Multiple sequence alignment - TraesCS3A01G117900

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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 TraesCS3A01G117900 chr3A 100.000 4891 0 0 1 4891 88552433 88547543 0.000000e+00 9033.0
1 TraesCS3A01G117900 chr3A 95.302 149 5 2 1446 1593 88550841 88550988 8.180000e-58 235.0
2 TraesCS3A01G117900 chr3D 95.780 3389 122 17 1520 4891 75148341 75144957 0.000000e+00 5446.0
3 TraesCS3A01G117900 chr3D 87.730 489 30 7 914 1387 75150756 75150283 1.200000e-150 544.0
4 TraesCS3A01G117900 chr3D 89.796 98 9 1 2 99 379001517 379001613 1.850000e-24 124.0
5 TraesCS3A01G117900 chr3D 98.551 69 1 0 1446 1514 75148268 75148336 6.650000e-24 122.0
6 TraesCS3A01G117900 chr3B 93.884 2093 89 16 1900 3963 120623372 120621290 0.000000e+00 3120.0
7 TraesCS3A01G117900 chr3B 87.298 1236 105 21 1606 2824 121468353 121467153 0.000000e+00 1365.0
8 TraesCS3A01G117900 chr3B 93.556 869 33 10 4032 4891 120621297 120620443 0.000000e+00 1273.0
9 TraesCS3A01G117900 chr3B 93.000 300 19 2 1139 1437 121482351 121482053 2.090000e-118 436.0
10 TraesCS3A01G117900 chr3B 90.397 302 28 1 1520 1820 120623673 120623372 3.550000e-106 396.0
11 TraesCS3A01G117900 chr3B 86.420 324 24 5 827 1138 120627818 120627503 2.180000e-88 337.0
12 TraesCS3A01G117900 chr3B 86.420 324 24 5 827 1138 120654384 120654069 2.180000e-88 337.0
13 TraesCS3A01G117900 chr3B 85.489 317 28 5 849 1155 121482677 121482369 1.020000e-81 315.0
14 TraesCS3A01G117900 chr3B 83.333 90 14 1 1796 1884 808274217 808274128 1.130000e-11 82.4
15 TraesCS3A01G117900 chr5D 77.538 650 82 30 96 733 331209534 331208937 2.820000e-87 333.0
16 TraesCS3A01G117900 chr5D 88.889 99 10 1 1 99 285024604 285024701 2.390000e-23 121.0
17 TraesCS3A01G117900 chr5D 82.667 75 11 2 3811 3884 406974003 406974076 1.140000e-06 65.8
18 TraesCS3A01G117900 chr1B 77.258 620 103 31 146 733 273506317 273506930 3.650000e-86 329.0
19 TraesCS3A01G117900 chr1A 79.223 515 75 26 212 706 524282705 524282203 3.650000e-86 329.0
20 TraesCS3A01G117900 chr1A 91.000 100 7 2 9 108 277004089 277004186 3.070000e-27 134.0
21 TraesCS3A01G117900 chr1A 90.909 99 7 1 2 100 485564173 485564269 1.100000e-26 132.0
22 TraesCS3A01G117900 chr7A 77.201 443 72 21 101 524 641446628 641446196 1.060000e-56 231.0
23 TraesCS3A01G117900 chr7A 87.129 101 8 3 636 734 634475131 634475228 5.180000e-20 110.0
24 TraesCS3A01G117900 chr7A 86.316 95 11 2 635 728 157949156 157949249 8.660000e-18 102.0
25 TraesCS3A01G117900 chr4B 81.333 300 43 12 230 522 67738600 67738893 1.060000e-56 231.0
26 TraesCS3A01G117900 chr7D 82.353 272 40 7 256 521 265266006 265266275 3.810000e-56 230.0
27 TraesCS3A01G117900 chr4D 81.985 272 40 8 256 520 451691978 451691709 6.370000e-54 222.0
28 TraesCS3A01G117900 chr4D 72.368 456 101 18 3267 3707 497647685 497648130 2.390000e-23 121.0
29 TraesCS3A01G117900 chr4D 80.142 141 21 6 3273 3411 497669062 497668927 1.120000e-16 99.0
30 TraesCS3A01G117900 chr5A 81.000 300 35 14 440 733 431668106 431667823 8.240000e-53 219.0
31 TraesCS3A01G117900 chr5A 91.262 103 8 1 1 103 440673156 440673257 6.600000e-29 139.0
32 TraesCS3A01G117900 chr5A 92.632 95 7 0 3332 3426 485602691 485602597 2.370000e-28 137.0
33 TraesCS3A01G117900 chr5A 72.588 456 100 18 3267 3707 677950660 677951105 5.140000e-25 126.0
34 TraesCS3A01G117900 chr5A 89.796 98 9 1 3 100 632873096 632873192 1.850000e-24 124.0
35 TraesCS3A01G117900 chr5A 89.535 86 8 1 1817 1901 559514677 559514592 1.860000e-19 108.0
36 TraesCS3A01G117900 chr5A 86.022 93 12 1 1817 1908 611977942 611977850 1.120000e-16 99.0
37 TraesCS3A01G117900 chr5A 97.143 35 1 0 3850 3884 512620813 512620779 5.290000e-05 60.2
38 TraesCS3A01G117900 chr6D 81.319 273 43 8 256 522 143660473 143660203 1.070000e-51 215.0
39 TraesCS3A01G117900 chr5B 81.716 268 35 12 256 514 398440651 398440389 1.380000e-50 211.0
40 TraesCS3A01G117900 chr5B 92.000 100 7 1 1 99 28481299 28481398 6.600000e-29 139.0
41 TraesCS3A01G117900 chr5B 88.679 106 12 0 3321 3426 461639910 461639805 3.970000e-26 130.0
42 TraesCS3A01G117900 chr5B 87.736 106 13 0 3321 3426 461861887 461861782 1.850000e-24 124.0
43 TraesCS3A01G117900 chr5B 97.143 35 1 0 3850 3884 488115405 488115371 5.290000e-05 60.2
44 TraesCS3A01G117900 chr2D 81.071 280 34 17 256 522 21014006 21013733 6.420000e-49 206.0
45 TraesCS3A01G117900 chr2D 88.095 84 10 0 1817 1900 629438877 629438794 3.120000e-17 100.0
46 TraesCS3A01G117900 chr2D 85.393 89 12 1 1813 1900 84679937 84679849 1.870000e-14 91.6
47 TraesCS3A01G117900 chr6A 91.753 97 8 0 2 98 16446998 16447094 8.540000e-28 135.0
