Multiple sequence alignment - TraesCS6D01G363200

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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 TraesCS6D01G363200 chr6D 100.000 7086 0 0 1 7086 453693150 453686065 0.000000e+00 13086.0
1 TraesCS6D01G363200 chr6D 83.238 698 101 12 4332 5025 453720678 453719993 1.680000e-175 627.0
2 TraesCS6D01G363200 chr6D 84.831 356 52 2 5812 6167 453718958 453718605 2.430000e-94 357.0
3 TraesCS6D01G363200 chr6D 86.452 310 36 4 5383 5689 453719463 453719157 1.140000e-87 335.0
4 TraesCS6D01G363200 chr6D 78.067 269 52 7 3181 3444 68915813 68915547 5.690000e-36 163.0
5 TraesCS6D01G363200 chr6B 89.557 2413 151 41 557 2947 689175483 689173150 0.000000e+00 2966.0
6 TraesCS6D01G363200 chr6B 94.448 1495 74 8 3163 4651 689172704 689171213 0.000000e+00 2292.0
7 TraesCS6D01G363200 chr6B 95.406 849 31 4 5382 6222 689169822 689168974 0.000000e+00 1345.0
8 TraesCS6D01G363200 chr6B 95.007 681 19 3 4683 5348 689170835 689170155 0.000000e+00 1055.0
9 TraesCS6D01G363200 chr6B 84.119 1039 110 22 809 1835 689069418 689068423 0.000000e+00 953.0
10 TraesCS6D01G363200 chr6B 88.191 796 67 20 10 798 689070418 689069643 0.000000e+00 924.0
11 TraesCS6D01G363200 chr6B 90.762 617 41 9 6441 7045 689165719 689165107 0.000000e+00 809.0
12 TraesCS6D01G363200 chr6B 78.033 1393 219 57 3771 5139 689067394 689066065 0.000000e+00 797.0
13 TraesCS6D01G363200 chr6B 80.559 823 125 20 4337 5139 689119032 689118225 2.830000e-168 603.0
14 TraesCS6D01G363200 chr6B 75.549 1002 179 46 3818 4806 689211047 689210099 3.930000e-117 433.0
15 TraesCS6D01G363200 chr6B 85.434 357 48 4 5812 6167 689097757 689097404 1.120000e-97 368.0
16 TraesCS6D01G363200 chr6B 85.434 357 48 4 5812 6167 689117326 689116973 1.120000e-97 368.0
17 TraesCS6D01G363200 chr6B 81.290 465 58 17 5814 6272 689065186 689064745 4.070000e-92 350.0
18 TraesCS6D01G363200 chr6B 95.067 223 9 2 2944 3165 689173038 689172817 4.070000e-92 350.0
19 TraesCS6D01G363200 chr6B 86.688 308 36 4 5383 5689 689065672 689065369 3.170000e-88 337.0
20 TraesCS6D01G363200 chr6B 90.116 172 14 3 6272 6442 689166194 689166025 3.330000e-53 220.0
21 TraesCS6D01G363200 chr6B 90.000 150 15 0 5411 5560 689208948 689208799 2.020000e-45 195.0
22 TraesCS6D01G363200 chr6B 81.778 225 33 7 3214 3434 704770219 704769999 1.570000e-41 182.0
23 TraesCS6D01G363200 chr6B 85.714 147 21 0 4881 5027 689209463 689209317 9.520000e-34 156.0
24 TraesCS6D01G363200 chr6A 91.857 1928 97 29 679 2579 599851305 599849411 0.000000e+00 2636.0
25 TraesCS6D01G363200 chr6A 96.067 839 32 1 5382 6219 599844866 599844028 0.000000e+00 1365.0
26 TraesCS6D01G363200 chr6A 94.240 625 25 8 4034 4649 599846759 599846137 0.000000e+00 944.0
27 TraesCS6D01G363200 chr6A 91.318 645 35 7 4707 5346 599845824 599845196 0.000000e+00 861.0
28 TraesCS6D01G363200 chr6A 86.239 654 38 13 2585 3228 599848652 599848041 0.000000e+00 662.0
29 TraesCS6D01G363200 chr6A 82.768 737 108 12 4337 5065 599868047 599867322 2.160000e-179 640.0
30 TraesCS6D01G363200 chr6A 90.269 483 43 4 3236 3717 599847593 599847114 4.670000e-176 628.0
31 TraesCS6D01G363200 chr6A 80.022 891 141 23 986 1859 599870119 599869249 6.040000e-175 625.0
32 TraesCS6D01G363200 chr6A 92.219 347 21 6 6244 6589 599843734 599843393 2.970000e-133 486.0
33 TraesCS6D01G363200 chr6A 95.736 258 11 0 3745 4002 599847008 599846751 3.950000e-112 416.0
34 TraesCS6D01G363200 chr6A 84.078 358 51 5 5812 6167 599866343 599865990 2.450000e-89 340.0
35 TraesCS6D01G363200 chr6A 86.774 310 35 4 5383 5689 599866829 599866523 2.450000e-89 340.0
36 TraesCS6D01G363200 chr6A 91.981 212 14 2 6604 6813 599842418 599842208 1.930000e-75 294.0
37 TraesCS6D01G363200 chr6A 79.259 270 38 14 3182 3441 136701849 136701588 9.450000e-39 172.0
38 TraesCS6D01G363200 chr6A 87.143 140 13 3 557 694 599851407 599851543 3.420000e-33 154.0
39 TraesCS6D01G363200 chrUn 84.216 1039 109 23 809 1835 216132539 216133534 0.000000e+00 959.0
40 TraesCS6D01G363200 chrUn 88.191 796 67 20 10 798 216131539 216132314 0.000000e+00 924.0
41 TraesCS6D01G363200 chrUn 78.033 1393 219 57 3771 5139 216134575 216135904 0.000000e+00 797.0
42 TraesCS6D01G363200 chrUn 81.290 465 58 17 5814 6272 216136783 216137224 4.070000e-92 350.0
43 TraesCS6D01G363200 chrUn 81.290 465 58 17 5814 6272 356425218 356424777 4.070000e-92 350.0
