Multiple sequence alignment - TraesCS6B01G064500

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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 TraesCS6B01G064500 chr6B 100.000 6333 0 0 1 6333 42745498 42751830 0.000000e+00 11695.0
1 TraesCS6B01G064500 chr6B 90.504 1906 115 22 1 1846 42772677 42774576 0.000000e+00 2457.0
2 TraesCS6B01G064500 chr6B 88.061 980 106 11 1843 2817 42774656 42775629 0.000000e+00 1151.0
3 TraesCS6B01G064500 chr6B 94.474 742 34 5 4739 5476 42778178 42778916 0.000000e+00 1136.0
4 TraesCS6B01G064500 chr6B 87.304 827 69 18 3153 3952 42776757 42777574 0.000000e+00 913.0
5 TraesCS6B01G064500 chr6B 84.570 337 30 2 3995 4310 42777557 42777892 1.330000e-81 315.0
6 TraesCS6B01G064500 chr6B 83.750 80 13 0 5017 5096 43353933 43354012 6.810000e-10 76.8
7 TraesCS6B01G064500 chrUn 87.337 2614 212 64 1 2553 93796371 93798926 0.000000e+00 2883.0
8 TraesCS6B01G064500 chrUn 93.582 1262 48 10 2555 3792 93798954 93800206 0.000000e+00 1851.0
9 TraesCS6B01G064500 chrUn 89.938 964 68 18 4532 5476 93800951 93801904 0.000000e+00 1216.0
10 TraesCS6B01G064500 chrUn 89.877 405 26 7 4076 4479 93800553 93800943 2.040000e-139 507.0
11 TraesCS6B01G064500 chrUn 93.143 175 12 0 3778 3952 93800289 93800463 2.270000e-64 257.0
12 TraesCS6B01G064500 chr6A 87.570 2325 206 41 17 2286 24325934 24328230 0.000000e+00 2615.0
13 TraesCS6B01G064500 chr6A 93.194 764 41 4 3035 3792 24328913 24329671 0.000000e+00 1112.0
14 TraesCS6B01G064500 chr6A 89.147 903 64 21 4595 5476 24331141 24332030 0.000000e+00 1094.0
15 TraesCS6B01G064500 chr6A 91.971 685 48 5 2325 3008 24328236 24328914 0.000000e+00 953.0
16 TraesCS6B01G064500 chr6A 89.630 405 28 6 4076 4479 24330014 24330405 2.640000e-138 503.0
17 TraesCS6B01G064500 chr6A 92.000 175 14 0 3778 3952 24329755 24329929 4.900000e-61 246.0
18 TraesCS6B01G064500 chr3B 85.283 795 103 7 5473 6261 333659701 333658915 0.000000e+00 808.0
19 TraesCS6B01G064500 chr3B 77.483 755 119 29 3128 3865 782637667 782638387 7.650000e-109 405.0
20 TraesCS6B01G064500 chr3B 77.273 440 74 24 4665 5101 782638991 782639407 1.060000e-57 235.0
21 TraesCS6B01G064500 chr3B 88.889 189 21 0 2325 2513 782636941 782637129 3.820000e-57 233.0
22 TraesCS6B01G064500 chr3B 85.321 218 31 1 5475 5691 703431910 703431693 2.300000e-54 224.0
23 TraesCS6B01G064500 chr2D 82.097 782 126 9 5554 6326 472484565 472483789 0.000000e+00 656.0
24 TraesCS6B01G064500 chr2D 80.100 804 142 14 5472 6266 281758854 281758060 3.290000e-162 582.0
25 TraesCS6B01G064500 chr4A 81.186 776 129 10 5572 6332 575773188 575773961 5.430000e-170 608.0
26 TraesCS6B01G064500 chr4A 97.959 49 1 0 3950 3998 740880626 740880674 1.130000e-12 86.1
27 TraesCS6B01G064500 chr1B 80.843 783 135 12 5475 6246 4293985 4294763 9.080000e-168 601.0
28 TraesCS6B01G064500 chr1B 92.982 57 3 1 3941 3997 22906914 22906969 1.460000e-11 82.4
29 TraesCS6B01G064500 chr2A 80.449 757 117 14 5473 6219 698073802 698073067 3.340000e-152 549.0
30 TraesCS6B01G064500 chr3A 78.835 841 150 17 5507 6332 608911213 608912040 5.580000e-150 542.0
31 TraesCS6B01G064500 chr3A 78.261 874 164 19 5475 6333 520794408 520795270 7.220000e-149 538.0
32 TraesCS6B01G064500 chr1A 79.420 758 132 20 5475 6219 335915776 335916522 1.220000e-141 514.0
33 TraesCS6B01G064500 chr3D 77.254 976 154 40 2922 3865 585927213 585928152 1.570000e-140 510.0
34 TraesCS6B01G064500 chr3D 83.824 272 28 4 2242 2513 585926519 585926774 1.760000e-60 244.0
35 TraesCS6B01G064500 chr3D 94.340 53 3 0 3945 3997 537032808 537032860 1.460000e-11 82.4
36 TraesCS6B01G064500 chr3D 92.857 56 3 1 3951 4005 40917129 40917074 5.260000e-11 80.5
37 TraesCS6B01G064500 chr6D 100.000 49 0 0 3951 3999 460808283 460808331 2.430000e-14 91.6
38 TraesCS6B01G064500 chr7A 97.959 49 1 0 3953 4001 174213598 174213646 1.130000e-12 86.1
39 TraesCS6B01G064500 chr2B 91.525 59 1 3 3944 3999 761895218 761895275 1.890000e-10 78.7
40 TraesCS6B01G064500 chr1D 89.831 59 4 2 3952 4009 470928452 470928395 2.450000e-09 75.0
41 TraesCS6B01G064500 chr5D 89.655 58 4 2 3954 4011 436771419 436771364 8.810000e-09 73.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G064500 chr6B 42745498 42751830 6332 False 11695.000000 11695 100.000000 1 6333 1 chr6B.!!$F1 6332
1 TraesCS6B01G064500 chr6B 42772677 42778916 6239 False 1194.400000 2457 88.982600 1 5476 5 chr6B.!!$F3 5475
2 TraesCS6B01G064500 chrUn 93796371 93801904 5533 False 1342.800000 2883 90.775400 1 5476 5 chrUn.!!$F1 5475
3 TraesCS6B01G064500 chr6A 24325934 24332030 6096 False 1087.166667 2615 90.585333 17 5476 6 chr6A.!!$F1 5459
4 TraesCS6B01G064500 chr3B 333658915 333659701 786 True 808.000000 808 85.283000 5473 6261 1 chr3B.!!$R1 788
5 TraesCS6B01G064500 chr3B 782636941 782639407 2466 False 291.000000 405 81.215000 2325 5101 3 chr3B.!!$F1 2776
6 TraesCS6B01G064500 chr2D 472483789 472484565 776 True 656.000000 656 82.097000 5554 6326 1 chr2D.!!$R2 772
