Multiple sequence alignment - TraesCS7A01G155200

Loading Multiple Alignment...

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 TraesCS7A01G155200 chr7A 100.000 4523 0 0 1 4523 108239654 108235132 0.000000e+00 8353.0
1 TraesCS7A01G155200 chr7A 90.016 641 42 8 3901 4523 36558069 36558705 0.000000e+00 809.0
2 TraesCS7A01G155200 chr7A 85.470 117 16 1 384 499 47303182 47303066 2.210000e-23 121.0
3 TraesCS7A01G155200 chr7D 95.861 3624 103 19 315 3901 104093551 104089938 0.000000e+00 5818.0
4 TraesCS7A01G155200 chr7D 87.952 415 37 11 3997 4405 477204777 477205184 1.140000e-130 477.0
5 TraesCS7A01G155200 chr7D 89.032 310 30 4 4215 4523 621064743 621065049 9.180000e-102 381.0
6 TraesCS7A01G155200 chr7D 82.075 106 15 3 2914 3017 46839212 46839109 2.240000e-13 87.9
7 TraesCS7A01G155200 chr7B 95.720 3341 87 15 505 3833 61911622 61908326 0.000000e+00 5326.0
8 TraesCS7A01G155200 chr6B 85.450 1244 140 20 2011 3253 654734424 654733221 0.000000e+00 1256.0
9 TraesCS7A01G155200 chr6B 89.522 649 45 9 3892 4523 695447712 695448354 0.000000e+00 800.0
10 TraesCS7A01G155200 chr6B 81.447 539 91 8 1047 1582 654735542 654735010 2.500000e-117 433.0
11 TraesCS7A01G155200 chr6D 85.370 1244 141 16 2011 3253 433477556 433476353 0.000000e+00 1251.0
12 TraesCS7A01G155200 chr6D 81.447 539 91 8 1047 1582 433478690 433478158 2.500000e-117 433.0
13 TraesCS7A01G155200 chr6A 85.164 1247 141 22 2011 3253 579438872 579437666 0.000000e+00 1238.0
14 TraesCS7A01G155200 chr6A 82.822 489 74 7 1047 1530 579439989 579439506 3.230000e-116 429.0
15 TraesCS7A01G155200 chr6A 92.308 78 6 0 430 507 2935984 2936061 1.330000e-20 111.0
16 TraesCS7A01G155200 chr4B 89.555 651 44 9 3892 4523 545181536 545180891 0.000000e+00 804.0
17 TraesCS7A01G155200 chr4B 85.000 120 14 3 382 499 23016046 23015929 7.950000e-23 119.0
18 TraesCS7A01G155200 chr4A 89.688 640 47 5 3901 4523 541885378 541886015 0.000000e+00 798.0
19 TraesCS7A01G155200 chr4A 82.645 121 18 3 390 507 550491976 550492096 2.230000e-18 104.0
20 TraesCS7A01G155200 chr4A 82.906 117 13 7 389 499 588590003 588590118 1.040000e-16 99.0
21 TraesCS7A01G155200 chr3B 89.425 643 45 8 3900 4523 602787853 602788491 0.000000e+00 789.0
22 TraesCS7A01G155200 chr3B 77.430 1214 243 25 2014 3216 377424465 377425658 0.000000e+00 695.0
23 TraesCS7A01G155200 chr2B 89.024 656 46 12 3887 4523 577600289 577600937 0.000000e+00 789.0
24 TraesCS7A01G155200 chr2B 83.603 494 63 16 4040 4523 432932468 432931983 8.930000e-122 448.0
25 TraesCS7A01G155200 chr2B 83.929 112 14 3 390 498 138086441 138086551 2.230000e-18 104.0
26 TraesCS7A01G155200 chr1A 89.482 637 45 8 3905 4523 494886004 494885372 0.000000e+00 785.0
27 TraesCS7A01G155200 chr1A 84.877 529 67 11 4001 4523 516453009 516453530 5.190000e-144 521.0
28 TraesCS7A01G155200 chr1A 81.970 538 65 20 4009 4521 472580796 472581326 1.160000e-115 427.0
29 TraesCS7A01G155200 chr5B 88.682 645 50 11 3898 4523 531155811 531156451 0.000000e+00 765.0
30 TraesCS7A01G155200 chr3D 77.329 1213 246 25 2014 3216 283316235 283317428 0.000000e+00 689.0
31 TraesCS7A01G155200 chr3A 77.228 1212 249 23 2014 3216 370239445 370240638 0.000000e+00 684.0
32 TraesCS7A01G155200 chr3A 85.333 75 8 3 308 381 532471587 532471515 1.750000e-09 75.0
33 TraesCS7A01G155200 chr2A 88.431 510 41 4 3900 4392 661588879 661588371 2.330000e-167 599.0
34 TraesCS7A01G155200 chr2A 86.769 325 38 4 4200 4523 13123100 13122780 1.550000e-94 357.0
35 TraesCS7A01G155200 chr2A 97.143 35 0 1 3868 3902 725988895 725988862 1.760000e-04 58.4
36 TraesCS7A01G155200 chr2D 85.847 537 57 15 3998 4523 87838620 87838092 1.840000e-153 553.0
37 TraesCS7A01G155200 chr1D 83.969 524 68 11 4009 4523 381967556 381967040 5.260000e-134 488.0
38 TraesCS7A01G155200 chr1D 86.866 335 38 5 4191 4523 41567626 41567956 1.990000e-98 370.0
39 TraesCS7A01G155200 chr1D 92.308 78 6 0 430 507 14667594 14667517 1.330000e-20 111.0
40 TraesCS7A01G155200 chr1D 85.714 98 12 1 412 507 26291171 26291268 8.000000e-18 102.0


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 TraesCS7A01G155200 chr7A 108235132 108239654 4522 True 8353.0 8353 100.0000 1 4523 1 chr7A.!!$R2 4522
1 TraesCS7A01G155200 chr7A 36558069 36558705 636 False 809.0 809 90.0160 3901 4523 1 chr7A.!!$F1 622
2 TraesCS7A01G155200 chr7D 104089938 104093551 3613 True 5818.0 5818 95.8610 315 3901 1 chr7D.!!$R2 3586
3 TraesCS7A01G155200 chr7B 61908326 61911622 3296 True 5326.0 5326 95.7200 505 3833 1 chr7B.!!$R1 3328
