Multiple sequence alignment - TraesCS6A01G195900

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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 TraesCS6A01G195900 chr6A 100.000 3321 0 0 1 3321 283883853 283880533 0.000000e+00 6133.0
1 TraesCS6A01G195900 chr6A 98.373 922 14 1 1136 2056 284938868 284937947 0.000000e+00 1618.0
2 TraesCS6A01G195900 chr6A 97.935 920 19 0 1133 2052 273088904 273089823 0.000000e+00 1594.0
3 TraesCS6A01G195900 chr2A 97.950 927 16 3 1133 2056 337517266 337518192 0.000000e+00 1604.0
4 TraesCS6A01G195900 chr2A 97.944 924 16 3 1136 2056 337887577 337886654 0.000000e+00 1598.0
5 TraesCS6A01G195900 chr2A 92.550 604 29 7 2263 2865 107526295 107526883 0.000000e+00 852.0
6 TraesCS6A01G195900 chr2A 92.384 604 30 7 2263 2865 107734935 107735523 0.000000e+00 846.0
7 TraesCS6A01G195900 chr2A 91.235 251 22 0 885 1135 67928874 67928624 3.170000e-90 342.0
8 TraesCS6A01G195900 chr2A 86.344 227 29 2 2053 2279 67928627 67928403 2.560000e-61 246.0
9 TraesCS6A01G195900 chr2A 92.941 85 5 1 1 85 580592061 580592144 4.500000e-24 122.0
10 TraesCS6A01G195900 chr3A 97.939 922 18 1 1136 2056 319923616 319924537 0.000000e+00 1596.0
11 TraesCS6A01G195900 chr3A 87.349 1075 93 23 2053 3099 234647189 234646130 0.000000e+00 1192.0
12 TraesCS6A01G195900 chr3A 89.423 832 70 11 2279 3107 606615126 606614310 0.000000e+00 1033.0
13 TraesCS6A01G195900 chr3A 91.722 604 27 5 2266 2868 688932643 688932062 0.000000e+00 817.0
14 TraesCS6A01G195900 chr3A 84.981 779 73 18 104 854 234648210 234647448 0.000000e+00 750.0
15 TraesCS6A01G195900 chr3A 84.217 792 78 20 84 848 606616428 606615657 0.000000e+00 726.0
16 TraesCS6A01G195900 chr3A 88.462 52 4 1 702 751 234647553 234647502 9.950000e-06 62.1
17 TraesCS6A01G195900 chr3A 88.462 52 4 1 702 751 606615756 606615705 9.950000e-06 62.1
18 TraesCS6A01G195900 chr3A 94.737 38 2 0 750 787 234647600 234647563 3.580000e-05 60.2
19 TraesCS6A01G195900 chr1A 97.642 933 17 5 1127 2056 278005459 278004529 0.000000e+00 1596.0
20 TraesCS6A01G195900 chr1A 97.838 925 17 3 1135 2056 214383866 214382942 0.000000e+00 1594.0
21 TraesCS6A01G195900 chrUn 97.937 921 18 1 1135 2054 72289384 72288464 0.000000e+00 1594.0
22 TraesCS6A01G195900 chrUn 92.982 114 7 1 972 1084 74596075 74596188 7.370000e-37 165.0
23 TraesCS6A01G195900 chr4A 97.234 940 20 6 1123 2056 270811864 270812803 0.000000e+00 1587.0
24 TraesCS6A01G195900 chr4A 92.033 841 57 3 2265 3104 410039559 410040390 0.000000e+00 1173.0
25 TraesCS6A01G195900 chr4A 90.040 251 25 0 885 1135 659370332 659370582 3.200000e-85 326.0
26 TraesCS6A01G195900 chr4A 90.164 244 23 1 885 1128 504813580 504813338 1.920000e-82 316.0
27 TraesCS6A01G195900 chr4A 93.720 207 12 1 3115 3321 410040460 410040665 3.220000e-80 309.0
28 TraesCS6A01G195900 chr4A 88.393 224 25 1 2056 2279 504813331 504813109 5.460000e-68 268.0
29 TraesCS6A01G195900 chr4A 81.197 234 16 16 2605 2819 743981432 743981656 2.650000e-36 163.0
30 TraesCS6A01G195900 chr7A 92.715 604 29 4 2263 2865 512540705 512541294 0.000000e+00 857.0
31 TraesCS6A01G195900 chr7A 92.257 607 31 6 2263 2868 211062107 211061516 0.000000e+00 846.0
32 TraesCS6A01G195900 chr7A 87.261 314 22 11 2568 2872 1317853 1317549 3.170000e-90 342.0
33 TraesCS6A01G195900 chr7A 82.412 398 48 8 84 461 287670645 287670250 8.880000e-86 327.0
34 TraesCS6A01G195900 chr7A 89.167 240 26 0 2868 3107 1317222 1316983 1.940000e-77 300.0
35 TraesCS6A01G195900 chr7A 90.640 203 18 1 2783 2985 633536157 633535956 5.460000e-68 268.0
36 TraesCS6A01G195900 chr7A 89.163 203 21 1 2783 2985 633541540 633541339 5.500000e-63 252.0
37 TraesCS6A01G195900 chr7A 92.920 113 8 0 885 997 633536997 633536885 7.370000e-37 165.0
38 TraesCS6A01G195900 chr7A 92.920 113 8 0 885 997 633542380 633542268 7.370000e-37 165.0
39 TraesCS6A01G195900 chr7A 97.826 46 1 0 3115 3160 1316916 1316871 2.750000e-11 80.5
40 TraesCS6A01G195900 chr5A 83.709 399 42 10 84 461 101314476 101314080 4.070000e-94 355.0
41 TraesCS6A01G195900 chr5A 81.704 399 49 8 84 461 456008134 456007739 8.950000e-81 311.0
42 TraesCS6A01G195900 chr6B 92.032 251 20 0 885 1135 686467483 686467733 1.470000e-93 353.0
43 TraesCS6A01G195900 chr6B 87.121 264 30 4 81 341 655257151 655257413 2.510000e-76 296.0
44 TraesCS6A01G195900 chr6B 91.626 203 16 1 2783 2985 76736587 76736386 2.520000e-71 279.0
45 TraesCS6A01G195900 chr6B 91.000 200 17 1 2783 2982 91949845 91950043 5.460000e-68 268.0
46 TraesCS6A01G195900 chr6B 92.941 85 5 1 1 85 464578977 464578894 4.500000e-24 122.0
47 TraesCS6A01G195900 chr3D 83.500 400 45 9 81 461 153647085 153647482 1.470000e-93 353.0