7 TraesCS6B01G064500 chr2D 281758060 281758854 794 True 582.000000 582 80.100000 5472 6266 1 chr2D.!!$R1 794
8 TraesCS6B01G064500 chr4A 575773188 575773961 773 False 608.000000 608 81.186000 5572 6332 1 chr4A.!!$F1 760
9 TraesCS6B01G064500 chr1B 4293985 4294763 778 False 601.000000 601 80.843000 5475 6246 1 chr1B.!!$F1 771
10 TraesCS6B01G064500 chr2A 698073067 698073802 735 True 549.000000 549 80.449000 5473 6219 1 chr2A.!!$R1 746
11 TraesCS6B01G064500 chr3A 608911213 608912040 827 False 542.000000 542 78.835000 5507 6332 1 chr3A.!!$F2 825
12 TraesCS6B01G064500 chr3A 520794408 520795270 862 False 538.000000 538 78.261000 5475 6333 1 chr3A.!!$F1 858
13 TraesCS6B01G064500 chr1A 335915776 335916522 746 False 514.000000 514 79.420000 5475 6219 1 chr1A.!!$F1 744
14 TraesCS6B01G064500 chr3D 585926519 585928152 1633 False 377.000000 510 80.539000 2242 3865 2 chr3D.!!$F2 1623

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
469 471 0.738975 CTGACGGCTAGGATTCGACA 59.261 55.000 0.0 0.0 0.00 4.35 F
1817 1899 0.391228 TACTGTTTGCGAGCCTCACA 59.609 50.000 0.0 0.0 0.00 3.58 F
1822 1904 0.966179 TTTGCGAGCCTCACAGACTA 59.034 50.000 0.0 0.0 0.00 2.59 F
2060 2235 1.354031 TGCTCTGCAAAATACTGGGGA 59.646 47.619 0.0 0.0 34.76 4.81 F
3885 5292 1.246649 TGCCAGCGACATTGTGAATT 58.753 45.000 0.0 0.0 0.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2245 2438 0.383949 AAGGCGCAATCGTTTTGTGT 59.616 45.000 10.83 0.00 38.14 3.72 R
2624 2848 0.871722 CGCCAGTTTTGAACGATCCA 59.128 50.000 0.00 0.00 36.23 3.41 R
3255 4534 1.299468 GGATGAGTACGGCGCAGAG 60.299 63.158 16.26 4.70 0.00 3.35 R
3954 5361 1.194547 GCTTACCACATGTGTCACGTG 59.805 52.381 23.79 21.25 40.80 4.49 R
5334 7531 1.098129 TGAGCGCTGCTAGATCGAGT 61.098 55.000 18.48 0.00 39.88 4.18 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
180 182 4.081917 TCAGCCGACTATAACATCACACAA 60.082 41.667 0.00 0.00 0.00 3.33
201 203 5.125739 ACAACAGTAGGAAGGAGATAGAACG 59.874 44.000 0.00 0.00 0.00 3.95
278 280 4.055710 TCCCATCTAGGTATGCGGATAA 57.944 45.455 0.00 0.00 34.66 1.75
319 321 4.037927 TCGACATCCTCCTTCCCTTTTAT 58.962 43.478 0.00 0.00 0.00 1.40
345 347 5.104374 CACCGATTTTCTACCTAAACGCTA 58.896 41.667 0.00 0.00 0.00 4.26
377 379 6.844388 TCAGATCCCTATACCAAGTATGTGTT 59.156 38.462 0.00 0.00 30.79 3.32
409 411 2.139917 GATTTTGGGGACGGTTTTTGC 58.860 47.619 0.00 0.00 0.00 3.68
422 424 1.065782 GTTTTTGCTGGTGGTTTGGGT 60.066 47.619 0.00 0.00 0.00 4.51
469 471 0.738975 CTGACGGCTAGGATTCGACA 59.261 55.000 0.00 0.00 0.00 4.35
624 637 3.706373 GGAAGCACTCCTCCGCCA 61.706 66.667 0.00 0.00 41.61 5.69
627 640 2.244117 GAAGCACTCCTCCGCCATCA 62.244 60.000 0.00 0.00 0.00 3.07
660 674 2.765807 CCCCCAGATCTGCCGTCT 60.766 66.667 17.76 0.00 0.00 4.18
672 686 2.107141 CCGTCTTGGAGATCGGCC 59.893 66.667 0.00 0.00 42.00 6.13
674 688 2.506472 GTCTTGGAGATCGGCCCC 59.494 66.667 0.00 0.00 0.00 5.80
675 689 2.040442 TCTTGGAGATCGGCCCCA 59.960 61.111 0.00 0.00 0.00 4.96
676 690 1.384502 TCTTGGAGATCGGCCCCAT 60.385 57.895 0.00 0.00 0.00 4.00
735 774 5.025986 TCGCGTTCTTGGTTTCTATTTTC 57.974 39.130 5.77 0.00 0.00 2.29
794 833 9.267096 GATCTGAGATTGTTTCGTTGTAATTTC 57.733 33.333 0.00 0.00 0.00 2.17
870 909 1.534729 ACCAAGGTGGAATTTCGCTC 58.465 50.000 0.18 0.00 40.96 5.03
881 920 4.766891 TGGAATTTCGCTCCTGAATTTCTT 59.233 37.500 0.00 0.00 37.90 2.52
1004 1061 2.356433 TGCCGCAACGACGATGAA 60.356 55.556 9.52 0.00 34.06 2.57
1008 1065 1.337150 CGCAACGACGATGAAGACG 59.663 57.895 9.52 0.00 34.06 4.18
1055 1113 5.652014 CCCTTGCTGGTATGTTCATTTCTTA 59.348 40.000 0.00 0.00 0.00 2.10
1081 1139 6.071952 ACAATTCAGTTATTAACCTGCCTGTG 60.072 38.462 2.92 0.00 0.00 3.66
1208 1279 3.428999 CGTGTCTTACTGTCTATGTGGGG 60.429 52.174 0.00 0.00 0.00 4.96
1372 1444 3.619038 CGTTTCTTCTTATGCAGGAGACC 59.381 47.826 1.57 0.00 36.78 3.85
1677 1751 4.478317 TCCAGAAGGGTGGAATGATAATGT 59.522 41.667 0.00 0.00 44.01 2.71
1703 1777 1.355796 TTGGCGTGCTCCGTATTTCG 61.356 55.000 0.00 0.00 39.32 3.46
1717 1791 4.022242 CCGTATTTCGACTGTATGATCCCT 60.022 45.833 0.00 0.00 42.86 4.20
1737 1811 2.803956 CTGCCTTCATTTTGTTTGCTGG 59.196 45.455 0.00 0.00 0.00 4.85
1776 1852 1.005097 ACATCCTGAAGCTCATGCCAA 59.995 47.619 0.00 0.00 40.80 4.52
1778 1854 1.538047 TCCTGAAGCTCATGCCAAAC 58.462 50.000 0.00 0.00 40.80 2.93
1807 1888 6.868339 ACAGCAAAATTCCTATTACTGTTTGC 59.132 34.615 9.55 9.55 41.54 3.68
1808 1889 6.033831 CAGCAAAATTCCTATTACTGTTTGCG 59.966 38.462 11.28 4.78 44.62 4.85
1809 1890 6.072175 AGCAAAATTCCTATTACTGTTTGCGA 60.072 34.615 11.28 0.00 44.62 5.10
1810 1891 6.251376 GCAAAATTCCTATTACTGTTTGCGAG 59.749 38.462 0.00 0.00 34.04 5.03
1817 1899 0.391228 TACTGTTTGCGAGCCTCACA 59.609 50.000 0.00 0.00 0.00 3.58
1822 1904 0.966179 TTTGCGAGCCTCACAGACTA 59.034 50.000 0.00 0.00 0.00 2.59
1871 2045 9.973450 ATTTCTAAGTGCTAGATATACACTGTG 57.027 33.333 6.19 6.19 43.63 3.66
1872 2046 7.511959 TCTAAGTGCTAGATATACACTGTGG 57.488 40.000 13.09 0.00 43.63 4.17
1875 2049 5.696030 AGTGCTAGATATACACTGTGGAGA 58.304 41.667 13.09 0.15 42.83 3.71
