Multiple sequence alignment - TraesCS1D01G449800

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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 TraesCS1D01G449800 chr1D 100.000 2803 0 0 1 2803 492135289 492138091 0.000000e+00 5177
1 TraesCS1D01G449800 chr1D 87.852 889 64 18 1001 1870 492104082 492104945 0.000000e+00 1003
2 TraesCS1D01G449800 chr1D 82.353 153 20 4 2376 2524 492428946 492428797 2.930000e-25 126
3 TraesCS1D01G449800 chr1A 95.292 1232 25 9 931 2129 590249554 590250785 0.000000e+00 1923
4 TraesCS1D01G449800 chr1A 82.735 1170 86 49 1004 2129 590560984 590559887 0.000000e+00 935
5 TraesCS1D01G449800 chr1A 82.822 489 71 10 2143 2622 590559765 590559281 2.580000e-115 425
6 TraesCS1D01G449800 chr1A 93.694 111 7 0 717 827 590249193 590249303 1.730000e-37 167
7 TraesCS1D01G449800 chr1A 96.117 103 1 2 847 946 590249290 590249392 6.210000e-37 165
8 TraesCS1D01G449800 chr7D 87.500 704 63 12 2 694 25329091 25329780 0.000000e+00 789
9 TraesCS1D01G449800 chr7D 86.872 716 68 15 1 702 119561672 119560969 0.000000e+00 778
10 TraesCS1D01G449800 chr7D 84.928 690 72 22 19 695 1604476 1605146 0.000000e+00 669
11 TraesCS1D01G449800 chr7D 87.952 581 53 6 3 577 53715180 53715749 0.000000e+00 669
12 TraesCS1D01G449800 chr7D 83.520 716 71 18 1 702 125840930 125840248 2.370000e-175 625
13 TraesCS1D01G449800 chr7D 85.515 573 57 18 139 696 518060934 518060373 2.420000e-160 575
14 TraesCS1D01G449800 chr2D 86.582 708 70 12 1 696 489573791 489573097 0.000000e+00 758
15 TraesCS1D01G449800 chr2D 85.574 714 74 13 1 696 480178483 480179185 0.000000e+00 721
16 TraesCS1D01G449800 chr5D 86.517 712 62 19 1 696 454030219 454029526 0.000000e+00 752
17 TraesCS1D01G449800 chr5D 87.187 679 60 14 30 696 544788126 544788789 0.000000e+00 747
18 TraesCS1D01G449800 chr5D 85.815 712 76 20 1 696 37641072 37640370 0.000000e+00 732
19 TraesCS1D01G449800 chr5D 87.640 623 51 16 1 610 478459662 478460271 0.000000e+00 701
20 TraesCS1D01G449800 chr5D 84.509 723 67 28 1 702 48457188 48456490 0.000000e+00 673
21 TraesCS1D01G449800 chr4A 86.080 704 70 16 1 696 30155896 30156579 0.000000e+00 732
22 TraesCS1D01G449800 chr4A 84.322 708 65 20 1 696 578274320 578274993 0.000000e+00 651
23 TraesCS1D01G449800 chr6D 85.615 716 70 15 1 696 402412070 402412772 0.000000e+00 721
24 TraesCS1D01G449800 chrUn 84.866 707 80 16 1 696 63257321 63258011 0.000000e+00 688
25 TraesCS1D01G449800 chr3D 84.182 727 85 21 1 702 467979058 467978337 0.000000e+00 678
26 TraesCS1D01G449800 chr3D 84.075 697 82 18 19 702 36363978 36363298 0.000000e+00 645
27 TraesCS1D01G449800 chr3A 84.583 707 81 17 1 695 588444396 588443706 0.000000e+00 676
28 TraesCS1D01G449800 chr5A 83.495 721 87 23 2 702 528934531 528933823 0.000000e+00 643
29 TraesCS1D01G449800 chr2B 83.024 701 82 21 10 696 486590824 486591501 3.990000e-168 601
30 TraesCS1D01G449800 chr2A 83.436 489 61 13 222 696 580050075 580050557 1.190000e-118 436
31 TraesCS1D01G449800 chr6B 84.175 297 29 11 403 695 652123536 652123254 3.560000e-69 272


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 TraesCS1D01G449800 chr1D 492135289 492138091 2802 False 5177.000000 5177 100.000000 1 2803 1 chr1D.!!$F2 2802
1 TraesCS1D01G449800 chr1D 492104082 492104945 863 False 1003.000000 1003 87.852000 1001 1870 1 chr1D.!!$F1 869
2 TraesCS1D01G449800 chr1A 590249193 590250785 1592 False 751.666667 1923 95.034333 717 2129 3 chr1A.!!$F1 1412
3 TraesCS1D01G449800 chr1A 590559281 590560984 1703 True 680.000000 935 82.778500 1004 2622 2 chr1A.!!$R1 1618
4 TraesCS1D01G449800 chr7D 25329091 25329780 689 False 789.000000 789 87.500000 2 694 1 chr7D.!!$F2 692
5 TraesCS1D01G449800 chr7D 119560969 119561672 703 True 778.000000 778 86.872000 1 702 1 chr7D.!!$R1 701
6 TraesCS1D01G449800 chr7D 1604476 1605146 670 False 669.000000 669 84.928000 19 695 1 chr7D.!!$F1 676
7 TraesCS1D01G449800 chr7D 53715180 53715749 569 False 669.000000 669 87.952000 3 577 1 chr7D.!!$F3 574
8 TraesCS1D01G449800 chr7D 125840248 125840930 682 True 625.000000 625 83.520000 1 702 1 chr7D.!!$R2 701
9 TraesCS1D01G449800 chr7D 518060373 518060934 561 True 575.000000 575 85.515000 139 696 1 chr7D.!!$R3 557
10 TraesCS1D01G449800 chr2D 489573097 489573791 694 True 758.000000 758 86.582000 1 696 1 chr2D.!!$R1 695
11 TraesCS1D01G449800 chr2D 480178483 480179185 702 False 721.000000 721 85.574000 1 696 1 chr2D.!!$F1 695
12 TraesCS1D01G449800 chr5D 454029526 454030219 693 True 752.000000 752 86.517000 1 696 1 chr5D.!!$R3 695
13 TraesCS1D01G449800 chr5D 544788126 544788789 663 False 747.000000 747 87.187000 30 696 1 chr5D.!!$F2 666
14 TraesCS1D01G449800 chr5D 37640370 37641072 702 True 732.000000 732 85.815000 1 696 1 chr5D.!!$R1 695
15 TraesCS1D01G449800 chr5D 478459662 478460271 609 False 701.000000 701 87.640000 1 610 1 chr5D.!!$F1 609
