Multiple sequence alignment - TraesCS4A01G308700

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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 TraesCS4A01G308700 chr4A 100.000 3134 0 0 1 3134 602259036 602262169 0.000000e+00 5788.0
1 TraesCS4A01G308700 chr4A 84.760 1273 128 12 871 2137 602863025 602864237 0.000000e+00 1216.0
2 TraesCS4A01G308700 chr4A 84.276 725 98 10 2419 3134 562411855 562411138 0.000000e+00 693.0
3 TraesCS4A01G308700 chr4D 91.895 2295 104 21 871 3134 3260934 3258691 0.000000e+00 3133.0
4 TraesCS4A01G308700 chr4D 87.140 1182 117 7 979 2160 2070963 2072109 0.000000e+00 1308.0
5 TraesCS4A01G308700 chr4D 83.862 725 99 11 2418 3134 38452505 38451791 0.000000e+00 675.0
6 TraesCS4A01G308700 chr4D 82.219 703 107 10 2444 3134 203645346 203646042 9.680000e-165 590.0
7 TraesCS4A01G308700 chr4D 90.873 252 20 2 105 355 3261310 3261061 5.010000e-88 335.0
8 TraesCS4A01G308700 chr4B 86.913 1299 135 12 862 2154 3784728 3785997 0.000000e+00 1424.0
9 TraesCS4A01G308700 chr4B 92.711 686 46 2 862 1547 3856295 3855614 0.000000e+00 987.0
10 TraesCS4A01G308700 chr4B 88.771 659 56 2 1543 2183 3854884 3854226 0.000000e+00 791.0
11 TraesCS4A01G308700 chr4B 93.333 180 12 0 206 385 3856469 3856290 1.850000e-67 267.0
12 TraesCS4A01G308700 chr4B 81.081 111 12 4 2291 2393 344467277 344467386 2.590000e-11 80.5
13 TraesCS4A01G308700 chr4B 79.070 129 15 8 2274 2393 413735121 413734996 9.320000e-11 78.7
14 TraesCS4A01G308700 chr2B 84.912 908 121 8 862 1758 713695293 713694391 0.000000e+00 904.0
15 TraesCS4A01G308700 chr2B 84.049 326 50 2 1830 2154 713694346 713694022 2.350000e-81 313.0
16 TraesCS4A01G308700 chr2B 79.751 321 53 9 1826 2137 25069943 25070260 4.070000e-54 222.0
17 TraesCS4A01G308700 chr2A 84.902 914 116 11 862 1758 723828696 723827788 0.000000e+00 904.0
18 TraesCS4A01G308700 chr2A 96.017 477 19 0 385 861 567923521 567923045 0.000000e+00 776.0
19 TraesCS4A01G308700 chr2A 95.397 478 22 0 384 861 567924897 567924420 0.000000e+00 761.0
20 TraesCS4A01G308700 chr2A 79.969 654 108 19 2494 3134 707211908 707211265 7.920000e-126 460.0
21 TraesCS4A01G308700 chr2A 82.659 346 60 0 1809 2154 723827764 723827419 1.090000e-79 307.0
22 TraesCS4A01G308700 chr2A 90.141 213 19 1 1554 1766 273358113 273357903 3.080000e-70 276.0
23 TraesCS4A01G308700 chr2D 83.315 911 134 10 862 1758 589503772 589502866 0.000000e+00 824.0
24 TraesCS4A01G308700 chr2D 81.023 743 111 22 2409 3134 388477808 388478537 5.870000e-157 564.0
25 TraesCS4A01G308700 chrUn 90.664 482 38 7 385 861 111045379 111044900 4.410000e-178 634.0
26 TraesCS4A01G308700 chrUn 78.273 718 130 14 873 1573 47781007 47780299 3.710000e-119 438.0
27 TraesCS4A01G308700 chr1D 90.795 478 38 6 389 862 460841722 460842197 4.410000e-178 634.0
28 TraesCS4A01G308700 chr1D 80.733 737 128 6 2406 3134 100660157 100659427 2.110000e-156 562.0
29 TraesCS4A01G308700 chr1D 80.180 111 13 4 2291 2393 60409613 60409722 1.210000e-09 75.0
30 TraesCS4A01G308700 chr7D 90.062 483 39 9 385 861 574111803 574111324 4.440000e-173 617.0
31 TraesCS4A01G308700 chr7D 89.648 483 41 9 385 861 574113181 574112702 9.610000e-170 606.0
32 TraesCS4A01G308700 chr7D 82.242 687 101 16 2418 3093 109516461 109517137 9.750000e-160 573.0
33 TraesCS4A01G308700 chr7D 77.013 770 128 27 1018 1758 48824895 48824146 2.270000e-106 396.0
34 TraesCS4A01G308700 chr5D 89.834 482 42 7 385 861 8962849 8962370 2.070000e-171 612.0
35 TraesCS4A01G308700 chr5D 80.828 725 119 17 2407 3121 30593769 30593055 4.570000e-153 551.0
36 TraesCS4A01G308700 chr3D 89.627 482 43 7 385 861 6034475 6033996 9.610000e-170 606.0
37 TraesCS4A01G308700 chr3D 84.375 64 9 1 2330 2393 97308953 97309015 9.390000e-06 62.1
38 TraesCS4A01G308700 chr1B 88.430 484 47 6 385 861 55010909 55010428 2.710000e-160 575.0
39 TraesCS4A01G308700 chr1B 81.651 109 11 3 2293 2393 453880938 453881045 7.200000e-12 82.4
40 TraesCS4A01G308700 chr7B 85.430 302 44 0 1859 2160 385435290 385434989 6.520000e-82 315.0
41 TraesCS4A01G308700 chr3B 83.962 106 16 1 2288 2393 256252460 256252564 1.990000e-17 100.0
42 TraesCS4A01G308700 chr3B 81.982 111 11 3 2291 2393 782637637 782637528 5.570000e-13 86.1
43 TraesCS4A01G308700 chr3B 95.455 44 0 2 2291 2333 819282620 819282578 5.610000e-08 69.4
44 TraesCS4A01G308700 chr5A 81.982 111 11 4 2291 2393 496606383 496606274 5.570000e-13 86.1
45 TraesCS4A01G308700 chr5A 81.250 112 11 6 2287 2389 537122645 537122535 7.200000e-12 82.4
46 TraesCS4A01G308700 chr1A 81.982 111 11 4 2291 2393 109578595 109578704 5.570000e-13 86.1
47 TraesCS4A01G308700 chr1A 100.000 33 0 0 2291 2323 21900988 21901020 9.390000e-06 62.1
48 TraesCS4A01G308700 chr6D 80.180 111 13 3 2291 2393 463869741 463869850 1.210000e-09 75.0
49 TraesCS4A01G308700 chr6B 85.938 64 8 1 2330 2393 250758232 250758170 2.020000e-07 67.6


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 TraesCS4A01G308700 chr4A 602259036 602262169 3133 False 5788.000000 5788 100.0000 1 3134 1 chr4A.!!$F1 3133
1 TraesCS4A01G308700 chr4A 602863025 602864237 1212 False 1216.000000 1216 84.7600 871 2137 1 chr4A.!!$F2 1266
2 TraesCS4A01G308700 chr4A 562411138 562411855 717 True 693.000000 693 84.2760 2419 3134 1 chr4A.!!$R1 715
3 TraesCS4A01G308700 chr4D 3258691 3261310 2619 True 1734.000000 3133 91.3840 105 3134 2 chr4D.!!$R2 3029
4 TraesCS4A01G308700 chr4D 2070963 2072109 1146 False 1308.000000 1308 87.1400 979 2160 1 chr4D.!!$F1 1181
