Multiple sequence alignment - TraesCS1D01G219400

Loading Multiple Alignment...

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 TraesCS1D01G219400 chr1D 100.000 5501 0 0 1 5501 307212225 307217725 0.000000e+00 10159.0
1 TraesCS1D01G219400 chr1B 92.198 2948 152 39 570 3465 414798137 414801058 0.000000e+00 4098.0
2 TraesCS1D01G219400 chr1B 92.940 1119 45 14 3784 4892 414801398 414802492 0.000000e+00 1598.0
3 TraesCS1D01G219400 chr1B 92.407 619 29 9 4894 5501 414805968 414806579 0.000000e+00 867.0
4 TraesCS1D01G219400 chr1B 92.500 40 2 1 3702 3741 45477927 45477965 7.700000e-04 56.5
5 TraesCS1D01G219400 chr1A 92.239 1572 86 15 962 2524 385656937 385658481 0.000000e+00 2194.0
6 TraesCS1D01G219400 chr1A 89.662 977 43 19 3597 4538 385659392 385660345 0.000000e+00 1192.0
7 TraesCS1D01G219400 chr1A 85.512 918 77 32 80 965 385655761 385656654 0.000000e+00 907.0
8 TraesCS1D01G219400 chr1A 93.494 538 31 4 4962 5498 385660471 385661005 0.000000e+00 797.0
9 TraesCS1D01G219400 chr1A 92.494 453 28 6 2894 3341 385658682 385659133 1.290000e-180 643.0
10 TraesCS1D01G219400 chr1A 92.308 104 5 2 4875 4975 385660354 385660457 1.600000e-30 145.0
11 TraesCS1D01G219400 chr1A 93.506 77 4 1 3340 3415 385659284 385659360 4.500000e-21 113.0
12 TraesCS1D01G219400 chr1A 84.112 107 7 3 2538 2643 385658590 385658493 1.630000e-15 95.3
13 TraesCS1D01G219400 chr1A 84.000 75 9 2 3667 3741 3790904 3790975 9.890000e-08 69.4
14 TraesCS1D01G219400 chr1A 100.000 28 0 0 3714 3741 6913504 6913477 1.000000e-02 52.8
15 TraesCS1D01G219400 chr6A 87.755 294 24 11 283 567 448651583 448651873 3.180000e-87 333.0
16 TraesCS1D01G219400 chr6A 89.219 269 23 6 301 566 421525105 421524840 1.140000e-86 331.0
17 TraesCS1D01G219400 chr6A 97.531 81 2 0 1 81 521479239 521479319 7.430000e-29 139.0
18 TraesCS1D01G219400 chr6A 97.531 81 2 0 1 81 596368716 596368796 7.430000e-29 139.0
19 TraesCS1D01G219400 chr5A 88.930 271 28 2 291 560 597832021 597832290 3.180000e-87 333.0
20 TraesCS1D01G219400 chr5A 88.192 271 29 3 292 561 603918583 603918315 2.470000e-83 320.0
21 TraesCS1D01G219400 chr5A 96.512 86 3 0 1 86 613408419 613408334 5.740000e-30 143.0
22 TraesCS1D01G219400 chr7A 89.695 262 24 3 301 560 350634801 350634541 1.140000e-86 331.0
23 TraesCS1D01G219400 chr7A 89.313 262 24 4 301 560 515222311 515222570 5.310000e-85 326.0
24 TraesCS1D01G219400 chr7A 97.590 83 2 0 1 83 263504056 263504138 5.740000e-30 143.0
25 TraesCS1D01G219400 chr7A 96.471 85 3 0 1 85 252742556 252742472 2.070000e-29 141.0
26 TraesCS1D01G219400 chr7A 97.561 82 2 0 1 82 718311847 718311928 2.070000e-29 141.0
27 TraesCS1D01G219400 chr2A 88.973 263 28 1 301 562 699241114 699240852 1.910000e-84 324.0
28 TraesCS1D01G219400 chr2A 88.136 118 9 4 1 115 77173321 77173206 9.610000e-28 135.0
29 TraesCS1D01G219400 chr5B 88.433 268 29 2 300 565 428579805 428579538 6.870000e-84 322.0
30 TraesCS1D01G219400 chr7D 97.561 82 2 0 1 82 439780696 439780777 2.070000e-29 141.0
31 TraesCS1D01G219400 chr2D 96.296 81 3 0 1 81 134786446 134786526 3.460000e-27 134.0
32 TraesCS1D01G219400 chr2D 82.178 101 16 2 3664 3764 5553575 5553673 9.820000e-13 86.1
33 TraesCS1D01G219400 chr6B 89.855 69 5 2 3706 3772 532385264 532385196 2.730000e-13 87.9
34 TraesCS1D01G219400 chr6D 90.769 65 5 1 3708 3772 402134745 402134808 9.820000e-13 86.1
35 TraesCS1D01G219400 chr6D 92.500 40 2 1 3702 3741 139418337 139418375 7.700000e-04 56.5
36 TraesCS1D01G219400 chr4A 88.679 53 6 0 3713 3765 19952393 19952445 1.280000e-06 65.8
37 TraesCS1D01G219400 chr4A 88.679 53 6 0 3713 3765 20001213 20001265 1.280000e-06 65.8
38 TraesCS1D01G219400 chr4A 84.058 69 9 2 3706 3772 731086752 731086684 1.280000e-06 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 TraesCS1D01G219400 chr1D 307212225 307217725 5500 False 10159.000000 10159 100.000000 1 5501 1 chr1D.!!$F1 5500
1 TraesCS1D01G219400 chr1B 414798137 414806579 8442 False 2187.666667 4098 92.515000 570 5501 3 chr1B.!!$F2 4931
2 TraesCS1D01G219400 chr1A 385655761 385661005 5244 False 855.857143 2194 91.316429 80 5498 7 chr1A.!!$F2 5418

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
803 836 0.320697 GTCTCCCTTTGTACGCTGGT 59.679 55.0 0.00 0.0 0.00 4.00 F
1080 1413 0.772124 TCCTCCACCTTTTCCTGGCT 60.772 55.0 0.00 0.0 0.00 4.75 F
2264 2609 0.331278 TTTGGGGACAGGATGCGAAT 59.669 50.0 0.00 0.0 44.54 3.34 F
2432 2777 0.478072 AGAAATGGGTGACTGGTGCA 59.522 50.0 0.00 0.0 0.00 4.57 F
2447 2792 0.819582 GTGCATTTGCTGGGCATACT 59.180 50.0 3.94 0.0 38.76 2.12 F
3193 3569 1.640917 TTGCTCCCTAGTCCTTTCGT 58.359 50.0 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 2285 0.608640 CCCATCCTATCCTGTACGGC 59.391 60.0 0.0 0.00 0.00 5.68 R
2301 2646 0.947244 CAAGGCTGAGAACGCTTGTT 59.053 50.0 0.0 0.00 38.91 2.83 R
3457 3991 0.102481 ATCCGTAGCTTACAGCACCG 59.898 55.0 0.0 0.00 45.56 4.94 R
4010 4722 0.748729 TCGCTGATGATGCCATGCAA 60.749 50.0 0.0 0.00 43.62 4.08 R
4246 4958 0.829333 ACTTGATCAGCCGAGCAGAT 59.171 50.0 0.0 3.99 39.09 2.90 R
