Multiple sequence alignment - TraesCS2D01G066900

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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 TraesCS2D01G066900 chr2D 100.000 5953 0 0 1 5953 28003420 27997468 0.000000e+00 10994.0
1 TraesCS2D01G066900 chr2D 89.883 3756 325 35 1277 5011 27956434 27960155 0.000000e+00 4780.0
2 TraesCS2D01G066900 chr2D 82.323 2376 355 35 2883 5244 28417361 28415037 0.000000e+00 2001.0
3 TraesCS2D01G066900 chr2D 95.861 1184 46 1 3086 4269 27977644 27976464 0.000000e+00 1912.0
4 TraesCS2D01G066900 chr2D 86.509 971 127 4 1712 2680 28060723 28059755 0.000000e+00 1064.0
5 TraesCS2D01G066900 chr2D 90.357 560 46 5 5243 5801 52621087 52621639 0.000000e+00 728.0
6 TraesCS2D01G066900 chr2D 78.069 953 113 52 604 1491 28010292 28009371 1.140000e-141 514.0
7 TraesCS2D01G066900 chr2D 81.232 682 81 21 4814 5491 27976408 27975770 1.910000e-139 507.0
8 TraesCS2D01G066900 chr2D 81.090 587 108 2 1688 2274 28417967 28417384 3.250000e-127 466.0
9 TraesCS2D01G066900 chr2D 80.145 690 73 35 627 1268 28095751 28095078 1.960000e-124 457.0
10 TraesCS2D01G066900 chr2D 77.123 577 75 36 703 1247 27955823 27956374 1.260000e-71 281.0
11 TraesCS2D01G066900 chr2D 87.500 240 24 5 5358 5593 27969266 27969029 7.600000e-69 272.0
12 TraesCS2D01G066900 chr2D 75.668 337 63 10 2 322 417543011 417542678 3.720000e-32 150.0
13 TraesCS2D01G066900 chr2B 93.354 4619 259 22 994 5589 44755401 44750808 0.000000e+00 6785.0
14 TraesCS2D01G066900 chr2B 93.395 2907 170 6 1468 4374 45542208 45545092 0.000000e+00 4285.0
15 TraesCS2D01G066900 chr2B 88.879 3453 322 23 1654 5103 45033130 45029737 0.000000e+00 4193.0
16 TraesCS2D01G066900 chr2B 89.980 2974 234 32 2553 5521 45135922 45133008 0.000000e+00 3783.0
17 TraesCS2D01G066900 chr2B 93.765 2037 99 11 2876 4886 45667348 45669382 0.000000e+00 3033.0
18 TraesCS2D01G066900 chr2B 92.308 936 57 11 4871 5802 45669711 45670635 0.000000e+00 1315.0
19 TraesCS2D01G066900 chr2B 81.486 1615 249 27 3638 5244 44926463 44928035 0.000000e+00 1280.0
20 TraesCS2D01G066900 chr2B 81.384 1590 253 28 3638 5220 45617054 45615501 0.000000e+00 1256.0
21 TraesCS2D01G066900 chr2B 81.150 1618 244 33 3638 5244 45625117 45626684 0.000000e+00 1242.0
22 TraesCS2D01G066900 chr2B 88.397 836 50 6 4366 5201 45545561 45546349 0.000000e+00 963.0
23 TraesCS2D01G066900 chr2B 90.949 685 49 5 278 960 44762367 44761694 0.000000e+00 909.0
24 TraesCS2D01G066900 chr2B 77.026 1271 177 68 7 1215 45035479 45034262 1.820000e-174 623.0
25 TraesCS2D01G066900 chr2B 82.689 647 51 16 363 975 45540321 45540940 8.840000e-143 518.0
26 TraesCS2D01G066900 chr2B 89.474 399 35 7 5198 5593 45546429 45546823 1.150000e-136 497.0
27 TraesCS2D01G066900 chr2B 88.571 245 26 2 722 966 105097485 105097727 4.510000e-76 296.0
28 TraesCS2D01G066900 chr2B 87.755 245 28 2 722 966 105083627 105083869 9.760000e-73 285.0
29 TraesCS2D01G066900 chr2B 76.006 646 99 33 620 1231 45137930 45137307 3.510000e-72 283.0
30 TraesCS2D01G066900 chr2B 85.081 248 25 6 5170 5415 45029713 45029476 5.960000e-60 243.0
31 TraesCS2D01G066900 chr2B 93.985 133 6 2 5785 5916 497854287 497854156 3.640000e-47 200.0
32 TraesCS2D01G066900 chr2B 93.023 129 8 1 850 978 44755923 44755796 2.830000e-43 187.0
33 TraesCS2D01G066900 chr2B 75.298 336 65 8 2 322 489364410 489364078 1.730000e-30 145.0
34 TraesCS2D01G066900 chr2A 90.277 4556 362 50 1277 5802 30165285 30160781 0.000000e+00 5884.0
35 TraesCS2D01G066900 chr2A 83.789 3547 521 31 1685 5215 30300994 30304502 0.000000e+00 3315.0
36 TraesCS2D01G066900 chr2A 84.350 3310 487 15 1701 5004 30272069 30268785 0.000000e+00 3214.0
37 TraesCS2D01G066900 chr2A 76.141 1446 205 91 607 1987 30213601 30212231 1.090000e-176 630.0
38 TraesCS2D01G066900 chr2A 74.895 956 126 67 605 1491 30189123 30188213 1.240000e-86 331.0
39 TraesCS2D01G066900 chr2A 90.722 194 7 4 1277 1461 22435733 22435924 1.280000e-61 248.0
40 TraesCS2D01G066900 chr2A 88.485 165 17 2 803 966 22435248 22435411 1.310000e-46 198.0
41 TraesCS2D01G066900 chr2A 100.000 40 0 0 994 1033 22435464 22435503 2.300000e-09 75.0
42 TraesCS2D01G066900 chr7D 84.540 2846 397 28 1685 4513 302743600 302746419 0.000000e+00 2778.0
43 TraesCS2D01G066900 chr7D 97.826 46 1 0 5591 5636 105653218 105653263 4.950000e-11 80.5
44 TraesCS2D01G066900 chr1A 78.858 473 78 13 1 456 449845519 449845986 3.490000e-77 300.0
45 TraesCS2D01G066900 chr1A 87.500 256 30 2 723 978 242073078 242072825 1.620000e-75 294.0
46 TraesCS2D01G066900 chr1A 95.370 108 4 1 1277 1384 242072496 242072390 2.850000e-38 171.0
