Multiple sequence alignment - TraesCS3A01G286000

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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 TraesCS3A01G286000 chr3A 100.000 3676 0 0 1 3676 514490827 514494502 0.000000e+00 6789.0
1 TraesCS3A01G286000 chr3A 87.709 179 22 0 1294 1472 547998707 547998885 3.720000e-50 209.0
2 TraesCS3A01G286000 chr3D 90.100 1596 115 25 302 1883 395035577 395037143 0.000000e+00 2032.0
3 TraesCS3A01G286000 chr3D 88.820 1136 68 23 2227 3311 395037839 395038966 0.000000e+00 1339.0
4 TraesCS3A01G286000 chr3D 91.262 721 32 9 2986 3676 395039260 395039979 0.000000e+00 953.0
5 TraesCS3A01G286000 chr3D 94.805 154 8 0 2836 2989 395038968 395039121 1.320000e-59 241.0
6 TraesCS3A01G286000 chr3B 92.488 812 41 9 835 1637 519397482 519398282 0.000000e+00 1144.0
7 TraesCS3A01G286000 chr3B 93.191 705 31 10 2313 3001 519399319 519400022 0.000000e+00 1020.0
8 TraesCS3A01G286000 chr3B 89.387 669 36 10 3017 3667 519400197 519400848 0.000000e+00 809.0
9 TraesCS3A01G286000 chr3B 87.326 718 50 23 1636 2318 519398369 519399080 0.000000e+00 784.0
10 TraesCS3A01G286000 chr3B 94.702 302 15 1 1 302 729975419 729975719 5.560000e-128 468.0
11 TraesCS3A01G286000 chr3B 91.071 56 4 1 1032 1086 403864919 403864974 1.420000e-09 75.0
12 TraesCS3A01G286000 chr3B 93.478 46 3 0 358 403 519397326 519397281 6.590000e-08 69.4
13 TraesCS3A01G286000 chr2A 96.117 309 7 3 1 308 755714412 755714108 1.970000e-137 499.0
14 TraesCS3A01G286000 chr1A 95.364 302 13 1 1 302 588982082 588981782 2.570000e-131 479.0
15 TraesCS3A01G286000 chr1A 94.059 303 16 2 1 302 432583916 432583615 3.350000e-125 459.0
16 TraesCS3A01G286000 chr1A 94.059 303 17 1 1 303 454545228 454545529 3.350000e-125 459.0
17 TraesCS3A01G286000 chr5D 94.389 303 16 1 1 303 365211808 365212109 7.190000e-127 464.0
18 TraesCS3A01G286000 chr5D 94.371 302 16 1 1 302 366761353 366761653 2.590000e-126 462.0
19 TraesCS3A01G286000 chr5D 88.514 148 17 0 1614 1761 164605002 164604855 2.920000e-41 180.0
20 TraesCS3A01G286000 chr5B 94.371 302 16 1 1 302 272848508 272848808 2.590000e-126 462.0
21 TraesCS3A01G286000 chr5B 89.865 148 14 1 1614 1761 176588381 176588235 4.850000e-44 189.0
22 TraesCS3A01G286000 chr5B 87.582 153 17 2 1609 1761 138770286 138770136 3.770000e-40 176.0
23 TraesCS3A01G286000 chr1B 93.333 315 17 4 1 312 681776880 681777193 2.590000e-126 462.0
24 TraesCS3A01G286000 chr1B 88.764 178 20 0 1293 1470 672840290 672840113 6.180000e-53 219.0
25 TraesCS3A01G286000 chr7B 91.053 190 14 2 1285 1472 498180786 498180598 1.690000e-63 254.0
26 TraesCS3A01G286000 chr7B 89.888 89 7 2 999 1086 498180987 498180900 3.000000e-21 113.0
27 TraesCS3A01G286000 chr7D 90.503 179 17 0 1294 1472 474084498 474084320 1.710000e-58 237.0
28 TraesCS3A01G286000 chr7D 91.824 159 13 0 1314 1472 591722460 591722302 4.780000e-54 222.0
29 TraesCS3A01G286000 chr7D 88.667 150 15 2 1613 1761 436961951 436961803 8.110000e-42 182.0
30 TraesCS3A01G286000 chr7D 89.888 89 7 2 999 1086 474084709 474084622 3.000000e-21 113.0
31 TraesCS3A01G286000 chr7A 89.617 183 19 0 1290 1472 521950239 521950421 2.210000e-57 233.0
32 TraesCS3A01G286000 chr7A 89.011 91 10 0 996 1086 521950029 521950119 3.000000e-21 113.0
33 TraesCS3A01G286000 chr5A 86.592 179 24 0 1294 1472 490521330 490521152 8.050000e-47 198.0
34 TraesCS3A01G286000 chr5A 90.476 147 13 1 1616 1761 556687381 556687527 3.750000e-45 193.0
35 TraesCS3A01G286000 chr5A 89.041 146 16 0 1616 1761 86662018 86662163 8.110000e-42 182.0
36 TraesCS3A01G286000 chr4B 88.591 149 15 2 1613 1761 483581985 483582131 2.920000e-41 180.0
37 TraesCS3A01G286000 chr2D 91.071 56 4 1 1032 1086 558945944 558945889 1.420000e-09 75.0
38 TraesCS3A01G286000 chr6B 92.000 50 3 1 1032 1080 98101652 98101701 6.590000e-08 69.4
39 TraesCS3A01G286000 chr2B 89.286 56 5 1 1032 1086 137137525 137137580 6.590000e-08 69.4


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 TraesCS3A01G286000 chr3A 514490827 514494502 3675 False 6789.00 6789 100.00000 1 3676 1 chr3A.!!$F1 3675
1 TraesCS3A01G286000 chr3D 395035577 395039979 4402 False 1141.25 2032 91.24675 302 3676 4 chr3D.!!$F1 3374
