Multiple sequence alignment - TraesCS3D01G119900

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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 TraesCS3D01G119900 chr3D 100.000 4153 0 0 1 4153 75542752 75546904 0.000000e+00 7670.0
1 TraesCS3D01G119900 chr3D 100.000 350 0 0 4294 4643 75547045 75547394 0.000000e+00 647.0
2 TraesCS3D01G119900 chr3D 93.396 212 10 4 120 329 70280645 70280436 1.250000e-80 311.0
3 TraesCS3D01G119900 chr3A 95.152 3486 134 18 694 4153 89577125 89580601 0.000000e+00 5469.0
4 TraesCS3D01G119900 chr3A 94.793 3438 126 20 734 4153 89665407 89668809 0.000000e+00 5308.0
5 TraesCS3D01G119900 chr3A 88.761 347 30 3 4304 4643 89580659 89581003 2.580000e-112 416.0
6 TraesCS3D01G119900 chr3A 86.297 343 28 3 4308 4643 89668853 89669183 5.710000e-94 355.0
7 TraesCS3D01G119900 chr3A 91.089 202 10 3 411 611 89576944 89577138 2.750000e-67 267.0
8 TraesCS3D01G119900 chr3A 89.873 158 3 3 433 590 89665258 89665402 1.710000e-44 191.0
9 TraesCS3D01G119900 chr3A 100.000 57 0 0 380 436 89664889 89664945 6.350000e-19 106.0
10 TraesCS3D01G119900 chr3A 100.000 35 0 0 380 414 89574781 89574815 1.080000e-06 65.8
11 TraesCS3D01G119900 chr3A 97.143 35 0 1 331 364 89664862 89664896 1.800000e-04 58.4
12 TraesCS3D01G119900 chr3B 94.784 2684 118 12 1321 3993 121641676 121644348 0.000000e+00 4161.0
13 TraesCS3D01G119900 chr3B 87.749 351 29 7 4302 4643 121647797 121648142 9.360000e-107 398.0
14 TraesCS3D01G119900 chr3B 91.038 212 15 4 120 329 183471220 183471429 2.730000e-72 283.0
15 TraesCS3D01G119900 chr3B 89.623 212 13 4 367 578 121641017 121641219 1.280000e-65 261.0
16 TraesCS3D01G119900 chr3B 92.308 169 12 1 3985 4153 121647590 121647757 6.000000e-59 239.0
17 TraesCS3D01G119900 chr3B 96.875 32 1 0 616 647 121641216 121641247 2.000000e-03 54.7
18 TraesCS3D01G119900 chr5D 80.456 1315 219 28 2390 3678 535643664 535644966 0.000000e+00 970.0
19 TraesCS3D01G119900 chr5D 78.028 1288 233 38 2397 3657 535816761 535818025 0.000000e+00 765.0
20 TraesCS3D01G119900 chr5D 88.754 329 27 6 1603 1923 535861919 535862245 1.210000e-105 394.0
21 TraesCS3D01G119900 chr5D 91.628 215 13 5 118 329 165608484 165608696 4.540000e-75 292.0
22 TraesCS3D01G119900 chr5D 78.873 426 82 8 2819 3242 499069513 499069094 9.840000e-72 281.0
23 TraesCS3D01G119900 chr5D 79.027 329 53 12 1571 1891 535556369 535556689 1.310000e-50 211.0
24 TraesCS3D01G119900 chr5D 97.753 89 2 0 1 89 31421802 31421890 2.240000e-33 154.0
25 TraesCS3D01G119900 chr5D 98.824 85 1 0 1 85 349794656 349794740 8.050000e-33 152.0
26 TraesCS3D01G119900 chr5D 96.667 90 3 0 1 90 395609892 395609803 2.890000e-32 150.0
27 TraesCS3D01G119900 chr4A 80.288 1319 212 32 2390 3677 636314976 636313675 0.000000e+00 952.0
28 TraesCS3D01G119900 chr4A 78.062 1486 276 38 2155 3611 635960942 635959478 0.000000e+00 893.0
29 TraesCS3D01G119900 chr4A 77.752 1317 236 46 2339 3625 636084667 636083378 0.000000e+00 756.0
30 TraesCS3D01G119900 chr4A 76.253 1377 262 52 2337 3674 636101120 636099770 0.000000e+00 671.0
31 TraesCS3D01G119900 chr4A 80.699 772 128 18 2147 2907 636044030 636043269 8.660000e-162 580.0
32 TraesCS3D01G119900 chr4A 83.850 613 84 10 1331 1931 635961750 635961141 1.870000e-158 569.0
33 TraesCS3D01G119900 chr4A 80.927 755 95 21 1200 1931 636044946 636044218 6.790000e-153 551.0
34 TraesCS3D01G119900 chr4A 81.259 699 107 17 1243 1932 636261407 636260724 1.140000e-150 544.0
35 TraesCS3D01G119900 chr4A 72.579 919 216 28 2772 3668 636034728 636033824 7.660000e-68 268.0
36 TraesCS3D01G119900 chr4A 97.802 91 2 0 1 91 583911777 583911687 1.730000e-34 158.0
37 TraesCS3D01G119900 chr5B 80.120 1328 212 33 2390 3678 676251104 676252418 0.000000e+00 942.0
38 TraesCS3D01G119900 chr5B 78.666 1289 213 41 2389 3649 676242499 676243753 0.000000e+00 800.0
39 TraesCS3D01G119900 chr5B 80.250 881 128 26 1080 1928 676271344 676272210 5.100000e-174 621.0
40 TraesCS3D01G119900 chr5B 77.494 431 86 11 2819 3245 619112796 619112373 9.980000e-62 248.0
41 TraesCS3D01G119900 chr5B 77.283 427 87 10 2819 3242 619156587 619156168 4.640000e-60 243.0
42 TraesCS3D01G119900 chr5B 76.869 428 86 10 2819 3242 619279442 619279024 3.610000e-56 230.0
43 TraesCS3D01G119900 chr7D 91.469 211 14 4 121 329 527466958 527466750 2.110000e-73 287.0
44 TraesCS3D01G119900 chr7D 98.876 89 1 0 1 89 588825509 588825421 4.810000e-35 159.0
45 TraesCS3D01G119900 chr7D 97.753 89 2 0 1 89 472848880 472848792 2.240000e-33 154.0
46 TraesCS3D01G119900 chr6A 91.429 210 13 5 121 329 530276152 530276357 2.730000e-72 283.0
47 TraesCS3D01G119900 chr1D 90.952 210 17 2 121 329 482994088 482993880 9.840000e-72 281.0
48 TraesCS3D01G119900 chrUn 89.593 221 15 7 121 336 200670027 200670244 1.650000e-69 274.0
49 TraesCS3D01G119900 chrUn 89.593 221 15 7 121 336 413842420 413842637 1.650000e-69 274.0
50 TraesCS3D01G119900 chrUn 77.049 427 88 10 2819 3242 334690501 334690920 2.160000e-58 237.0
51 TraesCS3D01G119900 chr7B 89.450 218 19 4 113 329 154674356 154674142 5.920000e-69 272.0
52 TraesCS3D01G119900 chr2B 97.802 91 2 0 1 91 535026668 535026578 1.730000e-34 158.0
53 TraesCS3D01G119900 chr2A 97.753 89 2 0 1 89 182736010 182735922 2.240000e-33 154.0
