Multiple sequence alignment - TraesCS7A01G129600

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 TraesCS7A01G129600 chr7A 100.000 3847 0 0 1 3847 83534726 83530880 0.000000e+00 7105
1 TraesCS7A01G129600 chr7A 88.047 594 47 6 3179 3754 696649778 696649191 0.000000e+00 682
2 TraesCS7A01G129600 chr7B 94.427 2853 114 28 233 3069 28306937 28304114 0.000000e+00 4346
3 TraesCS7A01G129600 chr7B 92.786 2523 124 32 584 3062 28002398 27999890 0.000000e+00 3598
4 TraesCS7A01G129600 chr7D 95.367 2633 82 24 465 3069 80782694 80780074 0.000000e+00 4150
5 TraesCS7A01G129600 chr7D 91.584 202 12 2 335 533 80782852 80782653 1.360000e-69 274
6 TraesCS7A01G129600 chr7D 87.778 180 20 2 3511 3690 6378760 6378583 3.890000e-50 209
7 TraesCS7A01G129600 chr6D 95.983 697 14 5 3163 3847 458051737 458052431 0.000000e+00 1120
8 TraesCS7A01G129600 chr2B 91.064 705 38 13 3163 3843 140774216 140773513 0.000000e+00 929
9 TraesCS7A01G129600 chr2B 87.517 753 89 4 1546 2294 245809893 245809142 0.000000e+00 865
10 TraesCS7A01G129600 chr2B 78.166 829 135 26 2271 3063 245809075 245808257 1.610000e-133 486
11 TraesCS7A01G129600 chr2B 86.500 200 16 5 3552 3740 864099 863900 3.890000e-50 209
12 TraesCS7A01G129600 chr1A 87.867 750 86 4 1546 2291 555689532 555690280 0.000000e+00 876
13 TraesCS7A01G129600 chr1A 77.563 829 130 30 2271 3063 555690350 555691158 2.110000e-122 449
14 TraesCS7A01G129600 chr4A 87.649 753 88 4 1546 2294 632936289 632935538 0.000000e+00 870
15 TraesCS7A01G129600 chr4A 87.741 726 26 24 3158 3847 522060106 522060804 0.000000e+00 789
16 TraesCS7A01G129600 chr4A 85.294 612 85 3 944 1550 668171125 668171736 9.070000e-176 627
17 TraesCS7A01G129600 chr4A 85.294 612 85 3 944 1550 668178997 668179608 9.070000e-176 627
18 TraesCS7A01G129600 chr4A 85.294 612 85 3 944 1550 668213664 668214275 9.070000e-176 627
19 TraesCS7A01G129600 chr4A 85.294 612 85 3 944 1550 668221450 668222061 9.070000e-176 627
20 TraesCS7A01G129600 chr4A 78.287 829 134 26 2271 3063 632935471 632934653 3.450000e-135 492
21 TraesCS7A01G129600 chr3B 87.733 750 87 4 1546 2291 752214641 752215389 0.000000e+00 870
22 TraesCS7A01G129600 chr3B 78.408 829 133 26 2271 3063 752215459 752216277 7.420000e-137 497
23 TraesCS7A01G129600 chr3B 88.268 179 19 2 3512 3690 542512884 542512708 3.010000e-51 213
24 TraesCS7A01G129600 chr1B 86.649 749 97 2 1546 2291 365016063 365016811 0.000000e+00 826
25 TraesCS7A01G129600 chr1B 86.569 752 98 2 1546 2294 366293028 366292277 0.000000e+00 826
26 TraesCS7A01G129600 chr2D 86.949 613 43 10 3163 3754 13402750 13403346 0.000000e+00 654
27 TraesCS7A01G129600 chr2D 82.645 605 73 9 3162 3753 448150785 448150200 1.230000e-139 507
28 TraesCS7A01G129600 chrUn 85.294 612 85 3 944 1550 272030143 272030754 9.070000e-176 627
29 TraesCS7A01G129600 chrUn 85.294 612 85 3 944 1550 296574642 296575253 9.070000e-176 627
30 TraesCS7A01G129600 chrUn 77.078 397 66 15 2689 3063 335557060 335557453 5.040000e-49 206
31 TraesCS7A01G129600 chr2A 94.560 386 21 0 3161 3546 654095292 654094907 7.110000e-167 597
32 TraesCS7A01G129600 chr2A 84.327 587 64 7 3163 3739 748960217 748959649 2.020000e-152 549
33 TraesCS7A01G129600 chr2A 89.362 188 9 2 3580 3757 654094908 654094722 3.870000e-55 226
34 TraesCS7A01G129600 chr2A 91.667 96 4 3 3753 3847 654094698 654094606 3.120000e-26 130
35 TraesCS7A01G129600 chr3D 84.553 615 61 15 3163 3754 143059182 143059785 2.580000e-161 579
36 TraesCS7A01G129600 chr3D 87.222 180 21 2 3511 3690 415688948 415688771 1.810000e-48 204
37 TraesCS7A01G129600 chr5B 84.874 595 48 22 3163 3747 620726144 620725582 2.590000e-156 562
38 TraesCS7A01G129600 chr5B 85.326 368 37 6 3163 3529 572516731 572516380 7.850000e-97 364
39 TraesCS7A01G129600 chr6B 78.488 688 125 17 2356 3027 29567899 29568579 2.750000e-116 429
40 TraesCS7A01G129600 chr4B 85.106 376 38 7 3151 3525 427071042 427071400 6.070000e-98 368
41 TraesCS7A01G129600 chr5A 83.463 387 34 14 3163 3547 490587092 490586734 2.210000e-87 333


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 TraesCS7A01G129600 chr7A 83530880 83534726 3846 True 7105.000000 7105 100.0000 1 3847 1 chr7A.!!$R1 3846
1 TraesCS7A01G129600 chr7A 696649191 696649778 587 True 682.000000 682 88.0470 3179 3754 1 chr7A.!!$R2 575
2 TraesCS7A01G129600 chr7B 28304114 28306937 2823 True 4346.000000 4346 94.4270 233 3069 1 chr7B.!!$R2 2836
3 TraesCS7A01G129600 chr7B 27999890 28002398 2508 True 3598.000000 3598 92.7860 584 3062 1 chr7B.!!$R1 2478
4 TraesCS7A01G129600 chr7D 80780074 80782852 2778 True 2212.000000 4150 93.4755 335 3069 2 chr7D.!!$R2 2734
5 TraesCS7A01G129600 chr6D 458051737 458052431 694 False 1120.000000 1120 95.9830 3163 3847 1 chr6D.!!$F1 684
6 TraesCS7A01G129600 chr2B 140773513 140774216 703 True 929.000000 929 91.0640 3163 3843 1 chr2B.!!$R2 680
7 TraesCS7A01G129600 chr2B 245808257 245809893 1636 True 675.500000 865 82.8415 1546 3063 2 chr2B.!!$R3 1517
