Multiple sequence alignment - TraesCS6D01G353300

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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 TraesCS6D01G353300 chr6D 100.000 6012 0 0 1 6012 449190554 449184543 0.000000e+00 11103.0
1 TraesCS6D01G353300 chr6D 88.930 804 74 11 3093 3887 449251411 449252208 0.000000e+00 977.0
2 TraesCS6D01G353300 chr6D 91.806 659 54 0 3113 3771 449217739 449217081 0.000000e+00 918.0
3 TraesCS6D01G353300 chr6D 86.618 822 74 21 4280 5080 449252778 449253584 0.000000e+00 876.0
4 TraesCS6D01G353300 chr6D 81.376 945 96 31 292 1223 449222096 449221219 0.000000e+00 697.0
5 TraesCS6D01G353300 chr6D 81.658 796 83 37 1722 2483 449219498 449218732 2.400000e-168 603.0
6 TraesCS6D01G353300 chr6D 78.046 788 89 47 1722 2475 449249754 449250491 2.590000e-113 420.0
7 TraesCS6D01G353300 chr6D 88.922 334 29 7 5126 5454 449214301 449213971 7.260000e-109 405.0
8 TraesCS6D01G353300 chr6D 89.700 233 21 3 4286 4518 449216847 449216618 1.640000e-75 294.0
9 TraesCS6D01G353300 chr6D 98.693 153 2 0 1041 1193 449247438 449247590 7.680000e-69 272.0
10 TraesCS6D01G353300 chr6D 77.662 479 67 27 1498 1942 449220065 449219593 7.730000e-64 255.0
11 TraesCS6D01G353300 chr6D 83.099 284 18 14 4875 5134 449214641 449214364 1.300000e-56 231.0
12 TraesCS6D01G353300 chr6D 80.272 294 32 13 1506 1785 449247593 449247874 1.320000e-46 198.0
13 TraesCS6D01G353300 chr6D 85.034 147 11 3 866 1011 449247306 449247442 8.130000e-29 139.0
14 TraesCS6D01G353300 chr6D 100.000 28 0 0 1423 1450 411719640 411719667 1.100000e-02 52.8
15 TraesCS6D01G353300 chr6B 93.423 2539 100 25 2912 5409 680860772 680863284 0.000000e+00 3701.0
16 TraesCS6D01G353300 chr6B 90.394 1572 80 18 4294 5825 680778090 680776550 0.000000e+00 2001.0
17 TraesCS6D01G353300 chr6B 91.568 1435 77 26 1501 2917 680858885 680860293 0.000000e+00 1940.0
18 TraesCS6D01G353300 chr6B 92.191 1319 76 10 2468 3774 680779545 680778242 0.000000e+00 1840.0
19 TraesCS6D01G353300 chr6B 88.199 805 82 8 3093 3887 680811981 680812782 0.000000e+00 948.0
20 TraesCS6D01G353300 chr6B 86.417 773 48 22 526 1274 680782351 680781612 0.000000e+00 793.0
21 TraesCS6D01G353300 chr6B 85.359 683 70 18 4267 4937 680813345 680814009 0.000000e+00 680.0
22 TraesCS6D01G353300 chr6B 82.578 838 63 30 1659 2465 680781103 680780318 0.000000e+00 662.0
23 TraesCS6D01G353300 chr6B 85.760 625 38 18 654 1271 680858019 680858599 1.110000e-171 614.0
24 TraesCS6D01G353300 chr6B 89.977 439 21 10 5405 5835 680863337 680863760 4.100000e-151 545.0
25 TraesCS6D01G353300 chr6B 79.445 793 99 30 1722 2475 680810233 680811000 2.500000e-138 503.0
26 TraesCS6D01G353300 chr6B 88.341 223 13 5 1052 1274 680809141 680809350 7.730000e-64 255.0
27 TraesCS6D01G353300 chr6B 84.492 187 21 5 1445 1629 680809590 680809770 1.720000e-40 178.0
28 TraesCS6D01G353300 chr6B 85.897 156 15 3 5814 5969 680776525 680776377 6.240000e-35 159.0
29 TraesCS6D01G353300 chr6A 91.196 1965 120 17 1831 3777 595026473 595024544 0.000000e+00 2621.0
30 TraesCS6D01G353300 chr6A 89.549 1263 98 24 2524 3771 595049414 595048171 0.000000e+00 1570.0
31 TraesCS6D01G353300 chr6A 86.070 1005 71 16 4989 5982 595023621 595022675 0.000000e+00 1016.0
32 TraesCS6D01G353300 chr6A 88.930 804 76 10 3095 3887 595073295 595074096 0.000000e+00 979.0
33 TraesCS6D01G353300 chr6A 86.649 749 46 12 488 1223 595030127 595029420 0.000000e+00 780.0
34 TraesCS6D01G353300 chr6A 82.201 927 120 31 1443 2347 595029003 595028100 0.000000e+00 756.0
35 TraesCS6D01G353300 chr6A 89.398 415 22 9 4589 4999 595024163 595023767 2.500000e-138 503.0
36 TraesCS6D01G353300 chr6A 84.542 524 46 16 4640 5134 595047677 595047160 2.520000e-133 486.0
37 TraesCS6D01G353300 chr6A 81.223 687 47 35 552 1223 595052581 595051962 4.210000e-131 479.0
38 TraesCS6D01G353300 chr6A 81.771 576 75 17 1908 2475 595049973 595049420 7.100000e-124 455.0
39 TraesCS6D01G353300 chr6A 88.785 321 24 7 5143 5453 595047078 595046760 3.400000e-102 383.0
40 TraesCS6D01G353300 chr6A 87.926 323 26 7 4280 4600 595076198 595076509 9.520000e-98 368.0
