Multiple sequence alignment - TraesCS3B01G484700

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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 TraesCS3B01G484700 chr3B 100.000 3652 0 0 1 3652 731126418 731130069 0.000000e+00 6745
1 TraesCS3B01G484700 chr3B 97.878 3016 51 3 626 3640 681202908 681199905 0.000000e+00 5203
2 TraesCS3B01G484700 chr3B 90.365 384 17 12 626 1004 731133878 731133510 1.520000e-133 486
3 TraesCS3B01G484700 chr3B 90.476 231 22 0 334 564 731134714 731134484 4.580000e-79 305
4 TraesCS3B01G484700 chr7B 98.543 2608 35 2 626 3233 554160477 554163081 0.000000e+00 4602
5 TraesCS3B01G484700 chr7B 98.010 603 11 1 3051 3652 554163425 554164027 0.000000e+00 1046
6 TraesCS3B01G484700 chr5A 98.084 2609 37 3 626 3233 346306298 346308894 0.000000e+00 4529
7 TraesCS3B01G484700 chr5A 94.729 645 30 4 3010 3652 346308720 346309362 0.000000e+00 1000
8 TraesCS3B01G484700 chr5A 91.781 292 24 0 335 626 669735946 669735655 1.220000e-109 407
9 TraesCS3B01G484700 chr5A 90.870 230 21 0 335 564 669734600 669734829 3.540000e-80 309
10 TraesCS3B01G484700 chr4B 98.084 2609 37 3 626 3233 139742625 139745221 0.000000e+00 4529
11 TraesCS3B01G484700 chr4B 97.826 2576 55 1 626 3201 2598691 2601265 0.000000e+00 4446
12 TraesCS3B01G484700 chr4B 94.419 645 32 4 3010 3652 139745047 139745689 0.000000e+00 989
13 TraesCS3B01G484700 chr4B 85.861 389 36 14 626 1004 147353293 147353672 2.640000e-106 396
14 TraesCS3B01G484700 chr4B 89.224 232 24 1 334 564 94794271 94794040 4.610000e-74 289
15 TraesCS3B01G484700 chr3A 97.931 2610 41 5 625 3233 199412058 199414655 0.000000e+00 4508
16 TraesCS3B01G484700 chr3A 94.237 642 33 4 3010 3649 199414481 199415120 0.000000e+00 977
17 TraesCS3B01G484700 chr3A 87.240 337 21 9 1 328 688595342 688595665 7.450000e-97 364
18 TraesCS3B01G484700 chr1A 97.984 2579 39 3 626 3203 63763699 63761133 0.000000e+00 4462
19 TraesCS3B01G484700 chr1A 95.302 596 25 3 3059 3652 320477390 320476796 0.000000e+00 942
20 TraesCS3B01G484700 chr1A 89.844 384 19 12 626 1004 320467920 320468288 3.300000e-130 475
21 TraesCS3B01G484700 chr1B 98.051 2566 37 3 626 3190 167930125 167927572 0.000000e+00 4449
22 TraesCS3B01G484700 chr1B 95.310 597 24 4 3059 3652 167927752 167927157 0.000000e+00 944
23 TraesCS3B01G484700 chr1B 87.838 370 30 9 626 990 676747589 676747948 1.570000e-113 420
24 TraesCS3B01G484700 chr2A 97.543 2401 46 3 623 3022 672536850 672539238 0.000000e+00 4095
25 TraesCS3B01G484700 chr2A 89.565 230 24 0 335 564 11810146 11809917 3.570000e-75 292
26 TraesCS3B01G484700 chr5B 95.638 596 23 3 3059 3652 56908667 56909261 0.000000e+00 953
27 TraesCS3B01G484700 chr4A 95.638 596 23 3 3059 3652 683249668 683249074 0.000000e+00 953
28 TraesCS3B01G484700 chrUn 89.583 384 20 12 626 1004 309589310 309589678 1.540000e-128 470
29 TraesCS3B01G484700 chrUn 89.583 384 20 12 626 1004 361599038 361598670 1.540000e-128 470
30 TraesCS3B01G484700 chr2B 86.735 392 33 17 626 1004 679642411 679642026 5.640000e-113 418
31 TraesCS3B01G484700 chr2B 92.123 292 22 1 335 626 11405976 11406266 9.440000e-111 411
32 TraesCS3B01G484700 chr3D 90.301 299 24 2 1 298 551428615 551428321 1.590000e-103 387
33 TraesCS3B01G484700 chr3D 81.818 297 13 5 32 328 551370258 551370513 1.030000e-50 211
34 TraesCS3B01G484700 chr6D 90.301 299 21 6 334 626 13852778 13852482 5.720000e-103 385
35 TraesCS3B01G484700 chr5D 89.706 272 24 4 338 606 519216955 519217225 9.710000e-91 344
36 TraesCS3B01G484700 chr1D 92.174 230 17 1 335 564 62694098 62694326 1.260000e-84 324


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 TraesCS3B01G484700 chr3B 731126418 731130069 3651 False 6745.0 6745 100.0000 1 3652 1 chr3B.!!$F1 3651
1 TraesCS3B01G484700 chr3B 681199905 681202908 3003 True 5203.0 5203 97.8780 626 3640 1 chr3B.!!$R1 3014
2 TraesCS3B01G484700 chr3B 731133510 731134714 1204 True 395.5 486 90.4205 334 1004 2 chr3B.!!$R2 670
3 TraesCS3B01G484700 chr7B 554160477 554164027 3550 False 2824.0 4602 98.2765 626 3652 2 chr7B.!!$F1 3026
4 TraesCS3B01G484700 chr5A 346306298 346309362 3064 False 2764.5 4529 96.4065 626 3652 2 chr5A.!!$F2 3026
5 TraesCS3B01G484700 chr4B 2598691 2601265 2574 False 4446.0 4446 97.8260 626 3201 1 chr4B.!!$F1 2575
6 TraesCS3B01G484700 chr4B 139742625 139745689 3064 False 2759.0 4529 96.2515 626 3652 2 chr4B.!!$F3 3026
7 TraesCS3B01G484700 chr3A 199412058 199415120 3062 False 2742.5 4508 96.0840 625 3649 2 chr3A.!!$F2 3024
8 TraesCS3B01G484700 chr1A 63761133 63763699 2566 True 4462.0 4462 97.9840 626 3203 1 chr1A.!!$R1 2577
9 TraesCS3B01G484700 chr1A 320476796 320477390 594 True 942.0 942 95.3020 3059 3652 1 chr1A.!!$R2 593
10 TraesCS3B01G484700 chr1B 167927157 167930125 2968 True 2696.5 4449 96.6805 626 3652 2 chr1B.!!$R1 3026
11 TraesCS3B01G484700 chr2A 672536850 672539238 2388 False 4095.0 4095 97.5430 623 3022 1 chr2A.!!$F1 2399
12 TraesCS3B01G484700 chr5B 56908667 56909261 594 False 953.0 953 95.6380 3059 3652 1 chr5B.!!$F1 593
13 TraesCS3B01G484700 chr4A 683249074 683249668 594 True 953.0 953 95.6380 3059 3652 1 chr4A.!!$R1 593

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
35 36 0.032130 GCGCTACCGATCCATCTGAA 59.968 55.0 0.00 0.00 36.29 3.02 F
221 222 0.182775 ATGGGAGCCGGTTATCCAAC 59.817 55.0 19.84 7.86 37.33 3.77 F
224 225 0.252197 GGAGCCGGTTATCCAACACT 59.748 55.0 15.18 0.00 36.29 3.55 F