8 TraesCS7A01G129600 chr1A 555689532 555691158 1626 False 662.500000 876 82.7150 1546 3063 2 chr1A.!!$F1 1517
9 TraesCS7A01G129600 chr4A 522060106 522060804 698 False 789.000000 789 87.7410 3158 3847 1 chr4A.!!$F1 689
10 TraesCS7A01G129600 chr4A 632934653 632936289 1636 True 681.000000 870 82.9680 1546 3063 2 chr4A.!!$R1 1517
11 TraesCS7A01G129600 chr4A 668171125 668171736 611 False 627.000000 627 85.2940 944 1550 1 chr4A.!!$F2 606
12 TraesCS7A01G129600 chr4A 668178997 668179608 611 False 627.000000 627 85.2940 944 1550 1 chr4A.!!$F3 606
13 TraesCS7A01G129600 chr4A 668213664 668214275 611 False 627.000000 627 85.2940 944 1550 1 chr4A.!!$F4 606
14 TraesCS7A01G129600 chr4A 668221450 668222061 611 False 627.000000 627 85.2940 944 1550 1 chr4A.!!$F5 606
15 TraesCS7A01G129600 chr3B 752214641 752216277 1636 False 683.500000 870 83.0705 1546 3063 2 chr3B.!!$F1 1517
16 TraesCS7A01G129600 chr1B 365016063 365016811 748 False 826.000000 826 86.6490 1546 2291 1 chr1B.!!$F1 745
17 TraesCS7A01G129600 chr1B 366292277 366293028 751 True 826.000000 826 86.5690 1546 2294 1 chr1B.!!$R1 748
18 TraesCS7A01G129600 chr2D 13402750 13403346 596 False 654.000000 654 86.9490 3163 3754 1 chr2D.!!$F1 591
19 TraesCS7A01G129600 chr2D 448150200 448150785 585 True 507.000000 507 82.6450 3162 3753 1 chr2D.!!$R1 591
20 TraesCS7A01G129600 chrUn 272030143 272030754 611 False 627.000000 627 85.2940 944 1550 1 chrUn.!!$F1 606
21 TraesCS7A01G129600 chrUn 296574642 296575253 611 False 627.000000 627 85.2940 944 1550 1 chrUn.!!$F2 606
22 TraesCS7A01G129600 chr2A 748959649 748960217 568 True 549.000000 549 84.3270 3163 3739 1 chr2A.!!$R1 576
23 TraesCS7A01G129600 chr2A 654094606 654095292 686 True 317.666667 597 91.8630 3161 3847 3 chr2A.!!$R2 686
24 TraesCS7A01G129600 chr3D 143059182 143059785 603 False 579.000000 579 84.5530 3163 3754 1 chr3D.!!$F1 591
25 TraesCS7A01G129600 chr5B 620725582 620726144 562 True 562.000000 562 84.8740 3163 3747 1 chr5B.!!$R2 584
26 TraesCS7A01G129600 chr6B 29567899 29568579 680 False 429.000000 429 78.4880 2356 3027 1 chr6B.!!$F1 671

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
105 106 0.462047 CCGCCGCCTCTTATTCAGTT 60.462 55.0 0.0 0.0 0.0 3.16 F
498 500 0.532862 GCCCATCACAGTATCACCGG 60.533 60.0 0.0 0.0 0.0 5.28 F
1389 1471 0.468226 TCAATATCACCCGTGCTCCC 59.532 55.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1070 1152 0.240945 ATTGCTTTCCCTTCGTTGCG 59.759 50.000 0.00 0.00 0.0 4.85 R
1881 1963 1.593006 CGATCAAGGACGTATTGTGGC 59.407 52.381 11.51 3.83 0.0 5.01 R
3070 3291 1.071471 CATGGGGGTTAGCTAGCGG 59.929 63.158 9.55 0.00 0.0 5.52 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
31 32 3.804193 CTTCTTTGGCGGCGGCTC 61.804 66.667 33.21 4.52 39.81 4.70
78 79 4.106925 CTGCCCTGCCCTCTCCAC 62.107 72.222 0.00 0.00 0.00 4.02
84 85 4.369591 TGCCCTCTCCACCCCCAT 62.370 66.667 0.00 0.00 0.00 4.00
85 86 3.493303 GCCCTCTCCACCCCCATC 61.493 72.222 0.00 0.00 0.00 3.51
86 87 2.774351 CCCTCTCCACCCCCATCC 60.774 72.222 0.00 0.00 0.00 3.51
87 88 2.774351 CCTCTCCACCCCCATCCC 60.774 72.222 0.00 0.00 0.00 3.85
88 89 3.164269 CTCTCCACCCCCATCCCG 61.164 72.222 0.00 0.00 0.00 5.14
98 99 3.546543 CCATCCCGCCGCCTCTTA 61.547 66.667 0.00 0.00 0.00 2.10
99 100 2.743718 CATCCCGCCGCCTCTTAT 59.256 61.111 0.00 0.00 0.00 1.73
100 101 1.071471 CATCCCGCCGCCTCTTATT 59.929 57.895 0.00 0.00 0.00 1.40
101 102 0.951040 CATCCCGCCGCCTCTTATTC 60.951 60.000 0.00 0.00 0.00 1.75
102 103 1.407656 ATCCCGCCGCCTCTTATTCA 61.408 55.000 0.00 0.00 0.00 2.57
103 104 1.595382 CCCGCCGCCTCTTATTCAG 60.595 63.158 0.00 0.00 0.00 3.02
104 105 1.144057 CCGCCGCCTCTTATTCAGT 59.856 57.895 0.00 0.00 0.00 3.41
105 106 0.462047 CCGCCGCCTCTTATTCAGTT 60.462 55.000 0.00 0.00 0.00 3.16
106 107 1.369625 CGCCGCCTCTTATTCAGTTT 58.630 50.000 0.00 0.00 0.00 2.66
107 108 1.737793 CGCCGCCTCTTATTCAGTTTT 59.262 47.619 0.00 0.00 0.00 2.43
108 109 2.223044 CGCCGCCTCTTATTCAGTTTTC 60.223 50.000 0.00 0.00 0.00 2.29
109 110 2.097629 GCCGCCTCTTATTCAGTTTTCC 59.902 50.000 0.00 0.00 0.00 3.13
110 111 3.610911 CCGCCTCTTATTCAGTTTTCCT 58.389 45.455 0.00 0.00 0.00 3.36
111 112 4.010349 CCGCCTCTTATTCAGTTTTCCTT 58.990 43.478 0.00 0.00 0.00 3.36
112 113 4.459337 CCGCCTCTTATTCAGTTTTCCTTT 59.541 41.667 0.00 0.00 0.00 3.11
113 114 5.392057 CCGCCTCTTATTCAGTTTTCCTTTC 60.392 44.000 0.00 0.00 0.00 2.62
114 115 5.412904 CGCCTCTTATTCAGTTTTCCTTTCT 59.587 40.000 0.00 0.00 0.00 2.52
115 116 6.402658 CGCCTCTTATTCAGTTTTCCTTTCTC 60.403 42.308 0.00 0.00 0.00 2.87
116 117 6.127869 GCCTCTTATTCAGTTTTCCTTTCTCC 60.128 42.308 0.00 0.00 0.00 3.71
117 118 6.092807 CCTCTTATTCAGTTTTCCTTTCTCCG 59.907 42.308 0.00 0.00 0.00 4.63
118 119 5.938125 TCTTATTCAGTTTTCCTTTCTCCGG 59.062 40.000 0.00 0.00 0.00 5.14
119 120 1.892209 TCAGTTTTCCTTTCTCCGGC 58.108 50.000 0.00 0.00 0.00 6.13
120 121 1.142060 TCAGTTTTCCTTTCTCCGGCA 59.858 47.619 0.00 0.00 0.00 5.69
121 122 1.953686 CAGTTTTCCTTTCTCCGGCAA 59.046 47.619 0.00 0.00 0.00 4.52
