Multiple sequence alignment - TraesCS4B01G057500

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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 TraesCS4B01G057500 chr4B 100.000 2481 0 0 1 2481 47504883 47502403 0.000000e+00 4582
1 TraesCS4B01G057500 chr4A 87.199 1578 83 47 96 1590 569876607 569878148 0.000000e+00 1685
2 TraesCS4B01G057500 chr4A 83.828 606 45 26 1899 2478 569878511 569879089 6.080000e-146 527
3 TraesCS4B01G057500 chr4D 85.009 1154 59 40 747 1833 32503126 32502020 0.000000e+00 1068
4 TraesCS4B01G057500 chr4D 91.791 402 13 9 364 751 32503846 32503451 2.170000e-150 542
5 TraesCS4B01G057500 chr4D 85.096 416 22 16 1899 2301 32501876 32501488 2.990000e-104 388
6 TraesCS4B01G057500 chr4D 91.304 92 3 1 2395 2481 32501449 32501358 1.210000e-23 121


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 TraesCS4B01G057500 chr4B 47502403 47504883 2480 True 4582.00 4582 100.0000 1 2481 1 chr4B.!!$R1 2480
1 TraesCS4B01G057500 chr4A 569876607 569879089 2482 False 1106.00 1685 85.5135 96 2478 2 chr4A.!!$F1 2382
2 TraesCS4B01G057500 chr4D 32501358 32503846 2488 True 529.75 1068 88.3000 364 2481 4 chr4D.!!$R1 2117

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
92 93 0.03563 GGTCAGGTTGCAGATGCTCT 60.036 55.0 6.35 0.0 42.66 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 2166 0.034896 ACACCGGCTCCAAACTACTG 59.965 55.0 0.0 0.0 0.0 2.74 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
18 19 4.016706 CGGTTTGAGAGGCCCGGT 62.017 66.667 0.00 0.00 36.84 5.28
19 20 2.434774 GGTTTGAGAGGCCCGGTT 59.565 61.111 0.00 0.00 0.00 4.44
20 21 1.681076 GGTTTGAGAGGCCCGGTTA 59.319 57.895 0.00 0.00 0.00 2.85
21 22 0.392595 GGTTTGAGAGGCCCGGTTAG 60.393 60.000 0.00 0.00 0.00 2.34
22 23 0.392595 GTTTGAGAGGCCCGGTTAGG 60.393 60.000 0.00 0.00 40.63 2.69
23 24 0.838987 TTTGAGAGGCCCGGTTAGGT 60.839 55.000 0.00 0.00 38.74 3.08
24 25 1.262640 TTGAGAGGCCCGGTTAGGTC 61.263 60.000 0.00 0.00 38.74 3.85
25 26 2.758737 AGAGGCCCGGTTAGGTCG 60.759 66.667 0.00 0.00 36.30 4.79
26 27 2.757099 GAGGCCCGGTTAGGTCGA 60.757 66.667 0.00 0.00 36.30 4.20
27 28 2.284112 AGGCCCGGTTAGGTCGAA 60.284 61.111 0.00 0.00 36.30 3.71
28 29 1.891722 GAGGCCCGGTTAGGTCGAAA 61.892 60.000 0.00 0.00 36.30 3.46
29 30 1.222661 GGCCCGGTTAGGTCGAAAT 59.777 57.895 0.00 0.00 38.74 2.17
30 31 0.393402 GGCCCGGTTAGGTCGAAATT 60.393 55.000 0.00 0.00 38.74 1.82
31 32 1.456296 GCCCGGTTAGGTCGAAATTT 58.544 50.000 0.00 0.00 38.74 1.82
32 33 1.399440 GCCCGGTTAGGTCGAAATTTC 59.601 52.381 8.20 8.20 38.74 2.17
33 34 1.662122 CCCGGTTAGGTCGAAATTTCG 59.338 52.381 30.11 30.11 43.90 3.46
34 35 2.932187 CCCGGTTAGGTCGAAATTTCGT 60.932 50.000 32.92 20.40 43.41 3.85
35 36 5.006995 CCCGGTTAGGTCGAAATTTCGTG 62.007 52.174 32.92 12.67 43.41 4.35
39 40 1.425412 AGGTCGAAATTTCGTGACCG 58.575 50.000 32.92 13.37 46.25 4.79
40 41 1.938016 AGGTCGAAATTTCGTGACCGG 60.938 52.381 32.92 0.00 46.25 5.28
41 42 4.233013 AGGTCGAAATTTCGTGACCGGA 62.233 50.000 32.92 14.68 46.25 5.14
42 43 3.941194 CGAAATTTCGTGACCGGAC 57.059 52.632 28.21 1.07 45.09 4.79
43 44 0.092351 CGAAATTTCGTGACCGGACG 59.908 55.000 28.21 9.36 45.09 4.79
44 45 0.441145 GAAATTTCGTGACCGGACGG 59.559 55.000 9.46 9.56 39.88 4.79
45 46 1.571215 AAATTTCGTGACCGGACGGC 61.571 55.000 9.46 4.51 39.88 5.68
46 47 2.718747 AATTTCGTGACCGGACGGCA 62.719 55.000 9.46 7.20 39.88 5.69
47 48 4.651008 TTCGTGACCGGACGGCAC 62.651 66.667 9.46 20.55 39.88 5.01
60 61 3.174788 GGCACCCGAGCGTTTAAG 58.825 61.111 0.00 0.00 34.64 1.85
61 62 1.375013 GGCACCCGAGCGTTTAAGA 60.375 57.895 0.00 0.00 34.64 2.10
62 63 0.952010 GGCACCCGAGCGTTTAAGAA 60.952 55.000 0.00 0.00 34.64 2.52
63 64 0.165295 GCACCCGAGCGTTTAAGAAC 59.835 55.000 0.00 0.00 0.00 3.01
74 75 3.909776 GTTTAAGAACGGTTGAAGGGG 57.090 47.619 0.00 0.00 0.00 4.79
75 76 3.216800 GTTTAAGAACGGTTGAAGGGGT 58.783 45.455 0.00 0.00 0.00 4.95
76 77 2.845363 TAAGAACGGTTGAAGGGGTC 57.155 50.000 0.00 0.00 0.00 4.46
77 78 0.841289 AAGAACGGTTGAAGGGGTCA 59.159 50.000 0.00 0.00 0.00 4.02
78 79 0.396811 AGAACGGTTGAAGGGGTCAG 59.603 55.000 0.00 0.00 37.61 3.51
79 80 0.605589 GAACGGTTGAAGGGGTCAGG 60.606 60.000 0.00 0.00 37.61 3.86
80 81 1.350310 AACGGTTGAAGGGGTCAGGT 61.350 55.000 0.00 0.00 37.61 4.00
81 82 1.350310 ACGGTTGAAGGGGTCAGGTT 61.350 55.000 0.00 0.00 37.61 3.50
82 83 0.889186 CGGTTGAAGGGGTCAGGTTG 60.889 60.000 0.00 0.00 37.61 3.77
83 84 1.179174 GGTTGAAGGGGTCAGGTTGC 61.179 60.000 0.00 0.00 37.61 4.17
84 85 0.467290 GTTGAAGGGGTCAGGTTGCA 60.467 55.000 0.00 0.00 37.61 4.08
85 86 0.178992 TTGAAGGGGTCAGGTTGCAG 60.179 55.000 0.00 0.00 37.61 4.41
86 87 1.059584 TGAAGGGGTCAGGTTGCAGA 61.060 55.000 0.00 0.00 0.00 4.26
87 88 0.329596 GAAGGGGTCAGGTTGCAGAT 59.670 55.000 0.00 0.00 0.00 2.90
88 89 0.038744 AAGGGGTCAGGTTGCAGATG 59.961 55.000 0.00 0.00 0.00 2.90
89 90 2.048603 GGGGTCAGGTTGCAGATGC 61.049 63.158 0.00 0.00 42.50 3.91
90 91 1.001641 GGGTCAGGTTGCAGATGCT 60.002 57.895 6.35 0.00 42.66 3.79
91 92 1.028868 GGGTCAGGTTGCAGATGCTC 61.029 60.000 6.35 0.00 42.66 4.26
92 93 0.035630 GGTCAGGTTGCAGATGCTCT 60.036 55.000 6.35 0.00 42.66 4.09