4 TraesCS7A01G155200 chr6B 654733221 654735542 2321 True 844.5 1256 83.4485 1047 3253 2 chr6B.!!$R1 2206
5 TraesCS7A01G155200 chr6B 695447712 695448354 642 False 800.0 800 89.5220 3892 4523 1 chr6B.!!$F1 631
6 TraesCS7A01G155200 chr6D 433476353 433478690 2337 True 842.0 1251 83.4085 1047 3253 2 chr6D.!!$R1 2206
7 TraesCS7A01G155200 chr6A 579437666 579439989 2323 True 833.5 1238 83.9930 1047 3253 2 chr6A.!!$R1 2206
8 TraesCS7A01G155200 chr4B 545180891 545181536 645 True 804.0 804 89.5550 3892 4523 1 chr4B.!!$R2 631
9 TraesCS7A01G155200 chr4A 541885378 541886015 637 False 798.0 798 89.6880 3901 4523 1 chr4A.!!$F1 622
10 TraesCS7A01G155200 chr3B 602787853 602788491 638 False 789.0 789 89.4250 3900 4523 1 chr3B.!!$F2 623
11 TraesCS7A01G155200 chr3B 377424465 377425658 1193 False 695.0 695 77.4300 2014 3216 1 chr3B.!!$F1 1202
12 TraesCS7A01G155200 chr2B 577600289 577600937 648 False 789.0 789 89.0240 3887 4523 1 chr2B.!!$F2 636
13 TraesCS7A01G155200 chr1A 494885372 494886004 632 True 785.0 785 89.4820 3905 4523 1 chr1A.!!$R1 618
14 TraesCS7A01G155200 chr1A 516453009 516453530 521 False 521.0 521 84.8770 4001 4523 1 chr1A.!!$F2 522
15 TraesCS7A01G155200 chr1A 472580796 472581326 530 False 427.0 427 81.9700 4009 4521 1 chr1A.!!$F1 512
16 TraesCS7A01G155200 chr5B 531155811 531156451 640 False 765.0 765 88.6820 3898 4523 1 chr5B.!!$F1 625
17 TraesCS7A01G155200 chr3D 283316235 283317428 1193 False 689.0 689 77.3290 2014 3216 1 chr3D.!!$F1 1202
18 TraesCS7A01G155200 chr3A 370239445 370240638 1193 False 684.0 684 77.2280 2014 3216 1 chr3A.!!$F1 1202
19 TraesCS7A01G155200 chr2A 661588371 661588879 508 True 599.0 599 88.4310 3900 4392 1 chr2A.!!$R2 492
20 TraesCS7A01G155200 chr2D 87838092 87838620 528 True 553.0 553 85.8470 3998 4523 1 chr2D.!!$R1 525
21 TraesCS7A01G155200 chr1D 381967040 381967556 516 True 488.0 488 83.9690 4009 4523 1 chr1D.!!$R2 514

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
111 112 0.034896 ACGTTAAGCCCCACACTCAG 59.965 55.0 0.00 0.00 0.00 3.35 F
113 114 0.036875 GTTAAGCCCCACACTCAGCT 59.963 55.0 0.00 0.00 37.10 4.24 F
125 126 0.260523 ACTCAGCTAGTCCTCCTCCC 59.739 60.0 0.00 0.00 30.33 4.30 F
179 180 0.320247 CATGCGAGCCAGGGATAGAC 60.320 60.0 0.00 0.00 0.00 2.59 F
1623 1684 0.526662 AGAAGTGGTCGATGTCGTCC 59.473 55.0 10.97 10.97 45.43 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1663 1724 2.279517 GAACGGCGAGCGGATGAT 60.280 61.111 16.62 0.0 0.00 2.45 R
2001 2197 3.445687 ACGTCGTCCATGCCGCTA 61.446 61.111 0.00 0.0 0.00 4.26 R
2952 3277 3.704231 CTTGACCCCCAGCATCCCG 62.704 68.421 0.00 0.0 0.00 5.14 R
3294 3619 1.373748 GTTGCTCTGGTACGCCGAA 60.374 57.895 0.00 0.0 37.67 4.30 R
3903 4239 0.596341 GCACCGCGTCCAAACATTTT 60.596 50.000 4.92 0.0 0.00 1.82 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
23 24 4.426313 GGACCCCCAAGGCGGAAG 62.426 72.222 0.00 0.00 40.58 3.46
56 57 3.044809 GGCGAACGAGAATAGCACA 57.955 52.632 0.00 0.00 0.00 4.57
57 58 0.645868 GGCGAACGAGAATAGCACAC 59.354 55.000 0.00 0.00 0.00 3.82
58 59 0.645868 GCGAACGAGAATAGCACACC 59.354 55.000 0.00 0.00 0.00 4.16
59 60 1.990799 CGAACGAGAATAGCACACCA 58.009 50.000 0.00 0.00 0.00 4.17
60 61 1.654105 CGAACGAGAATAGCACACCAC 59.346 52.381 0.00 0.00 0.00 4.16
61 62 2.000447 GAACGAGAATAGCACACCACC 59.000 52.381 0.00 0.00 0.00 4.61
62 63 0.249398 ACGAGAATAGCACACCACCC 59.751 55.000 0.00 0.00 0.00 4.61
63 64 0.462047 CGAGAATAGCACACCACCCC 60.462 60.000 0.00 0.00 0.00 4.95
64 65 0.107165 GAGAATAGCACACCACCCCC 60.107 60.000 0.00 0.00 0.00 5.40
65 66 1.451387 GAATAGCACACCACCCCCG 60.451 63.158 0.00 0.00 0.00 5.73
66 67 2.886730 GAATAGCACACCACCCCCGG 62.887 65.000 0.00 0.00 0.00 5.73
79 80 3.532155 CCCGGGGAGCGAAGAGAG 61.532 72.222 14.71 0.00 0.00 3.20
80 81 3.532155 CCGGGGAGCGAAGAGAGG 61.532 72.222 0.00 0.00 0.00 3.69
81 82 2.440430 CGGGGAGCGAAGAGAGGA 60.440 66.667 0.00 0.00 0.00 3.71
82 83 2.776913 CGGGGAGCGAAGAGAGGAC 61.777 68.421 0.00 0.00 0.00 3.85
83 84 2.776913 GGGGAGCGAAGAGAGGACG 61.777 68.421 0.00 0.00 0.00 4.79
84 85 2.776913 GGGAGCGAAGAGAGGACGG 61.777 68.421 0.00 0.00 0.00 4.79
85 86 2.776913 GGAGCGAAGAGAGGACGGG 61.777 68.421 0.00 0.00 0.00 5.28
86 87 2.756283 AGCGAAGAGAGGACGGGG 60.756 66.667 0.00 0.00 0.00 5.73
87 88 3.839432 GCGAAGAGAGGACGGGGG 61.839 72.222 0.00 0.00 0.00 5.40
88 89 2.044252 CGAAGAGAGGACGGGGGA 60.044 66.667 0.00 0.00 0.00 4.81
89 90 2.416432 CGAAGAGAGGACGGGGGAC 61.416 68.421 0.00 0.00 0.00 4.46
90 91 1.305046 GAAGAGAGGACGGGGGACA 60.305 63.158 0.00 0.00 0.00 4.02
91 92 1.605971 GAAGAGAGGACGGGGGACAC 61.606 65.000 0.00 0.00 0.00 3.67