122 123 2.558359 CAGTTTTCCTTTCTCCGGCAAT 59.442 45.455 0.00 0.00 0.00 3.56
123 124 3.005791 CAGTTTTCCTTTCTCCGGCAATT 59.994 43.478 0.00 0.00 0.00 2.32
124 125 3.641436 AGTTTTCCTTTCTCCGGCAATTT 59.359 39.130 0.00 0.00 0.00 1.82
125 126 3.658757 TTTCCTTTCTCCGGCAATTTG 57.341 42.857 0.00 0.00 0.00 2.32
126 127 2.286365 TCCTTTCTCCGGCAATTTGT 57.714 45.000 0.00 0.00 0.00 2.83
127 128 2.593026 TCCTTTCTCCGGCAATTTGTT 58.407 42.857 0.00 0.00 0.00 2.83
128 129 3.757270 TCCTTTCTCCGGCAATTTGTTA 58.243 40.909 0.00 0.00 0.00 2.41
129 130 4.145807 TCCTTTCTCCGGCAATTTGTTAA 58.854 39.130 0.00 0.00 0.00 2.01
130 131 4.770010 TCCTTTCTCCGGCAATTTGTTAAT 59.230 37.500 0.00 0.00 0.00 1.40
131 132 5.245075 TCCTTTCTCCGGCAATTTGTTAATT 59.755 36.000 0.00 0.00 34.29 1.40
132 133 5.931724 CCTTTCTCCGGCAATTTGTTAATTT 59.068 36.000 0.00 0.00 31.63 1.82
133 134 6.090763 CCTTTCTCCGGCAATTTGTTAATTTC 59.909 38.462 0.00 0.00 31.63 2.17
134 135 5.066968 TCTCCGGCAATTTGTTAATTTCC 57.933 39.130 0.00 0.00 34.77 3.13
135 136 4.081917 TCTCCGGCAATTTGTTAATTTCCC 60.082 41.667 0.00 0.00 34.66 3.97
136 137 3.055747 TCCGGCAATTTGTTAATTTCCCC 60.056 43.478 0.00 0.00 34.66 4.81
137 138 3.055458 CCGGCAATTTGTTAATTTCCCCT 60.055 43.478 0.00 0.00 34.66 4.79
138 139 4.160626 CCGGCAATTTGTTAATTTCCCCTA 59.839 41.667 0.00 0.00 34.66 3.53
139 140 5.348164 CGGCAATTTGTTAATTTCCCCTAG 58.652 41.667 0.00 0.00 34.66 3.02
140 141 5.126384 CGGCAATTTGTTAATTTCCCCTAGA 59.874 40.000 0.00 0.00 34.66 2.43
141 142 6.350612 CGGCAATTTGTTAATTTCCCCTAGAA 60.351 38.462 0.00 0.00 34.66 2.10
151 152 2.638480 TCCCCTAGAAATTCATGCCG 57.362 50.000 0.00 0.00 0.00 5.69
152 153 1.843851 TCCCCTAGAAATTCATGCCGT 59.156 47.619 0.00 0.00 0.00 5.68
153 154 1.949525 CCCCTAGAAATTCATGCCGTG 59.050 52.381 0.00 0.00 0.00 4.94
154 155 2.421388 CCCCTAGAAATTCATGCCGTGA 60.421 50.000 0.00 0.00 34.25 4.35
162 163 1.960417 TTCATGCCGTGAACACAAGA 58.040 45.000 0.00 0.00 41.79 3.02
163 164 2.183478 TCATGCCGTGAACACAAGAT 57.817 45.000 5.80 0.00 32.78 2.40
164 165 2.503331 TCATGCCGTGAACACAAGATT 58.497 42.857 5.80 0.00 32.78 2.40
165 166 2.884012 TCATGCCGTGAACACAAGATTT 59.116 40.909 5.80 0.00 32.78 2.17
166 167 3.317711 TCATGCCGTGAACACAAGATTTT 59.682 39.130 5.80 0.00 32.78 1.82
167 168 3.791973 TGCCGTGAACACAAGATTTTT 57.208 38.095 5.80 0.00 0.00 1.94
194 195 7.552050 TTTTTGAGGGAATGGACACATATTT 57.448 32.000 0.00 0.00 35.94 1.40
195 196 7.552050 TTTTGAGGGAATGGACACATATTTT 57.448 32.000 0.00 0.00 35.94 1.82
196 197 7.552050 TTTGAGGGAATGGACACATATTTTT 57.448 32.000 0.00 0.00 35.94 1.94
197 198 6.528537 TGAGGGAATGGACACATATTTTTG 57.471 37.500 0.00 0.00 35.94 2.44
198 199 6.252233 TGAGGGAATGGACACATATTTTTGA 58.748 36.000 0.00 0.00 35.94 2.69
199 200 6.723515 TGAGGGAATGGACACATATTTTTGAA 59.276 34.615 0.00 0.00 35.94 2.69
200 201 7.399765 TGAGGGAATGGACACATATTTTTGAAT 59.600 33.333 0.00 0.00 35.94 2.57
201 202 8.837099 AGGGAATGGACACATATTTTTGAATA 57.163 30.769 0.00 0.00 35.94 1.75
202 203 8.917088 AGGGAATGGACACATATTTTTGAATAG 58.083 33.333 0.00 0.00 35.94 1.73
203 204 8.912988 GGGAATGGACACATATTTTTGAATAGA 58.087 33.333 0.00 0.00 35.94 1.98
213 214 9.801873 ACATATTTTTGAATAGAAATGAACCCG 57.198 29.630 0.00 0.00 0.00 5.28
216 217 7.753309 TTTTTGAATAGAAATGAACCCGAGA 57.247 32.000 0.00 0.00 0.00 4.04
217 218 7.753309 TTTTGAATAGAAATGAACCCGAGAA 57.247 32.000 0.00 0.00 0.00 2.87
218 219 7.753309 TTTGAATAGAAATGAACCCGAGAAA 57.247 32.000 0.00 0.00 0.00 2.52
219 220 7.938140 TTGAATAGAAATGAACCCGAGAAAT 57.062 32.000 0.00 0.00 0.00 2.17
220 221 7.553881 TGAATAGAAATGAACCCGAGAAATC 57.446 36.000 0.00 0.00 0.00 2.17
221 222 7.338710 TGAATAGAAATGAACCCGAGAAATCT 58.661 34.615 0.00 0.00 0.00 2.40
222 223 7.495934 TGAATAGAAATGAACCCGAGAAATCTC 59.504 37.037 0.15 0.15 39.55 2.75
257 258 2.613026 ACGCCGGTGAATGATAATGA 57.387 45.000 24.59 0.00 0.00 2.57
258 259 3.126001 ACGCCGGTGAATGATAATGAT 57.874 42.857 24.59 0.00 0.00 2.45
259 260 4.265904 ACGCCGGTGAATGATAATGATA 57.734 40.909 24.59 0.00 0.00 2.15
260 261 4.637276 ACGCCGGTGAATGATAATGATAA 58.363 39.130 24.59 0.00 0.00 1.75
262 263 4.929211 CGCCGGTGAATGATAATGATAAGA 59.071 41.667 10.20 0.00 0.00 2.10
263 264 5.062683 CGCCGGTGAATGATAATGATAAGAG 59.937 44.000 10.20 0.00 0.00 2.85
264 265 6.166279 GCCGGTGAATGATAATGATAAGAGA 58.834 40.000 1.90 0.00 0.00 3.10
265 266 6.312426 GCCGGTGAATGATAATGATAAGAGAG 59.688 42.308 1.90 0.00 0.00 3.20
266 267 6.815641 CCGGTGAATGATAATGATAAGAGAGG 59.184 42.308 0.00 0.00 0.00 3.69
267 268 7.310052 CCGGTGAATGATAATGATAAGAGAGGA 60.310 40.741 0.00 0.00 0.00 3.71
268 269 8.090831 CGGTGAATGATAATGATAAGAGAGGAA 58.909 37.037 0.00 0.00 0.00 3.36
301 302 4.828829 AGGTAAAGTGCAGCTATTTACGT 58.171 39.130 18.77 17.49 39.29 3.57
308 309 3.802685 GTGCAGCTATTTACGTAGGGAAG 59.197 47.826 0.00 0.00 0.00 3.46
326 327 4.506802 GGGAAGAGAAAACCAGAAAGGCTA 60.507 45.833 0.00 0.00 43.14 3.93
331 332 4.652822 AGAAAACCAGAAAGGCTATTCGT 58.347 39.130 0.00 0.00 43.14 3.85
362 364 3.130160 CCAGAAAGGCAGCTCGGC 61.130 66.667 0.00 2.19 41.61 5.54
