Multiple sequence alignment - TraesCS2B01G407100

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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 TraesCS2B01G407100 chr2B 100.000 3333 0 0 1 3333 576746558 576743226 0.000000e+00 6156.0
1 TraesCS2B01G407100 chr2B 93.548 124 8 0 3 126 572186859 572186982 5.680000e-43 185.0
2 TraesCS2B01G407100 chr2B 100.000 30 0 0 1552 1581 23111457 23111428 4.650000e-04 56.5
3 TraesCS2B01G407100 chr2D 93.405 2335 103 20 478 2791 492023800 492021496 0.000000e+00 3411.0
4 TraesCS2B01G407100 chr2D 92.105 190 11 2 3148 3333 492021197 492021008 7.090000e-67 265.0
5 TraesCS2B01G407100 chr2D 100.000 33 0 0 1549 1581 183630571 183630539 9.980000e-06 62.1
6 TraesCS2B01G407100 chr2A 91.855 2345 96 35 478 2773 637224237 637221939 0.000000e+00 3184.0
7 TraesCS2B01G407100 chr2A 88.761 347 34 4 133 479 637227537 637227196 1.430000e-113 420.0
8 TraesCS2B01G407100 chr2A 93.684 190 7 2 3148 3333 637220073 637219885 2.530000e-71 279.0
9 TraesCS2B01G407100 chr2A 100.000 33 0 0 1549 1581 197925679 197925647 9.980000e-06 62.1
10 TraesCS2B01G407100 chr1B 97.360 303 8 0 2325 2627 482177759 482178061 1.770000e-142 516.0
11 TraesCS2B01G407100 chr6A 80.995 663 99 22 1659 2303 450107891 450107238 4.960000e-138 501.0
12 TraesCS2B01G407100 chr6A 92.063 126 10 0 1 126 570516242 570516117 9.500000e-41 178.0
13 TraesCS2B01G407100 chr6B 87.273 220 28 0 1427 1646 513135661 513135880 5.520000e-63 252.0
14 TraesCS2B01G407100 chr5D 93.651 126 8 0 1 126 403549433 403549558 4.390000e-44 189.0
15 TraesCS2B01G407100 chr5D 91.111 45 4 0 2012 2056 438361885 438361841 9.980000e-06 62.1
16 TraesCS2B01G407100 chr1D 92.857 126 9 0 1 126 99642880 99642755 2.040000e-42 183.0
17 TraesCS2B01G407100 chr7B 93.750 48 3 0 2011 2058 57633389 57633342 4.610000e-09 73.1
18 TraesCS2B01G407100 chr6D 93.182 44 3 0 2860 2903 320856947 320856990 7.720000e-07 65.8
19 TraesCS2B01G407100 chr3D 95.122 41 2 0 2008 2048 48365677 48365637 7.720000e-07 65.8
20 TraesCS2B01G407100 chr3D 89.583 48 5 0 2009 2056 516385275 516385228 9.980000e-06 62.1
21 TraesCS2B01G407100 chr3B 89.583 48 5 0 2009 2056 679646141 679646094 9.980000e-06 62.1
22 TraesCS2B01G407100 chr3A 89.583 48 5 0 2009 2056 651588232 651588185 9.980000e-06 62.1


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 TraesCS2B01G407100 chr2B 576743226 576746558 3332 True 6156.000000 6156 100.000000 1 3333 1 chr2B.!!$R2 3332
1 TraesCS2B01G407100 chr2D 492021008 492023800 2792 True 1838.000000 3411 92.755000 478 3333 2 chr2D.!!$R2 2855
2 TraesCS2B01G407100 chr2A 637219885 637227537 7652 True 1294.333333 3184 91.433333 133 3333 3 chr2A.!!$R2 3200
3 TraesCS2B01G407100 chr6A 450107238 450107891 653 True 501.000000 501 80.995000 1659 2303 1 chr6A.!!$R1 644

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
816 3777 0.106268 TTTCCAGCCCTCAAGCAACA 60.106 50.0 0.00 0.0 34.23 3.33 F
1190 4185 0.036388 CCCAAGCAAGCGTAGGAGAA 60.036 55.0 2.77 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 5017 0.109689 AAGCTGTACACGTCGCTCTC 60.110 55.0 7.7 0.0 31.3 3.20 R
2775 5795 0.317519 CCGTTTGAAACCCGCTTGAC 60.318 55.0 2.0 0.0 0.0 3.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.878086 TCTGCGAACAACAAATGAGAC 57.122 42.857 0.00 0.00 0.00 3.36
21 22 3.202097 TCTGCGAACAACAAATGAGACA 58.798 40.909 0.00 0.00 0.00 3.41
22 23 3.002246 TCTGCGAACAACAAATGAGACAC 59.998 43.478 0.00 0.00 0.00 3.67
23 24 2.680339 TGCGAACAACAAATGAGACACA 59.320 40.909 0.00 0.00 0.00 3.72
24 25 3.035942 GCGAACAACAAATGAGACACAC 58.964 45.455 0.00 0.00 0.00 3.82
25 26 3.617669 CGAACAACAAATGAGACACACC 58.382 45.455 0.00 0.00 0.00 4.16
26 27 3.548014 CGAACAACAAATGAGACACACCC 60.548 47.826 0.00 0.00 0.00 4.61
27 28 1.946768 ACAACAAATGAGACACACCCG 59.053 47.619 0.00 0.00 0.00 5.28
28 29 2.217750 CAACAAATGAGACACACCCGA 58.782 47.619 0.00 0.00 0.00 5.14
29 30 2.616376 CAACAAATGAGACACACCCGAA 59.384 45.455 0.00 0.00 0.00 4.30
30 31 2.494059 ACAAATGAGACACACCCGAAG 58.506 47.619 0.00 0.00 0.00 3.79
31 32 1.197721 CAAATGAGACACACCCGAAGC 59.802 52.381 0.00 0.00 0.00 3.86
32 33 0.687354 AATGAGACACACCCGAAGCT 59.313 50.000 0.00 0.00 0.00 3.74
33 34 0.247736 ATGAGACACACCCGAAGCTC 59.752 55.000 0.00 0.00 0.00 4.09
34 35 1.444553 GAGACACACCCGAAGCTCG 60.445 63.158 0.00 0.00 40.07 5.03
43 44 4.880537 CGAAGCTCGGCGGCAGAT 62.881 66.667 19.61 1.15 36.00 2.90
44 45 2.512515 GAAGCTCGGCGGCAGATT 60.513 61.111 19.61 10.60 34.17 2.40
45 46 2.045926 AAGCTCGGCGGCAGATTT 60.046 55.556 19.61 0.00 34.17 2.17
46 47 1.648467 GAAGCTCGGCGGCAGATTTT 61.648 55.000 19.61 1.33 34.17 1.82
47 48 1.648467 AAGCTCGGCGGCAGATTTTC 61.648 55.000 19.61 0.00 34.17 2.29
48 49 2.398554 GCTCGGCGGCAGATTTTCA 61.399 57.895 10.53 0.00 0.00 2.69
49 50 1.717937 CTCGGCGGCAGATTTTCAG 59.282 57.895 10.53 0.00 0.00 3.02
50 51 0.740868 CTCGGCGGCAGATTTTCAGA 60.741 55.000 10.53 0.00 0.00 3.27
51 52 0.740868 TCGGCGGCAGATTTTCAGAG 60.741 55.000 10.53 0.00 0.00 3.35
52 53 1.709147 CGGCGGCAGATTTTCAGAGG 61.709 60.000 10.53 0.00 0.00 3.69
53 54 0.678048 GGCGGCAGATTTTCAGAGGT 60.678 55.000 3.07 0.00 0.00 3.85
54 55 0.449388 GCGGCAGATTTTCAGAGGTG 59.551 55.000 0.00 0.00 0.00 4.00
55 56 1.813513 CGGCAGATTTTCAGAGGTGT 58.186 50.000 0.00 0.00 0.00 4.16