93 94 1.612726 GGTCAGGTTGCAGATGCTCTT 60.613 52.381 6.35 0.00 42.66 2.85
94 95 2.157738 GTCAGGTTGCAGATGCTCTTT 58.842 47.619 6.35 0.00 42.66 2.52
110 115 7.833183 AGATGCTCTTTATGAAACCATCTCTTT 59.167 33.333 0.00 0.00 33.61 2.52
138 143 6.783892 TTAATGAAATGGCAACTCTTTTGC 57.216 33.333 0.00 0.17 44.22 3.68
146 151 3.619233 GCAACTCTTTTGCCTCGTTTA 57.381 42.857 0.00 0.00 39.38 2.01
148 153 4.356289 GCAACTCTTTTGCCTCGTTTAAA 58.644 39.130 0.00 0.00 39.38 1.52
188 193 3.087031 CAACCTCATGAGCCTGAAATGT 58.913 45.455 17.76 4.23 0.00 2.71
192 197 3.370846 CCTCATGAGCCTGAAATGTACCA 60.371 47.826 17.76 0.00 0.00 3.25
202 207 5.106515 GCCTGAAATGTACCAAGAGAGAAAC 60.107 44.000 0.00 0.00 0.00 2.78
212 217 1.718280 AGAGAGAAACAGAACGGGGT 58.282 50.000 0.00 0.00 0.00 4.95
213 218 2.885616 AGAGAGAAACAGAACGGGGTA 58.114 47.619 0.00 0.00 0.00 3.69
214 219 3.442076 AGAGAGAAACAGAACGGGGTAT 58.558 45.455 0.00 0.00 0.00 2.73
215 220 3.447944 AGAGAGAAACAGAACGGGGTATC 59.552 47.826 0.00 0.00 0.00 2.24
216 221 3.442076 AGAGAAACAGAACGGGGTATCT 58.558 45.455 0.00 0.00 0.00 1.98
217 222 3.447944 AGAGAAACAGAACGGGGTATCTC 59.552 47.826 0.00 0.00 33.87 2.75
218 223 2.500504 AGAAACAGAACGGGGTATCTCC 59.499 50.000 0.00 0.00 0.00 3.71
270 278 4.450419 GTGTGGACTGAACTGAAGATCAAG 59.550 45.833 0.00 0.00 0.00 3.02
295 303 5.326069 AGTACTAGCATCGTTATCCATCCT 58.674 41.667 0.00 0.00 0.00 3.24
310 320 1.415659 CATCCTAGCTAGCTGCCTGTT 59.584 52.381 27.68 1.05 44.23 3.16
311 321 0.826715 TCCTAGCTAGCTGCCTGTTG 59.173 55.000 27.68 7.43 44.23 3.33
314 324 0.909610 TAGCTAGCTGCCTGTTGGGT 60.910 55.000 27.68 0.00 44.23 4.51
352 362 2.422377 CCCTATTTTCCGATCCCCGTTT 60.422 50.000 0.00 0.00 36.31 3.60
484 502 1.741770 CCCCCTGCTTCGTTTCTCG 60.742 63.158 0.00 0.00 41.41 4.04
488 506 1.678269 CCTGCTTCGTTTCTCGCTCG 61.678 60.000 0.00 0.00 39.67 5.03
489 507 0.729478 CTGCTTCGTTTCTCGCTCGA 60.729 55.000 0.00 0.00 39.67 4.04
490 508 0.729478 TGCTTCGTTTCTCGCTCGAG 60.729 55.000 8.45 8.45 43.21 4.04
645 699 2.433994 CCTGCTGCCTCTCTCTCCC 61.434 68.421 0.00 0.00 0.00 4.30
799 1187 3.264845 GGCCAACCCCTCCCTCAA 61.265 66.667 0.00 0.00 0.00 3.02
800 1188 2.035783 GCCAACCCCTCCCTCAAC 59.964 66.667 0.00 0.00 0.00 3.18
801 1189 2.763902 CCAACCCCTCCCTCAACC 59.236 66.667 0.00 0.00 0.00 3.77
802 1190 1.852626 CCAACCCCTCCCTCAACCT 60.853 63.158 0.00 0.00 0.00 3.50
803 1191 1.685820 CAACCCCTCCCTCAACCTC 59.314 63.158 0.00 0.00 0.00 3.85
804 1192 0.842467 CAACCCCTCCCTCAACCTCT 60.842 60.000 0.00 0.00 0.00 3.69
805 1193 0.547954 AACCCCTCCCTCAACCTCTC 60.548 60.000 0.00 0.00 0.00 3.20
806 1194 1.690985 CCCCTCCCTCAACCTCTCC 60.691 68.421 0.00 0.00 0.00 3.71
807 1195 1.690985 CCCTCCCTCAACCTCTCCC 60.691 68.421 0.00 0.00 0.00 4.30
808 1196 1.394151 CCTCCCTCAACCTCTCCCT 59.606 63.158 0.00 0.00 0.00 4.20
841 1231 2.042297 TGTGGACCATTTATTCCCAGCA 59.958 45.455 0.00 0.00 0.00 4.41
882 1272 2.107750 CCATGTGAGCGCGATCCT 59.892 61.111 23.12 2.50 0.00 3.24
904 1294 4.703645 TGATATAAGTAGCAGGCTAGCG 57.296 45.455 9.00 0.00 40.15 4.26
906 1296 1.705873 ATAAGTAGCAGGCTAGCGGT 58.294 50.000 9.00 4.00 40.15 5.68
907 1297 2.353357 TAAGTAGCAGGCTAGCGGTA 57.647 50.000 9.00 2.94 40.15 4.02
908 1298 0.745468 AAGTAGCAGGCTAGCGGTAC 59.255 55.000 18.61 18.61 40.15 3.34
909 1299 1.108132 AGTAGCAGGCTAGCGGTACC 61.108 60.000 21.10 0.16 36.91 3.34
910 1300 1.831286 TAGCAGGCTAGCGGTACCC 60.831 63.158 9.00 0.00 40.15 3.69
911 1301 2.294170 TAGCAGGCTAGCGGTACCCT 62.294 60.000 9.00 2.55 40.15 4.34
912 1302 1.831286 GCAGGCTAGCGGTACCCTA 60.831 63.158 9.00 8.03 0.00 3.53
958 1354 2.525368 TCAGTGAGTGCTTAGCTACCA 58.475 47.619 5.60 0.00 0.00 3.25
961 1357 0.530744 TGAGTGCTTAGCTACCACCG 59.469 55.000 16.25 0.00 0.00 4.94
990 1386 2.807878 GAGCCGATCGAGCTGAATC 58.192 57.895 28.07 14.66 41.75 2.52
993 1397 2.045280 CCGATCGAGCTGAATCCCT 58.955 57.895 18.66 0.00 0.00 4.20
1051 1464 2.948315 CTGCTTCTCCTTTTGCTATCCC 59.052 50.000 0.00 0.00 0.00 3.85
1077 1493 1.689892 GGCCTAGCCTCTACTCAAGGT 60.690 57.143 0.00 0.00 46.69 3.50
1078 1494 2.424523 GGCCTAGCCTCTACTCAAGGTA 60.425 54.545 0.00 0.00 46.69 3.08
1141 1557 1.880340 CGCCGCATCTTCCTCACTC 60.880 63.158 0.00 0.00 0.00 3.51
1142 1558 1.522580 GCCGCATCTTCCTCACTCC 60.523 63.158 0.00 0.00 0.00 3.85
1144 1560 1.144936 CGCATCTTCCTCACTCCCC 59.855 63.158 0.00 0.00 0.00 4.81
1161 1577 1.071128 CCCTGCCTCTAGCTGATGC 59.929 63.158 0.00 1.49 42.76 3.91
1164 1580 1.202782 CCTGCCTCTAGCTGATGCATT 60.203 52.381 0.00 0.00 43.45 3.56
1165 1581 2.573369 CTGCCTCTAGCTGATGCATTT 58.427 47.619 0.00 0.00 43.45 2.32
1173 1589 1.345089 AGCTGATGCATTTTGTTGCCA 59.655 42.857 0.00 0.00 42.06 4.92
1199 1619 2.284331 TTGCAGGTAGAGGGCCGA 60.284 61.111 0.00 0.00 0.00 5.54
1481 1913 1.823295 CCGATCCTCAACCCGTGAT 59.177 57.895 0.00 0.00 35.07 3.06
1482 1914 0.249489 CCGATCCTCAACCCGTGATC 60.249 60.000 0.00 0.00 35.07 2.92
1484 1916 0.744874 GATCCTCAACCCGTGATCGA 59.255 55.000 0.00 0.00 39.71 3.59
1486 1918 1.153628 CCTCAACCCGTGATCGACC 60.154 63.158 0.00 0.00 39.71 4.79
1487 1919 1.516386 CTCAACCCGTGATCGACCG 60.516 63.158 0.00 0.00 39.71 4.79
1488 1920 1.929806 CTCAACCCGTGATCGACCGA 61.930 60.000 0.00 0.00 39.71 4.69
