Multiple sequence alignment - TraesCS6A01G276800

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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 TraesCS6A01G276800 chr6A 100.000 5941 0 0 1 5941 503774989 503769049 0.000000e+00 10972.0
1 TraesCS6A01G276800 chr6D 95.465 3043 88 16 1745 4753 363068027 363065001 0.000000e+00 4809.0
2 TraesCS6A01G276800 chr6D 91.232 1015 40 8 686 1683 363069097 363068115 0.000000e+00 1336.0
3 TraesCS6A01G276800 chr6D 86.680 518 46 19 5040 5537 363064580 363064066 2.420000e-153 553.0
4 TraesCS6A01G276800 chr6D 88.837 430 41 3 262 687 363069615 363069189 6.820000e-144 521.0
5 TraesCS6A01G276800 chr6D 89.801 402 25 10 5554 5941 363064136 363063737 8.890000e-138 501.0
6 TraesCS6A01G276800 chr6D 92.830 265 19 0 1 265 363242239 363241975 9.340000e-103 385.0
7 TraesCS6A01G276800 chr6D 83.071 254 35 7 323 573 34310917 34310669 2.150000e-54 224.0
8 TraesCS6A01G276800 chr6D 91.304 92 7 1 4945 5036 472139041 472139131 2.250000e-24 124.0
9 TraesCS6A01G276800 chr6D 100.000 40 0 0 4763 4802 363065010 363064971 2.300000e-09 75.0
10 TraesCS6A01G276800 chr6B 92.376 1679 93 22 1745 3408 545258131 545256473 0.000000e+00 2359.0
11 TraesCS6A01G276800 chr6B 87.943 1551 114 29 3447 4959 545256254 545254739 0.000000e+00 1760.0
12 TraesCS6A01G276800 chr6B 93.918 559 24 3 627 1184 545259810 545259261 0.000000e+00 835.0
13 TraesCS6A01G276800 chr6B 90.172 641 50 5 1 641 545262538 545261911 0.000000e+00 822.0
14 TraesCS6A01G276800 chr6B 92.698 493 24 2 1202 1683 545258710 545258219 0.000000e+00 701.0
15 TraesCS6A01G276800 chr6B 84.465 663 45 22 5316 5938 545253911 545253267 8.520000e-168 601.0
16 TraesCS6A01G276800 chr6B 75.652 230 51 5 407 631 261661618 261661847 6.290000e-20 110.0
17 TraesCS6A01G276800 chr1A 85.425 247 30 5 326 570 548290947 548291189 9.880000e-63 252.0
18 TraesCS6A01G276800 chr1A 78.788 165 20 10 661 822 584498487 584498639 4.900000e-16 97.1
19 TraesCS6A01G276800 chr1A 93.478 46 3 0 774 819 522484607 522484562 1.070000e-07 69.4
20 TraesCS6A01G276800 chr3D 83.984 256 33 7 323 573 556115253 556115001 7.690000e-59 239.0
21 TraesCS6A01G276800 chr3D 82.278 158 11 6 655 810 415532971 415533113 2.910000e-23 121.0
22 TraesCS6A01G276800 chr3D 92.157 51 4 0 166 216 153779392 153779442 8.260000e-09 73.1
23 TraesCS6A01G276800 chr2D 83.137 255 37 6 323 573 390728895 390728643 1.670000e-55 228.0
24 TraesCS6A01G276800 chr2D 96.117 103 4 0 5707 5809 544610677 544610575 1.020000e-37 169.0
25 TraesCS6A01G276800 chr2D 97.826 46 1 0 774 819 64602219 64602174 4.940000e-11 80.5
26 TraesCS6A01G276800 chr5D 83.203 256 33 8 323 573 558062082 558061832 5.990000e-55 226.0
27 TraesCS6A01G276800 chr5D 83.267 251 35 5 323 570 28027129 28027375 2.150000e-54 224.0
28 TraesCS6A01G276800 chr5D 90.833 120 10 1 165 284 327746402 327746520 6.160000e-35 159.0
29 TraesCS6A01G276800 chr5D 95.238 84 3 1 4953 5036 470232504 470232586 1.340000e-26 132.0
30 TraesCS6A01G276800 chrUn 82.677 254 39 5 323 573 102576466 102576215 2.790000e-53 220.0
31 TraesCS6A01G276800 chr2A 79.715 281 42 9 5547 5815 686839605 686839328 7.860000e-44 189.0
32 TraesCS6A01G276800 chr2A 96.203 79 3 0 4958 5036 625011677 625011755 4.830000e-26 130.0
33 TraesCS6A01G276800 chr2A 93.617 47 3 0 774 820 659185135 659185089 2.970000e-08 71.3
34 TraesCS6A01G276800 chr4A 84.656 189 20 7 5649 5833 5552385 5552568 4.730000e-41 180.0
35 TraesCS6A01G276800 chr4A 92.308 91 6 1 4953 5042 18382480 18382570 1.740000e-25 128.0
36 TraesCS6A01G276800 chr4B 86.420 162 16 4 5648 5806 581069077 581068919 7.920000e-39 172.0
37 TraesCS6A01G276800 chr4B 92.308 91 6 1 4953 5042 525765548 525765458 1.740000e-25 128.0
38 TraesCS6A01G276800 chr2B 96.117 103 4 0 5707 5809 650164748 650164646 1.020000e-37 169.0
39 TraesCS6A01G276800 chr4D 88.462 130 11 3 5707 5833 464660638 464660510 2.870000e-33 154.0
40 TraesCS6A01G276800 chr7A 95.238 84 4 0 4953 5036 659022802 659022719 3.740000e-27 134.0
41 TraesCS6A01G276800 chr7A 94.118 85 3 2 4960 5042 394958919 394959003 1.740000e-25 128.0
42 TraesCS6A01G276800 chr7D 97.403 77 2 0 4960 5036 557416141 557416065 1.340000e-26 132.0
43 TraesCS6A01G276800 chr7D 84.685 111 9 4 662 768 115419061 115419167 2.930000e-18 104.0
44 TraesCS6A01G276800 chr7D 92.593 54 2 2 579 631 117579659 117579607 6.380000e-10 76.8
45 TraesCS6A01G276800 chr7D 90.566 53 4 1 579 631 611663509 611663560 1.070000e-07 69.4
46 TraesCS6A01G276800 chr5A 91.209 91 7 1 4953 5042 322220082 322220172 8.090000e-24 122.0
47 TraesCS6A01G276800 chr5A 93.333 45 2 1 587 631 9213057 9213100 1.380000e-06 65.8
48 TraesCS6A01G276800 chr3B 80.328 122 20 2 1484 1605 685077370 685077253 8.200000e-14 89.8


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 TraesCS6A01G276800 chr6A 503769049 503774989 5940 True 10972.000000 10972 100.0000 1 5941 1 chr6A.!!$R1 5940
1 TraesCS6A01G276800 chr6D 363063737 363069615 5878 True 1299.166667 4809 92.0025 262 5941 6 chr6D.!!$R3 5679
2 TraesCS6A01G276800 chr6B 545253267 545262538 9271 True 1179.666667 2359 90.2620 1 5938 6 chr6B.!!$R1 5937

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