16 TraesCS1D01G449800 chr5D 48456490 48457188 698 True 673.000000 673 84.509000 1 702 1 chr5D.!!$R2 701
17 TraesCS1D01G449800 chr4A 30155896 30156579 683 False 732.000000 732 86.080000 1 696 1 chr4A.!!$F1 695
18 TraesCS1D01G449800 chr4A 578274320 578274993 673 False 651.000000 651 84.322000 1 696 1 chr4A.!!$F2 695
19 TraesCS1D01G449800 chr6D 402412070 402412772 702 False 721.000000 721 85.615000 1 696 1 chr6D.!!$F1 695
20 TraesCS1D01G449800 chrUn 63257321 63258011 690 False 688.000000 688 84.866000 1 696 1 chrUn.!!$F1 695
21 TraesCS1D01G449800 chr3D 467978337 467979058 721 True 678.000000 678 84.182000 1 702 1 chr3D.!!$R2 701
22 TraesCS1D01G449800 chr3D 36363298 36363978 680 True 645.000000 645 84.075000 19 702 1 chr3D.!!$R1 683
23 TraesCS1D01G449800 chr3A 588443706 588444396 690 True 676.000000 676 84.583000 1 695 1 chr3A.!!$R1 694
24 TraesCS1D01G449800 chr5A 528933823 528934531 708 True 643.000000 643 83.495000 2 702 1 chr5A.!!$R1 700
25 TraesCS1D01G449800 chr2B 486590824 486591501 677 False 601.000000 601 83.024000 10 696 1 chr2B.!!$F1 686

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
696 771 0.16747 TCTTCGCAACGAGTACTCCG 59.833 55.0 17.23 14.1 37.14 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2381 2835 0.031994 GGCGAGGCAATGTTGTTTGT 59.968 50.0 0.0 0.0 0.0 2.83 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
82 83 2.657237 CGTGCCTCTCGGAAAGGT 59.343 61.111 0.00 0.00 36.21 3.50
125 130 0.601558 TTCTTTCGGGAGAGTCACGG 59.398 55.000 0.00 0.00 44.75 4.94
126 131 0.538977 TCTTTCGGGAGAGTCACGGT 60.539 55.000 0.00 0.00 44.75 4.83
127 132 0.317479 CTTTCGGGAGAGTCACGGTT 59.683 55.000 0.00 0.00 44.75 4.44
129 134 0.754472 TTCGGGAGAGTCACGGTTTT 59.246 50.000 0.00 0.00 44.75 2.43
130 135 0.316204 TCGGGAGAGTCACGGTTTTC 59.684 55.000 0.00 0.00 44.75 2.29
131 136 1.007336 CGGGAGAGTCACGGTTTTCG 61.007 60.000 0.00 0.00 40.12 3.46
142 147 0.782384 CGGTTTTCGTTCCGTGAGAG 59.218 55.000 0.00 0.00 41.58 3.20
242 265 2.872858 GAGAGTCACGGTTTTGCTTTCT 59.127 45.455 0.00 0.00 0.00 2.52
487 555 6.935741 TTCGTCAAAACCTATCAATATGGG 57.064 37.500 0.00 0.00 39.60 4.00
488 556 6.241882 TCGTCAAAACCTATCAATATGGGA 57.758 37.500 0.00 0.00 37.20 4.37
489 557 6.837312 TCGTCAAAACCTATCAATATGGGAT 58.163 36.000 0.00 0.00 37.20 3.85
490 558 6.934645 TCGTCAAAACCTATCAATATGGGATC 59.065 38.462 0.00 0.00 37.20 3.36
491 559 6.936900 CGTCAAAACCTATCAATATGGGATCT 59.063 38.462 0.00 0.00 37.20 2.75
577 646 4.946784 ACGCATGGTTTGAGAGATAAAC 57.053 40.909 0.00 0.00 37.31 2.01
651 725 0.456628 TAACGCGCTACATGCCACTA 59.543 50.000 5.73 0.00 38.78 2.74
654 728 0.806102 CGCGCTACATGCCACTAGTT 60.806 55.000 5.56 0.00 38.78 2.24
669 744 2.026822 ACTAGTTGCAACCAGGAGGATG 60.027 50.000 25.50 9.46 40.45 3.51
681 756 2.368221 CAGGAGGATGGAGGTGATCTTC 59.632 54.545 0.00 0.00 0.00 2.87
696 771 0.167470 TCTTCGCAACGAGTACTCCG 59.833 55.000 17.23 14.10 37.14 4.63
702 777 2.334838 GCAACGAGTACTCCGTGATTT 58.665 47.619 17.23 1.43 40.44 2.17
703 778 2.092211 GCAACGAGTACTCCGTGATTTG 59.908 50.000 17.23 12.94 40.44 2.32
704 779 2.649331 ACGAGTACTCCGTGATTTGG 57.351 50.000 17.23 2.42 38.97 3.28
705 780 2.165167 ACGAGTACTCCGTGATTTGGA 58.835 47.619 17.23 0.00 38.97 3.53
706 781 2.559668 ACGAGTACTCCGTGATTTGGAA 59.440 45.455 17.23 0.00 38.97 3.53
707 782 3.006110 ACGAGTACTCCGTGATTTGGAAA 59.994 43.478 17.23 0.00 38.97 3.13
708 783 4.181578 CGAGTACTCCGTGATTTGGAAAT 58.818 43.478 17.23 0.00 34.44 2.17
709 784 5.105635 ACGAGTACTCCGTGATTTGGAAATA 60.106 40.000 17.23 0.00 38.97 1.40
710 785 5.459107 CGAGTACTCCGTGATTTGGAAATAG 59.541 44.000 17.23 0.00 34.44 1.73
711 786 5.671493 AGTACTCCGTGATTTGGAAATAGG 58.329 41.667 0.00 0.00 34.44 2.57
712 787 4.837093 ACTCCGTGATTTGGAAATAGGA 57.163 40.909 0.00 0.00 34.44 2.94
713 788 5.174037 ACTCCGTGATTTGGAAATAGGAA 57.826 39.130 0.00 0.00 34.44 3.36
714 789 5.755849 ACTCCGTGATTTGGAAATAGGAAT 58.244 37.500 0.00 0.00 34.44 3.01
715 790 6.187682 ACTCCGTGATTTGGAAATAGGAATT 58.812 36.000 0.00 0.00 34.44 2.17
716 791 6.095440 ACTCCGTGATTTGGAAATAGGAATTG 59.905 38.462 0.00 0.00 34.44 2.32
717 792 5.043248 CCGTGATTTGGAAATAGGAATTGC 58.957 41.667 0.00 0.00 0.00 3.56
718 793 5.043248 CGTGATTTGGAAATAGGAATTGCC 58.957 41.667 0.00 0.00 40.90 4.52
736 811 2.185350 AGCATTCCCTCGCTGTCG 59.815 61.111 0.00 0.00 37.02 4.35
749 824 0.919981 GCTGTCGCAGAAATCGAGAG 59.080 55.000 10.46 5.38 46.11 3.20
762 837 0.755698 TCGAGAGATAGGTGTGCCCC 60.756 60.000 0.00 0.00 31.91 5.80
793 868 3.001330 CGTCAAATAGGATTCGGCTCAAC 59.999 47.826 0.00 0.00 0.00 3.18
858 933 7.568199 TTTTTGAGAAGAAGACCTAACCAAG 57.432 36.000 0.00 0.00 0.00 3.61
868 943 3.714798 AGACCTAACCAAGTGGACTTTCA 59.285 43.478 3.83 0.00 38.94 2.69
981 1237 2.897969 TGTTTGTGGTAGAGGAGGACTC 59.102 50.000 0.00 0.00 46.98 3.36
998 1271 6.351626 GGAGGACTCGAAAGGAAAACCTATAA 60.352 42.308 0.00 0.00 0.00 0.98
