Multiple sequence alignment - TraesCS5A01G033500

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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 TraesCS5A01G033500 chr5A 100.000 3929 0 0 1 3929 30411998 30415926 0.000000e+00 7256.0
1 TraesCS5A01G033500 chr5D 92.832 2567 112 34 445 2978 42037975 42040502 0.000000e+00 3655.0
2 TraesCS5A01G033500 chr5D 95.385 390 18 0 59 448 42037360 42037749 4.310000e-174 621.0
3 TraesCS5A01G033500 chr5D 82.796 744 44 23 3222 3929 42040857 42041552 4.370000e-164 588.0
4 TraesCS5A01G033500 chr5B 87.084 751 45 25 1767 2500 36730386 36731101 0.000000e+00 802.0
5 TraesCS5A01G033500 chr5B 94.523 493 18 3 2497 2980 36731190 36731682 0.000000e+00 752.0
6 TraesCS5A01G033500 chr5B 94.464 289 16 0 962 1250 36729867 36730155 2.790000e-121 446.0
7 TraesCS5A01G033500 chr5B 89.625 347 17 6 3269 3607 36733439 36733774 1.310000e-114 424.0
8 TraesCS5A01G033500 chr5B 87.205 297 17 14 3645 3929 36733776 36734063 6.340000e-83 318.0
9 TraesCS5A01G033500 chr5B 78.689 427 83 5 2497 2921 636898074 636898494 1.080000e-70 278.0
10 TraesCS5A01G033500 chr5B 94.118 153 9 0 782 934 36728344 36728496 2.360000e-57 233.0
11 TraesCS5A01G033500 chr5B 94.558 147 7 1 1502 1647 36730154 36730300 3.950000e-55 226.0
12 TraesCS5A01G033500 chr5B 80.556 288 50 3 2634 2921 636896705 636896986 2.380000e-52 217.0
13 TraesCS5A01G033500 chr5B 93.750 112 5 2 446 556 433216298 433216188 2.430000e-37 167.0
14 TraesCS5A01G033500 chr5B 100.000 29 0 0 922 950 36729841 36729869 2.000000e-03 54.7
15 TraesCS5A01G033500 chr1B 75.892 813 178 18 2124 2930 1472053 1472853 2.200000e-107 399.0
16 TraesCS5A01G033500 chr1B 78.170 623 126 7 2309 2930 1424395 1423782 4.760000e-104 388.0
17 TraesCS5A01G033500 chr1B 89.815 216 22 0 1 216 633852639 633852854 1.080000e-70 278.0
18 TraesCS5A01G033500 chr1B 83.688 141 21 2 2312 2451 160486855 160486994 8.860000e-27 132.0
19 TraesCS5A01G033500 chr1D 75.686 802 175 12 2127 2921 2125677 2124889 2.220000e-102 383.0
20 TraesCS5A01G033500 chr1D 75.646 813 167 24 2124 2921 2119956 2119160 3.710000e-100 375.0
21 TraesCS5A01G033500 chr1A 75.646 813 157 24 2124 2921 1229714 1228928 2.230000e-97 366.0
22 TraesCS5A01G033500 chr3B 88.626 211 21 1 240 447 125923630 125923420 1.810000e-63 254.0
23 TraesCS5A01G033500 chr2D 79.351 339 65 5 2 338 418737124 418737459 2.360000e-57 233.0
24 TraesCS5A01G033500 chr4B 76.584 363 75 8 2 356 22624943 22625303 1.440000e-44 191.0
25 TraesCS5A01G033500 chr6B 76.243 362 72 10 2 355 125088644 125088999 3.120000e-41 180.0
26 TraesCS5A01G033500 chr7D 75.549 364 77 10 2 356 374441728 374442088 6.750000e-38 169.0
27 TraesCS5A01G033500 chr7B 75.207 363 80 8 2 356 358054607 358054967 3.140000e-36 163.0


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 TraesCS5A01G033500 chr5A 30411998 30415926 3928 False 7256.000000 7256 100.000000 1 3929 1 chr5A.!!$F1 3928
1 TraesCS5A01G033500 chr5D 42037360 42041552 4192 False 1621.333333 3655 90.337667 59 3929 3 chr5D.!!$F1 3870
2 TraesCS5A01G033500 chr5B 36728344 36734063 5719 False 406.962500 802 92.697125 782 3929 8 chr5B.!!$F1 3147
3 TraesCS5A01G033500 chr5B 636896705 636898494 1789 False 247.500000 278 79.622500 2497 2921 2 chr5B.!!$F2 424
4 TraesCS5A01G033500 chr1B 1472053 1472853 800 False 399.000000 399 75.892000 2124 2930 1 chr1B.!!$F1 806
5 TraesCS5A01G033500 chr1B 1423782 1424395 613 True 388.000000 388 78.170000 2309 2930 1 chr1B.!!$R1 621
6 TraesCS5A01G033500 chr1D 2124889 2125677 788 True 383.000000 383 75.686000 2127 2921 1 chr1D.!!$R2 794
7 TraesCS5A01G033500 chr1D 2119160 2119956 796 True 375.000000 375 75.646000 2124 2921 1 chr1D.!!$R1 797
8 TraesCS5A01G033500 chr1A 1228928 1229714 786 True 366.000000 366 75.646000 2124 2921 1 chr1A.!!$R1 797

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
496 726 0.038310 TCTCGAGAGTGCTTCCTCCA 59.962 55.0 12.08 0.0 31.53 3.86 F
1540 3138 0.242017 GGAAGCGCAAGTTCAGCAAT 59.758 50.0 11.47 0.0 41.68 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 3453 0.250234 CGTCAATCTCCTTGGCCTCA 59.750 55.0 3.32 0.0 36.01 3.86 R
3216 5142 0.178964 TTCTGTTCCTTTGGGGCAGG 60.179 55.0 0.00 0.0 36.98 4.85 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
18 19 4.648626 GGTGAGCAGCACTGGCCA 62.649 66.667 4.71 4.71 46.86 5.36
19 20 2.360852 GTGAGCAGCACTGGCCAT 60.361 61.111 5.51 0.00 44.27 4.40
21 22 1.676635 TGAGCAGCACTGGCCATTC 60.677 57.895 5.51 0.00 42.56 2.67
