Multiple sequence alignment - TraesCS4A01G145300

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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 TraesCS4A01G145300 chr4A 100.000 6001 0 0 1 6001 246715054 246709054 0.000000e+00 11082.0
1 TraesCS4A01G145300 chr4A 75.972 283 52 11 148 427 662971344 662971075 1.360000e-26 132.0
2 TraesCS4A01G145300 chr4A 89.412 85 8 1 344 428 731503002 731502919 8.230000e-19 106.0
3 TraesCS4A01G145300 chr4A 88.235 85 10 0 2710 2794 625096058 625096142 1.060000e-17 102.0
4 TraesCS4A01G145300 chr4A 86.905 84 10 1 344 427 702146556 702146474 6.400000e-15 93.5
5 TraesCS4A01G145300 chr4A 95.745 47 1 1 3677 3723 681669801 681669846 2.320000e-09 75.0
6 TraesCS4A01G145300 chr4A 100.000 38 0 0 391 428 740519485 740519522 3.000000e-08 71.3
7 TraesCS4A01G145300 chr4D 96.974 2346 40 13 1701 4025 139042965 139045300 0.000000e+00 3910.0
8 TraesCS4A01G145300 chr4D 96.478 1164 11 4 4025 5166 139045928 139047083 0.000000e+00 1895.0
9 TraesCS4A01G145300 chr4D 94.145 1093 25 16 608 1662 139041882 139042973 0.000000e+00 1628.0
10 TraesCS4A01G145300 chr4D 89.171 905 69 16 2783 3678 49843772 49844656 0.000000e+00 1101.0
11 TraesCS4A01G145300 chr4D 98.148 216 2 1 5788 6001 139047073 139047288 5.680000e-100 375.0
12 TraesCS4A01G145300 chr4D 88.718 195 8 2 427 607 139040358 139040552 6.050000e-55 226.0
13 TraesCS4A01G145300 chr4B 96.916 2075 41 12 1416 3470 156533208 156531137 0.000000e+00 3456.0
14 TraesCS4A01G145300 chr4B 93.898 1180 28 12 4025 5165 156528342 156527168 0.000000e+00 1740.0
15 TraesCS4A01G145300 chr4B 92.216 835 27 15 603 1415 156534185 156533367 0.000000e+00 1147.0
16 TraesCS4A01G145300 chr4B 90.493 284 11 4 3758 4025 156530669 156530386 1.590000e-95 361.0
17 TraesCS4A01G145300 chr4B 97.585 207 5 0 3469 3675 156530877 156530671 7.400000e-94 355.0
18 TraesCS4A01G145300 chr4B 96.020 201 7 1 5802 6001 156527146 156526946 5.800000e-85 326.0
19 TraesCS4A01G145300 chr4B 82.381 210 11 8 427 611 156534644 156534436 6.230000e-35 159.0
20 TraesCS4A01G145300 chr7B 99.049 631 5 1 5164 5793 649443763 649444393 0.000000e+00 1131.0
21 TraesCS4A01G145300 chr7B 85.390 397 32 10 2952 3339 645260077 645259698 7.290000e-104 388.0
22 TraesCS4A01G145300 chr7B 83.636 385 40 12 50 427 144478415 144478783 2.070000e-89 340.0
23 TraesCS4A01G145300 chr7B 84.685 111 6 2 3687 3797 633244340 633244439 3.830000e-17 100.0
24 TraesCS4A01G145300 chr7B 87.805 82 4 4 3677 3752 450588408 450588327 2.300000e-14 91.6
25 TraesCS4A01G145300 chr2A 98.405 627 9 1 5163 5788 455680547 455681173 0.000000e+00 1101.0
26 TraesCS4A01G145300 chr2A 98.098 631 10 2 5167 5796 424165965 424165336 0.000000e+00 1098.0
27 TraesCS4A01G145300 chr2A 98.098 631 9 3 5167 5795 761297043 761296414 0.000000e+00 1096.0
28 TraesCS4A01G145300 chr2A 89.408 321 30 4 3362 3681 140062349 140062032 9.370000e-108 401.0
29 TraesCS4A01G145300 chr2A 94.805 77 4 0 3722 3798 694471456 694471532 2.940000e-23 121.0
30 TraesCS4A01G145300 chr2A 92.208 77 2 1 4284 4356 363365444 363365368 8.230000e-19 106.0
31 TraesCS4A01G145300 chr3B 97.516 644 14 2 5155 5797 581653091 581652449 0.000000e+00 1099.0
32 TraesCS4A01G145300 chr3B 98.240 625 10 1 5167 5790 433586550 433585926 0.000000e+00 1092.0
33 TraesCS4A01G145300 chr3B 88.244 689 60 11 3009 3684 723486643 723485963 0.000000e+00 804.0
34 TraesCS4A01G145300 chr3B 90.909 385 30 5 2836 3219 685612744 685613124 4.150000e-141 512.0
35 TraesCS4A01G145300 chr3B 84.842 442 40 15 3248 3678 685613109 685613534 2.590000e-113 420.0
36 TraesCS4A01G145300 chr3B 81.493 335 39 12 50 377 17613293 17613611 2.780000e-63 254.0
37 TraesCS4A01G145300 chr3B 78.378 222 29 8 2710 2931 702363916 702364118 6.310000e-25 126.0
38 TraesCS4A01G145300 chr3A 98.400 625 9 1 5167 5790 153593884 153593260 0.000000e+00 1098.0
39 TraesCS4A01G145300 chr3A 93.350 406 8 2 1 406 677837475 677837089 3.120000e-162 582.0
40 TraesCS4A01G145300 chr6A 97.799 636 10 4 5159 5790 189579387 189580022 0.000000e+00 1094.0
41 TraesCS4A01G145300 chr6A 96.495 428 15 0 1 428 119296330 119296757 0.000000e+00 708.0
42 TraesCS4A01G145300 chr6A 90.278 72 7 0 1590 1661 603354481 603354552 1.780000e-15 95.3
43 TraesCS4A01G145300 chr6A 82.883 111 5 3 4254 4350 422267965 422268075 2.980000e-13 87.9
44 TraesCS4A01G145300 chr1A 98.240 625 10 1 5167 5790 513163983 513163359 0.000000e+00 1092.0
45 TraesCS4A01G145300 chr1A 82.150 493 57 9 2853 3339 118278103 118278570 1.570000e-105 394.0
46 TraesCS4A01G145300 chr1A 95.652 69 3 0 1594 1662 432985327 432985395 1.770000e-20 111.0
47 TraesCS4A01G145300 chr1A 93.846 65 4 0 1598 1662 57303782 57303718 1.380000e-16 99.0
48 TraesCS4A01G145300 chr1A 85.366 82 12 0 2853 2934 232059725 232059644 1.070000e-12 86.1
49 TraesCS4A01G145300 chr1A 86.538 52 4 3 2835 2886 144561441 144561489 3.000000e-03 54.7
50 TraesCS4A01G145300 chr1B 87.459 909 72 23 2783 3677 60100211 60101091 0.000000e+00 1009.0
51 TraesCS4A01G145300 chr1B 87.918 687 64 9 3009 3684 496496100 496496778 0.000000e+00 791.0
