Multiple sequence alignment - TraesCS2D01G304700

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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 TraesCS2D01G304700 chr2D 100.000 2597 0 0 1 2597 390419402 390416806 0.000000e+00 4796.0
1 TraesCS2D01G304700 chr2A 93.771 1172 33 11 805 1956 526742584 526741433 0.000000e+00 1724.0
2 TraesCS2D01G304700 chr2A 89.925 665 23 13 1954 2597 526741293 526740652 0.000000e+00 817.0
3 TraesCS2D01G304700 chr2A 85.158 539 52 15 246 775 526743344 526742825 6.370000e-146 527.0
4 TraesCS2D01G304700 chr2A 91.566 249 21 0 1 249 526884258 526884010 6.880000e-91 344.0
5 TraesCS2D01G304700 chr2B 94.838 988 31 6 747 1731 461576554 461575584 0.000000e+00 1524.0
6 TraesCS2D01G304700 chr2B 96.620 355 7 3 1800 2153 461575587 461575237 3.720000e-163 584.0
7 TraesCS2D01G304700 chr2B 91.521 401 25 4 2201 2597 461572159 461571764 6.320000e-151 544.0
8 TraesCS2D01G304700 chr2B 97.368 38 1 0 2150 2187 461572556 461572519 6.000000e-07 65.8


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 TraesCS2D01G304700 chr2D 390416806 390419402 2596 True 4796.000000 4796 100.00000 1 2597 1 chr2D.!!$R1 2596
1 TraesCS2D01G304700 chr2A 526740652 526743344 2692 True 1022.666667 1724 89.61800 246 2597 3 chr2A.!!$R2 2351
2 TraesCS2D01G304700 chr2B 461571764 461576554 4790 True 679.450000 1524 95.08675 747 2597 4 chr2B.!!$R1 1850

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
586 587 0.035056 GTGGGATCAAGGTGGGTCAG 60.035 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2503 5960 0.179018 GCCAAATCCGCTGTCCCTAT 60.179 55.0 0.0 0.0 0.0 2.57 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
19 20 4.847444 GCAGGCTCGGAGGGCTTC 62.847 72.222 7.20 0.00 40.17 3.86
20 21 4.168291 CAGGCTCGGAGGGCTTCC 62.168 72.222 5.40 5.40 43.04 3.46
21 22 4.406763 AGGCTCGGAGGGCTTCCT 62.407 66.667 14.27 1.18 44.41 3.36
32 33 2.413601 AGGGCTTCCTCTTTCCTATCC 58.586 52.381 0.00 0.00 35.60 2.59
33 34 2.127708 GGGCTTCCTCTTTCCTATCCA 58.872 52.381 0.00 0.00 0.00 3.41
34 35 2.713708 GGGCTTCCTCTTTCCTATCCAT 59.286 50.000 0.00 0.00 0.00 3.41
35 36 3.497584 GGGCTTCCTCTTTCCTATCCATG 60.498 52.174 0.00 0.00 0.00 3.66
36 37 3.497584 GGCTTCCTCTTTCCTATCCATGG 60.498 52.174 4.97 4.97 0.00 3.66
37 38 3.749226 CTTCCTCTTTCCTATCCATGGC 58.251 50.000 6.96 0.00 0.00 4.40
38 39 1.694150 TCCTCTTTCCTATCCATGGCG 59.306 52.381 6.96 0.00 0.00 5.69
39 40 1.271054 CCTCTTTCCTATCCATGGCGG 60.271 57.143 6.96 7.55 0.00 6.13
40 41 1.417890 CTCTTTCCTATCCATGGCGGT 59.582 52.381 6.96 0.00 35.57 5.68
41 42 1.140852 TCTTTCCTATCCATGGCGGTG 59.859 52.381 6.96 0.00 35.57 4.94
42 43 0.916086 TTTCCTATCCATGGCGGTGT 59.084 50.000 6.96 0.00 35.57 4.16
43 44 0.180171 TTCCTATCCATGGCGGTGTG 59.820 55.000 6.96 0.00 35.57 3.82
44 45 0.980754 TCCTATCCATGGCGGTGTGT 60.981 55.000 6.96 0.00 35.57 3.72
45 46 0.815213 CCTATCCATGGCGGTGTGTG 60.815 60.000 6.96 0.00 35.57 3.82
46 47 0.177836 CTATCCATGGCGGTGTGTGA 59.822 55.000 6.96 0.00 35.57 3.58
47 48 0.107897 TATCCATGGCGGTGTGTGAC 60.108 55.000 6.96 0.00 35.57 3.67
48 49 1.841302 ATCCATGGCGGTGTGTGACT 61.841 55.000 6.96 0.00 35.57 3.41
49 50 2.034879 CCATGGCGGTGTGTGACTC 61.035 63.158 0.00 0.00 0.00 3.36
50 51 2.034879 CATGGCGGTGTGTGACTCC 61.035 63.158 0.00 0.00 0.00 3.85
55 56 2.048127 GGTGTGTGACTCCGGCTC 60.048 66.667 0.00 0.00 0.00 4.70
56 57 2.574955 GGTGTGTGACTCCGGCTCT 61.575 63.158 0.00 0.00 0.00 4.09
57 58 1.373497 GTGTGTGACTCCGGCTCTG 60.373 63.158 0.00 0.00 0.00 3.35
58 59 1.832608 TGTGTGACTCCGGCTCTGT 60.833 57.895 0.00 0.00 0.00 3.41
59 60 1.373497 GTGTGACTCCGGCTCTGTG 60.373 63.158 0.00 0.00 0.00 3.66
60 61 2.262915 GTGACTCCGGCTCTGTGG 59.737 66.667 0.00 0.00 0.00 4.17
61 62 3.695606 TGACTCCGGCTCTGTGGC 61.696 66.667 0.00 0.00 37.94 5.01
62 63 3.386237 GACTCCGGCTCTGTGGCT 61.386 66.667 0.00 0.00 39.32 4.75
63 64 2.925170 ACTCCGGCTCTGTGGCTT 60.925 61.111 0.00 0.00 39.32 4.35
64 65 2.125350 CTCCGGCTCTGTGGCTTC 60.125 66.667 0.00 0.00 39.32 3.86
65 66 3.672295 CTCCGGCTCTGTGGCTTCC 62.672 68.421 0.00 0.00 39.32 3.46
66 67 4.785453 CCGGCTCTGTGGCTTCCC 62.785 72.222 0.00 0.00 39.32 3.97