47 TraesCS2D01G066900 chr1A 96.491 57 1 1 1371 1426 240953575 240953519 6.350000e-15 93.5
48 TraesCS2D01G066900 chr4B 77.374 495 87 16 11 487 15432289 15432776 2.730000e-68 270.0
49 TraesCS2D01G066900 chr4B 79.600 250 46 4 217 463 496426492 496426739 2.210000e-39 174.0
50 TraesCS2D01G066900 chr4B 93.023 43 3 0 5591 5633 3861378 3861420 4.980000e-06 63.9
51 TraesCS2D01G066900 chr3A 76.969 508 96 13 1 490 16154516 16154012 2.730000e-68 270.0
52 TraesCS2D01G066900 chr3D 77.339 481 90 12 1 464 426881453 426880975 3.540000e-67 267.0
53 TraesCS2D01G066900 chr3D 77.778 369 67 7 129 483 580128148 580128515 4.670000e-51 213.0
54 TraesCS2D01G066900 chr3D 95.161 124 5 1 5796 5919 281906486 281906608 1.690000e-45 195.0
55 TraesCS2D01G066900 chr3D 97.826 46 1 0 5591 5636 35191611 35191656 4.950000e-11 80.5
56 TraesCS2D01G066900 chr5B 76.409 479 93 12 1 463 134061696 134062170 2.140000e-59 241.0
57 TraesCS2D01G066900 chr5B 95.868 121 5 0 5798 5918 70795772 70795652 4.710000e-46 196.0
58 TraesCS2D01G066900 chr4D 76.458 480 91 13 11 474 8152140 8152613 2.140000e-59 241.0
59 TraesCS2D01G066900 chr4D 75.630 476 94 12 1 460 479414634 479414165 3.610000e-52 217.0
60 TraesCS2D01G066900 chr4D 95.868 121 5 0 5798 5918 52629729 52629849 4.710000e-46 196.0
61 TraesCS2D01G066900 chr4D 78.387 310 53 10 164 461 417812547 417812854 7.880000e-44 189.0
62 TraesCS2D01G066900 chr3B 76.190 483 94 11 1 465 425723082 425723561 9.970000e-58 235.0
63 TraesCS2D01G066900 chr3B 74.844 481 86 24 1 464 3265349 3264887 1.020000e-42 185.0
64 TraesCS2D01G066900 chr6B 95.312 128 5 1 5794 5920 130306041 130306168 1.010000e-47 202.0
65 TraesCS2D01G066900 chr6B 90.972 144 11 2 5796 5939 27077968 27078109 6.090000e-45 193.0
66 TraesCS2D01G066900 chr6B 95.455 44 2 0 5595 5638 82186839 82186796 2.980000e-08 71.3
67 TraesCS2D01G066900 chrUn 96.639 119 4 0 5798 5916 88642464 88642582 1.310000e-46 198.0
68 TraesCS2D01G066900 chrUn 96.639 119 4 0 5798 5916 283732555 283732673 1.310000e-46 198.0
69 TraesCS2D01G066900 chr1D 75.208 480 87 18 12 483 365430059 365430514 1.310000e-46 198.0
70 TraesCS2D01G066900 chr6D 91.429 140 9 3 5778 5917 430998598 430998462 7.880000e-44 189.0
71 TraesCS2D01G066900 chr6D 95.652 46 2 0 5591 5636 449215598 449215643 2.300000e-09 75.0
72 TraesCS2D01G066900 chr5A 74.419 473 97 14 11 465 626985053 626985519 1.320000e-41 182.0
73 TraesCS2D01G066900 chr5A 92.857 42 3 0 5595 5636 677957887 677957928 1.790000e-05 62.1
74 TraesCS2D01G066900 chr7A 81.921 177 27 2 11 183 130068284 130068459 1.730000e-30 145.0


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 TraesCS2D01G066900 chr2D 27997468 28003420 5952 True 10994.000000 10994 100.00000 1 5953 1 chr2D.!!$R2 5952
1 TraesCS2D01G066900 chr2D 27955823 27960155 4332 False 2530.500000 4780 83.50300 703 5011 2 chr2D.!!$F2 4308
2 TraesCS2D01G066900 chr2D 28415037 28417967 2930 True 1233.500000 2001 81.70650 1688 5244 2 chr2D.!!$R8 3556
3 TraesCS2D01G066900 chr2D 27975770 27977644 1874 True 1209.500000 1912 88.54650 3086 5491 2 chr2D.!!$R7 2405
4 TraesCS2D01G066900 chr2D 28059755 28060723 968 True 1064.000000 1064 86.50900 1712 2680 1 chr2D.!!$R4 968
5 TraesCS2D01G066900 chr2D 52621087 52621639 552 False 728.000000 728 90.35700 5243 5801 1 chr2D.!!$F1 558
6 TraesCS2D01G066900 chr2D 28009371 28010292 921 True 514.000000 514 78.06900 604 1491 1 chr2D.!!$R3 887
7 TraesCS2D01G066900 chr2D 28095078 28095751 673 True 457.000000 457 80.14500 627 1268 1 chr2D.!!$R5 641
8 TraesCS2D01G066900 chr2B 44750808 44755923 5115 True 3486.000000 6785 93.18850 850 5589 2 chr2B.!!$R5 4739
9 TraesCS2D01G066900 chr2B 45667348 45670635 3287 False 2174.000000 3033 93.03650 2876 5802 2 chr2B.!!$F6 2926
10 TraesCS2D01G066900 chr2B 45133008 45137930 4922 True 2033.000000 3783 82.99300 620 5521 2 chr2B.!!$R7 4901
11 TraesCS2D01G066900 chr2B 45029476 45035479 6003 True 1686.333333 4193 83.66200 7 5415 3 chr2B.!!$R6 5408
12 TraesCS2D01G066900 chr2B 45540321 45546823 6502 False 1565.750000 4285 88.48875 363 5593 4 chr2B.!!$F5 5230
13 TraesCS2D01G066900 chr2B 44926463 44928035 1572 False 1280.000000 1280 81.48600 3638 5244 1 chr2B.!!$F1 1606
14 TraesCS2D01G066900 chr2B 45615501 45617054 1553 True 1256.000000 1256 81.38400 3638 5220 1 chr2B.!!$R2 1582
15 TraesCS2D01G066900 chr2B 45625117 45626684 1567 False 1242.000000 1242 81.15000 3638 5244 1 chr2B.!!$F2 1606
16 TraesCS2D01G066900 chr2B 44761694 44762367 673 True 909.000000 909 90.94900 278 960 1 chr2B.!!$R1 682