1233 1798 0.318120 ACTTGGATTTTGCTTGGGCG 59.682 50.0 0.00 0.00 42.25 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1024 1589 0.321996 GGGAGGCTTGAGTTCTCGTT 59.678 55.000 0.0 0.0 0.0 3.85 R
1279 1844 1.126890 CGCACAGCACTATCAGATCG 58.873 55.000 0.0 0.0 0.0 3.69 R
2423 2988 3.277715 CTCCAAATTCTCTTGAGCCTCC 58.722 50.000 0.0 0.0 0.0 4.30 R
3375 3991 2.042162 AGTGAATGCCTGGAATGGACTT 59.958 45.455 0.0 0.0 0.0 3.01 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
22 23 3.188786 CACTTGCTCCGGCGCTAC 61.189 66.667 18.73 0.00 42.25 3.58
23 24 4.452733 ACTTGCTCCGGCGCTACC 62.453 66.667 18.73 0.00 42.25 3.18
32 33 3.052081 GGCGCTACCGATCCATCT 58.948 61.111 7.64 0.00 36.29 2.90
33 34 1.373497 GGCGCTACCGATCCATCTG 60.373 63.158 7.64 0.00 36.29 2.90
34 35 1.660355 GCGCTACCGATCCATCTGA 59.340 57.895 0.00 0.00 36.29 3.27
35 36 0.032130 GCGCTACCGATCCATCTGAA 59.968 55.000 0.00 0.00 36.29 3.02
36 37 1.772182 CGCTACCGATCCATCTGAAC 58.228 55.000 0.00 0.00 36.29 3.18
37 38 1.067060 CGCTACCGATCCATCTGAACA 59.933 52.381 0.00 0.00 36.29 3.18
38 39 2.481276 CGCTACCGATCCATCTGAACAA 60.481 50.000 0.00 0.00 36.29 2.83
39 40 3.531538 GCTACCGATCCATCTGAACAAA 58.468 45.455 0.00 0.00 0.00 2.83
40 41 3.938963 GCTACCGATCCATCTGAACAAAA 59.061 43.478 0.00 0.00 0.00 2.44
41 42 4.201822 GCTACCGATCCATCTGAACAAAAC 60.202 45.833 0.00 0.00 0.00 2.43
42 43 3.081804 ACCGATCCATCTGAACAAAACC 58.918 45.455 0.00 0.00 0.00 3.27
43 44 3.244911 ACCGATCCATCTGAACAAAACCT 60.245 43.478 0.00 0.00 0.00 3.50
44 45 3.758554 CCGATCCATCTGAACAAAACCTT 59.241 43.478 0.00 0.00 0.00 3.50
45 46 4.218417 CCGATCCATCTGAACAAAACCTTT 59.782 41.667 0.00 0.00 0.00 3.11
46 47 5.156355 CGATCCATCTGAACAAAACCTTTG 58.844 41.667 0.00 0.00 0.00 2.77
47 48 5.048782 CGATCCATCTGAACAAAACCTTTGA 60.049 40.000 6.15 0.00 0.00 2.69
48 49 5.514274 TCCATCTGAACAAAACCTTTGAC 57.486 39.130 6.15 1.42 0.00 3.18
49 50 4.340950 TCCATCTGAACAAAACCTTTGACC 59.659 41.667 6.15 0.00 0.00 4.02
50 51 4.342092 CCATCTGAACAAAACCTTTGACCT 59.658 41.667 6.15 0.00 0.00 3.85
51 52 4.981806 TCTGAACAAAACCTTTGACCTG 57.018 40.909 6.15 2.49 0.00 4.00
52 53 3.130340 TCTGAACAAAACCTTTGACCTGC 59.870 43.478 6.15 0.00 0.00 4.85
53 54 2.167487 TGAACAAAACCTTTGACCTGCC 59.833 45.455 6.15 0.00 0.00 4.85
54 55 1.119684 ACAAAACCTTTGACCTGCCC 58.880 50.000 6.15 0.00 0.00 5.36
55 56 0.392706 CAAAACCTTTGACCTGCCCC 59.607 55.000 0.00 0.00 0.00 5.80
56 57 1.112916 AAAACCTTTGACCTGCCCCG 61.113 55.000 0.00 0.00 0.00 5.73
57 58 2.002018 AAACCTTTGACCTGCCCCGA 62.002 55.000 0.00 0.00 0.00 5.14
58 59 1.789576 AACCTTTGACCTGCCCCGAT 61.790 55.000 0.00 0.00 0.00 4.18
59 60 0.912487 ACCTTTGACCTGCCCCGATA 60.912 55.000 0.00 0.00 0.00 2.92
60 61 0.463833 CCTTTGACCTGCCCCGATAC 60.464 60.000 0.00 0.00 0.00 2.24
61 62 0.810031 CTTTGACCTGCCCCGATACG 60.810 60.000 0.00 0.00 0.00 3.06
62 63 1.546589 TTTGACCTGCCCCGATACGT 61.547 55.000 0.00 0.00 0.00 3.57
63 64 2.106332 GACCTGCCCCGATACGTG 59.894 66.667 0.00 0.00 0.00 4.49
64 65 4.157120 ACCTGCCCCGATACGTGC 62.157 66.667 0.00 0.00 0.00 5.34
65 66 4.910585 CCTGCCCCGATACGTGCC 62.911 72.222 0.00 0.00 0.00 5.01
66 67 4.155733 CTGCCCCGATACGTGCCA 62.156 66.667 0.00 0.00 0.00 4.92
67 68 4.460683 TGCCCCGATACGTGCCAC 62.461 66.667 0.00 0.00 0.00 5.01
114 115 4.950744 GCACTTGCCATGTCACAC 57.049 55.556 0.00 0.00 34.31 3.82
115 116 1.081906 GCACTTGCCATGTCACACG 60.082 57.895 0.00 0.00 34.31 4.49
116 117 1.081906 CACTTGCCATGTCACACGC 60.082 57.895 0.00 0.00 0.00 5.34
117 118 2.174107 CTTGCCATGTCACACGCG 59.826 61.111 3.53 3.53 0.00 6.01
118 119 3.933900 CTTGCCATGTCACACGCGC 62.934 63.158 5.73 0.00 0.00 6.86
119 120 4.986645 TGCCATGTCACACGCGCT 62.987 61.111 5.73 0.00 0.00 5.92
120 121 3.726517 GCCATGTCACACGCGCTT 61.727 61.111 5.73 0.00 0.00 4.68
121 122 2.174107 CCATGTCACACGCGCTTG 59.826 61.111 12.94 12.94 0.00 4.01
122 123 2.174107 CATGTCACACGCGCTTGG 59.826 61.111 18.82 7.38 0.00 3.61
123 124 3.049674 ATGTCACACGCGCTTGGG 61.050 61.111 18.82 14.93 0.00 4.12
132 133 4.715523 GCGCTTGGGGCTGGTACA 62.716 66.667 0.00 0.00 38.48 2.90
148 149 3.572682 TGGTACAGGTATCCAGATTAGCG 59.427 47.826 0.00 0.00 0.00 4.26
149 150 2.821991 ACAGGTATCCAGATTAGCGC 57.178 50.000 0.00 0.00 0.00 5.92
150 151 2.039418 ACAGGTATCCAGATTAGCGCA 58.961 47.619 11.47 0.00 0.00 6.09
151 152 2.634940 ACAGGTATCCAGATTAGCGCAT 59.365 45.455 11.47 0.00 0.00 4.73
152 153 3.257393 CAGGTATCCAGATTAGCGCATC 58.743 50.000 11.47 4.62 0.00 3.91
153 154 3.056250 CAGGTATCCAGATTAGCGCATCT 60.056 47.826 11.47 7.39 33.44 2.90
154 155 3.580458 AGGTATCCAGATTAGCGCATCTT 59.420 43.478 11.47 0.00 30.50 2.40
155 156 3.929610 GGTATCCAGATTAGCGCATCTTC 59.070 47.826 11.47 0.23 30.50 2.87
156 157 3.758755 ATCCAGATTAGCGCATCTTCA 57.241 42.857 11.47 0.00 30.50 3.02
157 158 3.541996 TCCAGATTAGCGCATCTTCAA 57.458 42.857 11.47 0.00 30.50 2.69
158 159 4.077300 TCCAGATTAGCGCATCTTCAAT 57.923 40.909 11.47 0.00 30.50 2.57
159 160 3.811497 TCCAGATTAGCGCATCTTCAATG 59.189 43.478 11.47 0.00 30.50 2.82
160 161 3.562973 CCAGATTAGCGCATCTTCAATGT 59.437 43.478 11.47 0.00 30.50 2.71
161 162 4.319333 CCAGATTAGCGCATCTTCAATGTC 60.319 45.833 11.47 0.00 30.50 3.06
162 163 4.510711 CAGATTAGCGCATCTTCAATGTCT 59.489 41.667 11.47 0.00 30.50 3.41
163 164 5.693555 CAGATTAGCGCATCTTCAATGTCTA 59.306 40.000 11.47 0.00 30.50 2.59
164 165 5.925397 AGATTAGCGCATCTTCAATGTCTAG 59.075 40.000 11.47 0.00 28.19 2.43
165 166 2.208431 AGCGCATCTTCAATGTCTAGC 58.792 47.619 11.47 0.00 0.00 3.42
166 167 1.262683 GCGCATCTTCAATGTCTAGCC 59.737 52.381 0.30 0.00 0.00 3.93
