Multiple sequence alignment - TraesCS4D01G148500

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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 TraesCS4D01G148500 chr4D 100.000 3941 0 0 1 3941 148416300 148420240 0.000000e+00 7278.0
1 TraesCS4D01G148500 chr4D 96.441 562 20 0 1097 1658 289987805 289988366 0.000000e+00 928.0
2 TraesCS4D01G148500 chr4D 93.684 95 3 3 383 476 289987687 289987779 5.310000e-29 139.0
3 TraesCS4D01G148500 chr4D 100.000 38 0 0 338 375 148416582 148416619 1.960000e-08 71.3
4 TraesCS4D01G148500 chr4D 100.000 38 0 0 283 320 148416637 148416674 1.960000e-08 71.3
5 TraesCS4D01G148500 chr6D 96.678 2378 71 4 1348 3720 234473256 234475630 0.000000e+00 3947.0
6 TraesCS4D01G148500 chr6D 97.403 616 16 0 3105 3720 68679302 68679917 0.000000e+00 1050.0
7 TraesCS4D01G148500 chr6D 95.045 222 9 2 3713 3934 68679999 68680218 8.110000e-92 348.0
8 TraesCS4D01G148500 chr6D 94.954 218 7 1 3717 3934 321603713 321603926 4.880000e-89 339.0
9 TraesCS4D01G148500 chr6D 94.318 88 4 1 2171 2258 469396390 469396304 2.470000e-27 134.0
10 TraesCS4D01G148500 chr6D 92.424 66 3 1 2943 3006 4870694 4870629 4.190000e-15 93.5
11 TraesCS4D01G148500 chr7A 96.369 1680 53 4 1644 3321 533340717 533339044 0.000000e+00 2758.0
12 TraesCS4D01G148500 chr7A 94.475 724 39 1 1346 2069 437683714 437682992 0.000000e+00 1114.0
13 TraesCS4D01G148500 chr7A 93.762 513 32 0 1557 2069 525546047 525545535 0.000000e+00 771.0
14 TraesCS4D01G148500 chr7A 94.828 232 12 0 1119 1350 686206611 686206380 2.890000e-96 363.0
15 TraesCS4D01G148500 chr7A 95.872 218 8 1 3717 3934 533338614 533338398 6.270000e-93 351.0
16 TraesCS4D01G148500 chr7A 95.876 97 4 0 1254 1350 437683890 437683794 1.470000e-34 158.0
17 TraesCS4D01G148500 chr7A 97.872 47 1 0 272 318 655545573 655545619 9.080000e-12 82.4
18 TraesCS4D01G148500 chr7A 100.000 36 0 0 338 373 655545584 655545619 2.540000e-07 67.6
19 TraesCS4D01G148500 chr5B 97.189 1103 27 2 2223 3321 591954129 591953027 0.000000e+00 1862.0
20 TraesCS4D01G148500 chr5B 95.056 445 19 2 1389 1833 37927006 37927447 0.000000e+00 697.0
21 TraesCS4D01G148500 chr5B 99.130 345 3 0 3376 3720 591953026 591952682 4.330000e-174 621.0
22 TraesCS4D01G148500 chr5B 93.255 341 19 1 3 339 652474220 652474560 2.110000e-137 499.0
23 TraesCS4D01G148500 chr5B 95.946 222 8 1 718 939 37926792 37927012 3.740000e-95 359.0
24 TraesCS4D01G148500 chr5B 95.413 218 9 1 3717 3934 591952597 591952381 2.920000e-91 346.0
25 TraesCS4D01G148500 chr5B 97.619 84 2 0 375 458 53323485 53323568 1.140000e-30 145.0
26 TraesCS4D01G148500 chr6A 97.094 1101 30 1 2223 3321 542013140 542014240 0.000000e+00 1855.0
27 TraesCS4D01G148500 chr6A 94.380 516 23 4 2422 2935 4928652 4928141 0.000000e+00 787.0
28 TraesCS4D01G148500 chr6A 98.551 345 5 0 3376 3720 542014241 542014585 9.360000e-171 610.0
29 TraesCS4D01G148500 chr6A 96.330 218 8 0 3717 3934 542014670 542014887 3.740000e-95 359.0
30 TraesCS4D01G148500 chr6A 93.277 119 7 1 2140 2258 614525296 614525179 1.460000e-39 174.0
31 TraesCS4D01G148500 chr6B 97.003 1101 30 2 2223 3321 104312582 104313681 0.000000e+00 1847.0
32 TraesCS4D01G148500 chr6B 96.235 664 24 1 3057 3720 76902230 76901568 0.000000e+00 1086.0
33 TraesCS4D01G148500 chr6B 93.077 650 21 6 2364 3011 14588302 14587675 0.000000e+00 929.0
34 TraesCS4D01G148500 chr6B 96.101 436 15 2 1398 1833 702628336 702627903 0.000000e+00 710.0
35 TraesCS4D01G148500 chr6B 96.000 225 8 1 718 942 702628559 702628336 8.050000e-97 364.0
36 TraesCS4D01G148500 chr6B 96.330 218 8 0 3717 3934 104314112 104314329 3.740000e-95 359.0
37 TraesCS4D01G148500 chr6B 94.495 218 12 0 3717 3934 76901483 76901266 1.750000e-88 337.0
38 TraesCS4D01G148500 chr6B 96.040 101 4 0 486 586 442428607 442428507 8.760000e-37 165.0
39 TraesCS4D01G148500 chr6B 96.667 60 2 0 3001 3060 76965379 76965320 2.510000e-17 100.0
40 TraesCS4D01G148500 chr6B 97.872 47 1 0 272 318 442428670 442428624 9.080000e-12 82.4
41 TraesCS4D01G148500 chr6B 95.833 48 2 0 2140 2187 715633434 715633387 1.170000e-10 78.7
42 TraesCS4D01G148500 chr6B 100.000 36 0 0 338 373 442428659 442428624 2.540000e-07 67.6
43 TraesCS4D01G148500 chr2B 96.458 1101 35 2 2223 3321 558684865 558685963 0.000000e+00 1814.0
44 TraesCS4D01G148500 chr2B 95.890 219 8 1 3717 3934 558686393 558686611 1.740000e-93 353.0
45 TraesCS4D01G148500 chr4A 94.890 724 37 0 1346 2069 374147185 374146462 0.000000e+00 1133.0
46 TraesCS4D01G148500 chr4A 92.415 501 37 1 1569 2069 193108326 193107827 0.000000e+00 713.0
47 TraesCS4D01G148500 chr4A 95.250 400 19 0 1670 2069 672616328 672615929 5.560000e-178 634.0
48 TraesCS4D01G148500 chr4A 95.370 108 4 1 1097 1203 193108431 193108324 1.880000e-38 171.0
49 TraesCS4D01G148500 chr4A 95.876 97 4 0 1254 1350 374147363 374147267 1.470000e-34 158.0
50 TraesCS4D01G148500 chr4A 93.137 102 6 1 375 476 193108557 193108457 8.820000e-32 148.0
51 TraesCS4D01G148500 chr4A 97.647 85 2 0 392 476 3775155 3775071 3.170000e-31 147.0
52 TraesCS4D01G148500 chr4A 100.000 68 0 0 1097 1164 3775045 3774978 4.130000e-25 126.0
53 TraesCS4D01G148500 chr3B 96.837 664 21 0 3057 3720 215292024 215291361 0.000000e+00 1110.0
54 TraesCS4D01G148500 chr3B 96.386 664 22 2 3057 3720 221919824 221919163 0.000000e+00 1092.0
55 TraesCS4D01G148500 chr3B 95.934 664 27 0 3057 3720 221508485 221507822 0.000000e+00 1077.0
56 TraesCS4D01G148500 chr3B 95.783 664 27 1 3057 3720 215340270 215339608 0.000000e+00 1070.0
