Multiple sequence alignment - TraesCS6B01G330100

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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 TraesCS6B01G330100 chr6B 100.000 4024 0 0 1 4024 579529285 579533308 0.000000e+00 7432
1 TraesCS6B01G330100 chr6B 97.030 202 6 0 1 202 579502585 579502786 1.390000e-89 340
2 TraesCS6B01G330100 chr6B 97.030 202 6 0 1 202 579512226 579512427 1.390000e-89 340
3 TraesCS6B01G330100 chr6D 90.622 1930 128 29 1780 3678 388117301 388119208 0.000000e+00 2512
4 TraesCS6B01G330100 chr6D 94.457 884 30 14 849 1721 388116395 388117270 0.000000e+00 1343
5 TraesCS6B01G330100 chr6D 88.475 564 23 14 235 773 388115833 388116379 0.000000e+00 643
6 TraesCS6B01G330100 chr6D 84.302 344 31 11 3703 4023 388119406 388119749 8.400000e-82 315
7 TraesCS6B01G330100 chr6A 85.120 1250 66 60 498 1707 533397728 533398897 0.000000e+00 1168
8 TraesCS6B01G330100 chr6A 93.333 705 42 2 2597 3301 533399603 533400302 0.000000e+00 1037
9 TraesCS6B01G330100 chr6A 89.744 663 46 14 1848 2499 533398899 533399550 0.000000e+00 828
10 TraesCS6B01G330100 chr6A 86.877 381 25 10 65 428 533397091 533397463 1.740000e-108 403
11 TraesCS6B01G330100 chr6A 90.533 169 16 0 3855 4023 533401252 533401420 1.460000e-54 224
12 TraesCS6B01G330100 chr6A 94.667 75 3 1 3306 3380 533400353 533400426 9.140000e-22 115
13 TraesCS6B01G330100 chr7D 86.607 224 30 0 1326 1549 135394342 135394565 8.640000e-62 248
14 TraesCS6B01G330100 chr7B 85.714 224 32 0 1326 1549 97306882 97307105 1.870000e-58 237
15 TraesCS6B01G330100 chr7A 85.714 224 32 0 1326 1549 134540973 134541196 1.870000e-58 237
16 TraesCS6B01G330100 chr2D 98.450 129 2 0 1721 1849 508728753 508728625 1.130000e-55 228
17 TraesCS6B01G330100 chr4D 96.850 127 4 0 1721 1847 330859717 330859843 3.150000e-51 213
18 TraesCS6B01G330100 chr4D 93.431 137 9 0 1721 1857 94769571 94769707 1.900000e-48 204
19 TraesCS6B01G330100 chr4D 93.431 137 9 0 1721 1857 94771752 94771888 1.900000e-48 204
20 TraesCS6B01G330100 chr4D 91.724 145 10 2 1721 1864 109463875 109464018 2.450000e-47 200
21 TraesCS6B01G330100 chr1B 95.455 132 4 2 1721 1852 540714519 540714648 4.080000e-50 209
22 TraesCS6B01G330100 chr3D 94.118 136 8 0 1721 1856 164330648 164330783 1.470000e-49 207
23 TraesCS6B01G330100 chr3B 92.414 145 7 4 1721 1863 752110369 752110227 1.900000e-48 204


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 TraesCS6B01G330100 chr6B 579529285 579533308 4023 False 7432.000000 7432 100.000000 1 4024 1 chr6B.!!$F3 4023
1 TraesCS6B01G330100 chr6D 388115833 388119749 3916 False 1203.250000 2512 89.464000 235 4023 4 chr6D.!!$F1 3788
2 TraesCS6B01G330100 chr6A 533397091 533401420 4329 False 629.166667 1168 90.045667 65 4023 6 chr6A.!!$F1 3958
3 TraesCS6B01G330100 chr4D 94769571 94771888 2317 False 204.000000 204 93.431000 1721 1857 2 chr4D.!!$F3 136

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
36 37 0.392863 TGGGTGCATCATCAACGAGG 60.393 55.000 0.00 0.0 0.00 4.63 F
37 38 0.392998 GGGTGCATCATCAACGAGGT 60.393 55.000 0.00 0.0 0.00 3.85 F
424 449 0.749454 AGCACATCCCCGCATTTCTC 60.749 55.000 0.00 0.0 0.00 2.87 F
559 779 0.763035 ACACCGCCCCTATAATCCAC 59.237 55.000 0.00 0.0 0.00 4.02 F
884 1118 1.211709 GCGTGCATAAAACCGCCTT 59.788 52.632 5.89 0.0 40.25 4.35 F
2747 5237 0.547954 AGGACCTCAAGGAAGACCCC 60.548 60.000 2.30 0.0 38.94 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1274 1524 0.757188 GATCAGGCGAGGGGAAGAGA 60.757 60.000 0.00 0.00 0.00 3.10 R
1550 1800 0.968393 AAGAGAGGAGAGGCGTGACC 60.968 60.000 0.00 0.00 39.61 4.02 R
2089 4562 0.883833 GGGACTGCTGGTGTTCATTG 59.116 55.000 0.00 0.00 0.00 2.82 R
2292 4765 2.486472 ATGTTGCAAGTAGCTGAGCT 57.514 45.000 13.25 13.25 45.94 4.09 R
2820 5310 1.076777 CAAGGGCCAACCGGATGAT 60.077 57.895 14.18 0.00 46.96 2.45 R
3758 6633 0.468226 TGAGACTGGGTTCGTTTGCT 59.532 50.000 0.00 0.00 0.00 3.91 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
20 21 3.669251 GAGGAAGAGGAATATCGTGGG 57.331 52.381 0.00 0.00 0.00 4.61
21 22 2.966516 GAGGAAGAGGAATATCGTGGGT 59.033 50.000 0.00 0.00 0.00 4.51
22 23 2.700897 AGGAAGAGGAATATCGTGGGTG 59.299 50.000 0.00 0.00 0.00 4.61
23 24 2.484889 GAAGAGGAATATCGTGGGTGC 58.515 52.381 0.00 0.00 0.00 5.01
