Multiple sequence alignment - TraesCS6A01G264600

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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 TraesCS6A01G264600 chr6A 100.000 4000 0 0 1 4000 488611826 488607827 0.000000e+00 7387
1 TraesCS6A01G264600 chr6B 94.776 1627 62 6 2049 3654 524967660 524966036 0.000000e+00 2512
2 TraesCS6A01G264600 chr6B 87.851 1638 124 33 451 2051 524969307 524967708 0.000000e+00 1853
3 TraesCS6A01G264600 chr6B 89.099 477 25 9 1 457 524970095 524969626 5.800000e-158 568
4 TraesCS6A01G264600 chr6B 95.699 186 5 1 3816 3998 524965975 524965790 3.020000e-76 296
5 TraesCS6A01G264600 chr6B 78.894 398 52 10 1244 1615 524968134 524967743 1.440000e-59 241
6 TraesCS6A01G264600 chr6B 91.667 84 4 1 3720 3803 524966041 524965961 3.270000e-21 113
7 TraesCS6A01G264600 chr6D 96.118 1520 46 7 2049 3559 353638973 353640488 0.000000e+00 2468
8 TraesCS6A01G264600 chr6D 87.755 1274 65 54 1 1201 353635897 353637152 0.000000e+00 1404
9 TraesCS6A01G264600 chr6D 90.693 505 46 1 1547 2051 353638422 353638925 0.000000e+00 671
10 TraesCS6A01G264600 chr6D 85.758 330 32 5 1226 1546 353637504 353637827 6.410000e-88 335
11 TraesCS6A01G264600 chr6D 95.161 186 6 1 3816 3998 353648067 353648252 1.410000e-74 291
12 TraesCS6A01G264600 chr6D 78.589 397 53 10 1247 1617 353638501 353638891 2.400000e-57 233
13 TraesCS6A01G264600 chr6D 97.403 77 2 0 3578 3654 353647930 353648006 9.020000e-27 132
14 TraesCS6A01G264600 chr6D 89.286 84 6 1 3720 3803 353648001 353648081 7.070000e-18 102


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 TraesCS6A01G264600 chr6A 488607827 488611826 3999 True 7387.0 7387 100.000000 1 4000 1 chr6A.!!$R1 3999
1 TraesCS6A01G264600 chr6B 524965790 524970095 4305 True 930.5 2512 89.664333 1 3998 6 chr6B.!!$R1 3997
2 TraesCS6A01G264600 chr6D 353635897 353640488 4591 False 1022.2 2468 87.782600 1 3559 5 chr6D.!!$F1 3558

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
33 34 0.177141 GTACAAGCTACGGATGGCCA 59.823 55.0 8.56 8.56 31.21 5.36 F
788 1213 0.180406 CCCTCTTTATCCACCACGGG 59.820 60.0 0.00 0.00 34.36 5.28 F
1519 2330 0.313987 GTTTGCAAGTGCCACCTACC 59.686 55.0 0.00 0.00 41.18 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 2987 0.534203 GCAACAAGGGTCGACAAGGA 60.534 55.0 18.91 0.00 0.00 3.36 R
1592 2997 0.877071 CTACAGCACAGCAACAAGGG 59.123 55.0 0.00 0.00 0.00 3.95 R
3328 4788 0.096976 ATTTTCTGACGGCGCAATCG 59.903 50.0 10.83 6.32 39.07 3.34 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
33 34 0.177141 GTACAAGCTACGGATGGCCA 59.823 55.000 8.56 8.56 31.21 5.36
108 109 0.608856 TGCTGGCCGTTTGATGTGAT 60.609 50.000 0.00 0.00 0.00 3.06
218 219 0.250166 ACACCCTACACGCCTGTTTC 60.250 55.000 0.00 0.00 0.00 2.78
327 368 1.215173 TGACCTATTGGCTGGGGAATG 59.785 52.381 0.00 0.00 36.63 2.67
333 374 0.413037 TTGGCTGGGGAATGGAATGT 59.587 50.000 0.00 0.00 0.00 2.71
334 375 0.413037 TGGCTGGGGAATGGAATGTT 59.587 50.000 0.00 0.00 0.00 2.71
359 400 6.738086 TCCCTCTCAGATAGTCAGATATACCT 59.262 42.308 0.00 0.00 0.00 3.08
374 416 5.536916 AGATATACCTTGTAGGCTGTGACTC 59.463 44.000 0.00 0.00 39.63 3.36
415 457 1.207089 TCATCCTGTAAGTTCCAGCCG 59.793 52.381 0.00 0.00 0.00 5.52
428 471 2.288666 TCCAGCCGCATTCTATTTGTC 58.711 47.619 0.00 0.00 0.00 3.18
449 492 2.599527 CAGTGTTGTGTCGTTCGTTACA 59.400 45.455 0.00 0.00 0.00 2.41
478 867 1.576421 CTCGTTGCTGGCCTCAAAC 59.424 57.895 3.32 4.58 0.00 2.93
557 958 9.851686 AATTGCTGTAATCTGAAGGATAATACA 57.148 29.630 0.00 0.00 33.71 2.29
643 1045 7.650504 CAGGAATACATTGATGGCATACAAAAG 59.349 37.037 0.00 6.89 0.00 2.27
711 1114 2.976840 GCCTGCATCGGCGACAAAA 61.977 57.895 13.76 0.00 45.35 2.44
749 1174 1.299620 CGACACGAAAGGACACCGT 60.300 57.895 0.00 0.00 36.95 4.83
788 1213 0.180406 CCCTCTTTATCCACCACGGG 59.820 60.000 0.00 0.00 34.36 5.28
960 1402 4.041917 GACGTGTACCGACGGGCA 62.042 66.667 20.00 13.86 43.84 5.36
1041 1483 0.673022 CTCTCCACAAGGTGAGCAGC 60.673 60.000 0.00 0.00 45.48 5.25
1042 1484 1.673665 CTCCACAAGGTGAGCAGCC 60.674 63.158 0.00 0.00 35.23 4.85
1043 1485 3.052082 CCACAAGGTGAGCAGCCG 61.052 66.667 0.00 0.00 35.23 5.52
1045 1487 4.254709 ACAAGGTGAGCAGCCGCA 62.255 61.111 0.00 0.00 42.27 5.69
1047 1489 2.980233 AAGGTGAGCAGCCGCAAC 60.980 61.111 0.00 0.00 42.27 4.17
1110 1579 7.988028 TCAACAGAGAGAGATCGAGTATCTTAA 59.012 37.037 0.00 0.00 45.35 1.85
