Multiple sequence alignment - TraesCS5A01G151100

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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 TraesCS5A01G151100 chr5A 100.000 9832 0 0 1 9832 328727784 328717953 0.000000e+00 18157.0
1 TraesCS5A01G151100 chr5A 98.359 2620 29 3 4160 6765 115021213 115023832 0.000000e+00 4588.0
2 TraesCS5A01G151100 chr5A 95.170 352 2 4 4154 4490 328721373 328721022 8.690000e-150 542.0
3 TraesCS5A01G151100 chr5A 94.886 352 3 4 4154 4490 115023479 115023830 4.040000e-148 536.0
4 TraesCS5A01G151100 chr5A 90.934 364 5 3 4154 4490 577953675 577953313 1.930000e-126 464.0
5 TraesCS5A01G151100 chr5A 85.251 339 31 6 4154 4474 4207990 4208327 2.050000e-86 331.0
6 TraesCS5A01G151100 chr5A 96.809 94 1 2 4074 4166 309680263 309680171 1.320000e-33 156.0
7 TraesCS5A01G151100 chr5A 97.143 35 1 0 2039 2073 328725710 328725676 1.070000e-04 60.2
8 TraesCS5A01G151100 chr5A 97.143 35 1 0 2075 2109 328725746 328725712 1.070000e-04 60.2
9 TraesCS5A01G151100 chr6A 98.319 2617 41 3 4154 6768 418951252 418953867 0.000000e+00 4586.0
10 TraesCS5A01G151100 chr5B 98.008 2611 52 0 4156 6766 678521699 678519089 0.000000e+00 4534.0
11 TraesCS5A01G151100 chr5B 92.511 3098 131 34 6767 9832 277640187 277637159 0.000000e+00 4342.0
12 TraesCS5A01G151100 chr5B 97.116 2011 48 7 2069 4076 277642189 277640186 0.000000e+00 3384.0
13 TraesCS5A01G151100 chr5B 89.068 2113 118 52 7 2073 277644194 277642149 0.000000e+00 2518.0
14 TraesCS5A01G151100 chr4B 97.810 2603 57 0 4161 6763 411531233 411528631 0.000000e+00 4492.0
15 TraesCS5A01G151100 chr7A 97.419 2635 52 5 4157 6776 201420624 201423257 0.000000e+00 4475.0
16 TraesCS5A01G151100 chr7A 97.479 2618 52 3 4161 6764 383176698 383179315 0.000000e+00 4457.0
17 TraesCS5A01G151100 chr1A 97.516 2617 50 4 4161 6763 566643949 566646564 0.000000e+00 4458.0
18 TraesCS5A01G151100 chr1A 96.809 94 2 1 4071 4164 57311853 57311945 1.320000e-33 156.0
19 TraesCS5A01G151100 chr2A 97.444 2621 51 5 4161 6765 86904537 86901917 0.000000e+00 4455.0
20 TraesCS5A01G151100 chr2A 93.768 353 6 4 4154 4490 86902271 86901919 5.260000e-142 516.0
21 TraesCS5A01G151100 chr6B 97.326 2618 56 3 4161 6764 308519640 308522257 0.000000e+00 4434.0
22 TraesCS5A01G151100 chr5D 98.401 2001 21 8 2039 4031 244373945 244371948 0.000000e+00 3507.0
23 TraesCS5A01G151100 chr5D 94.595 1887 68 11 6814 8681 244371933 244370062 0.000000e+00 2889.0
24 TraesCS5A01G151100 chr5D 96.636 1635 39 9 475 2109 244375529 244373911 0.000000e+00 2700.0
25 TraesCS5A01G151100 chr5D 90.899 934 55 14 8907 9832 244369631 244368720 0.000000e+00 1227.0
26 TraesCS5A01G151100 chr5D 88.423 501 32 10 1 491 244376027 244375543 1.840000e-161 580.0
27 TraesCS5A01G151100 chr5D 92.273 220 7 7 8679 8897 244369982 244369772 4.460000e-78 303.0
28 TraesCS5A01G151100 chr5D 96.739 92 2 1 4074 4165 276292432 276292522 1.710000e-32 152.0
29 TraesCS5A01G151100 chr5D 97.143 35 1 0 2075 2109 244373981 244373947 1.070000e-04 60.2
30 TraesCS5A01G151100 chr7B 96.451 1916 52 4 4155 6055 700578129 700576215 0.000000e+00 3147.0
31 TraesCS5A01G151100 chr7B 98.889 90 1 0 4072 4161 431678277 431678366 2.840000e-35 161.0
32 TraesCS5A01G151100 chr1B 98.864 88 1 0 4074 4161 133188855 133188942 3.680000e-34 158.0
33 TraesCS5A01G151100 chr4D 98.837 86 1 0 4075 4160 379169417 379169332 4.760000e-33 154.0
34 TraesCS5A01G151100 chr2D 97.753 89 2 0 4075 4163 107402954 107402866 4.760000e-33 154.0
35 TraesCS5A01G151100 chr2D 98.718 78 1 0 8104 8181 10777147 10777224 1.330000e-28 139.0
36 TraesCS5A01G151100 chr2B 95.789 95 3 1 4067 4160 799148677 799148771 1.710000e-32 152.0
37 TraesCS5A01G151100 chr1D 93.069 101 5 2 4075 4173 10183788 10183688 7.960000e-31 147.0
38 TraesCS5A01G151100 chr3B 76.023 171 36 3 2723 2891 738314706 738314873 6.330000e-12 84.2


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 TraesCS5A01G151100 chr5A 328717953 328727784 9831 True 18157.000000 18157 100.000000 1 9832 1 chr5A.!!$R2 9831
1 TraesCS5A01G151100 chr5A 115021213 115023832 2619 False 2562.000000 4588 96.622500 4154 6765 2 chr5A.!!$F2 2611
2 TraesCS5A01G151100 chr6A 418951252 418953867 2615 False 4586.000000 4586 98.319000 4154 6768 1 chr6A.!!$F1 2614
3 TraesCS5A01G151100 chr5B 678519089 678521699 2610 True 4534.000000 4534 98.008000 4156 6766 1 chr5B.!!$R1 2610
4 TraesCS5A01G151100 chr5B 277637159 277644194 7035 True 3414.666667 4342 92.898333 7 9832 3 chr5B.!!$R2 9825
5 TraesCS5A01G151100 chr4B 411528631 411531233 2602 True 4492.000000 4492 97.810000 4161 6763 1 chr4B.!!$R1 2602
6 TraesCS5A01G151100 chr7A 201420624 201423257 2633 False 4475.000000 4475 97.419000 4157 6776 1 chr7A.!!$F1 2619
7 TraesCS5A01G151100 chr7A 383176698 383179315 2617 False 4457.000000 4457 97.479000 4161 6764 1 chr7A.!!$F2 2603
8 TraesCS5A01G151100 chr1A 566643949 566646564 2615 False 4458.000000 4458 97.516000 4161 6763 1 chr1A.!!$F2 2602
9 TraesCS5A01G151100 chr2A 86901917 86904537 2620 True 2485.500000 4455 95.606000 4154 6765 2 chr2A.!!$R1 2611
10 TraesCS5A01G151100 chr6B 308519640 308522257 2617 False 4434.000000 4434 97.326000 4161 6764 1 chr6B.!!$F1 2603
11 TraesCS5A01G151100 chr5D 244368720 244376027 7307 True 1609.457143 3507 94.052857 1 9832 7 chr5D.!!$R1 9831
12 TraesCS5A01G151100 chr7B 700576215 700578129 1914 True 3147.000000 3147 96.451000 4155 6055 1 chr7B.!!$R1 1900

