Multiple sequence alignment - TraesCS7D01G242700

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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 TraesCS7D01G242700 chr7D 100.000 6955 0 0 1 6955 208555025 208548071 0.000000e+00 12844
1 TraesCS7D01G242700 chr7B 93.083 4496 190 48 2074 6495 192769257 192773705 0.000000e+00 6468
2 TraesCS7D01G242700 chr7B 96.010 1253 43 5 824 2072 192765991 192767240 0.000000e+00 2030
3 TraesCS7D01G242700 chr7B 88.854 646 62 6 69 709 192765224 192765864 0.000000e+00 785
4 TraesCS7D01G242700 chr7B 91.195 477 18 11 6488 6955 192786740 192787201 1.650000e-175 627
5 TraesCS7D01G242700 chr7A 93.542 2106 86 25 4587 6665 221681832 221679750 0.000000e+00 3090
6 TraesCS7D01G242700 chr7A 94.412 1879 67 13 824 2686 221686048 221684192 0.000000e+00 2854
7 TraesCS7D01G242700 chr7A 92.958 1917 71 18 2693 4555 221683738 221681832 0.000000e+00 2734
8 TraesCS7D01G242700 chr7A 95.477 199 7 2 6758 6955 221679595 221679398 4.050000e-82 316
9 TraesCS7D01G242700 chr7A 79.596 495 56 22 339 826 221686563 221686107 5.240000e-81 313
10 TraesCS7D01G242700 chr7A 82.270 282 45 4 4529 4808 74150790 74150512 9.020000e-59 239
11 TraesCS7D01G242700 chr6B 86.268 284 29 9 4531 4809 188141765 188142043 4.080000e-77 300
12 TraesCS7D01G242700 chr3D 89.912 228 19 4 4583 4808 611967387 611967162 2.450000e-74 291
13 TraesCS7D01G242700 chr4D 83.688 282 44 2 4530 4809 481411370 481411651 1.490000e-66 265
14 TraesCS7D01G242700 chr3B 85.837 233 27 6 4579 4808 763498050 763498279 6.970000e-60 243
15 TraesCS7D01G242700 chr3B 84.581 227 33 2 4583 4808 830588841 830588616 2.520000e-54 224
16 TraesCS7D01G242700 chr3B 91.463 82 6 1 4531 4612 717075553 717075473 2.050000e-20 111
17 TraesCS7D01G242700 chr5B 88.177 203 21 3 4533 4733 619296598 619296799 9.020000e-59 239
18 TraesCS7D01G242700 chr1D 81.955 266 40 5 4547 4809 439015627 439015887 1.170000e-52 219
19 TraesCS7D01G242700 chr4A 88.976 127 11 2 4685 4808 641448655 641448529 3.360000e-33 154


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 TraesCS7D01G242700 chr7D 208548071 208555025 6954 True 12844.000000 12844 100.000 1 6955 1 chr7D.!!$R1 6954
1 TraesCS7D01G242700 chr7B 192765224 192773705 8481 False 3094.333333 6468 92.649 69 6495 3 chr7B.!!$F2 6426
2 TraesCS7D01G242700 chr7A 221679398 221686563 7165 True 1861.400000 3090 91.197 339 6955 5 chr7A.!!$R2 6616

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
275 276 0.252881 AGATCAAGGAGGGCAGGTGA 60.253 55.000 0.00 0.00 0.0 4.02 F
936 1007 0.321564 CCAGAGAATGACCAACCGCA 60.322 55.000 0.00 0.00 0.0 5.69 F
1366 1437 0.395311 ACGGCTTCTCCCATCTCGTA 60.395 55.000 0.00 0.00 0.0 3.43 F
2075 4171 0.811281 GTGGATGGTGGCTAAAGTGC 59.189 55.000 0.00 0.00 0.0 4.40 F
2997 5577 0.546598 AATTGGAGGGAGTAAGCCGG 59.453 55.000 0.00 0.00 0.0 6.13 F
4070 6654 1.271379 TGCCTGAGCTTGCATTTTCAG 59.729 47.619 12.44 12.44 40.8 3.02 F
5681 8316 0.108615 AGGTCTCGGATGCTGAAACG 60.109 55.000 0.00 0.00 0.0 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1212 1283 0.179070 GGTCTGAGCTTCGGGATTCC 60.179 60.000 0.0 0.0 0.00 3.01 R
2687 4791 2.101783 CAGAGAGACACAGATGCCTCT 58.898 52.381 0.0 0.0 38.57 3.69 R
2993 5573 1.871080 CTCAGTGATAACATCCCGGC 58.129 55.000 0.0 0.0 0.00 6.13 R
3997 6581 2.191128 ACTTTGGATCAGGTGTCAGC 57.809 50.000 0.0 0.0 0.00 4.26 R
4635 7249 0.035739 TTCTGTCCACGTTTAGGCCC 59.964 55.000 0.0 0.0 0.00 5.80 R
5851 8489 0.108585 GAGAACTGGGGCTGTGTGAA 59.891 55.000 0.0 0.0 0.00 3.18 R
6639 9289 0.533308 CGGGTCCAGACGGAAAACAA 60.533 55.000 0.0 0.0 45.20 2.83 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
17 18 4.781959 CGCCGCCTGCCAATGTTG 62.782 66.667 0.00 0.00 36.24 3.33
19 20 4.440127 CCGCCTGCCAATGTTGCC 62.440 66.667 0.00 0.00 0.00 4.52
20 21 3.682885 CGCCTGCCAATGTTGCCA 61.683 61.111 0.00 0.00 0.00 4.92
21 22 2.047939 GCCTGCCAATGTTGCCAC 60.048 61.111 0.00 0.00 0.00 5.01
22 23 2.870119 GCCTGCCAATGTTGCCACA 61.870 57.895 0.00 0.00 37.31 4.17
23 24 1.747145 CCTGCCAATGTTGCCACAA 59.253 52.632 0.00 0.00 36.16 3.33
24 25 0.600782 CCTGCCAATGTTGCCACAAC 60.601 55.000 3.52 3.52 36.16 3.32
25 26 0.600782 CTGCCAATGTTGCCACAACC 60.601 55.000 7.91 0.00 36.16 3.77
26 27 1.664333 GCCAATGTTGCCACAACCG 60.664 57.895 7.91 0.00 36.16 4.44
27 28 1.739049 CCAATGTTGCCACAACCGT 59.261 52.632 7.91 0.00 36.16 4.83
28 29 0.318614 CCAATGTTGCCACAACCGTC 60.319 55.000 7.91 0.00 36.16 4.79
29 30 0.383590 CAATGTTGCCACAACCGTCA 59.616 50.000 7.91 0.00 36.16 4.35
30 31 0.667993 AATGTTGCCACAACCGTCAG 59.332 50.000 7.91 0.00 36.16 3.51
31 32 0.465460 ATGTTGCCACAACCGTCAGT 60.465 50.000 7.91 0.00 36.16 3.41
32 33 1.355210 GTTGCCACAACCGTCAGTG 59.645 57.895 0.00 0.00 35.56 3.66
36 37 4.361253 CACAACCGTCAGTGGGAG 57.639 61.111 0.00 0.00 32.24 4.30
37 38 1.301716 CACAACCGTCAGTGGGAGG 60.302 63.158 0.00 0.00 32.24 4.30
38 39 1.458777 ACAACCGTCAGTGGGAGGA 60.459 57.895 6.48 0.00 33.18 3.71
39 40 1.293498 CAACCGTCAGTGGGAGGAG 59.707 63.158 6.48 0.00 33.18 3.69
40 41 1.152312 AACCGTCAGTGGGAGGAGT 60.152 57.895 6.48 0.00 33.18 3.85
41 42 0.763223 AACCGTCAGTGGGAGGAGTT 60.763 55.000 6.48 0.00 33.18 3.01
42 43 1.293498 CCGTCAGTGGGAGGAGTTG 59.707 63.158 0.00 0.00 33.18 3.16
43 44 1.374758 CGTCAGTGGGAGGAGTTGC 60.375 63.158 0.00 0.00 33.18 4.17