1170 1639 7.573710 TGTAGCTCCTGTTGGTTTATGATTAT 58.426 34.615 0.00 0.00 34.23 1.28
1171 1640 8.052748 TGTAGCTCCTGTTGGTTTATGATTATT 58.947 33.333 0.00 0.00 34.23 1.40
1172 1641 9.555727 GTAGCTCCTGTTGGTTTATGATTATTA 57.444 33.333 0.00 0.00 34.23 0.98
1201 1676 7.652507 GGAATGAGTATAGTAGTACTGGTTTGC 59.347 40.741 13.29 0.00 35.14 3.68
1213 1688 2.564721 GGTTTGCTTTGGCCTCGCT 61.565 57.895 3.32 0.00 37.74 4.93
1234 2036 1.617947 GGGGGAGGAGCAGTGTACTG 61.618 65.000 7.64 7.64 46.40 2.74
1242 2044 3.389983 AGGAGCAGTGTACTGTTTGGTTA 59.610 43.478 13.08 0.00 45.45 2.85
1250 2052 7.095899 GCAGTGTACTGTTTGGTTAGTAGTTAC 60.096 40.741 13.08 0.00 45.45 2.50
1269 2071 7.578310 AGTTACATTTAGGCGTACTGATCTA 57.422 36.000 0.00 0.00 0.00 1.98
1295 2097 2.417243 GGGCGATTGGTCAAATTCCAAG 60.417 50.000 3.74 0.00 46.14 3.61
1299 2101 4.795962 GCGATTGGTCAAATTCCAAGTGTT 60.796 41.667 3.74 0.00 46.14 3.32
1300 2102 5.288804 CGATTGGTCAAATTCCAAGTGTTT 58.711 37.500 3.74 0.00 46.14 2.83
1301 2103 6.442952 CGATTGGTCAAATTCCAAGTGTTTA 58.557 36.000 3.74 0.00 46.14 2.01
1302 2104 7.090173 CGATTGGTCAAATTCCAAGTGTTTAT 58.910 34.615 3.74 0.00 46.14 1.40
1303 2105 7.273381 CGATTGGTCAAATTCCAAGTGTTTATC 59.727 37.037 3.74 0.00 46.14 1.75
1304 2106 7.595819 TTGGTCAAATTCCAAGTGTTTATCT 57.404 32.000 0.00 0.00 39.62 1.98
1319 2121 6.435277 AGTGTTTATCTTGTTGCTCATCCATT 59.565 34.615 0.00 0.00 0.00 3.16
1324 2126 4.143543 TCTTGTTGCTCATCCATTTGTGA 58.856 39.130 0.00 0.00 0.00 3.58
1338 2140 5.589855 TCCATTTGTGATATGTGTAAGGCAG 59.410 40.000 0.00 0.00 0.00 4.85
1344 2146 0.988063 TATGTGTAAGGCAGCACCCA 59.012 50.000 0.00 0.00 40.58 4.51
1354 2156 2.509548 AGGCAGCACCCATGTTTATCTA 59.490 45.455 0.00 0.00 40.58 1.98
1355 2157 3.053693 AGGCAGCACCCATGTTTATCTAA 60.054 43.478 0.00 0.00 40.58 2.10
1519 2330 0.313987 GTTTGCAAGTGCCACCTACC 59.686 55.000 0.00 0.00 41.18 3.18
1526 2337 1.224592 GTGCCACCTACCATGGGAG 59.775 63.158 18.13 18.13 38.37 4.30
1558 2963 5.871531 CAAACACTCAAACTTTTGGATCG 57.128 39.130 1.94 0.00 38.66 3.69
1560 2965 4.813296 ACACTCAAACTTTTGGATCGAC 57.187 40.909 1.94 0.00 38.66 4.20
1561 2966 4.451900 ACACTCAAACTTTTGGATCGACT 58.548 39.130 1.94 0.00 38.66 4.18
1564 2969 4.273480 ACTCAAACTTTTGGATCGACTGTG 59.727 41.667 1.94 0.00 38.66 3.66
1578 2983 3.378427 TCGACTGTGGACTGTGATATGAG 59.622 47.826 0.00 0.00 0.00 2.90
1582 2987 2.833943 TGTGGACTGTGATATGAGCACT 59.166 45.455 0.00 0.00 37.18 4.40
1592 2997 2.941453 TATGAGCACTCCTTGTCGAC 57.059 50.000 9.11 9.11 0.00 4.20
1603 3008 0.588252 CTTGTCGACCCTTGTTGCTG 59.412 55.000 14.12 0.00 0.00 4.41
1675 3080 3.157087 AGCGATTGGTCAAATTCCAACT 58.843 40.909 0.00 0.00 45.84 3.16
1678 3083 5.418840 AGCGATTGGTCAAATTCCAACTATT 59.581 36.000 0.00 0.00 45.84 1.73
1756 3161 5.037598 ACCTTGCCTACCTAAATTAGTCCT 58.962 41.667 0.00 0.00 0.00 3.85
1761 3166 9.628500 CTTGCCTACCTAAATTAGTCCTATTTT 57.372 33.333 0.00 0.00 0.00 1.82
1786 3191 5.355071 TGTTAGAAAGCTGATCGATGCATTT 59.645 36.000 0.54 4.01 0.00 2.32
1792 3197 2.793585 GCTGATCGATGCATTTGTGGTG 60.794 50.000 0.54 0.00 0.00 4.17
1796 3201 3.326836 TCGATGCATTTGTGGTGTCTA 57.673 42.857 0.00 0.00 0.00 2.59
1799 3204 3.374988 CGATGCATTTGTGGTGTCTATGT 59.625 43.478 0.00 0.00 0.00 2.29
1810 3215 3.181479 TGGTGTCTATGTGCCTAATCGAC 60.181 47.826 0.00 0.00 0.00 4.20
1823 3228 0.242017 AATCGACTTGCTTGCTTGGC 59.758 50.000 0.00 0.00 0.00 4.52
1824 3229 0.607489 ATCGACTTGCTTGCTTGGCT 60.607 50.000 0.00 0.00 0.00 4.75
1887 3292 1.518903 AAAACTCTGCTGCTTCGGCC 61.519 55.000 0.00 0.00 40.91 6.13
1888 3293 2.680974 AAACTCTGCTGCTTCGGCCA 62.681 55.000 2.24 0.00 40.91 5.36
1901 3306 4.642437 TGCTTCGGCCAAATATGTTTATCA 59.358 37.500 2.24 0.00 40.91 2.15
1909 3314 7.517101 CGGCCAAATATGTTTATCATTTGCAAG 60.517 37.037 2.24 0.00 38.00 4.01
1924 3329 1.065491 TGCAAGTGCCACCTACTATGG 60.065 52.381 0.00 0.00 41.18 2.74
1962 3367 7.461182 AATATTTGAACTTTTGGATCGGTCA 57.539 32.000 0.00 0.00 0.00 4.02
1964 3369 4.764679 TTGAACTTTTGGATCGGTCATG 57.235 40.909 0.00 0.00 0.00 3.07
1973 3378 1.414181 GGATCGGTCATGGACTGTGAT 59.586 52.381 0.00 2.93 39.68 3.06
1982 3387 2.988010 TGGACTGTGATATGAGCACC 57.012 50.000 0.00 0.00 35.43 5.01
2014 3419 3.131223 TCTCTGTTGCTATGCTGTAGACC 59.869 47.826 1.55 0.00 0.00 3.85
2027 3432 6.173427 TGCTGTAGACCATCTTATGCATAA 57.827 37.500 17.94 17.94 0.00 1.90
2056 3511 7.384932 TGAATATGCATTACCATCTACAACTCG 59.615 37.037 3.54 0.00 0.00 4.18