2 TraesCS3A01G286000 chr3B 519397482 519400848 3366 False 939.25 1144 90.59800 835 3667 4 chr3B.!!$F3 2832

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
335 336 0.178068 ACTTGGACACACGCTGAAGT 59.822 50.0 0.0 0.0 0.0 3.01 F
751 763 0.649992 TGAGGGGATGAGGGGATTCT 59.350 55.0 0.0 0.0 0.0 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1238 1265 0.038744 CCACCTGAACAGCCTCCATT 59.961 55.0 0.0 0.0 0.0 3.16 R
2691 3418 0.107116 ACCGCCGAGAGTGTAGATCT 60.107 55.0 0.0 0.0 0.0 2.75 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 4.701956 CTTGCTAAAACATCGTGGGAAT 57.298 40.909 0.00 0.00 0.00 3.01
22 23 4.414852 CTTGCTAAAACATCGTGGGAATG 58.585 43.478 0.00 0.00 0.00 2.67
23 24 3.680490 TGCTAAAACATCGTGGGAATGA 58.320 40.909 0.00 0.00 0.00 2.57
24 25 4.075682 TGCTAAAACATCGTGGGAATGAA 58.924 39.130 0.00 0.00 0.00 2.57
25 26 4.155826 TGCTAAAACATCGTGGGAATGAAG 59.844 41.667 0.00 0.00 0.00 3.02
26 27 3.575965 AAAACATCGTGGGAATGAAGC 57.424 42.857 0.00 0.00 0.00 3.86
27 28 2.496899 AACATCGTGGGAATGAAGCT 57.503 45.000 0.00 0.00 0.00 3.74
28 29 3.627395 AACATCGTGGGAATGAAGCTA 57.373 42.857 0.00 0.00 0.00 3.32
29 30 3.627395 ACATCGTGGGAATGAAGCTAA 57.373 42.857 0.00 0.00 0.00 3.09
30 31 3.950397 ACATCGTGGGAATGAAGCTAAA 58.050 40.909 0.00 0.00 0.00 1.85
31 32 3.941483 ACATCGTGGGAATGAAGCTAAAG 59.059 43.478 0.00 0.00 0.00 1.85
32 33 2.985896 TCGTGGGAATGAAGCTAAAGG 58.014 47.619 0.00 0.00 0.00 3.11
33 34 1.401905 CGTGGGAATGAAGCTAAAGGC 59.598 52.381 0.00 0.00 42.19 4.35
34 35 2.446435 GTGGGAATGAAGCTAAAGGCA 58.554 47.619 0.00 0.00 44.79 4.75
35 36 2.825532 GTGGGAATGAAGCTAAAGGCAA 59.174 45.455 0.00 0.00 44.79 4.52
36 37 2.825532 TGGGAATGAAGCTAAAGGCAAC 59.174 45.455 0.00 0.00 44.79 4.17
79 80 9.994432 AAAGAATTTCTTAAACGCATCATCTAG 57.006 29.630 11.92 0.00 35.27 2.43
80 81 8.948631 AGAATTTCTTAAACGCATCATCTAGA 57.051 30.769 0.00 0.00 0.00 2.43
81 82 9.553064 AGAATTTCTTAAACGCATCATCTAGAT 57.447 29.630 0.00 0.00 37.48 1.98
86 87 9.981114 TTCTTAAACGCATCATCTAGATATTGA 57.019 29.630 4.54 0.45 34.43 2.57
91 92 9.935241 AAACGCATCATCTAGATATTGATAGTT 57.065 29.630 4.54 11.84 34.43 2.24
92 93 9.935241 AACGCATCATCTAGATATTGATAGTTT 57.065 29.630 4.54 0.00 34.43 2.66
93 94 9.935241 ACGCATCATCTAGATATTGATAGTTTT 57.065 29.630 4.54 0.00 34.43 2.43
122 123 4.946784 ATGTTTAGTTGGAACATCGCTC 57.053 40.909 0.00 0.00 42.40 5.03
123 124 3.734463 TGTTTAGTTGGAACATCGCTCA 58.266 40.909 0.00 0.00 39.30 4.26
124 125 3.745975 TGTTTAGTTGGAACATCGCTCAG 59.254 43.478 0.00 0.00 39.30 3.35
125 126 3.678056 TTAGTTGGAACATCGCTCAGT 57.322 42.857 0.00 0.00 39.30 3.41
126 127 2.550830 AGTTGGAACATCGCTCAGTT 57.449 45.000 0.00 0.00 39.30 3.16
127 128 2.851195 AGTTGGAACATCGCTCAGTTT 58.149 42.857 0.00 0.00 39.30 2.66
128 129 2.549754 AGTTGGAACATCGCTCAGTTTG 59.450 45.455 0.00 0.00 39.30 2.93
129 130 2.254546 TGGAACATCGCTCAGTTTGT 57.745 45.000 0.00 0.00 0.00 2.83
130 131 2.571212 TGGAACATCGCTCAGTTTGTT 58.429 42.857 0.00 0.00 35.14 2.83
131 132 3.734463 TGGAACATCGCTCAGTTTGTTA 58.266 40.909 0.00 0.00 32.73 2.41
132 133 3.496884 TGGAACATCGCTCAGTTTGTTAC 59.503 43.478 0.00 0.00 34.23 2.50
133 134 3.496884 GGAACATCGCTCAGTTTGTTACA 59.503 43.478 0.00 0.00 33.90 2.41
134 135 4.154195 GGAACATCGCTCAGTTTGTTACAT 59.846 41.667 0.00 0.00 33.90 2.29
135 136 4.668576 ACATCGCTCAGTTTGTTACATG 57.331 40.909 0.00 0.00 0.00 3.21
136 137 3.436704 ACATCGCTCAGTTTGTTACATGG 59.563 43.478 0.00 0.00 0.00 3.66
137 138 3.394674 TCGCTCAGTTTGTTACATGGA 57.605 42.857 0.00 0.00 0.00 3.41
138 139 3.064207 TCGCTCAGTTTGTTACATGGAC 58.936 45.455 0.00 0.00 0.00 4.02
139 140 2.805671 CGCTCAGTTTGTTACATGGACA 59.194 45.455 0.00 0.00 0.00 4.02
140 141 3.436704 CGCTCAGTTTGTTACATGGACAT 59.563 43.478 0.00 0.00 0.00 3.06
141 142 4.669965 CGCTCAGTTTGTTACATGGACATG 60.670 45.833 10.57 10.57 44.15 3.21
155 156 6.668541 CATGGACATGTCGTTAATCTTTCT 57.331 37.500 19.33 0.00 34.23 2.52
156 157 7.076842 CATGGACATGTCGTTAATCTTTCTT 57.923 36.000 19.33 0.00 34.23 2.52
157 158 7.530010 CATGGACATGTCGTTAATCTTTCTTT 58.470 34.615 19.33 0.00 34.23 2.52
158 159 7.504924 TGGACATGTCGTTAATCTTTCTTTT 57.495 32.000 19.33 0.00 0.00 2.27
159 160 7.936584 TGGACATGTCGTTAATCTTTCTTTTT 58.063 30.769 19.33 0.00 0.00 1.94
160 161 9.058174 TGGACATGTCGTTAATCTTTCTTTTTA 57.942 29.630 19.33 0.00 0.00 1.52
