Multiple sequence alignment - TraesCS6B01G308100

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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 TraesCS6B01G308100 chr6B 100.000 8668 0 0 1 8668 552232998 552241665 0.000000e+00 16007.0
1 TraesCS6B01G308100 chr6D 96.945 4223 94 18 713 4915 366527891 366532098 0.000000e+00 7051.0
2 TraesCS6B01G308100 chr6D 93.832 3259 116 28 5437 8668 366532739 366535939 0.000000e+00 4826.0
3 TraesCS6B01G308100 chr6D 93.587 421 13 4 4993 5408 366532097 366532508 4.450000e-172 616.0
4 TraesCS6B01G308100 chr6D 91.071 448 38 2 1 446 445783935 445783488 9.630000e-169 604.0
5 TraesCS6B01G308100 chr6D 90.545 275 14 4 445 711 445782894 445782624 3.850000e-93 353.0
6 TraesCS6B01G308100 chr6A 96.602 4238 105 20 711 4915 507082134 507086365 0.000000e+00 6992.0
7 TraesCS6B01G308100 chr6A 94.888 3306 111 31 4993 8271 507086364 507089638 0.000000e+00 5116.0
8 TraesCS6B01G308100 chr6A 85.676 377 32 5 8308 8668 507089642 507090012 2.280000e-100 377.0
9 TraesCS6B01G308100 chr6A 89.873 79 4 1 4916 4990 338525499 338525577 1.990000e-16 99.0
10 TraesCS6B01G308100 chr1B 96.770 712 19 2 1 711 216096872 216097580 0.000000e+00 1184.0
11 TraesCS6B01G308100 chr3B 96.348 712 22 2 1 711 156872164 156872872 0.000000e+00 1168.0
12 TraesCS6B01G308100 chr3B 100.000 31 0 0 681 711 130631334 130631364 3.380000e-04 58.4
13 TraesCS6B01G308100 chr2B 95.652 713 27 2 2 713 195243289 195242580 0.000000e+00 1142.0
14 TraesCS6B01G308100 chr1D 91.518 448 36 2 1 446 256208814 256208367 4.450000e-172 616.0
15 TraesCS6B01G308100 chr1D 91.236 445 37 2 1 443 395979654 395980098 9.630000e-169 604.0
16 TraesCS6B01G308100 chr1D 89.818 275 15 4 445 711 256207773 256207504 3.000000e-89 340.0
17 TraesCS6B01G308100 chr1D 89.455 275 16 4 445 711 395980694 395980963 1.390000e-87 335.0
18 TraesCS6B01G308100 chr1A 91.441 444 37 1 1 443 406698466 406698909 7.440000e-170 608.0
19 TraesCS6B01G308100 chr1A 89.121 239 21 4 445 682 406699505 406699739 8.510000e-75 292.0
20 TraesCS6B01G308100 chr1A 90.244 82 4 1 4916 4993 238146399 238146318 4.280000e-18 104.0
21 TraesCS6B01G308100 chr1A 90.244 82 4 1 4916 4993 334070679 334070598 4.280000e-18 104.0
22 TraesCS6B01G308100 chr4D 90.848 448 39 2 1 446 49652753 49652306 4.480000e-167 599.0
23 TraesCS6B01G308100 chr4D 89.781 274 15 4 445 710 49651712 49651444 1.080000e-88 339.0
24 TraesCS6B01G308100 chr4D 91.139 79 3 1 4916 4990 123377650 123377728 4.280000e-18 104.0
25 TraesCS6B01G308100 chr4D 91.139 79 3 1 4916 4990 123588437 123588515 4.280000e-18 104.0
26 TraesCS6B01G308100 chr7A 89.647 425 41 3 21 443 101454828 101455251 9.900000e-149 538.0
27 TraesCS6B01G308100 chr2A 89.892 277 16 4 445 713 500950379 500950107 6.440000e-91 346.0
28 TraesCS6B01G308100 chr5D 87.770 278 19 6 445 714 83765357 83765087 2.350000e-80 311.0
29 TraesCS6B01G308100 chrUn 90.244 82 4 1 4916 4993 182471131 182471050 4.280000e-18 104.0
30 TraesCS6B01G308100 chrUn 90.244 82 4 1 4916 4993 446906753 446906672 4.280000e-18 104.0
31 TraesCS6B01G308100 chr7D 90.244 82 4 2 4916 4993 307055062 307054981 4.280000e-18 104.0
32 TraesCS6B01G308100 chr7D 89.873 79 4 1 4916 4990 307004791 307004869 1.990000e-16 99.0
33 TraesCS6B01G308100 chr2D 82.979 94 14 2 2626 2717 111995786 111995693 5.580000e-12 84.2
34 TraesCS6B01G308100 chr3D 94.872 39 1 1 678 715 489397905 489397943 9.400000e-05 60.2


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 TraesCS6B01G308100 chr6B 552232998 552241665 8667 False 16007.000000 16007 100.000000 1 8668 1 chr6B.!!$F1 8667
1 TraesCS6B01G308100 chr6D 366527891 366535939 8048 False 4164.333333 7051 94.788000 713 8668 3 chr6D.!!$F1 7955
2 TraesCS6B01G308100 chr6D 445782624 445783935 1311 True 478.500000 604 90.808000 1 711 2 chr6D.!!$R1 710
3 TraesCS6B01G308100 chr6A 507082134 507090012 7878 False 4161.666667 6992 92.388667 711 8668 3 chr6A.!!$F2 7957
4 TraesCS6B01G308100 chr1B 216096872 216097580 708 False 1184.000000 1184 96.770000 1 711 1 chr1B.!!$F1 710
5 TraesCS6B01G308100 chr3B 156872164 156872872 708 False 1168.000000 1168 96.348000 1 711 1 chr3B.!!$F2 710
6 TraesCS6B01G308100 chr2B 195242580 195243289 709 True 1142.000000 1142 95.652000 2 713 1 chr2B.!!$R1 711
7 TraesCS6B01G308100 chr1D 256207504 256208814 1310 True 478.000000 616 90.668000 1 711 2 chr1D.!!$R1 710
8 TraesCS6B01G308100 chr1D 395979654 395980963 1309 False 469.500000 604 90.345500 1 711 2 chr1D.!!$F1 710
9 TraesCS6B01G308100 chr1A 406698466 406699739 1273 False 450.000000 608 90.281000 1 682 2 chr1A.!!$F1 681
10 TraesCS6B01G308100 chr4D 49651444 49652753 1309 True 469.000000 599 90.314500 1 710 2 chr4D.!!$R1 709

