Multiple sequence alignment - TraesCS2A01G382600

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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 TraesCS2A01G382600 chr2A 100.000 3433 0 0 1 3433 627187356 627183924 0.000000e+00 6340
1 TraesCS2A01G382600 chr2A 90.931 1698 119 7 478 2165 472412677 472414349 0.000000e+00 2250
2 TraesCS2A01G382600 chr2A 89.273 1100 86 6 4 1094 648540021 648541097 0.000000e+00 1349
3 TraesCS2A01G382600 chr2A 89.780 1047 75 16 4 1045 732306198 732305179 0.000000e+00 1312
4 TraesCS2A01G382600 chr2A 93.785 708 42 2 2727 3433 472414981 472415687 0.000000e+00 1062
5 TraesCS2A01G382600 chr2A 92.464 491 34 3 2944 3433 698899524 698899036 0.000000e+00 699
6 TraesCS2A01G382600 chr2A 93.478 276 17 1 2163 2437 234437621 234437346 3.190000e-110 409
7 TraesCS2A01G382600 chr5D 91.663 2183 133 8 4 2175 473059083 473056939 0.000000e+00 2977
8 TraesCS2A01G382600 chr5D 91.791 402 10 2 2435 2835 473056400 473056021 3.900000e-149 538
9 TraesCS2A01G382600 chr5D 96.364 165 6 0 2163 2327 112833646 112833482 4.370000e-69 272
10 TraesCS2A01G382600 chr5D 95.758 165 5 2 2163 2327 300554604 300554442 7.310000e-67 265
11 TraesCS2A01G382600 chr4D 90.754 2174 159 14 4 2175 446598874 446596741 0.000000e+00 2863
12 TraesCS2A01G382600 chr4D 91.022 401 14 1 2435 2835 446596207 446595829 3.930000e-144 521
13 TraesCS2A01G382600 chr5B 89.312 2208 186 27 4 2175 617342256 617340063 0.000000e+00 2724
14 TraesCS2A01G382600 chr5B 90.909 1727 141 9 3 1720 494711876 494710157 0.000000e+00 2305
15 TraesCS2A01G382600 chr5B 92.580 903 50 5 2533 3433 617305418 617304531 0.000000e+00 1280
16 TraesCS2A01G382600 chr5B 90.797 891 74 5 4 888 440044323 440045211 0.000000e+00 1184
17 TraesCS2A01G382600 chr5B 92.105 76 6 0 2364 2439 496765429 496765504 1.300000e-19 108
18 TraesCS2A01G382600 chr7B 90.006 1801 132 9 4 1762 607378709 607376915 0.000000e+00 2285
19 TraesCS2A01G382600 chr7B 91.043 882 67 6 4 875 577427629 577428508 0.000000e+00 1181
20 TraesCS2A01G382600 chr7B 86.923 260 16 8 2443 2684 741569414 741569673 3.370000e-70 276
21 TraesCS2A01G382600 chr7B 85.345 116 15 2 2323 2437 545487391 545487505 6.020000e-23 119
22 TraesCS2A01G382600 chr2D 91.129 1612 119 7 4 1605 19721887 19723484 0.000000e+00 2163
23 TraesCS2A01G382600 chr2D 90.898 1615 120 7 4 1605 19745739 19747339 0.000000e+00 2143
24 TraesCS2A01G382600 chr2D 92.421 409 27 4 1764 2170 19723483 19723889 6.390000e-162 580
25 TraesCS2A01G382600 chr2D 94.865 370 18 1 1802 2170 19747373 19747742 8.260000e-161 577
26 TraesCS2A01G382600 chr2D 95.087 346 10 2 2435 2773 19724427 19724772 3.900000e-149 538
27 TraesCS2A01G382600 chr2D 95.087 346 10 2 2435 2773 19748280 19748625 3.900000e-149 538
28 TraesCS2A01G382600 chr2D 95.152 165 8 0 2163 2327 166480104 166480268 9.450000e-66 261
29 TraesCS2A01G382600 chr1B 87.882 1081 82 17 3 1045 637314968 637313899 0.000000e+00 1225
30 TraesCS2A01G382600 chr1B 90.684 526 48 1 1249 1774 34336599 34337123 0.000000e+00 699
31 TraesCS2A01G382600 chr1B 92.287 376 27 2 1801 2175 34337112 34337486 1.810000e-147 532
32 TraesCS2A01G382600 chr2B 91.246 891 70 6 4 888 22955128 22954240 0.000000e+00 1206
33 TraesCS2A01G382600 chr2B 90.919 892 70 7 4 888 70004703 70003816 0.000000e+00 1188
34 TraesCS2A01G382600 chr2B 90.347 518 44 6 2921 3433 48166686 48166170 0.000000e+00 675
35 TraesCS2A01G382600 chr2B 89.961 518 46 6 2921 3433 48238268 48237752 0.000000e+00 664
36 TraesCS2A01G382600 chr2B 83.968 630 64 11 1582 2175 748699186 748699814 1.380000e-158 569
37 TraesCS2A01G382600 chr2B 91.007 278 22 3 2163 2439 147729494 147729769 4.180000e-99 372
38 TraesCS2A01G382600 chr2B 88.288 111 13 0 2329 2439 35046209 35046099 2.150000e-27 134
39 TraesCS2A01G382600 chr2B 92.105 76 6 0 2364 2439 171092666 171092741 1.300000e-19 108
40 TraesCS2A01G382600 chr5A 91.134 891 71 6 4 888 168348166 168349054 0.000000e+00 1201
41 TraesCS2A01G382600 chr5A 90.123 81 8 0 2364 2444 706171824 706171904 4.690000e-19 106
42 TraesCS2A01G382600 chr3B 91.740 678 51 4 2761 3433 749280478 749279801 0.000000e+00 937
43 TraesCS2A01G382600 chr7D 88.076 629 67 6 965 1586 487724519 487723892 0.000000e+00 739
44 TraesCS2A01G382600 chr7D 91.313 518 39 6 2921 3433 609055604 609055088 0.000000e+00 702
45 TraesCS2A01G382600 chr7D 94.545 165 8 1 2163 2327 538580652 538580815 1.580000e-63 254
46 TraesCS2A01G382600 chr4B 90.734 518 42 6 2921 3433 218594339 218593823 0.000000e+00 686
47 TraesCS2A01G382600 chr4B 90.114 526 52 0 1249 1774 381142384 381141859 0.000000e+00 684
48 TraesCS2A01G382600 chr4B 90.347 518 44 5 2921 3433 352357468 352357984 0.000000e+00 675
49 TraesCS2A01G382600 chr4B 91.295 471 37 3 2684 3150 101791899 101792369 1.040000e-179 640
50 TraesCS2A01G382600 chr4B 92.021 376 28 2 1801 2175 381141870 381141496 8.440000e-146 527
51 TraesCS2A01G382600 chr4B 94.758 248 12 1 2437 2684 101791624 101791870 5.370000e-103 385
52 TraesCS2A01G382600 chrUn 95.087 346 10 2 2435 2773 340881357 340881702 3.900000e-149 538
53 TraesCS2A01G382600 chr3D 93.893 262 14 1 786 1045 9499601 9499340 8.930000e-106 394
54 TraesCS2A01G382600 chr3D 95.152 165 8 0 2163 2327 575277626 575277462 9.450000e-66 261
55 TraesCS2A01G382600 chr7A 85.375 253 26 5 2684 2925 731273856 731273604 5.690000e-63 252
