Multiple sequence alignment - TraesCS1D01G270000

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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 TraesCS1D01G270000 chr1D 100.000 3587 0 0 1 3587 365198810 365195224 0.000000e+00 6625.0
1 TraesCS1D01G270000 chr1D 100.000 216 0 0 3878 4093 365194933 365194718 2.290000e-107 399.0
2 TraesCS1D01G270000 chr1B 92.932 2943 160 27 572 3492 488645351 488642435 0.000000e+00 4239.0
3 TraesCS1D01G270000 chr1B 88.406 483 35 7 89 554 488645920 488645442 2.760000e-156 562.0
4 TraesCS1D01G270000 chr1A 94.577 1254 54 5 2103 3348 464088494 464087247 0.000000e+00 1927.0
5 TraesCS1D01G270000 chr1A 94.912 963 42 4 650 1609 464089490 464088532 0.000000e+00 1500.0
6 TraesCS1D01G270000 chr1A 93.075 491 26 6 92 577 464091394 464090907 0.000000e+00 712.0
7 TraesCS1D01G270000 chr1A 92.308 208 16 0 3886 4093 464081545 464081338 3.090000e-76 296.0
8 TraesCS1D01G270000 chr1A 84.615 208 13 10 3886 4093 464081019 464080831 5.400000e-44 189.0
9 TraesCS1D01G270000 chr6B 84.722 288 41 3 1610 1896 699541782 699541497 6.700000e-73 285.0
10 TraesCS1D01G270000 chr5B 84.536 291 42 3 1610 1899 684749894 684749606 6.700000e-73 285.0
11 TraesCS1D01G270000 chr5B 76.151 478 94 17 1077 1540 496828212 496828683 2.460000e-57 233.0
12 TraesCS1D01G270000 chr3D 83.681 288 44 3 1610 1896 55347854 55347569 6.740000e-68 268.0
13 TraesCS1D01G270000 chr3D 89.024 82 9 0 3 84 51477197 51477278 7.240000e-18 102.0
14 TraesCS1D01G270000 chr3D 87.805 82 10 0 3 84 47605166 47605085 3.370000e-16 97.1
15 TraesCS1D01G270000 chr5D 76.360 478 93 16 1077 1540 412464889 412465360 5.290000e-59 239.0
16 TraesCS1D01G270000 chr4A 77.817 284 45 8 1615 1896 648590804 648590537 4.230000e-35 159.0
17 TraesCS1D01G270000 chr7D 81.081 185 22 8 1614 1798 106982554 106982383 7.140000e-28 135.0
18 TraesCS1D01G270000 chr3B 78.226 248 29 14 1609 1853 45518620 45518845 7.140000e-28 135.0
19 TraesCS1D01G270000 chr4B 89.011 91 10 0 3 93 50464401 50464311 3.340000e-21 113.0
20 TraesCS1D01G270000 chr6D 87.234 94 12 0 3 96 264668137 264668044 1.560000e-19 108.0
21 TraesCS1D01G270000 chr2D 87.097 93 11 1 5 96 573916635 573916727 2.010000e-18 104.0
22 TraesCS1D01G270000 chr2D 85.714 91 13 0 3 93 125684125 125684035 3.370000e-16 97.1
23 TraesCS1D01G270000 chr2D 86.747 83 11 0 1611 1693 23336105 23336187 4.360000e-15 93.5
24 TraesCS1D01G270000 chr2D 88.333 60 7 0 1615 1674 558200319 558200260 5.680000e-09 73.1
25 TraesCS1D01G270000 chr7B 88.889 81 9 0 4 84 413102520 413102440 2.600000e-17 100.0
26 TraesCS1D01G270000 chr7B 94.444 36 2 0 3888 3923 715578623 715578588 5.720000e-04 56.5
27 TraesCS1D01G270000 chr4D 88.095 84 9 1 1 84 201904806 201904888 9.360000e-17 99.0
28 TraesCS1D01G270000 chr4D 87.500 72 9 0 3 74 82457555 82457484 2.620000e-12 84.2
29 TraesCS1D01G270000 chr3A 93.023 43 2 1 3881 3923 729473987 729473946 1.230000e-05 62.1


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 TraesCS1D01G270000 chr1D 365194718 365198810 4092 True 3512.000000 6625 100.0000 1 4093 2 chr1D.!!$R1 4092
1 TraesCS1D01G270000 chr1B 488642435 488645920 3485 True 2400.500000 4239 90.6690 89 3492 2 chr1B.!!$R1 3403
2 TraesCS1D01G270000 chr1A 464087247 464091394 4147 True 1379.666667 1927 94.1880 92 3348 3 chr1A.!!$R2 3256
3 TraesCS1D01G270000 chr1A 464080831 464081545 714 True 242.500000 296 88.4615 3886 4093 2 chr1A.!!$R1 207

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
801 2217 0.458716 TTCAATGTGCCATGCATGCG 60.459 50.0 21.69 15.04 41.91 4.73 F
2316 3737 0.104304 ACGCGGCTTATTACCTCCAG 59.896 55.0 12.47 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2400 3824 0.175760 TACTTGGCGACCATGCTCTC 59.824 55.0 10.32 0.0 32.73 3.20 R
3418 4850 0.481128 GGAGGGTGAAGGGTTGGAAA 59.519 55.0 0.00 0.0 0.00 3.13 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
26 27 9.436957 TTTCTCTCCTCATTAATTACTTGACAC 57.563 33.333 0.00 0.00 0.00 3.67
27 28 8.134202 TCTCTCCTCATTAATTACTTGACACA 57.866 34.615 0.00 0.00 0.00 3.72
28 29 8.762645 TCTCTCCTCATTAATTACTTGACACAT 58.237 33.333 0.00 0.00 0.00 3.21
29 30 8.948631 TCTCCTCATTAATTACTTGACACATC 57.051 34.615 0.00 0.00 0.00 3.06
30 31 8.539544 TCTCCTCATTAATTACTTGACACATCA 58.460 33.333 0.00 0.00 0.00 3.07
31 32 9.334947 CTCCTCATTAATTACTTGACACATCAT 57.665 33.333 0.00 0.00 33.85 2.45
77 78 9.478238 TGTATGTTACTAACTATGTTACTCCCA 57.522 33.333 0.71 0.00 0.00 4.37
88 89 8.497910 ACTATGTTACTCCCAATATGATGAGT 57.502 34.615 0.00 0.00 40.87 3.41
89 90 8.589338 ACTATGTTACTCCCAATATGATGAGTC 58.411 37.037 4.96 0.00 38.85 3.36
90 91 7.623999 ATGTTACTCCCAATATGATGAGTCT 57.376 36.000 4.96 0.00 38.85 3.24
91 92 8.727100 ATGTTACTCCCAATATGATGAGTCTA 57.273 34.615 4.96 0.00 38.85 2.59
92 93 8.547481 TGTTACTCCCAATATGATGAGTCTAA 57.453 34.615 4.96 0.00 38.85 2.10
93 94 8.421784 TGTTACTCCCAATATGATGAGTCTAAC 58.578 37.037 4.96 6.21 38.85 2.34
94 95 6.426646 ACTCCCAATATGATGAGTCTAACC 57.573 41.667 0.00 0.00 32.85 2.85
