Multiple sequence alignment - TraesCS3A01G403300

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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 TraesCS3A01G403300 chr3A 100.000 3881 0 0 1 3881 648313261 648309381 0.000000e+00 7167.0
1 TraesCS3A01G403300 chr3D 92.159 3839 125 66 98 3863 512708652 512704917 0.000000e+00 5260.0
2 TraesCS3A01G403300 chr3B 90.437 1830 77 45 2087 3860 675281246 675279459 0.000000e+00 2320.0
3 TraesCS3A01G403300 chr3B 86.465 1980 108 62 98 2037 675283107 675281248 0.000000e+00 2025.0
4 TraesCS3A01G403300 chr1D 92.395 263 16 4 1352 1612 355698587 355698327 4.740000e-99 372.0
5 TraesCS3A01G403300 chr1D 90.857 175 15 1 1085 1258 355698831 355698657 2.330000e-57 233.0
6 TraesCS3A01G403300 chr1A 92.395 263 16 4 1352 1612 456323326 456323066 4.740000e-99 372.0
7 TraesCS3A01G403300 chr1A 90.286 175 16 1 1085 1258 456323587 456323413 1.080000e-55 228.0
8 TraesCS3A01G403300 chr1B 92.015 263 17 4 1352 1612 478583492 478583232 2.200000e-97 366.0
9 TraesCS3A01G403300 chr1B 91.429 175 14 1 1085 1258 478583757 478583583 5.010000e-59 239.0
10 TraesCS3A01G403300 chr7D 86.102 295 33 7 1352 1642 401093668 401093378 1.050000e-80 311.0
11 TraesCS3A01G403300 chr7D 86.567 67 5 4 1120 1184 34151668 34151604 1.930000e-08 71.3
12 TraesCS3A01G403300 chr7D 100.000 37 0 0 1120 1156 34445002 34445038 6.960000e-08 69.4
13 TraesCS3A01G403300 chr7A 86.102 295 33 7 1352 1642 458934572 458934282 1.050000e-80 311.0
14 TraesCS3A01G403300 chr7B 85.424 295 36 6 1352 1642 410620575 410620284 2.270000e-77 300.0
15 TraesCS3A01G403300 chr5A 76.349 241 43 12 1366 1596 666525277 666525041 2.450000e-22 117.0
16 TraesCS3A01G403300 chr4A 100.000 36 0 0 1120 1155 690938211 690938176 2.500000e-07 67.6
17 TraesCS3A01G403300 chr4A 84.848 66 8 2 1120 1184 690689386 690689322 9.000000e-07 65.8


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 TraesCS3A01G403300 chr3A 648309381 648313261 3880 True 7167.0 7167 100.0000 1 3881 1 chr3A.!!$R1 3880
1 TraesCS3A01G403300 chr3D 512704917 512708652 3735 True 5260.0 5260 92.1590 98 3863 1 chr3D.!!$R1 3765
2 TraesCS3A01G403300 chr3B 675279459 675283107 3648 True 2172.5 2320 88.4510 98 3860 2 chr3B.!!$R1 3762
3 TraesCS3A01G403300 chr1D 355698327 355698831 504 True 302.5 372 91.6260 1085 1612 2 chr1D.!!$R1 527
4 TraesCS3A01G403300 chr1A 456323066 456323587 521 True 300.0 372 91.3405 1085 1612 2 chr1A.!!$R1 527
5 TraesCS3A01G403300 chr1B 478583232 478583757 525 True 302.5 366 91.7220 1085 1612 2 chr1B.!!$R1 527

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
46 47 0.100682 GTCTCGACTGCCGCTATGAA 59.899 55.0 0.00 0.0 38.37 2.57 F
54 55 0.459489 TGCCGCTATGAAAATTGGGC 59.541 50.0 0.00 0.0 39.48 5.36 F
55 56 0.459489 GCCGCTATGAAAATTGGGCA 59.541 50.0 0.00 0.0 38.88 5.36 F
66 67 0.968405 AATTGGGCAAACATGCTCGT 59.032 45.0 0.00 0.0 38.32 4.18 F
1773 1827 0.179134 CTGCGCCTGTAGTCCTGTAC 60.179 60.0 4.18 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1155 1171 0.030908 GGCGGAGGTAGAACTCGATG 59.969 60.000 0.00 0.0 38.39 3.84 R
1321 1373 2.051076 GCCACACACACACGCATG 60.051 61.111 0.00 0.0 0.00 4.06 R
1662 1714 3.439154 GCAGATGGATAGATCAGGAGGA 58.561 50.000 0.00 0.0 0.00 3.71 R
1778 1832 3.821033 GCACCCAACATCAAAGAACTAGT 59.179 43.478 0.00 0.0 0.00 2.57 R
3591 3734 0.033920 ATGACACGCTCTGACAAGCA 59.966 50.000 9.34 0.0 42.62 3.91 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.953158 ATACTCAAAGATAATGTGTGATCCG 57.047 36.000 0.00 0.00 0.00 4.18
25 26 4.572389 ACTCAAAGATAATGTGTGATCCGC 59.428 41.667 0.00 0.00 0.00 5.54
26 27 3.555547 TCAAAGATAATGTGTGATCCGCG 59.444 43.478 0.00 0.00 0.00 6.46
27 28 2.154854 AGATAATGTGTGATCCGCGG 57.845 50.000 22.12 22.12 0.00 6.46
28 29 1.412710 AGATAATGTGTGATCCGCGGT 59.587 47.619 27.15 12.96 0.00 5.68
29 30 1.792949 GATAATGTGTGATCCGCGGTC 59.207 52.381 27.15 21.38 0.00 4.79
30 31 0.821517 TAATGTGTGATCCGCGGTCT 59.178 50.000 27.15 14.32 0.00 3.85
31 32 0.460284 AATGTGTGATCCGCGGTCTC 60.460 55.000 27.15 22.42 0.00 3.36
32 33 2.579787 GTGTGATCCGCGGTCTCG 60.580 66.667 27.15 0.00 39.81 4.04
33 34 2.748647 TGTGATCCGCGGTCTCGA 60.749 61.111 27.15 5.24 39.00 4.04
34 35 2.278013 GTGATCCGCGGTCTCGAC 60.278 66.667 27.15 17.72 39.00 4.20
35 36 2.437895 TGATCCGCGGTCTCGACT 60.438 61.111 27.15 1.93 39.00 4.18
36 37 2.024871 GATCCGCGGTCTCGACTG 59.975 66.667 27.15 1.52 40.59 3.51
42 43 3.506096 CGGTCTCGACTGCCGCTA 61.506 66.667 4.90 0.00 38.99 4.26
43 44 2.835705 CGGTCTCGACTGCCGCTAT 61.836 63.158 4.90 0.00 38.99 2.97
