Multiple sequence alignment - TraesCS4D01G234900

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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 TraesCS4D01G234900 chr4D 100.000 4132 0 0 1 4132 395372659 395376790 0.000000e+00 7631.0
1 TraesCS4D01G234900 chr4D 100.000 2684 0 0 4269 6952 395376927 395379610 0.000000e+00 4957.0
2 TraesCS4D01G234900 chr4D 100.000 2269 0 0 7254 9522 395379912 395382180 0.000000e+00 4191.0
3 TraesCS4D01G234900 chr4D 98.958 96 0 1 6857 6952 333841113 333841019 4.570000e-38 171.0
4 TraesCS4D01G234900 chr4D 98.936 94 0 1 6859 6952 18320762 18320854 5.910000e-37 167.0
5 TraesCS4D01G234900 chr4D 80.423 189 29 7 9326 9510 7897618 7897802 4.640000e-28 137.0
6 TraesCS4D01G234900 chr4B 93.225 3749 168 38 441 4129 486274892 486278614 0.000000e+00 5437.0
7 TraesCS4D01G234900 chr4B 95.156 1734 43 14 5110 6828 486280065 486281772 0.000000e+00 2699.0
8 TraesCS4D01G234900 chr4B 94.488 1524 52 16 7254 8751 486282082 486283599 0.000000e+00 2320.0
9 TraesCS4D01G234900 chr4B 93.766 786 33 6 8749 9522 486283681 486284462 0.000000e+00 1166.0
10 TraesCS4D01G234900 chr4B 95.064 547 18 4 4434 4975 486279151 486279693 0.000000e+00 852.0
11 TraesCS4D01G234900 chr4B 94.131 426 18 6 1 423 486271659 486272080 8.060000e-180 641.0
12 TraesCS4D01G234900 chr4B 95.000 140 3 2 427 564 486274176 486274313 5.790000e-52 217.0
13 TraesCS4D01G234900 chr4B 92.086 139 8 1 4974 5112 486279817 486279952 9.760000e-45 193.0
14 TraesCS4D01G234900 chr4B 81.915 188 28 5 9326 9510 14267366 14267182 4.600000e-33 154.0
15 TraesCS4D01G234900 chr4B 93.056 72 4 1 639 709 486274821 486274892 4.700000e-18 104.0
16 TraesCS4D01G234900 chr4B 95.122 41 1 1 6830 6870 486281803 486281842 7.980000e-06 63.9
17 TraesCS4D01G234900 chr4A 91.434 3899 212 48 307 4129 76932742 76936594 0.000000e+00 5238.0
18 TraesCS4D01G234900 chr4A 93.935 2539 107 22 4307 6825 76936718 76939229 0.000000e+00 3792.0
19 TraesCS4D01G234900 chr4A 93.837 2304 86 24 7254 9522 76939565 76941847 0.000000e+00 3417.0
20 TraesCS4D01G234900 chr4A 94.719 303 14 2 1 303 76932270 76932570 4.030000e-128 470.0
21 TraesCS4D01G234900 chr4A 81.283 187 31 3 9326 9510 595418758 595418574 2.140000e-31 148.0
22 TraesCS4D01G234900 chr4A 95.238 42 1 1 6829 6870 76939262 76939302 2.220000e-06 65.8
23 TraesCS4D01G234900 chrUn 98.936 94 0 1 6859 6952 424751017 424750925 5.910000e-37 167.0
24 TraesCS4D01G234900 chr6D 98.936 94 0 1 6859 6952 389248513 389248605 5.910000e-37 167.0
25 TraesCS4D01G234900 chr6D 89.535 86 7 1 7457 7540 90111902 90111817 3.640000e-19 108.0
26 TraesCS4D01G234900 chr6A 98.936 94 0 1 6859 6952 608869614 608869522 5.910000e-37 167.0
27 TraesCS4D01G234900 chr5D 98.936 94 0 1 6859 6952 432331756 432331848 5.910000e-37 167.0
28 TraesCS4D01G234900 chr5D 89.655 87 7 1 7457 7541 442203812 442203726 1.010000e-19 110.0
29 TraesCS4D01G234900 chr5D 77.236 123 23 5 4903 5023 302878523 302878404 6.170000e-07 67.6
30 TraesCS4D01G234900 chr1D 98.936 94 0 1 6859 6952 176205879 176205971 5.910000e-37 167.0
31 TraesCS4D01G234900 chr1D 95.556 90 4 0 692 781 22889004 22888915 2.770000e-30 145.0
32 TraesCS4D01G234900 chr1D 95.506 89 3 1 693 781 22871574 22871487 3.590000e-29 141.0
33 TraesCS4D01G234900 chr1D 90.110 91 3 6 7454 7540 279101464 279101376 7.820000e-21 113.0
34 TraesCS4D01G234900 chr1B 98.936 94 0 1 6859 6952 89597380 89597288 5.910000e-37 167.0
35 TraesCS4D01G234900 chr1B 98.936 94 0 1 6859 6952 633745274 633745182 5.910000e-37 167.0
36 TraesCS4D01G234900 chr1B 95.604 91 3 1 693 782 38911785 38911875 2.770000e-30 145.0
37 TraesCS4D01G234900 chr1B 87.912 91 4 7 7454 7540 378835816 378835729 6.080000e-17 100.0
38 TraesCS4D01G234900 chr5B 95.604 91 3 1 693 783 70271997 70272086 2.770000e-30 145.0
39 TraesCS4D01G234900 chr1A 96.591 88 2 1 693 780 24303432 24303346 2.770000e-30 145.0
40 TraesCS4D01G234900 chr1A 95.556 90 3 1 693 781 23905648 23905559 9.970000e-30 143.0
41 TraesCS4D01G234900 chr2D 92.079 101 5 2 693 791 313227919 313228018 1.290000e-28 139.0
42 TraesCS4D01G234900 chr3D 93.023 86 4 1 7457 7540 45931418 45931333 3.610000e-24 124.0
43 TraesCS4D01G234900 chr7D 89.362 94 8 1 7449 7540 234807762 234807855 6.040000e-22 117.0