95 96 5.905331 ACTCCCAATATGATGAGTCTAACCA 59.095 40.000 0.00 0.00 32.85 3.67
96 97 6.560304 ACTCCCAATATGATGAGTCTAACCAT 59.440 38.462 0.00 0.00 32.85 3.55
97 98 6.772605 TCCCAATATGATGAGTCTAACCATG 58.227 40.000 0.00 0.00 0.00 3.66
98 99 6.329986 TCCCAATATGATGAGTCTAACCATGT 59.670 38.462 0.00 0.00 0.00 3.21
99 100 7.000472 CCCAATATGATGAGTCTAACCATGTT 59.000 38.462 0.00 0.00 0.00 2.71
100 101 7.040892 CCCAATATGATGAGTCTAACCATGTTG 60.041 40.741 0.00 0.00 36.64 3.33
101 102 7.040892 CCAATATGATGAGTCTAACCATGTTGG 60.041 40.741 5.81 5.81 44.18 3.77
110 111 4.440145 CCATGTTGGTTGGGGGAG 57.560 61.111 0.00 0.00 31.35 4.30
115 116 4.224971 TTGGTTGGGGGAGGGGGA 62.225 66.667 0.00 0.00 0.00 4.81
124 125 3.338250 GGAGGGGGATGGTGTGCA 61.338 66.667 0.00 0.00 0.00 4.57
128 129 1.454479 GGGGGATGGTGTGCATCTG 60.454 63.158 0.00 0.00 0.00 2.90
147 148 3.909086 GAGCAGTGTGAGGTGGCCC 62.909 68.421 0.00 0.00 0.00 5.80
165 166 0.790207 CCGTTTCATCACTGTCACCG 59.210 55.000 0.00 0.00 0.00 4.94
171 172 0.807667 CATCACTGTCACCGCTAGGC 60.808 60.000 0.00 0.00 42.76 3.93
310 326 2.109126 GGGATGCAAGTGAGGCGTC 61.109 63.158 0.00 0.00 44.59 5.19
342 358 2.363683 GAACAGAGGAAGCCATCAAGG 58.636 52.381 0.00 0.00 41.84 3.61
427 443 4.608073 TCGCGTTGTACGTACCTTTATA 57.392 40.909 22.43 0.00 44.73 0.98
501 517 6.287525 CCATCCAGATCTAGGTTTTCTCTTC 58.712 44.000 0.00 0.00 0.00 2.87
515 531 1.474478 TCTCTTCGTTGCTGGCTAGAG 59.526 52.381 0.00 0.00 0.00 2.43
526 542 1.268352 CTGGCTAGAGAGGACATACGC 59.732 57.143 0.00 0.00 0.00 4.42
536 607 5.070446 AGAGAGGACATACGCATATCCAAAA 59.930 40.000 0.00 0.00 33.33 2.44
577 662 7.667575 TTAGGCAAAATATGAGAGTCTCTCT 57.332 36.000 26.46 16.11 43.73 3.10
590 675 2.171448 AGTCTCTCTCTCTCTCTCTGCC 59.829 54.545 0.00 0.00 0.00 4.85
591 676 2.171448 GTCTCTCTCTCTCTCTCTGCCT 59.829 54.545 0.00 0.00 0.00 4.75
592 677 3.388024 GTCTCTCTCTCTCTCTCTGCCTA 59.612 52.174 0.00 0.00 0.00 3.93
594 679 3.111484 TCTCTCTCTCTCTCTGCCTACA 58.889 50.000 0.00 0.00 0.00 2.74
597 682 2.687935 CTCTCTCTCTCTGCCTACAACC 59.312 54.545 0.00 0.00 0.00 3.77
598 683 2.310349 TCTCTCTCTCTGCCTACAACCT 59.690 50.000 0.00 0.00 0.00 3.50
599 684 3.523972 TCTCTCTCTCTGCCTACAACCTA 59.476 47.826 0.00 0.00 0.00 3.08
600 685 3.622630 TCTCTCTCTGCCTACAACCTAC 58.377 50.000 0.00 0.00 0.00 3.18
601 686 3.010250 TCTCTCTCTGCCTACAACCTACA 59.990 47.826 0.00 0.00 0.00 2.74
602 687 3.764434 CTCTCTCTGCCTACAACCTACAA 59.236 47.826 0.00 0.00 0.00 2.41
603 688 4.353777 TCTCTCTGCCTACAACCTACAAT 58.646 43.478 0.00 0.00 0.00 2.71
604 689 4.777896 TCTCTCTGCCTACAACCTACAATT 59.222 41.667 0.00 0.00 0.00 2.32
605 690 5.248477 TCTCTCTGCCTACAACCTACAATTT 59.752 40.000 0.00 0.00 0.00 1.82
606 691 6.439375 TCTCTCTGCCTACAACCTACAATTTA 59.561 38.462 0.00 0.00 0.00 1.40
607 692 6.403878 TCTCTGCCTACAACCTACAATTTAC 58.596 40.000 0.00 0.00 0.00 2.01
611 981 5.047164 TGCCTACAACCTACAATTTACTCGA 60.047 40.000 0.00 0.00 0.00 4.04
665 2080 1.065709 GGGCCATTTCCTACGTGAGAA 60.066 52.381 4.39 0.00 0.00 2.87
774 2190 5.684030 GCAATTCATCTCTCCATTGCCATTT 60.684 40.000 4.68 0.00 43.80 2.32
801 2217 0.458716 TTCAATGTGCCATGCATGCG 60.459 50.000 21.69 15.04 41.91 4.73
818 2234 1.489070 GCGTCTGAGCTAGCTGCATG 61.489 60.000 24.99 11.65 45.94 4.06
849 2265 5.117745 CGGATAAGCGAACATCAATGTAGAG 59.882 44.000 0.00 0.00 40.80 2.43
850 2266 6.216569 GGATAAGCGAACATCAATGTAGAGA 58.783 40.000 0.00 0.00 40.80 3.10
859 2275 9.249457 CGAACATCAATGTAGAGATAAAGCTTA 57.751 33.333 0.00 0.00 40.80 3.09
861 2277 9.890629 AACATCAATGTAGAGATAAAGCTTACA 57.109 29.630 0.00 0.00 40.80 2.41
911 2327 0.812811 ACTGCTGCGGCACTGATATG 60.813 55.000 18.37 7.69 44.28 1.78
1011 2429 2.094906 TGTGTCCTGCATGTACTACGTC 60.095 50.000 0.00 0.00 0.00 4.34
1042 2460 4.428209 CTCTCCCAAGTGCATATATAGCG 58.572 47.826 0.00 0.00 33.85 4.26
1051 2469 3.243877 GTGCATATATAGCGCATCCGAAG 59.756 47.826 11.47 0.00 41.87 3.79
1253 2671 2.317609 GCTTCTTCCGCAGCAACGA 61.318 57.895 0.00 0.00 35.95 3.85
1254 2672 1.493311 CTTCTTCCGCAGCAACGAC 59.507 57.895 0.00 0.00 34.06 4.34
1257 2675 2.357034 TTCCGCAGCAACGACCTC 60.357 61.111 0.00 0.00 34.06 3.85
1258 2676 4.717629 TCCGCAGCAACGACCTCG 62.718 66.667 0.00 0.00 46.33 4.63
1622 3040 6.093633 AGGAAAGGTACGCATAGTTTTCAATC 59.906 38.462 0.00 0.00 0.00 2.67
1631 3049 6.204688 ACGCATAGTTTTCAATCTCAGTTTCA 59.795 34.615 0.00 0.00 0.00 2.69
1658 3076 0.871722 TTCAGCACCAACCGAAATCG 59.128 50.000 0.00 0.00 39.44 3.34
1667 3085 3.063485 CCAACCGAAATCGCCAAAATTT 58.937 40.909 0.00 0.00 38.18 1.82
1679 3097 7.816945 ATCGCCAAAATTTAGTGAATTTCAG 57.183 32.000 6.12 2.95 44.98 3.02
1693 3111 7.936584 AGTGAATTTCAGTAATTTCGGTTTGA 58.063 30.769 4.90 0.00 36.59 2.69
1700 3118 6.375377 TCAGTAATTTCGGTTTGAATTTCGG 58.625 36.000 0.00 0.00 36.22 4.30
1786 3204 9.015367 TCAAAAGAATATTTGAATTCCCGTGTA 57.985 29.630 2.27 0.00 44.11 2.90
1885 3303 4.551702 TTCACCGGAATCTCATTGAAGA 57.448 40.909 9.46 0.00 0.00 2.87
