Multiple sequence alignment - TraesCS5B01G092600

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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 TraesCS5B01G092600 chr5B 100.000 4288 0 0 1 4288 121557862 121553575 0.000000e+00 7919.0
1 TraesCS5B01G092600 chr5B 93.939 264 16 0 3959 4222 596287839 596287576 2.400000e-107 399.0
2 TraesCS5B01G092600 chr5B 89.394 132 13 1 2174 2304 490727680 490727811 9.540000e-37 165.0
3 TraesCS5B01G092600 chr5B 94.444 72 2 2 1472 1542 121556321 121556391 4.530000e-20 110.0
4 TraesCS5B01G092600 chr5D 95.996 2173 64 11 640 2796 112700369 112698204 0.000000e+00 3509.0
5 TraesCS5B01G092600 chr5D 98.407 565 7 2 2896 3458 112698208 112697644 0.000000e+00 992.0
6 TraesCS5B01G092600 chr5D 98.171 492 5 2 3469 3959 112697596 112697108 0.000000e+00 856.0
7 TraesCS5B01G092600 chr5D 84.536 485 58 7 5 473 238902736 238902253 8.400000e-127 464.0
8 TraesCS5B01G092600 chr5D 93.511 262 17 0 3958 4219 89074965 89075226 1.450000e-104 390.0
9 TraesCS5B01G092600 chr5D 78.507 670 86 34 5 646 112705903 112705264 1.870000e-103 387.0
10 TraesCS5B01G092600 chr5D 91.166 283 19 5 3942 4219 87808209 87807928 3.130000e-101 379.0
11 TraesCS5B01G092600 chr5D 89.674 184 15 4 466 645 238902224 238902041 9.270000e-57 231.0
12 TraesCS5B01G092600 chr5D 80.335 239 36 3 5 232 217747465 217747703 2.050000e-38 171.0
13 TraesCS5B01G092600 chr5D 88.976 127 12 2 511 635 446797150 446797276 5.740000e-34 156.0
14 TraesCS5B01G092600 chr5D 98.592 71 1 0 4218 4288 112697107 112697037 4.500000e-25 126.0
15 TraesCS5B01G092600 chr5D 92.982 57 4 0 514 570 296690593 296690649 2.750000e-12 84.2
16 TraesCS5B01G092600 chr5D 90.000 60 6 0 466 525 112705417 112705358 1.280000e-10 78.7
17 TraesCS5B01G092600 chr5D 97.297 37 0 1 2407 2442 112697644 112697608 1.290000e-05 62.1
18 TraesCS5B01G092600 chr5A 92.925 1258 52 20 1539 2787 115619154 115617925 0.000000e+00 1796.0
19 TraesCS5B01G092600 chr5A 92.268 1151 65 9 2814 3960 115617128 115615998 0.000000e+00 1611.0
20 TraesCS5B01G092600 chr5A 93.750 720 33 6 664 1372 115619872 115619154 0.000000e+00 1070.0
21 TraesCS5B01G092600 chr5A 95.402 87 3 1 2017 2102 705839144 705839058 2.080000e-28 137.0
22 TraesCS5B01G092600 chr5A 97.778 45 1 0 4244 4288 115615944 115615900 1.280000e-10 78.7
23 TraesCS5B01G092600 chr5A 95.652 46 2 0 2770 2815 115617194 115617149 1.650000e-09 75.0
24 TraesCS5B01G092600 chr3B 95.149 268 13 0 3959 4226 592641763 592642030 1.430000e-114 424.0
25 TraesCS5B01G092600 chr3B 80.412 485 77 8 5 473 566604006 566604488 1.900000e-93 353.0
26 TraesCS5B01G092600 chr7A 93.870 261 16 0 3959 4219 646560186 646560446 1.120000e-105 394.0
27 TraesCS5B01G092600 chr7A 89.394 132 13 1 2174 2304 183660411 183660280 9.540000e-37 165.0
28 TraesCS5B01G092600 chr7A 86.364 110 13 2 466 575 194810389 194810282 7.530000e-23 119.0
29 TraesCS5B01G092600 chr7A 95.349 43 2 0 466 508 731685213 731685255 7.690000e-08 69.4
30 TraesCS5B01G092600 chr1D 93.870 261 16 0 3959 4219 268120111 268120371 1.120000e-105 394.0
31 TraesCS5B01G092600 chr1D 93.870 261 16 0 3959 4219 331138321 331138581 1.120000e-105 394.0
32 TraesCS5B01G092600 chr1D 79.917 483 79 11 5 471 28031969 28032449 5.310000e-89 339.0
33 TraesCS5B01G092600 chr1D 78.279 488 73 13 1 465 479601139 479600662 2.520000e-72 283.0
34 TraesCS5B01G092600 chr1D 77.676 327 64 6 2297 2622 409313347 409313029 1.570000e-44 191.0
35 TraesCS5B01G092600 chr1D 89.041 73 8 0 1470 1542 401169130 401169202 1.640000e-14 91.6
36 TraesCS5B01G092600 chr1D 83.562 73 10 2 1471 1542 401169203 401169132 2.770000e-07 67.6
37 TraesCS5B01G092600 chr4A 91.873 283 20 3 3946 4227 611226873 611227153 4.020000e-105 392.0
38 TraesCS5B01G092600 chr1B 92.647 272 19 1 3958 4229 4324740 4324470 1.450000e-104 390.0
39 TraesCS5B01G092600 chr1B 80.738 488 76 9 5 476 642652749 642652264 8.760000e-97 364.0
40 TraesCS5B01G092600 chr2B 81.109 487 72 12 5 473 245300909 245301393 5.240000e-99 372.0
41 TraesCS5B01G092600 chr2B 83.246 382 56 6 97 471 110924356 110923976 1.140000e-90 344.0
42 TraesCS5B01G092600 chr2B 84.000 75 11 1 1471 1545 37574751 37574824 2.140000e-08 71.3
43 TraesCS5B01G092600 chr2B 84.000 75 11 1 1471 1545 37740741 37740814 2.140000e-08 71.3
44 TraesCS5B01G092600 chr7D 80.000 485 80 10 5 473 575712344 575712827 4.110000e-90 342.0
45 TraesCS5B01G092600 chr7D 83.965 343 46 6 127 462 433815883 433815543 1.920000e-83 320.0