1490 1922 2.707849 AACCCGTGATCGACCGAGG 61.708 63.158 0.00 0.00 39.71 4.63
1492 1924 3.822192 CCGTGATCGACCGAGGCA 61.822 66.667 0.00 0.00 39.71 4.75
1496 1928 1.453197 TGATCGACCGAGGCAGCTA 60.453 57.895 0.00 0.00 0.00 3.32
1497 1929 1.284408 GATCGACCGAGGCAGCTAG 59.716 63.158 0.00 0.00 0.00 3.42
1498 1930 2.741116 GATCGACCGAGGCAGCTAGC 62.741 65.000 6.62 6.62 44.65 3.42
1499 1931 3.522731 CGACCGAGGCAGCTAGCT 61.523 66.667 12.68 12.68 44.79 3.32
1500 1932 2.105930 GACCGAGGCAGCTAGCTG 59.894 66.667 35.54 35.54 46.15 4.24
1501 1933 2.681778 ACCGAGGCAGCTAGCTGT 60.682 61.111 37.91 24.35 45.24 4.40
1502 1934 2.232298 GACCGAGGCAGCTAGCTGTT 62.232 60.000 37.91 28.59 45.24 3.16
1503 1935 1.078848 CCGAGGCAGCTAGCTGTTT 60.079 57.895 37.91 28.27 45.24 2.83
1504 1936 0.674895 CCGAGGCAGCTAGCTGTTTT 60.675 55.000 37.91 26.06 45.24 2.43
1505 1937 0.723981 CGAGGCAGCTAGCTGTTTTC 59.276 55.000 37.91 29.83 45.24 2.29
1506 1938 1.674221 CGAGGCAGCTAGCTGTTTTCT 60.674 52.381 37.91 29.26 45.24 2.52
1507 1939 2.006169 GAGGCAGCTAGCTGTTTTCTC 58.994 52.381 37.91 31.39 45.24 2.87
1508 1940 1.090728 GGCAGCTAGCTGTTTTCTCC 58.909 55.000 37.91 27.54 45.24 3.71
1509 1941 1.339535 GGCAGCTAGCTGTTTTCTCCT 60.340 52.381 37.91 3.19 45.24 3.69
1530 1962 4.942483 CCTGAAGAAGATGTTTGATGAGCT 59.058 41.667 0.00 0.00 0.00 4.09
1586 2025 2.814336 CTGTAAGTTGTTGGGAGAAGCC 59.186 50.000 0.00 0.00 0.00 4.35
1590 2029 1.600636 TTGTTGGGAGAAGCCGCAG 60.601 57.895 0.00 0.00 37.63 5.18
1604 2076 2.680913 CGCAGGTGCAAGGTGTAGC 61.681 63.158 2.33 0.00 42.21 3.58
1613 2085 1.813513 CAAGGTGTAGCTGTTGGGAG 58.186 55.000 0.00 0.00 0.00 4.30
1633 2109 4.023107 GGAGAAGTTTTGGTCAGTTTAGGC 60.023 45.833 0.00 0.00 0.00 3.93
1660 2145 7.493743 AGAGTTTATGATGATGATGCTGAAC 57.506 36.000 0.00 0.00 0.00 3.18
1668 2153 1.869767 GATGATGCTGAACGATCCACC 59.130 52.381 0.00 0.00 0.00 4.61
1676 2161 3.181479 GCTGAACGATCCACCACATACTA 60.181 47.826 0.00 0.00 0.00 1.82
1680 2165 5.066893 TGAACGATCCACCACATACTACTAC 59.933 44.000 0.00 0.00 0.00 2.73
1681 2166 3.887716 ACGATCCACCACATACTACTACC 59.112 47.826 0.00 0.00 0.00 3.18
1711 2202 2.352388 GAGCCGGTGTTGCACTAATTA 58.648 47.619 1.90 0.00 34.40 1.40
1716 2226 4.380023 GCCGGTGTTGCACTAATTAATCAA 60.380 41.667 1.90 0.00 34.40 2.57
1717 2227 5.704888 CCGGTGTTGCACTAATTAATCAAA 58.295 37.500 0.00 0.00 34.40 2.69
1718 2228 5.799936 CCGGTGTTGCACTAATTAATCAAAG 59.200 40.000 0.00 0.00 34.40 2.77
1720 2230 6.348950 CGGTGTTGCACTAATTAATCAAAGGA 60.349 38.462 0.00 0.00 34.40 3.36
1721 2231 7.029563 GGTGTTGCACTAATTAATCAAAGGAG 58.970 38.462 0.00 0.00 34.40 3.69
1722 2232 6.528072 GTGTTGCACTAATTAATCAAAGGAGC 59.472 38.462 0.00 0.00 0.00 4.70
1723 2233 6.434028 TGTTGCACTAATTAATCAAAGGAGCT 59.566 34.615 0.00 0.00 0.00 4.09
1724 2234 7.609918 TGTTGCACTAATTAATCAAAGGAGCTA 59.390 33.333 0.00 0.00 0.00 3.32
1726 2236 6.260936 TGCACTAATTAATCAAAGGAGCTAGC 59.739 38.462 6.62 6.62 0.00 3.42
1727 2237 6.484977 GCACTAATTAATCAAAGGAGCTAGCT 59.515 38.462 19.45 19.45 0.00 3.32
1728 2238 7.657761 GCACTAATTAATCAAAGGAGCTAGCTA 59.342 37.037 19.38 0.08 0.00 3.32
1729 2239 9.547753 CACTAATTAATCAAAGGAGCTAGCTAA 57.452 33.333 19.38 5.15 0.00 3.09
1730 2240 9.771534 ACTAATTAATCAAAGGAGCTAGCTAAG 57.228 33.333 19.38 6.14 0.00 2.18
1731 2241 9.213799 CTAATTAATCAAAGGAGCTAGCTAAGG 57.786 37.037 19.38 6.13 0.00 2.69
1732 2242 6.561519 TTAATCAAAGGAGCTAGCTAAGGT 57.438 37.500 19.38 0.43 39.11 3.50
1733 2243 3.895232 TCAAAGGAGCTAGCTAAGGTG 57.105 47.619 19.38 13.76 35.60 4.00
1735 2245 3.055819 TCAAAGGAGCTAGCTAAGGTGTG 60.056 47.826 19.38 11.27 35.60 3.82
1736 2246 2.534042 AGGAGCTAGCTAAGGTGTGA 57.466 50.000 19.38 0.00 35.60 3.58
1737 2247 3.039252 AGGAGCTAGCTAAGGTGTGAT 57.961 47.619 19.38 0.00 35.60 3.06
1738 2248 2.697751 AGGAGCTAGCTAAGGTGTGATG 59.302 50.000 19.38 0.00 35.60 3.07
1740 2250 3.118592 GGAGCTAGCTAAGGTGTGATGTT 60.119 47.826 19.38 0.00 35.60 2.71
1741 2251 4.099573 GGAGCTAGCTAAGGTGTGATGTTA 59.900 45.833 19.38 0.00 35.60 2.41
1743 2253 5.665459 AGCTAGCTAAGGTGTGATGTTAAG 58.335 41.667 17.69 0.00 33.68 1.85
1744 2254 5.187967 AGCTAGCTAAGGTGTGATGTTAAGT 59.812 40.000 17.69 0.00 33.68 2.24
1745 2255 6.380274 AGCTAGCTAAGGTGTGATGTTAAGTA 59.620 38.462 17.69 0.00 33.68 2.24
1746 2256 6.697892 GCTAGCTAAGGTGTGATGTTAAGTAG 59.302 42.308 7.70 0.00 0.00 2.57
1747 2257 6.607004 AGCTAAGGTGTGATGTTAAGTAGT 57.393 37.500 0.00 0.00 0.00 2.73
1748 2258 7.005709 AGCTAAGGTGTGATGTTAAGTAGTT 57.994 36.000 0.00 0.00 0.00 2.24
1749 2259 7.097834 AGCTAAGGTGTGATGTTAAGTAGTTC 58.902 38.462 0.00 0.00 0.00 3.01
1750 2260 6.313164 GCTAAGGTGTGATGTTAAGTAGTTCC 59.687 42.308 0.00 0.00 0.00 3.62
1751 2261 6.435292 AAGGTGTGATGTTAAGTAGTTCCT 57.565 37.500 0.00 0.00 0.00 3.36
1752 2262 5.794894 AGGTGTGATGTTAAGTAGTTCCTG 58.205 41.667 0.00 0.00 0.00 3.86
1753 2263 4.392138 GGTGTGATGTTAAGTAGTTCCTGC 59.608 45.833 0.00 0.00 0.00 4.85
1754 2264 5.238583 GTGTGATGTTAAGTAGTTCCTGCT 58.761 41.667 0.00 0.00 0.00 4.24
1755 2265 5.120830 GTGTGATGTTAAGTAGTTCCTGCTG 59.879 44.000 0.00 0.00 0.00 4.41
1756 2266 5.011635 TGTGATGTTAAGTAGTTCCTGCTGA 59.988 40.000 0.00 0.00 0.00 4.26