1956 2131 5.244626 AGGCTTCAATAAAATTCAGCACTGT 59.755 36.000 0.00 0.00 0.00 3.55
1985 2160 8.842280 CCTTTGTACACCAGTAGTTCATTTTAA 58.158 33.333 0.00 0.00 0.00 1.52
2060 2235 1.354031 TGCTCTGCAAAATACTGGGGA 59.646 47.619 0.00 0.00 34.76 4.81
2073 2248 5.869649 ATACTGGGGAAATTAATTGGCAC 57.130 39.130 0.39 0.00 0.00 5.01
2074 2249 3.790126 ACTGGGGAAATTAATTGGCACT 58.210 40.909 0.39 0.00 0.00 4.40
2115 2292 5.087391 ACAATGTTGCATTTGATATGGCA 57.913 34.783 10.47 0.00 0.00 4.92
2126 2303 7.985752 TGCATTTGATATGGCATGTCATTTTTA 59.014 29.630 24.69 9.26 30.30 1.52
2130 2307 7.949903 TGATATGGCATGTCATTTTTATTGC 57.050 32.000 19.60 0.00 0.00 3.56
2163 2341 7.054491 AGTCTGGTTACATTTGCAAGATTTT 57.946 32.000 0.00 0.00 0.00 1.82
2170 2348 7.307870 GGTTACATTTGCAAGATTTTTGATGCA 60.308 33.333 0.00 0.00 46.21 3.96
2343 2537 7.040494 TGACTCTTGAGTCTTGATGATGATTC 58.960 38.462 25.21 2.05 39.41 2.52
2345 2539 6.817641 ACTCTTGAGTCTTGATGATGATTCAC 59.182 38.462 0.00 0.00 33.85 3.18
2405 2599 1.670811 ACCAAGTCTCAAGTTGTTGCG 59.329 47.619 2.11 0.00 34.54 4.85
2420 2614 1.401905 GTTGCGTCAATCCCAGGATTC 59.598 52.381 9.01 0.00 42.30 2.52
2480 2674 3.571590 AGCCAACAATGTTTTGGGAGTA 58.428 40.909 6.27 0.00 43.39 2.59
2505 2699 6.098838 AGCATTCTGTATTCAGGTCTGTCATA 59.901 38.462 0.00 0.00 41.59 2.15
2624 2848 5.374921 CAGGGAATTGAGATGCTATCACTT 58.625 41.667 0.00 0.00 0.00 3.16
2795 3022 8.128322 TCTCTGCTATCATAATCCTTACTTCC 57.872 38.462 0.00 0.00 0.00 3.46
2912 3244 8.045176 TCTAGAATTTTTGCTAGCCTTTCTTC 57.955 34.615 13.29 9.89 35.26 2.87
2926 3314 2.457366 TTCTTCTGGCCGTCTTTCTC 57.543 50.000 0.00 0.00 0.00 2.87
3030 4143 4.920640 TGCGTCCCTCTTCTCTTTATAG 57.079 45.455 0.00 0.00 0.00 1.31
3079 4200 5.458041 AAATGCATAGCAGTGTTCTTGTT 57.542 34.783 0.00 0.00 43.65 2.83
3096 4217 9.434420 TGTTCTTGTTCTTGTTTTCATGATTTT 57.566 25.926 0.00 0.00 34.68 1.82
3146 4418 9.436957 AGTCAATTACTTTTACTGTGGTGATAG 57.563 33.333 0.00 0.00 33.35 2.08
3164 4436 8.927411 TGGTGATAGTCTGAATGATTATTCTCA 58.073 33.333 11.13 3.31 42.56 3.27
3234 4513 3.712016 TTGGCAAGCTAACTATCCACA 57.288 42.857 0.00 0.00 29.98 4.17
3255 4534 7.335924 TCCACAATTGCCTTTTCTAGTATGTAC 59.664 37.037 5.05 0.00 0.00 2.90
3263 4542 3.984508 TTCTAGTATGTACTCTGCGCC 57.015 47.619 4.18 0.00 37.73 6.53
3350 4639 7.385778 AGTTCAACTTGTTTACTGCTTTACA 57.614 32.000 0.00 0.00 0.00 2.41
3409 4698 9.586435 GCATGCCTTATAAAAATGTTAGTTTCT 57.414 29.630 6.36 0.00 0.00 2.52
3498 4790 7.877097 TGCTTAATATTGTTTTGTGAATGGCTT 59.123 29.630 0.00 0.00 0.00 4.35
3511 4803 3.691118 TGAATGGCTTCTCAATTTCCTCG 59.309 43.478 0.00 0.00 32.29 4.63
3533 4825 4.550422 GTCAATTTCAGGCTGGACTTTTC 58.450 43.478 15.73 0.00 0.00 2.29
3572 4864 6.271391 TCTGGGTTTTCTTCACTCCAGTTATA 59.729 38.462 0.00 0.00 41.62 0.98
3573 4865 7.027874 TGGGTTTTCTTCACTCCAGTTATAT 57.972 36.000 0.00 0.00 0.00 0.86
3574 4866 8.153221 TGGGTTTTCTTCACTCCAGTTATATA 57.847 34.615 0.00 0.00 0.00 0.86
3575 4867 8.778059 TGGGTTTTCTTCACTCCAGTTATATAT 58.222 33.333 0.00 0.00 0.00 0.86
3653 4945 6.927294 GTGTATTCACTCTTTTATCCCCAG 57.073 41.667 0.00 0.00 40.98 4.45
3823 5227 8.579600 GTTTCGTCTCATATTCTAGCGATATTG 58.420 37.037 0.00 0.00 0.00 1.90
3846 5253 4.333926 GGCAGTGATACTGGATTTGTTCTC 59.666 45.833 10.62 0.00 46.01 2.87
3873 5280 6.299023 TGTGATTTAATAGTAATGCCAGCG 57.701 37.500 0.00 0.00 0.00 5.18
3885 5292 1.246649 TGCCAGCGACATTGTGAATT 58.753 45.000 0.00 0.00 0.00 2.17
3887 5294 3.016031 TGCCAGCGACATTGTGAATTAT 58.984 40.909 0.00 0.00 0.00 1.28
3943 5350 6.665992 AGTCTAACTGTCATAACAACAGGA 57.334 37.500 8.03 0.00 46.73 3.86
3944 5351 7.246171 AGTCTAACTGTCATAACAACAGGAT 57.754 36.000 8.03 0.00 46.73 3.24
3945 5352 7.680730 AGTCTAACTGTCATAACAACAGGATT 58.319 34.615 8.03 0.00 46.73 3.01
3946 5353 7.604164 AGTCTAACTGTCATAACAACAGGATTG 59.396 37.037 8.03 0.00 46.73 2.67
3947 5354 7.387948 GTCTAACTGTCATAACAACAGGATTGT 59.612 37.037 8.03 0.00 46.73 2.71
3958 5365 3.202829 ACAGGATTGTTGTTACCACGT 57.797 42.857 0.00 0.00 32.28 4.49
3959 5366 2.875933 ACAGGATTGTTGTTACCACGTG 59.124 45.455 9.08 9.08 32.28 4.49
3960 5367 3.135225 CAGGATTGTTGTTACCACGTGA 58.865 45.455 19.30 0.00 0.00 4.35
3961 5368 3.059188 CAGGATTGTTGTTACCACGTGAC 60.059 47.826 19.30 8.13 0.00 3.67
3962 5369 2.873472 GGATTGTTGTTACCACGTGACA 59.127 45.455 19.30 11.05 30.38 3.58
3963 5370 3.303526 GGATTGTTGTTACCACGTGACAC 60.304 47.826 19.30 10.78 31.98 3.67
3964 5371 2.381725 TGTTGTTACCACGTGACACA 57.618 45.000 19.30 13.38 31.98 3.72
3965 5372 2.907634 TGTTGTTACCACGTGACACAT 58.092 42.857 19.30 0.00 31.98 3.21
3966 5373 2.609916 TGTTGTTACCACGTGACACATG 59.390 45.455 19.30 0.00 31.98 3.21
3967 5374 2.605837 TGTTACCACGTGACACATGT 57.394 45.000 19.30 7.66 33.47 3.21
3974 5381 1.194547 CACGTGACACATGTGGTAAGC 59.805 52.381 28.64 13.03 44.71 3.09
3975 5382 1.202592 ACGTGACACATGTGGTAAGCA 60.203 47.619 28.64 15.24 31.87 3.91
3976 5383 1.870402 CGTGACACATGTGGTAAGCAA 59.130 47.619 28.64 4.27 34.19 3.91
3977 5384 2.483877 CGTGACACATGTGGTAAGCAAT 59.516 45.455 28.64 5.90 34.19 3.56