56 TraesCS2A01G382600 chr7A 86.802 197 19 4 2495 2684 731274085 731273889 2.680000e-51 213
57 TraesCS2A01G382600 chr7A 91.139 79 7 0 2364 2442 676402200 676402122 1.300000e-19 108
58 TraesCS2A01G382600 chr6A 94.012 167 7 2 2163 2327 413096972 413096807 2.050000e-62 250
59 TraesCS2A01G382600 chr6A 93.939 165 9 1 2163 2327 283879831 283879668 7.360000e-62 248
60 TraesCS2A01G382600 chr1D 87.705 122 9 3 2323 2439 390074151 390074271 1.660000e-28 137


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 TraesCS2A01G382600 chr2A 627183924 627187356 3432 True 6340.000000 6340 100.000000 1 3433 1 chr2A.!!$R2 3432
1 TraesCS2A01G382600 chr2A 472412677 472415687 3010 False 1656.000000 2250 92.358000 478 3433 2 chr2A.!!$F2 2955
2 TraesCS2A01G382600 chr2A 648540021 648541097 1076 False 1349.000000 1349 89.273000 4 1094 1 chr2A.!!$F1 1090
3 TraesCS2A01G382600 chr2A 732305179 732306198 1019 True 1312.000000 1312 89.780000 4 1045 1 chr2A.!!$R4 1041
4 TraesCS2A01G382600 chr5D 473056021 473059083 3062 True 1757.500000 2977 91.727000 4 2835 2 chr5D.!!$R3 2831
5 TraesCS2A01G382600 chr4D 446595829 446598874 3045 True 1692.000000 2863 90.888000 4 2835 2 chr4D.!!$R1 2831
6 TraesCS2A01G382600 chr5B 617340063 617342256 2193 True 2724.000000 2724 89.312000 4 2175 1 chr5B.!!$R3 2171
7 TraesCS2A01G382600 chr5B 494710157 494711876 1719 True 2305.000000 2305 90.909000 3 1720 1 chr5B.!!$R1 1717
8 TraesCS2A01G382600 chr5B 617304531 617305418 887 True 1280.000000 1280 92.580000 2533 3433 1 chr5B.!!$R2 900
9 TraesCS2A01G382600 chr5B 440044323 440045211 888 False 1184.000000 1184 90.797000 4 888 1 chr5B.!!$F1 884
10 TraesCS2A01G382600 chr7B 607376915 607378709 1794 True 2285.000000 2285 90.006000 4 1762 1 chr7B.!!$R1 1758
11 TraesCS2A01G382600 chr7B 577427629 577428508 879 False 1181.000000 1181 91.043000 4 875 1 chr7B.!!$F2 871
12 TraesCS2A01G382600 chr2D 19721887 19724772 2885 False 1093.666667 2163 92.879000 4 2773 3 chr2D.!!$F2 2769
13 TraesCS2A01G382600 chr2D 19745739 19748625 2886 False 1086.000000 2143 93.616667 4 2773 3 chr2D.!!$F3 2769
14 TraesCS2A01G382600 chr1B 637313899 637314968 1069 True 1225.000000 1225 87.882000 3 1045 1 chr1B.!!$R1 1042
15 TraesCS2A01G382600 chr1B 34336599 34337486 887 False 615.500000 699 91.485500 1249 2175 2 chr1B.!!$F1 926
16 TraesCS2A01G382600 chr2B 22954240 22955128 888 True 1206.000000 1206 91.246000 4 888 1 chr2B.!!$R1 884
17 TraesCS2A01G382600 chr2B 70003816 70004703 887 True 1188.000000 1188 90.919000 4 888 1 chr2B.!!$R5 884
18 TraesCS2A01G382600 chr2B 48166170 48166686 516 True 675.000000 675 90.347000 2921 3433 1 chr2B.!!$R3 512
19 TraesCS2A01G382600 chr2B 48237752 48238268 516 True 664.000000 664 89.961000 2921 3433 1 chr2B.!!$R4 512
20 TraesCS2A01G382600 chr2B 748699186 748699814 628 False 569.000000 569 83.968000 1582 2175 1 chr2B.!!$F3 593
21 TraesCS2A01G382600 chr5A 168348166 168349054 888 False 1201.000000 1201 91.134000 4 888 1 chr5A.!!$F1 884
22 TraesCS2A01G382600 chr3B 749279801 749280478 677 True 937.000000 937 91.740000 2761 3433 1 chr3B.!!$R1 672
23 TraesCS2A01G382600 chr7D 487723892 487724519 627 True 739.000000 739 88.076000 965 1586 1 chr7D.!!$R1 621
24 TraesCS2A01G382600 chr7D 609055088 609055604 516 True 702.000000 702 91.313000 2921 3433 1 chr7D.!!$R2 512
25 TraesCS2A01G382600 chr4B 218593823 218594339 516 True 686.000000 686 90.734000 2921 3433 1 chr4B.!!$R1 512
26 TraesCS2A01G382600 chr4B 352357468 352357984 516 False 675.000000 675 90.347000 2921 3433 1 chr4B.!!$F1 512
27 TraesCS2A01G382600 chr4B 381141496 381142384 888 True 605.500000 684 91.067500 1249 2175 2 chr4B.!!$R2 926
28 TraesCS2A01G382600 chr4B 101791624 101792369 745 False 512.500000 640 93.026500 2437 3150 2 chr4B.!!$F2 713

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
958 1084 0.531200 GATCTCGTCGGGAACAAGGT 59.469 55.0 0.00 0.0 0.0 3.50 F
1915 2180 0.096454 GTCGCGAAATTGGTAGGCAC 59.904 55.0 12.06 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2367 2792 0.105593 CCATCATCCTCCTCGTGGTG 59.894 60.0 2.99 0.65 34.23 4.17 R
3277 3962 1.291877 CGCACGAGCTAAGCAAACCT 61.292 55.0 2.73 0.00 39.10 3.50 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
38 39 2.057316 CAAAATGCGATCAAAACGGCA 58.943 42.857 0.00 0.00 0.00 5.69
69 70 4.504858 CGTTCCTAGCTAGTGGTTGAATT 58.495 43.478 19.31 0.00 0.00 2.17
75 76 5.888161 CCTAGCTAGTGGTTGAATTTTGGAT 59.112 40.000 19.31 0.00 0.00 3.41
78 80 7.775053 AGCTAGTGGTTGAATTTTGGATTTA 57.225 32.000 0.00 0.00 0.00 1.40
80 82 8.470002 AGCTAGTGGTTGAATTTTGGATTTATC 58.530 33.333 0.00 0.00 0.00 1.75
164 168 4.768968 AGAGCAAACTATGAGGCATTTGTT 59.231 37.500 0.00 0.00 35.06 2.83
246 251 3.181466 GGAACAAAGCTTTTGACACCCAT 60.181 43.478 9.53 0.00 0.00 4.00
476 495 5.336744 TGAAAACTCGTTCACATTTTGGTC 58.663 37.500 0.00 0.00 32.56 4.02
488 507 5.535783 TCACATTTTGGTCACACAATGAGAT 59.464 36.000 12.04 0.00 43.92 2.75
712 732 0.906775 CAACCCCGAAACCCTAGCTA 59.093 55.000 0.00 0.00 0.00 3.32
934 1049 2.123726 GTCCATGGCCACATCCCC 60.124 66.667 8.16 0.00 34.35 4.81
958 1084 0.531200 GATCTCGTCGGGAACAAGGT 59.469 55.000 0.00 0.00 0.00 3.50
960 1086 0.538977 TCTCGTCGGGAACAAGGTCT 60.539 55.000 0.00 0.00 0.00 3.85
971 1097 0.773644 ACAAGGTCTCCTGCAACCAT 59.226 50.000 7.99 0.00 38.06 3.55
978 1104 2.361610 CCTGCAACCATCGGCCTT 60.362 61.111 0.00 0.00 0.00 4.35
1026 1178 4.341783 GCAGCACTCCAGCCACCT 62.342 66.667 0.00 0.00 34.23 4.00