44 45 1.299468 GGTCTCGACTGCCGCTATG 60.299 63.158 0.00 0.00 38.37 2.23
45 46 1.725557 GGTCTCGACTGCCGCTATGA 61.726 60.000 0.00 0.00 38.37 2.15
46 47 0.100682 GTCTCGACTGCCGCTATGAA 59.899 55.000 0.00 0.00 38.37 2.57
47 48 0.815095 TCTCGACTGCCGCTATGAAA 59.185 50.000 0.00 0.00 38.37 2.69
48 49 1.203758 TCTCGACTGCCGCTATGAAAA 59.796 47.619 0.00 0.00 38.37 2.29
49 50 2.159099 TCTCGACTGCCGCTATGAAAAT 60.159 45.455 0.00 0.00 38.37 1.82
50 51 2.609459 CTCGACTGCCGCTATGAAAATT 59.391 45.455 0.00 0.00 38.37 1.82
51 52 2.351418 TCGACTGCCGCTATGAAAATTG 59.649 45.455 0.00 0.00 38.37 2.32
52 53 2.539547 CGACTGCCGCTATGAAAATTGG 60.540 50.000 0.00 0.00 0.00 3.16
53 54 1.750778 ACTGCCGCTATGAAAATTGGG 59.249 47.619 0.00 0.00 0.00 4.12
54 55 0.459489 TGCCGCTATGAAAATTGGGC 59.541 50.000 0.00 0.00 39.48 5.36
55 56 0.459489 GCCGCTATGAAAATTGGGCA 59.541 50.000 0.00 0.00 38.88 5.36
56 57 1.134848 GCCGCTATGAAAATTGGGCAA 60.135 47.619 0.00 0.00 38.88 4.52
57 58 2.676463 GCCGCTATGAAAATTGGGCAAA 60.676 45.455 0.00 0.00 38.88 3.68
58 59 2.929398 CCGCTATGAAAATTGGGCAAAC 59.071 45.455 0.00 0.00 0.00 2.93
59 60 3.583806 CGCTATGAAAATTGGGCAAACA 58.416 40.909 0.00 0.00 0.00 2.83
60 61 4.183101 CGCTATGAAAATTGGGCAAACAT 58.817 39.130 0.00 0.00 0.00 2.71
61 62 4.033129 CGCTATGAAAATTGGGCAAACATG 59.967 41.667 0.00 0.00 0.00 3.21
62 63 4.201841 GCTATGAAAATTGGGCAAACATGC 60.202 41.667 0.00 0.00 0.00 4.06
63 64 3.488778 TGAAAATTGGGCAAACATGCT 57.511 38.095 0.00 0.00 34.73 3.79
64 65 3.401182 TGAAAATTGGGCAAACATGCTC 58.599 40.909 0.00 0.00 35.46 4.26
65 66 2.083167 AAATTGGGCAAACATGCTCG 57.917 45.000 0.00 0.00 38.32 5.03
66 67 0.968405 AATTGGGCAAACATGCTCGT 59.032 45.000 0.00 0.00 38.32 4.18
67 68 1.832883 ATTGGGCAAACATGCTCGTA 58.167 45.000 0.00 0.00 38.32 3.43
68 69 1.832883 TTGGGCAAACATGCTCGTAT 58.167 45.000 0.00 0.00 38.32 3.06
69 70 1.378531 TGGGCAAACATGCTCGTATC 58.621 50.000 0.00 0.00 38.32 2.24
70 71 1.339535 TGGGCAAACATGCTCGTATCA 60.340 47.619 0.00 0.00 38.32 2.15
71 72 1.742831 GGGCAAACATGCTCGTATCAA 59.257 47.619 0.00 0.00 34.73 2.57
72 73 2.358898 GGGCAAACATGCTCGTATCAAT 59.641 45.455 0.00 0.00 34.73 2.57
73 74 3.365832 GGCAAACATGCTCGTATCAATG 58.634 45.455 0.00 0.00 34.73 2.82
74 75 3.065233 GGCAAACATGCTCGTATCAATGA 59.935 43.478 0.00 0.00 34.73 2.57
75 76 4.261322 GGCAAACATGCTCGTATCAATGAT 60.261 41.667 0.00 0.00 34.73 2.45
76 77 5.049474 GGCAAACATGCTCGTATCAATGATA 60.049 40.000 0.00 0.00 34.73 2.15
77 78 6.429624 GCAAACATGCTCGTATCAATGATAA 58.570 36.000 4.30 0.00 0.00 1.75
78 79 6.358030 GCAAACATGCTCGTATCAATGATAAC 59.642 38.462 4.30 0.00 0.00 1.89
79 80 7.633621 CAAACATGCTCGTATCAATGATAACT 58.366 34.615 4.30 0.00 0.00 2.24
80 81 7.792374 AACATGCTCGTATCAATGATAACTT 57.208 32.000 4.30 0.00 0.00 2.66
81 82 8.887036 AACATGCTCGTATCAATGATAACTTA 57.113 30.769 4.30 0.00 0.00 2.24
82 83 8.526218 ACATGCTCGTATCAATGATAACTTAG 57.474 34.615 4.30 2.09 0.00 2.18
83 84 7.116948 ACATGCTCGTATCAATGATAACTTAGC 59.883 37.037 4.30 11.18 0.00 3.09
84 85 5.629435 TGCTCGTATCAATGATAACTTAGCG 59.371 40.000 4.30 3.72 0.00 4.26
85 86 5.856986 GCTCGTATCAATGATAACTTAGCGA 59.143 40.000 4.30 7.69 0.00 4.93
86 87 6.032985 GCTCGTATCAATGATAACTTAGCGAG 59.967 42.308 22.95 22.95 37.05 5.03
87 88 7.198306 TCGTATCAATGATAACTTAGCGAGA 57.802 36.000 4.30 0.00 0.00 4.04
88 89 7.817641 TCGTATCAATGATAACTTAGCGAGAT 58.182 34.615 4.30 0.00 0.00 2.75
89 90 7.963465 TCGTATCAATGATAACTTAGCGAGATC 59.037 37.037 4.30 0.00 0.00 2.75
90 91 7.750903 CGTATCAATGATAACTTAGCGAGATCA 59.249 37.037 4.30 0.00 0.00 2.92
91 92 9.579768 GTATCAATGATAACTTAGCGAGATCAT 57.420 33.333 4.30 0.00 38.57 2.45
96 97 8.848948 ATGATAACTTAGCGAGATCATAATCG 57.151 34.615 0.00 0.00 41.79 3.34
110 111 9.502145 GAGATCATAATCGTTGATTAGCTCTAG 57.498 37.037 0.00 0.00 37.83 2.43
111 112 7.973388 AGATCATAATCGTTGATTAGCTCTAGC 59.027 37.037 0.00 0.00 37.83 3.42
162 164 4.464008 TCATTTGGACTTATGGAGATGCC 58.536 43.478 0.00 0.00 37.10 4.40
178 180 7.999679 TGGAGATGCCAGTAAAATCTAAAATG 58.000 34.615 0.00 0.00 43.33 2.32
179 181 7.615365 TGGAGATGCCAGTAAAATCTAAAATGT 59.385 33.333 0.00 0.00 43.33 2.71
190 192 9.202273 GTAAAATCTAAAATGTCAATGCCACAA 57.798 29.630 0.00 0.00 0.00 3.33
192 194 7.837202 AATCTAAAATGTCAATGCCACAATG 57.163 32.000 0.00 0.00 0.00 2.82
193 195 6.587206 TCTAAAATGTCAATGCCACAATGA 57.413 33.333 0.00 0.00 0.00 2.57
199 201 5.119931 TGTCAATGCCACAATGAAGTTAC 57.880 39.130 0.00 0.00 0.00 2.50
209 211 5.647658 CCACAATGAAGTTACTTATGCCAGA 59.352 40.000 0.00 0.00 0.00 3.86