1757 2267 5.578727 GTGATGTTAAGTAGTTCCTGCTGAG 59.421 44.000 0.00 0.00 0.00 3.35
1758 2268 5.246203 TGATGTTAAGTAGTTCCTGCTGAGT 59.754 40.000 0.00 0.00 0.00 3.41
1759 2269 6.436218 TGATGTTAAGTAGTTCCTGCTGAGTA 59.564 38.462 0.00 0.00 0.00 2.59
1760 2270 6.268825 TGTTAAGTAGTTCCTGCTGAGTAG 57.731 41.667 0.00 0.00 0.00 2.57
1761 2271 5.773680 TGTTAAGTAGTTCCTGCTGAGTAGT 59.226 40.000 0.00 0.00 0.00 2.73
1762 2272 6.944290 TGTTAAGTAGTTCCTGCTGAGTAGTA 59.056 38.462 0.00 0.00 0.00 1.82
1763 2273 7.614583 TGTTAAGTAGTTCCTGCTGAGTAGTAT 59.385 37.037 0.00 0.00 0.00 2.12
1764 2274 9.118300 GTTAAGTAGTTCCTGCTGAGTAGTATA 57.882 37.037 0.00 0.00 0.00 1.47
1765 2275 9.690913 TTAAGTAGTTCCTGCTGAGTAGTATAA 57.309 33.333 0.00 0.00 0.00 0.98
1766 2276 7.811117 AGTAGTTCCTGCTGAGTAGTATAAG 57.189 40.000 0.00 0.00 0.00 1.73
1767 2277 7.348033 AGTAGTTCCTGCTGAGTAGTATAAGT 58.652 38.462 0.00 0.00 0.00 2.24
1768 2278 8.492782 AGTAGTTCCTGCTGAGTAGTATAAGTA 58.507 37.037 0.00 0.00 0.00 2.24
1769 2279 9.287373 GTAGTTCCTGCTGAGTAGTATAAGTAT 57.713 37.037 0.00 0.00 0.00 2.12
1801 2311 6.894339 AACTTTGTGGTGTAATTAAGGGAG 57.106 37.500 0.00 0.00 0.00 4.30
1810 2320 8.157476 GTGGTGTAATTAAGGGAGTGATATCAT 58.843 37.037 9.02 0.00 0.00 2.45
1815 2325 9.899226 GTAATTAAGGGAGTGATATCATTTTGC 57.101 33.333 9.02 3.52 0.00 3.68
1823 2333 6.441093 AGTGATATCATTTTGCATTGTCGT 57.559 33.333 9.02 0.00 0.00 4.34
1825 2335 7.315142 AGTGATATCATTTTGCATTGTCGTTT 58.685 30.769 9.02 0.00 0.00 3.60
1833 2343 4.517952 TTGCATTGTCGTTTTGATGGAT 57.482 36.364 0.00 0.00 0.00 3.41
1834 2344 3.835779 TGCATTGTCGTTTTGATGGATG 58.164 40.909 0.00 0.00 0.00 3.51
1837 2351 3.829886 TTGTCGTTTTGATGGATGAGC 57.170 42.857 0.00 0.00 0.00 4.26
1843 2357 2.048444 TTTGATGGATGAGCTCCTGC 57.952 50.000 12.15 7.49 45.21 4.85
1851 2365 0.111061 ATGAGCTCCTGCCAACACAA 59.889 50.000 12.15 0.00 40.80 3.33
1853 2367 1.350684 TGAGCTCCTGCCAACACAATA 59.649 47.619 12.15 0.00 40.80 1.90
1856 2370 2.877300 AGCTCCTGCCAACACAATAGTG 60.877 50.000 0.00 0.00 45.31 2.74
1874 2472 3.205338 AGTGCTTGGCCAAAATGAAAAC 58.795 40.909 20.91 9.70 0.00 2.43
1883 2481 4.334203 GGCCAAAATGAAAACCGAGTTTTT 59.666 37.500 13.56 3.38 44.33 1.94
1884 2482 5.524281 GGCCAAAATGAAAACCGAGTTTTTA 59.476 36.000 13.56 10.94 44.33 1.52
1886 2484 7.068955 GCCAAAATGAAAACCGAGTTTTTATG 58.931 34.615 15.21 8.49 44.33 1.90
1887 2485 7.254624 GCCAAAATGAAAACCGAGTTTTTATGT 60.255 33.333 15.21 10.14 44.33 2.29
1888 2486 9.250624 CCAAAATGAAAACCGAGTTTTTATGTA 57.749 29.630 15.21 4.66 44.33 2.29
1918 2516 3.223157 GCAAGAAAAATGGTACGTGTCG 58.777 45.455 0.00 0.00 0.00 4.35
1977 2576 1.452145 GGGCCAAACAGCGAGACAAA 61.452 55.000 4.39 0.00 0.00 2.83
2085 2685 2.290260 TGTGATTCGCTTCCAGGACATT 60.290 45.455 0.00 0.00 0.00 2.71
2129 2729 0.037303 ACCATCTCCTTGCACACAGG 59.963 55.000 0.00 0.00 0.00 4.00
2131 2731 0.322277 CATCTCCTTGCACACAGGCT 60.322 55.000 0.00 0.00 34.04 4.58
2132 2732 0.035630 ATCTCCTTGCACACAGGCTC 60.036 55.000 0.00 0.00 34.04 4.70
2133 2733 1.673665 CTCCTTGCACACAGGCTCC 60.674 63.158 0.00 0.00 34.04 4.70
2134 2734 2.113774 CCTTGCACACAGGCTCCA 59.886 61.111 0.00 0.00 34.04 3.86
2135 2735 1.529010 CCTTGCACACAGGCTCCAA 60.529 57.895 0.00 0.00 34.04 3.53
2136 2736 0.896940 CCTTGCACACAGGCTCCAAT 60.897 55.000 0.00 0.00 34.04 3.16
2138 2738 0.961019 TTGCACACAGGCTCCAATTC 59.039 50.000 0.00 0.00 34.04 2.17
2139 2739 0.895100 TGCACACAGGCTCCAATTCC 60.895 55.000 0.00 0.00 34.04 3.01
2140 2740 0.895100 GCACACAGGCTCCAATTCCA 60.895 55.000 0.00 0.00 0.00 3.53
2141 2741 1.843368 CACACAGGCTCCAATTCCAT 58.157 50.000 0.00 0.00 0.00 3.41
2142 2742 1.747355 CACACAGGCTCCAATTCCATC 59.253 52.381 0.00 0.00 0.00 3.51
2144 2744 1.747355 CACAGGCTCCAATTCCATCAC 59.253 52.381 0.00 0.00 0.00 3.06
2145 2745 1.355381 ACAGGCTCCAATTCCATCACA 59.645 47.619 0.00 0.00 0.00 3.58
2147 2747 2.426024 CAGGCTCCAATTCCATCACAAG 59.574 50.000 0.00 0.00 0.00 3.16
2148 2748 2.309755 AGGCTCCAATTCCATCACAAGA 59.690 45.455 0.00 0.00 0.00 3.02
2149 2749 3.053095 AGGCTCCAATTCCATCACAAGAT 60.053 43.478 0.00 0.00 33.87 2.40
2150 2750 3.703052 GGCTCCAATTCCATCACAAGATT 59.297 43.478 0.00 0.00 30.20 2.40
2151 2751 4.161001 GGCTCCAATTCCATCACAAGATTT 59.839 41.667 0.00 0.00 30.20 2.17
2152 2752 5.107133 GCTCCAATTCCATCACAAGATTTG 58.893 41.667 0.00 0.00 30.20 2.32
2155 2755 7.156876 TCCAATTCCATCACAAGATTTGTAC 57.843 36.000 0.00 0.00 43.23 2.90
2156 2756 6.947733 TCCAATTCCATCACAAGATTTGTACT 59.052 34.615 0.00 0.00 43.23 2.73
2157 2757 7.031372 CCAATTCCATCACAAGATTTGTACTG 58.969 38.462 0.00 0.00 43.23 2.74
2160 2766 3.129287 CCATCACAAGATTTGTACTGCCC 59.871 47.826 0.00 0.00 43.23 5.36
2178 2784 2.356313 ACTCGCGTCAGCCAACAG 60.356 61.111 5.77 0.00 41.18 3.16
2193 2799 4.305769 GCCAACAGCATATGTGTTTTGAA 58.694 39.130 16.22 0.00 43.00 2.69
2248 2855 4.758165 GGAATGAACTGGAGGTCGTTTTTA 59.242 41.667 0.73 0.00 0.00 1.52
2264 2871 7.407337 GTCGTTTTTACCCATTGATGATCTAC 58.593 38.462 0.00 0.00 0.00 2.59
2265 2872 7.280205 GTCGTTTTTACCCATTGATGATCTACT 59.720 37.037 0.00 0.00 0.00 2.57
2266 2873 8.479689 TCGTTTTTACCCATTGATGATCTACTA 58.520 33.333 0.00 0.00 0.00 1.82