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
274 277 0.524862 GAGACGTCGCTTCAGGGTAA 59.475 55.000 12.41 0.0 0.00 2.85 F
880 1504 2.127758 CGAACGCACGGAACAAGC 60.128 61.111 0.00 0.0 0.00 4.01 F
881 1505 2.251371 GAACGCACGGAACAAGCC 59.749 61.111 0.00 0.0 0.00 4.35 F
2357 2988 0.313672 GTCCTGCAATCAAACCGCAA 59.686 50.000 0.00 0.0 34.75 4.85 F
2930 3568 0.393132 TTTTGCGTGAGGTGTGACCA 60.393 50.000 0.00 0.0 41.95 4.02 F
3188 3838 1.129058 AACACTTCGTTCCACCCTCT 58.871 50.000 0.00 0.0 29.27 3.69 F
3798 4449 1.629043 TAGAGTGCCCTTCGTCAAGT 58.371 50.000 0.00 0.0 0.00 3.16 F
5246 5897 1.730064 GACTAATTCGCGGTCAAGCAA 59.270 47.619 6.13 0.0 36.85 3.91 F
5521 6383 0.984230 CCTCCCACCACTAAGCTTCA 59.016 55.000 0.00 0.0 0.00 3.02 F
5526 6388 1.073923 CCACCACTAAGCTTCACCCTT 59.926 52.381 0.00 0.0 0.00 3.95 F
5753 6617 1.173043 AGGAGAGAGAAGCACGTGAG 58.827 55.000 22.23 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1465 2095 0.930726 ACTGTTCCAAGGGGTCCAAA 59.069 50.000 0.00 0.00 34.93 3.28 R
1818 2448 1.196766 TCACCCAGCTCATCTGCAGT 61.197 55.000 14.67 0.00 41.50 4.40 R
2514 3145 1.276622 AGCCTGTCTCGGTTGGTTAT 58.723 50.000 0.00 0.00 0.00 1.89 R
3583 4234 0.250124 TGTCAGCAGTACCAAACCGG 60.250 55.000 0.00 0.00 42.50 5.28 R
4735 5386 1.837439 AGAATGGACGACTTGGCCATA 59.163 47.619 6.09 0.00 41.36 2.74 R
5014 5665 0.465705 ATCGGTGCATCCAATCTCGT 59.534 50.000 0.00 0.00 35.57 4.18 R
5278 5929 0.735471 CGCGAGAGATGGAGAAGACA 59.265 55.000 0.00 0.00 0.00 3.41 R
6707 7583 1.133181 TGCAGGACCAGGAATCACCA 61.133 55.000 0.00 0.00 42.04 4.17 R
7076 7952 1.202758 AGTCCGCTGATTTGTTCCACA 60.203 47.619 0.00 0.00 0.00 4.17 R
7481 8357 1.497991 GCACGAGCTTGTGACTAACA 58.502 50.000 33.87 0.00 42.55 2.41 R
7736 8612 0.039165 GGCTTTTCTTTCCAGCGGTG 60.039 55.000 7.86 7.86 34.09 4.94 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
85 86 1.154205 GCTCGTTGTGTGCAGTGACT 61.154 55.000 0.00 0.00 37.06 3.41
236 239 4.322801 CCCGTACTTGAGGTCTGAATTCTT 60.323 45.833 7.05 0.00 0.00 2.52
243 246 3.071457 TGAGGTCTGAATTCTTGTCTGCA 59.929 43.478 7.05 0.00 0.00 4.41
274 277 0.524862 GAGACGTCGCTTCAGGGTAA 59.475 55.000 12.41 0.00 0.00 2.85
584 1182 3.371917 CCTGCAGGGTGAATATGGAGAAA 60.372 47.826 26.14 0.00 34.65 2.52
652 1254 9.726438 ATGTACTTGCTCTTACTGTAATTCTTT 57.274 29.630 0.00 0.00 0.00 2.52
713 1331 2.799917 GCACGGGCATCTTACTAGTCTG 60.800 54.545 3.77 0.00 40.72 3.51
714 1332 2.688446 CACGGGCATCTTACTAGTCTGA 59.312 50.000 0.00 0.00 0.00 3.27
715 1333 3.130516 CACGGGCATCTTACTAGTCTGAA 59.869 47.826 0.00 0.00 0.00 3.02
716 1334 3.381908 ACGGGCATCTTACTAGTCTGAAG 59.618 47.826 0.00 0.00 0.00 3.02
717 1335 3.243569 CGGGCATCTTACTAGTCTGAAGG 60.244 52.174 0.00 0.00 0.00 3.46
718 1336 3.961408 GGGCATCTTACTAGTCTGAAGGA 59.039 47.826 0.00 0.00 0.00 3.36
719 1337 4.038642 GGGCATCTTACTAGTCTGAAGGAG 59.961 50.000 0.00 0.00 0.00 3.69
720 1338 4.890581 GGCATCTTACTAGTCTGAAGGAGA 59.109 45.833 0.00 0.00 0.00 3.71
721 1339 5.361285 GGCATCTTACTAGTCTGAAGGAGAA 59.639 44.000 0.00 0.00 30.26 2.87
722 1340 6.127310 GGCATCTTACTAGTCTGAAGGAGAAA 60.127 42.308 0.00 0.00 30.26 2.52
723 1341 6.754675 GCATCTTACTAGTCTGAAGGAGAAAC 59.245 42.308 0.00 0.00 30.26 2.78
791 1413 2.350522 AGCACTCAAACCTCGCTATTG 58.649 47.619 0.00 0.00 0.00 1.90
880 1504 2.127758 CGAACGCACGGAACAAGC 60.128 61.111 0.00 0.00 0.00 4.01
881 1505 2.251371 GAACGCACGGAACAAGCC 59.749 61.111 0.00 0.00 0.00 4.35
882 1506 2.515057 AACGCACGGAACAAGCCA 60.515 55.556 0.00 0.00 0.00 4.75
1465 2095 4.540099 TCATCTGTGGGGATTAGGAACTTT 59.460 41.667 0.00 0.00 41.75 2.66
1474 2104 3.767673 GGATTAGGAACTTTTTGGACCCC 59.232 47.826 0.00 0.00 41.75 4.95
1501 2131 5.105473 GGAACAGTAGCAAGTGTAGTCCATA 60.105 44.000 0.00 0.00 38.36 2.74
1567 2197 6.726764 AGGTCTATAATCCAGGGAAGACATAC 59.273 42.308 15.93 3.65 36.03 2.39
1739 2369 6.968263 CTCACAAAGAGGATCCTATACTCA 57.032 41.667 16.16 0.00 42.97 3.41
1751 2381 8.317679 AGGATCCTATACTCACTTGATATTTGC 58.682 37.037 14.27 0.00 0.00 3.68
1789 2419 4.858850 TCAGTGACATGCCAATTAGGAAT 58.141 39.130 0.00 0.00 41.22 3.01
1949 2579 4.873259 GCATCTCTCCTCAAGTTAGTTTCC 59.127 45.833 0.00 0.00 0.00 3.13
1970 2600 4.122776 CCCAGACATGTTATTTCTCCTCG 58.877 47.826 0.00 0.00 0.00 4.63
1992 2622 4.034510 CGAGTTGAGAGTGAAAAAGCTTGT 59.965 41.667 0.00 0.00 0.00 3.16
2111 2741 5.057149 GCTGTGTTCCACATACTATAAGGG 58.943 45.833 0.00 0.00 43.71 3.95
2215 2845 2.709934 AGGATCCCTGTCTCATCCATTG 59.290 50.000 8.55 0.00 38.95 2.82
2268 2899 8.866093 ACCATTGTAGGCATAGTTTTAAAAACT 58.134 29.630 1.31 0.00 0.00 2.66
2357 2988 0.313672 GTCCTGCAATCAAACCGCAA 59.686 50.000 0.00 0.00 34.75 4.85
