
2883 3038 4.821589 CTCCTCTTCGCCACCCGC 62.822 72.222 0.00 0.00 36.73 6.13
2925 3105 4.529219 TCGCACCTAGCCCGCATG 62.529 66.667 0.00 0.00 41.38 4.06
2926 3106 4.530857 GTCGCACCTAGCCCGCAT 62.531 66.667 0.00 0.00 41.38 4.73
3176 3406 1.322538 GCCAAAATCCCTGTCGCCAT 61.323 55.000 0.00 0.00 0.00 4.40
3177 3407 1.976474 GCCAAAATCCCTGTCGCCA 60.976 57.895 0.00 0.00 0.00 5.69
3178 3408 2.885113 GCCAAAATCCCTGTCGCC 59.115 61.111 0.00 0.00 0.00 5.54
3179 3409 2.485122 CGCCAAAATCCCTGTCGC 59.515 61.111 0.00 0.00 0.00 5.19
3180 3410 1.674322 ACCGCCAAAATCCCTGTCG 60.674 57.895 0.00 0.00 0.00 4.35
3181 3411 1.595093 CCACCGCCAAAATCCCTGTC 61.595 60.000 0.00 0.00 0.00 3.51
3182 3412 1.606313 CCACCGCCAAAATCCCTGT 60.606 57.895 0.00 0.00 0.00 4.00
3183 3413 3.005540 GCCACCGCCAAAATCCCTG 62.006 63.158 0.00 0.00 0.00 4.45
3184 3414 2.679996 GCCACCGCCAAAATCCCT 60.680 61.111 0.00 0.00 0.00 4.20
3239 3469 4.595538 TTCACAGTCGCGCCCGTT 62.596 61.111 0.00 0.00 35.54 4.44


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

AutoCloner maintained by Alex Coulton.