Multiple sequence alignment - TraesCS4D01G225500

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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 TraesCS4D01G225500 chr4D 100.000 7080 0 0 1 7080 384263732 384270811 0.000000e+00 13075.0
1 TraesCS4D01G225500 chr4D 93.023 86 6 0 6154 6239 466837142 466837227 7.460000e-25 126.0
2 TraesCS4D01G225500 chr4D 82.243 107 6 7 4507 4611 89538657 89538562 5.890000e-11 80.5
3 TraesCS4D01G225500 chr4A 96.268 4930 109 23 24 4893 66141124 66146038 0.000000e+00 8015.0
4 TraesCS4D01G225500 chr4A 94.272 1222 33 12 4938 6139 66146206 66147410 0.000000e+00 1834.0
5 TraesCS4D01G225500 chr4A 85.070 710 41 31 6402 7080 66147405 66148080 0.000000e+00 664.0
6 TraesCS4D01G225500 chr4A 81.757 148 18 9 6241 6383 517032766 517032909 1.610000e-21 115.0
7 TraesCS4D01G225500 chr4B 97.579 4543 78 15 24 4548 471331179 471335707 0.000000e+00 7751.0
8 TraesCS4D01G225500 chr4B 96.473 1134 29 3 5031 6153 471336353 471337486 0.000000e+00 1862.0
9 TraesCS4D01G225500 chr4B 96.289 485 11 5 4551 5030 471335759 471336241 0.000000e+00 789.0
10 TraesCS4D01G225500 chr4B 92.505 547 16 9 6540 7080 471337676 471338203 0.000000e+00 760.0
11 TraesCS4D01G225500 chr7B 97.608 209 5 0 6872 7080 589740212 589740420 6.750000e-95 359.0
12 TraesCS4D01G225500 chr7B 85.586 111 12 3 6132 6241 173865770 173865877 5.800000e-21 113.0
13 TraesCS4D01G225500 chr7B 79.618 157 24 8 6233 6384 557435772 557435619 9.710000e-19 106.0
14 TraesCS4D01G225500 chr5D 97.608 209 5 0 6872 7080 405334397 405334605 6.750000e-95 359.0
15 TraesCS4D01G225500 chr5D 91.398 93 7 1 6149 6241 543829247 543829156 7.460000e-25 126.0
16 TraesCS4D01G225500 chr5B 97.608 209 5 0 6872 7080 486282945 486283153 6.750000e-95 359.0
17 TraesCS4D01G225500 chr5B 97.129 209 6 0 6872 7080 535715098 535715306 3.140000e-93 353.0
18 TraesCS4D01G225500 chr5B 81.308 107 8 5 4508 4613 34252088 34252183 7.620000e-10 76.8
19 TraesCS4D01G225500 chr5A 97.129 209 6 0 6872 7080 509043983 509043775 3.140000e-93 353.0
20 TraesCS4D01G225500 chr5A 95.556 45 1 1 4572 4615 11064129 11064173 3.540000e-08 71.3
21 TraesCS4D01G225500 chr5A 93.617 47 1 2 4573 4618 362173193 362173148 1.270000e-07 69.4
22 TraesCS4D01G225500 chr5A 95.122 41 2 0 4508 4548 699513180 699513140 1.650000e-06 65.8
23 TraesCS4D01G225500 chr1D 95.089 224 9 2 6859 7080 289782541 289782764 1.130000e-92 351.0
24 TraesCS4D01G225500 chr1D 97.115 208 6 0 6873 7080 445366502 445366709 1.130000e-92 351.0
25 TraesCS4D01G225500 chr2B 94.382 89 5 0 6155 6243 751183287 751183375 3.440000e-28 137.0
26 TraesCS4D01G225500 chr2B 89.691 97 10 0 6144 6240 165513045 165512949 2.680000e-24 124.0
27 TraesCS4D01G225500 chr2B 83.486 109 5 6 4508 4615 206114727 206114823 9.780000e-14 89.8
28 TraesCS4D01G225500 chr2B 78.626 131 24 4 6246 6373 463862031 463862160 4.550000e-12 84.2
29 TraesCS4D01G225500 chr2B 97.778 45 1 0 4502 4546 587241164 587241120 2.120000e-10 78.7
30 TraesCS4D01G225500 chr2B 97.436 39 1 0 4510 4548 202180139 202180177 4.580000e-07 67.6
31 TraesCS4D01G225500 chr6A 94.318 88 5 0 6154 6241 170907819 170907906 1.240000e-27 135.0
32 TraesCS4D01G225500 chr6A 80.537 149 21 8 6240 6384 499460381 499460237 2.700000e-19 108.0
33 TraesCS4D01G225500 chr7D 93.333 90 6 0 6155 6244 10855009 10855098 4.460000e-27 134.0
34 TraesCS4D01G225500 chr7D 92.135 89 7 0 6154 6242 575227936 575228024 7.460000e-25 126.0
35 TraesCS4D01G225500 chr7D 97.826 46 1 0 4503 4548 261818689 261818644 5.890000e-11 80.5
36 TraesCS4D01G225500 chr7D 92.000 50 3 1 4570 4618 618808602 618808553 1.270000e-07 69.4
37 TraesCS4D01G225500 chr6D 93.182 88 6 0 6154 6241 131945837 131945924 5.760000e-26 130.0
38 TraesCS4D01G225500 chr6D 85.714 98 11 3 6250 6344 111432693 111432790 4.520000e-17 100.0