46 TraesCS5B01G092600 chr7D 82.422 256 36 4 226 476 28051454 28051203 9.340000e-52 215.0
47 TraesCS5B01G092600 chr7D 82.979 235 37 3 97 329 37453437 37453670 4.340000e-50 209.0
48 TraesCS5B01G092600 chr7D 86.726 113 14 1 468 579 561664003 561663891 1.620000e-24 124.0
49 TraesCS5B01G092600 chr2D 79.381 485 83 8 5 473 218351697 218351214 4.140000e-85 326.0
50 TraesCS5B01G092600 chr6A 83.149 362 53 5 113 467 2817739 2818099 1.490000e-84 324.0
51 TraesCS5B01G092600 chr6A 88.679 106 9 1 468 570 614243507 614243612 4.500000e-25 126.0
52 TraesCS5B01G092600 chr6A 76.889 225 42 8 5 220 78849277 78849500 7.530000e-23 119.0
53 TraesCS5B01G092600 chr3A 81.612 397 63 6 85 473 724823297 724823691 1.920000e-83 320.0
54 TraesCS5B01G092600 chr3A 93.220 59 4 0 512 570 724824008 724824066 2.120000e-13 87.9
55 TraesCS5B01G092600 chr6B 79.698 463 77 9 5 452 192722179 192721719 6.920000e-83 318.0
56 TraesCS5B01G092600 chr6B 76.712 657 93 27 2174 2812 88216885 88216271 1.160000e-80 311.0
57 TraesCS5B01G092600 chr6B 76.950 564 101 17 2252 2803 88182806 88182260 1.170000e-75 294.0
58 TraesCS5B01G092600 chr1A 78.323 489 80 10 1 465 575906596 575906110 4.190000e-75 292.0
59 TraesCS5B01G092600 chr1A 76.667 240 45 4 5 233 589651719 589651480 5.820000e-24 122.0
60 TraesCS5B01G092600 chr1A 86.607 112 12 3 541 650 4640149 4640259 2.090000e-23 121.0
61 TraesCS5B01G092600 chr1A 91.781 73 6 0 1470 1542 497275852 497275924 7.590000e-18 102.0
62 TraesCS5B01G092600 chr1A 90.411 73 2 1 1470 1542 499442901 499442968 1.640000e-14 91.6
63 TraesCS5B01G092600 chr1A 86.301 73 8 2 1471 1542 497275925 497275854 1.280000e-10 78.7
64 TraesCS5B01G092600 chr4B 79.602 402 69 6 2359 2749 261680974 261681373 4.220000e-70 276.0
65 TraesCS5B01G092600 chr4B 83.390 295 28 8 2017 2310 665565309 665565583 1.980000e-63 254.0
66 TraesCS5B01G092600 chr4B 89.394 132 13 1 2174 2304 195446136 195446267 9.540000e-37 165.0
67 TraesCS5B01G092600 chr4B 95.402 87 3 1 2017 2102 665872158 665872072 2.080000e-28 137.0
68 TraesCS5B01G092600 chr4B 76.763 241 39 12 5 231 175200118 175200355 7.530000e-23 119.0
69 TraesCS5B01G092600 chr3D 80.101 397 55 10 89 479 68915031 68914653 1.520000e-69 274.0
70 TraesCS5B01G092600 chr3D 82.192 146 24 1 89 232 31942088 31942233 1.620000e-24 124.0
71 TraesCS5B01G092600 chr4D 85.141 249 31 3 230 473 425281912 425282159 2.560000e-62 250.0
72 TraesCS5B01G092600 chr4D 91.429 105 9 0 466 570 425282188 425282292 1.240000e-30 145.0
73 TraesCS5B01G092600 chrUn 81.962 316 32 11 2017 2326 108421852 108421556 1.190000e-60 244.0
74 TraesCS5B01G092600 chrUn 85.075 201 27 2 1784 1984 134250354 134250157 7.270000e-48 202.0
75 TraesCS5B01G092600 chrUn 76.235 425 71 14 2383 2797 108324547 108324951 9.410000e-47 198.0
76 TraesCS5B01G092600 chrUn 80.000 270 31 10 2174 2436 134270540 134270793 1.230000e-40 178.0
77 TraesCS5B01G092600 chrUn 88.889 126 14 0 2174 2299 108324387 108324512 5.740000e-34 156.0
78 TraesCS5B01G092600 chrUn 80.952 147 25 3 2661 2804 134275850 134275996 3.500000e-21 113.0
79 TraesCS5B01G092600 chrUn 84.722 72 9 2 3457 3527 134249278 134249208 2.140000e-08 71.3
80 TraesCS5B01G092600 chr6D 89.394 132 13 1 2174 2304 417348409 417348278 9.540000e-37 165.0
81 TraesCS5B01G092600 chr2A 86.087 115 14 2 2191 2304 735256929 735256816 5.820000e-24 122.0
82 TraesCS5B01G092600 chr2A 100.000 36 0 0 1181 1216 14991330 14991295 2.770000e-07 67.6


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 TraesCS5B01G092600 chr5B 121553575 121557862 4287 True 7919.00 7919 100.0000 1 4288 1 chr5B.!!$R1 4287
1 TraesCS5B01G092600 chr5D 112697037 112700369 3332 True 1109.02 3509 97.6926 640 4288 5 chr5D.!!$R2 3648
2 TraesCS5B01G092600 chr5D 238902041 238902736 695 True 347.50 464 87.1050 5 645 2 chr5D.!!$R4 640
3 TraesCS5B01G092600 chr5D 112705264 112705903 639 True 232.85 387 84.2535 5 646 2 chr5D.!!$R3 641
4 TraesCS5B01G092600 chr5A 115615900 115619872 3972 True 926.14 1796 94.4746 664 4288 5 chr5A.!!$R2 3624
5 TraesCS5B01G092600 chr3A 724823297 724824066 769 False 203.95 320 87.4160 85 570 2 chr3A.!!$F1 485
6 TraesCS5B01G092600 chr6B 88216271 88216885 614 True 311.00 311 76.7120 2174 2812 1 chr6B.!!$R2 638
7 TraesCS5B01G092600 chr6B 88182260 88182806 546 True 294.00 294 76.9500 2252 2803 1 chr6B.!!$R1 551

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
