Multiple sequence alignment - TraesCS3B01G442700

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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 TraesCS3B01G442700 chr3B 100.000 6649 0 0 1 6649 682792071 682785423 0.000000e+00 12279.0
1 TraesCS3B01G442700 chr3B 97.423 194 5 0 6456 6649 777007195 777007388 1.380000e-86 331.0
2 TraesCS3B01G442700 chr3B 96.891 193 5 1 6457 6649 699684312 699684121 8.320000e-84 322.0
3 TraesCS3B01G442700 chr3B 95.855 193 8 0 6457 6649 812314795 812314603 5.010000e-81 313.0
4 TraesCS3B01G442700 chr3B 88.601 193 22 0 6457 6649 777007929 777007737 1.110000e-57 235.0
5 TraesCS3B01G442700 chr3B 88.144 194 23 0 6456 6649 699683579 699683772 1.440000e-56 231.0
6 TraesCS3B01G442700 chr3B 86.154 195 27 0 6455 6649 682784884 682785078 1.880000e-50 211.0
7 TraesCS3B01G442700 chr3B 92.424 66 5 0 6584 6649 812314188 812314253 1.970000e-15 95.3
8 TraesCS3B01G442700 chr3D 95.128 4372 135 47 2107 6456 518155457 518151142 0.000000e+00 6822.0
9 TraesCS3B01G442700 chr3D 90.654 2172 100 46 1 2154 518157547 518155461 0.000000e+00 2791.0
10 TraesCS3B01G442700 chr3A 94.364 3726 110 57 2740 6421 653854768 653851099 0.000000e+00 5626.0
11 TraesCS3B01G442700 chr3A 92.249 2219 110 36 679 2885 653856880 653854712 0.000000e+00 3088.0
12 TraesCS3B01G442700 chr3A 90.887 406 19 10 1 397 653857723 653857327 4.570000e-146 529.0
13 TraesCS3B01G442700 chr3A 92.746 193 13 1 6457 6649 55741757 55741566 1.830000e-70 278.0
14 TraesCS3B01G442700 chr3A 88.083 193 23 0 6457 6649 55741029 55741221 5.190000e-56 230.0
15 TraesCS3B01G442700 chr3A 95.238 42 2 0 6415 6456 653850741 653850700 4.300000e-07 67.6
16 TraesCS3B01G442700 chr1D 85.343 962 139 2 4513 5473 362489985 362489025 0.000000e+00 994.0
17 TraesCS3B01G442700 chr1B 84.823 962 144 2 4513 5473 485289705 485288745 0.000000e+00 966.0
18 TraesCS3B01G442700 chr1A 82.716 1053 168 9 4513 5558 462002135 462001090 0.000000e+00 924.0
19 TraesCS3B01G442700 chr4D 96.970 33 0 1 5091 5122 105587469 105587437 3.000000e-03 54.7


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 TraesCS3B01G442700 chr3B 682785423 682792071 6648 True 12279.00 12279 100.0000 1 6649 1 chr3B.!!$R1 6648
1 TraesCS3B01G442700 chr3D 518151142 518157547 6405 True 4806.50 6822 92.8910 1 6456 2 chr3D.!!$R1 6455
2 TraesCS3B01G442700 chr3A 653850700 653857723 7023 True 2327.65 5626 93.1845 1 6456 4 chr3A.!!$R2 6455
3 TraesCS3B01G442700 chr1D 362489025 362489985 960 True 994.00 994 85.3430 4513 5473 1 chr1D.!!$R1 960
4 TraesCS3B01G442700 chr1B 485288745 485289705 960 True 966.00 966 84.8230 4513 5473 1 chr1B.!!$R1 960
5 TraesCS3B01G442700 chr1A 462001090 462002135 1045 True 924.00 924 82.7160 4513 5558 1 chr1A.!!$R1 1045

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
906 1092 0.107831 TGCCTGGTTTACTTCACGCT 59.892 50.0 0.00 0.0 0.00 5.07 F
1071 1264 0.601046 CACAGACTGAAAGCGAGCCA 60.601 55.0 10.08 0.0 37.60 4.75 F
1651 1844 0.694444 ATTACCGGCCAGGGATCTGT 60.694 55.0 16.44 0.0 46.96 3.41 F
2059 2252 0.515127 TGTTAACGGCATTGACGCTG 59.485 50.0 12.82 0.0 37.73 5.18 F
2112 2307 0.516877 TCATCTTCGTGCGGCTTTTG 59.483 50.0 0.00 0.0 0.00 2.44 F
3360 3701 0.595825 TCGCTATCATGTCTGCTGCG 60.596 55.0 0.00 0.0 42.70 5.18 F
5245 5588 1.244019 GGGAGTTTGCCAGCGACATT 61.244 55.0 0.00 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 2051 0.033504 CTACTCAACGTGCCCACTGT 59.966 55.000 0.0 0.0 0.00 3.55 R
2006 2199 0.108585 GACAGGAGACCAAGGTTGCA 59.891 55.000 0.0 0.0 0.00 4.08 R
2759 3011 1.064003 TCCCAAAGTAAGCAGGCAGA 58.936 50.000 0.0 0.0 0.00 4.26 R
3165 3506 1.338973 TCAGTAACGGAACAGCGAAGT 59.661 47.619 0.0 0.0 0.00 3.01 R
3523 3864 2.141517 CGATGAGCTTCAGGGCAATAG 58.858 52.381 0.0 0.0 34.17 1.73 R
5257 5600 0.250858 TGTCATGCACCTTCCACCAG 60.251 55.000 0.0 0.0 0.00 4.00 R
6478 7231 0.398696 TGTCAATACCGTTGGGCAGT 59.601 50.000 0.0 0.0 36.48 4.40 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
80 81 4.875713 CCCCTCCCCAAATCGCCG 62.876 72.222 0.00 0.00 0.00 6.46
182 188 3.859386 CGGCAGGCAAAGATTACATTTTC 59.141 43.478 0.00 0.00 0.00 2.29
303 317 8.115490 TCCCCTTCTCTCTCTCTATAAAACTA 57.885 38.462 0.00 0.00 0.00 2.24
349 365 0.679321 GCTTTTGCAGAGAGAGGGGG 60.679 60.000 3.58 0.00 46.58 5.40
399 418 2.254651 GACTGCGTTCGTCCGTCT 59.745 61.111 0.00 0.00 0.00 4.18
400 419 1.796749 GACTGCGTTCGTCCGTCTC 60.797 63.158 0.00 0.00 0.00 3.36
401 420 2.185103 GACTGCGTTCGTCCGTCTCT 62.185 60.000 0.00 0.00 0.00 3.10
403 422 1.066114 CTGCGTTCGTCCGTCTCTTC 61.066 60.000 0.00 0.00 0.00 2.87
404 423 1.209640 GCGTTCGTCCGTCTCTTCT 59.790 57.895 0.00 0.00 0.00 2.85
405 424 0.793853 GCGTTCGTCCGTCTCTTCTC 60.794 60.000 0.00 0.00 0.00 2.87
409 431 0.392729 TCGTCCGTCTCTTCTCCCTC 60.393 60.000 0.00 0.00 0.00 4.30
413 435 1.671901 CCGTCTCTTCTCCCTCCTGC 61.672 65.000 0.00 0.00 0.00 4.85
415 437 0.616111 GTCTCTTCTCCCTCCTGCCA 60.616 60.000 0.00 0.00 0.00 4.92
416 438 0.341258 TCTCTTCTCCCTCCTGCCAT 59.659 55.000 0.00 0.00 0.00 4.40
505 527 2.912624 GCGCTGTTCTTGGCTTGCT 61.913 57.895 0.00 0.00 0.00 3.91