22 23 2.362120 AGCAGCACTGGCCATTCC 60.362 61.111 5.51 0.00 42.56 3.01
23 24 3.455469 GCAGCACTGGCCATTCCC 61.455 66.667 5.51 0.00 42.56 3.97
24 25 2.357836 CAGCACTGGCCATTCCCT 59.642 61.111 5.51 0.00 42.56 4.20
25 26 2.050350 CAGCACTGGCCATTCCCTG 61.050 63.158 5.51 7.18 42.56 4.45
26 27 2.233566 AGCACTGGCCATTCCCTGA 61.234 57.895 5.51 0.00 42.56 3.86
27 28 1.304381 GCACTGGCCATTCCCTGAA 60.304 57.895 5.51 0.00 0.00 3.02
28 29 1.598701 GCACTGGCCATTCCCTGAAC 61.599 60.000 5.51 0.00 0.00 3.18
29 30 0.967380 CACTGGCCATTCCCTGAACC 60.967 60.000 5.51 0.00 0.00 3.62
30 31 1.142688 ACTGGCCATTCCCTGAACCT 61.143 55.000 5.51 0.00 0.00 3.50
31 32 0.682209 CTGGCCATTCCCTGAACCTG 60.682 60.000 5.51 0.00 0.00 4.00
32 33 1.139498 TGGCCATTCCCTGAACCTGA 61.139 55.000 0.00 0.00 0.00 3.86
33 34 0.259938 GGCCATTCCCTGAACCTGAT 59.740 55.000 0.00 0.00 0.00 2.90
34 35 1.396653 GCCATTCCCTGAACCTGATG 58.603 55.000 0.00 0.00 0.00 3.07
35 36 1.341383 GCCATTCCCTGAACCTGATGT 60.341 52.381 0.00 0.00 0.00 3.06
36 37 2.372264 CCATTCCCTGAACCTGATGTG 58.628 52.381 0.00 0.00 0.00 3.21
37 38 2.372264 CATTCCCTGAACCTGATGTGG 58.628 52.381 0.00 0.00 0.00 4.17
38 39 1.741028 TTCCCTGAACCTGATGTGGA 58.259 50.000 0.00 0.00 0.00 4.02
39 40 1.971149 TCCCTGAACCTGATGTGGAT 58.029 50.000 0.00 0.00 0.00 3.41
41 42 1.386533 CCTGAACCTGATGTGGATGC 58.613 55.000 0.00 0.00 0.00 3.91
42 43 1.386533 CTGAACCTGATGTGGATGCC 58.613 55.000 0.00 0.00 0.00 4.40
43 44 0.994247 TGAACCTGATGTGGATGCCT 59.006 50.000 0.00 0.00 0.00 4.75
44 45 1.340308 TGAACCTGATGTGGATGCCTG 60.340 52.381 0.00 0.00 0.00 4.85
45 46 0.682209 AACCTGATGTGGATGCCTGC 60.682 55.000 0.00 0.00 0.00 4.85
46 47 1.077285 CCTGATGTGGATGCCTGCA 60.077 57.895 0.00 0.00 0.00 4.41
47 48 1.101635 CCTGATGTGGATGCCTGCAG 61.102 60.000 6.78 6.78 0.00 4.41
48 49 1.077285 TGATGTGGATGCCTGCAGG 60.077 57.895 29.34 29.34 38.53 4.85
67 68 2.496070 AGGCGTGAAGACATACAAGCTA 59.504 45.455 0.00 0.00 40.25 3.32
112 113 5.665360 TGGTATTACTCATGTGATCTTCCCA 59.335 40.000 0.94 0.00 0.00 4.37
186 187 1.685765 CGATCCTGGGAGGGTCACA 60.686 63.158 3.82 0.00 46.02 3.58
273 274 0.751643 GCATGGGTGGTATGGTGTCC 60.752 60.000 0.00 0.00 0.00 4.02
398 399 0.173708 ATCTCCTTCAACTCGGTCGC 59.826 55.000 0.00 0.00 0.00 5.19
448 449 1.305201 TCAAGTCAACGCCAACTTCC 58.695 50.000 0.00 0.00 33.53 3.46
449 450 0.310854 CAAGTCAACGCCAACTTCCC 59.689 55.000 0.00 0.00 33.53 3.97
452 453 1.072505 TCAACGCCAACTTCCCCTC 59.927 57.895 0.00 0.00 0.00 4.30
470 700 3.452990 CCCTCTTACCTTTCTTCCTCCTC 59.547 52.174 0.00 0.00 0.00 3.71
496 726 0.038310 TCTCGAGAGTGCTTCCTCCA 59.962 55.000 12.08 0.00 31.53 3.86
505 735 2.000447 GTGCTTCCTCCATTCGTGTAC 59.000 52.381 0.00 0.00 0.00 2.90
580 810 6.049790 GTCCATCTATTCCCTTACACTTCAC 58.950 44.000 0.00 0.00 0.00 3.18
661 891 1.380785 CCTAGCCAGGTACGGTCCA 60.381 63.158 0.00 0.00 37.15 4.02
662 892 1.392710 CCTAGCCAGGTACGGTCCAG 61.393 65.000 0.00 0.00 37.15 3.86
663 893 1.380785 TAGCCAGGTACGGTCCAGG 60.381 63.158 5.46 5.46 37.23 4.45
664 894 1.866483 TAGCCAGGTACGGTCCAGGA 61.866 60.000 12.32 0.00 36.42 3.86
667 897 1.605058 CCAGGTACGGTCCAGGACTG 61.605 65.000 25.09 25.09 43.83 3.51
668 898 1.982938 AGGTACGGTCCAGGACTGC 60.983 63.158 26.40 12.27 42.17 4.40
670 900 3.066190 TACGGTCCAGGACTGCGG 61.066 66.667 26.40 12.47 42.17 5.69
694 924 3.583526 GGATGGTAATTAGGACCTCCTCC 59.416 52.174 0.00 0.00 44.77 4.30
711 941 3.850173 TCCTCCAAGGTAAATAACTGCCT 59.150 43.478 0.00 0.00 36.53 4.75
713 943 4.200092 CTCCAAGGTAAATAACTGCCTCC 58.800 47.826 0.00 0.00 0.00 4.30
715 945 4.229582 TCCAAGGTAAATAACTGCCTCCAT 59.770 41.667 0.00 0.00 0.00 3.41
716 946 4.956075 CCAAGGTAAATAACTGCCTCCATT 59.044 41.667 0.00 0.00 0.00 3.16
717 947 5.067805 CCAAGGTAAATAACTGCCTCCATTC 59.932 44.000 0.00 0.00 0.00 2.67
718 948 5.450818 AGGTAAATAACTGCCTCCATTCA 57.549 39.130 0.00 0.00 0.00 2.57
719 949 5.440610 AGGTAAATAACTGCCTCCATTCAG 58.559 41.667 0.00 0.00 36.45 3.02
720 950 5.044846 AGGTAAATAACTGCCTCCATTCAGT 60.045 40.000 0.00 0.00 44.64 3.41
778 1008 0.537188 CCCTGCACCGACAACTAGAT 59.463 55.000 0.00 0.00 0.00 1.98
780 1010 2.481449 CCCTGCACCGACAACTAGATAC 60.481 54.545 0.00 0.00 0.00 2.24
880 1110 6.252599 TCATAACATCCATAGGAGTTTGCT 57.747 37.500 6.32 0.00 34.05 3.91
951 2538 1.818642 AGCACTCACCTCTTGCATTC 58.181 50.000 0.00 0.00 38.81 2.67
1039 2627 0.593128 GTCGCAACAATGGAGCTTGT 59.407 50.000 0.00 0.00 41.01 3.16
1081 2669 2.930019 CTCTGTGGTGGGCCTGGA 60.930 66.667 4.53 0.00 35.27 3.86