52 TraesCS4A01G145300 chr1B 82.186 494 54 19 2853 3339 90433725 90433259 1.570000e-105 394.0
53 TraesCS4A01G145300 chr1B 83.750 400 42 12 35 427 665286685 665287068 2.060000e-94 357.0
54 TraesCS4A01G145300 chr1B 95.652 69 2 1 1594 1662 451737751 451737818 6.360000e-20 110.0
55 TraesCS4A01G145300 chr1B 85.859 99 7 5 4254 4347 60071994 60071898 1.380000e-16 99.0
56 TraesCS4A01G145300 chr7A 96.487 427 15 0 1 427 566353424 566352998 0.000000e+00 706.0
57 TraesCS4A01G145300 chr7A 86.585 82 11 0 2853 2934 660439533 660439452 2.300000e-14 91.6
58 TraesCS4A01G145300 chr7A 82.883 111 5 3 4254 4350 672983892 672984002 2.980000e-13 87.9
59 TraesCS4A01G145300 chr7A 96.970 33 0 1 2854 2886 672984039 672984008 3.000000e-03 54.7
60 TraesCS4A01G145300 chr5A 88.109 513 41 10 3009 3510 689428626 689428123 5.180000e-165 592.0
61 TraesCS4A01G145300 chr5A 82.051 117 7 3 4254 4356 598351184 598351068 2.980000e-13 87.9
62 TraesCS4A01G145300 chr5A 96.154 52 2 0 4305 4356 606395584 606395635 1.070000e-12 86.1
63 TraesCS4A01G145300 chr7D 89.389 311 27 6 120 427 170971596 170971289 2.620000e-103 387.0
64 TraesCS4A01G145300 chr7D 81.781 494 55 17 2853 3338 28801432 28800966 1.220000e-101 381.0
65 TraesCS4A01G145300 chr7D 90.435 115 4 3 3683 3797 431918972 431918865 1.740000e-30 145.0
66 TraesCS4A01G145300 chr7D 91.667 84 5 2 3722 3803 490902241 490902324 1.370000e-21 115.0
67 TraesCS4A01G145300 chr2D 86.350 337 40 6 95 428 57908140 57907807 4.420000e-96 363.0
68 TraesCS4A01G145300 chr2D 87.395 119 11 4 3683 3798 554308419 554308302 3.770000e-27 134.0
69 TraesCS4A01G145300 chr2B 82.946 387 42 12 50 428 549651747 549651377 1.610000e-85 327.0
70 TraesCS4A01G145300 chr2B 95.890 73 3 0 3724 3796 765397952 765398024 1.060000e-22 119.0
71 TraesCS4A01G145300 chr3D 90.972 144 12 1 3460 3603 501290201 501290343 6.140000e-45 193.0
72 TraesCS4A01G145300 chr3D 92.208 77 2 1 4282 4354 32172525 32172449 8.230000e-19 106.0
73 TraesCS4A01G145300 chr3D 96.226 53 2 0 4304 4356 16448318 16448266 2.980000e-13 87.9
74 TraesCS4A01G145300 chr6D 95.000 80 2 2 3721 3799 93644478 93644400 2.270000e-24 124.0
75 TraesCS4A01G145300 chr6D 93.590 78 5 0 3724 3801 93644411 93644488 3.800000e-22 117.0
76 TraesCS4A01G145300 chr6D 95.385 65 3 0 3796 3860 363018501 363018565 2.960000e-18 104.0
77 TraesCS4A01G145300 chr6D 91.781 73 6 0 1590 1662 456669649 456669721 1.060000e-17 102.0
78 TraesCS4A01G145300 chr6D 92.647 68 4 1 1595 1662 271006506 271006440 4.950000e-16 97.1
79 TraesCS4A01G145300 chr6B 92.405 79 2 1 4282 4356 247041993 247042071 6.360000e-20 110.0
80 TraesCS4A01G145300 chr6B 96.154 52 2 0 4305 4356 247036884 247036935 1.070000e-12 86.1
81 TraesCS4A01G145300 chr5B 91.304 69 6 0 1594 1662 693674595 693674527 1.780000e-15 95.3
82 TraesCS4A01G145300 chr5B 94.915 59 3 0 4254 4312 617237575 617237517 6.400000e-15 93.5
83 TraesCS4A01G145300 chr5B 94.118 51 3 0 3673 3723 635464463 635464513 1.790000e-10 78.7
84 TraesCS4A01G145300 chr5D 92.453 53 4 0 3671 3723 458811236 458811288 6.450000e-10 76.8
85 TraesCS4A01G145300 chr5D 85.915 71 9 1 3673 3743 505402863 505402932 2.320000e-09 75.0


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 TraesCS4A01G145300 chr4A 246709054 246715054 6000 True 11082.000000 11082 100.0000 1 6001 1 chr4A.!!$R1 6000
1 TraesCS4A01G145300 chr4D 139040358 139047288 6930 False 1606.800000 3910 94.8926 427 6001 5 chr4D.!!$F2 5574
2 TraesCS4A01G145300 chr4D 49843772 49844656 884 False 1101.000000 1101 89.1710 2783 3678 1 chr4D.!!$F1 895
3 TraesCS4A01G145300 chr4B 156526946 156534644 7698 True 1077.714286 3456 92.7870 427 6001 7 chr4B.!!$R1 5574
4 TraesCS4A01G145300 chr7B 649443763 649444393 630 False 1131.000000 1131 99.0490 5164 5793 1 chr7B.!!$F3 629
5 TraesCS4A01G145300 chr2A 455680547 455681173 626 False 1101.000000 1101 98.4050 5163 5788 1 chr2A.!!$F1 625
6 TraesCS4A01G145300 chr2A 424165336 424165965 629 True 1098.000000 1098 98.0980 5167 5796 1 chr2A.!!$R3 629
7 TraesCS4A01G145300 chr2A 761296414 761297043 629 True 1096.000000 1096 98.0980 5167 5795 1 chr2A.!!$R4 628
8 TraesCS4A01G145300 chr3B 581652449 581653091 642 True 1099.000000 1099 97.5160 5155 5797 1 chr3B.!!$R2 642
9 TraesCS4A01G145300 chr3B 433585926 433586550 624 True 1092.000000 1092 98.2400 5167 5790 1 chr3B.!!$R1 623
10 TraesCS4A01G145300 chr3B 723485963 723486643 680 True 804.000000 804 88.2440 3009 3684 1 chr3B.!!$R3 675
11 TraesCS4A01G145300 chr3B 685612744 685613534 790 False 466.000000 512 87.8755 2836 3678 2 chr3B.!!$F3 842
12 TraesCS4A01G145300 chr3A 153593260 153593884 624 True 1098.000000 1098 98.4000 5167 5790 1 chr3A.!!$R1 623
13 TraesCS4A01G145300 chr6A 189579387 189580022 635 False 1094.000000 1094 97.7990 5159 5790 1 chr6A.!!$F2 631
14 TraesCS4A01G145300 chr1A 513163359 513163983 624 True 1092.000000 1092 98.2400 5167 5790 1 chr1A.!!$R3 623
15 TraesCS4A01G145300 chr1B 60100211 60101091 880 False 1009.000000 1009 87.4590 2783 3677 1 chr1B.!!$F1 894