248 249 0.450184 CCGGTGCATAAGGAAAACGG 59.550 55.0 0.00 0.00 0.00 4.44 F
1795 4605 0.032403 TGCTGAACATGTGGCTTTGC 59.968 50.0 16.07 8.98 0.00 3.68 F
3525 6537 0.373716 GATAGTTTTCTGCGTGGCGG 59.626 55.0 0.00 0.00 36.06 6.13 F
4648 7695 0.321653 GGGCCGGCTTAGGATATGTG 60.322 60.0 28.56 0.00 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 4682 0.465460 GGCCCGCCATTCTGTTATCA 60.465 55.0 0.00 0.0 35.81 2.15 R
3747 6760 2.159184 ACTACTGCTGTCATCCATGTCG 60.159 50.0 0.00 0.0 0.00 4.35 R
4752 7807 0.031585 AGCTGCGACAAGTAACACGA 59.968 50.0 0.00 0.0 0.00 4.35 R
5480 9054 0.526954 CGGTTAGTGTAGCGGCGATT 60.527 55.0 12.98 0.0 35.53 3.34 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
36 37 9.875691 GGAAGAATAGCCAACAAGAAATAAAAT 57.124 29.630 0.00 0.00 0.00 1.82
130 131 2.039879 AGTTAGTCCACACACCATTCCC 59.960 50.000 0.00 0.00 0.00 3.97
150 151 4.469945 TCCCCGCTTATGATAATCTAAGGG 59.530 45.833 0.00 0.00 37.54 3.95
177 178 4.537135 AGAAAGAAGGCACGAGTATTCA 57.463 40.909 0.00 0.00 0.00 2.57
199 200 4.473477 AAGTAGAAGCGCTAACATTCCT 57.527 40.909 12.05 2.13 0.00 3.36
201 202 3.702045 AGTAGAAGCGCTAACATTCCTCT 59.298 43.478 12.05 10.02 0.00 3.69
205 206 3.618690 AGCGCTAACATTCCTCTTTCT 57.381 42.857 8.99 0.00 0.00 2.52
224 225 3.884895 TCTTTGAGAAAGCACTTGACCA 58.115 40.909 0.00 0.00 38.39 4.02
248 249 0.450184 CCGGTGCATAAGGAAAACGG 59.550 55.000 0.00 0.00 0.00 4.44
249 250 0.450184 CGGTGCATAAGGAAAACGGG 59.550 55.000 0.00 0.00 0.00 5.28
259 260 1.493446 AGGAAAACGGGTCTTCAGGTT 59.507 47.619 0.00 0.00 0.00 3.50
265 266 1.697432 ACGGGTCTTCAGGTTGATGAA 59.303 47.619 0.00 0.00 37.60 2.57
277 278 2.087646 GTTGATGAAGTCCTCCCAAGC 58.912 52.381 0.00 0.00 0.00 4.01
299 300 1.699730 TGTCTCTCAAACTCACCCGA 58.300 50.000 0.00 0.00 0.00 5.14
490 492 6.422776 ACACGAGGAATACAATGATGAAAC 57.577 37.500 0.00 0.00 0.00 2.78
528 530 6.093495 TGGACGCATGGTTTAAGAGATAAAAG 59.907 38.462 0.00 0.00 35.33 2.27
613 619 3.496160 GGGAGTGACCTTTGCAAAGAGTA 60.496 47.826 35.25 19.58 38.28 2.59
619 625 4.591498 TGACCTTTGCAAAGAGTACTCCTA 59.409 41.667 35.25 13.62 38.28 2.94
730 2945 4.748277 AGGCTAATGAAAATGCTTGCAT 57.252 36.364 1.81 1.81 31.43 3.96
768 2983 3.114606 TCAATGGCAGAGGACTTGGATA 58.885 45.455 0.00 0.00 0.00 2.59
769 2984 3.135348 TCAATGGCAGAGGACTTGGATAG 59.865 47.826 0.00 0.00 0.00 2.08
770 2985 2.254152 TGGCAGAGGACTTGGATAGT 57.746 50.000 0.00 0.00 40.71 2.12
771 2986 2.551270 TGGCAGAGGACTTGGATAGTT 58.449 47.619 0.00 0.00 37.17 2.24
772 2987 2.237143 TGGCAGAGGACTTGGATAGTTG 59.763 50.000 0.00 0.00 37.17 3.16
773 2988 2.420687 GGCAGAGGACTTGGATAGTTGG 60.421 54.545 0.00 0.00 37.17 3.77
774 2989 2.501723 GCAGAGGACTTGGATAGTTGGA 59.498 50.000 0.00 0.00 37.17 3.53
775 2990 3.135530 GCAGAGGACTTGGATAGTTGGAT 59.864 47.826 0.00 0.00 37.17 3.41
801 3016 7.710907 TGTGCAATATTTAGGACACATCTAGAC 59.289 37.037 0.00 0.00 33.41 2.59
830 3045 9.296400 GCTTTAACAAAACTGTTAGTGATTTCA 57.704 29.630 10.18 0.00 35.91 2.69
868 3089 5.159273 TGTGTGTACCAAAGATATGCAGA 57.841 39.130 0.00 0.00 0.00 4.26
878 3099 6.264744 ACCAAAGATATGCAGAGATGGAATTG 59.735 38.462 10.33 0.00 0.00 2.32
916 3137 3.354397 CAGCGATTAATTCAGAAACCGC 58.646 45.455 5.94 5.94 41.43 5.68
920 3141 1.455248 TTAATTCAGAAACCGCGGGG 58.545 50.000 31.76 18.33 40.11 5.73
1456 4210 1.939785 GAGTACGACTGCGCATCCG 60.940 63.158 23.81 23.81 42.48 4.18
1567 4321 9.014297 GCTACATAGGCTTTGGTATTTCATATT 57.986 33.333 9.76 0.00 0.00 1.28
1569 4323 7.661040 ACATAGGCTTTGGTATTTCATATTGC 58.339 34.615 9.76 0.00 0.00 3.56
1572 4326 5.893255 AGGCTTTGGTATTTCATATTGCTCA 59.107 36.000 0.00 0.00 0.00 4.26
1576 4330 9.185192 GCTTTGGTATTTCATATTGCTCATTAC 57.815 33.333 0.00 0.00 0.00 1.89
1594 4348 6.945218 TCATTACTTGCTTGGCCAATAAATT 58.055 32.000 20.85 12.70 0.00 1.82
1679 4444 2.496070 ACTCTACCAGATGCGCAAACTA 59.504 45.455 17.11 1.45 0.00 2.24
1683 4448 2.561569 ACCAGATGCGCAAACTATACC 58.438 47.619 17.11 0.00 0.00 2.73
1684 4449 2.170607 ACCAGATGCGCAAACTATACCT 59.829 45.455 17.11 0.00 0.00 3.08
1685 4450 3.206150 CCAGATGCGCAAACTATACCTT 58.794 45.455 17.11 0.00 0.00 3.50
1686 4451 3.248602 CCAGATGCGCAAACTATACCTTC 59.751 47.826 17.11 2.62 0.00 3.46
1687 4452 3.248602 CAGATGCGCAAACTATACCTTCC 59.751 47.826 17.11 0.00 0.00 3.46
1688 4453 2.772077 TGCGCAAACTATACCTTCCA 57.228 45.000 8.16 0.00 0.00 3.53
1689 4454 2.352388 TGCGCAAACTATACCTTCCAC 58.648 47.619 8.16 0.00 0.00 4.02
1693 4503 3.343617 GCAAACTATACCTTCCACTGCA 58.656 45.455 0.00 0.00 0.00 4.41
1733 4543 9.853555 GTATCTGACATCTTCTTACATATCTGG 57.146 37.037 0.00 0.00 0.00 3.86
1734 4544 6.753180 TCTGACATCTTCTTACATATCTGGC 58.247 40.000 0.00 0.00 0.00 4.85
1735 4545 5.858381 TGACATCTTCTTACATATCTGGCC 58.142 41.667 0.00 0.00 0.00 5.36
1736 4546 5.366477 TGACATCTTCTTACATATCTGGCCA 59.634 40.000 4.71 4.71 0.00 5.36
1737 4547 6.126796 TGACATCTTCTTACATATCTGGCCAA 60.127 38.462 7.01 0.00 0.00 4.52
1738 4548 6.845908 ACATCTTCTTACATATCTGGCCAAT 58.154 36.000 7.01 6.27 0.00 3.16
1739 4549 7.977818 ACATCTTCTTACATATCTGGCCAATA 58.022 34.615 7.01 8.45 0.00 1.90
1740 4550 7.880195 ACATCTTCTTACATATCTGGCCAATAC 59.120 37.037 7.01 0.00 0.00 1.89
1741 4551 7.618019 TCTTCTTACATATCTGGCCAATACT 57.382 36.000 7.01 0.00 0.00 2.12