224 226 4.386867 TGCCAGAAGAGTAATAACCTCG 57.613 45.455 0.00 0.00 34.08 4.63
401 403 3.083997 AGAGTAGCCGGGCCCAAG 61.084 66.667 24.92 14.18 0.00 3.61
415 419 2.355209 GGCCCAAGGAAAGAGTACAGAG 60.355 54.545 0.00 0.00 0.00 3.35
425 429 6.214412 AGGAAAGAGTACAGAGAATCACCAAT 59.786 38.462 0.00 0.00 37.82 3.16
569 573 5.572066 CGTCCTTTTCCCCCTATTTAACTCA 60.572 44.000 0.00 0.00 0.00 3.41
593 597 2.434359 CCGTCGCTTTCCACCTCC 60.434 66.667 0.00 0.00 0.00 4.30
595 599 2.434359 GTCGCTTTCCACCTCCCG 60.434 66.667 0.00 0.00 0.00 5.14
599 603 2.269241 CTTTCCACCTCCCGCCTC 59.731 66.667 0.00 0.00 0.00 4.70
600 604 3.327404 TTTCCACCTCCCGCCTCC 61.327 66.667 0.00 0.00 0.00 4.30
617 621 2.382746 CCCGTGTGTGATGCGTCAG 61.383 63.158 9.39 0.00 34.36 3.51
682 690 1.777101 GCATTCTAGCCAGCGTAGAG 58.223 55.000 0.00 0.00 0.00 2.43
823 836 6.353951 CCCAAACACTAATCTTATCCCTTCCT 60.354 42.308 0.00 0.00 0.00 3.36
824 837 7.119387 CCAAACACTAATCTTATCCCTTCCTT 58.881 38.462 0.00 0.00 0.00 3.36
830 845 6.839657 ACTAATCTTATCCCTTCCTTCTCGAA 59.160 38.462 0.00 0.00 0.00 3.71
1008 1024 2.373707 GGGAGGAGGCATGAGCAGT 61.374 63.158 0.00 0.00 44.61 4.40
1155 1171 3.213402 CCGACGGAGGAGGAGCTC 61.213 72.222 8.64 4.71 0.00 4.09
1287 1338 4.325204 CACAATCACTCAATTCAATTGCCG 59.675 41.667 5.12 1.88 40.05 5.69
1306 1358 4.393062 TGCCGTTTTCAGAATTCAGATCTC 59.607 41.667 8.44 0.00 0.00 2.75
1321 1373 5.417811 TCAGATCTCTGTGCTGAATTTCTC 58.582 41.667 7.07 0.00 44.12 2.87
1329 1381 2.095567 GTGCTGAATTTCTCATGCGTGT 60.096 45.455 5.68 0.00 33.43 4.49
1330 1382 2.095617 TGCTGAATTTCTCATGCGTGTG 60.096 45.455 5.68 3.44 33.43 3.82
1331 1383 2.095567 GCTGAATTTCTCATGCGTGTGT 60.096 45.455 5.68 0.00 32.14 3.72
1332 1384 3.485633 CTGAATTTCTCATGCGTGTGTG 58.514 45.455 5.68 0.00 32.14 3.82
1684 1736 2.166050 CCTCCTGATCTATCCATCTGCG 59.834 54.545 0.00 0.00 0.00 5.18
1765 1819 1.207593 GTTTGTGCTGCGCCTGTAG 59.792 57.895 11.12 0.00 0.00 2.74
1766 1820 1.227823 TTTGTGCTGCGCCTGTAGT 60.228 52.632 11.12 0.00 0.00 2.73
1767 1821 1.227999 TTTGTGCTGCGCCTGTAGTC 61.228 55.000 11.12 0.00 0.00 2.59
1768 1822 2.815647 GTGCTGCGCCTGTAGTCC 60.816 66.667 4.18 0.00 0.00 3.85
1769 1823 2.997315 TGCTGCGCCTGTAGTCCT 60.997 61.111 4.18 0.00 0.00 3.85
1770 1824 2.510238 GCTGCGCCTGTAGTCCTG 60.510 66.667 4.18 0.00 0.00 3.86
1771 1825 2.973899 CTGCGCCTGTAGTCCTGT 59.026 61.111 4.18 0.00 0.00 4.00
1772 1826 1.945354 GCTGCGCCTGTAGTCCTGTA 61.945 60.000 4.18 0.00 0.00 2.74
1773 1827 0.179134 CTGCGCCTGTAGTCCTGTAC 60.179 60.000 4.18 0.00 0.00 2.90
1774 1828 0.611062 TGCGCCTGTAGTCCTGTACT 60.611 55.000 4.18 0.00 42.62 2.73
1775 1829 1.340308 TGCGCCTGTAGTCCTGTACTA 60.340 52.381 4.18 0.00 39.80 1.82
1799 1853 6.231211 ACTACTAGTTCTTTGATGTTGGGTG 58.769 40.000 0.00 0.00 0.00 4.61
1855 1914 5.627780 TGTACTTCTTGTGCATATATACGCG 59.372 40.000 3.53 3.53 36.38 6.01
1909 1968 6.118852 AGGGCTTCAATCTTCTTCATCTTAC 58.881 40.000 0.00 0.00 0.00 2.34
1910 1969 5.882557 GGGCTTCAATCTTCTTCATCTTACA 59.117 40.000 0.00 0.00 0.00 2.41
1921 1980 5.428253 TCTTCATCTTACATACTTGCACCC 58.572 41.667 0.00 0.00 0.00 4.61
1933 1992 0.033601 TTGCACCCTGGTGTTCTTGT 60.034 50.000 17.19 0.00 46.90 3.16
1961 2031 3.119245 ACAACCTATACGCACTCGATTGT 60.119 43.478 4.58 0.00 39.41 2.71
1994 2075 6.462500 ACTAGCTAGCATCTTGAACATATGG 58.538 40.000 20.91 0.00 0.00 2.74
1995 2076 4.070716 AGCTAGCATCTTGAACATATGGC 58.929 43.478 18.83 0.00 0.00 4.40
1996 2077 4.070716 GCTAGCATCTTGAACATATGGCT 58.929 43.478 10.63 5.92 0.00 4.75
1997 2078 5.012458 AGCTAGCATCTTGAACATATGGCTA 59.988 40.000 18.83 6.75 0.00 3.93
1998 2079 5.879223 GCTAGCATCTTGAACATATGGCTAT 59.121 40.000 10.63 0.00 0.00 2.97
1999 2080 6.183360 GCTAGCATCTTGAACATATGGCTATG 60.183 42.308 10.63 3.54 40.56 2.23
2000 2081 5.872963 AGCATCTTGAACATATGGCTATGA 58.127 37.500 7.80 0.40 38.49 2.15
2001 2082 6.301486 AGCATCTTGAACATATGGCTATGAA 58.699 36.000 7.80 0.00 38.49 2.57
2059 2144 4.545208 TGACCGGAATCAATTGTAGTCA 57.455 40.909 9.46 7.83 0.00 3.41
2061 2146 4.935205 TGACCGGAATCAATTGTAGTCAAG 59.065 41.667 9.46 0.23 36.97 3.02
2066 2151 7.094933 ACCGGAATCAATTGTAGTCAAGTTTAC 60.095 37.037 9.46 0.00 36.97 2.01
2094 2179 9.678260 ATTGAATTTTAACTAGAGAGCAGACAT 57.322 29.630 0.00 0.00 0.00 3.06
2095 2180 8.709386 TGAATTTTAACTAGAGAGCAGACATC 57.291 34.615 0.00 0.00 0.00 3.06
2096 2181 7.489435 TGAATTTTAACTAGAGAGCAGACATCG 59.511 37.037 0.00 0.00 0.00 3.84
2116 2201 1.009078 TCCTCAATTCTTCGCATGCG 58.991 50.000 33.61 33.61 41.35 4.73
2128 2215 0.168788 CGCATGCGACATTTCCTTGT 59.831 50.000 35.82 0.00 42.83 3.16