54 TraesCS3D01G119900 chr7A 96.667 90 3 0 1 90 386601755 386601844 2.890000e-32 150.0


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 TraesCS3D01G119900 chr3D 75542752 75547394 4642 False 4158.50 7670 100.0000 1 4643 2 chr3D.!!$F1 4642
1 TraesCS3D01G119900 chr3A 89574781 89581003 6222 False 1554.45 5469 93.7505 380 4643 4 chr3A.!!$F1 4263
2 TraesCS3D01G119900 chr3A 89664862 89669183 4321 False 1203.68 5308 93.6212 331 4643 5 chr3A.!!$F2 4312
3 TraesCS3D01G119900 chr3B 121641017 121648142 7125 False 1022.74 4161 92.2678 367 4643 5 chr3B.!!$F2 4276
4 TraesCS3D01G119900 chr5D 535643664 535644966 1302 False 970.00 970 80.4560 2390 3678 1 chr5D.!!$F5 1288
5 TraesCS3D01G119900 chr5D 535816761 535818025 1264 False 765.00 765 78.0280 2397 3657 1 chr5D.!!$F6 1260
6 TraesCS3D01G119900 chr4A 636313675 636314976 1301 True 952.00 952 80.2880 2390 3677 1 chr4A.!!$R6 1287
7 TraesCS3D01G119900 chr4A 636083378 636084667 1289 True 756.00 756 77.7520 2339 3625 1 chr4A.!!$R3 1286
8 TraesCS3D01G119900 chr4A 635959478 635961750 2272 True 731.00 893 80.9560 1331 3611 2 chr4A.!!$R7 2280
9 TraesCS3D01G119900 chr4A 636099770 636101120 1350 True 671.00 671 76.2530 2337 3674 1 chr4A.!!$R4 1337
10 TraesCS3D01G119900 chr4A 636043269 636044946 1677 True 565.50 580 80.8130 1200 2907 2 chr4A.!!$R8 1707
11 TraesCS3D01G119900 chr4A 636260724 636261407 683 True 544.00 544 81.2590 1243 1932 1 chr4A.!!$R5 689
12 TraesCS3D01G119900 chr4A 636033824 636034728 904 True 268.00 268 72.5790 2772 3668 1 chr4A.!!$R2 896
13 TraesCS3D01G119900 chr5B 676251104 676252418 1314 False 942.00 942 80.1200 2390 3678 1 chr5B.!!$F2 1288
14 TraesCS3D01G119900 chr5B 676242499 676243753 1254 False 800.00 800 78.6660 2389 3649 1 chr5B.!!$F1 1260
15 TraesCS3D01G119900 chr5B 676271344 676272210 866 False 621.00 621 80.2500 1080 1928 1 chr5B.!!$F3 848

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
245 246 0.033503 ATTTTAAGAGGGTGGGGCCG 60.034 55.0 0.00 0.0 38.44 6.13 F
296 297 0.106335 CCTATGCAGAGCACAGAGGG 59.894 60.0 1.83 0.0 43.04 4.30 F
1296 3836 0.321298 AGGCATTGCGTAAGTTCGGT 60.321 50.0 1.23 0.0 41.68 4.69 F
3015 5673 1.586422 GTCATATGACATGTGCCGCT 58.414 50.0 27.33 0.0 44.18 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1105 3626 0.174617 GTCCAGTGGCTAGTCTCAGC 59.825 60.000 3.51 0.0 41.02 4.26 R
1378 3918 1.131126 CCCAAACATGCTTGTAGCTCG 59.869 52.381 5.56 0.0 42.97 5.03 R
3203 5865 0.109532 TGGGCAAGGTCGATCAAACA 59.890 50.000 0.00 0.0 0.00 2.83 R
4565 10550 1.302431 CGTCCCTGCCAATGACACA 60.302 57.895 0.00 0.0 0.00 3.72 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
22 23 3.240670 CCTATGACAGGTGGGCCTA 57.759 57.895 4.53 0.00 44.97 3.93
23 24 1.507140 CCTATGACAGGTGGGCCTAA 58.493 55.000 4.53 0.00 44.97 2.69
24 25 1.141053 CCTATGACAGGTGGGCCTAAC 59.859 57.143 4.53 0.00 44.97 2.34
25 26 1.837439 CTATGACAGGTGGGCCTAACA 59.163 52.381 7.01 0.00 44.97 2.41
26 27 0.620556 ATGACAGGTGGGCCTAACAG 59.379 55.000 7.01 0.00 44.97 3.16
27 28 1.299976 GACAGGTGGGCCTAACAGG 59.700 63.158 7.01 0.00 44.97 4.00
28 29 1.463410 ACAGGTGGGCCTAACAGGT 60.463 57.895 7.01 0.43 44.97 4.00
29 30 1.002134 CAGGTGGGCCTAACAGGTG 60.002 63.158 7.01 0.00 44.97 4.00
30 31 2.231380 AGGTGGGCCTAACAGGTGG 61.231 63.158 7.01 0.00 44.90 4.61
35 36 2.751837 GCCTAACAGGTGGCTGGC 60.752 66.667 0.00 0.00 45.26 4.85
36 37 2.044946 CCTAACAGGTGGCTGGCC 60.045 66.667 4.43 4.43 0.00 5.36
37 38 2.044946 CTAACAGGTGGCTGGCCC 60.045 66.667 9.28 0.00 34.56 5.80
38 39 2.856494 TAACAGGTGGCTGGCCCA 60.856 61.111 9.28 0.00 42.79 5.36
46 47 4.052518 GGCTGGCCCACCTGTCAT 62.053 66.667 0.00 0.00 39.22 3.06
47 48 2.679342 GGCTGGCCCACCTGTCATA 61.679 63.158 0.00 0.00 39.22 2.15
48 49 1.153086 GCTGGCCCACCTGTCATAG 60.153 63.158 0.00 0.00 37.23 2.23
49 50 1.626356 GCTGGCCCACCTGTCATAGA 61.626 60.000 0.00 0.00 37.23 1.98
50 51 0.179000 CTGGCCCACCTGTCATAGAC 59.821 60.000 0.00 0.00 36.63 2.59
51 52 1.271840 TGGCCCACCTGTCATAGACC 61.272 60.000 0.00 0.00 36.63 3.85
52 53 1.527370 GCCCACCTGTCATAGACCC 59.473 63.158 0.00 0.00 0.00 4.46
53 54 1.271840 GCCCACCTGTCATAGACCCA 61.272 60.000 0.00 0.00 0.00 4.51
54 55 1.285280 CCCACCTGTCATAGACCCAA 58.715 55.000 0.00 0.00 0.00 4.12
55 56 1.633432 CCCACCTGTCATAGACCCAAA 59.367 52.381 0.00 0.00 0.00 3.28
56 57 2.356125 CCCACCTGTCATAGACCCAAAG 60.356 54.545 0.00 0.00 0.00 2.77
57 58 2.356125 CCACCTGTCATAGACCCAAAGG 60.356 54.545 0.00 0.00 40.04 3.11
82 83 3.249687 CCTTTAAGGCACCGAAGCT 57.750 52.632 0.00 0.00 34.17 3.74
83 84 1.087501 CCTTTAAGGCACCGAAGCTC 58.912 55.000 0.00 0.00 34.17 4.09
84 85 1.610624 CCTTTAAGGCACCGAAGCTCA 60.611 52.381 0.00 0.00 34.17 4.26
85 86 2.151202 CTTTAAGGCACCGAAGCTCAA 58.849 47.619 0.00 0.00 34.17 3.02
86 87 2.489938 TTAAGGCACCGAAGCTCAAT 57.510 45.000 0.00 0.00 34.17 2.57
87 88 2.024176 TAAGGCACCGAAGCTCAATC 57.976 50.000 0.00 0.00 34.17 2.67
88 89 0.678048 AAGGCACCGAAGCTCAATCC 60.678 55.000 0.00 0.00 34.17 3.01
89 90 2.464459 GGCACCGAAGCTCAATCCG 61.464 63.158 0.00 0.00 34.17 4.18
90 91 1.741770 GCACCGAAGCTCAATCCGT 60.742 57.895 0.00 0.00 0.00 4.69
91 92 1.298859 GCACCGAAGCTCAATCCGTT 61.299 55.000 0.00 0.00 0.00 4.44
92 93 0.721718 CACCGAAGCTCAATCCGTTC 59.278 55.000 0.00 0.00 0.00 3.95