2410 3041 1.381165 CCGGGGAATAAAACCAGGCG 61.381 60.000 0.00 0.00 35.35 5.52
2514 3145 4.383118 GCTGAAGTACTAATCTCAGCCCAA 60.383 45.833 26.53 0.00 43.12 4.12
2684 3317 1.374758 CCTGAACCGCCAGACTCAC 60.375 63.158 0.00 0.00 36.29 3.51
2748 3385 7.939588 AGAAGTACTGTAAAGAAAGCCTTTCAT 59.060 33.333 18.81 4.46 43.61 2.57
2764 3401 5.417580 GCCTTTCATTTACACCCACTTGATA 59.582 40.000 0.00 0.00 0.00 2.15
2800 3438 8.237811 ACATGTGAATGACTTTTCTACCTTTT 57.762 30.769 0.00 0.00 0.00 2.27
2801 3439 8.137437 ACATGTGAATGACTTTTCTACCTTTTG 58.863 33.333 0.00 0.00 0.00 2.44
2864 3502 3.006940 TGCTGTTTATGCGGAGTTTAGG 58.993 45.455 0.00 0.00 0.00 2.69
2930 3568 0.393132 TTTTGCGTGAGGTGTGACCA 60.393 50.000 0.00 0.00 41.95 4.02
2946 3584 2.290260 TGACCAACAGTCCTATGCCTTG 60.290 50.000 0.00 0.00 45.68 3.61
3058 3697 4.082571 AGAGAAGCACCATTGTGTAAATGC 60.083 41.667 0.00 0.00 44.65 3.56
3167 3817 4.452455 AGCATTCACGAAAAGTAGTCCAAG 59.548 41.667 0.00 0.00 0.00 3.61
3188 3838 1.129058 AACACTTCGTTCCACCCTCT 58.871 50.000 0.00 0.00 29.27 3.69
3256 3906 2.018542 TCTGCCACCGTTGCTTATAC 57.981 50.000 0.00 0.00 0.00 1.47
3400 4051 7.060600 TCACTTTAAGATATCAACGTTGCTG 57.939 36.000 23.47 0.66 0.00 4.41
3583 4234 4.351111 ACTGTTCCAGATACAATATCCCCC 59.649 45.833 0.00 0.00 35.18 5.40
3798 4449 1.629043 TAGAGTGCCCTTCGTCAAGT 58.371 50.000 0.00 0.00 0.00 3.16
3820 4471 2.548480 GCAAATCTTACCGGTGATAGCC 59.452 50.000 19.93 0.53 0.00 3.93
3834 4485 4.381411 GTGATAGCCAAATACCTGACTCC 58.619 47.826 0.00 0.00 0.00 3.85
4047 4698 5.940470 AGCTGAAAGGTTTCAAGATTCGTAT 59.060 36.000 6.61 0.00 46.63 3.06
4196 4847 3.430333 AAAACTTTTTGATGGCGTCGT 57.570 38.095 1.67 0.00 0.00 4.34
4429 5080 4.452455 AGGAAATACAGCAAGAAGTTGTCG 59.548 41.667 0.00 0.00 41.10 4.35
4464 5115 7.881775 AGGAAAACATACATCCCAAGTTATC 57.118 36.000 0.00 0.00 33.55 1.75
4506 5157 4.859798 CAGTTGACGGAAGAATCTACTCAC 59.140 45.833 0.00 0.00 30.00 3.51
4735 5386 7.962964 TCTTCTACGTTGAATTCAGATGTTT 57.037 32.000 12.74 0.00 0.00 2.83
4746 5397 5.841957 ATTCAGATGTTTATGGCCAAGTC 57.158 39.130 10.96 1.11 0.00 3.01
4870 5521 8.537728 TCATTAAATTTTCATCCATGCTAGGT 57.462 30.769 0.00 0.00 0.00 3.08
4913 5564 7.513091 TGACAGAGACCAGAGTACTATCCTATA 59.487 40.741 0.00 0.00 0.00 1.31
4914 5565 8.457585 ACAGAGACCAGAGTACTATCCTATAT 57.542 38.462 0.00 0.00 0.00 0.86
4915 5566 8.325787 ACAGAGACCAGAGTACTATCCTATATG 58.674 40.741 0.00 0.00 0.00 1.78
4916 5567 8.544622 CAGAGACCAGAGTACTATCCTATATGA 58.455 40.741 0.00 0.00 0.00 2.15
4917 5568 9.118367 AGAGACCAGAGTACTATCCTATATGAA 57.882 37.037 0.00 0.00 0.00 2.57
4918 5569 9.914834 GAGACCAGAGTACTATCCTATATGAAT 57.085 37.037 0.00 0.00 0.00 2.57
4932 5583 7.999679 TCCTATATGAATTTTGCTTCAGTTGG 58.000 34.615 0.00 0.00 38.47 3.77
4933 5584 7.833682 TCCTATATGAATTTTGCTTCAGTTGGA 59.166 33.333 0.00 0.00 38.47 3.53
4934 5585 7.917505 CCTATATGAATTTTGCTTCAGTTGGAC 59.082 37.037 0.00 0.00 38.47 4.02
4935 5586 5.796424 ATGAATTTTGCTTCAGTTGGACT 57.204 34.783 0.00 0.00 38.47 3.85
4936 5587 5.596836 TGAATTTTGCTTCAGTTGGACTT 57.403 34.783 0.00 0.00 31.65 3.01
4937 5588 5.591099 TGAATTTTGCTTCAGTTGGACTTC 58.409 37.500 0.00 0.00 31.65 3.01
4938 5589 3.691049 TTTTGCTTCAGTTGGACTTCG 57.309 42.857 0.00 0.00 0.00 3.79
4939 5590 2.613026 TTGCTTCAGTTGGACTTCGA 57.387 45.000 0.00 0.00 0.00 3.71
4940 5591 2.839486 TGCTTCAGTTGGACTTCGAT 57.161 45.000 0.00 0.00 0.00 3.59
4941 5592 3.126001 TGCTTCAGTTGGACTTCGATT 57.874 42.857 0.00 0.00 0.00 3.34
4942 5593 3.476552 TGCTTCAGTTGGACTTCGATTT 58.523 40.909 0.00 0.00 0.00 2.17
4943 5594 3.882888 TGCTTCAGTTGGACTTCGATTTT 59.117 39.130 0.00 0.00 0.00 1.82
4944 5595 5.060506 TGCTTCAGTTGGACTTCGATTTTA 58.939 37.500 0.00 0.00 0.00 1.52
4945 5596 5.705441 TGCTTCAGTTGGACTTCGATTTTAT 59.295 36.000 0.00 0.00 0.00 1.40
4946 5597 6.024049 GCTTCAGTTGGACTTCGATTTTATG 58.976 40.000 0.00 0.00 0.00 1.90
4947 5598 6.128282 GCTTCAGTTGGACTTCGATTTTATGA 60.128 38.462 0.00 0.00 0.00 2.15
4948 5599 7.414540 GCTTCAGTTGGACTTCGATTTTATGAT 60.415 37.037 0.00 0.00 0.00 2.45
4949 5600 9.098355 CTTCAGTTGGACTTCGATTTTATGATA 57.902 33.333 0.00 0.00 0.00 2.15
4950 5601 8.648557 TCAGTTGGACTTCGATTTTATGATAG 57.351 34.615 0.00 0.00 0.00 2.08
4951 5602 8.474831 TCAGTTGGACTTCGATTTTATGATAGA 58.525 33.333 0.00 0.00 0.00 1.98
4952 5603 8.759641 CAGTTGGACTTCGATTTTATGATAGAG 58.240 37.037 0.00 0.00 0.00 2.43
4953 5604 8.478877 AGTTGGACTTCGATTTTATGATAGAGT 58.521 33.333 0.00 0.00 0.00 3.24
4954 5605 9.099454 GTTGGACTTCGATTTTATGATAGAGTT 57.901 33.333 0.00 0.00 0.00 3.01
4955 5606 8.873215 TGGACTTCGATTTTATGATAGAGTTC 57.127 34.615 0.00 0.00 0.00 3.01
4956 5607 8.474831 TGGACTTCGATTTTATGATAGAGTTCA 58.525 33.333 0.00 0.00 0.00 3.18