44 TraesCS6D01G363200 chrUn 85.902 305 38 4 5383 5686 216136297 216136597 3.190000e-83 320.0
45 TraesCS6D01G363200 chr3B 84.216 1039 109 23 809 1835 349680078 349681073 0.000000e+00 959.0
46 TraesCS6D01G363200 chr3B 78.033 1393 219 57 3771 5139 349682114 349683443 0.000000e+00 797.0
47 TraesCS6D01G363200 chr3B 85.902 305 38 4 5383 5686 349683836 349684136 3.190000e-83 320.0
48 TraesCS6D01G363200 chr7A 78.309 272 50 9 3181 3447 30627168 30627435 4.400000e-37 167.0
49 TraesCS6D01G363200 chr3D 78.599 257 49 6 3181 3433 550380518 550380772 1.580000e-36 165.0
50 TraesCS6D01G363200 chr4A 78.491 265 46 10 3182 3439 29806872 29806612 5.690000e-36 163.0
51 TraesCS6D01G363200 chr5D 77.698 278 52 9 3175 3447 440197526 440197798 2.050000e-35 161.0
52 TraesCS6D01G363200 chr2B 77.128 188 39 4 88 273 539285522 539285337 9.720000e-19 106.0
53 TraesCS6D01G363200 chr2B 92.500 40 3 0 462 501 169441162 169441123 2.760000e-04 58.4
54 TraesCS6D01G363200 chr4B 100.000 29 0 0 503 531 673094505 673094533 4.000000e-03 54.7
55 TraesCS6D01G363200 chr2A 92.308 39 2 1 463 501 438732957 438732920 4.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G363200 chr6D 453686065 453693150 7085 True 13086.000000 13086 100.000000 1 7086 1 chr6D.!!$R2 7085
1 TraesCS6D01G363200 chr6D 453718605 453720678 2073 True 439.666667 627 84.840333 4332 6167 3 chr6D.!!$R3 1835
2 TraesCS6D01G363200 chr6B 689165107 689175483 10376 True 1291.000000 2966 92.909000 557 7045 7 chr6B.!!$R5 6488
3 TraesCS6D01G363200 chr6B 689064745 689070418 5673 True 672.200000 953 83.664200 10 6272 5 chr6B.!!$R3 6262
4 TraesCS6D01G363200 chr6B 689116973 689119032 2059 True 485.500000 603 82.996500 4337 6167 2 chr6B.!!$R4 1830
5 TraesCS6D01G363200 chr6B 689208799 689211047 2248 True 261.333333 433 83.754333 3818 5560 3 chr6B.!!$R6 1742
6 TraesCS6D01G363200 chr6A 599842208 599851305 9097 True 921.333333 2636 92.214000 679 6813 9 chr6A.!!$R2 6134
7 TraesCS6D01G363200 chr6A 599865990 599870119 4129 True 486.250000 640 83.410500 986 6167 4 chr6A.!!$R3 5181
8 TraesCS6D01G363200 chrUn 216131539 216137224 5685 False 670.000000 959 83.526400 10 6272 5 chrUn.!!$F1 6262
9 TraesCS6D01G363200 chr3B 349680078 349684136 4058 False 692.000000 959 82.717000 809 5686 3 chr3B.!!$F1 4877

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
95 96 0.108472 TCTGGCTTGCGTCAGATGAG 60.108 55.000 0.00 0.00 46.36 2.90 F
216 217 0.399806 GGCTGGAAGAGGAGAGGGAT 60.400 60.000 0.00 0.00 34.07 3.85 F
329 330 0.460284 GAGGGACACGTGGCATGTAG 60.460 60.000 25.47 9.57 0.00 2.74 F
1541 1782 0.464013 CTGGCCATCTCCAGCTCAAG 60.464 60.000 5.51 0.00 46.11 3.02 F
1550 1791 1.142748 CCAGCTCAAGGGCGACTAG 59.857 63.158 0.00 0.00 37.29 2.57 F
2073 3388 1.957668 TGGCCAAGTCATCATCATCG 58.042 50.000 0.61 0.00 0.00 3.84 F
3339 6097 2.589798 TCTCGTTTCACTTCCAACGT 57.410 45.000 4.53 0.00 44.87 3.99 F
4451 7448 2.979813 CAAACGGCTTTCTCCAAATTCG 59.020 45.455 0.00 0.00 0.00 3.34 F
4658 7656 0.184933 TATAATGCCCACCCCACTGC 59.815 55.000 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1537 1778 0.171903 GCGTAACTAGTCGCCCTTGA 59.828 55.000 15.95 0.00 45.54 3.02 R
1544 1785 1.297158 CCGGTCGCGTAACTAGTCG 60.297 63.158 5.77 0.00 0.00 4.18 R
1803 2062 3.738282 GCATGTCGATCTTGATAGTGTCC 59.262 47.826 0.00 0.00 0.00 4.02 R
2450 3779 1.310904 TTGTGGGTTAGTTCGGTTGC 58.689 50.000 0.00 0.00 0.00 4.17 R
2569 3898 2.383245 ATAACCATGCGAGGAGGCCG 62.383 60.000 0.00 0.00 0.00 6.13 R
3959 6804 0.322456 TGCCAAATCCACCTTCTCCG 60.322 55.000 0.00 0.00 0.00 4.63 R
4520 7517 0.620030 TGCAGCATCCAAGAAGCCTA 59.380 50.000 0.00 0.00 0.00 3.93 R
5366 9317 0.439214 TAAACCGTATTGCGCACACG 59.561 50.000 27.99 27.99 44.07 4.49 R
6472 13938 0.181587 TGGGTCATTTGGTGTGACGT 59.818 50.000 0.00 0.00 45.32 4.34 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
21 22 1.385206 GGCAAGAGGAGGAGGGGAT 60.385 63.158 0.00 0.00 0.00 3.85
38 39 1.285078 GGATAGGGGGTGACAAGCTTT 59.715 52.381 0.00 0.00 0.00 3.51
39 40 2.291605 GGATAGGGGGTGACAAGCTTTT 60.292 50.000 0.00 0.00 0.00 2.27
51 52 2.223479 ACAAGCTTTTACAACCAGTGCG 60.223 45.455 0.00 0.00 0.00 5.34
54 55 1.334689 GCTTTTACAACCAGTGCGGAC 60.335 52.381 0.00 0.00 38.63 4.79
58 59 2.424705 TACAACCAGTGCGGACGACC 62.425 60.000 0.00 0.00 38.63 4.79