167 168 2.831333 CGCATCTTCAATGTCTAGCCT 58.169 47.619 0.00 0.00 0.00 4.58
168 169 3.201290 CGCATCTTCAATGTCTAGCCTT 58.799 45.455 0.00 0.00 0.00 4.35
169 170 4.371786 CGCATCTTCAATGTCTAGCCTTA 58.628 43.478 0.00 0.00 0.00 2.69
170 171 4.811024 CGCATCTTCAATGTCTAGCCTTAA 59.189 41.667 0.00 0.00 0.00 1.85
171 172 5.294306 CGCATCTTCAATGTCTAGCCTTAAA 59.706 40.000 0.00 0.00 0.00 1.52
172 173 6.183360 CGCATCTTCAATGTCTAGCCTTAAAA 60.183 38.462 0.00 0.00 0.00 1.52
173 174 7.538575 GCATCTTCAATGTCTAGCCTTAAAAA 58.461 34.615 0.00 0.00 0.00 1.94
174 175 7.699812 GCATCTTCAATGTCTAGCCTTAAAAAG 59.300 37.037 0.00 0.00 0.00 2.27
198 199 6.287107 GACATAATATTTGTCCACAGACCG 57.713 41.667 14.69 0.00 42.81 4.79
199 200 5.741011 ACATAATATTTGTCCACAGACCGT 58.259 37.500 0.00 0.00 42.81 4.83
200 201 6.880484 ACATAATATTTGTCCACAGACCGTA 58.120 36.000 0.00 0.00 42.81 4.02
201 202 7.506114 ACATAATATTTGTCCACAGACCGTAT 58.494 34.615 0.00 0.00 42.81 3.06
202 203 8.644216 ACATAATATTTGTCCACAGACCGTATA 58.356 33.333 0.00 0.00 42.81 1.47
203 204 9.653287 CATAATATTTGTCCACAGACCGTATAT 57.347 33.333 0.00 0.00 42.81 0.86
204 205 7.962964 AATATTTGTCCACAGACCGTATATG 57.037 36.000 0.00 0.00 42.81 1.78
205 206 3.812156 TTGTCCACAGACCGTATATGG 57.188 47.619 9.60 9.60 42.81 2.74
206 207 2.036387 TGTCCACAGACCGTATATGGG 58.964 52.381 15.56 3.70 42.81 4.00
207 208 2.313317 GTCCACAGACCGTATATGGGA 58.687 52.381 15.56 0.00 37.00 4.37
208 209 2.296471 GTCCACAGACCGTATATGGGAG 59.704 54.545 15.56 6.94 37.00 4.30
209 210 1.000955 CCACAGACCGTATATGGGAGC 59.999 57.143 15.56 4.54 0.00 4.70
210 211 1.000955 CACAGACCGTATATGGGAGCC 59.999 57.143 15.56 2.03 0.00 4.70
211 212 0.243907 CAGACCGTATATGGGAGCCG 59.756 60.000 15.56 0.00 0.00 5.52
212 213 0.898789 AGACCGTATATGGGAGCCGG 60.899 60.000 15.56 0.00 44.06 6.13
213 214 1.152398 ACCGTATATGGGAGCCGGT 60.152 57.895 15.56 5.76 46.31 5.28
214 215 2.055299 CCGTATATGGGAGCCGGTT 58.945 57.895 1.90 0.00 34.10 4.44
215 216 1.259609 CCGTATATGGGAGCCGGTTA 58.740 55.000 1.90 0.00 34.10 2.85
216 217 1.829222 CCGTATATGGGAGCCGGTTAT 59.171 52.381 1.90 0.00 34.10 1.89
217 218 2.159142 CCGTATATGGGAGCCGGTTATC 60.159 54.545 1.90 0.00 34.10 1.75
218 219 2.159142 CGTATATGGGAGCCGGTTATCC 60.159 54.545 1.90 8.70 34.64 2.59
219 220 2.038863 ATATGGGAGCCGGTTATCCA 57.961 50.000 19.84 16.95 37.33 3.41
220 221 1.809133 TATGGGAGCCGGTTATCCAA 58.191 50.000 19.84 12.09 37.33 3.53
221 222 0.182775 ATGGGAGCCGGTTATCCAAC 59.817 55.000 19.84 7.86 37.33 3.77
222 223 1.202099 TGGGAGCCGGTTATCCAACA 61.202 55.000 19.84 9.87 37.33 3.33
223 224 0.746923 GGGAGCCGGTTATCCAACAC 60.747 60.000 19.84 3.68 37.33 3.32
224 225 0.252197 GGAGCCGGTTATCCAACACT 59.748 55.000 15.18 0.00 36.29 3.55
225 226 1.369625 GAGCCGGTTATCCAACACTG 58.630 55.000 1.90 0.00 36.29 3.66
226 227 0.690762 AGCCGGTTATCCAACACTGT 59.309 50.000 1.90 0.00 36.29 3.55
227 228 1.084289 GCCGGTTATCCAACACTGTC 58.916 55.000 1.90 0.00 36.29 3.51
228 229 1.734163 CCGGTTATCCAACACTGTCC 58.266 55.000 0.00 0.00 36.29 4.02
229 230 1.677820 CCGGTTATCCAACACTGTCCC 60.678 57.143 0.00 0.00 36.29 4.46
230 231 1.677820 CGGTTATCCAACACTGTCCCC 60.678 57.143 0.00 0.00 36.29 4.81
231 232 1.353022 GGTTATCCAACACTGTCCCCA 59.647 52.381 0.00 0.00 36.29 4.96
232 233 2.224917 GGTTATCCAACACTGTCCCCAA 60.225 50.000 0.00 0.00 36.29 4.12
233 234 3.492337 GTTATCCAACACTGTCCCCAAA 58.508 45.455 0.00 0.00 34.60 3.28
234 235 1.995376 ATCCAACACTGTCCCCAAAC 58.005 50.000 0.00 0.00 0.00 2.93
235 236 0.626382 TCCAACACTGTCCCCAAACA 59.374 50.000 0.00 0.00 0.00 2.83
236 237 1.216678 TCCAACACTGTCCCCAAACAT 59.783 47.619 0.00 0.00 0.00 2.71
237 238 1.613437 CCAACACTGTCCCCAAACATC 59.387 52.381 0.00 0.00 0.00 3.06
238 239 2.586425 CAACACTGTCCCCAAACATCT 58.414 47.619 0.00 0.00 0.00 2.90
239 240 2.554032 CAACACTGTCCCCAAACATCTC 59.446 50.000 0.00 0.00 0.00 2.75
240 241 1.073923 ACACTGTCCCCAAACATCTCC 59.926 52.381 0.00 0.00 0.00 3.71
241 242 1.073763 CACTGTCCCCAAACATCTCCA 59.926 52.381 0.00 0.00 0.00 3.86
242 243 1.780309 ACTGTCCCCAAACATCTCCAA 59.220 47.619 0.00 0.00 0.00 3.53
243 244 2.379907 ACTGTCCCCAAACATCTCCAAT 59.620 45.455 0.00 0.00 0.00 3.16
244 245 3.591527 ACTGTCCCCAAACATCTCCAATA 59.408 43.478 0.00 0.00 0.00 1.90
245 246 3.947834 CTGTCCCCAAACATCTCCAATAC 59.052 47.826 0.00 0.00 0.00 1.89
246 247 3.591527 TGTCCCCAAACATCTCCAATACT 59.408 43.478 0.00 0.00 0.00 2.12
247 248 4.785914 TGTCCCCAAACATCTCCAATACTA 59.214 41.667 0.00 0.00 0.00 1.82
248 249 5.251932 TGTCCCCAAACATCTCCAATACTAA 59.748 40.000 0.00 0.00 0.00 2.24
249 250 5.589050 GTCCCCAAACATCTCCAATACTAAC 59.411 44.000 0.00 0.00 0.00 2.34
250 251 4.887655 CCCCAAACATCTCCAATACTAACC 59.112 45.833 0.00 0.00 0.00 2.85
251 252 5.340027 CCCCAAACATCTCCAATACTAACCT 60.340 44.000 0.00 0.00 0.00 3.50
252 253 6.126594 CCCCAAACATCTCCAATACTAACCTA 60.127 42.308 0.00 0.00 0.00 3.08
253 254 7.343357 CCCAAACATCTCCAATACTAACCTAA 58.657 38.462 0.00 0.00 0.00 2.69
254 255 7.832187 CCCAAACATCTCCAATACTAACCTAAA 59.168 37.037 0.00 0.00 0.00 1.85
255 256 9.238368 CCAAACATCTCCAATACTAACCTAAAA 57.762 33.333 0.00 0.00 0.00 1.52
263 264 8.732746 TCCAATACTAACCTAAAAAGATCAGC 57.267 34.615 0.00 0.00 0.00 4.26
264 265 7.773690 TCCAATACTAACCTAAAAAGATCAGCC 59.226 37.037 0.00 0.00 0.00 4.85
265 266 7.556275 CCAATACTAACCTAAAAAGATCAGCCA 59.444 37.037 0.00 0.00 0.00 4.75
266 267 8.956426 CAATACTAACCTAAAAAGATCAGCCAA 58.044 33.333 0.00 0.00 0.00 4.52
267 268 6.819397 ACTAACCTAAAAAGATCAGCCAAC 57.181 37.500 0.00 0.00 0.00 3.77
