Multiple sequence alignment - TraesCS4D01G221800

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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 TraesCS4D01G221800 chr4D 100.000 7269 0 0 1 7269 379144431 379151699 0.000000e+00 13424.0
1 TraesCS4D01G221800 chr4D 91.826 783 50 11 1 780 43412557 43413328 0.000000e+00 1079.0
2 TraesCS4D01G221800 chr4D 88.861 799 62 14 1 793 65103303 65102526 0.000000e+00 957.0
3 TraesCS4D01G221800 chr4D 100.000 58 0 0 4344 4401 379148831 379148774 2.770000e-19 108.0
4 TraesCS4D01G221800 chr4A 93.970 2156 82 21 4779 6912 85904502 85902373 0.000000e+00 3217.0
5 TraesCS4D01G221800 chr4A 92.995 1970 75 24 2846 4782 85906495 85904556 0.000000e+00 2815.0
6 TraesCS4D01G221800 chr4A 96.494 1255 33 4 1513 2765 85907738 85906493 0.000000e+00 2063.0
7 TraesCS4D01G221800 chr4A 90.775 542 23 7 780 1294 85908696 85908155 0.000000e+00 699.0
8 TraesCS4D01G221800 chr4A 88.000 275 18 4 7010 7269 85902372 85902098 1.970000e-80 311.0
9 TraesCS4D01G221800 chr4B 94.514 2005 75 12 780 2762 465729682 465731673 0.000000e+00 3061.0
10 TraesCS4D01G221800 chr4B 93.508 1987 81 15 5004 6957 465736474 465738445 0.000000e+00 2911.0
11 TraesCS4D01G221800 chr4B 92.806 1404 62 22 3399 4782 465732315 465733699 0.000000e+00 1997.0
12 TraesCS4D01G221800 chr4B 95.374 562 18 3 2847 3401 465731675 465732235 0.000000e+00 887.0
13 TraesCS4D01G221800 chr4B 87.833 263 18 12 7016 7269 465738457 465738714 5.510000e-76 296.0
14 TraesCS4D01G221800 chr4B 94.565 184 9 1 4831 5013 465733813 465733996 4.290000e-72 283.0
15 TraesCS4D01G221800 chr4B 94.624 93 4 1 2757 2848 192792739 192792831 7.600000e-30 143.0
16 TraesCS4D01G221800 chr5D 92.875 800 47 10 4 800 487917782 487916990 0.000000e+00 1153.0
17 TraesCS4D01G221800 chr3D 92.839 768 44 10 15 780 223472913 223472155 0.000000e+00 1103.0
18 TraesCS4D01G221800 chr3D 90.561 784 54 11 1 780 323486731 323485964 0.000000e+00 1020.0
19 TraesCS4D01G221800 chr7D 92.092 784 49 10 1 781 484795043 484795816 0.000000e+00 1092.0
20 TraesCS4D01G221800 chr7D 92.224 553 33 9 1 550 560997515 560998060 0.000000e+00 774.0
21 TraesCS4D01G221800 chr7D 89.305 187 19 1 600 785 560998352 560998538 4.380000e-57 233.0
22 TraesCS4D01G221800 chr7D 93.750 96 6 0 2760 2855 195626186 195626091 2.110000e-30 145.0
23 TraesCS4D01G221800 chr7D 96.154 52 0 1 3957 4008 366876788 366876739 4.670000e-12 84.2
24 TraesCS4D01G221800 chr7A 90.294 783 65 11 1 780 641245053 641245827 0.000000e+00 1014.0
25 TraesCS4D01G221800 chr7A 90.241 748 62 9 1 747 641264086 641264823 0.000000e+00 966.0
26 TraesCS4D01G221800 chr2A 91.145 463 33 5 328 784 747149647 747150107 8.010000e-174 621.0
27 TraesCS4D01G221800 chr2A 78.584 551 91 21 5399 5933 203005053 203004514 9.030000e-89 339.0
28 TraesCS4D01G221800 chr2A 87.342 79 5 3 4333 4406 32146295 32146217 1.300000e-12 86.1
29 TraesCS4D01G221800 chr2B 77.858 551 96 22 5399 5933 245009322 245008782 1.180000e-82 318.0
30 TraesCS4D01G221800 chr2D 76.461 599 115 16 5335 5921 188884858 188884274 1.190000e-77 302.0
31 TraesCS4D01G221800 chr2D 89.147 129 8 4 2740 2862 643235796 643235924 9.760000e-34 156.0
32 TraesCS4D01G221800 chr2D 95.745 94 3 1 2756 2848 382455931 382456024 4.540000e-32 150.0
33 TraesCS4D01G221800 chr6B 95.833 96 2 1 2755 2848 13827621 13827526 3.510000e-33 154.0
34 TraesCS4D01G221800 chr5A 96.629 89 3 0 2760 2848 450750704 450750792 1.630000e-31 148.0
35 TraesCS4D01G221800 chr1D 94.681 94 5 0 2763 2856 209139276 209139369 5.880000e-31 147.0
36 TraesCS4D01G221800 chr1A 94.681 94 5 0 2762 2855 530756573 530756666 5.880000e-31 147.0
37 TraesCS4D01G221800 chr1A 92.727 55 1 3 3957 4011 287086223 287086274 7.820000e-10 76.8
38 TraesCS4D01G221800 chr7B 90.476 105 9 1 2759 2863 639796288 639796185 3.540000e-28 137.0
39 TraesCS4D01G221800 chr7B 91.781 73 3 1 4339 4408 41635649 41635577 1.670000e-16 99.0
40 TraesCS4D01G221800 chr7B 89.041 73 5 3 4339 4410 540052587 540052517 3.610000e-13 87.9
41 TraesCS4D01G221800 chr7B 96.078 51 0 2 3957 4007 316235981 316236029 1.680000e-11 82.4
42 TraesCS4D01G221800 chr3B 91.667 72 4 1 4337 4406 750141491 750141420 1.670000e-16 99.0
43 TraesCS4D01G221800 chr3B 91.667 60 1 4 3957 4015 65762067 65762011 6.050000e-11 80.5
44 TraesCS4D01G221800 chr6D 97.917 48 1 0 3957 4004 372827549 372827502 4.670000e-12 84.2
45 TraesCS4D01G221800 chr5B 96.154 52 1 1 3957 4007 392344245 392344194 4.670000e-12 84.2
46 TraesCS4D01G221800 chr5B 100.000 43 0 0 3957 3999 221801029 221801071 6.050000e-11 80.5
47 TraesCS4D01G221800 chrUn 90.000 60 5 1 3957 4016 395405468 395405410 7.820000e-10 76.8
48 TraesCS4D01G221800 chr1B 90.000 60 4 2 3957 4015 458049321 458049263 7.820000e-10 76.8