539 561 1.130561 GGATGCGTTTTCTCTTTCGGG 59.869 52.381 0.00 0.00 0.00 5.14
565 587 1.612726 GCTGCCTGATCTGTTCTTGGT 60.613 52.381 0.00 0.00 0.00 3.67
567 589 3.869912 GCTGCCTGATCTGTTCTTGGTTA 60.870 47.826 0.00 0.00 0.00 2.85
574 596 5.556915 TGATCTGTTCTTGGTTATTCCGTT 58.443 37.500 0.00 0.00 39.52 4.44
575 597 5.411361 TGATCTGTTCTTGGTTATTCCGTTG 59.589 40.000 0.00 0.00 39.52 4.10
576 598 4.069304 TCTGTTCTTGGTTATTCCGTTGG 58.931 43.478 0.00 0.00 39.52 3.77
577 599 3.150767 TGTTCTTGGTTATTCCGTTGGG 58.849 45.455 0.00 0.00 39.52 4.12
578 600 3.151554 GTTCTTGGTTATTCCGTTGGGT 58.848 45.455 0.00 0.00 39.52 4.51
579 601 3.512219 TCTTGGTTATTCCGTTGGGTT 57.488 42.857 0.00 0.00 39.52 4.11
580 602 3.414269 TCTTGGTTATTCCGTTGGGTTC 58.586 45.455 0.00 0.00 39.52 3.62
581 603 1.810959 TGGTTATTCCGTTGGGTTCG 58.189 50.000 0.00 0.00 39.52 3.95
582 604 1.072015 TGGTTATTCCGTTGGGTTCGT 59.928 47.619 0.00 0.00 39.52 3.85
583 605 1.733912 GGTTATTCCGTTGGGTTCGTC 59.266 52.381 0.00 0.00 33.83 4.20
584 606 1.733912 GTTATTCCGTTGGGTTCGTCC 59.266 52.381 0.00 0.00 33.83 4.79
638 660 1.004440 GGTCGCTGGTTCTTGCTCT 60.004 57.895 0.00 0.00 0.00 4.09
643 665 1.337635 CGCTGGTTCTTGCTCTCTCTT 60.338 52.381 0.00 0.00 0.00 2.85
731 915 2.425592 GCTTTGGGTTGGTTGGGC 59.574 61.111 0.00 0.00 0.00 5.36
732 916 2.140138 GCTTTGGGTTGGTTGGGCT 61.140 57.895 0.00 0.00 0.00 5.19
782 966 2.481952 GCATTGCTCTCCGATATTCACC 59.518 50.000 0.16 0.00 0.00 4.02
783 967 3.732212 CATTGCTCTCCGATATTCACCA 58.268 45.455 0.00 0.00 0.00 4.17
839 1023 1.895131 GTTCATCCCCACATGCTTGTT 59.105 47.619 1.83 0.00 32.34 2.83
840 1024 2.299867 GTTCATCCCCACATGCTTGTTT 59.700 45.455 1.83 0.00 32.34 2.83
841 1025 1.894466 TCATCCCCACATGCTTGTTTG 59.106 47.619 1.83 0.00 32.34 2.93
842 1026 1.619827 CATCCCCACATGCTTGTTTGT 59.380 47.619 1.83 0.00 32.34 2.83
862 1048 4.093743 TGTCTGTTCATCTGCTTACCCTA 58.906 43.478 0.00 0.00 0.00 3.53
864 1050 5.163405 TGTCTGTTCATCTGCTTACCCTATC 60.163 44.000 0.00 0.00 0.00 2.08
866 1052 3.391296 TGTTCATCTGCTTACCCTATCCC 59.609 47.826 0.00 0.00 0.00 3.85
867 1053 3.637821 TCATCTGCTTACCCTATCCCT 57.362 47.619 0.00 0.00 0.00 4.20
902 1088 5.719173 GCATTATTTGCCTGGTTTACTTCA 58.281 37.500 0.00 0.00 46.15 3.02
903 1089 5.576774 GCATTATTTGCCTGGTTTACTTCAC 59.423 40.000 0.00 0.00 46.15 3.18
904 1090 3.915437 ATTTGCCTGGTTTACTTCACG 57.085 42.857 0.00 0.00 0.00 4.35
905 1091 0.948678 TTGCCTGGTTTACTTCACGC 59.051 50.000 0.00 0.00 0.00 5.34
906 1092 0.107831 TGCCTGGTTTACTTCACGCT 59.892 50.000 0.00 0.00 0.00 5.07
907 1093 0.796927 GCCTGGTTTACTTCACGCTC 59.203 55.000 0.00 0.00 0.00 5.03
908 1094 1.876416 GCCTGGTTTACTTCACGCTCA 60.876 52.381 0.00 0.00 0.00 4.26
909 1095 1.798813 CCTGGTTTACTTCACGCTCAC 59.201 52.381 0.00 0.00 0.00 3.51
910 1096 2.479837 CTGGTTTACTTCACGCTCACA 58.520 47.619 0.00 0.00 0.00 3.58
911 1097 2.206750 TGGTTTACTTCACGCTCACAC 58.793 47.619 0.00 0.00 0.00 3.82
914 1100 3.064271 GGTTTACTTCACGCTCACACAAA 59.936 43.478 0.00 0.00 0.00 2.83
915 1101 3.936902 TTACTTCACGCTCACACAAAC 57.063 42.857 0.00 0.00 0.00 2.93
917 1103 1.013596 CTTCACGCTCACACAAACCA 58.986 50.000 0.00 0.00 0.00 3.67
920 1106 1.601903 TCACGCTCACACAAACCATTC 59.398 47.619 0.00 0.00 0.00 2.67
936 1129 1.069022 CATTCCCGTGTTCTGCTGTTG 60.069 52.381 0.00 0.00 0.00 3.33
939 1132 0.813610 CCCGTGTTCTGCTGTTGTGA 60.814 55.000 0.00 0.00 0.00 3.58
1005 1198 3.071206 TGAGGTCGGAGAGGCAGC 61.071 66.667 0.00 0.00 36.95 5.25
1071 1264 0.601046 CACAGACTGAAAGCGAGCCA 60.601 55.000 10.08 0.00 37.60 4.75
1183 1376 8.084985 TCCAAAGAGAAAAATACCCACTTTTT 57.915 30.769 0.00 0.00 38.23 1.94
1184 1377 8.201464 TCCAAAGAGAAAAATACCCACTTTTTC 58.799 33.333 11.41 11.41 46.01 2.29
1190 1383 7.847166 GAAAAATACCCACTTTTTCTGTACG 57.153 36.000 11.88 0.00 43.94 3.67
1191 1384 5.366829 AAATACCCACTTTTTCTGTACGC 57.633 39.130 0.00 0.00 0.00 4.42
1192 1385 2.632987 ACCCACTTTTTCTGTACGCT 57.367 45.000 0.00 0.00 0.00 5.07
1471 1664 4.892965 TTGGTGGTTGCAGCGCCT 62.893 61.111 2.29 0.00 45.85 5.52
1474 1667 2.265182 GGTGGTTGCAGCGCCTTTA 61.265 57.895 2.29 0.00 42.60 1.85
1506 1699 5.455755 CCACCCATCCATCCATATATGCTAG 60.456 48.000 7.24 0.00 0.00 3.42
1507 1700 5.131642 CACCCATCCATCCATATATGCTAGT 59.868 44.000 7.24 0.00 0.00 2.57
1512 1705 6.791867 TCCATCCATATATGCTAGTACCAC 57.208 41.667 7.24 0.00 0.00 4.16
1513 1706 5.661312 TCCATCCATATATGCTAGTACCACC 59.339 44.000 7.24 0.00 0.00 4.61
1515 1708 6.407412 CCATCCATATATGCTAGTACCACCAG 60.407 46.154 7.24 0.00 0.00 4.00
1516 1709 4.466370 TCCATATATGCTAGTACCACCAGC 59.534 45.833 7.24 0.00 35.82 4.85
1517 1710 4.424626 CATATATGCTAGTACCACCAGCG 58.575 47.826 0.00 0.00 38.15 5.18
1566 1759 2.962569 GCCCTCTTTTCCGTTGCC 59.037 61.111 0.00 0.00 0.00 4.52
1651 1844 0.694444 ATTACCGGCCAGGGATCTGT 60.694 55.000 16.44 0.00 46.96 3.41
1658 1851 4.950479 CAGGGATCTGTCCTGCAC 57.050 61.111 3.86 0.00 44.29 4.57
1827 2020 7.124599 TGTCACCGAAACCCTATTAAATCTCTA 59.875 37.037 0.00 0.00 0.00 2.43
1858 2051 2.066700 TTGGCTCCATGTGCACTCCA 62.067 55.000 19.41 11.99 0.00 3.86
