Multiple sequence alignment - TraesCS2A01G331800

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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 TraesCS2A01G331800 chr2A 100.000 5610 0 0 1 5610 564621719 564616110 0.000000e+00 10360.0
1 TraesCS2A01G331800 chr2B 94.451 5010 166 47 1 4961 497794659 497799605 0.000000e+00 7609.0
2 TraesCS2A01G331800 chr2B 84.452 283 25 11 5091 5355 497799739 497800020 1.550000e-65 261.0
3 TraesCS2A01G331800 chr2B 94.949 99 2 3 5235 5331 548511126 548511223 9.730000e-33 152.0
4 TraesCS2A01G331800 chr2B 87.500 128 12 4 5364 5491 497800071 497800194 1.630000e-30 145.0
5 TraesCS2A01G331800 chr2B 86.667 120 15 1 5491 5610 135771066 135770948 1.270000e-26 132.0
6 TraesCS2A01G331800 chr2B 85.246 122 15 3 5489 5610 731194816 731194698 7.630000e-24 122.0
7 TraesCS2A01G331800 chr2D 92.742 5043 190 81 231 5203 423852695 423857631 0.000000e+00 7123.0
8 TraesCS2A01G331800 chr2D 94.706 170 8 1 1 170 423852525 423852693 4.310000e-66 263.0
9 TraesCS2A01G331800 chr2D 93.396 106 3 2 5222 5323 423859811 423859916 2.710000e-33 154.0
10 TraesCS2A01G331800 chr2D 85.366 123 16 2 5488 5609 540066817 540066696 5.900000e-25 126.0
11 TraesCS2A01G331800 chr2D 100.000 31 0 0 1110 1140 102979786 102979816 2.180000e-04 58.4
12 TraesCS2A01G331800 chr7B 96.842 95 0 3 5234 5326 164164795 164164702 7.530000e-34 156.0
13 TraesCS2A01G331800 chr7A 93.269 104 3 4 5225 5326 209593030 209592929 3.500000e-32 150.0
14 TraesCS2A01G331800 chr3B 100.000 79 0 0 5243 5321 821852354 821852432 4.530000e-31 147.0
15 TraesCS2A01G331800 chr3B 95.604 91 2 2 5236 5326 821733024 821733112 1.630000e-30 145.0
16 TraesCS2A01G331800 chr1A 98.795 83 0 1 5236 5318 495702269 495702350 4.530000e-31 147.0
17 TraesCS2A01G331800 chr1A 86.290 124 16 1 5487 5610 545755484 545755362 3.530000e-27 134.0
18 TraesCS2A01G331800 chr3D 95.556 90 3 1 5234 5323 610344636 610344724 5.860000e-30 143.0
19 TraesCS2A01G331800 chr3D 84.426 122 18 1 5489 5610 454499926 454500046 9.870000e-23 119.0
20 TraesCS2A01G331800 chr5D 86.667 120 15 1 5491 5610 483622361 483622479 1.270000e-26 132.0
21 TraesCS2A01G331800 chr4B 86.179 123 16 1 5488 5610 37726676 37726555 1.270000e-26 132.0
22 TraesCS2A01G331800 chr6D 84.553 123 18 1 5488 5610 419891665 419891786 2.750000e-23 121.0
23 TraesCS2A01G331800 chr6A 84.426 122 18 1 5489 5610 558125858 558125738 9.870000e-23 119.0


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 TraesCS2A01G331800 chr2A 564616110 564621719 5609 True 10360.000000 10360 100.000000 1 5610 1 chr2A.!!$R1 5609
1 TraesCS2A01G331800 chr2B 497794659 497800194 5535 False 2671.666667 7609 88.801000 1 5491 3 chr2B.!!$F2 5490
2 TraesCS2A01G331800 chr2D 423852525 423859916 7391 False 2513.333333 7123 93.614667 1 5323 3 chr2D.!!$F2 5322

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
797 809 0.186386 TTTTTCCTTTCCCTCCCGCA 59.814 50.0 0.0 0.0 0.0 5.69 F
1865 1889 0.178068 ACATAGTCGGGTCATGGCAC 59.822 55.0 0.0 0.0 0.0 5.01 F
2742 2814 0.314935 CACAGGTGATTGGTGGTTGC 59.685 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2448 2519 0.115152 TCTCTCTGGCCTGTGAGGAA 59.885 55.000 30.01 16.51 37.67 3.36 R
3067 3146 1.203622 AGAGACCCTTCCTTCCCCATT 60.204 52.381 0.00 0.00 0.00 3.16 R
4667 4762 0.037326 TCATCGGTGCTTCTTCGCTT 60.037 50.000 0.00 0.00 0.00 4.68 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
37 38 4.627035 GGTTGCCACTTCAATTATTCTTGC 59.373 41.667 0.00 0.00 0.00 4.01
43 44 6.128742 GCCACTTCAATTATTCTTGCTGTTTG 60.129 38.462 0.00 0.00 0.00 2.93
44 45 6.366877 CCACTTCAATTATTCTTGCTGTTTGG 59.633 38.462 0.00 0.00 0.00 3.28
118 123 6.204301 CGATAGTCAATCAAAAGATGGAGCAT 59.796 38.462 0.00 0.00 33.87 3.79
205 210 0.828022 AGATTGTGCATGCATTGGGG 59.172 50.000 25.64 0.00 0.00 4.96
249 254 2.928801 TTAGTGAAGGCTGTTCTGCA 57.071 45.000 0.00 0.00 34.04 4.41
277 282 3.004752 ACAGGGCAAGGACATGATAAC 57.995 47.619 0.00 0.00 0.00 1.89
307 312 1.659098 GCTCAAACGAGTTACCATCGG 59.341 52.381 0.00 0.00 44.36 4.18
314 319 2.289195 ACGAGTTACCATCGGCAGAAAA 60.289 45.455 0.00 0.00 44.36 2.29
332 337 8.992073 GGCAGAAAAATAGAATTTCACACAATT 58.008 29.630 0.00 0.00 38.86 2.32
360 365 5.593679 AATCAAGCACAGTACTATACGGT 57.406 39.130 0.00 0.00 37.58 4.83
388 393 1.464997 GACCAAAACTGGCACTCGATC 59.535 52.381 0.00 0.00 0.00 3.69
467 472 1.026718 AGCACCAAAGTCCTATGCGC 61.027 55.000 0.00 0.00 41.23 6.09
504 514 2.863137 CAATTTCTCTCTCTACCTGCGC 59.137 50.000 0.00 0.00 0.00 6.09
692 702 4.216257 TGCAGTAAAAACAGAGATCAAGCC 59.784 41.667 0.00 0.00 0.00 4.35
726 737 9.899661 AATATATACTGCTAGTGGTGTTTTTGA 57.100 29.630 0.00 0.00 0.00 2.69
727 738 7.849804 ATATACTGCTAGTGGTGTTTTTGAG 57.150 36.000 0.00 0.00 0.00 3.02