39 TraesCS4D01G225500 chrUn 79.661 177 24 11 6237 6407 60297729 60297899 4.490000e-22 117.0
40 TraesCS4D01G225500 chrUn 80.519 154 20 9 6237 6384 375799875 375800024 7.510000e-20 110.0
41 TraesCS4D01G225500 chrUn 80.795 151 19 9 6240 6384 391468891 391468745 7.510000e-20 110.0
42 TraesCS4D01G225500 chrUn 82.171 129 15 7 6262 6384 365985214 365985088 3.490000e-18 104.0
43 TraesCS4D01G225500 chr2D 84.466 103 3 6 4508 4609 145890407 145890497 9.780000e-14 89.8
44 TraesCS4D01G225500 chr1B 82.301 113 7 6 4505 4615 411568690 411568791 1.270000e-12 86.1
45 TraesCS4D01G225500 chr1A 81.081 111 10 6 4504 4613 381305833 381305733 2.120000e-10 78.7
46 TraesCS4D01G225500 chr7A 90.000 50 2 2 4568 4615 262465906 262465954 2.130000e-05 62.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G225500 chr4D 384263732 384270811 7079 False 13075.000000 13075 100.0000 1 7080 1 chr4D.!!$F1 7079
1 TraesCS4D01G225500 chr4A 66141124 66148080 6956 False 3504.333333 8015 91.8700 24 7080 3 chr4A.!!$F2 7056
2 TraesCS4D01G225500 chr4B 471331179 471338203 7024 False 2790.500000 7751 95.7115 24 7080 4 chr4B.!!$F1 7056

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
319 320 0.103026 GCGGATTGGGGATTCTTTGC 59.897 55.000 0.00 0.00 0.00 3.68 F
366 367 0.794605 GCGCACGCAGGAAAAAGATC 60.795 55.000 10.65 0.00 41.49 2.75 F
674 681 2.698797 AGGAACACCGTACATATCAGGG 59.301 50.000 0.00 0.00 0.00 4.45 F
1544 1571 7.323420 ACTTTTATTTTGCAGGAGGATAAAGC 58.677 34.615 0.00 0.00 0.00 3.51 F
2542 2570 4.521010 GTCTTGTTCGGAAAAAGTTACCG 58.479 43.478 17.85 0.00 46.71 4.02 F
3613 3641 1.053835 TGTCCAAGCACCAGAGACCA 61.054 55.000 0.00 0.00 0.00 4.02 F
4615 4707 0.108207 TCGGATCGGAGGGAGTACTC 59.892 60.000 14.87 14.87 36.76 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1450 1477 2.260844 ACACAAGACACTCATGTGGG 57.739 50.000 11.20 0.0 46.72 4.61 R
1758 1785 3.774216 ACCCAGATCCAGAAAAGAGAGAG 59.226 47.826 0.00 0.0 0.00 3.20 R
2491 2519 1.891150 CTTTGGCATTCAGCTTCCAGT 59.109 47.619 0.00 0.0 44.79 4.00 R
3166 3194 0.457166 CAACAGCATTGTCATGGCCG 60.457 55.000 0.00 0.0 36.23 6.13 R
4521 4563 3.609853 AGAGGCTGCGTCAATTAATTCA 58.390 40.909 22.55 0.0 0.00 2.57 R
5535 5896 0.323629 TTCTCGGGCAACTGGTTAGG 59.676 55.000 0.00 0.0 45.79 2.69 R
6534 6939 0.041312 ACGCTTCAACATGTTCGCAC 60.041 50.000 8.48 0.0 0.00 5.34 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.435372 TTGTTGGCCATGGTCCTATC 57.565 50.000 15.27 9.99 0.00 2.08
20 21 1.595311 TGTTGGCCATGGTCCTATCT 58.405 50.000 15.27 0.00 0.00 1.98
21 22 2.770447 TGTTGGCCATGGTCCTATCTA 58.230 47.619 15.27 0.00 0.00 1.98
22 23 3.326521 TGTTGGCCATGGTCCTATCTAT 58.673 45.455 15.27 0.00 0.00 1.98
63 64 1.740025 GCCCTAGCTGTGTGAATTGTC 59.260 52.381 0.00 0.00 35.50 3.18
76 77 0.884704 AATTGTCACGCAGGCTTCGT 60.885 50.000 6.32 6.32 41.28 3.85
180 181 2.229792 TCTGTTCTGTGGATTGGTTGC 58.770 47.619 0.00 0.00 0.00 4.17
194 195 0.240945 GGTTGCGAGTGGTTGATTGG 59.759 55.000 0.00 0.00 0.00 3.16
209 210 8.516234 GTGGTTGATTGGTTGTATTATTGTACA 58.484 33.333 0.00 0.00 32.99 2.90
296 297 4.081142 TCCCACTGTATGTGTATGACCTTG 60.081 45.833 0.00 0.00 44.81 3.61
317 318 1.272425 TGTGCGGATTGGGGATTCTTT 60.272 47.619 0.00 0.00 0.00 2.52
319 320 0.103026 GCGGATTGGGGATTCTTTGC 59.897 55.000 0.00 0.00 0.00 3.68
321 322 2.034124 CGGATTGGGGATTCTTTGCAT 58.966 47.619 0.00 0.00 0.00 3.96
348 349 7.043192 GCAGTGTGAATTATGGATGTTTTATGC 60.043 37.037 0.00 0.00 0.00 3.14
351 352 5.976534 GTGAATTATGGATGTTTTATGCGCA 59.023 36.000 14.96 14.96 0.00 6.09
366 367 0.794605 GCGCACGCAGGAAAAAGATC 60.795 55.000 10.65 0.00 41.49 2.75
496 503 3.878160 TTTTTGTGCGTTTCCCTTCTT 57.122 38.095 0.00 0.00 0.00 2.52
497 504 4.985538 TTTTTGTGCGTTTCCCTTCTTA 57.014 36.364 0.00 0.00 0.00 2.10
553 560 3.427573 TCGTCAATTCCACTGTCCTCTA 58.572 45.455 0.00 0.00 0.00 2.43
559 566 5.663106 TCAATTCCACTGTCCTCTATAGCTT 59.337 40.000 0.00 0.00 0.00 3.74