1315 2903 8.908903 AGCACGGTAAATAAATTAAATCCATCA 58.091 29.630 0.00 0.00 0.00 3.07
1388 2986 1.261619 GGTCACTTGTTCAGACTTGCG 59.738 52.381 0.00 0.00 32.98 4.85
1401 2999 2.101582 AGACTTGCGTGTCTGAAACTCT 59.898 45.455 10.09 0.00 44.64 3.24
1404 3002 3.318275 ACTTGCGTGTCTGAAACTCTAGA 59.682 43.478 6.45 0.00 0.00 2.43
1410 3008 5.700846 CGTGTCTGAAACTCTAGAAAGCTA 58.299 41.667 0.00 0.00 0.00 3.32
1498 3096 2.154567 AACTGGTGCGGGAGATACTA 57.845 50.000 0.00 0.00 0.00 1.82
1540 3138 0.242017 GGAAGCGCAAGTTCAGCAAT 59.758 50.000 11.47 0.00 41.68 3.56
1633 3231 2.214376 TCAACCCCGCATTTCATCTT 57.786 45.000 0.00 0.00 0.00 2.40
1667 3265 0.526739 AAGCGCGAAAACCAAACCAC 60.527 50.000 12.10 0.00 0.00 4.16
1669 3267 2.290082 CGCGAAAACCAAACCACGC 61.290 57.895 0.00 0.00 42.07 5.34
1672 3270 2.278271 AAAACCAAACCACGCGCG 60.278 55.556 30.96 30.96 0.00 6.86
1675 3273 2.452366 AAACCAAACCACGCGCGATC 62.452 55.000 39.36 0.00 0.00 3.69
1680 3278 2.488852 AAACCACGCGCGATCGTTTC 62.489 55.000 39.36 5.22 41.21 2.78
1683 3281 1.295220 CACGCGCGATCGTTTCTTC 60.295 57.895 39.36 0.00 41.21 2.87
1684 3282 1.443872 ACGCGCGATCGTTTCTTCT 60.444 52.632 39.36 5.95 40.07 2.85
1738 3343 2.002586 GCTTGCTCGCTTGTCTGAATA 58.997 47.619 0.00 0.00 0.00 1.75
1744 3349 4.142838 TGCTCGCTTGTCTGAATAATGTTG 60.143 41.667 0.00 0.00 0.00 3.33
1755 3360 8.149647 TGTCTGAATAATGTTGAATTTGCCTTT 58.850 29.630 0.00 0.00 0.00 3.11
1757 3362 7.603404 TCTGAATAATGTTGAATTTGCCTTTGG 59.397 33.333 0.00 0.00 0.00 3.28
1758 3363 7.222872 TGAATAATGTTGAATTTGCCTTTGGT 58.777 30.769 0.00 0.00 0.00 3.67
1759 3364 7.718753 TGAATAATGTTGAATTTGCCTTTGGTT 59.281 29.630 0.00 0.00 0.00 3.67
1760 3365 5.754543 AATGTTGAATTTGCCTTTGGTTG 57.245 34.783 0.00 0.00 0.00 3.77
1761 3366 4.213564 TGTTGAATTTGCCTTTGGTTGT 57.786 36.364 0.00 0.00 0.00 3.32
1762 3367 3.937706 TGTTGAATTTGCCTTTGGTTGTG 59.062 39.130 0.00 0.00 0.00 3.33
1763 3368 4.187694 GTTGAATTTGCCTTTGGTTGTGA 58.812 39.130 0.00 0.00 0.00 3.58
1764 3369 4.478206 TGAATTTGCCTTTGGTTGTGAA 57.522 36.364 0.00 0.00 0.00 3.18
1765 3370 4.187694 TGAATTTGCCTTTGGTTGTGAAC 58.812 39.130 0.00 0.00 0.00 3.18
1797 3402 0.887933 AAATGATGCCCGCTTTCGTT 59.112 45.000 0.00 0.00 0.00 3.85
1818 3423 3.164026 CTGCTGCAATGAGCTGGTA 57.836 52.632 3.02 0.00 45.94 3.25
1819 3424 1.015109 CTGCTGCAATGAGCTGGTAG 58.985 55.000 3.02 0.00 45.94 3.18
1836 3441 2.493687 GGTAGCTAGGTGGGAGGATCAT 60.494 54.545 4.27 0.00 36.25 2.45
1842 3447 0.988145 GGTGGGAGGATCATGTGGGA 60.988 60.000 0.00 0.00 36.25 4.37
1863 3468 0.471617 CCGATGAGGCCAAGGAGATT 59.528 55.000 5.01 0.00 0.00 2.40
1995 3600 2.681848 CCAGAATGTGGTGAAGATGCTC 59.318 50.000 0.00 0.00 42.17 4.26
2037 3647 3.936372 TTCAAGTGAGTCTCCCGTTAG 57.064 47.619 0.00 0.00 0.00 2.34
2085 3701 1.472480 GCACATTACCCGCTTGTGATT 59.528 47.619 6.47 0.00 42.59 2.57
2087 3703 3.315191 GCACATTACCCGCTTGTGATTAT 59.685 43.478 6.47 0.00 42.59 1.28
2095 3711 3.129287 CCCGCTTGTGATTATTGCTCTTT 59.871 43.478 0.00 0.00 0.00 2.52
2096 3712 4.380867 CCCGCTTGTGATTATTGCTCTTTT 60.381 41.667 0.00 0.00 0.00 2.27
2131 3756 3.138884 TCTTACCAATGCAGCTCAACA 57.861 42.857 0.00 0.00 0.00 3.33
2198 3823 2.289945 GCATAATCGGCAAGAGGGAGAT 60.290 50.000 0.00 0.00 0.00 2.75
2833 4592 3.724494 GGATACTGCAGCGCTTCC 58.276 61.111 15.27 7.66 0.00 3.46
2944 4708 3.056107 ACTCTAGCCGCAACATGTCTTAA 60.056 43.478 0.00 0.00 0.00 1.85
2958 4728 9.844790 CAACATGTCTTAAAATAAATCTCAGCA 57.155 29.630 0.00 0.00 0.00 4.41
2980 4750 9.330063 CAGCATATTGTAAACCAAGAGAGATAA 57.670 33.333 0.00 0.00 36.25 1.75
2986 4756 9.829507 ATTGTAAACCAAGAGAGATAATGAGAG 57.170 33.333 0.00 0.00 36.25 3.20
2987 4757 7.268586 TGTAAACCAAGAGAGATAATGAGAGC 58.731 38.462 0.00 0.00 0.00 4.09
2988 4758 6.558488 AAACCAAGAGAGATAATGAGAGCT 57.442 37.500 0.00 0.00 0.00 4.09
2989 4759 7.667575 AAACCAAGAGAGATAATGAGAGCTA 57.332 36.000 0.00 0.00 0.00 3.32
2992 4762 6.838612 ACCAAGAGAGATAATGAGAGCTAGTT 59.161 38.462 0.00 0.00 0.00 2.24
2993 4763 8.001875 ACCAAGAGAGATAATGAGAGCTAGTTA 58.998 37.037 0.00 0.00 0.00 2.24
3025 4850 8.994429 TCAACATGTATTTGTTTGTTTTCTGT 57.006 26.923 0.00 0.00 37.73 3.41
3026 4851 8.867935 TCAACATGTATTTGTTTGTTTTCTGTG 58.132 29.630 0.00 0.00 37.73 3.66
3037 4862 6.990349 TGTTTGTTTTCTGTGGGTTTTGTTTA 59.010 30.769 0.00 0.00 0.00 2.01
3038 4863 7.497909 TGTTTGTTTTCTGTGGGTTTTGTTTAA 59.502 29.630 0.00 0.00 0.00 1.52
3039 4864 7.659652 TTGTTTTCTGTGGGTTTTGTTTAAG 57.340 32.000 0.00 0.00 0.00 1.85
3040 4865 6.994221 TGTTTTCTGTGGGTTTTGTTTAAGA 58.006 32.000 0.00 0.00 0.00 2.10