4957 5608 8.973378 GGACTTCGATTTTATGATAGAGTTCAG 58.027 37.037 0.00 0.00 0.00 3.02
4958 5609 9.522804 GACTTCGATTTTATGATAGAGTTCAGT 57.477 33.333 0.00 0.00 0.00 3.41
4959 5610 9.307121 ACTTCGATTTTATGATAGAGTTCAGTG 57.693 33.333 0.00 0.00 0.00 3.66
4960 5611 8.648557 TTCGATTTTATGATAGAGTTCAGTGG 57.351 34.615 0.00 0.00 0.00 4.00
4961 5612 6.701841 TCGATTTTATGATAGAGTTCAGTGGC 59.298 38.462 0.00 0.00 0.00 5.01
4962 5613 6.073548 CGATTTTATGATAGAGTTCAGTGGCC 60.074 42.308 0.00 0.00 0.00 5.36
4963 5614 5.957771 TTTATGATAGAGTTCAGTGGCCT 57.042 39.130 3.32 0.00 0.00 5.19
4964 5615 5.957771 TTATGATAGAGTTCAGTGGCCTT 57.042 39.130 3.32 0.00 0.00 4.35
4965 5616 4.851639 ATGATAGAGTTCAGTGGCCTTT 57.148 40.909 3.32 0.00 0.00 3.11
4966 5617 4.207891 TGATAGAGTTCAGTGGCCTTTC 57.792 45.455 3.32 0.00 0.00 2.62
4967 5618 3.840666 TGATAGAGTTCAGTGGCCTTTCT 59.159 43.478 3.32 0.00 0.00 2.52
4968 5619 4.287067 TGATAGAGTTCAGTGGCCTTTCTT 59.713 41.667 3.32 0.00 0.00 2.52
4969 5620 2.856222 AGAGTTCAGTGGCCTTTCTTG 58.144 47.619 3.32 0.00 0.00 3.02
4970 5621 1.882623 GAGTTCAGTGGCCTTTCTTGG 59.117 52.381 3.32 0.00 0.00 3.61
4982 5633 2.424956 CCTTTCTTGGCAGAGGTAATGC 59.575 50.000 0.00 0.00 43.09 3.56
4983 5634 2.877097 TTCTTGGCAGAGGTAATGCA 57.123 45.000 0.00 0.00 45.68 3.96
4984 5635 3.370840 TTCTTGGCAGAGGTAATGCAT 57.629 42.857 0.00 0.00 45.68 3.96
4985 5636 4.502105 TTCTTGGCAGAGGTAATGCATA 57.498 40.909 0.00 0.00 45.68 3.14
4986 5637 4.077300 TCTTGGCAGAGGTAATGCATAG 57.923 45.455 0.00 0.00 45.68 2.23
4987 5638 2.936919 TGGCAGAGGTAATGCATAGG 57.063 50.000 0.00 0.00 45.68 2.57
4988 5639 2.407562 TGGCAGAGGTAATGCATAGGA 58.592 47.619 0.00 0.00 45.68 2.94
4989 5640 2.777114 TGGCAGAGGTAATGCATAGGAA 59.223 45.455 0.00 0.00 45.68 3.36
4990 5641 3.181451 TGGCAGAGGTAATGCATAGGAAG 60.181 47.826 0.00 0.00 45.68 3.46
4991 5642 3.071602 GGCAGAGGTAATGCATAGGAAGA 59.928 47.826 0.00 0.00 45.68 2.87
5059 5710 5.067674 CACCACATGAGTTGGAGAAGAAAAA 59.932 40.000 7.78 0.00 0.00 1.94
5069 5720 6.993308 AGTTGGAGAAGAAAAACCTAGAAGTC 59.007 38.462 0.00 0.00 0.00 3.01
5246 5897 1.730064 GACTAATTCGCGGTCAAGCAA 59.270 47.619 6.13 0.00 36.85 3.91
5278 5929 3.513119 TCAAGTCTGACAGCTGAGCTATT 59.487 43.478 23.35 0.00 36.40 1.73
5293 5944 5.207354 TGAGCTATTGTCTTCTCCATCTCT 58.793 41.667 0.00 0.00 0.00 3.10
5294 5945 5.301551 TGAGCTATTGTCTTCTCCATCTCTC 59.698 44.000 0.00 0.00 0.00 3.20
5311 5962 2.357517 CGCGGTTCTTCCACTGCT 60.358 61.111 0.00 0.00 45.56 4.24
5365 6016 3.399330 TCCATCACAGTTTTTCCTCGTC 58.601 45.455 0.00 0.00 0.00 4.20
5410 6066 3.181367 CAGTTGTCGCCTGCCATC 58.819 61.111 0.00 0.00 0.00 3.51
5450 6308 1.382629 GCCCCACATGTACCAACCT 59.617 57.895 0.00 0.00 0.00 3.50
5521 6383 0.984230 CCTCCCACCACTAAGCTTCA 59.016 55.000 0.00 0.00 0.00 3.02
5526 6388 1.073923 CCACCACTAAGCTTCACCCTT 59.926 52.381 0.00 0.00 0.00 3.95
5752 6616 1.621992 AAGGAGAGAGAAGCACGTGA 58.378 50.000 22.23 0.00 0.00 4.35
5753 6617 1.173043 AGGAGAGAGAAGCACGTGAG 58.827 55.000 22.23 0.00 0.00 3.51
5825 6689 3.388024 ACCGAGGATGTACAATGCATACT 59.612 43.478 0.00 0.00 40.01 2.12
5915 6779 7.979444 TGAGGAAACAAACTCTAACCATTAG 57.021 36.000 0.00 0.00 34.84 1.73
6130 7006 6.206438 GGAATATCAAGCTTTCTTCTCCATCC 59.794 42.308 0.00 0.00 0.00 3.51
6524 7400 7.765695 TTCTGGTGAGCTGAAAATTAATCTT 57.234 32.000 0.00 0.00 0.00 2.40
6707 7583 1.414919 TCAGTTCCCACGTTAGTTGCT 59.585 47.619 0.00 0.00 0.00 3.91
6920 7796 2.280628 CGAGAACCCTTGTTGCTATCC 58.719 52.381 0.00 0.00 33.97 2.59
6942 7818 1.410517 GGATCAGATCCTCAAGCGACA 59.589 52.381 21.00 0.00 46.19 4.35
7100 7976 2.540101 GGAACAAATCAGCGGACTATCG 59.460 50.000 0.00 0.00 0.00 2.92
7175 8051 1.877672 ATCCAAGGGCCAGCAATCCA 61.878 55.000 6.18 0.00 0.00 3.41
7481 8357 0.036765 TGCCGAAAACCGAGCATACT 60.037 50.000 0.00 0.00 41.76 2.12
7583 8459 1.003580 GCATTGACTCCTCCAACCTCA 59.996 52.381 0.00 0.00 0.00 3.86
7601 8477 0.518636 CAGCCACATCCGTCTTTGTG 59.481 55.000 0.00 0.00 42.25 3.33
7681 8557 3.614616 GTGAGCTAGATTTTCACAGACCG 59.385 47.826 0.00 0.00 40.62 4.79
7687 8563 0.958822 ATTTTCACAGACCGGGCAAC 59.041 50.000 11.69 0.00 0.00 4.17
7688 8564 0.106918 TTTTCACAGACCGGGCAACT 60.107 50.000 11.69 0.00 0.00 3.16
7694 8570 1.534235 AGACCGGGCAACTCACTCT 60.534 57.895 11.69 0.00 0.00 3.24
7699 8575 2.835764 ACCGGGCAACTCACTCTTTATA 59.164 45.455 6.32 0.00 0.00 0.98
7707 8583 5.806734 GCAACTCACTCTTTATACCCCCTTT 60.807 44.000 0.00 0.00 0.00 3.11
7708 8584 5.695424 ACTCACTCTTTATACCCCCTTTC 57.305 43.478 0.00 0.00 0.00 2.62
7709 8585 5.098663 ACTCACTCTTTATACCCCCTTTCA 58.901 41.667 0.00 0.00 0.00 2.69
7710 8586 5.550403 ACTCACTCTTTATACCCCCTTTCAA 59.450 40.000 0.00 0.00 0.00 2.69