24 25 1.496060 AGAGGAATATCGTGGGTGCA 58.504 50.000 0.00 0.00 0.00 4.57
25 26 2.050144 AGAGGAATATCGTGGGTGCAT 58.950 47.619 0.00 0.00 0.00 3.96
26 27 2.037772 AGAGGAATATCGTGGGTGCATC 59.962 50.000 0.00 0.00 0.00 3.91
27 28 1.768275 AGGAATATCGTGGGTGCATCA 59.232 47.619 0.00 0.00 0.00 3.07
28 29 2.373169 AGGAATATCGTGGGTGCATCAT 59.627 45.455 0.00 0.00 0.00 2.45
29 30 2.744202 GGAATATCGTGGGTGCATCATC 59.256 50.000 0.00 0.00 0.00 2.92
30 31 3.402110 GAATATCGTGGGTGCATCATCA 58.598 45.455 0.00 0.00 0.00 3.07
31 32 2.998316 TATCGTGGGTGCATCATCAA 57.002 45.000 0.00 0.00 0.00 2.57
32 33 1.382522 ATCGTGGGTGCATCATCAAC 58.617 50.000 0.00 0.00 0.00 3.18
33 34 1.018752 TCGTGGGTGCATCATCAACG 61.019 55.000 0.00 3.29 0.00 4.10
34 35 1.018752 CGTGGGTGCATCATCAACGA 61.019 55.000 0.00 0.00 0.00 3.85
35 36 0.729116 GTGGGTGCATCATCAACGAG 59.271 55.000 0.00 0.00 0.00 4.18
36 37 0.392863 TGGGTGCATCATCAACGAGG 60.393 55.000 0.00 0.00 0.00 4.63
37 38 0.392998 GGGTGCATCATCAACGAGGT 60.393 55.000 0.00 0.00 0.00 3.85
38 39 1.009829 GGTGCATCATCAACGAGGTC 58.990 55.000 0.00 0.00 0.00 3.85
39 40 1.675714 GGTGCATCATCAACGAGGTCA 60.676 52.381 0.00 0.00 0.00 4.02
40 41 2.076100 GTGCATCATCAACGAGGTCAA 58.924 47.619 0.00 0.00 0.00 3.18
41 42 2.483877 GTGCATCATCAACGAGGTCAAA 59.516 45.455 0.00 0.00 0.00 2.69
42 43 2.483877 TGCATCATCAACGAGGTCAAAC 59.516 45.455 0.00 0.00 0.00 2.93
43 44 2.483877 GCATCATCAACGAGGTCAAACA 59.516 45.455 0.00 0.00 0.00 2.83
44 45 3.425359 GCATCATCAACGAGGTCAAACAG 60.425 47.826 0.00 0.00 0.00 3.16
45 46 3.469008 TCATCAACGAGGTCAAACAGT 57.531 42.857 0.00 0.00 0.00 3.55
46 47 4.594123 TCATCAACGAGGTCAAACAGTA 57.406 40.909 0.00 0.00 0.00 2.74
47 48 5.147330 TCATCAACGAGGTCAAACAGTAT 57.853 39.130 0.00 0.00 0.00 2.12
48 49 4.929211 TCATCAACGAGGTCAAACAGTATG 59.071 41.667 0.00 0.00 46.00 2.39
49 50 3.064207 TCAACGAGGTCAAACAGTATGC 58.936 45.455 0.00 0.00 42.53 3.14
50 51 2.805671 CAACGAGGTCAAACAGTATGCA 59.194 45.455 0.00 0.00 42.53 3.96
51 52 3.334583 ACGAGGTCAAACAGTATGCAT 57.665 42.857 3.79 3.79 42.53 3.96
52 53 3.002791 ACGAGGTCAAACAGTATGCATG 58.997 45.455 10.16 0.00 42.53 4.06
53 54 3.002791 CGAGGTCAAACAGTATGCATGT 58.997 45.455 10.16 0.00 42.53 3.21
54 55 3.436704 CGAGGTCAAACAGTATGCATGTT 59.563 43.478 10.16 3.58 42.53 2.71
70 71 6.825284 TGCATGTTTGTTGAATTGTAGTTG 57.175 33.333 0.00 0.00 0.00 3.16
71 72 5.233902 TGCATGTTTGTTGAATTGTAGTTGC 59.766 36.000 0.00 0.00 0.00 4.17
81 82 8.602328 TGTTGAATTGTAGTTGCAAATTTGAAG 58.398 29.630 22.31 0.00 31.63 3.02
82 83 8.816144 GTTGAATTGTAGTTGCAAATTTGAAGA 58.184 29.630 22.31 3.57 31.63 2.87
118 119 8.774546 AATATAGATGCAGATAGGCTAGCTAA 57.225 34.615 12.63 4.40 34.04 3.09
126 127 4.985409 CAGATAGGCTAGCTAAGTTTTCCG 59.015 45.833 12.63 0.00 0.00 4.30
127 128 2.693267 AGGCTAGCTAAGTTTTCCGG 57.307 50.000 15.72 0.00 0.00 5.14
132 133 4.001652 GCTAGCTAAGTTTTCCGGTTCTT 58.998 43.478 7.70 4.99 0.00 2.52
143 144 1.142060 TCCGGTTCTTTTGCTCAAGGA 59.858 47.619 0.00 0.00 0.00 3.36
144 145 1.953686 CCGGTTCTTTTGCTCAAGGAA 59.046 47.619 0.00 0.00 0.00 3.36
147 148 3.304057 CGGTTCTTTTGCTCAAGGAAGAC 60.304 47.826 0.00 0.00 0.00 3.01
159 160 4.277476 TCAAGGAAGACACATGTTTGGTT 58.723 39.130 0.00 0.00 0.00 3.67
161 162 3.631250 AGGAAGACACATGTTTGGTTGT 58.369 40.909 0.00 0.00 0.00 3.32
189 192 6.187727 TCCCATGATCCTCTTTTATACCAC 57.812 41.667 0.00 0.00 0.00 4.16
256 262 1.138247 GTAATGTCGTCGGCGTCCT 59.862 57.895 10.18 0.00 39.49 3.85
267 273 2.590114 GGCGTCCTGTACCCCACTT 61.590 63.158 0.00 0.00 0.00 3.16
280 286 4.353383 ACCCCACTTTTCTTCTGTCTAC 57.647 45.455 0.00 0.00 0.00 2.59
376 401 8.507249 CACTCTGTCTAATCTAAAAACAAAGGG 58.493 37.037 0.00 0.00 0.00 3.95
424 449 0.749454 AGCACATCCCCGCATTTCTC 60.749 55.000 0.00 0.00 0.00 2.87
438 463 3.181476 GCATTTCTCCCGTTGGCATAATT 60.181 43.478 0.00 0.00 0.00 1.40
496 716 3.499737 CACCGACCAATCAGCGCC 61.500 66.667 2.29 0.00 0.00 6.53
516 736 2.161609 CCGATTAACCAAGTCCAAGTGC 59.838 50.000 0.00 0.00 0.00 4.40
559 779 0.763035 ACACCGCCCCTATAATCCAC 59.237 55.000 0.00 0.00 0.00 4.02
656 879 2.050714 GCACCGAAGTCGACGACA 60.051 61.111 28.31 0.00 43.02 4.35
657 880 1.443872 GCACCGAAGTCGACGACAT 60.444 57.895 28.31 18.19 43.02 3.06
658 881 1.674611 GCACCGAAGTCGACGACATG 61.675 60.000 28.31 17.92 43.02 3.21
