Multiple sequence alignment - TraesCS3A01G511700

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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 TraesCS3A01G511700 chr3A 100.000 6760 0 0 876 7635 731083587 731090346 0.000000e+00 12484.0
1 TraesCS3A01G511700 chr3A 100.000 375 0 0 1 375 731082712 731083086 0.000000e+00 693.0
2 TraesCS3A01G511700 chr3A 97.222 36 1 0 4657 4692 731087261 731087296 2.300000e-05 62.1
3 TraesCS3A01G511700 chr3A 97.222 36 1 0 4550 4585 731087368 731087403 2.300000e-05 62.1
4 TraesCS3A01G511700 chr3B 92.600 6351 348 55 881 7172 808879848 808873561 0.000000e+00 9012.0
5 TraesCS3A01G511700 chr3B 84.104 2271 257 56 4735 6933 808710328 808712566 0.000000e+00 2098.0
6 TraesCS3A01G511700 chr3B 87.638 453 54 2 3712 4164 808709293 808709743 6.790000e-145 525.0
7 TraesCS3A01G511700 chr3B 90.286 350 17 6 1 335 808880416 808880069 7.030000e-120 442.0
8 TraesCS3A01G511700 chr3B 87.138 311 27 3 4163 4460 808709902 808710212 2.640000e-89 340.0
9 TraesCS3A01G511700 chr3B 90.476 84 6 2 4584 4667 284561689 284561608 8.100000e-20 110.0
10 TraesCS3A01G511700 chr3B 100.000 36 0 0 4550 4585 808876077 808876042 4.940000e-07 67.6
11 TraesCS3A01G511700 chr3B 97.222 36 1 0 4657 4692 808876183 808876148 2.300000e-05 62.1
12 TraesCS3A01G511700 chr3D 92.600 3527 193 21 881 4382 601925074 601921591 0.000000e+00 5005.0
13 TraesCS3A01G511700 chr3D 92.786 2523 107 27 4657 7145 601920400 601917919 0.000000e+00 3581.0
14 TraesCS3A01G511700 chr3D 92.368 380 15 4 1 375 601925596 601925226 5.250000e-146 529.0
15 TraesCS3A01G511700 chr3D 87.828 419 41 6 7221 7635 601917920 601917508 4.140000e-132 483.0
16 TraesCS3A01G511700 chr6B 91.196 1045 63 16 923 1943 429704084 429705123 0.000000e+00 1393.0
17 TraesCS3A01G511700 chr1D 95.946 74 3 0 4584 4657 211684857 211684930 3.740000e-23 121.0
18 TraesCS3A01G511700 chr1D 94.595 74 4 0 4584 4657 86918609 86918682 1.740000e-21 115.0
19 TraesCS3A01G511700 chr6D 94.595 74 4 0 4584 4657 319689492 319689419 1.740000e-21 115.0
20 TraesCS3A01G511700 chr5D 94.595 74 4 0 4584 4657 162425225 162425298 1.740000e-21 115.0
21 TraesCS3A01G511700 chr2D 94.595 74 4 0 4584 4657 298290221 298290294 1.740000e-21 115.0
22 TraesCS3A01G511700 chr2D 91.463 82 6 1 4584 4665 459298776 459298696 2.250000e-20 111.0
23 TraesCS3A01G511700 chr5A 88.764 89 9 1 4584 4671 585407250 585407162 2.910000e-19 108.0


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 TraesCS3A01G511700 chr3A 731082712 731090346 7634 False 3325.300000 12484 98.611000 1 7635 4 chr3A.!!$F1 7634
1 TraesCS3A01G511700 chr3B 808873561 808880416 6855 True 2395.925000 9012 95.027000 1 7172 4 chr3B.!!$R2 7171
2 TraesCS3A01G511700 chr3B 808709293 808712566 3273 False 987.666667 2098 86.293333 3712 6933 3 chr3B.!!$F1 3221
3 TraesCS3A01G511700 chr3D 601917508 601925596 8088 True 2399.500000 5005 91.395500 1 7635 4 chr3D.!!$R1 7634
4 TraesCS3A01G511700 chr6B 429704084 429705123 1039 False 1393.000000 1393 91.196000 923 1943 1 chr6B.!!$F1 1020

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
907 959 1.441016 GCCGTTTCAGCTGCGAAAG 60.441 57.895 9.47 8.55 35.62 2.62 F
1706 1789 1.228245 TGAACAGTTGAGGCCTGCC 60.228 57.895 12.00 0.00 33.09 4.85 F
2298 2386 1.472728 CGGGAGTTATCTTTGTCCGGG 60.473 57.143 0.00 0.00 33.27 5.73 F
2872 2962 1.070601 GCCAATTGTTCTGCCCAAGTT 59.929 47.619 4.43 0.00 0.00 2.66 F
4317 4593 0.331616 TAAAGGGGGCTGGCTTCTTC 59.668 55.000 0.00 0.00 0.00 2.87 F
4616 5923 0.790993 TAGTGGTCAGACCCTTCCCT 59.209 55.000 17.59 7.46 37.50 4.20 F
4618 5925 0.836400 GTGGTCAGACCCTTCCCTGA 60.836 60.000 17.59 0.00 37.50 3.86 F
6142 7514 0.883370 GGAAGCGTTTCTCCCACGTT 60.883 55.000 11.94 0.00 39.92 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 1923 1.211457 CTGGTAGAAGCCTGCAATCCT 59.789 52.381 0.00 0.00 0.00 3.24 R
2849 2938 1.243342 TGGGCAGAACAATTGGCTCG 61.243 55.000 10.83 4.34 40.61 5.03 R
4134 4238 0.991146 TGCCAAGGAAGCTGTATGGA 59.009 50.000 11.16 0.00 32.82 3.41 R
4648 5955 0.538287 GACTCCATATTGGGCAGCCC 60.538 60.000 25.54 25.54 45.71 5.19 R
6239 7611 0.468226 ACGACCTTGGAGAAGTGCAA 59.532 50.000 0.00 0.00 32.33 4.08 R
6391 7781 0.948623 CCGCCGAGTTGATGTTCACA 60.949 55.000 0.00 0.00 0.00 3.58 R
6614 8004 4.844884 TCCTAGAACTCGTCATCAAGAGA 58.155 43.478 0.00 0.00 37.87 3.10 R
