Multiple sequence alignment - TraesCS4D01G049800

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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 TraesCS4D01G049800 chr4D 100.000 2411 0 0 1 2411 25490942 25493352 0.000000e+00 4453.0
1 TraesCS4D01G049800 chr4D 96.319 1141 24 3 313 1439 461374207 461375343 0.000000e+00 1858.0
2 TraesCS4D01G049800 chr4D 92.382 1142 59 8 313 1440 117431463 117430336 0.000000e+00 1602.0
3 TraesCS4D01G049800 chr6D 96.943 1145 20 2 313 1443 20292250 20291107 0.000000e+00 1906.0
4 TraesCS4D01G049800 chr6A 95.706 1141 28 4 313 1439 398542696 398543829 0.000000e+00 1816.0
5 TraesCS4D01G049800 chr2B 95.088 1140 40 3 313 1438 776897902 776896765 0.000000e+00 1781.0
6 TraesCS4D01G049800 chr2B 94.658 1142 37 5 313 1440 58835850 58836981 0.000000e+00 1749.0
7 TraesCS4D01G049800 chr2B 91.099 191 11 6 1940 2126 646964516 646964328 1.110000e-63 254.0
8 TraesCS4D01G049800 chr2B 88.889 90 6 4 46 134 84971882 84971968 9.110000e-20 108.0
9 TraesCS4D01G049800 chr1D 96.670 1051 21 1 404 1440 125758032 125759082 0.000000e+00 1735.0
10 TraesCS4D01G049800 chr1D 84.174 436 57 11 1771 2197 356143711 356143279 1.720000e-111 412.0
11 TraesCS4D01G049800 chr1D 88.889 135 14 1 1 134 470486140 470486274 5.330000e-37 165.0
12 TraesCS4D01G049800 chr2D 93.509 1140 58 8 313 1438 649290425 649289288 0.000000e+00 1681.0
13 TraesCS4D01G049800 chr2D 94.409 930 38 1 313 1228 604317670 604318599 0.000000e+00 1417.0
14 TraesCS4D01G049800 chr1B 92.308 1144 71 9 313 1442 37033243 37032103 0.000000e+00 1609.0
15 TraesCS4D01G049800 chr1B 80.371 647 82 26 1565 2185 478717748 478717121 1.310000e-122 449.0
16 TraesCS4D01G049800 chr1B 82.394 142 20 5 2 140 51942439 51942578 4.210000e-23 119.0
17 TraesCS4D01G049800 chr1A 93.015 1088 60 4 313 1386 495184527 495183442 0.000000e+00 1574.0
18 TraesCS4D01G049800 chr1A 81.085 645 88 24 1563 2185 456938253 456937621 3.600000e-133 484.0
19 TraesCS4D01G049800 chr3D 97.739 796 17 1 645 1440 554395580 554394786 0.000000e+00 1369.0
20 TraesCS4D01G049800 chr3D 93.855 358 8 1 313 656 554396259 554396616 5.900000e-146 527.0
21 TraesCS4D01G049800 chr4B 94.811 848 28 3 311 1143 3818731 3819577 0.000000e+00 1308.0
22 TraesCS4D01G049800 chr4B 86.228 639 46 24 1793 2403 37855315 37855939 0.000000e+00 654.0
23 TraesCS4D01G049800 chr4B 89.873 158 13 1 160 314 37854913 37855070 1.460000e-47 200.0
24 TraesCS4D01G049800 chr4B 79.670 182 14 6 1439 1613 37855055 37855220 2.530000e-20 110.0
25 TraesCS4D01G049800 chr4A 85.624 633 63 19 1793 2411 577541241 577540623 7.270000e-180 640.0
26 TraesCS4D01G049800 chr4A 83.025 324 32 17 1812 2122 622181993 622182306 3.050000e-69 272.0
27 TraesCS4D01G049800 chr4A 97.143 35 1 0 1656 1690 577541395 577541361 2.590000e-05 60.2
28 TraesCS4D01G049800 chrUn 90.642 374 15 6 313 686 311952727 311953080 1.680000e-131 479.0
29 TraesCS4D01G049800 chr3B 92.130 216 11 6 1924 2136 116146165 116145953 1.400000e-77 300.0
30 TraesCS4D01G049800 chr5B 83.175 315 36 11 1819 2122 689915357 689915665 3.050000e-69 272.0
31 TraesCS4D01G049800 chr3A 98.413 63 0 1 1374 1436 556456981 556456920 2.530000e-20 110.0


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 TraesCS4D01G049800 chr4D 25490942 25493352 2410 False 4453.000000 4453 100.0000 1 2411 1 chr4D.!!$F1 2410
1 TraesCS4D01G049800 chr4D 461374207 461375343 1136 False 1858.000000 1858 96.3190 313 1439 1 chr4D.!!$F2 1126
2 TraesCS4D01G049800 chr4D 117430336 117431463 1127 True 1602.000000 1602 92.3820 313 1440 1 chr4D.!!$R1 1127
3 TraesCS4D01G049800 chr6D 20291107 20292250 1143 True 1906.000000 1906 96.9430 313 1443 1 chr6D.!!$R1 1130
4 TraesCS4D01G049800 chr6A 398542696 398543829 1133 False 1816.000000 1816 95.7060 313 1439 1 chr6A.!!$F1 1126
5 TraesCS4D01G049800 chr2B 776896765 776897902 1137 True 1781.000000 1781 95.0880 313 1438 1 chr2B.!!$R2 1125
6 TraesCS4D01G049800 chr2B 58835850 58836981 1131 False 1749.000000 1749 94.6580 313 1440 1 chr2B.!!$F1 1127
7 TraesCS4D01G049800 chr1D 125758032 125759082 1050 False 1735.000000 1735 96.6700 404 1440 1 chr1D.!!$F1 1036
8 TraesCS4D01G049800 chr2D 649289288 649290425 1137 True 1681.000000 1681 93.5090 313 1438 1 chr2D.!!$R1 1125
9 TraesCS4D01G049800 chr2D 604317670 604318599 929 False 1417.000000 1417 94.4090 313 1228 1 chr2D.!!$F1 915
10 TraesCS4D01G049800 chr1B 37032103 37033243 1140 True 1609.000000 1609 92.3080 313 1442 1 chr1B.!!$R1 1129
11 TraesCS4D01G049800 chr1B 478717121 478717748 627 True 449.000000 449 80.3710 1565 2185 1 chr1B.!!$R2 620
12 TraesCS4D01G049800 chr1A 495183442 495184527 1085 True 1574.000000 1574 93.0150 313 1386 1 chr1A.!!$R2 1073
13 TraesCS4D01G049800 chr1A 456937621 456938253 632 True 484.000000 484 81.0850 1563 2185 1 chr1A.!!$R1 622
14 TraesCS4D01G049800 chr3D 554394786 554395580 794 True 1369.000000 1369 97.7390 645 1440 1 chr3D.!!$R1 795
15 TraesCS4D01G049800 chr4B 3818731 3819577 846 False 1308.000000 1308 94.8110 311 1143 1 chr4B.!!$F1 832