69 70 3.112709 GACGACCGCCTGTTCTGC 61.113 66.667 0.00 0.00 0.00 4.26
70 71 4.681978 ACGACCGCCTGTTCTGCC 62.682 66.667 0.00 0.00 0.00 4.85
78 79 1.919600 GCCTGTTCTGCCCCATCTCT 61.920 60.000 0.00 0.00 0.00 3.10
95 96 0.108472 TCTGGCTTGCGTCAGATGAG 60.108 55.000 0.00 0.00 46.36 2.90
114 115 2.182030 GGACGCAAGGAGGAGACG 59.818 66.667 0.00 0.00 46.39 4.18
129 130 0.679505 AGACGCCTACAACAGCTTGA 59.320 50.000 0.00 0.00 0.00 3.02
145 146 0.457166 TTGAGGCGGTTATCACGACG 60.457 55.000 0.00 0.00 45.85 5.12
162 163 1.125093 ACGAGGTCATGGTGGTGGAA 61.125 55.000 0.00 0.00 0.00 3.53
166 167 0.400213 GGTCATGGTGGTGGAAGACA 59.600 55.000 0.00 0.00 0.00 3.41
176 177 1.620822 GTGGAAGACAATGGGTTGCT 58.379 50.000 0.00 0.00 38.96 3.91
182 183 2.165167 AGACAATGGGTTGCTGACATG 58.835 47.619 0.00 0.00 38.96 3.21
183 184 0.604578 ACAATGGGTTGCTGACATGC 59.395 50.000 0.00 0.00 38.96 4.06
185 186 0.542467 AATGGGTTGCTGACATGCCA 60.542 50.000 0.00 0.00 0.00 4.92
186 187 1.252904 ATGGGTTGCTGACATGCCAC 61.253 55.000 0.00 0.00 0.00 5.01
187 188 1.902918 GGGTTGCTGACATGCCACA 60.903 57.895 0.00 0.00 31.24 4.17
191 192 2.548493 GGTTGCTGACATGCCACAAAAT 60.548 45.455 0.00 0.00 31.24 1.82
192 193 3.305950 GGTTGCTGACATGCCACAAAATA 60.306 43.478 0.00 0.00 31.24 1.40
203 204 2.214376 CACAAAATAGGTGGGCTGGA 57.786 50.000 0.00 0.00 32.65 3.86
216 217 0.399806 GGCTGGAAGAGGAGAGGGAT 60.400 60.000 0.00 0.00 34.07 3.85
222 223 1.618343 GAAGAGGAGAGGGATAGCTGC 59.382 57.143 0.00 0.00 0.00 5.25
225 226 0.560193 AGGAGAGGGATAGCTGCAGA 59.440 55.000 20.43 0.00 0.00 4.26
233 234 1.407936 GATAGCTGCAGAGGAGTGGA 58.592 55.000 20.43 0.00 0.00 4.02
245 246 2.362120 AGTGGAAGCTGCCATGCC 60.362 61.111 19.04 3.82 40.68 4.40
272 273 2.967076 CACACACAACCGCTCGCT 60.967 61.111 0.00 0.00 0.00 4.93
273 274 2.203015 ACACACAACCGCTCGCTT 60.203 55.556 0.00 0.00 0.00 4.68
279 280 1.076332 ACAACCGCTCGCTTCATAAC 58.924 50.000 0.00 0.00 0.00 1.89
299 300 1.727880 CAAATTGCAATGGAAGCGGTG 59.272 47.619 13.82 0.00 33.85 4.94
324 325 2.347114 CATGAGGGACACGTGGCA 59.653 61.111 25.47 11.40 32.36 4.92
325 326 1.078214 CATGAGGGACACGTGGCAT 60.078 57.895 25.47 11.45 32.36 4.40
326 327 1.078214 ATGAGGGACACGTGGCATG 60.078 57.895 25.47 4.87 0.00 4.06
327 328 1.841302 ATGAGGGACACGTGGCATGT 61.841 55.000 25.47 6.51 0.00 3.21
329 330 0.460284 GAGGGACACGTGGCATGTAG 60.460 60.000 25.47 9.57 0.00 2.74
335 336 0.744414 CACGTGGCATGTAGGGAAGG 60.744 60.000 12.81 0.00 0.00 3.46
336 337 1.198759 ACGTGGCATGTAGGGAAGGT 61.199 55.000 11.37 0.00 0.00 3.50
346 347 1.140312 TAGGGAAGGTGATGGATGCC 58.860 55.000 0.00 0.00 0.00 4.40
418 419 6.064717 GGGAAACTATGATAGCTGAAACCAT 58.935 40.000 0.00 0.00 0.00 3.55
440 441 6.872020 CCATCTTGAGGTAGACGAAAAAGTAA 59.128 38.462 0.00 0.00 0.00 2.24
448 449 6.774170 AGGTAGACGAAAAAGTAACCCAAATT 59.226 34.615 0.00 0.00 33.23 1.82
465 466 8.225603 ACCCAAATTCAATACATGATGTACTC 57.774 34.615 7.55 0.00 38.03 2.59
466 467 7.012327 ACCCAAATTCAATACATGATGTACTCG 59.988 37.037 7.55 0.00 38.03 4.18
471 472 6.877611 TCAATACATGATGTACTCGCTCTA 57.122 37.500 7.55 0.00 35.42 2.43
483 484 9.123709 GATGTACTCGCTCTATCTCAAAATAAG 57.876 37.037 0.00 0.00 0.00 1.73
484 485 7.997482 TGTACTCGCTCTATCTCAAAATAAGT 58.003 34.615 0.00 0.00 0.00 2.24
485 486 7.915923 TGTACTCGCTCTATCTCAAAATAAGTG 59.084 37.037 0.00 0.00 0.00 3.16
499 500 7.708998 TCAAAATAAGTGTCCCAACTTTGTAC 58.291 34.615 0.00 0.00 40.77 2.90
502 503 3.208747 AGTGTCCCAACTTTGTACTGG 57.791 47.619 0.00 0.00 0.00 4.00
523 524 7.659186 ACTGGTACTAAAGTTGAGACACTTAG 58.341 38.462 0.00 0.00 35.87 2.18
528 529 7.787725 ACTAAAGTTGAGACACTTAGTTTGG 57.212 36.000 0.00 0.00 35.87 3.28
564 567 1.205657 ACATAATGTTAGTCGGCGCG 58.794 50.000 0.00 0.00 0.00 6.86
598 601 4.272504 TCGTGGAACATTGACTTCAAGAAC 59.727 41.667 0.00 0.00 44.52 3.01
603 606 6.260050 TGGAACATTGACTTCAAGAACTGTAC 59.740 38.462 0.00 0.00 39.47 2.90
605 608 7.041098 GGAACATTGACTTCAAGAACTGTACAT 60.041 37.037 0.00 0.00 39.47 2.29
646 654 5.640783 CCAGTATAGTGTGCATATCCATGTG 59.359 44.000 6.81 0.00 34.40 3.21
804 820 1.821216 AACAAGCCAAGTACATCCCG 58.179 50.000 0.00 0.00 0.00 5.14
856 1086 1.680860 CGGTATTGGTTGGAAGACCCC 60.681 57.143 0.00 0.00 39.01 4.95
857 1087 1.680860 GGTATTGGTTGGAAGACCCCG 60.681 57.143 0.00 0.00 39.01 5.73
858 1088 1.003928 GTATTGGTTGGAAGACCCCGT 59.996 52.381 0.00 0.00 39.01 5.28