1027 1300 0.171679 TACGTGGTCGATCGTTGCAT 59.828 50.000 15.94 0.60 40.70 3.96
1252 1541 4.627035 TCGTGCTGTGATCAAAGATTGTAG 59.373 41.667 17.56 1.59 0.00 2.74
1404 1714 0.398381 TGGGCTTTTCCTTGGCAACT 60.398 50.000 0.00 0.00 34.39 3.16
1476 1786 2.029844 GCTCTCGGTGCAAGTCCAC 61.030 63.158 0.00 0.00 35.00 4.02
1509 1819 4.594123 TGATGTCTACTGGTTTGTTCGA 57.406 40.909 0.00 0.00 0.00 3.71
1512 1822 5.995282 TGATGTCTACTGGTTTGTTCGATTT 59.005 36.000 0.00 0.00 0.00 2.17
1605 1921 4.891727 CTAGGATGCGGCGGCGTT 62.892 66.667 32.35 20.35 44.10 4.84
1890 2219 8.957466 AGGTTTAGTTTGCTATCAATTTAGTCC 58.043 33.333 0.00 0.00 31.33 3.85
2129 2474 7.532571 ACTGTACAAAACCTCAACTAACAAAC 58.467 34.615 0.00 0.00 0.00 2.93
2130 2475 6.854778 TGTACAAAACCTCAACTAACAAACC 58.145 36.000 0.00 0.00 0.00 3.27
2131 2476 5.986501 ACAAAACCTCAACTAACAAACCA 57.013 34.783 0.00 0.00 0.00 3.67
2132 2477 5.716094 ACAAAACCTCAACTAACAAACCAC 58.284 37.500 0.00 0.00 0.00 4.16
2133 2478 5.479027 ACAAAACCTCAACTAACAAACCACT 59.521 36.000 0.00 0.00 0.00 4.00
2134 2479 5.830000 AAACCTCAACTAACAAACCACTC 57.170 39.130 0.00 0.00 0.00 3.51
2135 2480 3.816994 ACCTCAACTAACAAACCACTCC 58.183 45.455 0.00 0.00 0.00 3.85
2137 2482 3.815401 CCTCAACTAACAAACCACTCCAG 59.185 47.826 0.00 0.00 0.00 3.86
2138 2483 3.211045 TCAACTAACAAACCACTCCAGC 58.789 45.455 0.00 0.00 0.00 4.85
2139 2484 1.878953 ACTAACAAACCACTCCAGCG 58.121 50.000 0.00 0.00 0.00 5.18
2167 2621 3.522343 GTCCCTAAAACCCTCATGTAGGT 59.478 47.826 3.89 3.89 44.90 3.08
2178 2632 0.462047 CATGTAGGTGTTCCCGCTCC 60.462 60.000 0.00 0.00 38.74 4.70
2211 2665 0.036875 CCACACCCACCTCTTTCCTC 59.963 60.000 0.00 0.00 0.00 3.71
2224 2678 3.067106 TCTTTCCTCTTGCAATGACGAC 58.933 45.455 0.00 0.00 0.00 4.34
2225 2679 1.808411 TTCCTCTTGCAATGACGACC 58.192 50.000 0.00 0.00 0.00 4.79
2226 2680 0.036388 TCCTCTTGCAATGACGACCC 60.036 55.000 0.00 0.00 0.00 4.46
2229 2683 0.396435 TCTTGCAATGACGACCCTGT 59.604 50.000 0.00 0.00 0.00 4.00
2257 2711 3.945434 CTGCCATGCGCCGACATC 61.945 66.667 4.18 0.00 36.24 3.06
2259 2713 3.643978 GCCATGCGCCGACATCTC 61.644 66.667 4.18 0.00 0.00 2.75
2273 2727 3.957435 ATCTCGACGCCCACCTCCA 62.957 63.158 0.00 0.00 0.00 3.86
2274 2728 4.436998 CTCGACGCCCACCTCCAC 62.437 72.222 0.00 0.00 0.00 4.02
2278 2732 4.250305 ACGCCCACCTCCACACAC 62.250 66.667 0.00 0.00 0.00 3.82
2284 2738 1.351017 CCCACCTCCACACACTAATGT 59.649 52.381 0.00 0.00 40.80 2.71
2288 2742 1.065418 CCTCCACACACTAATGTCCCC 60.065 57.143 0.00 0.00 36.72 4.81
2289 2743 1.628340 CTCCACACACTAATGTCCCCA 59.372 52.381 0.00 0.00 36.72 4.96
2290 2744 2.239654 CTCCACACACTAATGTCCCCAT 59.760 50.000 0.00 0.00 36.72 4.00
2291 2745 3.454447 CTCCACACACTAATGTCCCCATA 59.546 47.826 0.00 0.00 36.72 2.74
2292 2746 4.044308 TCCACACACTAATGTCCCCATAT 58.956 43.478 0.00 0.00 36.72 1.78
2293 2747 4.102524 TCCACACACTAATGTCCCCATATC 59.897 45.833 0.00 0.00 36.72 1.63
2294 2748 4.103153 CCACACACTAATGTCCCCATATCT 59.897 45.833 0.00 0.00 36.72 1.98
2298 2752 4.841246 ACACTAATGTCCCCATATCTCCTC 59.159 45.833 0.00 0.00 31.55 3.71
2299 2753 4.840680 CACTAATGTCCCCATATCTCCTCA 59.159 45.833 0.00 0.00 0.00 3.86
2300 2754 4.841246 ACTAATGTCCCCATATCTCCTCAC 59.159 45.833 0.00 0.00 0.00 3.51
2306 2760 2.028658 CCCCATATCTCCTCACGATGTG 60.029 54.545 0.00 0.00 34.45 3.21
2307 2761 2.630098 CCCATATCTCCTCACGATGTGT 59.370 50.000 0.00 0.00 34.79 3.72
2313 2767 3.092301 TCTCCTCACGATGTGTCTCATT 58.908 45.455 0.00 0.00 36.83 2.57
2318 2772 2.495669 TCACGATGTGTCTCATTGCCTA 59.504 45.455 0.00 0.00 40.60 3.93
2328 2782 0.846015 TCATTGCCTACCCATCCCAG 59.154 55.000 0.00 0.00 0.00 4.45
2331 2785 0.548926 TTGCCTACCCATCCCAGACA 60.549 55.000 0.00 0.00 0.00 3.41
2340 2794 0.957395 CATCCCAGACACCACAGCAC 60.957 60.000 0.00 0.00 0.00 4.40
2343 2797 1.073722 CCAGACACCACAGCACCAT 59.926 57.895 0.00 0.00 0.00 3.55
2346 2800 0.250467 AGACACCACAGCACCATGTC 60.250 55.000 0.00 0.00 39.99 3.06
2347 2801 0.534877 GACACCACAGCACCATGTCA 60.535 55.000 0.00 0.00 39.57 3.58
2363 2817 0.543277 GTCACCATGCCTCCAGATCA 59.457 55.000 0.00 0.00 0.00 2.92
2367 2821 0.531532 CCATGCCTCCAGATCACGAC 60.532 60.000 0.00 0.00 0.00 4.34
2371 2825 1.608717 GCCTCCAGATCACGACACCT 61.609 60.000 0.00 0.00 0.00 4.00
2372 2826 1.763968 CCTCCAGATCACGACACCTA 58.236 55.000 0.00 0.00 0.00 3.08
2373 2827 2.311463 CCTCCAGATCACGACACCTAT 58.689 52.381 0.00 0.00 0.00 2.57
2374 2828 2.294791 CCTCCAGATCACGACACCTATC 59.705 54.545 0.00 0.00 0.00 2.08
2381 2835 1.542472 TCACGACACCTATCGCAAAGA 59.458 47.619 0.00 0.00 46.22 2.52
2385 2839 2.734606 CGACACCTATCGCAAAGACAAA 59.265 45.455 0.00 0.00 34.90 2.83
2392 2846 5.009610 ACCTATCGCAAAGACAAACAACATT 59.990 36.000 0.00 0.00 0.00 2.71
2396 2850 3.197265 GCAAAGACAAACAACATTGCCT 58.803 40.909 0.00 0.00 37.71 4.75
2397 2851 3.245990 GCAAAGACAAACAACATTGCCTC 59.754 43.478 0.00 0.00 37.71 4.70
2398 2852 3.354089 AAGACAAACAACATTGCCTCG 57.646 42.857 0.00 0.00 33.52 4.63
