Multiple sequence alignment - TraesCS4A01G281700

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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 TraesCS4A01G281700 chr4A 100.000 6226 0 0 1 6226 589608173 589601948 0.000000e+00 11498.0
1 TraesCS4A01G281700 chr4A 81.741 586 99 8 3052 3633 589604879 589604298 3.370000e-132 483.0
2 TraesCS4A01G281700 chr4A 81.741 586 99 8 3295 3876 589605122 589604541 3.370000e-132 483.0
3 TraesCS4A01G281700 chr4A 95.516 223 10 0 748 970 589616891 589616669 2.130000e-94 357.0
4 TraesCS4A01G281700 chr4A 96.970 33 1 0 4232 4264 589596379 589596411 8.720000e-04 56.5
5 TraesCS4A01G281700 chr4D 94.340 4876 230 25 740 5591 12704332 12699479 0.000000e+00 7433.0
6 TraesCS4A01G281700 chr4D 82.594 586 94 8 3052 3633 12701787 12701206 1.550000e-140 510.0
7 TraesCS4A01G281700 chr4D 80.371 647 113 13 3237 3876 12702088 12701449 4.370000e-131 479.0
8 TraesCS4A01G281700 chr4D 84.870 423 48 11 5759 6168 12698984 12698565 4.490000e-111 412.0
9 TraesCS4A01G281700 chr4D 94.286 35 2 0 3993 4027 12737540 12737574 3.000000e-03 54.7
10 TraesCS4A01G281700 chr4B 91.864 5359 287 58 780 6046 23408569 23403268 0.000000e+00 7343.0
11 TraesCS4A01G281700 chr4B 82.253 586 96 8 3052 3633 23406096 23405515 3.350000e-137 499.0
12 TraesCS4A01G281700 chr4B 81.293 588 98 11 3295 3876 23406339 23405758 3.400000e-127 466.0
13 TraesCS4A01G281700 chr2A 99.584 722 2 1 1 721 62229645 62230366 0.000000e+00 1315.0
14 TraesCS4A01G281700 chr2B 98.267 750 10 2 1 749 76854617 76855364 0.000000e+00 1310.0
15 TraesCS4A01G281700 chr2B 83.976 337 37 8 4961 5290 138121099 138120773 2.180000e-79 307.0
16 TraesCS4A01G281700 chr5D 97.330 749 15 3 1 748 458481554 458482298 0.000000e+00 1267.0
17 TraesCS4A01G281700 chr7D 97.200 750 15 4 1 749 465912066 465912810 0.000000e+00 1264.0
18 TraesCS4A01G281700 chr5B 96.552 754 20 3 1 754 161578660 161577913 0.000000e+00 1243.0
19 TraesCS4A01G281700 chr1D 96.538 751 16 5 1 749 374556968 374556226 0.000000e+00 1234.0
20 TraesCS4A01G281700 chr1D 85.294 340 38 4 4907 5241 51927282 51927614 2.150000e-89 340.0
21 TraesCS4A01G281700 chr6A 96.395 749 24 2 1 748 34741007 34741753 0.000000e+00 1230.0
22 TraesCS4A01G281700 chr7A 96.000 750 26 3 1 749 634060832 634060086 0.000000e+00 1216.0
23 TraesCS4A01G281700 chr2D 95.301 681 25 6 72 750 33846979 33847654 0.000000e+00 1074.0
24 TraesCS4A01G281700 chr3D 84.469 367 44 8 4906 5267 301345898 301345540 3.570000e-92 350.0
25 TraesCS4A01G281700 chr3B 82.493 337 29 10 4961 5290 646714410 646714097 1.030000e-67 268.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G281700 chr4A 589601948 589608173 6225 True 4154.666667 11498 87.827333 1 6226 3 chr4A.!!$R2 6225
1 TraesCS4A01G281700 chr4D 12698565 12704332 5767 True 2208.500000 7433 85.543750 740 6168 4 chr4D.!!$R1 5428
2 TraesCS4A01G281700 chr4B 23403268 23408569 5301 True 2769.333333 7343 85.136667 780 6046 3 chr4B.!!$R1 5266
3 TraesCS4A01G281700 chr2A 62229645 62230366 721 False 1315.000000 1315 99.584000 1 721 1 chr2A.!!$F1 720
4 TraesCS4A01G281700 chr2B 76854617 76855364 747 False 1310.000000 1310 98.267000 1 749 1 chr2B.!!$F1 748
5 TraesCS4A01G281700 chr5D 458481554 458482298 744 False 1267.000000 1267 97.330000 1 748 1 chr5D.!!$F1 747
6 TraesCS4A01G281700 chr7D 465912066 465912810 744 False 1264.000000 1264 97.200000 1 749 1 chr7D.!!$F1 748
7 TraesCS4A01G281700 chr5B 161577913 161578660 747 True 1243.000000 1243 96.552000 1 754 1 chr5B.!!$R1 753
8 TraesCS4A01G281700 chr1D 374556226 374556968 742 True 1234.000000 1234 96.538000 1 749 1 chr1D.!!$R1 748
9 TraesCS4A01G281700 chr6A 34741007 34741753 746 False 1230.000000 1230 96.395000 1 748 1 chr6A.!!$F1 747
10 TraesCS4A01G281700 chr7A 634060086 634060832 746 True 1216.000000 1216 96.000000 1 749 1 chr7A.!!$R1 748
11 TraesCS4A01G281700 chr2D 33846979 33847654 675 False 1074.000000 1074 95.301000 72 750 1 chr2D.!!$F1 678

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
775 783 1.167851 CGCTTCAGATTTTCCAGCCA 58.832 50.0 0.00 0.00 0.00 4.75 F
2301 2328 0.179094 TGGAGTATTGTAAGGCGCGG 60.179 55.0 8.83 0.00 0.00 6.46 F
3420 3447 0.387202 AGAGGGATCTTGATGTCGCG 59.613 55.0 0.00 0.00 33.09 5.87 F
4170 4197 0.179018 AGCTCGAAACAAGGCTTGGT 60.179 50.0 29.26 22.41 34.12 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2548 2575 0.877071 AACTCATTCTGCAACTGCCG 59.123 50.0 0.00 0.00 41.18 5.69 R
3719 3746 1.159285 TGCTTCATTGAGAGCAACCG 58.841 50.0 16.17 0.00 36.72 4.44 R