728 739 3.886123 ACTGCTAGTGGTGTTTTTGAGT 58.114 40.909 0.00 0.00 0.00 3.41
729 740 5.031066 ACTGCTAGTGGTGTTTTTGAGTA 57.969 39.130 0.00 0.00 0.00 2.59
730 741 4.814771 ACTGCTAGTGGTGTTTTTGAGTAC 59.185 41.667 0.00 0.00 0.00 2.73
735 746 6.145696 GCTAGTGGTGTTTTTGAGTACAGTAG 59.854 42.308 0.00 0.00 34.91 2.57
797 809 0.186386 TTTTTCCTTTCCCTCCCGCA 59.814 50.000 0.00 0.00 0.00 5.69
995 1019 2.667199 GCGGTGGTGTGGTGGTAC 60.667 66.667 0.00 0.00 0.00 3.34
1140 1164 1.607801 GCTTTGGATGGCCCCTTGTC 61.608 60.000 0.00 0.00 0.00 3.18
1218 1242 1.410882 GAGGATCACTGCTCCAGGTAC 59.589 57.143 1.79 0.00 35.51 3.34
1265 1289 0.822944 CATTCACCACAGCCACACCA 60.823 55.000 0.00 0.00 0.00 4.17
1266 1290 0.823356 ATTCACCACAGCCACACCAC 60.823 55.000 0.00 0.00 0.00 4.16
1267 1291 2.124362 CACCACAGCCACACCACA 60.124 61.111 0.00 0.00 0.00 4.17
1268 1292 2.124320 ACCACAGCCACACCACAC 60.124 61.111 0.00 0.00 0.00 3.82
1269 1293 2.906897 CCACAGCCACACCACACC 60.907 66.667 0.00 0.00 0.00 4.16
1383 1407 4.081420 TCCTGACTCAGCACCTTTATCTTC 60.081 45.833 0.00 0.00 0.00 2.87
1384 1408 4.187694 CTGACTCAGCACCTTTATCTTCC 58.812 47.826 0.00 0.00 0.00 3.46
1391 1415 5.006386 CAGCACCTTTATCTTCCTGTCTTT 58.994 41.667 0.00 0.00 0.00 2.52
1397 1421 4.908601 TTATCTTCCTGTCTTTGCTCCA 57.091 40.909 0.00 0.00 0.00 3.86
1483 1507 3.245264 ACCTATTGTTTTGTGGGGGAGAG 60.245 47.826 0.00 0.00 0.00 3.20
1485 1509 2.656947 TTGTTTTGTGGGGGAGAGAG 57.343 50.000 0.00 0.00 0.00 3.20
1509 1533 5.513962 GGATGGAAAGATCTCATAAGACCCC 60.514 48.000 0.00 0.00 33.32 4.95
1513 1537 5.788014 GGAAAGATCTCATAAGACCCCCTAT 59.212 44.000 0.00 0.00 33.32 2.57
1538 1562 6.645827 TCAAATGATGGCAACTTAACAACATG 59.354 34.615 0.00 0.00 29.72 3.21
1540 1564 5.781210 TGATGGCAACTTAACAACATGAA 57.219 34.783 0.00 0.00 37.61 2.57
1572 1596 5.654603 AACATTGCAGTTGATGTGATGAT 57.345 34.783 2.59 0.00 36.65 2.45
1573 1597 4.993905 ACATTGCAGTTGATGTGATGATG 58.006 39.130 0.96 0.00 35.31 3.07
1574 1598 4.703093 ACATTGCAGTTGATGTGATGATGA 59.297 37.500 0.96 0.00 35.31 2.92
1677 1701 1.202330 CCTGCAGAATGAGGAGAGGT 58.798 55.000 17.39 0.00 39.69 3.85
1745 1769 1.222936 CTCCATGCTGGTGGTCCTC 59.777 63.158 2.68 0.00 39.03 3.71
1787 1811 1.377856 GAACCTTGCTCTGGCCCTC 60.378 63.158 0.00 0.00 37.74 4.30
1799 1823 4.083862 GCCCTCGTCACCTCCACC 62.084 72.222 0.00 0.00 0.00 4.61
1856 1880 3.264897 GCGCTGCACATAGTCGGG 61.265 66.667 0.00 0.00 0.00 5.14
1865 1889 0.178068 ACATAGTCGGGTCATGGCAC 59.822 55.000 0.00 0.00 0.00 5.01
1915 1939 1.202940 GGAGGCAAGAAAGGTTGGTCT 60.203 52.381 0.00 0.00 0.00 3.85
1991 2015 2.107950 TGATCCCGTCAAACATGGAC 57.892 50.000 0.00 0.00 32.78 4.02
2011 2035 4.024387 GGACGAAAAACTCTGCACATGTTA 60.024 41.667 0.00 0.00 0.00 2.41
2340 2367 6.697641 ACTCTGGAATACCACCTTCTTAAA 57.302 37.500 0.00 0.00 41.77 1.52
2441 2512 2.027192 TGACTGAGGTTCTTGGGTATGC 60.027 50.000 0.00 0.00 0.00 3.14
2442 2513 1.282157 ACTGAGGTTCTTGGGTATGCC 59.718 52.381 0.00 0.00 0.00 4.40
2448 2519 2.487265 GGTTCTTGGGTATGCCGATCAT 60.487 50.000 0.00 0.00 39.17 2.45
2589 2660 1.542030 TCTGACGAGGAGAAAGTGAGC 59.458 52.381 0.00 0.00 0.00 4.26
2688 2759 3.027412 GTCAGCTCAAGATCTGGACCTA 58.973 50.000 0.00 0.00 0.00 3.08
2742 2814 0.314935 CACAGGTGATTGGTGGTTGC 59.685 55.000 0.00 0.00 0.00 4.17
2748 2820 1.177895 TGATTGGTGGTTGCGTGCAT 61.178 50.000 0.00 0.00 0.00 3.96
2749 2821 0.733566 GATTGGTGGTTGCGTGCATG 60.734 55.000 0.09 0.09 0.00 4.06
2982 3055 4.264352 ACATCCACCAAATATGTGACCCTT 60.264 41.667 0.00 0.00 35.74 3.95
2985 3058 3.696051 CCACCAAATATGTGACCCTTCAG 59.304 47.826 0.00 0.00 35.74 3.02
2988 3061 5.653769 CACCAAATATGTGACCCTTCAGAAT 59.346 40.000 0.00 0.00 35.74 2.40
2990 3063 6.725834 ACCAAATATGTGACCCTTCAGAATTT 59.274 34.615 0.00 0.00 30.10 1.82
4031 4114 5.298276 CCAAGGTACAAGCAAGAAGTTTACA 59.702 40.000 0.00 0.00 0.00 2.41
4034 4117 4.577283 GGTACAAGCAAGAAGTTTACACCA 59.423 41.667 0.00 0.00 0.00 4.17
4164 4247 6.682746 AGCCGATTAAGAGATACACATGTAG 58.317 40.000 0.00 0.00 33.52 2.74
4300 4392 6.641723 CACAGATTGATGCAGTCTCATACTAG 59.358 42.308 0.00 0.00 35.76 2.57
4311 4406 5.048782 CAGTCTCATACTAGTGGAGATGCTC 60.049 48.000 23.63 14.85 39.63 4.26
4667 4762 4.924305 AAAAAGAGATTGCAAGCAGTGA 57.076 36.364 18.24 0.00 0.00 3.41
4668 4763 4.924305 AAAAGAGATTGCAAGCAGTGAA 57.076 36.364 18.24 0.00 0.00 3.18
4669 4764 4.500603 AAAGAGATTGCAAGCAGTGAAG 57.499 40.909 18.24 0.00 0.00 3.02
4670 4765 1.811359 AGAGATTGCAAGCAGTGAAGC 59.189 47.619 18.24 0.00 0.00 3.86
4882 4978 9.113876 GGTGTTTACATTTACTTCTGAAATTCG 57.886 33.333 0.00 0.00 0.00 3.34
4883 4979 9.659830 GTGTTTACATTTACTTCTGAAATTCGT 57.340 29.630 0.00 0.00 0.00 3.85
4936 5032 4.390909 ACTGAAACTTCGAAACAACGTTCT 59.609 37.500 0.00 0.00 34.70 3.01
4940 5036 7.121272 TGAAACTTCGAAACAACGTTCTTATC 58.879 34.615 0.00 0.00 34.70 1.75
