Multiple sequence alignment - TraesCS7A01G061300

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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 TraesCS7A01G061300 chr7A 100.000 5829 0 0 1 5829 30136240 30142068 0.000000e+00 10765.0
1 TraesCS7A01G061300 chr7A 88.504 896 73 11 4142 5025 29243689 29242812 0.000000e+00 1057.0
2 TraesCS7A01G061300 chr7A 93.314 673 40 5 4263 4933 29260554 29259885 0.000000e+00 989.0
3 TraesCS7A01G061300 chr7A 95.673 208 7 2 3971 4177 29260754 29260548 3.370000e-87 333.0
4 TraesCS7A01G061300 chr7A 86.385 213 25 3 5111 5319 29237390 29237178 4.540000e-56 230.0
5 TraesCS7A01G061300 chr7A 85.915 213 26 3 5111 5319 29259164 29258952 2.110000e-54 224.0
6 TraesCS7A01G061300 chr7A 96.262 107 4 0 3530 3636 29260857 29260751 6.000000e-40 176.0
7 TraesCS7A01G061300 chr7D 94.840 3178 130 12 2236 5391 29876453 29879618 0.000000e+00 4929.0
8 TraesCS7A01G061300 chr7D 88.753 1716 109 35 1 1673 29874276 29875950 0.000000e+00 2023.0
9 TraesCS7A01G061300 chr7D 87.402 508 52 9 4421 4928 28789533 28789038 1.820000e-159 573.0
10 TraesCS7A01G061300 chr7D 90.051 392 26 7 1805 2183 29875947 29876338 4.060000e-136 496.0
11 TraesCS7A01G061300 chr7D 87.613 444 23 5 5415 5829 29879980 29880420 2.440000e-133 486.0
12 TraesCS7A01G061300 chr7D 89.444 360 37 1 4569 4928 28827116 28826758 2.480000e-123 453.0
13 TraesCS7A01G061300 chr7D 93.220 236 15 1 4360 4594 28819026 28818791 4.320000e-91 346.0
14 TraesCS7A01G061300 chr7D 89.623 212 22 0 5108 5319 28820253 28820042 2.680000e-68 270.0
15 TraesCS7A01G061300 chr7D 86.047 215 27 1 5108 5319 28817885 28817671 1.630000e-55 228.0
16 TraesCS7A01G061300 chr4A 94.985 2353 106 4 2768 5109 699792525 699790174 0.000000e+00 3681.0
17 TraesCS7A01G061300 chr4A 89.149 1751 94 35 1 1694 699794652 699792941 0.000000e+00 2093.0
18 TraesCS7A01G061300 chr4A 94.676 432 22 1 4280 4710 700962021 700962452 0.000000e+00 669.0
19 TraesCS7A01G061300 chr4A 91.379 406 28 4 1775 2173 699792932 699792527 3.070000e-152 549.0
20 TraesCS7A01G061300 chr4A 84.494 316 23 8 1 314 699803838 699803547 7.390000e-74 289.0
21 TraesCS7A01G061300 chr4A 80.180 444 31 17 5417 5829 699789673 699789256 4.450000e-71 279.0
22 TraesCS7A01G061300 chr4A 91.489 188 16 0 4353 4540 702574284 702574097 5.790000e-65 259.0
23 TraesCS7A01G061300 chr4A 91.489 188 16 0 4353 4540 702579095 702578908 5.790000e-65 259.0
24 TraesCS7A01G061300 chr4A 85.965 228 28 3 5095 5320 700543515 700543740 2.100000e-59 241.0
25 TraesCS7A01G061300 chr4A 87.255 204 22 4 4734 4935 699582159 699581958 4.540000e-56 230.0
26 TraesCS7A01G061300 chr4A 85.581 215 28 1 5108 5319 702573081 702572867 7.600000e-54 222.0
27 TraesCS7A01G061300 chr4A 85.581 215 28 1 5108 5319 702577892 702577678 7.600000e-54 222.0
28 TraesCS7A01G061300 chr4A 88.732 142 15 1 3490 3630 702613325 702613184 7.770000e-39 172.0
29 TraesCS7A01G061300 chr4A 84.940 166 25 0 3655 3820 700968150 700968315 1.000000e-37 169.0
30 TraesCS7A01G061300 chr4A 97.222 72 2 0 1699 1770 109936216 109936145 7.930000e-24 122.0
31 TraesCS7A01G061300 chr4A 97.143 35 1 0 1739 1773 255332194 255332228 6.310000e-05 60.2
32 TraesCS7A01G061300 chr4A 94.737 38 1 1 1744 1780 255332145 255332108 2.270000e-04 58.4
33 TraesCS7A01G061300 chr6A 92.084 379 24 4 1997 2369 611099443 611099065 4.000000e-146 529.0
34 TraesCS7A01G061300 chr6A 97.297 37 1 0 1739 1775 21048313 21048277 4.880000e-06 63.9
35 TraesCS7A01G061300 chr6A 94.737 38 2 0 3258 3295 532022077 532022040 6.310000e-05 60.2
36 TraesCS7A01G061300 chrUn 82.583 511 66 10 4419 4928 50236076 50236564 4.170000e-116 429.0
37 TraesCS7A01G061300 chrUn 86.601 306 31 3 999 1304 231905162 231905457 4.350000e-86 329.0
38 TraesCS7A01G061300 chrUn 83.923 311 47 3 4619 4928 478041824 478042132 1.590000e-75 294.0
39 TraesCS7A01G061300 chrUn 88.341 223 22 3 5095 5316 50236641 50236860 1.250000e-66 265.0
40 TraesCS7A01G061300 chr6B 87.055 309 35 5 1000 1307 456578456 456578152 1.560000e-90 344.0
41 TraesCS7A01G061300 chr6B 94.595 37 2 0 1744 1780 685672567 685672531 2.270000e-04 58.4
42 TraesCS7A01G061300 chr3D 87.013 231 27 2 1074 1304 203918101 203918328 2.080000e-64 257.0
43 TraesCS7A01G061300 chr5D 81.905 210 24 4 5633 5829 40891534 40891326 1.300000e-36 165.0
44 TraesCS7A01G061300 chr7B 90.291 103 8 2 1167 1268 673853529 673853428 3.660000e-27 134.0
45 TraesCS7A01G061300 chr1B 78.571 210 26 10 5633 5823 647140298 647140507 2.850000e-23 121.0
46 TraesCS7A01G061300 chr1B 80.220 91 13 2 3260 3349 606319316 606319230 4.880000e-06 63.9
47 TraesCS7A01G061300 chr1B 85.714 56 7 1 3245 3300 150361234 150361180 2.270000e-04 58.4
48 TraesCS7A01G061300 chr1B 92.500 40 1 2 3251 3289 610165040 610165078 8.160000e-04 56.5
49 TraesCS7A01G061300 chr4D 93.443 61 4 0 1074 1134 142309554 142309494 2.240000e-14 91.6