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 TraesCS4D01G221800 chr4D 379144431 379151699 7268 False 13424.0 13424 100.0000 1 7269 1 chr4D.!!$F2 7268
1 TraesCS4D01G221800 chr4D 43412557 43413328 771 False 1079.0 1079 91.8260 1 780 1 chr4D.!!$F1 779
2 TraesCS4D01G221800 chr4D 65102526 65103303 777 True 957.0 957 88.8610 1 793 1 chr4D.!!$R1 792
3 TraesCS4D01G221800 chr4A 85902098 85908696 6598 True 1821.0 3217 92.4468 780 7269 5 chr4A.!!$R1 6489
4 TraesCS4D01G221800 chr4B 465729682 465738714 9032 False 1572.5 3061 93.1000 780 7269 6 chr4B.!!$F2 6489
5 TraesCS4D01G221800 chr5D 487916990 487917782 792 True 1153.0 1153 92.8750 4 800 1 chr5D.!!$R1 796
6 TraesCS4D01G221800 chr3D 223472155 223472913 758 True 1103.0 1103 92.8390 15 780 1 chr3D.!!$R1 765
7 TraesCS4D01G221800 chr3D 323485964 323486731 767 True 1020.0 1020 90.5610 1 780 1 chr3D.!!$R2 779
8 TraesCS4D01G221800 chr7D 484795043 484795816 773 False 1092.0 1092 92.0920 1 781 1 chr7D.!!$F1 780
9 TraesCS4D01G221800 chr7D 560997515 560998538 1023 False 503.5 774 90.7645 1 785 2 chr7D.!!$F2 784
10 TraesCS4D01G221800 chr7A 641245053 641245827 774 False 1014.0 1014 90.2940 1 780 1 chr7A.!!$F1 779
11 TraesCS4D01G221800 chr7A 641264086 641264823 737 False 966.0 966 90.2410 1 747 1 chr7A.!!$F2 746
12 TraesCS4D01G221800 chr2A 203004514 203005053 539 True 339.0 339 78.5840 5399 5933 1 chr2A.!!$R2 534
13 TraesCS4D01G221800 chr2B 245008782 245009322 540 True 318.0 318 77.8580 5399 5933 1 chr2B.!!$R1 534
14 TraesCS4D01G221800 chr2D 188884274 188884858 584 True 302.0 302 76.4610 5335 5921 1 chr2D.!!$R1 586

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
258 267 0.239879 TGCCGCTCCGAATTGAAAAC 59.760 50.000 0.00 0.0 0.00 2.43 F
1010 1269 0.179034 GAAGGATCAATGGCCGCTCT 60.179 55.000 0.00 0.0 0.00 4.09 F
1481 1766 0.394625 GCACTCCTCTCGTACCTCCT 60.395 60.000 0.00 0.0 0.00 3.69 F
2318 2868 1.952296 CCTGGATGCTCTAAATGCACC 59.048 52.381 0.00 0.0 43.59 5.01 F
3323 3878 0.518636 CACCTTTGTGACCATCTGCG 59.481 55.000 0.00 0.0 45.76 5.18 F
4619 5287 0.307760 GTTGGTGACGGAGCAAGTTG 59.692 55.000 0.00 0.0 42.69 3.16 F
4622 5290 0.531974 GGTGACGGAGCAAGTTGTGA 60.532 55.000 4.48 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1352 1637 0.669619 TGTGAGCAGCAACAACATGG 59.330 50.0 0.00 0.00 0.00 3.66 R
2111 2661 1.493772 TCGGTAACAACAGTTCTGCG 58.506 50.0 0.00 0.00 0.00 5.18 R
3308 3863 0.035317 AGAGCGCAGATGGTCACAAA 59.965 50.0 11.47 0.00 38.81 2.83 R
4095 4746 0.535102 CCTCAGCAAAAGTCACCGGT 60.535 55.0 0.00 0.00 0.00 5.28 R
5194 8435 0.608640 GCGGGGGAGTATCGATCAAT 59.391 55.0 0.00 0.00 34.37 2.57 R
5657 8901 0.874390 CCTCCACATGTTCAACACCG 59.126 55.0 0.00 0.00 0.00 4.94 R
6516 9787 2.408271 TCCAGTGATCAGGCATGAAC 57.592 50.0 4.62 2.73 39.39 3.18 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
34 35 6.790461 ACCCCCTCAAGTTTTTGGTAATAAAT 59.210 34.615 0.00 0.00 34.97 1.40
219 226 8.835439 TGAAAACTTAATCAATAGCGCATGATA 58.165 29.630 19.33 7.97 35.29 2.15
238 247 6.785337 TGATAAGTCTTTCCTTCATACCGA 57.215 37.500 0.00 0.00 0.00 4.69
258 267 0.239879 TGCCGCTCCGAATTGAAAAC 59.760 50.000 0.00 0.00 0.00 2.43
373 382 7.095187 GGAGACGTCTTAAGATTGACAACATTT 60.095 37.037 21.08 0.00 33.18 2.32
420 430 4.838486 GCCAGCGTCGACGAGAGG 62.838 72.222 39.74 32.95 43.02 3.69
421 431 4.180946 CCAGCGTCGACGAGAGGG 62.181 72.222 39.74 27.60 43.02 4.30
583 595 2.500504 GAGGGGGACGTCTTAAGATTGT 59.499 50.000 16.46 10.52 41.92 2.71
596 608 7.855409 CGTCTTAAGATTGTCAACATTCAAACA 59.145 33.333 8.75 0.00 0.00 2.83
703 955 7.339466 GTGTTGAAATAAAGGACATGGACCTAT 59.661 37.037 12.86 3.25 36.67 2.57
729 982 8.718102 TGAAGTTTGGACTCATAGTTATTAGC 57.282 34.615 0.00 0.00 34.21 3.09
880 1138 1.153628 CCCTCACCGTCGGATTCAC 60.154 63.158 20.51 0.00 0.00 3.18
936 1194 0.744414 CACCCAACCGCAGTCCATAG 60.744 60.000 0.00 0.00 0.00 2.23
977 1236 2.909662 CCTGTTCTTCTTCTTCCCCTCT 59.090 50.000 0.00 0.00 0.00 3.69
1010 1269 0.179034 GAAGGATCAATGGCCGCTCT 60.179 55.000 0.00 0.00 0.00 4.09
1167 1441 3.773630 CGACGCAATGCCGACGTT 61.774 61.111 0.00 0.00 40.69 3.99
1224 1498 5.482878 TCTTCGGTCTAACTGGGACTTATTT 59.517 40.000 0.00 0.00 34.47 1.40
1352 1637 2.672195 GCAGCCTGTTTTGCCAATCTAC 60.672 50.000 0.00 0.00 34.28 2.59
1372 1657 1.067364 CCATGTTGTTGCTGCTCACAA 59.933 47.619 12.16 12.16 0.00 3.33
1399 1684 2.738846 ACTTGTAGTCTTGAGCAATGCG 59.261 45.455 0.00 0.00 0.00 4.73
1411 1696 1.764851 GCAATGCGTGTGCTTGTAAA 58.235 45.000 0.00 0.00 43.34 2.01
1412 1697 1.451651 GCAATGCGTGTGCTTGTAAAC 59.548 47.619 0.00 0.00 43.34 2.01
1481 1766 0.394625 GCACTCCTCTCGTACCTCCT 60.395 60.000 0.00 0.00 0.00 3.69
1485 1770 2.225066 ACTCCTCTCGTACCTCCTGTTT 60.225 50.000 0.00 0.00 0.00 2.83