2129 2216 1.621107 GCATGCGACATTTCCTTGTG 58.379 50.000 0.00 0.00 0.00 3.33
2130 2217 1.621107 CATGCGACATTTCCTTGTGC 58.379 50.000 0.00 0.00 0.00 4.57
2131 2218 0.168788 ATGCGACATTTCCTTGTGCG 59.831 50.000 0.00 0.00 30.94 5.34
2132 2219 0.882484 TGCGACATTTCCTTGTGCGA 60.882 50.000 0.00 0.00 30.94 5.10
2490 2594 1.535437 GGATACCTACAGTCAACCGCG 60.535 57.143 0.00 0.00 0.00 6.46
2571 2675 0.179045 AGAGCACAAACACCTTCGCT 60.179 50.000 0.00 0.00 0.00 4.93
2960 3070 2.711542 CAATTGGTACCACTCCACCTC 58.288 52.381 16.04 0.00 35.73 3.85
2961 3071 2.305927 CAATTGGTACCACTCCACCTCT 59.694 50.000 16.04 0.00 35.73 3.69
2972 3082 2.158295 ACTCCACCTCTTGTACACCTCT 60.158 50.000 0.00 0.00 0.00 3.69
2973 3083 2.494073 CTCCACCTCTTGTACACCTCTC 59.506 54.545 0.00 0.00 0.00 3.20
2974 3084 2.110188 TCCACCTCTTGTACACCTCTCT 59.890 50.000 0.00 0.00 0.00 3.10
2975 3085 2.494073 CCACCTCTTGTACACCTCTCTC 59.506 54.545 0.00 0.00 0.00 3.20
2976 3086 3.426615 CACCTCTTGTACACCTCTCTCT 58.573 50.000 0.00 0.00 0.00 3.10
2977 3087 3.442273 CACCTCTTGTACACCTCTCTCTC 59.558 52.174 0.00 0.00 0.00 3.20
2978 3088 3.332485 ACCTCTTGTACACCTCTCTCTCT 59.668 47.826 0.00 0.00 0.00 3.10
2979 3089 3.945285 CCTCTTGTACACCTCTCTCTCTC 59.055 52.174 0.00 0.00 0.00 3.20
2980 3090 4.324254 CCTCTTGTACACCTCTCTCTCTCT 60.324 50.000 0.00 0.00 0.00 3.10
2996 3107 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3004 3115 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3033 3144 8.012957 TCTCTCTCCACAGTTATTATTCTTCC 57.987 38.462 0.00 0.00 0.00 3.46
3107 3226 3.421394 TCACCCCATCTTCTCAGGTAT 57.579 47.619 0.00 0.00 0.00 2.73
3108 3227 3.309296 TCACCCCATCTTCTCAGGTATC 58.691 50.000 0.00 0.00 0.00 2.24
3109 3228 3.041211 CACCCCATCTTCTCAGGTATCA 58.959 50.000 0.00 0.00 0.00 2.15
3110 3229 3.649981 CACCCCATCTTCTCAGGTATCAT 59.350 47.826 0.00 0.00 0.00 2.45
3111 3230 3.906846 ACCCCATCTTCTCAGGTATCATC 59.093 47.826 0.00 0.00 0.00 2.92
3112 3231 3.906218 CCCCATCTTCTCAGGTATCATCA 59.094 47.826 0.00 0.00 0.00 3.07
3242 3376 1.733912 CGCATGTACTTGCATGTGTCT 59.266 47.619 27.33 0.00 46.43 3.41
3246 3380 4.201753 GCATGTACTTGCATGTGTCTAGTG 60.202 45.833 24.45 6.72 45.75 2.74
3366 3500 5.389520 TCATCGGAATGATTAGGAGAGAGT 58.610 41.667 0.00 0.00 36.98 3.24
3586 3729 9.236006 GTTAGTGCTATCATGGATTATTGGATT 57.764 33.333 0.00 0.00 0.00 3.01
3589 3732 7.555554 AGTGCTATCATGGATTATTGGATTAGC 59.444 37.037 0.00 0.00 0.00 3.09
3590 3733 7.555554 GTGCTATCATGGATTATTGGATTAGCT 59.444 37.037 0.00 0.00 0.00 3.32
3591 3734 8.111545 TGCTATCATGGATTATTGGATTAGCTT 58.888 33.333 0.00 0.00 0.00 3.74
3622 3765 1.702886 CGTGTCATGGACTCACTCAC 58.297 55.000 0.00 0.00 33.15 3.51
3623 3766 1.270826 CGTGTCATGGACTCACTCACT 59.729 52.381 0.00 0.00 33.15 3.41
3624 3767 2.669670 CGTGTCATGGACTCACTCACTC 60.670 54.545 0.00 0.00 33.15 3.51
3625 3768 2.297315 GTGTCATGGACTCACTCACTCA 59.703 50.000 0.00 0.00 33.15 3.41
3626 3769 2.297315 TGTCATGGACTCACTCACTCAC 59.703 50.000 0.00 0.00 33.15 3.51
3627 3770 2.297315 GTCATGGACTCACTCACTCACA 59.703 50.000 0.00 0.00 0.00 3.58
3779 3934 1.721664 CTTGGCCCGTGCATGAGATG 61.722 60.000 7.72 0.00 40.13 2.90
3780 3935 2.190313 GGCCCGTGCATGAGATGA 59.810 61.111 7.72 0.00 40.13 2.92
3781 3936 1.451927 GGCCCGTGCATGAGATGAA 60.452 57.895 7.72 0.00 40.13 2.57
3782 3937 1.031571 GGCCCGTGCATGAGATGAAA 61.032 55.000 7.72 0.00 40.13 2.69
3783 3938 1.027357 GCCCGTGCATGAGATGAAAT 58.973 50.000 7.72 0.00 37.47 2.17
3857 4012 8.659527 TCTGAAATATATATTGCTGGTCTTGGA 58.340 33.333 16.39 6.03 0.00 3.53
3858 4013 8.621532 TGAAATATATATTGCTGGTCTTGGAC 57.378 34.615 13.59 0.00 0.00 4.02
3859 4014 8.439971 TGAAATATATATTGCTGGTCTTGGACT 58.560 33.333 13.59 0.00 32.47 3.85
3860 4015 8.854614 AAATATATATTGCTGGTCTTGGACTC 57.145 34.615 8.74 0.00 32.47 3.36
3863 4018 2.260844 TTGCTGGTCTTGGACTCTTG 57.739 50.000 0.00 0.00 32.47 3.02
3864 4019 0.397941 TGCTGGTCTTGGACTCTTGG 59.602 55.000 0.00 0.00 32.47 3.61
3865 4020 0.398318 GCTGGTCTTGGACTCTTGGT 59.602 55.000 0.00 0.00 32.47 3.67
3866 4021 1.623811 GCTGGTCTTGGACTCTTGGTA 59.376 52.381 0.00 0.00 32.47 3.25
3867 4022 2.613223 GCTGGTCTTGGACTCTTGGTAC 60.613 54.545 0.00 0.00 32.47 3.34
3868 4023 2.900546 CTGGTCTTGGACTCTTGGTACT 59.099 50.000 0.00 0.00 32.47 2.73
3869 4024 3.314693 TGGTCTTGGACTCTTGGTACTT 58.685 45.455 0.00 0.00 32.47 2.24
3870 4025 3.714798 TGGTCTTGGACTCTTGGTACTTT 59.285 43.478 0.00 0.00 32.47 2.66
3871 4026 4.165372 TGGTCTTGGACTCTTGGTACTTTT 59.835 41.667 0.00 0.00 32.47 2.27
