Multiple sequence alignment - TraesCS7A01G054000

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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 TraesCS7A01G054000 chr7A 100.000 5806 0 0 1 5806 26106733 26100928 0.000000e+00 10722.0
1 TraesCS7A01G054000 chr7A 80.464 1464 228 41 3226 4660 26241110 26239676 0.000000e+00 1066.0
2 TraesCS7A01G054000 chr7A 89.535 774 74 4 3871 4641 26057502 26056733 0.000000e+00 974.0
3 TraesCS7A01G054000 chr7A 89.451 237 25 0 1228 1464 26060123 26059887 3.400000e-77 300.0
4 TraesCS7A01G054000 chr7A 89.785 186 19 0 3607 3792 26057818 26057633 7.520000e-59 239.0
5 TraesCS7A01G054000 chr7A 82.857 105 12 5 1081 1179 26243116 26243012 8.010000e-14 89.8
6 TraesCS7A01G054000 chr4A 89.972 3949 268 45 821 4679 709616466 709612556 0.000000e+00 4981.0
7 TraesCS7A01G054000 chr4A 89.495 3941 285 61 821 4679 709422372 709418479 0.000000e+00 4865.0
8 TraesCS7A01G054000 chr4A 89.416 3940 286 61 821 4679 709276038 709272149 0.000000e+00 4844.0
9 TraesCS7A01G054000 chr4A 89.292 3941 282 64 821 4679 709569988 709566106 0.000000e+00 4811.0
10 TraesCS7A01G054000 chr4A 82.429 2709 351 74 3162 5806 709207285 709204638 0.000000e+00 2250.0
11 TraesCS7A01G054000 chr4A 89.680 688 31 18 2 682 709570679 709570025 0.000000e+00 841.0
12 TraesCS7A01G054000 chr4A 89.260 689 34 18 1 682 709423064 709422409 0.000000e+00 826.0
13 TraesCS7A01G054000 chr4A 88.824 689 36 19 1 682 709276729 709276075 0.000000e+00 808.0
14 TraesCS7A01G054000 chr4A 80.000 800 124 17 3882 4660 709717140 709716356 5.080000e-155 558.0
15 TraesCS7A01G054000 chr4A 94.398 357 16 4 237 592 709616923 709616570 3.960000e-151 545.0
16 TraesCS7A01G054000 chr4A 82.180 578 92 9 3223 3795 709717810 709717239 2.430000e-133 486.0
17 TraesCS7A01G054000 chr4A 89.850 266 27 0 1199 1464 709209640 709209375 5.570000e-90 342.0
18 TraesCS7A01G054000 chr4A 87.766 188 15 4 32 218 709618567 709618387 4.560000e-51 213.0
19 TraesCS7A01G054000 chr4A 81.283 187 31 2 5351 5535 709268415 709268231 1.300000e-31 148.0
20 TraesCS7A01G054000 chr4A 81.283 187 31 2 5351 5535 709270504 709270320 1.300000e-31 148.0
21 TraesCS7A01G054000 chr4A 80.749 187 32 3 5351 5535 709266326 709266142 6.060000e-30 143.0
22 TraesCS7A01G054000 chr4A 89.474 95 10 0 4684 4778 709272102 709272008 2.840000e-23 121.0
23 TraesCS7A01G054000 chr4A 89.394 66 7 0 1081 1146 709720528 709720463 3.730000e-12 84.2
24 TraesCS7A01G054000 chr7D 92.916 2894 148 21 1817 4680 25291172 25288306 0.000000e+00 4156.0
25 TraesCS7A01G054000 chr7D 93.635 1791 78 20 1 1768 25292934 25291157 0.000000e+00 2643.0
26 TraesCS7A01G054000 chr7D 78.558 527 80 23 5201 5711 25287861 25287352 3.380000e-82 316.0
27 TraesCS7A01G054000 chr7D 82.199 382 50 15 4684 5057 25288260 25287889 4.370000e-81 313.0
28 TraesCS7A01G054000 chr7D 88.142 253 30 0 1230 1482 25338528 25338276 9.460000e-78 302.0
29 TraesCS7A01G054000 chr7D 89.394 66 7 0 1081 1146 25338665 25338600 3.730000e-12 84.2
30 TraesCS7A01G054000 chrUn 88.950 2172 171 35 1877 3998 350559132 350561284 0.000000e+00 2617.0
31 TraesCS7A01G054000 chrUn 87.484 1518 110 38 821 2291 346599899 346601383 0.000000e+00 1677.0
32 TraesCS7A01G054000 chrUn 89.673 581 26 16 108 682 346599310 346599862 0.000000e+00 710.0
33 TraesCS7A01G054000 chr3D 79.752 242 37 11 5171 5406 125693218 125693453 1.290000e-36 165.0
34 TraesCS7A01G054000 chr3D 95.455 44 2 0 1852 1895 197995596 197995639 2.900000e-08 71.3
35 TraesCS7A01G054000 chr3B 77.778 234 43 8 5171 5400 179658098 179658326 1.010000e-27 135.0
36 TraesCS7A01G054000 chr3A 86.441 118 13 2 5291 5406 134327829 134327945 6.110000e-25 126.0
37 TraesCS7A01G054000 chr4B 78.613 173 25 9 1739 1900 539498365 539498194 2.860000e-18 104.0
38 TraesCS7A01G054000 chr7B 83.036 112 19 0 1861 1972 680177794 680177683 1.030000e-17 102.0
39 TraesCS7A01G054000 chr2D 74.672 229 45 12 1739 1962 563307326 563307546 8.010000e-14 89.8
40 TraesCS7A01G054000 chr6B 84.375 64 10 0 5141 5204 409288957 409289020 4.860000e-06 63.9


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 TraesCS7A01G054000 chr7A 26100928 26106733 5805 True 10722.000000 10722 100.000000 1 5806 1 chr7A.!!$R1 5805
1 TraesCS7A01G054000 chr7A 26239676 26243116 3440 True 577.900000 1066 81.660500 1081 4660 2 chr7A.!!$R3 3579
2 TraesCS7A01G054000 chr7A 26056733 26060123 3390 True 504.333333 974 89.590333 1228 4641 3 chr7A.!!$R2 3413
3 TraesCS7A01G054000 chr4A 709418479 709423064 4585 True 2845.500000 4865 89.377500 1 4679 2 chr4A.!!$R3 4678
4 TraesCS7A01G054000 chr4A 709566106 709570679 4573 True 2826.000000 4811 89.486000 2 4679 2 chr4A.!!$R4 4677
5 TraesCS7A01G054000 chr4A 709612556 709618567 6011 True 1913.000000 4981 90.712000 32 4679 3 chr4A.!!$R5 4647