247 248 9.138062 TGTTTGTACATGTGAAATTTATCATGC 57.862 29.630 23.32 14.58 40.57 4.06
248 249 9.138062 GTTTGTACATGTGAAATTTATCATGCA 57.862 29.630 23.32 14.72 40.57 3.96
249 250 9.702494 TTTGTACATGTGAAATTTATCATGCAA 57.298 25.926 23.32 19.09 40.57 4.08
250 251 8.686397 TGTACATGTGAAATTTATCATGCAAC 57.314 30.769 23.32 21.43 40.57 4.17
251 252 8.522003 TGTACATGTGAAATTTATCATGCAACT 58.478 29.630 23.32 13.35 40.57 3.16
252 253 9.013490 GTACATGTGAAATTTATCATGCAACTC 57.987 33.333 23.32 12.52 40.57 3.01
253 254 7.833786 ACATGTGAAATTTATCATGCAACTCT 58.166 30.769 23.32 9.56 40.57 3.24
254 255 8.308931 ACATGTGAAATTTATCATGCAACTCTT 58.691 29.630 23.32 9.09 40.57 2.85
255 256 8.592155 CATGTGAAATTTATCATGCAACTCTTG 58.408 33.333 16.61 0.00 32.83 3.02
274 275 5.126067 TCTTGCATACTATTTCAAGAGCCC 58.874 41.667 0.00 0.00 39.70 5.19
275 276 3.466836 TGCATACTATTTCAAGAGCCCG 58.533 45.455 0.00 0.00 0.00 6.13
276 277 3.118408 TGCATACTATTTCAAGAGCCCGT 60.118 43.478 0.00 0.00 0.00 5.28
277 278 3.248602 GCATACTATTTCAAGAGCCCGTG 59.751 47.826 0.00 0.00 0.00 4.94
278 279 2.403252 ACTATTTCAAGAGCCCGTGG 57.597 50.000 0.00 0.00 0.00 4.94
296 297 2.048597 CAACGCACGGGCACTCTA 60.049 61.111 11.77 0.00 41.24 2.43
297 298 2.048503 AACGCACGGGCACTCTAC 60.049 61.111 11.77 0.00 41.24 2.59
298 299 2.571216 AACGCACGGGCACTCTACT 61.571 57.895 11.77 0.00 41.24 2.57
299 300 1.246056 AACGCACGGGCACTCTACTA 61.246 55.000 11.77 0.00 41.24 1.82
300 301 1.064296 CGCACGGGCACTCTACTAG 59.936 63.158 11.77 0.00 41.24 2.57
329 330 1.525619 GTTAGTGACTTGGACACACGC 59.474 52.381 0.00 0.00 40.25 5.34
335 336 0.178068 ACTTGGACACACGCTGAAGT 59.822 50.000 0.00 0.00 0.00 3.01
341 342 3.262420 GGACACACGCTGAAGTGATAAT 58.738 45.455 9.99 0.00 44.43 1.28
342 343 3.684788 GGACACACGCTGAAGTGATAATT 59.315 43.478 9.99 0.00 44.43 1.40
344 345 5.334879 GGACACACGCTGAAGTGATAATTTT 60.335 40.000 9.99 0.00 44.43 1.82
388 390 6.093495 TGTTGAAACTCCTAAGTTGTGACAAG 59.907 38.462 0.00 0.00 45.07 3.16
405 407 2.159707 ACAAGTGTCGCGCATGTAATTC 60.160 45.455 8.75 0.00 0.00 2.17
406 408 1.720805 AGTGTCGCGCATGTAATTCA 58.279 45.000 8.75 0.00 0.00 2.57
417 419 5.023920 CGCATGTAATTCATCACTTGTCAC 58.976 41.667 0.00 0.00 34.09 3.67
420 422 6.405065 GCATGTAATTCATCACTTGTCACCAT 60.405 38.462 0.00 0.00 34.09 3.55
475 477 7.048512 GGCACTCCATAACTAACTACTGATTT 58.951 38.462 0.00 0.00 0.00 2.17
477 479 7.043325 GCACTCCATAACTAACTACTGATTTCG 60.043 40.741 0.00 0.00 0.00 3.46
478 480 8.188799 CACTCCATAACTAACTACTGATTTCGA 58.811 37.037 0.00 0.00 0.00 3.71
488 490 2.413837 ACTGATTTCGAAACTCCCACG 58.586 47.619 13.81 6.17 0.00 4.94
509 511 4.530857 AGTGGCGCGGCTATGTCC 62.531 66.667 33.23 12.10 0.00 4.02
516 518 2.895372 CGGCTATGTCCCGCCAAC 60.895 66.667 0.00 0.00 46.62 3.77
542 544 1.975363 GCAGTAGCTTGCTTCGCCTG 61.975 60.000 3.04 4.11 40.89 4.85
557 559 1.078214 CCTGAAGGCAGCCGATTCA 60.078 57.895 13.98 13.98 40.91 2.57
566 568 3.599704 GCCGATTCATGGGCTGGC 61.600 66.667 5.61 4.16 46.64 4.85
577 579 3.240491 GGCTGGCCCAGTATAGCA 58.760 61.111 13.35 0.00 37.89 3.49
578 580 1.763770 GGCTGGCCCAGTATAGCAT 59.236 57.895 13.35 0.00 37.89 3.79
582 584 2.498167 CTGGCCCAGTATAGCATTGAC 58.502 52.381 1.39 0.00 0.00 3.18
591 593 0.810031 ATAGCATTGACGTCACGCCC 60.810 55.000 27.15 13.82 0.00 6.13
592 594 2.161078 TAGCATTGACGTCACGCCCA 62.161 55.000 27.15 17.01 0.00 5.36
593 595 2.612567 GCATTGACGTCACGCCCAA 61.613 57.895 19.90 2.14 0.00 4.12
599 601 1.002251 TGACGTCACGCCCAATTTTTC 60.002 47.619 15.76 0.00 0.00 2.29
613 615 7.600752 CGCCCAATTTTTCCTTTTGTTTATCTA 59.399 33.333 0.00 0.00 0.00 1.98
614 616 8.717821 GCCCAATTTTTCCTTTTGTTTATCTAC 58.282 33.333 0.00 0.00 0.00 2.59
703 713 3.674997 AGGCAATCTCACGAAGCTTTTA 58.325 40.909 0.00 0.00 0.00 1.52
740 752 7.125053 TGTTTACTCTTTTGTTTTTGAGGGGAT 59.875 33.333 0.00 0.00 0.00 3.85
741 753 5.535753 ACTCTTTTGTTTTTGAGGGGATG 57.464 39.130 0.00 0.00 0.00 3.51
742 754 5.208121 ACTCTTTTGTTTTTGAGGGGATGA 58.792 37.500 0.00 0.00 0.00 2.92
743 755 5.302823 ACTCTTTTGTTTTTGAGGGGATGAG 59.697 40.000 0.00 0.00 0.00 2.90
744 756 4.588528 TCTTTTGTTTTTGAGGGGATGAGG 59.411 41.667 0.00 0.00 0.00 3.86
745 757 2.603075 TGTTTTTGAGGGGATGAGGG 57.397 50.000 0.00 0.00 0.00 4.30