3872 4027 5.367352 TGGTCTTGGACTCTTGGTACTTTTA 59.633 40.000 0.00 0.00 32.47 1.52
3873 4028 5.932883 GGTCTTGGACTCTTGGTACTTTTAG 59.067 44.000 0.00 0.00 32.47 1.85
3874 4029 6.239515 GGTCTTGGACTCTTGGTACTTTTAGA 60.240 42.308 0.00 0.00 32.47 2.10
3875 4030 7.387643 GTCTTGGACTCTTGGTACTTTTAGAT 58.612 38.462 0.00 0.00 0.00 1.98
3876 4031 7.878644 GTCTTGGACTCTTGGTACTTTTAGATT 59.121 37.037 0.00 0.00 0.00 2.40
3877 4032 8.095169 TCTTGGACTCTTGGTACTTTTAGATTC 58.905 37.037 0.00 0.00 0.00 2.52
3878 4033 7.554959 TGGACTCTTGGTACTTTTAGATTCT 57.445 36.000 0.00 0.00 0.00 2.40
3879 4034 7.612677 TGGACTCTTGGTACTTTTAGATTCTC 58.387 38.462 0.00 0.00 0.00 2.87
3880 4035 7.455008 TGGACTCTTGGTACTTTTAGATTCTCT 59.545 37.037 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.425114 GCGGATCACACATTATCTTTGAGTAT 59.575 38.462 0.00 0.00 0.00 2.12
1 2 5.753438 GCGGATCACACATTATCTTTGAGTA 59.247 40.000 0.00 0.00 0.00 2.59
2 3 4.572389 GCGGATCACACATTATCTTTGAGT 59.428 41.667 0.00 0.00 0.00 3.41
3 4 4.318333 CGCGGATCACACATTATCTTTGAG 60.318 45.833 0.00 0.00 0.00 3.02
4 5 3.555547 CGCGGATCACACATTATCTTTGA 59.444 43.478 0.00 0.00 0.00 2.69
7 8 2.158957 ACCGCGGATCACACATTATCTT 60.159 45.455 35.90 0.00 0.00 2.40
8 9 1.412710 ACCGCGGATCACACATTATCT 59.587 47.619 35.90 0.00 0.00 1.98
9 10 1.792949 GACCGCGGATCACACATTATC 59.207 52.381 35.90 10.52 0.00 1.75
10 11 1.412710 AGACCGCGGATCACACATTAT 59.587 47.619 35.90 3.54 0.00 1.28
11 12 0.821517 AGACCGCGGATCACACATTA 59.178 50.000 35.90 0.00 0.00 1.90
12 13 0.460284 GAGACCGCGGATCACACATT 60.460 55.000 35.90 5.18 0.00 2.71
13 14 1.141881 GAGACCGCGGATCACACAT 59.858 57.895 35.90 6.14 0.00 3.21
14 15 2.571757 GAGACCGCGGATCACACA 59.428 61.111 35.90 0.00 0.00 3.72
15 16 2.579787 CGAGACCGCGGATCACAC 60.580 66.667 35.90 16.43 0.00 3.82
16 17 2.748647 TCGAGACCGCGGATCACA 60.749 61.111 35.90 15.04 35.37 3.58
17 18 2.278013 GTCGAGACCGCGGATCAC 60.278 66.667 35.90 21.47 35.37 3.06
18 19 2.437895 AGTCGAGACCGCGGATCA 60.438 61.111 35.90 16.01 35.37 2.92
19 20 2.024871 CAGTCGAGACCGCGGATC 59.975 66.667 35.90 26.58 35.37 3.36
20 21 4.194720 GCAGTCGAGACCGCGGAT 62.195 66.667 35.90 20.71 35.37 4.18
26 27 1.299468 CATAGCGGCAGTCGAGACC 60.299 63.158 0.00 0.00 42.43 3.85
27 28 0.100682 TTCATAGCGGCAGTCGAGAC 59.899 55.000 0.00 0.00 42.43 3.36
28 29 0.815095 TTTCATAGCGGCAGTCGAGA 59.185 50.000 0.00 0.00 42.43 4.04
29 30 1.640428 TTTTCATAGCGGCAGTCGAG 58.360 50.000 0.00 0.00 42.43 4.04
30 31 2.309528 ATTTTCATAGCGGCAGTCGA 57.690 45.000 0.00 0.00 42.43 4.20
31 32 2.539547 CCAATTTTCATAGCGGCAGTCG 60.540 50.000 1.45 0.00 42.76 4.18
32 33 2.223572 CCCAATTTTCATAGCGGCAGTC 60.224 50.000 1.45 0.00 0.00 3.51
33 34 1.750778 CCCAATTTTCATAGCGGCAGT 59.249 47.619 1.45 0.00 0.00 4.40
34 35 1.536709 GCCCAATTTTCATAGCGGCAG 60.537 52.381 1.45 0.00 34.98 4.85
35 36 0.459489 GCCCAATTTTCATAGCGGCA 59.541 50.000 1.45 0.00 34.98 5.69
36 37 0.459489 TGCCCAATTTTCATAGCGGC 59.541 50.000 0.00 0.00 35.44 6.53
37 38 2.929398 GTTTGCCCAATTTTCATAGCGG 59.071 45.455 0.00 0.00 0.00 5.52
38 39 3.583806 TGTTTGCCCAATTTTCATAGCG 58.416 40.909 0.00 0.00 0.00 4.26
39 40 4.201841 GCATGTTTGCCCAATTTTCATAGC 60.202 41.667 0.00 0.00 43.38 2.97
40 41 5.473796 GCATGTTTGCCCAATTTTCATAG 57.526 39.130 0.00 0.00 43.38 2.23
54 55 7.633621 AGTTATCATTGATACGAGCATGTTTG 58.366 34.615 5.86 0.00 0.00 2.93
55 56 7.792374 AGTTATCATTGATACGAGCATGTTT 57.208 32.000 5.86 0.00 0.00 2.83
56 57 7.792374 AAGTTATCATTGATACGAGCATGTT 57.208 32.000 5.86 0.00 0.00 2.71
57 58 7.116948 GCTAAGTTATCATTGATACGAGCATGT 59.883 37.037 5.86 0.00 0.00 3.21
58 59 7.451429 GCTAAGTTATCATTGATACGAGCATG 58.549 38.462 5.86 0.00 0.00 4.06
59 60 6.309009 CGCTAAGTTATCATTGATACGAGCAT 59.691 38.462 18.69 5.28 0.00 3.79
60 61 5.629435 CGCTAAGTTATCATTGATACGAGCA 59.371 40.000 18.69 1.90 0.00 4.26
61 62 5.856986 TCGCTAAGTTATCATTGATACGAGC 59.143 40.000 5.86 10.63 0.00 5.03
62 63 7.298854 TCTCGCTAAGTTATCATTGATACGAG 58.701 38.462 23.03 23.03 36.21 4.18
63 64 7.198306 TCTCGCTAAGTTATCATTGATACGA 57.802 36.000 5.86 9.48 0.00 3.43
64 65 7.750903 TGATCTCGCTAAGTTATCATTGATACG 59.249 37.037 5.86 5.95 0.00 3.06
65 66 8.972262 TGATCTCGCTAAGTTATCATTGATAC 57.028 34.615 5.86 2.78 0.00 2.24
70 71 9.295214 CGATTATGATCTCGCTAAGTTATCATT 57.705 33.333 0.00 0.00 38.10 2.57
71 72 8.462811 ACGATTATGATCTCGCTAAGTTATCAT 58.537 33.333 2.30 0.00 39.79 2.45
72 73 7.817641 ACGATTATGATCTCGCTAAGTTATCA 58.182 34.615 2.30 0.00 38.42 2.15
73 74 8.579600 CAACGATTATGATCTCGCTAAGTTATC 58.420 37.037 2.30 0.00 38.42 1.75