6 TraesCS7A01G054000 chr4A 709204638 709209640 5002 True 1296.000000 2250 86.139500 1199 5806 2 chr4A.!!$R1 4607
7 TraesCS7A01G054000 chr4A 709266142 709276729 10587 True 1035.333333 4844 85.171500 1 5535 6 chr4A.!!$R2 5534
8 TraesCS7A01G054000 chr4A 709716356 709720528 4172 True 376.066667 558 83.858000 1081 4660 3 chr4A.!!$R6 3579
9 TraesCS7A01G054000 chr7D 25287352 25292934 5582 True 1857.000000 4156 86.827000 1 5711 4 chr7D.!!$R1 5710
10 TraesCS7A01G054000 chrUn 350559132 350561284 2152 False 2617.000000 2617 88.950000 1877 3998 1 chrUn.!!$F1 2121
11 TraesCS7A01G054000 chrUn 346599310 346601383 2073 False 1193.500000 1677 88.578500 108 2291 2 chrUn.!!$F2 2183

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
529 1975 0.035056 CGATTGCTGGAAAGGGACCT 60.035 55.0 0.00 0.0 0.00 3.85 F
1464 2968 0.108945 GTTCTGGTCCGAACCCTACG 60.109 60.0 12.77 0.0 45.83 3.51 F
1881 4650 0.174162 GCATGTTGAGGTGGGCATTC 59.826 55.0 0.00 0.0 0.00 2.67 F
1928 4697 0.458669 CATGCTTGGATGTTGAGGGC 59.541 55.0 0.00 0.0 0.00 5.19 F
3831 8391 0.741221 CCTCCGTAGCTGCTTTCCAC 60.741 60.0 7.79 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 4174 1.529438 GGTAACGTGTGGTGTGTCATG 59.471 52.381 0.00 0.0 0.00 3.07 R
2747 6796 1.404717 GCCTGAGAGTTTGCAGATCGA 60.405 52.381 0.00 0.0 34.06 3.59 R
3865 8457 1.620822 ATCTGCAACAACAAGGTCCC 58.379 50.000 0.00 0.0 0.00 4.46 R
3898 8490 1.028330 CGCTTGTGGTGATCATGGCT 61.028 55.000 0.00 0.0 0.00 4.75 R
5502 13532 0.031857 CTCGAGCCCAGCTGTAGATG 59.968 60.000 13.81 0.0 39.88 2.90 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
33 34 1.878775 GCAAACCTGCCTAGCACAG 59.121 57.895 4.44 4.44 43.26 3.66
34 35 0.890996 GCAAACCTGCCTAGCACAGT 60.891 55.000 9.40 0.00 43.26 3.55
35 36 1.610624 GCAAACCTGCCTAGCACAGTA 60.611 52.381 9.40 0.00 43.26 2.74
36 37 2.076863 CAAACCTGCCTAGCACAGTAC 58.923 52.381 9.40 0.00 33.79 2.73
39 40 1.697432 ACCTGCCTAGCACAGTACAAA 59.303 47.619 9.40 0.00 33.79 2.83
73 74 1.984570 TGAAGACAGCCTCCCTCCG 60.985 63.158 0.00 0.00 0.00 4.63
175 176 6.849085 TGCACACCATATAAAATTTCCACT 57.151 33.333 0.00 0.00 0.00 4.00
332 1778 4.466827 TGGCAGATTCAGCATTATCACAT 58.533 39.130 3.34 0.00 0.00 3.21
529 1975 0.035056 CGATTGCTGGAAAGGGACCT 60.035 55.000 0.00 0.00 0.00 3.85
597 2043 3.054875 TGCAACTCTATCAAGCCACTGAT 60.055 43.478 0.00 0.00 39.41 2.90
598 2044 3.311871 GCAACTCTATCAAGCCACTGATG 59.688 47.826 4.27 0.00 36.69 3.07
600 2046 4.399004 ACTCTATCAAGCCACTGATGAC 57.601 45.455 4.27 0.00 36.69 3.06
732 2183 1.085091 CAGAGCACCAAGAGTCATGC 58.915 55.000 0.00 0.00 38.39 4.06
802 2255 9.993881 CAGCAAAATAAAACTCTAACATTTTCG 57.006 29.630 0.00 0.00 28.88 3.46
818 2271 2.358737 CGTCACTGAACTGGGCCC 60.359 66.667 17.59 17.59 0.00 5.80
891 2347 1.066587 GGAATCTCTCAGGCGTCGG 59.933 63.158 0.00 0.00 0.00 4.79
1007 2463 0.690411 CAGCCCTCCAGAGACCAGAT 60.690 60.000 0.00 0.00 0.00 2.90
1092 2551 2.239654 TCGAGGATCAAGAAGCCCAAAT 59.760 45.455 0.00 0.00 33.17 2.32
1146 2605 4.469945 CACTCTCCCCTTCATAGTTGGTAA 59.530 45.833 0.00 0.00 0.00 2.85
1205 2676 3.667497 TTCATGGTCACTCTCACTCAC 57.333 47.619 0.00 0.00 0.00 3.51
1208 2679 1.621992 TGGTCACTCTCACTCACTCC 58.378 55.000 0.00 0.00 0.00 3.85
1209 2680 1.133482 TGGTCACTCTCACTCACTCCA 60.133 52.381 0.00 0.00 0.00 3.86
1215 2686 0.610174 TCTCACTCACTCCATGGTGC 59.390 55.000 12.58 0.00 37.16 5.01
1252 2755 3.192630 ACCATGTTGGGGCTGGGT 61.193 61.111 0.00 0.00 43.37 4.51
1464 2968 0.108945 GTTCTGGTCCGAACCCTACG 60.109 60.000 12.77 0.00 45.83 3.51
1506 4061 2.801111 GTTCCGACCAACTTTGAGAGAC 59.199 50.000 0.00 0.00 0.00 3.36
1546 4101 2.836154 TGGCACACTGGTCCTTCC 59.164 61.111 0.00 0.00 0.00 3.46
1593 4174 7.165483 CGTCGGAAACACATCTTATAACTCTAC 59.835 40.741 0.00 0.00 0.00 2.59
1614 4195 0.535797 TGACACACCACACGTTACCA 59.464 50.000 0.00 0.00 0.00 3.25
1639 4220 7.170320 CACAGGAATTGCTTGCAATATATTTCC 59.830 37.037 19.35 20.27 0.00 3.13
1881 4650 0.174162 GCATGTTGAGGTGGGCATTC 59.826 55.000 0.00 0.00 0.00 2.67
1927 4696 1.747355 GACATGCTTGGATGTTGAGGG 59.253 52.381 9.02 0.00 36.67 4.30
1928 4697 0.458669 CATGCTTGGATGTTGAGGGC 59.541 55.000 0.00 0.00 0.00 5.19
1932 4701 2.291475 TGCTTGGATGTTGAGGGCAATA 60.291 45.455 0.00 0.00 36.22 1.90
1948 4717 3.371166 GGCAATAGGTTAGTGGGTGCTAA 60.371 47.826 0.00 0.00 0.00 3.09
2130 5034 3.254024 TTGAGGTGGCCCTTCGAGC 62.254 63.158 0.00 0.00 42.86 5.03
2248 5522 7.335924 TCATTTTAAGTACTCCCTTCAATTCCG 59.664 37.037 0.00 0.00 0.00 4.30
2430 5736 4.717877 TCATAAGGTCCTGCCATGTAATG 58.282 43.478 0.00 0.00 46.21 1.90
2454 5780 4.566545 ATGTCAAGAAAAACATGTCGCA 57.433 36.364 0.00 0.00 34.88 5.10
2455 5781 3.690422 TGTCAAGAAAAACATGTCGCAC 58.310 40.909 0.00 0.00 0.00 5.34
2554 5888 4.154015 CGACACATGCTCCTCACATAAAAA 59.846 41.667 0.00 0.00 0.00 1.94
2632 6010 9.949174 TCATATCCAAATGTGAATAAACGATTG 57.051 29.630 0.00 0.00 30.91 2.67
2685 6733 9.361315 GAAGTTTAGAGAGGTTTGAGAAGATAC 57.639 37.037 0.00 0.00 0.00 2.24