663 886 2.478031 CCGAAGTCGACGACATGAAGAT 60.478 50.000 28.31 4.29 43.02 2.40
664 887 3.172050 CGAAGTCGACGACATGAAGATT 58.828 45.455 28.31 12.81 43.02 2.40
686 910 2.284625 ACAGGGGCAGGTGATCGA 60.285 61.111 0.00 0.00 0.00 3.59
729 956 2.046507 CCCTCCACTGCACTCTGC 60.047 66.667 0.00 0.00 45.29 4.26
845 1077 3.400054 CCACTCCCCTTCCCCGAC 61.400 72.222 0.00 0.00 0.00 4.79
880 1114 4.035054 CACGCGTGCATAAAACCG 57.965 55.556 28.16 0.00 0.00 4.44
884 1118 1.211709 GCGTGCATAAAACCGCCTT 59.788 52.632 5.89 0.00 40.25 4.35
949 1183 3.893763 CGCCCACGCACCAACAAA 61.894 61.111 0.00 0.00 34.03 2.83
950 1184 2.733945 GCCCACGCACCAACAAAT 59.266 55.556 0.00 0.00 34.03 2.32
951 1185 1.372872 GCCCACGCACCAACAAATC 60.373 57.895 0.00 0.00 34.03 2.17
958 1192 1.402720 CGCACCAACAAATCCATCCAC 60.403 52.381 0.00 0.00 0.00 4.02
1296 1546 3.672338 TTCCCCTCGCCTGATCCGA 62.672 63.158 0.00 0.00 0.00 4.55
1299 1549 2.502492 CCCTCGCCTGATCCGATGT 61.502 63.158 0.00 0.00 33.83 3.06
1649 1927 2.825532 TCCAGACATCATGACAGAACGA 59.174 45.455 0.00 0.00 0.00 3.85
1656 1934 5.407502 ACATCATGACAGAACGACGAAATA 58.592 37.500 0.00 0.00 0.00 1.40
1728 2006 9.058174 TCGATTATACTCCTTTTGTTCAACAAA 57.942 29.630 11.83 11.83 45.37 2.83
1735 2013 8.237811 ACTCCTTTTGTTCAACAAATGACTAT 57.762 30.769 23.81 8.82 46.17 2.12
1752 2030 8.902540 AATGACTATATACGGAGCAAAATGAA 57.097 30.769 0.00 0.00 0.00 2.57
1817 4276 9.219603 TGTGGTAGTTCATTTGAAATCTCTAAG 57.780 33.333 0.00 0.00 35.58 2.18
1935 4399 4.620723 TCATGTTACTCTACATCCCACCT 58.379 43.478 0.00 0.00 36.64 4.00
2030 4499 2.094762 ATCTCCTGTTTTTCCGACGG 57.905 50.000 7.84 7.84 0.00 4.79
2039 4508 4.497300 TGTTTTTCCGACGGGATACTTAG 58.503 43.478 15.25 0.00 43.41 2.18
2053 4522 7.093858 ACGGGATACTTAGCCAGATCTAATAAC 60.094 40.741 0.00 0.00 32.16 1.89
2059 4528 7.371936 ACTTAGCCAGATCTAATAACACGATC 58.628 38.462 0.00 0.00 35.06 3.69
2079 4549 7.065085 CACGATCACAATTCTGAAATACTCCTT 59.935 37.037 0.00 0.00 0.00 3.36
2080 4550 7.065085 ACGATCACAATTCTGAAATACTCCTTG 59.935 37.037 0.00 0.00 0.00 3.61
2089 4562 3.696051 TGAAATACTCCTTGATTGCTGCC 59.304 43.478 0.00 0.00 0.00 4.85
2266 4739 3.323115 GGCCTACAGTGATGATGAGATCA 59.677 47.826 0.00 0.00 44.55 2.92
2292 4765 4.287067 AGGATTCTCACTACAAGGAGCAAA 59.713 41.667 0.00 0.00 0.00 3.68
2389 4862 3.616956 TCACCTCCTTGCTTACTCATG 57.383 47.619 0.00 0.00 0.00 3.07
2439 4916 7.254852 TGAAGACAAAAACACATCTTACAACC 58.745 34.615 0.00 0.00 31.58 3.77
2454 4931 7.166691 TCTTACAACCAGAACACCTATCTAC 57.833 40.000 0.00 0.00 0.00 2.59
2483 4960 5.082059 GCGTTTGAGTTGAACTATGTCATG 58.918 41.667 0.00 0.00 0.00 3.07
2572 5051 6.093771 AGAGAACTGCTTCACATGATTCATTC 59.906 38.462 0.00 0.00 0.00 2.67
2593 5072 1.333308 TGTTCACCAACATTGTCGCTG 59.667 47.619 0.00 0.00 37.61 5.18
2677 5163 7.553334 AGTAGTTCTTCACACTTGACAGTTTA 58.447 34.615 0.00 0.00 0.00 2.01
2688 5174 6.483640 ACACTTGACAGTTTAAGGAGACATTC 59.516 38.462 4.19 0.00 0.00 2.67
2704 5194 7.040409 AGGAGACATTCTTTTGTTGTTCATACC 60.040 37.037 0.00 0.00 0.00 2.73
2725 5215 4.333649 ACCGATGTATTTTGCTGATCACTG 59.666 41.667 0.00 0.00 0.00 3.66
2747 5237 0.547954 AGGACCTCAAGGAAGACCCC 60.548 60.000 2.30 0.00 38.94 4.95
2820 5310 4.081420 GCCCTGACAGATACTTTGAGAAGA 60.081 45.833 3.32 0.00 36.69 2.87
2823 5313 6.127225 CCCTGACAGATACTTTGAGAAGATCA 60.127 42.308 3.32 0.00 36.69 2.92
2963 5453 0.886490 CGCTGGACAAGGCTGTTTCT 60.886 55.000 0.00 0.00 35.30 2.52
2984 5474 6.026947 TCTAAGGAAACAAGCAGAGACTAC 57.973 41.667 0.00 0.00 0.00 2.73
2987 5477 3.057174 AGGAAACAAGCAGAGACTACGAG 60.057 47.826 0.00 0.00 0.00 4.18
2990 5480 1.813786 ACAAGCAGAGACTACGAGGAC 59.186 52.381 0.00 0.00 0.00 3.85
3085 5576 6.374333 GGGAATAAGAGTGCATAAAACTGTCA 59.626 38.462 0.00 0.00 0.00 3.58
3152 5643 6.076557 GCAGTACTCGTCCGATAAGTTATAC 58.923 44.000 0.00 0.00 0.00 1.47
3220 5711 9.739276 TGAAGTTTACTCCAGATTCACAATAAT 57.261 29.630 0.00 0.00 0.00 1.28
3243 5734 8.851541 AATCATTTGCATTGGTGTTATTCTTT 57.148 26.923 0.00 0.00 0.00 2.52
3251 5742 7.178274 TGCATTGGTGTTATTCTTTGTAGGATT 59.822 33.333 0.00 0.00 0.00 3.01
3256 5747 8.328758 TGGTGTTATTCTTTGTAGGATTCTCAT 58.671 33.333 0.00 0.00 0.00 2.90
3270 5761 9.853555 GTAGGATTCTCATGTCTATACAGAATG 57.146 37.037 7.95 0.00 39.49 2.67
3306 5842 8.727100 TCTACTGGTATGATTTATGAGGTCAT 57.273 34.615 0.00 0.00 40.22 3.06