268 269 6.303839 ACTAACCTAAAAAGATCAGCCAACA 58.696 36.000 0.00 0.00 0.00 3.33
269 270 6.948309 ACTAACCTAAAAAGATCAGCCAACAT 59.052 34.615 0.00 0.00 0.00 2.71
270 271 8.107095 ACTAACCTAAAAAGATCAGCCAACATA 58.893 33.333 0.00 0.00 0.00 2.29
271 272 7.961326 AACCTAAAAAGATCAGCCAACATAT 57.039 32.000 0.00 0.00 0.00 1.78
272 273 7.961326 ACCTAAAAAGATCAGCCAACATATT 57.039 32.000 0.00 0.00 0.00 1.28
273 274 8.000780 ACCTAAAAAGATCAGCCAACATATTC 57.999 34.615 0.00 0.00 0.00 1.75
274 275 7.134815 CCTAAAAAGATCAGCCAACATATTCG 58.865 38.462 0.00 0.00 0.00 3.34
275 276 6.515272 AAAAAGATCAGCCAACATATTCGT 57.485 33.333 0.00 0.00 0.00 3.85
276 277 7.624360 AAAAAGATCAGCCAACATATTCGTA 57.376 32.000 0.00 0.00 0.00 3.43
277 278 7.807977 AAAAGATCAGCCAACATATTCGTAT 57.192 32.000 0.00 0.00 0.00 3.06
278 279 8.902540 AAAAGATCAGCCAACATATTCGTATA 57.097 30.769 0.00 0.00 0.00 1.47
279 280 8.539770 AAAGATCAGCCAACATATTCGTATAG 57.460 34.615 0.00 0.00 0.00 1.31
280 281 7.233389 AGATCAGCCAACATATTCGTATAGT 57.767 36.000 0.00 0.00 0.00 2.12
281 282 7.671302 AGATCAGCCAACATATTCGTATAGTT 58.329 34.615 0.00 0.00 0.00 2.24
282 283 8.150945 AGATCAGCCAACATATTCGTATAGTTT 58.849 33.333 0.00 0.00 0.00 2.66
283 284 9.419297 GATCAGCCAACATATTCGTATAGTTTA 57.581 33.333 0.00 0.00 0.00 2.01
284 285 8.583810 TCAGCCAACATATTCGTATAGTTTAC 57.416 34.615 0.00 0.00 0.00 2.01
285 286 8.198778 TCAGCCAACATATTCGTATAGTTTACA 58.801 33.333 0.00 0.00 0.00 2.41
286 287 8.988934 CAGCCAACATATTCGTATAGTTTACAT 58.011 33.333 0.00 0.00 0.00 2.29
287 288 9.555727 AGCCAACATATTCGTATAGTTTACATT 57.444 29.630 0.00 0.00 0.00 2.71
288 289 9.594038 GCCAACATATTCGTATAGTTTACATTG 57.406 33.333 0.00 0.00 0.00 2.82
313 314 9.872757 TGAAGAAAAATAGTAACGAAACATGAC 57.127 29.630 0.00 0.00 0.00 3.06
315 316 9.878599 AAGAAAAATAGTAACGAAACATGACTG 57.121 29.630 0.00 0.00 0.00 3.51
316 317 8.504005 AGAAAAATAGTAACGAAACATGACTGG 58.496 33.333 0.00 0.00 0.00 4.00
317 318 6.737254 AAATAGTAACGAAACATGACTGGG 57.263 37.500 0.00 0.00 0.00 4.45
318 319 3.764237 AGTAACGAAACATGACTGGGT 57.236 42.857 0.00 0.00 0.00 4.51
319 320 3.399330 AGTAACGAAACATGACTGGGTG 58.601 45.455 0.00 0.00 0.00 4.61
320 321 1.604604 AACGAAACATGACTGGGTGG 58.395 50.000 0.00 0.00 0.00 4.61
321 322 0.762418 ACGAAACATGACTGGGTGGA 59.238 50.000 0.00 0.00 0.00 4.02
322 323 1.351017 ACGAAACATGACTGGGTGGAT 59.649 47.619 0.00 0.00 0.00 3.41
323 324 2.009774 CGAAACATGACTGGGTGGATC 58.990 52.381 0.00 0.00 0.00 3.36
324 325 2.615240 CGAAACATGACTGGGTGGATCA 60.615 50.000 0.00 0.00 0.00 2.92
325 326 2.795231 AACATGACTGGGTGGATCAG 57.205 50.000 0.00 0.00 38.16 2.90
326 327 1.956869 ACATGACTGGGTGGATCAGA 58.043 50.000 0.00 0.00 36.22 3.27
327 328 2.485659 ACATGACTGGGTGGATCAGAT 58.514 47.619 0.00 0.00 36.22 2.90
328 329 2.848694 ACATGACTGGGTGGATCAGATT 59.151 45.455 0.00 0.00 36.22 2.40
329 330 4.040047 ACATGACTGGGTGGATCAGATTA 58.960 43.478 0.00 0.00 36.22 1.75
330 331 4.662179 ACATGACTGGGTGGATCAGATTAT 59.338 41.667 0.00 0.00 36.22 1.28
331 332 4.694760 TGACTGGGTGGATCAGATTATG 57.305 45.455 0.00 0.00 36.22 1.90
332 333 3.392285 TGACTGGGTGGATCAGATTATGG 59.608 47.826 0.00 0.00 36.22 2.74
349 350 8.190784 CAGATTATGGGGAGTATTTGACAAAAC 58.809 37.037 4.41 5.14 0.00 2.43
364 365 5.885881 TGACAAAACACTACCACATTTCAC 58.114 37.500 0.00 0.00 0.00 3.18
369 370 3.128349 ACACTACCACATTTCACGTCAC 58.872 45.455 0.00 0.00 0.00 3.67
370 371 2.478894 CACTACCACATTTCACGTCACC 59.521 50.000 0.00 0.00 0.00 4.02
375 376 0.942410 ACATTTCACGTCACCGTCCG 60.942 55.000 0.00 0.00 46.28 4.79
405 406 5.654650 ACTACCACATTTTGAAAAGTGACCA 59.345 36.000 16.38 5.65 39.28 4.02
464 465 4.695455 ACTACCAAATTGAGTTGATGACCG 59.305 41.667 0.00 0.00 0.00 4.79
471 472 7.096230 CCAAATTGAGTTGATGACCGTTTTTAC 60.096 37.037 0.00 0.00 0.00 2.01
485 486 6.794374 ACCGTTTTTACGATTTTAAACCTGT 58.206 32.000 0.00 0.00 34.64 4.00
526 527 4.056125 CCAGAGCTGACGTGGCGA 62.056 66.667 0.00 0.00 34.52 5.54
527 528 2.807045 CAGAGCTGACGTGGCGAC 60.807 66.667 0.00 0.00 34.52 5.19
533 534 1.853319 CTGACGTGGCGACAAAGTC 59.147 57.895 18.21 18.21 46.06 3.01
538 539 0.655733 CGTGGCGACAAAGTCAACTT 59.344 50.000 0.00 0.00 46.06 2.66
557 558 9.493206 GTCAACTTCGTTTATTTTGACTGTTAA 57.507 29.630 5.69 0.00 41.78 2.01
558 559 9.710979 TCAACTTCGTTTATTTTGACTGTTAAG 57.289 29.630 0.00 0.00 0.00 1.85
564 565 8.885722 TCGTTTATTTTGACTGTTAAGTTGACT 58.114 29.630 0.00 0.00 36.52 3.41
579 589 3.976701 GACTGATGGGGCCCACACG 62.977 68.421 31.54 20.72 35.80 4.49
583 593 3.976701 GATGGGGCCCACACGTCAG 62.977 68.421 31.54 0.00 35.80 3.51
596 606 3.843426 CACGTCAGTGTCAACTTCTTC 57.157 47.619 0.00 0.00 43.15 2.87
597 607 2.540101 CACGTCAGTGTCAACTTCTTCC 59.460 50.000 0.00 0.00 43.15 3.46
598 608 2.431057 ACGTCAGTGTCAACTTCTTCCT 59.569 45.455 0.00 0.00 32.98 3.36
599 609 3.053455 CGTCAGTGTCAACTTCTTCCTC 58.947 50.000 0.00 0.00 32.98 3.71
601 611 3.070302 GTCAGTGTCAACTTCTTCCTCCT 59.930 47.826 0.00 0.00 32.98 3.69
602 612 3.711704 TCAGTGTCAACTTCTTCCTCCTT 59.288 43.478 0.00 0.00 32.98 3.36
603 613 4.061596 CAGTGTCAACTTCTTCCTCCTTC 58.938 47.826 0.00 0.00 32.98 3.46
604 614 3.970640 AGTGTCAACTTCTTCCTCCTTCT 59.029 43.478 0.00 0.00 30.14 2.85
605 615 4.039852 AGTGTCAACTTCTTCCTCCTTCTC 59.960 45.833 0.00 0.00 30.14 2.87
606 616 4.039852 GTGTCAACTTCTTCCTCCTTCTCT 59.960 45.833 0.00 0.00 0.00 3.10
607 617 4.282195 TGTCAACTTCTTCCTCCTTCTCTC 59.718 45.833 0.00 0.00 0.00 3.20
608 618 3.508012 TCAACTTCTTCCTCCTTCTCTCG 59.492 47.826 0.00 0.00 0.00 4.04
609 619 3.443145 ACTTCTTCCTCCTTCTCTCGA 57.557 47.619 0.00 0.00 0.00 4.04