1972 2522 3.974401 CCTTTTGTACGTTGCATGAACTG 59.026 43.478 0.00 0.00 31.70 3.16
2018 2568 8.258007 TGTAAACTGAGATTGGATAGTACAAGG 58.742 37.037 0.00 0.00 0.00 3.61
2071 2621 5.368145 CAGCATACTCCATAAGGCTACAAA 58.632 41.667 0.00 0.00 33.74 2.83
2111 2661 5.412904 GCATTATCTACTATTGGTTCTGGCC 59.587 44.000 0.00 0.00 0.00 5.36
2121 2671 2.828868 TTCTGGCCGCAGAACTGT 59.171 55.556 1.41 0.00 36.39 3.55
2196 2746 2.327325 TCAGTTTCTAGACCCCAGCT 57.673 50.000 0.00 0.00 0.00 4.24
2197 2747 3.468071 TCAGTTTCTAGACCCCAGCTA 57.532 47.619 0.00 0.00 0.00 3.32
2198 2748 3.097614 TCAGTTTCTAGACCCCAGCTAC 58.902 50.000 0.00 0.00 0.00 3.58
2199 2749 2.832129 CAGTTTCTAGACCCCAGCTACA 59.168 50.000 0.00 0.00 0.00 2.74
2318 2868 1.952296 CCTGGATGCTCTAAATGCACC 59.048 52.381 0.00 0.00 43.59 5.01
2370 2920 3.252701 CCAGAAATATCATCAGCCAGTGC 59.747 47.826 0.00 0.00 37.95 4.40
2762 3314 7.889873 TCATATGTTTGGTACCCAATAAAGG 57.110 36.000 10.07 0.00 43.55 3.11
2763 3315 7.415086 TCATATGTTTGGTACCCAATAAAGGT 58.585 34.615 10.07 0.00 43.55 3.50
2764 3316 8.558312 TCATATGTTTGGTACCCAATAAAGGTA 58.442 33.333 10.07 0.19 43.55 3.08
2772 3324 2.579400 ACCCAATAAAGGTACACCCTCC 59.421 50.000 0.00 0.00 45.47 4.30
2773 3325 2.420967 CCCAATAAAGGTACACCCTCCG 60.421 54.545 0.00 0.00 45.47 4.63
2774 3326 2.237893 CCAATAAAGGTACACCCTCCGT 59.762 50.000 0.00 0.00 45.47 4.69
2775 3327 3.451902 CCAATAAAGGTACACCCTCCGTA 59.548 47.826 0.00 0.00 45.47 4.02
2776 3328 4.080975 CCAATAAAGGTACACCCTCCGTAA 60.081 45.833 0.00 0.00 45.47 3.18
2777 3329 5.490159 CAATAAAGGTACACCCTCCGTAAA 58.510 41.667 0.00 0.00 45.47 2.01
2778 3330 3.690475 AAAGGTACACCCTCCGTAAAG 57.310 47.619 0.00 0.00 45.47 1.85
2779 3331 2.610438 AGGTACACCCTCCGTAAAGA 57.390 50.000 0.00 0.00 40.71 2.52
2780 3332 2.893424 AGGTACACCCTCCGTAAAGAA 58.107 47.619 0.00 0.00 40.71 2.52
2781 3333 3.242011 AGGTACACCCTCCGTAAAGAAA 58.758 45.455 0.00 0.00 40.71 2.52
2782 3334 3.842436 AGGTACACCCTCCGTAAAGAAAT 59.158 43.478 0.00 0.00 40.71 2.17
2783 3335 5.025453 AGGTACACCCTCCGTAAAGAAATA 58.975 41.667 0.00 0.00 40.71 1.40
2784 3336 5.664457 AGGTACACCCTCCGTAAAGAAATAT 59.336 40.000 0.00 0.00 40.71 1.28
2785 3337 6.840705 AGGTACACCCTCCGTAAAGAAATATA 59.159 38.462 0.00 0.00 40.71 0.86
2786 3338 7.345392 AGGTACACCCTCCGTAAAGAAATATAA 59.655 37.037 0.00 0.00 40.71 0.98
2787 3339 7.654923 GGTACACCCTCCGTAAAGAAATATAAG 59.345 40.741 0.00 0.00 0.00 1.73
2788 3340 7.427989 ACACCCTCCGTAAAGAAATATAAGA 57.572 36.000 0.00 0.00 0.00 2.10
2789 3341 7.498443 ACACCCTCCGTAAAGAAATATAAGAG 58.502 38.462 0.00 0.00 0.00 2.85
2790 3342 7.125356 ACACCCTCCGTAAAGAAATATAAGAGT 59.875 37.037 0.00 0.00 0.00 3.24
2791 3343 7.438459 CACCCTCCGTAAAGAAATATAAGAGTG 59.562 40.741 0.00 0.00 0.00 3.51
2792 3344 7.125356 ACCCTCCGTAAAGAAATATAAGAGTGT 59.875 37.037 0.00 0.00 0.00 3.55
2793 3345 7.985752 CCCTCCGTAAAGAAATATAAGAGTGTT 59.014 37.037 0.00 0.00 0.00 3.32
2794 3346 9.379791 CCTCCGTAAAGAAATATAAGAGTGTTT 57.620 33.333 0.00 0.00 0.00 2.83
2843 3395 9.892130 AACACTCTTATATTTCTTTACAGAGGG 57.108 33.333 0.00 0.00 36.55 4.30
2844 3396 9.268282 ACACTCTTATATTTCTTTACAGAGGGA 57.732 33.333 2.59 0.00 34.50 4.20
2944 3498 5.243060 ACTTTTGCTGTGGACCCTATTTAAC 59.757 40.000 0.00 0.00 0.00 2.01
2970 3524 5.528320 CAGACATGGTTTTCTTTTGGCAAAT 59.472 36.000 14.29 0.00 0.00 2.32
3026 3581 2.242043 CATGACCAAGTCAAGCCCTTT 58.758 47.619 0.91 0.00 45.96 3.11
3073 3628 6.096673 ACCGCAAAACATTTCCTTCTTTAT 57.903 33.333 0.00 0.00 0.00 1.40
3146 3701 5.882040 AGAGGTACATGATGCTAGCTAGTA 58.118 41.667 21.62 18.12 0.00 1.82
3238 3793 6.014584 TCTCTTGGTATAGTTTTGAGCAGTGA 60.015 38.462 0.00 0.00 0.00 3.41
3323 3878 0.518636 CACCTTTGTGACCATCTGCG 59.481 55.000 0.00 0.00 45.76 5.18
3379 3940 3.126686 GCTTCTGTGAGCTTCTTTCCATC 59.873 47.826 0.00 0.00 39.57 3.51
3468 4111 8.651389 ATGTGTATACATTAGCCTCTGTAATGT 58.349 33.333 9.18 11.61 45.01 2.71
3619 4262 8.924511 TTTGGTCTTGAATTCTAGATGTTCTT 57.075 30.769 20.12 0.00 31.04 2.52
3706 4349 5.946377 GGCAGGAATTAATGGTCTAATAGGG 59.054 44.000 0.00 0.00 0.00 3.53
3712 4355 6.877611 ATTAATGGTCTAATAGGGCAAACG 57.122 37.500 0.00 0.00 0.00 3.60
3780 4425 7.385205 TGTCTGTTCTCTTCTTGTGTATTTAGC 59.615 37.037 0.00 0.00 0.00 3.09
3804 4449 7.945109 AGCTTCCCTTAGAAATATTAATCACCC 59.055 37.037 0.00 0.00 32.88 4.61
3881 4532 9.161629 CTTGACCCAAATTGAAAATTATTACCC 57.838 33.333 0.00 0.00 0.00 3.69
3960 4611 1.579429 CCTTACGGTGCAAGCCAAC 59.421 57.895 0.00 0.00 0.00 3.77
3961 4612 0.889186 CCTTACGGTGCAAGCCAACT 60.889 55.000 0.00 0.00 0.00 3.16
3962 4613 0.951558 CTTACGGTGCAAGCCAACTT 59.048 50.000 0.00 0.00 36.19 2.66
3978 4629 3.977427 CAACTTGTTTGGGACTAAAGGC 58.023 45.455 0.00 0.00 0.00 4.35
3979 4630 3.595190 ACTTGTTTGGGACTAAAGGCT 57.405 42.857 0.00 0.00 0.00 4.58