746 758 1.077005 TGTTTTTGAGGGGATGAGGGG 59.923 52.381 0.00 0.00 0.00 4.79
747 759 1.357761 GTTTTTGAGGGGATGAGGGGA 59.642 52.381 0.00 0.00 0.00 4.81
748 760 2.000290 TTTTGAGGGGATGAGGGGAT 58.000 50.000 0.00 0.00 0.00 3.85
749 761 2.000290 TTTGAGGGGATGAGGGGATT 58.000 50.000 0.00 0.00 0.00 3.01
750 762 1.522900 TTGAGGGGATGAGGGGATTC 58.477 55.000 0.00 0.00 0.00 2.52
751 763 0.649992 TGAGGGGATGAGGGGATTCT 59.350 55.000 0.00 0.00 0.00 2.40
752 764 1.873049 TGAGGGGATGAGGGGATTCTA 59.127 52.381 0.00 0.00 0.00 2.10
753 765 2.252676 TGAGGGGATGAGGGGATTCTAA 59.747 50.000 0.00 0.00 0.00 2.10
754 766 2.909662 GAGGGGATGAGGGGATTCTAAG 59.090 54.545 0.00 0.00 0.00 2.18
755 767 2.254023 AGGGGATGAGGGGATTCTAAGT 59.746 50.000 0.00 0.00 0.00 2.24
756 768 3.056832 GGGGATGAGGGGATTCTAAGTT 58.943 50.000 0.00 0.00 0.00 2.66
757 769 3.463704 GGGGATGAGGGGATTCTAAGTTT 59.536 47.826 0.00 0.00 0.00 2.66
758 770 4.079154 GGGGATGAGGGGATTCTAAGTTTT 60.079 45.833 0.00 0.00 0.00 2.43
759 771 5.519808 GGGATGAGGGGATTCTAAGTTTTT 58.480 41.667 0.00 0.00 0.00 1.94
814 826 2.689658 TGTTTGAGAACTCTGAGGGGA 58.310 47.619 9.85 0.00 36.70 4.81
815 827 3.251484 TGTTTGAGAACTCTGAGGGGAT 58.749 45.455 9.85 0.00 36.70 3.85
817 829 4.257731 GTTTGAGAACTCTGAGGGGATTC 58.742 47.826 9.85 3.81 32.91 2.52
818 830 3.481559 TGAGAACTCTGAGGGGATTCT 57.518 47.619 9.85 8.61 32.36 2.40
819 831 3.102972 TGAGAACTCTGAGGGGATTCTG 58.897 50.000 9.85 0.00 29.85 3.02
820 832 3.245766 TGAGAACTCTGAGGGGATTCTGA 60.246 47.826 9.85 0.57 29.85 3.27
822 834 2.938428 ACTCTGAGGGGATTCTGAGT 57.062 50.000 9.85 9.00 45.67 3.41
824 836 2.465813 CTCTGAGGGGATTCTGAGTGT 58.534 52.381 0.00 0.00 37.97 3.55
1126 1153 2.746359 GGCTCCCAGGATCCATCG 59.254 66.667 15.82 1.33 31.27 3.84
1257 1284 0.038744 AATGGAGGCTGTTCAGGTGG 59.961 55.000 0.00 0.00 0.00 4.61
1382 1409 3.427425 TTCCGCACGCATTTCGGG 61.427 61.111 0.00 0.00 46.33 5.14
1558 1586 1.754803 CGTGTAGTCCAGCCCTAATCA 59.245 52.381 0.00 0.00 0.00 2.57
1570 1598 6.045318 CCAGCCCTAATCATCATTAGTATCG 58.955 44.000 0.00 0.00 39.98 2.92
1581 1609 8.693542 TCATCATTAGTATCGCTATCACAATG 57.306 34.615 0.00 0.00 0.00 2.82
1594 1622 4.994907 ATCACAATGTGTAGCAATGCAT 57.005 36.364 13.55 0.00 34.79 3.96
1716 1833 6.408858 TTTTCGCTCATTTCAGTCTGTATC 57.591 37.500 0.00 0.00 0.00 2.24
1858 1975 9.325198 TGTGCGTATCTAGATGACAAATTTATT 57.675 29.630 15.79 0.00 0.00 1.40
1884 2001 1.751351 GGCACTAGATTTCTTTGGGGC 59.249 52.381 0.00 0.00 0.00 5.80
1890 2007 1.203100 AGATTTCTTTGGGGCACTGCT 60.203 47.619 0.00 0.00 0.00 4.24
1896 2013 1.108727 TTTGGGGCACTGCTGACTTG 61.109 55.000 0.00 0.00 0.00 3.16
1901 2018 0.029834 GGCACTGCTGACTTGTTGTG 59.970 55.000 0.00 0.00 0.00 3.33
2040 2291 2.308570 GGATGGGGGATACATGTGCATA 59.691 50.000 9.11 0.00 39.74 3.14
2050 2301 8.028938 GGGGATACATGTGCATAATTTTGTATC 58.971 37.037 19.03 19.03 42.31 2.24
2072 2323 2.468831 TGTTTTCTTGCATTGAACCGC 58.531 42.857 2.65 0.00 0.00 5.68
2091 2343 2.139118 GCTCTGTGTTCTGTTGTCTCC 58.861 52.381 0.00 0.00 0.00 3.71
2215 2653 8.779303 CAATCTCCTAGGACTAGTATATATGCG 58.221 40.741 7.62 0.00 0.00 4.73
2278 2750 9.378551 GATGGTGTTAAAGAGTAATACATGACA 57.621 33.333 0.00 0.00 0.00 3.58
2327 3043 9.953697 TTAGTTACGCAGTTTTTAATTGATGTT 57.046 25.926 0.00 0.00 37.78 2.71
2335 3051 7.095102 GCAGTTTTTAATTGATGTTGCTGGATT 60.095 33.333 0.00 0.00 0.00 3.01
2567 3292 1.202533 CGTGGTGTCAAGAAGGTGAGT 60.203 52.381 0.00 0.00 0.00 3.41
2580 3305 5.431765 AGAAGGTGAGTTACTTATGCATGG 58.568 41.667 10.16 4.66 0.00 3.66
2590 3315 2.291153 ACTTATGCATGGTCTGTTGGCT 60.291 45.455 10.16 0.00 0.00 4.75
2608 3333 4.341487 TGGCTACTTTCTAGTGCTCACTA 58.659 43.478 9.17 9.17 42.54 2.74
2618 3343 5.582550 TCTAGTGCTCACTATGATCGTTTG 58.417 41.667 9.87 0.00 42.44 2.93
2628 3353 8.716646 TCACTATGATCGTTTGTGTTGATATT 57.283 30.769 15.65 0.00 0.00 1.28
2820 3550 2.029380 GCTGGTTTGGAATAACGCCTTT 60.029 45.455 0.00 0.00 0.00 3.11
2866 4106 6.211584 AGAGGTTAGAGCTAAAGTGTTCATGA 59.788 38.462 0.00 0.00 0.00 3.07
2923 4163 6.639632 AGTGTGTGATATGCAGTTTCTTTT 57.360 33.333 0.00 0.00 0.00 2.27
2944 4184 4.698201 TGTTGTCTGTCCACTCCATTTA 57.302 40.909 0.00 0.00 0.00 1.40
2945 4185 5.241403 TGTTGTCTGTCCACTCCATTTAT 57.759 39.130 0.00 0.00 0.00 1.40
2946 4186 5.003160 TGTTGTCTGTCCACTCCATTTATG 58.997 41.667 0.00 0.00 0.00 1.90