1028 1180 4.341783 AGCACTCCAGCCACCTGC 62.342 66.667 0.00 0.00 37.77 4.85
1045 1197 3.710722 CGCTCCTTCCCCAGCAGT 61.711 66.667 0.00 0.00 35.15 4.40
1125 1277 3.691342 CTCCCGAGCACCGACCAA 61.691 66.667 0.00 0.00 41.76 3.67
1221 1375 4.507916 CCTCCCGAGCTCCTCCGA 62.508 72.222 8.47 0.00 0.00 4.55
1271 1425 1.086067 CGTCTTCATCGCAGCACCAT 61.086 55.000 0.00 0.00 0.00 3.55
1339 1493 1.376942 CCAGTGAGCCAAGCCTCTG 60.377 63.158 0.00 0.00 33.02 3.35
1353 1507 1.681666 CTCTGCCTTGCCTTCTCCA 59.318 57.895 0.00 0.00 0.00 3.86
1381 1535 1.276421 TGCTCCCTTTCTTCTCTTCCG 59.724 52.381 0.00 0.00 0.00 4.30
1383 1537 2.289756 GCTCCCTTTCTTCTCTTCCGTT 60.290 50.000 0.00 0.00 0.00 4.44
1416 1570 2.416701 GCTCTCTCTGTCCTTTTCTCGG 60.417 54.545 0.00 0.00 0.00 4.63
1457 1611 3.182887 ACAGAGTCTGTCCAGGATCTT 57.817 47.619 20.34 0.00 41.21 2.40
1541 1696 3.402681 CCCACCTGGCAGATCCGT 61.403 66.667 17.94 1.59 37.80 4.69
1569 1724 2.125310 CCGTTGACCATGCCGCTA 60.125 61.111 0.00 0.00 0.00 4.26
1575 1736 4.227134 ACCATGCCGCTAGAGCCG 62.227 66.667 0.00 0.00 37.91 5.52
1577 1738 2.728180 CATGCCGCTAGAGCCGTA 59.272 61.111 0.00 0.00 37.91 4.02
1665 1826 3.616956 TTGATGTGGAGATGTGAGGAC 57.383 47.619 0.00 0.00 0.00 3.85
1668 1829 3.055602 TGATGTGGAGATGTGAGGACTTG 60.056 47.826 0.00 0.00 0.00 3.16
1676 1837 5.187186 GGAGATGTGAGGACTTGGTAGTTTA 59.813 44.000 0.00 0.00 33.84 2.01
1693 1854 0.600557 TTATTTGTGTGCTTGGCCGG 59.399 50.000 0.00 0.00 0.00 6.13
1735 1896 7.977818 TCTATTTGGTCTGTGCTGGATAATAT 58.022 34.615 0.00 0.00 0.00 1.28
1736 1897 6.889301 ATTTGGTCTGTGCTGGATAATATG 57.111 37.500 0.00 0.00 0.00 1.78
1742 1903 5.528690 GTCTGTGCTGGATAATATGCTGAAA 59.471 40.000 3.07 0.00 0.00 2.69
1777 2016 1.742831 GAACCATGTGTGTGTGTGTGT 59.257 47.619 0.00 0.00 0.00 3.72
1778 2017 2.700722 ACCATGTGTGTGTGTGTGTA 57.299 45.000 0.00 0.00 0.00 2.90
1779 2018 3.207265 ACCATGTGTGTGTGTGTGTAT 57.793 42.857 0.00 0.00 0.00 2.29
1780 2019 2.877786 ACCATGTGTGTGTGTGTGTATG 59.122 45.455 0.00 0.00 0.00 2.39
1781 2020 2.877786 CCATGTGTGTGTGTGTGTATGT 59.122 45.455 0.00 0.00 0.00 2.29
1782 2021 3.303924 CCATGTGTGTGTGTGTGTATGTG 60.304 47.826 0.00 0.00 0.00 3.21
1783 2022 2.979240 TGTGTGTGTGTGTGTATGTGT 58.021 42.857 0.00 0.00 0.00 3.72
1784 2023 2.675348 TGTGTGTGTGTGTGTATGTGTG 59.325 45.455 0.00 0.00 0.00 3.82
1785 2024 2.675844 GTGTGTGTGTGTGTATGTGTGT 59.324 45.455 0.00 0.00 0.00 3.72
1786 2025 2.675348 TGTGTGTGTGTGTATGTGTGTG 59.325 45.455 0.00 0.00 0.00 3.82
1787 2026 2.675844 GTGTGTGTGTGTATGTGTGTGT 59.324 45.455 0.00 0.00 0.00 3.72
1788 2027 2.675348 TGTGTGTGTGTATGTGTGTGTG 59.325 45.455 0.00 0.00 0.00 3.82
1789 2028 2.675844 GTGTGTGTGTATGTGTGTGTGT 59.324 45.455 0.00 0.00 0.00 3.72
1790 2029 2.675348 TGTGTGTGTATGTGTGTGTGTG 59.325 45.455 0.00 0.00 0.00 3.82
1791 2030 2.675844 GTGTGTGTATGTGTGTGTGTGT 59.324 45.455 0.00 0.00 0.00 3.72
1792 2031 2.675348 TGTGTGTATGTGTGTGTGTGTG 59.325 45.455 0.00 0.00 0.00 3.82
1793 2032 2.675844 GTGTGTATGTGTGTGTGTGTGT 59.324 45.455 0.00 0.00 0.00 3.72
1794 2033 2.675348 TGTGTATGTGTGTGTGTGTGTG 59.325 45.455 0.00 0.00 0.00 3.82
1795 2034 2.675844 GTGTATGTGTGTGTGTGTGTGT 59.324 45.455 0.00 0.00 0.00 3.72
1796 2035 2.675348 TGTATGTGTGTGTGTGTGTGTG 59.325 45.455 0.00 0.00 0.00 3.82
1797 2036 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
1798 2037 1.152510 TGTGTGTGTGTGTGTGTGTC 58.847 50.000 0.00 0.00 0.00 3.67
1799 2038 1.270571 TGTGTGTGTGTGTGTGTGTCT 60.271 47.619 0.00 0.00 0.00 3.41
1800 2039 2.028930 TGTGTGTGTGTGTGTGTGTCTA 60.029 45.455 0.00 0.00 0.00 2.59
1872 2137 6.214615 TGAATGGATTCTAGTGGTTAACTGGA 59.785 38.462 5.42 0.00 44.01 3.86
1915 2180 0.096454 GTCGCGAAATTGGTAGGCAC 59.904 55.000 12.06 0.00 0.00 5.01
1931 2196 2.038952 AGGCACACTGATGTCTTTGCTA 59.961 45.455 0.00 0.00 36.72 3.49
2080 2345 8.310406 GAAAATTTATGGAAGTTTTCTGGTGG 57.690 34.615 9.74 0.00 43.07 4.61
2092 2358 0.913934 TCTGGTGGGCCTGCAATAGA 60.914 55.000 4.53 0.00 34.18 1.98
2124 2390 3.740832 TCGAGTCATGTTGATGTTGTCAC 59.259 43.478 0.00 0.00 36.32 3.67
2173 2598 8.739039 TGGATTTGGATCAAGTTTGTATTACTG 58.261 33.333 0.00 0.00 33.77 2.74
2177 2602 7.864108 TGGATCAAGTTTGTATTACTGATGG 57.136 36.000 0.00 0.00 0.00 3.51
2179 2604 6.543831 GGATCAAGTTTGTATTACTGATGGCT 59.456 38.462 0.00 0.00 0.00 4.75
2180 2605 7.067494 GGATCAAGTTTGTATTACTGATGGCTT 59.933 37.037 0.00 0.00 0.00 4.35
2181 2606 9.109393 GATCAAGTTTGTATTACTGATGGCTTA 57.891 33.333 1.50 0.00 0.00 3.09
2182 2607 8.856153 TCAAGTTTGTATTACTGATGGCTTAA 57.144 30.769 0.00 0.00 0.00 1.85
2183 2608 9.461312 TCAAGTTTGTATTACTGATGGCTTAAT 57.539 29.630 0.00 0.00 0.00 1.40
2223 2648 9.595823 AGCTTGATTTGAAATTGAAATCATAGG 57.404 29.630 18.39 13.30 45.00 2.57
2224 2649 8.823818 GCTTGATTTGAAATTGAAATCATAGGG 58.176 33.333 18.39 11.47 45.00 3.53
2225 2650 9.880157 CTTGATTTGAAATTGAAATCATAGGGT 57.120 29.630 18.39 0.00 45.00 4.34
2227 2652 9.874205 TGATTTGAAATTGAAATCATAGGGTTC 57.126 29.630 14.83 0.00 42.29 3.62
2238 2663 9.973661 TGAAATCATAGGGTTCTTTTAATCTCA 57.026 29.630 0.00 0.00 0.00 3.27
2259 2684 8.351495 TCTCATTTTGAATTGTTTGTAGTTGC 57.649 30.769 0.00 0.00 0.00 4.17
2260 2685 8.196771 TCTCATTTTGAATTGTTTGTAGTTGCT 58.803 29.630 0.00 0.00 0.00 3.91
2262 2687 7.437862 TCATTTTGAATTGTTTGTAGTTGCTCC 59.562 33.333 0.00 0.00 0.00 4.70
2263 2688 5.843673 TTGAATTGTTTGTAGTTGCTCCA 57.156 34.783 0.00 0.00 0.00 3.86