67 68 4.020617 CGGCTCTGTGGCTTCCCA 62.021 66.667 1.84 0.00 39.32 4.37
76 77 3.081409 GGCTTCCCACGCCCTCTA 61.081 66.667 0.00 0.00 41.73 2.43
77 78 2.187163 GCTTCCCACGCCCTCTAC 59.813 66.667 0.00 0.00 0.00 2.59
78 79 2.901042 CTTCCCACGCCCTCTACC 59.099 66.667 0.00 0.00 0.00 3.18
79 80 1.686110 CTTCCCACGCCCTCTACCT 60.686 63.158 0.00 0.00 0.00 3.08
80 81 1.677637 CTTCCCACGCCCTCTACCTC 61.678 65.000 0.00 0.00 0.00 3.85
81 82 3.528370 CCCACGCCCTCTACCTCG 61.528 72.222 0.00 0.00 0.00 4.63
82 83 4.208686 CCACGCCCTCTACCTCGC 62.209 72.222 0.00 0.00 0.00 5.03
83 84 3.449227 CACGCCCTCTACCTCGCA 61.449 66.667 0.00 0.00 0.00 5.10
84 85 2.442272 ACGCCCTCTACCTCGCAT 60.442 61.111 0.00 0.00 0.00 4.73
85 86 2.028190 CGCCCTCTACCTCGCATG 59.972 66.667 0.00 0.00 0.00 4.06
86 87 2.490148 CGCCCTCTACCTCGCATGA 61.490 63.158 0.00 0.00 0.00 3.07
87 88 1.068250 GCCCTCTACCTCGCATGAC 59.932 63.158 0.00 0.00 0.00 3.06
88 89 1.360551 CCCTCTACCTCGCATGACG 59.639 63.158 0.00 0.00 45.62 4.35
89 90 1.360551 CCTCTACCTCGCATGACGG 59.639 63.158 0.00 0.00 43.89 4.79
90 91 1.360551 CTCTACCTCGCATGACGGG 59.639 63.158 0.00 0.00 44.02 5.28
91 92 2.279517 CTACCTCGCATGACGGGC 60.280 66.667 0.00 0.00 42.61 6.13
92 93 3.071837 TACCTCGCATGACGGGCA 61.072 61.111 0.00 0.00 42.61 5.36
93 94 3.365291 TACCTCGCATGACGGGCAC 62.365 63.158 0.00 0.00 42.61 5.01
109 110 4.388499 ACGCCGGTCCTTCGCATT 62.388 61.111 1.90 0.00 0.00 3.56
110 111 3.864686 CGCCGGTCCTTCGCATTG 61.865 66.667 1.90 0.00 0.00 2.82
111 112 3.508840 GCCGGTCCTTCGCATTGG 61.509 66.667 1.90 0.00 0.00 3.16
112 113 3.508840 CCGGTCCTTCGCATTGGC 61.509 66.667 0.00 0.00 0.00 4.52
113 114 2.436646 CGGTCCTTCGCATTGGCT 60.437 61.111 0.00 0.00 38.10 4.75
114 115 1.153449 CGGTCCTTCGCATTGGCTA 60.153 57.895 0.00 0.00 38.10 3.93
115 116 1.154205 CGGTCCTTCGCATTGGCTAG 61.154 60.000 0.00 0.00 38.10 3.42
116 117 0.815615 GGTCCTTCGCATTGGCTAGG 60.816 60.000 0.00 0.00 39.51 3.02
117 118 1.153168 TCCTTCGCATTGGCTAGGC 60.153 57.895 9.85 9.85 38.60 3.93
135 136 2.508439 CGTAAGGCATGCCGACGT 60.508 61.111 38.09 25.79 41.81 4.34
136 137 2.098233 CGTAAGGCATGCCGACGTT 61.098 57.895 38.09 27.62 41.81 3.99
137 138 1.423845 GTAAGGCATGCCGACGTTG 59.576 57.895 30.50 0.00 41.95 4.10
138 139 1.017177 GTAAGGCATGCCGACGTTGA 61.017 55.000 30.50 3.11 41.95 3.18
139 140 1.017177 TAAGGCATGCCGACGTTGAC 61.017 55.000 30.50 3.75 41.95 3.18
140 141 3.799755 GGCATGCCGACGTTGACC 61.800 66.667 23.48 0.00 0.00 4.02
141 142 2.742372 GCATGCCGACGTTGACCT 60.742 61.111 6.36 0.00 0.00 3.85
142 143 2.325082 GCATGCCGACGTTGACCTT 61.325 57.895 6.36 0.00 0.00 3.50
143 144 1.852067 GCATGCCGACGTTGACCTTT 61.852 55.000 6.36 0.00 0.00 3.11
144 145 0.110238 CATGCCGACGTTGACCTTTG 60.110 55.000 3.74 0.00 0.00 2.77
145 146 0.250124 ATGCCGACGTTGACCTTTGA 60.250 50.000 3.74 0.00 0.00 2.69
146 147 0.462225 TGCCGACGTTGACCTTTGAA 60.462 50.000 3.74 0.00 0.00 2.69
147 148 0.872388 GCCGACGTTGACCTTTGAAT 59.128 50.000 3.74 0.00 0.00 2.57
148 149 1.136057 GCCGACGTTGACCTTTGAATC 60.136 52.381 3.74 0.00 0.00 2.52
149 150 1.126113 CCGACGTTGACCTTTGAATCG 59.874 52.381 3.74 0.00 0.00 3.34
150 151 1.126113 CGACGTTGACCTTTGAATCGG 59.874 52.381 0.00 0.00 0.00 4.18
151 152 2.409975 GACGTTGACCTTTGAATCGGA 58.590 47.619 0.00 0.00 0.00 4.55
152 153 2.412089 GACGTTGACCTTTGAATCGGAG 59.588 50.000 0.00 0.00 0.00 4.63
153 154 1.128692 CGTTGACCTTTGAATCGGAGC 59.871 52.381 0.00 0.00 0.00 4.70
154 155 1.468914 GTTGACCTTTGAATCGGAGCC 59.531 52.381 0.00 0.00 0.00 4.70
155 156 0.035439 TGACCTTTGAATCGGAGCCC 60.035 55.000 0.00 0.00 0.00 5.19
181 182 4.035102 GGGGAGGAGGTGCCACAC 62.035 72.222 0.00 0.00 38.84 3.82
182 183 2.930562 GGGAGGAGGTGCCACACT 60.931 66.667 0.00 0.00 40.02 3.55
183 184 2.348998 GGAGGAGGTGCCACACTG 59.651 66.667 0.00 0.00 40.02 3.66
184 185 2.348998 GAGGAGGTGCCACACTGG 59.651 66.667 0.00 0.00 41.55 4.00
185 186 3.252284 AGGAGGTGCCACACTGGG 61.252 66.667 0.00 0.00 38.19 4.45
186 187 4.351054 GGAGGTGCCACACTGGGG 62.351 72.222 0.00 0.00 38.19 4.96
187 188 3.570212 GAGGTGCCACACTGGGGT 61.570 66.667 0.00 0.00 38.19 4.95
188 189 3.103213 AGGTGCCACACTGGGGTT 61.103 61.111 0.00 0.00 38.19 4.11
189 190 2.912025 GGTGCCACACTGGGGTTG 60.912 66.667 0.00 0.00 38.19 3.77