92 93 2.283676 GAGAGGACGGGGGACACA 60.284 66.667 0.00 0.00 0.00 3.72
93 94 2.603776 AGAGGACGGGGGACACAC 60.604 66.667 0.00 0.00 0.00 3.82
94 95 4.065281 GAGGACGGGGGACACACG 62.065 72.222 0.00 0.00 0.00 4.49
95 96 4.928140 AGGACGGGGGACACACGT 62.928 66.667 3.66 3.66 44.35 4.49
96 97 3.932483 GGACGGGGGACACACGTT 61.932 66.667 6.38 0.00 41.40 3.99
97 98 2.573083 GGACGGGGGACACACGTTA 61.573 63.158 6.38 0.00 41.40 3.18
98 99 1.367102 GACGGGGGACACACGTTAA 59.633 57.895 6.38 0.00 41.40 2.01
99 100 0.668401 GACGGGGGACACACGTTAAG 60.668 60.000 6.38 0.00 41.40 1.85
100 101 2.030958 CGGGGGACACACGTTAAGC 61.031 63.158 0.00 0.00 0.00 3.09
101 102 1.673337 GGGGGACACACGTTAAGCC 60.673 63.158 0.00 0.00 0.00 4.35
102 103 1.673337 GGGGACACACGTTAAGCCC 60.673 63.158 5.04 5.04 34.79 5.19
103 104 1.673337 GGGACACACGTTAAGCCCC 60.673 63.158 2.62 0.00 0.00 5.80
104 105 1.071814 GGACACACGTTAAGCCCCA 59.928 57.895 0.00 0.00 0.00 4.96
105 106 1.232621 GGACACACGTTAAGCCCCAC 61.233 60.000 0.00 0.00 0.00 4.61
106 107 0.533308 GACACACGTTAAGCCCCACA 60.533 55.000 0.00 0.00 0.00 4.17
107 108 0.816421 ACACACGTTAAGCCCCACAC 60.816 55.000 0.00 0.00 0.00 3.82
108 109 0.534203 CACACGTTAAGCCCCACACT 60.534 55.000 0.00 0.00 0.00 3.55
109 110 0.250166 ACACGTTAAGCCCCACACTC 60.250 55.000 0.00 0.00 0.00 3.51
110 111 0.250124 CACGTTAAGCCCCACACTCA 60.250 55.000 0.00 0.00 0.00 3.41
111 112 0.034896 ACGTTAAGCCCCACACTCAG 59.965 55.000 0.00 0.00 0.00 3.35
112 113 1.298859 CGTTAAGCCCCACACTCAGC 61.299 60.000 0.00 0.00 0.00 4.26
113 114 0.036875 GTTAAGCCCCACACTCAGCT 59.963 55.000 0.00 0.00 37.10 4.24
114 115 1.278127 GTTAAGCCCCACACTCAGCTA 59.722 52.381 0.00 0.00 34.49 3.32
115 116 1.195115 TAAGCCCCACACTCAGCTAG 58.805 55.000 0.00 0.00 34.49 3.42
116 117 0.838122 AAGCCCCACACTCAGCTAGT 60.838 55.000 0.00 0.00 39.81 2.57
117 118 1.219393 GCCCCACACTCAGCTAGTC 59.781 63.158 0.00 0.00 35.76 2.59
118 119 1.901085 CCCCACACTCAGCTAGTCC 59.099 63.158 0.00 0.00 35.76 3.85
119 120 0.616111 CCCCACACTCAGCTAGTCCT 60.616 60.000 0.00 0.00 35.76 3.85
120 121 0.820871 CCCACACTCAGCTAGTCCTC 59.179 60.000 0.00 0.00 35.76 3.71
121 122 0.820871 CCACACTCAGCTAGTCCTCC 59.179 60.000 0.00 0.00 35.76 4.30
122 123 1.618345 CCACACTCAGCTAGTCCTCCT 60.618 57.143 0.00 0.00 35.76 3.69
123 124 1.748493 CACACTCAGCTAGTCCTCCTC 59.252 57.143 0.00 0.00 35.76 3.71
124 125 1.341581 ACACTCAGCTAGTCCTCCTCC 60.342 57.143 0.00 0.00 35.76 4.30
125 126 0.260523 ACTCAGCTAGTCCTCCTCCC 59.739 60.000 0.00 0.00 30.33 4.30
126 127 0.469144 CTCAGCTAGTCCTCCTCCCC 60.469 65.000 0.00 0.00 0.00 4.81
127 128 1.458588 CAGCTAGTCCTCCTCCCCC 60.459 68.421 0.00 0.00 0.00 5.40
128 129 1.941820 AGCTAGTCCTCCTCCCCCA 60.942 63.158 0.00 0.00 0.00 4.96
129 130 1.003051 GCTAGTCCTCCTCCCCCAA 59.997 63.158 0.00 0.00 0.00 4.12
130 131 1.051556 GCTAGTCCTCCTCCCCCAAG 61.052 65.000 0.00 0.00 0.00 3.61
131 132 0.399233 CTAGTCCTCCTCCCCCAAGG 60.399 65.000 0.00 0.00 37.81 3.61
132 133 2.547123 TAGTCCTCCTCCCCCAAGGC 62.547 65.000 0.00 0.00 36.29 4.35
133 134 4.760220 TCCTCCTCCCCCAAGGCC 62.760 72.222 0.00 0.00 36.29 5.19
135 136 3.415087 CTCCTCCCCCAAGGCCAG 61.415 72.222 5.01 0.00 36.29 4.85
136 137 3.950861 CTCCTCCCCCAAGGCCAGA 62.951 68.421 5.01 0.00 36.29 3.86
137 138 3.732849 CCTCCCCCAAGGCCAGAC 61.733 72.222 5.01 0.00 34.51 3.51
138 139 3.732849 CTCCCCCAAGGCCAGACC 61.733 72.222 5.01 0.00 39.61 3.85
139 140 4.608514 TCCCCCAAGGCCAGACCA 62.609 66.667 5.01 0.00 43.14 4.02
140 141 3.350163 CCCCCAAGGCCAGACCAT 61.350 66.667 5.01 0.00 43.14 3.55
141 142 2.043652 CCCCAAGGCCAGACCATG 60.044 66.667 5.01 0.00 43.14 3.66
142 143 2.615465 CCCCAAGGCCAGACCATGA 61.615 63.158 5.01 0.00 39.64 3.07
143 144 1.379044 CCCAAGGCCAGACCATGAC 60.379 63.158 5.01 0.00 39.64 3.06
144 145 1.687612 CCAAGGCCAGACCATGACT 59.312 57.895 5.01 0.00 39.64 3.41
145 146 0.393537 CCAAGGCCAGACCATGACTC 60.394 60.000 5.01 0.00 39.64 3.36
146 147 0.742281 CAAGGCCAGACCATGACTCG 60.742 60.000 5.01 0.00 39.64 4.18
147 148 1.903877 AAGGCCAGACCATGACTCGG 61.904 60.000 5.01 0.00 43.14 4.63
148 149 2.187946 GCCAGACCATGACTCGGG 59.812 66.667 0.00 0.00 0.00 5.14
149 150 2.903357 CCAGACCATGACTCGGGG 59.097 66.667 0.00 0.00 0.00 5.73
150 151 1.685765 CCAGACCATGACTCGGGGA 60.686 63.158 0.00 0.00 0.00 4.81
151 152 1.680522 CCAGACCATGACTCGGGGAG 61.681 65.000 0.00 0.00 35.52 4.30
152 153 1.381872 AGACCATGACTCGGGGAGG 60.382 63.158 0.00 0.00 33.35 4.30
153 154 1.381327 GACCATGACTCGGGGAGGA 60.381 63.158 0.00 0.00 33.35 3.71
154 155 1.677637 GACCATGACTCGGGGAGGAC 61.678 65.000 0.00 0.00 33.35 3.85