50 TraesCS7A01G061300 chr4D 90.000 50 0 4 3241 3289 463695074 463695029 6.310000e-05 60.2
51 TraesCS7A01G061300 chr4D 97.143 35 1 0 1740 1774 469615133 469615099 6.310000e-05 60.2
52 TraesCS7A01G061300 chr5B 82.558 86 7 5 3260 3343 328226256 328226177 1.050000e-07 69.4
53 TraesCS7A01G061300 chr6D 97.143 35 1 0 1739 1773 395698959 395698925 6.310000e-05 60.2
54 TraesCS7A01G061300 chr2A 86.538 52 7 0 3250 3301 539394666 539394717 2.270000e-04 58.4
55 TraesCS7A01G061300 chr1A 100.000 31 0 0 1740 1770 580970499 580970529 2.270000e-04 58.4
56 TraesCS7A01G061300 chr3A 81.333 75 7 7 1740 1812 490814833 490814902 3.000000e-03 54.7


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 TraesCS7A01G061300 chr7A 30136240 30142068 5828 False 10765.000000 10765 100.00000 1 5829 1 chr7A.!!$F1 5828
1 TraesCS7A01G061300 chr7A 29242812 29243689 877 True 1057.000000 1057 88.50400 4142 5025 1 chr7A.!!$R2 883
2 TraesCS7A01G061300 chr7A 29258952 29260857 1905 True 430.500000 989 92.79100 3530 5319 4 chr7A.!!$R3 1789
3 TraesCS7A01G061300 chr7D 29874276 29880420 6144 False 1983.500000 4929 90.31425 1 5829 4 chr7D.!!$F1 5828
4 TraesCS7A01G061300 chr7D 28817671 28820253 2582 True 281.333333 346 89.63000 4360 5319 3 chr7D.!!$R3 959
5 TraesCS7A01G061300 chr4A 699789256 699794652 5396 True 1650.500000 3681 88.92325 1 5829 4 chr4A.!!$R6 5828
6 TraesCS7A01G061300 chr4A 702572867 702579095 6228 True 240.500000 259 88.53500 4353 5319 4 chr4A.!!$R7 966
7 TraesCS7A01G061300 chrUn 50236076 50236860 784 False 347.000000 429 85.46200 4419 5316 2 chrUn.!!$F3 897

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
149 151 0.108992 AGCGCCGACGAAATAACTCA 60.109 50.000 2.29 0.0 43.93 3.41 F
166 168 0.317799 TCAAAGCCTACCGCGTGTAA 59.682 50.000 4.92 0.0 44.76 2.41 F
354 388 0.537653 TATCGCGTTGGGTGGATCAA 59.462 50.000 5.77 0.0 0.00 2.57 F
1717 1816 0.669625 CTCCCTCCGTTCGGAAACAC 60.670 60.000 14.79 0.0 34.93 3.32 F
1772 1871 0.038744 TCCGAACGGAGGGAGTAGTT 59.961 55.000 12.04 0.0 39.76 2.24 F
1773 1872 0.172803 CCGAACGGAGGGAGTAGTTG 59.827 60.000 7.53 0.0 37.50 3.16 F
1861 1960 0.830648 TGTAGGCTGCTGGGATACAC 59.169 55.000 3.77 0.0 39.74 2.90 F
2599 2791 1.062880 TGCACGGTTTTGAACGACTTC 59.937 47.619 0.00 0.0 0.00 3.01 F
3091 3288 1.131126 CACTGATGGGCGTTCATTGTC 59.869 52.381 0.00 0.0 0.00 3.18 F
3766 3973 1.288188 TCATCCAGGACATGAAGGCA 58.712 50.000 0.00 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1288 1360 0.038251 CTAGTCTGCCGCAACAGTGA 60.038 55.000 0.00 0.00 38.84 3.41 R
1752 1851 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30 R
1754 1853 0.172803 CAACTACTCCCTCCGTTCGG 59.827 60.000 4.74 4.74 0.00 4.30 R
2865 3061 1.137282 GGGAAGCAGGAGTACTACAGC 59.863 57.143 14.41 14.41 0.00 4.40 R
3392 3599 1.607148 GTAAAGGACCACCACAAGCAC 59.393 52.381 0.00 0.00 38.94 4.40 R
3432 3639 4.177026 AGTCATAACTTCAGTAAGCTGCG 58.823 43.478 0.00 0.00 42.29 5.18 R
3844 4051 4.161189 GTCATCTCTTCAATCACCCTCTCA 59.839 45.833 0.00 0.00 0.00 3.27 R
4135 4343 0.729690 GCAGATCCTTCAAGTTCGCC 59.270 55.000 0.00 0.00 0.00 5.54 R
4669 5203 1.280421 GTCCCCAGATCTTTCTGCACT 59.720 52.381 0.00 0.00 46.76 4.40 R
5156 6978 0.320073 TTACCGAAGACAAGGCCACG 60.320 55.000 5.01 0.00 0.00 4.94 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
32 33 1.076533 CCTAATATAGCACGCGCCGG 61.077 60.000 5.73 0.00 39.83 6.13
59 61 6.971184 CAGGCTGAATAACACAATGAAAGATC 59.029 38.462 9.42 0.00 0.00 2.75
71 73 3.726557 TGAAAGATCATGGAGCTGGTT 57.273 42.857 0.00 0.00 0.00 3.67
89 91 5.505780 CTGGTTGGGACATTTATCACCTAA 58.494 41.667 0.00 0.00 39.30 2.69
135 137 2.644992 CTCCCACAAAACAGCGCC 59.355 61.111 2.29 0.00 0.00 6.53
136 138 3.254014 CTCCCACAAAACAGCGCCG 62.254 63.158 2.29 0.00 0.00 6.46
137 139 3.283684 CCCACAAAACAGCGCCGA 61.284 61.111 2.29 0.00 0.00 5.54
138 140 2.051345 CCACAAAACAGCGCCGAC 60.051 61.111 2.29 0.00 0.00 4.79
139 141 2.425124 CACAAAACAGCGCCGACG 60.425 61.111 2.29 0.00 44.07 5.12
140 142 2.586635 ACAAAACAGCGCCGACGA 60.587 55.556 2.29 0.00 43.93 4.20
143 145 0.385473 CAAAACAGCGCCGACGAAAT 60.385 50.000 2.29 0.00 43.93 2.17
145 147 1.149987 AAACAGCGCCGACGAAATAA 58.850 45.000 2.29 0.00 43.93 1.40
146 148 0.441145 AACAGCGCCGACGAAATAAC 59.559 50.000 2.29 0.00 43.93 1.89
148 150 0.297820 CAGCGCCGACGAAATAACTC 59.702 55.000 2.29 0.00 43.93 3.01
149 151 0.108992 AGCGCCGACGAAATAACTCA 60.109 50.000 2.29 0.00 43.93 3.41
150 152 0.717224 GCGCCGACGAAATAACTCAA 59.283 50.000 0.00 0.00 43.93 3.02
151 153 1.127213 GCGCCGACGAAATAACTCAAA 59.873 47.619 0.00 0.00 43.93 2.69
153 155 2.770532 GCCGACGAAATAACTCAAAGC 58.229 47.619 0.00 0.00 0.00 3.51
154 156 2.475685 GCCGACGAAATAACTCAAAGCC 60.476 50.000 0.00 0.00 0.00 4.35
155 157 3.000727 CCGACGAAATAACTCAAAGCCT 58.999 45.455 0.00 0.00 0.00 4.58
166 168 0.317799 TCAAAGCCTACCGCGTGTAA 59.682 50.000 4.92 0.00 44.76 2.41
169 171 1.648504 AAGCCTACCGCGTGTAATTC 58.351 50.000 4.92 0.00 44.76 2.17