44 45 1.003233 GTCAGTGGGAGGAGTTGCC 60.003 63.158 0.00 0.00 37.90 4.52
45 46 1.461268 TCAGTGGGAGGAGTTGCCA 60.461 57.895 0.00 0.00 46.23 4.92
48 49 2.206900 TGGGAGGAGTTGCCAGGA 59.793 61.111 0.00 0.00 43.15 3.86
49 50 1.229951 TGGGAGGAGTTGCCAGGAT 60.230 57.895 0.00 0.00 43.15 3.24
50 51 1.274703 TGGGAGGAGTTGCCAGGATC 61.275 60.000 0.00 0.00 43.15 3.36
51 52 0.985490 GGGAGGAGTTGCCAGGATCT 60.985 60.000 0.00 0.00 40.02 2.75
52 53 0.467804 GGAGGAGTTGCCAGGATCTC 59.532 60.000 0.00 0.00 40.02 2.75
53 54 1.494960 GAGGAGTTGCCAGGATCTCT 58.505 55.000 0.00 0.00 40.02 3.10
54 55 1.836802 GAGGAGTTGCCAGGATCTCTT 59.163 52.381 0.00 0.00 40.02 2.85
55 56 2.238395 GAGGAGTTGCCAGGATCTCTTT 59.762 50.000 0.00 0.00 40.02 2.52
56 57 3.452627 GAGGAGTTGCCAGGATCTCTTTA 59.547 47.826 0.00 0.00 40.02 1.85
57 58 3.198853 AGGAGTTGCCAGGATCTCTTTAC 59.801 47.826 0.00 0.00 40.02 2.01
58 59 3.536570 GAGTTGCCAGGATCTCTTTACC 58.463 50.000 0.00 0.00 0.00 2.85
59 60 3.185455 AGTTGCCAGGATCTCTTTACCT 58.815 45.455 0.00 0.00 34.02 3.08
60 61 3.198853 AGTTGCCAGGATCTCTTTACCTC 59.801 47.826 0.00 0.00 31.06 3.85
61 62 1.757118 TGCCAGGATCTCTTTACCTCG 59.243 52.381 0.00 0.00 31.06 4.63
62 63 1.069358 GCCAGGATCTCTTTACCTCGG 59.931 57.143 0.00 0.00 31.06 4.63
63 64 1.069358 CCAGGATCTCTTTACCTCGGC 59.931 57.143 0.00 0.00 31.06 5.54
64 65 2.035632 CAGGATCTCTTTACCTCGGCT 58.964 52.381 0.00 0.00 31.06 5.52
65 66 3.223435 CAGGATCTCTTTACCTCGGCTA 58.777 50.000 0.00 0.00 31.06 3.93
66 67 3.254657 CAGGATCTCTTTACCTCGGCTAG 59.745 52.174 0.00 0.00 31.06 3.42
67 68 3.117436 AGGATCTCTTTACCTCGGCTAGT 60.117 47.826 0.00 0.00 0.00 2.57
68 69 4.104420 AGGATCTCTTTACCTCGGCTAGTA 59.896 45.833 0.00 0.00 0.00 1.82
69 70 4.456566 GGATCTCTTTACCTCGGCTAGTAG 59.543 50.000 0.00 0.00 0.00 2.57
70 71 4.500499 TCTCTTTACCTCGGCTAGTAGT 57.500 45.455 0.00 0.00 0.00 2.73
71 72 5.620738 TCTCTTTACCTCGGCTAGTAGTA 57.379 43.478 0.00 0.00 0.00 1.82
72 73 5.609423 TCTCTTTACCTCGGCTAGTAGTAG 58.391 45.833 0.00 0.00 0.00 2.57
85 86 4.463539 GCTAGTAGTAGCCCTCTTAATCCC 59.536 50.000 17.43 0.00 45.37 3.85
88 89 4.902448 AGTAGTAGCCCTCTTAATCCCTTG 59.098 45.833 0.00 0.00 0.00 3.61
94 95 2.017049 CCTCTTAATCCCTTGCAACGG 58.983 52.381 8.07 8.07 0.00 4.44
101 102 1.304052 CCCTTGCAACGGGGATGAA 60.304 57.895 17.05 0.00 45.18 2.57
104 105 1.176527 CTTGCAACGGGGATGAATGT 58.823 50.000 0.00 0.00 0.00 2.71
105 106 1.545582 CTTGCAACGGGGATGAATGTT 59.454 47.619 0.00 0.00 0.00 2.71
113 114 2.122783 GGGATGAATGTTTCCCGTGA 57.877 50.000 0.00 0.00 42.18 4.35
154 155 3.494254 TTGACCCTGGGTTGCCGT 61.494 61.111 21.59 0.00 35.25 5.68
156 157 3.948719 GACCCTGGGTTGCCGTCA 61.949 66.667 21.59 0.00 35.25 4.35
158 159 3.636231 CCCTGGGTTGCCGTCAGA 61.636 66.667 3.97 0.00 0.00 3.27
159 160 2.358737 CCTGGGTTGCCGTCAGAC 60.359 66.667 0.00 0.00 0.00 3.51
173 174 2.031068 CGTCAGACATCTTCGACGAGAT 59.969 50.000 13.65 0.96 45.74 2.75
199 200 3.834726 TTGGGTGCCAAAGACACG 58.165 55.556 0.00 0.00 40.92 4.49
210 211 0.317479 AAAGACACGGGAGGAAGACG 59.683 55.000 0.00 0.00 0.00 4.18
228 229 2.280524 CGTGGGGTGCGAAAGACA 60.281 61.111 0.00 0.00 0.00 3.41
239 240 1.596220 GCGAAAGACACGGTGAAAACC 60.596 52.381 16.29 0.25 0.00 3.27
246 247 1.953686 ACACGGTGAAAACCCATGAAG 59.046 47.619 16.29 0.00 0.00 3.02
275 276 0.252881 AGATCAAGGAGGGCAGGTGA 60.253 55.000 0.00 0.00 0.00 4.02
287 289 2.532715 AGGTGATGTGGTGGCCCT 60.533 61.111 0.00 0.00 0.00 5.19
290 292 1.377725 GTGATGTGGTGGCCCTGAG 60.378 63.158 0.00 0.00 0.00 3.35
335 337 1.140052 TGTCCGAACAAGTGATGTGGT 59.860 47.619 0.00 0.00 42.99 4.16
505 510 1.996786 CTGCTGGTATTTGGCTGCCG 61.997 60.000 14.98 0.00 0.00 5.69
572 577 6.316390 CCCAACTGTACCAATCTGAATCTAAC 59.684 42.308 0.00 0.00 0.00 2.34
573 578 6.316390 CCAACTGTACCAATCTGAATCTAACC 59.684 42.308 0.00 0.00 0.00 2.85
600 606 4.268405 GTGTTCTTGCACAATTGAACCTTG 59.732 41.667 13.59 0.04 38.29 3.61
620 626 6.492087 ACCTTGAACGAAAATTATCTTCCCAA 59.508 34.615 0.00 0.00 0.00 4.12
635 641 6.045072 TCTTCCCAATCTTTTAGCGAAGTA 57.955 37.500 0.00 0.00 0.00 2.24
707 717 4.314440 TTGTCCAGCGGCGCTCTT 62.314 61.111 34.22 9.36 36.40 2.85
716 726 3.771160 GGCGCTCTTCCCTCGGAA 61.771 66.667 7.64 0.00 39.66 4.30
717 727 2.501610 GCGCTCTTCCCTCGGAAT 59.498 61.111 0.00 0.00 41.23 3.01
718 728 1.592939 GCGCTCTTCCCTCGGAATC 60.593 63.158 0.00 0.00 41.23 2.52
776 786 2.669569 CCCAACTCGCACACTGGG 60.670 66.667 0.00 0.00 42.60 4.45
826 836 1.883084 GCAGTATCCAAGACCGGCG 60.883 63.158 0.00 0.00 0.00 6.46
827 837 1.813859 CAGTATCCAAGACCGGCGA 59.186 57.895 9.30 0.00 0.00 5.54
828 838 0.389391 CAGTATCCAAGACCGGCGAT 59.611 55.000 9.30 0.00 0.00 4.58
829 839 0.389391 AGTATCCAAGACCGGCGATG 59.611 55.000 9.30 1.37 0.00 3.84
831 841 2.377628 TATCCAAGACCGGCGATGCC 62.378 60.000 9.30 0.00 46.75 4.40
936 1007 0.321564 CCAGAGAATGACCAACCGCA 60.322 55.000 0.00 0.00 0.00 5.69
1142 1213 3.248171 GCATCCTCGTCGTCGTGC 61.248 66.667 1.33 0.81 38.33 5.34
1257 1328 1.027792 AGAGTCCGAGAGCCGTCTTC 61.028 60.000 0.00 0.00 36.31 2.87
1260 1331 4.194720 CCGAGAGCCGTCTTCCCG 62.195 72.222 0.00 0.00 36.31 5.14
1366 1437 0.395311 ACGGCTTCTCCCATCTCGTA 60.395 55.000 0.00 0.00 0.00 3.43
1730 1801 1.207791 CCACTGCTCCCAGGTATTCT 58.792 55.000 0.00 0.00 43.53 2.40
1749 1820 3.585862 TCTTTGCCGTGATAACTGACTC 58.414 45.455 0.00 0.00 0.00 3.36