56 57 1.466167 CGGCAGATTTTCAGAGGTGTG 59.534 52.381 0.00 0.00 0.00 3.82
57 58 2.508526 GGCAGATTTTCAGAGGTGTGT 58.491 47.619 0.00 0.00 0.00 3.72
58 59 3.674997 GGCAGATTTTCAGAGGTGTGTA 58.325 45.455 0.00 0.00 0.00 2.90
59 60 3.686726 GGCAGATTTTCAGAGGTGTGTAG 59.313 47.826 0.00 0.00 0.00 2.74
60 61 4.319177 GCAGATTTTCAGAGGTGTGTAGT 58.681 43.478 0.00 0.00 0.00 2.73
61 62 4.390297 GCAGATTTTCAGAGGTGTGTAGTC 59.610 45.833 0.00 0.00 0.00 2.59
62 63 5.541845 CAGATTTTCAGAGGTGTGTAGTCA 58.458 41.667 0.00 0.00 0.00 3.41
63 64 5.406780 CAGATTTTCAGAGGTGTGTAGTCAC 59.593 44.000 0.00 0.00 44.08 3.67
74 75 4.945246 GTGTGTAGTCACCTTTCTCTTCA 58.055 43.478 0.00 0.00 43.26 3.02
75 76 4.745620 GTGTGTAGTCACCTTTCTCTTCAC 59.254 45.833 0.00 0.00 43.26 3.18
76 77 4.202223 TGTGTAGTCACCTTTCTCTTCACC 60.202 45.833 0.00 0.00 43.26 4.02
77 78 3.964688 TGTAGTCACCTTTCTCTTCACCA 59.035 43.478 0.00 0.00 0.00 4.17
78 79 4.593206 TGTAGTCACCTTTCTCTTCACCAT 59.407 41.667 0.00 0.00 0.00 3.55
79 80 4.278975 AGTCACCTTTCTCTTCACCATC 57.721 45.455 0.00 0.00 0.00 3.51
80 81 3.906846 AGTCACCTTTCTCTTCACCATCT 59.093 43.478 0.00 0.00 0.00 2.90
81 82 4.349342 AGTCACCTTTCTCTTCACCATCTT 59.651 41.667 0.00 0.00 0.00 2.40
82 83 5.066593 GTCACCTTTCTCTTCACCATCTTT 58.933 41.667 0.00 0.00 0.00 2.52
83 84 5.180304 GTCACCTTTCTCTTCACCATCTTTC 59.820 44.000 0.00 0.00 0.00 2.62
84 85 5.065914 CACCTTTCTCTTCACCATCTTTCA 58.934 41.667 0.00 0.00 0.00 2.69
85 86 5.532406 CACCTTTCTCTTCACCATCTTTCAA 59.468 40.000 0.00 0.00 0.00 2.69
86 87 5.532779 ACCTTTCTCTTCACCATCTTTCAAC 59.467 40.000 0.00 0.00 0.00 3.18
87 88 5.532406 CCTTTCTCTTCACCATCTTTCAACA 59.468 40.000 0.00 0.00 0.00 3.33
88 89 6.293845 CCTTTCTCTTCACCATCTTTCAACAG 60.294 42.308 0.00 0.00 0.00 3.16
89 90 4.645535 TCTCTTCACCATCTTTCAACAGG 58.354 43.478 0.00 0.00 0.00 4.00
90 91 3.754965 TCTTCACCATCTTTCAACAGGG 58.245 45.455 0.00 0.00 0.00 4.45
91 92 3.138283 TCTTCACCATCTTTCAACAGGGT 59.862 43.478 0.00 0.00 0.00 4.34
92 93 4.349636 TCTTCACCATCTTTCAACAGGGTA 59.650 41.667 0.00 0.00 0.00 3.69
93 94 4.286297 TCACCATCTTTCAACAGGGTAG 57.714 45.455 0.00 0.00 0.00 3.18
94 95 3.907474 TCACCATCTTTCAACAGGGTAGA 59.093 43.478 0.00 0.00 0.00 2.59
95 96 4.003648 CACCATCTTTCAACAGGGTAGAC 58.996 47.826 0.00 0.00 0.00 2.59
96 97 3.650942 ACCATCTTTCAACAGGGTAGACA 59.349 43.478 0.00 0.00 0.00 3.41
97 98 4.289672 ACCATCTTTCAACAGGGTAGACAT 59.710 41.667 0.00 0.00 0.00 3.06
98 99 5.487488 ACCATCTTTCAACAGGGTAGACATA 59.513 40.000 0.00 0.00 0.00 2.29
99 100 5.817816 CCATCTTTCAACAGGGTAGACATAC 59.182 44.000 0.00 0.00 0.00 2.39
113 114 6.830114 GTAGACATACCATCAGCAACTAAC 57.170 41.667 0.00 0.00 0.00 2.34
114 115 5.420725 AGACATACCATCAGCAACTAACA 57.579 39.130 0.00 0.00 0.00 2.41
115 116 5.804639 AGACATACCATCAGCAACTAACAA 58.195 37.500 0.00 0.00 0.00 2.83
116 117 5.877012 AGACATACCATCAGCAACTAACAAG 59.123 40.000 0.00 0.00 0.00 3.16
117 118 5.804639 ACATACCATCAGCAACTAACAAGA 58.195 37.500 0.00 0.00 0.00 3.02
118 119 6.237901 ACATACCATCAGCAACTAACAAGAA 58.762 36.000 0.00 0.00 0.00 2.52
119 120 6.149474 ACATACCATCAGCAACTAACAAGAAC 59.851 38.462 0.00 0.00 0.00 3.01
120 121 4.460263 ACCATCAGCAACTAACAAGAACA 58.540 39.130 0.00 0.00 0.00 3.18
121 122 4.887071 ACCATCAGCAACTAACAAGAACAA 59.113 37.500 0.00 0.00 0.00 2.83
122 123 5.009010 ACCATCAGCAACTAACAAGAACAAG 59.991 40.000 0.00 0.00 0.00 3.16
123 124 5.239306 CCATCAGCAACTAACAAGAACAAGA 59.761 40.000 0.00 0.00 0.00 3.02
124 125 6.238731 CCATCAGCAACTAACAAGAACAAGAA 60.239 38.462 0.00 0.00 0.00 2.52
125 126 6.119144 TCAGCAACTAACAAGAACAAGAAC 57.881 37.500 0.00 0.00 0.00 3.01
126 127 5.645929 TCAGCAACTAACAAGAACAAGAACA 59.354 36.000 0.00 0.00 0.00 3.18
127 128 6.318648 TCAGCAACTAACAAGAACAAGAACAT 59.681 34.615 0.00 0.00 0.00 2.71
128 129 6.415867 CAGCAACTAACAAGAACAAGAACATG 59.584 38.462 0.00 0.00 0.00 3.21
129 130 5.687285 GCAACTAACAAGAACAAGAACATGG 59.313 40.000 0.00 0.00 0.00 3.66
130 131 5.438761 ACTAACAAGAACAAGAACATGGC 57.561 39.130 0.00 0.00 0.00 4.40
131 132 4.887071 ACTAACAAGAACAAGAACATGGCA 59.113 37.500 0.00 0.00 0.00 4.92
132 133 3.996150 ACAAGAACAAGAACATGGCAG 57.004 42.857 0.00 0.00 0.00 4.85
133 134 3.554934 ACAAGAACAAGAACATGGCAGA 58.445 40.909 0.00 0.00 0.00 4.26
134 135 3.316308 ACAAGAACAAGAACATGGCAGAC 59.684 43.478 0.00 0.00 0.00 3.51
135 136 3.213206 AGAACAAGAACATGGCAGACA 57.787 42.857 0.00 0.00 0.00 3.41
136 137 3.759581 AGAACAAGAACATGGCAGACAT 58.240 40.909 0.00 0.00 41.57 3.06
162 163 2.223611 GCGAGCTCATCTCAATCAATGG 59.776 50.000 15.40 0.00 41.98 3.16
165 166 2.158505 AGCTCATCTCAATCAATGGGGG 60.159 50.000 0.00 0.00 0.00 5.40
166 167 2.423947 GCTCATCTCAATCAATGGGGGT 60.424 50.000 0.00 0.00 0.00 4.95
212 213 0.401738 TGGCTCAAGAAGGGGAGTTG 59.598 55.000 0.00 0.00 33.66 3.16
216 217 1.675641 CAAGAAGGGGAGTTGGCGG 60.676 63.158 0.00 0.00 0.00 6.13
257 258 2.483877 TGCAAAAGCGTAACAGATGAGG 59.516 45.455 0.00 0.00 0.00 3.86
267 268 1.276859 ACAGATGAGGATGGCCAGCA 61.277 55.000 24.75 12.88 36.29 4.41
269 270 0.110678 AGATGAGGATGGCCAGCATG 59.889 55.000 24.75 0.00 33.36 4.06
284 285 0.820891 GCATGGGCTGATCCGACATT 60.821 55.000 0.00 0.00 36.96 2.71
298 299 3.116300 CCGACATTAAGATCACGTCCAG 58.884 50.000 0.00 0.00 0.00 3.86
310 311 3.771160 GTCCAGGCGTGTCCGGAT 61.771 66.667 7.81 0.00 38.89 4.18
