Multiple sequence alignment - TraesCS3B01G115100

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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 TraesCS3B01G115100 chr3B 100.000 4252 0 0 1 4252 81812957 81817208 0.000000e+00 7853.0
1 TraesCS3B01G115100 chr3B 100.000 1506 0 0 4548 6053 81817504 81819009 0.000000e+00 2782.0
2 TraesCS3B01G115100 chr3D 95.239 4285 115 21 8 4252 51038422 51042657 0.000000e+00 6700.0
3 TraesCS3B01G115100 chr3D 89.084 1310 65 22 4548 5784 51042772 51044076 0.000000e+00 1555.0
4 TraesCS3B01G115100 chr3D 89.912 228 16 4 5832 6053 508391790 508392016 2.760000e-73 287.0
5 TraesCS3B01G115100 chr3A 94.803 4272 154 22 8 4252 63904838 63909068 0.000000e+00 6597.0
6 TraesCS3B01G115100 chr3A 88.961 1078 67 15 4548 5577 63909192 63910265 0.000000e+00 1284.0
7 TraesCS3B01G115100 chr3A 94.273 227 11 2 5580 5805 63911737 63911962 4.490000e-91 346.0
8 TraesCS3B01G115100 chr3A 92.609 230 17 0 5824 6053 646137944 646138173 1.260000e-86 331.0
9 TraesCS3B01G115100 chr4A 93.074 231 15 1 5824 6053 358853478 358853708 2.700000e-88 337.0
10 TraesCS3B01G115100 chr4A 88.983 236 25 1 5818 6053 493829455 493829221 2.130000e-74 291.0
11 TraesCS3B01G115100 chr2D 91.915 235 18 1 5820 6053 27615590 27615824 1.630000e-85 327.0
12 TraesCS3B01G115100 chr5A 91.026 234 20 1 5820 6053 262232326 262232558 1.270000e-81 315.0
13 TraesCS3B01G115100 chr7D 89.041 219 13 4 5835 6053 23195456 23195249 1.670000e-65 261.0
14 TraesCS3B01G115100 chr7D 89.362 188 20 0 5824 6011 12793174 12793361 2.820000e-58 237.0
15 TraesCS3B01G115100 chr5B 90.722 194 16 2 5819 6012 604743661 604743470 2.160000e-64 257.0
16 TraesCS3B01G115100 chr1D 78.818 203 34 9 3250 3448 108832269 108832072 1.770000e-25 128.0
17 TraesCS3B01G115100 chr1A 78.325 203 35 9 3250 3448 112038100 112037903 8.240000e-24 122.0
18 TraesCS3B01G115100 chr1B 71.748 492 111 24 2972 3448 164711460 164710982 4.960000e-21 113.0
19 TraesCS3B01G115100 chr5D 92.537 67 5 0 5984 6050 391379280 391379346 4.990000e-16 97.1


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 TraesCS3B01G115100 chr3B 81812957 81819009 6052 False 5317.500000 7853 100.0000 1 6053 2 chr3B.!!$F1 6052
1 TraesCS3B01G115100 chr3D 51038422 51044076 5654 False 4127.500000 6700 92.1615 8 5784 2 chr3D.!!$F2 5776
2 TraesCS3B01G115100 chr3A 63904838 63911962 7124 False 2742.333333 6597 92.6790 8 5805 3 chr3A.!!$F2 5797

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
452 458 0.036164 TGGCATGTAGGTGTGGTGTC 59.964 55.000 0.00 0.0 0.00 3.67 F
628 637 0.168788 CAGGCAGCGTTTGTATGGTG 59.831 55.000 0.00 0.0 40.83 4.17 F
748 806 0.476338 TGGTTTACCTGGCAAGCTCA 59.524 50.000 9.16 0.0 36.82 4.26 F
1851 1922 1.061566 GCGGAATTTTTCGGTACCTCG 59.938 52.381 10.90 0.0 33.09 4.63 F
1971 2042 1.142060 TGGTTCAACGGATGGTGAACT 59.858 47.619 21.41 0.0 37.11 3.01 F
2840 2911 0.517316 GTGTTCGTGCATTCCAGACC 59.483 55.000 0.00 0.0 0.00 3.85 F
3194 3265 2.292016 CACAGGTAAACATTGTTCGGCA 59.708 45.455 1.83 0.0 0.00 5.69 F
4844 4916 1.153229 GTACCTCATTGGCGGGTCC 60.153 63.158 0.00 0.0 40.22 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 2016 1.001974 CCATCCGTTGAACCAGACTCA 59.998 52.381 0.0 0.0 0.00 3.41 R
2295 2366 1.202114 TGGCGTTTGATGGATCTTTGC 59.798 47.619 0.0 0.0 0.00 3.68 R
2583 2654 4.694982 CCCAAAAGTTCAAAGCAAACAAGT 59.305 37.500 0.0 0.0 0.00 3.16 R
2824 2895 0.389817 CTCGGTCTGGAATGCACGAA 60.390 55.000 0.0 0.0 0.00 3.85 R
3172 3243 2.351350 GCCGAACAATGTTTACCTGTGG 60.351 50.000 0.0 0.0 0.00 4.17 R
4808 4880 1.221466 ACACATTGTCGTCCGCTGTG 61.221 55.000 0.0 0.0 42.19 3.66 R
4977 5049 0.252239 TAGACCAGCCTTGCCTCTCA 60.252 55.000 0.0 0.0 0.00 3.27 R
5943 7532 0.905357 AGCTCACGAATTGGCTAGGT 59.095 50.000 0.0 0.0 31.97 3.08 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
32 33 3.366985 GGGCGATTCGGTTTGATTTTTCT 60.367 43.478 8.34 0.00 0.00 2.52
39 40 3.075884 CGGTTTGATTTTTCTACGGGGA 58.924 45.455 0.00 0.00 0.00 4.81
54 55 1.341852 CGGGGAAACGGTGGAATTTTT 59.658 47.619 0.00 0.00 0.00 1.94
154 156 1.915614 GACACTGGTCGCTGCCATTG 61.916 60.000 10.66 10.66 42.63 2.82
167 169 3.655486 CTGCCATTGCTGATGTTTTTGA 58.345 40.909 0.00 0.00 38.61 2.69
225 227 5.179929 GGTTTATGGGGACGATATTTTACCG 59.820 44.000 0.00 0.00 0.00 4.02
231 233 3.432046 GGGACGATATTTTACCGGTTGGA 60.432 47.826 15.04 0.00 39.21 3.53
246 248 4.690280 CCGGTTGGATTTCATTGGAAAAAG 59.310 41.667 0.00 0.00 45.52 2.27
289 294 0.249155 TCCTGTCGAAACACGTCCAC 60.249 55.000 0.00 0.00 43.13 4.02
342 347 2.035961 TGTGAAGCAACTCGAGCTAGTT 59.964 45.455 13.61 0.96 42.53 2.24
401 407 0.973632 TTCCTGTAGCGAGCCTTTCA 59.026 50.000 0.00 0.00 0.00 2.69
402 408 0.532573 TCCTGTAGCGAGCCTTTCAG 59.467 55.000 0.00 0.00 0.00 3.02
407 413 1.066787 GTAGCGAGCCTTTCAGGACTT 60.067 52.381 0.00 0.00 37.67 3.01
425 431 5.187967 AGGACTTACATCCTCGAGTTTTGAT 59.812 40.000 12.31 3.84 46.92 2.57
451 457 0.698238 ATGGCATGTAGGTGTGGTGT 59.302 50.000 0.00 0.00 0.00 4.16
452 458 0.036164 TGGCATGTAGGTGTGGTGTC 59.964 55.000 0.00 0.00 0.00 3.67
453 459 0.676782 GGCATGTAGGTGTGGTGTCC 60.677 60.000 0.00 0.00 0.00 4.02
454 460 0.324943 GCATGTAGGTGTGGTGTCCT 59.675 55.000 0.00 0.00 37.80 3.85
455 461 1.553248 GCATGTAGGTGTGGTGTCCTA 59.447 52.381 0.00 0.00 35.51 2.94
533 542 1.810151 GTAATTTTGCCGTGGAGCTCA 59.190 47.619 17.19 0.00 0.00 4.26
