Multiple sequence alignment - TraesCS3D01G254400

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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 TraesCS3D01G254400 chr3D 100.000 3436 0 0 1 3436 355797115 355793680 0.000000e+00 6346.0
1 TraesCS3D01G254400 chr3D 87.082 867 81 18 2584 3436 548978419 548977570 0.000000e+00 952.0
2 TraesCS3D01G254400 chr3D 85.698 881 89 24 2575 3436 554035103 554034241 0.000000e+00 894.0
3 TraesCS3D01G254400 chr3D 87.724 391 48 0 1708 2098 23744723 23745113 1.120000e-124 457.0
4 TraesCS3D01G254400 chr3D 83.436 326 43 6 963 1285 23743991 23744308 3.350000e-75 292.0
5 TraesCS3D01G254400 chr3D 82.019 317 46 7 972 1285 23746315 23746623 3.400000e-65 259.0
6 TraesCS3D01G254400 chr3A 94.553 2313 99 19 289 2584 474812770 474810468 0.000000e+00 3548.0
7 TraesCS3D01G254400 chr3A 87.514 865 94 10 2584 3436 579648415 579647553 0.000000e+00 987.0
8 TraesCS3D01G254400 chr3A 86.191 869 82 23 2584 3436 686275057 686274211 0.000000e+00 905.0
9 TraesCS3D01G254400 chr3B 94.082 2315 99 18 280 2570 456982559 456980259 0.000000e+00 3482.0
10 TraesCS3D01G254400 chr3B 88.092 865 78 11 2584 3436 136103430 136104281 0.000000e+00 1003.0
11 TraesCS3D01G254400 chr3B 85.829 868 88 22 2584 3436 728291066 728290219 0.000000e+00 889.0
12 TraesCS3D01G254400 chr3B 80.720 778 92 25 1345 2122 41857381 41858100 1.390000e-153 553.0
13 TraesCS3D01G254400 chr3B 87.864 206 25 0 1080 1285 41857071 41857276 3.430000e-60 243.0
14 TraesCS3D01G254400 chr2B 84.395 1538 170 40 937 2440 144078575 144077074 0.000000e+00 1447.0
15 TraesCS3D01G254400 chr2B 85.623 786 77 25 1343 2122 144034724 144035479 0.000000e+00 793.0
16 TraesCS3D01G254400 chr2B 83.207 661 75 23 1467 2122 143969220 143969849 1.070000e-159 573.0
17 TraesCS3D01G254400 chr2B 87.383 214 24 2 2230 2440 144035496 144035709 3.430000e-60 243.0
18 TraesCS3D01G254400 chr7D 87.687 869 91 10 2580 3436 638314888 638315752 0.000000e+00 998.0
19 TraesCS3D01G254400 chr7D 85.862 870 82 23 2584 3436 180762257 180761412 0.000000e+00 887.0
20 TraesCS3D01G254400 chr7A 87.529 866 90 13 2584 3436 52433239 52434099 0.000000e+00 985.0
21 TraesCS3D01G254400 chr7A 86.605 866 95 16 2583 3436 27714845 27715701 0.000000e+00 937.0
22 TraesCS3D01G254400 chr7A 81.595 163 18 11 2575 2730 719746624 719746467 1.290000e-24 124.0
23 TraesCS3D01G254400 chr6D 87.543 867 88 15 2582 3436 372351756 372350898 0.000000e+00 985.0
24 TraesCS3D01G254400 chr2D 87.372 879 81 18 2572 3436 579072191 579071329 0.000000e+00 981.0
25 TraesCS3D01G254400 chr2D 83.317 1019 123 25 937 1938 92891476 92892464 0.000000e+00 896.0
26 TraesCS3D01G254400 chr2D 85.172 870 103 20 2584 3435 94717448 94718309 0.000000e+00 869.0
27 TraesCS3D01G254400 chr2D 85.369 786 82 22 1343 2122 92832185 92832943 0.000000e+00 784.0
28 TraesCS3D01G254400 chr2D 91.358 405 35 0 1717 2121 92889411 92889815 3.870000e-154 555.0
29 TraesCS3D01G254400 chr2D 88.670 406 37 3 2581 2978 591119671 591120075 1.430000e-133 486.0
30 TraesCS3D01G254400 chr2D 90.438 251 24 0 1870 2120 92863337 92863587 7.110000e-87 331.0
31 TraesCS3D01G254400 chr2D 88.722 266 21 3 1936 2194 92909759 92910022 1.990000e-82 316.0
32 TraesCS3D01G254400 chr2D 91.364 220 18 1 2218 2437 92912162 92912380 2.000000e-77 300.0
33 TraesCS3D01G254400 chr2D 79.500 400 74 6 1730 2122 92737190 92737588 9.390000e-71 278.0
34 TraesCS3D01G254400 chr2D 89.815 216 22 0 1068 1283 92831856 92832071 9.390000e-71 278.0
35 TraesCS3D01G254400 chr2D 90.000 200 20 0 2241 2440 92832971 92833170 3.400000e-65 259.0
36 TraesCS3D01G254400 chr2D 88.208 212 24 1 2230 2440 92863606 92863817 5.690000e-63 252.0
37 TraesCS3D01G254400 chr2D 85.135 148 21 1 2289 2435 92737693 92737840 2.140000e-32 150.0
38 TraesCS3D01G254400 chr1D 86.997 869 90 15 2580 3436 430064620 430063763 0.000000e+00 957.0
39 TraesCS3D01G254400 chr1D 90.283 247 19 4 46 290 452525658 452525901 5.530000e-83 318.0
40 TraesCS3D01G254400 chr5A 93.323 629 30 8 1962 2584 627486372 627485750 0.000000e+00 918.0
41 TraesCS3D01G254400 chr7B 87.010 816 84 17 2629 3436 594058405 594059206 0.000000e+00 900.0
42 TraesCS3D01G254400 chr7B 91.983 237 17 2 47 281 543042659 543042423 7.110000e-87 331.0
43 TraesCS3D01G254400 chr7B 91.845 233 17 1 48 280 598841111 598841341 1.190000e-84 324.0
44 TraesCS3D01G254400 chr7B 79.730 296 48 7 293 577 567798872 567799166 1.620000e-48 204.0
45 TraesCS3D01G254400 chr7B 78.065 155 30 4 2578 2731 750213364 750213213 1.020000e-15 95.3
46 TraesCS3D01G254400 chr5D 85.363 854 96 15 2584 3423 486093195 486094033 0.000000e+00 857.0
47 TraesCS3D01G254400 chr5D 78.804 184 35 4 2574 2756 382968846 382968666 1.670000e-23 121.0