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
338 362 0.890542 CTGTGCTTGCCCTGTTGCTA 60.891 55.000 0.00 0.0 0.00 3.49 F
585 665 1.071314 TGGGGCTTCAAAGGGGAAGA 61.071 55.000 7.08 0.0 45.66 2.87 F
2125 2244 1.537202 CGAGCTCAAACCAGAAAAGGG 59.463 52.381 15.40 0.0 0.00 3.95 F
4048 4176 2.039418 TGTCGGAGAATGGTCCATAGG 58.961 52.381 4.33 0.0 39.69 2.57 F
4089 4217 1.286849 TGATCTACTCCCTCCGTTCCA 59.713 52.381 0.00 0.0 0.00 3.53 F
5883 6026 1.002624 CTTTCAGGCCCAGGCGTAA 60.003 57.895 0.00 0.0 43.06 3.18 F
6663 6807 4.593864 CCCTTCTCCTAGCCGCGC 62.594 72.222 0.00 0.0 0.00 6.86 F
8394 8553 0.036952 CTGGAGCAATGTCGTCCACT 60.037 55.000 0.00 0.0 35.36 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2090 2209 0.179215 GCTCGTTGTTCCGCTCATTG 60.179 55.000 0.0 0.0 0.00 2.82 R
2434 2553 2.290514 CCTTCTGTTCCAGCTCCATTGA 60.291 50.000 0.0 0.0 0.00 2.57 R
4069 4197 1.286849 TGGAACGGAGGGAGTAGATCA 59.713 52.381 0.0 0.0 0.00 2.92 R
5340 5483 0.814010 GTGACGGTGGAAACTGCACT 60.814 55.000 0.0 0.0 38.83 4.40 R
6040 6183 1.006758 AGTCTGGGACGGTGATTCCTA 59.993 52.381 0.0 0.0 37.67 2.94 R
6820 6964 0.034089 GTGGTTTCCCCAGGAGATGG 60.034 60.000 0.0 0.0 46.45 3.51 R
8406 8565 0.035152 ATGACGGCATTCTTGGCTCA 60.035 50.000 0.0 2.1 45.85 4.26 R
9443 9846 0.033504 GGTCAGCACGTCCTCTTTCA 59.966 55.000 0.0 0.0 0.00 2.69 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
80 97 1.972223 CCTGCTCTTGCTGCTGCTT 60.972 57.895 17.00 0.00 40.48 3.91
81 98 1.502640 CTGCTCTTGCTGCTGCTTC 59.497 57.895 17.00 2.32 40.48 3.86
82 99 0.956410 CTGCTCTTGCTGCTGCTTCT 60.956 55.000 17.00 0.00 40.48 2.85
83 100 1.235281 TGCTCTTGCTGCTGCTTCTG 61.235 55.000 17.00 6.08 40.48 3.02
84 101 1.502640 CTCTTGCTGCTGCTTCTGC 59.497 57.895 17.00 1.02 40.48 4.26
85 102 1.924320 CTCTTGCTGCTGCTTCTGCC 61.924 60.000 17.00 0.00 40.48 4.85
141 161 2.091541 TCTTCGGATTTCCCATGCAAC 58.908 47.619 0.00 0.00 34.14 4.17
142 162 1.134946 CTTCGGATTTCCCATGCAACC 59.865 52.381 0.00 0.00 34.14 3.77
161 181 2.160221 CAACGGGATTGCGCAATGC 61.160 57.895 37.46 37.46 46.70 3.56
202 222 2.680913 GGCGCGTGCTCACATTTCT 61.681 57.895 21.89 0.00 42.25 2.52
338 362 0.890542 CTGTGCTTGCCCTGTTGCTA 60.891 55.000 0.00 0.00 0.00 3.49
355 379 2.200899 GCTAGCTTCTTCTGCTGCTAC 58.799 52.381 7.70 0.00 41.32 3.58
358 382 3.799281 AGCTTCTTCTGCTGCTACTAG 57.201 47.619 0.00 0.00 39.56 2.57
361 386 4.097286 AGCTTCTTCTGCTGCTACTAGTAC 59.903 45.833 0.00 0.00 39.56 2.73
363 388 5.393678 GCTTCTTCTGCTGCTACTAGTACTT 60.394 44.000 0.00 0.00 0.00 2.24
364 389 5.568685 TCTTCTGCTGCTACTAGTACTTG 57.431 43.478 0.00 0.59 0.00 3.16
366 391 6.178324 TCTTCTGCTGCTACTAGTACTTGTA 58.822 40.000 15.03 15.03 0.00 2.41
367 392 5.814764 TCTGCTGCTACTAGTACTTGTAC 57.185 43.478 12.37 10.27 0.00 2.90
370 395 7.108194 TCTGCTGCTACTAGTACTTGTACTAA 58.892 38.462 17.84 7.00 32.72 2.24
397 422 5.931146 TGTTTGGTTCCATCATTAATTGTGC 59.069 36.000 0.00 0.00 0.00 4.57
402 427 3.363627 TCCATCATTAATTGTGCCTGCA 58.636 40.909 0.00 0.00 0.00 4.41
436 461 7.981142 TCAGGTGTAACTGAGTTTTAGTTTTG 58.019 34.615 1.97 0.00 42.26 2.44
468 498 4.280174 TGATATACGACTAACTGGGGCTTC 59.720 45.833 0.00 0.00 0.00 3.86
491 521 9.953697 CTTCCAGTAATTATGTCTAGTGTACTC 57.046 37.037 0.00 0.00 0.00 2.59
520 600 3.509575 TGAATTGCCTACATGTTTGGTCC 59.490 43.478 2.30 0.00 0.00 4.46
552 632 6.992123 TCCCTTTATTGCTCTATACACACATG 59.008 38.462 0.00 0.00 0.00 3.21
585 665 1.071314 TGGGGCTTCAAAGGGGAAGA 61.071 55.000 7.08 0.00 45.66 2.87
726 808 3.463944 CTCTTTTATATGGCGTTCCGGT 58.536 45.455 0.00 0.00 34.14 5.28
730 812 3.478857 TTATATGGCGTTCCGGTTGAT 57.521 42.857 0.00 0.00 34.14 2.57
731 813 2.341846 ATATGGCGTTCCGGTTGATT 57.658 45.000 0.00 0.00 34.14 2.57
732 814 2.116827 TATGGCGTTCCGGTTGATTT 57.883 45.000 0.00 0.00 34.14 2.17
817 899 4.665212 ACAACTTGCTTCATATCAATGCG 58.335 39.130 0.00 0.00 32.76 4.73
823 905 3.735746 TGCTTCATATCAATGCGTAGACG 59.264 43.478 0.00 0.00 43.27 4.18
981 1063 4.091365 GCACTTTGTTTAATCATTTCCGCC 59.909 41.667 0.00 0.00 0.00 6.13
982 1064 4.625311 CACTTTGTTTAATCATTTCCGCCC 59.375 41.667 0.00 0.00 0.00 6.13
1033 1115 2.725221 ATCTTCATGGAGCCAGGTTC 57.275 50.000 0.00 0.00 0.00 3.62
1236 1318 6.424812 TCATACAAAGAAGTGACATGTCTGTG 59.575 38.462 25.55 13.08 35.14 3.66
1925 2008 5.074115 CCTCCTGTGTGGGTACAAAAATTA 58.926 41.667 0.00 0.00 38.82 1.40
2090 2209 3.476552 TGAGTGGAACAATGAGTGGAAC 58.523 45.455 0.00 0.00 44.16 3.62
2125 2244 1.537202 CGAGCTCAAACCAGAAAAGGG 59.463 52.381 15.40 0.00 0.00 3.95
2434 2553 8.299570 CCAGCAACTTAGTTCTGAATTTTATGT 58.700 33.333 18.89 0.00 0.00 2.29
2450 2569 2.885135 ATGTCAATGGAGCTGGAACA 57.115 45.000 0.00 0.00 0.00 3.18
2645 2764 8.779096 AGGTTAGTTATAACATAGCTACAGGT 57.221 34.615 17.65 0.00 42.66 4.00
2811 2930 5.130705 TGGAGAAGAAGCAGGTATCTCTA 57.869 43.478 8.89 2.48 37.33 2.43
2906 3025 9.422196 GAATCAATAAGTTAATCACAGCGTTAC 57.578 33.333 0.00 0.00 0.00 2.50
3750 3876 6.505044 TTCAACATGTCATCCTTGATTCAG 57.495 37.500 0.00 0.00 33.56 3.02
3937 4065 8.687824 AAATTAGTTGCTCCATTTTCAATACG 57.312 30.769 0.00 0.00 0.00 3.06
4048 4176 2.039418 TGTCGGAGAATGGTCCATAGG 58.961 52.381 4.33 0.00 39.69 2.57
4078 4206 9.490379 TGGAAAAAGTAACTCTTTGATCTACTC 57.510 33.333 0.00 0.00 44.50 2.59
4079 4207 8.937884 GGAAAAAGTAACTCTTTGATCTACTCC 58.062 37.037 0.00 0.00 44.50 3.85
4080 4208 8.850007 AAAAAGTAACTCTTTGATCTACTCCC 57.150 34.615 0.00 0.00 44.50 4.30