7218 8617 0.105709 TGGCATCCAGATACTCCGGA 60.106 55.000 2.93 2.93 0.00 5.14 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
21 22 4.957759 CTAAACCTACCACCAAAATCGG 57.042 45.455 0.00 0.00 0.00 4.18
116 122 9.920946 AGATAATTTATCTCCCAGCTACAAAAA 57.079 29.630 12.26 0.00 41.55 1.94
120 126 6.817765 TTATCTCCCAGCTACAAAAACAAG 57.182 37.500 0.00 0.00 0.00 3.16
323 372 3.083997 GGCACCGTCCTCCTCCAT 61.084 66.667 0.00 0.00 0.00 3.41
324 373 2.501610 GCACCGTCCTCCTCCATC 59.498 66.667 0.00 0.00 0.00 3.51
325 374 2.808315 CACCGTCCTCCTCCATCG 59.192 66.667 0.00 0.00 0.00 3.84
326 375 3.148279 ACCGTCCTCCTCCATCGC 61.148 66.667 0.00 0.00 0.00 4.58
327 376 3.917760 CCGTCCTCCTCCATCGCC 61.918 72.222 0.00 0.00 0.00 5.54
328 377 2.835431 CGTCCTCCTCCATCGCCT 60.835 66.667 0.00 0.00 0.00 5.52
329 378 2.851071 CGTCCTCCTCCATCGCCTC 61.851 68.421 0.00 0.00 0.00 4.70
330 379 2.519541 TCCTCCTCCATCGCCTCG 60.520 66.667 0.00 0.00 0.00 4.63
907 959 1.441016 GCCGTTTCAGCTGCGAAAG 60.441 57.895 9.47 8.55 35.62 2.62
965 1021 4.974438 TTCCGGCTCCAGGGGTGT 62.974 66.667 0.00 0.00 0.00 4.16
974 1030 2.488347 GCTCCAGGGGTGTTGAAGTTTA 60.488 50.000 0.00 0.00 0.00 2.01
1302 1367 4.576330 ATGCTTTCTTGTAGGCCTACTT 57.424 40.909 36.49 5.92 37.00 2.24
1374 1439 6.936968 AGAACCACCTATTCTGAGTAACTT 57.063 37.500 0.00 0.00 35.06 2.66
1456 1537 2.582052 CACCAAACACTTTGAGGCCTA 58.418 47.619 4.42 0.00 43.26 3.93
1500 1581 6.019108 ACTTCCAGGCAGAATAATTTTCCTT 58.981 36.000 0.00 0.00 0.00 3.36
1536 1617 9.378551 TGTTGAGGTGTATGTAGATAATGTTTC 57.621 33.333 0.00 0.00 0.00 2.78
1538 1619 8.002984 TGAGGTGTATGTAGATAATGTTTCGA 57.997 34.615 0.00 0.00 0.00 3.71
1540 1621 9.477484 GAGGTGTATGTAGATAATGTTTCGATT 57.523 33.333 0.00 0.00 0.00 3.34
1559 1640 6.570692 TCGATTGTTACCAGATTAGAAGGTC 58.429 40.000 0.00 0.00 36.87 3.85
1564 1645 5.105877 TGTTACCAGATTAGAAGGTCGTCAG 60.106 44.000 0.00 0.00 36.87 3.51
1614 1695 2.258109 GGAAACTCTGGGACTGTAGGT 58.742 52.381 0.00 0.00 0.00 3.08
1621 1702 4.773149 ACTCTGGGACTGTAGGTTTCTTAG 59.227 45.833 0.00 0.00 0.00 2.18
1678 1761 7.419204 ACTGATTTTGCCATTTCAAAAACATG 58.581 30.769 10.70 0.00 45.50 3.21
1688 1771 6.925165 CCATTTCAAAAACATGTAGAAGCACT 59.075 34.615 0.00 0.00 0.00 4.40
1706 1789 1.228245 TGAACAGTTGAGGCCTGCC 60.228 57.895 12.00 0.00 33.09 4.85
1731 1815 6.222038 AGACGTATTCAGCTGGAAGAAATA 57.778 37.500 15.13 7.27 39.30 1.40
1786 1870 7.749126 GGCGTATATAGATAATGTTTTGGTTGC 59.251 37.037 0.00 0.00 0.00 4.17
1846 1930 9.561270 GACATTTAGAAGAAACTAAAGGATTGC 57.439 33.333 15.93 3.59 42.71 3.56
1944 2028 2.564062 CAGAAACATGCAACCTTCCCAT 59.436 45.455 0.00 0.00 0.00 4.00
1956 2040 4.236527 ACCTTCCCATGATAGGTTTGTC 57.763 45.455 0.00 0.00 39.19 3.18
1978 2062 2.206900 TCCACCTTGGAGGGCAGA 59.793 61.111 3.39 0.00 42.67 4.26
1979 2063 2.224159 TCCACCTTGGAGGGCAGAC 61.224 63.158 3.39 0.00 42.67 3.51
1980 2064 2.528818 CCACCTTGGAGGGCAGACA 61.529 63.158 0.00 0.00 40.96 3.41
2005 2089 5.470368 TCAGTTGTGATGCTGTTCTAGTAC 58.530 41.667 0.00 0.00 34.57 2.73
2009 2093 3.576550 TGTGATGCTGTTCTAGTACCACA 59.423 43.478 5.02 5.02 32.63 4.17
2198 2282 6.710692 AGCTGCTTTAAATAATGTTTGTGC 57.289 33.333 0.00 0.00 0.00 4.57
2210 2294 8.885494 AATAATGTTTGTGCTGTGTTTACAAT 57.115 26.923 0.00 0.00 36.14 2.71
2211 2295 6.586868 AATGTTTGTGCTGTGTTTACAATG 57.413 33.333 0.00 0.00 36.14 2.82
2212 2296 5.065704 TGTTTGTGCTGTGTTTACAATGT 57.934 34.783 0.00 0.00 36.14 2.71
2213 2297 5.473931 TGTTTGTGCTGTGTTTACAATGTT 58.526 33.333 0.00 0.00 36.14 2.71
2298 2386 1.472728 CGGGAGTTATCTTTGTCCGGG 60.473 57.143 0.00 0.00 33.27 5.73
2388 2476 5.133221 AGTACCAAGTCACTTGCTTTTGAT 58.867 37.500 12.49 0.00 39.85 2.57
2582 2670 2.805099 CTCTGTGTTCTTGCTCCTTCAC 59.195 50.000 0.00 0.00 0.00 3.18
2583 2671 1.876156 CTGTGTTCTTGCTCCTTCACC 59.124 52.381 0.00 0.00 0.00 4.02
2632 2720 4.589216 TCTTTGACTGCCATTTTTCTGG 57.411 40.909 0.00 0.00 39.45 3.86
2675 2763 3.726557 ACATTCATGTCTGATGGGTGT 57.273 42.857 0.00 0.00 35.87 4.16
2759 2848 9.631257 AAATTTCATGTGAGATGTGACCATATA 57.369 29.630 0.00 0.00 0.00 0.86
2849 2938 5.231991 CACTGTTCTTGTTAAAACATGTGCC 59.768 40.000 0.00 0.00 38.95 5.01
2872 2962 1.070601 GCCAATTGTTCTGCCCAAGTT 59.929 47.619 4.43 0.00 0.00 2.66
2888 2978 5.689819 CCCAAGTTGTAAATCTGAACTTCG 58.310 41.667 1.45 0.00 37.74 3.79