328 329 2.611518 GATTTCCTCATATCCGCTCCG 58.388 52.381 0.00 0.00 0.00 4.63
352 353 5.947566 GCTTACAAGTTGGATTTAAGGGGTA 59.052 40.000 7.96 0.00 0.00 3.69
354 355 5.327737 ACAAGTTGGATTTAAGGGGTACA 57.672 39.130 7.96 0.00 0.00 2.90
394 395 1.123928 CCAGGTATGGGAGGTCAGAC 58.876 60.000 0.00 0.00 43.54 3.51
400 401 0.911525 ATGGGAGGTCAGACAGGGTG 60.912 60.000 2.17 0.00 0.00 4.61
411 412 0.243636 GACAGGGTGCGGATTTTTGG 59.756 55.000 0.00 0.00 0.00 3.28
412 413 0.469144 ACAGGGTGCGGATTTTTGGT 60.469 50.000 0.00 0.00 0.00 3.67
413 414 0.243636 CAGGGTGCGGATTTTTGGTC 59.756 55.000 0.00 0.00 0.00 4.02
414 415 0.178975 AGGGTGCGGATTTTTGGTCA 60.179 50.000 0.00 0.00 0.00 4.02
415 416 0.243636 GGGTGCGGATTTTTGGTCAG 59.756 55.000 0.00 0.00 0.00 3.51
418 419 1.215382 GCGGATTTTTGGTCAGGGC 59.785 57.895 0.00 0.00 0.00 5.19
442 443 1.241315 CGTGCCCGGAAAAATGAGGT 61.241 55.000 0.73 0.00 0.00 3.85
448 449 3.620472 GCCCGGAAAAATGAGGTGTAGTA 60.620 47.826 0.73 0.00 0.00 1.82
455 456 2.068834 ATGAGGTGTAGTAGGTCCGG 57.931 55.000 0.00 0.00 0.00 5.14
456 457 0.994247 TGAGGTGTAGTAGGTCCGGA 59.006 55.000 0.00 0.00 0.00 5.14
461 462 2.883386 GGTGTAGTAGGTCCGGATGTAG 59.117 54.545 7.81 0.00 0.00 2.74
468 469 2.780714 AGGTCCGGATGTAGATACTCG 58.219 52.381 7.81 0.00 0.00 4.18
472 473 5.188555 AGGTCCGGATGTAGATACTCGTATA 59.811 44.000 7.81 0.00 0.00 1.47
474 475 6.018098 GGTCCGGATGTAGATACTCGTATATG 60.018 46.154 7.81 0.00 0.00 1.78
477 478 8.427276 TCCGGATGTAGATACTCGTATATGTAT 58.573 37.037 0.00 0.00 32.71 2.29
478 479 9.702494 CCGGATGTAGATACTCGTATATGTATA 57.298 37.037 0.00 0.00 30.49 1.47
519 3477 1.910819 CATGTAAATGTTCGCAACGGC 59.089 47.619 0.00 0.00 0.00 5.68
529 3487 2.725815 GCAACGGCGCAACTGAAC 60.726 61.111 10.83 0.00 0.00 3.18
729 3689 7.201266 CCGTCGAAAAAGCTTGAATATCAAAAG 60.201 37.037 0.00 0.00 35.73 2.27
757 3718 2.887568 CCAAGCTAGCCGCGTCTG 60.888 66.667 12.13 0.00 45.59 3.51
770 3731 0.798776 GCGTCTGTGAACATTCCCAG 59.201 55.000 0.00 0.00 34.54 4.45
794 3755 8.208560 CAGTTAGAGCGATCGTCAATAAATAAC 58.791 37.037 17.81 14.02 0.00 1.89
816 3777 0.106268 TTTCCAGCCCTCAAGCAACA 60.106 50.000 0.00 0.00 34.23 3.33
866 3827 7.120726 CCACTGTAGGAAGGAAAACGAAATATT 59.879 37.037 0.00 0.00 0.00 1.28
907 3893 4.286910 GAGAGAGATGTTGATGACGTAGC 58.713 47.826 0.00 0.00 0.00 3.58
932 3920 1.279271 CCCCACTCTGAAAGAATCGGT 59.721 52.381 0.00 0.00 46.34 4.69
1006 3998 3.303990 GCGAGAAGAACACAAGATGCAAA 60.304 43.478 0.00 0.00 0.00 3.68
1175 4170 2.183679 AGAACCAGCAACAAAACCCAA 58.816 42.857 0.00 0.00 0.00 4.12
1190 4185 0.036388 CCCAAGCAAGCGTAGGAGAA 60.036 55.000 2.77 0.00 0.00 2.87
1192 4187 1.363744 CAAGCAAGCGTAGGAGAAGG 58.636 55.000 0.00 0.00 0.00 3.46
1279 4278 2.322999 GATCCGCGGGCACAATGTTC 62.323 60.000 27.83 4.90 0.00 3.18
1404 4406 4.144727 GGAGGAGGAGGAGGCCGA 62.145 72.222 0.00 0.00 0.00 5.54
1852 4857 2.342648 GCGTCCAACGTCCTCCTT 59.657 61.111 1.14 0.00 44.73 3.36
2006 5017 3.124921 CCGGCGTGGCTAACAAGG 61.125 66.667 6.01 0.00 0.00 3.61
2176 5187 3.420943 GGCAAATACAGCGCCGAT 58.579 55.556 2.29 0.00 35.79 4.18
2355 5369 2.439701 CTGGCTCATGGCTGGTGG 60.440 66.667 6.20 0.00 41.46 4.61
2356 5370 4.746309 TGGCTCATGGCTGGTGGC 62.746 66.667 6.20 0.00 41.46 5.01
2542 5561 3.149196 CAATGGCAGTGGTAGTTCAGTT 58.851 45.455 7.12 0.00 0.00 3.16
2622 5642 4.646572 TGGTTTTTGAGGCACTTTGTTTT 58.353 34.783 0.00 0.00 41.55 2.43
2623 5643 5.794894 TGGTTTTTGAGGCACTTTGTTTTA 58.205 33.333 0.00 0.00 41.55 1.52
2624 5644 6.410540 TGGTTTTTGAGGCACTTTGTTTTAT 58.589 32.000 0.00 0.00 41.55 1.40
2651 5671 2.031870 GGTGGAGGACAAGCTGTTTTT 58.968 47.619 0.00 0.00 0.00 1.94
2655 5675 4.097286 GTGGAGGACAAGCTGTTTTTGTTA 59.903 41.667 0.00 0.00 38.78 2.41
2705 5725 2.424601 CTGGCCATCAACGATTGAATGT 59.575 45.455 5.51 0.00 43.95 2.71
2707 5727 2.480073 GGCCATCAACGATTGAATGTGG 60.480 50.000 0.00 11.39 43.95 4.17
2709 5729 3.731867 GCCATCAACGATTGAATGTGGAC 60.732 47.826 16.37 8.69 43.95 4.02
2710 5730 3.439825 CCATCAACGATTGAATGTGGACA 59.560 43.478 10.70 0.00 43.95 4.02
2711 5731 4.082841 CCATCAACGATTGAATGTGGACAA 60.083 41.667 10.70 0.00 43.95 3.18
2713 5733 3.058293 TCAACGATTGAATGTGGACAAGC 60.058 43.478 0.00 0.00 36.59 4.01
2714 5734 2.783135 ACGATTGAATGTGGACAAGCT 58.217 42.857 0.00 0.00 31.51 3.74
2715 5735 2.485426 ACGATTGAATGTGGACAAGCTG 59.515 45.455 0.00 0.00 31.51 4.24
2716 5736 2.485426 CGATTGAATGTGGACAAGCTGT 59.515 45.455 0.00 0.00 31.51 4.40
2717 5737 3.058016 CGATTGAATGTGGACAAGCTGTT 60.058 43.478 0.00 0.00 31.51 3.16
2718 5738 4.557296 CGATTGAATGTGGACAAGCTGTTT 60.557 41.667 0.00 0.00 31.51 2.83
2719 5739 4.734398 TTGAATGTGGACAAGCTGTTTT 57.266 36.364 0.00 0.00 0.00 2.43
2720 5740 4.734398 TGAATGTGGACAAGCTGTTTTT 57.266 36.364 0.00 0.00 0.00 1.94
2721 5741 4.431809 TGAATGTGGACAAGCTGTTTTTG 58.568 39.130 0.00 0.00 0.00 2.44
2722 5742 4.081752 TGAATGTGGACAAGCTGTTTTTGT 60.082 37.500 0.00 0.00 41.21 2.83
2723 5743 3.951775 TGTGGACAAGCTGTTTTTGTT 57.048 38.095 0.00 0.00 38.78 2.83
2724 5744 3.583806 TGTGGACAAGCTGTTTTTGTTG 58.416 40.909 0.00 0.00 38.78 3.33
2739 5759 6.368243 TGTTTTTGTTGACAGACGTACTACAA 59.632 34.615 0.00 0.00 0.00 2.41
2741 5761 4.635833 TGTTGACAGACGTACTACAACA 57.364 40.909 19.32 19.32 44.19 3.33
2781 5801 3.082698 TGCATGTGAACAAAGTCAAGC 57.917 42.857 0.00 0.00 0.00 4.01