5 TraesCS4A01G308700 chr4D 38451791 38452505 714 True 675.000000 675 83.8620 2418 3134 1 chr4D.!!$R1 716
6 TraesCS4A01G308700 chr4D 203645346 203646042 696 False 590.000000 590 82.2190 2444 3134 1 chr4D.!!$F2 690
7 TraesCS4A01G308700 chr4B 3784728 3785997 1269 False 1424.000000 1424 86.9130 862 2154 1 chr4B.!!$F1 1292
8 TraesCS4A01G308700 chr4B 3854226 3856469 2243 True 681.666667 987 91.6050 206 2183 3 chr4B.!!$R2 1977
9 TraesCS4A01G308700 chr2B 713694022 713695293 1271 True 608.500000 904 84.4805 862 2154 2 chr2B.!!$R1 1292
10 TraesCS4A01G308700 chr2A 567923045 567924897 1852 True 768.500000 776 95.7070 384 861 2 chr2A.!!$R3 477
11 TraesCS4A01G308700 chr2A 723827419 723828696 1277 True 605.500000 904 83.7805 862 2154 2 chr2A.!!$R4 1292
12 TraesCS4A01G308700 chr2A 707211265 707211908 643 True 460.000000 460 79.9690 2494 3134 1 chr2A.!!$R2 640
13 TraesCS4A01G308700 chr2D 589502866 589503772 906 True 824.000000 824 83.3150 862 1758 1 chr2D.!!$R1 896
14 TraesCS4A01G308700 chr2D 388477808 388478537 729 False 564.000000 564 81.0230 2409 3134 1 chr2D.!!$F1 725
15 TraesCS4A01G308700 chrUn 47780299 47781007 708 True 438.000000 438 78.2730 873 1573 1 chrUn.!!$R1 700
16 TraesCS4A01G308700 chr1D 100659427 100660157 730 True 562.000000 562 80.7330 2406 3134 1 chr1D.!!$R1 728
17 TraesCS4A01G308700 chr7D 574111324 574113181 1857 True 611.500000 617 89.8550 385 861 2 chr7D.!!$R2 476
18 TraesCS4A01G308700 chr7D 109516461 109517137 676 False 573.000000 573 82.2420 2418 3093 1 chr7D.!!$F1 675
19 TraesCS4A01G308700 chr7D 48824146 48824895 749 True 396.000000 396 77.0130 1018 1758 1 chr7D.!!$R1 740
20 TraesCS4A01G308700 chr5D 30593055 30593769 714 True 551.000000 551 80.8280 2407 3121 1 chr5D.!!$R2 714

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
695 2083 0.027324 CCGTCCTCTACTACGCGTTC 59.973 60.0 20.78 0.0 37.78 3.95 F
856 2244 0.108329 CACCGCCGTGTCTTATTCCT 60.108 55.0 0.00 0.0 35.10 3.36 F
952 2346 0.396974 TTTGCACCAGCCCAGAGTTT 60.397 50.0 0.00 0.0 41.13 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 4057 1.032794 TTGTTGTTGTTGCCGCCATA 58.967 45.000 0.00 0.00 0.00 2.74 R
1878 4179 1.474478 GAGACGATCTGCAGGAAGTCA 59.526 52.381 26.08 6.15 37.79 3.41 R
2746 6056 1.677633 GTTGTACCCGGCAATGGCT 60.678 57.895 5.02 0.00 40.87 4.75 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
18 19 3.904586 GATCCGGCTTCCATCTCTC 57.095 57.895 0.00 0.00 0.00 3.20
19 20 0.320050 GATCCGGCTTCCATCTCTCC 59.680 60.000 0.00 0.00 0.00 3.71
20 21 0.399091 ATCCGGCTTCCATCTCTCCA 60.399 55.000 0.00 0.00 0.00 3.86
21 22 1.045350 TCCGGCTTCCATCTCTCCAG 61.045 60.000 0.00 0.00 0.00 3.86
22 23 1.333636 CCGGCTTCCATCTCTCCAGT 61.334 60.000 0.00 0.00 0.00 4.00
23 24 0.103937 CGGCTTCCATCTCTCCAGTC 59.896 60.000 0.00 0.00 0.00 3.51
24 25 0.103937 GGCTTCCATCTCTCCAGTCG 59.896 60.000 0.00 0.00 0.00 4.18
25 26 1.107114 GCTTCCATCTCTCCAGTCGA 58.893 55.000 0.00 0.00 0.00 4.20
26 27 1.686052 GCTTCCATCTCTCCAGTCGAT 59.314 52.381 0.00 0.00 0.00 3.59
27 28 2.102252 GCTTCCATCTCTCCAGTCGATT 59.898 50.000 0.00 0.00 0.00 3.34
28 29 3.798548 GCTTCCATCTCTCCAGTCGATTC 60.799 52.174 0.00 0.00 0.00 2.52
29 30 2.311463 TCCATCTCTCCAGTCGATTCC 58.689 52.381 0.00 0.00 0.00 3.01
30 31 2.034878 CCATCTCTCCAGTCGATTCCA 58.965 52.381 0.00 0.00 0.00 3.53
31 32 2.035704 CCATCTCTCCAGTCGATTCCAG 59.964 54.545 0.00 0.00 0.00 3.86
32 33 1.107114 TCTCTCCAGTCGATTCCAGC 58.893 55.000 0.00 0.00 0.00 4.85
33 34 1.110442 CTCTCCAGTCGATTCCAGCT 58.890 55.000 0.00 0.00 0.00 4.24
34 35 1.066908 CTCTCCAGTCGATTCCAGCTC 59.933 57.143 0.00 0.00 0.00 4.09
35 36 0.103937 CTCCAGTCGATTCCAGCTCC 59.896 60.000 0.00 0.00 0.00 4.70
36 37 0.614697 TCCAGTCGATTCCAGCTCCA 60.615 55.000 0.00 0.00 0.00 3.86
37 38 0.460987 CCAGTCGATTCCAGCTCCAC 60.461 60.000 0.00 0.00 0.00 4.02
38 39 0.460987 CAGTCGATTCCAGCTCCACC 60.461 60.000 0.00 0.00 0.00 4.61
39 40 0.904865 AGTCGATTCCAGCTCCACCA 60.905 55.000 0.00 0.00 0.00 4.17
40 41 0.741221 GTCGATTCCAGCTCCACCAC 60.741 60.000 0.00 0.00 0.00 4.16
41 42 1.191489 TCGATTCCAGCTCCACCACA 61.191 55.000 0.00 0.00 0.00 4.17
42 43 1.021390 CGATTCCAGCTCCACCACAC 61.021 60.000 0.00 0.00 0.00 3.82
43 44 0.326264 GATTCCAGCTCCACCACACT 59.674 55.000 0.00 0.00 0.00 3.55
44 45 1.555075 GATTCCAGCTCCACCACACTA 59.445 52.381 0.00 0.00 0.00 2.74
45 46 0.685097 TTCCAGCTCCACCACACTAC 59.315 55.000 0.00 0.00 0.00 2.73
46 47 0.178932 TCCAGCTCCACCACACTACT 60.179 55.000 0.00 0.00 0.00 2.57
47 48 1.076513 TCCAGCTCCACCACACTACTA 59.923 52.381 0.00 0.00 0.00 1.82
48 49 1.899814 CCAGCTCCACCACACTACTAA 59.100 52.381 0.00 0.00 0.00 2.24
49 50 2.301870 CCAGCTCCACCACACTACTAAA 59.698 50.000 0.00 0.00 0.00 1.85
50 51 3.589988 CAGCTCCACCACACTACTAAAG 58.410 50.000 0.00 0.00 0.00 1.85
51 52 3.258372 CAGCTCCACCACACTACTAAAGA 59.742 47.826 0.00 0.00 0.00 2.52
52 53 3.901844 AGCTCCACCACACTACTAAAGAA 59.098 43.478 0.00 0.00 0.00 2.52
53 54 4.532521 AGCTCCACCACACTACTAAAGAAT 59.467 41.667 0.00 0.00 0.00 2.40
54 55 5.013183 AGCTCCACCACACTACTAAAGAATT 59.987 40.000 0.00 0.00 0.00 2.17
55 56 5.122396 GCTCCACCACACTACTAAAGAATTG 59.878 44.000 0.00 0.00 0.00 2.32
56 57 6.428083 TCCACCACACTACTAAAGAATTGA 57.572 37.500 0.00 0.00 0.00 2.57
57 58 7.016153 TCCACCACACTACTAAAGAATTGAT 57.984 36.000 0.00 0.00 0.00 2.57
58 59 7.103641 TCCACCACACTACTAAAGAATTGATC 58.896 38.462 0.00 0.00 0.00 2.92