2992 4375 4.159135 ACTTTCTCCCTGCATGCTTAATTG 59.841 41.667 20.33 5.13 0.00 2.32
3042 4584 1.611977 CAGCATCCCCGATTCGTAGTA 59.388 52.381 5.20 0.00 0.00 1.82
3078 4620 2.791383 TTTCTCGCATTGGTTGTTGG 57.209 45.000 0.00 0.00 0.00 3.77
3079 4621 1.686355 TTCTCGCATTGGTTGTTGGT 58.314 45.000 0.00 0.00 0.00 3.67
3080 4622 2.552599 TCTCGCATTGGTTGTTGGTA 57.447 45.000 0.00 0.00 0.00 3.25
3081 4623 3.066291 TCTCGCATTGGTTGTTGGTAT 57.934 42.857 0.00 0.00 0.00 2.73
3082 4624 3.417101 TCTCGCATTGGTTGTTGGTATT 58.583 40.909 0.00 0.00 0.00 1.89
3083 4625 3.438781 TCTCGCATTGGTTGTTGGTATTC 59.561 43.478 0.00 0.00 0.00 1.75
3116 4658 1.617850 TGCATCCGAAATTGCCAAAGT 59.382 42.857 0.00 0.00 38.08 2.66
3190 4742 1.048160 TATGCTGATGGTCCTCCGCA 61.048 55.000 8.91 8.91 39.27 5.69
3210 4766 2.301505 GCAGCACAGCCTATGTACG 58.698 57.895 0.00 0.00 41.41 3.67
3212 4768 1.202371 GCAGCACAGCCTATGTACGTA 60.202 52.381 0.00 0.00 41.41 3.57
3221 4777 7.721239 ACAGCCTATGTACGTATTGGTACGC 62.721 48.000 0.00 0.00 45.12 4.42
3226 4782 3.713963 CGTATTGGTACGCTGGCC 58.286 61.111 0.00 0.00 46.03 5.36
3411 4967 0.031857 CTGCGCTCTCTCCATACCTG 59.968 60.000 9.73 0.00 0.00 4.00
3466 5022 5.659525 TCCAAATGCTGATCTGATTTTCCAT 59.340 36.000 3.42 0.00 0.00 3.41
3467 5023 6.834969 TCCAAATGCTGATCTGATTTTCCATA 59.165 34.615 3.42 0.00 0.00 2.74
3468 5024 7.507956 TCCAAATGCTGATCTGATTTTCCATAT 59.492 33.333 3.42 0.00 0.00 1.78
3470 5026 6.835819 ATGCTGATCTGATTTTCCATATGG 57.164 37.500 16.25 16.25 0.00 2.74
3471 5027 4.521639 TGCTGATCTGATTTTCCATATGGC 59.478 41.667 17.58 3.07 34.44 4.40
3472 5028 4.082354 GCTGATCTGATTTTCCATATGGCC 60.082 45.833 17.58 0.00 34.44 5.36
3515 5087 1.669115 CCTCTTGGACACTGCACCG 60.669 63.158 0.00 0.00 34.57 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.155826 TCATTCCCACGATGTTTTAGCAAG 59.844 41.667 0.00 0.00 0.00 4.01
1 2 4.075682 TCATTCCCACGATGTTTTAGCAA 58.924 39.130 0.00 0.00 0.00 3.91
2 3 3.680490 TCATTCCCACGATGTTTTAGCA 58.320 40.909 0.00 0.00 0.00 3.49
3 4 4.662145 CTTCATTCCCACGATGTTTTAGC 58.338 43.478 0.00 0.00 0.00 3.09
4 5 4.396166 AGCTTCATTCCCACGATGTTTTAG 59.604 41.667 0.00 0.00 0.00 1.85
5 6 4.331968 AGCTTCATTCCCACGATGTTTTA 58.668 39.130 0.00 0.00 0.00 1.52
6 7 3.157087 AGCTTCATTCCCACGATGTTTT 58.843 40.909 0.00 0.00 0.00 2.43
7 8 2.795329 AGCTTCATTCCCACGATGTTT 58.205 42.857 0.00 0.00 0.00 2.83
8 9 2.496899 AGCTTCATTCCCACGATGTT 57.503 45.000 0.00 0.00 0.00 2.71
9 10 3.627395 TTAGCTTCATTCCCACGATGT 57.373 42.857 0.00 0.00 0.00 3.06
10 11 3.313526 CCTTTAGCTTCATTCCCACGATG 59.686 47.826 0.00 0.00 0.00 3.84
11 12 3.545703 CCTTTAGCTTCATTCCCACGAT 58.454 45.455 0.00 0.00 0.00 3.73
12 13 2.939640 GCCTTTAGCTTCATTCCCACGA 60.940 50.000 0.00 0.00 38.99 4.35
13 14 1.401905 GCCTTTAGCTTCATTCCCACG 59.598 52.381 0.00 0.00 38.99 4.94
14 15 2.446435 TGCCTTTAGCTTCATTCCCAC 58.554 47.619 0.00 0.00 44.23 4.61
15 16 2.825532 GTTGCCTTTAGCTTCATTCCCA 59.174 45.455 0.00 0.00 44.23 4.37
16 17 3.092301 AGTTGCCTTTAGCTTCATTCCC 58.908 45.455 0.00 0.00 44.23 3.97
17 18 4.790765 AAGTTGCCTTTAGCTTCATTCC 57.209 40.909 0.00 0.00 44.23 3.01
18 19 6.018589 AGAAAGTTGCCTTTAGCTTCATTC 57.981 37.500 0.00 0.00 40.98 2.67
19 20 6.040842 TCAAGAAAGTTGCCTTTAGCTTCATT 59.959 34.615 0.00 0.00 40.98 2.57
20 21 5.536161 TCAAGAAAGTTGCCTTTAGCTTCAT 59.464 36.000 0.00 0.00 40.98 2.57
21 22 4.887071 TCAAGAAAGTTGCCTTTAGCTTCA 59.113 37.500 0.00 0.00 40.98 3.02
22 23 5.438761 TCAAGAAAGTTGCCTTTAGCTTC 57.561 39.130 0.00 0.00 40.98 3.86
23 24 7.709149 ATATCAAGAAAGTTGCCTTTAGCTT 57.291 32.000 0.00 0.00 40.98 3.74
24 25 7.709149 AATATCAAGAAAGTTGCCTTTAGCT 57.291 32.000 0.00 0.00 40.98 3.32
50 51 9.294030 GATGATGCGTTTAAGAAATTCTTTCAT 57.706 29.630 13.89 13.64 42.10 2.57
51 52 8.514594 AGATGATGCGTTTAAGAAATTCTTTCA 58.485 29.630 13.89 9.61 42.10 2.69
52 53 8.902040 AGATGATGCGTTTAAGAAATTCTTTC 57.098 30.769 13.89 4.19 37.89 2.62
53 54 9.994432 CTAGATGATGCGTTTAAGAAATTCTTT 57.006 29.630 13.89 0.00 37.89 2.52
54 55 9.383519 TCTAGATGATGCGTTTAAGAAATTCTT 57.616 29.630 13.20 13.20 40.35 2.52
55 56 8.948631 TCTAGATGATGCGTTTAAGAAATTCT 57.051 30.769 0.00 0.00 0.00 2.40
60 61 9.981114 TCAATATCTAGATGATGCGTTTAAGAA 57.019 29.630 15.79 0.00 36.65 2.52