3060 4885 9.823647 TTTAAGAGATTGTTATCAGAGGTGATC 57.176 33.333 0.00 0.00 42.80 2.92
3096 4922 5.071788 TGTTTCATCCATCATACTACTCCCC 59.928 44.000 0.00 0.00 0.00 4.81
3098 4924 3.143933 TCATCCATCATACTACTCCCCCA 59.856 47.826 0.00 0.00 0.00 4.96
3101 4927 3.730594 TCCATCATACTACTCCCCCAGTA 59.269 47.826 0.00 0.00 36.43 2.74
3106 4932 5.977533 TCATACTACTCCCCCAGTATCATT 58.022 41.667 0.00 0.00 36.96 2.57
3108 4934 7.182760 TCATACTACTCCCCCAGTATCATTAG 58.817 42.308 0.00 0.00 36.96 1.73
3109 4935 5.420215 ACTACTCCCCCAGTATCATTAGT 57.580 43.478 0.00 0.00 36.96 2.24
3111 4937 6.210522 ACTACTCCCCCAGTATCATTAGTTT 58.789 40.000 0.00 0.00 36.96 2.66
3112 4938 6.677076 ACTACTCCCCCAGTATCATTAGTTTT 59.323 38.462 0.00 0.00 36.96 2.43
3113 4939 6.402981 ACTCCCCCAGTATCATTAGTTTTT 57.597 37.500 0.00 0.00 31.37 1.94
3167 5007 7.878621 TTAGGATATCATCAAGATCCTTGGT 57.121 36.000 7.90 0.00 45.94 3.67
3168 5008 8.972662 TTAGGATATCATCAAGATCCTTGGTA 57.027 34.615 7.90 0.00 45.94 3.25
3169 5009 9.566331 TTAGGATATCATCAAGATCCTTGGTAT 57.434 33.333 7.90 2.17 45.94 2.73
3170 5010 8.460317 AGGATATCATCAAGATCCTTGGTATT 57.540 34.615 4.83 0.00 45.94 1.89
3172 5012 9.829507 GGATATCATCAAGATCCTTGGTATTAG 57.170 37.037 4.83 0.00 38.19 1.73
3175 5015 7.083062 TCATCAAGATCCTTGGTATTAGCAT 57.917 36.000 6.83 0.00 0.00 3.79
3176 5016 6.938596 TCATCAAGATCCTTGGTATTAGCATG 59.061 38.462 6.83 0.00 0.00 4.06
3177 5017 6.499106 TCAAGATCCTTGGTATTAGCATGA 57.501 37.500 0.00 4.72 0.00 3.07
3178 5018 6.528321 TCAAGATCCTTGGTATTAGCATGAG 58.472 40.000 0.00 0.19 0.00 2.90
3179 5019 4.904241 AGATCCTTGGTATTAGCATGAGC 58.096 43.478 0.00 6.68 42.56 4.26
3180 5020 4.349048 AGATCCTTGGTATTAGCATGAGCA 59.651 41.667 0.00 0.00 45.49 4.26
3182 5022 4.645535 TCCTTGGTATTAGCATGAGCATC 58.354 43.478 0.00 0.00 45.49 3.91
3202 5128 8.325421 AGCATCTCAAGCTAAATATTCATCAG 57.675 34.615 0.00 0.00 41.32 2.90
3207 5133 7.649705 TCTCAAGCTAAATATTCATCAGTCGAC 59.350 37.037 7.70 7.70 0.00 4.20
3208 5134 6.701841 TCAAGCTAAATATTCATCAGTCGACC 59.298 38.462 13.01 0.00 0.00 4.79
3209 5135 5.542779 AGCTAAATATTCATCAGTCGACCC 58.457 41.667 13.01 0.00 0.00 4.46
3210 5136 5.070446 AGCTAAATATTCATCAGTCGACCCA 59.930 40.000 13.01 0.00 0.00 4.51
3211 5137 5.177696 GCTAAATATTCATCAGTCGACCCAC 59.822 44.000 13.01 0.00 0.00 4.61
3212 5138 4.753516 AATATTCATCAGTCGACCCACA 57.246 40.909 13.01 0.00 0.00 4.17
3213 5139 4.963318 ATATTCATCAGTCGACCCACAT 57.037 40.909 13.01 0.00 0.00 3.21
3214 5140 2.385013 TTCATCAGTCGACCCACATG 57.615 50.000 13.01 9.36 0.00 3.21
3215 5141 1.266178 TCATCAGTCGACCCACATGT 58.734 50.000 13.01 0.00 0.00 3.21
3216 5142 1.204704 TCATCAGTCGACCCACATGTC 59.795 52.381 13.01 0.00 0.00 3.06
3217 5143 0.537188 ATCAGTCGACCCACATGTCC 59.463 55.000 13.01 0.00 31.35 4.02
3218 5144 0.541998 TCAGTCGACCCACATGTCCT 60.542 55.000 13.01 0.00 31.35 3.85
3219 5145 0.390340 CAGTCGACCCACATGTCCTG 60.390 60.000 13.01 0.00 31.35 3.86
3220 5146 1.741770 GTCGACCCACATGTCCTGC 60.742 63.158 3.51 0.00 31.35 4.85
3262 6619 9.956720 AGATCTTTACAACTGAAAACATTCTTG 57.043 29.630 0.00 0.00 0.00 3.02
3263 6620 9.736023 GATCTTTACAACTGAAAACATTCTTGT 57.264 29.630 0.00 0.00 37.82 3.16
3264 6621 8.909708 TCTTTACAACTGAAAACATTCTTGTG 57.090 30.769 6.50 0.00 35.83 3.33
3265 6622 8.735315 TCTTTACAACTGAAAACATTCTTGTGA 58.265 29.630 6.50 0.00 35.83 3.58
3266 6623 9.352784 CTTTACAACTGAAAACATTCTTGTGAA 57.647 29.630 6.50 4.65 35.83 3.18
3267 6624 8.909708 TTACAACTGAAAACATTCTTGTGAAG 57.090 30.769 6.50 0.00 35.83 3.02
3324 6681 2.838736 GTGTGAGACACCAGTTCATGT 58.161 47.619 0.00 0.00 43.05 3.21
3325 6682 3.990092 GTGTGAGACACCAGTTCATGTA 58.010 45.455 0.00 0.00 43.05 2.29
3326 6683 3.741344 GTGTGAGACACCAGTTCATGTAC 59.259 47.826 0.00 0.00 43.05 2.90
3327 6684 2.987149 GTGAGACACCAGTTCATGTACG 59.013 50.000 0.00 0.00 0.00 3.67
3328 6685 2.888414 TGAGACACCAGTTCATGTACGA 59.112 45.455 0.00 0.00 0.00 3.43
3329 6686 3.057526 TGAGACACCAGTTCATGTACGAG 60.058 47.826 0.00 0.00 0.00 4.18
3330 6687 2.891580 AGACACCAGTTCATGTACGAGT 59.108 45.455 0.00 0.00 0.00 4.18
3382 6755 4.400844 GTCGGTGCGAACATCATCGAAC 62.401 54.545 0.00 0.00 46.80 3.95
3486 6859 5.163663 TGGTTCACACTGAAAACTTGTGATC 60.164 40.000 4.59 4.39 46.78 2.92
3527 6900 6.094742 TGCAATCGCCTTGACATTAATCTAAA 59.905 34.615 2.21 0.00 36.97 1.85
3553 6926 1.474077 CATGCCCTCAAGCCAAACTAC 59.526 52.381 0.00 0.00 0.00 2.73
3607 6980 4.544683 TCATACATTTCCCATGCATCCAA 58.455 39.130 0.00 0.00 0.00 3.53