2403 2857 0.823356 AACAACATTGCCTCGCCACT 60.823 50.000 0.00 0.00 0.00 4.00
2404 2858 1.210931 CAACATTGCCTCGCCACTG 59.789 57.895 0.00 0.00 0.00 3.66
2405 2859 2.629656 AACATTGCCTCGCCACTGC 61.630 57.895 0.00 0.00 0.00 4.40
2409 2863 3.772853 TTGCCTCGCCACTGCTGTT 62.773 57.895 0.00 0.00 34.43 3.16
2421 2875 2.869801 CACTGCTGTTGTCGAAGGTTAA 59.130 45.455 0.00 0.00 0.00 2.01
2468 2925 8.205512 TCAATTTGAAATGGATGGTTCATATGG 58.794 33.333 2.13 0.00 33.90 2.74
2469 2926 6.482898 TTTGAAATGGATGGTTCATATGGG 57.517 37.500 2.13 0.00 33.90 4.00
2474 2931 6.923199 AATGGATGGTTCATATGGGAATTC 57.077 37.500 2.13 0.00 0.00 2.17
2476 2933 3.758554 GGATGGTTCATATGGGAATTCCG 59.241 47.826 18.30 4.22 38.76 4.30
2479 2936 5.060427 TGGTTCATATGGGAATTCCGAAT 57.940 39.130 18.30 15.82 38.76 3.34
2480 2937 5.454062 TGGTTCATATGGGAATTCCGAATT 58.546 37.500 18.30 6.04 38.76 2.17
2482 2939 5.534654 GGTTCATATGGGAATTCCGAATTGA 59.465 40.000 18.30 16.94 38.76 2.57
2485 2942 7.838079 TCATATGGGAATTCCGAATTGAAAT 57.162 32.000 18.30 0.21 38.76 2.17
2499 2956 9.566530 TCCGAATTGAAATTTTATATGTGTGTG 57.433 29.630 0.00 0.00 0.00 3.82
2515 2972 3.980775 GTGTGTGCACATGTTAAATGGAC 59.019 43.478 24.69 5.75 43.97 4.02
2622 3082 9.964253 GACATCATGAATATCAATGTCGATTAC 57.036 33.333 0.00 0.00 37.54 1.89
2623 3083 9.492973 ACATCATGAATATCAATGTCGATTACA 57.507 29.630 0.00 0.00 43.86 2.41
2624 3084 9.750882 CATCATGAATATCAATGTCGATTACAC 57.249 33.333 0.00 0.00 42.09 2.90
2625 3085 9.716531 ATCATGAATATCAATGTCGATTACACT 57.283 29.630 0.00 0.00 42.09 3.55
2647 3107 9.408069 ACACTACTAGAATTTTAGAGTTTGTCG 57.592 33.333 9.85 1.28 0.00 4.35
2648 3108 9.622004 CACTACTAGAATTTTAGAGTTTGTCGA 57.378 33.333 9.85 0.00 0.00 4.20
2649 3109 9.843334 ACTACTAGAATTTTAGAGTTTGTCGAG 57.157 33.333 9.85 0.00 0.00 4.04
2650 3110 9.843334 CTACTAGAATTTTAGAGTTTGTCGAGT 57.157 33.333 9.85 0.00 0.00 4.18
2652 3112 9.623350 ACTAGAATTTTAGAGTTTGTCGAGTAC 57.377 33.333 9.85 0.00 0.00 2.73
2653 3113 7.886405 AGAATTTTAGAGTTTGTCGAGTACC 57.114 36.000 0.00 0.00 0.00 3.34
2654 3114 6.585322 AGAATTTTAGAGTTTGTCGAGTACCG 59.415 38.462 0.00 0.00 40.25 4.02
2655 3115 3.837213 TTAGAGTTTGTCGAGTACCGG 57.163 47.619 0.00 0.00 39.14 5.28
2656 3116 1.901591 AGAGTTTGTCGAGTACCGGA 58.098 50.000 9.46 0.00 39.14 5.14
2657 3117 2.233271 AGAGTTTGTCGAGTACCGGAA 58.767 47.619 9.46 0.00 39.14 4.30
2658 3118 2.624838 AGAGTTTGTCGAGTACCGGAAA 59.375 45.455 9.46 0.00 39.14 3.13
2659 3119 3.068590 AGAGTTTGTCGAGTACCGGAAAA 59.931 43.478 9.46 0.00 39.14 2.29
2660 3120 3.795877 AGTTTGTCGAGTACCGGAAAAA 58.204 40.909 9.46 0.00 39.14 1.94
2661 3121 4.383173 AGTTTGTCGAGTACCGGAAAAAT 58.617 39.130 9.46 0.00 39.14 1.82
2662 3122 4.818005 AGTTTGTCGAGTACCGGAAAAATT 59.182 37.500 9.46 0.00 39.14 1.82
2663 3123 4.996062 TTGTCGAGTACCGGAAAAATTC 57.004 40.909 9.46 0.00 39.14 2.17
2664 3124 2.988493 TGTCGAGTACCGGAAAAATTCG 59.012 45.455 9.46 8.84 39.14 3.34
2673 3133 3.054166 CCGGAAAAATTCGGTGAAAACC 58.946 45.455 0.00 0.00 41.23 3.27
2685 3145 2.181426 TGAAAACCGTTTCGCACTTG 57.819 45.000 0.00 0.00 45.26 3.16
2686 3146 1.202200 TGAAAACCGTTTCGCACTTGG 60.202 47.619 0.00 0.00 45.26 3.61
2687 3147 0.526739 AAAACCGTTTCGCACTTGGC 60.527 50.000 0.00 0.00 39.90 4.52
2688 3148 1.658686 AAACCGTTTCGCACTTGGCA 61.659 50.000 0.00 0.00 45.17 4.92
2689 3149 2.058829 AACCGTTTCGCACTTGGCAG 62.059 55.000 0.00 0.00 45.17 4.85
2690 3150 2.250939 CCGTTTCGCACTTGGCAGA 61.251 57.895 0.00 0.00 45.17 4.26
2691 3151 1.205064 CGTTTCGCACTTGGCAGAG 59.795 57.895 0.00 0.00 45.17 3.35
2692 3152 1.221466 CGTTTCGCACTTGGCAGAGA 61.221 55.000 4.13 0.00 45.17 3.10
2693 3153 0.235926 GTTTCGCACTTGGCAGAGAC 59.764 55.000 4.13 0.00 45.17 3.36
2694 3154 0.106708 TTTCGCACTTGGCAGAGACT 59.893 50.000 4.13 0.00 45.17 3.24
2695 3155 0.319900 TTCGCACTTGGCAGAGACTC 60.320 55.000 0.00 0.00 45.17 3.36
2696 3156 1.181741 TCGCACTTGGCAGAGACTCT 61.182 55.000 0.00 0.00 45.17 3.24
2697 3157 1.013005 CGCACTTGGCAGAGACTCTG 61.013 60.000 25.45 25.45 46.90 3.35
2714 3174 3.867771 GCAGAGTGCAGTTCTCGG 58.132 61.111 0.00 0.00 44.26 4.63
2715 3175 2.386660 GCAGAGTGCAGTTCTCGGC 61.387 63.158 11.10 11.10 44.26 5.54
2716 3176 1.739562 CAGAGTGCAGTTCTCGGCC 60.740 63.158 0.00 0.00 37.07 6.13
2717 3177 1.910772 AGAGTGCAGTTCTCGGCCT 60.911 57.895 0.00 0.00 37.07 5.19
2718 3178 1.446966 GAGTGCAGTTCTCGGCCTC 60.447 63.158 0.00 0.00 34.03 4.70
2719 3179 2.811317 GTGCAGTTCTCGGCCTCG 60.811 66.667 0.00 0.00 34.03 4.63
2720 3180 4.069232 TGCAGTTCTCGGCCTCGG 62.069 66.667 0.00 0.00 36.95 4.63
2721 3181 4.821589 GCAGTTCTCGGCCTCGGG 62.822 72.222 0.00 0.00 38.44 5.14
2722 3182 3.382832 CAGTTCTCGGCCTCGGGT 61.383 66.667 0.00 0.00 38.21 5.28
2723 3183 2.050350 CAGTTCTCGGCCTCGGGTA 61.050 63.158 0.00 0.00 38.21 3.69
2724 3184 2.050934 AGTTCTCGGCCTCGGGTAC 61.051 63.158 0.00 0.00 37.41 3.34
2725 3185 2.050934 GTTCTCGGCCTCGGGTACT 61.051 63.158 0.00 0.00 38.21 2.73