93 94 0.608640 ACCGAAGCTCAATCCGTTCT 59.391 50.000 0.00 0.00 0.00 3.01
94 95 1.002366 CCGAAGCTCAATCCGTTCTG 58.998 55.000 0.00 0.00 0.00 3.02
95 96 1.404181 CCGAAGCTCAATCCGTTCTGA 60.404 52.381 0.00 0.00 0.00 3.27
96 97 2.544685 CGAAGCTCAATCCGTTCTGAT 58.455 47.619 0.00 0.00 0.00 2.90
97 98 2.537625 CGAAGCTCAATCCGTTCTGATC 59.462 50.000 0.00 0.00 0.00 2.92
98 99 3.525537 GAAGCTCAATCCGTTCTGATCA 58.474 45.455 0.00 0.00 0.00 2.92
99 100 3.176552 AGCTCAATCCGTTCTGATCAG 57.823 47.619 17.07 17.07 0.00 2.90
100 101 2.158986 AGCTCAATCCGTTCTGATCAGG 60.159 50.000 22.42 7.64 0.00 3.86
101 102 2.419297 GCTCAATCCGTTCTGATCAGGT 60.419 50.000 22.42 0.01 0.00 4.00
102 103 3.866651 CTCAATCCGTTCTGATCAGGTT 58.133 45.455 22.42 5.87 0.00 3.50
103 104 3.861840 TCAATCCGTTCTGATCAGGTTC 58.138 45.455 22.42 11.72 0.00 3.62
104 105 2.586258 ATCCGTTCTGATCAGGTTCG 57.414 50.000 22.42 20.86 0.00 3.95
105 106 0.108804 TCCGTTCTGATCAGGTTCGC 60.109 55.000 22.42 7.65 0.00 4.70
106 107 0.389817 CCGTTCTGATCAGGTTCGCA 60.390 55.000 22.42 0.00 0.00 5.10
107 108 0.716108 CGTTCTGATCAGGTTCGCAC 59.284 55.000 22.42 8.89 0.00 5.34
108 109 1.079503 GTTCTGATCAGGTTCGCACC 58.920 55.000 22.42 0.00 44.67 5.01
123 124 4.424711 ACCGCGGCATGTTGGGAT 62.425 61.111 28.58 0.00 0.00 3.85
124 125 3.585990 CCGCGGCATGTTGGGATC 61.586 66.667 14.67 0.00 0.00 3.36
125 126 3.585990 CGCGGCATGTTGGGATCC 61.586 66.667 1.92 1.92 0.00 3.36
126 127 3.585990 GCGGCATGTTGGGATCCG 61.586 66.667 5.45 0.00 42.68 4.18
127 128 2.901840 CGGCATGTTGGGATCCGG 60.902 66.667 5.45 0.00 36.73 5.14
128 129 3.219198 GGCATGTTGGGATCCGGC 61.219 66.667 5.45 0.00 0.00 6.13
129 130 2.124151 GCATGTTGGGATCCGGCT 60.124 61.111 5.45 0.00 0.00 5.52
130 131 1.754234 GCATGTTGGGATCCGGCTT 60.754 57.895 5.45 0.00 0.00 4.35
131 132 2.008268 GCATGTTGGGATCCGGCTTG 62.008 60.000 5.45 7.81 0.00 4.01
132 133 1.754234 ATGTTGGGATCCGGCTTGC 60.754 57.895 5.45 0.00 0.00 4.01
133 134 3.140814 GTTGGGATCCGGCTTGCC 61.141 66.667 5.45 1.50 0.00 4.52
134 135 3.338250 TTGGGATCCGGCTTGCCT 61.338 61.111 14.28 0.00 0.00 4.75
135 136 3.643595 TTGGGATCCGGCTTGCCTG 62.644 63.158 14.28 3.29 0.00 4.85
137 138 4.496336 GGATCCGGCTTGCCTGCT 62.496 66.667 10.12 0.00 0.00 4.24
138 139 2.899339 GATCCGGCTTGCCTGCTC 60.899 66.667 10.12 0.76 0.00 4.26
139 140 4.496336 ATCCGGCTTGCCTGCTCC 62.496 66.667 10.12 0.00 0.00 4.70
143 144 4.811364 GGCTTGCCTGCTCCCTCC 62.811 72.222 4.11 0.00 0.00 4.30
144 145 4.811364 GCTTGCCTGCTCCCTCCC 62.811 72.222 0.00 0.00 0.00 4.30
145 146 4.120755 CTTGCCTGCTCCCTCCCC 62.121 72.222 0.00 0.00 0.00 4.81
156 157 3.866582 CCTCCCCGTGCTCCCATC 61.867 72.222 0.00 0.00 0.00 3.51
157 158 3.866582 CTCCCCGTGCTCCCATCC 61.867 72.222 0.00 0.00 0.00 3.51
160 161 4.838152 CCCGTGCTCCCATCCGTG 62.838 72.222 0.00 0.00 0.00 4.94
162 163 4.457496 CGTGCTCCCATCCGTGCT 62.457 66.667 0.00 0.00 0.00 4.40
163 164 2.512515 GTGCTCCCATCCGTGCTC 60.513 66.667 0.00 0.00 0.00 4.26
164 165 3.785859 TGCTCCCATCCGTGCTCC 61.786 66.667 0.00 0.00 0.00 4.70
165 166 4.554036 GCTCCCATCCGTGCTCCC 62.554 72.222 0.00 0.00 0.00 4.30
166 167 3.083349 CTCCCATCCGTGCTCCCA 61.083 66.667 0.00 0.00 0.00 4.37
167 168 3.391665 CTCCCATCCGTGCTCCCAC 62.392 68.421 0.00 0.00 38.62 4.61
168 169 4.489771 CCCATCCGTGCTCCCACC 62.490 72.222 0.00 0.00 38.79 4.61
169 170 3.402681 CCATCCGTGCTCCCACCT 61.403 66.667 0.00 0.00 38.79 4.00
170 171 2.187946 CATCCGTGCTCCCACCTC 59.812 66.667 0.00 0.00 38.79 3.85
171 172 2.284625 ATCCGTGCTCCCACCTCA 60.285 61.111 0.00 0.00 38.79 3.86
172 173 1.690633 ATCCGTGCTCCCACCTCAT 60.691 57.895 0.00 0.00 38.79 2.90
173 174 1.690219 ATCCGTGCTCCCACCTCATC 61.690 60.000 0.00 0.00 38.79 2.92
174 175 2.187946 CGTGCTCCCACCTCATCC 59.812 66.667 0.00 0.00 38.79 3.51
175 176 2.362369 CGTGCTCCCACCTCATCCT 61.362 63.158 0.00 0.00 38.79 3.24
176 177 1.043116 CGTGCTCCCACCTCATCCTA 61.043 60.000 0.00 0.00 38.79 2.94
177 178 0.466124 GTGCTCCCACCTCATCCTAC 59.534 60.000 0.00 0.00 35.92 3.18
178 179 0.042581 TGCTCCCACCTCATCCTACA 59.957 55.000 0.00 0.00 0.00 2.74
179 180 0.755686 GCTCCCACCTCATCCTACAG 59.244 60.000 0.00 0.00 0.00 2.74
180 181 0.755686 CTCCCACCTCATCCTACAGC 59.244 60.000 0.00 0.00 0.00 4.40
181 182 0.339859 TCCCACCTCATCCTACAGCT 59.660 55.000 0.00 0.00 0.00 4.24
182 183 0.467384 CCCACCTCATCCTACAGCTG 59.533 60.000 13.48 13.48 0.00 4.24
183 184 1.198713 CCACCTCATCCTACAGCTGT 58.801 55.000 25.12 25.12 0.00 4.40
184 185 1.137872 CCACCTCATCCTACAGCTGTC 59.862 57.143 25.56 0.00 0.00 3.51
185 186 2.106566 CACCTCATCCTACAGCTGTCT 58.893 52.381 25.56 1.44 0.00 3.41
186 187 2.499289 CACCTCATCCTACAGCTGTCTT 59.501 50.000 25.56 0.54 0.00 3.01
187 188 3.055530 CACCTCATCCTACAGCTGTCTTT 60.056 47.826 25.56 4.03 0.00 2.52
188 189 3.584848 ACCTCATCCTACAGCTGTCTTTT 59.415 43.478 25.56 4.43 0.00 2.27
189 190 4.042187 ACCTCATCCTACAGCTGTCTTTTT 59.958 41.667 25.56 2.84 0.00 1.94
237 238 8.243961 TCATCTCTACTCTGATTTTAAGAGGG 57.756 38.462 5.51 0.00 44.58 4.30
238 239 7.841729 TCATCTCTACTCTGATTTTAAGAGGGT 59.158 37.037 5.51 0.00 44.58 4.34
239 240 7.411486 TCTCTACTCTGATTTTAAGAGGGTG 57.589 40.000 5.51 0.36 44.58 4.61
240 241 6.381420 TCTCTACTCTGATTTTAAGAGGGTGG 59.619 42.308 5.51 0.00 44.58 4.61