48 TraesCS6A01G195900 chr3D 92.857 84 5 1 1 84 584384184 584384102 1.620000e-23 121.0
49 TraesCS6A01G195900 chr3B 92.032 251 20 0 885 1135 779594424 779594174 1.470000e-93 353.0
50 TraesCS6A01G195900 chr3B 91.500 200 16 1 2783 2982 690614599 690614797 1.170000e-69 274.0
51 TraesCS6A01G195900 chr3B 91.500 200 16 1 2783 2982 690625671 690625869 1.170000e-69 274.0
52 TraesCS6A01G195900 chr3B 91.133 203 17 1 2783 2985 693619368 693619167 1.170000e-69 274.0
53 TraesCS6A01G195900 chr3B 97.561 41 0 1 3120 3160 31400196 31400235 5.950000e-08 69.4
54 TraesCS6A01G195900 chr7B 89.493 276 29 0 2832 3107 325185051 325184776 1.900000e-92 350.0
55 TraesCS6A01G195900 chr7B 91.235 251 22 0 885 1135 107951266 107951516 3.170000e-90 342.0
56 TraesCS6A01G195900 chr7B 87.833 263 29 3 81 341 634851974 634852235 4.160000e-79 305.0
57 TraesCS6A01G195900 chr7B 92.941 85 5 1 1 85 574616409 574616492 4.500000e-24 122.0
58 TraesCS6A01G195900 chr7B 92.941 85 5 1 1 85 708140865 708140948 4.500000e-24 122.0
59 TraesCS6A01G195900 chr7B 92.857 84 5 1 1 84 614254019 614253937 1.620000e-23 121.0
60 TraesCS6A01G195900 chr2B 91.633 251 21 0 885 1135 129710657 129710407 6.820000e-92 348.0
61 TraesCS6A01G195900 chr2B 92.941 85 5 1 1 85 669561914 669561831 4.500000e-24 122.0
62 TraesCS6A01G195900 chr7D 82.126 414 50 9 81 474 173524678 173525087 1.910000e-87 333.0
63 TraesCS6A01G195900 chr7D 87.452 263 30 3 81 341 610722272 610722533 1.940000e-77 300.0
64 TraesCS6A01G195900 chr7D 88.608 237 27 0 2868 3104 1324955 1325191 4.190000e-74 289.0
65 TraesCS6A01G195900 chr7D 80.236 339 26 24 2549 2872 1324316 1324628 2.010000e-52 217.0
66 TraesCS6A01G195900 chr7D 100.000 31 0 0 3130 3160 1325272 1325302 1.290000e-04 58.4
67 TraesCS6A01G195900 chr1D 82.382 403 45 10 81 461 65738371 65738769 8.880000e-86 327.0
68 TraesCS6A01G195900 chr4D 90.244 246 20 3 480 725 478770302 478770543 5.350000e-83 318.0
69 TraesCS6A01G195900 chr6D 87.072 263 30 4 81 341 93872883 93873143 9.010000e-76 294.0
70 TraesCS6A01G195900 chr6D 90.667 150 13 1 961 1109 431846285 431846434 7.270000e-47 198.0
71 TraesCS6A01G195900 chr6D 93.827 81 4 1 1 81 100661340 100661419 1.620000e-23 121.0
72 TraesCS6A01G195900 chr2D 93.827 81 4 1 1 81 477212756 477212835 1.620000e-23 121.0


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 TraesCS6A01G195900 chr6A 283880533 283883853 3320 True 6133.000000 6133 100.000000 1 3321 1 chr6A.!!$R1 3320
1 TraesCS6A01G195900 chr6A 284937947 284938868 921 True 1618.000000 1618 98.373000 1136 2056 1 chr6A.!!$R2 920
2 TraesCS6A01G195900 chr6A 273088904 273089823 919 False 1594.000000 1594 97.935000 1133 2052 1 chr6A.!!$F1 919
3 TraesCS6A01G195900 chr2A 337517266 337518192 926 False 1604.000000 1604 97.950000 1133 2056 1 chr2A.!!$F3 923
4 TraesCS6A01G195900 chr2A 337886654 337887577 923 True 1598.000000 1598 97.944000 1136 2056 1 chr2A.!!$R1 920
5 TraesCS6A01G195900 chr2A 107526295 107526883 588 False 852.000000 852 92.550000 2263 2865 1 chr2A.!!$F1 602
6 TraesCS6A01G195900 chr2A 107734935 107735523 588 False 846.000000 846 92.384000 2263 2865 1 chr2A.!!$F2 602
7 TraesCS6A01G195900 chr3A 319923616 319924537 921 False 1596.000000 1596 97.939000 1136 2056 1 chr3A.!!$F1 920
8 TraesCS6A01G195900 chr3A 688932062 688932643 581 True 817.000000 817 91.722000 2266 2868 1 chr3A.!!$R1 602
9 TraesCS6A01G195900 chr3A 606614310 606616428 2118 True 607.033333 1033 87.367333 84 3107 3 chr3A.!!$R3 3023
10 TraesCS6A01G195900 chr3A 234646130 234648210 2080 True 516.075000 1192 88.882250 104 3099 4 chr3A.!!$R2 2995
11 TraesCS6A01G195900 chr1A 278004529 278005459 930 True 1596.000000 1596 97.642000 1127 2056 1 chr1A.!!$R2 929
12 TraesCS6A01G195900 chr1A 214382942 214383866 924 True 1594.000000 1594 97.838000 1135 2056 1 chr1A.!!$R1 921
13 TraesCS6A01G195900 chrUn 72288464 72289384 920 True 1594.000000 1594 97.937000 1135 2054 1 chrUn.!!$R1 919
14 TraesCS6A01G195900 chr4A 270811864 270812803 939 False 1587.000000 1587 97.234000 1123 2056 1 chr4A.!!$F1 933
15 TraesCS6A01G195900 chr4A 410039559 410040665 1106 False 741.000000 1173 92.876500 2265 3321 2 chr4A.!!$F4 1056
16 TraesCS6A01G195900 chr7A 512540705 512541294 589 False 857.000000 857 92.715000 2263 2865 1 chr7A.!!$F1 602
17 TraesCS6A01G195900 chr7A 211061516 211062107 591 True 846.000000 846 92.257000 2263 2868 1 chr7A.!!$R1 605
18 TraesCS6A01G195900 chr7A 1316871 1317853 982 True 240.833333 342 91.418000 2568 3160 3 chr7A.!!$R3 592
19 TraesCS6A01G195900 chr7A 633535956 633536997 1041 True 216.500000 268 91.780000 885 2985 2 chr7A.!!$R4 2100