41 TraesCS6D01G353300 chr6A 93.004 243 12 2 1041 1282 595070417 595070655 3.450000e-92 350.0
42 TraesCS6D01G353300 chr6A 87.086 302 36 1 4596 4894 595076687 595076988 7.460000e-89 339.0
43 TraesCS6D01G353300 chr6A 95.074 203 10 0 4295 4497 595024381 595024179 2.700000e-83 320.0
44 TraesCS6D01G353300 chr6A 89.270 233 22 3 4286 4518 595047949 595047720 7.620000e-74 289.0
45 TraesCS6D01G353300 chr6A 87.310 197 19 5 105 299 595030523 595030331 2.820000e-53 220.0
46 TraesCS6D01G353300 chr6A 93.407 91 5 1 1308 1397 595029249 595029159 3.780000e-27 134.0
47 TraesCS6D01G353300 chr6A 91.667 96 3 3 1308 1398 595027393 595027298 1.760000e-25 128.0
48 TraesCS6D01G353300 chr6A 93.750 48 2 1 1894 1941 595050091 595050045 3.010000e-08 71.3
49 TraesCS6D01G353300 chr7D 90.588 680 61 2 3098 3774 419767416 419768095 0.000000e+00 898.0
50 TraesCS6D01G353300 chr7D 84.201 557 53 13 4306 4861 487739829 487740351 5.380000e-140 508.0
51 TraesCS6D01G353300 chr7D 88.136 118 5 1 1085 1193 487738043 487738160 1.360000e-26 132.0
52 TraesCS6D01G353300 chr7A 83.066 561 53 17 4306 4865 555650972 555651491 7.050000e-129 472.0
53 TraesCS6D01G353300 chr7A 92.857 98 5 2 1110 1206 513417483 513417387 2.260000e-29 141.0
54 TraesCS6D01G353300 chr7B 84.783 184 19 4 1868 2051 435788752 435788926 6.190000e-40 176.0
55 TraesCS6D01G353300 chr7B 88.983 118 4 1 1085 1193 516463169 516463286 2.920000e-28 137.0


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 TraesCS6D01G353300 chr6D 449184543 449190554 6011 True 11103.000000 11103 100.000000 1 6012 1 chr6D.!!$R1 6011
1 TraesCS6D01G353300 chr6D 449213971 449222096 8125 True 486.142857 918 84.889000 292 5454 7 chr6D.!!$R2 5162
2 TraesCS6D01G353300 chr6D 449247306 449253584 6278 False 480.333333 977 86.265500 866 5080 6 chr6D.!!$F2 4214
3 TraesCS6D01G353300 chr6B 680858019 680863760 5741 False 1700.000000 3701 90.182000 654 5835 4 chr6B.!!$F2 5181
4 TraesCS6D01G353300 chr6B 680776377 680782351 5974 True 1091.000000 2001 87.495400 526 5969 5 chr6B.!!$R1 5443
5 TraesCS6D01G353300 chr6B 680809141 680814009 4868 False 512.800000 948 85.167200 1052 4937 5 chr6B.!!$F1 3885
6 TraesCS6D01G353300 chr6A 595022675 595030523 7848 True 719.777778 2621 89.219111 105 5982 9 chr6A.!!$R1 5877
7 TraesCS6D01G353300 chr6A 595046760 595052581 5821 True 533.328571 1570 86.984286 552 5453 7 chr6A.!!$R2 4901
8 TraesCS6D01G353300 chr6A 595070417 595076988 6571 False 509.000000 979 89.236500 1041 4894 4 chr6A.!!$F1 3853
9 TraesCS6D01G353300 chr7D 419767416 419768095 679 False 898.000000 898 90.588000 3098 3774 1 chr7D.!!$F1 676
10 TraesCS6D01G353300 chr7D 487738043 487740351 2308 False 320.000000 508 86.168500 1085 4861 2 chr7D.!!$F2 3776
11 TraesCS6D01G353300 chr7A 555650972 555651491 519 False 472.000000 472 83.066000 4306 4865 1 chr7A.!!$F1 559

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
94 95 0.035056 CCGGATGGAAAAGTGGAGCT 60.035 55.000 0.00 0.00 37.49 4.09 F
102 103 0.185901 AAAAGTGGAGCTTGAGCCCA 59.814 50.000 8.52 8.52 43.38 5.36 F
103 104 0.251077 AAAGTGGAGCTTGAGCCCAG 60.251 55.000 11.77 0.00 40.37 4.45 F
956 1068 0.258194 ACCGTCGAACCTCCTCCTAT 59.742 55.000 0.00 0.00 0.00 2.57 F
957 1069 0.669077 CCGTCGAACCTCCTCCTATG 59.331 60.000 0.00 0.00 0.00 2.23 F
2281 9180 0.174162 AGACCGTACGTGCCCATTAC 59.826 55.000 15.21 0.00 0.00 1.89 F
2639 10314 2.030096 TGACCGTTTGCACGTATGACTA 60.030 45.455 0.00 0.00 45.62 2.59 F
3965 13252 0.108804 ACTCGCACCACCATAACTCG 60.109 55.000 0.00 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1479 3358 0.693049 AAGTAGGTGTGCAAGGGAGG 59.307 55.000 0.00 0.00 0.00 4.30 R
2100 8996 1.358877 TGCGAAAGACGTGATGATGG 58.641 50.000 0.00 0.00 44.60 3.51 R
2110 9006 6.663944 AGGTATTCACTATTTGCGAAAGAC 57.336 37.500 0.00 0.00 0.00 3.01 R
2263 9160 1.141591 CGTAATGGGCACGTACGGTC 61.142 60.000 21.06 9.94 34.74 4.79 R
2356 9255 1.144057 ATAGCACACTAGCACGGCC 59.856 57.895 0.00 0.00 36.85 6.13 R
3372 12643 0.390472 CAGTGGTTCTCGAAGCCCTC 60.390 60.000 6.41 0.00 37.97 4.30 R
4612 16161 0.389426 AATCAGCCACACGTACGTCC 60.389 55.000 19.94 7.33 0.00 4.79 R
