Multiple sequence alignment - TraesCS4B01G194100

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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 TraesCS4B01G194100 chr4B 100.000 5331 0 0 1 5331 417349154 417354484 0.000000e+00 9845.0
1 TraesCS4B01G194100 chr4B 90.519 1002 85 10 4334 5330 180943422 180942426 0.000000e+00 1315.0
2 TraesCS4B01G194100 chr4A 91.758 2184 95 25 61 2203 133844501 133842362 0.000000e+00 2957.0
3 TraesCS4B01G194100 chr4A 87.614 985 59 36 2459 3419 133841972 133841027 0.000000e+00 1085.0
4 TraesCS4B01G194100 chr4A 91.009 634 29 16 3711 4337 133840658 133840046 0.000000e+00 830.0
5 TraesCS4B01G194100 chr4A 89.051 274 15 10 3417 3687 133840996 133840735 5.150000e-85 326.0
6 TraesCS4B01G194100 chr4A 88.800 125 11 2 2238 2362 133842359 133842238 3.330000e-32 150.0
7 TraesCS4B01G194100 chr4A 100.000 30 0 0 12 41 38720317 38720288 7.460000e-04 56.5
8 TraesCS4B01G194100 chr4D 92.193 2139 80 29 156 2261 338365453 338367537 0.000000e+00 2944.0
9 TraesCS4B01G194100 chr4D 93.126 931 34 13 3415 4337 338368713 338369621 0.000000e+00 1338.0
10 TraesCS4B01G194100 chr4D 90.500 1000 88 7 4336 5331 50796177 50797173 0.000000e+00 1314.0
11 TraesCS4B01G194100 chr4D 91.641 323 9 4 3097 3419 338368380 338368684 1.060000e-116 431.0
12 TraesCS4B01G194100 chr4D 95.816 239 8 1 2458 2694 338367754 338367992 8.380000e-103 385.0
13 TraesCS4B01G194100 chr4D 98.585 212 3 0 2766 2977 338368083 338368294 5.040000e-100 375.0
14 TraesCS4B01G194100 chr4D 83.417 199 31 2 2770 2967 188963058 188963255 3.280000e-42 183.0
15 TraesCS4B01G194100 chr4D 93.750 112 7 0 61 172 338363761 338363872 9.180000e-38 169.0
16 TraesCS4B01G194100 chr4D 88.525 122 14 0 1939 2060 146029041 146028920 1.200000e-31 148.0
17 TraesCS4B01G194100 chr1B 92.331 1004 65 8 4332 5331 338013424 338012429 0.000000e+00 1417.0
18 TraesCS4B01G194100 chr1B 100.000 28 0 0 14 41 95662269 95662242 1.000000e-02 52.8
19 TraesCS4B01G194100 chr3D 91.908 1001 74 7 4335 5330 482860244 482861242 0.000000e+00 1393.0
20 TraesCS4B01G194100 chr3D 92.857 42 1 1 1 40 598084839 598084798 5.770000e-05 60.2
21 TraesCS4B01G194100 chr2D 91.045 1005 78 9 4335 5331 452373937 452372937 0.000000e+00 1347.0
22 TraesCS4B01G194100 chr2D 83.732 209 32 2 2770 2977 36535426 36535633 4.210000e-46 196.0
23 TraesCS4B01G194100 chr2D 81.860 215 35 3 2770 2981 288163014 288162801 1.530000e-40 178.0
24 TraesCS4B01G194100 chr2D 87.261 157 17 2 2498 2651 36535234 36535390 5.490000e-40 176.0
25 TraesCS4B01G194100 chr2D 81.183 186 29 4 1880 2059 36534957 36535142 1.550000e-30 145.0
26 TraesCS4B01G194100 chr2D 86.087 115 16 0 3144 3258 36535729 36535843 2.020000e-24 124.0
27 TraesCS4B01G194100 chr7B 91.304 989 81 5 4346 5330 639786245 639785258 0.000000e+00 1345.0
28 TraesCS4B01G194100 chr6B 90.746 1005 78 8 4336 5331 149166934 149165936 0.000000e+00 1327.0
29 TraesCS4B01G194100 chr6B 90.591 999 88 6 4336 5331 319558678 319559673 0.000000e+00 1319.0
30 TraesCS4B01G194100 chr5B 90.700 1000 86 7 4335 5330 504925771 504926767 0.000000e+00 1325.0
31 TraesCS4B01G194100 chr5B 85.366 123 18 0 2498 2620 634280200 634280078 1.560000e-25 128.0
32 TraesCS4B01G194100 chr2B 84.615 208 30 2 2770 2976 62546945 62547151 7.000000e-49 206.0
33 TraesCS4B01G194100 chr2B 90.244 123 12 0 2498 2620 62546753 62546875 1.540000e-35 161.0
34 TraesCS4B01G194100 chr2B 81.283 187 29 4 1880 2060 62546480 62546666 4.300000e-31 147.0
35 TraesCS4B01G194100 chr2B 86.087 115 16 0 3144 3258 62547296 62547410 2.020000e-24 124.0
36 TraesCS4B01G194100 chr2A 84.135 208 31 2 2770 2976 40537828 40538034 3.260000e-47 200.0
37 TraesCS4B01G194100 chr2A 86.364 154 18 2 2501 2651 40537639 40537792 1.190000e-36 165.0
38 TraesCS4B01G194100 chr2A 82.888 187 26 4 1880 2060 40537377 40537563 4.270000e-36 163.0
39 TraesCS4B01G194100 chr2A 84.677 124 19 0 3134 3257 40538149 40538272 2.020000e-24 124.0
40 TraesCS4B01G194100 chr2A 90.244 41 3 1 2 41 25331975 25331935 1.000000e-02 52.8
41 TraesCS4B01G194100 chr3A 83.920 199 30 2 2768 2965 598974869 598975066 7.050000e-44 189.0
42 TraesCS4B01G194100 chr3A 86.290 124 13 3 2493 2614 598974367 598974488 1.200000e-26 132.0
43 TraesCS4B01G194100 chr3A 96.774 31 1 0 11 41 13189861 13189891 1.000000e-02 52.8
44 TraesCS4B01G194100 chr3B 83.500 200 29 3 2768 2965 602584637 602584834 3.280000e-42 183.0
45 TraesCS4B01G194100 chr3B 86.325 117 16 0 2499 2615 602584148 602584264 1.560000e-25 128.0
46 TraesCS4B01G194100 chr1A 90.909 121 11 0 2501 2621 236303428 236303308 4.270000e-36 163.0
47 TraesCS4B01G194100 chr1A 87.705 122 15 0 1939 2060 514434109 514433988 5.570000e-30 143.0
48 TraesCS4B01G194100 chr1A 87.705 122 15 0 1939 2060 514503395 514503274 5.570000e-30 143.0
49 TraesCS4B01G194100 chrUn 87.705 122 15 0 1939 2060 427445272 427445393 5.570000e-30 143.0
50 TraesCS4B01G194100 chr5D 94.595 37 2 0 5 41 506089359 506089395 2.070000e-04 58.4
51 TraesCS4B01G194100 chr7D 100.000 29 0 0 12 40 93783327 93783299 3.000000e-03 54.7
52 TraesCS4B01G194100 chr7D 100.000 28 0 0 14 41 414373043 414373070 1.000000e-02 52.8
53 TraesCS4B01G194100 chr6D 100.000 29 0 0 13 41 451106522 451106550 3.000000e-03 54.7


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 TraesCS4B01G194100 chr4B 417349154 417354484 5330 False 9845.000000 9845 100.000000 1 5331 1 chr4B.!!$F1 5330
