Multiple sequence alignment - TraesCS3D01G113500

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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 TraesCS3D01G113500 chr3D 100.000 3592 0 0 1 3592 67533446 67537037 0.000000e+00 6634.0
1 TraesCS3D01G113500 chr3D 87.805 123 15 0 1 123 389080892 389081014 1.040000e-30 145.0
2 TraesCS3D01G113500 chr6D 97.898 2616 35 6 673 3279 454304979 454302375 0.000000e+00 4508.0
3 TraesCS3D01G113500 chr6D 99.045 314 3 0 3279 3592 454300447 454300134 6.730000e-157 564.0
4 TraesCS3D01G113500 chr6D 94.853 136 6 1 521 656 454305426 454305292 1.010000e-50 211.0
5 TraesCS3D01G113500 chr6D 83.333 126 19 2 1 126 60537222 60537345 8.150000e-22 115.0
6 TraesCS3D01G113500 chr2D 97.106 1935 36 4 526 2455 312028620 312030539 0.000000e+00 3245.0
7 TraesCS3D01G113500 chr2D 97.346 829 19 3 2453 3279 312043791 312044618 0.000000e+00 1406.0
8 TraesCS3D01G113500 chr2D 99.558 226 1 0 3279 3504 312046530 312046755 2.580000e-111 412.0
9 TraesCS3D01G113500 chr1D 88.007 1209 97 24 859 2048 403726312 403725133 0.000000e+00 1386.0
10 TraesCS3D01G113500 chr1D 96.296 54 2 0 1 54 469122583 469122530 4.940000e-14 89.8
11 TraesCS3D01G113500 chr1A 85.806 1240 103 49 859 2048 499445148 499443932 0.000000e+00 1247.0
12 TraesCS3D01G113500 chr1A 88.439 519 45 12 859 1363 584982516 584981999 2.370000e-171 612.0
13 TraesCS3D01G113500 chr1A 91.686 421 28 5 526 945 467181369 467180955 8.650000e-161 577.0
14 TraesCS3D01G113500 chr7A 95.549 719 28 3 2563 3279 333609387 333608671 0.000000e+00 1147.0
15 TraesCS3D01G113500 chr7A 94.264 645 32 3 525 1169 61494364 61493725 0.000000e+00 981.0
16 TraesCS3D01G113500 chr7A 86.283 904 88 23 1167 2057 333610268 333609388 0.000000e+00 950.0
17 TraesCS3D01G113500 chr7A 92.248 645 31 4 526 1169 109231410 109230784 0.000000e+00 896.0
18 TraesCS3D01G113500 chr7A 96.190 315 10 2 3279 3592 333606817 333606504 6.880000e-142 514.0
19 TraesCS3D01G113500 chr7A 84.615 169 21 4 2768 2934 581692504 581692669 2.870000e-36 163.0
20 TraesCS3D01G113500 chr7A 93.204 103 5 2 2050 2151 648669210 648669109 2.230000e-32 150.0
21 TraesCS3D01G113500 chr7A 93.204 103 5 2 2050 2151 648672266 648672165 2.230000e-32 150.0
22 TraesCS3D01G113500 chr7A 91.589 107 7 2 2046 2151 648675351 648675246 2.890000e-31 147.0
23 TraesCS3D01G113500 chr2B 90.785 586 40 8 2049 2620 18321644 18322229 0.000000e+00 771.0
24 TraesCS3D01G113500 chr2B 94.702 151 8 0 612 762 526417272 526417422 6.000000e-58 235.0
25 TraesCS3D01G113500 chr2B 89.744 117 7 4 2047 2163 283287049 283287160 1.040000e-30 145.0
26 TraesCS3D01G113500 chr1B 86.307 723 58 20 1350 2050 543087328 543086625 0.000000e+00 749.0
27 TraesCS3D01G113500 chr1B 90.448 513 30 11 859 1354 543089099 543088589 0.000000e+00 658.0
28 TraesCS3D01G113500 chr7B 96.092 435 17 0 726 1160 40952718 40953152 0.000000e+00 710.0
29 TraesCS3D01G113500 chr7B 87.646 429 43 8 2244 2670 584644398 584643978 1.160000e-134 490.0
30 TraesCS3D01G113500 chr7B 86.495 311 18 8 526 816 78319588 78319282 1.610000e-83 320.0
31 TraesCS3D01G113500 chr7B 87.783 221 21 5 2450 2670 40953199 40953413 1.660000e-63 254.0
32 TraesCS3D01G113500 chr3B 93.277 476 22 8 688 1160 644015158 644014690 0.000000e+00 693.0
33 TraesCS3D01G113500 chr3B 85.231 650 63 22 531 1160 309870574 309871210 3.910000e-179 638.0
34 TraesCS3D01G113500 chr3B 79.736 454 56 17 2401 2832 774133758 774134197 2.710000e-76 296.0
35 TraesCS3D01G113500 chr3B 83.696 184 25 4 244 425 748774925 748775105 6.170000e-38 169.0
36 TraesCS3D01G113500 chr5B 93.995 433 26 0 728 1160 290578141 290578573 0.000000e+00 656.0
37 TraesCS3D01G113500 chr5B 77.035 897 131 48 2395 3257 443270379 443271234 2.540000e-121 446.0
38 TraesCS3D01G113500 chr5B 88.208 212 19 5 2459 2670 290578629 290578834 7.700000e-62 248.0
39 TraesCS3D01G113500 chr5B 85.200 250 20 10 526 762 290577874 290578119 1.290000e-59 241.0
40 TraesCS3D01G113500 chr5B 84.127 126 18 2 3137 3261 443271247 443271371 1.750000e-23 121.0
41 TraesCS3D01G113500 chr3A 89.669 513 26 11 1 504 78898643 78899137 2.350000e-176 628.0
42 TraesCS3D01G113500 chr3A 84.302 172 22 4 2768 2937 719829586 719829418 2.870000e-36 163.0
43 TraesCS3D01G113500 chr3A 93.000 100 4 3 2047 2145 128095891 128095988 3.740000e-30 143.0
44 TraesCS3D01G113500 chr3A 78.261 138 22 8 302 434 560502638 560502772 8.270000e-12 82.4
45 TraesCS3D01G113500 chr3A 89.231 65 5 1 6 68 424231532 424231468 2.970000e-11 80.5
46 TraesCS3D01G113500 chr6A 88.292 521 46 12 859 1365 33174083 33173564 8.530000e-171 610.0
47 TraesCS3D01G113500 chr6A 84.024 169 22 4 2768 2934 185237254 185237419 1.340000e-34 158.0
48 TraesCS3D01G113500 chr4D 82.227 512 70 10 2768 3261 487010215 487010723 4.290000e-114 422.0
49 TraesCS3D01G113500 chr5A 84.150 347 43 9 2495 2832 64359183 64359526 3.460000e-85 326.0
50 TraesCS3D01G113500 chr5A 93.939 99 4 2 2047 2144 566581161 566581064 8.040000e-32 148.0
51 TraesCS3D01G113500 chr5D 90.984 244 10 5 525 762 416052718 416052481 5.790000e-83 318.0