3608 6981 4.341806 TCATACATTTCCCATGCATCCAAC 59.658 41.667 0.00 0.00 0.00 3.77
3609 6982 2.823959 ACATTTCCCATGCATCCAACT 58.176 42.857 0.00 0.00 0.00 3.16
3610 6983 3.979911 ACATTTCCCATGCATCCAACTA 58.020 40.909 0.00 0.00 0.00 2.24
3611 6984 3.956199 ACATTTCCCATGCATCCAACTAG 59.044 43.478 0.00 0.00 0.00 2.57
3612 6985 3.737559 TTTCCCATGCATCCAACTAGT 57.262 42.857 0.00 0.00 0.00 2.57
3613 6986 2.715749 TCCCATGCATCCAACTAGTG 57.284 50.000 0.00 0.00 0.00 2.74
3614 6987 1.027357 CCCATGCATCCAACTAGTGC 58.973 55.000 0.00 0.00 39.26 4.40
3615 6988 1.027357 CCATGCATCCAACTAGTGCC 58.973 55.000 0.00 0.00 38.06 5.01
3616 6989 1.409241 CCATGCATCCAACTAGTGCCT 60.409 52.381 0.00 0.00 38.06 4.75
3617 6990 1.674441 CATGCATCCAACTAGTGCCTG 59.326 52.381 0.00 0.00 38.06 4.85
3618 6991 0.677731 TGCATCCAACTAGTGCCTGC 60.678 55.000 0.00 4.65 38.06 4.85
3619 6992 1.379642 GCATCCAACTAGTGCCTGCC 61.380 60.000 0.00 0.00 32.88 4.85
3620 6993 0.254178 CATCCAACTAGTGCCTGCCT 59.746 55.000 0.00 0.00 0.00 4.75
3621 6994 0.995024 ATCCAACTAGTGCCTGCCTT 59.005 50.000 0.00 0.00 0.00 4.35
3622 6995 0.324943 TCCAACTAGTGCCTGCCTTC 59.675 55.000 0.00 0.00 0.00 3.46
3623 6996 0.036732 CCAACTAGTGCCTGCCTTCA 59.963 55.000 0.00 0.00 0.00 3.02
3624 6997 1.545428 CCAACTAGTGCCTGCCTTCAA 60.545 52.381 0.00 0.00 0.00 2.69
3638 7011 2.094338 GCCTTCAAGATTTCCAGCTTGG 60.094 50.000 0.00 0.00 41.31 3.61
3639 7012 3.424703 CCTTCAAGATTTCCAGCTTGGA 58.575 45.455 0.00 1.25 46.61 3.53
3653 7026 2.738480 TGGAGTTTCCACGGTCCG 59.262 61.111 10.48 10.48 42.67 4.79
3709 7082 6.142817 CACTAAACATCACAAAACTGGTAGC 58.857 40.000 0.00 0.00 0.00 3.58
3722 7095 0.338467 TGGTAGCCCAGCCTCTCTTA 59.662 55.000 0.00 0.00 35.17 2.10
3784 7161 3.405831 CTGCAGAATCAAGAGACACCAA 58.594 45.455 8.42 0.00 0.00 3.67
3798 7177 3.059166 GACACCAATGAACACAAATGCC 58.941 45.455 0.00 0.00 0.00 4.40
3810 7189 5.125100 ACACAAATGCCAGTGACAAATAG 57.875 39.130 0.00 0.00 39.03 1.73
3814 7193 5.126061 ACAAATGCCAGTGACAAATAGGATC 59.874 40.000 0.00 0.00 0.00 3.36
3851 7237 6.403866 AGGCATTTTGTTCAAGTATCAACA 57.596 33.333 0.00 0.00 0.00 3.33
3891 7301 6.128035 CCAGGTTTAACATCAATCACGATTCA 60.128 38.462 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.930908 GAATGGCCAGTGCTGCTCAC 61.931 60.000 12.17 0.00 45.98 3.51
3 4 1.676635 GAATGGCCAGTGCTGCTCA 60.677 57.895 12.17 0.00 37.74 4.26
4 5 2.413142 GGAATGGCCAGTGCTGCTC 61.413 63.158 18.18 0.00 37.74 4.26
5 6 2.362120 GGAATGGCCAGTGCTGCT 60.362 61.111 18.18 0.00 37.74 4.24
6 7 3.455469 GGGAATGGCCAGTGCTGC 61.455 66.667 24.15 4.86 38.95 5.25
7 8 2.050350 CAGGGAATGGCCAGTGCTG 61.050 63.158 24.15 15.71 38.95 4.41
8 9 1.792757 TTCAGGGAATGGCCAGTGCT 61.793 55.000 24.15 7.71 38.95 4.40
9 10 1.304381 TTCAGGGAATGGCCAGTGC 60.304 57.895 17.19 17.19 38.95 4.40
12 13 0.682209 CAGGTTCAGGGAATGGCCAG 60.682 60.000 13.05 0.00 38.95 4.85
13 14 1.139498 TCAGGTTCAGGGAATGGCCA 61.139 55.000 8.56 8.56 38.95 5.36
15 16 1.341383 ACATCAGGTTCAGGGAATGGC 60.341 52.381 0.00 0.00 0.00 4.40
16 17 2.372264 CACATCAGGTTCAGGGAATGG 58.628 52.381 0.00 0.00 0.00 3.16
17 18 2.025981 TCCACATCAGGTTCAGGGAATG 60.026 50.000 0.00 0.00 0.00 2.67
18 19 2.278245 TCCACATCAGGTTCAGGGAAT 58.722 47.619 0.00 0.00 0.00 3.01
19 20 1.741028 TCCACATCAGGTTCAGGGAA 58.259 50.000 0.00 0.00 0.00 3.97
21 22 2.020694 GCATCCACATCAGGTTCAGGG 61.021 57.143 0.00 0.00 0.00 4.45
22 23 1.386533 GCATCCACATCAGGTTCAGG 58.613 55.000 0.00 0.00 0.00 3.86
23 24 1.064906 AGGCATCCACATCAGGTTCAG 60.065 52.381 0.00 0.00 0.00 3.02
24 25 0.994247 AGGCATCCACATCAGGTTCA 59.006 50.000 0.00 0.00 0.00 3.18
25 26 1.386533 CAGGCATCCACATCAGGTTC 58.613 55.000 0.00 0.00 0.00 3.62
26 27 0.682209 GCAGGCATCCACATCAGGTT 60.682 55.000 0.00 0.00 0.00 3.50
27 28 1.077212 GCAGGCATCCACATCAGGT 60.077 57.895 0.00 0.00 0.00 4.00
28 29 1.077285 TGCAGGCATCCACATCAGG 60.077 57.895 0.00 0.00 0.00 3.86
29 30 1.101635 CCTGCAGGCATCCACATCAG 61.102 60.000 22.33 0.00 0.00 2.90
30 31 1.077285 CCTGCAGGCATCCACATCA 60.077 57.895 22.33 0.00 0.00 3.07
31 32 3.837578 CCTGCAGGCATCCACATC 58.162 61.111 22.33 0.00 0.00 3.06
41 42 0.108186 TATGTCTTCACGCCTGCAGG 60.108 55.000 29.34 29.34 38.53 4.85
42 43 1.002366 GTATGTCTTCACGCCTGCAG 58.998 55.000 6.78 6.78 0.00 4.41
43 44 0.320050 TGTATGTCTTCACGCCTGCA 59.680 50.000 0.00 0.00 0.00 4.41
44 45 1.394917 CTTGTATGTCTTCACGCCTGC 59.605 52.381 0.00 0.00 0.00 4.85
45 46 1.394917 GCTTGTATGTCTTCACGCCTG 59.605 52.381 0.00 0.00 0.00 4.85
46 47 1.276421 AGCTTGTATGTCTTCACGCCT 59.724 47.619 0.00 0.00 30.84 5.52
