Multiple sequence alignment - TraesCS3B01G326600

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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 TraesCS3B01G326600 chr3B 100.000 5740 0 0 1 5740 527292504 527298243 0.000000e+00 10600
1 TraesCS3B01G326600 chr3D 95.676 2035 71 12 594 2619 401870105 401872131 0.000000e+00 3254
2 TraesCS3B01G326600 chr3D 95.847 1517 52 5 2621 4137 401872184 401873689 0.000000e+00 2442
3 TraesCS3B01G326600 chr3D 92.011 751 45 6 4841 5588 401874485 401875223 0.000000e+00 1040
4 TraesCS3B01G326600 chr3D 91.948 534 28 10 4301 4821 401873889 401874420 0.000000e+00 734
5 TraesCS3B01G326600 chr3D 83.611 360 31 15 1 335 401850020 401850376 4.320000e-81 313
6 TraesCS3B01G326600 chr3D 87.624 202 21 2 342 542 401850430 401850628 1.240000e-56 231
7 TraesCS3B01G326600 chr3A 93.544 2091 90 22 555 2616 522172568 522174642 0.000000e+00 3072
8 TraesCS3B01G326600 chr3A 89.574 1410 86 32 4301 5658 522176783 522178183 0.000000e+00 1733
9 TraesCS3B01G326600 chr3A 90.786 1183 90 14 2958 4137 522175130 522176296 0.000000e+00 1563
10 TraesCS3B01G326600 chr3A 94.937 316 13 2 2621 2934 522174825 522175139 5.170000e-135 492
11 TraesCS3B01G326600 chr3A 87.081 209 16 4 336 542 522172388 522172587 5.790000e-55 226
12 TraesCS3B01G326600 chr5B 86.726 1115 75 28 4557 5629 261373886 261374969 0.000000e+00 1171
13 TraesCS3B01G326600 chr4A 87.559 1053 79 20 4614 5629 225583548 225582511 0.000000e+00 1171
14 TraesCS3B01G326600 chr4A 86.275 1122 80 29 4561 5629 195312018 195313118 0.000000e+00 1151
15 TraesCS3B01G326600 chr5D 87.382 1062 72 21 4611 5629 437570622 437571664 0.000000e+00 1162
16 TraesCS3B01G326600 chr7B 83.828 606 84 10 3339 3939 659871234 659871830 1.080000e-156 564
17 TraesCS3B01G326600 chrUn 86.386 404 49 5 3530 3932 114314594 114314196 2.460000e-118 436


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 TraesCS3B01G326600 chr3B 527292504 527298243 5739 False 10600.0 10600 100.0000 1 5740 1 chr3B.!!$F1 5739
1 TraesCS3B01G326600 chr3D 401870105 401875223 5118 False 1867.5 3254 93.8705 594 5588 4 chr3D.!!$F2 4994
2 TraesCS3B01G326600 chr3D 401850020 401850628 608 False 272.0 313 85.6175 1 542 2 chr3D.!!$F1 541
3 TraesCS3B01G326600 chr3A 522172388 522178183 5795 False 1417.2 3072 91.1844 336 5658 5 chr3A.!!$F1 5322
4 TraesCS3B01G326600 chr5B 261373886 261374969 1083 False 1171.0 1171 86.7260 4557 5629 1 chr5B.!!$F1 1072
5 TraesCS3B01G326600 chr4A 225582511 225583548 1037 True 1171.0 1171 87.5590 4614 5629 1 chr4A.!!$R1 1015
6 TraesCS3B01G326600 chr4A 195312018 195313118 1100 False 1151.0 1151 86.2750 4561 5629 1 chr4A.!!$F1 1068
7 TraesCS3B01G326600 chr5D 437570622 437571664 1042 False 1162.0 1162 87.3820 4611 5629 1 chr5D.!!$F1 1018
8 TraesCS3B01G326600 chr7B 659871234 659871830 596 False 564.0 564 83.8280 3339 3939 1 chr7B.!!$F1 600

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
239 263 0.112412 GAAAGGGCCTCCTGGTCAAA 59.888 55.0 6.46 0.00 44.07 2.69 F
244 268 0.112412 GGCCTCCTGGTCAAAGGAAA 59.888 55.0 0.00 0.00 45.81 3.13 F
392 463 0.179086 AAACCGAACGTACAACCCGT 60.179 50.0 0.00 0.00 40.92 5.28 F
1713 1802 0.671251 GCCACTCCTACCTCTCATCG 59.329 60.0 0.00 0.00 0.00 3.84 F
2281 2392 1.369839 TTCCGTTTGCTGCGTTGACA 61.370 50.0 0.00 0.00 0.00 3.58 F
3868 4164 1.118838 ATCTTCTGAGAAGAGGCGGG 58.881 55.0 26.73 0.28 35.07 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1335 1420 0.105964 TAATCCTGATTCCCCGCGTG 59.894 55.0 4.92 0.00 32.50 5.34 R
1336 1421 0.393077 CTAATCCTGATTCCCCGCGT 59.607 55.0 4.92 0.00 32.50 6.01 R
2281 2392 0.937304 CATATAAAGCACGCCACGCT 59.063 50.0 0.00 0.00 42.98 5.07 R
3261 3551 0.322975 ACAGCTAGCAGTCCCTTGTG 59.677 55.0 18.83 5.36 0.00 3.33 R
3961 4257 0.755686 AAGCTGCCTCTCCCTAATCG 59.244 55.0 0.00 0.00 0.00 3.34 R
5265 6113 0.178932 GGGTTCTTCCAAGGGCCTTT 60.179 55.0 18.16 0.00 38.11 3.11 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