44 TraesCS4D01G234900 chr3B 88.764 89 6 3 7458 7544 481625314 481625400 1.310000e-18 106.0


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 TraesCS4D01G234900 chr4D 395372659 395382180 9521 False 5593.00 7631 100.0000 1 9522 3 chr4D.!!$F3 9521
1 TraesCS4D01G234900 chr4B 486271659 486284462 12803 False 1369.29 5437 94.1094 1 9522 10 chr4B.!!$F1 9521
2 TraesCS4D01G234900 chr4A 76932270 76941847 9577 False 2596.56 5238 93.8326 1 9522 5 chr4A.!!$F1 9521

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
875 3864 0.962356 CCACGCCATTTGCTCCTCTT 60.962 55.000 0.00 0.0 38.05 2.85 F
1326 4334 0.105964 AGCACCTTCGTGTAGTTGCA 59.894 50.000 7.07 0.0 42.39 4.08 F
1525 4539 0.608640 AAGGACCGTCAGTGGATCAC 59.391 55.000 0.00 0.0 34.10 3.06 F
1549 4563 1.071699 CCCCGGATTCCGTTGTATGAT 59.928 52.381 22.83 0.0 46.80 2.45 F
1570 4584 1.127567 ACAGCTTGCCCTCAGGTGTA 61.128 55.000 3.02 0.0 41.62 2.90 F
2485 5522 1.889829 GCTCTGTCACTGGTGAGTAGT 59.110 52.381 3.47 0.0 40.75 2.73 F
3781 6851 1.762957 TCCTTCGGAGAATTGCCCTAG 59.237 52.381 0.00 0.0 45.90 3.02 F
4029 7100 1.204704 CTGACATGTAGCGTTCTCCCA 59.795 52.381 0.00 0.0 0.00 4.37 F
5002 8440 1.707427 AGCAGTGACCCTCTTGGAAAT 59.293 47.619 0.00 0.0 38.00 2.17 F
5189 8742 2.198827 ATCCTGCACATTTGTCCGAA 57.801 45.000 0.00 0.0 0.00 4.30 F
6272 9839 2.450609 TACCTTCTGAAAGTGTCGCC 57.549 50.000 1.96 0.0 33.76 5.54 F
6916 10514 0.394938 TGCGGTTAGGCACTCTTCAA 59.605 50.000 0.00 0.0 41.75 2.69 F
6917 10515 1.202710 TGCGGTTAGGCACTCTTCAAA 60.203 47.619 0.00 0.0 41.75 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2545 5590 0.608035 ACCCATAACTGCAACACCCG 60.608 55.000 0.00 0.00 0.00 5.28 R
3264 6321 3.282021 AGCTGCAGAGAAAACTTGACAA 58.718 40.909 20.43 0.00 0.00 3.18 R
3269 6326 4.036144 GTCAAGAAGCTGCAGAGAAAACTT 59.964 41.667 20.43 9.95 0.00 2.66 R
3398 6456 5.489249 AGCTCATGCATATAGATCACCAAG 58.511 41.667 11.45 0.00 42.74 3.61 R
3563 6623 5.917462 AGTGCCAAATGATTATTAAAGGCC 58.083 37.500 14.55 0.00 37.72 5.19 R
3986 7057 2.103153 AGGTGAACTTGGAGAGGACA 57.897 50.000 0.00 0.00 0.00 4.02 R
4702 8015 1.272592 TGATCCAGGCCATCTTTTGCA 60.273 47.619 5.01 0.00 0.00 4.08 R
5046 8484 1.953686 GGCACCACAAGAAAAGCACTA 59.046 47.619 0.00 0.00 0.00 2.74 R
6894 10492 0.392998 AAGAGTGCCTAACCGCATGG 60.393 55.000 0.00 0.00 41.70 3.66 R
6896 10494 0.613260 TGAAGAGTGCCTAACCGCAT 59.387 50.000 0.00 0.00 41.70 4.73 R
7804 11421 3.862267 CGACTTCATCCACTGATCTCAAC 59.138 47.826 0.00 0.00 32.72 3.18 R
8446 12070 0.249489 ACGATCCTTCTGCATACGCC 60.249 55.000 0.00 0.00 37.32 5.68 R
8848 12559 1.117994 TGGCCAAACTTGCACATGAA 58.882 45.000 0.61 0.00 0.00 2.57 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
160 164 5.065704 TGCTCAGAAGTCAGAAGTGTATC 57.934 43.478 0.00 0.00 0.00 2.24
161 165 4.769488 TGCTCAGAAGTCAGAAGTGTATCT 59.231 41.667 0.00 0.00 0.00 1.98
163 167 5.576384 GCTCAGAAGTCAGAAGTGTATCTTG 59.424 44.000 0.00 0.00 36.40 3.02
164 168 6.656632 TCAGAAGTCAGAAGTGTATCTTGT 57.343 37.500 0.00 0.00 36.40 3.16
165 169 7.575909 GCTCAGAAGTCAGAAGTGTATCTTGTA 60.576 40.741 0.00 0.00 36.40 2.41
168 172 5.662674 AGTCAGAAGTGTATCTTGTACCC 57.337 43.478 0.00 0.00 36.40 3.69
169 173 5.084519 AGTCAGAAGTGTATCTTGTACCCA 58.915 41.667 0.00 0.00 36.40 4.51
211 215 3.855950 GCACAGTTAATTTCTGAGCATGC 59.144 43.478 10.51 10.51 44.49 4.06
225 229 4.252878 TGAGCATGCTTTCGTCTCAAATA 58.747 39.130 23.61 0.00 31.62 1.40
303 308 2.946329 TCTGCTAGTCGAATCTCTCACC 59.054 50.000 0.00 0.00 0.00 4.02
384 558 5.697067 TGGAGCCTTTACTTTGGAAACTTA 58.303 37.500 0.00 0.00 0.00 2.24
473 3438 9.965824 CTGTAAAGTTTCATGGTGAAAAATACT 57.034 29.630 6.69 0.00 46.53 2.12
553 3518 6.480524 TGTACAGCTCACATCAAAATGTAC 57.519 37.500 0.00 5.80 44.41 2.90
556 3521 6.639632 ACAGCTCACATCAAAATGTACTTT 57.360 33.333 0.00 0.00 44.41 2.66
660 3643 7.056006 AGTTGATTTTTGGAAAATTCAGGCTT 58.944 30.769 8.60 0.00 38.62 4.35
794 3778 9.504708 AATGGATTTGTGAAAGCAAATATTTCA 57.495 25.926 0.00 0.00 45.68 2.69
795 3779 8.537049 TGGATTTGTGAAAGCAAATATTTCAG 57.463 30.769 0.00 0.00 45.68 3.02
798 3782 9.195411 GATTTGTGAAAGCAAATATTTCAGTGA 57.805 29.630 0.00 0.00 45.68 3.41
805 3789 9.674824 GAAAGCAAATATTTCAGTGATATCTGG 57.325 33.333 3.98 0.00 36.79 3.86
875 3864 0.962356 CCACGCCATTTGCTCCTCTT 60.962 55.000 0.00 0.00 38.05 2.85