3980 4631 3.910989 ACTTGTTTGGGACTAAAGGCTT 58.089 40.909 0.00 0.00 0.00 4.35
3981 4632 4.286707 ACTTGTTTGGGACTAAAGGCTTT 58.713 39.130 17.76 17.76 0.00 3.51
3982 4633 4.099419 ACTTGTTTGGGACTAAAGGCTTTG 59.901 41.667 22.32 13.97 0.00 2.77
3983 4634 3.637769 TGTTTGGGACTAAAGGCTTTGT 58.362 40.909 22.32 16.86 0.00 2.83
3984 4635 4.027437 TGTTTGGGACTAAAGGCTTTGTT 58.973 39.130 22.32 8.73 0.00 2.83
3985 4636 4.142049 TGTTTGGGACTAAAGGCTTTGTTG 60.142 41.667 22.32 13.85 0.00 3.33
3986 4637 3.306472 TGGGACTAAAGGCTTTGTTGT 57.694 42.857 22.32 16.69 0.00 3.32
3987 4638 3.637769 TGGGACTAAAGGCTTTGTTGTT 58.362 40.909 22.32 1.84 0.00 2.83
3988 4639 3.383185 TGGGACTAAAGGCTTTGTTGTTG 59.617 43.478 22.32 7.79 0.00 3.33
3991 4642 4.803613 GGACTAAAGGCTTTGTTGTTGTTG 59.196 41.667 22.32 0.00 0.00 3.33
3994 4645 5.637387 ACTAAAGGCTTTGTTGTTGTTGTTG 59.363 36.000 22.32 0.00 0.00 3.33
4089 4740 7.302948 TCGATGCCCCTACATATAATATACCT 58.697 38.462 0.00 0.00 0.00 3.08
4095 4746 8.989131 GCCCCTACATATAATATACCTGAGAAA 58.011 37.037 0.00 0.00 0.00 2.52
4390 5058 5.769484 TTGGCCAAAACGTCTTACATTTA 57.231 34.783 17.98 0.00 0.00 1.40
4436 5104 6.669736 AGGGCATATAGGGAGTATGTACTA 57.330 41.667 0.00 0.00 36.50 1.82
4476 5144 1.001487 CAGGCATGTGCGAAGTTTTCA 60.001 47.619 0.00 0.00 43.26 2.69
4516 5184 2.815963 GCATCATCCTCTCTCCTCGGTA 60.816 54.545 0.00 0.00 0.00 4.02
4524 5192 1.775459 TCTCTCCTCGGTAGTAGCCAT 59.225 52.381 0.00 0.00 0.00 4.40
4613 5281 2.668550 GTGGGTTGGTGACGGAGC 60.669 66.667 0.00 0.00 0.00 4.70
4619 5287 0.307760 GTTGGTGACGGAGCAAGTTG 59.692 55.000 0.00 0.00 42.69 3.16
4622 5290 0.531974 GGTGACGGAGCAAGTTGTGA 60.532 55.000 4.48 0.00 0.00 3.58
4628 5296 1.160329 GGAGCAAGTTGTGACGCTGT 61.160 55.000 4.48 0.00 34.12 4.40
4629 5297 0.657840 GAGCAAGTTGTGACGCTGTT 59.342 50.000 4.48 0.00 34.12 3.16
4688 5356 1.489560 AAGCCACCTCACCTGGTACC 61.490 60.000 4.43 4.43 38.45 3.34
4734 5402 8.603304 ACATCTCCTTGGTAGTAACAAATACTT 58.397 33.333 1.57 0.00 42.31 2.24
4803 5555 2.216898 GCCATGTCTATCTGAACTGCC 58.783 52.381 0.00 0.00 0.00 4.85
4816 5568 2.037902 TGAACTGCCGGAATTCACTGTA 59.962 45.455 5.05 0.00 0.00 2.74
4827 5579 7.352739 CCGGAATTCACTGTAGTTAATATTGC 58.647 38.462 7.93 0.00 0.00 3.56
4902 5656 5.162637 TCTGGAGGCCTTGTGGTATATATT 58.837 41.667 6.77 0.00 35.27 1.28
4933 5687 8.691661 TGCTTGTATATTCTATTTCCCCTTTC 57.308 34.615 0.00 0.00 0.00 2.62
4959 5713 2.108168 TGTGCCACTACCTATCACCTC 58.892 52.381 0.00 0.00 0.00 3.85
5026 8267 8.796278 GTCGTTCATTAGTAATCTACACACTTC 58.204 37.037 0.00 0.00 0.00 3.01
5042 8283 2.909244 CACTTCTCGTGTTACGCTGTAG 59.091 50.000 0.00 0.00 42.21 2.74
5047 8288 3.498018 TCTCGTGTTACGCTGTAGTACAA 59.502 43.478 4.21 0.00 42.21 2.41
5062 8303 3.403038 AGTACAATGTCACAACCAGCTC 58.597 45.455 0.00 0.00 0.00 4.09
5147 8388 9.447040 CTTACACAATAGAATTCATGCTCATTG 57.553 33.333 8.44 9.10 0.00 2.82
5193 8434 2.297701 AGCATGTTGTCAGTTTCCGTT 58.702 42.857 0.00 0.00 0.00 4.44
5194 8435 3.472652 AGCATGTTGTCAGTTTCCGTTA 58.527 40.909 0.00 0.00 0.00 3.18
5195 8436 4.072131 AGCATGTTGTCAGTTTCCGTTAT 58.928 39.130 0.00 0.00 0.00 1.89
5198 8439 5.561919 GCATGTTGTCAGTTTCCGTTATTGA 60.562 40.000 0.00 0.00 0.00 2.57
5199 8440 6.611381 CATGTTGTCAGTTTCCGTTATTGAT 58.389 36.000 0.00 0.00 0.00 2.57
5200 8441 6.236017 TGTTGTCAGTTTCCGTTATTGATC 57.764 37.500 0.00 0.00 0.00 2.92
5208 8450 6.144080 CAGTTTCCGTTATTGATCGATACTCC 59.856 42.308 0.00 0.00 0.00 3.85
5270 8512 6.581919 TGATATGTTTTGTCAGTTTGAATGCG 59.418 34.615 0.00 0.00 0.00 4.73
5333 8575 2.102420 TGGCTACGTATTCATCTGTGGG 59.898 50.000 0.00 0.00 0.00 4.61
5364 8606 2.512692 AGATGCCTGTGGTATTTGCA 57.487 45.000 0.00 0.00 36.23 4.08
5365 8607 2.094675 AGATGCCTGTGGTATTTGCAC 58.905 47.619 0.00 0.00 34.33 4.57
5487 8729 5.125739 CAGGTTTGTGGGTGTTAGTGTTTTA 59.874 40.000 0.00 0.00 0.00 1.52
5618 8862 2.075426 AAAGCAGAAACCGTGCAGCC 62.075 55.000 0.00 0.00 43.82 4.85
5657 8901 1.630878 AGGGTTTGGACAGATGAGGAC 59.369 52.381 0.00 0.00 0.00 3.85
6023 9280 3.056107 CGTGGAAAGGAACACTAGGATGA 60.056 47.826 0.00 0.00 35.51 2.92
6301 9558 4.536489 AGACCATAGTTGCTAGGAACCTTT 59.464 41.667 21.97 7.92 0.00 3.11
6315 9572 4.542525 AGGAACCTTTGGTAATATGGGTCA 59.457 41.667 0.00 0.00 36.31 4.02
6328 9585 1.061546 TGGGTCAAGGAACTGGGTAC 58.938 55.000 0.00 0.00 40.86 3.34
6392 9649 2.105821 CCTCTTTGGGTTAGGTGTGACA 59.894 50.000 0.00 0.00 0.00 3.58
6393 9650 3.434453 CCTCTTTGGGTTAGGTGTGACAA 60.434 47.826 0.00 0.00 0.00 3.18
6516 9787 6.820470 TTTTTAGAACATTGTTGAAAGCCG 57.180 33.333 6.80 0.00 0.00 5.52
6692 9980 7.095910 TCTGAAAAGAAATGTTTCAAAGCACA 58.904 30.769 8.09 0.00 42.73 4.57
6717 10005 9.442047 CAACCCTAATTGTATGGATAGATTCTC 57.558 37.037 0.00 0.00 0.00 2.87