1945 2025 7.291566 TCCTAAACAAAGGGTAAATTGTGAGA 58.708 34.615 0.00 0.00 39.57 3.27
1951 2031 9.758651 AACAAAGGGTAAATTGTGAGAAATTAC 57.241 29.630 0.00 0.00 39.57 1.89
1957 2037 8.749354 GGGTAAATTGTGAGAAATTACAGGATT 58.251 33.333 3.24 0.00 0.00 3.01
2026 2107 5.047306 CGGCTCACATAATATCCACCTCTTA 60.047 44.000 0.00 0.00 0.00 2.10
2072 2153 1.004745 AGTGGTGGATGGTGGCTAAAG 59.995 52.381 0.00 0.00 0.00 1.85
2075 4171 0.811281 GTGGATGGTGGCTAAAGTGC 59.189 55.000 0.00 0.00 0.00 4.40
2098 4194 6.859508 TGCGTATAACTGTGTATACTGCATAC 59.140 38.462 19.45 9.65 39.15 2.39
2109 4205 9.019656 TGTGTATACTGCATACCAAAAGAAAAT 57.980 29.630 4.17 0.00 39.08 1.82
2155 4251 3.565902 AGTAACTGCCAGCAACTTTTCTC 59.434 43.478 0.00 0.00 0.00 2.87
2227 4329 6.429078 TGCTGCAAATTCAGTATCAGATATCC 59.571 38.462 0.00 0.00 36.49 2.59
2441 4545 4.623167 CAGACTCTGTGTGAAATAGAACGG 59.377 45.833 0.00 0.00 0.00 4.44
2449 4553 9.226606 TCTGTGTGAAATAGAACGGATAATTTT 57.773 29.630 0.00 0.00 0.00 1.82
2462 4566 7.239763 ACGGATAATTTTTGGGAAGTTCAAT 57.760 32.000 5.01 0.00 0.00 2.57
2479 4583 9.827411 GAAGTTCAATAAGGACTTTACATGAAC 57.173 33.333 19.64 19.64 43.43 3.18
2547 4651 4.562082 TGTGTGGTAGTTCAAATAGGTCG 58.438 43.478 0.00 0.00 0.00 4.79
2571 4675 5.972973 GCTCATATTGAATTGCGATGTTTCA 59.027 36.000 0.00 0.00 0.00 2.69
2586 4690 5.220472 CGATGTTTCATGATGCGTTTAGAGT 60.220 40.000 0.00 0.00 0.00 3.24
2687 4791 8.141268 CCAAGTTTACTTCCTCAAGCAATTTAA 58.859 33.333 0.00 0.00 33.11 1.52
2690 4794 8.787852 AGTTTACTTCCTCAAGCAATTTAAGAG 58.212 33.333 0.00 0.00 32.09 2.85
2724 5276 6.642950 GTCTCTCTGTACATGCCACATATTAC 59.357 42.308 0.00 0.00 0.00 1.89
2739 5291 9.182214 GCCACATATTACATAGGAATGAATGAT 57.818 33.333 0.00 0.00 36.54 2.45
2769 5321 5.365021 AAGTAGTGAATCATAGCAGGCTT 57.635 39.130 0.00 0.00 0.00 4.35
2948 5502 6.462500 ACATATAGTCTAGGAAGCTGCAATG 58.538 40.000 1.02 0.00 0.00 2.82
2997 5577 0.546598 AATTGGAGGGAGTAAGCCGG 59.453 55.000 0.00 0.00 0.00 6.13
3030 5610 6.934083 TCACTGAGCAATCAAACTGTTACATA 59.066 34.615 0.00 0.00 0.00 2.29
3186 5766 6.634805 TGGTTCAGTTTCAGTTTATTGCAAA 58.365 32.000 1.71 0.00 0.00 3.68
3236 5816 5.344128 CACAGTTTATGCTTCAATTGTGCTC 59.656 40.000 20.35 5.64 0.00 4.26
3257 5837 5.791666 CTCATATACCAGTGATGCATGTCT 58.208 41.667 2.46 0.00 0.00 3.41
3627 6210 3.917329 TGTTAGTTCCAGAGTCACGAG 57.083 47.619 0.00 0.00 0.00 4.18
3732 6315 7.267857 TGACTCTTGGTACATTACATGAGATG 58.732 38.462 15.12 5.62 39.75 2.90
3742 6325 6.927416 ACATTACATGAGATGTGTTGCATTT 58.073 32.000 14.76 0.00 44.60 2.32
3817 6400 5.658634 ACTTGAGAGTTATGTGCCTGATCTA 59.341 40.000 0.00 0.00 29.87 1.98
3819 6402 6.737720 TGAGAGTTATGTGCCTGATCTATT 57.262 37.500 0.00 0.00 0.00 1.73
3829 6412 5.123820 TGTGCCTGATCTATTGTTTGTTAGC 59.876 40.000 0.00 0.00 0.00 3.09
3841 6424 9.554724 CTATTGTTTGTTAGCGTGTTCATATTT 57.445 29.630 0.00 0.00 0.00 1.40
3997 6581 7.064371 CAGATACAAATTCCTGAGAACTCTGTG 59.936 40.741 3.51 0.54 33.97 3.66
4070 6654 1.271379 TGCCTGAGCTTGCATTTTCAG 59.729 47.619 12.44 12.44 40.80 3.02
4133 6717 3.254657 TGCAGCTTAAAGTGCGGTTTATT 59.745 39.130 0.00 0.00 42.96 1.40
4143 6727 6.716898 AAGTGCGGTTTATTGTAACTACTC 57.283 37.500 0.00 0.00 0.00 2.59
4145 6729 5.867716 AGTGCGGTTTATTGTAACTACTCAG 59.132 40.000 0.00 0.00 0.00 3.35
4146 6730 5.636543 GTGCGGTTTATTGTAACTACTCAGT 59.363 40.000 0.00 0.00 36.19 3.41
4147 6731 6.808212 GTGCGGTTTATTGTAACTACTCAGTA 59.192 38.462 0.00 0.00 33.48 2.74
4148 6732 7.329226 GTGCGGTTTATTGTAACTACTCAGTAA 59.671 37.037 0.00 0.00 33.48 2.24
4150 6734 8.164790 GCGGTTTATTGTAACTACTCAGTAAAC 58.835 37.037 11.82 11.82 41.50 2.01
4172 6774 6.149129 ACTTTGAAGAAAGAATGGAACACC 57.851 37.500 0.00 0.00 40.92 4.16
4232 6841 6.531503 TTACCAAAATCAGTCAACCAAACA 57.468 33.333 0.00 0.00 0.00 2.83
4246 6855 2.070783 CCAAACAATTCTGTGGCATGC 58.929 47.619 9.90 9.90 35.37 4.06
4263 6872 3.759086 GCATGCCTCATCAATCATCTCAT 59.241 43.478 6.36 0.00 0.00 2.90
4298 6907 7.554118 CACCTGTTCATGGAATAGTTAGAACAT 59.446 37.037 0.00 0.00 42.77 2.71
4320 6929 8.297470 ACATTGCCATACTTTTGATAGTTGAT 57.703 30.769 0.00 0.00 0.00 2.57
4321 6930 8.192774 ACATTGCCATACTTTTGATAGTTGATG 58.807 33.333 0.00 0.00 0.00 3.07
4322 6931 7.701539 TTGCCATACTTTTGATAGTTGATGT 57.298 32.000 0.00 0.00 0.00 3.06
4323 6932 7.087409 TGCCATACTTTTGATAGTTGATGTG 57.913 36.000 0.00 0.00 0.00 3.21
4328 6937 6.942532 ACTTTTGATAGTTGATGTGTGTGT 57.057 33.333 0.00 0.00 0.00 3.72
4352 6961 3.376859 TGTGTGCTGTTTGTAACTCCTTG 59.623 43.478 0.00 0.00 0.00 3.61
4369 6978 6.122277 ACTCCTTGTCAGAACATTTGAAGAA 58.878 36.000 0.00 0.00 34.73 2.52
4507 7116 3.011818 CACAAGAACATGAGCAGCCATA 58.988 45.455 0.00 0.00 0.00 2.74
4556 7165 4.030452 GCACGCACCAGCCAGTTC 62.030 66.667 0.00 0.00 37.52 3.01
4585 7194 1.813477 GCTCAAGCTGATAGGGGAAGC 60.813 57.143 0.00 0.00 38.21 3.86
4635 7249 3.633094 CTCACGTGTGGCTCCCTCG 62.633 68.421 16.51 0.00 0.00 4.63
4651 7265 2.162338 CTCGGGCCTAAACGTGGACA 62.162 60.000 0.84 0.00 33.26 4.02
4667 7281 1.032014 GACAGAAAGTGGGCTGCAAA 58.968 50.000 0.50 0.00 35.57 3.68
4672 7293 3.495753 CAGAAAGTGGGCTGCAAATTTTC 59.504 43.478 0.50 7.69 0.00 2.29
4734 7355 4.586421 TCTTGGCTCTGATACCATGTAGAG 59.414 45.833 10.55 0.00 39.64 2.43
4739 7361 5.981088 CTCTGATACCATGTAGAGCTCAT 57.019 43.478 17.77 3.63 31.35 2.90
4744 7366 1.836166 ACCATGTAGAGCTCATGCACT 59.164 47.619 17.77 0.00 42.50 4.40