1742 4552 7.445121 TCTTCTTACATATCTGGCCAATACTG 58.555 38.462 7.01 5.15 0.00 2.74
1743 4553 5.551233 TCTTACATATCTGGCCAATACTGC 58.449 41.667 7.01 0.00 0.00 4.40
1744 4554 3.862877 ACATATCTGGCCAATACTGCA 57.137 42.857 7.01 0.00 0.00 4.41
1745 4555 4.169059 ACATATCTGGCCAATACTGCAA 57.831 40.909 7.01 0.00 0.00 4.08
1746 4556 4.535781 ACATATCTGGCCAATACTGCAAA 58.464 39.130 7.01 0.00 0.00 3.68
1747 4557 5.142639 ACATATCTGGCCAATACTGCAAAT 58.857 37.500 7.01 0.00 0.00 2.32
1748 4558 5.599656 ACATATCTGGCCAATACTGCAAATT 59.400 36.000 7.01 0.00 0.00 1.82
1774 4584 5.117355 GCATGTAGCAGCATATGAAATGT 57.883 39.130 6.97 0.00 44.79 2.71
1778 4588 5.342433 TGTAGCAGCATATGAAATGTTTGC 58.658 37.500 6.97 4.22 34.41 3.68
1794 4604 2.512485 TTGCTGAACATGTGGCTTTG 57.488 45.000 16.07 0.49 0.00 2.77
1795 4605 0.032403 TGCTGAACATGTGGCTTTGC 59.968 50.000 16.07 8.98 0.00 3.68
1854 4664 3.300934 CTCGCTGGCCTGTGCTACA 62.301 63.158 17.70 0.47 37.74 2.74
1860 4670 1.680735 CTGGCCTGTGCTACAACAAAA 59.319 47.619 3.32 0.00 37.74 2.44
1903 4713 1.434696 GCGGGCCACAATGAATCAG 59.565 57.895 4.39 0.00 0.00 2.90
1970 4780 4.132336 GTGCATAAAGATCCTCATGCTCA 58.868 43.478 18.42 3.09 43.30 4.26
1980 4790 3.635591 TCCTCATGCTCATAGTGTCTCA 58.364 45.455 0.00 0.00 0.00 3.27
2010 4820 4.022935 TCTGCTGGAACAAGCAAAAGTATG 60.023 41.667 5.38 0.00 40.62 2.39
2017 4827 5.008613 GGAACAAGCAAAAGTATGTCACTGA 59.991 40.000 0.00 0.00 37.63 3.41
2018 4828 6.294176 GGAACAAGCAAAAGTATGTCACTGAT 60.294 38.462 0.00 0.00 37.63 2.90
2019 4829 6.639632 ACAAGCAAAAGTATGTCACTGATT 57.360 33.333 0.00 0.00 37.63 2.57
2021 4831 6.262944 ACAAGCAAAAGTATGTCACTGATTCA 59.737 34.615 0.00 0.00 37.63 2.57
2022 4832 6.246420 AGCAAAAGTATGTCACTGATTCAC 57.754 37.500 0.00 0.00 37.63 3.18
2023 4833 6.000219 AGCAAAAGTATGTCACTGATTCACT 59.000 36.000 0.00 0.00 37.63 3.41
2024 4834 6.072838 AGCAAAAGTATGTCACTGATTCACTG 60.073 38.462 0.00 0.00 37.63 3.66
2025 4835 5.869753 AAAGTATGTCACTGATTCACTGC 57.130 39.130 0.00 0.00 37.63 4.40
2026 4836 4.541973 AGTATGTCACTGATTCACTGCA 57.458 40.909 0.00 0.00 35.62 4.41
2028 4838 4.874396 AGTATGTCACTGATTCACTGCATG 59.126 41.667 0.00 0.00 35.62 4.06
2031 4841 2.095532 GTCACTGATTCACTGCATGCTC 59.904 50.000 20.33 7.35 0.00 4.26
2032 4842 1.400846 CACTGATTCACTGCATGCTCC 59.599 52.381 20.33 0.85 0.00 4.70
2046 4856 7.117667 CACTGCATGCTCCGTAATACATATTAA 59.882 37.037 20.33 0.00 30.64 1.40
2071 4882 8.586570 AGTAGATTCTGATATTTCTTGAAGCG 57.413 34.615 0.00 0.00 31.63 4.68
2073 4884 4.882671 TTCTGATATTTCTTGAAGCGGC 57.117 40.909 0.00 0.00 0.00 6.53
2095 4906 3.376859 CGCAGGACTTTGGCATGTAAATA 59.623 43.478 0.00 0.00 0.00 1.40
2127 4938 1.073177 ACTTTTTCGGGCGTGTATCG 58.927 50.000 0.00 0.00 43.12 2.92
2135 4946 3.011818 TCGGGCGTGTATCGTATATGAT 58.988 45.455 12.07 12.07 42.13 2.45
2267 5078 2.745968 TGCTGGGGAACAAGAAGTTTT 58.254 42.857 0.00 0.00 41.51 2.43
2581 5392 3.046283 AGGAAGGGAAGCCAAAAGTTT 57.954 42.857 0.00 0.00 0.00 2.66
3070 5881 4.096532 TGAGTTCTCGAGGCAGTATAACAG 59.903 45.833 13.56 0.00 0.00 3.16
3093 5904 5.009811 AGAGCGCGAGATTATTTAGGTAGTT 59.990 40.000 12.10 0.00 0.00 2.24
3174 6006 7.766278 AGCAGTTAGTGTAATAACCTTCATCAG 59.234 37.037 0.00 0.00 36.49 2.90
3516 6528 5.948162 AGTCATGCATGTTGGATAGTTTTCT 59.052 36.000 25.43 0.00 0.00 2.52
3525 6537 0.373716 GATAGTTTTCTGCGTGGCGG 59.626 55.000 0.00 0.00 36.06 6.13
3640 6652 6.186957 TGTTATGCCCTCACAAAACATATCT 58.813 36.000 0.00 0.00 0.00 1.98
3747 6760 1.135859 CAGCTTCCGTTGACAGATTGC 60.136 52.381 0.00 0.00 0.00 3.56
3982 6996 6.414408 AGATCAATTTTGCTCAGTAGAACG 57.586 37.500 0.00 0.00 0.00 3.95
3983 6997 5.352569 AGATCAATTTTGCTCAGTAGAACGG 59.647 40.000 0.00 0.00 0.00 4.44
3984 6998 4.637276 TCAATTTTGCTCAGTAGAACGGA 58.363 39.130 0.00 0.00 0.00 4.69
3985 6999 5.060506 TCAATTTTGCTCAGTAGAACGGAA 58.939 37.500 0.00 0.00 0.00 4.30
3986 7000 5.049680 TCAATTTTGCTCAGTAGAACGGAAC 60.050 40.000 0.00 0.00 0.00 3.62
4014 7028 7.950236 AGATACTTATTTCACAAACGAAGACG 58.050 34.615 0.00 0.00 45.75 4.18
4039 7053 5.335583 CCATGAATCGAAACTAACCAAGCAA 60.336 40.000 0.00 0.00 0.00 3.91
4097 7117 1.353022 GACCCTCACCAACCCATTACA 59.647 52.381 0.00 0.00 0.00 2.41
4132 7152 6.035650 CCATGCTTCAGAATTTTTGCAGTATG 59.964 38.462 9.41 9.41 33.92 2.39
4331 7373 1.593006 GGTGGTGCGATTAATGTCTCG 59.407 52.381 0.00 0.00 37.92 4.04
4364 7407 3.040147 TGTAGCTCTTGTTTTCCTCGG 57.960 47.619 0.00 0.00 0.00 4.63
4380 7423 8.446599 TTTTCCTCGGAAAACATAGGATTATC 57.553 34.615 17.48 0.00 45.59 1.75
4400 7443 7.900782 TTATCTTTTTGTACAGCTAGGTCAC 57.099 36.000 0.00 0.00 0.00 3.67
4407 7450 1.251527 ACAGCTAGGTCACCGTGGAG 61.252 60.000 0.00 0.00 0.00 3.86
4424 7467 2.760650 TGGAGCTGCGATCTTCTCTTTA 59.239 45.455 0.00 0.00 0.00 1.85
4477 7520 5.563475 CGCAGAATTCAGGAATTTGACAACT 60.563 40.000 8.44 0.00 40.77 3.16
4592 7635 4.464069 ACTCGAGATCCTTCTTTTCTGG 57.536 45.455 21.68 0.00 30.30 3.86
4614 7657 4.368315 GAAAACAAAAGGAAGGCGATGTT 58.632 39.130 0.00 0.00 32.78 2.71
4644 7691 1.841556 CAGGGGCCGGCTTAGGATA 60.842 63.158 28.56 0.00 0.00 2.59
4648 7695 0.321653 GGGCCGGCTTAGGATATGTG 60.322 60.000 28.56 0.00 0.00 3.21
4653 7700 3.614390 GCCGGCTTAGGATATGTGTAGTC 60.614 52.174 22.15 0.00 0.00 2.59