4081 4209 7.800300 AAAGTAACTCTTTGATCTACTCCCT 57.200 36.000 0.00 0.00 43.72 4.20
4082 4210 7.412853 AAGTAACTCTTTGATCTACTCCCTC 57.587 40.000 0.00 0.00 31.57 4.30
4083 4211 5.894964 AGTAACTCTTTGATCTACTCCCTCC 59.105 44.000 0.00 0.00 0.00 4.30
4084 4212 3.292460 ACTCTTTGATCTACTCCCTCCG 58.708 50.000 0.00 0.00 0.00 4.63
4085 4213 3.292460 CTCTTTGATCTACTCCCTCCGT 58.708 50.000 0.00 0.00 0.00 4.69
4086 4214 3.702045 CTCTTTGATCTACTCCCTCCGTT 59.298 47.826 0.00 0.00 0.00 4.44
4087 4215 3.700038 TCTTTGATCTACTCCCTCCGTTC 59.300 47.826 0.00 0.00 0.00 3.95
4088 4216 2.068834 TGATCTACTCCCTCCGTTCC 57.931 55.000 0.00 0.00 0.00 3.62
4089 4217 1.286849 TGATCTACTCCCTCCGTTCCA 59.713 52.381 0.00 0.00 0.00 3.53
4090 4218 2.091278 TGATCTACTCCCTCCGTTCCAT 60.091 50.000 0.00 0.00 0.00 3.41
4091 4219 3.139584 TGATCTACTCCCTCCGTTCCATA 59.860 47.826 0.00 0.00 0.00 2.74
4092 4220 3.897657 TCTACTCCCTCCGTTCCATAT 57.102 47.619 0.00 0.00 0.00 1.78
4093 4221 4.194678 TCTACTCCCTCCGTTCCATATT 57.805 45.455 0.00 0.00 0.00 1.28
4094 4222 5.329191 TCTACTCCCTCCGTTCCATATTA 57.671 43.478 0.00 0.00 0.00 0.98
4095 4223 5.075493 TCTACTCCCTCCGTTCCATATTAC 58.925 45.833 0.00 0.00 0.00 1.89
4096 4224 3.924922 ACTCCCTCCGTTCCATATTACT 58.075 45.455 0.00 0.00 0.00 2.24
4097 4225 4.296056 ACTCCCTCCGTTCCATATTACTT 58.704 43.478 0.00 0.00 0.00 2.24
4098 4226 4.101119 ACTCCCTCCGTTCCATATTACTTG 59.899 45.833 0.00 0.00 0.00 3.16
4099 4227 4.035112 TCCCTCCGTTCCATATTACTTGT 58.965 43.478 0.00 0.00 0.00 3.16
4100 4228 4.100498 TCCCTCCGTTCCATATTACTTGTC 59.900 45.833 0.00 0.00 0.00 3.18
4101 4229 4.049186 CCTCCGTTCCATATTACTTGTCG 58.951 47.826 0.00 0.00 0.00 4.35
4102 4230 3.450578 TCCGTTCCATATTACTTGTCGC 58.549 45.455 0.00 0.00 0.00 5.19
4103 4231 3.131577 TCCGTTCCATATTACTTGTCGCT 59.868 43.478 0.00 0.00 0.00 4.93
4104 4232 3.245284 CCGTTCCATATTACTTGTCGCTG 59.755 47.826 0.00 0.00 0.00 5.18
4105 4233 4.109766 CGTTCCATATTACTTGTCGCTGA 58.890 43.478 0.00 0.00 0.00 4.26
4106 4234 4.745125 CGTTCCATATTACTTGTCGCTGAT 59.255 41.667 0.00 0.00 0.00 2.90
4107 4235 5.234329 CGTTCCATATTACTTGTCGCTGATT 59.766 40.000 0.00 0.00 0.00 2.57
4108 4236 6.238103 CGTTCCATATTACTTGTCGCTGATTT 60.238 38.462 0.00 0.00 0.00 2.17
4109 4237 7.042992 CGTTCCATATTACTTGTCGCTGATTTA 60.043 37.037 0.00 0.00 0.00 1.40
4110 4238 7.946655 TCCATATTACTTGTCGCTGATTTAG 57.053 36.000 0.00 0.00 0.00 1.85
4111 4239 7.497595 TCCATATTACTTGTCGCTGATTTAGT 58.502 34.615 0.00 0.00 0.00 2.24
4112 4240 8.635328 TCCATATTACTTGTCGCTGATTTAGTA 58.365 33.333 0.00 0.00 0.00 1.82
4113 4241 8.700644 CCATATTACTTGTCGCTGATTTAGTAC 58.299 37.037 0.00 0.00 0.00 2.73
4114 4242 9.244799 CATATTACTTGTCGCTGATTTAGTACA 57.755 33.333 0.00 0.00 0.00 2.90
4115 4243 9.811995 ATATTACTTGTCGCTGATTTAGTACAA 57.188 29.630 0.00 0.00 34.99 2.41
4116 4244 7.949903 TTACTTGTCGCTGATTTAGTACAAA 57.050 32.000 0.00 0.00 35.46 2.83
4117 4245 6.467723 ACTTGTCGCTGATTTAGTACAAAG 57.532 37.500 0.00 0.00 35.46 2.77
4118 4246 5.989777 ACTTGTCGCTGATTTAGTACAAAGT 59.010 36.000 0.00 0.00 35.46 2.66
4119 4247 6.482308 ACTTGTCGCTGATTTAGTACAAAGTT 59.518 34.615 0.00 0.00 35.46 2.66
4120 4248 6.223138 TGTCGCTGATTTAGTACAAAGTTG 57.777 37.500 0.00 0.00 0.00 3.16
4121 4249 5.756347 TGTCGCTGATTTAGTACAAAGTTGT 59.244 36.000 1.75 1.75 44.86 3.32
4122 4250 6.924612 TGTCGCTGATTTAGTACAAAGTTGTA 59.075 34.615 0.00 0.00 42.35 2.41
4136 4264 6.814343 ACAAAGTTGTACTAAATTAGCGACG 58.186 36.000 0.00 0.00 40.16 5.12
4137 4265 6.642131 ACAAAGTTGTACTAAATTAGCGACGA 59.358 34.615 0.00 0.00 40.16 4.20
4138 4266 6.866179 AAGTTGTACTAAATTAGCGACGAG 57.134 37.500 0.00 0.00 0.00 4.18
4139 4267 5.947443 AGTTGTACTAAATTAGCGACGAGT 58.053 37.500 0.00 0.00 0.00 4.18
4140 4268 7.076842 AGTTGTACTAAATTAGCGACGAGTA 57.923 36.000 0.00 0.00 0.00 2.59
4141 4269 7.530010 AGTTGTACTAAATTAGCGACGAGTAA 58.470 34.615 0.00 0.00 0.00 2.24
4142 4270 8.186821 AGTTGTACTAAATTAGCGACGAGTAAT 58.813 33.333 0.00 0.00 0.00 1.89
4143 4271 9.438291 GTTGTACTAAATTAGCGACGAGTAATA 57.562 33.333 0.00 0.00 0.00 0.98
4145 4273 9.603298 TGTACTAAATTAGCGACGAGTAATATG 57.397 33.333 0.00 0.00 0.00 1.78
4146 4274 9.059485 GTACTAAATTAGCGACGAGTAATATGG 57.941 37.037 0.00 0.00 0.00 2.74
4147 4275 7.879070 ACTAAATTAGCGACGAGTAATATGGA 58.121 34.615 0.00 0.00 0.00 3.41
4148 4276 8.355169 ACTAAATTAGCGACGAGTAATATGGAA 58.645 33.333 0.00 0.00 0.00 3.53
4149 4277 7.404139 AAATTAGCGACGAGTAATATGGAAC 57.596 36.000 0.00 0.00 0.00 3.62
4150 4278 2.996155 AGCGACGAGTAATATGGAACG 58.004 47.619 0.00 0.00 0.00 3.95
4151 4279 2.049228 GCGACGAGTAATATGGAACGG 58.951 52.381 0.00 0.00 0.00 4.44
4152 4280 2.287188 GCGACGAGTAATATGGAACGGA 60.287 50.000 0.00 0.00 0.00 4.69
4153 4281 3.552541 CGACGAGTAATATGGAACGGAG 58.447 50.000 0.00 0.00 0.00 4.63
4154 4282 3.608707 CGACGAGTAATATGGAACGGAGG 60.609 52.174 0.00 0.00 0.00 4.30
4710 4853 4.980805 GTCCAACACTCGCCGCCA 62.981 66.667 0.00 0.00 0.00 5.69
5374 5517 3.860605 CACCATCGCCGATCCCCA 61.861 66.667 0.00 0.00 0.00 4.96
5868 6011 2.126189 GACTACGCCGACCGCTTT 60.126 61.111 0.00 0.00 41.76 3.51
5876 6019 4.697756 CGACCGCTTTCAGGCCCA 62.698 66.667 0.00 0.00 0.00 5.36
5882 6025 2.668632 CTTTCAGGCCCAGGCGTA 59.331 61.111 0.00 0.00 43.06 4.42
5883 6026 1.002624 CTTTCAGGCCCAGGCGTAA 60.003 57.895 0.00 0.00 43.06 3.18
6663 6807 4.593864 CCCTTCTCCTAGCCGCGC 62.594 72.222 0.00 0.00 0.00 6.86