4756 7378 3.430098 GCTCATGCACTAGCTAGTTCACT 60.430 47.826 25.41 13.53 42.74 3.41
4780 7403 3.271250 GCTCAAGCTGATGGGGAAA 57.729 52.632 0.00 0.00 38.21 3.13
4782 7405 1.340405 GCTCAAGCTGATGGGGAAAGA 60.340 52.381 0.00 0.00 38.21 2.52
4801 7424 6.434028 GGAAAGATGGGCTATGCATTTATACA 59.566 38.462 3.54 0.00 0.00 2.29
4808 7431 6.548993 TGGGCTATGCATTTATACATCAACAA 59.451 34.615 3.54 0.00 0.00 2.83
4864 7496 9.088512 AGTTTCGAGTGTATTTTATCTGCTAAG 57.911 33.333 0.00 0.00 0.00 2.18
4890 7522 5.824421 AGGAGTGAAATCATTCTTGTCCAT 58.176 37.500 5.98 0.00 36.48 3.41
4891 7523 6.962182 AGGAGTGAAATCATTCTTGTCCATA 58.038 36.000 5.98 0.00 36.48 2.74
5173 7808 1.873591 ACTGCACGGTTGTCTGAATTC 59.126 47.619 0.00 0.00 0.00 2.17
5640 8275 3.618019 GCAAGTATCCCAGACGTTACCAA 60.618 47.826 0.00 0.00 0.00 3.67
5681 8316 0.108615 AGGTCTCGGATGCTGAAACG 60.109 55.000 0.00 0.00 0.00 3.60
5685 8320 0.807667 CTCGGATGCTGAAACGGAGG 60.808 60.000 0.00 0.00 0.00 4.30
5686 8321 1.079127 CGGATGCTGAAACGGAGGT 60.079 57.895 0.00 0.00 0.00 3.85
5693 8328 4.811969 TGCTGAAACGGAGGTATTCTTA 57.188 40.909 0.00 0.00 0.00 2.10
5694 8329 5.155278 TGCTGAAACGGAGGTATTCTTAA 57.845 39.130 0.00 0.00 0.00 1.85
5709 8344 6.753744 GGTATTCTTAACGTTGAGGTATTCGT 59.246 38.462 18.77 2.31 38.15 3.85
5747 8384 5.765510 AGCATTGTTGGGTGGATAATTCTA 58.234 37.500 0.00 0.00 0.00 2.10
5806 8444 3.077359 GCTTGCAGTTACAGTTGGAGAT 58.923 45.455 0.00 0.00 0.00 2.75
5831 8469 5.645067 CACTCTCTGCTGGTTATTCATTCAA 59.355 40.000 0.00 0.00 0.00 2.69
5842 8480 1.083489 TTCATTCAATCACGCCCGTC 58.917 50.000 0.00 0.00 0.00 4.79
5852 8490 3.117372 CGCCCGTCGTCTAGGATT 58.883 61.111 0.00 0.00 0.00 3.01
5871 8509 1.669115 CACACAGCCCCAGTTCTCG 60.669 63.158 0.00 0.00 0.00 4.04
5912 8550 3.258372 GCCAGATGTAGACCGATATTCCA 59.742 47.826 0.00 0.00 0.00 3.53
5987 8625 1.752501 CGACGTGTTCGCCATGATCC 61.753 60.000 0.00 0.00 41.87 3.36
5988 8626 0.460284 GACGTGTTCGCCATGATCCT 60.460 55.000 0.00 0.00 41.18 3.24
5989 8627 0.740868 ACGTGTTCGCCATGATCCTG 60.741 55.000 0.00 0.00 41.18 3.86
5990 8628 1.431488 CGTGTTCGCCATGATCCTGG 61.431 60.000 12.39 12.39 39.45 4.45
5991 8629 1.097547 GTGTTCGCCATGATCCTGGG 61.098 60.000 17.59 8.70 36.75 4.45
5992 8630 2.189499 GTTCGCCATGATCCTGGGC 61.189 63.158 17.59 13.07 44.27 5.36
5993 8631 3.420206 TTCGCCATGATCCTGGGCC 62.420 63.158 17.59 0.00 44.90 5.80
5994 8632 3.882326 CGCCATGATCCTGGGCCT 61.882 66.667 17.59 0.00 44.90 5.19
5995 8633 2.203451 GCCATGATCCTGGGCCTG 60.203 66.667 17.59 3.68 41.90 4.85
5996 8634 2.519441 CCATGATCCTGGGCCTGG 59.481 66.667 22.66 22.66 32.28 4.45
5997 8635 2.203451 CATGATCCTGGGCCTGGC 60.203 66.667 23.72 11.05 0.00 4.85
5998 8636 2.369291 ATGATCCTGGGCCTGGCT 60.369 61.111 23.72 15.24 0.00 4.75
5999 8637 1.073474 ATGATCCTGGGCCTGGCTA 60.073 57.895 23.72 12.62 0.00 3.93
6065 8704 5.220303 GCTTGAACGTTTTTGTGTTGCAATA 60.220 36.000 0.59 0.00 36.89 1.90
6073 8712 4.624336 TTTGTGTTGCAATACGAGTGTT 57.376 36.364 19.67 0.00 36.89 3.32
6097 8739 3.114616 CTCCCACTGCGCAGTTCG 61.115 66.667 39.13 29.55 40.20 3.95
6129 8775 0.801872 TTGTGCACGGTGTATGATGC 59.198 50.000 13.13 0.00 38.59 3.91
6509 9159 3.700154 CATGTGTCTCGTATGAGTGAGG 58.300 50.000 11.71 0.00 43.09 3.86
6624 9274 4.332543 TCTGGGAGGGGTCGCCTT 62.333 66.667 10.26 0.00 33.08 4.35
6625 9275 4.101448 CTGGGAGGGGTCGCCTTG 62.101 72.222 10.26 0.00 33.08 3.61
6639 9289 1.704641 GCCTTGGTTGGGTTTCTTCT 58.295 50.000 0.00 0.00 0.00 2.85
6683 9333 4.686191 CCTGAAGGCTATGAGAGATTGT 57.314 45.455 0.00 0.00 0.00 2.71
6684 9334 4.378774 CCTGAAGGCTATGAGAGATTGTG 58.621 47.826 0.00 0.00 0.00 3.33
6685 9335 3.801698 TGAAGGCTATGAGAGATTGTGC 58.198 45.455 0.00 0.00 0.00 4.57
6686 9336 2.522836 AGGCTATGAGAGATTGTGCG 57.477 50.000 0.00 0.00 0.00 5.34
6687 9337 2.034878 AGGCTATGAGAGATTGTGCGA 58.965 47.619 0.00 0.00 0.00 5.10
6688 9338 2.035704 AGGCTATGAGAGATTGTGCGAG 59.964 50.000 0.00 0.00 0.00 5.03
6689 9339 2.223923 GGCTATGAGAGATTGTGCGAGT 60.224 50.000 0.00 0.00 0.00 4.18
6690 9340 3.452474 GCTATGAGAGATTGTGCGAGTT 58.548 45.455 0.00 0.00 0.00 3.01
6691 9341 3.868077 GCTATGAGAGATTGTGCGAGTTT 59.132 43.478 0.00 0.00 0.00 2.66
6692 9342 4.331168 GCTATGAGAGATTGTGCGAGTTTT 59.669 41.667 0.00 0.00 0.00 2.43
6693 9343 5.163814 GCTATGAGAGATTGTGCGAGTTTTT 60.164 40.000 0.00 0.00 0.00 1.94
6694 9344 4.732285 TGAGAGATTGTGCGAGTTTTTC 57.268 40.909 0.00 0.00 0.00 2.29
6695 9345 4.380531 TGAGAGATTGTGCGAGTTTTTCT 58.619 39.130 0.00 0.00 0.00 2.52
6696 9346 4.816385 TGAGAGATTGTGCGAGTTTTTCTT 59.184 37.500 0.00 0.00 0.00 2.52
6697 9347 5.296780 TGAGAGATTGTGCGAGTTTTTCTTT 59.703 36.000 0.00 0.00 0.00 2.52
6698 9348 6.136541 AGAGATTGTGCGAGTTTTTCTTTT 57.863 33.333 0.00 0.00 0.00 2.27
6699 9349 6.202226 AGAGATTGTGCGAGTTTTTCTTTTC 58.798 36.000 0.00 0.00 0.00 2.29
6700 9350 6.038714 AGAGATTGTGCGAGTTTTTCTTTTCT 59.961 34.615 0.00 0.00 0.00 2.52
6701 9351 6.202226 AGATTGTGCGAGTTTTTCTTTTCTC 58.798 36.000 0.00 0.00 0.00 2.87
6702 9352 5.560966 TTGTGCGAGTTTTTCTTTTCTCT 57.439 34.783 0.00 0.00 0.00 3.10
6703 9353 5.560966 TGTGCGAGTTTTTCTTTTCTCTT 57.439 34.783 0.00 0.00 0.00 2.85
6704 9354 5.949735 TGTGCGAGTTTTTCTTTTCTCTTT 58.050 33.333 0.00 0.00 0.00 2.52
6705 9355 5.799936 TGTGCGAGTTTTTCTTTTCTCTTTG 59.200 36.000 0.00 0.00 0.00 2.77