3053 3143 2.157640 AGGAGATGTCTGACAGGAGG 57.842 55.000 16.46 0.00 0.00 4.30
3101 3191 4.189231 ACATTAGTTTCAGGGATGCGTAC 58.811 43.478 0.00 0.00 0.00 3.67
3266 3359 3.369381 CCATCTCTGTAGTTGGGCG 57.631 57.895 0.00 0.00 38.47 6.13
3473 3575 4.872664 AGAGCTATTCGTGTATAGGTTGC 58.127 43.478 0.00 0.00 38.55 4.17
3579 3682 6.205853 AGCTCGGTGATTTATGTTTTTGTGTA 59.794 34.615 0.00 0.00 0.00 2.90
3626 3729 2.353208 GCGACTGAGATTTGTGGAGTCT 60.353 50.000 0.00 0.00 32.50 3.24
3632 3735 4.416516 TGAGATTTGTGGAGTCTAGTCCA 58.583 43.478 2.25 2.25 44.82 4.02
3660 3763 4.920640 TCTTATGCTTCGAAGGAGGTAG 57.079 45.455 25.77 19.48 0.00 3.18
3819 3922 3.615110 CGAGTGGCTGAGTAGTGTTCAAT 60.615 47.826 0.00 0.00 0.00 2.57
3937 4040 9.793252 TCTGTACCTTCGTTGTAAGTATAAATC 57.207 33.333 0.00 0.00 0.00 2.17
3942 4045 8.483758 ACCTTCGTTGTAAGTATAAATCCTGAT 58.516 33.333 0.00 0.00 0.00 2.90
3995 4098 8.470805 TCAACTCTCAGCTCTTAACCTATAAAG 58.529 37.037 0.00 0.00 0.00 1.85
3998 4101 8.856103 ACTCTCAGCTCTTAACCTATAAAGATC 58.144 37.037 0.00 0.00 31.60 2.75
4074 4177 5.363005 TGATCTTCACCCCTAGTACTTTAGC 59.637 44.000 0.00 0.00 0.00 3.09
4092 4195 6.801862 ACTTTAGCTGCGTGTTAATTTTGATC 59.198 34.615 0.00 0.00 0.00 2.92
4168 4432 6.618287 TCCTTGGCATTGATTTATAGTTCG 57.382 37.500 0.00 0.00 0.00 3.95
4192 4456 7.441760 TCGTGATAGTGTCTAGAGTTAGGATTC 59.558 40.741 0.00 0.00 0.00 2.52
4317 4593 0.331616 TAAAGGGGGCTGGCTTCTTC 59.668 55.000 0.00 0.00 0.00 2.87
4321 4597 1.379176 GGGGCTGGCTTCTTCCTTC 60.379 63.158 0.00 0.00 0.00 3.46
4329 4605 2.693074 TGGCTTCTTCCTTCCACAAAAC 59.307 45.455 0.00 0.00 0.00 2.43
4334 4610 5.067283 GCTTCTTCCTTCCACAAAACAAGTA 59.933 40.000 0.00 0.00 0.00 2.24
4612 5919 1.203440 ACCCATAGTGGTCAGACCCTT 60.203 52.381 17.59 7.61 37.50 3.95
4616 5923 0.790993 TAGTGGTCAGACCCTTCCCT 59.209 55.000 17.59 7.46 37.50 4.20
4618 5925 0.836400 GTGGTCAGACCCTTCCCTGA 60.836 60.000 17.59 0.00 37.50 3.86
4648 5955 4.115279 CGGGAGCTACATGCACTG 57.885 61.111 0.00 0.00 45.94 3.66
4649 5956 1.522355 CGGGAGCTACATGCACTGG 60.522 63.158 0.00 0.00 45.94 4.00
4879 6200 4.149221 GCAAACAATGTGATGTGTGATGTG 59.851 41.667 1.90 0.00 40.35 3.21
4994 6315 3.951663 GGCACCAGTTTATAGTGACCTT 58.048 45.455 0.00 0.00 33.18 3.50
5181 6511 1.904144 TGATCTCTTAAACGTCGCCG 58.096 50.000 0.00 0.00 40.83 6.46
5197 6527 4.319333 CGTCGCCGTAGAAAGTAGACATAT 60.319 45.833 0.00 0.00 0.00 1.78
5320 6650 3.802948 ACCTGGTCGTTAGCTTAGATG 57.197 47.619 0.00 0.00 0.00 2.90
5321 6651 2.159085 ACCTGGTCGTTAGCTTAGATGC 60.159 50.000 0.00 0.00 0.00 3.91
5322 6652 2.474816 CTGGTCGTTAGCTTAGATGCC 58.525 52.381 0.00 0.00 0.00 4.40
5376 6733 7.040494 CAGATCACATGGCTAGATAACTATGG 58.960 42.308 0.00 0.00 0.00 2.74
5433 6790 7.902087 AGAGGTATAAGATAGTGCATTTCCTC 58.098 38.462 0.00 0.00 37.44 3.71
5477 6835 9.886132 AAAGGGTATAAGATGTGTAAGTACTTG 57.114 33.333 18.56 0.00 0.00 3.16
5599 6964 3.228188 TCCAATCCTGGTGGCATTATC 57.772 47.619 0.00 0.00 43.97 1.75
5604 6969 5.163280 CCAATCCTGGTGGCATTATCAAAAT 60.163 40.000 0.00 0.00 38.00 1.82
5616 6981 1.930567 ATCAAAATTGGATGCGCTGC 58.069 45.000 9.73 0.00 0.00 5.25
5712 7078 5.750352 ATTTGGGAATGATGAAAACAGCT 57.250 34.783 0.00 0.00 0.00 4.24
5730 7096 4.901849 ACAGCTGTAGCATTAGAATAGGGA 59.098 41.667 20.16 0.00 45.16 4.20
5822 7191 4.334552 TGTGGATCAACATTGCACACTAT 58.665 39.130 0.00 0.00 31.69 2.12
5872 7241 1.486310 TGACAGTTGCCACTCAGTTCT 59.514 47.619 0.00 0.00 0.00 3.01
5889 7258 7.337942 ACTCAGTTCTGGGTTTGATGATATTTC 59.662 37.037 0.00 0.00 0.00 2.17
5944 7316 3.222173 ACTTTGGTGCAGGTTGATGTA 57.778 42.857 0.00 0.00 0.00 2.29
6066 7438 1.065854 CCAGCTCGAAGATGACCCTTT 60.066 52.381 2.35 0.00 32.38 3.11
6142 7514 0.883370 GGAAGCGTTTCTCCCACGTT 60.883 55.000 11.94 0.00 39.92 3.99
6202 7574 1.103803 CAGGAGCACGGCTAGAAGTA 58.896 55.000 0.00 0.00 39.88 2.24
6239 7611 4.527038 TCAAGAAGATACTGTTCCTTCGGT 59.473 41.667 12.81 6.06 40.71 4.69
6283 7655 3.699894 CACTCCGTCAGGCAGCCT 61.700 66.667 8.70 8.70 37.47 4.58
6614 8004 0.674534 GCCCGATGACGAGGATTACT 59.325 55.000 0.00 0.00 42.66 2.24
6616 8006 2.231529 CCCGATGACGAGGATTACTCT 58.768 52.381 0.00 0.00 44.33 3.24
6638 8028 6.592870 TCTCTTGATGACGAGTTCTAGGATA 58.407 40.000 0.00 0.00 0.00 2.59
6742 8132 5.048991 GCGGGTGAAAGATTTAGAGTTTTCA 60.049 40.000 0.00 0.00 37.25 2.69