52 TraesCS3D01G113500 chr5D 83.803 142 14 8 319 457 117783940 117783805 3.760000e-25 126.0
53 TraesCS3D01G113500 chr5D 83.333 126 19 2 3137 3261 373206010 373206134 8.150000e-22 115.0
54 TraesCS3D01G113500 chr4A 87.778 180 18 2 1268 1443 623982616 623982437 1.310000e-49 207.0
55 TraesCS3D01G113500 chr7D 92.857 112 5 3 526 637 140763566 140763458 3.710000e-35 159.0
56 TraesCS3D01G113500 chr7D 93.878 49 2 1 1 49 472283409 472283456 4.970000e-09 73.1
57 TraesCS3D01G113500 chrUn 92.105 114 6 2 524 637 92586352 92586242 1.340000e-34 158.0
58 TraesCS3D01G113500 chr6B 84.800 125 14 4 1 121 16590304 16590427 1.750000e-23 121.0
59 TraesCS3D01G113500 chr6B 82.979 94 10 4 1 89 674556569 674556661 2.970000e-11 80.5
60 TraesCS3D01G113500 chr2A 81.102 127 19 4 1 124 558594877 558595001 2.950000e-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 TraesCS3D01G113500 chr3D 67533446 67537037 3591 False 6634.000000 6634 100.000000 1 3592 1 chr3D.!!$F1 3591
1 TraesCS3D01G113500 chr6D 454300134 454305426 5292 True 1761.000000 4508 97.265333 521 3592 3 chr6D.!!$R1 3071
2 TraesCS3D01G113500 chr2D 312028620 312030539 1919 False 3245.000000 3245 97.106000 526 2455 1 chr2D.!!$F1 1929
3 TraesCS3D01G113500 chr2D 312043791 312046755 2964 False 909.000000 1406 98.452000 2453 3504 2 chr2D.!!$F2 1051
4 TraesCS3D01G113500 chr1D 403725133 403726312 1179 True 1386.000000 1386 88.007000 859 2048 1 chr1D.!!$R1 1189
5 TraesCS3D01G113500 chr1A 499443932 499445148 1216 True 1247.000000 1247 85.806000 859 2048 1 chr1A.!!$R2 1189
6 TraesCS3D01G113500 chr1A 584981999 584982516 517 True 612.000000 612 88.439000 859 1363 1 chr1A.!!$R3 504
7 TraesCS3D01G113500 chr7A 61493725 61494364 639 True 981.000000 981 94.264000 525 1169 1 chr7A.!!$R1 644
8 TraesCS3D01G113500 chr7A 109230784 109231410 626 True 896.000000 896 92.248000 526 1169 1 chr7A.!!$R2 643
9 TraesCS3D01G113500 chr7A 333606504 333610268 3764 True 870.333333 1147 92.674000 1167 3592 3 chr7A.!!$R3 2425
10 TraesCS3D01G113500 chr2B 18321644 18322229 585 False 771.000000 771 90.785000 2049 2620 1 chr2B.!!$F1 571
11 TraesCS3D01G113500 chr1B 543086625 543089099 2474 True 703.500000 749 88.377500 859 2050 2 chr1B.!!$R1 1191
12 TraesCS3D01G113500 chr7B 40952718 40953413 695 False 482.000000 710 91.937500 726 2670 2 chr7B.!!$F1 1944
13 TraesCS3D01G113500 chr3B 309870574 309871210 636 False 638.000000 638 85.231000 531 1160 1 chr3B.!!$F1 629
14 TraesCS3D01G113500 chr5B 290577874 290578834 960 False 381.666667 656 89.134333 526 2670 3 chr5B.!!$F1 2144
15 TraesCS3D01G113500 chr5B 443270379 443271371 992 False 283.500000 446 80.581000 2395 3261 2 chr5B.!!$F2 866
16 TraesCS3D01G113500 chr6A 33173564 33174083 519 True 610.000000 610 88.292000 859 1365 1 chr6A.!!$R1 506
17 TraesCS3D01G113500 chr4D 487010215 487010723 508 False 422.000000 422 82.227000 2768 3261 1 chr4D.!!$F1 493

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
104 105 0.037590 AACAAACCCTGCATAGCGGA 59.962 50.0 0.0 0.0 37.02 5.54 F
110 111 0.396435 CCCTGCATAGCGGAACCATA 59.604 55.0 0.0 0.0 37.02 2.74 F
217 218 0.405585 ACACAGGGGAGAATGGTTGG 59.594 55.0 0.0 0.0 0.00 3.77 F
218 219 0.405585 CACAGGGGAGAATGGTTGGT 59.594 55.0 0.0 0.0 0.00 3.67 F
219 220 0.405585 ACAGGGGAGAATGGTTGGTG 59.594 55.0 0.0 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1591 3284 1.061131 CCATTCTCTTGCGTAAGTGCG 59.939 52.381 13.14 3.78 41.68 5.34 R
2109 3839 0.509929 GGACGAAGAAAAACCGGACG 59.490 55.000 9.46 3.12 0.00 4.79 R
2205 3964 4.030134 CTGCGTCTTCGTAGGTTATTCT 57.970 45.455 0.00 0.00 43.88 2.40 R
2262 4027 1.074395 GTTAGGGGAGGAGGGGAGG 60.074 68.421 0.00 0.00 0.00 4.30 R
2863 4645 2.303600 AGGCATTGGCATCACAAACAAT 59.696 40.909 13.20 0.00 43.71 2.71 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
36 37 9.883142 TGTGTAATATGTGAGATATGTGTCAAA 57.117 29.630 0.00 0.00 28.36 2.69
45 46 9.942850 TGTGAGATATGTGTCAAATTTAGAAGA 57.057 29.630 0.00 0.00 28.36 2.87
87 88 4.639171 CACGGGTTGCGGCCAAAC 62.639 66.667 2.24 6.66 37.94 2.93
89 90 3.905678 CGGGTTGCGGCCAAACAA 61.906 61.111 17.57 9.29 40.49 2.83
90 91 2.501610 GGGTTGCGGCCAAACAAA 59.498 55.556 17.57 0.00 40.49 2.83
91 92 1.885388 GGGTTGCGGCCAAACAAAC 60.885 57.895 17.57 13.57 40.49 2.93
92 93 1.885388 GGTTGCGGCCAAACAAACC 60.885 57.895 17.57 11.97 38.55 3.27
93 94 1.885388 GTTGCGGCCAAACAAACCC 60.885 57.895 12.35 0.00 31.68 4.11
94 95 2.060980 TTGCGGCCAAACAAACCCT 61.061 52.632 2.24 0.00 0.00 4.34
95 96 2.028925 GCGGCCAAACAAACCCTG 59.971 61.111 2.24 0.00 0.00 4.45
96 97 2.028925 CGGCCAAACAAACCCTGC 59.971 61.111 2.24 0.00 0.00 4.85
97 98 2.790791 CGGCCAAACAAACCCTGCA 61.791 57.895 2.24 0.00 0.00 4.41
98 99 1.754107 GGCCAAACAAACCCTGCAT 59.246 52.632 0.00 0.00 0.00 3.96
99 100 0.972883 GGCCAAACAAACCCTGCATA 59.027 50.000 0.00 0.00 0.00 3.14
100 101 1.066929 GGCCAAACAAACCCTGCATAG 60.067 52.381 0.00 0.00 0.00 2.23
101 102 1.672737 GCCAAACAAACCCTGCATAGC 60.673 52.381 0.00 0.00 0.00 2.97