1 TraesCS4B01G194100 chr4B 180942426 180943422 996 True 1315.000000 1315 90.519000 4334 5330 1 chr4B.!!$R1 996
2 TraesCS4B01G194100 chr4A 133840046 133844501 4455 True 1069.600000 2957 89.646400 61 4337 5 chr4A.!!$R2 4276
3 TraesCS4B01G194100 chr4D 50796177 50797173 996 False 1314.000000 1314 90.500000 4336 5331 1 chr4D.!!$F1 995
4 TraesCS4B01G194100 chr4D 338363761 338369621 5860 False 940.333333 2944 94.185167 61 4337 6 chr4D.!!$F3 4276
5 TraesCS4B01G194100 chr1B 338012429 338013424 995 True 1417.000000 1417 92.331000 4332 5331 1 chr1B.!!$R2 999
6 TraesCS4B01G194100 chr3D 482860244 482861242 998 False 1393.000000 1393 91.908000 4335 5330 1 chr3D.!!$F1 995
7 TraesCS4B01G194100 chr2D 452372937 452373937 1000 True 1347.000000 1347 91.045000 4335 5331 1 chr2D.!!$R2 996
8 TraesCS4B01G194100 chr7B 639785258 639786245 987 True 1345.000000 1345 91.304000 4346 5330 1 chr7B.!!$R1 984
9 TraesCS4B01G194100 chr6B 149165936 149166934 998 True 1327.000000 1327 90.746000 4336 5331 1 chr6B.!!$R1 995
10 TraesCS4B01G194100 chr6B 319558678 319559673 995 False 1319.000000 1319 90.591000 4336 5331 1 chr6B.!!$F1 995
11 TraesCS4B01G194100 chr5B 504925771 504926767 996 False 1325.000000 1325 90.700000 4335 5330 1 chr5B.!!$F1 995

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
125 126 0.592637 CTGCGGTTTTCAGTGCATGA 59.407 50.0 0.0 0.0 36.64 3.07 F
2088 3740 0.321653 CCTTCCTTCTTCCCGTGTGG 60.322 60.0 0.0 0.0 0.00 4.17 F
3273 5208 0.035439 CCACATCACGTAAGCCCCTT 60.035 55.0 0.0 0.0 45.62 3.95 F
3279 5214 0.323629 CACGTAAGCCCCTTCTTCCA 59.676 55.0 0.0 0.0 45.62 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2120 3772 0.179073 AATCTCAGATCGCAACCCCG 60.179 55.000 0.00 0.00 0.00 5.73 R
3433 5403 1.337387 GGTCCCTCTCTCGATAAACCG 59.663 57.143 0.00 0.00 0.00 4.44 R
4114 6145 0.179067 ACGTTGGAGCTCCGTTTGAA 60.179 50.000 27.43 13.16 39.43 2.69 R
4694 6752 0.616679 AGCTAGACCGGGCAAGGTAA 60.617 55.000 11.69 0.00 46.09 2.85 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
24 25 5.750352 AAACAAAGTAATACTCCCTCCGA 57.250 39.130 0.00 0.00 0.00 4.55
25 26 5.952347 AACAAAGTAATACTCCCTCCGAT 57.048 39.130 0.00 0.00 0.00 4.18
26 27 5.952347 ACAAAGTAATACTCCCTCCGATT 57.048 39.130 0.00 0.00 0.00 3.34
27 28 5.915175 ACAAAGTAATACTCCCTCCGATTC 58.085 41.667 0.00 0.00 0.00 2.52
28 29 5.424252 ACAAAGTAATACTCCCTCCGATTCA 59.576 40.000 0.00 0.00 0.00 2.57
29 30 6.099845 ACAAAGTAATACTCCCTCCGATTCAT 59.900 38.462 0.00 0.00 0.00 2.57
30 31 7.289317 ACAAAGTAATACTCCCTCCGATTCATA 59.711 37.037 0.00 0.00 0.00 2.15
31 32 8.314751 CAAAGTAATACTCCCTCCGATTCATAT 58.685 37.037 0.00 0.00 0.00 1.78
32 33 8.437274 AAGTAATACTCCCTCCGATTCATATT 57.563 34.615 0.00 0.00 0.00 1.28
33 34 9.543231 AAGTAATACTCCCTCCGATTCATATTA 57.457 33.333 0.00 0.00 0.00 0.98
34 35 8.968969 AGTAATACTCCCTCCGATTCATATTAC 58.031 37.037 0.00 0.00 35.74 1.89
35 36 8.968969 GTAATACTCCCTCCGATTCATATTACT 58.031 37.037 0.00 0.00 34.03 2.24
36 37 8.437274 AATACTCCCTCCGATTCATATTACTT 57.563 34.615 0.00 0.00 0.00 2.24
37 38 6.102897 ACTCCCTCCGATTCATATTACTTG 57.897 41.667 0.00 0.00 0.00 3.16
38 39 5.602978 ACTCCCTCCGATTCATATTACTTGT 59.397 40.000 0.00 0.00 0.00 3.16
39 40 6.097915 TCCCTCCGATTCATATTACTTGTC 57.902 41.667 0.00 0.00 0.00 3.18
40 41 4.923871 CCCTCCGATTCATATTACTTGTCG 59.076 45.833 0.00 0.00 0.00 4.35
41 42 4.923871 CCTCCGATTCATATTACTTGTCGG 59.076 45.833 4.65 4.65 46.12 4.79
42 43 4.304110 TCCGATTCATATTACTTGTCGGC 58.696 43.478 6.06 0.00 44.84 5.54
43 44 4.055360 CCGATTCATATTACTTGTCGGCA 58.945 43.478 0.00 0.00 40.32 5.69
44 45 4.084537 CCGATTCATATTACTTGTCGGCAC 60.085 45.833 0.00 0.00 40.32 5.01
45 46 4.506288 CGATTCATATTACTTGTCGGCACA 59.494 41.667 0.00 0.00 0.00 4.57
46 47 5.006261 CGATTCATATTACTTGTCGGCACAA 59.994 40.000 0.00 0.00 40.40 3.33
56 57 3.897141 TGTCGGCACAAGTAATATGGA 57.103 42.857 0.00 0.00 0.00 3.41
57 58 4.415881 TGTCGGCACAAGTAATATGGAT 57.584 40.909 0.00 0.00 0.00 3.41
58 59 4.377021 TGTCGGCACAAGTAATATGGATC 58.623 43.478 0.00 0.00 0.00 3.36
59 60 3.428870 GTCGGCACAAGTAATATGGATCG 59.571 47.826 0.00 0.00 0.00 3.69
63 64 2.736721 CACAAGTAATATGGATCGGCGG 59.263 50.000 7.21 0.00 0.00 6.13
66 67 4.222145 ACAAGTAATATGGATCGGCGGTAT 59.778 41.667 7.21 0.00 0.00 2.73
125 126 0.592637 CTGCGGTTTTCAGTGCATGA 59.407 50.000 0.00 0.00 36.64 3.07
166 1764 2.439507 ACTCTGAAGCCTCAAAACCTCA 59.560 45.455 0.00 0.00 0.00 3.86
190 1788 1.827969 ACAGCCTCGCAGTCTAATTCT 59.172 47.619 0.00 0.00 0.00 2.40
212 1810 3.610040 TCAATCACGGCTGAACTGTAT 57.390 42.857 0.00 0.00 35.54 2.29
225 1823 6.702282 GGCTGAACTGTATAGAATACAAGTCC 59.298 42.308 0.00 0.29 0.00 3.85
227 1825 7.222999 GCTGAACTGTATAGAATACAAGTCCAC 59.777 40.741 0.00 0.00 0.00 4.02
237 1836 0.815734 ACAAGTCCACGGATAGGTCG 59.184 55.000 0.00 0.00 0.00 4.79
265 1864 4.655963 CACCAAGGAAGGAAAGATCTTGA 58.344 43.478 9.17 0.00 37.57 3.02
337 1940 2.508887 CTGCTGCTGCCTCGTCTC 60.509 66.667 13.47 0.00 38.71 3.36
373 1985 1.153549 GCTTGCTTCCCGATCTCGT 60.154 57.895 0.00 0.00 37.74 4.18
402 2015 3.782244 GCAAGCGAGACAGGCACG 61.782 66.667 0.00 0.00 0.00 5.34
486 2106 3.181525 ACCAAAAACGAAAAGCGCAAAAG 60.182 39.130 11.47 0.00 46.04 2.27
502 2122 6.321181 AGCGCAAAAGGAGGAATATCAATTAA 59.679 34.615 11.47 0.00 0.00 1.40
568 2188 1.094785 CAAGGCAAGTAACGGATGGG 58.905 55.000 0.00 0.00 0.00 4.00
604 2224 3.304659 GCAATGCCAATGTATAACCTCCG 60.305 47.826 0.00 0.00 0.00 4.63