901 1131 1.741401 TGATGTTCGCAAGCTCCCG 60.741 57.895 0.00 0.00 37.18 5.14
902 1132 3.100862 GATGTTCGCAAGCTCCCGC 62.101 63.158 0.00 0.00 37.18 6.13
977 1209 1.725931 CGAACGTACGTACCTCACCAC 60.726 57.143 23.12 4.27 0.00 4.16
1024 1256 0.752376 CACGTACCTCCTCCTCCTCC 60.752 65.000 0.00 0.00 0.00 4.30
1405 1646 3.996744 GACGACGAGCGGTCCTTCG 62.997 68.421 24.03 24.03 46.49 3.79
1503 1744 0.541063 TGGAGACGGTGGTGAAGCTA 60.541 55.000 0.00 0.00 0.00 3.32
1534 1775 3.083349 CCGACCTGGCCATCTCCA 61.083 66.667 5.51 0.00 34.42 3.86
1539 1780 3.317109 CTGGCCATCTCCAGCTCA 58.683 61.111 5.51 0.00 46.11 4.26
1540 1781 1.605992 CTGGCCATCTCCAGCTCAA 59.394 57.895 5.51 0.00 46.11 3.02
1541 1782 0.464013 CTGGCCATCTCCAGCTCAAG 60.464 60.000 5.51 0.00 46.11 3.02
1542 1783 1.153005 GGCCATCTCCAGCTCAAGG 60.153 63.158 0.00 0.00 0.00 3.61
1543 1784 1.153005 GCCATCTCCAGCTCAAGGG 60.153 63.158 0.00 0.00 0.00 3.95
1544 1785 1.153005 CCATCTCCAGCTCAAGGGC 60.153 63.158 0.00 0.00 0.00 5.19
1548 1789 2.604686 TCCAGCTCAAGGGCGACT 60.605 61.111 0.00 0.00 37.29 4.18
1550 1791 1.142748 CCAGCTCAAGGGCGACTAG 59.857 63.158 0.00 0.00 37.29 2.57
1803 2062 5.331876 ACTTATTCTTCGAGGAGACAAGG 57.668 43.478 14.79 2.93 0.00 3.61
1856 2119 2.388121 GCACTGCTTTGCTGTTTACAG 58.612 47.619 5.52 5.52 46.40 2.74
1862 2125 2.604614 GCTTTGCTGTTTACAGTTCCCG 60.605 50.000 11.23 0.00 45.45 5.14
1880 2143 5.670792 TCCCGTGACAGTATATTTCAAGT 57.329 39.130 0.00 0.00 0.00 3.16
1886 2149 7.896274 CCGTGACAGTATATTTCAAGTAAAACG 59.104 37.037 0.00 0.00 0.00 3.60
1902 2165 7.823149 AGTAAAACGCAATAGTGGTACTTAG 57.177 36.000 0.00 0.00 0.00 2.18
1978 2558 7.148255 TGTGTTTATGATTGTCATAGTTGGAGC 60.148 37.037 0.56 0.00 40.13 4.70
2073 3388 1.957668 TGGCCAAGTCATCATCATCG 58.042 50.000 0.61 0.00 0.00 3.84
2206 3524 4.805219 ACCCTTTTCGTTGCATAATTCAC 58.195 39.130 0.00 0.00 0.00 3.18
2705 4790 9.175060 CTCATTTATGTACTCTGTTGATACTCG 57.825 37.037 0.00 0.00 0.00 4.18
2763 4848 6.500684 TTGTATTGCTCTTGTGGAATTCTC 57.499 37.500 5.23 0.09 30.80 2.87
2766 4851 7.568349 TGTATTGCTCTTGTGGAATTCTCTAT 58.432 34.615 5.23 0.00 30.80 1.98
2792 4877 7.070798 GCTGATAGTACGAAGTGTCTACATAC 58.929 42.308 0.00 0.00 45.73 2.39
2798 4883 4.845387 ACGAAGTGTCTACATACATAGCG 58.155 43.478 0.00 0.00 42.51 4.26
2858 4943 5.369833 TCCATTGACTAGTTTTTCGTTGGA 58.630 37.500 0.00 1.08 0.00 3.53
2908 4993 8.345565 GTTTTAGATTAGCATTGGAGTATGTGG 58.654 37.037 0.00 0.00 0.00 4.17
2942 5027 6.740110 ACATGTTCAAAACAGGCGTAAAATA 58.260 32.000 4.55 0.00 46.37 1.40
2947 5032 8.569641 TGTTCAAAACAGGCGTAAAATATACTT 58.430 29.630 0.00 0.00 36.25 2.24
2948 5033 9.401873 GTTCAAAACAGGCGTAAAATATACTTT 57.598 29.630 0.00 0.00 0.00 2.66
2949 5034 9.968870 TTCAAAACAGGCGTAAAATATACTTTT 57.031 25.926 0.00 0.00 0.00 2.27
2973 5172 7.922505 TTTGTGTGCATAAAATGTACTTGTC 57.077 32.000 9.10 0.44 44.74 3.18
2993 5192 9.148104 ACTTGTCGTTTATAGTTCACCTAATTC 57.852 33.333 0.00 0.00 0.00 2.17
3189 5505 8.093307 ACATGCATACATACAACAAAAATTGGA 58.907 29.630 0.00 0.00 33.67 3.53
3339 6097 2.589798 TCTCGTTTCACTTCCAACGT 57.410 45.000 4.53 0.00 44.87 3.99
3462 6220 5.398581 CCCAGGGTGTTGTAATATGGTGTAT 60.399 44.000 0.00 0.00 0.00 2.29
3538 6296 7.778083 TCTTCTCTATTGCGGTTTGAGTATAA 58.222 34.615 0.00 0.00 0.00 0.98
3572 6330 5.573337 AAATGCAATGTTCTTAGAGAGGC 57.427 39.130 0.00 0.00 0.00 4.70
3577 6335 4.436183 GCAATGTTCTTAGAGAGGCGTTTC 60.436 45.833 0.00 0.00 0.00 2.78
3592 6350 7.892609 AGAGGCGTTTCTAAAAATAAACCAAT 58.107 30.769 0.00 0.00 33.05 3.16
3646 6404 7.865706 ATAACAAGGTTCCTAGTTAAGCATG 57.134 36.000 6.93 7.24 31.11 4.06
3668 6426 6.892658 TGTGCACTTTACAAATATGAACCT 57.107 33.333 19.41 0.00 0.00 3.50
3998 6843 4.326009 GGCATTGTTTACAAGGTAATTGCG 59.674 41.667 8.77 0.00 43.15 4.85
4278 7140 6.511416 CACCCAACATAGAATTGTGAACAAA 58.489 36.000 0.00 0.00 39.55 2.83
4451 7448 2.979813 CAAACGGCTTTCTCCAAATTCG 59.020 45.455 0.00 0.00 0.00 3.34
4520 7517 5.882557 CAGCCTACAACATAAGAATCTGGTT 59.117 40.000 0.00 0.00 0.00 3.67
4653 7651 5.823861 ATGAAAAATATAATGCCCACCCC 57.176 39.130 0.00 0.00 0.00 4.95
4654 7652 4.624913 TGAAAAATATAATGCCCACCCCA 58.375 39.130 0.00 0.00 0.00 4.96
4655 7653 4.407296 TGAAAAATATAATGCCCACCCCAC 59.593 41.667 0.00 0.00 0.00 4.61
4656 7654 3.991628 AAATATAATGCCCACCCCACT 57.008 42.857 0.00 0.00 0.00 4.00
4657 7655 2.978156 ATATAATGCCCACCCCACTG 57.022 50.000 0.00 0.00 0.00 3.66