102 103 1.402720 CCAAACAAACCCTGCATAGCG 60.403 52.381 0.00 0.00 0.00 4.26
103 104 0.887933 AAACAAACCCTGCATAGCGG 59.112 50.000 0.00 0.00 34.23 5.52
104 105 0.037590 AACAAACCCTGCATAGCGGA 59.962 50.000 0.00 0.00 37.02 5.54
105 106 0.037590 ACAAACCCTGCATAGCGGAA 59.962 50.000 0.00 0.00 37.02 4.30
106 107 0.451783 CAAACCCTGCATAGCGGAAC 59.548 55.000 0.00 0.00 37.02 3.62
107 108 0.679960 AAACCCTGCATAGCGGAACC 60.680 55.000 0.00 0.00 37.02 3.62
108 109 1.847798 AACCCTGCATAGCGGAACCA 61.848 55.000 0.00 0.00 37.02 3.67
109 110 1.149174 CCCTGCATAGCGGAACCAT 59.851 57.895 0.00 0.00 37.02 3.55
110 111 0.396435 CCCTGCATAGCGGAACCATA 59.604 55.000 0.00 0.00 37.02 2.74
111 112 1.202758 CCCTGCATAGCGGAACCATAA 60.203 52.381 0.00 0.00 37.02 1.90
112 113 2.571212 CCTGCATAGCGGAACCATAAA 58.429 47.619 0.00 0.00 37.02 1.40
113 114 2.948979 CCTGCATAGCGGAACCATAAAA 59.051 45.455 0.00 0.00 37.02 1.52
114 115 3.380004 CCTGCATAGCGGAACCATAAAAA 59.620 43.478 0.00 0.00 37.02 1.94
140 141 8.388484 AGAATATTCACACTTCTAATGCATCC 57.612 34.615 17.56 0.00 0.00 3.51
141 142 8.216423 AGAATATTCACACTTCTAATGCATCCT 58.784 33.333 17.56 0.00 0.00 3.24
142 143 9.494271 GAATATTCACACTTCTAATGCATCCTA 57.506 33.333 10.68 0.00 0.00 2.94
143 144 9.851686 AATATTCACACTTCTAATGCATCCTAA 57.148 29.630 0.00 0.00 0.00 2.69
144 145 9.851686 ATATTCACACTTCTAATGCATCCTAAA 57.148 29.630 0.00 0.00 0.00 1.85
145 146 8.757982 ATTCACACTTCTAATGCATCCTAAAT 57.242 30.769 0.00 0.00 0.00 1.40
146 147 8.579850 TTCACACTTCTAATGCATCCTAAATT 57.420 30.769 0.00 0.00 0.00 1.82
147 148 8.579850 TCACACTTCTAATGCATCCTAAATTT 57.420 30.769 0.00 0.00 0.00 1.82
148 149 8.677300 TCACACTTCTAATGCATCCTAAATTTC 58.323 33.333 0.00 0.00 0.00 2.17
149 150 8.461222 CACACTTCTAATGCATCCTAAATTTCA 58.539 33.333 0.00 0.00 0.00 2.69
150 151 9.023962 ACACTTCTAATGCATCCTAAATTTCAA 57.976 29.630 0.00 0.00 0.00 2.69
191 192 4.640789 AAATCACTAGACGAGCTGTAGG 57.359 45.455 0.00 0.00 0.00 3.18
192 193 3.562343 ATCACTAGACGAGCTGTAGGA 57.438 47.619 0.00 0.00 0.00 2.94
193 194 2.907634 TCACTAGACGAGCTGTAGGAG 58.092 52.381 0.00 0.00 0.00 3.69
204 205 2.949451 CTGTAGGAGCAGTACACAGG 57.051 55.000 0.00 0.00 34.35 4.00
205 206 1.478510 CTGTAGGAGCAGTACACAGGG 59.521 57.143 0.00 0.00 34.35 4.45
206 207 0.824759 GTAGGAGCAGTACACAGGGG 59.175 60.000 0.00 0.00 0.00 4.79
207 208 0.708209 TAGGAGCAGTACACAGGGGA 59.292 55.000 0.00 0.00 0.00 4.81
208 209 0.616111 AGGAGCAGTACACAGGGGAG 60.616 60.000 0.00 0.00 0.00 4.30
209 210 0.614979 GGAGCAGTACACAGGGGAGA 60.615 60.000 0.00 0.00 0.00 3.71
210 211 1.267121 GAGCAGTACACAGGGGAGAA 58.733 55.000 0.00 0.00 0.00 2.87
211 212 1.834263 GAGCAGTACACAGGGGAGAAT 59.166 52.381 0.00 0.00 0.00 2.40
212 213 1.556911 AGCAGTACACAGGGGAGAATG 59.443 52.381 0.00 0.00 0.00 2.67
213 214 1.407437 GCAGTACACAGGGGAGAATGG 60.407 57.143 0.00 0.00 0.00 3.16
214 215 1.909302 CAGTACACAGGGGAGAATGGT 59.091 52.381 0.00 0.00 0.00 3.55
215 216 2.305927 CAGTACACAGGGGAGAATGGTT 59.694 50.000 0.00 0.00 0.00 3.67
216 217 2.305927 AGTACACAGGGGAGAATGGTTG 59.694 50.000 0.00 0.00 0.00 3.77
217 218 0.405585 ACACAGGGGAGAATGGTTGG 59.594 55.000 0.00 0.00 0.00 3.77
218 219 0.405585 CACAGGGGAGAATGGTTGGT 59.594 55.000 0.00 0.00 0.00 3.67
219 220 0.405585 ACAGGGGAGAATGGTTGGTG 59.594 55.000 0.00 0.00 0.00 4.17
220 221 0.698238 CAGGGGAGAATGGTTGGTGA 59.302 55.000 0.00 0.00 0.00 4.02
221 222 1.285962 CAGGGGAGAATGGTTGGTGAT 59.714 52.381 0.00 0.00 0.00 3.06
222 223 2.509548 CAGGGGAGAATGGTTGGTGATA 59.490 50.000 0.00 0.00 0.00 2.15
223 224 2.509964 AGGGGAGAATGGTTGGTGATAC 59.490 50.000 0.00 0.00 0.00 2.24
224 225 2.422945 GGGGAGAATGGTTGGTGATACC 60.423 54.545 0.00 0.00 39.22 2.73
239 240 4.672587 TGATACCATCACTTAGTGCTCC 57.327 45.455 7.61 0.00 33.59 4.70
240 241 3.388024 TGATACCATCACTTAGTGCTCCC 59.612 47.826 7.61 0.00 33.59 4.30
241 242 1.656587 ACCATCACTTAGTGCTCCCA 58.343 50.000 7.61 0.00 32.98 4.37
242 243 2.200081 ACCATCACTTAGTGCTCCCAT 58.800 47.619 7.61 0.00 32.98 4.00
243 244 2.092753 ACCATCACTTAGTGCTCCCATG 60.093 50.000 7.61 5.82 32.98 3.66
244 245 2.171237 CCATCACTTAGTGCTCCCATGA 59.829 50.000 7.61 0.00 32.98 3.07
245 246 3.181447 CCATCACTTAGTGCTCCCATGAT 60.181 47.826 7.61 0.00 32.98 2.45
246 247 4.040829 CCATCACTTAGTGCTCCCATGATA 59.959 45.833 7.61 0.00 32.98 2.15
247 248 5.455183 CCATCACTTAGTGCTCCCATGATAA 60.455 44.000 7.61 0.00 32.98 1.75
248 249 5.692115 TCACTTAGTGCTCCCATGATAAA 57.308 39.130 7.61 0.00 32.98 1.40
249 250 6.252599 TCACTTAGTGCTCCCATGATAAAT 57.747 37.500 7.61 0.00 32.98 1.40
250 251 6.662755 TCACTTAGTGCTCCCATGATAAATT 58.337 36.000 7.61 0.00 32.98 1.82
251 252 6.767902 TCACTTAGTGCTCCCATGATAAATTC 59.232 38.462 7.61 0.00 32.98 2.17
252 253 6.543465 CACTTAGTGCTCCCATGATAAATTCA 59.457 38.462 0.00 0.00 39.12 2.57
253 254 6.769822 ACTTAGTGCTCCCATGATAAATTCAG 59.230 38.462 0.00 0.00 37.89 3.02
254 255 3.887716 AGTGCTCCCATGATAAATTCAGC 59.112 43.478 0.00 0.00 37.89 4.26
255 256 3.633525 GTGCTCCCATGATAAATTCAGCA 59.366 43.478 0.00 0.00 37.89 4.41