20 TraesCS6A01G195900 chr7A 633541339 633542380 1041 True 208.500000 252 91.041500 885 2985 2 chr7A.!!$R5 2100

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
685 706 0.027586 GCGCGCGTCTGGAATAAAAT 59.972 50.0 32.35 0.0 0.0 1.82 F
734 755 0.031111 TCCCACTCGATCCCCTCATT 60.031 55.0 0.00 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2255 3110 0.105964 CGACCCAACAACTCACCAGA 59.894 55.0 0.0 0.0 0.0 3.86 R
2321 3216 0.887387 CCCCGAAACACCGTCAACAT 60.887 55.0 0.0 0.0 0.0 2.71 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
21 22 3.829886 ACAAACTATGCCGTGAATGTG 57.170 42.857 0.00 0.00 0.00 3.21
22 23 2.487762 ACAAACTATGCCGTGAATGTGG 59.512 45.455 0.00 0.00 0.00 4.17
27 28 4.234019 GCCGTGAATGTGGCCATA 57.766 55.556 9.72 6.71 45.73 2.74
28 29 2.487918 GCCGTGAATGTGGCCATAA 58.512 52.632 9.72 0.00 45.73 1.90
29 30 0.381801 GCCGTGAATGTGGCCATAAG 59.618 55.000 9.72 0.00 45.73 1.73
30 31 2.016604 GCCGTGAATGTGGCCATAAGA 61.017 52.381 9.72 0.00 45.73 2.10
31 32 2.575532 CCGTGAATGTGGCCATAAGAT 58.424 47.619 9.72 0.00 0.00 2.40
32 33 2.951642 CCGTGAATGTGGCCATAAGATT 59.048 45.455 9.72 5.27 0.00 2.40
33 34 3.381272 CCGTGAATGTGGCCATAAGATTT 59.619 43.478 9.72 0.00 0.00 2.17
34 35 4.578516 CCGTGAATGTGGCCATAAGATTTA 59.421 41.667 9.72 0.00 0.00 1.40
35 36 5.241506 CCGTGAATGTGGCCATAAGATTTAT 59.758 40.000 9.72 0.00 0.00 1.40
36 37 6.373779 CGTGAATGTGGCCATAAGATTTATC 58.626 40.000 9.72 0.00 0.00 1.75
37 38 6.017192 CGTGAATGTGGCCATAAGATTTATCA 60.017 38.462 9.72 0.00 0.00 2.15
38 39 7.308770 CGTGAATGTGGCCATAAGATTTATCAT 60.309 37.037 9.72 0.00 0.00 2.45
39 40 8.362639 GTGAATGTGGCCATAAGATTTATCATT 58.637 33.333 9.72 9.78 0.00 2.57
40 41 8.926374 TGAATGTGGCCATAAGATTTATCATTT 58.074 29.630 9.72 0.00 0.00 2.32
41 42 9.199982 GAATGTGGCCATAAGATTTATCATTTG 57.800 33.333 9.72 0.00 0.00 2.32
42 43 7.053316 TGTGGCCATAAGATTTATCATTTGG 57.947 36.000 9.72 1.60 0.00 3.28
43 44 6.610830 TGTGGCCATAAGATTTATCATTTGGT 59.389 34.615 9.72 0.00 0.00 3.67
44 45 7.125507 TGTGGCCATAAGATTTATCATTTGGTT 59.874 33.333 9.72 0.00 0.00 3.67
45 46 7.986889 GTGGCCATAAGATTTATCATTTGGTTT 59.013 33.333 9.72 0.00 0.00 3.27
46 47 7.986320 TGGCCATAAGATTTATCATTTGGTTTG 59.014 33.333 0.00 0.00 0.00 2.93
47 48 8.203485 GGCCATAAGATTTATCATTTGGTTTGA 58.797 33.333 0.00 0.00 0.00 2.69
48 49 9.598517 GCCATAAGATTTATCATTTGGTTTGAA 57.401 29.630 6.39 0.00 0.00 2.69
60 61 8.325421 TCATTTGGTTTGAAAATCCATGAATG 57.675 30.769 0.00 5.99 44.58 2.67
61 62 7.937942 TCATTTGGTTTGAAAATCCATGAATGT 59.062 29.630 0.00 0.00 44.58 2.71
62 63 8.569641 CATTTGGTTTGAAAATCCATGAATGTT 58.430 29.630 0.00 0.00 44.58 2.71
63 64 7.727331 TTGGTTTGAAAATCCATGAATGTTC 57.273 32.000 0.00 0.00 44.58 3.18
64 65 6.824553 TGGTTTGAAAATCCATGAATGTTCA 58.175 32.000 0.00 0.00 40.60 3.18
65 66 6.705381 TGGTTTGAAAATCCATGAATGTTCAC 59.295 34.615 0.00 0.00 40.60 3.18
66 67 6.705381 GGTTTGAAAATCCATGAATGTTCACA 59.295 34.615 0.00 0.00 40.49 3.58
67 68 7.307337 GGTTTGAAAATCCATGAATGTTCACAC 60.307 37.037 5.74 5.74 40.49 3.82
68 69 6.402456 TGAAAATCCATGAATGTTCACACA 57.598 33.333 0.00 0.00 40.49 3.72
69 70 6.995364 TGAAAATCCATGAATGTTCACACAT 58.005 32.000 0.00 0.00 46.34 3.21
70 71 6.869388 TGAAAATCCATGAATGTTCACACATG 59.131 34.615 0.00 0.00 43.34 3.21
71 72 6.593268 AAATCCATGAATGTTCACACATGA 57.407 33.333 0.00 8.06 43.34 3.07
72 73 6.785337 AATCCATGAATGTTCACACATGAT 57.215 33.333 0.00 9.28 43.34 2.45
73 74 7.885009 AATCCATGAATGTTCACACATGATA 57.115 32.000 0.00 8.91 43.34 2.15
74 75 6.930667 TCCATGAATGTTCACACATGATAG 57.069 37.500 0.00 0.00 43.34 2.08
75 76 5.297527 TCCATGAATGTTCACACATGATAGC 59.702 40.000 0.00 0.00 43.34 2.97
76 77 5.298527 CCATGAATGTTCACACATGATAGCT 59.701 40.000 0.00 0.00 43.34 3.32
77 78 6.427974 CATGAATGTTCACACATGATAGCTC 58.572 40.000 0.00 0.00 43.34 4.09
78 79 5.490159 TGAATGTTCACACATGATAGCTCA 58.510 37.500 0.00 0.00 43.34 4.26
79 80 6.117488 TGAATGTTCACACATGATAGCTCAT 58.883 36.000 0.00 0.00 43.34 2.90
80 81 6.600427 TGAATGTTCACACATGATAGCTCATT 59.400 34.615 0.00 3.86 43.34 2.57
81 82 7.769970 TGAATGTTCACACATGATAGCTCATTA 59.230 33.333 0.00 0.00 43.34 1.90
82 83 6.908870 TGTTCACACATGATAGCTCATTAC 57.091 37.500 0.00 0.00 40.20 1.89
86 87 5.129320 TCACACATGATAGCTCATTACTGGT 59.871 40.000 0.00 0.00 40.20 4.00
89 90 6.051074 CACATGATAGCTCATTACTGGTTGA 58.949 40.000 0.00 0.00 40.20 3.18
92 93 8.432013 ACATGATAGCTCATTACTGGTTGAATA 58.568 33.333 0.00 0.00 40.20 1.75
100 101 8.250332 GCTCATTACTGGTTGAATATTGGAAAA 58.750 33.333 0.00 0.00 0.00 2.29
102 103 9.921637 TCATTACTGGTTGAATATTGGAAAAAC 57.078 29.630 0.00 0.00 0.00 2.43