2689 6737 6.865834 AGAGAGGTTTGAGAAGATACATGT 57.134 37.500 2.69 2.69 0.00 3.21
2763 6813 4.094212 GCAAAATCGATCTGCAAACTCTC 58.906 43.478 21.45 0.00 36.09 3.20
2800 6851 2.033407 CACTCACTCTTTGCACAAGACG 60.033 50.000 7.09 6.79 0.00 4.18
2803 6854 2.100749 TCACTCTTTGCACAAGACGAGA 59.899 45.455 7.09 6.03 0.00 4.04
2883 6935 5.389830 CGTCATTTACACTGTCAACATCTGG 60.390 44.000 0.00 0.00 0.00 3.86
2918 6970 4.826733 AGGAAACATGACTGCACAATAACA 59.173 37.500 0.00 0.00 0.00 2.41
2939 6991 6.224665 ACATTTATATGCTTGCAACACCAT 57.775 33.333 0.00 1.37 35.03 3.55
2975 7027 3.685756 CCACAAATGAATGCAACAATCCC 59.314 43.478 0.00 0.00 0.00 3.85
2980 7032 5.841957 AATGAATGCAACAATCCCTAGAC 57.158 39.130 0.00 0.00 0.00 2.59
2989 7041 5.880332 GCAACAATCCCTAGACTGAATTACA 59.120 40.000 0.00 0.00 0.00 2.41
3021 7074 8.335532 TCATTCGATTTGTAAGATTTTGGAGT 57.664 30.769 0.00 0.00 0.00 3.85
3305 7537 1.081906 CCACACTGCACATTGTCGC 60.082 57.895 4.81 4.81 0.00 5.19
3307 7539 1.227943 ACACTGCACATTGTCGCCT 60.228 52.632 8.19 0.00 0.00 5.52
3792 8278 6.569801 GCACCAAGTAAAAGCTTAAGGTAAGG 60.570 42.308 7.76 5.24 36.31 2.69
3831 8391 0.741221 CCTCCGTAGCTGCTTTCCAC 60.741 60.000 7.79 0.00 0.00 4.02
3862 8454 2.350102 CGGATTGGTGAATCATGCATCG 60.350 50.000 0.00 0.00 39.98 3.84
3865 8457 1.280746 GGTGAATCATGCATCGGCG 59.719 57.895 0.00 0.00 45.35 6.46
3898 8490 2.976589 TGCAGATTTCTGAATCGAGCA 58.023 42.857 11.70 8.92 46.23 4.26
3910 8502 0.250209 ATCGAGCAGCCATGATCACC 60.250 55.000 0.00 0.00 42.09 4.02
3998 8593 2.206900 TGGAGGACCTCAAGGCCA 59.793 61.111 23.06 9.28 39.32 5.36
4035 8630 0.532862 CTGTGGTCATCCGGCATACC 60.533 60.000 10.91 10.91 36.30 2.73
4439 9049 0.912486 CTACCAGGAGTTCCCCAAGG 59.088 60.000 0.00 0.00 36.42 3.61
4660 9270 2.472816 CGTTACAAGTACCACAACCGT 58.527 47.619 0.00 0.00 0.00 4.83
4681 9291 1.258982 GCGGCGATGTAGACAAGATTG 59.741 52.381 12.98 0.00 0.00 2.67
4682 9292 1.860950 CGGCGATGTAGACAAGATTGG 59.139 52.381 0.00 0.00 0.00 3.16
4689 9341 4.890158 TGTAGACAAGATTGGCTCTTCA 57.110 40.909 3.70 0.95 45.29 3.02
4695 9347 6.054295 AGACAAGATTGGCTCTTCATGTATC 58.946 40.000 0.00 0.00 45.29 2.24
4700 9352 3.564053 TGGCTCTTCATGTATCATGCA 57.436 42.857 5.03 0.00 0.00 3.96
4704 9356 4.517832 GGCTCTTCATGTATCATGCATTCA 59.482 41.667 0.00 0.00 0.00 2.57
4716 9368 2.957402 TGCATTCAGGGAAGAGTTGT 57.043 45.000 0.00 0.00 0.00 3.32
4727 9379 2.427095 GGAAGAGTTGTGTTGCACCTTT 59.573 45.455 0.00 0.00 32.73 3.11
4736 9388 2.223377 GTGTTGCACCTTTCTACTTCGG 59.777 50.000 0.00 0.00 0.00 4.30
4740 9392 1.630148 CACCTTTCTACTTCGGAGCG 58.370 55.000 0.00 0.00 0.00 5.03
4784 9436 5.352284 ACATCGTAGCAAGGAAGAACTATG 58.648 41.667 0.00 0.00 0.00 2.23
4816 9470 9.970395 ATATGCACAATGAATACATTTTAGTGG 57.030 29.630 0.00 0.00 43.17 4.00
4828 9482 2.030490 TTTAGTGGCACGACACCGGT 62.030 55.000 12.71 0.00 42.28 5.28
4849 9503 4.290155 GTCTTTTGTGTTGATTGATGCGT 58.710 39.130 0.00 0.00 0.00 5.24
4850 9504 4.146961 GTCTTTTGTGTTGATTGATGCGTG 59.853 41.667 0.00 0.00 0.00 5.34
4870 9524 5.672819 GCGTGCAACCTTACTTTATTACCAG 60.673 44.000 0.00 0.00 0.00 4.00
4874 9528 5.708697 GCAACCTTACTTTATTACCAGGTGT 59.291 40.000 0.76 0.00 34.76 4.16
4893 9548 4.142249 GGTGTTCAGTTGTTACAAAAGCCT 60.142 41.667 0.00 0.00 0.00 4.58
4906 9561 4.394729 ACAAAAGCCTAAAAGATCGGTCA 58.605 39.130 0.00 0.00 0.00 4.02
4919 9574 4.713946 GGTCAACCGATCAAGGCA 57.286 55.556 0.00 0.00 33.69 4.75
4922 9577 1.234821 GTCAACCGATCAAGGCAACA 58.765 50.000 0.00 0.00 41.41 3.33
4930 9586 3.310774 CCGATCAAGGCAACACAATAGAG 59.689 47.826 0.00 0.00 41.41 2.43
4936 9592 5.880332 TCAAGGCAACACAATAGAGATTACC 59.120 40.000 0.00 0.00 41.41 2.85
4937 9593 5.435686 AGGCAACACAATAGAGATTACCA 57.564 39.130 0.00 0.00 41.41 3.25
4938 9594 5.431765 AGGCAACACAATAGAGATTACCAG 58.568 41.667 0.00 0.00 41.41 4.00
4940 9596 5.186198 GCAACACAATAGAGATTACCAGGT 58.814 41.667 0.00 0.00 0.00 4.00
4941 9597 5.065218 GCAACACAATAGAGATTACCAGGTG 59.935 44.000 0.76 0.00 0.00 4.00
4942 9598 6.173339 CAACACAATAGAGATTACCAGGTGT 58.827 40.000 0.76 0.00 38.47 4.16
4943 9599 6.374417 ACACAATAGAGATTACCAGGTGTT 57.626 37.500 0.76 0.00 33.59 3.32
4944 9600 6.407202 ACACAATAGAGATTACCAGGTGTTC 58.593 40.000 0.76 0.00 33.59 3.18
4946 9602 6.536582 CACAATAGAGATTACCAGGTGTTCAG 59.463 42.308 0.76 0.00 0.00 3.02
4949 9605 4.899502 AGAGATTACCAGGTGTTCAGTTG 58.100 43.478 0.76 0.00 0.00 3.16
4951 9607 5.048846 AGATTACCAGGTGTTCAGTTGTT 57.951 39.130 0.76 0.00 0.00 2.83
4953 9614 5.995897 AGATTACCAGGTGTTCAGTTGTTAC 59.004 40.000 0.76 0.00 0.00 2.50
4957 9618 4.338118 ACCAGGTGTTCAGTTGTTACAATG 59.662 41.667 0.00 1.53 0.00 2.82
4962 9623 3.242903 TGTTCAGTTGTTACAATGCCACG 60.243 43.478 0.00 0.00 0.00 4.94
4972 9637 3.925630 AATGCCACGGCCACCTCAG 62.926 63.158 2.24 0.00 41.09 3.35
4990 10920 4.397417 CCTCAGAAATAGGCTGAACAAAGG 59.603 45.833 0.00 0.00 41.45 3.11