48 TraesCS3A01G117900 chr6A 93.590 78 5 0 1817 1894 548408060 548408137 3.090000e-22 117.0
49 TraesCS3A01G117900 chr4A 89.524 105 9 2 1 105 624353253 624353355 1.100000e-26 132.0
50 TraesCS3A01G117900 chr6B 86.747 83 11 0 1817 1899 538070732 538070650 5.210000e-15 93.5


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 TraesCS3A01G117900 chr3A 88547543 88552433 4890 True 9033.0 9033 100.00000 1 4891 1 chr3A.!!$R1 4890
1 TraesCS3A01G117900 chr3D 75144957 75150756 5799 True 2995.0 5446 91.75500 914 4891 2 chr3D.!!$R1 3977
2 TraesCS3A01G117900 chr3B 121467153 121468353 1200 True 1365.0 1365 87.29800 1606 2824 1 chr3B.!!$R2 1218
3 TraesCS3A01G117900 chr3B 120620443 120627818 7375 True 1281.5 3120 91.06425 827 4891 4 chr3B.!!$R4 4064
4 TraesCS3A01G117900 chr3B 121482053 121482677 624 True 375.5 436 89.24450 849 1437 2 chr3B.!!$R5 588
5 TraesCS3A01G117900 chr5D 331208937 331209534 597 True 333.0 333 77.53800 96 733 1 chr5D.!!$R1 637
6 TraesCS3A01G117900 chr1B 273506317 273506930 613 False 329.0 329 77.25800 146 733 1 chr1B.!!$F1 587
7 TraesCS3A01G117900 chr1A 524282203 524282705 502 True 329.0 329 79.22300 212 706 1 chr1A.!!$R1 494

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
843 1050 0.036306 ATCACGGGTGTGTTTCTCCC 59.964 55.000 0.00 0.00 46.49 4.30 F
1033 1252 0.311165 GCTCATGTGGATGCAGCATC 59.689 55.000 25.16 25.16 39.87 3.91 F
1065 1284 1.078426 CCAGATCCAACCCCACGTC 60.078 63.158 0.00 0.00 0.00 4.34 F
1439 4078 1.268352 TGGCGCAAAACCACAATAGTC 59.732 47.619 10.83 0.00 30.29 2.59 F
1441 4080 1.268352 GCGCAAAACCACAATAGTCCA 59.732 47.619 0.30 0.00 0.00 4.02 F
1442 4081 2.287909 GCGCAAAACCACAATAGTCCAA 60.288 45.455 0.30 0.00 0.00 3.53 F
2855 7382 2.289444 CGAGTTAGGGTGCCTTCTTTCA 60.289 50.000 0.00 0.00 34.61 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 6771 0.813184 CTTGTAGAGGCGACCGGTTA 59.187 55.000 9.42 0.0 0.00 2.85 R
2320 6826 0.924823 ATGAGCCCAGATTTCCTGCT 59.075 50.000 0.00 0.0 41.57 4.24 R
2716 7240 2.890311 AGATCCCGAATTGTGTTTGCAA 59.110 40.909 0.00 0.0 0.00 4.08 R
3152 7679 2.396590 TTACCGCCAAAGATGAGGTC 57.603 50.000 0.00 0.0 38.06 3.85 R
3303 7831 2.949963 GCCCCTGCTGATACCATGAAAA 60.950 50.000 0.00 0.0 33.53 2.29 R
3414 7942 6.496565 ACACTAGATATCCTTGGGAAGATGAG 59.503 42.308 0.00 0.0 34.34 2.90 R
4251 8788 0.690762 TCCCAACCTCAGGCAGTTAC 59.309 55.000 0.00 0.0 0.00 2.50 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
47 48 9.893305 ATAGAAATTCGGTCAAACTTTGTAAAG 57.107 29.630 2.94 2.94 41.73 1.85
76 77 9.594478 TGACTTGATAAAAATCTAATACGCAGA 57.406 29.630 0.00 0.00 0.00 4.26
78 79 9.601217 ACTTGATAAAAATCTAATACGCAGAGT 57.399 29.630 0.00 0.00 0.00 3.24
86 87 9.444600 AAAATCTAATACGCAGAGTAAAAAGGA 57.555 29.630 0.00 0.00 39.04 3.36
87 88 8.421673 AATCTAATACGCAGAGTAAAAAGGAC 57.578 34.615 0.00 0.00 39.04 3.85
88 89 6.335777 TCTAATACGCAGAGTAAAAAGGACC 58.664 40.000 0.00 0.00 39.04 4.46
89 90 1.792006 ACGCAGAGTAAAAAGGACCG 58.208 50.000 0.00 0.00 0.00 4.79
90 91 1.342174 ACGCAGAGTAAAAAGGACCGA 59.658 47.619 0.00 0.00 0.00 4.69
91 92 2.224113 ACGCAGAGTAAAAAGGACCGAA 60.224 45.455 0.00 0.00 0.00 4.30
92 93 2.412089 CGCAGAGTAAAAAGGACCGAAG 59.588 50.000 0.00 0.00 0.00 3.79
93 94 7.791857 TACGCAGAGTAAAAAGGACCGAAGG 62.792 48.000 0.00 0.00 43.51 3.46
112 113 4.883021 AGGGAGTACTAGGATCAAGACA 57.117 45.455 0.00 0.00 0.00 3.41
123 124 5.073437 AGGATCAAGACATACTAGAGGCT 57.927 43.478 0.00 0.00 0.00 4.58
125 126 6.799827 AGGATCAAGACATACTAGAGGCTAT 58.200 40.000 0.00 0.00 0.00 2.97
127 128 6.889722 GGATCAAGACATACTAGAGGCTATCT 59.110 42.308 0.00 0.00 42.47 1.98
128 129 8.050325 GGATCAAGACATACTAGAGGCTATCTA 58.950 40.741 0.00 0.33 39.64 1.98
143 144 2.420058 ATCTAAGCCAGTTTTCCCCG 57.580 50.000 0.00 0.00 0.00 5.73
452 618 9.651913 ACTTGTTCACATTTTTCAAATAGTTGT 57.348 25.926 2.43 0.00 36.07 3.32
455 621 9.645059 TGTTCACATTTTTCAAATAGTTGTTCA 57.355 25.926 2.43 0.00 36.07 3.18
458 624 8.802856 TCACATTTTTCAAATAGTTGTTCAACG 58.197 29.630 2.43 0.00 36.07 4.10
459 625 8.591312 CACATTTTTCAAATAGTTGTTCAACGT 58.409 29.630 2.43 0.00 36.07 3.99
460 626 8.591312 ACATTTTTCAAATAGTTGTTCAACGTG 58.409 29.630 2.43 7.40 36.07 4.49
622 822 9.578439 TTAAATTAAAAAGGAAACCGAAAACGA 57.422 25.926 0.00 0.00 0.00 3.85
750 957 4.982749 GGTATAGCCGCGCCCACC 62.983 72.222 0.00 0.00 0.00 4.61
751 958 4.230002 GTATAGCCGCGCCCACCA 62.230 66.667 0.00 0.00 0.00 4.17
752 959 3.471806 TATAGCCGCGCCCACCAA 61.472 61.111 0.00 0.00 0.00 3.67
753 960 3.032667 TATAGCCGCGCCCACCAAA 62.033 57.895 0.00 0.00 0.00 3.28
762 969 2.600173 CCCACCAAACACGCCCAT 60.600 61.111 0.00 0.00 0.00 4.00
763 970 2.635443 CCCACCAAACACGCCCATC 61.635 63.158 0.00 0.00 0.00 3.51