334 368 2.093447 CCCCAGTATCCAGTGTGTTCTC 60.093 54.545 0.00 0.00 0.00 2.87
354 388 0.537653 TATCGCGTTGGGTGGATCAA 59.462 50.000 5.77 0.00 0.00 2.57
359 393 0.726827 CGTTGGGTGGATCAACATCG 59.273 55.000 1.86 0.00 43.18 3.84
389 423 4.222847 GGGAGATCGACCGTGGCC 62.223 72.222 0.00 0.00 0.00 5.36
729 786 2.123897 GCCTCGCCTCTCCTCTCT 60.124 66.667 0.00 0.00 0.00 3.10
768 825 5.669904 TCTTTCTCCCAAAATTCCCCTTTTT 59.330 36.000 0.00 0.00 0.00 1.94
1169 1233 1.296715 CCTTCAAGTGGGAGGTCGG 59.703 63.158 0.00 0.00 0.00 4.79
1279 1351 2.432628 CGGTTCCTGCTCCGTGAC 60.433 66.667 0.00 0.00 41.58 3.67
1354 1426 1.140312 GGGGAATAGGCCATGTGAGA 58.860 55.000 5.01 0.00 0.00 3.27
1355 1427 1.202818 GGGGAATAGGCCATGTGAGAC 60.203 57.143 5.01 0.00 0.00 3.36
1356 1428 1.771255 GGGAATAGGCCATGTGAGACT 59.229 52.381 5.01 0.00 0.00 3.24
1385 1457 1.141858 TGGTGTGTTAGTGTGCCATGA 59.858 47.619 0.00 0.00 0.00 3.07
1482 1554 3.181472 GCCCTCTGGAATGCTTAATTTGG 60.181 47.826 0.00 0.00 0.00 3.28
1487 1559 7.428826 CCTCTGGAATGCTTAATTTGGATTAC 58.571 38.462 0.00 0.00 0.00 1.89
1520 1592 4.141846 TGTCTGTTTGCTCTCTGGATATCC 60.142 45.833 15.39 15.39 0.00 2.59
1522 1594 4.125703 CTGTTTGCTCTCTGGATATCCAC 58.874 47.826 20.98 11.07 42.01 4.02
1528 1600 3.006323 GCTCTCTGGATATCCACATCGTT 59.994 47.826 20.98 0.00 42.01 3.85
1529 1601 4.502259 GCTCTCTGGATATCCACATCGTTT 60.502 45.833 20.98 0.00 42.01 3.60
1530 1602 5.605534 CTCTCTGGATATCCACATCGTTTT 58.394 41.667 20.98 0.00 42.01 2.43
1564 1657 0.731417 ATGCTGTCGAATTGCTGAGC 59.269 50.000 0.00 0.00 0.00 4.26
1582 1676 3.500680 TGAGCGAAACAAGGGTAAATGTC 59.499 43.478 0.00 0.00 0.00 3.06
1614 1713 1.050988 TGAGATGCCCCTCTAGGTGC 61.051 60.000 0.00 0.00 34.38 5.01
1645 1744 1.896694 CTCTCCCTCTGTCCAGTGC 59.103 63.158 0.00 0.00 0.00 4.40
1673 1772 2.948979 TGCTAACAGGACAGGTTTGTTG 59.051 45.455 11.24 5.42 37.76 3.33
1676 1775 1.762708 ACAGGACAGGTTTGTTGGTG 58.237 50.000 0.00 0.00 37.76 4.17
1694 1793 1.404035 GTGGTGGTTCAGTTGTGGAAC 59.596 52.381 0.00 0.00 42.99 3.62
1696 1795 1.375551 GTGGTTCAGTTGTGGAACGT 58.624 50.000 0.00 0.00 44.29 3.99
1698 1797 2.286025 GTGGTTCAGTTGTGGAACGTAC 59.714 50.000 0.00 0.00 44.29 3.67
1700 1799 2.798847 GGTTCAGTTGTGGAACGTACTC 59.201 50.000 0.00 0.00 44.29 2.59
1701 1800 2.798847 GTTCAGTTGTGGAACGTACTCC 59.201 50.000 0.00 0.00 42.39 3.85
1702 1801 1.342174 TCAGTTGTGGAACGTACTCCC 59.658 52.381 3.84 0.00 42.39 4.30
1706 1805 1.246056 TGTGGAACGTACTCCCTCCG 61.246 60.000 3.84 0.00 42.39 4.63
1711 1810 1.589716 AACGTACTCCCTCCGTTCGG 61.590 60.000 4.74 4.74 40.46 4.30
1712 1811 1.746615 CGTACTCCCTCCGTTCGGA 60.747 63.158 13.34 13.34 0.00 4.55
1716 1815 1.117142 ACTCCCTCCGTTCGGAAACA 61.117 55.000 14.79 1.28 34.93 2.83
1717 1816 0.669625 CTCCCTCCGTTCGGAAACAC 60.670 60.000 14.79 0.00 34.93 3.32
1721 1820 1.578583 CTCCGTTCGGAAACACTTGT 58.421 50.000 14.79 0.00 34.93 3.16
1722 1821 1.525619 CTCCGTTCGGAAACACTTGTC 59.474 52.381 14.79 0.00 34.93 3.18
1723 1822 1.137479 TCCGTTCGGAAACACTTGTCT 59.863 47.619 11.66 0.00 34.93 3.41
1724 1823 1.937899 CCGTTCGGAAACACTTGTCTT 59.062 47.619 5.19 0.00 34.93 3.01
1727 1826 4.046462 CGTTCGGAAACACTTGTCTTAGA 58.954 43.478 0.00 0.00 34.93 2.10
1728 1827 4.505191 CGTTCGGAAACACTTGTCTTAGAA 59.495 41.667 0.00 0.00 34.93 2.10
1729 1828 5.005971 CGTTCGGAAACACTTGTCTTAGAAA 59.994 40.000 0.00 0.00 34.93 2.52
1730 1829 6.292703 CGTTCGGAAACACTTGTCTTAGAAAT 60.293 38.462 0.00 0.00 34.93 2.17
1731 1830 6.539649 TCGGAAACACTTGTCTTAGAAATG 57.460 37.500 0.00 0.00 0.00 2.32
1735 1834 6.918022 GGAAACACTTGTCTTAGAAATGGTTG 59.082 38.462 0.00 0.00 0.00 3.77
1736 1835 7.404671 AAACACTTGTCTTAGAAATGGTTGT 57.595 32.000 0.00 0.00 0.00 3.32
1737 1836 8.514330 AAACACTTGTCTTAGAAATGGTTGTA 57.486 30.769 0.00 0.00 0.00 2.41
1739 1838 8.324163 ACACTTGTCTTAGAAATGGTTGTATC 57.676 34.615 0.00 0.00 0.00 2.24
1741 1840 9.003658 CACTTGTCTTAGAAATGGTTGTATCTT 57.996 33.333 0.00 0.00 0.00 2.40
1742 1841 9.003658 ACTTGTCTTAGAAATGGTTGTATCTTG 57.996 33.333 0.00 0.00 0.00 3.02
1743 1842 7.921786 TGTCTTAGAAATGGTTGTATCTTGG 57.078 36.000 0.00 0.00 0.00 3.61
1744 1843 7.685481 TGTCTTAGAAATGGTTGTATCTTGGA 58.315 34.615 0.00 0.00 0.00 3.53
1745 1844 7.606456 TGTCTTAGAAATGGTTGTATCTTGGAC 59.394 37.037 0.00 0.00 0.00 4.02
1746 1845 7.606456 GTCTTAGAAATGGTTGTATCTTGGACA 59.394 37.037 0.00 0.00 0.00 4.02
1747 1846 8.160765 TCTTAGAAATGGTTGTATCTTGGACAA 58.839 33.333 0.00 0.00 34.46 3.18
1748 1847 6.824305 AGAAATGGTTGTATCTTGGACAAG 57.176 37.500 5.72 5.72 37.47 3.16
1750 1849 7.458397 AGAAATGGTTGTATCTTGGACAAGTA 58.542 34.615 11.44 2.10 37.47 2.24
1752 1851 8.650143 AAATGGTTGTATCTTGGACAAGTATT 57.350 30.769 11.44 2.11 37.47 1.89
1753 1852 8.650143 AATGGTTGTATCTTGGACAAGTATTT 57.350 30.769 11.44 0.00 37.47 1.40
1754 1853 7.681939 TGGTTGTATCTTGGACAAGTATTTC 57.318 36.000 11.44 1.78 37.47 2.17