2726 3186 1.751927 TTCTCGGCCTCGGGTACTC 60.752 63.158 0.00 0.00 38.21 2.59
2727 3187 3.584052 CTCGGCCTCGGGTACTCG 61.584 72.222 9.43 9.43 36.95 4.18
2734 3194 4.738998 TCGGGTACTCGGCCGGAA 62.739 66.667 27.83 5.67 33.33 4.30
2735 3195 3.762247 CGGGTACTCGGCCGGAAA 61.762 66.667 27.83 7.82 0.00 3.13
2736 3196 2.125391 GGGTACTCGGCCGGAAAC 60.125 66.667 27.83 19.57 0.00 2.78
2737 3197 2.125391 GGTACTCGGCCGGAAACC 60.125 66.667 27.83 24.34 0.00 3.27
2738 3198 2.653087 GGTACTCGGCCGGAAACCT 61.653 63.158 27.83 3.83 31.18 3.50
2739 3199 1.447314 GTACTCGGCCGGAAACCTG 60.447 63.158 27.83 9.32 0.00 4.00
2740 3200 3.305177 TACTCGGCCGGAAACCTGC 62.305 63.158 27.83 0.00 32.93 4.85
2746 3206 2.597217 CCGGAAACCTGCCAGCAA 60.597 61.111 0.00 0.00 0.00 3.91
2747 3207 2.199652 CCGGAAACCTGCCAGCAAA 61.200 57.895 0.00 0.00 0.00 3.68
2748 3208 1.286880 CGGAAACCTGCCAGCAAAG 59.713 57.895 0.00 0.00 0.00 2.77
2749 3209 1.172180 CGGAAACCTGCCAGCAAAGA 61.172 55.000 0.00 0.00 0.00 2.52
2750 3210 0.315251 GGAAACCTGCCAGCAAAGAC 59.685 55.000 0.00 0.00 0.00 3.01
2751 3211 0.315251 GAAACCTGCCAGCAAAGACC 59.685 55.000 0.00 0.00 0.00 3.85
2752 3212 0.396974 AAACCTGCCAGCAAAGACCA 60.397 50.000 0.00 0.00 0.00 4.02
2753 3213 1.109323 AACCTGCCAGCAAAGACCAC 61.109 55.000 0.00 0.00 0.00 4.16
2754 3214 1.228367 CCTGCCAGCAAAGACCACT 60.228 57.895 0.00 0.00 0.00 4.00
2755 3215 0.825010 CCTGCCAGCAAAGACCACTT 60.825 55.000 0.00 0.00 38.05 3.16
2756 3216 1.035139 CTGCCAGCAAAGACCACTTT 58.965 50.000 0.00 0.00 45.75 2.66
2763 3223 3.021451 AAAGACCACTTTGCCGAGG 57.979 52.632 0.00 0.00 43.57 4.63
2764 3224 0.537371 AAAGACCACTTTGCCGAGGG 60.537 55.000 0.00 0.00 43.57 4.30
2784 3244 2.981302 GCCATTTGGGGACTTGGC 59.019 61.111 0.00 0.00 46.94 4.52
2785 3245 4.537260 CCATTTGGGGACTTGGCA 57.463 55.556 0.00 0.00 0.00 4.92
2786 3246 2.757313 CCATTTGGGGACTTGGCAA 58.243 52.632 0.00 0.00 0.00 4.52
2787 3247 1.055040 CCATTTGGGGACTTGGCAAA 58.945 50.000 0.00 0.00 0.00 3.68
2788 3248 1.002315 CCATTTGGGGACTTGGCAAAG 59.998 52.381 0.00 0.00 39.49 2.77
2790 3250 2.757894 TTTGGGGACTTGGCAAAGTA 57.242 45.000 6.43 0.00 46.84 2.24
2791 3251 2.990740 TTGGGGACTTGGCAAAGTAT 57.009 45.000 6.43 0.00 46.84 2.12
2792 3252 2.990740 TGGGGACTTGGCAAAGTATT 57.009 45.000 6.43 0.00 46.84 1.89
2793 3253 3.252554 TGGGGACTTGGCAAAGTATTT 57.747 42.857 6.43 0.00 46.84 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 113 0.317479 AACCGTGACTCTCCCGAAAG 59.683 55.000 0.00 0.00 0.00 2.62
113 118 2.823628 CGAAAACCGTGACTCTCCC 58.176 57.895 0.00 0.00 0.00 4.30
135 140 1.007336 GCACAACCGTACCTCTCACG 61.007 60.000 0.00 0.00 39.10 4.35
136 141 0.317479 AGCACAACCGTACCTCTCAC 59.683 55.000 0.00 0.00 0.00 3.51
138 143 2.067013 GAAAGCACAACCGTACCTCTC 58.933 52.381 0.00 0.00 0.00 3.20
139 144 1.604693 CGAAAGCACAACCGTACCTCT 60.605 52.381 0.00 0.00 0.00 3.69
140 145 0.788391 CGAAAGCACAACCGTACCTC 59.212 55.000 0.00 0.00 0.00 3.85
242 265 4.454948 CACAACCGTGCCTCTTGA 57.545 55.556 0.00 0.00 36.06 3.02
461 529 8.247562 CCCATATTGATAGGTTTTGACGAAAAA 58.752 33.333 0.00 0.00 35.35 1.94
488 556 9.391227 AGATCTTCAAAACTAGATCCCATAGAT 57.609 33.333 0.00 0.00 38.24 1.98
489 557 8.789767 AGATCTTCAAAACTAGATCCCATAGA 57.210 34.615 0.00 0.00 38.24 1.98
490 558 7.812191 CGAGATCTTCAAAACTAGATCCCATAG 59.188 40.741 0.00 0.00 38.24 2.23
491 559 7.505923 TCGAGATCTTCAAAACTAGATCCCATA 59.494 37.037 0.00 0.00 38.24 2.74
614 684 4.171005 CGTTACTTATCGCAACCTGAGAA 58.829 43.478 0.00 0.00 28.16 2.87
651 725 0.038744 CCATCCTCCTGGTTGCAACT 59.961 55.000 27.64 3.64 32.96 3.16
654 728 1.565390 CCTCCATCCTCCTGGTTGCA 61.565 60.000 0.00 0.00 37.57 4.08
669 744 0.108804 TCGTTGCGAAGATCACCTCC 60.109 55.000 0.00 0.00 31.06 4.30
681 756 0.179171 ATCACGGAGTACTCGTTGCG 60.179 55.000 16.56 15.71 41.61 4.85
696 771 5.976458 TGGCAATTCCTATTTCCAAATCAC 58.024 37.500 0.00 0.00 34.67 3.06
702 777 3.098774 TGCTGGCAATTCCTATTTCCA 57.901 42.857 0.00 0.00 35.13 3.53
703 778 4.502087 GGAATGCTGGCAATTCCTATTTCC 60.502 45.833 19.29 13.28 40.39 3.13
704 779 4.502087 GGGAATGCTGGCAATTCCTATTTC 60.502 45.833 23.48 8.81 42.51 2.17
705 780 3.389002 GGGAATGCTGGCAATTCCTATTT 59.611 43.478 23.48 5.55 42.51 1.40
706 781 2.967887 GGGAATGCTGGCAATTCCTATT 59.032 45.455 23.48 4.63 42.51 1.73
707 782 2.178544 AGGGAATGCTGGCAATTCCTAT 59.821 45.455 23.48 13.85 42.51 2.57
708 783 1.570501 AGGGAATGCTGGCAATTCCTA 59.429 47.619 23.48 0.00 42.51 2.94
709 784 0.337428 AGGGAATGCTGGCAATTCCT 59.663 50.000 23.48 16.31 42.51 3.36
710 785 0.749049 GAGGGAATGCTGGCAATTCC 59.251 55.000 18.64 18.64 42.24 3.01
711 786 0.383231 CGAGGGAATGCTGGCAATTC 59.617 55.000 0.00 3.75 0.00 2.17
712 787 1.669999 GCGAGGGAATGCTGGCAATT 61.670 55.000 0.00 0.00 0.00 2.32
713 788 2.123428 GCGAGGGAATGCTGGCAAT 61.123 57.895 0.00 0.00 0.00 3.56
714 789 2.751436 GCGAGGGAATGCTGGCAA 60.751 61.111 0.00 0.00 0.00 4.52