155 156 2.786495 CCATGACTCGGGGAGGACG 61.786 68.421 0.00 0.00 33.35 4.79
156 157 2.442272 ATGACTCGGGGAGGACGG 60.442 66.667 0.00 0.00 33.35 4.79
177 178 4.689484 CATGCGAGCCAGGGATAG 57.311 61.111 0.00 0.00 0.00 2.08
178 179 2.052779 CATGCGAGCCAGGGATAGA 58.947 57.895 0.00 0.00 0.00 1.98
179 180 0.320247 CATGCGAGCCAGGGATAGAC 60.320 60.000 0.00 0.00 0.00 2.59
180 181 1.476007 ATGCGAGCCAGGGATAGACC 61.476 60.000 0.00 0.00 38.08 3.85
181 182 3.043419 CGAGCCAGGGATAGACCG 58.957 66.667 0.00 0.00 40.11 4.79
182 183 2.565645 CGAGCCAGGGATAGACCGG 61.566 68.421 0.00 0.00 40.11 5.28
183 184 2.844839 AGCCAGGGATAGACCGGC 60.845 66.667 0.00 9.13 44.83 6.13
184 185 4.301027 GCCAGGGATAGACCGGCG 62.301 72.222 0.00 0.00 39.25 6.46
185 186 3.616721 CCAGGGATAGACCGGCGG 61.617 72.222 27.06 27.06 40.11 6.13
186 187 4.301027 CAGGGATAGACCGGCGGC 62.301 72.222 28.71 19.04 40.11 6.53
216 217 4.208686 CCGAGCGGTAGTCCCAGC 62.209 72.222 0.00 0.00 34.31 4.85
217 218 4.208686 CGAGCGGTAGTCCCAGCC 62.209 72.222 0.00 0.00 34.54 4.85
221 222 3.834799 CGGTAGTCCCAGCCGGTC 61.835 72.222 1.90 0.00 41.60 4.79
222 223 3.468140 GGTAGTCCCAGCCGGTCC 61.468 72.222 1.90 0.00 0.00 4.46
223 224 2.682494 GTAGTCCCAGCCGGTCCA 60.682 66.667 1.90 0.00 0.00 4.02
224 225 2.120940 TAGTCCCAGCCGGTCCAA 59.879 61.111 1.90 0.00 0.00 3.53
225 226 2.288025 TAGTCCCAGCCGGTCCAAC 61.288 63.158 1.90 0.00 0.00 3.77
228 229 4.323477 CCCAGCCGGTCCAACGAA 62.323 66.667 1.90 0.00 35.47 3.85
229 230 3.047877 CCAGCCGGTCCAACGAAC 61.048 66.667 1.90 0.00 35.47 3.95
234 235 2.735857 CGGTCCAACGAACGTCCC 60.736 66.667 0.00 0.00 44.44 4.46
235 236 2.357881 GGTCCAACGAACGTCCCC 60.358 66.667 0.00 0.00 0.00 4.81
236 237 2.357881 GTCCAACGAACGTCCCCC 60.358 66.667 0.00 0.00 0.00 5.40
255 256 4.175337 GATGGCGGCAGGGCTACA 62.175 66.667 19.29 0.00 42.84 2.74
256 257 4.489771 ATGGCGGCAGGGCTACAC 62.490 66.667 19.29 0.00 42.84 2.90
284 285 3.089874 CCTGGGCGAAGGGGATGA 61.090 66.667 0.00 0.00 33.28 2.92
285 286 2.679342 CCTGGGCGAAGGGGATGAA 61.679 63.158 0.00 0.00 33.28 2.57
286 287 1.302949 CTGGGCGAAGGGGATGAAA 59.697 57.895 0.00 0.00 0.00 2.69
287 288 1.001393 TGGGCGAAGGGGATGAAAC 60.001 57.895 0.00 0.00 0.00 2.78
288 289 1.001393 GGGCGAAGGGGATGAAACA 60.001 57.895 0.00 0.00 0.00 2.83
289 290 0.610785 GGGCGAAGGGGATGAAACAA 60.611 55.000 0.00 0.00 0.00 2.83
290 291 1.253100 GGCGAAGGGGATGAAACAAA 58.747 50.000 0.00 0.00 0.00 2.83
291 292 1.824852 GGCGAAGGGGATGAAACAAAT 59.175 47.619 0.00 0.00 0.00 2.32
292 293 3.020984 GGCGAAGGGGATGAAACAAATA 58.979 45.455 0.00 0.00 0.00 1.40
293 294 3.445805 GGCGAAGGGGATGAAACAAATAA 59.554 43.478 0.00 0.00 0.00 1.40
294 295 4.081917 GGCGAAGGGGATGAAACAAATAAA 60.082 41.667 0.00 0.00 0.00 1.40
295 296 5.395214 GGCGAAGGGGATGAAACAAATAAAT 60.395 40.000 0.00 0.00 0.00 1.40
296 297 6.183360 GGCGAAGGGGATGAAACAAATAAATA 60.183 38.462 0.00 0.00 0.00 1.40
297 298 6.695713 GCGAAGGGGATGAAACAAATAAATAC 59.304 38.462 0.00 0.00 0.00 1.89
298 299 7.416326 GCGAAGGGGATGAAACAAATAAATACT 60.416 37.037 0.00 0.00 0.00 2.12
299 300 8.129211 CGAAGGGGATGAAACAAATAAATACTC 58.871 37.037 0.00 0.00 0.00 2.59
300 301 9.190317 GAAGGGGATGAAACAAATAAATACTCT 57.810 33.333 0.00 0.00 0.00 3.24
301 302 8.753497 AGGGGATGAAACAAATAAATACTCTC 57.247 34.615 0.00 0.00 0.00 3.20
302 303 8.560903 AGGGGATGAAACAAATAAATACTCTCT 58.439 33.333 0.00 0.00 0.00 3.10
303 304 9.190317 GGGGATGAAACAAATAAATACTCTCTT 57.810 33.333 0.00 0.00 0.00 2.85
305 306 9.922305 GGATGAAACAAATAAATACTCTCTTCG 57.078 33.333 0.00 0.00 0.00 3.79
310 311 8.664211 AACAAATAAATACTCTCTTCGATCCC 57.336 34.615 0.00 0.00 0.00 3.85
311 312 8.024145 ACAAATAAATACTCTCTTCGATCCCT 57.976 34.615 0.00 0.00 0.00 4.20
312 313 9.144298 ACAAATAAATACTCTCTTCGATCCCTA 57.856 33.333 0.00 0.00 0.00 3.53
416 417 2.394930 ACACAGTACACACACAAGCA 57.605 45.000 0.00 0.00 0.00 3.91
422 423 3.561310 CAGTACACACACAAGCACTCATT 59.439 43.478 0.00 0.00 0.00 2.57
423 424 4.035558 CAGTACACACACAAGCACTCATTT 59.964 41.667 0.00 0.00 0.00 2.32
427 428 7.824289 AGTACACACACAAGCACTCATTTATAT 59.176 33.333 0.00 0.00 0.00 0.86
435 466 3.002656 AGCACTCATTTATATGCGCACAC 59.997 43.478 14.90 0.00 42.98 3.82
441 472 3.830744 TTTATATGCGCACACCCTACT 57.169 42.857 14.90 0.00 0.00 2.57
455 486 2.022918 ACCCTACTCCTATGAGCACCTT 60.023 50.000 0.00 0.00 42.74 3.50
462 493 7.948301 TACTCCTATGAGCACCTTCGAGAGG 62.948 52.000 10.85 10.85 46.06 3.69
502 533 5.060506 TCTTGAGATTTTACAAAGTCGCCA 58.939 37.500 0.03 0.00 30.86 5.69
647 685 5.880332 TGGAACAAATAAAAGAGAGGATCCG 59.120 40.000 5.98 0.00 29.61 4.18