3978 5385 3.424829 CGTGACACATGTGGTAAGCAATC 60.425 47.826 28.64 14.99 34.19 2.67
3979 5386 3.081061 TGACACATGTGGTAAGCAATCC 58.919 45.455 28.64 6.08 34.19 3.01
3980 5387 3.081061 GACACATGTGGTAAGCAATCCA 58.919 45.455 28.64 0.00 34.19 3.41
3981 5388 3.495331 ACACATGTGGTAAGCAATCCAA 58.505 40.909 28.64 0.00 35.38 3.53
3982 5389 3.894427 ACACATGTGGTAAGCAATCCAAA 59.106 39.130 28.64 0.00 35.38 3.28
3983 5390 4.236935 CACATGTGGTAAGCAATCCAAAC 58.763 43.478 18.51 0.00 35.38 2.93
3984 5391 4.022068 CACATGTGGTAAGCAATCCAAACT 60.022 41.667 18.51 0.00 35.38 2.66
3985 5392 5.182950 CACATGTGGTAAGCAATCCAAACTA 59.817 40.000 18.51 0.00 35.38 2.24
3986 5393 5.951747 ACATGTGGTAAGCAATCCAAACTAT 59.048 36.000 0.00 0.00 35.38 2.12
3987 5394 6.437162 ACATGTGGTAAGCAATCCAAACTATT 59.563 34.615 0.00 0.00 35.38 1.73
3988 5395 6.509418 TGTGGTAAGCAATCCAAACTATTC 57.491 37.500 0.00 0.00 35.38 1.75
3989 5396 6.007076 TGTGGTAAGCAATCCAAACTATTCA 58.993 36.000 0.00 0.00 35.38 2.57
3990 5397 6.491745 TGTGGTAAGCAATCCAAACTATTCAA 59.508 34.615 0.00 0.00 35.38 2.69
3991 5398 7.014711 TGTGGTAAGCAATCCAAACTATTCAAA 59.985 33.333 0.00 0.00 35.38 2.69
3992 5399 7.870445 GTGGTAAGCAATCCAAACTATTCAAAA 59.130 33.333 0.00 0.00 35.38 2.44
3993 5400 8.424918 TGGTAAGCAATCCAAACTATTCAAAAA 58.575 29.630 0.00 0.00 0.00 1.94
4128 5619 1.065782 CACCACATGACCGGTTCCATA 60.066 52.381 9.42 0.00 31.41 2.74
4131 5622 3.456644 ACCACATGACCGGTTCCATATTA 59.543 43.478 9.42 0.00 28.43 0.98
4133 5624 4.884744 CCACATGACCGGTTCCATATTAAA 59.115 41.667 9.42 0.00 0.00 1.52
4199 5690 3.815401 GTGCATTCACTCCTGTGTAGTTT 59.185 43.478 0.00 0.00 44.14 2.66
4212 5703 5.431420 TGTGTAGTTTGTTGCCAATACAG 57.569 39.130 0.00 0.00 30.55 2.74
4215 5706 1.618343 AGTTTGTTGCCAATACAGCCC 59.382 47.619 0.00 0.00 0.00 5.19
4265 5756 4.893829 TGTAGGTATGCAGTAACACCAA 57.106 40.909 0.00 0.00 33.27 3.67
4285 5776 8.311109 ACACCAAAAAGTAATTATGATTGGACC 58.689 33.333 20.14 0.00 38.44 4.46
4326 5818 2.949177 ATGCCAACTGAGTTGTGGTA 57.051 45.000 22.40 10.32 41.41 3.25
4360 5854 5.065988 TGGAGACAACAAAACTTAGCTTGAC 59.934 40.000 0.00 0.00 37.44 3.18
4376 5872 9.239002 CTTAGCTTGACACTACTATGTTGTATC 57.761 37.037 0.00 0.00 31.24 2.24
4381 5877 9.755804 CTTGACACTACTATGTTGTATCATGAT 57.244 33.333 13.81 13.81 27.03 2.45
4392 5888 8.631480 ATGTTGTATCATGATGATGTATGCTT 57.369 30.769 18.72 0.00 37.70 3.91
4394 5890 8.905850 TGTTGTATCATGATGATGTATGCTTTT 58.094 29.630 18.72 0.00 37.70 2.27
4482 5991 3.243101 GGATGCTCAGACAATTGATGCAG 60.243 47.826 13.59 10.30 35.91 4.41
4483 5992 2.786777 TGCTCAGACAATTGATGCAGT 58.213 42.857 13.59 0.00 31.93 4.40
4484 5993 3.941573 TGCTCAGACAATTGATGCAGTA 58.058 40.909 13.59 6.92 31.93 2.74
4485 5994 3.937079 TGCTCAGACAATTGATGCAGTAG 59.063 43.478 13.59 5.22 31.93 2.57
4486 5995 4.186926 GCTCAGACAATTGATGCAGTAGA 58.813 43.478 13.59 0.00 0.00 2.59
4487 5996 4.033817 GCTCAGACAATTGATGCAGTAGAC 59.966 45.833 13.59 0.00 0.00 2.59
4488 5997 5.411831 TCAGACAATTGATGCAGTAGACT 57.588 39.130 13.59 0.00 0.00 3.24
4489 5998 5.414360 TCAGACAATTGATGCAGTAGACTC 58.586 41.667 13.59 0.00 0.00 3.36
4490 5999 5.047092 TCAGACAATTGATGCAGTAGACTCA 60.047 40.000 13.59 0.00 0.00 3.41
4491 6000 5.816258 CAGACAATTGATGCAGTAGACTCAT 59.184 40.000 13.59 0.00 0.00 2.90
4492 6001 6.982724 CAGACAATTGATGCAGTAGACTCATA 59.017 38.462 13.59 0.00 0.00 2.15
4493 6002 7.656542 CAGACAATTGATGCAGTAGACTCATAT 59.343 37.037 13.59 0.00 0.00 1.78
4494 6003 8.864087 AGACAATTGATGCAGTAGACTCATATA 58.136 33.333 13.59 0.00 0.00 0.86
4495 6004 9.481340 GACAATTGATGCAGTAGACTCATATAA 57.519 33.333 13.59 0.00 0.00 0.98
4505 6014 9.796120 GCAGTAGACTCATATAATATCTGTTCC 57.204 37.037 0.00 0.00 0.00 3.62
4509 6018 8.964533 AGACTCATATAATATCTGTTCCCAGT 57.035 34.615 0.00 0.00 39.82 4.00
4510 6019 8.811017 AGACTCATATAATATCTGTTCCCAGTG 58.189 37.037 0.00 0.00 39.82 3.66
4511 6020 8.727100 ACTCATATAATATCTGTTCCCAGTGA 57.273 34.615 0.00 0.00 39.82 3.41
4512 6021 9.331466 ACTCATATAATATCTGTTCCCAGTGAT 57.669 33.333 0.00 0.00 39.82 3.06
4513 6022 9.814899 CTCATATAATATCTGTTCCCAGTGATC 57.185 37.037 0.00 0.00 39.82 2.92
4514 6023 9.325248 TCATATAATATCTGTTCCCAGTGATCA 57.675 33.333 0.00 0.00 39.82 2.92
4515 6024 9.597170 CATATAATATCTGTTCCCAGTGATCAG 57.403 37.037 0.00 0.00 40.64 2.90
4516 6025 5.965033 AATATCTGTTCCCAGTGATCAGT 57.035 39.130 0.00 0.00 40.32 3.41
4517 6026 5.965033 ATATCTGTTCCCAGTGATCAGTT 57.035 39.130 0.00 0.00 40.32 3.16
4518 6027 4.647564 ATCTGTTCCCAGTGATCAGTTT 57.352 40.909 0.00 0.00 40.32 2.66
4519 6028 3.743521 TCTGTTCCCAGTGATCAGTTTG 58.256 45.455 0.00 0.00 40.32 2.93
4520 6029 3.136443 TCTGTTCCCAGTGATCAGTTTGT 59.864 43.478 0.00 0.00 40.32 2.83
4521 6030 3.213506 TGTTCCCAGTGATCAGTTTGTG 58.786 45.455 0.00 0.00 0.00 3.33
4522 6031 2.554032 GTTCCCAGTGATCAGTTTGTGG 59.446 50.000 0.00 0.00 0.00 4.17
4523 6032 2.054021 TCCCAGTGATCAGTTTGTGGA 58.946 47.619 0.00 2.32 0.00 4.02
4524 6033 2.644299 TCCCAGTGATCAGTTTGTGGAT 59.356 45.455 0.00 0.00 0.00 3.41
4525 6034 3.074390 TCCCAGTGATCAGTTTGTGGATT 59.926 43.478 0.00 0.00 0.00 3.01
