Multiple sequence alignment - TraesCS2A01G035200

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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 TraesCS2A01G035200 chr2A 100.000 4097 0 0 1 4097 15354834 15358930 0.000000e+00 7566.0
1 TraesCS2A01G035200 chr2A 81.340 209 15 10 456 653 15292191 15292386 9.180000e-32 148.0
2 TraesCS2A01G035200 chr2A 97.297 74 1 1 1 73 14572882 14572955 1.550000e-24 124.0
3 TraesCS2A01G035200 chr2A 95.946 74 1 2 1 73 15364300 15364228 7.190000e-23 119.0
4 TraesCS2A01G035200 chr2A 94.521 73 2 2 1 73 15369487 15369417 1.200000e-20 111.0
5 TraesCS2A01G035200 chr2A 94.521 73 2 2 1 73 15814890 15814960 1.200000e-20 111.0
6 TraesCS2A01G035200 chr2A 81.553 103 6 6 532 634 15365758 15365669 5.680000e-09 73.1
7 TraesCS2A01G035200 chr2B 89.840 3622 196 71 532 4094 23965183 23968691 0.000000e+00 4492.0
8 TraesCS2A01G035200 chr2B 85.811 592 74 6 2265 2853 23343108 23343692 1.620000e-173 619.0
9 TraesCS2A01G035200 chr2B 85.792 183 24 2 954 1135 23980577 23980396 4.180000e-45 193.0
10 TraesCS2A01G035200 chr2B 84.956 113 5 7 1 102 511131561 511131672 2.010000e-18 104.0
11 TraesCS2A01G035200 chr2B 100.000 35 0 0 73 107 135024661 135024695 9.510000e-07 65.8
12 TraesCS2A01G035200 chr2D 93.621 2524 125 13 985 3482 13320317 13322830 0.000000e+00 3736.0
13 TraesCS2A01G035200 chr2D 82.306 876 67 33 105 946 13319495 13320316 0.000000e+00 678.0
14 TraesCS2A01G035200 chr2D 83.833 600 51 21 3489 4065 13322997 13323573 2.800000e-146 529.0
15 TraesCS2A01G035200 chr2D 100.000 34 0 0 72 105 89616548 89616581 3.420000e-06 63.9
16 TraesCS2A01G035200 chr2D 94.737 38 2 0 72 109 627832722 627832759 4.420000e-05 60.2
17 TraesCS2A01G035200 chr3D 89.450 673 59 7 2265 2937 511670121 511670781 0.000000e+00 839.0
18 TraesCS2A01G035200 chr1D 88.872 674 66 5 2265 2938 455512078 455512742 0.000000e+00 821.0
19 TraesCS2A01G035200 chr4D 88.676 680 64 7 2265 2938 31720468 31721140 0.000000e+00 817.0
20 TraesCS2A01G035200 chr3B 86.647 674 79 8 2265 2938 464329804 464329142 0.000000e+00 736.0
21 TraesCS2A01G035200 chr3B 84.421 674 77 14 2265 2938 464162820 464162175 4.470000e-179 638.0
22 TraesCS2A01G035200 chr3A 86.647 674 79 9 2265 2938 478051309 478050647 0.000000e+00 736.0
23 TraesCS2A01G035200 chr7A 86.478 673 64 9 2265 2937 195750342 195750987 0.000000e+00 713.0
24 TraesCS2A01G035200 chr6B 95.890 73 2 1 1 73 559355134 559355063 2.590000e-22 117.0
25 TraesCS2A01G035200 chr6B 97.222 36 1 0 72 107 559355050 559355015 1.230000e-05 62.1
26 TraesCS2A01G035200 chr6B 97.222 36 1 0 72 107 630861535 630861500 1.230000e-05 62.1
27 TraesCS2A01G035200 chr6A 95.890 73 2 1 1 73 70570880 70570951 2.590000e-22 117.0
28 TraesCS2A01G035200 chr6A 95.890 73 2 1 1 73 326797617 326797688 2.590000e-22 117.0
29 TraesCS2A01G035200 chr5A 94.595 74 2 2 1 73 659881052 659880980 3.350000e-21 113.0
30 TraesCS2A01G035200 chr5A 97.222 36 1 0 72 107 659880967 659880932 1.230000e-05 62.1
31 TraesCS2A01G035200 chr7D 97.222 36 1 0 72 107 576159153 576159188 1.230000e-05 62.1
32 TraesCS2A01G035200 chr6D 97.222 36 1 0 72 107 335057970 335057935 1.230000e-05 62.1
33 TraesCS2A01G035200 chr6D 94.872 39 1 1 72 109 14977662 14977624 4.420000e-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 TraesCS2A01G035200 chr2A 15354834 15358930 4096 False 7566.000000 7566 100.000000 1 4097 1 chr2A.!!$F3 4096
1 TraesCS2A01G035200 chr2B 23965183 23968691 3508 False 4492.000000 4492 89.840000 532 4094 1 chr2B.!!$F2 3562
2 TraesCS2A01G035200 chr2B 23343108 23343692 584 False 619.000000 619 85.811000 2265 2853 1 chr2B.!!$F1 588
3 TraesCS2A01G035200 chr2D 13319495 13323573 4078 False 1647.666667 3736 86.586667 105 4065 3 chr2D.!!$F3 3960
4 TraesCS2A01G035200 chr3D 511670121 511670781 660 False 839.000000 839 89.450000 2265 2937 1 chr3D.!!$F1 672
5 TraesCS2A01G035200 chr1D 455512078 455512742 664 False 821.000000 821 88.872000 2265 2938 1 chr1D.!!$F1 673
6 TraesCS2A01G035200 chr4D 31720468 31721140 672 False 817.000000 817 88.676000 2265 2938 1 chr4D.!!$F1 673
7 TraesCS2A01G035200 chr3B 464329142 464329804 662 True 736.000000 736 86.647000 2265 2938 1 chr3B.!!$R2 673