241 242 4.576330 ACTCTGATTTTAAGAGGGTGGG 57.424 45.455 5.51 0.00 44.58 4.61
242 243 3.267031 ACTCTGATTTTAAGAGGGTGGGG 59.733 47.826 5.51 0.00 44.58 4.96
243 244 2.025321 TCTGATTTTAAGAGGGTGGGGC 60.025 50.000 0.00 0.00 0.00 5.80
244 245 1.006639 TGATTTTAAGAGGGTGGGGCC 59.993 52.381 0.00 0.00 0.00 5.80
245 246 0.033503 ATTTTAAGAGGGTGGGGCCG 60.034 55.000 0.00 0.00 38.44 6.13
246 247 2.144859 TTTTAAGAGGGTGGGGCCGG 62.145 60.000 0.00 0.00 38.44 6.13
253 254 3.094498 GGTGGGGCCGGGTCTTAT 61.094 66.667 2.18 0.00 0.00 1.73
254 255 2.686572 GGTGGGGCCGGGTCTTATT 61.687 63.158 2.18 0.00 0.00 1.40
255 256 1.305287 GTGGGGCCGGGTCTTATTT 59.695 57.895 2.18 0.00 0.00 1.40
256 257 0.323999 GTGGGGCCGGGTCTTATTTT 60.324 55.000 2.18 0.00 0.00 1.82
257 258 0.323908 TGGGGCCGGGTCTTATTTTG 60.324 55.000 2.18 0.00 0.00 2.44
258 259 0.323999 GGGGCCGGGTCTTATTTTGT 60.324 55.000 2.18 0.00 0.00 2.83
259 260 1.552578 GGGCCGGGTCTTATTTTGTT 58.447 50.000 2.18 0.00 0.00 2.83
260 261 1.475280 GGGCCGGGTCTTATTTTGTTC 59.525 52.381 2.18 0.00 0.00 3.18
261 262 1.475280 GGCCGGGTCTTATTTTGTTCC 59.525 52.381 2.18 0.00 0.00 3.62
262 263 2.164338 GCCGGGTCTTATTTTGTTCCA 58.836 47.619 2.18 0.00 0.00 3.53
263 264 2.559231 GCCGGGTCTTATTTTGTTCCAA 59.441 45.455 2.18 0.00 0.00 3.53
264 265 3.194755 GCCGGGTCTTATTTTGTTCCAAT 59.805 43.478 2.18 0.00 0.00 3.16
265 266 4.676986 GCCGGGTCTTATTTTGTTCCAATC 60.677 45.833 2.18 0.00 0.00 2.67
266 267 4.461081 CCGGGTCTTATTTTGTTCCAATCA 59.539 41.667 0.00 0.00 0.00 2.57
267 268 5.047660 CCGGGTCTTATTTTGTTCCAATCAA 60.048 40.000 0.00 0.00 0.00 2.57
268 269 6.451393 CGGGTCTTATTTTGTTCCAATCAAA 58.549 36.000 0.00 0.00 33.76 2.69
269 270 7.096551 CGGGTCTTATTTTGTTCCAATCAAAT 58.903 34.615 0.00 0.00 35.25 2.32
270 271 7.275560 CGGGTCTTATTTTGTTCCAATCAAATC 59.724 37.037 0.00 0.00 35.25 2.17
271 272 8.093927 GGGTCTTATTTTGTTCCAATCAAATCA 58.906 33.333 0.00 0.00 35.25 2.57
272 273 9.487790 GGTCTTATTTTGTTCCAATCAAATCAA 57.512 29.630 0.00 0.00 35.25 2.57
274 275 9.206870 TCTTATTTTGTTCCAATCAAATCAAGC 57.793 29.630 0.00 0.00 35.25 4.01
275 276 6.806388 ATTTTGTTCCAATCAAATCAAGCC 57.194 33.333 0.00 0.00 35.25 4.35
276 277 4.952071 TTGTTCCAATCAAATCAAGCCA 57.048 36.364 0.00 0.00 0.00 4.75
277 278 4.255833 TGTTCCAATCAAATCAAGCCAC 57.744 40.909 0.00 0.00 0.00 5.01
278 279 3.006752 TGTTCCAATCAAATCAAGCCACC 59.993 43.478 0.00 0.00 0.00 4.61
279 280 3.173953 TCCAATCAAATCAAGCCACCT 57.826 42.857 0.00 0.00 0.00 4.00
280 281 4.314522 TCCAATCAAATCAAGCCACCTA 57.685 40.909 0.00 0.00 0.00 3.08
281 282 4.870636 TCCAATCAAATCAAGCCACCTAT 58.129 39.130 0.00 0.00 0.00 2.57
282 283 4.646040 TCCAATCAAATCAAGCCACCTATG 59.354 41.667 0.00 0.00 0.00 2.23
283 284 4.365723 CAATCAAATCAAGCCACCTATGC 58.634 43.478 0.00 0.00 0.00 3.14
284 285 3.084536 TCAAATCAAGCCACCTATGCA 57.915 42.857 0.00 0.00 0.00 3.96
285 286 3.018856 TCAAATCAAGCCACCTATGCAG 58.981 45.455 0.00 0.00 0.00 4.41
286 287 3.018856 CAAATCAAGCCACCTATGCAGA 58.981 45.455 0.00 0.00 0.00 4.26
287 288 2.634815 ATCAAGCCACCTATGCAGAG 57.365 50.000 0.00 0.00 0.00 3.35
288 289 0.107508 TCAAGCCACCTATGCAGAGC 60.108 55.000 1.83 0.00 0.00 4.09
289 290 0.393402 CAAGCCACCTATGCAGAGCA 60.393 55.000 1.83 0.00 44.86 4.26
290 291 0.393537 AAGCCACCTATGCAGAGCAC 60.394 55.000 1.83 0.00 43.04 4.40
291 292 1.078214 GCCACCTATGCAGAGCACA 60.078 57.895 1.83 0.00 43.04 4.57
292 293 1.094073 GCCACCTATGCAGAGCACAG 61.094 60.000 1.83 0.00 43.04 3.66
293 294 0.538584 CCACCTATGCAGAGCACAGA 59.461 55.000 1.83 0.00 43.04 3.41
294 295 1.472904 CCACCTATGCAGAGCACAGAG 60.473 57.143 1.83 0.00 43.04 3.35
295 296 0.829333 ACCTATGCAGAGCACAGAGG 59.171 55.000 1.83 12.37 43.04 3.69
296 297 0.106335 CCTATGCAGAGCACAGAGGG 59.894 60.000 1.83 0.00 43.04 4.30
297 298 0.106335 CTATGCAGAGCACAGAGGGG 59.894 60.000 0.00 0.00 43.04 4.79
298 299 1.976132 TATGCAGAGCACAGAGGGGC 61.976 60.000 0.00 0.00 43.04 5.80
323 324 3.710722 CGGGGAGCAGGCAAGTCT 61.711 66.667 0.00 0.00 0.00 3.24
324 325 2.270527 GGGGAGCAGGCAAGTCTC 59.729 66.667 0.00 0.00 0.00 3.36
325 326 2.297129 GGGGAGCAGGCAAGTCTCT 61.297 63.158 0.00 0.00 0.00 3.10
326 327 1.078567 GGGAGCAGGCAAGTCTCTG 60.079 63.158 0.00 0.00 0.00 3.35
327 328 1.676384 GGAGCAGGCAAGTCTCTGT 59.324 57.895 0.00 0.00 33.81 3.41
328 329 0.390998 GGAGCAGGCAAGTCTCTGTC 60.391 60.000 0.00 0.00 33.81 3.51
329 330 0.607620 GAGCAGGCAAGTCTCTGTCT 59.392 55.000 0.00 0.00 33.81 3.41
357 358 2.604174 GGGTCGCACGTTGGAGTTG 61.604 63.158 0.00 0.00 0.00 3.16
358 359 2.248431 GTCGCACGTTGGAGTTGC 59.752 61.111 0.00 0.00 0.00 4.17
359 360 2.970324 TCGCACGTTGGAGTTGCC 60.970 61.111 0.00 0.00 37.10 4.52
360 361 4.368808 CGCACGTTGGAGTTGCCG 62.369 66.667 0.00 0.00 40.66 5.69
361 362 3.276846 GCACGTTGGAGTTGCCGT 61.277 61.111 0.00 0.00 40.66 5.68
362 363 2.830285 GCACGTTGGAGTTGCCGTT 61.830 57.895 0.00 0.00 40.66 4.44
363 364 1.278637 CACGTTGGAGTTGCCGTTC 59.721 57.895 0.00 0.00 40.66 3.95
364 365 2.241880 ACGTTGGAGTTGCCGTTCG 61.242 57.895 0.00 0.00 40.66 3.95
365 366 1.952133 CGTTGGAGTTGCCGTTCGA 60.952 57.895 0.00 0.00 40.66 3.71
368 369 2.035237 TTGGAGTTGCCGTTCGAGGT 62.035 55.000 0.00 0.00 40.66 3.85
375 376 2.882876 CCGTTCGAGGTCGGTGAT 59.117 61.111 14.56 0.00 41.58 3.06