6706 9356 6.027749 GTGCGAGTTTTTCTTTTCTCTTTGA 58.972 36.000 0.00 0.00 0.00 2.69
6707 9357 6.195428 GTGCGAGTTTTTCTTTTCTCTTTGAG 59.805 38.462 0.00 0.00 0.00 3.02
6708 9358 5.683302 GCGAGTTTTTCTTTTCTCTTTGAGG 59.317 40.000 0.00 0.00 0.00 3.86
6709 9359 6.458342 GCGAGTTTTTCTTTTCTCTTTGAGGA 60.458 38.462 0.00 0.00 0.00 3.71
6710 9360 7.472543 CGAGTTTTTCTTTTCTCTTTGAGGAA 58.527 34.615 0.00 0.00 0.00 3.36
6711 9361 7.968405 CGAGTTTTTCTTTTCTCTTTGAGGAAA 59.032 33.333 1.67 1.67 35.08 3.13
6712 9362 9.639601 GAGTTTTTCTTTTCTCTTTGAGGAAAA 57.360 29.630 3.10 0.00 36.80 2.29
6713 9363 9.996554 AGTTTTTCTTTTCTCTTTGAGGAAAAA 57.003 25.926 13.13 13.13 36.80 1.94
6739 9389 1.871039 CCGTGTTGAAATATAGGGCCG 59.129 52.381 0.00 0.00 0.00 6.13
6753 9403 0.881796 GGGCCGGCTATAAAATCAGC 59.118 55.000 28.56 4.14 37.05 4.26
6766 9522 1.813513 AATCAGCGACCCTGTTGAAG 58.186 50.000 0.00 0.00 42.38 3.02
6778 9534 6.986817 CGACCCTGTTGAAGTATATCATTCTT 59.013 38.462 2.55 0.00 0.00 2.52
6809 9565 0.935898 CTCTCGAGGAACATGCATGC 59.064 55.000 26.53 11.82 0.00 4.06
6865 9621 0.883833 AGCAAACAGTGTATGGCTGC 59.116 50.000 13.51 9.72 39.61 5.25
6878 9634 2.731571 GGCTGCTCATACGGGTCCA 61.732 63.158 0.00 0.00 0.00 4.02
6899 9655 0.247695 GATACGCGAGTTTGCTTGCC 60.248 55.000 15.93 0.00 46.84 4.52
6933 9689 0.459899 TCCTATGTGCTCGCGTGAAT 59.540 50.000 13.13 4.68 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.781959 CAACATTGGCAGGCGGCG 62.782 66.667 0.51 0.51 46.16 6.46
14 15 1.355210 CACTGACGGTTGTGGCAAC 59.645 57.895 3.62 3.62 0.00 4.17
15 16 1.821759 CCACTGACGGTTGTGGCAA 60.822 57.895 17.11 0.00 45.68 4.52
16 17 2.203139 CCACTGACGGTTGTGGCA 60.203 61.111 17.11 0.00 45.68 4.92
19 20 1.301716 CCTCCCACTGACGGTTGTG 60.302 63.158 7.83 7.83 0.00 3.33
20 21 1.458777 TCCTCCCACTGACGGTTGT 60.459 57.895 0.00 0.00 0.00 3.32
21 22 1.293498 CTCCTCCCACTGACGGTTG 59.707 63.158 0.00 0.00 0.00 3.77
22 23 0.763223 AACTCCTCCCACTGACGGTT 60.763 55.000 0.00 0.00 0.00 4.44
23 24 1.152312 AACTCCTCCCACTGACGGT 60.152 57.895 0.00 0.00 0.00 4.83
24 25 1.293498 CAACTCCTCCCACTGACGG 59.707 63.158 0.00 0.00 0.00 4.79
25 26 1.374758 GCAACTCCTCCCACTGACG 60.375 63.158 0.00 0.00 0.00 4.35
26 27 1.003233 GGCAACTCCTCCCACTGAC 60.003 63.158 0.00 0.00 0.00 3.51
27 28 1.461268 TGGCAACTCCTCCCACTGA 60.461 57.895 0.00 0.00 35.26 3.41
28 29 1.002868 CTGGCAACTCCTCCCACTG 60.003 63.158 0.00 0.00 35.26 3.66
29 30 2.227036 CCTGGCAACTCCTCCCACT 61.227 63.158 0.00 0.00 35.26 4.00
30 31 1.566298 ATCCTGGCAACTCCTCCCAC 61.566 60.000 0.00 0.00 35.26 4.61
31 32 1.229951 ATCCTGGCAACTCCTCCCA 60.230 57.895 0.00 0.00 35.26 4.37
32 33 0.985490 AGATCCTGGCAACTCCTCCC 60.985 60.000 0.00 0.00 35.26 4.30
33 34 0.467804 GAGATCCTGGCAACTCCTCC 59.532 60.000 0.00 0.00 35.26 4.30
34 35 1.494960 AGAGATCCTGGCAACTCCTC 58.505 55.000 9.65 0.00 35.26 3.71
35 36 1.963985 AAGAGATCCTGGCAACTCCT 58.036 50.000 9.65 0.00 35.26 3.69
36 37 2.797177 AAAGAGATCCTGGCAACTCC 57.203 50.000 9.65 0.00 37.61 3.85
37 38 3.198853 AGGTAAAGAGATCCTGGCAACTC 59.801 47.826 0.00 0.00 37.61 3.01
38 39 3.185455 AGGTAAAGAGATCCTGGCAACT 58.815 45.455 0.00 0.00 37.61 3.16
39 40 3.536570 GAGGTAAAGAGATCCTGGCAAC 58.463 50.000 0.00 0.00 0.00 4.17
40 41 2.168521 CGAGGTAAAGAGATCCTGGCAA 59.831 50.000 0.00 0.00 0.00 4.52
41 42 1.757118 CGAGGTAAAGAGATCCTGGCA 59.243 52.381 0.00 0.00 0.00 4.92
42 43 1.069358 CCGAGGTAAAGAGATCCTGGC 59.931 57.143 0.00 0.00 0.00 4.85
43 44 1.069358 GCCGAGGTAAAGAGATCCTGG 59.931 57.143 0.00 0.00 0.00 4.45
44 45 2.035632 AGCCGAGGTAAAGAGATCCTG 58.964 52.381 0.00 0.00 0.00 3.86
45 46 2.463047 AGCCGAGGTAAAGAGATCCT 57.537 50.000 0.00 0.00 0.00 3.24
46 47 3.224269 ACTAGCCGAGGTAAAGAGATCC 58.776 50.000 0.00 0.00 0.00 3.36
47 48 5.065235 ACTACTAGCCGAGGTAAAGAGATC 58.935 45.833 0.00 0.00 0.00 2.75
48 49 5.051409 ACTACTAGCCGAGGTAAAGAGAT 57.949 43.478 0.00 0.00 0.00 2.75
49 50 4.500499 ACTACTAGCCGAGGTAAAGAGA 57.500 45.455 0.00 0.00 0.00 3.10
50 51 4.213906 GCTACTACTAGCCGAGGTAAAGAG 59.786 50.000 0.00 0.00 39.79 2.85
51 52 4.133078 GCTACTACTAGCCGAGGTAAAGA 58.867 47.826 0.00 0.00 39.79 2.52
52 53 4.486574 GCTACTACTAGCCGAGGTAAAG 57.513 50.000 0.00 0.00 39.79 1.85
62 63 4.463539 GGGATTAAGAGGGCTACTACTAGC 59.536 50.000 0.00 0.00 44.34 3.42
63 64 5.894653 AGGGATTAAGAGGGCTACTACTAG 58.105 45.833 0.00 0.00 0.00 2.57
64 65 5.944809 AGGGATTAAGAGGGCTACTACTA 57.055 43.478 0.00 0.00 0.00 1.82
65 66 4.836255 AGGGATTAAGAGGGCTACTACT 57.164 45.455 0.00 0.00 0.00 2.57
66 67 4.503469 GCAAGGGATTAAGAGGGCTACTAC 60.503 50.000 0.00 0.00 0.00 2.73
67 68 3.646637 GCAAGGGATTAAGAGGGCTACTA 59.353 47.826 0.00 0.00 0.00 1.82
68 69 2.439880 GCAAGGGATTAAGAGGGCTACT 59.560 50.000 0.00 0.00 0.00 2.57
69 70 2.172717 TGCAAGGGATTAAGAGGGCTAC 59.827 50.000 0.00 0.00 0.00 3.58
70 71 2.487775 TGCAAGGGATTAAGAGGGCTA 58.512 47.619 0.00 0.00 0.00 3.93
71 72 1.298953 TGCAAGGGATTAAGAGGGCT 58.701 50.000 0.00 0.00 0.00 5.19
72 73 1.751351 GTTGCAAGGGATTAAGAGGGC 59.249 52.381 0.00 0.00 0.00 5.19
73 74 2.017049 CGTTGCAAGGGATTAAGAGGG 58.983 52.381 11.31 0.00 0.00 4.30
74 75 2.017049 CCGTTGCAAGGGATTAAGAGG 58.983 52.381 30.03 2.32 36.04 3.69
85 86 1.176527 ACATTCATCCCCGTTGCAAG 58.823 50.000 0.00 0.00 0.00 4.01
88 89 1.135112 GGAAACATTCATCCCCGTTGC 60.135 52.381 0.00 0.00 0.00 4.17
124 125 2.814835 GGTCAACCTCCCCGTGTGT 61.815 63.158 0.00 0.00 0.00 3.72