48 TraesCS3D01G254400 chr5B 92.050 239 16 3 48 283 105072257 105072495 1.980000e-87 333.0
49 TraesCS3D01G254400 chr4B 91.667 240 14 4 47 281 311018934 311019172 9.190000e-86 327.0
50 TraesCS3D01G254400 chr4B 91.597 238 17 1 43 280 399290010 399290244 3.310000e-85 326.0
51 TraesCS3D01G254400 chr2A 91.701 241 13 3 47 281 280966332 280966571 9.190000e-86 327.0
52 TraesCS3D01G254400 chr6A 91.880 234 17 1 47 280 319442111 319441880 3.310000e-85 326.0
53 TraesCS3D01G254400 chr6A 95.000 40 2 0 2574 2613 428660979 428661018 2.860000e-06 63.9
54 TraesCS3D01G254400 chr4A 91.880 234 16 1 47 280 55822750 55822520 1.190000e-84 324.0
55 TraesCS3D01G254400 chr1B 76.418 564 100 20 2576 3114 27159290 27158735 1.210000e-69 274.0
56 TraesCS3D01G254400 chr6B 100.000 36 0 0 2578 2613 445886772 445886807 2.210000e-07 67.6


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 TraesCS3D01G254400 chr3D 355793680 355797115 3435 True 6346.000000 6346 100.000000 1 3436 1 chr3D.!!$R1 3435
1 TraesCS3D01G254400 chr3D 548977570 548978419 849 True 952.000000 952 87.082000 2584 3436 1 chr3D.!!$R2 852
2 TraesCS3D01G254400 chr3D 554034241 554035103 862 True 894.000000 894 85.698000 2575 3436 1 chr3D.!!$R3 861
3 TraesCS3D01G254400 chr3D 23743991 23746623 2632 False 336.000000 457 84.393000 963 2098 3 chr3D.!!$F1 1135
4 TraesCS3D01G254400 chr3A 474810468 474812770 2302 True 3548.000000 3548 94.553000 289 2584 1 chr3A.!!$R1 2295
5 TraesCS3D01G254400 chr3A 579647553 579648415 862 True 987.000000 987 87.514000 2584 3436 1 chr3A.!!$R2 852
6 TraesCS3D01G254400 chr3A 686274211 686275057 846 True 905.000000 905 86.191000 2584 3436 1 chr3A.!!$R3 852
7 TraesCS3D01G254400 chr3B 456980259 456982559 2300 True 3482.000000 3482 94.082000 280 2570 1 chr3B.!!$R1 2290
8 TraesCS3D01G254400 chr3B 136103430 136104281 851 False 1003.000000 1003 88.092000 2584 3436 1 chr3B.!!$F1 852
9 TraesCS3D01G254400 chr3B 728290219 728291066 847 True 889.000000 889 85.829000 2584 3436 1 chr3B.!!$R2 852
10 TraesCS3D01G254400 chr3B 41857071 41858100 1029 False 398.000000 553 84.292000 1080 2122 2 chr3B.!!$F2 1042
11 TraesCS3D01G254400 chr2B 144077074 144078575 1501 True 1447.000000 1447 84.395000 937 2440 1 chr2B.!!$R1 1503
12 TraesCS3D01G254400 chr2B 143969220 143969849 629 False 573.000000 573 83.207000 1467 2122 1 chr2B.!!$F1 655
13 TraesCS3D01G254400 chr2B 144034724 144035709 985 False 518.000000 793 86.503000 1343 2440 2 chr2B.!!$F2 1097
14 TraesCS3D01G254400 chr7D 638314888 638315752 864 False 998.000000 998 87.687000 2580 3436 1 chr7D.!!$F1 856
15 TraesCS3D01G254400 chr7D 180761412 180762257 845 True 887.000000 887 85.862000 2584 3436 1 chr7D.!!$R1 852
16 TraesCS3D01G254400 chr7A 52433239 52434099 860 False 985.000000 985 87.529000 2584 3436 1 chr7A.!!$F2 852
17 TraesCS3D01G254400 chr7A 27714845 27715701 856 False 937.000000 937 86.605000 2583 3436 1 chr7A.!!$F1 853
18 TraesCS3D01G254400 chr6D 372350898 372351756 858 True 985.000000 985 87.543000 2582 3436 1 chr6D.!!$R1 854
19 TraesCS3D01G254400 chr2D 579071329 579072191 862 True 981.000000 981 87.372000 2572 3436 1 chr2D.!!$R1 864
20 TraesCS3D01G254400 chr2D 94717448 94718309 861 False 869.000000 869 85.172000 2584 3435 1 chr2D.!!$F1 851
21 TraesCS3D01G254400 chr2D 92889411 92892464 3053 False 725.500000 896 87.337500 937 2121 2 chr2D.!!$F6 1184
22 TraesCS3D01G254400 chr2D 92831856 92833170 1314 False 440.333333 784 88.394667 1068 2440 3 chr2D.!!$F4 1372
23 TraesCS3D01G254400 chr2D 92909759 92912380 2621 False 308.000000 316 90.043000 1936 2437 2 chr2D.!!$F7 501
24 TraesCS3D01G254400 chr2D 92737190 92737840 650 False 214.000000 278 82.317500 1730 2435 2 chr2D.!!$F3 705
25 TraesCS3D01G254400 chr1D 430063763 430064620 857 True 957.000000 957 86.997000 2580 3436 1 chr1D.!!$R1 856
26 TraesCS3D01G254400 chr5A 627485750 627486372 622 True 918.000000 918 93.323000 1962 2584 1 chr5A.!!$R1 622
27 TraesCS3D01G254400 chr7B 594058405 594059206 801 False 900.000000 900 87.010000 2629 3436 1 chr7B.!!$F2 807
28 TraesCS3D01G254400 chr5D 486093195 486094033 838 False 857.000000 857 85.363000 2584 3423 1 chr5D.!!$F1 839
29 TraesCS3D01G254400 chr1B 27158735 27159290 555 True 274.000000 274 76.418000 2576 3114 1 chr1B.!!$R1 538

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
99 100 0.033796 ATGGTGTTCCTGCCATCCTG 60.034 55.0 0.0 0.0 41.24 3.86 F
103 104 0.040058 TGTTCCTGCCATCCTGCAAT 59.960 50.0 0.0 0.0 41.51 3.56 F
173 174 0.104882 TTGTACCACACCCCTCTCCA 60.105 55.0 0.0 0.0 0.00 3.86 F
176 177 0.118346 TACCACACCCCTCTCCACAT 59.882 55.0 0.0 0.0 0.00 3.21 F