16 TraesCS4A01G145300 chr1B 496496100 496496778 678 False 791.000000 791 87.9180 3009 3684 1 chr1B.!!$F3 675
17 TraesCS4A01G145300 chr5A 689428123 689428626 503 True 592.000000 592 88.1090 3009 3510 1 chr5A.!!$R2 501

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
666 2024 0.039798 TCGTTCCGTGTTCCTCTTCG 60.040 55.000 0.00 0.00 0.00 3.79 F
1172 2570 1.139947 GTACCGTCTGCTCCTCTGC 59.860 63.158 0.00 0.00 0.00 4.26 F
1612 3168 1.270147 CCCAAGGTTTTCGAGTCGACT 60.270 52.381 20.18 20.18 34.89 4.18 F
2563 4134 1.197721 GCCGTCTCACTGAATTTGTGG 59.802 52.381 11.05 4.61 36.21 4.17 F
4055 7971 2.167281 AGGACATCTCACAATGAGGACG 59.833 50.000 6.01 0.00 44.39 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1612 3168 0.035152 TCGCTACCCAAGACCGACTA 60.035 55.000 0.0 0.0 0.00 2.59 R
2305 3876 2.625639 AGAAGGGTGTCTCATCTTGGT 58.374 47.619 0.0 0.0 0.00 3.67 R
3339 4927 1.946267 CAACCAGTACCAACGCCAC 59.054 57.895 0.0 0.0 0.00 5.01 R
4378 8333 4.618338 CACGAATGCAAACAACATGAAG 57.382 40.909 0.0 0.0 0.00 3.02 R
5157 9112 0.109342 GCACAGGGCTATATGCAGGT 59.891 55.000 0.0 0.0 45.15 4.00 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
34 35 8.519492 AATGGACGAACATTTCTACAAATTTG 57.481 30.769 16.67 16.67 37.81 2.32
35 36 7.265647 TGGACGAACATTTCTACAAATTTGA 57.734 32.000 24.64 7.56 28.97 2.69
36 37 7.881142 TGGACGAACATTTCTACAAATTTGAT 58.119 30.769 24.64 11.17 28.97 2.57
37 38 7.807433 TGGACGAACATTTCTACAAATTTGATG 59.193 33.333 24.64 17.76 28.97 3.07
38 39 8.020819 GGACGAACATTTCTACAAATTTGATGA 58.979 33.333 24.64 17.10 28.97 2.92
39 40 9.393249 GACGAACATTTCTACAAATTTGATGAA 57.607 29.630 24.64 21.14 28.97 2.57
40 41 9.180678 ACGAACATTTCTACAAATTTGATGAAC 57.819 29.630 24.64 13.51 28.97 3.18
41 42 9.398170 CGAACATTTCTACAAATTTGATGAACT 57.602 29.630 24.64 16.56 28.97 3.01
80 81 8.939201 TGAACTTTTTACAAATTTGATGAGCA 57.061 26.923 24.64 7.68 0.00 4.26
81 82 9.545105 TGAACTTTTTACAAATTTGATGAGCAT 57.455 25.926 24.64 2.89 0.00 3.79
94 95 7.804843 TTTGATGAGCATTTTCAAATTTGGT 57.195 28.000 17.90 0.00 35.16 3.67
95 96 6.788684 TGATGAGCATTTTCAAATTTGGTG 57.211 33.333 17.90 12.29 0.00 4.17
96 97 6.522946 TGATGAGCATTTTCAAATTTGGTGA 58.477 32.000 17.90 4.77 0.00 4.02
97 98 6.990939 TGATGAGCATTTTCAAATTTGGTGAA 59.009 30.769 17.90 10.46 33.21 3.18
98 99 6.601741 TGAGCATTTTCAAATTTGGTGAAC 57.398 33.333 17.90 4.47 34.78 3.18
99 100 6.347696 TGAGCATTTTCAAATTTGGTGAACT 58.652 32.000 17.90 8.87 34.78 3.01
100 101 6.822676 TGAGCATTTTCAAATTTGGTGAACTT 59.177 30.769 17.90 0.45 34.78 2.66
101 102 7.336427 TGAGCATTTTCAAATTTGGTGAACTTT 59.664 29.630 17.90 0.00 34.78 2.66
102 103 8.054152 AGCATTTTCAAATTTGGTGAACTTTT 57.946 26.923 17.90 0.00 34.78 2.27
103 104 8.522003 AGCATTTTCAAATTTGGTGAACTTTTT 58.478 25.926 17.90 0.00 34.78 1.94
176 177 8.409358 AATTAGGAAATCCAATAAATAGCGCT 57.591 30.769 17.26 17.26 38.89 5.92
177 178 9.515226 AATTAGGAAATCCAATAAATAGCGCTA 57.485 29.630 21.30 21.30 38.89 4.26
178 179 8.911918 TTAGGAAATCCAATAAATAGCGCTAA 57.088 30.769 22.98 5.33 38.89 3.09
179 180 9.515226 TTAGGAAATCCAATAAATAGCGCTAAT 57.485 29.630 22.98 10.86 38.89 1.73
180 181 8.409358 AGGAAATCCAATAAATAGCGCTAATT 57.591 30.769 22.98 21.70 38.89 1.40
181 182 8.860088 AGGAAATCCAATAAATAGCGCTAATTT 58.140 29.630 22.98 21.51 38.89 1.82
196 197 8.671384 AGCGCTAATTTATTGGTTCTTATACA 57.329 30.769 8.99 0.00 0.00 2.29
197 198 8.557029 AGCGCTAATTTATTGGTTCTTATACAC 58.443 33.333 8.99 0.00 0.00 2.90
198 199 8.557029 GCGCTAATTTATTGGTTCTTATACACT 58.443 33.333 0.00 0.00 0.00 3.55
203 204 6.578020 TTATTGGTTCTTATACACTTCGCG 57.422 37.500 0.00 0.00 0.00 5.87
204 205 3.581024 TGGTTCTTATACACTTCGCGT 57.419 42.857 5.77 0.00 0.00 6.01
205 206 3.916761 TGGTTCTTATACACTTCGCGTT 58.083 40.909 5.77 0.00 0.00 4.84
206 207 3.922240 TGGTTCTTATACACTTCGCGTTC 59.078 43.478 5.77 0.00 0.00 3.95
207 208 3.922240 GGTTCTTATACACTTCGCGTTCA 59.078 43.478 5.77 0.00 0.00 3.18
208 209 4.565564 GGTTCTTATACACTTCGCGTTCAT 59.434 41.667 5.77 0.00 0.00 2.57
209 210 5.063060 GGTTCTTATACACTTCGCGTTCATT 59.937 40.000 5.77 0.00 0.00 2.57
210 211 6.401796 GGTTCTTATACACTTCGCGTTCATTT 60.402 38.462 5.77 0.00 0.00 2.32
211 212 6.089920 TCTTATACACTTCGCGTTCATTTG 57.910 37.500 5.77 0.00 0.00 2.32
212 213 5.636121 TCTTATACACTTCGCGTTCATTTGT 59.364 36.000 5.77 4.98 0.00 2.83
213 214 6.807720 TCTTATACACTTCGCGTTCATTTGTA 59.192 34.615 5.77 7.07 0.00 2.41
214 215 3.515071 ACACTTCGCGTTCATTTGTAC 57.485 42.857 5.77 0.00 0.00 2.90
215 216 3.128349 ACACTTCGCGTTCATTTGTACT 58.872 40.909 5.77 0.00 0.00 2.73
216 217 4.300803 ACACTTCGCGTTCATTTGTACTA 58.699 39.130 5.77 0.00 0.00 1.82
217 218 4.746115 ACACTTCGCGTTCATTTGTACTAA 59.254 37.500 5.77 0.00 0.00 2.24
218 219 5.070862 CACTTCGCGTTCATTTGTACTAAC 58.929 41.667 5.77 0.00 0.00 2.34
219 220 4.986659 ACTTCGCGTTCATTTGTACTAACT 59.013 37.500 5.77 0.00 0.00 2.24
220 221 6.088483 CACTTCGCGTTCATTTGTACTAACTA 59.912 38.462 5.77 0.00 0.00 2.24
221 222 6.307318 ACTTCGCGTTCATTTGTACTAACTAG 59.693 38.462 5.77 0.00 0.00 2.57