7711 8587 6.045106 ACTCACTCTTTATACCCCCTTTCAAA 59.955 38.462 0.00 0.00 0.00 2.69
7712 8588 6.243148 TCACTCTTTATACCCCCTTTCAAAC 58.757 40.000 0.00 0.00 0.00 2.93
7714 8590 4.591929 TCTTTATACCCCCTTTCAAACGG 58.408 43.478 0.00 0.00 0.00 4.44
7715 8591 3.369242 TTATACCCCCTTTCAAACGGG 57.631 47.619 0.00 0.00 41.71 5.28
7716 8592 0.323999 ATACCCCCTTTCAAACGGGC 60.324 55.000 0.00 0.00 39.34 6.13
7717 8593 1.428718 TACCCCCTTTCAAACGGGCT 61.429 55.000 0.00 0.00 39.34 5.19
7718 8594 2.275380 CCCCCTTTCAAACGGGCTG 61.275 63.158 0.00 0.00 39.22 4.85
7719 8595 1.530655 CCCCTTTCAAACGGGCTGT 60.531 57.895 0.00 0.00 39.22 4.40
7721 8597 1.659794 CCTTTCAAACGGGCTGTGG 59.340 57.895 0.00 0.00 0.00 4.17
7722 8598 1.106944 CCTTTCAAACGGGCTGTGGT 61.107 55.000 0.00 0.00 0.00 4.16
7724 8600 2.010582 TTTCAAACGGGCTGTGGTGC 62.011 55.000 0.00 0.00 0.00 5.01
7725 8601 2.902423 TTCAAACGGGCTGTGGTGCT 62.902 55.000 0.00 0.00 0.00 4.40
7727 8603 3.414136 AAACGGGCTGTGGTGCTCA 62.414 57.895 0.00 0.00 31.82 4.26
7728 8604 2.902423 AAACGGGCTGTGGTGCTCAA 62.902 55.000 0.00 0.00 31.82 3.02
7729 8605 3.052082 CGGGCTGTGGTGCTCAAG 61.052 66.667 0.00 0.00 31.82 3.02
7730 8606 3.368571 GGGCTGTGGTGCTCAAGC 61.369 66.667 0.00 0.00 42.50 4.01
7750 8626 1.048601 AGAGTCACCGCTGGAAAGAA 58.951 50.000 1.50 0.00 0.00 2.52
7768 8644 4.762289 AGAAAAGCCTATCGGTGATTCT 57.238 40.909 0.00 0.00 0.00 2.40
7770 8646 2.246719 AAGCCTATCGGTGATTCTGC 57.753 50.000 0.00 0.00 0.00 4.26
7772 8648 0.603975 GCCTATCGGTGATTCTGCCC 60.604 60.000 0.00 0.00 0.00 5.36
7800 8676 0.466007 TGCTGAACAGGCTTGAAGCA 60.466 50.000 19.89 16.94 44.75 3.91
7804 8680 3.801293 GCTGAACAGGCTTGAAGCAAAAT 60.801 43.478 19.89 1.88 44.75 1.82
7805 8681 3.719924 TGAACAGGCTTGAAGCAAAATG 58.280 40.909 19.89 13.35 44.75 2.32
7806 8682 2.159327 ACAGGCTTGAAGCAAAATGC 57.841 45.000 19.89 0.00 44.75 3.56
7817 8693 2.405892 GCAAAATGCTGTTGTCGAGT 57.594 45.000 0.00 0.00 40.96 4.18
7905 8783 4.568072 AGACCACATATGCCTTGTAACA 57.432 40.909 1.58 0.00 0.00 2.41
8026 8904 3.589288 GGGAATAAGTGAGCCCCATATCT 59.411 47.826 0.00 0.00 37.04 1.98
8027 8905 4.783227 GGGAATAAGTGAGCCCCATATCTA 59.217 45.833 0.00 0.00 37.04 1.98
8028 8906 5.430089 GGGAATAAGTGAGCCCCATATCTAT 59.570 44.000 0.00 0.00 37.04 1.98
8029 8907 6.408662 GGGAATAAGTGAGCCCCATATCTATC 60.409 46.154 0.00 0.00 37.04 2.08
8076 8954 3.668447 TCTTCAGGTTCATTGTCTCTGC 58.332 45.455 0.00 0.00 0.00 4.26
8137 9020 6.017400 ACAAGCTTTCATATCCAGTGTTTG 57.983 37.500 0.00 0.00 0.00 2.93
8193 9076 7.348080 AGGCTTTTTACTCCCTATATTTTGC 57.652 36.000 0.00 0.00 0.00 3.68
8213 9096 2.168313 GCCCCCATTTGTAATGGTGAAG 59.832 50.000 15.28 2.63 37.48 3.02
8248 9131 8.655651 TTCCAGTAATTTTTACTGCCTTTTTG 57.344 30.769 17.85 6.58 42.53 2.44
8259 9142 0.249868 GCCTTTTTGACCCCAGTTGC 60.250 55.000 0.00 0.00 0.00 4.17
8261 9144 1.069049 CCTTTTTGACCCCAGTTGCAG 59.931 52.381 0.00 0.00 0.00 4.41
8284 9167 6.196538 CAGTGCAAGATTTTGATCGATCAATG 59.803 38.462 34.66 29.04 45.30 2.82
8361 9244 3.704566 TGCTACTAGTAATCACCACCTGG 59.295 47.826 3.76 0.00 42.17 4.45
8512 9405 2.802816 CTCTCTCGCCCATAAAAATCCG 59.197 50.000 0.00 0.00 0.00 4.18
8550 9443 1.098050 AATCCAAACTCGCTGCCATC 58.902 50.000 0.00 0.00 0.00 3.51
8563 9456 0.464373 TGCCATCTTCCCTGATTCGC 60.464 55.000 0.00 0.00 0.00 4.70
8564 9457 0.179034 GCCATCTTCCCTGATTCGCT 60.179 55.000 0.00 0.00 0.00 4.93
8565 9458 1.876322 CCATCTTCCCTGATTCGCTC 58.124 55.000 0.00 0.00 0.00 5.03
8566 9459 1.495878 CATCTTCCCTGATTCGCTCG 58.504 55.000 0.00 0.00 0.00 5.03
8567 9460 0.249657 ATCTTCCCTGATTCGCTCGC 60.250 55.000 0.00 0.00 0.00 5.03
8635 9528 1.226916 ACGGCGACAAACACGTACA 60.227 52.632 16.62 0.00 37.85 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
243 246 2.345244 CGTCTCTGCCTTGCCACT 59.655 61.111 0.00 0.00 0.00 4.00
249 252 1.080434 GAAGCGACGTCTCTGCCTT 60.080 57.895 14.70 7.83 0.00 4.35
531 1129 9.099454 CTTCTTGTACTTTATTATTCCTCGCTT 57.901 33.333 0.00 0.00 0.00 4.68
584 1182 5.659440 AATGTACCGAGCCAAATGATTTT 57.341 34.783 0.00 0.00 0.00 1.82
667 1269 2.228822 GCAACGGAAGACCACATGAAAT 59.771 45.455 0.00 0.00 35.59 2.17
713 1331 1.531578 GGCACGTTCTGTTTCTCCTTC 59.468 52.381 0.00 0.00 0.00 3.46
714 1332 1.594331 GGCACGTTCTGTTTCTCCTT 58.406 50.000 0.00 0.00 0.00 3.36
715 1333 0.250338 GGGCACGTTCTGTTTCTCCT 60.250 55.000 0.00 0.00 0.00 3.69
716 1334 0.534203 TGGGCACGTTCTGTTTCTCC 60.534 55.000 0.00 0.00 0.00 3.71
717 1335 1.305201 TTGGGCACGTTCTGTTTCTC 58.695 50.000 0.00 0.00 0.00 2.87
718 1336 1.757682 TTTGGGCACGTTCTGTTTCT 58.242 45.000 0.00 0.00 0.00 2.52
719 1337 2.570442 TTTTGGGCACGTTCTGTTTC 57.430 45.000 0.00 0.00 0.00 2.78