4658 7656 0.184933 TATAATGCCCACCCCACTGC 59.815 55.000 0.00 0.00 0.00 4.40
4659 7657 2.588029 ATAATGCCCACCCCACTGCC 62.588 60.000 0.00 0.00 0.00 4.85
4990 8905 0.391597 ATACGACAACGGCTATGGGG 59.608 55.000 0.00 0.00 44.46 4.96
5021 8937 8.691797 TGTAAGGTTTTGATTTTACAAGCTTCT 58.308 29.630 0.00 0.00 34.21 2.85
5110 9047 6.647334 TTTCTTGAAGTGCCATGTTAATCA 57.353 33.333 0.00 0.00 0.00 2.57
5165 9103 5.339118 GCCCCCTGGTTTCAAAATATTTCAT 60.339 40.000 0.10 0.00 0.00 2.57
5335 9286 7.171167 GTCAAAAGTTTGTCCTAACTAGACCTC 59.829 40.741 0.00 0.00 37.37 3.85
5346 9297 2.667470 ACTAGACCTCTGTGTGTGTGT 58.333 47.619 0.00 0.00 0.00 3.72
5347 9298 2.362397 ACTAGACCTCTGTGTGTGTGTG 59.638 50.000 0.00 0.00 0.00 3.82
5348 9299 1.195115 AGACCTCTGTGTGTGTGTGT 58.805 50.000 0.00 0.00 0.00 3.72
5349 9300 1.134699 AGACCTCTGTGTGTGTGTGTG 60.135 52.381 0.00 0.00 0.00 3.82
5350 9301 0.613260 ACCTCTGTGTGTGTGTGTGT 59.387 50.000 0.00 0.00 0.00 3.72
5351 9302 1.009078 CCTCTGTGTGTGTGTGTGTG 58.991 55.000 0.00 0.00 0.00 3.82
5352 9303 1.675714 CCTCTGTGTGTGTGTGTGTGT 60.676 52.381 0.00 0.00 0.00 3.72
5353 9304 1.394572 CTCTGTGTGTGTGTGTGTGTG 59.605 52.381 0.00 0.00 0.00 3.82
5354 9305 1.155889 CTGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
5356 9307 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
5357 9308 1.225991 GTGTGTGTGTGTGTGTGCG 60.226 57.895 0.00 0.00 0.00 5.34
5358 9309 2.277247 GTGTGTGTGTGTGTGCGC 60.277 61.111 0.00 0.00 0.00 6.09
5359 9310 3.858989 TGTGTGTGTGTGTGCGCG 61.859 61.111 0.00 0.00 0.00 6.86
5542 9849 1.739196 GCCGTCGGTTCCTACCAAC 60.739 63.158 13.94 0.00 45.31 3.77
5753 10078 6.391227 TCATCTCCTTGTTTTCCTTTTCAC 57.609 37.500 0.00 0.00 0.00 3.18
6009 10432 3.376234 ACGATGATGTTGAGCAATGGAAG 59.624 43.478 0.00 0.00 0.00 3.46
6090 10516 5.234466 ACTGAAATAGAGTTGTGAGCCTT 57.766 39.130 0.00 0.00 0.00 4.35
6164 10590 7.013178 TGTTGTAGAAAAGCAATGTGAAGATGA 59.987 33.333 0.00 0.00 0.00 2.92
6171 10597 9.443283 GAAAAGCAATGTGAAGATGATACATAC 57.557 33.333 0.00 0.00 34.18 2.39
6242 13377 1.079888 CGGCCAAAAATGCCCTCAC 60.080 57.895 2.24 0.00 46.48 3.51
6305 13462 7.657336 TGTTGTCAAAAAGAGGATCATAAACC 58.343 34.615 0.00 0.00 37.82 3.27
6390 13547 4.351192 CAGTTGCAAGACGCTAAACTTTT 58.649 39.130 0.00 0.00 43.06 2.27
6397 13554 5.741982 GCAAGACGCTAAACTTTTCTTTTCA 59.258 36.000 0.00 0.00 37.77 2.69
6560 14030 4.402474 AGGGAATTAAGCCTACAATGTTGC 59.598 41.667 0.00 0.00 0.00 4.17
6566 14036 1.241315 GCCTACAATGTTGCGGTGGT 61.241 55.000 0.00 0.00 0.00 4.16
6585 14055 8.230486 GCGGTGGTAATATCTGATTGAAAATAG 58.770 37.037 0.00 0.00 0.00 1.73
6657 15088 2.642311 ACACATCTGTAACCCATGTCCA 59.358 45.455 0.00 0.00 0.00 4.02
6661 15092 4.968719 ACATCTGTAACCCATGTCCATAGA 59.031 41.667 0.00 0.00 0.00 1.98
6727 15158 3.213506 CAAATGATTAGGCGATGTGGGA 58.786 45.455 0.00 0.00 0.00 4.37
6730 15161 1.837439 TGATTAGGCGATGTGGGACTT 59.163 47.619 0.00 0.00 0.00 3.01
6809 15241 6.824196 TGTGAACCTTTACACTTCACATGTAA 59.176 34.615 0.00 0.00 45.55 2.41
6811 15243 5.941948 ACCTTTACACTTCACATGTAAGC 57.058 39.130 0.00 0.00 42.06 3.09
6839 15276 1.896220 TTGCTCCGTTTCTCAGCAAT 58.104 45.000 1.48 0.00 45.91 3.56
6846 15283 2.420022 CCGTTTCTCAGCAATCCGATTT 59.580 45.455 0.00 0.00 0.00 2.17
6847 15284 3.485877 CCGTTTCTCAGCAATCCGATTTC 60.486 47.826 0.00 0.00 0.00 2.17
6853 15290 0.106519 AGCAATCCGATTTCCCCCTG 60.107 55.000 0.00 0.00 0.00 4.45
6872 15309 3.363844 GAGACCTCCACCTCAGCGC 62.364 68.421 0.00 0.00 0.00 5.92
6946 15383 2.287368 CCAACAACCGGCTACTTGTTTC 60.287 50.000 15.95 0.00 38.30 2.78
6950 15387 3.066203 ACAACCGGCTACTTGTTTCTTTG 59.934 43.478 0.00 0.00 0.00 2.77
6953 15390 2.095718 CCGGCTACTTGTTTCTTTGCTC 60.096 50.000 0.00 0.00 0.00 4.26
6972 15409 2.177950 GGTTCACGAGGTAGCGAGA 58.822 57.895 0.00 0.00 34.83 4.04
6980 15417 0.528470 GAGGTAGCGAGACAGTGCTT 59.472 55.000 0.00 0.00 42.48 3.91
6996 15433 2.032799 GTGCTTGTTCGATTGGTTCACA 59.967 45.455 0.00 0.00 0.00 3.58
7000 15437 3.961477 TGTTCGATTGGTTCACAGTTG 57.039 42.857 0.00 0.00 0.00 3.16
7003 15440 3.469008 TCGATTGGTTCACAGTTGACT 57.531 42.857 0.00 0.00 0.00 3.41
7019 15456 2.582052 TGACTGGTCAACAATTCACCC 58.418 47.619 0.51 0.00 36.53 4.61
7022 15459 1.175983 TGGTCAACAATTCACCCGGC 61.176 55.000 0.00 0.00 0.00 6.13
7026 15463 2.490115 GTCAACAATTCACCCGGCAATA 59.510 45.455 0.00 0.00 0.00 1.90