481 482 0.181114 CAAGGATGAGGATCGGGCAA 59.819 55.0 0.0 0.0 38.61 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 3068 1.135139 CGATGGACAGAACGATGGACT 59.865 52.381 0.00 0.0 0.00 3.85 R
1872 3092 2.496341 CGCCCAGCTCGATCAGAA 59.504 61.111 0.00 0.0 0.00 3.02 R
2172 3405 0.729116 GCCGTTCTGGACATGATGTG 59.271 55.000 1.23 0.0 42.00 3.21 R
2173 3406 0.615331 AGCCGTTCTGGACATGATGT 59.385 50.000 0.00 0.0 42.00 3.06 R
2492 5896 9.507329 AGTACTATTGATGACACTTTGACAATT 57.493 29.630 0.00 0.0 31.85 2.32 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
27 28 9.149225 CTGTTCATATAGCTTCCAATCTATCAC 57.851 37.037 0.00 0.00 0.00 3.06
29 30 6.867550 TCATATAGCTTCCAATCTATCACCG 58.132 40.000 0.00 0.00 0.00 4.94
31 32 1.202698 AGCTTCCAATCTATCACCGCC 60.203 52.381 0.00 0.00 0.00 6.13
33 34 1.140852 CTTCCAATCTATCACCGCCCA 59.859 52.381 0.00 0.00 0.00 5.36
34 35 0.468226 TCCAATCTATCACCGCCCAC 59.532 55.000 0.00 0.00 0.00 4.61
35 36 0.880278 CCAATCTATCACCGCCCACG 60.880 60.000 0.00 0.00 39.67 4.94
45 46 3.607163 CGCCCACGGGTAGTAAGA 58.393 61.111 3.54 0.00 37.65 2.10
46 47 1.892338 CGCCCACGGGTAGTAAGAA 59.108 57.895 3.54 0.00 37.65 2.52
47 48 0.462789 CGCCCACGGGTAGTAAGAAT 59.537 55.000 3.54 0.00 37.65 2.40
48 49 1.537562 CGCCCACGGGTAGTAAGAATC 60.538 57.143 3.54 0.00 37.65 2.52
49 50 1.761198 GCCCACGGGTAGTAAGAATCT 59.239 52.381 3.54 0.00 37.65 2.40
50 51 2.223994 GCCCACGGGTAGTAAGAATCTC 60.224 54.545 3.54 0.00 37.65 2.75
52 53 4.467769 CCCACGGGTAGTAAGAATCTCTA 58.532 47.826 0.00 0.00 0.00 2.43
53 54 4.277921 CCCACGGGTAGTAAGAATCTCTAC 59.722 50.000 0.00 1.70 34.93 2.59
54 55 5.131784 CCACGGGTAGTAAGAATCTCTACT 58.868 45.833 8.44 8.77 35.69 2.57
56 57 6.056884 CACGGGTAGTAAGAATCTCTACTCT 58.943 44.000 7.22 0.00 34.23 3.24
58 59 7.714377 CACGGGTAGTAAGAATCTCTACTCTTA 59.286 40.741 7.22 0.00 34.23 2.10
59 60 8.439172 ACGGGTAGTAAGAATCTCTACTCTTAT 58.561 37.037 7.22 0.00 36.72 1.73
83 84 5.458041 AAAAACAGAGTTGGTGATGATGG 57.542 39.130 0.00 0.00 0.00 3.51
84 85 3.795688 AACAGAGTTGGTGATGATGGT 57.204 42.857 0.00 0.00 0.00 3.55
86 87 2.373169 ACAGAGTTGGTGATGATGGTGT 59.627 45.455 0.00 0.00 0.00 4.16
87 88 3.181440 ACAGAGTTGGTGATGATGGTGTT 60.181 43.478 0.00 0.00 0.00 3.32
89 90 2.749621 GAGTTGGTGATGATGGTGTTCC 59.250 50.000 0.00 0.00 0.00 3.62
90 91 2.376518 AGTTGGTGATGATGGTGTTCCT 59.623 45.455 0.00 0.00 34.23 3.36
92 93 1.098050 GGTGATGATGGTGTTCCTGC 58.902 55.000 0.00 0.00 34.23 4.85
94 95 0.697658 TGATGATGGTGTTCCTGCCA 59.302 50.000 0.00 0.00 39.33 4.92
98 99 2.402238 ATGGTGTTCCTGCCATCCT 58.598 52.632 0.00 0.00 41.24 3.24
99 100 0.033796 ATGGTGTTCCTGCCATCCTG 60.034 55.000 0.00 0.00 41.24 3.86
100 101 2.048603 GGTGTTCCTGCCATCCTGC 61.049 63.158 0.00 0.00 0.00 4.85
101 102 1.303561 GTGTTCCTGCCATCCTGCA 60.304 57.895 0.00 0.00 39.37 4.41
102 103 0.895100 GTGTTCCTGCCATCCTGCAA 60.895 55.000 0.00 0.00 41.51 4.08
103 104 0.040058 TGTTCCTGCCATCCTGCAAT 59.960 50.000 0.00 0.00 41.51 3.56
104 105 1.284491 TGTTCCTGCCATCCTGCAATA 59.716 47.619 0.00 0.00 41.51 1.90
106 107 3.138098 TGTTCCTGCCATCCTGCAATATA 59.862 43.478 0.00 0.00 41.51 0.86
107 108 4.202599 TGTTCCTGCCATCCTGCAATATAT 60.203 41.667 0.00 0.00 41.51 0.86
129 130 8.883954 ATATGCCATCTGATTTATATCTGACG 57.116 34.615 5.18 0.00 40.26 4.35
130 131 5.482006 TGCCATCTGATTTATATCTGACGG 58.518 41.667 9.68 9.68 41.96 4.79
132 133 6.070596 TGCCATCTGATTTATATCTGACGGAT 60.071 38.462 15.73 1.60 41.74 4.18
133 134 7.124147 TGCCATCTGATTTATATCTGACGGATA 59.876 37.037 15.73 6.45 41.74 2.59
134 135 7.651304 GCCATCTGATTTATATCTGACGGATAG 59.349 40.741 15.73 0.00 41.74 2.08
135 136 8.140628 CCATCTGATTTATATCTGACGGATAGG 58.859 40.741 9.78 0.00 41.74 2.57
136 137 8.907885 CATCTGATTTATATCTGACGGATAGGA 58.092 37.037 9.78 0.00 40.26 2.94
138 139 8.961634 TCTGATTTATATCTGACGGATAGGAAG 58.038 37.037 9.78 2.74 39.89 3.46
139 140 8.067751 TGATTTATATCTGACGGATAGGAAGG 57.932 38.462 9.78 0.00 39.89 3.46
140 141 7.893833 TGATTTATATCTGACGGATAGGAAGGA 59.106 37.037 9.78 0.00 39.89 3.36
141 142 8.666129 ATTTATATCTGACGGATAGGAAGGAA 57.334 34.615 9.78 0.15 39.89 3.36
142 143 8.486942 TTTATATCTGACGGATAGGAAGGAAA 57.513 34.615 9.78 1.82 39.89 3.13
145 146 4.863548 TCTGACGGATAGGAAGGAAACTA 58.136 43.478 0.00 0.00 42.68 2.24
147 148 5.302059 TCTGACGGATAGGAAGGAAACTATG 59.698 44.000 0.00 0.00 42.68 2.23
148 149 4.960469 TGACGGATAGGAAGGAAACTATGT 59.040 41.667 0.00 0.00 42.68 2.29
149 150 5.068723 TGACGGATAGGAAGGAAACTATGTC 59.931 44.000 0.00 0.00 42.68 3.06
150 151 4.960469 ACGGATAGGAAGGAAACTATGTCA 59.040 41.667 0.00 0.00 42.68 3.58
151 152 5.424252 ACGGATAGGAAGGAAACTATGTCAA 59.576 40.000 0.00 0.00 42.68 3.18
152 153 6.099845 ACGGATAGGAAGGAAACTATGTCAAT 59.900 38.462 0.00 0.00 42.68 2.57