74 75 8.297426 TCAACGATTATGATCTCGCTAAGTTAT 58.703 33.333 2.30 0.00 38.42 1.89
75 76 7.645402 TCAACGATTATGATCTCGCTAAGTTA 58.355 34.615 2.30 0.00 38.42 2.24
76 77 6.504398 TCAACGATTATGATCTCGCTAAGTT 58.496 36.000 2.30 0.00 38.42 2.66
77 78 6.073327 TCAACGATTATGATCTCGCTAAGT 57.927 37.500 2.30 0.00 38.42 2.24
78 79 7.573916 AATCAACGATTATGATCTCGCTAAG 57.426 36.000 2.30 0.00 36.53 2.18
79 80 7.273598 GCTAATCAACGATTATGATCTCGCTAA 59.726 37.037 2.30 0.00 36.53 3.09
80 81 6.747739 GCTAATCAACGATTATGATCTCGCTA 59.252 38.462 2.30 0.00 36.53 4.26
81 82 5.574830 GCTAATCAACGATTATGATCTCGCT 59.425 40.000 2.30 0.00 36.53 4.93
82 83 5.574830 AGCTAATCAACGATTATGATCTCGC 59.425 40.000 2.30 0.00 36.53 5.03
83 84 7.026562 AGAGCTAATCAACGATTATGATCTCG 58.973 38.462 0.00 0.94 36.53 4.04
84 85 9.502145 CTAGAGCTAATCAACGATTATGATCTC 57.498 37.037 12.75 9.81 36.53 2.75
85 86 7.973388 GCTAGAGCTAATCAACGATTATGATCT 59.027 37.037 0.00 13.39 35.90 2.75
86 87 7.757173 TGCTAGAGCTAATCAACGATTATGATC 59.243 37.037 2.72 0.00 42.66 2.92
87 88 7.606349 TGCTAGAGCTAATCAACGATTATGAT 58.394 34.615 2.72 0.00 42.66 2.45
88 89 6.981722 TGCTAGAGCTAATCAACGATTATGA 58.018 36.000 2.72 0.00 42.66 2.15
89 90 7.643528 TTGCTAGAGCTAATCAACGATTATG 57.356 36.000 2.72 0.00 42.66 1.90
90 91 8.715998 CATTTGCTAGAGCTAATCAACGATTAT 58.284 33.333 8.02 0.00 42.76 1.28
91 92 7.710907 ACATTTGCTAGAGCTAATCAACGATTA 59.289 33.333 8.02 0.00 42.76 1.75
92 93 6.540189 ACATTTGCTAGAGCTAATCAACGATT 59.460 34.615 8.02 0.00 42.76 3.34
93 94 6.051717 ACATTTGCTAGAGCTAATCAACGAT 58.948 36.000 8.02 0.00 42.76 3.73
94 95 5.419542 ACATTTGCTAGAGCTAATCAACGA 58.580 37.500 8.02 0.00 42.76 3.85
95 96 5.725110 ACATTTGCTAGAGCTAATCAACG 57.275 39.130 8.02 1.52 42.76 4.10
96 97 6.846350 ACAACATTTGCTAGAGCTAATCAAC 58.154 36.000 8.02 0.00 42.76 3.18
110 111 3.490526 CCACTAGCACAAACAACATTTGC 59.509 43.478 0.00 0.00 32.93 3.68
111 112 4.930963 TCCACTAGCACAAACAACATTTG 58.069 39.130 0.00 0.00 35.64 2.32
139 141 4.889409 GGCATCTCCATAAGTCCAAATGAA 59.111 41.667 0.00 0.00 34.01 2.57
162 164 8.863049 GTGGCATTGACATTTTAGATTTTACTG 58.137 33.333 0.00 0.00 0.00 2.74
165 167 9.941325 ATTGTGGCATTGACATTTTAGATTTTA 57.059 25.926 0.00 0.00 0.00 1.52
171 173 6.869913 ACTTCATTGTGGCATTGACATTTTAG 59.130 34.615 0.00 0.00 0.00 1.85
172 174 6.757237 ACTTCATTGTGGCATTGACATTTTA 58.243 32.000 0.00 0.00 0.00 1.52
173 175 5.613329 ACTTCATTGTGGCATTGACATTTT 58.387 33.333 0.00 0.00 0.00 1.82
174 176 5.217978 ACTTCATTGTGGCATTGACATTT 57.782 34.783 0.00 0.00 0.00 2.32
175 177 4.877378 ACTTCATTGTGGCATTGACATT 57.123 36.364 0.00 0.00 0.00 2.71
176 178 4.877378 AACTTCATTGTGGCATTGACAT 57.123 36.364 0.00 0.00 0.00 3.06
177 179 4.826733 AGTAACTTCATTGTGGCATTGACA 59.173 37.500 0.00 0.00 0.00 3.58
178 180 5.376854 AGTAACTTCATTGTGGCATTGAC 57.623 39.130 0.00 0.00 0.00 3.18
179 181 7.537715 CATAAGTAACTTCATTGTGGCATTGA 58.462 34.615 0.00 0.00 0.00 2.57
190 192 6.951971 ACTCTTCTGGCATAAGTAACTTCAT 58.048 36.000 11.77 0.00 0.00 2.57
192 194 8.950208 ATTACTCTTCTGGCATAAGTAACTTC 57.050 34.615 11.77 0.00 35.81 3.01
199 201 6.642950 CGAGGTTATTACTCTTCTGGCATAAG 59.357 42.308 6.30 6.30 32.83 1.73
209 211 8.696374 TCATCTTGAATCGAGGTTATTACTCTT 58.304 33.333 0.00 0.00 32.83 2.85
340 342 9.185680 AGTCTGGTAGTAAATGTTTTCAACTTT 57.814 29.630 0.00 0.00 0.00 2.66
341 343 8.747538 AGTCTGGTAGTAAATGTTTTCAACTT 57.252 30.769 0.00 0.00 0.00 2.66
342 344 8.747538 AAGTCTGGTAGTAAATGTTTTCAACT 57.252 30.769 0.00 0.00 0.00 3.16
343 345 9.874215 GTAAGTCTGGTAGTAAATGTTTTCAAC 57.126 33.333 0.00 0.00 0.00 3.18
344 346 9.616156 TGTAAGTCTGGTAGTAAATGTTTTCAA 57.384 29.630 0.00 0.00 0.00 2.69
345 347 9.787435 ATGTAAGTCTGGTAGTAAATGTTTTCA 57.213 29.630 0.00 0.00 0.00 2.69
348 350 9.569122 ACAATGTAAGTCTGGTAGTAAATGTTT 57.431 29.630 0.00 0.00 0.00 2.83
349 351 8.999431 CACAATGTAAGTCTGGTAGTAAATGTT 58.001 33.333 0.00 0.00 0.00 2.71
350 352 7.606456 CCACAATGTAAGTCTGGTAGTAAATGT 59.394 37.037 0.00 0.00 0.00 2.71
351 353 7.822334 TCCACAATGTAAGTCTGGTAGTAAATG 59.178 37.037 0.00 0.00 0.00 2.32
352 354 7.822822 GTCCACAATGTAAGTCTGGTAGTAAAT 59.177 37.037 0.00 0.00 0.00 1.40
353 355 7.156673 GTCCACAATGTAAGTCTGGTAGTAAA 58.843 38.462 0.00 0.00 0.00 2.01
354 356 6.295462 GGTCCACAATGTAAGTCTGGTAGTAA 60.295 42.308 0.00 0.00 0.00 2.24
355 357 5.186409 GGTCCACAATGTAAGTCTGGTAGTA 59.814 44.000 0.00 0.00 0.00 1.82
356 358 4.020485 GGTCCACAATGTAAGTCTGGTAGT 60.020 45.833 0.00 0.00 0.00 2.73
357 359 4.504858 GGTCCACAATGTAAGTCTGGTAG 58.495 47.826 0.00 0.00 0.00 3.18