7037 15474 2.556622 ACCCGGCAATACTTCACTTTTG 59.443 45.455 0.00 0.00 0.00 2.44
7038 15475 2.817258 CCCGGCAATACTTCACTTTTGA 59.183 45.455 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.674220 CCCTCCTCCTCTTGCCACC 61.674 68.421 0.00 0.00 0.00 4.61
1 2 2.674220 CCCCTCCTCCTCTTGCCAC 61.674 68.421 0.00 0.00 0.00 5.01
2 3 2.200373 ATCCCCTCCTCCTCTTGCCA 62.200 60.000 0.00 0.00 0.00 4.92
3 4 0.104934 TATCCCCTCCTCCTCTTGCC 60.105 60.000 0.00 0.00 0.00 4.52
4 5 1.347062 CTATCCCCTCCTCCTCTTGC 58.653 60.000 0.00 0.00 0.00 4.01
5 6 1.484065 CCCTATCCCCTCCTCCTCTTG 60.484 61.905 0.00 0.00 0.00 3.02
6 7 0.871024 CCCTATCCCCTCCTCCTCTT 59.129 60.000 0.00 0.00 0.00 2.85
7 8 1.083363 CCCCTATCCCCTCCTCCTCT 61.083 65.000 0.00 0.00 0.00 3.69
8 9 1.471999 CCCCTATCCCCTCCTCCTC 59.528 68.421 0.00 0.00 0.00 3.71
21 22 2.712087 TGTAAAAGCTTGTCACCCCCTA 59.288 45.455 0.00 0.00 0.00 3.53
38 39 0.598158 GTCGTCCGCACTGGTTGTAA 60.598 55.000 0.00 0.00 39.52 2.41
39 40 1.007038 GTCGTCCGCACTGGTTGTA 60.007 57.895 0.00 0.00 39.52 2.41
51 52 2.432628 CAGAACAGGCGGTCGTCC 60.433 66.667 0.00 0.00 0.00 4.79
58 59 2.825836 GATGGGGCAGAACAGGCG 60.826 66.667 0.00 0.00 34.40 5.52
69 70 2.515523 CGCAAGCCAGAGATGGGG 60.516 66.667 0.00 0.00 0.00 4.96
70 71 1.817099 GACGCAAGCCAGAGATGGG 60.817 63.158 0.00 0.00 45.62 4.00
78 79 1.078918 CCTCATCTGACGCAAGCCA 60.079 57.895 0.00 0.00 45.62 4.75
95 96 2.683933 TCTCCTCCTTGCGTCCCC 60.684 66.667 0.00 0.00 0.00 4.81
101 102 1.142097 GTAGGCGTCTCCTCCTTGC 59.858 63.158 0.00 0.00 43.20 4.01
114 115 1.639298 CGCCTCAAGCTGTTGTAGGC 61.639 60.000 14.20 14.20 44.85 3.93
121 122 0.613260 TGATAACCGCCTCAAGCTGT 59.387 50.000 0.00 0.00 41.19 4.40
129 130 1.432251 CTCGTCGTGATAACCGCCT 59.568 57.895 0.00 0.00 0.00 5.52
145 146 0.984230 TCTTCCACCACCATGACCTC 59.016 55.000 0.00 0.00 0.00 3.85
162 163 2.165167 CATGTCAGCAACCCATTGTCT 58.835 47.619 0.00 0.00 38.17 3.41
166 167 0.542467 TGGCATGTCAGCAACCCATT 60.542 50.000 0.00 0.00 35.83 3.16
176 177 2.824936 CCACCTATTTTGTGGCATGTCA 59.175 45.455 0.00 0.00 46.13 3.58
185 186 2.378547 TCTTCCAGCCCACCTATTTTGT 59.621 45.455 0.00 0.00 0.00 2.83
186 187 3.019564 CTCTTCCAGCCCACCTATTTTG 58.980 50.000 0.00 0.00 0.00 2.44
187 188 2.024941 CCTCTTCCAGCCCACCTATTTT 60.025 50.000 0.00 0.00 0.00 1.82
191 192 0.325671 CTCCTCTTCCAGCCCACCTA 60.326 60.000 0.00 0.00 0.00 3.08
192 193 1.614824 CTCCTCTTCCAGCCCACCT 60.615 63.158 0.00 0.00 0.00 4.00
201 202 2.247358 CAGCTATCCCTCTCCTCTTCC 58.753 57.143 0.00 0.00 0.00 3.46
203 204 1.062581 TGCAGCTATCCCTCTCCTCTT 60.063 52.381 0.00 0.00 0.00 2.85
216 217 1.189752 CTTCCACTCCTCTGCAGCTA 58.810 55.000 9.47 0.00 0.00 3.32
222 223 1.078567 GGCAGCTTCCACTCCTCTG 60.079 63.158 0.00 0.00 0.00 3.35
225 226 1.302285 CATGGCAGCTTCCACTCCT 59.698 57.895 7.43 0.00 39.25 3.69
245 246 0.235665 GTTGTGTGTGGATCGTGCTG 59.764 55.000 0.00 0.00 0.00 4.41
250 251 1.626654 GAGCGGTTGTGTGTGGATCG 61.627 60.000 0.00 0.00 0.00 3.69
272 273 5.348179 CGCTTCCATTGCAATTTGTTATGAA 59.652 36.000 9.83 3.76 0.00 2.57
273 274 4.863689 CGCTTCCATTGCAATTTGTTATGA 59.136 37.500 9.83 0.00 0.00 2.15
279 280 1.727880 CACCGCTTCCATTGCAATTTG 59.272 47.619 9.83 4.21 0.00 2.32
307 308 1.078214 ATGCCACGTGTCCCTCATG 60.078 57.895 15.65 0.00 38.86 3.07
311 312 1.596934 CTACATGCCACGTGTCCCT 59.403 57.895 15.65 0.00 0.00 4.20
315 316 0.036388 CTTCCCTACATGCCACGTGT 60.036 55.000 15.65 0.00 0.00 4.49
321 322 1.477558 CCATCACCTTCCCTACATGCC 60.478 57.143 0.00 0.00 0.00 4.40
324 325 2.107204 GCATCCATCACCTTCCCTACAT 59.893 50.000 0.00 0.00 0.00 2.29
325 326 1.490490 GCATCCATCACCTTCCCTACA 59.510 52.381 0.00 0.00 0.00 2.74
326 327 1.202818 GGCATCCATCACCTTCCCTAC 60.203 57.143 0.00 0.00 0.00 3.18
327 328 1.140312 GGCATCCATCACCTTCCCTA 58.860 55.000 0.00 0.00 0.00 3.53
329 330 1.526917 CGGCATCCATCACCTTCCC 60.527 63.158 0.00 0.00 0.00 3.97
335 336 2.903855 CAGCCCGGCATCCATCAC 60.904 66.667 13.15 0.00 0.00 3.06
336 337 4.881440 GCAGCCCGGCATCCATCA 62.881 66.667 13.15 0.00 0.00 3.07
359 360 8.871686 AATAAAAACACTTCAAATCACCTGAC 57.128 30.769 0.00 0.00 0.00 3.51
408 409 3.935828 GTCTACCTCAAGATGGTTTCAGC 59.064 47.826 0.00 0.00 38.88 4.26
418 419 6.218746 GGTTACTTTTTCGTCTACCTCAAGA 58.781 40.000 0.00 0.00 0.00 3.02
440 441 7.012327 CGAGTACATCATGTATTGAATTTGGGT 59.988 37.037 0.00 0.00 38.03 4.51