16 TraesCS4D01G049800 chr4B 37854913 37855939 1026 False 321.333333 654 85.2570 160 2403 3 chr4B.!!$F2 2243
17 TraesCS4D01G049800 chr4A 577540623 577541395 772 True 350.100000 640 91.3835 1656 2411 2 chr4A.!!$R1 755

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
406 410 1.514678 GACAAACTCATGGCGCCACA 61.515 55.0 35.5 21.01 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2270 2777 0.036388 CCTAAAGGGCGCAGTCTTGA 60.036 55.0 10.83 1.88 0.0 3.02 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
37 38 9.981114 AAAAACTAGGGTTCATAATTTTGTGAG 57.019 29.630 0.00 0.00 34.14 3.51
38 39 8.934023 AAACTAGGGTTCATAATTTTGTGAGA 57.066 30.769 0.00 0.00 34.14 3.27
39 40 9.533831 AAACTAGGGTTCATAATTTTGTGAGAT 57.466 29.630 0.00 0.00 34.14 2.75
40 41 9.533831 AACTAGGGTTCATAATTTTGTGAGATT 57.466 29.630 0.00 0.00 29.93 2.40
61 62 7.374272 AGATTAATCTCATGTCGTGTATCTGG 58.626 38.462 12.37 0.00 29.30 3.86
62 63 4.327982 AATCTCATGTCGTGTATCTGGG 57.672 45.455 0.00 0.00 0.00 4.45
63 64 2.735151 TCTCATGTCGTGTATCTGGGT 58.265 47.619 0.00 0.00 0.00 4.51
64 65 3.096852 TCTCATGTCGTGTATCTGGGTT 58.903 45.455 0.00 0.00 0.00 4.11
65 66 4.274978 TCTCATGTCGTGTATCTGGGTTA 58.725 43.478 0.00 0.00 0.00 2.85
66 67 4.097437 TCTCATGTCGTGTATCTGGGTTAC 59.903 45.833 0.00 0.00 0.00 2.50
67 68 4.021229 TCATGTCGTGTATCTGGGTTACT 58.979 43.478 0.00 0.00 0.00 2.24
68 69 4.464951 TCATGTCGTGTATCTGGGTTACTT 59.535 41.667 0.00 0.00 0.00 2.24
69 70 4.182693 TGTCGTGTATCTGGGTTACTTG 57.817 45.455 0.00 0.00 0.00 3.16
70 71 3.575256 TGTCGTGTATCTGGGTTACTTGT 59.425 43.478 0.00 0.00 0.00 3.16
71 72 4.766373 TGTCGTGTATCTGGGTTACTTGTA 59.234 41.667 0.00 0.00 0.00 2.41
72 73 5.243507 TGTCGTGTATCTGGGTTACTTGTAA 59.756 40.000 0.00 0.00 0.00 2.41
73 74 5.574443 GTCGTGTATCTGGGTTACTTGTAAC 59.426 44.000 13.49 13.49 0.00 2.50
74 75 5.243507 TCGTGTATCTGGGTTACTTGTAACA 59.756 40.000 20.70 5.30 0.00 2.41
75 76 5.927689 CGTGTATCTGGGTTACTTGTAACAA 59.072 40.000 20.70 10.49 0.00 2.83
76 77 6.424509 CGTGTATCTGGGTTACTTGTAACAAA 59.575 38.462 20.70 10.22 0.00 2.83
77 78 7.569957 CGTGTATCTGGGTTACTTGTAACAAAC 60.570 40.741 20.70 12.77 0.00 2.93
78 79 7.443272 GTGTATCTGGGTTACTTGTAACAAACT 59.557 37.037 20.70 7.64 0.00 2.66
79 80 7.658575 TGTATCTGGGTTACTTGTAACAAACTC 59.341 37.037 20.70 7.01 0.00 3.01
80 81 6.243216 TCTGGGTTACTTGTAACAAACTCT 57.757 37.500 20.70 0.00 0.00 3.24
81 82 7.364149 TCTGGGTTACTTGTAACAAACTCTA 57.636 36.000 20.70 4.98 0.00 2.43
82 83 7.970102 TCTGGGTTACTTGTAACAAACTCTAT 58.030 34.615 20.70 0.00 0.00 1.98
83 84 8.434392 TCTGGGTTACTTGTAACAAACTCTATT 58.566 33.333 20.70 0.00 0.00 1.73
84 85 8.983702 TGGGTTACTTGTAACAAACTCTATTT 57.016 30.769 20.70 0.00 0.00 1.40
85 86 9.059260 TGGGTTACTTGTAACAAACTCTATTTC 57.941 33.333 20.70 3.82 0.00 2.17
86 87 9.281371 GGGTTACTTGTAACAAACTCTATTTCT 57.719 33.333 20.70 0.00 0.00 2.52
89 90 7.981102 ACTTGTAACAAACTCTATTTCTCCC 57.019 36.000 0.00 0.00 0.00 4.30
90 91 7.746703 ACTTGTAACAAACTCTATTTCTCCCT 58.253 34.615 0.00 0.00 0.00 4.20
91 92 8.218488 ACTTGTAACAAACTCTATTTCTCCCTT 58.782 33.333 0.00 0.00 0.00 3.95
92 93 9.720769 CTTGTAACAAACTCTATTTCTCCCTTA 57.279 33.333 0.00 0.00 0.00 2.69
107 108 7.765695 TTCTCCCTTATTTAATGGATGATGC 57.234 36.000 0.00 0.00 31.11 3.91
108 109 6.851318 TCTCCCTTATTTAATGGATGATGCA 58.149 36.000 0.00 0.00 31.11 3.96
109 110 7.296856 TCTCCCTTATTTAATGGATGATGCAA 58.703 34.615 0.00 0.00 31.11 4.08
110 111 7.784073 TCTCCCTTATTTAATGGATGATGCAAA 59.216 33.333 0.00 0.00 31.11 3.68
111 112 7.954835 TCCCTTATTTAATGGATGATGCAAAG 58.045 34.615 0.00 0.00 0.00 2.77
112 113 6.647895 CCCTTATTTAATGGATGATGCAAAGC 59.352 38.462 0.00 0.00 0.00 3.51
113 114 7.439381 CCTTATTTAATGGATGATGCAAAGCT 58.561 34.615 0.00 0.00 0.00 3.74
114 115 7.929785 CCTTATTTAATGGATGATGCAAAGCTT 59.070 33.333 0.00 0.00 0.00 3.74
115 116 9.321562 CTTATTTAATGGATGATGCAAAGCTTT 57.678 29.630 5.69 5.69 0.00 3.51
116 117 9.669887 TTATTTAATGGATGATGCAAAGCTTTT 57.330 25.926 9.53 0.00 0.00 2.27
117 118 6.971527 TTAATGGATGATGCAAAGCTTTTG 57.028 33.333 9.53 6.62 0.00 2.44
118 119 4.546829 ATGGATGATGCAAAGCTTTTGT 57.453 36.364 9.53 0.00 0.00 2.83
119 120 3.916761 TGGATGATGCAAAGCTTTTGTC 58.083 40.909 9.53 8.45 0.00 3.18
120 121 3.575256 TGGATGATGCAAAGCTTTTGTCT 59.425 39.130 9.53 0.00 0.00 3.41
121 122 4.039488 TGGATGATGCAAAGCTTTTGTCTT 59.961 37.500 9.53 6.20 0.00 3.01
122 123 4.624452 GGATGATGCAAAGCTTTTGTCTTC 59.376 41.667 9.53 13.70 0.00 2.87
123 124 3.631144 TGATGCAAAGCTTTTGTCTTCG 58.369 40.909 9.53 0.00 0.00 3.79
124 125 3.066621 TGATGCAAAGCTTTTGTCTTCGT 59.933 39.130 9.53 0.00 0.00 3.85
125 126 3.502191 TGCAAAGCTTTTGTCTTCGTT 57.498 38.095 9.53 0.00 0.00 3.85
126 127 3.843999 TGCAAAGCTTTTGTCTTCGTTT 58.156 36.364 9.53 0.00 0.00 3.60
127 128 4.241681 TGCAAAGCTTTTGTCTTCGTTTT 58.758 34.783 9.53 0.00 0.00 2.43
128 129 5.403246 TGCAAAGCTTTTGTCTTCGTTTTA 58.597 33.333 9.53 0.00 0.00 1.52
129 130 5.864474 TGCAAAGCTTTTGTCTTCGTTTTAA 59.136 32.000 9.53 0.00 0.00 1.52
130 131 6.366332 TGCAAAGCTTTTGTCTTCGTTTTAAA 59.634 30.769 9.53 0.00 0.00 1.52