2794 5814 0.317519 GTCAAGCGGGTTTCAAACGG 60.318 55.000 0.00 0.00 0.00 4.44
2795 5815 1.007849 CAAGCGGGTTTCAAACGGG 60.008 57.895 0.00 0.00 0.00 5.28
2803 5833 1.677052 GGTTTCAAACGGGCAGTTACA 59.323 47.619 2.82 0.00 43.37 2.41
2804 5834 2.295070 GGTTTCAAACGGGCAGTTACAT 59.705 45.455 2.82 0.00 43.37 2.29
2807 5837 2.577700 TCAAACGGGCAGTTACATTGT 58.422 42.857 2.82 0.00 43.37 2.71
2808 5838 2.292016 TCAAACGGGCAGTTACATTGTG 59.708 45.455 2.82 0.00 43.37 3.33
2813 5843 3.243267 ACGGGCAGTTACATTGTGAAAAC 60.243 43.478 0.00 0.00 0.00 2.43
2816 5846 4.278419 GGGCAGTTACATTGTGAAAACTCT 59.722 41.667 0.00 0.00 29.51 3.24
2819 5849 4.905866 CAGTTACATTGTGAAAACTCTGCG 59.094 41.667 0.00 0.00 29.51 5.18
2836 7458 2.354821 CTGCGGCTCTTATTTTACCCAC 59.645 50.000 0.00 0.00 0.00 4.61
2846 7468 7.148355 TCTTATTTTACCCACTTTAAAGCCG 57.852 36.000 15.24 6.68 0.00 5.52
2849 7471 4.834357 TTTACCCACTTTAAAGCCGTTC 57.166 40.909 15.24 0.00 0.00 3.95
2851 7473 3.775261 ACCCACTTTAAAGCCGTTCTA 57.225 42.857 15.24 0.00 0.00 2.10
2855 7477 4.201783 CCCACTTTAAAGCCGTTCTAATCG 60.202 45.833 15.24 0.00 0.00 3.34
2861 7483 6.875926 TTAAAGCCGTTCTAATCGTTCTAC 57.124 37.500 0.00 0.00 0.00 2.59
2862 7484 4.715527 AAGCCGTTCTAATCGTTCTACT 57.284 40.909 0.00 0.00 0.00 2.57
2864 7486 3.066481 AGCCGTTCTAATCGTTCTACTCC 59.934 47.826 0.00 0.00 0.00 3.85
2865 7487 3.794812 GCCGTTCTAATCGTTCTACTCCC 60.795 52.174 0.00 0.00 0.00 4.30
2866 7488 3.631227 CCGTTCTAATCGTTCTACTCCCT 59.369 47.826 0.00 0.00 0.00 4.20
2867 7489 4.261114 CCGTTCTAATCGTTCTACTCCCTC 60.261 50.000 0.00 0.00 0.00 4.30
2868 7490 4.261114 CGTTCTAATCGTTCTACTCCCTCC 60.261 50.000 0.00 0.00 0.00 4.30
2869 7491 3.474600 TCTAATCGTTCTACTCCCTCCG 58.525 50.000 0.00 0.00 0.00 4.63
2870 7492 2.140839 AATCGTTCTACTCCCTCCGT 57.859 50.000 0.00 0.00 0.00 4.69
2871 7493 1.677942 ATCGTTCTACTCCCTCCGTC 58.322 55.000 0.00 0.00 0.00 4.79
2872 7494 0.393537 TCGTTCTACTCCCTCCGTCC 60.394 60.000 0.00 0.00 0.00 4.79
2873 7495 1.382692 CGTTCTACTCCCTCCGTCCC 61.383 65.000 0.00 0.00 0.00 4.46
2874 7496 1.077212 TTCTACTCCCTCCGTCCCG 60.077 63.158 0.00 0.00 0.00 5.14
2875 7497 1.856539 TTCTACTCCCTCCGTCCCGT 61.857 60.000 0.00 0.00 0.00 5.28
2876 7498 0.982852 TCTACTCCCTCCGTCCCGTA 60.983 60.000 0.00 0.00 0.00 4.02
2877 7499 0.107017 CTACTCCCTCCGTCCCGTAA 60.107 60.000 0.00 0.00 0.00 3.18
2878 7500 0.331278 TACTCCCTCCGTCCCGTAAA 59.669 55.000 0.00 0.00 0.00 2.01
2879 7501 0.542702 ACTCCCTCCGTCCCGTAAAA 60.543 55.000 0.00 0.00 0.00 1.52
2880 7502 0.828677 CTCCCTCCGTCCCGTAAAAT 59.171 55.000 0.00 0.00 0.00 1.82
2881 7503 2.034124 CTCCCTCCGTCCCGTAAAATA 58.966 52.381 0.00 0.00 0.00 1.40
2882 7504 2.431782 CTCCCTCCGTCCCGTAAAATAA 59.568 50.000 0.00 0.00 0.00 1.40
2883 7505 2.431782 TCCCTCCGTCCCGTAAAATAAG 59.568 50.000 0.00 0.00 0.00 1.73
2884 7506 2.431782 CCCTCCGTCCCGTAAAATAAGA 59.568 50.000 0.00 0.00 0.00 2.10
2885 7507 3.118665 CCCTCCGTCCCGTAAAATAAGAA 60.119 47.826 0.00 0.00 0.00 2.52
2886 7508 4.443881 CCCTCCGTCCCGTAAAATAAGAAT 60.444 45.833 0.00 0.00 0.00 2.40
2887 7509 4.510340 CCTCCGTCCCGTAAAATAAGAATG 59.490 45.833 0.00 0.00 0.00 2.67
2888 7510 5.088680 TCCGTCCCGTAAAATAAGAATGT 57.911 39.130 0.00 0.00 0.00 2.71
2889 7511 5.490159 TCCGTCCCGTAAAATAAGAATGTT 58.510 37.500 0.00 0.00 0.00 2.71
2890 7512 5.939296 TCCGTCCCGTAAAATAAGAATGTTT 59.061 36.000 0.00 0.00 0.00 2.83
2891 7513 6.430616 TCCGTCCCGTAAAATAAGAATGTTTT 59.569 34.615 0.00 0.00 34.68 2.43
2892 7514 7.040548 TCCGTCCCGTAAAATAAGAATGTTTTT 60.041 33.333 0.00 0.00 32.84 1.94
2893 7515 7.061326 CCGTCCCGTAAAATAAGAATGTTTTTG 59.939 37.037 0.00 0.00 32.84 2.44
2894 7516 7.061326 CGTCCCGTAAAATAAGAATGTTTTTGG 59.939 37.037 0.00 0.00 32.84 3.28
2895 7517 6.869388 TCCCGTAAAATAAGAATGTTTTTGGC 59.131 34.615 0.00 0.00 32.84 4.52
2896 7518 6.647067 CCCGTAAAATAAGAATGTTTTTGGCA 59.353 34.615 0.00 0.00 32.84 4.92
2897 7519 7.359681 CCCGTAAAATAAGAATGTTTTTGGCAC 60.360 37.037 0.00 0.00 32.84 5.01
2898 7520 7.383843 CCGTAAAATAAGAATGTTTTTGGCACT 59.616 33.333 0.00 0.00 32.84 4.40
2899 7521 9.400638 CGTAAAATAAGAATGTTTTTGGCACTA 57.599 29.630 0.00 0.00 32.84 2.74
2929 7551 7.683437 AATATTGTGAGGCATGACATATGAG 57.317 36.000 10.38 0.00 0.00 2.90
2936 7558 4.458397 AGGCATGACATATGAGTTCTTGG 58.542 43.478 10.38 0.00 0.00 3.61
2937 7559 3.004106 GGCATGACATATGAGTTCTTGGC 59.996 47.826 10.38 12.86 0.00 4.52
2938 7560 3.628942 GCATGACATATGAGTTCTTGGCA 59.371 43.478 10.38 0.00 0.00 4.92
2939 7561 4.277672 GCATGACATATGAGTTCTTGGCAT 59.722 41.667 10.38 0.00 38.34 4.40
2944 7566 6.484308 TGACATATGAGTTCTTGGCATACATG 59.516 38.462 10.38 0.00 0.00 3.21
2984 7607 1.748493 GACAACTTGGTGCTTGTGGAA 59.252 47.619 0.00 0.00 30.59 3.53
3036 7660 8.706492 ATGCACTATAATGTTTGTTGAAATGG 57.294 30.769 0.00 0.00 0.00 3.16
3050 7674 7.026631 TGTTGAAATGGTTGTGAAGAACTAG 57.973 36.000 0.00 0.00 0.00 2.57
3055 7680 7.227910 TGAAATGGTTGTGAAGAACTAGTTACC 59.772 37.037 8.42 11.00 26.69 2.85
3071 7696 2.554272 CCGTTTTGGTCGCTTCGG 59.446 61.111 0.00 0.00 0.00 4.30
3072 7697 2.554272 CGTTTTGGTCGCTTCGGG 59.446 61.111 0.00 0.00 0.00 5.14
3073 7698 2.254350 GTTTTGGTCGCTTCGGGC 59.746 61.111 0.00 0.00 37.64 6.13
3074 7699 2.112297 TTTTGGTCGCTTCGGGCT 59.888 55.556 0.52 0.00 39.13 5.19
3075 7700 1.527380 TTTTGGTCGCTTCGGGCTT 60.527 52.632 0.52 0.00 39.13 4.35