2264 2689 5.437289 TGAATTGTTTGTAGTTGCTCCAG 57.563 39.130 0.00 0.00 0.00 3.86
2266 2691 3.290948 TTGTTTGTAGTTGCTCCAGGT 57.709 42.857 0.00 0.00 0.00 4.00
2267 2692 2.846193 TGTTTGTAGTTGCTCCAGGTC 58.154 47.619 0.00 0.00 0.00 3.85
2269 2694 1.729586 TTGTAGTTGCTCCAGGTCCT 58.270 50.000 0.00 0.00 0.00 3.85
2270 2695 1.729586 TGTAGTTGCTCCAGGTCCTT 58.270 50.000 0.00 0.00 0.00 3.36
2272 2697 1.903183 GTAGTTGCTCCAGGTCCTTCT 59.097 52.381 0.00 0.00 0.00 2.85
2273 2698 0.980423 AGTTGCTCCAGGTCCTTCTC 59.020 55.000 0.00 0.00 0.00 2.87
2274 2699 0.980423 GTTGCTCCAGGTCCTTCTCT 59.020 55.000 0.00 0.00 0.00 3.10
2275 2700 2.180276 GTTGCTCCAGGTCCTTCTCTA 58.820 52.381 0.00 0.00 0.00 2.43
2276 2701 2.151502 TGCTCCAGGTCCTTCTCTAG 57.848 55.000 0.00 0.00 0.00 2.43
2277 2702 1.359474 TGCTCCAGGTCCTTCTCTAGT 59.641 52.381 0.00 0.00 0.00 2.57
2278 2703 2.225394 TGCTCCAGGTCCTTCTCTAGTT 60.225 50.000 0.00 0.00 0.00 2.24
2280 2705 3.436243 CTCCAGGTCCTTCTCTAGTTGT 58.564 50.000 0.00 0.00 0.00 3.32
2282 2707 2.900546 CCAGGTCCTTCTCTAGTTGTGT 59.099 50.000 0.00 0.00 0.00 3.72
2283 2708 3.325135 CCAGGTCCTTCTCTAGTTGTGTT 59.675 47.826 0.00 0.00 0.00 3.32
2284 2709 4.202367 CCAGGTCCTTCTCTAGTTGTGTTT 60.202 45.833 0.00 0.00 0.00 2.83
2285 2710 5.011738 CCAGGTCCTTCTCTAGTTGTGTTTA 59.988 44.000 0.00 0.00 0.00 2.01
2286 2711 6.295916 CCAGGTCCTTCTCTAGTTGTGTTTAT 60.296 42.308 0.00 0.00 0.00 1.40
2287 2712 7.093465 CCAGGTCCTTCTCTAGTTGTGTTTATA 60.093 40.741 0.00 0.00 0.00 0.98
2289 2714 8.312564 AGGTCCTTCTCTAGTTGTGTTTATAAC 58.687 37.037 0.00 0.00 0.00 1.89
2290 2715 8.312564 GGTCCTTCTCTAGTTGTGTTTATAACT 58.687 37.037 0.00 0.00 40.69 2.24
2291 2716 9.141400 GTCCTTCTCTAGTTGTGTTTATAACTG 57.859 37.037 0.00 0.00 38.50 3.16
2292 2717 8.867097 TCCTTCTCTAGTTGTGTTTATAACTGT 58.133 33.333 0.00 0.00 38.50 3.55
2293 2718 9.141400 CCTTCTCTAGTTGTGTTTATAACTGTC 57.859 37.037 0.00 0.00 38.50 3.51
2294 2719 9.915629 CTTCTCTAGTTGTGTTTATAACTGTCT 57.084 33.333 0.00 0.00 38.50 3.41
2298 2723 9.826574 TCTAGTTGTGTTTATAACTGTCTTTGT 57.173 29.630 0.00 0.00 38.50 2.83
2301 2726 8.403236 AGTTGTGTTTATAACTGTCTTTGTTCC 58.597 33.333 0.00 0.00 36.95 3.62
2302 2727 8.403236 GTTGTGTTTATAACTGTCTTTGTTCCT 58.597 33.333 0.00 0.00 0.00 3.36
2304 2729 8.962679 TGTGTTTATAACTGTCTTTGTTCCTTT 58.037 29.630 0.00 0.00 0.00 3.11
2305 2730 9.797556 GTGTTTATAACTGTCTTTGTTCCTTTT 57.202 29.630 0.00 0.00 0.00 2.27
2329 2754 7.880160 TTTGATAATAGGACCAGTTTGATGG 57.120 36.000 0.00 0.00 46.47 3.51
2330 2755 6.823286 TGATAATAGGACCAGTTTGATGGA 57.177 37.500 0.00 0.00 43.57 3.41
2331 2756 6.830912 TGATAATAGGACCAGTTTGATGGAG 58.169 40.000 0.00 0.00 43.57 3.86
2332 2757 6.386927 TGATAATAGGACCAGTTTGATGGAGT 59.613 38.462 0.00 0.00 43.57 3.85
2333 2758 5.520748 AATAGGACCAGTTTGATGGAGTT 57.479 39.130 0.00 0.00 43.57 3.01
2334 2759 3.425162 AGGACCAGTTTGATGGAGTTC 57.575 47.619 0.00 0.00 43.57 3.01
2335 2760 2.040412 AGGACCAGTTTGATGGAGTTCC 59.960 50.000 0.00 0.00 43.57 3.62
2336 2761 2.437413 GACCAGTTTGATGGAGTTCCC 58.563 52.381 0.00 0.00 43.57 3.97
2347 2772 0.610785 GGAGTTCCCAAAATGCCCGA 60.611 55.000 0.00 0.00 34.14 5.14
2354 2779 0.243636 CCAAAATGCCCGACTCCAAC 59.756 55.000 0.00 0.00 0.00 3.77
2355 2780 0.109781 CAAAATGCCCGACTCCAACG 60.110 55.000 0.00 0.00 0.00 4.10
2362 2787 1.375396 CCGACTCCAACGGCAATGA 60.375 57.895 0.00 0.00 43.74 2.57
2364 2789 0.948623 CGACTCCAACGGCAATGACA 60.949 55.000 0.00 0.00 0.00 3.58
2365 2790 1.453155 GACTCCAACGGCAATGACAT 58.547 50.000 0.00 0.00 0.00 3.06
2367 2792 0.179156 CTCCAACGGCAATGACATGC 60.179 55.000 0.00 0.00 45.67 4.06
2379 2804 1.448540 GACATGCACCACGAGGAGG 60.449 63.158 5.68 0.00 38.69 4.30
2380 2805 1.888436 GACATGCACCACGAGGAGGA 61.888 60.000 5.68 0.00 38.69 3.71
2381 2806 1.267574 ACATGCACCACGAGGAGGAT 61.268 55.000 5.68 0.89 37.03 3.24
2382 2807 0.812811 CATGCACCACGAGGAGGATG 60.813 60.000 14.76 14.76 44.83 3.51
2383 2808 0.977627 ATGCACCACGAGGAGGATGA 60.978 55.000 5.68 0.00 35.36 2.92
2384 2809 0.977627 TGCACCACGAGGAGGATGAT 60.978 55.000 5.68 0.00 38.69 2.45
2385 2810 0.531532 GCACCACGAGGAGGATGATG 60.532 60.000 5.68 0.00 38.69 3.07
2386 2811 0.105593 CACCACGAGGAGGATGATGG 59.894 60.000 5.68 0.00 38.69 3.51
2388 2813 1.070445 CACGAGGAGGATGATGGCC 59.930 63.158 0.00 0.00 0.00 5.36
2389 2814 1.074926 ACGAGGAGGATGATGGCCT 60.075 57.895 3.32 0.00 38.81 5.19
2395 2820 2.252976 GAGGATGATGGCCTCTTCAC 57.747 55.000 3.32 2.46 46.70 3.18
2396 2821 0.842635 AGGATGATGGCCTCTTCACC 59.157 55.000 3.32 8.87 31.23 4.02
2397 2822 0.842635 GGATGATGGCCTCTTCACCT 59.157 55.000 3.32 0.00 31.23 4.00
2398 2823 2.050144 GGATGATGGCCTCTTCACCTA 58.950 52.381 3.32 0.00 31.23 3.08
2400 2825 2.254152 TGATGGCCTCTTCACCTACT 57.746 50.000 3.32 0.00 0.00 2.57
2401 2826 2.111384 TGATGGCCTCTTCACCTACTC 58.889 52.381 3.32 0.00 0.00 2.59
2403 2828 0.970937 TGGCCTCTTCACCTACTCCG 60.971 60.000 3.32 0.00 0.00 4.63
2404 2829 0.683504 GGCCTCTTCACCTACTCCGA 60.684 60.000 0.00 0.00 0.00 4.55
2406 2831 1.104630 CCTCTTCACCTACTCCGACC 58.895 60.000 0.00 0.00 0.00 4.79
2407 2832 1.104630 CTCTTCACCTACTCCGACCC 58.895 60.000 0.00 0.00 0.00 4.46
2408 2833 0.324091 TCTTCACCTACTCCGACCCC 60.324 60.000 0.00 0.00 0.00 4.95
2412 2837 2.832201 CCTACTCCGACCCCGTCC 60.832 72.222 0.00 0.00 0.00 4.79
2414 2839 1.823041 CTACTCCGACCCCGTCCTC 60.823 68.421 0.00 0.00 0.00 3.71
2426 2851 3.775654 GTCCTCCCTGACGCCTGG 61.776 72.222 0.00 0.00 0.00 4.45