5045 10975 2.326550 CACGTTGGTTGTCGGTGC 59.673 61.111 0.00 0.00 0.00 5.01
5054 10984 1.583054 GTTGTCGGTGCTTTGAGACT 58.417 50.000 0.00 0.00 34.92 3.24
5056 10986 0.249868 TGTCGGTGCTTTGAGACTGG 60.250 55.000 0.00 0.00 34.92 4.00
5057 10987 1.301716 TCGGTGCTTTGAGACTGGC 60.302 57.895 0.00 0.00 0.00 4.85
5058 10988 2.328099 CGGTGCTTTGAGACTGGCC 61.328 63.158 0.00 0.00 0.00 5.36
5066 10996 0.037326 TTGAGACTGGCCGTGATGTC 60.037 55.000 4.94 4.99 0.00 3.06
5091 11021 8.085909 TCAAGTGACGACATATTTGTTTAGAGA 58.914 33.333 0.00 0.00 35.79 3.10
5096 11026 5.189145 ACGACATATTTGTTTAGAGAGGGGT 59.811 40.000 0.00 0.00 35.79 4.95
5108 11038 2.687200 AGGGGTATGTGAGCGGCA 60.687 61.111 1.45 0.00 0.00 5.69
5125 11055 2.735126 CGGCACATTGAAATGGTAAGGC 60.735 50.000 7.87 5.96 40.70 4.35
5126 11056 2.233431 GGCACATTGAAATGGTAAGGCA 59.767 45.455 7.87 0.00 40.70 4.75
5141 11071 2.191128 AGGCACAAGACATGGAGTTC 57.809 50.000 0.00 0.00 0.00 3.01
5147 11077 4.641396 CACAAGACATGGAGTTCACCTAA 58.359 43.478 0.00 0.00 0.00 2.69
5151 11081 6.777580 ACAAGACATGGAGTTCACCTAAATTT 59.222 34.615 0.00 0.00 0.00 1.82
5152 11082 6.824305 AGACATGGAGTTCACCTAAATTTG 57.176 37.500 0.00 0.00 0.00 2.32
5154 11084 5.640147 ACATGGAGTTCACCTAAATTTGGA 58.360 37.500 2.65 0.00 0.00 3.53
5155 11085 5.476945 ACATGGAGTTCACCTAAATTTGGAC 59.523 40.000 2.65 0.00 0.00 4.02
5156 11086 4.403734 TGGAGTTCACCTAAATTTGGACC 58.596 43.478 2.65 0.00 0.00 4.46
5160 11090 4.354087 AGTTCACCTAAATTTGGACCCTCT 59.646 41.667 2.65 0.00 0.00 3.69
5181 11111 1.290130 GGGAGGAGGTAAGACCCTACA 59.710 57.143 0.00 0.00 39.75 2.74
5185 11115 3.203934 GAGGAGGTAAGACCCTACACCTA 59.796 52.174 0.00 0.00 41.49 3.08
5188 11118 2.931771 AGGTAAGACCCTACACCTACCT 59.068 50.000 0.00 0.00 39.75 3.08
5191 11121 5.016675 AGGTAAGACCCTACACCTACCTTTA 59.983 44.000 0.00 0.00 39.75 1.85
5225 11155 3.989698 AAGTGCTCGCCGGTGATCG 62.990 63.158 19.93 9.18 38.88 3.69
5244 11175 2.570442 GGAGGATCGCCGAAGATATC 57.430 55.000 0.00 0.00 39.96 1.63
5262 11193 6.659824 AGATATCCGTTTCTTGGGTTACAAT 58.340 36.000 0.00 0.00 38.65 2.71
5270 11201 7.197703 CGTTTCTTGGGTTACAATTTACAAGT 58.802 34.615 0.00 0.00 38.65 3.16
5284 11219 2.526873 AAGTCCTCGGCTGGTGGT 60.527 61.111 0.00 0.00 0.00 4.16
5306 11241 0.722676 AGGGGAAGATGGTGGTAGGA 59.277 55.000 0.00 0.00 0.00 2.94
5315 11252 4.897051 AGATGGTGGTAGGAGAACCTTAT 58.103 43.478 0.00 0.00 45.36 1.73
5316 11253 6.039415 AGATGGTGGTAGGAGAACCTTATA 57.961 41.667 0.00 0.00 45.36 0.98
5346 11287 7.073470 AGGATGATCTAGAATTTGTTGGATCCT 59.927 37.037 14.23 0.00 31.89 3.24
5349 11290 7.632861 TGATCTAGAATTTGTTGGATCCTTCA 58.367 34.615 14.23 9.22 31.55 3.02
5355 11296 8.021898 AGAATTTGTTGGATCCTTCAAAAAGA 57.978 30.769 26.10 13.01 34.14 2.52
5400 11341 2.421529 GGTCAAGCTAGGGTTACATGGG 60.422 54.545 0.00 0.00 0.00 4.00
5409 11350 1.226262 GTTACATGGGTCGGGGCAT 59.774 57.895 0.00 0.00 0.00 4.40
5412 11353 0.399376 TACATGGGTCGGGGCATACT 60.399 55.000 0.00 0.00 0.00 2.12
5413 11354 1.227943 CATGGGTCGGGGCATACTG 60.228 63.158 0.00 0.00 0.00 2.74
5418 11359 3.845259 TCGGGGCATACTGTCGGC 61.845 66.667 0.00 0.00 0.00 5.54
5426 11367 3.675619 ATACTGTCGGCGGGTTGGC 62.676 63.158 7.21 0.00 40.44 4.52
5443 11384 1.453745 GCGCCCTTTGATCCCATCA 60.454 57.895 0.00 0.00 37.55 3.07
5468 11409 2.055838 GTGTCGTGCGATGTTGTCTTA 58.944 47.619 0.00 0.00 0.00 2.10
5473 11414 1.126113 GTGCGATGTTGTCTTACCACG 59.874 52.381 0.00 0.00 0.00 4.94
5477 11418 2.608506 CGATGTTGTCTTACCACGTCCA 60.609 50.000 0.00 0.00 0.00 4.02
5491 11432 0.311790 CGTCCATGCTTGCAAGTTGT 59.688 50.000 26.55 10.94 0.00 3.32
5494 11435 1.755959 TCCATGCTTGCAAGTTGTTGT 59.244 42.857 26.55 5.14 35.92 3.32
5502 13532 4.354587 CTTGCAAGTTGTTGTCTTCCTTC 58.645 43.478 18.65 0.00 35.92 3.46
5537 13567 3.006940 CTCGAGAAGCTGACTCAGTACT 58.993 50.000 6.58 5.02 34.47 2.73
5550 13580 2.171237 CTCAGTACTTGGCCATGGATGA 59.829 50.000 18.40 18.67 0.00 2.92
5552 13582 1.212935 AGTACTTGGCCATGGATGACC 59.787 52.381 18.40 7.65 0.00 4.02
5558 13588 0.179034 GGCCATGGATGACCTGAGTC 60.179 60.000 18.40 0.00 43.83 3.36
5563 13594 3.570540 CATGGATGACCTGAGTCTCCTA 58.429 50.000 0.00 2.40 43.91 2.94
5567 13598 4.027437 GGATGACCTGAGTCTCCTACTTT 58.973 47.826 0.00 0.00 43.91 2.66
5568 13599 5.202004 GGATGACCTGAGTCTCCTACTTTA 58.798 45.833 0.00 0.00 43.91 1.85
5569 13600 5.300792 GGATGACCTGAGTCTCCTACTTTAG 59.699 48.000 0.00 0.00 43.91 1.85
5570 13601 4.017808 TGACCTGAGTCTCCTACTTTAGC 58.982 47.826 0.00 0.00 43.91 3.09
5572 13603 3.018149 CCTGAGTCTCCTACTTTAGCGT 58.982 50.000 0.00 0.00 39.07 5.07
5573 13604 3.181495 CCTGAGTCTCCTACTTTAGCGTG 60.181 52.174 0.00 0.00 39.07 5.34
5574 13605 2.163815 TGAGTCTCCTACTTTAGCGTGC 59.836 50.000 0.00 0.00 39.07 5.34
5576 13607 0.822164 TCTCCTACTTTAGCGTGCCC 59.178 55.000 0.00 0.00 0.00 5.36