126 127 3.246880 GGGTCAACCTCCCCGTGT 61.247 66.667 0.00 0.00 39.08 4.49
154 155 3.682372 CATCTCGTCGAAGATGTCTGA 57.318 47.619 15.94 4.69 45.01 3.27
197 198 4.052229 CACGCGTCTTCCTCCCGT 62.052 66.667 9.86 0.00 0.00 5.28
198 199 4.796231 CCACGCGTCTTCCTCCCG 62.796 72.222 9.86 0.00 0.00 5.14
199 200 4.452733 CCCACGCGTCTTCCTCCC 62.453 72.222 9.86 0.00 0.00 4.30
210 211 3.723348 GTCTTTCGCACCCCACGC 61.723 66.667 0.00 0.00 0.00 5.34
221 222 2.018515 TGGGTTTTCACCGTGTCTTTC 58.981 47.619 0.00 0.00 45.39 2.62
228 229 1.616159 CCTTCATGGGTTTTCACCGT 58.384 50.000 0.00 0.00 45.39 4.83
239 240 6.439636 TTGATCTACCTTATCCCTTCATGG 57.560 41.667 0.00 0.00 0.00 3.66
246 247 3.841255 CCCTCCTTGATCTACCTTATCCC 59.159 52.174 0.00 0.00 0.00 3.85
290 292 2.983030 TTCACGGCCACATGTGCC 60.983 61.111 20.81 21.62 45.70 5.01
303 305 0.249573 TTCGGACAACTCCCGTTCAC 60.250 55.000 0.00 0.00 46.53 3.18
306 308 0.178533 TTGTTCGGACAACTCCCGTT 59.821 50.000 4.79 0.00 46.53 4.44
314 316 2.217750 CCACATCACTTGTTCGGACAA 58.782 47.619 9.39 9.39 43.23 3.18
318 320 1.593196 ACACCACATCACTTGTTCGG 58.407 50.000 0.00 0.00 36.00 4.30
323 325 1.460743 CGCACTACACCACATCACTTG 59.539 52.381 0.00 0.00 0.00 3.16
327 329 1.403647 GCTACGCACTACACCACATCA 60.404 52.381 0.00 0.00 0.00 3.07
335 337 1.065102 GATCCTTCGCTACGCACTACA 59.935 52.381 0.00 0.00 0.00 2.74
359 361 3.330853 GTGCATCGTCGGATCCGC 61.331 66.667 29.62 21.78 39.59 5.54
407 409 1.338337 CTAATGATGACTCGAGCCGGT 59.662 52.381 13.61 0.00 0.00 5.28
410 412 1.789506 GGCTAATGATGACTCGAGCC 58.210 55.000 13.61 0.65 42.45 4.70
482 487 2.941415 GCAGCCAAATACCAGCAGTAGT 60.941 50.000 0.00 0.00 33.42 2.73
488 493 2.800736 CGGCAGCCAAATACCAGC 59.199 61.111 13.30 0.00 0.00 4.85
505 510 3.441572 AGGTGACTTACATCTTTGCATGC 59.558 43.478 11.82 11.82 36.42 4.06
517 522 6.310711 CGACTTAAATGGAAGAGGTGACTTAC 59.689 42.308 0.00 0.00 44.43 2.34
591 597 8.079809 GGAAGATAATTTTCGTTCAAGGTTCAA 58.920 33.333 0.00 0.00 0.00 2.69
600 606 9.639601 AAAAGATTGGGAAGATAATTTTCGTTC 57.360 29.630 0.00 0.00 0.00 3.95
620 626 7.377766 TCATTTGCTTACTTCGCTAAAAGAT 57.622 32.000 0.00 0.00 0.00 2.40
628 634 6.934561 AGAATTTTCATTTGCTTACTTCGC 57.065 33.333 0.00 0.00 0.00 4.70
635 641 7.575720 CGTTCCTCCTAGAATTTTCATTTGCTT 60.576 37.037 0.00 0.00 0.00 3.91
712 722 0.597377 TCGGCATGTGATCGATTCCG 60.597 55.000 0.00 8.67 37.00 4.30
713 723 0.861837 GTCGGCATGTGATCGATTCC 59.138 55.000 0.00 0.00 35.35 3.01
714 724 0.504384 CGTCGGCATGTGATCGATTC 59.496 55.000 0.00 0.00 35.35 2.52
715 725 0.875908 CCGTCGGCATGTGATCGATT 60.876 55.000 0.00 0.00 35.35 3.34
716 726 1.300156 CCGTCGGCATGTGATCGAT 60.300 57.895 0.00 0.00 35.35 3.59
717 727 2.104132 CCGTCGGCATGTGATCGA 59.896 61.111 0.00 0.00 0.00 3.59
807 817 1.522569 GCCGGTCTTGGATACTGCT 59.477 57.895 1.90 0.00 37.61 4.24
808 818 1.883084 CGCCGGTCTTGGATACTGC 60.883 63.158 1.90 0.00 37.61 4.40
809 819 0.389391 ATCGCCGGTCTTGGATACTG 59.611 55.000 1.90 0.00 37.61 2.74
829 839 4.451150 TGTCGCCGGAGACATGGC 62.451 66.667 33.57 11.21 45.18 4.40
936 1007 2.047274 CATCGGACGGTTGCTGGT 60.047 61.111 0.00 0.00 0.00 4.00
949 1020 2.890474 GCGTGGTGGGTAGCATCG 60.890 66.667 0.00 0.00 36.58 3.84
1212 1283 0.179070 GGTCTGAGCTTCGGGATTCC 60.179 60.000 0.00 0.00 0.00 3.01
1213 1284 0.179070 GGGTCTGAGCTTCGGGATTC 60.179 60.000 6.83 0.00 0.00 2.52
1216 1287 1.306141 ATGGGTCTGAGCTTCGGGA 60.306 57.895 6.83 0.00 0.00 5.14
1730 1801 3.244078 ACAGAGTCAGTTATCACGGCAAA 60.244 43.478 0.00 0.00 0.00 3.68
1749 1820 6.992063 ATCAGTTATAGGTTGCTGAAACAG 57.008 37.500 0.11 0.00 40.71 3.16
1945 2025 8.870075 GGAATATCCTAGCAATCCTGTAATTT 57.130 34.615 0.00 0.00 32.53 1.82
1991 2072 6.665992 ATTATGTGAGCCGGAGTAAGATTA 57.334 37.500 5.05 0.00 0.00 1.75
2026 2107 2.159043 CCATAAGCACGAGTGGAGTGAT 60.159 50.000 5.32 0.00 41.83 3.06
2072 2153 5.038683 TGCAGTATACACAGTTATACGCAC 58.961 41.667 5.50 9.33 35.73 5.34
2075 4171 7.364970 TGGTATGCAGTATACACAGTTATACG 58.635 38.462 10.48 0.00 42.85 3.06
2098 4194 8.689972 ACTATGGCTTAGATCATTTTCTTTTGG 58.310 33.333 13.76 0.00 0.00 3.28
2109 4205 4.199002 TGAGGGACTATGGCTTAGATCA 57.801 45.455 13.76 9.00 41.55 2.92
2155 4251 4.734854 CGATTTGTTGTCAGAGGTTGTTTG 59.265 41.667 0.00 0.00 0.00 2.93
2227 4329 2.159226 GGAGAGAATACACACCACTCGG 60.159 54.545 0.00 0.00 38.77 4.63
2279 4381 6.547510 ACCATTTAAGGGCTCTGATTTACATC 59.452 38.462 0.00 0.00 0.00 3.06
2424 4526 9.840427 AAAAATTATCCGTTCTATTTCACACAG 57.160 29.630 0.00 0.00 0.00 3.66
2449 4553 7.291566 TGTAAAGTCCTTATTGAACTTCCCAA 58.708 34.615 0.00 0.00 32.24 4.12
2479 4583 7.562454 TGTTGGTTTCTTGAACTACCTTTAG 57.438 36.000 5.99 0.00 38.35 1.85
2547 4651 5.972973 TGAAACATCGCAATTCAATATGAGC 59.027 36.000 0.00 0.00 30.60 4.26
2571 4675 5.552870 AATAGGGACTCTAAACGCATCAT 57.447 39.130 0.00 0.00 41.75 2.45
2586 4690 5.702065 TGTATGCAGTTACCAAATAGGGA 57.298 39.130 0.00 0.00 43.89 4.20
2662 4766 9.185192 CTTAAATTGCTTGAGGAAGTAAACTTG 57.815 33.333 0.00 0.00 37.34 3.16
2687 4791 2.101783 CAGAGAGACACAGATGCCTCT 58.898 52.381 0.00 0.00 38.57 3.69
2690 4794 2.493675 TGTACAGAGAGACACAGATGCC 59.506 50.000 0.00 0.00 0.00 4.40
2739 5291 9.702494 CTGCTATGATTCACTACTTTCATATCA 57.298 33.333 0.00 0.00 32.33 2.15
2819 5371 5.906073 ACTGAAAAACTTGTTAGCTGCAAT 58.094 33.333 1.02 0.00 0.00 3.56