618 2238 1.711942 ACCTCCGAATTAAACCCCCAA 59.288 47.619 0.00 0.00 0.00 4.12
619 2239 2.313643 ACCTCCGAATTAAACCCCCAAT 59.686 45.455 0.00 0.00 0.00 3.16
620 2240 2.693074 CCTCCGAATTAAACCCCCAATG 59.307 50.000 0.00 0.00 0.00 2.82
621 2241 2.693074 CTCCGAATTAAACCCCCAATGG 59.307 50.000 0.00 0.00 0.00 3.16
622 2242 2.312140 TCCGAATTAAACCCCCAATGGA 59.688 45.455 0.00 0.00 35.39 3.41
715 2335 6.801575 ACCACTTGTGGTAAATGTTGTAAAG 58.198 36.000 22.33 0.00 41.04 1.85
786 2406 9.381038 AGTTCCTACCAAATATATAAGCAGAGA 57.619 33.333 0.00 0.00 0.00 3.10
787 2407 9.646427 GTTCCTACCAAATATATAAGCAGAGAG 57.354 37.037 0.00 0.00 0.00 3.20
788 2408 9.601810 TTCCTACCAAATATATAAGCAGAGAGA 57.398 33.333 0.00 0.00 0.00 3.10
789 2409 9.249053 TCCTACCAAATATATAAGCAGAGAGAG 57.751 37.037 0.00 0.00 0.00 3.20
887 2509 2.034812 GGCGAACCAAACCAAACATACA 59.965 45.455 0.00 0.00 35.26 2.29
888 2510 3.305110 GCGAACCAAACCAAACATACAG 58.695 45.455 0.00 0.00 0.00 2.74
889 2511 3.243267 GCGAACCAAACCAAACATACAGT 60.243 43.478 0.00 0.00 0.00 3.55
891 2513 5.445845 CGAACCAAACCAAACATACAGTAC 58.554 41.667 0.00 0.00 0.00 2.73
892 2514 5.561339 CGAACCAAACCAAACATACAGTACC 60.561 44.000 0.00 0.00 0.00 3.34
893 2515 4.794334 ACCAAACCAAACATACAGTACCA 58.206 39.130 0.00 0.00 0.00 3.25
897 2519 6.212955 CAAACCAAACATACAGTACCAAAGG 58.787 40.000 0.00 0.00 0.00 3.11
898 2520 4.403734 ACCAAACATACAGTACCAAAGGG 58.596 43.478 0.00 0.00 41.29 3.95
905 2527 3.306472 ACAGTACCAAAGGGAAGCAAA 57.694 42.857 0.00 0.00 38.05 3.68
1065 2711 7.535139 TCTCCATTTTCCGTTTCATTTCATAC 58.465 34.615 0.00 0.00 0.00 2.39
1088 2734 2.225017 GGGAGAGAGCTAGATAGGCACT 60.225 54.545 0.00 0.00 46.37 4.40
1118 2764 3.181519 GCTAGCAAAGCGGAGAAGTAAAC 60.182 47.826 10.63 0.00 42.53 2.01
1140 2786 6.783708 ACAAGTTTTTGTTTACTCCATCCA 57.216 33.333 0.00 0.00 45.01 3.41
1141 2787 7.360113 ACAAGTTTTTGTTTACTCCATCCAT 57.640 32.000 0.00 0.00 45.01 3.41
1142 2788 7.433680 ACAAGTTTTTGTTTACTCCATCCATC 58.566 34.615 0.00 0.00 45.01 3.51
1143 2789 7.287696 ACAAGTTTTTGTTTACTCCATCCATCT 59.712 33.333 0.00 0.00 45.01 2.90
1144 2790 7.839680 AGTTTTTGTTTACTCCATCCATCTT 57.160 32.000 0.00 0.00 0.00 2.40
1145 2791 7.886338 AGTTTTTGTTTACTCCATCCATCTTC 58.114 34.615 0.00 0.00 0.00 2.87
1658 3307 3.897122 GGGTGGTGGTGGCCAAGA 61.897 66.667 7.24 0.00 40.68 3.02
2088 3740 0.321653 CCTTCCTTCTTCCCGTGTGG 60.322 60.000 0.00 0.00 0.00 4.17
2120 3772 1.487482 GGTTTTTCTGAGCGGTTTGC 58.513 50.000 0.00 0.00 46.98 3.68
2211 3868 0.110147 GTACGAGCCGGAGATCATCG 60.110 60.000 5.05 6.86 39.22 3.84
2219 3876 1.335810 CCGGAGATCATCGTCGGTTTA 59.664 52.381 11.93 0.00 34.15 2.01
2253 3910 4.454847 GGCCACTTGTTTTTACTACTCCTC 59.545 45.833 0.00 0.00 0.00 3.71
2320 3977 2.775384 ACAAACACCACTAGGAGGTCAA 59.225 45.455 6.19 0.00 37.23 3.18
2322 3979 0.966920 ACACCACTAGGAGGTCAACG 59.033 55.000 6.19 0.00 37.23 4.10
2329 3986 1.202582 CTAGGAGGTCAACGGTGTCAG 59.797 57.143 0.00 0.00 0.00 3.51
2334 3991 4.308458 TCAACGGTGTCAGGGGCG 62.308 66.667 0.00 0.00 0.00 6.13
2335 3992 4.619227 CAACGGTGTCAGGGGCGT 62.619 66.667 0.00 0.00 0.00 5.68
2336 3993 4.309950 AACGGTGTCAGGGGCGTC 62.310 66.667 0.00 0.00 0.00 5.19
2351 4008 2.034001 GGGCGTCGAAATAGAATGTTCG 60.034 50.000 0.00 0.00 46.17 3.95
2400 4059 1.200716 TCTACTCCTGTTACCGCGTTG 59.799 52.381 4.92 0.00 0.00 4.10
2411 4070 1.154225 CCGCGTTGGTTTGAGCATC 60.154 57.895 4.92 0.00 0.00 3.91
2446 4105 2.639970 TCCATGCGGGAAACTGTTG 58.360 52.632 0.00 0.00 44.80 3.33
2456 4115 3.615099 AAACTGTTGTTTCCGCACG 57.385 47.368 0.00 0.00 42.11 5.34
2470 4345 1.521681 GCACGACTAGGGATGTGGC 60.522 63.158 0.00 0.00 33.04 5.01
2471 4346 1.897423 CACGACTAGGGATGTGGCA 59.103 57.895 0.00 0.00 0.00 4.92
2489 4364 3.256879 TGGCACTGAAAAGTGTTGAACAA 59.743 39.130 0.00 0.00 41.53 2.83
2490 4365 4.081752 TGGCACTGAAAAGTGTTGAACAAT 60.082 37.500 0.00 0.00 41.53 2.71
2560 4437 2.264480 CGGCTGATGTTCGTGGGA 59.736 61.111 0.00 0.00 0.00 4.37
2717 4594 2.682155 TCAACCGCATGCAGTACATA 57.318 45.000 19.57 0.00 36.64 2.29
2718 4595 2.276201 TCAACCGCATGCAGTACATAC 58.724 47.619 19.57 0.00 36.64 2.39
2719 4596 2.006169 CAACCGCATGCAGTACATACA 58.994 47.619 19.57 0.00 36.64 2.29
2720 4597 1.651987 ACCGCATGCAGTACATACAC 58.348 50.000 19.57 0.00 36.64 2.90
2722 4599 2.212652 CCGCATGCAGTACATACACAT 58.787 47.619 19.57 0.00 36.64 3.21
2723 4600 2.613595 CCGCATGCAGTACATACACATT 59.386 45.455 19.57 0.00 36.64 2.71
2724 4601 3.303329 CCGCATGCAGTACATACACATTC 60.303 47.826 19.57 0.00 36.64 2.67
2726 4603 4.201802 CGCATGCAGTACATACACATTCAA 60.202 41.667 19.57 0.00 36.64 2.69
2727 4604 5.030295 GCATGCAGTACATACACATTCAAC 58.970 41.667 14.21 0.00 36.64 3.18
2728 4605 5.391843 GCATGCAGTACATACACATTCAACA 60.392 40.000 14.21 0.00 36.64 3.33
2729 4606 5.861222 TGCAGTACATACACATTCAACAG 57.139 39.130 0.00 0.00 0.00 3.16
2730 4607 5.546526 TGCAGTACATACACATTCAACAGA 58.453 37.500 0.00 0.00 0.00 3.41
2731 4608 6.172630 TGCAGTACATACACATTCAACAGAT 58.827 36.000 0.00 0.00 0.00 2.90
2732 4609 6.313658 TGCAGTACATACACATTCAACAGATC 59.686 38.462 0.00 0.00 0.00 2.75
2747 4624 3.146066 ACAGATCGATCTAGCCTGAGAC 58.854 50.000 26.87 0.00 34.85 3.36
2762 4639 1.006400 TGAGACAGAGGAGCTCATGGA 59.994 52.381 17.19 0.00 34.02 3.41
2764 4641 0.102120 GACAGAGGAGCTCATGGACG 59.898 60.000 17.19 0.76 32.06 4.79
2805 4712 2.202756 GAGTTCTACTGGGCGCCG 60.203 66.667 22.54 10.51 0.00 6.46