715 790 3.720601 AGCGAGGGAATGCTGGCA 61.721 61.111 0.00 0.00 40.62 4.92
733 808 3.003897 ACCTATCTCTCGATTTCTGCGAC 59.996 47.826 0.00 0.00 33.71 5.19
736 811 4.047822 CACACCTATCTCTCGATTTCTGC 58.952 47.826 0.00 0.00 0.00 4.26
749 824 0.179468 TTAAGCGGGGCACACCTATC 59.821 55.000 0.00 0.00 40.03 2.08
793 868 0.105039 GGACCATGAAGCCTACTCGG 59.895 60.000 0.00 0.00 0.00 4.63
834 909 7.067008 CACTTGGTTAGGTCTTCTTCTCAAAAA 59.933 37.037 0.00 0.00 0.00 1.94
835 910 6.542370 CACTTGGTTAGGTCTTCTTCTCAAAA 59.458 38.462 0.00 0.00 0.00 2.44
836 911 6.055588 CACTTGGTTAGGTCTTCTTCTCAAA 58.944 40.000 0.00 0.00 0.00 2.69
837 912 5.454755 CCACTTGGTTAGGTCTTCTTCTCAA 60.455 44.000 0.00 0.00 0.00 3.02
838 913 4.040461 CCACTTGGTTAGGTCTTCTTCTCA 59.960 45.833 0.00 0.00 0.00 3.27
839 914 4.283722 TCCACTTGGTTAGGTCTTCTTCTC 59.716 45.833 0.00 0.00 36.34 2.87
840 915 4.040584 GTCCACTTGGTTAGGTCTTCTTCT 59.959 45.833 0.00 0.00 36.34 2.85
841 916 4.040584 AGTCCACTTGGTTAGGTCTTCTTC 59.959 45.833 0.00 0.00 36.34 2.87
842 917 3.974642 AGTCCACTTGGTTAGGTCTTCTT 59.025 43.478 0.00 0.00 36.34 2.52
843 918 3.588569 AGTCCACTTGGTTAGGTCTTCT 58.411 45.455 0.00 0.00 36.34 2.85
844 919 4.353383 AAGTCCACTTGGTTAGGTCTTC 57.647 45.455 0.00 0.00 34.38 2.87
845 920 4.165372 TGAAAGTCCACTTGGTTAGGTCTT 59.835 41.667 0.00 0.00 36.12 3.01
846 921 3.714798 TGAAAGTCCACTTGGTTAGGTCT 59.285 43.478 0.00 0.00 36.12 3.85
847 922 4.081322 TGAAAGTCCACTTGGTTAGGTC 57.919 45.455 0.00 0.00 36.12 3.85
848 923 4.165372 TCTTGAAAGTCCACTTGGTTAGGT 59.835 41.667 0.00 0.00 36.12 3.08
849 924 4.714632 TCTTGAAAGTCCACTTGGTTAGG 58.285 43.478 0.00 0.00 36.12 2.69
850 925 6.294176 CCAATCTTGAAAGTCCACTTGGTTAG 60.294 42.308 0.00 0.00 36.12 2.34
851 926 5.534654 CCAATCTTGAAAGTCCACTTGGTTA 59.465 40.000 0.00 0.00 36.12 2.85
852 927 4.342092 CCAATCTTGAAAGTCCACTTGGTT 59.658 41.667 0.00 0.00 36.12 3.67
853 928 3.891366 CCAATCTTGAAAGTCCACTTGGT 59.109 43.478 0.00 0.00 36.12 3.67
854 929 3.256631 CCCAATCTTGAAAGTCCACTTGG 59.743 47.826 0.00 0.00 36.12 3.61
855 930 3.305608 GCCCAATCTTGAAAGTCCACTTG 60.306 47.826 0.00 0.00 36.12 3.16
856 931 2.893489 GCCCAATCTTGAAAGTCCACTT 59.107 45.455 0.00 0.00 37.91 3.16
857 932 2.108952 AGCCCAATCTTGAAAGTCCACT 59.891 45.455 0.00 0.00 0.00 4.00
858 933 2.519013 AGCCCAATCTTGAAAGTCCAC 58.481 47.619 0.00 0.00 0.00 4.02
868 943 0.337428 ATCAGCCCAAGCCCAATCTT 59.663 50.000 0.00 0.00 41.25 2.40
920 998 8.067751 TCTTGAAAGGAGATCGAATTAAGAGA 57.932 34.615 0.00 0.00 0.00 3.10
998 1271 7.783090 ACGATCGACCACGTATTATATCTAT 57.217 36.000 24.34 0.00 40.92 1.98
1018 1291 0.179084 CGGGTCTGGTATGCAACGAT 60.179 55.000 0.00 0.00 0.00 3.73
1027 1300 1.559368 TTTTCGGATCGGGTCTGGTA 58.441 50.000 0.00 0.00 33.78 3.25
1272 1564 4.680708 GCAGGGTGAAGAATAAGATCGACA 60.681 45.833 0.00 0.00 0.00 4.35
1404 1714 1.158484 CGCGAGGGAGATCGTACTCA 61.158 60.000 0.00 0.00 44.53 3.41
1476 1786 0.921896 AGACATCATTGGGTCTGGGG 59.078 55.000 9.98 0.00 42.49 4.96
1604 1920 1.139654 CGCTTCATCCTCTCCATCCAA 59.860 52.381 0.00 0.00 0.00 3.53
1605 1921 0.755079 CGCTTCATCCTCTCCATCCA 59.245 55.000 0.00 0.00 0.00 3.41
2129 2474 1.374758 GACCTCAACGCTGGAGTGG 60.375 63.158 0.00 0.00 0.00 4.00
2130 2475 1.374758 GGACCTCAACGCTGGAGTG 60.375 63.158 0.00 0.00 0.00 3.51
2131 2476 2.584391 GGGACCTCAACGCTGGAGT 61.584 63.158 0.00 0.00 0.00 3.85
2132 2477 0.970937 TAGGGACCTCAACGCTGGAG 60.971 60.000 0.00 0.00 32.98 3.86
2133 2478 0.543410 TTAGGGACCTCAACGCTGGA 60.543 55.000 0.00 0.00 32.98 3.86
2134 2479 0.323629 TTTAGGGACCTCAACGCTGG 59.676 55.000 0.00 0.00 32.98 4.85
2135 2480 1.804748 GTTTTAGGGACCTCAACGCTG 59.195 52.381 0.00 0.00 32.98 5.18
2137 2482 1.162698 GGTTTTAGGGACCTCAACGC 58.837 55.000 0.00 0.00 34.27 4.84
2138 2483 1.350019 AGGGTTTTAGGGACCTCAACG 59.650 52.381 0.00 0.00 37.34 4.10
2139 2484 3.069079 GAGGGTTTTAGGGACCTCAAC 57.931 52.381 4.78 0.00 46.81 3.18
2167 2621 4.974438 AGGGTGGGAGCGGGAACA 62.974 66.667 0.00 0.00 0.00 3.18
2190 2644 0.537371 GGAAAGAGGTGGGTGTGGTG 60.537 60.000 0.00 0.00 0.00 4.17
2196 2650 0.402121 GCAAGAGGAAAGAGGTGGGT 59.598 55.000 0.00 0.00 0.00 4.51
2200 2654 3.416156 GTCATTGCAAGAGGAAAGAGGT 58.584 45.455 4.94 0.00 0.00 3.85
2211 2665 0.798776 GACAGGGTCGTCATTGCAAG 59.201 55.000 4.94 0.00 35.88 4.01
2224 2678 2.104859 CAGCAGATGCACGACAGGG 61.105 63.158 7.68 0.00 45.16 4.45
2225 2679 3.482809 CAGCAGATGCACGACAGG 58.517 61.111 7.68 0.00 45.16 4.00
2256 2710 4.671590 TGGAGGTGGGCGTCGAGA 62.672 66.667 0.00 0.00 0.00 4.04
2257 2711 4.436998 GTGGAGGTGGGCGTCGAG 62.437 72.222 0.00 0.00 0.00 4.04
2263 2717 0.328258 ATTAGTGTGTGGAGGTGGGC 59.672 55.000 0.00 0.00 0.00 5.36
2284 2738 2.158310 ACATCGTGAGGAGATATGGGGA 60.158 50.000 0.00 0.00 0.00 4.81
2288 2742 4.276926 TGAGACACATCGTGAGGAGATATG 59.723 45.833 0.24 0.00 36.96 1.78
2289 2743 4.464947 TGAGACACATCGTGAGGAGATAT 58.535 43.478 0.24 0.00 36.96 1.63