2948 5502 2.291741 GGCACATAGGCTTACAATGCTC 59.708 50.000 0.00 0.00 40.24 4.26
2993 5573 1.871080 CTCAGTGATAACATCCCGGC 58.129 55.000 0.00 0.00 0.00 6.13
2997 5577 6.094603 AGTTTGATTGCTCAGTGATAACATCC 59.905 38.462 0.00 0.00 31.68 3.51
3152 5732 5.103290 TGAAACTGAACCAAATAGCGAAC 57.897 39.130 0.00 0.00 0.00 3.95
3231 5811 3.732212 TGCATCACTGGTATATGAGCAC 58.268 45.455 0.00 0.00 29.75 4.40
3236 5816 5.857822 CAGACATGCATCACTGGTATATG 57.142 43.478 17.11 0.00 0.00 1.78
3257 5837 5.221028 CCATTCCTTGATATTAAAGTGCGCA 60.221 40.000 5.66 5.66 0.00 6.09
3291 5874 4.464008 CATGGAAATATGGCACCACTAGT 58.536 43.478 0.00 0.00 35.19 2.57
3627 6210 5.873164 ACAACATTAGGACGATCAGGTAAAC 59.127 40.000 0.00 0.00 0.00 2.01
3817 6400 8.810652 AAAATATGAACACGCTAACAAACAAT 57.189 26.923 0.00 0.00 0.00 2.71
3819 6402 7.915923 TGAAAAATATGAACACGCTAACAAACA 59.084 29.630 0.00 0.00 0.00 2.83
3841 6424 8.390354 CAAACGAGCAAAGATATCTATGTGAAA 58.610 33.333 5.46 0.00 0.00 2.69
3997 6581 2.191128 ACTTTGGATCAGGTGTCAGC 57.809 50.000 0.00 0.00 0.00 4.26
4070 6654 8.887717 ACAAAGAGAATAACATGATAGAGCAAC 58.112 33.333 0.00 0.00 0.00 4.17
4143 6727 9.237846 GTTCCATTCTTTCTTCAAAGTTTACTG 57.762 33.333 0.00 0.00 40.16 2.74
4145 6729 9.020813 GTGTTCCATTCTTTCTTCAAAGTTTAC 57.979 33.333 0.00 0.00 40.16 2.01
4146 6730 8.194769 GGTGTTCCATTCTTTCTTCAAAGTTTA 58.805 33.333 0.00 0.00 40.16 2.01
4147 6731 7.041721 GGTGTTCCATTCTTTCTTCAAAGTTT 58.958 34.615 0.00 0.00 40.16 2.66
4148 6732 6.573434 GGTGTTCCATTCTTTCTTCAAAGTT 58.427 36.000 0.00 0.00 40.16 2.66
4150 6734 5.215160 CGGTGTTCCATTCTTTCTTCAAAG 58.785 41.667 0.00 0.00 40.56 2.77
4172 6774 1.946768 TCAAAACTCAAACTCTGCCCG 59.053 47.619 0.00 0.00 0.00 6.13
4232 6841 2.029623 GATGAGGCATGCCACAGAATT 58.970 47.619 34.81 22.26 39.86 2.17
4246 6855 4.629092 ACGTGATGAGATGATTGATGAGG 58.371 43.478 0.00 0.00 0.00 3.86
4263 6872 0.756294 ATGAACAGGTGGTGACGTGA 59.244 50.000 0.00 0.00 39.85 4.35
4298 6907 7.176515 ACACATCAACTATCAAAAGTATGGCAA 59.823 33.333 0.00 0.00 0.00 4.52
4320 6929 0.605050 ACAGCACACACACACACACA 60.605 50.000 0.00 0.00 0.00 3.72
4321 6930 0.521291 AACAGCACACACACACACAC 59.479 50.000 0.00 0.00 0.00 3.82
4322 6931 1.068679 CAAACAGCACACACACACACA 60.069 47.619 0.00 0.00 0.00 3.72
4323 6932 1.068610 ACAAACAGCACACACACACAC 60.069 47.619 0.00 0.00 0.00 3.82
4328 6937 2.680841 GGAGTTACAAACAGCACACACA 59.319 45.455 0.00 0.00 0.00 3.72
4352 6961 5.774498 ACCCTTTCTTCAAATGTTCTGAC 57.226 39.130 0.00 0.00 0.00 3.51
4369 6978 6.410853 CCATTATTCTTCACCATCCTACCCTT 60.411 42.308 0.00 0.00 0.00 3.95
4448 7057 8.612145 ACATAAGTTAGTTTTGGTAGGAAGGAT 58.388 33.333 0.00 0.00 0.00 3.24
4507 7116 2.211250 ACAATGGCAGAACTGAGCAT 57.789 45.000 5.97 0.00 0.00 3.79
4581 7190 4.142816 CGTATAAATGCATAGCCCAGCTTC 60.143 45.833 0.00 0.00 40.44 3.86
4583 7192 3.244561 ACGTATAAATGCATAGCCCAGCT 60.245 43.478 0.00 0.00 43.41 4.24
4585 7194 4.314961 TGACGTATAAATGCATAGCCCAG 58.685 43.478 0.00 0.00 0.00 4.45
4635 7249 0.035739 TTCTGTCCACGTTTAGGCCC 59.964 55.000 0.00 0.00 0.00 5.80
4651 7265 3.389002 AGAAAATTTGCAGCCCACTTTCT 59.611 39.130 0.00 0.00 0.00 2.52
4667 7281 5.334802 GGCTGGCGCAATTTAAAAAGAAAAT 60.335 36.000 10.83 0.00 38.10 1.82
4672 7293 1.389784 CGGCTGGCGCAATTTAAAAAG 59.610 47.619 11.55 0.00 38.10 2.27
4725 7346 2.616634 AGTGCATGAGCTCTACATGG 57.383 50.000 16.19 0.00 42.36 3.66
4734 7355 2.863137 GTGAACTAGCTAGTGCATGAGC 59.137 50.000 32.57 18.63 43.42 4.26
4739 7361 4.600692 TTTGAGTGAACTAGCTAGTGCA 57.399 40.909 27.85 27.85 39.52 4.57
4744 7366 5.468540 TGAGCTTTTGAGTGAACTAGCTA 57.531 39.130 5.64 0.00 38.94 3.32
4777 7400 7.452880 TGTATAAATGCATAGCCCATCTTTC 57.547 36.000 0.00 0.00 0.00 2.62
4780 7403 6.724351 TGATGTATAAATGCATAGCCCATCT 58.276 36.000 18.80 0.00 33.17 2.90
4782 7405 6.720748 TGTTGATGTATAAATGCATAGCCCAT 59.279 34.615 0.00 0.00 33.17 4.00
4801 7424 9.961265 CAAGCAGTTGATATCAATATTGTTGAT 57.039 29.630 20.65 12.48 38.06 2.57
4808 7431 8.915057 AAGTAGCAAGCAGTTGATATCAATAT 57.085 30.769 20.65 10.37 36.93 1.28
4864 7496 6.655003 TGGACAAGAATGATTTCACTCCTTAC 59.345 38.462 0.00 0.00 34.08 2.34
4890 7522 7.915930 ACATGGGGAAAACAAATGAATCATTA 58.084 30.769 9.09 0.00 32.43 1.90
4891 7523 6.781943 ACATGGGGAAAACAAATGAATCATT 58.218 32.000 2.07 2.07 35.39 2.57
4990 7625 3.019564 GCTCTTGGCATAGGTCACATTT 58.980 45.455 0.00 0.00 41.35 2.32
5173 7808 5.413309 AAGAAGCTATAATCATCTCCCCG 57.587 43.478 0.00 0.00 0.00 5.73
5302 7937 4.770795 TGCTTAGCCTAGATTCAACCTTC 58.229 43.478 0.29 0.00 0.00 3.46
5640 8275 6.160459 ACCTTTCAGTATATTCCCCAACTCAT 59.840 38.462 0.00 0.00 0.00 2.90
5681 8316 5.082251 ACCTCAACGTTAAGAATACCTCC 57.918 43.478 0.00 0.00 0.00 4.30
5685 8320 7.305076 CGACGAATACCTCAACGTTAAGAATAC 60.305 40.741 0.00 0.00 39.04 1.89
5686 8321 6.688385 CGACGAATACCTCAACGTTAAGAATA 59.312 38.462 0.00 0.00 39.04 1.75
5693 8328 2.030893 TCACGACGAATACCTCAACGTT 60.031 45.455 0.00 0.00 39.04 3.99
5694 8329 1.536766 TCACGACGAATACCTCAACGT 59.463 47.619 0.00 0.00 41.57 3.99
5747 8384 8.318412 TGTGTGACCAGTGTATATGAACTAAAT 58.682 33.333 0.00 0.00 0.00 1.40
5806 8444 5.046376 TGAATGAATAACCAGCAGAGAGTGA 60.046 40.000 0.00 0.00 0.00 3.41
5842 8480 1.471676 GGGCTGTGTGAATCCTAGACG 60.472 57.143 0.00 0.00 0.00 4.18
5851 8489 0.108585 GAGAACTGGGGCTGTGTGAA 59.891 55.000 0.00 0.00 0.00 3.18