2164 3619 7.815383 ACCTGTCCATTTAATCCATCTTATCA 58.185 34.615 0.00 0.00 0.00 2.15
2259 3714 4.051237 TCTGACGACAACATCAAACTGAG 58.949 43.478 0.00 0.00 0.00 3.35
2276 3731 7.435488 TCAAACTGAGTTATAGAAGATTAGCGC 59.565 37.037 0.00 0.00 0.00 5.92
2281 3736 6.489022 TGAGTTATAGAAGATTAGCGCTGGTA 59.511 38.462 22.90 5.57 0.00 3.25
2318 3773 1.544691 TCTCTTCTGCGAACCACTACC 59.455 52.381 0.00 0.00 0.00 3.18
2550 4007 1.279271 GGCAGGGTCACACTTCACTAT 59.721 52.381 0.00 0.00 0.00 2.12
2561 4019 7.148573 GGTCACACTTCACTATACACAATTCTG 60.149 40.741 0.00 0.00 0.00 3.02
2586 4044 8.134895 TGAAAACTTCTTTTACCTAATGCACTG 58.865 33.333 0.00 0.00 29.21 3.66
2696 4154 6.430616 ACGTGTAAGAGCTCTTCTTTACTAGT 59.569 38.462 31.67 21.62 43.68 2.57
2930 4388 3.650139 GCCTCAGAGAGTGTTTTTCGTA 58.350 45.455 0.00 0.00 0.00 3.43
2931 4389 4.246458 GCCTCAGAGAGTGTTTTTCGTAT 58.754 43.478 0.00 0.00 0.00 3.06
2962 4420 6.093771 TGTTGACGTTGTGTACTTATGGTTTT 59.906 34.615 0.00 0.00 0.00 2.43
2969 4427 4.076394 GTGTACTTATGGTTTTCAGGGCA 58.924 43.478 0.00 0.00 0.00 5.36
3041 4499 4.618920 ATTCCCGAACTTGTTCAGTAGT 57.381 40.909 13.05 0.00 32.94 2.73
3058 4516 2.593346 AGTGTCTCTGATGGCGATTC 57.407 50.000 0.00 0.00 0.00 2.52
3193 4653 2.780065 TTGACTTGTCACAAGCATGC 57.220 45.000 17.93 10.51 0.00 4.06
3195 4655 1.605232 TGACTTGTCACAAGCATGCTG 59.395 47.619 23.48 17.40 0.00 4.41
3218 4678 7.067008 GCTGGTAATAGTTCCTTTTCAGCATAA 59.933 37.037 0.00 0.00 42.95 1.90
3225 4685 5.362430 AGTTCCTTTTCAGCATAAACCACAA 59.638 36.000 0.00 0.00 0.00 3.33
3281 4741 7.383687 AGGAAAGAGAACAACATATCGTGTAA 58.616 34.615 0.00 0.00 41.14 2.41
3328 4788 4.137116 ACAGAAAAGGAAGTTTTTGGGC 57.863 40.909 0.00 0.00 38.54 5.36
3334 4794 1.000843 AGGAAGTTTTTGGGCGATTGC 59.999 47.619 0.00 0.00 41.71 3.56
3354 4814 1.126846 CGCCGTCAGAAAATCTGTGAC 59.873 52.381 7.21 0.00 44.58 3.67
3392 4854 2.274437 TGAGCGTTGATCATCAAGCTC 58.726 47.619 27.82 27.82 46.09 4.09
3438 4900 4.809193 AGGCATAGAGACACCTAGATGAA 58.191 43.478 0.00 0.00 0.00 2.57
3466 4932 4.973168 AGAGCAAGTACAACAGGAATTGA 58.027 39.130 0.00 0.00 33.57 2.57
3497 4963 1.931906 CTGATCATCAGTCCACGGTG 58.068 55.000 6.48 0.00 39.58 4.94
3509 4975 2.282180 ACGGTGTGAATGGGGCAC 60.282 61.111 0.00 0.00 36.81 5.01
3521 4987 1.363246 TGGGGCACACTATGTTGGTA 58.637 50.000 0.00 0.00 0.00 3.25
3645 5128 6.699575 AATCTATTTGGTCCATAGTGCAAC 57.300 37.500 0.00 0.00 0.00 4.17
3648 5131 6.894682 TCTATTTGGTCCATAGTGCAACATA 58.105 36.000 0.00 0.00 41.43 2.29
3649 5132 5.835113 ATTTGGTCCATAGTGCAACATAC 57.165 39.130 0.00 0.00 41.43 2.39
3650 5133 4.568072 TTGGTCCATAGTGCAACATACT 57.432 40.909 0.00 0.00 41.43 2.12
3651 5134 3.872696 TGGTCCATAGTGCAACATACTG 58.127 45.455 0.00 0.00 41.43 2.74
3652 5135 3.517500 TGGTCCATAGTGCAACATACTGA 59.482 43.478 0.00 0.00 41.43 3.41
3653 5136 4.019771 TGGTCCATAGTGCAACATACTGAA 60.020 41.667 0.00 0.00 41.43 3.02
3654 5137 4.941263 GGTCCATAGTGCAACATACTGAAA 59.059 41.667 0.00 0.00 41.43 2.69
3655 5138 5.065218 GGTCCATAGTGCAACATACTGAAAG 59.935 44.000 0.00 0.00 41.43 2.62
3656 5139 4.635765 TCCATAGTGCAACATACTGAAAGC 59.364 41.667 0.00 0.00 41.43 3.51
3657 5140 4.395854 CCATAGTGCAACATACTGAAAGCA 59.604 41.667 0.00 0.00 41.43 3.91
3658 5141 5.448225 CCATAGTGCAACATACTGAAAGCAG 60.448 44.000 0.00 0.00 43.99 4.24
3659 5142 3.743521 AGTGCAACATACTGAAAGCAGA 58.256 40.909 0.00 0.00 41.95 4.26
3660 5143 4.330250 AGTGCAACATACTGAAAGCAGAT 58.670 39.130 0.00 0.00 41.95 2.90
3661 5144 5.491070 AGTGCAACATACTGAAAGCAGATA 58.509 37.500 0.00 0.00 41.95 1.98
3662 5145 6.118170 AGTGCAACATACTGAAAGCAGATAT 58.882 36.000 0.00 0.00 41.95 1.63
3663 5146 6.037940 AGTGCAACATACTGAAAGCAGATATG 59.962 38.462 0.00 0.00 41.95 1.78
3664 5147 6.037500 GTGCAACATACTGAAAGCAGATATGA 59.962 38.462 15.60 0.54 39.99 2.15
3665 5148 6.598850 TGCAACATACTGAAAGCAGATATGAA 59.401 34.615 15.60 0.00 45.17 2.57
3666 5149 7.283807 TGCAACATACTGAAAGCAGATATGAAT 59.716 33.333 15.60 7.16 45.17 2.57
3667 5150 8.133627 GCAACATACTGAAAGCAGATATGAATT 58.866 33.333 15.60 0.00 45.17 2.17
3668 5151 9.447040 CAACATACTGAAAGCAGATATGAATTG 57.553 33.333 15.60 10.25 45.17 2.32
3669 5152 7.646314 ACATACTGAAAGCAGATATGAATTGC 58.354 34.615 15.60 0.00 45.17 3.56
3670 5153 7.283807 ACATACTGAAAGCAGATATGAATTGCA 59.716 33.333 15.60 0.00 45.17 4.08
3671 5154 6.519679 ACTGAAAGCAGATATGAATTGCAA 57.480 33.333 0.00 0.00 45.17 4.08