59 60 6.878923 CCACCACACTACTAAAGAATTGATCA 59.121 38.462 0.00 0.00 0.00 2.92
60 61 7.554118 CCACCACACTACTAAAGAATTGATCAT 59.446 37.037 0.00 0.00 0.00 2.45
61 62 8.607459 CACCACACTACTAAAGAATTGATCATC 58.393 37.037 0.00 0.00 0.00 2.92
62 63 8.543774 ACCACACTACTAAAGAATTGATCATCT 58.456 33.333 0.00 0.00 0.00 2.90
63 64 9.039870 CCACACTACTAAAGAATTGATCATCTC 57.960 37.037 0.00 0.00 0.00 2.75
64 65 9.814899 CACACTACTAAAGAATTGATCATCTCT 57.185 33.333 0.00 0.00 0.00 3.10
78 79 7.312657 TGATCATCTCTTCAATTTAGTGTGC 57.687 36.000 0.00 0.00 0.00 4.57
79 80 6.880529 TGATCATCTCTTCAATTTAGTGTGCA 59.119 34.615 0.00 0.00 0.00 4.57
80 81 6.486253 TCATCTCTTCAATTTAGTGTGCAC 57.514 37.500 10.75 10.75 0.00 4.57
81 82 6.233434 TCATCTCTTCAATTTAGTGTGCACT 58.767 36.000 19.41 9.90 45.02 4.40
82 83 6.712095 TCATCTCTTCAATTTAGTGTGCACTT 59.288 34.615 19.41 9.00 42.54 3.16
83 84 6.942532 TCTCTTCAATTTAGTGTGCACTTT 57.057 33.333 19.41 8.62 42.54 2.66
84 85 6.959361 TCTCTTCAATTTAGTGTGCACTTTC 58.041 36.000 19.41 8.65 42.54 2.62
85 86 6.767902 TCTCTTCAATTTAGTGTGCACTTTCT 59.232 34.615 19.41 15.25 42.54 2.52
86 87 7.931407 TCTCTTCAATTTAGTGTGCACTTTCTA 59.069 33.333 19.41 14.29 42.54 2.10
87 88 8.621532 TCTTCAATTTAGTGTGCACTTTCTAT 57.378 30.769 19.41 3.57 42.54 1.98
88 89 9.066892 TCTTCAATTTAGTGTGCACTTTCTATT 57.933 29.630 19.41 9.44 42.54 1.73
89 90 9.121517 CTTCAATTTAGTGTGCACTTTCTATTG 57.878 33.333 19.41 19.37 42.54 1.90
90 91 7.592938 TCAATTTAGTGTGCACTTTCTATTGG 58.407 34.615 19.41 6.97 42.54 3.16
91 92 5.957842 TTTAGTGTGCACTTTCTATTGGG 57.042 39.130 19.41 0.00 42.54 4.12
92 93 3.508845 AGTGTGCACTTTCTATTGGGT 57.491 42.857 19.41 0.00 38.83 4.51
93 94 3.149196 AGTGTGCACTTTCTATTGGGTG 58.851 45.455 19.41 0.00 38.83 4.61
98 99 3.221964 CACTTTCTATTGGGTGCAAGC 57.778 47.619 0.00 0.00 0.00 4.01
99 100 2.821969 CACTTTCTATTGGGTGCAAGCT 59.178 45.455 0.00 0.00 0.00 3.74
100 101 4.009675 CACTTTCTATTGGGTGCAAGCTA 58.990 43.478 0.00 0.00 0.00 3.32
101 102 4.010349 ACTTTCTATTGGGTGCAAGCTAC 58.990 43.478 0.00 0.00 0.00 3.58
102 103 3.712016 TTCTATTGGGTGCAAGCTACA 57.288 42.857 0.00 0.00 0.00 2.74
103 104 2.985896 TCTATTGGGTGCAAGCTACAC 58.014 47.619 10.59 10.59 37.31 2.90
125 126 4.289342 CGATAGTCTCTGCTGAGTGAATG 58.711 47.826 18.82 4.35 40.98 2.67
139 140 6.611613 TGAGTGAATGTGACTATCCTTCTT 57.388 37.500 0.00 0.00 0.00 2.52
142 143 7.604164 TGAGTGAATGTGACTATCCTTCTTTTC 59.396 37.037 0.00 0.00 0.00 2.29
144 145 6.655003 GTGAATGTGACTATCCTTCTTTTCCA 59.345 38.462 0.00 0.00 0.00 3.53
146 147 7.723616 TGAATGTGACTATCCTTCTTTTCCAAA 59.276 33.333 0.00 0.00 0.00 3.28
148 149 9.753674 AATGTGACTATCCTTCTTTTCCAAATA 57.246 29.630 0.00 0.00 0.00 1.40
149 150 9.927081 ATGTGACTATCCTTCTTTTCCAAATAT 57.073 29.630 0.00 0.00 0.00 1.28
150 151 9.177608 TGTGACTATCCTTCTTTTCCAAATATG 57.822 33.333 0.00 0.00 0.00 1.78
157 158 8.593945 TCCTTCTTTTCCAAATATGTTAGCAT 57.406 30.769 0.00 0.00 39.03 3.79
161 162 7.546358 TCTTTTCCAAATATGTTAGCATGTGG 58.454 34.615 1.80 7.26 36.58 4.17
184 185 4.275936 GCTGTTGATGTGTGAAAGGTAGTT 59.724 41.667 0.00 0.00 0.00 2.24
232 233 0.035881 TTCCAGCTCAAGCCACTGAG 59.964 55.000 0.00 4.15 44.82 3.35
238 239 2.360852 CAAGCCACTGAGCCCTGG 60.361 66.667 0.00 0.00 0.00 4.45
256 257 1.073763 TGGAAGGCTGCAGCTTCTTAA 59.926 47.619 35.82 19.81 41.70 1.85
341 342 6.064060 TGATAGGGAAACAATGATGGATCAC 58.936 40.000 0.00 0.00 40.03 3.06
484 1872 3.103875 GGCAACAAACCACGACGT 58.896 55.556 0.00 0.00 0.00 4.34
592 1980 0.391228 AACAAACCAAATCACCGCCC 59.609 50.000 0.00 0.00 0.00 6.13
692 2080 2.327244 GCCGTCCTCTACTACGCG 59.673 66.667 3.53 3.53 37.78 6.01
693 2081 2.467826 GCCGTCCTCTACTACGCGT 61.468 63.158 19.17 19.17 37.78 6.01
694 2082 1.986575 GCCGTCCTCTACTACGCGTT 61.987 60.000 20.78 1.73 37.78 4.84
695 2083 0.027324 CCGTCCTCTACTACGCGTTC 59.973 60.000 20.78 0.00 37.78 3.95
696 2084 1.005340 CGTCCTCTACTACGCGTTCT 58.995 55.000 20.78 5.14 31.66 3.01
697 2085 1.267433 CGTCCTCTACTACGCGTTCTG 60.267 57.143 20.78 11.20 31.66 3.02
698 2086 2.005451 GTCCTCTACTACGCGTTCTGA 58.995 52.381 20.78 10.31 0.00 3.27
699 2087 2.005451 TCCTCTACTACGCGTTCTGAC 58.995 52.381 20.78 0.00 0.00 3.51
708 2096 3.470567 CGTTCTGACGCGTCCAGC 61.471 66.667 34.34 21.58 43.03 4.85
709 2097 3.112709 GTTCTGACGCGTCCAGCC 61.113 66.667 34.34 19.61 44.76 4.85
710 2098 4.717629 TTCTGACGCGTCCAGCCG 62.718 66.667 34.34 17.76 44.76 5.52
724 2112 3.854459 GCCGCGACTGCTGCTAAC 61.854 66.667 8.23 0.00 46.47 2.34
725 2113 2.125912 CCGCGACTGCTGCTAACT 60.126 61.111 8.23 0.00 39.65 2.24
726 2114 2.447887 CCGCGACTGCTGCTAACTG 61.448 63.158 8.23 0.00 39.65 3.16
727 2115 1.444383 CGCGACTGCTGCTAACTGA 60.444 57.895 0.00 0.00 39.65 3.41
728 2116 1.678269 CGCGACTGCTGCTAACTGAC 61.678 60.000 0.00 0.00 39.65 3.51
729 2117 0.389166 GCGACTGCTGCTAACTGACT 60.389 55.000 0.00 0.00 38.39 3.41
730 2118 1.135373 GCGACTGCTGCTAACTGACTA 60.135 52.381 0.00 0.00 38.39 2.59
731 2119 2.520979 CGACTGCTGCTAACTGACTAC 58.479 52.381 0.00 0.00 0.00 2.73
732 2120 2.520979 GACTGCTGCTAACTGACTACG 58.479 52.381 0.00 0.00 0.00 3.51
733 2121 2.160205 ACTGCTGCTAACTGACTACGA 58.840 47.619 0.00 0.00 0.00 3.43
734 2122 2.095161 ACTGCTGCTAACTGACTACGAC 60.095 50.000 0.00 0.00 0.00 4.34
735 2123 1.201647 TGCTGCTAACTGACTACGACC 59.798 52.381 0.00 0.00 0.00 4.79
736 2124 1.469423 GCTGCTAACTGACTACGACCC 60.469 57.143 0.00 0.00 0.00 4.46
737 2125 1.816835 CTGCTAACTGACTACGACCCA 59.183 52.381 0.00 0.00 0.00 4.51
738 2126 2.230508 CTGCTAACTGACTACGACCCAA 59.769 50.000 0.00 0.00 0.00 4.12