625 634 4.771684 GCAGGCAGCGTTTGTATG 57.228 55.556 0.00 0.00 0.00 2.39
626 635 1.137404 GCAGGCAGCGTTTGTATGG 59.863 57.895 0.00 0.00 0.00 2.74
627 636 1.586154 GCAGGCAGCGTTTGTATGGT 61.586 55.000 0.00 0.00 0.00 3.55
628 637 0.168788 CAGGCAGCGTTTGTATGGTG 59.831 55.000 0.00 0.00 40.83 4.17
631 640 3.975992 CAGCGTTTGTATGGTGCTC 57.024 52.632 0.00 0.00 32.66 4.26
632 641 1.442769 CAGCGTTTGTATGGTGCTCT 58.557 50.000 0.00 0.00 32.66 4.09
633 642 1.806542 CAGCGTTTGTATGGTGCTCTT 59.193 47.619 0.00 0.00 32.66 2.85
634 643 1.806542 AGCGTTTGTATGGTGCTCTTG 59.193 47.619 0.00 0.00 0.00 3.02
635 644 1.804151 GCGTTTGTATGGTGCTCTTGA 59.196 47.619 0.00 0.00 0.00 3.02
636 645 2.225491 GCGTTTGTATGGTGCTCTTGAA 59.775 45.455 0.00 0.00 0.00 2.69
637 646 3.304391 GCGTTTGTATGGTGCTCTTGAAA 60.304 43.478 0.00 0.00 0.00 2.69
640 649 5.920273 CGTTTGTATGGTGCTCTTGAAATTT 59.080 36.000 0.00 0.00 0.00 1.82
708 736 2.206750 TGACGGAAACACAACTACAGC 58.793 47.619 0.00 0.00 0.00 4.40
712 740 2.616842 CGGAAACACAACTACAGCCTTT 59.383 45.455 0.00 0.00 0.00 3.11
737 795 4.526650 ACATTCCCATTGTTCTGGTTTACC 59.473 41.667 0.00 0.00 34.23 2.85
748 806 0.476338 TGGTTTACCTGGCAAGCTCA 59.524 50.000 9.16 0.00 36.82 4.26
1034 1105 2.284190 GAAGGCAGAGACCTACAATGC 58.716 52.381 0.00 0.00 39.93 3.56
1523 1594 5.934043 TCATGATGGTAGAACAAAGACACAG 59.066 40.000 0.00 0.00 0.00 3.66
1592 1663 7.889589 TCTGTCACTTCAGTTTGTATGTATG 57.110 36.000 0.00 0.00 36.85 2.39
1593 1664 7.666623 TCTGTCACTTCAGTTTGTATGTATGA 58.333 34.615 0.00 0.00 36.85 2.15
1594 1665 8.314021 TCTGTCACTTCAGTTTGTATGTATGAT 58.686 33.333 0.00 0.00 36.85 2.45
1595 1666 8.846943 TGTCACTTCAGTTTGTATGTATGATT 57.153 30.769 0.00 0.00 0.00 2.57
1596 1667 9.283768 TGTCACTTCAGTTTGTATGTATGATTT 57.716 29.630 0.00 0.00 0.00 2.17
1599 1670 8.853345 CACTTCAGTTTGTATGTATGATTTTGC 58.147 33.333 0.00 0.00 0.00 3.68
1600 1671 8.796475 ACTTCAGTTTGTATGTATGATTTTGCT 58.204 29.630 0.00 0.00 0.00 3.91
1601 1672 8.969121 TTCAGTTTGTATGTATGATTTTGCTG 57.031 30.769 0.00 0.00 0.00 4.41
1602 1673 7.537715 TCAGTTTGTATGTATGATTTTGCTGG 58.462 34.615 0.00 0.00 0.00 4.85
1603 1674 7.176515 TCAGTTTGTATGTATGATTTTGCTGGT 59.823 33.333 0.00 0.00 0.00 4.00
1604 1675 7.814107 CAGTTTGTATGTATGATTTTGCTGGTT 59.186 33.333 0.00 0.00 0.00 3.67
1605 1676 9.019656 AGTTTGTATGTATGATTTTGCTGGTTA 57.980 29.630 0.00 0.00 0.00 2.85
1606 1677 9.801873 GTTTGTATGTATGATTTTGCTGGTTAT 57.198 29.630 0.00 0.00 0.00 1.89
1609 1680 9.845740 TGTATGTATGATTTTGCTGGTTATAGT 57.154 29.630 0.00 0.00 0.00 2.12
1851 1922 1.061566 GCGGAATTTTTCGGTACCTCG 59.938 52.381 10.90 0.00 33.09 4.63
1945 2016 1.509644 TTCGTGGCGTAGTGTCGACT 61.510 55.000 17.92 0.00 39.83 4.18
1971 2042 1.142060 TGGTTCAACGGATGGTGAACT 59.858 47.619 21.41 0.00 37.11 3.01
1994 2065 1.667236 TGCCGGTTCAGCATATTCAG 58.333 50.000 1.90 0.00 34.69 3.02
2057 2128 4.762956 AAGAGCAACTTTGATGAAGAGC 57.237 40.909 0.00 0.00 38.77 4.09
2141 2212 3.076333 TGGCCATCCACATATCAATCCAT 59.924 43.478 0.00 0.00 37.47 3.41
2144 2215 8.627654 TGGCCATCCACATATCAATCCATTGA 62.628 42.308 0.00 4.47 43.17 2.57
2244 2315 2.354704 CCTCGGAGGTTGCTGTTGATTA 60.355 50.000 16.15 0.00 0.00 1.75
2295 2366 1.364901 CACTGGGTGCTGCTTTTGG 59.635 57.895 0.00 0.00 0.00 3.28
2583 2654 6.013812 AGCAATTGGGAAAAAGCAGGTATTAA 60.014 34.615 7.72 0.00 0.00 1.40
2688 2759 6.620678 TGTCTTAAGTTCTTATTTGGCATGC 58.379 36.000 9.90 9.90 0.00 4.06
2709 2780 7.648142 CATGCCCGTAACTATGTGATTTTAAT 58.352 34.615 0.00 0.00 0.00 1.40
2824 2895 4.330250 CATTCCCTCTGTCTTGATTGTGT 58.670 43.478 0.00 0.00 0.00 3.72
2839 2910 1.225855 TGTGTTCGTGCATTCCAGAC 58.774 50.000 0.00 0.00 0.00 3.51
2840 2911 0.517316 GTGTTCGTGCATTCCAGACC 59.483 55.000 0.00 0.00 0.00 3.85
2924 2995 3.117888 AGGAACTGCAGTACCAATATGGG 60.118 47.826 22.01 0.00 38.99 4.00
3062 3133 5.685075 CGATTCCTTTTACCCTACAGCAGAT 60.685 44.000 0.00 0.00 0.00 2.90
3172 3243 2.348666 GCGATGGCGATTCATGGTATAC 59.651 50.000 0.00 0.00 40.82 1.47
3191 3262 5.873179 ATACCACAGGTAAACATTGTTCG 57.127 39.130 1.83 0.00 41.85 3.95
3194 3265 2.292016 CACAGGTAAACATTGTTCGGCA 59.708 45.455 1.83 0.00 0.00 5.69
3494 3565 5.831525 TCCCTCTAACGCTTATATTCAGTGA 59.168 40.000 0.00 0.00 0.00 3.41
3668 3739 8.918202 TGTTCTTAATCACTTAAATCTGGTGT 57.082 30.769 0.00 0.00 33.30 4.16
3679 3750 8.616076 CACTTAAATCTGGTGTATTCTTCATCC 58.384 37.037 0.00 0.00 0.00 3.51
3722 3793 9.077885 CCTGGCATTATTGTATTATGGTTTACT 57.922 33.333 0.00 0.00 0.00 2.24
3939 4010 4.757149 GGTGCTACATTAATCCACTCCATC 59.243 45.833 0.00 0.00 0.00 3.51
3953 4024 3.196039 CACTCCATCATGCATTTTTCCCA 59.804 43.478 0.00 0.00 0.00 4.37
4073 4144 5.596361 TGTTGTTGGTGGTTATGATTTCAGT 59.404 36.000 0.00 0.00 0.00 3.41
4078 4149 4.250464 GGTGGTTATGATTTCAGTGACGA 58.750 43.478 0.00 0.00 0.00 4.20
4099 4170 8.343366 TGACGACTCATACTTACAGTAATGATC 58.657 37.037 0.00 0.00 33.89 2.92
4591 4663 6.600882 ATTCTTTCATTCACTCAGGCAATT 57.399 33.333 0.00 0.00 0.00 2.32
4592 4664 6.409524 TTCTTTCATTCACTCAGGCAATTT 57.590 33.333 0.00 0.00 0.00 1.82
4634 4706 9.778993 GACGTCTCTTAAACATACAACTACATA 57.221 33.333 8.70 0.00 0.00 2.29
4808 4880 1.765314 AGAGGATATGGGTGTGCAGTC 59.235 52.381 0.00 0.00 0.00 3.51
4820 4892 3.106407 GCAGTCACAGCGGACGAC 61.106 66.667 0.00 0.00 42.62 4.34
4844 4916 1.153229 GTACCTCATTGGCGGGTCC 60.153 63.158 0.00 0.00 40.22 4.46