190 191 3.605664 GTGCCACACTGGGGTTGC 61.606 66.667 0.00 0.00 38.19 4.17
215 216 2.618053 CCAGTCGATGGTCTTTACACC 58.382 52.381 0.00 0.00 44.91 4.16
216 217 2.618053 CAGTCGATGGTCTTTACACCC 58.382 52.381 0.00 0.00 35.26 4.61
217 218 1.203994 AGTCGATGGTCTTTACACCCG 59.796 52.381 0.00 0.00 35.26 5.28
218 219 0.533491 TCGATGGTCTTTACACCCGG 59.467 55.000 0.00 0.00 35.26 5.73
219 220 1.087771 CGATGGTCTTTACACCCGGC 61.088 60.000 0.00 0.00 35.26 6.13
220 221 1.078708 ATGGTCTTTACACCCGGCG 60.079 57.895 0.00 0.00 35.26 6.46
221 222 1.546589 ATGGTCTTTACACCCGGCGA 61.547 55.000 9.30 0.00 35.26 5.54
222 223 1.447314 GGTCTTTACACCCGGCGAG 60.447 63.158 9.30 0.00 0.00 5.03
223 224 1.447314 GTCTTTACACCCGGCGAGG 60.447 63.158 9.30 11.01 40.63 4.63
224 225 2.818274 CTTTACACCCGGCGAGGC 60.818 66.667 9.30 0.00 39.21 4.70
225 226 4.397832 TTTACACCCGGCGAGGCC 62.398 66.667 9.30 0.00 46.75 5.19
242 243 4.829518 CGCGATCACGTGCCTCGA 62.830 66.667 31.25 9.98 42.78 4.04
243 244 2.951745 GCGATCACGTGCCTCGAG 60.952 66.667 31.25 5.13 42.86 4.04
244 245 2.951745 CGATCACGTGCCTCGAGC 60.952 66.667 26.25 6.90 42.86 5.03
276 277 2.126888 GCGTCATTTGTGTGGGCG 60.127 61.111 0.00 0.00 0.00 6.13
293 294 2.480610 CGCAATGGATTCCCACCGG 61.481 63.158 0.00 0.00 46.98 5.28
311 312 1.643832 GATCAACTCGGATTGCGGC 59.356 57.895 0.00 0.00 0.00 6.53
313 314 2.257409 ATCAACTCGGATTGCGGCCT 62.257 55.000 0.00 0.00 0.00 5.19
320 321 2.401766 GGATTGCGGCCTGACACAG 61.402 63.158 0.00 0.00 0.00 3.66
330 331 1.595882 CTGACACAGCCCTCTCAGG 59.404 63.158 0.00 0.00 34.30 3.86
353 354 3.680786 CGGAGAGCCACACGGACA 61.681 66.667 0.00 0.00 0.00 4.02
371 372 1.028905 CAGTCATCTCCTCCTCGTCC 58.971 60.000 0.00 0.00 0.00 4.79
374 375 1.143277 GTCATCTCCTCCTCGTCCCTA 59.857 57.143 0.00 0.00 0.00 3.53
404 405 3.543680 AAGGTCCCAGTTGATGTATCG 57.456 47.619 0.00 0.00 0.00 2.92
450 451 0.534412 CCGTCATGCAGGAGAAGACT 59.466 55.000 0.00 0.00 0.00 3.24
460 461 3.364549 CAGGAGAAGACTGGAGATCACT 58.635 50.000 0.00 0.00 32.38 3.41
470 471 0.980231 GGAGATCACTGGCCAGGAGT 60.980 60.000 35.42 20.50 0.00 3.85
479 480 0.840288 TGGCCAGGAGTTTAGGAGCA 60.840 55.000 0.00 0.00 0.00 4.26
481 482 0.905357 GCCAGGAGTTTAGGAGCAGA 59.095 55.000 0.00 0.00 0.00 4.26
490 491 3.898123 AGTTTAGGAGCAGAGTGAAGTGA 59.102 43.478 0.00 0.00 0.00 3.41
491 492 4.021544 AGTTTAGGAGCAGAGTGAAGTGAG 60.022 45.833 0.00 0.00 0.00 3.51
495 496 2.165437 GGAGCAGAGTGAAGTGAGGTAG 59.835 54.545 0.00 0.00 0.00 3.18
502 503 3.020984 AGTGAAGTGAGGTAGCTAGAGC 58.979 50.000 0.00 0.00 42.49 4.09
544 545 4.888917 TGAACGAACATATGTGAGGTCAA 58.111 39.130 21.93 10.82 31.98 3.18
554 555 0.035458 GTGAGGTCAAGGTGGGTCAG 59.965 60.000 0.00 0.00 0.00 3.51
559 560 0.603975 GTCAAGGTGGGTCAGACTGC 60.604 60.000 0.00 0.00 0.00 4.40
560 561 1.053835 TCAAGGTGGGTCAGACTGCA 61.054 55.000 0.00 0.00 0.00 4.41
561 562 0.179020 CAAGGTGGGTCAGACTGCAA 60.179 55.000 0.00 0.00 0.00 4.08
563 564 1.148273 GGTGGGTCAGACTGCAACA 59.852 57.895 0.00 0.00 0.00 3.33
564 565 0.250901 GGTGGGTCAGACTGCAACAT 60.251 55.000 0.00 0.00 0.00 2.71
565 566 1.003118 GGTGGGTCAGACTGCAACATA 59.997 52.381 0.00 0.00 0.00 2.29
567 568 2.679837 GTGGGTCAGACTGCAACATATG 59.320 50.000 0.00 0.00 0.00 1.78
568 569 2.305635 TGGGTCAGACTGCAACATATGT 59.694 45.455 1.41 1.41 0.00 2.29
570 571 2.679837 GGTCAGACTGCAACATATGTGG 59.320 50.000 9.63 7.62 0.00 4.17
571 572 2.679837 GTCAGACTGCAACATATGTGGG 59.320 50.000 9.63 6.27 0.00 4.61
574 575 3.562973 CAGACTGCAACATATGTGGGATC 59.437 47.826 9.63 7.46 0.00 3.36
575 576 3.200605 AGACTGCAACATATGTGGGATCA 59.799 43.478 9.63 0.00 0.00 2.92
576 577 3.947196 GACTGCAACATATGTGGGATCAA 59.053 43.478 9.63 0.00 0.00 2.57
577 578 3.949754 ACTGCAACATATGTGGGATCAAG 59.050 43.478 9.63 0.00 0.00 3.02
578 579 3.289836 TGCAACATATGTGGGATCAAGG 58.710 45.455 9.63 0.00 0.00 3.61
579 580 3.290710 GCAACATATGTGGGATCAAGGT 58.709 45.455 9.63 0.00 0.00 3.50
580 581 3.067180 GCAACATATGTGGGATCAAGGTG 59.933 47.826 9.63 0.80 0.00 4.00
581 582 3.582998 ACATATGTGGGATCAAGGTGG 57.417 47.619 7.78 0.00 0.00 4.61
582 583 2.175499 ACATATGTGGGATCAAGGTGGG 59.825 50.000 7.78 0.00 0.00 4.61