4785 4812 1.252904 TGATCCTTGCCAAGCTTGCC 61.253 55.0 21.43 11.17 0.00 4.52 R
5795 6162 0.032615 ACAAAGTGAACCTGGGGCAA 60.033 50.0 0.00 0.00 0.00 4.52 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
144 145 5.163301 GGAATGTCAGCTGTCTAGGGAAATA 60.163 44.000 14.67 0.00 0.00 1.40
756 764 6.587608 ACGTGCCATTTACTAGTACTGTAAAC 59.412 38.462 22.02 14.91 40.98 2.01
758 766 5.577945 TGCCATTTACTAGTACTGTAAACGC 59.422 40.000 22.02 23.01 40.98 4.84
766 774 6.921914 ACTAGTACTGTAAACGCTTCAGATT 58.078 36.000 5.39 0.00 33.93 2.40
768 776 7.871463 ACTAGTACTGTAAACGCTTCAGATTTT 59.129 33.333 5.39 0.00 33.93 1.82
773 781 2.997485 AACGCTTCAGATTTTCCAGC 57.003 45.000 0.00 0.00 0.00 4.85
775 783 1.167851 CGCTTCAGATTTTCCAGCCA 58.832 50.000 0.00 0.00 0.00 4.75
778 787 3.733077 CGCTTCAGATTTTCCAGCCATTC 60.733 47.826 0.00 0.00 0.00 2.67
793 802 3.006752 AGCCATTCTGAAAATTCGGCAAA 59.993 39.130 15.63 0.00 40.58 3.68
797 806 6.536688 CCATTCTGAAAATTCGGCAAATTTC 58.463 36.000 8.86 0.97 44.88 2.17
802 811 4.509600 TGAAAATTCGGCAAATTTCACCAC 59.490 37.500 8.86 2.40 44.88 4.16
803 812 3.742433 AATTCGGCAAATTTCACCACA 57.258 38.095 7.39 0.00 33.69 4.17
805 814 3.296322 TTCGGCAAATTTCACCACATC 57.704 42.857 7.39 0.00 0.00 3.06
806 815 2.513753 TCGGCAAATTTCACCACATCT 58.486 42.857 7.39 0.00 0.00 2.90
841 850 4.035102 GGACCCCACTGTCAGCCC 62.035 72.222 0.00 0.00 36.97 5.19
845 854 2.348998 CCCACTGTCAGCCCACTC 59.651 66.667 0.00 0.00 0.00 3.51
1042 1063 2.280524 CGCCGAACCCACTGACAA 60.281 61.111 0.00 0.00 0.00 3.18
1128 1149 4.623886 GCCCAAATTCCAAATCTTTCCTCC 60.624 45.833 0.00 0.00 0.00 4.30
1138 1159 2.204244 TTTCCTCCCCTGTCCCCC 60.204 66.667 0.00 0.00 0.00 5.40
1139 1160 4.733725 TTCCTCCCCTGTCCCCCG 62.734 72.222 0.00 0.00 0.00 5.73
1195 1216 2.524394 GGATCTCTAGCCCCCGCA 60.524 66.667 0.00 0.00 37.52 5.69
1308 1329 4.700365 CGCGTGCCTGACTGACGA 62.700 66.667 0.00 0.00 35.05 4.20
1803 1830 2.604686 AGGTGCTCGGAGGCTGAA 60.605 61.111 7.20 0.00 0.00 3.02
1812 1839 2.297129 GGAGGCTGAACAGAGGGCT 61.297 63.158 5.97 0.00 38.56 5.19
2049 2076 2.558359 GTTGGATTCCAAGACAAGGGTG 59.442 50.000 18.49 0.00 44.82 4.61
2088 2115 1.580942 GCTCGAAATGTGCAGCCAA 59.419 52.632 0.00 0.00 37.06 4.52
2143 2170 3.519579 CTCGAAGCAGAGATGTGTGATT 58.480 45.455 0.00 0.00 40.57 2.57
2203 2230 1.296715 GCCAGGTCGACCATTGAGT 59.703 57.895 35.00 11.85 38.89 3.41
2301 2328 0.179094 TGGAGTATTGTAAGGCGCGG 60.179 55.000 8.83 0.00 0.00 6.46
2313 2340 2.398554 GGCGCGGCTTGATCAAGAA 61.399 57.895 34.43 2.24 40.79 2.52
2319 2346 3.174375 GCGGCTTGATCAAGAAAATGAC 58.826 45.455 34.43 16.87 40.79 3.06
2394 2421 1.304381 TGCAGGGATGTTGAAGGGC 60.304 57.895 0.00 0.00 0.00 5.19
2479 2506 4.639135 AAAGAAACAGAGTGGAAAGCAC 57.361 40.909 0.00 0.00 0.00 4.40
2511 2538 4.462133 AGCTTGAGAATGATCTTGATGGG 58.538 43.478 0.00 0.00 35.54 4.00
2548 2575 6.127786 GCTGGATTCCAAAGATATGCTAATCC 60.128 42.308 6.88 0.00 39.43 3.01
2593 2620 3.636679 AGCAGTTATAGCTCACTGGAGA 58.363 45.455 17.81 0.00 44.26 3.71
2685 2712 9.330063 TCCTGCTCATGTATTGATACTTTAAAG 57.670 33.333 13.76 13.76 32.72 1.85
2792 2819 0.607489 CAGTCCCAAGCTGAACAGGG 60.607 60.000 3.99 0.00 42.86 4.45
2846 2873 5.728898 GCGGAAGAATTGAACAGCTAGAATG 60.729 44.000 0.00 0.00 0.00 2.67
3171 3198 5.221224 CCATGTACTGAAGAGAGATCTGGAC 60.221 48.000 0.00 0.00 32.05 4.02
3209 3236 1.949799 ATTGGAGCTGAGGTGTCTCT 58.050 50.000 0.00 0.00 40.58 3.10
3221 3248 3.318313 AGGTGTCTCTCAGGGAAGAAAA 58.682 45.455 0.00 0.00 0.00 2.29
3225 3252 3.973973 TGTCTCTCAGGGAAGAAAAGGAA 59.026 43.478 0.00 0.00 0.00 3.36
3250 3277 8.779354 AAAGTTACTAGGTGCTCTTAATGAAG 57.221 34.615 0.00 0.00 0.00 3.02
3270 3297 0.593128 CAAACTGTGCCCTTTCCGAG 59.407 55.000 0.00 0.00 0.00 4.63
3283 3310 3.193691 CCTTTCCGAGAGTAAGAGCAAGA 59.806 47.826 0.00 0.00 0.00 3.02
3303 3330 5.613358 AGATTTGTGAGAACGAAATCACC 57.387 39.130 13.32 2.23 44.19 4.02
3309 3336 3.186613 GTGAGAACGAAATCACCCTTCAC 59.813 47.826 0.00 0.00 39.94 3.18
3330 3357 3.817647 ACCAGCAAAAGCAAGAAGTAGAG 59.182 43.478 0.00 0.00 0.00 2.43
3360 3387 5.163364 GGAAGAGCTGAGAGTTGATATGGAA 60.163 44.000 0.00 0.00 0.00 3.53
3379 3406 4.103469 TGGAAACTAAACTCAAGGGCTACA 59.897 41.667 0.00 0.00 0.00 2.74
3420 3447 0.387202 AGAGGGATCTTGATGTCGCG 59.613 55.000 0.00 0.00 33.09 5.87
3474 3501 4.024218 CACACAGAAGAAAAGGAGAAGCTG 60.024 45.833 0.00 0.00 0.00 4.24
3552 3579 7.348815 TGGACCAACTCAAGATCAATATTCAT 58.651 34.615 0.00 0.00 0.00 2.57