17 TraesCS2D01G066900 chr2A 30160781 30165285 4504 True 5884.000000 5884 90.27700 1277 5802 1 chr2A.!!$R1 4525
18 TraesCS2D01G066900 chr2A 30300994 30304502 3508 False 3315.000000 3315 83.78900 1685 5215 1 chr2A.!!$F1 3530
19 TraesCS2D01G066900 chr2A 30268785 30272069 3284 True 3214.000000 3214 84.35000 1701 5004 1 chr2A.!!$R4 3303
20 TraesCS2D01G066900 chr2A 30212231 30213601 1370 True 630.000000 630 76.14100 607 1987 1 chr2A.!!$R3 1380
21 TraesCS2D01G066900 chr2A 30188213 30189123 910 True 331.000000 331 74.89500 605 1491 1 chr2A.!!$R2 886
22 TraesCS2D01G066900 chr7D 302743600 302746419 2819 False 2778.000000 2778 84.54000 1685 4513 1 chr7D.!!$F2 2828
23 TraesCS2D01G066900 chr1A 242072390 242073078 688 True 232.500000 294 91.43500 723 1384 2 chr1A.!!$R2 661
24 TraesCS2D01G066900 chr3A 16154012 16154516 504 True 270.000000 270 76.96900 1 490 1 chr3A.!!$R1 489

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
245 259 0.107410 AGTGGGTTCAACTGCGACAA 60.107 50.000 0.00 0.0 0.00 3.18 F
1093 1307 0.180171 CCATTGTCCCATCCTGCGTA 59.820 55.000 0.00 0.0 0.00 4.42 F
1895 4509 0.979709 TGCAGATGGAGAGGGGTCAG 60.980 60.000 0.00 0.0 0.00 3.51 F
2698 5346 1.213296 GGGCCTGATCCCTACTTCAA 58.787 55.000 0.84 0.0 43.13 2.69 F
3393 6041 0.037303 CTGGTGCTGGTCCAACATCT 59.963 55.000 7.06 0.0 30.94 2.90 F
4446 7601 1.202359 TCAGCAAAGTTTTTGTCGCCC 60.202 47.619 3.77 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 4227 0.756442 TTGGGAGTGCTTGCTGCTTT 60.756 50.000 0.00 0.00 43.37 3.51 R
2040 4654 1.351350 GGAAGCTTACCCAACTCACCT 59.649 52.381 0.00 0.00 0.00 4.00 R
2901 5549 1.561542 ACTGCAATAGGTAAGCTGCCT 59.438 47.619 13.74 13.74 40.00 4.75 R
4376 7531 3.000041 TCATCGTCCAAAAGGATGTTCG 59.000 45.455 3.85 0.00 45.99 3.95 R
4792 7952 1.939381 GCGTCCATACTTCTGCACACA 60.939 52.381 0.00 0.00 0.00 3.72 R
5883 9500 0.030369 CCGGAAATACTCGTCGGAGG 59.970 60.000 0.00 0.00 44.93 4.30 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
28 29 8.989131 TCTGCTCTGGTTAGTAATTTAGGTTAT 58.011 33.333 0.00 0.00 0.00 1.89
33 34 9.895138 TCTGGTTAGTAATTTAGGTTATGGTTC 57.105 33.333 0.00 0.00 0.00 3.62
51 52 2.488153 GTTCTTTAATCCTTGCAGGCGT 59.512 45.455 0.00 0.00 34.61 5.68
72 73 4.814294 GCTCGGGCGAATGACGGT 62.814 66.667 0.00 0.00 42.83 4.83
99 100 1.000506 TCTTCGAGTTTGTCTTCCGGG 59.999 52.381 0.00 0.00 0.00 5.73
116 117 1.066430 CGGGTTTTGATCCTCCTCGAA 60.066 52.381 0.00 0.00 0.00 3.71
126 131 2.752030 TCCTCCTCGAATTCATCTGGT 58.248 47.619 6.22 0.00 0.00 4.00
147 152 1.025647 GTAGTCGACGGAGCTCAGGT 61.026 60.000 18.37 13.69 0.00 4.00
165 170 2.755655 AGGTGTAGATTCCTGTCGTCTG 59.244 50.000 0.00 0.00 32.29 3.51
172 177 2.731691 TTCCTGTCGTCTGCTTGGGC 62.732 60.000 0.00 0.00 39.26 5.36
188 193 0.470341 GGGCCAGTGAGGTTAGGATC 59.530 60.000 4.39 0.00 40.61 3.36
215 220 8.663167 TCTCCTCATATGGTGATATTTGATGTT 58.337 33.333 2.13 0.00 35.97 2.71
238 252 3.521126 AGATCTATGCAGTGGGTTCAACT 59.479 43.478 0.00 0.00 0.00 3.16
245 259 0.107410 AGTGGGTTCAACTGCGACAA 60.107 50.000 0.00 0.00 0.00 3.18
256 270 0.388649 CTGCGACAAACTACGGCTCT 60.389 55.000 0.00 0.00 0.00 4.09
261 275 2.358267 CGACAAACTACGGCTCTAGGAT 59.642 50.000 0.00 0.00 0.00 3.24
268 282 0.978146 ACGGCTCTAGGATGCTGGTT 60.978 55.000 0.00 0.00 39.67 3.67
270 284 0.833287 GGCTCTAGGATGCTGGTTCA 59.167 55.000 0.00 0.00 0.00 3.18
273 287 3.306641 GGCTCTAGGATGCTGGTTCATAG 60.307 52.174 0.00 0.00 0.00 2.23
275 289 2.634940 TCTAGGATGCTGGTTCATAGGC 59.365 50.000 0.00 0.00 30.46 3.93
276 290 1.216064 AGGATGCTGGTTCATAGGCA 58.784 50.000 0.00 0.00 39.06 4.75
277 291 1.133976 AGGATGCTGGTTCATAGGCAC 60.134 52.381 0.00 0.00 37.52 5.01
278 292 0.940126 GATGCTGGTTCATAGGCACG 59.060 55.000 0.00 0.00 37.52 5.34
279 293 0.464373 ATGCTGGTTCATAGGCACGG 60.464 55.000 0.00 0.00 37.52 4.94
280 294 1.220749 GCTGGTTCATAGGCACGGA 59.779 57.895 0.00 0.00 0.00 4.69
282 296 0.249120 CTGGTTCATAGGCACGGACA 59.751 55.000 0.00 0.00 0.00 4.02
283 297 0.908910 TGGTTCATAGGCACGGACAT 59.091 50.000 0.00 0.00 0.00 3.06
346 363 2.144833 TAGGAAAGCGGCGACAACGA 62.145 55.000 12.98 0.00 42.66 3.85
394 411 2.710096 AGTGGTTGTTCGGGGATATG 57.290 50.000 0.00 0.00 0.00 1.78
402 419 2.371841 TGTTCGGGGATATGGGAATCTG 59.628 50.000 0.00 0.00 0.00 2.90
686 739 2.509336 CCGACGGTGTGATGCTCC 60.509 66.667 5.48 0.00 0.00 4.70
756 840 4.162690 GCATCGAAGGCCTCCGGT 62.163 66.667 12.95 0.00 0.00 5.28
859 993 3.478540 GAGCATCGCCTAGGGTTTT 57.521 52.632 11.72 0.00 0.00 2.43
1071 1284 6.183360 GGATGAAGTGCAGTTACCTACAAATC 60.183 42.308 6.80 0.00 0.00 2.17