674 681 2.698797 AGGAACACCGTACATATCAGGG 59.301 50.000 0.00 0.00 0.00 4.45
1275 1302 7.708322 TCAGTAGCACAGATGTTCTTATGATTC 59.292 37.037 0.00 0.00 0.00 2.52
1544 1571 7.323420 ACTTTTATTTTGCAGGAGGATAAAGC 58.677 34.615 0.00 0.00 0.00 3.51
1755 1782 8.827677 GGTGCGTAAAAGAACTCTATATTCATT 58.172 33.333 0.00 0.00 0.00 2.57
1756 1783 9.851043 GTGCGTAAAAGAACTCTATATTCATTC 57.149 33.333 0.00 0.00 0.00 2.67
1757 1784 9.817809 TGCGTAAAAGAACTCTATATTCATTCT 57.182 29.630 0.00 0.00 0.00 2.40
2491 2519 8.243961 TGGAGGATGTTAAGAAAATCACAAAA 57.756 30.769 0.00 0.00 0.00 2.44
2542 2570 4.521010 GTCTTGTTCGGAAAAAGTTACCG 58.479 43.478 17.85 0.00 46.71 4.02
2587 2615 5.241403 TGAAAATGGAAGTTGAGAGCCTA 57.759 39.130 0.00 0.00 0.00 3.93
3140 3168 5.661503 TGACTTCCTAGAGATGGAGAGAT 57.338 43.478 0.00 0.00 34.76 2.75
3166 3194 1.408702 TGTTTGCCTTCTGAAGCCAAC 59.591 47.619 12.77 14.34 35.73 3.77
3394 3422 5.193099 ACAATGCTGGGAAGGTACTAAAT 57.807 39.130 0.00 0.00 38.49 1.40
3447 3475 7.613022 TGAAGAAGAGGCAGATTTAATGAATGT 59.387 33.333 0.00 0.00 0.00 2.71
3448 3476 7.330900 AGAAGAGGCAGATTTAATGAATGTG 57.669 36.000 0.00 0.00 40.87 3.21
3613 3641 1.053835 TGTCCAAGCACCAGAGACCA 61.054 55.000 0.00 0.00 0.00 4.02
4069 4097 6.371825 GTCGGTTTAGTGAGATGGAGAAAAAT 59.628 38.462 0.00 0.00 0.00 1.82
4263 4291 4.692625 CGGTGATGAAAGACAAAGTCATCT 59.307 41.667 12.61 0.00 45.20 2.90
4466 4507 7.617225 TCAAAGCAGGTACTAATAAGTGCTAA 58.383 34.615 0.00 0.00 38.31 3.09
4521 4563 4.828387 GTGATTTAGTACTCCCTCCGATCT 59.172 45.833 0.00 0.00 0.00 2.75
4547 4638 3.819564 AATTGACGCAGCCTCTATACA 57.180 42.857 0.00 0.00 0.00 2.29
4584 4675 8.954950 AATTCAGTTGACATTGTATAGAGGAG 57.045 34.615 0.00 0.00 0.00 3.69
4585 4676 7.482169 TTCAGTTGACATTGTATAGAGGAGT 57.518 36.000 0.00 0.00 0.00 3.85
4614 4706 0.549950 TTCGGATCGGAGGGAGTACT 59.450 55.000 0.00 0.00 0.00 2.73
4615 4707 0.108207 TCGGATCGGAGGGAGTACTC 59.892 60.000 14.87 14.87 36.76 2.59
4744 4837 6.615316 TCTTCCCTTTTGGATCCTTTTTCTTT 59.385 34.615 14.23 0.00 44.66 2.52
5180 5538 0.757188 ATCGGTGGCAGGAGGTAGAG 60.757 60.000 0.00 0.00 0.00 2.43
5535 5896 4.457834 TCCTCATCTTCTTCCTCGTTTC 57.542 45.455 0.00 0.00 0.00 2.78
6010 6390 4.651778 ACAGCTAAGTTAACCTGCATCAA 58.348 39.130 14.56 0.00 0.00 2.57
6032 6412 9.643693 ATCAATTTGAAGGTTATCATTGTGTTC 57.356 29.630 2.68 0.00 0.00 3.18
6129 6510 3.177228 ACATCCTTACTGCTGGAAGACT 58.823 45.455 16.67 1.05 35.81 3.24
6142 6523 2.289694 TGGAAGACTGCTTAGACCTTGC 60.290 50.000 0.00 0.00 33.61 4.01
6161 6542 1.808411 CACAATGCAAGGTACTCCGT 58.192 50.000 0.00 0.00 38.49 4.69
6162 6543 1.732259 CACAATGCAAGGTACTCCGTC 59.268 52.381 0.00 0.00 38.49 4.79
6163 6544 1.623811 ACAATGCAAGGTACTCCGTCT 59.376 47.619 0.00 0.00 38.49 4.18
6164 6545 2.002586 CAATGCAAGGTACTCCGTCTG 58.997 52.381 0.00 0.00 38.49 3.51
6165 6546 1.267121 ATGCAAGGTACTCCGTCTGT 58.733 50.000 0.00 0.00 38.49 3.41
6166 6547 1.913778 TGCAAGGTACTCCGTCTGTA 58.086 50.000 0.00 0.00 38.49 2.74
6167 6548 2.241160 TGCAAGGTACTCCGTCTGTAA 58.759 47.619 0.00 0.00 38.49 2.41
6168 6549 2.629137 TGCAAGGTACTCCGTCTGTAAA 59.371 45.455 0.00 0.00 38.49 2.01
6169 6550 2.991866 GCAAGGTACTCCGTCTGTAAAC 59.008 50.000 0.00 0.00 38.49 2.01
6170 6551 3.553508 GCAAGGTACTCCGTCTGTAAACA 60.554 47.826 0.00 0.00 38.49 2.83
6171 6552 4.624015 CAAGGTACTCCGTCTGTAAACAA 58.376 43.478 0.00 0.00 38.49 2.83
6172 6553 4.942761 AGGTACTCCGTCTGTAAACAAA 57.057 40.909 0.00 0.00 39.05 2.83
6173 6554 5.479124 AGGTACTCCGTCTGTAAACAAAT 57.521 39.130 0.00 0.00 39.05 2.32
6174 6555 6.594788 AGGTACTCCGTCTGTAAACAAATA 57.405 37.500 0.00 0.00 39.05 1.40
6175 6556 7.179076 AGGTACTCCGTCTGTAAACAAATAT 57.821 36.000 0.00 0.00 39.05 1.28
6176 6557 8.297470 AGGTACTCCGTCTGTAAACAAATATA 57.703 34.615 0.00 0.00 39.05 0.86
6177 6558 8.752187 AGGTACTCCGTCTGTAAACAAATATAA 58.248 33.333 0.00 0.00 39.05 0.98