426 428 1.017387 CCTCGCCCTAATTGCTGAAC 58.983 55.000 0.00 0.00 0.00 3.18
436 438 6.049149 CCCTAATTGCTGAACGAGATTTCTA 58.951 40.000 0.00 0.00 0.00 2.10
474 476 3.799755 CGCCTAAACCGCTGTGGC 61.800 66.667 7.27 0.00 43.94 5.01
498 500 0.532862 GCCCATCACAGTATCACCGG 60.533 60.000 0.00 0.00 0.00 5.28
521 553 1.144057 CGCCCATCAGAGTACACCC 59.856 63.158 0.00 0.00 0.00 4.61
631 663 4.560128 GAGGTTCCTTTTCAATTCTTGCC 58.440 43.478 0.00 0.00 0.00 4.52
632 664 3.324846 AGGTTCCTTTTCAATTCTTGCCC 59.675 43.478 0.00 0.00 0.00 5.36
662 694 6.451393 GTCTAGCTATTTTCGATCAGGTCAT 58.549 40.000 0.00 0.00 0.00 3.06
663 695 6.364706 GTCTAGCTATTTTCGATCAGGTCATG 59.635 42.308 0.00 0.00 0.00 3.07
724 774 3.561725 GCTCTCTGTAATGTGTAATGGCC 59.438 47.826 0.00 0.00 0.00 5.36
747 797 2.368548 TGCTCTTGAGTTGGCTGTAAGA 59.631 45.455 0.00 0.00 34.07 2.10
884 940 5.527214 CGGAGCACCATTTACTGATTTGATA 59.473 40.000 0.00 0.00 35.59 2.15
885 941 6.205464 CGGAGCACCATTTACTGATTTGATAT 59.795 38.462 0.00 0.00 35.59 1.63
886 942 7.365741 GGAGCACCATTTACTGATTTGATATG 58.634 38.462 0.00 0.00 35.97 1.78
955 1032 7.086376 GCCAGCATTTAGGTCAATATGTTATG 58.914 38.462 0.00 0.00 0.00 1.90
1070 1152 0.870307 AGCGATGACGACGGCATTAC 60.870 55.000 19.04 12.95 42.66 1.89
1109 1191 3.455469 GGAGCTTGCACATGGCCC 61.455 66.667 0.00 0.00 43.89 5.80
1280 1362 4.826733 TGGACAACTGAAGTACCTTACGTA 59.173 41.667 0.00 0.00 0.00 3.57
1389 1471 0.468226 TCAATATCACCCGTGCTCCC 59.532 55.000 0.00 0.00 0.00 4.30
1605 1687 5.679734 AGCAATTTCAATCAGCCTATACG 57.320 39.130 0.00 0.00 0.00 3.06
1881 1963 3.821033 ACAAGAAAATCAAGGAGGTTCCG 59.179 43.478 0.00 0.00 42.75 4.30
2117 2199 5.841957 AGCAACTCAAGTTCTGAAAATGT 57.158 34.783 0.00 0.00 35.83 2.71
2219 2301 0.546267 AGGTGTGCTGGATGTCCTCT 60.546 55.000 0.09 0.00 36.82 3.69
2317 2492 8.126700 AGGTATTGTTGCTTATATTACGTTTGC 58.873 33.333 0.00 0.00 0.00 3.68
2401 2583 2.660670 TAAACAAGAAAAGGCCCCGA 57.339 45.000 0.00 0.00 0.00 5.14
2442 2624 7.500992 TCAGTGGATGATATTCTAGAACAACC 58.499 38.462 7.48 10.17 31.12 3.77
2476 2659 9.099454 GAACATTCGGTATCTAATCTTGTTCTT 57.901 33.333 0.00 0.00 38.12 2.52
2598 2782 8.654997 AGTAGCATCACATCTCAGGTATATTTT 58.345 33.333 0.00 0.00 0.00 1.82
2865 3052 2.245546 TGATGGAATTGGAGGGCTCAAT 59.754 45.455 0.00 0.00 36.50 2.57
2870 3057 6.024563 TGGAATTGGAGGGCTCAATAATAA 57.975 37.500 0.00 0.00 34.15 1.40
2902 3089 7.713750 TCGGAGTTAGACAGGATTTATGTAAG 58.286 38.462 0.00 0.00 0.00 2.34
2905 3092 9.315525 GGAGTTAGACAGGATTTATGTAAGTTC 57.684 37.037 0.00 0.00 0.00 3.01
2910 3097 8.779354 AGACAGGATTTATGTAAGTTCAAGAC 57.221 34.615 0.00 0.00 0.00 3.01
2918 3107 4.350368 TGTAAGTTCAAGACTGGATGCA 57.650 40.909 0.00 0.00 39.00 3.96
2923 3112 4.764172 AGTTCAAGACTGGATGCAGTATC 58.236 43.478 20.79 8.91 37.17 2.24
2999 3212 2.450867 TCTCATCTGGTCTCTCCCTG 57.549 55.000 0.00 0.00 34.77 4.45
3056 3277 5.417754 TTGCAAATTTCCAAGGATATGCA 57.582 34.783 0.00 11.88 0.00 3.96
3074 3295 2.906388 TGTGTGCACATTGCCGCT 60.906 55.556 24.69 0.00 44.23 5.52
3075 3296 1.599240 TGTGTGCACATTGCCGCTA 60.599 52.632 24.69 0.00 44.23 4.26
3076 3297 1.135315 GTGTGCACATTGCCGCTAG 59.865 57.895 24.69 0.00 44.23 3.42
3077 3298 2.100991 GTGCACATTGCCGCTAGC 59.899 61.111 13.17 4.06 44.23 3.42
3078 3299 2.046023 TGCACATTGCCGCTAGCT 60.046 55.556 13.93 0.00 44.23 3.32
3079 3300 1.089481 GTGCACATTGCCGCTAGCTA 61.089 55.000 13.17 0.00 44.23 3.32
3080 3301 0.392327 TGCACATTGCCGCTAGCTAA 60.392 50.000 13.93 5.80 44.23 3.09
3081 3302 0.028110 GCACATTGCCGCTAGCTAAC 59.972 55.000 13.93 2.25 44.23 2.34
3082 3303 0.657840 CACATTGCCGCTAGCTAACC 59.342 55.000 13.93 0.00 44.23 2.85
3083 3304 0.463833 ACATTGCCGCTAGCTAACCC 60.464 55.000 13.93 0.00 44.23 4.11
3084 3305 1.148498 ATTGCCGCTAGCTAACCCC 59.852 57.895 13.93 0.00 44.23 4.95
3085 3306 2.339275 ATTGCCGCTAGCTAACCCCC 62.339 60.000 13.93 0.00 44.23 5.40
3086 3307 3.476419 GCCGCTAGCTAACCCCCA 61.476 66.667 13.93 0.00 38.99 4.96
3087 3308 2.819284 GCCGCTAGCTAACCCCCAT 61.819 63.158 13.93 0.00 38.99 4.00
3088 3309 1.071471 CCGCTAGCTAACCCCCATG 59.929 63.158 13.93 0.00 0.00 3.66
3089 3310 1.071471 CGCTAGCTAACCCCCATGG 59.929 63.158 13.93 4.14 41.37 3.66
3100 3321 2.058593 CCCCCATGGTTTAGAGCTTC 57.941 55.000 11.73 0.00 0.00 3.86
3101 3322 1.410224 CCCCCATGGTTTAGAGCTTCC 60.410 57.143 11.73 0.00 0.00 3.46
3102 3323 1.284785 CCCCATGGTTTAGAGCTTCCA 59.715 52.381 11.73 0.00 0.00 3.53
3103 3324 2.648059 CCCATGGTTTAGAGCTTCCAG 58.352 52.381 11.73 0.00 33.33 3.86
3104 3325 2.025887 CCCATGGTTTAGAGCTTCCAGT 60.026 50.000 11.73 0.00 33.33 4.00
3105 3326 3.562176 CCCATGGTTTAGAGCTTCCAGTT 60.562 47.826 11.73 0.00 33.33 3.16
3106 3327 3.691609 CCATGGTTTAGAGCTTCCAGTTC 59.308 47.826 2.57 0.00 33.33 3.01
3107 3328 4.326826 CATGGTTTAGAGCTTCCAGTTCA 58.673 43.478 0.00 0.00 33.33 3.18
3108 3329 4.431416 TGGTTTAGAGCTTCCAGTTCAA 57.569 40.909 0.00 0.00 0.00 2.69
3109 3330 4.787551 TGGTTTAGAGCTTCCAGTTCAAA 58.212 39.130 0.00 0.00 0.00 2.69