739 2127 2.629137 TGCTAACTGACTACGACCCAAA 59.371 45.455 0.00 0.00 0.00 3.28
740 2128 2.991866 GCTAACTGACTACGACCCAAAC 59.008 50.000 0.00 0.00 0.00 2.93
741 2129 3.553508 GCTAACTGACTACGACCCAAACA 60.554 47.826 0.00 0.00 0.00 2.83
742 2130 3.764237 AACTGACTACGACCCAAACAT 57.236 42.857 0.00 0.00 0.00 2.71
743 2131 4.877378 AACTGACTACGACCCAAACATA 57.123 40.909 0.00 0.00 0.00 2.29
744 2132 4.877378 ACTGACTACGACCCAAACATAA 57.123 40.909 0.00 0.00 0.00 1.90
745 2133 4.817517 ACTGACTACGACCCAAACATAAG 58.182 43.478 0.00 0.00 0.00 1.73
746 2134 3.592059 TGACTACGACCCAAACATAAGC 58.408 45.455 0.00 0.00 0.00 3.09
747 2135 3.007074 TGACTACGACCCAAACATAAGCA 59.993 43.478 0.00 0.00 0.00 3.91
748 2136 3.332034 ACTACGACCCAAACATAAGCAC 58.668 45.455 0.00 0.00 0.00 4.40
749 2137 2.264005 ACGACCCAAACATAAGCACA 57.736 45.000 0.00 0.00 0.00 4.57
750 2138 2.151202 ACGACCCAAACATAAGCACAG 58.849 47.619 0.00 0.00 0.00 3.66
751 2139 2.224426 ACGACCCAAACATAAGCACAGA 60.224 45.455 0.00 0.00 0.00 3.41
752 2140 2.159627 CGACCCAAACATAAGCACAGAC 59.840 50.000 0.00 0.00 0.00 3.51
753 2141 3.412386 GACCCAAACATAAGCACAGACT 58.588 45.455 0.00 0.00 0.00 3.24
754 2142 3.412386 ACCCAAACATAAGCACAGACTC 58.588 45.455 0.00 0.00 0.00 3.36
755 2143 2.416547 CCCAAACATAAGCACAGACTCG 59.583 50.000 0.00 0.00 0.00 4.18
756 2144 3.325870 CCAAACATAAGCACAGACTCGA 58.674 45.455 0.00 0.00 0.00 4.04
757 2145 3.123621 CCAAACATAAGCACAGACTCGAC 59.876 47.826 0.00 0.00 0.00 4.20
758 2146 3.660501 AACATAAGCACAGACTCGACA 57.339 42.857 0.00 0.00 0.00 4.35
759 2147 2.947852 ACATAAGCACAGACTCGACAC 58.052 47.619 0.00 0.00 0.00 3.67
760 2148 1.914051 CATAAGCACAGACTCGACACG 59.086 52.381 0.00 0.00 0.00 4.49
761 2149 0.386858 TAAGCACAGACTCGACACGC 60.387 55.000 0.00 0.00 0.00 5.34
762 2150 2.349969 AAGCACAGACTCGACACGCA 62.350 55.000 0.00 0.00 0.00 5.24
763 2151 2.649257 GCACAGACTCGACACGCAC 61.649 63.158 0.00 0.00 0.00 5.34
764 2152 2.016704 CACAGACTCGACACGCACC 61.017 63.158 0.00 0.00 0.00 5.01
765 2153 2.430921 CAGACTCGACACGCACCC 60.431 66.667 0.00 0.00 0.00 4.61
766 2154 2.910479 AGACTCGACACGCACCCA 60.910 61.111 0.00 0.00 0.00 4.51
767 2155 2.028484 GACTCGACACGCACCCAA 59.972 61.111 0.00 0.00 0.00 4.12
768 2156 2.279918 ACTCGACACGCACCCAAC 60.280 61.111 0.00 0.00 0.00 3.77
769 2157 3.403057 CTCGACACGCACCCAACG 61.403 66.667 0.00 0.00 0.00 4.10
772 2160 4.307908 GACACGCACCCAACGCAC 62.308 66.667 0.00 0.00 0.00 5.34
778 2166 4.605967 CACCCAACGCACGCACAC 62.606 66.667 0.00 0.00 0.00 3.82
780 2168 4.605967 CCCAACGCACGCACACAC 62.606 66.667 0.00 0.00 0.00 3.82
781 2169 4.936248 CCAACGCACGCACACACG 62.936 66.667 0.00 0.00 39.50 4.49
787 2175 3.563088 CACGCACACACGCACACT 61.563 61.111 0.00 0.00 36.19 3.55
788 2176 3.261951 ACGCACACACGCACACTC 61.262 61.111 0.00 0.00 36.19 3.51
789 2177 4.339809 CGCACACACGCACACTCG 62.340 66.667 0.00 0.00 0.00 4.18
790 2178 4.649954 GCACACACGCACACTCGC 62.650 66.667 0.00 0.00 0.00 5.03
791 2179 4.000557 CACACACGCACACTCGCC 62.001 66.667 0.00 0.00 0.00 5.54
792 2180 4.522689 ACACACGCACACTCGCCA 62.523 61.111 0.00 0.00 0.00 5.69
793 2181 4.000557 CACACGCACACTCGCCAC 62.001 66.667 0.00 0.00 0.00 5.01
818 2206 4.307908 GGCACGACCAACACGCAC 62.308 66.667 0.00 0.00 38.86 5.34
819 2207 4.643385 GCACGACCAACACGCACG 62.643 66.667 0.00 0.00 0.00 5.34
820 2208 4.643385 CACGACCAACACGCACGC 62.643 66.667 0.00 0.00 0.00 5.34
822 2210 4.643385 CGACCAACACGCACGCAC 62.643 66.667 0.00 0.00 0.00 5.34
823 2211 3.568743 GACCAACACGCACGCACA 61.569 61.111 0.00 0.00 0.00 4.57
824 2212 3.783588 GACCAACACGCACGCACAC 62.784 63.158 0.00 0.00 0.00 3.82
825 2213 3.870422 CCAACACGCACGCACACA 61.870 61.111 0.00 0.00 0.00 3.72
826 2214 2.647481 CAACACGCACGCACACAC 60.647 61.111 0.00 0.00 0.00 3.82
827 2215 2.817834 AACACGCACGCACACACT 60.818 55.556 0.00 0.00 0.00 3.55
828 2216 3.094661 AACACGCACGCACACACTG 62.095 57.895 0.00 0.00 0.00 3.66
829 2217 4.297891 CACGCACGCACACACTGG 62.298 66.667 0.00 0.00 0.00 4.00
830 2218 4.830765 ACGCACGCACACACTGGT 62.831 61.111 0.00 0.00 0.00 4.00
831 2219 4.000557 CGCACGCACACACTGGTC 62.001 66.667 0.00 0.00 0.00 4.02
832 2220 2.894879 GCACGCACACACTGGTCA 60.895 61.111 0.00 0.00 0.00 4.02
833 2221 3.014036 CACGCACACACTGGTCAC 58.986 61.111 0.00 0.00 0.00 3.67
834 2222 2.203015 ACGCACACACTGGTCACC 60.203 61.111 0.00 0.00 0.00 4.02
835 2223 2.203001 CGCACACACTGGTCACCA 60.203 61.111 0.00 0.00 0.00 4.17
836 2224 2.534019 CGCACACACTGGTCACCAC 61.534 63.158 0.00 0.00 0.00 4.16
837 2225 2.186826 GCACACACTGGTCACCACC 61.187 63.158 0.00 0.00 44.10 4.61
839 2227 1.095228 CACACACTGGTCACCACCAC 61.095 60.000 0.00 0.00 46.63 4.16
840 2228 1.525995 CACACTGGTCACCACCACC 60.526 63.158 0.00 0.00 46.63 4.61
841 2229 2.280797 CACTGGTCACCACCACCG 60.281 66.667 0.00 0.00 46.63 4.94
842 2230 4.250305 ACTGGTCACCACCACCGC 62.250 66.667 0.00 0.00 46.63 5.68
850 2238 4.619227 CCACCACCGCCGTGTCTT 62.619 66.667 4.49 0.00 38.41 3.01
851 2239 2.340809 CACCACCGCCGTGTCTTA 59.659 61.111 4.49 0.00 38.41 2.10
852 2240 1.079405 CACCACCGCCGTGTCTTAT 60.079 57.895 4.49 0.00 38.41 1.73
853 2241 0.672401 CACCACCGCCGTGTCTTATT 60.672 55.000 4.49 0.00 38.41 1.40
854 2242 0.390735 ACCACCGCCGTGTCTTATTC 60.391 55.000 4.49 0.00 38.41 1.75
855 2243 1.087771 CCACCGCCGTGTCTTATTCC 61.088 60.000 4.49 0.00 38.41 3.01
856 2244 0.108329 CACCGCCGTGTCTTATTCCT 60.108 55.000 0.00 0.00 35.10 3.36
857 2245 1.135527 CACCGCCGTGTCTTATTCCTA 59.864 52.381 0.00 0.00 35.10 2.94