3562 3589 9.181061 TCAAGATCAATATTCATCAGCAAAAGA 57.819 29.630 1.95 0.00 0.00 2.52
3694 3721 5.008514 GCTAAAATGAAAGCTGAGGAGATCC 59.991 44.000 0.00 0.00 35.80 3.36
3718 3745 7.939039 TCCACACAGAAGAAAATGAGAAGTTAT 59.061 33.333 0.00 0.00 0.00 1.89
3719 3746 8.233190 CCACACAGAAGAAAATGAGAAGTTATC 58.767 37.037 0.00 0.00 0.00 1.75
3721 3748 7.118390 ACACAGAAGAAAATGAGAAGTTATCGG 59.882 37.037 0.00 0.00 0.00 4.18
3743 3770 4.225208 GTTGCTCTCAATGAAGCAAACTC 58.775 43.478 23.70 14.08 46.72 3.01
3790 3817 3.760684 GCTGGACCAACTCAAGATCAATT 59.239 43.478 0.00 0.00 0.00 2.32
3817 3844 0.386838 GCAAAAGCAAGCACTGGAGT 59.613 50.000 0.00 0.00 0.00 3.85
3921 3948 5.817296 GGTTCTTTCTCTTGTTGCCAAATTT 59.183 36.000 0.00 0.00 0.00 1.82
3994 4021 3.379688 TGATGAGAGAGACAGGAACATCG 59.620 47.826 0.00 0.00 36.49 3.84
4054 4081 9.492973 AAGATAATTTGGGTCAAAAACTTGATG 57.507 29.630 0.00 0.00 36.90 3.07
4170 4197 0.179018 AGCTCGAAACAAGGCTTGGT 60.179 50.000 29.26 22.41 34.12 3.67
4194 4221 3.536158 TTTGAGCAGAAATACACACGC 57.464 42.857 0.00 0.00 0.00 5.34
4207 4234 1.082679 CACACGCAGAGAGCATGAGG 61.083 60.000 0.00 0.00 39.14 3.86
4275 4302 7.886629 AATTGCAGAGAAGGAAAATGCTATA 57.113 32.000 0.00 0.00 37.76 1.31
4289 4316 7.201767 GGAAAATGCTATAGCTGACATTCAACT 60.202 37.037 24.61 0.00 42.66 3.16
4329 4356 9.548208 GTTCAACTTAACATAAAGCATCTTCTC 57.452 33.333 0.00 0.00 0.00 2.87
4391 4418 1.547372 CCAGCAGCTTTATGGCTTTGT 59.453 47.619 0.00 0.00 41.00 2.83
4480 4507 0.250467 GTGCCAAAGAGAGCTGGTGA 60.250 55.000 0.00 0.00 34.97 4.02
4746 4773 1.674962 GAGCTGAATGGAATCACCTGC 59.325 52.381 0.00 0.00 39.86 4.85
4785 4812 3.725490 TCATGCGGATGAAGATCTGAAG 58.275 45.455 17.99 0.00 37.16 3.02
4935 4962 1.344114 GCAGCTCTCCCAGATAGAAGG 59.656 57.143 0.00 0.00 0.00 3.46
4959 4986 7.930325 AGGTTACCACTAAAAGAGAACAACTAC 59.070 37.037 3.51 0.00 0.00 2.73
4987 5014 4.974645 TGGTAGGTGAAGTCAGATTGTT 57.025 40.909 0.00 0.00 0.00 2.83
4988 5015 4.894784 TGGTAGGTGAAGTCAGATTGTTC 58.105 43.478 0.00 0.00 0.00 3.18
5017 5044 7.981789 TGACATTGTTGTAATCTCTGTATCCTC 59.018 37.037 0.00 0.00 35.79 3.71
5018 5045 7.275920 ACATTGTTGTAATCTCTGTATCCTCC 58.724 38.462 0.00 0.00 33.16 4.30
5021 5048 6.878317 TGTTGTAATCTCTGTATCCTCCTTG 58.122 40.000 0.00 0.00 0.00 3.61
5032 5059 3.423154 CTCCTTGTTGCCGCCGTC 61.423 66.667 0.00 0.00 0.00 4.79
5045 5072 1.533731 CCGCCGTCTGTGTTATTTTGT 59.466 47.619 0.00 0.00 0.00 2.83
5083 5110 6.627065 GCCATGTTTATCCGAAATTTCTTCCA 60.627 38.462 15.92 3.93 0.00 3.53
5084 5111 6.751888 CCATGTTTATCCGAAATTTCTTCCAC 59.248 38.462 15.92 6.03 0.00 4.02
5104 5131 7.125792 TCCACCAGTTGCCTTTAAATTAAAA 57.874 32.000 0.00 0.00 0.00 1.52
5145 5172 9.733556 AATAGAATGTGTTTGTTGTAGTCCATA 57.266 29.630 0.00 0.00 0.00 2.74
5161 5188 1.280710 CCATAGCCCACAACTGTACCA 59.719 52.381 0.00 0.00 0.00 3.25
5171 5198 6.049149 CCCACAACTGTACCATTATCTACTG 58.951 44.000 0.00 0.00 0.00 2.74
5172 5199 5.523916 CCACAACTGTACCATTATCTACTGC 59.476 44.000 0.00 0.00 0.00 4.40
5196 5223 9.742144 TGCTGAATAGTTGGGTTAATAAACTTA 57.258 29.630 5.92 0.00 35.77 2.24
5240 5272 7.284489 TGCAAAGTTCTCACCTGTTTATAACTT 59.716 33.333 0.00 0.00 37.30 2.66
5272 5304 5.472137 TCCTGAGTTGTTATTTGTAAGGTGC 59.528 40.000 0.00 0.00 0.00 5.01
5278 5310 6.714810 AGTTGTTATTTGTAAGGTGCTGATGA 59.285 34.615 0.00 0.00 0.00 2.92
5285 5317 5.101648 TGTAAGGTGCTGATGATTGATGA 57.898 39.130 0.00 0.00 0.00 2.92
5288 5320 4.498894 AGGTGCTGATGATTGATGAGAA 57.501 40.909 0.00 0.00 0.00 2.87
5292 5324 7.058525 AGGTGCTGATGATTGATGAGAATTTA 58.941 34.615 0.00 0.00 0.00 1.40
5297 5329 7.523216 GCTGATGATTGATGAGAATTTATGCCA 60.523 37.037 0.00 0.00 0.00 4.92
5317 5349 8.627208 ATGCCATCTATTTACTGGATTACAAG 57.373 34.615 0.00 0.00 31.38 3.16
5354 5386 4.792513 ATCATCATTCTTTCTCCTGCCT 57.207 40.909 0.00 0.00 0.00 4.75
5357 5389 1.561542 TCATTCTTTCTCCTGCCTCCC 59.438 52.381 0.00 0.00 0.00 4.30
5366 5398 1.305633 CCTGCCTCCCTCTGTCTGA 60.306 63.158 0.00 0.00 0.00 3.27
5378 5410 4.998033 CCCTCTGTCTGAAGAGTTAAAACC 59.002 45.833 12.59 0.00 41.89 3.27
5381 5413 2.798283 TGTCTGAAGAGTTAAAACCGCG 59.202 45.455 0.00 0.00 0.00 6.46
5383 5415 3.983344 GTCTGAAGAGTTAAAACCGCGTA 59.017 43.478 4.92 0.00 0.00 4.42
5389 5421 3.446516 AGAGTTAAAACCGCGTATCTCCT 59.553 43.478 4.92 0.00 0.00 3.69
5390 5422 3.778618 AGTTAAAACCGCGTATCTCCTC 58.221 45.455 4.92 0.00 0.00 3.71
5391 5423 3.194116 AGTTAAAACCGCGTATCTCCTCA 59.806 43.478 4.92 0.00 0.00 3.86
5392 5424 2.005971 AAAACCGCGTATCTCCTCAC 57.994 50.000 4.92 0.00 0.00 3.51