47 48 1.726853 AGCTTGTATGTCTTCACGCC 58.273 50.000 0.00 0.00 30.84 5.68
48 49 3.250744 TGTAGCTTGTATGTCTTCACGC 58.749 45.455 0.00 0.00 0.00 5.34
49 50 5.275927 CGATTGTAGCTTGTATGTCTTCACG 60.276 44.000 0.00 0.00 0.00 4.35
51 52 5.961272 TCGATTGTAGCTTGTATGTCTTCA 58.039 37.500 0.00 0.00 0.00 3.02
54 55 4.202161 CCCTCGATTGTAGCTTGTATGTCT 60.202 45.833 0.00 0.00 0.00 3.41
56 57 3.181465 CCCCTCGATTGTAGCTTGTATGT 60.181 47.826 0.00 0.00 0.00 2.29
57 58 3.181465 ACCCCTCGATTGTAGCTTGTATG 60.181 47.826 0.00 0.00 0.00 2.39
67 68 1.677552 GTGGACACCCCTCGATTGT 59.322 57.895 0.00 0.00 35.38 2.71
112 113 1.152963 AAACGGCAACTGGAGCACT 60.153 52.632 0.00 0.00 0.00 4.40
174 175 2.449518 TGCCTTGTGACCCTCCCA 60.450 61.111 0.00 0.00 0.00 4.37
186 187 5.879223 CAGTTGAATATCAGAAGTCTGCCTT 59.121 40.000 3.30 0.00 43.46 4.35
250 251 2.203337 CATACCACCCATGCCCGG 60.203 66.667 0.00 0.00 0.00 5.73
261 262 2.187958 CAGGAAGAGGACACCATACCA 58.812 52.381 0.00 0.00 0.00 3.25
273 274 4.187694 GTCCTTGATTGTAGCAGGAAGAG 58.812 47.826 0.00 0.00 0.00 2.85
406 407 1.255667 ACGTGGGGGTAGTAGCTGTG 61.256 60.000 0.00 0.00 0.00 3.66
409 410 1.751927 CGACGTGGGGGTAGTAGCT 60.752 63.158 0.00 0.00 0.00 3.32
410 411 1.598701 AACGACGTGGGGGTAGTAGC 61.599 60.000 0.00 0.00 0.00 3.58
448 449 3.452990 GAGGAGGAAGAAAGGTAAGAGGG 59.547 52.174 0.00 0.00 0.00 4.30
449 450 3.131400 CGAGGAGGAAGAAAGGTAAGAGG 59.869 52.174 0.00 0.00 0.00 3.69
452 453 2.418884 GCCGAGGAGGAAGAAAGGTAAG 60.419 54.545 0.00 0.00 45.00 2.34
470 700 3.106552 CACTCTCGAGAGGAGCCG 58.893 66.667 38.23 20.92 46.13 5.52
505 735 2.386661 AGCAGGTTACAGTTCATCGG 57.613 50.000 0.00 0.00 0.00 4.18
539 769 1.822990 GGACACAGGGTTCGATCTACA 59.177 52.381 0.00 0.00 0.00 2.74
580 810 3.587923 CAATTGTGTAATGGTTGGCTGG 58.412 45.455 0.00 0.00 0.00 4.85
661 891 0.325296 TTACCATCCTCCGCAGTCCT 60.325 55.000 0.00 0.00 0.00 3.85
662 892 0.759346 ATTACCATCCTCCGCAGTCC 59.241 55.000 0.00 0.00 0.00 3.85
663 893 2.622064 AATTACCATCCTCCGCAGTC 57.378 50.000 0.00 0.00 0.00 3.51
664 894 2.368875 CCTAATTACCATCCTCCGCAGT 59.631 50.000 0.00 0.00 0.00 4.40
667 897 2.289506 GGTCCTAATTACCATCCTCCGC 60.290 54.545 0.00 0.00 36.96 5.54
668 898 3.240302 AGGTCCTAATTACCATCCTCCG 58.760 50.000 0.00 0.00 39.64 4.63
670 900 4.494591 AGGAGGTCCTAATTACCATCCTC 58.505 47.826 0.00 9.90 46.48 3.71
694 924 5.652014 TGAATGGAGGCAGTTATTTACCTTG 59.348 40.000 0.00 0.00 30.95 3.61
711 941 2.294233 GAGTTTTGCAGCACTGAATGGA 59.706 45.455 0.00 0.00 0.00 3.41
713 943 3.637998 AGAGTTTTGCAGCACTGAATG 57.362 42.857 0.00 0.00 0.00 2.67
715 945 3.016031 TGAAGAGTTTTGCAGCACTGAA 58.984 40.909 0.00 0.00 0.00 3.02
716 946 2.642427 TGAAGAGTTTTGCAGCACTGA 58.358 42.857 0.00 0.00 0.00 3.41
717 947 3.637998 ATGAAGAGTTTTGCAGCACTG 57.362 42.857 0.00 0.00 0.00 3.66
718 948 3.887716 AGAATGAAGAGTTTTGCAGCACT 59.112 39.130 0.00 0.00 0.00 4.40
719 949 3.979495 CAGAATGAAGAGTTTTGCAGCAC 59.021 43.478 0.00 0.00 39.69 4.40
720 950 3.633525 ACAGAATGAAGAGTTTTGCAGCA 59.366 39.130 0.00 0.00 39.69 4.41
778 1008 2.542205 GCCATCAGTGCGTACGTATGTA 60.542 50.000 17.90 9.07 0.00 2.29
780 1010 0.852777 GCCATCAGTGCGTACGTATG 59.147 55.000 17.90 10.54 0.00 2.39
880 1110 9.057911 AGGGAAGCCACTTATATATAATAAGCA 57.942 33.333 16.69 0.00 35.57 3.91
951 2538 0.033781 CAGTTTGGTGTTGGGCATGG 59.966 55.000 0.00 0.00 0.00 3.66
1239 2827 2.541437 CGCGCTGTGATATCGTGC 59.459 61.111 5.56 1.65 0.00 5.34
1343 2941 5.804639 TCACAGCCATGTTCACTAATAACT 58.195 37.500 0.00 0.00 37.65 2.24
1388 2986 7.948278 TTTAGCTTTCTAGAGTTTCAGACAC 57.052 36.000 0.00 0.00 0.00 3.67
1415 3013 1.134280 CACGGAGATCTTCCCTGCAAT 60.134 52.381 0.00 0.00 43.63 3.56
1453 3051 1.810030 GTTCACGATCACCCTCGGC 60.810 63.158 0.00 0.00 42.88 5.54
1477 3075 2.463752 AGTATCTCCCGCACCAGTTTA 58.536 47.619 0.00 0.00 0.00 2.01
1498 3096 3.884774 TGCCCGGACTTGTTGGCT 61.885 61.111 0.73 0.00 44.32 4.75
1633 3231 1.229428 CGCTTGCCTTGAGTTTCTCA 58.771 50.000 0.00 0.00 38.87 3.27
1667 3265 0.313547 GAAGAAGAAACGATCGCGCG 60.314 55.000 26.76 26.76 42.48 6.86
1669 3267 2.661675 TGAAGAAGAAGAAACGATCGCG 59.338 45.455 16.60 0.00 44.79 5.87
1672 3270 6.587990 TCTGACATGAAGAAGAAGAAACGATC 59.412 38.462 0.00 0.00 0.00 3.69
1675 3273 6.018751 TGTTCTGACATGAAGAAGAAGAAACG 60.019 38.462 13.53 0.00 34.40 3.60
1738 3343 5.066246 CACAACCAAAGGCAAATTCAACATT 59.934 36.000 0.00 0.00 0.00 2.71
1744 3349 4.441792 AGTTCACAACCAAAGGCAAATTC 58.558 39.130 0.00 0.00 0.00 2.17