4863 4935 4.383770 GGTCCGAATCCAATGGAGAAACTA 60.384 45.833 8.40 0.00 34.05 2.24
4907 4979 5.971763 ACAGTTTACTCTGGATCACTGATC 58.028 41.667 10.22 10.22 39.48 2.92
4913 4985 3.766591 ACTCTGGATCACTGATCGTTTCT 59.233 43.478 12.06 0.00 39.72 2.52
4918 4990 6.322456 TCTGGATCACTGATCGTTTCTTCTAT 59.678 38.462 12.06 0.00 39.72 1.98
4935 5007 7.898014 TCTTCTATGTATTCAAGCCTCACTA 57.102 36.000 0.00 0.00 0.00 2.74
4936 5008 7.717568 TCTTCTATGTATTCAAGCCTCACTAC 58.282 38.462 0.00 0.00 0.00 2.73
4947 5019 4.545208 AGCCTCACTACTTTCCTTCTTC 57.455 45.455 0.00 0.00 0.00 2.87
4955 5027 2.576615 ACTTTCCTTCTTCTGTGTGGC 58.423 47.619 0.00 0.00 0.00 5.01
4977 5049 3.134574 TCGCAGGTGGAAGTTTACAAT 57.865 42.857 0.00 0.00 0.00 2.71
4993 5065 0.323178 CAATGAGAGGCAAGGCTGGT 60.323 55.000 0.00 0.00 0.00 4.00
5097 5169 2.295885 CCCACATTTTGCTTTTTGCCA 58.704 42.857 0.00 0.00 42.00 4.92
5103 5175 0.106521 TTTGCTTTTTGCCAGAGCCC 59.893 50.000 0.00 0.00 42.00 5.19
5104 5176 1.047596 TTGCTTTTTGCCAGAGCCCA 61.048 50.000 0.00 0.00 42.00 5.36
5156 5253 5.125097 TCACAGTATACCCTCTTCTCGAAAC 59.875 44.000 0.00 0.00 0.00 2.78
5177 5274 1.228429 CCGCTGGGGGTTTGAGAAA 60.228 57.895 2.21 0.00 0.00 2.52
5183 5280 4.065088 GCTGGGGGTTTGAGAAATTTTTC 58.935 43.478 1.81 1.81 37.45 2.29
5187 5284 2.154963 GGGTTTGAGAAATTTTTCGCGC 59.845 45.455 0.00 0.00 41.92 6.86
5189 5286 2.058913 TTGAGAAATTTTTCGCGCCC 57.941 45.000 0.00 0.00 41.92 6.13
5190 5287 0.109964 TGAGAAATTTTTCGCGCCCG 60.110 50.000 0.00 0.00 41.92 6.13
5191 5288 1.403225 GAGAAATTTTTCGCGCCCGC 61.403 55.000 0.00 1.98 41.92 6.13
5252 5349 1.802960 GTGCTTGTCTCAGACACCATG 59.197 52.381 7.12 0.00 42.60 3.66
5257 5354 3.114643 TGTCTCAGACACCATGGGATA 57.885 47.619 18.09 0.00 37.67 2.59
5282 5379 3.133901 TCTCACAGCAACACAAGGTCTTA 59.866 43.478 0.00 0.00 0.00 2.10
5323 5420 1.270305 GCATATCCTCCTGCTGCGTTA 60.270 52.381 0.00 0.00 35.49 3.18
5340 5437 0.323302 TTATTGAGTGGGCGCAGACA 59.677 50.000 10.83 4.63 37.00 3.41
5341 5438 0.323302 TATTGAGTGGGCGCAGACAA 59.677 50.000 19.21 19.21 37.00 3.18
5343 5440 3.426568 GAGTGGGCGCAGACAAGC 61.427 66.667 10.83 0.00 37.00 4.01
5368 5465 6.598525 GGTTCCTTGTTTCTGTTTGTTTTTG 58.401 36.000 0.00 0.00 0.00 2.44
5369 5466 6.425417 GGTTCCTTGTTTCTGTTTGTTTTTGA 59.575 34.615 0.00 0.00 0.00 2.69
5382 5480 5.356882 TTGTTTTTGAGGCGATACTTGAG 57.643 39.130 0.00 0.00 0.00 3.02
5399 5497 1.271652 TGAGGGCGCCTGAACAAATTA 60.272 47.619 28.56 0.00 31.76 1.40
5405 5503 2.408368 GCGCCTGAACAAATTAAACTGC 59.592 45.455 0.00 0.00 0.00 4.40
5417 5515 1.803334 TAAACTGCTCGCGGTTCATT 58.197 45.000 15.71 4.35 43.92 2.57
5434 5532 4.386867 TCATTAGTGGCTACTCCGAAAG 57.613 45.455 5.78 0.00 38.36 2.62
5443 5541 3.596214 GCTACTCCGAAAGTTGGAATGA 58.404 45.455 0.00 0.00 39.55 2.57
5474 5594 6.194677 AACAACTGTTTTTGCAATGTGCGG 62.195 41.667 0.00 0.00 39.96 5.69
5488 5608 2.830370 GCGGCCTGGGGATTCTTG 60.830 66.667 0.00 0.00 0.00 3.02
5553 5673 2.556257 GCTAGTAGCTCTGCCTTTTCC 58.444 52.381 15.16 0.00 38.45 3.13
5577 5697 3.393800 CAGCCGGTGGAGATAAATAGTG 58.606 50.000 1.90 0.00 0.00 2.74
5578 5698 2.368875 AGCCGGTGGAGATAAATAGTGG 59.631 50.000 1.90 0.00 0.00 4.00
5580 5700 2.368875 CCGGTGGAGATAAATAGTGGCT 59.631 50.000 0.00 0.00 0.00 4.75
5581 5701 3.393800 CGGTGGAGATAAATAGTGGCTG 58.606 50.000 0.00 0.00 0.00 4.85
5611 7199 2.007608 GTTGGACTATTCTGGCGGTTC 58.992 52.381 0.00 0.00 0.00 3.62
5612 7200 0.539986 TGGACTATTCTGGCGGTTCC 59.460 55.000 0.00 0.00 0.00 3.62
5704 7293 5.014858 CCCCGCCTAACTGTCTATCTATTA 58.985 45.833 0.00 0.00 0.00 0.98
5761 7350 0.990374 AGGCACCTTGAGAGATTGCT 59.010 50.000 0.00 0.00 34.16 3.91
5786 7375 2.239654 CAGTGGATAGTTCCCATGGTGT 59.760 50.000 11.73 0.00 41.83 4.16
5793 7382 1.971167 TTCCCATGGTGTGAAGCGC 60.971 57.895 11.73 0.00 0.00 5.92
5809 7398 2.798689 GCCGGGGCGAAATCTTTC 59.201 61.111 2.18 0.00 0.00 2.62
5825 7414 8.482437 GAAATCTTTCGAACTTCTCTTTGTTC 57.518 34.615 0.00 0.00 39.15 3.18
5826 7415 7.793927 AATCTTTCGAACTTCTCTTTGTTCT 57.206 32.000 0.00 0.00 40.04 3.01
5827 7416 7.793927 ATCTTTCGAACTTCTCTTTGTTCTT 57.206 32.000 0.00 0.00 40.04 2.52
5828 7417 7.611213 TCTTTCGAACTTCTCTTTGTTCTTT 57.389 32.000 0.00 0.00 40.04 2.52
5829 7418 8.712285 TCTTTCGAACTTCTCTTTGTTCTTTA 57.288 30.769 0.00 0.00 40.04 1.85
5830 7419 8.601476 TCTTTCGAACTTCTCTTTGTTCTTTAC 58.399 33.333 0.00 0.00 40.04 2.01
5831 7420 7.837202 TTCGAACTTCTCTTTGTTCTTTACA 57.163 32.000 0.00 0.00 40.04 2.41
5832 7421 7.837202 TCGAACTTCTCTTTGTTCTTTACAA 57.163 32.000 0.00 0.00 44.81 2.41
5833 7422 7.681903 TCGAACTTCTCTTTGTTCTTTACAAC 58.318 34.615 0.00 0.00 46.09 3.32
5834 7423 7.548075 TCGAACTTCTCTTTGTTCTTTACAACT 59.452 33.333 0.00 0.00 46.09 3.16
5835 7424 8.814235 CGAACTTCTCTTTGTTCTTTACAACTA 58.186 33.333 0.00 0.00 46.09 2.24
5840 7429 9.490379 TTCTCTTTGTTCTTTACAACTATCTCC 57.510 33.333 0.00 0.00 46.09 3.71
5841 7430 8.871125 TCTCTTTGTTCTTTACAACTATCTCCT 58.129 33.333 0.00 0.00 46.09 3.69
5842 7431 9.145865 CTCTTTGTTCTTTACAACTATCTCCTC 57.854 37.037 0.00 0.00 46.09 3.71
5843 7432 8.647796 TCTTTGTTCTTTACAACTATCTCCTCA 58.352 33.333 0.00 0.00 46.09 3.86
5844 7433 9.442047 CTTTGTTCTTTACAACTATCTCCTCAT 57.558 33.333 0.00 0.00 46.09 2.90
5845 7434 9.793259 TTTGTTCTTTACAACTATCTCCTCATT 57.207 29.630 0.00 0.00 46.09 2.57