5393 5425 1.183549 AAACCGCGTATCTCCTCACT 58.816 50.000 4.92 0.00 0.00 3.41
5396 5428 1.880675 ACCGCGTATCTCCTCACTATG 59.119 52.381 4.92 0.00 0.00 2.23
5397 5429 2.152016 CCGCGTATCTCCTCACTATGA 58.848 52.381 4.92 0.00 0.00 2.15
5407 5447 6.716934 TCTCCTCACTATGAAATCAGGTAC 57.283 41.667 0.00 0.00 0.00 3.34
5432 5472 8.806146 ACCAGATGAACATTTTAGCAATTACTT 58.194 29.630 0.00 0.00 0.00 2.24
5436 5476 7.636259 TGAACATTTTAGCAATTACTTGTGC 57.364 32.000 0.00 0.00 41.22 4.57
5466 5506 9.129532 AGAATCTTTTGATGTCTCTGTTTTCTT 57.870 29.630 0.00 0.00 39.48 2.52
5473 5513 8.994429 TTGATGTCTCTGTTTTCTTATCTCTC 57.006 34.615 0.00 0.00 0.00 3.20
5521 5561 5.761726 TGCAAGGCAATACTAATCATCTGAG 59.238 40.000 0.00 0.00 34.76 3.35
5553 5593 4.343526 TCTCCATTTGGCTTTGCAGTTTTA 59.656 37.500 0.00 0.00 34.44 1.52
5554 5594 4.630111 TCCATTTGGCTTTGCAGTTTTAG 58.370 39.130 0.00 0.00 34.44 1.85
5555 5595 3.187022 CCATTTGGCTTTGCAGTTTTAGC 59.813 43.478 0.00 0.00 0.00 3.09
5591 5632 3.274288 GGTCTCATCCAACAGGAATGAC 58.726 50.000 0.00 0.00 34.49 3.06
5592 5633 3.054802 GGTCTCATCCAACAGGAATGACT 60.055 47.826 11.63 0.00 34.49 3.41
5593 5634 4.566488 GGTCTCATCCAACAGGAATGACTT 60.566 45.833 11.63 0.00 34.49 3.01
5594 5635 5.006386 GTCTCATCCAACAGGAATGACTTT 58.994 41.667 0.00 0.00 34.49 2.66
5595 5636 5.005740 TCTCATCCAACAGGAATGACTTTG 58.994 41.667 0.00 0.00 34.49 2.77
5596 5637 4.081406 TCATCCAACAGGAATGACTTTGG 58.919 43.478 0.00 0.00 38.48 3.28
5597 5638 2.875296 TCCAACAGGAATGACTTTGGG 58.125 47.619 0.00 0.00 37.82 4.12
5598 5639 1.895131 CCAACAGGAATGACTTTGGGG 59.105 52.381 0.00 0.00 34.26 4.96
5599 5640 2.597455 CAACAGGAATGACTTTGGGGT 58.403 47.619 0.00 0.00 0.00 4.95
5600 5641 3.499563 CCAACAGGAATGACTTTGGGGTA 60.500 47.826 0.00 0.00 34.26 3.69
5601 5642 4.148838 CAACAGGAATGACTTTGGGGTAA 58.851 43.478 0.00 0.00 0.00 2.85
5602 5643 4.675063 ACAGGAATGACTTTGGGGTAAT 57.325 40.909 0.00 0.00 0.00 1.89
5603 5644 5.789574 ACAGGAATGACTTTGGGGTAATA 57.210 39.130 0.00 0.00 0.00 0.98
5614 5670 7.037153 TGACTTTGGGGTAATAATAACCTGTCT 60.037 37.037 0.00 0.00 39.05 3.41
5616 5672 7.832685 ACTTTGGGGTAATAATAACCTGTCTTC 59.167 37.037 0.00 0.00 39.05 2.87
5638 5694 8.458212 CTTCATTTTGAAGCTAACTCCAATTC 57.542 34.615 4.46 0.00 46.03 2.17
5639 5695 7.765695 TCATTTTGAAGCTAACTCCAATTCT 57.234 32.000 0.00 0.00 0.00 2.40
5651 5707 7.121315 GCTAACTCCAATTCTTGTACCAAAGAT 59.879 37.037 0.00 0.00 36.12 2.40
5654 5710 9.533831 AACTCCAATTCTTGTACCAAAGATAAT 57.466 29.630 0.00 0.00 36.12 1.28
5662 5718 8.786826 TCTTGTACCAAAGATAATGAAATCGT 57.213 30.769 0.00 0.00 31.19 3.73
5805 6172 0.540365 CTCAATGTGTTGCCCCAGGT 60.540 55.000 0.00 0.00 35.26 4.00
5816 6183 1.215673 TGCCCCAGGTTCACTTTGTTA 59.784 47.619 0.00 0.00 0.00 2.41
5817 6184 1.611977 GCCCCAGGTTCACTTTGTTAC 59.388 52.381 0.00 0.00 0.00 2.50
5818 6185 2.751816 GCCCCAGGTTCACTTTGTTACT 60.752 50.000 0.00 0.00 0.00 2.24
5819 6186 3.562182 CCCCAGGTTCACTTTGTTACTT 58.438 45.455 0.00 0.00 0.00 2.24
5824 6194 5.588648 CCAGGTTCACTTTGTTACTTCTCAA 59.411 40.000 0.00 0.00 0.00 3.02
5830 6200 9.439537 GTTCACTTTGTTACTTCTCAATTTCTC 57.560 33.333 0.00 0.00 0.00 2.87
5835 6205 9.787532 CTTTGTTACTTCTCAATTTCTCAAACA 57.212 29.630 0.00 0.00 0.00 2.83
5838 6208 5.100751 ACTTCTCAATTTCTCAAACAGCG 57.899 39.130 0.00 0.00 0.00 5.18
5856 6226 1.685224 GACCTCTGGTGGCATTCCA 59.315 57.895 0.00 0.00 40.85 3.53
5869 6239 1.030457 CATTCCATGCTTCTCAGGCC 58.970 55.000 0.00 0.00 0.00 5.19
5870 6240 0.627451 ATTCCATGCTTCTCAGGCCA 59.373 50.000 5.01 0.00 0.00 5.36
5874 6244 2.444388 TCCATGCTTCTCAGGCCATTAT 59.556 45.455 5.01 0.00 0.00 1.28
5877 6247 3.482156 TGCTTCTCAGGCCATTATCTC 57.518 47.619 5.01 0.00 0.00 2.75
5890 6264 4.079970 CCATTATCTCTCTACGGCCACTA 58.920 47.826 2.24 0.00 0.00 2.74
5903 6277 2.095263 CGGCCACTACTCATTGTTTTGG 60.095 50.000 2.24 0.00 34.34 3.28
5904 6278 2.352715 GGCCACTACTCATTGTTTTGGC 60.353 50.000 0.00 0.92 46.43 4.52
5916 6290 4.414337 TTGTTTTGGCCATTTACTTGCT 57.586 36.364 6.09 0.00 0.00 3.91
5928 6302 6.115446 CCATTTACTTGCTCAATCAGAGGTA 58.885 40.000 0.00 0.00 44.86 3.08
5929 6303 6.769822 CCATTTACTTGCTCAATCAGAGGTAT 59.230 38.462 0.00 0.00 44.86 2.73
5932 6306 5.426689 ACTTGCTCAATCAGAGGTATTGA 57.573 39.130 0.00 0.00 44.86 2.57
5949 6323 9.167311 GAGGTATTGATCTTGTATGTTCTTTGT 57.833 33.333 0.00 0.00 0.00 2.83
5982 6358 3.151554 GGGTGGGTGGTAAGTTACTTTG 58.848 50.000 12.65 0.00 0.00 2.77
5983 6359 3.151554 GGTGGGTGGTAAGTTACTTTGG 58.848 50.000 12.65 0.00 0.00 3.28
6023 6399 3.735237 ACTGTCATGTGTTCTCGTCTT 57.265 42.857 0.00 0.00 0.00 3.01