2006 2199 0.736325 CGGCGAACGGAGTGAATTCT 60.736 55.000 0.00 0.00 45.00 2.40
2029 2222 0.898320 ACCTTGGTCTCCTGTCATCG 59.102 55.000 0.00 0.00 0.00 3.84
2034 2227 1.283905 TGGTCTCCTGTCATCGGTCTA 59.716 52.381 0.00 0.00 0.00 2.59
2059 2252 0.515127 TGTTAACGGCATTGACGCTG 59.485 50.000 12.82 0.00 37.73 5.18
2112 2307 0.516877 TCATCTTCGTGCGGCTTTTG 59.483 50.000 0.00 0.00 0.00 2.44
2144 2391 6.809196 TGTTTGCCGGTATTAAAATTGCTAAG 59.191 34.615 1.90 0.00 0.00 2.18
2252 2500 9.364989 CTCTCCTTTTCTAAAAGATGTGACTAG 57.635 37.037 15.16 0.00 46.39 2.57
2337 2585 1.885388 CGGTGTGGAGAAACGTGCA 60.885 57.895 0.00 0.00 0.00 4.57
2338 2586 1.647084 GGTGTGGAGAAACGTGCAC 59.353 57.895 6.82 6.82 39.13 4.57
2352 2600 1.754621 TGCACGCTTTTGTTCCCCA 60.755 52.632 0.00 0.00 0.00 4.96
2517 2768 5.424895 AGTCTTCTGAACCTTCTGAGCATAT 59.575 40.000 0.00 0.00 36.67 1.78
2593 2845 6.676456 GCACTATGAAAGCTATCTTTGTGGTG 60.676 42.308 0.00 5.11 42.24 4.17
2664 2916 5.768317 TGCTTGTAGGCTTATTTTGTTGTC 58.232 37.500 0.00 0.00 0.00 3.18
2700 2952 3.009033 TGGTTGTTCTGATAGGGACCTTG 59.991 47.826 0.00 0.00 0.00 3.61
2702 2954 2.915869 TGTTCTGATAGGGACCTTGGT 58.084 47.619 0.00 0.00 0.00 3.67
2787 3039 5.888161 CCTGCTTACTTTGGGAAATCATACT 59.112 40.000 0.00 0.00 0.00 2.12
2789 3041 7.556275 CCTGCTTACTTTGGGAAATCATACTTA 59.444 37.037 0.00 0.00 0.00 2.24
2790 3042 9.125026 CTGCTTACTTTGGGAAATCATACTTAT 57.875 33.333 0.00 0.00 0.00 1.73
2819 3071 7.615582 TCATAAGTGCCTATTTCAGAGTTTG 57.384 36.000 0.00 0.00 0.00 2.93
2823 3075 3.440522 GTGCCTATTTCAGAGTTTGGGTC 59.559 47.826 0.00 0.00 0.00 4.46
2831 3083 2.368875 TCAGAGTTTGGGTCTTGGACTC 59.631 50.000 0.00 0.00 37.57 3.36
2841 3095 5.009631 TGGGTCTTGGACTCACAAATAATG 58.990 41.667 0.00 0.00 38.21 1.90
2943 3283 1.737838 TTGTTTCATCTGCCTAGCCG 58.262 50.000 0.00 0.00 0.00 5.52
3165 3506 6.779860 ACTTTCTCTTGGCCAGAATTAGTAA 58.220 36.000 5.11 0.20 29.89 2.24
3196 3537 2.061773 CCGTTACTGACTTGCTGTCTG 58.938 52.381 12.80 12.80 45.54 3.51
3252 3593 4.321304 GCTAAAAGAAGGACCCAGAAAAGC 60.321 45.833 0.00 0.00 0.00 3.51
3360 3701 0.595825 TCGCTATCATGTCTGCTGCG 60.596 55.000 0.00 0.00 42.70 5.18
3489 3830 5.603596 ACACGTAGAACATTACTTTCCACA 58.396 37.500 0.00 0.00 0.00 4.17
3523 3864 6.464222 TGTTATCTGTATATGGTAAGCTGCC 58.536 40.000 0.00 0.00 0.00 4.85
3628 3969 4.276183 CCGCGATATGTATCTACTATGCCT 59.724 45.833 8.23 0.00 0.00 4.75
4063 4404 1.261238 CGGAGTGCTTCCCTCTTCCT 61.261 60.000 2.76 0.00 43.63 3.36
4112 4453 1.636148 ACATGAAGGCAATGCTTGGT 58.364 45.000 4.82 0.00 0.00 3.67
4119 4460 4.398988 TGAAGGCAATGCTTGGTTATACAG 59.601 41.667 4.82 0.00 0.00 2.74
4363 4704 3.084039 TCCATCTGTGGCAGTTGAAATC 58.916 45.455 8.32 0.00 45.63 2.17
4479 4822 6.177610 TGTTGTCCCTGTATTACTTGGATTC 58.822 40.000 7.76 4.18 0.00 2.52
4489 4832 9.605275 CTGTATTACTTGGATTCTTCTGATGAA 57.395 33.333 8.23 8.23 0.00 2.57
5245 5588 1.244019 GGGAGTTTGCCAGCGACATT 61.244 55.000 0.00 0.00 0.00 2.71
5314 5657 0.628522 AGAGCTACTGCCTCCTGAGA 59.371 55.000 0.00 0.00 40.80 3.27
5425 5768 3.893813 ACAAGAGGCTCAAGATTTGCTTT 59.106 39.130 18.26 0.00 33.60 3.51
5483 5826 4.660938 GCGAGGCCCCCAACAACT 62.661 66.667 0.00 0.00 0.00 3.16
5565 5914 1.784593 TGTGTAGATATCCTCCCCCGA 59.215 52.381 0.00 0.00 0.00 5.14
5713 6067 4.220382 AGCTATACATTTTGTTTGCTGCCA 59.780 37.500 0.00 0.00 31.53 4.92
5753 6107 3.189473 CTCTCGCTGCTGCTGCTG 61.189 66.667 25.43 16.73 40.48 4.41
5754 6108 3.644399 CTCTCGCTGCTGCTGCTGA 62.644 63.158 25.43 21.60 40.01 4.26
5755 6109 2.511829 CTCGCTGCTGCTGCTGAT 60.512 61.111 25.43 0.00 40.01 2.90
5756 6110 2.510918 TCGCTGCTGCTGCTGATC 60.511 61.111 25.43 8.03 40.01 2.92
5757 6111 3.574445 CGCTGCTGCTGCTGATCC 61.574 66.667 25.43 7.40 40.01 3.36
5758 6112 3.574445 GCTGCTGCTGCTGATCCG 61.574 66.667 23.39 4.45 40.01 4.18
5759 6113 2.186125 CTGCTGCTGCTGATCCGA 59.814 61.111 17.00 0.00 40.01 4.55
5760 6114 2.125391 TGCTGCTGCTGATCCGAC 60.125 61.111 17.00 0.00 40.48 4.79
5761 6115 2.894387 GCTGCTGCTGATCCGACC 60.894 66.667 10.92 0.00 36.03 4.79
5762 6116 2.898738 CTGCTGCTGATCCGACCT 59.101 61.111 0.00 0.00 0.00 3.85
5763 6117 1.227205 CTGCTGCTGATCCGACCTC 60.227 63.158 0.00 0.00 0.00 3.85
5764 6118 2.279120 GCTGCTGATCCGACCTCG 60.279 66.667 0.00 0.00 39.44 4.63
5765 6119 2.775856 GCTGCTGATCCGACCTCGA 61.776 63.158 0.00 0.00 43.02 4.04
5766 6120 1.809869 CTGCTGATCCGACCTCGAA 59.190 57.895 0.00 0.00 43.02 3.71
5767 6121 0.173481 CTGCTGATCCGACCTCGAAA 59.827 55.000 0.00 0.00 43.02 3.46
5768 6122 0.173481 TGCTGATCCGACCTCGAAAG 59.827 55.000 0.00 0.00 43.02 2.62
5769 6123 1.148759 GCTGATCCGACCTCGAAAGC 61.149 60.000 0.00 0.00 43.02 3.51
5770 6124 0.173481 CTGATCCGACCTCGAAAGCA 59.827 55.000 0.00 0.00 43.02 3.91
5771 6125 0.173481 TGATCCGACCTCGAAAGCAG 59.827 55.000 0.00 0.00 43.02 4.24
5772 6126 1.148759 GATCCGACCTCGAAAGCAGC 61.149 60.000 0.00 0.00 43.02 5.25
5773 6127 2.579684 ATCCGACCTCGAAAGCAGCC 62.580 60.000 0.00 0.00 43.02 4.85
5774 6128 3.181967 CGACCTCGAAAGCAGCCG 61.182 66.667 0.00 0.00 43.02 5.52
5775 6129 3.491652 GACCTCGAAAGCAGCCGC 61.492 66.667 0.00 0.00 38.99 6.53