583 584 1.979809 TATGTGGGATCAAGGTGGGT 58.020 50.000 0.00 0.00 0.00 4.51
584 585 0.625849 ATGTGGGATCAAGGTGGGTC 59.374 55.000 0.00 0.00 0.00 4.46
585 586 0.770166 TGTGGGATCAAGGTGGGTCA 60.770 55.000 0.00 0.00 0.00 4.02
586 587 0.035056 GTGGGATCAAGGTGGGTCAG 60.035 60.000 0.00 0.00 0.00 3.51
587 588 0.178876 TGGGATCAAGGTGGGTCAGA 60.179 55.000 0.00 0.00 0.00 3.27
588 589 0.253327 GGGATCAAGGTGGGTCAGAC 59.747 60.000 0.00 0.00 0.00 3.51
589 590 1.280457 GGATCAAGGTGGGTCAGACT 58.720 55.000 0.00 0.00 0.00 3.24
590 591 2.467880 GGATCAAGGTGGGTCAGACTA 58.532 52.381 0.00 0.00 0.00 2.59
591 592 2.168728 GGATCAAGGTGGGTCAGACTAC 59.831 54.545 0.00 0.44 0.00 2.73
592 593 2.391926 TCAAGGTGGGTCAGACTACA 57.608 50.000 0.00 0.00 0.00 2.74
593 594 2.684943 TCAAGGTGGGTCAGACTACAA 58.315 47.619 0.00 0.00 0.00 2.41
608 609 3.945285 GACTACAACATATGTGGGGTTGG 59.055 47.826 14.82 9.68 44.27 3.77
662 663 0.110678 TGAGGAGTGTCGGTCAGTCT 59.889 55.000 9.38 0.00 43.76 3.24
664 665 0.110678 AGGAGTGTCGGTCAGTCTGA 59.889 55.000 0.00 0.00 43.76 3.27
667 668 2.608261 GGAGTGTCGGTCAGTCTGAAAG 60.608 54.545 3.51 1.79 43.76 2.62
669 670 0.318699 TGTCGGTCAGTCTGAAAGCG 60.319 55.000 3.51 5.47 32.76 4.68
674 675 1.719780 GGTCAGTCTGAAAGCGTAACG 59.280 52.381 3.51 0.00 0.00 3.18
675 676 2.391879 GTCAGTCTGAAAGCGTAACGT 58.608 47.619 3.51 0.00 0.00 3.99
682 683 0.984829 GAAAGCGTAACGTCGGTACC 59.015 55.000 14.62 0.16 40.62 3.34
686 687 0.522076 GCGTAACGTCGGTACCAGAG 60.522 60.000 14.62 4.30 0.00 3.35
701 702 1.997874 AGAGGGGTGGCTGGATCAC 60.998 63.158 0.00 0.00 34.61 3.06
703 704 4.489771 GGGGTGGCTGGATCACGG 62.490 72.222 0.00 0.00 36.09 4.94
712 713 1.464997 GCTGGATCACGGTTTTCTGAC 59.535 52.381 0.00 0.00 0.00 3.51
714 715 2.480419 CTGGATCACGGTTTTCTGACAC 59.520 50.000 0.00 0.00 0.00 3.67
715 716 1.804748 GGATCACGGTTTTCTGACACC 59.195 52.381 0.00 0.00 0.00 4.16
783 793 3.342377 TGCCTCCAAATTCACGATACA 57.658 42.857 0.00 0.00 0.00 2.29
852 1086 8.228035 ACTAGTAAAATAGTACTCCAGCTCTG 57.772 38.462 0.00 0.00 35.85 3.35
1195 1440 1.796796 GACGGCATGGAAGAGCAAC 59.203 57.895 0.00 0.00 0.00 4.17
1201 1446 1.377725 ATGGAAGAGCAACAGCCCG 60.378 57.895 0.00 0.00 0.00 6.13
1657 1907 1.375853 TACAGCATGCACAATCGCCC 61.376 55.000 21.98 0.00 42.53 6.13
1689 1939 2.816672 TGTGATGCAAATGCCGAGTAAA 59.183 40.909 2.46 0.00 41.18 2.01
1716 1968 7.642082 AAGTTATACTAGACGGACATGAGTT 57.358 36.000 0.00 0.00 0.00 3.01
1717 1969 7.028926 AGTTATACTAGACGGACATGAGTTG 57.971 40.000 0.00 0.00 0.00 3.16
1759 2011 5.711036 GGTGTAACTAGAGTCCATCGGATAT 59.289 44.000 0.00 0.00 36.74 1.63
1770 2022 6.256819 AGTCCATCGGATATAGAGGAATTCA 58.743 40.000 7.93 0.00 32.73 2.57
1801 2053 4.523558 TCACTCCATTGTTTTGCATCATCA 59.476 37.500 0.00 0.00 0.00 3.07
1802 2054 5.186215 TCACTCCATTGTTTTGCATCATCAT 59.814 36.000 0.00 0.00 0.00 2.45
1803 2055 5.518847 CACTCCATTGTTTTGCATCATCATC 59.481 40.000 0.00 0.00 0.00 2.92
1804 2056 4.674475 TCCATTGTTTTGCATCATCATCG 58.326 39.130 0.00 0.00 0.00 3.84
1810 2062 4.940654 TGTTTTGCATCATCATCGTTCCTA 59.059 37.500 0.00 0.00 0.00 2.94
2198 5640 2.125106 GCTAAGTGGTCGCCCCAG 60.125 66.667 0.00 0.00 46.45 4.45
2199 5641 2.656069 GCTAAGTGGTCGCCCCAGA 61.656 63.158 0.00 0.00 46.45 3.86
2200 5642 1.218316 CTAAGTGGTCGCCCCAGAC 59.782 63.158 0.00 0.00 46.45 3.51
2282 5725 1.271054 GCCCAGATTCTGTATGCCGAT 60.271 52.381 12.54 0.00 0.00 4.18
2289 5733 6.238842 CCAGATTCTGTATGCCGATCATTTTT 60.239 38.462 12.54 0.00 36.63 1.94
2293 5737 7.624360 TTCTGTATGCCGATCATTTTTACTT 57.376 32.000 0.00 0.00 36.63 2.24
2321 5765 0.404040 TGAACTGGAAAAGGGGCGAT 59.596 50.000 0.00 0.00 0.00 4.58
2322 5766 1.095600 GAACTGGAAAAGGGGCGATC 58.904 55.000 0.00 0.00 0.00 3.69
2323 5767 0.676782 AACTGGAAAAGGGGCGATCG 60.677 55.000 11.69 11.69 0.00 3.69
2324 5768 1.819632 CTGGAAAAGGGGCGATCGG 60.820 63.158 18.30 0.00 0.00 4.18
2504 5961 4.862092 CGCTCGCTCGGCTCACAT 62.862 66.667 0.00 0.00 0.00 3.21
2514 5971 1.227380 GGCTCACATAGGGACAGCG 60.227 63.158 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.847444 GAAGCCCTCCGAGCCTGC 62.847 72.222 0.00 0.00 0.00 4.85
3 4 4.168291 GGAAGCCCTCCGAGCCTG 62.168 72.222 0.00 0.00 33.37 4.85
13 14 2.127708 TGGATAGGAAAGAGGAAGCCC 58.872 52.381 0.00 0.00 0.00 5.19