3309 5845 8.455903 ACTGGTATGATTTATGAGGTCATTTG 57.544 34.615 0.00 0.00 37.76 2.32
3343 5879 7.998964 ACCCCAAACTATAAAATCAGGTATCAG 59.001 37.037 0.00 0.00 0.00 2.90
3381 6073 5.450818 AAACCCAACTGGCTGATTATAGA 57.549 39.130 0.00 0.00 37.83 1.98
3382 6074 5.653255 AACCCAACTGGCTGATTATAGAT 57.347 39.130 0.00 0.00 37.83 1.98
3383 6075 6.763715 AACCCAACTGGCTGATTATAGATA 57.236 37.500 0.00 0.00 37.83 1.98
3384 6076 6.365970 ACCCAACTGGCTGATTATAGATAG 57.634 41.667 0.00 0.00 37.83 2.08
3388 6080 7.364232 CCCAACTGGCTGATTATAGATAGTAGG 60.364 44.444 0.00 0.00 0.00 3.18
3389 6081 7.364232 CCAACTGGCTGATTATAGATAGTAGGG 60.364 44.444 0.00 0.00 0.00 3.53
3414 6106 1.202110 GCGCACACAGATGGAGAAATG 60.202 52.381 0.30 0.00 0.00 2.32
3419 6111 2.821969 ACACAGATGGAGAAATGTTGCC 59.178 45.455 0.00 0.00 0.00 4.52
3450 6142 5.189736 TCCTATCCTAATCCGCATAATGCTT 59.810 40.000 0.00 0.00 42.25 3.91
3451 6143 5.882557 CCTATCCTAATCCGCATAATGCTTT 59.117 40.000 0.00 0.00 42.25 3.51
3458 6150 7.281774 CCTAATCCGCATAATGCTTTATCTCAT 59.718 37.037 2.00 0.00 42.25 2.90
3482 6174 9.298774 CATCCTATTTTGCATTTTCTTCTTCTC 57.701 33.333 0.00 0.00 0.00 2.87
3523 6215 3.521531 TGTAGTGCTGAATACCCATTCCA 59.478 43.478 0.00 0.00 39.97 3.53
3530 6222 4.646492 GCTGAATACCCATTCCAAGAACAT 59.354 41.667 0.00 0.00 39.97 2.71
3538 6230 3.055891 CCATTCCAAGAACATGGTTTCCC 60.056 47.826 0.00 0.00 41.46 3.97
3540 6232 0.887933 CCAAGAACATGGTTTCCCGG 59.112 55.000 0.00 0.00 35.65 5.73
3541 6233 0.243636 CAAGAACATGGTTTCCCGGC 59.756 55.000 0.00 0.00 0.00 6.13
3553 6245 1.182385 TTCCCGGCCACCATTTTCAC 61.182 55.000 2.24 0.00 0.00 3.18
3559 6257 2.029110 CGGCCACCATTTTCACTTCATT 60.029 45.455 2.24 0.00 0.00 2.57
3561 6259 4.388485 GGCCACCATTTTCACTTCATTTT 58.612 39.130 0.00 0.00 0.00 1.82
3562 6260 4.452114 GGCCACCATTTTCACTTCATTTTC 59.548 41.667 0.00 0.00 0.00 2.29
3568 6266 8.090214 CACCATTTTCACTTCATTTTCACCTAT 58.910 33.333 0.00 0.00 0.00 2.57
3577 6275 7.596248 CACTTCATTTTCACCTATGTCCTTTTG 59.404 37.037 0.00 0.00 0.00 2.44
3609 6310 3.724508 ATGAGCTACCTGAAGACATCG 57.275 47.619 0.00 0.00 0.00 3.84
3610 6311 2.447443 TGAGCTACCTGAAGACATCGT 58.553 47.619 0.00 0.00 0.00 3.73
3616 6317 2.973945 ACCTGAAGACATCGTAAAGGC 58.026 47.619 0.00 0.00 0.00 4.35
3649 6350 2.104859 CATCAGGGCACAGTGAGCG 61.105 63.158 4.15 0.00 0.00 5.03
3650 6351 2.285773 ATCAGGGCACAGTGAGCGA 61.286 57.895 4.15 0.00 0.00 4.93
3670 6371 7.172190 TGAGCGACTATGTAGTATGTACCTTAC 59.828 40.741 0.00 0.00 36.50 2.34
3671 6372 6.994496 AGCGACTATGTAGTATGTACCTTACA 59.006 38.462 6.02 3.17 38.80 2.41
3695 6542 9.871238 ACAAAATACAGTATCTTTACATCGAGT 57.129 29.630 0.00 0.00 0.00 4.18
3708 6582 4.474226 ACATCGAGTTTTCTTCAACTGC 57.526 40.909 0.00 0.00 37.11 4.40
3709 6583 3.876914 ACATCGAGTTTTCTTCAACTGCA 59.123 39.130 0.00 0.00 37.11 4.41
3757 6632 9.515226 TTATCAACATATTTAGGCCCAGTATTC 57.485 33.333 0.00 0.00 0.00 1.75
3758 6633 6.905736 TCAACATATTTAGGCCCAGTATTCA 58.094 36.000 0.00 0.00 0.00 2.57
3764 6639 1.839424 AGGCCCAGTATTCAGCAAAC 58.161 50.000 0.00 0.00 0.00 2.93
3766 6641 1.448985 GCCCAGTATTCAGCAAACGA 58.551 50.000 0.00 0.00 0.00 3.85
3793 6684 4.517075 CAGTCTCAGTCTAGACAACACTCA 59.483 45.833 24.44 0.00 46.89 3.41
3796 6687 2.552743 TCAGTCTAGACAACACTCACCG 59.447 50.000 24.44 0.67 0.00 4.94
3827 6724 5.352293 TGCAAGCAAGATAACAGAGTATGTG 59.648 40.000 0.00 0.00 43.00 3.21
3892 6830 4.877773 AGATCTCTGACCCAGTGAATACT 58.122 43.478 0.00 2.16 37.50 2.12
3933 6871 4.991687 GTCCTAACCATCGGATGATTTCTC 59.008 45.833 19.30 1.31 30.49 2.87
3964 6902 4.108501 TCTACAACGGGCTATCCAGATA 57.891 45.455 0.00 0.00 34.36 1.98
3968 6906 0.252284 ACGGGCTATCCAGATAGGGG 60.252 60.000 14.86 0.00 40.77 4.79
3970 6908 0.417841 GGGCTATCCAGATAGGGGGA 59.582 60.000 14.86 0.00 40.77 4.81
3986 6924 4.990526 AGGGGGATAAAGTGCATTCTATG 58.009 43.478 0.00 0.00 0.00 2.23
3991 6929 6.128172 GGGGATAAAGTGCATTCTATGATTCG 60.128 42.308 0.00 0.00 0.00 3.34
3993 6931 6.073058 GGATAAAGTGCATTCTATGATTCGCA 60.073 38.462 0.00 0.00 0.00 5.10
3995 6933 5.762825 AAGTGCATTCTATGATTCGCAAT 57.237 34.783 0.00 0.00 0.00 3.56
4000 6938 5.990996 TGCATTCTATGATTCGCAATACAGA 59.009 36.000 0.00 0.00 0.00 3.41
4014 6952 2.751166 TACAGAAGCAGCCTCAAGTC 57.249 50.000 0.00 0.00 0.00 3.01