57 TraesCS4D01G148500 chr3B 99.242 264 2 0 836 1099 695558640 695558377 9.910000e-131 477.0
58 TraesCS4D01G148500 chr3B 94.958 238 8 1 604 837 695558908 695558671 1.730000e-98 370.0
59 TraesCS4D01G148500 chr3B 94.037 218 12 1 3717 3934 221507737 221507521 2.940000e-86 329.0
60 TraesCS4D01G148500 chr3B 94.690 113 5 1 473 584 695559127 695559015 1.460000e-39 174.0
61 TraesCS4D01G148500 chr3B 97.561 82 2 0 377 458 759966121 759966040 1.480000e-29 141.0
62 TraesCS4D01G148500 chr3B 98.333 60 1 0 3001 3060 215399696 215399637 5.390000e-19 106.0
63 TraesCS4D01G148500 chr3B 98.333 60 1 0 3001 3060 221898066 221898007 5.390000e-19 106.0
64 TraesCS4D01G148500 chr3D 97.627 632 10 2 473 1099 526279633 526279002 0.000000e+00 1079.0
65 TraesCS4D01G148500 chr3D 95.000 400 20 0 1670 2069 568318624 568318225 2.580000e-176 628.0
66 TraesCS4D01G148500 chr5D 95.489 665 24 3 2273 2935 524291309 524291969 0.000000e+00 1057.0
67 TraesCS4D01G148500 chr5D 93.529 340 19 1 3 342 518793082 518793418 1.630000e-138 503.0
68 TraesCS4D01G148500 chr3A 95.768 638 15 5 473 1099 660512958 660512322 0.000000e+00 1018.0
69 TraesCS4D01G148500 chr5A 95.730 562 24 0 1097 1658 433439390 433439951 0.000000e+00 905.0
70 TraesCS4D01G148500 chr5A 95.378 238 11 0 3 240 645406680 645406917 2.870000e-101 379.0
71 TraesCS4D01G148500 chr5A 96.471 85 3 0 392 476 433439280 433439364 1.480000e-29 141.0
72 TraesCS4D01G148500 chr2D 93.555 512 30 2 2422 2932 65812240 65812749 0.000000e+00 760.0
73 TraesCS4D01G148500 chr7D 95.500 400 18 0 1670 2069 449805444 449805843 1.190000e-179 640.0
74 TraesCS4D01G148500 chr1A 94.444 306 17 0 3 308 364020063 364019758 4.610000e-129 472.0
75 TraesCS4D01G148500 chr1A 94.118 306 18 0 3 308 11441856 11441551 2.140000e-127 466.0
76 TraesCS4D01G148500 chr1A 93.651 63 2 1 2943 3003 419296534 419296596 4.190000e-15 93.5
77 TraesCS4D01G148500 chr7B 93.286 283 16 1 1376 1658 738629084 738629363 7.880000e-112 414.0
78 TraesCS4D01G148500 chr7B 90.171 234 9 3 1117 1350 667450578 667450797 3.850000e-75 292.0
79 TraesCS4D01G148500 chr7B 96.429 84 3 0 375 458 738629005 738629088 5.310000e-29 139.0
80 TraesCS4D01G148500 chr7B 96.429 84 3 0 375 458 738759545 738759628 5.310000e-29 139.0
81 TraesCS4D01G148500 chr7B 95.000 40 2 0 1130 1169 629480690 629480651 3.290000e-06 63.9
82 TraesCS4D01G148500 chr4B 97.619 84 2 0 375 458 1729506 1729423 1.140000e-30 145.0
83 TraesCS4D01G148500 chr2A 95.312 64 3 0 1287 1350 744206974 744207037 6.970000e-18 102.0


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 TraesCS4D01G148500 chr4D 148416300 148420240 3940 False 2473.533333 7278 100.000000 1 3941 3 chr4D.!!$F1 3940
1 TraesCS4D01G148500 chr4D 289987687 289988366 679 False 533.500000 928 95.062500 383 1658 2 chr4D.!!$F2 1275
2 TraesCS4D01G148500 chr6D 234473256 234475630 2374 False 3947.000000 3947 96.678000 1348 3720 1 chr6D.!!$F1 2372
3 TraesCS4D01G148500 chr6D 68679302 68680218 916 False 699.000000 1050 96.224000 3105 3934 2 chr6D.!!$F3 829
4 TraesCS4D01G148500 chr7A 533338398 533340717 2319 True 1554.500000 2758 96.120500 1644 3934 2 chr7A.!!$R4 2290
5 TraesCS4D01G148500 chr7A 525545535 525546047 512 True 771.000000 771 93.762000 1557 2069 1 chr7A.!!$R1 512
6 TraesCS4D01G148500 chr7A 437682992 437683890 898 True 636.000000 1114 95.175500 1254 2069 2 chr7A.!!$R3 815
7 TraesCS4D01G148500 chr5B 591952381 591954129 1748 True 943.000000 1862 97.244000 2223 3934 3 chr5B.!!$R1 1711
8 TraesCS4D01G148500 chr5B 37926792 37927447 655 False 528.000000 697 95.501000 718 1833 2 chr5B.!!$F3 1115
9 TraesCS4D01G148500 chr6A 542013140 542014887 1747 False 941.333333 1855 97.325000 2223 3934 3 chr6A.!!$F1 1711
10 TraesCS4D01G148500 chr6A 4928141 4928652 511 True 787.000000 787 94.380000 2422 2935 1 chr6A.!!$R1 513
11 TraesCS4D01G148500 chr6B 104312582 104314329 1747 False 1103.000000 1847 96.666500 2223 3934 2 chr6B.!!$F1 1711
12 TraesCS4D01G148500 chr6B 14587675 14588302 627 True 929.000000 929 93.077000 2364 3011 1 chr6B.!!$R1 647
13 TraesCS4D01G148500 chr6B 76901266 76902230 964 True 711.500000 1086 95.365000 3057 3934 2 chr6B.!!$R4 877
14 TraesCS4D01G148500 chr6B 702627903 702628559 656 True 537.000000 710 96.050500 718 1833 2 chr6B.!!$R6 1115
15 TraesCS4D01G148500 chr2B 558684865 558686611 1746 False 1083.500000 1814 96.174000 2223 3934 2 chr2B.!!$F1 1711
16 TraesCS4D01G148500 chr4A 374146462 374147363 901 True 645.500000 1133 95.383000 1254 2069 2 chr4A.!!$R4 815
17 TraesCS4D01G148500 chr4A 193107827 193108557 730 True 344.000000 713 93.640667 375 2069 3 chr4A.!!$R3 1694
18 TraesCS4D01G148500 chr3B 215291361 215292024 663 True 1110.000000 1110 96.837000 3057 3720 1 chr3B.!!$R1 663
19 TraesCS4D01G148500 chr3B 221919163 221919824 661 True 1092.000000 1092 96.386000 3057 3720 1 chr3B.!!$R5 663
20 TraesCS4D01G148500 chr3B 215339608 215340270 662 True 1070.000000 1070 95.783000 3057 3720 1 chr3B.!!$R2 663
21 TraesCS4D01G148500 chr3B 221507521 221508485 964 True 703.000000 1077 94.985500 3057 3934 2 chr3B.!!$R7 877
22 TraesCS4D01G148500 chr3B 695558377 695559127 750 True 340.333333 477 96.296667 473 1099 3 chr3B.!!$R8 626
23 TraesCS4D01G148500 chr3D 526279002 526279633 631 True 1079.000000 1079 97.627000 473 1099 1 chr3D.!!$R1 626
24 TraesCS4D01G148500 chr5D 524291309 524291969 660 False 1057.000000 1057 95.489000 2273 2935 1 chr5D.!!$F2 662
25 TraesCS4D01G148500 chr3A 660512322 660512958 636 True 1018.000000 1018 95.768000 473 1099 1 chr3A.!!$R1 626