6766 6910 5.459982 AGAGTACTTGATCCTACCAGAGT 57.540 43.478 0.00 0.00 0.00 3.24
6812 6956 5.475564 TGTTGCTGGGTATTTTTCCTACTTC 59.524 40.000 0.00 0.00 0.00 3.01
6819 6963 6.664816 TGGGTATTTTTCCTACTTCTAGTCGA 59.335 38.462 0.00 0.00 0.00 4.20
6820 6964 6.977502 GGGTATTTTTCCTACTTCTAGTCGAC 59.022 42.308 7.70 7.70 0.00 4.20
6916 7060 3.670627 CGGGTTGCTCTTGCTTGAATTAC 60.671 47.826 0.00 0.00 40.48 1.89
6917 7061 3.367395 GGGTTGCTCTTGCTTGAATTACC 60.367 47.826 0.00 0.00 40.48 2.85
6918 7062 3.255642 GGTTGCTCTTGCTTGAATTACCA 59.744 43.478 0.00 0.00 40.48 3.25
6919 7063 4.082026 GGTTGCTCTTGCTTGAATTACCAT 60.082 41.667 0.00 0.00 40.48 3.55
6920 7064 5.125417 GGTTGCTCTTGCTTGAATTACCATA 59.875 40.000 0.00 0.00 40.48 2.74
6921 7065 6.350110 GGTTGCTCTTGCTTGAATTACCATAA 60.350 38.462 0.00 0.00 40.48 1.90
6922 7066 6.194796 TGCTCTTGCTTGAATTACCATAAC 57.805 37.500 0.00 0.00 40.48 1.89
6923 7067 5.945784 TGCTCTTGCTTGAATTACCATAACT 59.054 36.000 0.00 0.00 40.48 2.24
6951 7095 4.159557 AGTTGGCCTAACATTGTTCCATT 58.840 39.130 16.93 0.00 41.88 3.16
7038 7182 6.275494 TGTCTTTGACATACTCGATGGTTA 57.725 37.500 0.00 0.00 37.67 2.85
7042 7186 6.811665 TCTTTGACATACTCGATGGTTACTTG 59.188 38.462 0.00 0.00 40.18 3.16
7137 7282 0.112412 GGAAAGAAACAGGGGCTCCA 59.888 55.000 4.79 0.00 34.83 3.86
7178 7323 7.406916 TGTATGGAATTTAGAAGTTTGCCCTA 58.593 34.615 0.00 0.00 0.00 3.53
7412 7563 8.696043 TTATGGAAAGATAATGATTGTCCTGG 57.304 34.615 0.00 0.00 0.00 4.45
7749 7900 6.072673 CCCAGCAAAAGTAAGTAGTTTAGTGG 60.073 42.308 0.00 1.09 0.00 4.00
7847 7998 1.865865 TCGAGCAACAGAGAAACACC 58.134 50.000 0.00 0.00 0.00 4.16
7936 8087 7.147976 GCCTATTTTCTTTATGGCTTACATGG 58.852 38.462 0.00 0.00 40.82 3.66
8236 8394 2.794631 CGGGGATCAGCGTAAATTTTGC 60.795 50.000 0.00 1.18 0.00 3.68
8258 8416 1.270305 CGATGTCGGCCCATGTAATCT 60.270 52.381 0.00 0.00 35.37 2.40
8394 8553 0.036952 CTGGAGCAATGTCGTCCACT 60.037 55.000 0.00 0.00 35.36 4.00
8403 8562 2.218953 TGTCGTCCACTGTTGAGTTC 57.781 50.000 0.00 0.00 0.00 3.01
8406 8565 3.572682 TGTCGTCCACTGTTGAGTTCTAT 59.427 43.478 0.00 0.00 0.00 1.98
8428 8587 1.031571 GCCAAGAATGCCGTCATGGA 61.032 55.000 11.11 0.00 38.42 3.41
8644 8826 4.005650 CTGCCTAGATTTCAGTTTCAGCA 58.994 43.478 0.00 0.00 0.00 4.41
8738 9001 2.756760 CCTCTTGTGTTGGATGGATTGG 59.243 50.000 0.00 0.00 0.00 3.16
8777 9040 0.755327 AAGGCTGTGGTTGGGTGAAC 60.755 55.000 0.00 0.00 0.00 3.18
8832 9095 2.008329 GCTCTGCCATTGTTCTCTGAG 58.992 52.381 0.00 0.00 0.00 3.35
8833 9096 2.354503 GCTCTGCCATTGTTCTCTGAGA 60.355 50.000 2.58 2.58 0.00 3.27
8834 9097 3.260740 CTCTGCCATTGTTCTCTGAGAC 58.739 50.000 6.92 3.80 0.00 3.36
8835 9098 2.902486 TCTGCCATTGTTCTCTGAGACT 59.098 45.455 6.92 0.00 0.00 3.24
8836 9099 3.056250 TCTGCCATTGTTCTCTGAGACTC 60.056 47.826 6.92 4.62 0.00 3.36
8837 9100 2.902486 TGCCATTGTTCTCTGAGACTCT 59.098 45.455 6.92 0.00 0.00 3.24
8838 9101 3.260740 GCCATTGTTCTCTGAGACTCTG 58.739 50.000 6.92 3.34 0.00 3.35
8839 9102 3.056250 GCCATTGTTCTCTGAGACTCTGA 60.056 47.826 6.92 11.15 0.00 3.27
8847 9110 2.259875 CTGAGACTCTGACCGACCGC 62.260 65.000 3.68 0.00 0.00 5.68
8853 9116 2.434359 CTGACCGACCGCCTTTCC 60.434 66.667 0.00 0.00 0.00 3.13
8929 9327 1.326852 GCTGCTGATGATGAGTGAACG 59.673 52.381 0.00 0.00 0.00 3.95
8979 9377 3.833070 GGTCCTCTCTTTGTCCTTGTCTA 59.167 47.826 0.00 0.00 0.00 2.59
9019 9417 0.782384 CTGAACCGAGAAAACCGTCG 59.218 55.000 0.00 0.00 35.91 5.12
9020 9418 0.385029 TGAACCGAGAAAACCGTCGA 59.615 50.000 0.00 0.00 38.50 4.20
9076 9475 4.754372 TCTTAATTGACAGTGCAGCAAG 57.246 40.909 0.00 0.00 0.00 4.01
9141 9540 7.169308 ACGAACTATATGGACGAACATTTGATC 59.831 37.037 14.16 0.00 32.39 2.92
9157 9556 2.710377 TGATCTGTTGCCGTATGCTTT 58.290 42.857 0.00 0.00 42.00 3.51
9158 9557 3.081061 TGATCTGTTGCCGTATGCTTTT 58.919 40.909 0.00 0.00 42.00 2.27
9159 9558 2.987413 TCTGTTGCCGTATGCTTTTG 57.013 45.000 0.00 0.00 42.00 2.44
9191 9590 0.590230 TTTTTCGCTGTCGTTTGCCG 60.590 50.000 0.00 0.00 36.96 5.69
9247 9646 0.590195 CACAGCAAGAGAACACCAGC 59.410 55.000 0.00 0.00 0.00 4.85
9263 9662 1.407437 CCAGCGTTTAGATTCAGGCCT 60.407 52.381 0.00 0.00 0.00 5.19
9290 9689 2.814805 AACCCTGACATGATCCTTGG 57.185 50.000 0.00 0.00 0.00 3.61
9297 9696 4.082026 CCTGACATGATCCTTGGTTTTTCC 60.082 45.833 0.00 0.00 0.00 3.13
9316 9715 7.495135 TTTTCCAAAATTTCTTGAAGATGGC 57.505 32.000 6.85 0.00 0.00 4.40
9348 9748 9.706846 GATCTTTTTGTTTGCCATATTTTATGC 57.293 29.630 0.00 0.00 0.00 3.14
9350 9750 8.719648 TCTTTTTGTTTGCCATATTTTATGCAG 58.280 29.630 0.00 0.00 34.81 4.41
9351 9751 6.981762 TTTGTTTGCCATATTTTATGCAGG 57.018 33.333 0.00 0.00 34.81 4.85
9352 9752 5.929058 TGTTTGCCATATTTTATGCAGGA 57.071 34.783 0.00 0.00 34.81 3.86
9353 9753 5.904941 TGTTTGCCATATTTTATGCAGGAG 58.095 37.500 0.00 0.00 34.81 3.69
9355 9755 6.605194 TGTTTGCCATATTTTATGCAGGAGTA 59.395 34.615 0.00 0.00 34.81 2.59
9356 9756 6.633500 TTGCCATATTTTATGCAGGAGTAC 57.367 37.500 0.00 0.00 34.81 2.73
9361 9764 9.014297 GCCATATTTTATGCAGGAGTACTTTAT 57.986 33.333 0.00 0.00 0.00 1.40
9401 9804 4.802918 GCAGAACTGTAGAAGTAGGGCAAA 60.803 45.833 3.77 0.00 38.56 3.68
9402 9805 5.491982 CAGAACTGTAGAAGTAGGGCAAAT 58.508 41.667 0.00 0.00 38.56 2.32
9403 9806 6.640518 CAGAACTGTAGAAGTAGGGCAAATA 58.359 40.000 0.00 0.00 38.56 1.40
9404 9807 7.275920 CAGAACTGTAGAAGTAGGGCAAATAT 58.724 38.462 0.00 0.00 38.56 1.28
9405 9808 7.225538 CAGAACTGTAGAAGTAGGGCAAATATG 59.774 40.741 0.00 0.00 38.56 1.78