117 118 6.353404 TGGAAAAACTTTTGGTGTTTCTCT 57.647 33.333 10.10 0.00 46.22 3.10
118 119 6.764379 TGGAAAAACTTTTGGTGTTTCTCTT 58.236 32.000 10.10 0.00 46.22 2.85
183 186 2.393271 AGGAGAAAACGATGAGGCAG 57.607 50.000 0.00 0.00 0.00 4.85
192 195 1.303799 CGATGAGGCAGCTGCAGTTT 61.304 55.000 37.63 20.81 44.36 2.66
197 200 2.892852 TGAGGCAGCTGCAGTTTAAATT 59.107 40.909 37.63 12.44 44.36 1.82
203 206 4.797275 GCAGCTGCAGTTTAAATTTGACCT 60.797 41.667 33.36 0.00 41.59 3.85
210 213 5.230182 CAGTTTAAATTTGACCTGCTTCCC 58.770 41.667 0.00 0.00 0.00 3.97
220 223 1.153568 CTGCTTCCCGCTGAATCGA 60.154 57.895 0.00 0.00 39.69 3.59
222 225 1.447838 GCTTCCCGCTGAATCGACA 60.448 57.895 0.00 0.00 35.14 4.35
250 253 3.149196 TGTCTTTTTCATGAGAGGTGGC 58.851 45.455 0.00 0.00 0.00 5.01
253 256 2.099141 TTTTCATGAGAGGTGGCTCG 57.901 50.000 0.00 0.00 37.73 5.03
262 265 3.070446 TGAGAGGTGGCTCGAAACTTTTA 59.930 43.478 0.00 0.00 37.73 1.52
263 266 3.665190 AGAGGTGGCTCGAAACTTTTAG 58.335 45.455 0.00 0.00 0.00 1.85
264 267 2.152016 AGGTGGCTCGAAACTTTTAGC 58.848 47.619 0.00 0.00 0.00 3.09
267 270 2.289547 GTGGCTCGAAACTTTTAGCACA 59.710 45.455 10.37 5.27 36.68 4.57
271 274 4.347813 GCTCGAAACTTTTAGCACACAAA 58.652 39.130 5.39 0.00 35.05 2.83
276 279 6.809196 TCGAAACTTTTAGCACACAAACATTT 59.191 30.769 0.00 0.00 0.00 2.32
277 280 6.893995 CGAAACTTTTAGCACACAAACATTTG 59.106 34.615 2.77 2.77 43.62 2.32
287 290 5.521735 GCACACAAACATTTGGTCAATTGTA 59.478 36.000 5.13 0.00 42.34 2.41
326 330 9.801873 CCTAATATTTTCTAAAATGGTGTGGTG 57.198 33.333 10.26 0.00 38.90 4.17
341 345 4.201802 GGTGTGGTGAAATTTTGCAACAAG 60.202 41.667 0.00 0.00 32.84 3.16
344 348 6.091441 GTGTGGTGAAATTTTGCAACAAGTAA 59.909 34.615 0.00 0.00 32.84 2.24
346 350 7.173218 TGTGGTGAAATTTTGCAACAAGTAAAA 59.827 29.630 0.00 0.00 44.14 1.52
375 396 8.212317 ACTCATTTTGGAAACTTGAAAAATGG 57.788 30.769 15.72 10.83 44.45 3.16
384 405 9.236006 TGGAAACTTGAAAAATGGAAAATGAAA 57.764 25.926 0.00 0.00 0.00 2.69
468 489 6.648725 GCACCCTTCTGCACATATTTTAAAAA 59.351 34.615 4.44 0.00 37.11 1.94
515 536 9.784531 ACTAATATTTGGTAGATTCTCCACATG 57.215 33.333 0.00 0.00 33.12 3.21
523 544 7.069344 TGGTAGATTCTCCACATGAATAGAGA 58.931 38.462 0.00 2.19 34.67 3.10
630 651 4.724602 GACAGCGGCTCGAGCACA 62.725 66.667 36.27 0.00 44.36 4.57
647 668 1.812922 CAGCCTGCCGTCAGATGTC 60.813 63.158 0.00 0.00 42.95 3.06
650 671 1.517257 CCTGCCGTCAGATGTCGAC 60.517 63.158 9.11 9.11 42.95 4.20
651 672 1.212751 CTGCCGTCAGATGTCGACA 59.787 57.895 22.48 22.48 42.95 4.35
684 705 1.422269 GCGCGCGTCTGGAATAAAA 59.578 52.632 32.35 0.00 0.00 1.52
685 706 0.027586 GCGCGCGTCTGGAATAAAAT 59.972 50.000 32.35 0.00 0.00 1.82
698 719 7.222999 GTCTGGAATAAAATAGACACTTCCTCG 59.777 40.741 0.00 0.00 39.39 4.63
732 753 1.075970 CTCCCACTCGATCCCCTCA 60.076 63.158 0.00 0.00 0.00 3.86
733 754 0.470833 CTCCCACTCGATCCCCTCAT 60.471 60.000 0.00 0.00 0.00 2.90
734 755 0.031111 TCCCACTCGATCCCCTCATT 60.031 55.000 0.00 0.00 0.00 2.57
736 757 1.418334 CCACTCGATCCCCTCATTCT 58.582 55.000 0.00 0.00 0.00 2.40
738 759 2.315176 CACTCGATCCCCTCATTCTCT 58.685 52.381 0.00 0.00 0.00 3.10
739 760 2.697751 CACTCGATCCCCTCATTCTCTT 59.302 50.000 0.00 0.00 0.00 2.85
740 761 3.133721 CACTCGATCCCCTCATTCTCTTT 59.866 47.826 0.00 0.00 0.00 2.52
741 762 3.386402 ACTCGATCCCCTCATTCTCTTTC 59.614 47.826 0.00 0.00 0.00 2.62
742 763 3.640967 CTCGATCCCCTCATTCTCTTTCT 59.359 47.826 0.00 0.00 0.00 2.52
743 764 3.639094 TCGATCCCCTCATTCTCTTTCTC 59.361 47.826 0.00 0.00 0.00 2.87
744 765 3.551863 CGATCCCCTCATTCTCTTTCTCG 60.552 52.174 0.00 0.00 0.00 4.04
745 766 3.101643 TCCCCTCATTCTCTTTCTCGA 57.898 47.619 0.00 0.00 0.00 4.04
746 767 3.647636 TCCCCTCATTCTCTTTCTCGAT 58.352 45.455 0.00 0.00 0.00 3.59
747 768 3.639094 TCCCCTCATTCTCTTTCTCGATC 59.361 47.826 0.00 0.00 0.00 3.69
748 769 3.244044 CCCCTCATTCTCTTTCTCGATCC 60.244 52.174 0.00 0.00 0.00 3.36
749 770 3.244044 CCCTCATTCTCTTTCTCGATCCC 60.244 52.174 0.00 0.00 0.00 3.85
750 771 3.244044 CCTCATTCTCTTTCTCGATCCCC 60.244 52.174 0.00 0.00 0.00 4.81
751 772 3.640967 CTCATTCTCTTTCTCGATCCCCT 59.359 47.826 0.00 0.00 0.00 4.79
752 773 3.639094 TCATTCTCTTTCTCGATCCCCTC 59.361 47.826 0.00 0.00 0.00 4.30
753 774 3.390175 TTCTCTTTCTCGATCCCCTCT 57.610 47.619 0.00 0.00 0.00 3.69
754 775 2.660572 TCTCTTTCTCGATCCCCTCTG 58.339 52.381 0.00 0.00 0.00 3.35
755 776 1.686052 CTCTTTCTCGATCCCCTCTGG 59.314 57.143 0.00 0.00 0.00 3.86
777 798 1.003573 CCCTAGCCTCCTCCCACTT 59.996 63.158 0.00 0.00 0.00 3.16
783 804 0.985490 GCCTCCTCCCACTTGATCCT 60.985 60.000 0.00 0.00 0.00 3.24
798 819 6.772233 CACTTGATCCTCTCTCATTCTCTCTA 59.228 42.308 0.00 0.00 0.00 2.43
801 822 4.079980 TCCTCTCTCATTCTCTCTACCG 57.920 50.000 0.00 0.00 0.00 4.02