858 2246 1.826720 ACCGCCGTGTCTTATTCCTAA 59.173 47.619 0.00 0.00 0.00 2.69
859 2247 2.199236 CCGCCGTGTCTTATTCCTAAC 58.801 52.381 0.00 0.00 0.00 2.34
860 2248 2.417651 CCGCCGTGTCTTATTCCTAACA 60.418 50.000 0.00 0.00 0.00 2.41
868 2256 7.345192 CGTGTCTTATTCCTAACATTGCATAC 58.655 38.462 0.00 0.00 0.00 2.39
952 2346 0.396974 TTTGCACCAGCCCAGAGTTT 60.397 50.000 0.00 0.00 41.13 2.66
987 2381 6.268617 AGCAGCAATAATCATCTAGTGGAGTA 59.731 38.462 0.00 0.00 0.00 2.59
989 2383 7.665690 CAGCAATAATCATCTAGTGGAGTAGT 58.334 38.462 0.00 0.00 0.00 2.73
990 2384 8.797438 CAGCAATAATCATCTAGTGGAGTAGTA 58.203 37.037 0.00 0.00 0.00 1.82
991 2385 8.798402 AGCAATAATCATCTAGTGGAGTAGTAC 58.202 37.037 0.00 0.00 0.00 2.73
992 2386 8.577296 GCAATAATCATCTAGTGGAGTAGTACA 58.423 37.037 2.52 0.00 0.00 2.90
1016 2417 2.704464 TTGATGATGGCCTCAGACTG 57.296 50.000 3.32 0.00 37.28 3.51
1137 2549 0.745845 CACTGCCCATAGAGCACACC 60.746 60.000 0.00 0.00 36.01 4.16
1532 2966 2.655364 CATCGCGCTGGAGTACGG 60.655 66.667 5.56 0.00 0.00 4.02
1686 3969 3.941188 CCGCACCTGACACTGGGT 61.941 66.667 0.00 0.00 36.07 4.51
1774 4057 3.764972 GGTGCTACTCAAGGAAGACTACT 59.235 47.826 0.00 0.00 0.00 2.57
1827 4128 0.650512 ACAACAACAAGTCGTCTGCG 59.349 50.000 0.00 0.00 39.92 5.18
1878 4179 1.302511 GCTGGTGGTGAATGTCGGT 60.303 57.895 0.00 0.00 0.00 4.69
2138 5178 1.743091 GCACCTGAGGCTCTGAATCAG 60.743 57.143 21.42 3.38 40.13 2.90
2192 5475 6.053632 TGGAAGATGCATACATATACAGGG 57.946 41.667 0.00 0.00 36.35 4.45
2193 5476 5.547666 TGGAAGATGCATACATATACAGGGT 59.452 40.000 0.00 0.00 36.35 4.34
2250 5546 5.048013 GGAAGGCAGTAAAAACATAAGCACT 60.048 40.000 0.00 0.00 0.00 4.40
2257 5553 6.795114 CAGTAAAAACATAAGCACTTACCGTG 59.205 38.462 0.00 0.00 46.58 4.94
2269 5565 4.618927 GCACTTACCGTGTTCACTATACCA 60.619 45.833 1.53 0.00 45.57 3.25
2277 5573 5.113383 CGTGTTCACTATACCAGGCAATAA 58.887 41.667 1.53 0.00 0.00 1.40
2300 5596 1.846439 ACATACATGTAAGGGCAGCCT 59.154 47.619 12.43 0.00 39.68 4.58
2380 5676 5.935789 ACGCAGCCTTTTACTACATTTTCTA 59.064 36.000 0.00 0.00 0.00 2.10
2480 5776 6.467677 TCCAGCCTCTGCATTAATAAGATAC 58.532 40.000 0.00 0.00 41.13 2.24
2597 5906 0.250295 GCAGCACTCTAACCACCACA 60.250 55.000 0.00 0.00 0.00 4.17
2699 6008 2.831333 CCCGATCAAGGATCTTCAGTG 58.169 52.381 4.86 0.00 36.96 3.66
2715 6024 5.766670 TCTTCAGTGTTCATGCAGAAGAAAT 59.233 36.000 7.96 0.00 38.67 2.17
2746 6056 3.493877 CGCAAATCAATGCCTTCAACAAA 59.506 39.130 0.00 0.00 43.47 2.83
2952 6274 4.956075 ACCAAAAATCCTCTTCGCCATTAT 59.044 37.500 0.00 0.00 0.00 1.28
2978 6300 0.745486 CTGATCGCAGCCACCATGAA 60.745 55.000 0.00 0.00 34.95 2.57
3015 6337 4.986659 GTCAACGCCGTGGAAATATATACT 59.013 41.667 0.00 0.00 0.00 2.12
3016 6338 5.464389 GTCAACGCCGTGGAAATATATACTT 59.536 40.000 0.00 0.00 0.00 2.24
3017 6339 6.642131 GTCAACGCCGTGGAAATATATACTTA 59.358 38.462 0.00 0.00 0.00 2.24
3018 6340 7.169645 GTCAACGCCGTGGAAATATATACTTAA 59.830 37.037 0.00 0.00 0.00 1.85
3042 6364 3.338250 ATGTCCCATGGCACCGGT 61.338 61.111 6.09 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.320050 GGAGAGATGGAAGCCGGATC 59.680 60.000 5.05 1.46 0.00 3.36
1 2 0.399091 TGGAGAGATGGAAGCCGGAT 60.399 55.000 5.05 0.00 0.00 4.18
3 4 1.333636 ACTGGAGAGATGGAAGCCGG 61.334 60.000 0.00 0.00 0.00 6.13
6 7 1.107114 TCGACTGGAGAGATGGAAGC 58.893 55.000 0.00 0.00 0.00 3.86
7 8 3.243704 GGAATCGACTGGAGAGATGGAAG 60.244 52.174 0.00 0.00 0.00 3.46
8 9 2.695666 GGAATCGACTGGAGAGATGGAA 59.304 50.000 0.00 0.00 0.00 3.53
9 10 2.311463 GGAATCGACTGGAGAGATGGA 58.689 52.381 0.00 0.00 0.00 3.41
10 11 2.034878 TGGAATCGACTGGAGAGATGG 58.965 52.381 0.00 0.00 0.00 3.51
11 12 2.545532 GCTGGAATCGACTGGAGAGATG 60.546 54.545 0.00 0.00 0.00 2.90
12 13 1.686052 GCTGGAATCGACTGGAGAGAT 59.314 52.381 0.00 0.00 0.00 2.75
13 14 1.107114 GCTGGAATCGACTGGAGAGA 58.893 55.000 0.00 0.00 0.00 3.10
14 15 1.066908 GAGCTGGAATCGACTGGAGAG 59.933 57.143 0.00 0.00 0.00 3.20
15 16 1.107114 GAGCTGGAATCGACTGGAGA 58.893 55.000 0.00 0.00 0.00 3.71
16 17 0.103937 GGAGCTGGAATCGACTGGAG 59.896 60.000 0.00 0.00 0.00 3.86
17 18 0.614697 TGGAGCTGGAATCGACTGGA 60.615 55.000 0.00 0.00 0.00 3.86
18 19 0.460987 GTGGAGCTGGAATCGACTGG 60.461 60.000 0.00 0.00 0.00 4.00
19 20 0.460987 GGTGGAGCTGGAATCGACTG 60.461 60.000 0.00 0.00 0.00 3.51
20 21 0.904865 TGGTGGAGCTGGAATCGACT 60.905 55.000 0.00 0.00 0.00 4.18
21 22 0.741221 GTGGTGGAGCTGGAATCGAC 60.741 60.000 0.00 0.00 0.00 4.20
22 23 1.191489 TGTGGTGGAGCTGGAATCGA 61.191 55.000 0.00 0.00 0.00 3.59
23 24 1.021390 GTGTGGTGGAGCTGGAATCG 61.021 60.000 0.00 0.00 0.00 3.34
24 25 0.326264 AGTGTGGTGGAGCTGGAATC 59.674 55.000 0.00 0.00 0.00 2.52
25 26 1.279271 GTAGTGTGGTGGAGCTGGAAT 59.721 52.381 0.00 0.00 0.00 3.01
26 27 0.685097 GTAGTGTGGTGGAGCTGGAA 59.315 55.000 0.00 0.00 0.00 3.53
27 28 0.178932 AGTAGTGTGGTGGAGCTGGA 60.179 55.000 0.00 0.00 0.00 3.86
28 29 1.557099 TAGTAGTGTGGTGGAGCTGG 58.443 55.000 0.00 0.00 0.00 4.85
29 30 3.258372 TCTTTAGTAGTGTGGTGGAGCTG 59.742 47.826 0.00 0.00 0.00 4.24
30 31 3.507411 TCTTTAGTAGTGTGGTGGAGCT 58.493 45.455 0.00 0.00 0.00 4.09
31 32 3.955650 TCTTTAGTAGTGTGGTGGAGC 57.044 47.619 0.00 0.00 0.00 4.70
32 33 6.464222 TCAATTCTTTAGTAGTGTGGTGGAG 58.536 40.000 0.00 0.00 0.00 3.86
33 34 6.428083 TCAATTCTTTAGTAGTGTGGTGGA 57.572 37.500 0.00 0.00 0.00 4.02
34 35 6.878923 TGATCAATTCTTTAGTAGTGTGGTGG 59.121 38.462 0.00 0.00 0.00 4.61
35 36 7.905604 TGATCAATTCTTTAGTAGTGTGGTG 57.094 36.000 0.00 0.00 0.00 4.17