5735 19347 0.537143 TGGTTGTGGAGTGTGGATGC 60.537 55.000 0.00 0.00 0.00 3.91 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
40 41 8.640063 AGCTTATATGAATCAATTGCATACCA 57.360 30.769 0.00 0.00 0.00 3.25
41 42 9.081204 AGCTTATATGAATCAATTGCATACCAA 57.919 29.630 0.00 1.68 37.94 3.67
42 43 9.865321 GCTTATATGAATCAATTGCATACCAAT 57.135 29.630 0.00 0.00 45.90 3.16
69 70 1.249407 TGGTTTTACCATGTTCGGGC 58.751 50.000 0.00 0.00 44.79 6.13
70 71 1.202952 TGGTTTTACCATGTTCGGGCT 60.203 47.619 0.00 0.00 44.79 5.19
71 72 1.890489 GGTTTTACCATGTTCGGGCTT 59.110 47.619 0.00 0.00 38.42 4.35
72 73 2.297880 GGTTTTACCATGTTCGGGCTTT 59.702 45.455 0.00 0.00 38.42 3.51
73 74 3.243941 GGTTTTACCATGTTCGGGCTTTT 60.244 43.478 0.00 0.00 38.42 2.27
74 75 3.926821 TTTACCATGTTCGGGCTTTTC 57.073 42.857 0.00 0.00 0.00 2.29
75 76 1.828979 TACCATGTTCGGGCTTTTCC 58.171 50.000 0.00 0.00 0.00 3.13
91 92 2.780264 TCCCGGATGGAAAAGTGGA 58.220 52.632 0.73 0.00 41.40 4.02
92 93 0.618458 TCCCGGATGGAAAAGTGGAG 59.382 55.000 0.73 0.00 41.40 3.86
93 94 1.032114 CCCGGATGGAAAAGTGGAGC 61.032 60.000 0.73 0.00 37.49 4.70
94 95 0.035056 CCGGATGGAAAAGTGGAGCT 60.035 55.000 0.00 0.00 37.49 4.09
95 96 1.614317 CCGGATGGAAAAGTGGAGCTT 60.614 52.381 0.00 0.00 36.73 3.74
96 97 1.470098 CGGATGGAAAAGTGGAGCTTG 59.530 52.381 0.00 0.00 37.52 4.01
97 98 2.795329 GGATGGAAAAGTGGAGCTTGA 58.205 47.619 0.00 0.00 37.52 3.02
98 99 2.751806 GGATGGAAAAGTGGAGCTTGAG 59.248 50.000 0.00 0.00 37.52 3.02
99 100 1.609208 TGGAAAAGTGGAGCTTGAGC 58.391 50.000 0.00 0.00 37.52 4.26
100 101 0.884514 GGAAAAGTGGAGCTTGAGCC 59.115 55.000 0.00 0.00 43.38 4.70
101 102 0.884514 GAAAAGTGGAGCTTGAGCCC 59.115 55.000 0.00 1.80 43.38 5.19
102 103 0.185901 AAAAGTGGAGCTTGAGCCCA 59.814 50.000 8.52 8.52 43.38 5.36
103 104 0.251077 AAAGTGGAGCTTGAGCCCAG 60.251 55.000 11.77 0.00 40.37 4.45
107 108 2.438075 GAGCTTGAGCCCAGCCTG 60.438 66.667 0.00 0.00 43.38 4.85
113 114 0.322816 TTGAGCCCAGCCTGAATGTC 60.323 55.000 0.00 0.00 0.00 3.06
175 176 7.898014 TGCTCAAGTCTATCTGTAAGGATTA 57.102 36.000 0.00 0.00 0.00 1.75
358 423 4.874970 TCTGGTAGTTAAAAGGACACGAC 58.125 43.478 0.00 0.00 0.00 4.34
377 442 6.072508 ACACGACAACAATGAATTGAGCTTAT 60.073 34.615 9.94 0.00 40.14 1.73
416 481 4.650734 TCTTGTGATGGAACTTGCACATA 58.349 39.130 0.00 0.00 40.51 2.29
418 483 5.355071 TCTTGTGATGGAACTTGCACATATC 59.645 40.000 0.00 0.00 40.51 1.63
421 486 5.711506 TGTGATGGAACTTGCACATATCTTT 59.288 36.000 0.00 0.00 36.44 2.52
445 510 5.424121 TTCAAGTTCTAGACTTTGCAAGC 57.576 39.130 0.00 0.00 46.34 4.01
449 514 4.645535 AGTTCTAGACTTTGCAAGCATGA 58.354 39.130 0.00 0.00 33.92 3.07
451 516 5.123502 AGTTCTAGACTTTGCAAGCATGATG 59.876 40.000 0.00 0.00 33.92 3.07
454 519 2.230508 AGACTTTGCAAGCATGATGGTG 59.769 45.455 0.00 0.00 0.00 4.17
455 520 1.337447 ACTTTGCAAGCATGATGGTGC 60.337 47.619 0.00 5.09 45.38 5.01
462 527 1.430632 GCATGATGGTGCGTTCCTG 59.569 57.895 0.00 0.00 35.10 3.86
468 533 2.026729 TGATGGTGCGTTCCTGGATTTA 60.027 45.455 0.00 0.00 0.00 1.40
474 539 3.560068 GTGCGTTCCTGGATTTAGTATGG 59.440 47.826 0.00 0.00 0.00 2.74
476 541 3.804036 CGTTCCTGGATTTAGTATGGCA 58.196 45.455 0.00 0.00 0.00 4.92
477 542 4.389374 CGTTCCTGGATTTAGTATGGCAT 58.611 43.478 4.88 4.88 0.00 4.40
481 546 3.141398 CTGGATTTAGTATGGCATGCGT 58.859 45.455 12.44 5.48 0.00 5.24
482 547 2.877786 TGGATTTAGTATGGCATGCGTG 59.122 45.455 12.44 0.09 0.00 5.34
499 564 1.388093 CGTGCTGACAAGACTTCATCG 59.612 52.381 0.00 0.00 0.00 3.84
504 569 3.506810 CTGACAAGACTTCATCGGTCTC 58.493 50.000 0.00 0.00 42.39 3.36
620 692 4.727655 GCGTTTACGTCTATACTGACTGAC 59.272 45.833 0.00 0.00 42.22 3.51
637 709 7.019774 TGACTGACATGTTTCTGAAAAGAAG 57.980 36.000 4.09 4.97 0.00 2.85
667 743 2.625828 GAAAACGTCGCAGTCTTGTTC 58.374 47.619 0.00 0.00 0.00 3.18
692 768 4.408276 CTTTCACCCCCTCGATCTAGATA 58.592 47.826 4.89 0.00 0.00 1.98
861 960 1.739929 CGCGCTCACCACAACCATA 60.740 57.895 5.56 0.00 0.00 2.74
906 1017 4.505217 GACGCGCTTGGCACATCG 62.505 66.667 5.73 0.00 43.84 3.84
940 1052 1.647346 TGTAGCATAAAAGGCGACCG 58.353 50.000 0.00 0.00 36.25 4.79
949 1061 2.760387 AAAGGCGACCGTCGAACCTC 62.760 60.000 24.78 6.05 43.74 3.85