2969 4876 0.737715 GCGCTCGACATGAAAGTCCT 60.738 55.000 0.00 0.00 35.07 3.85
2970 4877 0.994995 CGCTCGACATGAAAGTCCTG 59.005 55.000 0.00 0.00 35.07 3.86
2971 4878 1.670087 CGCTCGACATGAAAGTCCTGT 60.670 52.381 0.00 0.00 35.07 4.00
2972 4879 2.415491 CGCTCGACATGAAAGTCCTGTA 60.415 50.000 0.00 0.00 35.07 2.74
2973 4880 3.585862 GCTCGACATGAAAGTCCTGTAA 58.414 45.455 0.00 0.00 35.07 2.41
2974 4881 3.614616 GCTCGACATGAAAGTCCTGTAAG 59.385 47.826 0.00 0.00 35.07 2.34
2975 4882 4.810790 CTCGACATGAAAGTCCTGTAAGT 58.189 43.478 0.00 0.00 35.07 2.24
2976 4883 5.209818 TCGACATGAAAGTCCTGTAAGTT 57.790 39.130 0.00 0.00 35.07 2.66
2977 4884 5.227908 TCGACATGAAAGTCCTGTAAGTTC 58.772 41.667 0.00 0.00 35.07 3.01
2978 4885 4.389077 CGACATGAAAGTCCTGTAAGTTCC 59.611 45.833 0.00 0.00 35.07 3.62
2979 4886 4.315803 ACATGAAAGTCCTGTAAGTTCCG 58.684 43.478 0.00 0.00 0.00 4.30
2980 4887 4.202326 ACATGAAAGTCCTGTAAGTTCCGT 60.202 41.667 0.00 0.00 0.00 4.69
2981 4888 4.411256 TGAAAGTCCTGTAAGTTCCGTT 57.589 40.909 0.00 0.00 0.00 4.44
2982 4889 4.773013 TGAAAGTCCTGTAAGTTCCGTTT 58.227 39.130 0.00 0.00 0.00 3.60
2983 4890 5.916318 TGAAAGTCCTGTAAGTTCCGTTTA 58.084 37.500 0.00 0.00 0.00 2.01
2984 4891 6.347696 TGAAAGTCCTGTAAGTTCCGTTTAA 58.652 36.000 0.00 0.00 0.00 1.52
2985 4892 6.822676 TGAAAGTCCTGTAAGTTCCGTTTAAA 59.177 34.615 0.00 0.00 0.00 1.52
2986 4893 7.336427 TGAAAGTCCTGTAAGTTCCGTTTAAAA 59.664 33.333 0.00 0.00 0.00 1.52
2987 4894 7.628769 AAGTCCTGTAAGTTCCGTTTAAAAA 57.371 32.000 0.00 0.00 0.00 1.94
3036 4949 3.568007 GTGGACATTTCAGTTGCTTGGTA 59.432 43.478 0.00 0.00 0.00 3.25
3037 4950 3.820467 TGGACATTTCAGTTGCTTGGTAG 59.180 43.478 0.00 0.00 0.00 3.18
3056 4969 0.733729 GCATCTCGACTACTCGTGGT 59.266 55.000 0.00 0.00 41.02 4.16
3057 4970 1.532090 GCATCTCGACTACTCGTGGTG 60.532 57.143 3.62 3.62 44.03 4.17
3060 4973 1.909141 CTCGACTACTCGTGGTGCGT 61.909 60.000 0.00 0.00 41.02 5.24
3061 4974 1.081641 CGACTACTCGTGGTGCGTT 60.082 57.895 0.00 0.00 42.13 4.84
3064 4977 0.240411 ACTACTCGTGGTGCGTTCTC 59.760 55.000 0.00 0.00 42.13 2.87
3080 5012 5.789774 CGTTCTCCTTTTGAATTTGAACG 57.210 39.130 10.15 10.15 45.25 3.95
3095 5030 9.292846 TGAATTTGAACGAAATGATGATGAATC 57.707 29.630 0.00 0.00 34.30 2.52
3242 5177 0.613260 CCACCGTCTTCTTCATGGGA 59.387 55.000 0.00 0.00 0.00 4.37
3271 5206 0.322187 AACCACATCACGTAAGCCCC 60.322 55.000 0.00 0.00 45.62 5.80
3272 5207 1.198759 ACCACATCACGTAAGCCCCT 61.199 55.000 0.00 0.00 45.62 4.79
3273 5208 0.035439 CCACATCACGTAAGCCCCTT 60.035 55.000 0.00 0.00 45.62 3.95
3274 5209 1.369625 CACATCACGTAAGCCCCTTC 58.630 55.000 0.00 0.00 45.62 3.46
3275 5210 1.066143 CACATCACGTAAGCCCCTTCT 60.066 52.381 0.00 0.00 45.62 2.85
3277 5212 2.280628 CATCACGTAAGCCCCTTCTTC 58.719 52.381 0.00 0.00 45.62 2.87
3279 5214 0.323629 CACGTAAGCCCCTTCTTCCA 59.676 55.000 0.00 0.00 45.62 3.53
3280 5215 0.323957 ACGTAAGCCCCTTCTTCCAC 59.676 55.000 0.00 0.00 45.62 4.02
3281 5216 0.323629 CGTAAGCCCCTTCTTCCACA 59.676 55.000 0.00 0.00 0.00 4.17
3282 5217 1.822506 GTAAGCCCCTTCTTCCACAC 58.177 55.000 0.00 0.00 0.00 3.82
3283 5218 1.351350 GTAAGCCCCTTCTTCCACACT 59.649 52.381 0.00 0.00 0.00 3.55
3284 5219 1.742308 AAGCCCCTTCTTCCACACTA 58.258 50.000 0.00 0.00 0.00 2.74
3285 5220 0.984995 AGCCCCTTCTTCCACACTAC 59.015 55.000 0.00 0.00 0.00 2.73
3286 5221 0.984995 GCCCCTTCTTCCACACTACT 59.015 55.000 0.00 0.00 0.00 2.57
3293 5228 5.450137 CCCTTCTTCCACACTACTATACGTG 60.450 48.000 0.00 0.00 37.18 4.49
3295 5230 6.349944 CCTTCTTCCACACTACTATACGTGTT 60.350 42.308 0.00 0.00 42.05 3.32
3323 5258 4.475028 TCATTCTTTGCTTGCATTGTACG 58.525 39.130 0.00 0.00 0.00 3.67
3324 5259 3.980646 TTCTTTGCTTGCATTGTACGT 57.019 38.095 0.00 0.00 0.00 3.57
3325 5260 5.180304 TCATTCTTTGCTTGCATTGTACGTA 59.820 36.000 0.00 0.00 0.00 3.57
3326 5261 4.398549 TCTTTGCTTGCATTGTACGTAC 57.601 40.909 18.90 18.90 0.00 3.67
3327 5262 2.865556 TTGCTTGCATTGTACGTACG 57.134 45.000 20.18 15.01 0.00 3.67
3328 5263 1.785768 TGCTTGCATTGTACGTACGT 58.214 45.000 25.98 25.98 0.00 3.57
3329 5264 2.943993 TGCTTGCATTGTACGTACGTA 58.056 42.857 23.60 23.60 0.00 3.57
3433 5403 8.193438 CAGAAAAATATGGTTTCCTTGAGGATC 58.807 37.037 0.00 0.00 44.98 3.36
3481 5451 2.462889 GCAGCGAGATCTCTCTTTCAG 58.537 52.381 20.26 7.21 40.75 3.02
3540 5510 1.486439 ATTCGCACAAAAGGCAAACG 58.514 45.000 0.00 0.00 0.00 3.60
3542 5512 2.584967 CGCACAAAAGGCAAACGGC 61.585 57.895 0.00 0.00 43.74 5.68
3553 5523 1.862602 GCAAACGGCGACAGGGATTT 61.863 55.000 16.62 0.00 0.00 2.17
3557 5527 1.375396 CGGCGACAGGGATTTGTCA 60.375 57.895 0.00 0.00 46.11 3.58
3565 5535 4.935205 CGACAGGGATTTGTCAGATGTTAA 59.065 41.667 6.91 0.00 46.11 2.01
3570 5540 7.390718 ACAGGGATTTGTCAGATGTTAACTAAC 59.609 37.037 7.22 0.00 36.74 2.34
3681 5655 9.567776 CCACCTATCTATTCTCGATCATATACT 57.432 37.037 0.00 0.00 0.00 2.12
3706 5680 9.341899 CTATTGTTTGTGGTGCTAATTAAACTC 57.658 33.333 0.00 0.00 0.00 3.01
4068 6099 2.792947 TTCCTCTACGCCCGCATCC 61.793 63.158 0.00 0.00 0.00 3.51
4077 6108 4.247380 CCCGCATCCTCTCCAGCC 62.247 72.222 0.00 0.00 0.00 4.85
4111 6142 0.618968 CAACAGTAGCCTCCCTCCCT 60.619 60.000 0.00 0.00 0.00 4.20
4112 6143 1.016415 AACAGTAGCCTCCCTCCCTA 58.984 55.000 0.00 0.00 0.00 3.53
4113 6144 0.558712 ACAGTAGCCTCCCTCCCTAG 59.441 60.000 0.00 0.00 0.00 3.02
4114 6145 0.558712 CAGTAGCCTCCCTCCCTAGT 59.441 60.000 0.00 0.00 0.00 2.57
4115 6146 1.062810 CAGTAGCCTCCCTCCCTAGTT 60.063 57.143 0.00 0.00 0.00 2.24