5079 9309 0.037232 GGTTTCGAGTGAGTGAGGGG 60.037 60.0 0.0 0.00 0.00 4.79 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 8.840833 AAATTTGGTCAAACTTTGTGTAGTTT 57.159 26.923 1.44 0.00 46.42 2.66
33 34 8.474006 AATTTGGTCAAACTTTGTGTAGTTTC 57.526 30.769 1.44 0.00 44.33 2.78
34 35 6.576662 TTGGTCAAACTTTGTGTAGTTTCA 57.423 33.333 1.44 0.00 44.33 2.69
35 36 5.945155 TGGTCAAACTTTGTGTAGTTTCAC 58.055 37.500 1.44 0.00 44.33 3.18
36 37 5.708230 TGGTCAAACTTTGTGTAGTTTCACT 59.292 36.000 0.00 0.00 44.33 3.41
37 38 6.207810 TGGTCAAACTTTGTGTAGTTTCACTT 59.792 34.615 0.00 0.00 44.33 3.16
38 39 7.088272 GGTCAAACTTTGTGTAGTTTCACTTT 58.912 34.615 0.00 0.00 44.33 2.66
39 40 7.061789 GGTCAAACTTTGTGTAGTTTCACTTTG 59.938 37.037 0.00 0.00 44.33 2.77
40 41 7.806014 GTCAAACTTTGTGTAGTTTCACTTTGA 59.194 33.333 1.44 0.00 44.33 2.69
41 42 7.806014 TCAAACTTTGTGTAGTTTCACTTTGAC 59.194 33.333 1.44 0.00 44.33 3.18
42 43 6.190954 ACTTTGTGTAGTTTCACTTTGACC 57.809 37.500 0.00 0.00 38.90 4.02
43 44 5.708230 ACTTTGTGTAGTTTCACTTTGACCA 59.292 36.000 0.00 0.00 38.90 4.02
44 45 6.207810 ACTTTGTGTAGTTTCACTTTGACCAA 59.792 34.615 0.00 0.00 38.90 3.67
45 46 6.576662 TTGTGTAGTTTCACTTTGACCAAA 57.423 33.333 0.00 0.00 38.90 3.28
46 47 6.767524 TGTGTAGTTTCACTTTGACCAAAT 57.232 33.333 0.00 0.00 38.90 2.32
47 48 6.791303 TGTGTAGTTTCACTTTGACCAAATC 58.209 36.000 0.00 0.00 38.90 2.17
48 49 6.601613 TGTGTAGTTTCACTTTGACCAAATCT 59.398 34.615 0.00 0.00 38.90 2.40
49 50 7.122055 TGTGTAGTTTCACTTTGACCAAATCTT 59.878 33.333 0.00 0.00 38.90 2.40
50 51 8.617809 GTGTAGTTTCACTTTGACCAAATCTTA 58.382 33.333 0.00 0.00 35.68 2.10
51 52 9.349713 TGTAGTTTCACTTTGACCAAATCTTAT 57.650 29.630 0.00 0.00 0.00 1.73
55 56 9.076596 GTTTCACTTTGACCAAATCTTATATGC 57.923 33.333 0.00 0.00 0.00 3.14
56 57 7.936496 TCACTTTGACCAAATCTTATATGCA 57.064 32.000 0.00 0.00 0.00 3.96
57 58 8.347004 TCACTTTGACCAAATCTTATATGCAA 57.653 30.769 0.00 0.00 0.00 4.08
58 59 8.801299 TCACTTTGACCAAATCTTATATGCAAA 58.199 29.630 0.00 0.00 0.00 3.68
59 60 9.079833 CACTTTGACCAAATCTTATATGCAAAG 57.920 33.333 0.00 0.00 42.99 2.77
60 61 8.806146 ACTTTGACCAAATCTTATATGCAAAGT 58.194 29.630 0.00 0.00 44.45 2.66
72 73 9.834628 TCTTATATGCAAAGTAAAAAGAAACGG 57.165 29.630 0.00 0.00 0.00 4.44
73 74 9.834628 CTTATATGCAAAGTAAAAAGAAACGGA 57.165 29.630 0.00 0.00 0.00 4.69
74 75 9.834628 TTATATGCAAAGTAAAAAGAAACGGAG 57.165 29.630 0.00 0.00 0.00 4.63
75 76 4.927422 TGCAAAGTAAAAAGAAACGGAGG 58.073 39.130 0.00 0.00 0.00 4.30
76 77 4.202070 TGCAAAGTAAAAAGAAACGGAGGG 60.202 41.667 0.00 0.00 0.00 4.30
77 78 4.037089 GCAAAGTAAAAAGAAACGGAGGGA 59.963 41.667 0.00 0.00 0.00 4.20
78 79 5.758924 CAAAGTAAAAAGAAACGGAGGGAG 58.241 41.667 0.00 0.00 0.00 4.30
93 94 1.915489 AGGGAGTATGTCATGTTGCCA 59.085 47.619 10.25 0.00 0.00 4.92
100 101 5.423015 AGTATGTCATGTTGCCAGAGTAAG 58.577 41.667 0.00 0.00 0.00 2.34
103 104 4.318332 TGTCATGTTGCCAGAGTAAGAAG 58.682 43.478 0.00 0.00 0.00 2.85
143 145 1.740025 GCAGAAGAAAATCTGGGACCG 59.260 52.381 6.46 0.00 45.60 4.79
145 147 3.003480 CAGAAGAAAATCTGGGACCGAC 58.997 50.000 0.00 0.00 42.52 4.79
152 154 0.684805 ATCTGGGACCGACTGACCTC 60.685 60.000 0.00 0.00 0.00 3.85
156 158 2.567049 GACCGACTGACCTCCACG 59.433 66.667 0.00 0.00 0.00 4.94
165 167 4.566987 GACTGACCTCCACGATTAGTTTT 58.433 43.478 0.00 0.00 0.00 2.43
172 174 3.602483 TCCACGATTAGTTTTGTAGGCC 58.398 45.455 0.00 0.00 0.00 5.19
198 200 1.451567 TCGGTGGTTCGTTTTGGCA 60.452 52.632 0.00 0.00 0.00 4.92
216 218 1.587034 GCAGTAGTAATGGTCGTTCGC 59.413 52.381 0.00 0.00 0.00 4.70
220 222 0.739813 AGTAATGGTCGTTCGCTGGC 60.740 55.000 0.00 0.00 0.00 4.85
223 225 2.748058 AATGGTCGTTCGCTGGCCTT 62.748 55.000 3.32 0.00 0.00 4.35
225 227 1.375013 GGTCGTTCGCTGGCCTTAA 60.375 57.895 3.32 0.00 0.00 1.85
231 233 2.223044 CGTTCGCTGGCCTTAAAATCTC 60.223 50.000 3.32 0.00 0.00 2.75
272 274 3.374220 TGAGATGGTTTGTACGTTCGT 57.626 42.857 0.00 2.91 0.00 3.85
275 277 3.719924 AGATGGTTTGTACGTTCGTTGA 58.280 40.909 2.62 0.00 0.00 3.18
281 283 4.725280 GGTTTGTACGTTCGTTGAACTTTC 59.275 41.667 2.62 0.00 40.05 2.62
288 290 8.427012 TGTACGTTCGTTGAACTTTCATAATAC 58.573 33.333 2.62 0.00 40.05 1.89
291 293 8.500773 ACGTTCGTTGAACTTTCATAATACATT 58.499 29.630 7.95 0.00 40.05 2.71
324 326 8.728337 ATACTCCTTCGGTTTTTATTTAGACC 57.272 34.615 0.00 0.00 0.00 3.85
360 362 9.696917 CTTTGGTCAAAGTCAAGCTTTATAAAT 57.303 29.630 13.58 0.00 44.95 1.40
575 607 6.905776 AGAGGGAGTATATATATGGCAAAGCT 59.094 38.462 5.44 0.00 0.00 3.74
674 707 2.541178 CGAGGTCCGTTATAGCTGTGTC 60.541 54.545 0.00 0.00 0.00 3.67
675 708 1.755380 AGGTCCGTTATAGCTGTGTCC 59.245 52.381 0.00 0.00 0.00 4.02
676 709 1.755380 GGTCCGTTATAGCTGTGTCCT 59.245 52.381 0.00 0.00 0.00 3.85
677 710 2.954318 GGTCCGTTATAGCTGTGTCCTA 59.046 50.000 0.00 0.00 0.00 2.94
726 759 0.321122 CAAGCTTGAGTTCTCGCCCT 60.321 55.000 22.31 0.00 0.00 5.19
779 812 1.519751 CGGTCCAAAATTCCCGTGCA 61.520 55.000 0.00 0.00 35.78 4.57
780 813 0.894835 GGTCCAAAATTCCCGTGCAT 59.105 50.000 0.00 0.00 0.00 3.96
792 825 2.990479 GTGCATCCGGTCTCCCTT 59.010 61.111 0.00 0.00 0.00 3.95
803 836 0.320697 GTCTCCCTTTGTACGCTGGT 59.679 55.000 0.00 0.00 0.00 4.00
838 871 5.810587 AGAAAAAGGGAAGAAAAGAAAACGC 59.189 36.000 0.00 0.00 0.00 4.84