610 620 3.976015 ACTTCTTCCTCCTTCTCTCGAT 58.024 45.455 0.00 0.00 0.00 3.59
611 621 3.699038 ACTTCTTCCTCCTTCTCTCGATG 59.301 47.826 0.00 0.00 0.00 3.84
612 622 3.374042 TCTTCCTCCTTCTCTCGATGT 57.626 47.619 0.00 0.00 0.00 3.06
614 624 1.769026 TCCTCCTTCTCTCGATGTGG 58.231 55.000 0.00 0.00 0.00 4.17
616 626 0.820226 CTCCTTCTCTCGATGTGGCA 59.180 55.000 0.00 0.00 0.00 4.92
617 627 1.411977 CTCCTTCTCTCGATGTGGCAT 59.588 52.381 0.00 0.00 0.00 4.40
618 628 1.833630 TCCTTCTCTCGATGTGGCATT 59.166 47.619 0.00 0.00 0.00 3.56
619 629 2.237143 TCCTTCTCTCGATGTGGCATTT 59.763 45.455 0.00 0.00 0.00 2.32
621 631 3.264947 CTTCTCTCGATGTGGCATTTGA 58.735 45.455 0.00 0.00 0.00 2.69
622 632 3.333029 TCTCTCGATGTGGCATTTGAA 57.667 42.857 0.00 0.00 0.00 2.69
623 633 3.002791 TCTCTCGATGTGGCATTTGAAC 58.997 45.455 0.00 0.00 0.00 3.18
1024 1589 2.238942 TTTTGAAGACGAGAGCAGCA 57.761 45.000 0.00 0.00 0.00 4.41
1196 1761 4.359706 GTTTGATTTGCTTTGTCCTCGTT 58.640 39.130 0.00 0.00 0.00 3.85
1233 1798 0.318120 ACTTGGATTTTGCTTGGGCG 59.682 50.000 0.00 0.00 42.25 6.13
1279 1844 3.557595 CGGATTACAATGGTCTTGAGCTC 59.442 47.826 6.82 6.82 0.00 4.09
1642 2207 7.147724 TGCTTAGTACTCACATTAGCCATTAGT 60.148 37.037 0.00 0.00 0.00 2.24
1651 2216 6.658816 TCACATTAGCCATTAGTTGATGTGTT 59.341 34.615 11.97 0.00 41.96 3.32
2234 2799 4.033358 GTGGATTTCAGTTATCTGCAGTCG 59.967 45.833 14.67 0.00 41.10 4.18
2423 2988 5.892160 TGAAAGAGAAGCAATTGAGGATG 57.108 39.130 10.34 0.00 0.00 3.51
2518 3083 4.503296 GCTAGAGTTGAAGTTCCAGGTTGA 60.503 45.833 0.00 0.00 0.00 3.18
2696 3261 2.224257 GCATTGCAGACCTTTTGGGAAA 60.224 45.455 3.15 0.00 46.08 3.13
2704 3269 3.333680 AGACCTTTTGGGAAAGATGGCTA 59.666 43.478 0.70 0.00 44.03 3.93
2786 3351 4.091509 GTGAACTCTGGCTGTTTATGTACG 59.908 45.833 0.00 0.00 0.00 3.67
2854 3419 7.826744 TGTGCATTTGAACTCCACTATGTAATA 59.173 33.333 0.00 0.00 0.00 0.98
3254 3868 9.487790 CCACCAAAACATAGACAACATAAAAAT 57.512 29.630 0.00 0.00 0.00 1.82
3357 3973 5.129815 ACCATCCAAGCTTGCATAATCAATT 59.870 36.000 21.43 0.00 0.00 2.32
3375 3991 8.985315 AATCAATTACTCCAGCATATCAAGAA 57.015 30.769 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.188786 GTAGCGCCGGAGCAAGTG 61.189 66.667 32.12 0.00 39.83 3.16
6 7 4.452733 GGTAGCGCCGGAGCAAGT 62.453 66.667 32.12 14.36 39.83 3.16
15 16 1.373497 CAGATGGATCGGTAGCGCC 60.373 63.158 9.99 6.74 0.00 6.53
16 17 0.032130 TTCAGATGGATCGGTAGCGC 59.968 55.000 9.99 0.00 0.00 5.92
17 18 1.067060 TGTTCAGATGGATCGGTAGCG 59.933 52.381 8.29 8.29 0.00 4.26
18 19 2.890808 TGTTCAGATGGATCGGTAGC 57.109 50.000 0.00 0.00 0.00 3.58
19 20 4.332819 GGTTTTGTTCAGATGGATCGGTAG 59.667 45.833 0.00 0.00 0.00 3.18
20 21 4.019681 AGGTTTTGTTCAGATGGATCGGTA 60.020 41.667 0.00 0.00 0.00 4.02
21 22 3.081804 GGTTTTGTTCAGATGGATCGGT 58.918 45.455 0.00 0.00 0.00 4.69
22 23 3.347216 AGGTTTTGTTCAGATGGATCGG 58.653 45.455 0.00 0.00 0.00 4.18
23 24 5.048782 TCAAAGGTTTTGTTCAGATGGATCG 60.049 40.000 1.92 0.00 0.00 3.69
24 25 6.152379 GTCAAAGGTTTTGTTCAGATGGATC 58.848 40.000 1.92 0.00 0.00 3.36
25 26 5.011023 GGTCAAAGGTTTTGTTCAGATGGAT 59.989 40.000 1.92 0.00 0.00 3.41
26 27 4.340950 GGTCAAAGGTTTTGTTCAGATGGA 59.659 41.667 1.92 0.00 0.00 3.41
27 28 4.342092 AGGTCAAAGGTTTTGTTCAGATGG 59.658 41.667 1.92 0.00 0.00 3.51
28 29 5.284079 CAGGTCAAAGGTTTTGTTCAGATG 58.716 41.667 1.92 0.00 0.00 2.90
29 30 4.202151 GCAGGTCAAAGGTTTTGTTCAGAT 60.202 41.667 1.92 0.00 0.00 2.90
30 31 3.130340 GCAGGTCAAAGGTTTTGTTCAGA 59.870 43.478 1.92 0.00 0.00 3.27
31 32 3.447742 GCAGGTCAAAGGTTTTGTTCAG 58.552 45.455 1.92 0.00 0.00 3.02
32 33 2.167487 GGCAGGTCAAAGGTTTTGTTCA 59.833 45.455 1.92 0.00 0.00 3.18
33 34 2.483013 GGGCAGGTCAAAGGTTTTGTTC 60.483 50.000 1.92 0.00 0.00 3.18
34 35 1.484653 GGGCAGGTCAAAGGTTTTGTT 59.515 47.619 1.92 0.00 0.00 2.83
35 36 1.119684 GGGCAGGTCAAAGGTTTTGT 58.880 50.000 1.92 0.00 0.00 2.83
36 37 0.392706 GGGGCAGGTCAAAGGTTTTG 59.607 55.000 0.00 0.00 0.00 2.44
37 38 1.112916 CGGGGCAGGTCAAAGGTTTT 61.113 55.000 0.00 0.00 0.00 2.43
38 39 1.530655 CGGGGCAGGTCAAAGGTTT 60.531 57.895 0.00 0.00 0.00 3.27
39 40 1.789576 ATCGGGGCAGGTCAAAGGTT 61.790 55.000 0.00 0.00 0.00 3.50
40 41 0.912487 TATCGGGGCAGGTCAAAGGT 60.912 55.000 0.00 0.00 0.00 3.50
41 42 0.463833 GTATCGGGGCAGGTCAAAGG 60.464 60.000 0.00 0.00 0.00 3.11
42 43 0.810031 CGTATCGGGGCAGGTCAAAG 60.810 60.000 0.00 0.00 0.00 2.77
43 44 1.219664 CGTATCGGGGCAGGTCAAA 59.780 57.895 0.00 0.00 0.00 2.69
44 45 1.985662 ACGTATCGGGGCAGGTCAA 60.986 57.895 0.00 0.00 0.00 3.18
45 46 2.363276 ACGTATCGGGGCAGGTCA 60.363 61.111 0.00 0.00 0.00 4.02
46 47 2.106332 CACGTATCGGGGCAGGTC 59.894 66.667 0.00 0.00 0.00 3.85
47 48 4.157120 GCACGTATCGGGGCAGGT 62.157 66.667 0.00 0.00 33.04 4.00
54 55 4.508128 AGGCGTGGCACGTATCGG 62.508 66.667 36.68 12.45 44.73 4.18
55 56 3.254654 CAGGCGTGGCACGTATCG 61.255 66.667 36.68 21.00 44.73 2.92
56 57 3.564027 GCAGGCGTGGCACGTATC 61.564 66.667 36.68 26.17 44.73 2.24
57 58 3.680620 ATGCAGGCGTGGCACGTAT 62.681 57.895 36.68 24.48 45.23 3.06
58 59 4.386951 ATGCAGGCGTGGCACGTA 62.387 61.111 36.68 20.26 45.23 3.57
97 98 1.081906 CGTGTGACATGGCAAGTGC 60.082 57.895 0.58 0.00 41.14 4.40
98 99 1.081906 GCGTGTGACATGGCAAGTG 60.082 57.895 0.58 0.00 0.00 3.16
99 100 2.606961 CGCGTGTGACATGGCAAGT 61.607 57.895 0.58 0.00 0.00 3.16
100 101 2.174107 CGCGTGTGACATGGCAAG 59.826 61.111 0.58 0.00 0.00 4.01
101 102 4.024143 GCGCGTGTGACATGGCAA 62.024 61.111 0.58 0.00 0.00 4.52
102 103 4.986645 AGCGCGTGTGACATGGCA 62.987 61.111 8.43 0.00 0.00 4.92