2427 2852 4.316823 TCCTCCCTGACGCCTGGT 62.317 66.667 0.00 0.00 0.00 4.00
2428 2853 3.775654 CCTCCCTGACGCCTGGTC 61.776 72.222 0.00 0.00 46.27 4.02
2439 3006 2.056223 GCCTGGTCGTAGCCCTGTA 61.056 63.158 0.00 0.00 0.00 2.74
2501 3127 2.375174 AGTTCCTTGGCACATAGGTTGA 59.625 45.455 3.74 0.00 39.30 3.18
2502 3128 3.010584 AGTTCCTTGGCACATAGGTTGAT 59.989 43.478 3.74 0.00 39.30 2.57
2503 3129 3.281727 TCCTTGGCACATAGGTTGATC 57.718 47.619 3.74 0.00 39.30 2.92
2504 3130 2.846206 TCCTTGGCACATAGGTTGATCT 59.154 45.455 3.74 0.00 39.30 2.75
2505 3131 2.947652 CCTTGGCACATAGGTTGATCTG 59.052 50.000 0.00 0.00 39.30 2.90
2506 3132 2.042686 TGGCACATAGGTTGATCTGC 57.957 50.000 0.00 0.00 0.00 4.26
2507 3133 1.312815 GGCACATAGGTTGATCTGCC 58.687 55.000 2.95 2.95 37.71 4.85
2508 3134 1.133976 GGCACATAGGTTGATCTGCCT 60.134 52.381 10.27 11.24 40.28 4.75
2509 3135 1.945394 GCACATAGGTTGATCTGCCTG 59.055 52.381 15.76 6.43 36.38 4.85
2510 3136 2.681976 GCACATAGGTTGATCTGCCTGT 60.682 50.000 15.76 8.65 36.38 4.00
2511 3137 2.941064 CACATAGGTTGATCTGCCTGTG 59.059 50.000 21.73 21.73 45.63 3.66
2512 3138 2.840038 ACATAGGTTGATCTGCCTGTGA 59.160 45.455 26.56 8.79 43.77 3.58
2513 3139 3.264193 ACATAGGTTGATCTGCCTGTGAA 59.736 43.478 26.56 8.52 43.77 3.18
2514 3140 4.080129 ACATAGGTTGATCTGCCTGTGAAT 60.080 41.667 26.56 12.00 43.77 2.57
2515 3141 2.719739 AGGTTGATCTGCCTGTGAATG 58.280 47.619 7.66 0.00 33.13 2.67
2516 3142 2.306805 AGGTTGATCTGCCTGTGAATGA 59.693 45.455 7.66 0.00 33.13 2.57
2517 3143 3.053842 AGGTTGATCTGCCTGTGAATGAT 60.054 43.478 7.66 0.00 33.13 2.45
2518 3144 4.164796 AGGTTGATCTGCCTGTGAATGATA 59.835 41.667 7.66 0.00 33.13 2.15
2519 3145 4.514441 GGTTGATCTGCCTGTGAATGATAG 59.486 45.833 0.00 0.00 0.00 2.08
2520 3146 5.121811 GTTGATCTGCCTGTGAATGATAGT 58.878 41.667 0.00 0.00 0.00 2.12
2521 3147 4.700700 TGATCTGCCTGTGAATGATAGTG 58.299 43.478 0.00 0.00 0.00 2.74
2522 3148 4.162888 TGATCTGCCTGTGAATGATAGTGT 59.837 41.667 0.00 0.00 0.00 3.55
2647 3297 0.982852 AGGGATGGATGCGTCTTGGA 60.983 55.000 5.77 0.00 0.00 3.53
2670 3321 3.487372 ACCACAAGAAAAAGGCTACTCC 58.513 45.455 0.00 0.00 0.00 3.85
2697 3377 8.836413 GCTTTTGTTATGTAGTATATGCTTCCA 58.164 33.333 0.00 0.00 0.00 3.53
2714 3394 4.823989 GCTTCCATGTTGCTCTTATACCAT 59.176 41.667 0.00 0.00 0.00 3.55
2715 3395 5.997746 GCTTCCATGTTGCTCTTATACCATA 59.002 40.000 0.00 0.00 0.00 2.74
2722 3402 6.364701 TGTTGCTCTTATACCATAATGGCTT 58.635 36.000 0.00 0.00 42.67 4.35
2774 3454 2.116533 CCTGGCAGATGCATTGCGA 61.117 57.895 17.94 17.29 44.36 5.10
2802 3482 5.445939 CCGTGATAGCATCTGTTTGTGTAAC 60.446 44.000 0.00 0.00 37.26 2.50
2835 3515 1.273048 TCCATGTTGCTGCACCATTTC 59.727 47.619 10.14 0.00 0.00 2.17
2843 3523 1.732405 GCTGCACCATTTCCGCTTAAC 60.732 52.381 0.00 0.00 0.00 2.01
2959 3639 4.580167 GGCCATGACAATGCTAATGTTCTA 59.420 41.667 0.00 0.00 31.93 2.10
3065 3750 5.397447 GGATGGTTATGTCCTGGTTGTCATA 60.397 44.000 0.00 0.00 0.00 2.15
3079 3764 9.046296 CCTGGTTGTCATAAGAATATGTTACTC 57.954 37.037 0.00 0.00 39.94 2.59
3107 3792 6.472486 GCTTTTGTTATTTATCGCCTTTCCTC 59.528 38.462 0.00 0.00 0.00 3.71
3135 3820 3.785887 AGTTTATCCCTGGTATGCTTCCA 59.214 43.478 0.00 0.00 0.00 3.53
3194 3879 7.663827 TCTCATTGTGCTCTTTTTCATTTCAT 58.336 30.769 0.00 0.00 0.00 2.57
3202 3887 8.292448 GTGCTCTTTTTCATTTCATAAGTCAGA 58.708 33.333 0.00 0.00 0.00 3.27
3203 3888 8.849168 TGCTCTTTTTCATTTCATAAGTCAGAA 58.151 29.630 0.00 0.00 0.00 3.02
3215 3900 0.620556 AGTCAGAATTCGGCCATGGT 59.379 50.000 14.67 0.00 0.00 3.55
3260 3945 3.413327 GACCAAAGAGGAAGAAGGTTCC 58.587 50.000 0.00 0.00 41.22 3.62
3307 3993 2.678580 TCGTGCGGATGGGAGACA 60.679 61.111 0.00 0.00 0.00 3.41
3413 4099 2.309755 TCAATTCATGGTTGAGCCTCCT 59.690 45.455 9.47 0.00 38.35 3.69
3425 4111 3.124066 TGAGCCTCCTTCTACCTCTCTA 58.876 50.000 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.159077 CGCATTTTGAAACGAGCATAAAAATAA 58.841 29.630 0.00 0.00 0.00 1.40
12 13 4.145585 CGTTTTGATCGCATTTTGAAACGA 59.854 37.500 11.60 0.00 46.09 3.85
38 39 2.911143 CTAGGAACGGGCATGCCT 59.089 61.111 34.70 17.16 36.10 4.75
69 70 7.230747 TCAGAGAAACACCAGATAAATCCAAA 58.769 34.615 0.00 0.00 0.00 3.28
164 168 5.098893 CAGGAAACACGTCAAATTTGAACA 58.901 37.500 22.07 0.00 39.21 3.18
179 183 0.250684 TGCCGATTCAGCAGGAAACA 60.251 50.000 0.00 0.00 39.39 2.83
246 251 4.620589 AATGCACAATTGACCAAATGGA 57.379 36.364 13.59 0.00 38.94 3.41
355 364 8.499403 AAAAACATTTTTCATTTTTCGAGGGA 57.501 26.923 0.00 0.00 35.61 4.20
476 495 9.132521 GAAAATAGAAAACCATCTCATTGTGTG 57.867 33.333 0.00 0.00 0.00 3.82
558 578 7.062322 ACCATCTAAATTGATCATAGTTGCCA 58.938 34.615 0.00 0.00 0.00 4.92
570 590 9.440773 GTATGATGCTATGACCATCTAAATTGA 57.559 33.333 0.00 0.00 39.76 2.57
712 732 1.007118 GGGGGTGGATGGAAAATGACT 59.993 52.381 0.00 0.00 0.00 3.41
784 857 1.142870 GGAGGCAGCTCTCTCTCTCTA 59.857 57.143 11.32 0.00 34.39 2.43
853 950 4.195334 GTGCGGGAGGCCATGGAT 62.195 66.667 18.40 1.89 42.61 3.41
958 1084 2.268920 GCCGATGGTTGCAGGAGA 59.731 61.111 0.00 0.00 0.00 3.71
960 1086 2.819984 GAAGGCCGATGGTTGCAGGA 62.820 60.000 0.00 0.00 0.00 3.86
971 1097 0.179084 GTTGGATCGATGAAGGCCGA 60.179 55.000 0.54 0.00 39.25 5.54
978 1104 2.038952 GGATGGATGGTTGGATCGATGA 59.961 50.000 0.54 0.00 0.00 2.92
1019 1171 4.400961 GAAGGAGCGCAGGTGGCT 62.401 66.667 11.47 0.00 45.00 4.75
1118 1270 4.821589 GCTCGGGCTCTTGGTCGG 62.822 72.222 0.00 0.00 35.22 4.79