1887 3305 4.445453 TCACCGGAATCTCATTGAAGATG 58.555 43.478 9.46 0.00 36.14 2.90
1932 3350 6.591750 TCTAAGTTGCTAGCTCTAGTTTGT 57.408 37.500 17.23 1.53 35.65 2.83
1946 3364 8.560374 AGCTCTAGTTTGTCTAAAAACAATGTC 58.440 33.333 2.97 0.00 41.56 3.06
1947 3365 8.342634 GCTCTAGTTTGTCTAAAAACAATGTCA 58.657 33.333 2.97 0.00 41.56 3.58
2024 3443 9.742144 CTAGGAGATCTAGCTATAGGTACAAAA 57.258 37.037 7.58 0.00 39.02 2.44
2064 3485 2.225491 GTGGCTCGTGAACAGCATTTTA 59.775 45.455 0.00 0.00 38.77 1.52
2080 3501 4.595116 CATTTTAATGCCTTCTCTGCTCG 58.405 43.478 0.00 0.00 0.00 5.03
2112 3533 5.428253 TCCATGTAGGCACTAATCTTGAAC 58.572 41.667 0.00 0.00 45.48 3.18
2117 3538 5.647658 TGTAGGCACTAATCTTGAACCATTG 59.352 40.000 0.00 0.00 45.48 2.82
2119 3540 5.079643 AGGCACTAATCTTGAACCATTGTT 58.920 37.500 0.00 0.00 36.02 2.83
2127 3548 3.890756 TCTTGAACCATTGTTGACATGCT 59.109 39.130 0.00 0.00 33.97 3.79
2128 3549 4.341806 TCTTGAACCATTGTTGACATGCTT 59.658 37.500 0.00 0.00 33.97 3.91
2129 3550 5.534278 TCTTGAACCATTGTTGACATGCTTA 59.466 36.000 0.00 0.00 33.97 3.09
2198 3619 2.493030 CATAACCTCGCCGACGGT 59.507 61.111 16.73 2.93 40.63 4.83
2301 3722 1.633171 GAGCTGCTAACATCACGCG 59.367 57.895 3.53 3.53 0.00 6.01
2312 3733 1.138266 ACATCACGCGGCTTATTACCT 59.862 47.619 12.47 0.00 0.00 3.08
2315 3736 0.179094 CACGCGGCTTATTACCTCCA 60.179 55.000 12.47 0.00 0.00 3.86
2316 3737 0.104304 ACGCGGCTTATTACCTCCAG 59.896 55.000 12.47 0.00 0.00 3.86
2317 3738 0.104304 CGCGGCTTATTACCTCCAGT 59.896 55.000 0.00 0.00 0.00 4.00
2320 3741 2.419574 GCGGCTTATTACCTCCAGTCAA 60.420 50.000 0.00 0.00 0.00 3.18
2335 3759 1.254954 GTCAACCGACTCTACCCAGT 58.745 55.000 0.00 0.00 39.22 4.00
2340 3764 1.215647 CGACTCTACCCAGTGCACC 59.784 63.158 14.63 0.00 0.00 5.01
2350 3774 1.453745 CAGTGCACCAACCACCAGT 60.454 57.895 14.63 0.00 33.75 4.00
2444 3868 1.993391 CTTCGGGCCAAGGGAGGTA 60.993 63.158 4.39 0.00 0.00 3.08
2671 4095 2.122813 CTCCCCCATAGCGGAGGT 60.123 66.667 0.00 0.00 41.79 3.85
2831 4255 4.202641 ACCATGGACAGGATATACGAGGTA 60.203 45.833 21.47 0.00 0.00 3.08
2900 4324 4.483243 CTGGCCGGCGGTGGTATT 62.483 66.667 28.82 0.00 0.00 1.89
3023 4447 1.366111 CGGCCATGGACAGGTTTACG 61.366 60.000 20.22 0.00 0.00 3.18
3127 4554 2.747446 CGGGGTATTGAAACTTCACCAG 59.253 50.000 0.00 0.00 36.83 4.00
3201 4628 2.030823 GTCCATGTCACACGCACATATG 59.969 50.000 0.00 0.00 32.48 1.78
3244 4676 9.432077 CATTAATTTAAAGTTTGGTTGTGCAAC 57.568 29.630 6.52 6.52 40.45 4.17
3310 4742 8.991243 CACATTTGGATCAATTCTTTGTATGT 57.009 30.769 0.00 0.00 34.32 2.29
3317 4749 7.448161 TGGATCAATTCTTTGTATGTGTGACTT 59.552 33.333 0.00 0.00 34.32 3.01
3410 4842 8.865590 AATTAAGTTTGCGAGTTTTTGTACAT 57.134 26.923 0.00 0.00 0.00 2.29
3411 4843 7.901874 TTAAGTTTGCGAGTTTTTGTACATC 57.098 32.000 0.00 0.00 0.00 3.06
3412 4844 4.855531 AGTTTGCGAGTTTTTGTACATCC 58.144 39.130 0.00 0.00 0.00 3.51
3413 4845 3.907894 TTGCGAGTTTTTGTACATCCC 57.092 42.857 0.00 0.00 0.00 3.85
3414 4846 3.134574 TGCGAGTTTTTGTACATCCCT 57.865 42.857 0.00 0.00 0.00 4.20
3415 4847 3.482436 TGCGAGTTTTTGTACATCCCTT 58.518 40.909 0.00 0.00 0.00 3.95
3416 4848 3.886505 TGCGAGTTTTTGTACATCCCTTT 59.113 39.130 0.00 0.00 0.00 3.11
3417 4849 4.226761 GCGAGTTTTTGTACATCCCTTTG 58.773 43.478 0.00 0.00 0.00 2.77
3418 4850 4.261447 GCGAGTTTTTGTACATCCCTTTGT 60.261 41.667 0.00 0.00 0.00 2.83
3419 4851 5.735070 GCGAGTTTTTGTACATCCCTTTGTT 60.735 40.000 0.00 0.00 0.00 2.83
3420 4852 6.270064 CGAGTTTTTGTACATCCCTTTGTTT 58.730 36.000 0.00 0.00 0.00 2.83
3421 4853 6.416750 CGAGTTTTTGTACATCCCTTTGTTTC 59.583 38.462 0.00 0.00 0.00 2.78
3422 4854 6.578944 AGTTTTTGTACATCCCTTTGTTTCC 58.421 36.000 0.00 0.00 0.00 3.13
3423 4855 6.155393 AGTTTTTGTACATCCCTTTGTTTCCA 59.845 34.615 0.00 0.00 0.00 3.53
3424 4856 6.546428 TTTTGTACATCCCTTTGTTTCCAA 57.454 33.333 0.00 0.00 0.00 3.53
3425 4857 5.523438 TTGTACATCCCTTTGTTTCCAAC 57.477 39.130 0.00 0.00 0.00 3.77
3426 4858 3.892588 TGTACATCCCTTTGTTTCCAACC 59.107 43.478 0.00 0.00 0.00 3.77
3427 4859 2.325484 ACATCCCTTTGTTTCCAACCC 58.675 47.619 0.00 0.00 0.00 4.11
3428 4860 2.090775 ACATCCCTTTGTTTCCAACCCT 60.091 45.455 0.00 0.00 0.00 4.34
3429 4861 2.858787 TCCCTTTGTTTCCAACCCTT 57.141 45.000 0.00 0.00 0.00 3.95
3430 4862 2.673258 TCCCTTTGTTTCCAACCCTTC 58.327 47.619 0.00 0.00 0.00 3.46
3431 4863 2.023888 TCCCTTTGTTTCCAACCCTTCA 60.024 45.455 0.00 0.00 0.00 3.02
3432 4864 2.102420 CCCTTTGTTTCCAACCCTTCAC 59.898 50.000 0.00 0.00 0.00 3.18
3433 4865 2.102420 CCTTTGTTTCCAACCCTTCACC 59.898 50.000 0.00 0.00 0.00 4.02
3434 4866 1.783071 TTGTTTCCAACCCTTCACCC 58.217 50.000 0.00 0.00 0.00 4.61
3435 4867 0.930726 TGTTTCCAACCCTTCACCCT 59.069 50.000 0.00 0.00 0.00 4.34
3436 4868 1.133606 TGTTTCCAACCCTTCACCCTC 60.134 52.381 0.00 0.00 0.00 4.30
3437 4869 0.481128 TTTCCAACCCTTCACCCTCC 59.519 55.000 0.00 0.00 0.00 4.30
3438 4870 0.699577 TTCCAACCCTTCACCCTCCA 60.700 55.000 0.00 0.00 0.00 3.86
3439 4871 1.074951 CCAACCCTTCACCCTCCAC 59.925 63.158 0.00 0.00 0.00 4.02