8 TraesCS2A01G035200 chr3B 464162175 464162820 645 True 638.000000 638 84.421000 2265 2938 1 chr3B.!!$R1 673
9 TraesCS2A01G035200 chr3A 478050647 478051309 662 True 736.000000 736 86.647000 2265 2938 1 chr3A.!!$R1 673
10 TraesCS2A01G035200 chr7A 195750342 195750987 645 False 713.000000 713 86.478000 2265 2937 1 chr7A.!!$F1 672

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
344 345 0.036732 TGACAGATCAAGGGGTGTGC 59.963 55.0 0.0 0.0 0.00 4.57 F
946 1008 0.178068 AACACCTCGTTGCACTCTGT 59.822 50.0 0.0 0.0 36.12 3.41 F
999 1061 0.338467 TCAAAGGGAGATCGGGAGGA 59.662 55.0 0.0 0.0 0.00 3.71 F
1230 1295 0.395036 TCAGCTCTCCTTCTCCCTCG 60.395 60.0 0.0 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1301 1366 0.035056 GAACCACTCCCCATGGACTG 60.035 60.000 15.22 4.75 39.87 3.51 R
2812 2907 1.376037 GTCTTGTTGCGGAGGAGGG 60.376 63.158 0.00 0.00 0.00 4.30 R
2857 2952 1.669115 CCTTCACCGTGCTCCACAG 60.669 63.158 0.00 0.00 33.40 3.66 R
3286 3394 3.595758 GCACGCACACCAAGGCTT 61.596 61.111 0.00 0.00 0.00 4.35 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
22 23 4.740268 GATCTTGCATTGAGATTTGTGCA 58.260 39.130 1.03 0.00 44.97 4.57
26 27 4.056092 TGCATTGAGATTTGTGCAAACA 57.944 36.364 0.00 0.00 43.83 2.83
27 28 4.439968 TGCATTGAGATTTGTGCAAACAA 58.560 34.783 0.00 1.37 43.83 2.83
28 29 5.057819 TGCATTGAGATTTGTGCAAACAAT 58.942 33.333 0.00 3.49 43.83 2.71
29 30 5.527951 TGCATTGAGATTTGTGCAAACAATT 59.472 32.000 0.00 0.00 43.83 2.32
30 31 6.038382 TGCATTGAGATTTGTGCAAACAATTT 59.962 30.769 0.00 0.00 43.83 1.82
31 32 6.913673 GCATTGAGATTTGTGCAAACAATTTT 59.086 30.769 0.00 0.00 37.52 1.82
32 33 7.432838 GCATTGAGATTTGTGCAAACAATTTTT 59.567 29.630 0.00 0.00 37.52 1.94
72 73 8.962884 TTCTTCTTGCATACTATATTGCTTGA 57.037 30.769 0.00 0.00 39.60 3.02
73 74 8.962884 TCTTCTTGCATACTATATTGCTTGAA 57.037 30.769 0.00 3.20 39.60 2.69
74 75 9.049523 TCTTCTTGCATACTATATTGCTTGAAG 57.950 33.333 17.05 17.05 42.71 3.02
75 76 8.737168 TTCTTGCATACTATATTGCTTGAAGT 57.263 30.769 0.00 0.00 39.60 3.01
76 77 8.370493 TCTTGCATACTATATTGCTTGAAGTC 57.630 34.615 0.00 0.00 39.60 3.01
77 78 8.206867 TCTTGCATACTATATTGCTTGAAGTCT 58.793 33.333 0.00 0.00 39.60 3.24
78 79 7.953158 TGCATACTATATTGCTTGAAGTCTC 57.047 36.000 0.00 0.00 39.60 3.36
79 80 7.500141 TGCATACTATATTGCTTGAAGTCTCA 58.500 34.615 0.00 0.00 39.60 3.27
80 81 7.654923 TGCATACTATATTGCTTGAAGTCTCAG 59.345 37.037 0.00 0.00 39.60 3.35
81 82 7.655328 GCATACTATATTGCTTGAAGTCTCAGT 59.345 37.037 0.00 0.00 35.95 3.41
82 83 9.190858 CATACTATATTGCTTGAAGTCTCAGTC 57.809 37.037 0.00 0.00 31.69 3.51
83 84 6.269315 ACTATATTGCTTGAAGTCTCAGTCG 58.731 40.000 0.00 0.00 31.69 4.18
84 85 3.667497 ATTGCTTGAAGTCTCAGTCGA 57.333 42.857 0.00 0.00 31.69 4.20
85 86 2.423926 TGCTTGAAGTCTCAGTCGAC 57.576 50.000 7.70 7.70 31.69 4.20
86 87 1.957177 TGCTTGAAGTCTCAGTCGACT 59.043 47.619 13.58 13.58 45.73 4.18
87 88 2.287849 TGCTTGAAGTCTCAGTCGACTG 60.288 50.000 34.76 34.76 43.14 3.51
98 99 2.701107 CAGTCGACTGAGACCTAGACA 58.299 52.381 36.73 0.00 46.59 3.41
99 100 3.075148 CAGTCGACTGAGACCTAGACAA 58.925 50.000 36.73 0.00 46.59 3.18
100 101 3.502595 CAGTCGACTGAGACCTAGACAAA 59.497 47.826 36.73 0.00 46.59 2.83
101 102 3.502979 AGTCGACTGAGACCTAGACAAAC 59.497 47.826 19.30 0.00 41.83 2.93
102 103 3.502979 GTCGACTGAGACCTAGACAAACT 59.497 47.826 8.70 0.00 35.22 2.66
103 104 3.752222 TCGACTGAGACCTAGACAAACTC 59.248 47.826 0.00 0.00 0.00 3.01
109 110 7.832769 ACTGAGACCTAGACAAACTCTTTATC 58.167 38.462 0.00 0.00 0.00 1.75
117 118 4.452455 AGACAAACTCTTTATCTTGCGTGG 59.548 41.667 0.00 0.00 0.00 4.94
123 124 5.245531 ACTCTTTATCTTGCGTGGAATTGA 58.754 37.500 0.00 0.00 0.00 2.57
136 137 5.392380 GCGTGGAATTGAGTGAATTTGAGAT 60.392 40.000 0.00 0.00 34.18 2.75
166 167 0.695924 AATGGGGTGTCCGATTGTGA 59.304 50.000 0.00 0.00 39.53 3.58
172 173 2.882137 GGGTGTCCGATTGTGAAAAAGA 59.118 45.455 0.00 0.00 0.00 2.52
177 178 4.201970 TGTCCGATTGTGAAAAAGAACACC 60.202 41.667 0.00 0.00 36.35 4.16
194 195 4.814900 CGAAGGGTGATCGGTCAG 57.185 61.111 0.00 0.00 36.68 3.51
196 197 0.246635 CGAAGGGTGATCGGTCAGTT 59.753 55.000 0.00 0.00 36.68 3.16
201 202 1.359459 GGTGATCGGTCAGTTTCCGC 61.359 60.000 0.00 0.00 46.49 5.54
202 203 1.445410 TGATCGGTCAGTTTCCGCG 60.445 57.895 0.00 0.00 46.49 6.46