2290 2744 3.886123 TGAGACACATCGTGAGGAGATA 58.114 45.455 0.24 0.00 36.96 1.98
2291 2745 2.728007 TGAGACACATCGTGAGGAGAT 58.272 47.619 0.24 0.00 36.96 2.75
2292 2746 2.200373 TGAGACACATCGTGAGGAGA 57.800 50.000 0.24 0.00 36.96 3.71
2293 2747 3.185330 CAATGAGACACATCGTGAGGAG 58.815 50.000 0.24 0.00 38.38 3.69
2294 2748 2.675032 GCAATGAGACACATCGTGAGGA 60.675 50.000 0.24 0.00 38.38 3.71
2298 2752 1.730501 AGGCAATGAGACACATCGTG 58.269 50.000 0.00 0.00 38.38 4.35
2299 2753 2.418746 GGTAGGCAATGAGACACATCGT 60.419 50.000 0.00 0.00 38.38 3.73
2300 2754 2.205074 GGTAGGCAATGAGACACATCG 58.795 52.381 0.00 0.00 38.38 3.84
2306 2760 1.202818 GGGATGGGTAGGCAATGAGAC 60.203 57.143 0.00 0.00 0.00 3.36
2307 2761 1.140312 GGGATGGGTAGGCAATGAGA 58.860 55.000 0.00 0.00 0.00 3.27
2313 2767 1.082019 TGTCTGGGATGGGTAGGCA 59.918 57.895 0.00 0.00 0.00 4.75
2318 2772 1.463214 TGTGGTGTCTGGGATGGGT 60.463 57.895 0.00 0.00 0.00 4.51
2328 2782 0.534877 TGACATGGTGCTGTGGTGTC 60.535 55.000 0.00 0.00 39.58 3.67
2331 2785 1.228245 GGTGACATGGTGCTGTGGT 60.228 57.895 0.00 0.00 0.00 4.16
2346 2800 0.812811 CGTGATCTGGAGGCATGGTG 60.813 60.000 0.00 0.00 0.00 4.17
2347 2801 0.977627 TCGTGATCTGGAGGCATGGT 60.978 55.000 0.00 0.00 0.00 3.55
2363 2817 1.271379 TGTCTTTGCGATAGGTGTCGT 59.729 47.619 0.00 0.00 43.27 4.34
2367 2821 4.219033 GTTGTTTGTCTTTGCGATAGGTG 58.781 43.478 0.00 0.00 0.00 4.00
2371 2825 4.679197 GCAATGTTGTTTGTCTTTGCGATA 59.321 37.500 0.00 0.00 35.93 2.92
2372 2826 3.490526 GCAATGTTGTTTGTCTTTGCGAT 59.509 39.130 0.00 0.00 35.93 4.58
2373 2827 2.857152 GCAATGTTGTTTGTCTTTGCGA 59.143 40.909 0.00 0.00 35.93 5.10
2374 2828 2.033832 GGCAATGTTGTTTGTCTTTGCG 60.034 45.455 0.00 0.00 41.96 4.85
2381 2835 0.031994 GGCGAGGCAATGTTGTTTGT 59.968 50.000 0.00 0.00 0.00 2.83
2385 2839 1.228245 AGTGGCGAGGCAATGTTGT 60.228 52.632 0.00 0.00 0.00 3.32
2398 2852 1.571460 CTTCGACAACAGCAGTGGC 59.429 57.895 0.00 0.00 41.61 5.01
2403 2857 3.500680 GGAATTAACCTTCGACAACAGCA 59.499 43.478 0.00 0.00 0.00 4.41
2404 2858 3.500680 TGGAATTAACCTTCGACAACAGC 59.499 43.478 0.00 0.00 0.00 4.40
2405 2859 5.880054 ATGGAATTAACCTTCGACAACAG 57.120 39.130 0.00 0.00 0.00 3.16
2474 2931 8.320295 GCACACACATATAAAATTTCAATTCGG 58.680 33.333 0.00 0.00 0.00 4.30
2476 2933 9.956797 GTGCACACACATATAAAATTTCAATTC 57.043 29.630 13.17 0.00 46.61 2.17
2494 2951 3.304324 CGTCCATTTAACATGTGCACACA 60.304 43.478 24.37 5.85 46.44 3.72
2495 2952 3.058570 TCGTCCATTTAACATGTGCACAC 60.059 43.478 24.37 3.47 0.00 3.82
2498 2955 4.457257 TGAATCGTCCATTTAACATGTGCA 59.543 37.500 0.00 0.00 0.00 4.57
2499 2956 4.980590 TGAATCGTCCATTTAACATGTGC 58.019 39.130 0.00 0.00 0.00 4.57
2505 2962 7.693952 ACATACACATGAATCGTCCATTTAAC 58.306 34.615 0.00 0.00 35.96 2.01
2515 2972 8.075593 TCACATATGAACATACACATGAATCG 57.924 34.615 10.38 0.00 35.96 3.34
2544 3004 8.463456 CACATATACACATGTGCAAAATTCAA 57.537 30.769 25.68 1.89 46.66 2.69
2555 3015 9.230122 TGAAATTGACTTCACATATACACATGT 57.770 29.630 0.00 0.00 39.76 3.21
2595 3055 8.843885 AATCGACATTGATATTCATGATGTCT 57.156 30.769 16.99 2.06 42.59 3.41
2598 3058 9.750882 GTGTAATCGACATTGATATTCATGATG 57.249 33.333 0.00 0.00 41.14 3.07
2599 3059 9.716531 AGTGTAATCGACATTGATATTCATGAT 57.283 29.630 0.00 0.00 41.14 2.45
2622 3082 9.622004 TCGACAAACTCTAAAATTCTAGTAGTG 57.378 33.333 0.00 0.00 0.00 2.74
2623 3083 9.843334 CTCGACAAACTCTAAAATTCTAGTAGT 57.157 33.333 0.00 0.00 0.00 2.73
2624 3084 9.843334 ACTCGACAAACTCTAAAATTCTAGTAG 57.157 33.333 0.00 0.00 0.00 2.57
2626 3086 9.623350 GTACTCGACAAACTCTAAAATTCTAGT 57.377 33.333 0.00 0.00 0.00 2.57
2627 3087 9.074443 GGTACTCGACAAACTCTAAAATTCTAG 57.926 37.037 0.00 0.00 0.00 2.43
2628 3088 7.752239 CGGTACTCGACAAACTCTAAAATTCTA 59.248 37.037 0.00 0.00 42.43 2.10
2629 3089 6.585322 CGGTACTCGACAAACTCTAAAATTCT 59.415 38.462 0.00 0.00 42.43 2.40
2630 3090 6.183360 CCGGTACTCGACAAACTCTAAAATTC 60.183 42.308 0.00 0.00 42.43 2.17
2631 3091 5.636543 CCGGTACTCGACAAACTCTAAAATT 59.363 40.000 0.00 0.00 42.43 1.82
2632 3092 5.047802 TCCGGTACTCGACAAACTCTAAAAT 60.048 40.000 0.00 0.00 42.43 1.82
2633 3093 4.278170 TCCGGTACTCGACAAACTCTAAAA 59.722 41.667 0.00 0.00 42.43 1.52
2634 3094 3.820467 TCCGGTACTCGACAAACTCTAAA 59.180 43.478 0.00 0.00 42.43 1.85
2635 3095 3.411446 TCCGGTACTCGACAAACTCTAA 58.589 45.455 0.00 0.00 42.43 2.10
2636 3096 3.057969 TCCGGTACTCGACAAACTCTA 57.942 47.619 0.00 0.00 42.43 2.43
2637 3097 1.901591 TCCGGTACTCGACAAACTCT 58.098 50.000 0.00 0.00 42.43 3.24
2638 3098 2.712057 TTCCGGTACTCGACAAACTC 57.288 50.000 0.00 0.00 42.43 3.01
2639 3099 3.457610 TTTTCCGGTACTCGACAAACT 57.542 42.857 0.00 0.00 42.43 2.66
2640 3100 4.737353 ATTTTTCCGGTACTCGACAAAC 57.263 40.909 0.00 0.00 42.43 2.93
2641 3101 4.084433 CGAATTTTTCCGGTACTCGACAAA 60.084 41.667 0.00 2.02 42.43 2.83
2642 3102 3.429543 CGAATTTTTCCGGTACTCGACAA 59.570 43.478 0.00 0.00 42.43 3.18