26 TraesCS4D01G148500 chr5A 433439280 433439951 671 False 523.000000 905 96.100500 392 1658 2 chr5A.!!$F2 1266
27 TraesCS4D01G148500 chr2D 65812240 65812749 509 False 760.000000 760 93.555000 2422 2932 1 chr2D.!!$F1 510

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
241 242 0.175073 GTCTCCGGCAAGGTACGAAT 59.825 55.000 0.00 0.00 41.99 3.34 F
647 743 0.324738 TAGCTAGTCTGCAGTGGCCT 60.325 55.000 14.67 8.23 40.13 5.19 F
1875 2101 1.227438 CCACCGGTTCGTCAAGTGT 60.227 57.895 2.97 0.00 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1875 2101 0.034186 GGATGCACATGACCTTGGGA 60.034 55.0 0.0 0.0 0.00 4.37 R
1956 2182 0.175073 GGTTCTTATCGAGGGTGCGT 59.825 55.0 0.0 0.0 0.00 5.24 R
2981 3220 0.899717 ACAATGATGGCTTTGGCGGT 60.900 50.0 0.0 0.0 39.81 5.68 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
17 18 2.893398 GTGGTGTAGAGGGAGCCG 59.107 66.667 0.00 0.00 0.00 5.52
18 19 2.363795 TGGTGTAGAGGGAGCCGG 60.364 66.667 0.00 0.00 0.00 6.13
19 20 3.851128 GGTGTAGAGGGAGCCGGC 61.851 72.222 21.89 21.89 0.00 6.13
20 21 4.208686 GTGTAGAGGGAGCCGGCG 62.209 72.222 23.20 0.00 0.00 6.46
71 72 4.754667 GCGAGGGACGGGGTGTTC 62.755 72.222 0.00 0.00 42.83 3.18
72 73 3.307906 CGAGGGACGGGGTGTTCA 61.308 66.667 0.00 0.00 38.46 3.18
73 74 2.346365 GAGGGACGGGGTGTTCAC 59.654 66.667 0.00 0.00 0.00 3.18
74 75 3.584868 GAGGGACGGGGTGTTCACG 62.585 68.421 0.00 0.00 0.00 4.35
75 76 3.932483 GGGACGGGGTGTTCACGT 61.932 66.667 0.00 0.00 44.35 4.49
76 77 2.663852 GGACGGGGTGTTCACGTG 60.664 66.667 9.94 9.94 41.40 4.49
77 78 2.663852 GACGGGGTGTTCACGTGG 60.664 66.667 17.00 0.00 41.40 4.94
78 79 4.244463 ACGGGGTGTTCACGTGGG 62.244 66.667 17.00 0.00 39.64 4.61
79 80 3.931247 CGGGGTGTTCACGTGGGA 61.931 66.667 17.00 1.64 0.00 4.37
80 81 2.281276 GGGGTGTTCACGTGGGAC 60.281 66.667 17.00 15.05 0.00 4.46
82 83 2.418356 GGTGTTCACGTGGGACGA 59.582 61.111 17.00 3.82 46.05 4.20
83 84 1.952635 GGTGTTCACGTGGGACGAC 60.953 63.158 17.00 13.90 46.05 4.34
84 85 2.026445 TGTTCACGTGGGACGACG 59.974 61.111 17.00 5.33 46.05 5.12
85 86 2.332514 GTTCACGTGGGACGACGA 59.667 61.111 17.00 0.00 46.05 4.20
86 87 1.728426 GTTCACGTGGGACGACGAG 60.728 63.158 17.00 5.95 46.05 4.18
87 88 2.911484 TTCACGTGGGACGACGAGG 61.911 63.158 17.00 5.60 46.05 4.63
88 89 3.359523 CACGTGGGACGACGAGGA 61.360 66.667 13.59 0.00 46.05 3.71
89 90 3.054503 ACGTGGGACGACGAGGAG 61.055 66.667 13.59 0.00 46.05 3.69
90 91 2.745100 CGTGGGACGACGAGGAGA 60.745 66.667 0.00 0.00 46.05 3.71
91 92 2.876219 GTGGGACGACGAGGAGAC 59.124 66.667 0.00 0.00 0.00 3.36
92 93 1.970114 GTGGGACGACGAGGAGACA 60.970 63.158 0.00 0.00 0.00 3.41
93 94 1.674651 TGGGACGACGAGGAGACAG 60.675 63.158 0.00 0.00 0.00 3.51
94 95 1.376942 GGGACGACGAGGAGACAGA 60.377 63.158 0.00 0.00 0.00 3.41
95 96 1.370587 GGGACGACGAGGAGACAGAG 61.371 65.000 0.00 0.00 0.00 3.35
96 97 1.370587 GGACGACGAGGAGACAGAGG 61.371 65.000 0.00 0.00 0.00 3.69
97 98 1.984321 GACGACGAGGAGACAGAGGC 61.984 65.000 0.00 0.00 0.00 4.70
98 99 2.766400 CGACGAGGAGACAGAGGCC 61.766 68.421 0.00 0.00 0.00 5.19
99 100 2.752238 ACGAGGAGACAGAGGCCG 60.752 66.667 0.00 0.00 0.00 6.13
100 101 3.522731 CGAGGAGACAGAGGCCGG 61.523 72.222 0.00 0.00 0.00 6.13
101 102 3.151022 GAGGAGACAGAGGCCGGG 61.151 72.222 2.18 0.00 0.00 5.73
102 103 3.663815 GAGGAGACAGAGGCCGGGA 62.664 68.421 2.18 0.00 0.00 5.14
103 104 2.683933 GGAGACAGAGGCCGGGAA 60.684 66.667 2.18 0.00 0.00 3.97
104 105 2.726351 GGAGACAGAGGCCGGGAAG 61.726 68.421 2.18 0.00 0.00 3.46
105 106 2.685380 AGACAGAGGCCGGGAAGG 60.685 66.667 2.18 0.00 44.97 3.46
106 107 2.683933 GACAGAGGCCGGGAAGGA 60.684 66.667 2.18 0.00 45.00 3.36
107 108 2.685380 ACAGAGGCCGGGAAGGAG 60.685 66.667 2.18 0.00 45.00 3.69
108 109 3.474570 CAGAGGCCGGGAAGGAGG 61.475 72.222 2.18 0.00 45.00 4.30
109 110 4.012721 AGAGGCCGGGAAGGAGGT 62.013 66.667 2.18 0.00 45.00 3.85
110 111 3.787001 GAGGCCGGGAAGGAGGTG 61.787 72.222 2.18 0.00 45.00 4.00
113 114 4.035102 GCCGGGAAGGAGGTGCTT 62.035 66.667 2.18 0.00 45.00 3.91
114 115 2.269241 CCGGGAAGGAGGTGCTTC 59.731 66.667 2.77 2.77 45.00 3.86
115 116 2.125512 CGGGAAGGAGGTGCTTCG 60.126 66.667 5.29 0.00 0.00 3.79
116 117 2.646175 CGGGAAGGAGGTGCTTCGA 61.646 63.158 5.29 0.00 0.00 3.71
117 118 1.219393 GGGAAGGAGGTGCTTCGAG 59.781 63.158 5.29 0.00 0.00 4.04
118 119 1.219393 GGAAGGAGGTGCTTCGAGG 59.781 63.158 5.29 0.00 0.00 4.63
119 120 1.448717 GAAGGAGGTGCTTCGAGGC 60.449 63.158 13.36 13.36 0.00 4.70
120 121 2.172483 GAAGGAGGTGCTTCGAGGCA 62.172 60.000 19.30 19.30 40.15 4.75
121 122 1.557269 AAGGAGGTGCTTCGAGGCAT 61.557 55.000 25.75 10.67 44.34 4.40
122 123 1.522580 GGAGGTGCTTCGAGGCATC 60.523 63.158 25.75 24.86 44.34 3.91
123 124 1.880340 GAGGTGCTTCGAGGCATCG 60.880 63.158 25.75 15.81 46.77 3.84
132 133 3.941081 GAGGCATCGACCTGGAGA 58.059 61.111 0.00 0.00 41.32 3.71
133 134 2.435418 GAGGCATCGACCTGGAGAT 58.565 57.895 0.00 1.90 41.32 2.75
134 135 0.316841 GAGGCATCGACCTGGAGATC 59.683 60.000 0.00 0.00 41.32 2.75
135 136 1.118356 AGGCATCGACCTGGAGATCC 61.118 60.000 0.00 8.51 39.13 3.36
136 137 1.006805 GCATCGACCTGGAGATCCG 60.007 63.158 0.00 0.00 39.43 4.18
137 138 1.006805 CATCGACCTGGAGATCCGC 60.007 63.158 0.00 0.00 39.43 5.54
138 139 1.455773 ATCGACCTGGAGATCCGCA 60.456 57.895 0.00 0.00 39.43 5.69
139 140 1.459455 ATCGACCTGGAGATCCGCAG 61.459 60.000 0.00 0.00 39.43 5.18
140 141 2.107953 GACCTGGAGATCCGCAGC 59.892 66.667 0.00 0.00 39.43 5.25
141 142 3.781770 GACCTGGAGATCCGCAGCG 62.782 68.421 8.18 8.18 39.43 5.18