5846 7435 9.793259 TTGTTCTTTACAACTATCTCCTCATTT 57.207 29.630 0.00 0.00 41.73 2.32
5871 7460 9.970395 TTATTCATTGATCAAAATAGTGGCATC 57.030 29.630 13.09 0.00 0.00 3.91
5872 7461 6.063640 TCATTGATCAAAATAGTGGCATCG 57.936 37.500 13.09 0.00 0.00 3.84
5873 7462 3.969117 TGATCAAAATAGTGGCATCGC 57.031 42.857 0.00 0.00 0.00 4.58
5874 7463 3.544684 TGATCAAAATAGTGGCATCGCT 58.455 40.909 0.00 0.00 37.51 4.93
5875 7464 3.947196 TGATCAAAATAGTGGCATCGCTT 59.053 39.130 0.00 0.00 35.12 4.68
5876 7465 5.122519 TGATCAAAATAGTGGCATCGCTTA 58.877 37.500 0.00 0.00 35.12 3.09
5877 7466 4.875544 TCAAAATAGTGGCATCGCTTAC 57.124 40.909 0.00 0.00 35.12 2.34
5878 7467 4.257731 TCAAAATAGTGGCATCGCTTACA 58.742 39.130 0.00 0.00 35.12 2.41
5879 7468 4.697828 TCAAAATAGTGGCATCGCTTACAA 59.302 37.500 0.00 0.00 35.12 2.41
5880 7469 5.356751 TCAAAATAGTGGCATCGCTTACAAT 59.643 36.000 0.00 0.00 35.12 2.71
5881 7470 6.540551 TCAAAATAGTGGCATCGCTTACAATA 59.459 34.615 0.00 0.00 35.12 1.90
5882 7471 6.935741 AAATAGTGGCATCGCTTACAATAA 57.064 33.333 0.00 0.00 35.12 1.40
5883 7472 6.935741 AATAGTGGCATCGCTTACAATAAA 57.064 33.333 0.00 0.00 35.12 1.40
5884 7473 4.882671 AGTGGCATCGCTTACAATAAAG 57.117 40.909 0.00 0.00 0.00 1.85
5885 7474 3.627577 AGTGGCATCGCTTACAATAAAGG 59.372 43.478 0.00 0.00 0.00 3.11
5886 7475 2.948979 TGGCATCGCTTACAATAAAGGG 59.051 45.455 0.00 0.00 39.94 3.95
5893 7482 6.930667 TCGCTTACAATAAAGGGAATAACC 57.069 37.500 1.39 0.00 43.15 2.85
5894 7483 5.524646 TCGCTTACAATAAAGGGAATAACCG 59.475 40.000 1.39 0.00 43.15 4.44
5895 7484 5.516996 GCTTACAATAAAGGGAATAACCGC 58.483 41.667 0.00 0.00 40.11 5.68
5896 7485 5.066764 GCTTACAATAAAGGGAATAACCGCA 59.933 40.000 0.00 0.00 40.11 5.69
5897 7486 6.238925 GCTTACAATAAAGGGAATAACCGCAT 60.239 38.462 0.00 0.00 40.11 4.73
5898 7487 7.648039 TTACAATAAAGGGAATAACCGCATT 57.352 32.000 0.00 0.00 40.11 3.56
5899 7488 8.749026 TTACAATAAAGGGAATAACCGCATTA 57.251 30.769 0.00 0.00 40.11 1.90
5900 7489 7.272037 ACAATAAAGGGAATAACCGCATTAG 57.728 36.000 0.00 0.00 40.11 1.73
5901 7490 7.057894 ACAATAAAGGGAATAACCGCATTAGA 58.942 34.615 0.00 0.00 40.11 2.10
5902 7491 7.558444 ACAATAAAGGGAATAACCGCATTAGAA 59.442 33.333 0.00 0.00 40.11 2.10
5903 7492 5.830000 AAAGGGAATAACCGCATTAGAAC 57.170 39.130 0.00 0.00 40.11 3.01
5904 7493 4.772886 AGGGAATAACCGCATTAGAACT 57.227 40.909 0.00 0.00 40.11 3.01
5905 7494 5.881923 AGGGAATAACCGCATTAGAACTA 57.118 39.130 0.00 0.00 40.11 2.24
5906 7495 5.855045 AGGGAATAACCGCATTAGAACTAG 58.145 41.667 0.00 0.00 40.11 2.57
5907 7496 5.365895 AGGGAATAACCGCATTAGAACTAGT 59.634 40.000 0.00 0.00 40.11 2.57
5908 7497 6.552350 AGGGAATAACCGCATTAGAACTAGTA 59.448 38.462 0.00 0.00 40.11 1.82
5909 7498 7.234988 AGGGAATAACCGCATTAGAACTAGTAT 59.765 37.037 0.00 0.00 40.11 2.12
5910 7499 7.544915 GGGAATAACCGCATTAGAACTAGTATC 59.455 40.741 0.00 0.00 40.11 2.24
5911 7500 7.544915 GGAATAACCGCATTAGAACTAGTATCC 59.455 40.741 0.00 0.00 0.00 2.59
5912 7501 5.864418 AACCGCATTAGAACTAGTATCCA 57.136 39.130 0.00 0.00 0.00 3.41
5913 7502 6.420913 AACCGCATTAGAACTAGTATCCAT 57.579 37.500 0.00 0.00 0.00 3.41
5914 7503 6.026947 ACCGCATTAGAACTAGTATCCATC 57.973 41.667 0.00 0.00 0.00 3.51
5915 7504 5.047235 ACCGCATTAGAACTAGTATCCATCC 60.047 44.000 0.00 0.00 0.00 3.51
5916 7505 5.186021 CCGCATTAGAACTAGTATCCATCCT 59.814 44.000 0.00 0.00 0.00 3.24
5917 7506 6.377429 CCGCATTAGAACTAGTATCCATCCTA 59.623 42.308 0.00 0.00 0.00 2.94
5918 7507 7.251994 CGCATTAGAACTAGTATCCATCCTAC 58.748 42.308 0.00 0.00 0.00 3.18
5919 7508 7.094334 CGCATTAGAACTAGTATCCATCCTACA 60.094 40.741 0.00 0.00 0.00 2.74
5920 7509 8.585881 GCATTAGAACTAGTATCCATCCTACAA 58.414 37.037 0.00 0.00 0.00 2.41
5921 7510 9.915629 CATTAGAACTAGTATCCATCCTACAAC 57.084 37.037 0.00 0.00 0.00 3.32
5922 7511 9.884814 ATTAGAACTAGTATCCATCCTACAACT 57.115 33.333 0.00 0.00 0.00 3.16
5924 7513 8.927675 AGAACTAGTATCCATCCTACAACTAG 57.072 38.462 0.00 5.92 41.27 2.57
5925 7514 7.945664 AGAACTAGTATCCATCCTACAACTAGG 59.054 40.741 0.00 0.00 40.32 3.02
5926 7515 6.553857 ACTAGTATCCATCCTACAACTAGGG 58.446 44.000 10.94 0.00 40.32 3.53
5927 7516 4.753186 AGTATCCATCCTACAACTAGGGG 58.247 47.826 0.00 0.00 40.31 4.79
5928 7517 2.489528 TCCATCCTACAACTAGGGGG 57.510 55.000 0.00 0.00 40.31 5.40
5929 7518 1.941682 TCCATCCTACAACTAGGGGGA 59.058 52.381 0.00 4.78 40.31 4.81
5930 7519 2.090719 TCCATCCTACAACTAGGGGGAG 60.091 54.545 0.00 0.00 40.31 4.30
5931 7520 2.090719 CCATCCTACAACTAGGGGGAGA 60.091 54.545 0.00 0.00 40.31 3.71
5932 7521 3.632645 CCATCCTACAACTAGGGGGAGAA 60.633 52.174 0.00 0.00 40.31 2.87
5933 7522 3.858696 TCCTACAACTAGGGGGAGAAA 57.141 47.619 0.00 0.00 40.31 2.52
5934 7523 4.150516 TCCTACAACTAGGGGGAGAAAA 57.849 45.455 0.00 0.00 40.31 2.29
5935 7524 4.706616 TCCTACAACTAGGGGGAGAAAAT 58.293 43.478 0.00 0.00 40.31 1.82
5936 7525 5.105853 TCCTACAACTAGGGGGAGAAAATT 58.894 41.667 0.00 0.00 40.31 1.82
5937 7526 5.554350 TCCTACAACTAGGGGGAGAAAATTT 59.446 40.000 0.00 0.00 40.31 1.82
5938 7527 5.652452 CCTACAACTAGGGGGAGAAAATTTG 59.348 44.000 0.00 0.00 36.56 2.32
5939 7528 4.416516 ACAACTAGGGGGAGAAAATTTGG 58.583 43.478 0.00 0.00 0.00 3.28
5940 7529 3.101643 ACTAGGGGGAGAAAATTTGGC 57.898 47.619 0.00 0.00 0.00 4.52
5941 7530 2.654896 ACTAGGGGGAGAAAATTTGGCT 59.345 45.455 0.00 0.00 0.00 4.75
5942 7531 3.856206 ACTAGGGGGAGAAAATTTGGCTA 59.144 43.478 0.00 0.00 0.00 3.93