1755 3360 2.358582 CTGCATCACAAGTTCACAACCA 59.641 45.455 0.00 0.00 0.00 3.67
1757 3362 3.969117 TCTGCATCACAAGTTCACAAC 57.031 42.857 0.00 0.00 0.00 3.32
1758 3363 4.979943 TTTCTGCATCACAAGTTCACAA 57.020 36.364 0.00 0.00 0.00 3.33
1759 3364 4.979943 TTTTCTGCATCACAAGTTCACA 57.020 36.364 0.00 0.00 0.00 3.58
1760 3365 5.522456 TCATTTTCTGCATCACAAGTTCAC 58.478 37.500 0.00 0.00 0.00 3.18
1761 3366 5.771153 TCATTTTCTGCATCACAAGTTCA 57.229 34.783 0.00 0.00 0.00 3.18
1762 3367 5.061808 GCATCATTTTCTGCATCACAAGTTC 59.938 40.000 0.00 0.00 38.28 3.01
1763 3368 4.927425 GCATCATTTTCTGCATCACAAGTT 59.073 37.500 0.00 0.00 38.28 2.66
1764 3369 4.491676 GCATCATTTTCTGCATCACAAGT 58.508 39.130 0.00 0.00 38.28 3.16
1765 3370 3.863424 GGCATCATTTTCTGCATCACAAG 59.137 43.478 0.00 0.00 40.18 3.16
1818 3423 1.061812 ACATGATCCTCCCACCTAGCT 60.062 52.381 0.00 0.00 0.00 3.32
1819 3424 1.071385 CACATGATCCTCCCACCTAGC 59.929 57.143 0.00 0.00 0.00 3.42
1836 3441 2.443394 GGCCTCATCGGATCCCACA 61.443 63.158 6.06 0.00 33.16 4.17
1842 3447 0.399091 TCTCCTTGGCCTCATCGGAT 60.399 55.000 3.32 0.00 33.16 4.18
1848 3453 0.250234 CGTCAATCTCCTTGGCCTCA 59.750 55.000 3.32 0.00 36.01 3.86
1863 3468 3.509137 GAACTCCGGCCACACGTCA 62.509 63.158 2.24 0.00 0.00 4.35
1995 3600 1.768870 CCTGGGAGGTATAGGGTGTTG 59.231 57.143 0.00 0.00 0.00 3.33
2037 3647 2.752903 GACCAGAGAGAGACCAAGAGTC 59.247 54.545 0.00 0.00 46.71 3.36
2053 3665 3.305335 GGGTAATGTGCAAAAGTGACCAG 60.305 47.826 0.00 0.00 0.00 4.00
2100 3716 5.245531 TGCATTGGTAAGAACCTACTCAAG 58.754 41.667 0.00 0.00 46.91 3.02
2103 3719 3.623510 GCTGCATTGGTAAGAACCTACTC 59.376 47.826 0.00 0.00 46.91 2.59
2104 3720 3.264450 AGCTGCATTGGTAAGAACCTACT 59.736 43.478 1.02 0.00 46.91 2.57
2115 3740 1.242076 GTCTGTTGAGCTGCATTGGT 58.758 50.000 1.02 0.00 0.00 3.67
2118 3743 0.957395 CCCGTCTGTTGAGCTGCATT 60.957 55.000 1.02 0.00 0.00 3.56
2131 3756 2.342648 GTTCGCCTTCACCCGTCT 59.657 61.111 0.00 0.00 0.00 4.18
2198 3823 1.605992 CTGCCTTCTCTCATGGCCA 59.394 57.895 8.56 8.56 43.53 5.36
2216 3841 4.166011 GGTCATCGTTGCTGGCGC 62.166 66.667 0.00 0.00 0.00 6.53
2287 3927 0.632835 ATGGTCATGATGGGCTTGGT 59.367 50.000 0.00 0.00 0.00 3.67
2604 4360 2.107953 GGCAGCGAGAGGATCACC 59.892 66.667 0.00 0.00 37.82 4.02
2868 4627 1.995626 CAGGGTGGAGACCGGGAAT 60.996 63.158 6.32 0.00 44.23 3.01
2961 4731 7.766278 GCTCTCATTATCTCTCTTGGTTTACAA 59.234 37.037 0.00 0.00 37.55 2.41
2982 4752 9.757227 ACATGTTGAGATTTATAACTAGCTCTC 57.243 33.333 0.00 0.00 0.00 3.20
2998 4768 9.299963 CAGAAAACAAACAAATACATGTTGAGA 57.700 29.630 2.30 0.00 42.49 3.27
2999 4769 9.086336 ACAGAAAACAAACAAATACATGTTGAG 57.914 29.630 2.30 0.00 42.49 3.02
3000 4770 8.867935 CACAGAAAACAAACAAATACATGTTGA 58.132 29.630 2.30 0.00 42.49 3.18
3001 4771 8.115520 CCACAGAAAACAAACAAATACATGTTG 58.884 33.333 2.30 0.00 42.49 3.33
3004 4774 6.760770 ACCCACAGAAAACAAACAAATACATG 59.239 34.615 0.00 0.00 0.00 3.21
3006 4776 6.287589 ACCCACAGAAAACAAACAAATACA 57.712 33.333 0.00 0.00 0.00 2.29
3025 4850 9.137459 TGATAACAATCTCTTAAACAAAACCCA 57.863 29.630 0.00 0.00 0.00 4.51
3026 4851 9.626045 CTGATAACAATCTCTTAAACAAAACCC 57.374 33.333 0.00 0.00 0.00 4.11
3037 4862 6.614906 AGGATCACCTCTGATAACAATCTCTT 59.385 38.462 0.00 0.00 44.13 2.85
3038 4863 6.142498 AGGATCACCTCTGATAACAATCTCT 58.858 40.000 0.00 0.00 44.13 3.10
3039 4864 6.418057 AGGATCACCTCTGATAACAATCTC 57.582 41.667 0.00 0.00 44.13 2.75
3060 4885 8.229253 TGATGGATGAAACAATCTATTTGAGG 57.771 34.615 0.00 0.00 38.76 3.86
3074 4899 4.597507 GGGGGAGTAGTATGATGGATGAAA 59.402 45.833 0.00 0.00 0.00 2.69
3111 4937 7.941238 ACTACTACTCACTCCACTAGTACAAAA 59.059 37.037 0.00 0.00 35.76 2.44
3112 4938 7.456725 ACTACTACTCACTCCACTAGTACAAA 58.543 38.462 0.00 0.00 35.76 2.83
3113 4939 7.013823 ACTACTACTCACTCCACTAGTACAA 57.986 40.000 0.00 0.00 35.76 2.41
3114 4940 6.617782 ACTACTACTCACTCCACTAGTACA 57.382 41.667 0.00 0.00 35.76 2.90
3154 4994 6.499106 TCATGCTAATACCAAGGATCTTGA 57.501 37.500 9.01 0.00 0.00 3.02
3155 4995 5.180868 GCTCATGCTAATACCAAGGATCTTG 59.819 44.000 0.00 1.00 36.03 3.02
3157 4997 4.349048 TGCTCATGCTAATACCAAGGATCT 59.651 41.667 0.00 0.00 40.48 2.75
3158 4998 4.645535 TGCTCATGCTAATACCAAGGATC 58.354 43.478 0.00 0.00 40.48 3.36
3159 4999 4.712051 TGCTCATGCTAATACCAAGGAT 57.288 40.909 0.00 0.00 40.48 3.24
3161 5001 4.649692 AGATGCTCATGCTAATACCAAGG 58.350 43.478 0.00 0.00 40.48 3.61
3162 5002 5.303165 TGAGATGCTCATGCTAATACCAAG 58.697 41.667 0.00 0.00 35.39 3.61