131 132 7.095607 TGCAAAGCTTTTGTCTTCGTTTTAAAA 60.096 29.630 9.53 0.00 0.00 1.52
132 133 7.742525 GCAAAGCTTTTGTCTTCGTTTTAAAAA 59.257 29.630 9.53 0.00 0.00 1.94
173 174 7.786178 TTCATCCTATTTCATCCTAACGTTG 57.214 36.000 11.99 0.68 0.00 4.10
178 179 4.946784 ATTTCATCCTAACGTTGTCTGC 57.053 40.909 11.99 0.00 0.00 4.26
197 198 4.780021 TCTGCCTCAACCTAGAGAAGATTT 59.220 41.667 0.00 0.00 37.87 2.17
200 201 5.940470 TGCCTCAACCTAGAGAAGATTTTTC 59.060 40.000 0.00 0.00 37.87 2.29
201 202 5.355630 GCCTCAACCTAGAGAAGATTTTTCC 59.644 44.000 0.00 0.00 37.87 3.13
221 222 2.026449 CCAAAGCCTTGAGGATCTGTCT 60.026 50.000 0.06 0.00 37.39 3.41
234 235 6.427853 TGAGGATCTGTCTGTTTTGTACAATG 59.572 38.462 9.56 1.00 33.66 2.82
237 238 6.349611 GGATCTGTCTGTTTTGTACAATGCAT 60.350 38.462 9.56 0.00 36.02 3.96
277 278 8.818622 ATGATTTGGGATATCTGATATGGTTG 57.181 34.615 14.60 0.00 0.00 3.77
278 279 7.987820 TGATTTGGGATATCTGATATGGTTGA 58.012 34.615 14.60 0.00 0.00 3.18
310 314 5.925506 AATGTGGATCAATGATTTGCAGA 57.074 34.783 0.00 0.00 32.61 4.26
311 315 5.925506 ATGTGGATCAATGATTTGCAGAA 57.074 34.783 0.00 0.00 32.61 3.02
406 410 1.514678 GACAAACTCATGGCGCCACA 61.515 55.000 35.50 21.01 0.00 4.17
414 418 1.674322 ATGGCGCCACAGGTACAAC 60.674 57.895 35.50 0.00 0.00 3.32
1205 1605 4.023707 GCTTGCACAGATACAAAACAGTCT 60.024 41.667 0.00 0.00 0.00 3.24
1307 1707 7.101652 TGAAAGTTAAAAACAGCCATGTACA 57.898 32.000 0.00 0.00 39.29 2.90
1371 1780 3.582164 GGATTCCCTCTCTGTATCCAGT 58.418 50.000 0.00 0.00 39.82 4.00
1464 1873 2.435586 CAGAACTGCCAGCTCCGG 60.436 66.667 0.00 0.00 0.00 5.14
1465 1874 3.710722 AGAACTGCCAGCTCCGGG 61.711 66.667 0.00 0.00 0.00 5.73
1466 1875 3.706373 GAACTGCCAGCTCCGGGA 61.706 66.667 0.00 0.00 0.00 5.14
1467 1876 3.011517 AACTGCCAGCTCCGGGAT 61.012 61.111 0.00 0.00 0.00 3.85
1468 1877 2.932130 GAACTGCCAGCTCCGGGATC 62.932 65.000 0.00 0.00 0.00 3.36
1469 1878 3.473647 CTGCCAGCTCCGGGATCA 61.474 66.667 0.00 0.00 0.00 2.92
1470 1879 2.769621 TGCCAGCTCCGGGATCAT 60.770 61.111 0.00 0.00 0.00 2.45
1471 1880 1.459348 TGCCAGCTCCGGGATCATA 60.459 57.895 0.00 0.00 0.00 2.15
1472 1881 0.837691 TGCCAGCTCCGGGATCATAT 60.838 55.000 0.00 0.00 0.00 1.78
1473 1882 1.195115 GCCAGCTCCGGGATCATATA 58.805 55.000 0.00 0.00 0.00 0.86
1474 1883 1.555075 GCCAGCTCCGGGATCATATAA 59.445 52.381 0.00 0.00 0.00 0.98
1475 1884 2.171448 GCCAGCTCCGGGATCATATAAT 59.829 50.000 0.00 0.00 0.00 1.28
1476 1885 3.370953 GCCAGCTCCGGGATCATATAATT 60.371 47.826 0.00 0.00 0.00 1.40
1477 1886 4.848357 CCAGCTCCGGGATCATATAATTT 58.152 43.478 0.00 0.00 0.00 1.82
1478 1887 5.629133 GCCAGCTCCGGGATCATATAATTTA 60.629 44.000 0.00 0.00 0.00 1.40
1479 1888 6.595682 CCAGCTCCGGGATCATATAATTTAT 58.404 40.000 0.00 0.00 0.00 1.40
1480 1889 7.689313 GCCAGCTCCGGGATCATATAATTTATA 60.689 40.741 0.00 0.00 0.00 0.98
1481 1890 8.210946 CCAGCTCCGGGATCATATAATTTATAA 58.789 37.037 0.00 0.00 0.00 0.98
1482 1891 9.784531 CAGCTCCGGGATCATATAATTTATAAT 57.215 33.333 0.00 0.00 0.00 1.28
1501 1910 4.762956 AATCTCTGAAGCAAAACTCTGC 57.237 40.909 0.00 0.00 42.97 4.26
1516 1925 3.296322 CTCTGCGAGAGTTTCTCTTGT 57.704 47.619 13.42 0.00 41.35 3.16
1517 1926 4.427096 CTCTGCGAGAGTTTCTCTTGTA 57.573 45.455 13.42 9.34 41.35 2.41
1518 1927 4.799678 CTCTGCGAGAGTTTCTCTTGTAA 58.200 43.478 13.42 4.50 41.35 2.41
1519 1928 5.196341 TCTGCGAGAGTTTCTCTTGTAAA 57.804 39.130 13.42 0.00 41.35 2.01
1520 1929 5.784177 TCTGCGAGAGTTTCTCTTGTAAAT 58.216 37.500 13.42 0.00 41.35 1.40
1521 1930 5.864474 TCTGCGAGAGTTTCTCTTGTAAATC 59.136 40.000 13.42 0.00 41.35 2.17
1522 1931 5.784177 TGCGAGAGTTTCTCTTGTAAATCT 58.216 37.500 13.42 0.00 41.35 2.40
1523 1932 5.635280 TGCGAGAGTTTCTCTTGTAAATCTG 59.365 40.000 13.42 0.00 41.35 2.90
1524 1933 5.445275 GCGAGAGTTTCTCTTGTAAATCTGC 60.445 44.000 13.42 0.00 41.35 4.26
1525 1934 5.866633 CGAGAGTTTCTCTTGTAAATCTGCT 59.133 40.000 4.73 0.00 41.35 4.24
1526 1935 6.034470 CGAGAGTTTCTCTTGTAAATCTGCTC 59.966 42.308 4.73 0.00 41.35 4.26
1527 1936 5.866633 AGAGTTTCTCTTGTAAATCTGCTCG 59.133 40.000 0.00 0.00 37.60 5.03
1528 1937 4.390297 AGTTTCTCTTGTAAATCTGCTCGC 59.610 41.667 0.00 0.00 0.00 5.03
1529 1938 3.592898 TCTCTTGTAAATCTGCTCGCA 57.407 42.857 0.00 0.00 0.00 5.10
1530 1939 3.515630 TCTCTTGTAAATCTGCTCGCAG 58.484 45.455 12.54 12.54 44.86 5.18
1531 1940 2.002586 TCTTGTAAATCTGCTCGCAGC 58.997 47.619 13.83 0.00 43.31 5.25
1532 1941 1.063174 CTTGTAAATCTGCTCGCAGCC 59.937 52.381 13.83 0.86 41.51 4.85
1533 1942 0.250234 TGTAAATCTGCTCGCAGCCT 59.750 50.000 13.83 1.41 41.51 4.58
1534 1943 0.654683 GTAAATCTGCTCGCAGCCTG 59.345 55.000 13.83 0.00 41.51 4.85
1535 1944 0.536724 TAAATCTGCTCGCAGCCTGA 59.463 50.000 13.83 0.00 41.51 3.86
1536 1945 0.321919 AAATCTGCTCGCAGCCTGAA 60.322 50.000 13.83 0.00 41.51 3.02
1537 1946 0.321919 AATCTGCTCGCAGCCTGAAA 60.322 50.000 13.83 0.00 41.51 2.69
1538 1947 0.743701 ATCTGCTCGCAGCCTGAAAG 60.744 55.000 13.83 0.00 41.51 2.62
1539 1948 3.036783 CTGCTCGCAGCCTGAAAGC 62.037 63.158 5.91 10.75 41.51 3.51
1540 1949 2.745492 GCTCGCAGCCTGAAAGCT 60.745 61.111 10.48 0.00 46.45 3.74
1541 1950 2.748843 GCTCGCAGCCTGAAAGCTC 61.749 63.158 10.48 0.00 42.61 4.09