802 823 3.712218 TCCTCTCTCATTCTCTCTACCGA 59.288 47.826 0.00 0.00 0.00 4.69
808 837 2.158856 TCATTCTCTCTACCGACGCCTA 60.159 50.000 0.00 0.00 0.00 3.93
816 845 1.028330 TACCGACGCCTACTCCACAG 61.028 60.000 0.00 0.00 0.00 3.66
819 848 1.292223 GACGCCTACTCCACAGCAA 59.708 57.895 0.00 0.00 0.00 3.91
827 856 0.035317 ACTCCACAGCAAATCGAGCA 59.965 50.000 0.00 0.00 0.00 4.26
897 956 1.147824 CAGCGAGGCCATCCAAGAT 59.852 57.895 5.01 0.00 33.74 2.40
968 1027 1.070134 CAGGAAGACGGTGAACCTCAA 59.930 52.381 0.00 0.00 0.00 3.02
1013 1072 0.329596 AGCAAGATGGTGAAGGGACC 59.670 55.000 0.00 0.00 36.43 4.46
1038 1097 2.415010 CAGCGCGTGAGGCTCTAT 59.585 61.111 16.72 0.00 39.08 1.98
1057 1116 2.606213 TCCGTGGCACCATCCTCA 60.606 61.111 12.86 0.00 0.00 3.86
1078 1137 3.382865 CAGATACAAGAGGTGAGCAGCTA 59.617 47.826 0.00 0.00 39.57 3.32
1083 1142 4.042251 AGGTGAGCAGCTACCTCC 57.958 61.111 14.55 6.06 43.69 4.30
1111 1170 0.912006 GGCTCTGGTCCTTCTCCCTT 60.912 60.000 0.00 0.00 0.00 3.95
1114 1173 0.473694 TCTGGTCCTTCTCCCTTGCA 60.474 55.000 0.00 0.00 0.00 4.08
1372 2223 1.512926 AGAACACGCATGGAGTTGAC 58.487 50.000 0.00 0.00 0.00 3.18
1496 2347 5.056480 TGCCACTTCATAATATTCGTCCAG 58.944 41.667 0.00 0.00 0.00 3.86
1651 2503 2.238701 AGGGCCACGAAATTCCCCT 61.239 57.895 6.18 2.26 41.19 4.79
1875 2727 0.586319 TTCGTTTGCTCGCAGGAAAG 59.414 50.000 3.74 0.00 36.21 2.62
1883 2735 0.610687 CTCGCAGGAAAGAGACCCTT 59.389 55.000 0.00 0.00 36.65 3.95
2075 2929 1.926511 CTTGGTTGGGCACGCAGATC 61.927 60.000 0.00 0.00 0.00 2.75
2089 2943 2.372264 GCAGATCCAAGCAGATCCAAA 58.628 47.619 7.54 0.00 43.14 3.28
2098 2952 2.086869 AGCAGATCCAAATGAACACCG 58.913 47.619 0.00 0.00 0.00 4.94
2099 2953 2.083774 GCAGATCCAAATGAACACCGA 58.916 47.619 0.00 0.00 0.00 4.69
2107 2961 0.246635 AATGAACACCGAGGAGGACG 59.753 55.000 0.00 0.00 45.00 4.79
2110 2964 2.488087 GAACACCGAGGAGGACGTGG 62.488 65.000 0.00 0.00 45.00 4.94
2111 2965 4.436998 CACCGAGGAGGACGTGGC 62.437 72.222 0.00 0.00 45.00 5.01
2121 2975 3.688159 GACGTGGCCTGGTACGGT 61.688 66.667 22.74 12.55 44.07 4.83
2155 3009 1.549170 CCTACGTCTACAAGGCCAAGT 59.451 52.381 5.01 5.24 0.00 3.16
2251 3106 4.324991 AAGTTCACCCCCGCCGAC 62.325 66.667 0.00 0.00 0.00 4.79
2280 3175 1.208535 TGAGTTGTTGGGTCGAACTGT 59.791 47.619 0.00 0.00 30.01 3.55
2321 3216 2.022934 TGACTTGTGTTGCATGCTGAA 58.977 42.857 20.33 2.28 0.00 3.02
2501 3430 2.046892 GAGATGCACCACACGCCT 60.047 61.111 0.00 0.00 0.00 5.52
2553 3482 4.344448 TCATTTTGTTTCACGTCGTTTCC 58.656 39.130 0.00 0.00 0.00 3.13
2596 3525 6.589907 CGTGCATGGTATCTAGCAATGTAATA 59.410 38.462 0.00 0.00 38.91 0.98
2633 3563 8.539544 TGTCCTTCACATCATCTAATTAGTGAA 58.460 33.333 12.19 12.36 41.88 3.18
2802 3795 5.179045 AGAAAATGCAGAGAACACACTTG 57.821 39.130 0.00 0.00 0.00 3.16
2923 4247 3.391296 GGGATCTGGATAGGTTGCAACTA 59.609 47.826 27.64 17.87 0.00 2.24
2970 4294 1.000394 TCTCTGGTGCGAAAATCGACA 60.000 47.619 3.61 0.00 43.74 4.35
2991 4315 3.064900 ACCAAGATCCACTTCAGCTTC 57.935 47.619 0.00 0.00 36.61 3.86
3000 4324 2.288213 CCACTTCAGCTTCGTAGTGACA 60.288 50.000 11.06 0.00 40.24 3.58
3020 4344 0.610174 TGTGAGAGATCTGTGGTGGC 59.390 55.000 0.00 0.00 0.00 5.01
3061 4385 2.421388 CCTGGGCATCGGTTCATTTCTA 60.421 50.000 0.00 0.00 0.00 2.10
3078 4402 4.314522 TTCTAATGTTTGATCCTGGCCA 57.685 40.909 4.71 4.71 0.00 5.36
3107 4431 2.429058 CCGGGATGGCAGATCCTG 59.571 66.667 13.63 13.63 42.78 3.86
3108 4432 2.429058 CGGGATGGCAGATCCTGG 59.571 66.667 12.99 0.00 40.15 4.45
3120 4503 2.103094 CAGATCCTGGCCATCGAGTAAA 59.897 50.000 5.51 0.00 0.00 2.01
3177 4560 0.318120 ACGTAGTTTGGTGGTACCCG 59.682 55.000 10.07 4.61 37.78 5.28
3204 4587 3.117926 TGGCAGGCTTGAGATGCTTATAA 60.118 43.478 0.00 0.00 39.88 0.98
3209 4592 5.180868 CAGGCTTGAGATGCTTATAATGTCC 59.819 44.000 0.00 0.00 0.00 4.02
3227 4610 3.377485 TGTCCGATGTAGAAGTAGCTGAC 59.623 47.826 0.00 0.00 0.00 3.51
3228 4611 3.628487 GTCCGATGTAGAAGTAGCTGACT 59.372 47.826 0.00 0.00 41.56 3.41
3230 4613 3.303461 CCGATGTAGAAGTAGCTGACTCG 60.303 52.174 0.00 0.00 37.44 4.18
3302 4685 5.449177 GGAAAGCTTCAGTTATGTGTATGGC 60.449 44.000 0.00 0.00 0.00 4.40
3314 4697 1.064003 TGTATGGCAGGACAACACCT 58.936 50.000 2.73 0.00 41.43 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.057596 CCACATTCACGGCATAGTTTGTT 60.058 43.478 0.00 0.00 0.00 2.83
1 2 2.487762 CCACATTCACGGCATAGTTTGT 59.512 45.455 0.00 0.00 0.00 2.83
2 3 3.135414 CCACATTCACGGCATAGTTTG 57.865 47.619 0.00 0.00 0.00 2.93
11 12 2.036958 TCTTATGGCCACATTCACGG 57.963 50.000 8.16 0.00 38.53 4.94
12 13 4.637483 AAATCTTATGGCCACATTCACG 57.363 40.909 8.16 0.00 38.53 4.35