4944 5040 5.585500 TCGAAACAACGTTCTTATCCTTG 57.415 39.130 0.00 0.00 34.70 3.61
4950 5046 4.226761 CAACGTTCTTATCCTTGCCAAAC 58.773 43.478 0.00 0.00 0.00 2.93
4961 5061 2.890311 CCTTGCCAAACAGACCATGTAA 59.110 45.455 0.00 0.00 43.00 2.41
4963 5063 3.222173 TGCCAAACAGACCATGTAAGT 57.778 42.857 0.00 0.00 43.00 2.24
4964 5064 3.146066 TGCCAAACAGACCATGTAAGTC 58.854 45.455 0.00 0.00 43.00 3.01
4965 5065 2.488153 GCCAAACAGACCATGTAAGTCC 59.512 50.000 0.00 0.00 43.00 3.85
4966 5066 3.081804 CCAAACAGACCATGTAAGTCCC 58.918 50.000 0.00 0.00 43.00 4.46
4969 5069 4.447138 AACAGACCATGTAAGTCCCAAA 57.553 40.909 0.00 0.00 43.00 3.28
4971 5071 4.798882 ACAGACCATGTAAGTCCCAAAAA 58.201 39.130 0.00 0.00 41.60 1.94
4997 5097 6.824305 AAAGACCATGTAAGAGAACATTGG 57.176 37.500 0.00 0.00 38.01 3.16
4998 5098 4.848357 AGACCATGTAAGAGAACATTGGG 58.152 43.478 0.00 0.00 38.01 4.12
4999 5099 4.536090 AGACCATGTAAGAGAACATTGGGA 59.464 41.667 0.00 0.00 38.01 4.37
5000 5100 5.014123 AGACCATGTAAGAGAACATTGGGAA 59.986 40.000 0.00 0.00 38.01 3.97
5001 5101 5.831103 ACCATGTAAGAGAACATTGGGAAT 58.169 37.500 0.00 0.00 38.01 3.01
5005 5105 6.588719 TGTAAGAGAACATTGGGAATTTGG 57.411 37.500 0.00 0.00 0.00 3.28
5015 5115 2.533916 TGGGAATTTGGCATAAGCACA 58.466 42.857 0.00 0.00 44.61 4.57
5021 5121 1.533625 TTGGCATAAGCACACCAGTC 58.466 50.000 0.00 0.00 44.61 3.51
5023 5123 1.089920 GGCATAAGCACACCAGTCAG 58.910 55.000 0.00 0.00 44.61 3.51
5043 5143 5.698545 GTCAGCAGAGAGTGAAGTTATTGTT 59.301 40.000 0.00 0.00 0.00 2.83
5053 5153 9.185680 AGAGTGAAGTTATTGTTTAAAACTGGT 57.814 29.630 0.00 0.00 33.85 4.00
5111 5225 7.567250 TGTAAATCAGTATGGGGAGATTCTACA 59.433 37.037 0.00 0.00 36.16 2.74
5118 5258 2.225779 TGGGGAGATTCTACAAGGGACA 60.226 50.000 0.00 0.00 0.00 4.02
5125 5265 6.332976 AGATTCTACAAGGGACATTTGGAT 57.667 37.500 0.00 0.00 0.00 3.41
5134 5274 4.514401 AGGGACATTTGGATAGAACGAAC 58.486 43.478 0.00 0.00 0.00 3.95
5159 5299 6.625873 AGTCCTTCAGAATTCAGTTGAAAC 57.374 37.500 8.44 5.62 37.61 2.78
5197 5344 7.622502 TGGATAATGAGAGGAGATCAATGAA 57.377 36.000 0.00 0.00 0.00 2.57
5218 5365 2.173569 ACAGAGGCTTTGTTCAGGAGTT 59.826 45.455 4.61 0.00 0.00 3.01
5230 7538 8.924511 TTTGTTCAGGAGTTTAGAGAATGATT 57.075 30.769 0.00 0.00 0.00 2.57
5231 7539 7.912056 TGTTCAGGAGTTTAGAGAATGATTG 57.088 36.000 0.00 0.00 0.00 2.67
5232 7540 6.372659 TGTTCAGGAGTTTAGAGAATGATTGC 59.627 38.462 0.00 0.00 0.00 3.56
5233 7541 6.053632 TCAGGAGTTTAGAGAATGATTGCA 57.946 37.500 0.00 0.00 0.00 4.08
5234 7542 6.111382 TCAGGAGTTTAGAGAATGATTGCAG 58.889 40.000 0.00 0.00 0.00 4.41
5240 7548 9.122613 GAGTTTAGAGAATGATTGCAGAAAAAC 57.877 33.333 0.00 0.00 0.00 2.43
5241 7549 8.854117 AGTTTAGAGAATGATTGCAGAAAAACT 58.146 29.630 0.00 0.00 0.00 2.66
5324 7641 2.571653 TGAGCTAATAGGCCTTGTGTGT 59.428 45.455 12.58 0.00 0.00 3.72
5326 7643 4.224147 TGAGCTAATAGGCCTTGTGTGTAA 59.776 41.667 12.58 0.00 0.00 2.41
5327 7644 5.174037 AGCTAATAGGCCTTGTGTGTAAA 57.826 39.130 12.58 0.00 0.00 2.01
5328 7645 4.941873 AGCTAATAGGCCTTGTGTGTAAAC 59.058 41.667 12.58 0.00 0.00 2.01
5329 7646 4.941873 GCTAATAGGCCTTGTGTGTAAACT 59.058 41.667 12.58 0.00 0.00 2.66
5332 7649 2.851195 AGGCCTTGTGTGTAAACTGAG 58.149 47.619 0.00 0.00 0.00 3.35
5334 7651 1.266989 GCCTTGTGTGTAAACTGAGCC 59.733 52.381 0.00 0.00 0.00 4.70
5341 7658 4.814234 TGTGTGTAAACTGAGCCAGTAAAG 59.186 41.667 8.07 0.00 44.62 1.85
5343 7660 3.813166 GTGTAAACTGAGCCAGTAAAGCA 59.187 43.478 8.07 3.98 44.62 3.91
5344 7661 3.813166 TGTAAACTGAGCCAGTAAAGCAC 59.187 43.478 8.07 4.09 44.62 4.40
5349 7666 5.677319 ACTGAGCCAGTAAAGCACTTATA 57.323 39.130 6.10 0.00 43.46 0.98
5355 7672 8.428852 TGAGCCAGTAAAGCACTTATATATGAA 58.571 33.333 2.80 0.00 34.26 2.57
5356 7673 9.442047 GAGCCAGTAAAGCACTTATATATGAAT 57.558 33.333 2.80 0.00 34.26 2.57
5357 7674 9.442047 AGCCAGTAAAGCACTTATATATGAATC 57.558 33.333 2.80 0.00 34.26 2.52
5397 7755 4.081697 TCCAGAATCAGTCAAAGCGTATGA 60.082 41.667 0.00 0.00 0.00 2.15
5403 7761 3.119459 TCAGTCAAAGCGTATGACCTCTC 60.119 47.826 13.59 0.00 46.60 3.20
5407 7765 5.361285 AGTCAAAGCGTATGACCTCTCTTAT 59.639 40.000 13.59 0.00 46.60 1.73
5408 7766 6.043411 GTCAAAGCGTATGACCTCTCTTATT 58.957 40.000 7.96 0.00 41.02 1.40
5409 7767 6.535508 GTCAAAGCGTATGACCTCTCTTATTT 59.464 38.462 7.96 0.00 41.02 1.40
5448 7806 0.537188 AGTCAGGGCGTATGTTGGAG 59.463 55.000 0.00 0.00 0.00 3.86
5449 7807 0.535335 GTCAGGGCGTATGTTGGAGA 59.465 55.000 0.00 0.00 0.00 3.71
5459 7817 5.295787 GGCGTATGTTGGAGAAAATATGACA 59.704 40.000 0.00 0.00 0.00 3.58
5471 7829 5.755375 AGAAAATATGACATACTGGCAGACG 59.245 40.000 23.66 11.09 39.76 4.18
5478 7836 3.782046 ACATACTGGCAGACGACAATAC 58.218 45.455 23.66 0.00 0.00 1.89
5484 7842 0.522705 GCAGACGACAATACGCTCGA 60.523 55.000 0.00 0.00 36.70 4.04