3440 4872 1.302511 CAACCCTTCACCCTCCACG 60.303 63.158 0.00 0.00 0.00 4.94
3441 4873 2.526046 AACCCTTCACCCTCCACGG 61.526 63.158 0.00 0.00 0.00 4.94
3442 4874 2.928396 CCCTTCACCCTCCACGGT 60.928 66.667 0.00 0.00 36.18 4.83
3457 4889 3.920144 CGGTGGTCGTCAGAGTATC 57.080 57.895 0.00 0.00 0.00 2.24
3470 4902 2.211353 GAGTATCTGTCACGGCCTTC 57.789 55.000 0.00 0.00 0.00 3.46
3471 4903 1.751924 GAGTATCTGTCACGGCCTTCT 59.248 52.381 0.00 0.00 0.00 2.85
3472 4904 2.950309 GAGTATCTGTCACGGCCTTCTA 59.050 50.000 0.00 0.00 0.00 2.10
3473 4905 3.567397 AGTATCTGTCACGGCCTTCTAT 58.433 45.455 0.00 0.00 0.00 1.98
3474 4906 2.898729 ATCTGTCACGGCCTTCTATG 57.101 50.000 0.00 0.00 0.00 2.23
3475 4907 1.557099 TCTGTCACGGCCTTCTATGT 58.443 50.000 0.00 0.00 0.00 2.29
3476 4908 1.204704 TCTGTCACGGCCTTCTATGTG 59.795 52.381 0.00 0.00 0.00 3.21
3477 4909 0.973632 TGTCACGGCCTTCTATGTGT 59.026 50.000 0.00 0.00 34.08 3.72
3478 4910 1.346395 TGTCACGGCCTTCTATGTGTT 59.654 47.619 0.00 0.00 34.08 3.32
3479 4911 1.732259 GTCACGGCCTTCTATGTGTTG 59.268 52.381 0.00 0.00 34.08 3.33
3480 4912 1.346395 TCACGGCCTTCTATGTGTTGT 59.654 47.619 0.00 0.00 34.08 3.32
3481 4913 2.151202 CACGGCCTTCTATGTGTTGTT 58.849 47.619 0.00 0.00 0.00 2.83
3482 4914 3.007074 TCACGGCCTTCTATGTGTTGTTA 59.993 43.478 0.00 0.00 34.08 2.41
3483 4915 3.370978 CACGGCCTTCTATGTGTTGTTAG 59.629 47.826 0.00 0.00 0.00 2.34
3484 4916 3.007614 ACGGCCTTCTATGTGTTGTTAGT 59.992 43.478 0.00 0.00 0.00 2.24
3485 4917 3.370978 CGGCCTTCTATGTGTTGTTAGTG 59.629 47.826 0.00 0.00 0.00 2.74
3486 4918 4.324267 GGCCTTCTATGTGTTGTTAGTGT 58.676 43.478 0.00 0.00 0.00 3.55
3487 4919 4.392138 GGCCTTCTATGTGTTGTTAGTGTC 59.608 45.833 0.00 0.00 0.00 3.67
3488 4920 5.238583 GCCTTCTATGTGTTGTTAGTGTCT 58.761 41.667 0.00 0.00 0.00 3.41
3489 4921 6.395629 GCCTTCTATGTGTTGTTAGTGTCTA 58.604 40.000 0.00 0.00 0.00 2.59
3490 4922 6.310711 GCCTTCTATGTGTTGTTAGTGTCTAC 59.689 42.308 0.00 0.00 0.00 2.59
3491 4923 7.603651 CCTTCTATGTGTTGTTAGTGTCTACT 58.396 38.462 0.00 0.00 40.99 2.57
3492 4924 8.088981 CCTTCTATGTGTTGTTAGTGTCTACTT 58.911 37.037 0.00 0.00 38.36 2.24
3493 4925 9.477484 CTTCTATGTGTTGTTAGTGTCTACTTT 57.523 33.333 0.00 0.00 38.36 2.66
3494 4926 9.826574 TTCTATGTGTTGTTAGTGTCTACTTTT 57.173 29.630 0.00 0.00 38.36 2.27
3495 4927 9.472361 TCTATGTGTTGTTAGTGTCTACTTTTC 57.528 33.333 0.00 0.00 38.36 2.29
3496 4928 9.256477 CTATGTGTTGTTAGTGTCTACTTTTCA 57.744 33.333 0.00 0.00 38.36 2.69
3497 4929 7.908827 TGTGTTGTTAGTGTCTACTTTTCAA 57.091 32.000 0.00 0.00 38.36 2.69
3498 4930 8.325421 TGTGTTGTTAGTGTCTACTTTTCAAA 57.675 30.769 0.00 0.00 38.36 2.69
3499 4931 8.447833 TGTGTTGTTAGTGTCTACTTTTCAAAG 58.552 33.333 0.00 0.00 41.73 2.77
3500 4932 8.662141 GTGTTGTTAGTGTCTACTTTTCAAAGA 58.338 33.333 6.29 0.00 39.31 2.52
3501 4933 9.391006 TGTTGTTAGTGTCTACTTTTCAAAGAT 57.609 29.630 6.29 0.00 39.31 2.40
3520 4952 8.853126 TCAAAGATTTCAATATAGATGCAAGGG 58.147 33.333 0.00 0.00 0.00 3.95
3521 4953 8.636213 CAAAGATTTCAATATAGATGCAAGGGT 58.364 33.333 0.00 0.00 0.00 4.34
3522 4954 8.773033 AAGATTTCAATATAGATGCAAGGGTT 57.227 30.769 0.00 0.00 0.00 4.11
3523 4955 8.174733 AGATTTCAATATAGATGCAAGGGTTG 57.825 34.615 0.00 0.00 0.00 3.77
3524 4956 7.781693 AGATTTCAATATAGATGCAAGGGTTGT 59.218 33.333 0.00 0.00 0.00 3.32
3525 4957 7.716799 TTTCAATATAGATGCAAGGGTTGTT 57.283 32.000 0.00 0.00 0.00 2.83
3526 4958 8.815565 TTTCAATATAGATGCAAGGGTTGTTA 57.184 30.769 0.00 0.00 0.00 2.41
3527 4959 8.995027 TTCAATATAGATGCAAGGGTTGTTAT 57.005 30.769 0.00 0.00 0.00 1.89
3528 4960 8.394971 TCAATATAGATGCAAGGGTTGTTATG 57.605 34.615 0.00 0.00 0.00 1.90
3529 4961 7.448161 TCAATATAGATGCAAGGGTTGTTATGG 59.552 37.037 0.00 0.00 0.00 2.74
3530 4962 3.737559 AGATGCAAGGGTTGTTATGGA 57.262 42.857 0.00 0.00 0.00 3.41
3531 4963 4.046286 AGATGCAAGGGTTGTTATGGAA 57.954 40.909 0.00 0.00 0.00 3.53
3532 4964 4.415596 AGATGCAAGGGTTGTTATGGAAA 58.584 39.130 0.00 0.00 0.00 3.13
3533 4965 4.837860 AGATGCAAGGGTTGTTATGGAAAA 59.162 37.500 0.00 0.00 0.00 2.29
3534 4966 5.484998 AGATGCAAGGGTTGTTATGGAAAAT 59.515 36.000 0.00 0.00 0.00 1.82
3535 4967 4.892433 TGCAAGGGTTGTTATGGAAAATG 58.108 39.130 0.00 0.00 0.00 2.32
3536 4968 4.590647 TGCAAGGGTTGTTATGGAAAATGA 59.409 37.500 0.00 0.00 0.00 2.57
3537 4969 5.070981 TGCAAGGGTTGTTATGGAAAATGAA 59.929 36.000 0.00 0.00 0.00 2.57
3538 4970 5.639082 GCAAGGGTTGTTATGGAAAATGAAG 59.361 40.000 0.00 0.00 0.00 3.02
3539 4971 6.741240 GCAAGGGTTGTTATGGAAAATGAAGT 60.741 38.462 0.00 0.00 0.00 3.01
3540 4972 6.590234 AGGGTTGTTATGGAAAATGAAGTC 57.410 37.500 0.00 0.00 0.00 3.01
3541 4973 6.314917 AGGGTTGTTATGGAAAATGAAGTCT 58.685 36.000 0.00 0.00 0.00 3.24
3542 4974 6.209391 AGGGTTGTTATGGAAAATGAAGTCTG 59.791 38.462 0.00 0.00 0.00 3.51
3543 4975 5.863935 GGTTGTTATGGAAAATGAAGTCTGC 59.136 40.000 0.00 0.00 0.00 4.26
3544 4976 6.446318 GTTGTTATGGAAAATGAAGTCTGCA 58.554 36.000 0.00 0.00 0.00 4.41
3545 4977 6.647334 TGTTATGGAAAATGAAGTCTGCAA 57.353 33.333 0.00 0.00 0.00 4.08