720 1338 2.232696 AGTTTTTGGGCACGTTCTGTTT 59.767 40.909 0.00 0.00 0.00 2.83
721 1339 1.822371 AGTTTTTGGGCACGTTCTGTT 59.178 42.857 0.00 0.00 0.00 3.16
722 1340 1.134175 CAGTTTTTGGGCACGTTCTGT 59.866 47.619 0.00 0.00 0.00 3.41
723 1341 1.838913 CAGTTTTTGGGCACGTTCTG 58.161 50.000 0.00 0.00 0.00 3.02
791 1413 1.746991 GTCTGGCTTGGCTAGGTGC 60.747 63.158 3.28 0.00 37.73 5.01
878 1502 0.107312 GATCTGTGATGGCTGTGGCT 60.107 55.000 0.00 0.00 38.73 4.75
879 1503 1.099879 GGATCTGTGATGGCTGTGGC 61.100 60.000 0.00 0.00 37.82 5.01
880 1504 0.812811 CGGATCTGTGATGGCTGTGG 60.813 60.000 0.00 0.00 0.00 4.17
881 1505 0.176449 TCGGATCTGTGATGGCTGTG 59.824 55.000 0.42 0.00 0.00 3.66
882 1506 0.463204 CTCGGATCTGTGATGGCTGT 59.537 55.000 0.42 0.00 0.00 4.40
998 1622 1.075525 TCCGGGTAGTCCTCCATGG 60.076 63.158 4.97 4.97 37.10 3.66
1436 2066 4.884164 CCTAATCCCCACAGATGAAAAGAC 59.116 45.833 0.00 0.00 0.00 3.01
1465 2095 0.930726 ACTGTTCCAAGGGGTCCAAA 59.069 50.000 0.00 0.00 34.93 3.28
1474 2104 4.632153 ACTACACTTGCTACTGTTCCAAG 58.368 43.478 14.60 14.60 41.20 3.61
1567 2197 5.943416 TGTACAAGGATCACCACCAATTTAG 59.057 40.000 0.00 0.00 38.94 1.85
1789 2419 9.900710 ATAATTGTGTGTTTGCTTAAAATCGTA 57.099 25.926 0.00 0.00 0.00 3.43
1818 2448 1.196766 TCACCCAGCTCATCTGCAGT 61.197 55.000 14.67 0.00 41.50 4.40
1949 2579 5.011090 TCGAGGAGAAATAACATGTCTGG 57.989 43.478 0.00 0.00 0.00 3.86
1970 2600 5.491635 ACAAGCTTTTTCACTCTCAACTC 57.508 39.130 0.00 0.00 0.00 3.01
2111 2741 2.298610 CTTTTATCCTTCGCCCTTCCC 58.701 52.381 0.00 0.00 0.00 3.97
2215 2845 9.379791 ACTTGGAACACTTATTAATAGCACTAC 57.620 33.333 0.00 0.00 39.29 2.73
2357 2988 2.493278 CCATCTGGTTCAGCCGATTTTT 59.507 45.455 0.00 0.00 41.21 1.94
2410 3041 1.677633 CCCATCAACCGGTCCAACC 60.678 63.158 8.04 0.00 34.05 3.77
2493 3124 5.957771 ATTGGGCTGAGATTAGTACTTCA 57.042 39.130 0.00 0.00 0.00 3.02
2514 3145 1.276622 AGCCTGTCTCGGTTGGTTAT 58.723 50.000 0.00 0.00 0.00 1.89
2613 3244 3.205338 TCGATTGTCGGTTCGATAGGTA 58.795 45.455 0.00 0.00 40.88 3.08
2665 3298 1.533033 TGAGTCTGGCGGTTCAGGA 60.533 57.895 0.00 0.00 35.58 3.86
2684 3317 1.442769 CCAGACTGGTGATCAAACCG 58.557 55.000 13.84 0.00 43.73 4.44
2748 3385 5.163184 TGGTGAACTATCAAGTGGGTGTAAA 60.163 40.000 0.00 0.00 37.30 2.01
2827 3465 3.626028 CAGCAACCTGGTGTAAGAAAC 57.374 47.619 0.00 0.00 40.68 2.78
2864 3502 3.521796 GCTTCTGGCCAATCCCGC 61.522 66.667 7.01 1.28 34.27 6.13
2946 3584 5.665459 ACTGTTGACAAGGCTATATCAGTC 58.335 41.667 0.00 0.00 0.00 3.51
3024 3663 9.077885 ACAATGGTGCTTCTCTTAATTCTTTTA 57.922 29.630 0.00 0.00 0.00 1.52
3028 3667 6.506500 CACAATGGTGCTTCTCTTAATTCT 57.493 37.500 0.00 0.00 38.37 2.40
3167 3817 0.818040 AGGGTGGAACGAAGTGTTGC 60.818 55.000 0.00 0.00 45.00 4.17
3188 3838 9.420118 AGAAGGCAATGTATAAACATAAATGGA 57.580 29.630 0.00 0.00 45.79 3.41
3216 3866 7.274250 GGCAGATCAATCAAACTGTAACAAATC 59.726 37.037 0.00 0.00 33.57 2.17
3400 4051 1.372087 CGACCTTCCCAGCATGAAGC 61.372 60.000 0.00 0.00 39.69 3.86
3583 4234 0.250124 TGTCAGCAGTACCAAACCGG 60.250 55.000 0.00 0.00 42.50 5.28
3718 4369 4.279982 TGCCAGAAGGAAATGCATGATAA 58.720 39.130 0.00 0.00 36.89 1.75
3725 4376 2.159324 GCTAACTGCCAGAAGGAAATGC 60.159 50.000 0.00 0.00 36.89 3.56
3798 4449 3.202906 GCTATCACCGGTAAGATTTGCA 58.797 45.455 6.87 0.00 0.00 4.08
3820 4471 5.661458 AGACATTACGGAGTCAGGTATTTG 58.339 41.667 0.00 0.38 43.93 2.32
3834 4485 6.073765 GGCCAACATATACAGAAGACATTACG 60.074 42.308 0.00 0.00 0.00 3.18
4047 4698 7.543172 GCTTTTCTGAACAATGCAATTATCTCA 59.457 33.333 0.00 0.00 32.46 3.27
4464 5115 9.430838 GTCAACTGAAGATTAAATTCATCATCG 57.569 33.333 6.87 0.02 36.16 3.84
4485 5136 4.082136 AGGTGAGTAGATTCTTCCGTCAAC 60.082 45.833 0.00 0.00 0.00 3.18
4735 5386 1.837439 AGAATGGACGACTTGGCCATA 59.163 47.619 6.09 0.00 41.36 2.74
4746 5397 7.036220 ACAATGTAAGAGAAGTAGAATGGACG 58.964 38.462 0.00 0.00 0.00 4.79
4870 5521 8.668353 GTCTCTGTCAATTAACATCAAATGCTA 58.332 33.333 0.00 0.00 0.00 3.49
4889 5540 6.773583 ATAGGATAGTACTCTGGTCTCTGT 57.226 41.667 0.00 0.00 0.00 3.41
4913 5564 5.796424 AGTCCAACTGAAGCAAAATTCAT 57.204 34.783 0.00 0.00 38.47 2.57
4914 5565 5.591099 GAAGTCCAACTGAAGCAAAATTCA 58.409 37.500 0.00 0.00 37.60 2.57
4915 5566 4.676924 CGAAGTCCAACTGAAGCAAAATTC 59.323 41.667 0.00 0.00 0.00 2.17
4916 5567 4.338118 TCGAAGTCCAACTGAAGCAAAATT 59.662 37.500 0.00 0.00 0.00 1.82
4917 5568 3.882888 TCGAAGTCCAACTGAAGCAAAAT 59.117 39.130 0.00 0.00 0.00 1.82
4918 5569 3.275143 TCGAAGTCCAACTGAAGCAAAA 58.725 40.909 0.00 0.00 0.00 2.44
4919 5570 2.912771 TCGAAGTCCAACTGAAGCAAA 58.087 42.857 0.00 0.00 0.00 3.68
4920 5571 2.613026 TCGAAGTCCAACTGAAGCAA 57.387 45.000 0.00 0.00 0.00 3.91
4921 5572 2.839486 ATCGAAGTCCAACTGAAGCA 57.161 45.000 0.00 0.00 0.00 3.91