1623 1684 0.526662 AGAAGTGGTCGATGTCGTCC 59.473 55.000 10.97 10.97 45.43 4.79
1636 1697 3.536917 CGTCCAGGGGCAGCGATA 61.537 66.667 0.00 0.00 0.00 2.92
1823 2010 2.419159 CGGACATCTCCTTCATCAGCAA 60.419 50.000 0.00 0.00 33.79 3.91
2001 2197 2.057408 CGCCTCCTCCTTCTGCTCT 61.057 63.158 0.00 0.00 0.00 4.09
2952 3277 2.722201 CCCGGAGTACCAGCAGACC 61.722 68.421 0.73 0.00 35.59 3.85
3306 3631 2.380410 GCACAGTTCGGCGTACCAG 61.380 63.158 13.15 8.87 34.57 4.00
3351 3676 1.401018 GCCGTAAGCTTTTCGTGCAAT 60.401 47.619 3.20 0.00 38.99 3.56
3352 3677 2.505866 CCGTAAGCTTTTCGTGCAATC 58.494 47.619 3.20 0.00 0.00 2.67
3410 3738 3.508840 GCAAGCACGCCGGCTAAT 61.509 61.111 26.68 6.92 45.07 1.73
3518 3846 0.317479 CCTCCGAGAAGAACCAACGT 59.683 55.000 0.00 0.00 0.00 3.99
3547 3875 4.845447 TCCATGGGCTGGCCATGC 62.845 66.667 42.01 12.55 45.52 4.06
3549 3877 2.842462 CATGGGCTGGCCATGCAT 60.842 61.111 39.29 18.05 38.55 3.96
3550 3878 2.842462 ATGGGCTGGCCATGCATG 60.842 61.111 32.13 20.19 37.98 4.06
3576 3909 4.043200 GTCTTGGTGCTTGCGGGC 62.043 66.667 0.00 0.00 0.00 6.13
3619 3952 0.528924 GAACATGCAGCAAGATGGCA 59.471 50.000 4.23 0.00 42.43 4.92
3620 3953 0.245539 AACATGCAGCAAGATGGCAC 59.754 50.000 4.23 0.00 40.83 5.01
3623 3956 0.530744 ATGCAGCAAGATGGCACTTG 59.469 50.000 19.08 19.08 46.69 3.16
3628 3961 3.863400 GCAGCAAGATGGCACTTGAAATT 60.863 43.478 24.35 10.23 46.85 1.82
3824 4159 3.748048 GCTGTAATTTGTGACTCTCTGCA 59.252 43.478 0.00 0.00 0.00 4.41
3825 4160 4.142945 GCTGTAATTTGTGACTCTCTGCAG 60.143 45.833 7.63 7.63 0.00 4.41
3850 4186 1.065410 TTGAGGGCAGTGGGAAAGGA 61.065 55.000 0.00 0.00 0.00 3.36
3853 4189 0.846427 AGGGCAGTGGGAAAGGATCA 60.846 55.000 0.00 0.00 0.00 2.92
3858 4194 3.372025 GGCAGTGGGAAAGGATCAGTAAT 60.372 47.826 0.00 0.00 0.00 1.89
3903 4239 2.030007 CGGCTGATCTTTTGCAAAAGGA 60.030 45.455 38.33 28.49 44.22 3.36
3914 4250 6.656693 TCTTTTGCAAAAGGAAAATGTTTGGA 59.343 30.769 38.33 20.09 44.22 3.53
3937 4273 0.533978 GGTGCACCGGCCAAAATTTT 60.534 50.000 22.49 0.00 40.13 1.82
3988 4325 1.802508 CGCAATACGCAGTGATCCTCA 60.803 52.381 0.00 0.00 45.73 3.86
4011 4348 2.125066 ATCCCGCCTCCATCCCCTAT 62.125 60.000 0.00 0.00 0.00 2.57
4017 4354 1.766499 GCCTCCATCCCCTATCTCCAA 60.766 57.143 0.00 0.00 0.00 3.53
4124 4475 4.753662 CCTGCCATGGCTGCCTGT 62.754 66.667 35.53 5.74 42.51 4.00
4127 4478 2.993264 GCCATGGCTGCCTGTTGT 60.993 61.111 29.98 0.00 38.26 3.32
4194 4565 1.731324 CCCCTCCTCTCCTATCGGGT 61.731 65.000 0.00 0.00 36.25 5.28
4349 4740 7.817418 AAGCTTTAACCATAGACACAGAAAA 57.183 32.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.426313 CTTCCGCCTTGGGGGTCC 62.426 72.222 20.05 0.00 38.76 4.46
32 33 2.008268 TATTCTCGTTCGCCGGGGTC 62.008 60.000 19.13 11.77 37.74 4.46
33 34 2.012902 CTATTCTCGTTCGCCGGGGT 62.013 60.000 19.13 0.00 37.74 4.95
34 35 1.299926 CTATTCTCGTTCGCCGGGG 60.300 63.158 13.31 13.31 37.74 5.73
35 36 1.949631 GCTATTCTCGTTCGCCGGG 60.950 63.158 2.18 0.00 38.86 5.73
36 37 1.226859 TGCTATTCTCGTTCGCCGG 60.227 57.895 0.00 0.00 37.11 6.13
37 38 0.800683 TGTGCTATTCTCGTTCGCCG 60.801 55.000 0.00 0.00 38.13 6.46
38 39 0.645868 GTGTGCTATTCTCGTTCGCC 59.354 55.000 0.00 0.00 0.00 5.54
39 40 0.645868 GGTGTGCTATTCTCGTTCGC 59.354 55.000 0.00 0.00 0.00 4.70
40 41 1.654105 GTGGTGTGCTATTCTCGTTCG 59.346 52.381 0.00 0.00 0.00 3.95
41 42 2.000447 GGTGGTGTGCTATTCTCGTTC 59.000 52.381 0.00 0.00 0.00 3.95
42 43 1.338769 GGGTGGTGTGCTATTCTCGTT 60.339 52.381 0.00 0.00 0.00 3.85
43 44 0.249398 GGGTGGTGTGCTATTCTCGT 59.751 55.000 0.00 0.00 0.00 4.18
44 45 0.462047 GGGGTGGTGTGCTATTCTCG 60.462 60.000 0.00 0.00 0.00 4.04
45 46 0.107165 GGGGGTGGTGTGCTATTCTC 60.107 60.000 0.00 0.00 0.00 2.87
46 47 1.910580 CGGGGGTGGTGTGCTATTCT 61.911 60.000 0.00 0.00 0.00 2.40
47 48 1.451387 CGGGGGTGGTGTGCTATTC 60.451 63.158 0.00 0.00 0.00 1.75
48 49 2.674754 CGGGGGTGGTGTGCTATT 59.325 61.111 0.00 0.00 0.00 1.73
49 50 3.407967 CCGGGGGTGGTGTGCTAT 61.408 66.667 0.00 0.00 0.00 2.97
62 63 3.532155 CTCTCTTCGCTCCCCGGG 61.532 72.222 15.80 15.80 37.59 5.73
63 64 3.532155 CCTCTCTTCGCTCCCCGG 61.532 72.222 0.00 0.00 37.59 5.73
64 65 2.440430 TCCTCTCTTCGCTCCCCG 60.440 66.667 0.00 0.00 38.61 5.73
65 66 2.776913 CGTCCTCTCTTCGCTCCCC 61.777 68.421 0.00 0.00 0.00 4.81
66 67 2.776913 CCGTCCTCTCTTCGCTCCC 61.777 68.421 0.00 0.00 0.00 4.30
67 68 2.776913 CCCGTCCTCTCTTCGCTCC 61.777 68.421 0.00 0.00 0.00 4.70
68 69 2.776913 CCCCGTCCTCTCTTCGCTC 61.777 68.421 0.00 0.00 0.00 5.03
69 70 2.756283 CCCCGTCCTCTCTTCGCT 60.756 66.667 0.00 0.00 0.00 4.93
70 71 3.839432 CCCCCGTCCTCTCTTCGC 61.839 72.222 0.00 0.00 0.00 4.70