5486 7844 1.085091 AGACGACAATACGCTCGACT 58.915 50.000 0.00 0.00 36.70 4.18
5491 7849 3.242349 ACGACAATACGCTCGACTCTAAG 60.242 47.826 0.00 0.00 36.70 2.18
5492 7850 3.619729 GACAATACGCTCGACTCTAAGG 58.380 50.000 0.00 0.00 0.00 2.69
5493 7851 2.358267 ACAATACGCTCGACTCTAAGGG 59.642 50.000 0.00 0.00 0.00 3.95
5494 7852 0.953003 ATACGCTCGACTCTAAGGGC 59.047 55.000 0.00 0.00 0.00 5.19
5495 7853 0.393402 TACGCTCGACTCTAAGGGCA 60.393 55.000 0.00 0.00 0.00 5.36
5496 7854 1.038130 ACGCTCGACTCTAAGGGCAT 61.038 55.000 0.00 0.00 0.00 4.40
5497 7855 0.596083 CGCTCGACTCTAAGGGCATG 60.596 60.000 0.00 0.00 0.00 4.06
5498 7856 0.461961 GCTCGACTCTAAGGGCATGT 59.538 55.000 0.00 0.00 0.00 3.21
5499 7857 1.681793 GCTCGACTCTAAGGGCATGTA 59.318 52.381 0.00 0.00 0.00 2.29
5500 7858 2.544069 GCTCGACTCTAAGGGCATGTAC 60.544 54.545 0.00 0.00 0.00 2.90
5501 7859 2.688446 CTCGACTCTAAGGGCATGTACA 59.312 50.000 0.00 0.00 0.00 2.90
5502 7860 3.093814 TCGACTCTAAGGGCATGTACAA 58.906 45.455 0.00 0.00 0.00 2.41
5503 7861 3.704566 TCGACTCTAAGGGCATGTACAAT 59.295 43.478 0.00 0.00 0.00 2.71
5504 7862 3.804325 CGACTCTAAGGGCATGTACAATG 59.196 47.826 0.00 0.12 0.00 2.82
5505 7863 4.441495 CGACTCTAAGGGCATGTACAATGA 60.441 45.833 0.00 0.00 0.00 2.57
5506 7864 5.615289 GACTCTAAGGGCATGTACAATGAT 58.385 41.667 0.00 0.00 0.00 2.45
5507 7865 5.371526 ACTCTAAGGGCATGTACAATGATG 58.628 41.667 0.00 0.00 0.00 3.07
5508 7866 4.717877 TCTAAGGGCATGTACAATGATGG 58.282 43.478 0.00 0.00 0.00 3.51
5509 7867 1.696063 AGGGCATGTACAATGATGGC 58.304 50.000 11.25 11.25 42.82 4.40
5510 7868 1.063792 AGGGCATGTACAATGATGGCA 60.064 47.619 18.87 0.00 44.77 4.92
5511 7869 1.965643 GGGCATGTACAATGATGGCAT 59.034 47.619 18.87 0.00 44.77 4.40
5512 7870 3.156293 GGGCATGTACAATGATGGCATA 58.844 45.455 18.87 0.00 44.77 3.14
5513 7871 3.765511 GGGCATGTACAATGATGGCATAT 59.234 43.478 18.87 0.00 44.77 1.78
5514 7872 4.381185 GGGCATGTACAATGATGGCATATG 60.381 45.833 18.87 2.78 44.77 1.78
5515 7873 4.381185 GGCATGTACAATGATGGCATATGG 60.381 45.833 14.01 0.00 43.00 2.74
5516 7874 4.460034 GCATGTACAATGATGGCATATGGA 59.540 41.667 0.00 0.00 33.44 3.41
5517 7875 5.126545 GCATGTACAATGATGGCATATGGAT 59.873 40.000 0.00 0.00 33.44 3.41
5518 7876 6.319405 GCATGTACAATGATGGCATATGGATA 59.681 38.462 0.00 0.00 33.44 2.59
5519 7877 7.680350 GCATGTACAATGATGGCATATGGATAC 60.680 40.741 0.00 2.02 33.44 2.24
5520 7878 6.777782 TGTACAATGATGGCATATGGATACA 58.222 36.000 0.00 4.71 43.07 2.29
5537 7895 7.894753 TGGATACATATGCCTCATTGAAAAA 57.105 32.000 1.58 0.00 46.17 1.94
5560 7918 8.581253 AAAAAGTAGCTTGAGGCAATTATACT 57.419 30.769 0.00 0.00 44.79 2.12
5561 7919 7.559590 AAAGTAGCTTGAGGCAATTATACTG 57.440 36.000 0.00 0.00 44.79 2.74
5562 7920 6.485830 AGTAGCTTGAGGCAATTATACTGA 57.514 37.500 0.00 0.00 44.79 3.41
5563 7921 7.072263 AGTAGCTTGAGGCAATTATACTGAT 57.928 36.000 0.00 0.00 44.79 2.90
5564 7922 7.512992 AGTAGCTTGAGGCAATTATACTGATT 58.487 34.615 0.00 0.00 44.79 2.57
5565 7923 7.995488 AGTAGCTTGAGGCAATTATACTGATTT 59.005 33.333 0.00 0.00 44.79 2.17
5566 7924 7.651027 AGCTTGAGGCAATTATACTGATTTT 57.349 32.000 0.00 0.00 44.79 1.82
5567 7925 7.710896 AGCTTGAGGCAATTATACTGATTTTC 58.289 34.615 0.00 0.00 44.79 2.29
5568 7926 7.559170 AGCTTGAGGCAATTATACTGATTTTCT 59.441 33.333 0.00 0.00 44.79 2.52
5569 7927 7.859875 GCTTGAGGCAATTATACTGATTTTCTC 59.140 37.037 0.00 0.00 41.35 2.87
5570 7928 9.118300 CTTGAGGCAATTATACTGATTTTCTCT 57.882 33.333 0.00 0.00 0.00 3.10
5571 7929 8.668510 TGAGGCAATTATACTGATTTTCTCTC 57.331 34.615 0.00 0.00 0.00 3.20
5572 7930 7.716998 TGAGGCAATTATACTGATTTTCTCTCC 59.283 37.037 0.00 0.00 0.00 3.71
5573 7931 7.001073 AGGCAATTATACTGATTTTCTCTCCC 58.999 38.462 0.00 0.00 0.00 4.30
5574 7932 6.207614 GGCAATTATACTGATTTTCTCTCCCC 59.792 42.308 0.00 0.00 0.00 4.81
5575 7933 6.772716 GCAATTATACTGATTTTCTCTCCCCA 59.227 38.462 0.00 0.00 0.00 4.96
5576 7934 7.285401 GCAATTATACTGATTTTCTCTCCCCAA 59.715 37.037 0.00 0.00 0.00 4.12
5577 7935 9.359653 CAATTATACTGATTTTCTCTCCCCAAT 57.640 33.333 0.00 0.00 0.00 3.16
5580 7938 5.779241 ACTGATTTTCTCTCCCCAATACA 57.221 39.130 0.00 0.00 0.00 2.29
5581 7939 6.139679 ACTGATTTTCTCTCCCCAATACAA 57.860 37.500 0.00 0.00 0.00 2.41
5582 7940 6.552008 ACTGATTTTCTCTCCCCAATACAAA 58.448 36.000 0.00 0.00 0.00 2.83
5583 7941 6.434340 ACTGATTTTCTCTCCCCAATACAAAC 59.566 38.462 0.00 0.00 0.00 2.93
5584 7942 6.552008 TGATTTTCTCTCCCCAATACAAACT 58.448 36.000 0.00 0.00 0.00 2.66
5585 7943 7.695055 TGATTTTCTCTCCCCAATACAAACTA 58.305 34.615 0.00 0.00 0.00 2.24
5586 7944 7.610305 TGATTTTCTCTCCCCAATACAAACTAC 59.390 37.037 0.00 0.00 0.00 2.73
5587 7945 6.697641 TTTCTCTCCCCAATACAAACTACT 57.302 37.500 0.00 0.00 0.00 2.57