4922 5573 4.489679 AAAATCGAAGTCCAACTGAAGC 57.510 40.909 0.00 0.00 0.00 3.86
4923 5574 7.364522 TCATAAAATCGAAGTCCAACTGAAG 57.635 36.000 0.00 0.00 0.00 3.02
4924 5575 7.921786 ATCATAAAATCGAAGTCCAACTGAA 57.078 32.000 0.00 0.00 0.00 3.02
4925 5576 8.474831 TCTATCATAAAATCGAAGTCCAACTGA 58.525 33.333 0.00 0.00 0.00 3.41
4926 5577 8.648557 TCTATCATAAAATCGAAGTCCAACTG 57.351 34.615 0.00 0.00 0.00 3.16
4927 5578 8.478877 ACTCTATCATAAAATCGAAGTCCAACT 58.521 33.333 0.00 0.00 0.00 3.16
4928 5579 8.649973 ACTCTATCATAAAATCGAAGTCCAAC 57.350 34.615 0.00 0.00 0.00 3.77
4929 5580 9.314321 GAACTCTATCATAAAATCGAAGTCCAA 57.686 33.333 0.00 0.00 0.00 3.53
4930 5581 8.474831 TGAACTCTATCATAAAATCGAAGTCCA 58.525 33.333 0.00 0.00 0.00 4.02
4931 5582 8.873215 TGAACTCTATCATAAAATCGAAGTCC 57.127 34.615 0.00 0.00 0.00 3.85
4932 5583 9.522804 ACTGAACTCTATCATAAAATCGAAGTC 57.477 33.333 0.00 0.00 0.00 3.01
4933 5584 9.307121 CACTGAACTCTATCATAAAATCGAAGT 57.693 33.333 0.00 0.00 0.00 3.01
4934 5585 8.759641 CCACTGAACTCTATCATAAAATCGAAG 58.240 37.037 0.00 0.00 0.00 3.79
4935 5586 7.224753 GCCACTGAACTCTATCATAAAATCGAA 59.775 37.037 0.00 0.00 0.00 3.71
4936 5587 6.701841 GCCACTGAACTCTATCATAAAATCGA 59.298 38.462 0.00 0.00 0.00 3.59
4937 5588 6.073548 GGCCACTGAACTCTATCATAAAATCG 60.074 42.308 0.00 0.00 0.00 3.34
4938 5589 6.995091 AGGCCACTGAACTCTATCATAAAATC 59.005 38.462 5.01 0.00 0.00 2.17
4939 5590 6.904626 AGGCCACTGAACTCTATCATAAAAT 58.095 36.000 5.01 0.00 0.00 1.82
4940 5591 6.313519 AGGCCACTGAACTCTATCATAAAA 57.686 37.500 5.01 0.00 0.00 1.52
4941 5592 5.957771 AGGCCACTGAACTCTATCATAAA 57.042 39.130 5.01 0.00 0.00 1.40
4942 5593 5.957771 AAGGCCACTGAACTCTATCATAA 57.042 39.130 5.01 0.00 0.00 1.90
4943 5594 5.663106 AGAAAGGCCACTGAACTCTATCATA 59.337 40.000 5.01 0.00 0.00 2.15
4944 5595 4.472833 AGAAAGGCCACTGAACTCTATCAT 59.527 41.667 5.01 0.00 0.00 2.45
4945 5596 3.840666 AGAAAGGCCACTGAACTCTATCA 59.159 43.478 5.01 0.00 0.00 2.15
4946 5597 4.479786 AGAAAGGCCACTGAACTCTATC 57.520 45.455 5.01 0.00 0.00 2.08
4947 5598 4.566488 CCAAGAAAGGCCACTGAACTCTAT 60.566 45.833 5.01 0.00 0.00 1.98
4948 5599 3.244561 CCAAGAAAGGCCACTGAACTCTA 60.245 47.826 5.01 0.00 0.00 2.43
4949 5600 2.487986 CCAAGAAAGGCCACTGAACTCT 60.488 50.000 5.01 0.00 0.00 3.24
4950 5601 1.882623 CCAAGAAAGGCCACTGAACTC 59.117 52.381 5.01 0.00 0.00 3.01
4951 5602 1.986882 CCAAGAAAGGCCACTGAACT 58.013 50.000 5.01 0.00 0.00 3.01
4961 5612 2.424956 GCATTACCTCTGCCAAGAAAGG 59.575 50.000 0.00 0.00 33.44 3.11
4962 5613 3.084039 TGCATTACCTCTGCCAAGAAAG 58.916 45.455 0.00 0.00 38.89 2.62
4963 5614 3.153369 TGCATTACCTCTGCCAAGAAA 57.847 42.857 0.00 0.00 38.89 2.52
4964 5615 2.877097 TGCATTACCTCTGCCAAGAA 57.123 45.000 0.00 0.00 38.89 2.52
4965 5616 3.181451 CCTATGCATTACCTCTGCCAAGA 60.181 47.826 3.54 0.00 38.89 3.02
4966 5617 3.144506 CCTATGCATTACCTCTGCCAAG 58.855 50.000 3.54 0.00 38.89 3.61
4967 5618 2.777114 TCCTATGCATTACCTCTGCCAA 59.223 45.455 3.54 0.00 38.89 4.52
4968 5619 2.407562 TCCTATGCATTACCTCTGCCA 58.592 47.619 3.54 0.00 38.89 4.92
4969 5620 3.071602 TCTTCCTATGCATTACCTCTGCC 59.928 47.826 3.54 0.00 38.89 4.85
4970 5621 4.342862 TCTTCCTATGCATTACCTCTGC 57.657 45.455 3.54 0.00 40.10 4.26
5014 5665 0.465705 ATCGGTGCATCCAATCTCGT 59.534 50.000 0.00 0.00 35.57 4.18
5059 5710 5.952347 AATTAATGGGACGACTTCTAGGT 57.048 39.130 0.00 0.00 0.00 3.08
5069 5720 6.823689 CCCCTTCTATCATAATTAATGGGACG 59.176 42.308 0.00 0.00 36.15 4.79
5278 5929 0.735471 CGCGAGAGATGGAGAAGACA 59.265 55.000 0.00 0.00 0.00 3.41
5553 6415 1.376037 GGTGAAGGCTGGAACGAGG 60.376 63.158 0.00 0.00 0.00 4.63
5752 6616 3.212397 ACACCTTTATCTCCCCCTATCCT 59.788 47.826 0.00 0.00 0.00 3.24
5753 6617 3.328050 CACACCTTTATCTCCCCCTATCC 59.672 52.174 0.00 0.00 0.00 2.59
5825 6689 8.821894 GTTGTTTATTTGCCAAGTTATGTGAAA 58.178 29.630 0.00 0.00 0.00 2.69
5915 6779 5.275067 TGCATGGTTAATAAATCCCAAGC 57.725 39.130 0.00 0.00 40.95 4.01
6075 6951 5.511386 AGAAGCAAATAGGCAGGCTATAT 57.489 39.130 16.61 5.13 35.11 0.86
6707 7583 1.133181 TGCAGGACCAGGAATCACCA 61.133 55.000 0.00 0.00 42.04 4.17
7076 7952 1.202758 AGTCCGCTGATTTGTTCCACA 60.203 47.619 0.00 0.00 0.00 4.17
7100 7976 1.531058 GCAACAACCGCGTATTCATCC 60.531 52.381 4.92 0.00 0.00 3.51
7175 8051 7.505923 AGGCAAAGTTCACCTAAATAAAAGTCT 59.494 33.333 0.00 0.00 29.98 3.24
7481 8357 1.497991 GCACGAGCTTGTGACTAACA 58.502 50.000 33.87 0.00 42.55 2.41
7583 8459 2.932663 CACAAAGACGGATGTGGCT 58.067 52.632 0.00 0.00 42.46 4.75
7601 8477 0.179018 ATTTGGGCTCGCTGGGATAC 60.179 55.000 0.00 0.00 0.00 2.24
7671 8547 1.070786 GAGTTGCCCGGTCTGTGAA 59.929 57.895 0.00 0.00 0.00 3.18