28 29 8.934023 ATTTTAGAACATTGAAACTGGGTAGA 57.066 30.769 0.00 0.00 0.00 2.59
61 62 2.299993 AATGCTCTCAGCGATTTCGA 57.700 45.000 3.77 0.00 46.26 3.71
64 65 0.458543 GCTCTCAGCGATTTCGACCA 60.459 55.000 3.77 0.00 43.02 4.02
67 68 0.848942 CTCAGCGATTTCGACCATCG 59.151 55.000 17.94 17.94 45.26 3.84
85 86 1.966451 GGACTTTGCACCCTGGTCG 60.966 63.158 0.00 0.00 0.00 4.79
92 94 2.276116 GCACCCTGGTCGTCTCTGA 61.276 63.158 0.00 0.00 0.00 3.27
102 104 1.550976 GTCGTCTCTGACCCTTGGATT 59.449 52.381 0.00 0.00 32.61 3.01
105 107 2.761208 CGTCTCTGACCCTTGGATTACT 59.239 50.000 0.00 0.00 0.00 2.24
106 108 3.952323 CGTCTCTGACCCTTGGATTACTA 59.048 47.826 0.00 0.00 0.00 1.82
109 111 4.901849 TCTCTGACCCTTGGATTACTATGG 59.098 45.833 0.00 0.00 0.00 2.74
110 112 3.973973 TCTGACCCTTGGATTACTATGGG 59.026 47.826 0.00 0.00 43.96 4.00
111 113 2.441750 TGACCCTTGGATTACTATGGGC 59.558 50.000 0.00 0.00 42.79 5.36
112 114 2.441750 GACCCTTGGATTACTATGGGCA 59.558 50.000 0.00 0.00 42.79 5.36
113 115 3.063650 ACCCTTGGATTACTATGGGCAT 58.936 45.455 0.00 0.00 42.79 4.40
114 116 3.467103 ACCCTTGGATTACTATGGGCATT 59.533 43.478 0.00 0.00 42.79 3.56
150 163 5.123344 GGACAAACGTCAATGGTAGCTATTT 59.877 40.000 0.00 0.00 34.92 1.40
154 167 3.377172 ACGTCAATGGTAGCTATTTTGGC 59.623 43.478 0.00 2.46 0.00 4.52
155 168 3.546020 CGTCAATGGTAGCTATTTTGGCG 60.546 47.826 18.95 18.95 38.75 5.69
156 169 3.377172 GTCAATGGTAGCTATTTTGGCGT 59.623 43.478 0.00 0.00 34.52 5.68
165 178 2.929398 GCTATTTTGGCGTTTGATTGGG 59.071 45.455 0.00 0.00 0.00 4.12
167 180 0.598680 TTTTGGCGTTTGATTGGGCG 60.599 50.000 0.00 0.00 0.00 6.13
186 199 1.377594 TGCCTAGCACGTCGAGGTA 60.378 57.895 10.91 0.00 39.49 3.08
191 204 1.329906 CTAGCACGTCGAGGTAACGAT 59.670 52.381 10.91 0.15 43.93 3.73
201 225 0.389391 AGGTAACGATGAGCCGATGG 59.611 55.000 0.00 0.00 46.39 3.51
225 249 6.869388 GGCCTATCGATAAAAGTAGAGAAAGG 59.131 42.308 6.58 2.27 0.00 3.11
237 261 1.151810 AGAAAGGGCCTCCTGGTCA 60.152 57.895 6.46 0.00 44.07 4.02
239 263 0.112412 GAAAGGGCCTCCTGGTCAAA 59.888 55.000 6.46 0.00 44.07 2.69
240 264 0.113190 AAAGGGCCTCCTGGTCAAAG 59.887 55.000 6.46 0.00 44.07 2.77
244 268 0.112412 GGCCTCCTGGTCAAAGGAAA 59.888 55.000 0.00 0.00 45.81 3.13
339 363 3.956848 GGGATTTTAGCTTGCAAGATCCT 59.043 43.478 29.15 20.77 37.03 3.24
344 415 2.695127 AGCTTGCAAGATCCTCTCAG 57.305 50.000 30.39 0.00 0.00 3.35
354 425 1.045911 ATCCTCTCAGTCCCCTTCGC 61.046 60.000 0.00 0.00 0.00 4.70
385 456 0.532640 ACCCACCAAACCGAACGTAC 60.533 55.000 0.00 0.00 0.00 3.67
392 463 0.179086 AAACCGAACGTACAACCCGT 60.179 50.000 0.00 0.00 40.92 5.28
404 475 2.014128 ACAACCCGTCTGAAGTTTGTG 58.986 47.619 6.91 0.00 0.00 3.33
461 532 0.673437 CCTTGAGCCTTTTCCGCAAA 59.327 50.000 0.00 0.00 0.00 3.68
462 533 1.068434 CCTTGAGCCTTTTCCGCAAAA 59.932 47.619 0.00 0.00 0.00 2.44
463 534 2.397549 CTTGAGCCTTTTCCGCAAAAG 58.602 47.619 4.50 4.50 45.73 2.27
568 640 7.692460 TTTTGCATGAAGTATCATTCAGACT 57.308 32.000 0.00 0.00 43.89 3.24
569 641 6.915544 TTGCATGAAGTATCATTCAGACTC 57.084 37.500 0.00 0.00 43.89 3.36
570 642 6.231258 TGCATGAAGTATCATTCAGACTCT 57.769 37.500 0.00 0.00 43.89 3.24
584 656 5.443185 TCAGACTCTTTTGCTCCAAAATG 57.557 39.130 3.87 3.75 41.53 2.32
638 710 2.277084 GGAAAATCACCGTAGCACGAT 58.723 47.619 9.75 0.00 46.05 3.73
639 711 2.284417 GGAAAATCACCGTAGCACGATC 59.716 50.000 9.75 0.00 46.05 3.69
665 737 2.067013 GCCGTACAAAGAGTGAAGTCC 58.933 52.381 0.00 0.00 0.00 3.85
844 917 3.650647 ATGTCCCCACATGTCACAC 57.349 52.632 0.00 0.00 42.05 3.82
845 918 0.770499 ATGTCCCCACATGTCACACA 59.230 50.000 0.00 0.00 42.05 3.72
864 937 1.611977 CACCCACGAGGCTCGATTATA 59.388 52.381 40.35 0.00 43.74 0.98
877 950 5.336610 GGCTCGATTATACTTAACCCTCTCC 60.337 48.000 0.00 0.00 0.00 3.71
937 1015 1.603455 CAGGGGTGTCGCCATTGTT 60.603 57.895 4.48 0.00 39.05 2.83
938 1016 1.603455 AGGGGTGTCGCCATTGTTG 60.603 57.895 4.48 0.00 39.05 3.33
939 1017 1.901464 GGGGTGTCGCCATTGTTGT 60.901 57.895 4.48 0.00 39.65 3.32
948 1026 0.674895 GCCATTGTTGTCGCCTCTCT 60.675 55.000 0.00 0.00 0.00 3.10