3076 7701 1.104577 TTTTGGTCGCTTCGGGCTTT 61.105 50.000 0.52 0.00 39.13 3.51
3077 7702 1.791103 TTTGGTCGCTTCGGGCTTTG 61.791 55.000 0.52 0.00 39.13 2.77
3100 7727 4.037690 GCTGCAACTTTAAACTCACACTG 58.962 43.478 0.00 0.00 0.00 3.66
3142 7769 6.588348 AATTTCCAGTTTCTTTCTTTTGCG 57.412 33.333 0.00 0.00 0.00 4.85
3143 7770 3.708563 TCCAGTTTCTTTCTTTTGCGG 57.291 42.857 0.00 0.00 0.00 5.69
3144 7771 3.020984 TCCAGTTTCTTTCTTTTGCGGT 58.979 40.909 0.00 0.00 0.00 5.68
3145 7772 4.200874 TCCAGTTTCTTTCTTTTGCGGTA 58.799 39.130 0.00 0.00 0.00 4.02
3146 7773 4.035909 TCCAGTTTCTTTCTTTTGCGGTAC 59.964 41.667 0.00 0.00 0.00 3.34
3147 7774 4.201970 CCAGTTTCTTTCTTTTGCGGTACA 60.202 41.667 0.00 0.00 0.00 2.90
3161 7788 3.886505 TGCGGTACAGAAATTTCCAGTTT 59.113 39.130 14.61 0.00 0.00 2.66
3178 7805 6.115446 TCCAGTTTTATATCAGCTTCACCAG 58.885 40.000 0.00 0.00 0.00 4.00
3204 7835 0.464013 TTCCGAAACGAAAGCCACCA 60.464 50.000 0.00 0.00 0.00 4.17
3206 7837 1.574428 CGAAACGAAAGCCACCAGG 59.426 57.895 0.00 0.00 38.23 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.242706 TGTGTCTCATTTGTTGTTCGCAG 60.243 43.478 0.00 0.00 0.00 5.18
4 5 3.548014 GGGTGTGTCTCATTTGTTGTTCG 60.548 47.826 0.00 0.00 0.00 3.95
5 6 3.548014 CGGGTGTGTCTCATTTGTTGTTC 60.548 47.826 0.00 0.00 0.00 3.18
6 7 2.357637 CGGGTGTGTCTCATTTGTTGTT 59.642 45.455 0.00 0.00 0.00 2.83
7 8 1.946768 CGGGTGTGTCTCATTTGTTGT 59.053 47.619 0.00 0.00 0.00 3.32
8 9 2.217750 TCGGGTGTGTCTCATTTGTTG 58.782 47.619 0.00 0.00 0.00 3.33
9 10 2.631160 TCGGGTGTGTCTCATTTGTT 57.369 45.000 0.00 0.00 0.00 2.83
10 11 2.494059 CTTCGGGTGTGTCTCATTTGT 58.506 47.619 0.00 0.00 0.00 2.83
11 12 1.197721 GCTTCGGGTGTGTCTCATTTG 59.802 52.381 0.00 0.00 0.00 2.32
12 13 1.072331 AGCTTCGGGTGTGTCTCATTT 59.928 47.619 0.00 0.00 0.00 2.32
13 14 0.687354 AGCTTCGGGTGTGTCTCATT 59.313 50.000 0.00 0.00 0.00 2.57
14 15 0.247736 GAGCTTCGGGTGTGTCTCAT 59.752 55.000 0.00 0.00 0.00 2.90
15 16 1.666011 GAGCTTCGGGTGTGTCTCA 59.334 57.895 0.00 0.00 0.00 3.27
16 17 1.444553 CGAGCTTCGGGTGTGTCTC 60.445 63.158 0.00 0.00 36.00 3.36
17 18 2.651361 CGAGCTTCGGGTGTGTCT 59.349 61.111 0.00 0.00 36.00 3.41
26 27 4.880537 ATCTGCCGCCGAGCTTCG 62.881 66.667 0.00 0.00 40.07 3.79
27 28 1.648467 AAAATCTGCCGCCGAGCTTC 61.648 55.000 0.00 0.00 0.00 3.86
28 29 1.648467 GAAAATCTGCCGCCGAGCTT 61.648 55.000 0.00 0.00 0.00 3.74
29 30 2.045926 AAAATCTGCCGCCGAGCT 60.046 55.556 0.00 0.00 0.00 4.09
30 31 2.315038 CTGAAAATCTGCCGCCGAGC 62.315 60.000 0.00 0.00 0.00 5.03
31 32 0.740868 TCTGAAAATCTGCCGCCGAG 60.741 55.000 0.00 0.00 0.00 4.63
32 33 0.740868 CTCTGAAAATCTGCCGCCGA 60.741 55.000 0.00 0.00 0.00 5.54
33 34 1.709147 CCTCTGAAAATCTGCCGCCG 61.709 60.000 0.00 0.00 0.00 6.46
34 35 0.678048 ACCTCTGAAAATCTGCCGCC 60.678 55.000 0.00 0.00 0.00 6.13
35 36 0.449388 CACCTCTGAAAATCTGCCGC 59.551 55.000 0.00 0.00 0.00 6.53
36 37 1.466167 CACACCTCTGAAAATCTGCCG 59.534 52.381 0.00 0.00 0.00 5.69
37 38 2.508526 ACACACCTCTGAAAATCTGCC 58.491 47.619 0.00 0.00 0.00 4.85
38 39 4.319177 ACTACACACCTCTGAAAATCTGC 58.681 43.478 0.00 0.00 0.00 4.26
39 40 5.406780 GTGACTACACACCTCTGAAAATCTG 59.593 44.000 0.00 0.00 45.32 2.90
40 41 5.542779 GTGACTACACACCTCTGAAAATCT 58.457 41.667 0.00 0.00 45.32 2.40
41 42 5.847670 GTGACTACACACCTCTGAAAATC 57.152 43.478 0.00 0.00 45.32 2.17
54 55 4.202223 TGGTGAAGAGAAAGGTGACTACAC 60.202 45.833 0.00 0.00 42.68 2.90
55 56 3.964688 TGGTGAAGAGAAAGGTGACTACA 59.035 43.478 0.00 0.00 42.68 2.74
56 57 4.602340 TGGTGAAGAGAAAGGTGACTAC 57.398 45.455 0.00 0.00 42.68 2.73
57 58 5.087323 AGATGGTGAAGAGAAAGGTGACTA 58.913 41.667 0.00 0.00 42.68 2.59
59 60 4.278975 AGATGGTGAAGAGAAAGGTGAC 57.721 45.455 0.00 0.00 0.00 3.67
60 61 4.982241 AAGATGGTGAAGAGAAAGGTGA 57.018 40.909 0.00 0.00 0.00 4.02
61 62 5.065914 TGAAAGATGGTGAAGAGAAAGGTG 58.934 41.667 0.00 0.00 0.00 4.00
62 63 5.310409 TGAAAGATGGTGAAGAGAAAGGT 57.690 39.130 0.00 0.00 0.00 3.50
63 64 5.532406 TGTTGAAAGATGGTGAAGAGAAAGG 59.468 40.000 0.00 0.00 0.00 3.11
64 65 6.293845 CCTGTTGAAAGATGGTGAAGAGAAAG 60.294 42.308 0.00 0.00 0.00 2.62
65 66 5.532406 CCTGTTGAAAGATGGTGAAGAGAAA 59.468 40.000 0.00 0.00 0.00 2.52
66 67 5.065914 CCTGTTGAAAGATGGTGAAGAGAA 58.934 41.667 0.00 0.00 0.00 2.87
67 68 4.505566 CCCTGTTGAAAGATGGTGAAGAGA 60.506 45.833 0.00 0.00 0.00 3.10
68 69 3.755378 CCCTGTTGAAAGATGGTGAAGAG 59.245 47.826 0.00 0.00 0.00 2.85
69 70 3.138283 ACCCTGTTGAAAGATGGTGAAGA 59.862 43.478 0.00 0.00 0.00 2.87
70 71 3.490348 ACCCTGTTGAAAGATGGTGAAG 58.510 45.455 0.00 0.00 0.00 3.02
71 72 3.593442 ACCCTGTTGAAAGATGGTGAA 57.407 42.857 0.00 0.00 0.00 3.18
72 73 3.907474 TCTACCCTGTTGAAAGATGGTGA 59.093 43.478 0.00 0.00 0.00 4.02
73 74 4.003648 GTCTACCCTGTTGAAAGATGGTG 58.996 47.826 0.00 0.00 0.00 4.17
74 75 3.650942 TGTCTACCCTGTTGAAAGATGGT 59.349 43.478 0.00 0.00 0.00 3.55
75 76 4.286297 TGTCTACCCTGTTGAAAGATGG 57.714 45.455 0.00 0.00 0.00 3.51
76 77 5.817816 GGTATGTCTACCCTGTTGAAAGATG 59.182 44.000 0.00 0.00 41.50 2.90
77 78 5.487488 TGGTATGTCTACCCTGTTGAAAGAT 59.513 40.000 0.00 0.00 46.01 2.40
78 79 4.841813 TGGTATGTCTACCCTGTTGAAAGA 59.158 41.667 0.00 0.00 46.01 2.52
79 80 5.160607 TGGTATGTCTACCCTGTTGAAAG 57.839 43.478 0.00 0.00 46.01 2.62
80 81 5.249622 TGATGGTATGTCTACCCTGTTGAAA 59.750 40.000 0.00 0.00 46.01 2.69