206 207 2.741211 GGTCAGTTTCCGCGGACC 60.741 66.667 31.19 21.90 44.00 4.46
210 211 3.932483 AGTTTCCGCGGACCCGTT 61.932 61.111 31.19 9.29 42.09 4.44
226 227 1.081641 GTTCGGACGAGTTCGCAGA 60.082 57.895 0.73 0.00 44.43 4.26
229 230 1.154016 CGGACGAGTTCGCAGATGT 60.154 57.895 0.73 0.00 44.43 3.06
240 241 3.953712 TCGCAGATGTTTAGAGGACAA 57.046 42.857 0.00 0.00 0.00 3.18
253 254 8.780249 TGTTTAGAGGACAAATTTGCTAAGTAC 58.220 33.333 18.12 12.37 0.00 2.73
254 255 7.591006 TTAGAGGACAAATTTGCTAAGTACG 57.409 36.000 18.12 0.00 0.00 3.67
256 257 4.007659 AGGACAAATTTGCTAAGTACGGG 58.992 43.478 18.12 0.00 0.00 5.28
268 269 2.299326 AGTACGGGTGTAGAAGTGGT 57.701 50.000 0.00 0.00 0.00 4.16
309 310 1.082821 CACGCCGTCACATGTGTTG 60.083 57.895 24.63 17.35 0.00 3.33
310 311 2.250939 ACGCCGTCACATGTGTTGG 61.251 57.895 24.63 24.99 0.00 3.77
337 338 2.738846 CGGACAAGTTGACAGATCAAGG 59.261 50.000 10.54 0.00 45.58 3.61
344 345 0.036732 TGACAGATCAAGGGGTGTGC 59.963 55.000 0.00 0.00 0.00 4.57
354 355 3.383185 TCAAGGGGTGTGCTTAAACAAAG 59.617 43.478 0.00 0.00 38.32 2.77
361 365 4.202111 GGTGTGCTTAAACAAAGTGTCCAT 60.202 41.667 0.00 0.00 37.53 3.41
367 371 0.831711 AACAAAGTGTCCATGGGGCC 60.832 55.000 13.02 0.00 0.00 5.80
370 374 2.445492 AAAGTGTCCATGGGGCCCAG 62.445 60.000 31.98 21.46 36.75 4.45
384 388 1.445095 CCCAGGGAGCAAGAGATCG 59.555 63.158 0.00 0.00 0.00 3.69
410 415 6.969828 TTTTTGAAAAACAAACGGCATACT 57.030 29.167 0.00 0.00 46.32 2.12
411 416 6.576551 TTTTGAAAAACAAACGGCATACTC 57.423 33.333 0.00 0.00 46.32 2.59
412 417 4.231718 TGAAAAACAAACGGCATACTCC 57.768 40.909 0.00 0.00 0.00 3.85
413 418 3.632604 TGAAAAACAAACGGCATACTCCA 59.367 39.130 0.00 0.00 0.00 3.86
414 419 4.279671 TGAAAAACAAACGGCATACTCCAT 59.720 37.500 0.00 0.00 0.00 3.41
415 420 4.864704 AAAACAAACGGCATACTCCATT 57.135 36.364 0.00 0.00 0.00 3.16
416 421 4.864704 AAACAAACGGCATACTCCATTT 57.135 36.364 0.00 0.00 0.00 2.32
417 422 4.864704 AACAAACGGCATACTCCATTTT 57.135 36.364 0.00 0.00 0.00 1.82
418 423 4.864704 ACAAACGGCATACTCCATTTTT 57.135 36.364 0.00 0.00 0.00 1.94
449 454 1.722034 AACAGAGAGAGGCAGTCCAA 58.278 50.000 0.00 0.00 33.74 3.53
450 455 1.949799 ACAGAGAGAGGCAGTCCAAT 58.050 50.000 0.00 0.00 33.74 3.16
452 457 3.030291 ACAGAGAGAGGCAGTCCAATAG 58.970 50.000 0.00 0.00 33.74 1.73
529 534 3.473625 CATCAGCCTCACTGCATGATAA 58.526 45.455 0.00 0.00 46.76 1.75
530 535 3.189618 TCAGCCTCACTGCATGATAAG 57.810 47.619 0.00 0.00 46.76 1.73
555 560 6.088824 GCATGATAACAACTTTCTCCTGTTG 58.911 40.000 0.00 0.00 46.19 3.33
592 609 2.288395 CCAACAAACAATCACCCAGCTC 60.288 50.000 0.00 0.00 0.00 4.09
593 610 1.620822 ACAAACAATCACCCAGCTCC 58.379 50.000 0.00 0.00 0.00 4.70
595 612 2.173519 CAAACAATCACCCAGCTCCAT 58.826 47.619 0.00 0.00 0.00 3.41
613 630 2.107726 CCATGTCCATCATCCATCCACT 59.892 50.000 0.00 0.00 34.09 4.00
653 671 2.826428 CACCACCACCAGATTCTATCG 58.174 52.381 0.00 0.00 0.00 2.92
655 673 1.414181 CCACCACCAGATTCTATCGCT 59.586 52.381 0.00 0.00 0.00 4.93
657 675 2.363680 CACCACCAGATTCTATCGCTCT 59.636 50.000 0.00 0.00 0.00 4.09
658 676 2.625790 ACCACCAGATTCTATCGCTCTC 59.374 50.000 0.00 0.00 0.00 3.20
659 677 2.890311 CCACCAGATTCTATCGCTCTCT 59.110 50.000 0.00 0.00 0.00 3.10
660 678 3.305267 CCACCAGATTCTATCGCTCTCTG 60.305 52.174 0.00 0.00 34.48 3.35
662 680 2.295629 CCAGATTCTATCGCTCTCTGCA 59.704 50.000 0.00 0.00 43.06 4.41
663 681 3.567530 CAGATTCTATCGCTCTCTGCAG 58.432 50.000 7.63 7.63 43.06 4.41
664 682 2.557924 AGATTCTATCGCTCTCTGCAGG 59.442 50.000 15.13 4.77 43.06 4.85
720 772 1.002544 CACCTCCTCCCACTCTGAAAC 59.997 57.143 0.00 0.00 0.00 2.78
762 818 1.181786 CCTCACTCACTCACTCTCCC 58.818 60.000 0.00 0.00 0.00 4.30
763 819 1.272425 CCTCACTCACTCACTCTCCCT 60.272 57.143 0.00 0.00 0.00 4.20
764 820 2.091541 CTCACTCACTCACTCTCCCTC 58.908 57.143 0.00 0.00 0.00 4.30
766 822 1.080638 ACTCACTCACTCTCCCTCCT 58.919 55.000 0.00 0.00 0.00 3.69
767 823 1.272425 ACTCACTCACTCTCCCTCCTG 60.272 57.143 0.00 0.00 0.00 3.86
768 824 0.780637 TCACTCACTCTCCCTCCTGT 59.219 55.000 0.00 0.00 0.00 4.00
769 825 1.993301 TCACTCACTCTCCCTCCTGTA 59.007 52.381 0.00 0.00 0.00 2.74
770 826 2.096248 CACTCACTCTCCCTCCTGTAC 58.904 57.143 0.00 0.00 0.00 2.90
946 1008 0.178068 AACACCTCGTTGCACTCTGT 59.822 50.000 0.00 0.00 36.12 3.41