764 971 2.560861 CACCAAACACGCCCATCG 59.439 61.111 0.00 0.00 45.38 3.84
765 972 1.963855 CACCAAACACGCCCATCGA 60.964 57.895 0.00 0.00 41.67 3.59
766 973 1.671054 ACCAAACACGCCCATCGAG 60.671 57.895 0.00 0.00 41.67 4.04
767 974 2.398554 CCAAACACGCCCATCGAGG 61.399 63.158 0.00 0.00 41.67 4.63
775 982 4.722193 CCCATCGAGGCTGTTGTT 57.278 55.556 0.00 0.00 35.39 2.83
776 983 2.174334 CCCATCGAGGCTGTTGTTG 58.826 57.895 0.00 0.00 35.39 3.33
777 984 0.606401 CCCATCGAGGCTGTTGTTGT 60.606 55.000 0.00 0.00 35.39 3.32
778 985 1.238439 CCATCGAGGCTGTTGTTGTT 58.762 50.000 0.00 0.00 0.00 2.83
779 986 1.069022 CCATCGAGGCTGTTGTTGTTG 60.069 52.381 0.00 0.00 0.00 3.33
780 987 1.069022 CATCGAGGCTGTTGTTGTTGG 60.069 52.381 0.00 0.00 0.00 3.77
781 988 0.179234 TCGAGGCTGTTGTTGTTGGA 59.821 50.000 0.00 0.00 0.00 3.53
782 989 0.588252 CGAGGCTGTTGTTGTTGGAG 59.412 55.000 0.00 0.00 0.00 3.86
783 990 1.680338 GAGGCTGTTGTTGTTGGAGT 58.320 50.000 0.00 0.00 0.00 3.85
784 991 1.334869 GAGGCTGTTGTTGTTGGAGTG 59.665 52.381 0.00 0.00 0.00 3.51
785 992 1.102978 GGCTGTTGTTGTTGGAGTGT 58.897 50.000 0.00 0.00 0.00 3.55
786 993 1.476488 GGCTGTTGTTGTTGGAGTGTT 59.524 47.619 0.00 0.00 0.00 3.32
787 994 2.094234 GGCTGTTGTTGTTGGAGTGTTT 60.094 45.455 0.00 0.00 0.00 2.83
788 995 3.584834 GCTGTTGTTGTTGGAGTGTTTT 58.415 40.909 0.00 0.00 0.00 2.43
789 996 3.993736 GCTGTTGTTGTTGGAGTGTTTTT 59.006 39.130 0.00 0.00 0.00 1.94
806 1013 2.333291 TTTTCCCGTCGAAAAGGCC 58.667 52.632 0.00 0.00 43.89 5.19
807 1014 1.174078 TTTTCCCGTCGAAAAGGCCC 61.174 55.000 0.00 0.00 43.89 5.80
808 1015 2.340673 TTTCCCGTCGAAAAGGCCCA 62.341 55.000 0.00 0.00 37.53 5.36
809 1016 2.281900 CCCGTCGAAAAGGCCCAA 60.282 61.111 0.00 0.00 0.00 4.12
810 1017 2.622962 CCCGTCGAAAAGGCCCAAC 61.623 63.158 0.00 0.00 0.00 3.77
811 1018 1.894756 CCGTCGAAAAGGCCCAACA 60.895 57.895 0.00 0.00 0.00 3.33
812 1019 1.574428 CGTCGAAAAGGCCCAACAG 59.426 57.895 0.00 0.00 0.00 3.16
813 1020 1.852067 CGTCGAAAAGGCCCAACAGG 61.852 60.000 0.00 0.00 39.47 4.00
833 1040 1.769733 CAGTTTTTGCATCACGGGTG 58.230 50.000 0.00 0.00 0.00 4.61
834 1041 1.066908 CAGTTTTTGCATCACGGGTGT 59.933 47.619 0.00 0.00 0.00 4.16
843 1050 0.036306 ATCACGGGTGTGTTTCTCCC 59.964 55.000 0.00 0.00 46.49 4.30
851 1058 1.192146 TGTGTTTCTCCCCCTCTCGG 61.192 60.000 0.00 0.00 0.00 4.63
956 1165 1.412710 AGAACGCTTGTCTGGACTTCA 59.587 47.619 2.38 0.00 0.00 3.02
991 1200 0.522180 ACCTCAGTCATCGTCGACAC 59.478 55.000 17.16 5.98 38.43 3.67
1022 1241 3.200593 GCTCCAGCGGCTCATGTG 61.201 66.667 0.00 0.00 0.00 3.21
1031 1250 1.751544 GGCTCATGTGGATGCAGCA 60.752 57.895 3.51 0.00 35.82 4.41
1032 1251 1.107538 GGCTCATGTGGATGCAGCAT 61.108 55.000 7.91 7.91 35.82 3.79
1033 1252 0.311165 GCTCATGTGGATGCAGCATC 59.689 55.000 25.16 25.16 39.87 3.91
1063 1282 1.377202 CACCAGATCCAACCCCACG 60.377 63.158 0.00 0.00 0.00 4.94
1064 1283 1.846124 ACCAGATCCAACCCCACGT 60.846 57.895 0.00 0.00 0.00 4.49
1065 1284 1.078426 CCAGATCCAACCCCACGTC 60.078 63.158 0.00 0.00 0.00 4.34
1066 1285 1.078426 CAGATCCAACCCCACGTCC 60.078 63.158 0.00 0.00 0.00 4.79
1067 1286 2.271173 GATCCAACCCCACGTCCC 59.729 66.667 0.00 0.00 0.00 4.46
1068 1287 3.335729 ATCCAACCCCACGTCCCC 61.336 66.667 0.00 0.00 0.00 4.81
1069 1288 4.902258 TCCAACCCCACGTCCCCA 62.902 66.667 0.00 0.00 0.00 4.96
1070 1289 4.653888 CCAACCCCACGTCCCCAC 62.654 72.222 0.00 0.00 0.00 4.61
1101 1320 3.305964 CTTCTTCTCTGTTTACGTCGCA 58.694 45.455 0.00 0.00 0.00 5.10
1151 3776 7.171630 TCACTGAGTTAAGAGTAGGGAATTC 57.828 40.000 0.00 0.00 0.00 2.17
1212 3837 8.763601 AGTAATAAGAAGAAACACAGATAGCCT 58.236 33.333 0.00 0.00 0.00 4.58
1224 3849 7.701539 ACACAGATAGCCTTAGATCTAGATG 57.298 40.000 10.74 0.00 31.09 2.90
1298 3937 2.149578 CCTGACACAAGAGCTCCTTTG 58.850 52.381 10.93 12.04 31.42 2.77
1321 3960 6.061441 TGTTTGTTTGAGCTCCATCTTAGAA 58.939 36.000 12.15 0.00 0.00 2.10
1342 3981 6.807789 AGAATCTATTTCTACTTGGTCGGAC 58.192 40.000 0.00 0.00 43.03 4.79
1372 4011 4.779696 AGGAAATTGCACAAAACACCAAT 58.220 34.783 0.00 0.00 0.00 3.16
1437 4076 2.288152 ACTTGGCGCAAAACCACAATAG 60.288 45.455 10.83 0.00 36.76 1.73
1438 4077 1.323412 TGGCGCAAAACCACAATAGT 58.677 45.000 10.83 0.00 30.29 2.12
1439 4078 1.268352 TGGCGCAAAACCACAATAGTC 59.732 47.619 10.83 0.00 30.29 2.59
1440 4079 1.402325 GGCGCAAAACCACAATAGTCC 60.402 52.381 10.83 0.00 0.00 3.85
1441 4080 1.268352 GCGCAAAACCACAATAGTCCA 59.732 47.619 0.30 0.00 0.00 4.02
1442 4081 2.287909 GCGCAAAACCACAATAGTCCAA 60.288 45.455 0.30 0.00 0.00 3.53
1443 4082 3.797184 GCGCAAAACCACAATAGTCCAAA 60.797 43.478 0.30 0.00 0.00 3.28
1444 4083 3.733727 CGCAAAACCACAATAGTCCAAAC 59.266 43.478 0.00 0.00 0.00 2.93