541 2991 3.431725 CCCCTCGAAAGCGTTGGC 61.432 66.667 0.00 0.00 38.98 4.52
608 3058 3.673597 TCGGAGAGACTGGGCCCT 61.674 66.667 25.70 2.15 0.00 5.19
609 3059 3.465403 CGGAGAGACTGGGCCCTG 61.465 72.222 26.14 26.14 0.00 4.45
610 3060 3.791586 GGAGAGACTGGGCCCTGC 61.792 72.222 27.51 19.45 0.00 4.85
926 3436 1.775039 CGCAACTATGTCCCATGCCG 61.775 60.000 0.00 0.00 33.55 5.69
1021 3540 7.307160 GGTTGATGATGATGCAGCAAATATTTG 60.307 37.037 21.54 21.54 44.57 2.32
1028 3547 3.587923 TGCAGCAAATATTTGGTCAAGC 58.412 40.909 25.92 24.65 46.06 4.01
1085 3606 0.539051 CCTGTCCCTGCAGAAGTAGG 59.461 60.000 17.39 13.39 46.19 3.18
1105 3626 4.458397 AGGATACAATCAATCCACTGCAG 58.542 43.478 13.48 13.48 44.62 4.41
1202 3740 7.668469 TGACAGTTCTACTACTTGATGTCCTTA 59.332 37.037 0.00 0.00 0.00 2.69
1296 3836 0.321298 AGGCATTGCGTAAGTTCGGT 60.321 50.000 1.23 0.00 41.68 4.69
1378 3918 6.418057 ACATCTATGATCTCTTTCCTCACC 57.582 41.667 0.00 0.00 0.00 4.02
1396 3936 1.806542 ACCGAGCTACAAGCATGTTTG 59.193 47.619 19.42 19.42 45.56 2.93
1428 3968 1.985684 GCAGCTAAATTGCCGTTCAAC 59.014 47.619 0.00 0.00 37.53 3.18
1434 3974 4.742659 GCTAAATTGCCGTTCAACTTTTCA 59.257 37.500 0.00 0.00 37.53 2.69
1491 4045 5.295292 AGAGTGATTAAATGAATCTGCACCG 59.705 40.000 0.00 0.00 43.90 4.94
1999 4591 7.819900 AGTCTCTGCACTTAAATTTACTGGTAG 59.180 37.037 0.00 0.02 0.00 3.18
2084 4676 7.323420 TGTGTCATCTCTTTTAGTCATCGATT 58.677 34.615 0.00 0.00 0.00 3.34
2088 4680 7.492669 GTCATCTCTTTTAGTCATCGATTTGGA 59.507 37.037 0.00 0.00 0.00 3.53
2193 4821 8.000127 TGGATCTGATTGTATGGAATGATTGAA 59.000 33.333 0.00 0.00 0.00 2.69
2335 4966 8.512138 AGTCAACTTCGAAAATTATTTAGGGTG 58.488 33.333 0.00 0.00 0.00 4.61
2601 5240 4.202202 ACAGAATCTGCACTGCTATACCTC 60.202 45.833 10.62 0.00 37.61 3.85
2604 5243 2.587522 TCTGCACTGCTATACCTCGAT 58.412 47.619 1.98 0.00 0.00 3.59
2708 5347 7.009179 AGATTTTAGACAAGTGAGTGATCCA 57.991 36.000 0.00 0.00 0.00 3.41
3015 5673 1.586422 GTCATATGACATGTGCCGCT 58.414 50.000 27.33 0.00 44.18 5.52
3203 5865 2.481104 CCAAACATGTGAAAGCGGTTGT 60.481 45.455 0.00 0.00 0.00 3.32
3249 5919 9.490379 CAGGTTATAGTTTACATGGATCTAACC 57.510 37.037 0.00 5.37 37.11 2.85
3406 6082 6.962182 TGGCTAGGGATATATGGAAATTCTG 58.038 40.000 0.00 0.00 0.00 3.02
3482 6179 5.049405 CAGGAAAATTCTTGAGCAAGTACGT 60.049 40.000 9.79 0.00 36.49 3.57
3730 6448 2.379005 CAGCCAGGAAGTTTAATCCCC 58.621 52.381 0.00 0.00 37.71 4.81
3807 6530 5.521516 CTGCAAGTCAGTAGTAACATGTG 57.478 43.478 0.00 0.00 38.02 3.21
3808 6531 4.956085 TGCAAGTCAGTAGTAACATGTGT 58.044 39.130 0.00 0.00 0.00 3.72
3816 6539 3.807622 AGTAGTAACATGTGTGTGTGTGC 59.192 43.478 0.00 0.00 38.92 4.57
3948 6671 0.721718 GATTCCGACTTGGTGCTTCG 59.278 55.000 0.00 0.00 39.52 3.79
4049 10022 4.021925 AGTCAGCGGTTCAGGGCC 62.022 66.667 0.00 0.00 0.00 5.80
4106 10079 1.679032 CGGATCGCCCCTCTTCTTTTT 60.679 52.381 0.00 0.00 0.00 1.94
4119 10092 4.435425 TCTTCTTTTTCGTTCGTCCTTCA 58.565 39.130 0.00 0.00 0.00 3.02
4129 10102 2.074547 TCGTCCTTCAAATGTCGACC 57.925 50.000 14.12 0.00 0.00 4.79
4444 10422 2.665603 GTGCTCTTCCTTCGCCCT 59.334 61.111 0.00 0.00 0.00 5.19
4446 10424 1.021920 GTGCTCTTCCTTCGCCCTTC 61.022 60.000 0.00 0.00 0.00 3.46
4573 10558 3.726517 GGTGCGCGCTGTGTCATT 61.727 61.111 33.29 0.00 0.00 2.57
4582 10567 1.589716 GCTGTGTCATTGGCAGGGAC 61.590 60.000 12.13 12.13 0.00 4.46
4584 10569 1.003839 GTGTCATTGGCAGGGACGA 60.004 57.895 13.58 3.57 34.32 4.20
4596 10582 3.434319 GGACGAGACGGGTGCGTA 61.434 66.667 0.00 0.00 38.51 4.42
4634 10620 1.170919 GGATACGGACAGCTCGGCTA 61.171 60.000 0.00 0.00 36.40 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.355115 CCACCTGTTAGGCCCACC 59.645 66.667 0.00 0.00 39.63 4.61
14 15 2.361230 GCCACCTGTTAGGCCCAC 60.361 66.667 0.00 0.00 45.18 4.61
19 20 2.044946 GGCCAGCCACCTGTTAGG 60.045 66.667 3.12 0.00 42.49 2.69
20 21 2.044946 GGGCCAGCCACCTGTTAG 60.045 66.667 11.50 0.00 37.38 2.34
21 22 2.856494 TGGGCCAGCCACCTGTTA 60.856 61.111 11.50 0.00 37.38 2.41
22 23 4.603535 GTGGGCCAGCCACCTGTT 62.604 66.667 6.40 0.00 37.38 3.16
29 30 2.615227 CTATGACAGGTGGGCCAGCC 62.615 65.000 30.80 22.20 37.19 4.85
30 31 1.153086 CTATGACAGGTGGGCCAGC 60.153 63.158 27.81 27.81 37.19 4.85
31 32 0.179000 GTCTATGACAGGTGGGCCAG 59.821 60.000 6.40 0.00 37.19 4.85
32 33 1.271840 GGTCTATGACAGGTGGGCCA 61.272 60.000 0.00 0.00 37.19 5.36
33 34 1.527370 GGTCTATGACAGGTGGGCC 59.473 63.158 0.00 0.00 33.68 5.80
34 35 1.271840 TGGGTCTATGACAGGTGGGC 61.272 60.000 0.07 0.00 33.68 5.36
35 36 1.285280 TTGGGTCTATGACAGGTGGG 58.715 55.000 0.07 0.00 33.68 4.61
36 37 2.356125 CCTTTGGGTCTATGACAGGTGG 60.356 54.545 0.07 0.00 33.68 4.61
37 38 2.305927 ACCTTTGGGTCTATGACAGGTG 59.694 50.000 6.65 0.00 43.38 4.00
38 39 2.632537 ACCTTTGGGTCTATGACAGGT 58.367 47.619 0.07 1.60 43.38 4.00
39 40 3.134804 CCTACCTTTGGGTCTATGACAGG 59.865 52.174 0.07 1.03 45.98 4.00
40 41 3.775316 ACCTACCTTTGGGTCTATGACAG 59.225 47.826 0.07 0.00 45.98 3.51
41 42 3.517901 CACCTACCTTTGGGTCTATGACA 59.482 47.826 0.07 0.00 45.98 3.58
42 43 3.681874 GCACCTACCTTTGGGTCTATGAC 60.682 52.174 0.00 0.00 45.98 3.06
43 44 2.504175 GCACCTACCTTTGGGTCTATGA 59.496 50.000 0.00 0.00 45.98 2.15
44 45 2.421529 GGCACCTACCTTTGGGTCTATG 60.422 54.545 0.00 0.00 45.98 2.23