401 403 5.407407 TGGTGATTCTCTGTACTCTTTCC 57.593 43.478 0.00 0.00 0.00 3.13
415 419 1.139520 GCGGTGGCATTGGTGATTC 59.860 57.895 0.00 0.00 39.62 2.52
569 573 2.574399 GAAAGCGACGGAGGAGCT 59.426 61.111 0.00 0.00 43.90 4.09
593 597 4.082523 ATCACACACGGGAGGCGG 62.083 66.667 0.00 0.00 0.00 6.13
595 599 3.127533 GCATCACACACGGGAGGC 61.128 66.667 0.00 0.00 33.46 4.70
597 601 2.048222 ACGCATCACACACGGGAG 60.048 61.111 0.00 0.00 0.00 4.30
599 603 2.356913 TGACGCATCACACACGGG 60.357 61.111 0.00 0.00 0.00 5.28
600 604 2.382746 CCTGACGCATCACACACGG 61.383 63.158 0.00 0.00 0.00 4.94
601 605 2.382746 CCCTGACGCATCACACACG 61.383 63.158 0.00 0.00 0.00 4.49
617 621 2.024319 GCGATATGTGAGCGAGCCC 61.024 63.158 0.00 0.00 40.14 5.19
663 667 1.067821 ACTCTACGCTGGCTAGAATGC 59.932 52.381 0.00 0.00 0.00 3.56
664 668 3.566322 ACTACTCTACGCTGGCTAGAATG 59.434 47.826 0.00 0.00 0.00 2.67
673 681 3.242804 GCTCTAACCACTACTCTACGCTG 60.243 52.174 0.00 0.00 0.00 5.18
682 690 1.817447 ACTGGTCGCTCTAACCACTAC 59.183 52.381 0.00 0.00 41.84 2.73
823 836 3.575630 CAAGTGGAGAATCGTTCGAGAA 58.424 45.455 0.80 0.00 34.37 2.87
824 837 2.671351 GCAAGTGGAGAATCGTTCGAGA 60.671 50.000 0.80 0.00 34.37 4.04
830 845 2.540515 CGTATGCAAGTGGAGAATCGT 58.459 47.619 0.00 0.00 34.37 3.73
931 947 0.462759 GCTGGGTGTTAGCTAGGCAG 60.463 60.000 0.00 0.00 38.14 4.85
932 948 1.602237 GCTGGGTGTTAGCTAGGCA 59.398 57.895 0.00 0.00 38.14 4.75
933 949 4.542075 GCTGGGTGTTAGCTAGGC 57.458 61.111 0.00 0.00 38.14 3.93
1068 1084 1.069935 GCCGCCCTCCTTGATACTC 59.930 63.158 0.00 0.00 0.00 2.59
1155 1171 0.030908 GGCGGAGGTAGAACTCGATG 59.969 60.000 0.00 0.00 38.39 3.84
1266 1282 4.487948 ACGGCAATTGAATTGAGTGATTG 58.512 39.130 21.14 4.89 42.83 2.67
1267 1283 4.789012 ACGGCAATTGAATTGAGTGATT 57.211 36.364 21.14 0.00 42.83 2.57
1287 1338 6.149142 AGCACAGAGATCTGAATTCTGAAAAC 59.851 38.462 21.34 12.25 46.59 2.43
1306 1358 2.161012 ACGCATGAGAAATTCAGCACAG 59.839 45.455 2.50 0.00 39.68 3.66
1321 1373 2.051076 GCCACACACACACGCATG 60.051 61.111 0.00 0.00 0.00 4.06
1329 1381 4.927782 GCCGGTCAGCCACACACA 62.928 66.667 1.90 0.00 34.09 3.72
1642 1694 6.440328 GGAGGAGAATTTCTAGGAGATGCTAT 59.560 42.308 0.00 0.00 0.00 2.97
1652 1704 7.673504 TGGATAGATCAGGAGGAGAATTTCTAG 59.326 40.741 0.00 0.00 0.00 2.43
1662 1714 3.439154 GCAGATGGATAGATCAGGAGGA 58.561 50.000 0.00 0.00 0.00 3.71
1765 1819 8.558973 TCAAAGAACTAGTAGTAGTACAGGAC 57.441 38.462 10.68 0.00 38.66 3.85
1766 1820 9.175312 CATCAAAGAACTAGTAGTAGTACAGGA 57.825 37.037 10.68 6.18 38.66 3.86
1767 1821 8.958506 ACATCAAAGAACTAGTAGTAGTACAGG 58.041 37.037 10.68 4.78 38.66 4.00
1770 1824 9.570488 CCAACATCAAAGAACTAGTAGTAGTAC 57.430 37.037 10.68 0.00 38.66 2.73
1771 1825 8.746530 CCCAACATCAAAGAACTAGTAGTAGTA 58.253 37.037 10.68 0.00 38.66 1.82
1772 1826 7.234988 ACCCAACATCAAAGAACTAGTAGTAGT 59.765 37.037 2.50 4.29 41.61 2.73
1773 1827 7.545965 CACCCAACATCAAAGAACTAGTAGTAG 59.454 40.741 2.50 2.87 0.00 2.57
1774 1828 7.383687 CACCCAACATCAAAGAACTAGTAGTA 58.616 38.462 2.50 0.00 0.00 1.82
1775 1829 6.231211 CACCCAACATCAAAGAACTAGTAGT 58.769 40.000 0.00 0.00 0.00 2.73
1776 1830 5.122396 GCACCCAACATCAAAGAACTAGTAG 59.878 44.000 0.00 0.00 0.00 2.57
1777 1831 5.001232 GCACCCAACATCAAAGAACTAGTA 58.999 41.667 0.00 0.00 0.00 1.82
1778 1832 3.821033 GCACCCAACATCAAAGAACTAGT 59.179 43.478 0.00 0.00 0.00 2.57
1855 1914 7.044798 AGCTGATTACTTGTAGATCTGAAACC 58.955 38.462 5.18 0.00 0.00 3.27
1902 1961 3.879295 CCAGGGTGCAAGTATGTAAGATG 59.121 47.826 0.00 0.00 0.00 2.90
1933 1992 4.430007 GAGTGCGTATAGGTTGTTCATGA 58.570 43.478 0.00 0.00 0.00 3.07
1946 2016 9.327628 AGTATAGATATACAATCGAGTGCGTAT 57.672 33.333 13.64 11.15 40.70 3.06
1994 2075 6.652900 GGATGGAATTCTAGGTTCTTCATAGC 59.347 42.308 5.23 0.00 31.40 2.97
1995 2076 7.972301 AGGATGGAATTCTAGGTTCTTCATAG 58.028 38.462 5.23 0.00 22.12 2.23
1996 2077 7.937700 AGGATGGAATTCTAGGTTCTTCATA 57.062 36.000 5.23 0.00 22.12 2.15
1997 2078 6.838401 AGGATGGAATTCTAGGTTCTTCAT 57.162 37.500 5.23 0.00 22.12 2.57
1998 2079 7.366847 CTAGGATGGAATTCTAGGTTCTTCA 57.633 40.000 5.23 0.00 46.82 3.02
1999 2080 8.201242 ATCTAGGATGGAATTCTAGGTTCTTC 57.799 38.462 5.23 0.00 43.54 2.87
2066 2151 9.766277 GTCTGCTCTCTAGTTAAAATTCAATTG 57.234 33.333 0.00 0.00 0.00 2.32
2069 2154 9.155975 GATGTCTGCTCTCTAGTTAAAATTCAA 57.844 33.333 0.00 0.00 0.00 2.69
2071 2156 7.489757 ACGATGTCTGCTCTCTAGTTAAAATTC 59.510 37.037 0.00 0.00 0.00 2.17
2078 2163 2.685897 GGACGATGTCTGCTCTCTAGTT 59.314 50.000 0.00 0.00 32.47 2.24