256 257 4.280174 GTGCTCCCATGATAAATTCAGCAT 59.720 41.667 0.00 0.00 37.89 3.79
257 258 4.279922 TGCTCCCATGATAAATTCAGCATG 59.720 41.667 0.00 0.00 41.04 4.06
274 275 6.805713 TCAGCATGAATAGTGTCGATAAAGA 58.194 36.000 0.00 0.00 45.97 2.52
275 276 7.264947 TCAGCATGAATAGTGTCGATAAAGAA 58.735 34.615 0.00 0.00 45.97 2.52
276 277 7.763985 TCAGCATGAATAGTGTCGATAAAGAAA 59.236 33.333 0.00 0.00 45.97 2.52
277 278 8.390354 CAGCATGAATAGTGTCGATAAAGAAAA 58.610 33.333 0.00 0.00 39.69 2.29
278 279 8.946085 AGCATGAATAGTGTCGATAAAGAAAAA 58.054 29.630 0.00 0.00 0.00 1.94
301 302 7.736447 AAAACATGAAAAGTGTGAAAAACCA 57.264 28.000 0.00 0.00 0.00 3.67
302 303 6.720012 AACATGAAAAGTGTGAAAAACCAC 57.280 33.333 0.00 0.00 37.55 4.16
303 304 5.788450 ACATGAAAAGTGTGAAAAACCACA 58.212 33.333 0.00 0.00 43.98 4.17
314 315 6.806120 GTGAAAAACCACACTATTCACAAC 57.194 37.500 10.98 0.00 45.63 3.32
315 316 6.326375 GTGAAAAACCACACTATTCACAACA 58.674 36.000 10.98 0.00 45.63 3.33
316 317 6.472163 GTGAAAAACCACACTATTCACAACAG 59.528 38.462 10.98 0.00 45.63 3.16
317 318 5.514274 AAAACCACACTATTCACAACAGG 57.486 39.130 0.00 0.00 0.00 4.00
318 319 3.857157 ACCACACTATTCACAACAGGT 57.143 42.857 0.00 0.00 0.00 4.00
319 320 4.164843 ACCACACTATTCACAACAGGTT 57.835 40.909 0.00 0.00 0.00 3.50
320 321 4.532834 ACCACACTATTCACAACAGGTTT 58.467 39.130 0.00 0.00 0.00 3.27
321 322 4.338118 ACCACACTATTCACAACAGGTTTG 59.662 41.667 0.00 0.00 0.00 2.93
322 323 4.338118 CCACACTATTCACAACAGGTTTGT 59.662 41.667 0.00 0.00 39.87 2.83
323 324 5.505654 CCACACTATTCACAACAGGTTTGTC 60.506 44.000 0.00 0.00 36.23 3.18
324 325 5.296780 CACACTATTCACAACAGGTTTGTCT 59.703 40.000 0.00 0.00 36.23 3.41
325 326 5.885912 ACACTATTCACAACAGGTTTGTCTT 59.114 36.000 0.00 0.00 36.23 3.01
326 327 6.377146 ACACTATTCACAACAGGTTTGTCTTT 59.623 34.615 0.00 0.00 36.23 2.52
327 328 7.093945 ACACTATTCACAACAGGTTTGTCTTTT 60.094 33.333 0.00 0.00 36.23 2.27
328 329 7.759433 CACTATTCACAACAGGTTTGTCTTTTT 59.241 33.333 0.00 0.00 36.23 1.94
355 356 9.791820 TGCTTCTCAATGTGTATATCAAATTTG 57.208 29.630 12.15 12.15 32.17 2.32
356 357 9.241317 GCTTCTCAATGTGTATATCAAATTTGG 57.759 33.333 17.90 0.12 32.17 3.28
390 391 6.627395 TTTTAGGGTTTGTAGACACATGTG 57.373 37.500 24.25 24.25 33.76 3.21
392 393 4.164843 AGGGTTTGTAGACACATGTGTT 57.835 40.909 31.03 21.78 45.05 3.32
393 394 3.882888 AGGGTTTGTAGACACATGTGTTG 59.117 43.478 31.03 6.60 45.05 3.33
394 395 3.550030 GGGTTTGTAGACACATGTGTTGC 60.550 47.826 31.03 22.31 45.05 4.17
395 396 3.066064 GGTTTGTAGACACATGTGTTGCA 59.934 43.478 31.03 24.24 45.05 4.08
396 397 4.439426 GGTTTGTAGACACATGTGTTGCAA 60.439 41.667 31.03 27.46 45.05 4.08
397 398 4.972514 TTGTAGACACATGTGTTGCAAA 57.027 36.364 31.03 19.91 45.05 3.68
398 399 4.667262 TTGTAGACACATGTGTTGCAAAC 58.333 39.130 31.03 22.28 45.05 2.93
399 400 4.156739 TTGTAGACACATGTGTTGCAAACA 59.843 37.500 31.03 24.16 44.57 2.83
400 401 5.163571 TTGTAGACACATGTGTTGCAAACAT 60.164 36.000 31.03 16.54 46.73 2.71
401 402 6.950651 TTGTAGACACATGTGTTGCAAACATC 60.951 38.462 31.03 15.46 46.73 3.06
402 403 9.746233 TTGTAGACACATGTGTTGCAAACATCC 62.746 40.741 31.03 14.76 46.73 3.51
467 468 5.811399 TTGAATTTGTATCTAAGTGGCGG 57.189 39.130 0.00 0.00 0.00 6.13
468 469 4.839121 TGAATTTGTATCTAAGTGGCGGT 58.161 39.130 0.00 0.00 0.00 5.68
469 470 5.979993 TGAATTTGTATCTAAGTGGCGGTA 58.020 37.500 0.00 0.00 0.00 4.02
470 471 6.588204 TGAATTTGTATCTAAGTGGCGGTAT 58.412 36.000 0.00 0.00 0.00 2.73
471 472 6.704493 TGAATTTGTATCTAAGTGGCGGTATC 59.296 38.462 0.00 0.00 0.00 2.24
472 473 5.601583 TTTGTATCTAAGTGGCGGTATCA 57.398 39.130 0.00 0.00 0.00 2.15
473 474 4.579454 TGTATCTAAGTGGCGGTATCAC 57.421 45.455 0.00 0.00 35.51 3.06
474 475 2.795175 ATCTAAGTGGCGGTATCACG 57.205 50.000 0.00 0.00 39.86 4.35
475 476 1.466856 TCTAAGTGGCGGTATCACGT 58.533 50.000 0.00 0.00 39.86 4.49
476 477 1.133598 TCTAAGTGGCGGTATCACGTG 59.866 52.381 9.94 9.94 39.86 4.49
477 478 1.133598 CTAAGTGGCGGTATCACGTGA 59.866 52.381 22.48 22.48 39.86 4.35
478 479 0.535335 AAGTGGCGGTATCACGTGAT 59.465 50.000 31.93 31.93 39.86 3.06
479 480 1.395635 AGTGGCGGTATCACGTGATA 58.604 50.000 29.79 29.79 39.86 2.15
480 481 1.961394 AGTGGCGGTATCACGTGATAT 59.039 47.619 34.15 17.92 39.03 1.63
481 482 2.364324 AGTGGCGGTATCACGTGATATT 59.636 45.455 34.15 17.21 39.03 1.28
482 483 2.729882 GTGGCGGTATCACGTGATATTC 59.270 50.000 34.15 27.12 39.03 1.75
483 484 2.626266 TGGCGGTATCACGTGATATTCT 59.374 45.455 34.15 16.50 39.03 2.40
484 485 3.243336 GGCGGTATCACGTGATATTCTC 58.757 50.000 34.15 24.20 39.03 2.87
485 486 3.243336 GCGGTATCACGTGATATTCTCC 58.757 50.000 34.15 28.27 39.03 3.71
486 487 3.834610 CGGTATCACGTGATATTCTCCC 58.165 50.000 34.15 27.97 39.03 4.30
487 488 3.367087 CGGTATCACGTGATATTCTCCCC 60.367 52.174 34.15 27.39 39.03 4.81
488 489 3.576982 GGTATCACGTGATATTCTCCCCA 59.423 47.826 34.15 13.69 39.03 4.96
489 490 4.223032 GGTATCACGTGATATTCTCCCCAT 59.777 45.833 34.15 12.52 39.03 4.00
490 491 4.982241 ATCACGTGATATTCTCCCCATT 57.018 40.909 29.05 1.01 32.01 3.16