666 962 0.033796 TAGTCCTCCCGATCCGTGTT 60.034 55.0 0.00 0.0 0.0 3.32 F
692 988 0.739462 CGCTTTCATCGTGTAGGGCA 60.739 55.0 0.00 0.0 0.0 5.36 F
1058 1364 0.868406 CTCCCTGTTGCGAGTTGTTC 59.132 55.0 0.00 0.0 0.0 3.18 F
1501 1809 0.458889 TCCGGAATTACTTGTCGCGG 60.459 55.0 6.13 0.0 0.0 6.46 F
1946 2271 1.855295 TTCCTATGTACGCCTCACCA 58.145 50.0 0.00 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1468 1776 0.109342 TCCGGACGGAGGGAGTATAC 59.891 60.000 9.76 0.0 39.76 1.47 R
1501 1809 1.737793 ACTTGTCGCGGAAATGGATTC 59.262 47.619 6.13 0.0 37.31 2.52 R
1971 2296 2.094182 ACGCAATGAGATCAGTACGGTT 60.094 45.455 7.68 0.0 0.00 4.44 R
3266 4402 1.376424 CATCAGCTGGTTGCCGACT 60.376 57.895 15.13 0.0 44.23 4.18 R
3448 4584 2.279582 AGACCTTACAACATCGCTCG 57.720 50.000 0.00 0.0 0.00 5.03 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
26 27 3.161866 CTGGAAGACTAGATCCTAGGGC 58.838 54.545 9.46 1.32 36.64 5.19
30 31 3.536075 AGACTAGATCCTAGGGCTTCC 57.464 52.381 9.46 0.73 0.00 3.46
46 47 3.252974 CTTCCCTCGAAGCAGTACAAT 57.747 47.619 0.00 0.00 39.21 2.71
53 54 2.037902 TCGAAGCAGTACAATTGGGTCA 59.962 45.455 10.83 0.00 0.00 4.02
55 56 3.440173 CGAAGCAGTACAATTGGGTCAAT 59.560 43.478 10.83 0.00 35.39 2.57
68 69 7.556275 ACAATTGGGTCAATAGTAGTTACATGG 59.444 37.037 10.83 0.00 32.43 3.66
75 76 2.979814 AGTAGTTACATGGCGATGCA 57.020 45.000 8.81 0.00 32.14 3.96
86 96 0.589729 GGCGATGCAGTAACAATGCG 60.590 55.000 0.00 0.00 46.87 4.73
122 132 3.156334 CCGTCAGCTCGGTTTTCG 58.844 61.111 5.70 0.00 44.77 3.46
141 151 1.972660 GCCGGCAACTATGTCTCCCT 61.973 60.000 24.80 0.00 0.00 4.20
175 185 5.662657 TCAGGACTACATGATGGATCTCAAA 59.337 40.000 0.00 0.00 31.79 2.69
191 201 0.609131 CAAAATCCGACCACCCAGCT 60.609 55.000 0.00 0.00 0.00 4.24
224 236 1.686325 CCCCGACGGATGAGAACCAT 61.686 60.000 17.49 0.00 38.43 3.55
309 321 0.035439 ACCACGATCCAAAGCCGAAT 60.035 50.000 0.00 0.00 0.00 3.34
318 330 4.829872 TCCAAAGCCGAATTAGAGGTTA 57.170 40.909 0.00 0.00 0.00 2.85
322 334 3.906720 AGCCGAATTAGAGGTTAAGCA 57.093 42.857 7.52 0.00 0.00 3.91
401 418 2.358125 CGTTGTCCGCCATCACCA 60.358 61.111 0.00 0.00 0.00 4.17
427 444 2.102252 GGAGATCAAGATCAGAACCGCT 59.898 50.000 12.21 0.00 40.22 5.52
497 550 1.679305 GCGGAGAGGAGAGTGGTGA 60.679 63.158 0.00 0.00 0.00 4.02
525 820 2.204090 AAAGAGGGAGGCGGGGAA 60.204 61.111 0.00 0.00 0.00 3.97
586 881 2.202756 GTCGGGTGAGATGGCGAC 60.203 66.667 0.00 0.00 0.00 5.19
587 882 2.362503 TCGGGTGAGATGGCGACT 60.363 61.111 0.00 0.00 0.00 4.18
622 917 3.023118 CGGCGCTAGATCGAGTCA 58.977 61.111 7.64 0.00 0.00 3.41
666 962 0.033796 TAGTCCTCCCGATCCGTGTT 60.034 55.000 0.00 0.00 0.00 3.32
692 988 0.739462 CGCTTTCATCGTGTAGGGCA 60.739 55.000 0.00 0.00 0.00 5.36
697 993 3.342377 TTCATCGTGTAGGGCATTCAA 57.658 42.857 0.00 0.00 0.00 2.69
921 1217 2.025863 GCCCTTGCTTGCAGATACCAT 61.026 52.381 0.00 0.00 33.53 3.55
1024 1330 1.134699 TGATGCCGTTTCTAGCTCAGG 60.135 52.381 0.00 0.00 0.00 3.86
1040 1346 2.564947 CTCAGGCCTCTCAAACTACACT 59.435 50.000 0.00 0.00 0.00 3.55
1058 1364 0.868406 CTCCCTGTTGCGAGTTGTTC 59.132 55.000 0.00 0.00 0.00 3.18
1126 1432 7.469870 GTCAGATCTTGATCTAGCTCTTGCTTA 60.470 40.741 12.18 0.00 41.85 3.09
1147 1454 7.027161 GCTTAATCTTTATGCGTTTTCCAAGA 58.973 34.615 0.00 0.00 0.00 3.02
1173 1480 5.895636 TGCATATACCCAACTTTGAACTG 57.104 39.130 0.00 0.00 0.00 3.16
1185 1492 3.823304 ACTTTGAACTGAATCTTCCTGGC 59.177 43.478 0.00 0.00 0.00 4.85
1322 1629 7.324178 ACTCTTGTTCGAGCTAATAATTCACT 58.676 34.615 0.00 0.00 34.35 3.41
1346 1654 8.474025 ACTTTGAGACCACAAAATTGAATGTTA 58.526 29.630 0.00 0.00 38.90 2.41
1497 1805 2.537401 CTCCGTCCGGAATTACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1501 1809 0.458889 TCCGGAATTACTTGTCGCGG 60.459 55.000 6.13 0.00 0.00 6.46
1946 2271 1.855295 TTCCTATGTACGCCTCACCA 58.145 50.000 0.00 0.00 0.00 4.17
1971 2296 5.568825 CGTAATCCTCCTTTCCAGTTCTTCA 60.569 44.000 0.00 0.00 0.00 3.02
2105 2430 2.484241 GGGGCGAGGTAACGTAATTGAT 60.484 50.000 0.00 0.00 46.39 2.57
2145 2470 4.571176 CCGTTATCTCCCTCTTTTGCTTAC 59.429 45.833 0.00 0.00 0.00 2.34
2148 2473 6.697892 CGTTATCTCCCTCTTTTGCTTACTAG 59.302 42.308 0.00 0.00 0.00 2.57
2534 2880 4.281898 TGCTGTCTGGATCATATGGATG 57.718 45.455 2.13 0.00 36.00 3.51
2607 2954 5.757808 CCCTACATTTTGTTTTTGTTCCCTG 59.242 40.000 0.00 0.00 0.00 4.45
2701 3063 5.351458 ACAATTTTCTTGTTTCCTGCAGTC 58.649 37.500 13.81 0.88 0.00 3.51