5577 13608 0.527817 CTCCTACTTTAGCGTGCCCG 60.528 60.000 0.00 0.00 37.07 6.13
5578 13609 0.966875 TCCTACTTTAGCGTGCCCGA 60.967 55.000 0.00 0.00 35.63 5.14
5579 13610 0.108520 CCTACTTTAGCGTGCCCGAA 60.109 55.000 0.00 0.00 35.63 4.30
5580 13611 1.472728 CCTACTTTAGCGTGCCCGAAT 60.473 52.381 0.00 0.00 35.63 3.34
5581 13612 1.593006 CTACTTTAGCGTGCCCGAATG 59.407 52.381 0.00 0.00 35.63 2.67
5591 13622 4.743018 CCCGAATGGCACTTCCTT 57.257 55.556 0.00 0.00 35.26 3.36
5592 13623 2.961424 CCCGAATGGCACTTCCTTT 58.039 52.632 0.00 0.00 35.16 3.11
5593 13624 0.527565 CCCGAATGGCACTTCCTTTG 59.472 55.000 0.00 0.00 32.87 2.77
5594 13625 1.533625 CCGAATGGCACTTCCTTTGA 58.466 50.000 0.00 0.00 32.87 2.69
5595 13626 2.094675 CCGAATGGCACTTCCTTTGAT 58.905 47.619 0.00 0.00 32.87 2.57
5608 13641 1.766496 CCTTTGATAGTAGCCCCCGAA 59.234 52.381 0.00 0.00 0.00 4.30
5613 13646 2.249139 GATAGTAGCCCCCGAATGTCT 58.751 52.381 0.00 0.00 0.00 3.41
5614 13647 2.170012 TAGTAGCCCCCGAATGTCTT 57.830 50.000 0.00 0.00 0.00 3.01
5615 13648 0.541863 AGTAGCCCCCGAATGTCTTG 59.458 55.000 0.00 0.00 0.00 3.02
5638 13671 0.253327 CCCTCCTGCCAGAAGGTTAC 59.747 60.000 0.00 0.00 38.58 2.50
5640 13673 1.561542 CCTCCTGCCAGAAGGTTACAT 59.438 52.381 0.00 0.00 38.58 2.29
5660 13694 4.042187 ACATGGGCTTGTTAAGTCTCTTCT 59.958 41.667 0.00 0.00 32.49 2.85
5661 13695 4.706842 TGGGCTTGTTAAGTCTCTTCTT 57.293 40.909 0.00 0.00 32.49 2.52
5667 13701 4.848562 TGTTAAGTCTCTTCTTGCTCGA 57.151 40.909 0.00 0.00 0.00 4.04
5672 13706 0.826715 TCTCTTCTTGCTCGATGGGG 59.173 55.000 0.00 0.00 0.00 4.96
5693 13727 3.370633 GGAGCTACCCGAGAAGGAATTTT 60.371 47.826 0.00 0.00 45.00 1.82
5705 13739 7.335924 CCGAGAAGGAATTTTAGTGGTTGAATA 59.664 37.037 0.00 0.00 45.00 1.75
5711 13745 6.761242 GGAATTTTAGTGGTTGAATAATGGGC 59.239 38.462 0.00 0.00 0.00 5.36
5713 13747 4.601406 TTAGTGGTTGAATAATGGGCCT 57.399 40.909 4.53 0.00 0.00 5.19
5714 13748 2.738743 AGTGGTTGAATAATGGGCCTG 58.261 47.619 4.53 0.00 0.00 4.85
5715 13749 1.136891 GTGGTTGAATAATGGGCCTGC 59.863 52.381 4.53 0.00 0.00 4.85
5716 13750 1.272928 TGGTTGAATAATGGGCCTGCA 60.273 47.619 4.53 0.00 0.00 4.41
5717 13751 2.041701 GGTTGAATAATGGGCCTGCAT 58.958 47.619 4.53 0.00 0.00 3.96
5718 13752 2.036346 GGTTGAATAATGGGCCTGCATC 59.964 50.000 4.53 0.00 0.00 3.91
5719 13753 2.961062 GTTGAATAATGGGCCTGCATCT 59.039 45.455 4.53 0.00 0.00 2.90
5720 13754 2.589720 TGAATAATGGGCCTGCATCTG 58.410 47.619 4.53 0.00 0.00 2.90
5722 13756 0.541296 ATAATGGGCCTGCATCTGGC 60.541 55.000 4.53 6.91 45.73 4.85
5728 13762 2.119655 GCCTGCATCTGGCCAGAAG 61.120 63.158 38.02 33.53 41.62 2.85
5729 13763 1.605992 CCTGCATCTGGCCAGAAGA 59.394 57.895 38.02 22.76 43.89 2.87
5730 13764 0.183014 CCTGCATCTGGCCAGAAGAT 59.817 55.000 38.02 20.56 43.89 2.40
5732 13766 0.179065 TGCATCTGGCCAGAAGATCG 60.179 55.000 38.02 23.36 43.89 3.69
5733 13767 0.179062 GCATCTGGCCAGAAGATCGT 60.179 55.000 38.02 18.96 41.36 3.73
5734 13768 1.579698 CATCTGGCCAGAAGATCGTG 58.420 55.000 38.02 25.92 41.36 4.35
5737 13771 1.612146 TGGCCAGAAGATCGTGGGA 60.612 57.895 0.00 0.00 34.06 4.37
5746 13780 6.405842 GCCAGAAGATCGTGGGAAAAATATTT 60.406 38.462 12.18 0.00 34.06 1.40
5771 13805 2.036475 CGATCTCCACTCCACCAATAGG 59.964 54.545 0.00 0.00 42.21 2.57
5775 13809 0.469917 CCACTCCACCAATAGGCGAT 59.530 55.000 0.00 0.00 39.06 4.58
5778 13812 3.016736 CACTCCACCAATAGGCGATTTT 58.983 45.455 0.00 0.00 39.06 1.82
5780 13814 3.443681 ACTCCACCAATAGGCGATTTTTG 59.556 43.478 0.00 0.00 39.06 2.44
5785 13819 4.157656 CACCAATAGGCGATTTTTGGAAGA 59.842 41.667 13.09 0.00 40.89 2.87
5791 13825 4.089361 AGGCGATTTTTGGAAGAGGAATT 58.911 39.130 0.00 0.00 0.00 2.17
5799 13833 0.804989 GGAAGAGGAATTGTGTGCCG 59.195 55.000 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 7.659799 TCTTGCTCTTTTATTTGTACTGTGCTA 59.340 33.333 0.00 0.00 0.00 3.49
29 30 8.345565 ACTTCTTGCTCTTTTATTTGTACTGTG 58.654 33.333 0.00 0.00 0.00 3.66
33 34 9.387123 CTTCACTTCTTGCTCTTTTATTTGTAC 57.613 33.333 0.00 0.00 0.00 2.90
34 35 9.337396 TCTTCACTTCTTGCTCTTTTATTTGTA 57.663 29.630 0.00 0.00 0.00 2.41
35 36 8.131731 GTCTTCACTTCTTGCTCTTTTATTTGT 58.868 33.333 0.00 0.00 0.00 2.83
36 37 8.131100 TGTCTTCACTTCTTGCTCTTTTATTTG 58.869 33.333 0.00 0.00 0.00 2.32
39 40 6.072783 GCTGTCTTCACTTCTTGCTCTTTTAT 60.073 38.462 0.00 0.00 0.00 1.40
73 74 4.892934 TGGGCATATTGTTAGACATTTCCC 59.107 41.667 0.00 0.00 0.00 3.97
126 127 4.262549 CCTGAAATTTGCTGGGTGATTTGA 60.263 41.667 0.00 0.00 0.00 2.69
332 1778 3.694072 CCGGCAATCCTTCATGTTCTTTA 59.306 43.478 0.00 0.00 0.00 1.85
529 1975 7.618117 TCAACACTCTTCCTGATGGTATAGTTA 59.382 37.037 0.00 0.00 34.23 2.24
597 2043 2.226674 TCGTTTGTGTTGCTTTGTGTCA 59.773 40.909 0.00 0.00 0.00 3.58
598 2044 2.845967 CTCGTTTGTGTTGCTTTGTGTC 59.154 45.455 0.00 0.00 0.00 3.67
600 2046 3.129852 TCTCGTTTGTGTTGCTTTGTG 57.870 42.857 0.00 0.00 0.00 3.33