6025 6401 3.319405 ACTGTCATGTGTTCTCGTCTTCT 59.681 43.478 0.00 0.00 0.00 2.85
6062 6438 0.785979 GCAAGCAAATGAAGCAACCG 59.214 50.000 0.00 0.00 0.00 4.44
6082 6458 3.427503 CCGCTGGTCCATTTTGATTGTAC 60.428 47.826 0.00 0.00 0.00 2.90
6102 6478 5.880332 TGTACCTTGAGCCATTATCTGTTTC 59.120 40.000 0.00 0.00 0.00 2.78
6107 6483 4.183865 TGAGCCATTATCTGTTTCGAGTG 58.816 43.478 0.00 0.00 0.00 3.51
6108 6484 4.184629 GAGCCATTATCTGTTTCGAGTGT 58.815 43.478 0.00 0.00 0.00 3.55
6110 6486 5.730550 AGCCATTATCTGTTTCGAGTGTTA 58.269 37.500 0.00 0.00 0.00 2.41
6121 6501 9.970395 TCTGTTTCGAGTGTTATTTTTACTCTA 57.030 29.630 0.00 0.00 38.87 2.43
6129 6509 6.318900 AGTGTTATTTTTACTCTATGCCAGCC 59.681 38.462 0.00 0.00 0.00 4.85
6132 6512 3.560636 TTTTACTCTATGCCAGCCTCC 57.439 47.619 0.00 0.00 0.00 4.30
6138 6518 0.036448 CTATGCCAGCCTCCTCCATG 59.964 60.000 0.00 0.00 0.00 3.66
6141 6521 2.988839 GCCAGCCTCCTCCATGGTT 61.989 63.158 12.58 0.00 35.17 3.67
6148 6528 2.716217 CCTCCTCCATGGTTCTGTTTC 58.284 52.381 12.58 0.00 37.07 2.78
6152 6532 4.081406 TCCTCCATGGTTCTGTTTCATTG 58.919 43.478 12.58 0.00 37.07 2.82
6155 6535 5.452078 TCCATGGTTCTGTTTCATTGTTC 57.548 39.130 12.58 0.00 0.00 3.18
6156 6536 5.139727 TCCATGGTTCTGTTTCATTGTTCT 58.860 37.500 12.58 0.00 0.00 3.01
6157 6537 5.009911 TCCATGGTTCTGTTTCATTGTTCTG 59.990 40.000 12.58 0.00 0.00 3.02
6161 6541 6.929625 TGGTTCTGTTTCATTGTTCTGAAAA 58.070 32.000 1.16 0.00 44.38 2.29
6162 6542 7.382110 TGGTTCTGTTTCATTGTTCTGAAAAA 58.618 30.769 0.00 0.00 44.38 1.94
6163 6543 8.040132 TGGTTCTGTTTCATTGTTCTGAAAAAT 58.960 29.630 0.00 0.00 44.38 1.82
6164 6544 8.330302 GGTTCTGTTTCATTGTTCTGAAAAATG 58.670 33.333 21.95 21.95 44.38 2.32
6166 6546 9.650539 TTCTGTTTCATTGTTCTGAAAAATGAA 57.349 25.926 30.93 30.93 44.38 2.57
6167 6547 9.820725 TCTGTTTCATTGTTCTGAAAAATGAAT 57.179 25.926 33.15 10.25 45.07 2.57
6198 6578 7.849804 TCTCACTTAAATACTCTGAAATGGC 57.150 36.000 0.00 0.00 0.00 4.40
6199 6579 7.394016 TCTCACTTAAATACTCTGAAATGGCA 58.606 34.615 0.00 0.00 0.00 4.92
6200 6580 7.334421 TCTCACTTAAATACTCTGAAATGGCAC 59.666 37.037 0.00 0.00 0.00 5.01
6201 6581 6.374333 TCACTTAAATACTCTGAAATGGCACC 59.626 38.462 0.00 0.00 0.00 5.01
6202 6582 5.354234 ACTTAAATACTCTGAAATGGCACCG 59.646 40.000 0.00 0.00 0.00 4.94
6203 6583 3.627395 AATACTCTGAAATGGCACCGA 57.373 42.857 0.00 0.00 0.00 4.69
6204 6584 3.845781 ATACTCTGAAATGGCACCGAT 57.154 42.857 0.00 0.00 0.00 4.18
6205 6585 1.742761 ACTCTGAAATGGCACCGATG 58.257 50.000 0.00 0.00 0.00 3.84
6218 6598 3.925238 CGATGCTGGGCGCGTTAC 61.925 66.667 8.43 0.00 43.27 2.50
6219 6599 2.511600 GATGCTGGGCGCGTTACT 60.512 61.111 8.43 0.00 43.27 2.24
6220 6600 2.511600 ATGCTGGGCGCGTTACTC 60.512 61.111 8.43 0.00 43.27 2.59
6221 6601 2.907897 GATGCTGGGCGCGTTACTCT 62.908 60.000 8.43 0.00 43.27 3.24
6222 6602 2.434359 GCTGGGCGCGTTACTCTT 60.434 61.111 8.43 0.00 0.00 2.85
6223 6603 2.453638 GCTGGGCGCGTTACTCTTC 61.454 63.158 8.43 0.00 0.00 2.87
6224 6604 1.215647 CTGGGCGCGTTACTCTTCT 59.784 57.895 8.43 0.00 0.00 2.85
6225 6605 0.389948 CTGGGCGCGTTACTCTTCTT 60.390 55.000 8.43 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 145 4.278419 AGGCTAAACTTCTTCGCAAAACAT 59.722 37.500 0.00 0.00 0.00 2.71
756 764 1.167851 TGGCTGGAAAATCTGAAGCG 58.832 50.000 0.00 0.00 34.66 4.68
758 766 4.703575 TCAGAATGGCTGGAAAATCTGAAG 59.296 41.667 1.10 0.00 44.98 3.02
768 776 2.754552 CCGAATTTTCAGAATGGCTGGA 59.245 45.455 0.00 0.00 44.98 3.86
773 781 6.147492 TGAAATTTGCCGAATTTTCAGAATGG 59.853 34.615 4.19 0.00 45.54 3.16
775 783 6.147656 GGTGAAATTTGCCGAATTTTCAGAAT 59.852 34.615 4.19 0.00 45.54 2.40
778 787 4.749099 TGGTGAAATTTGCCGAATTTTCAG 59.251 37.500 4.19 0.00 45.54 3.02
802 811 7.331687 GGTCCACATGAATTTACCAAAAAGATG 59.668 37.037 0.00 0.00 0.00 2.90
803 812 7.386059 GGTCCACATGAATTTACCAAAAAGAT 58.614 34.615 0.00 0.00 0.00 2.40
805 814 5.931724 GGGTCCACATGAATTTACCAAAAAG 59.068 40.000 0.00 0.00 0.00 2.27
806 815 5.221742 GGGGTCCACATGAATTTACCAAAAA 60.222 40.000 0.00 0.00 0.00 1.94
841 850 6.505044 TCATCAATTTTGGATGAGTGAGTG 57.495 37.500 3.47 0.00 44.51 3.51
1026 1046 1.070786 TCTTGTCAGTGGGTTCGGC 59.929 57.895 0.00 0.00 0.00 5.54
1029 1049 1.228657 GCCGTCTTGTCAGTGGGTTC 61.229 60.000 0.00 0.00 0.00 3.62
1031 1051 2.426023 GCCGTCTTGTCAGTGGGT 59.574 61.111 0.00 0.00 0.00 4.51
1075 1096 0.463833 CGATTTACTCACCTGGGGGC 60.464 60.000 0.00 0.00 35.63 5.80
1138 1159 1.457831 CTAGAAGGGGGAGGGGACG 60.458 68.421 0.00 0.00 0.00 4.79