4116 6147 1.218450 AGTAGCCTCCCTCCCTAGTTC 59.782 57.143 0.00 0.00 0.00 3.01
4133 6169 0.179067 TTCAAACGGAGCTCCAACGT 60.179 50.000 31.67 20.71 43.43 3.99
4180 6227 4.162509 ACAGATACAGAAGAGTAAAGGGCC 59.837 45.833 0.00 0.00 0.00 5.80
4191 6238 3.558033 AGTAAAGGGCCGTTGAAAGAAA 58.442 40.909 15.31 0.00 0.00 2.52
4219 6267 1.449353 GATGCCCGCCATCTCTCTT 59.551 57.895 6.95 0.00 45.58 2.85
4221 6269 0.179034 ATGCCCGCCATCTCTCTTTC 60.179 55.000 0.00 0.00 0.00 2.62
4264 6312 0.739813 GCGTAAAGCCGTCATGTCCT 60.740 55.000 0.00 0.00 40.81 3.85
4323 6373 9.938280 CGGAAGGTTAGGATAATGAAATATGTA 57.062 33.333 0.00 0.00 0.00 2.29
4362 6412 2.047296 TCTTAAATGGAGGAGGACCCCT 59.953 50.000 1.40 1.40 39.77 4.79
4380 6430 0.471191 CTGGCCTCTGCATATGGACA 59.529 55.000 3.32 7.87 40.13 4.02
4384 6434 1.884579 GCCTCTGCATATGGACAATGG 59.115 52.381 4.56 0.84 37.47 3.16
4410 6464 9.403110 GATGCAGCCACTTTATTAATTATTCAG 57.597 33.333 0.00 0.00 0.00 3.02
4428 6482 8.974060 TTATTCAGACAAGACCTTACAAAGTT 57.026 30.769 0.00 0.00 0.00 2.66
4515 6570 1.061812 AGGGATGCTGATAGTCTGGGT 60.062 52.381 0.00 0.00 0.00 4.51
4526 6582 6.998673 GCTGATAGTCTGGGTTAATACCAAAT 59.001 38.462 3.80 0.00 46.96 2.32
4543 6599 2.684881 CAAATAGACCTCGCAGCCAAAT 59.315 45.455 0.00 0.00 0.00 2.32
4586 6643 1.831286 AACCAGGACGTCTGTCGGT 60.831 57.895 16.46 13.37 46.49 4.69
4589 6646 0.109412 CCAGGACGTCTGTCGGTTAC 60.109 60.000 16.46 0.00 46.49 2.50
4686 6744 4.701651 CCAATCCATCTTCAAAGCTGTACA 59.298 41.667 0.00 0.00 0.00 2.90
4694 6752 4.580167 TCTTCAAAGCTGTACAACTGCATT 59.420 37.500 0.00 0.00 44.20 3.56
4783 6841 0.737367 CATCGCCACACATCTGACGT 60.737 55.000 0.00 0.00 0.00 4.34
4850 6908 1.725164 GTAGAAAGAAACACCGCTCCG 59.275 52.381 0.00 0.00 0.00 4.63
4894 6952 2.780094 CGAGCCCGAGTGCATCTCT 61.780 63.158 12.45 0.00 40.75 3.10
4896 6954 0.313672 GAGCCCGAGTGCATCTCTAG 59.686 60.000 12.45 6.47 40.75 2.43
4984 7044 0.419865 TCCCCCAGAGGTATTGGTGA 59.580 55.000 0.00 0.00 33.73 4.02
4990 7050 2.571653 CCAGAGGTATTGGTGAGGTTGA 59.428 50.000 0.00 0.00 0.00 3.18
5000 7060 2.503765 TGGTGAGGTTGAGAGTTTCACA 59.496 45.455 5.44 0.00 39.81 3.58
5036 7096 6.233905 TCATGAAGGAAACGATGATAAGGA 57.766 37.500 0.00 0.00 0.00 3.36
5172 7233 2.792947 GCCACCTAGATCCGGCGAA 61.793 63.158 9.30 0.00 34.26 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.243604 TCGGAGGGAGTATTACTTTGTTTAA 57.756 36.000 0.00 0.00 0.00 1.52
1 2 6.855763 TCGGAGGGAGTATTACTTTGTTTA 57.144 37.500 0.00 0.00 0.00 2.01
2 3 5.750352 TCGGAGGGAGTATTACTTTGTTT 57.250 39.130 0.00 0.00 0.00 2.83
3 4 5.952347 ATCGGAGGGAGTATTACTTTGTT 57.048 39.130 0.00 0.00 0.00 2.83
4 5 5.424252 TGAATCGGAGGGAGTATTACTTTGT 59.576 40.000 0.00 0.00 0.00 2.83
5 6 5.914033 TGAATCGGAGGGAGTATTACTTTG 58.086 41.667 0.00 0.00 0.00 2.77
6 7 6.749036 ATGAATCGGAGGGAGTATTACTTT 57.251 37.500 0.00 0.00 0.00 2.66
7 8 8.437274 AATATGAATCGGAGGGAGTATTACTT 57.563 34.615 0.00 0.00 0.00 2.24
8 9 8.968969 GTAATATGAATCGGAGGGAGTATTACT 58.031 37.037 0.00 0.00 33.90 2.24
9 10 8.968969 AGTAATATGAATCGGAGGGAGTATTAC 58.031 37.037 0.00 0.00 35.54 1.89
10 11 9.543231 AAGTAATATGAATCGGAGGGAGTATTA 57.457 33.333 0.00 0.00 0.00 0.98
11 12 8.314751 CAAGTAATATGAATCGGAGGGAGTATT 58.685 37.037 0.00 0.00 0.00 1.89
12 13 7.455008 ACAAGTAATATGAATCGGAGGGAGTAT 59.545 37.037 0.00 0.00 0.00 2.12
13 14 6.781014 ACAAGTAATATGAATCGGAGGGAGTA 59.219 38.462 0.00 0.00 0.00 2.59
14 15 5.602978 ACAAGTAATATGAATCGGAGGGAGT 59.397 40.000 0.00 0.00 0.00 3.85
15 16 6.102897 ACAAGTAATATGAATCGGAGGGAG 57.897 41.667 0.00 0.00 0.00 4.30
16 17 5.278808 CGACAAGTAATATGAATCGGAGGGA 60.279 44.000 0.00 0.00 0.00 4.20
17 18 4.923871 CGACAAGTAATATGAATCGGAGGG 59.076 45.833 0.00 0.00 0.00 4.30
22 23 4.506288 TGTGCCGACAAGTAATATGAATCG 59.494 41.667 0.00 0.00 0.00 3.34
23 24 5.984233 TGTGCCGACAAGTAATATGAATC 57.016 39.130 0.00 0.00 0.00 2.52
35 36 4.209307 TCCATATTACTTGTGCCGACAA 57.791 40.909 0.00 0.00 39.88 3.18
36 37 3.897141 TCCATATTACTTGTGCCGACA 57.103 42.857 0.00 0.00 0.00 4.35
37 38 3.428870 CGATCCATATTACTTGTGCCGAC 59.571 47.826 0.00 0.00 0.00 4.79
38 39 3.554129 CCGATCCATATTACTTGTGCCGA 60.554 47.826 0.00 0.00 0.00 5.54
39 40 2.736721 CCGATCCATATTACTTGTGCCG 59.263 50.000 0.00 0.00 0.00 5.69
40 41 2.484264 GCCGATCCATATTACTTGTGCC 59.516 50.000 0.00 0.00 0.00 5.01
41 42 2.157668 CGCCGATCCATATTACTTGTGC 59.842 50.000 0.00 0.00 0.00 4.57
42 43 2.736721 CCGCCGATCCATATTACTTGTG 59.263 50.000 0.00 0.00 0.00 3.33
43 44 2.367567 ACCGCCGATCCATATTACTTGT 59.632 45.455 0.00 0.00 0.00 3.16
44 45 3.040147 ACCGCCGATCCATATTACTTG 57.960 47.619 0.00 0.00 0.00 3.16
45 46 5.416271 AATACCGCCGATCCATATTACTT 57.584 39.130 0.00 0.00 0.00 2.24
46 47 6.726490 ATAATACCGCCGATCCATATTACT 57.274 37.500 0.00 0.00 0.00 2.24
47 48 6.982141 TCAATAATACCGCCGATCCATATTAC 59.018 38.462 0.00 0.00 0.00 1.89
48 49 7.114866 TCAATAATACCGCCGATCCATATTA 57.885 36.000 0.00 0.00 0.00 0.98
49 50 5.984725 TCAATAATACCGCCGATCCATATT 58.015 37.500 0.00 0.00 0.00 1.28
50 51 5.601662 CTCAATAATACCGCCGATCCATAT 58.398 41.667 0.00 0.00 0.00 1.78
51 52 4.679639 GCTCAATAATACCGCCGATCCATA 60.680 45.833 0.00 0.00 0.00 2.74
52 53 3.861840 CTCAATAATACCGCCGATCCAT 58.138 45.455 0.00 0.00 0.00 3.41
53 54 2.611971 GCTCAATAATACCGCCGATCCA 60.612 50.000 0.00 0.00 0.00 3.41
54 55 2.000447 GCTCAATAATACCGCCGATCC 59.000 52.381 0.00 0.00 0.00 3.36