947 1009 1.037493 ACACCTCGTTGCACTCTGTA 58.963 50.000 0.00 0.00 0.00 2.74
948 1010 1.618837 ACACCTCGTTGCACTCTGTAT 59.381 47.619 0.00 0.00 0.00 2.29
949 1011 2.263077 CACCTCGTTGCACTCTGTATC 58.737 52.381 0.00 0.00 0.00 2.24
950 1012 1.893137 ACCTCGTTGCACTCTGTATCA 59.107 47.619 0.00 0.00 0.00 2.15
951 1013 2.094494 ACCTCGTTGCACTCTGTATCAG 60.094 50.000 0.00 0.00 0.00 2.90
952 1014 1.923204 CTCGTTGCACTCTGTATCAGC 59.077 52.381 0.00 0.00 0.00 4.26
953 1015 1.546029 TCGTTGCACTCTGTATCAGCT 59.454 47.619 0.00 0.00 0.00 4.24
954 1016 1.923204 CGTTGCACTCTGTATCAGCTC 59.077 52.381 0.00 0.00 0.00 4.09
955 1017 2.672195 CGTTGCACTCTGTATCAGCTCA 60.672 50.000 0.00 0.00 0.00 4.26
956 1018 2.928757 GTTGCACTCTGTATCAGCTCAG 59.071 50.000 0.00 0.00 0.00 3.35
957 1019 1.134877 TGCACTCTGTATCAGCTCAGC 60.135 52.381 0.00 0.00 0.00 4.26
958 1020 1.136695 GCACTCTGTATCAGCTCAGCT 59.863 52.381 0.00 0.00 40.77 4.24
959 1021 2.799207 GCACTCTGTATCAGCTCAGCTC 60.799 54.545 0.00 0.00 36.40 4.09
960 1022 1.675483 ACTCTGTATCAGCTCAGCTCG 59.325 52.381 0.00 0.00 36.40 5.03
961 1023 1.675483 CTCTGTATCAGCTCAGCTCGT 59.325 52.381 0.00 0.00 36.40 4.18
962 1024 2.095461 TCTGTATCAGCTCAGCTCGTT 58.905 47.619 0.00 0.00 36.40 3.85
963 1025 2.098280 TCTGTATCAGCTCAGCTCGTTC 59.902 50.000 0.00 0.00 36.40 3.95
964 1026 2.095461 TGTATCAGCTCAGCTCGTTCT 58.905 47.619 0.00 0.00 36.40 3.01
968 1030 1.201181 TCAGCTCAGCTCGTTCTCTTC 59.799 52.381 0.00 0.00 36.40 2.87
999 1061 0.338467 TCAAAGGGAGATCGGGAGGA 59.662 55.000 0.00 0.00 0.00 3.71
1014 1076 2.838202 GGGAGGAATGAAGTGGTACTCA 59.162 50.000 0.00 0.00 0.00 3.41
1015 1077 3.263425 GGGAGGAATGAAGTGGTACTCAA 59.737 47.826 0.00 0.00 0.00 3.02
1101 1166 2.767445 CGGCTGCATGTCCATGGTG 61.767 63.158 12.58 3.82 39.16 4.17
1160 1225 3.157949 CCCTCCCTCCTCCGCTTC 61.158 72.222 0.00 0.00 0.00 3.86
1173 1238 2.048127 GCTTCCAACGACTCCGCT 60.048 61.111 0.00 0.00 39.95 5.52
1230 1295 0.395036 TCAGCTCTCCTTCTCCCTCG 60.395 60.000 0.00 0.00 0.00 4.63
1233 1298 2.440430 TCTCCTTCTCCCTCGCCG 60.440 66.667 0.00 0.00 0.00 6.46
1253 1318 1.400242 GCACGAGAAAGGTACGTACGT 60.400 52.381 25.98 25.98 38.47 3.57
1254 1319 2.499896 CACGAGAAAGGTACGTACGTC 58.500 52.381 26.53 15.93 38.47 4.34
1257 1322 3.189287 ACGAGAAAGGTACGTACGTCAAT 59.811 43.478 26.53 8.82 38.47 2.57
1300 1365 2.878580 CAACTGAGTGCAGAGAGCTAG 58.121 52.381 0.00 0.00 45.17 3.42
1301 1366 0.817013 ACTGAGTGCAGAGAGCTAGC 59.183 55.000 6.62 6.62 45.17 3.42
1312 1377 1.053264 AGAGCTAGCAGTCCATGGGG 61.053 60.000 18.83 3.12 0.00 4.96
1320 1385 2.387952 AGTCCATGGGGAGTGGTTC 58.612 57.895 13.02 0.00 45.40 3.62
1333 1403 5.505173 GGAGTGGTTCCATTTGACATATG 57.495 43.478 0.00 0.00 46.01 1.78
1337 1407 3.376859 TGGTTCCATTTGACATATGCGAC 59.623 43.478 1.58 2.11 0.00 5.19
1594 1669 4.082523 CGCCGGGCCTCAAGAAGA 62.083 66.667 14.55 0.00 0.00 2.87
1597 1672 2.510238 CGGGCCTCAAGAAGAGCG 60.510 66.667 0.84 0.00 43.31 5.03
1598 1673 2.124942 GGGCCTCAAGAAGAGCGG 60.125 66.667 0.84 0.00 43.31 5.52
1600 1675 3.191539 GCCTCAAGAAGAGCGGCG 61.192 66.667 0.51 0.51 43.31 6.46
1601 1676 2.510238 CCTCAAGAAGAGCGGCGG 60.510 66.667 9.78 0.00 43.31 6.13
2104 2185 2.331265 GTGGTCCAAGTTCCAGCAC 58.669 57.895 0.00 0.00 34.16 4.40
2177 2258 3.617143 AAGCCGATCAGCAGCAGCA 62.617 57.895 3.17 0.00 45.49 4.41
2178 2259 3.574445 GCCGATCAGCAGCAGCAG 61.574 66.667 3.17 0.00 45.49 4.24
2179 2260 3.574445 CCGATCAGCAGCAGCAGC 61.574 66.667 3.17 0.46 45.49 5.25
2281 2362 0.804544 TCATCCAATTCCGACGACGC 60.805 55.000 0.64 0.00 38.29 5.19
2503 2589 0.876342 CCGCCGCAGATTACTTCCTC 60.876 60.000 0.00 0.00 0.00 3.71
2508 2594 0.466124 GCAGATTACTTCCTCCCGCT 59.534 55.000 0.00 0.00 0.00 5.52
2509 2595 1.808133 GCAGATTACTTCCTCCCGCTG 60.808 57.143 0.00 0.00 0.00 5.18
2510 2596 1.482593 CAGATTACTTCCTCCCGCTGT 59.517 52.381 0.00 0.00 0.00 4.40
2785 2880 1.071542 TCACGCAAGAAATCCTCACCA 59.928 47.619 0.00 0.00 43.62 4.17
2798 2893 1.842381 CTCACCAACCTCCTCCACCC 61.842 65.000 0.00 0.00 0.00 4.61
3286 3394 2.767445 CGATGACGACGGGTGGCTA 61.767 63.158 0.00 0.00 42.66 3.93
3287 3395 1.514087 GATGACGACGGGTGGCTAA 59.486 57.895 0.00 0.00 0.00 3.09
3419 3530 8.722480 TTGAGATTTCAGGTGTACATAATGAG 57.278 34.615 0.00 0.00 34.15 2.90