895 3884 1.380403 CCAACTTCCGTGGTTGTGCA 61.380 55.000 10.08 0.00 41.47 4.57
902 3902 2.730094 GTGGTTGTGCAGCCCAAG 59.270 61.111 2.69 0.00 0.00 3.61
1023 4023 4.631247 TGCTGCTGCTTCCGTGCT 62.631 61.111 17.00 0.00 40.48 4.40
1162 4167 0.669318 GCACGGTTCGACAGATTGGA 60.669 55.000 0.00 0.00 0.00 3.53
1185 4190 1.532728 GAGAGGGCCCGTAGAGAGA 59.467 63.158 18.44 0.00 0.00 3.10
1186 4191 0.536460 GAGAGGGCCCGTAGAGAGAG 60.536 65.000 18.44 0.00 0.00 3.20
1187 4192 0.989212 AGAGGGCCCGTAGAGAGAGA 60.989 60.000 18.44 0.00 0.00 3.10
1188 4193 0.106619 GAGGGCCCGTAGAGAGAGAA 60.107 60.000 18.44 0.00 0.00 2.87
1189 4194 0.335361 AGGGCCCGTAGAGAGAGAAA 59.665 55.000 18.44 0.00 0.00 2.52
1190 4195 1.192428 GGGCCCGTAGAGAGAGAAAA 58.808 55.000 5.69 0.00 0.00 2.29
1305 4313 6.080406 GGATAAAGTTTCTTCTTGTTCAGCG 58.920 40.000 0.00 0.00 0.00 5.18
1326 4334 0.105964 AGCACCTTCGTGTAGTTGCA 59.894 50.000 7.07 0.00 42.39 4.08
1416 4430 8.402472 CCTTAATGTTTTCTAATGCGAATACCA 58.598 33.333 0.00 0.00 0.00 3.25
1419 4433 8.856490 AATGTTTTCTAATGCGAATACCAATC 57.144 30.769 0.00 0.00 0.00 2.67
1427 4441 9.337396 TCTAATGCGAATACCAATCAATTACTT 57.663 29.630 0.00 0.00 0.00 2.24
1525 4539 0.608640 AAGGACCGTCAGTGGATCAC 59.391 55.000 0.00 0.00 34.10 3.06
1531 4545 3.399181 TCAGTGGATCACGCCCCC 61.399 66.667 0.00 0.00 39.64 5.40
1549 4563 1.071699 CCCCGGATTCCGTTGTATGAT 59.928 52.381 22.83 0.00 46.80 2.45
1570 4584 1.127567 ACAGCTTGCCCTCAGGTGTA 61.128 55.000 3.02 0.00 41.62 2.90
1627 4641 2.015587 CCTGCTGATCCTTCAAAGAGC 58.984 52.381 0.00 0.00 0.00 4.09
1701 4715 7.741554 AGATATTAGGTCAGTGTTTTCCTCT 57.258 36.000 0.00 0.00 0.00 3.69
1831 4852 6.721571 TCCTCAAGACATTTCGTTTCATAC 57.278 37.500 0.00 0.00 0.00 2.39
1850 4871 2.914059 ACGCTTGGTAAGTTGTCTTGT 58.086 42.857 0.00 0.00 35.36 3.16
1977 4998 7.941919 AGTATAGCAGAATTCTGTCGTTATCA 58.058 34.615 30.88 11.83 45.45 2.15
2051 5080 3.381272 CCATAACAACATGACATGGGACC 59.619 47.826 19.39 0.00 32.50 4.46
2101 5130 3.059884 TGCATCGTTTTCAGAGACTGAC 58.940 45.455 0.74 0.00 40.46 3.51
2191 5228 2.795231 ACTGTGTGCTATGCTTGGAT 57.205 45.000 0.00 0.00 0.00 3.41
2213 5250 4.993705 AGAAACTCCTAACCAATGTCCA 57.006 40.909 0.00 0.00 0.00 4.02
2485 5522 1.889829 GCTCTGTCACTGGTGAGTAGT 59.110 52.381 3.47 0.00 40.75 2.73
2607 5652 4.154918 GTGAAACACAATCTTCTAGGGCAG 59.845 45.833 0.00 0.00 36.32 4.85
2619 5664 4.706842 TCTAGGGCAGTTCTGTTTCTTT 57.293 40.909 1.78 0.00 0.00 2.52
2627 5672 6.861572 GGGCAGTTCTGTTTCTTTATTTGTAC 59.138 38.462 1.78 0.00 0.00 2.90
3041 6098 8.974060 AACTACAAAAGTTTATCCTCAGTTGA 57.026 30.769 0.00 0.00 46.61 3.18
3157 6214 5.357742 AATGATGGATTAACCTTTTGCCC 57.642 39.130 0.00 0.00 39.86 5.36
3185 6242 7.995463 TGCTTTTTCATGTACCAAACTTTAC 57.005 32.000 0.00 0.00 0.00 2.01
3264 6321 9.426837 CATGATCCTTTGTTGTGATTTGTAATT 57.573 29.630 0.00 0.00 0.00 1.40
3269 6326 8.253810 TCCTTTGTTGTGATTTGTAATTTGTCA 58.746 29.630 0.00 0.00 0.00 3.58
3781 6851 1.762957 TCCTTCGGAGAATTGCCCTAG 59.237 52.381 0.00 0.00 45.90 3.02
4029 7100 1.204704 CTGACATGTAGCGTTCTCCCA 59.795 52.381 0.00 0.00 0.00 4.37
4033 7104 3.296854 ACATGTAGCGTTCTCCCATAGA 58.703 45.455 0.00 0.00 0.00 1.98
4043 7114 4.230657 GTTCTCCCATAGATGATCGTTCG 58.769 47.826 0.00 0.00 33.05 3.95
4065 7137 9.031360 GTTCGTGCTCATGATTTAATACTCTTA 57.969 33.333 0.00 0.00 0.00 2.10
4102 7176 4.007659 AGTTCTCGAACCAAACAAAGTGT 58.992 39.130 6.20 0.00 42.06 3.55
4129 7203 5.673337 TTCCTCACTTTCTTTTGACATCG 57.327 39.130 0.00 0.00 0.00 3.84
4298 7372 8.316640 TGGTGCAAATTCAAACAAATATTACC 57.683 30.769 0.00 0.00 0.00 2.85
4299 7373 7.116948 TGGTGCAAATTCAAACAAATATTACCG 59.883 33.333 0.00 0.00 0.00 4.02
4300 7374 7.329717 GGTGCAAATTCAAACAAATATTACCGA 59.670 33.333 0.00 0.00 0.00 4.69
4301 7375 8.159709 GTGCAAATTCAAACAAATATTACCGAC 58.840 33.333 0.00 0.00 0.00 4.79
4302 7376 8.085296 TGCAAATTCAAACAAATATTACCGACT 58.915 29.630 0.00 0.00 0.00 4.18
4303 7377 8.921670 GCAAATTCAAACAAATATTACCGACTT 58.078 29.630 0.00 0.00 0.00 3.01
4308 7382 8.836268 TCAAACAAATATTACCGACTTACTGT 57.164 30.769 0.00 0.00 0.00 3.55
4309 7383 9.275398 TCAAACAAATATTACCGACTTACTGTT 57.725 29.630 0.00 0.00 0.00 3.16
4321 7395 7.710896 ACCGACTTACTGTTACCATATTAGTC 58.289 38.462 0.00 0.00 0.00 2.59
4323 7397 9.060347 CCGACTTACTGTTACCATATTAGTCTA 57.940 37.037 0.00 0.00 0.00 2.59