1081 1295 7.626452 GCAGTTACCTACAAATCTTCCATTGTC 60.626 40.741 0.00 0.00 40.14 3.18
1093 1307 0.180171 CCATTGTCCCATCCTGCGTA 59.820 55.000 0.00 0.00 0.00 4.42
1111 1327 3.058639 GCGTAATCCCATTCAGATTCAGC 60.059 47.826 0.00 0.00 35.59 4.26
1112 1328 4.384056 CGTAATCCCATTCAGATTCAGCT 58.616 43.478 0.00 0.00 35.59 4.24
1114 1330 2.723322 TCCCATTCAGATTCAGCTGG 57.277 50.000 15.13 0.00 36.55 4.85
1165 1390 3.567530 TGCAATTCTGAATCAGTTTGCG 58.432 40.909 29.18 13.35 45.15 4.85
1200 1830 4.202461 TGTCTAATGAGTGGTTCAGGCTTT 60.202 41.667 0.00 0.00 39.68 3.51
1219 2569 4.744631 GCTTTTGTTTATGTGTTCTGGGTG 59.255 41.667 0.00 0.00 0.00 4.61
1233 2583 1.837439 CTGGGTGGATGCTACCAAGTA 59.163 52.381 4.19 0.00 41.87 2.24
1271 2648 2.357952 GTGTCACCTCTTGGTTTGTTCC 59.642 50.000 0.00 0.00 46.05 3.62
1274 2651 2.507886 TCACCTCTTGGTTTGTTCCTCA 59.492 45.455 0.00 0.00 46.05 3.86
1344 2732 2.037136 AGCATCCTTGTGTCGCTGC 61.037 57.895 0.00 0.00 0.00 5.25
1577 4177 4.393062 ACATAACTTCTGGCAGACAAATCG 59.607 41.667 18.55 7.59 0.00 3.34
1580 4180 2.808543 ACTTCTGGCAGACAAATCGTTC 59.191 45.455 18.55 0.00 0.00 3.95
1623 4227 1.899437 GATCGTCCAGGCTCCAACCA 61.899 60.000 0.00 0.00 0.00 3.67
1881 4494 3.462982 TGACTCGCTAAACTTTTGCAGA 58.537 40.909 8.38 5.83 0.00 4.26
1895 4509 0.979709 TGCAGATGGAGAGGGGTCAG 60.980 60.000 0.00 0.00 0.00 3.51
1947 4561 3.761218 TCTCTCTTAACCTCAGCTCTGTG 59.239 47.826 0.00 0.00 0.00 3.66
2146 4760 4.083217 GCGCTAGCAGTTCTCTTAGCTATA 60.083 45.833 16.45 0.00 44.35 1.31
2241 4855 6.637254 CACTTATACTGTCACGTAATAGCCTG 59.363 42.308 0.00 0.00 0.00 4.85
2428 5042 8.677148 TTCAATAGGAAATATTTCTTCCCTCG 57.323 34.615 23.85 9.95 42.98 4.63
2500 5114 8.366671 GACTTTGAGTCACATTACTAAACTGT 57.633 34.615 0.00 0.00 44.45 3.55
2698 5346 1.213296 GGGCCTGATCCCTACTTCAA 58.787 55.000 0.84 0.00 43.13 2.69
2703 5351 3.326297 GCCTGATCCCTACTTCAATAGCT 59.674 47.826 0.00 0.00 0.00 3.32
2722 5370 9.941664 CAATAGCTAACATGTTAAATCTTCAGG 57.058 33.333 18.55 5.69 0.00 3.86
2745 5393 7.012327 CAGGTACTTGATCTTTCAAACAACTCA 59.988 37.037 0.00 0.00 41.22 3.41
2807 5455 5.766174 ACTTGCGTCAGTTAATTTTAGGGAA 59.234 36.000 0.00 0.00 0.00 3.97
2901 5549 4.044065 TCCTTGGAAGGGAATGCTCTAAAA 59.956 41.667 5.58 0.00 46.47 1.52
2916 5564 5.126779 GCTCTAAAAGGCAGCTTACCTATT 58.873 41.667 5.47 1.01 36.14 1.73
2945 5593 4.693566 TGTTAATCTTTCCACAACGCTAGG 59.306 41.667 0.00 0.00 0.00 3.02
3027 5675 6.920817 TCTTGTTAATCTCACTTCGCTTAGA 58.079 36.000 0.00 0.00 0.00 2.10
3393 6041 0.037303 CTGGTGCTGGTCCAACATCT 59.963 55.000 7.06 0.00 30.94 2.90
3828 6505 7.038659 CGGTATTCTTATTTTTCCAATTGGCA 58.961 34.615 20.33 6.08 34.44 4.92
4050 6728 3.367703 GGAGATTGGTTGCCATCAAAGTG 60.368 47.826 0.00 0.00 33.37 3.16
4176 6854 5.747565 TCGACACTTGATTCACAAAATCAC 58.252 37.500 0.13 0.00 38.08 3.06
4376 7531 2.231964 TCCATTGTGATTTGAAGCCAGC 59.768 45.455 0.00 0.00 0.00 4.85
4446 7601 1.202359 TCAGCAAAGTTTTTGTCGCCC 60.202 47.619 3.77 0.00 0.00 6.13
4792 7952 1.211457 GGGACATGAGGAGCATCAAGT 59.789 52.381 0.00 0.00 36.25 3.16
5036 8552 7.736893 AGTAAAGTTCATTCTTCACAGTACCT 58.263 34.615 0.00 0.00 0.00 3.08
5196 8805 4.615912 GCTGTGTGTATGGCGAAATTCTTT 60.616 41.667 0.00 0.00 0.00 2.52
5310 8920 5.782893 TTTAGGTCAACTTTTGGTCCATG 57.217 39.130 0.00 0.00 0.00 3.66
5513 9126 6.765512 TGGGAACTTCCATTTTCAAAAATCAC 59.234 34.615 10.11 0.00 38.64 3.06
5596 9210 5.286267 AGGACAGACCGAAAAGAAAGTTA 57.714 39.130 0.00 0.00 44.74 2.24
5629 9243 5.234329 CAGCGACAACTAATATGAAACGGAT 59.766 40.000 0.00 0.00 0.00 4.18
5630 9244 5.234329 AGCGACAACTAATATGAAACGGATG 59.766 40.000 0.00 0.00 0.00 3.51
5665 9279 7.510630 AGATTAGACGTGTTTTTGAAGAATCG 58.489 34.615 0.00 0.00 0.00 3.34
5679 9293 4.635765 TGAAGAATCGGGAAACATGATGTC 59.364 41.667 0.00 0.00 0.00 3.06
5685 9300 5.873179 TCGGGAAACATGATGTCTTTTAC 57.127 39.130 0.00 0.00 0.00 2.01
5694 9309 5.065218 ACATGATGTCTTTTACGAATGCTCC 59.935 40.000 0.00 0.00 0.00 4.70
5727 9343 3.755112 TGTGGAGTTCCGTACATGAAA 57.245 42.857 0.00 0.00 39.43 2.69
5733 9349 5.180492 TGGAGTTCCGTACATGAAAAATCAC 59.820 40.000 0.00 0.00 39.43 3.06
5734 9351 5.391629 GGAGTTCCGTACATGAAAAATCACC 60.392 44.000 0.00 0.00 0.00 4.02
5781 9398 6.951198 ACCTCATAGTCTCTCTTCTTCAAAGA 59.049 38.462 0.00 0.00 0.00 2.52
5802 9419 6.952935 AGAAAGAATTCATGTGACGTACTC 57.047 37.500 8.44 0.00 38.06 2.59
5803 9420 5.869888 AGAAAGAATTCATGTGACGTACTCC 59.130 40.000 8.44 0.00 38.06 3.85
5804 9421 4.124851 AGAATTCATGTGACGTACTCCC 57.875 45.455 8.44 0.00 0.00 4.30
5805 9422 3.769844 AGAATTCATGTGACGTACTCCCT 59.230 43.478 8.44 0.00 0.00 4.20