491 492 4.336889 TCACGTGATATTCTCCCCATTC 57.663 45.455 15.76 0.00 0.00 2.67
492 493 3.071023 TCACGTGATATTCTCCCCATTCC 59.929 47.826 15.76 0.00 0.00 3.01
493 494 2.372172 ACGTGATATTCTCCCCATTCCC 59.628 50.000 0.00 0.00 0.00 3.97
494 495 2.290323 CGTGATATTCTCCCCATTCCCC 60.290 54.545 0.00 0.00 0.00 4.81
495 496 2.716424 GTGATATTCTCCCCATTCCCCA 59.284 50.000 0.00 0.00 0.00 4.96
496 497 3.140144 GTGATATTCTCCCCATTCCCCAA 59.860 47.826 0.00 0.00 0.00 4.12
497 498 3.996465 TGATATTCTCCCCATTCCCCAAT 59.004 43.478 0.00 0.00 0.00 3.16
498 499 5.015178 GTGATATTCTCCCCATTCCCCAATA 59.985 44.000 0.00 0.00 0.00 1.90
499 500 3.903530 ATTCTCCCCATTCCCCAATAC 57.096 47.619 0.00 0.00 0.00 1.89
500 501 2.295269 TCTCCCCATTCCCCAATACA 57.705 50.000 0.00 0.00 0.00 2.29
501 502 1.850345 TCTCCCCATTCCCCAATACAC 59.150 52.381 0.00 0.00 0.00 2.90
502 503 1.568597 CTCCCCATTCCCCAATACACA 59.431 52.381 0.00 0.00 0.00 3.72
503 504 2.177669 CTCCCCATTCCCCAATACACAT 59.822 50.000 0.00 0.00 0.00 3.21
504 505 3.397618 CTCCCCATTCCCCAATACACATA 59.602 47.826 0.00 0.00 0.00 2.29
505 506 3.993692 TCCCCATTCCCCAATACACATAT 59.006 43.478 0.00 0.00 0.00 1.78
506 507 4.088634 CCCCATTCCCCAATACACATATG 58.911 47.826 0.00 0.00 0.00 1.78
507 508 3.511146 CCCATTCCCCAATACACATATGC 59.489 47.826 1.58 0.00 0.00 3.14
508 509 4.151121 CCATTCCCCAATACACATATGCA 58.849 43.478 1.58 0.00 0.00 3.96
509 510 4.773674 CCATTCCCCAATACACATATGCAT 59.226 41.667 3.79 3.79 0.00 3.96
510 511 5.105635 CCATTCCCCAATACACATATGCATC 60.106 44.000 0.19 0.00 0.00 3.91
511 512 4.720775 TCCCCAATACACATATGCATCA 57.279 40.909 0.19 0.00 0.00 3.07
512 513 4.654915 TCCCCAATACACATATGCATCAG 58.345 43.478 0.19 0.00 0.00 2.90
513 514 4.104579 TCCCCAATACACATATGCATCAGT 59.895 41.667 0.19 0.00 0.00 3.41
514 515 4.216902 CCCCAATACACATATGCATCAGTG 59.783 45.833 22.70 22.70 37.95 3.66
579 580 2.479656 CGTTCCGGGTTTATTTTCGTCA 59.520 45.455 0.00 0.00 0.00 4.35
911 1292 4.074526 GCTGGACGAGCTGAGGCA 62.075 66.667 1.67 0.00 45.21 4.75
1162 1565 4.210331 GTTTGGTCCAATATCATCTGCCT 58.790 43.478 4.80 0.00 0.00 4.75
1450 3128 9.537192 AGCAATAACAATCATTTTGTCATATGG 57.463 29.630 2.13 0.00 0.00 2.74
1524 3217 4.223032 CCTTGTAGAACTTCCTGCTTCCTA 59.777 45.833 0.00 0.00 0.00 2.94
1591 3284 1.339151 ACACCTTCGGAAGAGAATGGC 60.339 52.381 19.06 0.00 43.69 4.40
1916 3627 2.192664 TTATTCCTTGTGCTGCCGAA 57.807 45.000 0.00 0.00 0.00 4.30
2205 3964 0.900182 AGTCCCATGCTCGTCACAGA 60.900 55.000 0.00 0.00 0.00 3.41
3058 4857 1.154197 GTTCTTGTAGTTGGGGACGC 58.846 55.000 0.00 0.00 0.00 5.19
3146 5076 7.205992 TGATGATAATGCTTCACTACTGAGTC 58.794 38.462 0.00 0.00 31.73 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.883142 TTTGACACATATCTCACATATTACACA 57.117 29.630 0.00 0.00 0.00 3.72
19 20 9.942850 TCTTCTAAATTTGACACATATCTCACA 57.057 29.630 0.00 0.00 0.00 3.58
70 71 4.639171 GTTTGGCCGCAACCCGTG 62.639 66.667 6.38 0.00 34.38 4.94
72 73 3.432051 TTTGTTTGGCCGCAACCCG 62.432 57.895 13.65 0.00 0.00 5.28
73 74 1.885388 GTTTGTTTGGCCGCAACCC 60.885 57.895 13.65 2.56 0.00 4.11
74 75 1.885388 GGTTTGTTTGGCCGCAACC 60.885 57.895 13.65 9.65 0.00 3.77
75 76 1.885388 GGGTTTGTTTGGCCGCAAC 60.885 57.895 10.14 10.14 0.00 4.17
76 77 2.060980 AGGGTTTGTTTGGCCGCAA 61.061 52.632 0.00 0.00 0.00 4.85
77 78 2.443016 AGGGTTTGTTTGGCCGCA 60.443 55.556 0.00 0.00 0.00 5.69
78 79 2.028925 CAGGGTTTGTTTGGCCGC 59.971 61.111 0.00 0.00 0.00 6.53
79 80 2.028925 GCAGGGTTTGTTTGGCCG 59.971 61.111 0.00 0.00 0.00 6.13
80 81 0.972883 TATGCAGGGTTTGTTTGGCC 59.027 50.000 0.00 0.00 0.00 5.36
81 82 1.672737 GCTATGCAGGGTTTGTTTGGC 60.673 52.381 0.00 0.00 0.00 4.52
82 83 1.402720 CGCTATGCAGGGTTTGTTTGG 60.403 52.381 0.00 0.00 0.00 3.28
83 84 1.402720 CCGCTATGCAGGGTTTGTTTG 60.403 52.381 0.00 0.00 32.93 2.93
84 85 0.887933 CCGCTATGCAGGGTTTGTTT 59.112 50.000 0.00 0.00 32.93 2.83
85 86 0.037590 TCCGCTATGCAGGGTTTGTT 59.962 50.000 0.00 0.00 32.93 2.83
86 87 0.037590 TTCCGCTATGCAGGGTTTGT 59.962 50.000 0.00 0.00 32.93 2.83
87 88 0.451783 GTTCCGCTATGCAGGGTTTG 59.548 55.000 0.00 0.00 32.93 2.93
88 89 0.679960 GGTTCCGCTATGCAGGGTTT 60.680 55.000 0.00 0.00 32.93 3.27
89 90 1.077716 GGTTCCGCTATGCAGGGTT 60.078 57.895 0.00 0.00 32.93 4.11
90 91 1.635817 ATGGTTCCGCTATGCAGGGT 61.636 55.000 0.00 0.00 32.93 4.34
91 92 0.396435 TATGGTTCCGCTATGCAGGG 59.604 55.000 0.00 0.00 34.56 4.45
92 93 2.254546 TTATGGTTCCGCTATGCAGG 57.745 50.000 0.00 0.00 0.00 4.85
93 94 4.630894 TTTTTATGGTTCCGCTATGCAG 57.369 40.909 0.00 0.00 0.00 4.41
114 115 8.844244 GGATGCATTAGAAGTGTGAATATTCTT 58.156 33.333 16.24 2.41 35.09 2.52
115 116 8.216423 AGGATGCATTAGAAGTGTGAATATTCT 58.784 33.333 16.24 0.00 37.13 2.40
116 117 8.388484 AGGATGCATTAGAAGTGTGAATATTC 57.612 34.615 8.60 8.60 0.00 1.75
117 118 9.851686 TTAGGATGCATTAGAAGTGTGAATATT 57.148 29.630 0.00 0.00 0.00 1.28
118 119 9.851686 TTTAGGATGCATTAGAAGTGTGAATAT 57.148 29.630 0.00 0.00 0.00 1.28
119 120 9.851686 ATTTAGGATGCATTAGAAGTGTGAATA 57.148 29.630 0.00 0.00 0.00 1.75
120 121 8.757982 ATTTAGGATGCATTAGAAGTGTGAAT 57.242 30.769 0.00 0.00 0.00 2.57