14 15 3.497584 CCATGGATAGGAAAGAGGAAGCC 60.498 52.174 5.56 0.00 0.00 4.35
15 16 3.749226 CCATGGATAGGAAAGAGGAAGC 58.251 50.000 5.56 0.00 0.00 3.86
16 17 3.749226 GCCATGGATAGGAAAGAGGAAG 58.251 50.000 18.40 0.00 0.00 3.46
17 18 2.104792 CGCCATGGATAGGAAAGAGGAA 59.895 50.000 18.40 0.00 0.00 3.36
18 19 1.694150 CGCCATGGATAGGAAAGAGGA 59.306 52.381 18.40 0.00 0.00 3.71
19 20 1.271054 CCGCCATGGATAGGAAAGAGG 60.271 57.143 18.40 0.00 42.00 3.69
20 21 1.417890 ACCGCCATGGATAGGAAAGAG 59.582 52.381 18.40 0.00 42.00 2.85
21 22 1.140852 CACCGCCATGGATAGGAAAGA 59.859 52.381 18.40 0.00 42.00 2.52
22 23 1.134098 ACACCGCCATGGATAGGAAAG 60.134 52.381 18.40 12.36 42.00 2.62
23 24 0.916086 ACACCGCCATGGATAGGAAA 59.084 50.000 18.40 0.00 42.00 3.13
24 25 0.180171 CACACCGCCATGGATAGGAA 59.820 55.000 18.40 0.00 42.00 3.36
25 26 0.980754 ACACACCGCCATGGATAGGA 60.981 55.000 18.40 0.00 42.00 2.94
26 27 0.815213 CACACACCGCCATGGATAGG 60.815 60.000 18.40 17.35 42.00 2.57
27 28 0.177836 TCACACACCGCCATGGATAG 59.822 55.000 18.40 5.12 42.00 2.08
28 29 0.107897 GTCACACACCGCCATGGATA 60.108 55.000 18.40 0.00 42.00 2.59
29 30 1.377202 GTCACACACCGCCATGGAT 60.377 57.895 18.40 0.00 42.00 3.41
30 31 2.031919 GTCACACACCGCCATGGA 59.968 61.111 18.40 0.00 42.00 3.41
31 32 2.032528 AGTCACACACCGCCATGG 59.967 61.111 7.63 7.63 46.41 3.66
32 33 2.034879 GGAGTCACACACCGCCATG 61.035 63.158 0.00 0.00 0.00 3.66
33 34 2.347490 GGAGTCACACACCGCCAT 59.653 61.111 0.00 0.00 0.00 4.40
34 35 4.293648 CGGAGTCACACACCGCCA 62.294 66.667 0.00 0.00 44.58 5.69
38 39 2.048127 GAGCCGGAGTCACACACC 60.048 66.667 5.05 0.00 0.00 4.16
39 40 1.373497 CAGAGCCGGAGTCACACAC 60.373 63.158 5.05 0.00 0.00 3.82
40 41 1.832608 ACAGAGCCGGAGTCACACA 60.833 57.895 5.05 0.00 0.00 3.72
41 42 1.373497 CACAGAGCCGGAGTCACAC 60.373 63.158 5.05 0.00 0.00 3.82
42 43 2.574018 CCACAGAGCCGGAGTCACA 61.574 63.158 5.05 0.00 0.00 3.58
43 44 2.262915 CCACAGAGCCGGAGTCAC 59.737 66.667 5.05 0.00 0.00 3.67
44 45 3.695606 GCCACAGAGCCGGAGTCA 61.696 66.667 5.05 0.00 0.00 3.41
45 46 2.844072 GAAGCCACAGAGCCGGAGTC 62.844 65.000 5.05 0.00 0.00 3.36
46 47 2.925170 AAGCCACAGAGCCGGAGT 60.925 61.111 5.05 0.00 0.00 3.85
47 48 2.125350 GAAGCCACAGAGCCGGAG 60.125 66.667 5.05 0.00 0.00 4.63
48 49 3.706373 GGAAGCCACAGAGCCGGA 61.706 66.667 5.05 0.00 0.00 5.14
49 50 4.785453 GGGAAGCCACAGAGCCGG 62.785 72.222 0.00 0.00 0.00 6.13
50 51 4.020617 TGGGAAGCCACAGAGCCG 62.021 66.667 0.00 0.00 0.00 5.52
51 52 2.360475 GTGGGAAGCCACAGAGCC 60.360 66.667 0.00 0.00 40.13 4.70
52 53 2.743928 CGTGGGAAGCCACAGAGC 60.744 66.667 0.00 0.00 40.38 4.09
53 54 2.743928 GCGTGGGAAGCCACAGAG 60.744 66.667 0.00 0.00 40.38 3.35
60 61 2.187163 GTAGAGGGCGTGGGAAGC 59.813 66.667 0.00 0.00 0.00 3.86
61 62 1.677637 GAGGTAGAGGGCGTGGGAAG 61.678 65.000 0.00 0.00 0.00 3.46
62 63 1.684734 GAGGTAGAGGGCGTGGGAA 60.685 63.158 0.00 0.00 0.00 3.97
63 64 2.043248 GAGGTAGAGGGCGTGGGA 60.043 66.667 0.00 0.00 0.00 4.37
64 65 3.528370 CGAGGTAGAGGGCGTGGG 61.528 72.222 0.00 0.00 0.00 4.61
65 66 4.208686 GCGAGGTAGAGGGCGTGG 62.209 72.222 0.00 0.00 0.00 4.94
66 67 2.786495 ATGCGAGGTAGAGGGCGTG 61.786 63.158 0.00 0.00 0.00 5.34
67 68 2.442272 ATGCGAGGTAGAGGGCGT 60.442 61.111 0.00 0.00 0.00 5.68
68 69 2.028190 CATGCGAGGTAGAGGGCG 59.972 66.667 0.00 0.00 0.00 6.13
69 70 1.068250 GTCATGCGAGGTAGAGGGC 59.932 63.158 0.00 0.00 0.00 5.19
70 71 1.360551 CGTCATGCGAGGTAGAGGG 59.639 63.158 3.85 0.00 44.77 4.30
71 72 1.360551 CCGTCATGCGAGGTAGAGG 59.639 63.158 10.48 0.00 44.77 3.69
72 73 1.360551 CCCGTCATGCGAGGTAGAG 59.639 63.158 10.48 0.00 44.77 2.43
73 74 2.782222 GCCCGTCATGCGAGGTAGA 61.782 63.158 10.48 0.00 44.77 2.59
74 75 2.279517 GCCCGTCATGCGAGGTAG 60.280 66.667 10.48 0.00 44.77 3.18
75 76 3.071837 TGCCCGTCATGCGAGGTA 61.072 61.111 10.48 7.21 44.77 3.08
76 77 4.760047 GTGCCCGTCATGCGAGGT 62.760 66.667 10.48 0.00 44.77 3.85
92 93 4.388499 AATGCGAAGGACCGGCGT 62.388 61.111 6.01 3.09 0.00 5.68
93 94 3.864686 CAATGCGAAGGACCGGCG 61.865 66.667 0.00 0.00 0.00 6.46
94 95 3.508840 CCAATGCGAAGGACCGGC 61.509 66.667 0.00 0.00 0.00 6.13
95 96 2.587322 TAGCCAATGCGAAGGACCGG 62.587 60.000 0.00 0.00 44.33 5.28