4349 7423 7.476667 TGTAACTCAACTTAACATGTTTGGTG 58.523 34.615 17.78 17.80 0.00 4.17
4394 7691 1.971695 GCGGCTTTGCAGGGTTAGT 60.972 57.895 0.00 0.00 34.15 2.24
4418 7716 7.040132 AGTCTTTCTGTTTGGATTTCTTCATCC 60.040 37.037 0.00 0.00 43.03 3.51
4486 7798 2.262211 TGCGAATTCAGACACATCTCG 58.738 47.619 6.22 0.00 30.42 4.04
4554 7866 6.213397 CAGGAGTCCCATATGGTCATTATACA 59.787 42.308 20.46 0.00 34.77 2.29
4690 8003 5.819991 TCACTTTCTAGGCAGATCCAATTT 58.180 37.500 0.00 0.00 37.29 1.82
4792 8105 8.757982 ATACAATGTTTAAGGCTTCATCTCAT 57.242 30.769 1.30 0.48 0.00 2.90
4793 8106 6.860080 ACAATGTTTAAGGCTTCATCTCATG 58.140 36.000 1.30 0.00 0.00 3.07
4837 8150 3.760580 AGGGAGTGTTCTTGTTCTCTG 57.239 47.619 0.00 0.00 0.00 3.35
4840 8153 3.070302 GGGAGTGTTCTTGTTCTCTGTCT 59.930 47.826 0.00 0.00 0.00 3.41
4886 8199 4.766891 TGGATTGAAAGAATCTTGTGGGAC 59.233 41.667 0.00 0.00 0.00 4.46
4928 8241 2.108075 TGTTTGAAGGAATGAGCCCTCA 59.892 45.455 0.00 0.00 44.59 3.86
4985 8423 9.440773 CCAATTCTATATGATAGCTAACAAGCA 57.559 33.333 7.86 0.00 37.25 3.91
5002 8440 1.707427 AGCAGTGACCCTCTTGGAAAT 59.293 47.619 0.00 0.00 38.00 2.17
5006 8444 4.202253 GCAGTGACCCTCTTGGAAATTTTT 60.202 41.667 0.00 0.00 38.00 1.94
5028 8466 4.898320 TCTTTGTGTCTATGACATGCACT 58.102 39.130 15.58 0.00 44.63 4.40
5043 8481 2.826428 TGCACTCAGTGTCTTCAGAAC 58.174 47.619 6.68 0.00 35.75 3.01
5046 8484 3.243704 GCACTCAGTGTCTTCAGAACTCT 60.244 47.826 6.68 0.00 35.75 3.24
5119 8672 6.375455 GTGTTCACAATCTTTGTAGGATCCAT 59.625 38.462 15.82 1.47 43.23 3.41
5134 8687 7.781219 TGTAGGATCCATCATGTCATGAAATTT 59.219 33.333 19.17 5.64 43.50 1.82
5189 8742 2.198827 ATCCTGCACATTTGTCCGAA 57.801 45.000 0.00 0.00 0.00 4.30
5277 8830 2.801063 CTCATTTGTATTTGCTGCGGG 58.199 47.619 0.00 0.00 0.00 6.13
5427 8981 5.971763 ACACTAACTGAATTTTGGTTTGCA 58.028 33.333 0.00 0.00 0.00 4.08
5429 8983 7.047271 ACACTAACTGAATTTTGGTTTGCAAT 58.953 30.769 0.00 0.00 0.00 3.56
5430 8984 7.011295 ACACTAACTGAATTTTGGTTTGCAATG 59.989 33.333 0.00 0.00 0.00 2.82
5470 9025 9.847224 TCTTAACAGTTATCTCCAATATTTCCC 57.153 33.333 0.00 0.00 0.00 3.97
5957 9513 7.558444 ACAATTGTTCCTACCACTTTTACTTGA 59.442 33.333 4.92 0.00 0.00 3.02
5958 9514 8.576442 CAATTGTTCCTACCACTTTTACTTGAT 58.424 33.333 0.00 0.00 0.00 2.57
6272 9839 2.450609 TACCTTCTGAAAGTGTCGCC 57.549 50.000 1.96 0.00 33.76 5.54
6321 9888 8.279970 TCATGATTTTAACATACTGGAGGTTG 57.720 34.615 0.00 0.00 33.24 3.77
6458 10025 8.454106 CAAAGCTGATAATATACCAGGTATTGC 58.546 37.037 17.72 10.30 37.63 3.56
6485 10052 4.513692 TGTTGCTGTTGTATCTTGTACCAC 59.486 41.667 0.00 0.00 0.00 4.16
6496 10063 7.325694 TGTATCTTGTACCACTTTAGTTAGGC 58.674 38.462 0.00 0.00 0.00 3.93
6638 10207 5.712152 ACAGGCAGAAACTTCCTAATTTG 57.288 39.130 0.00 0.00 0.00 2.32
6671 10240 3.222173 AGTGTGTTGCATGGGTTAGAA 57.778 42.857 0.00 0.00 0.00 2.10
6740 10309 2.548067 CCAAGTTAGCCTGAGACACGTT 60.548 50.000 0.00 0.00 0.00 3.99
6876 10474 5.229423 ACCATTTGTGATCCAAAATTGACG 58.771 37.500 11.70 0.00 45.72 4.35
6878 10476 3.932545 TTGTGATCCAAAATTGACGGG 57.067 42.857 0.00 0.00 0.00 5.28
6881 10479 4.399219 TGTGATCCAAAATTGACGGGTTA 58.601 39.130 0.00 0.00 0.00 2.85
6882 10480 4.827835 TGTGATCCAAAATTGACGGGTTAA 59.172 37.500 0.00 0.00 0.00 2.01
6883 10481 5.478679 TGTGATCCAAAATTGACGGGTTAAT 59.521 36.000 0.00 0.00 0.00 1.40
6884 10482 5.804979 GTGATCCAAAATTGACGGGTTAATG 59.195 40.000 0.00 0.00 0.00 1.90
6887 10485 4.827835 TCCAAAATTGACGGGTTAATGTGA 59.172 37.500 0.00 0.00 0.00 3.58
6888 10486 5.048364 TCCAAAATTGACGGGTTAATGTGAG 60.048 40.000 0.00 0.00 0.00 3.51
6890 10488 2.851263 TTGACGGGTTAATGTGAGCT 57.149 45.000 0.00 0.00 0.00 4.09
6891 10489 2.851263 TGACGGGTTAATGTGAGCTT 57.149 45.000 0.00 0.00 0.00 3.74
6893 10491 4.481368 TGACGGGTTAATGTGAGCTTAT 57.519 40.909 0.00 0.00 0.00 1.73
6894 10492 4.439057 TGACGGGTTAATGTGAGCTTATC 58.561 43.478 0.00 0.00 0.00 1.75
6895 10493 3.805207 ACGGGTTAATGTGAGCTTATCC 58.195 45.455 0.00 0.00 0.00 2.59
6896 10494 3.199071 ACGGGTTAATGTGAGCTTATCCA 59.801 43.478 0.00 0.00 0.00 3.41
6899 10497 4.022849 GGGTTAATGTGAGCTTATCCATGC 60.023 45.833 0.00 0.00 0.00 4.06
6900 10498 4.319766 GGTTAATGTGAGCTTATCCATGCG 60.320 45.833 0.00 0.00 0.00 4.73
6901 10499 1.888215 ATGTGAGCTTATCCATGCGG 58.112 50.000 0.00 0.00 0.00 5.69