950 1028 1.066573 CCATTGTTGTCGCCTCTCTCT 60.067 52.381 0.00 0.00 0.00 3.10
1332 1417 5.638596 AAACAGTCGTTTCCTTTTGTTCT 57.361 34.783 0.00 0.00 41.60 3.01
1333 1418 4.616181 ACAGTCGTTTCCTTTTGTTCTG 57.384 40.909 0.00 0.00 0.00 3.02
1334 1419 4.258543 ACAGTCGTTTCCTTTTGTTCTGA 58.741 39.130 0.00 0.00 0.00 3.27
1335 1420 4.094442 ACAGTCGTTTCCTTTTGTTCTGAC 59.906 41.667 0.00 0.00 0.00 3.51
1336 1421 4.094294 CAGTCGTTTCCTTTTGTTCTGACA 59.906 41.667 0.00 0.00 0.00 3.58
1337 1422 4.094442 AGTCGTTTCCTTTTGTTCTGACAC 59.906 41.667 0.00 0.00 34.98 3.67
1362 1451 2.234143 GGAATCAGGATTAGCTTGGGC 58.766 52.381 0.00 0.00 39.06 5.36
1380 1469 2.415426 CGTTGGGCGCCTGTTTTT 59.585 55.556 28.56 0.00 0.00 1.94
1394 1483 4.394920 GCCTGTTTTTATCTGAACCGATCA 59.605 41.667 0.00 0.00 36.38 2.92
1437 1526 4.083324 CCACTCACTAATTTGTTGCGATGT 60.083 41.667 0.00 0.00 0.00 3.06
1713 1802 0.671251 GCCACTCCTACCTCTCATCG 59.329 60.000 0.00 0.00 0.00 3.84
1862 1951 3.849911 TCTTTCACAGGATGAGCTTACG 58.150 45.455 0.00 0.00 39.69 3.18
1893 1982 3.288092 TCTACGCTCACTCATGTGGTAT 58.712 45.455 0.00 0.00 43.94 2.73
1921 2010 5.188434 TCACTGAAATCCTATCCTTTGCAG 58.812 41.667 0.00 0.00 0.00 4.41
1927 2016 4.965200 ATCCTATCCTTTGCAGTCTACC 57.035 45.455 0.00 0.00 0.00 3.18
1935 2024 6.121776 TCCTTTGCAGTCTACCATTTCTTA 57.878 37.500 0.00 0.00 0.00 2.10
2095 2185 2.890945 AGGTTGCACATTTGGTAGTTCC 59.109 45.455 0.00 0.00 0.00 3.62
2096 2186 2.029380 GGTTGCACATTTGGTAGTTCCC 60.029 50.000 0.00 0.00 34.77 3.97
2145 2249 6.579666 TTGGTGATGGAGAGAAGAATTTTG 57.420 37.500 0.00 0.00 0.00 2.44
2188 2296 8.201464 TGACTGAAGACATAGTGTTTAGTTTGA 58.799 33.333 6.05 0.00 36.21 2.69
2281 2392 1.369839 TTCCGTTTGCTGCGTTGACA 61.370 50.000 0.00 0.00 0.00 3.58
2379 2490 2.604462 CCTTTGTTGCTGTTTCTTGTGC 59.396 45.455 0.00 0.00 0.00 4.57
2386 2497 2.168106 TGCTGTTTCTTGTGCATTGGTT 59.832 40.909 0.00 0.00 0.00 3.67
2456 2567 6.987386 ACTGCTATGTTCATGATCTAGGTAC 58.013 40.000 0.00 0.00 0.00 3.34
2575 2687 9.630098 CATGCTACTGTCAAAAGTTAATTCATT 57.370 29.630 0.00 0.00 0.00 2.57
2619 2731 4.882671 ATATTTTGCGCTACAGTTCCTG 57.117 40.909 9.73 0.00 37.52 3.86
2664 2954 4.222124 ACCAATCTGTTAGTTAGGCCAG 57.778 45.455 5.01 0.00 0.00 4.85
2935 3225 4.987912 CCTTCAGAAGTCAGAACTCTTGTC 59.012 45.833 9.41 0.00 33.48 3.18
2940 3230 6.016192 TCAGAAGTCAGAACTCTTGTCGTTAT 60.016 38.462 0.00 0.00 33.48 1.89
2946 3236 7.033791 GTCAGAACTCTTGTCGTTATCCATAA 58.966 38.462 0.00 0.00 0.00 1.90
2947 3237 7.707035 GTCAGAACTCTTGTCGTTATCCATAAT 59.293 37.037 0.00 0.00 0.00 1.28
2948 3238 7.706607 TCAGAACTCTTGTCGTTATCCATAATG 59.293 37.037 0.00 0.00 0.00 1.90
2949 3239 7.706607 CAGAACTCTTGTCGTTATCCATAATGA 59.293 37.037 0.00 0.00 36.28 2.57
2950 3240 8.424918 AGAACTCTTGTCGTTATCCATAATGAT 58.575 33.333 4.84 0.00 39.61 2.45
2951 3241 7.953158 ACTCTTGTCGTTATCCATAATGATG 57.047 36.000 4.84 0.00 39.61 3.07
2952 3242 6.425114 ACTCTTGTCGTTATCCATAATGATGC 59.575 38.462 4.84 0.00 39.61 3.91
2953 3243 6.287525 TCTTGTCGTTATCCATAATGATGCA 58.712 36.000 4.84 0.00 39.61 3.96
2954 3244 6.424812 TCTTGTCGTTATCCATAATGATGCAG 59.575 38.462 4.84 2.93 39.61 4.41
2955 3245 5.610398 TGTCGTTATCCATAATGATGCAGT 58.390 37.500 4.84 0.00 39.61 4.40
3005 3295 5.163353 TGACCTCAACAACATAGTGAAGTCA 60.163 40.000 1.25 1.25 0.00 3.41
3006 3296 5.869579 ACCTCAACAACATAGTGAAGTCAT 58.130 37.500 0.00 0.00 0.00 3.06
3007 3297 5.702670 ACCTCAACAACATAGTGAAGTCATG 59.297 40.000 0.00 0.00 0.00 3.07
3008 3298 5.702670 CCTCAACAACATAGTGAAGTCATGT 59.297 40.000 0.00 0.00 34.42 3.21
3009 3299 6.873605 CCTCAACAACATAGTGAAGTCATGTA 59.126 38.462 0.00 0.00 32.70 2.29
3010 3300 7.550551 CCTCAACAACATAGTGAAGTCATGTAT 59.449 37.037 0.00 0.00 32.70 2.29
3027 3317 6.874134 GTCATGTATATGTATGTCCCTGGTTC 59.126 42.308 0.00 0.00 35.73 3.62
3100 3390 7.852263 AGGAATGCATATAGTGGGATAGTTAC 58.148 38.462 0.00 0.00 0.00 2.50
3125 3415 6.849811 CGTATTAGTATGGTACTCAAGACACG 59.150 42.308 0.00 0.00 40.14 4.49