448 449 5.774498 AGAGCGAGTACATCATGTATTGA 57.226 39.130 0.00 0.00 35.05 2.57
465 466 5.463724 GGGACACTTATTTTGAGATAGAGCG 59.536 44.000 0.00 0.00 0.00 5.03
466 467 6.349300 TGGGACACTTATTTTGAGATAGAGC 58.651 40.000 0.00 0.00 0.00 4.09
471 472 7.287696 ACAAAGTTGGGACACTTATTTTGAGAT 59.712 33.333 0.00 0.00 39.29 2.75
483 484 2.927028 ACCAGTACAAAGTTGGGACAC 58.073 47.619 0.00 0.00 39.29 3.67
484 485 3.712733 AGTACCAGTACAAAGTTGGGACA 59.287 43.478 14.19 0.00 46.32 4.02
485 486 4.347360 AGTACCAGTACAAAGTTGGGAC 57.653 45.455 10.41 5.49 44.62 4.46
499 500 7.659186 ACTAAGTGTCTCAACTTTAGTACCAG 58.341 38.462 0.00 0.00 40.77 4.00
502 503 8.762426 CCAAACTAAGTGTCTCAACTTTAGTAC 58.238 37.037 0.00 0.00 40.77 2.73
514 515 3.387050 AGTTCGTCCCAAACTAAGTGTCT 59.613 43.478 0.00 0.00 35.25 3.41
523 524 6.567050 TGTATATACTCAGTTCGTCCCAAAC 58.433 40.000 13.89 0.00 0.00 2.93
528 529 9.909644 AACATTATGTATATACTCAGTTCGTCC 57.090 33.333 13.89 0.00 0.00 4.79
555 556 1.735376 ATGAATAGACCGCGCCGACT 61.735 55.000 0.00 3.54 0.00 4.18
564 567 5.584649 TCAATGTTCCACGAATGAATAGACC 59.415 40.000 0.00 0.00 0.00 3.85
598 601 4.632538 TGGATGTGACGACTATGTACAG 57.367 45.455 0.33 0.00 0.00 2.74
603 606 4.053983 CTGGATTGGATGTGACGACTATG 58.946 47.826 0.00 0.00 0.00 2.23
605 608 3.096852 ACTGGATTGGATGTGACGACTA 58.903 45.455 0.00 0.00 0.00 2.59
690 701 4.514441 CAGAGCAGAAGTTTTGTGACTGAT 59.486 41.667 0.00 0.00 34.50 2.90
856 1086 2.178783 GACGACCAACCAAAACAAACG 58.821 47.619 0.00 0.00 0.00 3.60
857 1087 2.918600 GTGACGACCAACCAAAACAAAC 59.081 45.455 0.00 0.00 0.00 2.93
858 1088 2.414293 CGTGACGACCAACCAAAACAAA 60.414 45.455 0.00 0.00 0.00 2.83
901 1131 2.174349 CTTTGACTGGAAGCGCGC 59.826 61.111 26.66 26.66 37.60 6.86
902 1132 2.863153 CCTTTGACTGGAAGCGCG 59.137 61.111 0.00 0.00 37.60 6.86
903 1133 1.916697 GAGCCTTTGACTGGAAGCGC 61.917 60.000 0.00 0.00 37.60 5.92
904 1134 1.301677 GGAGCCTTTGACTGGAAGCG 61.302 60.000 0.00 0.00 37.60 4.68
950 1182 0.625351 GTACGTACGTTCGAGCGTTG 59.375 55.000 31.48 24.69 43.04 4.10
977 1209 1.302033 GTGACTGGTGACTGCTGGG 60.302 63.158 0.00 0.00 0.00 4.45
1296 1537 2.283894 TGGAAGGCGGCTCTGAGA 60.284 61.111 13.70 0.00 0.00 3.27
1405 1646 2.253452 CTCGTTGCTGGTGCTTGC 59.747 61.111 0.00 0.00 40.48 4.01
1407 1648 2.980233 GGCTCGTTGCTGGTGCTT 60.980 61.111 3.58 0.00 42.39 3.91
1503 1744 1.375523 GTCGGCCAGGTCGTTCATT 60.376 57.895 14.52 0.00 30.45 2.57
1529 1770 2.283894 TCGCCCTTGAGCTGGAGA 60.284 61.111 0.00 0.00 0.00 3.71
1534 1775 1.477295 GTAACTAGTCGCCCTTGAGCT 59.523 52.381 0.00 0.00 0.00 4.09
1537 1778 0.171903 GCGTAACTAGTCGCCCTTGA 59.828 55.000 15.95 0.00 45.54 3.02
1538 1779 2.662150 GCGTAACTAGTCGCCCTTG 58.338 57.895 15.95 0.00 45.54 3.61
1544 1785 1.297158 CCGGTCGCGTAACTAGTCG 60.297 63.158 5.77 0.00 0.00 4.18
1803 2062 3.738282 GCATGTCGATCTTGATAGTGTCC 59.262 47.826 0.00 0.00 0.00 4.02
1856 2119 5.873164 ACTTGAAATATACTGTCACGGGAAC 59.127 40.000 0.00 0.00 0.00 3.62
1862 2125 8.225107 TGCGTTTTACTTGAAATATACTGTCAC 58.775 33.333 0.00 0.00 0.00 3.67
1880 2143 9.439500 AATTCTAAGTACCACTATTGCGTTTTA 57.561 29.630 0.00 0.00 0.00 1.52
1978 2558 4.442753 GGATGAGCAAAACTAGGAGAGGAG 60.443 50.000 0.00 0.00 0.00 3.69
2292 3620 8.805688 GTCTAAATACCACGAGTTAGATGTTTC 58.194 37.037 0.00 0.00 35.60 2.78
2450 3779 1.310904 TTGTGGGTTAGTTCGGTTGC 58.689 50.000 0.00 0.00 0.00 4.17
2569 3898 2.383245 ATAACCATGCGAGGAGGCCG 62.383 60.000 0.00 0.00 0.00 6.13
2705 4790 2.412089 GAGAGTGATTACGCACCAACAC 59.588 50.000 0.00 0.00 39.59 3.32
2763 4848 6.307031 AGACACTTCGTACTATCAGCATAG 57.693 41.667 0.00 0.00 38.45 2.23
2766 4851 4.939439 TGTAGACACTTCGTACTATCAGCA 59.061 41.667 0.00 0.00 0.00 4.41
2815 4900 9.987272 CAATGGAAAAATCTCCTCTTACTTTTT 57.013 29.630 0.00 0.00 36.35 1.94
2816 4901 9.367160 TCAATGGAAAAATCTCCTCTTACTTTT 57.633 29.630 0.00 0.00 36.35 2.27
2817 4902 8.797438 GTCAATGGAAAAATCTCCTCTTACTTT 58.203 33.333 0.00 0.00 36.35 2.66
2818 4903 8.166726 AGTCAATGGAAAAATCTCCTCTTACTT 58.833 33.333 0.00 0.00 36.35 2.24
2819 4904 7.694093 AGTCAATGGAAAAATCTCCTCTTACT 58.306 34.615 0.00 0.00 36.35 2.24
2820 4905 7.929941 AGTCAATGGAAAAATCTCCTCTTAC 57.070 36.000 0.00 0.00 36.35 2.34
2821 4906 8.826765 ACTAGTCAATGGAAAAATCTCCTCTTA 58.173 33.333 0.00 0.00 36.35 2.10
2908 4993 6.475402 CCTGTTTTGAACATGTTGGTTCTAAC 59.525 38.462 17.58 11.18 45.74 2.34