103 104 3.726517 AAGCGCGTGTGACATGGC 61.727 61.111 8.43 8.34 0.00 4.40
104 105 2.174107 CAAGCGCGTGTGACATGG 59.826 61.111 15.58 0.00 0.00 3.66
105 106 2.174107 CCAAGCGCGTGTGACATG 59.826 61.111 21.67 0.00 0.00 3.21
106 107 3.049674 CCCAAGCGCGTGTGACAT 61.050 61.111 21.67 0.00 0.00 3.06
117 118 1.559065 TACCTGTACCAGCCCCAAGC 61.559 60.000 0.00 0.00 44.25 4.01
118 119 1.141053 GATACCTGTACCAGCCCCAAG 59.859 57.143 0.00 0.00 0.00 3.61
119 120 1.209621 GATACCTGTACCAGCCCCAA 58.790 55.000 0.00 0.00 0.00 4.12
120 121 0.693092 GGATACCTGTACCAGCCCCA 60.693 60.000 0.00 0.00 0.00 4.96
121 122 0.693092 TGGATACCTGTACCAGCCCC 60.693 60.000 0.00 0.00 0.00 5.80
122 123 0.759346 CTGGATACCTGTACCAGCCC 59.241 60.000 0.00 0.00 43.32 5.19
126 127 3.572682 CGCTAATCTGGATACCTGTACCA 59.427 47.826 0.00 0.00 0.00 3.25
127 128 3.614390 GCGCTAATCTGGATACCTGTACC 60.614 52.174 0.00 0.00 0.00 3.34
128 129 3.005472 TGCGCTAATCTGGATACCTGTAC 59.995 47.826 9.73 0.00 0.00 2.90
129 130 3.227614 TGCGCTAATCTGGATACCTGTA 58.772 45.455 9.73 0.00 0.00 2.74
130 131 2.039418 TGCGCTAATCTGGATACCTGT 58.961 47.619 9.73 0.00 0.00 4.00
131 132 2.820059 TGCGCTAATCTGGATACCTG 57.180 50.000 9.73 0.00 0.00 4.00
132 133 3.169099 AGATGCGCTAATCTGGATACCT 58.831 45.455 9.73 0.00 35.54 3.08
133 134 3.601443 AGATGCGCTAATCTGGATACC 57.399 47.619 9.73 0.00 35.54 2.73
134 135 4.560128 TGAAGATGCGCTAATCTGGATAC 58.440 43.478 9.73 1.49 36.99 2.24
135 136 4.871933 TGAAGATGCGCTAATCTGGATA 57.128 40.909 9.73 0.00 36.99 2.59
136 137 3.758755 TGAAGATGCGCTAATCTGGAT 57.241 42.857 9.73 0.00 36.99 3.41
137 138 3.541996 TTGAAGATGCGCTAATCTGGA 57.458 42.857 9.73 0.00 36.99 3.86
138 139 3.562973 ACATTGAAGATGCGCTAATCTGG 59.437 43.478 9.73 1.25 36.99 3.86
139 140 4.510711 AGACATTGAAGATGCGCTAATCTG 59.489 41.667 9.73 0.77 36.99 2.90
140 141 4.701765 AGACATTGAAGATGCGCTAATCT 58.298 39.130 9.73 6.70 38.59 2.40
141 142 5.389307 GCTAGACATTGAAGATGCGCTAATC 60.389 44.000 9.73 3.94 0.00 1.75
142 143 4.450419 GCTAGACATTGAAGATGCGCTAAT 59.550 41.667 9.73 0.00 0.00 1.73
143 144 3.804325 GCTAGACATTGAAGATGCGCTAA 59.196 43.478 9.73 0.00 0.00 3.09
144 145 3.384668 GCTAGACATTGAAGATGCGCTA 58.615 45.455 9.73 0.00 0.00 4.26
145 146 2.208431 GCTAGACATTGAAGATGCGCT 58.792 47.619 9.73 0.00 0.00 5.92
146 147 1.262683 GGCTAGACATTGAAGATGCGC 59.737 52.381 0.00 0.00 0.00 6.09
147 148 2.831333 AGGCTAGACATTGAAGATGCG 58.169 47.619 0.00 0.00 0.00 4.73
148 149 6.683974 TTTAAGGCTAGACATTGAAGATGC 57.316 37.500 0.00 0.00 0.00 3.91
149 150 8.186821 CCTTTTTAAGGCTAGACATTGAAGATG 58.813 37.037 0.00 0.00 42.78 2.90
150 151 8.286191 CCTTTTTAAGGCTAGACATTGAAGAT 57.714 34.615 0.00 0.00 42.78 2.40
151 152 7.687941 CCTTTTTAAGGCTAGACATTGAAGA 57.312 36.000 0.00 0.00 42.78 2.87
175 176 5.815740 ACGGTCTGTGGACAAATATTATGTC 59.184 40.000 16.22 16.22 45.08 3.06
176 177 5.741011 ACGGTCTGTGGACAAATATTATGT 58.259 37.500 0.00 0.00 43.77 2.29
177 178 7.962964 ATACGGTCTGTGGACAAATATTATG 57.037 36.000 0.00 0.00 43.77 1.90
178 179 9.653287 CATATACGGTCTGTGGACAAATATTAT 57.347 33.333 0.00 0.00 43.77 1.28
179 180 8.092068 CCATATACGGTCTGTGGACAAATATTA 58.908 37.037 3.62 0.00 43.77 0.98
180 181 6.934645 CCATATACGGTCTGTGGACAAATATT 59.065 38.462 3.62 0.00 43.77 1.28
181 182 6.464222 CCATATACGGTCTGTGGACAAATAT 58.536 40.000 3.62 0.00 43.77 1.28
182 183 5.221561 CCCATATACGGTCTGTGGACAAATA 60.222 44.000 10.28 0.00 43.77 1.40
183 184 4.444306 CCCATATACGGTCTGTGGACAAAT 60.444 45.833 10.28 0.00 43.77 2.32
184 185 3.118555 CCCATATACGGTCTGTGGACAAA 60.119 47.826 10.28 0.00 43.77 2.83
185 186 2.432874 CCCATATACGGTCTGTGGACAA 59.567 50.000 10.28 0.00 43.77 3.18
186 187 2.036387 CCCATATACGGTCTGTGGACA 58.964 52.381 10.28 0.00 43.77 4.02
187 188 2.296471 CTCCCATATACGGTCTGTGGAC 59.704 54.545 10.28 0.00 41.43 4.02
188 189 2.594131 CTCCCATATACGGTCTGTGGA 58.406 52.381 10.28 0.00 31.59 4.02
189 190 1.000955 GCTCCCATATACGGTCTGTGG 59.999 57.143 2.81 2.81 0.00 4.17
190 191 1.000955 GGCTCCCATATACGGTCTGTG 59.999 57.143 0.00 0.00 0.00 3.66
191 192 1.339097 GGCTCCCATATACGGTCTGT 58.661 55.000 0.00 0.00 0.00 3.41
192 193 0.243907 CGGCTCCCATATACGGTCTG 59.756 60.000 0.00 0.00 0.00 3.51
193 194 0.898789 CCGGCTCCCATATACGGTCT 60.899 60.000 0.00 0.00 39.70 3.85
194 195 1.590147 CCGGCTCCCATATACGGTC 59.410 63.158 0.00 0.00 39.70 4.79
195 196 3.787394 CCGGCTCCCATATACGGT 58.213 61.111 0.00 0.00 39.70 4.83
197 198 2.159142 GGATAACCGGCTCCCATATACG 60.159 54.545 0.00 0.00 0.00 3.06
198 199 2.835764 TGGATAACCGGCTCCCATATAC 59.164 50.000 13.99 0.90 39.42 1.47
199 200 3.193395 TGGATAACCGGCTCCCATATA 57.807 47.619 13.99 0.00 39.42 0.86
200 201 2.038863 TGGATAACCGGCTCCCATAT 57.961 50.000 13.99 0.00 39.42 1.78
201 202 1.418637 GTTGGATAACCGGCTCCCATA 59.581 52.381 13.99 0.04 39.42 2.74
202 203 0.182775 GTTGGATAACCGGCTCCCAT 59.817 55.000 13.99 0.00 39.42 4.00
203 204 1.202099 TGTTGGATAACCGGCTCCCA 61.202 55.000 13.99 8.31 39.42 4.37
204 205 0.746923 GTGTTGGATAACCGGCTCCC 60.747 60.000 13.99 5.94 39.42 4.30
205 206 0.252197 AGTGTTGGATAACCGGCTCC 59.748 55.000 0.00 6.34 39.42 4.70
206 207 1.338769 ACAGTGTTGGATAACCGGCTC 60.339 52.381 0.00 0.00 39.42 4.70
207 208 0.690762 ACAGTGTTGGATAACCGGCT 59.309 50.000 0.00 0.00 39.42 5.52
208 209 1.084289 GACAGTGTTGGATAACCGGC 58.916 55.000 0.00 0.00 39.42 6.13
209 210 1.677820 GGGACAGTGTTGGATAACCGG 60.678 57.143 0.00 0.00 39.42 5.28
210 211 1.677820 GGGGACAGTGTTGGATAACCG 60.678 57.143 0.00 0.00 39.42 4.44