1542 1951 2.433145 TCGCAGCCTGAAAGCTCG 60.433 61.111 0.00 0.00 42.61 5.03
1543 1952 3.494336 CGCAGCCTGAAAGCTCGG 61.494 66.667 0.00 0.00 42.61 4.63
1544 1953 2.046892 GCAGCCTGAAAGCTCGGA 60.047 61.111 0.00 0.00 42.61 4.55
1545 1954 1.672356 GCAGCCTGAAAGCTCGGAA 60.672 57.895 0.00 0.00 42.61 4.30
1546 1955 1.916697 GCAGCCTGAAAGCTCGGAAC 61.917 60.000 0.00 0.00 42.61 3.62
1547 1956 0.603707 CAGCCTGAAAGCTCGGAACA 60.604 55.000 0.00 0.00 42.61 3.18
1548 1957 0.108585 AGCCTGAAAGCTCGGAACAA 59.891 50.000 0.00 0.00 39.48 2.83
1549 1958 0.951558 GCCTGAAAGCTCGGAACAAA 59.048 50.000 0.00 0.00 0.00 2.83
1550 1959 1.541588 GCCTGAAAGCTCGGAACAAAT 59.458 47.619 0.00 0.00 0.00 2.32
1551 1960 2.669391 GCCTGAAAGCTCGGAACAAATG 60.669 50.000 0.00 0.00 0.00 2.32
1552 1961 2.589014 CTGAAAGCTCGGAACAAATGC 58.411 47.619 0.00 0.00 0.00 3.56
1553 1962 1.952990 TGAAAGCTCGGAACAAATGCA 59.047 42.857 0.00 0.00 0.00 3.96
1554 1963 2.287547 TGAAAGCTCGGAACAAATGCAC 60.288 45.455 0.00 0.00 0.00 4.57
1555 1964 1.317613 AAGCTCGGAACAAATGCACA 58.682 45.000 0.00 0.00 0.00 4.57
1556 1965 1.538047 AGCTCGGAACAAATGCACAT 58.462 45.000 0.00 0.00 0.00 3.21
1557 1966 2.710377 AGCTCGGAACAAATGCACATA 58.290 42.857 0.00 0.00 0.00 2.29
1558 1967 3.282021 AGCTCGGAACAAATGCACATAT 58.718 40.909 0.00 0.00 0.00 1.78
1559 1968 4.450976 AGCTCGGAACAAATGCACATATA 58.549 39.130 0.00 0.00 0.00 0.86
1560 1969 4.273480 AGCTCGGAACAAATGCACATATAC 59.727 41.667 0.00 0.00 0.00 1.47
1561 1970 4.035091 GCTCGGAACAAATGCACATATACA 59.965 41.667 0.00 0.00 0.00 2.29
1562 1971 5.277974 GCTCGGAACAAATGCACATATACAT 60.278 40.000 0.00 0.00 0.00 2.29
1563 1972 6.073276 GCTCGGAACAAATGCACATATACATA 60.073 38.462 0.00 0.00 0.00 2.29
1628 2044 4.145807 ACGGAGTATGGACTATGAAGAGG 58.854 47.826 0.00 0.00 41.94 3.69
1630 2046 3.259625 GGAGTATGGACTATGAAGAGGGC 59.740 52.174 0.00 0.00 35.45 5.19
1653 2069 3.368571 GCTGCCTCCTGTGTTGGC 61.369 66.667 0.00 0.00 46.26 4.52
1711 2127 8.492673 AAAAATTGAGGAAAAGAAAACCAGTC 57.507 30.769 0.00 0.00 0.00 3.51
1714 2130 6.850752 TTGAGGAAAAGAAAACCAGTCTTT 57.149 33.333 0.00 0.00 45.14 2.52
1739 2155 2.579410 TTGAGGGGCAGTAGAAAACC 57.421 50.000 0.00 0.00 0.00 3.27
1742 2158 1.351350 GAGGGGCAGTAGAAAACCAGT 59.649 52.381 0.00 0.00 0.00 4.00
1743 2159 1.351350 AGGGGCAGTAGAAAACCAGTC 59.649 52.381 0.00 0.00 0.00 3.51
1745 2161 2.488347 GGGGCAGTAGAAAACCAGTCAA 60.488 50.000 0.00 0.00 0.00 3.18
1775 2192 0.109723 TCTCCCCCACGGTGAAAAAG 59.890 55.000 10.28 2.26 31.05 2.27
1800 2293 2.401766 CCACATCGGCAAGGCTCAC 61.402 63.158 0.00 0.00 0.00 3.51
1832 2325 0.751643 GCATGAAGGCCCATTACGGT 60.752 55.000 0.00 0.00 0.00 4.83
1864 2357 1.274703 TGGGCCAGACCAAGAGATCC 61.275 60.000 0.00 0.00 42.05 3.36
1869 2362 0.179936 CAGACCAAGAGATCCAGCCC 59.820 60.000 0.00 0.00 0.00 5.19
1876 2369 0.616111 AGAGATCCAGCCCACTCGTT 60.616 55.000 0.00 0.00 34.98 3.85
1896 2389 4.953868 CCACCGCACGTTCCGACA 62.954 66.667 6.92 0.00 0.00 4.35
1910 2403 3.749064 GACAGCGCTCCCGTCTGA 61.749 66.667 7.13 0.00 39.37 3.27
1912 2405 2.048222 CAGCGCTCCCGTCTGAAA 60.048 61.111 7.13 0.00 39.37 2.69
1915 2408 0.951040 AGCGCTCCCGTCTGAAAAAG 60.951 55.000 2.64 0.00 36.67 2.27
1918 2411 0.519077 GCTCCCGTCTGAAAAAGCAG 59.481 55.000 0.00 0.00 37.24 4.24
1967 2460 1.153449 CCCACATCGGCTAGCGAAA 60.153 57.895 9.00 0.00 0.00 3.46
1975 2468 1.132643 TCGGCTAGCGAAAGAGAGAAC 59.867 52.381 9.00 0.00 0.00 3.01
2135 2634 0.330267 GGATTTTCCGGTCCCTGGAA 59.670 55.000 0.00 0.32 43.59 3.53
2140 2639 0.109723 TTCCGGTCCCTGGAAACTTG 59.890 55.000 0.00 0.00 42.37 3.16
2159 2660 4.043200 GTTGAGCCCCTTGTGCGC 62.043 66.667 0.00 0.00 0.00 6.09
2166 2667 4.034258 CCCTTGTGCGCAGTGCTG 62.034 66.667 12.22 8.05 46.63 4.41
2185 2686 3.630312 GCTGTTTTACAAAGTGGTCCTCA 59.370 43.478 0.00 0.00 0.00 3.86
2187 2688 5.472137 GCTGTTTTACAAAGTGGTCCTCATA 59.528 40.000 0.00 0.00 0.00 2.15
2188 2689 6.348540 GCTGTTTTACAAAGTGGTCCTCATAG 60.349 42.308 0.00 0.00 0.00 2.23
2189 2690 5.472137 TGTTTTACAAAGTGGTCCTCATAGC 59.528 40.000 0.00 0.00 0.00 2.97
2190 2691 5.499004 TTTACAAAGTGGTCCTCATAGCT 57.501 39.130 0.00 0.00 0.00 3.32
2195 2696 4.373156 AAGTGGTCCTCATAGCTTTTGT 57.627 40.909 0.00 0.00 0.00 2.83
2196 2697 4.373156 AGTGGTCCTCATAGCTTTTGTT 57.627 40.909 0.00 0.00 0.00 2.83
2197 2698 4.729868 AGTGGTCCTCATAGCTTTTGTTT 58.270 39.130 0.00 0.00 0.00 2.83
2198 2699 5.140454 AGTGGTCCTCATAGCTTTTGTTTT 58.860 37.500 0.00 0.00 0.00 2.43
2199 2700 5.598417 AGTGGTCCTCATAGCTTTTGTTTTT 59.402 36.000 0.00 0.00 0.00 1.94
2200 2701 5.691754 GTGGTCCTCATAGCTTTTGTTTTTG 59.308 40.000 0.00 0.00 0.00 2.44
2201 2702 4.686091 GGTCCTCATAGCTTTTGTTTTTGC 59.314 41.667 0.00 0.00 0.00 3.68
2202 2703 5.509670 GGTCCTCATAGCTTTTGTTTTTGCT 60.510 40.000 0.00 0.00 39.30 3.91
2203 2704 5.403466 GTCCTCATAGCTTTTGTTTTTGCTG 59.597 40.000 0.00 0.00 37.02 4.41
2204 2705 4.687483 CCTCATAGCTTTTGTTTTTGCTGG 59.313 41.667 0.00 0.00 37.02 4.85
2205 2706 4.630111 TCATAGCTTTTGTTTTTGCTGGG 58.370 39.130 0.00 0.00 37.02 4.45
2206 2707 4.100808 TCATAGCTTTTGTTTTTGCTGGGT 59.899 37.500 0.00 0.00 37.02 4.51