6178 6559 9.028185 GGTACTCCGTCTGTAAACAAATATAAG 57.972 37.037 0.00 0.00 0.00 1.73
6179 6560 9.793252 GTACTCCGTCTGTAAACAAATATAAGA 57.207 33.333 0.00 0.00 0.00 2.10
6180 6561 8.928270 ACTCCGTCTGTAAACAAATATAAGAG 57.072 34.615 0.00 0.00 0.00 2.85
6181 6562 7.491696 ACTCCGTCTGTAAACAAATATAAGAGC 59.508 37.037 0.00 0.00 0.00 4.09
6182 6563 6.474427 TCCGTCTGTAAACAAATATAAGAGCG 59.526 38.462 0.00 0.00 0.00 5.03
6183 6564 6.255020 CCGTCTGTAAACAAATATAAGAGCGT 59.745 38.462 0.00 0.00 0.00 5.07
6184 6565 7.201496 CCGTCTGTAAACAAATATAAGAGCGTT 60.201 37.037 0.00 0.00 0.00 4.84
6185 6566 8.166706 CGTCTGTAAACAAATATAAGAGCGTTT 58.833 33.333 0.00 0.00 0.00 3.60
6235 6616 9.841295 ACGCTTTTATATTTATTTACAGAGGGA 57.159 29.630 0.00 0.00 0.00 4.20
6245 6626 9.725206 ATTTATTTACAGAGGGAGTACTTAGGA 57.275 33.333 0.00 0.00 0.00 2.94
6246 6627 8.763984 TTATTTACAGAGGGAGTACTTAGGAG 57.236 38.462 0.00 0.00 0.00 3.69
6247 6628 6.398655 TTTACAGAGGGAGTACTTAGGAGA 57.601 41.667 0.00 0.00 0.00 3.71
6248 6629 4.513406 ACAGAGGGAGTACTTAGGAGAG 57.487 50.000 0.00 0.00 0.00 3.20
6249 6630 4.113085 ACAGAGGGAGTACTTAGGAGAGA 58.887 47.826 0.00 0.00 0.00 3.10
6250 6631 4.165372 ACAGAGGGAGTACTTAGGAGAGAG 59.835 50.000 0.00 0.00 0.00 3.20
6251 6632 3.720002 AGAGGGAGTACTTAGGAGAGAGG 59.280 52.174 0.00 0.00 0.00 3.69
6252 6633 3.460712 GAGGGAGTACTTAGGAGAGAGGT 59.539 52.174 0.00 0.00 0.00 3.85
6253 6634 3.203487 AGGGAGTACTTAGGAGAGAGGTG 59.797 52.174 0.00 0.00 0.00 4.00
6254 6635 2.953648 GGAGTACTTAGGAGAGAGGTGC 59.046 54.545 0.00 0.00 0.00 5.01
6255 6636 3.372241 GGAGTACTTAGGAGAGAGGTGCT 60.372 52.174 0.00 0.00 0.00 4.40
6256 6637 4.274978 GAGTACTTAGGAGAGAGGTGCTT 58.725 47.826 0.00 0.00 0.00 3.91
6257 6638 4.020543 AGTACTTAGGAGAGAGGTGCTTG 58.979 47.826 0.00 0.00 0.00 4.01
6258 6639 3.176924 ACTTAGGAGAGAGGTGCTTGA 57.823 47.619 0.00 0.00 0.00 3.02
6308 6701 7.855545 CATCAGTGCTTATTTGTACAGGATAC 58.144 38.462 0.00 0.00 0.00 2.24
6310 6703 7.564793 TCAGTGCTTATTTGTACAGGATACAT 58.435 34.615 0.00 0.00 41.41 2.29
6325 6718 7.006509 ACAGGATACATGCTTAATTAGGCATT 58.993 34.615 27.14 20.62 45.19 3.56
6327 6720 9.013229 CAGGATACATGCTTAATTAGGCATTTA 57.987 33.333 27.14 24.83 45.19 1.40
6328 6721 9.014297 AGGATACATGCTTAATTAGGCATTTAC 57.986 33.333 27.14 19.01 45.19 2.01
6329 6722 9.014297 GGATACATGCTTAATTAGGCATTTACT 57.986 33.333 27.14 16.50 45.19 2.24
6333 6726 9.627123 ACATGCTTAATTAGGCATTTACTCTAA 57.373 29.630 27.14 2.38 45.19 2.10
6342 6735 9.640952 ATTAGGCATTTACTCTAAAAATAGGCA 57.359 29.630 0.00 0.00 0.00 4.75
6343 6736 7.334844 AGGCATTTACTCTAAAAATAGGCAC 57.665 36.000 0.00 0.00 0.00 5.01
6344 6737 6.321435 AGGCATTTACTCTAAAAATAGGCACC 59.679 38.462 0.00 0.00 0.00 5.01
6345 6738 6.321435 GGCATTTACTCTAAAAATAGGCACCT 59.679 38.462 0.00 0.00 0.00 4.00
6350 6743 5.631119 ACTCTAAAAATAGGCACCTGTGTT 58.369 37.500 0.00 0.00 0.00 3.32
6358 6751 6.575162 AATAGGCACCTGTGTTTTAGAAAG 57.425 37.500 0.00 0.00 0.00 2.62
6360 6753 4.729868 AGGCACCTGTGTTTTAGAAAGAT 58.270 39.130 0.00 0.00 0.00 2.40
6361 6754 4.762251 AGGCACCTGTGTTTTAGAAAGATC 59.238 41.667 0.00 0.00 0.00 2.75
6367 6760 6.371825 ACCTGTGTTTTAGAAAGATCCGATTC 59.628 38.462 0.00 0.00 0.00 2.52
6386 6779 5.352569 CGATTCATTTTTCTGAGCACCTAGT 59.647 40.000 0.00 0.00 0.00 2.57
6394 6787 6.599356 TTTCTGAGCACCTAGTATTGTACA 57.401 37.500 0.00 0.00 0.00 2.90
6398 6791 6.210784 TCTGAGCACCTAGTATTGTACAAAGT 59.789 38.462 13.23 7.70 0.00 2.66
6425 6818 8.223100 CCTATAGCAATTCAAAAACAGCAAAAC 58.777 33.333 0.00 0.00 0.00 2.43
6429 6822 5.512434 GCAATTCAAAAACAGCAAAACCAAG 59.488 36.000 0.00 0.00 0.00 3.61
6430 6823 4.676849 TTCAAAAACAGCAAAACCAAGC 57.323 36.364 0.00 0.00 0.00 4.01
6462 6855 8.595533 GTTTTCTTTCTCAACAATCCAGAAAAC 58.404 33.333 15.17 15.17 45.33 2.43
6468 6861 5.417266 TCTCAACAATCCAGAAAACACAACA 59.583 36.000 0.00 0.00 0.00 3.33