4017 6955 1.055040 AGAAGCAGCCTCAAGTCAGT 58.945 50.000 0.00 0.00 0.00 3.41
4023 6961 2.703416 CAGCCTCAAGTCAGTGCAATA 58.297 47.619 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.966516 ACCCACGATATTCCTCTTCCTC 59.033 50.000 0.00 0.00 0.00 3.71
2 3 2.807108 GCACCCACGATATTCCTCTTCC 60.807 54.545 0.00 0.00 0.00 3.46
3 4 2.158957 TGCACCCACGATATTCCTCTTC 60.159 50.000 0.00 0.00 0.00 2.87
4 5 1.837439 TGCACCCACGATATTCCTCTT 59.163 47.619 0.00 0.00 0.00 2.85
5 6 1.496060 TGCACCCACGATATTCCTCT 58.504 50.000 0.00 0.00 0.00 3.69
6 7 2.224281 TGATGCACCCACGATATTCCTC 60.224 50.000 0.00 0.00 0.00 3.71
7 8 1.768275 TGATGCACCCACGATATTCCT 59.232 47.619 0.00 0.00 0.00 3.36
8 9 2.254546 TGATGCACCCACGATATTCC 57.745 50.000 0.00 0.00 0.00 3.01
9 10 3.402110 TGATGATGCACCCACGATATTC 58.598 45.455 0.00 0.00 0.00 1.75
10 11 3.490439 TGATGATGCACCCACGATATT 57.510 42.857 0.00 0.00 0.00 1.28
11 12 3.141398 GTTGATGATGCACCCACGATAT 58.859 45.455 0.00 0.00 0.00 1.63
12 13 2.560504 GTTGATGATGCACCCACGATA 58.439 47.619 0.00 0.00 0.00 2.92
13 14 1.382522 GTTGATGATGCACCCACGAT 58.617 50.000 0.00 0.00 0.00 3.73
14 15 1.018752 CGTTGATGATGCACCCACGA 61.019 55.000 0.00 0.00 0.00 4.35
15 16 1.018752 TCGTTGATGATGCACCCACG 61.019 55.000 0.00 0.00 0.00 4.94
16 17 0.729116 CTCGTTGATGATGCACCCAC 59.271 55.000 0.00 0.00 0.00 4.61
17 18 0.392863 CCTCGTTGATGATGCACCCA 60.393 55.000 0.00 0.00 0.00 4.51
18 19 0.392998 ACCTCGTTGATGATGCACCC 60.393 55.000 0.00 0.00 0.00 4.61
19 20 1.009829 GACCTCGTTGATGATGCACC 58.990 55.000 0.00 0.00 0.00 5.01
20 21 1.725641 TGACCTCGTTGATGATGCAC 58.274 50.000 0.00 0.00 0.00 4.57
21 22 2.470983 TTGACCTCGTTGATGATGCA 57.529 45.000 0.00 0.00 0.00 3.96
22 23 2.483877 TGTTTGACCTCGTTGATGATGC 59.516 45.455 0.00 0.00 0.00 3.91
23 24 3.748048 ACTGTTTGACCTCGTTGATGATG 59.252 43.478 0.00 0.00 0.00 3.07
24 25 4.008074 ACTGTTTGACCTCGTTGATGAT 57.992 40.909 0.00 0.00 0.00 2.45
25 26 3.469008 ACTGTTTGACCTCGTTGATGA 57.531 42.857 0.00 0.00 0.00 2.92
26 27 4.436050 GCATACTGTTTGACCTCGTTGATG 60.436 45.833 2.29 0.00 0.00 3.07
27 28 3.684788 GCATACTGTTTGACCTCGTTGAT 59.315 43.478 2.29 0.00 0.00 2.57
28 29 3.064207 GCATACTGTTTGACCTCGTTGA 58.936 45.455 2.29 0.00 0.00 3.18
29 30 2.805671 TGCATACTGTTTGACCTCGTTG 59.194 45.455 2.29 0.00 0.00 4.10
30 31 3.120321 TGCATACTGTTTGACCTCGTT 57.880 42.857 2.29 0.00 0.00 3.85
31 32 2.831685 TGCATACTGTTTGACCTCGT 57.168 45.000 2.29 0.00 0.00 4.18
32 33 3.002791 ACATGCATACTGTTTGACCTCG 58.997 45.455 0.00 0.00 0.00 4.63
33 34 5.376854 AAACATGCATACTGTTTGACCTC 57.623 39.130 14.47 0.00 43.31 3.85
39 40 7.495279 ACAATTCAACAAACATGCATACTGTTT 59.505 29.630 10.41 10.41 45.23 2.83
40 41 6.985645 ACAATTCAACAAACATGCATACTGTT 59.014 30.769 0.00 6.64 38.44 3.16
41 42 6.514947 ACAATTCAACAAACATGCATACTGT 58.485 32.000 0.00 0.00 0.00 3.55
42 43 7.809331 ACTACAATTCAACAAACATGCATACTG 59.191 33.333 0.00 0.00 0.00 2.74
43 44 7.885297 ACTACAATTCAACAAACATGCATACT 58.115 30.769 0.00 0.00 0.00 2.12
44 45 8.427012 CAACTACAATTCAACAAACATGCATAC 58.573 33.333 0.00 0.00 0.00 2.39
45 46 7.116090 GCAACTACAATTCAACAAACATGCATA 59.884 33.333 0.00 0.00 0.00 3.14
46 47 6.073657 GCAACTACAATTCAACAAACATGCAT 60.074 34.615 0.00 0.00 0.00 3.96
47 48 5.233902 GCAACTACAATTCAACAAACATGCA 59.766 36.000 0.00 0.00 0.00 3.96
48 49 5.233902 TGCAACTACAATTCAACAAACATGC 59.766 36.000 0.00 0.00 0.00 4.06
49 50 6.825284 TGCAACTACAATTCAACAAACATG 57.175 33.333 0.00 0.00 0.00 3.21
50 51 7.840342 TTTGCAACTACAATTCAACAAACAT 57.160 28.000 0.00 0.00 0.00 2.71
51 52 7.840342 ATTTGCAACTACAATTCAACAAACA 57.160 28.000 0.00 0.00 0.00 2.83
52 53 8.997960 CAAATTTGCAACTACAATTCAACAAAC 58.002 29.630 5.01 0.00 0.00 2.93
53 54 8.939929 TCAAATTTGCAACTACAATTCAACAAA 58.060 25.926 13.54 0.00 0.00 2.83
54 55 8.484641 TCAAATTTGCAACTACAATTCAACAA 57.515 26.923 13.54 0.00 0.00 2.83
55 56 8.484641 TTCAAATTTGCAACTACAATTCAACA 57.515 26.923 13.54 0.00 0.00 3.33
56 57 8.816144 TCTTCAAATTTGCAACTACAATTCAAC 58.184 29.630 13.54 0.00 0.00 3.18
57 58 8.939201 TCTTCAAATTTGCAACTACAATTCAA 57.061 26.923 13.54 0.00 0.00 2.69
58 59 9.195411 GATCTTCAAATTTGCAACTACAATTCA 57.805 29.630 13.54 0.00 0.00 2.57
59 60 8.368126 CGATCTTCAAATTTGCAACTACAATTC 58.632 33.333 13.54 1.40 0.00 2.17
60 61 7.867403 ACGATCTTCAAATTTGCAACTACAATT 59.133 29.630 13.54 0.00 0.00 2.32