121 122 8.579850 AATTTAGGATGCATTAGAAGTGTGAA 57.420 30.769 0.00 0.00 0.00 3.18
122 123 8.579850 AAATTTAGGATGCATTAGAAGTGTGA 57.420 30.769 0.00 0.00 0.00 3.58
123 124 8.461222 TGAAATTTAGGATGCATTAGAAGTGTG 58.539 33.333 0.00 0.00 0.00 3.82
124 125 8.579850 TGAAATTTAGGATGCATTAGAAGTGT 57.420 30.769 0.00 0.00 0.00 3.55
168 169 5.185249 TCCTACAGCTCGTCTAGTGATTTTT 59.815 40.000 0.00 0.00 0.00 1.94
169 170 4.705507 TCCTACAGCTCGTCTAGTGATTTT 59.294 41.667 0.00 0.00 0.00 1.82
170 171 4.270834 TCCTACAGCTCGTCTAGTGATTT 58.729 43.478 0.00 0.00 0.00 2.17
171 172 3.880490 CTCCTACAGCTCGTCTAGTGATT 59.120 47.826 0.00 0.00 0.00 2.57
172 173 3.472652 CTCCTACAGCTCGTCTAGTGAT 58.527 50.000 0.00 0.00 0.00 3.06
173 174 2.907634 CTCCTACAGCTCGTCTAGTGA 58.092 52.381 0.00 0.00 0.00 3.41
174 175 1.332375 GCTCCTACAGCTCGTCTAGTG 59.668 57.143 0.00 0.00 45.83 2.74
175 176 1.670791 GCTCCTACAGCTCGTCTAGT 58.329 55.000 0.00 0.00 45.83 2.57
185 186 1.478510 CCCTGTGTACTGCTCCTACAG 59.521 57.143 0.00 0.00 43.59 2.74
186 187 1.557099 CCCTGTGTACTGCTCCTACA 58.443 55.000 0.00 0.00 0.00 2.74
187 188 0.824759 CCCCTGTGTACTGCTCCTAC 59.175 60.000 0.00 0.00 0.00 3.18
188 189 0.708209 TCCCCTGTGTACTGCTCCTA 59.292 55.000 0.00 0.00 0.00 2.94
189 190 0.616111 CTCCCCTGTGTACTGCTCCT 60.616 60.000 0.00 0.00 0.00 3.69
190 191 0.614979 TCTCCCCTGTGTACTGCTCC 60.615 60.000 0.00 0.00 0.00 4.70
191 192 1.267121 TTCTCCCCTGTGTACTGCTC 58.733 55.000 0.00 0.00 0.00 4.26
192 193 1.556911 CATTCTCCCCTGTGTACTGCT 59.443 52.381 0.00 0.00 0.00 4.24
193 194 1.407437 CCATTCTCCCCTGTGTACTGC 60.407 57.143 0.00 0.00 0.00 4.40
194 195 1.909302 ACCATTCTCCCCTGTGTACTG 59.091 52.381 0.00 0.00 0.00 2.74
195 196 2.305927 CAACCATTCTCCCCTGTGTACT 59.694 50.000 0.00 0.00 0.00 2.73
196 197 2.618045 CCAACCATTCTCCCCTGTGTAC 60.618 54.545 0.00 0.00 0.00 2.90
197 198 1.633432 CCAACCATTCTCCCCTGTGTA 59.367 52.381 0.00 0.00 0.00 2.90
198 199 0.405585 CCAACCATTCTCCCCTGTGT 59.594 55.000 0.00 0.00 0.00 3.72
199 200 0.405585 ACCAACCATTCTCCCCTGTG 59.594 55.000 0.00 0.00 0.00 3.66
200 201 0.405585 CACCAACCATTCTCCCCTGT 59.594 55.000 0.00 0.00 0.00 4.00
201 202 0.698238 TCACCAACCATTCTCCCCTG 59.302 55.000 0.00 0.00 0.00 4.45
202 203 1.686236 ATCACCAACCATTCTCCCCT 58.314 50.000 0.00 0.00 0.00 4.79
203 204 2.422945 GGTATCACCAACCATTCTCCCC 60.423 54.545 0.00 0.00 38.42 4.81
204 205 2.932261 GGTATCACCAACCATTCTCCC 58.068 52.381 0.00 0.00 38.42 4.30
218 219 3.388024 GGGAGCACTAAGTGATGGTATCA 59.612 47.826 0.00 0.00 35.23 2.15
219 220 3.388024 TGGGAGCACTAAGTGATGGTATC 59.612 47.826 0.00 0.00 35.23 2.24
220 221 3.384168 TGGGAGCACTAAGTGATGGTAT 58.616 45.455 0.00 0.00 35.23 2.73
221 222 2.827755 TGGGAGCACTAAGTGATGGTA 58.172 47.619 0.00 0.00 35.23 3.25
222 223 1.656587 TGGGAGCACTAAGTGATGGT 58.343 50.000 0.00 0.00 35.23 3.55
223 224 2.171237 TCATGGGAGCACTAAGTGATGG 59.829 50.000 0.00 0.00 35.23 3.51
224 225 3.548745 TCATGGGAGCACTAAGTGATG 57.451 47.619 0.00 0.00 35.23 3.07
225 226 5.894298 TTATCATGGGAGCACTAAGTGAT 57.106 39.130 0.00 0.00 35.23 3.06
226 227 5.692115 TTTATCATGGGAGCACTAAGTGA 57.308 39.130 0.00 0.00 35.23 3.41
227 228 6.543465 TGAATTTATCATGGGAGCACTAAGTG 59.457 38.462 0.00 0.00 32.68 3.16
228 229 6.662755 TGAATTTATCATGGGAGCACTAAGT 58.337 36.000 0.00 0.00 31.50 2.24
229 230 6.293845 GCTGAATTTATCATGGGAGCACTAAG 60.294 42.308 0.00 0.00 37.44 2.18
230 231 5.532406 GCTGAATTTATCATGGGAGCACTAA 59.468 40.000 0.00 0.00 37.44 2.24
231 232 5.065914 GCTGAATTTATCATGGGAGCACTA 58.934 41.667 0.00 0.00 37.44 2.74
232 233 3.887716 GCTGAATTTATCATGGGAGCACT 59.112 43.478 0.00 0.00 37.44 4.40
233 234 3.633525 TGCTGAATTTATCATGGGAGCAC 59.366 43.478 0.00 0.00 37.44 4.40
234 235 3.900971 TGCTGAATTTATCATGGGAGCA 58.099 40.909 0.00 0.00 37.44 4.26
235 236 4.521639 TCATGCTGAATTTATCATGGGAGC 59.478 41.667 12.46 0.00 37.44 4.70
236 237 6.644248 TTCATGCTGAATTTATCATGGGAG 57.356 37.500 12.46 0.00 37.44 4.30
237 238 7.946219 ACTATTCATGCTGAATTTATCATGGGA 59.054 33.333 12.46 4.59 44.03 4.37
238 239 8.027189 CACTATTCATGCTGAATTTATCATGGG 58.973 37.037 12.46 5.50 44.03 4.00
239 240 8.573885 ACACTATTCATGCTGAATTTATCATGG 58.426 33.333 12.46 1.88 44.03 3.66
240 241 9.608617 GACACTATTCATGCTGAATTTATCATG 57.391 33.333 14.02 7.52 44.03 3.07
241 242 8.501580 CGACACTATTCATGCTGAATTTATCAT 58.498 33.333 14.02 0.00 44.03 2.45
242 243 7.710475 TCGACACTATTCATGCTGAATTTATCA 59.290 33.333 14.02 0.00 44.03 2.15
243 244 8.076714 TCGACACTATTCATGCTGAATTTATC 57.923 34.615 14.02 8.32 44.03 1.75
244 245 8.613060 ATCGACACTATTCATGCTGAATTTAT 57.387 30.769 14.02 2.42 44.03 1.40
245 246 9.541143 TTATCGACACTATTCATGCTGAATTTA 57.459 29.630 14.02 0.98 44.03 1.40
246 247 6.932356 ATCGACACTATTCATGCTGAATTT 57.068 33.333 14.02 3.21 44.03 1.82
247 248 8.437360 TTTATCGACACTATTCATGCTGAATT 57.563 30.769 14.02 0.54 44.03 2.17
249 250 7.264947 TCTTTATCGACACTATTCATGCTGAA 58.735 34.615 0.00 1.85 41.09 3.02
250 251 6.805713 TCTTTATCGACACTATTCATGCTGA 58.194 36.000 0.00 0.00 0.00 4.26