36 37 8.543774 AGATGATCAATTCTTTAGTAGTGTGGT 58.456 33.333 0.00 0.00 0.00 4.16
37 38 8.954950 AGATGATCAATTCTTTAGTAGTGTGG 57.045 34.615 0.00 0.00 0.00 4.17
38 39 9.814899 AGAGATGATCAATTCTTTAGTAGTGTG 57.185 33.333 0.00 0.00 0.00 3.82
52 53 8.404000 GCACACTAAATTGAAGAGATGATCAAT 58.596 33.333 0.00 0.00 34.68 2.57
53 54 7.391275 TGCACACTAAATTGAAGAGATGATCAA 59.609 33.333 0.00 0.00 0.00 2.57
54 55 6.880529 TGCACACTAAATTGAAGAGATGATCA 59.119 34.615 0.00 0.00 0.00 2.92
55 56 7.065563 AGTGCACACTAAATTGAAGAGATGATC 59.934 37.037 21.04 0.00 40.43 2.92
56 57 6.883217 AGTGCACACTAAATTGAAGAGATGAT 59.117 34.615 21.04 0.00 40.43 2.45
57 58 6.233434 AGTGCACACTAAATTGAAGAGATGA 58.767 36.000 21.04 0.00 40.43 2.92
58 59 6.492007 AGTGCACACTAAATTGAAGAGATG 57.508 37.500 21.04 0.00 40.43 2.90
59 60 7.446625 AGAAAGTGCACACTAAATTGAAGAGAT 59.553 33.333 21.04 0.00 41.58 2.75
60 61 6.767902 AGAAAGTGCACACTAAATTGAAGAGA 59.232 34.615 21.04 0.00 41.58 3.10
61 62 6.963796 AGAAAGTGCACACTAAATTGAAGAG 58.036 36.000 21.04 0.00 41.58 2.85
62 63 6.942532 AGAAAGTGCACACTAAATTGAAGA 57.057 33.333 21.04 0.00 41.58 2.87
63 64 9.121517 CAATAGAAAGTGCACACTAAATTGAAG 57.878 33.333 21.04 0.00 41.58 3.02
64 65 8.081633 CCAATAGAAAGTGCACACTAAATTGAA 58.918 33.333 21.04 0.00 41.58 2.69
65 66 7.309133 CCCAATAGAAAGTGCACACTAAATTGA 60.309 37.037 21.04 0.00 41.58 2.57
66 67 6.808212 CCCAATAGAAAGTGCACACTAAATTG 59.192 38.462 21.04 19.87 41.58 2.32
67 68 6.493458 ACCCAATAGAAAGTGCACACTAAATT 59.507 34.615 21.04 9.97 41.58 1.82
68 69 6.010219 ACCCAATAGAAAGTGCACACTAAAT 58.990 36.000 21.04 9.77 41.58 1.40
69 70 5.240623 CACCCAATAGAAAGTGCACACTAAA 59.759 40.000 21.04 1.29 41.58 1.85
70 71 4.759693 CACCCAATAGAAAGTGCACACTAA 59.240 41.667 21.04 0.09 41.58 2.24
71 72 4.323417 CACCCAATAGAAAGTGCACACTA 58.677 43.478 21.04 18.19 41.58 2.74
72 73 3.149196 CACCCAATAGAAAGTGCACACT 58.851 45.455 21.04 16.66 44.94 3.55
73 74 3.559238 CACCCAATAGAAAGTGCACAC 57.441 47.619 21.04 10.00 0.00 3.82
78 79 2.821969 AGCTTGCACCCAATAGAAAGTG 59.178 45.455 0.00 0.00 0.00 3.16
79 80 3.160679 AGCTTGCACCCAATAGAAAGT 57.839 42.857 0.00 0.00 0.00 2.66
80 81 4.009675 TGTAGCTTGCACCCAATAGAAAG 58.990 43.478 0.00 0.00 0.00 2.62
81 82 3.756434 GTGTAGCTTGCACCCAATAGAAA 59.244 43.478 9.23 0.00 0.00 2.52
82 83 3.343617 GTGTAGCTTGCACCCAATAGAA 58.656 45.455 9.23 0.00 0.00 2.10
83 84 2.676750 CGTGTAGCTTGCACCCAATAGA 60.677 50.000 13.28 0.00 33.61 1.98
84 85 1.665679 CGTGTAGCTTGCACCCAATAG 59.334 52.381 13.28 0.00 33.61 1.73
85 86 1.276705 TCGTGTAGCTTGCACCCAATA 59.723 47.619 13.28 0.00 33.61 1.90
86 87 0.036164 TCGTGTAGCTTGCACCCAAT 59.964 50.000 13.28 0.00 33.61 3.16
87 88 0.036164 ATCGTGTAGCTTGCACCCAA 59.964 50.000 13.28 3.06 33.61 4.12
88 89 0.899019 TATCGTGTAGCTTGCACCCA 59.101 50.000 13.28 3.68 33.61 4.51
89 90 1.134788 ACTATCGTGTAGCTTGCACCC 60.135 52.381 13.28 0.00 33.61 4.61
90 91 2.159226 AGACTATCGTGTAGCTTGCACC 60.159 50.000 13.28 1.79 33.61 5.01
91 92 3.109619 GAGACTATCGTGTAGCTTGCAC 58.890 50.000 10.09 10.09 0.00 4.57
92 93 3.017442 AGAGACTATCGTGTAGCTTGCA 58.983 45.455 0.00 0.00 0.00 4.08
93 94 3.367607 CAGAGACTATCGTGTAGCTTGC 58.632 50.000 0.00 0.00 0.00 4.01
94 95 3.066064 AGCAGAGACTATCGTGTAGCTTG 59.934 47.826 0.00 0.00 27.91 4.01
95 96 3.066064 CAGCAGAGACTATCGTGTAGCTT 59.934 47.826 0.00 0.00 29.31 3.74
96 97 2.616376 CAGCAGAGACTATCGTGTAGCT 59.384 50.000 0.00 0.00 31.07 3.32
97 98 2.614520 TCAGCAGAGACTATCGTGTAGC 59.385 50.000 0.00 0.00 0.00 3.58
98 99 3.874543 ACTCAGCAGAGACTATCGTGTAG 59.125 47.826 13.73 0.00 44.98 2.74
99 100 3.623510 CACTCAGCAGAGACTATCGTGTA 59.376 47.826 13.73 0.00 44.98 2.90
100 101 2.421775 CACTCAGCAGAGACTATCGTGT 59.578 50.000 13.73 0.00 44.98 4.49
101 102 2.680339 TCACTCAGCAGAGACTATCGTG 59.320 50.000 13.73 0.00 44.98 4.35
102 103 2.992593 TCACTCAGCAGAGACTATCGT 58.007 47.619 13.73 0.00 44.98 3.73
103 104 4.202000 ACATTCACTCAGCAGAGACTATCG 60.202 45.833 13.73 0.00 44.98 2.92
115 116 6.219417 AGAAGGATAGTCACATTCACTCAG 57.781 41.667 0.00 0.00 31.75 3.35
119 120 6.655003 TGGAAAAGAAGGATAGTCACATTCAC 59.345 38.462 0.00 0.00 31.75 3.18
120 121 6.778821 TGGAAAAGAAGGATAGTCACATTCA 58.221 36.000 0.00 0.00 31.75 2.57
121 122 7.687941 TTGGAAAAGAAGGATAGTCACATTC 57.312 36.000 0.00 0.00 0.00 2.67
125 126 9.178758 ACATATTTGGAAAAGAAGGATAGTCAC 57.821 33.333 0.00 0.00 0.00 3.67
139 140 5.659463 GCCACATGCTAACATATTTGGAAA 58.341 37.500 0.00 0.00 34.15 3.13
157 158 2.049888 TTCACACATCAACAGCCACA 57.950 45.000 0.00 0.00 0.00 4.17
161 162 3.815401 ACTACCTTTCACACATCAACAGC 59.185 43.478 0.00 0.00 0.00 4.40
238 239 2.154462 TGTTAAGAAGCTGCAGCCTTC 58.846 47.619 34.39 30.84 43.38 3.46
287 288 8.073768 TCCGAAAAACAATCATTGTAGTTCTTC 58.926 33.333 17.69 10.16 44.59 2.87
341 342 1.586422 CTGATTATCAGTGCGGTGGG 58.414 55.000 13.65 0.00 39.58 4.61
481 1869 0.100146 GGATAAGAGGCGTTCGACGT 59.900 55.000 8.72 0.00 44.73 4.34
484 1872 0.744874 CAGGGATAAGAGGCGTTCGA 59.255 55.000 0.00 0.00 0.00 3.71
592 1980 0.719465 GTCCCGTGTGATACAAAGCG 59.281 55.000 0.00 0.00 0.00 4.68
615 2003 1.603739 GGAAAGGAAGCTTGGGCGT 60.604 57.895 2.10 0.00 44.37 5.68
692 2080 3.112709 GGCTGGACGCGTCAGAAC 61.113 66.667 37.26 23.37 40.44 3.01
693 2081 4.717629 CGGCTGGACGCGTCAGAA 62.718 66.667 37.26 22.22 40.44 3.02
708 2096 2.125912 AGTTAGCAGCAGTCGCGG 60.126 61.111 6.13 0.00 45.49 6.46
709 2097 1.444383 TCAGTTAGCAGCAGTCGCG 60.444 57.895 0.00 0.00 45.49 5.87