3168 3458 9.922305 GCTTTTATCTAGCACTGTAGTTTTATG 57.078 33.333 0.00 0.00 38.51 1.90
3261 3551 2.551459 ACTTTGCTCTGTGATGCTGAAC 59.449 45.455 0.00 0.00 0.00 3.18
3267 3557 2.483106 CTCTGTGATGCTGAACACAAGG 59.517 50.000 0.00 0.00 44.50 3.61
3312 3603 9.822185 ATCATTATCTCCTTTTATGTTTTTGCC 57.178 29.630 0.00 0.00 0.00 4.52
3518 3809 2.299867 TGTATGTGAGCTTGAGCAGTCA 59.700 45.455 5.70 0.00 45.16 3.41
3662 3957 9.283768 TCTTTCTGCAGTTTGATGAAATAGTTA 57.716 29.630 14.67 0.00 0.00 2.24
3729 4024 4.207165 TCCTAGCCTTGAATACCATTTGC 58.793 43.478 0.00 0.00 0.00 3.68
3868 4164 1.118838 ATCTTCTGAGAAGAGGCGGG 58.881 55.000 26.73 0.28 35.07 6.13
3914 4210 5.617609 TCAATCTGCACGTTTAATCTTTCG 58.382 37.500 0.00 0.00 0.00 3.46
3961 4257 6.490566 TCCTTATTGTCTTTCCTTTTACGC 57.509 37.500 0.00 0.00 0.00 4.42
4177 4705 7.144000 AGAAAATGCTGTTTTTGCAACAAAAA 58.856 26.923 12.80 12.80 44.01 1.94
4254 4782 6.877611 AACACTACTAGGATTTGGTTGTTG 57.122 37.500 0.00 0.00 0.00 3.33
4255 4783 4.760204 ACACTACTAGGATTTGGTTGTTGC 59.240 41.667 0.00 0.00 0.00 4.17
4326 5065 7.864108 TTCCATTATCTGTGTAAGATGTTGG 57.136 36.000 10.08 10.08 45.64 3.77
4430 5169 1.039068 ATGAGATCCAGAGGCTGTCG 58.961 55.000 0.00 0.00 0.00 4.35
4454 5193 4.113354 GAGCTGGAAAACTACAGATACCG 58.887 47.826 0.00 0.00 36.86 4.02
4457 5196 4.430908 CTGGAAAACTACAGATACCGGTC 58.569 47.826 12.40 0.00 36.86 4.79
4514 5253 2.097825 CATGAGGCCAAGGAGAAAAGG 58.902 52.381 5.01 0.00 0.00 3.11
4669 5421 3.568007 TGTGGCTTAATTTGCTCGTTCTT 59.432 39.130 3.70 0.00 0.00 2.52
4702 5454 6.133356 ACTCCAAAGGTTATTTTGTCAGGAA 58.867 36.000 0.00 0.00 36.54 3.36
4709 5461 7.158099 AGGTTATTTTGTCAGGAATTAGTGC 57.842 36.000 0.00 0.00 0.00 4.40
4749 5510 9.764363 AATGATATGCAATACGAAGAGACTTAA 57.236 29.630 0.00 0.00 0.00 1.85
4750 5511 9.764363 ATGATATGCAATACGAAGAGACTTAAA 57.236 29.630 0.00 0.00 0.00 1.52
4764 5525 6.418946 AGAGACTTAAATCAAAGGATCCCAC 58.581 40.000 8.55 0.00 31.88 4.61
4821 5586 2.529780 TACGTTTGTGGATGGACGTT 57.470 45.000 5.69 0.00 45.32 3.99
4835 5631 1.061485 GACGTTGAACGAGCTTCCTC 58.939 55.000 25.62 5.59 46.05 3.71
4907 5717 6.600882 AAAATCACTTTCATGCCAGAAGAT 57.399 33.333 0.00 0.00 0.00 2.40
5003 5819 2.689983 CAATTCCAGGCACCTCATTACC 59.310 50.000 0.00 0.00 0.00 2.85
5136 5972 1.267806 ACAAATCTCAGCGCTGGTTTG 59.732 47.619 35.10 35.10 35.76 2.93
5440 6300 1.081892 CATCTCCGCACAACTCTTGG 58.918 55.000 0.00 0.00 34.12 3.61
5463 6323 4.580167 GCAAGATTGTATGTAGGGCATGAA 59.420 41.667 0.00 0.00 38.47 2.57
5487 6347 4.324402 CCAAATTAACTGTCAGCGATTTGC 59.676 41.667 20.18 0.00 46.98 3.68
5578 6438 2.894126 AGAGTAGAGTCCACAACACAGG 59.106 50.000 0.00 0.00 0.00 4.00
5643 6503 9.973661 TCCTAGAAATCTCATGTTTTCCATTAA 57.026 29.630 11.98 0.00 34.25 1.40
5669 6529 9.730420 AAAATATGTTAGTGTGAAAACTGTGTC 57.270 29.630 0.00 0.00 0.00 3.67
5670 6530 8.677148 AATATGTTAGTGTGAAAACTGTGTCT 57.323 30.769 0.00 0.00 0.00 3.41
5671 6531 6.604735 ATGTTAGTGTGAAAACTGTGTCTC 57.395 37.500 0.00 0.00 0.00 3.36
5672 6532 5.730550 TGTTAGTGTGAAAACTGTGTCTCT 58.269 37.500 0.00 0.00 0.00 3.10
5673 6533 5.810587 TGTTAGTGTGAAAACTGTGTCTCTC 59.189 40.000 0.00 0.00 0.00 3.20
5674 6534 4.471904 AGTGTGAAAACTGTGTCTCTCA 57.528 40.909 0.00 0.00 0.00 3.27
5675 6535 4.437239 AGTGTGAAAACTGTGTCTCTCAG 58.563 43.478 0.00 0.00 38.68 3.35
5676 6536 4.081420 AGTGTGAAAACTGTGTCTCTCAGT 60.081 41.667 0.00 0.00 46.30 3.41
5677 6537 4.033358 GTGTGAAAACTGTGTCTCTCAGTG 59.967 45.833 5.46 0.00 44.03 3.66
5678 6538 4.081697 TGTGAAAACTGTGTCTCTCAGTGA 60.082 41.667 5.46 0.00 44.03 3.41
5679 6539 4.505922 GTGAAAACTGTGTCTCTCAGTGAG 59.494 45.833 14.36 14.36 44.03 3.51
5692 6552 5.995055 CTCTCAGTGAGAACAATTTGAACC 58.005 41.667 22.83 0.00 45.39 3.62
5693 6553 5.436175 TCTCAGTGAGAACAATTTGAACCA 58.564 37.500 20.65 0.00 35.59 3.67
5694 6554 5.885352 TCTCAGTGAGAACAATTTGAACCAA 59.115 36.000 20.65 0.00 35.59 3.67
5695 6555 6.547141 TCTCAGTGAGAACAATTTGAACCAAT 59.453 34.615 20.65 0.00 35.59 3.16
5696 6556 6.738114 TCAGTGAGAACAATTTGAACCAATC 58.262 36.000 2.79 0.00 0.00 2.67