3163 5003 5.294734 TGAGATGCTCATGCTAATACCAA 57.705 39.130 0.00 0.00 35.39 3.67
3165 5005 5.859521 CTTGAGATGCTCATGCTAATACC 57.140 43.478 0.00 0.00 40.39 2.73
3175 5015 7.935210 TGATGAATATTTAGCTTGAGATGCTCA 59.065 33.333 0.00 0.00 41.46 4.26
3176 5016 8.320396 TGATGAATATTTAGCTTGAGATGCTC 57.680 34.615 0.00 0.00 41.46 4.26
3177 5017 7.937942 ACTGATGAATATTTAGCTTGAGATGCT 59.062 33.333 0.00 0.00 43.79 3.79
3178 5018 8.097078 ACTGATGAATATTTAGCTTGAGATGC 57.903 34.615 0.00 0.00 0.00 3.91
3179 5019 8.433893 CGACTGATGAATATTTAGCTTGAGATG 58.566 37.037 0.00 0.00 0.00 2.90
3180 5020 8.363390 TCGACTGATGAATATTTAGCTTGAGAT 58.637 33.333 0.00 0.00 0.00 2.75
3182 5022 7.095857 GGTCGACTGATGAATATTTAGCTTGAG 60.096 40.741 16.46 0.00 0.00 3.02
3202 5128 1.741770 GCAGGACATGTGGGTCGAC 60.742 63.158 1.15 7.13 38.70 4.20
3207 5133 2.728460 TTTGGGGCAGGACATGTGGG 62.728 60.000 1.15 0.00 0.00 4.61
3208 5134 1.228831 TTTGGGGCAGGACATGTGG 60.229 57.895 1.15 0.00 0.00 4.17
3209 5135 1.252904 CCTTTGGGGCAGGACATGTG 61.253 60.000 1.15 0.00 32.41 3.21
3210 5136 1.077265 CCTTTGGGGCAGGACATGT 59.923 57.895 0.00 0.00 32.41 3.21
3211 5137 0.251742 TTCCTTTGGGGCAGGACATG 60.252 55.000 0.00 0.00 40.37 3.21
3212 5138 0.251787 GTTCCTTTGGGGCAGGACAT 60.252 55.000 0.00 0.00 40.37 3.06
3213 5139 1.152830 GTTCCTTTGGGGCAGGACA 59.847 57.895 0.00 0.00 40.37 4.02
3214 5140 0.895559 CTGTTCCTTTGGGGCAGGAC 60.896 60.000 0.00 0.00 40.37 3.85
3215 5141 1.065410 TCTGTTCCTTTGGGGCAGGA 61.065 55.000 0.00 0.00 38.79 3.86
3216 5142 0.178964 TTCTGTTCCTTTGGGGCAGG 60.179 55.000 0.00 0.00 36.98 4.85
3217 5143 1.615392 CTTTCTGTTCCTTTGGGGCAG 59.385 52.381 0.00 0.00 37.36 4.85
3218 5144 1.216678 TCTTTCTGTTCCTTTGGGGCA 59.783 47.619 0.00 0.00 34.39 5.36
3219 5145 1.995376 TCTTTCTGTTCCTTTGGGGC 58.005 50.000 0.00 0.00 34.39 5.80
3220 5146 4.039603 AGATCTTTCTGTTCCTTTGGGG 57.960 45.455 0.00 0.00 0.00 4.96
3259 6616 4.758674 ACCTGATCATCACAACTTCACAAG 59.241 41.667 0.00 0.00 0.00 3.16
3260 6617 4.717877 ACCTGATCATCACAACTTCACAA 58.282 39.130 0.00 0.00 0.00 3.33
3261 6618 4.318332 GACCTGATCATCACAACTTCACA 58.682 43.478 0.00 0.00 0.00 3.58
3262 6619 3.369147 CGACCTGATCATCACAACTTCAC 59.631 47.826 0.00 0.00 0.00 3.18
3263 6620 3.258123 TCGACCTGATCATCACAACTTCA 59.742 43.478 0.00 0.00 0.00 3.02
3264 6621 3.614616 GTCGACCTGATCATCACAACTTC 59.385 47.826 3.51 0.00 0.00 3.01
3265 6622 3.006859 TGTCGACCTGATCATCACAACTT 59.993 43.478 14.12 0.00 0.00 2.66
3266 6623 2.562738 TGTCGACCTGATCATCACAACT 59.437 45.455 14.12 0.00 0.00 3.16
3267 6624 2.959516 TGTCGACCTGATCATCACAAC 58.040 47.619 14.12 0.00 0.00 3.32
3486 6859 1.934589 TGCAAGATCCGGTTGTATCG 58.065 50.000 0.00 0.00 0.00 2.92
3527 6900 1.001641 GCTTGAGGGCATGGACTGT 60.002 57.895 0.00 0.00 0.00 3.55
3553 6926 7.487484 AGCTAGTCATGGATTATACATCATCG 58.513 38.462 0.00 0.00 0.00 3.84
3607 6980 1.352083 TCTTGAAGGCAGGCACTAGT 58.648 50.000 0.00 0.00 36.02 2.57
3608 6981 2.706339 ATCTTGAAGGCAGGCACTAG 57.294 50.000 0.00 0.00 36.02 2.57
3609 6982 3.347216 GAAATCTTGAAGGCAGGCACTA 58.653 45.455 0.00 0.00 36.02 2.74
3610 6983 2.165998 GAAATCTTGAAGGCAGGCACT 58.834 47.619 0.00 0.00 43.88 4.40
3611 6984 1.203287 GGAAATCTTGAAGGCAGGCAC 59.797 52.381 0.00 0.00 0.00 5.01
3612 6985 1.203038 TGGAAATCTTGAAGGCAGGCA 60.203 47.619 0.00 0.00 0.00 4.75
3613 6986 1.475682 CTGGAAATCTTGAAGGCAGGC 59.524 52.381 0.00 0.00 0.00 4.85
3614 6987 1.475682 GCTGGAAATCTTGAAGGCAGG 59.524 52.381 0.00 0.00 0.00 4.85
3615 6988 2.444421 AGCTGGAAATCTTGAAGGCAG 58.556 47.619 0.00 0.00 0.00 4.85
3616 6989 2.559668 CAAGCTGGAAATCTTGAAGGCA 59.440 45.455 0.00 0.00 41.50 4.75
3617 6990 2.094338 CCAAGCTGGAAATCTTGAAGGC 60.094 50.000 0.00 0.00 40.96 4.35
3618 6991 3.424703 TCCAAGCTGGAAATCTTGAAGG 58.575 45.455 2.78 0.00 45.00 3.46
3638 7011 1.203052 TGATACGGACCGTGGAAACTC 59.797 52.381 29.55 15.06 41.39 3.01
3639 7012 1.067354 GTGATACGGACCGTGGAAACT 60.067 52.381 29.55 6.76 41.39 2.66
3646 7019 1.747355 CTTACTGGTGATACGGACCGT 59.253 52.381 25.14 25.14 44.35 4.83
3653 7026 1.538419 GCGGGCTCTTACTGGTGATAC 60.538 57.143 0.00 0.00 0.00 2.24
3709 7082 6.325286 AGTTAAACTATCTAAGAGAGGCTGGG 59.675 42.308 0.00 0.00 0.00 4.45
3784 7161 2.957680 TGTCACTGGCATTTGTGTTCAT 59.042 40.909 5.42 0.00 35.82 2.57
3828 7213 6.183360 TGTGTTGATACTTGAACAAAATGCCT 60.183 34.615 0.00 0.00 33.96 4.75
3851 7237 3.795688 ACCTGGTTTCATGAGTCATGT 57.204 42.857 28.03 7.75 41.98 3.21


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

AutoCloner maintained by Alex Coulton.