96 97 1.153449 TAGCCAATGCGAAGGACCG 60.153 57.895 0.00 0.00 44.33 4.79
97 98 0.815615 CCTAGCCAATGCGAAGGACC 60.816 60.000 3.73 0.00 44.03 4.46
98 99 1.440145 GCCTAGCCAATGCGAAGGAC 61.440 60.000 11.58 2.21 44.03 3.85
99 100 1.153168 GCCTAGCCAATGCGAAGGA 60.153 57.895 11.58 0.00 44.03 3.36
100 101 3.425422 GCCTAGCCAATGCGAAGG 58.575 61.111 0.00 5.07 44.09 3.46
117 118 3.261951 CGTCGGCATGCCTTACGG 61.262 66.667 35.57 22.61 38.56 4.02
118 119 2.098233 AACGTCGGCATGCCTTACG 61.098 57.895 38.50 38.50 43.77 3.18
119 120 1.017177 TCAACGTCGGCATGCCTTAC 61.017 55.000 33.07 27.23 0.00 2.34
120 121 1.017177 GTCAACGTCGGCATGCCTTA 61.017 55.000 33.07 19.13 0.00 2.69
121 122 2.031919 TCAACGTCGGCATGCCTT 59.968 55.556 33.07 18.54 0.00 4.35
122 123 2.742372 GTCAACGTCGGCATGCCT 60.742 61.111 33.07 13.08 0.00 4.75
123 124 3.799755 GGTCAACGTCGGCATGCC 61.800 66.667 27.67 27.67 0.00 4.40
124 125 1.852067 AAAGGTCAACGTCGGCATGC 61.852 55.000 9.90 9.90 0.00 4.06
125 126 0.110238 CAAAGGTCAACGTCGGCATG 60.110 55.000 0.00 0.00 0.00 4.06
126 127 0.250124 TCAAAGGTCAACGTCGGCAT 60.250 50.000 0.00 0.00 0.00 4.40
127 128 0.462225 TTCAAAGGTCAACGTCGGCA 60.462 50.000 0.00 0.00 0.00 5.69
128 129 0.872388 ATTCAAAGGTCAACGTCGGC 59.128 50.000 0.00 0.00 0.00 5.54
129 130 1.126113 CGATTCAAAGGTCAACGTCGG 59.874 52.381 0.00 0.00 0.00 4.79
130 131 1.126113 CCGATTCAAAGGTCAACGTCG 59.874 52.381 0.00 0.00 0.00 5.12
131 132 2.409975 TCCGATTCAAAGGTCAACGTC 58.590 47.619 0.00 0.00 0.00 4.34
132 133 2.413837 CTCCGATTCAAAGGTCAACGT 58.586 47.619 0.00 0.00 0.00 3.99
133 134 1.128692 GCTCCGATTCAAAGGTCAACG 59.871 52.381 0.00 0.00 0.00 4.10
134 135 1.468914 GGCTCCGATTCAAAGGTCAAC 59.531 52.381 0.00 0.00 0.00 3.18
135 136 1.613255 GGGCTCCGATTCAAAGGTCAA 60.613 52.381 0.00 0.00 0.00 3.18
136 137 0.035439 GGGCTCCGATTCAAAGGTCA 60.035 55.000 0.00 0.00 0.00 4.02
137 138 2.781911 GGGCTCCGATTCAAAGGTC 58.218 57.895 0.00 0.00 0.00 3.85
164 165 4.035102 GTGTGGCACCTCCTCCCC 62.035 72.222 16.26 0.00 35.26 4.81
165 166 2.930562 AGTGTGGCACCTCCTCCC 60.931 66.667 16.26 0.00 34.49 4.30
166 167 2.348998 CAGTGTGGCACCTCCTCC 59.651 66.667 16.26 0.00 34.49 4.30
167 168 2.348998 CCAGTGTGGCACCTCCTC 59.651 66.667 16.26 0.72 34.49 3.71
168 169 3.252284 CCCAGTGTGGCACCTCCT 61.252 66.667 16.26 5.44 35.79 3.69
169 170 4.351054 CCCCAGTGTGGCACCTCC 62.351 72.222 16.26 2.93 35.79 4.30
170 171 3.133365 AACCCCAGTGTGGCACCTC 62.133 63.158 16.26 8.47 35.79 3.85
171 172 3.103213 AACCCCAGTGTGGCACCT 61.103 61.111 16.26 8.98 35.79 4.00
172 173 2.912025 CAACCCCAGTGTGGCACC 60.912 66.667 16.26 6.59 35.79 5.01
173 174 3.605664 GCAACCCCAGTGTGGCAC 61.606 66.667 11.55 11.55 35.79 5.01
196 197 2.618053 GGGTGTAAAGACCATCGACTG 58.382 52.381 0.00 0.00 37.80 3.51
197 198 1.203994 CGGGTGTAAAGACCATCGACT 59.796 52.381 0.00 0.00 37.80 4.18
198 199 1.636988 CGGGTGTAAAGACCATCGAC 58.363 55.000 0.00 0.00 37.80 4.20
199 200 0.533491 CCGGGTGTAAAGACCATCGA 59.467 55.000 0.00 0.00 37.80 3.59
200 201 1.087771 GCCGGGTGTAAAGACCATCG 61.088 60.000 2.18 0.00 37.80 3.84
201 202 1.087771 CGCCGGGTGTAAAGACCATC 61.088 60.000 2.18 0.00 37.80 3.51
202 203 1.078708 CGCCGGGTGTAAAGACCAT 60.079 57.895 2.18 0.00 37.80 3.55
203 204 2.162338 CTCGCCGGGTGTAAAGACCA 62.162 60.000 2.18 0.00 37.80 4.02
204 205 1.447314 CTCGCCGGGTGTAAAGACC 60.447 63.158 2.18 0.00 34.96 3.85
205 206 1.447314 CCTCGCCGGGTGTAAAGAC 60.447 63.158 2.18 0.00 0.00 3.01
206 207 2.975536 CCTCGCCGGGTGTAAAGA 59.024 61.111 2.18 0.00 0.00 2.52
207 208 2.818274 GCCTCGCCGGGTGTAAAG 60.818 66.667 2.18 0.00 0.00 1.85
208 209 4.397832 GGCCTCGCCGGGTGTAAA 62.398 66.667 2.18 0.00 39.62 2.01
225 226 4.829518 TCGAGGCACGTGATCGCG 62.830 66.667 28.34 26.14 43.13 5.87
226 227 2.951745 CTCGAGGCACGTGATCGC 60.952 66.667 28.34 17.08 43.13 4.58
227 228 2.951745 GCTCGAGGCACGTGATCG 60.952 66.667 27.66 27.66 43.13 3.69
228 229 2.583593 GGCTCGAGGCACGTGATC 60.584 66.667 31.94 15.14 44.01 2.92
229 230 3.381983 TGGCTCGAGGCACGTGAT 61.382 61.111 35.14 6.57 46.12 3.06
238 239 4.933064 GATCCGCGGTGGCTCGAG 62.933 72.222 27.15 8.45 37.80 4.04
241 242 4.467084 TTGGATCCGCGGTGGCTC 62.467 66.667 27.15 16.85 37.80 4.70