153 154 6.992715 CGGATAGGAAGGAAACTATGTCAATT 59.007 38.462 0.00 0.00 42.68 2.32
154 155 7.499232 CGGATAGGAAGGAAACTATGTCAATTT 59.501 37.037 0.00 0.00 42.68 1.82
155 156 9.190317 GGATAGGAAGGAAACTATGTCAATTTT 57.810 33.333 0.00 0.00 42.68 1.82
157 158 7.839680 AGGAAGGAAACTATGTCAATTTTGT 57.160 32.000 0.00 0.00 42.68 2.83
158 159 8.934023 AGGAAGGAAACTATGTCAATTTTGTA 57.066 30.769 0.00 0.00 42.68 2.41
159 160 8.793592 AGGAAGGAAACTATGTCAATTTTGTAC 58.206 33.333 0.00 0.00 42.68 2.90
160 161 8.027189 GGAAGGAAACTATGTCAATTTTGTACC 58.973 37.037 0.00 0.00 42.68 3.34
161 162 8.472007 AAGGAAACTATGTCAATTTTGTACCA 57.528 30.769 0.00 0.00 42.68 3.25
162 163 7.882179 AGGAAACTATGTCAATTTTGTACCAC 58.118 34.615 0.00 0.00 40.61 4.16
163 164 7.504238 AGGAAACTATGTCAATTTTGTACCACA 59.496 33.333 0.00 0.00 40.61 4.17
164 165 7.593644 GGAAACTATGTCAATTTTGTACCACAC 59.406 37.037 0.00 0.00 0.00 3.82
165 166 6.569179 ACTATGTCAATTTTGTACCACACC 57.431 37.500 0.00 0.00 0.00 4.16
166 167 4.864704 ATGTCAATTTTGTACCACACCC 57.135 40.909 0.00 0.00 0.00 4.61
170 171 3.139397 TCAATTTTGTACCACACCCCTCT 59.861 43.478 0.00 0.00 0.00 3.69
171 172 2.943036 TTTTGTACCACACCCCTCTC 57.057 50.000 0.00 0.00 0.00 3.20
173 174 0.104882 TTGTACCACACCCCTCTCCA 60.105 55.000 0.00 0.00 0.00 3.86
175 176 0.834687 GTACCACACCCCTCTCCACA 60.835 60.000 0.00 0.00 0.00 4.17
176 177 0.118346 TACCACACCCCTCTCCACAT 59.882 55.000 0.00 0.00 0.00 3.21
177 178 0.772124 ACCACACCCCTCTCCACATT 60.772 55.000 0.00 0.00 0.00 2.71
178 179 0.405585 CCACACCCCTCTCCACATTT 59.594 55.000 0.00 0.00 0.00 2.32
179 180 1.538047 CACACCCCTCTCCACATTTG 58.462 55.000 0.00 0.00 0.00 2.32
181 182 0.251297 CACCCCTCTCCACATTTGCA 60.251 55.000 0.00 0.00 0.00 4.08
183 184 1.133199 ACCCCTCTCCACATTTGCAAA 60.133 47.619 15.44 15.44 0.00 3.68
184 185 2.181975 CCCCTCTCCACATTTGCAAAT 58.818 47.619 18.99 18.99 0.00 2.32
185 186 3.245586 ACCCCTCTCCACATTTGCAAATA 60.246 43.478 23.69 8.18 0.00 1.40
187 188 4.142093 CCCCTCTCCACATTTGCAAATAAG 60.142 45.833 23.69 17.76 0.00 1.73
189 190 4.427312 CTCTCCACATTTGCAAATAAGGC 58.573 43.478 23.69 0.00 0.00 4.35
190 191 3.831333 TCTCCACATTTGCAAATAAGGCA 59.169 39.130 23.69 14.31 40.00 4.75
191 192 4.467082 TCTCCACATTTGCAAATAAGGCAT 59.533 37.500 23.69 0.00 41.58 4.40
192 193 5.046448 TCTCCACATTTGCAAATAAGGCATT 60.046 36.000 23.69 0.00 41.58 3.56
193 194 5.177326 TCCACATTTGCAAATAAGGCATTC 58.823 37.500 23.69 0.00 41.58 2.67
194 195 4.333372 CCACATTTGCAAATAAGGCATTCC 59.667 41.667 23.69 0.00 41.58 3.01
195 196 4.333372 CACATTTGCAAATAAGGCATTCCC 59.667 41.667 23.69 0.00 41.58 3.97
197 198 4.470334 TTTGCAAATAAGGCATTCCCTC 57.530 40.909 8.05 0.00 45.62 4.30
198 199 2.023673 TGCAAATAAGGCATTCCCTCG 58.976 47.619 0.00 0.00 45.62 4.63
199 200 2.024414 GCAAATAAGGCATTCCCTCGT 58.976 47.619 0.00 0.00 45.62 4.18
201 202 3.489229 GCAAATAAGGCATTCCCTCGTTC 60.489 47.826 0.00 0.00 45.62 3.95
202 203 3.644966 AATAAGGCATTCCCTCGTTCA 57.355 42.857 0.00 0.00 45.62 3.18
203 204 3.864789 ATAAGGCATTCCCTCGTTCAT 57.135 42.857 0.00 0.00 45.62 2.57
205 206 1.207791 AGGCATTCCCTCGTTCATCT 58.792 50.000 0.00 0.00 41.21 2.90
206 207 1.561542 AGGCATTCCCTCGTTCATCTT 59.438 47.619 0.00 0.00 41.21 2.40
208 209 2.755103 GGCATTCCCTCGTTCATCTTTT 59.245 45.455 0.00 0.00 0.00 2.27
209 210 3.193479 GGCATTCCCTCGTTCATCTTTTT 59.807 43.478 0.00 0.00 0.00 1.94
210 211 4.415735 GCATTCCCTCGTTCATCTTTTTC 58.584 43.478 0.00 0.00 0.00 2.29
211 212 4.156739 GCATTCCCTCGTTCATCTTTTTCT 59.843 41.667 0.00 0.00 0.00 2.52
212 213 5.674820 GCATTCCCTCGTTCATCTTTTTCTC 60.675 44.000 0.00 0.00 0.00 2.87
213 214 3.939066 TCCCTCGTTCATCTTTTTCTCC 58.061 45.455 0.00 0.00 0.00 3.71
217 218 4.065088 CTCGTTCATCTTTTTCTCCCACA 58.935 43.478 0.00 0.00 0.00 4.17
218 219 4.456535 TCGTTCATCTTTTTCTCCCACAA 58.543 39.130 0.00 0.00 0.00 3.33
219 220 4.515191 TCGTTCATCTTTTTCTCCCACAAG 59.485 41.667 0.00 0.00 0.00 3.16
220 221 4.515191 CGTTCATCTTTTTCTCCCACAAGA 59.485 41.667 0.00 0.00 0.00 3.02
221 222 5.182001 CGTTCATCTTTTTCTCCCACAAGAT 59.818 40.000 0.00 0.00 36.59 2.40
223 224 7.094805 CGTTCATCTTTTTCTCCCACAAGATAA 60.095 37.037 0.00 0.00 34.80 1.75
224 225 8.576442 GTTCATCTTTTTCTCCCACAAGATAAA 58.424 33.333 0.00 0.00 34.80 1.40
225 226 8.110860 TCATCTTTTTCTCCCACAAGATAAAC 57.889 34.615 0.00 0.00 34.80 2.01
226 227 7.944554 TCATCTTTTTCTCCCACAAGATAAACT 59.055 33.333 0.00 0.00 34.80 2.66
227 228 9.231297 CATCTTTTTCTCCCACAAGATAAACTA 57.769 33.333 0.00 0.00 34.80 2.24
228 229 9.807921 ATCTTTTTCTCCCACAAGATAAACTAA 57.192 29.630 0.00 0.00 34.80 2.24
229 230 9.807921 TCTTTTTCTCCCACAAGATAAACTAAT 57.192 29.630 0.00 0.00 0.00 1.73