710 2098 0.389166 AGTCAGTTAGCAGCAGTCGC 60.389 55.000 0.00 0.00 38.99 5.19
711 2099 2.520979 GTAGTCAGTTAGCAGCAGTCG 58.479 52.381 0.00 0.00 0.00 4.18
712 2100 2.161808 TCGTAGTCAGTTAGCAGCAGTC 59.838 50.000 0.00 0.00 0.00 3.51
713 2101 2.095161 GTCGTAGTCAGTTAGCAGCAGT 60.095 50.000 0.00 0.00 0.00 4.40
714 2102 2.520979 GTCGTAGTCAGTTAGCAGCAG 58.479 52.381 0.00 0.00 0.00 4.24
715 2103 1.201647 GGTCGTAGTCAGTTAGCAGCA 59.798 52.381 0.00 0.00 0.00 4.41
716 2104 1.469423 GGGTCGTAGTCAGTTAGCAGC 60.469 57.143 0.00 0.00 0.00 5.25
717 2105 1.816835 TGGGTCGTAGTCAGTTAGCAG 59.183 52.381 0.00 0.00 0.00 4.24
718 2106 1.913778 TGGGTCGTAGTCAGTTAGCA 58.086 50.000 0.00 0.00 0.00 3.49
719 2107 2.991866 GTTTGGGTCGTAGTCAGTTAGC 59.008 50.000 0.00 0.00 0.00 3.09
720 2108 4.247267 TGTTTGGGTCGTAGTCAGTTAG 57.753 45.455 0.00 0.00 0.00 2.34
721 2109 4.877378 ATGTTTGGGTCGTAGTCAGTTA 57.123 40.909 0.00 0.00 0.00 2.24
722 2110 3.764237 ATGTTTGGGTCGTAGTCAGTT 57.236 42.857 0.00 0.00 0.00 3.16
723 2111 4.817517 CTTATGTTTGGGTCGTAGTCAGT 58.182 43.478 0.00 0.00 0.00 3.41
724 2112 3.617263 GCTTATGTTTGGGTCGTAGTCAG 59.383 47.826 0.00 0.00 0.00 3.51
725 2113 3.007074 TGCTTATGTTTGGGTCGTAGTCA 59.993 43.478 0.00 0.00 0.00 3.41
726 2114 3.370061 GTGCTTATGTTTGGGTCGTAGTC 59.630 47.826 0.00 0.00 0.00 2.59
727 2115 3.244284 TGTGCTTATGTTTGGGTCGTAGT 60.244 43.478 0.00 0.00 0.00 2.73
728 2116 3.331150 TGTGCTTATGTTTGGGTCGTAG 58.669 45.455 0.00 0.00 0.00 3.51
729 2117 3.007074 TCTGTGCTTATGTTTGGGTCGTA 59.993 43.478 0.00 0.00 0.00 3.43
730 2118 2.151202 CTGTGCTTATGTTTGGGTCGT 58.849 47.619 0.00 0.00 0.00 4.34
731 2119 2.159627 GTCTGTGCTTATGTTTGGGTCG 59.840 50.000 0.00 0.00 0.00 4.79
732 2120 3.412386 AGTCTGTGCTTATGTTTGGGTC 58.588 45.455 0.00 0.00 0.00 4.46
733 2121 3.412386 GAGTCTGTGCTTATGTTTGGGT 58.588 45.455 0.00 0.00 0.00 4.51
734 2122 2.416547 CGAGTCTGTGCTTATGTTTGGG 59.583 50.000 0.00 0.00 0.00 4.12
735 2123 3.123621 GTCGAGTCTGTGCTTATGTTTGG 59.876 47.826 0.00 0.00 0.00 3.28
736 2124 3.740832 TGTCGAGTCTGTGCTTATGTTTG 59.259 43.478 0.00 0.00 0.00 2.93
737 2125 3.741344 GTGTCGAGTCTGTGCTTATGTTT 59.259 43.478 0.00 0.00 0.00 2.83
738 2126 3.318017 GTGTCGAGTCTGTGCTTATGTT 58.682 45.455 0.00 0.00 0.00 2.71
739 2127 2.668556 CGTGTCGAGTCTGTGCTTATGT 60.669 50.000 0.00 0.00 0.00 2.29
740 2128 1.914051 CGTGTCGAGTCTGTGCTTATG 59.086 52.381 0.00 0.00 0.00 1.90
741 2129 1.732732 GCGTGTCGAGTCTGTGCTTAT 60.733 52.381 0.00 0.00 0.00 1.73
742 2130 0.386858 GCGTGTCGAGTCTGTGCTTA 60.387 55.000 0.00 0.00 0.00 3.09
743 2131 1.661821 GCGTGTCGAGTCTGTGCTT 60.662 57.895 0.00 0.00 0.00 3.91
744 2132 2.049985 GCGTGTCGAGTCTGTGCT 60.050 61.111 0.00 0.00 0.00 4.40
745 2133 2.354656 TGCGTGTCGAGTCTGTGC 60.355 61.111 0.00 0.00 0.00 4.57
746 2134 2.016704 GGTGCGTGTCGAGTCTGTG 61.017 63.158 0.00 0.00 0.00 3.66
747 2135 2.335369 GGTGCGTGTCGAGTCTGT 59.665 61.111 0.00 0.00 0.00 3.41
748 2136 2.430921 GGGTGCGTGTCGAGTCTG 60.431 66.667 0.00 0.00 0.00 3.51
749 2137 2.495409 TTGGGTGCGTGTCGAGTCT 61.495 57.895 0.00 0.00 0.00 3.24
750 2138 2.028484 TTGGGTGCGTGTCGAGTC 59.972 61.111 0.00 0.00 0.00 3.36
751 2139 2.279918 GTTGGGTGCGTGTCGAGT 60.280 61.111 0.00 0.00 0.00 4.18
752 2140 3.403057 CGTTGGGTGCGTGTCGAG 61.403 66.667 0.00 0.00 0.00 4.04
755 2143 4.307908 GTGCGTTGGGTGCGTGTC 62.308 66.667 0.00 0.00 34.24 3.67
761 2149 4.605967 GTGTGCGTGCGTTGGGTG 62.606 66.667 0.00 0.00 0.00 4.61
763 2151 4.605967 GTGTGTGCGTGCGTTGGG 62.606 66.667 0.00 0.00 0.00 4.12
764 2152 4.936248 CGTGTGTGCGTGCGTTGG 62.936 66.667 0.00 0.00 0.00 3.77
770 2158 3.491508 GAGTGTGCGTGTGTGCGTG 62.492 63.158 0.00 0.00 37.81 5.34
771 2159 3.261951 GAGTGTGCGTGTGTGCGT 61.262 61.111 0.00 0.00 37.81 5.24
772 2160 4.339809 CGAGTGTGCGTGTGTGCG 62.340 66.667 0.00 0.00 37.81 5.34
773 2161 4.649954 GCGAGTGTGCGTGTGTGC 62.650 66.667 0.00 0.00 0.00 4.57
774 2162 4.000557 GGCGAGTGTGCGTGTGTG 62.001 66.667 0.00 0.00 35.06 3.82
775 2163 4.522689 TGGCGAGTGTGCGTGTGT 62.523 61.111 0.00 0.00 35.06 3.72
776 2164 4.000557 GTGGCGAGTGTGCGTGTG 62.001 66.667 0.00 0.00 35.06 3.82
801 2189 4.307908 GTGCGTGTTGGTCGTGCC 62.308 66.667 0.00 0.00 37.90 5.01
802 2190 4.643385 CGTGCGTGTTGGTCGTGC 62.643 66.667 0.00 0.00 0.00 5.34
803 2191 4.643385 GCGTGCGTGTTGGTCGTG 62.643 66.667 0.00 0.00 0.00 4.35
805 2193 4.643385 GTGCGTGCGTGTTGGTCG 62.643 66.667 0.00 0.00 0.00 4.79
806 2194 3.568743 TGTGCGTGCGTGTTGGTC 61.569 61.111 0.00 0.00 0.00 4.02
807 2195 3.871574 GTGTGCGTGCGTGTTGGT 61.872 61.111 0.00 0.00 0.00 3.67
808 2196 3.870422 TGTGTGCGTGCGTGTTGG 61.870 61.111 0.00 0.00 0.00 3.77
809 2197 2.647481 GTGTGTGCGTGCGTGTTG 60.647 61.111 0.00 0.00 0.00 3.33
810 2198 2.817834 AGTGTGTGCGTGCGTGTT 60.818 55.556 0.00 0.00 0.00 3.32
811 2199 3.563088 CAGTGTGTGCGTGCGTGT 61.563 61.111 0.00 0.00 0.00 4.49
812 2200 4.297891 CCAGTGTGTGCGTGCGTG 62.298 66.667 0.00 0.00 0.00 5.34
813 2201 4.830765 ACCAGTGTGTGCGTGCGT 62.831 61.111 0.00 0.00 0.00 5.24
814 2202 4.000557 GACCAGTGTGTGCGTGCG 62.001 66.667 0.00 0.00 0.00 5.34
815 2203 2.894879 TGACCAGTGTGTGCGTGC 60.895 61.111 0.00 0.00 0.00 5.34
816 2204 2.534019 GGTGACCAGTGTGTGCGTG 61.534 63.158 0.00 0.00 0.00 5.34
817 2205 2.203015 GGTGACCAGTGTGTGCGT 60.203 61.111 0.00 0.00 0.00 5.24
818 2206 2.203001 TGGTGACCAGTGTGTGCG 60.203 61.111 0.00 0.00 0.00 5.34
819 2207 2.186826 GGTGGTGACCAGTGTGTGC 61.187 63.158 3.58 0.00 42.59 4.57
820 2208 4.141144 GGTGGTGACCAGTGTGTG 57.859 61.111 3.58 0.00 42.59 3.82