4526 6035 3.441572 CCCAGTGATCAGTTTGTGGATTC 59.558 47.826 0.00 0.00 0.00 2.52
4527 6036 4.330250 CCAGTGATCAGTTTGTGGATTCT 58.670 43.478 0.00 0.00 0.00 2.40
4528 6037 4.763793 CCAGTGATCAGTTTGTGGATTCTT 59.236 41.667 0.00 0.00 0.00 2.52
4529 6038 5.335426 CCAGTGATCAGTTTGTGGATTCTTG 60.335 44.000 0.00 0.00 0.00 3.02
4530 6039 5.240183 CAGTGATCAGTTTGTGGATTCTTGT 59.760 40.000 0.00 0.00 0.00 3.16
4545 6054 4.946160 TTCTTGTATTTCCCAGGGATGT 57.054 40.909 9.80 3.48 0.00 3.06
4554 6063 2.066592 TCCCAGGGATGTGTTTGGTTA 58.933 47.619 3.01 0.00 0.00 2.85
4591 6101 9.755804 TTTGTTGAAACATGCATTATAAACTCA 57.244 25.926 0.00 0.00 38.95 3.41
4662 6850 7.544804 AAAAATCCTAAGCAGTTCTCCATTT 57.455 32.000 0.00 0.00 0.00 2.32
4666 6854 9.920946 AAATCCTAAGCAGTTCTCCATTTTATA 57.079 29.630 0.00 0.00 0.00 0.98
4690 6878 5.048504 ACAATACTGAAAACACATGCAGAGG 60.049 40.000 0.00 0.00 32.86 3.69
4718 6906 5.126869 CCCATGTTTCCATAAGCATGTAACA 59.873 40.000 12.08 5.31 46.89 2.41
4953 7144 8.563732 TCTTCTCATCTTGTCGTTCTCTATATG 58.436 37.037 0.00 0.00 0.00 1.78
5102 7296 2.102925 CGGGGAAGTAAAGCCGGTAATA 59.897 50.000 1.90 0.00 0.00 0.98
5122 7316 6.506500 AATAAAGCTTGTTCACCTCTGATG 57.493 37.500 0.00 0.00 0.00 3.07
5124 7318 3.996921 AGCTTGTTCACCTCTGATGAT 57.003 42.857 0.00 0.00 0.00 2.45
5125 7319 3.871485 AGCTTGTTCACCTCTGATGATC 58.129 45.455 0.00 0.00 0.00 2.92
5126 7320 3.262660 AGCTTGTTCACCTCTGATGATCA 59.737 43.478 0.00 0.00 0.00 2.92
5127 7321 3.622163 GCTTGTTCACCTCTGATGATCAG 59.378 47.826 16.15 16.15 45.59 2.90
5334 7531 0.250727 AGCAAAAAGGCGGACTAGCA 60.251 50.000 0.00 0.00 39.27 3.49
5376 7573 6.330778 TCAGGTCTTTTTAGTTAGGGGAAGAA 59.669 38.462 0.00 0.00 0.00 2.52
5453 7652 8.186821 CCATTCACATCATAGAACCTCTTTTTC 58.813 37.037 0.00 0.00 0.00 2.29
5456 7656 7.679783 TCACATCATAGAACCTCTTTTTCTCA 58.320 34.615 0.00 0.00 34.99 3.27
5597 7801 5.309543 TGAGGAAGGATTTTAGTTGACTGGA 59.690 40.000 0.00 0.00 0.00 3.86
5623 7827 2.450609 TAAGTGAGTTCCCTGCGTTC 57.549 50.000 0.00 0.00 0.00 3.95
5624 7828 0.468226 AAGTGAGTTCCCTGCGTTCA 59.532 50.000 0.00 0.00 0.00 3.18
5633 7837 7.225931 GTGAGTTCCCTGCGTTCATTTAATATA 59.774 37.037 0.00 0.00 0.00 0.86
5737 7945 7.849322 AAAGAAAACTTAGGGGCTTGAATTA 57.151 32.000 0.00 0.00 0.00 1.40
5762 7972 4.800993 CGAAGAGAACGAGCATTCAAGTAT 59.199 41.667 0.00 0.00 0.00 2.12
5764 7974 8.778285 TCGAAGAGAACGAGCATTCAAGTATTG 61.778 40.741 0.00 0.00 40.18 1.90
5779 7990 5.804173 CAAGTATTGCAACTCTACATGCTC 58.196 41.667 0.00 0.00 40.39 4.26
5804 8015 5.885230 TTTGATTGACTTGATAGCACCTG 57.115 39.130 0.00 0.00 0.00 4.00
5819 8030 7.928167 TGATAGCACCTGTTGATAGAGTTATTG 59.072 37.037 0.00 0.00 27.00 1.90
5845 8056 9.354673 GGGAGGAATGAATATTTAAAGTGATCA 57.645 33.333 0.00 0.00 0.00 2.92
5873 8084 9.691362 GGTTATGCCAAAATTTATTCACGATAT 57.309 29.630 0.00 0.00 37.17 1.63
5940 8156 7.940178 ATATGTTGAGATAATTCGCGTAACA 57.060 32.000 5.77 5.70 0.00 2.41
5967 8183 1.993370 CCGTCACGAACTTGGAGATTC 59.007 52.381 0.00 0.00 0.00 2.52
6025 8241 5.584649 TGTATGTGGTAAATAAGAGCACTGC 59.415 40.000 6.54 0.00 43.95 4.40
6061 8281 4.927978 AGAGACAACCATTCTAGATCCG 57.072 45.455 0.00 0.00 0.00 4.18
6091 8312 6.644775 CACAAAATTAAACCACAATGGAACG 58.355 36.000 0.84 0.00 40.96 3.95
6092 8313 5.755861 ACAAAATTAAACCACAATGGAACGG 59.244 36.000 0.84 0.00 40.96 4.44
6098 8319 1.892474 ACCACAATGGAACGGAATTGG 59.108 47.619 0.84 0.00 40.96 3.16
6099 8320 1.404047 CCACAATGGAACGGAATTGGC 60.404 52.381 0.00 0.00 40.96 4.52
6112 8333 7.860872 GGAACGGAATTGGCTATAGTAAATTTG 59.139 37.037 12.95 11.57 0.00 2.32
6132 8353 2.664402 GGCATAACCCCATCACTGAT 57.336 50.000 0.00 0.00 0.00 2.90
6148 8370 7.040478 CCATCACTGATAGTTGAAGTTCCAAAA 60.040 37.037 0.00 0.00 0.00 2.44
6171 8393 6.749923 AGATAATGGTTGAAAGAAGTGCTC 57.250 37.500 0.00 0.00 0.00 4.26
6252 8474 5.074515 TCTCTTTGTTTCCCAAACTCCCTAT 59.925 40.000 1.11 0.00 41.90 2.57
6266 8490 6.418057 AACTCCCTATTGCATTTGTTGAAA 57.582 33.333 0.00 0.00 0.00 2.69
6267 8494 6.418057 ACTCCCTATTGCATTTGTTGAAAA 57.582 33.333 0.00 0.00 0.00 2.29
6269 8496 7.452562 ACTCCCTATTGCATTTGTTGAAAAAT 58.547 30.769 0.00 0.00 0.00 1.82
6273 8503 7.804129 CCCTATTGCATTTGTTGAAAAATGTTG 59.196 33.333 10.40 0.00 45.37 3.33
6274 8504 7.804129 CCTATTGCATTTGTTGAAAAATGTTGG 59.196 33.333 10.40 0.40 45.37 3.77
6316 8548 5.378292 AAGAAATTCTTTCGCTTTCCTCC 57.622 39.130 1.80 0.00 44.29 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 162 3.930229 TGTTGTGTGATGTTATAGTCGGC 59.070 43.478 0.00 0.00 0.00 5.54
180 182 5.113446 TCGTTCTATCTCCTTCCTACTGT 57.887 43.478 0.00 0.00 0.00 3.55
201 203 2.884087 TTCGTGGAGCTTCGCCGATC 62.884 60.000 7.35 0.00 0.00 3.69
278 280 2.418746 CGAAATGGACCAAGATCTCGGT 60.419 50.000 4.59 4.59 38.56 4.69
319 321 3.985019 TTAGGTAGAAAATCGGTGCCA 57.015 42.857 0.00 0.00 0.00 4.92
345 347 8.050316 ACTTGGTATAGGGATCTGAATTTCAT 57.950 34.615 0.00 0.00 0.00 2.57
377 379 2.092646 CCCCAAAATCCATCTACCACGA 60.093 50.000 0.00 0.00 0.00 4.35
409 411 0.035439 ATCGCTACCCAAACCACCAG 60.035 55.000 0.00 0.00 0.00 4.00