3672 5155 7.108841 ACTGAAAGCAGATATGAATTGCAAT 57.891 32.000 5.99 5.99 45.17 3.56
3673 5156 7.553334 ACTGAAAGCAGATATGAATTGCAATT 58.447 30.769 24.33 24.33 45.17 2.32
3674 5157 8.038944 ACTGAAAGCAGATATGAATTGCAATTT 58.961 29.630 24.81 13.20 45.17 1.82
3675 5158 8.192068 TGAAAGCAGATATGAATTGCAATTTG 57.808 30.769 24.81 18.10 40.22 2.32
3676 5159 7.820386 TGAAAGCAGATATGAATTGCAATTTGT 59.180 29.630 24.81 17.98 40.22 2.83
3677 5160 9.304731 GAAAGCAGATATGAATTGCAATTTGTA 57.695 29.630 24.81 19.34 40.22 2.41
3678 5161 8.867112 AAGCAGATATGAATTGCAATTTGTAG 57.133 30.769 24.81 12.58 40.22 2.74
3679 5162 6.921857 AGCAGATATGAATTGCAATTTGTAGC 59.078 34.615 24.81 20.66 40.22 3.58
3680 5163 6.698329 GCAGATATGAATTGCAATTTGTAGCA 59.302 34.615 24.81 17.56 37.75 3.49
3681 5164 7.096189 GCAGATATGAATTGCAATTTGTAGCAG 60.096 37.037 24.81 18.73 42.39 4.24
3682 5165 8.132995 CAGATATGAATTGCAATTTGTAGCAGA 58.867 33.333 24.81 15.22 42.39 4.26
3683 5166 8.350722 AGATATGAATTGCAATTTGTAGCAGAG 58.649 33.333 24.81 0.00 42.39 3.35
3684 5167 4.487948 TGAATTGCAATTTGTAGCAGAGC 58.512 39.130 24.81 9.27 42.39 4.09
3685 5168 3.515330 ATTGCAATTTGTAGCAGAGCC 57.485 42.857 5.99 0.00 42.39 4.70
3686 5169 1.176527 TGCAATTTGTAGCAGAGCCC 58.823 50.000 0.00 0.00 35.51 5.19
3687 5170 0.099436 GCAATTTGTAGCAGAGCCCG 59.901 55.000 0.00 0.00 0.00 6.13
3688 5171 1.453155 CAATTTGTAGCAGAGCCCGT 58.547 50.000 0.00 0.00 0.00 5.28
3689 5172 1.812571 CAATTTGTAGCAGAGCCCGTT 59.187 47.619 0.00 0.00 0.00 4.44
3690 5173 2.200373 ATTTGTAGCAGAGCCCGTTT 57.800 45.000 0.00 0.00 0.00 3.60
3691 5174 1.975660 TTTGTAGCAGAGCCCGTTTT 58.024 45.000 0.00 0.00 0.00 2.43
3692 5175 1.975660 TTGTAGCAGAGCCCGTTTTT 58.024 45.000 0.00 0.00 0.00 1.94
3693 5176 2.843401 TGTAGCAGAGCCCGTTTTTA 57.157 45.000 0.00 0.00 0.00 1.52
3694 5177 3.128852 TGTAGCAGAGCCCGTTTTTAA 57.871 42.857 0.00 0.00 0.00 1.52
3695 5178 3.478509 TGTAGCAGAGCCCGTTTTTAAA 58.521 40.909 0.00 0.00 0.00 1.52
3696 5179 4.076394 TGTAGCAGAGCCCGTTTTTAAAT 58.924 39.130 0.00 0.00 0.00 1.40
3697 5180 3.575965 AGCAGAGCCCGTTTTTAAATG 57.424 42.857 0.00 0.00 0.00 2.32
3698 5181 2.890945 AGCAGAGCCCGTTTTTAAATGT 59.109 40.909 0.00 0.00 0.00 2.71
3699 5182 3.320826 AGCAGAGCCCGTTTTTAAATGTT 59.679 39.130 0.00 0.00 0.00 2.71
3700 5183 3.428534 GCAGAGCCCGTTTTTAAATGTTG 59.571 43.478 0.00 0.00 0.00 3.33
3701 5184 4.794655 GCAGAGCCCGTTTTTAAATGTTGA 60.795 41.667 0.00 0.00 0.00 3.18
3702 5185 5.285651 CAGAGCCCGTTTTTAAATGTTGAA 58.714 37.500 0.00 0.00 0.00 2.69
3703 5186 5.174943 CAGAGCCCGTTTTTAAATGTTGAAC 59.825 40.000 0.00 0.00 0.00 3.18
3704 5187 5.012328 AGCCCGTTTTTAAATGTTGAACA 57.988 34.783 0.00 0.00 0.00 3.18
3705 5188 4.806775 AGCCCGTTTTTAAATGTTGAACAC 59.193 37.500 0.00 0.00 0.00 3.32
3706 5189 4.567159 GCCCGTTTTTAAATGTTGAACACA 59.433 37.500 0.00 0.00 40.71 3.72
3707 5190 5.276631 GCCCGTTTTTAAATGTTGAACACAG 60.277 40.000 0.00 0.00 39.40 3.66
3708 5191 5.808030 CCCGTTTTTAAATGTTGAACACAGT 59.192 36.000 0.00 0.00 39.40 3.55
3709 5192 6.237701 CCCGTTTTTAAATGTTGAACACAGTG 60.238 38.462 0.00 0.00 39.40 3.66
3710 5193 6.237701 CCGTTTTTAAATGTTGAACACAGTGG 60.238 38.462 0.00 0.00 39.40 4.00
3711 5194 6.309251 CGTTTTTAAATGTTGAACACAGTGGT 59.691 34.615 0.00 0.00 39.40 4.16
3712 5195 7.148722 CGTTTTTAAATGTTGAACACAGTGGTT 60.149 33.333 0.00 0.00 39.40 3.67
3713 5196 7.588143 TTTTAAATGTTGAACACAGTGGTTG 57.412 32.000 0.00 0.00 39.40 3.77
3714 5197 4.799564 AAATGTTGAACACAGTGGTTGT 57.200 36.364 0.00 0.00 39.40 3.32
3715 5198 5.906113 AAATGTTGAACACAGTGGTTGTA 57.094 34.783 0.00 0.00 39.40 2.41
3716 5199 4.893424 ATGTTGAACACAGTGGTTGTAC 57.107 40.909 0.00 0.00 39.40 2.90
3717 5200 3.676093 TGTTGAACACAGTGGTTGTACA 58.324 40.909 5.31 1.57 38.16 2.90
3718 5201 3.687212 TGTTGAACACAGTGGTTGTACAG 59.313 43.478 5.31 0.00 38.16 2.74
3722 5205 4.403113 TGAACACAGTGGTTGTACAGACTA 59.597 41.667 5.31 0.00 38.16 2.59
3755 5238 2.042686 TCTGCTCCAATGGCATGTAC 57.957 50.000 0.00 0.00 39.07 2.90
3756 5239 1.561076 TCTGCTCCAATGGCATGTACT 59.439 47.619 0.00 0.00 39.07 2.73
3757 5240 2.771372 TCTGCTCCAATGGCATGTACTA 59.229 45.455 0.00 0.00 39.07 1.82
3799 5282 6.838382 AGTAGGAACCATAAAGAAACACACT 58.162 36.000 0.00 0.00 0.00 3.55
3800 5283 7.287810 AGTAGGAACCATAAAGAAACACACTT 58.712 34.615 0.00 0.00 0.00 3.16
3801 5284 7.778382 AGTAGGAACCATAAAGAAACACACTTT 59.222 33.333 0.00 0.00 40.13 2.66
3802 5285 7.418337 AGGAACCATAAAGAAACACACTTTT 57.582 32.000 0.00 0.00 38.34 2.27