242 243 4.473520 CTTGGATCCGCGGTGGCT 62.474 66.667 27.15 8.59 37.80 4.75
249 250 0.248215 CAAATGACGCTTGGATCCGC 60.248 55.000 7.39 4.26 0.00 5.54
262 263 0.038435 CATTGCGCCCACACAAATGA 60.038 50.000 4.18 0.00 0.00 2.57
263 264 1.015085 CCATTGCGCCCACACAAATG 61.015 55.000 4.18 6.15 0.00 2.32
276 277 1.077068 TCCGGTGGGAATCCATTGC 60.077 57.895 0.00 0.00 46.09 3.56
293 294 1.643832 GCCGCAATCCGAGTTGATC 59.356 57.895 4.25 0.00 40.02 2.92
311 312 1.595882 CTGAGAGGGCTGTGTCAGG 59.404 63.158 6.65 0.00 34.06 3.86
313 314 0.902048 CTCCTGAGAGGGCTGTGTCA 60.902 60.000 0.00 0.00 35.59 3.58
338 339 1.080434 GACTGTCCGTGTGGCTCTC 60.080 63.158 0.00 0.00 34.14 3.20
352 353 1.028905 GGACGAGGAGGAGATGACTG 58.971 60.000 0.00 0.00 0.00 3.51
353 354 0.106419 GGGACGAGGAGGAGATGACT 60.106 60.000 0.00 0.00 0.00 3.41
385 386 2.747177 TCGATACATCAACTGGGACCT 58.253 47.619 0.00 0.00 0.00 3.85
392 393 9.877178 ACTCTAAGATTTTTCGATACATCAACT 57.123 29.630 5.08 0.00 0.00 3.16
395 396 9.521503 CAGACTCTAAGATTTTTCGATACATCA 57.478 33.333 5.08 0.00 0.00 3.07
396 397 9.737427 TCAGACTCTAAGATTTTTCGATACATC 57.263 33.333 0.00 0.00 0.00 3.06
404 405 9.928236 GCAATGTATCAGACTCTAAGATTTTTC 57.072 33.333 0.00 0.00 0.00 2.29
426 427 1.452651 CTCCTGCATGACGGGCAAT 60.453 57.895 0.00 0.00 45.54 3.56
427 428 2.046023 CTCCTGCATGACGGGCAA 60.046 61.111 0.00 0.00 45.54 4.52
450 451 0.979709 CTCCTGGCCAGTGATCTCCA 60.980 60.000 30.63 5.14 0.00 3.86
460 461 0.840288 TGCTCCTAAACTCCTGGCCA 60.840 55.000 4.71 4.71 0.00 5.36
470 471 3.259374 CCTCACTTCACTCTGCTCCTAAA 59.741 47.826 0.00 0.00 0.00 1.85
479 480 4.523083 CTCTAGCTACCTCACTTCACTCT 58.477 47.826 0.00 0.00 0.00 3.24
481 482 3.020984 GCTCTAGCTACCTCACTTCACT 58.979 50.000 0.00 0.00 38.21 3.41
495 496 2.746269 CATCTCTGAGCAAGCTCTAGC 58.254 52.381 21.35 0.00 43.12 3.42
502 503 2.808523 TATCCGCATCTCTGAGCAAG 57.191 50.000 0.00 0.00 0.00 4.01
544 545 1.344953 TGTTGCAGTCTGACCCACCT 61.345 55.000 3.32 0.00 0.00 4.00
554 555 3.544684 TGATCCCACATATGTTGCAGTC 58.455 45.455 5.37 2.25 0.00 3.51
559 560 3.633525 CCACCTTGATCCCACATATGTTG 59.366 47.826 5.37 2.32 0.00 3.33
560 561 3.373001 CCCACCTTGATCCCACATATGTT 60.373 47.826 5.37 0.00 0.00 2.71
561 562 2.175499 CCCACCTTGATCCCACATATGT 59.825 50.000 1.41 1.41 0.00 2.29
563 564 2.443255 GACCCACCTTGATCCCACATAT 59.557 50.000 0.00 0.00 0.00 1.78
564 565 1.843851 GACCCACCTTGATCCCACATA 59.156 52.381 0.00 0.00 0.00 2.29
565 566 0.625849 GACCCACCTTGATCCCACAT 59.374 55.000 0.00 0.00 0.00 3.21
567 568 0.035056 CTGACCCACCTTGATCCCAC 60.035 60.000 0.00 0.00 0.00 4.61
568 569 0.178876 TCTGACCCACCTTGATCCCA 60.179 55.000 0.00 0.00 0.00 4.37
570 571 1.280457 AGTCTGACCCACCTTGATCC 58.720 55.000 3.76 0.00 0.00 3.36
571 572 2.832129 TGTAGTCTGACCCACCTTGATC 59.168 50.000 3.76 0.00 0.00 2.92
574 575 2.104111 TGTTGTAGTCTGACCCACCTTG 59.896 50.000 3.76 0.00 0.00 3.61
575 576 2.404559 TGTTGTAGTCTGACCCACCTT 58.595 47.619 3.76 0.00 0.00 3.50
576 577 2.097110 TGTTGTAGTCTGACCCACCT 57.903 50.000 3.76 0.00 0.00 4.00
577 578 4.081087 ACATATGTTGTAGTCTGACCCACC 60.081 45.833 1.41 0.00 36.57 4.61
578 579 4.870426 CACATATGTTGTAGTCTGACCCAC 59.130 45.833 5.37 3.79 36.57 4.61
579 580 4.081142 CCACATATGTTGTAGTCTGACCCA 60.081 45.833 5.37 0.00 36.57 4.51
580 581 4.442706 CCACATATGTTGTAGTCTGACCC 58.557 47.826 5.37 0.00 36.57 4.46
581 582 4.442706 CCCACATATGTTGTAGTCTGACC 58.557 47.826 5.37 0.00 36.57 4.02
582 583 4.081087 ACCCCACATATGTTGTAGTCTGAC 60.081 45.833 5.37 0.00 36.57 3.51
583 584 4.101114 ACCCCACATATGTTGTAGTCTGA 58.899 43.478 5.37 0.00 36.57 3.27
584 585 4.487714 ACCCCACATATGTTGTAGTCTG 57.512 45.455 5.37 0.00 36.57 3.51
585 586 4.324254 CCAACCCCACATATGTTGTAGTCT 60.324 45.833 5.37 0.00 38.10 3.24
586 587 3.945285 CCAACCCCACATATGTTGTAGTC 59.055 47.826 5.37 0.00 38.10 2.59
587 588 3.308832 CCCAACCCCACATATGTTGTAGT 60.309 47.826 5.37 0.00 38.10 2.73
588 589 3.287222 CCCAACCCCACATATGTTGTAG 58.713 50.000 5.37 0.00 38.10 2.74
589 590 2.024846 CCCCAACCCCACATATGTTGTA 60.025 50.000 5.37 0.00 38.10 2.41
590 591 1.272985 CCCCAACCCCACATATGTTGT 60.273 52.381 5.37 1.04 38.10 3.32
591 592 1.272985 ACCCCAACCCCACATATGTTG 60.273 52.381 5.37 2.32 39.20 3.33