3110 3331 4.578928 TGGTTTAGAGCTTCCAGTTCAAAC 59.421 41.667 0.00 0.00 32.07 2.93
3111 3332 4.578928 GGTTTAGAGCTTCCAGTTCAAACA 59.421 41.667 0.00 0.00 33.18 2.83
3112 3333 5.278022 GGTTTAGAGCTTCCAGTTCAAACAG 60.278 44.000 0.00 0.00 33.18 3.16
3113 3334 3.567478 AGAGCTTCCAGTTCAAACAGT 57.433 42.857 0.00 0.00 0.00 3.55
3114 3335 3.891049 AGAGCTTCCAGTTCAAACAGTT 58.109 40.909 0.00 0.00 0.00 3.16
3115 3336 4.273318 AGAGCTTCCAGTTCAAACAGTTT 58.727 39.130 0.00 0.00 0.00 2.66
3116 3337 4.706962 AGAGCTTCCAGTTCAAACAGTTTT 59.293 37.500 0.00 0.00 0.00 2.43
3117 3338 4.747810 AGCTTCCAGTTCAAACAGTTTTG 58.252 39.130 0.00 0.00 43.17 2.44
3118 3339 4.220602 AGCTTCCAGTTCAAACAGTTTTGT 59.779 37.500 0.00 0.00 42.51 2.83
3119 3340 4.562789 GCTTCCAGTTCAAACAGTTTTGTC 59.437 41.667 0.00 0.00 42.51 3.18
3120 3341 5.622233 GCTTCCAGTTCAAACAGTTTTGTCT 60.622 40.000 0.00 0.00 42.51 3.41
3121 3342 5.560966 TCCAGTTCAAACAGTTTTGTCTC 57.439 39.130 0.00 0.00 42.51 3.36
3122 3343 5.007034 TCCAGTTCAAACAGTTTTGTCTCA 58.993 37.500 0.00 0.00 42.51 3.27
3123 3344 5.123820 TCCAGTTCAAACAGTTTTGTCTCAG 59.876 40.000 0.00 0.00 42.51 3.35
3124 3345 5.123820 CCAGTTCAAACAGTTTTGTCTCAGA 59.876 40.000 0.00 0.00 42.51 3.27
3125 3346 6.024049 CAGTTCAAACAGTTTTGTCTCAGAC 58.976 40.000 0.00 0.00 42.51 3.51
3126 3347 5.705441 AGTTCAAACAGTTTTGTCTCAGACA 59.295 36.000 2.36 2.36 42.51 3.41
3127 3348 6.375455 AGTTCAAACAGTTTTGTCTCAGACAT 59.625 34.615 8.74 0.00 42.40 3.06
3128 3349 6.363577 TCAAACAGTTTTGTCTCAGACATC 57.636 37.500 8.74 2.81 42.40 3.06
3129 3350 6.115446 TCAAACAGTTTTGTCTCAGACATCT 58.885 36.000 8.74 5.17 42.40 2.90
3130 3351 5.998454 AACAGTTTTGTCTCAGACATCTG 57.002 39.130 22.56 22.56 42.40 2.90
3131 3352 3.812053 ACAGTTTTGTCTCAGACATCTGC 59.188 43.478 23.41 11.03 42.40 4.26
3132 3353 3.811497 CAGTTTTGTCTCAGACATCTGCA 59.189 43.478 8.74 0.00 42.40 4.41
3133 3354 4.274214 CAGTTTTGTCTCAGACATCTGCAA 59.726 41.667 8.74 0.00 42.40 4.08
3134 3355 5.048921 CAGTTTTGTCTCAGACATCTGCAAT 60.049 40.000 8.74 0.00 42.40 3.56
3135 3356 5.533903 AGTTTTGTCTCAGACATCTGCAATT 59.466 36.000 8.74 0.00 42.40 2.32
3136 3357 6.040166 AGTTTTGTCTCAGACATCTGCAATTT 59.960 34.615 8.74 0.00 42.40 1.82
3137 3358 5.366829 TTGTCTCAGACATCTGCAATTTG 57.633 39.130 8.74 0.00 42.40 2.32
3138 3359 3.189910 TGTCTCAGACATCTGCAATTTGC 59.810 43.478 14.49 14.49 43.46 3.68
3139 3360 2.751259 TCTCAGACATCTGCAATTTGCC 59.249 45.455 18.27 2.20 44.23 4.52
3140 3361 2.490509 CTCAGACATCTGCAATTTGCCA 59.509 45.455 18.27 5.80 44.23 4.92
3141 3362 3.093814 TCAGACATCTGCAATTTGCCAT 58.906 40.909 18.27 7.87 44.23 4.40
3142 3363 4.271661 TCAGACATCTGCAATTTGCCATA 58.728 39.130 18.27 4.58 44.23 2.74
3143 3364 4.337274 TCAGACATCTGCAATTTGCCATAG 59.663 41.667 18.27 9.54 44.23 2.23
3144 3365 4.337274 CAGACATCTGCAATTTGCCATAGA 59.663 41.667 18.27 14.31 44.23 1.98
3145 3366 5.009710 CAGACATCTGCAATTTGCCATAGAT 59.990 40.000 18.27 15.79 44.23 1.98
3146 3367 6.206048 CAGACATCTGCAATTTGCCATAGATA 59.794 38.462 18.27 0.00 44.23 1.98
3147 3368 6.946583 AGACATCTGCAATTTGCCATAGATAT 59.053 34.615 18.27 9.40 44.23 1.63
3148 3369 6.920817 ACATCTGCAATTTGCCATAGATATG 58.079 36.000 18.27 12.25 44.23 1.78
3149 3370 5.381174 TCTGCAATTTGCCATAGATATGC 57.619 39.130 18.27 0.00 44.23 3.14
3150 3371 4.219070 TCTGCAATTTGCCATAGATATGCC 59.781 41.667 18.27 0.00 44.23 4.40
3151 3372 3.896272 TGCAATTTGCCATAGATATGCCA 59.104 39.130 18.27 0.00 44.23 4.92
3152 3373 4.528987 TGCAATTTGCCATAGATATGCCAT 59.471 37.500 18.27 0.00 44.23 4.40
3153 3374 5.715753 TGCAATTTGCCATAGATATGCCATA 59.284 36.000 18.27 0.00 44.23 2.74
3154 3375 6.381707 TGCAATTTGCCATAGATATGCCATAT 59.618 34.615 18.27 0.00 44.23 1.78
3155 3376 6.700081 GCAATTTGCCATAGATATGCCATATG 59.300 38.462 10.34 0.00 37.42 1.78
3156 3377 7.632028 GCAATTTGCCATAGATATGCCATATGT 60.632 37.037 10.34 0.26 37.42 2.29
3157 3378 6.762702 TTTGCCATAGATATGCCATATGTG 57.237 37.500 0.99 0.00 32.40 3.21
3158 3379 4.201657 TGCCATAGATATGCCATATGTGC 58.798 43.478 0.99 5.66 32.40 4.57
3159 3380 4.201657 GCCATAGATATGCCATATGTGCA 58.798 43.478 17.54 17.54 43.97 4.57
3240 3461 3.043713 CAGCGCTCAAGCCGAACA 61.044 61.111 7.13 0.00 37.91 3.18
3327 3548 7.683578 TCCATCCAGACCATTTTCTAGATATG 58.316 38.462 0.00 0.85 0.00 1.78
3389 3611 1.210967 ACTGGAACGTTGGACTTGGAA 59.789 47.619 5.00 0.00 0.00 3.53
3410 3632 1.871039 CCCAAACTTGACCTGTACGTG 59.129 52.381 0.00 0.00 0.00 4.49
3435 3678 2.346803 ACTACGAAACGCATGAAGCAT 58.653 42.857 0.00 0.00 46.13 3.79
3568 3863 3.741476 GCCGGCTGCAAGACCTTG 61.741 66.667 22.15 5.44 40.92 3.61
3757 4091 1.908619 TCTGCATGAAGGAGTTGGCTA 59.091 47.619 0.00 0.00 36.95 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.804193 GAGCCGCCGCCAAAGAAG 61.804 66.667 0.00 0.00 34.57 2.85
61 62 4.106925 GTGGAGAGGGCAGGGCAG 62.107 72.222 0.00 0.00 0.00 4.85
67 68 4.369591 ATGGGGGTGGAGAGGGCA 62.370 66.667 0.00 0.00 0.00 5.36
68 69 3.493303 GATGGGGGTGGAGAGGGC 61.493 72.222 0.00 0.00 0.00 5.19
69 70 2.774351 GGATGGGGGTGGAGAGGG 60.774 72.222 0.00 0.00 0.00 4.30