902 935 1.757682 AACAAACCACTGAGCCGAAA 58.242 45.000 0.00 0.00 0.00 3.46
972 1016 1.512926 CGCATAGATAAGTGGTGCCC 58.487 55.000 0.00 0.00 32.39 5.36
1060 1393 2.524394 TGCCTATCCTCCTCGCCC 60.524 66.667 0.00 0.00 0.00 6.13
1080 1413 0.772124 TCCTCCACCTTTTCCTGGCT 60.772 55.000 0.00 0.00 0.00 4.75
1272 1605 3.386237 GTCCTCAGCCTCACGCCT 61.386 66.667 0.00 0.00 38.78 5.52
1291 1624 2.112297 GTCCCCGTGGAAGCAACA 59.888 61.111 0.00 0.00 44.07 3.33
1347 1680 2.290896 CCTCAAGGTGCCCTTACATTGA 60.291 50.000 6.20 4.34 45.61 2.57
1419 1754 6.370593 TGATTAACTTCGACTTTGATGTTGC 58.629 36.000 7.64 0.00 37.00 4.17
1422 1757 4.630894 ACTTCGACTTTGATGTTGCAAA 57.369 36.364 0.00 0.00 36.43 3.68
1423 1758 4.992688 ACTTCGACTTTGATGTTGCAAAA 58.007 34.783 0.00 0.00 37.32 2.44
1424 1759 5.406649 ACTTCGACTTTGATGTTGCAAAAA 58.593 33.333 0.00 0.00 37.32 1.94
1499 1836 5.304686 TCGCATAGGATTCCCAGTATTTT 57.695 39.130 0.00 0.00 33.88 1.82
1509 1846 7.123247 AGGATTCCCAGTATTTTGTTCTCATTG 59.877 37.037 0.00 0.00 33.88 2.82
1555 1898 4.939439 TGTCTTCATGTGAATGTGATCCAG 59.061 41.667 0.00 0.00 33.01 3.86
1558 1901 3.877559 TCATGTGAATGTGATCCAGACC 58.122 45.455 0.00 0.00 0.00 3.85
1572 1915 2.894765 TCCAGACCAGACATACGACAAA 59.105 45.455 0.00 0.00 0.00 2.83
1590 1933 8.161699 ACGACAAAGGCTAAAAATAGAAAAGA 57.838 30.769 0.00 0.00 0.00 2.52
1617 1960 5.116069 TGATTCCCACGAAAACTAAAAGC 57.884 39.130 0.00 0.00 0.00 3.51
1699 2042 5.404366 CACGGGTTATATCATTCGTTAGTGG 59.596 44.000 0.00 0.00 0.00 4.00
1747 2090 4.550395 GCCAAATTGCGAGCGAAA 57.450 50.000 0.00 0.00 0.00 3.46
1796 2139 2.548707 GGACGATTAGAGGCATGCATGA 60.549 50.000 30.64 8.50 0.00 3.07
1842 2185 6.235231 TCATTTACTGAACCATAGTCCCTC 57.765 41.667 0.00 0.00 0.00 4.30
1937 2282 3.631686 GCATGGACCTGTATGTATTTGCA 59.368 43.478 0.00 0.00 0.00 4.08
1940 2285 3.687212 TGGACCTGTATGTATTTGCAACG 59.313 43.478 0.00 0.00 0.00 4.10
2009 2354 4.063689 CCTTCGAGATCAAATCATGGGAG 58.936 47.826 0.00 0.00 0.00 4.30
2037 2382 5.527582 GCAGGAGAAATGGAATATGTACGTT 59.472 40.000 0.00 0.00 0.00 3.99
2078 2423 6.294231 GGTTGTTTTCAGATTTCTCCTCCTTC 60.294 42.308 0.00 0.00 0.00 3.46
2106 2451 4.743151 GGCCACTTGTTAGTTTTGCTTTAC 59.257 41.667 0.00 0.00 30.26 2.01
2198 2543 2.974698 CCATCCGGAATGCTCGGC 60.975 66.667 9.01 0.00 46.43 5.54
2258 2603 1.084018 ACACCATTTGGGGACAGGAT 58.916 50.000 5.70 0.00 42.67 3.24
2261 2606 1.386525 CCATTTGGGGACAGGATGCG 61.387 60.000 0.00 0.00 44.54 4.73
2264 2609 0.331278 TTTGGGGACAGGATGCGAAT 59.669 50.000 0.00 0.00 44.54 3.34
2301 2646 1.006998 AGCACATGGGGGCTTCATTTA 59.993 47.619 0.00 0.00 36.92 1.40
2303 2648 2.418609 GCACATGGGGGCTTCATTTAAC 60.419 50.000 0.00 0.00 0.00 2.01
2335 2680 0.611618 CCTTGGGCTGCCAACATACA 60.612 55.000 22.05 4.88 0.00 2.29
2432 2777 0.478072 AGAAATGGGTGACTGGTGCA 59.522 50.000 0.00 0.00 0.00 4.57
2447 2792 0.819582 GTGCATTTGCTGGGCATACT 59.180 50.000 3.94 0.00 38.76 2.12
2477 2822 2.542020 TGAAAGATGAGAACGGCACA 57.458 45.000 0.00 0.00 0.00 4.57
2480 2825 3.006430 TGAAAGATGAGAACGGCACACTA 59.994 43.478 0.00 0.00 0.00 2.74
2518 2863 8.098220 TCAGGTTACGAAAATAAAAAGGTACC 57.902 34.615 2.73 2.73 0.00 3.34
2536 2881 4.218417 GGTACCACATGCAATCTCTTGTTT 59.782 41.667 7.15 0.00 34.69 2.83
2614 2960 9.621629 AATTAGGAAAATAATACGACATGACCA 57.378 29.630 0.00 0.00 0.00 4.02
2615 2961 9.621629 ATTAGGAAAATAATACGACATGACCAA 57.378 29.630 0.00 0.00 0.00 3.67
2616 2962 7.931578 AGGAAAATAATACGACATGACCAAA 57.068 32.000 0.00 0.00 0.00 3.28
2617 2963 8.519799 AGGAAAATAATACGACATGACCAAAT 57.480 30.769 0.00 0.00 0.00 2.32
2618 2964 9.621629 AGGAAAATAATACGACATGACCAAATA 57.378 29.630 0.00 0.00 0.00 1.40
2619 2965 9.659830 GGAAAATAATACGACATGACCAAATAC 57.340 33.333 0.00 0.00 0.00 1.89
2700 3050 3.814945 GCATAGGCGAAAAGTCATATGC 58.185 45.455 0.00 3.68 35.82 3.14
2723 3073 5.351740 GCTATCCACTGGAACAAAGAACTAC 59.648 44.000 0.66 0.00 38.70 2.73
2876 3228 7.090173 CGTTGGGTCAAATCTATGAATTGTTT 58.910 34.615 0.00 0.00 0.00 2.83
2893 3245 8.750416 TGAATTGTTTTGTGAACATTGATAACG 58.250 29.630 0.00 0.00 0.00 3.18
2894 3246 8.641499 AATTGTTTTGTGAACATTGATAACGT 57.359 26.923 0.00 0.00 0.00 3.99
2914 3290 4.521256 ACGTTGGCTTTATGTGGTACAATT 59.479 37.500 0.00 0.00 44.16 2.32
3027 3403 2.383245 CTTGCACCCTGACGTGAGGT 62.383 60.000 20.16 7.61 35.68 3.85
3140 3516 7.504924 TGATACAATGTCGGAAAATTATCCC 57.495 36.000 0.00 0.00 36.00 3.85
3149 3525 3.372675 CGGAAAATTATCCCCCACCTCTT 60.373 47.826 0.00 0.00 36.00 2.85
3166 3542 5.070446 CACCTCTTGATGCTAACCTGGTATA 59.930 44.000 0.00 0.00 0.00 1.47
3180 3556 4.042187 ACCTGGTATAATCTCCATTGCTCC 59.958 45.833 0.00 0.00 33.01 4.70
3193 3569 1.640917 TTGCTCCCTAGTCCTTTCGT 58.359 50.000 0.00 0.00 0.00 3.85
3284 3663 6.238484 GCTGTTATCTTCATTCATGTGGGTAC 60.238 42.308 0.00 0.00 0.00 3.34
3297 3677 3.887352 TGTGGGTACTTTGCACTAACAA 58.113 40.909 0.00 0.00 0.00 2.83
3383 3916 7.390162 TGAAAGTGTATGTGCATTCTATGTTGA 59.610 33.333 0.00 0.00 0.00 3.18
3459 3993 7.581476 TCTAATCTTTTGAGTAAACTTTGCGG 58.419 34.615 0.00 0.00 0.00 5.69
3496 4075 2.054799 TGCACAGGTCCTCCTAAACTT 58.945 47.619 0.00 0.00 43.07 2.66