5588 7946 7.801893 TTTCTCTCCCCAATACAAACTACTA 57.198 36.000 0.00 0.00 0.00 1.82
5589 7947 6.786967 TCTCTCCCCAATACAAACTACTAC 57.213 41.667 0.00 0.00 0.00 2.73
5590 7948 6.500336 TCTCTCCCCAATACAAACTACTACT 58.500 40.000 0.00 0.00 0.00 2.57
5591 7949 7.645942 TCTCTCCCCAATACAAACTACTACTA 58.354 38.462 0.00 0.00 0.00 1.82
5592 7950 8.117956 TCTCTCCCCAATACAAACTACTACTAA 58.882 37.037 0.00 0.00 0.00 2.24
5593 7951 8.849543 TCTCCCCAATACAAACTACTACTAAT 57.150 34.615 0.00 0.00 0.00 1.73
5594 7952 8.701895 TCTCCCCAATACAAACTACTACTAATG 58.298 37.037 0.00 0.00 0.00 1.90
5595 7953 7.798071 TCCCCAATACAAACTACTACTAATGG 58.202 38.462 0.00 0.00 0.00 3.16
5596 7954 6.996282 CCCCAATACAAACTACTACTAATGGG 59.004 42.308 0.00 0.00 41.78 4.00
5597 7955 7.366191 CCCCAATACAAACTACTACTAATGGGT 60.366 40.741 0.00 0.00 40.77 4.51
5598 7956 7.713942 CCCAATACAAACTACTACTAATGGGTC 59.286 40.741 0.00 0.00 38.20 4.46
5599 7957 8.483758 CCAATACAAACTACTACTAATGGGTCT 58.516 37.037 0.00 0.00 0.00 3.85
5600 7958 9.530633 CAATACAAACTACTACTAATGGGTCTC 57.469 37.037 0.00 0.00 0.00 3.36
5601 7959 8.834004 ATACAAACTACTACTAATGGGTCTCA 57.166 34.615 0.00 0.00 0.00 3.27
5602 7960 7.735326 ACAAACTACTACTAATGGGTCTCAT 57.265 36.000 0.00 0.00 37.79 2.90
5603 7961 7.783042 ACAAACTACTACTAATGGGTCTCATC 58.217 38.462 0.00 0.00 34.44 2.92
5604 7962 7.399191 ACAAACTACTACTAATGGGTCTCATCA 59.601 37.037 0.00 0.00 34.44 3.07
5605 7963 7.973048 AACTACTACTAATGGGTCTCATCAA 57.027 36.000 0.00 0.00 34.44 2.57
5606 7964 7.589958 ACTACTACTAATGGGTCTCATCAAG 57.410 40.000 0.00 0.00 34.44 3.02
5607 7965 7.355101 ACTACTACTAATGGGTCTCATCAAGA 58.645 38.462 2.75 0.00 34.44 3.02
5608 7966 7.839705 ACTACTACTAATGGGTCTCATCAAGAA 59.160 37.037 2.75 0.00 35.21 2.52
5609 7967 7.496346 ACTACTAATGGGTCTCATCAAGAAA 57.504 36.000 2.75 0.00 35.21 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 0.682209 CAGGCTCATCCCCCAAACAG 60.682 60.000 0.00 0.00 34.51 3.16
43 44 1.077429 GTCAACAGGCTCATCCCCC 60.077 63.158 0.00 0.00 34.51 5.40
44 45 0.038166 TTGTCAACAGGCTCATCCCC 59.962 55.000 0.00 0.00 34.51 4.81
105 110 9.606631 CTAGAGTAAGTTAATGCTCCATCTTTT 57.393 33.333 0.00 0.00 33.07 2.27
118 123 4.142227 CCGCTTGGAGCTAGAGTAAGTTAA 60.142 45.833 0.00 0.00 39.60 2.01
157 162 6.440647 TGTCCTATCTGAACATGTACCTCTTT 59.559 38.462 0.00 0.00 0.00 2.52
205 210 3.315191 TGTGCTCAAAACTCAAAGCTACC 59.685 43.478 0.00 0.00 35.76 3.18
249 254 0.486879 TCCTTGCCCTGTTTTCCCAT 59.513 50.000 0.00 0.00 0.00 4.00
277 282 2.609459 ACTCGTTTGAGCAGTGTTCTTG 59.391 45.455 8.54 0.00 46.69 3.02
332 337 9.726232 CGTATAGTACTGTGCTTGATTAGTTTA 57.274 33.333 5.39 0.00 0.00 2.01
360 365 1.679139 CCAGTTTTGGTCACAGCAGA 58.321 50.000 0.00 0.00 39.79 4.26
467 472 4.272504 AGAAATTGTATCGGGTTACATGCG 59.727 41.667 0.00 0.00 32.39 4.73
504 514 0.040958 GCTCAAGGTGCAGTCAAACG 60.041 55.000 0.00 0.00 0.00 3.60
649 659 1.298859 GACCCGGCTGCTTGTACTTG 61.299 60.000 0.00 0.00 0.00 3.16
797 809 2.105766 GGCAGGAAGGATCTTTGCAAT 58.894 47.619 11.58 0.00 37.65 3.56
979 1003 2.356553 CGTACCACCACACCACCG 60.357 66.667 0.00 0.00 0.00 4.94
995 1019 2.203252 CCCCCACCATCATGCTCG 60.203 66.667 0.00 0.00 0.00 5.03
1140 1164 3.358076 GAACCTGAGGGTCTCGCCG 62.358 68.421 9.85 0.00 46.67 6.46
1265 1289 2.632996 TCGTGGAGAAATCTTGAGGTGT 59.367 45.455 0.00 0.00 0.00 4.16
1266 1290 3.319137 TCGTGGAGAAATCTTGAGGTG 57.681 47.619 0.00 0.00 0.00 4.00
1267 1291 3.866651 CATCGTGGAGAAATCTTGAGGT 58.133 45.455 0.00 0.00 0.00 3.85
1268 1292 2.611292 GCATCGTGGAGAAATCTTGAGG 59.389 50.000 0.00 0.00 0.00 3.86
1269 1293 3.264947 TGCATCGTGGAGAAATCTTGAG 58.735 45.455 0.00 0.00 0.00 3.02
1383 1407 0.251077 AGCCTTGGAGCAAAGACAGG 60.251 55.000 0.00 0.00 34.23 4.00
1384 1408 0.879765 CAGCCTTGGAGCAAAGACAG 59.120 55.000 0.00 0.00 34.23 3.51
1391 1415 4.712051 AATATATCACAGCCTTGGAGCA 57.288 40.909 0.00 0.00 34.23 4.26
1455 1479 5.305902 CCCCCACAAAACAATAGGTAAAACT 59.694 40.000 0.00 0.00 0.00 2.66
1460 1484 3.917629 TCTCCCCCACAAAACAATAGGTA 59.082 43.478 0.00 0.00 0.00 3.08
1483 1507 6.463360 GGTCTTATGAGATCTTTCCATCCTC 58.537 44.000 0.00 0.00 33.70 3.71
1485 1509 5.513962 GGGGTCTTATGAGATCTTTCCATCC 60.514 48.000 0.00 0.00 33.33 3.51
1509 1533 7.099266 TGTTAAGTTGCCATCATTTGATAGG 57.901 36.000 0.00 0.00 32.63 2.57
1513 1537 6.154203 TGTTGTTAAGTTGCCATCATTTGA 57.846 33.333 0.00 0.00 0.00 2.69
1540 1564 8.362639 ACATCAACTGCAATGTTAGATCTTTTT 58.637 29.630 0.00 0.00 32.24 1.94
1548 1572 6.185852 TCATCACATCAACTGCAATGTTAG 57.814 37.500 0.00 0.00 33.92 2.34
1557 1581 4.261197 CCTGCATCATCATCACATCAACTG 60.261 45.833 0.00 0.00 0.00 3.16
1572 1596 0.327480 ACCCTCCCATACCTGCATCA 60.327 55.000 0.00 0.00 0.00 3.07
1573 1597 0.109342 CACCCTCCCATACCTGCATC 59.891 60.000 0.00 0.00 0.00 3.91
1574 1598 0.624500 ACACCCTCCCATACCTGCAT 60.625 55.000 0.00 0.00 0.00 3.96