682 2132 5.951747 CCCTTAAAATCTCATTCCTTGGACA 59.048 40.000 0.00 0.00 0.00 4.02
732 2183 7.104290 ACAGTGATGATATAGCAAGATGATGG 58.896 38.462 0.00 0.00 0.00 3.51
802 2255 1.003233 GAGGGCCCAGTTCAGTGAC 60.003 63.158 27.56 0.00 0.00 3.67
818 2271 2.052104 GGGGTTGAAATGGCCGGAG 61.052 63.158 5.05 0.00 0.00 4.63
826 2279 3.918544 CCGCATCGGGGTTGAAAT 58.081 55.556 0.00 0.00 44.15 2.17
1007 2463 4.603094 TGATCCTCCTACTAGTTGGTGA 57.397 45.455 21.98 18.74 0.00 4.02
1092 2551 2.672996 GCTTTCCGCCTGCCTTCA 60.673 61.111 0.00 0.00 0.00 3.02
1146 2605 3.857217 CAGAGAGGCTGCATTCACT 57.143 52.632 0.50 0.00 37.90 3.41
1205 2676 3.241493 TGGTTTACGCACCATGGAG 57.759 52.632 21.47 12.70 42.27 3.86
1215 2686 0.027979 CGCTGCATCCATGGTTTACG 59.972 55.000 12.58 5.98 0.00 3.18
1464 2968 3.126343 ACGGAGTGCGACAAAATAATTCC 59.874 43.478 12.27 0.00 42.51 3.01
1471 2975 2.313267 GGAACGGAGTGCGACAAAA 58.687 52.632 12.27 0.00 45.00 2.44
1546 4101 6.074544 ACGCTACTTATAGTTTGGCTCTAG 57.925 41.667 0.00 0.00 0.00 2.43
1593 4174 1.529438 GGTAACGTGTGGTGTGTCATG 59.471 52.381 0.00 0.00 0.00 3.07
1614 4195 7.147689 TGGAAATATATTGCAAGCAATTCCTGT 60.148 33.333 25.37 12.61 43.32 4.00
1927 4696 2.420058 AGCACCCACTAACCTATTGC 57.580 50.000 0.00 0.00 0.00 3.56
2240 5514 5.008811 ACCACGACAAAAATTACGGAATTGA 59.991 36.000 6.32 0.00 35.38 2.57
2248 5522 9.453325 TTGATCTAAAACCACGACAAAAATTAC 57.547 29.630 0.00 0.00 0.00 1.89
2413 5719 4.079787 ACATTACATTACATGGCAGGACCT 60.080 41.667 5.99 0.00 40.22 3.85
2430 5736 5.912396 TGCGACATGTTTTTCTTGACATTAC 59.088 36.000 0.00 0.00 34.42 1.89
2454 5780 9.739276 TCAAATGGTTATTTTGACAGATAGAGT 57.261 29.630 0.00 0.00 34.34 3.24
2554 5888 5.560966 TGCACGAAAGAGAGTTTTCTTTT 57.439 34.783 2.88 0.00 45.00 2.27
2627 6005 2.811431 TGTGTAAAGTTCCTGGCAATCG 59.189 45.455 0.00 0.00 0.00 3.34
2628 6006 6.509418 TTATGTGTAAAGTTCCTGGCAATC 57.491 37.500 0.00 0.00 0.00 2.67
2632 6010 9.869757 AAAATATTTATGTGTAAAGTTCCTGGC 57.130 29.630 0.01 0.00 33.57 4.85
2665 6713 7.068839 GGACATGTATCTTCTCAAACCTCTCTA 59.931 40.741 0.00 0.00 0.00 2.43
2689 6737 8.100164 TCACTATAATGTTTCATGTCAACAGGA 58.900 33.333 15.35 0.00 37.55 3.86
2747 6796 1.404717 GCCTGAGAGTTTGCAGATCGA 60.405 52.381 0.00 0.00 34.06 3.59
2763 6813 2.049156 TGAGTTCTCACGCGCCTG 60.049 61.111 5.73 0.00 0.00 4.85
2857 6908 5.989168 AGATGTTGACAGTGTAAATGACGAA 59.011 36.000 0.00 0.00 34.17 3.85
2883 6935 5.594317 AGTCATGTTTCCTTATTGGTATGGC 59.406 40.000 0.00 0.00 37.07 4.40
2918 6970 6.097270 ACTGATGGTGTTGCAAGCATATAAAT 59.903 34.615 0.00 0.00 38.35 1.40
2939 6991 4.288366 TCATTTGTGGTGATAAGGGACTGA 59.712 41.667 0.00 0.00 40.86 3.41
2975 7027 9.868277 GAATGATCCCTATGTAATTCAGTCTAG 57.132 37.037 0.00 0.00 0.00 2.43
2980 7032 8.783833 AATCGAATGATCCCTATGTAATTCAG 57.216 34.615 0.00 0.00 32.24 3.02
2989 7041 9.799106 AAATCTTACAAATCGAATGATCCCTAT 57.201 29.630 8.40 0.00 32.24 2.57
3792 8278 3.131755 AGGAAATGCCACCTACGTACTAC 59.868 47.826 0.00 0.00 40.02 2.73
3831 8391 4.301505 CCAATCCGGTGTCCTGTG 57.698 61.111 0.00 0.00 0.00 3.66
3862 8454 3.039134 CAACAACAAGGTCCCGCC 58.961 61.111 0.00 0.00 37.58 6.13
3865 8457 1.620822 ATCTGCAACAACAAGGTCCC 58.379 50.000 0.00 0.00 0.00 4.46
3898 8490 1.028330 CGCTTGTGGTGATCATGGCT 61.028 55.000 0.00 0.00 0.00 4.75
3910 8502 1.202065 CCGGATGATTTGTCGCTTGTG 60.202 52.381 0.00 0.00 0.00 3.33
3998 8593 2.490217 CGGGAAGACGCTGACGAT 59.510 61.111 0.00 0.00 43.93 3.73
4035 8630 1.920051 CCGATCGACATGAACAGCG 59.080 57.895 18.66 0.00 0.00 5.18
4202 8800 1.522355 CGGTGATCTTGCGCCAGAT 60.522 57.895 22.78 22.78 38.35 2.90
4660 9270 0.459899 ATCTTGTCTACATCGCCGCA 59.540 50.000 0.00 0.00 0.00 5.69
4681 9291 4.517832 TGAATGCATGATACATGAAGAGCC 59.482 41.667 14.65 0.00 0.00 4.70
4682 9292 5.334957 CCTGAATGCATGATACATGAAGAGC 60.335 44.000 14.65 0.00 0.00 4.09
4689 9341 5.163120 ACTCTTCCCTGAATGCATGATACAT 60.163 40.000 0.00 0.00 0.00 2.29
4695 9347 3.087031 ACAACTCTTCCCTGAATGCATG 58.913 45.455 0.00 0.00 0.00 4.06
4700 9352 2.887152 GCAACACAACTCTTCCCTGAAT 59.113 45.455 0.00 0.00 0.00 2.57
4704 9356 1.680338 GTGCAACACAACTCTTCCCT 58.320 50.000 0.00 0.00 36.32 4.20
4716 9368 2.103432 TCCGAAGTAGAAAGGTGCAACA 59.897 45.455 3.64 0.00 39.98 3.33
4736 9388 3.896648 TCCATTTTGTTCACTTCGCTC 57.103 42.857 0.00 0.00 0.00 5.03
4740 9392 5.841810 TGTTCCATCCATTTTGTTCACTTC 58.158 37.500 0.00 0.00 0.00 3.01
4802 9456 4.155280 GGTGTCGTGCCACTAAAATGTATT 59.845 41.667 0.00 0.00 35.63 1.89
4816 9470 1.278637 CAAAAGACCGGTGTCGTGC 59.721 57.895 14.63 0.00 46.51 5.34
4828 9482 4.289342 CACGCATCAATCAACACAAAAGA 58.711 39.130 0.00 0.00 0.00 2.52
4849 9503 5.708230 CACCTGGTAATAAAGTAAGGTTGCA 59.292 40.000 0.00 0.00 35.87 4.08
4850 9504 5.708697 ACACCTGGTAATAAAGTAAGGTTGC 59.291 40.000 0.00 0.00 35.87 4.17
4870 9524 4.109766 GGCTTTTGTAACAACTGAACACC 58.890 43.478 0.00 0.00 0.00 4.16