170 171 3.747976 GCGGTGGTTGGCATGGTC 61.748 66.667 0.00 0.00 0.00 4.02
171 172 3.430862 CGGTGGTTGGCATGGTCG 61.431 66.667 0.00 0.00 0.00 4.79
172 173 3.061848 GGTGGTTGGCATGGTCGG 61.062 66.667 0.00 0.00 0.00 4.79
173 174 3.061848 GTGGTTGGCATGGTCGGG 61.062 66.667 0.00 0.00 0.00 5.14
174 175 3.575247 TGGTTGGCATGGTCGGGT 61.575 61.111 0.00 0.00 0.00 5.28
175 176 2.750237 GGTTGGCATGGTCGGGTC 60.750 66.667 0.00 0.00 0.00 4.46
176 177 2.750237 GTTGGCATGGTCGGGTCC 60.750 66.667 0.00 0.00 0.00 4.46
177 178 4.402528 TTGGCATGGTCGGGTCCG 62.403 66.667 2.52 2.52 41.35 4.79
181 182 4.402528 CATGGTCGGGTCCGGCAA 62.403 66.667 16.07 4.75 46.91 4.52
182 183 4.096003 ATGGTCGGGTCCGGCAAG 62.096 66.667 16.07 0.00 46.91 4.01
184 185 4.754667 GGTCGGGTCCGGCAAGTC 62.755 72.222 16.07 0.00 46.91 3.01
190 191 4.719369 GTCCGGCAAGTCGTCGCT 62.719 66.667 0.00 0.00 42.98 4.93
191 192 4.717629 TCCGGCAAGTCGTCGCTG 62.718 66.667 0.00 0.00 42.98 5.18
194 195 3.482783 GGCAAGTCGTCGCTGCTC 61.483 66.667 11.76 0.00 0.00 4.26
195 196 3.832171 GCAAGTCGTCGCTGCTCG 61.832 66.667 0.00 2.88 40.15 5.03
196 197 3.175240 CAAGTCGTCGCTGCTCGG 61.175 66.667 12.40 0.00 39.05 4.63
206 207 2.588314 CTGCTCGGCTGCATCCTC 60.588 66.667 4.84 0.00 42.48 3.71
207 208 4.519437 TGCTCGGCTGCATCCTCG 62.519 66.667 4.84 0.00 38.12 4.63
213 214 4.212913 GCTGCATCCTCGGCGAGA 62.213 66.667 36.47 22.57 0.00 4.04
214 215 2.733301 CTGCATCCTCGGCGAGAT 59.267 61.111 36.47 23.69 0.00 2.75
215 216 1.664017 CTGCATCCTCGGCGAGATG 60.664 63.158 36.47 31.76 0.00 2.90
216 217 3.040763 GCATCCTCGGCGAGATGC 61.041 66.667 35.17 35.17 45.38 3.91
226 227 3.698382 CGAGATGCGCAAGGTCTC 58.302 61.111 23.50 23.50 36.02 3.36
227 228 1.880340 CGAGATGCGCAAGGTCTCC 60.880 63.158 25.92 13.42 35.99 3.71
228 229 1.880340 GAGATGCGCAAGGTCTCCG 60.880 63.158 23.08 0.00 33.85 4.63
229 230 2.892425 GATGCGCAAGGTCTCCGG 60.892 66.667 17.11 0.00 38.28 5.14
233 234 3.121030 CGCAAGGTCTCCGGCAAG 61.121 66.667 0.00 0.00 0.00 4.01
234 235 2.747855 GCAAGGTCTCCGGCAAGG 60.748 66.667 0.00 0.00 42.97 3.61
235 236 2.750350 CAAGGTCTCCGGCAAGGT 59.250 61.111 0.00 0.00 41.99 3.50
236 237 1.980052 CAAGGTCTCCGGCAAGGTA 59.020 57.895 0.00 0.00 41.99 3.08
237 238 0.391263 CAAGGTCTCCGGCAAGGTAC 60.391 60.000 0.00 0.00 41.99 3.34
238 239 1.885163 AAGGTCTCCGGCAAGGTACG 61.885 60.000 0.00 0.00 41.99 3.67
239 240 2.345760 GGTCTCCGGCAAGGTACGA 61.346 63.158 0.00 0.00 41.99 3.43
240 241 1.588082 GTCTCCGGCAAGGTACGAA 59.412 57.895 0.00 0.00 41.99 3.85
241 242 0.175073 GTCTCCGGCAAGGTACGAAT 59.825 55.000 0.00 0.00 41.99 3.34
242 243 1.406539 GTCTCCGGCAAGGTACGAATA 59.593 52.381 0.00 0.00 41.99 1.75
243 244 2.035576 GTCTCCGGCAAGGTACGAATAT 59.964 50.000 0.00 0.00 41.99 1.28
244 245 2.295349 TCTCCGGCAAGGTACGAATATC 59.705 50.000 0.00 0.00 41.99 1.63
245 246 1.342174 TCCGGCAAGGTACGAATATCC 59.658 52.381 0.00 0.00 41.99 2.59
246 247 1.069513 CCGGCAAGGTACGAATATCCA 59.930 52.381 0.00 0.00 34.51 3.41
247 248 2.289444 CCGGCAAGGTACGAATATCCAT 60.289 50.000 0.00 0.00 34.51 3.41
248 249 2.993899 CGGCAAGGTACGAATATCCATC 59.006 50.000 0.00 0.00 0.00 3.51
249 250 2.993899 GGCAAGGTACGAATATCCATCG 59.006 50.000 0.00 0.00 45.47 3.84
250 251 3.305813 GGCAAGGTACGAATATCCATCGA 60.306 47.826 2.65 0.00 42.76 3.59
251 252 4.495422 GCAAGGTACGAATATCCATCGAT 58.505 43.478 2.65 0.00 42.76 3.59
252 253 4.563184 GCAAGGTACGAATATCCATCGATC 59.437 45.833 0.00 0.00 42.76 3.69
253 254 5.622460 GCAAGGTACGAATATCCATCGATCT 60.622 44.000 0.00 0.00 42.76 2.75
254 255 5.821516 AGGTACGAATATCCATCGATCTC 57.178 43.478 0.00 0.00 42.76 2.75
255 256 5.502079 AGGTACGAATATCCATCGATCTCT 58.498 41.667 0.00 0.00 42.76 3.10
256 257 5.946972 AGGTACGAATATCCATCGATCTCTT 59.053 40.000 0.00 0.00 42.76 2.85
257 258 6.030849 GGTACGAATATCCATCGATCTCTTG 58.969 44.000 0.00 0.00 42.76 3.02
258 259 4.489810 ACGAATATCCATCGATCTCTTGC 58.510 43.478 0.00 0.00 42.76 4.01
259 260 4.021981 ACGAATATCCATCGATCTCTTGCA 60.022 41.667 0.00 0.00 42.76 4.08
260 261 4.562000 CGAATATCCATCGATCTCTTGCAG 59.438 45.833 0.00 0.00 42.76 4.41
261 262 5.477510 GAATATCCATCGATCTCTTGCAGT 58.522 41.667 0.00 0.00 0.00 4.40
262 263 3.834489 ATCCATCGATCTCTTGCAGTT 57.166 42.857 0.00 0.00 0.00 3.16
263 264 4.944619 ATCCATCGATCTCTTGCAGTTA 57.055 40.909 0.00 0.00 0.00 2.24
264 265 4.736126 TCCATCGATCTCTTGCAGTTAA 57.264 40.909 0.00 0.00 0.00 2.01
265 266 5.282055 TCCATCGATCTCTTGCAGTTAAT 57.718 39.130 0.00 0.00 0.00 1.40
266 267 6.405278 TCCATCGATCTCTTGCAGTTAATA 57.595 37.500 0.00 0.00 0.00 0.98
267 268 6.997655 TCCATCGATCTCTTGCAGTTAATAT 58.002 36.000 0.00 0.00 0.00 1.28
268 269 6.870439 TCCATCGATCTCTTGCAGTTAATATG 59.130 38.462 0.00 0.00 0.00 1.78
269 270 6.870439 CCATCGATCTCTTGCAGTTAATATGA 59.130 38.462 0.00 0.00 0.00 2.15
270 271 7.548427 CCATCGATCTCTTGCAGTTAATATGAT 59.452 37.037 0.00 0.00 0.00 2.45
271 272 7.880059 TCGATCTCTTGCAGTTAATATGATG 57.120 36.000 0.00 0.00 0.00 3.07
272 273 6.367149 TCGATCTCTTGCAGTTAATATGATGC 59.633 38.462 0.00 0.00 39.14 3.91
273 274 6.146673 CGATCTCTTGCAGTTAATATGATGCA 59.853 38.462 0.00 0.00 46.29 3.96
279 280 5.823353 TGCAGTTAATATGATGCATGTGTG 58.177 37.500 2.46 0.00 43.34 3.82
280 281 5.217393 GCAGTTAATATGATGCATGTGTGG 58.783 41.667 2.46 0.00 38.54 4.17
281 282 5.221106 GCAGTTAATATGATGCATGTGTGGT 60.221 40.000 2.46 0.00 38.54 4.16
282 283 6.681120 GCAGTTAATATGATGCATGTGTGGTT 60.681 38.462 2.46 0.00 38.54 3.67
283 284 6.693978 CAGTTAATATGATGCATGTGTGGTTG 59.306 38.462 2.46 0.00 0.00 3.77
284 285 3.720949 ATATGATGCATGTGTGGTTGC 57.279 42.857 2.46 0.00 39.33 4.17