1755 1854 6.657541 TGGTTGTATCTTGGACAAGTATTTCC 59.342 38.462 11.44 9.00 37.47 3.13
1756 1855 6.183360 GGTTGTATCTTGGACAAGTATTTCCG 60.183 42.308 11.44 0.00 37.47 4.30
1760 1859 3.991773 TCTTGGACAAGTATTTCCGAACG 59.008 43.478 11.44 0.00 39.38 3.95
1761 1860 2.690786 TGGACAAGTATTTCCGAACGG 58.309 47.619 6.94 6.94 34.24 4.44
1762 1861 2.299582 TGGACAAGTATTTCCGAACGGA 59.700 45.455 12.04 12.04 43.52 4.69
1763 1862 2.928116 GGACAAGTATTTCCGAACGGAG 59.072 50.000 15.34 5.60 46.06 4.63
1764 1863 2.928116 GACAAGTATTTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
1765 1864 2.277084 CAAGTATTTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
1767 1866 1.755380 AGTATTTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
1768 1867 1.479730 GTATTTCCGAACGGAGGGAGT 59.520 52.381 15.34 1.96 46.06 3.85
1772 1871 0.038744 TCCGAACGGAGGGAGTAGTT 59.961 55.000 12.04 0.00 39.76 2.24
1773 1872 0.172803 CCGAACGGAGGGAGTAGTTG 59.827 60.000 7.53 0.00 37.50 3.16
1784 1883 2.104281 GGGAGTAGTTGTGAGTGGTGTT 59.896 50.000 0.00 0.00 0.00 3.32
1790 1889 4.008074 AGTTGTGAGTGGTGTTGGATAG 57.992 45.455 0.00 0.00 0.00 2.08
1805 1904 9.520204 GGTGTTGGATAGATATGAATTTTGTTG 57.480 33.333 0.00 0.00 0.00 3.33
1825 1924 1.541588 GTTCAAGTCATGCCCTGTTCC 59.458 52.381 0.00 0.00 0.00 3.62
1832 1931 2.275380 ATGCCCTGTTCCGGTTTGC 61.275 57.895 0.00 0.00 0.00 3.68
1861 1960 0.830648 TGTAGGCTGCTGGGATACAC 59.169 55.000 3.77 0.00 39.74 2.90
1924 2026 5.684704 TGTCCATAGATTGACTCCATTTCC 58.315 41.667 0.00 0.00 32.67 3.13
1928 2030 5.511373 CCATAGATTGACTCCATTTCCGCTA 60.511 44.000 0.00 0.00 0.00 4.26
1983 2086 2.543641 TCATCTGTATGCTTCACTGCG 58.456 47.619 0.00 0.00 35.36 5.18
1991 2094 4.875536 TGTATGCTTCACTGCGTTGATAAT 59.124 37.500 0.00 0.00 35.36 1.28
2036 2140 2.235898 ACCTTTAGCTTCTCTCTGCCTG 59.764 50.000 0.00 0.00 0.00 4.85
2095 2200 2.104622 TGTCTTGGCACTGTCTCATTCA 59.895 45.455 0.00 0.00 0.00 2.57
2138 2249 5.532406 TCATTCTAAATAAGCATGGCCTCAC 59.468 40.000 3.32 0.00 30.58 3.51
2139 2250 3.466836 TCTAAATAAGCATGGCCTCACG 58.533 45.455 3.32 0.00 0.00 4.35
2184 2296 7.592938 TGTTGTTGTCAATAATCAAGGTGATC 58.407 34.615 0.00 0.00 34.43 2.92
2185 2297 7.448161 TGTTGTTGTCAATAATCAAGGTGATCT 59.552 33.333 0.00 0.00 34.43 2.75
2186 2298 8.946085 GTTGTTGTCAATAATCAAGGTGATCTA 58.054 33.333 0.00 0.00 34.43 1.98
2187 2299 9.685276 TTGTTGTCAATAATCAAGGTGATCTAT 57.315 29.630 0.00 0.00 35.76 1.98
2190 2302 8.908786 TGTCAATAATCAAGGTGATCTATTCC 57.091 34.615 0.00 0.00 35.76 3.01
2191 2303 7.939039 TGTCAATAATCAAGGTGATCTATTCCC 59.061 37.037 0.00 0.00 35.76 3.97
2192 2304 7.391833 GTCAATAATCAAGGTGATCTATTCCCC 59.608 40.741 0.00 0.00 35.76 4.81
2193 2305 7.073598 TCAATAATCAAGGTGATCTATTCCCCA 59.926 37.037 0.00 0.00 35.76 4.96
2194 2306 5.937492 AATCAAGGTGATCTATTCCCCAT 57.063 39.130 0.00 0.00 35.76 4.00
2195 2307 4.712051 TCAAGGTGATCTATTCCCCATG 57.288 45.455 0.00 0.00 0.00 3.66
2196 2308 4.047166 TCAAGGTGATCTATTCCCCATGT 58.953 43.478 0.00 0.00 0.00 3.21
2197 2309 4.103153 TCAAGGTGATCTATTCCCCATGTC 59.897 45.833 0.00 0.00 0.00 3.06
2198 2310 3.946824 AGGTGATCTATTCCCCATGTCT 58.053 45.455 0.00 0.00 0.00 3.41
2199 2311 4.310740 AGGTGATCTATTCCCCATGTCTT 58.689 43.478 0.00 0.00 0.00 3.01
2200 2312 5.476983 AGGTGATCTATTCCCCATGTCTTA 58.523 41.667 0.00 0.00 0.00 2.10
2207 2319 7.392766 TCTATTCCCCATGTCTTACATCATT 57.607 36.000 0.00 0.00 36.53 2.57
2228 2340 4.621068 TGCAAGTTGCTATGCTTGTATC 57.379 40.909 27.17 0.00 45.31 2.24
2229 2341 4.009002 TGCAAGTTGCTATGCTTGTATCA 58.991 39.130 27.17 0.45 45.31 2.15
2230 2342 4.641541 TGCAAGTTGCTATGCTTGTATCAT 59.358 37.500 27.17 0.00 45.31 2.45
2232 2344 6.487668 TGCAAGTTGCTATGCTTGTATCATAT 59.512 34.615 27.17 0.00 45.31 1.78
2365 2557 2.388310 TTCGGATGTTTGTCGCCATA 57.612 45.000 0.00 0.00 0.00 2.74
2419 2611 8.675705 ACCTAATGCTTTTAAATGTGCTTTTT 57.324 26.923 11.61 6.20 0.00 1.94
2445 2637 6.536582 CCATACTCAGTGTGAACCTTTCTATG 59.463 42.308 2.50 0.00 0.00 2.23
2512 2704 5.700402 AGATAACTGTCTAACTGGGCATT 57.300 39.130 0.00 0.00 0.00 3.56
2527 2719 3.894427 TGGGCATTTGACTTTTCTAGCAA 59.106 39.130 0.00 0.00 0.00 3.91
2528 2720 4.527816 TGGGCATTTGACTTTTCTAGCAAT 59.472 37.500 0.00 0.00 0.00 3.56
2599 2791 1.062880 TGCACGGTTTTGAACGACTTC 59.937 47.619 0.00 0.00 0.00 3.01
2772 2967 8.873215 ATTATAGAACTGGTCTGTAATTGTCG 57.127 34.615 16.21 0.00 44.10 4.35
2792 2988 8.786826 TTGTCGACTCAATGGAAATAATACTT 57.213 30.769 17.92 0.00 0.00 2.24
2799 2995 8.522830 ACTCAATGGAAATAATACTTTGTGTGG 58.477 33.333 0.00 0.00 30.26 4.17
2865 3061 2.014857 CCATGACTGCTTGACATCTGG 58.985 52.381 0.00 0.00 0.00 3.86
2876 3072 4.677584 CTTGACATCTGGCTGTAGTACTC 58.322 47.826 0.00 0.00 0.00 2.59
2884 3080 1.137282 GGCTGTAGTACTCCTGCTTCC 59.863 57.143 15.22 0.00 0.00 3.46
2935 3132 3.252458 GGTTAGTTGCCTACCAAGTTGTG 59.748 47.826 1.45 0.00 38.11 3.33
2958 3155 4.130118 CACTCTAGTTCTGTTGCAACCTT 58.870 43.478 26.14 9.84 0.00 3.50