70 71 2.774351 GGGATGGGGGTGGAGAGG 60.774 72.222 0.00 0.00 0.00 3.69
71 72 3.164269 CGGGATGGGGGTGGAGAG 61.164 72.222 0.00 0.00 0.00 3.20
81 82 2.397413 AATAAGAGGCGGCGGGATGG 62.397 60.000 9.78 0.00 0.00 3.51
82 83 0.951040 GAATAAGAGGCGGCGGGATG 60.951 60.000 9.78 0.00 0.00 3.51
83 84 1.371558 GAATAAGAGGCGGCGGGAT 59.628 57.895 9.78 0.00 0.00 3.85
84 85 2.028125 CTGAATAAGAGGCGGCGGGA 62.028 60.000 9.78 0.00 0.00 5.14
85 86 1.595382 CTGAATAAGAGGCGGCGGG 60.595 63.158 9.78 0.00 0.00 6.13
86 87 0.462047 AACTGAATAAGAGGCGGCGG 60.462 55.000 9.78 0.00 0.00 6.13
87 88 1.369625 AAACTGAATAAGAGGCGGCG 58.630 50.000 0.51 0.51 0.00 6.46
88 89 2.097629 GGAAAACTGAATAAGAGGCGGC 59.902 50.000 0.00 0.00 0.00 6.53
89 90 3.610911 AGGAAAACTGAATAAGAGGCGG 58.389 45.455 0.00 0.00 0.00 6.13
90 91 5.412904 AGAAAGGAAAACTGAATAAGAGGCG 59.587 40.000 0.00 0.00 0.00 5.52
91 92 6.127869 GGAGAAAGGAAAACTGAATAAGAGGC 60.128 42.308 0.00 0.00 0.00 4.70
92 93 6.092807 CGGAGAAAGGAAAACTGAATAAGAGG 59.907 42.308 0.00 0.00 0.00 3.69
93 94 6.092807 CCGGAGAAAGGAAAACTGAATAAGAG 59.907 42.308 0.00 0.00 0.00 2.85
94 95 5.938125 CCGGAGAAAGGAAAACTGAATAAGA 59.062 40.000 0.00 0.00 0.00 2.10
95 96 5.392057 GCCGGAGAAAGGAAAACTGAATAAG 60.392 44.000 5.05 0.00 0.00 1.73
96 97 4.457949 GCCGGAGAAAGGAAAACTGAATAA 59.542 41.667 5.05 0.00 0.00 1.40
97 98 4.007659 GCCGGAGAAAGGAAAACTGAATA 58.992 43.478 5.05 0.00 0.00 1.75
98 99 2.820197 GCCGGAGAAAGGAAAACTGAAT 59.180 45.455 5.05 0.00 0.00 2.57
99 100 2.227194 GCCGGAGAAAGGAAAACTGAA 58.773 47.619 5.05 0.00 0.00 3.02
100 101 1.142060 TGCCGGAGAAAGGAAAACTGA 59.858 47.619 5.05 0.00 0.00 3.41
101 102 1.604604 TGCCGGAGAAAGGAAAACTG 58.395 50.000 5.05 0.00 0.00 3.16
102 103 2.358322 TTGCCGGAGAAAGGAAAACT 57.642 45.000 5.05 0.00 0.00 2.66
103 104 3.660501 AATTGCCGGAGAAAGGAAAAC 57.339 42.857 5.05 0.00 28.46 2.43
104 105 3.386402 ACAAATTGCCGGAGAAAGGAAAA 59.614 39.130 5.05 0.00 28.46 2.29
105 106 2.962421 ACAAATTGCCGGAGAAAGGAAA 59.038 40.909 5.05 0.00 0.00 3.13
106 107 2.593026 ACAAATTGCCGGAGAAAGGAA 58.407 42.857 5.05 0.00 0.00 3.36
107 108 2.286365 ACAAATTGCCGGAGAAAGGA 57.714 45.000 5.05 0.00 0.00 3.36
108 109 4.513198 TTAACAAATTGCCGGAGAAAGG 57.487 40.909 5.05 0.00 0.00 3.11
109 110 6.090763 GGAAATTAACAAATTGCCGGAGAAAG 59.909 38.462 5.05 0.00 28.66 2.62
110 111 5.929415 GGAAATTAACAAATTGCCGGAGAAA 59.071 36.000 5.05 0.00 28.66 2.52
111 112 5.474825 GGAAATTAACAAATTGCCGGAGAA 58.525 37.500 5.05 0.00 28.66 2.87
112 113 4.081917 GGGAAATTAACAAATTGCCGGAGA 60.082 41.667 5.05 0.00 38.52 3.71
113 114 4.180817 GGGAAATTAACAAATTGCCGGAG 58.819 43.478 5.05 0.00 38.52 4.63
114 115 3.055747 GGGGAAATTAACAAATTGCCGGA 60.056 43.478 5.05 0.00 38.52 5.14
115 116 3.055458 AGGGGAAATTAACAAATTGCCGG 60.055 43.478 0.00 0.00 38.52 6.13
116 117 4.200838 AGGGGAAATTAACAAATTGCCG 57.799 40.909 0.00 0.00 38.52 5.69
117 118 6.538945 TCTAGGGGAAATTAACAAATTGCC 57.461 37.500 0.00 0.00 37.16 4.52
130 131 3.287222 CGGCATGAATTTCTAGGGGAAA 58.713 45.455 0.00 0.00 46.33 3.13
131 132 2.241176 ACGGCATGAATTTCTAGGGGAA 59.759 45.455 0.00 0.00 0.00 3.97
132 133 1.843851 ACGGCATGAATTTCTAGGGGA 59.156 47.619 0.00 0.00 0.00 4.81
133 134 1.949525 CACGGCATGAATTTCTAGGGG 59.050 52.381 0.00 0.00 0.00 4.79
134 135 2.917933 TCACGGCATGAATTTCTAGGG 58.082 47.619 0.00 0.00 33.02 3.53
143 144 1.960417 TCTTGTGTTCACGGCATGAA 58.040 45.000 0.00 0.00 45.39 2.57
144 145 2.183478 ATCTTGTGTTCACGGCATGA 57.817 45.000 0.00 0.00 34.65 3.07
145 146 2.995466 AATCTTGTGTTCACGGCATG 57.005 45.000 0.00 0.00 0.00 4.06
146 147 4.320608 AAAAATCTTGTGTTCACGGCAT 57.679 36.364 0.00 0.00 0.00 4.40
147 148 3.791973 AAAAATCTTGTGTTCACGGCA 57.208 38.095 0.00 0.00 0.00 5.69
170 171 7.552050 AAATATGTGTCCATTCCCTCAAAAA 57.448 32.000 0.00 0.00 32.29 1.94
171 172 7.552050 AAAATATGTGTCCATTCCCTCAAAA 57.448 32.000 0.00 0.00 32.29 2.44
172 173 7.234371 TCAAAAATATGTGTCCATTCCCTCAAA 59.766 33.333 0.00 0.00 32.29 2.69
173 174 6.723515 TCAAAAATATGTGTCCATTCCCTCAA 59.276 34.615 0.00 0.00 32.29 3.02
174 175 6.252233 TCAAAAATATGTGTCCATTCCCTCA 58.748 36.000 0.00 0.00 32.29 3.86
175 176 6.773976 TCAAAAATATGTGTCCATTCCCTC 57.226 37.500 0.00 0.00 32.29 4.30
176 177 7.738437 ATTCAAAAATATGTGTCCATTCCCT 57.262 32.000 0.00 0.00 32.29 4.20
177 178 8.912988 TCTATTCAAAAATATGTGTCCATTCCC 58.087 33.333 0.00 0.00 32.29 3.97
187 188 9.801873 CGGGTTCATTTCTATTCAAAAATATGT 57.198 29.630 0.00 0.00 0.00 2.29
190 191 9.456147 TCTCGGGTTCATTTCTATTCAAAAATA 57.544 29.630 0.00 0.00 0.00 1.40
191 192 8.348285 TCTCGGGTTCATTTCTATTCAAAAAT 57.652 30.769 0.00 0.00 0.00 1.82
192 193 7.753309 TCTCGGGTTCATTTCTATTCAAAAA 57.247 32.000 0.00 0.00 0.00 1.94
193 194 7.753309 TTCTCGGGTTCATTTCTATTCAAAA 57.247 32.000 0.00 0.00 0.00 2.44
194 195 7.753309 TTTCTCGGGTTCATTTCTATTCAAA 57.247 32.000 0.00 0.00 0.00 2.69
195 196 7.829211 AGATTTCTCGGGTTCATTTCTATTCAA 59.171 33.333 0.00 0.00 0.00 2.69
196 197 7.338710 AGATTTCTCGGGTTCATTTCTATTCA 58.661 34.615 0.00 0.00 0.00 2.57