288 289 3.039452 TGCATGTGTGGTTGCATCT 57.961 47.368 0.00 0.00 43.54 2.90
289 290 0.599060 TGCATGTGTGGTTGCATCTG 59.401 50.000 0.00 0.00 43.54 2.90
290 291 0.734942 GCATGTGTGGTTGCATCTGC 60.735 55.000 0.00 0.00 38.72 4.26
300 301 3.900855 GCATCTGCACTGGTCCTG 58.099 61.111 0.00 0.00 41.59 3.86
301 302 1.002868 GCATCTGCACTGGTCCTGT 60.003 57.895 0.00 0.00 41.59 4.00
302 303 1.023513 GCATCTGCACTGGTCCTGTC 61.024 60.000 0.00 0.00 41.59 3.51
303 304 0.738762 CATCTGCACTGGTCCTGTCG 60.739 60.000 0.00 0.00 0.00 4.35
304 305 1.892819 ATCTGCACTGGTCCTGTCGG 61.893 60.000 0.00 0.57 0.00 4.79
305 306 3.596066 CTGCACTGGTCCTGTCGGG 62.596 68.421 0.00 0.00 0.00 5.14
306 307 3.311110 GCACTGGTCCTGTCGGGA 61.311 66.667 0.00 0.00 42.77 5.14
307 308 2.973899 CACTGGTCCTGTCGGGAG 59.026 66.667 0.00 0.00 46.10 4.30
308 309 1.606601 CACTGGTCCTGTCGGGAGA 60.607 63.158 0.00 0.00 46.10 3.71
328 329 2.760634 CCACACATGGTACTACTGCA 57.239 50.000 0.00 0.00 41.64 4.41
329 330 3.266510 CCACACATGGTACTACTGCAT 57.733 47.619 0.00 0.00 41.64 3.96
330 331 4.400529 CCACACATGGTACTACTGCATA 57.599 45.455 0.00 0.00 41.64 3.14
331 332 4.119862 CCACACATGGTACTACTGCATAC 58.880 47.826 0.00 0.00 41.64 2.39
332 333 4.141937 CCACACATGGTACTACTGCATACT 60.142 45.833 0.00 0.00 41.64 2.12
333 334 5.043903 CACACATGGTACTACTGCATACTC 58.956 45.833 0.00 0.00 0.00 2.59
334 335 4.709886 ACACATGGTACTACTGCATACTCA 59.290 41.667 0.00 0.00 0.00 3.41
335 336 5.363868 ACACATGGTACTACTGCATACTCAT 59.636 40.000 0.00 0.00 0.00 2.90
336 337 6.549736 ACACATGGTACTACTGCATACTCATA 59.450 38.462 0.00 0.00 0.00 2.15
337 338 7.233553 ACACATGGTACTACTGCATACTCATAT 59.766 37.037 0.00 0.00 0.00 1.78
338 339 7.543520 CACATGGTACTACTGCATACTCATATG 59.456 40.741 0.00 0.00 41.16 1.78
355 356 3.900855 GCATCTGCACTGGTCCTG 58.099 61.111 0.00 0.00 41.59 3.86
356 357 1.002868 GCATCTGCACTGGTCCTGT 60.003 57.895 0.00 0.00 41.59 4.00
357 358 1.023513 GCATCTGCACTGGTCCTGTC 61.024 60.000 0.00 0.00 41.59 3.51
358 359 0.738762 CATCTGCACTGGTCCTGTCG 60.739 60.000 0.00 0.00 0.00 4.35
359 360 1.892819 ATCTGCACTGGTCCTGTCGG 61.893 60.000 0.00 0.57 0.00 4.79
360 361 3.596066 CTGCACTGGTCCTGTCGGG 62.596 68.421 0.00 0.00 0.00 5.14
361 362 3.311110 GCACTGGTCCTGTCGGGA 61.311 66.667 0.00 0.00 42.77 5.14
362 363 2.973899 CACTGGTCCTGTCGGGAG 59.026 66.667 0.00 0.00 46.10 4.30
363 364 1.606601 CACTGGTCCTGTCGGGAGA 60.607 63.158 0.00 0.00 46.10 3.71
476 477 5.977635 TCTAGGACAGTGTTATGTGATTGG 58.022 41.667 0.00 0.00 32.25 3.16
484 485 6.939730 ACAGTGTTATGTGATTGGTGTTCATA 59.060 34.615 0.00 0.00 30.46 2.15
578 579 8.366401 AGATCCTATACTTCTGATGTGTTGATG 58.634 37.037 6.46 0.00 0.00 3.07
594 595 6.209589 TGTGTTGATGCTAAGACTCTAAGAGT 59.790 38.462 0.00 0.00 46.42 3.24
647 743 0.324738 TAGCTAGTCTGCAGTGGCCT 60.325 55.000 14.67 8.23 40.13 5.19
715 811 1.267806 GCATGGGTTTCTGTCAGTGTG 59.732 52.381 0.00 0.00 0.00 3.82
1061 1199 8.141268 TGGTTTTGTCCAGTTCTCAAATAATTC 58.859 33.333 0.00 0.00 32.41 2.17
1199 1338 3.706594 GACCTCCTGGACTCACATGATAA 59.293 47.826 0.00 0.00 37.04 1.75
1206 1345 5.337894 CCTGGACTCACATGATAACAAGAGT 60.338 44.000 0.00 6.02 38.45 3.24
1281 1420 5.298989 ACAACAGGGTGTGAACATACTTA 57.701 39.130 0.00 0.00 0.00 2.24
1318 1457 7.806690 TGTTTGCTTGTTTCTGTATGAGATAC 58.193 34.615 0.00 0.00 34.22 2.24
1334 1473 3.097614 AGATACGCTACTTGTGAAGGGT 58.902 45.455 0.00 0.00 41.27 4.34
1393 1619 5.715279 AGCACTTGTAGTGGACAACTAGATA 59.285 40.000 8.73 0.00 46.01 1.98
1530 1756 8.743714 GTTATGAGAATTGTTCCTTCAAGGATT 58.256 33.333 7.07 0.00 45.34 3.01
1626 1852 2.645838 TTTCTTGAAGCTCCACTGCT 57.354 45.000 0.00 0.00 46.40 4.24
1629 1855 1.909141 CTTGAAGCTCCACTGCTGCG 61.909 60.000 0.00 0.00 43.24 5.18
1875 2101 1.227438 CCACCGGTTCGTCAAGTGT 60.227 57.895 2.97 0.00 0.00 3.55
1897 2123 1.615116 CCAAGGTCATGTGCATCCAGT 60.615 52.381 0.00 0.00 0.00 4.00
1956 2182 2.280797 GCGCTCCACCAGTTCACA 60.281 61.111 0.00 0.00 0.00 3.58
1968 2194 1.374252 GTTCACACGCACCCTCGAT 60.374 57.895 0.00 0.00 0.00 3.59
2100 2326 3.706600 ACATGGATTGGCTGCAATTTT 57.293 38.095 0.50 0.00 0.00 1.82
2126 2352 5.919141 GGCTACATTGTACTCCACGTATTAG 59.081 44.000 0.00 0.00 0.00 1.73
2299 2528 6.942163 ATATCTGGCTACATTGTACTCCAT 57.058 37.500 11.41 3.91 0.00 3.41
2429 2658 4.040952 AGCTTGGAAGAATGACTACACACT 59.959 41.667 0.00 0.00 0.00 3.55
2496 2725 9.989869 CATAAAATATTTGCATGCATGACAAAA 57.010 25.926 32.88 26.41 37.35 2.44
2536 2766 9.196139 ACTCTCATGCTTACTTAGATTAGAAGT 57.804 33.333 0.00 0.00 40.27 3.01
2787 3024 4.083110 AGCATGCATGTGTGACTTAGTTTC 60.083 41.667 26.79 5.87 0.00 2.78
2808 3045 1.153597 GGTGTGTTTTGCTTGCAGGC 61.154 55.000 14.88 14.88 0.00 4.85
2970 3209 8.871125 TGGGTGAACTAAGCCATTTTTATTTAA 58.129 29.630 0.00 0.00 42.69 1.52
3081 3322 8.724229 CATGTTCATATAGCTAATTTGCTGCTA 58.276 33.333 22.30 14.28 43.87 3.49
3374 3669 6.435591 TGACAATGGTCTGATCCTAGCTATAG 59.564 42.308 1.02 0.00 44.61 1.31
3512 3808 8.279800 TGTTGTAGACAAATGTATGAAACTTCG 58.720 33.333 0.00 0.00 37.63 3.79
3795 4179 5.060506 TCTATTTTCTTGCGTCACCTTTCA 58.939 37.500 0.00 0.00 0.00 2.69
3934 4319 2.238521 TGGCTCCAGTGTTTTGATTCC 58.761 47.619 0.00 0.00 0.00 3.01
3935 4320 2.158475 TGGCTCCAGTGTTTTGATTCCT 60.158 45.455 0.00 0.00 0.00 3.36
3936 4321 2.893489 GGCTCCAGTGTTTTGATTCCTT 59.107 45.455 0.00 0.00 0.00 3.36
3937 4322 3.321968 GGCTCCAGTGTTTTGATTCCTTT 59.678 43.478 0.00 0.00 0.00 3.11
3938 4323 4.301628 GCTCCAGTGTTTTGATTCCTTTG 58.698 43.478 0.00 0.00 0.00 2.77