6807 8198 2.227865 TGGGTTTTTCGCAGTAATGAGC 59.772 45.455 0.00 0.00 34.88 4.26
6948 8343 5.122082 ACTGTTTTGGTTTTGCATTGTCAAG 59.878 36.000 0.00 0.00 0.00 3.02
6962 8357 5.618640 GCATTGTCAAGAGATTCAGGTGTTC 60.619 44.000 0.00 0.00 0.00 3.18
7076 8475 6.147492 TCCAGCAATGCAATGTAATTTGTTTC 59.853 34.615 8.35 0.00 31.22 2.78
7109 8508 9.778741 ATGTTAATAAATCGATATGTCTGGTGT 57.221 29.630 0.00 0.00 0.00 4.16
7123 8522 2.618241 TCTGGTGTTTCTTGTGATGTGC 59.382 45.455 0.00 0.00 0.00 4.57
7150 8549 8.349245 TCTTTCAAAATTTCTTTATCGTGCTGA 58.651 29.630 0.00 0.00 0.00 4.26
7155 8554 8.840867 CAAAATTTCTTTATCGTGCTGAAGTAC 58.159 33.333 0.00 0.00 0.00 2.73
7157 8556 7.849804 ATTTCTTTATCGTGCTGAAGTACAT 57.150 32.000 0.00 0.00 0.00 2.29
7166 8565 5.992829 TCGTGCTGAAGTACATAAGGAAAAA 59.007 36.000 0.00 0.00 0.00 1.94
7172 8571 7.435068 TGAAGTACATAAGGAAAAACAGAGC 57.565 36.000 0.00 0.00 0.00 4.09
7173 8572 6.147164 TGAAGTACATAAGGAAAAACAGAGCG 59.853 38.462 0.00 0.00 0.00 5.03
7174 8573 3.831715 ACATAAGGAAAAACAGAGCGC 57.168 42.857 0.00 0.00 0.00 5.92
7175 8574 2.488153 ACATAAGGAAAAACAGAGCGCC 59.512 45.455 2.29 0.00 0.00 6.53
7176 8575 2.264005 TAAGGAAAAACAGAGCGCCA 57.736 45.000 2.29 0.00 0.00 5.69
7177 8576 1.398692 AAGGAAAAACAGAGCGCCAA 58.601 45.000 2.29 0.00 0.00 4.52
7178 8577 1.398692 AGGAAAAACAGAGCGCCAAA 58.601 45.000 2.29 0.00 0.00 3.28
7179 8578 1.963515 AGGAAAAACAGAGCGCCAAAT 59.036 42.857 2.29 0.00 0.00 2.32
7180 8579 2.061028 GGAAAAACAGAGCGCCAAATG 58.939 47.619 2.29 0.00 0.00 2.32
7181 8580 2.288152 GGAAAAACAGAGCGCCAAATGA 60.288 45.455 2.29 0.00 0.00 2.57
7182 8581 2.712057 AAAACAGAGCGCCAAATGAG 57.288 45.000 2.29 0.00 0.00 2.90
7183 8582 1.896220 AAACAGAGCGCCAAATGAGA 58.104 45.000 2.29 0.00 0.00 3.27
7184 8583 2.119801 AACAGAGCGCCAAATGAGAT 57.880 45.000 2.29 0.00 0.00 2.75
7185 8584 1.376543 ACAGAGCGCCAAATGAGATG 58.623 50.000 2.29 0.00 0.00 2.90
7186 8585 0.029035 CAGAGCGCCAAATGAGATGC 59.971 55.000 2.29 0.00 0.00 3.91
7187 8586 0.393402 AGAGCGCCAAATGAGATGCA 60.393 50.000 2.29 0.00 0.00 3.96
7188 8587 0.029035 GAGCGCCAAATGAGATGCAG 59.971 55.000 2.29 0.00 0.00 4.41
7189 8588 0.393402 AGCGCCAAATGAGATGCAGA 60.393 50.000 2.29 0.00 0.00 4.26
7190 8589 0.248377 GCGCCAAATGAGATGCAGAC 60.248 55.000 0.00 0.00 0.00 3.51
7191 8590 1.089112 CGCCAAATGAGATGCAGACA 58.911 50.000 0.00 0.00 0.00 3.41
7192 8591 1.674441 CGCCAAATGAGATGCAGACAT 59.326 47.619 0.00 0.00 39.98 3.06
7193 8592 2.098607 CGCCAAATGAGATGCAGACATT 59.901 45.455 9.09 9.09 36.35 2.71
7194 8593 3.428452 CGCCAAATGAGATGCAGACATTT 60.428 43.478 16.99 16.99 42.42 2.32
7195 8594 4.201940 CGCCAAATGAGATGCAGACATTTA 60.202 41.667 20.10 0.00 40.63 1.40
7196 8595 5.279384 GCCAAATGAGATGCAGACATTTAG 58.721 41.667 20.10 16.42 40.63 1.85
7197 8596 5.735354 GCCAAATGAGATGCAGACATTTAGG 60.735 44.000 20.10 21.08 40.63 2.69
7198 8597 5.279384 CAAATGAGATGCAGACATTTAGGC 58.721 41.667 20.10 0.00 40.63 3.93
7199 8598 2.923121 TGAGATGCAGACATTTAGGCC 58.077 47.619 0.00 0.00 36.35 5.19
7200 8599 2.225467 GAGATGCAGACATTTAGGCCC 58.775 52.381 0.00 0.00 36.35 5.80
7201 8600 0.947244 GATGCAGACATTTAGGCCCG 59.053 55.000 0.00 0.00 36.35 6.13
7202 8601 0.255890 ATGCAGACATTTAGGCCCGT 59.744 50.000 0.00 0.00 30.07 5.28
7203 8602 0.392461 TGCAGACATTTAGGCCCGTC 60.392 55.000 0.00 0.00 0.00 4.79
7204 8603 1.095807 GCAGACATTTAGGCCCGTCC 61.096 60.000 0.00 0.00 0.00 4.79
7206 8605 1.065418 CAGACATTTAGGCCCGTCCTT 60.065 52.381 0.00 0.00 44.75 3.36
7207 8606 1.209747 AGACATTTAGGCCCGTCCTTC 59.790 52.381 0.00 0.00 44.75 3.46
7208 8607 0.255033 ACATTTAGGCCCGTCCTTCC 59.745 55.000 0.00 0.00 44.75 3.46
7209 8608 0.814010 CATTTAGGCCCGTCCTTCCG 60.814 60.000 0.00 0.00 44.75 4.30
7210 8609 2.604299 ATTTAGGCCCGTCCTTCCGC 62.604 60.000 0.00 0.00 44.75 5.54
7215 8614 4.891727 CCCGTCCTTCCGCCGATG 62.892 72.222 0.00 0.00 0.00 3.84
7216 8615 3.833645 CCGTCCTTCCGCCGATGA 61.834 66.667 0.00 0.00 0.00 2.92
7217 8616 2.417516 CGTCCTTCCGCCGATGAT 59.582 61.111 0.00 0.00 0.00 2.45
7218 8617 1.227263 CGTCCTTCCGCCGATGATT 60.227 57.895 0.00 0.00 0.00 2.57
7219 8618 1.215655 CGTCCTTCCGCCGATGATTC 61.216 60.000 0.00 0.00 0.00 2.52
7220 8619 0.880718 GTCCTTCCGCCGATGATTCC 60.881 60.000 0.00 0.00 0.00 3.01
7221 8620 1.956170 CCTTCCGCCGATGATTCCG 60.956 63.158 0.00 0.00 0.00 4.30