2643 3103 2.988493 CGAATTTTTCCGGTACTCGACA 59.012 45.455 0.00 0.00 42.43 4.35
2644 3104 2.346545 CCGAATTTTTCCGGTACTCGAC 59.653 50.000 0.00 0.00 42.43 4.20
2645 3105 2.609350 CCGAATTTTTCCGGTACTCGA 58.391 47.619 0.00 0.00 42.43 4.04
2664 3124 0.379316 AGTGCGAAACGGTTTTCACC 59.621 50.000 23.77 13.56 41.22 4.02
2665 3125 1.843753 CAAGTGCGAAACGGTTTTCAC 59.156 47.619 21.72 21.72 41.22 3.18
2666 3126 1.202200 CCAAGTGCGAAACGGTTTTCA 60.202 47.619 7.65 6.50 41.22 2.69
2667 3127 1.472990 CCAAGTGCGAAACGGTTTTC 58.527 50.000 7.65 4.01 38.23 2.29
2668 3128 0.526739 GCCAAGTGCGAAACGGTTTT 60.527 50.000 7.65 0.00 0.00 2.43
2669 3129 1.065109 GCCAAGTGCGAAACGGTTT 59.935 52.632 5.68 5.68 0.00 3.27
2670 3130 2.058829 CTGCCAAGTGCGAAACGGTT 62.059 55.000 0.00 0.00 45.60 4.44
2671 3131 2.515057 TGCCAAGTGCGAAACGGT 60.515 55.556 0.00 0.00 45.60 4.83
2672 3132 2.175184 CTCTGCCAAGTGCGAAACGG 62.175 60.000 0.00 0.00 45.60 4.44
2673 3133 1.205064 CTCTGCCAAGTGCGAAACG 59.795 57.895 0.00 0.00 45.60 3.60
2674 3134 0.235926 GTCTCTGCCAAGTGCGAAAC 59.764 55.000 0.00 0.00 45.60 2.78
2675 3135 0.106708 AGTCTCTGCCAAGTGCGAAA 59.893 50.000 0.00 0.00 45.60 3.46
2676 3136 0.319900 GAGTCTCTGCCAAGTGCGAA 60.320 55.000 0.00 0.00 45.60 4.70
2677 3137 1.181741 AGAGTCTCTGCCAAGTGCGA 61.182 55.000 0.18 0.00 45.60 5.10
2678 3138 1.013005 CAGAGTCTCTGCCAAGTGCG 61.013 60.000 16.81 0.00 45.60 5.34
2679 3139 2.838286 CAGAGTCTCTGCCAAGTGC 58.162 57.895 16.81 0.00 37.72 4.40
2697 3157 2.386660 GCCGAGAACTGCACTCTGC 61.387 63.158 3.98 3.98 45.29 4.26
2698 3158 1.739562 GGCCGAGAACTGCACTCTG 60.740 63.158 0.00 0.00 32.87 3.35
2699 3159 1.882989 GAGGCCGAGAACTGCACTCT 61.883 60.000 0.00 0.00 32.87 3.24
2700 3160 1.446966 GAGGCCGAGAACTGCACTC 60.447 63.158 0.00 0.00 0.00 3.51
2701 3161 2.659610 GAGGCCGAGAACTGCACT 59.340 61.111 0.00 0.00 0.00 4.40
2702 3162 2.811317 CGAGGCCGAGAACTGCAC 60.811 66.667 0.00 0.00 38.22 4.57
2703 3163 4.069232 CCGAGGCCGAGAACTGCA 62.069 66.667 0.00 0.00 38.22 4.41
2704 3164 4.821589 CCCGAGGCCGAGAACTGC 62.822 72.222 0.00 0.00 38.22 4.40
2705 3165 2.050350 TACCCGAGGCCGAGAACTG 61.050 63.158 0.00 0.00 38.22 3.16
2706 3166 2.050934 GTACCCGAGGCCGAGAACT 61.051 63.158 0.00 0.00 38.22 3.01
2707 3167 2.002509 GAGTACCCGAGGCCGAGAAC 62.003 65.000 0.00 0.00 38.22 3.01
2708 3168 1.751927 GAGTACCCGAGGCCGAGAA 60.752 63.158 0.00 0.00 38.22 2.87
2709 3169 2.124403 GAGTACCCGAGGCCGAGA 60.124 66.667 0.00 0.00 38.22 4.04
2710 3170 3.584052 CGAGTACCCGAGGCCGAG 61.584 72.222 0.00 0.00 38.22 4.63
2718 3178 3.762247 TTTCCGGCCGAGTACCCG 61.762 66.667 30.73 8.04 43.97 5.28
2719 3179 2.125391 GTTTCCGGCCGAGTACCC 60.125 66.667 30.73 5.13 0.00 3.69
2720 3180 2.125391 GGTTTCCGGCCGAGTACC 60.125 66.667 30.73 24.78 0.00 3.34
2721 3181 1.447314 CAGGTTTCCGGCCGAGTAC 60.447 63.158 30.73 19.94 0.00 2.73
2722 3182 2.975536 CAGGTTTCCGGCCGAGTA 59.024 61.111 30.73 9.00 0.00 2.59
2723 3183 4.699522 GCAGGTTTCCGGCCGAGT 62.700 66.667 30.73 0.15 38.74 4.18
2729 3189 2.146073 CTTTGCTGGCAGGTTTCCGG 62.146 60.000 17.64 0.00 0.00 5.14
2730 3190 1.172180 TCTTTGCTGGCAGGTTTCCG 61.172 55.000 17.64 0.00 0.00 4.30
2731 3191 0.315251 GTCTTTGCTGGCAGGTTTCC 59.685 55.000 17.64 0.00 0.00 3.13
2732 3192 0.315251 GGTCTTTGCTGGCAGGTTTC 59.685 55.000 17.64 0.00 0.00 2.78
2733 3193 0.396974 TGGTCTTTGCTGGCAGGTTT 60.397 50.000 17.64 0.00 0.00 3.27
2734 3194 1.109323 GTGGTCTTTGCTGGCAGGTT 61.109 55.000 17.64 0.00 0.00 3.50
2735 3195 1.529244 GTGGTCTTTGCTGGCAGGT 60.529 57.895 17.64 0.00 0.00 4.00
2736 3196 0.825010 AAGTGGTCTTTGCTGGCAGG 60.825 55.000 17.64 0.00 0.00 4.85
2737 3197 1.035139 AAAGTGGTCTTTGCTGGCAG 58.965 50.000 10.94 10.94 41.62 4.85
2738 3198 3.205815 AAAGTGGTCTTTGCTGGCA 57.794 47.368 0.00 0.00 41.62 4.92
2745 3205 0.537371 CCCTCGGCAAAGTGGTCTTT 60.537 55.000 0.00 0.00 43.66 2.52
2746 3206 1.073199 CCCTCGGCAAAGTGGTCTT 59.927 57.895 0.00 0.00 35.14 3.01
2747 3207 2.750350 CCCTCGGCAAAGTGGTCT 59.250 61.111 0.00 0.00 0.00 3.85
2763 3223 4.759205 AGTCCCCAAATGGCGGCC 62.759 66.667 13.32 13.32 0.00 6.13
2764 3224 2.679996 AAGTCCCCAAATGGCGGC 60.680 61.111 0.00 0.00 0.00 6.53
2765 3225 2.350458 CCAAGTCCCCAAATGGCGG 61.350 63.158 0.00 0.00 0.00 6.13
2766 3226 3.287445 CCAAGTCCCCAAATGGCG 58.713 61.111 0.00 0.00 0.00 5.69
2768 3228 1.002315 CTTTGCCAAGTCCCCAAATGG 59.998 52.381 0.00 0.00 36.00 3.16
2769 3229 1.693606 ACTTTGCCAAGTCCCCAAATG 59.306 47.619 0.00 0.00 39.15 2.32
2770 3230 2.101640 ACTTTGCCAAGTCCCCAAAT 57.898 45.000 0.00 0.00 39.15 2.32
2771 3231 2.757894 TACTTTGCCAAGTCCCCAAA 57.242 45.000 6.43 0.00 42.66 3.28
2772 3232 2.990740 ATACTTTGCCAAGTCCCCAA 57.009 45.000 6.43 0.00 42.66 4.12
2773 3233 2.896685 CAAATACTTTGCCAAGTCCCCA 59.103 45.455 6.43 0.00 42.66 4.96
2774 3234 3.592898 CAAATACTTTGCCAAGTCCCC 57.407 47.619 6.43 0.00 42.66 4.81


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

AutoCloner maintained by Alex Coulton.