3939 4324 4.202151 GCTCCAGTGTTTTGATTCCTTTGT 60.202 41.667 0.00 0.00 0.00 2.83
3940 4325 5.682212 GCTCCAGTGTTTTGATTCCTTTGTT 60.682 40.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.851128 GCCGGCTCCCTCTACACC 61.851 72.222 22.15 0.00 0.00 4.16
54 55 4.754667 GAACACCCCGTCCCTCGC 62.755 72.222 0.00 0.00 38.35 5.03
55 56 3.307906 TGAACACCCCGTCCCTCG 61.308 66.667 0.00 0.00 39.52 4.63
56 57 2.346365 GTGAACACCCCGTCCCTC 59.654 66.667 0.00 0.00 0.00 4.30
57 58 3.622826 CGTGAACACCCCGTCCCT 61.623 66.667 0.00 0.00 0.00 4.20
58 59 3.932483 ACGTGAACACCCCGTCCC 61.932 66.667 0.00 0.00 0.00 4.46
59 60 2.663852 CACGTGAACACCCCGTCC 60.664 66.667 10.90 0.00 31.46 4.79
60 61 2.663852 CCACGTGAACACCCCGTC 60.664 66.667 19.30 0.00 31.46 4.79
61 62 4.244463 CCCACGTGAACACCCCGT 62.244 66.667 19.30 0.00 34.71 5.28
62 63 3.931247 TCCCACGTGAACACCCCG 61.931 66.667 19.30 0.00 0.00 5.73
63 64 2.281276 GTCCCACGTGAACACCCC 60.281 66.667 19.30 0.00 0.00 4.95
64 65 2.663852 CGTCCCACGTGAACACCC 60.664 66.667 19.30 0.00 36.74 4.61
65 66 1.952635 GTCGTCCCACGTGAACACC 60.953 63.158 19.30 4.39 43.14 4.16
66 67 2.297912 CGTCGTCCCACGTGAACAC 61.298 63.158 19.30 9.19 43.14 3.32
67 68 2.026445 CGTCGTCCCACGTGAACA 59.974 61.111 19.30 0.00 43.14 3.18
68 69 1.728426 CTCGTCGTCCCACGTGAAC 60.728 63.158 19.30 13.72 43.14 3.18
69 70 2.640989 CTCGTCGTCCCACGTGAA 59.359 61.111 19.30 1.09 43.14 3.18
70 71 3.359523 CCTCGTCGTCCCACGTGA 61.360 66.667 19.30 0.00 43.14 4.35
71 72 3.324099 CTCCTCGTCGTCCCACGTG 62.324 68.421 9.08 9.08 43.14 4.49
72 73 3.054503 CTCCTCGTCGTCCCACGT 61.055 66.667 0.00 0.00 43.14 4.49
73 74 2.745100 TCTCCTCGTCGTCCCACG 60.745 66.667 0.00 0.00 44.19 4.94
74 75 1.924320 CTGTCTCCTCGTCGTCCCAC 61.924 65.000 0.00 0.00 0.00 4.61
75 76 1.674651 CTGTCTCCTCGTCGTCCCA 60.675 63.158 0.00 0.00 0.00 4.37
76 77 1.370587 CTCTGTCTCCTCGTCGTCCC 61.371 65.000 0.00 0.00 0.00 4.46
77 78 1.370587 CCTCTGTCTCCTCGTCGTCC 61.371 65.000 0.00 0.00 0.00 4.79
78 79 1.984321 GCCTCTGTCTCCTCGTCGTC 61.984 65.000 0.00 0.00 0.00 4.20
79 80 2.041686 GCCTCTGTCTCCTCGTCGT 61.042 63.158 0.00 0.00 0.00 4.34
80 81 2.766400 GGCCTCTGTCTCCTCGTCG 61.766 68.421 0.00 0.00 0.00 5.12
81 82 2.766400 CGGCCTCTGTCTCCTCGTC 61.766 68.421 0.00 0.00 0.00 4.20
82 83 2.752238 CGGCCTCTGTCTCCTCGT 60.752 66.667 0.00 0.00 0.00 4.18
83 84 3.522731 CCGGCCTCTGTCTCCTCG 61.523 72.222 0.00 0.00 0.00 4.63
84 85 3.151022 CCCGGCCTCTGTCTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
85 86 3.239627 TTCCCGGCCTCTGTCTCCT 62.240 63.158 0.00 0.00 0.00 3.69
86 87 2.683933 TTCCCGGCCTCTGTCTCC 60.684 66.667 0.00 0.00 0.00 3.71
87 88 2.726351 CCTTCCCGGCCTCTGTCTC 61.726 68.421 0.00 0.00 0.00 3.36
88 89 2.685380 CCTTCCCGGCCTCTGTCT 60.685 66.667 0.00 0.00 0.00 3.41
89 90 2.683933 TCCTTCCCGGCCTCTGTC 60.684 66.667 0.00 0.00 0.00 3.51
90 91 2.685380 CTCCTTCCCGGCCTCTGT 60.685 66.667 0.00 0.00 0.00 3.41
91 92 3.474570 CCTCCTTCCCGGCCTCTG 61.475 72.222 0.00 0.00 0.00 3.35
92 93 4.012721 ACCTCCTTCCCGGCCTCT 62.013 66.667 0.00 0.00 0.00 3.69
93 94 3.787001 CACCTCCTTCCCGGCCTC 61.787 72.222 0.00 0.00 0.00 4.70
96 97 3.978571 GAAGCACCTCCTTCCCGGC 62.979 68.421 0.00 0.00 36.15 6.13
97 98 2.269241 GAAGCACCTCCTTCCCGG 59.731 66.667 0.00 0.00 36.15 5.73
98 99 2.125512 CGAAGCACCTCCTTCCCG 60.126 66.667 0.00 0.00 38.35 5.14
99 100 1.219393 CTCGAAGCACCTCCTTCCC 59.781 63.158 0.00 0.00 38.35 3.97
100 101 1.219393 CCTCGAAGCACCTCCTTCC 59.781 63.158 0.00 0.00 38.35 3.46
101 102 1.448717 GCCTCGAAGCACCTCCTTC 60.449 63.158 0.00 0.00 38.24 3.46
102 103 2.217038 TGCCTCGAAGCACCTCCTT 61.217 57.895 4.15 0.00 38.00 3.36
103 104 2.604686 TGCCTCGAAGCACCTCCT 60.605 61.111 4.15 0.00 38.00 3.69
114 115 1.459455 ATCTCCAGGTCGATGCCTCG 61.459 60.000 4.89 4.89 46.41 4.63
115 116 0.316841 GATCTCCAGGTCGATGCCTC 59.683 60.000 0.00 0.00 36.58 4.70
116 117 1.118356 GGATCTCCAGGTCGATGCCT 61.118 60.000 0.00 0.00 39.99 4.75
117 118 1.369321 GGATCTCCAGGTCGATGCC 59.631 63.158 0.00 0.00 35.64 4.40
118 119 1.006805 CGGATCTCCAGGTCGATGC 60.007 63.158 0.00 1.92 35.14 3.91
119 120 1.006805 GCGGATCTCCAGGTCGATG 60.007 63.158 0.00 0.00 35.14 3.84
120 121 1.455773 TGCGGATCTCCAGGTCGAT 60.456 57.895 0.00 0.00 35.14 3.59
121 122 2.044352 TGCGGATCTCCAGGTCGA 60.044 61.111 0.00 0.00 35.14 4.20
122 123 2.415010 CTGCGGATCTCCAGGTCG 59.585 66.667 0.00 0.00 35.14 4.79
123 124 2.107953 GCTGCGGATCTCCAGGTC 59.892 66.667 0.00 0.00 35.14 3.85
124 125 3.842923 CGCTGCGGATCTCCAGGT 61.843 66.667 15.40 0.00 35.14 4.00
153 154 3.747976 GACCATGCCAACCACCGC 61.748 66.667 0.00 0.00 0.00 5.68
154 155 3.430862 CGACCATGCCAACCACCG 61.431 66.667 0.00 0.00 0.00 4.94
155 156 3.061848 CCGACCATGCCAACCACC 61.062 66.667 0.00 0.00 0.00 4.61
156 157 3.061848 CCCGACCATGCCAACCAC 61.062 66.667 0.00 0.00 0.00 4.16
157 158 3.561120 GACCCGACCATGCCAACCA 62.561 63.158 0.00 0.00 0.00 3.67
158 159 2.750237 GACCCGACCATGCCAACC 60.750 66.667 0.00 0.00 0.00 3.77
159 160 2.750237 GGACCCGACCATGCCAAC 60.750 66.667 0.00 0.00 0.00 3.77
160 161 4.402528 CGGACCCGACCATGCCAA 62.403 66.667 1.54 0.00 42.83 4.52
164 165 4.402528 TTGCCGGACCCGACCATG 62.403 66.667 5.05 0.00 42.83 3.66
165 166 4.096003 CTTGCCGGACCCGACCAT 62.096 66.667 5.05 0.00 42.83 3.55
167 168 4.754667 GACTTGCCGGACCCGACC 62.755 72.222 5.05 1.28 42.83 4.79
173 174 4.719369 AGCGACGACTTGCCGGAC 62.719 66.667 5.05 0.00 0.00 4.79
174 175 4.717629 CAGCGACGACTTGCCGGA 62.718 66.667 5.05 0.00 0.00 5.14
177 178 3.482783 GAGCAGCGACGACTTGCC 61.483 66.667 13.44 4.75 38.58 4.52