3803 5286 7.847096 AGGAACCATAAAGAAACACACTTTTT 58.153 30.769 0.00 0.00 38.34 1.94
3824 5307 4.681835 TTTTCGAAACGGAAGAAACACA 57.318 36.364 10.79 0.00 34.14 3.72
3825 5308 3.661758 TTCGAAACGGAAGAAACACAC 57.338 42.857 0.00 0.00 0.00 3.82
3826 5309 2.896168 TCGAAACGGAAGAAACACACT 58.104 42.857 0.00 0.00 0.00 3.55
3892 5375 0.178068 CTAGCATGGTAACCAGCCGT 59.822 55.000 6.04 0.00 36.75 5.68
3934 5420 5.504010 CGAAACACACAGCAAGTAAATCACT 60.504 40.000 0.00 0.00 40.05 3.41
3998 5484 2.173782 TGCTTTGACCTGTAAAGTCCCA 59.826 45.455 0.00 0.00 37.44 4.37
3999 5485 2.814336 GCTTTGACCTGTAAAGTCCCAG 59.186 50.000 0.00 0.00 37.44 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.146342 CCACTGCACGAAGAACTGATT 58.854 47.619 0.00 0.00 0.00 2.57
108 109 8.064389 TCCCAAATATCATTTAAGGGTGAATCA 58.936 33.333 0.00 0.00 36.24 2.57
118 119 6.831353 ACGATGGTGTCCCAAATATCATTTAA 59.169 34.615 0.00 0.00 46.04 1.52
286 327 6.218746 GTCAGCCTTGAAAGACAATTTTGAT 58.781 36.000 0.00 0.00 37.88 2.57
305 346 1.152881 CCCCAGCCAATAGGTCAGC 60.153 63.158 0.00 0.00 37.19 4.26
327 368 4.651503 TGACTATCTGAGAGGGAACATTCC 59.348 45.833 4.13 1.70 46.82 3.01
333 374 7.240828 AGGTATATCTGACTATCTGAGAGGGAA 59.759 40.741 4.13 0.00 0.00 3.97
334 375 6.738086 AGGTATATCTGACTATCTGAGAGGGA 59.262 42.308 4.13 0.07 0.00 4.20
341 382 7.613801 AGCCTACAAGGTATATCTGACTATCTG 59.386 40.741 0.00 0.00 37.80 2.90
342 383 7.613801 CAGCCTACAAGGTATATCTGACTATCT 59.386 40.741 0.00 0.00 37.80 1.98
343 384 7.394923 ACAGCCTACAAGGTATATCTGACTATC 59.605 40.741 5.02 0.00 37.80 2.08
344 385 7.177568 CACAGCCTACAAGGTATATCTGACTAT 59.822 40.741 5.02 0.00 37.80 2.12
345 386 6.490381 CACAGCCTACAAGGTATATCTGACTA 59.510 42.308 5.02 0.00 37.80 2.59
346 387 5.303078 CACAGCCTACAAGGTATATCTGACT 59.697 44.000 5.02 0.00 37.80 3.41
347 388 5.302059 TCACAGCCTACAAGGTATATCTGAC 59.698 44.000 5.02 0.00 37.80 3.51
348 389 5.302059 GTCACAGCCTACAAGGTATATCTGA 59.698 44.000 5.02 0.00 37.80 3.27
359 400 1.001293 CTGCAGAGTCACAGCCTACAA 59.999 52.381 8.42 0.00 0.00 2.41
374 416 3.733337 AGGTTTACACTTGACTCTGCAG 58.267 45.455 7.63 7.63 0.00 4.41
415 457 5.762045 ACACAACACTGACAAATAGAATGC 58.238 37.500 0.00 0.00 0.00 3.56
428 471 2.599527 TGTAACGAACGACACAACACTG 59.400 45.455 0.14 0.00 0.00 3.66
449 492 2.620115 CCAGCAACGAGGCATGATAAAT 59.380 45.455 0.00 0.00 35.83 1.40
478 867 1.512926 CAGTTTTCCCTCTGGTGACG 58.487 55.000 0.00 0.00 0.00 4.35
607 1008 7.070322 CCATCAATGTATTCCTGGGAAAATTCT 59.930 37.037 6.14 0.00 37.69 2.40
711 1114 2.203070 GAGCGTCCCCGATTGCAT 60.203 61.111 0.00 0.00 35.63 3.96
788 1213 8.791355 TTCTCCGCTGTTTATTTTTAAGAAAC 57.209 30.769 3.44 3.44 34.37 2.78
874 1315 2.919856 AGGGGATGATCGCGAGGG 60.920 66.667 16.66 0.00 0.00 4.30
938 1380 4.783734 GTCGGTACACGTCCCGCC 62.784 72.222 11.84 0.00 43.87 6.13
1041 1483 3.057734 GAGATTATCTTACGGGTTGCGG 58.942 50.000 0.00 0.00 0.00 5.69
1042 1484 3.057734 GGAGATTATCTTACGGGTTGCG 58.942 50.000 0.00 0.00 0.00 4.85
1043 1485 3.057734 CGGAGATTATCTTACGGGTTGC 58.942 50.000 10.84 0.00 0.00 4.17
1045 1487 3.303049 ACCGGAGATTATCTTACGGGTT 58.697 45.455 29.02 15.55 45.42 4.11
1047 1489 2.095364 CGACCGGAGATTATCTTACGGG 60.095 54.545 29.02 18.78 45.42 5.28
1048 1490 2.551459 ACGACCGGAGATTATCTTACGG 59.449 50.000 26.26 26.26 46.07 4.02
1050 1492 4.929781 ACAACGACCGGAGATTATCTTAC 58.070 43.478 9.46 0.00 0.00 2.34
1170 1639 9.570468 CCAGTACTACTATACTCATTCCAGTAA 57.430 37.037 0.00 0.00 32.92 2.24
1171 1640 8.721479 ACCAGTACTACTATACTCATTCCAGTA 58.279 37.037 0.00 0.00 32.92 2.74
1172 1641 7.584532 ACCAGTACTACTATACTCATTCCAGT 58.415 38.462 0.00 0.00 32.92 4.00
1228 2030 9.835389 AAATGTAACTACTAACCAAACAGTACA 57.165 29.630 0.00 0.00 0.00 2.90
1231 2033 9.498176 CCTAAATGTAACTACTAACCAAACAGT 57.502 33.333 0.00 0.00 0.00 3.55
1234 2036 7.118245 ACGCCTAAATGTAACTACTAACCAAAC 59.882 37.037 0.00 0.00 0.00 2.93
1242 2044 6.764308 TCAGTACGCCTAAATGTAACTACT 57.236 37.500 0.00 0.00 0.00 2.57
1250 2052 4.627467 GCCATAGATCAGTACGCCTAAATG 59.373 45.833 0.00 0.00 0.00 2.32
1269 2071 3.636929 TTGACCAATCGCCCGCCAT 62.637 57.895 0.00 0.00 0.00 4.40
1295 2097 5.627499 TGGATGAGCAACAAGATAAACAC 57.373 39.130 0.00 0.00 0.00 3.32
1299 2101 6.433716 TCACAAATGGATGAGCAACAAGATAA 59.566 34.615 0.00 0.00 0.00 1.75
1300 2102 5.945191 TCACAAATGGATGAGCAACAAGATA 59.055 36.000 0.00 0.00 0.00 1.98