81 82 4.780554 TGATGGTATGTCTACCCTGTTGAA 59.219 41.667 0.00 0.00 46.01 2.69
82 83 4.358214 TGATGGTATGTCTACCCTGTTGA 58.642 43.478 0.00 0.00 46.01 3.18
83 84 4.697514 CTGATGGTATGTCTACCCTGTTG 58.302 47.826 0.00 0.00 46.01 3.33
84 85 3.134804 GCTGATGGTATGTCTACCCTGTT 59.865 47.826 0.00 0.00 46.01 3.16
85 86 2.700897 GCTGATGGTATGTCTACCCTGT 59.299 50.000 0.00 0.00 46.01 4.00
86 87 2.700371 TGCTGATGGTATGTCTACCCTG 59.300 50.000 0.00 0.00 46.01 4.45
87 88 3.046283 TGCTGATGGTATGTCTACCCT 57.954 47.619 0.00 0.00 46.01 4.34
88 89 3.134804 AGTTGCTGATGGTATGTCTACCC 59.865 47.826 0.00 0.00 46.01 3.69
89 90 4.408182 AGTTGCTGATGGTATGTCTACC 57.592 45.455 0.00 0.00 46.65 3.18
90 91 6.338146 TGTTAGTTGCTGATGGTATGTCTAC 58.662 40.000 0.00 0.00 0.00 2.59
91 92 6.538945 TGTTAGTTGCTGATGGTATGTCTA 57.461 37.500 0.00 0.00 0.00 2.59
92 93 5.420725 TGTTAGTTGCTGATGGTATGTCT 57.579 39.130 0.00 0.00 0.00 3.41
93 94 5.874810 TCTTGTTAGTTGCTGATGGTATGTC 59.125 40.000 0.00 0.00 0.00 3.06
94 95 5.804639 TCTTGTTAGTTGCTGATGGTATGT 58.195 37.500 0.00 0.00 0.00 2.29
95 96 6.149308 TGTTCTTGTTAGTTGCTGATGGTATG 59.851 38.462 0.00 0.00 0.00 2.39
96 97 6.237901 TGTTCTTGTTAGTTGCTGATGGTAT 58.762 36.000 0.00 0.00 0.00 2.73
97 98 5.616270 TGTTCTTGTTAGTTGCTGATGGTA 58.384 37.500 0.00 0.00 0.00 3.25
98 99 4.460263 TGTTCTTGTTAGTTGCTGATGGT 58.540 39.130 0.00 0.00 0.00 3.55
99 100 5.239306 TCTTGTTCTTGTTAGTTGCTGATGG 59.761 40.000 0.00 0.00 0.00 3.51
100 101 6.304356 TCTTGTTCTTGTTAGTTGCTGATG 57.696 37.500 0.00 0.00 0.00 3.07
101 102 6.318648 TGTTCTTGTTCTTGTTAGTTGCTGAT 59.681 34.615 0.00 0.00 0.00 2.90
102 103 5.645929 TGTTCTTGTTCTTGTTAGTTGCTGA 59.354 36.000 0.00 0.00 0.00 4.26
103 104 5.879237 TGTTCTTGTTCTTGTTAGTTGCTG 58.121 37.500 0.00 0.00 0.00 4.41
104 105 6.460123 CCATGTTCTTGTTCTTGTTAGTTGCT 60.460 38.462 0.00 0.00 0.00 3.91
105 106 5.687285 CCATGTTCTTGTTCTTGTTAGTTGC 59.313 40.000 0.00 0.00 0.00 4.17
106 107 5.687285 GCCATGTTCTTGTTCTTGTTAGTTG 59.313 40.000 0.00 0.00 0.00 3.16
107 108 5.359576 TGCCATGTTCTTGTTCTTGTTAGTT 59.640 36.000 0.00 0.00 0.00 2.24
108 109 4.887071 TGCCATGTTCTTGTTCTTGTTAGT 59.113 37.500 0.00 0.00 0.00 2.24
109 110 5.239306 TCTGCCATGTTCTTGTTCTTGTTAG 59.761 40.000 0.00 0.00 0.00 2.34
110 111 5.008613 GTCTGCCATGTTCTTGTTCTTGTTA 59.991 40.000 0.00 0.00 0.00 2.41
111 112 3.953612 TCTGCCATGTTCTTGTTCTTGTT 59.046 39.130 0.00 0.00 0.00 2.83
112 113 3.316308 GTCTGCCATGTTCTTGTTCTTGT 59.684 43.478 0.00 0.00 0.00 3.16
113 114 3.316029 TGTCTGCCATGTTCTTGTTCTTG 59.684 43.478 0.00 0.00 0.00 3.02
114 115 3.554934 TGTCTGCCATGTTCTTGTTCTT 58.445 40.909 0.00 0.00 0.00 2.52
115 116 3.213206 TGTCTGCCATGTTCTTGTTCT 57.787 42.857 0.00 0.00 0.00 3.01
116 117 3.829948 CATGTCTGCCATGTTCTTGTTC 58.170 45.455 0.00 0.00 44.96 3.18
117 118 3.928727 CATGTCTGCCATGTTCTTGTT 57.071 42.857 0.00 0.00 44.96 2.83
130 131 4.827087 AGCTCGCCGCCATGTCTG 62.827 66.667 0.00 0.00 40.39 3.51
131 132 4.521062 GAGCTCGCCGCCATGTCT 62.521 66.667 0.00 0.00 40.39 3.41
132 133 4.819761 TGAGCTCGCCGCCATGTC 62.820 66.667 9.64 0.00 40.39 3.06
133 134 4.166888 ATGAGCTCGCCGCCATGT 62.167 61.111 9.64 0.00 40.39 3.21
134 135 3.344215 GATGAGCTCGCCGCCATG 61.344 66.667 9.64 0.00 40.39 3.66
135 136 3.512223 GAGATGAGCTCGCCGCCAT 62.512 63.158 9.64 0.00 40.39 4.40
136 137 4.212913 GAGATGAGCTCGCCGCCA 62.213 66.667 9.64 0.00 40.39 5.69
149 150 1.412074 GCCACCCCCATTGATTGAGAT 60.412 52.381 0.00 0.00 0.00 2.75
178 179 2.671070 CCACCATGGTCGGCTCTT 59.329 61.111 16.53 0.00 31.35 2.85
179 180 4.101448 GCCACCATGGTCGGCTCT 62.101 66.667 33.48 6.97 40.46 4.09
246 247 1.141657 GCTGGCCATCCTCATCTGTTA 59.858 52.381 5.51 0.00 0.00 2.41
267 268 2.705658 TCTTAATGTCGGATCAGCCCAT 59.294 45.455 0.00 0.00 0.00 4.00
269 270 2.910688 TCTTAATGTCGGATCAGCCC 57.089 50.000 0.00 0.00 0.00 5.19
273 274 4.499188 GGACGTGATCTTAATGTCGGATCA 60.499 45.833 0.00 0.00 42.06 2.92
275 276 3.383505 TGGACGTGATCTTAATGTCGGAT 59.616 43.478 0.00 0.00 34.91 4.18
284 285 2.575108 ACGCCTGGACGTGATCTTA 58.425 52.632 13.83 0.00 46.28 2.10
298 299 1.814169 GAGGAAATCCGGACACGCC 60.814 63.158 6.12 6.31 42.08 5.68
328 329 4.770531 ACCCCTTAAATCCAACTTGTAAGC 59.229 41.667 0.00 0.00 0.00 3.09
352 353 4.437239 CTCAAATGTCCGAGCTATCTTGT 58.563 43.478 0.00 0.00 0.00 3.16
375 376 1.123928 GTCTGACCTCCCATACCTGG 58.876 60.000 0.00 0.00 42.73 4.45
384 385 2.665603 GCACCCTGTCTGACCTCC 59.334 66.667 5.17 0.00 0.00 4.30
386 387 3.314331 CCGCACCCTGTCTGACCT 61.314 66.667 5.17 0.00 0.00 3.85
391 392 1.247567 CAAAAATCCGCACCCTGTCT 58.752 50.000 0.00 0.00 0.00 3.41
392 393 0.243636 CCAAAAATCCGCACCCTGTC 59.756 55.000 0.00 0.00 0.00 3.51
394 395 0.243636 GACCAAAAATCCGCACCCTG 59.756 55.000 0.00 0.00 0.00 4.45
400 401 1.215382 GCCCTGACCAAAAATCCGC 59.785 57.895 0.00 0.00 0.00 5.54
442 443 4.719026 ATCTACATCCGGACCTACTACA 57.281 45.455 6.12 0.00 0.00 2.74
448 449 2.106166 ACGAGTATCTACATCCGGACCT 59.894 50.000 6.12 0.00 0.00 3.85
472 473 7.703621 GCAAGCAAAACATCACTTCATATACAT 59.296 33.333 0.00 0.00 0.00 2.29
474 475 6.473455 GGCAAGCAAAACATCACTTCATATAC 59.527 38.462 0.00 0.00 0.00 1.47
477 478 4.280425 TGGCAAGCAAAACATCACTTCATA 59.720 37.500 0.00 0.00 0.00 2.15
478 479 3.069872 TGGCAAGCAAAACATCACTTCAT 59.930 39.130 0.00 0.00 0.00 2.57