6902 10500 0.541392 TGTGAGCTTATCCATGCGGT 59.459 50.000 0.00 0.00 0.00 5.68
6903 10501 1.065491 TGTGAGCTTATCCATGCGGTT 60.065 47.619 0.00 0.00 0.00 4.44
6904 10502 2.169561 TGTGAGCTTATCCATGCGGTTA 59.830 45.455 0.00 0.00 0.00 2.85
6905 10503 2.802816 GTGAGCTTATCCATGCGGTTAG 59.197 50.000 0.00 0.00 0.00 2.34
6915 10513 2.054458 TGCGGTTAGGCACTCTTCA 58.946 52.632 0.00 0.00 41.75 3.02
6916 10514 0.394938 TGCGGTTAGGCACTCTTCAA 59.605 50.000 0.00 0.00 41.75 2.69
6917 10515 1.202710 TGCGGTTAGGCACTCTTCAAA 60.203 47.619 0.00 0.00 41.75 2.69
6918 10516 2.084546 GCGGTTAGGCACTCTTCAAAT 58.915 47.619 0.00 0.00 41.75 2.32
6920 10518 3.309954 GCGGTTAGGCACTCTTCAAATAG 59.690 47.826 0.00 0.00 41.75 1.73
6922 10520 4.382685 CGGTTAGGCACTCTTCAAATAGGA 60.383 45.833 0.00 0.00 41.75 2.94
6925 10523 6.261158 GGTTAGGCACTCTTCAAATAGGAATC 59.739 42.308 0.00 0.00 41.75 2.52
6928 10526 5.103771 AGGCACTCTTCAAATAGGAATCCAT 60.104 40.000 0.61 0.00 0.00 3.41
6929 10527 5.595952 GGCACTCTTCAAATAGGAATCCATT 59.404 40.000 0.61 0.00 0.00 3.16
6931 10529 7.364144 GGCACTCTTCAAATAGGAATCCATTTT 60.364 37.037 0.61 0.00 0.00 1.82
6933 10531 8.964772 CACTCTTCAAATAGGAATCCATTTTCT 58.035 33.333 0.61 0.00 0.00 2.52
6940 10538 7.588497 AATAGGAATCCATTTTCTAACTGGC 57.412 36.000 0.61 0.00 0.00 4.85
6941 10539 5.198602 AGGAATCCATTTTCTAACTGGCT 57.801 39.130 0.61 0.00 0.00 4.75
6942 10540 5.583932 AGGAATCCATTTTCTAACTGGCTT 58.416 37.500 0.61 0.00 0.00 4.35
6945 10543 5.567138 ATCCATTTTCTAACTGGCTTTCG 57.433 39.130 0.00 0.00 0.00 3.46
6946 10544 4.394729 TCCATTTTCTAACTGGCTTTCGT 58.605 39.130 0.00 0.00 0.00 3.85
6947 10545 4.215399 TCCATTTTCTAACTGGCTTTCGTG 59.785 41.667 0.00 0.00 0.00 4.35
6948 10546 3.619233 TTTTCTAACTGGCTTTCGTGC 57.381 42.857 0.00 0.00 0.00 5.34
6949 10547 2.543777 TTCTAACTGGCTTTCGTGCT 57.456 45.000 0.00 0.00 0.00 4.40
6951 10549 2.846193 TCTAACTGGCTTTCGTGCTTT 58.154 42.857 0.00 0.00 0.00 3.51
7561 11163 9.335891 GAGTATGTATCAAACTATCGATCACTG 57.664 37.037 0.00 0.00 0.00 3.66
7569 11171 2.158798 ACTATCGATCACTGGAGGACGA 60.159 50.000 0.00 0.00 33.90 4.20
7571 11173 1.763968 TCGATCACTGGAGGACGATT 58.236 50.000 0.00 0.00 0.00 3.34
7624 11237 6.054860 ACTGATTGAGCTAGGTACACAATT 57.945 37.500 8.29 0.00 32.50 2.32
7682 11299 7.277760 TGACTGATGTTCCATTACTAATTCACG 59.722 37.037 0.00 0.00 0.00 4.35
7687 11304 6.693466 TGTTCCATTACTAATTCACGAGTGA 58.307 36.000 1.24 1.24 37.91 3.41
7744 11361 4.819630 TGAAAGTATGGAACGGCATTATCC 59.180 41.667 0.00 0.00 0.00 2.59
7755 11372 3.692791 GGCATTATCCGAAACCTTGAC 57.307 47.619 0.00 0.00 0.00 3.18
7804 11421 4.994852 TGAATAGGTTCGTTGGAGAACTTG 59.005 41.667 9.31 0.00 46.99 3.16
7853 11470 3.751175 CCAGCGAATCAAACAGGTAAGAA 59.249 43.478 0.00 0.00 0.00 2.52
7909 11529 5.589452 TGCAAAAATGGCATCTGAACTTTTT 59.411 32.000 0.00 0.00 36.11 1.94
7984 11605 4.019174 CAACTTATGGTCTCCCAAATGCT 58.981 43.478 0.00 0.00 46.04 3.79
8019 11640 5.272405 TCCAGTAGAGTTCTTCCCTACTT 57.728 43.478 0.00 0.00 40.58 2.24
8134 11755 5.479027 GCCTGGTAATTTTTCTTCCTAACCA 59.521 40.000 0.00 0.00 34.72 3.67
8149 11773 7.993183 TCTTCCTAACCATCTTTCATGAATACC 59.007 37.037 9.40 0.00 0.00 2.73
8265 11889 3.755112 TTACGTTGTGACCTTCCATCA 57.245 42.857 0.00 0.00 0.00 3.07
8350 11974 9.981114 CCATAGGCATCATATATCGTTAATACA 57.019 33.333 0.00 0.00 0.00 2.29
8446 12070 1.446907 ATCTGTTGCGAGCTTTGGAG 58.553 50.000 0.00 0.00 0.00 3.86
8560 12184 4.593206 TCAGTAGTGACCCAGAAGAATGTT 59.407 41.667 0.00 0.00 0.00 2.71
8589 12213 9.203421 CATAATTGCACGATAAGATAGGTTACA 57.797 33.333 0.00 0.00 0.00 2.41
8668 12294 2.253452 GTCTTGTTGCTGGCTGCG 59.747 61.111 11.85 0.00 46.63 5.18
8848 12559 2.541178 GGCTGATTAGTTCGTCGATCGT 60.541 50.000 15.94 0.00 40.80 3.73
8879 12590 5.730289 GCAAGTTTGGCCATTTTTCTTTGTC 60.730 40.000 6.09 0.00 0.00 3.18
8883 12594 2.295909 TGGCCATTTTTCTTTGTCCTCG 59.704 45.455 0.00 0.00 0.00 4.63
8909 12620 5.088739 CGGTGAATTCTTATGCACAAAGAC 58.911 41.667 11.82 3.67 41.46 3.01
8912 12623 6.363357 GGTGAATTCTTATGCACAAAGACAAC 59.637 38.462 11.82 7.22 41.46 3.32
9009 12733 4.021544 AGCAAAACACCAAACAAGACAAGA 60.022 37.500 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.165319 ACCGGCTCTACACAAGTTTC 57.835 50.000 0.00 0.00 0.00 2.78