222 223 5.097529 TCGCGTTCATTTGTACTAACTAGG 58.902 41.667 5.77 0.00 0.00 3.02
223 224 4.266976 CGCGTTCATTTGTACTAACTAGGG 59.733 45.833 0.00 0.00 0.00 3.53
224 225 4.569564 GCGTTCATTTGTACTAACTAGGGG 59.430 45.833 0.00 0.00 0.00 4.79
225 226 5.727434 CGTTCATTTGTACTAACTAGGGGT 58.273 41.667 0.00 0.00 0.00 4.95
226 227 6.168389 CGTTCATTTGTACTAACTAGGGGTT 58.832 40.000 0.00 0.00 41.54 4.11
227 228 6.312180 CGTTCATTTGTACTAACTAGGGGTTC 59.688 42.308 0.00 0.00 39.17 3.62
228 229 6.303903 TCATTTGTACTAACTAGGGGTTCC 57.696 41.667 0.00 0.00 39.17 3.62
229 230 6.027482 TCATTTGTACTAACTAGGGGTTCCT 58.973 40.000 0.00 0.00 46.96 3.36
230 231 6.502863 TCATTTGTACTAACTAGGGGTTCCTT 59.497 38.462 0.00 0.00 41.56 3.36
231 232 5.750352 TTGTACTAACTAGGGGTTCCTTG 57.250 43.478 0.00 0.00 41.56 3.61
238 239 3.595021 ACTAGGGGTTCCTTGTTGTAGT 58.405 45.455 0.00 0.00 44.64 2.73
239 240 2.951229 AGGGGTTCCTTGTTGTAGTG 57.049 50.000 0.00 0.00 41.56 2.74
240 241 1.423921 AGGGGTTCCTTGTTGTAGTGG 59.576 52.381 0.00 0.00 41.56 4.00
241 242 1.144298 GGGGTTCCTTGTTGTAGTGGT 59.856 52.381 0.00 0.00 0.00 4.16
242 243 2.423803 GGGGTTCCTTGTTGTAGTGGTT 60.424 50.000 0.00 0.00 0.00 3.67
243 244 3.181441 GGGGTTCCTTGTTGTAGTGGTTA 60.181 47.826 0.00 0.00 0.00 2.85
244 245 4.070009 GGGTTCCTTGTTGTAGTGGTTAG 58.930 47.826 0.00 0.00 0.00 2.34
245 246 3.501062 GGTTCCTTGTTGTAGTGGTTAGC 59.499 47.826 0.00 0.00 0.00 3.09
246 247 3.034721 TCCTTGTTGTAGTGGTTAGCG 57.965 47.619 0.00 0.00 0.00 4.26
247 248 2.073816 CCTTGTTGTAGTGGTTAGCGG 58.926 52.381 0.00 0.00 0.00 5.52
248 249 2.289195 CCTTGTTGTAGTGGTTAGCGGA 60.289 50.000 0.00 0.00 0.00 5.54
249 250 3.395639 CTTGTTGTAGTGGTTAGCGGAA 58.604 45.455 0.00 0.00 0.00 4.30
250 251 3.688694 TGTTGTAGTGGTTAGCGGAAT 57.311 42.857 0.00 0.00 0.00 3.01
251 252 3.331150 TGTTGTAGTGGTTAGCGGAATG 58.669 45.455 0.00 0.00 0.00 2.67
252 253 2.676342 GTTGTAGTGGTTAGCGGAATGG 59.324 50.000 0.00 0.00 0.00 3.16
253 254 1.903860 TGTAGTGGTTAGCGGAATGGT 59.096 47.619 0.00 0.00 0.00 3.55
254 255 2.303600 TGTAGTGGTTAGCGGAATGGTT 59.696 45.455 0.00 0.00 0.00 3.67
255 256 2.109425 AGTGGTTAGCGGAATGGTTC 57.891 50.000 0.00 0.00 0.00 3.62
256 257 1.092348 GTGGTTAGCGGAATGGTTCC 58.908 55.000 0.00 0.00 46.62 3.62
267 268 4.302559 GGAATGGTTCCTCCTTTGTAGT 57.697 45.455 1.52 0.00 46.57 2.73
268 269 4.663334 GGAATGGTTCCTCCTTTGTAGTT 58.337 43.478 1.52 0.00 46.57 2.24
269 270 5.077564 GGAATGGTTCCTCCTTTGTAGTTT 58.922 41.667 1.52 0.00 46.57 2.66
270 271 5.183331 GGAATGGTTCCTCCTTTGTAGTTTC 59.817 44.000 1.52 0.00 46.57 2.78
271 272 4.781775 TGGTTCCTCCTTTGTAGTTTCA 57.218 40.909 0.00 0.00 37.07 2.69
272 273 5.118729 TGGTTCCTCCTTTGTAGTTTCAA 57.881 39.130 0.00 0.00 37.07 2.69
273 274 5.130350 TGGTTCCTCCTTTGTAGTTTCAAG 58.870 41.667 0.00 0.00 37.07 3.02
274 275 4.519350 GGTTCCTCCTTTGTAGTTTCAAGG 59.481 45.833 0.00 0.00 0.00 3.61
275 276 3.751518 TCCTCCTTTGTAGTTTCAAGGC 58.248 45.455 0.00 0.00 0.00 4.35
276 277 3.137544 TCCTCCTTTGTAGTTTCAAGGCA 59.862 43.478 0.00 0.00 0.00 4.75
277 278 4.082125 CCTCCTTTGTAGTTTCAAGGCAT 58.918 43.478 0.00 0.00 0.00 4.40
278 279 4.082571 CCTCCTTTGTAGTTTCAAGGCATG 60.083 45.833 0.00 0.00 0.00 4.06
279 280 4.724399 TCCTTTGTAGTTTCAAGGCATGA 58.276 39.130 0.00 0.00 35.85 3.07
280 281 4.761739 TCCTTTGTAGTTTCAAGGCATGAG 59.238 41.667 0.00 0.00 39.77 2.90
281 282 4.520492 CCTTTGTAGTTTCAAGGCATGAGT 59.480 41.667 0.00 0.00 39.77 3.41
282 283 5.010012 CCTTTGTAGTTTCAAGGCATGAGTT 59.990 40.000 0.00 0.00 39.77 3.01
283 284 6.461509 CCTTTGTAGTTTCAAGGCATGAGTTT 60.462 38.462 0.00 0.00 39.77 2.66
284 285 5.437289 TGTAGTTTCAAGGCATGAGTTTG 57.563 39.130 0.00 0.00 39.77 2.93
285 286 5.129634 TGTAGTTTCAAGGCATGAGTTTGA 58.870 37.500 0.00 0.00 39.77 2.69
286 287 4.843220 AGTTTCAAGGCATGAGTTTGAG 57.157 40.909 0.00 0.00 39.77 3.02
287 288 4.210331 AGTTTCAAGGCATGAGTTTGAGT 58.790 39.130 0.00 0.00 39.77 3.41
288 289 4.037208 AGTTTCAAGGCATGAGTTTGAGTG 59.963 41.667 0.00 0.00 39.77 3.51
289 290 3.490439 TCAAGGCATGAGTTTGAGTGA 57.510 42.857 0.00 0.00 33.04 3.41
290 291 3.141398 TCAAGGCATGAGTTTGAGTGAC 58.859 45.455 0.00 0.00 33.04 3.67
291 292 1.800805 AGGCATGAGTTTGAGTGACG 58.199 50.000 0.00 0.00 0.00 4.35
292 293 0.798776 GGCATGAGTTTGAGTGACGG 59.201 55.000 0.00 0.00 0.00 4.79
293 294 1.512926 GCATGAGTTTGAGTGACGGT 58.487 50.000 0.00 0.00 0.00 4.83
294 295 2.611971 GGCATGAGTTTGAGTGACGGTA 60.612 50.000 0.00 0.00 0.00 4.02
295 296 2.412089 GCATGAGTTTGAGTGACGGTAC 59.588 50.000 0.00 0.00 0.00 3.34
296 297 2.806608 TGAGTTTGAGTGACGGTACC 57.193 50.000 0.16 0.16 0.00 3.34
297 298 1.001048 TGAGTTTGAGTGACGGTACCG 60.001 52.381 32.22 32.22 46.03 4.02
298 299 0.316204 AGTTTGAGTGACGGTACCGG 59.684 55.000 35.86 19.18 44.69 5.28
306 307 4.883240 ACGGTACCGGCAGTTTTT 57.117 50.000 35.86 11.64 44.69 1.94
351 352 2.902705 TTTCTTCTACAGCGTGTGGT 57.097 45.000 1.58 0.00 30.33 4.16
389 390 3.969802 GCGTGCAAGTGCCAGCTT 61.970 61.111 11.32 0.00 41.18 3.74
390 391 2.050714 CGTGCAAGTGCCAGCTTG 60.051 61.111 0.00 7.99 46.21 4.01
394 395 3.754068 CAAGTGCCAGCTTGCTGA 58.246 55.556 22.50 2.14 39.26 4.26