480 481 3.096489 TGGCAAGCAAAACATCACTTC 57.904 42.857 0.00 0.00 0.00 3.01
481 482 3.181463 ACATGGCAAGCAAAACATCACTT 60.181 39.130 0.00 0.00 0.00 3.16
489 3447 4.447054 CGAACATTTACATGGCAAGCAAAA 59.553 37.500 0.00 0.00 34.27 2.44
519 3477 3.811722 TTATTGCAGAGTTCAGTTGCG 57.188 42.857 0.00 0.00 40.62 4.85
603 3562 0.038159 GTCAGGAGTGTCGGTTCCAG 60.038 60.000 0.00 0.00 35.88 3.86
674 3634 9.232473 AGGAGGATTTTAAACATGTTTCTAGTC 57.768 33.333 26.46 19.15 34.23 2.59
729 3689 1.471153 GCTAGCTTGGGTCCTACGTTC 60.471 57.143 7.70 0.00 0.00 3.95
757 3718 2.673368 CGCTCTAACTGGGAATGTTCAC 59.327 50.000 0.00 0.00 0.00 3.18
770 3731 7.168637 TGGTTATTTATTGACGATCGCTCTAAC 59.831 37.037 16.60 13.35 0.00 2.34
794 3755 0.612732 TGCTTGAGGGCTGGAAATGG 60.613 55.000 0.00 0.00 0.00 3.16
816 3777 0.834612 TCCAACGTGTTCTTGACCCT 59.165 50.000 0.00 0.00 0.00 4.34
866 3827 9.238368 TCTCTCTCCAACTTTGTTTTCTTTTAA 57.762 29.630 0.00 0.00 0.00 1.52
907 3893 0.679505 TCTTTCAGAGTGGGGACGTG 59.320 55.000 0.00 0.00 0.00 4.49
932 3920 1.301716 GCTGCGTGACAAGGGAGAA 60.302 57.895 1.15 0.00 31.87 2.87
1022 4014 7.344352 TGCATACCTGTGTATATATATGCCAGA 59.656 37.037 20.53 10.31 42.64 3.86
1055 4047 1.227147 GGCGCCTTGTATGCTACGA 60.227 57.895 22.15 0.00 0.00 3.43
1175 4170 0.614979 TCCCTTCTCCTACGCTTGCT 60.615 55.000 0.00 0.00 0.00 3.91
1190 4185 2.007636 AGGTTCTCTCTTCTCCTCCCT 58.992 52.381 0.00 0.00 0.00 4.20
1192 4187 5.454966 AGAATAGGTTCTCTCTTCTCCTCC 58.545 45.833 0.00 0.00 40.68 4.30
1253 4248 4.421479 GCCCGCGGATCGATCGAT 62.421 66.667 29.76 29.76 41.67 3.59
1268 4267 0.318120 CACCCTTGGAACATTGTGCC 59.682 55.000 6.89 6.89 39.30 5.01
1279 4278 4.974721 AACAGGCCGCACCCTTGG 62.975 66.667 0.00 0.00 40.58 3.61
1657 4659 3.288308 CTCGAAGACCAGCACGCCT 62.288 63.158 0.00 0.00 0.00 5.52
1852 4857 3.047280 GCGTCCATGTTGCCGTCA 61.047 61.111 0.00 0.00 0.00 4.35
1999 5010 0.956633 ACACGTCGCTCTCCTTGTTA 59.043 50.000 0.00 0.00 0.00 2.41
2006 5017 0.109689 AAGCTGTACACGTCGCTCTC 60.110 55.000 7.70 0.00 31.30 3.20
2183 5194 3.735029 GAGCTCCACGACGACGGT 61.735 66.667 12.58 0.00 44.46 4.83
2355 5369 6.086222 ACTATTCACAAATCACAATCAACGC 58.914 36.000 0.00 0.00 0.00 4.84
2356 5370 9.773328 ATTACTATTCACAAATCACAATCAACG 57.227 29.630 0.00 0.00 0.00 4.10
2542 5561 2.100087 TGATACGCGCCAGAATTAGACA 59.900 45.455 5.73 0.00 0.00 3.41
2622 5642 3.578716 GCTTGTCCTCCACCAGCTATATA 59.421 47.826 0.00 0.00 40.08 0.86
2623 5643 2.370189 GCTTGTCCTCCACCAGCTATAT 59.630 50.000 0.00 0.00 40.08 0.86
2624 5644 1.762957 GCTTGTCCTCCACCAGCTATA 59.237 52.381 0.00 0.00 40.08 1.31
2705 5725 3.256879 TGTCAACAAAAACAGCTTGTCCA 59.743 39.130 0.00 0.00 35.98 4.02
2707 5727 4.558860 GTCTGTCAACAAAAACAGCTTGTC 59.441 41.667 0.00 0.00 42.10 3.18
2709 5729 3.543494 CGTCTGTCAACAAAAACAGCTTG 59.457 43.478 0.00 0.00 42.10 4.01
2710 5730 3.190535 ACGTCTGTCAACAAAAACAGCTT 59.809 39.130 0.00 0.00 42.10 3.74
2711 5731 2.747446 ACGTCTGTCAACAAAAACAGCT 59.253 40.909 0.00 0.00 42.10 4.24
2713 5733 5.464965 AGTACGTCTGTCAACAAAAACAG 57.535 39.130 0.00 0.00 43.41 3.16
2714 5734 5.868258 TGTAGTACGTCTGTCAACAAAAACA 59.132 36.000 0.00 0.00 0.00 2.83
2715 5735 6.335176 TGTAGTACGTCTGTCAACAAAAAC 57.665 37.500 0.00 0.00 0.00 2.43
2716 5736 6.368243 TGTTGTAGTACGTCTGTCAACAAAAA 59.632 34.615 21.74 10.73 42.59 1.94
2717 5737 5.868258 TGTTGTAGTACGTCTGTCAACAAAA 59.132 36.000 21.74 9.55 42.59 2.44
2718 5738 5.289193 GTGTTGTAGTACGTCTGTCAACAAA 59.711 40.000 23.45 12.29 44.50 2.83
2719 5739 4.799949 GTGTTGTAGTACGTCTGTCAACAA 59.200 41.667 23.45 13.57 44.50 2.83
2720 5740 4.353737 GTGTTGTAGTACGTCTGTCAACA 58.646 43.478 21.02 21.02 42.91 3.33
2721 5741 3.732721 GGTGTTGTAGTACGTCTGTCAAC 59.267 47.826 18.48 18.48 39.80 3.18
2722 5742 3.380954 TGGTGTTGTAGTACGTCTGTCAA 59.619 43.478 0.00 0.00 0.00 3.18
2723 5743 2.950975 TGGTGTTGTAGTACGTCTGTCA 59.049 45.455 0.00 0.00 0.00 3.58
2724 5744 3.631145 TGGTGTTGTAGTACGTCTGTC 57.369 47.619 0.00 0.00 0.00 3.51
2739 5759 3.806380 TGTTAACGTACATGGTTGGTGT 58.194 40.909 0.26 0.00 0.00 4.16
2773 5793 1.064952 CGTTTGAAACCCGCTTGACTT 59.935 47.619 2.00 0.00 0.00 3.01
2775 5795 0.317519 CCGTTTGAAACCCGCTTGAC 60.318 55.000 2.00 0.00 0.00 3.18
2776 5796 1.448922 CCCGTTTGAAACCCGCTTGA 61.449 55.000 2.00 0.00 0.00 3.02
2781 5801 1.730451 AACTGCCCGTTTGAAACCCG 61.730 55.000 2.00 0.00 29.63 5.28
2794 5814 5.215160 CAGAGTTTTCACAATGTAACTGCC 58.785 41.667 4.91 0.00 31.41 4.85
2795 5815 4.676924 GCAGAGTTTTCACAATGTAACTGC 59.323 41.667 4.91 0.00 31.41 4.40
2803 5833 1.537202 GAGCCGCAGAGTTTTCACAAT 59.463 47.619 0.00 0.00 0.00 2.71
2804 5834 0.944386 GAGCCGCAGAGTTTTCACAA 59.056 50.000 0.00 0.00 0.00 3.33
2807 5837 2.831685 TAAGAGCCGCAGAGTTTTCA 57.168 45.000 0.00 0.00 0.00 2.69
2808 5838 4.686839 AAATAAGAGCCGCAGAGTTTTC 57.313 40.909 0.00 0.00 0.00 2.29
2813 5843 2.872858 GGGTAAAATAAGAGCCGCAGAG 59.127 50.000 0.00 0.00 0.00 3.35
2816 5846 2.026636 AGTGGGTAAAATAAGAGCCGCA 60.027 45.455 6.46 0.00 44.40 5.69
2819 5849 7.033791 GCTTTAAAGTGGGTAAAATAAGAGCC 58.966 38.462 16.38 0.00 0.00 4.70
2836 7458 6.404712 AGAACGATTAGAACGGCTTTAAAG 57.595 37.500 11.02 11.02 34.93 1.85
2846 7468 4.261114 CGGAGGGAGTAGAACGATTAGAAC 60.261 50.000 0.00 0.00 0.00 3.01
2849 7471 3.212685 ACGGAGGGAGTAGAACGATTAG 58.787 50.000 0.00 0.00 0.00 1.73