178 179 3.832171 CGAGCAGCGACGACTTGC 61.832 66.667 0.00 5.13 44.57 4.01
179 180 3.175240 CCGAGCAGCGACGACTTG 61.175 66.667 14.76 0.00 44.57 3.16
196 197 3.512223 ATCTCGCCGAGGATGCAGC 62.512 63.158 15.08 0.00 0.00 5.25
197 198 1.664017 CATCTCGCCGAGGATGCAG 60.664 63.158 15.08 0.00 33.98 4.41
198 199 2.418777 CATCTCGCCGAGGATGCA 59.581 61.111 15.08 0.00 33.98 3.96
200 201 2.732468 CGCATCTCGCCGAGGATG 60.732 66.667 15.08 16.20 41.36 3.51
209 210 1.880340 GGAGACCTTGCGCATCTCG 60.880 63.158 25.34 11.44 39.89 4.04
210 211 1.880340 CGGAGACCTTGCGCATCTC 60.880 63.158 24.74 24.74 38.53 2.75
211 212 2.185350 CGGAGACCTTGCGCATCT 59.815 61.111 12.75 12.10 32.64 2.90
212 213 2.892425 CCGGAGACCTTGCGCATC 60.892 66.667 12.75 6.06 39.57 3.91
216 217 3.121030 CTTGCCGGAGACCTTGCG 61.121 66.667 5.05 0.00 40.71 4.85
217 218 2.180159 TACCTTGCCGGAGACCTTGC 62.180 60.000 5.05 0.00 36.31 4.01
218 219 0.391263 GTACCTTGCCGGAGACCTTG 60.391 60.000 5.05 0.00 36.31 3.61
219 220 1.885163 CGTACCTTGCCGGAGACCTT 61.885 60.000 5.05 0.00 36.31 3.50
220 221 2.348888 CGTACCTTGCCGGAGACCT 61.349 63.158 5.05 0.00 36.31 3.85
221 222 1.880819 TTCGTACCTTGCCGGAGACC 61.881 60.000 5.05 0.00 36.31 3.85
222 223 0.175073 ATTCGTACCTTGCCGGAGAC 59.825 55.000 5.05 0.00 36.31 3.36
223 224 1.766494 TATTCGTACCTTGCCGGAGA 58.234 50.000 5.05 0.00 36.31 3.71
224 225 2.609737 GGATATTCGTACCTTGCCGGAG 60.610 54.545 5.05 0.00 36.31 4.63
225 226 1.342174 GGATATTCGTACCTTGCCGGA 59.658 52.381 5.05 0.00 36.31 5.14
226 227 1.069513 TGGATATTCGTACCTTGCCGG 59.930 52.381 0.00 0.00 39.35 6.13
227 228 2.519377 TGGATATTCGTACCTTGCCG 57.481 50.000 0.00 0.00 0.00 5.69
228 229 2.993899 CGATGGATATTCGTACCTTGCC 59.006 50.000 0.00 0.00 32.08 4.52
229 230 3.909430 TCGATGGATATTCGTACCTTGC 58.091 45.455 0.00 0.00 37.82 4.01
230 231 5.955488 AGATCGATGGATATTCGTACCTTG 58.045 41.667 0.54 0.00 37.82 3.61
231 232 5.946972 AGAGATCGATGGATATTCGTACCTT 59.053 40.000 0.54 0.00 37.82 3.50
232 233 5.502079 AGAGATCGATGGATATTCGTACCT 58.498 41.667 0.54 0.00 37.82 3.08
233 234 5.821516 AGAGATCGATGGATATTCGTACC 57.178 43.478 0.54 0.00 37.82 3.34
234 235 5.513495 GCAAGAGATCGATGGATATTCGTAC 59.487 44.000 0.54 0.00 37.82 3.67
235 236 5.183140 TGCAAGAGATCGATGGATATTCGTA 59.817 40.000 0.54 0.00 37.82 3.43
236 237 4.021981 TGCAAGAGATCGATGGATATTCGT 60.022 41.667 0.54 0.00 37.82 3.85
237 238 4.488879 TGCAAGAGATCGATGGATATTCG 58.511 43.478 0.54 0.00 37.94 3.34
238 239 5.477510 ACTGCAAGAGATCGATGGATATTC 58.522 41.667 0.54 0.00 37.43 1.75
239 240 5.480642 ACTGCAAGAGATCGATGGATATT 57.519 39.130 0.54 0.00 37.43 1.28
240 241 5.480642 AACTGCAAGAGATCGATGGATAT 57.519 39.130 0.54 0.00 37.43 1.63
241 242 4.944619 AACTGCAAGAGATCGATGGATA 57.055 40.909 0.54 0.00 37.43 2.59
242 243 3.834489 AACTGCAAGAGATCGATGGAT 57.166 42.857 0.54 0.00 37.43 3.41
243 244 4.736126 TTAACTGCAAGAGATCGATGGA 57.264 40.909 0.54 0.00 37.43 3.41
244 245 6.870439 TCATATTAACTGCAAGAGATCGATGG 59.130 38.462 0.54 0.00 37.43 3.51
245 246 7.880059 TCATATTAACTGCAAGAGATCGATG 57.120 36.000 0.54 0.00 37.43 3.84
246 247 7.064371 GCATCATATTAACTGCAAGAGATCGAT 59.936 37.037 0.00 0.00 37.43 3.59
247 248 6.367149 GCATCATATTAACTGCAAGAGATCGA 59.633 38.462 0.00 0.00 37.43 3.59
248 249 6.146673 TGCATCATATTAACTGCAAGAGATCG 59.853 38.462 0.00 0.00 41.33 3.69
249 250 7.430992 TGCATCATATTAACTGCAAGAGATC 57.569 36.000 0.00 0.00 41.33 2.75
250 251 7.447545 ACATGCATCATATTAACTGCAAGAGAT 59.552 33.333 0.00 0.00 46.59 2.75
251 252 6.769341 ACATGCATCATATTAACTGCAAGAGA 59.231 34.615 0.00 0.00 46.59 3.10
252 253 6.856426 CACATGCATCATATTAACTGCAAGAG 59.144 38.462 0.00 0.41 46.59 2.85
253 254 6.319405 ACACATGCATCATATTAACTGCAAGA 59.681 34.615 0.00 0.00 46.59 3.02
254 255 6.416750 CACACATGCATCATATTAACTGCAAG 59.583 38.462 0.00 0.00 46.59 4.01
255 256 6.267070 CACACATGCATCATATTAACTGCAA 58.733 36.000 0.00 0.00 46.59 4.08
257 258 5.217393 CCACACATGCATCATATTAACTGC 58.783 41.667 0.00 0.00 35.21 4.40
258 259 6.381481 ACCACACATGCATCATATTAACTG 57.619 37.500 0.00 0.00 0.00 3.16
259 260 6.681120 GCAACCACACATGCATCATATTAACT 60.681 38.462 0.00 0.00 42.12 2.24
260 261 5.459762 GCAACCACACATGCATCATATTAAC 59.540 40.000 0.00 0.00 42.12 2.01
261 262 5.126707 TGCAACCACACATGCATCATATTAA 59.873 36.000 0.00 0.00 46.87 1.40
262 263 4.643784 TGCAACCACACATGCATCATATTA 59.356 37.500 0.00 0.00 46.87 0.98
263 264 3.447944 TGCAACCACACATGCATCATATT 59.552 39.130 0.00 0.00 46.87 1.28
264 265 3.025262 TGCAACCACACATGCATCATAT 58.975 40.909 0.00 0.00 46.87 1.78
265 266 2.444421 TGCAACCACACATGCATCATA 58.556 42.857 0.00 0.00 46.87 2.15
266 267 1.258676 TGCAACCACACATGCATCAT 58.741 45.000 0.00 0.00 46.87 2.45
267 268 2.729692 TGCAACCACACATGCATCA 58.270 47.368 0.00 0.00 46.87 3.07
271 272 0.734942 GCAGATGCAACCACACATGC 60.735 55.000 0.00 0.00 42.86 4.06
272 273 3.411808 GCAGATGCAACCACACATG 57.588 52.632 0.00 0.00 41.59 3.21
283 284 1.002868 ACAGGACCAGTGCAGATGC 60.003 57.895 0.00 0.00 42.50 3.91
284 285 0.738762 CGACAGGACCAGTGCAGATG 60.739 60.000 0.00 0.00 0.00 2.90
285 286 1.593787 CGACAGGACCAGTGCAGAT 59.406 57.895 0.00 0.00 0.00 2.90
286 287 2.574018 CCGACAGGACCAGTGCAGA 61.574 63.158 0.00 0.00 41.02 4.26
287 288 2.047844 CCGACAGGACCAGTGCAG 60.048 66.667 0.00 0.00 41.02 4.41
288 289 3.625897 CCCGACAGGACCAGTGCA 61.626 66.667 0.00 0.00 41.02 4.57
289 290 3.302347 CTCCCGACAGGACCAGTGC 62.302 68.421 0.00 0.00 40.93 4.40
290 291 1.606601 TCTCCCGACAGGACCAGTG 60.607 63.158 0.00 0.00 40.93 3.66
291 292 1.606889 GTCTCCCGACAGGACCAGT 60.607 63.158 0.00 0.00 40.93 4.00