5697 6557 6.320926 TCAGTGAGAACAATTTGAACCAATCA 59.679 34.615 2.79 0.00 35.85 2.57
5698 6558 7.014518 TCAGTGAGAACAATTTGAACCAATCAT 59.985 33.333 2.79 0.00 38.03 2.45
5699 6559 7.327761 CAGTGAGAACAATTTGAACCAATCATC 59.672 37.037 2.79 0.00 38.03 2.92
5700 6560 7.232127 AGTGAGAACAATTTGAACCAATCATCT 59.768 33.333 2.79 0.00 38.03 2.90
5701 6561 7.869429 GTGAGAACAATTTGAACCAATCATCTT 59.131 33.333 2.79 0.00 38.03 2.40
5702 6562 8.423349 TGAGAACAATTTGAACCAATCATCTTT 58.577 29.630 2.79 0.00 38.03 2.52
5703 6563 9.264719 GAGAACAATTTGAACCAATCATCTTTT 57.735 29.630 2.79 0.00 38.03 2.27
5704 6564 9.617523 AGAACAATTTGAACCAATCATCTTTTT 57.382 25.926 2.79 0.00 38.03 1.94
5738 6598 3.310652 GGTGAGTACCCTGGCCTC 58.689 66.667 3.32 0.00 41.36 4.70
5739 6599 1.306226 GGTGAGTACCCTGGCCTCT 60.306 63.158 3.32 0.00 41.36 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.362151 TCTACCCAGTTTCAATGTTCTAAAATT 57.638 29.630 0.00 0.00 0.00 1.82
7 8 6.464222 CAGTCTACCCAGTTTCAATGTTCTA 58.536 40.000 0.00 0.00 0.00 2.10
20 21 2.893398 GACGCCCAGTCTACCCAG 59.107 66.667 0.00 0.00 46.13 4.45
28 29 0.328258 AGCATTAAAGGACGCCCAGT 59.672 50.000 0.00 0.00 33.88 4.00
61 62 1.303317 GGGTGCAAAGTCCGATGGT 60.303 57.895 0.00 0.00 0.00 3.55
64 65 1.002134 CCAGGGTGCAAAGTCCGAT 60.002 57.895 0.00 0.00 0.00 4.18
67 68 1.966451 CGACCAGGGTGCAAAGTCC 60.966 63.158 0.00 0.00 0.00 3.85
85 86 5.221541 CCATAGTAATCCAAGGGTCAGAGAC 60.222 48.000 0.00 0.00 0.00 3.36
92 94 2.498441 TGCCCATAGTAATCCAAGGGT 58.502 47.619 0.00 0.00 38.56 4.34
111 113 4.672542 CGTTTGTCCCACTTAGCATGAATG 60.673 45.833 0.00 0.00 0.00 2.67
112 114 3.440173 CGTTTGTCCCACTTAGCATGAAT 59.560 43.478 0.00 0.00 0.00 2.57
113 115 2.811431 CGTTTGTCCCACTTAGCATGAA 59.189 45.455 0.00 0.00 0.00 2.57
114 116 2.224426 ACGTTTGTCCCACTTAGCATGA 60.224 45.455 0.00 0.00 0.00 3.07
150 163 2.196925 ACGCCCAATCAAACGCCAA 61.197 52.632 0.00 0.00 0.00 4.52
154 167 1.302383 TAGGCACGCCCAATCAAACG 61.302 55.000 3.95 0.00 36.58 3.60
155 168 0.451783 CTAGGCACGCCCAATCAAAC 59.548 55.000 3.95 0.00 36.58 2.93
156 169 1.312371 GCTAGGCACGCCCAATCAAA 61.312 55.000 3.95 0.00 36.58 2.69
201 225 6.869388 CCCTTTCTCTACTTTTATCGATAGGC 59.131 42.308 5.09 0.00 0.00 3.93
210 234 4.225267 CAGGAGGCCCTTTCTCTACTTTTA 59.775 45.833 0.00 0.00 42.02 1.52
215 239 0.833949 CCAGGAGGCCCTTTCTCTAC 59.166 60.000 0.00 0.00 42.02 2.59
225 249 0.112412 TTTCCTTTGACCAGGAGGCC 59.888 55.000 0.00 0.00 44.18 5.19
244 268 4.983671 AGAAAAAGAAGACACCGCTTTT 57.016 36.364 0.00 0.00 41.95 2.27
294 318 5.306160 CCCCTCAATTTTCCATTGCATATCT 59.694 40.000 0.00 0.00 0.00 1.98
295 319 5.511888 CCCCCTCAATTTTCCATTGCATATC 60.512 44.000 0.00 0.00 0.00 1.63
296 320 4.348754 CCCCCTCAATTTTCCATTGCATAT 59.651 41.667 0.00 0.00 0.00 1.78
297 321 3.710677 CCCCCTCAATTTTCCATTGCATA 59.289 43.478 0.00 0.00 0.00 3.14
298 322 2.506644 CCCCCTCAATTTTCCATTGCAT 59.493 45.455 0.00 0.00 0.00 3.96
299 323 1.907936 CCCCCTCAATTTTCCATTGCA 59.092 47.619 0.00 0.00 0.00 4.08
300 324 2.187100 TCCCCCTCAATTTTCCATTGC 58.813 47.619 0.00 0.00 0.00 3.56
301 325 5.440207 AAATCCCCCTCAATTTTCCATTG 57.560 39.130 0.00 0.00 0.00 2.82
339 363 2.683933 GGGCGAAGGGGACTGAGA 60.684 66.667 0.00 0.00 42.68 3.27
385 456 1.333619 CCACAAACTTCAGACGGGTTG 59.666 52.381 0.00 0.00 0.00 3.77
392 463 0.179234 TGCCGTCCACAAACTTCAGA 59.821 50.000 0.00 0.00 0.00 3.27
404 475 1.173043 TCATCATTTGGTTGCCGTCC 58.827 50.000 0.00 0.00 0.00 4.79
543 615 8.114331 AGTCTGAATGATACTTCATGCAAAAA 57.886 30.769 0.00 0.00 45.46 1.94
544 616 7.609146 AGAGTCTGAATGATACTTCATGCAAAA 59.391 33.333 0.00 0.00 45.46 2.44
545 617 7.108194 AGAGTCTGAATGATACTTCATGCAAA 58.892 34.615 0.00 0.00 45.46 3.68
546 618 6.647229 AGAGTCTGAATGATACTTCATGCAA 58.353 36.000 0.00 0.00 45.46 4.08
547 619 6.231258 AGAGTCTGAATGATACTTCATGCA 57.769 37.500 0.00 0.00 44.27 3.96
548 620 7.551035 AAAGAGTCTGAATGATACTTCATGC 57.449 36.000 0.00 0.00 41.83 4.06
549 621 7.909121 GCAAAAGAGTCTGAATGATACTTCATG 59.091 37.037 0.00 0.00 41.83 3.07