6477 6870 4.434067 CCAGAAAACACAACAAACGCAAAG 60.434 41.667 0.00 0.00 0.00 2.77
6479 6872 4.384547 AGAAAACACAACAAACGCAAAGTC 59.615 37.500 0.00 0.00 0.00 3.01
6480 6873 3.569250 AACACAACAAACGCAAAGTCT 57.431 38.095 0.00 0.00 0.00 3.24
6481 6874 3.569250 ACACAACAAACGCAAAGTCTT 57.431 38.095 0.00 0.00 0.00 3.01
6482 6875 3.241701 ACACAACAAACGCAAAGTCTTG 58.758 40.909 0.00 0.00 35.49 3.02
6496 6889 5.222631 CAAAGTCTTGCCAGTTTACAATCC 58.777 41.667 0.00 0.00 0.00 3.01
6498 6891 5.499004 AGTCTTGCCAGTTTACAATCCTA 57.501 39.130 0.00 0.00 0.00 2.94
6509 6914 2.789409 ACAATCCTAGGTGACAAGGC 57.211 50.000 9.08 0.00 32.55 4.35
6530 6935 3.732471 GCAAAAAGCACCGCCGATATTTA 60.732 43.478 0.00 0.00 44.79 1.40
6534 6939 2.210116 AGCACCGCCGATATTTACTTG 58.790 47.619 0.00 0.00 0.00 3.16
6553 6958 0.041312 GTGCGAACATGTTGAAGCGT 60.041 50.000 17.58 0.00 0.00 5.07
6682 7087 9.369904 GCAAAGCAATTATCCAAAGAAGAAATA 57.630 29.630 0.00 0.00 0.00 1.40
6708 7116 1.128507 CAAAAGAGAAGCGCACGCATA 59.871 47.619 18.24 0.00 44.88 3.14
6713 7121 0.103026 AGAAGCGCACGCATATCTGA 59.897 50.000 18.24 0.00 44.88 3.27
6829 7237 3.135994 ACATTCGACACCAAACTACCAC 58.864 45.455 0.00 0.00 0.00 4.16
6836 7244 0.920438 ACCAAACTACCACCACCACA 59.080 50.000 0.00 0.00 0.00 4.17
6837 7245 1.314730 CCAAACTACCACCACCACAC 58.685 55.000 0.00 0.00 0.00 3.82
6838 7246 1.314730 CAAACTACCACCACCACACC 58.685 55.000 0.00 0.00 0.00 4.16
6839 7247 0.920438 AAACTACCACCACCACACCA 59.080 50.000 0.00 0.00 0.00 4.17
6840 7248 0.181824 AACTACCACCACCACACCAC 59.818 55.000 0.00 0.00 0.00 4.16
6841 7249 1.072505 CTACCACCACCACACCACC 59.927 63.158 0.00 0.00 0.00 4.61
6842 7250 1.693103 TACCACCACCACACCACCA 60.693 57.895 0.00 0.00 0.00 4.17
6843 7251 1.701031 TACCACCACCACACCACCAG 61.701 60.000 0.00 0.00 0.00 4.00
6844 7252 2.906897 CACCACCACACCACCAGC 60.907 66.667 0.00 0.00 0.00 4.85
6865 7289 0.669625 AACAAGCCGCTACGAGGAAC 60.670 55.000 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.922447 AGATAGGACCATGGCCAACAA 59.078 47.619 22.33 9.05 0.00 2.83
1 2 1.595311 AGATAGGACCATGGCCAACA 58.405 50.000 22.33 10.74 0.00 3.33
2 3 3.584848 AGATAGATAGGACCATGGCCAAC 59.415 47.826 22.33 14.30 0.00 3.77
3 4 3.874316 AGATAGATAGGACCATGGCCAA 58.126 45.455 22.33 0.00 0.00 4.52
4 5 3.567375 AGATAGATAGGACCATGGCCA 57.433 47.619 22.33 8.56 0.00 5.36
5 6 5.463154 AGATAGATAGATAGGACCATGGCC 58.537 45.833 13.04 14.36 0.00 5.36
6 7 7.782644 ACTAAGATAGATAGATAGGACCATGGC 59.217 40.741 13.04 4.47 0.00 4.40
63 64 0.453282 CAAATGACGAAGCCTGCGTG 60.453 55.000 0.30 0.00 42.77 5.34
180 181 6.677781 ATAATACAACCAATCAACCACTCG 57.322 37.500 0.00 0.00 0.00 4.18
231 232 4.769688 ACACACTTCAGTTGAGATCACAA 58.230 39.130 1.02 1.02 0.00 3.33
296 297 0.394352 AGAATCCCCAATCCGCACAC 60.394 55.000 0.00 0.00 0.00 3.82
317 318 3.354467 TCCATAATTCACACTGCATGCA 58.646 40.909 21.29 21.29 0.00 3.96
319 320 5.509716 ACATCCATAATTCACACTGCATG 57.490 39.130 0.00 0.00 0.00 4.06
321 322 5.981088 AAACATCCATAATTCACACTGCA 57.019 34.783 0.00 0.00 0.00 4.41
348 349 0.516877 TGATCTTTTTCCTGCGTGCG 59.483 50.000 0.00 0.00 0.00 5.34
351 352 3.126001 TCAGTGATCTTTTTCCTGCGT 57.874 42.857 0.00 0.00 0.00 5.24
366 367 8.204160 TGTCACTATATGGAAAGGTTATCAGTG 58.796 37.037 0.00 0.00 0.00 3.66
488 495 8.477256 CATCATAAGCCAATTTTTAAGAAGGGA 58.523 33.333 4.07 0.00 0.00 4.20
489 496 8.260114 ACATCATAAGCCAATTTTTAAGAAGGG 58.740 33.333 0.00 0.00 0.00 3.95
578 585 7.733402 ACTCCAATAGCGTAAGTTTTTGTAA 57.267 32.000 0.00 0.00 37.69 2.41
591 598 4.319766 GCATGTATCCAAACTCCAATAGCG 60.320 45.833 0.00 0.00 0.00 4.26
621 628 4.072131 GGTTTCCTACAATGAGCTGACAA 58.928 43.478 0.00 0.00 0.00 3.18
674 681 3.555956 CACCGTTGTCACTATATGGAAGC 59.444 47.826 0.00 0.00 0.00 3.86
1167 1194 3.470709 AGAATGACACCACTGACACTTG 58.529 45.455 0.00 0.00 0.00 3.16