611 624 0.601311 GTATGATGGCGGAGGAGTGC 60.601 60.000 0.00 0.00 0.00 4.40
660 674 2.452064 GGATGGGGCCGATCTCCAA 61.452 63.158 25.08 0.00 33.90 3.53
671 685 3.781307 TGAAGCGACGGGATGGGG 61.781 66.667 0.00 0.00 0.00 4.96
672 686 2.511600 GTGAAGCGACGGGATGGG 60.512 66.667 0.00 0.00 0.00 4.00
735 774 1.129326 GGTTCGACACTCGTGAACTG 58.871 55.000 3.74 0.00 41.27 3.16
794 833 3.070302 CCTACCCAGCTAAGCTTCCTAAG 59.930 52.174 0.00 0.00 36.40 2.18
870 909 6.683974 ACACCGATGAATAAGAAATTCAGG 57.316 37.500 6.58 5.77 40.80 3.86
1008 1065 3.792047 TTCGCAGCACGCTCATGC 61.792 61.111 0.00 0.00 46.50 4.06
1055 1113 6.493458 ACAGGCAGGTTAATAACTGAATTGTT 59.507 34.615 2.96 0.00 36.86 2.83
1081 1139 1.739067 ACGAACTAGCAAATCAGGCC 58.261 50.000 0.00 0.00 0.00 5.19
1208 1279 1.529865 GCCTTGACAGAACGGTAACAC 59.470 52.381 0.00 0.00 0.00 3.32
1372 1444 2.743752 CGCGTGCTCCTTGGACATG 61.744 63.158 0.00 0.00 36.78 3.21
1633 1707 3.850122 AGAAAACGCTTTATGGAAGGC 57.150 42.857 0.00 0.00 35.82 4.35
1703 1777 2.435805 TGAAGGCAGGGATCATACAGTC 59.564 50.000 0.00 0.00 0.00 3.51
1717 1791 2.170187 ACCAGCAAACAAAATGAAGGCA 59.830 40.909 0.00 0.00 0.00 4.75
1802 1883 0.601311 AGTCTGTGAGGCTCGCAAAC 60.601 55.000 28.69 26.07 36.34 2.93
1803 1884 0.966179 TAGTCTGTGAGGCTCGCAAA 59.034 50.000 28.69 16.12 36.34 3.68
1806 1887 4.974368 ATATATAGTCTGTGAGGCTCGC 57.026 45.455 20.87 20.87 29.80 5.03
1807 1888 6.550843 CAGAATATATAGTCTGTGAGGCTCG 58.449 44.000 25.22 3.71 41.86 5.03
1859 2025 6.637254 CACATTACGTCTCCACAGTGTATATC 59.363 42.308 0.00 0.00 0.00 1.63
1871 2045 5.348986 TCTTGATTAGCACATTACGTCTCC 58.651 41.667 0.00 0.00 0.00 3.71
1872 2046 6.037098 ACTCTTGATTAGCACATTACGTCTC 58.963 40.000 0.00 0.00 0.00 3.36
1875 2049 5.109903 GGACTCTTGATTAGCACATTACGT 58.890 41.667 0.00 0.00 0.00 3.57
1925 2100 6.976088 TGAATTTTATTGAAGCCTGTTCGAA 58.024 32.000 0.00 0.00 0.00 3.71
1927 2102 5.287035 GCTGAATTTTATTGAAGCCTGTTCG 59.713 40.000 0.00 0.00 0.00 3.95
1956 2131 3.849563 ACTACTGGTGTACAAAGGCAA 57.150 42.857 0.00 0.00 0.00 4.52
1985 2160 0.701310 ACAGTTTCCCAGTTCCCCCT 60.701 55.000 0.00 0.00 0.00 4.79
2052 2227 4.941713 AGTGCCAATTAATTTCCCCAGTA 58.058 39.130 0.00 0.00 0.00 2.74
2101 2278 6.854496 AAAATGACATGCCATATCAAATGC 57.146 33.333 0.00 0.00 0.00 3.56
2115 2292 7.394359 ACTCCAGTACAGCAATAAAAATGACAT 59.606 33.333 0.00 0.00 0.00 3.06
2126 2303 2.260822 ACCAGACTCCAGTACAGCAAT 58.739 47.619 0.00 0.00 0.00 3.56
2130 2307 5.407407 AATGTAACCAGACTCCAGTACAG 57.593 43.478 0.00 0.00 0.00 2.74
2234 2427 7.270365 CGCAATCGTTTTGTGTTTGTAAGATAT 59.730 33.333 6.34 0.00 0.00 1.63
2235 2428 6.575572 CGCAATCGTTTTGTGTTTGTAAGATA 59.424 34.615 6.34 0.00 0.00 1.98
2236 2429 5.398122 CGCAATCGTTTTGTGTTTGTAAGAT 59.602 36.000 6.34 0.00 0.00 2.40
2237 2430 4.731000 CGCAATCGTTTTGTGTTTGTAAGA 59.269 37.500 6.34 0.00 0.00 2.10
2238 2431 4.602957 GCGCAATCGTTTTGTGTTTGTAAG 60.603 41.667 0.30 0.00 38.14 2.34
2239 2432 3.240861 GCGCAATCGTTTTGTGTTTGTAA 59.759 39.130 0.30 0.00 38.14 2.41
2240 2433 2.784380 GCGCAATCGTTTTGTGTTTGTA 59.216 40.909 0.30 0.00 38.14 2.41
2245 2438 0.383949 AAGGCGCAATCGTTTTGTGT 59.616 45.000 10.83 0.00 38.14 3.72
2296 2490 5.944007 TCAAGCTTGTAAAGGGGAATAGAAC 59.056 40.000 25.19 0.00 46.35 3.01
2298 2492 5.250774 AGTCAAGCTTGTAAAGGGGAATAGA 59.749 40.000 25.19 0.00 46.35 1.98
2343 2537 5.688823 TGAAATGTGAAGTTAATGAGCGTG 58.311 37.500 0.00 0.00 0.00 5.34
2345 2539 4.790140 GCTGAAATGTGAAGTTAATGAGCG 59.210 41.667 0.00 0.00 0.00 5.03
2405 2599 4.880696 CAGAAGAAGAATCCTGGGATTGAC 59.119 45.833 18.27 6.32 43.98 3.18
2420 2614 2.802816 GGCATACCATACGCAGAAGAAG 59.197 50.000 0.00 0.00 35.26 2.85
2480 2674 4.223700 TGACAGACCTGAATACAGAATGCT 59.776 41.667 3.76 0.00 46.03 3.79
2505 2699 7.442666 GCATATTAACCTTAAGCTCTAGCAGTT 59.557 37.037 4.54 2.87 45.16 3.16
2624 2848 0.871722 CGCCAGTTTTGAACGATCCA 59.128 50.000 0.00 0.00 36.23 3.41
2795 3022 9.657419 TTATTGTACATATATGTCATGCTCCAG 57.343 33.333 21.49 0.00 41.97 3.86
2847 3179 8.456471 CAAATTGTATCTATCCTACATGCATGG 58.544 37.037 29.41 13.24 0.00 3.66
2879 3211 9.061435 GGCTAGCAAAAATTCTAGAATATCAGT 57.939 33.333 18.23 0.00 35.48 3.41
2912 3244 1.461127 CTTTTCGAGAAAGACGGCCAG 59.539 52.381 2.24 0.00 0.00 4.85
2926 3314 4.811158 CACTGCATAACATTGCTTTTCG 57.189 40.909 0.00 0.00 43.18 3.46
3030 4143 8.239998 AGTGAGCTGCTAGAAATTTGTTAATTC 58.760 33.333 0.15 0.00 32.85 2.17
3164 4436 3.886505 TGCTGAAGTACGGAACCAAAATT 59.113 39.130 0.00 0.00 0.00 1.82
3234 4513 7.281100 GCAGAGTACATACTAGAAAAGGCAATT 59.719 37.037 0.00 0.00 36.50 2.32
3255 4534 1.299468 GGATGAGTACGGCGCAGAG 60.299 63.158 16.26 4.70 0.00 3.35
3263 4542 1.478510 ACTTGCCAGAGGATGAGTACG 59.521 52.381 0.00 0.00 0.00 3.67
3343 4632 7.283127 TGGAAAATCTGTGGATATCTGTAAAGC 59.717 37.037 2.05 0.00 0.00 3.51
3409 4698 3.130633 CAACAGGACTGACGAAATGACA 58.869 45.455 6.29 0.00 0.00 3.58
3498 4790 5.412594 CCTGAAATTGACGAGGAAATTGAGA 59.587 40.000 0.00 0.00 0.00 3.27
3511 4803 4.279420 AGAAAAGTCCAGCCTGAAATTGAC 59.721 41.667 0.00 0.00 0.00 3.18