6752 10043 6.042143 AGAACATGTCATTGCGTTTTCTTTT 58.958 32.000 0.00 0.00 0.00 2.27
6777 10068 0.958382 TGGCGATGGTACTTGCAACC 60.958 55.000 0.00 0.00 37.53 3.77
6819 10114 6.446318 TGATTTCCTTTGTGAATTTTCCTCG 58.554 36.000 0.00 0.00 0.00 4.63
6831 10126 9.757227 TGTGAATTTTCCTCGACAATAATTTTT 57.243 25.926 0.00 0.00 0.00 1.94
6921 10216 6.115446 AGATAATCTTGTTCAAGCGATCCAA 58.885 36.000 7.58 0.00 0.00 3.53
6929 10224 2.952714 AAGCGATCCAAGCAAGCTT 58.047 47.368 0.59 0.59 42.51 3.74
6953 10248 5.013287 TGCTCCCTACTGGTTTTATGTTACA 59.987 40.000 0.00 0.00 34.77 2.41
6957 10252 6.270463 TCCCTACTGGTTTTATGTTACAGTGA 59.730 38.462 0.00 0.00 41.93 3.41
6958 10253 6.370718 CCCTACTGGTTTTATGTTACAGTGAC 59.629 42.308 0.00 0.00 41.93 3.67
6960 10255 5.362263 ACTGGTTTTATGTTACAGTGACGT 58.638 37.500 0.00 0.00 40.56 4.34
6961 10256 5.235616 ACTGGTTTTATGTTACAGTGACGTG 59.764 40.000 0.00 0.00 40.56 4.49
6962 10257 4.024725 TGGTTTTATGTTACAGTGACGTGC 60.025 41.667 0.00 0.00 0.00 5.34
6963 10258 4.460505 GTTTTATGTTACAGTGACGTGCC 58.539 43.478 0.00 0.00 0.00 5.01
6964 10259 3.388345 TTATGTTACAGTGACGTGCCA 57.612 42.857 0.00 0.00 0.00 4.92
6965 10260 1.508632 ATGTTACAGTGACGTGCCAC 58.491 50.000 0.00 0.00 37.32 5.01
6966 10261 0.531090 TGTTACAGTGACGTGCCACC 60.531 55.000 0.00 0.00 37.76 4.61
6968 10263 0.394938 TTACAGTGACGTGCCACCAT 59.605 50.000 0.00 0.00 37.76 3.55
6969 10264 1.258676 TACAGTGACGTGCCACCATA 58.741 50.000 0.00 0.00 37.76 2.74
6970 10265 0.613260 ACAGTGACGTGCCACCATAT 59.387 50.000 0.00 0.00 37.76 1.78
6971 10266 1.003118 ACAGTGACGTGCCACCATATT 59.997 47.619 0.00 0.00 37.76 1.28
6972 10267 2.083774 CAGTGACGTGCCACCATATTT 58.916 47.619 0.00 0.00 37.76 1.40
6973 10268 2.083774 AGTGACGTGCCACCATATTTG 58.916 47.619 0.00 0.00 37.76 2.32
6974 10269 2.080693 GTGACGTGCCACCATATTTGA 58.919 47.619 0.00 0.00 0.00 2.69
6975 10270 2.486203 GTGACGTGCCACCATATTTGAA 59.514 45.455 0.00 0.00 0.00 2.69
6976 10271 2.746904 TGACGTGCCACCATATTTGAAG 59.253 45.455 0.00 0.00 0.00 3.02
6977 10272 2.091541 ACGTGCCACCATATTTGAAGG 58.908 47.619 0.00 0.00 0.00 3.46
6978 10273 1.202290 CGTGCCACCATATTTGAAGGC 60.202 52.381 10.40 10.40 40.73 4.35
6979 10274 1.824230 GTGCCACCATATTTGAAGGCA 59.176 47.619 14.27 14.27 44.77 4.75
6980 10275 1.824230 TGCCACCATATTTGAAGGCAC 59.176 47.619 14.27 0.00 43.26 5.01
6981 10276 2.557229 TGCCACCATATTTGAAGGCACT 60.557 45.455 14.27 0.00 43.26 4.40
6997 10292 5.852282 AGGCACTTGAAACTGTTATTTGT 57.148 34.783 0.00 0.00 27.25 2.83
6998 10293 5.591099 AGGCACTTGAAACTGTTATTTGTG 58.409 37.500 0.00 3.29 27.25 3.33
6999 10294 5.359576 AGGCACTTGAAACTGTTATTTGTGA 59.640 36.000 15.61 0.00 27.25 3.58
7000 10295 6.040842 AGGCACTTGAAACTGTTATTTGTGAT 59.959 34.615 15.61 5.55 27.25 3.06
7001 10296 6.363357 GGCACTTGAAACTGTTATTTGTGATC 59.637 38.462 15.61 0.00 0.00 2.92
7002 10297 6.917477 GCACTTGAAACTGTTATTTGTGATCA 59.083 34.615 15.61 0.00 0.00 2.92
7003 10298 7.096477 GCACTTGAAACTGTTATTTGTGATCAC 60.096 37.037 19.27 19.27 0.00 3.06
7004 10299 8.131100 CACTTGAAACTGTTATTTGTGATCACT 58.869 33.333 25.55 9.24 0.00 3.41
7005 10300 8.345565 ACTTGAAACTGTTATTTGTGATCACTC 58.654 33.333 25.55 11.14 0.00 3.51
7006 10301 7.202016 TGAAACTGTTATTTGTGATCACTCC 57.798 36.000 25.55 8.33 0.00 3.85
7007 10302 6.206634 TGAAACTGTTATTTGTGATCACTCCC 59.793 38.462 25.55 8.97 0.00 4.30
7008 10303 4.253685 ACTGTTATTTGTGATCACTCCCG 58.746 43.478 25.55 9.08 0.00 5.14
7009 10304 4.253685 CTGTTATTTGTGATCACTCCCGT 58.746 43.478 25.55 10.39 0.00 5.28
7010 10305 4.250464 TGTTATTTGTGATCACTCCCGTC 58.750 43.478 25.55 12.85 0.00 4.79
7011 10306 4.250464 GTTATTTGTGATCACTCCCGTCA 58.750 43.478 25.55 1.47 0.00 4.35
7012 10307 3.634397 ATTTGTGATCACTCCCGTCAT 57.366 42.857 25.55 5.49 0.00 3.06
7020 10315 6.096036 GTGATCACTCCCGTCATATAATCTG 58.904 44.000 18.83 0.00 0.00 2.90
7055 10350 6.410540 TCTTTTTACCAAAATGTTTGGCTGT 58.589 32.000 17.65 3.66 43.23 4.40
7131 10436 2.130426 GGCTGCGAGGAGGATGAGA 61.130 63.158 0.00 0.00 0.00 3.27
7136 10441 0.755686 GCGAGGAGGATGAGATTGGT 59.244 55.000 0.00 0.00 0.00 3.67
7153 10458 3.430497 TAGGAGGCGAGGGGAGCT 61.430 66.667 0.00 0.00 34.52 4.09
7162 10467 1.668101 CGAGGGGAGCTACACTGTCC 61.668 65.000 4.68 0.00 0.00 4.02
7163 10468 0.614979 GAGGGGAGCTACACTGTCCA 60.615 60.000 4.68 0.00 31.31 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.082140 ACCAAAAACTTGAGGGGGTC 57.918 50.000 0.00 0.00 0.00 4.46
198 205 7.875041 AGACTTATCATGCGCTATTGATTAAGT 59.125 33.333 20.53 22.07 0.00 2.24
219 226 4.192317 GCATCGGTATGAAGGAAAGACTT 58.808 43.478 0.00 0.00 34.84 3.01
238 247 1.135402 GTTTTCAATTCGGAGCGGCAT 60.135 47.619 1.45 0.00 0.00 4.40
373 382 3.532542 TCACACCATCACAACACGTTTA 58.467 40.909 0.00 0.00 0.00 2.01
420 430 6.546403 GTGTTTCTATTTATCCTTCTTCCCCC 59.454 42.308 0.00 0.00 0.00 5.40