231 232 9.581289 TTTTTCTCCCACAAGATAAACTAATCA 57.419 29.630 0.00 0.00 0.00 2.57
232 233 9.753674 TTTTCTCCCACAAGATAAACTAATCAT 57.246 29.630 0.00 0.00 0.00 2.45
234 235 9.832445 TTCTCCCACAAGATAAACTAATCATAC 57.168 33.333 0.00 0.00 0.00 2.39
235 236 8.988060 TCTCCCACAAGATAAACTAATCATACA 58.012 33.333 0.00 0.00 0.00 2.29
236 237 9.613428 CTCCCACAAGATAAACTAATCATACAA 57.387 33.333 0.00 0.00 0.00 2.41
237 238 9.967451 TCCCACAAGATAAACTAATCATACAAA 57.033 29.630 0.00 0.00 0.00 2.83
249 250 9.961265 AACTAATCATACAAATGCATCTTGATG 57.039 29.630 20.96 18.39 32.76 3.07
250 251 9.128404 ACTAATCATACAAATGCATCTTGATGT 57.872 29.630 20.96 14.21 32.76 3.06
251 252 9.961265 CTAATCATACAAATGCATCTTGATGTT 57.039 29.630 20.96 16.78 32.76 2.71
252 253 8.867112 AATCATACAAATGCATCTTGATGTTC 57.133 30.769 20.96 0.00 32.76 3.18
255 256 3.507233 ACAAATGCATCTTGATGTTCCGT 59.493 39.130 20.96 2.07 0.00 4.69
256 257 3.770263 AATGCATCTTGATGTTCCGTG 57.230 42.857 0.00 0.00 0.00 4.94
258 259 0.804364 GCATCTTGATGTTCCGTGCA 59.196 50.000 11.61 0.00 0.00 4.57
259 260 1.199789 GCATCTTGATGTTCCGTGCAA 59.800 47.619 11.61 0.00 0.00 4.08
260 261 2.855180 CATCTTGATGTTCCGTGCAAC 58.145 47.619 0.00 0.00 0.00 4.17
272 273 2.361483 TGCAACGCATGGGCATCT 60.361 55.556 10.10 0.00 41.24 2.90
274 275 1.517694 GCAACGCATGGGCATCTTG 60.518 57.895 10.10 7.97 41.24 3.02
276 277 1.679977 AACGCATGGGCATCTTGCT 60.680 52.632 10.10 0.00 44.28 3.91
277 278 0.394216 AACGCATGGGCATCTTGCTA 60.394 50.000 10.10 0.00 44.28 3.49
278 279 0.816825 ACGCATGGGCATCTTGCTAG 60.817 55.000 10.10 0.00 44.28 3.42
286 287 5.366482 TGGGCATCTTGCTAGTATGTTTA 57.634 39.130 0.00 0.00 44.28 2.01
312 313 1.300697 GTTACTAGGGCGCATCCGG 60.301 63.158 10.83 0.00 34.94 5.14
334 335 2.802816 AGTTGAAGTGTCAGAATCGTGC 59.197 45.455 0.00 0.00 34.49 5.34
362 363 3.536158 TGCGCTTTACTTTGTGTCATC 57.464 42.857 9.73 0.00 0.00 2.92
449 450 3.942130 CATCAGCTGGATCCATACGTA 57.058 47.619 16.63 0.00 32.57 3.57
481 482 0.181114 CAAGGATGAGGATCGGGCAA 59.819 55.000 0.00 0.00 38.61 4.52
484 485 2.203070 ATGAGGATCGGGCAACGC 60.203 61.111 0.00 0.00 43.86 4.84
503 504 1.731433 CCTTTGGATGCAGCCGATGG 61.731 60.000 24.42 24.42 32.19 3.51
719 729 3.257469 CATCACTTGCAGAGGCTAAGA 57.743 47.619 1.89 0.00 41.91 2.10
841 853 6.183309 ACGATTTCAAAATGTTAGAGCTCC 57.817 37.500 10.93 0.00 0.00 4.70
860 872 5.481824 AGCTCCCATCGTGATGAAATAGATA 59.518 40.000 11.35 0.00 41.20 1.98
1551 2760 1.528542 CTCCCTCGGCGTCCAGATA 60.529 63.158 6.85 0.00 0.00 1.98
1872 3092 1.135139 CATCGTTCTGTCCATCGAGGT 59.865 52.381 0.00 0.00 39.02 3.85
2163 3396 1.772182 CGCTAGCAAGAATCCTACCG 58.228 55.000 16.45 0.00 0.00 4.02
2215 3457 7.798982 GGCTTTGATCTTACTGTATATTTTCGC 59.201 37.037 0.00 0.00 0.00 4.70
2566 5977 6.880529 AGCACCTCCATTTTTCCAATAAATTG 59.119 34.615 0.00 0.00 37.52 2.32
2719 6134 1.169577 GAGCTGTGGTCTTCTCTCGA 58.830 55.000 0.00 0.00 0.00 4.04
2786 6205 1.890510 GGCGACGACCAACCAACTT 60.891 57.895 0.00 0.00 0.00 2.66
2794 6215 2.303175 GACCAACCAACTTGTGCCTTA 58.697 47.619 0.00 0.00 0.00 2.69
2920 6390 5.705609 ACCGGATGGAATATTAATTGCAC 57.294 39.130 9.46 0.00 44.89 4.57
2942 6519 8.225107 TGCACTACGTAAATCAAGTTTCATTAC 58.775 33.333 0.00 0.00 0.00 1.89
3015 6597 6.494842 TCTTTGATTATTTTAGCGGTCATGC 58.505 36.000 0.00 0.00 0.00 4.06
3023 6605 0.762842 TAGCGGTCATGCCCCTACAT 60.763 55.000 0.00 0.00 34.65 2.29
3055 6641 2.097825 AGAGCCAATTCAGCATGTTCC 58.902 47.619 0.00 0.00 37.40 3.62
3133 6882 0.810648 ATCGTCAAATTGCGCATGGT 59.189 45.000 12.75 0.00 0.00 3.55
3146 6895 1.257936 CGCATGGTACGCACAATAGTC 59.742 52.381 0.00 0.00 0.00 2.59
3197 7465 4.773149 ACCAAAAGGACCTGTGTTTGTAAA 59.227 37.500 13.61 0.00 30.61 2.01
3255 7528 4.326548 GGATCGAACTCACGACCTAAAAAG 59.673 45.833 0.00 0.00 44.84 2.27
3301 7575 3.247648 CGAATAAATGGTCCTGCTTACCG 59.752 47.826 0.00 0.00 40.08 4.02
3351 7636 5.957798 ACTGCATCACCATATTCAAAACAG 58.042 37.500 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.149225 GTGATAGATTGGAAGCTATATGAACAG 57.851 37.037 0.00 0.00 37.71 3.16
6 7 5.521735 GCGGTGATAGATTGGAAGCTATATG 59.478 44.000 0.00 0.00 37.71 1.78
10 11 2.037251 GGCGGTGATAGATTGGAAGCTA 59.963 50.000 0.00 0.00 0.00 3.32
12 13 1.230324 GGCGGTGATAGATTGGAAGC 58.770 55.000 0.00 0.00 0.00 3.86
13 14 1.140852 TGGGCGGTGATAGATTGGAAG 59.859 52.381 0.00 0.00 0.00 3.46
14 15 1.134220 GTGGGCGGTGATAGATTGGAA 60.134 52.381 0.00 0.00 0.00 3.53
15 16 0.468226 GTGGGCGGTGATAGATTGGA 59.532 55.000 0.00 0.00 0.00 3.53
16 17 0.880278 CGTGGGCGGTGATAGATTGG 60.880 60.000 0.00 0.00 0.00 3.16
17 18 2.605094 CGTGGGCGGTGATAGATTG 58.395 57.895 0.00 0.00 0.00 2.67
29 30 1.761198 AGATTCTTACTACCCGTGGGC 59.239 52.381 4.41 0.00 39.32 5.36