3533 4825 7.108847 AGAAAACCCAGAAGATGTCATAGAAG 58.891 38.462 0.00 0.00 0.00 2.85
3572 4864 7.886629 AATGATTTAGCAACACTGACCATAT 57.113 32.000 0.00 0.00 0.00 1.78
3573 4865 7.392953 TCAAATGATTTAGCAACACTGACCATA 59.607 33.333 0.00 0.00 0.00 2.74
3574 4866 6.209192 TCAAATGATTTAGCAACACTGACCAT 59.791 34.615 0.00 0.00 0.00 3.55
3575 4867 5.534278 TCAAATGATTTAGCAACACTGACCA 59.466 36.000 0.00 0.00 0.00 4.02
3823 5227 4.265073 AGAACAAATCCAGTATCACTGCC 58.735 43.478 0.64 0.00 44.63 4.85
3846 5253 7.165812 GCTGGCATTACTATTAAATCACAAACG 59.834 37.037 0.00 0.00 0.00 3.60
3885 5292 8.909923 TCCATTTATCACGAGAACAGAGTTATA 58.090 33.333 0.00 0.00 0.00 0.98
3887 5294 7.122204 TCTCCATTTATCACGAGAACAGAGTTA 59.878 37.037 0.00 0.00 0.00 2.24
3899 5306 7.484975 AGACTAGAAGTTCTCCATTTATCACG 58.515 38.462 9.12 0.00 0.00 4.35
3949 5356 1.529438 CCACATGTGTCACGTGGTAAC 59.471 52.381 25.31 11.98 44.27 2.50
3950 5357 1.872388 CCACATGTGTCACGTGGTAA 58.128 50.000 25.31 0.00 44.27 2.85
3951 5358 3.597550 CCACATGTGTCACGTGGTA 57.402 52.632 25.31 1.73 44.27 3.25
3952 5359 4.454948 CCACATGTGTCACGTGGT 57.545 55.556 25.31 11.12 44.27 4.16
3954 5361 1.194547 GCTTACCACATGTGTCACGTG 59.805 52.381 23.79 21.25 40.80 4.49
3955 5362 1.202592 TGCTTACCACATGTGTCACGT 60.203 47.619 23.79 16.29 0.00 4.49
3956 5363 1.507562 TGCTTACCACATGTGTCACG 58.492 50.000 23.79 11.29 0.00 4.35
3957 5364 3.119849 GGATTGCTTACCACATGTGTCAC 60.120 47.826 23.79 9.40 0.00 3.67
3958 5365 3.081061 GGATTGCTTACCACATGTGTCA 58.919 45.455 23.79 8.71 0.00 3.58
3959 5366 3.081061 TGGATTGCTTACCACATGTGTC 58.919 45.455 23.79 11.95 0.00 3.67
3960 5367 3.153369 TGGATTGCTTACCACATGTGT 57.847 42.857 23.79 14.29 0.00 3.72
3961 5368 4.022068 AGTTTGGATTGCTTACCACATGTG 60.022 41.667 19.31 19.31 35.81 3.21
3962 5369 4.151883 AGTTTGGATTGCTTACCACATGT 58.848 39.130 0.00 0.00 35.81 3.21
3963 5370 4.789012 AGTTTGGATTGCTTACCACATG 57.211 40.909 0.00 0.00 35.81 3.21
3964 5371 6.663093 TGAATAGTTTGGATTGCTTACCACAT 59.337 34.615 0.00 0.00 35.81 3.21
3965 5372 6.007076 TGAATAGTTTGGATTGCTTACCACA 58.993 36.000 0.00 0.00 35.81 4.17
3966 5373 6.509418 TGAATAGTTTGGATTGCTTACCAC 57.491 37.500 0.00 0.00 35.81 4.16
3967 5374 7.531857 TTTGAATAGTTTGGATTGCTTACCA 57.468 32.000 0.00 0.00 0.00 3.25
3968 5375 8.825667 TTTTTGAATAGTTTGGATTGCTTACC 57.174 30.769 0.00 0.00 0.00 2.85
3995 5402 9.927668 CCCTTATATCAACAACAATTCTGTTTT 57.072 29.630 0.58 0.00 43.45 2.43
3996 5403 9.308000 TCCCTTATATCAACAACAATTCTGTTT 57.692 29.630 0.58 0.00 43.45 2.83
3998 5405 8.906867 CATCCCTTATATCAACAACAATTCTGT 58.093 33.333 0.00 0.00 37.39 3.41
3999 5406 8.906867 ACATCCCTTATATCAACAACAATTCTG 58.093 33.333 0.00 0.00 0.00 3.02
4000 5407 9.479549 AACATCCCTTATATCAACAACAATTCT 57.520 29.630 0.00 0.00 0.00 2.40
4199 5690 8.893388 AGCATATATGGGCTGTATTGGCAACA 62.893 42.308 14.51 0.00 42.23 3.33
4212 5703 0.394899 GGCCTGGAGCATATATGGGC 60.395 60.000 17.14 17.14 46.50 5.36
4215 5706 3.928005 ATCAGGCCTGGAGCATATATG 57.072 47.619 32.23 8.45 46.50 1.78
4265 5756 8.749354 GGAAGTGGTCCAATCATAATTACTTTT 58.251 33.333 0.00 0.00 46.97 2.27
4360 5854 9.702494 ACATCATCATGATACAACATAGTAGTG 57.298 33.333 8.15 0.00 34.28 2.74
4392 5888 8.934825 CAAAAAGAAGAATCCACAACTGAAAAA 58.065 29.630 0.00 0.00 0.00 1.94
4394 5890 7.610865 ACAAAAAGAAGAATCCACAACTGAAA 58.389 30.769 0.00 0.00 0.00 2.69
4397 5893 7.930217 TCTACAAAAAGAAGAATCCACAACTG 58.070 34.615 0.00 0.00 0.00 3.16
4398 5894 8.697507 ATCTACAAAAAGAAGAATCCACAACT 57.302 30.769 0.00 0.00 0.00 3.16
4399 5895 8.023706 GGATCTACAAAAAGAAGAATCCACAAC 58.976 37.037 0.00 0.00 0.00 3.32
4400 5896 7.944554 AGGATCTACAAAAAGAAGAATCCACAA 59.055 33.333 0.00 0.00 0.00 3.33
4402 5898 7.929941 AGGATCTACAAAAAGAAGAATCCAC 57.070 36.000 0.00 0.00 0.00 4.02
4433 5942 9.950496 ATGTTAAACATCTGATTCAGTCTAGTT 57.050 29.630 13.23 10.52 32.38 2.24
4434 5943 9.376075 CATGTTAAACATCTGATTCAGTCTAGT 57.624 33.333 13.23 5.62 36.53 2.57
4448 5957 5.355071 TGTCTGAGCATCCATGTTAAACATC 59.645 40.000 0.00 0.00 36.53 3.06
4500 6009 3.213506 CACAAACTGATCACTGGGAACA 58.786 45.455 0.00 0.00 39.59 3.18
4501 6010 2.554032 CCACAAACTGATCACTGGGAAC 59.446 50.000 0.00 0.00 0.00 3.62
4502 6011 2.441375 TCCACAAACTGATCACTGGGAA 59.559 45.455 0.00 0.00 0.00 3.97
4503 6012 2.054021 TCCACAAACTGATCACTGGGA 58.946 47.619 0.00 0.00 0.00 4.37
4504 6013 2.566833 TCCACAAACTGATCACTGGG 57.433 50.000 0.00 0.00 0.00 4.45
4505 6014 4.330250 AGAATCCACAAACTGATCACTGG 58.670 43.478 0.00 0.00 0.00 4.00
4506 6015 5.240183 ACAAGAATCCACAAACTGATCACTG 59.760 40.000 0.00 0.00 0.00 3.66
4507 6016 5.380043 ACAAGAATCCACAAACTGATCACT 58.620 37.500 0.00 0.00 0.00 3.41
4508 6017 5.695851 ACAAGAATCCACAAACTGATCAC 57.304 39.130 0.00 0.00 0.00 3.06
4509 6018 8.408043 AAATACAAGAATCCACAAACTGATCA 57.592 30.769 0.00 0.00 0.00 2.92
4510 6019 7.970614 GGAAATACAAGAATCCACAAACTGATC 59.029 37.037 0.00 0.00 32.08 2.92
4511 6020 7.093771 GGGAAATACAAGAATCCACAAACTGAT 60.094 37.037 0.00 0.00 33.48 2.90
4512 6021 6.208599 GGGAAATACAAGAATCCACAAACTGA 59.791 38.462 0.00 0.00 33.48 3.41