421 431 7.116736 TGTGTTTCTATTTATCCTTCTTCCCC 58.883 38.462 0.00 0.00 0.00 4.81
450 460 5.337410 CCTTTATTTCAACACATGGCATCCA 60.337 40.000 0.00 0.00 38.19 3.41
565 577 3.604875 TGACAATCTTAAGACGTCCCC 57.395 47.619 24.06 9.41 32.05 4.81
567 579 6.147164 TGAATGTTGACAATCTTAAGACGTCC 59.853 38.462 24.06 15.14 32.05 4.79
615 867 3.112709 GTCGACGCTGGCCTCAAC 61.113 66.667 3.32 0.00 0.00 3.18
616 868 4.717629 CGTCGACGCTGGCCTCAA 62.718 66.667 26.59 0.00 0.00 3.02
703 955 9.162764 GCTAATAACTATGAGTCCAAACTTCAA 57.837 33.333 0.00 0.00 35.28 2.69
880 1138 3.487376 CCGTTCCATCCAATGTTCGATTG 60.487 47.826 0.00 0.00 0.00 2.67
936 1194 1.270893 GCGAGATGGGGGAAATAGGAC 60.271 57.143 0.00 0.00 0.00 3.85
977 1236 0.762418 TCCTTCTCGTTTGCTTGGGA 59.238 50.000 0.00 0.00 0.00 4.37
1010 1269 1.984026 TGGAGCAGCCTCGTGATCA 60.984 57.895 0.00 0.00 39.06 2.92
1167 1441 1.080093 GACAATGGCGTCGAGACCA 60.080 57.895 8.70 8.70 41.06 4.02
1224 1498 4.529377 ACCAAAGAAGACACCTCGGTATAA 59.471 41.667 0.00 0.00 0.00 0.98
1335 1620 3.511146 ACATGGTAGATTGGCAAAACAGG 59.489 43.478 3.01 0.64 0.00 4.00
1352 1637 0.669619 TGTGAGCAGCAACAACATGG 59.330 50.000 0.00 0.00 0.00 3.66
1372 1657 5.984695 TGCTCAAGACTACAAGTAGATGT 57.015 39.130 13.79 0.00 36.97 3.06
1439 1724 8.113675 GTGCTGGTAGTTTACAAACAAAATTTG 58.886 33.333 3.89 3.89 41.30 2.32
1918 2468 1.801242 TTCACAAGACCAGGACTCCA 58.199 50.000 0.00 0.00 0.00 3.86
1972 2522 3.128068 ACAAAACCTCGTTGGACAAAGTC 59.872 43.478 4.38 0.00 39.71 3.01
2018 2568 3.603532 TGACTGTTCATGATGCTCTTCC 58.396 45.455 0.00 0.00 0.00 3.46
2111 2661 1.493772 TCGGTAACAACAGTTCTGCG 58.506 50.000 0.00 0.00 0.00 5.18
2121 2671 8.205512 TGCTAATCTGGTATATTTCGGTAACAA 58.794 33.333 0.00 0.00 0.00 2.83
2184 2734 2.894126 CCTGTATGTAGCTGGGGTCTAG 59.106 54.545 0.00 0.00 0.00 2.43
2196 2746 7.334921 GCTTTGTAACACCATTACCTGTATGTA 59.665 37.037 0.00 0.00 0.00 2.29
2197 2747 6.150474 GCTTTGTAACACCATTACCTGTATGT 59.850 38.462 0.00 0.00 0.00 2.29
2198 2748 6.150307 TGCTTTGTAACACCATTACCTGTATG 59.850 38.462 0.00 0.00 0.00 2.39
2199 2749 6.242396 TGCTTTGTAACACCATTACCTGTAT 58.758 36.000 0.00 0.00 0.00 2.29
2318 2868 2.715046 ACATCAGCCACCATGTAAGTG 58.285 47.619 0.00 0.00 31.20 3.16
2504 3054 8.331931 ACATAGATAAGAGATGTTACCCCAAA 57.668 34.615 0.00 0.00 29.46 3.28
2505 3055 7.931015 ACATAGATAAGAGATGTTACCCCAA 57.069 36.000 0.00 0.00 29.46 4.12
2506 3056 7.567250 TGAACATAGATAAGAGATGTTACCCCA 59.433 37.037 0.00 0.00 42.40 4.96
2507 3057 7.963532 TGAACATAGATAAGAGATGTTACCCC 58.036 38.462 0.00 0.00 42.40 4.95
2508 3058 9.482627 CTTGAACATAGATAAGAGATGTTACCC 57.517 37.037 0.00 0.00 42.40 3.69
2643 3195 2.494059 TGCTCTCAAAGAAAGGTTCCG 58.506 47.619 0.00 0.00 0.00 4.30
2762 3314 8.416329 TCTTATATTTCTTTACGGAGGGTGTAC 58.584 37.037 0.00 0.00 0.00 2.90
2763 3315 8.537728 TCTTATATTTCTTTACGGAGGGTGTA 57.462 34.615 0.00 0.00 0.00 2.90
2764 3316 7.125356 ACTCTTATATTTCTTTACGGAGGGTGT 59.875 37.037 0.00 0.00 0.00 4.16
2765 3317 7.438459 CACTCTTATATTTCTTTACGGAGGGTG 59.562 40.741 0.00 0.00 0.00 4.61
2766 3318 7.125356 ACACTCTTATATTTCTTTACGGAGGGT 59.875 37.037 0.00 0.00 31.26 4.34
2767 3319 7.498443 ACACTCTTATATTTCTTTACGGAGGG 58.502 38.462 0.00 0.00 0.00 4.30
2768 3320 8.943909 AACACTCTTATATTTCTTTACGGAGG 57.056 34.615 0.00 0.00 0.00 4.30
2817 3369 9.892130 CCCTCTGTAAAGAAATATAAGAGTGTT 57.108 33.333 0.00 0.00 0.00 3.32
2818 3370 9.268282 TCCCTCTGTAAAGAAATATAAGAGTGT 57.732 33.333 0.00 0.00 0.00 3.55
2819 3371 9.757227 CTCCCTCTGTAAAGAAATATAAGAGTG 57.243 37.037 0.00 0.00 0.00 3.51
2820 3372 9.495382 ACTCCCTCTGTAAAGAAATATAAGAGT 57.505 33.333 0.00 0.00 0.00 3.24
2944 3498 3.052036 CCAAAAGAAAACCATGTCTGCG 58.948 45.455 0.00 0.00 0.00 5.18
3026 3581 3.173151 TCCTGCATTGTCAGAGGACTAA 58.827 45.455 8.94 0.00 44.61 2.24
3073 3628 5.663106 AGGAGTAAGATGCAGATGACCTTAA 59.337 40.000 0.00 0.00 0.00 1.85
3187 3742 7.875971 AGACTAAAACAAGCAGGAAAATGTAG 58.124 34.615 0.00 0.00 0.00 2.74
3308 3863 0.035317 AGAGCGCAGATGGTCACAAA 59.965 50.000 11.47 0.00 38.81 2.83
3323 3878 2.094494 TGCTTAGTCAGTACTGCAGAGC 60.094 50.000 23.35 20.97 36.36 4.09
3531 4174 2.413371 GCAGAACCTTTTCAGCGTGATC 60.413 50.000 0.00 0.00 34.90 2.92
3589 4232 7.609532 ACATCTAGAATTCAAGACCAAAGAAGG 59.390 37.037 8.44 0.00 0.00 3.46
3619 4262 5.645056 TCCTAATTGGGTTATCTCATGCA 57.355 39.130 7.83 0.00 36.20 3.96
3684 4327 6.542821 TGCCCTATTAGACCATTAATTCCTG 58.457 40.000 0.00 0.00 0.00 3.86
3706 4349 6.199393 ACTCTAAACAACAGAATTCGTTTGC 58.801 36.000 17.28 0.00 33.79 3.68
3780 4425 9.640952 TTGGGTGATTAATATTTCTAAGGGAAG 57.359 33.333 0.00 0.00 35.16 3.46
3879 4530 7.989416 TTAAACCATACAAAGAGTACTTGGG 57.011 36.000 11.28 0.37 37.23 4.12
3960 4611 4.099419 ACAAAGCCTTTAGTCCCAAACAAG 59.901 41.667 0.00 0.00 0.00 3.16