211 212 1.353022 TGGGGACAGTGTTGGATAACC 59.647 52.381 0.00 0.00 33.95 2.85
212 213 2.871096 TGGGGACAGTGTTGGATAAC 57.129 50.000 0.00 0.00 34.87 1.89
213 214 3.117474 TGTTTGGGGACAGTGTTGGATAA 60.117 43.478 0.00 0.00 44.54 1.75
214 215 2.443632 TGTTTGGGGACAGTGTTGGATA 59.556 45.455 0.00 0.00 44.54 2.59
215 216 1.216678 TGTTTGGGGACAGTGTTGGAT 59.783 47.619 0.00 0.00 44.54 3.41
216 217 0.626382 TGTTTGGGGACAGTGTTGGA 59.374 50.000 0.00 0.00 44.54 3.53
217 218 1.613437 GATGTTTGGGGACAGTGTTGG 59.387 52.381 0.00 0.00 44.54 3.77
218 219 2.554032 GAGATGTTTGGGGACAGTGTTG 59.446 50.000 0.00 0.00 44.54 3.33
219 220 2.489073 GGAGATGTTTGGGGACAGTGTT 60.489 50.000 0.00 0.00 44.54 3.32
220 221 1.073923 GGAGATGTTTGGGGACAGTGT 59.926 52.381 0.00 0.00 44.54 3.55
221 222 1.073763 TGGAGATGTTTGGGGACAGTG 59.926 52.381 0.00 0.00 44.54 3.66
222 223 1.444933 TGGAGATGTTTGGGGACAGT 58.555 50.000 0.00 0.00 44.54 3.55
223 224 2.584835 TTGGAGATGTTTGGGGACAG 57.415 50.000 0.00 0.00 44.54 3.51
224 225 3.591527 AGTATTGGAGATGTTTGGGGACA 59.408 43.478 0.00 0.00 39.83 4.02
225 226 4.236527 AGTATTGGAGATGTTTGGGGAC 57.763 45.455 0.00 0.00 0.00 4.46
226 227 5.339695 GGTTAGTATTGGAGATGTTTGGGGA 60.340 44.000 0.00 0.00 0.00 4.81
227 228 4.887655 GGTTAGTATTGGAGATGTTTGGGG 59.112 45.833 0.00 0.00 0.00 4.96
228 229 5.755849 AGGTTAGTATTGGAGATGTTTGGG 58.244 41.667 0.00 0.00 0.00 4.12
229 230 8.801882 TTTAGGTTAGTATTGGAGATGTTTGG 57.198 34.615 0.00 0.00 0.00 3.28
237 238 8.831550 GCTGATCTTTTTAGGTTAGTATTGGAG 58.168 37.037 0.00 0.00 0.00 3.86
238 239 7.773690 GGCTGATCTTTTTAGGTTAGTATTGGA 59.226 37.037 0.00 0.00 0.00 3.53
239 240 7.556275 TGGCTGATCTTTTTAGGTTAGTATTGG 59.444 37.037 0.00 0.00 0.00 3.16
240 241 8.506168 TGGCTGATCTTTTTAGGTTAGTATTG 57.494 34.615 0.00 0.00 0.00 1.90
241 242 8.957466 GTTGGCTGATCTTTTTAGGTTAGTATT 58.043 33.333 0.00 0.00 0.00 1.89
242 243 8.107095 TGTTGGCTGATCTTTTTAGGTTAGTAT 58.893 33.333 0.00 0.00 0.00 2.12
243 244 7.455058 TGTTGGCTGATCTTTTTAGGTTAGTA 58.545 34.615 0.00 0.00 0.00 1.82
244 245 6.303839 TGTTGGCTGATCTTTTTAGGTTAGT 58.696 36.000 0.00 0.00 0.00 2.24
245 246 6.817765 TGTTGGCTGATCTTTTTAGGTTAG 57.182 37.500 0.00 0.00 0.00 2.34
246 247 9.474313 AATATGTTGGCTGATCTTTTTAGGTTA 57.526 29.630 0.00 0.00 0.00 2.85
247 248 7.961326 ATATGTTGGCTGATCTTTTTAGGTT 57.039 32.000 0.00 0.00 0.00 3.50
248 249 7.201732 CGAATATGTTGGCTGATCTTTTTAGGT 60.202 37.037 0.00 0.00 0.00 3.08
249 250 7.134815 CGAATATGTTGGCTGATCTTTTTAGG 58.865 38.462 0.00 0.00 0.00 2.69
250 251 7.697691 ACGAATATGTTGGCTGATCTTTTTAG 58.302 34.615 0.00 0.00 0.00 1.85
251 252 7.624360 ACGAATATGTTGGCTGATCTTTTTA 57.376 32.000 0.00 0.00 0.00 1.52
252 253 6.515272 ACGAATATGTTGGCTGATCTTTTT 57.485 33.333 0.00 0.00 0.00 1.94
253 254 7.807977 ATACGAATATGTTGGCTGATCTTTT 57.192 32.000 0.00 0.00 0.00 2.27
254 255 8.150945 ACTATACGAATATGTTGGCTGATCTTT 58.849 33.333 0.00 0.00 0.00 2.52
255 256 7.671302 ACTATACGAATATGTTGGCTGATCTT 58.329 34.615 0.00 0.00 0.00 2.40
256 257 7.233389 ACTATACGAATATGTTGGCTGATCT 57.767 36.000 0.00 0.00 0.00 2.75
257 258 7.891183 AACTATACGAATATGTTGGCTGATC 57.109 36.000 0.00 0.00 0.00 2.92
258 259 9.204570 GTAAACTATACGAATATGTTGGCTGAT 57.795 33.333 0.00 0.00 0.00 2.90
259 260 8.198778 TGTAAACTATACGAATATGTTGGCTGA 58.801 33.333 0.00 0.00 0.00 4.26
260 261 8.360325 TGTAAACTATACGAATATGTTGGCTG 57.640 34.615 0.00 0.00 0.00 4.85
261 262 9.555727 AATGTAAACTATACGAATATGTTGGCT 57.444 29.630 0.00 0.00 0.00 4.75
262 263 9.594038 CAATGTAAACTATACGAATATGTTGGC 57.406 33.333 0.00 0.00 0.00 4.52
287 288 9.872757 GTCATGTTTCGTTACTATTTTTCTTCA 57.127 29.630 0.00 0.00 0.00 3.02
289 290 9.878599 CAGTCATGTTTCGTTACTATTTTTCTT 57.121 29.630 0.00 0.00 0.00 2.52
290 291 8.504005 CCAGTCATGTTTCGTTACTATTTTTCT 58.496 33.333 0.00 0.00 0.00 2.52
291 292 7.749126 CCCAGTCATGTTTCGTTACTATTTTTC 59.251 37.037 0.00 0.00 0.00 2.29
292 293 7.229907 ACCCAGTCATGTTTCGTTACTATTTTT 59.770 33.333 0.00 0.00 0.00 1.94
293 294 6.713450 ACCCAGTCATGTTTCGTTACTATTTT 59.287 34.615 0.00 0.00 0.00 1.82
294 295 6.148811 CACCCAGTCATGTTTCGTTACTATTT 59.851 38.462 0.00 0.00 0.00 1.40
295 296 5.642063 CACCCAGTCATGTTTCGTTACTATT 59.358 40.000 0.00 0.00 0.00 1.73
296 297 5.175859 CACCCAGTCATGTTTCGTTACTAT 58.824 41.667 0.00 0.00 0.00 2.12
297 298 4.561938 CCACCCAGTCATGTTTCGTTACTA 60.562 45.833 0.00 0.00 0.00 1.82
298 299 3.399330 CACCCAGTCATGTTTCGTTACT 58.601 45.455 0.00 0.00 0.00 2.24
299 300 2.482721 CCACCCAGTCATGTTTCGTTAC 59.517 50.000 0.00 0.00 0.00 2.50
300 301 2.369203 TCCACCCAGTCATGTTTCGTTA 59.631 45.455 0.00 0.00 0.00 3.18
301 302 1.142060 TCCACCCAGTCATGTTTCGTT 59.858 47.619 0.00 0.00 0.00 3.85
302 303 0.762418 TCCACCCAGTCATGTTTCGT 59.238 50.000 0.00 0.00 0.00 3.85
303 304 2.009774 GATCCACCCAGTCATGTTTCG 58.990 52.381 0.00 0.00 0.00 3.46
304 305 3.012518 CTGATCCACCCAGTCATGTTTC 58.987 50.000 0.00 0.00 0.00 2.78
305 306 2.644299 TCTGATCCACCCAGTCATGTTT 59.356 45.455 0.00 0.00 33.57 2.83
306 307 2.269023 TCTGATCCACCCAGTCATGTT 58.731 47.619 0.00 0.00 33.57 2.71
307 308 1.956869 TCTGATCCACCCAGTCATGT 58.043 50.000 0.00 0.00 33.57 3.21
308 309 3.572632 AATCTGATCCACCCAGTCATG 57.427 47.619 0.00 0.00 33.57 3.07
309 310 4.042560 CCATAATCTGATCCACCCAGTCAT 59.957 45.833 0.00 0.00 33.57 3.06
310 311 3.392285 CCATAATCTGATCCACCCAGTCA 59.608 47.826 0.00 0.00 33.57 3.41
311 312 3.244700 CCCATAATCTGATCCACCCAGTC 60.245 52.174 0.00 0.00 33.57 3.51
312 313 2.713167 CCCATAATCTGATCCACCCAGT 59.287 50.000 0.00 0.00 33.57 4.00