1435 1462 5.750524 TCATGTGGGCAAAATAAGTAGCTA 58.249 37.500 0.00 0.00 0.00 3.32
1450 1477 2.260844 ACACAAGACACTCATGTGGG 57.739 50.000 11.20 0.00 46.72 4.61
1523 1550 5.594317 GGAGCTTTATCCTCCTGCAAAATAA 59.406 40.000 0.00 0.00 44.40 1.40
1544 1571 4.618489 GTGAAATCTGCACAAATTTCGGAG 59.382 41.667 14.80 0.00 42.27 4.63
1755 1782 4.955450 CCAGATCCAGAAAAGAGAGAGAGA 59.045 45.833 0.00 0.00 0.00 3.10
1756 1783 4.099881 CCCAGATCCAGAAAAGAGAGAGAG 59.900 50.000 0.00 0.00 0.00 3.20
1757 1784 4.029520 CCCAGATCCAGAAAAGAGAGAGA 58.970 47.826 0.00 0.00 0.00 3.10
1758 1785 3.774216 ACCCAGATCCAGAAAAGAGAGAG 59.226 47.826 0.00 0.00 0.00 3.20
1811 1838 6.708285 TGGAAAATGAGGAAGGTCTAGTAAC 58.292 40.000 0.00 0.00 0.00 2.50
1944 1972 9.184523 TCTCCCAACCTAACATAACAAAATATG 57.815 33.333 0.00 0.00 38.86 1.78
2491 2519 1.891150 CTTTGGCATTCAGCTTCCAGT 59.109 47.619 0.00 0.00 44.79 4.00
2587 2615 3.330110 CTCCATAATCTCTGCCCATTCCT 59.670 47.826 0.00 0.00 0.00 3.36
3140 3168 3.004734 GCTTCAGAAGGCAAACAAGCTAA 59.995 43.478 12.30 0.00 34.64 3.09
3166 3194 0.457166 CAACAGCATTGTCATGGCCG 60.457 55.000 0.00 0.00 36.23 6.13
3447 3475 4.276678 CAGAAACTTCAACCATCTTGCTCA 59.723 41.667 0.00 0.00 0.00 4.26
3448 3476 4.516698 TCAGAAACTTCAACCATCTTGCTC 59.483 41.667 0.00 0.00 0.00 4.26
3613 3641 6.715718 CAGAAAGCCCATCATAATCAGAAGAT 59.284 38.462 0.00 0.00 35.53 2.40
4046 4074 6.595716 AGATTTTTCTCCATCTCACTAAACCG 59.404 38.462 0.00 0.00 0.00 4.44
4069 4097 3.840666 ACTTGGATGTAAGCTCTTCCAGA 59.159 43.478 9.23 2.92 40.81 3.86
4263 4291 5.425217 TCTTTGTATCTGGCTAAGTCATCCA 59.575 40.000 0.00 0.00 0.00 3.41
4466 4507 4.016444 TGTGTGTTTGAGAAAAGGAGCTT 58.984 39.130 0.00 0.00 0.00 3.74
4521 4563 3.609853 AGAGGCTGCGTCAATTAATTCA 58.390 40.909 22.55 0.00 0.00 2.57
4547 4638 7.490962 TGTCAACTGAATTAATTGTCGAAGT 57.509 32.000 5.17 0.00 0.00 3.01
4584 4675 4.211374 CCTCCGATCCGAATTAATTGACAC 59.789 45.833 5.17 0.00 0.00 3.67
4585 4676 4.377021 CCTCCGATCCGAATTAATTGACA 58.623 43.478 5.17 0.00 0.00 3.58
4744 4837 8.885494 ACAGTATAGTACAACGTTACCAAAAA 57.115 30.769 0.00 0.00 0.00 1.94
5106 5464 9.801873 TTTTGTAAGTCTTGAATTTCCAGAAAG 57.198 29.630 2.01 0.00 33.32 2.62
5180 5538 1.091771 TTTCTGCTGCAGCCGCTATC 61.092 55.000 34.64 7.29 41.18 2.08
5344 5705 0.392461 TGGTTTCTGGGCATACTCGC 60.392 55.000 0.00 0.00 0.00 5.03
5535 5896 0.323629 TTCTCGGGCAACTGGTTAGG 59.676 55.000 0.00 0.00 45.79 2.69
5664 6025 0.107214 ATGACCCGCATTCATCCGTT 60.107 50.000 0.00 0.00 31.73 4.44
6129 6510 1.541147 GCATTGTGCAAGGTCTAAGCA 59.459 47.619 0.00 0.00 44.26 3.91
6142 6523 1.808411 ACGGAGTACCTTGCATTGTG 58.192 50.000 0.00 0.00 41.94 3.33
6156 6537 7.306051 CGCTCTTATATTTGTTTACAGACGGAG 60.306 40.741 0.00 0.00 0.00 4.63
6158 6539 6.255020 ACGCTCTTATATTTGTTTACAGACGG 59.745 38.462 0.00 0.00 0.00 4.79
6159 6540 7.218145 ACGCTCTTATATTTGTTTACAGACG 57.782 36.000 0.00 0.00 0.00 4.18
6209 6590 9.841295 TCCCTCTGTAAATAAATATAAAAGCGT 57.159 29.630 0.00 0.00 0.00 5.07
6219 6600 9.725206 TCCTAAGTACTCCCTCTGTAAATAAAT 57.275 33.333 0.00 0.00 0.00 1.40
6220 6601 9.198475 CTCCTAAGTACTCCCTCTGTAAATAAA 57.802 37.037 0.00 0.00 0.00 1.40
6221 6602 8.563502 TCTCCTAAGTACTCCCTCTGTAAATAA 58.436 37.037 0.00 0.00 0.00 1.40
6222 6603 8.110743 TCTCCTAAGTACTCCCTCTGTAAATA 57.889 38.462 0.00 0.00 0.00 1.40
6223 6604 6.982899 TCTCCTAAGTACTCCCTCTGTAAAT 58.017 40.000 0.00 0.00 0.00 1.40
6224 6605 6.217074 TCTCTCCTAAGTACTCCCTCTGTAAA 59.783 42.308 0.00 0.00 0.00 2.01
6225 6606 5.730207 TCTCTCCTAAGTACTCCCTCTGTAA 59.270 44.000 0.00 0.00 0.00 2.41
6226 6607 5.287042 TCTCTCCTAAGTACTCCCTCTGTA 58.713 45.833 0.00 0.00 0.00 2.74
6227 6608 4.113085 TCTCTCCTAAGTACTCCCTCTGT 58.887 47.826 0.00 0.00 0.00 3.41
6228 6609 4.445735 CCTCTCTCCTAAGTACTCCCTCTG 60.446 54.167 0.00 0.00 0.00 3.35
6229 6610 3.720002 CCTCTCTCCTAAGTACTCCCTCT 59.280 52.174 0.00 0.00 0.00 3.69