5806 9423 3.802948 ATTCATGTGACGTACTCCCTC 57.197 47.619 0.00 0.00 0.00 4.30
5807 9424 1.471119 TCATGTGACGTACTCCCTCC 58.529 55.000 0.00 0.00 0.00 4.30
5808 9425 1.182667 CATGTGACGTACTCCCTCCA 58.817 55.000 0.00 0.00 0.00 3.86
5809 9426 1.757118 CATGTGACGTACTCCCTCCAT 59.243 52.381 0.00 0.00 0.00 3.41
5810 9427 1.471119 TGTGACGTACTCCCTCCATC 58.529 55.000 0.00 0.00 0.00 3.51
5811 9428 0.745468 GTGACGTACTCCCTCCATCC 59.255 60.000 0.00 0.00 0.00 3.51
5812 9429 0.750546 TGACGTACTCCCTCCATCCG 60.751 60.000 0.00 0.00 0.00 4.18
5813 9430 1.453762 GACGTACTCCCTCCATCCGG 61.454 65.000 0.00 0.00 0.00 5.14
5814 9431 1.152819 CGTACTCCCTCCATCCGGA 60.153 63.158 6.61 6.61 39.79 5.14
5815 9432 0.754217 CGTACTCCCTCCATCCGGAA 60.754 60.000 9.01 0.00 42.21 4.30
5816 9433 1.492764 GTACTCCCTCCATCCGGAAA 58.507 55.000 9.01 0.00 42.21 3.13
5817 9434 2.047830 GTACTCCCTCCATCCGGAAAT 58.952 52.381 9.01 0.00 42.21 2.17
5818 9435 2.489528 ACTCCCTCCATCCGGAAATA 57.510 50.000 9.01 0.00 42.21 1.40
5819 9436 2.047830 ACTCCCTCCATCCGGAAATAC 58.952 52.381 9.01 0.00 42.21 1.89
5820 9437 2.330216 CTCCCTCCATCCGGAAATACT 58.670 52.381 9.01 0.00 42.21 2.12
5821 9438 2.706190 CTCCCTCCATCCGGAAATACTT 59.294 50.000 9.01 0.00 42.21 2.24
5822 9439 2.438021 TCCCTCCATCCGGAAATACTTG 59.562 50.000 9.01 0.00 42.21 3.16
5823 9440 2.172717 CCCTCCATCCGGAAATACTTGT 59.827 50.000 9.01 0.00 42.21 3.16
5824 9441 3.467803 CCTCCATCCGGAAATACTTGTC 58.532 50.000 9.01 0.00 42.21 3.18
5825 9442 3.118408 CCTCCATCCGGAAATACTTGTCA 60.118 47.826 9.01 0.00 42.21 3.58
5826 9443 4.122776 CTCCATCCGGAAATACTTGTCAG 58.877 47.826 9.01 0.00 42.21 3.51
5827 9444 3.772572 TCCATCCGGAAATACTTGTCAGA 59.227 43.478 9.01 0.00 38.83 3.27
5828 9445 4.122776 CCATCCGGAAATACTTGTCAGAG 58.877 47.826 9.01 0.00 0.00 3.35
5829 9446 4.141937 CCATCCGGAAATACTTGTCAGAGA 60.142 45.833 9.01 0.00 0.00 3.10
5830 9447 5.419542 CATCCGGAAATACTTGTCAGAGAA 58.580 41.667 9.01 0.00 0.00 2.87
5831 9448 5.477607 TCCGGAAATACTTGTCAGAGAAA 57.522 39.130 0.00 0.00 0.00 2.52
5832 9449 6.049955 TCCGGAAATACTTGTCAGAGAAAT 57.950 37.500 0.00 0.00 0.00 2.17
5833 9450 5.874810 TCCGGAAATACTTGTCAGAGAAATG 59.125 40.000 0.00 0.00 0.00 2.32
5834 9451 5.447818 CCGGAAATACTTGTCAGAGAAATGC 60.448 44.000 0.00 0.00 0.00 3.56
5835 9452 5.122239 CGGAAATACTTGTCAGAGAAATGCA 59.878 40.000 0.00 0.00 0.00 3.96
5836 9453 6.183360 CGGAAATACTTGTCAGAGAAATGCAT 60.183 38.462 0.00 0.00 0.00 3.96
5837 9454 7.011389 CGGAAATACTTGTCAGAGAAATGCATA 59.989 37.037 0.00 0.00 0.00 3.14
5838 9455 8.677300 GGAAATACTTGTCAGAGAAATGCATAA 58.323 33.333 0.00 0.00 0.00 1.90
5843 9460 8.752766 ACTTGTCAGAGAAATGCATAAAAATG 57.247 30.769 0.00 0.00 0.00 2.32
5844 9461 8.579006 ACTTGTCAGAGAAATGCATAAAAATGA 58.421 29.630 0.00 0.00 0.00 2.57
5845 9462 9.414295 CTTGTCAGAGAAATGCATAAAAATGAA 57.586 29.630 0.00 0.00 0.00 2.57
5846 9463 9.932207 TTGTCAGAGAAATGCATAAAAATGAAT 57.068 25.926 0.00 0.00 0.00 2.57
5847 9464 9.361315 TGTCAGAGAAATGCATAAAAATGAATG 57.639 29.630 0.00 0.00 0.00 2.67
5848 9465 9.362539 GTCAGAGAAATGCATAAAAATGAATGT 57.637 29.630 0.00 0.00 0.00 2.71
5887 9504 6.865834 ACATCTAGATACATCCAATCCTCC 57.134 41.667 4.54 0.00 0.00 4.30
5888 9505 5.420421 ACATCTAGATACATCCAATCCTCCG 59.580 44.000 4.54 0.00 0.00 4.63
5889 9506 5.256806 TCTAGATACATCCAATCCTCCGA 57.743 43.478 0.00 0.00 0.00 4.55
5890 9507 5.010933 TCTAGATACATCCAATCCTCCGAC 58.989 45.833 0.00 0.00 0.00 4.79
5891 9508 2.558795 AGATACATCCAATCCTCCGACG 59.441 50.000 0.00 0.00 0.00 5.12
5892 9509 2.061509 TACATCCAATCCTCCGACGA 57.938 50.000 0.00 0.00 0.00 4.20
5893 9510 0.747255 ACATCCAATCCTCCGACGAG 59.253 55.000 0.00 0.00 35.72 4.18
5894 9511 0.747255 CATCCAATCCTCCGACGAGT 59.253 55.000 0.00 0.00 33.93 4.18
5895 9512 1.954382 CATCCAATCCTCCGACGAGTA 59.046 52.381 0.00 0.00 33.93 2.59
5896 9513 2.359981 TCCAATCCTCCGACGAGTAT 57.640 50.000 0.00 0.00 33.93 2.12
5897 9514 2.662866 TCCAATCCTCCGACGAGTATT 58.337 47.619 0.00 0.00 33.93 1.89
5898 9515 3.028850 TCCAATCCTCCGACGAGTATTT 58.971 45.455 0.00 0.00 33.93 1.40
5899 9516 3.067742 TCCAATCCTCCGACGAGTATTTC 59.932 47.826 0.00 0.00 33.93 2.17
5900 9517 3.381949 CAATCCTCCGACGAGTATTTCC 58.618 50.000 0.00 0.00 33.93 3.13
5901 9518 1.019673 TCCTCCGACGAGTATTTCCG 58.980 55.000 0.00 0.00 33.93 4.30
5902 9519 0.030369 CCTCCGACGAGTATTTCCGG 59.970 60.000 0.00 0.00 41.36 5.14
5903 9520 1.019673 CTCCGACGAGTATTTCCGGA 58.980 55.000 0.00 0.00 45.74 5.14
5904 9521 0.734889 TCCGACGAGTATTTCCGGAC 59.265 55.000 1.83 0.00 43.47 4.79
5905 9522 0.590732 CCGACGAGTATTTCCGGACG 60.591 60.000 1.83 5.89 42.49 4.79