395 396 2.035421 CAAGTGCCAGCTTGCTGAA 58.965 52.632 22.50 8.73 39.26 3.02
396 397 0.318445 CAAGTGCCAGCTTGCTGAAC 60.318 55.000 22.50 18.54 39.26 3.18
397 398 1.458639 AAGTGCCAGCTTGCTGAACC 61.459 55.000 22.50 11.34 0.00 3.62
398 399 2.979676 TGCCAGCTTGCTGAACCG 60.980 61.111 22.50 8.01 0.00 4.44
399 400 3.741476 GCCAGCTTGCTGAACCGG 61.741 66.667 22.50 0.00 0.00 5.28
400 401 3.741476 CCAGCTTGCTGAACCGGC 61.741 66.667 22.50 0.00 36.10 6.13
401 402 4.093952 CAGCTTGCTGAACCGGCG 62.094 66.667 16.78 0.00 38.82 6.46
404 405 3.357079 CTTGCTGAACCGGCGCTT 61.357 61.111 7.64 0.00 38.82 4.68
405 406 2.031314 TTGCTGAACCGGCGCTTA 59.969 55.556 7.64 0.00 38.82 3.09
406 407 1.573829 CTTGCTGAACCGGCGCTTAA 61.574 55.000 7.64 0.00 38.82 1.85
407 408 1.573829 TTGCTGAACCGGCGCTTAAG 61.574 55.000 7.64 0.00 38.82 1.85
408 409 2.750888 GCTGAACCGGCGCTTAAGG 61.751 63.158 7.64 8.80 0.00 2.69
409 410 2.744709 TGAACCGGCGCTTAAGGC 60.745 61.111 7.64 6.03 37.64 4.35
418 419 3.406559 GCTTAAGGCGCCGGTTAG 58.593 61.111 23.20 17.07 0.00 2.34
419 420 2.178235 GCTTAAGGCGCCGGTTAGG 61.178 63.158 23.20 16.37 44.97 2.69
420 421 1.518774 CTTAAGGCGCCGGTTAGGA 59.481 57.895 23.20 3.11 45.00 2.94
421 422 0.529992 CTTAAGGCGCCGGTTAGGAG 60.530 60.000 23.20 9.54 45.00 3.69
475 483 4.168291 GGAGCCTGGAGCCTTCGG 62.168 72.222 0.00 0.00 45.47 4.30
666 2024 0.039798 TCGTTCCGTGTTCCTCTTCG 60.040 55.000 0.00 0.00 0.00 3.79
791 2151 2.126228 CTGTTTCCTCGCGCCGTA 60.126 61.111 0.00 0.00 0.00 4.02
912 2278 2.088423 TCTCGCTCCTCTCTTGTCTTC 58.912 52.381 0.00 0.00 0.00 2.87
915 2281 2.091541 CGCTCCTCTCTTGTCTTCTCT 58.908 52.381 0.00 0.00 0.00 3.10
919 2285 4.618227 GCTCCTCTCTTGTCTTCTCTTGTC 60.618 50.000 0.00 0.00 0.00 3.18
920 2286 3.504134 TCCTCTCTTGTCTTCTCTTGTCG 59.496 47.826 0.00 0.00 0.00 4.35
922 2288 1.982223 CTCTTGTCTTCTCTTGTCGCG 59.018 52.381 0.00 0.00 0.00 5.87
923 2289 1.337071 TCTTGTCTTCTCTTGTCGCGT 59.663 47.619 5.77 0.00 0.00 6.01
926 2292 2.658285 TGTCTTCTCTTGTCGCGTAAC 58.342 47.619 5.77 0.00 0.00 2.50
927 2293 2.033675 TGTCTTCTCTTGTCGCGTAACA 59.966 45.455 5.77 0.00 0.00 2.41
985 2378 3.629398 AGATTGAGATTGATTTCGGTGCC 59.371 43.478 0.00 0.00 0.00 5.01
1172 2570 1.139947 GTACCGTCTGCTCCTCTGC 59.860 63.158 0.00 0.00 0.00 4.26
1612 3168 1.270147 CCCAAGGTTTTCGAGTCGACT 60.270 52.381 20.18 20.18 34.89 4.18
1683 3239 5.949735 ACACGTTGTTGAGTCTTGAATTTT 58.050 33.333 0.00 0.00 0.00 1.82
1709 3278 7.892778 TTTATGACTACAATTAGTTGCGACA 57.107 32.000 6.90 0.00 38.77 4.35
1710 3279 7.520119 TTATGACTACAATTAGTTGCGACAG 57.480 36.000 6.90 0.00 38.77 3.51
1866 3436 1.630369 AGGAGCCTAACAGTTGCATGA 59.370 47.619 0.00 0.00 0.00 3.07
2563 4134 1.197721 GCCGTCTCACTGAATTTGTGG 59.802 52.381 11.05 4.61 36.21 4.17
2632 4203 2.306847 ACTTTGGCAGGTTGGTACTTG 58.693 47.619 0.00 0.00 34.68 3.16
3240 4821 5.911752 TCTCTATCTGCTTCTTTCCATGTC 58.088 41.667 0.00 0.00 0.00 3.06
3296 4879 9.312146 GACAGTTTTGTTTTGTAACACATTTTG 57.688 29.630 0.00 0.00 43.66 2.44
3339 4927 4.931661 ATTGGCTTGAGCTCCATTATTG 57.068 40.909 12.15 0.00 41.70 1.90
3409 4997 8.110860 TCTTATCTCTCCAATTTGACCAAAAC 57.889 34.615 0.00 0.00 33.56 2.43
3644 5499 3.793129 GCTTTGGGTGTAATGCATGATCG 60.793 47.826 0.00 0.00 32.71 3.69
3692 5547 7.756395 TCATACTTAATAAGTACTCCCTCCG 57.244 40.000 14.37 0.00 45.99 4.63
3717 5572 6.007936 TCCATAATTCTTGTCGTGGTTTTG 57.992 37.500 0.00 0.00 0.00 2.44
3728 5583 2.359531 TCGTGGTTTTGGTTCATTCCAC 59.640 45.455 0.00 0.00 41.00 4.02
3866 5722 8.786826 AAGAACAGATATACCAAATTTGTCGA 57.213 30.769 16.73 2.24 0.00 4.20
3867 5723 8.197988 AGAACAGATATACCAAATTTGTCGAC 57.802 34.615 16.73 9.11 0.00 4.20
3869 5725 8.561738 AACAGATATACCAAATTTGTCGACTT 57.438 30.769 17.92 0.00 0.00 3.01
3996 5867 9.753674 TTTCATGAAAAATCATAGTAGGGAGTT 57.246 29.630 18.45 0.00 0.00 3.01
4055 7971 2.167281 AGGACATCTCACAATGAGGACG 59.833 50.000 6.01 0.00 44.39 4.79
4378 8333 6.396829 AGGCTGGATTTTTGCTTATGTATC 57.603 37.500 0.00 0.00 0.00 2.24
4610 8565 5.898972 ACAACCACATAATATGGAAGCCAAT 59.101 36.000 5.16 0.00 39.87 3.16
4751 8706 2.541547 TTTCTGAGCCATCCAGCCCG 62.542 60.000 0.00 0.00 0.00 6.13
5545 9501 6.170506 TGTAGGTGCTTAGTAGTGAATTTGG 58.829 40.000 0.00 0.00 0.00 3.28
5819 9793 8.788806 GCATAGAGTTGTGTATATCTCACTAGT 58.211 37.037 10.77 0.00 36.83 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.541143 AATTTGTAGAAATGTTCGTCCATTTTT 57.459 25.926 13.51 11.31 43.28 1.94
7 8 9.541143 AAATTTGTAGAAATGTTCGTCCATTTT 57.459 25.926 13.51 8.37 43.28 1.82
10 11 7.881142 TCAAATTTGTAGAAATGTTCGTCCAT 58.119 30.769 17.47 0.00 31.83 3.41
11 12 7.265647 TCAAATTTGTAGAAATGTTCGTCCA 57.734 32.000 17.47 0.00 31.83 4.02
12 13 8.020819 TCATCAAATTTGTAGAAATGTTCGTCC 58.979 33.333 17.47 0.00 31.83 4.79
13 14 8.948853 TCATCAAATTTGTAGAAATGTTCGTC 57.051 30.769 17.47 0.00 31.83 4.20
14 15 9.180678 GTTCATCAAATTTGTAGAAATGTTCGT 57.819 29.630 21.06 0.00 31.83 3.85
15 16 9.398170 AGTTCATCAAATTTGTAGAAATGTTCG 57.602 29.630 21.06 0.13 31.83 3.95
54 55 9.545105 TGCTCATCAAATTTGTAAAAAGTTCAT 57.455 25.926 17.47 0.00 0.00 2.57