950 1062 4.790861 GGCGACCGTCGAACCTCC 62.791 72.222 24.78 11.56 43.74 4.30
951 1063 3.745803 GCGACCGTCGAACCTCCT 61.746 66.667 24.78 0.00 43.74 3.69
952 1064 2.484203 CGACCGTCGAACCTCCTC 59.516 66.667 16.03 0.00 43.74 3.71
953 1065 2.883621 GACCGTCGAACCTCCTCC 59.116 66.667 0.00 0.00 0.00 4.30
954 1066 1.678300 GACCGTCGAACCTCCTCCT 60.678 63.158 0.00 0.00 0.00 3.69
955 1067 0.393537 GACCGTCGAACCTCCTCCTA 60.394 60.000 0.00 0.00 0.00 2.94
956 1068 0.258194 ACCGTCGAACCTCCTCCTAT 59.742 55.000 0.00 0.00 0.00 2.57
957 1069 0.669077 CCGTCGAACCTCCTCCTATG 59.331 60.000 0.00 0.00 0.00 2.23
1020 1132 2.217038 AGAGACGCACCACCACCAT 61.217 57.895 0.00 0.00 0.00 3.55
1021 1133 1.741770 GAGACGCACCACCACCATC 60.742 63.158 0.00 0.00 0.00 3.51
1022 1134 2.031919 GACGCACCACCACCATCA 59.968 61.111 0.00 0.00 0.00 3.07
1023 1135 2.281484 ACGCACCACCACCATCAC 60.281 61.111 0.00 0.00 0.00 3.06
1262 1400 2.205152 ACTTGTCCGGCGGTGTAGT 61.205 57.895 27.32 22.06 0.00 2.73
1310 1582 3.060000 CTCGGCCGGTTTTTCCCC 61.060 66.667 27.83 0.00 0.00 4.81
1462 3122 7.881775 AGGGAGTATGATTTTAGCGAAATTT 57.118 32.000 0.00 0.00 38.06 1.82
1477 3356 4.606961 CGAAATTTGTGTGGCTAACAGTT 58.393 39.130 0.00 0.00 40.26 3.16
1479 3358 2.861462 TTTGTGTGGCTAACAGTTGC 57.139 45.000 0.00 0.00 40.26 4.17
1492 3371 1.529244 AGTTGCCTCCCTTGCACAC 60.529 57.895 0.00 0.00 38.72 3.82
1495 3380 1.422977 TTGCCTCCCTTGCACACCTA 61.423 55.000 0.00 0.00 38.72 3.08
1550 3437 6.808704 CGACACAGATTCTCAAAATAGTCTCA 59.191 38.462 0.00 0.00 0.00 3.27
1562 3454 6.371548 TCAAAATAGTCTCAGTGGCATGTAAC 59.628 38.462 0.00 0.00 0.00 2.50
1607 3499 2.352323 GGTGGTTATTGGGTTGCTTTCG 60.352 50.000 0.00 0.00 0.00 3.46
1618 3543 3.985279 GGGTTGCTTTCGGTGTTATTTTC 59.015 43.478 0.00 0.00 0.00 2.29
1766 5619 2.754946 TTGGAATCTTTAGGCGACGT 57.245 45.000 0.00 0.00 0.00 4.34
1785 5638 5.456497 CGACGTCACTGTTAGTTGTAAAAGA 59.544 40.000 17.16 0.00 29.07 2.52
1787 5640 5.521372 ACGTCACTGTTAGTTGTAAAAGACC 59.479 40.000 0.00 0.00 29.07 3.85
2001 8882 0.744281 AGAGGTTGTGGCGTTTTTGG 59.256 50.000 0.00 0.00 0.00 3.28
2100 8996 8.014517 GCTAGAGAATGAGCTATGCAATTTAAC 58.985 37.037 0.00 0.00 35.73 2.01
2110 9006 5.626543 GCTATGCAATTTAACCATCATCACG 59.373 40.000 0.00 0.00 0.00 4.35
2189 9086 3.011119 TGTACCACCACAAGTTTGTCAC 58.989 45.455 0.00 0.00 39.91 3.67
2263 9160 1.617850 TGCTACCAAAAATGTGGGCAG 59.382 47.619 0.00 0.00 43.56 4.85
2281 9180 0.174162 AGACCGTACGTGCCCATTAC 59.826 55.000 15.21 0.00 0.00 1.89
2356 9255 9.244799 TGCTAGTAGTTTTATGTCGTTATCATG 57.755 33.333 0.00 0.00 0.00 3.07
2414 9316 2.418368 TGGATGGTAAGGATGTGCAC 57.582 50.000 10.75 10.75 0.00 4.57
2594 10267 7.874940 TGAAATTCAGTGGTTTGATTAGACAG 58.125 34.615 0.00 0.00 0.00 3.51
2639 10314 2.030096 TGACCGTTTGCACGTATGACTA 60.030 45.455 0.00 0.00 45.62 2.59
3695 12966 3.060020 GATCAGTTCGTCGCCGGGA 62.060 63.158 2.18 0.00 33.95 5.14
3965 13252 0.108804 ACTCGCACCACCATAACTCG 60.109 55.000 0.00 0.00 0.00 4.18
3971 13258 0.824759 ACCACCATAACTCGAGCTCC 59.175 55.000 13.61 0.00 0.00 4.70
3985 13272 4.683832 TCGAGCTCCTAGTGCTAAAATTC 58.316 43.478 8.47 0.00 41.30 2.17
3993 13280 6.235664 TCCTAGTGCTAAAATTCGTCCTTTT 58.764 36.000 0.00 0.00 0.00 2.27
4034 13321 1.000607 GAACCCGAGGTTTTTGGAAGC 60.001 52.381 9.31 0.00 46.95 3.86
4035 13322 0.185175 ACCCGAGGTTTTTGGAAGCT 59.815 50.000 0.00 0.00 27.29 3.74
4045 13332 3.624326 TTTTGGAAGCTGTTGACATCG 57.376 42.857 0.00 0.00 0.00 3.84
4088 13500 1.276421 CCCGCCAAGACATATAGAGGG 59.724 57.143 0.00 0.00 0.00 4.30
4089 13501 1.276421 CCGCCAAGACATATAGAGGGG 59.724 57.143 0.00 0.00 0.00 4.79
4090 13502 1.276421 CGCCAAGACATATAGAGGGGG 59.724 57.143 0.00 0.00 0.00 5.40
4094 13506 4.141251 GCCAAGACATATAGAGGGGGAAAA 60.141 45.833 0.00 0.00 0.00 2.29
4123 13535 6.608610 GTTGAATCAACGCAATAGTAAACCT 58.391 36.000 10.58 0.00 34.63 3.50
4161 13573 1.281656 GCAACAACGCCAGGTACAC 59.718 57.895 0.00 0.00 0.00 2.90
4163 13575 1.228033 AACAACGCCAGGTACACCC 60.228 57.895 0.00 0.00 36.42 4.61
4164 13576 2.359478 CAACGCCAGGTACACCCC 60.359 66.667 0.00 0.00 36.42 4.95
4165 13577 2.528378 AACGCCAGGTACACCCCT 60.528 61.111 0.00 0.00 36.42 4.79