5906 9523 0.590732 CGACGAGTATTTCCGGACGG 60.591 60.000 1.83 3.96 0.00 4.79
5907 9524 0.734889 GACGAGTATTTCCGGACGGA 59.265 55.000 1.83 9.76 43.52 4.69
5908 9525 0.737219 ACGAGTATTTCCGGACGGAG 59.263 55.000 13.64 3.15 46.06 4.63
5909 9526 0.030369 CGAGTATTTCCGGACGGAGG 59.970 60.000 13.64 0.00 46.06 4.30
5910 9527 0.388294 GAGTATTTCCGGACGGAGGG 59.612 60.000 13.64 0.00 46.06 4.30
5911 9528 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
5912 9529 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
5913 9530 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
5914 9531 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
5915 9532 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
5916 9533 1.856539 TTCCGGACGGAGGGAGTACT 61.857 60.000 13.64 0.00 46.06 2.73
5917 9534 1.379576 CCGGACGGAGGGAGTACTT 60.380 63.158 4.40 0.00 37.50 2.24
5918 9535 0.107017 CCGGACGGAGGGAGTACTTA 60.107 60.000 4.40 0.00 37.50 2.24
5919 9536 1.478288 CCGGACGGAGGGAGTACTTAT 60.478 57.143 4.40 0.00 37.50 1.73
5920 9537 2.224621 CCGGACGGAGGGAGTACTTATA 60.225 54.545 4.40 0.00 37.50 0.98
5921 9538 3.480470 CGGACGGAGGGAGTACTTATAA 58.520 50.000 0.00 0.00 0.00 0.98
5922 9539 3.501445 CGGACGGAGGGAGTACTTATAAG 59.499 52.174 11.05 11.05 0.00 1.73
5923 9540 4.723309 GGACGGAGGGAGTACTTATAAGA 58.277 47.826 19.38 0.27 0.00 2.10
5924 9541 5.136105 GGACGGAGGGAGTACTTATAAGAA 58.864 45.833 19.38 0.00 0.00 2.52
5925 9542 5.241285 GGACGGAGGGAGTACTTATAAGAAG 59.759 48.000 19.38 0.00 0.00 2.85
5926 9543 5.139001 ACGGAGGGAGTACTTATAAGAAGG 58.861 45.833 19.38 0.00 0.00 3.46
5927 9544 5.139001 CGGAGGGAGTACTTATAAGAAGGT 58.861 45.833 19.38 0.00 0.00 3.50
5928 9545 5.597594 CGGAGGGAGTACTTATAAGAAGGTT 59.402 44.000 19.38 0.00 0.00 3.50
5929 9546 6.774656 CGGAGGGAGTACTTATAAGAAGGTTA 59.225 42.308 19.38 0.00 0.00 2.85
5930 9547 7.286316 CGGAGGGAGTACTTATAAGAAGGTTAA 59.714 40.741 19.38 0.00 0.00 2.01
5931 9548 8.420222 GGAGGGAGTACTTATAAGAAGGTTAAC 58.580 40.741 19.38 0.00 0.00 2.01
5932 9549 8.906238 AGGGAGTACTTATAAGAAGGTTAACA 57.094 34.615 19.38 0.00 0.00 2.41
5933 9550 9.330220 AGGGAGTACTTATAAGAAGGTTAACAA 57.670 33.333 19.38 0.00 0.00 2.83
5934 9551 9.376075 GGGAGTACTTATAAGAAGGTTAACAAC 57.624 37.037 19.38 0.00 0.00 3.32
5935 9552 9.933723 GGAGTACTTATAAGAAGGTTAACAACA 57.066 33.333 19.38 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.990886 CCATAACCTAAATTACTAACCAGAGCA 59.009 37.037 0.00 0.00 0.00 4.26
64 65 2.069273 CGAAGAAGAAGCACCGTCATT 58.931 47.619 0.00 0.00 0.00 2.57
68 69 0.674534 ACTCGAAGAAGAAGCACCGT 59.325 50.000 0.00 0.00 34.09 4.83
72 73 4.060038 AGACAAACTCGAAGAAGAAGCA 57.940 40.909 0.00 0.00 34.09 3.91
99 100 5.819901 AGATGAATTCGAGGAGGATCAAAAC 59.180 40.000 0.04 0.00 36.25 2.43
144 149 2.755655 CAGACGACAGGAATCTACACCT 59.244 50.000 0.00 0.00 36.92 4.00
147 152 2.447443 AGCAGACGACAGGAATCTACA 58.553 47.619 0.00 0.00 0.00 2.74
165 170 0.678048 CTAACCTCACTGGCCCAAGC 60.678 60.000 0.00 0.00 40.22 4.01
172 177 2.962421 GGAGAGATCCTAACCTCACTGG 59.038 54.545 0.00 0.00 42.93 4.00
188 193 8.319881 ACATCAAATATCACCATATGAGGAGAG 58.680 37.037 3.65 0.00 41.91 3.20
205 210 7.879677 CCCACTGCATAGATCTAACATCAAATA 59.120 37.037 6.52 0.00 0.00 1.40
215 220 4.716784 AGTTGAACCCACTGCATAGATCTA 59.283 41.667 4.57 4.57 0.00 1.98
227 241 0.736053 TTTGTCGCAGTTGAACCCAC 59.264 50.000 0.00 0.00 0.00 4.61
228 242 0.736053 GTTTGTCGCAGTTGAACCCA 59.264 50.000 0.00 0.00 0.00 4.51
238 252 0.883153 TAGAGCCGTAGTTTGTCGCA 59.117 50.000 0.00 0.00 0.00 5.10
245 259 1.683917 CAGCATCCTAGAGCCGTAGTT 59.316 52.381 0.00 0.00 0.00 2.24
256 270 2.104792 GTGCCTATGAACCAGCATCCTA 59.895 50.000 0.00 0.00 37.60 2.94
261 275 1.078497 CCGTGCCTATGAACCAGCA 60.078 57.895 0.00 0.00 0.00 4.41
268 282 2.107366 TCTTCATGTCCGTGCCTATGA 58.893 47.619 0.00 0.00 0.00 2.15
270 284 2.111384 AGTCTTCATGTCCGTGCCTAT 58.889 47.619 0.00 0.00 0.00 2.57
273 287 1.079503 GAAGTCTTCATGTCCGTGCC 58.920 55.000 7.76 0.00 0.00 5.01
275 289 1.726853 GGGAAGTCTTCATGTCCGTG 58.273 55.000 14.49 0.00 0.00 4.94
276 290 0.246635 CGGGAAGTCTTCATGTCCGT 59.753 55.000 14.49 0.00 0.00 4.69
277 291 0.530744 TCGGGAAGTCTTCATGTCCG 59.469 55.000 17.23 17.23 37.61 4.79
278 292 1.550976 AGTCGGGAAGTCTTCATGTCC 59.449 52.381 14.49 5.38 0.00 4.02
279 293 2.028930 ACAGTCGGGAAGTCTTCATGTC 60.029 50.000 14.49 4.14 0.00 3.06
280 294 1.971357 ACAGTCGGGAAGTCTTCATGT 59.029 47.619 14.49 7.61 0.00 3.21
282 296 2.248248 TGACAGTCGGGAAGTCTTCAT 58.752 47.619 14.49 0.00 33.56 2.57
283 297 1.699730 TGACAGTCGGGAAGTCTTCA 58.300 50.000 14.49 0.00 33.56 3.02