13 14 7.275888 TGATAAATCTTATGGCCACATTCAC 57.724 36.000 8.16 1.03 38.53 3.18
14 15 8.481492 AATGATAAATCTTATGGCCACATTCA 57.519 30.769 8.16 1.67 38.53 2.57
15 16 9.199982 CAAATGATAAATCTTATGGCCACATTC 57.800 33.333 8.16 0.00 38.53 2.67
16 17 8.152246 CCAAATGATAAATCTTATGGCCACATT 58.848 33.333 8.16 6.31 38.53 2.71
17 18 7.290714 ACCAAATGATAAATCTTATGGCCACAT 59.709 33.333 8.16 0.00 41.13 3.21
18 19 6.610830 ACCAAATGATAAATCTTATGGCCACA 59.389 34.615 8.16 0.00 0.00 4.17
19 20 7.054491 ACCAAATGATAAATCTTATGGCCAC 57.946 36.000 8.16 0.00 0.00 5.01
20 21 7.673641 AACCAAATGATAAATCTTATGGCCA 57.326 32.000 8.56 8.56 0.00 5.36
21 22 8.203485 TCAAACCAAATGATAAATCTTATGGCC 58.797 33.333 0.00 0.00 0.00 5.36
22 23 9.598517 TTCAAACCAAATGATAAATCTTATGGC 57.401 29.630 0.00 0.00 0.00 4.40
34 35 8.952278 CATTCATGGATTTTCAAACCAAATGAT 58.048 29.630 0.00 0.00 35.59 2.45
35 36 7.937942 ACATTCATGGATTTTCAAACCAAATGA 59.062 29.630 13.20 2.67 36.36 2.57
36 37 8.101654 ACATTCATGGATTTTCAAACCAAATG 57.898 30.769 0.00 0.00 37.64 2.32
37 38 8.694581 AACATTCATGGATTTTCAAACCAAAT 57.305 26.923 0.00 0.00 37.24 2.32
38 39 7.772292 TGAACATTCATGGATTTTCAAACCAAA 59.228 29.630 12.30 0.00 37.24 3.28
39 40 7.226325 GTGAACATTCATGGATTTTCAAACCAA 59.774 33.333 15.63 0.00 39.73 3.67
40 41 6.705381 GTGAACATTCATGGATTTTCAAACCA 59.295 34.615 15.63 0.00 39.73 3.67
41 42 6.705381 TGTGAACATTCATGGATTTTCAAACC 59.295 34.615 15.63 6.18 39.73 3.27
42 43 7.224362 TGTGTGAACATTCATGGATTTTCAAAC 59.776 33.333 22.07 22.07 39.73 2.93
43 44 7.270779 TGTGTGAACATTCATGGATTTTCAAA 58.729 30.769 15.63 9.07 39.73 2.69
44 45 6.814043 TGTGTGAACATTCATGGATTTTCAA 58.186 32.000 15.63 5.67 39.73 2.69
45 46 6.402456 TGTGTGAACATTCATGGATTTTCA 57.598 33.333 10.91 10.91 39.73 2.69
46 47 7.092079 TCATGTGTGAACATTCATGGATTTTC 58.908 34.615 5.99 5.99 39.73 2.29
47 48 6.995364 TCATGTGTGAACATTCATGGATTTT 58.005 32.000 11.81 0.00 39.73 1.82
48 49 6.593268 TCATGTGTGAACATTCATGGATTT 57.407 33.333 11.81 0.00 39.73 2.17
49 50 6.785337 ATCATGTGTGAACATTCATGGATT 57.215 33.333 11.81 0.00 39.73 3.01
50 51 6.016527 GCTATCATGTGTGAACATTCATGGAT 60.017 38.462 11.81 0.00 39.73 3.41
51 52 5.297527 GCTATCATGTGTGAACATTCATGGA 59.702 40.000 11.81 0.00 39.73 3.41
52 53 5.298527 AGCTATCATGTGTGAACATTCATGG 59.701 40.000 11.81 1.64 39.73 3.66
53 54 6.037830 TGAGCTATCATGTGTGAACATTCATG 59.962 38.462 7.41 7.41 39.73 3.07
54 55 6.117488 TGAGCTATCATGTGTGAACATTCAT 58.883 36.000 0.00 0.00 39.73 2.57
55 56 5.490159 TGAGCTATCATGTGTGAACATTCA 58.510 37.500 0.00 0.00 38.01 2.57
56 57 6.615264 ATGAGCTATCATGTGTGAACATTC 57.385 37.500 0.00 0.00 44.67 2.67
57 58 7.772292 AGTAATGAGCTATCATGTGTGAACATT 59.228 33.333 0.00 0.00 45.67 2.71
58 59 7.226128 CAGTAATGAGCTATCATGTGTGAACAT 59.774 37.037 0.00 0.00 45.67 2.71
59 60 6.536224 CAGTAATGAGCTATCATGTGTGAACA 59.464 38.462 0.00 0.00 45.67 3.18
60 61 6.018425 CCAGTAATGAGCTATCATGTGTGAAC 60.018 42.308 0.00 0.00 45.67 3.18
61 62 6.051074 CCAGTAATGAGCTATCATGTGTGAA 58.949 40.000 0.00 0.00 45.67 3.18
62 63 5.129320 ACCAGTAATGAGCTATCATGTGTGA 59.871 40.000 0.00 0.00 45.67 3.58
63 64 5.363101 ACCAGTAATGAGCTATCATGTGTG 58.637 41.667 0.00 0.00 45.67 3.82
64 65 5.620738 ACCAGTAATGAGCTATCATGTGT 57.379 39.130 0.00 0.00 45.67 3.72
65 66 6.051074 TCAACCAGTAATGAGCTATCATGTG 58.949 40.000 0.00 0.00 45.67 3.21
66 67 6.239217 TCAACCAGTAATGAGCTATCATGT 57.761 37.500 0.00 0.00 45.67 3.21
67 68 7.741027 ATTCAACCAGTAATGAGCTATCATG 57.259 36.000 0.00 0.00 45.67 3.07
69 70 9.276590 CAATATTCAACCAGTAATGAGCTATCA 57.723 33.333 0.00 0.00 40.50 2.15
70 71 8.725148 CCAATATTCAACCAGTAATGAGCTATC 58.275 37.037 0.00 0.00 0.00 2.08
71 72 8.439971 TCCAATATTCAACCAGTAATGAGCTAT 58.560 33.333 0.00 0.00 0.00 2.97
72 73 7.801104 TCCAATATTCAACCAGTAATGAGCTA 58.199 34.615 0.00 0.00 0.00 3.32
73 74 6.662755 TCCAATATTCAACCAGTAATGAGCT 58.337 36.000 0.00 0.00 0.00 4.09
74 75 6.942532 TCCAATATTCAACCAGTAATGAGC 57.057 37.500 0.00 0.00 0.00 4.26
76 77 9.921637 GTTTTTCCAATATTCAACCAGTAATGA 57.078 29.630 0.00 0.00 0.00 2.57
77 78 9.927668 AGTTTTTCCAATATTCAACCAGTAATG 57.072 29.630 0.00 0.00 0.00 1.90
81 82 9.108284 CAAAAGTTTTTCCAATATTCAACCAGT 57.892 29.630 0.00 0.00 0.00 4.00
82 83 8.558700 CCAAAAGTTTTTCCAATATTCAACCAG 58.441 33.333 0.00 0.00 0.00 4.00
86 87 9.454859 AACACCAAAAGTTTTTCCAATATTCAA 57.545 25.926 0.00 0.00 0.00 2.69
89 90 9.679661 AGAAACACCAAAAGTTTTTCCAATATT 57.320 25.926 0.00 0.00 43.33 1.28
92 93 7.394016 AGAGAAACACCAAAAGTTTTTCCAAT 58.606 30.769 0.00 0.00 43.33 3.16
165 168 0.729690 GCTGCCTCATCGTTTTCTCC 59.270 55.000 0.00 0.00 0.00 3.71
169 172 0.890542 TGCAGCTGCCTCATCGTTTT 60.891 50.000 34.64 0.00 41.18 2.43