45 46 1.844497 GGCACCTACCTTTGGGTCTAT 59.156 52.381 0.00 0.00 45.98 1.98
46 47 1.203389 AGGCACCTACCTTTGGGTCTA 60.203 52.381 0.00 0.00 45.98 2.59
47 48 0.475828 AGGCACCTACCTTTGGGTCT 60.476 55.000 0.00 0.00 45.98 3.85
48 49 2.075837 AGGCACCTACCTTTGGGTC 58.924 57.895 0.00 0.00 45.98 4.46
64 65 1.087501 GAGCTTCGGTGCCTTAAAGG 58.912 55.000 0.00 0.00 38.80 3.11
65 66 1.808411 TGAGCTTCGGTGCCTTAAAG 58.192 50.000 0.00 0.00 0.00 1.85
66 67 2.264005 TTGAGCTTCGGTGCCTTAAA 57.736 45.000 0.00 0.00 0.00 1.52
67 68 2.356135 GATTGAGCTTCGGTGCCTTAA 58.644 47.619 0.00 0.00 0.00 1.85
68 69 1.406887 GGATTGAGCTTCGGTGCCTTA 60.407 52.381 0.00 0.00 0.00 2.69
69 70 0.678048 GGATTGAGCTTCGGTGCCTT 60.678 55.000 0.00 0.00 0.00 4.35
70 71 1.078143 GGATTGAGCTTCGGTGCCT 60.078 57.895 0.00 0.00 0.00 4.75
71 72 2.464459 CGGATTGAGCTTCGGTGCC 61.464 63.158 0.00 0.00 0.00 5.01
72 73 1.298859 AACGGATTGAGCTTCGGTGC 61.299 55.000 0.00 0.00 0.00 5.01
73 74 0.721718 GAACGGATTGAGCTTCGGTG 59.278 55.000 0.00 0.00 0.00 4.94
74 75 0.608640 AGAACGGATTGAGCTTCGGT 59.391 50.000 0.00 0.00 0.00 4.69
75 76 1.002366 CAGAACGGATTGAGCTTCGG 58.998 55.000 0.00 0.00 0.00 4.30
76 77 1.996292 TCAGAACGGATTGAGCTTCG 58.004 50.000 0.00 0.00 0.00 3.79
77 78 3.525537 TGATCAGAACGGATTGAGCTTC 58.474 45.455 0.00 0.00 31.34 3.86
78 79 3.529533 CTGATCAGAACGGATTGAGCTT 58.470 45.455 18.34 0.00 31.34 3.74
79 80 2.158986 CCTGATCAGAACGGATTGAGCT 60.159 50.000 24.62 0.00 31.34 4.09
80 81 2.208431 CCTGATCAGAACGGATTGAGC 58.792 52.381 24.62 0.00 0.00 4.26
81 82 3.533606 ACCTGATCAGAACGGATTGAG 57.466 47.619 24.62 5.56 0.00 3.02
82 83 3.676049 CGAACCTGATCAGAACGGATTGA 60.676 47.826 24.62 0.00 0.00 2.57
83 84 2.604914 CGAACCTGATCAGAACGGATTG 59.395 50.000 24.62 7.03 0.00 2.67
84 85 2.893637 CGAACCTGATCAGAACGGATT 58.106 47.619 24.62 7.95 0.00 3.01
85 86 1.471676 GCGAACCTGATCAGAACGGAT 60.472 52.381 24.62 2.49 0.00 4.18
86 87 0.108804 GCGAACCTGATCAGAACGGA 60.109 55.000 24.62 0.00 0.00 4.69
87 88 0.389817 TGCGAACCTGATCAGAACGG 60.390 55.000 24.62 10.75 0.00 4.44
88 89 0.716108 GTGCGAACCTGATCAGAACG 59.284 55.000 24.62 23.04 0.00 3.95
89 90 1.079503 GGTGCGAACCTGATCAGAAC 58.920 55.000 24.62 12.88 0.00 3.01
90 91 0.389817 CGGTGCGAACCTGATCAGAA 60.390 55.000 24.62 0.00 0.00 3.02
91 92 1.215382 CGGTGCGAACCTGATCAGA 59.785 57.895 24.62 0.00 0.00 3.27
92 93 2.456119 GCGGTGCGAACCTGATCAG 61.456 63.158 16.24 16.24 0.00 2.90
93 94 2.434185 GCGGTGCGAACCTGATCA 60.434 61.111 11.82 0.00 0.00 2.92
106 107 4.424711 ATCCCAACATGCCGCGGT 62.425 61.111 28.70 4.23 0.00 5.68
107 108 3.585990 GATCCCAACATGCCGCGG 61.586 66.667 24.05 24.05 0.00 6.46
108 109 3.585990 GGATCCCAACATGCCGCG 61.586 66.667 0.00 0.00 0.00 6.46
109 110 3.585990 CGGATCCCAACATGCCGC 61.586 66.667 6.06 0.00 35.17 6.53
110 111 2.901840 CCGGATCCCAACATGCCG 60.902 66.667 6.06 0.00 41.53 5.69
111 112 3.219198 GCCGGATCCCAACATGCC 61.219 66.667 5.05 0.00 0.00 4.40
112 113 1.754234 AAGCCGGATCCCAACATGC 60.754 57.895 5.05 0.00 0.00 4.06
113 114 2.008268 GCAAGCCGGATCCCAACATG 62.008 60.000 5.05 0.00 0.00 3.21
114 115 1.754234 GCAAGCCGGATCCCAACAT 60.754 57.895 5.05 0.00 0.00 2.71
115 116 2.361104 GCAAGCCGGATCCCAACA 60.361 61.111 5.05 0.00 0.00 3.33
116 117 3.140814 GGCAAGCCGGATCCCAAC 61.141 66.667 5.05 0.00 0.00 3.77
117 118 3.338250 AGGCAAGCCGGATCCCAA 61.338 61.111 5.05 0.00 41.95 4.12
118 119 4.113815 CAGGCAAGCCGGATCCCA 62.114 66.667 5.05 0.00 41.95 4.37
120 121 4.496336 AGCAGGCAAGCCGGATCC 62.496 66.667 15.46 0.00 41.95 3.36
121 122 2.899339 GAGCAGGCAAGCCGGATC 60.899 66.667 15.46 14.32 39.23 3.36
122 123 4.496336 GGAGCAGGCAAGCCGGAT 62.496 66.667 15.46 8.74 41.95 4.18
126 127 4.811364 GGAGGGAGCAGGCAAGCC 62.811 72.222 2.02 2.02 34.23 4.35
127 128 4.811364 GGGAGGGAGCAGGCAAGC 62.811 72.222 0.00 0.00 0.00 4.01
128 129 4.120755 GGGGAGGGAGCAGGCAAG 62.121 72.222 0.00 0.00 0.00 4.01
139 140 3.866582 GATGGGAGCACGGGGAGG 61.867 72.222 0.00 0.00 0.00 4.30
140 141 3.866582 GGATGGGAGCACGGGGAG 61.867 72.222 0.00 0.00 0.00 4.30
143 144 4.838152 CACGGATGGGAGCACGGG 62.838 72.222 0.00 0.00 0.00 5.28
145 146 4.457496 AGCACGGATGGGAGCACG 62.457 66.667 0.00 0.00 0.00 5.34
146 147 2.512515 GAGCACGGATGGGAGCAC 60.513 66.667 0.00 0.00 0.00 4.40
147 148 3.785859 GGAGCACGGATGGGAGCA 61.786 66.667 0.00 0.00 0.00 4.26
148 149 4.554036 GGGAGCACGGATGGGAGC 62.554 72.222 0.00 0.00 0.00 4.70
149 150 3.083349 TGGGAGCACGGATGGGAG 61.083 66.667 0.00 0.00 0.00 4.30
150 151 3.399181 GTGGGAGCACGGATGGGA 61.399 66.667 0.00 0.00 0.00 4.37
151 152 4.489771 GGTGGGAGCACGGATGGG 62.490 72.222 0.00 0.00 0.00 4.00
152 153 3.391665 GAGGTGGGAGCACGGATGG 62.392 68.421 0.00 0.00 0.00 3.51
153 154 1.976132 ATGAGGTGGGAGCACGGATG 61.976 60.000 0.00 0.00 0.00 3.51
154 155 1.690219 GATGAGGTGGGAGCACGGAT 61.690 60.000 0.00 0.00 0.00 4.18
155 156 2.284625 ATGAGGTGGGAGCACGGA 60.285 61.111 0.00 0.00 0.00 4.69
156 157 2.187946 GATGAGGTGGGAGCACGG 59.812 66.667 0.00 0.00 0.00 4.94
157 158 1.043116 TAGGATGAGGTGGGAGCACG 61.043 60.000 0.00 0.00 0.00 5.34
158 159 0.466124 GTAGGATGAGGTGGGAGCAC 59.534 60.000 0.00 0.00 0.00 4.40
159 160 0.042581 TGTAGGATGAGGTGGGAGCA 59.957 55.000 0.00 0.00 0.00 4.26
160 161 0.755686 CTGTAGGATGAGGTGGGAGC 59.244 60.000 0.00 0.00 0.00 4.70