4167 13579 0.619543 AACGCCAGGTACACCCCTAT 60.620 55.000 0.00 0.00 36.42 2.57
4168 13580 1.047034 ACGCCAGGTACACCCCTATC 61.047 60.000 0.00 0.00 36.42 2.08
4208 13639 0.109319 GTACCAAGCCGGCAATGTTG 60.109 55.000 31.54 23.18 39.03 3.33
4262 13700 2.408271 AGACGATGTTGCCATGACAT 57.592 45.000 0.00 0.00 40.27 3.06
4325 15691 0.323302 TATGTCGTCTTTGCAGGCCA 59.677 50.000 5.01 0.00 0.00 5.36
4612 16161 2.642139 AACTGACCGGTACACATACG 57.358 50.000 7.34 0.00 31.40 3.06
4736 16285 2.431942 GACGTGACGGCGGACATT 60.432 61.111 13.24 2.64 35.98 2.71
4766 16315 2.084681 CGCCGAGTACGTGAACACC 61.085 63.158 0.00 0.00 37.88 4.16
4904 18163 7.062839 GTCAGCAGTAACAAGAGAGACAATTAG 59.937 40.741 0.00 0.00 0.00 1.73
4941 18201 1.068417 TGTGTGAAAGCGTACGCCT 59.932 52.632 34.88 21.93 43.17 5.52
4968 18255 5.070047 AGGTATAGGCGCTACTTGTTGTATT 59.930 40.000 7.64 0.00 0.00 1.89
4974 18261 9.720769 ATAGGCGCTACTTGTTGTATTTATAAT 57.279 29.630 7.64 0.00 0.00 1.28
5053 18499 4.646040 TGTTGCATGATATCCCAAGAAAGG 59.354 41.667 0.00 0.00 0.00 3.11
5371 18906 1.065709 ACGGGAATACTCGGTGCATTT 60.066 47.619 0.00 0.00 45.17 2.32
5413 19013 9.169592 TGGTTGTAATTGGAAATTACTAGCTAC 57.830 33.333 23.59 14.32 38.01 3.58
5584 19187 5.124776 CGAGGAATAAGCAACCAAATAACCA 59.875 40.000 0.00 0.00 0.00 3.67
5735 19347 1.004200 GTGGTAGGTTGGGGTGTCG 60.004 63.158 0.00 0.00 0.00 4.35
5750 19367 1.005037 GTCGCATCCACACTCCACA 60.005 57.895 0.00 0.00 0.00 4.17
5795 19412 2.449031 AAATGGCTCACGACCTCGCA 62.449 55.000 0.00 0.00 44.43 5.10
5800 19418 1.208358 CTCACGACCTCGCACGTTA 59.792 57.895 0.00 0.00 44.43 3.18
5812 19466 1.498865 GCACGTTATCCCGCTCATGG 61.499 60.000 0.00 0.00 0.00 3.66
5825 19479 4.385825 CCGCTCATGGGTTTAGCTTAATA 58.614 43.478 0.00 0.00 34.03 0.98
5843 19497 8.137437 AGCTTAATACATCCATGTTACAATTGC 58.863 33.333 5.05 0.00 41.97 3.56
5868 19522 8.414923 GCAAAGTTTACATTAAGCTACGAAAAC 58.585 33.333 0.00 0.00 0.00 2.43
5876 19530 5.840940 TTAAGCTACGAAAACTCTCAAGC 57.159 39.130 0.00 0.00 0.00 4.01
5877 19531 3.386768 AGCTACGAAAACTCTCAAGCA 57.613 42.857 0.00 0.00 0.00 3.91
5883 19537 2.411748 CGAAAACTCTCAAGCATGCGTA 59.588 45.455 13.01 0.42 0.00 4.42
5912 19566 2.402787 GTCCTCGCGTCGTCCTAC 59.597 66.667 5.77 0.00 0.00 3.18
5913 19567 2.046988 TCCTCGCGTCGTCCTACA 60.047 61.111 5.77 0.00 0.00 2.74
5916 19570 1.060622 CTCGCGTCGTCCTACACTC 59.939 63.158 5.77 0.00 0.00 3.51
5955 19609 2.486918 TGCATATTGATGACGCAGAGG 58.513 47.619 0.00 0.00 34.73 3.69
5961 19615 0.813821 TGATGACGCAGAGGAGACAG 59.186 55.000 0.00 0.00 0.00 3.51
5982 19636 6.631016 ACAGACGTGTACATCAGTTGATTAT 58.369 36.000 0.00 0.00 34.05 1.28
5983 19637 6.752351 ACAGACGTGTACATCAGTTGATTATC 59.248 38.462 0.00 0.00 34.05 1.75
5984 19638 6.975197 CAGACGTGTACATCAGTTGATTATCT 59.025 38.462 0.00 0.00 31.21 1.98
5985 19639 6.975197 AGACGTGTACATCAGTTGATTATCTG 59.025 38.462 0.00 0.00 31.21 2.90
5986 19640 5.520288 ACGTGTACATCAGTTGATTATCTGC 59.480 40.000 0.00 0.00 31.21 4.26
5987 19641 5.331830 CGTGTACATCAGTTGATTATCTGCG 60.332 44.000 0.00 0.00 31.21 5.18
5988 19642 5.748630 GTGTACATCAGTTGATTATCTGCGA 59.251 40.000 0.00 0.00 31.21 5.10
5989 19643 6.255670 GTGTACATCAGTTGATTATCTGCGAA 59.744 38.462 0.00 0.00 31.21 4.70
5990 19644 6.816140 TGTACATCAGTTGATTATCTGCGAAA 59.184 34.615 0.00 0.00 31.21 3.46
5991 19645 6.741992 ACATCAGTTGATTATCTGCGAAAA 57.258 33.333 0.00 0.00 31.21 2.29
5992 19646 6.546395 ACATCAGTTGATTATCTGCGAAAAC 58.454 36.000 0.00 0.00 31.21 2.43
5993 19647 6.372659 ACATCAGTTGATTATCTGCGAAAACT 59.627 34.615 0.00 0.00 31.21 2.66
5994 19648 6.408858 TCAGTTGATTATCTGCGAAAACTC 57.591 37.500 0.00 0.00 0.00 3.01
5995 19649 6.166279 TCAGTTGATTATCTGCGAAAACTCT 58.834 36.000 0.00 0.00 0.00 3.24
5996 19650 6.650807 TCAGTTGATTATCTGCGAAAACTCTT 59.349 34.615 0.00 0.00 0.00 2.85
5997 19651 7.173218 TCAGTTGATTATCTGCGAAAACTCTTT 59.827 33.333 0.00 0.00 0.00 2.52
5998 19652 8.443160 CAGTTGATTATCTGCGAAAACTCTTTA 58.557 33.333 0.00 0.00 0.00 1.85
5999 19653 8.999431 AGTTGATTATCTGCGAAAACTCTTTAA 58.001 29.630 0.00 0.00 0.00 1.52
6000 19654 9.774742 GTTGATTATCTGCGAAAACTCTTTAAT 57.225 29.630 0.00 0.00 0.00 1.40