3511 4090 2.191128 AACTTGTTCAGGCTAGGCTG 57.809 50.000 34.38 34.38 0.00 4.85
3525 4104 4.276926 GGCTAGGCTGAAATTACCTTCATG 59.723 45.833 9.46 0.00 34.86 3.07
3533 4112 8.470002 GGCTGAAATTACCTTCATGACTTTAAT 58.530 33.333 0.00 0.00 34.86 1.40
3534 4113 9.860898 GCTGAAATTACCTTCATGACTTTAATT 57.139 29.630 0.00 2.12 34.86 1.40
3598 4177 7.676683 ATACTTTCCCTATTCTACTTGCTGA 57.323 36.000 0.00 0.00 0.00 4.26
3599 4178 6.567602 ACTTTCCCTATTCTACTTGCTGAT 57.432 37.500 0.00 0.00 0.00 2.90
3600 4179 7.676683 ACTTTCCCTATTCTACTTGCTGATA 57.323 36.000 0.00 0.00 0.00 2.15
3601 4180 8.090788 ACTTTCCCTATTCTACTTGCTGATAA 57.909 34.615 0.00 0.00 0.00 1.75
3602 4181 8.718656 ACTTTCCCTATTCTACTTGCTGATAAT 58.281 33.333 0.00 0.00 0.00 1.28
3605 4184 7.841956 TCCCTATTCTACTTGCTGATAATAGC 58.158 38.462 0.00 0.00 43.95 2.97
3606 4185 7.676043 TCCCTATTCTACTTGCTGATAATAGCT 59.324 37.037 0.00 0.00 44.01 3.32
3607 4186 7.978975 CCCTATTCTACTTGCTGATAATAGCTC 59.021 40.741 0.00 0.00 44.01 4.09
3628 4207 5.523916 GCTCTTTAGAACGCTTGATTCCATA 59.476 40.000 0.00 0.00 0.00 2.74
3629 4208 6.510317 GCTCTTTAGAACGCTTGATTCCATAC 60.510 42.308 0.00 0.00 0.00 2.39
3631 4210 3.247006 AGAACGCTTGATTCCATACGT 57.753 42.857 0.00 0.00 36.27 3.57
3632 4211 3.187700 AGAACGCTTGATTCCATACGTC 58.812 45.455 0.00 0.00 34.50 4.34
3652 4342 4.304110 GTCGTCTTCTGTCATGTTGGTTA 58.696 43.478 0.00 0.00 0.00 2.85
3654 4344 4.055360 CGTCTTCTGTCATGTTGGTTACA 58.945 43.478 0.00 0.00 41.97 2.41
3666 4356 6.597672 TCATGTTGGTTACATCTGTTCATACC 59.402 38.462 0.00 0.00 45.71 2.73
3680 4370 2.773487 TCATACCCGTGGTTGTCTTTG 58.227 47.619 0.72 0.00 37.09 2.77
3684 4374 1.746787 ACCCGTGGTTGTCTTTGTTTC 59.253 47.619 0.00 0.00 27.29 2.78
3701 4391 8.038944 TCTTTGTTTCGTACTCTGCCTAATAAT 58.961 33.333 0.00 0.00 0.00 1.28
3704 4396 8.638685 TGTTTCGTACTCTGCCTAATAATTAC 57.361 34.615 0.00 0.00 0.00 1.89
3728 4426 5.981088 AATAAAGATGGTTGTGTGCATCA 57.019 34.783 0.00 0.00 0.00 3.07
3905 4617 5.411669 GGACTGAGGTTGTTATAACCAACTG 59.588 44.000 11.74 11.71 42.69 3.16
3958 4670 4.346418 ACAGAGGACTGAGAAATTGACAGT 59.654 41.667 10.69 10.69 46.03 3.55
3964 4676 7.379750 AGGACTGAGAAATTGACAGTAAGTAC 58.620 38.462 10.81 0.00 43.49 2.73
3965 4677 7.233757 AGGACTGAGAAATTGACAGTAAGTACT 59.766 37.037 10.81 0.00 43.49 2.73
3966 4678 8.521176 GGACTGAGAAATTGACAGTAAGTACTA 58.479 37.037 0.00 0.00 43.49 1.82
3985 4697 8.358582 AGTACTATATGATGATGATGTGCTCA 57.641 34.615 0.00 0.00 38.53 4.26
3993 4705 3.346315 TGATGATGTGCTCAATTCCGTT 58.654 40.909 0.00 0.00 37.44 4.44
4010 4722 2.124903 CGTTCGTGTAGCAACTTGACT 58.875 47.619 0.00 0.00 0.00 3.41
4138 4850 2.956964 GTCGCCTTCATCCTCGCG 60.957 66.667 0.00 0.00 45.76 5.87
4153 4865 2.511600 GCGATGTACAAGGCGGCT 60.512 61.111 5.25 5.25 0.00 5.52
4241 4953 2.281970 CAGTCAAGCTGCCTGCCA 60.282 61.111 0.00 0.00 44.23 4.92
4246 4958 1.545582 GTCAAGCTGCCTGCCATTTTA 59.454 47.619 0.00 0.00 44.23 1.52
4248 4960 2.428171 TCAAGCTGCCTGCCATTTTATC 59.572 45.455 0.00 0.00 44.23 1.75
4249 4961 2.429610 CAAGCTGCCTGCCATTTTATCT 59.570 45.455 0.00 0.00 44.23 1.98
4250 4962 2.029623 AGCTGCCTGCCATTTTATCTG 58.970 47.619 0.00 0.00 44.23 2.90
4273 4994 0.108945 GGCTGATCAAGTGCTTTGCC 60.109 55.000 0.00 0.00 36.70 4.52
4434 5158 0.328258 AGTACAACACCATCCAGCCC 59.672 55.000 0.00 0.00 0.00 5.19
4510 5234 0.590195 GCGCTGTTGATCATGGATCC 59.410 55.000 4.20 4.20 38.20 3.36
4546 5270 6.955963 CGTCGAAAGGAAAGATGATTTTACAG 59.044 38.462 0.00 0.00 0.00 2.74
4578 5302 4.634004 CCTGTGCAATCAATTAGGACGTAA 59.366 41.667 0.00 0.00 0.00 3.18
4579 5303 5.123186 CCTGTGCAATCAATTAGGACGTAAA 59.877 40.000 0.00 0.00 0.00 2.01
4580 5304 6.183360 CCTGTGCAATCAATTAGGACGTAAAT 60.183 38.462 0.00 0.00 0.00 1.40
4581 5305 7.011950 CCTGTGCAATCAATTAGGACGTAAATA 59.988 37.037 0.00 0.00 0.00 1.40
4582 5306 7.915508 TGTGCAATCAATTAGGACGTAAATAG 58.084 34.615 0.00 0.00 0.00 1.73
4583 5307 7.766738 TGTGCAATCAATTAGGACGTAAATAGA 59.233 33.333 0.00 0.00 0.00 1.98
4584 5308 8.062448 GTGCAATCAATTAGGACGTAAATAGAC 58.938 37.037 0.00 0.00 0.00 2.59
4586 5310 7.225931 GCAATCAATTAGGACGTAAATAGACCA 59.774 37.037 0.00 0.00 0.00 4.02
4588 5312 6.267817 TCAATTAGGACGTAAATAGACCACG 58.732 40.000 0.00 0.00 41.32 4.94
4593 5317 2.785679 ACGTAAATAGACCACGTACGC 58.214 47.619 16.72 0.00 46.23 4.42
4594 5318 2.420022 ACGTAAATAGACCACGTACGCT 59.580 45.455 16.72 6.78 46.23 5.07
4595 5319 3.119849 ACGTAAATAGACCACGTACGCTT 60.120 43.478 16.72 0.00 46.23 4.68
4596 5320 3.853671 CGTAAATAGACCACGTACGCTTT 59.146 43.478 16.72 0.00 32.18 3.51
4597 5321 4.324402 CGTAAATAGACCACGTACGCTTTT 59.676 41.667 16.72 9.64 32.18 2.27
4598 5322 5.511377 CGTAAATAGACCACGTACGCTTTTA 59.489 40.000 16.72 8.83 32.18 1.52
4599 5323 5.768333 AAATAGACCACGTACGCTTTTAC 57.232 39.130 16.72 2.51 0.00 2.01
4600 5324 4.708726 ATAGACCACGTACGCTTTTACT 57.291 40.909 16.72 9.93 0.00 2.24
4601 5325 2.938869 AGACCACGTACGCTTTTACTC 58.061 47.619 16.72 0.57 0.00 2.59
4602 5326 1.988467 GACCACGTACGCTTTTACTCC 59.012 52.381 16.72 0.00 0.00 3.85
4603 5327 1.340889 ACCACGTACGCTTTTACTCCA 59.659 47.619 16.72 0.00 0.00 3.86
4621 5345 1.600663 CCACATCGTACGCTCTCATCC 60.601 57.143 11.24 0.00 0.00 3.51