1220 1374 2.887568 CGAGTGGAGGCACGCATC 60.888 66.667 0.00 0.00 0.00 3.91
1221 1375 3.240134 AACGAGTGGAGGCACGCAT 62.240 57.895 0.00 0.00 0.00 4.73
1339 1493 0.820226 GGAAATGGAGAAGGCAAGGC 59.180 55.000 0.00 0.00 0.00 4.35
1353 1507 0.698818 AGAAAGGGAGCACGGGAAAT 59.301 50.000 0.00 0.00 0.00 2.17
1381 1535 0.460459 GAGAGCGGGAGGTTAGCAAC 60.460 60.000 0.00 0.00 43.00 4.17
1383 1537 1.000486 AGAGAGCGGGAGGTTAGCA 60.000 57.895 0.00 0.00 43.00 3.49
1416 1570 0.378257 CATGGCGTTGGCTGTCATAC 59.622 55.000 0.00 0.00 39.81 2.39
1541 1696 2.119611 TCAACGGGCAGGAGAGGA 59.880 61.111 0.00 0.00 0.00 3.71
1575 1736 1.144057 CCAGTGAGGGGCGATGTAC 59.856 63.158 0.00 0.00 0.00 2.90
1577 1738 2.185310 GAACCAGTGAGGGGCGATGT 62.185 60.000 0.00 0.00 43.89 3.06
1665 1826 5.920273 CCAAGCACACAAATAAACTACCAAG 59.080 40.000 0.00 0.00 0.00 3.61
1668 1829 4.234574 GCCAAGCACACAAATAAACTACC 58.765 43.478 0.00 0.00 0.00 3.18
1676 1837 0.538516 TACCGGCCAAGCACACAAAT 60.539 50.000 0.00 0.00 0.00 2.32
1693 1854 5.977489 AATAGAGCCAAAAACAACCCTAC 57.023 39.130 0.00 0.00 0.00 3.18
1735 1896 1.825090 ATCGCCTTCATGTTTCAGCA 58.175 45.000 0.00 0.00 0.00 4.41
1736 1897 2.289002 CCTATCGCCTTCATGTTTCAGC 59.711 50.000 0.00 0.00 0.00 4.26
1742 1903 1.837439 TGGTTCCTATCGCCTTCATGT 59.163 47.619 0.00 0.00 0.00 3.21
1777 2016 2.933260 GACACACACACACACACACATA 59.067 45.455 0.00 0.00 0.00 2.29
1778 2017 1.737236 GACACACACACACACACACAT 59.263 47.619 0.00 0.00 0.00 3.21
1779 2018 1.152510 GACACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
1780 2019 1.438651 AGACACACACACACACACAC 58.561 50.000 0.00 0.00 0.00 3.82
1781 2020 3.194062 CATAGACACACACACACACACA 58.806 45.455 0.00 0.00 0.00 3.72
1782 2021 3.001228 CACATAGACACACACACACACAC 59.999 47.826 0.00 0.00 0.00 3.82
1783 2022 3.194062 CACATAGACACACACACACACA 58.806 45.455 0.00 0.00 0.00 3.72
1784 2023 3.001228 CACACATAGACACACACACACAC 59.999 47.826 0.00 0.00 0.00 3.82
1785 2024 3.194062 CACACATAGACACACACACACA 58.806 45.455 0.00 0.00 0.00 3.72
1786 2025 3.001228 CACACACATAGACACACACACAC 59.999 47.826 0.00 0.00 0.00 3.82
1787 2026 3.194062 CACACACATAGACACACACACA 58.806 45.455 0.00 0.00 0.00 3.72
1788 2027 3.001228 CACACACACATAGACACACACAC 59.999 47.826 0.00 0.00 0.00 3.82
1789 2028 3.194062 CACACACACATAGACACACACA 58.806 45.455 0.00 0.00 0.00 3.72
1790 2029 3.194861 ACACACACACATAGACACACAC 58.805 45.455 0.00 0.00 0.00 3.82
1791 2030 3.535280 ACACACACACATAGACACACA 57.465 42.857 0.00 0.00 0.00 3.72
1792 2031 6.617879 TCTATACACACACACATAGACACAC 58.382 40.000 0.00 0.00 0.00 3.82
1793 2032 6.827586 TCTATACACACACACATAGACACA 57.172 37.500 0.00 0.00 0.00 3.72
1794 2033 6.530534 GGTTCTATACACACACACATAGACAC 59.469 42.308 0.00 0.00 31.43 3.67
1795 2034 6.436218 AGGTTCTATACACACACACATAGACA 59.564 38.462 0.00 0.00 31.43 3.41
1796 2035 6.864342 AGGTTCTATACACACACACATAGAC 58.136 40.000 0.00 0.00 31.43 2.59
1797 2036 7.177744 TCAAGGTTCTATACACACACACATAGA 59.822 37.037 0.00 0.00 0.00 1.98
1798 2037 7.320399 TCAAGGTTCTATACACACACACATAG 58.680 38.462 0.00 0.00 0.00 2.23
1799 2038 7.234661 TCAAGGTTCTATACACACACACATA 57.765 36.000 0.00 0.00 0.00 2.29
1800 2039 6.109156 TCAAGGTTCTATACACACACACAT 57.891 37.500 0.00 0.00 0.00 3.21
1872 2137 9.233232 GACTAAATTCACGAATGTTTCAGTTTT 57.767 29.630 0.00 0.00 0.00 2.43
1915 2180 8.886719 TCAATCTTTATAGCAAAGACATCAGTG 58.113 33.333 1.76 0.00 38.88 3.66
2062 2327 2.556559 GGCCCACCAGAAAACTTCCATA 60.557 50.000 0.00 0.00 35.26 2.74
2064 2329 0.469144 GGCCCACCAGAAAACTTCCA 60.469 55.000 0.00 0.00 35.26 3.53
2078 2343 0.925558 TTCCATCTATTGCAGGCCCA 59.074 50.000 0.00 0.00 0.00 5.36
2080 2345 5.392380 CGATTATTTCCATCTATTGCAGGCC 60.392 44.000 0.00 0.00 0.00 5.19
2092 2358 7.500227 ACATCAACATGACTCGATTATTTCCAT 59.500 33.333 0.00 0.00 33.72 3.41
2124 2390 2.159517 GCCAAACTGAATCTACCAAGCG 60.160 50.000 0.00 0.00 0.00 4.68
2212 2637 9.973661 TGAGATTAAAAGAACCCTATGATTTCA 57.026 29.630 0.00 0.00 0.00 2.69
2233 2658 8.981647 GCAACTACAAACAATTCAAAATGAGAT 58.018 29.630 0.00 0.00 0.00 2.75
2234 2659 8.196771 AGCAACTACAAACAATTCAAAATGAGA 58.803 29.630 0.00 0.00 0.00 3.27
2235 2660 8.356533 AGCAACTACAAACAATTCAAAATGAG 57.643 30.769 0.00 0.00 0.00 2.90
2236 2661 7.437862 GGAGCAACTACAAACAATTCAAAATGA 59.562 33.333 0.00 0.00 0.00 2.57
2237 2662 7.224362 TGGAGCAACTACAAACAATTCAAAATG 59.776 33.333 0.00 0.00 0.00 2.32
2238 2663 7.271511 TGGAGCAACTACAAACAATTCAAAAT 58.728 30.769 0.00 0.00 0.00 1.82
2239 2664 6.634805 TGGAGCAACTACAAACAATTCAAAA 58.365 32.000 0.00 0.00 0.00 2.44
2240 2665 6.214191 TGGAGCAACTACAAACAATTCAAA 57.786 33.333 0.00 0.00 0.00 2.69
2241 2666 5.221224 CCTGGAGCAACTACAAACAATTCAA 60.221 40.000 0.00 0.00 0.00 2.69
2242 2667 4.278170 CCTGGAGCAACTACAAACAATTCA 59.722 41.667 0.00 0.00 0.00 2.57
2245 2670 3.821033 GACCTGGAGCAACTACAAACAAT 59.179 43.478 0.00 0.00 0.00 2.71
2247 2672 2.486548 GGACCTGGAGCAACTACAAACA 60.487 50.000 0.00 0.00 0.00 2.83
2248 2673 2.152016 GGACCTGGAGCAACTACAAAC 58.848 52.381 0.00 0.00 0.00 2.93
2249 2674 2.054799 AGGACCTGGAGCAACTACAAA 58.945 47.619 0.00 0.00 0.00 2.83
2250 2675 1.729586 AGGACCTGGAGCAACTACAA 58.270 50.000 0.00 0.00 0.00 2.41
2251 2676 1.623811 GAAGGACCTGGAGCAACTACA 59.376 52.381 0.00 0.00 0.00 2.74
2253 2678 2.180276 GAGAAGGACCTGGAGCAACTA 58.820 52.381 0.00 0.00 0.00 2.24
2254 2679 0.980423 GAGAAGGACCTGGAGCAACT 59.020 55.000 0.00 0.00 0.00 3.16