1139 1160 1.074395 CCTAGAAGGGGGAGGGGAC 60.074 68.421 0.00 0.00 0.00 4.46
1195 1216 2.610859 AAGGAGCGGGACATGGGT 60.611 61.111 0.00 0.00 0.00 4.51
1269 1290 3.124560 GGGAGAAAATCGACGGAATCTC 58.875 50.000 0.00 3.92 33.32 2.75
1275 1296 2.171725 GCGGGGAGAAAATCGACGG 61.172 63.158 0.00 0.00 0.00 4.79
1314 1341 1.243342 CGGCTGCCCAAATCAGAACA 61.243 55.000 14.12 0.00 33.54 3.18
1323 1350 3.008517 TCCATCTCGGCTGCCCAA 61.009 61.111 14.12 0.09 33.14 4.12
1326 1353 3.157252 TCCTCCATCTCGGCTGCC 61.157 66.667 9.11 9.11 33.14 4.85
1768 1795 3.576118 CACCTCTTCTCCTTCTCTGACAA 59.424 47.826 0.00 0.00 0.00 3.18
1803 1830 1.228367 CTGTGCCAAAGCCCTCTGT 60.228 57.895 0.00 0.00 38.69 3.41
1812 1839 1.059584 TGACCTCCCTCTGTGCCAAA 61.060 55.000 0.00 0.00 0.00 3.28
1932 1959 3.020274 CTCATCTCGGACCTTCTTGAGA 58.980 50.000 5.79 2.84 41.33 3.27
2138 2165 3.489738 GCCATACATGTGCCTCAAATCAC 60.490 47.826 9.11 0.00 0.00 3.06
2143 2170 2.212812 TTGCCATACATGTGCCTCAA 57.787 45.000 9.11 5.07 0.00 3.02
2203 2230 1.176619 TCCCTCTTCGACGTCAGCAA 61.177 55.000 17.16 3.94 0.00 3.91
2301 2328 4.154918 AGGTCGTCATTTTCTTGATCAAGC 59.845 41.667 27.45 12.58 38.28 4.01
2337 2364 2.167487 CTGAGCCTCTTGGTACTCCTTC 59.833 54.545 0.00 0.00 35.27 3.46
2394 2421 1.661341 CTCGGAATTTCTCCTGCAGG 58.339 55.000 27.87 27.87 42.85 4.85
2479 2506 4.267536 TCATTCTCAAGCTTTCCCATCTG 58.732 43.478 0.00 0.00 0.00 2.90
2511 2538 1.198637 GAATCCAGCTGTGACAAGCAC 59.801 52.381 13.81 0.00 46.08 4.40
2548 2575 0.877071 AACTCATTCTGCAACTGCCG 59.123 50.000 0.00 0.00 41.18 5.69
2593 2620 5.825593 TCCAAGTTCTCTACAGTTTGGAT 57.174 39.130 0.00 0.00 39.17 3.41
2728 2755 5.279106 CCTCCAATTGATTTTTCACAGCAGA 60.279 40.000 7.12 0.00 0.00 4.26
2792 2819 2.427095 GCCATTACCTCCAATTGGTGTC 59.573 50.000 23.76 0.00 38.42 3.67
2823 2850 5.352569 ACATTCTAGCTGTTCAATTCTTCCG 59.647 40.000 0.00 0.00 0.00 4.30
2846 2873 2.627515 TTCATGCTCCTGCTCCATAC 57.372 50.000 0.00 0.00 40.48 2.39
2883 2910 1.750778 AGCATTTCTTTGTATGCCCCG 59.249 47.619 0.00 0.00 46.42 5.73
2975 3002 5.420104 AGATCACTTAAAGCTTTCCCCAATG 59.580 40.000 16.57 7.15 0.00 2.82
3209 3236 6.669631 AGTAACTTTTCCTTTTCTTCCCTGA 58.330 36.000 0.00 0.00 0.00 3.86
3221 3248 5.827326 AAGAGCACCTAGTAACTTTTCCT 57.173 39.130 0.00 0.00 0.00 3.36
3225 3252 7.334671 GCTTCATTAAGAGCACCTAGTAACTTT 59.665 37.037 4.04 0.00 34.37 2.66
3270 3297 6.400515 CGTTCTCACAAATCTTGCTCTTACTC 60.401 42.308 0.00 0.00 0.00 2.59
3283 3310 4.398319 AGGGTGATTTCGTTCTCACAAAT 58.602 39.130 13.21 0.00 42.83 2.32
3330 3357 1.481772 ACTCTCAGCTCTTCCAGATGC 59.518 52.381 0.00 0.00 38.52 3.91
3360 3387 5.876357 TCAATGTAGCCCTTGAGTTTAGTT 58.124 37.500 0.00 0.00 0.00 2.24
3420 3447 7.066284 TCCTCAGCTTTCATTTTAGCAATAGTC 59.934 37.037 0.00 0.00 39.85 2.59
3474 3501 3.968649 TGCTTCATTGAGAGCAAACAAC 58.031 40.909 16.17 0.00 37.59 3.32
3552 3579 2.620115 CTCCACTGCTTTCTTTTGCTGA 59.380 45.455 0.00 0.00 33.38 4.26
3562 3589 2.435372 TCCAAACACTCCACTGCTTT 57.565 45.000 0.00 0.00 0.00 3.51
3655 3682 4.514545 TTTTAGCAATAGTCGCGACATG 57.485 40.909 37.85 30.94 0.00 3.21
3694 3721 7.954248 CGATAACTTCTCATTTTCTTCTGTGTG 59.046 37.037 0.00 0.00 0.00 3.82
3718 3745 1.270785 TGCTTCATTGAGAGCAACCGA 60.271 47.619 16.17 0.14 36.72 4.69
3719 3746 1.159285 TGCTTCATTGAGAGCAACCG 58.841 50.000 16.17 0.00 36.72 4.44
3721 3748 4.023365 AGAGTTTGCTTCATTGAGAGCAAC 60.023 41.667 23.66 19.74 45.32 4.17
3743 3770 2.005451 CCTTCATCTCAGAAACGGCAG 58.995 52.381 0.00 0.00 0.00 4.85
3817 3844 8.930760 CATGTCAACTTTTAACTTTTCCAAACA 58.069 29.630 0.00 0.00 0.00 2.83
3921 3948 4.002006 AGGGTGCCCTCAACTTCA 57.998 55.556 3.45 0.00 44.43 3.02
3994 4021 3.801698 TGATGTATTGCTGAAGCTCCTC 58.198 45.455 3.61 0.00 42.66 3.71
4054 4081 3.055819 TCTGACTTGATAAGACTGGCCAC 60.056 47.826 0.00 0.00 0.00 5.01
4207 4234 8.455903 TCCTCTTGATCAAATATTTCCATGAC 57.544 34.615 9.88 0.00 0.00 3.06
4267 4294 8.915057 ATTAGTTGAATGTCAGCTATAGCATT 57.085 30.769 26.07 16.24 39.38 3.56
4391 4418 8.105197 TGAGATTCAGAGAATTCAGATTTTCCA 58.895 33.333 8.44 0.00 29.05 3.53
4480 4507 7.175104 TCTAGAACTAATTTCATTTGCAGGGT 58.825 34.615 0.00 0.00 36.57 4.34
4518 4545 5.224888 TCAAGAACATGCTTCAAATTGCTC 58.775 37.500 0.00 0.00 0.00 4.26
4746 4773 3.306917 TGAATTGCTGCTCCAATGTTG 57.693 42.857 0.00 0.00 35.70 3.33
4770 4797 2.617774 GCTTGCCTTCAGATCTTCATCC 59.382 50.000 0.00 0.00 0.00 3.51
4785 4812 1.252904 TGATCCTTGCCAAGCTTGCC 61.253 55.000 21.43 11.17 0.00 4.52
4935 4962 8.883954 AGTAGTTGTTCTCTTTTAGTGGTAAC 57.116 34.615 0.00 0.00 0.00 2.50