313 314 2.040813 CCCCATAATCTGATCCACCCAG 59.959 54.545 0.00 0.00 0.00 4.45
314 315 2.065007 CCCCATAATCTGATCCACCCA 58.935 52.381 0.00 0.00 0.00 4.51
315 316 2.307098 CTCCCCATAATCTGATCCACCC 59.693 54.545 0.00 0.00 0.00 4.61
316 317 2.982488 ACTCCCCATAATCTGATCCACC 59.018 50.000 0.00 0.00 0.00 4.61
317 318 6.380079 AATACTCCCCATAATCTGATCCAC 57.620 41.667 0.00 0.00 0.00 4.02
318 319 6.562223 TCAAATACTCCCCATAATCTGATCCA 59.438 38.462 0.00 0.00 0.00 3.41
319 320 6.881602 GTCAAATACTCCCCATAATCTGATCC 59.118 42.308 0.00 0.00 0.00 3.36
320 321 7.453393 TGTCAAATACTCCCCATAATCTGATC 58.547 38.462 0.00 0.00 0.00 2.92
321 322 7.392766 TGTCAAATACTCCCCATAATCTGAT 57.607 36.000 0.00 0.00 0.00 2.90
322 323 6.823286 TGTCAAATACTCCCCATAATCTGA 57.177 37.500 0.00 0.00 0.00 3.27
323 324 7.880160 TTTGTCAAATACTCCCCATAATCTG 57.120 36.000 0.00 0.00 0.00 2.90
324 325 7.893302 TGTTTTGTCAAATACTCCCCATAATCT 59.107 33.333 0.00 0.00 0.00 2.40
325 326 7.973944 GTGTTTTGTCAAATACTCCCCATAATC 59.026 37.037 0.00 0.00 32.62 1.75
326 327 7.673926 AGTGTTTTGTCAAATACTCCCCATAAT 59.326 33.333 0.00 0.00 39.46 1.28
327 328 7.007723 AGTGTTTTGTCAAATACTCCCCATAA 58.992 34.615 0.00 0.00 39.46 1.90
328 329 6.548321 AGTGTTTTGTCAAATACTCCCCATA 58.452 36.000 0.00 0.00 39.46 2.74
329 330 5.393866 AGTGTTTTGTCAAATACTCCCCAT 58.606 37.500 0.00 0.00 39.46 4.00
330 331 4.798882 AGTGTTTTGTCAAATACTCCCCA 58.201 39.130 0.00 0.00 39.46 4.96
331 332 5.182570 GGTAGTGTTTTGTCAAATACTCCCC 59.817 44.000 15.18 13.24 41.87 4.81
332 333 5.766174 TGGTAGTGTTTTGTCAAATACTCCC 59.234 40.000 15.18 14.29 41.87 4.30
349 350 2.478894 GGTGACGTGAAATGTGGTAGTG 59.521 50.000 0.00 0.00 35.18 2.74
369 370 0.109412 GTGGTAGTTCTGTCGGACGG 60.109 60.000 10.78 10.78 0.00 4.79
370 371 0.594602 TGTGGTAGTTCTGTCGGACG 59.405 55.000 3.34 0.00 0.00 4.79
375 376 7.432252 CACTTTTCAAAATGTGGTAGTTCTGTC 59.568 37.037 11.62 0.00 39.20 3.51
435 436 8.474025 TCATCAACTCAATTTGGTAGTTTTTGT 58.526 29.630 1.78 0.00 31.21 2.83
436 437 8.755018 GTCATCAACTCAATTTGGTAGTTTTTG 58.245 33.333 1.78 3.58 31.21 2.44
449 450 5.467399 TCGTAAAAACGGTCATCAACTCAAT 59.533 36.000 0.00 0.00 0.00 2.57
471 472 7.253288 CGCATGTCATAAACAGGTTTAAAATCG 60.253 37.037 8.53 3.84 41.70 3.34
485 486 0.462937 CGGGTCCCGCATGTCATAAA 60.463 55.000 19.48 0.00 41.17 1.40
505 506 3.108289 CACGTCAGCTCTGGCACG 61.108 66.667 8.84 8.84 41.52 5.34
509 510 4.056125 TCGCCACGTCAGCTCTGG 62.056 66.667 5.62 0.00 0.00 3.86
538 539 8.885722 AGTCAACTTAACAGTCAAAATAAACGA 58.114 29.630 0.00 0.00 30.45 3.85
552 553 2.554344 GGCCCCATCAGTCAACTTAACA 60.554 50.000 0.00 0.00 0.00 2.41
557 558 1.852157 TGGGCCCCATCAGTCAACT 60.852 57.895 22.27 0.00 0.00 3.16
558 559 1.678970 GTGGGCCCCATCAGTCAAC 60.679 63.158 22.27 2.75 35.28 3.18
564 565 4.028490 GACGTGTGGGCCCCATCA 62.028 66.667 22.27 13.49 35.28 3.07
579 589 3.070302 AGGAGGAAGAAGTTGACACTGAC 59.930 47.826 0.00 0.00 31.60 3.51
583 593 4.039852 AGAGAAGGAGGAAGAAGTTGACAC 59.960 45.833 0.00 0.00 0.00 3.67
585 595 4.617298 CGAGAGAAGGAGGAAGAAGTTGAC 60.617 50.000 0.00 0.00 0.00 3.18
587 597 3.508012 TCGAGAGAAGGAGGAAGAAGTTG 59.492 47.826 0.00 0.00 37.03 3.16
588 598 3.768878 TCGAGAGAAGGAGGAAGAAGTT 58.231 45.455 0.00 0.00 37.03 2.66
589 599 3.443145 TCGAGAGAAGGAGGAAGAAGT 57.557 47.619 0.00 0.00 37.03 3.01
603 613 2.743664 TGTTCAAATGCCACATCGAGAG 59.256 45.455 0.00 0.00 0.00 3.20
604 614 2.777094 TGTTCAAATGCCACATCGAGA 58.223 42.857 0.00 0.00 0.00 4.04
605 615 3.058016 ACTTGTTCAAATGCCACATCGAG 60.058 43.478 0.00 0.00 0.00 4.04
606 616 2.884012 ACTTGTTCAAATGCCACATCGA 59.116 40.909 0.00 0.00 0.00 3.59
607 617 3.287312 ACTTGTTCAAATGCCACATCG 57.713 42.857 0.00 0.00 0.00 3.84
608 618 7.512297 CAATTTACTTGTTCAAATGCCACATC 58.488 34.615 0.00 0.00 0.00 3.06
609 619 6.073112 GCAATTTACTTGTTCAAATGCCACAT 60.073 34.615 0.00 0.00 37.18 3.21
610 620 5.236047 GCAATTTACTTGTTCAAATGCCACA 59.764 36.000 0.00 0.00 37.18 4.17
611 621 5.236047 TGCAATTTACTTGTTCAAATGCCAC 59.764 36.000 0.00 0.00 37.18 5.01
612 622 5.236047 GTGCAATTTACTTGTTCAAATGCCA 59.764 36.000 0.00 0.00 37.18 4.92
614 624 6.200665 TCTGTGCAATTTACTTGTTCAAATGC 59.799 34.615 0.00 0.00 37.18 3.56
616 626 7.981225 ACTTCTGTGCAATTTACTTGTTCAAAT 59.019 29.630 0.00 0.00 37.18 2.32
617 627 7.319646 ACTTCTGTGCAATTTACTTGTTCAAA 58.680 30.769 0.00 0.00 37.18 2.69
618 628 6.862209 ACTTCTGTGCAATTTACTTGTTCAA 58.138 32.000 0.00 0.00 37.18 2.69
619 629 6.449635 ACTTCTGTGCAATTTACTTGTTCA 57.550 33.333 0.00 0.00 37.18 3.18
621 631 6.320164 TGGTACTTCTGTGCAATTTACTTGTT 59.680 34.615 0.00 0.00 37.18 2.83
622 632 5.825679 TGGTACTTCTGTGCAATTTACTTGT 59.174 36.000 0.00 0.00 37.18 3.16
623 633 6.142817 GTGGTACTTCTGTGCAATTTACTTG 58.857 40.000 0.00 0.00 37.94 3.16
925 1485 4.103342 AGGCAGAGAGAAGGAAGAAGAAT 58.897 43.478 0.00 0.00 0.00 2.40
1024 1589 0.321996 GGGAGGCTTGAGTTCTCGTT 59.678 55.000 0.00 0.00 0.00 3.85
1233 1798 1.339535 CCTGAAGAGAGAAAGGCACCC 60.340 57.143 0.00 0.00 0.00 4.61
1279 1844 1.126890 CGCACAGCACTATCAGATCG 58.873 55.000 0.00 0.00 0.00 3.69
2423 2988 3.277715 CTCCAAATTCTCTTGAGCCTCC 58.722 50.000 0.00 0.00 0.00 4.30
2696 3261 3.047039 GGCCATTGCATAGCCATCT 57.953 52.632 15.24 0.00 46.34 2.90
2704 3269 5.630415 TCTAAGTTACTAGGCCATTGCAT 57.370 39.130 5.01 0.00 40.13 3.96
3254 3868 5.069318 TGTTGTCTATGCTCAAAATGGTCA 58.931 37.500 0.00 0.00 0.00 4.02
3357 3973 5.425217 TGGACTTTCTTGATATGCTGGAGTA 59.575 40.000 0.00 0.00 0.00 2.59
3375 3991 2.042162 AGTGAATGCCTGGAATGGACTT 59.958 45.455 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.