5943 7532 3.845109 AGGGGGAGAAAATTTGGCTAA 57.155 42.857 0.00 0.00 0.00 3.09
5944 7533 3.441101 AGGGGGAGAAAATTTGGCTAAC 58.559 45.455 0.00 0.00 0.00 2.34
5945 7534 2.500098 GGGGGAGAAAATTTGGCTAACC 59.500 50.000 0.00 0.00 0.00 2.85
5946 7535 3.441101 GGGGAGAAAATTTGGCTAACCT 58.559 45.455 0.00 0.00 36.63 3.50
5947 7536 4.571148 GGGGGAGAAAATTTGGCTAACCTA 60.571 45.833 0.00 0.00 36.63 3.08
5948 7537 4.645136 GGGGAGAAAATTTGGCTAACCTAG 59.355 45.833 0.00 0.00 36.63 3.02
5959 7548 2.901249 GCTAACCTAGCCAATTCGTGA 58.099 47.619 0.00 0.00 45.95 4.35
5960 7549 2.866762 GCTAACCTAGCCAATTCGTGAG 59.133 50.000 0.00 0.00 45.95 3.51
5961 7550 1.739067 AACCTAGCCAATTCGTGAGC 58.261 50.000 0.00 0.00 0.00 4.26
5962 7551 0.905357 ACCTAGCCAATTCGTGAGCT 59.095 50.000 0.00 0.00 37.47 4.09
5963 7552 2.108168 ACCTAGCCAATTCGTGAGCTA 58.892 47.619 0.00 0.00 35.90 3.32
5964 7553 2.159085 ACCTAGCCAATTCGTGAGCTAC 60.159 50.000 0.00 0.00 35.90 3.58
5965 7554 2.101582 CCTAGCCAATTCGTGAGCTACT 59.898 50.000 0.00 0.00 35.90 2.57
5966 7555 2.770164 AGCCAATTCGTGAGCTACTT 57.230 45.000 0.00 0.00 33.54 2.24
5967 7556 2.350522 AGCCAATTCGTGAGCTACTTG 58.649 47.619 0.00 0.00 33.54 3.16
5968 7557 2.028112 AGCCAATTCGTGAGCTACTTGA 60.028 45.455 0.00 0.00 33.54 3.02
5969 7558 2.939103 GCCAATTCGTGAGCTACTTGAT 59.061 45.455 0.00 0.00 0.00 2.57
5970 7559 3.375299 GCCAATTCGTGAGCTACTTGATT 59.625 43.478 0.00 0.00 0.00 2.57
5971 7560 4.728882 GCCAATTCGTGAGCTACTTGATTG 60.729 45.833 0.00 0.00 0.00 2.67
5972 7561 4.337763 CAATTCGTGAGCTACTTGATTGC 58.662 43.478 0.00 0.00 0.00 3.56
5973 7562 3.319137 TTCGTGAGCTACTTGATTGCT 57.681 42.857 0.00 0.00 42.55 3.91
5982 7571 6.729690 AGCTACTTGATTGCTCTCTCTATT 57.270 37.500 0.00 0.00 33.81 1.73
5983 7572 7.831691 AGCTACTTGATTGCTCTCTCTATTA 57.168 36.000 0.00 0.00 33.81 0.98
5984 7573 7.657336 AGCTACTTGATTGCTCTCTCTATTAC 58.343 38.462 0.00 0.00 33.81 1.89
5985 7574 7.286546 AGCTACTTGATTGCTCTCTCTATTACA 59.713 37.037 0.00 0.00 33.81 2.41
5986 7575 7.923344 GCTACTTGATTGCTCTCTCTATTACAA 59.077 37.037 0.00 0.00 0.00 2.41
5987 7576 9.979578 CTACTTGATTGCTCTCTCTATTACAAT 57.020 33.333 0.00 0.00 0.00 2.71
5988 7577 8.659925 ACTTGATTGCTCTCTCTATTACAATG 57.340 34.615 0.00 0.00 0.00 2.82
5989 7578 8.263640 ACTTGATTGCTCTCTCTATTACAATGT 58.736 33.333 0.00 0.00 0.00 2.71
5990 7579 9.107177 CTTGATTGCTCTCTCTATTACAATGTT 57.893 33.333 0.00 0.00 0.00 2.71
5991 7580 8.654230 TGATTGCTCTCTCTATTACAATGTTC 57.346 34.615 0.00 0.00 0.00 3.18
5992 7581 8.260114 TGATTGCTCTCTCTATTACAATGTTCA 58.740 33.333 0.00 0.00 0.00 3.18
5993 7582 9.270640 GATTGCTCTCTCTATTACAATGTTCAT 57.729 33.333 0.00 0.00 0.00 2.57
6023 7612 9.398538 TGACATGATTGAAATCTAATGACATGA 57.601 29.630 0.00 0.00 36.92 3.07
6052 7641 8.681486 AACAATCATTGAATATAGCACTAGCA 57.319 30.769 3.79 0.00 45.49 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.969250 GAATCGCCCCGCACCTGAA 62.969 63.158 0.00 0.00 0.00 3.02
1 2 4.467084 GAATCGCCCCGCACCTGA 62.467 66.667 0.00 0.00 0.00 3.86
6 7 4.708386 AAACCGAATCGCCCCGCA 62.708 61.111 0.00 0.00 0.00 5.69
10 11 2.647529 AAAATCAAACCGAATCGCCC 57.352 45.000 0.00 0.00 0.00 6.13
32 33 0.691904 AATTCCACCGTTTCCCCGTA 59.308 50.000 0.00 0.00 0.00 4.02
54 55 4.020543 ACCAGTTGCTTAGAAAACACCAA 58.979 39.130 2.07 0.00 0.00 3.67
154 156 2.729156 GCTAGGCGTCAAAAACATCAGC 60.729 50.000 0.00 0.00 0.00 4.26
167 169 2.357034 CACACGGTTGCTAGGCGT 60.357 61.111 0.00 0.00 0.00 5.68
225 227 6.765512 TGAACTTTTTCCAATGAAATCCAACC 59.234 34.615 0.00 0.00 40.08 3.77
231 233 6.155475 TCCGTGAACTTTTTCCAATGAAAT 57.845 33.333 0.00 0.00 40.08 2.17
263 268 1.464997 GTGTTTCGACAGGATTCTGCC 59.535 52.381 0.00 0.00 44.59 4.85
289 294 3.614870 GCAACAAAATAGCAACCCCAGAG 60.615 47.826 0.00 0.00 0.00 3.35
342 347 6.980593 ACTGCAAATTAGAACAAGTTATGCA 58.019 32.000 0.00 0.00 38.78 3.96
402 408 4.817517 TCAAAACTCGAGGATGTAAGTCC 58.182 43.478 18.41 0.00 38.62 3.85
407 413 4.221924 TCCACATCAAAACTCGAGGATGTA 59.778 41.667 25.07 14.17 46.18 2.29
425 431 2.224992 ACACCTACATGCCATTTCCACA 60.225 45.455 0.00 0.00 0.00 4.17
451 457 3.572682 CACACAACAGTAGGAGTGTAGGA 59.427 47.826 0.00 0.00 42.79 2.94
452 458 3.321111 ACACACAACAGTAGGAGTGTAGG 59.679 47.826 6.58 0.00 42.79 3.18
453 459 4.547532 GACACACAACAGTAGGAGTGTAG 58.452 47.826 7.90 0.00 42.79 2.74
454 460 3.319972 GGACACACAACAGTAGGAGTGTA 59.680 47.826 7.90 0.00 42.79 2.90
455 461 2.102588 GGACACACAACAGTAGGAGTGT 59.897 50.000 7.71 7.71 45.29 3.55
456 462 2.548067 GGGACACACAACAGTAGGAGTG 60.548 54.545 0.00 0.00 37.95 3.51
457 463 1.692519 GGGACACACAACAGTAGGAGT 59.307 52.381 0.00 0.00 0.00 3.85
458 464 1.971357 AGGGACACACAACAGTAGGAG 59.029 52.381 0.00 0.00 0.00 3.69
533 542 5.163581 GCACCAGAAAATAGATTCACTGCAT 60.164 40.000 0.00 0.00 31.16 3.96
616 625 4.481930 TTTCAAGAGCACCATACAAACG 57.518 40.909 0.00 0.00 0.00 3.60
619 628 8.801299 TGATAAAATTTCAAGAGCACCATACAA 58.199 29.630 0.00 0.00 0.00 2.41
620 629 8.347004 TGATAAAATTTCAAGAGCACCATACA 57.653 30.769 0.00 0.00 0.00 2.29
621 630 9.638239 TTTGATAAAATTTCAAGAGCACCATAC 57.362 29.630 0.00 0.00 34.76 2.39
622 631 9.638239 GTTTGATAAAATTTCAAGAGCACCATA 57.362 29.630 0.00 0.00 34.76 2.74
623 632 8.149647 TGTTTGATAAAATTTCAAGAGCACCAT 58.850 29.630 0.00 0.00 34.76 3.55
624 633 7.495901 TGTTTGATAAAATTTCAAGAGCACCA 58.504 30.769 0.00 0.00 34.76 4.17