161 162 0.755686 GCTGTAGGATGAGGTGGGAG 59.244 60.000 0.00 0.00 0.00 4.30
162 163 0.339859 AGCTGTAGGATGAGGTGGGA 59.660 55.000 0.00 0.00 0.00 4.37
163 164 0.467384 CAGCTGTAGGATGAGGTGGG 59.533 60.000 5.25 0.00 34.68 4.61
164 165 1.137872 GACAGCTGTAGGATGAGGTGG 59.862 57.143 21.73 0.00 41.13 4.61
165 166 2.106566 AGACAGCTGTAGGATGAGGTG 58.893 52.381 21.73 0.00 42.26 4.00
166 167 2.541233 AGACAGCTGTAGGATGAGGT 57.459 50.000 21.73 0.00 35.04 3.85
167 168 3.902881 AAAGACAGCTGTAGGATGAGG 57.097 47.619 21.73 0.00 35.04 3.86
211 212 8.869109 CCCTCTTAAAATCAGAGTAGAGATGAT 58.131 37.037 0.00 0.00 36.75 2.45
212 213 7.841729 ACCCTCTTAAAATCAGAGTAGAGATGA 59.158 37.037 0.00 0.00 36.75 2.92
213 214 7.925483 CACCCTCTTAAAATCAGAGTAGAGATG 59.075 40.741 0.00 0.00 36.75 2.90
214 215 7.070571 CCACCCTCTTAAAATCAGAGTAGAGAT 59.929 40.741 0.00 0.00 36.75 2.75
215 216 6.381420 CCACCCTCTTAAAATCAGAGTAGAGA 59.619 42.308 0.00 0.00 36.75 3.10
216 217 6.407525 CCCACCCTCTTAAAATCAGAGTAGAG 60.408 46.154 0.00 0.00 36.75 2.43
217 218 5.425539 CCCACCCTCTTAAAATCAGAGTAGA 59.574 44.000 0.00 0.00 36.75 2.59
218 219 5.396884 CCCCACCCTCTTAAAATCAGAGTAG 60.397 48.000 0.00 0.00 36.75 2.57
219 220 4.473559 CCCCACCCTCTTAAAATCAGAGTA 59.526 45.833 0.00 0.00 36.75 2.59
220 221 3.267031 CCCCACCCTCTTAAAATCAGAGT 59.733 47.826 0.00 0.00 36.75 3.24
221 222 3.891049 CCCCACCCTCTTAAAATCAGAG 58.109 50.000 0.00 0.00 38.03 3.35
222 223 2.025321 GCCCCACCCTCTTAAAATCAGA 60.025 50.000 0.00 0.00 0.00 3.27
223 224 2.379005 GCCCCACCCTCTTAAAATCAG 58.621 52.381 0.00 0.00 0.00 2.90
224 225 1.006639 GGCCCCACCCTCTTAAAATCA 59.993 52.381 0.00 0.00 0.00 2.57
225 226 1.776662 GGCCCCACCCTCTTAAAATC 58.223 55.000 0.00 0.00 0.00 2.17
226 227 0.033503 CGGCCCCACCCTCTTAAAAT 60.034 55.000 0.00 0.00 33.26 1.82
227 228 1.381076 CGGCCCCACCCTCTTAAAA 59.619 57.895 0.00 0.00 33.26 1.52
228 229 2.608550 CCGGCCCCACCCTCTTAAA 61.609 63.158 0.00 0.00 33.26 1.52
229 230 3.012722 CCGGCCCCACCCTCTTAA 61.013 66.667 0.00 0.00 33.26 1.85
236 237 2.219449 AAATAAGACCCGGCCCCACC 62.219 60.000 0.00 0.00 0.00 4.61
237 238 0.323999 AAAATAAGACCCGGCCCCAC 60.324 55.000 0.00 0.00 0.00 4.61
238 239 0.323908 CAAAATAAGACCCGGCCCCA 60.324 55.000 0.00 0.00 0.00 4.96
239 240 0.323999 ACAAAATAAGACCCGGCCCC 60.324 55.000 0.00 0.00 0.00 5.80
240 241 1.475280 GAACAAAATAAGACCCGGCCC 59.525 52.381 0.00 0.00 0.00 5.80
241 242 1.475280 GGAACAAAATAAGACCCGGCC 59.525 52.381 0.00 0.00 0.00 6.13
242 243 2.164338 TGGAACAAAATAAGACCCGGC 58.836 47.619 0.00 0.00 31.92 6.13
256 257 3.006752 GGTGGCTTGATTTGATTGGAACA 59.993 43.478 0.00 0.00 0.00 3.18
257 258 3.259123 AGGTGGCTTGATTTGATTGGAAC 59.741 43.478 0.00 0.00 0.00 3.62
258 259 3.509442 AGGTGGCTTGATTTGATTGGAA 58.491 40.909 0.00 0.00 0.00 3.53
259 260 3.173953 AGGTGGCTTGATTTGATTGGA 57.826 42.857 0.00 0.00 0.00 3.53
260 261 4.738541 GCATAGGTGGCTTGATTTGATTGG 60.739 45.833 0.00 0.00 0.00 3.16
261 262 4.142116 TGCATAGGTGGCTTGATTTGATTG 60.142 41.667 0.00 0.00 0.00 2.67
262 263 4.025360 TGCATAGGTGGCTTGATTTGATT 58.975 39.130 0.00 0.00 0.00 2.57
263 264 3.634504 TGCATAGGTGGCTTGATTTGAT 58.365 40.909 0.00 0.00 0.00 2.57
264 265 3.018856 CTGCATAGGTGGCTTGATTTGA 58.981 45.455 0.00 0.00 0.00 2.69
265 266 3.018856 TCTGCATAGGTGGCTTGATTTG 58.981 45.455 0.00 0.00 0.00 2.32
266 267 3.285484 CTCTGCATAGGTGGCTTGATTT 58.715 45.455 0.00 0.00 0.00 2.17
267 268 2.928334 CTCTGCATAGGTGGCTTGATT 58.072 47.619 0.00 0.00 0.00 2.57
268 269 1.476471 GCTCTGCATAGGTGGCTTGAT 60.476 52.381 0.83 0.00 0.00 2.57
269 270 0.107508 GCTCTGCATAGGTGGCTTGA 60.108 55.000 0.83 0.00 0.00 3.02
270 271 0.393402 TGCTCTGCATAGGTGGCTTG 60.393 55.000 0.83 0.00 31.71 4.01
271 272 0.393537 GTGCTCTGCATAGGTGGCTT 60.394 55.000 0.83 0.00 41.91 4.35
272 273 1.222936 GTGCTCTGCATAGGTGGCT 59.777 57.895 0.83 0.00 41.91 4.75
273 274 1.078214 TGTGCTCTGCATAGGTGGC 60.078 57.895 0.83 0.00 41.91 5.01
274 275 0.538584 TCTGTGCTCTGCATAGGTGG 59.461 55.000 14.46 0.00 45.54 4.61
275 276 1.472904 CCTCTGTGCTCTGCATAGGTG 60.473 57.143 14.46 8.92 45.54 4.00
276 277 0.829333 CCTCTGTGCTCTGCATAGGT 59.171 55.000 14.46 0.00 45.54 3.08
277 278 0.106335 CCCTCTGTGCTCTGCATAGG 59.894 60.000 14.46 11.97 45.54 2.57
278 279 0.106335 CCCCTCTGTGCTCTGCATAG 59.894 60.000 9.50 9.50 46.57 2.23
279 280 1.976132 GCCCCTCTGTGCTCTGCATA 61.976 60.000 0.00 0.00 41.91 3.14
280 281 2.996395 CCCCTCTGTGCTCTGCAT 59.004 61.111 0.00 0.00 41.91 3.96
281 282 4.025858 GCCCCTCTGTGCTCTGCA 62.026 66.667 0.00 0.00 35.60 4.41
306 307 3.672295 GAGACTTGCCTGCTCCCCG 62.672 68.421 0.00 0.00 0.00 5.73
307 308 2.270527 GAGACTTGCCTGCTCCCC 59.729 66.667 0.00 0.00 0.00 4.81
308 309 1.078567 CAGAGACTTGCCTGCTCCC 60.079 63.158 0.00 0.00 0.00 4.30
309 310 0.390998 GACAGAGACTTGCCTGCTCC 60.391 60.000 0.00 0.00 33.90 4.70
310 311 0.607620 AGACAGAGACTTGCCTGCTC 59.392 55.000 0.00 0.00 33.90 4.26
311 312 0.321021 CAGACAGAGACTTGCCTGCT 59.679 55.000 0.00 0.00 33.90 4.24
312 313 0.673022 CCAGACAGAGACTTGCCTGC 60.673 60.000 0.00 0.00 33.90 4.85
313 314 0.673022 GCCAGACAGAGACTTGCCTG 60.673 60.000 0.00 0.00 36.53 4.85
314 315 1.123861 TGCCAGACAGAGACTTGCCT 61.124 55.000 0.00 0.00 0.00 4.75
315 316 0.035630 ATGCCAGACAGAGACTTGCC 60.036 55.000 0.00 0.00 0.00 4.52