2207 2708 5.303078 TCATAGCTTTTGTTTTTGCTGGGTA 59.697 36.000 0.00 0.00 37.02 3.69
2209 2710 5.799827 AGCTTTTGTTTTTGCTGGGTATA 57.200 34.783 0.00 0.00 34.19 1.47
2210 2711 6.168270 AGCTTTTGTTTTTGCTGGGTATAA 57.832 33.333 0.00 0.00 34.19 0.98
2211 2712 6.223120 AGCTTTTGTTTTTGCTGGGTATAAG 58.777 36.000 0.00 0.00 34.19 1.73
2218 2725 5.715434 TTTTGCTGGGTATAAGTCCAAAC 57.285 39.130 0.00 0.00 31.97 2.93
2225 2732 3.014623 GGTATAAGTCCAAACTGGGTGC 58.985 50.000 0.00 0.00 38.32 5.01
2227 2734 2.561478 TAAGTCCAAACTGGGTGCTC 57.439 50.000 0.00 0.00 38.32 4.26
2231 2738 1.338020 GTCCAAACTGGGTGCTCTTTG 59.662 52.381 0.00 0.00 38.32 2.77
2253 2760 3.433615 GCTATTGCAGATACGCCCTTTAG 59.566 47.826 0.00 0.00 39.41 1.85
2257 2764 3.236047 TGCAGATACGCCCTTTAGGATA 58.764 45.455 0.00 0.00 38.24 2.59
2260 2767 5.482526 TGCAGATACGCCCTTTAGGATAATA 59.517 40.000 0.00 0.00 38.24 0.98
2261 2768 6.156256 TGCAGATACGCCCTTTAGGATAATAT 59.844 38.462 0.00 0.00 38.24 1.28
2262 2769 7.343574 TGCAGATACGCCCTTTAGGATAATATA 59.656 37.037 0.00 0.00 38.24 0.86
2288 2795 1.808411 TTCAAGACTGCGCCCTTTAG 58.192 50.000 4.18 0.00 0.00 1.85
2292 2799 0.912486 AGACTGCGCCCTTTAGGATT 59.088 50.000 4.18 0.00 38.24 3.01
2294 2801 2.504175 AGACTGCGCCCTTTAGGATTTA 59.496 45.455 4.18 0.00 38.24 1.40
2296 2803 3.883489 GACTGCGCCCTTTAGGATTTAAT 59.117 43.478 4.18 0.00 38.24 1.40
2310 2817 8.713708 TTAGGATTTAATGTTTTGGACCTTGA 57.286 30.769 0.00 0.00 0.00 3.02
2312 2819 8.028652 AGGATTTAATGTTTTGGACCTTGAAA 57.971 30.769 0.00 0.00 0.00 2.69
2313 2820 8.659527 AGGATTTAATGTTTTGGACCTTGAAAT 58.340 29.630 0.00 0.00 0.00 2.17
2314 2821 9.283768 GGATTTAATGTTTTGGACCTTGAAATT 57.716 29.630 0.00 0.00 0.00 1.82
2323 2830 8.604035 GTTTTGGACCTTGAAATTTCTTTCTTC 58.396 33.333 18.64 8.73 41.18 2.87
2324 2831 6.072112 TGGACCTTGAAATTTCTTTCTTCG 57.928 37.500 18.64 2.91 41.18 3.79
2381 2888 7.474364 GCCACACCCATATAGGAGTACTTTATT 60.474 40.741 0.00 0.00 41.22 1.40
2382 2889 9.096823 CCACACCCATATAGGAGTACTTTATTA 57.903 37.037 0.00 0.00 41.22 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.981114 CTCACAAAATTATGAACCCTAGTTTTT 57.019 29.630 0.00 0.00 35.94 1.94
12 13 9.362151 TCTCACAAAATTATGAACCCTAGTTTT 57.638 29.630 0.00 0.00 35.94 2.43
13 14 8.934023 TCTCACAAAATTATGAACCCTAGTTT 57.066 30.769 0.00 0.00 35.94 2.66
14 15 9.533831 AATCTCACAAAATTATGAACCCTAGTT 57.466 29.630 0.00 0.00 39.54 2.24
36 37 7.374272 CCAGATACACGACATGAGATTAATCT 58.626 38.462 17.96 17.96 40.50 2.40
37 38 6.587990 CCCAGATACACGACATGAGATTAATC 59.412 42.308 7.41 7.41 0.00 1.75
38 39 6.042093 ACCCAGATACACGACATGAGATTAAT 59.958 38.462 0.00 0.00 0.00 1.40
39 40 5.362717 ACCCAGATACACGACATGAGATTAA 59.637 40.000 0.00 0.00 0.00 1.40
40 41 4.893524 ACCCAGATACACGACATGAGATTA 59.106 41.667 0.00 0.00 0.00 1.75
41 42 3.706594 ACCCAGATACACGACATGAGATT 59.293 43.478 0.00 0.00 0.00 2.40
42 43 3.300388 ACCCAGATACACGACATGAGAT 58.700 45.455 0.00 0.00 0.00 2.75
43 44 2.735151 ACCCAGATACACGACATGAGA 58.265 47.619 0.00 0.00 0.00 3.27
44 45 3.526931 AACCCAGATACACGACATGAG 57.473 47.619 0.00 0.00 0.00 2.90
45 46 4.021229 AGTAACCCAGATACACGACATGA 58.979 43.478 0.00 0.00 0.00 3.07
46 47 4.386867 AGTAACCCAGATACACGACATG 57.613 45.455 0.00 0.00 0.00 3.21
47 48 4.222145 ACAAGTAACCCAGATACACGACAT 59.778 41.667 0.00 0.00 0.00 3.06
48 49 3.575256 ACAAGTAACCCAGATACACGACA 59.425 43.478 0.00 0.00 0.00 4.35
49 50 4.184079 ACAAGTAACCCAGATACACGAC 57.816 45.455 0.00 0.00 0.00 4.34
50 51 5.243507 TGTTACAAGTAACCCAGATACACGA 59.756 40.000 17.66 0.00 43.47 4.35
51 52 5.472148 TGTTACAAGTAACCCAGATACACG 58.528 41.667 17.66 0.00 43.47 4.49
52 53 7.443272 AGTTTGTTACAAGTAACCCAGATACAC 59.557 37.037 17.66 4.55 43.47 2.90
53 54 7.511268 AGTTTGTTACAAGTAACCCAGATACA 58.489 34.615 17.66 0.00 43.47 2.29
54 55 7.876582 AGAGTTTGTTACAAGTAACCCAGATAC 59.123 37.037 17.66 6.99 43.47 2.24
55 56 7.970102 AGAGTTTGTTACAAGTAACCCAGATA 58.030 34.615 17.66 0.00 43.47 1.98
56 57 6.838382 AGAGTTTGTTACAAGTAACCCAGAT 58.162 36.000 17.66 3.54 43.47 2.90
57 58 6.243216 AGAGTTTGTTACAAGTAACCCAGA 57.757 37.500 17.66 0.00 43.47 3.86
58 59 8.617290 AATAGAGTTTGTTACAAGTAACCCAG 57.383 34.615 17.66 0.00 43.47 4.45
59 60 8.983702 AAATAGAGTTTGTTACAAGTAACCCA 57.016 30.769 17.66 4.76 43.47 4.51
60 61 9.281371 AGAAATAGAGTTTGTTACAAGTAACCC 57.719 33.333 17.66 8.03 43.47 4.11
63 64 9.498176 GGGAGAAATAGAGTTTGTTACAAGTAA 57.502 33.333 0.00 0.00 0.00 2.24
64 65 8.877195 AGGGAGAAATAGAGTTTGTTACAAGTA 58.123 33.333 0.00 0.00 0.00 2.24
65 66 7.746703 AGGGAGAAATAGAGTTTGTTACAAGT 58.253 34.615 0.00 0.00 0.00 3.16
66 67 8.622948 AAGGGAGAAATAGAGTTTGTTACAAG 57.377 34.615 0.00 0.00 0.00 3.16
87 88 6.647895 GCTTTGCATCATCCATTAAATAAGGG 59.352 38.462 0.00 0.00 38.42 3.95
88 89 7.439381 AGCTTTGCATCATCCATTAAATAAGG 58.561 34.615 0.00 0.00 0.00 2.69
89 90 8.882415 AAGCTTTGCATCATCCATTAAATAAG 57.118 30.769 0.00 0.00 0.00 1.73
90 91 9.669887 AAAAGCTTTGCATCATCCATTAAATAA 57.330 25.926 13.54 0.00 0.00 1.40
91 92 9.100554 CAAAAGCTTTGCATCATCCATTAAATA 57.899 29.630 13.54 0.00 0.00 1.40