31 32 5.131784 AGTAGAGATTCTTACTACCCGTGG 58.868 45.833 8.28 0.00 37.71 4.94
33 34 6.251255 AGAGTAGAGATTCTTACTACCCGT 57.749 41.667 8.28 0.00 37.71 5.28
34 35 8.851541 ATAAGAGTAGAGATTCTTACTACCCG 57.148 38.462 8.28 0.00 36.89 5.28
61 62 4.895297 ACCATCATCACCAACTCTGTTTTT 59.105 37.500 0.00 0.00 0.00 1.94
62 63 4.279169 CACCATCATCACCAACTCTGTTTT 59.721 41.667 0.00 0.00 0.00 2.43
64 65 3.181440 ACACCATCATCACCAACTCTGTT 60.181 43.478 0.00 0.00 0.00 3.16
65 66 2.373169 ACACCATCATCACCAACTCTGT 59.627 45.455 0.00 0.00 0.00 3.41
66 67 3.063510 ACACCATCATCACCAACTCTG 57.936 47.619 0.00 0.00 0.00 3.35
67 68 3.560025 GGAACACCATCATCACCAACTCT 60.560 47.826 0.00 0.00 0.00 3.24
68 69 2.749621 GGAACACCATCATCACCAACTC 59.250 50.000 0.00 0.00 0.00 3.01
70 71 2.489329 CAGGAACACCATCATCACCAAC 59.511 50.000 0.00 0.00 0.00 3.77
71 72 2.794103 CAGGAACACCATCATCACCAA 58.206 47.619 0.00 0.00 0.00 3.67
72 73 1.614051 GCAGGAACACCATCATCACCA 60.614 52.381 0.00 0.00 0.00 4.17
73 74 1.098050 GCAGGAACACCATCATCACC 58.902 55.000 0.00 0.00 0.00 4.02
74 75 1.098050 GGCAGGAACACCATCATCAC 58.902 55.000 0.00 0.00 0.00 3.06
75 76 0.697658 TGGCAGGAACACCATCATCA 59.302 50.000 0.00 0.00 31.77 3.07
76 77 2.062971 ATGGCAGGAACACCATCATC 57.937 50.000 0.00 0.00 42.69 2.92
83 84 0.895100 TTGCAGGATGGCAGGAACAC 60.895 55.000 0.00 0.00 45.88 3.32
84 85 0.040058 ATTGCAGGATGGCAGGAACA 59.960 50.000 0.00 0.00 45.88 3.18
86 87 4.338012 CATATATTGCAGGATGGCAGGAA 58.662 43.478 0.00 0.00 45.88 3.36
87 88 3.959293 CATATATTGCAGGATGGCAGGA 58.041 45.455 0.00 0.00 45.88 3.86
103 104 9.971922 CGTCAGATATAAATCAGATGGCATATA 57.028 33.333 0.00 0.00 33.29 0.86
104 105 7.930325 CCGTCAGATATAAATCAGATGGCATAT 59.070 37.037 0.00 0.00 43.68 1.78
106 107 6.070596 TCCGTCAGATATAAATCAGATGGCAT 60.071 38.462 0.00 0.00 46.74 4.40
107 108 5.245977 TCCGTCAGATATAAATCAGATGGCA 59.754 40.000 11.97 0.00 46.74 4.92
111 112 9.480861 TTCCTATCCGTCAGATATAAATCAGAT 57.519 33.333 0.00 0.00 36.84 2.90
112 113 8.879427 TTCCTATCCGTCAGATATAAATCAGA 57.121 34.615 0.00 0.00 36.84 3.27
115 116 8.294954 TCCTTCCTATCCGTCAGATATAAATC 57.705 38.462 0.00 0.00 36.84 2.17
116 117 8.666129 TTCCTTCCTATCCGTCAGATATAAAT 57.334 34.615 0.00 0.00 36.84 1.40
118 119 7.728981 AGTTTCCTTCCTATCCGTCAGATATAA 59.271 37.037 0.00 0.00 36.84 0.98
119 120 7.239438 AGTTTCCTTCCTATCCGTCAGATATA 58.761 38.462 0.00 0.00 36.84 0.86
120 121 6.078664 AGTTTCCTTCCTATCCGTCAGATAT 58.921 40.000 0.00 0.00 36.84 1.63
121 122 5.455872 AGTTTCCTTCCTATCCGTCAGATA 58.544 41.667 0.00 0.00 36.33 1.98
122 123 4.290942 AGTTTCCTTCCTATCCGTCAGAT 58.709 43.478 0.00 0.00 39.15 2.90
123 124 3.709587 AGTTTCCTTCCTATCCGTCAGA 58.290 45.455 0.00 0.00 0.00 3.27
124 125 5.069251 ACATAGTTTCCTTCCTATCCGTCAG 59.931 44.000 0.00 0.00 0.00 3.51
125 126 4.960469 ACATAGTTTCCTTCCTATCCGTCA 59.040 41.667 0.00 0.00 0.00 4.35
126 127 5.068723 TGACATAGTTTCCTTCCTATCCGTC 59.931 44.000 0.00 0.00 0.00 4.79
127 128 4.960469 TGACATAGTTTCCTTCCTATCCGT 59.040 41.667 0.00 0.00 0.00 4.69
128 129 5.531122 TGACATAGTTTCCTTCCTATCCG 57.469 43.478 0.00 0.00 0.00 4.18
129 130 8.753497 AAATTGACATAGTTTCCTTCCTATCC 57.247 34.615 0.00 0.00 0.00 2.59
132 133 8.934023 ACAAAATTGACATAGTTTCCTTCCTA 57.066 30.769 0.00 0.00 0.00 2.94
133 134 7.839680 ACAAAATTGACATAGTTTCCTTCCT 57.160 32.000 0.00 0.00 0.00 3.36
134 135 8.027189 GGTACAAAATTGACATAGTTTCCTTCC 58.973 37.037 0.00 0.00 0.00 3.46
135 136 8.573035 TGGTACAAAATTGACATAGTTTCCTTC 58.427 33.333 0.00 0.00 31.92 3.46
136 137 8.357402 GTGGTACAAAATTGACATAGTTTCCTT 58.643 33.333 0.00 0.00 44.16 3.36
138 139 7.593644 GTGTGGTACAAAATTGACATAGTTTCC 59.406 37.037 0.00 0.00 44.16 3.13
139 140 7.593644 GGTGTGGTACAAAATTGACATAGTTTC 59.406 37.037 0.00 0.00 44.16 2.78
140 141 7.430441 GGTGTGGTACAAAATTGACATAGTTT 58.570 34.615 0.00 0.00 44.16 2.66
141 142 6.015772 GGGTGTGGTACAAAATTGACATAGTT 60.016 38.462 0.00 0.00 44.16 2.24
142 143 5.475564 GGGTGTGGTACAAAATTGACATAGT 59.524 40.000 0.00 0.00 44.16 2.12
145 146 3.576550 GGGGTGTGGTACAAAATTGACAT 59.423 43.478 0.00 0.00 44.16 3.06
147 148 3.227614 AGGGGTGTGGTACAAAATTGAC 58.772 45.455 0.00 0.00 44.16 3.18
148 149 3.139397 AGAGGGGTGTGGTACAAAATTGA 59.861 43.478 0.00 0.00 44.16 2.57
149 150 3.496331 AGAGGGGTGTGGTACAAAATTG 58.504 45.455 0.00 0.00 44.16 2.32
150 151 3.499745 GGAGAGGGGTGTGGTACAAAATT 60.500 47.826 0.00 0.00 44.16 1.82
151 152 2.041216 GGAGAGGGGTGTGGTACAAAAT 59.959 50.000 0.00 0.00 44.16 1.82
152 153 1.422402 GGAGAGGGGTGTGGTACAAAA 59.578 52.381 0.00 0.00 44.16 2.44
153 154 1.061546 GGAGAGGGGTGTGGTACAAA 58.938 55.000 0.00 0.00 44.16 2.83
154 155 0.104882 TGGAGAGGGGTGTGGTACAA 60.105 55.000 0.00 0.00 44.16 2.41