1301 2103 4.768448 TCACAAATGGATGAGCAACAAGAT 59.232 37.500 0.00 0.00 0.00 2.40
1302 2104 4.143543 TCACAAATGGATGAGCAACAAGA 58.856 39.130 0.00 0.00 0.00 3.02
1303 2105 4.508461 TCACAAATGGATGAGCAACAAG 57.492 40.909 0.00 0.00 0.00 3.16
1304 2106 6.153170 ACATATCACAAATGGATGAGCAACAA 59.847 34.615 0.00 0.00 0.00 2.83
1319 2121 3.689161 GTGCTGCCTTACACATATCACAA 59.311 43.478 0.00 0.00 36.77 3.33
1324 2126 1.563879 TGGGTGCTGCCTTACACATAT 59.436 47.619 0.00 0.00 38.57 1.78
1464 2275 1.808945 CGAAGCAGCAGAGTTTTCCAT 59.191 47.619 0.00 0.00 0.00 3.41
1555 2960 3.954258 TCATATCACAGTCCACAGTCGAT 59.046 43.478 0.00 0.00 0.00 3.59
1558 2963 3.118992 TGCTCATATCACAGTCCACAGTC 60.119 47.826 0.00 0.00 0.00 3.51
1560 2965 3.118847 AGTGCTCATATCACAGTCCACAG 60.119 47.826 0.00 0.00 36.93 3.66
1561 2966 2.833943 AGTGCTCATATCACAGTCCACA 59.166 45.455 0.00 0.00 36.93 4.17
1564 2969 3.104843 GGAGTGCTCATATCACAGTCC 57.895 52.381 7.08 7.08 44.36 3.85
1578 2983 0.951040 CAAGGGTCGACAAGGAGTGC 60.951 60.000 18.91 0.00 0.00 4.40
1582 2987 0.534203 GCAACAAGGGTCGACAAGGA 60.534 55.000 18.91 0.00 0.00 3.36
1592 2997 0.877071 CTACAGCACAGCAACAAGGG 59.123 55.000 0.00 0.00 0.00 3.95
1603 3008 6.636562 ACTACCATACATAGTCTACAGCAC 57.363 41.667 0.00 0.00 0.00 4.40
1756 3161 7.910162 GCATCGATCAGCTTTCTAACAAAAATA 59.090 33.333 0.00 0.00 0.00 1.40
1761 3166 4.252878 TGCATCGATCAGCTTTCTAACAA 58.747 39.130 8.93 0.00 0.00 2.83
1766 3171 3.693085 ACAAATGCATCGATCAGCTTTCT 59.307 39.130 0.00 0.00 0.00 2.52
1786 3191 3.430236 CGATTAGGCACATAGACACCACA 60.430 47.826 0.00 0.00 0.00 4.17
1792 3197 3.491267 GCAAGTCGATTAGGCACATAGAC 59.509 47.826 0.00 0.00 0.00 2.59
1796 3201 2.679837 CAAGCAAGTCGATTAGGCACAT 59.320 45.455 7.15 0.00 0.00 3.21
1799 3204 1.086696 GCAAGCAAGTCGATTAGGCA 58.913 50.000 7.15 0.00 0.00 4.75
1810 3215 0.944311 CAAGCAGCCAAGCAAGCAAG 60.944 55.000 6.77 0.00 35.04 4.01
1823 3228 5.694910 ACTCAATGCAAAATTCTTCAAGCAG 59.305 36.000 0.00 0.00 35.26 4.24
1824 3229 5.603596 ACTCAATGCAAAATTCTTCAAGCA 58.396 33.333 0.00 0.00 36.34 3.91
1860 3265 3.290710 AGCAGCAGAGTTTTCCAGAAAA 58.709 40.909 1.45 1.45 37.90 2.29
1887 3292 8.117988 GGCACTTGCAAATGATAAACATATTTG 58.882 33.333 12.91 0.00 44.36 2.32
1888 3293 7.823310 TGGCACTTGCAAATGATAAACATATTT 59.177 29.630 12.91 0.00 44.36 1.40
1901 3306 2.292828 AGTAGGTGGCACTTGCAAAT 57.707 45.000 19.09 0.00 44.36 2.32
1909 3314 3.577805 AAATCCCATAGTAGGTGGCAC 57.422 47.619 9.70 9.70 35.35 5.01
1944 3349 3.081061 CCATGACCGATCCAAAAGTTCA 58.919 45.455 0.00 0.00 0.00 3.18
1959 3364 3.806521 GTGCTCATATCACAGTCCATGAC 59.193 47.826 0.00 0.00 34.73 3.06
1962 3367 2.105477 GGGTGCTCATATCACAGTCCAT 59.895 50.000 0.00 0.00 36.22 3.41
1964 3369 1.202698 GGGGTGCTCATATCACAGTCC 60.203 57.143 0.00 0.00 36.22 3.85
1982 3387 1.372087 GCAACAGAGATCGGCAAGGG 61.372 60.000 0.00 0.00 0.00 3.95
1993 3398 3.118992 TGGTCTACAGCATAGCAACAGAG 60.119 47.826 0.00 0.00 0.00 3.35
2027 3432 7.078249 TGTAGATGGTAATGCATATTCAGGT 57.922 36.000 0.00 0.00 0.00 4.00
2043 3448 3.850122 TCACACTCGAGTTGTAGATGG 57.150 47.619 17.26 4.41 0.00 3.51
2056 3511 2.766263 TCCATAGGACCACATCACACTC 59.234 50.000 0.00 0.00 0.00 3.51
2138 3593 7.939039 TGATAAGATGGATTAAATGGACAGGTC 59.061 37.037 0.00 0.00 0.00 3.85
2259 3714 7.941795 TTTACCAGCGCTAATCTTCTATAAC 57.058 36.000 10.99 0.00 0.00 1.89
2276 3731 3.825328 AGCAGGGCATAAGATTTACCAG 58.175 45.455 0.00 0.00 0.00 4.00
2281 3736 4.516652 AGAGAAGCAGGGCATAAGATTT 57.483 40.909 0.00 0.00 0.00 2.17
2561 4019 8.135529 ACAGTGCATTAGGTAAAAGAAGTTTTC 58.864 33.333 0.00 0.00 37.12 2.29
2586 4044 9.827411 GATCACTTAAAACTGGAAAGACAATAC 57.173 33.333 0.00 0.00 0.00 1.89
2712 4170 7.661040 AGCAAACTTAAACAGAAAGCACATAT 58.339 30.769 0.00 0.00 0.00 1.78
2914 4372 3.673809 GCGTGATACGAAAAACACTCTCT 59.326 43.478 5.44 0.00 46.05 3.10
2930 4388 0.581529 CACAACGTCAACAGCGTGAT 59.418 50.000 0.00 0.00 42.10 3.06
2931 4389 0.738063 ACACAACGTCAACAGCGTGA 60.738 50.000 0.00 0.00 42.10 4.35
2962 4420 0.321564 CCTCAAATGTCGTGCCCTGA 60.322 55.000 0.00 0.00 0.00 3.86
2969 4427 1.633432 TCCCATTCCCTCAAATGTCGT 59.367 47.619 0.00 0.00 35.31 4.34
3041 4499 0.103026 CCGAATCGCCATCAGAGACA 59.897 55.000 0.00 0.00 0.00 3.41
3058 4516 5.046910 ACAGAAGAACAAAATACATGCCG 57.953 39.130 0.00 0.00 0.00 5.69
3193 4653 8.506168 TTATGCTGAAAAGGAACTATTACCAG 57.494 34.615 0.00 0.00 38.49 4.00
3195 4655 8.188799 GGTTTATGCTGAAAAGGAACTATTACC 58.811 37.037 0.00 0.00 38.49 2.85