6002 19656 9.773328 TGATTATCTGCGAAAACTCTTTAATTG 57.227 29.630 0.00 0.00 0.00 2.32
6003 19657 9.774742 GATTATCTGCGAAAACTCTTTAATTGT 57.225 29.630 0.00 0.00 0.00 2.71
6006 19660 6.586751 TCTGCGAAAACTCTTTAATTGTACG 58.413 36.000 0.00 0.00 0.00 3.67
6007 19661 6.201425 TCTGCGAAAACTCTTTAATTGTACGT 59.799 34.615 0.00 0.00 0.00 3.57
6008 19662 6.130723 TGCGAAAACTCTTTAATTGTACGTG 58.869 36.000 0.00 0.00 0.00 4.49
6009 19663 6.018913 TGCGAAAACTCTTTAATTGTACGTGA 60.019 34.615 0.00 0.00 0.00 4.35
6010 19664 7.013529 GCGAAAACTCTTTAATTGTACGTGAT 58.986 34.615 0.00 0.00 0.00 3.06
6011 19665 7.213891 GCGAAAACTCTTTAATTGTACGTGATC 59.786 37.037 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.737844 TGGTATGCAATTGATTCATATAAGCTA 57.262 29.630 10.34 0.00 0.00 3.32
15 16 8.640063 TGGTATGCAATTGATTCATATAAGCT 57.360 30.769 10.34 0.00 0.00 3.74
16 17 9.865321 ATTGGTATGCAATTGATTCATATAAGC 57.135 29.630 10.34 0.00 0.00 3.09
51 52 1.541379 AGCCCGAACATGGTAAAACC 58.459 50.000 0.00 0.00 39.22 3.27
52 53 3.653539 AAAGCCCGAACATGGTAAAAC 57.346 42.857 0.00 0.00 0.00 2.43
53 54 3.006003 GGAAAAGCCCGAACATGGTAAAA 59.994 43.478 0.00 0.00 0.00 1.52
54 55 2.559231 GGAAAAGCCCGAACATGGTAAA 59.441 45.455 0.00 0.00 0.00 2.01
55 56 2.164338 GGAAAAGCCCGAACATGGTAA 58.836 47.619 0.00 0.00 0.00 2.85
56 57 1.828979 GGAAAAGCCCGAACATGGTA 58.171 50.000 0.00 0.00 0.00 3.25
57 58 2.653557 GGAAAAGCCCGAACATGGT 58.346 52.632 0.00 0.00 0.00 3.55
73 74 0.618458 CTCCACTTTTCCATCCGGGA 59.382 55.000 0.00 0.00 46.61 5.14
74 75 1.032114 GCTCCACTTTTCCATCCGGG 61.032 60.000 0.00 0.00 38.37 5.73
75 76 0.035056 AGCTCCACTTTTCCATCCGG 60.035 55.000 0.00 0.00 0.00 5.14
76 77 1.470098 CAAGCTCCACTTTTCCATCCG 59.530 52.381 0.00 0.00 36.04 4.18
77 78 2.751806 CTCAAGCTCCACTTTTCCATCC 59.248 50.000 0.00 0.00 36.04 3.51
78 79 2.163211 GCTCAAGCTCCACTTTTCCATC 59.837 50.000 0.00 0.00 36.04 3.51
79 80 2.165998 GCTCAAGCTCCACTTTTCCAT 58.834 47.619 0.00 0.00 36.04 3.41
80 81 1.609208 GCTCAAGCTCCACTTTTCCA 58.391 50.000 0.00 0.00 36.04 3.53
81 82 0.884514 GGCTCAAGCTCCACTTTTCC 59.115 55.000 1.46 0.00 41.70 3.13
82 83 0.884514 GGGCTCAAGCTCCACTTTTC 59.115 55.000 1.46 0.00 41.70 2.29
83 84 0.185901 TGGGCTCAAGCTCCACTTTT 59.814 50.000 0.00 0.00 41.95 2.27
84 85 0.251077 CTGGGCTCAAGCTCCACTTT 60.251 55.000 0.00 0.00 41.95 2.66
85 86 1.377994 CTGGGCTCAAGCTCCACTT 59.622 57.895 0.00 0.00 41.95 3.16
86 87 3.076092 CTGGGCTCAAGCTCCACT 58.924 61.111 0.00 0.00 41.95 4.00
87 88 2.749441 GCTGGGCTCAAGCTCCAC 60.749 66.667 0.00 0.00 41.95 4.02
88 89 4.039092 GGCTGGGCTCAAGCTCCA 62.039 66.667 0.00 5.82 41.95 3.86
89 90 3.726144 AGGCTGGGCTCAAGCTCC 61.726 66.667 0.00 1.28 41.95 4.70
90 91 2.438075 CAGGCTGGGCTCAAGCTC 60.438 66.667 6.61 0.00 43.24 4.09
91 92 1.860944 ATTCAGGCTGGGCTCAAGCT 61.861 55.000 15.73 0.00 41.70 3.74
92 93 1.379576 ATTCAGGCTGGGCTCAAGC 60.380 57.895 15.73 0.00 41.14 4.01
93 94 0.323178 ACATTCAGGCTGGGCTCAAG 60.323 55.000 15.73 0.90 0.00 3.02
94 95 0.322816 GACATTCAGGCTGGGCTCAA 60.323 55.000 15.73 0.81 0.00 3.02
95 96 1.300963 GACATTCAGGCTGGGCTCA 59.699 57.895 15.73 0.00 0.00 4.26
96 97 0.747283 CTGACATTCAGGCTGGGCTC 60.747 60.000 15.73 5.17 40.71 4.70
97 98 1.302285 CTGACATTCAGGCTGGGCT 59.698 57.895 15.73 0.00 40.71 5.19
98 99 3.915575 CTGACATTCAGGCTGGGC 58.084 61.111 15.73 0.74 40.71 5.36
107 108 2.475666 GCCAGACAGCCTGACATTC 58.524 57.895 0.00 0.00 45.78 2.67
265 267 8.990163 ACAAAACTCCCGAATATAATAACCAT 57.010 30.769 0.00 0.00 0.00 3.55
274 276 6.658188 TCCAAAAACAAAACTCCCGAATAT 57.342 33.333 0.00 0.00 0.00 1.28
276 278 5.346181 TTCCAAAAACAAAACTCCCGAAT 57.654 34.783 0.00 0.00 0.00 3.34
294 359 5.885352 TCAAAAGAAGACTGTTGTGATTCCA 59.115 36.000 0.00 0.00 40.93 3.53
358 423 6.869913 ACCAACATAAGCTCAATTCATTGTTG 59.130 34.615 0.00 0.00 41.27 3.33
377 442 5.592282 TCACAAGAAATCTAAGCAACCAACA 59.408 36.000 0.00 0.00 0.00 3.33
442 507 0.322816 AGGAACGCACCATCATGCTT 60.323 50.000 1.50 0.00 43.80 3.91
443 508 1.028330 CAGGAACGCACCATCATGCT 61.028 55.000 1.50 0.00 43.80 3.79
445 510 0.392863 TCCAGGAACGCACCATCATG 60.393 55.000 0.00 0.00 0.00 3.07