92 93 7.608761 ACAAAAGCTTTGCATCATCCATTAAAT 59.391 29.630 13.54 0.00 0.00 1.40
93 94 6.935771 ACAAAAGCTTTGCATCATCCATTAAA 59.064 30.769 13.54 0.00 0.00 1.52
94 95 6.465948 ACAAAAGCTTTGCATCATCCATTAA 58.534 32.000 13.54 0.00 0.00 1.40
95 96 6.040209 ACAAAAGCTTTGCATCATCCATTA 57.960 33.333 13.54 0.00 0.00 1.90
96 97 4.901868 ACAAAAGCTTTGCATCATCCATT 58.098 34.783 13.54 0.00 0.00 3.16
97 98 4.222145 AGACAAAAGCTTTGCATCATCCAT 59.778 37.500 13.54 0.00 0.00 3.41
98 99 3.575256 AGACAAAAGCTTTGCATCATCCA 59.425 39.130 13.54 0.00 0.00 3.41
99 100 4.184079 AGACAAAAGCTTTGCATCATCC 57.816 40.909 13.54 0.00 0.00 3.51
100 101 4.322804 CGAAGACAAAAGCTTTGCATCATC 59.677 41.667 13.54 11.57 0.00 2.92
101 102 4.232221 CGAAGACAAAAGCTTTGCATCAT 58.768 39.130 13.54 3.86 0.00 2.45
102 103 3.066621 ACGAAGACAAAAGCTTTGCATCA 59.933 39.130 13.54 0.00 31.31 3.07
103 104 3.632189 ACGAAGACAAAAGCTTTGCATC 58.368 40.909 13.54 10.61 31.31 3.91
104 105 3.715628 ACGAAGACAAAAGCTTTGCAT 57.284 38.095 13.54 0.72 31.31 3.96
105 106 3.502191 AACGAAGACAAAAGCTTTGCA 57.498 38.095 13.54 0.00 31.31 4.08
106 107 4.840401 AAAACGAAGACAAAAGCTTTGC 57.160 36.364 13.54 5.68 31.31 3.68
144 145 9.712305 CGTTAGGATGAAATAGGATGAAACTAT 57.288 33.333 0.00 0.00 32.72 2.12
145 146 8.701895 ACGTTAGGATGAAATAGGATGAAACTA 58.298 33.333 0.00 0.00 0.00 2.24
146 147 7.565680 ACGTTAGGATGAAATAGGATGAAACT 58.434 34.615 0.00 0.00 0.00 2.66
147 148 7.787725 ACGTTAGGATGAAATAGGATGAAAC 57.212 36.000 0.00 0.00 0.00 2.78
148 149 7.827236 ACAACGTTAGGATGAAATAGGATGAAA 59.173 33.333 0.00 0.00 0.00 2.69
149 150 7.335627 ACAACGTTAGGATGAAATAGGATGAA 58.664 34.615 0.00 0.00 0.00 2.57
150 151 6.884832 ACAACGTTAGGATGAAATAGGATGA 58.115 36.000 0.00 0.00 0.00 2.92
151 152 6.986817 AGACAACGTTAGGATGAAATAGGATG 59.013 38.462 0.00 0.00 0.00 3.51
152 153 6.986817 CAGACAACGTTAGGATGAAATAGGAT 59.013 38.462 0.00 0.00 0.00 3.24
153 154 6.338146 CAGACAACGTTAGGATGAAATAGGA 58.662 40.000 0.00 0.00 0.00 2.94
154 155 5.006746 GCAGACAACGTTAGGATGAAATAGG 59.993 44.000 0.00 0.00 0.00 2.57
155 156 5.006746 GGCAGACAACGTTAGGATGAAATAG 59.993 44.000 0.00 0.00 0.00 1.73
156 157 4.873827 GGCAGACAACGTTAGGATGAAATA 59.126 41.667 0.00 0.00 0.00 1.40
157 158 3.689649 GGCAGACAACGTTAGGATGAAAT 59.310 43.478 0.00 0.00 0.00 2.17
158 159 3.071479 GGCAGACAACGTTAGGATGAAA 58.929 45.455 0.00 0.00 0.00 2.69
166 167 1.414919 AGGTTGAGGCAGACAACGTTA 59.585 47.619 0.00 0.00 45.56 3.18
169 170 1.272490 TCTAGGTTGAGGCAGACAACG 59.728 52.381 13.04 0.00 45.56 4.10
173 174 3.093057 TCTTCTCTAGGTTGAGGCAGAC 58.907 50.000 0.00 0.00 34.98 3.51
178 179 6.476378 TGGAAAAATCTTCTCTAGGTTGAGG 58.524 40.000 0.00 0.00 34.98 3.86
197 198 3.181429 ACAGATCCTCAAGGCTTTGGAAA 60.181 43.478 18.81 2.38 34.97 3.13
200 201 2.026449 AGACAGATCCTCAAGGCTTTGG 60.026 50.000 8.88 3.11 34.97 3.28
201 202 3.008330 CAGACAGATCCTCAAGGCTTTG 58.992 50.000 1.35 1.35 35.57 2.77
221 222 7.264221 AGTTCTCAAATGCATTGTACAAAACA 58.736 30.769 13.82 13.79 40.11 2.83
234 235 6.374565 AATCATAGCAGAGTTCTCAAATGC 57.625 37.500 2.64 3.94 37.15 3.56
237 238 5.649395 CCCAAATCATAGCAGAGTTCTCAAA 59.351 40.000 2.64 0.00 0.00 2.69
288 289 5.925506 TCTGCAAATCATTGATCCACATT 57.074 34.783 0.00 0.00 38.94 2.71
310 314 3.507411 TGTCTAGCTGGTAGGTCAAGTT 58.493 45.455 13.43 0.00 0.00 2.66
311 315 3.093057 CTGTCTAGCTGGTAGGTCAAGT 58.907 50.000 13.43 0.00 0.00 3.16
414 418 4.397417 CCTAAGAAGTCTCCAAGCAAATGG 59.603 45.833 0.00 0.00 42.12 3.16
1205 1605 5.410067 CAACTTTGCCACTCTGAAAAGAAA 58.590 37.500 5.94 0.00 34.47 2.52
1307 1707 5.617751 GCATCAAGACATAAGCAACGAAACT 60.618 40.000 0.00 0.00 0.00 2.66
1371 1780 0.662619 CAAGCGTGAAAGGAAGCACA 59.337 50.000 0.00 0.00 34.78 4.57
1443 1852 1.174712 GGAGCTGGCAGTTCTGCAAA 61.175 55.000 27.00 11.83 36.33 3.68
1444 1853 1.601759 GGAGCTGGCAGTTCTGCAA 60.602 57.895 27.00 13.55 36.33 4.08
1445 1854 2.033141 GGAGCTGGCAGTTCTGCA 59.967 61.111 27.00 10.72 36.33 4.41
1446 1855 3.123620 CGGAGCTGGCAGTTCTGC 61.124 66.667 27.00 15.69 0.00 4.26
1447 1856 2.435586 CCGGAGCTGGCAGTTCTG 60.436 66.667 27.53 27.53 32.39 3.02
1448 1857 3.710722 CCCGGAGCTGGCAGTTCT 61.711 66.667 27.00 12.45 0.00 3.01
1449 1858 2.932130 GATCCCGGAGCTGGCAGTTC 62.932 65.000 21.55 21.55 0.00 3.01
1450 1859 3.011517 ATCCCGGAGCTGGCAGTT 61.012 61.111 17.16 10.61 0.00 3.16
1451 1860 3.474570 GATCCCGGAGCTGGCAGT 61.475 66.667 17.16 2.59 0.00 4.40
1452 1861 1.475169 TATGATCCCGGAGCTGGCAG 61.475 60.000 10.94 10.94 0.00 4.85
1453 1862 0.837691 ATATGATCCCGGAGCTGGCA 60.838 55.000 0.73 0.00 0.00 4.92
1454 1863 1.195115 TATATGATCCCGGAGCTGGC 58.805 55.000 0.73 0.00 0.00 4.85
1455 1864 4.494091 AATTATATGATCCCGGAGCTGG 57.506 45.455 0.73 0.00 0.00 4.85
1456 1865 9.784531 ATTATAAATTATATGATCCCGGAGCTG 57.215 33.333 0.73 0.00 0.00 4.24
1475 1884 8.454106 GCAGAGTTTTGCTTCAGAGATTATAAA 58.546 33.333 0.00 0.00 40.89 1.40
1476 1885 7.201556 CGCAGAGTTTTGCTTCAGAGATTATAA 60.202 37.037 0.00 0.00 41.90 0.98
1477 1886 6.256539 CGCAGAGTTTTGCTTCAGAGATTATA 59.743 38.462 0.00 0.00 41.90 0.98