3546 4978 6.680810 TGTTATGGAAAATGAAGTCTGCAAG 58.319 36.000 0.00 0.00 0.00 4.01
3547 4979 6.265196 TGTTATGGAAAATGAAGTCTGCAAGT 59.735 34.615 0.00 0.00 33.76 3.16
3548 4980 7.446931 TGTTATGGAAAATGAAGTCTGCAAGTA 59.553 33.333 0.00 0.00 33.76 2.24
3549 4981 6.899393 ATGGAAAATGAAGTCTGCAAGTAA 57.101 33.333 0.00 0.00 33.76 2.24
3550 4982 6.707440 TGGAAAATGAAGTCTGCAAGTAAA 57.293 33.333 0.00 0.00 33.76 2.01
3551 4983 7.288810 TGGAAAATGAAGTCTGCAAGTAAAT 57.711 32.000 0.00 0.00 33.76 1.40
3552 4984 8.402798 TGGAAAATGAAGTCTGCAAGTAAATA 57.597 30.769 0.00 0.00 33.76 1.40
3553 4985 8.855110 TGGAAAATGAAGTCTGCAAGTAAATAA 58.145 29.630 0.00 0.00 33.76 1.40
3554 4986 9.860898 GGAAAATGAAGTCTGCAAGTAAATAAT 57.139 29.630 0.00 0.00 33.76 1.28
3563 4995 9.573133 AGTCTGCAAGTAAATAATAAACAATGC 57.427 29.630 0.00 0.00 33.76 3.56
3564 4996 9.352784 GTCTGCAAGTAAATAATAAACAATGCA 57.647 29.630 0.00 0.00 36.51 3.96
3565 4997 9.920133 TCTGCAAGTAAATAATAAACAATGCAA 57.080 25.926 0.00 0.00 37.59 4.08
3566 4998 9.956797 CTGCAAGTAAATAATAAACAATGCAAC 57.043 29.630 0.00 0.00 37.59 4.17
3567 4999 9.481340 TGCAAGTAAATAATAAACAATGCAACA 57.519 25.926 0.00 0.00 36.17 3.33
3578 5010 9.662545 AATAAACAATGCAACAATAAAGTTTGC 57.337 25.926 0.00 0.00 31.33 3.68
3579 5011 6.674694 AACAATGCAACAATAAAGTTTGCA 57.325 29.167 10.38 10.38 38.70 4.08
3580 5012 6.674694 ACAATGCAACAATAAAGTTTGCAA 57.325 29.167 11.84 0.00 38.25 4.08
3581 5013 6.717413 ACAATGCAACAATAAAGTTTGCAAG 58.283 32.000 11.84 10.07 38.25 4.01
3582 5014 6.315891 ACAATGCAACAATAAAGTTTGCAAGT 59.684 30.769 11.84 10.62 38.25 3.16
3583 5015 7.493971 ACAATGCAACAATAAAGTTTGCAAGTA 59.506 29.630 11.84 0.00 38.25 2.24
3584 5016 8.333908 CAATGCAACAATAAAGTTTGCAAGTAA 58.666 29.630 11.84 0.00 38.25 2.24
3585 5017 7.462109 TGCAACAATAAAGTTTGCAAGTAAG 57.538 32.000 5.78 0.00 34.78 2.34
3586 5018 6.478344 TGCAACAATAAAGTTTGCAAGTAAGG 59.522 34.615 5.78 0.00 34.78 2.69
3954 5386 7.015226 TGCACATACTTGCTACAATTGATAC 57.985 36.000 13.59 0.89 43.41 2.24
3958 5390 8.071967 CACATACTTGCTACAATTGATACATGG 58.928 37.037 13.59 5.63 0.00 3.66
3991 5423 3.570975 TGCTCAACTCACTGCAAAATCAT 59.429 39.130 0.00 0.00 32.12 2.45
3998 5430 4.083643 ACTCACTGCAAAATCATTGACTCG 60.084 41.667 0.00 0.00 0.00 4.18
4021 5453 8.336498 TCGTGTCTTATTTACGATGAAATCTC 57.664 34.615 0.00 0.00 42.58 2.75
4025 5457 9.098355 TGTCTTATTTACGATGAAATCTCCAAG 57.902 33.333 0.00 0.00 42.58 3.61
4027 5459 8.482943 TCTTATTTACGATGAAATCTCCAAGGA 58.517 33.333 0.00 0.00 42.58 3.36
4033 5465 3.507162 TGAAATCTCCAAGGAGCAACA 57.493 42.857 11.31 6.22 41.71 3.33
4034 5466 4.038271 TGAAATCTCCAAGGAGCAACAT 57.962 40.909 11.31 0.00 41.71 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.593679 TGTGTCAAGTAATTAATGAGGAGAGAA 58.406 33.333 3.16 0.00 0.00 2.87
3 4 8.954950 ATGTGTCAAGTAATTAATGAGGAGAG 57.045 34.615 3.16 0.00 0.00 3.20
4 5 8.539544 TGATGTGTCAAGTAATTAATGAGGAGA 58.460 33.333 3.16 0.00 0.00 3.71
51 52 9.478238 TGGGAGTAACATAGTTAGTAACATACA 57.522 33.333 15.28 0.00 0.00 2.29
62 63 8.938883 ACTCATCATATTGGGAGTAACATAGTT 58.061 33.333 0.00 0.00 38.74 2.24
63 64 8.497910 ACTCATCATATTGGGAGTAACATAGT 57.502 34.615 0.00 0.00 38.74 2.12
64 65 8.811017 AGACTCATCATATTGGGAGTAACATAG 58.189 37.037 0.00 0.00 40.48 2.23
65 66 8.727100 AGACTCATCATATTGGGAGTAACATA 57.273 34.615 0.00 0.00 40.48 2.29
66 67 7.623999 AGACTCATCATATTGGGAGTAACAT 57.376 36.000 0.00 0.00 40.48 2.71
67 68 8.421784 GTTAGACTCATCATATTGGGAGTAACA 58.578 37.037 0.00 0.00 40.48 2.41
68 69 7.873505 GGTTAGACTCATCATATTGGGAGTAAC 59.126 40.741 0.00 0.00 40.48 2.50
69 70 7.567250 TGGTTAGACTCATCATATTGGGAGTAA 59.433 37.037 0.00 0.00 40.48 2.24
70 71 7.073208 TGGTTAGACTCATCATATTGGGAGTA 58.927 38.462 0.00 0.00 40.48 2.59
71 72 5.905331 TGGTTAGACTCATCATATTGGGAGT 59.095 40.000 0.00 0.00 42.90 3.85
72 73 6.425210 TGGTTAGACTCATCATATTGGGAG 57.575 41.667 0.00 0.00 0.00 4.30
73 74 6.329986 ACATGGTTAGACTCATCATATTGGGA 59.670 38.462 0.00 0.00 0.00 4.37
74 75 6.537355 ACATGGTTAGACTCATCATATTGGG 58.463 40.000 0.00 0.00 0.00 4.12
75 76 7.040892 CCAACATGGTTAGACTCATCATATTGG 60.041 40.741 5.71 5.71 31.35 3.16
76 77 7.868775 CCAACATGGTTAGACTCATCATATTG 58.131 38.462 0.00 0.00 31.35 1.90
93 94 1.305213 CCTCCCCCAACCAACATGG 60.305 63.158 0.00 0.00 45.02 3.66
94 95 1.305213 CCCTCCCCCAACCAACATG 60.305 63.158 0.00 0.00 0.00 3.21
95 96 2.557181 CCCCTCCCCCAACCAACAT 61.557 63.158 0.00 0.00 0.00 2.71
96 97 3.189646 CCCCTCCCCCAACCAACA 61.190 66.667 0.00 0.00 0.00 3.33
97 98 3.992641 CCCCCTCCCCCAACCAAC 61.993 72.222 0.00 0.00 0.00 3.77
98 99 3.548934 ATCCCCCTCCCCCAACCAA 62.549 63.158 0.00 0.00 0.00 3.67
99 100 3.980600 ATCCCCCTCCCCCAACCA 61.981 66.667 0.00 0.00 0.00 3.67
100 101 3.429580 CATCCCCCTCCCCCAACC 61.430 72.222 0.00 0.00 0.00 3.77
101 102 3.429580 CCATCCCCCTCCCCCAAC 61.430 72.222 0.00 0.00 0.00 3.77
102 103 3.980600 ACCATCCCCCTCCCCCAA 61.981 66.667 0.00 0.00 0.00 4.12
103 104 4.777546 CACCATCCCCCTCCCCCA 62.778 72.222 0.00 0.00 0.00 4.96