4708 5435 9.893634 TTCTTTATAATCTTTAACACGGATGGA 57.106 29.630 0.00 0.00 0.00 3.41
4711 5438 8.615878 TTATAATCTTTAACACGGATGGATGG 57.384 34.615 0.00 0.00 0.00 3.51
4753 5480 6.434018 ACCCAAAATGTGATGTTTTGTTTG 57.566 33.333 9.60 0.00 42.25 2.93
4833 5560 1.144057 CCATTCGTCTCCTTCCCCG 59.856 63.158 0.00 0.00 0.00 5.73
4894 5621 4.183865 CGTCATCTTGCACTGAGGATTTA 58.816 43.478 6.54 0.00 30.74 1.40
4896 5623 5.277202 CGTCATCTTGCACTGAGGATTTATG 60.277 44.000 6.54 0.00 30.74 1.90
5060 9290 4.627058 TGATCGCATCCGCTCTATAAAAA 58.373 39.130 0.00 0.00 35.30 1.94
5061 9291 4.447724 TGATCGCATCCGCTCTATAAAAAC 59.552 41.667 0.00 0.00 35.30 2.43
5079 9309 1.215647 CGAGTACCTCCACAGCACC 59.784 63.158 0.00 0.00 0.00 5.01
5140 9377 2.046892 CTCGGCCACAGGAACCAG 60.047 66.667 2.24 0.00 0.00 4.00
5231 9468 1.171549 TCTCGCACAGGCATTGCAAA 61.172 50.000 11.39 0.00 40.20 3.68
5233 9470 2.366584 CGCACAGGCATTGCAAACG 61.367 57.895 11.39 0.00 40.20 3.60
5234 9471 1.007502 GCACAGGCATTGCAAACGA 60.008 52.632 11.39 0.00 39.93 3.85
5243 9480 0.743688 ATTGCAAACGACCAGCACAA 59.256 45.000 1.71 0.00 38.11 3.33
5353 9591 0.393402 ATCATGCACATGCGTCTGGT 60.393 50.000 5.73 0.00 45.83 4.00
5424 9664 1.340889 TGTGTCTGCAAATTTCAGGCC 59.659 47.619 15.16 0.00 35.43 5.19
5441 9681 6.036577 TCAGGCCAAATTTCCTAAATTGAC 57.963 37.500 5.01 0.00 40.05 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.930693 AAACTACACAAAGTTTGACCAAATTTA 57.069 25.926 22.23 0.00 45.60 1.40
7 8 8.840833 AAACTACACAAAGTTTGACCAAATTT 57.159 26.923 22.23 11.30 45.60 1.82
8 9 8.091449 TGAAACTACACAAAGTTTGACCAAATT 58.909 29.630 22.23 9.70 46.92 1.82
9 10 7.544217 GTGAAACTACACAAAGTTTGACCAAAT 59.456 33.333 22.23 2.84 46.92 2.32
10 11 6.864165 GTGAAACTACACAAAGTTTGACCAAA 59.136 34.615 22.23 2.34 46.92 3.28
11 12 6.383415 GTGAAACTACACAAAGTTTGACCAA 58.617 36.000 22.23 3.97 46.92 3.67
12 13 5.945155 GTGAAACTACACAAAGTTTGACCA 58.055 37.500 22.23 5.30 46.92 4.02
29 30 9.076596 GCATATAAGATTTGGTCAAAGTGAAAC 57.923 33.333 2.55 0.00 33.32 2.78
30 31 8.801299 TGCATATAAGATTTGGTCAAAGTGAAA 58.199 29.630 2.55 0.00 33.32 2.69
31 32 8.347004 TGCATATAAGATTTGGTCAAAGTGAA 57.653 30.769 2.55 0.00 33.32 3.18
32 33 7.936496 TGCATATAAGATTTGGTCAAAGTGA 57.064 32.000 2.55 0.00 33.32 3.41
33 34 8.984891 TTTGCATATAAGATTTGGTCAAAGTG 57.015 30.769 2.55 0.00 33.32 3.16
34 35 8.806146 ACTTTGCATATAAGATTTGGTCAAAGT 58.194 29.630 9.78 9.78 43.26 2.66
46 47 9.834628 CCGTTTCTTTTTACTTTGCATATAAGA 57.165 29.630 3.66 0.00 0.00 2.10
47 48 9.834628 TCCGTTTCTTTTTACTTTGCATATAAG 57.165 29.630 0.00 0.00 0.00 1.73
48 49 9.834628 CTCCGTTTCTTTTTACTTTGCATATAA 57.165 29.630 0.00 0.00 0.00 0.98
49 50 8.455682 CCTCCGTTTCTTTTTACTTTGCATATA 58.544 33.333 0.00 0.00 0.00 0.86
50 51 7.312899 CCTCCGTTTCTTTTTACTTTGCATAT 58.687 34.615 0.00 0.00 0.00 1.78
51 52 6.294286 CCCTCCGTTTCTTTTTACTTTGCATA 60.294 38.462 0.00 0.00 0.00 3.14
52 53 5.508994 CCCTCCGTTTCTTTTTACTTTGCAT 60.509 40.000 0.00 0.00 0.00 3.96
53 54 4.202070 CCCTCCGTTTCTTTTTACTTTGCA 60.202 41.667 0.00 0.00 0.00 4.08
54 55 4.037089 TCCCTCCGTTTCTTTTTACTTTGC 59.963 41.667 0.00 0.00 0.00 3.68
55 56 5.298527 ACTCCCTCCGTTTCTTTTTACTTTG 59.701 40.000 0.00 0.00 0.00 2.77
56 57 5.443283 ACTCCCTCCGTTTCTTTTTACTTT 58.557 37.500 0.00 0.00 0.00 2.66
57 58 5.045012 ACTCCCTCCGTTTCTTTTTACTT 57.955 39.130 0.00 0.00 0.00 2.24
58 59 4.701651 ACTCCCTCCGTTTCTTTTTACT 57.298 40.909 0.00 0.00 0.00 2.24
59 60 5.936372 ACATACTCCCTCCGTTTCTTTTTAC 59.064 40.000 0.00 0.00 0.00 2.01
60 61 6.117975 ACATACTCCCTCCGTTTCTTTTTA 57.882 37.500 0.00 0.00 0.00 1.52
61 62 4.981812 ACATACTCCCTCCGTTTCTTTTT 58.018 39.130 0.00 0.00 0.00 1.94
62 63 4.041198 TGACATACTCCCTCCGTTTCTTTT 59.959 41.667 0.00 0.00 0.00 2.27
63 64 3.581332 TGACATACTCCCTCCGTTTCTTT 59.419 43.478 0.00 0.00 0.00 2.52
64 65 3.170717 TGACATACTCCCTCCGTTTCTT 58.829 45.455 0.00 0.00 0.00 2.52
65 66 2.816411 TGACATACTCCCTCCGTTTCT 58.184 47.619 0.00 0.00 0.00 2.52
66 67 3.118738 ACATGACATACTCCCTCCGTTTC 60.119 47.826 0.00 0.00 0.00 2.78
67 68 2.838202 ACATGACATACTCCCTCCGTTT 59.162 45.455 0.00 0.00 0.00 3.60
68 69 2.467880 ACATGACATACTCCCTCCGTT 58.532 47.619 0.00 0.00 0.00 4.44
69 70 2.160721 ACATGACATACTCCCTCCGT 57.839 50.000 0.00 0.00 0.00 4.69
70 71 2.826428 CAACATGACATACTCCCTCCG 58.174 52.381 0.00 0.00 0.00 4.63
71 72 2.565841 GCAACATGACATACTCCCTCC 58.434 52.381 0.00 0.00 0.00 4.30
72 73 2.092968 TGGCAACATGACATACTCCCTC 60.093 50.000 0.00 0.00 46.17 4.30
73 74 1.915489 TGGCAACATGACATACTCCCT 59.085 47.619 0.00 0.00 46.17 4.20
74 75 2.418368 TGGCAACATGACATACTCCC 57.582 50.000 0.00 0.00 46.17 4.30
93 94 6.284459 CCAGAACAACACTTCTTCTTACTCT 58.716 40.000 0.00 0.00 0.00 3.24
100 101 3.809905 ACTCCCAGAACAACACTTCTTC 58.190 45.455 0.00 0.00 0.00 2.87
103 104 2.033424 GCAACTCCCAGAACAACACTTC 59.967 50.000 0.00 0.00 0.00 3.01
137 139 2.283676 TGGAGGTCAGTCGGTCCC 60.284 66.667 0.00 0.00 0.00 4.46
143 145 3.870633 AACTAATCGTGGAGGTCAGTC 57.129 47.619 0.00 0.00 0.00 3.51
145 147 4.315803 ACAAAACTAATCGTGGAGGTCAG 58.684 43.478 0.00 0.00 0.00 3.51
152 154 3.374058 CAGGCCTACAAAACTAATCGTGG 59.626 47.826 3.98 0.00 0.00 4.94