3421 3532 5.755375 AGATTTCAGGTGTACATAATGAGCG 59.245 40.000 0.00 0.00 0.00 5.03
3455 3566 7.809331 TCATCTTGTAATTTTGATCAACAGCAC 59.191 33.333 7.89 4.69 0.00 4.40
3486 3602 5.948758 ACATTCCCTTCTCTCATTTTCCTTC 59.051 40.000 0.00 0.00 0.00 3.46
3544 3820 0.984109 GCGTCGACGAACCGAAAATA 59.016 50.000 39.74 0.00 43.02 1.40
3545 3821 1.585214 GCGTCGACGAACCGAAAATAT 59.415 47.619 39.74 0.00 43.02 1.28
3549 3825 4.201513 CGTCGACGAACCGAAAATATTTGA 60.202 41.667 33.35 0.00 43.02 2.69
3582 3859 3.129462 TGGAACTTTGCGAAAATGTCACA 59.871 39.130 0.00 0.00 0.00 3.58
3627 3904 2.664402 ATGGAATGAGGTGGGTATGC 57.336 50.000 0.00 0.00 0.00 3.14
3628 3905 1.595311 TGGAATGAGGTGGGTATGCT 58.405 50.000 0.00 0.00 0.00 3.79
3693 3971 9.260002 CAGCTTGAAAAACACCATAAAAGTATT 57.740 29.630 0.00 0.00 0.00 1.89
3706 3984 8.362639 ACCATAAAAGTATTGGATTGATGATGC 58.637 33.333 0.00 0.00 0.00 3.91
3709 3987 7.414222 AAAAGTATTGGATTGATGATGCTGT 57.586 32.000 0.00 0.00 0.00 4.40
3730 4031 1.964223 AGTACCATCGCCTAGGATGTG 59.036 52.381 14.75 6.85 41.76 3.21
3763 4064 3.118334 GCTGATGCATATGCTAGATCCCT 60.118 47.826 27.13 3.30 42.66 4.20
3764 4065 4.443621 CTGATGCATATGCTAGATCCCTG 58.556 47.826 27.13 11.39 42.66 4.45
3765 4066 2.775911 TGCATATGCTAGATCCCTGC 57.224 50.000 27.13 0.00 42.66 4.85
3766 4067 1.980036 TGCATATGCTAGATCCCTGCA 59.020 47.619 27.13 2.04 42.66 4.41
3768 4069 2.943690 GCATATGCTAGATCCCTGCATG 59.056 50.000 20.64 12.02 45.52 4.06
3769 4070 2.775911 TATGCTAGATCCCTGCATGC 57.224 50.000 20.75 11.82 45.52 4.06
3770 4071 0.769247 ATGCTAGATCCCTGCATGCA 59.231 50.000 21.29 21.29 44.48 3.96
3847 4148 0.608856 TAATGTGGGCAGCAGTGGTG 60.609 55.000 18.01 18.01 0.00 4.17
3878 4179 2.615747 GGTAGGGACAGACAAAAGAGGC 60.616 54.545 0.00 0.00 0.00 4.70
3882 4183 1.528129 GACAGACAAAAGAGGCAGGG 58.472 55.000 0.00 0.00 0.00 4.45
3885 4186 0.037447 AGACAAAAGAGGCAGGGAGC 59.963 55.000 0.00 0.00 44.65 4.70
3933 4234 8.770438 AGTACTAGTACTACTACACACTGAAC 57.230 38.462 29.96 3.26 43.98 3.18
4018 4320 5.546621 TTAACTATCCCATCAGTACCTGC 57.453 43.478 0.00 0.00 0.00 4.85
4019 4321 3.046283 ACTATCCCATCAGTACCTGCA 57.954 47.619 0.00 0.00 0.00 4.41
4020 4322 2.700897 ACTATCCCATCAGTACCTGCAC 59.299 50.000 0.00 0.00 0.00 4.57
4021 4323 0.839946 ATCCCATCAGTACCTGCACC 59.160 55.000 0.00 0.00 0.00 5.01
4022 4324 0.252696 TCCCATCAGTACCTGCACCT 60.253 55.000 0.00 0.00 0.00 4.00
4023 4325 0.107508 CCCATCAGTACCTGCACCTG 60.108 60.000 0.00 0.00 0.00 4.00
4066 4368 3.978687 TCAAACTGAAACGGAGAGAGAC 58.021 45.455 0.00 0.00 0.00 3.36
4081 4383 2.487762 GAGAGACAGAGAGAGTGTGTGG 59.512 54.545 0.00 0.00 31.30 4.17
4094 4396 1.326213 TGTGTGGGTGTTGCAAAGGG 61.326 55.000 0.00 0.00 0.00 3.95
4095 4397 1.000993 TGTGGGTGTTGCAAAGGGT 59.999 52.632 0.00 0.00 0.00 4.34
4096 4398 1.040339 TGTGGGTGTTGCAAAGGGTC 61.040 55.000 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.740268 TGCACAAATCTCAATGCAAGATC 58.260 39.130 0.00 0.00 44.72 2.75
1 2 4.794278 TGCACAAATCTCAATGCAAGAT 57.206 36.364 0.00 0.00 44.72 2.40
5 6 4.056092 TGTTTGCACAAATCTCAATGCA 57.944 36.364 0.00 0.00 45.94 3.96
6 7 5.600908 ATTGTTTGCACAAATCTCAATGC 57.399 34.783 8.70 0.00 46.17 3.56
7 8 8.844441 AAAAATTGTTTGCACAAATCTCAATG 57.156 26.923 9.74 0.00 46.17 2.82
46 47 9.394767 TCAAGCAATATAGTATGCAAGAAGAAA 57.605 29.630 9.71 0.00 44.95 2.52
47 48 8.962884 TCAAGCAATATAGTATGCAAGAAGAA 57.037 30.769 9.71 0.00 44.95 2.52
48 49 8.962884 TTCAAGCAATATAGTATGCAAGAAGA 57.037 30.769 9.71 0.12 44.95 2.87
50 51 8.737168 ACTTCAAGCAATATAGTATGCAAGAA 57.263 30.769 9.71 10.55 44.95 2.52
51 52 8.206867 AGACTTCAAGCAATATAGTATGCAAGA 58.793 33.333 9.71 5.11 44.95 3.02
52 53 8.375608 AGACTTCAAGCAATATAGTATGCAAG 57.624 34.615 9.71 7.43 44.95 4.01
53 54 7.986889 TGAGACTTCAAGCAATATAGTATGCAA 59.013 33.333 9.71 0.00 44.95 4.08
54 55 7.500141 TGAGACTTCAAGCAATATAGTATGCA 58.500 34.615 9.71 0.00 44.95 3.96
55 56 7.655328 ACTGAGACTTCAAGCAATATAGTATGC 59.345 37.037 0.00 0.89 42.87 3.14
56 57 9.190858 GACTGAGACTTCAAGCAATATAGTATG 57.809 37.037 0.00 0.00 31.69 2.39
57 58 8.079203 CGACTGAGACTTCAAGCAATATAGTAT 58.921 37.037 0.00 0.00 31.69 2.12
58 59 7.282450 TCGACTGAGACTTCAAGCAATATAGTA 59.718 37.037 0.00 0.00 31.69 1.82
59 60 6.095580 TCGACTGAGACTTCAAGCAATATAGT 59.904 38.462 0.00 0.00 31.69 2.12