4686 7741 2.829720 GACACTGGTGTATGTACTGGGA 59.170 50.000 6.35 0.00 45.05 4.37
4744 7799 5.413833 AGAGATTGAGCCAGTTTTGTATGTG 59.586 40.000 0.00 0.00 0.00 3.21
4745 7800 5.072741 AGATTGAGCCAGTTTTGTATGTGT 58.927 37.500 0.00 0.00 0.00 3.72
4747 7802 3.146066 TGAGCCAGTTTTGTATGTGTCC 58.854 45.455 0.00 0.00 0.00 4.02
4748 7803 2.488153 GAGCCAGTTTTGTATGTGTCCC 59.512 50.000 0.00 0.00 0.00 4.46
4751 7806 2.228822 CCAGTTTTGTATGTGTCCCTGC 59.771 50.000 0.00 0.00 0.00 4.85
4752 7807 3.149196 CAGTTTTGTATGTGTCCCTGCT 58.851 45.455 0.00 0.00 0.00 4.24
4753 7808 3.189287 CAGTTTTGTATGTGTCCCTGCTC 59.811 47.826 0.00 0.00 0.00 4.26
4843 7901 2.223112 GCCTCGTAGACAATGTTGCATG 60.223 50.000 0.00 0.00 0.00 4.06
4852 7910 2.027929 ACAATGTTGCATGGGACCATTG 60.028 45.455 0.00 6.48 44.85 2.82
4853 7911 1.941377 ATGTTGCATGGGACCATTGT 58.059 45.000 0.00 0.00 33.90 2.71
4874 7933 1.153939 GTGTTGCACCGCACACAAA 60.154 52.632 13.27 0.00 38.71 2.83
4875 7934 0.527385 GTGTTGCACCGCACACAAAT 60.527 50.000 13.27 0.00 38.71 2.32
4889 7949 5.164196 CGCACACAAATAAAGAATGTTTCCG 60.164 40.000 0.00 0.00 0.00 4.30
4895 7955 9.619316 CACAAATAAAGAATGTTTCCGTCATAA 57.381 29.630 0.00 0.00 0.00 1.90
4899 7959 9.801873 AATAAAGAATGTTTCCGTCATAAATGG 57.198 29.630 0.00 0.00 35.07 3.16
4900 7960 7.461182 AAAGAATGTTTCCGTCATAAATGGA 57.539 32.000 0.00 0.00 41.56 3.41
4924 7988 0.326264 ACTGTCCCCATTCAGCACTC 59.674 55.000 0.00 0.00 35.37 3.51
4925 7989 0.325933 CTGTCCCCATTCAGCACTCA 59.674 55.000 0.00 0.00 0.00 3.41
4943 8010 6.919662 AGCACTCAAAATATTATGCGGAAATG 59.080 34.615 0.00 0.00 38.12 2.32
4959 8026 6.021596 GCGGAAATGTATGTTTCTTGTGTAG 58.978 40.000 0.00 0.00 38.02 2.74
4960 8027 6.348213 GCGGAAATGTATGTTTCTTGTGTAGT 60.348 38.462 0.00 0.00 38.02 2.73
4962 8029 8.166706 CGGAAATGTATGTTTCTTGTGTAGTAC 58.833 37.037 0.00 0.00 38.02 2.73
4970 8037 2.719739 TCTTGTGTAGTACTCCCTCCG 58.280 52.381 0.00 0.00 0.00 4.63
4971 8038 1.749634 CTTGTGTAGTACTCCCTCCGG 59.250 57.143 0.00 0.00 0.00 5.14
4973 8040 1.340405 TGTGTAGTACTCCCTCCGGTC 60.340 57.143 0.00 0.00 0.00 4.79
4974 8041 0.257039 TGTAGTACTCCCTCCGGTCC 59.743 60.000 0.00 0.00 0.00 4.46
4980 8047 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
4981 8048 1.907255 ACTCCCTCCGGTCCTTTTTAG 59.093 52.381 0.00 0.00 0.00 1.85
4982 8049 1.907255 CTCCCTCCGGTCCTTTTTAGT 59.093 52.381 0.00 0.00 0.00 2.24
4985 8052 2.817844 CCCTCCGGTCCTTTTTAGTTTG 59.182 50.000 0.00 0.00 0.00 2.93
4986 8053 2.228103 CCTCCGGTCCTTTTTAGTTTGC 59.772 50.000 0.00 0.00 0.00 3.68
4987 8054 2.882137 CTCCGGTCCTTTTTAGTTTGCA 59.118 45.455 0.00 0.00 0.00 4.08
4990 8057 5.258051 TCCGGTCCTTTTTAGTTTGCATAT 58.742 37.500 0.00 0.00 0.00 1.78
4991 8058 6.416415 TCCGGTCCTTTTTAGTTTGCATATA 58.584 36.000 0.00 0.00 0.00 0.86
4993 8060 7.066525 TCCGGTCCTTTTTAGTTTGCATATAAG 59.933 37.037 0.00 0.00 0.00 1.73
4995 8062 7.908601 CGGTCCTTTTTAGTTTGCATATAAGAC 59.091 37.037 0.00 0.00 0.00 3.01
4996 8063 8.957466 GGTCCTTTTTAGTTTGCATATAAGACT 58.043 33.333 0.00 0.00 0.00 3.24
5004 8071 9.719355 TTAGTTTGCATATAAGACTTGTCTGAA 57.281 29.630 3.87 0.00 0.00 3.02
5005 8072 8.261492 AGTTTGCATATAAGACTTGTCTGAAG 57.739 34.615 3.87 0.00 0.00 3.02
5006 8073 7.880195 AGTTTGCATATAAGACTTGTCTGAAGT 59.120 33.333 3.87 0.00 0.00 3.01
5008 8075 6.935167 TGCATATAAGACTTGTCTGAAGTCA 58.065 36.000 15.11 0.00 46.78 3.41
5009 8076 7.386059 TGCATATAAGACTTGTCTGAAGTCAA 58.614 34.615 15.11 5.12 46.78 3.18
5010 8077 7.877612 TGCATATAAGACTTGTCTGAAGTCAAA 59.122 33.333 15.11 4.82 46.78 2.69
5011 8078 8.171840 GCATATAAGACTTGTCTGAAGTCAAAC 58.828 37.037 15.11 0.00 46.78 2.93
5012 8079 8.660373 CATATAAGACTTGTCTGAAGTCAAACC 58.340 37.037 15.11 0.00 46.78 3.27
5013 8080 4.762289 AGACTTGTCTGAAGTCAAACCT 57.238 40.909 15.11 0.00 46.78 3.50
5014 8081 4.698575 AGACTTGTCTGAAGTCAAACCTC 58.301 43.478 15.11 0.00 46.78 3.85
5015 8082 3.458189 ACTTGTCTGAAGTCAAACCTCG 58.542 45.455 0.00 0.00 0.00 4.63
5016 8083 3.118738 ACTTGTCTGAAGTCAAACCTCGT 60.119 43.478 0.00 0.00 0.00 4.18
5017 8084 4.098960 ACTTGTCTGAAGTCAAACCTCGTA 59.901 41.667 0.00 0.00 0.00 3.43
5022 8089 5.522824 GTCTGAAGTCAAACCTCGTAAACTT 59.477 40.000 0.00 0.00 0.00 2.66
5023 8090 6.036844 GTCTGAAGTCAAACCTCGTAAACTTT 59.963 38.462 0.00 0.00 0.00 2.66
5024 8091 6.036735 TCTGAAGTCAAACCTCGTAAACTTTG 59.963 38.462 0.00 0.00 0.00 2.77
5026 8093 5.729974 AGTCAAACCTCGTAAACTTTGAC 57.270 39.130 12.19 12.19 46.84 3.18
5027 8094 4.840911 GTCAAACCTCGTAAACTTTGACC 58.159 43.478 9.86 0.00 43.35 4.02
5029 8096 4.942483 TCAAACCTCGTAAACTTTGACCAA 59.058 37.500 0.00 0.00 29.66 3.67
5032 8099 6.459670 AACCTCGTAAACTTTGACCAAATT 57.540 33.333 0.00 0.00 0.00 1.82
5033 8100 6.459670 ACCTCGTAAACTTTGACCAAATTT 57.540 33.333 0.00 0.00 0.00 1.82
5034 8101 7.571080 ACCTCGTAAACTTTGACCAAATTTA 57.429 32.000 0.00 2.26 0.00 1.40
5038 8278 6.579292 TCGTAAACTTTGACCAAATTTATGCG 59.421 34.615 15.32 12.44 30.78 4.73
5044 8284 6.420604 ACTTTGACCAAATTTATGCGAAACTG 59.579 34.615 0.00 0.00 0.00 3.16
5067 8307 3.433306 TTGAAAGGATCAATCACCCGT 57.567 42.857 0.00 0.00 43.08 5.28
5074 8314 2.482142 GGATCAATCACCCGTCTGTCTC 60.482 54.545 0.00 0.00 0.00 3.36