625 634 7.653311 ACTGTTTGATAAAATTTCAAGAGCACC 59.347 33.333 0.00 0.00 34.76 5.01
626 635 8.482429 CACTGTTTGATAAAATTTCAAGAGCAC 58.518 33.333 0.00 0.00 34.76 4.40
627 636 7.652909 CCACTGTTTGATAAAATTTCAAGAGCA 59.347 33.333 0.00 0.00 34.76 4.26
628 637 7.116805 CCCACTGTTTGATAAAATTTCAAGAGC 59.883 37.037 0.00 0.00 34.76 4.09
629 638 8.143835 ACCCACTGTTTGATAAAATTTCAAGAG 58.856 33.333 0.00 0.00 34.76 2.85
630 639 7.925483 CACCCACTGTTTGATAAAATTTCAAGA 59.075 33.333 0.00 0.00 34.76 3.02
631 640 7.710475 ACACCCACTGTTTGATAAAATTTCAAG 59.290 33.333 0.00 0.00 34.76 3.02
632 641 7.560368 ACACCCACTGTTTGATAAAATTTCAA 58.440 30.769 0.00 0.00 0.00 2.69
633 642 7.118496 ACACCCACTGTTTGATAAAATTTCA 57.882 32.000 0.00 0.00 0.00 2.69
708 736 5.245977 ACCAGAACAATGGGAATGTAAAAGG 59.754 40.000 0.00 0.00 45.25 3.11
712 740 6.209788 GGTAAACCAGAACAATGGGAATGTAA 59.790 38.462 0.00 0.00 45.25 2.41
737 795 0.798776 CGTAAACCTGAGCTTGCCAG 59.201 55.000 0.00 0.00 0.00 4.85
748 806 2.232941 ACATCATGACGTCCGTAAACCT 59.767 45.455 14.12 0.00 0.00 3.50
1034 1105 1.273327 GATCTTGTTTTGGTGCTGGGG 59.727 52.381 0.00 0.00 0.00 4.96
1523 1594 1.605712 GCTGATACCTGTGCGGGATAC 60.606 57.143 3.74 0.00 36.03 2.24
1594 1665 9.522804 CAGTTTACAAAACTATAACCAGCAAAA 57.477 29.630 4.81 0.00 0.00 2.44
1595 1666 8.904834 TCAGTTTACAAAACTATAACCAGCAAA 58.095 29.630 4.81 0.00 0.00 3.68
1596 1667 8.453238 TCAGTTTACAAAACTATAACCAGCAA 57.547 30.769 4.81 0.00 0.00 3.91
1597 1668 8.630054 ATCAGTTTACAAAACTATAACCAGCA 57.370 30.769 4.81 0.00 0.00 4.41
1598 1669 9.341899 CAATCAGTTTACAAAACTATAACCAGC 57.658 33.333 4.81 0.00 0.00 4.85
1605 1676 9.897744 CACATCACAATCAGTTTACAAAACTAT 57.102 29.630 4.81 0.00 0.00 2.12
1606 1677 8.898761 ACACATCACAATCAGTTTACAAAACTA 58.101 29.630 4.81 0.00 0.00 2.24
1607 1678 7.701924 CACACATCACAATCAGTTTACAAAACT 59.298 33.333 0.00 0.00 0.00 2.66
1608 1679 7.700234 TCACACATCACAATCAGTTTACAAAAC 59.300 33.333 0.00 0.00 0.00 2.43
1609 1680 7.766283 TCACACATCACAATCAGTTTACAAAA 58.234 30.769 0.00 0.00 0.00 2.44
1851 1922 2.959357 GCAGCGTCAACAGGAGCAC 61.959 63.158 0.00 0.00 0.00 4.40
1945 2016 1.001974 CCATCCGTTGAACCAGACTCA 59.998 52.381 0.00 0.00 0.00 3.41
1994 2065 4.498682 GGCATGGTCAGCATTTCTATCAAC 60.499 45.833 0.00 0.00 0.00 3.18
2057 2128 3.054139 TCCAAATCATCCCACTCAGAAGG 60.054 47.826 0.00 0.00 0.00 3.46
2141 2212 3.921119 GTCATGCTGTTGACCATTCAA 57.079 42.857 4.32 0.00 40.11 2.69
2295 2366 1.202114 TGGCGTTTGATGGATCTTTGC 59.798 47.619 0.00 0.00 0.00 3.68
2583 2654 4.694982 CCCAAAAGTTCAAAGCAAACAAGT 59.305 37.500 0.00 0.00 0.00 3.16
2688 2759 9.663904 CATGAATTAAAATCACATAGTTACGGG 57.336 33.333 0.00 0.00 0.00 5.28
2795 2866 4.409901 TCAAGACAGAGGGAATGCATATCA 59.590 41.667 0.00 0.00 0.00 2.15
2797 2868 5.579753 ATCAAGACAGAGGGAATGCATAT 57.420 39.130 0.00 0.00 0.00 1.78
2824 2895 0.389817 CTCGGTCTGGAATGCACGAA 60.390 55.000 0.00 0.00 0.00 3.85
2839 2910 6.102663 ACAAGTATTTCTTCATCTGACTCGG 58.897 40.000 0.00 0.00 33.63 4.63
2840 2911 8.864069 ATACAAGTATTTCTTCATCTGACTCG 57.136 34.615 0.00 0.00 33.63 4.18
2924 2995 7.377766 TGCTGAATACTCCAACTGTAATTTC 57.622 36.000 0.00 0.00 0.00 2.17
3062 3133 2.795165 CCTCAGCGGCACTAGTCTA 58.205 57.895 1.45 0.00 0.00 2.59
3172 3243 2.351350 GCCGAACAATGTTTACCTGTGG 60.351 50.000 0.00 0.00 0.00 4.17
3191 3262 6.690194 ACAGAGATCTTTATTTGTCATGCC 57.310 37.500 0.00 0.00 0.00 4.40
3226 3297 5.710513 AAGCAATGCAGATAGTCAAACAA 57.289 34.783 8.35 0.00 0.00 2.83
3539 3610 8.933653 TCTAACCCTGATCACATATCACAAATA 58.066 33.333 0.00 0.00 0.00 1.40
3640 3711 9.178758 ACCAGATTTAAGTGATTAAGAACATCC 57.821 33.333 0.00 0.00 0.00 3.51
3722 3793 6.811954 TCCTATTGATCGTATGCAACTACAA 58.188 36.000 0.00 0.00 0.00 2.41
3735 3806 8.879342 ATGTCTAACTTCTTTCCTATTGATCG 57.121 34.615 0.00 0.00 0.00 3.69
3939 4010 4.096231 TCGACATAGTGGGAAAAATGCATG 59.904 41.667 0.00 0.00 0.00 4.06
3953 4024 8.053026 ACTGTTAGTTCTAACATCGACATAGT 57.947 34.615 20.76 12.37 39.00 2.12
4591 4663 8.827177 AGAGACGTCAAACTTATTAACATCAA 57.173 30.769 19.50 0.00 0.00 2.57
4592 4664 8.827177 AAGAGACGTCAAACTTATTAACATCA 57.173 30.769 19.50 0.00 0.00 3.07
4808 4880 1.221466 ACACATTGTCGTCCGCTGTG 61.221 55.000 0.00 0.00 42.19 3.66
4844 4916 6.925610 TCAATAGTTTCTCCATTGGATTCG 57.074 37.500 5.70 0.00 31.88 3.34
4888 4960 5.661056 AACGATCAGTGATCCAGAGTAAA 57.339 39.130 24.23 0.00 35.83 2.01
4907 4979 6.535150 TGAGGCTTGAATACATAGAAGAAACG 59.465 38.462 0.00 0.00 0.00 3.60
4913 4985 7.661536 AGTAGTGAGGCTTGAATACATAGAA 57.338 36.000 0.00 0.00 0.00 2.10
4918 4990 5.248477 AGGAAAGTAGTGAGGCTTGAATACA 59.752 40.000 0.00 0.00 0.00 2.29
4935 5007 2.173569 AGCCACACAGAAGAAGGAAAGT 59.826 45.455 0.00 0.00 0.00 2.66
4936 5008 2.856222 AGCCACACAGAAGAAGGAAAG 58.144 47.619 0.00 0.00 0.00 2.62
4955 5027 2.489971 TGTAAACTTCCACCTGCGAAG 58.510 47.619 0.00 0.00 42.06 3.79
4977 5049 0.252239 TAGACCAGCCTTGCCTCTCA 60.252 55.000 0.00 0.00 0.00 3.27
4993 5065 1.424638 GCCTTGTAGCCAGGGATAGA 58.575 55.000 0.00 0.00 40.20 1.98
5097 5169 0.912486 GTACAGAACCCATGGGCTCT 59.088 55.000 28.07 28.07 40.98 4.09
5103 5175 5.598416 TCTCATACTGTACAGAACCCATG 57.402 43.478 29.30 19.92 0.00 3.66
5104 5176 5.453903 GCATCTCATACTGTACAGAACCCAT 60.454 44.000 29.30 8.24 0.00 4.00
5156 5253 4.659172 TCAAACCCCCAGCGGCTG 62.659 66.667 22.84 22.84 0.00 4.85