3961 4612 4.027437 ACAAAGCCTTTAGTCCCAAACAA 58.973 39.130 0.00 0.00 0.00 2.83
3962 4613 3.637769 ACAAAGCCTTTAGTCCCAAACA 58.362 40.909 0.00 0.00 0.00 2.83
3963 4614 4.142026 ACAACAAAGCCTTTAGTCCCAAAC 60.142 41.667 0.00 0.00 0.00 2.93
3964 4615 4.027437 ACAACAAAGCCTTTAGTCCCAAA 58.973 39.130 0.00 0.00 0.00 3.28
3965 4616 3.637769 ACAACAAAGCCTTTAGTCCCAA 58.362 40.909 0.00 0.00 0.00 4.12
3966 4617 3.306472 ACAACAAAGCCTTTAGTCCCA 57.694 42.857 0.00 0.00 0.00 4.37
3967 4618 3.383505 ACAACAACAAAGCCTTTAGTCCC 59.616 43.478 0.00 0.00 0.00 4.46
3968 4619 4.649088 ACAACAACAAAGCCTTTAGTCC 57.351 40.909 0.00 0.00 0.00 3.85
3969 4620 5.407502 ACAACAACAACAAAGCCTTTAGTC 58.592 37.500 0.00 0.00 0.00 2.59
3970 4621 5.400066 ACAACAACAACAAAGCCTTTAGT 57.600 34.783 0.00 0.00 0.00 2.24
3971 4622 5.637387 ACAACAACAACAACAAAGCCTTTAG 59.363 36.000 0.00 0.00 0.00 1.85
3973 4624 4.384940 ACAACAACAACAACAAAGCCTTT 58.615 34.783 0.00 0.00 0.00 3.11
3974 4625 4.001618 ACAACAACAACAACAAAGCCTT 57.998 36.364 0.00 0.00 0.00 4.35
3975 4626 3.676291 ACAACAACAACAACAAAGCCT 57.324 38.095 0.00 0.00 0.00 4.58
3976 4627 5.726413 GCAATACAACAACAACAACAAAGCC 60.726 40.000 0.00 0.00 0.00 4.35
3977 4628 5.063312 AGCAATACAACAACAACAACAAAGC 59.937 36.000 0.00 0.00 0.00 3.51
3978 4629 6.645700 AGCAATACAACAACAACAACAAAG 57.354 33.333 0.00 0.00 0.00 2.77
3979 4630 8.709386 ATAAGCAATACAACAACAACAACAAA 57.291 26.923 0.00 0.00 0.00 2.83
3980 4631 9.457110 CTATAAGCAATACAACAACAACAACAA 57.543 29.630 0.00 0.00 0.00 2.83
3981 4632 8.841300 TCTATAAGCAATACAACAACAACAACA 58.159 29.630 0.00 0.00 0.00 3.33
3982 4633 9.840427 ATCTATAAGCAATACAACAACAACAAC 57.160 29.630 0.00 0.00 0.00 3.32
3984 4635 9.225436 TGATCTATAAGCAATACAACAACAACA 57.775 29.630 0.00 0.00 0.00 3.33
3988 4639 9.173939 GCAATGATCTATAAGCAATACAACAAC 57.826 33.333 0.00 0.00 0.00 3.32
3991 4642 7.175641 AGGGCAATGATCTATAAGCAATACAAC 59.824 37.037 0.00 0.00 0.00 3.32
3994 4645 7.108847 AGAGGGCAATGATCTATAAGCAATAC 58.891 38.462 0.00 0.00 0.00 1.89
4011 4662 2.774234 CTCCTGAGGATAAAGAGGGCAA 59.226 50.000 0.00 0.00 0.00 4.52
4089 4740 1.673920 GCAAAAGTCACCGGTTTCTCA 59.326 47.619 2.97 0.00 0.00 3.27
4095 4746 0.535102 CCTCAGCAAAAGTCACCGGT 60.535 55.000 0.00 0.00 0.00 5.28
4291 4942 8.396272 ACCATAATGAGATATAACCAACAAGC 57.604 34.615 0.00 0.00 0.00 4.01
4381 5049 5.805728 ACACCCTCTGTTCCTAAATGTAAG 58.194 41.667 0.00 0.00 0.00 2.34
4390 5058 2.638363 GGAAAGTACACCCTCTGTTCCT 59.362 50.000 0.00 0.00 33.91 3.36
4436 5104 5.745227 CCTGATGTGGTATTTCTTAGTGGT 58.255 41.667 0.00 0.00 0.00 4.16
4476 5144 4.640771 TGCTTAACACTGGAGAGGAAAT 57.359 40.909 0.00 0.00 0.00 2.17
4688 5356 1.010419 GCAATGTGCCTTTGAAGCCG 61.010 55.000 5.41 0.00 37.42 5.52
4713 5381 7.170277 GGGAAAGTATTTGTTACTACCAAGGA 58.830 38.462 0.00 0.00 40.37 3.36
4785 5537 2.101415 TCCGGCAGTTCAGATAGACATG 59.899 50.000 0.00 0.00 0.00 3.21
4803 5555 7.915508 TGCAATATTAACTACAGTGAATTCCG 58.084 34.615 2.27 0.00 31.72 4.30
4816 5568 9.104965 TCGCTAACAAAGTATGCAATATTAACT 57.895 29.630 0.00 0.00 0.00 2.24
4902 5656 8.594550 GGGAAATAGAATATACAAGCAGGTAGA 58.405 37.037 0.00 0.00 0.00 2.59
4919 5673 5.016173 CACACAATGGAAAGGGGAAATAGA 58.984 41.667 0.00 0.00 0.00 1.98
4959 5713 1.929836 GGAGCAGCTAGAACATCAACG 59.070 52.381 0.00 0.00 0.00 4.10
5026 8267 3.460362 TGTACTACAGCGTAACACGAG 57.540 47.619 2.35 0.00 46.05 4.18
5031 8272 4.919168 TGTGACATTGTACTACAGCGTAAC 59.081 41.667 0.00 0.00 0.00 2.50
5042 8283 3.187227 CAGAGCTGGTTGTGACATTGTAC 59.813 47.826 0.00 0.00 0.00 2.90
5047 8288 1.888215 CACAGAGCTGGTTGTGACAT 58.112 50.000 14.36 0.00 45.79 3.06
5062 8303 1.269883 TGCCAAGAAATGCAAGCACAG 60.270 47.619 0.00 0.00 33.87 3.66
5147 8388 6.327279 ACAAAAACTTAACATCCAGGCTAC 57.673 37.500 0.00 0.00 0.00 3.58
5193 8434 1.822990 GCGGGGGAGTATCGATCAATA 59.177 52.381 0.00 0.00 34.37 1.90
5194 8435 0.608640 GCGGGGGAGTATCGATCAAT 59.391 55.000 0.00 0.00 34.37 2.57
5195 8436 1.469335 GGCGGGGGAGTATCGATCAA 61.469 60.000 0.00 0.00 34.37 2.57
5198 8439 1.908793 CTGGCGGGGGAGTATCGAT 60.909 63.158 2.16 2.16 34.37 3.59
5199 8440 2.367586 ATCTGGCGGGGGAGTATCGA 62.368 60.000 0.00 0.00 34.37 3.59
5200 8441 1.472662 AATCTGGCGGGGGAGTATCG 61.473 60.000 0.00 0.00 34.37 2.92
5208 8450 2.348411 ATTCAGTAAATCTGGCGGGG 57.652 50.000 0.00 0.00 43.76 5.73
5294 8536 4.612932 GCCAAAAGCAATGTGAAAAACA 57.387 36.364 0.00 0.00 42.18 2.83
5364 8606 2.549754 CAATCTCACTTTCAGGTTGCGT 59.450 45.455 0.00 0.00 0.00 5.24
5365 8607 2.666619 GCAATCTCACTTTCAGGTTGCG 60.667 50.000 2.10 0.00 45.55 4.85
5618 8862 1.393539 CTGTTTGGAATACGCTGTCGG 59.606 52.381 0.00 0.00 40.69 4.79
5657 8901 0.874390 CCTCCACATGTTCAACACCG 59.126 55.000 0.00 0.00 0.00 4.94