1478 1887 5.064452 CGCAGAGTTTTGCTTCAGAGATTAT 59.936 40.000 0.00 0.00 41.90 1.28
1479 1888 4.389992 CGCAGAGTTTTGCTTCAGAGATTA 59.610 41.667 0.00 0.00 41.90 1.75
1480 1889 3.188048 CGCAGAGTTTTGCTTCAGAGATT 59.812 43.478 0.00 0.00 41.90 2.40
1481 1890 2.740981 CGCAGAGTTTTGCTTCAGAGAT 59.259 45.455 0.00 0.00 41.90 2.75
1482 1891 2.138320 CGCAGAGTTTTGCTTCAGAGA 58.862 47.619 0.00 0.00 41.90 3.10
1483 1892 2.138320 TCGCAGAGTTTTGCTTCAGAG 58.862 47.619 0.00 0.00 41.90 3.35
1484 1893 2.238942 TCGCAGAGTTTTGCTTCAGA 57.761 45.000 0.00 0.00 41.90 3.27
1502 1911 6.034470 CGAGCAGATTTACAAGAGAAACTCTC 59.966 42.308 1.71 0.00 40.28 3.20
1503 1912 5.866633 CGAGCAGATTTACAAGAGAAACTCT 59.133 40.000 0.00 0.00 43.37 3.24
1504 1913 5.445275 GCGAGCAGATTTACAAGAGAAACTC 60.445 44.000 0.00 0.00 0.00 3.01
1505 1914 4.390297 GCGAGCAGATTTACAAGAGAAACT 59.610 41.667 0.00 0.00 0.00 2.66
1506 1915 4.152402 TGCGAGCAGATTTACAAGAGAAAC 59.848 41.667 0.00 0.00 0.00 2.78
1507 1916 4.314961 TGCGAGCAGATTTACAAGAGAAA 58.685 39.130 0.00 0.00 0.00 2.52
1508 1917 3.925379 TGCGAGCAGATTTACAAGAGAA 58.075 40.909 0.00 0.00 0.00 2.87
1509 1918 3.515630 CTGCGAGCAGATTTACAAGAGA 58.484 45.455 19.40 0.00 46.30 3.10
1510 1919 2.030213 GCTGCGAGCAGATTTACAAGAG 59.970 50.000 27.09 0.00 46.30 2.85
1511 1920 2.002586 GCTGCGAGCAGATTTACAAGA 58.997 47.619 27.09 0.00 46.30 3.02
1512 1921 1.063174 GGCTGCGAGCAGATTTACAAG 59.937 52.381 27.09 0.22 44.75 3.16
1513 1922 1.086696 GGCTGCGAGCAGATTTACAA 58.913 50.000 27.09 0.00 44.75 2.41
1514 1923 0.250234 AGGCTGCGAGCAGATTTACA 59.750 50.000 27.09 0.00 44.75 2.41
1515 1924 0.654683 CAGGCTGCGAGCAGATTTAC 59.345 55.000 27.09 9.79 44.75 2.01
1516 1925 0.536724 TCAGGCTGCGAGCAGATTTA 59.463 50.000 27.09 7.74 44.75 1.40
1517 1926 0.321919 TTCAGGCTGCGAGCAGATTT 60.322 50.000 27.09 9.51 44.75 2.17
1518 1927 0.321919 TTTCAGGCTGCGAGCAGATT 60.322 50.000 27.09 11.89 44.75 2.40
1519 1928 0.743701 CTTTCAGGCTGCGAGCAGAT 60.744 55.000 27.09 12.60 44.75 2.90
1520 1929 1.375140 CTTTCAGGCTGCGAGCAGA 60.375 57.895 27.09 5.00 44.75 4.26
1521 1930 3.036783 GCTTTCAGGCTGCGAGCAG 62.037 63.158 26.48 19.76 44.75 4.24
1522 1931 3.052082 GCTTTCAGGCTGCGAGCA 61.052 61.111 26.48 3.25 44.75 4.26
1523 1932 2.745492 AGCTTTCAGGCTGCGAGC 60.745 61.111 25.03 25.03 41.43 5.03
1524 1933 2.451167 CGAGCTTTCAGGCTGCGAG 61.451 63.158 10.34 10.87 43.20 5.03
1525 1934 2.433145 CGAGCTTTCAGGCTGCGA 60.433 61.111 10.34 0.00 43.20 5.10
1526 1935 3.494336 CCGAGCTTTCAGGCTGCG 61.494 66.667 10.34 6.29 43.20 5.18
1527 1936 1.672356 TTCCGAGCTTTCAGGCTGC 60.672 57.895 10.34 0.00 43.20 5.25
1528 1937 0.603707 TGTTCCGAGCTTTCAGGCTG 60.604 55.000 8.58 8.58 43.20 4.85
1529 1938 0.108585 TTGTTCCGAGCTTTCAGGCT 59.891 50.000 0.00 0.00 46.11 4.58
1530 1939 0.951558 TTTGTTCCGAGCTTTCAGGC 59.048 50.000 0.00 0.00 0.00 4.85
1531 1940 2.669391 GCATTTGTTCCGAGCTTTCAGG 60.669 50.000 0.00 0.00 0.00 3.86
1532 1941 2.030893 TGCATTTGTTCCGAGCTTTCAG 60.031 45.455 0.00 0.00 0.00 3.02
1533 1942 1.952990 TGCATTTGTTCCGAGCTTTCA 59.047 42.857 0.00 0.00 0.00 2.69
1534 1943 2.287547 TGTGCATTTGTTCCGAGCTTTC 60.288 45.455 0.00 0.00 0.00 2.62
1535 1944 1.680735 TGTGCATTTGTTCCGAGCTTT 59.319 42.857 0.00 0.00 0.00 3.51
1536 1945 1.317613 TGTGCATTTGTTCCGAGCTT 58.682 45.000 0.00 0.00 0.00 3.74
1537 1946 1.538047 ATGTGCATTTGTTCCGAGCT 58.462 45.000 0.00 0.00 0.00 4.09
1538 1947 3.698029 ATATGTGCATTTGTTCCGAGC 57.302 42.857 0.00 0.00 0.00 5.03
1539 1948 5.733226 TGTATATGTGCATTTGTTCCGAG 57.267 39.130 0.00 0.00 0.00 4.63
1540 1949 7.977789 ATATGTATATGTGCATTTGTTCCGA 57.022 32.000 0.00 0.00 32.63 4.55
1612 2028 5.402630 TGTATGCCCTCTTCATAGTCCATA 58.597 41.667 0.00 0.00 0.00 2.74
1630 2046 0.251354 ACACAGGAGGCAGCTGTATG 59.749 55.000 16.64 9.54 0.00 2.39
1653 2069 3.849911 TCTCTCGATGTAAAGCAACAGG 58.150 45.455 0.00 0.00 31.70 4.00
1687 2103 7.851228 AGACTGGTTTTCTTTTCCTCAATTTT 58.149 30.769 0.00 0.00 0.00 1.82
1688 2104 7.423844 AGACTGGTTTTCTTTTCCTCAATTT 57.576 32.000 0.00 0.00 0.00 1.82
1689 2105 7.423844 AAGACTGGTTTTCTTTTCCTCAATT 57.576 32.000 0.00 0.00 28.36 2.32
1690 2106 7.423844 AAAGACTGGTTTTCTTTTCCTCAAT 57.576 32.000 0.00 0.00 39.77 2.57
1692 2108 6.850752 AAAAGACTGGTTTTCTTTTCCTCA 57.149 33.333 4.59 0.00 45.89 3.86
1717 2133 3.639561 GGTTTTCTACTGCCCCTCAAAAA 59.360 43.478 0.00 0.00 0.00 1.94
1722 2138 1.351350 ACTGGTTTTCTACTGCCCCTC 59.649 52.381 0.00 0.00 0.00 4.30
1723 2139 1.351350 GACTGGTTTTCTACTGCCCCT 59.649 52.381 0.00 0.00 0.00 4.79
1724 2140 1.073284 TGACTGGTTTTCTACTGCCCC 59.927 52.381 0.00 0.00 0.00 5.80
1725 2141 2.561478 TGACTGGTTTTCTACTGCCC 57.439 50.000 0.00 0.00 0.00 5.36
1726 2142 6.379386 GTTATTTGACTGGTTTTCTACTGCC 58.621 40.000 0.00 0.00 0.00 4.85
1727 2143 6.016610 TGGTTATTTGACTGGTTTTCTACTGC 60.017 38.462 0.00 0.00 0.00 4.40
1728 2144 7.504924 TGGTTATTTGACTGGTTTTCTACTG 57.495 36.000 0.00 0.00 0.00 2.74
1729 2145 6.206829 GCTGGTTATTTGACTGGTTTTCTACT 59.793 38.462 0.00 0.00 0.00 2.57
1730 2146 6.379386 GCTGGTTATTTGACTGGTTTTCTAC 58.621 40.000 0.00 0.00 0.00 2.59
1733 2149 4.226761 CGCTGGTTATTTGACTGGTTTTC 58.773 43.478 0.00 0.00 0.00 2.29