5075 8315 0.895530 TCAATCACCCGTCTGTCTCC 59.104 55.000 0.00 0.00 0.00 3.71
5105 8345 3.947910 AAATGCTCCCAGACAAATGTG 57.052 42.857 0.00 0.00 0.00 3.21
5114 8354 6.491403 GCTCCCAGACAAATGTGGAATATATT 59.509 38.462 0.00 0.00 42.06 1.28
5175 8568 5.520022 TCGGATTTACGAGTAAAAACAGC 57.480 39.130 11.77 0.00 38.38 4.40
5180 8573 0.475044 ACGAGTAAAAACAGCCCCCA 59.525 50.000 0.00 0.00 0.00 4.96
5183 8576 2.618045 CGAGTAAAAACAGCCCCCAGAT 60.618 50.000 0.00 0.00 0.00 2.90
5197 8590 6.769822 CAGCCCCCAGATGTTGAATATATATC 59.230 42.308 0.00 0.00 0.00 1.63
5203 8604 9.091784 CCCAGATGTTGAATATATATCGTGAAG 57.908 37.037 0.00 0.00 0.00 3.02
5222 8623 5.123979 GTGAAGTCCCAGAATGATTACAACC 59.876 44.000 0.00 0.00 39.69 3.77
5306 8707 5.606348 AGGCTGAATCTTAACACCTAGAG 57.394 43.478 0.00 0.00 0.00 2.43
5307 8708 4.123506 GGCTGAATCTTAACACCTAGAGC 58.876 47.826 0.00 0.00 0.00 4.09
5366 8925 0.318360 CACTGTAACTGCCGTCACGA 60.318 55.000 0.00 0.00 0.00 4.35
5437 8996 2.827642 GTGCAGCTCATCCAGGCC 60.828 66.667 0.00 0.00 0.00 5.19
5443 9002 4.227134 CTCATCCAGGCCCGACGG 62.227 72.222 6.99 6.99 0.00 4.79
5481 9055 2.813474 CCCGCGCGTCATTCTCAA 60.813 61.111 29.95 0.00 0.00 3.02
5482 9056 2.173669 CCCGCGCGTCATTCTCAAT 61.174 57.895 29.95 0.00 0.00 2.57
5483 9057 1.273887 CCGCGCGTCATTCTCAATC 59.726 57.895 29.95 0.00 0.00 2.67
5484 9058 1.084666 CGCGCGTCATTCTCAATCG 60.085 57.895 24.19 0.00 0.00 3.34
5486 9060 1.273887 CGCGTCATTCTCAATCGCC 59.726 57.895 0.00 0.00 43.18 5.54
5487 9061 1.273887 GCGTCATTCTCAATCGCCG 59.726 57.895 0.00 0.00 40.83 6.46
5489 9063 1.148157 CGTCATTCTCAATCGCCGCT 61.148 55.000 0.00 0.00 0.00 5.52
5490 9064 1.852942 GTCATTCTCAATCGCCGCTA 58.147 50.000 0.00 0.00 0.00 4.26
5491 9065 1.523095 GTCATTCTCAATCGCCGCTAC 59.477 52.381 0.00 0.00 0.00 3.58
5492 9066 1.136110 TCATTCTCAATCGCCGCTACA 59.864 47.619 0.00 0.00 0.00 2.74
5493 9067 1.258982 CATTCTCAATCGCCGCTACAC 59.741 52.381 0.00 0.00 0.00 2.90
5494 9068 0.530744 TTCTCAATCGCCGCTACACT 59.469 50.000 0.00 0.00 0.00 3.55
5533 9107 2.139118 GGGAATGAGATAGCTTGACGC 58.861 52.381 0.00 0.00 39.57 5.19
5796 9376 1.305930 GGTGACCTTGACGCCATTCC 61.306 60.000 0.00 0.00 37.78 3.01
5806 9389 1.224315 CGCCATTCCTGTCCATGGA 59.776 57.895 11.44 11.44 42.49 3.41
5812 9395 3.484407 CATTCCTGTCCATGGATCCTTC 58.516 50.000 19.62 4.90 33.09 3.46
5815 9398 1.419387 CCTGTCCATGGATCCTTCCTC 59.581 57.143 19.62 2.45 43.07 3.71
5853 9460 3.002348 CACCTTTGGTCAGTTTTCTCGAC 59.998 47.826 0.00 0.00 31.02 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 8.934023 TCAGTTCCACCTATTTTATTTCTTGT 57.066 30.769 0.00 0.00 0.00 3.16
36 37 7.510675 AATCTATTCCTTTCAGTTCCACCTA 57.489 36.000 0.00 0.00 0.00 3.08
38 39 7.468141 AAAATCTATTCCTTTCAGTTCCACC 57.532 36.000 0.00 0.00 0.00 4.61
95 96 6.264518 TGTGGACTAACTATTCATGCGATAGA 59.735 38.462 17.57 2.05 39.76 1.98
130 131 4.832248 TGCCCTTAGATTATCATAAGCGG 58.168 43.478 0.00 5.30 0.00 5.52
150 151 3.045688 CTCGTGCCTTCTTTCTTTTTGC 58.954 45.455 0.00 0.00 0.00 3.68
177 178 4.833390 AGGAATGTTAGCGCTTCTACTTT 58.167 39.130 18.68 15.43 0.00 2.66
201 202 4.704540 TGGTCAAGTGCTTTCTCAAAGAAA 59.295 37.500 0.01 2.44 41.51 2.52
205 206 3.351740 TGTGGTCAAGTGCTTTCTCAAA 58.648 40.909 0.00 0.00 0.00 2.69
224 225 0.037590 TTCCTTATGCACCGGCTTGT 59.962 50.000 0.00 0.00 41.91 3.16
259 260 1.361204 TGCTTGGGAGGACTTCATCA 58.639 50.000 0.00 0.00 0.00 3.07
265 266 1.280421 GAGACAATGCTTGGGAGGACT 59.720 52.381 1.84 0.00 34.12 3.85
277 278 2.738846 CGGGTGAGTTTGAGAGACAATG 59.261 50.000 0.00 0.00 38.36 2.82
299 300 9.503369 AAACTAATACTTCTACCTATCACCCTT 57.497 33.333 0.00 0.00 0.00 3.95
317 318 4.617959 CCTCTCGCGGAATCAAACTAATA 58.382 43.478 6.13 0.00 0.00 0.98
370 371 2.291457 AAACCAGGCGCACGCTTTTT 62.291 50.000 15.36 3.09 41.60 1.94
371 372 2.781158 AAACCAGGCGCACGCTTTT 61.781 52.632 15.36 6.78 41.60 2.27
422 424 8.722480 TCTCATGTTGATAGATTTTGACGAAT 57.278 30.769 0.00 0.00 0.00 3.34
490 492 0.168128 GCGTCCAAATCTTGAACCGG 59.832 55.000 0.00 0.00 0.00 5.28
497 499 4.764823 TCTTAAACCATGCGTCCAAATCTT 59.235 37.500 0.00 0.00 0.00 2.40
556 558 8.101419 AGGTTACGATAATCTGGAAGTTTTTCT 58.899 33.333 0.00 0.00 33.68 2.52
557 559 8.175716 CAGGTTACGATAATCTGGAAGTTTTTC 58.824 37.037 9.05 0.00 33.76 2.29
573 579 3.170717 TCCCACTTTCTCAGGTTACGAT 58.829 45.455 0.00 0.00 0.00 3.73
577 583 3.323979 GTCACTCCCACTTTCTCAGGTTA 59.676 47.826 0.00 0.00 0.00 2.85
613 619 8.611051 ACAGACCTAATCACTAATTTAGGAGT 57.389 34.615 14.04 7.65 0.00 3.85
619 625 7.556635 GCCCTAAACAGACCTAATCACTAATTT 59.443 37.037 0.00 0.00 0.00 1.82
730 2945 7.838884 TGCCATTGATTTTACATGAAGATTCA 58.161 30.769 0.00 0.00 42.14 2.57
768 2983 6.095440 GTGTCCTAAATATTGCACATCCAACT 59.905 38.462 0.00 0.00 0.00 3.16
769 2984 6.127758 TGTGTCCTAAATATTGCACATCCAAC 60.128 38.462 0.00 0.00 32.79 3.77
770 2985 5.948758 TGTGTCCTAAATATTGCACATCCAA 59.051 36.000 0.00 0.00 32.79 3.53
771 2986 5.504853 TGTGTCCTAAATATTGCACATCCA 58.495 37.500 0.00 0.00 32.79 3.41
772 2987 6.639632 ATGTGTCCTAAATATTGCACATCC 57.360 37.500 12.75 0.00 41.81 3.51
774 2989 8.432013 TCTAGATGTGTCCTAAATATTGCACAT 58.568 33.333 15.93 15.93 46.19 3.21
775 2990 7.710907 GTCTAGATGTGTCCTAAATATTGCACA 59.289 37.037 0.00 0.00 40.42 4.57