2980 3177 4.428294 TCATCTGAATGTCCCTCAATCC 57.572 45.455 0.00 0.00 34.32 3.01
3091 3288 1.131126 CACTGATGGGCGTTCATTGTC 59.869 52.381 0.00 0.00 0.00 3.18
3269 3466 5.132648 ACAGAAAATGCATATACTCCCTCCA 59.867 40.000 0.00 0.00 0.00 3.86
3289 3486 6.207417 CCTCCAATCCATATTAATTGACGCTT 59.793 38.462 7.95 0.00 35.35 4.68
3303 3500 6.946229 ATTGACGCTTACTTAGTACAAGTG 57.054 37.500 16.26 10.15 36.19 3.16
3304 3501 4.801891 TGACGCTTACTTAGTACAAGTGG 58.198 43.478 16.26 11.57 34.78 4.00
3432 3639 8.692710 CCTTTACCCCTTCTATTGTTTATTTCC 58.307 37.037 0.00 0.00 0.00 3.13
3636 3843 4.187694 GAGTTAATGACTGAGAAGGCTGG 58.812 47.826 0.00 0.00 39.19 4.85
3682 3889 2.223665 GCTCAACTTTGCTTTCACTGCT 60.224 45.455 0.00 0.00 0.00 4.24
3715 3922 6.594159 ACAACAGCTTAATGACACTATACACC 59.406 38.462 0.00 0.00 0.00 4.16
3766 3973 1.288188 TCATCCAGGACATGAAGGCA 58.712 50.000 0.00 0.00 0.00 4.75
3793 4000 6.701340 TGATGTATTGCCTGATGTCTATACC 58.299 40.000 0.00 0.00 0.00 2.73
3829 4036 1.301716 GTCCCTTGCAGCTCGTCAA 60.302 57.895 0.00 0.00 0.00 3.18
3844 4051 4.443034 GCTCGTCAAGACATATTAGGGGTT 60.443 45.833 0.72 0.00 0.00 4.11
3941 4148 1.656652 ATACGTTGATGCTGGACTGC 58.343 50.000 0.00 0.00 0.00 4.40
3993 4200 2.180131 GAGAAGCGCAACACTGGCAG 62.180 60.000 14.16 14.16 0.00 4.85
4135 4343 7.714377 AGCTATCTTAACATGATTCAGGTTCTG 59.286 37.037 18.96 13.13 39.15 3.02
4588 5122 4.045781 TGGGTGCCGCCACATGAT 62.046 61.111 0.00 0.00 43.88 2.45
4669 5203 3.374220 TTCGTCGAGGTGCTAAAGAAA 57.626 42.857 4.85 0.00 0.00 2.52
4816 5350 2.499693 TGACAAGCTGGTCGATTCCATA 59.500 45.455 16.52 0.00 40.72 2.74
4878 5412 4.223700 TCCATCTCAATAACAGACAGCAGT 59.776 41.667 0.00 0.00 0.00 4.40
5156 6978 5.931441 ATACTCTGCTTTTCAGTTGTGTC 57.069 39.130 0.00 0.00 43.32 3.67
5158 6980 2.609459 CTCTGCTTTTCAGTTGTGTCGT 59.391 45.455 0.00 0.00 43.32 4.34
5159 6981 2.351418 TCTGCTTTTCAGTTGTGTCGTG 59.649 45.455 0.00 0.00 43.32 4.35
5170 6992 0.531974 TGTGTCGTGGCCTTGTCTTC 60.532 55.000 3.32 0.00 0.00 2.87
5208 7030 6.034256 GCTATACATGCTTTGCTTGTTTGAAG 59.966 38.462 14.48 9.23 42.78 3.02
5233 7055 7.159437 CAAAAATTGAATTTGCGTGTGAGTA 57.841 32.000 3.62 0.00 31.70 2.59
5266 7088 6.532657 GCAATGCCCTTAAATATGTGATATGC 59.467 38.462 0.00 0.00 0.00 3.14
5268 7090 4.699735 TGCCCTTAAATATGTGATATGCGG 59.300 41.667 0.00 0.00 0.00 5.69
5274 7096 7.041440 CCTTAAATATGTGATATGCGGTGTGAA 60.041 37.037 0.00 0.00 0.00 3.18
5281 7103 4.512944 GTGATATGCGGTGTGAAGAATGAT 59.487 41.667 0.00 0.00 0.00 2.45
5283 7105 5.589855 TGATATGCGGTGTGAAGAATGATTT 59.410 36.000 0.00 0.00 0.00 2.17
5334 7164 3.135712 TGTGACATTGTGACTGGGTACTT 59.864 43.478 7.89 0.00 0.00 2.24
5372 7202 3.931468 AGACTCTGAATGCGTCTGAATTG 59.069 43.478 0.00 0.00 39.07 2.32
5373 7203 3.668447 ACTCTGAATGCGTCTGAATTGT 58.332 40.909 0.00 0.00 34.16 2.71
5374 7204 4.820897 ACTCTGAATGCGTCTGAATTGTA 58.179 39.130 0.00 0.00 34.16 2.41
5375 7205 4.627467 ACTCTGAATGCGTCTGAATTGTAC 59.373 41.667 0.00 0.00 34.16 2.90
5405 7235 8.583810 AAAATTGTGAACATTGTGAAGATCTG 57.416 30.769 0.00 0.00 0.00 2.90
5408 7238 4.516321 TGTGAACATTGTGAAGATCTGTGG 59.484 41.667 0.00 0.00 0.00 4.17
5409 7239 3.503363 TGAACATTGTGAAGATCTGTGGC 59.497 43.478 0.00 0.00 0.00 5.01
5411 7241 3.693807 ACATTGTGAAGATCTGTGGCAT 58.306 40.909 0.00 0.00 0.00 4.40
5412 7242 4.084287 ACATTGTGAAGATCTGTGGCATT 58.916 39.130 0.00 0.00 0.00 3.56
5413 7243 4.082408 ACATTGTGAAGATCTGTGGCATTG 60.082 41.667 0.00 3.59 0.00 2.82
5427 7596 4.002316 GTGGCATTGTTATTGCAACCATT 58.998 39.130 0.00 0.00 41.95 3.16
5473 7642 9.477484 AATAAATAGAAGCTGTATACCTTGTCG 57.523 33.333 0.00 0.00 0.00 4.35
5475 7644 2.496070 AGAAGCTGTATACCTTGTCGCA 59.504 45.455 0.00 0.00 0.00 5.10
5493 7662 2.271800 GCAGAGATTACAAGTGGACGG 58.728 52.381 0.00 0.00 0.00 4.79
5551 7720 3.973206 TTTCTCGTTGAGCAGGGAATA 57.027 42.857 0.00 0.00 0.00 1.75
5558 7727 1.216064 TGAGCAGGGAATAGCCACAT 58.784 50.000 0.00 0.00 38.95 3.21
5575 7744 4.675146 GCCACATAAATGATCAACACGCTT 60.675 41.667 0.00 0.00 0.00 4.68
5623 7792 3.024547 TGATCTAGCCTTTAGTCGCTGT 58.975 45.455 0.00 0.00 36.53 4.40
5628 7797 1.000506 AGCCTTTAGTCGCTGTTTCGA 59.999 47.619 0.00 0.00 32.98 3.71
5686 7872 5.666718 TGGGGAAATGATATTTTGCCTGAAT 59.333 36.000 9.49 0.00 44.11 2.57
5748 7946 4.096984 ACTCTTTTCTTTGCAGTGTCCTTG 59.903 41.667 0.00 0.00 0.00 3.61
5770 7968 7.309499 CCTTGTTTGGCATTACTAACAACCATA 60.309 37.037 9.68 0.00 36.05 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.176958 CGCGTGCTATATTAGGTTTAGCTTT 59.823 40.000 0.00 0.00 39.24 3.51
12 13 0.388134 CGGCGCGTGCTATATTAGGT 60.388 55.000 21.89 0.00 42.25 3.08
32 33 5.627499 TTCATTGTGTTATTCAGCCTGAC 57.373 39.130 0.00 0.00 0.00 3.51
59 61 0.033796 ATGTCCCAACCAGCTCCATG 60.034 55.000 0.00 0.00 0.00 3.66
71 73 8.096621 TCAGTATTTAGGTGATAAATGTCCCA 57.903 34.615 3.68 0.00 42.73 4.37
89 91 5.670485 TGTCGGAATATGCTGTTCAGTATT 58.330 37.500 8.49 2.88 0.00 1.89