316 317 1.085091 CATGCCAGACAGAGACTTGC 58.915 55.000 0.00 0.00 0.00 4.01
317 318 2.469274 ACATGCCAGACAGAGACTTG 57.531 50.000 0.00 0.00 0.00 3.16
318 319 2.551721 CCAACATGCCAGACAGAGACTT 60.552 50.000 0.00 0.00 0.00 3.01
319 320 1.002888 CCAACATGCCAGACAGAGACT 59.997 52.381 0.00 0.00 0.00 3.24
320 321 1.446907 CCAACATGCCAGACAGAGAC 58.553 55.000 0.00 0.00 0.00 3.36
321 322 0.325933 CCCAACATGCCAGACAGAGA 59.674 55.000 0.00 0.00 0.00 3.10
322 323 0.679002 CCCCAACATGCCAGACAGAG 60.679 60.000 0.00 0.00 0.00 3.35
323 324 1.379916 CCCCAACATGCCAGACAGA 59.620 57.895 0.00 0.00 0.00 3.41
324 325 0.962356 GACCCCAACATGCCAGACAG 60.962 60.000 0.00 0.00 0.00 3.51
325 326 1.074775 GACCCCAACATGCCAGACA 59.925 57.895 0.00 0.00 0.00 3.41
326 327 2.040544 CGACCCCAACATGCCAGAC 61.041 63.158 0.00 0.00 0.00 3.51
327 328 2.350895 CGACCCCAACATGCCAGA 59.649 61.111 0.00 0.00 0.00 3.86
328 329 3.443045 GCGACCCCAACATGCCAG 61.443 66.667 0.00 0.00 0.00 4.85
329 330 4.277009 TGCGACCCCAACATGCCA 62.277 61.111 0.00 0.00 0.00 4.92
359 360 0.797249 GTCATCACCGACCTCGAACG 60.797 60.000 0.00 0.00 43.02 3.95
360 361 0.797249 CGTCATCACCGACCTCGAAC 60.797 60.000 0.00 0.00 43.02 3.95
361 362 1.504900 CGTCATCACCGACCTCGAA 59.495 57.895 0.00 0.00 43.02 3.71
362 363 3.047718 GCGTCATCACCGACCTCGA 62.048 63.158 0.00 0.00 43.02 4.04
363 364 2.579787 GCGTCATCACCGACCTCG 60.580 66.667 0.00 0.00 39.44 4.63
364 365 2.202756 GGCGTCATCACCGACCTC 60.203 66.667 0.00 0.00 31.91 3.85
523 2973 2.746277 CCAACGCTTTCGAGGGGG 60.746 66.667 8.77 6.02 39.41 5.40
541 2991 1.043673 CCTGGACCGTAAGAGGGGAG 61.044 65.000 0.00 0.00 43.02 4.30
590 3040 3.151022 GGGCCCAGTCTCTCCGAG 61.151 72.222 19.95 0.00 0.00 4.63
680 3187 0.539438 AGGTGGAAATTGCTCGCCAA 60.539 50.000 7.12 0.00 37.94 4.52
738 3245 2.047179 GGTGCCGTTGGAGGAGTC 60.047 66.667 0.00 0.00 0.00 3.36
739 3246 4.003788 CGGTGCCGTTGGAGGAGT 62.004 66.667 1.93 0.00 34.35 3.85
765 3275 2.187946 CATGTGCGTCCTCCTCCC 59.812 66.667 0.00 0.00 0.00 4.30
773 3283 2.103042 GCTCCAGACCATGTGCGTC 61.103 63.158 0.00 0.00 0.00 5.19
913 3423 0.980754 ACCACTCGGCATGGGACATA 60.981 55.000 0.00 0.00 41.97 2.29
1021 3540 4.082026 ACAGCTAAATCCAAATGCTTGACC 60.082 41.667 0.00 0.00 34.14 4.02
1028 3547 4.789012 ACACCACAGCTAAATCCAAATG 57.211 40.909 0.00 0.00 0.00 2.32
1085 3606 3.881688 AGCTGCAGTGGATTGATTGTATC 59.118 43.478 16.64 0.00 0.00 2.24
1105 3626 0.174617 GTCCAGTGGCTAGTCTCAGC 59.825 60.000 3.51 0.00 41.02 4.26
1296 3836 8.596271 TTCGTCAGATAAGTATTTGACACAAA 57.404 30.769 17.39 8.83 43.86 2.83
1378 3918 1.131126 CCCAAACATGCTTGTAGCTCG 59.869 52.381 5.56 0.00 42.97 5.03
1491 4045 8.911247 AAAATACTTGAAACACTCTGTTCAAC 57.089 30.769 0.00 0.00 40.14 3.18
1752 4335 8.099364 TGAAGCTTATTAGAAACTTGAACTGG 57.901 34.615 0.00 0.00 0.00 4.00
1907 4493 9.181061 ACTAAAAATAGTAACACAACCACAGTT 57.819 29.630 0.00 0.00 36.33 3.16
1999 4591 6.791887 ATATATACAGTGTGCATGCTGAAC 57.208 37.500 20.33 13.86 36.62 3.18
2164 4761 7.991084 TCATTCCATACAATCAGATCCAATC 57.009 36.000 0.00 0.00 0.00 2.67
2193 4821 3.334881 AGTTGGGAGGAATCCAAGTGATT 59.665 43.478 0.61 0.00 46.46 2.57
2369 5000 8.176365 CAGAAAAATCATAAGAGAGCAGTTCAG 58.824 37.037 0.00 0.00 0.00 3.02
2601 5240 2.149578 GAAAGGGAGCATGGATGATCG 58.850 52.381 0.00 0.00 43.72 3.69
2604 5243 3.293337 CATTGAAAGGGAGCATGGATGA 58.707 45.455 0.00 0.00 0.00 2.92
3203 5865 0.109532 TGGGCAAGGTCGATCAAACA 59.890 50.000 0.00 0.00 0.00 2.83
3406 6082 0.935196 AAACACGACGAGCCTGAAAC 59.065 50.000 0.00 0.00 0.00 2.78
3430 6127 1.405105 TGTCCTTGCAGCAAACTCAAC 59.595 47.619 9.65 4.02 0.00 3.18
3482 6179 0.391130 GCTGAATGTGTGCCTACCGA 60.391 55.000 0.00 0.00 0.00 4.69
3730 6448 3.332445 TTACCCCGGACAATGCCCG 62.332 63.158 0.73 0.00 46.10 6.13
3764 6485 4.072131 AGTAGCAACCGATCAACAACAAT 58.928 39.130 0.00 0.00 0.00 2.71
3765 6486 3.249799 CAGTAGCAACCGATCAACAACAA 59.750 43.478 0.00 0.00 0.00 2.83
3766 6487 2.805671 CAGTAGCAACCGATCAACAACA 59.194 45.455 0.00 0.00 0.00 3.33
3807 6530 4.649954 GTCAGCGCGCACACACAC 62.650 66.667 35.10 15.42 0.00 3.82
3808 6531 4.889856 AGTCAGCGCGCACACACA 62.890 61.111 35.10 6.71 0.00 3.72
3863 6586 2.099592 ACCATTCGCACAGGCATAAATG 59.900 45.455 0.00 0.00 41.24 2.32
3948 6671 8.410141 ACTATAGTAAGTCAGATGAAAGCAGTC 58.590 37.037 2.75 0.00 0.00 3.51
4049 10022 2.033049 GGATGAGCTTGTAGCAATGCAG 59.967 50.000 8.35 0.00 45.56 4.41
4106 10079 2.055838 CGACATTTGAAGGACGAACGA 58.944 47.619 0.14 0.00 30.22 3.85
4119 10092 3.813166 ACTTCACAAATCGGTCGACATTT 59.187 39.130 18.91 12.56 0.00 2.32
4129 10102 3.155998 CGCTTAAGCACTTCACAAATCG 58.844 45.455 26.29 2.21 42.21 3.34
4419 10397 4.475135 GGAAGAGCACCCCTCCGC 62.475 72.222 0.00 0.00 41.74 5.54
4421 10399 1.604915 GAAGGAAGAGCACCCCTCC 59.395 63.158 0.00 0.00 41.74 4.30
4524 10502 3.269347 CCCTTTCATACCGCCGCG 61.269 66.667 5.59 5.59 0.00 6.46
4532 10510 2.243810 GCAACCCACAACCCTTTCATA 58.756 47.619 0.00 0.00 0.00 2.15
4563 10548 1.303561 TCCCTGCCAATGACACAGC 60.304 57.895 0.00 0.00 0.00 4.40
4565 10550 1.302431 CGTCCCTGCCAATGACACA 60.302 57.895 0.00 0.00 0.00 3.72
4584 10569 1.793134 GATCCGATACGCACCCGTCT 61.793 60.000 0.00 0.00 46.39 4.18


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

AutoCloner maintained by Alex Coulton.