5845 6204 5.163530 TGGGTAATAATTCGTCGCTTGTAGA 60.164 40.000 0.00 0.00 0.00 2.59
5847 6206 6.423001 GGGTAATAATTCGTCGCTTGTAGATT 59.577 38.462 0.00 0.00 0.00 2.40
5895 6254 0.534877 CTGGCTGTGTTGGTGCAGTA 60.535 55.000 0.00 0.00 35.33 2.74
6092 6453 4.207281 CTGCTCGGCGATTCGGGA 62.207 66.667 11.27 0.00 31.16 5.14
6095 6456 2.728180 CTCGGCGATTCGGGATGA 59.272 61.111 11.27 0.00 31.16 2.92
6096 6457 1.290324 CTCGGCGATTCGGGATGAT 59.710 57.895 11.27 0.00 31.16 2.45
6097 6458 0.319900 CTCGGCGATTCGGGATGATT 60.320 55.000 11.27 0.00 31.16 2.57
6100 6461 1.151668 GGCGATTCGGGATGATTGAG 58.848 55.000 8.34 0.00 0.00 3.02
6104 6479 1.528586 GATTCGGGATGATTGAGCGTG 59.471 52.381 0.00 0.00 0.00 5.34
6119 6494 3.058293 TGAGCGTGTGAAATTGTTCATCC 60.058 43.478 0.00 0.00 45.38 3.51
6238 6619 1.171549 TTGAAATGGCGTGCTGCTGA 61.172 50.000 0.00 0.00 45.43 4.26
6239 6620 1.136147 GAAATGGCGTGCTGCTGAG 59.864 57.895 0.00 0.00 45.43 3.35
6240 6621 1.580845 GAAATGGCGTGCTGCTGAGT 61.581 55.000 0.00 0.00 45.43 3.41
6241 6622 1.859427 AAATGGCGTGCTGCTGAGTG 61.859 55.000 0.00 0.00 45.43 3.51
6242 6623 2.736579 AATGGCGTGCTGCTGAGTGA 62.737 55.000 0.00 0.00 45.43 3.41
6246 6627 2.745492 GTGCTGCTGAGTGAGGGC 60.745 66.667 0.00 0.00 0.00 5.19
6247 6628 3.243816 TGCTGCTGAGTGAGGGCA 61.244 61.111 0.00 0.00 34.66 5.36
6251 6632 4.792804 GCTGAGTGAGGGCAGGGC 62.793 72.222 0.00 0.00 32.83 5.19
6252 6633 3.324930 CTGAGTGAGGGCAGGGCA 61.325 66.667 0.00 0.00 0.00 5.36
6253 6634 3.324930 TGAGTGAGGGCAGGGCAG 61.325 66.667 0.00 0.00 0.00 4.85
6261 6642 0.401105 AGGGCAGGGCAGAGATGTAT 60.401 55.000 0.00 0.00 0.00 2.29
6266 6647 3.071602 GGCAGGGCAGAGATGTATAAGAA 59.928 47.826 0.00 0.00 0.00 2.52
6290 6673 4.511246 ACATGGGGCGCATGGAGG 62.511 66.667 37.29 20.14 34.56 4.30
6307 6690 2.674380 GGTTGGGTGAGCTGCCTG 60.674 66.667 0.00 0.00 0.00 4.85
6326 6709 4.854924 CGTGCCGATGCCATGGGA 62.855 66.667 15.13 12.25 36.33 4.37
6383 6770 3.047877 CGTGCTCCGTTGGGTTCC 61.048 66.667 0.00 0.00 33.83 3.62
6384 6771 2.112297 GTGCTCCGTTGGGTTCCA 59.888 61.111 0.00 0.00 33.83 3.53
6385 6772 1.966451 GTGCTCCGTTGGGTTCCAG 60.966 63.158 0.00 0.00 33.81 3.86
6452 7205 1.974265 TTTCCGACAGCATGGAAACA 58.026 45.000 2.45 0.00 46.48 2.83
6483 7236 4.911514 TTGTCCAAAAAGACTAACTGCC 57.088 40.909 0.00 0.00 37.66 4.85
6484 7237 3.219281 TGTCCAAAAAGACTAACTGCCC 58.781 45.455 0.00 0.00 37.66 5.36
6485 7238 3.219281 GTCCAAAAAGACTAACTGCCCA 58.781 45.455 0.00 0.00 33.79 5.36
6486 7239 3.634910 GTCCAAAAAGACTAACTGCCCAA 59.365 43.478 0.00 0.00 33.79 4.12
6487 7240 3.634910 TCCAAAAAGACTAACTGCCCAAC 59.365 43.478 0.00 0.00 0.00 3.77
6488 7241 3.550030 CCAAAAAGACTAACTGCCCAACG 60.550 47.826 0.00 0.00 0.00 4.10
6489 7242 1.892209 AAAGACTAACTGCCCAACGG 58.108 50.000 0.00 0.00 0.00 4.44
6490 7243 0.763035 AAGACTAACTGCCCAACGGT 59.237 50.000 0.00 0.00 40.66 4.83
6491 7244 1.636148 AGACTAACTGCCCAACGGTA 58.364 50.000 0.00 0.00 36.64 4.02
6492 7245 2.185387 AGACTAACTGCCCAACGGTAT 58.815 47.619 0.00 0.00 36.64 2.73
6493 7246 2.570302 AGACTAACTGCCCAACGGTATT 59.430 45.455 0.00 0.00 36.64 1.89
6494 7247 2.676342 GACTAACTGCCCAACGGTATTG 59.324 50.000 0.00 0.00 36.64 1.90
6495 7248 2.303600 ACTAACTGCCCAACGGTATTGA 59.696 45.455 0.00 0.00 36.64 2.57
6496 7249 1.530323 AACTGCCCAACGGTATTGAC 58.470 50.000 0.00 0.00 36.64 3.18
6497 7250 0.398696 ACTGCCCAACGGTATTGACA 59.601 50.000 0.00 0.00 35.54 3.58
6498 7251 1.202830 ACTGCCCAACGGTATTGACAA 60.203 47.619 0.00 0.00 35.54 3.18
6499 7252 1.883275 CTGCCCAACGGTATTGACAAA 59.117 47.619 0.00 0.00 0.00 2.83
6500 7253 2.294791 CTGCCCAACGGTATTGACAAAA 59.705 45.455 0.00 0.00 0.00 2.44
6501 7254 2.693591 TGCCCAACGGTATTGACAAAAA 59.306 40.909 0.00 0.00 0.00 1.94
6519 7272 4.351874 AAAAAGACCATCTTCCAGACGA 57.648 40.909 0.00 0.00 35.27 4.20
6520 7273 4.351874 AAAAGACCATCTTCCAGACGAA 57.648 40.909 0.00 0.00 35.27 3.85
6521 7274 4.559862 AAAGACCATCTTCCAGACGAAT 57.440 40.909 0.00 0.00 35.27 3.34
6522 7275 4.559862 AAGACCATCTTCCAGACGAATT 57.440 40.909 0.00 0.00 28.99 2.17
6523 7276 3.866651 AGACCATCTTCCAGACGAATTG 58.133 45.455 0.00 0.00 0.00 2.32
6524 7277 3.515502 AGACCATCTTCCAGACGAATTGA 59.484 43.478 0.00 0.00 0.00 2.57
6525 7278 3.600388 ACCATCTTCCAGACGAATTGAC 58.400 45.455 0.00 0.00 0.00 3.18
6526 7279 3.007940 ACCATCTTCCAGACGAATTGACA 59.992 43.478 0.00 0.00 0.00 3.58
6527 7280 4.002982 CCATCTTCCAGACGAATTGACAA 58.997 43.478 0.00 0.00 0.00 3.18
6528 7281 4.455533 CCATCTTCCAGACGAATTGACAAA 59.544 41.667 0.00 0.00 0.00 2.83
6529 7282 5.048782 CCATCTTCCAGACGAATTGACAAAA 60.049 40.000 0.00 0.00 0.00 2.44
6530 7283 5.418310 TCTTCCAGACGAATTGACAAAAC 57.582 39.130 0.00 0.00 0.00 2.43
6531 7284 4.878971 TCTTCCAGACGAATTGACAAAACA 59.121 37.500 0.00 0.00 0.00 2.83
6532 7285 4.811555 TCCAGACGAATTGACAAAACAG 57.188 40.909 0.00 0.00 0.00 3.16
6533 7286 4.447290 TCCAGACGAATTGACAAAACAGA 58.553 39.130 0.00 0.00 0.00 3.41
6534 7287 4.272504 TCCAGACGAATTGACAAAACAGAC 59.727 41.667 0.00 0.00 0.00 3.51
6535 7288 4.273480 CCAGACGAATTGACAAAACAGACT 59.727 41.667 0.00 0.00 0.00 3.24