2301 2908 7.226325 ACAGAATTTCAAGTTCAGTCAGAGAAG 59.774 37.037 0.00 0.00 0.00 2.85
2302 2909 5.938438 ATTTCAAGTTCAGTCAGAGAAGC 57.062 39.130 0.00 0.00 0.00 3.86
2305 2912 0.980423 AGTTCAGTCAGAGAAGCCCC 59.020 55.000 0.00 0.00 0.00 5.80
2306 2913 0.035915 GTTCAGTCAGAGAAGCCCCC 60.036 60.000 0.00 0.00 0.00 5.40
2307 2914 1.544825 TTCAGTCAGAGAAGCCCCCG 61.545 60.000 0.00 0.00 0.00 5.73
2309 2916 4.475135 GTCAGAGAAGCCCCCGCC 62.475 72.222 0.00 0.00 34.57 6.13
2320 2927 4.426313 CCCCGCCCCCTCAAGTTC 62.426 72.222 0.00 0.00 0.00 3.01
2321 2928 4.426313 CCCGCCCCCTCAAGTTCC 62.426 72.222 0.00 0.00 0.00 3.62
2331 2938 2.698797 CCCTCAAGTTCCGCCTCTATAA 59.301 50.000 0.00 0.00 0.00 0.98
2336 2943 1.413077 AGTTCCGCCTCTATAACCTGC 59.587 52.381 0.00 0.00 0.00 4.85
2338 2945 1.664965 CCGCCTCTATAACCTGCGC 60.665 63.158 0.00 0.00 43.59 6.09
2339 2946 1.067416 CGCCTCTATAACCTGCGCA 59.933 57.895 10.98 10.98 38.69 6.09
2358 2976 0.949397 ATGCATGCATGGCTAACTCG 59.051 50.000 31.74 0.00 35.03 4.18
2385 3003 6.861065 CTTGAGCAAAGGTTACTAACTCAA 57.139 37.500 0.00 0.00 37.53 3.02
2386 3004 6.861065 TTGAGCAAAGGTTACTAACTCAAG 57.139 37.500 0.00 0.00 36.21 3.02
2387 3005 4.755123 TGAGCAAAGGTTACTAACTCAAGC 59.245 41.667 0.00 0.40 31.24 4.01
2388 3006 4.072839 AGCAAAGGTTACTAACTCAAGCC 58.927 43.478 0.00 0.00 0.00 4.35
2389 3007 4.072839 GCAAAGGTTACTAACTCAAGCCT 58.927 43.478 0.00 0.00 0.00 4.58
2390 3008 4.519350 GCAAAGGTTACTAACTCAAGCCTT 59.481 41.667 0.00 0.00 36.53 4.35
2391 3009 5.562890 GCAAAGGTTACTAACTCAAGCCTTG 60.563 44.000 0.00 0.00 35.35 3.61
2392 3010 5.562298 AAGGTTACTAACTCAAGCCTTGA 57.438 39.130 7.00 7.00 38.17 3.02
2478 3103 0.888619 TACCAACCTGAGTGCGAGAG 59.111 55.000 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.175035 TAACCGGGCCTCTCAAACCG 62.175 60.000 6.32 0.00 45.57 4.44
2 3 0.392595 CTAACCGGGCCTCTCAAACC 60.393 60.000 6.32 0.00 0.00 3.27
3 4 0.392595 CCTAACCGGGCCTCTCAAAC 60.393 60.000 6.32 0.00 0.00 2.93
4 5 0.838987 ACCTAACCGGGCCTCTCAAA 60.839 55.000 6.32 0.00 36.97 2.69
5 6 1.229400 ACCTAACCGGGCCTCTCAA 60.229 57.895 6.32 0.00 36.97 3.02
6 7 1.684734 GACCTAACCGGGCCTCTCA 60.685 63.158 6.32 0.00 33.11 3.27
7 8 2.783288 CGACCTAACCGGGCCTCTC 61.783 68.421 6.32 0.00 37.62 3.20
8 9 2.758737 CGACCTAACCGGGCCTCT 60.759 66.667 6.32 0.00 37.62 3.69
9 10 1.891722 TTTCGACCTAACCGGGCCTC 61.892 60.000 6.32 0.00 37.62 4.70
10 11 1.269703 ATTTCGACCTAACCGGGCCT 61.270 55.000 6.32 0.00 37.62 5.19
11 12 0.393402 AATTTCGACCTAACCGGGCC 60.393 55.000 6.32 0.00 37.62 5.80
12 13 1.399440 GAAATTTCGACCTAACCGGGC 59.601 52.381 6.32 0.00 37.50 6.13
25 26 0.441145 CCGTCCGGTCACGAAATTTC 59.559 55.000 16.59 8.20 42.69 2.17
26 27 1.571215 GCCGTCCGGTCACGAAATTT 61.571 55.000 16.59 0.00 42.69 1.82
27 28 2.030958 GCCGTCCGGTCACGAAATT 61.031 57.895 16.59 0.00 42.69 1.82
28 29 2.433664 GCCGTCCGGTCACGAAAT 60.434 61.111 16.59 0.00 42.69 2.17
29 30 3.914117 TGCCGTCCGGTCACGAAA 61.914 61.111 16.59 2.18 42.69 3.46
30 31 4.651008 GTGCCGTCCGGTCACGAA 62.651 66.667 16.59 2.52 42.69 3.85
43 44 0.952010 TTCTTAAACGCTCGGGTGCC 60.952 55.000 0.00 0.00 0.00 5.01
44 45 0.165295 GTTCTTAAACGCTCGGGTGC 59.835 55.000 0.00 0.00 0.00 5.01
54 55 3.216800 ACCCCTTCAACCGTTCTTAAAC 58.783 45.455 0.00 0.00 0.00 2.01
55 56 3.117963 TGACCCCTTCAACCGTTCTTAAA 60.118 43.478 0.00 0.00 0.00 1.52
56 57 2.438763 TGACCCCTTCAACCGTTCTTAA 59.561 45.455 0.00 0.00 0.00 1.85
57 58 2.038033 CTGACCCCTTCAACCGTTCTTA 59.962 50.000 0.00 0.00 32.21 2.10
58 59 0.841289 TGACCCCTTCAACCGTTCTT 59.159 50.000 0.00 0.00 0.00 2.52
59 60 0.396811 CTGACCCCTTCAACCGTTCT 59.603 55.000 0.00 0.00 32.21 3.01
60 61 0.605589 CCTGACCCCTTCAACCGTTC 60.606 60.000 0.00 0.00 32.21 3.95
61 62 1.350310 ACCTGACCCCTTCAACCGTT 61.350 55.000 0.00 0.00 32.21 4.44
62 63 1.350310 AACCTGACCCCTTCAACCGT 61.350 55.000 0.00 0.00 32.21 4.83
63 64 0.889186 CAACCTGACCCCTTCAACCG 60.889 60.000 0.00 0.00 32.21 4.44
64 65 1.179174 GCAACCTGACCCCTTCAACC 61.179 60.000 0.00 0.00 32.21 3.77
65 66 0.467290 TGCAACCTGACCCCTTCAAC 60.467 55.000 0.00 0.00 32.21 3.18
66 67 0.178992 CTGCAACCTGACCCCTTCAA 60.179 55.000 0.00 0.00 32.21 2.69
67 68 1.059584 TCTGCAACCTGACCCCTTCA 61.060 55.000 0.00 0.00 0.00 3.02
68 69 0.329596 ATCTGCAACCTGACCCCTTC 59.670 55.000 0.00 0.00 0.00 3.46
69 70 0.038744 CATCTGCAACCTGACCCCTT 59.961 55.000 0.00 0.00 0.00 3.95
70 71 1.687612 CATCTGCAACCTGACCCCT 59.312 57.895 0.00 0.00 0.00 4.79
71 72 2.048603 GCATCTGCAACCTGACCCC 61.049 63.158 0.00 0.00 41.59 4.95
72 73 1.001641 AGCATCTGCAACCTGACCC 60.002 57.895 4.79 0.00 45.16 4.46
73 74 2.475666 GAGCATCTGCAACCTGACC 58.524 57.895 4.79 0.00 45.16 4.02
79 80 8.362993 GATGGTTTCATAAAGAGCATCTGCAAC 61.363 40.741 4.79 0.00 42.17 4.17
80 81 6.405065 GATGGTTTCATAAAGAGCATCTGCAA 60.405 38.462 4.79 0.00 42.17 4.08
81 82 5.066893 GATGGTTTCATAAAGAGCATCTGCA 59.933 40.000 4.79 0.00 42.17 4.41
82 83 5.517904 GATGGTTTCATAAAGAGCATCTGC 58.482 41.667 7.32 0.00 42.17 4.26
85 86 7.565323 AAGAGATGGTTTCATAAAGAGCATC 57.435 36.000 6.65 6.65 44.43 3.91
86 87 7.951347 AAAGAGATGGTTTCATAAAGAGCAT 57.049 32.000 0.00 0.00 32.98 3.79