104 105 4.779486 ACACCATCCCCCTCCCCC 62.779 72.222 0.00 0.00 0.00 5.40
105 106 3.420482 CACACCATCCCCCTCCCC 61.420 72.222 0.00 0.00 0.00 4.81
106 107 4.129148 GCACACCATCCCCCTCCC 62.129 72.222 0.00 0.00 0.00 4.30
107 108 2.631012 GATGCACACCATCCCCCTCC 62.631 65.000 0.00 0.00 43.72 4.30
115 116 0.393944 CTGCTCCAGATGCACACCAT 60.394 55.000 0.00 0.00 36.37 3.55
124 125 0.612229 CACCTCACACTGCTCCAGAT 59.388 55.000 0.00 0.00 35.18 2.90
128 129 2.359230 GCCACCTCACACTGCTCC 60.359 66.667 0.00 0.00 0.00 4.70
147 148 0.163788 GCGGTGACAGTGATGAAACG 59.836 55.000 0.00 0.00 0.00 3.60
148 149 1.512926 AGCGGTGACAGTGATGAAAC 58.487 50.000 0.00 0.00 0.00 2.78
171 172 3.375782 GGCTGCAGGGCAATAAATAAG 57.624 47.619 17.12 0.00 38.41 1.73
342 358 4.846779 TGACCAAATTTTACCAGCTGAC 57.153 40.909 17.39 0.00 0.00 3.51
501 517 0.179124 GTCCTCTCTAGCCAGCAACG 60.179 60.000 0.00 0.00 0.00 4.10
515 531 4.213482 GGTTTTGGATATGCGTATGTCCTC 59.787 45.833 25.24 14.65 43.08 3.71
526 542 7.767198 AGAAAAATCATGCAGGTTTTGGATATG 59.233 33.333 8.07 0.00 35.41 1.78
536 607 4.527816 TGCCTAAAGAAAAATCATGCAGGT 59.472 37.500 0.00 0.00 0.00 4.00
571 642 2.481441 AGGCAGAGAGAGAGAGAGAGA 58.519 52.381 0.00 0.00 0.00 3.10
577 662 2.310349 AGGTTGTAGGCAGAGAGAGAGA 59.690 50.000 0.00 0.00 0.00 3.10
590 675 9.630098 TTTAGTCGAGTAAATTGTAGGTTGTAG 57.370 33.333 19.20 0.00 0.00 2.74
591 676 9.979578 TTTTAGTCGAGTAAATTGTAGGTTGTA 57.020 29.630 22.65 4.25 0.00 2.41
592 677 8.891671 TTTTAGTCGAGTAAATTGTAGGTTGT 57.108 30.769 22.65 0.00 0.00 3.32
594 679 9.768662 TCTTTTTAGTCGAGTAAATTGTAGGTT 57.231 29.630 22.65 0.00 0.00 3.50
603 688 9.897744 TTCGTCTTATCTTTTTAGTCGAGTAAA 57.102 29.630 19.20 19.20 32.77 2.01
604 689 9.334693 GTTCGTCTTATCTTTTTAGTCGAGTAA 57.665 33.333 8.66 8.66 32.77 2.24
605 690 8.506437 TGTTCGTCTTATCTTTTTAGTCGAGTA 58.494 33.333 0.00 0.00 32.77 2.59
606 691 7.365741 TGTTCGTCTTATCTTTTTAGTCGAGT 58.634 34.615 0.00 0.00 32.77 4.18
607 692 7.792383 TGTTCGTCTTATCTTTTTAGTCGAG 57.208 36.000 0.00 0.00 32.77 4.04
626 996 4.499696 GGCCCCATATTCAGAAATTGTTCG 60.500 45.833 0.00 0.00 38.90 3.95
641 2045 1.142060 CACGTAGGAAATGGCCCCATA 59.858 52.381 0.00 0.00 35.31 2.74
665 2080 7.224557 CCTTTCCGTTTGTCAAATCATTTCTTT 59.775 33.333 0.40 0.00 0.00 2.52
774 2190 2.572812 GCACATTGAATGGCCGCA 59.427 55.556 10.27 0.00 33.60 5.69
801 2217 1.489070 CGCATGCAGCTAGCTCAGAC 61.489 60.000 16.15 10.74 45.94 3.51
818 2234 0.024619 GTTCGCTTATCCGTTCACGC 59.975 55.000 0.00 0.00 38.18 5.34
849 2265 8.315391 TCTCATATGTGCATGTAAGCTTTATC 57.685 34.615 3.20 0.00 34.99 1.75
850 2266 8.859236 ATCTCATATGTGCATGTAAGCTTTAT 57.141 30.769 3.20 0.00 34.99 1.40
859 2275 6.147328 CGAATTGAGATCTCATATGTGCATGT 59.853 38.462 25.64 6.10 39.64 3.21
861 2277 5.121925 GCGAATTGAGATCTCATATGTGCAT 59.878 40.000 25.64 11.67 39.64 3.96
920 2336 2.731217 CTGCCAGTTGTAAAGTTGTGC 58.269 47.619 0.00 0.00 0.00 4.57
1011 2429 1.142748 CTTGGGAGAGGTAGCAGCG 59.857 63.158 0.00 0.00 0.00 5.18
1042 2460 2.395690 CGTTCGTGCTTCGGATGC 59.604 61.111 8.78 8.78 40.32 3.91
1051 2469 3.340721 CTGCTTCGAGCGTTCGTGC 62.341 63.158 24.86 24.86 46.26 5.34
1425 2843 3.068691 TCGCCGAACTCCTCCAGG 61.069 66.667 0.00 0.00 0.00 4.45
1646 3064 2.362169 ATTTTGGCGATTTCGGTTGG 57.638 45.000 1.75 0.00 40.23 3.77
1667 3085 9.058174 TCAAACCGAAATTACTGAAATTCACTA 57.942 29.630 0.00 0.00 36.76 2.74
1679 3097 4.325204 GGCCGAAATTCAAACCGAAATTAC 59.675 41.667 0.00 0.00 37.12 1.89
1766 3184 8.548721 CAGTAGTACACGGGAATTCAAATATTC 58.451 37.037 7.93 0.00 34.48 1.75
1779 3197 4.571919 TGGAAATTTCAGTAGTACACGGG 58.428 43.478 19.49 0.00 0.00 5.28
1780 3198 6.548441 TTTGGAAATTTCAGTAGTACACGG 57.452 37.500 19.49 0.00 0.00 4.94
1856 3274 5.414789 TGAGATTCCGGTGAAATTCACTA 57.585 39.130 23.30 8.76 46.19 2.74
1885 3303 9.778741 AGATATATGTGTCGTAATGGTTTTCAT 57.221 29.630 0.00 0.00 37.79 2.57
2037 3456 0.392706 TGTTCACGAGCCACAGTGAT 59.607 50.000 0.62 0.00 45.40 3.06
2064 3485 1.277557 AGAACGAGCAGAGAAGGCATT 59.722 47.619 0.00 0.00 0.00 3.56
2076 3497 2.593346 ACATGGATGAGAGAACGAGC 57.407 50.000 0.00 0.00 0.00 5.03
2078 3499 2.362397 GCCTACATGGATGAGAGAACGA 59.638 50.000 0.00 0.00 38.35 3.85
2079 3500 2.101415 TGCCTACATGGATGAGAGAACG 59.899 50.000 0.00 0.00 38.35 3.95
2080 3501 3.133721 AGTGCCTACATGGATGAGAGAAC 59.866 47.826 0.00 0.00 38.35 3.01
2112 3533 3.507233 ACCTGTAAGCATGTCAACAATGG 59.493 43.478 0.00 0.00 0.00 3.16
2117 3538 3.058914 GTGTCACCTGTAAGCATGTCAAC 60.059 47.826 0.00 0.00 0.00 3.18
2119 3540 2.766313 GTGTCACCTGTAAGCATGTCA 58.234 47.619 0.00 0.00 0.00 3.58
2127 3548 3.804786 TTTGAGTCGTGTCACCTGTAA 57.195 42.857 0.00 0.00 0.00 2.41
2128 3549 3.649073 CATTTGAGTCGTGTCACCTGTA 58.351 45.455 0.00 0.00 0.00 2.74
2129 3550 2.483876 CATTTGAGTCGTGTCACCTGT 58.516 47.619 0.00 0.00 0.00 4.00
2198 3619 0.250684 TGAACTGAGCCATGCCGAAA 60.251 50.000 0.00 0.00 0.00 3.46
2301 3722 3.542648 GGTTGACTGGAGGTAATAAGCC 58.457 50.000 0.00 0.00 0.00 4.35
2316 3737 1.067776 CACTGGGTAGAGTCGGTTGAC 60.068 57.143 0.00 0.00 45.86 3.18