5766 9019 4.593634 AGCCCCCTATAGTGAACTTGTATC 59.406 45.833 0.00 0.00 0.00 2.24
5780 9035 4.413520 CCACTATATATTGCAGCCCCCTAT 59.586 45.833 0.00 0.00 0.00 2.57
5933 9190 2.783135 AGAAGCCATCACACGACAAAT 58.217 42.857 0.00 0.00 0.00 2.32
5944 9201 9.403110 CATATATAAAACTTGCAAGAAGCCATC 57.597 33.333 32.50 0.00 44.83 3.51
6275 9532 4.081087 GGTTCCTAGCAACTATGGTCTCAA 60.081 45.833 0.00 0.00 38.46 3.02
6301 9558 4.080015 CCAGTTCCTTGACCCATATTACCA 60.080 45.833 0.00 0.00 0.00 3.25
6392 9649 6.239289 CCATGTCCCAAAAATGTGTACTCTTT 60.239 38.462 0.00 0.00 0.00 2.52
6393 9650 5.243730 CCATGTCCCAAAAATGTGTACTCTT 59.756 40.000 0.00 0.00 0.00 2.85
6516 9787 2.408271 TCCAGTGATCAGGCATGAAC 57.592 50.000 4.62 2.73 39.39 3.18
6613 9901 5.862845 AGAAAGAGCATCGGATATCATGTT 58.137 37.500 4.83 0.00 42.67 2.71
6621 9909 5.012458 TCCAATCATAGAAAGAGCATCGGAT 59.988 40.000 0.00 0.00 42.67 4.18
6625 9913 7.441017 ACTACTCCAATCATAGAAAGAGCATC 58.559 38.462 0.00 0.00 0.00 3.91
6717 10005 7.637519 CGCAATGACATGTTCTAAATTAGTCAG 59.362 37.037 0.00 0.00 37.85 3.51
6752 10043 0.986019 AAGTACCATCGCCATCCCCA 60.986 55.000 0.00 0.00 0.00 4.96
6831 10126 8.961634 TGATCCCAACGTTTGATAATGATAAAA 58.038 29.630 0.00 0.00 0.00 1.52
6832 10127 8.512966 TGATCCCAACGTTTGATAATGATAAA 57.487 30.769 0.00 0.00 0.00 1.40
6929 10224 4.650972 AACATAAAACCAGTAGGGAGCA 57.349 40.909 0.00 0.00 41.15 4.26
6953 10248 2.083774 CAAATATGGTGGCACGTCACT 58.916 47.619 12.17 0.00 37.75 3.41
6957 10252 2.091541 CCTTCAAATATGGTGGCACGT 58.908 47.619 12.17 5.45 0.00 4.49
6958 10253 1.202290 GCCTTCAAATATGGTGGCACG 60.202 52.381 12.17 0.00 41.60 5.34
6960 10255 1.824230 GTGCCTTCAAATATGGTGGCA 59.176 47.619 0.00 0.00 45.76 4.92
6961 10256 2.102578 AGTGCCTTCAAATATGGTGGC 58.897 47.619 0.00 0.00 42.01 5.01
6962 10257 3.763360 TCAAGTGCCTTCAAATATGGTGG 59.237 43.478 0.00 0.00 0.00 4.61
6963 10258 5.389859 TTCAAGTGCCTTCAAATATGGTG 57.610 39.130 0.00 0.00 0.00 4.17
6964 10259 5.539955 AGTTTCAAGTGCCTTCAAATATGGT 59.460 36.000 0.00 0.00 0.00 3.55
6965 10260 5.865552 CAGTTTCAAGTGCCTTCAAATATGG 59.134 40.000 0.00 0.00 0.00 2.74
6966 10261 6.449698 ACAGTTTCAAGTGCCTTCAAATATG 58.550 36.000 0.00 0.00 32.54 1.78
6968 10263 6.463995 AACAGTTTCAAGTGCCTTCAAATA 57.536 33.333 0.00 0.00 32.54 1.40
6969 10264 5.343307 AACAGTTTCAAGTGCCTTCAAAT 57.657 34.783 0.00 0.00 32.54 2.32
6970 10265 4.799564 AACAGTTTCAAGTGCCTTCAAA 57.200 36.364 0.00 0.00 32.54 2.69
6971 10266 6.463995 AATAACAGTTTCAAGTGCCTTCAA 57.536 33.333 0.00 0.00 32.54 2.69
6972 10267 6.127479 ACAAATAACAGTTTCAAGTGCCTTCA 60.127 34.615 0.00 0.00 32.54 3.02
6973 10268 6.198966 CACAAATAACAGTTTCAAGTGCCTTC 59.801 38.462 0.00 0.00 32.54 3.46
6974 10269 6.042143 CACAAATAACAGTTTCAAGTGCCTT 58.958 36.000 0.00 0.00 32.54 4.35
6975 10270 5.359576 TCACAAATAACAGTTTCAAGTGCCT 59.640 36.000 0.00 0.00 32.54 4.75
6976 10271 5.587289 TCACAAATAACAGTTTCAAGTGCC 58.413 37.500 0.00 0.00 32.54 5.01
6977 10272 6.917477 TGATCACAAATAACAGTTTCAAGTGC 59.083 34.615 0.00 0.00 32.54 4.40
6978 10273 8.131100 AGTGATCACAAATAACAGTTTCAAGTG 58.869 33.333 27.02 0.00 35.47 3.16
6979 10274 8.225603 AGTGATCACAAATAACAGTTTCAAGT 57.774 30.769 27.02 0.00 0.00 3.16
6980 10275 7.805071 GGAGTGATCACAAATAACAGTTTCAAG 59.195 37.037 27.02 0.00 0.00 3.02
6981 10276 7.255451 GGGAGTGATCACAAATAACAGTTTCAA 60.255 37.037 27.02 0.00 0.00 2.69
6982 10277 6.206634 GGGAGTGATCACAAATAACAGTTTCA 59.793 38.462 27.02 0.00 0.00 2.69
6983 10278 6.612306 GGGAGTGATCACAAATAACAGTTTC 58.388 40.000 27.02 11.06 0.00 2.78
6984 10279 5.181245 CGGGAGTGATCACAAATAACAGTTT 59.819 40.000 27.02 1.97 0.00 2.66
6985 10280 4.695455 CGGGAGTGATCACAAATAACAGTT 59.305 41.667 27.02 2.52 0.00 3.16
6986 10281 4.253685 CGGGAGTGATCACAAATAACAGT 58.746 43.478 27.02 3.30 0.00 3.55
6987 10282 4.253685 ACGGGAGTGATCACAAATAACAG 58.746 43.478 27.02 12.62 44.82 3.16
6988 10283 4.280436 ACGGGAGTGATCACAAATAACA 57.720 40.909 27.02 0.00 44.82 2.41
7003 10298 7.595502 GTCAAACTACAGATTATATGACGGGAG 59.404 40.741 0.00 0.00 0.00 4.30
7004 10299 7.068962 TGTCAAACTACAGATTATATGACGGGA 59.931 37.037 0.00 0.00 38.93 5.14
7005 10300 7.207383 TGTCAAACTACAGATTATATGACGGG 58.793 38.462 0.00 0.00 38.93 5.28
7006 10301 8.818141 ATGTCAAACTACAGATTATATGACGG 57.182 34.615 0.00 0.00 38.93 4.79
7007 10302 9.684448 AGATGTCAAACTACAGATTATATGACG 57.316 33.333 0.00 0.00 38.93 4.35
7055 10350 5.055812 GCAAAGTGATGAATTCAAACCCAA 58.944 37.500 13.09 0.00 35.70 4.12
7131 10436 1.766461 CCCCTCGCCTCCTACCAAT 60.766 63.158 0.00 0.00 0.00 3.16
7136 10441 2.083042 TAGCTCCCCTCGCCTCCTA 61.083 63.158 0.00 0.00 0.00 2.94
7178 10489 5.105997 CCTGATCCATCACCTCTTTTTGTTC 60.106 44.000 0.00 0.00 32.50 3.18


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

AutoCloner maintained by Alex Coulton.