7 8 4.708421 AGACTATTTACCGGCTCTACACAA 59.292 41.667 0.00 0.00 0.00 3.33
160 164 1.135689 GCTGAACGCAATGGGTACAAG 60.136 52.381 2.68 3.28 38.92 3.16
161 165 0.878416 GCTGAACGCAATGGGTACAA 59.122 50.000 2.68 0.00 38.92 2.41
163 167 1.800681 GGCTGAACGCAATGGGTAC 59.199 57.895 2.68 0.00 41.67 3.34
164 168 1.743623 CGGCTGAACGCAATGGGTA 60.744 57.895 2.68 0.00 41.67 3.69
165 169 3.055719 CGGCTGAACGCAATGGGT 61.056 61.111 0.00 0.00 41.67 4.51
168 172 0.725784 GTGAACGGCTGAACGCAATG 60.726 55.000 0.00 0.00 41.67 2.82
169 173 0.884704 AGTGAACGGCTGAACGCAAT 60.885 50.000 0.00 0.00 41.67 3.56
261 265 5.647658 CAGATTAGCCCACACATTTTACAGA 59.352 40.000 0.00 0.00 0.00 3.41
553 3518 7.650504 AGATGTGTGTGAAATTTCATGACAAAG 59.349 33.333 25.70 0.00 39.73 2.77
556 3521 6.638096 AGATGTGTGTGAAATTTCATGACA 57.362 33.333 23.05 22.77 39.73 3.58
660 3643 0.908910 TTTGCTCTCGGGCTCCATAA 59.091 50.000 0.00 0.00 0.00 1.90
735 3719 3.318017 CGGTTAGGATATCTGGCTTTCG 58.682 50.000 2.05 0.00 0.00 3.46
794 3778 8.034313 TGCTCCTAAATTTACCAGATATCACT 57.966 34.615 5.32 0.00 0.00 3.41
795 3779 8.560374 GTTGCTCCTAAATTTACCAGATATCAC 58.440 37.037 5.32 0.00 0.00 3.06
798 3782 8.052748 TGTGTTGCTCCTAAATTTACCAGATAT 58.947 33.333 0.00 0.00 0.00 1.63
800 3784 6.245408 TGTGTTGCTCCTAAATTTACCAGAT 58.755 36.000 0.00 0.00 0.00 2.90
802 3786 5.619981 GCTGTGTTGCTCCTAAATTTACCAG 60.620 44.000 0.00 0.00 0.00 4.00
804 3788 4.380550 GGCTGTGTTGCTCCTAAATTTACC 60.381 45.833 0.00 0.00 0.00 2.85
805 3789 4.217550 TGGCTGTGTTGCTCCTAAATTTAC 59.782 41.667 0.00 0.00 0.00 2.01
902 3902 2.116556 TTTTGGAGGCGGTTCCCC 59.883 61.111 0.00 0.00 36.35 4.81
916 3916 4.174305 CCGTGGGCAAGGAGTTTT 57.826 55.556 0.00 0.00 31.21 2.43
1162 4167 4.075793 TACGGGCCCTCTCCAGCT 62.076 66.667 22.43 0.00 0.00 4.24
1208 4213 6.147328 CCGATTTTACTAGGGCTAGTTAATGC 59.853 42.308 0.00 0.00 43.35 3.56
1317 4325 2.954989 TCCAACTTGCAATGCAACTACA 59.045 40.909 17.55 0.00 43.99 2.74
1326 4334 1.825090 TGAGCGATCCAACTTGCAAT 58.175 45.000 0.00 0.00 0.00 3.56
1388 4401 9.434559 GTATTCGCATTAGAAAACATTAAGGTC 57.565 33.333 0.00 0.00 33.43 3.85
1419 4433 9.658799 TCAGAGACAAAATAGGAGAAGTAATTG 57.341 33.333 0.00 0.00 0.00 2.32
1427 4441 6.611613 ATGTGTCAGAGACAAAATAGGAGA 57.388 37.500 4.18 0.00 44.49 3.71
1442 4456 3.262420 CCGAGAAACCCTAATGTGTCAG 58.738 50.000 0.00 0.00 0.00 3.51
1549 4563 2.149383 ACCTGAGGGCAAGCTGTCA 61.149 57.895 2.38 0.00 35.63 3.58
1570 4584 5.011738 ACCAGGATTCGTTAATATGGTCGAT 59.988 40.000 0.00 0.00 39.42 3.59
1627 4641 4.976224 TCCATCAACAAGCATGATTCTG 57.024 40.909 0.00 0.00 35.38 3.02
1701 4715 6.658816 ACAAGATGTACCAATAATGAGTGCAA 59.341 34.615 0.00 0.00 30.70 4.08
1831 4852 4.271533 TGTTACAAGACAACTTACCAAGCG 59.728 41.667 0.00 0.00 34.70 4.68
1850 4871 8.615878 ACAAGTGCTGACTTAAATACATGTTA 57.384 30.769 2.30 0.00 40.68 2.41
1977 4998 9.461312 TGTAATATTTCTTTTGCCAGTGTCTAT 57.539 29.630 0.00 0.00 0.00 1.98
2191 5228 6.636454 ATGGACATTGGTTAGGAGTTTCTA 57.364 37.500 0.00 0.00 0.00 2.10
2530 5575 8.277490 TGCAACACCCGTTATATACAAATTTA 57.723 30.769 0.00 0.00 32.75 1.40
2545 5590 0.608035 ACCCATAACTGCAACACCCG 60.608 55.000 0.00 0.00 0.00 5.28
2598 5643 4.706842 AAAGAAACAGAACTGCCCTAGA 57.293 40.909 1.46 0.00 0.00 2.43
2935 5980 8.732531 CAAAACTCGTCCCTATAATGGTAAAAA 58.267 33.333 0.00 0.00 0.00 1.94
2939 5984 5.163280 CCCAAAACTCGTCCCTATAATGGTA 60.163 44.000 0.00 0.00 0.00 3.25
2953 6010 7.538678 CAGAATATTGTCTTTTCCCAAAACTCG 59.461 37.037 0.00 0.00 0.00 4.18
3185 6242 7.206981 AGGAAACAGTTCTACAATGTCAATG 57.793 36.000 0.00 0.00 33.92 2.82
3238 6295 8.991243 ATTACAAATCACAACAAAGGATCATG 57.009 30.769 0.00 0.00 0.00 3.07
3264 6321 3.282021 AGCTGCAGAGAAAACTTGACAA 58.718 40.909 20.43 0.00 0.00 3.18
3269 6326 4.036144 GTCAAGAAGCTGCAGAGAAAACTT 59.964 41.667 20.43 9.95 0.00 2.66
3384 6441 9.739276 ATAGATCACCAAGATGTAGTTTTTCAA 57.261 29.630 0.00 0.00 36.11 2.69
3398 6456 5.489249 AGCTCATGCATATAGATCACCAAG 58.511 41.667 11.45 0.00 42.74 3.61
3563 6623 5.917462 AGTGCCAAATGATTATTAAAGGCC 58.083 37.500 14.55 0.00 37.72 5.19
3662 6732 9.582648 AGGCTAAGAGGAAAACAAATAAAAGTA 57.417 29.630 0.00 0.00 0.00 2.24
3663 6733 8.478775 AGGCTAAGAGGAAAACAAATAAAAGT 57.521 30.769 0.00 0.00 0.00 2.66
3775 6845 6.951062 AGATTAAAAAGAATGAGCTAGGGC 57.049 37.500 0.00 0.00 39.06 5.19