1445 4084 4.055360 GCAAAACCACAATAGTCCAAACC 58.945 43.478 0.00 0.00 0.00 3.27
1446 4085 4.442192 GCAAAACCACAATAGTCCAAACCA 60.442 41.667 0.00 0.00 0.00 3.67
1447 4086 4.929819 AAACCACAATAGTCCAAACCAC 57.070 40.909 0.00 0.00 0.00 4.16
1452 4091 4.700213 CCACAATAGTCCAAACCACCTTAG 59.300 45.833 0.00 0.00 0.00 2.18
1453 4092 5.313712 CACAATAGTCCAAACCACCTTAGT 58.686 41.667 0.00 0.00 0.00 2.24
1454 4093 5.411669 CACAATAGTCCAAACCACCTTAGTC 59.588 44.000 0.00 0.00 0.00 2.59
1456 4095 2.414612 AGTCCAAACCACCTTAGTCCA 58.585 47.619 0.00 0.00 0.00 4.02
1457 4096 2.781174 AGTCCAAACCACCTTAGTCCAA 59.219 45.455 0.00 0.00 0.00 3.53
1458 4097 3.203487 AGTCCAAACCACCTTAGTCCAAA 59.797 43.478 0.00 0.00 0.00 3.28
1462 4101 3.895041 CAAACCACCTTAGTCCAAACCAT 59.105 43.478 0.00 0.00 0.00 3.55
1465 4104 5.327737 ACCACCTTAGTCCAAACCATAAA 57.672 39.130 0.00 0.00 0.00 1.40
1467 4106 4.157840 CCACCTTAGTCCAAACCATAAAGC 59.842 45.833 0.00 0.00 0.00 3.51
1470 4109 4.399303 CCTTAGTCCAAACCATAAAGCCAG 59.601 45.833 0.00 0.00 0.00 4.85
1473 4112 3.153919 GTCCAAACCATAAAGCCAGTGA 58.846 45.455 0.00 0.00 0.00 3.41
1474 4113 3.572255 GTCCAAACCATAAAGCCAGTGAA 59.428 43.478 0.00 0.00 0.00 3.18
1475 4114 4.038642 GTCCAAACCATAAAGCCAGTGAAA 59.961 41.667 0.00 0.00 0.00 2.69
1476 4115 4.280677 TCCAAACCATAAAGCCAGTGAAAG 59.719 41.667 0.00 0.00 0.00 2.62
1477 4116 3.942130 AACCATAAAGCCAGTGAAAGC 57.058 42.857 0.00 0.00 0.00 3.51
1478 4117 3.160679 ACCATAAAGCCAGTGAAAGCT 57.839 42.857 0.00 0.00 42.40 3.74
1486 4125 4.858389 AAGCCAGTGAAAGCTTTCAGAGC 61.858 47.826 36.07 33.41 46.99 4.09
1500 4139 5.551760 TTTCAGAGCAGCACTTAAATAGC 57.448 39.130 0.00 0.00 0.00 2.97
1501 4140 4.478206 TCAGAGCAGCACTTAAATAGCT 57.522 40.909 0.00 0.00 39.63 3.32
1502 4141 4.836825 TCAGAGCAGCACTTAAATAGCTT 58.163 39.130 0.00 0.00 36.26 3.74
1506 5990 6.705381 CAGAGCAGCACTTAAATAGCTTCTAT 59.295 38.462 0.00 0.00 36.26 1.98
1507 5991 6.928492 AGAGCAGCACTTAAATAGCTTCTATC 59.072 38.462 0.00 0.00 36.26 2.08
1508 5992 6.825610 AGCAGCACTTAAATAGCTTCTATCT 58.174 36.000 0.00 0.00 36.26 1.98
1510 5994 7.772757 AGCAGCACTTAAATAGCTTCTATCTTT 59.227 33.333 0.00 0.00 36.26 2.52
1517 6001 9.430623 CTTAAATAGCTTCTATCTTTCCTAGGC 57.569 37.037 2.96 0.00 0.00 3.93
1518 6002 7.380423 AAATAGCTTCTATCTTTCCTAGGCA 57.620 36.000 2.96 0.00 0.00 4.75
1523 6007 3.995636 TCTATCTTTCCTAGGCACCACT 58.004 45.455 2.96 0.00 0.00 4.00
1526 6010 3.468071 TCTTTCCTAGGCACCACTAGA 57.532 47.619 2.96 0.00 42.40 2.43
1538 6023 4.572795 GGCACCACTAGAAAAGATAGAAGC 59.427 45.833 0.00 0.00 0.00 3.86
1603 6088 7.175990 GGTTTGGACTAAGGTGTTGATTTCATA 59.824 37.037 0.00 0.00 0.00 2.15
1616 6101 5.885230 TGATTTCATAACAGTGCTTCCTG 57.115 39.130 0.00 0.00 38.45 3.86
1688 6174 4.128925 TGACATTCTATCTGGTCTGTGC 57.871 45.455 0.00 0.00 0.00 4.57
1745 6231 6.199908 GCTCATGTCATGTATCTTCACTGTAC 59.800 42.308 12.54 0.00 0.00 2.90
1790 6276 7.154435 TGTTACACGGGCTTCTAGATATATC 57.846 40.000 4.42 4.42 0.00 1.63
1845 6331 4.075682 TCCAATCCAAAATAAGTGTCGCA 58.924 39.130 0.00 0.00 0.00 5.10
1876 6373 6.348540 GGACTATGGTTAGTTCAAAACTGCAG 60.349 42.308 13.48 13.48 42.84 4.41
2034 6532 6.449698 CATCTTGTTTGACTAAAATGCACCT 58.550 36.000 0.00 0.00 0.00 4.00
2061 6560 8.774586 ACTAACATTGTTGAATGTCAGTTACTC 58.225 33.333 12.30 0.00 45.35 2.59
2187 6689 3.303395 GCGCAATGCTCAATCTAACTACC 60.303 47.826 0.30 0.00 41.73 3.18
2231 6733 2.429610 AGCACGTAGTTCCGAATGGTAT 59.570 45.455 0.00 0.00 41.61 2.73
2257 6761 5.793457 CACTACGGCCTTATTTTTCTTTTCG 59.207 40.000 0.00 0.00 0.00 3.46
2293 6797 2.429610 GGTCGCCTCTACAAGTCCAATA 59.570 50.000 0.00 0.00 0.00 1.90
2320 6826 4.377021 ACTTTTCTCTAACACATGTGCGA 58.623 39.130 25.68 17.31 0.00 5.10
2524 7048 6.986817 AGTGATCTTGTCAGGATAATTTACCG 59.013 38.462 0.00 0.00 37.56 4.02
2716 7240 7.564660 TCCATGCTCAATTTTACTTAATGGGAT 59.435 33.333 0.00 0.00 34.19 3.85
2855 7382 2.289444 CGAGTTAGGGTGCCTTCTTTCA 60.289 50.000 0.00 0.00 34.61 2.69
2864 7391 4.522789 GGGTGCCTTCTTTCATGTTCTTTA 59.477 41.667 0.00 0.00 0.00 1.85
2904 7431 6.418226 GGTACTCACGTATTGCAAAGAGATAG 59.582 42.308 1.71 0.31 0.00 2.08
3152 7679 6.016024 TCCCAAATCTTGAAACTCTTGACATG 60.016 38.462 0.00 0.00 0.00 3.21
3280 7808 4.502431 CCGTTTTTACCTGGCAAATTCCTT 60.502 41.667 0.00 0.00 0.00 3.36
3303 7831 4.887071 TCACCTCAAGCACTTGTGTATTTT 59.113 37.500 10.05 0.00 41.16 1.82
3414 7942 5.391310 CCTTGATGTTGTCTGTAAGTCATGC 60.391 44.000 0.00 0.00 30.71 4.06
3595 8125 2.753043 GCCAGGACACTGCCATGG 60.753 66.667 7.63 7.63 43.53 3.66
3632 8162 2.611225 AGATCATCGGTTTCTGCTCC 57.389 50.000 0.00 0.00 0.00 4.70
3683 8213 0.856641 TTCTTGAGAACGCGGTTTCG 59.143 50.000 12.47 0.00 39.81 3.46