251 252 7.468922 TTCTTTATCGACACTATTCATGCTG 57.531 36.000 0.00 0.00 0.00 4.41
252 253 8.492673 TTTTCTTTATCGACACTATTCATGCT 57.507 30.769 0.00 0.00 0.00 3.79
276 277 8.073167 GTGGTTTTTCACACTTTTCATGTTTTT 58.927 29.630 0.00 0.00 37.57 1.94
277 278 7.227512 TGTGGTTTTTCACACTTTTCATGTTTT 59.772 29.630 0.00 0.00 42.05 2.43
278 279 6.708054 TGTGGTTTTTCACACTTTTCATGTTT 59.292 30.769 0.00 0.00 42.05 2.83
279 280 6.226787 TGTGGTTTTTCACACTTTTCATGTT 58.773 32.000 0.00 0.00 42.05 2.71
280 281 5.788450 TGTGGTTTTTCACACTTTTCATGT 58.212 33.333 0.00 0.00 42.05 3.21
291 292 6.326375 TGTTGTGAATAGTGTGGTTTTTCAC 58.674 36.000 7.05 7.05 43.96 3.18
292 293 6.405286 CCTGTTGTGAATAGTGTGGTTTTTCA 60.405 38.462 0.00 0.00 0.00 2.69
293 294 5.977129 CCTGTTGTGAATAGTGTGGTTTTTC 59.023 40.000 0.00 0.00 0.00 2.29
294 295 5.420739 ACCTGTTGTGAATAGTGTGGTTTTT 59.579 36.000 0.00 0.00 0.00 1.94
295 296 4.953579 ACCTGTTGTGAATAGTGTGGTTTT 59.046 37.500 0.00 0.00 0.00 2.43
296 297 4.532834 ACCTGTTGTGAATAGTGTGGTTT 58.467 39.130 0.00 0.00 0.00 3.27
297 298 4.164843 ACCTGTTGTGAATAGTGTGGTT 57.835 40.909 0.00 0.00 0.00 3.67
298 299 3.857157 ACCTGTTGTGAATAGTGTGGT 57.143 42.857 0.00 0.00 0.00 4.16
299 300 4.338118 ACAAACCTGTTGTGAATAGTGTGG 59.662 41.667 0.00 0.00 28.57 4.17
300 301 5.296780 AGACAAACCTGTTGTGAATAGTGTG 59.703 40.000 0.00 0.00 35.30 3.82
301 302 5.437060 AGACAAACCTGTTGTGAATAGTGT 58.563 37.500 0.00 0.00 35.30 3.55
302 303 6.377327 AAGACAAACCTGTTGTGAATAGTG 57.623 37.500 0.00 0.00 35.30 2.74
303 304 7.404671 AAAAGACAAACCTGTTGTGAATAGT 57.595 32.000 0.00 0.00 35.30 2.12
329 330 9.791820 CAAATTTGATATACACATTGAGAAGCA 57.208 29.630 13.08 0.00 30.58 3.91
330 331 9.241317 CCAAATTTGATATACACATTGAGAAGC 57.759 33.333 19.86 0.00 30.58 3.86
366 367 6.603997 ACACATGTGTCTACAAACCCTAAAAA 59.396 34.615 25.76 0.00 40.24 1.94
367 368 6.123651 ACACATGTGTCTACAAACCCTAAAA 58.876 36.000 25.76 0.00 40.24 1.52
368 369 5.686753 ACACATGTGTCTACAAACCCTAAA 58.313 37.500 25.76 0.00 40.24 1.85
369 370 5.298989 ACACATGTGTCTACAAACCCTAA 57.701 39.130 25.76 0.00 40.24 2.69
370 371 4.967084 ACACATGTGTCTACAAACCCTA 57.033 40.909 25.76 0.00 40.24 3.53
371 372 3.857157 ACACATGTGTCTACAAACCCT 57.143 42.857 25.76 0.00 40.24 4.34
372 373 3.550030 GCAACACATGTGTCTACAAACCC 60.550 47.826 30.64 8.53 44.13 4.11
373 374 3.066064 TGCAACACATGTGTCTACAAACC 59.934 43.478 30.64 13.21 44.13 3.27
374 375 4.285807 TGCAACACATGTGTCTACAAAC 57.714 40.909 30.64 15.16 44.13 2.93
375 376 4.972514 TTGCAACACATGTGTCTACAAA 57.027 36.364 30.64 17.46 44.13 2.83
376 377 4.156739 TGTTTGCAACACATGTGTCTACAA 59.843 37.500 30.64 27.44 44.13 2.41
377 378 3.691609 TGTTTGCAACACATGTGTCTACA 59.308 39.130 30.64 23.95 44.13 2.74
378 379 4.285807 TGTTTGCAACACATGTGTCTAC 57.714 40.909 30.64 21.86 44.13 2.59
379 380 4.023279 GGATGTTTGCAACACATGTGTCTA 60.023 41.667 30.64 17.13 45.50 2.59
380 381 3.243501 GGATGTTTGCAACACATGTGTCT 60.244 43.478 30.64 17.91 45.50 3.41
381 382 3.052036 GGATGTTTGCAACACATGTGTC 58.948 45.455 30.64 19.70 45.50 3.67
382 383 2.429971 TGGATGTTTGCAACACATGTGT 59.570 40.909 25.76 25.76 45.50 3.72
383 384 3.095102 TGGATGTTTGCAACACATGTG 57.905 42.857 24.25 24.25 45.50 3.21
384 385 3.815856 TTGGATGTTTGCAACACATGT 57.184 38.095 23.13 0.00 45.50 3.21
385 386 5.676532 AAATTGGATGTTTGCAACACATG 57.323 34.783 23.13 0.00 45.50 3.21
386 387 6.696441 AAAAATTGGATGTTTGCAACACAT 57.304 29.167 20.13 20.13 45.50 3.21
442 443 7.087639 CCGCCACTTAGATACAAATTCAAAAA 58.912 34.615 0.00 0.00 0.00 1.94
443 444 6.207810 ACCGCCACTTAGATACAAATTCAAAA 59.792 34.615 0.00 0.00 0.00 2.44
444 445 5.708230 ACCGCCACTTAGATACAAATTCAAA 59.292 36.000 0.00 0.00 0.00 2.69
445 446 5.250200 ACCGCCACTTAGATACAAATTCAA 58.750 37.500 0.00 0.00 0.00 2.69
446 447 4.839121 ACCGCCACTTAGATACAAATTCA 58.161 39.130 0.00 0.00 0.00 2.57
447 448 6.704493 TGATACCGCCACTTAGATACAAATTC 59.296 38.462 0.00 0.00 0.00 2.17
448 449 6.482308 GTGATACCGCCACTTAGATACAAATT 59.518 38.462 0.00 0.00 0.00 1.82
449 450 5.989777 GTGATACCGCCACTTAGATACAAAT 59.010 40.000 0.00 0.00 0.00 2.32
450 451 5.353938 GTGATACCGCCACTTAGATACAAA 58.646 41.667 0.00 0.00 0.00 2.83
451 452 4.498513 CGTGATACCGCCACTTAGATACAA 60.499 45.833 0.00 0.00 32.64 2.41
452 453 3.004002 CGTGATACCGCCACTTAGATACA 59.996 47.826 0.00 0.00 32.64 2.29
453 454 3.004106 ACGTGATACCGCCACTTAGATAC 59.996 47.826 0.00 0.00 32.64 2.24
454 455 3.004002 CACGTGATACCGCCACTTAGATA 59.996 47.826 10.90 0.00 32.64 1.98
455 456 2.029623 ACGTGATACCGCCACTTAGAT 58.970 47.619 0.00 0.00 32.64 1.98
456 457 1.133598 CACGTGATACCGCCACTTAGA 59.866 52.381 10.90 0.00 32.64 2.10
457 458 1.133598 TCACGTGATACCGCCACTTAG 59.866 52.381 15.76 0.00 32.64 2.18
458 459 1.175654 TCACGTGATACCGCCACTTA 58.824 50.000 15.76 0.00 32.64 2.24
459 460 0.535335 ATCACGTGATACCGCCACTT 59.465 50.000 29.05 1.82 32.01 3.16
460 461 1.395635 TATCACGTGATACCGCCACT 58.604 50.000 29.79 10.59 36.05 4.00
461 462 2.433868 ATATCACGTGATACCGCCAC 57.566 50.000 34.29 0.00 39.57 5.01