61 62 7.326789 CACGATCTTCAAATTTGCAACTACAAT 59.673 33.333 13.54 0.00 0.00 2.71
62 63 6.636447 CACGATCTTCAAATTTGCAACTACAA 59.364 34.615 13.54 0.04 0.00 2.41
63 64 6.142139 CACGATCTTCAAATTTGCAACTACA 58.858 36.000 13.54 0.00 0.00 2.74
70 71 4.168014 TGATGCACGATCTTCAAATTTGC 58.832 39.130 13.54 0.00 31.55 3.68
71 72 6.693761 TTTGATGCACGATCTTCAAATTTG 57.306 33.333 12.15 12.15 36.11 2.32
98 99 4.415596 ACTTAGCTAGCCTATCTGCATCT 58.584 43.478 12.13 0.00 0.00 2.90
109 110 2.398252 ACCGGAAAACTTAGCTAGCC 57.602 50.000 9.46 0.00 0.00 3.93
118 119 3.020984 TGAGCAAAAGAACCGGAAAACT 58.979 40.909 9.46 0.00 0.00 2.66
126 127 3.632145 TGTCTTCCTTGAGCAAAAGAACC 59.368 43.478 0.25 0.00 30.10 3.62
127 128 4.096382 TGTGTCTTCCTTGAGCAAAAGAAC 59.904 41.667 0.25 2.98 30.10 3.01
132 133 3.554934 ACATGTGTCTTCCTTGAGCAAA 58.445 40.909 0.00 0.00 0.00 3.68
143 144 3.766591 TGGAACAACCAAACATGTGTCTT 59.233 39.130 0.00 0.00 46.75 3.01
144 145 3.360867 TGGAACAACCAAACATGTGTCT 58.639 40.909 0.00 0.00 46.75 3.41
159 160 2.780414 AGAGGATCATGGGATGGAACA 58.220 47.619 0.00 0.00 40.67 3.18
161 162 4.886755 AAAAGAGGATCATGGGATGGAA 57.113 40.909 0.00 0.00 37.82 3.53
189 192 9.425893 GTTTTATTGATCATAGTTCACATGTCG 57.574 33.333 0.00 0.00 0.00 4.35
239 245 1.138036 CAGGACGCCGACGACATTA 59.862 57.895 0.00 0.00 43.93 1.90
256 262 3.714798 AGACAGAAGAAAAGTGGGGTACA 59.285 43.478 0.00 0.00 0.00 2.90
280 286 7.149918 GGCACGTTTTTCTTTCTTTCTTTAG 57.850 36.000 0.00 0.00 0.00 1.85
376 401 1.560860 GGCGCGATATCAGTGGCTTC 61.561 60.000 12.10 4.95 40.80 3.86
424 449 4.202101 TGCTTGATTAATTATGCCAACGGG 60.202 41.667 13.40 0.00 37.18 5.28
438 463 3.119388 GGCAACATCAGCTTGCTTGATTA 60.119 43.478 7.24 0.00 43.08 1.75
496 716 2.161609 GGCACTTGGACTTGGTTAATCG 59.838 50.000 0.00 0.00 0.00 3.34
591 814 2.665185 ACGTCGTGCTTTGGAGGC 60.665 61.111 0.00 0.00 0.00 4.70
593 816 2.954753 GCCACGTCGTGCTTTGGAG 61.955 63.158 20.01 5.56 31.34 3.86
656 879 4.467769 CTGCCCCTGTCAATAATCTTCAT 58.532 43.478 0.00 0.00 0.00 2.57
657 880 3.371917 CCTGCCCCTGTCAATAATCTTCA 60.372 47.826 0.00 0.00 0.00 3.02
658 881 3.217626 CCTGCCCCTGTCAATAATCTTC 58.782 50.000 0.00 0.00 0.00 2.87
663 886 1.367346 TCACCTGCCCCTGTCAATAA 58.633 50.000 0.00 0.00 0.00 1.40
664 887 1.490490 GATCACCTGCCCCTGTCAATA 59.510 52.381 0.00 0.00 0.00 1.90
729 956 0.312416 GACAGTCTCCGATCCCGATG 59.688 60.000 0.00 0.00 38.22 3.84
825 1057 4.048470 GGGGAAGGGGAGTGGCAC 62.048 72.222 10.29 10.29 0.00 5.01
830 1062 4.735599 GGGTCGGGGAAGGGGAGT 62.736 72.222 0.00 0.00 0.00 3.85
931 1165 4.858680 TTGTTGGTGCGTGGGCGA 62.859 61.111 0.00 0.00 44.10 5.54
933 1167 1.372872 GATTTGTTGGTGCGTGGGC 60.373 57.895 0.00 0.00 40.52 5.36
934 1168 1.288752 GGATTTGTTGGTGCGTGGG 59.711 57.895 0.00 0.00 0.00 4.61
935 1169 0.602562 ATGGATTTGTTGGTGCGTGG 59.397 50.000 0.00 0.00 0.00 4.94
936 1170 1.402720 GGATGGATTTGTTGGTGCGTG 60.403 52.381 0.00 0.00 0.00 5.34
937 1171 0.887933 GGATGGATTTGTTGGTGCGT 59.112 50.000 0.00 0.00 0.00 5.24
939 1173 1.066929 GGTGGATGGATTTGTTGGTGC 60.067 52.381 0.00 0.00 0.00 5.01
940 1174 2.493278 GAGGTGGATGGATTTGTTGGTG 59.507 50.000 0.00 0.00 0.00 4.17
941 1175 2.557452 GGAGGTGGATGGATTTGTTGGT 60.557 50.000 0.00 0.00 0.00 3.67
942 1176 2.102578 GGAGGTGGATGGATTTGTTGG 58.897 52.381 0.00 0.00 0.00 3.77
945 1179 0.631212 GGGGAGGTGGATGGATTTGT 59.369 55.000 0.00 0.00 0.00 2.83
949 1183 0.401979 ATTCGGGGAGGTGGATGGAT 60.402 55.000 0.00 0.00 0.00 3.41
950 1184 1.004230 ATTCGGGGAGGTGGATGGA 59.996 57.895 0.00 0.00 0.00 3.41
951 1185 1.451936 GATTCGGGGAGGTGGATGG 59.548 63.158 0.00 0.00 0.00 3.51
986 1220 2.746803 GCCATTTTCGTCCGGTCCG 61.747 63.158 3.60 3.60 0.00 4.79
989 1223 2.030958 GTCGCCATTTTCGTCCGGT 61.031 57.895 0.00 0.00 0.00 5.28
990 1224 2.782615 GTCGCCATTTTCGTCCGG 59.217 61.111 0.00 0.00 0.00 5.14
991 1225 2.394136 CGTCGCCATTTTCGTCCG 59.606 61.111 0.00 0.00 0.00 4.79
992 1226 2.097728 GCGTCGCCATTTTCGTCC 59.902 61.111 5.75 0.00 0.00 4.79
993 1227 1.058903 GAGCGTCGCCATTTTCGTC 59.941 57.895 14.86 0.00 0.00 4.20
996 1230 1.716172 GGAGAGCGTCGCCATTTTC 59.284 57.895 14.86 4.30 36.28 2.29
997 1231 2.100631 CGGAGAGCGTCGCCATTTT 61.101 57.895 14.86 0.00 35.99 1.82
1272 1522 1.380515 CAGGCGAGGGGAAGAGAGA 60.381 63.158 0.00 0.00 0.00 3.10