7255 8654 3.420839 CCATATCTTGGCGGTTGAAAC 57.579 47.619 0.00 0.00 39.09 2.78
7259 8658 0.536460 TCTTGGCGGTTGAAACCCTC 60.536 55.000 6.64 0.34 46.53 4.30
7281 8680 2.769663 GGGGGTTCTTTTCTGTTGGTTT 59.230 45.455 0.00 0.00 0.00 3.27
7282 8681 3.199071 GGGGGTTCTTTTCTGTTGGTTTT 59.801 43.478 0.00 0.00 0.00 2.43
7294 8693 1.380771 GTTGGTTTTGTTTATCGCGCG 59.619 47.619 26.76 26.76 0.00 6.86
7318 8717 1.871676 GTGAAAACCGTCACTCCCTTC 59.128 52.381 0.00 0.00 43.82 3.46
7331 8730 5.980715 GTCACTCCCTTCGAAGATTAAGATC 59.019 44.000 26.61 6.81 35.04 2.75
7345 8744 5.821470 AGATTAAGATCTTGTGTGATGGCTG 59.179 40.000 18.47 0.00 39.63 4.85
7346 8745 1.747709 AGATCTTGTGTGATGGCTGC 58.252 50.000 0.00 0.00 0.00 5.25
7347 8746 1.281287 AGATCTTGTGTGATGGCTGCT 59.719 47.619 0.00 0.00 0.00 4.24
7382 8781 1.002430 TCTCTTCGCCAAGCTGAATGT 59.998 47.619 0.00 0.00 0.00 2.71
7391 8790 3.293311 CAAGCTGAATGTTCTTGGTGG 57.707 47.619 0.00 0.00 34.98 4.61
7454 8856 3.131396 GTTCACGACAATGACTTGGACT 58.869 45.455 0.00 0.00 36.64 3.85
7455 8857 3.026630 TCACGACAATGACTTGGACTC 57.973 47.619 0.00 0.00 36.64 3.36
7466 8868 2.544267 GACTTGGACTCTTTGGACAACG 59.456 50.000 0.00 0.00 0.00 4.10
7487 8889 5.060506 ACGTGTAACAAGATGGTGATCAAA 58.939 37.500 0.00 0.00 35.74 2.69
7500 8902 6.633500 TGGTGATCAAACAGGTCTTTTTAG 57.367 37.500 0.00 0.00 0.00 1.85
7513 8915 2.844348 TCTTTTTAGGAGGGGCCACTAG 59.156 50.000 8.04 0.00 40.02 2.57
7521 8923 2.291605 GGAGGGGCCACTAGTTTCATTT 60.292 50.000 8.04 0.00 36.34 2.32
7552 8954 4.821805 TCTAGCATTTTTACAGCATAGGCC 59.178 41.667 0.00 0.00 42.56 5.19
7555 8957 3.299503 CATTTTTACAGCATAGGCCCCT 58.700 45.455 0.00 0.00 42.56 4.79
7557 8959 1.295020 TTTACAGCATAGGCCCCTGT 58.705 50.000 16.84 16.84 42.56 4.00
7561 8963 0.257039 CAGCATAGGCCCCTGTTCTT 59.743 55.000 0.00 0.00 42.56 2.52
7562 8964 1.490490 CAGCATAGGCCCCTGTTCTTA 59.510 52.381 0.00 0.00 42.56 2.10
7563 8965 1.771255 AGCATAGGCCCCTGTTCTTAG 59.229 52.381 0.00 0.00 42.56 2.18
7564 8966 1.768870 GCATAGGCCCCTGTTCTTAGA 59.231 52.381 0.00 0.00 0.00 2.10
7565 8967 2.485657 GCATAGGCCCCTGTTCTTAGAC 60.486 54.545 0.00 0.00 0.00 2.59
7566 8968 2.942604 TAGGCCCCTGTTCTTAGACT 57.057 50.000 0.00 0.00 0.00 3.24
7567 8969 1.280457 AGGCCCCTGTTCTTAGACTG 58.720 55.000 0.00 0.00 0.00 3.51
7568 8970 0.393132 GGCCCCTGTTCTTAGACTGC 60.393 60.000 0.00 0.00 0.00 4.40
7571 8973 0.895530 CCCTGTTCTTAGACTGCGGA 59.104 55.000 0.00 0.00 0.00 5.54
7577 8979 3.190874 GTTCTTAGACTGCGGAATCAGG 58.809 50.000 0.00 0.00 38.36 3.86
7578 8980 1.757118 TCTTAGACTGCGGAATCAGGG 59.243 52.381 0.00 0.00 38.36 4.45
7598 9000 2.484062 CGGCTTGGTGGGATGATGC 61.484 63.158 0.00 0.00 0.00 3.91
7603 9005 3.576356 GGTGGGATGATGCACGCG 61.576 66.667 3.53 3.53 0.00 6.01
7612 9014 0.878086 TGATGCACGCGTTGACTTCA 60.878 50.000 10.22 13.14 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.777832 AGTGAGAGCCATTGACTTCC 57.222 50.000 0.00 0.00 0.00 3.46
21 22 4.083057 GGAAAAGTGAGAGCCATTGACTTC 60.083 45.833 0.00 0.00 0.00 3.01
116 122 6.071391 AGTGACATTCCACTTTTGTTTCTTGT 60.071 34.615 0.00 0.00 44.32 3.16
120 126 5.650543 ACAGTGACATTCCACTTTTGTTTC 58.349 37.500 0.00 0.00 44.32 2.78
907 959 0.457337 ACGACGCGGTTAGACAATCC 60.457 55.000 12.47 0.00 0.00 3.01
965 1021 0.806241 GGCGCCGGAATAAACTTCAA 59.194 50.000 12.58 0.00 0.00 2.69
1284 1340 5.407407 TCTGAAGTAGGCCTACAAGAAAG 57.593 43.478 37.94 26.77 38.48 2.62
1292 1348 3.786553 TCCTTGTTCTGAAGTAGGCCTA 58.213 45.455 8.91 8.91 0.00 3.93
1294 1350 3.008049 TCTTCCTTGTTCTGAAGTAGGCC 59.992 47.826 11.17 0.00 39.19 5.19
1302 1367 5.551305 TTCTGTCATCTTCCTTGTTCTGA 57.449 39.130 0.00 0.00 0.00 3.27
1374 1439 8.635765 AGGATGATTTTACTCTTAAAAGTGCA 57.364 30.769 0.00 0.00 39.89 4.57
1456 1537 7.455953 TGGAAGTGGCAGAATACATATCTCTAT 59.544 37.037 0.00 0.00 0.00 1.98
1500 1581 6.530120 ACATACACCTCAACATTACTCACAA 58.470 36.000 0.00 0.00 0.00 3.33
1512 1593 8.471609 TCGAAACATTATCTACATACACCTCAA 58.528 33.333 0.00 0.00 0.00 3.02
1559 1640 8.141909 TCCAAATATCTAACCTGATAACTGACG 58.858 37.037 0.00 0.00 33.31 4.35
1607 1688 3.437049 GCAACCTGCTAAGAAACCTACAG 59.563 47.826 0.00 0.00 40.96 2.74
1678 1761 3.743396 CCTCAACTGTTCAGTGCTTCTAC 59.257 47.826 6.22 0.00 0.00 2.59
1688 1771 1.228245 GGCAGGCCTCAACTGTTCA 60.228 57.895 0.00 0.00 38.22 3.18
1706 1789 4.902443 TCTTCCAGCTGAATACGTCTAG 57.098 45.455 17.39 0.00 31.06 2.43