156 158 2.354821 CGCCAGGCCTACAAAACTAATC 59.645 50.000 3.98 0.00 0.00 1.75
165 167 4.063967 CGACACGCCAGGCCTACA 62.064 66.667 3.98 0.00 0.00 2.74
172 174 3.041940 GAACCACCGACACGCCAG 61.042 66.667 0.00 0.00 0.00 4.85
187 189 4.391155 ACCATTACTACTGCCAAAACGAA 58.609 39.130 0.00 0.00 0.00 3.85
198 200 2.159282 CCAGCGAACGACCATTACTACT 60.159 50.000 0.00 0.00 0.00 2.57
216 218 2.711542 ACACCGAGATTTTAAGGCCAG 58.288 47.619 5.01 0.00 0.00 4.85
231 233 9.950680 ATCTCAAGCATAATAAAAATTACACCG 57.049 29.630 0.00 0.00 0.00 4.94
533 565 6.655425 ACTCCCTCTGTTTTTATTTAGTCTGC 59.345 38.462 0.00 0.00 0.00 4.26
534 566 9.892130 ATACTCCCTCTGTTTTTATTTAGTCTG 57.108 33.333 0.00 0.00 0.00 3.51
544 576 8.890472 TGCCATATATATACTCCCTCTGTTTTT 58.110 33.333 0.00 0.00 0.00 1.94
550 582 6.905776 AGCTTTGCCATATATATACTCCCTCT 59.094 38.462 0.00 0.00 0.00 3.69
561 593 3.257375 TCCGTCGTAGCTTTGCCATATAT 59.743 43.478 0.00 0.00 0.00 0.86
566 598 1.373748 GTCCGTCGTAGCTTTGCCA 60.374 57.895 0.00 0.00 0.00 4.92
575 607 2.114670 GGATCCACCGTCCGTCGTA 61.115 63.158 6.95 0.00 37.94 3.43
620 652 1.190323 CGTTCTTTGCACTCACGAGAC 59.810 52.381 0.00 0.00 32.51 3.36
674 707 2.722201 GCAGTGGGTCCGGACTAGG 61.722 68.421 32.52 18.55 0.00 3.02
675 708 1.668101 GAGCAGTGGGTCCGGACTAG 61.668 65.000 32.52 18.50 35.49 2.57
676 709 1.681327 GAGCAGTGGGTCCGGACTA 60.681 63.158 32.52 19.78 35.49 2.59
677 710 2.997897 GAGCAGTGGGTCCGGACT 60.998 66.667 32.52 12.43 35.49 3.85
708 741 0.036858 GAGGGCGAGAACTCAAGCTT 60.037 55.000 0.00 0.00 33.95 3.74
739 772 0.734889 CCGAGGTTTGATCCATGCAC 59.265 55.000 0.00 0.00 0.00 4.57
803 836 1.036707 CCTTTTTCTTTCCACCGCCA 58.963 50.000 0.00 0.00 0.00 5.69
902 935 0.607489 ATTTGCTGCTCTGCCGAGTT 60.607 50.000 7.01 0.00 39.53 3.01
1060 1393 0.322906 GCCAGGAAAAGGTGGAGGAG 60.323 60.000 0.00 0.00 35.67 3.69
1153 1486 3.170585 GTCGACGGCGCTGTGTAC 61.171 66.667 29.82 20.01 37.46 2.90
1347 1680 4.980339 ATTCAAAAGGCAATTTGGAGGT 57.020 36.364 13.55 0.00 40.04 3.85
1468 1803 6.542821 TGGGAATCCTATGCGAAATTAAGAT 58.457 36.000 0.00 0.00 0.00 2.40
1469 1804 5.935945 TGGGAATCCTATGCGAAATTAAGA 58.064 37.500 0.00 0.00 0.00 2.10
1470 1805 5.765182 ACTGGGAATCCTATGCGAAATTAAG 59.235 40.000 0.00 0.00 0.00 1.85
1555 1898 2.000447 GCCTTTGTCGTATGTCTGGTC 59.000 52.381 0.00 0.00 0.00 4.02
1558 1901 5.856126 TTTTAGCCTTTGTCGTATGTCTG 57.144 39.130 0.00 0.00 0.00 3.51
1590 1933 6.702716 TTAGTTTTCGTGGGAATCAACTTT 57.297 33.333 0.00 0.00 35.72 2.66
1699 2042 2.237393 TTGGAATGGTTGCAACTTGC 57.763 45.000 27.64 20.09 45.29 4.01
1710 2053 4.111916 GGCGTTGTTATTGATTGGAATGG 58.888 43.478 0.00 0.00 0.00 3.16
1746 2089 3.411446 TGACAGATTCGCATGAAGGTTT 58.589 40.909 0.00 0.00 37.57 3.27
1747 2090 3.057969 TGACAGATTCGCATGAAGGTT 57.942 42.857 0.00 0.00 37.57 3.50
1779 2122 4.333690 AGGAATCATGCATGCCTCTAATC 58.666 43.478 22.25 6.82 0.00 1.75
1842 2185 4.565166 TCGTCAGGCAAAACTCGTTATATG 59.435 41.667 0.00 0.00 0.00 1.78
1937 2282 1.340248 CATCCTATCCTGTACGGCGTT 59.660 52.381 21.24 0.10 0.00 4.84
1940 2285 0.608640 CCCATCCTATCCTGTACGGC 59.391 60.000 0.00 0.00 0.00 5.68
2009 2354 5.136105 ACATATTCCATTTCTCCTGCTTCC 58.864 41.667 0.00 0.00 0.00 3.46
2078 2423 4.050553 CAAAACTAACAAGTGGCCATGTG 58.949 43.478 9.72 13.24 0.00 3.21
2106 2451 6.146837 CCAGAGATGCCGATTGTTAGAATTAG 59.853 42.308 0.00 0.00 0.00 1.73
2198 2543 5.458126 CACATCGATCAGAGATAACAGTGTG 59.542 44.000 0.00 0.00 0.00 3.82
2258 2603 3.255395 TCTGAAGAAATGCCAAATTCGCA 59.745 39.130 2.92 2.92 41.28 5.10
2261 2606 5.119743 GTGCTTCTGAAGAAATGCCAAATTC 59.880 40.000 21.06 0.00 33.07 2.17
2264 2609 3.384146 TGTGCTTCTGAAGAAATGCCAAA 59.616 39.130 21.06 0.77 33.07 3.28
2301 2646 0.947244 CAAGGCTGAGAACGCTTGTT 59.053 50.000 0.00 0.00 38.91 2.83
2303 2648 1.580845 CCCAAGGCTGAGAACGCTTG 61.581 60.000 0.00 0.00 0.00 4.01
2335 2680 3.521126 ACCAGAGTGCACATCCTCTTTAT 59.479 43.478 21.04 0.00 35.90 1.40
2447 2792 1.952990 TCATCTTTCAAGCAAACCGCA 59.047 42.857 0.00 0.00 46.13 5.69
2477 2822 2.578021 ACCTGATTCTGCAACCCATAGT 59.422 45.455 0.00 0.00 0.00 2.12
2480 2825 2.610438 AACCTGATTCTGCAACCCAT 57.390 45.000 0.00 0.00 0.00 4.00
2518 2863 6.831727 TTTTCAAACAAGAGATTGCATGTG 57.168 33.333 0.00 0.00 0.00 3.21
2592 2938 7.931578 TTTGGTCATGTCGTATTATTTTCCT 57.068 32.000 0.00 0.00 0.00 3.36
2593 2939 9.659830 GTATTTGGTCATGTCGTATTATTTTCC 57.340 33.333 0.00 0.00 0.00 3.13
2601 2947 6.479001 GCAGTAAGTATTTGGTCATGTCGTAT 59.521 38.462 0.00 0.00 0.00 3.06
2603 2949 4.630069 GCAGTAAGTATTTGGTCATGTCGT 59.370 41.667 0.00 0.00 0.00 4.34
2604 2950 4.629634 TGCAGTAAGTATTTGGTCATGTCG 59.370 41.667 0.00 0.00 0.00 4.35
2606 2952 6.237901 TCTTGCAGTAAGTATTTGGTCATGT 58.762 36.000 0.00 0.00 37.65 3.21
2607 2953 6.741992 TCTTGCAGTAAGTATTTGGTCATG 57.258 37.500 0.00 0.00 37.65 3.07
2610 2956 8.662781 TCATATCTTGCAGTAAGTATTTGGTC 57.337 34.615 0.00 0.00 37.65 4.02
2640 2986 6.677913 ACGGAAATGATGAAAACGAGAAAAT 58.322 32.000 0.00 0.00 0.00 1.82
2700 3050 6.702329 AGTAGTTCTTTGTTCCAGTGGATAG 58.298 40.000 14.00 8.55 0.00 2.08
2795 3145 3.321950 ACTTGCTGAGGCCTAGGATTAT 58.678 45.455 14.75 0.00 37.74 1.28