60 61 6.416455 GTCGACTGAGACTTCAAGCAATATAG 59.584 42.308 8.70 0.00 38.09 1.31
61 62 6.266323 GTCGACTGAGACTTCAAGCAATATA 58.734 40.000 8.70 0.00 38.09 0.86
62 63 5.105752 GTCGACTGAGACTTCAAGCAATAT 58.894 41.667 8.70 0.00 38.09 1.28
63 64 4.486090 GTCGACTGAGACTTCAAGCAATA 58.514 43.478 8.70 0.00 38.09 1.90
64 65 3.321497 GTCGACTGAGACTTCAAGCAAT 58.679 45.455 8.70 0.00 38.09 3.56
65 66 2.743938 GTCGACTGAGACTTCAAGCAA 58.256 47.619 8.70 0.00 38.09 3.91
66 67 2.423926 GTCGACTGAGACTTCAAGCA 57.576 50.000 8.70 0.00 38.09 3.91
78 79 2.701107 TGTCTAGGTCTCAGTCGACTG 58.299 52.381 34.76 34.76 45.08 3.51
79 80 3.420300 TTGTCTAGGTCTCAGTCGACT 57.580 47.619 13.58 13.58 34.38 4.18
80 81 3.502979 AGTTTGTCTAGGTCTCAGTCGAC 59.497 47.826 7.70 7.70 0.00 4.20
81 82 3.752222 GAGTTTGTCTAGGTCTCAGTCGA 59.248 47.826 0.00 0.00 0.00 4.20
82 83 3.754323 AGAGTTTGTCTAGGTCTCAGTCG 59.246 47.826 0.00 0.00 31.71 4.18
83 84 5.715434 AAGAGTTTGTCTAGGTCTCAGTC 57.285 43.478 0.00 0.00 32.65 3.51
84 85 7.672239 AGATAAAGAGTTTGTCTAGGTCTCAGT 59.328 37.037 0.00 0.00 39.02 3.41
85 86 8.062065 AGATAAAGAGTTTGTCTAGGTCTCAG 57.938 38.462 0.00 0.00 39.02 3.35
86 87 8.307483 CAAGATAAAGAGTTTGTCTAGGTCTCA 58.693 37.037 0.00 0.00 39.74 3.27
87 88 7.276878 GCAAGATAAAGAGTTTGTCTAGGTCTC 59.723 40.741 0.00 0.00 39.74 3.36
88 89 7.100409 GCAAGATAAAGAGTTTGTCTAGGTCT 58.900 38.462 0.00 0.00 39.74 3.85
89 90 6.035112 CGCAAGATAAAGAGTTTGTCTAGGTC 59.965 42.308 0.00 0.00 39.74 3.85
90 91 5.869888 CGCAAGATAAAGAGTTTGTCTAGGT 59.130 40.000 0.00 0.00 39.74 3.08
91 92 5.869888 ACGCAAGATAAAGAGTTTGTCTAGG 59.130 40.000 0.00 0.00 39.74 3.02
92 93 6.183360 CCACGCAAGATAAAGAGTTTGTCTAG 60.183 42.308 0.00 0.00 39.74 2.43
93 94 5.637810 CCACGCAAGATAAAGAGTTTGTCTA 59.362 40.000 0.00 0.00 39.74 2.59
94 95 4.452455 CCACGCAAGATAAAGAGTTTGTCT 59.548 41.667 0.00 0.00 42.00 3.41
95 96 4.451096 TCCACGCAAGATAAAGAGTTTGTC 59.549 41.667 0.00 0.00 43.62 3.18
96 97 4.385825 TCCACGCAAGATAAAGAGTTTGT 58.614 39.130 0.00 0.00 43.62 2.83
97 98 5.356882 TTCCACGCAAGATAAAGAGTTTG 57.643 39.130 0.00 0.00 43.62 2.93
98 99 6.206634 TCAATTCCACGCAAGATAAAGAGTTT 59.793 34.615 0.00 0.00 43.62 2.66
99 100 5.705441 TCAATTCCACGCAAGATAAAGAGTT 59.295 36.000 0.00 0.00 43.62 3.01
100 101 5.245531 TCAATTCCACGCAAGATAAAGAGT 58.754 37.500 0.00 0.00 43.62 3.24
101 102 5.352569 ACTCAATTCCACGCAAGATAAAGAG 59.647 40.000 0.00 0.00 43.62 2.85
102 103 5.122239 CACTCAATTCCACGCAAGATAAAGA 59.878 40.000 0.00 0.00 43.62 2.52
103 104 5.122239 TCACTCAATTCCACGCAAGATAAAG 59.878 40.000 0.00 0.00 43.62 1.85
109 110 4.164822 AATTCACTCAATTCCACGCAAG 57.835 40.909 0.00 0.00 34.34 4.01
144 145 1.308998 CAATCGGACACCCCATTAGC 58.691 55.000 0.00 0.00 34.14 3.09
147 148 0.695924 TCACAATCGGACACCCCATT 59.304 50.000 0.00 0.00 34.14 3.16
151 152 2.882137 TCTTTTTCACAATCGGACACCC 59.118 45.455 0.00 0.00 0.00 4.61
155 156 4.287720 GGTGTTCTTTTTCACAATCGGAC 58.712 43.478 0.00 0.00 36.43 4.79
177 178 0.246635 AACTGACCGATCACCCTTCG 59.753 55.000 0.00 0.00 36.38 3.79
189 190 2.741211 GGTCCGCGGAAACTGACC 60.741 66.667 32.93 22.77 40.40 4.02
194 195 3.417224 GAACGGGTCCGCGGAAAC 61.417 66.667 32.93 25.22 44.19 2.78
210 211 1.136774 CATCTGCGAACTCGTCCGA 59.863 57.895 0.51 0.00 42.22 4.55
212 213 1.429463 AAACATCTGCGAACTCGTCC 58.571 50.000 0.51 0.00 42.22 4.79
215 216 2.854777 CCTCTAAACATCTGCGAACTCG 59.145 50.000 0.00 0.00 43.27 4.18
219 220 3.953712 TGTCCTCTAAACATCTGCGAA 57.046 42.857 0.00 0.00 0.00 4.70
220 221 3.953712 TTGTCCTCTAAACATCTGCGA 57.046 42.857 0.00 0.00 0.00 5.10
224 225 8.635765 TTAGCAAATTTGTCCTCTAAACATCT 57.364 30.769 19.03 5.83 0.00 2.90
226 227 8.409358 ACTTAGCAAATTTGTCCTCTAAACAT 57.591 30.769 19.03 4.91 0.00 2.71
229 230 7.118680 CCGTACTTAGCAAATTTGTCCTCTAAA 59.881 37.037 19.03 2.77 0.00 1.85
240 241 5.410355 TCTACACCCGTACTTAGCAAATT 57.590 39.130 0.00 0.00 0.00 1.82
253 254 0.677288 TCACACCACTTCTACACCCG 59.323 55.000 0.00 0.00 0.00 5.28
254 255 1.692519 ACTCACACCACTTCTACACCC 59.307 52.381 0.00 0.00 0.00 4.61
256 257 3.728076 TCACTCACACCACTTCTACAC 57.272 47.619 0.00 0.00 0.00 2.90
268 269 1.445871 GCACATCAGCATCACTCACA 58.554 50.000 0.00 0.00 0.00 3.58
294 295 2.255252 GCCAACACATGTGACGGC 59.745 61.111 32.36 32.36 41.42 5.68