2815 3925 8.893563 TTCTGTTATTAATGGGTTTGGAAGAT 57.106 30.769 0.00 0.00 0.00 2.40
3266 4402 0.533085 TGCATTTTGTCGTCGACCCA 60.533 50.000 22.05 6.59 0.00 4.51
3334 4470 3.891366 CTGAACCTGAAATGGAACCTTGT 59.109 43.478 0.00 0.00 0.00 3.16
3448 4584 1.373497 CCACGAGGCAGTGACTGAC 60.373 63.158 18.18 14.89 44.43 3.51
3960 5137 9.924650 AGGATCGTATGGAGTATTATGTTTTAC 57.075 33.333 0.00 0.00 0.00 2.01
3961 5138 9.924650 GGATCGTATGGAGTATTATGTTTTACT 57.075 33.333 0.00 0.00 0.00 2.24
3969 5146 6.803366 AGTATTATGTTTTACTCCCTCCGT 57.197 37.500 0.00 0.00 0.00 4.69
3970 5147 7.191593 AGTATTATGTTTTACTCCCTCCGTT 57.808 36.000 0.00 0.00 0.00 4.44
3971 5148 7.270779 AGTATTATGTTTTACTCCCTCCGTTC 58.729 38.462 0.00 0.00 0.00 3.95
3972 5149 2.845363 TGTTTTACTCCCTCCGTTCC 57.155 50.000 0.00 0.00 0.00 3.62
3973 5150 2.332117 TGTTTTACTCCCTCCGTTCCT 58.668 47.619 0.00 0.00 0.00 3.36
3974 5151 2.707257 TGTTTTACTCCCTCCGTTCCTT 59.293 45.455 0.00 0.00 0.00 3.36
3975 5152 3.136992 TGTTTTACTCCCTCCGTTCCTTT 59.863 43.478 0.00 0.00 0.00 3.11
3976 5153 4.347583 TGTTTTACTCCCTCCGTTCCTTTA 59.652 41.667 0.00 0.00 0.00 1.85
3977 5154 5.013391 TGTTTTACTCCCTCCGTTCCTTTAT 59.987 40.000 0.00 0.00 0.00 1.40
3978 5155 6.213195 TGTTTTACTCCCTCCGTTCCTTTATA 59.787 38.462 0.00 0.00 0.00 0.98
3979 5156 7.092757 TGTTTTACTCCCTCCGTTCCTTTATAT 60.093 37.037 0.00 0.00 0.00 0.86
3980 5157 8.424133 GTTTTACTCCCTCCGTTCCTTTATATA 58.576 37.037 0.00 0.00 0.00 0.86
3981 5158 8.551682 TTTACTCCCTCCGTTCCTTTATATAA 57.448 34.615 0.00 0.00 0.00 0.98
3982 5159 6.667558 ACTCCCTCCGTTCCTTTATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3983 5160 5.543020 ACTCCCTCCGTTCCTTTATATAAGG 59.457 44.000 0.00 0.00 38.78 2.69
3984 5161 5.470501 TCCCTCCGTTCCTTTATATAAGGT 58.529 41.667 4.13 0.00 38.55 3.50
3985 5162 5.306160 TCCCTCCGTTCCTTTATATAAGGTG 59.694 44.000 4.13 0.00 38.55 4.00
3986 5163 5.071384 CCCTCCGTTCCTTTATATAAGGTGT 59.929 44.000 4.13 0.00 38.55 4.16
3987 5164 6.268387 CCCTCCGTTCCTTTATATAAGGTGTA 59.732 42.308 4.13 0.00 38.55 2.90
3988 5165 7.038516 CCCTCCGTTCCTTTATATAAGGTGTAT 60.039 40.741 4.13 0.00 38.55 2.29
3989 5166 8.373220 CCTCCGTTCCTTTATATAAGGTGTATT 58.627 37.037 4.13 0.00 38.55 1.89
3990 5167 9.774413 CTCCGTTCCTTTATATAAGGTGTATTT 57.226 33.333 4.13 0.00 38.55 1.40
3991 5168 9.550406 TCCGTTCCTTTATATAAGGTGTATTTG 57.450 33.333 4.13 0.00 38.55 2.32
3992 5169 9.333724 CCGTTCCTTTATATAAGGTGTATTTGT 57.666 33.333 4.13 0.00 38.55 2.83
4013 5190 8.973835 TTTGTATTTTCAAAAGTCAAACGAGT 57.026 26.923 9.67 0.00 34.90 4.18
4014 5191 7.962934 TGTATTTTCAAAAGTCAAACGAGTG 57.037 32.000 0.00 0.00 0.00 3.51
4015 5192 5.949233 ATTTTCAAAAGTCAAACGAGTGC 57.051 34.783 0.00 0.00 0.00 4.40
4016 5193 4.427096 TTTCAAAAGTCAAACGAGTGCA 57.573 36.364 0.00 0.00 0.00 4.57
4017 5194 4.630894 TTCAAAAGTCAAACGAGTGCAT 57.369 36.364 0.00 0.00 0.00 3.96
4018 5195 3.951306 TCAAAAGTCAAACGAGTGCATG 58.049 40.909 0.00 0.00 0.00 4.06
4019 5196 3.376859 TCAAAAGTCAAACGAGTGCATGT 59.623 39.130 0.00 0.00 0.00 3.21
4020 5197 4.104776 CAAAAGTCAAACGAGTGCATGTT 58.895 39.130 0.00 0.00 0.00 2.71
4021 5198 4.370364 AAAGTCAAACGAGTGCATGTTT 57.630 36.364 8.36 8.36 38.76 2.83
4025 5202 2.774439 AAACGAGTGCATGTTTGACC 57.226 45.000 12.15 0.00 36.96 4.02
4026 5203 1.674359 AACGAGTGCATGTTTGACCA 58.326 45.000 0.00 0.00 0.00 4.02
4027 5204 1.674359 ACGAGTGCATGTTTGACCAA 58.326 45.000 0.00 0.00 0.00 3.67
4028 5205 2.020720 ACGAGTGCATGTTTGACCAAA 58.979 42.857 0.00 0.00 0.00 3.28
4029 5206 2.622942 ACGAGTGCATGTTTGACCAAAT 59.377 40.909 0.00 0.00 32.36 2.32
4030 5207 3.068024 ACGAGTGCATGTTTGACCAAATT 59.932 39.130 0.00 0.00 32.36 1.82
4031 5208 4.050553 CGAGTGCATGTTTGACCAAATTT 58.949 39.130 0.00 0.00 32.36 1.82
4032 5209 4.507388 CGAGTGCATGTTTGACCAAATTTT 59.493 37.500 0.00 0.00 32.36 1.82
4033 5210 5.006552 CGAGTGCATGTTTGACCAAATTTTT 59.993 36.000 0.00 0.00 32.36 1.94
4034 5211 6.199908 CGAGTGCATGTTTGACCAAATTTTTA 59.800 34.615 0.00 0.00 32.36 1.52
4035 5212 7.481275 AGTGCATGTTTGACCAAATTTTTAG 57.519 32.000 0.00 0.00 32.36 1.85
4036 5213 7.271511 AGTGCATGTTTGACCAAATTTTTAGA 58.728 30.769 0.00 0.00 32.36 2.10
4037 5214 7.768120 AGTGCATGTTTGACCAAATTTTTAGAA 59.232 29.630 0.00 0.00 32.36 2.10
4038 5215 8.394121 GTGCATGTTTGACCAAATTTTTAGAAA 58.606 29.630 0.00 0.00 32.36 2.52
4039 5216 8.950210 TGCATGTTTGACCAAATTTTTAGAAAA 58.050 25.926 0.00 0.00 32.36 2.29
4040 5217 9.780413 GCATGTTTGACCAAATTTTTAGAAAAA 57.220 25.926 2.82 2.82 41.59 1.94