801 3016 6.252281 TCACTAACAGTTTTGTTAAAGCACG 58.748 36.000 0.00 0.00 46.21 5.34
830 3045 3.420482 CAGGGCCGGGGAATCCTT 61.420 66.667 2.18 0.00 0.00 3.36
878 3099 7.665080 AATCGCTGCGTATCTTTTTATTTTC 57.335 32.000 22.48 0.00 0.00 2.29
916 3137 4.918201 GCGAGAGGAATGGCCCCG 62.918 72.222 0.00 0.00 37.37 5.73
920 3141 1.372087 CCTTGTGCGAGAGGAATGGC 61.372 60.000 0.00 0.00 34.91 4.40
1434 4188 0.592500 ATGCGCAGTCGTACTCATCG 60.593 55.000 18.32 0.00 38.14 3.84
1456 4210 1.028868 GGGTGCTGGTGAGAATGAGC 61.029 60.000 0.00 0.00 0.00 4.26
1567 4321 1.176527 GGCCAAGCAAGTAATGAGCA 58.823 50.000 0.00 0.00 0.00 4.26
1568 4322 1.176527 TGGCCAAGCAAGTAATGAGC 58.823 50.000 0.61 0.00 0.00 4.26
1569 4323 5.581126 TTATTGGCCAAGCAAGTAATGAG 57.419 39.130 24.94 0.00 0.00 2.90
1572 4326 7.393216 TGAAATTTATTGGCCAAGCAAGTAAT 58.607 30.769 24.94 12.71 0.00 1.89
1576 4330 7.846644 TTATGAAATTTATTGGCCAAGCAAG 57.153 32.000 24.94 0.00 0.00 4.01
1594 4348 5.450592 TGAGCTGCAACAATGTTTATGAA 57.549 34.783 1.02 0.00 0.00 2.57
1679 4444 5.906073 GCATAAAAATGCAGTGGAAGGTAT 58.094 37.500 5.51 0.00 46.25 2.73
1707 4517 9.853555 CCAGATATGTAAGAAGATGTCAGATAC 57.146 37.037 0.00 0.00 0.00 2.24
1719 4529 5.997746 GCAGTATTGGCCAGATATGTAAGAA 59.002 40.000 5.11 0.00 0.00 2.52
1720 4530 5.071653 TGCAGTATTGGCCAGATATGTAAGA 59.928 40.000 5.11 0.00 0.00 2.10
1721 4531 5.308014 TGCAGTATTGGCCAGATATGTAAG 58.692 41.667 5.11 0.00 0.00 2.34
1723 4533 4.972751 TGCAGTATTGGCCAGATATGTA 57.027 40.909 5.11 0.85 0.00 2.29
1725 4535 5.717078 ATTTGCAGTATTGGCCAGATATG 57.283 39.130 5.11 5.61 0.00 1.78
1727 4537 5.221028 CGAAATTTGCAGTATTGGCCAGATA 60.221 40.000 5.11 4.51 0.00 1.98
1728 4538 4.440525 CGAAATTTGCAGTATTGGCCAGAT 60.441 41.667 5.11 5.57 0.00 2.90
1729 4539 3.119531 CGAAATTTGCAGTATTGGCCAGA 60.120 43.478 5.11 0.00 0.00 3.86
1730 4540 3.181397 CGAAATTTGCAGTATTGGCCAG 58.819 45.455 5.11 0.00 0.00 4.85
1731 4541 2.094286 CCGAAATTTGCAGTATTGGCCA 60.094 45.455 0.00 0.00 0.00 5.36
1732 4542 2.539476 CCGAAATTTGCAGTATTGGCC 58.461 47.619 0.00 0.00 0.00 5.36
1733 4543 1.926510 GCCGAAATTTGCAGTATTGGC 59.073 47.619 0.00 6.43 0.00 4.52
1734 4544 3.229276 TGCCGAAATTTGCAGTATTGG 57.771 42.857 0.00 0.00 32.77 3.16
1735 4545 4.175516 ACATGCCGAAATTTGCAGTATTG 58.824 39.130 8.87 5.23 41.46 1.90
1736 4546 4.454728 ACATGCCGAAATTTGCAGTATT 57.545 36.364 8.87 0.00 41.46 1.89
1737 4547 4.498009 GCTACATGCCGAAATTTGCAGTAT 60.498 41.667 8.87 0.98 41.46 2.12
1738 4548 3.181501 GCTACATGCCGAAATTTGCAGTA 60.182 43.478 8.87 9.51 41.46 2.74
1739 4549 2.415893 GCTACATGCCGAAATTTGCAGT 60.416 45.455 8.87 9.01 41.46 4.40
1740 4550 2.187707 GCTACATGCCGAAATTTGCAG 58.812 47.619 8.87 4.61 41.46 4.41
1741 4551 1.543358 TGCTACATGCCGAAATTTGCA 59.457 42.857 5.74 5.74 42.52 4.08
1742 4552 2.187707 CTGCTACATGCCGAAATTTGC 58.812 47.619 0.00 0.00 42.00 3.68
1743 4553 2.187707 GCTGCTACATGCCGAAATTTG 58.812 47.619 0.00 0.00 42.00 2.32
1744 4554 1.818060 TGCTGCTACATGCCGAAATTT 59.182 42.857 0.00 0.00 42.00 1.82
1745 4555 1.462616 TGCTGCTACATGCCGAAATT 58.537 45.000 0.00 0.00 42.00 1.82
1746 4556 1.683943 ATGCTGCTACATGCCGAAAT 58.316 45.000 0.00 0.00 42.00 2.17
1747 4557 2.323968 TATGCTGCTACATGCCGAAA 57.676 45.000 0.00 0.00 42.00 3.46
1748 4558 2.145536 CATATGCTGCTACATGCCGAA 58.854 47.619 0.00 0.00 42.00 4.30
1774 4584 2.823984 CAAAGCCACATGTTCAGCAAA 58.176 42.857 13.21 0.00 0.00 3.68
1794 4604 8.850156 ACATCCTGTTGATATACAATAAAAGGC 58.150 33.333 0.00 0.00 40.76 4.35
1860 4670 7.507829 CCATTCTGTTATCATCCTCTCTCTTT 58.492 38.462 0.00 0.00 0.00 2.52
1870 4680 1.537202 GCCCGCCATTCTGTTATCATC 59.463 52.381 0.00 0.00 0.00 2.92
1872 4682 0.465460 GGCCCGCCATTCTGTTATCA 60.465 55.000 0.00 0.00 35.81 2.15
1903 4713 2.295885 CTGAACTTCATCCCAGATGGC 58.704 52.381 4.83 0.00 0.00 4.40
1970 4780 4.826733 CAGCAGATAGGAGTGAGACACTAT 59.173 45.833 4.36 0.30 45.44 2.12
1980 4790 2.093235 GCTTGTTCCAGCAGATAGGAGT 60.093 50.000 0.00 0.00 39.83 3.85
2010 4820 2.082231 AGCATGCAGTGAATCAGTGAC 58.918 47.619 21.18 12.61 36.99 3.67
2017 4827 2.401583 TTACGGAGCATGCAGTGAAT 57.598 45.000 21.98 0.00 0.00 2.57
2018 4828 2.401583 ATTACGGAGCATGCAGTGAA 57.598 45.000 21.98 7.47 0.00 3.18
2019 4829 2.167487 TGTATTACGGAGCATGCAGTGA 59.833 45.455 21.98 13.54 0.00 3.41
2021 4831 2.979814 TGTATTACGGAGCATGCAGT 57.020 45.000 21.98 18.26 0.00 4.40
2022 4832 7.331934 ACTTAATATGTATTACGGAGCATGCAG 59.668 37.037 21.98 13.16 0.00 4.41
2023 4833 7.158697 ACTTAATATGTATTACGGAGCATGCA 58.841 34.615 21.98 0.00 0.00 3.96
2024 4834 7.596749 ACTTAATATGTATTACGGAGCATGC 57.403 36.000 10.51 10.51 0.00 4.06
2046 4856 7.655328 CCGCTTCAAGAAATATCAGAATCTACT 59.345 37.037 0.00 0.00 0.00 2.57
2071 4882 3.064324 ATGCCAAAGTCCTGCGCC 61.064 61.111 4.18 0.00 0.00 6.53
2073 4884 1.164411 TTACATGCCAAAGTCCTGCG 58.836 50.000 0.00 0.00 0.00 5.18
2095 4906 5.408299 GCCCGAAAAAGTTATGCAAGAAAAT 59.592 36.000 0.00 0.00 0.00 1.82
2267 5078 1.375908 GCTGGTCGCATTCCTGACA 60.376 57.895 0.00 0.00 38.92 3.58
2464 5275 2.819608 TGAAGCAGCACCAAGAAATACC 59.180 45.455 0.00 0.00 0.00 2.73
2581 5392 5.740290 AGTATTTTCTTCCCTGAAGTCGA 57.260 39.130 3.95 0.00 40.24 4.20
2646 5457 2.679837 CGTTTCACCAATAGCATGCTCT 59.320 45.455 26.57 12.51 0.00 4.09