299 300 1.575922 CGTCCTGCCAACACATGTG 59.424 57.895 24.25 24.25 0.00 3.21
309 310 1.070786 TCAACTTGTCCGTCCTGCC 59.929 57.895 0.00 0.00 0.00 4.85
310 311 0.531974 TGTCAACTTGTCCGTCCTGC 60.532 55.000 0.00 0.00 0.00 4.85
337 338 3.490249 GGACACTTTGTTTAAGCACACCC 60.490 47.826 0.00 0.00 37.37 4.61
344 345 3.306019 GCCCCATGGACACTTTGTTTAAG 60.306 47.826 15.22 0.00 39.87 1.85
354 355 4.447342 CCTGGGCCCCATGGACAC 62.447 72.222 22.27 6.68 44.10 3.67
367 371 1.047002 ATCGATCTCTTGCTCCCTGG 58.953 55.000 0.00 0.00 0.00 4.45
417 422 8.426489 TGCCTCTCTCTGTTTTACTACTAAAAA 58.574 33.333 0.00 0.00 34.33 1.94
418 423 7.959175 TGCCTCTCTCTGTTTTACTACTAAAA 58.041 34.615 0.00 0.00 30.72 1.52
419 424 7.232941 ACTGCCTCTCTCTGTTTTACTACTAAA 59.767 37.037 0.00 0.00 0.00 1.85
420 425 6.720288 ACTGCCTCTCTCTGTTTTACTACTAA 59.280 38.462 0.00 0.00 0.00 2.24
421 426 6.246919 ACTGCCTCTCTCTGTTTTACTACTA 58.753 40.000 0.00 0.00 0.00 1.82
422 427 5.081032 ACTGCCTCTCTCTGTTTTACTACT 58.919 41.667 0.00 0.00 0.00 2.57
423 428 5.394224 ACTGCCTCTCTCTGTTTTACTAC 57.606 43.478 0.00 0.00 0.00 2.73
424 429 4.463186 GGACTGCCTCTCTCTGTTTTACTA 59.537 45.833 0.00 0.00 0.00 1.82
425 430 3.259625 GGACTGCCTCTCTCTGTTTTACT 59.740 47.826 0.00 0.00 0.00 2.24
426 431 3.006967 TGGACTGCCTCTCTCTGTTTTAC 59.993 47.826 0.00 0.00 34.31 2.01
427 432 3.239449 TGGACTGCCTCTCTCTGTTTTA 58.761 45.455 0.00 0.00 34.31 1.52
428 433 2.050144 TGGACTGCCTCTCTCTGTTTT 58.950 47.619 0.00 0.00 34.31 2.43
429 434 1.722034 TGGACTGCCTCTCTCTGTTT 58.278 50.000 0.00 0.00 34.31 2.83
430 435 1.722034 TTGGACTGCCTCTCTCTGTT 58.278 50.000 0.00 0.00 34.31 3.16
431 436 1.949799 ATTGGACTGCCTCTCTCTGT 58.050 50.000 0.00 0.00 34.31 3.41
432 437 3.295093 TCTATTGGACTGCCTCTCTCTG 58.705 50.000 0.00 0.00 34.31 3.35
439 444 0.978146 ACGCCTCTATTGGACTGCCT 60.978 55.000 0.00 0.00 34.31 4.75
441 446 1.432270 GCACGCCTCTATTGGACTGC 61.432 60.000 0.00 0.00 0.00 4.40
449 454 2.072487 ACCCCATGCACGCCTCTAT 61.072 57.895 0.00 0.00 0.00 1.98
450 455 2.687200 ACCCCATGCACGCCTCTA 60.687 61.111 0.00 0.00 0.00 2.43
471 476 3.775654 CACACCTCTCGGAGCCCC 61.776 72.222 0.00 0.00 0.00 5.80
472 477 3.775654 CCACACCTCTCGGAGCCC 61.776 72.222 0.00 0.00 0.00 5.19
473 478 4.459089 GCCACACCTCTCGGAGCC 62.459 72.222 0.00 0.00 0.00 4.70
493 498 4.923942 ATGGCGATGCTGGCTCCG 62.924 66.667 0.00 0.00 35.06 4.63
494 499 2.976903 GATGGCGATGCTGGCTCC 60.977 66.667 0.00 0.00 35.06 4.70
495 500 2.203112 TGATGGCGATGCTGGCTC 60.203 61.111 0.00 0.00 35.06 4.70
496 501 2.203167 CTGATGGCGATGCTGGCT 60.203 61.111 0.00 0.00 35.06 4.75
497 502 3.962421 GCTGATGGCGATGCTGGC 61.962 66.667 0.00 0.00 0.00 4.85
498 503 3.285215 GGCTGATGGCGATGCTGG 61.285 66.667 0.00 0.00 42.94 4.85
499 504 2.203167 AGGCTGATGGCGATGCTG 60.203 61.111 0.00 0.00 44.18 4.41
500 505 2.110627 GAGGCTGATGGCGATGCT 59.889 61.111 0.00 0.00 44.18 3.79
501 506 2.203112 TGAGGCTGATGGCGATGC 60.203 61.111 0.00 0.00 44.18 3.91
502 507 1.145598 AGTGAGGCTGATGGCGATG 59.854 57.895 0.00 0.00 44.18 3.84
529 534 4.946157 CAGGAGAAAGTTGTTATCATGCCT 59.054 41.667 0.00 0.00 0.00 4.75
530 535 4.702131 ACAGGAGAAAGTTGTTATCATGCC 59.298 41.667 0.00 0.00 0.00 4.40
555 560 0.960364 TTGGCCGGAGAAGACAATGC 60.960 55.000 5.05 0.00 0.00 3.56
592 609 2.107726 AGTGGATGGATGATGGACATGG 59.892 50.000 0.00 0.00 39.56 3.66
593 610 3.503800 AGTGGATGGATGATGGACATG 57.496 47.619 0.00 0.00 39.56 3.21
595 612 2.845586 TGAAGTGGATGGATGATGGACA 59.154 45.455 0.00 0.00 0.00 4.02
613 630 1.548798 ATTGGGGGATGGGGGTGAA 60.549 57.895 0.00 0.00 0.00 3.18
707 755 2.221299 CCGGGGTTTCAGAGTGGGA 61.221 63.158 0.00 0.00 0.00 4.37
708 756 2.351276 CCGGGGTTTCAGAGTGGG 59.649 66.667 0.00 0.00 0.00 4.61
946 1008 2.649190 AGAGAACGAGCTGAGCTGATA 58.351 47.619 13.71 0.00 39.88 2.15
947 1009 1.473258 AGAGAACGAGCTGAGCTGAT 58.527 50.000 13.71 0.00 39.88 2.90
948 1010 1.201181 GAAGAGAACGAGCTGAGCTGA 59.799 52.381 13.71 0.00 39.88 4.26
949 1011 1.627879 GAAGAGAACGAGCTGAGCTG 58.372 55.000 13.71 7.04 39.88 4.24
950 1012 0.530288 GGAAGAGAACGAGCTGAGCT 59.470 55.000 6.69 6.69 43.88 4.09
951 1013 0.459411 GGGAAGAGAACGAGCTGAGC 60.459 60.000 0.00 0.00 0.00 4.26
952 1014 0.891373 TGGGAAGAGAACGAGCTGAG 59.109 55.000 0.00 0.00 0.00 3.35