1731 1815 9.643693 CATTAGCATTACTCAAACTGGAAAAAT 57.356 29.630 0.00 0.00 0.00 1.82
1838 1922 1.635487 TGGTAGAAGCCTGCAATCCTT 59.365 47.619 0.00 0.00 0.00 3.36
1839 1923 1.211457 CTGGTAGAAGCCTGCAATCCT 59.789 52.381 0.00 0.00 0.00 3.24
1846 1930 2.191128 AGCAAACTGGTAGAAGCCTG 57.809 50.000 0.00 0.00 0.00 4.85
1944 2028 4.044065 AGGTGGAAATGGACAAACCTATCA 59.956 41.667 0.00 0.00 36.28 2.15
1978 2062 4.139786 AGAACAGCATCACAACTGAATGT 58.860 39.130 0.00 0.00 37.35 2.71
1979 2063 4.761235 AGAACAGCATCACAACTGAATG 57.239 40.909 0.00 0.00 37.35 2.67
1980 2064 5.555017 ACTAGAACAGCATCACAACTGAAT 58.445 37.500 0.00 0.00 37.35 2.57
2005 2089 5.562696 GCACATAAATCATAATCCCGTGTGG 60.563 44.000 0.00 0.00 36.03 4.17
2009 2093 4.216257 GCAGCACATAAATCATAATCCCGT 59.784 41.667 0.00 0.00 0.00 5.28
2198 2282 8.472683 TTTTTCTCCAAACATTGTAAACACAG 57.527 30.769 0.00 0.00 0.00 3.66
2298 2386 3.511146 TGAACAGGCCAGATGGAATTTTC 59.489 43.478 5.01 0.00 37.39 2.29
2522 2610 7.171653 TCAATGAGTACATGATTTTGGGTACA 58.828 34.615 0.00 0.00 38.78 2.90
2523 2611 7.624360 TCAATGAGTACATGATTTTGGGTAC 57.376 36.000 0.00 0.00 36.79 3.34
2582 2670 5.047731 TGCTATCATCCTATCAAGACTTCGG 60.048 44.000 0.00 0.00 0.00 4.30
2583 2671 6.018589 TGCTATCATCCTATCAAGACTTCG 57.981 41.667 0.00 0.00 0.00 3.79
2675 2763 1.476891 GGAGTCGGTGCTCAGACAATA 59.523 52.381 18.83 0.00 40.31 1.90
2849 2938 1.243342 TGGGCAGAACAATTGGCTCG 61.243 55.000 10.83 4.34 40.61 5.03
2872 2962 8.717821 CAATTAAGGTCGAAGTTCAGATTTACA 58.282 33.333 3.32 0.00 0.00 2.41
2888 2978 5.385509 TGCAAGGTTAAGCAATTAAGGTC 57.614 39.130 7.52 0.00 37.90 3.85
3053 3143 3.042871 TGCCCATTTGCATCAAGAAAC 57.957 42.857 0.00 0.00 36.04 2.78
3101 3191 4.222366 GGTAATACCTTATCCTCCTTCCCG 59.778 50.000 1.41 0.00 34.73 5.14
3150 3242 2.348411 AATATGCAAGGGGAAGTCGG 57.652 50.000 0.00 0.00 0.00 4.79
3473 3575 5.026462 GCATGATGTTCGAATTCAAGTGAG 58.974 41.667 15.09 6.96 0.00 3.51
3579 3682 1.973515 TCTTCTGTCACTCTGCATGGT 59.026 47.619 0.00 0.00 0.00 3.55
3626 3729 7.778083 TCGAAGCATAAGAATTTAGTGGACTA 58.222 34.615 0.00 0.00 0.00 2.59
3632 3735 6.763610 CCTCCTTCGAAGCATAAGAATTTAGT 59.236 38.462 19.99 0.00 0.00 2.24
3682 3785 7.726033 ACACTTCTCCTATGAACAGTCTTAT 57.274 36.000 0.00 0.00 0.00 1.73
3685 3788 7.726033 ATAACACTTCTCCTATGAACAGTCT 57.274 36.000 0.00 0.00 0.00 3.24
3819 3922 5.360999 ACATCGAGATAACATCAGGTTCTGA 59.639 40.000 0.00 0.00 44.99 3.27
3937 4040 2.163815 CAGCAAGCTTGAAAGGATCAGG 59.836 50.000 30.39 0.00 39.77 3.86
3942 4045 4.655963 ACTATTCAGCAAGCTTGAAAGGA 58.344 39.130 30.39 16.56 0.00 3.36
3972 4075 8.776061 ATCTTTATAGGTTAAGAGCTGAGAGT 57.224 34.615 0.00 0.00 34.17 3.24
3995 4098 6.074142 GCAGTTCCAACTTTCAACATTTGATC 60.074 38.462 0.00 0.00 36.97 2.92
3998 4101 4.869297 TGCAGTTCCAACTTTCAACATTTG 59.131 37.500 0.00 0.00 37.08 2.32
4059 4162 1.755380 ACGCAGCTAAAGTACTAGGGG 59.245 52.381 0.00 0.00 0.00 4.79
4074 4177 7.565450 TGAAATGATCAAAATTAACACGCAG 57.435 32.000 0.00 0.00 34.30 5.18
4133 4237 1.354031 TGCCAAGGAAGCTGTATGGAA 59.646 47.619 11.16 0.00 32.82 3.53
4134 4238 0.991146 TGCCAAGGAAGCTGTATGGA 59.009 50.000 11.16 0.00 32.82 3.41
4137 4241 3.370840 TCAATGCCAAGGAAGCTGTAT 57.629 42.857 0.00 0.00 0.00 2.29
4151 4255 8.765219 ACACTATCACGAACTATAAATCAATGC 58.235 33.333 0.00 0.00 0.00 3.56
4168 4432 8.685838 AGAATCCTAACTCTAGACACTATCAC 57.314 38.462 0.00 0.00 0.00 3.06
4192 4456 6.199393 CGAAAAACACAAGTTCTTTCCCTAG 58.801 40.000 0.00 0.00 36.84 3.02
4317 4593 6.264518 ACAATAGGTACTTGTTTTGTGGAAGG 59.735 38.462 0.00 0.00 41.75 3.46
4594 5901 1.486726 GGAAGGGTCTGACCACTATGG 59.513 57.143 26.94 0.00 41.02 2.74
4597 5904 0.790993 AGGGAAGGGTCTGACCACTA 59.209 55.000 26.94 0.00 41.02 2.74
4604 5911 0.842467 AGGGTTCAGGGAAGGGTCTG 60.842 60.000 0.00 0.00 0.00 3.51
4605 5912 0.842467 CAGGGTTCAGGGAAGGGTCT 60.842 60.000 0.00 0.00 0.00 3.85
4612 5919 3.551496 CTTGCGCAGGGTTCAGGGA 62.551 63.158 12.39 0.00 0.00 4.20
4648 5955 0.538287 GACTCCATATTGGGCAGCCC 60.538 60.000 25.54 25.54 45.71 5.19
4649 5956 0.538287 GGACTCCATATTGGGCAGCC 60.538 60.000 1.26 1.26 38.32 4.85
5235 6565 9.774742 GTAGAATAAGAATTTGAATGGTCACAC 57.225 33.333 0.00 0.00 31.90 3.82
5320 6650 3.694072 TGTGAGTTGCAACATATAAGGGC 59.306 43.478 30.11 10.44 0.00 5.19
5321 6651 5.415701 AGTTGTGAGTTGCAACATATAAGGG 59.584 40.000 30.11 0.00 46.09 3.95