346 363 0.033504 AGAACGAGCCATCAACGTGT 59.966 50.000 0.00 0.00 40.10 4.49
348 365 0.670546 CCAGAACGAGCCATCAACGT 60.671 55.000 0.00 0.00 41.97 3.99
352 369 1.296392 CCACCAGAACGAGCCATCA 59.704 57.895 0.00 0.00 0.00 3.07
356 373 2.167398 TACTGCCACCAGAACGAGCC 62.167 60.000 0.00 0.00 41.77 4.70
418 437 6.149633 ACGGAAATACAAAGCATCTCAAAAC 58.850 36.000 0.00 0.00 0.00 2.43
756 840 3.515286 CGAGGCGGCGAGGAACTA 61.515 66.667 12.98 0.00 41.55 2.24
845 979 1.880941 AGGAGAAAACCCTAGGCGAT 58.119 50.000 2.05 0.00 30.92 4.58
1093 1307 3.053095 ACCAGCTGAATCTGAATGGGATT 60.053 43.478 17.39 0.00 36.19 3.01
1111 1327 3.554524 CACAAACATGCTTCGTAACCAG 58.445 45.455 0.00 0.00 0.00 4.00
1112 1328 2.287308 GCACAAACATGCTTCGTAACCA 60.287 45.455 0.00 0.00 42.62 3.67
1114 1330 2.973224 CTGCACAAACATGCTTCGTAAC 59.027 45.455 0.00 0.00 46.28 2.50
1135 1356 4.622313 TGATTCAGAATTGCAATTTCGTGC 59.378 37.500 24.81 12.23 45.15 5.34
1165 1390 6.036953 CCACTCATTAGACATTTCTTCAGAGC 59.963 42.308 0.00 0.00 32.75 4.09
1200 1830 4.171878 TCCACCCAGAACACATAAACAA 57.828 40.909 0.00 0.00 0.00 2.83
1219 2569 3.068307 AGTCGTCATACTTGGTAGCATCC 59.932 47.826 0.00 0.00 0.00 3.51
1271 2648 1.598132 GCTGCAGAGCACACATATGAG 59.402 52.381 20.43 3.79 45.46 2.90
1344 2732 9.196552 GAAGAGGAAAAGTGACAATTATTTTGG 57.803 33.333 0.00 0.00 0.00 3.28
1441 2833 4.462483 AGTGGAACAAAGACTTTTGCAAGA 59.538 37.500 0.00 0.00 46.05 3.02
1577 4177 7.861630 TGTGTGTAAGATTAGCTCTTTTGAAC 58.138 34.615 0.00 0.00 41.60 3.18
1580 4180 8.087982 TCTTGTGTGTAAGATTAGCTCTTTTG 57.912 34.615 0.00 0.00 41.60 2.44
1623 4227 0.756442 TTGGGAGTGCTTGCTGCTTT 60.756 50.000 0.00 0.00 43.37 3.51
1881 4494 2.373707 GCAGCTGACCCCTCTCCAT 61.374 63.158 20.43 0.00 0.00 3.41
1895 4509 1.658409 GGAAACGTTGTGCTGCAGC 60.658 57.895 31.89 31.89 42.50 5.25
1947 4561 3.019564 AGATAATTGCCCACTGAGTTGC 58.980 45.455 0.00 0.00 0.00 4.17
2040 4654 1.351350 GGAAGCTTACCCAACTCACCT 59.649 52.381 0.00 0.00 0.00 4.00
2043 4657 3.219281 GTTTGGAAGCTTACCCAACTCA 58.781 45.455 16.95 3.07 41.67 3.41
2146 4760 3.052036 GCGTGTTGTTTGCAAGATTGAT 58.948 40.909 0.00 0.00 34.94 2.57
2241 4855 4.178956 AGTAGAAGGGATCTCTCCAGAC 57.821 50.000 0.00 0.00 44.08 3.51
2428 5042 2.169832 TGGCCGAGCAATATAGAAGC 57.830 50.000 0.00 0.00 0.00 3.86
2493 5107 8.677148 AACTTAGATCAAGCTCAAACAGTTTA 57.323 30.769 0.00 0.00 37.83 2.01
2500 5114 7.283127 ACTGTTGAAACTTAGATCAAGCTCAAA 59.717 33.333 16.05 10.53 39.37 2.69
2721 5369 7.259290 TGAGTTGTTTGAAAGATCAAGTACC 57.741 36.000 0.00 0.00 45.82 3.34
2797 5445 6.375736 GCTTCTAGCAAGTTCTTCCCTAAAAT 59.624 38.462 0.00 0.00 41.89 1.82
2901 5549 1.561542 ACTGCAATAGGTAAGCTGCCT 59.438 47.619 13.74 13.74 40.00 4.75
2916 5564 5.587289 GTTGTGGAAAGATTAACAACTGCA 58.413 37.500 9.61 0.00 45.62 4.41
2945 5593 4.972440 GGTTTGATGCAAGCGATAAATCTC 59.028 41.667 0.00 0.00 0.00 2.75
3828 6505 4.273480 CGAAACATCTTCTTGGACACAACT 59.727 41.667 0.00 0.00 32.14 3.16
3969 6647 7.231722 CCAGTAGAGGTTGAGCTAATAGTATGT 59.768 40.741 0.00 0.00 0.00 2.29
4050 6728 4.511826 CCACTAGGTTCACTCAAGTTGAAC 59.488 45.833 7.06 6.67 40.63 3.18
4176 6854 3.306973 TGAATATCAGCGCTTTGAACTCG 59.693 43.478 7.50 0.00 0.00 4.18
4376 7531 3.000041 TCATCGTCCAAAAGGATGTTCG 59.000 45.455 3.85 0.00 45.99 3.95
4446 7601 6.293626 CCAGGCTTTCAGGAATAAACATATCG 60.294 42.308 0.00 0.00 0.00 2.92
4792 7952 1.939381 GCGTCCATACTTCTGCACACA 60.939 52.381 0.00 0.00 0.00 3.72
5291 8900 3.593442 TCATGGACCAAAAGTTGACCT 57.407 42.857 0.00 0.00 0.00 3.85
5488 9101 6.765512 GTGATTTTTGAAAATGGAAGTTCCCA 59.234 34.615 19.42 6.58 38.64 4.37
5642 9256 6.348213 CCCGATTCTTCAAAAACACGTCTAAT 60.348 38.462 0.00 0.00 0.00 1.73
5648 9262 3.889196 TCCCGATTCTTCAAAAACACG 57.111 42.857 0.00 0.00 0.00 4.49
5649 9263 5.344884 TGTTTCCCGATTCTTCAAAAACAC 58.655 37.500 0.00 0.00 32.10 3.32
5650 9264 5.584253 TGTTTCCCGATTCTTCAAAAACA 57.416 34.783 0.00 0.00 33.98 2.83
5651 9265 6.212955 TCATGTTTCCCGATTCTTCAAAAAC 58.787 36.000 0.00 0.00 0.00 2.43
5665 9279 5.873179 TCGTAAAAGACATCATGTTTCCC 57.127 39.130 0.00 0.00 0.00 3.97
5679 9293 8.873215 TCTTTATCTAGGAGCATTCGTAAAAG 57.127 34.615 0.00 0.00 0.00 2.27
5685 9300 7.307632 CCACAAATCTTTATCTAGGAGCATTCG 60.308 40.741 0.00 0.00 0.00 3.34
5694 9309 7.042335 ACGGAACTCCACAAATCTTTATCTAG 58.958 38.462 0.00 0.00 35.14 2.43
5781 9398 4.935808 GGGAGTACGTCACATGAATTCTTT 59.064 41.667 7.05 0.00 0.00 2.52
5805 9422 3.772572 TCTGACAAGTATTTCCGGATGGA 59.227 43.478 4.15 0.00 44.61 3.41
5806 9423 4.122776 CTCTGACAAGTATTTCCGGATGG 58.877 47.826 4.15 0.00 0.00 3.51