71 72 2.044252 TCCCCCGTCCTCTCTTCG 60.044 66.667 0.00 0.00 0.00 3.79
72 73 1.305046 TGTCCCCCGTCCTCTCTTC 60.305 63.158 0.00 0.00 0.00 2.87
73 74 1.609794 GTGTCCCCCGTCCTCTCTT 60.610 63.158 0.00 0.00 0.00 2.85
74 75 2.037527 GTGTCCCCCGTCCTCTCT 59.962 66.667 0.00 0.00 0.00 3.10
75 76 2.283676 TGTGTCCCCCGTCCTCTC 60.284 66.667 0.00 0.00 0.00 3.20
76 77 2.603776 GTGTGTCCCCCGTCCTCT 60.604 66.667 0.00 0.00 0.00 3.69
77 78 4.065281 CGTGTGTCCCCCGTCCTC 62.065 72.222 0.00 0.00 0.00 3.71
78 79 4.928140 ACGTGTGTCCCCCGTCCT 62.928 66.667 0.00 0.00 0.00 3.85
79 80 2.098426 TTAACGTGTGTCCCCCGTCC 62.098 60.000 0.00 0.00 32.95 4.79
80 81 0.668401 CTTAACGTGTGTCCCCCGTC 60.668 60.000 0.00 0.00 32.95 4.79
81 82 1.368579 CTTAACGTGTGTCCCCCGT 59.631 57.895 0.00 0.00 36.17 5.28
82 83 2.030958 GCTTAACGTGTGTCCCCCG 61.031 63.158 0.00 0.00 0.00 5.73
83 84 1.673337 GGCTTAACGTGTGTCCCCC 60.673 63.158 0.00 0.00 0.00 5.40
84 85 1.673337 GGGCTTAACGTGTGTCCCC 60.673 63.158 0.00 0.00 0.00 4.81
85 86 1.673337 GGGGCTTAACGTGTGTCCC 60.673 63.158 9.17 9.17 0.00 4.46
86 87 1.071814 TGGGGCTTAACGTGTGTCC 59.928 57.895 0.00 0.00 0.00 4.02
87 88 0.533308 TGTGGGGCTTAACGTGTGTC 60.533 55.000 0.00 0.00 0.00 3.67
88 89 0.816421 GTGTGGGGCTTAACGTGTGT 60.816 55.000 0.00 0.00 0.00 3.72
89 90 0.534203 AGTGTGGGGCTTAACGTGTG 60.534 55.000 0.00 0.00 0.00 3.82
90 91 0.250166 GAGTGTGGGGCTTAACGTGT 60.250 55.000 0.00 0.00 0.00 4.49
91 92 0.250124 TGAGTGTGGGGCTTAACGTG 60.250 55.000 0.00 0.00 0.00 4.49
92 93 0.034896 CTGAGTGTGGGGCTTAACGT 59.965 55.000 0.00 0.00 0.00 3.99
93 94 1.298859 GCTGAGTGTGGGGCTTAACG 61.299 60.000 0.00 0.00 0.00 3.18
94 95 0.036875 AGCTGAGTGTGGGGCTTAAC 59.963 55.000 0.00 0.00 0.00 2.01
95 96 1.555075 CTAGCTGAGTGTGGGGCTTAA 59.445 52.381 0.00 0.00 36.40 1.85
96 97 1.195115 CTAGCTGAGTGTGGGGCTTA 58.805 55.000 0.00 0.00 36.40 3.09
97 98 0.838122 ACTAGCTGAGTGTGGGGCTT 60.838 55.000 0.00 0.00 36.87 4.35
98 99 1.229336 ACTAGCTGAGTGTGGGGCT 60.229 57.895 0.00 0.00 36.87 5.19
99 100 1.219393 GACTAGCTGAGTGTGGGGC 59.781 63.158 0.00 0.00 39.06 5.80
100 101 0.616111 AGGACTAGCTGAGTGTGGGG 60.616 60.000 0.00 0.00 39.06 4.96
101 102 0.820871 GAGGACTAGCTGAGTGTGGG 59.179 60.000 0.00 0.00 39.06 4.61
102 103 0.820871 GGAGGACTAGCTGAGTGTGG 59.179 60.000 0.00 0.00 39.06 4.17
103 104 1.748493 GAGGAGGACTAGCTGAGTGTG 59.252 57.143 0.00 0.00 39.06 3.82
104 105 1.341581 GGAGGAGGACTAGCTGAGTGT 60.342 57.143 0.00 0.00 39.06 3.55
105 106 1.398692 GGAGGAGGACTAGCTGAGTG 58.601 60.000 0.00 0.00 39.06 3.51
106 107 0.260523 GGGAGGAGGACTAGCTGAGT 59.739 60.000 0.00 0.00 42.90 3.41
107 108 0.469144 GGGGAGGAGGACTAGCTGAG 60.469 65.000 0.00 0.00 0.00 3.35
108 109 1.621377 GGGGAGGAGGACTAGCTGA 59.379 63.158 0.00 0.00 0.00 4.26
109 110 1.458588 GGGGGAGGAGGACTAGCTG 60.459 68.421 0.00 0.00 0.00 4.24
110 111 1.528341 TTGGGGGAGGAGGACTAGCT 61.528 60.000 0.00 0.00 0.00 3.32
111 112 1.003051 TTGGGGGAGGAGGACTAGC 59.997 63.158 0.00 0.00 0.00 3.42
112 113 0.399233 CCTTGGGGGAGGAGGACTAG 60.399 65.000 0.00 0.00 39.25 2.57
113 114 1.710341 CCTTGGGGGAGGAGGACTA 59.290 63.158 0.00 0.00 39.25 2.59
114 115 2.456840 CCTTGGGGGAGGAGGACT 59.543 66.667 0.00 0.00 39.25 3.85
115 116 3.412408 GCCTTGGGGGAGGAGGAC 61.412 72.222 0.00 0.00 39.25 3.85
116 117 4.760220 GGCCTTGGGGGAGGAGGA 62.760 72.222 0.00 0.00 39.25 3.71
118 119 3.415087 CTGGCCTTGGGGGAGGAG 61.415 72.222 3.32 0.00 39.25 3.69
119 120 3.953652 TCTGGCCTTGGGGGAGGA 61.954 66.667 3.32 0.00 39.25 3.71
120 121 3.732849 GTCTGGCCTTGGGGGAGG 61.733 72.222 3.32 0.00 39.93 4.30
121 122 3.732849 GGTCTGGCCTTGGGGGAG 61.733 72.222 3.32 0.00 37.23 4.30
122 123 3.908712 ATGGTCTGGCCTTGGGGGA 62.909 63.158 3.32 0.00 38.35 4.81
123 124 3.350163 ATGGTCTGGCCTTGGGGG 61.350 66.667 3.32 0.00 38.35 5.40
124 125 2.043652 CATGGTCTGGCCTTGGGG 60.044 66.667 3.32 0.00 38.39 4.96
125 126 1.379044 GTCATGGTCTGGCCTTGGG 60.379 63.158 13.47 0.00 41.33 4.12
126 127 0.393537 GAGTCATGGTCTGGCCTTGG 60.394 60.000 13.47 0.00 41.33 3.61
127 128 0.742281 CGAGTCATGGTCTGGCCTTG 60.742 60.000 3.32 7.81 42.09 3.61
128 129 1.599047 CGAGTCATGGTCTGGCCTT 59.401 57.895 3.32 0.00 38.35 4.35
129 130 2.362369 CCGAGTCATGGTCTGGCCT 61.362 63.158 3.32 0.00 38.35 5.19
130 131 2.187946 CCGAGTCATGGTCTGGCC 59.812 66.667 0.00 0.00 37.90 5.36
131 132 2.187946 CCCGAGTCATGGTCTGGC 59.812 66.667 0.00 0.00 0.00 4.85
132 133 1.680522 CTCCCCGAGTCATGGTCTGG 61.681 65.000 0.00 0.00 0.00 3.86
133 134 1.680522 CCTCCCCGAGTCATGGTCTG 61.681 65.000 0.00 0.00 0.00 3.51