1735 2151 3.219281 ACGCTGGTTATTTGACTGGTTT 58.781 40.909 0.00 0.00 0.00 3.27
1739 2155 2.673368 GGAGACGCTGGTTATTTGACTG 59.327 50.000 0.00 0.00 0.00 3.51
1742 2158 1.065709 GGGGAGACGCTGGTTATTTGA 60.066 52.381 0.00 0.00 40.76 2.69
1743 2159 1.379527 GGGGAGACGCTGGTTATTTG 58.620 55.000 0.00 0.00 40.76 2.32
1745 2161 0.912487 TGGGGGAGACGCTGGTTATT 60.912 55.000 0.00 0.00 44.03 1.40
1775 2192 1.586154 CTTGCCGATGTGGTGGGTTC 61.586 60.000 0.00 0.00 41.21 3.62
1800 2293 3.817647 GCCTTCATGCTTGTAGGGAATAG 59.182 47.826 21.74 1.85 39.98 1.73
1832 2325 2.647299 TCTGGCCCAAAATAGTGGAAGA 59.353 45.455 0.00 0.00 41.65 2.87
1864 2357 4.641645 TGGGCAACGAGTGGGCTG 62.642 66.667 4.16 0.00 37.60 4.85
1896 2389 0.951040 CTTTTTCAGACGGGAGCGCT 60.951 55.000 11.27 11.27 0.00 5.92
1910 2403 3.365265 CTCCCCGCGCTGCTTTTT 61.365 61.111 5.56 0.00 0.00 1.94
1941 2434 0.981183 AGCCGATGTGGGACTAAACA 59.019 50.000 0.00 0.00 38.63 2.83
1967 2460 5.394333 GGCTTATAAACTGGTCGTTCTCTCT 60.394 44.000 0.00 0.00 33.90 3.10
1975 2468 0.575390 CGCGGCTTATAAACTGGTCG 59.425 55.000 0.00 0.00 0.00 4.79
2122 2616 1.057851 ACAAGTTTCCAGGGACCGGA 61.058 55.000 9.46 0.00 0.00 5.14
2135 2634 1.341976 ACAAGGGGCTCAACACAAGTT 60.342 47.619 0.00 0.00 38.88 2.66
2136 2635 0.258774 ACAAGGGGCTCAACACAAGT 59.741 50.000 0.00 0.00 0.00 3.16
2140 2639 2.908073 CGCACAAGGGGCTCAACAC 61.908 63.158 0.00 0.00 0.00 3.32
2159 2660 4.351192 GACCACTTTGTAAAACAGCACTG 58.649 43.478 0.00 0.00 0.00 3.66
2161 2662 3.380320 AGGACCACTTTGTAAAACAGCAC 59.620 43.478 0.00 0.00 0.00 4.40
2166 2667 5.705905 AGCTATGAGGACCACTTTGTAAAAC 59.294 40.000 0.00 0.00 0.00 2.43
2185 2686 4.687901 ACCCAGCAAAAACAAAAGCTAT 57.312 36.364 0.00 0.00 35.19 2.97
2187 2688 4.687901 ATACCCAGCAAAAACAAAAGCT 57.312 36.364 0.00 0.00 37.95 3.74
2188 2689 5.989168 ACTTATACCCAGCAAAAACAAAAGC 59.011 36.000 0.00 0.00 0.00 3.51
2189 2690 6.645003 GGACTTATACCCAGCAAAAACAAAAG 59.355 38.462 0.00 0.00 0.00 2.27
2190 2691 6.098409 TGGACTTATACCCAGCAAAAACAAAA 59.902 34.615 0.00 0.00 0.00 2.44
2195 2696 5.836358 AGTTTGGACTTATACCCAGCAAAAA 59.164 36.000 0.00 0.00 33.43 1.94
2196 2697 5.242838 CAGTTTGGACTTATACCCAGCAAAA 59.757 40.000 0.00 0.00 32.54 2.44
2197 2698 4.764823 CAGTTTGGACTTATACCCAGCAAA 59.235 41.667 0.00 0.00 32.54 3.68
2198 2699 4.331968 CAGTTTGGACTTATACCCAGCAA 58.668 43.478 0.00 0.00 32.54 3.91
2199 2700 3.308117 CCAGTTTGGACTTATACCCAGCA 60.308 47.826 0.00 0.00 40.96 4.41
2200 2701 3.279434 CCAGTTTGGACTTATACCCAGC 58.721 50.000 0.00 0.00 40.96 4.85
2201 2702 3.265995 ACCCAGTTTGGACTTATACCCAG 59.734 47.826 0.00 0.00 40.96 4.45
2202 2703 3.009695 CACCCAGTTTGGACTTATACCCA 59.990 47.826 0.00 0.00 40.96 4.51
2203 2704 3.617284 CACCCAGTTTGGACTTATACCC 58.383 50.000 0.00 0.00 40.96 3.69
2204 2705 3.014623 GCACCCAGTTTGGACTTATACC 58.985 50.000 0.00 0.00 40.96 2.73
2205 2706 3.939592 GAGCACCCAGTTTGGACTTATAC 59.060 47.826 0.00 0.00 40.96 1.47
2206 2707 3.844211 AGAGCACCCAGTTTGGACTTATA 59.156 43.478 0.00 0.00 40.96 0.98
2207 2708 2.644798 AGAGCACCCAGTTTGGACTTAT 59.355 45.455 0.00 0.00 40.96 1.73
2209 2710 0.846693 AGAGCACCCAGTTTGGACTT 59.153 50.000 0.00 0.00 40.96 3.01
2210 2711 0.846693 AAGAGCACCCAGTTTGGACT 59.153 50.000 0.00 0.00 40.96 3.85
2211 2712 1.338020 CAAAGAGCACCCAGTTTGGAC 59.662 52.381 0.00 0.00 40.96 4.02
2231 2738 1.884235 AAGGGCGTATCTGCAATAGC 58.116 50.000 0.00 0.00 42.57 2.97
2257 2764 8.893727 GGGCGCAGTCTTGAAAATATATATATT 58.106 33.333 10.83 11.51 34.59 1.28
2260 2767 6.476378 AGGGCGCAGTCTTGAAAATATATAT 58.524 36.000 10.83 0.00 0.00 0.86
2261 2768 5.865085 AGGGCGCAGTCTTGAAAATATATA 58.135 37.500 10.83 0.00 0.00 0.86
2262 2769 4.718961 AGGGCGCAGTCTTGAAAATATAT 58.281 39.130 10.83 0.00 0.00 0.86
2264 2771 3.004752 AGGGCGCAGTCTTGAAAATAT 57.995 42.857 10.83 0.00 0.00 1.28
2265 2772 2.489938 AGGGCGCAGTCTTGAAAATA 57.510 45.000 10.83 0.00 0.00 1.40
2266 2773 1.620822 AAGGGCGCAGTCTTGAAAAT 58.379 45.000 10.83 0.00 0.00 1.82
2267 2774 1.398692 AAAGGGCGCAGTCTTGAAAA 58.601 45.000 10.83 0.00 0.00 2.29
2268 2775 2.151202 CTAAAGGGCGCAGTCTTGAAA 58.849 47.619 10.83 0.00 0.00 2.69
2269 2776 1.610624 CCTAAAGGGCGCAGTCTTGAA 60.611 52.381 10.83 1.66 0.00 2.69
2270 2777 0.036388 CCTAAAGGGCGCAGTCTTGA 60.036 55.000 10.83 1.88 0.00 3.02
2280 2787 6.816640 GTCCAAAACATTAAATCCTAAAGGGC 59.183 38.462 0.00 0.00 35.41 5.19
2288 2795 8.846943 ATTTCAAGGTCCAAAACATTAAATCC 57.153 30.769 0.00 0.00 29.05 3.01
2292 2799 9.898152 AAGAAATTTCAAGGTCCAAAACATTAA 57.102 25.926 19.99 0.00 29.05 1.40
2294 2801 8.806429 AAAGAAATTTCAAGGTCCAAAACATT 57.194 26.923 19.99 0.00 30.45 2.71
2296 2803 7.619965 AGAAAGAAATTTCAAGGTCCAAAACA 58.380 30.769 19.99 0.00 33.53 2.83
2314 2821 9.659830 GCTCTTTTTGTAATAACGAAGAAAGAA 57.340 29.630 0.00 0.00 30.61 2.52
2315 2822 8.287503 GGCTCTTTTTGTAATAACGAAGAAAGA 58.712 33.333 0.00 0.00 30.40 2.52
2316 2823 7.537649 GGGCTCTTTTTGTAATAACGAAGAAAG 59.462 37.037 0.00 0.00 30.55 2.62


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

AutoCloner maintained by Alex Coulton.