5322 6652 6.149308 TCAGTTGTGAGTTGCAACATATAAGG 59.851 38.462 30.11 16.15 46.09 2.69
5376 6733 4.433615 TCGCTCTTGAGTGATAATTGGTC 58.566 43.478 9.52 0.00 0.00 4.02
5422 6779 4.305989 TGTTTTCACTGAGGAAATGCAC 57.694 40.909 0.00 0.00 36.71 4.57
5433 6790 5.105917 ACCCTTTGTACTGTTGTTTTCACTG 60.106 40.000 0.00 0.00 0.00 3.66
5532 6893 8.729805 ATATTTTTCAGTTTCAGGTTTTTGCA 57.270 26.923 0.00 0.00 0.00 4.08
5563 6928 4.694339 GATTGGATCCAAAGCGTACTAGT 58.306 43.478 30.28 10.38 39.55 2.57
5599 6964 2.159338 AGTAGCAGCGCATCCAATTTTG 60.159 45.455 11.47 0.00 0.00 2.44
5604 6969 1.111277 TAGAGTAGCAGCGCATCCAA 58.889 50.000 11.47 0.00 0.00 3.53
5616 6981 9.276590 TGATTGATGTAATGCCAAATAGAGTAG 57.723 33.333 0.00 0.00 0.00 2.57
5803 7172 7.657354 TCTGTATATAGTGTGCAATGTTGATCC 59.343 37.037 0.00 0.00 0.00 3.36
5860 7229 0.954452 CAAACCCAGAACTGAGTGGC 59.046 55.000 3.19 0.00 31.85 5.01
5889 7258 8.090214 TGCTCAAAAAGGGAAGAAAATTGATAG 58.910 33.333 0.00 0.00 0.00 2.08
5905 7276 7.653311 ACCAAAGTTATAAAGCTGCTCAAAAAG 59.347 33.333 1.00 0.00 0.00 2.27
5944 7316 2.167662 CCCGTAATTGGTCTTTTGCCT 58.832 47.619 0.00 0.00 0.00 4.75
6066 7438 2.557317 GTTCTGGAGTTCGGTTGTTGA 58.443 47.619 0.00 0.00 0.00 3.18
6239 7611 0.468226 ACGACCTTGGAGAAGTGCAA 59.532 50.000 0.00 0.00 32.33 4.08
6304 7676 1.330655 GGCCCGACTTCTGGATCAGA 61.331 60.000 0.00 0.00 38.87 3.27
6391 7781 0.948623 CCGCCGAGTTGATGTTCACA 60.949 55.000 0.00 0.00 0.00 3.58
6601 7991 5.066634 GTCATCAAGAGAGTAATCCTCGTCA 59.933 44.000 0.00 0.00 45.44 4.35
6614 8004 4.844884 TCCTAGAACTCGTCATCAAGAGA 58.155 43.478 0.00 0.00 37.87 3.10
6616 8006 5.531659 GGTATCCTAGAACTCGTCATCAAGA 59.468 44.000 0.00 0.00 0.00 3.02
6638 8028 7.308589 CGTTTCATTCTGATTGTTTTCTAGGGT 60.309 37.037 0.00 0.00 0.00 4.34
6807 8198 1.081892 CTCCATTTCAGGACACAGCG 58.918 55.000 0.00 0.00 33.19 5.18
6948 8343 6.015940 ACAATTTCCTTGAACACCTGAATCTC 60.016 38.462 0.00 0.00 38.29 2.75
6962 8357 4.329528 CACACCACAACAACAATTTCCTTG 59.670 41.667 0.00 0.00 40.90 3.61
7084 8483 9.607988 AACACCAGACATATCGATTTATTAACA 57.392 29.630 1.71 0.00 0.00 2.41
7092 8491 6.092670 CACAAGAAACACCAGACATATCGATT 59.907 38.462 1.71 0.00 0.00 3.34
7095 8494 4.929211 TCACAAGAAACACCAGACATATCG 59.071 41.667 0.00 0.00 0.00 2.92
7109 8508 5.833406 TTGAAAGAGCACATCACAAGAAA 57.167 34.783 0.00 0.00 0.00 2.52
7111 8510 5.833406 TTTTGAAAGAGCACATCACAAGA 57.167 34.783 0.00 0.00 0.00 3.02
7123 8522 8.633408 CAGCACGATAAAGAAATTTTGAAAGAG 58.367 33.333 0.00 0.00 0.00 2.85
7150 8549 5.106673 GCGCTCTGTTTTTCCTTATGTACTT 60.107 40.000 0.00 0.00 0.00 2.24
7155 8554 2.487762 TGGCGCTCTGTTTTTCCTTATG 59.512 45.455 7.64 0.00 0.00 1.90
7157 8556 2.264005 TGGCGCTCTGTTTTTCCTTA 57.736 45.000 7.64 0.00 0.00 2.69
7166 8565 1.376543 CATCTCATTTGGCGCTCTGT 58.623 50.000 7.64 0.00 0.00 3.41
7172 8571 1.089112 TGTCTGCATCTCATTTGGCG 58.911 50.000 0.00 0.00 0.00 5.69
7173 8572 3.795623 AATGTCTGCATCTCATTTGGC 57.204 42.857 0.00 0.00 33.50 4.52
7174 8573 5.735354 GCCTAAATGTCTGCATCTCATTTGG 60.735 44.000 22.40 20.36 40.45 3.28
7175 8574 5.279384 GCCTAAATGTCTGCATCTCATTTG 58.721 41.667 22.40 15.86 40.45 2.32
7176 8575 4.340381 GGCCTAAATGTCTGCATCTCATTT 59.660 41.667 19.75 19.75 42.11 2.32
7177 8576 3.887716 GGCCTAAATGTCTGCATCTCATT 59.112 43.478 0.00 0.00 33.50 2.57
7178 8577 3.484407 GGCCTAAATGTCTGCATCTCAT 58.516 45.455 0.00 0.00 33.50 2.90
7179 8578 2.421952 GGGCCTAAATGTCTGCATCTCA 60.422 50.000 0.84 0.00 33.50 3.27
7180 8579 2.225467 GGGCCTAAATGTCTGCATCTC 58.775 52.381 0.84 0.00 33.50 2.75
7181 8580 1.475751 CGGGCCTAAATGTCTGCATCT 60.476 52.381 0.84 0.00 33.50 2.90
7182 8581 0.947244 CGGGCCTAAATGTCTGCATC 59.053 55.000 0.84 0.00 33.50 3.91
7183 8582 0.255890 ACGGGCCTAAATGTCTGCAT 59.744 50.000 0.84 0.00 36.80 3.96
7184 8583 0.392461 GACGGGCCTAAATGTCTGCA 60.392 55.000 0.84 0.00 0.00 4.41
7185 8584 1.095807 GGACGGGCCTAAATGTCTGC 61.096 60.000 0.84 0.00 0.00 4.26
7186 8585 3.080647 GGACGGGCCTAAATGTCTG 57.919 57.895 0.84 0.00 0.00 3.51
7201 8600 0.880718 GGAATCATCGGCGGAAGGAC 60.881 60.000 7.21 0.00 0.00 3.85
7202 8601 1.445942 GGAATCATCGGCGGAAGGA 59.554 57.895 7.21 0.00 0.00 3.36
7203 8602 1.956170 CGGAATCATCGGCGGAAGG 60.956 63.158 7.21 0.00 0.00 3.46
7204 8603 1.956170 CCGGAATCATCGGCGGAAG 60.956 63.158 7.21 0.00 41.07 3.46