65 66 9.935241 AACTATCAATATCTAGATGATGCGTTT 57.065 29.630 15.79 2.08 35.53 3.60
66 67 9.935241 AAACTATCAATATCTAGATGATGCGTT 57.065 29.630 15.79 14.11 35.53 4.84
67 68 9.935241 AAAACTATCAATATCTAGATGATGCGT 57.065 29.630 15.79 9.73 35.53 5.24
102 103 3.734463 TGAGCGATGTTCCAACTAAACA 58.266 40.909 0.00 0.00 40.63 2.83
103 104 3.746492 ACTGAGCGATGTTCCAACTAAAC 59.254 43.478 0.00 0.00 0.00 2.01
104 105 4.002906 ACTGAGCGATGTTCCAACTAAA 57.997 40.909 0.00 0.00 0.00 1.85
105 106 3.678056 ACTGAGCGATGTTCCAACTAA 57.322 42.857 0.00 0.00 0.00 2.24
106 107 3.678056 AACTGAGCGATGTTCCAACTA 57.322 42.857 0.00 0.00 0.00 2.24
107 108 2.549754 CAAACTGAGCGATGTTCCAACT 59.450 45.455 0.00 0.00 0.00 3.16
108 109 2.290641 ACAAACTGAGCGATGTTCCAAC 59.709 45.455 0.00 0.00 0.00 3.77
109 110 2.571212 ACAAACTGAGCGATGTTCCAA 58.429 42.857 0.00 0.00 0.00 3.53
110 111 2.254546 ACAAACTGAGCGATGTTCCA 57.745 45.000 0.00 0.00 0.00 3.53
111 112 3.496884 TGTAACAAACTGAGCGATGTTCC 59.503 43.478 2.08 0.00 37.25 3.62
112 113 4.725556 TGTAACAAACTGAGCGATGTTC 57.274 40.909 2.08 0.00 37.25 3.18
113 114 4.083324 CCATGTAACAAACTGAGCGATGTT 60.083 41.667 4.06 4.06 39.23 2.71
114 115 3.436704 CCATGTAACAAACTGAGCGATGT 59.563 43.478 0.00 0.00 0.00 3.06
115 116 3.684305 TCCATGTAACAAACTGAGCGATG 59.316 43.478 0.00 0.00 0.00 3.84
116 117 3.684788 GTCCATGTAACAAACTGAGCGAT 59.315 43.478 0.00 0.00 0.00 4.58
117 118 3.064207 GTCCATGTAACAAACTGAGCGA 58.936 45.455 0.00 0.00 0.00 4.93
118 119 2.805671 TGTCCATGTAACAAACTGAGCG 59.194 45.455 0.00 0.00 0.00 5.03
119 120 4.726416 CATGTCCATGTAACAAACTGAGC 58.274 43.478 2.65 0.00 34.23 4.26
132 133 6.668541 AGAAAGATTAACGACATGTCCATG 57.331 37.500 20.03 8.85 44.15 3.66
133 134 7.687941 AAAGAAAGATTAACGACATGTCCAT 57.312 32.000 20.03 11.31 0.00 3.41
134 135 7.504924 AAAAGAAAGATTAACGACATGTCCA 57.495 32.000 20.03 2.86 0.00 4.02
221 222 9.138062 GCATGATAAATTTCACATGTACAAACA 57.862 29.630 24.75 0.00 41.14 2.83
222 223 9.138062 TGCATGATAAATTTCACATGTACAAAC 57.862 29.630 24.75 14.88 41.14 2.93
223 224 9.702494 TTGCATGATAAATTTCACATGTACAAA 57.298 25.926 24.75 16.79 41.14 2.83
224 225 9.138062 GTTGCATGATAAATTTCACATGTACAA 57.862 29.630 24.75 20.45 41.14 2.41
225 226 8.522003 AGTTGCATGATAAATTTCACATGTACA 58.478 29.630 24.75 17.67 41.14 2.90
226 227 8.915871 AGTTGCATGATAAATTTCACATGTAC 57.084 30.769 24.75 22.44 41.14 2.90
227 228 8.959548 AGAGTTGCATGATAAATTTCACATGTA 58.040 29.630 24.75 21.21 41.14 2.29
228 229 7.833786 AGAGTTGCATGATAAATTTCACATGT 58.166 30.769 24.75 13.79 41.14 3.21
229 230 8.592155 CAAGAGTTGCATGATAAATTTCACATG 58.408 33.333 22.26 22.26 41.72 3.21
230 231 8.697846 CAAGAGTTGCATGATAAATTTCACAT 57.302 30.769 0.00 0.00 0.00 3.21
251 252 5.126067 GGGCTCTTGAAATAGTATGCAAGA 58.874 41.667 19.58 19.58 43.00 3.02
252 253 4.024556 CGGGCTCTTGAAATAGTATGCAAG 60.025 45.833 15.11 15.11 39.17 4.01
253 254 3.876914 CGGGCTCTTGAAATAGTATGCAA 59.123 43.478 0.00 0.00 0.00 4.08
254 255 3.118408 ACGGGCTCTTGAAATAGTATGCA 60.118 43.478 0.00 0.00 0.00 3.96
255 256 3.248602 CACGGGCTCTTGAAATAGTATGC 59.751 47.826 0.00 0.00 0.00 3.14
256 257 3.809832 CCACGGGCTCTTGAAATAGTATG 59.190 47.826 0.00 0.00 0.00 2.39
257 258 3.744530 GCCACGGGCTCTTGAAATAGTAT 60.745 47.826 7.58 0.00 46.69 2.12
258 259 2.419574 GCCACGGGCTCTTGAAATAGTA 60.420 50.000 7.58 0.00 46.69 1.82
259 260 1.679032 GCCACGGGCTCTTGAAATAGT 60.679 52.381 7.58 0.00 46.69 2.12
260 261 1.017387 GCCACGGGCTCTTGAAATAG 58.983 55.000 7.58 0.00 46.69 1.73
261 262 3.168773 GCCACGGGCTCTTGAAATA 57.831 52.632 7.58 0.00 46.69 1.40
262 263 4.002797 GCCACGGGCTCTTGAAAT 57.997 55.556 7.58 0.00 46.69 2.17
279 280 2.048597 TAGAGTGCCCGTGCGTTG 60.049 61.111 0.00 0.00 41.78 4.10
280 281 1.246056 TAGTAGAGTGCCCGTGCGTT 61.246 55.000 0.00 0.00 41.78 4.84
281 282 1.654954 CTAGTAGAGTGCCCGTGCGT 61.655 60.000 0.00 0.00 41.78 5.24
282 283 1.064296 CTAGTAGAGTGCCCGTGCG 59.936 63.158 0.00 0.00 41.78 5.34
283 284 2.190756 ACTAGTAGAGTGCCCGTGC 58.809 57.895 3.59 0.00 36.87 5.34
291 292 6.946583 TCACTAACCATTGTCACTAGTAGAGT 59.053 38.462 3.59 0.00 39.82 3.24
292 293 7.121463 AGTCACTAACCATTGTCACTAGTAGAG 59.879 40.741 3.59 0.00 0.00 2.43
293 294 6.946583 AGTCACTAACCATTGTCACTAGTAGA 59.053 38.462 3.59 0.00 0.00 2.59