2080 2165 2.548057 GAGGACGATGTCTGCTCTCTAG 59.452 54.545 0.00 0.00 32.47 2.43
2081 2166 2.092914 TGAGGACGATGTCTGCTCTCTA 60.093 50.000 0.00 0.00 32.47 2.43
2088 2173 3.549471 CGAAGAATTGAGGACGATGTCTG 59.451 47.826 0.00 0.00 32.47 3.51
2094 2179 2.270923 CATGCGAAGAATTGAGGACGA 58.729 47.619 0.00 0.00 0.00 4.20
2095 2180 1.267732 GCATGCGAAGAATTGAGGACG 60.268 52.381 0.00 0.00 0.00 4.79
2096 2181 1.267732 CGCATGCGAAGAATTGAGGAC 60.268 52.381 35.82 0.00 42.83 3.85
2116 2201 1.999735 TCGATCGCACAAGGAAATGTC 59.000 47.619 11.09 0.00 0.00 3.06
2128 2215 1.064134 CACGTGAGGATCGATCGCA 59.936 57.895 18.81 15.93 38.61 5.10
2129 2216 0.525668 AACACGTGAGGATCGATCGC 60.526 55.000 25.01 13.60 38.61 4.58
2130 2217 2.373269 GTAACACGTGAGGATCGATCG 58.627 52.381 25.01 9.36 38.61 3.69
2131 2218 2.373269 CGTAACACGTGAGGATCGATC 58.627 52.381 25.01 17.36 36.74 3.69
2132 2219 2.470196 CGTAACACGTGAGGATCGAT 57.530 50.000 25.01 0.00 36.74 3.59
2277 2378 1.141053 GACCCTTGTCTGTTGTCCTGT 59.859 52.381 0.00 0.00 38.53 4.00
2322 2423 4.467084 TTGGATGGAGTCGGCGGC 62.467 66.667 1.71 1.71 0.00 6.53
2443 2547 4.021925 ACCTGAGGGCTTGACGGC 62.022 66.667 2.38 0.00 35.63 5.68
2457 2561 3.352611 AGGTATCCTAATGAGCCACCT 57.647 47.619 0.00 0.00 31.87 4.00
2502 2606 1.129917 CTCCCTCCTGCTGATGATGT 58.870 55.000 0.00 0.00 0.00 3.06
2571 2675 1.211969 GAGCAGCGAGTACGTGGAA 59.788 57.895 0.00 0.00 41.98 3.53
2671 2775 3.391382 GTAGGACGGCAGCTGGGT 61.391 66.667 17.12 0.00 0.00 4.51
2960 3070 4.843728 AGAGAGAGAGAGAGGTGTACAAG 58.156 47.826 0.00 0.00 0.00 3.16
2961 3071 4.534500 AGAGAGAGAGAGAGAGGTGTACAA 59.466 45.833 0.00 0.00 0.00 2.41
2972 3082 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2973 3083 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2974 3084 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2975 3085 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2976 3086 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2977 3087 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2978 3088 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2979 3089 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2980 3090 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2996 3107 3.706594 GTGGAGAGAGAGAGAGAGAGAGA 59.293 52.174 0.00 0.00 0.00 3.10
3004 3115 8.278639 AGAATAATAACTGTGGAGAGAGAGAGA 58.721 37.037 0.00 0.00 0.00 3.10
3033 3144 6.642683 ATGGTCTAATTGTTCGTTTACTCG 57.357 37.500 0.00 0.00 0.00 4.18
3200 3330 2.158755 CCCATCCAGGTCCTACATTGTC 60.159 54.545 0.00 0.00 34.66 3.18
3242 3376 6.316890 AGTTAAAAACGAGGCACTTTTCACTA 59.683 34.615 0.00 0.00 41.55 2.74
3246 3380 5.337554 ACAGTTAAAAACGAGGCACTTTTC 58.662 37.500 0.00 0.00 41.55 2.29
3346 3480 4.793201 TCACTCTCTCCTAATCATTCCGA 58.207 43.478 0.00 0.00 0.00 4.55
3366 3500 2.032528 CCGGCCTGCAAGTTCTCA 59.967 61.111 0.00 0.00 0.00 3.27
3586 3729 0.318441 ACGCTCTGACAAGCAAGCTA 59.682 50.000 0.00 0.00 42.62 3.32
3588 3731 1.206072 CACGCTCTGACAAGCAAGC 59.794 57.895 9.34 0.00 42.62 4.01
3589 3732 0.510359 GACACGCTCTGACAAGCAAG 59.490 55.000 9.34 4.56 42.62 4.01
3590 3733 0.179086 TGACACGCTCTGACAAGCAA 60.179 50.000 9.34 0.00 42.62 3.91
3591 3734 0.033920 ATGACACGCTCTGACAAGCA 59.966 50.000 9.34 0.00 42.62 3.91
3622 3765 1.300931 CCACCGGTGAGTGTGTGAG 60.301 63.158 36.07 11.77 35.93 3.51
3623 3766 1.118965 ATCCACCGGTGAGTGTGTGA 61.119 55.000 36.07 21.73 35.93 3.58
3624 3767 0.950555 CATCCACCGGTGAGTGTGTG 60.951 60.000 36.07 16.95 35.93 3.82
3625 3768 1.371183 CATCCACCGGTGAGTGTGT 59.629 57.895 36.07 11.42 35.93 3.72
3626 3769 1.375908 CCATCCACCGGTGAGTGTG 60.376 63.158 36.07 24.32 35.93 3.82
3627 3770 0.543410 TACCATCCACCGGTGAGTGT 60.543 55.000 36.07 25.51 37.33 3.55
3671 3814 1.377725 CATCTGCGAGGCCCAAACT 60.378 57.895 0.00 0.00 0.00 2.66
3779 3934 6.097915 TGTCCTATCCAAGGTATCGATTTC 57.902 41.667 1.71 0.00 46.62 2.17
3780 3935 5.602978 ACTGTCCTATCCAAGGTATCGATTT 59.397 40.000 1.71 0.00 46.62 2.17
3781 3936 5.148502 ACTGTCCTATCCAAGGTATCGATT 58.851 41.667 1.71 0.00 46.62 3.34
3782 3937 4.742012 ACTGTCCTATCCAAGGTATCGAT 58.258 43.478 2.16 2.16 46.62 3.59
3783 3938 4.141228 AGACTGTCCTATCCAAGGTATCGA 60.141 45.833 3.76 0.00 46.62 3.59
3796 3951 5.150715 TCCCTACGAGTATAGACTGTCCTA 58.849 45.833 3.76 0.00 35.45 2.94
3825 3980 7.094463 ACCAGCAATATATATTTCAGAAGCAGC 60.094 37.037 5.18 3.40 0.00 5.25
3826 3981 8.332996 ACCAGCAATATATATTTCAGAAGCAG 57.667 34.615 5.18 2.72 0.00 4.24


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

AutoCloner maintained by Alex Coulton.