55 56 8.939201 TGCTCATCAAATTTGTAAAAAGTTCA 57.061 26.923 17.47 3.82 0.00 3.18
70 71 7.498239 TCACCAAATTTGAAAATGCTCATCAAA 59.502 29.630 19.86 3.02 44.44 2.69
71 72 6.990939 TCACCAAATTTGAAAATGCTCATCAA 59.009 30.769 19.86 0.00 0.00 2.57
72 73 6.522946 TCACCAAATTTGAAAATGCTCATCA 58.477 32.000 19.86 0.00 0.00 3.07
73 74 7.172019 AGTTCACCAAATTTGAAAATGCTCATC 59.828 33.333 19.86 0.00 34.78 2.92
74 75 6.993902 AGTTCACCAAATTTGAAAATGCTCAT 59.006 30.769 19.86 0.00 34.78 2.90
75 76 6.347696 AGTTCACCAAATTTGAAAATGCTCA 58.652 32.000 19.86 0.00 34.78 4.26
76 77 6.849588 AGTTCACCAAATTTGAAAATGCTC 57.150 33.333 19.86 8.17 34.78 4.26
77 78 7.628769 AAAGTTCACCAAATTTGAAAATGCT 57.371 28.000 19.86 7.38 34.78 3.79
78 79 8.686397 AAAAAGTTCACCAAATTTGAAAATGC 57.314 26.923 19.86 5.34 34.78 3.56
150 151 9.515226 AGCGCTATTTATTGGATTTCCTAATTA 57.485 29.630 8.99 0.00 36.82 1.40
151 152 8.409358 AGCGCTATTTATTGGATTTCCTAATT 57.591 30.769 8.99 0.00 36.82 1.40
152 153 9.515226 TTAGCGCTATTTATTGGATTTCCTAAT 57.485 29.630 19.60 0.00 36.82 1.73
153 154 8.911918 TTAGCGCTATTTATTGGATTTCCTAA 57.088 30.769 19.60 0.00 36.82 2.69
154 155 9.515226 AATTAGCGCTATTTATTGGATTTCCTA 57.485 29.630 19.60 0.00 36.82 2.94
155 156 8.409358 AATTAGCGCTATTTATTGGATTTCCT 57.591 30.769 19.60 0.00 36.82 3.36
170 171 9.767228 TGTATAAGAACCAATAAATTAGCGCTA 57.233 29.630 14.45 14.45 0.00 4.26
171 172 8.557029 GTGTATAAGAACCAATAAATTAGCGCT 58.443 33.333 17.26 17.26 0.00 5.92
172 173 8.557029 AGTGTATAAGAACCAATAAATTAGCGC 58.443 33.333 0.00 0.00 0.00 5.92
177 178 8.120465 CGCGAAGTGTATAAGAACCAATAAATT 58.880 33.333 0.00 0.00 0.00 1.82
178 179 7.627340 CGCGAAGTGTATAAGAACCAATAAAT 58.373 34.615 0.00 0.00 0.00 1.40
179 180 6.996106 CGCGAAGTGTATAAGAACCAATAAA 58.004 36.000 0.00 0.00 0.00 1.40
180 181 6.578020 CGCGAAGTGTATAAGAACCAATAA 57.422 37.500 0.00 0.00 0.00 1.40
196 197 4.986659 AGTTAGTACAAATGAACGCGAAGT 59.013 37.500 15.93 0.00 0.00 3.01
197 198 5.511088 AGTTAGTACAAATGAACGCGAAG 57.489 39.130 15.93 0.00 0.00 3.79
198 199 5.574055 CCTAGTTAGTACAAATGAACGCGAA 59.426 40.000 15.93 0.00 0.00 4.70
199 200 5.097529 CCTAGTTAGTACAAATGAACGCGA 58.902 41.667 15.93 0.00 0.00 5.87
200 201 4.266976 CCCTAGTTAGTACAAATGAACGCG 59.733 45.833 3.53 3.53 0.00 6.01
201 202 4.569564 CCCCTAGTTAGTACAAATGAACGC 59.430 45.833 0.00 0.00 0.00 4.84
202 203 5.727434 ACCCCTAGTTAGTACAAATGAACG 58.273 41.667 0.00 0.00 0.00 3.95
203 204 6.596888 GGAACCCCTAGTTAGTACAAATGAAC 59.403 42.308 0.00 0.00 39.40 3.18
204 205 6.502863 AGGAACCCCTAGTTAGTACAAATGAA 59.497 38.462 0.00 0.00 42.15 2.57
205 206 6.027482 AGGAACCCCTAGTTAGTACAAATGA 58.973 40.000 0.00 0.00 42.15 2.57
206 207 6.309389 AGGAACCCCTAGTTAGTACAAATG 57.691 41.667 0.00 0.00 42.15 2.32
207 208 6.273965 ACAAGGAACCCCTAGTTAGTACAAAT 59.726 38.462 0.00 0.00 43.48 2.32
208 209 5.608015 ACAAGGAACCCCTAGTTAGTACAAA 59.392 40.000 0.00 0.00 43.48 2.83
209 210 5.157395 ACAAGGAACCCCTAGTTAGTACAA 58.843 41.667 0.00 0.00 43.48 2.41
210 211 4.755437 ACAAGGAACCCCTAGTTAGTACA 58.245 43.478 0.00 0.00 43.48 2.90
211 212 5.012458 ACAACAAGGAACCCCTAGTTAGTAC 59.988 44.000 0.00 0.00 43.48 2.73
212 213 5.157395 ACAACAAGGAACCCCTAGTTAGTA 58.843 41.667 0.00 0.00 43.48 1.82
213 214 3.978672 ACAACAAGGAACCCCTAGTTAGT 59.021 43.478 0.00 0.00 43.48 2.24
214 215 4.635699 ACAACAAGGAACCCCTAGTTAG 57.364 45.455 0.00 0.00 43.48 2.34
215 216 5.012354 CACTACAACAAGGAACCCCTAGTTA 59.988 44.000 0.00 0.00 43.48 2.24
216 217 3.978672 ACTACAACAAGGAACCCCTAGTT 59.021 43.478 0.00 0.00 43.48 2.24
217 218 3.326880 CACTACAACAAGGAACCCCTAGT 59.673 47.826 0.00 0.00 43.48 2.57
218 219 3.307480 CCACTACAACAAGGAACCCCTAG 60.307 52.174 0.00 0.00 43.48 3.02
219 220 2.640826 CCACTACAACAAGGAACCCCTA 59.359 50.000 0.00 0.00 43.48 3.53
221 222 1.144298 ACCACTACAACAAGGAACCCC 59.856 52.381 0.00 0.00 0.00 4.95
222 223 2.651382 ACCACTACAACAAGGAACCC 57.349 50.000 0.00 0.00 0.00 4.11
223 224 3.501062 GCTAACCACTACAACAAGGAACC 59.499 47.826 0.00 0.00 0.00 3.62
224 225 3.185797 CGCTAACCACTACAACAAGGAAC 59.814 47.826 0.00 0.00 0.00 3.62
225 226 3.395639 CGCTAACCACTACAACAAGGAA 58.604 45.455 0.00 0.00 0.00 3.36
226 227 2.289195 CCGCTAACCACTACAACAAGGA 60.289 50.000 0.00 0.00 0.00 3.36
227 228 2.073816 CCGCTAACCACTACAACAAGG 58.926 52.381 0.00 0.00 0.00 3.61
228 229 3.034721 TCCGCTAACCACTACAACAAG 57.965 47.619 0.00 0.00 0.00 3.16
229 230 3.472283 TTCCGCTAACCACTACAACAA 57.528 42.857 0.00 0.00 0.00 2.83
230 231 3.331150 CATTCCGCTAACCACTACAACA 58.669 45.455 0.00 0.00 0.00 3.33
231 232 2.676342 CCATTCCGCTAACCACTACAAC 59.324 50.000 0.00 0.00 0.00 3.32
232 233 2.303600 ACCATTCCGCTAACCACTACAA 59.696 45.455 0.00 0.00 0.00 2.41
233 234 1.903860 ACCATTCCGCTAACCACTACA 59.096 47.619 0.00 0.00 0.00 2.74
234 235 2.685850 ACCATTCCGCTAACCACTAC 57.314 50.000 0.00 0.00 0.00 2.73
235 236 2.093341 GGAACCATTCCGCTAACCACTA 60.093 50.000 0.00 0.00 40.59 2.74
236 237 1.339727 GGAACCATTCCGCTAACCACT 60.340 52.381 0.00 0.00 40.59 4.00
237 238 1.092348 GGAACCATTCCGCTAACCAC 58.908 55.000 0.00 0.00 40.59 4.16