550 622 7.828223 AGCAAAAGAGTCTGAATGATACTTCAT 59.172 33.333 0.00 0.00 44.62 2.57
551 623 7.164122 AGCAAAAGAGTCTGAATGATACTTCA 58.836 34.615 0.00 0.00 36.00 3.02
552 624 7.201600 GGAGCAAAAGAGTCTGAATGATACTTC 60.202 40.741 0.00 0.00 0.00 3.01
553 625 6.597280 GGAGCAAAAGAGTCTGAATGATACTT 59.403 38.462 0.00 0.00 0.00 2.24
554 626 6.112058 GGAGCAAAAGAGTCTGAATGATACT 58.888 40.000 0.00 0.00 0.00 2.12
555 627 5.877012 TGGAGCAAAAGAGTCTGAATGATAC 59.123 40.000 0.00 0.00 0.00 2.24
556 628 6.053632 TGGAGCAAAAGAGTCTGAATGATA 57.946 37.500 0.00 0.00 0.00 2.15
557 629 4.914983 TGGAGCAAAAGAGTCTGAATGAT 58.085 39.130 0.00 0.00 0.00 2.45
558 630 4.356405 TGGAGCAAAAGAGTCTGAATGA 57.644 40.909 0.00 0.00 0.00 2.57
559 631 5.443185 TTTGGAGCAAAAGAGTCTGAATG 57.557 39.130 0.00 0.00 29.89 2.67
560 632 6.041296 ACATTTTGGAGCAAAAGAGTCTGAAT 59.959 34.615 0.00 0.00 44.72 2.57
561 633 5.360714 ACATTTTGGAGCAAAAGAGTCTGAA 59.639 36.000 0.00 0.00 44.72 3.02
562 634 4.889409 ACATTTTGGAGCAAAAGAGTCTGA 59.111 37.500 0.00 0.00 44.72 3.27
563 635 5.192327 ACATTTTGGAGCAAAAGAGTCTG 57.808 39.130 0.00 0.00 44.72 3.51
564 636 6.321181 TGTTACATTTTGGAGCAAAAGAGTCT 59.679 34.615 0.00 0.00 44.72 3.24
565 637 6.417930 GTGTTACATTTTGGAGCAAAAGAGTC 59.582 38.462 0.00 0.00 44.72 3.36
566 638 6.273071 GTGTTACATTTTGGAGCAAAAGAGT 58.727 36.000 0.00 0.00 44.72 3.24
567 639 5.691754 GGTGTTACATTTTGGAGCAAAAGAG 59.308 40.000 0.00 0.00 44.72 2.85
568 640 5.362430 AGGTGTTACATTTTGGAGCAAAAGA 59.638 36.000 0.00 0.00 44.72 2.52
569 641 5.600696 AGGTGTTACATTTTGGAGCAAAAG 58.399 37.500 0.00 0.00 44.72 2.27
570 642 5.606348 AGGTGTTACATTTTGGAGCAAAA 57.394 34.783 0.00 0.00 45.41 2.44
638 710 2.753452 CACTCTTTGTACGGCTCTAGGA 59.247 50.000 0.00 0.00 0.00 2.94
639 711 2.753452 TCACTCTTTGTACGGCTCTAGG 59.247 50.000 0.00 0.00 0.00 3.02
665 737 1.226603 GATCTCGTCCGTCCGTTGG 60.227 63.158 0.00 0.00 0.00 3.77
842 915 2.507110 AATCGAGCCTCGTGGGTGTG 62.507 60.000 13.76 5.62 45.24 3.82
843 916 0.968901 TAATCGAGCCTCGTGGGTGT 60.969 55.000 13.76 0.00 45.24 4.16
844 917 0.389391 ATAATCGAGCCTCGTGGGTG 59.611 55.000 13.76 5.94 45.24 4.61
887 960 3.148279 CGGAGAAGGAGACGGGGG 61.148 72.222 0.00 0.00 0.00 5.40
937 1015 2.359975 TGCGAGAGAGAGGCGACA 60.360 61.111 0.00 0.00 0.00 4.35
938 1016 2.407210 CTGCGAGAGAGAGGCGAC 59.593 66.667 0.00 0.00 0.00 5.19
939 1017 2.826287 CCTGCGAGAGAGAGGCGA 60.826 66.667 0.00 0.00 0.00 5.54
1152 1230 3.721706 CACCCCCTGCCTCACCTC 61.722 72.222 0.00 0.00 0.00 3.85
1293 1375 0.468226 TTTCACCAGACAGTTCCGCT 59.532 50.000 0.00 0.00 0.00 5.52
1294 1376 0.586802 GTTTCACCAGACAGTTCCGC 59.413 55.000 0.00 0.00 0.00 5.54
1295 1377 1.867233 CTGTTTCACCAGACAGTTCCG 59.133 52.381 0.00 0.00 38.70 4.30
1331 1416 1.811266 CTGATTCCCCGCGTGTCAG 60.811 63.158 4.92 7.17 0.00 3.51
1332 1417 2.264480 CTGATTCCCCGCGTGTCA 59.736 61.111 4.92 0.67 0.00 3.58
1333 1418 2.311688 ATCCTGATTCCCCGCGTGTC 62.312 60.000 4.92 0.00 0.00 3.67
1334 1419 1.910580 AATCCTGATTCCCCGCGTGT 61.911 55.000 4.92 0.00 0.00 4.49
1335 1420 0.105964 TAATCCTGATTCCCCGCGTG 59.894 55.000 4.92 0.00 32.50 5.34
1336 1421 0.393077 CTAATCCTGATTCCCCGCGT 59.607 55.000 4.92 0.00 32.50 6.01
1337 1422 0.951040 GCTAATCCTGATTCCCCGCG 60.951 60.000 0.00 0.00 32.50 6.46
1362 1451 1.797211 TAAAAACAGGCGCCCAACGG 61.797 55.000 26.15 10.57 43.93 4.44
1380 1469 5.596772 TCCTACAATGTGATCGGTTCAGATA 59.403 40.000 0.00 0.00 37.35 1.98
1394 1483 5.957774 AGTGGCCAATAAATTCCTACAATGT 59.042 36.000 7.24 0.00 0.00 2.71
1437 1526 5.738619 TCCTCACACTATTCAGTAGCAAA 57.261 39.130 0.00 0.00 33.47 3.68
1571 1660 7.284716 TCTGCAAGCAGATTCATTTATTCTGAT 59.715 33.333 20.00 0.00 46.80 2.90
1593 1682 4.892433 AGCACCAGACTGATATAATCTGC 58.108 43.478 3.32 0.00 38.84 4.26
1713 1802 2.040544 CACTGATGTCCCGGCCAAC 61.041 63.158 2.24 0.00 0.00 3.77
1862 1951 4.142447 TGAGTGAGCGTAGATGGTTTAGAC 60.142 45.833 0.00 0.00 0.00 2.59
1893 1982 4.293494 AGGATAGGATTTCAGTGAGCTCA 58.707 43.478 13.74 13.74 0.00 4.26