3744 8274 1.359848 GTGTTCGGATGGTGCTAGTG 58.640 55.000 0.00 0.00 0.00 2.74
3745 8275 0.249120 TGTTCGGATGGTGCTAGTGG 59.751 55.000 0.00 0.00 0.00 4.00
3784 8314 3.678289 TGAATATGATCATGGAAGCCCG 58.322 45.455 18.72 0.00 34.29 6.13
3791 8321 0.326595 TCATGGAAGCCCGTAAAGCA 59.673 50.000 0.00 0.00 34.29 3.91
3884 8414 1.808531 GCCAGTGCCATGCTGTTGAA 61.809 55.000 0.00 0.00 32.41 2.69
3963 8494 6.238130 GCTCGTTTCATTAAGTTATCTCACCC 60.238 42.308 0.00 0.00 0.00 4.61
4082 8614 2.104111 TGTTATAGAACCGCCTCATGGG 59.896 50.000 0.00 0.00 34.38 4.00
4144 8676 6.349860 CCAAGAACTTCTGCAATGATCATCAA 60.350 38.462 9.06 0.00 0.00 2.57
4145 8677 6.829229 AGAACTTCTGCAATGATCATCAAA 57.171 33.333 9.06 0.00 0.00 2.69
4146 8678 7.406031 AGAACTTCTGCAATGATCATCAAAT 57.594 32.000 9.06 0.00 0.00 2.32
4147 8679 7.481642 AGAACTTCTGCAATGATCATCAAATC 58.518 34.615 9.06 0.00 0.00 2.17
4148 8680 6.769134 ACTTCTGCAATGATCATCAAATCA 57.231 33.333 9.06 2.43 39.85 2.57
4251 8788 4.280819 ACAATACAACTTGATCCATGGGG 58.719 43.478 13.02 0.17 0.00 4.96
4311 8848 4.591498 ACATGCCCATTATGCAAAGATGAT 59.409 37.500 8.40 0.00 42.92 2.45
4340 8877 6.782000 AGCCCATAATATTTGCCACTGATAAA 59.218 34.615 0.00 0.00 0.00 1.40
4518 9066 4.695455 ACGTGGGAGACATTATTTCTGTTG 59.305 41.667 0.00 0.00 0.00 3.33
4704 9255 5.105917 CCCTTGAAATTTGGCGTACATACTT 60.106 40.000 0.00 0.00 0.00 2.24
4712 9263 9.820725 AAATTTGGCGTACATACTTGTAGTATA 57.179 29.630 0.00 0.00 39.26 1.47
4713 9264 9.991906 AATTTGGCGTACATACTTGTAGTATAT 57.008 29.630 0.00 0.00 39.26 0.86
4744 9300 4.010349 AGCTCTGCAAGTTTTATACACCC 58.990 43.478 0.00 0.00 33.76 4.61
4851 9407 1.965414 TGGGGTGATTAAGCAGGAGA 58.035 50.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 9.893305 CTTTACAAAGTTTGACCGAATTTCTAT 57.107 29.630 22.23 0.00 0.00 1.98
22 23 8.895737 ACTTTACAAAGTTTGACCGAATTTCTA 58.104 29.630 22.23 0.00 46.52 2.10
23 24 7.768240 ACTTTACAAAGTTTGACCGAATTTCT 58.232 30.769 22.23 0.00 46.52 2.52
24 25 7.980742 ACTTTACAAAGTTTGACCGAATTTC 57.019 32.000 22.23 0.00 46.52 2.17
50 51 9.594478 TCTGCGTATTAGATTTTTATCAAGTCA 57.406 29.630 0.00 0.00 0.00 3.41
52 53 9.601217 ACTCTGCGTATTAGATTTTTATCAAGT 57.399 29.630 0.00 0.00 0.00 3.16
60 61 9.444600 TCCTTTTTACTCTGCGTATTAGATTTT 57.555 29.630 0.00 0.00 0.00 1.82
61 62 8.880750 GTCCTTTTTACTCTGCGTATTAGATTT 58.119 33.333 0.00 0.00 0.00 2.17
62 63 7.494952 GGTCCTTTTTACTCTGCGTATTAGATT 59.505 37.037 0.00 0.00 0.00 2.40
63 64 6.985059 GGTCCTTTTTACTCTGCGTATTAGAT 59.015 38.462 0.00 0.00 0.00 1.98
64 65 6.335777 GGTCCTTTTTACTCTGCGTATTAGA 58.664 40.000 0.00 0.00 0.00 2.10
65 66 5.231568 CGGTCCTTTTTACTCTGCGTATTAG 59.768 44.000 0.00 0.00 0.00 1.73
66 67 5.104374 CGGTCCTTTTTACTCTGCGTATTA 58.896 41.667 0.00 0.00 0.00 0.98
67 68 3.930848 CGGTCCTTTTTACTCTGCGTATT 59.069 43.478 0.00 0.00 0.00 1.89
68 69 3.194116 TCGGTCCTTTTTACTCTGCGTAT 59.806 43.478 0.00 0.00 0.00 3.06
69 70 2.557924 TCGGTCCTTTTTACTCTGCGTA 59.442 45.455 0.00 0.00 0.00 4.42
70 71 1.342174 TCGGTCCTTTTTACTCTGCGT 59.658 47.619 0.00 0.00 0.00 5.24
71 72 2.074547 TCGGTCCTTTTTACTCTGCG 57.925 50.000 0.00 0.00 0.00 5.18
72 73 2.742589 CCTTCGGTCCTTTTTACTCTGC 59.257 50.000 0.00 0.00 0.00 4.26
73 74 3.007614 TCCCTTCGGTCCTTTTTACTCTG 59.992 47.826 0.00 0.00 0.00 3.35
74 75 3.245441 TCCCTTCGGTCCTTTTTACTCT 58.755 45.455 0.00 0.00 0.00 3.24
75 76 3.007723 ACTCCCTTCGGTCCTTTTTACTC 59.992 47.826 0.00 0.00 0.00 2.59
76 77 2.977580 ACTCCCTTCGGTCCTTTTTACT 59.022 45.455 0.00 0.00 0.00 2.24
77 78 3.413846 ACTCCCTTCGGTCCTTTTTAC 57.586 47.619 0.00 0.00 0.00 2.01
78 79 4.162651 AGTACTCCCTTCGGTCCTTTTTA 58.837 43.478 0.00 0.00 0.00 1.52
79 80 2.977580 AGTACTCCCTTCGGTCCTTTTT 59.022 45.455 0.00 0.00 0.00 1.94
80 81 2.617658 AGTACTCCCTTCGGTCCTTTT 58.382 47.619 0.00 0.00 0.00 2.27
81 82 2.322339 AGTACTCCCTTCGGTCCTTT 57.678 50.000 0.00 0.00 0.00 3.11
82 83 2.357986 CCTAGTACTCCCTTCGGTCCTT 60.358 54.545 0.00 0.00 0.00 3.36
83 84 1.214923 CCTAGTACTCCCTTCGGTCCT 59.785 57.143 0.00 0.00 0.00 3.85
84 85 1.213926 TCCTAGTACTCCCTTCGGTCC 59.786 57.143 0.00 0.00 0.00 4.46
85 86 2.725221 TCCTAGTACTCCCTTCGGTC 57.275 55.000 0.00 0.00 0.00 4.79
86 87 2.512896 TGATCCTAGTACTCCCTTCGGT 59.487 50.000 0.00 0.00 0.00 4.69
87 88 3.225177 TGATCCTAGTACTCCCTTCGG 57.775 52.381 0.00 0.00 0.00 4.30
88 89 4.276431 GTCTTGATCCTAGTACTCCCTTCG 59.724 50.000 0.00 0.00 0.00 3.79
89 90 5.202004 TGTCTTGATCCTAGTACTCCCTTC 58.798 45.833 0.00 0.00 0.00 3.46
90 91 5.208294 TGTCTTGATCCTAGTACTCCCTT 57.792 43.478 0.00 0.00 0.00 3.95
91 92 4.883021 TGTCTTGATCCTAGTACTCCCT 57.117 45.455 0.00 0.00 0.00 4.20