2255 2680 0.980423 AGAGAAGGACCTGGAGCAAC 59.020 55.000 0.00 0.00 0.00 4.17
2256 2681 2.225394 ACTAGAGAAGGACCTGGAGCAA 60.225 50.000 0.00 0.00 0.00 3.91
2257 2682 1.359474 ACTAGAGAAGGACCTGGAGCA 59.641 52.381 0.00 0.00 0.00 4.26
2258 2683 2.153034 ACTAGAGAAGGACCTGGAGC 57.847 55.000 0.00 0.00 0.00 4.70
2259 2684 3.194542 CACAACTAGAGAAGGACCTGGAG 59.805 52.174 0.00 0.00 0.00 3.86
2260 2685 3.165875 CACAACTAGAGAAGGACCTGGA 58.834 50.000 0.00 0.00 0.00 3.86
2262 2687 4.608948 AACACAACTAGAGAAGGACCTG 57.391 45.455 0.00 0.00 0.00 4.00
2263 2688 6.936968 ATAAACACAACTAGAGAAGGACCT 57.063 37.500 0.00 0.00 0.00 3.85
2264 2689 8.312564 AGTTATAAACACAACTAGAGAAGGACC 58.687 37.037 0.00 0.00 0.00 4.46
2266 2691 8.867097 ACAGTTATAAACACAACTAGAGAAGGA 58.133 33.333 0.00 0.00 0.00 3.36
2267 2692 9.141400 GACAGTTATAAACACAACTAGAGAAGG 57.859 37.037 0.00 0.00 0.00 3.46
2272 2697 9.826574 ACAAAGACAGTTATAAACACAACTAGA 57.173 29.630 0.00 0.00 0.00 2.43
2275 2700 8.403236 GGAACAAAGACAGTTATAAACACAACT 58.597 33.333 0.00 0.00 0.00 3.16
2276 2701 8.403236 AGGAACAAAGACAGTTATAAACACAAC 58.597 33.333 0.00 0.00 0.00 3.32
2277 2702 8.514330 AGGAACAAAGACAGTTATAAACACAA 57.486 30.769 0.00 0.00 0.00 3.33
2278 2703 8.514330 AAGGAACAAAGACAGTTATAAACACA 57.486 30.769 0.00 0.00 0.00 3.72
2304 2729 8.112822 TCCATCAAACTGGTCCTATTATCAAAA 58.887 33.333 0.00 0.00 37.57 2.44
2305 2730 7.638444 TCCATCAAACTGGTCCTATTATCAAA 58.362 34.615 0.00 0.00 37.57 2.69
2306 2731 7.092444 ACTCCATCAAACTGGTCCTATTATCAA 60.092 37.037 0.00 0.00 37.57 2.57
2307 2732 6.386927 ACTCCATCAAACTGGTCCTATTATCA 59.613 38.462 0.00 0.00 37.57 2.15
2309 2734 6.831664 ACTCCATCAAACTGGTCCTATTAT 57.168 37.500 0.00 0.00 37.57 1.28
2310 2735 6.352737 GGAACTCCATCAAACTGGTCCTATTA 60.353 42.308 0.00 0.00 37.57 0.98
2311 2736 5.501156 GAACTCCATCAAACTGGTCCTATT 58.499 41.667 0.00 0.00 37.57 1.73
2314 2739 2.040412 GGAACTCCATCAAACTGGTCCT 59.960 50.000 0.00 0.00 37.57 3.85
2315 2740 2.437413 GGAACTCCATCAAACTGGTCC 58.563 52.381 0.00 0.00 37.57 4.46
2316 2741 2.224769 TGGGAACTCCATCAAACTGGTC 60.225 50.000 0.00 0.00 41.46 4.02
2317 2742 1.780309 TGGGAACTCCATCAAACTGGT 59.220 47.619 0.00 0.00 41.46 4.00
2318 2743 2.584835 TGGGAACTCCATCAAACTGG 57.415 50.000 0.00 0.00 41.46 4.00
2319 2744 4.935352 TTTTGGGAACTCCATCAAACTG 57.065 40.909 0.00 0.00 46.52 3.16
2320 2745 4.262592 GCATTTTGGGAACTCCATCAAACT 60.263 41.667 0.00 0.00 46.52 2.66
2321 2746 3.996363 GCATTTTGGGAACTCCATCAAAC 59.004 43.478 0.00 0.00 46.52 2.93
2322 2747 3.007831 GGCATTTTGGGAACTCCATCAAA 59.992 43.478 0.00 0.00 46.52 2.69
2323 2748 2.566724 GGCATTTTGGGAACTCCATCAA 59.433 45.455 0.00 0.00 46.52 2.57
2324 2749 2.178580 GGCATTTTGGGAACTCCATCA 58.821 47.619 0.00 0.00 46.52 3.07
2325 2750 1.482182 GGGCATTTTGGGAACTCCATC 59.518 52.381 0.00 0.00 46.52 3.51
2326 2751 1.571955 GGGCATTTTGGGAACTCCAT 58.428 50.000 0.00 0.00 46.52 3.41
2327 2752 0.897863 CGGGCATTTTGGGAACTCCA 60.898 55.000 0.00 0.00 45.43 3.86
2328 2753 0.610785 TCGGGCATTTTGGGAACTCC 60.611 55.000 0.00 0.00 0.00 3.85
2329 2754 0.526211 GTCGGGCATTTTGGGAACTC 59.474 55.000 0.00 0.00 0.00 3.01
2330 2755 0.112412 AGTCGGGCATTTTGGGAACT 59.888 50.000 0.00 0.00 0.00 3.01
2331 2756 0.526211 GAGTCGGGCATTTTGGGAAC 59.474 55.000 0.00 0.00 0.00 3.62
2332 2757 0.610785 GGAGTCGGGCATTTTGGGAA 60.611 55.000 0.00 0.00 0.00 3.97
2333 2758 1.001393 GGAGTCGGGCATTTTGGGA 60.001 57.895 0.00 0.00 0.00 4.37
2334 2759 0.897863 TTGGAGTCGGGCATTTTGGG 60.898 55.000 0.00 0.00 0.00 4.12
2335 2760 0.243636 GTTGGAGTCGGGCATTTTGG 59.756 55.000 0.00 0.00 0.00 3.28
2336 2761 0.109781 CGTTGGAGTCGGGCATTTTG 60.110 55.000 0.00 0.00 0.00 2.44
2337 2762 1.241315 CCGTTGGAGTCGGGCATTTT 61.241 55.000 0.00 0.00 43.68 1.82
2338 2763 1.674322 CCGTTGGAGTCGGGCATTT 60.674 57.895 0.00 0.00 43.68 2.32
2339 2764 2.046314 CCGTTGGAGTCGGGCATT 60.046 61.111 0.00 0.00 43.68 3.56
2347 2772 1.167851 CATGTCATTGCCGTTGGAGT 58.832 50.000 0.00 0.00 0.00 3.85
2354 2779 1.153978 GTGGTGCATGTCATTGCCG 60.154 57.895 0.00 0.00 42.06 5.69
2355 2780 1.153978 CGTGGTGCATGTCATTGCC 60.154 57.895 0.00 0.00 42.06 4.52
2356 2781 0.179181 CTCGTGGTGCATGTCATTGC 60.179 55.000 0.00 0.00 43.07 3.56
2360 2785 1.293179 CTCCTCGTGGTGCATGTCA 59.707 57.895 2.99 0.00 34.23 3.58
2362 2787 1.267574 ATCCTCCTCGTGGTGCATGT 61.268 55.000 2.99 0.00 34.23 3.21
2364 2789 0.977627 TCATCCTCCTCGTGGTGCAT 60.978 55.000 2.99 0.00 34.23 3.96
2365 2790 0.977627 ATCATCCTCCTCGTGGTGCA 60.978 55.000 2.99 0.00 34.23 4.57
2367 2792 0.105593 CCATCATCCTCCTCGTGGTG 59.894 60.000 2.99 0.65 34.23 4.17
2368 2793 1.690219 GCCATCATCCTCCTCGTGGT 61.690 60.000 2.99 0.00 34.23 4.16
2369 2794 1.070445 GCCATCATCCTCCTCGTGG 59.930 63.158 0.00 0.00 0.00 4.94
2370 2795 1.070445 GGCCATCATCCTCCTCGTG 59.930 63.158 0.00 0.00 0.00 4.35
2372 2797 1.670590 GAGGCCATCATCCTCCTCG 59.329 63.158 5.01 0.00 43.32 4.63
2379 2804 2.703007 AGTAGGTGAAGAGGCCATCATC 59.297 50.000 5.01 6.96 0.00 2.92
2380 2805 2.703007 GAGTAGGTGAAGAGGCCATCAT 59.297 50.000 5.01 0.00 0.00 2.45
2381 2806 2.111384 GAGTAGGTGAAGAGGCCATCA 58.889 52.381 5.01 3.24 0.00 3.07
2382 2807 1.414550 GGAGTAGGTGAAGAGGCCATC 59.585 57.143 5.01 0.00 0.00 3.51
2383 2808 1.501582 GGAGTAGGTGAAGAGGCCAT 58.498 55.000 5.01 0.00 0.00 4.40
2384 2809 0.970937 CGGAGTAGGTGAAGAGGCCA 60.971 60.000 5.01 0.00 0.00 5.36