7677 8553 0.250338 AAAGAGTGAGTTGCCCGGTC 60.250 55.000 0.00 0.00 0.00 4.79
7681 8557 3.542648 GGGTATAAAGAGTGAGTTGCCC 58.457 50.000 0.00 0.00 0.00 5.36
7687 8563 5.693769 TGAAAGGGGGTATAAAGAGTGAG 57.306 43.478 0.00 0.00 0.00 3.51
7688 8564 6.243148 GTTTGAAAGGGGGTATAAAGAGTGA 58.757 40.000 0.00 0.00 0.00 3.41
7707 8583 2.904866 GCACCACAGCCCGTTTGA 60.905 61.111 0.00 0.00 0.00 2.69
7708 8584 2.906897 AGCACCACAGCCCGTTTG 60.907 61.111 0.00 0.00 34.23 2.93
7709 8585 2.594592 GAGCACCACAGCCCGTTT 60.595 61.111 0.00 0.00 34.23 3.60
7710 8586 3.414136 TTGAGCACCACAGCCCGTT 62.414 57.895 0.00 0.00 34.23 4.44
7711 8587 3.832237 CTTGAGCACCACAGCCCGT 62.832 63.158 0.00 0.00 34.23 5.28
7712 8588 3.052082 CTTGAGCACCACAGCCCG 61.052 66.667 0.00 0.00 34.23 6.13
7730 8606 0.318441 TCTTTCCAGCGGTGACTCTG 59.682 55.000 17.83 0.00 0.00 3.35
7731 8607 1.048601 TTCTTTCCAGCGGTGACTCT 58.951 50.000 17.83 0.00 0.00 3.24
7732 8608 1.878953 TTTCTTTCCAGCGGTGACTC 58.121 50.000 17.83 0.00 0.00 3.36
7733 8609 2.222027 CTTTTCTTTCCAGCGGTGACT 58.778 47.619 17.83 0.00 0.00 3.41
7734 8610 1.335051 GCTTTTCTTTCCAGCGGTGAC 60.335 52.381 17.83 0.00 0.00 3.67
7735 8611 0.951558 GCTTTTCTTTCCAGCGGTGA 59.048 50.000 17.83 0.00 0.00 4.02
7736 8612 0.039165 GGCTTTTCTTTCCAGCGGTG 60.039 55.000 7.86 7.86 34.09 4.94
7737 8613 0.178990 AGGCTTTTCTTTCCAGCGGT 60.179 50.000 0.00 0.00 34.09 5.68
7768 8644 3.970410 CAGCAAGGAGGTGGGGCA 61.970 66.667 0.00 0.00 41.98 5.36
7770 8646 1.303643 GTTCAGCAAGGAGGTGGGG 60.304 63.158 0.00 0.00 45.66 4.96
7772 8648 0.607489 CCTGTTCAGCAAGGAGGTGG 60.607 60.000 0.00 0.00 45.66 4.61
7800 8676 3.376859 TCAACACTCGACAACAGCATTTT 59.623 39.130 0.00 0.00 0.00 1.82
7804 8680 2.135139 GATCAACACTCGACAACAGCA 58.865 47.619 0.00 0.00 0.00 4.41
7805 8681 1.125021 CGATCAACACTCGACAACAGC 59.875 52.381 0.00 0.00 38.38 4.40
7806 8682 1.721389 CCGATCAACACTCGACAACAG 59.279 52.381 0.00 0.00 38.38 3.16
7807 8683 1.778334 CCGATCAACACTCGACAACA 58.222 50.000 0.00 0.00 38.38 3.33
7808 8684 0.438830 GCCGATCAACACTCGACAAC 59.561 55.000 0.00 0.00 38.38 3.32
7809 8685 0.032815 TGCCGATCAACACTCGACAA 59.967 50.000 0.00 0.00 38.38 3.18
7811 8687 1.674611 CGTGCCGATCAACACTCGAC 61.675 60.000 11.95 0.00 38.38 4.20
7812 8688 1.443702 CGTGCCGATCAACACTCGA 60.444 57.895 11.95 0.00 38.38 4.04
7813 8689 2.444624 CCGTGCCGATCAACACTCG 61.445 63.158 11.95 2.00 34.58 4.18
7814 8690 2.740714 GCCGTGCCGATCAACACTC 61.741 63.158 11.95 2.41 34.58 3.51
7899 8777 9.679661 AACAATGGAGTATAATCACATGTTACA 57.320 29.630 12.16 0.00 0.00 2.41
8071 8949 5.406649 TGGTTAAACACAAGTTTTGCAGAG 58.593 37.500 0.00 0.00 45.32 3.35
8076 8954 7.971168 TGTCAGTATGGTTAAACACAAGTTTTG 59.029 33.333 0.00 0.00 40.12 2.44
8137 9020 5.917447 GCTGAAAGAAAAACTGGAGAATGAC 59.083 40.000 0.00 0.00 34.07 3.06
8193 9076 3.195396 CACTTCACCATTACAAATGGGGG 59.805 47.826 18.44 11.97 42.75 5.40
8213 9096 1.102978 ATTACTGGAAATGGCGCCAC 58.897 50.000 35.50 20.34 0.00 5.01
8248 9131 1.799258 CTTGCACTGCAACTGGGGTC 61.799 60.000 12.59 0.00 43.99 4.46
8259 9142 5.225899 TGATCGATCAAAATCTTGCACTG 57.774 39.130 25.44 0.00 33.08 3.66
8294 9177 1.626654 ATTCCACGCGAAACAGCTCG 61.627 55.000 15.93 0.00 41.84 5.03
8295 9178 0.095417 GATTCCACGCGAAACAGCTC 59.905 55.000 15.93 0.00 33.08 4.09
8296 9179 0.320771 AGATTCCACGCGAAACAGCT 60.321 50.000 15.93 0.00 33.08 4.24
8297 9180 0.179215 CAGATTCCACGCGAAACAGC 60.179 55.000 15.93 0.00 33.08 4.40
8298 9181 1.136252 CACAGATTCCACGCGAAACAG 60.136 52.381 15.93 0.00 33.08 3.16
8299 9182 0.865111 CACAGATTCCACGCGAAACA 59.135 50.000 15.93 0.00 33.08 2.83
8300 9183 0.452784 GCACAGATTCCACGCGAAAC 60.453 55.000 15.93 0.00 33.08 2.78
8301 9184 1.573829 GGCACAGATTCCACGCGAAA 61.574 55.000 15.93 4.20 33.08 3.46
8302 9185 2.032634 GGCACAGATTCCACGCGAA 61.033 57.895 15.93 0.00 34.14 4.70
8303 9186 2.434185 GGCACAGATTCCACGCGA 60.434 61.111 15.93 0.00 0.00 5.87
8304 9187 3.853330 CGGCACAGATTCCACGCG 61.853 66.667 3.53 3.53 0.00 6.01
8361 9244 0.390472 CCAGACCACCGAGCTCTTTC 60.390 60.000 12.85 0.74 0.00 2.62
8477 9370 3.615110 GCGAGAGAGATTGTTTGGTCTGA 60.615 47.826 0.00 0.00 0.00 3.27
8512 9405 0.746563 TTCCATGGACGAAATCGCCC 60.747 55.000 15.91 0.83 44.43 6.13
8544 9437 0.464373 GCGAATCAGGGAAGATGGCA 60.464 55.000 0.00 0.00 31.99 4.92
8545 9438 0.179034 AGCGAATCAGGGAAGATGGC 60.179 55.000 0.00 0.00 0.00 4.40
8550 9443 1.884926 GGCGAGCGAATCAGGGAAG 60.885 63.158 0.00 0.00 0.00 3.46
8565 9458 4.508128 TTAAGGCGAGGCGAGGCG 62.508 66.667 0.00 0.00 39.33 5.52
8566 9459 2.125269 TTTAAGGCGAGGCGAGGC 60.125 61.111 0.00 0.92 0.00 4.70
8567 9460 1.814169 GGTTTAAGGCGAGGCGAGG 60.814 63.158 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.