9406 9809 5.930135 ACTGTAGAAGTAGGGCAAATATGG 58.070 41.667 0.00 0.00 37.36 2.74
9407 9810 5.428783 ACTGTAGAAGTAGGGCAAATATGGT 59.571 40.000 0.00 0.00 37.36 3.55
9408 9811 5.680619 TGTAGAAGTAGGGCAAATATGGTG 58.319 41.667 0.00 0.00 0.00 4.17
9409 9812 4.862641 AGAAGTAGGGCAAATATGGTGT 57.137 40.909 0.00 0.00 0.00 4.16
9410 9813 4.526970 AGAAGTAGGGCAAATATGGTGTG 58.473 43.478 0.00 0.00 0.00 3.82
9411 9814 2.654863 AGTAGGGCAAATATGGTGTGC 58.345 47.619 0.00 0.00 37.55 4.57
9412 9815 2.242196 AGTAGGGCAAATATGGTGTGCT 59.758 45.455 0.00 0.00 38.36 4.40
9413 9816 1.477553 AGGGCAAATATGGTGTGCTG 58.522 50.000 0.00 0.00 38.36 4.41
9414 9817 1.005805 AGGGCAAATATGGTGTGCTGA 59.994 47.619 0.00 0.00 38.36 4.26
9415 9818 1.824230 GGGCAAATATGGTGTGCTGAA 59.176 47.619 0.00 0.00 38.36 3.02
9416 9819 2.417243 GGGCAAATATGGTGTGCTGAAC 60.417 50.000 0.00 0.00 38.36 3.18
9417 9820 2.417243 GGCAAATATGGTGTGCTGAACC 60.417 50.000 0.00 0.00 38.36 3.62
9418 9821 2.493278 GCAAATATGGTGTGCTGAACCT 59.507 45.455 4.94 0.00 38.60 3.50
9435 9838 0.040067 CCTGAAAGCGGTTGTTGAGC 60.040 55.000 0.00 0.00 0.00 4.26
9442 9845 3.611766 AGCGGTTGTTGAGCTAGTAAT 57.388 42.857 0.00 0.00 39.74 1.89
9443 9846 3.939066 AGCGGTTGTTGAGCTAGTAATT 58.061 40.909 0.00 0.00 39.74 1.40
9444 9847 3.684788 AGCGGTTGTTGAGCTAGTAATTG 59.315 43.478 0.00 0.00 39.74 2.32
9445 9848 3.682858 GCGGTTGTTGAGCTAGTAATTGA 59.317 43.478 0.00 0.00 0.00 2.57
9446 9849 4.153475 GCGGTTGTTGAGCTAGTAATTGAA 59.847 41.667 0.00 0.00 0.00 2.69
9448 9851 6.307155 CGGTTGTTGAGCTAGTAATTGAAAG 58.693 40.000 0.00 0.00 0.00 2.62
9449 9852 6.147164 CGGTTGTTGAGCTAGTAATTGAAAGA 59.853 38.462 0.00 0.00 0.00 2.52
9450 9853 7.522374 GGTTGTTGAGCTAGTAATTGAAAGAG 58.478 38.462 0.00 0.00 0.00 2.85
9452 9855 7.004555 TGTTGAGCTAGTAATTGAAAGAGGA 57.995 36.000 0.00 0.00 0.00 3.71
9453 9856 6.874134 TGTTGAGCTAGTAATTGAAAGAGGAC 59.126 38.462 0.00 0.00 0.00 3.85
9455 9858 5.185249 TGAGCTAGTAATTGAAAGAGGACGT 59.815 40.000 0.00 0.00 0.00 4.34
9456 9859 5.411781 AGCTAGTAATTGAAAGAGGACGTG 58.588 41.667 0.00 0.00 0.00 4.49
9488 9893 1.679898 GTCCCCATCGATCCCATCC 59.320 63.158 0.00 0.00 0.00 3.51
9491 9896 1.376466 CCCATCGATCCCATCCCAC 59.624 63.158 0.00 0.00 0.00 4.61
9493 9898 1.418097 CCATCGATCCCATCCCACCA 61.418 60.000 0.00 0.00 0.00 4.17
9544 9950 4.637489 CTCTCCATCTCCGGCGCG 62.637 72.222 0.00 0.00 0.00 6.86
9665 10071 0.518636 CTCCGACTACGACGACCAAA 59.481 55.000 0.00 0.00 42.66 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.125673 CGCGGTTGGGTGTAGAGG 60.126 66.667 0.00 0.00 0.00 3.69
80 97 2.752358 CCACCAAGCAGAGGCAGA 59.248 61.111 0.00 0.00 44.61 4.26
81 98 3.060615 GCCACCAAGCAGAGGCAG 61.061 66.667 0.00 0.00 46.26 4.85
84 101 4.335647 ACCGCCACCAAGCAGAGG 62.336 66.667 0.00 0.00 0.00 3.69
85 102 3.052082 CACCGCCACCAAGCAGAG 61.052 66.667 0.00 0.00 0.00 3.35
107 124 3.665675 GAAGAGTCGCGCCACCCAT 62.666 63.158 0.00 0.00 0.00 4.00
108 125 4.373116 GAAGAGTCGCGCCACCCA 62.373 66.667 0.00 0.00 0.00 4.51
115 135 1.146358 GGGAAATCCGAAGAGTCGCG 61.146 60.000 0.00 0.00 46.28 5.87
119 139 1.281867 TGCATGGGAAATCCGAAGAGT 59.718 47.619 0.00 0.00 38.76 3.24
142 162 1.516821 CATTGCGCAATCCCGTTGG 60.517 57.895 31.88 15.61 38.29 3.77
161 181 2.916527 ATTCCCCCGCTTGCATCCTG 62.917 60.000 0.00 0.00 0.00 3.86
195 215 3.503827 TCACTCGCGTGATAGAAATGT 57.496 42.857 16.04 0.00 44.85 2.71
238 261 4.202357 ACAACAGAGCATTCACAGTAGGAA 60.202 41.667 0.00 0.00 0.00 3.36
239 262 3.324846 ACAACAGAGCATTCACAGTAGGA 59.675 43.478 0.00 0.00 0.00 2.94
244 267 3.308053 CGGATACAACAGAGCATTCACAG 59.692 47.826 0.00 0.00 0.00 3.66
338 362 3.096092 ACTAGTAGCAGCAGAAGAAGCT 58.904 45.455 0.00 0.00 44.62 3.74
355 379 9.538508 AACCAAACAAGTTAGTACAAGTACTAG 57.461 33.333 16.88 10.15 45.92 2.57
358 382 7.280652 TGGAACCAAACAAGTTAGTACAAGTAC 59.719 37.037 2.18 2.18 36.35 2.73
361 386 6.687081 TGGAACCAAACAAGTTAGTACAAG 57.313 37.500 0.00 0.00 0.00 3.16
363 388 6.358178 TGATGGAACCAAACAAGTTAGTACA 58.642 36.000 0.00 0.00 0.00 2.90
364 389 6.870971 TGATGGAACCAAACAAGTTAGTAC 57.129 37.500 0.00 0.00 0.00 2.73
366 391 6.976934 AATGATGGAACCAAACAAGTTAGT 57.023 33.333 0.00 0.00 0.00 2.24
367 392 9.927668 AATTAATGATGGAACCAAACAAGTTAG 57.072 29.630 0.00 0.00 0.00 2.34
370 395 7.656948 CACAATTAATGATGGAACCAAACAAGT 59.343 33.333 0.00 0.00 0.00 3.16
402 427 3.324846 TCAGTTACACCTGAGACTGCATT 59.675 43.478 0.00 0.00 39.39 3.56
431 456 6.924060 AGTCGTATATCACCTCATAGCAAAAC 59.076 38.462 0.00 0.00 0.00 2.43
432 457 7.050970 AGTCGTATATCACCTCATAGCAAAA 57.949 36.000 0.00 0.00 0.00 2.44
433 458 6.650427 AGTCGTATATCACCTCATAGCAAA 57.350 37.500 0.00 0.00 0.00 3.68
434 459 7.447545 AGTTAGTCGTATATCACCTCATAGCAA 59.552 37.037 0.00 0.00 0.00 3.91
435 460 6.940867 AGTTAGTCGTATATCACCTCATAGCA 59.059 38.462 0.00 0.00 0.00 3.49
436 461 7.244898 CAGTTAGTCGTATATCACCTCATAGC 58.755 42.308 0.00 0.00 0.00 2.97
468 498 9.121658 TCTGAGTACACTAGACATAATTACTGG 57.878 37.037 0.00 0.00 0.00 4.00
491 521 5.571784 ACATGTAGGCAATTCAACATCTG 57.428 39.130 0.00 0.00 30.32 2.90
520 600 7.987458 TGTATAGAGCAATAAAGGGAACTGAAG 59.013 37.037 0.00 0.00 42.68 3.02
552 632 3.469008 AGCCCCAAACTTACAAAAAGC 57.531 42.857 0.00 0.00 0.00 3.51
585 665 9.826574 AGAAAATGCATGCACTTTCAATAATAT 57.173 25.926 39.93 23.90 42.43 1.28
746 828 9.941664 CATATGAAATCAAAGTGAATCACCTAC 57.058 33.333 10.12 0.00 34.49 3.18
784 866 4.022935 TGAAGCAAGTTGTTTAGGCATGAG 60.023 41.667 4.81 0.00 0.00 2.90