92 93 6.308566 AGTATGTCTTGATCCTAGTACTCCC 58.691 44.000 0.00 0.00 0.00 4.30
93 94 8.377034 TCTAGTATGTCTTGATCCTAGTACTCC 58.623 40.741 0.00 0.00 0.00 3.85
94 95 9.431887 CTCTAGTATGTCTTGATCCTAGTACTC 57.568 40.741 0.00 0.00 0.00 2.59
99 100 6.245408 AGCCTCTAGTATGTCTTGATCCTAG 58.755 44.000 0.00 0.00 0.00 3.02
107 108 7.696992 GCTTAGATAGCCTCTAGTATGTCTT 57.303 40.000 0.00 0.00 44.48 3.01
123 124 2.841881 ACGGGGAAAACTGGCTTAGATA 59.158 45.455 0.00 0.00 0.00 1.98
125 126 1.061546 ACGGGGAAAACTGGCTTAGA 58.938 50.000 0.00 0.00 0.00 2.10
127 128 2.368311 AAACGGGGAAAACTGGCTTA 57.632 45.000 0.00 0.00 0.00 3.09
128 129 1.491668 AAAACGGGGAAAACTGGCTT 58.508 45.000 0.00 0.00 0.00 4.35
435 601 8.591312 ACACGTTGAACAACTATTTGAAAAATG 58.409 29.630 14.31 0.00 39.08 2.32
436 602 8.696410 ACACGTTGAACAACTATTTGAAAAAT 57.304 26.923 14.31 0.00 39.08 1.82
437 603 8.522178 AACACGTTGAACAACTATTTGAAAAA 57.478 26.923 14.31 0.00 39.08 1.94
439 605 9.790389 ATAAACACGTTGAACAACTATTTGAAA 57.210 25.926 14.31 0.00 39.08 2.69
447 613 9.210329 TCATGTATATAAACACGTTGAACAACT 57.790 29.630 14.31 0.13 39.08 3.16
448 614 9.982291 ATCATGTATATAAACACGTTGAACAAC 57.018 29.630 7.51 7.51 37.92 3.32
450 616 9.372369 TGATCATGTATATAAACACGTTGAACA 57.628 29.630 0.00 0.00 30.75 3.18
693 900 2.452105 GTTATGCGAGACGAGAGGTTC 58.548 52.381 0.00 0.00 0.00 3.62
733 940 4.982749 GGTGGGCGCGGCTATACC 62.983 72.222 32.30 29.39 0.00 2.73
734 941 3.743534 TTGGTGGGCGCGGCTATAC 62.744 63.158 32.30 25.35 0.00 1.47
735 942 3.032667 TTTGGTGGGCGCGGCTATA 62.033 57.895 32.30 16.71 0.00 1.31
736 943 4.418328 TTTGGTGGGCGCGGCTAT 62.418 61.111 32.30 0.00 0.00 2.97
745 952 2.600173 ATGGGCGTGTTTGGTGGG 60.600 61.111 0.00 0.00 0.00 4.61
746 953 2.961768 GATGGGCGTGTTTGGTGG 59.038 61.111 0.00 0.00 0.00 4.61
747 954 1.911293 CTCGATGGGCGTGTTTGGTG 61.911 60.000 0.00 0.00 41.80 4.17
748 955 1.671054 CTCGATGGGCGTGTTTGGT 60.671 57.895 0.00 0.00 41.80 3.67
749 956 2.398554 CCTCGATGGGCGTGTTTGG 61.399 63.158 0.00 0.00 41.80 3.28
750 957 3.039202 GCCTCGATGGGCGTGTTTG 62.039 63.158 0.00 0.00 42.82 2.93
751 958 2.746277 GCCTCGATGGGCGTGTTT 60.746 61.111 0.00 0.00 42.82 2.83
758 965 0.606401 ACAACAACAGCCTCGATGGG 60.606 55.000 3.56 0.00 36.00 4.00
759 966 1.069022 CAACAACAACAGCCTCGATGG 60.069 52.381 0.00 0.00 39.35 3.51
760 967 1.069022 CCAACAACAACAGCCTCGATG 60.069 52.381 0.00 0.00 0.00 3.84
761 968 1.202758 TCCAACAACAACAGCCTCGAT 60.203 47.619 0.00 0.00 0.00 3.59
762 969 0.179234 TCCAACAACAACAGCCTCGA 59.821 50.000 0.00 0.00 0.00 4.04
763 970 0.588252 CTCCAACAACAACAGCCTCG 59.412 55.000 0.00 0.00 0.00 4.63
764 971 1.334869 CACTCCAACAACAACAGCCTC 59.665 52.381 0.00 0.00 0.00 4.70
765 972 1.340991 ACACTCCAACAACAACAGCCT 60.341 47.619 0.00 0.00 0.00 4.58
766 973 1.102978 ACACTCCAACAACAACAGCC 58.897 50.000 0.00 0.00 0.00 4.85
767 974 2.939460 AACACTCCAACAACAACAGC 57.061 45.000 0.00 0.00 0.00 4.40
789 996 1.601477 GGGCCTTTTCGACGGGAAA 60.601 57.895 0.84 0.41 42.75 3.13
790 997 2.032987 GGGCCTTTTCGACGGGAA 59.967 61.111 0.84 0.00 0.00 3.97
791 998 2.820400 TTGGGCCTTTTCGACGGGA 61.820 57.895 4.53 0.00 0.00 5.14
792 999 2.281900 TTGGGCCTTTTCGACGGG 60.282 61.111 4.53 0.00 0.00 5.28
793 1000 1.852067 CTGTTGGGCCTTTTCGACGG 61.852 60.000 4.53 0.00 0.00 4.79
794 1001 1.574428 CTGTTGGGCCTTTTCGACG 59.426 57.895 4.53 0.00 0.00 5.12
795 1002 1.956802 CCTGTTGGGCCTTTTCGAC 59.043 57.895 4.53 0.00 0.00 4.20
796 1003 4.492604 CCTGTTGGGCCTTTTCGA 57.507 55.556 4.53 0.00 0.00 3.71
805 1012 2.990642 GCAAAAACTGCCTGTTGGG 58.009 52.632 0.00 0.00 46.13 4.12
814 1021 1.066908 ACACCCGTGATGCAAAAACTG 59.933 47.619 0.96 0.00 0.00 3.16
815 1022 1.066908 CACACCCGTGATGCAAAAACT 59.933 47.619 0.96 0.00 46.80 2.66
816 1023 1.202359 ACACACCCGTGATGCAAAAAC 60.202 47.619 0.96 0.00 46.80 2.43
817 1024 1.107114 ACACACCCGTGATGCAAAAA 58.893 45.000 0.96 0.00 46.80 1.94
818 1025 1.107114 AACACACCCGTGATGCAAAA 58.893 45.000 0.96 0.00 46.80 2.44
819 1026 1.066303 GAAACACACCCGTGATGCAAA 59.934 47.619 0.96 0.00 46.80 3.68
820 1027 0.665835 GAAACACACCCGTGATGCAA 59.334 50.000 0.96 0.00 46.80 4.08
821 1028 0.179032 AGAAACACACCCGTGATGCA 60.179 50.000 0.96 0.00 46.80 3.96
822 1029 0.517316 GAGAAACACACCCGTGATGC 59.483 55.000 0.96 0.00 46.80 3.91
823 1030 1.156736 GGAGAAACACACCCGTGATG 58.843 55.000 0.96 0.00 46.80 3.07
824 1031 0.036306 GGGAGAAACACACCCGTGAT 59.964 55.000 0.96 0.00 46.80 3.06
825 1032 1.448497 GGGAGAAACACACCCGTGA 59.552 57.895 0.96 0.00 46.80 4.35
829 1036 1.134438 AGAGGGGGAGAAACACACCC 61.134 60.000 0.00 0.00 46.50 4.61
830 1037 0.325272 GAGAGGGGGAGAAACACACC 59.675 60.000 0.00 0.00 0.00 4.16
831 1038 0.037232 CGAGAGGGGGAGAAACACAC 60.037 60.000 0.00 0.00 0.00 3.82