4093 5270 8.859236 ATATCATTCGATTGATCATGAAAGGT 57.141 30.769 22.40 2.81 37.51 3.50
4094 5271 9.948964 ATATCATTCGATTGATCATGAAAGGTA 57.051 29.630 22.40 5.56 37.51 3.08
4095 5272 7.719778 TCATTCGATTGATCATGAAAGGTAG 57.280 36.000 0.00 0.00 0.00 3.18
4096 5273 7.275183 TCATTCGATTGATCATGAAAGGTAGT 58.725 34.615 0.00 0.00 0.00 2.73
4097 5274 7.770433 TCATTCGATTGATCATGAAAGGTAGTT 59.230 33.333 0.00 0.00 0.00 2.24
4098 5275 7.921786 TTCGATTGATCATGAAAGGTAGTTT 57.078 32.000 0.00 0.00 0.00 2.66
4099 5276 7.539712 TCGATTGATCATGAAAGGTAGTTTC 57.460 36.000 0.00 0.00 44.41 2.78
4169 5346 5.930837 TCTTGGTCAAACTTTCAAATGGT 57.069 34.783 0.00 0.00 0.00 3.55
4170 5347 6.293004 TCTTGGTCAAACTTTCAAATGGTT 57.707 33.333 0.00 0.00 0.00 3.67
4171 5348 6.105333 TCTTGGTCAAACTTTCAAATGGTTG 58.895 36.000 1.14 1.14 33.47 3.77
4172 5349 5.667539 TGGTCAAACTTTCAAATGGTTGA 57.332 34.783 5.32 5.32 42.12 3.18
4173 5350 6.232581 TGGTCAAACTTTCAAATGGTTGAT 57.767 33.333 10.99 0.00 43.29 2.57
4174 5351 6.648192 TGGTCAAACTTTCAAATGGTTGATT 58.352 32.000 10.99 0.00 43.29 2.57
4175 5352 7.108847 TGGTCAAACTTTCAAATGGTTGATTT 58.891 30.769 10.99 0.00 43.29 2.17
4176 5353 8.260818 TGGTCAAACTTTCAAATGGTTGATTTA 58.739 29.630 10.99 1.44 43.29 1.40
4177 5354 8.547894 GGTCAAACTTTCAAATGGTTGATTTAC 58.452 33.333 10.99 1.72 43.29 2.01
4178 5355 9.092876 GTCAAACTTTCAAATGGTTGATTTACA 57.907 29.630 10.99 0.00 43.29 2.41
4179 5356 9.092876 TCAAACTTTCAAATGGTTGATTTACAC 57.907 29.630 5.32 0.00 43.29 2.90
4180 5357 8.877779 CAAACTTTCAAATGGTTGATTTACACA 58.122 29.630 1.29 0.00 43.29 3.72
4181 5358 8.647143 AACTTTCAAATGGTTGATTTACACAG 57.353 30.769 0.00 0.00 43.29 3.66
4182 5359 8.006298 ACTTTCAAATGGTTGATTTACACAGA 57.994 30.769 0.00 0.00 43.29 3.41
4183 5360 8.474025 ACTTTCAAATGGTTGATTTACACAGAA 58.526 29.630 0.00 0.00 43.29 3.02
4184 5361 9.311916 CTTTCAAATGGTTGATTTACACAGAAA 57.688 29.630 0.00 0.00 43.29 2.52
4185 5362 8.641499 TTCAAATGGTTGATTTACACAGAAAC 57.359 30.769 0.00 0.00 43.29 2.78
4186 5363 7.206687 TCAAATGGTTGATTTACACAGAAACC 58.793 34.615 0.00 0.00 38.88 3.27
4189 5366 6.723298 TGGTTGATTTACACAGAAACCAAT 57.277 33.333 2.71 0.00 42.94 3.16
4190 5367 7.825331 TGGTTGATTTACACAGAAACCAATA 57.175 32.000 2.71 0.00 42.94 1.90
4191 5368 7.653647 TGGTTGATTTACACAGAAACCAATAC 58.346 34.615 2.71 0.00 42.94 1.89
4192 5369 7.285629 TGGTTGATTTACACAGAAACCAATACA 59.714 33.333 2.71 0.00 42.94 2.29
4193 5370 7.593644 GGTTGATTTACACAGAAACCAATACAC 59.406 37.037 0.00 0.00 37.57 2.90
4194 5371 7.209471 TGATTTACACAGAAACCAATACACC 57.791 36.000 0.00 0.00 0.00 4.16
4195 5372 7.001674 TGATTTACACAGAAACCAATACACCT 58.998 34.615 0.00 0.00 0.00 4.00
4196 5373 7.504238 TGATTTACACAGAAACCAATACACCTT 59.496 33.333 0.00 0.00 0.00 3.50
4197 5374 8.927675 ATTTACACAGAAACCAATACACCTTA 57.072 30.769 0.00 0.00 0.00 2.69
4198 5375 8.927675 TTTACACAGAAACCAATACACCTTAT 57.072 30.769 0.00 0.00 0.00 1.73
4202 5379 9.174166 ACACAGAAACCAATACACCTTATATTC 57.826 33.333 0.00 0.00 0.00 1.75
4203 5380 9.396022 CACAGAAACCAATACACCTTATATTCT 57.604 33.333 0.00 0.00 0.00 2.40
4209 5386 9.760077 AACCAATACACCTTATATTCTAGAACG 57.240 33.333 7.48 0.00 0.00 3.95
4210 5387 8.365647 ACCAATACACCTTATATTCTAGAACGG 58.634 37.037 7.48 6.23 0.00 4.44
4211 5388 8.582437 CCAATACACCTTATATTCTAGAACGGA 58.418 37.037 7.48 0.00 0.00 4.69
4212 5389 9.627395 CAATACACCTTATATTCTAGAACGGAG 57.373 37.037 7.48 3.93 0.00 4.63
4213 5390 6.651975 ACACCTTATATTCTAGAACGGAGG 57.348 41.667 7.48 14.30 0.00 4.30
4214 5391 5.539193 ACACCTTATATTCTAGAACGGAGGG 59.461 44.000 20.99 16.60 0.00 4.30
4215 5392 5.773680 CACCTTATATTCTAGAACGGAGGGA 59.226 44.000 20.99 0.00 0.00 4.20
4216 5393 6.011481 ACCTTATATTCTAGAACGGAGGGAG 58.989 44.000 20.99 9.75 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.403734 CCCTAGGATCTAGTCTTCCAGAC 58.596 52.174 11.48 0.00 45.38 3.51
30 31 2.009774 CCCAATTGTACTGCTTCGAGG 58.990 52.381 4.43 0.00 0.00 4.63
32 33 2.037902 TGACCCAATTGTACTGCTTCGA 59.962 45.455 4.43 0.00 0.00 3.71
35 36 5.570320 ACTATTGACCCAATTGTACTGCTT 58.430 37.500 4.43 0.00 37.84 3.91
41 42 9.607988 CATGTAACTACTATTGACCCAATTGTA 57.392 33.333 4.43 11.37 39.57 2.41
44 45 6.546034 GCCATGTAACTACTATTGACCCAATT 59.454 38.462 0.00 0.00 35.54 2.32
46 47 5.433526 GCCATGTAACTACTATTGACCCAA 58.566 41.667 0.00 0.00 0.00 4.12
53 54 4.956085 TGCATCGCCATGTAACTACTATT 58.044 39.130 0.00 0.00 31.86 1.73