174 177 1.742761 TAAACTGCAGCTGCCTCATC 58.257 50.000 34.64 8.07 41.18 2.92
210 213 4.070581 ACAAATTTCTGTCGATTCAGCG 57.929 40.909 0.00 0.00 35.63 5.18
220 223 8.139989 CCTCTCATGAAAAAGACAAATTTCTGT 58.860 33.333 0.00 0.00 36.68 3.41
222 225 8.139989 CACCTCTCATGAAAAAGACAAATTTCT 58.860 33.333 0.00 0.00 36.68 2.52
250 253 5.328691 TGTTTGTGTGCTAAAAGTTTCGAG 58.671 37.500 0.00 0.00 0.00 4.04
253 256 7.148490 ACCAAATGTTTGTGTGCTAAAAGTTTC 60.148 33.333 4.92 0.00 36.45 2.78
262 265 3.883830 TTGACCAAATGTTTGTGTGCT 57.116 38.095 4.92 0.00 36.45 4.40
263 266 4.332268 ACAATTGACCAAATGTTTGTGTGC 59.668 37.500 13.59 0.00 30.86 4.57
264 267 6.533012 TGTACAATTGACCAAATGTTTGTGTG 59.467 34.615 13.59 0.00 36.07 3.82
267 270 9.823647 TTAATGTACAATTGACCAAATGTTTGT 57.176 25.926 13.59 6.70 36.07 2.83
276 279 7.563188 AGGCCATATTTAATGTACAATTGACCA 59.437 33.333 13.59 8.31 0.00 4.02
277 280 7.951591 AGGCCATATTTAATGTACAATTGACC 58.048 34.615 13.59 2.25 0.00 4.02
391 412 9.987272 CTAAGGAAGTTTTCATTTTCTTTGGAT 57.013 29.630 0.00 0.00 35.11 3.41
475 496 8.374743 ACCAAATATTAGTTGCAAAATTGGACT 58.625 29.630 17.73 6.13 38.47 3.85
476 497 8.546597 ACCAAATATTAGTTGCAAAATTGGAC 57.453 30.769 17.73 0.00 38.47 4.02
539 560 7.224362 CAGTTGAGCAGAATAATTAGGACAGAG 59.776 40.741 0.00 0.00 0.00 3.35
546 567 4.276926 GGCCCAGTTGAGCAGAATAATTAG 59.723 45.833 0.00 0.00 0.00 1.73
550 571 1.678728 CGGCCCAGTTGAGCAGAATAA 60.679 52.381 0.00 0.00 0.00 1.40
555 576 1.172180 TTTTCGGCCCAGTTGAGCAG 61.172 55.000 0.00 0.00 0.00 4.24
608 629 3.573772 CTCGAGCCGCTGTCCAACA 62.574 63.158 0.00 0.00 0.00 3.33
630 651 2.581354 GACATCTGACGGCAGGCT 59.419 61.111 20.50 2.98 42.53 4.58
638 659 2.862536 CACCATCATGTCGACATCTGAC 59.137 50.000 27.79 0.00 33.61 3.51
640 661 2.207590 CCACCATCATGTCGACATCTG 58.792 52.381 27.79 24.49 33.61 2.90
647 668 1.524621 GCTCCCCACCATCATGTCG 60.525 63.158 0.00 0.00 0.00 4.35
650 671 2.903855 GCGCTCCCCACCATCATG 60.904 66.667 0.00 0.00 0.00 3.07
651 672 4.552365 CGCGCTCCCCACCATCAT 62.552 66.667 5.56 0.00 0.00 2.45
684 705 2.500504 GGTTTCCCGAGGAAGTGTCTAT 59.499 50.000 5.66 0.00 43.06 1.98
685 706 1.897802 GGTTTCCCGAGGAAGTGTCTA 59.102 52.381 5.66 0.00 43.06 2.59
698 719 1.346479 GGAGGAGGCTAGGGTTTCCC 61.346 65.000 0.00 0.00 45.90 3.97
732 753 3.640967 CAGAGGGGATCGAGAAAGAGAAT 59.359 47.826 0.00 0.00 0.00 2.40
733 754 3.027412 CAGAGGGGATCGAGAAAGAGAA 58.973 50.000 0.00 0.00 0.00 2.87
734 755 2.660572 CAGAGGGGATCGAGAAAGAGA 58.339 52.381 0.00 0.00 0.00 3.10
736 757 1.288037 TCCAGAGGGGATCGAGAAAGA 59.712 52.381 0.00 0.00 42.15 2.52
746 767 0.620700 GCTAGGGTTTCCAGAGGGGA 60.621 60.000 0.00 0.00 46.61 4.81
747 768 1.636769 GGCTAGGGTTTCCAGAGGGG 61.637 65.000 0.00 0.00 34.83 4.79
748 769 0.621862 AGGCTAGGGTTTCCAGAGGG 60.622 60.000 0.00 0.00 34.83 4.30
749 770 0.833949 GAGGCTAGGGTTTCCAGAGG 59.166 60.000 0.00 0.00 34.83 3.69
750 771 0.833949 GGAGGCTAGGGTTTCCAGAG 59.166 60.000 0.00 0.00 34.83 3.35
751 772 0.417841 AGGAGGCTAGGGTTTCCAGA 59.582 55.000 0.00 0.00 34.83 3.86
752 773 0.833949 GAGGAGGCTAGGGTTTCCAG 59.166 60.000 0.00 0.00 34.83 3.86
753 774 0.620700 GGAGGAGGCTAGGGTTTCCA 60.621 60.000 0.00 0.00 34.83 3.53
754 775 1.346479 GGGAGGAGGCTAGGGTTTCC 61.346 65.000 0.00 0.00 0.00 3.13
755 776 0.620700 TGGGAGGAGGCTAGGGTTTC 60.621 60.000 0.00 0.00 0.00 2.78
777 798 5.630121 GGTAGAGAGAATGAGAGAGGATCA 58.370 45.833 0.00 0.00 37.82 2.92
783 804 3.459145 CGTCGGTAGAGAGAATGAGAGA 58.541 50.000 0.00 0.00 0.00 3.10
798 819 2.282674 TGTGGAGTAGGCGTCGGT 60.283 61.111 0.00 0.00 0.00 4.69
801 822 0.320421 TTTGCTGTGGAGTAGGCGTC 60.320 55.000 0.00 0.00 0.00 5.19
802 823 0.324943 ATTTGCTGTGGAGTAGGCGT 59.675 50.000 0.00 0.00 0.00 5.68
808 837 0.035317 TGCTCGATTTGCTGTGGAGT 59.965 50.000 0.00 0.00 0.00 3.85
816 845 2.653130 GCGGCATGCTCGATTTGC 60.653 61.111 26.00 12.46 41.73 3.68
956 1015 1.003718 GGGGAGTTGAGGTTCACCG 60.004 63.158 0.00 0.00 42.08 4.94
985 1044 4.531912 CATCTTGCTGCTGCGGCG 62.532 66.667 26.64 14.66 43.34 6.46
1006 1065 3.260100 CTGGCTGGTGGGTCCCTT 61.260 66.667 10.00 0.00 34.77 3.95
1030 1089 1.685765 TGCCACGGACATAGAGCCT 60.686 57.895 0.00 0.00 0.00 4.58
1038 1097 2.927856 AGGATGGTGCCACGGACA 60.928 61.111 0.00 0.00 0.00 4.02
1057 1116 2.465813 AGCTGCTCACCTCTTGTATCT 58.534 47.619 0.00 0.00 0.00 1.98
1111 1170 1.768275 ACGGATTCAGATACCCATGCA 59.232 47.619 0.00 0.00 0.00 3.96
1114 1173 2.408565 ACCACGGATTCAGATACCCAT 58.591 47.619 0.00 0.00 0.00 4.00
1119 1178 4.202253 CCTCATCAACCACGGATTCAGATA 60.202 45.833 0.00 0.00 0.00 1.98
1120 1179 3.432749 CCTCATCAACCACGGATTCAGAT 60.433 47.826 0.00 0.00 0.00 2.90