592 593 1.089123 ACCCCAACCCCACATATGTT 58.911 50.000 5.37 0.00 0.00 2.71
593 594 0.334676 CACCCCAACCCCACATATGT 59.665 55.000 1.41 1.41 0.00 2.29
608 609 3.403558 GAGGAGGCTGACCCACCC 61.404 72.222 0.00 0.00 44.78 4.61
662 663 1.665735 GGTACCGACGTTACGCTTTCA 60.666 52.381 4.09 0.00 0.00 2.69
664 665 0.313672 TGGTACCGACGTTACGCTTT 59.686 50.000 7.57 0.00 0.00 3.51
667 668 0.522076 CTCTGGTACCGACGTTACGC 60.522 60.000 7.57 0.00 0.00 4.42
669 670 0.453390 CCCTCTGGTACCGACGTTAC 59.547 60.000 7.57 0.00 0.00 2.50
682 683 1.997311 TGATCCAGCCACCCCTCTG 60.997 63.158 0.00 0.00 0.00 3.35
686 687 4.489771 CCGTGATCCAGCCACCCC 62.490 72.222 0.00 0.00 0.00 4.95
690 691 0.400213 AGAAAACCGTGATCCAGCCA 59.600 50.000 0.00 0.00 0.00 4.75
691 692 0.804989 CAGAAAACCGTGATCCAGCC 59.195 55.000 0.00 0.00 0.00 4.85
703 704 2.140717 CTACACCCGGTGTCAGAAAAC 58.859 52.381 26.70 0.00 43.92 2.43
712 713 0.821517 TACAGCATCTACACCCGGTG 59.178 55.000 16.47 16.47 39.75 4.94
714 715 1.801395 CGTTACAGCATCTACACCCGG 60.801 57.143 0.00 0.00 0.00 5.73
715 716 1.135199 ACGTTACAGCATCTACACCCG 60.135 52.381 0.00 0.00 0.00 5.28
716 717 2.537401 GACGTTACAGCATCTACACCC 58.463 52.381 0.00 0.00 0.00 4.61
783 793 1.352156 GCGACCGAGCGAATTCTGTT 61.352 55.000 3.52 0.00 0.00 3.16
852 1086 1.469423 GGTACTTGCTACGAGTGCTCC 60.469 57.143 0.00 0.00 31.47 4.70
1592 1840 2.827642 CTGCTGCCTTGGCCTAGC 60.828 66.667 8.91 14.63 36.72 3.42
1657 1907 4.451241 CATCACAGGGATGCCTCG 57.549 61.111 1.06 1.66 46.35 4.63
1689 1939 9.352191 ACTCATGTCCGTCTAGTATAACTTAAT 57.648 33.333 0.00 0.00 0.00 1.40
1716 1968 3.627123 CACCCATCATGAACGCTTAATCA 59.373 43.478 0.00 0.00 0.00 2.57
1717 1969 3.627577 ACACCCATCATGAACGCTTAATC 59.372 43.478 0.00 0.00 0.00 1.75
1759 2011 7.675619 TGGAGTGATATATGCTGAATTCCTCTA 59.324 37.037 2.27 0.00 0.00 2.43
1770 2022 6.321945 TGCAAAACAATGGAGTGATATATGCT 59.678 34.615 0.00 0.00 0.00 3.79
1801 2053 4.466726 ACAAAAGGAGTAGCTAGGAACGAT 59.533 41.667 0.00 0.00 0.00 3.73
1802 2054 3.830755 ACAAAAGGAGTAGCTAGGAACGA 59.169 43.478 0.00 0.00 0.00 3.85
1803 2055 4.189639 ACAAAAGGAGTAGCTAGGAACG 57.810 45.455 0.00 0.00 0.00 3.95
1804 2056 6.147985 CAGAAACAAAAGGAGTAGCTAGGAAC 59.852 42.308 0.00 0.00 0.00 3.62
1810 2062 7.875327 TTTTACAGAAACAAAAGGAGTAGCT 57.125 32.000 0.00 0.00 0.00 3.32
1851 2104 6.496338 AAATACAAAAGAATCTCCACGGAC 57.504 37.500 0.00 0.00 0.00 4.79
1852 2105 6.596497 GGTAAATACAAAAGAATCTCCACGGA 59.404 38.462 0.00 0.00 0.00 4.69
1956 2214 2.805671 CACTTACGCCACTCATGAACAA 59.194 45.455 0.00 0.00 0.00 2.83
2080 2483 7.786178 TCCGTTGGTCTTGATTTTCTATATG 57.214 36.000 0.00 0.00 0.00 1.78
2198 5640 2.851263 TACATTGTGTCACTGGGGTC 57.149 50.000 4.27 0.00 0.00 4.46
2199 5641 3.073798 TCATTACATTGTGTCACTGGGGT 59.926 43.478 4.27 0.57 0.00 4.95
2200 5642 3.684908 TCATTACATTGTGTCACTGGGG 58.315 45.455 4.27 0.00 0.00 4.96
2201 5643 4.943093 TGATCATTACATTGTGTCACTGGG 59.057 41.667 4.27 0.00 0.00 4.45
2202 5644 6.499234 TTGATCATTACATTGTGTCACTGG 57.501 37.500 4.27 0.00 0.00 4.00
2203 5645 7.483691 CACATTGATCATTACATTGTGTCACTG 59.516 37.037 4.27 0.00 41.01 3.66
2204 5646 7.362315 CCACATTGATCATTACATTGTGTCACT 60.362 37.037 16.11 0.00 42.67 3.41
2321 5765 0.323629 AGACGAAAAATGAGCCCCGA 59.676 50.000 0.00 0.00 0.00 5.14
2322 5766 2.018542 TAGACGAAAAATGAGCCCCG 57.981 50.000 0.00 0.00 0.00 5.73
2323 5767 4.776795 TTTTAGACGAAAAATGAGCCCC 57.223 40.909 0.00 0.00 34.00 5.80
2496 5953 1.227380 CGCTGTCCCTATGTGAGCC 60.227 63.158 0.00 0.00 0.00 4.70
2497 5954 1.227380 CCGCTGTCCCTATGTGAGC 60.227 63.158 0.00 0.00 0.00 4.26
2498 5955 1.043816 ATCCGCTGTCCCTATGTGAG 58.956 55.000 0.00 0.00 0.00 3.51
2500 5957 1.942657 CAAATCCGCTGTCCCTATGTG 59.057 52.381 0.00 0.00 0.00 3.21
2501 5958 1.134098 CCAAATCCGCTGTCCCTATGT 60.134 52.381 0.00 0.00 0.00 2.29
2502 5959 1.597742 CCAAATCCGCTGTCCCTATG 58.402 55.000 0.00 0.00 0.00 2.23
2503 5960 0.179018 GCCAAATCCGCTGTCCCTAT 60.179 55.000 0.00 0.00 0.00 2.57
2504 5961 1.223487 GCCAAATCCGCTGTCCCTA 59.777 57.895 0.00 0.00 0.00 3.53
2514 5971 1.401905 CCTTTAGTGCGAGCCAAATCC 59.598 52.381 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.