6536 7289 5.465390 CCAGACGAATTGACAAAACAGACTA 59.535 40.000 0.00 0.00 0.00 2.59
6537 7290 6.346919 CCAGACGAATTGACAAAACAGACTAG 60.347 42.308 0.00 0.00 0.00 2.57
6538 7291 5.177696 AGACGAATTGACAAAACAGACTAGC 59.822 40.000 0.00 0.00 0.00 3.42
6539 7292 4.213482 ACGAATTGACAAAACAGACTAGCC 59.787 41.667 0.00 0.00 0.00 3.93
6540 7293 4.452455 CGAATTGACAAAACAGACTAGCCT 59.548 41.667 0.00 0.00 0.00 4.58
6541 7294 5.637810 CGAATTGACAAAACAGACTAGCCTA 59.362 40.000 0.00 0.00 0.00 3.93
6542 7295 6.183360 CGAATTGACAAAACAGACTAGCCTAG 60.183 42.308 0.00 0.00 0.00 3.02
6543 7296 3.926616 TGACAAAACAGACTAGCCTAGC 58.073 45.455 0.00 0.00 0.00 3.42
6544 7297 3.263261 GACAAAACAGACTAGCCTAGCC 58.737 50.000 0.00 0.00 0.00 3.93
6545 7298 2.271800 CAAAACAGACTAGCCTAGCCG 58.728 52.381 0.00 0.00 0.00 5.52
6546 7299 1.558233 AAACAGACTAGCCTAGCCGT 58.442 50.000 0.00 0.00 0.00 5.68
6547 7300 0.818296 AACAGACTAGCCTAGCCGTG 59.182 55.000 0.00 0.00 0.00 4.94
6548 7301 1.038130 ACAGACTAGCCTAGCCGTGG 61.038 60.000 0.00 0.00 0.00 4.94
6566 7319 3.716006 CGGCAGGCGTGACAGTTG 61.716 66.667 13.58 0.00 0.00 3.16
6567 7320 2.280797 GGCAGGCGTGACAGTTGA 60.281 61.111 11.29 0.00 0.00 3.18
6568 7321 2.607892 GGCAGGCGTGACAGTTGAC 61.608 63.158 11.29 0.00 0.00 3.18
6569 7322 2.943345 GCAGGCGTGACAGTTGACG 61.943 63.158 11.29 2.40 38.63 4.35
6573 7326 2.539503 CGTGACAGTTGACGCGTG 59.460 61.111 20.70 3.72 38.48 5.34
6574 7327 2.927618 CGTGACAGTTGACGCGTGG 61.928 63.158 20.70 2.87 38.48 4.94
6575 7328 2.964925 TGACAGTTGACGCGTGGC 60.965 61.111 20.70 3.93 0.00 5.01
6594 7347 2.438254 CCTGCCGCCACATGCTAA 60.438 61.111 0.00 0.00 38.05 3.09
6595 7348 2.475466 CCTGCCGCCACATGCTAAG 61.475 63.158 0.00 0.00 38.05 2.18
6596 7349 2.438254 TGCCGCCACATGCTAAGG 60.438 61.111 0.00 0.00 38.05 2.69
6597 7350 3.892581 GCCGCCACATGCTAAGGC 61.893 66.667 7.03 7.03 44.89 4.35
6600 7353 3.892581 GCCACATGCTAAGGCGGC 61.893 66.667 0.00 0.00 42.25 6.53
6601 7354 2.438254 CCACATGCTAAGGCGGCA 60.438 61.111 13.08 0.00 44.05 5.69
6602 7355 2.475466 CCACATGCTAAGGCGGCAG 61.475 63.158 13.08 0.98 43.15 4.85
6603 7356 2.825836 ACATGCTAAGGCGGCAGC 60.826 61.111 13.08 13.38 43.15 5.25
6620 7373 4.511246 CCCCTGCCGCCATGATGT 62.511 66.667 0.00 0.00 0.00 3.06
6621 7374 3.214123 CCCTGCCGCCATGATGTG 61.214 66.667 0.00 0.00 0.00 3.21
6622 7375 2.124612 CCTGCCGCCATGATGTGA 60.125 61.111 0.00 0.00 0.00 3.58
6623 7376 2.184830 CCTGCCGCCATGATGTGAG 61.185 63.158 0.00 0.00 0.00 3.51
6624 7377 2.124612 TGCCGCCATGATGTGAGG 60.125 61.111 0.00 0.00 0.00 3.86
6625 7378 3.589881 GCCGCCATGATGTGAGGC 61.590 66.667 11.38 11.38 44.89 4.70
6628 7381 3.589881 GCCATGATGTGAGGCGGC 61.590 66.667 0.00 0.00 38.86 6.53
6629 7382 2.903855 CCATGATGTGAGGCGGCC 60.904 66.667 12.11 12.11 0.00 6.13
6630 7383 3.274586 CATGATGTGAGGCGGCCG 61.275 66.667 24.05 24.05 0.00 6.13
6631 7384 4.552365 ATGATGTGAGGCGGCCGG 62.552 66.667 29.38 8.95 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.445582 GTCGCCGTCGGTGAGAATT 60.446 57.895 27.28 0.00 43.30 2.17
38 39 2.181021 GTCGCCGTCGGTGAGAAT 59.819 61.111 27.28 0.00 43.30 2.40
39 40 4.047059 GGTCGCCGTCGGTGAGAA 62.047 66.667 27.28 4.02 43.30 2.87
80 81 1.996187 GAGGGACCAGGAGGGGTTC 60.996 68.421 0.00 0.00 42.53 3.62
303 317 1.385206 GGGGGAAGCAGGGAGAGAT 60.385 63.158 0.00 0.00 0.00 2.75
338 352 4.150454 CCGGCTCCCCCTCTCTCT 62.150 72.222 0.00 0.00 0.00 3.10
339 353 4.144727 TCCGGCTCCCCCTCTCTC 62.145 72.222 0.00 0.00 0.00 3.20
349 365 2.743928 CTTGTGTGGCTCCGGCTC 60.744 66.667 0.00 0.00 38.73 4.70
390 409 0.392729 GAGGGAGAAGAGACGGACGA 60.393 60.000 0.00 0.00 0.00 4.20
399 418 1.045350 CGATGGCAGGAGGGAGAAGA 61.045 60.000 0.00 0.00 0.00 2.87
400 419 1.445095 CGATGGCAGGAGGGAGAAG 59.555 63.158 0.00 0.00 0.00 2.85
401 420 2.735772 GCGATGGCAGGAGGGAGAA 61.736 63.158 0.00 0.00 39.62 2.87
403 422 4.247380 GGCGATGGCAGGAGGGAG 62.247 72.222 1.01 0.00 42.47 4.30
405 424 3.426309 AATGGCGATGGCAGGAGGG 62.426 63.158 1.01 0.00 42.43 4.30
486 508 3.033184 CAAGCCAAGAACAGCGCA 58.967 55.556 11.47 0.00 0.00 6.09
488 510 1.208614 GAGCAAGCCAAGAACAGCG 59.791 57.895 0.00 0.00 0.00 5.18
547 569 2.957402 AACCAAGAACAGATCAGGCA 57.043 45.000 0.00 0.00 0.00 4.75
565 587 2.097680 GGACGAACCCAACGGAATAA 57.902 50.000 0.00 0.00 34.93 1.40
567 589 4.707791 GGACGAACCCAACGGAAT 57.292 55.556 0.00 0.00 34.93 3.01
592 614 1.754234 AAATGAGGCGACCCATGGC 60.754 57.895 6.09 0.00 0.00 4.40
593 615 2.008268 GCAAATGAGGCGACCCATGG 62.008 60.000 4.14 4.14 0.00 3.66
594 616 1.434696 GCAAATGAGGCGACCCATG 59.565 57.895 0.00 0.00 0.00 3.66
595 617 1.754234 GGCAAATGAGGCGACCCAT 60.754 57.895 0.00 0.00 0.00 4.00
638 660 1.208052 CAAATCTGCTCGGGGAAGAGA 59.792 52.381 0.00 0.00 40.57 3.10
717 901 1.002274 ACAAGCCCAACCAACCCAA 59.998 52.632 0.00 0.00 0.00 4.12
731 915 2.664916 CGGCAAACCAAATCTGACAAG 58.335 47.619 0.00 0.00 34.57 3.16
732 916 1.269517 GCGGCAAACCAAATCTGACAA 60.270 47.619 0.00 0.00 34.57 3.18
782 966 9.741647 GGGAGAAAATAAGAGCAGAAAAATATG 57.258 33.333 0.00 0.00 0.00 1.78
783 967 8.918116 GGGGAGAAAATAAGAGCAGAAAAATAT 58.082 33.333 0.00 0.00 0.00 1.28