462 463 2.626266 AGAATATCACGTGATACCGCCA 59.374 45.455 34.29 18.09 39.57 5.69
463 464 3.243336 GAGAATATCACGTGATACCGCC 58.757 50.000 34.29 23.28 39.57 6.13
464 465 3.243336 GGAGAATATCACGTGATACCGC 58.757 50.000 34.29 27.78 39.57 5.68
465 466 3.367087 GGGGAGAATATCACGTGATACCG 60.367 52.174 34.29 0.74 39.57 4.02
466 467 3.576982 TGGGGAGAATATCACGTGATACC 59.423 47.826 34.29 28.85 39.57 2.73
467 468 4.866508 TGGGGAGAATATCACGTGATAC 57.133 45.455 34.29 24.16 39.57 2.24
468 469 5.046591 GGAATGGGGAGAATATCACGTGATA 60.047 44.000 33.83 33.83 40.85 2.15
469 470 4.263068 GGAATGGGGAGAATATCACGTGAT 60.263 45.833 31.93 31.93 38.51 3.06
470 471 3.071023 GGAATGGGGAGAATATCACGTGA 59.929 47.826 22.48 22.48 28.88 4.35
471 472 3.403038 GGAATGGGGAGAATATCACGTG 58.597 50.000 9.94 9.94 28.88 4.49
472 473 2.372172 GGGAATGGGGAGAATATCACGT 59.628 50.000 0.00 0.00 28.88 4.49
473 474 2.290323 GGGGAATGGGGAGAATATCACG 60.290 54.545 0.00 0.00 28.88 4.35
474 475 2.716424 TGGGGAATGGGGAGAATATCAC 59.284 50.000 0.00 0.00 0.00 3.06
475 476 3.087956 TGGGGAATGGGGAGAATATCA 57.912 47.619 0.00 0.00 0.00 2.15
476 477 4.682021 ATTGGGGAATGGGGAGAATATC 57.318 45.455 0.00 0.00 0.00 1.63
477 478 4.925734 TGTATTGGGGAATGGGGAGAATAT 59.074 41.667 0.00 0.00 0.00 1.28
478 479 4.105697 GTGTATTGGGGAATGGGGAGAATA 59.894 45.833 0.00 0.00 0.00 1.75
479 480 3.117131 GTGTATTGGGGAATGGGGAGAAT 60.117 47.826 0.00 0.00 0.00 2.40
480 481 2.243736 GTGTATTGGGGAATGGGGAGAA 59.756 50.000 0.00 0.00 0.00 2.87
481 482 1.850345 GTGTATTGGGGAATGGGGAGA 59.150 52.381 0.00 0.00 0.00 3.71
482 483 1.568597 TGTGTATTGGGGAATGGGGAG 59.431 52.381 0.00 0.00 0.00 4.30
483 484 1.687492 TGTGTATTGGGGAATGGGGA 58.313 50.000 0.00 0.00 0.00 4.81
484 485 2.773525 ATGTGTATTGGGGAATGGGG 57.226 50.000 0.00 0.00 0.00 4.96
485 486 3.511146 GCATATGTGTATTGGGGAATGGG 59.489 47.826 4.29 0.00 0.00 4.00
486 487 4.151121 TGCATATGTGTATTGGGGAATGG 58.849 43.478 4.29 0.00 0.00 3.16
487 488 5.477637 TGATGCATATGTGTATTGGGGAATG 59.522 40.000 0.00 0.00 30.30 2.67
488 489 5.643176 TGATGCATATGTGTATTGGGGAAT 58.357 37.500 0.00 0.00 30.30 3.01
489 490 5.059134 TGATGCATATGTGTATTGGGGAA 57.941 39.130 0.00 0.00 30.30 3.97
490 491 4.104579 ACTGATGCATATGTGTATTGGGGA 59.895 41.667 0.00 0.00 30.30 4.81
491 492 4.216902 CACTGATGCATATGTGTATTGGGG 59.783 45.833 18.17 0.00 30.30 4.96
492 493 5.366829 CACTGATGCATATGTGTATTGGG 57.633 43.478 18.17 0.00 30.30 4.12
507 508 5.417811 AGAGATTAGAAGTGTGCACTGATG 58.582 41.667 19.41 0.00 41.58 3.07
508 509 5.674052 AGAGATTAGAAGTGTGCACTGAT 57.326 39.130 19.41 3.29 41.58 2.90
509 510 5.712446 AGTAGAGATTAGAAGTGTGCACTGA 59.288 40.000 19.41 0.00 41.58 3.41
510 511 5.960113 AGTAGAGATTAGAAGTGTGCACTG 58.040 41.667 19.41 0.00 41.58 3.66
511 512 5.126384 GGAGTAGAGATTAGAAGTGTGCACT 59.874 44.000 19.41 0.00 44.94 4.40
512 513 5.126384 AGGAGTAGAGATTAGAAGTGTGCAC 59.874 44.000 10.75 10.75 0.00 4.57
513 514 5.265191 AGGAGTAGAGATTAGAAGTGTGCA 58.735 41.667 0.00 0.00 0.00 4.57
514 515 5.845391 AGGAGTAGAGATTAGAAGTGTGC 57.155 43.478 0.00 0.00 0.00 4.57
515 516 8.908903 ACATTAGGAGTAGAGATTAGAAGTGTG 58.091 37.037 0.00 0.00 0.00 3.82
516 517 9.127277 GACATTAGGAGTAGAGATTAGAAGTGT 57.873 37.037 0.00 0.00 0.00 3.55
517 518 9.349713 AGACATTAGGAGTAGAGATTAGAAGTG 57.650 37.037 0.00 0.00 0.00 3.16
518 519 9.569122 GAGACATTAGGAGTAGAGATTAGAAGT 57.431 37.037 0.00 0.00 0.00 3.01
519 520 9.567776 TGAGACATTAGGAGTAGAGATTAGAAG 57.432 37.037 0.00 0.00 0.00 2.85
520 521 9.567776 CTGAGACATTAGGAGTAGAGATTAGAA 57.432 37.037 0.00 0.00 0.00 2.10
521 522 8.719596 ACTGAGACATTAGGAGTAGAGATTAGA 58.280 37.037 0.00 0.00 0.00 2.10
522 523 8.918202 ACTGAGACATTAGGAGTAGAGATTAG 57.082 38.462 0.00 0.00 0.00 1.73
523 524 9.126151 CAACTGAGACATTAGGAGTAGAGATTA 57.874 37.037 0.00 0.00 0.00 1.75
579 580 1.682740 AAACCGGACGAAAATGGTGT 58.317 45.000 9.46 0.00 34.26 4.16
656 685 4.408821 ACGGATGGTGGCGCATGT 62.409 61.111 10.83 0.00 0.00 3.21
660 689 4.148825 AGAGACGGATGGTGGCGC 62.149 66.667 0.00 0.00 0.00 6.53
864 1245 3.382832 CGCACCGACTCCCTCCTT 61.383 66.667 0.00 0.00 0.00 3.36
1524 3217 9.365906 TGGTGTAATTTCATCATAAATGGCTAT 57.634 29.630 0.00 0.00 0.00 2.97
1591 3284 1.061131 CCATTCTCTTGCGTAAGTGCG 59.939 52.381 13.14 3.78 41.68 5.34
2109 3839 0.509929 GGACGAAGAAAAACCGGACG 59.490 55.000 9.46 3.12 0.00 4.79
2205 3964 4.030134 CTGCGTCTTCGTAGGTTATTCT 57.970 45.455 0.00 0.00 43.88 2.40
2262 4027 1.074395 GTTAGGGGAGGAGGGGAGG 60.074 68.421 0.00 0.00 0.00 4.30
2863 4645 2.303600 AGGCATTGGCATCACAAACAAT 59.696 40.909 13.20 0.00 43.71 2.71
3058 4857 4.742201 CTGTCACGGGCTCACGGG 62.742 72.222 0.00 0.00 38.97 5.28
3146 5076 3.571571 TCGTCTCACCGTTTCTTACATG 58.428 45.455 0.00 0.00 0.00 3.21
3275 5208 6.750148 ACGTCTTGAGAATAAAGAACTCACT 58.250 36.000 0.00 0.00 39.80 3.41
3276 5209 7.382759 AGAACGTCTTGAGAATAAAGAACTCAC 59.617 37.037 0.00 0.00 39.80 3.51
3277 5210 7.434492 AGAACGTCTTGAGAATAAAGAACTCA 58.566 34.615 0.00 0.00 38.61 3.41


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

AutoCloner maintained by Alex Coulton.