6230 6611 3.460712 ACCTCTCTCCTAAGTACTCCCTC 59.539 52.174 0.00 0.00 0.00 4.30
6231 6612 3.203487 CACCTCTCTCCTAAGTACTCCCT 59.797 52.174 0.00 0.00 0.00 4.20
6232 6613 3.558033 CACCTCTCTCCTAAGTACTCCC 58.442 54.545 0.00 0.00 0.00 4.30
6233 6614 2.953648 GCACCTCTCTCCTAAGTACTCC 59.046 54.545 0.00 0.00 0.00 3.85
6234 6615 3.893521 AGCACCTCTCTCCTAAGTACTC 58.106 50.000 0.00 0.00 0.00 2.59
6235 6616 4.020543 CAAGCACCTCTCTCCTAAGTACT 58.979 47.826 0.00 0.00 0.00 2.73
6236 6617 4.017808 TCAAGCACCTCTCTCCTAAGTAC 58.982 47.826 0.00 0.00 0.00 2.73
6237 6618 4.317530 TCAAGCACCTCTCTCCTAAGTA 57.682 45.455 0.00 0.00 0.00 2.24
6238 6619 3.176924 TCAAGCACCTCTCTCCTAAGT 57.823 47.619 0.00 0.00 0.00 2.24
6239 6620 3.766591 TCTTCAAGCACCTCTCTCCTAAG 59.233 47.826 0.00 0.00 0.00 2.18
6240 6621 3.779444 TCTTCAAGCACCTCTCTCCTAA 58.221 45.455 0.00 0.00 0.00 2.69
6241 6622 3.458044 TCTTCAAGCACCTCTCTCCTA 57.542 47.619 0.00 0.00 0.00 2.94
6242 6623 2.317371 TCTTCAAGCACCTCTCTCCT 57.683 50.000 0.00 0.00 0.00 3.69
6243 6624 3.409026 TTTCTTCAAGCACCTCTCTCC 57.591 47.619 0.00 0.00 0.00 3.71
6244 6625 7.335422 TGATTTATTTCTTCAAGCACCTCTCTC 59.665 37.037 0.00 0.00 0.00 3.20
6245 6626 7.170965 TGATTTATTTCTTCAAGCACCTCTCT 58.829 34.615 0.00 0.00 0.00 3.10
6246 6627 7.383102 TGATTTATTTCTTCAAGCACCTCTC 57.617 36.000 0.00 0.00 0.00 3.20
6247 6628 6.376581 CCTGATTTATTTCTTCAAGCACCTCT 59.623 38.462 0.00 0.00 0.00 3.69
6248 6629 6.151817 ACCTGATTTATTTCTTCAAGCACCTC 59.848 38.462 0.00 0.00 0.00 3.85
6249 6630 6.012745 ACCTGATTTATTTCTTCAAGCACCT 58.987 36.000 0.00 0.00 0.00 4.00
6250 6631 6.272822 ACCTGATTTATTTCTTCAAGCACC 57.727 37.500 0.00 0.00 0.00 5.01
6251 6632 8.593492 AAAACCTGATTTATTTCTTCAAGCAC 57.407 30.769 0.00 0.00 0.00 4.40
6252 6633 8.641541 AGAAAACCTGATTTATTTCTTCAAGCA 58.358 29.630 0.00 0.00 38.59 3.91
6253 6634 9.481340 AAGAAAACCTGATTTATTTCTTCAAGC 57.519 29.630 6.54 0.00 44.51 4.01
6285 6666 6.941857 TGTATCCTGTACAAATAAGCACTGA 58.058 36.000 0.00 0.00 0.00 3.41
6287 6668 6.260936 GCATGTATCCTGTACAAATAAGCACT 59.739 38.462 0.00 0.00 0.00 4.40
6320 6713 6.321435 AGGTGCCTATTTTTAGAGTAAATGCC 59.679 38.462 0.00 0.00 0.00 4.40
6325 6718 6.775708 ACACAGGTGCCTATTTTTAGAGTAA 58.224 36.000 0.00 0.00 0.00 2.24
6327 6720 5.242795 ACACAGGTGCCTATTTTTAGAGT 57.757 39.130 0.00 0.00 0.00 3.24
6328 6721 6.575162 AAACACAGGTGCCTATTTTTAGAG 57.425 37.500 0.00 0.00 0.00 2.43
6329 6722 6.969993 AAAACACAGGTGCCTATTTTTAGA 57.030 33.333 0.00 0.00 0.00 2.10
6332 6725 6.969993 TCTAAAACACAGGTGCCTATTTTT 57.030 33.333 0.00 9.16 0.00 1.94
6333 6726 6.969993 TTCTAAAACACAGGTGCCTATTTT 57.030 33.333 0.00 2.15 0.00 1.82
6335 6728 6.303839 TCTTTCTAAAACACAGGTGCCTATT 58.696 36.000 0.00 0.00 0.00 1.73
6337 6730 5.298989 TCTTTCTAAAACACAGGTGCCTA 57.701 39.130 0.00 0.00 0.00 3.93
6338 6731 4.164843 TCTTTCTAAAACACAGGTGCCT 57.835 40.909 0.00 0.00 0.00 4.75
6339 6732 4.082733 GGATCTTTCTAAAACACAGGTGCC 60.083 45.833 0.00 0.00 0.00 5.01
6340 6733 4.378459 CGGATCTTTCTAAAACACAGGTGC 60.378 45.833 0.00 0.00 0.00 5.01
6341 6734 4.994852 TCGGATCTTTCTAAAACACAGGTG 59.005 41.667 0.00 0.00 0.00 4.00
6342 6735 5.223449 TCGGATCTTTCTAAAACACAGGT 57.777 39.130 0.00 0.00 0.00 4.00
6343 6736 6.371548 TGAATCGGATCTTTCTAAAACACAGG 59.628 38.462 0.00 0.00 0.00 4.00
6344 6737 7.364522 TGAATCGGATCTTTCTAAAACACAG 57.635 36.000 0.00 0.00 0.00 3.66
6345 6738 7.921786 ATGAATCGGATCTTTCTAAAACACA 57.078 32.000 0.00 0.00 0.00 3.72
6358 6751 5.269313 GTGCTCAGAAAAATGAATCGGATC 58.731 41.667 0.00 0.00 0.00 3.36
6360 6753 3.440173 GGTGCTCAGAAAAATGAATCGGA 59.560 43.478 0.00 0.00 0.00 4.55
6361 6754 3.441572 AGGTGCTCAGAAAAATGAATCGG 59.558 43.478 0.00 0.00 0.00 4.18
6367 6760 7.383102 ACAATACTAGGTGCTCAGAAAAATG 57.617 36.000 0.00 0.00 0.00 2.32
6376 6769 5.811100 GGACTTTGTACAATACTAGGTGCTC 59.189 44.000 9.56 0.00 31.90 4.26