55 56 3.383505 ACTGCATCGCCATGTAACTACTA 59.616 43.478 0.00 0.00 31.86 1.82
68 69 0.589729 CCGCATTGTTACTGCATCGC 60.590 55.000 0.00 0.00 39.64 4.58
122 132 1.523938 GGGAGACATAGTTGCCGGC 60.524 63.158 22.73 22.73 0.00 6.13
160 170 4.214971 GGTCGGATTTTGAGATCCATCATG 59.785 45.833 4.92 0.00 44.83 3.07
175 185 1.299976 GAAGCTGGGTGGTCGGATT 59.700 57.895 0.00 0.00 0.00 3.01
191 201 2.926242 GGGGGTGGTCGTCCTGAA 60.926 66.667 0.00 0.00 34.23 3.02
215 225 1.883638 GCTTGGCAGTGATGGTTCTCA 60.884 52.381 0.00 0.00 0.00 3.27
224 236 3.970410 CCCTGGGCTTGGCAGTGA 61.970 66.667 0.00 0.00 0.00 3.41
293 305 3.458189 CTCTAATTCGGCTTTGGATCGT 58.542 45.455 0.00 0.00 0.00 3.73
309 321 3.074412 GTTGCAGCTGCTTAACCTCTAA 58.926 45.455 36.61 18.12 42.66 2.10
318 330 2.654877 GCCATGTTGCAGCTGCTT 59.345 55.556 36.61 17.69 42.66 3.91
401 418 3.304911 TCTGATCTTGATCTCCTCGGT 57.695 47.619 11.31 0.00 0.00 4.69
427 444 0.323957 AGCTGCTCAAGATCACTGCA 59.676 50.000 0.00 0.00 0.00 4.41
508 562 2.204090 TTCCCCGCCTCCCTCTTT 60.204 61.111 0.00 0.00 0.00 2.52
586 881 2.419198 CGCCGGATCCTTCCTCAG 59.581 66.667 5.05 0.00 40.17 3.35
587 882 3.154473 CCGCCGGATCCTTCCTCA 61.154 66.667 5.05 0.00 40.17 3.86
622 917 0.896019 CAGTCACCAGGAGGACTCGT 60.896 60.000 13.56 0.00 42.22 4.18
637 933 0.537653 GGGAGGACTAGCAACCAGTC 59.462 60.000 0.00 0.00 41.43 3.51
638 934 1.258445 CGGGAGGACTAGCAACCAGT 61.258 60.000 0.00 0.00 0.00 4.00
648 944 0.903454 AAACACGGATCGGGAGGACT 60.903 55.000 5.18 0.00 32.98 3.85
692 988 7.201857 CCTTGACTTTCTTTCCAGACTTTGAAT 60.202 37.037 0.00 0.00 0.00 2.57
697 993 5.117406 ACCTTGACTTTCTTTCCAGACTT 57.883 39.130 0.00 0.00 0.00 3.01
774 1070 6.650807 CGTATGGCTCTAAACATACCAATCAT 59.349 38.462 8.67 0.00 43.99 2.45
815 1111 4.574674 TCTGATATTTCTTGTGGCCAGT 57.425 40.909 5.11 0.00 0.00 4.00
921 1217 1.918293 CTGGGGTGGAGCTGTGGTA 60.918 63.158 0.00 0.00 0.00 3.25
1024 1330 1.903183 AGGGAGTGTAGTTTGAGAGGC 59.097 52.381 0.00 0.00 0.00 4.70
1040 1346 0.468226 AGAACAACTCGCAACAGGGA 59.532 50.000 0.00 0.00 0.00 4.20
1126 1432 9.520204 CATATTCTTGGAAAACGCATAAAGATT 57.480 29.630 0.00 0.00 0.00 2.40
1137 1443 8.177119 TGGGTATATGCATATTCTTGGAAAAC 57.823 34.615 23.71 12.21 0.00 2.43
1147 1454 8.632679 CAGTTCAAAGTTGGGTATATGCATATT 58.367 33.333 23.71 8.88 0.00 1.28
1173 1480 1.332997 CAATCTGCGCCAGGAAGATTC 59.667 52.381 14.90 0.00 31.51 2.52
1185 1492 1.586422 CCCACCATCTACAATCTGCG 58.414 55.000 0.00 0.00 0.00 5.18
1322 1629 9.829507 ATTAACATTCAATTTTGTGGTCTCAAA 57.170 25.926 0.00 0.00 35.83 2.69
1346 1654 4.156455 ACGCCATGTAAATCTGAGGATT 57.844 40.909 0.00 0.00 43.26 3.01
1468 1776 0.109342 TCCGGACGGAGGGAGTATAC 59.891 60.000 9.76 0.00 39.76 1.47
1476 1784 1.206371 ACAAGTAATTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1501 1809 1.737793 ACTTGTCGCGGAAATGGATTC 59.262 47.619 6.13 0.00 37.31 2.52
1804 2129 2.726351 GCTCTCGCTGTTAGGGCCT 61.726 63.158 12.58 12.58 34.17 5.19
1946 2271 3.838903 AGAACTGGAAAGGAGGATTACGT 59.161 43.478 0.00 0.00 0.00 3.57
1971 2296 2.094182 ACGCAATGAGATCAGTACGGTT 60.094 45.455 7.68 0.00 0.00 4.44
2105 2430 2.899838 GTCCGTGCCAGCACAACA 60.900 61.111 21.67 2.66 46.47 3.33
2123 2448 5.420409 AGTAAGCAAAAGAGGGAGATAACG 58.580 41.667 0.00 0.00 0.00 3.18
2145 2470 8.752254 CAAAATTATGTTCAGATGCAATGCTAG 58.248 33.333 6.82 0.00 0.00 3.42
2148 2473 6.036735 AGCAAAATTATGTTCAGATGCAATGC 59.963 34.615 0.00 0.00 35.11 3.56
2534 2880 3.108521 CAGCGTGACTGTACAGACC 57.891 57.895 29.30 19.01 41.86 3.85
2607 2954 7.201956 ACATCTATGTAATTCAGGGACTCTGAC 60.202 40.741 3.94 0.00 44.68 3.51
2701 3063 6.310467 TCTCCTTGAATAATTTGAAGTCGTCG 59.690 38.462 0.00 0.00 0.00 5.12
2853 3985 5.572896 ACAAAAGCGAAACAAGTTTTCAGAG 59.427 36.000 0.00 0.00 32.11 3.35
2939 4074 6.702282 AGACTGCAACAGTTACTTAGTTCTTC 59.298 38.462 1.15 0.00 45.44 2.87
2940 4075 6.583562 AGACTGCAACAGTTACTTAGTTCTT 58.416 36.000 1.15 0.00 45.44 2.52
2941 4076 6.163135 AGACTGCAACAGTTACTTAGTTCT 57.837 37.500 1.15 0.00 45.44 3.01
3266 4402 1.376424 CATCAGCTGGTTGCCGACT 60.376 57.895 15.13 0.00 44.23 4.18
3334 4470 4.039245 ACAAGAACTCTCTTTCGGATGTGA 59.961 41.667 0.00 0.00 40.05 3.58
3448 4584 2.279582 AGACCTTACAACATCGCTCG 57.720 50.000 0.00 0.00 0.00 5.03
3633 4809 4.418013 TTGCAGATAACATTTGGACGTG 57.582 40.909 0.00 0.00 0.00 4.49
3959 5136 5.543020 CCTTATATAAAGGAACGGAGGGAGT 59.457 44.000 0.00 0.00 39.81 3.85
3960 5137 5.543020 ACCTTATATAAAGGAACGGAGGGAG 59.457 44.000 10.67 0.00 39.81 4.30