238 239 3.562397 GGAACCATTCCGCTAACCA 57.438 52.632 0.00 0.00 40.59 3.67
247 248 5.768164 TGAAACTACAAAGGAGGAACCATTC 59.232 40.000 0.00 0.00 42.04 2.67
248 249 5.701224 TGAAACTACAAAGGAGGAACCATT 58.299 37.500 0.00 0.00 42.04 3.16
249 250 5.319043 TGAAACTACAAAGGAGGAACCAT 57.681 39.130 0.00 0.00 42.04 3.55
250 251 4.781775 TGAAACTACAAAGGAGGAACCA 57.218 40.909 0.00 0.00 42.04 3.67
251 252 4.519350 CCTTGAAACTACAAAGGAGGAACC 59.481 45.833 0.00 0.00 39.35 3.62
252 253 4.023107 GCCTTGAAACTACAAAGGAGGAAC 60.023 45.833 4.88 0.00 0.00 3.62
253 254 4.142038 GCCTTGAAACTACAAAGGAGGAA 58.858 43.478 4.88 0.00 0.00 3.36
254 255 3.137544 TGCCTTGAAACTACAAAGGAGGA 59.862 43.478 4.88 0.00 0.00 3.71
255 256 3.486383 TGCCTTGAAACTACAAAGGAGG 58.514 45.455 4.88 0.00 0.00 4.30
256 257 4.761739 TCATGCCTTGAAACTACAAAGGAG 59.238 41.667 4.88 0.00 0.00 3.69
257 258 4.724399 TCATGCCTTGAAACTACAAAGGA 58.276 39.130 4.88 0.00 0.00 3.36
258 259 4.520492 ACTCATGCCTTGAAACTACAAAGG 59.480 41.667 0.00 0.00 32.78 3.11
259 260 5.695851 ACTCATGCCTTGAAACTACAAAG 57.304 39.130 0.00 0.00 32.78 2.77
260 261 6.096141 TCAAACTCATGCCTTGAAACTACAAA 59.904 34.615 0.00 0.00 32.78 2.83
261 262 5.592282 TCAAACTCATGCCTTGAAACTACAA 59.408 36.000 0.00 0.00 32.78 2.41
262 263 5.129634 TCAAACTCATGCCTTGAAACTACA 58.870 37.500 0.00 0.00 32.78 2.74
263 264 5.239525 ACTCAAACTCATGCCTTGAAACTAC 59.760 40.000 5.74 0.00 32.78 2.73
264 265 5.239306 CACTCAAACTCATGCCTTGAAACTA 59.761 40.000 5.74 0.00 32.78 2.24
265 266 4.037208 CACTCAAACTCATGCCTTGAAACT 59.963 41.667 5.74 0.00 32.78 2.66
266 267 4.036734 TCACTCAAACTCATGCCTTGAAAC 59.963 41.667 5.74 0.00 32.78 2.78
267 268 4.036734 GTCACTCAAACTCATGCCTTGAAA 59.963 41.667 5.74 0.00 32.78 2.69
268 269 3.565482 GTCACTCAAACTCATGCCTTGAA 59.435 43.478 5.74 0.00 32.78 2.69
269 270 3.141398 GTCACTCAAACTCATGCCTTGA 58.859 45.455 0.00 0.00 0.00 3.02
270 271 2.096069 CGTCACTCAAACTCATGCCTTG 60.096 50.000 0.00 0.00 0.00 3.61
271 272 2.146342 CGTCACTCAAACTCATGCCTT 58.854 47.619 0.00 0.00 0.00 4.35
272 273 1.609061 CCGTCACTCAAACTCATGCCT 60.609 52.381 0.00 0.00 0.00 4.75
273 274 0.798776 CCGTCACTCAAACTCATGCC 59.201 55.000 0.00 0.00 0.00 4.40
274 275 1.512926 ACCGTCACTCAAACTCATGC 58.487 50.000 0.00 0.00 0.00 4.06
275 276 2.993899 GGTACCGTCACTCAAACTCATG 59.006 50.000 0.00 0.00 0.00 3.07
276 277 2.352421 CGGTACCGTCACTCAAACTCAT 60.352 50.000 26.39 0.00 34.35 2.90
277 278 1.001048 CGGTACCGTCACTCAAACTCA 60.001 52.381 26.39 0.00 34.35 3.41
278 279 1.668047 CCGGTACCGTCACTCAAACTC 60.668 57.143 31.24 0.00 37.81 3.01
279 280 0.316204 CCGGTACCGTCACTCAAACT 59.684 55.000 31.24 0.00 37.81 2.66
280 281 1.287041 GCCGGTACCGTCACTCAAAC 61.287 60.000 31.24 6.66 37.81 2.93
281 282 1.005867 GCCGGTACCGTCACTCAAA 60.006 57.895 31.24 0.00 37.81 2.69
282 283 2.149803 CTGCCGGTACCGTCACTCAA 62.150 60.000 31.24 2.66 37.81 3.02
283 284 2.598099 TGCCGGTACCGTCACTCA 60.598 61.111 31.24 17.51 37.81 3.41
284 285 2.151049 AACTGCCGGTACCGTCACTC 62.151 60.000 31.24 15.32 37.81 3.51
285 286 1.751349 AAACTGCCGGTACCGTCACT 61.751 55.000 31.24 12.51 37.81 3.41
286 287 0.881600 AAAACTGCCGGTACCGTCAC 60.882 55.000 31.24 20.58 37.81 3.67
287 288 0.179051 AAAAACTGCCGGTACCGTCA 60.179 50.000 31.24 25.10 37.81 4.35
288 289 2.620562 AAAAACTGCCGGTACCGTC 58.379 52.632 31.24 21.47 37.81 4.79
289 290 4.883240 AAAAACTGCCGGTACCGT 57.117 50.000 31.24 11.57 37.81 4.83
330 331 3.311322 CACCACACGCTGTAGAAGAAAAA 59.689 43.478 0.00 0.00 0.00 1.94
331 332 2.869801 CACCACACGCTGTAGAAGAAAA 59.130 45.455 0.00 0.00 0.00 2.29
332 333 2.479837 CACCACACGCTGTAGAAGAAA 58.520 47.619 0.00 0.00 0.00 2.52
333 334 1.270094 CCACCACACGCTGTAGAAGAA 60.270 52.381 0.00 0.00 0.00 2.52
334 335 0.317160 CCACCACACGCTGTAGAAGA 59.683 55.000 0.00 0.00 0.00 2.87
335 336 0.670546 CCCACCACACGCTGTAGAAG 60.671 60.000 0.00 0.00 0.00 2.85
336 337 1.369692 CCCACCACACGCTGTAGAA 59.630 57.895 0.00 0.00 0.00 2.10
337 338 3.056458 CCCACCACACGCTGTAGA 58.944 61.111 0.00 0.00 0.00 2.59
338 339 2.742372 GCCCACCACACGCTGTAG 60.742 66.667 0.00 0.00 0.00 2.74
339 340 4.323477 GGCCCACCACACGCTGTA 62.323 66.667 0.00 0.00 35.26 2.74
372 373 3.969802 AAGCTGGCACTTGCACGC 61.970 61.111 3.15 4.80 44.36 5.34
373 374 2.050714 CAAGCTGGCACTTGCACG 60.051 61.111 13.99 0.00 40.53 5.34
378 379 1.458639 GGTTCAGCAAGCTGGCACTT 61.459 55.000 17.28 0.00 43.75 3.16
379 380 1.900498 GGTTCAGCAAGCTGGCACT 60.900 57.895 17.28 0.00 43.75 4.40
380 381 2.647297 GGTTCAGCAAGCTGGCAC 59.353 61.111 17.28 16.71 43.75 5.01
381 382 2.979676 CGGTTCAGCAAGCTGGCA 60.980 61.111 17.28 6.50 43.75 4.92
382 383 3.741476 CCGGTTCAGCAAGCTGGC 61.741 66.667 20.78 4.37 43.75 4.85
383 384 3.741476 GCCGGTTCAGCAAGCTGG 61.741 66.667 20.78 6.61 43.75 4.85
384 385 4.093952 CGCCGGTTCAGCAAGCTG 62.094 66.667 15.67 15.67 44.86 4.24
387 388 1.573829 TTAAGCGCCGGTTCAGCAAG 61.574 55.000 4.18 0.00 0.00 4.01
388 389 1.573829 CTTAAGCGCCGGTTCAGCAA 61.574 55.000 4.18 0.00 0.00 3.91
389 390 2.031314 TTAAGCGCCGGTTCAGCA 59.969 55.556 4.18 0.00 0.00 4.41