197 198 7.793927 AGATTTCTCGGGTTCATTTCTATTC 57.206 36.000 0.00 0.00 0.00 1.75
198 199 7.793927 GAGATTTCTCGGGTTCATTTCTATT 57.206 36.000 0.00 0.00 32.78 1.73
220 221 1.078759 GTGACCCAGTTGATCGCGAG 61.079 60.000 16.66 0.00 0.00 5.03
221 222 1.080093 GTGACCCAGTTGATCGCGA 60.080 57.895 13.09 13.09 0.00 5.87
222 223 2.444624 CGTGACCCAGTTGATCGCG 61.445 63.158 0.00 0.00 39.65 5.87
223 224 2.740714 GCGTGACCCAGTTGATCGC 61.741 63.158 0.00 0.00 35.86 4.58
224 225 2.100631 GGCGTGACCCAGTTGATCG 61.101 63.158 0.00 0.00 0.00 3.69
225 226 2.100631 CGGCGTGACCCAGTTGATC 61.101 63.158 0.00 0.00 33.26 2.92
226 227 2.047274 CGGCGTGACCCAGTTGAT 60.047 61.111 0.00 0.00 33.26 2.57
227 228 4.308458 CCGGCGTGACCCAGTTGA 62.308 66.667 6.01 0.00 33.26 3.18
228 229 4.619227 ACCGGCGTGACCCAGTTG 62.619 66.667 6.01 0.00 33.26 3.16
229 230 4.619227 CACCGGCGTGACCCAGTT 62.619 66.667 6.01 0.00 43.14 3.16
268 269 5.509670 GCTGCACTTTACCTTCTCCATTTTT 60.510 40.000 0.00 0.00 0.00 1.94
277 278 5.350640 ACGTAAATAGCTGCACTTTACCTTC 59.649 40.000 21.20 6.78 33.72 3.46
281 282 5.233689 CCCTACGTAAATAGCTGCACTTTAC 59.766 44.000 19.03 19.03 33.86 2.01
290 291 6.786967 TTTCTCTTCCCTACGTAAATAGCT 57.213 37.500 0.00 0.00 0.00 3.32
301 302 4.506802 GCCTTTCTGGTTTTCTCTTCCCTA 60.507 45.833 0.00 0.00 38.35 3.53
308 309 4.695928 ACGAATAGCCTTTCTGGTTTTCTC 59.304 41.667 0.00 0.00 38.35 2.87
341 342 1.580845 CGAGCTGCCTTTCTGGGTTG 61.581 60.000 0.00 0.00 36.00 3.77
362 364 3.104843 GATCTGGTCGATCTGGGAAAG 57.895 52.381 2.47 0.00 44.21 2.62
436 438 1.940613 GTGAGACTGTTTTTCTGCCGT 59.059 47.619 0.00 0.00 0.00 5.68
474 476 3.460672 ATACTGTGATGGGCGGCGG 62.461 63.158 9.78 0.00 0.00 6.13
631 663 3.067742 TCGAAAATAGCTAGACGGAAGGG 59.932 47.826 0.00 0.00 0.00 3.95
632 664 4.303086 TCGAAAATAGCTAGACGGAAGG 57.697 45.455 0.00 0.00 0.00 3.46
662 694 1.065053 ACCAAACACACACAGCCTACA 60.065 47.619 0.00 0.00 0.00 2.74
663 695 1.675552 ACCAAACACACACAGCCTAC 58.324 50.000 0.00 0.00 0.00 3.18
724 774 0.882042 ACAGCCAACTCAAGAGCACG 60.882 55.000 0.00 0.00 0.00 5.34
747 797 5.131142 CCTGATCAGATAAGTAACAACCCCT 59.869 44.000 24.62 0.00 0.00 4.79
885 941 3.038788 TCATGCTGAACTTAACGAGCA 57.961 42.857 0.00 0.00 45.12 4.26
886 942 3.726190 GCTTCATGCTGAACTTAACGAGC 60.726 47.826 0.00 0.00 38.95 5.03
908 964 5.392380 GGCAATCTAACCATGAACTTGTGAG 60.392 44.000 0.00 0.00 0.00 3.51
955 1032 8.937634 ATTAATCATTCTCATTCAAAGGCAAC 57.062 30.769 0.00 0.00 0.00 4.17
1070 1152 0.240945 ATTGCTTTCCCTTCGTTGCG 59.759 50.000 0.00 0.00 0.00 4.85
1109 1191 1.738350 CATCTGGTTGAGCTTCAGCAG 59.262 52.381 15.70 15.70 45.16 4.24
1377 1459 4.838152 CCATCGGGAGCACGGGTG 62.838 72.222 0.00 0.00 35.59 4.61
1389 1471 2.609459 CGAAAGATGAAACCTCCCATCG 59.391 50.000 0.00 0.00 42.81 3.84
1605 1687 9.450807 TCTTGAAATTCTTTGAACTTCGAATTC 57.549 29.630 0.00 5.90 35.65 2.17
1881 1963 1.593006 CGATCAAGGACGTATTGTGGC 59.407 52.381 11.51 3.83 0.00 5.01
1920 2002 6.654582 TGCATCTGATAAAGTTGTGCTTTCTA 59.345 34.615 0.00 0.00 43.42 2.10
2117 2199 3.749088 CCGTGTAGCAACATGTTCCTTAA 59.251 43.478 7.96 0.00 40.44 1.85
2219 2301 6.873997 TCAAGCATAGATTCTTTTCTCGGTA 58.126 36.000 0.00 0.00 0.00 4.02
2317 2492 9.326339 GAGTTTTTATAAAAAGTGGCTTACGAG 57.674 33.333 27.73 0.00 40.56 4.18
2865 3052 6.131264 TGTCTAACTCCGATCCACCTTATTA 58.869 40.000 0.00 0.00 0.00 0.98
2870 3057 2.379972 CTGTCTAACTCCGATCCACCT 58.620 52.381 0.00 0.00 0.00 4.00
2910 3097 7.268586 ACTACACTAAAAGATACTGCATCCAG 58.731 38.462 0.00 0.00 44.80 3.86
2923 3112 6.697892 GTGCCTATCAGCTACTACACTAAAAG 59.302 42.308 0.00 0.00 0.00 2.27
2981 3194 2.450867 TCAGGGAGAGACCAGATGAG 57.549 55.000 0.00 0.00 41.20 2.90
3023 3244 8.658609 CCTTGGAAATTTGCAAATGTACAATAG 58.341 33.333 31.33 23.17 36.20 1.73
3028 3249 8.819974 CATATCCTTGGAAATTTGCAAATGTAC 58.180 33.333 24.74 20.57 38.05 2.90
3040 3261 5.524971 CACACATGCATATCCTTGGAAAT 57.475 39.130 0.00 0.00 0.00 2.17
3069 3290 2.819284 ATGGGGGTTAGCTAGCGGC 61.819 63.158 9.55 3.36 42.19 6.53
3070 3291 1.071471 CATGGGGGTTAGCTAGCGG 59.929 63.158 9.55 0.00 0.00 5.52
3071 3292 1.071471 CCATGGGGGTTAGCTAGCG 59.929 63.158 9.55 0.00 0.00 4.26
3081 3302 1.410224 GGAAGCTCTAAACCATGGGGG 60.410 57.143 18.09 0.00 44.81 5.40
3082 3303 1.284785 TGGAAGCTCTAAACCATGGGG 59.715 52.381 18.09 3.33 41.29 4.96
3083 3304 2.025887 ACTGGAAGCTCTAAACCATGGG 60.026 50.000 18.09 0.00 37.60 4.00
3084 3305 3.356529 ACTGGAAGCTCTAAACCATGG 57.643 47.619 11.19 11.19 37.60 3.66
3085 3306 4.326826 TGAACTGGAAGCTCTAAACCATG 58.673 43.478 0.00 0.00 37.60 3.66
3086 3307 4.640771 TGAACTGGAAGCTCTAAACCAT 57.359 40.909 0.00 0.00 37.60 3.55
3087 3308 4.431416 TTGAACTGGAAGCTCTAAACCA 57.569 40.909 0.00 0.00 37.60 3.67
3088 3309 4.578928 TGTTTGAACTGGAAGCTCTAAACC 59.421 41.667 0.00 0.00 37.60 3.27
3089 3310 5.297029 ACTGTTTGAACTGGAAGCTCTAAAC 59.703 40.000 0.00 0.00 37.60 2.01
3090 3311 5.437060 ACTGTTTGAACTGGAAGCTCTAAA 58.563 37.500 0.00 0.00 37.60 1.85
3091 3312 5.036117 ACTGTTTGAACTGGAAGCTCTAA 57.964 39.130 0.00 0.00 37.60 2.10