2981 5792 4.398988 CCATAATAACCAGCTCTGCACAAA 59.601 41.667 0.00 0.00 0.00 2.83
2983 5794 3.199727 TCCATAATAACCAGCTCTGCACA 59.800 43.478 0.00 0.00 0.00 4.57
3070 5881 4.796369 ACTACCTAAATAATCTCGCGCTC 58.204 43.478 5.56 0.00 0.00 5.03
3093 5904 6.688578 AGTTCACGATAGCAAAACTAAGAGA 58.311 36.000 0.00 0.00 42.67 3.10
3525 6537 3.248363 GCAATTCAAAAAGAGTGGCCAAC 59.752 43.478 7.24 4.78 0.00 3.77
3640 6652 6.512514 TGTTAGAACTTACCCCCAGTAAAA 57.487 37.500 0.00 0.00 40.43 1.52
3698 6710 5.856126 ACACAAATACACTGATAACACCG 57.144 39.130 0.00 0.00 0.00 4.94
3747 6760 2.159184 ACTACTGCTGTCATCCATGTCG 60.159 50.000 0.00 0.00 0.00 4.35
3982 6996 7.461918 GTTTGTGAAATAAGTATCTCCGTTCC 58.538 38.462 0.00 0.00 0.00 3.62
3983 6997 7.062605 TCGTTTGTGAAATAAGTATCTCCGTTC 59.937 37.037 0.00 0.00 0.00 3.95
3984 6998 6.869913 TCGTTTGTGAAATAAGTATCTCCGTT 59.130 34.615 0.00 0.00 0.00 4.44
3985 6999 6.392354 TCGTTTGTGAAATAAGTATCTCCGT 58.608 36.000 0.00 0.00 0.00 4.69
3986 7000 6.880822 TCGTTTGTGAAATAAGTATCTCCG 57.119 37.500 0.00 0.00 0.00 4.63
4014 7028 4.662145 CTTGGTTAGTTTCGATTCATGGC 58.338 43.478 0.00 0.00 0.00 4.40
4039 7053 5.723860 AGAAGCTCTCCCCATATTTTTCT 57.276 39.130 0.00 0.00 0.00 2.52
4068 7088 2.706190 GTTGGTGAGGGTCTATGGCTAT 59.294 50.000 0.00 0.00 0.00 2.97
4069 7089 2.116238 GTTGGTGAGGGTCTATGGCTA 58.884 52.381 0.00 0.00 0.00 3.93
4070 7090 0.912486 GTTGGTGAGGGTCTATGGCT 59.088 55.000 0.00 0.00 0.00 4.75
4071 7091 0.107165 GGTTGGTGAGGGTCTATGGC 60.107 60.000 0.00 0.00 0.00 4.40
4072 7092 0.546598 GGGTTGGTGAGGGTCTATGG 59.453 60.000 0.00 0.00 0.00 2.74
4073 7093 1.285280 TGGGTTGGTGAGGGTCTATG 58.715 55.000 0.00 0.00 0.00 2.23
4132 7152 2.356135 TGGGCTCTAAACGAAGATTGC 58.644 47.619 0.00 0.00 0.00 3.56
4143 7163 7.437713 TCAAATTTCTCTAGATGGGCTCTAA 57.562 36.000 0.00 0.00 36.02 2.10
4318 7338 1.185121 CGACACGCGAGACATTAATCG 59.815 52.381 15.93 4.39 44.57 3.34
4331 7373 3.011760 GCTACAAGCACCGACACGC 62.012 63.158 0.00 0.00 41.89 5.34
4333 7375 0.038159 AGAGCTACAAGCACCGACAC 60.038 55.000 1.22 0.00 45.56 3.67
4335 7377 1.071605 CAAGAGCTACAAGCACCGAC 58.928 55.000 1.22 0.00 45.56 4.79
4371 7414 8.989131 ACCTAGCTGTACAAAAAGATAATCCTA 58.011 33.333 0.00 0.00 0.00 2.94
4373 7416 7.769044 TGACCTAGCTGTACAAAAAGATAATCC 59.231 37.037 0.00 0.00 0.00 3.01
4375 7418 7.553044 GGTGACCTAGCTGTACAAAAAGATAAT 59.447 37.037 0.00 0.00 0.00 1.28
4378 7421 5.246307 GGTGACCTAGCTGTACAAAAAGAT 58.754 41.667 0.00 0.00 0.00 2.40
4379 7422 4.638304 GGTGACCTAGCTGTACAAAAAGA 58.362 43.478 0.00 0.00 0.00 2.52
4380 7423 3.432252 CGGTGACCTAGCTGTACAAAAAG 59.568 47.826 0.00 0.00 0.00 2.27
4400 7443 1.880340 GAAGATCGCAGCTCCACGG 60.880 63.158 0.94 0.00 0.00 4.94
4407 7450 5.677936 CATGAATAAAGAGAAGATCGCAGC 58.322 41.667 0.00 0.00 0.00 5.25
4412 7455 7.225538 TCCGAAAGCATGAATAAAGAGAAGATC 59.774 37.037 0.00 0.00 0.00 2.75
4424 7467 2.092212 AGACCCATCCGAAAGCATGAAT 60.092 45.455 0.00 0.00 0.00 2.57
4477 7520 3.593942 TCTTTCCTGTTGAGGTAAGGGA 58.406 45.455 7.41 0.00 43.65 4.20
4592 7635 3.977427 ACATCGCCTTCCTTTTGTTTTC 58.023 40.909 0.00 0.00 0.00 2.29
4640 7684 6.952773 AGAGTTCTCAGACTACACATATCC 57.047 41.667 2.64 0.00 0.00 2.59
4641 7685 8.770828 GTCTAGAGTTCTCAGACTACACATATC 58.229 40.741 16.95 0.00 36.57 1.63
4644 7691 6.373216 GTGTCTAGAGTTCTCAGACTACACAT 59.627 42.308 20.93 0.00 39.54 3.21
4648 7695 5.353123 CCAGTGTCTAGAGTTCTCAGACTAC 59.647 48.000 20.93 18.05 39.54 2.73
4653 7700 3.823873 ACACCAGTGTCTAGAGTTCTCAG 59.176 47.826 0.00 0.00 40.24 3.35
4686 7741 2.035961 ACACACAGCGACACATACTCTT 59.964 45.455 0.00 0.00 0.00 2.85
4744 7799 1.270147 ACAAGTAACACGAGCAGGGAC 60.270 52.381 0.00 0.00 0.00 4.46
4745 7800 1.000506 GACAAGTAACACGAGCAGGGA 59.999 52.381 0.00 0.00 0.00 4.20
4747 7802 1.060713 CGACAAGTAACACGAGCAGG 58.939 55.000 0.00 0.00 0.00 4.85
4748 7803 0.435008 GCGACAAGTAACACGAGCAG 59.565 55.000 0.00 0.00 0.00 4.24
4751 7806 0.435008 GCTGCGACAAGTAACACGAG 59.565 55.000 0.00 0.00 0.00 4.18
4752 7807 0.031585 AGCTGCGACAAGTAACACGA 59.968 50.000 0.00 0.00 0.00 4.35
4753 7808 0.161658 CAGCTGCGACAAGTAACACG 59.838 55.000 0.00 0.00 0.00 4.49
4825 7880 2.027653 TCCCATGCAACATTGTCTACGA 60.028 45.455 0.00 0.00 0.00 3.43
4826 7881 2.095853 GTCCCATGCAACATTGTCTACG 59.904 50.000 0.00 0.00 0.00 3.51
4831 7889 1.941377 ATGGTCCCATGCAACATTGT 58.059 45.000 0.00 0.00 35.03 2.71
4843 7901 1.862602 GCAACACCGACAATGGTCCC 61.863 60.000 0.00 0.00 41.38 4.46
4865 7924 5.164196 CGGAAACATTCTTTATTTGTGTGCG 60.164 40.000 0.00 0.00 36.37 5.34
4874 7933 9.184523 TCCATTTATGACGGAAACATTCTTTAT 57.815 29.630 0.00 0.00 0.00 1.40
4875 7934 8.568676 TCCATTTATGACGGAAACATTCTTTA 57.431 30.769 0.00 0.00 0.00 1.85
4909 7973 2.673775 TTTTGAGTGCTGAATGGGGA 57.326 45.000 0.00 0.00 0.00 4.81
4913 7977 6.361481 CCGCATAATATTTTGAGTGCTGAATG 59.639 38.462 9.76 0.00 0.00 2.67
4914 7978 6.262944 TCCGCATAATATTTTGAGTGCTGAAT 59.737 34.615 9.76 0.00 0.00 2.57
4916 7980 5.122519 TCCGCATAATATTTTGAGTGCTGA 58.877 37.500 9.76 5.26 0.00 4.26
4943 8010 6.932947 AGGGAGTACTACACAAGAAACATAC 58.067 40.000 7.57 0.00 0.00 2.39
4970 8037 8.957466 AGTCTTATATGCAAACTAAAAAGGACC 58.043 33.333 0.00 0.00 0.00 4.46