55 56 2.412089 GTGCTCAATAATACCGCCGATC 59.588 50.000 0.00 0.00 0.00 3.69
56 57 2.037251 AGTGCTCAATAATACCGCCGAT 59.963 45.455 0.00 0.00 0.00 4.18
57 58 1.411246 AGTGCTCAATAATACCGCCGA 59.589 47.619 0.00 0.00 0.00 5.54
58 59 1.526887 CAGTGCTCAATAATACCGCCG 59.473 52.381 0.00 0.00 0.00 6.46
59 60 2.833794 TCAGTGCTCAATAATACCGCC 58.166 47.619 0.00 0.00 0.00 6.13
63 64 7.364522 TCACAAGTTCAGTGCTCAATAATAC 57.635 36.000 0.00 0.00 36.93 1.89
66 67 5.764686 ACATCACAAGTTCAGTGCTCAATAA 59.235 36.000 0.00 0.00 36.93 1.40
125 126 6.817641 CAGAGTTCAGAATCTTCAGCTATTGT 59.182 38.462 0.00 0.00 0.00 2.71
166 1764 4.385405 GACTGCGAGGCTGTGGCT 62.385 66.667 4.84 0.00 40.59 4.75
190 1788 2.571212 ACAGTTCAGCCGTGATTGAAA 58.429 42.857 0.00 0.00 35.29 2.69
212 1810 5.452255 ACCTATCCGTGGACTTGTATTCTA 58.548 41.667 0.00 0.00 0.00 2.10
225 1823 0.174845 TGCTTTCCGACCTATCCGTG 59.825 55.000 0.00 0.00 0.00 4.94
227 1825 0.529992 GGTGCTTTCCGACCTATCCG 60.530 60.000 0.00 0.00 0.00 4.18
237 1836 1.995376 TTCCTTCCTTGGTGCTTTCC 58.005 50.000 0.00 0.00 0.00 3.13
265 1864 4.022849 GCTACTCCATTTTGTGTTCTTGCT 60.023 41.667 0.00 0.00 0.00 3.91
337 1940 2.278857 AATGGCGAGCGAGCGTAG 60.279 61.111 0.00 0.00 38.18 3.51
373 1985 4.284550 GCTTGCCTGGGGTGGTGA 62.285 66.667 0.00 0.00 0.00 4.02
387 2000 3.575351 GACCGTGCCTGTCTCGCTT 62.575 63.158 0.00 0.00 0.00 4.68
402 2015 2.301870 TGTGACATGGAGTGGTTAGACC 59.698 50.000 0.00 0.00 39.22 3.85
486 2106 7.771183 TGTTGCTTGTTAATTGATATTCCTCC 58.229 34.615 0.00 0.00 0.00 4.30
502 2122 7.264947 GGGTAGCATATTTAATTGTTGCTTGT 58.735 34.615 12.49 0.00 43.08 3.16
568 2188 2.001872 GCATTGCCTTGCCAAACATAC 58.998 47.619 0.00 0.00 36.60 2.39
596 2216 2.918266 TGGGGGTTTAATTCGGAGGTTA 59.082 45.455 0.00 0.00 0.00 2.85
597 2217 1.711942 TGGGGGTTTAATTCGGAGGTT 59.288 47.619 0.00 0.00 0.00 3.50
604 2224 4.719273 TCCATTCCATTGGGGGTTTAATTC 59.281 41.667 2.09 0.00 37.37 2.17
731 2351 8.115490 TCTCTTCAATTTCCTCCATTCTTTTC 57.885 34.615 0.00 0.00 0.00 2.29
732 2352 8.482852 TTCTCTTCAATTTCCTCCATTCTTTT 57.517 30.769 0.00 0.00 0.00 2.27
779 2399 3.378512 TCTCTCTCTCTCTCTCTCTGCT 58.621 50.000 0.00 0.00 0.00 4.24
780 2400 3.133721 ACTCTCTCTCTCTCTCTCTCTGC 59.866 52.174 0.00 0.00 0.00 4.26
781 2401 6.471233 TTACTCTCTCTCTCTCTCTCTCTG 57.529 45.833 0.00 0.00 0.00 3.35
782 2402 7.682787 AATTACTCTCTCTCTCTCTCTCTCT 57.317 40.000 0.00 0.00 0.00 3.10
783 2403 8.091449 CCTAATTACTCTCTCTCTCTCTCTCTC 58.909 44.444 0.00 0.00 0.00 3.20
784 2404 7.789831 TCCTAATTACTCTCTCTCTCTCTCTCT 59.210 40.741 0.00 0.00 0.00 3.10
785 2405 7.963532 TCCTAATTACTCTCTCTCTCTCTCTC 58.036 42.308 0.00 0.00 0.00 3.20
786 2406 7.016661 CCTCCTAATTACTCTCTCTCTCTCTCT 59.983 44.444 0.00 0.00 0.00 3.10
787 2407 7.016268 TCCTCCTAATTACTCTCTCTCTCTCTC 59.984 44.444 0.00 0.00 0.00 3.20
788 2408 6.849697 TCCTCCTAATTACTCTCTCTCTCTCT 59.150 42.308 0.00 0.00 0.00 3.10
789 2409 7.074653 TCCTCCTAATTACTCTCTCTCTCTC 57.925 44.000 0.00 0.00 0.00 3.20
887 2509 2.239400 GCTTTGCTTCCCTTTGGTACT 58.761 47.619 0.00 0.00 0.00 2.73
888 2510 1.960689 TGCTTTGCTTCCCTTTGGTAC 59.039 47.619 0.00 0.00 0.00 3.34
889 2511 2.364002 GTTGCTTTGCTTCCCTTTGGTA 59.636 45.455 0.00 0.00 0.00 3.25
891 2513 1.869342 CGTTGCTTTGCTTCCCTTTGG 60.869 52.381 0.00 0.00 0.00 3.28
892 2514 1.490621 CGTTGCTTTGCTTCCCTTTG 58.509 50.000 0.00 0.00 0.00 2.77
893 2515 0.389025 CCGTTGCTTTGCTTCCCTTT 59.611 50.000 0.00 0.00 0.00 3.11
897 2519 2.200170 ATCGCCGTTGCTTTGCTTCC 62.200 55.000 0.00 0.00 34.43 3.46
898 2520 0.794605 GATCGCCGTTGCTTTGCTTC 60.795 55.000 0.00 0.00 34.43 3.86
905 2527 1.574428 GTGTTTGATCGCCGTTGCT 59.426 52.632 0.00 0.00 34.43 3.91
1065 2711 2.224992 TGCCTATCTAGCTCTCTCCCTG 60.225 54.545 0.00 0.00 0.00 4.45
1118 2764 7.661040 AGATGGATGGAGTAAACAAAAACTTG 58.339 34.615 0.00 0.00 0.00 3.16
1138 2784 1.228510 GCCCAGGGAAGGAAGATGG 59.771 63.158 10.89 0.00 0.00 3.51
1139 2785 0.627986 AAGCCCAGGGAAGGAAGATG 59.372 55.000 10.89 0.00 0.00 2.90
1140 2786 0.627986 CAAGCCCAGGGAAGGAAGAT 59.372 55.000 10.89 0.00 0.00 2.40
1141 2787 2.078452 CAAGCCCAGGGAAGGAAGA 58.922 57.895 10.89 0.00 0.00 2.87
1142 2788 1.680314 GCAAGCCCAGGGAAGGAAG 60.680 63.158 10.89 0.00 0.00 3.46
1143 2789 2.017668 TTGCAAGCCCAGGGAAGGAA 62.018 55.000 10.89 2.00 0.00 3.36
1144 2790 2.430704 CTTGCAAGCCCAGGGAAGGA 62.431 60.000 14.65 0.00 0.00 3.36
1145 2791 1.980772 CTTGCAAGCCCAGGGAAGG 60.981 63.158 14.65 0.00 0.00 3.46
1360 3006 1.337817 CGAAGAGCGAGAACACCACG 61.338 60.000 0.00 0.00 44.57 4.94
1366 3012 1.252235 CGAAGACGAAGAGCGAGAAC 58.748 55.000 0.00 0.00 44.57 3.01
1677 3326 4.659874 CGACCGTGTTGGCGTTGC 62.660 66.667 0.00 0.00 43.94 4.17
2069 3721 0.321653 CCACACGGGAAGAAGGAAGG 60.322 60.000 0.00 0.00 40.01 3.46
2070 3722 0.955919 GCCACACGGGAAGAAGGAAG 60.956 60.000 0.00 0.00 40.01 3.46
2071 3723 1.072505 GCCACACGGGAAGAAGGAA 59.927 57.895 0.00 0.00 40.01 3.36
2073 3725 2.359975 GGCCACACGGGAAGAAGG 60.360 66.667 0.00 0.00 40.01 3.46
2075 3727 2.612095 AAACGGCCACACGGGAAGAA 62.612 55.000 2.24 0.00 40.01 2.52
2077 3729 0.885596 TAAAACGGCCACACGGGAAG 60.886 55.000 2.24 0.00 40.01 3.46
2078 3730 1.147824 TAAAACGGCCACACGGGAA 59.852 52.632 2.24 0.00 40.01 3.97
2080 3732 2.948323 GTAAAACGGCCACACGGG 59.052 61.111 2.24 0.00 38.39 5.28
2081 3733 2.552268 CGTAAAACGGCCACACGG 59.448 61.111 2.24 0.00 38.08 4.94
2120 3772 0.179073 AATCTCAGATCGCAACCCCG 60.179 55.000 0.00 0.00 0.00 5.73