155 156 0.834687 GTGGAGAGGGGTGTGGTACA 60.835 60.000 0.00 0.00 0.00 2.90
156 157 0.834687 TGTGGAGAGGGGTGTGGTAC 60.835 60.000 0.00 0.00 0.00 3.34
157 158 0.118346 ATGTGGAGAGGGGTGTGGTA 59.882 55.000 0.00 0.00 0.00 3.25
158 159 0.772124 AATGTGGAGAGGGGTGTGGT 60.772 55.000 0.00 0.00 0.00 4.16
159 160 0.405585 AAATGTGGAGAGGGGTGTGG 59.594 55.000 0.00 0.00 0.00 4.17
160 161 1.538047 CAAATGTGGAGAGGGGTGTG 58.462 55.000 0.00 0.00 0.00 3.82
161 162 0.251341 GCAAATGTGGAGAGGGGTGT 60.251 55.000 0.00 0.00 0.00 4.16
162 163 0.251297 TGCAAATGTGGAGAGGGGTG 60.251 55.000 0.00 0.00 0.00 4.61
163 164 0.482446 TTGCAAATGTGGAGAGGGGT 59.518 50.000 0.00 0.00 0.00 4.95
164 165 1.631405 TTTGCAAATGTGGAGAGGGG 58.369 50.000 8.05 0.00 0.00 4.79
165 166 4.142093 CCTTATTTGCAAATGTGGAGAGGG 60.142 45.833 30.43 17.11 0.00 4.30
166 167 4.678840 GCCTTATTTGCAAATGTGGAGAGG 60.679 45.833 31.67 25.73 0.00 3.69
170 171 4.822685 ATGCCTTATTTGCAAATGTGGA 57.177 36.364 31.67 22.57 42.92 4.02
171 172 4.333372 GGAATGCCTTATTTGCAAATGTGG 59.667 41.667 30.43 28.46 42.92 4.17
173 174 4.225717 AGGGAATGCCTTATTTGCAAATGT 59.774 37.500 30.43 12.33 42.92 2.71
175 176 4.441913 CGAGGGAATGCCTTATTTGCAAAT 60.442 41.667 26.72 26.72 42.92 2.32
176 177 3.119173 CGAGGGAATGCCTTATTTGCAAA 60.119 43.478 15.44 15.44 42.92 3.68
177 178 2.426738 CGAGGGAATGCCTTATTTGCAA 59.573 45.455 0.00 0.00 42.92 4.08
178 179 2.023673 CGAGGGAATGCCTTATTTGCA 58.976 47.619 0.00 0.00 43.97 4.08
179 180 2.024414 ACGAGGGAATGCCTTATTTGC 58.976 47.619 0.00 0.00 0.00 3.68
181 182 3.963129 TGAACGAGGGAATGCCTTATTT 58.037 40.909 0.00 0.00 0.00 1.40
183 184 3.392616 AGATGAACGAGGGAATGCCTTAT 59.607 43.478 0.00 0.00 0.00 1.73
184 185 2.771943 AGATGAACGAGGGAATGCCTTA 59.228 45.455 0.00 0.00 0.00 2.69
185 186 1.561542 AGATGAACGAGGGAATGCCTT 59.438 47.619 0.00 0.00 0.00 4.35
187 188 2.044123 AAGATGAACGAGGGAATGCC 57.956 50.000 0.00 0.00 0.00 4.40
189 190 5.163713 GGAGAAAAAGATGAACGAGGGAATG 60.164 44.000 0.00 0.00 0.00 2.67
190 191 4.944317 GGAGAAAAAGATGAACGAGGGAAT 59.056 41.667 0.00 0.00 0.00 3.01
191 192 4.324267 GGAGAAAAAGATGAACGAGGGAA 58.676 43.478 0.00 0.00 0.00 3.97
192 193 3.307480 GGGAGAAAAAGATGAACGAGGGA 60.307 47.826 0.00 0.00 0.00 4.20
193 194 3.010420 GGGAGAAAAAGATGAACGAGGG 58.990 50.000 0.00 0.00 0.00 4.30
194 195 3.437049 GTGGGAGAAAAAGATGAACGAGG 59.563 47.826 0.00 0.00 0.00 4.63
195 196 4.065088 TGTGGGAGAAAAAGATGAACGAG 58.935 43.478 0.00 0.00 0.00 4.18
196 197 4.079980 TGTGGGAGAAAAAGATGAACGA 57.920 40.909 0.00 0.00 0.00 3.85
197 198 4.515191 TCTTGTGGGAGAAAAAGATGAACG 59.485 41.667 0.00 0.00 0.00 3.95
198 199 6.581171 ATCTTGTGGGAGAAAAAGATGAAC 57.419 37.500 0.00 0.00 37.84 3.18
199 200 8.576442 GTTTATCTTGTGGGAGAAAAAGATGAA 58.424 33.333 6.95 3.02 39.20 2.57
201 202 8.115490 AGTTTATCTTGTGGGAGAAAAAGATG 57.885 34.615 6.95 0.00 39.20 2.90
202 203 9.807921 TTAGTTTATCTTGTGGGAGAAAAAGAT 57.192 29.630 0.00 0.00 41.18 2.40
203 204 9.807921 ATTAGTTTATCTTGTGGGAGAAAAAGA 57.192 29.630 0.00 0.00 29.99 2.52
205 206 9.581289 TGATTAGTTTATCTTGTGGGAGAAAAA 57.419 29.630 0.00 0.00 29.99 1.94
206 207 9.753674 ATGATTAGTTTATCTTGTGGGAGAAAA 57.246 29.630 0.00 0.00 29.99 2.29
208 209 9.832445 GTATGATTAGTTTATCTTGTGGGAGAA 57.168 33.333 0.00 0.00 0.00 2.87
209 210 8.988060 TGTATGATTAGTTTATCTTGTGGGAGA 58.012 33.333 0.00 0.00 0.00 3.71
210 211 9.613428 TTGTATGATTAGTTTATCTTGTGGGAG 57.387 33.333 0.00 0.00 0.00 4.30
211 212 9.967451 TTTGTATGATTAGTTTATCTTGTGGGA 57.033 29.630 0.00 0.00 0.00 4.37
223 224 9.961265 CATCAAGATGCATTTGTATGATTAGTT 57.039 29.630 0.00 0.00 33.37 2.24
224 225 9.128404 ACATCAAGATGCATTTGTATGATTAGT 57.872 29.630 22.17 13.28 42.39 2.24
225 226 9.961265 AACATCAAGATGCATTTGTATGATTAG 57.039 29.630 22.17 12.92 42.39 1.73
226 227 9.955208 GAACATCAAGATGCATTTGTATGATTA 57.045 29.630 22.17 8.59 42.39 1.75
227 228 7.924412 GGAACATCAAGATGCATTTGTATGATT 59.076 33.333 22.17 17.12 42.39 2.57
228 229 7.431249 GGAACATCAAGATGCATTTGTATGAT 58.569 34.615 22.17 16.27 42.39 2.45
229 230 6.458615 CGGAACATCAAGATGCATTTGTATGA 60.459 38.462 22.17 15.31 42.39 2.15
230 231 5.684184 CGGAACATCAAGATGCATTTGTATG 59.316 40.000 9.85 13.57 42.39 2.39
231 232 5.357878 ACGGAACATCAAGATGCATTTGTAT 59.642 36.000 9.85 1.80 42.39 2.29
232 233 4.699735 ACGGAACATCAAGATGCATTTGTA 59.300 37.500 9.85 0.00 42.39 2.41
233 234 3.507233 ACGGAACATCAAGATGCATTTGT 59.493 39.130 9.85 0.00 42.39 2.83
234 235 3.855379 CACGGAACATCAAGATGCATTTG 59.145 43.478 9.85 7.88 42.39 2.32
235 236 3.674138 GCACGGAACATCAAGATGCATTT 60.674 43.478 9.85 0.00 42.39 2.32
236 237 2.159338 GCACGGAACATCAAGATGCATT 60.159 45.455 9.85 0.00 42.39 3.56
237 238 1.402968 GCACGGAACATCAAGATGCAT 59.597 47.619 9.85 0.00 42.39 3.96