5852 8490 1.754745 GAGAACTGGGGCTGTGTGA 59.245 57.895 0.00 0.00 0.00 3.58
5871 8509 0.453390 CAGCAGAAAATTCCTCCGCC 59.547 55.000 0.00 0.00 0.00 6.13
5874 8512 1.475682 CTGGCAGCAGAAAATTCCTCC 59.524 52.381 0.00 0.00 0.00 4.30
5912 8550 4.221482 TCATGTCATCAGTAGCTTGTCAGT 59.779 41.667 0.00 0.00 0.00 3.41
5982 8620 2.072487 GTAGCCAGGCCCAGGATCA 61.072 63.158 15.78 0.00 0.00 2.92
5984 8622 2.074948 CAGTAGCCAGGCCCAGGAT 61.075 63.158 15.78 11.80 0.00 3.24
5987 8625 3.801997 CCCAGTAGCCAGGCCCAG 61.802 72.222 8.22 0.00 0.00 4.45
5991 8629 4.115199 CACCCCCAGTAGCCAGGC 62.115 72.222 1.84 1.84 0.00 4.85
5992 8630 3.411517 CCACCCCCAGTAGCCAGG 61.412 72.222 0.00 0.00 0.00 4.45
5993 8631 1.694169 ATCCACCCCCAGTAGCCAG 60.694 63.158 0.00 0.00 0.00 4.85
5994 8632 1.692749 GATCCACCCCCAGTAGCCA 60.693 63.158 0.00 0.00 0.00 4.75
5995 8633 1.279025 TTGATCCACCCCCAGTAGCC 61.279 60.000 0.00 0.00 0.00 3.93
5996 8634 0.623723 TTTGATCCACCCCCAGTAGC 59.376 55.000 0.00 0.00 0.00 3.58
5997 8635 1.916181 AGTTTGATCCACCCCCAGTAG 59.084 52.381 0.00 0.00 0.00 2.57
5998 8636 1.633432 CAGTTTGATCCACCCCCAGTA 59.367 52.381 0.00 0.00 0.00 2.74
5999 8637 0.405585 CAGTTTGATCCACCCCCAGT 59.594 55.000 0.00 0.00 0.00 4.00
6034 8672 2.996621 CAAAAACGTTCAAGCCCAAACA 59.003 40.909 0.00 0.00 0.00 2.83
6097 8739 3.228749 CGTGCACAAGAATGTTCATCAC 58.771 45.455 18.64 0.00 37.82 3.06
6129 8775 1.533756 CGTTGGCAGAAATAATGGGCG 60.534 52.381 0.00 0.00 0.00 6.13
6411 9061 0.793861 TCCGGAAAATTCAAGACGCG 59.206 50.000 0.00 3.53 0.00 6.01
6486 9136 1.848608 CACTCATACGAGACACATGCG 59.151 52.381 0.00 0.00 42.34 4.73
6534 9184 1.429148 CTAATCTCGGCCGGCAACAC 61.429 60.000 30.85 9.91 0.00 3.32
6535 9185 1.153449 CTAATCTCGGCCGGCAACA 60.153 57.895 30.85 10.14 0.00 3.33
6536 9186 2.534903 GCTAATCTCGGCCGGCAAC 61.535 63.158 30.85 11.20 0.00 4.17
6622 9272 4.736126 AACAAGAAGAAACCCAACCAAG 57.264 40.909 0.00 0.00 0.00 3.61
6623 9273 5.483811 GAAAACAAGAAGAAACCCAACCAA 58.516 37.500 0.00 0.00 0.00 3.67
6624 9274 4.081365 GGAAAACAAGAAGAAACCCAACCA 60.081 41.667 0.00 0.00 0.00 3.67
6625 9275 4.439057 GGAAAACAAGAAGAAACCCAACC 58.561 43.478 0.00 0.00 0.00 3.77
6626 9276 4.109766 CGGAAAACAAGAAGAAACCCAAC 58.890 43.478 0.00 0.00 0.00 3.77
6639 9289 0.533308 CGGGTCCAGACGGAAAACAA 60.533 55.000 0.00 0.00 45.20 2.83
6662 9312 4.378774 CACAATCTCTCATAGCCTTCAGG 58.621 47.826 0.00 0.00 38.53 3.86
6665 9315 2.799412 CGCACAATCTCTCATAGCCTTC 59.201 50.000 0.00 0.00 0.00 3.46
6666 9316 2.432146 TCGCACAATCTCTCATAGCCTT 59.568 45.455 0.00 0.00 0.00 4.35
6670 9320 6.312426 AGAAAAACTCGCACAATCTCTCATAG 59.688 38.462 0.00 0.00 0.00 2.23
6671 9321 6.166279 AGAAAAACTCGCACAATCTCTCATA 58.834 36.000 0.00 0.00 0.00 2.15
6673 9323 4.380531 AGAAAAACTCGCACAATCTCTCA 58.619 39.130 0.00 0.00 0.00 3.27
6674 9324 4.999751 AGAAAAACTCGCACAATCTCTC 57.000 40.909 0.00 0.00 0.00 3.20
6675 9325 5.757850 AAAGAAAAACTCGCACAATCTCT 57.242 34.783 0.00 0.00 0.00 3.10
6676 9326 6.202226 AGAAAAGAAAAACTCGCACAATCTC 58.798 36.000 0.00 0.00 0.00 2.75
6677 9327 6.038714 AGAGAAAAGAAAAACTCGCACAATCT 59.961 34.615 0.00 0.00 34.98 2.40
6678 9328 6.202226 AGAGAAAAGAAAAACTCGCACAATC 58.798 36.000 0.00 0.00 34.98 2.67
6679 9329 6.136541 AGAGAAAAGAAAAACTCGCACAAT 57.863 33.333 0.00 0.00 34.98 2.71
6680 9330 5.560966 AGAGAAAAGAAAAACTCGCACAA 57.439 34.783 0.00 0.00 34.98 3.33
6681 9331 5.560966 AAGAGAAAAGAAAAACTCGCACA 57.439 34.783 0.00 0.00 34.98 4.57
6682 9332 6.027749 TCAAAGAGAAAAGAAAAACTCGCAC 58.972 36.000 0.00 0.00 34.98 5.34
6683 9333 6.189677 TCAAAGAGAAAAGAAAAACTCGCA 57.810 33.333 0.00 0.00 34.98 5.10
6684 9334 5.683302 CCTCAAAGAGAAAAGAAAAACTCGC 59.317 40.000 0.00 0.00 34.98 5.03
6685 9335 7.016361 TCCTCAAAGAGAAAAGAAAAACTCG 57.984 36.000 0.00 0.00 34.98 4.18
6686 9336 9.639601 TTTTCCTCAAAGAGAAAAGAAAAACTC 57.360 29.630 0.00 0.00 31.91 3.01
6687 9337 9.996554 TTTTTCCTCAAAGAGAAAAGAAAAACT 57.003 25.926 13.00 0.00 36.23 2.66
6712 9362 7.417003 GGCCCTATATTTCAACACGGTATTTTT 60.417 37.037 0.00 0.00 0.00 1.94
6713 9363 6.040054 GGCCCTATATTTCAACACGGTATTTT 59.960 38.462 0.00 0.00 0.00 1.82
6714 9364 5.533528 GGCCCTATATTTCAACACGGTATTT 59.466 40.000 0.00 0.00 0.00 1.40
6715 9365 5.067954 GGCCCTATATTTCAACACGGTATT 58.932 41.667 0.00 0.00 0.00 1.89
6716 9366 4.648651 GGCCCTATATTTCAACACGGTAT 58.351 43.478 0.00 0.00 0.00 2.73
6717 9367 3.493002 CGGCCCTATATTTCAACACGGTA 60.493 47.826 0.00 0.00 0.00 4.02
6718 9368 2.743838 CGGCCCTATATTTCAACACGGT 60.744 50.000 0.00 0.00 0.00 4.83
6725 9375 5.765576 TTTATAGCCGGCCCTATATTTCA 57.234 39.130 26.15 1.79 32.08 2.69
6729 9379 5.687706 GCTGATTTTATAGCCGGCCCTATAT 60.688 44.000 26.15 16.88 32.08 0.86
6734 9384 0.881796 GCTGATTTTATAGCCGGCCC 59.118 55.000 26.15 0.00 33.89 5.80
6739 9389 2.808543 CAGGGTCGCTGATTTTATAGCC 59.191 50.000 11.37 0.00 36.60 3.93
6753 9403 6.516718 AGAATGATATACTTCAACAGGGTCG 58.483 40.000 0.97 0.00 0.00 4.79
6794 9550 0.736636 ATGTGCATGCATGTTCCTCG 59.263 50.000 25.64 0.81 0.00 4.63
6809 9565 1.708193 ATCATCGCCGTGCACATGTG 61.708 55.000 21.83 21.83 0.00 3.21
6865 9621 2.607282 GCGTATCTTGGACCCGTATGAG 60.607 54.545 0.00 0.00 0.00 2.90
6878 9634 1.128692 GCAAGCAAACTCGCGTATCTT 59.871 47.619 5.77 0.00 36.85 2.40
6933 9689 1.413812 CATGATGAGATCGACCACCCA 59.586 52.381 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.