2211 3868 1.528161 CCACAGTTTCCGTAAACCGAC 59.472 52.381 0.00 0.00 45.11 4.79
2219 3876 1.101049 CAAGTGGCCACAGTTTCCGT 61.101 55.000 36.39 11.61 38.17 4.69
2229 3886 4.139038 GGAGTAGTAAAAACAAGTGGCCA 58.861 43.478 0.00 0.00 0.00 5.36
2253 3910 8.487028 AGAAAATGGTAGTACTCCCAGATTAAG 58.513 37.037 13.17 0.00 33.39 1.85
2268 3925 6.072286 ACTCTGACAAATGCAGAAAATGGTAG 60.072 38.462 0.00 0.00 41.45 3.18
2322 3979 2.798148 ATTTCGACGCCCCTGACACC 62.798 60.000 0.00 0.00 0.00 4.16
2329 3986 1.949465 ACATTCTATTTCGACGCCCC 58.051 50.000 0.00 0.00 0.00 5.80
2357 4014 8.768501 AGAGAACATCAGTGGTATTCATAGTA 57.231 34.615 0.00 0.00 0.00 1.82
2362 4019 6.096987 GGAGTAGAGAACATCAGTGGTATTCA 59.903 42.308 0.00 0.00 0.00 2.57
2363 4020 6.322712 AGGAGTAGAGAACATCAGTGGTATTC 59.677 42.308 0.00 0.00 0.00 1.75
2364 4021 6.097554 CAGGAGTAGAGAACATCAGTGGTATT 59.902 42.308 0.00 0.00 0.00 1.89
2365 4022 5.596361 CAGGAGTAGAGAACATCAGTGGTAT 59.404 44.000 0.00 0.00 0.00 2.73
2366 4023 4.950475 CAGGAGTAGAGAACATCAGTGGTA 59.050 45.833 0.00 0.00 0.00 3.25
2367 4024 3.766591 CAGGAGTAGAGAACATCAGTGGT 59.233 47.826 0.00 0.00 0.00 4.16
2368 4025 3.766591 ACAGGAGTAGAGAACATCAGTGG 59.233 47.826 0.00 0.00 0.00 4.00
2369 4026 5.398603 AACAGGAGTAGAGAACATCAGTG 57.601 43.478 0.00 0.00 0.00 3.66
2370 4027 5.419471 GGTAACAGGAGTAGAGAACATCAGT 59.581 44.000 0.00 0.00 0.00 3.41
2371 4028 5.449314 CGGTAACAGGAGTAGAGAACATCAG 60.449 48.000 0.00 0.00 0.00 2.90
2372 4029 4.398358 CGGTAACAGGAGTAGAGAACATCA 59.602 45.833 0.00 0.00 0.00 3.07
2373 4030 4.734108 GCGGTAACAGGAGTAGAGAACATC 60.734 50.000 0.00 0.00 0.00 3.06
2374 4031 3.130693 GCGGTAACAGGAGTAGAGAACAT 59.869 47.826 0.00 0.00 0.00 2.71
2400 4059 1.648467 GCTGTCGGGATGCTCAAACC 61.648 60.000 0.00 0.00 0.00 3.27
2446 4105 0.175073 ATCCCTAGTCGTGCGGAAAC 59.825 55.000 0.00 0.00 0.00 2.78
2449 4108 1.379443 ACATCCCTAGTCGTGCGGA 60.379 57.895 0.00 0.00 0.00 5.54
2450 4109 1.226974 CACATCCCTAGTCGTGCGG 60.227 63.158 0.00 0.00 0.00 5.69
2451 4110 1.226974 CCACATCCCTAGTCGTGCG 60.227 63.158 0.00 0.00 0.00 5.34
2452 4111 1.521681 GCCACATCCCTAGTCGTGC 60.522 63.158 0.00 0.00 0.00 5.34
2453 4112 0.460284 GTGCCACATCCCTAGTCGTG 60.460 60.000 0.00 0.00 0.00 4.35
2454 4113 0.614979 AGTGCCACATCCCTAGTCGT 60.615 55.000 0.00 0.00 0.00 4.34
2455 4114 0.179100 CAGTGCCACATCCCTAGTCG 60.179 60.000 0.00 0.00 0.00 4.18
2456 4115 1.195115 TCAGTGCCACATCCCTAGTC 58.805 55.000 0.00 0.00 0.00 2.59
2471 4346 9.301153 GTTTCATATTGTTCAACACTTTTCAGT 57.699 29.630 0.00 0.00 0.00 3.41
2489 4364 2.930040 CGTCGAACCTGCAGTTTCATAT 59.070 45.455 22.00 0.00 39.40 1.78
2490 4365 2.333926 CGTCGAACCTGCAGTTTCATA 58.666 47.619 22.00 8.16 39.40 2.15
2560 4437 0.391263 GGTTCCGGTTCAGCGAATCT 60.391 55.000 0.00 0.00 0.00 2.40
2694 4571 2.359214 TGTACTGCATGCGGTTGAAAAA 59.641 40.909 35.52 15.30 36.80 1.94
2695 4572 1.950216 TGTACTGCATGCGGTTGAAAA 59.050 42.857 35.52 16.07 36.80 2.29
2697 4574 1.819928 ATGTACTGCATGCGGTTGAA 58.180 45.000 35.52 21.54 36.26 2.69
2698 4575 2.276201 GTATGTACTGCATGCGGTTGA 58.724 47.619 35.52 22.56 38.47 3.18
2700 4577 2.006888 GTGTATGTACTGCATGCGGTT 58.993 47.619 35.52 21.09 42.13 4.44
2701 4578 1.066502 TGTGTATGTACTGCATGCGGT 60.067 47.619 33.24 33.24 42.13 5.68
2702 4579 1.650825 TGTGTATGTACTGCATGCGG 58.349 50.000 25.08 25.08 42.13 5.69
2703 4580 3.309410 TGAATGTGTATGTACTGCATGCG 59.691 43.478 14.09 10.50 42.13 4.73
2706 4583 6.172630 TCTGTTGAATGTGTATGTACTGCAT 58.827 36.000 0.00 0.00 41.42 3.96
2707 4584 5.546526 TCTGTTGAATGTGTATGTACTGCA 58.453 37.500 0.00 0.00 0.00 4.41
2708 4585 6.508563 CGATCTGTTGAATGTGTATGTACTGC 60.509 42.308 0.00 0.00 0.00 4.40
2709 4586 6.751888 TCGATCTGTTGAATGTGTATGTACTG 59.248 38.462 0.00 0.00 0.00 2.74
2710 4587 6.863275 TCGATCTGTTGAATGTGTATGTACT 58.137 36.000 0.00 0.00 0.00 2.73
2712 4589 7.716612 AGATCGATCTGTTGAATGTGTATGTA 58.283 34.615 26.78 0.00 35.42 2.29
2713 4590 6.577103 AGATCGATCTGTTGAATGTGTATGT 58.423 36.000 26.78 0.00 35.42 2.29
2717 4594 5.046529 GCTAGATCGATCTGTTGAATGTGT 58.953 41.667 33.22 9.12 37.76 3.72
2718 4595 4.447054 GGCTAGATCGATCTGTTGAATGTG 59.553 45.833 33.22 14.43 37.76 3.21
2719 4596 4.343526 AGGCTAGATCGATCTGTTGAATGT 59.656 41.667 33.22 10.31 37.76 2.71
2720 4597 4.685165 CAGGCTAGATCGATCTGTTGAATG 59.315 45.833 33.22 20.47 37.76 2.67
2722 4599 3.954258 TCAGGCTAGATCGATCTGTTGAA 59.046 43.478 33.22 15.28 37.76 2.69
2723 4600 3.555966 TCAGGCTAGATCGATCTGTTGA 58.444 45.455 33.22 25.38 37.76 3.18
2724 4601 3.567585 TCTCAGGCTAGATCGATCTGTTG 59.432 47.826 33.22 23.91 37.76 3.33
2726 4603 3.146066 GTCTCAGGCTAGATCGATCTGT 58.854 50.000 33.22 14.55 37.76 3.41
2727 4604 3.145286 TGTCTCAGGCTAGATCGATCTG 58.855 50.000 33.22 23.72 37.76 2.90
2728 4605 3.072330 TCTGTCTCAGGCTAGATCGATCT 59.928 47.826 29.58 29.58 35.14 2.75
2729 4606 3.407698 TCTGTCTCAGGCTAGATCGATC 58.592 50.000 17.91 17.91 31.51 3.69
2730 4607 3.411446 CTCTGTCTCAGGCTAGATCGAT 58.589 50.000 0.00 0.00 31.51 3.59
2731 4608 2.486370 CCTCTGTCTCAGGCTAGATCGA 60.486 54.545 0.00 0.00 31.51 3.59
2732 4609 1.879380 CCTCTGTCTCAGGCTAGATCG 59.121 57.143 0.00 0.00 31.51 3.69
2747 4624 0.179116 CACGTCCATGAGCTCCTCTG 60.179 60.000 12.15 6.17 0.00 3.35
2762 4639 1.623081 CGCGTTGTAATCCTGCACGT 61.623 55.000 0.00 0.00 0.00 4.49
2764 4641 0.094730 GTCGCGTTGTAATCCTGCAC 59.905 55.000 5.77 0.00 0.00 4.57
2805 4712 0.765510 AGTTGGACTCCACCAGGAAC 59.234 55.000 0.00 0.00 45.19 3.62