2317 3738 1.254026 CACTGGGTAGAGTCGGTTGA 58.746 55.000 0.00 0.00 0.00 3.18
2320 3741 1.228769 TGCACTGGGTAGAGTCGGT 60.229 57.895 0.00 0.00 0.00 4.69
2327 3751 0.889186 GTGGTTGGTGCACTGGGTAG 60.889 60.000 17.98 0.00 0.00 3.18
2335 3759 1.034838 GTTCACTGGTGGTTGGTGCA 61.035 55.000 0.70 0.00 0.00 4.57
2340 3764 1.507141 GAGCCGTTCACTGGTGGTTG 61.507 60.000 0.70 0.00 0.00 3.77
2400 3824 0.175760 TACTTGGCGACCATGCTCTC 59.824 55.000 10.32 0.00 32.73 3.20
2444 3868 2.491022 GCGGTCTCGTAGGGCTGAT 61.491 63.158 0.00 0.00 38.89 2.90
2495 3919 0.526524 CGGTCACCAGCTCGAAGATC 60.527 60.000 0.00 0.00 33.89 2.75
2831 4255 1.002888 GCCATCCATCTCACATCCGAT 59.997 52.381 0.00 0.00 0.00 4.18
3023 4447 1.587054 CCATACCGCGATCTCCTCC 59.413 63.158 8.23 0.00 0.00 4.30
3127 4554 8.792830 TCATATAACCTTCCAATAGCAATAGC 57.207 34.615 0.00 0.00 42.56 2.97
3157 4584 7.363793 GGACCACAGGAATAATTAATGCTGTTT 60.364 37.037 21.16 13.21 44.47 2.83
3161 4588 5.765510 TGGACCACAGGAATAATTAATGCT 58.234 37.500 0.00 0.00 0.00 3.79
3176 4603 1.596752 GCGTGTGACATGGACCACA 60.597 57.895 6.95 11.97 40.56 4.17
3201 4628 7.739498 AATTAATGGACGGGAACATACATAC 57.261 36.000 0.00 0.00 0.00 2.39
3269 4701 5.163530 CCAAATGTGGGATGAATTGAATCGA 60.164 40.000 0.00 0.00 41.77 3.59
3310 4742 7.441157 ACGAAGACTAAAATTCATGAAGTCACA 59.559 33.333 21.01 5.81 39.20 3.58
3317 4749 8.378172 AGAAACACGAAGACTAAAATTCATGA 57.622 30.769 0.00 0.00 0.00 3.07
3400 4832 6.546428 TGGAAACAAAGGGATGTACAAAAA 57.454 33.333 0.00 0.00 37.44 1.94
3418 4850 0.481128 GGAGGGTGAAGGGTTGGAAA 59.519 55.000 0.00 0.00 0.00 3.13
3419 4851 0.699577 TGGAGGGTGAAGGGTTGGAA 60.700 55.000 0.00 0.00 0.00 3.53
3420 4852 1.073319 TGGAGGGTGAAGGGTTGGA 60.073 57.895 0.00 0.00 0.00 3.53
3421 4853 1.074951 GTGGAGGGTGAAGGGTTGG 59.925 63.158 0.00 0.00 0.00 3.77
3422 4854 1.302511 CGTGGAGGGTGAAGGGTTG 60.303 63.158 0.00 0.00 0.00 3.77
3423 4855 2.526046 CCGTGGAGGGTGAAGGGTT 61.526 63.158 0.00 0.00 35.97 4.11
3424 4856 2.928396 CCGTGGAGGGTGAAGGGT 60.928 66.667 0.00 0.00 35.97 4.34
3425 4857 2.928396 ACCGTGGAGGGTGAAGGG 60.928 66.667 0.00 0.00 46.96 3.95
3439 4871 1.380524 AGATACTCTGACGACCACCG 58.619 55.000 0.00 0.00 45.44 4.94
3450 4882 1.751924 GAAGGCCGTGACAGATACTCT 59.248 52.381 0.00 0.00 0.00 3.24
3451 4883 1.751924 AGAAGGCCGTGACAGATACTC 59.248 52.381 0.00 0.00 0.00 2.59
3452 4884 1.853963 AGAAGGCCGTGACAGATACT 58.146 50.000 0.00 0.00 0.00 2.12
3453 4885 3.068307 ACATAGAAGGCCGTGACAGATAC 59.932 47.826 0.00 0.00 0.00 2.24
3454 4886 3.068165 CACATAGAAGGCCGTGACAGATA 59.932 47.826 0.00 0.00 0.00 1.98
3455 4887 2.111384 ACATAGAAGGCCGTGACAGAT 58.889 47.619 0.00 0.00 0.00 2.90
3456 4888 1.204704 CACATAGAAGGCCGTGACAGA 59.795 52.381 0.00 0.00 0.00 3.41
3457 4889 1.066858 ACACATAGAAGGCCGTGACAG 60.067 52.381 12.44 0.00 33.56 3.51
3458 4890 0.973632 ACACATAGAAGGCCGTGACA 59.026 50.000 12.44 0.00 33.56 3.58
3459 4891 1.732259 CAACACATAGAAGGCCGTGAC 59.268 52.381 12.44 0.00 33.56 3.67
3460 4892 1.346395 ACAACACATAGAAGGCCGTGA 59.654 47.619 12.44 0.00 33.56 4.35
3461 4893 1.808411 ACAACACATAGAAGGCCGTG 58.192 50.000 0.00 0.00 35.48 4.94
3462 4894 2.561478 AACAACACATAGAAGGCCGT 57.439 45.000 0.00 0.00 0.00 5.68
3463 4895 3.370978 CACTAACAACACATAGAAGGCCG 59.629 47.826 0.00 0.00 0.00 6.13
3464 4896 4.324267 ACACTAACAACACATAGAAGGCC 58.676 43.478 0.00 0.00 0.00 5.19
3465 4897 5.238583 AGACACTAACAACACATAGAAGGC 58.761 41.667 0.00 0.00 0.00 4.35
3466 4898 7.603651 AGTAGACACTAACAACACATAGAAGG 58.396 38.462 0.00 0.00 31.45 3.46
3467 4899 9.477484 AAAGTAGACACTAACAACACATAGAAG 57.523 33.333 0.00 0.00 33.48 2.85
3468 4900 9.826574 AAAAGTAGACACTAACAACACATAGAA 57.173 29.630 0.00 0.00 33.48 2.10
3469 4901 9.472361 GAAAAGTAGACACTAACAACACATAGA 57.528 33.333 0.00 0.00 33.48 1.98
3470 4902 9.256477 TGAAAAGTAGACACTAACAACACATAG 57.744 33.333 0.00 0.00 33.48 2.23
3471 4903 9.602568 TTGAAAAGTAGACACTAACAACACATA 57.397 29.630 0.00 0.00 33.48 2.29
3472 4904 8.500753 TTGAAAAGTAGACACTAACAACACAT 57.499 30.769 0.00 0.00 33.48 3.21
3473 4905 7.908827 TTGAAAAGTAGACACTAACAACACA 57.091 32.000 0.00 0.00 33.48 3.72
3474 4906 8.662141 TCTTTGAAAAGTAGACACTAACAACAC 58.338 33.333 2.88 0.00 37.31 3.32
3475 4907 8.780846 TCTTTGAAAAGTAGACACTAACAACA 57.219 30.769 2.88 0.00 37.31 3.33
3494 4926 8.853126 CCCTTGCATCTATATTGAAATCTTTGA 58.147 33.333 0.00 0.00 0.00 2.69
3495 4927 8.636213 ACCCTTGCATCTATATTGAAATCTTTG 58.364 33.333 0.00 0.00 0.00 2.77
3496 4928 8.773033 ACCCTTGCATCTATATTGAAATCTTT 57.227 30.769 0.00 0.00 0.00 2.52
3497 4929 8.636213 CAACCCTTGCATCTATATTGAAATCTT 58.364 33.333 0.00 0.00 0.00 2.40
3498 4930 7.781693 ACAACCCTTGCATCTATATTGAAATCT 59.218 33.333 0.00 0.00 0.00 2.40
3499 4931 7.945134 ACAACCCTTGCATCTATATTGAAATC 58.055 34.615 0.00 0.00 0.00 2.17
3500 4932 7.902920 ACAACCCTTGCATCTATATTGAAAT 57.097 32.000 0.00 0.00 0.00 2.17
3501 4933 7.716799 AACAACCCTTGCATCTATATTGAAA 57.283 32.000 0.00 0.00 0.00 2.69