953 1015 1.478510 GATGGGAAGAGAACGAGCTGA 59.521 52.381 0.00 0.00 0.00 4.26
954 1016 1.800655 CGATGGGAAGAGAACGAGCTG 60.801 57.143 0.00 0.00 0.00 4.24
955 1017 0.457851 CGATGGGAAGAGAACGAGCT 59.542 55.000 0.00 0.00 0.00 4.09
956 1018 0.456221 TCGATGGGAAGAGAACGAGC 59.544 55.000 0.00 0.00 0.00 5.03
957 1019 2.359214 TGATCGATGGGAAGAGAACGAG 59.641 50.000 0.54 0.00 33.58 4.18
958 1020 2.375146 TGATCGATGGGAAGAGAACGA 58.625 47.619 0.54 0.00 0.00 3.85
959 1021 2.871182 TGATCGATGGGAAGAGAACG 57.129 50.000 0.54 0.00 0.00 3.95
960 1022 4.697514 TGATTGATCGATGGGAAGAGAAC 58.302 43.478 0.54 0.00 0.00 3.01
961 1023 5.357742 TTGATTGATCGATGGGAAGAGAA 57.642 39.130 0.54 0.00 0.00 2.87
962 1024 5.357742 TTTGATTGATCGATGGGAAGAGA 57.642 39.130 0.54 0.00 0.00 3.10
963 1025 4.514441 CCTTTGATTGATCGATGGGAAGAG 59.486 45.833 0.54 0.00 33.82 2.85
964 1026 4.454678 CCTTTGATTGATCGATGGGAAGA 58.545 43.478 0.54 0.00 33.82 2.87
999 1061 3.307762 GGCTCCTTGAGTACCACTTCATT 60.308 47.826 0.00 0.00 31.39 2.57
1101 1166 0.530870 GGGCGAAGATGAGGTAGTGC 60.531 60.000 0.00 0.00 0.00 4.40
1157 1222 3.862124 CAGCGGAGTCGTTGGAAG 58.138 61.111 0.00 0.00 42.56 3.46
1230 1295 2.442188 CGTACCTTTCTCGTGCGGC 61.442 63.158 0.00 0.00 35.95 6.53
1233 1298 1.253999 CGTACGTACCTTTCTCGTGC 58.746 55.000 19.67 0.00 38.27 5.34
1300 1365 2.142292 AACCACTCCCCATGGACTGC 62.142 60.000 15.22 0.00 39.87 4.40
1301 1366 0.035056 GAACCACTCCCCATGGACTG 60.035 60.000 15.22 4.75 39.87 3.51
1312 1377 4.496341 CGCATATGTCAAATGGAACCACTC 60.496 45.833 4.29 0.00 0.00 3.51
1320 1385 2.355444 TGCAGTCGCATATGTCAAATGG 59.645 45.455 4.29 0.00 45.36 3.16
1386 1461 4.457496 ATGTCCCGCAGCTGGTCG 62.457 66.667 17.12 11.37 0.00 4.79
1533 1608 2.501128 CCGTCGATGCCCATGAGT 59.499 61.111 0.00 0.00 0.00 3.41
2025 2106 4.927782 TTGTCGTTGCAGCCCGCT 62.928 61.111 0.00 0.00 43.06 5.52
2104 2185 2.892425 GACGATGGAAGCTGCCGG 60.892 66.667 6.16 0.00 0.00 6.13
2364 2447 4.760047 TCGGCTGGCGGCTTCTTC 62.760 66.667 23.59 0.00 41.46 2.87
2510 2596 3.620300 GACGACGATGTGGACGCCA 62.620 63.158 0.00 0.00 0.00 5.69
2785 2880 2.606826 GTCGGGGTGGAGGAGGTT 60.607 66.667 0.00 0.00 0.00 3.50
2812 2907 1.376037 GTCTTGTTGCGGAGGAGGG 60.376 63.158 0.00 0.00 0.00 4.30
2857 2952 1.669115 CCTTCACCGTGCTCCACAG 60.669 63.158 0.00 0.00 33.40 3.66
3286 3394 3.595758 GCACGCACACCAAGGCTT 61.596 61.111 0.00 0.00 0.00 4.35
3391 3502 9.941664 CATTATGTACACCTGAAATCTCAAATC 57.058 33.333 0.00 0.00 0.00 2.17
3419 3530 8.124823 TCAAAATTACAAGATGAGATTGATCGC 58.875 33.333 0.00 0.00 0.00 4.58
3455 3566 5.459536 TGAGAGAAGGGAATGTATCATCG 57.540 43.478 0.00 0.00 0.00 3.84
3544 3820 6.966534 AAGTTCCACATTCTTCACTCAAAT 57.033 33.333 0.00 0.00 0.00 2.32
3545 3821 6.563422 CAAAGTTCCACATTCTTCACTCAAA 58.437 36.000 0.00 0.00 0.00 2.69
3549 3825 3.003689 CGCAAAGTTCCACATTCTTCACT 59.996 43.478 0.00 0.00 0.00 3.41
3618 3895 5.841957 AATCTTCATTTGAGCATACCCAC 57.158 39.130 0.00 0.00 0.00 4.61
3693 3971 4.408596 TGGTACTACAGCATCATCAATCCA 59.591 41.667 0.00 0.00 0.00 3.41
3706 3984 2.860009 TCCTAGGCGATGGTACTACAG 58.140 52.381 2.96 0.00 0.00 2.74
3709 3987 3.154710 CACATCCTAGGCGATGGTACTA 58.845 50.000 13.53 0.00 43.34 1.82
3782 4083 8.498054 TGAGATCTACATTCAAAACTCCAATC 57.502 34.615 0.00 0.00 0.00 2.67
3847 4148 1.377333 GTCCCTACCAGCACAAGGC 60.377 63.158 0.00 0.00 45.30 4.35
3878 4179 2.114616 ACTCCTACTTGATGCTCCCTG 58.885 52.381 0.00 0.00 0.00 4.45
3882 4183 5.907207 TGTTGATACTCCTACTTGATGCTC 58.093 41.667 0.00 0.00 0.00 4.26
3912 4213 9.086336 GACTAGTTCAGTGTGTAGTAGTACTAG 57.914 40.741 10.38 0.00 35.12 2.57
3931 4232 2.158842 GCATGCTGATCCAGGACTAGTT 60.159 50.000 11.37 0.00 34.07 2.24
3933 4234 1.415289 TGCATGCTGATCCAGGACTAG 59.585 52.381 20.33 0.00 34.07 2.57
4018 4320 6.982141 ACAATATAAAAATGATGCTGCAGGTG 59.018 34.615 17.12 0.00 0.00 4.00
4019 4321 7.116075 ACAATATAAAAATGATGCTGCAGGT 57.884 32.000 17.12 0.00 0.00 4.00
4020 4322 8.428186 AAACAATATAAAAATGATGCTGCAGG 57.572 30.769 17.12 0.00 0.00 4.85
4021 4323 9.089601 TGAAACAATATAAAAATGATGCTGCAG 57.910 29.630 10.11 10.11 0.00 4.41
4022 4324 8.999220 TGAAACAATATAAAAATGATGCTGCA 57.001 26.923 4.13 4.13 0.00 4.41
4066 4368 1.043816 ACACCCACACACTCTCTCTG 58.956 55.000 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.