135 137 4.032558 GGTAGGCTTTGAGTTATTTCGTCG 59.967 45.833 0.00 0.00 0.00 5.12
136 138 4.032558 CGGTAGGCTTTGAGTTATTTCGTC 59.967 45.833 0.00 0.00 0.00 4.20
137 139 3.930848 CGGTAGGCTTTGAGTTATTTCGT 59.069 43.478 0.00 0.00 0.00 3.85
138 140 3.242316 GCGGTAGGCTTTGAGTTATTTCG 60.242 47.826 0.00 0.00 39.11 3.46
139 141 3.242316 CGCGGTAGGCTTTGAGTTATTTC 60.242 47.826 0.00 0.00 40.44 2.17
140 142 2.676342 CGCGGTAGGCTTTGAGTTATTT 59.324 45.455 0.00 0.00 40.44 1.40
143 145 0.604578 ACGCGGTAGGCTTTGAGTTA 59.395 50.000 12.47 0.00 40.44 2.24
145 147 1.374252 CACGCGGTAGGCTTTGAGT 60.374 57.895 12.47 0.00 40.44 3.41
146 148 0.108992 TACACGCGGTAGGCTTTGAG 60.109 55.000 12.47 0.00 40.44 3.02
148 150 1.365699 ATTACACGCGGTAGGCTTTG 58.634 50.000 12.47 0.00 40.44 2.77
149 151 2.004733 GAATTACACGCGGTAGGCTTT 58.995 47.619 12.47 3.16 40.44 3.51
150 152 1.648504 GAATTACACGCGGTAGGCTT 58.351 50.000 12.47 5.26 40.44 4.35
151 153 0.179092 GGAATTACACGCGGTAGGCT 60.179 55.000 12.47 0.00 40.44 4.58
153 155 0.176219 TGGGAATTACACGCGGTAGG 59.824 55.000 12.47 0.00 32.49 3.18
154 156 1.662122 GTTGGGAATTACACGCGGTAG 59.338 52.381 12.47 1.86 32.49 3.18
155 157 1.001746 TGTTGGGAATTACACGCGGTA 59.998 47.619 12.47 7.24 0.00 4.02
230 235 7.119387 GGGGGAAATGCTAGTTATATTATGCT 58.881 38.462 0.00 0.00 0.00 3.79
237 242 6.523035 TCAATGGGGGAAATGCTAGTTATA 57.477 37.500 0.00 0.00 0.00 0.98
334 368 0.104120 TGATCCACCCAACGCGATAG 59.896 55.000 15.93 0.89 0.00 2.08
389 423 5.392380 CCGATCTCCAAGGTGATTTCTTTTG 60.392 44.000 5.25 0.00 0.00 2.44
712 763 2.123897 AGAGAGGAGAGGCGAGGC 60.124 66.667 0.00 0.00 0.00 4.70
717 768 2.520741 CGGGGAGAGAGGAGAGGC 60.521 72.222 0.00 0.00 0.00 4.70
729 786 1.779061 AAAGAAAGGAGCAGCGGGGA 61.779 55.000 0.00 0.00 0.00 4.81
870 929 2.359967 GCTTCCCTAGCCCGTCACT 61.360 63.158 0.00 0.00 44.48 3.41
1113 1177 3.003763 AAGCCGTCCACCTCCTCC 61.004 66.667 0.00 0.00 0.00 4.30
1279 1351 2.738521 CAACAGTGACGGAGGGCG 60.739 66.667 0.00 0.00 0.00 6.13
1288 1360 0.038251 CTAGTCTGCCGCAACAGTGA 60.038 55.000 0.00 0.00 38.84 3.41
1289 1361 0.038251 TCTAGTCTGCCGCAACAGTG 60.038 55.000 0.00 0.00 38.84 3.66
1290 1362 0.898320 ATCTAGTCTGCCGCAACAGT 59.102 50.000 0.00 0.00 38.84 3.55
1354 1426 3.641906 ACTAACACACCAGTAAGCAGAGT 59.358 43.478 0.00 0.00 0.00 3.24
1355 1427 3.990469 CACTAACACACCAGTAAGCAGAG 59.010 47.826 0.00 0.00 0.00 3.35
1356 1428 3.386726 ACACTAACACACCAGTAAGCAGA 59.613 43.478 0.00 0.00 0.00 4.26
1385 1457 6.650807 TCTCGATCTTTGCATGAAAAGTAACT 59.349 34.615 22.95 8.95 38.16 2.24
1426 1498 2.027192 TGATTTTGAGGCCTACGAAGCT 60.027 45.455 4.42 0.00 0.00 3.74
1482 1554 6.237861 GCAAACAGACAAGACGGATAGTAATC 60.238 42.308 0.00 0.00 0.00 1.75
1487 1559 3.589988 AGCAAACAGACAAGACGGATAG 58.410 45.455 0.00 0.00 0.00 2.08
1495 1567 3.117491 TCCAGAGAGCAAACAGACAAG 57.883 47.619 0.00 0.00 0.00 3.16
1500 1572 4.412796 TGGATATCCAGAGAGCAAACAG 57.587 45.455 20.98 0.00 42.01 3.16
1522 1594 1.036707 AACCCCCACACAAAACGATG 58.963 50.000 0.00 0.00 0.00 3.84
1528 1600 1.139853 GCATCAAAACCCCCACACAAA 59.860 47.619 0.00 0.00 0.00 2.83
1529 1601 0.755686 GCATCAAAACCCCCACACAA 59.244 50.000 0.00 0.00 0.00 3.33
1530 1602 0.105760 AGCATCAAAACCCCCACACA 60.106 50.000 0.00 0.00 0.00 3.72
1564 1657 4.735662 TTCGACATTTACCCTTGTTTCG 57.264 40.909 0.00 0.00 0.00 3.46
1582 1676 4.107622 GGGCATCTCATTTCAATGTTTCG 58.892 43.478 0.00 0.00 37.65 3.46
1595 1694 3.230608 CACCTAGAGGGGCATCTCA 57.769 57.895 0.00 0.00 40.27 3.27
1614 1713 2.036089 GAGGGAGAGCATAAACGTAGGG 59.964 54.545 0.00 0.00 0.00 3.53
1673 1772 0.106918 TCCACAACTGAACCACCACC 60.107 55.000 0.00 0.00 0.00 4.61
1676 1775 0.661020 CGTTCCACAACTGAACCACC 59.339 55.000 0.00 0.00 39.10 4.61
1694 1793 1.308069 TTCCGAACGGAGGGAGTACG 61.308 60.000 15.34 0.00 46.06 3.67
1696 1795 0.890683 GTTTCCGAACGGAGGGAGTA 59.109 55.000 15.34 0.00 46.06 2.59
1698 1797 0.669625 GTGTTTCCGAACGGAGGGAG 60.670 60.000 15.34 0.00 46.06 4.30
1700 1799 0.250166 AAGTGTTTCCGAACGGAGGG 60.250 55.000 15.34 0.00 46.06 4.30
1701 1800 0.865769 CAAGTGTTTCCGAACGGAGG 59.134 55.000 15.34 0.00 46.06 4.30
1702 1801 1.525619 GACAAGTGTTTCCGAACGGAG 59.474 52.381 15.34 5.60 46.06 4.63
1706 1805 5.978934 TTCTAAGACAAGTGTTTCCGAAC 57.021 39.130 0.00 0.00 36.29 3.95
1709 1808 5.238650 ACCATTTCTAAGACAAGTGTTTCCG 59.761 40.000 0.00 0.00 0.00 4.30
1711 1810 7.480810 ACAACCATTTCTAAGACAAGTGTTTC 58.519 34.615 0.00 0.00 0.00 2.78
1712 1811 7.404671 ACAACCATTTCTAAGACAAGTGTTT 57.595 32.000 0.00 0.00 0.00 2.83
1716 1815 9.003658 CAAGATACAACCATTTCTAAGACAAGT 57.996 33.333 0.00 0.00 0.00 3.16
1717 1816 8.454106 CCAAGATACAACCATTTCTAAGACAAG 58.546 37.037 0.00 0.00 0.00 3.16
1721 1820 7.685481 TGTCCAAGATACAACCATTTCTAAGA 58.315 34.615 0.00 0.00 0.00 2.10
1722 1821 7.921786 TGTCCAAGATACAACCATTTCTAAG 57.078 36.000 0.00 0.00 0.00 2.18