5807 9424 5.011090 TCTCTGACAAGTATTTCCGGATG 57.989 43.478 4.15 0.97 0.00 3.51
5808 9425 5.677319 TTCTCTGACAAGTATTTCCGGAT 57.323 39.130 4.15 0.00 0.00 4.18
5809 9426 5.477607 TTTCTCTGACAAGTATTTCCGGA 57.522 39.130 0.00 0.00 0.00 5.14
5810 9427 5.447818 GCATTTCTCTGACAAGTATTTCCGG 60.448 44.000 0.00 0.00 0.00 5.14
5811 9428 5.122239 TGCATTTCTCTGACAAGTATTTCCG 59.878 40.000 0.00 0.00 0.00 4.30
5812 9429 6.500684 TGCATTTCTCTGACAAGTATTTCC 57.499 37.500 0.00 0.00 0.00 3.13
5817 9434 9.844790 CATTTTTATGCATTTCTCTGACAAGTA 57.155 29.630 3.54 0.00 0.00 2.24
5818 9435 8.579006 TCATTTTTATGCATTTCTCTGACAAGT 58.421 29.630 3.54 0.00 0.00 3.16
5819 9436 8.975410 TCATTTTTATGCATTTCTCTGACAAG 57.025 30.769 3.54 0.00 0.00 3.16
5820 9437 9.932207 ATTCATTTTTATGCATTTCTCTGACAA 57.068 25.926 3.54 0.00 0.00 3.18
5821 9438 9.361315 CATTCATTTTTATGCATTTCTCTGACA 57.639 29.630 3.54 0.00 0.00 3.58
5822 9439 9.362539 ACATTCATTTTTATGCATTTCTCTGAC 57.637 29.630 3.54 0.00 0.00 3.51
5861 9478 8.986991 GGAGGATTGGATGTATCTAGATGTATT 58.013 37.037 15.79 0.00 0.00 1.89
5862 9479 7.286546 CGGAGGATTGGATGTATCTAGATGTAT 59.713 40.741 15.79 9.11 0.00 2.29
5863 9480 6.603599 CGGAGGATTGGATGTATCTAGATGTA 59.396 42.308 15.79 4.44 0.00 2.29
5864 9481 5.420421 CGGAGGATTGGATGTATCTAGATGT 59.580 44.000 15.79 1.25 0.00 3.06
5865 9482 5.654209 TCGGAGGATTGGATGTATCTAGATG 59.346 44.000 15.79 0.00 0.00 2.90
5866 9483 5.654650 GTCGGAGGATTGGATGTATCTAGAT 59.345 44.000 10.73 10.73 0.00 1.98
5867 9484 5.010933 GTCGGAGGATTGGATGTATCTAGA 58.989 45.833 0.00 0.00 0.00 2.43
5868 9485 4.142578 CGTCGGAGGATTGGATGTATCTAG 60.143 50.000 0.00 0.00 0.00 2.43
5869 9486 3.756963 CGTCGGAGGATTGGATGTATCTA 59.243 47.826 0.00 0.00 0.00 1.98
5870 9487 2.558795 CGTCGGAGGATTGGATGTATCT 59.441 50.000 0.00 0.00 0.00 1.98
5871 9488 2.557056 TCGTCGGAGGATTGGATGTATC 59.443 50.000 0.00 0.00 0.00 2.24
5872 9489 2.558795 CTCGTCGGAGGATTGGATGTAT 59.441 50.000 0.27 0.00 36.61 2.29
5873 9490 1.954382 CTCGTCGGAGGATTGGATGTA 59.046 52.381 0.27 0.00 36.61 2.29
5874 9491 0.747255 CTCGTCGGAGGATTGGATGT 59.253 55.000 0.27 0.00 36.61 3.06
5875 9492 0.747255 ACTCGTCGGAGGATTGGATG 59.253 55.000 0.27 0.00 44.93 3.51
5876 9493 2.359981 TACTCGTCGGAGGATTGGAT 57.640 50.000 0.27 0.00 44.93 3.41
5877 9494 2.359981 ATACTCGTCGGAGGATTGGA 57.640 50.000 0.27 0.00 41.24 3.53
5881 9498 1.607628 CGGAAATACTCGTCGGAGGAT 59.392 52.381 0.27 0.00 46.19 3.24
5882 9499 1.019673 CGGAAATACTCGTCGGAGGA 58.980 55.000 0.00 0.00 44.93 3.71
5883 9500 0.030369 CCGGAAATACTCGTCGGAGG 59.970 60.000 0.00 0.00 44.93 4.30
5884 9501 1.019673 TCCGGAAATACTCGTCGGAG 58.980 55.000 0.00 0.00 43.84 4.63
5885 9502 0.734889 GTCCGGAAATACTCGTCGGA 59.265 55.000 5.23 0.00 46.06 4.55
5886 9503 0.590732 CGTCCGGAAATACTCGTCGG 60.591 60.000 5.23 0.00 41.80 4.79
5887 9504 0.590732 CCGTCCGGAAATACTCGTCG 60.591 60.000 5.23 1.25 37.50 5.12
5888 9505 0.734889 TCCGTCCGGAAATACTCGTC 59.265 55.000 5.23 0.00 42.05 4.20
5889 9506 0.737219 CTCCGTCCGGAAATACTCGT 59.263 55.000 5.23 0.00 44.66 4.18
5890 9507 0.030369 CCTCCGTCCGGAAATACTCG 59.970 60.000 5.23 3.90 44.66 4.18
5891 9508 0.388294 CCCTCCGTCCGGAAATACTC 59.612 60.000 5.23 0.00 44.66 2.59
5892 9509 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
5893 9510 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
5894 9511 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
5895 9512 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
5896 9513 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
5897 9514 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
5898 9515 1.856539 AAGTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
5899 9516 0.107017 TAAGTACTCCCTCCGTCCGG 60.107 60.000 0.00 0.00 0.00 5.14
5900 9517 1.978454 ATAAGTACTCCCTCCGTCCG 58.022 55.000 0.00 0.00 0.00 4.79
5901 9518 4.723309 TCTTATAAGTACTCCCTCCGTCC 58.277 47.826 12.19 0.00 0.00 4.79
5902 9519 5.241285 CCTTCTTATAAGTACTCCCTCCGTC 59.759 48.000 12.19 0.00 0.00 4.79
5903 9520 5.139001 CCTTCTTATAAGTACTCCCTCCGT 58.861 45.833 12.19 0.00 0.00 4.69
5904 9521 5.139001 ACCTTCTTATAAGTACTCCCTCCG 58.861 45.833 12.19 0.00 0.00 4.63
5905 9522 8.420222 GTTAACCTTCTTATAAGTACTCCCTCC 58.580 40.741 12.19 0.00 0.00 4.30
5906 9523 8.975295 TGTTAACCTTCTTATAAGTACTCCCTC 58.025 37.037 12.19 1.24 0.00 4.30
5907 9524 8.906238 TGTTAACCTTCTTATAAGTACTCCCT 57.094 34.615 12.19 0.00 0.00 4.20
5908 9525 9.376075 GTTGTTAACCTTCTTATAAGTACTCCC 57.624 37.037 12.19 0.00 0.00 4.30
5909 9526 9.933723 TGTTGTTAACCTTCTTATAAGTACTCC 57.066 33.333 12.19 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.