817 899 4.175787 AGGTTCAGTGAACATCGTCTAC 57.824 45.455 31.52 15.23 43.54 2.59
823 905 3.876914 TGTGTGAAGGTTCAGTGAACATC 59.123 43.478 31.52 27.21 43.54 3.06
866 948 9.722184 CTAACACCATCTCAATATCTCATCATT 57.278 33.333 0.00 0.00 0.00 2.57
867 949 8.878211 ACTAACACCATCTCAATATCTCATCAT 58.122 33.333 0.00 0.00 0.00 2.45
868 950 8.255111 ACTAACACCATCTCAATATCTCATCA 57.745 34.615 0.00 0.00 0.00 3.07
869 951 8.986847 CAACTAACACCATCTCAATATCTCATC 58.013 37.037 0.00 0.00 0.00 2.92
870 952 8.708378 TCAACTAACACCATCTCAATATCTCAT 58.292 33.333 0.00 0.00 0.00 2.90
871 953 8.078060 TCAACTAACACCATCTCAATATCTCA 57.922 34.615 0.00 0.00 0.00 3.27
872 954 9.553064 AATCAACTAACACCATCTCAATATCTC 57.447 33.333 0.00 0.00 0.00 2.75
873 955 9.911788 AAATCAACTAACACCATCTCAATATCT 57.088 29.630 0.00 0.00 0.00 1.98
874 956 9.941664 CAAATCAACTAACACCATCTCAATATC 57.058 33.333 0.00 0.00 0.00 1.63
875 957 8.408601 GCAAATCAACTAACACCATCTCAATAT 58.591 33.333 0.00 0.00 0.00 1.28
876 958 7.413988 CGCAAATCAACTAACACCATCTCAATA 60.414 37.037 0.00 0.00 0.00 1.90
877 959 6.623549 CGCAAATCAACTAACACCATCTCAAT 60.624 38.462 0.00 0.00 0.00 2.57
878 960 5.334802 CGCAAATCAACTAACACCATCTCAA 60.335 40.000 0.00 0.00 0.00 3.02
884 966 1.950216 TGCGCAAATCAACTAACACCA 59.050 42.857 8.16 0.00 0.00 4.17
952 1034 2.033927 TGATTAAACAAAGTGCAGCGCA 59.966 40.909 11.47 0.00 35.60 6.09
981 1063 3.488047 CCATTGCATTAAGCTGAGAACGG 60.488 47.826 0.00 0.00 45.94 4.44
982 1064 3.127548 ACCATTGCATTAAGCTGAGAACG 59.872 43.478 0.00 0.00 45.94 3.95
1194 1276 6.096673 TGTATGAAAGAAAAAGAAAGGGCC 57.903 37.500 0.00 0.00 0.00 5.80
1248 1331 4.476297 TGCATCAAATGGAGAAGGCATAT 58.524 39.130 0.00 0.00 0.00 1.78
1628 1711 6.926272 CCTAGATAATTGGAAGAGTACAGTGC 59.074 42.308 0.00 0.00 0.00 4.40
1691 1774 9.732130 ATAATAGCATTCCTGAATTTACTCTCC 57.268 33.333 0.00 0.00 0.00 3.71
1925 2008 4.583871 CTTTGAGCTCATTGTTACCCTCT 58.416 43.478 19.04 0.00 0.00 3.69
2001 2084 6.214412 ACATCTCTTAGTCCAACTCCTTCAAT 59.786 38.462 0.00 0.00 0.00 2.57
2006 2089 3.772025 CCACATCTCTTAGTCCAACTCCT 59.228 47.826 0.00 0.00 0.00 3.69
2090 2209 0.179215 GCTCGTTGTTCCGCTCATTG 60.179 55.000 0.00 0.00 0.00 2.82
2125 2244 6.319405 TGACACTAAACCCTTTTCTGGTAAAC 59.681 38.462 0.00 0.00 34.15 2.01
2434 2553 2.290514 CCTTCTGTTCCAGCTCCATTGA 60.291 50.000 0.00 0.00 0.00 2.57
2645 2764 7.816031 CAGACAAGAAATAAGGACGGTAGTAAA 59.184 37.037 0.00 0.00 0.00 2.01
2682 2801 2.494059 TGAAGCTGTTTGCAGGAGTAC 58.506 47.619 0.00 0.00 45.94 2.73
2811 2930 8.480501 AGGCATTTGAAGATATTACAGCATTTT 58.519 29.630 0.00 0.00 0.00 1.82
2893 3012 3.436704 CACCATGAAGTAACGCTGTGATT 59.563 43.478 0.00 0.00 0.00 2.57
2898 3017 1.732259 GGTCACCATGAAGTAACGCTG 59.268 52.381 0.00 0.00 0.00 5.18
2906 3025 3.432749 CCATCCTGTAGGTCACCATGAAG 60.433 52.174 0.00 0.00 36.34 3.02
3002 3126 3.167485 AGCTGAATTTTGCAGGATTCCA 58.833 40.909 16.73 8.04 34.00 3.53
3750 3876 4.970662 TCATTCTGCAATGAAGGTAAGC 57.029 40.909 0.00 0.00 44.56 3.09
3937 4065 9.235537 GATAAAAGTTGGTACTATCTCGTCTTC 57.764 37.037 0.00 0.00 33.17 2.87
4069 4197 1.286849 TGGAACGGAGGGAGTAGATCA 59.713 52.381 0.00 0.00 0.00 2.92
4076 4204 4.101119 ACAAGTAATATGGAACGGAGGGAG 59.899 45.833 0.00 0.00 0.00 4.30
4077 4205 4.035112 ACAAGTAATATGGAACGGAGGGA 58.965 43.478 0.00 0.00 0.00 4.20
4078 4206 4.377897 GACAAGTAATATGGAACGGAGGG 58.622 47.826 0.00 0.00 0.00 4.30
4079 4207 4.049186 CGACAAGTAATATGGAACGGAGG 58.951 47.826 0.00 0.00 0.00 4.30
4080 4208 3.489785 GCGACAAGTAATATGGAACGGAG 59.510 47.826 0.00 0.00 0.00 4.63
4081 4209 3.131577 AGCGACAAGTAATATGGAACGGA 59.868 43.478 0.00 0.00 0.00 4.69
4082 4210 3.245284 CAGCGACAAGTAATATGGAACGG 59.755 47.826 0.00 0.00 0.00 4.44
4083 4211 4.109766 TCAGCGACAAGTAATATGGAACG 58.890 43.478 0.00 0.00 0.00 3.95
4084 4212 6.604735 AATCAGCGACAAGTAATATGGAAC 57.395 37.500 0.00 0.00 0.00 3.62
4085 4213 7.985184 ACTAAATCAGCGACAAGTAATATGGAA 59.015 33.333 0.00 0.00 0.00 3.53
4086 4214 7.497595 ACTAAATCAGCGACAAGTAATATGGA 58.502 34.615 0.00 0.00 0.00 3.41
4087 4215 7.715265 ACTAAATCAGCGACAAGTAATATGG 57.285 36.000 0.00 0.00 0.00 2.74
4088 4216 9.244799 TGTACTAAATCAGCGACAAGTAATATG 57.755 33.333 0.00 0.00 0.00 1.78
4089 4217 9.811995 TTGTACTAAATCAGCGACAAGTAATAT 57.188 29.630 0.00 0.00 31.65 1.28
4090 4218 9.642327 TTTGTACTAAATCAGCGACAAGTAATA 57.358 29.630 0.00 0.00 35.77 0.98
4091 4219 8.542497 TTTGTACTAAATCAGCGACAAGTAAT 57.458 30.769 0.00 0.00 35.77 1.89
4092 4220 7.654520 ACTTTGTACTAAATCAGCGACAAGTAA 59.345 33.333 0.00 0.00 35.77 2.24
4093 4221 7.149973 ACTTTGTACTAAATCAGCGACAAGTA 58.850 34.615 0.00 0.00 35.77 2.24
4094 4222 5.989777 ACTTTGTACTAAATCAGCGACAAGT 59.010 36.000 0.00 0.00 35.77 3.16
4095 4223 6.467723 ACTTTGTACTAAATCAGCGACAAG 57.532 37.500 0.00 0.00 35.77 3.16
4096 4224 6.259167 ACAACTTTGTACTAAATCAGCGACAA 59.741 34.615 0.00 0.00 40.16 3.18
4097 4225 5.756347 ACAACTTTGTACTAAATCAGCGACA 59.244 36.000 0.00 0.00 40.16 4.35
4098 4226 6.224420 ACAACTTTGTACTAAATCAGCGAC 57.776 37.500 0.00 0.00 40.16 5.19
4111 4239 7.807433 TCGTCGCTAATTTAGTACAACTTTGTA 59.193 33.333 5.38 0.00 42.35 2.41
4112 4240 6.642131 TCGTCGCTAATTTAGTACAACTTTGT 59.358 34.615 5.38 0.00 44.86 2.83
4113 4241 7.041187 TCGTCGCTAATTTAGTACAACTTTG 57.959 36.000 5.38 0.00 0.00 2.77
4114 4242 6.865205 ACTCGTCGCTAATTTAGTACAACTTT 59.135 34.615 5.38 0.00 0.00 2.66