449 514 2.026262 ACTAAATCCAGGAACGCACCAT 60.026 45.455 0.00 0.00 0.00 3.55
451 516 2.109425 ACTAAATCCAGGAACGCACC 57.891 50.000 0.00 0.00 0.00 5.01
454 519 2.548480 GCCATACTAAATCCAGGAACGC 59.452 50.000 0.00 0.00 0.00 4.84
455 520 3.804036 TGCCATACTAAATCCAGGAACG 58.196 45.455 0.00 0.00 0.00 3.95
462 527 2.350772 GCACGCATGCCATACTAAATCC 60.351 50.000 13.15 0.00 46.97 3.01
476 541 1.151668 GAAGTCTTGTCAGCACGCAT 58.848 50.000 0.00 0.00 0.00 4.73
477 542 0.179086 TGAAGTCTTGTCAGCACGCA 60.179 50.000 0.00 0.00 0.00 5.24
481 546 1.344438 ACCGATGAAGTCTTGTCAGCA 59.656 47.619 0.00 0.00 30.75 4.41
482 547 1.996191 GACCGATGAAGTCTTGTCAGC 59.004 52.381 0.00 0.00 0.00 4.26
483 548 3.057245 TGAGACCGATGAAGTCTTGTCAG 60.057 47.826 0.00 0.00 44.55 3.51
485 550 3.577649 TGAGACCGATGAAGTCTTGTC 57.422 47.619 0.00 0.00 44.55 3.18
499 564 2.740981 CAAGCAGACATGTCTTGAGACC 59.259 50.000 25.84 9.84 44.15 3.85
504 569 2.740981 GAGACCAAGCAGACATGTCTTG 59.259 50.000 25.84 20.26 37.98 3.02
620 692 8.811378 GTTTTTCCTCTTCTTTTCAGAAACATG 58.189 33.333 0.00 0.00 38.63 3.21
667 743 0.462759 GATCGAGGGGGTGAAAGCAG 60.463 60.000 0.00 0.00 34.77 4.24
692 768 3.498614 TTTCTTCCCCTCTCCATCTCT 57.501 47.619 0.00 0.00 0.00 3.10
906 1017 1.369091 CTACAAGGCCCGCACATGTC 61.369 60.000 0.00 0.00 0.00 3.06
907 1018 1.377202 CTACAAGGCCCGCACATGT 60.377 57.895 0.00 0.00 0.00 3.21
940 1052 1.682323 GGACATAGGAGGAGGTTCGAC 59.318 57.143 0.00 0.00 0.00 4.20
949 1061 2.096248 GAGGCGATAGGACATAGGAGG 58.904 57.143 0.00 0.00 0.00 4.30
950 1062 2.796557 TGAGGCGATAGGACATAGGAG 58.203 52.381 0.00 0.00 0.00 3.69
951 1063 2.971901 TGAGGCGATAGGACATAGGA 57.028 50.000 0.00 0.00 0.00 2.94
952 1064 2.098280 CGATGAGGCGATAGGACATAGG 59.902 54.545 0.00 0.00 0.00 2.57
953 1065 2.098280 CCGATGAGGCGATAGGACATAG 59.902 54.545 0.00 0.00 0.00 2.23
954 1066 2.092323 CCGATGAGGCGATAGGACATA 58.908 52.381 0.00 0.00 0.00 2.29
955 1067 0.891373 CCGATGAGGCGATAGGACAT 59.109 55.000 0.00 0.00 0.00 3.06
956 1068 0.467474 ACCGATGAGGCGATAGGACA 60.467 55.000 5.86 0.00 46.52 4.02
957 1069 0.241481 GACCGATGAGGCGATAGGAC 59.759 60.000 5.86 0.00 46.52 3.85
1020 1132 0.916086 AACTTCAGTGGGTGGTGTGA 59.084 50.000 0.00 0.00 0.00 3.58
1021 1133 2.158813 AGTAACTTCAGTGGGTGGTGTG 60.159 50.000 0.00 0.00 0.00 3.82
1022 1134 2.104281 GAGTAACTTCAGTGGGTGGTGT 59.896 50.000 0.00 0.00 0.00 4.16
1023 1135 2.104111 TGAGTAACTTCAGTGGGTGGTG 59.896 50.000 0.00 0.00 0.00 4.17
1288 1528 1.574702 GAAAAACCGGCCGAGACCAG 61.575 60.000 30.73 11.56 0.00 4.00
1300 1561 2.579657 CCAAGGGCGGGGAAAAACC 61.580 63.158 0.00 0.00 38.08 3.27
1310 1582 3.682885 TGCATGCAACCAAGGGCG 61.683 61.111 20.30 0.00 0.00 6.13
1436 3096 6.920569 TTTCGCTAAAATCATACTCCCTTC 57.079 37.500 0.00 0.00 0.00 3.46
1437 3097 7.881775 AATTTCGCTAAAATCATACTCCCTT 57.118 32.000 0.00 0.00 36.54 3.95
1477 3356 1.845664 TAGGTGTGCAAGGGAGGCA 60.846 57.895 0.00 0.00 39.32 4.75
1479 3358 0.693049 AAGTAGGTGTGCAAGGGAGG 59.307 55.000 0.00 0.00 0.00 4.30
1481 3360 3.054655 GGATAAAGTAGGTGTGCAAGGGA 60.055 47.826 0.00 0.00 0.00 4.20
1482 3361 3.279434 GGATAAAGTAGGTGTGCAAGGG 58.721 50.000 0.00 0.00 0.00 3.95
1521 3408 3.319137 TTTGAGAATCTGTGTCGGGAG 57.681 47.619 0.00 0.00 34.92 4.30
1550 3437 3.320826 GGGAAACAAAGTTACATGCCACT 59.679 43.478 0.00 0.00 0.00 4.00
1562 3454 7.557719 ACCATGTATGAATCTAGGGAAACAAAG 59.442 37.037 0.00 0.00 0.00 2.77
1607 3499 6.695713 GGCCGAATTTCATAGAAAATAACACC 59.304 38.462 0.00 0.00 0.00 4.16
1618 3543 6.272318 TGCAAATTAAGGCCGAATTTCATAG 58.728 36.000 21.74 14.65 34.93 2.23
1668 3603 7.412137 ACTTGTATTTGTTACGGTTGTACTC 57.588 36.000 0.00 0.00 33.15 2.59
1766 5619 5.991861 TGGGTCTTTTACAACTAACAGTGA 58.008 37.500 0.00 0.00 0.00 3.41
1785 5638 7.315066 TGACATATCACATGTATGTATGGGT 57.685 36.000 19.81 7.61 41.50 4.51
2001 8882 8.001549 CCAAATAAGCGAACAAACAACAATAAC 58.998 33.333 0.00 0.00 0.00 1.89
2100 8996 1.358877 TGCGAAAGACGTGATGATGG 58.641 50.000 0.00 0.00 44.60 3.51
2110 9006 6.663944 AGGTATTCACTATTTGCGAAAGAC 57.336 37.500 0.00 0.00 0.00 3.01
2263 9160 1.141591 CGTAATGGGCACGTACGGTC 61.142 60.000 21.06 9.94 34.74 4.79