1723 1822 7.942341 ACTTGTCCAAGATACAACCATTTCTAA 59.058 33.333 13.69 0.00 40.79 2.10
1724 1823 7.458397 ACTTGTCCAAGATACAACCATTTCTA 58.542 34.615 13.69 0.00 40.79 2.10
1727 1826 8.650143 AATACTTGTCCAAGATACAACCATTT 57.350 30.769 13.69 0.00 40.79 2.32
1728 1827 8.650143 AAATACTTGTCCAAGATACAACCATT 57.350 30.769 13.69 0.00 40.79 3.16
1729 1828 7.339466 GGAAATACTTGTCCAAGATACAACCAT 59.661 37.037 13.69 0.00 40.79 3.55
1730 1829 6.657541 GGAAATACTTGTCCAAGATACAACCA 59.342 38.462 13.69 0.00 40.79 3.67
1731 1830 6.183360 CGGAAATACTTGTCCAAGATACAACC 60.183 42.308 13.69 8.32 40.79 3.77
1735 1834 6.237755 CGTTCGGAAATACTTGTCCAAGATAC 60.238 42.308 13.69 1.40 40.79 2.24
1736 1835 5.808540 CGTTCGGAAATACTTGTCCAAGATA 59.191 40.000 13.69 3.55 40.79 1.98
1737 1836 4.630069 CGTTCGGAAATACTTGTCCAAGAT 59.370 41.667 13.69 1.05 40.79 2.40
1739 1838 3.124636 CCGTTCGGAAATACTTGTCCAAG 59.875 47.826 5.19 5.51 43.79 3.61
1741 1840 2.299582 TCCGTTCGGAAATACTTGTCCA 59.700 45.455 11.66 0.00 33.10 4.02
1742 1841 2.928116 CTCCGTTCGGAAATACTTGTCC 59.072 50.000 14.79 0.00 33.41 4.02
1743 1842 2.928116 CCTCCGTTCGGAAATACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
1744 1843 2.354403 CCCTCCGTTCGGAAATACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
1745 1844 2.093869 TCCCTCCGTTCGGAAATACTTG 60.094 50.000 14.79 1.97 33.41 3.16
1746 1845 2.167900 CTCCCTCCGTTCGGAAATACTT 59.832 50.000 14.79 0.00 33.41 2.24
1747 1846 1.755380 CTCCCTCCGTTCGGAAATACT 59.245 52.381 14.79 0.00 33.41 2.12
1748 1847 1.479730 ACTCCCTCCGTTCGGAAATAC 59.520 52.381 14.79 0.00 33.41 1.89
1750 1849 1.755380 CTACTCCCTCCGTTCGGAAAT 59.245 52.381 14.79 2.39 33.41 2.17
1752 1851 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
1753 1852 0.038744 AACTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
1754 1853 0.172803 CAACTACTCCCTCCGTTCGG 59.827 60.000 4.74 4.74 0.00 4.30
1755 1854 0.886563 ACAACTACTCCCTCCGTTCG 59.113 55.000 0.00 0.00 0.00 3.95
1756 1855 1.891150 TCACAACTACTCCCTCCGTTC 59.109 52.381 0.00 0.00 0.00 3.95
1760 1859 1.550976 CCACTCACAACTACTCCCTCC 59.449 57.143 0.00 0.00 0.00 4.30
1761 1860 2.028930 CACCACTCACAACTACTCCCTC 60.029 54.545 0.00 0.00 0.00 4.30
1762 1861 1.971357 CACCACTCACAACTACTCCCT 59.029 52.381 0.00 0.00 0.00 4.20
1763 1862 1.692519 ACACCACTCACAACTACTCCC 59.307 52.381 0.00 0.00 0.00 4.30
1764 1863 3.131396 CAACACCACTCACAACTACTCC 58.869 50.000 0.00 0.00 0.00 3.85
1765 1864 3.131396 CCAACACCACTCACAACTACTC 58.869 50.000 0.00 0.00 0.00 2.59
1767 1866 3.188159 TCCAACACCACTCACAACTAC 57.812 47.619 0.00 0.00 0.00 2.73
1768 1867 4.836175 TCTATCCAACACCACTCACAACTA 59.164 41.667 0.00 0.00 0.00 2.24
1772 1871 5.660864 TCATATCTATCCAACACCACTCACA 59.339 40.000 0.00 0.00 0.00 3.58
1773 1872 6.161855 TCATATCTATCCAACACCACTCAC 57.838 41.667 0.00 0.00 0.00 3.51
1805 1904 1.541588 GGAACAGGGCATGACTTGAAC 59.458 52.381 19.00 10.16 0.00 3.18
1861 1960 2.605338 CCAAAGTGTGCGATCCAACTTG 60.605 50.000 0.00 0.00 33.30 3.16
1924 2026 5.050091 ACACAGAAATGACAGACTTTTAGCG 60.050 40.000 0.00 0.00 0.00 4.26
1928 2030 7.624360 TGTAACACAGAAATGACAGACTTTT 57.376 32.000 0.00 0.00 0.00 2.27
1991 2094 6.449635 AATTCATAAAACCGCAGATAAGCA 57.550 33.333 0.00 0.00 0.00 3.91
2036 2140 9.194271 CTAAGAACCTAACTGTGTAAGAGAAAC 57.806 37.037 0.00 0.00 0.00 2.78
2138 2249 1.792949 GTCAACAGGTAACAGAGCACG 59.207 52.381 0.00 0.00 41.41 5.34
2139 2250 2.802816 CAGTCAACAGGTAACAGAGCAC 59.197 50.000 0.00 0.00 41.41 4.40
2184 2296 6.072286 GCAATGATGTAAGACATGGGGAATAG 60.072 42.308 0.00 0.00 39.27 1.73
2185 2297 5.769662 GCAATGATGTAAGACATGGGGAATA 59.230 40.000 0.00 0.00 39.27 1.75
2186 2298 4.586001 GCAATGATGTAAGACATGGGGAAT 59.414 41.667 0.00 0.00 39.27 3.01
2187 2299 3.953612 GCAATGATGTAAGACATGGGGAA 59.046 43.478 0.00 0.00 39.27 3.97
2189 2301 3.289836 TGCAATGATGTAAGACATGGGG 58.710 45.455 0.00 0.00 39.27 4.96
2190 2302 4.987408 TTGCAATGATGTAAGACATGGG 57.013 40.909 0.00 0.00 39.27 4.00
2256 2448 7.361286 CCTGTGAAAAGATACTAAGCAAACTCC 60.361 40.741 0.00 0.00 0.00 3.85
2391 2583 5.480073 AGCACATTTAAAAGCATTAGGTCCA 59.520 36.000 11.57 0.00 0.00 4.02
2392 2584 5.965922 AGCACATTTAAAAGCATTAGGTCC 58.034 37.500 11.57 0.00 0.00 4.46
2395 2587 8.229811 GGAAAAAGCACATTTAAAAGCATTAGG 58.770 33.333 11.57 0.00 0.00 2.69
2419 2611 4.593206 AGAAAGGTTCACACTGAGTATGGA 59.407 41.667 0.00 0.00 0.00 3.41
2599 2791 5.397142 AAAAAGCAGGCCAAAGAATAGAG 57.603 39.130 5.01 0.00 0.00 2.43
2716 2911 6.851222 ATGTTATGTAGCAGTGTAGATTGC 57.149 37.500 0.00 0.00 40.57 3.56
2772 2967 9.559958 CACACAAAGTATTATTTCCATTGAGTC 57.440 33.333 0.00 0.00 0.00 3.36
2792 2988 3.073798 ACAGACCATAATGGACCACACAA 59.926 43.478 0.00 0.00 40.96 3.33
2799 2995 5.368145 TGCATCTAACAGACCATAATGGAC 58.632 41.667 0.00 0.00 40.96 4.02
2865 3061 1.137282 GGGAAGCAGGAGTACTACAGC 59.863 57.143 14.41 14.41 0.00 4.40
2935 3132 2.224314 GGTTGCAACAGAACTAGAGTGC 59.776 50.000 29.55 4.98 0.00 4.40