2385 2810 0.683504 TCGGAGTAGGTGAAGAGGCC 60.684 60.000 0.00 0.00 0.00 5.19
2386 2811 0.456628 GTCGGAGTAGGTGAAGAGGC 59.543 60.000 0.00 0.00 0.00 4.70
2388 2813 1.104630 GGGTCGGAGTAGGTGAAGAG 58.895 60.000 0.00 0.00 0.00 2.85
2389 2814 0.324091 GGGGTCGGAGTAGGTGAAGA 60.324 60.000 0.00 0.00 0.00 2.87
2391 2816 1.679977 CGGGGTCGGAGTAGGTGAA 60.680 63.158 0.00 0.00 0.00 3.18
2393 2818 2.362120 ACGGGGTCGGAGTAGGTG 60.362 66.667 0.00 0.00 41.39 4.00
2394 2819 2.044551 GACGGGGTCGGAGTAGGT 60.045 66.667 0.00 0.00 41.39 3.08
2395 2820 2.832201 GGACGGGGTCGGAGTAGG 60.832 72.222 0.00 0.00 41.39 3.18
2396 2821 1.823041 GAGGACGGGGTCGGAGTAG 60.823 68.421 0.00 0.00 41.39 2.57
2397 2822 2.273449 GAGGACGGGGTCGGAGTA 59.727 66.667 0.00 0.00 41.39 2.59
2398 2823 4.755507 GGAGGACGGGGTCGGAGT 62.756 72.222 0.00 0.00 41.39 3.85
2403 2828 3.075641 GTCAGGGAGGACGGGGTC 61.076 72.222 0.00 0.00 0.00 4.46
2412 2837 4.135153 CGACCAGGCGTCAGGGAG 62.135 72.222 2.64 0.00 42.07 4.30
2414 2839 3.064987 CTACGACCAGGCGTCAGGG 62.065 68.421 0.00 0.00 44.39 4.45
2416 2841 2.202623 GCTACGACCAGGCGTCAG 60.203 66.667 0.00 0.00 44.39 3.51
2417 2842 3.755628 GGCTACGACCAGGCGTCA 61.756 66.667 0.00 0.00 44.39 4.35
2418 2843 4.509737 GGGCTACGACCAGGCGTC 62.510 72.222 0.00 0.00 44.39 5.19
2421 2846 2.056223 TACAGGGCTACGACCAGGC 61.056 63.158 0.00 0.00 40.27 4.85
2422 2847 0.968901 TGTACAGGGCTACGACCAGG 60.969 60.000 0.00 0.00 29.21 4.45
2426 2851 2.686915 AGTACATGTACAGGGCTACGAC 59.313 50.000 32.02 8.61 38.48 4.34
2427 2852 3.008835 AGTACATGTACAGGGCTACGA 57.991 47.619 32.02 0.00 38.48 3.43
2428 2853 3.380637 AGAAGTACATGTACAGGGCTACG 59.619 47.826 32.02 0.00 38.48 3.51
2429 2854 4.401519 TGAGAAGTACATGTACAGGGCTAC 59.598 45.833 32.02 18.14 38.48 3.58
2430 2855 4.606210 TGAGAAGTACATGTACAGGGCTA 58.394 43.478 32.02 14.49 38.48 3.93
2432 2857 3.887621 TGAGAAGTACATGTACAGGGC 57.112 47.619 32.02 20.29 38.48 5.19
2433 2858 4.405680 TCCATGAGAAGTACATGTACAGGG 59.594 45.833 32.02 22.91 42.16 4.45
2439 3006 5.503927 AGCAATTCCATGAGAAGTACATGT 58.496 37.500 2.69 2.69 42.16 3.21
2501 3127 4.408270 AGACACTATCATTCACAGGCAGAT 59.592 41.667 0.00 0.00 0.00 2.90
2502 3128 3.771479 AGACACTATCATTCACAGGCAGA 59.229 43.478 0.00 0.00 0.00 4.26
2503 3129 4.118410 GAGACACTATCATTCACAGGCAG 58.882 47.826 0.00 0.00 0.00 4.85
2504 3130 3.771479 AGAGACACTATCATTCACAGGCA 59.229 43.478 0.00 0.00 0.00 4.75
2505 3131 4.399004 AGAGACACTATCATTCACAGGC 57.601 45.455 0.00 0.00 0.00 4.85
2506 3132 6.276847 GGTAAGAGACACTATCATTCACAGG 58.723 44.000 0.00 0.00 0.00 4.00
2507 3133 6.097554 AGGGTAAGAGACACTATCATTCACAG 59.902 42.308 0.00 0.00 41.34 3.66
2508 3134 5.958380 AGGGTAAGAGACACTATCATTCACA 59.042 40.000 0.00 0.00 41.34 3.58
2509 3135 6.322712 AGAGGGTAAGAGACACTATCATTCAC 59.677 42.308 0.00 0.00 44.07 3.18
2510 3136 6.436027 AGAGGGTAAGAGACACTATCATTCA 58.564 40.000 0.00 0.00 44.07 2.57
2511 3137 6.969993 AGAGGGTAAGAGACACTATCATTC 57.030 41.667 0.00 0.00 44.07 2.67
2512 3138 7.355101 TGTAGAGGGTAAGAGACACTATCATT 58.645 38.462 0.00 0.00 44.07 2.57
2513 3139 6.912426 TGTAGAGGGTAAGAGACACTATCAT 58.088 40.000 0.00 0.00 44.07 2.45
2514 3140 6.323210 TGTAGAGGGTAAGAGACACTATCA 57.677 41.667 0.00 0.00 44.07 2.15
2515 3141 6.773685 ACATGTAGAGGGTAAGAGACACTATC 59.226 42.308 0.00 0.00 44.07 2.08
2516 3142 6.674573 ACATGTAGAGGGTAAGAGACACTAT 58.325 40.000 0.00 0.00 44.07 2.12
2517 3143 6.075949 ACATGTAGAGGGTAAGAGACACTA 57.924 41.667 0.00 0.00 44.07 2.74
2519 3145 5.185249 TCAACATGTAGAGGGTAAGAGACAC 59.815 44.000 0.00 0.00 0.00 3.67
2520 3146 5.185249 GTCAACATGTAGAGGGTAAGAGACA 59.815 44.000 0.00 0.00 0.00 3.41
2521 3147 5.394333 GGTCAACATGTAGAGGGTAAGAGAC 60.394 48.000 0.00 0.00 0.00 3.36
2522 3148 4.710375 GGTCAACATGTAGAGGGTAAGAGA 59.290 45.833 0.00 0.00 0.00 3.10
2647 3297 4.341235 GGAGTAGCCTTTTTCTTGTGGTTT 59.659 41.667 0.00 0.00 0.00 3.27
2670 3321 8.009974 GGAAGCATATACTACATAACAAAAGCG 58.990 37.037 0.00 0.00 0.00 4.68
2697 3377 6.546484 AGCCATTATGGTATAAGAGCAACAT 58.454 36.000 13.28 0.00 40.46 2.71
2714 3394 8.607441 CATGAGTAATGTTAGCTAAGCCATTA 57.393 34.615 18.59 18.59 0.00 1.90
2715 3395 7.502120 CATGAGTAATGTTAGCTAAGCCATT 57.498 36.000 20.08 20.08 0.00 3.16
2774 3454 3.827008 AACAGATGCTATCACGGACAT 57.173 42.857 0.00 0.00 0.00 3.06
2802 3482 3.190744 GCAACATGGATGAGCATATCCTG 59.809 47.826 17.06 14.57 45.59 3.86
2835 3515 8.709646 GTCATATAATGGTAAGAAGTTAAGCGG 58.290 37.037 0.00 0.00 0.00 5.52
2890 3570 4.341520 GGGGTGTATCAATAAGACTCGTCT 59.658 45.833 0.00 0.00 42.75 4.18
2966 3650 5.815581 AGAAATTGTACACAGGCAAGGATA 58.184 37.500 0.00 0.00 0.00 2.59
2968 3652 4.098914 AGAAATTGTACACAGGCAAGGA 57.901 40.909 0.00 0.00 0.00 3.36
3020 3704 5.756918 TCCCGATTCCATTTTACCATGTAA 58.243 37.500 0.00 0.00 0.00 2.41
3065 3750 8.409358 AACAAAAGCAGGAGTAACATATTCTT 57.591 30.769 0.00 0.00 0.00 2.52
3079 3764 5.248870 AGGCGATAAATAACAAAAGCAGG 57.751 39.130 0.00 0.00 0.00 4.85
3107 3792 5.057149 GCATACCAGGGATAAACTGTACAG 58.943 45.833 21.44 21.44 34.16 2.74
3135 3820 9.259832 TGAGCCATGATGATATAGTAGTAACAT 57.740 33.333 0.00 0.00 0.00 2.71
3194 3879 2.238646 ACCATGGCCGAATTCTGACTTA 59.761 45.455 13.04 0.00 0.00 2.24
3277 3962 1.291877 CGCACGAGCTAAGCAAACCT 61.292 55.000 2.73 0.00 39.10 3.50
3307 3993 4.241555 GGATCCGTGCGGGCATCT 62.242 66.667 10.94 0.00 34.94 2.90


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

AutoCloner maintained by Alex Coulton.