2947 5032 8.709386 ACAAGTACATTTTATGCACACAAAAA 57.291 26.923 6.75 4.33 0.00 1.94
2948 5033 7.166638 CGACAAGTACATTTTATGCACACAAAA 59.833 33.333 0.00 0.00 0.00 2.44
2949 5034 6.634837 CGACAAGTACATTTTATGCACACAAA 59.365 34.615 0.00 0.00 0.00 2.83
2951 5036 5.237561 ACGACAAGTACATTTTATGCACACA 59.762 36.000 0.00 0.00 0.00 3.72
2952 5037 5.685841 ACGACAAGTACATTTTATGCACAC 58.314 37.500 0.00 0.00 0.00 3.82
3021 5220 5.679734 AGTTGCACTTACACAAATCTCAG 57.320 39.130 0.00 0.00 0.00 3.35
3339 6097 8.632906 TTTACATCCCGTAAATTTTGTCCTAA 57.367 30.769 0.00 0.00 43.57 2.69
3389 6147 5.970640 AGGAATAGTTATTCTTCACCCCTCA 59.029 40.000 10.71 0.00 41.33 3.86
3462 6220 6.370442 TCGCAAAGAAGCAAAATAGCTAGTTA 59.630 34.615 6.89 0.00 45.89 2.24
3538 6296 8.757982 AGAACATTGCATTTAAGATGGACTAT 57.242 30.769 0.00 0.00 0.00 2.12
3607 6365 6.815089 ACCTTGTTATTGAAAAACAGCATCA 58.185 32.000 0.00 0.00 38.05 3.07
3608 6366 7.095649 GGAACCTTGTTATTGAAAAACAGCATC 60.096 37.037 0.00 0.00 38.05 3.91
3646 6404 7.432252 GCATAGGTTCATATTTGTAAAGTGCAC 59.568 37.037 9.40 9.40 0.00 4.57
3959 6804 0.322456 TGCCAAATCCACCTTCTCCG 60.322 55.000 0.00 0.00 0.00 4.63
4196 7056 4.219919 TGTGATTGATGCATCATTGGGAT 58.780 39.130 29.13 19.05 36.56 3.85
4242 7103 3.742433 TGTTGGGTGCATTTTGTAAGG 57.258 42.857 0.00 0.00 0.00 2.69
4520 7517 0.620030 TGCAGCATCCAAGAAGCCTA 59.380 50.000 0.00 0.00 0.00 3.93
4659 7657 3.774216 TGCCTTTTCTCATTTTATGGGGG 59.226 43.478 0.00 0.00 0.00 5.40
5021 8937 8.701895 ACTAACTATAATTCCGGTCTCAAATGA 58.298 33.333 0.00 0.00 0.00 2.57
5110 9047 7.453393 TGAATCATGGAACTCAACTTACTCTT 58.547 34.615 0.00 0.00 0.00 2.85
5335 9286 1.136000 CACACACACACACACACACAG 60.136 52.381 0.00 0.00 0.00 3.66
5366 9317 0.439214 TAAACCGTATTGCGCACACG 59.561 50.000 27.99 27.99 44.07 4.49
5367 9318 2.817538 ATAAACCGTATTGCGCACAC 57.182 45.000 11.12 10.78 39.71 3.82
5368 9319 3.307512 CACTATAAACCGTATTGCGCACA 59.692 43.478 11.12 1.31 39.71 4.57
5369 9320 3.552699 TCACTATAAACCGTATTGCGCAC 59.447 43.478 11.12 0.00 39.71 5.34
5370 9321 3.783191 TCACTATAAACCGTATTGCGCA 58.217 40.909 5.66 5.66 39.71 6.09
5372 9323 4.049186 AGCTCACTATAAACCGTATTGCG 58.951 43.478 0.00 0.00 40.95 4.85
5374 9325 7.306632 GCAGTAAGCTCACTATAAACCGTATTG 60.307 40.741 0.00 0.00 41.15 1.90
5377 9328 5.450965 GGCAGTAAGCTCACTATAAACCGTA 60.451 44.000 0.00 0.00 44.79 4.02
5378 9329 4.430908 GCAGTAAGCTCACTATAAACCGT 58.569 43.478 0.00 0.00 41.15 4.83
5379 9330 3.802685 GGCAGTAAGCTCACTATAAACCG 59.197 47.826 0.00 0.00 44.79 4.44
5380 9331 4.766375 TGGCAGTAAGCTCACTATAAACC 58.234 43.478 0.00 0.00 44.79 3.27
5542 9849 3.692101 AGCTCGTATGATCTTCCGGATAG 59.308 47.826 4.15 6.12 34.33 2.08
5753 10078 9.801714 AAGTAAGTACGTAAACGATCATTTTTG 57.198 29.630 9.86 0.00 43.02 2.44
5974 10397 2.949678 ATCGTCACGTCGCGCATC 60.950 61.111 8.75 0.00 0.00 3.91
6009 10432 1.153269 GGTAGGAGCAGCCTCTTGC 60.153 63.158 0.92 0.00 46.97 4.01
6164 10590 7.345691 TGGGATCATCAAAACAGTGTATGTAT 58.654 34.615 0.00 0.00 43.00 2.29
6242 13377 0.460311 ACGGGTCTAAAGATCGCCAG 59.540 55.000 5.87 0.00 0.00 4.85
6472 13938 0.181587 TGGGTCATTTGGTGTGACGT 59.818 50.000 0.00 0.00 45.32 4.34
6484 13950 1.267574 ACTCCGTCTGCATGGGTCAT 61.268 55.000 0.00 0.00 0.00 3.06
6560 14030 8.721478 CCTATTTTCAATCAGATATTACCACCG 58.279 37.037 0.00 0.00 0.00 4.94
6566 14036 7.685481 TCCGCCCTATTTTCAATCAGATATTA 58.315 34.615 0.00 0.00 0.00 0.98
6787 15219 6.017440 TGCTTACATGTGAAGTGTAAAGGTTC 60.017 38.462 9.11 0.00 40.41 3.62
6831 15268 1.312815 GGGGAAATCGGATTGCTGAG 58.687 55.000 8.57 0.00 31.75 3.35
6839 15276 0.981277 GTCTCCAGGGGGAAATCGGA 60.981 60.000 0.00 0.00 44.38 4.55
6880 15317 1.575423 CGCTACCTCGCTACCTAGC 59.425 63.158 0.00 0.00 45.62 3.42
6953 15390 1.226323 CTCGCTACCTCGTGAACCG 60.226 63.158 0.00 0.00 38.13 4.44
6972 15409 1.967319 ACCAATCGAACAAGCACTGT 58.033 45.000 0.00 0.00 41.27 3.55
6980 15417 3.311322 GTCAACTGTGAACCAATCGAACA 59.689 43.478 0.00 0.00 34.87 3.18
7000 15437 1.535462 CGGGTGAATTGTTGACCAGTC 59.465 52.381 0.99 0.00 0.00 3.51
7003 15440 1.175983 GCCGGGTGAATTGTTGACCA 61.176 55.000 2.18 0.00 0.00 4.02
7007 15444 2.491693 AGTATTGCCGGGTGAATTGTTG 59.508 45.455 2.18 0.00 0.00 3.33
7019 15456 6.820470 TTTTTCAAAAGTGAAGTATTGCCG 57.180 33.333 0.00 0.00 44.49 5.69


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

AutoCloner maintained by Alex Coulton.