4513 6022 6.015519 TGGGAAATACAAGAATCCACAAACTG 60.016 38.462 0.00 0.00 33.48 3.16
4514 6023 6.074648 TGGGAAATACAAGAATCCACAAACT 58.925 36.000 0.00 0.00 33.48 2.66
4515 6024 6.339587 TGGGAAATACAAGAATCCACAAAC 57.660 37.500 0.00 0.00 33.48 2.93
4516 6025 5.480073 CCTGGGAAATACAAGAATCCACAAA 59.520 40.000 0.00 0.00 33.48 2.83
4517 6026 5.016173 CCTGGGAAATACAAGAATCCACAA 58.984 41.667 0.00 0.00 33.48 3.33
4518 6027 4.569653 CCCTGGGAAATACAAGAATCCACA 60.570 45.833 7.01 0.00 33.48 4.17
4519 6028 3.954258 CCCTGGGAAATACAAGAATCCAC 59.046 47.826 7.01 0.00 33.48 4.02
4520 6029 3.855599 TCCCTGGGAAATACAAGAATCCA 59.144 43.478 14.48 0.00 33.48 3.41
4521 6030 4.519906 TCCCTGGGAAATACAAGAATCC 57.480 45.455 14.48 0.00 0.00 3.01
4522 6031 5.300286 CACATCCCTGGGAAATACAAGAATC 59.700 44.000 21.42 0.00 34.34 2.52
4523 6032 5.203528 CACATCCCTGGGAAATACAAGAAT 58.796 41.667 21.42 0.00 34.34 2.40
4524 6033 4.044065 ACACATCCCTGGGAAATACAAGAA 59.956 41.667 21.42 0.00 34.34 2.52
4525 6034 3.591527 ACACATCCCTGGGAAATACAAGA 59.408 43.478 21.42 0.00 34.34 3.02
4526 6035 3.968265 ACACATCCCTGGGAAATACAAG 58.032 45.455 21.42 8.17 34.34 3.16
4527 6036 4.396357 AACACATCCCTGGGAAATACAA 57.604 40.909 21.42 0.00 34.34 2.41
4528 6037 4.085733 CAAACACATCCCTGGGAAATACA 58.914 43.478 21.42 0.00 34.34 2.29
4529 6038 3.447229 CCAAACACATCCCTGGGAAATAC 59.553 47.826 21.42 0.00 34.34 1.89
4530 6039 3.076785 ACCAAACACATCCCTGGGAAATA 59.923 43.478 21.42 0.00 34.34 1.40
4545 6054 8.499162 CAACAAAACATTTTCACTAACCAAACA 58.501 29.630 0.00 0.00 0.00 2.83
4661 6849 9.838975 CTGCATGTGTTTTCAGTATTGTATAAA 57.161 29.630 0.00 0.00 0.00 1.40
4662 6850 9.225436 TCTGCATGTGTTTTCAGTATTGTATAA 57.775 29.630 0.00 0.00 0.00 0.98
4666 6854 5.048504 CCTCTGCATGTGTTTTCAGTATTGT 60.049 40.000 0.00 0.00 0.00 2.71
4953 7144 7.400627 AGGTAATAATATTCCAGAGACTAGGGC 59.599 40.741 0.00 0.00 0.00 5.19
5102 7296 4.090761 TCATCAGAGGTGAACAAGCTTT 57.909 40.909 0.00 0.00 36.52 3.51
5137 7331 3.973425 ACATGGGAAATGAGGAAAGGAG 58.027 45.455 0.00 0.00 0.00 3.69
5140 7334 5.713861 AGAAGAACATGGGAAATGAGGAAAG 59.286 40.000 0.00 0.00 0.00 2.62
5150 7344 6.550854 AGATGAAACAAAGAAGAACATGGGAA 59.449 34.615 0.00 0.00 0.00 3.97
5195 7389 5.504010 CGCAGTTTTGACAGTGAATTGTAGT 60.504 40.000 0.00 0.00 0.00 2.73
5199 7393 3.951306 TCGCAGTTTTGACAGTGAATTG 58.049 40.909 0.00 0.00 0.00 2.32
5269 7463 1.402107 TATCATCAGCCTGCGCCTCA 61.402 55.000 4.18 0.00 34.57 3.86
5334 7531 1.098129 TGAGCGCTGCTAGATCGAGT 61.098 55.000 18.48 0.00 39.88 4.18
5376 7573 3.312736 TTGAAACTCCTCCTTTGGCTT 57.687 42.857 0.00 0.00 0.00 4.35
5552 7755 8.796475 TCCTCAAATAATATTGCAAGATAAGGC 58.204 33.333 7.05 0.00 0.00 4.35
5581 7784 5.886960 AGTGCATCCAGTCAACTAAAATC 57.113 39.130 0.00 0.00 0.00 2.17
5597 7801 3.679389 CAGGGAACTCACTTAAGTGCAT 58.321 45.455 27.49 16.30 45.25 3.96
5737 7945 3.510388 TGAATGCTCGTTCTCTTCGAT 57.490 42.857 3.81 0.00 36.73 3.59
5762 7972 5.241285 TCAAATTGAGCATGTAGAGTTGCAA 59.759 36.000 0.00 0.00 41.35 4.08
5764 7974 5.300969 TCAAATTGAGCATGTAGAGTTGC 57.699 39.130 0.00 0.00 39.17 4.17
5779 7990 6.750501 CAGGTGCTATCAAGTCAATCAAATTG 59.249 38.462 0.00 0.00 41.57 2.32
5804 8015 7.509546 TCATTCCTCCCAATAACTCTATCAAC 58.490 38.462 0.00 0.00 0.00 3.18
5819 8030 9.354673 TGATCACTTTAAATATTCATTCCTCCC 57.645 33.333 0.00 0.00 0.00 4.30
5845 8056 7.607250 TCGTGAATAAATTTTGGCATAACCTT 58.393 30.769 0.00 0.00 40.22 3.50
5873 8084 5.332743 AGGGCTGAAGTTCCATGATTTTAA 58.667 37.500 0.00 0.00 0.00 1.52
5886 8097 1.692519 ACGTGAAACTAGGGCTGAAGT 59.307 47.619 0.00 0.00 31.75 3.01
5967 8183 4.759782 AGAAGGTCGATCATTTACCACAG 58.240 43.478 0.00 0.00 35.64 3.66
6025 8241 3.384668 TGTCTCTTTCGAGCTCAACAAG 58.615 45.455 15.40 11.81 37.19 3.16
6055 8275 6.349033 GGTTTAATTTTGTGCACTACGGATCT 60.349 38.462 19.41 0.00 0.00 2.75
6061 8281 7.307101 CCATTGTGGTTTAATTTTGTGCACTAC 60.307 37.037 19.41 3.38 31.35 2.73
6091 8312 6.041523 TGCCCAAATTTACTATAGCCAATTCC 59.958 38.462 0.00 0.00 0.00 3.01
6092 8313 7.049799 TGCCCAAATTTACTATAGCCAATTC 57.950 36.000 0.00 0.00 0.00 2.17
6132 8353 8.934023 ACCATTATCTTTTGGAACTTCAACTA 57.066 30.769 0.00 0.00 36.79 2.24
6148 8370 5.352569 CGAGCACTTCTTTCAACCATTATCT 59.647 40.000 0.00 0.00 0.00 1.98
6171 8393 1.089920 CCTCCTTGTCATGGCTTTCG 58.910 55.000 0.00 0.00 0.00 3.46
6220 8442 4.473444 TGGGAAACAAAGAGAGCAAAGAT 58.527 39.130 0.00 0.00 0.00 2.40
6252 8474 5.416952 ACCCAACATTTTTCAACAAATGCAA 59.583 32.000 6.14 0.00 44.76 4.08
6266 8490 5.963253 TGGATGGATATTCAACCCAACATTT 59.037 36.000 7.80 0.00 33.15 2.32
6267 8494 5.527385 TGGATGGATATTCAACCCAACATT 58.473 37.500 7.80 0.00 33.15 2.71
6269 8496 4.599720 TGGATGGATATTCAACCCAACA 57.400 40.909 7.80 0.00 33.15 3.33
6273 8503 6.129179 TCTTTCTTGGATGGATATTCAACCC 58.871 40.000 7.80 3.67 28.80 4.11
6274 8504 7.645058 TTCTTTCTTGGATGGATATTCAACC 57.355 36.000 3.27 3.27 28.80 3.77
6301 8532 1.416401 AGTGTGGAGGAAAGCGAAAGA 59.584 47.619 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.