5196 5293 1.942657 CATCTGTACATCGGCAAAGGG 59.057 52.381 0.00 0.00 0.00 3.95
5197 5294 2.632377 ACATCTGTACATCGGCAAAGG 58.368 47.619 0.00 0.00 0.00 3.11
5198 5295 4.034048 GGTTACATCTGTACATCGGCAAAG 59.966 45.833 0.00 0.00 0.00 2.77
5199 5296 3.936453 GGTTACATCTGTACATCGGCAAA 59.064 43.478 0.00 0.00 0.00 3.68
5200 5297 3.527533 GGTTACATCTGTACATCGGCAA 58.472 45.455 0.00 0.00 0.00 4.52
5252 5349 3.118629 TGTGTTGCTGTGAGATCTATCCC 60.119 47.826 0.00 0.00 0.00 3.85
5257 5354 2.105477 ACCTTGTGTTGCTGTGAGATCT 59.895 45.455 0.00 0.00 0.00 2.75
5323 5420 0.957395 CTTGTCTGCGCCCACTCAAT 60.957 55.000 4.18 0.00 0.00 2.57
5340 5437 2.052782 ACAGAAACAAGGAACCGCTT 57.947 45.000 0.00 0.00 0.00 4.68
5341 5438 2.052782 AACAGAAACAAGGAACCGCT 57.947 45.000 0.00 0.00 0.00 5.52
5343 5440 3.775661 ACAAACAGAAACAAGGAACCG 57.224 42.857 0.00 0.00 0.00 4.44
5368 5465 1.300233 CGCCCTCAAGTATCGCCTC 60.300 63.158 0.00 0.00 0.00 4.70
5369 5466 2.815308 CGCCCTCAAGTATCGCCT 59.185 61.111 0.00 0.00 0.00 5.52
5382 5480 2.029380 AGTTTAATTTGTTCAGGCGCCC 60.029 45.455 26.15 8.39 0.00 6.13
5399 5497 1.732259 CTAATGAACCGCGAGCAGTTT 59.268 47.619 8.23 0.00 0.00 2.66
5405 5503 0.460284 AGCCACTAATGAACCGCGAG 60.460 55.000 8.23 0.00 0.00 5.03
5417 5515 2.232941 CCAACTTTCGGAGTAGCCACTA 59.767 50.000 0.00 0.00 37.72 2.74
5449 5547 5.152804 GCACATTGCAAAAACAGTTGTTTT 58.847 33.333 15.26 15.26 45.32 2.43
5450 5548 4.668686 CGCACATTGCAAAAACAGTTGTTT 60.669 37.500 1.71 4.48 46.02 2.83
5451 5549 3.181522 CGCACATTGCAAAAACAGTTGTT 60.182 39.130 1.71 0.00 45.36 2.83
5452 5550 2.348059 CGCACATTGCAAAAACAGTTGT 59.652 40.909 1.71 0.00 45.36 3.32
5474 5594 2.054453 GCACCAAGAATCCCCAGGC 61.054 63.158 0.00 0.00 0.00 4.85
5477 5597 0.776810 TTCAGCACCAAGAATCCCCA 59.223 50.000 0.00 0.00 0.00 4.96
5506 5626 8.549338 AAGCTAGGTACAAGAACAGAATAAAC 57.451 34.615 0.00 0.00 0.00 2.01
5510 5630 6.155393 AGCTAAGCTAGGTACAAGAACAGAAT 59.845 38.462 0.00 0.00 36.99 2.40
5577 5697 2.365293 AGTCCAACATTCCAAAACAGCC 59.635 45.455 0.00 0.00 0.00 4.85
5578 5698 3.733443 AGTCCAACATTCCAAAACAGC 57.267 42.857 0.00 0.00 0.00 4.40
5580 5700 6.015519 CCAGAATAGTCCAACATTCCAAAACA 60.016 38.462 0.00 0.00 32.61 2.83
5581 5701 6.389906 CCAGAATAGTCCAACATTCCAAAAC 58.610 40.000 0.00 0.00 32.61 2.43
5611 7199 0.965363 CATCCCAACTTTCCCACCGG 60.965 60.000 0.00 0.00 0.00 5.28
5612 7200 0.965363 CCATCCCAACTTTCCCACCG 60.965 60.000 0.00 0.00 0.00 4.94
5648 7237 5.655090 TGTGAGTTAGGACCATATTCTTCGA 59.345 40.000 0.00 0.00 0.00 3.71
5704 7293 1.818674 CGAACAAAGCTTTGCCCCTAT 59.181 47.619 33.72 14.57 41.79 2.57
5805 7394 8.388103 TGTAAAGAACAAAGAGAAGTTCGAAAG 58.612 33.333 0.00 0.00 46.54 2.62
5806 7395 8.259049 TGTAAAGAACAAAGAGAAGTTCGAAA 57.741 30.769 0.00 0.00 46.54 3.46
5807 7396 7.837202 TGTAAAGAACAAAGAGAAGTTCGAA 57.163 32.000 0.00 0.00 46.54 3.71
5808 7397 7.837202 TTGTAAAGAACAAAGAGAAGTTCGA 57.163 32.000 0.00 0.00 45.11 3.71
5820 7409 9.793259 AAATGAGGAGATAGTTGTAAAGAACAA 57.207 29.630 0.00 0.00 45.90 2.83
5845 7434 9.970395 GATGCCACTATTTTGATCAATGAATAA 57.030 29.630 9.40 0.08 0.00 1.40
5846 7435 8.291740 CGATGCCACTATTTTGATCAATGAATA 58.708 33.333 9.40 10.19 0.00 1.75
5847 7436 7.143340 CGATGCCACTATTTTGATCAATGAAT 58.857 34.615 9.40 9.56 0.00 2.57
5848 7437 6.497437 CGATGCCACTATTTTGATCAATGAA 58.503 36.000 9.40 1.68 0.00 2.57
5849 7438 5.506151 GCGATGCCACTATTTTGATCAATGA 60.506 40.000 9.40 1.60 0.00 2.57
5850 7439 4.678287 GCGATGCCACTATTTTGATCAATG 59.322 41.667 9.40 3.97 0.00 2.82
5851 7440 4.581824 AGCGATGCCACTATTTTGATCAAT 59.418 37.500 9.40 0.00 0.00 2.57
5852 7441 3.947196 AGCGATGCCACTATTTTGATCAA 59.053 39.130 3.38 3.38 0.00 2.57
5853 7442 3.544684 AGCGATGCCACTATTTTGATCA 58.455 40.909 0.00 0.00 0.00 2.92
5854 7443 4.558538 AAGCGATGCCACTATTTTGATC 57.441 40.909 0.00 0.00 0.00 2.92
5855 7444 4.881273 TGTAAGCGATGCCACTATTTTGAT 59.119 37.500 0.00 0.00 0.00 2.57
5856 7445 4.257731 TGTAAGCGATGCCACTATTTTGA 58.742 39.130 0.00 0.00 0.00 2.69
5857 7446 4.614555 TGTAAGCGATGCCACTATTTTG 57.385 40.909 0.00 0.00 0.00 2.44
5858 7447 5.835113 ATTGTAAGCGATGCCACTATTTT 57.165 34.783 0.00 0.00 0.00 1.82
5859 7448 6.935741 TTATTGTAAGCGATGCCACTATTT 57.064 33.333 0.00 0.00 0.00 1.40
5860 7449 6.017109 CCTTTATTGTAAGCGATGCCACTATT 60.017 38.462 0.00 0.00 0.00 1.73
5861 7450 5.470098 CCTTTATTGTAAGCGATGCCACTAT 59.530 40.000 0.00 0.00 0.00 2.12
5862 7451 4.814234 CCTTTATTGTAAGCGATGCCACTA 59.186 41.667 0.00 0.00 0.00 2.74
5863 7452 3.627577 CCTTTATTGTAAGCGATGCCACT 59.372 43.478 0.00 0.00 0.00 4.00
5864 7453 3.243068 CCCTTTATTGTAAGCGATGCCAC 60.243 47.826 0.00 0.00 0.00 5.01
5865 7454 2.948979 CCCTTTATTGTAAGCGATGCCA 59.051 45.455 0.00 0.00 0.00 4.92
5866 7455 3.211045 TCCCTTTATTGTAAGCGATGCC 58.789 45.455 0.00 0.00 0.00 4.40
5867 7456 4.893424 TTCCCTTTATTGTAAGCGATGC 57.107 40.909 0.00 0.00 0.00 3.91
5868 7457 7.360361 GGTTATTCCCTTTATTGTAAGCGATG 58.640 38.462 0.00 0.00 0.00 3.84
5869 7458 6.204108 CGGTTATTCCCTTTATTGTAAGCGAT 59.796 38.462 8.32 0.00 42.27 4.58
5870 7459 5.524646 CGGTTATTCCCTTTATTGTAAGCGA 59.475 40.000 8.32 0.00 42.27 4.93
5871 7460 5.744490 CGGTTATTCCCTTTATTGTAAGCG 58.256 41.667 0.00 0.00 36.93 4.68
5872 7461 5.066764 TGCGGTTATTCCCTTTATTGTAAGC 59.933 40.000 0.00 0.00 0.00 3.09
5873 7462 6.687081 TGCGGTTATTCCCTTTATTGTAAG 57.313 37.500 0.00 0.00 0.00 2.34