1677 1701 0.250727 GGGTAGCTGCACTGGAACAA 60.251 55.000 3.61 0.00 38.70 2.83
1745 1769 4.760047 CGCTTGTGGTCCTCCCCG 62.760 72.222 0.00 0.00 0.00 5.73
1787 1811 1.374758 GAGCTTGGTGGAGGTGACG 60.375 63.158 0.00 0.00 0.00 4.35
1856 1880 3.443045 CCCTTGCCGTGCCATGAC 61.443 66.667 0.00 0.00 0.00 3.06
1879 1903 0.809241 CTCCTCGCAGAAGGTGATGC 60.809 60.000 0.00 0.00 39.09 3.91
1953 1977 1.878088 CATGTCCCTACTGATGCATGC 59.122 52.381 11.82 11.82 0.00 4.06
1981 2005 3.730715 GCAGAGTTTTTCGTCCATGTTTG 59.269 43.478 0.00 0.00 0.00 2.93
1991 2015 4.024048 AGGTAACATGTGCAGAGTTTTTCG 60.024 41.667 0.00 0.00 41.41 3.46
2011 2035 3.586174 AGCATGATGATGTAGCCATAGGT 59.414 43.478 0.00 0.00 31.50 3.08
2154 2181 3.681897 CCTGCTTCACTATCACACTGAAC 59.318 47.826 0.00 0.00 0.00 3.18
2190 2217 2.267324 GTGACAGGCTCCTCTGGC 59.733 66.667 0.00 0.00 42.93 4.85
2324 2351 7.778382 ACTTTGACAGTTTAAGAAGGTGGTATT 59.222 33.333 3.35 0.00 27.32 1.89
2340 2367 3.004752 AGTGCTGGAAACTTTGACAGT 57.995 42.857 0.00 0.00 37.30 3.55
2420 2491 2.027192 GCATACCCAAGAACCTCAGTCA 60.027 50.000 0.00 0.00 0.00 3.41
2421 2492 2.633488 GCATACCCAAGAACCTCAGTC 58.367 52.381 0.00 0.00 0.00 3.51
2422 2493 1.282157 GGCATACCCAAGAACCTCAGT 59.718 52.381 0.00 0.00 0.00 3.41
2423 2494 1.743772 CGGCATACCCAAGAACCTCAG 60.744 57.143 0.00 0.00 0.00 3.35
2441 2512 0.533755 GGCCTGTGAGGAATGATCGG 60.534 60.000 0.00 0.00 37.67 4.18
2442 2513 0.178767 TGGCCTGTGAGGAATGATCG 59.821 55.000 3.32 0.00 37.67 3.69
2448 2519 0.115152 TCTCTCTGGCCTGTGAGGAA 59.885 55.000 30.01 16.51 37.67 3.36
2589 2660 1.239968 GCAGGGAGTCCAGCACAAAG 61.240 60.000 18.06 0.00 44.00 2.77
2619 2690 1.177401 TCATGAGTGAGGTGGTCTCG 58.823 55.000 0.00 0.00 45.32 4.04
2742 2814 9.139174 TCATATATAATAAGTGACACATGCACG 57.861 33.333 8.59 0.00 41.04 5.34
2944 3016 7.675161 TGGTGGATGTCTGATAATAGAAAGA 57.325 36.000 0.00 0.00 0.00 2.52
2959 3031 3.269381 AGGGTCACATATTTGGTGGATGT 59.731 43.478 0.00 0.00 36.90 3.06
2965 3037 4.927267 TCTGAAGGGTCACATATTTGGT 57.073 40.909 0.00 0.00 0.00 3.67
3006 3085 4.826274 TTCCAGATATAGGCAGGCATAC 57.174 45.455 0.00 0.00 0.00 2.39
3067 3146 1.203622 AGAGACCCTTCCTTCCCCATT 60.204 52.381 0.00 0.00 0.00 3.16
3617 3696 7.755618 AGGCTTCCCTAAACAAGCATATTATA 58.244 34.615 6.04 0.00 45.85 0.98
4164 4247 0.453449 GCTCTTGCTGCGTTAGTTGC 60.453 55.000 0.00 0.00 36.03 4.17
4445 4540 7.271511 AGATTCAGTAAGCACTTATCTCCTTG 58.728 38.462 0.00 0.00 32.13 3.61
4629 4724 1.686355 TTTTCACTCACCGCCATGTT 58.314 45.000 0.00 0.00 0.00 2.71
4664 4759 0.944311 TCGGTGCTTCTTCGCTTCAC 60.944 55.000 0.00 0.00 0.00 3.18
4666 4761 0.371645 CATCGGTGCTTCTTCGCTTC 59.628 55.000 0.00 0.00 0.00 3.86
4667 4762 0.037326 TCATCGGTGCTTCTTCGCTT 60.037 50.000 0.00 0.00 0.00 4.68
4668 4763 0.737715 GTCATCGGTGCTTCTTCGCT 60.738 55.000 0.00 0.00 0.00 4.93
4669 4764 0.737715 AGTCATCGGTGCTTCTTCGC 60.738 55.000 0.00 0.00 0.00 4.70
4670 4765 2.455032 CTAGTCATCGGTGCTTCTTCG 58.545 52.381 0.00 0.00 0.00 3.79
4707 4802 0.471617 CTCAGCTACCCCATTCCAGG 59.528 60.000 0.00 0.00 0.00 4.45
4882 4978 6.106673 CGGTTCATACATATCTCCCCATAAC 58.893 44.000 0.00 0.00 0.00 1.89
4883 4979 5.188948 CCGGTTCATACATATCTCCCCATAA 59.811 44.000 0.00 0.00 0.00 1.90
4936 5032 3.517296 TGGTCTGTTTGGCAAGGATAA 57.483 42.857 0.00 0.00 0.00 1.75
4940 5036 1.331214 ACATGGTCTGTTTGGCAAGG 58.669 50.000 0.00 0.00 32.90 3.61
4944 5040 2.488153 GGACTTACATGGTCTGTTTGGC 59.512 50.000 0.00 0.00 39.39 4.52
4971 5071 8.960591 CCAATGTTCTCTTACATGGTCTTTATT 58.039 33.333 0.00 0.00 38.69 1.40
4972 5072 7.557719 CCCAATGTTCTCTTACATGGTCTTTAT 59.442 37.037 0.00 0.00 38.69 1.40
4973 5073 6.884295 CCCAATGTTCTCTTACATGGTCTTTA 59.116 38.462 0.00 0.00 38.69 1.85
4974 5074 5.711976 CCCAATGTTCTCTTACATGGTCTTT 59.288 40.000 0.00 0.00 38.69 2.52
4975 5075 5.014123 TCCCAATGTTCTCTTACATGGTCTT 59.986 40.000 0.00 0.00 38.69 3.01
4976 5076 4.536090 TCCCAATGTTCTCTTACATGGTCT 59.464 41.667 0.00 0.00 38.69 3.85
4977 5077 4.843728 TCCCAATGTTCTCTTACATGGTC 58.156 43.478 0.00 0.00 38.69 4.02
4978 5078 4.927267 TCCCAATGTTCTCTTACATGGT 57.073 40.909 0.00 0.00 38.69 3.55
4979 5079 6.780457 AATTCCCAATGTTCTCTTACATGG 57.220 37.500 0.00 0.00 38.69 3.66
4980 5080 7.037438 CCAAATTCCCAATGTTCTCTTACATG 58.963 38.462 0.00 0.00 38.69 3.21
4981 5081 6.351286 GCCAAATTCCCAATGTTCTCTTACAT 60.351 38.462 0.00 0.00 40.37 2.29
4982 5082 5.047377 GCCAAATTCCCAATGTTCTCTTACA 60.047 40.000 0.00 0.00 0.00 2.41
4983 5083 5.047377 TGCCAAATTCCCAATGTTCTCTTAC 60.047 40.000 0.00 0.00 0.00 2.34
4984 5084 5.083122 TGCCAAATTCCCAATGTTCTCTTA 58.917 37.500 0.00 0.00 0.00 2.10
4985 5085 3.903090 TGCCAAATTCCCAATGTTCTCTT 59.097 39.130 0.00 0.00 0.00 2.85
4986 5086 3.509442 TGCCAAATTCCCAATGTTCTCT 58.491 40.909 0.00 0.00 0.00 3.10