838 2226 1.477553 TAGGAATAAGACACGGCGGT 58.522 50.000 13.24 6.25 0.00 5.68
839 2227 2.199236 GTTAGGAATAAGACACGGCGG 58.801 52.381 13.24 2.35 0.00 6.13
840 2228 2.883574 TGTTAGGAATAAGACACGGCG 58.116 47.619 4.80 4.80 0.00 6.46
841 2229 4.495844 GCAATGTTAGGAATAAGACACGGC 60.496 45.833 0.00 0.00 0.00 5.68
842 2230 4.634004 TGCAATGTTAGGAATAAGACACGG 59.366 41.667 0.00 0.00 0.00 4.94
843 2231 5.794687 TGCAATGTTAGGAATAAGACACG 57.205 39.130 0.00 0.00 0.00 4.49
844 2232 7.282224 TGGTATGCAATGTTAGGAATAAGACAC 59.718 37.037 0.00 0.00 0.00 3.67
845 2233 7.342581 TGGTATGCAATGTTAGGAATAAGACA 58.657 34.615 0.00 0.00 0.00 3.41
846 2234 7.499232 ACTGGTATGCAATGTTAGGAATAAGAC 59.501 37.037 0.00 0.00 0.00 3.01
847 2235 7.573710 ACTGGTATGCAATGTTAGGAATAAGA 58.426 34.615 0.00 0.00 0.00 2.10
848 2236 7.807977 ACTGGTATGCAATGTTAGGAATAAG 57.192 36.000 0.00 0.00 0.00 1.73
849 2237 7.068103 CCAACTGGTATGCAATGTTAGGAATAA 59.932 37.037 0.00 0.00 0.00 1.40
850 2238 6.545666 CCAACTGGTATGCAATGTTAGGAATA 59.454 38.462 0.00 0.00 0.00 1.75
851 2239 5.360714 CCAACTGGTATGCAATGTTAGGAAT 59.639 40.000 0.00 0.00 0.00 3.01
852 2240 4.704540 CCAACTGGTATGCAATGTTAGGAA 59.295 41.667 0.00 0.00 0.00 3.36
853 2241 4.018870 TCCAACTGGTATGCAATGTTAGGA 60.019 41.667 0.00 0.22 36.34 2.94
854 2242 4.269183 TCCAACTGGTATGCAATGTTAGG 58.731 43.478 0.00 0.00 36.34 2.69
855 2243 5.895636 TTCCAACTGGTATGCAATGTTAG 57.104 39.130 0.00 0.00 36.34 2.34
856 2244 6.007076 TCTTTCCAACTGGTATGCAATGTTA 58.993 36.000 0.00 0.00 36.34 2.41
857 2245 4.832266 TCTTTCCAACTGGTATGCAATGTT 59.168 37.500 0.00 0.00 36.34 2.71
858 2246 4.406456 TCTTTCCAACTGGTATGCAATGT 58.594 39.130 0.00 0.00 36.34 2.71
859 2247 4.701651 TCTCTTTCCAACTGGTATGCAATG 59.298 41.667 0.00 0.00 36.34 2.82
860 2248 4.922206 TCTCTTTCCAACTGGTATGCAAT 58.078 39.130 0.00 0.00 36.34 3.56
868 2256 5.529060 GCATTACCTATCTCTTTCCAACTGG 59.471 44.000 0.00 0.00 0.00 4.00
902 2290 6.861572 CGAGAAAAGCACGATCCACTATATAA 59.138 38.462 0.00 0.00 31.96 0.98
952 2346 7.718314 AGATGATTATTGCTGCTCACTCAAATA 59.282 33.333 0.00 0.00 0.00 1.40
987 2381 6.604171 TGAGGCCATCATCAATTATTGTACT 58.396 36.000 5.01 0.00 31.12 2.73
989 2383 6.712095 GTCTGAGGCCATCATCAATTATTGTA 59.288 38.462 5.01 0.00 37.28 2.41
990 2384 5.533903 GTCTGAGGCCATCATCAATTATTGT 59.466 40.000 5.01 0.00 37.28 2.71
991 2385 5.768662 AGTCTGAGGCCATCATCAATTATTG 59.231 40.000 5.01 0.00 37.28 1.90
992 2386 5.768662 CAGTCTGAGGCCATCATCAATTATT 59.231 40.000 5.01 0.00 37.28 1.40
993 2387 5.314529 CAGTCTGAGGCCATCATCAATTAT 58.685 41.667 5.01 0.00 37.28 1.28
994 2388 4.711399 CAGTCTGAGGCCATCATCAATTA 58.289 43.478 5.01 0.00 37.28 1.40
995 2389 3.552875 CAGTCTGAGGCCATCATCAATT 58.447 45.455 5.01 0.00 37.28 2.32
996 2390 2.748798 GCAGTCTGAGGCCATCATCAAT 60.749 50.000 5.01 0.00 37.28 2.57
997 2391 1.407851 GCAGTCTGAGGCCATCATCAA 60.408 52.381 5.01 0.00 37.28 2.57
998 2392 0.179702 GCAGTCTGAGGCCATCATCA 59.820 55.000 5.01 0.00 37.28 3.07
999 2393 0.879400 CGCAGTCTGAGGCCATCATC 60.879 60.000 5.01 0.00 37.28 2.92
1137 2549 2.868583 GGTGAAGTGGTGATCATGATCG 59.131 50.000 26.52 0.00 40.63 3.69
1686 3969 1.663739 GTCAGAGTGGCGTGTGGTA 59.336 57.895 0.00 0.00 0.00 3.25
1749 4032 2.563179 GTCTTCCTTGAGTAGCACCTGA 59.437 50.000 0.00 0.00 0.00 3.86
1774 4057 1.032794 TTGTTGTTGTTGCCGCCATA 58.967 45.000 0.00 0.00 0.00 2.74
1827 4128 2.344872 GGTACGTCCACCCACACC 59.655 66.667 0.00 0.00 35.97 4.16
1878 4179 1.474478 GAGACGATCTGCAGGAAGTCA 59.526 52.381 26.08 6.15 37.79 3.41
2138 5178 4.352887 GTGCTAGGTAGTTTCGATCAGAC 58.647 47.826 0.00 0.00 0.00 3.51
2192 5475 3.341823 TGTTCTAGACCGTACCTCTCAC 58.658 50.000 0.00 0.00 0.00 3.51
2193 5476 3.708403 TGTTCTAGACCGTACCTCTCA 57.292 47.619 0.00 0.00 0.00 3.27
2250 5546 3.119029 GCCTGGTATAGTGAACACGGTAA 60.119 47.826 0.00 0.00 36.20 2.85
2257 5553 8.671384 TGTATTTATTGCCTGGTATAGTGAAC 57.329 34.615 0.00 0.00 0.00 3.18
2269 5565 7.176690 GCCCTTACATGTATGTATTTATTGCCT 59.823 37.037 6.36 0.00 42.32 4.75
2277 5573 4.104738 AGGCTGCCCTTACATGTATGTATT 59.895 41.667 16.57 0.00 42.32 1.89
2289 5585 2.615465 ATGCACCAGGCTGCCCTTA 61.615 57.895 16.57 0.00 45.15 2.69
2345 5641 2.660670 AGGCTGCGTACTATAGACCT 57.339 50.000 6.78 0.00 0.00 3.85
2353 5649 3.947910 TGTAGTAAAAGGCTGCGTACT 57.052 42.857 9.24 9.24 0.00 2.73
2354 5650 5.541098 AAATGTAGTAAAAGGCTGCGTAC 57.459 39.130 0.00 0.00 0.00 3.67
2380 5676 9.456147 TGTATGTATTTATTAACAGCCTGTTGT 57.544 29.630 20.12 10.86 41.30 3.32
2439 5735 8.168725 AGAGGCTGGATGTAATTGATATCATTT 58.831 33.333 15.21 15.21 0.00 2.32
2480 5776 4.330074 GTGTGTATTCTGGATGTCTTTCGG 59.670 45.833 0.00 0.00 0.00 4.30
2538 5845 2.378084 GCGACGGGGTCTTCGTTTC 61.378 63.158 0.00 0.00 41.22 2.78
2573 5882 1.801178 GTGGTTAGAGTGCTGCTGTTC 59.199 52.381 0.00 0.00 0.00 3.18
2610 5919 2.224402 GGAGAGCCTATTTTGCGATCCT 60.224 50.000 0.00 0.00 36.14 3.24
2614 5923 2.779755 TTGGAGAGCCTATTTTGCGA 57.220 45.000 0.00 0.00 34.31 5.10
2661 5970 3.917870 CGACGACAACGCTTCTGT 58.082 55.556 0.00 0.00 43.96 3.41
2699 6008 4.870426 TCTCGGTATTTCTTCTGCATGAAC 59.130 41.667 0.00 0.00 0.00 3.18
2715 6024 2.543848 GCATTGATTTGCGATCTCGGTA 59.456 45.455 1.34 0.00 40.23 4.02
2746 6056 1.677633 GTTGTACCCGGCAATGGCT 60.678 57.895 5.02 0.00 40.87 4.75
2952 6274 0.967380 TGGCTGCGATCAGAGACTGA 60.967 55.000 3.95 3.95 44.99 3.41
2978 6300 2.808543 GCGTTGACAGAGGTGAAGAAAT 59.191 45.455 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.