6394 6787 7.814587 GCTGTTTTTGAATTGCTATAGGACTTT 59.185 33.333 1.04 0.00 0.00 2.66
6398 6791 6.832520 TGCTGTTTTTGAATTGCTATAGGA 57.167 33.333 1.04 0.00 0.00 2.94
6425 6818 2.814336 AGAAAGAAAACTAGGCGCTTGG 59.186 45.455 7.64 3.66 0.00 3.61
6429 6822 3.250040 TGTTGAGAAAGAAAACTAGGCGC 59.750 43.478 0.00 0.00 0.00 6.53
6430 6823 5.418310 TTGTTGAGAAAGAAAACTAGGCG 57.582 39.130 0.00 0.00 0.00 5.52
6462 6855 3.887069 CAAGACTTTGCGTTTGTTGTG 57.113 42.857 0.00 0.00 0.00 3.33
6477 6870 4.636206 CCTAGGATTGTAAACTGGCAAGAC 59.364 45.833 1.05 0.00 0.00 3.01
6479 6872 4.396166 CACCTAGGATTGTAAACTGGCAAG 59.604 45.833 17.98 0.00 0.00 4.01
6480 6873 4.042311 TCACCTAGGATTGTAAACTGGCAA 59.958 41.667 17.98 0.00 0.00 4.52
6481 6874 3.585289 TCACCTAGGATTGTAAACTGGCA 59.415 43.478 17.98 0.00 0.00 4.92
6482 6875 3.939592 GTCACCTAGGATTGTAAACTGGC 59.060 47.826 17.98 0.00 0.00 4.85
6483 6876 5.160607 TGTCACCTAGGATTGTAAACTGG 57.839 43.478 17.98 0.00 0.00 4.00
6485 6878 5.803470 GCCTTGTCACCTAGGATTGTAAACT 60.803 44.000 17.98 0.00 35.83 2.66
6486 6879 4.395231 GCCTTGTCACCTAGGATTGTAAAC 59.605 45.833 17.98 0.00 35.83 2.01
6487 6880 4.042311 TGCCTTGTCACCTAGGATTGTAAA 59.958 41.667 17.98 2.98 35.83 2.01
6488 6881 3.585289 TGCCTTGTCACCTAGGATTGTAA 59.415 43.478 17.98 4.07 35.83 2.41
6490 6883 1.985159 TGCCTTGTCACCTAGGATTGT 59.015 47.619 17.98 0.00 35.83 2.71
6491 6884 2.787473 TGCCTTGTCACCTAGGATTG 57.213 50.000 17.98 4.10 35.83 2.67
6492 6885 3.806949 TTTGCCTTGTCACCTAGGATT 57.193 42.857 17.98 0.00 35.83 3.01
6493 6886 3.806949 TTTTGCCTTGTCACCTAGGAT 57.193 42.857 17.98 0.00 35.83 3.24
6494 6887 3.486383 CTTTTTGCCTTGTCACCTAGGA 58.514 45.455 17.98 0.00 35.83 2.94
6495 6888 2.029918 GCTTTTTGCCTTGTCACCTAGG 60.030 50.000 7.41 7.41 36.75 3.02
6496 6889 2.622942 TGCTTTTTGCCTTGTCACCTAG 59.377 45.455 0.00 0.00 42.00 3.02
6498 6891 1.136891 GTGCTTTTTGCCTTGTCACCT 59.863 47.619 0.00 0.00 42.00 4.00
6509 6914 2.559998 AATATCGGCGGTGCTTTTTG 57.440 45.000 7.21 0.00 0.00 2.44
6522 6927 5.795766 ACATGTTCGCACAAGTAAATATCG 58.204 37.500 0.00 0.00 33.01 2.92
6523 6928 7.240674 TCAACATGTTCGCACAAGTAAATATC 58.759 34.615 8.48 0.00 33.66 1.63
6530 6935 2.541588 GCTTCAACATGTTCGCACAAGT 60.542 45.455 8.48 0.00 36.37 3.16
6534 6939 0.041312 ACGCTTCAACATGTTCGCAC 60.041 50.000 8.48 0.00 0.00 5.34
6553 6958 3.640498 TGAAACTGCCAAATTGGTGATGA 59.360 39.130 14.17 0.00 40.46 2.92
6609 7014 2.143925 GCCAGTGGTGTTGTTCTAGAC 58.856 52.381 11.74 0.00 0.00 2.59
6614 7019 0.318955 GCATGCCAGTGGTGTTGTTC 60.319 55.000 11.74 0.00 0.00 3.18
6648 7053 5.260424 TGGATAATTGCTTTGCTCTGGTTA 58.740 37.500 0.00 0.00 0.00 2.85
6682 7087 1.576421 CGCTTCTCTTTTGCGGCTT 59.424 52.632 0.00 0.00 45.07 4.35
6708 7116 4.651045 GCCCCTTTTAATCCAATGTCAGAT 59.349 41.667 0.00 0.00 0.00 2.90
6713 7121 3.515562 TGTGCCCCTTTTAATCCAATGT 58.484 40.909 0.00 0.00 0.00 2.71
6829 7237 1.756172 TTTGCTGGTGGTGTGGTGG 60.756 57.895 0.00 0.00 0.00 4.61
6836 7244 2.489275 CGGCTTGTTTGCTGGTGGT 61.489 57.895 0.00 0.00 35.80 4.16
6837 7245 2.336088 CGGCTTGTTTGCTGGTGG 59.664 61.111 0.00 0.00 35.80 4.61
6838 7246 2.355009 GCGGCTTGTTTGCTGGTG 60.355 61.111 0.00 0.00 39.56 4.17
6839 7247 2.519302 AGCGGCTTGTTTGCTGGT 60.519 55.556 0.00 0.00 44.09 4.00
6840 7248 1.210155 GTAGCGGCTTGTTTGCTGG 59.790 57.895 8.26 0.00 39.73 4.85
6841 7249 1.154413 CGTAGCGGCTTGTTTGCTG 60.154 57.895 8.26 0.00 39.73 4.41
6842 7250 1.291877 CTCGTAGCGGCTTGTTTGCT 61.292 55.000 8.26 0.00 42.58 3.91
6843 7251 1.132640 CTCGTAGCGGCTTGTTTGC 59.867 57.895 8.26 0.00 0.00 3.68
6844 7252 0.669318 TCCTCGTAGCGGCTTGTTTG 60.669 55.000 8.26 0.00 28.70 2.93
6924 7348 3.118454 GTCACCGCCATGGACGTG 61.118 66.667 18.40 19.60 42.00 4.49
6957 7381 1.511305 CGTCACCTACACGGAGCAT 59.489 57.895 0.00 0.00 36.31 3.79


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

AutoCloner maintained by Alex Coulton.