4959 4986 5.010933 TCTGACTTCACCTACCAAGACTAG 58.989 45.833 0.00 0.00 0.00 2.57
4987 5014 6.524734 ACAGAGATTACAACAATGTCAGTGA 58.475 36.000 7.39 0.00 41.05 3.41
4988 5015 6.791887 ACAGAGATTACAACAATGTCAGTG 57.208 37.500 0.00 0.00 41.05 3.66
5017 5044 3.726517 CAGACGGCGGCAACAAGG 61.727 66.667 18.30 0.00 0.00 3.61
5018 5045 2.972505 ACAGACGGCGGCAACAAG 60.973 61.111 18.30 0.95 0.00 3.16
5021 5048 1.296056 ATAACACAGACGGCGGCAAC 61.296 55.000 18.30 1.04 0.00 4.17
5045 5072 6.127479 GGATAAACATGGCCATTCTGTGTAAA 60.127 38.462 17.92 4.33 0.00 2.01
5161 5188 7.380423 ACCCAACTATTCAGCAGTAGATAAT 57.620 36.000 0.00 0.00 0.00 1.28
5247 5279 6.151144 GCACCTTACAAATAACAACTCAGGAT 59.849 38.462 0.00 0.00 0.00 3.24
5272 5304 7.882179 TGGCATAAATTCTCATCAATCATCAG 58.118 34.615 0.00 0.00 0.00 2.90
5292 5324 7.667219 CCTTGTAATCCAGTAAATAGATGGCAT 59.333 37.037 0.00 0.00 33.92 4.40
5303 5335 8.842280 CACTGTTTTTACCTTGTAATCCAGTAA 58.158 33.333 10.61 0.00 0.00 2.24
5314 5346 7.881142 TGATGATTACCACTGTTTTTACCTTG 58.119 34.615 0.00 0.00 0.00 3.61
5317 5349 8.739972 AGAATGATGATTACCACTGTTTTTACC 58.260 33.333 0.00 0.00 0.00 2.85
5354 5386 5.221661 GGTTTTAACTCTTCAGACAGAGGGA 60.222 44.000 11.87 0.88 44.23 4.20
5357 5389 4.150804 GCGGTTTTAACTCTTCAGACAGAG 59.849 45.833 7.64 7.64 45.29 3.35
5366 5398 4.081807 AGGAGATACGCGGTTTTAACTCTT 60.082 41.667 12.47 0.68 0.00 2.85
5378 5410 3.898517 TTCATAGTGAGGAGATACGCG 57.101 47.619 3.53 3.53 0.00 6.01
5381 5413 7.296628 ACCTGATTTCATAGTGAGGAGATAC 57.703 40.000 0.00 0.00 0.00 2.24
5383 5415 6.268847 GGTACCTGATTTCATAGTGAGGAGAT 59.731 42.308 4.06 0.00 0.00 2.75
5389 5421 6.611236 TCATCTGGTACCTGATTTCATAGTGA 59.389 38.462 26.76 18.46 33.34 3.41
5390 5422 6.820335 TCATCTGGTACCTGATTTCATAGTG 58.180 40.000 26.76 16.78 33.34 2.74
5391 5423 7.092891 TGTTCATCTGGTACCTGATTTCATAGT 60.093 37.037 26.76 6.51 33.34 2.12
5392 5424 7.275183 TGTTCATCTGGTACCTGATTTCATAG 58.725 38.462 26.76 16.59 33.34 2.23
5393 5425 7.194112 TGTTCATCTGGTACCTGATTTCATA 57.806 36.000 26.76 12.27 33.34 2.15
5396 5428 7.396540 AAATGTTCATCTGGTACCTGATTTC 57.603 36.000 26.76 19.81 33.34 2.17
5397 5429 7.781324 AAAATGTTCATCTGGTACCTGATTT 57.219 32.000 26.76 17.29 33.34 2.17
5407 5447 9.079833 CAAGTAATTGCTAAAATGTTCATCTGG 57.920 33.333 0.00 0.00 0.00 3.86
5432 5472 6.233434 AGACATCAAAAGATTCTACAGCACA 58.767 36.000 0.00 0.00 0.00 4.57
5436 5476 8.545229 AACAGAGACATCAAAAGATTCTACAG 57.455 34.615 0.00 0.00 0.00 2.74
5437 5477 8.908786 AAACAGAGACATCAAAAGATTCTACA 57.091 30.769 0.00 0.00 0.00 2.74
5444 5484 9.784531 AGATAAGAAAACAGAGACATCAAAAGA 57.215 29.630 0.00 0.00 0.00 2.52
5466 5506 6.136155 TGTCCCAACATATCACAGAGAGATA 58.864 40.000 0.00 0.00 32.93 1.98
5473 5513 3.691118 CCAGTTGTCCCAACATATCACAG 59.309 47.826 9.53 0.00 34.73 3.66
5485 5525 2.270986 CCTTGCAGCCAGTTGTCCC 61.271 63.158 0.00 0.00 0.00 4.46
5514 5554 9.846689 CCAAATGGAGATCCTCATCCTCAGATG 62.847 48.148 0.00 0.00 43.84 2.90
5515 5555 3.919304 TGGAGATCCTCATCCTCAGAT 57.081 47.619 0.00 0.00 36.50 2.90
5521 5561 2.107901 AGCCAAATGGAGATCCTCATCC 59.892 50.000 2.98 0.00 37.39 3.51
5534 5574 4.060205 AGCTAAAACTGCAAAGCCAAATG 58.940 39.130 0.00 0.00 35.54 2.32
5553 5593 2.578021 AGACCACATTATCACCCAAGCT 59.422 45.455 0.00 0.00 0.00 3.74
5554 5594 2.945668 GAGACCACATTATCACCCAAGC 59.054 50.000 0.00 0.00 0.00 4.01
5555 5595 4.220693 TGAGACCACATTATCACCCAAG 57.779 45.455 0.00 0.00 0.00 3.61
5591 5632 7.832187 TGAAGACAGGTTATTATTACCCCAAAG 59.168 37.037 0.00 0.00 36.27 2.77
5592 5633 7.700846 TGAAGACAGGTTATTATTACCCCAAA 58.299 34.615 0.00 0.00 36.27 3.28
5593 5634 7.273457 TGAAGACAGGTTATTATTACCCCAA 57.727 36.000 0.00 0.00 36.27 4.12
5594 5635 6.894735 TGAAGACAGGTTATTATTACCCCA 57.105 37.500 0.00 0.00 36.27 4.96
5595 5636 8.762481 AAATGAAGACAGGTTATTATTACCCC 57.238 34.615 0.00 0.00 36.27 4.95
5614 5670 8.181904 AGAATTGGAGTTAGCTTCAAAATGAA 57.818 30.769 4.22 0.00 42.95 2.57
5616 5672 8.236084 CAAGAATTGGAGTTAGCTTCAAAATG 57.764 34.615 4.22 0.00 42.95 2.32
5763 6099 9.616156 TGAGTTATGTGTACTTTTTAAACCAGA 57.384 29.630 0.00 0.00 0.00 3.86
5781 6148 3.508744 GGGGCAACACATTGAGTTATG 57.491 47.619 0.00 0.00 42.67 1.90
5795 6162 0.032615 ACAAAGTGAACCTGGGGCAA 60.033 50.000 0.00 0.00 0.00 4.52
5799 6166 4.461198 AGAAGTAACAAAGTGAACCTGGG 58.539 43.478 0.00 0.00 0.00 4.45
5800 6167 5.123227 TGAGAAGTAACAAAGTGAACCTGG 58.877 41.667 0.00 0.00 0.00 4.45
5805 6172 9.173021 TGAGAAATTGAGAAGTAACAAAGTGAA 57.827 29.630 0.00 0.00 0.00 3.18