1273 1523 0.758685 ATCAGGCGAGGGGAAGAGAG 60.759 60.000 0.00 0.00 0.00 3.20
1274 1524 0.757188 GATCAGGCGAGGGGAAGAGA 60.757 60.000 0.00 0.00 0.00 3.10
1279 1529 3.452621 ATCGGATCAGGCGAGGGGA 62.453 63.158 0.00 0.00 0.00 4.81
1316 1566 2.186384 CGCCCTCTGCAGGAGAAG 59.814 66.667 15.13 3.26 43.65 2.85
1470 1720 4.468689 GGTCGTGGTAGGCCTGCC 62.469 72.222 31.52 31.52 35.78 4.85
1537 1787 1.303317 GTGACCCACCTTGCGGAAT 60.303 57.895 0.00 0.00 0.00 3.01
1549 1799 2.363147 AGAGGAGAGGCGTGACCC 60.363 66.667 0.00 0.00 40.58 4.46
1550 1800 0.968393 AAGAGAGGAGAGGCGTGACC 60.968 60.000 0.00 0.00 39.61 4.02
1649 1927 5.295152 GGAAGGATATCGTTGGTATTTCGT 58.705 41.667 15.07 0.00 0.00 3.85
1656 1934 1.141053 GCTGGGAAGGATATCGTTGGT 59.859 52.381 15.07 0.00 0.00 3.67
1728 2006 8.939929 CATTCATTTTGCTCCGTATATAGTCAT 58.060 33.333 0.00 0.00 0.00 3.06
1735 2013 8.988934 GTAGATTCATTCATTTTGCTCCGTATA 58.011 33.333 0.00 0.00 0.00 1.47
1787 2065 8.862325 AGATTTCAAATGAACTACCACATACA 57.138 30.769 0.00 0.00 33.13 2.29
1817 4276 6.260271 CCCTCCGTTCCTAAATATTTGTCTTC 59.740 42.308 11.05 0.00 0.00 2.87
1909 4368 6.657541 GGTGGGATGTAGAGTAACATGAAAAA 59.342 38.462 0.00 0.00 40.17 1.94
1913 4372 4.620723 AGGTGGGATGTAGAGTAACATGA 58.379 43.478 0.00 0.00 40.17 3.07
1915 4374 6.388619 AAAAGGTGGGATGTAGAGTAACAT 57.611 37.500 0.00 0.00 42.75 2.71
1916 4375 5.836024 AAAAGGTGGGATGTAGAGTAACA 57.164 39.130 0.00 0.00 0.00 2.41
1917 4376 5.414765 CCAAAAAGGTGGGATGTAGAGTAAC 59.585 44.000 0.00 0.00 34.77 2.50
1918 4377 5.566469 CCAAAAAGGTGGGATGTAGAGTAA 58.434 41.667 0.00 0.00 34.77 2.24
1919 4378 5.174037 CCAAAAAGGTGGGATGTAGAGTA 57.826 43.478 0.00 0.00 34.77 2.59
1920 4379 4.034285 CCAAAAAGGTGGGATGTAGAGT 57.966 45.455 0.00 0.00 34.77 3.24
2030 4499 7.755822 CGTGTTATTAGATCTGGCTAAGTATCC 59.244 40.741 5.18 0.00 34.16 2.59
2039 4508 5.289595 TGTGATCGTGTTATTAGATCTGGC 58.710 41.667 5.18 0.00 40.84 4.85
2053 4522 6.536582 AGGAGTATTTCAGAATTGTGATCGTG 59.463 38.462 6.07 0.00 0.00 4.35
2059 4528 7.487189 GCAATCAAGGAGTATTTCAGAATTGTG 59.513 37.037 0.00 0.00 0.00 3.33
2079 4549 1.273048 GGTGTTCATTGGCAGCAATCA 59.727 47.619 0.00 0.00 33.77 2.57
2080 4550 1.273048 TGGTGTTCATTGGCAGCAATC 59.727 47.619 10.13 0.00 39.68 2.67
2089 4562 0.883833 GGGACTGCTGGTGTTCATTG 59.116 55.000 0.00 0.00 0.00 2.82
2266 4739 4.100808 GCTCCTTGTAGTGAGAATCCTGAT 59.899 45.833 0.00 0.00 0.00 2.90
2292 4765 2.486472 ATGTTGCAAGTAGCTGAGCT 57.514 45.000 13.25 13.25 45.94 4.09
2439 4916 2.852413 CGCAACGTAGATAGGTGTTCTG 59.148 50.000 0.00 0.00 0.00 3.02
2507 4986 9.492973 AACCAAATTCATCATTCTTTTCGAAAT 57.507 25.926 12.12 0.00 34.79 2.17
2550 5029 6.028368 CAGAATGAATCATGTGAAGCAGTTC 58.972 40.000 0.00 0.00 39.69 3.01
2572 5051 1.603802 AGCGACAATGTTGGTGAACAG 59.396 47.619 4.30 0.00 45.29 3.16
2677 5163 6.773976 TGAACAACAAAAGAATGTCTCCTT 57.226 33.333 0.00 0.00 31.81 3.36
2688 5174 8.964420 AAATACATCGGTATGAACAACAAAAG 57.036 30.769 0.00 0.00 40.09 2.27
2704 5194 5.063817 TGTCAGTGATCAGCAAAATACATCG 59.936 40.000 0.00 0.00 0.00 3.84
2725 5215 1.276705 GGTCTTCCTTGAGGTCCTGTC 59.723 57.143 0.00 0.00 36.34 3.51
2820 5310 1.076777 CAAGGGCCAACCGGATGAT 60.077 57.895 14.18 0.00 46.96 2.45
2823 5313 2.938798 TCCAAGGGCCAACCGGAT 60.939 61.111 9.46 0.00 46.96 4.18
2963 5453 4.521639 TCGTAGTCTCTGCTTGTTTCCTTA 59.478 41.667 0.00 0.00 0.00 2.69
2984 5474 0.376152 GTGCAAGCATCATGTCCTCG 59.624 55.000 0.00 0.00 0.00 4.63
2987 5477 2.089980 AGAAGTGCAAGCATCATGTCC 58.910 47.619 0.00 0.00 0.00 4.02
2990 5480 1.134367 CCCAGAAGTGCAAGCATCATG 59.866 52.381 0.00 0.00 0.00 3.07
3062 5553 8.507249 ACTTGACAGTTTTATGCACTCTTATTC 58.493 33.333 0.00 0.00 0.00 1.75
3085 5576 6.219417 TCATCCATGAAAAACAACACACTT 57.781 33.333 0.00 0.00 33.08 3.16
3152 5643 2.095110 TGCAGCTCAAATGACGAAATGG 60.095 45.455 0.00 0.00 0.00 3.16
3220 5711 7.215789 ACAAAGAATAACACCAATGCAAATGA 58.784 30.769 4.54 0.00 0.00 2.57
3240 5731 9.689976 CTGTATAGACATGAGAATCCTACAAAG 57.310 37.037 0.00 0.00 34.24 2.77
3243 5734 8.996651 TTCTGTATAGACATGAGAATCCTACA 57.003 34.615 0.00 0.00 34.24 2.74
3343 5879 1.272313 GGTTTTAGGGGTTCAGGGGTC 60.272 57.143 0.00 0.00 0.00 4.46
3381 6073 1.837499 GTGCGCCCCTCCCTACTAT 60.837 63.158 4.18 0.00 0.00 2.12
3382 6074 2.443390 GTGCGCCCCTCCCTACTA 60.443 66.667 4.18 0.00 0.00 1.82