4115 4243 6.385033 ACTCGTCGCTAATTTAGTACAACTT 58.615 36.000 5.38 0.00 0.00 2.66
4116 4244 5.947443 ACTCGTCGCTAATTTAGTACAACT 58.053 37.500 5.38 0.00 0.00 3.16
4117 4245 7.725610 TTACTCGTCGCTAATTTAGTACAAC 57.274 36.000 5.38 0.00 0.00 3.32
4119 4247 9.603298 CATATTACTCGTCGCTAATTTAGTACA 57.397 33.333 5.38 0.00 0.00 2.90
4120 4248 9.059485 CCATATTACTCGTCGCTAATTTAGTAC 57.941 37.037 5.38 3.82 0.00 2.73
4121 4249 9.002600 TCCATATTACTCGTCGCTAATTTAGTA 57.997 33.333 5.38 0.00 0.00 1.82
4122 4250 7.879070 TCCATATTACTCGTCGCTAATTTAGT 58.121 34.615 5.38 0.00 0.00 2.24
4123 4251 8.636843 GTTCCATATTACTCGTCGCTAATTTAG 58.363 37.037 0.00 0.00 0.00 1.85
4124 4252 7.324375 CGTTCCATATTACTCGTCGCTAATTTA 59.676 37.037 0.00 0.00 0.00 1.40
4125 4253 6.143438 CGTTCCATATTACTCGTCGCTAATTT 59.857 38.462 0.00 0.00 0.00 1.82
4126 4254 5.628193 CGTTCCATATTACTCGTCGCTAATT 59.372 40.000 0.00 0.00 0.00 1.40
4127 4255 5.152097 CGTTCCATATTACTCGTCGCTAAT 58.848 41.667 0.00 0.00 0.00 1.73
4128 4256 4.530388 CGTTCCATATTACTCGTCGCTAA 58.470 43.478 0.00 0.00 0.00 3.09
4129 4257 3.058708 CCGTTCCATATTACTCGTCGCTA 60.059 47.826 0.00 0.00 0.00 4.26
4130 4258 2.287427 CCGTTCCATATTACTCGTCGCT 60.287 50.000 0.00 0.00 0.00 4.93
4131 4259 2.049228 CCGTTCCATATTACTCGTCGC 58.951 52.381 0.00 0.00 0.00 5.19
4132 4260 3.552541 CTCCGTTCCATATTACTCGTCG 58.447 50.000 0.00 0.00 0.00 5.12
4133 4261 3.305199 CCCTCCGTTCCATATTACTCGTC 60.305 52.174 0.00 0.00 0.00 4.20
4134 4262 2.626743 CCCTCCGTTCCATATTACTCGT 59.373 50.000 0.00 0.00 0.00 4.18
4135 4263 2.889045 TCCCTCCGTTCCATATTACTCG 59.111 50.000 0.00 0.00 0.00 4.18
4136 4264 3.896272 ACTCCCTCCGTTCCATATTACTC 59.104 47.826 0.00 0.00 0.00 2.59
4137 4265 3.924922 ACTCCCTCCGTTCCATATTACT 58.075 45.455 0.00 0.00 0.00 2.24
4138 4266 5.245526 ACATACTCCCTCCGTTCCATATTAC 59.754 44.000 0.00 0.00 0.00 1.89
4139 4267 5.399991 ACATACTCCCTCCGTTCCATATTA 58.600 41.667 0.00 0.00 0.00 0.98
4140 4268 4.232091 ACATACTCCCTCCGTTCCATATT 58.768 43.478 0.00 0.00 0.00 1.28
4141 4269 3.858135 ACATACTCCCTCCGTTCCATAT 58.142 45.455 0.00 0.00 0.00 1.78
4142 4270 3.323774 ACATACTCCCTCCGTTCCATA 57.676 47.619 0.00 0.00 0.00 2.74
4143 4271 2.176247 ACATACTCCCTCCGTTCCAT 57.824 50.000 0.00 0.00 0.00 3.41
4144 4272 1.946984 AACATACTCCCTCCGTTCCA 58.053 50.000 0.00 0.00 0.00 3.53
4145 4273 3.244112 CCATAACATACTCCCTCCGTTCC 60.244 52.174 0.00 0.00 0.00 3.62
4146 4274 3.802675 GCCATAACATACTCCCTCCGTTC 60.803 52.174 0.00 0.00 0.00 3.95
4147 4275 2.104281 GCCATAACATACTCCCTCCGTT 59.896 50.000 0.00 0.00 0.00 4.44
4148 4276 1.692519 GCCATAACATACTCCCTCCGT 59.307 52.381 0.00 0.00 0.00 4.69
4149 4277 1.002087 GGCCATAACATACTCCCTCCG 59.998 57.143 0.00 0.00 0.00 4.63
4150 4278 1.002087 CGGCCATAACATACTCCCTCC 59.998 57.143 2.24 0.00 0.00 4.30
4151 4279 1.002087 CCGGCCATAACATACTCCCTC 59.998 57.143 2.24 0.00 0.00 4.30
4152 4280 1.056660 CCGGCCATAACATACTCCCT 58.943 55.000 2.24 0.00 0.00 4.20
4153 4281 0.605589 GCCGGCCATAACATACTCCC 60.606 60.000 18.11 0.00 0.00 4.30
4154 4282 0.605589 GGCCGGCCATAACATACTCC 60.606 60.000 40.73 7.78 35.81 3.85
4508 4651 0.246635 CGGAGACATGGTCGAAACCT 59.753 55.000 0.00 0.00 46.60 3.50
4594 4737 3.893763 CGAGAGCGAGGCCGTGAT 61.894 66.667 0.00 0.00 40.82 3.06
5340 5483 0.814010 GTGACGGTGGAAACTGCACT 60.814 55.000 0.00 0.00 38.83 4.40
5868 6011 2.925706 TGTTACGCCTGGGCCTGA 60.926 61.111 12.58 0.00 37.98 3.86
5911 6054 1.302383 CCCACAAATAACTCGGCGCA 61.302 55.000 10.83 0.00 0.00 6.09
6040 6183 1.006758 AGTCTGGGACGGTGATTCCTA 59.993 52.381 0.00 0.00 37.67 2.94
6766 6910 5.899547 ACAACAGAGGAGACCATCACATATA 59.100 40.000 0.00 0.00 0.00 0.86
6820 6964 0.034089 GTGGTTTCCCCAGGAGATGG 60.034 60.000 0.00 0.00 46.45 3.51
6923 7067 9.821765 TGGAACAATGTTAGGCCAACTTATGGA 62.822 40.741 5.01 0.00 45.28 3.41
6951 7095 7.726291 TGGTGAAATCTACAACTTTGGGATAAA 59.274 33.333 0.00 0.00 0.00 1.40
6974 7118 0.696501 GGTGTGGAGGTTATGGTGGT 59.303 55.000 0.00 0.00 0.00 4.16
7178 7323 2.829120 GAGACTGTCTCCCTGCTTAAGT 59.171 50.000 24.05 0.00 37.55 2.24
7249 7395 5.046591 TGGAGACCAACACCTAGAAGTTATG 60.047 44.000 0.00 0.00 0.00 1.90
7352 7503 3.702548 TGATGCCAGCTTTAGATGCATTT 59.297 39.130 0.00 0.00 31.86 2.32
7353 7504 3.293337 TGATGCCAGCTTTAGATGCATT 58.707 40.909 0.00 0.00 31.86 3.56
7354 7505 2.940158 TGATGCCAGCTTTAGATGCAT 58.060 42.857 0.00 0.00 33.41 3.96
7412 7563 6.972977 ACTACAGAAGTACGCACTTTTGCAC 61.973 44.000 16.70 0.00 46.03 4.57
7447 7598 9.899226 AATAGCAAATAGAGAAACAAGAACAAC 57.101 29.630 0.00 0.00 0.00 3.32
7715 7866 5.473504 ACTTACTTTTGCTGGGTTGATAGTG 59.526 40.000 0.00 0.00 0.00 2.74
7749 7900 4.022849 AGACTTTTGCAGGTTGTATTGCTC 60.023 41.667 0.00 0.00 40.87 4.26
7847 7998 6.274157 ACATACTGCTTCGATATAAGGAGG 57.726 41.667 10.45 0.00 46.04 4.30
7891 8042 4.644685 AGGCTAATGAATACCGTGCAATTT 59.355 37.500 0.00 0.00 0.00 1.82
7972 8123 6.751425 TCGTAGCATTAGCAAAATGGAAATTG 59.249 34.615 12.19 0.00 45.49 2.32
8069 8220 3.187700 CCGTATGACAACCTCTTACTGC 58.812 50.000 0.00 0.00 30.52 4.40
8236 8394 0.461163 TTACATGGGCCGACATCGTG 60.461 55.000 0.00 0.00 37.74 4.35
8314 8473 1.002134 ACGGCATTGCTAAGCACCT 60.002 52.632 8.82 0.00 38.71 4.00
8386 8545 3.824443 TCATAGAACTCAACAGTGGACGA 59.176 43.478 0.00 0.00 31.06 4.20
8394 8553 4.890158 TCTTGGCTCATAGAACTCAACA 57.110 40.909 0.00 0.00 0.00 3.33
8403 8562 1.869767 GACGGCATTCTTGGCTCATAG 59.130 52.381 0.00 0.00 45.85 2.23