2958 3155 4.227982 TGGATTGAGGGACATTCAGATGAA 59.772 41.667 0.00 0.00 36.73 2.57
2980 3177 7.265673 ACATACACATTTACAGGCTACTACTG 58.734 38.462 0.00 0.00 41.64 2.74
3091 3288 6.331369 TCCAGGCAAACTAAGAATGAAAAG 57.669 37.500 0.00 0.00 0.00 2.27
3289 3486 8.640063 TGATACAACTCCACTTGTACTAAGTA 57.360 34.615 9.43 0.00 39.00 2.24
3301 3498 3.074412 CACCCACTTGATACAACTCCAC 58.926 50.000 0.00 0.00 0.00 4.02
3303 3500 3.244422 TGACACCCACTTGATACAACTCC 60.244 47.826 0.00 0.00 0.00 3.85
3304 3501 4.002906 TGACACCCACTTGATACAACTC 57.997 45.455 0.00 0.00 0.00 3.01
3392 3599 1.607148 GTAAAGGACCACCACAAGCAC 59.393 52.381 0.00 0.00 38.94 4.40
3432 3639 4.177026 AGTCATAACTTCAGTAAGCTGCG 58.823 43.478 0.00 0.00 42.29 5.18
3636 3843 4.889995 CCTTCATTTTCTCCATAAGGGACC 59.110 45.833 0.00 0.00 42.15 4.46
3682 3889 6.816640 GTGTCATTAAGCTGTTGTAGGACATA 59.183 38.462 0.00 0.00 35.51 2.29
3766 3973 5.563876 AGACATCAGGCAATACATCATCT 57.436 39.130 0.00 0.00 0.00 2.90
3829 4036 4.235372 CCCTCTCAACCCCTAATATGTCT 58.765 47.826 0.00 0.00 0.00 3.41
3844 4051 4.161189 GTCATCTCTTCAATCACCCTCTCA 59.839 45.833 0.00 0.00 0.00 3.27
3993 4200 3.618690 ACTGGTAGGCTTCAAGATCAC 57.381 47.619 2.13 0.00 0.00 3.06
4135 4343 0.729690 GCAGATCCTTCAAGTTCGCC 59.270 55.000 0.00 0.00 0.00 5.54
4195 4403 4.340381 GCTTTAGTCTTAGGTGGACGGATA 59.660 45.833 0.00 0.00 38.58 2.59
4567 5101 3.286694 ATGTGGCGGCACCCAGATT 62.287 57.895 35.54 13.18 35.52 2.40
4588 5122 1.625315 CCCATCAAGGTCTCAGTCACA 59.375 52.381 0.00 0.00 34.66 3.58
4594 5128 2.254152 AGTAGCCCATCAAGGTCTCA 57.746 50.000 0.00 0.00 34.66 3.27
4669 5203 1.280421 GTCCCCAGATCTTTCTGCACT 59.720 52.381 0.00 0.00 46.76 4.40
4878 5412 8.885494 AAACAGCAAAAACAATTTAGAGCATA 57.115 26.923 0.00 0.00 0.00 3.14
4886 5420 7.022979 GCAGAAGAAAACAGCAAAAACAATTT 58.977 30.769 0.00 0.00 0.00 1.82
4891 5427 5.529014 TTGCAGAAGAAAACAGCAAAAAC 57.471 34.783 0.00 0.00 41.65 2.43
4938 6094 2.420722 TGGCGAACCGAAATAAATGTCC 59.579 45.455 0.00 0.00 39.70 4.02
5156 6978 0.320073 TTACCGAAGACAAGGCCACG 60.320 55.000 5.01 0.00 0.00 4.94
5158 6980 1.695242 TCTTTACCGAAGACAAGGCCA 59.305 47.619 5.01 0.00 39.44 5.36
5159 6981 2.467566 TCTTTACCGAAGACAAGGCC 57.532 50.000 0.00 0.00 39.44 5.19
5170 6992 5.928839 AGCATGTATAGCTCATTCTTTACCG 59.071 40.000 0.00 0.00 38.01 4.02
5224 7046 2.636768 TGCAGTCAGATACTCACACG 57.363 50.000 0.00 0.00 35.76 4.49
5233 7055 3.370840 TTAAGGGCATTGCAGTCAGAT 57.629 42.857 11.39 0.00 0.00 2.90
5283 7105 8.486210 ACCATGTATAATTCAGAGTAGCAAAGA 58.514 33.333 0.00 0.00 0.00 2.52
5334 7164 3.323115 AGAGTCTCACAGATGCACTTTCA 59.677 43.478 1.94 0.00 0.00 2.69
5391 7221 4.082408 ACAATGCCACAGATCTTCACAATG 60.082 41.667 0.00 0.00 0.00 2.82
5394 7224 3.144657 ACAATGCCACAGATCTTCACA 57.855 42.857 0.00 0.00 0.00 3.58
5395 7225 5.824904 ATAACAATGCCACAGATCTTCAC 57.175 39.130 0.00 0.00 0.00 3.18
5396 7226 5.393352 GCAATAACAATGCCACAGATCTTCA 60.393 40.000 0.00 0.00 37.85 3.02
5397 7227 5.039333 GCAATAACAATGCCACAGATCTTC 58.961 41.667 0.00 0.00 37.85 2.87
5398 7228 4.463539 TGCAATAACAATGCCACAGATCTT 59.536 37.500 0.00 0.00 43.16 2.40
5400 7230 4.374843 TGCAATAACAATGCCACAGATC 57.625 40.909 0.00 0.00 43.16 2.75
5402 7232 3.305950 GGTTGCAATAACAATGCCACAGA 60.306 43.478 0.59 0.00 43.16 3.41
5405 7235 3.037431 TGGTTGCAATAACAATGCCAC 57.963 42.857 0.59 0.00 43.16 5.01
5408 7238 7.188157 CCAAATAATGGTTGCAATAACAATGC 58.812 34.615 0.59 0.00 44.85 3.56
5473 7642 2.094182 TCCGTCCACTTGTAATCTCTGC 60.094 50.000 0.00 0.00 0.00 4.26
5475 7644 3.769844 ACATCCGTCCACTTGTAATCTCT 59.230 43.478 0.00 0.00 0.00 3.10
5527 7696 2.158813 TCCCTGCTCAACGAGAAAAAGT 60.159 45.455 0.00 0.00 0.00 2.66
5531 7700 2.859165 ATTCCCTGCTCAACGAGAAA 57.141 45.000 0.00 0.00 0.00 2.52
5532 7701 2.418746 GCTATTCCCTGCTCAACGAGAA 60.419 50.000 0.00 0.00 0.00 2.87
5533 7702 1.137086 GCTATTCCCTGCTCAACGAGA 59.863 52.381 0.00 0.00 0.00 4.04
5551 7720 3.181497 GCGTGTTGATCATTTATGTGGCT 60.181 43.478 0.00 0.00 0.00 4.75
5558 7727 4.323417 AGTCCAAGCGTGTTGATCATTTA 58.677 39.130 0.00 0.00 0.00 1.40
5623 7792 3.429547 GGAGATAGAAGCAGCAGTCGAAA 60.430 47.826 0.00 0.00 0.00 3.46
5628 7797 2.430332 GTGAGGAGATAGAAGCAGCAGT 59.570 50.000 0.00 0.00 0.00 4.40
5629 7798 2.224018 GGTGAGGAGATAGAAGCAGCAG 60.224 54.545 0.00 0.00 0.00 4.24
5630 7799 1.759445 GGTGAGGAGATAGAAGCAGCA 59.241 52.381 0.00 0.00 0.00 4.41
5631 7800 1.759445 TGGTGAGGAGATAGAAGCAGC 59.241 52.381 0.00 0.00 0.00 5.25
5674 7860 9.211485 CTGATGAAAACTAAATTCAGGCAAAAT 57.789 29.630 0.00 0.00 39.92 1.82
5675 7861 7.171337 GCTGATGAAAACTAAATTCAGGCAAAA 59.829 33.333 0.00 0.00 39.92 2.44
5686 7872 5.538053 TGGGTGAATGCTGATGAAAACTAAA 59.462 36.000 0.00 0.00 0.00 1.85
5748 7946 9.511144 GTTATATGGTTGTTAGTAATGCCAAAC 57.489 33.333 6.99 1.39 0.00 2.93
5770 7968 6.215636 ACTCCTACCCATCTGAAACAAGTTAT 59.784 38.462 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.