1121 1180 2.093500 CCTCATCAACCACGGATTCAGA 60.093 50.000 0.00 0.00 0.00 3.27
1122 1181 2.093500 TCCTCATCAACCACGGATTCAG 60.093 50.000 0.00 0.00 0.00 3.02
1123 1182 1.905894 TCCTCATCAACCACGGATTCA 59.094 47.619 0.00 0.00 0.00 2.57
1124 1183 2.280628 GTCCTCATCAACCACGGATTC 58.719 52.381 0.00 0.00 0.00 2.52
1496 2347 1.414181 TGCAGCACCTAGAATAGCCTC 59.586 52.381 0.00 0.00 37.37 4.70
1651 2503 5.016782 AGGGCTGTATATATGGAGGAAGAGA 59.983 44.000 0.00 0.00 0.00 3.10
1819 2671 6.114187 ACTGAGATTGCAATCGGGATATTA 57.886 37.500 28.88 10.31 40.35 0.98
1883 2735 1.346395 AGCACGATCAACCTAACCACA 59.654 47.619 0.00 0.00 0.00 4.17
2075 2929 3.367703 GGTGTTCATTTGGATCTGCTTGG 60.368 47.826 0.00 0.00 0.00 3.61
2089 2943 0.898789 ACGTCCTCCTCGGTGTTCAT 60.899 55.000 0.00 0.00 0.00 2.57
2098 2952 3.775654 CCAGGCCACGTCCTCCTC 61.776 72.222 5.01 0.00 33.25 3.71
2099 2953 3.233919 TACCAGGCCACGTCCTCCT 62.234 63.158 5.01 0.00 33.25 3.69
2110 2964 2.536997 ATCTTGGCACCGTACCAGGC 62.537 60.000 0.00 0.00 38.73 4.85
2111 2965 0.744414 CATCTTGGCACCGTACCAGG 60.744 60.000 0.00 0.00 38.73 4.45
2123 2977 1.414181 AGACGTAGGCCATCATCTTGG 59.586 52.381 5.01 0.00 39.94 3.61
2139 2993 0.320374 TGGACTTGGCCTTGTAGACG 59.680 55.000 3.32 0.00 0.00 4.18
2155 3009 2.363306 AGTTGGTGTCATTGCTTGGA 57.637 45.000 0.00 0.00 0.00 3.53
2245 3100 4.794439 TCACCAGATGCGTCGGCG 62.794 66.667 4.29 4.29 44.10 6.46
2251 3106 0.518636 CCAACAACTCACCAGATGCG 59.481 55.000 0.00 0.00 0.00 4.73
2254 3109 1.270839 CGACCCAACAACTCACCAGAT 60.271 52.381 0.00 0.00 0.00 2.90
2255 3110 0.105964 CGACCCAACAACTCACCAGA 59.894 55.000 0.00 0.00 0.00 3.86
2256 3111 0.105964 TCGACCCAACAACTCACCAG 59.894 55.000 0.00 0.00 0.00 4.00
2280 3175 3.740832 CAGTACATCAAAGAGCAACACGA 59.259 43.478 0.00 0.00 0.00 4.35
2321 3216 0.887387 CCCCGAAACACCGTCAACAT 60.887 55.000 0.00 0.00 0.00 2.71
2553 3482 3.563508 CACGATGTGCAGCTAGATAGAG 58.436 50.000 0.00 0.00 0.00 2.43
2625 3555 4.973168 TCTGCACCTCTTGTTTCACTAAT 58.027 39.130 0.00 0.00 0.00 1.73
2633 3563 3.806941 TGCTTCTGCACCTCTTGTT 57.193 47.368 0.00 0.00 45.31 2.83
2679 3609 3.892588 TGACATACTGTAGTGTGGTGTCA 59.107 43.478 12.99 12.99 40.79 3.58
2680 3610 4.514781 TGACATACTGTAGTGTGGTGTC 57.485 45.455 12.41 9.09 40.79 3.67
2682 3612 4.820897 ACATGACATACTGTAGTGTGGTG 58.179 43.478 12.41 10.13 40.79 4.17
2683 3613 4.526650 TGACATGACATACTGTAGTGTGGT 59.473 41.667 12.41 1.97 40.79 4.16
2684 3614 5.072040 TGACATGACATACTGTAGTGTGG 57.928 43.478 12.41 0.00 40.79 4.17
2685 3615 5.714047 ACTGACATGACATACTGTAGTGTG 58.286 41.667 0.00 7.15 41.98 3.82
2712 3657 1.274728 GCATGTTGCATGTTGGGGTTA 59.725 47.619 10.31 0.00 44.26 2.85
2737 3682 1.152963 GCAGACAACCACACTGGGT 60.153 57.895 0.00 0.00 43.37 4.51
2802 3795 4.227538 GCATGCATGATTGATTAGTCTGC 58.772 43.478 30.64 7.16 0.00 4.26
2923 4247 5.812642 CAGTTCAGACGCATATTTTACTCCT 59.187 40.000 0.00 0.00 0.00 3.69
2970 4294 3.416156 GAAGCTGAAGTGGATCTTGGTT 58.584 45.455 0.00 0.00 36.40 3.67
2991 4315 4.095632 ACAGATCTCTCACATGTCACTACG 59.904 45.833 0.00 0.00 0.00 3.51
3000 4324 1.209019 GCCACCACAGATCTCTCACAT 59.791 52.381 0.00 0.00 0.00 3.21
3020 4344 1.891060 GAGAAGACACGTGCCGCTTG 61.891 60.000 17.22 0.00 0.00 4.01
3036 4360 2.285368 AACCGATGCCCAGGGAGA 60.285 61.111 10.89 0.00 0.00 3.71
3037 4361 1.987807 ATGAACCGATGCCCAGGGAG 61.988 60.000 10.89 0.00 0.00 4.30
3061 4385 2.026641 CGATGGCCAGGATCAAACATT 58.973 47.619 13.05 0.00 0.00 2.71
3104 4428 3.753294 ATAGTTTACTCGATGGCCAGG 57.247 47.619 13.05 5.82 0.00 4.45
3107 4431 4.448210 TCCAAATAGTTTACTCGATGGCC 58.552 43.478 0.00 0.00 0.00 5.36
3108 4432 4.024809 GCTCCAAATAGTTTACTCGATGGC 60.025 45.833 0.00 0.00 0.00 4.40
3109 4433 5.235186 CAGCTCCAAATAGTTTACTCGATGG 59.765 44.000 0.00 0.00 0.00 3.51
3111 4435 5.978814 ACAGCTCCAAATAGTTTACTCGAT 58.021 37.500 0.00 0.00 0.00 3.59
3112 4436 5.401531 ACAGCTCCAAATAGTTTACTCGA 57.598 39.130 0.00 0.00 0.00 4.04
3113 4437 6.331061 AGTACAGCTCCAAATAGTTTACTCG 58.669 40.000 0.00 0.00 0.00 4.18
3120 4503 4.559862 AGCAAGTACAGCTCCAAATAGT 57.440 40.909 6.98 0.00 38.01 2.12
3176 4559 0.533531 TCTCAAGCCTGCCATATGCG 60.534 55.000 0.00 0.00 45.60 4.73
3177 4560 1.540267 CATCTCAAGCCTGCCATATGC 59.460 52.381 0.00 0.00 41.77 3.14
3204 4587 4.036971 GTCAGCTACTTCTACATCGGACAT 59.963 45.833 0.00 0.00 0.00 3.06
3209 4592 3.846744 GCGAGTCAGCTACTTCTACATCG 60.847 52.174 0.00 0.00 39.07 3.84
3227 4610 3.126514 AGAAAACATCTCAAGCATGCGAG 59.873 43.478 13.01 13.86 30.46 5.03
3228 4611 3.076621 AGAAAACATCTCAAGCATGCGA 58.923 40.909 13.01 3.47 30.46 5.10
3276 4659 4.373156 ACACATAACTGAAGCTTTCCCT 57.627 40.909 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.