2991 4898 9.817809 CCACATAGTATTACAACTTACATGACT 57.182 33.333 0.00 0.00 0.00 3.41
2992 4899 9.811995 TCCACATAGTATTACAACTTACATGAC 57.188 33.333 0.00 0.00 0.00 3.06
2993 4900 9.811995 GTCCACATAGTATTACAACTTACATGA 57.188 33.333 0.00 0.00 0.00 3.07
2994 4901 9.594478 TGTCCACATAGTATTACAACTTACATG 57.406 33.333 0.00 0.00 0.00 3.21
3056 4969 4.909696 TCAAATTCAAAAGGAGAACGCA 57.090 36.364 0.00 0.00 0.00 5.24
3057 4970 4.146443 CGTTCAAATTCAAAAGGAGAACGC 59.854 41.667 11.07 0.00 46.30 4.84
3060 4973 8.194104 TCATTTCGTTCAAATTCAAAAGGAGAA 58.806 29.630 0.00 0.00 31.79 2.87
3061 4974 7.711846 TCATTTCGTTCAAATTCAAAAGGAGA 58.288 30.769 0.00 0.00 31.79 3.71
3064 4977 8.296799 TCATCATTTCGTTCAAATTCAAAAGG 57.703 30.769 0.00 0.00 31.79 3.11
3080 5012 6.609237 TTCCTGTCGATTCATCATCATTTC 57.391 37.500 0.00 0.00 0.00 2.17
3242 5177 2.238521 GTGATGTGGTTGGGTGACATT 58.761 47.619 0.00 0.00 30.39 2.71
3280 5215 6.915544 TGAGAGGTAACACGTATAGTAGTG 57.084 41.667 0.00 2.46 43.46 2.74
3281 5216 7.992033 AGAATGAGAGGTAACACGTATAGTAGT 59.008 37.037 0.00 0.00 41.41 2.73
3282 5217 8.380743 AGAATGAGAGGTAACACGTATAGTAG 57.619 38.462 0.00 0.00 41.41 2.57
3283 5218 8.743085 AAGAATGAGAGGTAACACGTATAGTA 57.257 34.615 0.00 0.00 41.41 1.82
3284 5219 7.642082 AAGAATGAGAGGTAACACGTATAGT 57.358 36.000 0.00 0.00 41.41 2.12
3285 5220 7.043325 GCAAAGAATGAGAGGTAACACGTATAG 60.043 40.741 0.00 0.00 41.41 1.31
3286 5221 6.755141 GCAAAGAATGAGAGGTAACACGTATA 59.245 38.462 0.00 0.00 41.41 1.47
3293 5228 4.216257 TGCAAGCAAAGAATGAGAGGTAAC 59.784 41.667 0.00 0.00 0.00 2.50
3295 5230 4.019792 TGCAAGCAAAGAATGAGAGGTA 57.980 40.909 0.00 0.00 0.00 3.08
3331 5266 7.417496 AAGAAAAAGATGGAACGTGTACTAC 57.583 36.000 0.00 0.00 0.00 2.73
3332 5267 7.519328 GCAAAGAAAAAGATGGAACGTGTACTA 60.519 37.037 0.00 0.00 0.00 1.82
3333 5268 6.725246 CAAAGAAAAAGATGGAACGTGTACT 58.275 36.000 0.00 0.00 0.00 2.73
3387 5324 4.758674 TCTGAATCTGAACTGAAGCAAAGG 59.241 41.667 0.00 0.00 0.00 3.11
3433 5403 1.337387 GGTCCCTCTCTCGATAAACCG 59.663 57.143 0.00 0.00 0.00 4.44
3481 5451 5.915196 GCTCAACTCAACACCTAATTGAAAC 59.085 40.000 0.00 0.00 35.70 2.78
3553 5523 7.985184 ACTTGACTTGTTAGTTAACATCTGACA 59.015 33.333 8.61 0.00 44.72 3.58
3557 5527 7.985184 TGTGACTTGACTTGTTAGTTAACATCT 59.015 33.333 8.61 0.00 44.72 2.90
3681 5655 8.301002 GGAGTTTAATTAGCACCACAAACAATA 58.699 33.333 0.00 0.00 0.00 1.90
3691 5665 5.527582 ACATGATCGGAGTTTAATTAGCACC 59.472 40.000 0.00 0.00 0.00 5.01
4068 6099 3.086600 GGTGGAGGGGCTGGAGAG 61.087 72.222 0.00 0.00 0.00 3.20
4077 6108 1.530655 GTTGGTGTTGGGTGGAGGG 60.531 63.158 0.00 0.00 0.00 4.30
4111 6142 2.762745 GTTGGAGCTCCGTTTGAACTA 58.237 47.619 27.43 3.73 39.43 2.24
4112 6143 1.594331 GTTGGAGCTCCGTTTGAACT 58.406 50.000 27.43 0.00 39.43 3.01
4113 6144 0.234884 CGTTGGAGCTCCGTTTGAAC 59.765 55.000 27.43 22.38 39.43 3.18
4114 6145 0.179067 ACGTTGGAGCTCCGTTTGAA 60.179 50.000 27.43 13.16 39.43 2.69
4115 6146 0.878523 CACGTTGGAGCTCCGTTTGA 60.879 55.000 27.43 6.98 39.43 2.69
4116 6147 1.569493 CACGTTGGAGCTCCGTTTG 59.431 57.895 27.43 18.55 39.43 2.93
4133 6169 0.764369 AACACTCACTGGAGGAGCCA 60.764 55.000 0.00 0.00 45.81 4.75
4180 6227 5.181690 TCCATCCTTTGTTTCTTTCAACG 57.818 39.130 0.00 0.00 0.00 4.10
4191 6238 1.754234 GCGGGCATCCATCCTTTGT 60.754 57.895 0.00 0.00 0.00 2.83
4262 6310 6.805713 ACAAAAAGAATCACAGGTTAACAGG 58.194 36.000 8.10 0.96 0.00 4.00
4264 6312 7.831753 TGAACAAAAAGAATCACAGGTTAACA 58.168 30.769 8.10 0.00 0.00 2.41
4297 6345 8.848474 ACATATTTCATTATCCTAACCTTCCG 57.152 34.615 0.00 0.00 0.00 4.30
4342 6392 2.173569 CAGGGGTCCTCCTCCATTTAAG 59.826 54.545 0.00 0.00 33.94 1.85
4343 6393 2.205342 CAGGGGTCCTCCTCCATTTAA 58.795 52.381 0.00 0.00 33.94 1.52
4344 6394 1.628043 CCAGGGGTCCTCCTCCATTTA 60.628 57.143 0.00 0.00 33.94 1.40
4362 6412 0.918258 TTGTCCATATGCAGAGGCCA 59.082 50.000 5.01 0.00 40.13 5.36
4380 6430 6.736110 ATTAATAAAGTGGCTGCATCCATT 57.264 33.333 13.31 5.54 38.57 3.16
4384 6434 9.403110 CTGAATAATTAATAAAGTGGCTGCATC 57.597 33.333 0.50 0.00 0.00 3.91
4410 6464 9.048446 TGTTGTATAACTTTGTAAGGTCTTGTC 57.952 33.333 3.89 0.00 37.68 3.18
4428 6482 6.821665 GGTGGCTTCAGTCTTATTGTTGTATA 59.178 38.462 0.00 0.00 0.00 1.47
4515 6570 5.054477 GCTGCGAGGTCTATTTGGTATTAA 58.946 41.667 0.00 0.00 0.00 1.40
4526 6582 1.195115 AGATTTGGCTGCGAGGTCTA 58.805 50.000 0.00 0.00 0.00 2.59
4586 6643 2.400269 GAACTGGTGGGTGCCCGTAA 62.400 60.000 2.44 0.00 39.42 3.18
4604 6661 4.373116 GGTTGAGGAGCACGCCGA 62.373 66.667 0.00 0.00 0.00 5.54
4686 6744 0.887933 CGGGCAAGGTAAATGCAGTT 59.112 50.000 4.23 4.23 45.60 3.16
4694 6752 0.616679 AGCTAGACCGGGCAAGGTAA 60.617 55.000 11.69 0.00 46.09 2.85
4750 6808 1.815003 CGATGGACATGCGCAGGAA 60.815 57.895 30.79 14.02 0.00 3.36
4850 6908 3.056328 GTGGTTGGCTCCTTCGGC 61.056 66.667 1.63 0.00 0.00 5.54
4894 6952 3.018193 TTGGGGGCGGCATTCCTA 61.018 61.111 12.47 3.26 0.00 2.94
4970 7029 3.515502 TCTCAACCTCACCAATACCTCTG 59.484 47.826 0.00 0.00 0.00 3.35
4984 7044 4.021104 TCATCGATGTGAAACTCTCAACCT 60.021 41.667 24.09 0.00 38.04 3.50
4990 7050 3.118482 AGGCATCATCGATGTGAAACTCT 60.118 43.478 24.09 11.17 41.60 3.24
5036 7096 1.141881 GAGCCGGTGATGACGATGT 59.858 57.895 1.90 0.00 0.00 3.06
5084 7144 1.138266 GATTCCTTGGGACGGATTCGA 59.862 52.381 0.00 0.00 40.11 3.71


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

AutoCloner maintained by Alex Coulton.