3383 6075 4.715130 TGTGCGCCCCTCCCTACT 62.715 66.667 4.18 0.00 0.00 2.57
3384 6076 4.468689 GTGTGCGCCCCTCCCTAC 62.469 72.222 4.18 0.00 0.00 3.18
3388 6080 4.101448 ATCTGTGTGCGCCCCTCC 62.101 66.667 4.18 0.00 0.00 4.30
3389 6081 2.821366 CATCTGTGTGCGCCCCTC 60.821 66.667 4.18 0.00 0.00 4.30
3414 6106 5.552870 TTAGGATAGGAGAGATTGGCAAC 57.447 43.478 0.00 0.00 0.00 4.17
3419 6111 4.464244 TGCGGATTAGGATAGGAGAGATTG 59.536 45.833 0.00 0.00 0.00 2.67
3458 6150 8.408043 TGAGAAGAAGAAAATGCAAAATAGGA 57.592 30.769 0.00 0.00 0.00 2.94
3482 6174 5.747197 ACTACACGTACAAGACTTGTCTTTG 59.253 40.000 23.79 19.10 44.12 2.77
3497 6189 3.090790 TGGGTATTCAGCACTACACGTA 58.909 45.455 0.00 0.00 0.00 3.57
3500 6192 3.877508 GGAATGGGTATTCAGCACTACAC 59.122 47.826 0.00 0.00 43.62 2.90
3503 6195 4.473196 TCTTGGAATGGGTATTCAGCACTA 59.527 41.667 0.00 0.00 43.62 2.74
3538 6230 0.958091 TGAAGTGAAAATGGTGGCCG 59.042 50.000 0.00 0.00 0.00 6.13
3540 6232 5.050159 GTGAAAATGAAGTGAAAATGGTGGC 60.050 40.000 0.00 0.00 0.00 5.01
3541 6233 5.466393 GGTGAAAATGAAGTGAAAATGGTGG 59.534 40.000 0.00 0.00 0.00 4.61
3553 6245 7.661040 ACAAAAGGACATAGGTGAAAATGAAG 58.339 34.615 0.00 0.00 0.00 3.02
3559 6257 5.055265 TGGACAAAAGGACATAGGTGAAA 57.945 39.130 0.00 0.00 0.00 2.69
3561 6259 4.715534 TTGGACAAAAGGACATAGGTGA 57.284 40.909 0.00 0.00 0.00 4.02
3562 6260 5.982890 AATTGGACAAAAGGACATAGGTG 57.017 39.130 0.00 0.00 0.00 4.00
3568 6266 8.250332 GCTCATTAATAATTGGACAAAAGGACA 58.750 33.333 0.00 0.00 0.00 4.02
3577 6275 8.677148 TTCAGGTAGCTCATTAATAATTGGAC 57.323 34.615 0.00 0.00 0.00 4.02
3609 6310 5.985911 TGTGAAGGGATTACTAGCCTTTAC 58.014 41.667 11.64 11.64 28.10 2.01
3610 6311 6.385759 TGATGTGAAGGGATTACTAGCCTTTA 59.614 38.462 0.78 0.00 28.10 1.85
3678 6379 9.706691 TTGAAGAAAACTCGATGTAAAGATACT 57.293 29.630 0.00 0.00 32.98 2.12
3693 6540 7.068716 ACTCCTTATTTGCAGTTGAAGAAAACT 59.931 33.333 0.00 0.00 41.08 2.66
3694 6541 7.203218 ACTCCTTATTTGCAGTTGAAGAAAAC 58.797 34.615 0.00 0.00 0.00 2.43
3695 6542 7.346751 ACTCCTTATTTGCAGTTGAAGAAAA 57.653 32.000 0.00 0.00 0.00 2.29
3696 6543 6.959639 ACTCCTTATTTGCAGTTGAAGAAA 57.040 33.333 0.00 0.00 0.00 2.52
3697 6544 7.719633 AGTTACTCCTTATTTGCAGTTGAAGAA 59.280 33.333 0.00 0.00 0.00 2.52
3698 6545 7.224297 AGTTACTCCTTATTTGCAGTTGAAGA 58.776 34.615 0.00 0.00 0.00 2.87
3699 6546 7.440523 AGTTACTCCTTATTTGCAGTTGAAG 57.559 36.000 0.00 0.00 0.00 3.02
3700 6547 8.946085 CATAGTTACTCCTTATTTGCAGTTGAA 58.054 33.333 0.00 0.00 0.00 2.69
3701 6548 8.318412 TCATAGTTACTCCTTATTTGCAGTTGA 58.682 33.333 0.00 0.00 0.00 3.18
3733 6608 7.526041 TGAATACTGGGCCTAAATATGTTGAT 58.474 34.615 4.53 0.00 0.00 2.57
3742 6617 3.730215 TTGCTGAATACTGGGCCTAAA 57.270 42.857 4.53 0.00 0.00 1.85
3757 6632 0.868406 GAGACTGGGTTCGTTTGCTG 59.132 55.000 0.00 0.00 0.00 4.41
3758 6633 0.468226 TGAGACTGGGTTCGTTTGCT 59.532 50.000 0.00 0.00 0.00 3.91
3764 6639 2.420722 GTCTAGACTGAGACTGGGTTCG 59.579 54.545 15.91 0.00 42.26 3.95
3766 6641 3.527507 TGTCTAGACTGAGACTGGGTT 57.472 47.619 23.01 0.00 45.21 4.11
3793 6684 2.828095 TGCTTGCAACAGCACGGT 60.828 55.556 9.02 0.00 45.14 4.83
3809 6700 4.433615 ACCGCACATACTCTGTTATCTTG 58.566 43.478 0.00 0.00 35.29 3.02
3812 6703 4.928601 TGTACCGCACATACTCTGTTATC 58.071 43.478 0.00 0.00 35.29 1.75
3813 6704 4.401519 ACTGTACCGCACATACTCTGTTAT 59.598 41.667 0.00 0.00 35.29 1.89
3814 6705 3.760151 ACTGTACCGCACATACTCTGTTA 59.240 43.478 0.00 0.00 35.29 2.41
3892 6830 2.091994 GGACTACTGTAGCCCCTGACTA 60.092 54.545 14.55 0.00 0.00 2.59
3933 6871 0.852777 CCGTTGTAGATCCAATCGCG 59.147 55.000 0.00 0.00 0.00 5.87
3964 6902 4.665009 TCATAGAATGCACTTTATCCCCCT 59.335 41.667 0.00 0.00 0.00 4.79
3968 6906 6.073058 TGCGAATCATAGAATGCACTTTATCC 60.073 38.462 0.00 0.00 0.00 2.59
3970 6908 6.866010 TGCGAATCATAGAATGCACTTTAT 57.134 33.333 0.00 0.00 0.00 1.40
3986 6924 2.286654 GGCTGCTTCTGTATTGCGAATC 60.287 50.000 0.00 0.00 0.00 2.52
3991 6929 1.742761 TGAGGCTGCTTCTGTATTGC 58.257 50.000 13.13 0.00 0.00 3.56
3993 6931 3.008375 TGACTTGAGGCTGCTTCTGTATT 59.992 43.478 13.13 0.00 0.00 1.89
3995 6933 1.970640 TGACTTGAGGCTGCTTCTGTA 59.029 47.619 13.13 0.00 0.00 2.74
4000 6938 0.888285 GCACTGACTTGAGGCTGCTT 60.888 55.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.