2851 7473 2.022934 GACGGAGGGAGTAGAACGATT 58.977 52.381 0.00 0.00 0.00 3.34
2855 7477 2.502633 GGGACGGAGGGAGTAGAAC 58.497 63.158 0.00 0.00 0.00 3.01
2869 7491 7.148705 GCCAAAAACATTCTTATTTTACGGGAC 60.149 37.037 0.00 0.00 0.00 4.46
2870 7492 6.869388 GCCAAAAACATTCTTATTTTACGGGA 59.131 34.615 0.00 0.00 0.00 5.14
2871 7493 6.647067 TGCCAAAAACATTCTTATTTTACGGG 59.353 34.615 0.00 0.00 0.00 5.28
2872 7494 7.383843 AGTGCCAAAAACATTCTTATTTTACGG 59.616 33.333 0.00 0.00 0.00 4.02
2873 7495 8.293114 AGTGCCAAAAACATTCTTATTTTACG 57.707 30.769 0.00 0.00 0.00 3.18
2876 7498 9.040939 GTGTAGTGCCAAAAACATTCTTATTTT 57.959 29.630 0.00 0.00 0.00 1.82
2877 7499 8.200792 TGTGTAGTGCCAAAAACATTCTTATTT 58.799 29.630 0.00 0.00 0.00 1.40
2878 7500 7.721402 TGTGTAGTGCCAAAAACATTCTTATT 58.279 30.769 0.00 0.00 0.00 1.40
2879 7501 7.283625 TGTGTAGTGCCAAAAACATTCTTAT 57.716 32.000 0.00 0.00 0.00 1.73
2880 7502 6.701145 TGTGTAGTGCCAAAAACATTCTTA 57.299 33.333 0.00 0.00 0.00 2.10
2881 7503 5.590530 TGTGTAGTGCCAAAAACATTCTT 57.409 34.783 0.00 0.00 0.00 2.52
2882 7504 5.590530 TTGTGTAGTGCCAAAAACATTCT 57.409 34.783 0.00 0.00 0.00 2.40
2883 7505 6.654793 TTTTGTGTAGTGCCAAAAACATTC 57.345 33.333 5.56 0.00 37.55 2.67
2884 7506 8.900983 ATATTTTGTGTAGTGCCAAAAACATT 57.099 26.923 10.09 0.76 42.07 2.71
2885 7507 8.772705 CAATATTTTGTGTAGTGCCAAAAACAT 58.227 29.630 10.09 6.00 42.07 2.71
2886 7508 7.766278 ACAATATTTTGTGTAGTGCCAAAAACA 59.234 29.630 0.33 4.54 44.36 2.83
2887 7509 8.137210 ACAATATTTTGTGTAGTGCCAAAAAC 57.863 30.769 0.33 0.00 44.36 2.43
2912 7534 5.121105 CAAGAACTCATATGTCATGCCTCA 58.879 41.667 1.90 0.00 0.00 3.86
2939 7561 9.660180 TCAGTATTTACTACAACAATGCATGTA 57.340 29.630 0.00 0.00 36.53 2.29
2944 7566 8.504005 AGTTGTCAGTATTTACTACAACAATGC 58.496 33.333 24.91 12.99 43.48 3.56
2962 7584 1.066002 CCACAAGCACCAAGTTGTCAG 59.934 52.381 1.45 0.00 34.62 3.51
3015 7638 9.474920 CACAACCATTTCAACAAACATTATAGT 57.525 29.630 0.00 0.00 0.00 2.12
3019 7643 8.253810 TCTTCACAACCATTTCAACAAACATTA 58.746 29.630 0.00 0.00 0.00 1.90
3028 7652 7.639113 AACTAGTTCTTCACAACCATTTCAA 57.361 32.000 1.12 0.00 0.00 2.69
3031 7655 6.204108 CGGTAACTAGTTCTTCACAACCATTT 59.796 38.462 12.39 0.00 0.00 2.32
3036 7660 6.594284 AAACGGTAACTAGTTCTTCACAAC 57.406 37.500 12.39 2.53 0.00 3.32
3055 7680 2.554272 CCCGAAGCGACCAAAACG 59.446 61.111 0.00 0.00 0.00 3.60
3071 7696 2.524569 TTAAAGTTGCAGCCAAAGCC 57.475 45.000 0.00 0.00 41.25 4.35
3072 7697 3.457234 AGTTTAAAGTTGCAGCCAAAGC 58.543 40.909 0.00 0.00 40.32 3.51
3073 7698 4.504097 GTGAGTTTAAAGTTGCAGCCAAAG 59.496 41.667 0.00 0.00 31.68 2.77
3074 7699 4.081972 TGTGAGTTTAAAGTTGCAGCCAAA 60.082 37.500 0.00 0.00 31.68 3.28
3075 7700 3.445450 TGTGAGTTTAAAGTTGCAGCCAA 59.555 39.130 0.00 0.00 0.00 4.52
3076 7701 3.020274 TGTGAGTTTAAAGTTGCAGCCA 58.980 40.909 0.00 0.00 0.00 4.75
3077 7702 3.066760 AGTGTGAGTTTAAAGTTGCAGCC 59.933 43.478 0.00 0.00 0.00 4.85
3117 7744 7.223777 CCGCAAAAGAAAGAAACTGGAAATTTA 59.776 33.333 0.00 0.00 0.00 1.40
3118 7745 6.037062 CCGCAAAAGAAAGAAACTGGAAATTT 59.963 34.615 0.00 0.00 0.00 1.82
3120 7747 5.049828 CCGCAAAAGAAAGAAACTGGAAAT 58.950 37.500 0.00 0.00 0.00 2.17
3121 7748 4.081917 ACCGCAAAAGAAAGAAACTGGAAA 60.082 37.500 0.00 0.00 0.00 3.13
3122 7749 3.445805 ACCGCAAAAGAAAGAAACTGGAA 59.554 39.130 0.00 0.00 0.00 3.53
3123 7750 3.020984 ACCGCAAAAGAAAGAAACTGGA 58.979 40.909 0.00 0.00 0.00 3.86
3124 7751 3.436700 ACCGCAAAAGAAAGAAACTGG 57.563 42.857 0.00 0.00 0.00 4.00
3125 7752 4.915704 TGTACCGCAAAAGAAAGAAACTG 58.084 39.130 0.00 0.00 0.00 3.16
3126 7753 4.879545 TCTGTACCGCAAAAGAAAGAAACT 59.120 37.500 0.00 0.00 0.00 2.66
3127 7754 5.164606 TCTGTACCGCAAAAGAAAGAAAC 57.835 39.130 0.00 0.00 0.00 2.78
3128 7755 5.821516 TTCTGTACCGCAAAAGAAAGAAA 57.178 34.783 0.00 0.00 0.00 2.52
3129 7756 5.821516 TTTCTGTACCGCAAAAGAAAGAA 57.178 34.783 0.93 0.00 34.56 2.52
3130 7757 6.385649 AATTTCTGTACCGCAAAAGAAAGA 57.614 33.333 9.02 0.00 40.79 2.52
3131 7758 6.143919 GGAAATTTCTGTACCGCAAAAGAAAG 59.856 38.462 17.42 0.00 40.79 2.62
3132 7759 5.980715 GGAAATTTCTGTACCGCAAAAGAAA 59.019 36.000 17.42 6.34 41.47 2.52
3133 7760 5.067936 TGGAAATTTCTGTACCGCAAAAGAA 59.932 36.000 17.42 0.00 0.00 2.52
3134 7761 4.580995 TGGAAATTTCTGTACCGCAAAAGA 59.419 37.500 17.42 0.00 0.00 2.52
3135 7762 4.865776 TGGAAATTTCTGTACCGCAAAAG 58.134 39.130 17.42 0.00 0.00 2.27
3136 7763 4.339814 ACTGGAAATTTCTGTACCGCAAAA 59.660 37.500 17.42 0.00 0.00 2.44
3137 7764 3.886505 ACTGGAAATTTCTGTACCGCAAA 59.113 39.130 17.42 0.00 0.00 3.68
3138 7765 3.482436 ACTGGAAATTTCTGTACCGCAA 58.518 40.909 17.42 0.00 0.00 4.85
3139 7766 3.134574 ACTGGAAATTTCTGTACCGCA 57.865 42.857 17.42 4.76 0.00 5.69
3140 7767 4.499037 AAACTGGAAATTTCTGTACCGC 57.501 40.909 17.42 0.22 0.00 5.68
3141 7768 9.931210 GATATAAAACTGGAAATTTCTGTACCG 57.069 33.333 17.42 0.81 0.00 4.02
3145 7772 9.247861 AGCTGATATAAAACTGGAAATTTCTGT 57.752 29.630 17.42 13.32 0.00 3.41
3178 7805 3.161306 GCTTTCGTTTCGGAATGCTTAC 58.839 45.455 6.08 0.00 41.35 2.34
3204 7835 0.402121 GGCCAGAACACTTTCTCCCT 59.598 55.000 0.00 0.00 40.34 4.20
3206 7837 1.202818 AGTGGCCAGAACACTTTCTCC 60.203 52.381 5.11 0.00 46.38 3.71


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

AutoCloner maintained by Alex Coulton.