3257 4717 7.591006 TTACACGATATGTTGTTCTCTTTCC 57.409 36.000 0.00 0.00 43.19 3.13
3267 4727 8.817100 ACACATACTTGATTACACGATATGTTG 58.183 33.333 0.00 0.00 43.19 3.33
3328 4788 0.096976 ATTTTCTGACGGCGCAATCG 59.903 50.000 10.83 6.32 39.07 3.34
3354 4814 4.610122 CGCTCATTTATCGCATTTAGCTTG 59.390 41.667 0.00 0.00 42.61 4.01
3392 4854 0.103208 GGTGGCTGACTATCGTGGAG 59.897 60.000 0.00 0.00 0.00 3.86
3438 4900 5.865085 TCCTGTTGTACTTGCTCTTATGTT 58.135 37.500 0.00 0.00 0.00 2.71
3466 4932 5.867903 CTGATGATCAGTCTTCCTAGGTT 57.132 43.478 14.17 0.00 39.58 3.50
3497 4963 2.128771 ACATAGTGTGCCCCATTCAC 57.871 50.000 0.00 0.00 35.14 3.18
3532 4998 7.249858 GTGCACAAACTTGAATGGAAATTTTT 58.750 30.769 13.17 0.00 0.00 1.94
3645 5128 7.645402 TGCAATTCATATCTGCTTTCAGTATG 58.355 34.615 0.00 0.00 41.10 2.39
3648 5131 6.519679 TTGCAATTCATATCTGCTTTCAGT 57.480 33.333 0.00 0.00 41.10 3.41
3649 5132 8.328146 CAAATTGCAATTCATATCTGCTTTCAG 58.672 33.333 24.28 0.00 41.67 3.02
3650 5133 7.820386 ACAAATTGCAATTCATATCTGCTTTCA 59.180 29.630 24.28 0.00 37.00 2.69
3651 5134 8.193250 ACAAATTGCAATTCATATCTGCTTTC 57.807 30.769 24.28 0.00 37.00 2.62
3652 5135 9.309516 CTACAAATTGCAATTCATATCTGCTTT 57.690 29.630 24.28 2.89 37.00 3.51
3653 5136 7.437267 GCTACAAATTGCAATTCATATCTGCTT 59.563 33.333 24.28 2.58 37.00 3.91
3654 5137 6.921857 GCTACAAATTGCAATTCATATCTGCT 59.078 34.615 24.28 10.88 37.00 4.24
3655 5138 6.698329 TGCTACAAATTGCAATTCATATCTGC 59.302 34.615 24.28 19.63 36.15 4.26
3656 5139 8.132995 TCTGCTACAAATTGCAATTCATATCTG 58.867 33.333 24.28 18.84 38.81 2.90
3657 5140 8.229253 TCTGCTACAAATTGCAATTCATATCT 57.771 30.769 24.28 5.56 38.81 1.98
3658 5141 7.114529 GCTCTGCTACAAATTGCAATTCATATC 59.885 37.037 24.28 14.84 38.81 1.63
3659 5142 6.921857 GCTCTGCTACAAATTGCAATTCATAT 59.078 34.615 24.28 12.58 38.81 1.78
3660 5143 6.267817 GCTCTGCTACAAATTGCAATTCATA 58.732 36.000 24.28 17.32 38.81 2.15
3661 5144 5.107133 GCTCTGCTACAAATTGCAATTCAT 58.893 37.500 24.28 17.13 38.81 2.57
3662 5145 4.487948 GCTCTGCTACAAATTGCAATTCA 58.512 39.130 24.28 15.94 38.81 2.57
3663 5146 3.861689 GGCTCTGCTACAAATTGCAATTC 59.138 43.478 24.28 12.29 38.81 2.17
3664 5147 3.368739 GGGCTCTGCTACAAATTGCAATT 60.369 43.478 18.99 18.99 38.81 2.32
3665 5148 2.167075 GGGCTCTGCTACAAATTGCAAT 59.833 45.455 5.99 5.99 38.81 3.56
3666 5149 1.545582 GGGCTCTGCTACAAATTGCAA 59.454 47.619 0.00 0.00 38.81 4.08
3667 5150 1.176527 GGGCTCTGCTACAAATTGCA 58.823 50.000 0.00 0.00 37.63 4.08
3668 5151 0.099436 CGGGCTCTGCTACAAATTGC 59.901 55.000 0.00 0.00 0.00 3.56
3669 5152 1.453155 ACGGGCTCTGCTACAAATTG 58.547 50.000 0.00 0.00 0.00 2.32
3670 5153 2.200373 AACGGGCTCTGCTACAAATT 57.800 45.000 0.00 0.00 0.00 1.82
3671 5154 2.200373 AAACGGGCTCTGCTACAAAT 57.800 45.000 0.00 0.00 0.00 2.32
3672 5155 1.975660 AAAACGGGCTCTGCTACAAA 58.024 45.000 0.00 0.00 0.00 2.83
3673 5156 1.975660 AAAAACGGGCTCTGCTACAA 58.024 45.000 0.00 0.00 0.00 2.41
3674 5157 2.843401 TAAAAACGGGCTCTGCTACA 57.157 45.000 0.00 0.00 0.00 2.74
3675 5158 4.082949 ACATTTAAAAACGGGCTCTGCTAC 60.083 41.667 0.00 0.00 0.00 3.58
3676 5159 4.076394 ACATTTAAAAACGGGCTCTGCTA 58.924 39.130 0.00 0.00 0.00 3.49
3677 5160 2.890945 ACATTTAAAAACGGGCTCTGCT 59.109 40.909 0.00 0.00 0.00 4.24
3678 5161 3.297830 ACATTTAAAAACGGGCTCTGC 57.702 42.857 0.00 0.00 0.00 4.26
3679 5162 4.865776 TCAACATTTAAAAACGGGCTCTG 58.134 39.130 0.00 0.00 0.00 3.35
3680 5163 5.163499 TGTTCAACATTTAAAAACGGGCTCT 60.163 36.000 0.00 0.00 0.00 4.09
3681 5164 5.044558 TGTTCAACATTTAAAAACGGGCTC 58.955 37.500 0.00 0.00 0.00 4.70
3682 5165 4.806775 GTGTTCAACATTTAAAAACGGGCT 59.193 37.500 0.00 0.00 0.00 5.19
3683 5166 4.567159 TGTGTTCAACATTTAAAAACGGGC 59.433 37.500 0.00 0.00 32.36 6.13
3684 5167 5.808030 ACTGTGTTCAACATTTAAAAACGGG 59.192 36.000 0.00 0.00 38.39 5.28
3685 5168 6.237701 CCACTGTGTTCAACATTTAAAAACGG 60.238 38.462 7.08 0.00 38.39 4.44
3686 5169 6.309251 ACCACTGTGTTCAACATTTAAAAACG 59.691 34.615 7.08 0.00 38.39 3.60
3687 5170 7.589574 ACCACTGTGTTCAACATTTAAAAAC 57.410 32.000 7.08 0.00 38.39 2.43
3688 5171 7.657761 ACAACCACTGTGTTCAACATTTAAAAA 59.342 29.630 7.08 0.00 38.39 1.94
3689 5172 7.155328 ACAACCACTGTGTTCAACATTTAAAA 58.845 30.769 7.08 0.00 38.39 1.52
3690 5173 6.692486 ACAACCACTGTGTTCAACATTTAAA 58.308 32.000 7.08 0.00 38.39 1.52
3691 5174 6.274157 ACAACCACTGTGTTCAACATTTAA 57.726 33.333 7.08 0.00 38.39 1.52