5816 6183 4.816385 TCGCTGTTTGAGAAATTGAGAAGT 59.184 37.500 0.00 0.00 0.00 3.01
5817 6184 5.142962 GTCGCTGTTTGAGAAATTGAGAAG 58.857 41.667 0.00 0.00 0.00 2.85
5818 6185 4.024048 GGTCGCTGTTTGAGAAATTGAGAA 60.024 41.667 0.00 0.00 0.00 2.87
5819 6186 3.498397 GGTCGCTGTTTGAGAAATTGAGA 59.502 43.478 0.00 0.00 0.00 3.27
5824 6194 3.070018 CAGAGGTCGCTGTTTGAGAAAT 58.930 45.455 0.00 0.00 0.00 2.17
5830 6200 1.230635 CCACCAGAGGTCGCTGTTTG 61.231 60.000 1.43 0.00 31.02 2.93
5835 6205 2.527951 GAATGCCACCAGAGGTCGCT 62.528 60.000 7.28 0.00 40.40 4.93
5838 6208 1.685224 TGGAATGCCACCAGAGGTC 59.315 57.895 0.00 0.00 39.92 3.85
5856 6226 3.651904 AGAGATAATGGCCTGAGAAGCAT 59.348 43.478 3.32 0.00 0.00 3.79
5869 6239 4.762765 AGTAGTGGCCGTAGAGAGATAATG 59.237 45.833 0.00 0.00 0.00 1.90
5870 6240 4.988029 AGTAGTGGCCGTAGAGAGATAAT 58.012 43.478 0.00 0.00 0.00 1.28
5874 6244 1.558294 TGAGTAGTGGCCGTAGAGAGA 59.442 52.381 0.00 0.00 0.00 3.10
5877 6247 2.427453 ACAATGAGTAGTGGCCGTAGAG 59.573 50.000 0.00 0.00 0.00 2.43
5890 6264 5.806654 AGTAAATGGCCAAAACAATGAGT 57.193 34.783 10.96 0.00 0.00 3.41
5903 6277 4.201990 CCTCTGATTGAGCAAGTAAATGGC 60.202 45.833 0.00 0.00 41.35 4.40
5904 6278 4.946157 ACCTCTGATTGAGCAAGTAAATGG 59.054 41.667 0.00 0.00 41.35 3.16
5916 6290 8.708378 ACATACAAGATCAATACCTCTGATTGA 58.292 33.333 0.00 0.88 45.01 2.57
5949 6323 3.594232 ACCACCCACCCAAATCTATGTAA 59.406 43.478 0.00 0.00 0.00 2.41
5982 6358 6.038271 ACAGTATCATCCTTCGCAAATTTACC 59.962 38.462 0.00 0.00 0.00 2.85
5983 6359 7.016361 ACAGTATCATCCTTCGCAAATTTAC 57.984 36.000 0.00 0.00 0.00 2.01
6018 6394 3.549019 CGTATGATCTGGACCAGAAGACG 60.549 52.174 27.69 24.51 44.04 4.18
6019 6395 3.797184 GCGTATGATCTGGACCAGAAGAC 60.797 52.174 27.69 17.77 44.04 3.01
6023 6399 0.668535 CGCGTATGATCTGGACCAGA 59.331 55.000 26.28 26.28 44.99 3.86
6025 6401 1.739667 CCGCGTATGATCTGGACCA 59.260 57.895 4.92 0.00 0.00 4.02
6082 6458 4.191544 TCGAAACAGATAATGGCTCAAGG 58.808 43.478 0.00 0.00 0.00 3.61
6102 6478 7.534085 TGGCATAGAGTAAAAATAACACTCG 57.466 36.000 0.00 0.00 42.80 4.18
6107 6483 6.017026 GGAGGCTGGCATAGAGTAAAAATAAC 60.017 42.308 3.38 0.00 0.00 1.89
6108 6484 6.062095 GGAGGCTGGCATAGAGTAAAAATAA 58.938 40.000 3.38 0.00 0.00 1.40
6110 6486 4.166919 AGGAGGCTGGCATAGAGTAAAAAT 59.833 41.667 3.38 0.00 0.00 1.82
6118 6498 0.104777 ATGGAGGAGGCTGGCATAGA 60.105 55.000 3.38 0.00 0.00 1.98
6121 6501 2.764737 CCATGGAGGAGGCTGGCAT 61.765 63.158 5.56 0.00 41.22 4.40
6129 6509 3.423539 TGAAACAGAACCATGGAGGAG 57.576 47.619 21.47 8.10 41.22 3.69
6132 6512 5.242393 AGAACAATGAAACAGAACCATGGAG 59.758 40.000 21.47 7.72 0.00 3.86
6138 6518 7.826260 TTTTTCAGAACAATGAAACAGAACC 57.174 32.000 1.57 0.00 46.12 3.62
6141 6521 9.820725 ATTCATTTTTCAGAACAATGAAACAGA 57.179 25.926 28.81 14.87 46.12 3.41
6172 6552 9.547753 GCCATTTCAGAGTATTTAAGTGAGATA 57.452 33.333 0.00 0.00 0.00 1.98
6173 6553 8.049117 TGCCATTTCAGAGTATTTAAGTGAGAT 58.951 33.333 0.00 0.00 0.00 2.75
6174 6554 7.334421 GTGCCATTTCAGAGTATTTAAGTGAGA 59.666 37.037 0.00 0.00 0.00 3.27
6175 6555 7.414540 GGTGCCATTTCAGAGTATTTAAGTGAG 60.415 40.741 0.00 0.00 0.00 3.51
6176 6556 6.374333 GGTGCCATTTCAGAGTATTTAAGTGA 59.626 38.462 0.00 0.00 0.00 3.41
6177 6557 6.555315 GGTGCCATTTCAGAGTATTTAAGTG 58.445 40.000 0.00 0.00 0.00 3.16
6178 6558 5.354234 CGGTGCCATTTCAGAGTATTTAAGT 59.646 40.000 0.00 0.00 0.00 2.24
6179 6559 5.584649 TCGGTGCCATTTCAGAGTATTTAAG 59.415 40.000 0.00 0.00 0.00 1.85
6180 6560 5.492895 TCGGTGCCATTTCAGAGTATTTAA 58.507 37.500 0.00 0.00 0.00 1.52
6181 6561 5.092554 TCGGTGCCATTTCAGAGTATTTA 57.907 39.130 0.00 0.00 0.00 1.40
6182 6562 3.950397 TCGGTGCCATTTCAGAGTATTT 58.050 40.909 0.00 0.00 0.00 1.40
6183 6563 3.627395 TCGGTGCCATTTCAGAGTATT 57.373 42.857 0.00 0.00 0.00 1.89
6184 6564 3.470709 CATCGGTGCCATTTCAGAGTAT 58.529 45.455 0.00 0.00 0.00 2.12
6185 6565 2.905075 CATCGGTGCCATTTCAGAGTA 58.095 47.619 0.00 0.00 0.00 2.59
6186 6566 1.742761 CATCGGTGCCATTTCAGAGT 58.257 50.000 0.00 0.00 0.00 3.24
6187 6567 0.379669 GCATCGGTGCCATTTCAGAG 59.620 55.000 10.29 0.00 45.76 3.35
6188 6568 2.481212 GCATCGGTGCCATTTCAGA 58.519 52.632 10.29 0.00 45.76 3.27
6205 6585 2.434359 AAGAGTAACGCGCCCAGC 60.434 61.111 5.73 0.00 43.95 4.85
6206 6586 0.389948 AAGAAGAGTAACGCGCCCAG 60.390 55.000 5.73 0.00 0.00 4.45
6207 6587 1.669440 AAGAAGAGTAACGCGCCCA 59.331 52.632 5.73 0.00 0.00 5.36
6208 6588 4.592426 AAGAAGAGTAACGCGCCC 57.408 55.556 5.73 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.