8406 8565 0.035152 ATGACGGCATTCTTGGCTCA 60.035 50.000 0.00 2.10 45.85 4.26
8428 8587 2.159382 GTTCATTGGTTCCACCGTCAT 58.841 47.619 0.00 0.00 42.58 3.06
8432 8591 2.482721 GTGTAGTTCATTGGTTCCACCG 59.517 50.000 0.00 0.00 42.58 4.94
8600 8770 5.527582 CAGTAATGTAGGTTGGATGTTAGCC 59.472 44.000 0.00 0.00 0.00 3.93
8644 8826 7.041098 ACAGCGAGAAAATCAAGTGATAAAACT 60.041 33.333 0.00 0.00 33.73 2.66
8738 9001 2.047274 TTGTAGCGCTCCACCTGC 60.047 61.111 16.34 0.00 0.00 4.85
8777 9040 2.283298 CCGATTGACTTCATCCCTGTG 58.717 52.381 0.00 0.00 0.00 3.66
8832 9095 2.156051 AAAGGCGGTCGGTCAGAGTC 62.156 60.000 0.00 0.00 0.00 3.36
8833 9096 2.156051 GAAAGGCGGTCGGTCAGAGT 62.156 60.000 0.00 0.00 0.00 3.24
8834 9097 1.446272 GAAAGGCGGTCGGTCAGAG 60.446 63.158 0.00 0.00 0.00 3.35
8835 9098 2.654877 GAAAGGCGGTCGGTCAGA 59.345 61.111 0.00 0.00 0.00 3.27
8836 9099 2.434359 GGAAAGGCGGTCGGTCAG 60.434 66.667 0.00 0.00 0.00 3.51
8837 9100 4.011517 GGGAAAGGCGGTCGGTCA 62.012 66.667 0.00 0.00 0.00 4.02
8838 9101 4.772687 GGGGAAAGGCGGTCGGTC 62.773 72.222 0.00 0.00 0.00 4.79
8847 9110 2.500098 TGTCAAGTAGATCGGGGAAAGG 59.500 50.000 0.00 0.00 0.00 3.11
8853 9116 1.065701 CGGAGTGTCAAGTAGATCGGG 59.934 57.143 0.00 0.00 0.00 5.14
8916 9314 1.470098 GCTTTGCCGTTCACTCATCAT 59.530 47.619 0.00 0.00 0.00 2.45
8929 9327 3.381045 GGTCTTAACAGTTTGCTTTGCC 58.619 45.455 0.00 0.00 0.00 4.52
8979 9377 2.174360 GAGGCAAGGGCTTCTGAATTT 58.826 47.619 0.00 0.00 42.43 1.82
9019 9417 2.673833 ACGAGAAATTGGACAGTCGTC 58.326 47.619 0.00 0.00 35.89 4.20
9020 9418 2.814280 ACGAGAAATTGGACAGTCGT 57.186 45.000 0.00 0.00 35.90 4.34
9076 9475 6.005583 TCAGTTCAGTTTCAAATCAGATGC 57.994 37.500 0.00 0.00 0.00 3.91
9157 9556 5.341993 CAGCGAAAAACGATCATAAAAGCAA 59.658 36.000 0.00 0.00 45.77 3.91
9158 9557 4.851014 CAGCGAAAAACGATCATAAAAGCA 59.149 37.500 0.00 0.00 45.77 3.91
9159 9558 4.851558 ACAGCGAAAAACGATCATAAAAGC 59.148 37.500 0.00 0.00 45.77 3.51
9160 9559 5.223094 CGACAGCGAAAAACGATCATAAAAG 59.777 40.000 0.00 0.00 45.77 2.27
9161 9560 5.076765 CGACAGCGAAAAACGATCATAAAA 58.923 37.500 0.00 0.00 45.77 1.52
9162 9561 4.150980 ACGACAGCGAAAAACGATCATAAA 59.849 37.500 0.00 0.00 45.77 1.40
9163 9562 3.676172 ACGACAGCGAAAAACGATCATAA 59.324 39.130 0.00 0.00 45.77 1.90
9164 9563 3.247442 ACGACAGCGAAAAACGATCATA 58.753 40.909 0.00 0.00 45.77 2.15
9191 9590 4.335594 AGTTGCTTCAGTAAACAACAGGAC 59.664 41.667 7.39 0.00 43.74 3.85
9247 9646 1.017387 GCCAGGCCTGAATCTAAACG 58.983 55.000 34.91 14.69 0.00 3.60
9272 9671 1.673767 ACCAAGGATCATGTCAGGGT 58.326 50.000 0.00 0.00 0.00 4.34
9290 9689 7.857389 GCCATCTTCAAGAAATTTTGGAAAAAC 59.143 33.333 8.01 0.00 0.00 2.43
9316 9715 8.767478 ATATGGCAAACAAAAAGATCTTGAAG 57.233 30.769 9.17 4.32 0.00 3.02
9322 9721 9.706846 GCATAAAATATGGCAAACAAAAAGATC 57.293 29.630 0.00 0.00 0.00 2.75
9324 9723 8.613060 TGCATAAAATATGGCAAACAAAAAGA 57.387 26.923 0.00 0.00 32.54 2.52
9325 9724 7.964011 CCTGCATAAAATATGGCAAACAAAAAG 59.036 33.333 0.00 0.00 35.59 2.27
9331 9731 5.906073 ACTCCTGCATAAAATATGGCAAAC 58.094 37.500 0.00 0.00 35.59 2.93
9361 9764 8.614346 ACAGTTCTGCTACAATTTTACGTTTTA 58.386 29.630 0.00 0.00 0.00 1.52
9378 9781 2.233922 TGCCCTACTTCTACAGTTCTGC 59.766 50.000 0.00 0.00 36.88 4.26
9379 9782 4.537135 TTGCCCTACTTCTACAGTTCTG 57.463 45.455 0.00 0.00 36.88 3.02
9401 9804 3.719268 TTCAGGTTCAGCACACCATAT 57.281 42.857 2.20 0.00 36.67 1.78
9402 9805 3.411446 CTTTCAGGTTCAGCACACCATA 58.589 45.455 2.20 0.00 36.67 2.74
9403 9806 2.233271 CTTTCAGGTTCAGCACACCAT 58.767 47.619 2.20 0.00 36.67 3.55
9404 9807 1.679139 CTTTCAGGTTCAGCACACCA 58.321 50.000 2.20 0.00 36.67 4.17
9405 9808 0.312102 GCTTTCAGGTTCAGCACACC 59.688 55.000 0.00 0.00 33.45 4.16
9406 9809 0.040958 CGCTTTCAGGTTCAGCACAC 60.041 55.000 0.00 0.00 32.71 3.82
9407 9810 1.165907 CCGCTTTCAGGTTCAGCACA 61.166 55.000 0.00 0.00 32.71 4.57
9408 9811 1.166531 ACCGCTTTCAGGTTCAGCAC 61.167 55.000 0.00 0.00 39.29 4.40
9409 9812 1.148273 ACCGCTTTCAGGTTCAGCA 59.852 52.632 0.00 0.00 39.29 4.41
9410 9813 4.065110 ACCGCTTTCAGGTTCAGC 57.935 55.556 0.00 0.00 39.29 4.26
9415 9818 1.308998 CTCAACAACCGCTTTCAGGT 58.691 50.000 0.00 0.00 45.29 4.00
9416 9819 0.040067 GCTCAACAACCGCTTTCAGG 60.040 55.000 0.00 0.00 0.00 3.86
9417 9820 0.947244 AGCTCAACAACCGCTTTCAG 59.053 50.000 0.00 0.00 0.00 3.02
9418 9821 2.143122 CTAGCTCAACAACCGCTTTCA 58.857 47.619 0.00 0.00 35.33 2.69
9435 9838 5.289675 CAGCACGTCCTCTTTCAATTACTAG 59.710 44.000 0.00 0.00 0.00 2.57
9442 9845 1.540363 GGTCAGCACGTCCTCTTTCAA 60.540 52.381 0.00 0.00 0.00 2.69
9443 9846 0.033504 GGTCAGCACGTCCTCTTTCA 59.966 55.000 0.00 0.00 0.00 2.69
9444 9847 0.318762 AGGTCAGCACGTCCTCTTTC 59.681 55.000 0.00 0.00 0.00 2.62
9445 9848 0.759346 AAGGTCAGCACGTCCTCTTT 59.241 50.000 0.00 0.00 31.16 2.52
9446 9849 0.759346 AAAGGTCAGCACGTCCTCTT 59.241 50.000 0.00 0.00 31.16 2.85
9448 9851 1.000506 TGTAAAGGTCAGCACGTCCTC 59.999 52.381 0.00 0.00 31.16 3.71
9449 9852 1.045407 TGTAAAGGTCAGCACGTCCT 58.955 50.000 0.00 0.00 34.21 3.85
9450 9853 1.145803 GTGTAAAGGTCAGCACGTCC 58.854 55.000 0.00 0.00 0.00 4.79
9452 9855 2.895039 CGTGTAAAGGTCAGCACGT 58.105 52.632 7.63 0.00 46.30 4.49
9455 9858 0.034337 GGGACGTGTAAAGGTCAGCA 59.966 55.000 7.98 0.00 34.87 4.41
9456 9859 0.672711 GGGGACGTGTAAAGGTCAGC 60.673 60.000 7.98 0.00 34.87 4.26
9488 9893 2.359850 CATCGGTGGGTGTGGTGG 60.360 66.667 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.