832 1039 2.362242 CGAGAGGGGGAGAAACACA 58.638 57.895 0.00 0.00 0.00 3.72
956 1165 0.263172 AGGTGGAGACTCGGGATGAT 59.737 55.000 0.00 0.00 0.00 2.45
991 1200 0.109153 TGGAGCCCCATGATTCGATG 59.891 55.000 0.00 0.00 37.58 3.84
1004 1223 4.479993 ACATGAGCCGCTGGAGCC 62.480 66.667 0.00 0.00 37.91 4.70
1022 1241 2.952245 GCCGATGATGCTGCATCC 59.048 61.111 32.90 20.59 41.21 3.51
1063 1282 0.900421 AAGCTTACTACGGTGGGGAC 59.100 55.000 0.00 0.00 0.00 4.46
1064 1283 1.188863 GAAGCTTACTACGGTGGGGA 58.811 55.000 0.00 0.00 0.00 4.81
1065 1284 1.192428 AGAAGCTTACTACGGTGGGG 58.808 55.000 0.00 0.00 0.00 4.96
1066 1285 2.496470 AGAAGAAGCTTACTACGGTGGG 59.504 50.000 0.00 0.00 0.00 4.61
1067 1286 3.444388 AGAGAAGAAGCTTACTACGGTGG 59.556 47.826 0.00 0.00 0.00 4.61
1068 1287 4.082679 ACAGAGAAGAAGCTTACTACGGTG 60.083 45.833 0.00 0.00 0.00 4.94
1069 1288 4.080687 ACAGAGAAGAAGCTTACTACGGT 58.919 43.478 0.00 0.00 0.00 4.83
1070 1289 4.705337 ACAGAGAAGAAGCTTACTACGG 57.295 45.455 0.00 0.00 0.00 4.02
1073 1292 7.211966 ACGTAAACAGAGAAGAAGCTTACTA 57.788 36.000 0.00 0.00 0.00 1.82
1101 1320 5.196341 TCGATTCCTTTACGCAGATACAT 57.804 39.130 0.00 0.00 0.00 2.29
1151 3776 4.821805 TCCTTTTGCTTCCAAGTTACTCTG 59.178 41.667 0.00 0.00 31.52 3.35
1224 3849 6.652900 GGATGGCTAAGATGACTCTTAATTCC 59.347 42.308 0.00 0.00 42.11 3.01
1298 3937 6.560253 TTCTAAGATGGAGCTCAAACAAAC 57.440 37.500 17.19 3.87 0.00 2.93
1321 3960 6.540438 TTGTCCGACCAAGTAGAAATAGAT 57.460 37.500 0.00 0.00 0.00 1.98
1342 3981 9.008289 GTGTTTTGTGCAATTTCCTTTTATTTG 57.992 29.630 0.00 0.00 0.00 2.32
1372 4011 4.083003 GCATCAATCAAGTAACCCAACGAA 60.083 41.667 0.00 0.00 0.00 3.85
1416 4055 0.463620 ATTGTGGTTTTGCGCCAAGT 59.536 45.000 4.18 0.00 37.81 3.16
1437 4076 2.943036 TGGACTAAGGTGGTTTGGAC 57.057 50.000 0.00 0.00 0.00 4.02
1438 4077 3.558033 GTTTGGACTAAGGTGGTTTGGA 58.442 45.455 0.00 0.00 0.00 3.53
1439 4078 2.626266 GGTTTGGACTAAGGTGGTTTGG 59.374 50.000 0.00 0.00 0.00 3.28
1440 4079 3.292460 TGGTTTGGACTAAGGTGGTTTG 58.708 45.455 0.00 0.00 0.00 2.93
1441 4080 3.673543 TGGTTTGGACTAAGGTGGTTT 57.326 42.857 0.00 0.00 0.00 3.27
1442 4081 3.895704 ATGGTTTGGACTAAGGTGGTT 57.104 42.857 0.00 0.00 0.00 3.67
1443 4082 5.321927 CTTTATGGTTTGGACTAAGGTGGT 58.678 41.667 0.00 0.00 0.00 4.16
1444 4083 4.157840 GCTTTATGGTTTGGACTAAGGTGG 59.842 45.833 0.00 0.00 0.00 4.61
1445 4084 4.157840 GGCTTTATGGTTTGGACTAAGGTG 59.842 45.833 0.00 0.00 0.00 4.00
1446 4085 4.202631 TGGCTTTATGGTTTGGACTAAGGT 60.203 41.667 0.00 0.00 0.00 3.50
1447 4086 4.340617 TGGCTTTATGGTTTGGACTAAGG 58.659 43.478 0.00 0.00 0.00 2.69
1452 4091 3.153919 TCACTGGCTTTATGGTTTGGAC 58.846 45.455 0.00 0.00 0.00 4.02
1453 4092 3.517296 TCACTGGCTTTATGGTTTGGA 57.483 42.857 0.00 0.00 0.00 3.53
1454 4093 4.559153 CTTTCACTGGCTTTATGGTTTGG 58.441 43.478 0.00 0.00 0.00 3.28
1456 4095 3.897505 AGCTTTCACTGGCTTTATGGTTT 59.102 39.130 0.00 0.00 34.96 3.27
1457 4096 3.500343 AGCTTTCACTGGCTTTATGGTT 58.500 40.909 0.00 0.00 34.96 3.67
1458 4097 3.160679 AGCTTTCACTGGCTTTATGGT 57.839 42.857 0.00 0.00 34.96 3.55
1465 4104 2.502295 CTCTGAAAGCTTTCACTGGCT 58.498 47.619 32.86 0.00 41.88 4.75
1477 4116 5.353678 AGCTATTTAAGTGCTGCTCTGAAAG 59.646 40.000 16.73 7.85 35.54 2.62
1478 4117 5.248640 AGCTATTTAAGTGCTGCTCTGAAA 58.751 37.500 14.68 14.68 35.54 2.69
1479 4118 4.836825 AGCTATTTAAGTGCTGCTCTGAA 58.163 39.130 4.83 0.93 35.54 3.02
1481 4120 4.874966 AGAAGCTATTTAAGTGCTGCTCTG 59.125 41.667 4.83 0.00 38.21 3.35
1482 4121 5.096443 AGAAGCTATTTAAGTGCTGCTCT 57.904 39.130 0.00 0.00 38.21 4.09
1483 4122 6.928492 AGATAGAAGCTATTTAAGTGCTGCTC 59.072 38.462 9.33 0.00 41.41 4.26
1486 4125 8.555361 GGAAAGATAGAAGCTATTTAAGTGCTG 58.445 37.037 0.00 0.00 37.11 4.41
1487 4126 8.490311 AGGAAAGATAGAAGCTATTTAAGTGCT 58.510 33.333 0.00 0.00 38.87 4.40
1488 4127 8.669946 AGGAAAGATAGAAGCTATTTAAGTGC 57.330 34.615 0.00 0.00 0.00 4.40
1491 4130 9.430623 GCCTAGGAAAGATAGAAGCTATTTAAG 57.569 37.037 14.75 0.00 0.00 1.85
1493 4132 8.368668 GTGCCTAGGAAAGATAGAAGCTATTTA 58.631 37.037 14.75 0.00 0.00 1.40
1494 4133 7.220740 GTGCCTAGGAAAGATAGAAGCTATTT 58.779 38.462 14.75 0.00 0.00 1.40
1496 4135 5.247337 GGTGCCTAGGAAAGATAGAAGCTAT 59.753 44.000 14.75 0.00 0.00 2.97
1498 4137 3.389656 GGTGCCTAGGAAAGATAGAAGCT 59.610 47.826 14.75 0.00 0.00 3.74
1499 4138 3.134804 TGGTGCCTAGGAAAGATAGAAGC 59.865 47.826 14.75 0.00 0.00 3.86
1500 4139 4.407296 AGTGGTGCCTAGGAAAGATAGAAG 59.593 45.833 14.75 0.00 0.00 2.85
1501 4140 4.362677 AGTGGTGCCTAGGAAAGATAGAA 58.637 43.478 14.75 0.00 0.00 2.10
1502 4141 3.995636 AGTGGTGCCTAGGAAAGATAGA 58.004 45.455 14.75 0.00 0.00 1.98