3910 6980 8.785329 AAGACAAATGCTTAAAGGAAACAAAA 57.215 26.923 0.00 0.00 0.00 2.44
3912 6982 9.877178 TTTAAGACAAATGCTTAAAGGAAACAA 57.123 25.926 13.68 0.00 40.77 2.83
3986 7057 2.103153 AGGTGAACTTGGAGAGGACA 57.897 50.000 0.00 0.00 0.00 4.02
4029 7100 3.990318 TGAGCACGAACGATCATCTAT 57.010 42.857 0.14 0.00 0.00 1.98
4033 7104 2.584492 TCATGAGCACGAACGATCAT 57.416 45.000 0.14 5.13 32.70 2.45
4065 7137 7.041303 GGTTCGAGAACTAAAAGAAAACCAGAT 60.041 37.037 14.62 0.00 40.94 2.90
4084 7158 7.043656 GGAAAATAACACTTTGTTTGGTTCGAG 60.044 37.037 0.00 0.00 41.45 4.04
4102 7176 9.965824 GATGTCAAAAGAAAGTGAGGAAAATAA 57.034 29.630 0.00 0.00 0.00 1.40
4321 7395 9.825972 CCAAACATGTTAAGTTGAGTTACATAG 57.174 33.333 12.39 0.00 0.00 2.23
4323 7397 8.134895 CACCAAACATGTTAAGTTGAGTTACAT 58.865 33.333 12.39 0.00 0.00 2.29
4394 7691 6.209391 GGGATGAAGAAATCCAAACAGAAAGA 59.791 38.462 5.63 0.00 46.94 2.52
4418 7716 6.478129 TCACAAACTATAGTAAACAAGGGGG 58.522 40.000 5.65 0.00 0.00 5.40
4431 7739 9.016438 GTATTGGGGTTCTTTTCACAAACTATA 57.984 33.333 0.00 0.00 0.00 1.31
4432 7740 6.994421 ATTGGGGTTCTTTTCACAAACTAT 57.006 33.333 0.00 0.00 0.00 2.12
4554 7866 1.760613 CATTCTTTGGATGGCATGGCT 59.239 47.619 21.08 5.86 0.00 4.75
4702 8015 1.272592 TGATCCAGGCCATCTTTTGCA 60.273 47.619 5.01 0.00 0.00 4.08
4837 8150 3.948473 GGGCAAAGAAAGGAGGATTAGAC 59.052 47.826 0.00 0.00 0.00 2.59
4840 8153 2.356741 CGGGGCAAAGAAAGGAGGATTA 60.357 50.000 0.00 0.00 0.00 1.75
4886 8199 5.969423 ACAAAATGGTGCTTTCTATGGATG 58.031 37.500 0.00 0.00 0.00 3.51
4895 8208 5.096443 TCCTTCAAACAAAATGGTGCTTT 57.904 34.783 0.00 0.00 0.00 3.51
4951 8264 9.760926 AGCTATCATATAGAATTGGAGTGTAGA 57.239 33.333 0.00 0.00 0.00 2.59
4985 8423 5.458595 AGAAAAATTTCCAAGAGGGTCACT 58.541 37.500 2.37 0.00 37.92 3.41
5002 8440 6.917477 GTGCATGTCATAGACACAAAGAAAAA 59.083 34.615 1.43 0.00 45.65 1.94
5006 8444 4.898320 AGTGCATGTCATAGACACAAAGA 58.102 39.130 1.43 0.00 45.65 2.52
5028 8466 4.022762 GCACTAGAGTTCTGAAGACACTGA 60.023 45.833 0.00 0.00 0.00 3.41
5043 8481 3.058639 GCACCACAAGAAAAGCACTAGAG 60.059 47.826 0.00 0.00 0.00 2.43
5046 8484 1.953686 GGCACCACAAGAAAAGCACTA 59.046 47.619 0.00 0.00 0.00 2.74
5156 8709 4.764308 TGTGCAGGATTTGTAAAGTGCATA 59.236 37.500 12.18 8.68 42.47 3.14
5189 8742 3.767711 TCTGTCATGTGTACTGGACTCT 58.232 45.455 0.00 0.00 0.00 3.24
5277 8830 4.394300 CACATGTCCAGATTTCAGAAGGAC 59.606 45.833 10.97 10.97 46.86 3.85
5500 9055 4.283722 TCCTAGGAGAACACAAGAAAGACC 59.716 45.833 7.62 0.00 0.00 3.85
5694 9250 8.972458 TTTGACGATCCCATATATCAAAAGAA 57.028 30.769 0.00 0.00 34.16 2.52
5706 9262 7.587037 ACATTGATAATTTTGACGATCCCAT 57.413 32.000 0.00 0.00 0.00 4.00
5856 9412 6.238402 CCAGTGCATGTAAGATTCATGAAGAG 60.238 42.308 14.54 0.00 43.47 2.85
5896 9452 3.181453 TGTTACCGGAAATCCAGTCAACA 60.181 43.478 9.46 4.19 35.14 3.33
5957 9513 4.471386 ACTCCAGCCATTGTCTAGTTGTAT 59.529 41.667 0.00 0.00 0.00 2.29
5958 9514 3.838317 ACTCCAGCCATTGTCTAGTTGTA 59.162 43.478 0.00 0.00 0.00 2.41
6458 10025 5.679734 ACAAGATACAACAGCAACAGAAG 57.320 39.130 0.00 0.00 0.00 2.85
6485 10052 6.056428 AGTTTTGTTGACGCCTAACTAAAG 57.944 37.500 6.80 0.00 34.92 1.85
6513 10080 1.978617 GTCATGCCAACCCACCAGG 60.979 63.158 0.00 0.00 43.78 4.45
6638 10207 1.687563 ACACACTTAACCAACTGCCC 58.312 50.000 0.00 0.00 0.00 5.36
6671 10240 1.692411 GCCAAACAGTCCAGAAACCT 58.308 50.000 0.00 0.00 0.00 3.50
6740 10309 2.208132 AGGGTGACAACAACACAACA 57.792 45.000 0.00 0.00 39.65 3.33
6747 10316 2.930950 CAAGGAGAAGGGTGACAACAA 58.069 47.619 0.00 0.00 0.00 2.83
6862 10460 5.804979 CACATTAACCCGTCAATTTTGGATC 59.195 40.000 0.00 0.00 0.00 3.36
6863 10461 5.478679 TCACATTAACCCGTCAATTTTGGAT 59.521 36.000 0.00 0.00 0.00 3.41
6864 10462 4.827835 TCACATTAACCCGTCAATTTTGGA 59.172 37.500 0.00 0.00 0.00 3.53
6866 10464 4.621034 GCTCACATTAACCCGTCAATTTTG 59.379 41.667 0.00 0.00 0.00 2.44
6869 10467 3.686016 AGCTCACATTAACCCGTCAATT 58.314 40.909 0.00 0.00 0.00 2.32
6870 10468 3.350219 AGCTCACATTAACCCGTCAAT 57.650 42.857 0.00 0.00 0.00 2.57
6871 10469 2.851263 AGCTCACATTAACCCGTCAA 57.149 45.000 0.00 0.00 0.00 3.18
6874 10472 3.199071 TGGATAAGCTCACATTAACCCGT 59.801 43.478 0.00 0.00 0.00 5.28
6876 10474 4.022849 GCATGGATAAGCTCACATTAACCC 60.023 45.833 0.00 0.00 0.00 4.11