7205 8604 2.108157 CCGGAATCATCGGCGGAA 59.892 61.111 7.21 0.00 41.07 4.30
7206 8605 2.835895 TCCGGAATCATCGGCGGA 60.836 61.111 0.00 0.00 46.43 5.54
7207 8606 1.802337 TACTCCGGAATCATCGGCGG 61.802 60.000 5.23 0.00 46.43 6.13
7208 8607 0.243907 ATACTCCGGAATCATCGGCG 59.756 55.000 5.23 0.00 46.43 6.46
7209 8608 1.546476 AGATACTCCGGAATCATCGGC 59.454 52.381 16.62 0.00 46.43 5.54
7211 8610 2.820197 TCCAGATACTCCGGAATCATCG 59.180 50.000 16.62 1.93 0.00 3.84
7212 8611 4.753233 CATCCAGATACTCCGGAATCATC 58.247 47.826 16.62 13.33 31.18 2.92
7213 8612 3.055530 GCATCCAGATACTCCGGAATCAT 60.056 47.826 16.62 5.49 31.18 2.45
7214 8613 2.300152 GCATCCAGATACTCCGGAATCA 59.700 50.000 16.62 0.65 31.18 2.57
7215 8614 2.354203 GGCATCCAGATACTCCGGAATC 60.354 54.545 5.23 6.84 31.18 2.52
7216 8615 1.625818 GGCATCCAGATACTCCGGAAT 59.374 52.381 5.23 0.00 31.18 3.01
7217 8616 1.048601 GGCATCCAGATACTCCGGAA 58.951 55.000 5.23 0.00 31.18 4.30
7218 8617 0.105709 TGGCATCCAGATACTCCGGA 60.106 55.000 2.93 2.93 0.00 5.14
7219 8618 0.979665 ATGGCATCCAGATACTCCGG 59.020 55.000 0.00 0.00 36.75 5.14
7220 8619 3.703556 AGATATGGCATCCAGATACTCCG 59.296 47.826 1.65 0.00 35.41 4.63
7221 8620 5.426504 CAAGATATGGCATCCAGATACTCC 58.573 45.833 1.65 0.00 35.41 3.85
7222 8621 5.426504 CCAAGATATGGCATCCAGATACTC 58.573 45.833 1.65 0.00 43.80 2.59
7223 8622 5.432680 CCAAGATATGGCATCCAGATACT 57.567 43.478 1.65 0.00 43.80 2.12
7259 8658 0.958822 CCAACAGAAAAGAACCCCCG 59.041 55.000 0.00 0.00 0.00 5.73
7264 8663 8.318167 CGATAAACAAAACCAACAGAAAAGAAC 58.682 33.333 0.00 0.00 0.00 3.01
7268 8667 5.230306 CGCGATAAACAAAACCAACAGAAAA 59.770 36.000 0.00 0.00 0.00 2.29
7281 8680 0.436913 CACAGACGCGCGATAAACAA 59.563 50.000 39.36 0.00 0.00 2.83
7282 8681 0.387494 TCACAGACGCGCGATAAACA 60.387 50.000 39.36 13.10 0.00 2.83
7331 8730 1.211969 GCAGCAGCCATCACACAAG 59.788 57.895 0.00 0.00 33.58 3.16
7352 8751 0.813210 GGCGAAGAGAGGCAATCCTG 60.813 60.000 0.00 0.00 44.46 3.86
7353 8752 2.792952 TTGGCGAAGAGAGGCAATCCT 61.793 52.381 1.05 0.00 46.81 3.24
7361 8760 1.664659 CATTCAGCTTGGCGAAGAGAG 59.335 52.381 13.20 1.01 0.00 3.20
7382 8781 2.443632 TGACATAACCCACCACCAAGAA 59.556 45.455 0.00 0.00 0.00 2.52
7388 8787 4.776349 TCATATGTGACATAACCCACCAC 58.224 43.478 9.61 0.00 32.61 4.16
7389 8788 4.141505 CCTCATATGTGACATAACCCACCA 60.142 45.833 9.61 0.00 32.61 4.17
7391 8790 5.070446 TCTCCTCATATGTGACATAACCCAC 59.930 44.000 9.61 0.00 0.00 4.61
7421 8823 8.162880 GTCATTGTCGTGAACACTAATTAGAAG 58.837 37.037 19.38 12.70 37.70 2.85
7426 8828 6.293407 CCAAGTCATTGTCGTGAACACTAATT 60.293 38.462 3.51 0.00 37.70 1.40
7454 8856 4.505808 TCTTGTTACACGTTGTCCAAAGA 58.494 39.130 0.00 0.00 0.00 2.52
7455 8857 4.868450 TCTTGTTACACGTTGTCCAAAG 57.132 40.909 0.00 0.00 0.00 2.77
7466 8868 6.312399 TGTTTGATCACCATCTTGTTACAC 57.688 37.500 0.00 0.00 0.00 2.90
7487 8889 1.354705 GCCCCTCCTAAAAAGACCTGT 59.645 52.381 0.00 0.00 0.00 4.00
7500 8902 0.919710 ATGAAACTAGTGGCCCCTCC 59.080 55.000 0.00 0.00 0.00 4.30
7547 8949 2.467880 CAGTCTAAGAACAGGGGCCTA 58.532 52.381 0.84 0.00 0.00 3.93
7548 8950 1.280457 CAGTCTAAGAACAGGGGCCT 58.720 55.000 0.84 0.00 0.00 5.19
7550 8952 0.741221 CGCAGTCTAAGAACAGGGGC 60.741 60.000 0.00 0.00 0.00 5.80
7552 8954 0.895530 TCCGCAGTCTAAGAACAGGG 59.104 55.000 0.00 0.00 0.00 4.45
7555 8957 3.368427 CCTGATTCCGCAGTCTAAGAACA 60.368 47.826 0.00 0.00 34.06 3.18
7557 8959 2.168521 CCCTGATTCCGCAGTCTAAGAA 59.831 50.000 0.00 0.00 34.06 2.52
7561 8963 1.686325 GGCCCTGATTCCGCAGTCTA 61.686 60.000 0.00 0.00 34.06 2.59
7562 8964 2.586792 GCCCTGATTCCGCAGTCT 59.413 61.111 0.00 0.00 34.06 3.24
7563 8965 2.514824 GGCCCTGATTCCGCAGTC 60.515 66.667 0.00 0.00 34.06 3.51
7564 8966 4.473520 CGGCCCTGATTCCGCAGT 62.474 66.667 0.00 0.00 39.14 4.40
7568 8970 4.489771 AAGCCGGCCCTGATTCCG 62.490 66.667 26.15 0.00 44.89 4.30
7571 8973 3.661648 ACCAAGCCGGCCCTGATT 61.662 61.111 26.15 7.59 39.03 2.57
7578 8980 3.721370 ATCATCCCACCAAGCCGGC 62.721 63.158 21.89 21.89 39.03 6.13
7592 8994 0.443869 GAAGTCAACGCGTGCATCAT 59.556 50.000 14.98 0.00 0.00 2.45
7598 9000 0.383491 CTTGCTGAAGTCAACGCGTG 60.383 55.000 14.98 7.52 0.00 5.34
7603 9005 2.032178 GTGGTGTCTTGCTGAAGTCAAC 59.968 50.000 0.00 0.00 36.00 3.18


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

AutoCloner maintained by Alex Coulton.