3961 5138 5.306160 CACCTTATATAAAGGAACGGAGGGA 59.694 44.000 10.67 0.00 39.81 4.20
3962 5139 5.071384 ACACCTTATATAAAGGAACGGAGGG 59.929 44.000 10.67 4.11 39.81 4.30
3963 5140 6.170846 ACACCTTATATAAAGGAACGGAGG 57.829 41.667 10.67 4.52 39.81 4.30
3964 5141 9.774413 AAATACACCTTATATAAAGGAACGGAG 57.226 33.333 10.67 5.47 39.81 4.63
3965 5142 9.550406 CAAATACACCTTATATAAAGGAACGGA 57.450 33.333 10.67 0.00 39.81 4.69
3966 5143 9.333724 ACAAATACACCTTATATAAAGGAACGG 57.666 33.333 10.67 6.38 39.81 4.44
3987 5164 9.581099 ACTCGTTTGACTTTTGAAAATACAAAT 57.419 25.926 17.92 6.66 39.09 2.32
3988 5165 8.855279 CACTCGTTTGACTTTTGAAAATACAAA 58.145 29.630 13.89 13.89 37.87 2.83
3989 5166 7.008810 GCACTCGTTTGACTTTTGAAAATACAA 59.991 33.333 0.00 0.00 0.00 2.41
3990 5167 6.470877 GCACTCGTTTGACTTTTGAAAATACA 59.529 34.615 0.00 0.00 0.00 2.29
3991 5168 6.470877 TGCACTCGTTTGACTTTTGAAAATAC 59.529 34.615 0.00 0.00 0.00 1.89
3992 5169 6.556212 TGCACTCGTTTGACTTTTGAAAATA 58.444 32.000 0.00 0.00 0.00 1.40
3993 5170 5.406649 TGCACTCGTTTGACTTTTGAAAAT 58.593 33.333 0.00 0.00 0.00 1.82
3994 5171 4.799678 TGCACTCGTTTGACTTTTGAAAA 58.200 34.783 0.00 0.00 0.00 2.29
3995 5172 4.427096 TGCACTCGTTTGACTTTTGAAA 57.573 36.364 0.00 0.00 0.00 2.69
3996 5173 4.142491 ACATGCACTCGTTTGACTTTTGAA 60.142 37.500 0.00 0.00 0.00 2.69
3997 5174 3.376859 ACATGCACTCGTTTGACTTTTGA 59.623 39.130 0.00 0.00 0.00 2.69
3998 5175 3.694734 ACATGCACTCGTTTGACTTTTG 58.305 40.909 0.00 0.00 0.00 2.44
3999 5176 4.370364 AACATGCACTCGTTTGACTTTT 57.630 36.364 0.00 0.00 0.00 2.27
4000 5177 4.370364 AAACATGCACTCGTTTGACTTT 57.630 36.364 9.29 0.00 34.16 2.66
4006 5183 2.020720 TGGTCAAACATGCACTCGTTT 58.979 42.857 5.20 5.20 35.76 3.60
4007 5184 1.674359 TGGTCAAACATGCACTCGTT 58.326 45.000 0.00 0.00 0.00 3.85
4008 5185 1.674359 TTGGTCAAACATGCACTCGT 58.326 45.000 0.00 0.00 0.00 4.18
4009 5186 2.772568 TTTGGTCAAACATGCACTCG 57.227 45.000 0.00 0.00 0.00 4.18
4010 5187 5.989551 AAAATTTGGTCAAACATGCACTC 57.010 34.783 0.00 0.00 32.51 3.51
4011 5188 7.271511 TCTAAAAATTTGGTCAAACATGCACT 58.728 30.769 0.00 0.00 32.51 4.40
4012 5189 7.475771 TCTAAAAATTTGGTCAAACATGCAC 57.524 32.000 0.00 0.00 32.51 4.57
4013 5190 8.498054 TTTCTAAAAATTTGGTCAAACATGCA 57.502 26.923 0.00 0.00 32.51 3.96
4014 5191 9.780413 TTTTTCTAAAAATTTGGTCAAACATGC 57.220 25.926 0.00 0.00 33.29 4.06
4067 5244 9.948964 ACCTTTCATGATCAATCGAATGATATA 57.051 29.630 15.79 8.83 40.08 0.86
4068 5245 8.859236 ACCTTTCATGATCAATCGAATGATAT 57.141 30.769 15.79 7.56 40.08 1.63
4069 5246 9.428097 CTACCTTTCATGATCAATCGAATGATA 57.572 33.333 15.79 5.69 40.08 2.15
4070 5247 7.935755 ACTACCTTTCATGATCAATCGAATGAT 59.064 33.333 15.76 15.76 42.62 2.45
4071 5248 7.275183 ACTACCTTTCATGATCAATCGAATGA 58.725 34.615 5.48 5.48 0.00 2.57
4072 5249 7.488187 ACTACCTTTCATGATCAATCGAATG 57.512 36.000 0.00 5.77 0.00 2.67
4073 5250 8.511604 AAACTACCTTTCATGATCAATCGAAT 57.488 30.769 0.00 0.00 0.00 3.34
4074 5251 7.606073 TGAAACTACCTTTCATGATCAATCGAA 59.394 33.333 0.00 0.16 42.85 3.71
4075 5252 7.102993 TGAAACTACCTTTCATGATCAATCGA 58.897 34.615 0.00 0.00 42.85 3.59
4076 5253 7.307493 TGAAACTACCTTTCATGATCAATCG 57.693 36.000 0.00 0.00 42.85 3.34
4143 5320 8.650490 ACCATTTGAAAGTTTGACCAAGATTAT 58.350 29.630 0.00 0.00 0.00 1.28
4144 5321 8.017418 ACCATTTGAAAGTTTGACCAAGATTA 57.983 30.769 0.00 0.00 0.00 1.75
4145 5322 6.888105 ACCATTTGAAAGTTTGACCAAGATT 58.112 32.000 0.00 0.00 0.00 2.40
4146 5323 6.484364 ACCATTTGAAAGTTTGACCAAGAT 57.516 33.333 0.00 0.00 0.00 2.40
4147 5324 5.930837 ACCATTTGAAAGTTTGACCAAGA 57.069 34.783 0.00 0.00 0.00 3.02
4148 5325 6.105333 TCAACCATTTGAAAGTTTGACCAAG 58.895 36.000 0.00 0.00 38.87 3.61
4149 5326 6.042638 TCAACCATTTGAAAGTTTGACCAA 57.957 33.333 0.00 0.00 38.87 3.67
4150 5327 5.667539 TCAACCATTTGAAAGTTTGACCA 57.332 34.783 0.00 0.00 38.87 4.02
4151 5328 7.552458 AAATCAACCATTTGAAAGTTTGACC 57.448 32.000 0.00 0.00 45.01 4.02
4152 5329 9.092876 TGTAAATCAACCATTTGAAAGTTTGAC 57.907 29.630 0.00 0.00 45.01 3.18
4153 5330 9.092876 GTGTAAATCAACCATTTGAAAGTTTGA 57.907 29.630 0.00 2.42 45.01 2.69
4154 5331 8.877779 TGTGTAAATCAACCATTTGAAAGTTTG 58.122 29.630 0.00 0.00 45.01 2.93
4155 5332 9.097257 CTGTGTAAATCAACCATTTGAAAGTTT 57.903 29.630 0.00 0.00 45.01 2.66
4156 5333 8.474025 TCTGTGTAAATCAACCATTTGAAAGTT 58.526 29.630 0.00 0.00 45.01 2.66
4157 5334 8.006298 TCTGTGTAAATCAACCATTTGAAAGT 57.994 30.769 0.00 0.00 45.01 2.66