1506 5990 3.468071 TCTAGTGGTGCCTAGGAAAGA 57.532 47.619 14.75 0.00 36.02 2.52
1507 5991 4.553330 TTTCTAGTGGTGCCTAGGAAAG 57.447 45.455 14.75 0.00 36.02 2.62
1508 5992 4.595781 TCTTTTCTAGTGGTGCCTAGGAAA 59.404 41.667 14.75 0.00 39.25 3.13
1510 5994 3.786553 TCTTTTCTAGTGGTGCCTAGGA 58.213 45.455 14.75 0.00 36.02 2.94
1516 6000 5.423886 AGCTTCTATCTTTTCTAGTGGTGC 58.576 41.667 0.00 0.00 0.00 5.01
1517 6001 9.606631 AAATAGCTTCTATCTTTTCTAGTGGTG 57.393 33.333 0.00 0.00 0.00 4.17
1526 6010 8.401709 GCAGCACTTAAATAGCTTCTATCTTTT 58.598 33.333 0.00 0.00 36.26 2.27
1603 6088 4.899352 ACTAGAATCAGGAAGCACTGTT 57.101 40.909 0.00 0.00 39.48 3.16
1688 6174 8.567285 AACTAAGGTGAGAGGATAACAAATTG 57.433 34.615 0.00 0.00 0.00 2.32
1762 6248 4.060205 TCTAGAAGCCCGTGTAACAAAAC 58.940 43.478 0.00 0.00 35.74 2.43
1765 6251 5.864418 ATATCTAGAAGCCCGTGTAACAA 57.136 39.130 0.00 0.00 35.74 2.83
1767 6253 7.393841 AGATATATCTAGAAGCCCGTGTAAC 57.606 40.000 13.76 0.00 34.85 2.50
1814 6300 8.217799 CACTTATTTTGGATTGGAGGGAGTATA 58.782 37.037 0.00 0.00 0.00 1.47
1826 6312 5.705609 AACTGCGACACTTATTTTGGATT 57.294 34.783 0.00 0.00 0.00 3.01
1845 6331 8.528044 TTTTGAACTAACCATAGTCCAAAACT 57.472 30.769 8.46 0.00 44.17 2.66
1876 6373 2.304761 TCCCCCGATCCATAATAAGTGC 59.695 50.000 0.00 0.00 0.00 4.40
2053 6552 4.847757 CACGAAATGTGCATTGAGTAACTG 59.152 41.667 0.00 0.00 42.70 3.16
2187 6689 2.430956 CGCTAAGTAAAGTGCATTGCG 58.569 47.619 3.84 0.00 35.22 4.85
2231 6733 6.887626 AAAGAAAAATAAGGCCGTAGTGAA 57.112 33.333 4.31 0.00 0.00 3.18
2257 6761 2.159612 GGCGACCGGTTACTTCAATTTC 60.160 50.000 9.42 0.00 0.00 2.17
2267 6771 0.813184 CTTGTAGAGGCGACCGGTTA 59.187 55.000 9.42 0.00 0.00 2.85
2293 6797 7.141363 GCACATGTGTTAGAGAAAAGTTCAAT 58.859 34.615 26.01 0.00 0.00 2.57
2320 6826 0.924823 ATGAGCCCAGATTTCCTGCT 59.075 50.000 0.00 0.00 41.57 4.24
2490 6996 4.273480 CCTGACAAGATCACTCGTTGTTTT 59.727 41.667 0.00 0.00 34.55 2.43
2524 7048 3.858503 GCCTGAGTGGTTTTTCAGAATGC 60.859 47.826 3.22 0.00 42.67 3.56
2716 7240 2.890311 AGATCCCGAATTGTGTTTGCAA 59.110 40.909 0.00 0.00 0.00 4.08
2855 7382 6.071165 CCAATTCCTCCAAAGCTAAAGAACAT 60.071 38.462 0.00 0.00 0.00 2.71
2864 7391 3.330701 TGAGTACCAATTCCTCCAAAGCT 59.669 43.478 0.00 0.00 0.00 3.74
2958 7485 8.934023 TTTATAACCTCCAGATTTTCACAGTT 57.066 30.769 0.00 0.00 0.00 3.16
3152 7679 2.396590 TTACCGCCAAAGATGAGGTC 57.603 50.000 0.00 0.00 38.06 3.85
3196 7723 6.737254 AATAATATACCAAGGAAATCGCCG 57.263 37.500 0.00 0.00 0.00 6.46
3239 7766 8.836268 AAAAACGGTATGTCTGTCTGTATAAA 57.164 30.769 0.00 0.00 34.09 1.40
3280 7808 3.769739 ATACACAAGTGCTTGAGGTGA 57.230 42.857 17.62 2.14 42.93 4.02
3303 7831 2.949963 GCCCCTGCTGATACCATGAAAA 60.950 50.000 0.00 0.00 33.53 2.29
3414 7942 6.496565 ACACTAGATATCCTTGGGAAGATGAG 59.503 42.308 0.00 0.00 34.34 2.90
3595 8125 2.362736 TCTTCACATCCTTGATGCTGC 58.637 47.619 4.05 0.00 43.15 5.25
3632 8162 1.067199 GCTCAACCATGCTTTTCGCG 61.067 55.000 0.00 0.00 43.27 5.87
3683 8213 2.103042 CAGTGTAAGGCGCTCCAGC 61.103 63.158 7.64 0.00 35.42 4.85
3744 8274 4.090761 TCATATTCCCAACTGAGCATCC 57.909 45.455 0.00 0.00 0.00 3.51
3745 8275 7.609146 TCATATTCATATTCCCAACTGAGCATC 59.391 37.037 0.00 0.00 0.00 3.91
3784 8314 2.206750 TCACAACCACGAGTGCTTTAC 58.793 47.619 0.00 0.00 35.76 2.01
3791 8321 2.981859 AACTTCTCACAACCACGAGT 57.018 45.000 0.00 0.00 0.00 4.18
3996 8528 3.854286 AAACAGTAGTGAAACGAAGCG 57.146 42.857 4.09 0.00 45.86 4.68
4028 8560 4.248859 AGATGAAATAATCGGCAGATCGG 58.751 43.478 0.00 0.00 35.74 4.18
4082 8614 1.535437 GCACTAGCATTGGAAGCATGC 60.535 52.381 10.51 10.51 46.39 4.06
4251 8788 0.690762 TCCCAACCTCAGGCAGTTAC 59.309 55.000 0.00 0.00 0.00 2.50
4311 8848 6.609212 TCAGTGGCAAATATTATGGGCTTAAA 59.391 34.615 0.00 0.00 0.00 1.52
4340 8877 3.870419 ACATGAAACTGCAACGCATTTTT 59.130 34.783 0.00 1.54 40.50 1.94
4395 8932 2.358737 GTCACAAGTCAGGCCCCG 60.359 66.667 0.00 0.00 0.00 5.73
4396 8933 0.690762 TAAGTCACAAGTCAGGCCCC 59.309 55.000 0.00 0.00 0.00 5.80
4547 9095 9.793259 AACAGATAATGAAACTTTGGAAGAGTA 57.207 29.630 0.00 0.00 0.00 2.59
4548 9096 8.571336 CAACAGATAATGAAACTTTGGAAGAGT 58.429 33.333 0.00 0.00 0.00 3.24
4591 9140 0.762418 TGGACATGGTTCCGTTCTGT 59.238 50.000 0.00 0.00 38.69 3.41
4669 9220 7.231467 GCCAAATTTCAAGGGATAGATACCTA 58.769 38.462 0.00 0.00 41.42 3.08
4671 9222 5.048713 CGCCAAATTTCAAGGGATAGATACC 60.049 44.000 0.00 0.00 0.00 2.73
4851 9407 5.819901 CACATGTTTTTGGTTAACCCACATT 59.180 36.000 21.97 11.53 45.19 2.71
4865 9421 8.746922 CTATACTTTGTGCATCACATGTTTTT 57.253 30.769 0.00 0.00 44.16 1.94


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

AutoCloner maintained by Alex Coulton.