2281 9180 9.834628 TTTTATTTCCTATTGCAAACTACTTCG 57.165 29.630 1.71 0.00 0.00 3.79
2356 9255 1.144057 ATAGCACACTAGCACGGCC 59.856 57.895 0.00 0.00 36.85 6.13
2414 9316 3.940209 TTGCAAAGCAAATGGTAGGAG 57.060 42.857 0.00 0.00 45.96 3.69
2601 10274 5.115480 ACGGTCAATTTTTGTTTTGCTGAT 58.885 33.333 0.00 0.00 0.00 2.90
2602 10275 4.499183 ACGGTCAATTTTTGTTTTGCTGA 58.501 34.783 0.00 0.00 0.00 4.26
2606 10279 5.282544 GTGCAAACGGTCAATTTTTGTTTTG 59.717 36.000 0.00 0.00 33.57 2.44
2639 10314 5.252547 ACAAGGTTCAAAAGCCAAACAATT 58.747 33.333 0.00 0.00 0.00 2.32
3372 12643 0.390472 CAGTGGTTCTCGAAGCCCTC 60.390 60.000 6.41 0.00 37.97 4.30
3551 12822 1.064003 ACTTCATGGGGCTGTACACA 58.936 50.000 0.00 0.00 0.00 3.72
3695 12966 1.688211 GAGGGCCTCCTGCTTCTTT 59.312 57.895 23.49 0.00 45.05 2.52
3965 13252 4.434520 ACGAATTTTAGCACTAGGAGCTC 58.565 43.478 14.28 4.71 42.32 4.09
3985 13272 7.625828 AGAGGTAAATCCATTAAAAAGGACG 57.374 36.000 0.00 0.00 36.60 4.79
3993 13280 6.661805 GGTTCCACAAGAGGTAAATCCATTAA 59.338 38.462 0.00 0.00 39.02 1.40
4059 13346 1.004595 GTCTTGGCGGGTATTTCGAC 58.995 55.000 0.00 0.00 35.97 4.20
4108 13520 2.028748 ACACGGAGGTTTACTATTGCGT 60.029 45.455 0.00 0.00 38.12 5.24
4119 13531 3.025924 TCTGTCGTACACGGAGGTT 57.974 52.632 1.39 0.00 35.25 3.50
4123 13535 1.471287 CCAATCTCTGTCGTACACGGA 59.529 52.381 1.39 0.52 38.15 4.69
4151 13563 2.249139 CTAGATAGGGGTGTACCTGGC 58.751 57.143 0.44 0.00 42.02 4.85
4164 13576 2.755655 CCGTGGATGCCTACCTAGATAG 59.244 54.545 0.00 0.00 0.00 2.08
4165 13577 2.556782 CCCGTGGATGCCTACCTAGATA 60.557 54.545 0.00 0.00 0.00 1.98
4167 13579 0.469331 CCCGTGGATGCCTACCTAGA 60.469 60.000 0.00 0.00 0.00 2.43
4168 13580 0.759436 ACCCGTGGATGCCTACCTAG 60.759 60.000 0.00 0.00 0.00 3.02
4208 13639 1.512926 TCTTTCGAGCCTTTGTGAGC 58.487 50.000 0.00 0.00 0.00 4.26
4262 13700 3.423539 AGCATCAACCAGTAAGCTTCA 57.576 42.857 0.00 0.00 0.00 3.02
4612 16161 0.389426 AATCAGCCACACGTACGTCC 60.389 55.000 19.94 7.33 0.00 4.79
4736 16285 1.741401 CTCGGCGCCAATCACTTCA 60.741 57.895 28.98 0.00 0.00 3.02
4941 18201 1.068588 CAAGTAGCGCCTATACCTGCA 59.931 52.381 2.29 0.00 0.00 4.41
5141 18662 5.886960 AACAATGCTGTATCTTCCAACTC 57.113 39.130 0.00 0.00 33.45 3.01
5176 18705 4.632153 AGCTAAGGACCATAAATAGCGTG 58.368 43.478 0.00 0.00 42.82 5.34
5413 19013 8.132995 TCATTACTTTAGCATGCATGATTTCTG 58.867 33.333 30.64 16.19 0.00 3.02
5584 19187 8.424133 TGAGCTGATGTATGTATTAAGACACAT 58.576 33.333 4.80 5.60 38.81 3.21
5672 19281 0.813184 TAACTAACTCTCACCCGCCG 59.187 55.000 0.00 0.00 0.00 6.46
5735 19347 0.537143 TGGTTGTGGAGTGTGGATGC 60.537 55.000 0.00 0.00 0.00 3.91
5750 19367 1.147600 GTTGGTGGGACGAGTGGTT 59.852 57.895 0.00 0.00 0.00 3.67
5812 19466 9.116067 TGTAACATGGATGTATTAAGCTAAACC 57.884 33.333 0.00 0.00 40.80 3.27
5825 19479 6.100404 ACTTTGCAATTGTAACATGGATGT 57.900 33.333 8.60 0.00 44.20 3.06
5843 19497 9.659830 AGTTTTCGTAGCTTAATGTAAACTTTG 57.340 29.630 7.34 0.00 34.33 2.77
5861 19515 1.195448 CGCATGCTTGAGAGTTTTCGT 59.805 47.619 17.13 0.00 0.00 3.85
5868 19522 1.195347 CGAGTACGCATGCTTGAGAG 58.805 55.000 17.13 0.80 0.00 3.20
5876 19530 1.742900 CGCAAGACCGAGTACGCATG 61.743 60.000 0.00 0.00 43.02 4.06
5877 19531 1.516386 CGCAAGACCGAGTACGCAT 60.516 57.895 0.00 0.00 43.02 4.73
5916 19570 2.229784 GCAGGAAACCAAACTCATGAGG 59.770 50.000 26.08 12.16 0.00 3.86
5927 19581 3.627123 CGTCATCAATATGCAGGAAACCA 59.373 43.478 0.00 0.00 32.76 3.67
5930 19584 3.277715 TGCGTCATCAATATGCAGGAAA 58.722 40.909 0.00 0.00 34.03 3.13
5955 19609 3.833545 ACTGATGTACACGTCTGTCTC 57.166 47.619 0.00 0.00 38.98 3.36
5961 19615 6.291849 GCAGATAATCAACTGATGTACACGTC 60.292 42.308 0.00 0.00 36.38 4.34
5982 19636 6.201425 ACGTACAATTAAAGAGTTTTCGCAGA 59.799 34.615 0.00 0.00 0.00 4.26
5983 19637 6.299966 CACGTACAATTAAAGAGTTTTCGCAG 59.700 38.462 0.00 0.00 0.00 5.18
5984 19638 6.018913 TCACGTACAATTAAAGAGTTTTCGCA 60.019 34.615 0.00 0.00 0.00 5.10
5985 19639 6.357198 TCACGTACAATTAAAGAGTTTTCGC 58.643 36.000 0.00 0.00 0.00 4.70
5986 19640 8.570123 GATCACGTACAATTAAAGAGTTTTCG 57.430 34.615 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.