3092 3313 4.689612 ACTGTTTGAACTGGAAGCTCTA 57.310 40.909 0.00 0.00 37.60 2.43
3093 3314 3.567478 ACTGTTTGAACTGGAAGCTCT 57.433 42.857 0.00 0.00 37.60 4.09
3094 3315 4.639135 AAACTGTTTGAACTGGAAGCTC 57.361 40.909 4.73 0.00 37.60 4.09
3095 3316 4.220602 ACAAAACTGTTTGAACTGGAAGCT 59.779 37.500 6.53 0.00 45.99 3.74
3096 3317 4.494484 ACAAAACTGTTTGAACTGGAAGC 58.506 39.130 6.53 0.00 45.99 3.86
3097 3318 5.954335 AGACAAAACTGTTTGAACTGGAAG 58.046 37.500 6.53 0.00 45.99 3.46
3098 3319 5.475220 TGAGACAAAACTGTTTGAACTGGAA 59.525 36.000 6.53 0.00 45.99 3.53
3099 3320 5.007034 TGAGACAAAACTGTTTGAACTGGA 58.993 37.500 6.53 0.00 45.99 3.86
3100 3321 5.123820 TCTGAGACAAAACTGTTTGAACTGG 59.876 40.000 6.53 3.07 45.99 4.00
3101 3322 6.024049 GTCTGAGACAAAACTGTTTGAACTG 58.976 40.000 7.90 3.98 45.99 3.16
3102 3323 5.705441 TGTCTGAGACAAAACTGTTTGAACT 59.295 36.000 13.74 6.34 45.99 3.01
3103 3324 5.938322 TGTCTGAGACAAAACTGTTTGAAC 58.062 37.500 13.74 1.71 45.99 3.18
3104 3325 6.599244 AGATGTCTGAGACAAAACTGTTTGAA 59.401 34.615 20.26 0.00 45.96 2.69
3105 3326 6.037500 CAGATGTCTGAGACAAAACTGTTTGA 59.962 38.462 20.26 0.00 45.96 2.69
3106 3327 6.197276 CAGATGTCTGAGACAAAACTGTTTG 58.803 40.000 20.26 3.69 45.96 2.93
3107 3328 5.220931 GCAGATGTCTGAGACAAAACTGTTT 60.221 40.000 29.17 12.81 45.96 2.83
3108 3329 4.274459 GCAGATGTCTGAGACAAAACTGTT 59.726 41.667 29.17 13.38 45.96 3.16
3109 3330 3.812053 GCAGATGTCTGAGACAAAACTGT 59.188 43.478 29.17 13.94 45.96 3.55
3110 3331 3.811497 TGCAGATGTCTGAGACAAAACTG 59.189 43.478 27.10 27.10 45.96 3.16
3111 3332 4.077300 TGCAGATGTCTGAGACAAAACT 57.923 40.909 20.26 15.37 45.96 2.66
3112 3333 4.818534 TTGCAGATGTCTGAGACAAAAC 57.181 40.909 20.26 13.45 45.96 2.43
3113 3334 6.210796 CAAATTGCAGATGTCTGAGACAAAA 58.789 36.000 20.26 9.46 45.96 2.44
3114 3335 5.765176 CAAATTGCAGATGTCTGAGACAAA 58.235 37.500 20.26 9.20 45.96 2.83
3115 3336 4.320714 GCAAATTGCAGATGTCTGAGACAA 60.321 41.667 20.26 1.75 43.78 3.18
3116 3337 3.189910 GCAAATTGCAGATGTCTGAGACA 59.810 43.478 18.64 18.64 46.59 3.41
3117 3338 3.756069 GCAAATTGCAGATGTCTGAGAC 58.244 45.455 13.73 5.47 46.59 3.36
3147 3368 4.766373 CCAGGTTTATATGCACATATGGCA 59.234 41.667 17.54 17.54 46.66 4.92
3148 3369 4.158394 CCCAGGTTTATATGCACATATGGC 59.842 45.833 12.41 8.32 35.71 4.40
3149 3370 5.569355 TCCCAGGTTTATATGCACATATGG 58.431 41.667 12.41 6.18 35.71 2.74
3150 3371 7.707624 ATTCCCAGGTTTATATGCACATATG 57.292 36.000 12.41 0.00 35.71 1.78
3151 3372 8.614814 ACTATTCCCAGGTTTATATGCACATAT 58.385 33.333 8.16 8.16 37.69 1.78
3152 3373 7.984475 ACTATTCCCAGGTTTATATGCACATA 58.016 34.615 0.00 0.00 0.00 2.29
3153 3374 6.852404 ACTATTCCCAGGTTTATATGCACAT 58.148 36.000 0.00 0.00 0.00 3.21
3154 3375 6.260700 ACTATTCCCAGGTTTATATGCACA 57.739 37.500 0.00 0.00 0.00 4.57
3155 3376 7.068226 ACAAACTATTCCCAGGTTTATATGCAC 59.932 37.037 0.00 0.00 32.80 4.57
3156 3377 7.122715 ACAAACTATTCCCAGGTTTATATGCA 58.877 34.615 0.00 0.00 32.80 3.96
3157 3378 7.582667 ACAAACTATTCCCAGGTTTATATGC 57.417 36.000 0.00 0.00 32.80 3.14
3240 3461 5.543507 TGTACCATTTGCAATCTGGTTTT 57.456 34.783 28.91 14.16 40.34 2.43
3327 3548 5.242434 AGTTTGAAACTTTGGGTTCAAACC 58.758 37.500 31.15 20.76 44.74 3.27
3389 3611 1.487558 ACGTACAGGTCAAGTTTGGGT 59.512 47.619 0.00 0.00 0.00 4.51
3410 3632 2.911120 TCATGCGTTTCGTAGTTTTGC 58.089 42.857 0.00 0.00 0.00 3.68
3435 3678 1.153901 GCTAGCCGCTGTTCGTACA 60.154 57.895 2.29 0.00 36.19 2.90
3559 3854 1.942657 CACATATCCGGCAAGGTCTTG 59.057 52.381 0.00 6.36 43.14 3.02
3560 3855 1.747206 GCACATATCCGGCAAGGTCTT 60.747 52.381 0.00 0.00 41.99 3.01
3561 3856 0.179045 GCACATATCCGGCAAGGTCT 60.179 55.000 0.00 0.00 41.99 3.85
3562 3857 0.463654 TGCACATATCCGGCAAGGTC 60.464 55.000 0.00 0.00 41.99 3.85
3563 3858 0.034574 TTGCACATATCCGGCAAGGT 60.035 50.000 0.00 0.00 42.12 3.50
3564 3859 2.792500 TTGCACATATCCGGCAAGG 58.208 52.632 0.00 0.00 42.12 3.61
3566 3861 1.378531 GTCTTGCACATATCCGGCAA 58.621 50.000 0.00 0.00 44.50 4.52
3567 3862 0.463654 GGTCTTGCACATATCCGGCA 60.464 55.000 0.00 0.00 35.41 5.69
3568 3863 1.166531 GGGTCTTGCACATATCCGGC 61.167 60.000 0.00 0.00 0.00 6.13
3569 3864 0.469917 AGGGTCTTGCACATATCCGG 59.530 55.000 0.00 0.00 0.00 5.14
3570 3865 2.332063 AAGGGTCTTGCACATATCCG 57.668 50.000 0.00 0.00 0.00 4.18
3571 3866 2.689983 CCAAAGGGTCTTGCACATATCC 59.310 50.000 0.00 0.00 0.00 2.59
3572 3867 2.099756 GCCAAAGGGTCTTGCACATATC 59.900 50.000 0.00 0.00 36.17 1.63
3573 3868 2.102578 GCCAAAGGGTCTTGCACATAT 58.897 47.619 0.00 0.00 36.17 1.78
3574 3869 1.202989 TGCCAAAGGGTCTTGCACATA 60.203 47.619 0.00 0.00 36.17 2.29
3575 3870 0.469705 TGCCAAAGGGTCTTGCACAT 60.470 50.000 0.00 0.00 36.17 3.21
3576 3871 1.076412 TGCCAAAGGGTCTTGCACA 60.076 52.632 0.00 0.00 36.17 4.57
3577 3872 0.823356 TCTGCCAAAGGGTCTTGCAC 60.823 55.000 0.00 0.00 36.17 4.57
3757 4091 0.106708 ACATGAGTGTGCGTTCACCT 59.893 50.000 0.00 0.00 42.46 4.00


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

AutoCloner maintained by Alex Coulton.