3692 5175 5.906113 ACAACCACTGTGTTCAACATTTA 57.094 34.783 7.08 0.00 38.39 1.40
3693 5176 4.799564 ACAACCACTGTGTTCAACATTT 57.200 36.364 7.08 0.00 38.39 2.32
3694 5177 4.702612 TGTACAACCACTGTGTTCAACATT 59.297 37.500 7.08 0.00 39.20 2.71
3695 5178 4.265893 TGTACAACCACTGTGTTCAACAT 58.734 39.130 7.08 0.00 39.20 2.71
3696 5179 3.676093 TGTACAACCACTGTGTTCAACA 58.324 40.909 7.08 0.00 39.20 3.33
3697 5180 3.936453 TCTGTACAACCACTGTGTTCAAC 59.064 43.478 7.08 0.00 39.20 3.18
3698 5181 3.936453 GTCTGTACAACCACTGTGTTCAA 59.064 43.478 7.08 0.00 39.20 2.69
3699 5182 3.196901 AGTCTGTACAACCACTGTGTTCA 59.803 43.478 7.08 0.00 39.20 3.18
3700 5183 3.793559 AGTCTGTACAACCACTGTGTTC 58.206 45.455 7.08 0.00 39.20 3.18
3701 5184 3.906720 AGTCTGTACAACCACTGTGTT 57.093 42.857 7.08 0.00 39.20 3.32
3702 5185 5.128171 TCTTTAGTCTGTACAACCACTGTGT 59.872 40.000 7.08 0.00 39.20 3.72
3703 5186 5.597806 TCTTTAGTCTGTACAACCACTGTG 58.402 41.667 10.63 0.00 39.20 3.66
3704 5187 5.864418 TCTTTAGTCTGTACAACCACTGT 57.136 39.130 10.63 0.00 42.47 3.55
3705 5188 5.696724 CCTTCTTTAGTCTGTACAACCACTG 59.303 44.000 10.63 0.00 0.00 3.66
3706 5189 5.221661 CCCTTCTTTAGTCTGTACAACCACT 60.222 44.000 0.00 2.12 0.00 4.00
3707 5190 4.995487 CCCTTCTTTAGTCTGTACAACCAC 59.005 45.833 0.00 0.00 0.00 4.16
3708 5191 4.504340 GCCCTTCTTTAGTCTGTACAACCA 60.504 45.833 0.00 0.00 0.00 3.67
3709 5192 4.001652 GCCCTTCTTTAGTCTGTACAACC 58.998 47.826 0.00 0.00 0.00 3.77
3710 5193 4.638304 TGCCCTTCTTTAGTCTGTACAAC 58.362 43.478 0.00 0.00 0.00 3.32
3711 5194 4.967084 TGCCCTTCTTTAGTCTGTACAA 57.033 40.909 0.00 0.00 0.00 2.41
3712 5195 4.967084 TTGCCCTTCTTTAGTCTGTACA 57.033 40.909 0.00 0.00 0.00 2.90
3713 5196 6.655425 AGAATTTGCCCTTCTTTAGTCTGTAC 59.345 38.462 0.00 0.00 28.55 2.90
3714 5197 6.655003 CAGAATTTGCCCTTCTTTAGTCTGTA 59.345 38.462 0.00 0.00 30.60 2.74
3715 5198 5.474876 CAGAATTTGCCCTTCTTTAGTCTGT 59.525 40.000 0.00 0.00 30.60 3.41
3716 5199 5.947443 CAGAATTTGCCCTTCTTTAGTCTG 58.053 41.667 0.00 0.00 30.60 3.51
3742 5225 4.898320 TCATAGCTAGTACATGCCATTGG 58.102 43.478 0.00 0.00 0.00 3.16
3802 5285 4.852650 GTGTGTTTCTTCCGTTTCGAAAAA 59.147 37.500 13.10 2.65 0.00 1.94
3803 5286 4.154556 AGTGTGTTTCTTCCGTTTCGAAAA 59.845 37.500 13.10 0.00 0.00 2.29
3804 5287 3.685756 AGTGTGTTTCTTCCGTTTCGAAA 59.314 39.130 6.47 6.47 0.00 3.46
3805 5288 3.264104 AGTGTGTTTCTTCCGTTTCGAA 58.736 40.909 0.00 0.00 0.00 3.71
3806 5289 2.896168 AGTGTGTTTCTTCCGTTTCGA 58.104 42.857 0.00 0.00 0.00 3.71
3807 5290 3.668596 AAGTGTGTTTCTTCCGTTTCG 57.331 42.857 0.00 0.00 0.00 3.46
3808 5291 4.494410 CGAAAAGTGTGTTTCTTCCGTTTC 59.506 41.667 0.00 0.00 35.70 2.78
3809 5292 4.083164 ACGAAAAGTGTGTTTCTTCCGTTT 60.083 37.500 0.00 0.00 35.70 3.60
3810 5293 3.437741 ACGAAAAGTGTGTTTCTTCCGTT 59.562 39.130 0.00 0.00 35.70 4.44
3811 5294 3.004862 ACGAAAAGTGTGTTTCTTCCGT 58.995 40.909 0.00 0.00 35.70 4.69
3812 5295 3.308866 AGACGAAAAGTGTGTTTCTTCCG 59.691 43.478 0.00 0.00 36.78 4.30
3813 5296 4.331717 TCAGACGAAAAGTGTGTTTCTTCC 59.668 41.667 0.00 0.00 43.78 3.46
3814 5297 5.464965 TCAGACGAAAAGTGTGTTTCTTC 57.535 39.130 0.00 0.00 43.78 2.87
3815 5298 5.873179 TTCAGACGAAAAGTGTGTTTCTT 57.127 34.783 0.00 0.00 43.78 2.52
3816 5299 5.163754 CCTTTCAGACGAAAAGTGTGTTTCT 60.164 40.000 0.00 0.00 43.78 2.52
3817 5300 5.028375 CCTTTCAGACGAAAAGTGTGTTTC 58.972 41.667 0.00 0.00 43.78 2.78
3818 5301 4.698304 TCCTTTCAGACGAAAAGTGTGTTT 59.302 37.500 0.00 0.00 43.78 2.83
3819 5302 4.258543 TCCTTTCAGACGAAAAGTGTGTT 58.741 39.130 0.00 0.00 43.78 3.32
3820 5303 3.869065 TCCTTTCAGACGAAAAGTGTGT 58.131 40.909 0.00 0.00 43.78 3.72
3821 5304 4.119862 TCTCCTTTCAGACGAAAAGTGTG 58.880 43.478 0.00 0.00 44.63 3.82
3822 5305 4.402056 TCTCCTTTCAGACGAAAAGTGT 57.598 40.909 0.00 0.00 40.57 3.55
3823 5306 4.319118 GCTTCTCCTTTCAGACGAAAAGTG 60.319 45.833 0.00 0.00 40.57 3.16
3824 5307 3.810386 GCTTCTCCTTTCAGACGAAAAGT 59.190 43.478 0.00 0.00 40.57 2.66
3825 5308 3.187432 GGCTTCTCCTTTCAGACGAAAAG 59.813 47.826 0.00 0.00 40.57 2.27
3826 5309 3.139077 GGCTTCTCCTTTCAGACGAAAA 58.861 45.455 0.00 0.00 40.57 2.29
3918 5404 7.229306 TCAAAAGATCAGTGATTTACTTGCTGT 59.771 33.333 7.16 0.00 37.60 4.40
3922 5408 7.025963 GGCTCAAAAGATCAGTGATTTACTTG 58.974 38.462 7.16 9.08 37.60 3.16
3934 5420 8.274322 TGAATAGAATAAGGGCTCAAAAGATCA 58.726 33.333 0.00 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.