87 88 7.765695 AAAAGAGATGGTTTCATAAAGAGCA 57.234 32.000 0.00 0.00 32.98 4.26
115 120 6.783892 GCAAAAGAGTTGCCATTTCATTAA 57.216 33.333 0.00 0.00 39.38 1.40
166 171 2.205022 TTTCAGGCTCATGAGGTTGG 57.795 50.000 23.89 0.00 0.00 3.77
172 177 3.998913 TGGTACATTTCAGGCTCATGA 57.001 42.857 0.00 0.00 0.00 3.07
188 193 3.006537 CCCGTTCTGTTTCTCTCTTGGTA 59.993 47.826 0.00 0.00 0.00 3.25
192 197 2.047830 ACCCCGTTCTGTTTCTCTCTT 58.952 47.619 0.00 0.00 0.00 2.85
212 217 4.725490 TGGTGATGTCAGATACGGAGATA 58.275 43.478 0.00 0.00 0.00 1.98
213 218 3.566351 TGGTGATGTCAGATACGGAGAT 58.434 45.455 0.00 0.00 0.00 2.75
214 219 3.012934 TGGTGATGTCAGATACGGAGA 57.987 47.619 0.00 0.00 0.00 3.71
215 220 3.319122 TGATGGTGATGTCAGATACGGAG 59.681 47.826 0.00 0.00 0.00 4.63
216 221 3.295973 TGATGGTGATGTCAGATACGGA 58.704 45.455 0.00 0.00 0.00 4.69
217 222 3.733443 TGATGGTGATGTCAGATACGG 57.267 47.619 0.00 0.00 0.00 4.02
218 223 4.874970 TGATGATGGTGATGTCAGATACG 58.125 43.478 0.00 0.00 0.00 3.06
219 224 5.575995 CGATGATGATGGTGATGTCAGATAC 59.424 44.000 0.00 0.00 0.00 2.24
220 225 5.337009 CCGATGATGATGGTGATGTCAGATA 60.337 44.000 0.00 0.00 0.00 1.98
270 278 6.071840 AGGATGGATAACGATGCTAGTACTTC 60.072 42.308 0.00 0.00 32.15 3.01
295 303 0.909610 ACCCAACAGGCAGCTAGCTA 60.910 55.000 18.86 0.00 44.79 3.32
310 320 1.347062 GGGCCAAGAATTTCAACCCA 58.653 50.000 4.39 0.00 35.84 4.51
311 321 0.246360 CGGGCCAAGAATTTCAACCC 59.754 55.000 4.39 3.08 0.00 4.11
314 324 1.540435 GGGCGGGCCAAGAATTTCAA 61.540 55.000 16.76 0.00 37.98 2.69
352 362 1.003355 CCTTCTTCCCTGCAAGCGA 60.003 57.895 0.00 0.00 0.00 4.93
488 506 2.802816 TGCGAGAAAAGAAACAGCTCTC 59.197 45.455 0.00 0.00 0.00 3.20
489 507 2.838736 TGCGAGAAAAGAAACAGCTCT 58.161 42.857 0.00 0.00 0.00 4.09
490 508 3.486584 CATGCGAGAAAAGAAACAGCTC 58.513 45.455 0.00 0.00 0.00 4.09
491 509 2.227388 CCATGCGAGAAAAGAAACAGCT 59.773 45.455 0.00 0.00 0.00 4.24
492 510 2.589014 CCATGCGAGAAAAGAAACAGC 58.411 47.619 0.00 0.00 0.00 4.40
495 513 1.729149 CGGCCATGCGAGAAAAGAAAC 60.729 52.381 2.24 0.00 0.00 2.78
645 699 1.303643 GGGAGCACAAGAGTTGGGG 60.304 63.158 0.00 0.00 33.68 4.96
794 1182 1.287739 AGAGAGAGGGAGAGGTTGAGG 59.712 57.143 0.00 0.00 0.00 3.86
796 1184 2.241176 GAGAGAGAGAGGGAGAGGTTGA 59.759 54.545 0.00 0.00 0.00 3.18
797 1185 2.242196 AGAGAGAGAGAGGGAGAGGTTG 59.758 54.545 0.00 0.00 0.00 3.77
798 1186 2.509964 GAGAGAGAGAGAGGGAGAGGTT 59.490 54.545 0.00 0.00 0.00 3.50
799 1187 2.127708 GAGAGAGAGAGAGGGAGAGGT 58.872 57.143 0.00 0.00 0.00 3.85
800 1188 2.105477 CAGAGAGAGAGAGAGGGAGAGG 59.895 59.091 0.00 0.00 0.00 3.69
801 1189 2.774234 ACAGAGAGAGAGAGAGGGAGAG 59.226 54.545 0.00 0.00 0.00 3.20
802 1190 2.505407 CACAGAGAGAGAGAGAGGGAGA 59.495 54.545 0.00 0.00 0.00 3.71
803 1191 2.421952 CCACAGAGAGAGAGAGAGGGAG 60.422 59.091 0.00 0.00 0.00 4.30
804 1192 1.563879 CCACAGAGAGAGAGAGAGGGA 59.436 57.143 0.00 0.00 0.00 4.20
805 1193 1.563879 TCCACAGAGAGAGAGAGAGGG 59.436 57.143 0.00 0.00 0.00 4.30
806 1194 2.643551 GTCCACAGAGAGAGAGAGAGG 58.356 57.143 0.00 0.00 0.00 3.69
807 1195 2.026356 TGGTCCACAGAGAGAGAGAGAG 60.026 54.545 0.00 0.00 0.00 3.20
808 1196 1.988846 TGGTCCACAGAGAGAGAGAGA 59.011 52.381 0.00 0.00 0.00 3.10
841 1231 0.400594 GGGTTCCTTGTAGCTGTGGT 59.599 55.000 0.00 0.00 0.00 4.16
882 1272 4.082190 CCGCTAGCCTGCTACTTATATCAA 60.082 45.833 9.66 0.00 0.00 2.57
908 1298 4.176752 GGAAGCAGCCGGGTAGGG 62.177 72.222 5.47 0.00 41.48 3.53
909 1299 4.176752 GGGAAGCAGCCGGGTAGG 62.177 72.222 5.47 0.00 44.97 3.18
910 1300 3.083997 AGGGAAGCAGCCGGGTAG 61.084 66.667 5.47 1.79 0.00 3.18
911 1301 3.081409 GAGGGAAGCAGCCGGGTA 61.081 66.667 5.47 0.00 0.00 3.69
958 1354 2.569134 GCTCGACTGAAGCTCGGT 59.431 61.111 0.00 0.00 39.01 4.69
961 1357 0.593773 GATCGGCTCGACTGAAGCTC 60.594 60.000 0.00 0.00 39.18 4.09
988 1384 0.628668 AGCTTCATGGGGGAAGGGAT 60.629 55.000 5.22 0.00 43.54 3.85
989 1385 1.230281 AGCTTCATGGGGGAAGGGA 60.230 57.895 5.22 0.00 43.54 4.20
990 1386 1.228510 GAGCTTCATGGGGGAAGGG 59.771 63.158 5.22 0.00 43.54 3.95
993 1397 2.001803 CAGGAGCTTCATGGGGGAA 58.998 57.895 0.00 0.00 0.00 3.97
1014 1418 1.646189 GCAGAAGCGAGGAGTAAAGG 58.354 55.000 0.00 0.00 0.00 3.11
1077 1493 1.407618 AGATCTTGGCACGCACGTATA 59.592 47.619 0.00 0.00 0.00 1.47
1078 1494 0.175760 AGATCTTGGCACGCACGTAT 59.824 50.000 0.00 0.00 0.00 3.06
1141 1557 1.461075 ATCAGCTAGAGGCAGGGGG 60.461 63.158 0.00 0.00 44.79 5.40
1142 1558 1.753470 CATCAGCTAGAGGCAGGGG 59.247 63.158 0.00 0.00 44.79 4.79
1164 1580 5.594247 TGCAAGAAAGCGATGGCAACAAA 62.594 43.478 1.50 0.00 45.09 2.83
1165 1581 4.162049 TGCAAGAAAGCGATGGCAACAA 62.162 45.455 1.50 0.00 45.09 2.83
1173 1589 2.419297 CCTCTACCTGCAAGAAAGCGAT 60.419 50.000 0.00 0.00 34.07 4.58
1199 1619 2.928334 CTCCTTGAGCTGGTAATGCAT 58.072 47.619 0.00 0.00 0.00 3.96
1226 1646 2.843545 GCCCTCCACCACCTTTGA 59.156 61.111 0.00 0.00 0.00 2.69
1481 1913 3.518998 GCTAGCTGCCTCGGTCGA 61.519 66.667 7.70 0.00 35.15 4.20
1482 1914 3.522731 AGCTAGCTGCCTCGGTCG 61.523 66.667 18.57 0.00 44.23 4.79
1490 1922 5.914686 CTTCAGGAGAAAACAGCTAGCTGC 61.915 50.000 38.47 24.54 39.29 5.25
1492 1924 3.580458 TCTTCAGGAGAAAACAGCTAGCT 59.420 43.478 12.68 12.68 32.35 3.32