2876 3228 4.277174 AGCCAACGTTATCAATGTTCACAA 59.723 37.500 0.00 0.00 38.51 3.33
2888 3240 5.247084 TGTACCACATAAAGCCAACGTTAT 58.753 37.500 0.00 0.00 31.62 1.89
2889 3241 4.639334 TGTACCACATAAAGCCAACGTTA 58.361 39.130 0.00 0.00 0.00 3.18
2892 3244 4.695217 ATTGTACCACATAAAGCCAACG 57.305 40.909 0.00 0.00 0.00 4.10
2893 3245 8.349983 CCTATAATTGTACCACATAAAGCCAAC 58.650 37.037 0.00 0.00 0.00 3.77
2894 3246 7.504238 CCCTATAATTGTACCACATAAAGCCAA 59.496 37.037 0.00 0.00 0.00 4.52
2914 3290 5.957771 AGCAATGACTTCTTCACCCTATA 57.042 39.130 0.00 0.00 36.92 1.31
3027 3403 3.192001 GCAGCACTTTCATTGAATCTGGA 59.808 43.478 0.00 0.00 0.00 3.86
3140 3516 1.561542 AGGTTAGCATCAAGAGGTGGG 59.438 52.381 0.00 0.00 0.00 4.61
3149 3525 5.843969 TGGAGATTATACCAGGTTAGCATCA 59.156 40.000 0.00 0.00 0.00 3.07
3166 3542 2.708325 GGACTAGGGAGCAATGGAGATT 59.292 50.000 0.00 0.00 0.00 2.40
3180 3556 8.712285 TGAAACAATTATACGAAAGGACTAGG 57.288 34.615 0.00 0.00 0.00 3.02
3236 3613 3.030291 TGAAGCTCCAAAAGGCAGAAAA 58.970 40.909 0.00 0.00 0.00 2.29
3239 3616 2.165167 CATGAAGCTCCAAAAGGCAGA 58.835 47.619 0.00 0.00 0.00 4.26
3284 3663 5.385617 CCTCGAGAAATTGTTAGTGCAAAG 58.614 41.667 15.71 0.00 31.63 2.77
3297 3677 2.168496 TCGTGAAGTCCCTCGAGAAAT 58.832 47.619 15.71 0.00 0.00 2.17
3443 3977 2.032799 CAGCACCGCAAAGTTTACTCAA 59.967 45.455 0.00 0.00 0.00 3.02
3444 3978 1.601903 CAGCACCGCAAAGTTTACTCA 59.398 47.619 0.00 0.00 0.00 3.41
3451 3985 0.535102 AGCTTACAGCACCGCAAAGT 60.535 50.000 0.00 0.00 45.56 2.66
3452 3986 1.128692 GTAGCTTACAGCACCGCAAAG 59.871 52.381 0.00 0.00 45.56 2.77
3455 3989 1.445410 CGTAGCTTACAGCACCGCA 60.445 57.895 0.00 0.00 45.56 5.69
3456 3990 2.165301 CCGTAGCTTACAGCACCGC 61.165 63.158 0.00 0.00 45.56 5.68
3457 3991 0.102481 ATCCGTAGCTTACAGCACCG 59.898 55.000 0.00 0.00 45.56 4.94
3459 3993 0.931005 GCATCCGTAGCTTACAGCAC 59.069 55.000 0.00 0.00 45.56 4.40
3580 4159 7.676043 AGCTATTATCAGCAAGTAGAATAGGGA 59.324 37.037 0.00 0.00 44.35 4.20
3581 4160 7.846066 AGCTATTATCAGCAAGTAGAATAGGG 58.154 38.462 0.00 0.00 44.35 3.53
3582 4161 8.748412 AGAGCTATTATCAGCAAGTAGAATAGG 58.252 37.037 0.00 0.00 44.35 2.57
3586 4165 9.973450 CTAAAGAGCTATTATCAGCAAGTAGAA 57.027 33.333 0.00 0.00 44.35 2.10
3587 4166 9.355916 TCTAAAGAGCTATTATCAGCAAGTAGA 57.644 33.333 0.00 0.00 44.35 2.59
3588 4167 9.973450 TTCTAAAGAGCTATTATCAGCAAGTAG 57.027 33.333 0.00 0.00 44.35 2.57
3589 4168 9.751542 GTTCTAAAGAGCTATTATCAGCAAGTA 57.248 33.333 0.00 0.00 44.35 2.24
3590 4169 7.436673 CGTTCTAAAGAGCTATTATCAGCAAGT 59.563 37.037 0.00 0.00 44.35 3.16
3591 4170 7.568497 GCGTTCTAAAGAGCTATTATCAGCAAG 60.568 40.741 0.00 0.00 44.35 4.01
3593 4172 5.692204 GCGTTCTAAAGAGCTATTATCAGCA 59.308 40.000 0.00 0.00 44.35 4.41
3594 4173 5.923684 AGCGTTCTAAAGAGCTATTATCAGC 59.076 40.000 0.00 0.00 42.12 4.26
3595 4174 7.649705 TCAAGCGTTCTAAAGAGCTATTATCAG 59.350 37.037 0.00 0.00 39.25 2.90
3596 4175 7.489160 TCAAGCGTTCTAAAGAGCTATTATCA 58.511 34.615 0.00 0.00 39.25 2.15
3597 4176 7.932120 TCAAGCGTTCTAAAGAGCTATTATC 57.068 36.000 0.00 0.00 39.25 1.75
3598 4177 8.894768 AATCAAGCGTTCTAAAGAGCTATTAT 57.105 30.769 0.00 0.00 39.25 1.28
3599 4178 7.438459 GGAATCAAGCGTTCTAAAGAGCTATTA 59.562 37.037 0.00 0.00 39.25 0.98
3600 4179 6.258947 GGAATCAAGCGTTCTAAAGAGCTATT 59.741 38.462 0.00 0.00 39.25 1.73
3601 4180 5.755861 GGAATCAAGCGTTCTAAAGAGCTAT 59.244 40.000 0.00 0.00 39.25 2.97
3602 4181 5.109903 GGAATCAAGCGTTCTAAAGAGCTA 58.890 41.667 0.00 0.00 39.25 3.32
3603 4182 3.935828 GGAATCAAGCGTTCTAAAGAGCT 59.064 43.478 0.00 0.00 42.35 4.09
3604 4183 3.684788 TGGAATCAAGCGTTCTAAAGAGC 59.315 43.478 0.00 0.00 0.00 4.09
3605 4184 6.291849 CGTATGGAATCAAGCGTTCTAAAGAG 60.292 42.308 0.00 0.00 0.00 2.85
3606 4185 5.518847 CGTATGGAATCAAGCGTTCTAAAGA 59.481 40.000 0.00 0.00 0.00 2.52
3607 4186 5.291128 ACGTATGGAATCAAGCGTTCTAAAG 59.709 40.000 0.00 0.00 35.14 1.85
3628 4207 2.394708 CAACATGACAGAAGACGACGT 58.605 47.619 0.00 0.00 0.00 4.34
3629 4208 1.721389 CCAACATGACAGAAGACGACG 59.279 52.381 0.00 0.00 0.00 5.12
3631 4210 3.469008 AACCAACATGACAGAAGACGA 57.531 42.857 0.00 0.00 0.00 4.20
3632 4211 4.055360 TGTAACCAACATGACAGAAGACG 58.945 43.478 0.00 0.00 31.43 4.18
3652 4342 1.906574 ACCACGGGTATGAACAGATGT 59.093 47.619 0.00 0.00 32.11 3.06
3654 4344 2.304761 ACAACCACGGGTATGAACAGAT 59.695 45.455 0.00 0.00 33.12 2.90
3666 4356 1.399089 ACGAAACAAAGACAACCACGG 59.601 47.619 0.00 0.00 0.00 4.94
3680 4370 8.868635 AGTAATTATTAGGCAGAGTACGAAAC 57.131 34.615 0.00 0.00 0.00 2.78
3701 4391 7.987750 TGCACACAACCATCTTTATTAGTAA 57.012 32.000 0.00 0.00 0.00 2.24
3704 4396 7.087409 TGATGCACACAACCATCTTTATTAG 57.913 36.000 0.00 0.00 38.84 1.73
3734 4432 6.075732 GGTTAAAACCCCTTGCTTCTGCAT 62.076 45.833 0.02 0.00 45.15 3.96
3780 4492 5.354234 CGCCATTACCTGAAAACAGAATACT 59.646 40.000 0.00 0.00 0.00 2.12
3781 4493 5.448632 CCGCCATTACCTGAAAACAGAATAC 60.449 44.000 0.00 0.00 0.00 1.89
3782 4494 4.638421 CCGCCATTACCTGAAAACAGAATA 59.362 41.667 0.00 0.00 0.00 1.75
3905 4617 4.819769 TGAAGTGAAATTTATTGCAGGGC 58.180 39.130 0.00 0.00 0.00 5.19