5874 7463 7.648039 AATGCGGTTATTCCCTTTATTGTAA 57.352 32.000 0.00 0.00 0.00 2.41
5875 7464 8.212312 TCTAATGCGGTTATTCCCTTTATTGTA 58.788 33.333 0.00 0.00 0.00 2.41
5876 7465 7.057894 TCTAATGCGGTTATTCCCTTTATTGT 58.942 34.615 0.00 0.00 0.00 2.71
5877 7466 7.504924 TCTAATGCGGTTATTCCCTTTATTG 57.495 36.000 0.00 0.00 0.00 1.90
5878 7467 7.778382 AGTTCTAATGCGGTTATTCCCTTTATT 59.222 33.333 0.00 0.00 0.00 1.40
5879 7468 7.287810 AGTTCTAATGCGGTTATTCCCTTTAT 58.712 34.615 0.00 0.00 0.00 1.40
5880 7469 6.655930 AGTTCTAATGCGGTTATTCCCTTTA 58.344 36.000 0.00 0.00 0.00 1.85
5881 7470 5.506708 AGTTCTAATGCGGTTATTCCCTTT 58.493 37.500 0.00 0.00 0.00 3.11
5882 7471 5.112129 AGTTCTAATGCGGTTATTCCCTT 57.888 39.130 0.00 0.00 0.00 3.95
5883 7472 4.772886 AGTTCTAATGCGGTTATTCCCT 57.227 40.909 0.00 0.00 0.00 4.20
5884 7473 5.608449 ACTAGTTCTAATGCGGTTATTCCC 58.392 41.667 0.00 0.00 0.00 3.97
5885 7474 7.544915 GGATACTAGTTCTAATGCGGTTATTCC 59.455 40.741 0.00 0.00 0.00 3.01
5886 7475 8.086522 TGGATACTAGTTCTAATGCGGTTATTC 58.913 37.037 0.00 0.00 37.61 1.75
5887 7476 7.959175 TGGATACTAGTTCTAATGCGGTTATT 58.041 34.615 0.00 0.00 37.61 1.40
5888 7477 7.534723 TGGATACTAGTTCTAATGCGGTTAT 57.465 36.000 0.00 0.00 37.61 1.89
5889 7478 6.964807 TGGATACTAGTTCTAATGCGGTTA 57.035 37.500 0.00 0.00 37.61 2.85
5890 7479 5.864418 TGGATACTAGTTCTAATGCGGTT 57.136 39.130 0.00 0.00 37.61 4.44
5891 7480 5.047235 GGATGGATACTAGTTCTAATGCGGT 60.047 44.000 0.00 0.00 37.61 5.68
5892 7481 5.186021 AGGATGGATACTAGTTCTAATGCGG 59.814 44.000 0.00 0.00 37.61 5.69
5893 7482 6.274157 AGGATGGATACTAGTTCTAATGCG 57.726 41.667 0.00 0.00 37.61 4.73
5894 7483 8.123639 TGTAGGATGGATACTAGTTCTAATGC 57.876 38.462 0.00 0.00 37.61 3.56
5895 7484 9.915629 GTTGTAGGATGGATACTAGTTCTAATG 57.084 37.037 0.00 0.00 37.61 1.90
5896 7485 9.884814 AGTTGTAGGATGGATACTAGTTCTAAT 57.115 33.333 0.00 0.00 37.61 1.73
5899 7488 8.927675 CTAGTTGTAGGATGGATACTAGTTCT 57.072 38.462 0.00 0.00 33.61 3.01
5914 7503 5.452341 AATTTTCTCCCCCTAGTTGTAGG 57.548 43.478 0.00 0.00 45.25 3.18
5915 7504 5.652452 CCAAATTTTCTCCCCCTAGTTGTAG 59.348 44.000 0.00 0.00 0.00 2.74
5916 7505 5.576128 CCAAATTTTCTCCCCCTAGTTGTA 58.424 41.667 0.00 0.00 0.00 2.41
5917 7506 4.416516 CCAAATTTTCTCCCCCTAGTTGT 58.583 43.478 0.00 0.00 0.00 3.32
5918 7507 3.195610 GCCAAATTTTCTCCCCCTAGTTG 59.804 47.826 0.00 0.00 0.00 3.16
5919 7508 3.077543 AGCCAAATTTTCTCCCCCTAGTT 59.922 43.478 0.00 0.00 0.00 2.24
5920 7509 2.654896 AGCCAAATTTTCTCCCCCTAGT 59.345 45.455 0.00 0.00 0.00 2.57
5921 7510 3.388552 AGCCAAATTTTCTCCCCCTAG 57.611 47.619 0.00 0.00 0.00 3.02
5922 7511 4.571148 GGTTAGCCAAATTTTCTCCCCCTA 60.571 45.833 0.00 0.00 34.09 3.53
5923 7512 3.441101 GTTAGCCAAATTTTCTCCCCCT 58.559 45.455 0.00 0.00 0.00 4.79
5924 7513 2.500098 GGTTAGCCAAATTTTCTCCCCC 59.500 50.000 0.00 0.00 34.09 5.40
5925 7514 3.441101 AGGTTAGCCAAATTTTCTCCCC 58.559 45.455 0.00 0.00 37.19 4.81
5926 7515 4.098044 GCTAGGTTAGCCAAATTTTCTCCC 59.902 45.833 0.00 0.00 45.95 4.30
5927 7516 5.250235 GCTAGGTTAGCCAAATTTTCTCC 57.750 43.478 0.00 0.00 45.95 3.71
5940 7529 2.866762 GCTCACGAATTGGCTAGGTTAG 59.133 50.000 0.00 0.00 0.00 2.34
5941 7530 2.500098 AGCTCACGAATTGGCTAGGTTA 59.500 45.455 0.00 0.00 31.97 2.85
5942 7531 1.279271 AGCTCACGAATTGGCTAGGTT 59.721 47.619 0.00 0.00 31.97 3.50
5943 7532 0.905357 AGCTCACGAATTGGCTAGGT 59.095 50.000 0.00 0.00 31.97 3.08
5944 7533 2.101582 AGTAGCTCACGAATTGGCTAGG 59.898 50.000 0.00 0.00 35.74 3.02
5945 7534 3.444703 AGTAGCTCACGAATTGGCTAG 57.555 47.619 0.00 0.00 35.74 3.42
5946 7535 3.194755 TCAAGTAGCTCACGAATTGGCTA 59.805 43.478 0.00 0.00 34.62 3.93
5947 7536 2.028112 TCAAGTAGCTCACGAATTGGCT 60.028 45.455 0.00 0.00 36.22 4.75
5948 7537 2.346803 TCAAGTAGCTCACGAATTGGC 58.653 47.619 0.00 0.00 29.05 4.52
5949 7538 4.728882 GCAATCAAGTAGCTCACGAATTGG 60.729 45.833 0.00 0.00 31.42 3.16
5950 7539 4.093998 AGCAATCAAGTAGCTCACGAATTG 59.906 41.667 0.00 0.00 32.05 2.32
5951 7540 4.256920 AGCAATCAAGTAGCTCACGAATT 58.743 39.130 0.00 0.00 32.05 2.17
5952 7541 3.866651 AGCAATCAAGTAGCTCACGAAT 58.133 40.909 0.00 0.00 32.05 3.34
5953 7542 3.319137 AGCAATCAAGTAGCTCACGAA 57.681 42.857 0.00 0.00 32.05 3.85
5959 7548 6.729690 AATAGAGAGAGCAATCAAGTAGCT 57.270 37.500 0.00 0.00 42.17 3.32
5960 7549 7.429633 TGTAATAGAGAGAGCAATCAAGTAGC 58.570 38.462 0.00 0.00 0.00 3.58
5961 7550 9.979578 ATTGTAATAGAGAGAGCAATCAAGTAG 57.020 33.333 0.00 0.00 0.00 2.57
5962 7551 9.755804 CATTGTAATAGAGAGAGCAATCAAGTA 57.244 33.333 0.00 0.00 0.00 2.24
5963 7552 8.263640 ACATTGTAATAGAGAGAGCAATCAAGT 58.736 33.333 0.00 0.00 0.00 3.16
5964 7553 8.659925 ACATTGTAATAGAGAGAGCAATCAAG 57.340 34.615 0.00 0.00 0.00 3.02
5965 7554 9.102757 GAACATTGTAATAGAGAGAGCAATCAA 57.897 33.333 0.00 0.00 0.00 2.57
5966 7555 8.260114 TGAACATTGTAATAGAGAGAGCAATCA 58.740 33.333 0.00 0.00 0.00 2.57
5967 7556 8.654230 TGAACATTGTAATAGAGAGAGCAATC 57.346 34.615 0.00 0.00 0.00 2.67
5997 7586 9.398538 TCATGTCATTAGATTTCAATCATGTCA 57.601 29.630 2.43 3.26 37.89 3.58
6026 7615 9.777297 TGCTAGTGCTATATTCAATGATTGTTA 57.223 29.630 4.93 0.00 40.48 2.41
6027 7616 8.681486 TGCTAGTGCTATATTCAATGATTGTT 57.319 30.769 4.93 0.00 40.48 2.83


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

AutoCloner maintained by Alex Coulton.