6878 10476 4.319766 CCGCATGGATAAGCTCACATTAAC 60.320 45.833 0.00 0.00 37.49 2.01
6881 10479 2.224606 CCGCATGGATAAGCTCACATT 58.775 47.619 0.00 0.00 37.49 2.71
6882 10480 1.141657 ACCGCATGGATAAGCTCACAT 59.858 47.619 0.00 0.00 39.21 3.21
6883 10481 0.541392 ACCGCATGGATAAGCTCACA 59.459 50.000 0.00 0.00 39.21 3.58
6884 10482 1.668419 AACCGCATGGATAAGCTCAC 58.332 50.000 0.00 0.00 39.21 3.51
6887 10485 1.543429 GCCTAACCGCATGGATAAGCT 60.543 52.381 0.00 0.00 39.21 3.74
6888 10486 0.875059 GCCTAACCGCATGGATAAGC 59.125 55.000 0.00 0.00 39.21 3.09
6890 10488 1.488812 AGTGCCTAACCGCATGGATAA 59.511 47.619 0.00 0.00 41.70 1.75
6891 10489 1.070134 GAGTGCCTAACCGCATGGATA 59.930 52.381 0.00 0.00 41.70 2.59
6893 10491 1.220749 GAGTGCCTAACCGCATGGA 59.779 57.895 0.00 0.00 41.70 3.41
6894 10492 0.392998 AAGAGTGCCTAACCGCATGG 60.393 55.000 0.00 0.00 41.70 3.66
6895 10493 1.009829 GAAGAGTGCCTAACCGCATG 58.990 55.000 0.00 0.00 41.70 4.06
6896 10494 0.613260 TGAAGAGTGCCTAACCGCAT 59.387 50.000 0.00 0.00 41.70 4.73
6899 10497 3.871594 CCTATTTGAAGAGTGCCTAACCG 59.128 47.826 0.00 0.00 0.00 4.44
6900 10498 5.099042 TCCTATTTGAAGAGTGCCTAACC 57.901 43.478 0.00 0.00 0.00 2.85
6901 10499 6.261158 GGATTCCTATTTGAAGAGTGCCTAAC 59.739 42.308 0.00 0.00 0.00 2.34
6902 10500 6.069673 TGGATTCCTATTTGAAGAGTGCCTAA 60.070 38.462 3.95 0.00 0.00 2.69
6903 10501 5.428457 TGGATTCCTATTTGAAGAGTGCCTA 59.572 40.000 3.95 0.00 0.00 3.93
6904 10502 4.228210 TGGATTCCTATTTGAAGAGTGCCT 59.772 41.667 3.95 0.00 0.00 4.75
6905 10503 4.526970 TGGATTCCTATTTGAAGAGTGCC 58.473 43.478 3.95 0.00 0.00 5.01
6913 10511 9.189156 CCAGTTAGAAAATGGATTCCTATTTGA 57.811 33.333 3.95 0.00 36.09 2.69
6915 10513 7.841222 AGCCAGTTAGAAAATGGATTCCTATTT 59.159 33.333 10.12 5.25 36.09 1.40
6916 10514 7.357471 AGCCAGTTAGAAAATGGATTCCTATT 58.643 34.615 10.12 0.00 36.09 1.73
6917 10515 6.915786 AGCCAGTTAGAAAATGGATTCCTAT 58.084 36.000 10.12 0.00 36.09 2.57
6918 10516 6.327386 AGCCAGTTAGAAAATGGATTCCTA 57.673 37.500 10.12 0.00 36.09 2.94
6920 10518 5.921962 AAGCCAGTTAGAAAATGGATTCC 57.078 39.130 10.12 0.00 38.26 3.01
6922 10520 5.476945 ACGAAAGCCAGTTAGAAAATGGATT 59.523 36.000 10.12 7.03 44.20 3.01
6925 10523 4.475944 CACGAAAGCCAGTTAGAAAATGG 58.524 43.478 1.87 1.87 37.15 3.16
6928 10526 3.211045 AGCACGAAAGCCAGTTAGAAAA 58.789 40.909 0.00 0.00 34.23 2.29
6929 10527 2.846193 AGCACGAAAGCCAGTTAGAAA 58.154 42.857 0.00 0.00 34.23 2.52
6931 10529 2.543777 AAGCACGAAAGCCAGTTAGA 57.456 45.000 0.00 0.00 34.23 2.10
7437 11036 7.202011 GGGAGTATCTAATAAGCACTCAGGAAA 60.202 40.741 0.00 0.00 36.76 3.13
7561 11163 4.156008 ACATTAAAGCAACAATCGTCCTCC 59.844 41.667 0.00 0.00 0.00 4.30
7607 11220 5.705441 CCTTTCAAATTGTGTACCTAGCTCA 59.295 40.000 0.00 0.00 0.00 4.26
7624 11237 5.502079 TCTGTGTACAAAACCTCCTTTCAA 58.498 37.500 0.00 0.00 0.00 2.69
7744 11361 4.976116 GGACAATTTTCAGTCAAGGTTTCG 59.024 41.667 0.00 0.00 36.50 3.46
7755 11372 5.181690 TCCAACGAAAGGACAATTTTCAG 57.818 39.130 0.00 0.00 34.90 3.02
7804 11421 3.862267 CGACTTCATCCACTGATCTCAAC 59.138 47.826 0.00 0.00 32.72 3.18
7853 11470 5.426689 TCTGCAAGATTAGAATGGTCTGT 57.573 39.130 0.00 0.00 38.67 3.41
7984 11605 9.186837 AGAACTCTACTGGAATAAATTACTCGA 57.813 33.333 0.00 0.00 0.00 4.04
8019 11640 5.920903 TCTCAACCTTTTCCTTACGAGAAA 58.079 37.500 0.00 0.00 0.00 2.52
8134 11755 6.263168 GGTGGAATTCGGTATTCATGAAAGAT 59.737 38.462 13.09 0.00 43.72 2.40
8265 11889 5.516044 GGGGTCTTAAAAGGAACCATGTAT 58.484 41.667 0.21 0.00 42.01 2.29
8350 11974 7.516198 AGCACAAAATCAACAGAATCTAGTT 57.484 32.000 0.00 0.00 0.00 2.24
8446 12070 0.249489 ACGATCCTTCTGCATACGCC 60.249 55.000 0.00 0.00 37.32 5.68
8572 12196 7.604927 TGCTGTTTTTGTAACCTATCTTATCGT 59.395 33.333 0.00 0.00 0.00 3.73
8589 12213 2.412089 GCTAGACGATCGTGCTGTTTTT 59.588 45.455 28.12 0.00 0.00 1.94
8668 12294 3.602265 GCTTCAGCAAAACGCAAAATGTC 60.602 43.478 0.00 0.00 46.13 3.06
8848 12559 1.117994 TGGCCAAACTTGCACATGAA 58.882 45.000 0.61 0.00 0.00 2.57
8879 12590 2.953466 TAAGAATTCACCGGTCGAGG 57.047 50.000 2.59 0.00 37.30 4.63
8883 12594 3.006940 TGTGCATAAGAATTCACCGGTC 58.993 45.455 2.59 0.00 0.00 4.79
8912 12623 1.203313 GACTTTTGGAACGCGACCG 59.797 57.895 15.93 5.69 41.14 4.79


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

AutoCloner maintained by Alex Coulton.