238 239 0.804364 GCACGGAACATCAAGATGCA 59.196 50.000 9.85 0.00 42.39 3.96
239 240 0.804364 TGCACGGAACATCAAGATGC 59.196 50.000 9.85 0.00 42.39 3.91
241 242 1.464608 CGTTGCACGGAACATCAAGAT 59.535 47.619 2.31 0.00 38.08 2.40
242 243 0.865111 CGTTGCACGGAACATCAAGA 59.135 50.000 2.31 0.00 38.08 3.02
243 244 0.725784 GCGTTGCACGGAACATCAAG 60.726 55.000 10.02 0.00 42.82 3.02
244 245 1.281353 GCGTTGCACGGAACATCAA 59.719 52.632 10.02 0.00 42.82 2.57
245 246 1.233950 ATGCGTTGCACGGAACATCA 61.234 50.000 6.93 0.00 46.78 3.07
246 247 0.794229 CATGCGTTGCACGGAACATC 60.794 55.000 6.93 0.00 46.78 3.06
247 248 1.209898 CATGCGTTGCACGGAACAT 59.790 52.632 6.93 2.04 46.78 2.71
248 249 2.636462 CATGCGTTGCACGGAACA 59.364 55.556 6.93 0.00 46.78 3.18
249 250 2.126888 CCATGCGTTGCACGGAAC 60.127 61.111 0.00 0.00 45.44 3.62
250 251 3.361158 CCCATGCGTTGCACGGAA 61.361 61.111 5.32 0.00 45.44 4.30
255 256 1.978080 AAGATGCCCATGCGTTGCA 60.978 52.632 2.57 2.57 44.86 4.08
256 257 1.517694 CAAGATGCCCATGCGTTGC 60.518 57.895 0.00 0.00 41.78 4.17
258 259 0.394216 TAGCAAGATGCCCATGCGTT 60.394 50.000 0.00 0.00 46.52 4.84
259 260 0.816825 CTAGCAAGATGCCCATGCGT 60.817 55.000 0.00 0.00 46.52 5.24
260 261 0.816825 ACTAGCAAGATGCCCATGCG 60.817 55.000 0.00 0.00 46.52 4.73
261 262 2.260844 TACTAGCAAGATGCCCATGC 57.739 50.000 0.00 0.00 46.52 4.06
264 265 3.931907 AACATACTAGCAAGATGCCCA 57.068 42.857 0.00 0.00 46.52 5.36
269 270 9.686683 ACCAATTTCTAAACATACTAGCAAGAT 57.313 29.630 0.00 0.00 0.00 2.40
270 271 9.515226 AACCAATTTCTAAACATACTAGCAAGA 57.485 29.630 0.00 0.00 0.00 3.02
277 278 9.901172 CCCTAGTAACCAATTTCTAAACATACT 57.099 33.333 0.00 0.00 0.00 2.12
278 279 8.618677 GCCCTAGTAACCAATTTCTAAACATAC 58.381 37.037 0.00 0.00 0.00 2.39
286 287 2.026636 TGCGCCCTAGTAACCAATTTCT 60.027 45.455 4.18 0.00 0.00 2.52
312 313 3.120854 GCACGATTCTGACACTTCAACTC 60.121 47.826 0.00 0.00 0.00 3.01
334 335 2.629639 AAGTAAAGCGCAAATTCCCG 57.370 45.000 11.47 0.00 0.00 5.14
449 450 0.246635 ATCCTTGCGCAGTAACGACT 59.753 50.000 11.31 0.00 35.80 4.18
459 460 1.958205 CCGATCCTCATCCTTGCGC 60.958 63.158 0.00 0.00 0.00 6.09
481 482 3.064324 GGCTGCATCCAAAGGCGT 61.064 61.111 0.55 0.00 34.08 5.68
484 485 1.731433 CCATCGGCTGCATCCAAAGG 61.731 60.000 7.47 0.65 0.00 3.11
503 504 2.938956 AATCCCGAATGACCATCTCC 57.061 50.000 0.00 0.00 0.00 3.71
537 538 4.748277 TTCTTATTAGTAGGCGCCAACT 57.252 40.909 31.54 11.17 0.00 3.16
700 703 2.170187 CCTCTTAGCCTCTGCAAGTGAT 59.830 50.000 0.00 0.00 41.13 3.06
802 814 3.152400 GTCCGTACCCATCGGCCT 61.152 66.667 0.00 0.00 46.49 5.19
841 853 6.111382 AGCCATATCTATTTCATCACGATGG 58.889 40.000 7.17 0.00 39.24 3.51
860 872 2.868253 GCCAACTTCCGTTAGCCAT 58.132 52.632 0.00 0.00 32.59 4.40
882 894 6.976925 GCTATTTGTAATGTCCTACGTAGTGT 59.023 38.462 20.73 4.26 45.73 3.55
1332 2529 2.290367 CTCCACTGCACGAAACAATTCA 59.710 45.455 0.00 0.00 35.15 2.57
1333 2530 2.548057 TCTCCACTGCACGAAACAATTC 59.452 45.455 0.00 0.00 0.00 2.17
1551 2760 3.557595 CGAGCACTTTCTTGAACAAGTCT 59.442 43.478 13.15 4.16 39.38 3.24
1833 3053 3.432051 GACTCGATGACCTGGGGCG 62.432 68.421 0.00 0.00 0.00 6.13
1847 3067 2.796383 CGATGGACAGAACGATGGACTC 60.796 54.545 0.00 0.00 0.00 3.36
1848 3068 1.135139 CGATGGACAGAACGATGGACT 59.865 52.381 0.00 0.00 0.00 3.85
1872 3092 2.496341 CGCCCAGCTCGATCAGAA 59.504 61.111 0.00 0.00 0.00 3.02
2163 3396 1.068333 GGACATGATGTGTGTTGCCAC 60.068 52.381 1.23 0.00 42.36 5.01
2172 3405 0.729116 GCCGTTCTGGACATGATGTG 59.271 55.000 1.23 0.00 42.00 3.21
2173 3406 0.615331 AGCCGTTCTGGACATGATGT 59.385 50.000 0.00 0.00 42.00 3.06
2492 5896 9.507329 AGTACTATTGATGACACTTTGACAATT 57.493 29.630 0.00 0.00 31.85 2.32
2633 6047 7.201609 GCACACATTAATTATCTCTTCCGTTGA 60.202 37.037 0.00 0.00 0.00 3.18
2640 6054 7.701539 TTGGTGCACACATTAATTATCTCTT 57.298 32.000 20.43 0.00 0.00 2.85
2719 6134 0.813184 CTCGCAGGCCAAACATGATT 59.187 50.000 5.01 0.00 0.00 2.57
2786 6205 3.582164 ACCCAAAGGAAAATAAGGCACA 58.418 40.909 0.00 0.00 36.73 4.57
2860 6301 2.703007 AGAGTGATGATACCCTGAAGGC 59.297 50.000 0.00 0.00 40.58 4.35
2870 6311 8.610369 ACATCATAGTAGGAGAGAGTGATGATA 58.390 37.037 16.54 0.00 42.30 2.15
3015 6597 6.039829 GGCTCTAATGAAAAGAAATGTAGGGG 59.960 42.308 0.00 0.00 0.00 4.79
3023 6605 7.092716 GCTGAATTGGCTCTAATGAAAAGAAA 58.907 34.615 0.00 0.00 0.00 2.52
3171 7439 0.033601 ACACAGGTCCTTTTGGTGCA 60.034 50.000 6.93 0.00 41.38 4.57
3228 7501 1.536149 GTCGTGAGTTCGATCCTTCG 58.464 55.000 0.00 0.00 46.87 3.79
3255 7528 1.597027 CCAACACCCAGTGGTCGAC 60.597 63.158 7.13 7.13 45.57 4.20
3301 7575 1.355971 TAAAGTTCGCGCTGGTCATC 58.644 50.000 5.56 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.