1496 1928 4.696479 TCTTCTTCAGGAGAAAACAGCT 57.304 40.909 0.00 0.00 43.56 4.24
1497 1929 4.759183 ACATCTTCTTCAGGAGAAAACAGC 59.241 41.667 0.00 0.00 43.56 4.40
1498 1930 6.874288 AACATCTTCTTCAGGAGAAAACAG 57.126 37.500 0.00 0.00 43.56 3.16
1499 1931 6.828273 TCAAACATCTTCTTCAGGAGAAAACA 59.172 34.615 0.00 0.00 43.56 2.83
1500 1932 7.264373 TCAAACATCTTCTTCAGGAGAAAAC 57.736 36.000 0.00 0.00 43.56 2.43
1501 1933 7.720957 TCATCAAACATCTTCTTCAGGAGAAAA 59.279 33.333 0.00 0.00 43.56 2.29
1502 1934 7.226441 TCATCAAACATCTTCTTCAGGAGAAA 58.774 34.615 0.00 0.00 43.56 2.52
1503 1935 6.772605 TCATCAAACATCTTCTTCAGGAGAA 58.227 36.000 0.00 0.00 42.03 2.87
1504 1936 6.364568 TCATCAAACATCTTCTTCAGGAGA 57.635 37.500 0.00 0.00 0.00 3.71
1505 1937 5.064962 GCTCATCAAACATCTTCTTCAGGAG 59.935 44.000 0.00 0.00 0.00 3.69
1506 1938 4.940046 GCTCATCAAACATCTTCTTCAGGA 59.060 41.667 0.00 0.00 0.00 3.86
1507 1939 4.942483 AGCTCATCAAACATCTTCTTCAGG 59.058 41.667 0.00 0.00 0.00 3.86
1508 1940 6.403418 GGAAGCTCATCAAACATCTTCTTCAG 60.403 42.308 0.00 0.00 32.77 3.02
1509 1941 5.413833 GGAAGCTCATCAAACATCTTCTTCA 59.586 40.000 0.00 0.00 32.77 3.02
1530 1962 3.559069 GGATGGATCAAAGATGCTGGAA 58.441 45.455 0.00 0.00 0.00 3.53
1586 2025 2.680913 GCTACACCTTGCACCTGCG 61.681 63.158 0.00 0.00 45.83 5.18
1590 2029 0.593128 CAACAGCTACACCTTGCACC 59.407 55.000 0.00 0.00 0.00 5.01
1599 2071 3.857157 AAACTTCTCCCAACAGCTACA 57.143 42.857 0.00 0.00 0.00 2.74
1602 2074 2.310538 CCAAAACTTCTCCCAACAGCT 58.689 47.619 0.00 0.00 0.00 4.24
1604 2076 3.287222 TGACCAAAACTTCTCCCAACAG 58.713 45.455 0.00 0.00 0.00 3.16
1613 2085 4.911514 TGCCTAAACTGACCAAAACTTC 57.088 40.909 0.00 0.00 0.00 3.01
1633 2109 8.773404 TCAGCATCATCATCATAAACTCTATG 57.227 34.615 0.00 0.00 0.00 2.23
1660 2145 3.887110 TGGTAGTAGTATGTGGTGGATCG 59.113 47.826 0.00 0.00 0.00 3.69
1680 2165 0.673644 CACCGGCTCCAAACTACTGG 60.674 60.000 0.00 0.00 37.87 4.00
1681 2166 0.034896 ACACCGGCTCCAAACTACTG 59.965 55.000 0.00 0.00 0.00 2.74
1711 2202 4.226168 ACACCTTAGCTAGCTCCTTTGATT 59.774 41.667 23.26 0.00 0.00 2.57
1716 2226 2.821437 TCACACCTTAGCTAGCTCCTT 58.179 47.619 23.26 0.00 0.00 3.36
1717 2227 2.534042 TCACACCTTAGCTAGCTCCT 57.466 50.000 23.26 0.00 0.00 3.69
1718 2228 2.432510 ACATCACACCTTAGCTAGCTCC 59.567 50.000 23.26 0.00 0.00 4.70
1720 2230 5.187967 ACTTAACATCACACCTTAGCTAGCT 59.812 40.000 23.12 23.12 0.00 3.32
1721 2231 5.420409 ACTTAACATCACACCTTAGCTAGC 58.580 41.667 6.62 6.62 0.00 3.42
1722 2232 7.773149 ACTACTTAACATCACACCTTAGCTAG 58.227 38.462 0.00 0.00 0.00 3.42
1723 2233 7.713734 ACTACTTAACATCACACCTTAGCTA 57.286 36.000 0.00 0.00 0.00 3.32
1724 2234 6.607004 ACTACTTAACATCACACCTTAGCT 57.393 37.500 0.00 0.00 0.00 3.32
1726 2236 7.545965 CAGGAACTACTTAACATCACACCTTAG 59.454 40.741 0.00 0.00 36.02 2.18
1727 2237 7.383687 CAGGAACTACTTAACATCACACCTTA 58.616 38.462 0.00 0.00 36.02 2.69
1728 2238 6.231211 CAGGAACTACTTAACATCACACCTT 58.769 40.000 0.00 0.00 36.02 3.50
1729 2239 5.794894 CAGGAACTACTTAACATCACACCT 58.205 41.667 0.00 0.00 36.02 4.00
1730 2240 4.392138 GCAGGAACTACTTAACATCACACC 59.608 45.833 0.00 0.00 36.02 4.16
1731 2241 5.120830 CAGCAGGAACTACTTAACATCACAC 59.879 44.000 0.00 0.00 36.02 3.82
1732 2242 5.011635 TCAGCAGGAACTACTTAACATCACA 59.988 40.000 0.00 0.00 36.02 3.58
1733 2243 5.479306 TCAGCAGGAACTACTTAACATCAC 58.521 41.667 0.00 0.00 36.02 3.06
1735 2245 5.725362 ACTCAGCAGGAACTACTTAACATC 58.275 41.667 0.00 0.00 36.02 3.06
1736 2246 5.746990 ACTCAGCAGGAACTACTTAACAT 57.253 39.130 0.00 0.00 36.02 2.71
1737 2247 5.773680 ACTACTCAGCAGGAACTACTTAACA 59.226 40.000 0.00 0.00 36.02 2.41
1738 2248 6.270156 ACTACTCAGCAGGAACTACTTAAC 57.730 41.667 0.00 0.00 36.02 2.01
1740 2250 9.339850 CTTATACTACTCAGCAGGAACTACTTA 57.660 37.037 0.00 0.00 36.02 2.24
1741 2251 7.835181 ACTTATACTACTCAGCAGGAACTACTT 59.165 37.037 0.00 0.00 36.02 2.24
1743 2253 7.571080 ACTTATACTACTCAGCAGGAACTAC 57.429 40.000 0.00 0.00 36.02 2.73
1748 2258 9.809395 ACAATATACTTATACTACTCAGCAGGA 57.191 33.333 0.00 0.00 0.00 3.86
1779 2289 5.768164 CACTCCCTTAATTACACCACAAAGT 59.232 40.000 0.00 0.00 0.00 2.66
1783 2293 5.772393 ATCACTCCCTTAATTACACCACA 57.228 39.130 0.00 0.00 0.00 4.17
1798 2308 5.911280 CGACAATGCAAAATGATATCACTCC 59.089 40.000 7.78 0.00 0.00 3.85
1801 2311 7.510428 AAACGACAATGCAAAATGATATCAC 57.490 32.000 7.78 0.00 0.00 3.06
1810 2320 4.686972 TCCATCAAAACGACAATGCAAAA 58.313 34.783 0.00 0.00 0.00 2.44
1813 2323 3.505293 TCATCCATCAAAACGACAATGCA 59.495 39.130 0.00 0.00 0.00 3.96
1815 2325 4.100529 GCTCATCCATCAAAACGACAATG 58.899 43.478 0.00 0.00 0.00 2.82
1833 2343 0.111061 ATTGTGTTGGCAGGAGCTCA 59.889 50.000 17.19 0.00 41.70 4.26
1834 2344 2.012673 CTATTGTGTTGGCAGGAGCTC 58.987 52.381 4.71 4.71 41.70 4.09
1837 2351 1.470098 GCACTATTGTGTTGGCAGGAG 59.530 52.381 9.05 0.00 45.44 3.69
1843 2357 1.067635 GGCCAAGCACTATTGTGTTGG 60.068 52.381 23.63 23.63 46.20 3.77
1851 2365 4.888326 TTTCATTTTGGCCAAGCACTAT 57.112 36.364 19.48 5.85 0.00 2.12
1853 2367 3.205338 GTTTTCATTTTGGCCAAGCACT 58.795 40.909 19.48 1.73 0.00 4.40
1856 2370 1.530720 CGGTTTTCATTTTGGCCAAGC 59.469 47.619 19.48 3.40 0.00 4.01