4987 5087 3.959535 TGCCAAATTCCCAATGTTCTC 57.040 42.857 0.00 0.00 0.00 2.87
4988 5088 5.627503 GCTTATGCCAAATTCCCAATGTTCT 60.628 40.000 0.00 0.00 0.00 3.01
4989 5089 4.571984 GCTTATGCCAAATTCCCAATGTTC 59.428 41.667 0.00 0.00 0.00 3.18
4990 5090 4.019501 TGCTTATGCCAAATTCCCAATGTT 60.020 37.500 0.00 0.00 38.71 2.71
4991 5091 3.518705 TGCTTATGCCAAATTCCCAATGT 59.481 39.130 0.00 0.00 38.71 2.71
4992 5092 3.872771 GTGCTTATGCCAAATTCCCAATG 59.127 43.478 0.00 0.00 38.71 2.82
4993 5093 3.518705 TGTGCTTATGCCAAATTCCCAAT 59.481 39.130 0.00 0.00 38.71 3.16
4994 5094 2.902486 TGTGCTTATGCCAAATTCCCAA 59.098 40.909 0.00 0.00 38.71 4.12
4995 5095 2.233431 GTGTGCTTATGCCAAATTCCCA 59.767 45.455 0.00 0.00 38.71 4.37
4996 5096 2.418609 GGTGTGCTTATGCCAAATTCCC 60.419 50.000 0.00 0.00 38.71 3.97
4997 5097 2.233431 TGGTGTGCTTATGCCAAATTCC 59.767 45.455 0.00 0.00 38.71 3.01
4998 5098 3.056607 ACTGGTGTGCTTATGCCAAATTC 60.057 43.478 0.00 0.00 38.71 2.17
4999 5099 2.899256 ACTGGTGTGCTTATGCCAAATT 59.101 40.909 0.00 0.00 38.71 1.82
5000 5100 2.493278 GACTGGTGTGCTTATGCCAAAT 59.507 45.455 0.00 0.00 38.71 2.32
5001 5101 1.885887 GACTGGTGTGCTTATGCCAAA 59.114 47.619 0.00 0.00 38.71 3.28
5005 5105 0.449388 GCTGACTGGTGTGCTTATGC 59.551 55.000 0.00 0.00 40.20 3.14
5015 5115 1.617850 CTTCACTCTCTGCTGACTGGT 59.382 52.381 0.00 0.00 0.00 4.00
5021 5121 6.551385 AAACAATAACTTCACTCTCTGCTG 57.449 37.500 0.00 0.00 0.00 4.41
5023 5123 9.170584 GTTTTAAACAATAACTTCACTCTCTGC 57.829 33.333 2.62 0.00 0.00 4.26
5074 5174 8.906867 CCCATACTGATTTACATGAATCTTTGT 58.093 33.333 0.00 3.60 37.04 2.83
5075 5175 8.355169 CCCCATACTGATTTACATGAATCTTTG 58.645 37.037 0.00 0.00 37.04 2.77
5078 5178 7.293299 TCTCCCCATACTGATTTACATGAATCT 59.707 37.037 0.00 0.00 37.04 2.40
5079 5179 7.453393 TCTCCCCATACTGATTTACATGAATC 58.547 38.462 0.00 0.00 36.73 2.52
5092 5205 4.040952 CCCTTGTAGAATCTCCCCATACTG 59.959 50.000 0.00 0.00 0.00 2.74
5111 5225 4.837093 TCGTTCTATCCAAATGTCCCTT 57.163 40.909 0.00 0.00 0.00 3.95
5118 5258 5.805728 AGGACTTGTTCGTTCTATCCAAAT 58.194 37.500 0.00 0.00 0.00 2.32
5125 5265 5.524971 TTCTGAAGGACTTGTTCGTTCTA 57.475 39.130 7.88 0.00 45.58 2.10
5134 5274 6.624352 TTCAACTGAATTCTGAAGGACTTG 57.376 37.500 18.13 10.86 0.00 3.16
5159 5299 5.074804 TCATTATCCATTTGAGCATGGGAG 58.925 41.667 0.00 0.00 43.74 4.30
5177 5317 7.201983 CCTCTGTTCATTGATCTCCTCTCATTA 60.202 40.741 0.00 0.00 0.00 1.90
5197 5344 1.771255 ACTCCTGAACAAAGCCTCTGT 59.229 47.619 0.00 0.00 0.00 3.41
5230 7538 2.300956 TGGGCCATAGTTTTTCTGCA 57.699 45.000 0.00 0.00 0.00 4.41
5231 7539 3.699038 TGTATGGGCCATAGTTTTTCTGC 59.301 43.478 26.28 11.67 0.00 4.26
5232 7540 4.339247 CCTGTATGGGCCATAGTTTTTCTG 59.661 45.833 26.28 15.77 0.00 3.02
5233 7541 4.017499 ACCTGTATGGGCCATAGTTTTTCT 60.017 41.667 26.28 0.52 41.11 2.52
5234 7542 4.278310 ACCTGTATGGGCCATAGTTTTTC 58.722 43.478 26.28 13.76 41.11 2.29
5324 7641 4.351874 AGTGCTTTACTGGCTCAGTTTA 57.648 40.909 12.22 0.89 42.59 2.01
5326 7643 2.938956 AGTGCTTTACTGGCTCAGTT 57.061 45.000 12.22 0.00 42.59 3.16
5328 7645 8.090831 TCATATATAAGTGCTTTACTGGCTCAG 58.909 37.037 1.16 1.16 40.26 3.35
5329 7646 7.962441 TCATATATAAGTGCTTTACTGGCTCA 58.038 34.615 0.00 0.00 40.26 4.26
5332 7649 9.219603 TGATTCATATATAAGTGCTTTACTGGC 57.780 33.333 0.00 0.00 40.26 4.85
5360 7677 9.099454 GACTGATTCTGGAACTTACGAAAATAT 57.901 33.333 0.00 0.00 0.00 1.28
5362 7679 6.934645 TGACTGATTCTGGAACTTACGAAAAT 59.065 34.615 0.00 0.00 0.00 1.82
5367 7684 5.389935 GCTTTGACTGATTCTGGAACTTACG 60.390 44.000 0.00 0.00 0.00 3.18
5368 7685 5.389935 CGCTTTGACTGATTCTGGAACTTAC 60.390 44.000 0.00 0.00 0.00 2.34
5374 7732 2.839486 ACGCTTTGACTGATTCTGGA 57.161 45.000 0.00 0.00 0.00 3.86
5377 7735 4.081420 AGGTCATACGCTTTGACTGATTCT 60.081 41.667 11.33 0.12 42.48 2.40
5378 7736 4.184629 AGGTCATACGCTTTGACTGATTC 58.815 43.478 11.33 0.00 42.48 2.52
5448 7806 5.753438 TCGTCTGCCAGTATGTCATATTTTC 59.247 40.000 0.00 0.00 0.00 2.29
5449 7807 5.523916 GTCGTCTGCCAGTATGTCATATTTT 59.476 40.000 0.00 0.00 0.00 1.82
5459 7817 2.798499 GCGTATTGTCGTCTGCCAGTAT 60.798 50.000 0.00 0.00 0.00 2.12
5471 7829 3.548415 CCCTTAGAGTCGAGCGTATTGTC 60.548 52.174 0.00 0.00 0.00 3.18
5478 7836 0.596083 CATGCCCTTAGAGTCGAGCG 60.596 60.000 0.00 0.00 0.00 5.03
5484 7842 5.371526 CATCATTGTACATGCCCTTAGAGT 58.628 41.667 0.00 0.00 0.00 3.24
5486 7844 4.717877 CCATCATTGTACATGCCCTTAGA 58.282 43.478 0.00 0.00 0.00 2.10
5491 7849 1.401761 TGCCATCATTGTACATGCCC 58.598 50.000 0.00 0.00 0.00 5.36
5492 7850 4.381185 CCATATGCCATCATTGTACATGCC 60.381 45.833 0.00 0.00 34.22 4.40
5493 7851 4.460034 TCCATATGCCATCATTGTACATGC 59.540 41.667 0.00 0.00 34.22 4.06
5494 7852 6.769134 ATCCATATGCCATCATTGTACATG 57.231 37.500 0.00 0.00 34.22 3.21