294 295 7.159322 AGTCACTAACCATTGTCACTAGTAG 57.841 40.000 0.00 0.00 0.00 2.57
295 296 7.375834 CAAGTCACTAACCATTGTCACTAGTA 58.624 38.462 0.00 0.00 0.00 1.82
296 297 6.223852 CAAGTCACTAACCATTGTCACTAGT 58.776 40.000 0.00 0.00 0.00 2.57
297 298 5.639506 CCAAGTCACTAACCATTGTCACTAG 59.360 44.000 0.00 0.00 0.00 2.57
298 299 5.305902 TCCAAGTCACTAACCATTGTCACTA 59.694 40.000 0.00 0.00 0.00 2.74
299 300 4.102524 TCCAAGTCACTAACCATTGTCACT 59.897 41.667 0.00 0.00 0.00 3.41
300 301 4.213482 GTCCAAGTCACTAACCATTGTCAC 59.787 45.833 0.00 0.00 0.00 3.67
348 349 8.073768 GGAGTTTCAACATAGATTCGTTTTTCA 58.926 33.333 0.00 0.00 0.00 2.69
366 368 5.584649 CACTTGTCACAACTTAGGAGTTTCA 59.415 40.000 0.00 0.00 43.48 2.69
388 390 2.030335 TGATGAATTACATGCGCGACAC 59.970 45.455 12.10 0.00 39.56 3.67
395 397 5.106197 TGGTGACAAGTGATGAATTACATGC 60.106 40.000 0.00 0.00 36.97 4.06
417 419 3.024547 TCACTCCTACCTTCTTCGATGG 58.975 50.000 0.00 0.00 33.73 3.51
420 422 2.041350 AGGTCACTCCTACCTTCTTCGA 59.959 50.000 0.00 0.00 45.26 3.71
445 447 4.589908 AGTTAGTTATGGAGTGCCCTTTG 58.410 43.478 0.00 0.00 35.38 2.77
455 457 9.362539 GTTTCGAAATCAGTAGTTAGTTATGGA 57.637 33.333 14.69 0.00 0.00 3.41
458 460 9.583765 GGAGTTTCGAAATCAGTAGTTAGTTAT 57.416 33.333 14.69 0.00 0.00 1.89
475 477 3.234630 CTGCCCGTGGGAGTTTCGA 62.235 63.158 9.72 0.00 36.37 3.71
512 514 1.741770 GCTACTGCCTCACGGTTGG 60.742 63.158 0.00 0.00 39.22 3.77
513 515 0.320771 AAGCTACTGCCTCACGGTTG 60.321 55.000 0.00 0.00 39.22 3.77
514 516 0.320771 CAAGCTACTGCCTCACGGTT 60.321 55.000 0.00 0.00 39.22 4.44
516 518 2.103042 GCAAGCTACTGCCTCACGG 61.103 63.158 0.00 0.00 40.80 4.94
542 544 1.450531 CCCATGAATCGGCTGCCTTC 61.451 60.000 17.92 14.76 0.00 3.46
549 551 3.599704 GCCAGCCCATGAATCGGC 61.600 66.667 2.71 2.71 46.09 5.54
563 565 1.202639 CGTCAATGCTATACTGGGCCA 60.203 52.381 5.85 5.85 0.00 5.36
566 568 3.123804 GTGACGTCAATGCTATACTGGG 58.876 50.000 21.95 0.00 0.00 4.45
577 579 1.243902 AAATTGGGCGTGACGTCAAT 58.756 45.000 21.95 15.99 35.70 2.57
578 580 1.025812 AAAATTGGGCGTGACGTCAA 58.974 45.000 21.95 14.41 30.88 3.18
582 584 0.596082 AGGAAAAATTGGGCGTGACG 59.404 50.000 0.00 0.00 0.00 4.35
720 732 5.279156 CCTCATCCCCTCAAAAACAAAAGAG 60.279 44.000 0.00 0.00 0.00 2.85
728 740 1.766951 TCCCCTCATCCCCTCAAAAA 58.233 50.000 0.00 0.00 0.00 1.94
758 770 6.601332 AGAATCACCTCAGAGTTACCAAAAA 58.399 36.000 0.00 0.00 0.00 1.94
759 771 6.187727 AGAATCACCTCAGAGTTACCAAAA 57.812 37.500 0.00 0.00 0.00 2.44
760 772 5.825593 AGAATCACCTCAGAGTTACCAAA 57.174 39.130 0.00 0.00 0.00 3.28
761 773 6.497259 ACTTAGAATCACCTCAGAGTTACCAA 59.503 38.462 0.00 0.00 0.00 3.67
762 774 6.017192 ACTTAGAATCACCTCAGAGTTACCA 58.983 40.000 0.00 0.00 0.00 3.25
763 775 6.532988 ACTTAGAATCACCTCAGAGTTACC 57.467 41.667 0.00 0.00 0.00 2.85
764 776 8.834749 AAAACTTAGAATCACCTCAGAGTTAC 57.165 34.615 0.00 0.00 0.00 2.50
795 807 3.990959 ATCCCCTCAGAGTTCTCAAAC 57.009 47.619 0.00 0.00 35.50 2.93
796 808 4.019860 CAGAATCCCCTCAGAGTTCTCAAA 60.020 45.833 0.00 0.00 0.00 2.69
799 811 3.370104 TCAGAATCCCCTCAGAGTTCTC 58.630 50.000 0.00 0.00 0.00 2.87
800 812 3.245948 ACTCAGAATCCCCTCAGAGTTCT 60.246 47.826 0.00 0.00 38.60 3.01
801 813 3.103742 ACTCAGAATCCCCTCAGAGTTC 58.896 50.000 0.00 0.00 38.60 3.01
802 814 2.836981 CACTCAGAATCCCCTCAGAGTT 59.163 50.000 0.00 0.00 39.41 3.01
805 817 2.568956 CAACACTCAGAATCCCCTCAGA 59.431 50.000 0.00 0.00 0.00 3.27
806 818 2.304180 ACAACACTCAGAATCCCCTCAG 59.696 50.000 0.00 0.00 0.00 3.35
808 820 3.244561 TGAACAACACTCAGAATCCCCTC 60.245 47.826 0.00 0.00 0.00 4.30
809 821 2.711009 TGAACAACACTCAGAATCCCCT 59.289 45.455 0.00 0.00 0.00 4.79
811 823 4.142816 CGAATGAACAACACTCAGAATCCC 60.143 45.833 0.00 0.00 0.00 3.85
838 857 0.820074 AGATGGGCTCGAGGAGTACG 60.820 60.000 15.58 0.00 31.39 3.67
1114 1141 0.975135 AGAGATGCGATGGATCCTGG 59.025 55.000 14.23 3.07 0.00 4.45
1126 1153 7.201600 GGAAAGAGTTAGTGATTTGAGAGATGC 60.202 40.741 0.00 0.00 0.00 3.91
1237 1264 1.548582 CCACCTGAACAGCCTCCATTT 60.549 52.381 0.00 0.00 0.00 2.32
1238 1265 0.038744 CCACCTGAACAGCCTCCATT 59.961 55.000 0.00 0.00 0.00 3.16
1397 1424 2.617308 GTCGTAGATGAGACCGAATCCA 59.383 50.000 0.00 0.00 40.67 3.41
1517 1545 0.741221 GGCAAAGAACGATCGAGCCT 60.741 55.000 24.34 12.13 38.09 4.58