839 1023 3.327757 AGGGTAAGCAGATGAACAGACAA 59.672 43.478 0.00 0.00 0.00 3.18
840 1024 2.906389 AGGGTAAGCAGATGAACAGACA 59.094 45.455 0.00 0.00 0.00 3.41
841 1025 3.618690 AGGGTAAGCAGATGAACAGAC 57.381 47.619 0.00 0.00 0.00 3.51
842 1026 4.345257 GGATAGGGTAAGCAGATGAACAGA 59.655 45.833 0.00 0.00 0.00 3.41
862 1048 0.618458 TGCTACGCAGGAAAAGGGAT 59.382 50.000 0.00 0.00 33.32 3.85
864 1050 1.463674 AATGCTACGCAGGAAAAGGG 58.536 50.000 0.00 0.00 43.65 3.95
889 1075 1.798813 GTGAGCGTGAAGTAAACCAGG 59.201 52.381 0.00 0.00 0.00 4.45
892 1078 2.206750 TGTGTGAGCGTGAAGTAAACC 58.793 47.619 0.00 0.00 0.00 3.27
894 1080 3.064271 GGTTTGTGTGAGCGTGAAGTAAA 59.936 43.478 0.00 0.00 0.00 2.01
896 1082 2.206750 GGTTTGTGTGAGCGTGAAGTA 58.793 47.619 0.00 0.00 0.00 2.24
897 1083 1.014352 GGTTTGTGTGAGCGTGAAGT 58.986 50.000 0.00 0.00 0.00 3.01
898 1084 1.013596 TGGTTTGTGTGAGCGTGAAG 58.986 50.000 0.00 0.00 0.00 3.02
899 1085 1.674359 ATGGTTTGTGTGAGCGTGAA 58.326 45.000 0.00 0.00 0.00 3.18
900 1086 1.601903 GAATGGTTTGTGTGAGCGTGA 59.398 47.619 0.00 0.00 0.00 4.35
901 1087 1.334960 GGAATGGTTTGTGTGAGCGTG 60.335 52.381 0.00 0.00 0.00 5.34
902 1088 0.951558 GGAATGGTTTGTGTGAGCGT 59.048 50.000 0.00 0.00 0.00 5.07
903 1089 0.240945 GGGAATGGTTTGTGTGAGCG 59.759 55.000 0.00 0.00 0.00 5.03
904 1090 0.240945 CGGGAATGGTTTGTGTGAGC 59.759 55.000 0.00 0.00 0.00 4.26
905 1091 1.266718 CACGGGAATGGTTTGTGTGAG 59.733 52.381 0.00 0.00 0.00 3.51
906 1092 1.313772 CACGGGAATGGTTTGTGTGA 58.686 50.000 0.00 0.00 0.00 3.58
907 1093 1.028905 ACACGGGAATGGTTTGTGTG 58.971 50.000 0.00 0.00 41.81 3.82
908 1094 1.679153 GAACACGGGAATGGTTTGTGT 59.321 47.619 0.00 0.00 45.01 3.72
909 1095 1.953686 AGAACACGGGAATGGTTTGTG 59.046 47.619 0.00 0.00 36.64 3.33
910 1096 1.953686 CAGAACACGGGAATGGTTTGT 59.046 47.619 0.00 0.00 0.00 2.83
911 1097 1.335872 GCAGAACACGGGAATGGTTTG 60.336 52.381 0.00 0.00 0.00 2.93
914 1100 0.606401 CAGCAGAACACGGGAATGGT 60.606 55.000 0.00 0.00 0.00 3.55
915 1101 0.606401 ACAGCAGAACACGGGAATGG 60.606 55.000 0.00 0.00 0.00 3.16
917 1103 1.238439 CAACAGCAGAACACGGGAAT 58.762 50.000 0.00 0.00 0.00 3.01
920 1106 0.813610 TCACAACAGCAGAACACGGG 60.814 55.000 0.00 0.00 0.00 5.28
936 1129 3.242349 CGCTGCTTCTCATCTGAAATCAC 60.242 47.826 0.00 0.00 0.00 3.06
939 1132 1.669779 GCGCTGCTTCTCATCTGAAAT 59.330 47.619 0.00 0.00 0.00 2.17
1005 1198 4.065281 GCTTTGCAGCCTGCCTGG 62.065 66.667 15.29 4.92 44.23 4.45
1071 1264 2.693864 CTCCAGGGAGCCCATGGT 60.694 66.667 19.98 0.00 38.92 3.55
1220 1413 2.821366 CGCAAGCGGCATCTCCTT 60.821 61.111 6.55 0.00 45.17 3.36
1294 1487 1.435577 GTAATCGCCACAGAAACGGT 58.564 50.000 0.00 0.00 0.00 4.83
1295 1488 0.725117 GGTAATCGCCACAGAAACGG 59.275 55.000 0.00 0.00 0.00 4.44
1296 1489 1.434555 TGGTAATCGCCACAGAAACG 58.565 50.000 0.00 0.00 32.81 3.60
1318 1511 1.678101 GCGGGTACAGGATTACTACGT 59.322 52.381 0.00 0.00 0.00 3.57
1420 1613 6.100424 CCTACAAGATCAGGGAAGTTAAGGAT 59.900 42.308 0.00 0.00 0.00 3.24
1471 1664 1.683629 GGATGGGTGGACGCCATTAAA 60.684 52.381 4.09 0.00 35.28 1.52
1474 1667 1.936767 ATGGATGGGTGGACGCCATT 61.937 55.000 4.09 0.00 35.95 3.16
1480 1673 4.785301 CATATATGGATGGATGGGTGGAC 58.215 47.826 4.68 0.00 0.00 4.02
1506 1699 2.032071 AAGTGGCGCTGGTGGTAC 59.968 61.111 7.64 0.00 0.00 3.34
1507 1700 2.345991 GAAGTGGCGCTGGTGGTA 59.654 61.111 7.64 0.00 0.00 3.25
1512 1705 3.599285 TAACGGGAAGTGGCGCTGG 62.599 63.158 7.64 0.00 0.00 4.85
1513 1706 2.047655 TAACGGGAAGTGGCGCTG 60.048 61.111 7.64 0.00 0.00 5.18
1515 1708 1.810030 CTCTAACGGGAAGTGGCGC 60.810 63.158 0.00 0.00 0.00 6.53
1516 1709 0.460311 ATCTCTAACGGGAAGTGGCG 59.540 55.000 0.00 0.00 0.00 5.69
1517 1710 1.941325 CATCTCTAACGGGAAGTGGC 58.059 55.000 0.00 0.00 0.00 5.01
1566 1759 1.675310 TGGCAGTTCGGGCATCTTG 60.675 57.895 0.00 0.00 38.55 3.02
1651 1844 3.241530 ACCGCCAGAAGTGCAGGA 61.242 61.111 0.00 0.00 0.00 3.86
1658 1851 1.200020 GATCAAAACCACCGCCAGAAG 59.800 52.381 0.00 0.00 0.00 2.85
1827 2020 0.108138 GGAGCCAATGCGTCAGTAGT 60.108 55.000 0.00 0.00 44.33 2.73
1858 2051 0.033504 CTACTCAACGTGCCCACTGT 59.966 55.000 0.00 0.00 0.00 3.55
2006 2199 0.108585 GACAGGAGACCAAGGTTGCA 59.891 55.000 0.00 0.00 0.00 4.08
2029 2222 3.527533 TGCCGTTAACATCACATAGACC 58.472 45.455 6.39 0.00 0.00 3.85
2034 2227 3.181511 CGTCAATGCCGTTAACATCACAT 60.182 43.478 6.39 0.52 0.00 3.21
2059 2252 5.351740 GGTGTAGAGATGGAAACTTTGTAGC 59.648 44.000 0.00 0.00 0.00 3.58
2112 2307 1.903783 ATACCGGCAAACACGCGAAC 61.904 55.000 15.93 0.00 0.00 3.95
2252 2500 1.153349 CTCCGGGCCTCTGCTTTAC 60.153 63.158 0.84 0.00 37.74 2.01
2324 2572 1.092921 AAAGCGTGCACGTTTCTCCA 61.093 50.000 35.69 0.00 41.75 3.86
2337 2585 1.173913 GCTATGGGGAACAAAAGCGT 58.826 50.000 0.00 0.00 34.01 5.07
2338 2586 0.455815 GGCTATGGGGAACAAAAGCG 59.544 55.000 0.00 0.00 40.92 4.68
2593 2845 1.066929 CACCCCATTGCTTTGCTTACC 60.067 52.381 0.00 0.00 0.00 2.85
2664 2916 7.925993 TCAGAACAACCACTTGTACTAAAATG 58.074 34.615 0.00 0.00 39.88 2.32
2670 2922 5.280011 CCCTATCAGAACAACCACTTGTACT 60.280 44.000 0.00 0.00 39.88 2.73