3502 4934 8.849168 CATAACAACCCTTGCATCTATATTGAA 58.151 33.333 0.00 0.00 0.00 2.69
3503 4935 7.448161 CCATAACAACCCTTGCATCTATATTGA 59.552 37.037 0.00 0.00 0.00 2.57
3504 4936 7.448161 TCCATAACAACCCTTGCATCTATATTG 59.552 37.037 0.00 0.00 0.00 1.90
3505 4937 7.526041 TCCATAACAACCCTTGCATCTATATT 58.474 34.615 0.00 0.00 0.00 1.28
3506 4938 7.090319 TCCATAACAACCCTTGCATCTATAT 57.910 36.000 0.00 0.00 0.00 0.86
3507 4939 6.508030 TCCATAACAACCCTTGCATCTATA 57.492 37.500 0.00 0.00 0.00 1.31
3508 4940 5.387113 TCCATAACAACCCTTGCATCTAT 57.613 39.130 0.00 0.00 0.00 1.98
3509 4941 4.853468 TCCATAACAACCCTTGCATCTA 57.147 40.909 0.00 0.00 0.00 1.98
3510 4942 3.737559 TCCATAACAACCCTTGCATCT 57.262 42.857 0.00 0.00 0.00 2.90
3511 4943 4.799564 TTTCCATAACAACCCTTGCATC 57.200 40.909 0.00 0.00 0.00 3.91
3512 4944 5.248020 TCATTTTCCATAACAACCCTTGCAT 59.752 36.000 0.00 0.00 0.00 3.96
3513 4945 4.590647 TCATTTTCCATAACAACCCTTGCA 59.409 37.500 0.00 0.00 0.00 4.08
3514 4946 5.146010 TCATTTTCCATAACAACCCTTGC 57.854 39.130 0.00 0.00 0.00 4.01
3515 4947 6.758254 ACTTCATTTTCCATAACAACCCTTG 58.242 36.000 0.00 0.00 0.00 3.61
3516 4948 6.782494 AGACTTCATTTTCCATAACAACCCTT 59.218 34.615 0.00 0.00 0.00 3.95
3517 4949 6.209391 CAGACTTCATTTTCCATAACAACCCT 59.791 38.462 0.00 0.00 0.00 4.34
3518 4950 6.389906 CAGACTTCATTTTCCATAACAACCC 58.610 40.000 0.00 0.00 0.00 4.11
3519 4951 5.863935 GCAGACTTCATTTTCCATAACAACC 59.136 40.000 0.00 0.00 0.00 3.77
3520 4952 6.446318 TGCAGACTTCATTTTCCATAACAAC 58.554 36.000 0.00 0.00 0.00 3.32
3521 4953 6.647334 TGCAGACTTCATTTTCCATAACAA 57.353 33.333 0.00 0.00 0.00 2.83
3522 4954 6.265196 ACTTGCAGACTTCATTTTCCATAACA 59.735 34.615 0.00 0.00 0.00 2.41
3523 4955 6.681777 ACTTGCAGACTTCATTTTCCATAAC 58.318 36.000 0.00 0.00 0.00 1.89
3524 4956 6.899393 ACTTGCAGACTTCATTTTCCATAA 57.101 33.333 0.00 0.00 0.00 1.90
3525 4957 7.994425 TTACTTGCAGACTTCATTTTCCATA 57.006 32.000 0.00 0.00 0.00 2.74
3526 4958 6.899393 TTACTTGCAGACTTCATTTTCCAT 57.101 33.333 0.00 0.00 0.00 3.41
3527 4959 6.707440 TTTACTTGCAGACTTCATTTTCCA 57.293 33.333 0.00 0.00 0.00 3.53
3528 4960 9.860898 ATTATTTACTTGCAGACTTCATTTTCC 57.139 29.630 0.00 0.00 0.00 3.13
3537 4969 9.573133 GCATTGTTTATTATTTACTTGCAGACT 57.427 29.630 0.00 0.00 0.00 3.24
3538 4970 9.352784 TGCATTGTTTATTATTTACTTGCAGAC 57.647 29.630 0.00 0.00 32.22 3.51
3539 4971 9.920133 TTGCATTGTTTATTATTTACTTGCAGA 57.080 25.926 0.00 0.00 35.08 4.26
3540 4972 9.956797 GTTGCATTGTTTATTATTTACTTGCAG 57.043 29.630 0.00 0.00 35.08 4.41
3541 4973 9.481340 TGTTGCATTGTTTATTATTTACTTGCA 57.519 25.926 0.00 0.00 33.25 4.08
3552 4984 9.662545 GCAAACTTTATTGTTGCATTGTTTATT 57.337 25.926 2.88 0.00 32.80 1.40
3553 4985 8.834465 TGCAAACTTTATTGTTGCATTGTTTAT 58.166 25.926 6.22 0.00 33.02 1.40
3554 4986 8.201554 TGCAAACTTTATTGTTGCATTGTTTA 57.798 26.923 6.22 0.00 33.02 2.01
3555 4987 7.081526 TGCAAACTTTATTGTTGCATTGTTT 57.918 28.000 6.22 0.00 33.02 2.83
3556 4988 6.674694 TGCAAACTTTATTGTTGCATTGTT 57.325 29.167 6.22 0.00 33.02 2.83
3557 4989 6.315891 ACTTGCAAACTTTATTGTTGCATTGT 59.684 30.769 10.74 9.98 35.58 2.71
3558 4990 6.717413 ACTTGCAAACTTTATTGTTGCATTG 58.283 32.000 10.74 9.45 35.58 2.82
3559 4991 6.923928 ACTTGCAAACTTTATTGTTGCATT 57.076 29.167 10.74 0.00 35.58 3.56
3560 4992 7.171337 CCTTACTTGCAAACTTTATTGTTGCAT 59.829 33.333 10.74 0.83 35.58 3.96
3561 4993 6.478344 CCTTACTTGCAAACTTTATTGTTGCA 59.522 34.615 0.00 6.22 34.66 4.08
3562 4994 6.876804 CCTTACTTGCAAACTTTATTGTTGC 58.123 36.000 0.00 0.76 32.80 4.17
3877 5309 4.514401 GGATAATTCCACAACGACCTTCT 58.486 43.478 0.00 0.00 42.12 2.85
3878 5310 3.626217 GGGATAATTCCACAACGACCTTC 59.374 47.826 0.00 0.00 44.60 3.46
3879 5311 3.265995 AGGGATAATTCCACAACGACCTT 59.734 43.478 0.00 0.00 44.60 3.50
3880 5312 2.844348 AGGGATAATTCCACAACGACCT 59.156 45.455 0.00 0.00 44.60 3.85
3881 5313 3.277142 AGGGATAATTCCACAACGACC 57.723 47.619 0.00 0.00 44.60 4.79
3882 5314 4.377897 CCTAGGGATAATTCCACAACGAC 58.622 47.826 0.00 0.00 44.60 4.34
3883 5315 3.181458 GCCTAGGGATAATTCCACAACGA 60.181 47.826 11.72 0.00 44.60 3.85
3884 5316 3.139077 GCCTAGGGATAATTCCACAACG 58.861 50.000 11.72 0.00 44.60 4.10
3890 5322 3.511540 GCCAATTGCCTAGGGATAATTCC 59.488 47.826 11.72 0.00 41.77 3.01
3917 5349 5.102953 AGTATGTGCATCGGCCATATTAT 57.897 39.130 2.24 0.00 40.13 1.28
3954 5386 3.639672 TGAGCATAGGCATATCCCATG 57.360 47.619 0.67 0.00 44.61 3.66
3958 5390 3.999663 GTGAGTTGAGCATAGGCATATCC 59.000 47.826 0.67 0.00 44.61 2.59
3991 5423 6.614160 TCATCGTAAATAAGACACGAGTCAA 58.386 36.000 15.47 3.30 46.60 3.18
3998 5430 8.420374 TGGAGATTTCATCGTAAATAAGACAC 57.580 34.615 0.00 0.00 0.00 3.67
4010 5442 2.910199 TGCTCCTTGGAGATTTCATCG 58.090 47.619 19.85 0.00 0.00 3.84
4021 5453 5.895636 TTGTTATGTATGTTGCTCCTTGG 57.104 39.130 0.00 0.00 0.00 3.61
4025 5457 9.801873 ATTTACAATTGTTATGTATGTTGCTCC 57.198 29.630 17.78 0.00 33.55 4.70


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

AutoCloner maintained by Alex Coulton.