2077 2167 1.883275 CGGGAACTACCAAATGTGCAA 59.117 47.619 0.00 0.00 41.20 4.08
2095 2185 3.934457 AAAATAACAGACCCTTTGCGG 57.066 42.857 0.00 0.00 0.00 5.69
2154 2258 6.870965 ACACTATGTCTTCAGTCATCAACTTC 59.129 38.462 0.00 0.00 35.45 3.01
2281 2392 0.937304 CATATAAAGCACGCCACGCT 59.063 50.000 0.00 0.00 42.98 5.07
2379 2490 3.109044 TCAACCAATGTGCAACCAATG 57.891 42.857 0.00 0.00 34.36 2.82
2386 2497 5.781210 TTCAGTAAATCAACCAATGTGCA 57.219 34.783 0.00 0.00 0.00 4.57
2425 2536 8.545229 AGATCATGAACATAGCAGTAAATAGC 57.455 34.615 0.00 0.00 0.00 2.97
2456 2567 6.603237 TTCAGAAACCATCTAATGCATACG 57.397 37.500 0.00 0.00 36.32 3.06
2619 2731 4.853924 TCAGAACAATCAAAAGGGAAGC 57.146 40.909 0.00 0.00 0.00 3.86
2831 3121 0.400213 TACTTTGGGCTCCACAGGTG 59.600 55.000 10.82 0.00 35.79 4.00
2935 3225 8.087982 ACTTTACTGCATCATTATGGATAACG 57.912 34.615 0.00 0.00 32.46 3.18
2940 3230 7.129457 AGAGACTTTACTGCATCATTATGGA 57.871 36.000 0.00 0.00 33.38 3.41
2946 3236 5.046014 AGGTCAAGAGACTTTACTGCATCAT 60.046 40.000 0.00 0.00 44.36 2.45
2947 3237 4.284490 AGGTCAAGAGACTTTACTGCATCA 59.716 41.667 0.00 0.00 44.36 3.07
2948 3238 4.826556 AGGTCAAGAGACTTTACTGCATC 58.173 43.478 0.00 0.00 44.36 3.91
2949 3239 4.899352 AGGTCAAGAGACTTTACTGCAT 57.101 40.909 0.00 0.00 44.36 3.96
2950 3240 4.345257 AGAAGGTCAAGAGACTTTACTGCA 59.655 41.667 0.00 0.00 43.23 4.41
2951 3241 4.888917 AGAAGGTCAAGAGACTTTACTGC 58.111 43.478 0.00 0.00 43.23 4.40
2998 3288 7.256296 CCAGGGACATACATATACATGACTTCA 60.256 40.741 0.00 0.00 35.96 3.02
3005 3295 5.542635 ACGAACCAGGGACATACATATACAT 59.457 40.000 0.00 0.00 0.00 2.29
3006 3296 4.897076 ACGAACCAGGGACATACATATACA 59.103 41.667 0.00 0.00 0.00 2.29
3007 3297 5.221382 ACACGAACCAGGGACATACATATAC 60.221 44.000 0.00 0.00 0.00 1.47
3008 3298 4.897076 ACACGAACCAGGGACATACATATA 59.103 41.667 0.00 0.00 0.00 0.86
3009 3299 3.709653 ACACGAACCAGGGACATACATAT 59.290 43.478 0.00 0.00 0.00 1.78
3010 3300 3.101437 ACACGAACCAGGGACATACATA 58.899 45.455 0.00 0.00 0.00 2.29
3027 3317 8.628882 TCATTGTACAGTGAAATATCTACACG 57.371 34.615 17.76 0.00 39.19 4.49
3100 3390 6.849811 CGTGTCTTGAGTACCATACTAATACG 59.150 42.308 0.00 0.00 39.59 3.06
3125 3415 7.965107 AGATAAAAGCGACAGAAATGAAATGTC 59.035 33.333 0.00 0.00 39.93 3.06
3168 3458 1.767759 ATTTACCAGCTCATGTGGCC 58.232 50.000 0.00 0.00 38.83 5.36
3261 3551 0.322975 ACAGCTAGCAGTCCCTTGTG 59.677 55.000 18.83 5.36 0.00 3.33
3267 3557 2.743636 TACACAACAGCTAGCAGTCC 57.256 50.000 18.83 0.00 0.00 3.85
3312 3603 4.046938 TCGAAGAGAAATGGGAGATTCG 57.953 45.455 0.00 0.00 39.38 3.34
3473 3764 0.983467 TACTGGCACCAAGAGCATGA 59.017 50.000 0.00 0.00 0.00 3.07
3518 3809 2.156917 CACAGACACATGGAGTTGCAT 58.843 47.619 0.00 0.00 0.00 3.96
3662 3957 1.789523 TATGAGAGGGTAGCGGCTTT 58.210 50.000 8.26 0.00 0.00 3.51
3770 4066 2.695359 TCCTGTAACCGTTGATTCAGC 58.305 47.619 0.00 0.00 0.00 4.26
3914 4210 7.148474 GGAAAGGAGAAACAAAAGAAAAACACC 60.148 37.037 0.00 0.00 0.00 4.16
3961 4257 0.755686 AAGCTGCCTCTCCCTAATCG 59.244 55.000 0.00 0.00 0.00 3.34
4128 4425 2.224548 GCCAGTTACTGACCAAGTTCCT 60.225 50.000 14.66 0.00 40.56 3.36
4177 4705 8.682936 TGTATTTCTTGCTTCTTCTTCTTCTT 57.317 30.769 0.00 0.00 0.00 2.52
4178 4706 8.682936 TTGTATTTCTTGCTTCTTCTTCTTCT 57.317 30.769 0.00 0.00 0.00 2.85
4179 4707 9.392021 CTTTGTATTTCTTGCTTCTTCTTCTTC 57.608 33.333 0.00 0.00 0.00 2.87
4236 4764 4.980573 ACTGCAACAACCAAATCCTAGTA 58.019 39.130 0.00 0.00 0.00 1.82
4250 4778 8.983724 GGTAAAGCATTTTATAAAACTGCAACA 58.016 29.630 27.83 17.80 40.09 3.33
4254 4782 9.020813 GCTAGGTAAAGCATTTTATAAAACTGC 57.979 33.333 23.47 23.47 42.30 4.40
4430 5169 3.636153 ATCTGTAGTTTTCCAGCTCCC 57.364 47.619 0.00 0.00 0.00 4.30
4454 5193 5.326200 TGATAGGAAAAGTCTTCTCGACC 57.674 43.478 0.00 0.00 43.91 4.79
4457 5196 4.116238 GGCTGATAGGAAAAGTCTTCTCG 58.884 47.826 0.00 0.00 0.00 4.04
4514 5253 4.982701 ACCTTGCCAGGCACCAGC 62.983 66.667 15.89 0.00 45.56 4.85
4649 5394 4.846779 AAAGAACGAGCAAATTAAGCCA 57.153 36.364 0.00 0.00 0.00 4.75