2700 2952 3.353557 GAAGGGATCCAACTTGGTTACC 58.646 50.000 15.23 11.19 40.00 2.85
2717 2969 4.891992 TCTGAAGTACAAGGAAGGAAGG 57.108 45.455 0.00 0.00 0.00 3.46
2759 3011 1.064003 TCCCAAAGTAAGCAGGCAGA 58.936 50.000 0.00 0.00 0.00 4.26
2760 3012 1.909700 TTCCCAAAGTAAGCAGGCAG 58.090 50.000 0.00 0.00 0.00 4.85
2761 3013 2.373335 TTTCCCAAAGTAAGCAGGCA 57.627 45.000 0.00 0.00 0.00 4.75
2762 3014 2.825532 TGATTTCCCAAAGTAAGCAGGC 59.174 45.455 0.00 0.00 0.00 4.85
2763 3015 5.888161 AGTATGATTTCCCAAAGTAAGCAGG 59.112 40.000 0.00 0.00 0.00 4.85
2789 3041 9.118300 CTCTGAAATAGGCACTTATGAAGAAAT 57.882 33.333 0.00 0.00 41.75 2.17
2790 3042 8.103305 ACTCTGAAATAGGCACTTATGAAGAAA 58.897 33.333 0.00 0.00 41.75 2.52
2798 3050 5.222048 ACCCAAACTCTGAAATAGGCACTTA 60.222 40.000 0.00 0.00 41.75 2.24
2819 3071 5.010282 ACATTATTTGTGAGTCCAAGACCC 58.990 41.667 0.00 0.00 37.11 4.46
2943 3283 3.274288 CTCAATAGGCACTGGGAACTTC 58.726 50.000 0.00 0.00 41.52 3.01
3107 3448 8.778358 CAGAAGCTGTCTCTACAATAAAAAGTT 58.222 33.333 0.00 0.00 34.49 2.66
3125 3466 2.447244 AAGTCGGAACTCAGAAGCTG 57.553 50.000 0.00 0.00 33.48 4.24
3165 3506 1.338973 TCAGTAACGGAACAGCGAAGT 59.661 47.619 0.00 0.00 0.00 3.01
3196 3537 4.180057 CTGCAACAGAGGAGATAGTCAAC 58.820 47.826 0.00 0.00 32.44 3.18
3360 3701 5.800941 CGGAGTGTATAGAAGTGTCAGAAAC 59.199 44.000 0.00 0.00 0.00 2.78
3449 3790 5.288543 ACGTGTAGTACTAGCTGTTACAC 57.711 43.478 1.87 7.73 38.52 2.90
3523 3864 2.141517 CGATGAGCTTCAGGGCAATAG 58.858 52.381 0.00 0.00 34.17 1.73
3628 3969 4.842531 ATACACATCATCCCACTGAACA 57.157 40.909 0.00 0.00 0.00 3.18
4112 4453 2.693591 CCTTCGAGTCAGGCCTGTATAA 59.306 50.000 31.58 17.76 0.00 0.98
4438 4780 5.631929 GGACAACAATAAAAGGCGTAAAAGG 59.368 40.000 0.00 0.00 0.00 3.11
4479 4822 5.651139 AGGATTTGGTGTCATTCATCAGAAG 59.349 40.000 0.00 0.00 38.49 2.85
4489 4832 6.542821 TGTAAGAGAAAGGATTTGGTGTCAT 58.457 36.000 0.00 0.00 39.27 3.06
5140 5483 2.830651 AGTGGAGGACGTAGAGGATT 57.169 50.000 0.00 0.00 0.00 3.01
5176 5519 1.523938 GTCCCGGAAGCATAGCCAC 60.524 63.158 0.73 0.00 0.00 5.01
5257 5600 0.250858 TGTCATGCACCTTCCACCAG 60.251 55.000 0.00 0.00 0.00 4.00
5483 5826 1.673337 TCGAGGCCTTCTTCGTCGA 60.673 57.895 6.77 6.84 44.89 4.20
5565 5914 9.851686 TGTATCATCTGGTATGCTAAAATTTCT 57.148 29.630 0.00 0.00 0.00 2.52
5753 6107 1.148759 GCTGCTTTCGAGGTCGGATC 61.149 60.000 0.00 0.00 40.29 3.36
5754 6108 1.153549 GCTGCTTTCGAGGTCGGAT 60.154 57.895 0.00 0.00 40.29 4.18
5755 6109 2.261671 GCTGCTTTCGAGGTCGGA 59.738 61.111 0.00 0.00 40.29 4.55
5756 6110 2.815647 GGCTGCTTTCGAGGTCGG 60.816 66.667 0.00 0.00 40.29 4.79
5757 6111 3.181967 CGGCTGCTTTCGAGGTCG 61.182 66.667 0.00 0.00 41.45 4.79
5758 6112 3.491652 GCGGCTGCTTTCGAGGTC 61.492 66.667 11.21 0.00 38.39 3.85
5804 6163 3.788933 ACCCATCCATGATGAAACCAAA 58.211 40.909 5.67 0.00 42.09 3.28
5845 6204 3.763057 AGTCTTGCCCGGAAAAGTTAAT 58.237 40.909 0.73 0.00 0.00 1.40
5847 6206 2.882137 CAAGTCTTGCCCGGAAAAGTTA 59.118 45.455 0.73 0.00 0.00 2.24
6092 6453 4.771590 ACAATTTCACACGCTCAATCAT 57.228 36.364 0.00 0.00 0.00 2.45
6095 6456 4.566545 TGAACAATTTCACACGCTCAAT 57.433 36.364 0.00 0.00 36.79 2.57
6096 6457 4.536065 GATGAACAATTTCACACGCTCAA 58.464 39.130 0.00 0.00 44.66 3.02
6097 6458 3.058293 GGATGAACAATTTCACACGCTCA 60.058 43.478 0.00 0.00 44.66 4.26
6100 6461 2.241722 CGGATGAACAATTTCACACGC 58.758 47.619 0.00 0.00 44.66 5.34
6104 6479 5.173131 GTCAAACACGGATGAACAATTTCAC 59.827 40.000 0.00 0.00 44.66 3.18
6119 6494 2.185867 TGCACAACATGTCAAACACG 57.814 45.000 0.00 0.00 0.00 4.49
6238 6619 2.836672 ATCTCTGCCCTGCCCTCACT 62.837 60.000 0.00 0.00 0.00 3.41
6239 6620 2.373707 ATCTCTGCCCTGCCCTCAC 61.374 63.158 0.00 0.00 0.00 3.51
6240 6621 2.041762 ATCTCTGCCCTGCCCTCA 59.958 61.111 0.00 0.00 0.00 3.86
6241 6622 1.050988 TACATCTCTGCCCTGCCCTC 61.051 60.000 0.00 0.00 0.00 4.30
6242 6623 0.401105 ATACATCTCTGCCCTGCCCT 60.401 55.000 0.00 0.00 0.00 5.19
6246 6627 5.279406 CCTCTTCTTATACATCTCTGCCCTG 60.279 48.000 0.00 0.00 0.00 4.45
6247 6628 4.837860 CCTCTTCTTATACATCTCTGCCCT 59.162 45.833 0.00 0.00 0.00 5.19
6248 6629 4.835615 TCCTCTTCTTATACATCTCTGCCC 59.164 45.833 0.00 0.00 0.00 5.36
6251 6632 7.340122 TGTGTCCTCTTCTTATACATCTCTG 57.660 40.000 0.00 0.00 0.00 3.35
6252 6633 7.015098 CCATGTGTCCTCTTCTTATACATCTCT 59.985 40.741 0.00 0.00 0.00 3.10
6253 6634 7.151308 CCATGTGTCCTCTTCTTATACATCTC 58.849 42.308 0.00 0.00 0.00 2.75
6261 6642 1.559682 GCCCCATGTGTCCTCTTCTTA 59.440 52.381 0.00 0.00 0.00 2.10
6266 6647 4.101448 GCGCCCCATGTGTCCTCT 62.101 66.667 0.00 0.00 0.00 3.69
6290 6673 2.674380 CAGGCAGCTCACCCAACC 60.674 66.667 0.00 0.00 0.00 3.77
6315 6698 0.538977 CATGTCCCTCCCATGGCATC 60.539 60.000 6.09 0.00 36.81 3.91
6320 6703 2.196776 GGCCATGTCCCTCCCATG 59.803 66.667 0.00 0.00 39.50 3.66
6321 6704 3.105928 GGGCCATGTCCCTCCCAT 61.106 66.667 4.01 0.00 43.13 4.00
6459 7212 6.103330 GGCAGTTAGTCTTTTTGGACAAAAA 58.897 36.000 18.58 18.58 44.98 1.94
6460 7213 5.394773 GGGCAGTTAGTCTTTTTGGACAAAA 60.395 40.000 6.14 6.14 38.57 2.44