4874 9528 8.057536 TCTTTTAGGCTTTTGTAACAACTGAA 57.942 30.769 0.00 0.00 0.00 3.02
4906 9561 1.686355 TTGTGTTGCCTTGATCGGTT 58.314 45.000 0.00 0.00 0.00 4.44
4916 9571 4.576463 CCTGGTAATCTCTATTGTGTTGCC 59.424 45.833 0.00 0.00 0.00 4.52
4918 9573 6.173339 ACACCTGGTAATCTCTATTGTGTTG 58.827 40.000 0.00 0.00 28.25 3.33
4919 9574 6.374417 ACACCTGGTAATCTCTATTGTGTT 57.626 37.500 0.00 0.00 28.25 3.32
4922 9577 6.213600 ACTGAACACCTGGTAATCTCTATTGT 59.786 38.462 0.00 0.00 0.00 2.71
4930 9586 5.761234 TGTAACAACTGAACACCTGGTAATC 59.239 40.000 0.00 1.26 0.00 1.75
4936 9592 4.290155 GCATTGTAACAACTGAACACCTG 58.710 43.478 0.00 0.00 0.00 4.00
4937 9593 3.317993 GGCATTGTAACAACTGAACACCT 59.682 43.478 0.00 0.00 0.00 4.00
4938 9594 3.067461 TGGCATTGTAACAACTGAACACC 59.933 43.478 0.00 0.00 0.00 4.16
4940 9596 3.242903 CGTGGCATTGTAACAACTGAACA 60.243 43.478 0.00 0.00 0.00 3.18
4941 9597 3.296628 CGTGGCATTGTAACAACTGAAC 58.703 45.455 0.00 0.00 0.00 3.18
4942 9598 2.292016 CCGTGGCATTGTAACAACTGAA 59.708 45.455 0.00 0.00 0.00 3.02
4943 9599 1.876799 CCGTGGCATTGTAACAACTGA 59.123 47.619 0.00 0.00 0.00 3.41
4944 9600 1.665735 GCCGTGGCATTGTAACAACTG 60.666 52.381 5.89 0.00 41.49 3.16
4946 9602 0.388006 GGCCGTGGCATTGTAACAAC 60.388 55.000 13.76 0.00 44.11 3.32
4949 9605 1.211709 GTGGCCGTGGCATTGTAAC 59.788 57.895 13.76 0.00 44.11 2.50
4951 9607 2.360600 GGTGGCCGTGGCATTGTA 60.361 61.111 13.76 0.00 44.11 2.41
4953 9614 3.443045 GAGGTGGCCGTGGCATTG 61.443 66.667 13.76 0.00 44.11 2.82
4957 9618 3.723912 TATTTCTGAGGTGGCCGTGGC 62.724 57.143 1.16 1.16 41.06 5.01
4962 9623 0.548510 AGCCTATTTCTGAGGTGGCC 59.451 55.000 0.00 0.00 41.08 5.36
4972 9637 3.426292 GCGTCCTTTGTTCAGCCTATTTC 60.426 47.826 0.00 0.00 0.00 2.17
4990 10920 2.928116 ACTAAACTTTGGATAGCGCGTC 59.072 45.455 8.43 4.28 0.00 5.19
5030 10960 0.591236 CAAAGCACCGACAACCAACG 60.591 55.000 0.00 0.00 0.00 4.10
5035 10965 1.261619 CAGTCTCAAAGCACCGACAAC 59.738 52.381 0.00 0.00 0.00 3.32
5045 10975 1.081892 CATCACGGCCAGTCTCAAAG 58.918 55.000 2.24 0.00 0.00 2.77
5054 10984 0.602638 GTCACTTGACATCACGGCCA 60.603 55.000 2.24 0.00 44.18 5.36
5056 10986 0.666274 TCGTCACTTGACATCACGGC 60.666 55.000 9.94 0.00 44.99 5.68
5057 10987 1.060713 GTCGTCACTTGACATCACGG 58.939 55.000 9.94 0.00 44.99 4.94
5058 10988 1.766069 TGTCGTCACTTGACATCACG 58.234 50.000 9.94 0.00 44.99 4.35
5066 10996 8.239681 TCTCTAAACAAATATGTCGTCACTTG 57.760 34.615 0.00 0.00 39.40 3.16
5085 11015 2.307768 CGCTCACATACCCCTCTCTAA 58.692 52.381 0.00 0.00 0.00 2.10
5087 11017 0.757188 CCGCTCACATACCCCTCTCT 60.757 60.000 0.00 0.00 0.00 3.10
5091 11021 2.687200 TGCCGCTCACATACCCCT 60.687 61.111 0.00 0.00 0.00 4.79
5108 11038 4.832266 TCTTGTGCCTTACCATTTCAATGT 59.168 37.500 0.00 0.00 34.60 2.71
5109 11039 5.163513 GTCTTGTGCCTTACCATTTCAATG 58.836 41.667 0.00 0.00 36.17 2.82
5115 11045 3.091545 CCATGTCTTGTGCCTTACCATT 58.908 45.455 0.00 0.00 0.00 3.16
5125 11055 3.131709 AGGTGAACTCCATGTCTTGTG 57.868 47.619 0.00 0.00 0.00 3.33
5126 11056 4.974645 TTAGGTGAACTCCATGTCTTGT 57.025 40.909 0.00 0.00 0.00 3.16
5141 11071 3.356290 CCAGAGGGTCCAAATTTAGGTG 58.644 50.000 0.00 0.00 0.00 4.00
5147 11077 1.002857 CCTCCCAGAGGGTCCAAATT 58.997 55.000 2.49 0.00 45.43 1.82
5160 11090 1.290130 GTAGGGTCTTACCTCCTCCCA 59.710 57.143 0.00 0.00 42.09 4.37
5181 11111 5.013808 AGCAATACAACCACTAAAGGTAGGT 59.986 40.000 0.00 0.00 42.25 3.08
5185 11115 4.980573 TGAGCAATACAACCACTAAAGGT 58.019 39.130 0.00 0.00 45.91 3.50
5188 11118 5.278266 GCACTTGAGCAATACAACCACTAAA 60.278 40.000 0.00 0.00 0.00 1.85
5191 11121 2.554032 GCACTTGAGCAATACAACCACT 59.446 45.455 0.00 0.00 0.00 4.00
5225 11155 1.135333 GGATATCTTCGGCGATCCTCC 59.865 57.143 11.76 9.42 35.86 4.30
5227 11157 0.811915 CGGATATCTTCGGCGATCCT 59.188 55.000 20.49 7.66 36.49 3.24
5228 11158 0.526662 ACGGATATCTTCGGCGATCC 59.473 55.000 11.76 13.66 35.47 3.36
5231 11161 1.679680 AGAAACGGATATCTTCGGCGA 59.320 47.619 4.99 4.99 0.00 5.54
5232 11162 2.135664 AGAAACGGATATCTTCGGCG 57.864 50.000 0.00 0.00 0.00 6.46
5233 11163 2.544267 CCAAGAAACGGATATCTTCGGC 59.456 50.000 2.05 0.00 33.73 5.54
5236 11166 6.110707 TGTAACCCAAGAAACGGATATCTTC 58.889 40.000 2.05 0.00 33.73 2.87
5241 11172 7.664731 TGTAAATTGTAACCCAAGAAACGGATA 59.335 33.333 0.00 0.00 36.25 2.59
5244 11175 6.074544 TGTAAATTGTAACCCAAGAAACGG 57.925 37.500 0.00 0.00 36.25 4.44
5262 11193 1.053424 ACCAGCCGAGGACTTGTAAA 58.947 50.000 0.00 0.00 0.00 2.01
5270 11201 4.631740 TCCACCACCAGCCGAGGA 62.632 66.667 0.00 0.00 0.00 3.71
5284 11219 0.419865 TACCACCATCTTCCCCTCCA 59.580 55.000 0.00 0.00 0.00 3.86
5290 11225 2.170817 GGTTCTCCTACCACCATCTTCC 59.829 54.545 0.00 0.00 38.12 3.46
5316 11253 9.163894 TCCAACAAATTCTAGATCATCCTAGAT 57.836 33.333 0.00 0.00 43.14 1.98
5346 11287 3.763897 GGCAAGCTAGGGATCTTTTTGAA 59.236 43.478 0.00 0.00 0.00 2.69