134 135 1.381872 CCTCCCCGAGTCATGGTCT 60.382 63.158 0.00 0.00 0.00 3.85
135 136 1.381327 TCCTCCCCGAGTCATGGTC 60.381 63.158 0.00 0.00 0.00 4.02
136 137 1.686110 GTCCTCCCCGAGTCATGGT 60.686 63.158 0.00 0.00 0.00 3.55
137 138 2.786495 CGTCCTCCCCGAGTCATGG 61.786 68.421 0.00 0.00 0.00 3.66
138 139 2.786495 CCGTCCTCCCCGAGTCATG 61.786 68.421 0.00 0.00 0.00 3.07
139 140 2.442272 CCGTCCTCCCCGAGTCAT 60.442 66.667 0.00 0.00 0.00 3.06
158 159 3.182590 TATCCCTGGCTCGCATGGC 62.183 63.158 0.00 0.00 0.00 4.40
159 160 1.004080 CTATCCCTGGCTCGCATGG 60.004 63.158 0.00 0.00 0.00 3.66
160 161 0.320247 GTCTATCCCTGGCTCGCATG 60.320 60.000 0.00 0.00 0.00 4.06
161 162 1.476007 GGTCTATCCCTGGCTCGCAT 61.476 60.000 0.00 0.00 0.00 4.73
162 163 2.134287 GGTCTATCCCTGGCTCGCA 61.134 63.158 0.00 0.00 0.00 5.10
163 164 2.737830 GGTCTATCCCTGGCTCGC 59.262 66.667 0.00 0.00 0.00 5.03
164 165 2.565645 CCGGTCTATCCCTGGCTCG 61.566 68.421 0.00 0.00 0.00 5.03
165 166 2.873525 GCCGGTCTATCCCTGGCTC 61.874 68.421 1.90 0.00 39.52 4.70
166 167 2.844839 GCCGGTCTATCCCTGGCT 60.845 66.667 1.90 0.00 39.52 4.75
167 168 4.301027 CGCCGGTCTATCCCTGGC 62.301 72.222 1.90 0.05 39.36 4.85
168 169 3.616721 CCGCCGGTCTATCCCTGG 61.617 72.222 1.90 0.00 0.00 4.45
169 170 4.301027 GCCGCCGGTCTATCCCTG 62.301 72.222 4.45 0.00 0.00 4.45
199 200 4.208686 GCTGGGACTACCGCTCGG 62.209 72.222 6.79 6.79 44.64 4.63
200 201 4.208686 GGCTGGGACTACCGCTCG 62.209 72.222 0.00 0.00 44.64 5.03
201 202 4.208686 CGGCTGGGACTACCGCTC 62.209 72.222 0.00 0.00 44.64 5.03
204 205 3.834799 GACCGGCTGGGACTACCG 61.835 72.222 18.00 0.00 44.64 4.02
205 206 3.468140 GGACCGGCTGGGACTACC 61.468 72.222 18.00 7.35 40.75 3.18
206 207 2.288025 TTGGACCGGCTGGGACTAC 61.288 63.158 18.00 0.00 40.75 2.73
207 208 2.120940 TTGGACCGGCTGGGACTA 59.879 61.111 18.00 4.68 40.75 2.59
208 209 3.637273 GTTGGACCGGCTGGGACT 61.637 66.667 18.00 0.00 40.75 3.85
211 212 4.323477 TTCGTTGGACCGGCTGGG 62.323 66.667 18.00 4.46 40.75 4.45
212 213 3.047877 GTTCGTTGGACCGGCTGG 61.048 66.667 11.02 11.02 42.84 4.85
213 214 3.411351 CGTTCGTTGGACCGGCTG 61.411 66.667 0.00 0.00 0.00 4.85
214 215 3.853597 GACGTTCGTTGGACCGGCT 62.854 63.158 0.00 0.00 32.65 5.52
215 216 3.408851 GACGTTCGTTGGACCGGC 61.409 66.667 0.00 0.00 31.67 6.13
216 217 2.735857 GGACGTTCGTTGGACCGG 60.736 66.667 0.00 0.00 31.67 5.28
217 218 2.735857 GGGACGTTCGTTGGACCG 60.736 66.667 0.00 0.00 33.88 4.79
218 219 2.357881 GGGGACGTTCGTTGGACC 60.358 66.667 0.00 0.00 0.00 4.46
219 220 2.357881 GGGGGACGTTCGTTGGAC 60.358 66.667 0.00 0.00 0.00 4.02
238 239 4.175337 TGTAGCCCTGCCGCCATC 62.175 66.667 0.00 0.00 0.00 3.51
239 240 4.489771 GTGTAGCCCTGCCGCCAT 62.490 66.667 0.00 0.00 0.00 4.40
267 268 2.210144 TTTCATCCCCTTCGCCCAGG 62.210 60.000 0.00 0.00 0.00 4.45
268 269 1.032114 GTTTCATCCCCTTCGCCCAG 61.032 60.000 0.00 0.00 0.00 4.45
269 270 1.001393 GTTTCATCCCCTTCGCCCA 60.001 57.895 0.00 0.00 0.00 5.36
270 271 0.610785 TTGTTTCATCCCCTTCGCCC 60.611 55.000 0.00 0.00 0.00 6.13
271 272 1.253100 TTTGTTTCATCCCCTTCGCC 58.747 50.000 0.00 0.00 0.00 5.54
272 273 4.712122 TTATTTGTTTCATCCCCTTCGC 57.288 40.909 0.00 0.00 0.00 4.70
273 274 7.996385 AGTATTTATTTGTTTCATCCCCTTCG 58.004 34.615 0.00 0.00 0.00 3.79
274 275 9.190317 AGAGTATTTATTTGTTTCATCCCCTTC 57.810 33.333 0.00 0.00 0.00 3.46
275 276 9.190317 GAGAGTATTTATTTGTTTCATCCCCTT 57.810 33.333 0.00 0.00 0.00 3.95
276 277 8.560903 AGAGAGTATTTATTTGTTTCATCCCCT 58.439 33.333 0.00 0.00 0.00 4.79
277 278 8.753497 AGAGAGTATTTATTTGTTTCATCCCC 57.247 34.615 0.00 0.00 0.00 4.81
279 280 9.922305 CGAAGAGAGTATTTATTTGTTTCATCC 57.078 33.333 0.00 0.00 0.00 3.51
284 285 9.110502 GGGATCGAAGAGAGTATTTATTTGTTT 57.889 33.333 0.00 0.00 43.63 2.83
285 286 8.487028 AGGGATCGAAGAGAGTATTTATTTGTT 58.513 33.333 0.00 0.00 43.63 2.83
286 287 8.024145 AGGGATCGAAGAGAGTATTTATTTGT 57.976 34.615 0.00 0.00 43.63 2.83
292 293 9.369672 ACTTAATAGGGATCGAAGAGAGTATTT 57.630 33.333 0.00 0.00 43.63 1.40
293 294 8.798402 CACTTAATAGGGATCGAAGAGAGTATT 58.202 37.037 0.00 0.00 43.63 1.89
294 295 7.945664 ACACTTAATAGGGATCGAAGAGAGTAT 59.054 37.037 0.00 0.00 43.63 2.12
295 296 7.288560 ACACTTAATAGGGATCGAAGAGAGTA 58.711 38.462 0.00 0.00 43.63 2.59
296 297 6.130569 ACACTTAATAGGGATCGAAGAGAGT 58.869 40.000 0.00 0.00 43.63 3.24
297 298 6.263392 TGACACTTAATAGGGATCGAAGAGAG 59.737 42.308 0.00 0.00 43.63 3.20
298 299 6.039493 GTGACACTTAATAGGGATCGAAGAGA 59.961 42.308 0.00 0.00 43.63 3.10
299 300 6.039941 AGTGACACTTAATAGGGATCGAAGAG 59.960 42.308 1.07 0.00 43.63 2.85
300 301 5.892119 AGTGACACTTAATAGGGATCGAAGA 59.108 40.000 1.07 0.00 45.75 2.87