292 293 2.352032 GGTCTCCCGACAGGACCAG 61.352 68.421 6.49 0.00 46.14 4.00
293 294 2.283676 GGTCTCCCGACAGGACCA 60.284 66.667 6.49 0.00 46.14 4.02
294 295 2.283676 TGGTCTCCCGACAGGACC 60.284 66.667 0.00 0.00 46.80 4.46
295 296 1.906824 TGTGGTCTCCCGACAGGAC 60.907 63.158 0.00 0.00 40.93 3.85
296 297 1.906824 GTGTGGTCTCCCGACAGGA 60.907 63.158 0.00 0.00 44.91 3.86
297 298 1.544825 ATGTGTGGTCTCCCGACAGG 61.545 60.000 0.00 0.00 42.05 4.00
298 299 0.390340 CATGTGTGGTCTCCCGACAG 60.390 60.000 0.00 0.00 42.05 3.51
299 300 1.671166 CATGTGTGGTCTCCCGACA 59.329 57.895 0.00 0.00 42.05 4.35
300 301 1.079127 CCATGTGTGGTCTCCCGAC 60.079 63.158 0.00 0.00 40.83 4.79
301 302 3.387716 CCATGTGTGGTCTCCCGA 58.612 61.111 0.00 0.00 40.83 5.14
310 311 5.011090 AGTATGCAGTAGTACCATGTGTG 57.989 43.478 0.00 0.00 0.00 3.82
311 312 4.709886 TGAGTATGCAGTAGTACCATGTGT 59.290 41.667 0.00 0.00 0.00 3.72
312 313 5.262588 TGAGTATGCAGTAGTACCATGTG 57.737 43.478 0.00 0.00 0.00 3.21
313 314 7.606349 CATATGAGTATGCAGTAGTACCATGT 58.394 38.462 0.00 0.00 31.98 3.21
338 339 1.002868 ACAGGACCAGTGCAGATGC 60.003 57.895 0.00 0.00 42.50 3.91
339 340 0.738762 CGACAGGACCAGTGCAGATG 60.739 60.000 0.00 0.00 0.00 2.90
340 341 1.593787 CGACAGGACCAGTGCAGAT 59.406 57.895 0.00 0.00 0.00 2.90
341 342 2.574018 CCGACAGGACCAGTGCAGA 61.574 63.158 0.00 0.00 41.02 4.26
342 343 2.047844 CCGACAGGACCAGTGCAG 60.048 66.667 0.00 0.00 41.02 4.41
343 344 3.625897 CCCGACAGGACCAGTGCA 61.626 66.667 0.00 0.00 41.02 4.57
344 345 3.302347 CTCCCGACAGGACCAGTGC 62.302 68.421 0.00 0.00 40.93 4.40
345 346 1.606601 TCTCCCGACAGGACCAGTG 60.607 63.158 0.00 0.00 40.93 3.66
346 347 1.606889 GTCTCCCGACAGGACCAGT 60.607 63.158 0.00 0.00 40.93 4.00
347 348 2.352032 GGTCTCCCGACAGGACCAG 61.352 68.421 6.49 0.00 46.14 4.00
348 349 2.283676 GGTCTCCCGACAGGACCA 60.284 66.667 6.49 0.00 46.14 4.02
349 350 2.283676 TGGTCTCCCGACAGGACC 60.284 66.667 0.00 0.00 46.80 4.46
350 351 1.906824 TGTGGTCTCCCGACAGGAC 60.907 63.158 0.00 0.00 40.93 3.85
351 352 1.906824 GTGTGGTCTCCCGACAGGA 60.907 63.158 0.00 0.00 44.91 3.86
352 353 1.544825 ATGTGTGGTCTCCCGACAGG 61.545 60.000 0.00 0.00 42.05 4.00
353 354 0.390340 CATGTGTGGTCTCCCGACAG 60.390 60.000 0.00 0.00 42.05 3.51
354 355 1.671166 CATGTGTGGTCTCCCGACA 59.329 57.895 0.00 0.00 42.05 4.35
355 356 1.079127 CCATGTGTGGTCTCCCGAC 60.079 63.158 0.00 0.00 40.83 4.79
356 357 3.387716 CCATGTGTGGTCTCCCGA 58.612 61.111 0.00 0.00 40.83 5.14
365 366 6.653228 ACAACAACTGTAGACACCATGTGTG 61.653 44.000 4.33 11.40 41.08 3.82
366 367 4.625324 ACAACAACTGTAGACACCATGTGT 60.625 41.667 0.00 0.00 42.68 3.72
367 368 3.876914 ACAACAACTGTAGACACCATGTG 59.123 43.478 0.00 0.00 36.10 3.21
368 369 4.150897 ACAACAACTGTAGACACCATGT 57.849 40.909 0.00 0.00 36.10 3.21
381 382 3.881089 GCTACAACCAACCTACAACAACT 59.119 43.478 0.00 0.00 0.00 3.16
461 462 7.994425 TTATGAACACCAATCACATAACACT 57.006 32.000 0.00 0.00 31.46 3.55
476 477 5.581085 AGGACGCAACTAGATTTATGAACAC 59.419 40.000 0.00 0.00 0.00 3.32
484 485 4.695928 GGAAGAAAGGACGCAACTAGATTT 59.304 41.667 0.00 0.00 0.00 2.17
578 579 5.838531 TGGCTAACTCTTAGAGTCTTAGC 57.161 43.478 26.04 26.04 42.59 3.09
647 743 4.591498 ACAGAGTAATGTACACTTGTGGGA 59.409 41.667 0.00 0.00 0.00 4.37
715 811 7.823149 AACTTGCTCAAAATAGAAATGATGC 57.177 32.000 0.00 0.00 0.00 3.91
1199 1338 7.416964 AATCAGCATTAGTCTAGACTCTTGT 57.583 36.000 28.42 13.92 42.54 3.16
1206 1345 6.511416 GCTCAGAAATCAGCATTAGTCTAGA 58.489 40.000 0.00 0.00 35.56 2.43
1318 1457 1.878953 ACAACCCTTCACAAGTAGCG 58.121 50.000 0.00 0.00 0.00 4.26
1334 1473 5.356190 CCACACGAGTCTAATCTAGGTACAA 59.644 44.000 0.00 0.00 0.00 2.41
1393 1619 5.537674 ACTGGAACAAGAAGATTTGCAGAAT 59.462 36.000 8.78 0.00 40.15 2.40
1530 1756 7.920160 TTGAACACATATGTCATTCTAGCAA 57.080 32.000 21.64 11.29 38.45 3.91
1626 1852 1.116536 TGTACCAGGAACAGGACGCA 61.117 55.000 0.00 0.00 37.04 5.24
1629 1855 0.685097 TGCTGTACCAGGAACAGGAC 59.315 55.000 0.00 0.00 43.71 3.85
1795 2021 0.677288 TTCGGCCTCTTCTCGAACAA 59.323 50.000 0.00 0.00 37.88 2.83
1835 2061 4.351054 CCTTCTTGGGCGGCAGGT 62.351 66.667 12.47 0.00 0.00 4.00
1875 2101 0.034186 GGATGCACATGACCTTGGGA 60.034 55.000 0.00 0.00 0.00 4.37
1938 2164 3.414700 GTGAACTGGTGGAGCGCG 61.415 66.667 0.00 0.00 0.00 6.86
1956 2182 0.175073 GGTTCTTATCGAGGGTGCGT 59.825 55.000 0.00 0.00 0.00 5.24
1968 2194 7.807977 AGTTTCGTATATACCGAGGTTCTTA 57.192 36.000 7.30 0.00 35.49 2.10
2100 2326 2.300723 ACGTGGAGTACAATGTAGCCAA 59.699 45.455 14.16 0.50 0.00 4.52
2126 2352 6.425504 CAAGAATCTGAACACTGACAAGAAC 58.574 40.000 0.00 0.00 0.00 3.01
2496 2725 2.304092 TGAGAGTGTACGTGTTGGAGT 58.696 47.619 0.00 0.00 0.00 3.85
2787 3024 1.563111 CTGCAAGCAAAACACACCAG 58.437 50.000 0.00 0.00 0.00 4.00
2808 3045 1.080569 GCGGCCTTCACAACAATGG 60.081 57.895 0.00 0.00 0.00 3.16
2970 3209 2.359900 CTTTGGCGGTAGAGAGCAAAT 58.640 47.619 0.00 0.00 34.54 2.32
2981 3220 0.899717 ACAATGATGGCTTTGGCGGT 60.900 50.000 0.00 0.00 39.81 5.68
3081 3322 7.836183 AGACCTTCCTAGAATTTTATGCACAAT 59.164 33.333 0.00 0.00 0.00 2.71
3374 3669 6.463995 TGCAAATTATTGTCCCCTACATTC 57.536 37.500 0.00 0.00 38.10 2.67
3512 3808 3.888093 AGTTGTCGTCCACAGCTAC 57.112 52.632 0.00 0.00 44.28 3.58
3752 4136 4.511527 AGAGCACTTTACTCATGTCATGG 58.488 43.478 12.90 6.40 36.58 3.66
3758 4142 7.695618 GCAAGAAAATAGAGCACTTTACTCATG 59.304 37.037 0.00 0.00 36.58 3.07
3891 4275 8.177663 GCCAATATATTATGAACAGACCATTCG 58.822 37.037 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.