4669 5421 9.729281 CAAAATAACCTTTGGAGTACTACCTAA 57.271 33.333 1.66 5.53 33.48 2.69
4749 5510 9.887862 AATAATAATGAGTGGGATCCTTTGATT 57.112 29.630 12.58 6.21 0.00 2.57
4750 5511 9.887862 AAATAATAATGAGTGGGATCCTTTGAT 57.112 29.630 12.58 0.00 0.00 2.57
4790 5555 0.725117 CAAACGTATTCTGGCGGGAC 59.275 55.000 0.00 0.00 0.00 4.46
4835 5631 3.677121 CAGAACACAGAAGGAACATCGAG 59.323 47.826 0.00 0.00 0.00 4.04
4838 5644 3.406764 AGCAGAACACAGAAGGAACATC 58.593 45.455 0.00 0.00 0.00 3.06
4907 5717 7.737869 TCAAGGTAACAACTCAAGTGGTAATA 58.262 34.615 0.00 0.00 41.41 0.98
4953 5763 4.579340 ACTTCGTGTTCAGACTTCAGAGTA 59.421 41.667 0.00 0.00 35.88 2.59
5003 5819 4.346127 TCAGAGGATGATATGTTCCTGGTG 59.654 45.833 7.61 5.78 42.48 4.17
5044 5872 3.446873 AGCTGTCGATGGAGGATGATATC 59.553 47.826 0.00 0.00 0.00 1.63
5136 5972 0.381801 AATGATTCCATCGCGTTGGC 59.618 50.000 27.66 16.22 36.66 4.52
5265 6113 0.178932 GGGTTCTTCCAAGGGCCTTT 60.179 55.000 18.16 0.00 38.11 3.11
5440 6300 4.136796 TCATGCCCTACATACAATCTTGC 58.863 43.478 0.00 0.00 36.64 4.01
5463 6323 5.460646 CAAATCGCTGACAGTTAATTTGGT 58.539 37.500 20.23 0.00 32.92 3.67
5487 6347 7.201591 CCTGCACTTACATATCAAGAGACAAAG 60.202 40.741 1.45 0.00 0.00 2.77
5578 6438 4.296690 ACACGACAGAAAGTGCTAGTAAC 58.703 43.478 0.00 0.00 41.72 2.50
5643 6503 9.730420 GACACAGTTTTCACACTAACATATTTT 57.270 29.630 0.00 0.00 0.00 1.82
5651 6511 5.972935 TGAGAGACACAGTTTTCACACTAA 58.027 37.500 0.00 0.00 0.00 2.24
5652 6512 5.127194 ACTGAGAGACACAGTTTTCACACTA 59.873 40.000 0.00 0.00 44.69 2.74
5669 6529 5.528690 TGGTTCAAATTGTTCTCACTGAGAG 59.471 40.000 8.76 0.00 46.14 3.20
5670 6530 5.436175 TGGTTCAAATTGTTCTCACTGAGA 58.564 37.500 4.50 4.50 36.86 3.27
5671 6531 5.756195 TGGTTCAAATTGTTCTCACTGAG 57.244 39.130 0.00 0.00 0.00 3.35
5672 6532 6.320926 TGATTGGTTCAAATTGTTCTCACTGA 59.679 34.615 0.00 0.00 0.00 3.41
5673 6533 6.506147 TGATTGGTTCAAATTGTTCTCACTG 58.494 36.000 0.00 0.00 0.00 3.66
5674 6534 6.713762 TGATTGGTTCAAATTGTTCTCACT 57.286 33.333 0.00 0.00 0.00 3.41
5675 6535 7.373493 AGATGATTGGTTCAAATTGTTCTCAC 58.627 34.615 0.00 0.00 38.03 3.51
5676 6536 7.528996 AGATGATTGGTTCAAATTGTTCTCA 57.471 32.000 0.00 0.00 38.03 3.27
5677 6537 8.822652 AAAGATGATTGGTTCAAATTGTTCTC 57.177 30.769 0.00 0.00 38.03 2.87
5678 6538 9.617523 AAAAAGATGATTGGTTCAAATTGTTCT 57.382 25.926 0.00 0.00 38.03 3.01
5704 6564 9.210329 GGTACTCACCTTTTTGAAAAAGAAAAA 57.790 29.630 26.93 11.50 42.11 1.94
5705 6565 7.820386 GGGTACTCACCTTTTTGAAAAAGAAAA 59.180 33.333 26.93 12.94 45.04 2.29
5706 6566 7.179516 AGGGTACTCACCTTTTTGAAAAAGAAA 59.820 33.333 26.93 13.23 45.04 2.52
5707 6567 6.666113 AGGGTACTCACCTTTTTGAAAAAGAA 59.334 34.615 26.93 13.52 45.04 2.52
5708 6568 6.096282 CAGGGTACTCACCTTTTTGAAAAAGA 59.904 38.462 26.93 10.45 45.04 2.52
5709 6569 6.273071 CAGGGTACTCACCTTTTTGAAAAAG 58.727 40.000 20.45 20.45 45.04 2.27
5710 6570 5.128008 CCAGGGTACTCACCTTTTTGAAAAA 59.872 40.000 2.83 2.83 45.04 1.94
5711 6571 4.647399 CCAGGGTACTCACCTTTTTGAAAA 59.353 41.667 0.00 0.00 45.04 2.29
5712 6572 4.211920 CCAGGGTACTCACCTTTTTGAAA 58.788 43.478 0.00 0.00 45.04 2.69
5713 6573 3.827722 CCAGGGTACTCACCTTTTTGAA 58.172 45.455 0.00 0.00 45.04 2.69
5714 6574 2.488347 GCCAGGGTACTCACCTTTTTGA 60.488 50.000 0.00 0.00 45.04 2.69
5715 6575 1.886542 GCCAGGGTACTCACCTTTTTG 59.113 52.381 0.00 0.00 45.04 2.44
5716 6576 1.203013 GGCCAGGGTACTCACCTTTTT 60.203 52.381 0.00 0.00 45.04 1.94
5717 6577 0.404426 GGCCAGGGTACTCACCTTTT 59.596 55.000 0.00 0.00 45.04 2.27
5718 6578 0.475828 AGGCCAGGGTACTCACCTTT 60.476 55.000 5.01 0.00 45.04 3.11
5719 6579 0.910088 GAGGCCAGGGTACTCACCTT 60.910 60.000 5.01 0.00 45.04 3.50
5720 6580 1.306226 GAGGCCAGGGTACTCACCT 60.306 63.158 5.01 1.86 45.04 4.00
5721 6581 1.306226 AGAGGCCAGGGTACTCACC 60.306 63.158 5.01 0.00 44.96 4.02
5722 6582 4.463043 AGAGGCCAGGGTACTCAC 57.537 61.111 5.01 0.00 33.76 3.51


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

AutoCloner maintained by Alex Coulton.