301 302 6.150396 AGTGACACTTAATAGGGATCGAAG 57.850 41.667 1.07 0.00 0.00 3.79
302 303 7.649533 TTAGTGACACTTAATAGGGATCGAA 57.350 36.000 14.50 0.00 0.00 3.71
303 304 7.834881 ATTAGTGACACTTAATAGGGATCGA 57.165 36.000 14.50 0.00 0.00 3.59
304 305 8.888579 AAATTAGTGACACTTAATAGGGATCG 57.111 34.615 14.50 0.00 0.00 3.69
399 400 2.093711 TGAGTGCTTGTGTGTGTACTGT 60.094 45.455 0.00 0.00 29.71 3.55
400 401 2.549926 TGAGTGCTTGTGTGTGTACTG 58.450 47.619 0.00 0.00 29.71 2.74
401 402 2.979814 TGAGTGCTTGTGTGTGTACT 57.020 45.000 0.00 0.00 32.11 2.73
402 403 4.552166 AAATGAGTGCTTGTGTGTGTAC 57.448 40.909 0.00 0.00 0.00 2.90
403 404 7.413988 GCATATAAATGAGTGCTTGTGTGTGTA 60.414 37.037 0.00 0.00 34.84 2.90
407 408 4.965762 CGCATATAAATGAGTGCTTGTGTG 59.034 41.667 0.00 0.00 34.84 3.82
410 411 3.627123 TGCGCATATAAATGAGTGCTTGT 59.373 39.130 5.66 0.00 35.53 3.16
416 417 2.878406 GGGTGTGCGCATATAAATGAGT 59.122 45.455 15.91 0.00 35.53 3.41
422 423 2.036733 GGAGTAGGGTGTGCGCATATAA 59.963 50.000 15.91 0.00 0.00 0.98
423 424 1.616865 GGAGTAGGGTGTGCGCATATA 59.383 52.381 15.91 0.00 0.00 0.86
427 428 0.686441 ATAGGAGTAGGGTGTGCGCA 60.686 55.000 5.66 5.66 0.00 6.09
435 466 2.390225 AGGTGCTCATAGGAGTAGGG 57.610 55.000 6.23 0.00 43.37 3.53
441 472 2.302260 CTCTCGAAGGTGCTCATAGGA 58.698 52.381 0.00 0.00 0.00 2.94
462 493 0.036577 AGATGATATGCCGGCTCAGC 60.037 55.000 29.70 24.79 0.00 4.26
467 498 2.462456 TCTCAAGATGATATGCCGGC 57.538 50.000 22.73 22.73 0.00 6.13
469 500 7.425577 TGTAAAATCTCAAGATGATATGCCG 57.574 36.000 0.00 0.00 34.49 5.69
499 530 6.852420 TCAGTATTACATACTCCCTATGGC 57.148 41.667 0.00 0.00 43.93 4.40
549 580 1.361793 GCATGTGCAATGCGGAAAAT 58.638 45.000 14.98 0.00 41.59 1.82
632 670 2.829023 ACCACCGGATCCTCTCTTTTA 58.171 47.619 9.46 0.00 0.00 1.52
660 698 0.673985 GTGGGTTCTTGGCTGTTTCC 59.326 55.000 0.00 0.00 0.00 3.13
896 935 5.474825 GCTCCTAGCTAGCTAAGGTTATTG 58.525 45.833 24.20 10.57 38.45 1.90
901 940 1.218196 TGGCTCCTAGCTAGCTAAGGT 59.782 52.381 24.20 2.08 41.99 3.50
953 992 1.084289 CAACCTTACTTACGCCTGGC 58.916 55.000 9.11 9.11 0.00 4.85
1623 1684 2.588877 CCGTTATCGCTGCCCCTG 60.589 66.667 0.00 0.00 35.54 4.45
1634 1695 2.440796 TCGGCGTCTCCCCGTTAT 60.441 61.111 6.85 0.00 45.71 1.89
1635 1696 3.136123 CTCGGCGTCTCCCCGTTA 61.136 66.667 6.85 0.00 45.71 3.18
1663 1724 2.279517 GAACGGCGAGCGGATGAT 60.280 61.111 16.62 0.00 0.00 2.45
2001 2197 3.445687 ACGTCGTCCATGCCGCTA 61.446 61.111 0.00 0.00 0.00 4.26
2952 3277 3.704231 CTTGACCCCCAGCATCCCG 62.704 68.421 0.00 0.00 0.00 5.14
3294 3619 1.373748 GTTGCTCTGGTACGCCGAA 60.374 57.895 0.00 0.00 37.67 4.30
3372 3697 2.125512 ATTCGTGGAGGTCGCAGC 60.126 61.111 0.00 0.00 0.00 5.25
3375 3700 1.586564 CGAGATTCGTGGAGGTCGC 60.587 63.158 0.00 0.00 34.72 5.19
3408 3736 8.533657 TGCAAATTTTCACATCCAGATTAGATT 58.466 29.630 0.00 0.00 0.00 2.40
3409 3737 8.070034 TGCAAATTTTCACATCCAGATTAGAT 57.930 30.769 0.00 0.00 0.00 1.98
3410 3738 7.363181 CCTGCAAATTTTCACATCCAGATTAGA 60.363 37.037 0.00 0.00 0.00 2.10
3493 3821 1.092345 GTTCTTCTCGGAGGCATGGC 61.092 60.000 12.14 12.14 0.00 4.40
3551 3879 2.989055 AAGCACCAAGACGTCCACGG 62.989 60.000 13.01 12.77 44.95 4.94
3619 3952 6.130298 TCACGATCAAACACAATTTCAAGT 57.870 33.333 0.00 0.00 0.00 3.16
3620 3953 6.201517 ACTCACGATCAAACACAATTTCAAG 58.798 36.000 0.00 0.00 0.00 3.02
3623 3956 8.555166 TTAAACTCACGATCAAACACAATTTC 57.445 30.769 0.00 0.00 0.00 2.17
3628 3961 5.529430 ACCATTAAACTCACGATCAAACACA 59.471 36.000 0.00 0.00 0.00 3.72
3839 4175 5.131142 CCACTATTACTGATCCTTTCCCACT 59.869 44.000 0.00 0.00 0.00 4.00
3845 4181 3.181454 CGGCCCACTATTACTGATCCTTT 60.181 47.826 0.00 0.00 0.00 3.11
3850 4186 1.202651 GCACGGCCCACTATTACTGAT 60.203 52.381 0.00 0.00 0.00 2.90
3853 4189 1.411612 GTAGCACGGCCCACTATTACT 59.588 52.381 0.00 0.00 0.00 2.24
3903 4239 0.596341 GCACCGCGTCCAAACATTTT 60.596 50.000 4.92 0.00 0.00 1.82
3933 4269 3.134127 GAGCGAGCCGGCCAAAAT 61.134 61.111 26.15 2.91 0.00 1.82
3993 4330 2.748641 GATAGGGGATGGAGGCGGGA 62.749 65.000 0.00 0.00 0.00 5.14
4194 4565 4.947147 GTGGTGGCCCAGTCGCAA 62.947 66.667 0.00 0.00 42.94 4.85
4327 4718 7.203255 AGTTTTCTGTGTCTATGGTTAAAGC 57.797 36.000 0.00 0.00 0.00 3.51
4331 4722 8.783093 CATTGAAGTTTTCTGTGTCTATGGTTA 58.217 33.333 0.00 0.00 0.00 2.85
4349 4740 5.047802 CCTTGTTATGAAGTGCCATTGAAGT 60.048 40.000 0.00 0.00 0.00 3.01
4476 4869 4.671766 GCAAAAATCTACTACGGTTGCAGG 60.672 45.833 0.00 0.00 39.65 4.85


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

AutoCloner maintained by Alex Coulton.