390 391 2.750888 CCTTAAGCGCCGGTTCAGC 61.751 63.158 4.18 4.12 0.00 4.26
391 392 2.750888 GCCTTAAGCGCCGGTTCAG 61.751 63.158 4.18 3.71 0.00 3.02
392 393 2.744709 GCCTTAAGCGCCGGTTCA 60.745 61.111 4.18 0.00 0.00 3.18
401 402 2.178235 CCTAACCGGCGCCTTAAGC 61.178 63.158 26.68 0.00 38.52 3.09
402 403 0.529992 CTCCTAACCGGCGCCTTAAG 60.530 60.000 26.68 15.67 0.00 1.85
403 404 1.518774 CTCCTAACCGGCGCCTTAA 59.481 57.895 26.68 6.15 0.00 1.85
404 405 3.085119 GCTCCTAACCGGCGCCTTA 62.085 63.158 26.68 16.18 37.54 2.69
405 406 4.468689 GCTCCTAACCGGCGCCTT 62.469 66.667 26.68 15.87 37.54 4.35
407 408 4.893601 GAGCTCCTAACCGGCGCC 62.894 72.222 19.07 19.07 44.75 6.53
408 409 4.893601 GGAGCTCCTAACCGGCGC 62.894 72.222 26.25 0.00 43.98 6.53
409 410 4.222847 GGGAGCTCCTAACCGGCG 62.223 72.222 31.36 0.00 35.95 6.46
410 411 3.862991 GGGGAGCTCCTAACCGGC 61.863 72.222 31.36 13.25 35.95 6.13
411 412 2.365105 TGGGGAGCTCCTAACCGG 60.365 66.667 31.36 0.00 35.95 5.28
412 413 2.901042 GTGGGGAGCTCCTAACCG 59.099 66.667 31.36 0.00 35.95 4.44
413 414 2.732619 CCGTGGGGAGCTCCTAACC 61.733 68.421 31.36 23.82 35.95 2.85
414 415 1.988406 ACCGTGGGGAGCTCCTAAC 60.988 63.158 31.36 25.74 36.97 2.34
415 416 1.987855 CACCGTGGGGAGCTCCTAA 60.988 63.158 31.36 17.49 36.97 2.69
416 417 2.363795 CACCGTGGGGAGCTCCTA 60.364 66.667 31.36 18.38 36.97 2.94
441 442 2.188994 CAGCTCCTGCCTACCTGC 59.811 66.667 0.00 0.00 40.80 4.85
446 447 2.765807 GGCTCCAGCTCCTGCCTA 60.766 66.667 11.78 0.00 41.92 3.93
475 483 4.176752 GGGCCACCTCGGATGACC 62.177 72.222 4.39 0.00 36.56 4.02
666 2024 2.291741 CCTCTTCTGTTTGTTGGAGCAC 59.708 50.000 0.00 0.00 0.00 4.40
725 2085 2.018542 TTTTTATGGGCCGTCTCTCG 57.981 50.000 0.00 0.00 39.52 4.04
791 2151 3.425162 AAGAAAGATCCGTGGAAAGCT 57.575 42.857 0.00 0.00 0.00 3.74
915 2281 0.810426 TGCCTTGTGTTACGCGACAA 60.810 50.000 15.93 12.33 0.00 3.18
919 2285 2.860293 CCTGCCTTGTGTTACGCG 59.140 61.111 3.53 3.53 0.00 6.01
920 2286 2.561373 GCCTGCCTTGTGTTACGC 59.439 61.111 0.00 0.00 0.00 4.42
922 2288 1.574428 CACGCCTGCCTTGTGTTAC 59.426 57.895 0.00 0.00 0.00 2.50
923 2289 1.599518 CCACGCCTGCCTTGTGTTA 60.600 57.895 0.00 0.00 31.75 2.41
959 2352 6.567321 GCACCGAAATCAATCTCAATCTATGG 60.567 42.308 0.00 0.00 0.00 2.74
1172 2570 4.345288 CACAACAAACACACACAGAGATG 58.655 43.478 0.00 0.00 0.00 2.90
1243 2641 1.519455 GAAGAGGATGACCGTGCCG 60.519 63.158 0.00 0.00 41.83 5.69
1383 2781 2.270923 CAGCGCAAGACTAGTGCATAA 58.729 47.619 11.47 0.00 44.55 1.90
1612 3168 0.035152 TCGCTACCCAAGACCGACTA 60.035 55.000 0.00 0.00 0.00 2.59
1618 3174 1.544691 TCAAGAGTCGCTACCCAAGAC 59.455 52.381 0.00 0.00 35.30 3.01
1622 3178 3.362706 ACTATTCAAGAGTCGCTACCCA 58.637 45.455 0.00 0.00 0.00 4.51
1683 3239 8.775527 TGTCGCAACTAATTGTAGTCATAAAAA 58.224 29.630 0.00 0.00 39.79 1.94
1689 3245 4.878439 ACTGTCGCAACTAATTGTAGTCA 58.122 39.130 0.00 0.00 39.79 3.41
1710 3279 3.305094 TCACTGTTTTTGAGTCGAACGAC 59.695 43.478 17.79 17.79 44.86 4.34
1753 3323 7.493367 AGCCACATTCAGTTATTAGAGAGTAC 58.507 38.462 0.00 0.00 0.00 2.73
1866 3436 3.588569 AGGGGAAAAGAGTAGTGTGAGT 58.411 45.455 0.00 0.00 0.00 3.41
2305 3876 2.625639 AGAAGGGTGTCTCATCTTGGT 58.374 47.619 0.00 0.00 0.00 3.67
2563 4134 2.821991 AGTCCACTCTGCAGTAACAC 57.178 50.000 14.67 5.61 0.00 3.32
2714 4285 7.728847 AAAATGCCAAATTAGAGGAACAAAC 57.271 32.000 0.00 0.00 0.00 2.93
3296 4879 9.864628 CCAATAGATTTCATTGGGCTGCATAGC 62.865 44.444 0.50 0.00 45.83 2.97
3322 4910 2.223665 GCCACAATAATGGAGCTCAAGC 60.224 50.000 17.19 0.00 43.02 4.01
3339 4927 1.946267 CAACCAGTACCAACGCCAC 59.054 57.895 0.00 0.00 0.00 5.01
3644 5499 9.477484 TGATAAAACACTGAGACTAGAAAACTC 57.523 33.333 0.00 0.70 0.00 3.01
3692 5547 5.622770 AACCACGACAAGAATTATGGAAC 57.377 39.130 0.00 0.00 0.00 3.62
3728 5583 7.888839 TGTGAACTAAAACCACGACAAGAATTG 60.889 37.037 0.00 0.00 41.82 2.32
3996 5867 9.745880 TTTTTCCAAAAGTACGTAAATTATGCA 57.254 25.926 0.00 0.00 0.00 3.96
4378 8333 4.618338 CACGAATGCAAACAACATGAAG 57.382 40.909 0.00 0.00 0.00 3.02
4751 8706 2.810852 CAGCTGTTCAAGGAAGGACTTC 59.189 50.000 5.25 3.48 38.80 3.01
5063 9018 6.371548 TCAGATTTACAGCAATTACACTCACC 59.628 38.462 0.00 0.00 0.00 4.02
5155 9110 1.417517 CACAGGGCTATATGCAGGTCA 59.582 52.381 0.00 0.00 45.15 4.02
5156 9111 1.879796 GCACAGGGCTATATGCAGGTC 60.880 57.143 0.00 0.00 45.15 3.85
5157 9112 0.109342 GCACAGGGCTATATGCAGGT 59.891 55.000 0.00 0.00 45.15 4.00
5158 9113 0.952497 CGCACAGGGCTATATGCAGG 60.952 60.000 0.00 0.00 45.15 4.85
5159 9114 0.250038 ACGCACAGGGCTATATGCAG 60.250 55.000 0.00 0.00 45.15 4.41
5160 9115 0.180171 AACGCACAGGGCTATATGCA 59.820 50.000 0.00 0.00 45.15 3.96
5165 9120 2.180159 AACCGAACGCACAGGGCTAT 62.180 55.000 0.00 0.00 41.67 2.97
5545 9501 7.141363 AGTTGTCATTTTTCTTGTACATGAGC 58.859 34.615 10.92 0.00 0.00 4.26
5692 9649 3.773418 TGGTTTCTGGTTTCGGTATGA 57.227 42.857 0.00 0.00 0.00 2.15
5734 9691 6.904463 ACCATACCGAAAATAAACCAAACT 57.096 33.333 0.00 0.00 0.00 2.66
5819 9793 7.438160 CGAATACTCCTTTATAATGTGCAGTGA 59.562 37.037 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.