3964 4676 8.613482 GGAATTGAGCACATCATCATCATATAG 58.387 37.037 0.00 0.00 37.89 1.31
3965 4677 7.279313 CGGAATTGAGCACATCATCATCATATA 59.721 37.037 0.00 0.00 37.89 0.86
3966 4678 6.093633 CGGAATTGAGCACATCATCATCATAT 59.906 38.462 0.00 0.00 37.89 1.78
3984 4696 2.478894 AGTTGCTACACGAACGGAATTG 59.521 45.455 0.13 0.00 0.00 2.32
3985 4697 2.762745 AGTTGCTACACGAACGGAATT 58.237 42.857 0.13 0.00 0.00 2.17
3988 4700 1.067364 TCAAGTTGCTACACGAACGGA 59.933 47.619 0.13 0.00 0.00 4.69
4010 4722 0.748729 TCGCTGATGATGCCATGCAA 60.749 50.000 0.00 0.00 43.62 4.08
4138 4850 1.819632 CCCAGCCGCCTTGTACATC 60.820 63.158 0.00 0.00 0.00 3.06
4236 4948 1.002033 GCCGAGCAGATAAAATGGCAG 60.002 52.381 0.00 0.00 40.66 4.85
4241 4953 4.077300 TGATCAGCCGAGCAGATAAAAT 57.923 40.909 0.00 0.00 35.03 1.82
4246 4958 0.829333 ACTTGATCAGCCGAGCAGAT 59.171 50.000 0.00 3.99 39.09 2.90
4248 4960 1.703438 GCACTTGATCAGCCGAGCAG 61.703 60.000 0.00 0.00 39.09 4.24
4249 4961 1.742880 GCACTTGATCAGCCGAGCA 60.743 57.895 0.00 0.00 35.25 4.26
4250 4962 1.023513 AAGCACTTGATCAGCCGAGC 61.024 55.000 0.00 0.00 0.00 5.03
4273 4994 1.549037 CCGGATCTAGGGGAGGAAGAG 60.549 61.905 0.00 0.00 0.00 2.85
4434 5158 1.990799 TCTCGTTCATGTTGGCGTAG 58.009 50.000 0.00 0.00 0.00 3.51
4510 5234 3.521560 TCCTTTCGACGGAAGAATGATG 58.478 45.455 17.69 0.00 32.80 3.07
4568 5292 5.220586 CGTACGTGGTCTATTTACGTCCTAA 60.221 44.000 7.22 0.00 46.81 2.69
4578 5302 5.064441 AGTAAAAGCGTACGTGGTCTATT 57.936 39.130 17.90 5.62 0.00 1.73
4579 5303 4.439289 GGAGTAAAAGCGTACGTGGTCTAT 60.439 45.833 17.90 0.00 0.00 1.98
4580 5304 3.119849 GGAGTAAAAGCGTACGTGGTCTA 60.120 47.826 17.90 0.00 0.00 2.59
4581 5305 2.352127 GGAGTAAAAGCGTACGTGGTCT 60.352 50.000 17.90 8.15 0.00 3.85
4582 5306 1.988467 GGAGTAAAAGCGTACGTGGTC 59.012 52.381 17.90 0.00 0.00 4.02
4583 5307 1.340889 TGGAGTAAAAGCGTACGTGGT 59.659 47.619 17.90 2.74 0.00 4.16
4584 5308 1.723003 GTGGAGTAAAAGCGTACGTGG 59.277 52.381 17.90 0.00 0.00 4.94
4586 5310 2.798976 TGTGGAGTAAAAGCGTACGT 57.201 45.000 17.90 0.00 0.00 3.57
4588 5312 3.248266 ACGATGTGGAGTAAAAGCGTAC 58.752 45.455 0.00 0.00 0.00 3.67
4589 5313 3.581024 ACGATGTGGAGTAAAAGCGTA 57.419 42.857 0.00 0.00 0.00 4.42
4590 5314 2.450609 ACGATGTGGAGTAAAAGCGT 57.549 45.000 0.00 0.00 0.00 5.07
4591 5315 2.278094 CGTACGATGTGGAGTAAAAGCG 59.722 50.000 10.44 0.00 0.00 4.68
4592 5316 2.028883 GCGTACGATGTGGAGTAAAAGC 59.971 50.000 21.65 0.00 0.00 3.51
4593 5317 3.508762 AGCGTACGATGTGGAGTAAAAG 58.491 45.455 21.65 0.00 0.00 2.27
4594 5318 3.192001 AGAGCGTACGATGTGGAGTAAAA 59.808 43.478 21.65 0.00 0.00 1.52
4595 5319 2.751259 AGAGCGTACGATGTGGAGTAAA 59.249 45.455 21.65 0.00 0.00 2.01
4596 5320 2.353889 GAGAGCGTACGATGTGGAGTAA 59.646 50.000 21.65 0.00 0.00 2.24
4597 5321 1.938577 GAGAGCGTACGATGTGGAGTA 59.061 52.381 21.65 0.00 0.00 2.59
4598 5322 0.733729 GAGAGCGTACGATGTGGAGT 59.266 55.000 21.65 0.00 0.00 3.85
4599 5323 0.733150 TGAGAGCGTACGATGTGGAG 59.267 55.000 21.65 0.00 0.00 3.86
4600 5324 1.333931 GATGAGAGCGTACGATGTGGA 59.666 52.381 21.65 0.00 0.00 4.02
4601 5325 1.600663 GGATGAGAGCGTACGATGTGG 60.601 57.143 21.65 0.00 0.00 4.17
4602 5326 1.065551 TGGATGAGAGCGTACGATGTG 59.934 52.381 21.65 0.00 0.00 3.21
4603 5327 1.335182 CTGGATGAGAGCGTACGATGT 59.665 52.381 21.65 12.30 0.00 3.06
4621 5345 7.385205 ACAGTAGTACTTCTTTACATGTTGCTG 59.615 37.037 2.30 3.53 0.00 4.41
4657 5384 3.371487 CCATCACAATTAGGGCAGGTGTA 60.371 47.826 0.00 0.00 0.00 2.90
4693 5420 4.766375 ACTACCATCCATCCGTGTTAAAG 58.234 43.478 0.00 0.00 0.00 1.85
4700 5427 6.667848 TCATCATATAACTACCATCCATCCGT 59.332 38.462 0.00 0.00 0.00 4.69
4708 5435 7.737607 TGGGTTAGGTCATCATATAACTACCAT 59.262 37.037 0.00 0.00 0.00 3.55
4709 5436 7.077095 TGGGTTAGGTCATCATATAACTACCA 58.923 38.462 0.00 0.00 0.00 3.25
4710 5437 7.549147 TGGGTTAGGTCATCATATAACTACC 57.451 40.000 0.00 0.00 0.00 3.18
4711 5438 9.841295 TTTTGGGTTAGGTCATCATATAACTAC 57.159 33.333 0.00 0.00 0.00 2.73
4753 5480 1.012086 GTCCGGGCGGAGAAAATTAC 58.988 55.000 0.00 0.00 46.16 1.89
4833 5560 1.522580 GCAGGAGAGCCGGATTCAC 60.523 63.158 5.05 0.00 39.96 3.18
4894 5621 3.864921 GCACTTTGTCTCGTCCCTTACAT 60.865 47.826 0.00 0.00 0.00 2.29
4896 5623 2.067013 GCACTTTGTCTCGTCCCTTAC 58.933 52.381 0.00 0.00 0.00 2.34
5079 9309 0.037232 GGTTTCGAGTGAGTGAGGGG 60.037 60.000 0.00 0.00 0.00 4.79
5140 9377 3.942351 TCCATGGATCGATGGATGC 57.058 52.632 29.58 2.14 45.85 3.91
5183 9420 3.803082 CCCATCTTGTGCGGCGTG 61.803 66.667 9.37 0.00 0.00 5.34
5231 9468 1.909700 ATGGAAATTGTGCTGGTCGT 58.090 45.000 0.00 0.00 0.00 4.34
5233 9470 3.940209 TGAATGGAAATTGTGCTGGTC 57.060 42.857 0.00 0.00 0.00 4.02
5234 9471 3.618019 GCATGAATGGAAATTGTGCTGGT 60.618 43.478 0.00 0.00 0.00 4.00
5243 9480 3.254166 GCTACGATGGCATGAATGGAAAT 59.746 43.478 3.81 0.00 0.00 2.17
5330 9568 0.042708 GACGCATGTGCATGATCGAC 60.043 55.000 15.53 7.42 41.20 4.20
5451 9691 6.227298 TCAGGCAGATTTGGTAAAACAAAA 57.773 33.333 0.00 0.00 42.91 2.44
5452 9692 5.860941 TCAGGCAGATTTGGTAAAACAAA 57.139 34.783 0.00 0.00 43.69 2.83
5459 9699 9.639563 TCAATATTATTTCAGGCAGATTTGGTA 57.360 29.630 0.00 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.