5349 11290 3.746792 AGGCAAGCTAGGGATCTTTTT 57.253 42.857 0.00 0.00 0.00 1.94
5355 11296 6.069963 CCAAGTATATAAGGCAAGCTAGGGAT 60.070 42.308 0.00 0.00 0.00 3.85
5400 11341 2.106332 CCGACAGTATGCCCCGAC 59.894 66.667 0.00 0.00 42.53 4.79
5409 11350 4.382320 GCCAACCCGCCGACAGTA 62.382 66.667 0.00 0.00 0.00 2.74
5426 11367 3.189568 TTGATGGGATCAAAGGGCG 57.810 52.632 0.00 0.00 45.57 6.13
5435 11376 0.323629 ACGACACGGTTTGATGGGAT 59.676 50.000 0.00 0.00 0.00 3.85
5443 11384 1.155424 AACATCGCACGACACGGTTT 61.155 50.000 0.00 0.00 0.00 3.27
5468 11409 1.518056 CTTGCAAGCATGGACGTGGT 61.518 55.000 14.65 0.00 0.00 4.16
5473 11414 2.129607 CAACAACTTGCAAGCATGGAC 58.870 47.619 26.27 0.00 0.00 4.02
5477 11418 3.491447 GGAAGACAACAACTTGCAAGCAT 60.491 43.478 26.27 12.84 36.12 3.79
5491 11432 4.323028 CCAGCTGTAGATGAAGGAAGACAA 60.323 45.833 13.81 0.00 32.25 3.18
5494 11435 2.768527 CCCAGCTGTAGATGAAGGAAGA 59.231 50.000 13.81 0.00 32.25 2.87
5502 13532 0.031857 CTCGAGCCCAGCTGTAGATG 59.968 60.000 13.81 0.00 39.88 2.90
5550 13580 3.018149 CGCTAAAGTAGGAGACTCAGGT 58.982 50.000 4.53 0.00 43.67 4.00
5552 13582 3.732471 GCACGCTAAAGTAGGAGACTCAG 60.732 52.174 4.53 0.00 43.67 3.35
5558 13588 0.527817 CGGGCACGCTAAAGTAGGAG 60.528 60.000 0.00 0.00 0.00 3.69
5563 13594 1.024579 CCATTCGGGCACGCTAAAGT 61.025 55.000 1.67 0.00 40.69 2.66
5574 13605 0.527565 CAAAGGAAGTGCCATTCGGG 59.472 55.000 0.00 0.00 40.02 5.14
5576 13607 3.941483 ACTATCAAAGGAAGTGCCATTCG 59.059 43.478 0.00 0.00 40.02 3.34
5577 13608 5.008118 GCTACTATCAAAGGAAGTGCCATTC 59.992 44.000 0.00 0.00 40.02 2.67
5578 13609 4.884164 GCTACTATCAAAGGAAGTGCCATT 59.116 41.667 0.00 0.00 40.02 3.16
5579 13610 4.455606 GCTACTATCAAAGGAAGTGCCAT 58.544 43.478 0.00 0.00 40.02 4.40
5580 13611 3.370527 GGCTACTATCAAAGGAAGTGCCA 60.371 47.826 0.00 0.00 40.02 4.92
5581 13612 3.206964 GGCTACTATCAAAGGAAGTGCC 58.793 50.000 0.00 0.00 33.49 5.01
5583 13614 3.433740 GGGGGCTACTATCAAAGGAAGTG 60.434 52.174 0.00 0.00 0.00 3.16
5584 13615 2.778270 GGGGGCTACTATCAAAGGAAGT 59.222 50.000 0.00 0.00 0.00 3.01
5586 13617 1.766496 CGGGGGCTACTATCAAAGGAA 59.234 52.381 0.00 0.00 0.00 3.36
5587 13618 1.062734 TCGGGGGCTACTATCAAAGGA 60.063 52.381 0.00 0.00 0.00 3.36
5589 13620 3.181454 ACATTCGGGGGCTACTATCAAAG 60.181 47.826 0.00 0.00 0.00 2.77
5591 13622 2.367567 GACATTCGGGGGCTACTATCAA 59.632 50.000 0.00 0.00 0.00 2.57
5592 13623 1.968493 GACATTCGGGGGCTACTATCA 59.032 52.381 0.00 0.00 0.00 2.15
5593 13624 2.249139 AGACATTCGGGGGCTACTATC 58.751 52.381 0.00 0.00 0.00 2.08
5594 13625 2.368875 CAAGACATTCGGGGGCTACTAT 59.631 50.000 0.00 0.00 0.00 2.12
5595 13626 1.760613 CAAGACATTCGGGGGCTACTA 59.239 52.381 0.00 0.00 0.00 1.82
5608 13641 0.610232 GCAGGAGGGTTGCAAGACAT 60.610 55.000 0.00 0.00 41.17 3.06
5613 13646 2.005606 TTCTGGCAGGAGGGTTGCAA 62.006 55.000 15.73 0.00 43.28 4.08
5614 13647 2.416107 CTTCTGGCAGGAGGGTTGCA 62.416 60.000 15.47 0.00 43.28 4.08
5615 13648 1.676967 CTTCTGGCAGGAGGGTTGC 60.677 63.158 15.47 0.00 40.80 4.17
5638 13671 4.583871 AGAAGAGACTTAACAAGCCCATG 58.416 43.478 0.00 0.00 0.00 3.66
5640 13673 4.389374 CAAGAAGAGACTTAACAAGCCCA 58.611 43.478 0.00 0.00 0.00 5.36
5672 13706 3.545366 AAATTCCTTCTCGGGTAGCTC 57.455 47.619 0.00 0.00 0.00 4.09
5679 13713 5.001232 TCAACCACTAAAATTCCTTCTCGG 58.999 41.667 0.00 0.00 0.00 4.63
5693 13727 3.897239 CAGGCCCATTATTCAACCACTA 58.103 45.455 0.00 0.00 0.00 2.74
5705 13739 2.443390 GCCAGATGCAGGCCCATT 60.443 61.111 0.00 0.00 46.50 3.16
5711 13745 0.183014 ATCTTCTGGCCAGATGCAGG 59.817 55.000 35.42 21.22 43.89 4.85
5713 13747 0.179065 CGATCTTCTGGCCAGATGCA 60.179 55.000 35.42 24.40 43.89 3.96
5714 13748 0.179062 ACGATCTTCTGGCCAGATGC 60.179 55.000 35.42 22.44 37.29 3.91
5715 13749 1.579698 CACGATCTTCTGGCCAGATG 58.420 55.000 35.42 34.00 37.29 2.90
5716 13750 0.467384 CCACGATCTTCTGGCCAGAT 59.533 55.000 35.42 21.73 37.29 2.90
5717 13751 1.617018 CCCACGATCTTCTGGCCAGA 61.617 60.000 32.00 32.00 35.27 3.86
5718 13752 1.153289 CCCACGATCTTCTGGCCAG 60.153 63.158 27.87 27.87 0.00 4.85
5719 13753 1.198094 TTCCCACGATCTTCTGGCCA 61.198 55.000 4.71 4.71 0.00 5.36
5720 13754 0.035439 TTTCCCACGATCTTCTGGCC 60.035 55.000 0.00 0.00 0.00 5.36
5722 13756 6.699575 AATATTTTTCCCACGATCTTCTGG 57.300 37.500 0.00 0.00 0.00 3.86
5737 13771 6.318900 GGAGTGGAGATCGTGGAAATATTTTT 59.681 38.462 1.43 0.00 0.00 1.94
5746 13780 0.970937 GGTGGAGTGGAGATCGTGGA 60.971 60.000 0.00 0.00 0.00 4.02
5771 13805 4.622740 CACAATTCCTCTTCCAAAAATCGC 59.377 41.667 0.00 0.00 0.00 4.58
5775 13809 4.442753 GGCACACAATTCCTCTTCCAAAAA 60.443 41.667 0.00 0.00 0.00 1.94
5778 13812 2.238521 GGCACACAATTCCTCTTCCAA 58.761 47.619 0.00 0.00 0.00 3.53
5780 13814 0.804989 CGGCACACAATTCCTCTTCC 59.195 55.000 0.00 0.00 0.00 3.46
5785 13819 0.608856 TCATGCGGCACACAATTCCT 60.609 50.000 4.03 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.