5495 7853 7.404481 TGTATCCATATGCCATCATTGTACAT 58.596 34.615 0.00 0.00 34.22 2.29
5496 7854 6.777782 TGTATCCATATGCCATCATTGTACA 58.222 36.000 0.00 0.00 34.22 2.90
5497 7855 7.870509 ATGTATCCATATGCCATCATTGTAC 57.129 36.000 0.00 0.00 34.22 2.90
5510 7868 9.758021 TTTTCAATGAGGCATATGTATCCATAT 57.242 29.630 4.29 0.00 43.54 1.78
5511 7869 9.585369 TTTTTCAATGAGGCATATGTATCCATA 57.415 29.630 4.29 0.00 37.92 2.74
5512 7870 8.481492 TTTTTCAATGAGGCATATGTATCCAT 57.519 30.769 4.29 1.04 34.97 3.41
5513 7871 7.894753 TTTTTCAATGAGGCATATGTATCCA 57.105 32.000 4.29 0.00 0.00 3.41
5535 7893 8.462016 CAGTATAATTGCCTCAAGCTACTTTTT 58.538 33.333 0.00 0.00 44.23 1.94
5536 7894 7.829211 TCAGTATAATTGCCTCAAGCTACTTTT 59.171 33.333 0.00 0.00 44.23 2.27
5537 7895 7.338710 TCAGTATAATTGCCTCAAGCTACTTT 58.661 34.615 0.00 0.00 44.23 2.66
5538 7896 6.889198 TCAGTATAATTGCCTCAAGCTACTT 58.111 36.000 0.00 0.00 44.23 2.24
5539 7897 6.485830 TCAGTATAATTGCCTCAAGCTACT 57.514 37.500 0.00 0.00 44.23 2.57
5540 7898 7.736447 AATCAGTATAATTGCCTCAAGCTAC 57.264 36.000 0.00 0.00 44.23 3.58
5541 7899 8.752005 AAAATCAGTATAATTGCCTCAAGCTA 57.248 30.769 0.00 0.00 44.23 3.32
5542 7900 7.559170 AGAAAATCAGTATAATTGCCTCAAGCT 59.441 33.333 0.00 0.00 44.23 3.74
5543 7901 7.710896 AGAAAATCAGTATAATTGCCTCAAGC 58.289 34.615 0.00 0.00 44.14 4.01
5544 7902 9.118300 AGAGAAAATCAGTATAATTGCCTCAAG 57.882 33.333 0.00 0.00 0.00 3.02
5545 7903 9.113838 GAGAGAAAATCAGTATAATTGCCTCAA 57.886 33.333 0.00 0.00 0.00 3.02
5546 7904 7.716998 GGAGAGAAAATCAGTATAATTGCCTCA 59.283 37.037 0.00 0.00 0.00 3.86
5547 7905 7.174080 GGGAGAGAAAATCAGTATAATTGCCTC 59.826 40.741 0.00 0.00 0.00 4.70
5548 7906 7.001073 GGGAGAGAAAATCAGTATAATTGCCT 58.999 38.462 0.00 0.00 0.00 4.75
5549 7907 6.207614 GGGGAGAGAAAATCAGTATAATTGCC 59.792 42.308 0.00 0.00 0.00 4.52
5550 7908 6.772716 TGGGGAGAGAAAATCAGTATAATTGC 59.227 38.462 0.00 0.00 0.00 3.56
5551 7909 8.752005 TTGGGGAGAGAAAATCAGTATAATTG 57.248 34.615 0.00 0.00 0.00 2.32
5554 7912 8.998814 TGTATTGGGGAGAGAAAATCAGTATAA 58.001 33.333 0.00 0.00 0.00 0.98
5555 7913 8.561536 TGTATTGGGGAGAGAAAATCAGTATA 57.438 34.615 0.00 0.00 0.00 1.47
5556 7914 7.451731 TGTATTGGGGAGAGAAAATCAGTAT 57.548 36.000 0.00 0.00 0.00 2.12
5557 7915 6.884472 TGTATTGGGGAGAGAAAATCAGTA 57.116 37.500 0.00 0.00 0.00 2.74
5558 7916 5.779241 TGTATTGGGGAGAGAAAATCAGT 57.221 39.130 0.00 0.00 0.00 3.41
5559 7917 6.660949 AGTTTGTATTGGGGAGAGAAAATCAG 59.339 38.462 0.00 0.00 0.00 2.90
5560 7918 6.552008 AGTTTGTATTGGGGAGAGAAAATCA 58.448 36.000 0.00 0.00 0.00 2.57
5561 7919 7.829706 AGTAGTTTGTATTGGGGAGAGAAAATC 59.170 37.037 0.00 0.00 0.00 2.17
5562 7920 7.699878 AGTAGTTTGTATTGGGGAGAGAAAAT 58.300 34.615 0.00 0.00 0.00 1.82
5563 7921 7.086685 AGTAGTTTGTATTGGGGAGAGAAAA 57.913 36.000 0.00 0.00 0.00 2.29
5564 7922 6.697641 AGTAGTTTGTATTGGGGAGAGAAA 57.302 37.500 0.00 0.00 0.00 2.52
5565 7923 6.958192 AGTAGTAGTTTGTATTGGGGAGAGAA 59.042 38.462 0.00 0.00 0.00 2.87
5566 7924 6.500336 AGTAGTAGTTTGTATTGGGGAGAGA 58.500 40.000 0.00 0.00 0.00 3.10
5567 7925 6.793505 AGTAGTAGTTTGTATTGGGGAGAG 57.206 41.667 0.00 0.00 0.00 3.20
5568 7926 8.701895 CATTAGTAGTAGTTTGTATTGGGGAGA 58.298 37.037 0.00 0.00 0.00 3.71
5569 7927 7.931948 CCATTAGTAGTAGTTTGTATTGGGGAG 59.068 40.741 0.00 0.00 0.00 4.30
5570 7928 7.147444 CCCATTAGTAGTAGTTTGTATTGGGGA 60.147 40.741 0.00 0.00 33.44 4.81
5571 7929 6.996282 CCCATTAGTAGTAGTTTGTATTGGGG 59.004 42.308 0.00 0.00 33.44 4.96
5572 7930 7.571025 ACCCATTAGTAGTAGTTTGTATTGGG 58.429 38.462 0.00 0.00 39.02 4.12
5573 7931 8.483758 AGACCCATTAGTAGTAGTTTGTATTGG 58.516 37.037 0.00 0.00 0.00 3.16
5574 7932 9.530633 GAGACCCATTAGTAGTAGTTTGTATTG 57.469 37.037 0.00 0.00 0.00 1.90
5575 7933 9.263446 TGAGACCCATTAGTAGTAGTTTGTATT 57.737 33.333 0.00 0.00 0.00 1.89
5576 7934 8.834004 TGAGACCCATTAGTAGTAGTTTGTAT 57.166 34.615 0.00 0.00 0.00 2.29
5577 7935 8.834004 ATGAGACCCATTAGTAGTAGTTTGTA 57.166 34.615 0.00 0.00 29.34 2.41
5578 7936 7.399191 TGATGAGACCCATTAGTAGTAGTTTGT 59.601 37.037 0.00 0.00 35.17 2.83
5579 7937 7.782049 TGATGAGACCCATTAGTAGTAGTTTG 58.218 38.462 0.00 0.00 35.17 2.93
5580 7938 7.973048 TGATGAGACCCATTAGTAGTAGTTT 57.027 36.000 0.00 0.00 35.17 2.66
5581 7939 7.839705 TCTTGATGAGACCCATTAGTAGTAGTT 59.160 37.037 0.00 0.00 35.17 2.24
5582 7940 7.355101 TCTTGATGAGACCCATTAGTAGTAGT 58.645 38.462 0.00 0.00 35.17 2.73
5583 7941 7.825331 TCTTGATGAGACCCATTAGTAGTAG 57.175 40.000 0.00 0.00 35.17 2.57
5584 7942 8.603898 TTTCTTGATGAGACCCATTAGTAGTA 57.396 34.615 0.00 0.00 35.17 1.82
5585 7943 7.496346 TTTCTTGATGAGACCCATTAGTAGT 57.504 36.000 0.00 0.00 35.17 2.73


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

AutoCloner maintained by Alex Coulton.