4158 5335 8.870160 TTCTGTGTAAATCAACCATTTGAAAG 57.130 30.769 0.00 0.00 45.01 2.62
4159 5336 9.092876 GTTTCTGTGTAAATCAACCATTTGAAA 57.907 29.630 0.00 0.00 45.01 2.69
4160 5337 7.708752 GGTTTCTGTGTAAATCAACCATTTGAA 59.291 33.333 0.00 0.00 45.01 2.69
4161 5338 7.147828 TGGTTTCTGTGTAAATCAACCATTTGA 60.148 33.333 0.00 0.00 45.93 2.69
4162 5339 6.983307 TGGTTTCTGTGTAAATCAACCATTTG 59.017 34.615 0.00 0.00 35.34 2.32
4163 5340 7.118496 TGGTTTCTGTGTAAATCAACCATTT 57.882 32.000 0.00 0.00 38.35 2.32
4164 5341 6.723298 TGGTTTCTGTGTAAATCAACCATT 57.277 33.333 0.00 0.00 34.50 3.16
4165 5342 6.723298 TTGGTTTCTGTGTAAATCAACCAT 57.277 33.333 2.54 0.00 35.16 3.55
4166 5343 6.723298 ATTGGTTTCTGTGTAAATCAACCA 57.277 33.333 0.00 0.00 41.06 3.67
4167 5344 7.593644 GTGTATTGGTTTCTGTGTAAATCAACC 59.406 37.037 0.00 0.00 41.06 3.77
4168 5345 7.593644 GGTGTATTGGTTTCTGTGTAAATCAAC 59.406 37.037 0.00 0.00 41.06 3.18
4169 5346 7.504238 AGGTGTATTGGTTTCTGTGTAAATCAA 59.496 33.333 0.00 0.00 42.10 2.57
4170 5347 7.001674 AGGTGTATTGGTTTCTGTGTAAATCA 58.998 34.615 0.00 0.00 0.00 2.57
4171 5348 7.448748 AGGTGTATTGGTTTCTGTGTAAATC 57.551 36.000 0.00 0.00 0.00 2.17
4172 5349 7.833285 AAGGTGTATTGGTTTCTGTGTAAAT 57.167 32.000 0.00 0.00 0.00 1.40
4173 5350 8.927675 ATAAGGTGTATTGGTTTCTGTGTAAA 57.072 30.769 0.00 0.00 0.00 2.01
4176 5353 9.174166 GAATATAAGGTGTATTGGTTTCTGTGT 57.826 33.333 0.00 0.00 0.00 3.72
4177 5354 9.396022 AGAATATAAGGTGTATTGGTTTCTGTG 57.604 33.333 0.00 0.00 0.00 3.66
4183 5360 9.760077 CGTTCTAGAATATAAGGTGTATTGGTT 57.240 33.333 8.75 0.00 0.00 3.67
4184 5361 8.365647 CCGTTCTAGAATATAAGGTGTATTGGT 58.634 37.037 8.75 0.00 0.00 3.67
4185 5362 8.582437 TCCGTTCTAGAATATAAGGTGTATTGG 58.418 37.037 8.75 0.00 0.00 3.16
4186 5363 9.627395 CTCCGTTCTAGAATATAAGGTGTATTG 57.373 37.037 8.75 0.00 0.00 1.90
4187 5364 8.804204 CCTCCGTTCTAGAATATAAGGTGTATT 58.196 37.037 8.75 0.00 0.00 1.89
4188 5365 7.396623 CCCTCCGTTCTAGAATATAAGGTGTAT 59.603 40.741 8.75 0.00 0.00 2.29
4189 5366 6.718454 CCCTCCGTTCTAGAATATAAGGTGTA 59.282 42.308 8.75 0.00 0.00 2.90
4190 5367 5.539193 CCCTCCGTTCTAGAATATAAGGTGT 59.461 44.000 8.75 0.00 0.00 4.16
4191 5368 5.773680 TCCCTCCGTTCTAGAATATAAGGTG 59.226 44.000 8.75 8.25 0.00 4.00
4192 5369 5.961897 TCCCTCCGTTCTAGAATATAAGGT 58.038 41.667 8.75 0.00 0.00 3.50
4193 5370 6.011481 ACTCCCTCCGTTCTAGAATATAAGG 58.989 44.000 8.75 12.50 0.00 2.69
4194 5371 8.513774 GTTACTCCCTCCGTTCTAGAATATAAG 58.486 40.741 8.75 4.58 0.00 1.73
4195 5372 8.223330 AGTTACTCCCTCCGTTCTAGAATATAA 58.777 37.037 8.75 0.00 0.00 0.98
4196 5373 7.753630 AGTTACTCCCTCCGTTCTAGAATATA 58.246 38.462 8.75 0.00 0.00 0.86
4197 5374 6.612741 AGTTACTCCCTCCGTTCTAGAATAT 58.387 40.000 8.75 0.00 0.00 1.28
4198 5375 6.011122 AGTTACTCCCTCCGTTCTAGAATA 57.989 41.667 8.75 0.00 0.00 1.75
4199 5376 4.869451 AGTTACTCCCTCCGTTCTAGAAT 58.131 43.478 8.75 0.00 0.00 2.40
4200 5377 4.313020 AGTTACTCCCTCCGTTCTAGAA 57.687 45.455 0.00 0.00 0.00 2.10
4201 5378 4.313020 AAGTTACTCCCTCCGTTCTAGA 57.687 45.455 0.00 0.00 0.00 2.43
4202 5379 5.192176 AGTAAGTTACTCCCTCCGTTCTAG 58.808 45.833 9.85 0.00 32.47 2.43
4203 5380 5.184892 AGTAAGTTACTCCCTCCGTTCTA 57.815 43.478 9.85 0.00 32.47 2.10
4204 5381 4.044946 AGTAAGTTACTCCCTCCGTTCT 57.955 45.455 9.85 0.00 32.47 3.01
4205 5382 6.096001 TGAATAGTAAGTTACTCCCTCCGTTC 59.904 42.308 18.77 12.25 40.14 3.95
4206 5383 5.954150 TGAATAGTAAGTTACTCCCTCCGTT 59.046 40.000 18.77 4.69 40.14 4.44
4207 5384 5.513233 TGAATAGTAAGTTACTCCCTCCGT 58.487 41.667 18.77 0.00 40.14 4.69
4208 5385 6.568081 CGATGAATAGTAAGTTACTCCCTCCG 60.568 46.154 18.77 12.37 40.14 4.63
4209 5386 6.264970 ACGATGAATAGTAAGTTACTCCCTCC 59.735 42.308 18.77 6.40 40.14 4.30
4210 5387 7.274603 ACGATGAATAGTAAGTTACTCCCTC 57.725 40.000 18.77 13.52 40.14 4.30
4211 5388 7.447853 CCTACGATGAATAGTAAGTTACTCCCT 59.552 40.741 18.77 5.13 40.14 4.20
4212 5389 7.446625 TCCTACGATGAATAGTAAGTTACTCCC 59.553 40.741 18.77 9.85 40.14 4.30
4213 5390 8.388484 TCCTACGATGAATAGTAAGTTACTCC 57.612 38.462 18.77 10.17 40.14 3.85
4214 5391 8.016801 GCTCCTACGATGAATAGTAAGTTACTC 58.983 40.741 18.77 6.34 40.14 2.59
4215 5392 7.501559 TGCTCCTACGATGAATAGTAAGTTACT 59.498 37.037 19.15 19.15 42.68 2.24
4216 5393 7.590689 GTGCTCCTACGATGAATAGTAAGTTAC 59.409 40.741 4.78 4.78 0.00 2.50


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

AutoCloner maintained by Alex Coulton.