4980 8047 7.880195 ACTTCAGACAAGTCTTATATGCAAACT 59.120 33.333 0.00 0.00 37.98 2.66
4981 8048 8.034058 ACTTCAGACAAGTCTTATATGCAAAC 57.966 34.615 0.00 0.00 37.98 2.93
4982 8049 7.877612 TGACTTCAGACAAGTCTTATATGCAAA 59.122 33.333 14.05 0.00 45.13 3.68
4985 8052 7.834068 TTGACTTCAGACAAGTCTTATATGC 57.166 36.000 14.05 0.00 45.13 3.14
4986 8053 8.660373 GGTTTGACTTCAGACAAGTCTTATATG 58.340 37.037 14.05 0.00 45.13 1.78
4987 8054 8.598041 AGGTTTGACTTCAGACAAGTCTTATAT 58.402 33.333 14.05 0.00 45.13 0.86
4990 8057 6.235231 AGGTTTGACTTCAGACAAGTCTTA 57.765 37.500 14.05 0.00 45.13 2.10
4991 8058 5.104259 AGGTTTGACTTCAGACAAGTCTT 57.896 39.130 14.05 0.00 45.13 3.01
4993 8060 3.491267 CGAGGTTTGACTTCAGACAAGTC 59.509 47.826 7.43 7.43 45.12 3.01
4995 8062 3.458189 ACGAGGTTTGACTTCAGACAAG 58.542 45.455 2.66 0.00 33.14 3.16
4996 8063 3.536956 ACGAGGTTTGACTTCAGACAA 57.463 42.857 2.66 0.00 33.14 3.18
4998 8065 5.048507 AGTTTACGAGGTTTGACTTCAGAC 58.951 41.667 0.00 0.00 0.00 3.51
5001 8068 5.875910 TCAAAGTTTACGAGGTTTGACTTCA 59.124 36.000 0.00 0.00 34.72 3.02
5002 8069 6.354039 TCAAAGTTTACGAGGTTTGACTTC 57.646 37.500 0.00 0.00 34.72 3.01
5006 8073 4.515361 TGGTCAAAGTTTACGAGGTTTGA 58.485 39.130 0.00 0.00 36.74 2.69
5008 8075 5.900865 TTTGGTCAAAGTTTACGAGGTTT 57.099 34.783 0.00 0.00 0.00 3.27
5009 8076 6.459670 AATTTGGTCAAAGTTTACGAGGTT 57.540 33.333 2.55 0.00 33.32 3.50
5010 8077 6.459670 AAATTTGGTCAAAGTTTACGAGGT 57.540 33.333 3.69 0.00 35.39 3.85
5011 8078 7.061789 GCATAAATTTGGTCAAAGTTTACGAGG 59.938 37.037 13.08 0.95 39.07 4.63
5012 8079 7.201232 CGCATAAATTTGGTCAAAGTTTACGAG 60.201 37.037 13.08 4.94 39.07 4.18
5013 8080 6.579292 CGCATAAATTTGGTCAAAGTTTACGA 59.421 34.615 13.08 0.00 39.07 3.43
5014 8081 6.579292 TCGCATAAATTTGGTCAAAGTTTACG 59.421 34.615 13.08 13.48 39.07 3.18
5015 8082 7.861176 TCGCATAAATTTGGTCAAAGTTTAC 57.139 32.000 13.08 4.57 39.07 2.01
5016 8083 8.756864 GTTTCGCATAAATTTGGTCAAAGTTTA 58.243 29.630 13.08 11.48 39.07 2.01
5017 8084 7.494298 AGTTTCGCATAAATTTGGTCAAAGTTT 59.506 29.630 13.08 10.11 39.07 2.66
5022 8089 5.226396 CCAGTTTCGCATAAATTTGGTCAA 58.774 37.500 0.00 0.00 0.00 3.18
5023 8090 4.321601 CCCAGTTTCGCATAAATTTGGTCA 60.322 41.667 0.00 0.00 0.00 4.02
5024 8091 4.173256 CCCAGTTTCGCATAAATTTGGTC 58.827 43.478 0.00 0.00 0.00 4.02
5026 8093 4.186856 ACCCAGTTTCGCATAAATTTGG 57.813 40.909 0.00 0.00 0.00 3.28
5027 8094 5.226396 TCAACCCAGTTTCGCATAAATTTG 58.774 37.500 0.00 0.00 0.00 2.32
5029 8096 5.461032 TTCAACCCAGTTTCGCATAAATT 57.539 34.783 0.00 0.00 0.00 1.82
5032 8099 3.254657 CCTTTCAACCCAGTTTCGCATAA 59.745 43.478 0.00 0.00 0.00 1.90
5033 8100 2.817258 CCTTTCAACCCAGTTTCGCATA 59.183 45.455 0.00 0.00 0.00 3.14
5034 8101 1.613437 CCTTTCAACCCAGTTTCGCAT 59.387 47.619 0.00 0.00 0.00 4.73
5038 8278 5.243730 TGATTGATCCTTTCAACCCAGTTTC 59.756 40.000 0.00 0.00 46.80 2.78
5044 8284 2.760650 GGGTGATTGATCCTTTCAACCC 59.239 50.000 10.99 7.34 46.80 4.11
5083 8323 4.503643 CCACATTTGTCTGGGAGCATTTTT 60.504 41.667 0.00 0.00 0.00 1.94
5097 8337 7.850193 AGGCACAAAATATATTCCACATTTGT 58.150 30.769 0.00 2.14 40.49 2.83
5105 8345 5.707764 GGAGAGGAGGCACAAAATATATTCC 59.292 44.000 0.00 0.00 0.00 3.01
5114 8354 1.270907 GAGAGGAGAGGAGGCACAAA 58.729 55.000 0.00 0.00 0.00 2.83
5156 8549 4.142534 GGGGGCTGTTTTTACTCGTAAATC 60.143 45.833 3.36 2.10 35.27 2.17
5175 8568 6.763135 CACGATATATATTCAACATCTGGGGG 59.237 42.308 0.00 0.00 0.00 5.40
5180 8573 9.862371 GGACTTCACGATATATATTCAACATCT 57.138 33.333 0.00 0.00 0.00 2.90
5183 8576 7.958088 TGGGACTTCACGATATATATTCAACA 58.042 34.615 0.00 0.00 0.00 3.33
5197 8590 4.503910 TGTAATCATTCTGGGACTTCACG 58.496 43.478 0.00 0.00 0.00 4.35
5203 8604 6.177610 TGTAAGGTTGTAATCATTCTGGGAC 58.822 40.000 0.00 0.00 0.00 4.46
5293 8694 3.006967 ACACACAGGCTCTAGGTGTTAAG 59.993 47.826 5.68 0.00 42.72 1.85
5464 9038 2.094126 GATTGAGAATGACGCGCGGG 62.094 60.000 35.22 22.69 0.00 6.13
5478 9052 1.470285 GGTTAGTGTAGCGGCGATTGA 60.470 52.381 12.98 0.00 0.00 2.57
5480 9054 0.526954 CGGTTAGTGTAGCGGCGATT 60.527 55.000 12.98 0.00 35.53 3.34
5481 9055 1.065273 CGGTTAGTGTAGCGGCGAT 59.935 57.895 12.98 7.15 35.53 4.58
5482 9056 2.486504 CGGTTAGTGTAGCGGCGA 59.513 61.111 12.98 0.00 35.53 5.54
5486 9060 2.202837 GGCCCGGTTAGTGTAGCG 60.203 66.667 0.00 0.00 38.65 4.26
5487 9061 1.153429 CAGGCCCGGTTAGTGTAGC 60.153 63.158 0.00 0.00 0.00 3.58
5489 9063 2.662070 GGCAGGCCCGGTTAGTGTA 61.662 63.158 0.00 0.00 0.00 2.90
5490 9064 4.029809 GGCAGGCCCGGTTAGTGT 62.030 66.667 0.00 0.00 0.00 3.55
5603 9177 1.571919 GACCGTCAAGCTATCGCATT 58.428 50.000 0.00 0.00 39.10 3.56
5697 9277 4.619227 CACCGGCAACTCACCCGT 62.619 66.667 0.00 0.00 42.87 5.28
5806 9389 1.403814 TCGATCAAGCGAGGAAGGAT 58.596 50.000 0.00 0.00 35.01 3.24
5812 9395 3.084686 CTCGATCGATCAAGCGAGG 57.915 57.895 24.40 7.01 44.58 4.63
5815 9398 1.543941 GGTGCTCGATCGATCAAGCG 61.544 60.000 28.14 14.68 39.65 4.68
5832 9421 3.203716 GTCGAGAAAACTGACCAAAGGT 58.796 45.455 0.00 0.00 39.44 3.50
5892 9503 0.534203 ATGACACACACAACCCCGAC 60.534 55.000 0.00 0.00 0.00 4.79
5895 9506 0.823356 AGCATGACACACACAACCCC 60.823 55.000 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.