1859 2373 2.035632 ACTCGGTTTTCATTTTGGCCA 58.964 42.857 0.00 0.00 0.00 5.36
1860 2374 2.812358 ACTCGGTTTTCATTTTGGCC 57.188 45.000 0.00 0.00 0.00 5.36
1861 2375 5.478233 AAAAACTCGGTTTTCATTTTGGC 57.522 34.783 12.95 0.00 43.67 4.52
1862 2376 8.137210 ACATAAAAACTCGGTTTTCATTTTGG 57.863 30.769 12.95 0.00 43.67 3.28
1889 2487 9.515020 CACGTACCATTTTTCTTGCATTATTAT 57.485 29.630 0.00 0.00 0.00 1.28
1890 2488 8.516234 ACACGTACCATTTTTCTTGCATTATTA 58.484 29.630 0.00 0.00 0.00 0.98
1891 2489 7.375053 ACACGTACCATTTTTCTTGCATTATT 58.625 30.769 0.00 0.00 0.00 1.40
1892 2490 6.919721 ACACGTACCATTTTTCTTGCATTAT 58.080 32.000 0.00 0.00 0.00 1.28
1893 2491 6.320494 ACACGTACCATTTTTCTTGCATTA 57.680 33.333 0.00 0.00 0.00 1.90
1894 2492 5.195001 ACACGTACCATTTTTCTTGCATT 57.805 34.783 0.00 0.00 0.00 3.56
1895 2493 4.612712 CGACACGTACCATTTTTCTTGCAT 60.613 41.667 0.00 0.00 0.00 3.96
1896 2494 3.303461 CGACACGTACCATTTTTCTTGCA 60.303 43.478 0.00 0.00 0.00 4.08
1897 2495 3.223157 CGACACGTACCATTTTTCTTGC 58.777 45.455 0.00 0.00 0.00 4.01
2129 2729 4.996788 AATCTTGTGATGGAATTGGAGC 57.003 40.909 0.00 0.00 32.44 4.70
2131 2731 6.947733 AGTACAAATCTTGTGATGGAATTGGA 59.052 34.615 2.30 0.00 45.03 3.53
2132 2732 7.031372 CAGTACAAATCTTGTGATGGAATTGG 58.969 38.462 2.30 0.00 45.03 3.16
2133 2733 6.529125 GCAGTACAAATCTTGTGATGGAATTG 59.471 38.462 2.30 0.00 45.03 2.32
2134 2734 6.350445 GGCAGTACAAATCTTGTGATGGAATT 60.350 38.462 2.30 0.00 45.03 2.17
2135 2735 5.126061 GGCAGTACAAATCTTGTGATGGAAT 59.874 40.000 2.30 0.00 45.03 3.01
2136 2736 4.458989 GGCAGTACAAATCTTGTGATGGAA 59.541 41.667 2.30 0.00 45.03 3.53
2138 2738 3.129287 GGGCAGTACAAATCTTGTGATGG 59.871 47.826 2.30 0.00 45.03 3.51
2139 2739 3.758023 TGGGCAGTACAAATCTTGTGATG 59.242 43.478 2.30 2.69 45.03 3.07
2140 2740 3.758554 GTGGGCAGTACAAATCTTGTGAT 59.241 43.478 2.30 0.00 45.03 3.06
2141 2741 3.146066 GTGGGCAGTACAAATCTTGTGA 58.854 45.455 2.30 0.00 45.03 3.58
2142 2742 3.149196 AGTGGGCAGTACAAATCTTGTG 58.851 45.455 2.30 0.00 45.03 3.33
2144 2744 2.416547 CGAGTGGGCAGTACAAATCTTG 59.583 50.000 0.00 0.00 0.00 3.02
2145 2745 2.699954 CGAGTGGGCAGTACAAATCTT 58.300 47.619 0.00 0.00 0.00 2.40
2147 2747 0.727398 GCGAGTGGGCAGTACAAATC 59.273 55.000 0.00 0.00 0.00 2.17
2148 2748 1.019278 CGCGAGTGGGCAGTACAAAT 61.019 55.000 0.00 0.00 0.00 2.32
2149 2749 1.666553 CGCGAGTGGGCAGTACAAA 60.667 57.895 0.00 0.00 0.00 2.83
2150 2750 2.048597 CGCGAGTGGGCAGTACAA 60.049 61.111 0.00 0.00 0.00 2.41
2151 2751 3.299977 ACGCGAGTGGGCAGTACA 61.300 61.111 15.93 0.00 46.97 2.90
2178 2784 4.532276 TCACACGTTCAAAACACATATGC 58.468 39.130 1.58 0.00 0.00 3.14
2183 2789 5.123186 AGAGAAATCACACGTTCAAAACACA 59.877 36.000 0.00 0.00 0.00 3.72
2187 2793 6.538742 AGAAGAGAGAAATCACACGTTCAAAA 59.461 34.615 0.00 0.00 0.00 2.44
2193 2799 5.461032 AGAAGAAGAGAGAAATCACACGT 57.539 39.130 0.00 0.00 0.00 4.49
2233 2840 2.554370 TGGGTAAAAACGACCTCCAG 57.446 50.000 0.00 0.00 37.13 3.86
2305 2912 4.778143 CGGAACTTGAGGGGGCGG 62.778 72.222 0.00 0.00 0.00 6.13
2309 2916 0.976073 TAGAGGCGGAACTTGAGGGG 60.976 60.000 0.00 0.00 0.00 4.79
2311 2918 3.492829 GGTTATAGAGGCGGAACTTGAGG 60.493 52.174 0.00 0.00 0.00 3.86
2312 2919 3.385111 AGGTTATAGAGGCGGAACTTGAG 59.615 47.826 0.00 0.00 0.00 3.02
2314 2921 3.458189 CAGGTTATAGAGGCGGAACTTG 58.542 50.000 0.00 0.00 0.00 3.16
2315 2922 2.158943 GCAGGTTATAGAGGCGGAACTT 60.159 50.000 0.00 0.00 0.00 2.66
2316 2923 1.413077 GCAGGTTATAGAGGCGGAACT 59.587 52.381 0.00 0.00 0.00 3.01
2317 2924 1.867166 GCAGGTTATAGAGGCGGAAC 58.133 55.000 0.00 0.00 0.00 3.62
2318 2925 0.387929 CGCAGGTTATAGAGGCGGAA 59.612 55.000 0.00 0.00 43.63 4.30
2319 2926 2.038690 CGCAGGTTATAGAGGCGGA 58.961 57.895 0.00 0.00 43.63 5.54
2320 2927 4.655527 CGCAGGTTATAGAGGCGG 57.344 61.111 0.00 0.00 43.63 6.13
2339 2946 0.949397 CGAGTTAGCCATGCATGCAT 59.051 50.000 27.46 27.46 37.08 3.96
2382 3000 5.648526 CAGTACTACTCTACTCAAGGCTTGA 59.351 44.000 27.01 27.01 38.17 3.02
2383 3001 5.163602 CCAGTACTACTCTACTCAAGGCTTG 60.164 48.000 21.17 21.17 0.00 4.01
2384 3002 4.951094 CCAGTACTACTCTACTCAAGGCTT 59.049 45.833 0.00 0.00 0.00 4.35
2385 3003 4.528920 CCAGTACTACTCTACTCAAGGCT 58.471 47.826 0.00 0.00 0.00 4.58
2386 3004 3.067040 GCCAGTACTACTCTACTCAAGGC 59.933 52.174 0.00 0.00 30.40 4.35
2387 3005 4.270834 TGCCAGTACTACTCTACTCAAGG 58.729 47.826 0.00 0.00 0.00 3.61
2388 3006 5.416326 AGTTGCCAGTACTACTCTACTCAAG 59.584 44.000 0.00 0.00 0.00 3.02
2389 3007 5.183331 CAGTTGCCAGTACTACTCTACTCAA 59.817 44.000 0.00 0.00 0.00 3.02
2390 3008 4.700692 CAGTTGCCAGTACTACTCTACTCA 59.299 45.833 0.00 0.00 0.00 3.41
2391 3009 4.439016 GCAGTTGCCAGTACTACTCTACTC 60.439 50.000 0.00 0.00 34.31 2.59
2392 3010 3.444388 GCAGTTGCCAGTACTACTCTACT 59.556 47.826 0.00 0.00 34.31 2.57
2393 3011 3.192844 TGCAGTTGCCAGTACTACTCTAC 59.807 47.826 0.00 0.00 41.18 2.59
2394 3012 3.427573 TGCAGTTGCCAGTACTACTCTA 58.572 45.455 0.00 0.00 41.18 2.43
2395 3013 2.248248 TGCAGTTGCCAGTACTACTCT 58.752 47.619 0.00 0.00 41.18 3.24


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

AutoCloner maintained by Alex Coulton.