6461 7214 4.098807 GGGCAGTTAGTCTTTTTGGACAAA 59.901 41.667 0.00 0.00 38.57 2.83
6462 7215 3.634910 GGGCAGTTAGTCTTTTTGGACAA 59.365 43.478 0.00 0.00 38.57 3.18
6463 7216 3.219281 GGGCAGTTAGTCTTTTTGGACA 58.781 45.455 0.00 0.00 38.57 4.02
6464 7217 3.219281 TGGGCAGTTAGTCTTTTTGGAC 58.781 45.455 0.00 0.00 36.56 4.02
6465 7218 3.586470 TGGGCAGTTAGTCTTTTTGGA 57.414 42.857 0.00 0.00 0.00 3.53
6466 7219 3.550030 CGTTGGGCAGTTAGTCTTTTTGG 60.550 47.826 0.00 0.00 0.00 3.28
6467 7220 3.550030 CCGTTGGGCAGTTAGTCTTTTTG 60.550 47.826 0.00 0.00 0.00 2.44
6468 7221 2.621526 CCGTTGGGCAGTTAGTCTTTTT 59.378 45.455 0.00 0.00 0.00 1.94
6469 7222 2.227194 CCGTTGGGCAGTTAGTCTTTT 58.773 47.619 0.00 0.00 0.00 2.27
6470 7223 1.142262 ACCGTTGGGCAGTTAGTCTTT 59.858 47.619 0.00 0.00 36.48 2.52
6471 7224 0.763035 ACCGTTGGGCAGTTAGTCTT 59.237 50.000 0.00 0.00 36.48 3.01
6472 7225 1.636148 TACCGTTGGGCAGTTAGTCT 58.364 50.000 0.00 0.00 36.48 3.24
6473 7226 2.676342 CAATACCGTTGGGCAGTTAGTC 59.324 50.000 0.00 0.00 36.48 2.59
6474 7227 2.303600 TCAATACCGTTGGGCAGTTAGT 59.696 45.455 0.00 0.00 36.48 2.24
6475 7228 2.676342 GTCAATACCGTTGGGCAGTTAG 59.324 50.000 0.00 0.00 36.48 2.34
6476 7229 2.038689 TGTCAATACCGTTGGGCAGTTA 59.961 45.455 0.00 0.00 36.48 2.24
6477 7230 1.202830 TGTCAATACCGTTGGGCAGTT 60.203 47.619 0.00 0.00 36.48 3.16
6478 7231 0.398696 TGTCAATACCGTTGGGCAGT 59.601 50.000 0.00 0.00 36.48 4.40
6479 7232 1.529226 TTGTCAATACCGTTGGGCAG 58.471 50.000 0.00 0.00 36.48 4.85
6480 7233 1.982660 TTTGTCAATACCGTTGGGCA 58.017 45.000 0.00 0.00 36.48 5.36
6481 7234 3.372660 TTTTTGTCAATACCGTTGGGC 57.627 42.857 0.00 0.00 36.48 5.36
6508 7261 4.878971 TGTTTTGTCAATTCGTCTGGAAGA 59.121 37.500 0.00 0.00 43.69 2.87
6509 7262 5.007626 TCTGTTTTGTCAATTCGTCTGGAAG 59.992 40.000 0.00 0.00 38.24 3.46
6510 7263 4.878971 TCTGTTTTGTCAATTCGTCTGGAA 59.121 37.500 0.00 0.00 39.42 3.53
6511 7264 4.272504 GTCTGTTTTGTCAATTCGTCTGGA 59.727 41.667 0.00 0.00 0.00 3.86
6512 7265 4.273480 AGTCTGTTTTGTCAATTCGTCTGG 59.727 41.667 0.00 0.00 0.00 3.86
6513 7266 5.409643 AGTCTGTTTTGTCAATTCGTCTG 57.590 39.130 0.00 0.00 0.00 3.51
6514 7267 5.177696 GCTAGTCTGTTTTGTCAATTCGTCT 59.822 40.000 0.00 0.00 0.00 4.18
6515 7268 5.374898 GCTAGTCTGTTTTGTCAATTCGTC 58.625 41.667 0.00 0.00 0.00 4.20
6516 7269 4.213482 GGCTAGTCTGTTTTGTCAATTCGT 59.787 41.667 0.00 0.00 0.00 3.85
6517 7270 4.452455 AGGCTAGTCTGTTTTGTCAATTCG 59.548 41.667 0.00 0.00 0.00 3.34
6518 7271 5.948992 AGGCTAGTCTGTTTTGTCAATTC 57.051 39.130 0.00 0.00 0.00 2.17
6519 7272 5.412904 GCTAGGCTAGTCTGTTTTGTCAATT 59.587 40.000 21.92 0.00 0.00 2.32
6520 7273 4.938226 GCTAGGCTAGTCTGTTTTGTCAAT 59.062 41.667 21.92 0.00 0.00 2.57
6521 7274 4.315803 GCTAGGCTAGTCTGTTTTGTCAA 58.684 43.478 21.92 0.00 0.00 3.18
6522 7275 3.306780 GGCTAGGCTAGTCTGTTTTGTCA 60.307 47.826 21.92 0.00 0.00 3.58
6523 7276 3.263261 GGCTAGGCTAGTCTGTTTTGTC 58.737 50.000 21.92 2.07 0.00 3.18
6524 7277 2.353803 CGGCTAGGCTAGTCTGTTTTGT 60.354 50.000 22.69 0.00 0.00 2.83
6525 7278 2.271800 CGGCTAGGCTAGTCTGTTTTG 58.728 52.381 22.69 3.49 0.00 2.44
6526 7279 1.900486 ACGGCTAGGCTAGTCTGTTTT 59.100 47.619 22.69 0.55 0.00 2.43
6527 7280 1.204941 CACGGCTAGGCTAGTCTGTTT 59.795 52.381 22.69 2.94 0.00 2.83
6528 7281 0.818296 CACGGCTAGGCTAGTCTGTT 59.182 55.000 22.69 5.37 0.00 3.16
6529 7282 1.038130 CCACGGCTAGGCTAGTCTGT 61.038 60.000 22.69 20.36 0.00 3.41
6530 7283 1.736586 CCACGGCTAGGCTAGTCTG 59.263 63.158 22.69 19.80 0.00 3.51
6531 7284 4.261701 CCACGGCTAGGCTAGTCT 57.738 61.111 22.69 0.74 0.00 3.24
6549 7302 3.716006 CAACTGTCACGCCTGCCG 61.716 66.667 0.00 0.00 44.21 5.69
6550 7303 2.280797 TCAACTGTCACGCCTGCC 60.281 61.111 0.00 0.00 0.00 4.85
6551 7304 2.939022 GTCAACTGTCACGCCTGC 59.061 61.111 0.00 0.00 0.00 4.85
6552 7305 3.234390 CGTCAACTGTCACGCCTG 58.766 61.111 0.05 0.00 0.00 4.85
6556 7309 2.539503 CACGCGTCAACTGTCACG 59.460 61.111 9.86 7.64 39.09 4.35
6557 7310 2.928361 CCACGCGTCAACTGTCAC 59.072 61.111 9.86 0.00 0.00 3.67
6558 7311 2.964925 GCCACGCGTCAACTGTCA 60.965 61.111 9.86 0.00 0.00 3.58
6584 7337 2.438254 TGCCGCCTTAGCATGTGG 60.438 61.111 0.00 0.00 39.83 4.17
6585 7338 3.104766 CTGCCGCCTTAGCATGTG 58.895 61.111 0.00 0.00 40.04 3.21
6586 7339 2.825836 GCTGCCGCCTTAGCATGT 60.826 61.111 0.00 0.00 40.04 3.21
6603 7356 4.511246 ACATCATGGCGGCAGGGG 62.511 66.667 23.81 17.72 0.00 4.79
6604 7357 3.214123 CACATCATGGCGGCAGGG 61.214 66.667 23.81 15.06 0.00 4.45
6605 7358 2.124612 TCACATCATGGCGGCAGG 60.125 61.111 18.43 18.43 0.00 4.85
6606 7359 2.184830 CCTCACATCATGGCGGCAG 61.185 63.158 19.29 9.89 0.00 4.85
6607 7360 2.124612 CCTCACATCATGGCGGCA 60.125 61.111 16.34 16.34 0.00 5.69
6608 7361 3.589881 GCCTCACATCATGGCGGC 61.590 66.667 0.00 0.00 37.87 6.53
6611 7364 3.589881 GCCGCCTCACATCATGGC 61.590 66.667 0.00 0.00 42.94 4.40
6612 7365 2.903855 GGCCGCCTCACATCATGG 60.904 66.667 0.71 0.00 0.00 3.66
6613 7366 3.274586 CGGCCGCCTCACATCATG 61.275 66.667 14.67 0.00 0.00 3.07
6614 7367 4.552365 CCGGCCGCCTCACATCAT 62.552 66.667 22.85 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.