1528 1556 1.139256 TGGACTACACGTGGCAAAGAA 59.861 47.619 21.57 0.00 0.00 2.52
1558 1586 8.090831 ACACATTGTGATAGCGATACTAATGAT 58.909 33.333 23.12 0.00 36.96 2.45
1570 1598 4.201940 TGCATTGCTACACATTGTGATAGC 60.202 41.667 26.88 26.88 40.24 2.97
1594 1622 9.751542 GAGTACTATTCTTTTAGCAGATTAGCA 57.248 33.333 0.00 0.00 33.04 3.49
1601 1629 6.517605 GGAGGGAGTACTATTCTTTTAGCAG 58.482 44.000 0.00 0.00 0.00 4.24
1657 1773 9.778741 AAATGTGTCTACATACATCCGATTTAT 57.221 29.630 0.00 0.00 46.54 1.40
1759 1876 1.677637 CTACTCCCTCCGTTCAGGCC 61.678 65.000 0.00 0.00 40.77 5.19
1884 2001 3.976793 ATTCACAACAAGTCAGCAGTG 57.023 42.857 0.00 0.00 0.00 3.66
1890 2007 4.704540 AGGAACACAATTCACAACAAGTCA 59.295 37.500 0.00 0.00 0.00 3.41
1896 2013 4.900635 AGTCAGGAACACAATTCACAAC 57.099 40.909 0.00 0.00 0.00 3.32
1901 2018 5.248870 ACAACAAGTCAGGAACACAATTC 57.751 39.130 0.00 0.00 0.00 2.17
1956 2205 8.818622 AATATAAATCTATGATGCATGGCAGT 57.181 30.769 2.46 0.00 43.65 4.40
1985 2235 4.820897 TCTGAACATCACAGACACCATAC 58.179 43.478 0.00 0.00 39.10 2.39
2050 2301 3.120923 GCGGTTCAATGCAAGAAAACATG 60.121 43.478 6.54 0.00 0.00 3.21
2072 2323 3.126831 GTGGAGACAACAGAACACAGAG 58.873 50.000 0.00 0.00 46.06 3.35
2091 2343 8.050778 TCTGTATGGGCTTTAACTAAAATGTG 57.949 34.615 0.00 0.00 0.00 3.21
2215 2653 6.699575 ATATCAGACCTAATTGTTGTTGCC 57.300 37.500 0.00 0.00 0.00 4.52
2318 3034 7.879160 ACAATTACAAATCCAGCAACATCAATT 59.121 29.630 0.00 0.00 0.00 2.32
2327 3043 8.347004 TCTTCATAACAATTACAAATCCAGCA 57.653 30.769 0.00 0.00 0.00 4.41
2567 3292 3.694072 GCCAACAGACCATGCATAAGTAA 59.306 43.478 0.00 0.00 0.00 2.24
2580 3305 3.680458 GCACTAGAAAGTAGCCAACAGAC 59.320 47.826 0.00 0.00 33.48 3.51
2590 3315 6.542735 ACGATCATAGTGAGCACTAGAAAGTA 59.457 38.462 14.82 0.00 45.94 2.24
2608 3333 7.063308 GCCAAAAATATCAACACAAACGATCAT 59.937 33.333 0.00 0.00 0.00 2.45
2618 3343 4.749099 TGCACAAGCCAAAAATATCAACAC 59.251 37.500 0.00 0.00 41.13 3.32
2628 3353 1.136695 CTTGGTCTGCACAAGCCAAAA 59.863 47.619 2.94 0.00 39.80 2.44
2691 3418 0.107116 ACCGCCGAGAGTGTAGATCT 60.107 55.000 0.00 0.00 0.00 2.75
2693 3420 1.183549 AAACCGCCGAGAGTGTAGAT 58.816 50.000 0.00 0.00 0.00 1.98
2695 3422 1.471684 ACTAAACCGCCGAGAGTGTAG 59.528 52.381 0.00 0.00 31.24 2.74
2760 3487 4.138487 ACGAGAAAAACCTCACTTCAGT 57.862 40.909 0.00 0.00 32.86 3.41
2820 3550 6.543465 CCTCTAAGCATGGATGTAAATGTCAA 59.457 38.462 0.00 0.00 0.00 3.18
2866 4106 5.977635 AGAAAGCTGCCTTGTTAAAGTTTT 58.022 33.333 0.00 0.00 0.00 2.43
2923 4163 3.576078 AAATGGAGTGGACAGACAACA 57.424 42.857 0.00 0.00 0.00 3.33
2944 4184 6.874664 TGCATAATCAAAATGAACAAGTGCAT 59.125 30.769 0.00 0.00 33.36 3.96
2945 4185 6.145858 GTGCATAATCAAAATGAACAAGTGCA 59.854 34.615 0.00 0.00 33.67 4.57
2946 4186 6.366877 AGTGCATAATCAAAATGAACAAGTGC 59.633 34.615 0.00 0.00 35.62 4.40
2992 4375 1.439679 CCCTAGCCAAACACGACTTC 58.560 55.000 0.00 0.00 0.00 3.01
3042 4584 6.127925 TGCGAGAAATCATAAATCAGTTGCTT 60.128 34.615 0.00 0.00 0.00 3.91
3078 4620 6.183360 CGGATGCACTGATATGTCATGAATAC 60.183 42.308 0.00 0.00 32.98 1.89
3079 4621 5.870978 CGGATGCACTGATATGTCATGAATA 59.129 40.000 0.00 0.00 32.98 1.75
3080 4622 4.694037 CGGATGCACTGATATGTCATGAAT 59.306 41.667 0.00 0.00 32.98 2.57
3081 4623 4.060205 CGGATGCACTGATATGTCATGAA 58.940 43.478 0.00 0.00 32.98 2.57
3082 4624 3.321682 TCGGATGCACTGATATGTCATGA 59.678 43.478 0.00 0.00 32.98 3.07
3083 4625 3.656559 TCGGATGCACTGATATGTCATG 58.343 45.455 0.00 0.00 32.98 3.07
3210 4766 1.153509 ACGGCCAGCGTACCAATAC 60.154 57.895 2.24 0.00 0.00 1.89
3212 4768 2.435938 CACGGCCAGCGTACCAAT 60.436 61.111 2.24 0.00 0.00 3.16
3466 5022 1.609239 CACCTCAAGCCAGGCCATA 59.391 57.895 8.22 0.00 36.98 2.74
3467 5023 2.357836 CACCTCAAGCCAGGCCAT 59.642 61.111 8.22 0.00 36.98 4.40
3468 5024 4.666253 GCACCTCAAGCCAGGCCA 62.666 66.667 8.22 0.00 36.98 5.36
3470 5026 2.833604 ATCAGCACCTCAAGCCAGGC 62.834 60.000 1.84 1.84 36.98 4.85
3471 5027 1.030488 CATCAGCACCTCAAGCCAGG 61.030 60.000 0.00 0.00 39.80 4.45
3472 5028 0.322277 ACATCAGCACCTCAAGCCAG 60.322 55.000 0.00 0.00 0.00 4.85
3515 5087 1.535226 GCAACCTCCAACGTTGTTTCC 60.535 52.381 25.63 4.90 42.12 3.13


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

AutoCloner maintained by Alex Coulton.